Directory

#ncbi_accession source_identifier label sequence_cutoff domain_cutoff hmm_length family_type for_structural_annotation for_naming for_AMRFinder product_name gene_symbol gene_synonyms ec_numbers go_terms pmids taxonomic_range taxonomic_range_name taxonomic_rank_name n_refseq_protein_hits source name_orig hmm_name comment NF000008.1 trim_DfrA1_rpt 420 420 187 exception Y Y Y trimethoprim-resistant repeat-containing dihydrofolate reductase DfrA1 dfrA1 GO:0004146 0 NCBIFAM trimethoprim-resistant repeat-containing dihydrofolate reductase DfrA1 trimethoprim-resistant repeat-containing dihydrofolate reductase DfrA1 NF000019.2 trim_DfrA3 350 350 162 exception Y Y Y trimethoprim-resistant dihydrofolate reductase DfrA3 dfrA3 1.5.1.3 GO:0004146 0 NCBIFAM trimethoprim-resistant dihydrofolate reductase DfrA3 trimethoprim-resistant dihydrofolate reductase DfrA3 NF000032.1 D_ala_D_ser_VanL 750 750 349 exception Y Y Y D-alanine--D-serine ligase VanL vanL 6.3.2.35 0 NCBIFAM D-alanine--D-serine ligase VanL D-alanine--D-serine ligase VanL NF000033.1 vanT-L-mem 675 675 329 exception Y Y Y serine racemase VanT-L membrane subunit vanTm 0 NCBIFAM serine racemase VanT-L membrane subunit serine racemase VanT-L membrane subunit NF000048.1 AAC_6p_A40 400 400 184 exception Y Y Y aminoglycoside 6'-N-acetyltransferase AacA40 aacA40 0 NCBIFAM aminoglycoside 6'-N-acetyltransferase AacA40 aminoglycoside 6'-N-acetyltransferase AacA40 NF000059.1 tet_redox_37 225 225 108 exception Y Y Y tetracycline resistance NADPH-dependent oxidoreductase Tet(37) tet(37) 0 NCBIFAM tetracycline resistance NADPH-dependent oxidoreductase Tet(37) tetracycline resistance NADPH-dependent oxidoreductase Tet(37) NF000072.1 MFS_efflux_PexA 800 800 415 equivalog Y Y Y phenicol efflux MFS transporter PexA pexA 0 NCBIFAM phenicol efflux MFS transporter PexA phenicol efflux MFS transporter PexA NF000101.1 stregram_VatA 450 450 219 exception Y Y Y streptogramin A O-acetyltransferase Vat(A) vat(A) GO:0016740 0 NCBIFAM streptogramin A O-acetyltransferase Vat(A) streptogramin A O-acetyltransferase Vat(A) NF000106.1 40850658_otr 750 750 351 exception Y Y N oxytetracycline efflux ABC transporter Otr(C) ATP-binding subunit 0 NCBIFAM oxytetracycline efflux ABC transporter Otr(C) ATP-binding subunit oxytetracycline efflux ABC transporter Otr(C) ATP-binding subunit NF000115.2 AAC_6p_Iad 275 275 144 exception Y Y Y aminoglycoside N-acetyltransferase AAC(6')-Iad aac(6')-Iad 0 NCBIFAM aminoglycoside N-acetyltransferase AAC(6')-Iad aminoglycoside N-acetyltransferase AAC(6')-Iad NF000122.1 485965_fosC 350 350 182 equivalog Y Y Y fosfomycin resistance kinase FosC fosC 0 NCBIFAM fosfomycin resistance kinase FosC fosfomycin resistance kinase FosC NF000258.1 MupB 1900 1900 1033 exception Y Y Y mupirocin-resistant isoleucine--tRNA ligase MupB mupB 6.1.1.5 0 NCBIFAM mupirocin-resistant isoleucine--tRNA ligase MupB mupirocin-resistant isoleucine--tRNA ligase MupB NF000342.3 glpA_Cterm 500 500 228 exception Y Y N aminoglycoside O-phosphotransferase APH(4)-Ib glpA 0 NCBIFAM aminoglycoside O-phosphotransferase APH(4)-Ib aminoglycoside O-phosphotransferase APH(4)-Ib The C-terminal half of CAA52372.1 shows homology to hygromycin-modifying enzyme APH(4)-Ia. The N-terminal region shows no homology to any other protein. The gene glpA was identified as one of two in a 3.0-kb DNA segment capable of conferring on E. coli the ability to degrade and use the phosphonate herbicide glyphosate as a sole carbon source. The expressed protein conferred minor (3-fold) increase in tolerance to hygromycin, but this protein probably should not be considered an aminoglycoside modifying enzyme associated with the spread of resistance in bacteria toward clinically important antimicrobials. NF000359.1 sat3 360 360 180 exception Y Y Y streptothricin N-acetyltransferase Sat3 sat3 0 NCBIFAM streptothricin N-acetyltransferase Sat3 streptothricin N-acetyltransferase Sat3 NF000415.3 blaOXA-372_like 535 535 257 exception Y Y Y OXA-372 family carbapenem-hydrolyzing class D beta-lactamase blaOXA 3.5.2.6 GO:0008800 26126492 0 NCBIFAM OXA-372 family carbapenem-hydrolyzing class D beta-lactamase OXA-372 family carbapenem-hydrolyzing class D beta-lactamase NF000449.2 blaBIC 640 640 294 exception Y Y Y BIC family carbapenem-hydrolyzing class A beta-lactamase blaBIC 3.5.2.6 GO:0008800 0 NCBIFAM BIC family class A beta-lactamase BIC family carbapenem-hydrolyzing class A beta-lactamase NF000456.2 blaMSI-1_fam 550 550 289 exception Y Y Y MSI-1 family subclass B3 metallo-beta-lactamase blaMSI GO:0008800 0 NCBIFAM MSI-1 family subclass B3 metallo-beta-lactamase MSI-1 family subclass B3 metallo-beta-lactamase NF000459.2 blaSPG-1_fam 550 550 285 exception Y Y Y SPG-1 family subclass B3 metallo-beta-lactamase blaSPG 3.5.2.6 GO:0008800 0 NCBIFAM SPG-1 family subclass B3 metallo-beta-lactamase SPG-1 family subclass B3 metallo-beta-lactamase NF000486.1 AAC_6p_Ip 390 390 173 exception Y Y Y aminoglycoside 6'-N-acetyltransferase AAC(6')-Ip aac(6')-Ip GO:0008080 0 NCBIFAM aminoglycoside N-acetyltransferase AAC(6')-Ip aminoglycoside 6'-N-acetyltransferase AAC(6')-Ip NF001990.1 PRK00790 PRK00790.1-1 147 147 111 equivalog Y Y N flagellar hook-basal body complex protein FliE fliE GO:0003774,GO:0005198,GO:0009288,GO:0071973 17098908,9161424 0 NCBI Protein Cluster (PRK) flagellar hook-basal body protein FliE flagellar hook-basal body complex protein FliE NF002513.0 PRK01903 PRK01903.2-4 240 240 118 equivalog Y N N ribonuclease P 0 NCBI Protein Cluster (PRK) ribonuclease P ribonuclease P NF002515.0 PRK01903 PRK01903.3-2 175 175 85 subfamily Y N N ribonuclease P 0 NCBI Protein Cluster (PRK) ribonuclease P ribonuclease P NF004243.1 PRK05682 PRK05682.2-2 801 801 420 equivalog Y Y N flagellar hook protein FlgE flgE 15839898 0 NCBI Protein Cluster (PRK) flagellar hook protein FlgE flagellar hook protein FlgE NF005256.0 PRK06762 PRK06762.3-1 160 160 67 equivalog Y N N hypothetical protein 0 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF012180.1 tet_MFS_43 999 999 484 exception Y Y Y tetracycline efflux MFS transporter Tet(43) tet(43) GO:0008493,GO:0015904 0 NCBIFAM tetracycline efflux MFS transporter Tet(43) tetracycline efflux MFS transporter Tet(43) NF012732.5 PF00522.23 VPR 25.5 25.5 83 domain Y Y N Vpr/Vpx protein GO:0019058,GO:0042025 0 EBI-EMBL VPR/VPX protein Vpr/Vpx protein NF012749.5 PF00539.23 Tat 22.5 22.5 64 domain Y Y N tat protein GO:0001070,GO:0042025,GO:0050434 10506122,2478293,7502045,7515512,9126842 0 EBI-EMBL Transactivating regulatory protein (Tat) tat protein Tat (Trans-Activator of Transcription) is an regulatory protein from HIV-1. NF012919.5 PF00716.22 Peptidase_S21 27 27 337 PfamEq Y Y N S21 family capsid maturation serine protease 3.4.21.- GO:0004252,GO:0006508 8805708 0 EBI-EMBL Assemblin (Peptidase family S21) S21 family capsid maturation serine protease NF013000.5 PF00802.24 Glycoprotein_G 27 27 263 domain Y Y N attachment glycoprotein G GO:0055036 2441388 0 EBI-EMBL Pneumovirus attachment glycoprotein G attachment glycoprotein G This family includes attachment proteins from respiratory synctial virus. Glycoprotein G has not been shown to have any neuraminidase or hemagglutinin activity (Swiss-Prot). The amino terminus is thought to be cytoplasmic, and the carboxyl terminus extracellular. The extracellular region contains four completely conserved cysteine residues. [1]. 2441388. The G glycoprotein of human respiratory syncytial viruses of subgroups A and B: extensive sequence divergence between antigenically related proteins. Johnson PR, Spriggs MK, Olmsted RA, Collins PL;. Proc Natl Acad Sci U S A 1987;84:5625-5629. (from Pfam) NF013040.5 PF00844.23 Gemini_coat 33.9 33.9 244 domain Y Y N capsid/nuclear shuttle family protein GO:0005198,GO:0019028 8124726,9191917,9778251 0 EBI-EMBL Geminivirus coat protein/nuclear export factor BR1 family capsid/nuclear shuttle family protein It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically [1]. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus [3]. [1]. 9191917. Maize streak virus coat protein binds single- and double-stranded DNA in vitro. Liu H, Boulton MI, Davies JW;. J Gen Virol 1997;78:1265-1270. [2]. 9778251. Bean Dwarf mosaic geminivirus movement proteins recognize DNA in a form- and size-specific manner. Rojas MR, Noueiry AO, Lucas WJ, Gilbertson RL;. Cell 1998;95:105-130. [3]. 8124726. Two proteins of a plant DNA virus coordinate nuclear and plasmodesmal transport. Noueiry AO, Lucas WJ, Gilbertson RL;. Cell 1994;76:925-932. (from Pfam) NF013054.5 PF00858.29 ASC 23.6 23.6 455 domain Y Y N amiloride-sensitive sodium channel family protein GO:0005272,GO:0006814,GO:0016020 0 EBI-EMBL Amiloride-sensitive sodium channel amiloride-sensitive sodium channel family protein NF013092.5 PF00897.22 Orbi_VP7 25 25 348 PfamEq Y Y N inner capsid protein VP7 GO:0005198,GO:0019028 9261081 0 EBI-EMBL Orbivirus inner capsid protein VP7 orbivirus inner capsid protein VP7 In BTV, 260 trimers of VP7 are found in the core. The major proteins of the core are VP7 and VP3. VP7 forms an outer layer around VP3 [1]. Crystal structure. [1]. 9261081. Structures of orbivirus VP7: implications for the role of this protein in the viral life cycle. Basak AK, Grimes JM, Gouet P, Roy P, Stuart DI;. Structure 1997;5:871-883. (from Pfam) NF013452.5 PF01284.28 MARVEL 32.8 32.8 135 domain Y Y N MARVEL domain-containing protein GO:0016020 12468223 0 EBI-EMBL Membrane-associating domain Membrane-associating domain MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins [1]. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis. [1]. 12468223. MARVEL: a conserved domain involved in membrane apposition events. Sanchez-Pulido L, Marti;n-Belmonte F, Valencia A, Alonso MA;. Trends Biochem Sci 2002;27:599-601. (from Pfam) NF013513.5 PF01350.22 Flavi_NS4A 27 27 144 domain Y Y N non-structural protein NS4A GO:0016032,GO:0016070,GO:0044423 2174669,2541547 0 EBI-EMBL Flavivirus non-structural protein NS4A Flavivirus non-structural protein NS4A Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4A protein is small and poorly conserved among the Flaviviruses. NS4A contains multiple hydrophobic potential membrane spanning regions [1]. NS4A has only been found in cells infected by Kunjin virus [2]. [1]. 2174669. Flavivirus genome organization, expression, and replication. Chambers TJ, Hahn CS, Galler R, Rice CM;. Annu Rev Microbiol 1990;44:649-688. [2]. 2541547. Positive identification of NS4A, the last of the hypothetical nonstructural proteins of flaviviruses. Speight G, Westaway EG;. Virology 1989;170:299-301. (from Pfam) NF013711.5 PF01562.24 Pep_M12B_propep 23.7 23.7 93 domain Y Y N reprolysin family propeptide-containing metallopeptidase 7674922 0 EBI-EMBL Reprolysin family propeptide reprolysin family propeptide domain Certified not prok. NF013818.5 PF01683.23 EB 24.3 24.3 52 domain Y Y N EB domain-containing protein 0 EBI-EMBL EB module EB module This domain has no known function. It is found in several C. elegans proteins. The domain contains 8 conserved cysteines that probably form four disulphide bridges. This domain is found associated with kunitz domains Pfam:PF00014. (from Pfam) NF014450.5 PF02393.21 US22 35 35 124 domain Y Y N US22 domain-containing protein 10405367,1321206,21306995 0 EBI-EMBL US22 like US22 like US22 proteins have been found across many animal DNA viruses and some vertebrates [3]. The name sake of this family US22 Swiss:P09722 is an early nuclear protein that is secreted from cells [2]. The US22 family may have a role in virus replication and pathogenesis [1]. Domain analysis showed that US22 proteins usually contain two copies of conserved modules which is homologous to several other families like SMI1 and SYD (commonly called SUKH superfamily) [3]. Bacterial operon analysis revealed that all bacterial SUKH members function as immunity proteins against various toxins. Thus US22 family is predicted to counter diverse anti-viral responses by interacting with specific host proteins [3]. [1]. 10405367. Transcriptional analysis of the murine cytomegalovirus HindIII-I region: identification of a novel immediate-early gene region. Hanson LK, Dalton BL, Karabekian Z, Farrell HE, Rawlinson WD, Stenberg RM, Campbell AE;. Virology 1999;260:156-164. [2]. 1321206. Identification of homologues to the human cytomegalovirus US22 gene family in human herpesvirus 6. Efstathiou S, Lawrence GL, Brown CM, Barrell BG;. J Gen Virol 1992;73:1661-1671. [3]. 21306995. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Zhang D, Iyer LM, Aravind L;. Nucleic Acids Res. 2011;39:4532-4552. (from Pfam) NF014495.5 PF02442.22 L1R_F9L 27 27 200 domain Y Y N L1 family membrane protein 11689653,8938976 0 EBI-EMBL Lipid membrane protein of large eukaryotic DNA viruses L1 family membrane protein The four families of large eukaryotic DNA viruses, Poxviridae, Asfarviridae, Iridoviridae, and Phycodnaviridae, referred to collectively as nucleocytoplasmic large DNA viruses or NCLDV, have all been shown to have a lipid membrane, in spite of the major differences in virion structure. The paralogous genes L1R and F9L encode membrane proteins that have a conserved domain architecture, with a single, C-terminal transmembrane helix, and an N-terminal, multiple-disulfide-bonded domain. The conservation of the myristoylated, disulfide-bonded protein L1R/F9L in most of the NCLDV correlates with the conservation of the thiol-disulfide oxidoreductase E10R which, in vaccinia virus, is required for the formation of disulfide bonds in L1R and F9L [2]. [1]. 8938976. Sequence analysis of a Molluscum contagiosum virus DNA region which includes the gene encoding protein kinase 2 and other genes with unique organization. Martin-Gallardo A, Moratilla M, Funes JM, Agromayor M, Nunez A, Varas AJ, Collado M, Valencia A, Lopez-Estebaranz JL, Esteban M;. Virus Genes 1996;13:19-29. [2]. 11689653. Common origin of four diverse families of large eukaryotic DNA viruses. Iyer LM, Aravind L, Koonin EV;. J Virol. 2001;75:11720-11734. (from Pfam) NF014532.5 PF02480.21 Herpes_gE 26.7 26.7 175 domain Y N N Alphaherpesvirus glycoprotein E 10881679,16646632 0 EBI-EMBL Alphaherpesvirus glycoprotein E Alphaherpesvirus glycoprotein E Glycoprotein E (gE) of Alphaherpesvirus forms a complex with glycoprotein I (gI) (Pfam:PF01688), functioning as an immunoglobulin G (IgG) Fc binding protein. gE is involved in virus spread but is not essential for propagation [1]. This entry represents the Ig-like domain of gE, identified as the Fc-binding domain [2]. [1]. 10881679. Epitopes on glycoprotein E and on the glycoprotein E/glycoprotein I complex of bovine herpesvirus 1 are expressed by all of 222 isolates and 11 vaccine strains. Rijsewijk FA, Kaashoek MJ, Langeveld JP, Maris-Veldhuis MA, Magdalena J, Verschuren SB, Meloen RH, van Oirschot JT;. Arch Virol 2000;145:921-936. [2]. 16646632. Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging. Sprague ER, Wang C, Baker D, Bjorkman PJ;. PLoS Biol. 2006;4:e148. (from Pfam) NF014737.5 PF02713.19 DUF220 29.4 29.4 73 domain Y Y N DUF220 domain-containing protein 31068459 0 EBI-EMBL Domain of unknown function DUF220 Domain of unknown function DUF220 This is family consists of a region in several Arabidopsis thaliana hypothetical proteins none of which have any known function. The aligned region contains two cysteine residues. This domain shows structural similarity to members of the Bet v1-like superfamily [1] and may be involved in lipid binding. [1]. 31068459. JASSY, a chloroplast outer membrane protein required for jasmonate biosynthesis. Guan L, Denkert N, Eisa A, Lehmann M, Sjuts I, Weiberg A, Soll J, Meinecke M, Schwenkert S;. Proc Natl Acad Sci U S A. 2019;116:10568-10575. (from Pfam) NF015088.5 PF03103.22 DUF243 25 25 98 domain Y Y N DUF243 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF243) Domain of unknown function (DUF243) This family of uncharacterised proteins is only found in fly proteins. It is found associated with YLP motifs Pfam:PF02757 in some proteins. (from Pfam) NF015105.5 PF03121.20 Herpes_UL52 21 21 75 domain Y Y N herpesvirus-type DNA primase 10501495,11278618,8659123,9242911 0 EBI-EMBL Herpesviridae UL52/UL70 DNA primase herpesvirus DNA primase Herpes simplex virus type 1 DNA replication in host cells is known to be mediated by seven viral-encoded proteins, three of which form a heterotrimeric DNA helicase-primase complex. This complex consists of UL5, UL8, and UL52 subunits. Heterodimers consisting of UL5 and UL52 have been shown to retain both helicase and primase activities. Nevertheless, UL8 is still essential for replication: though it lacks any DNA binding or catalytic activities, it is involved in the transport of UL5-UL52 and it also interacts with other replication proteins. The molecular mechanisms of the UL5-UL52 catalytic activities are not known. While UL5 is associated with DNA helicase activity and UL52 with DNA primase activity, the helicase activity requires the interaction of UL5 and UL52 [see 2,3]. It is not known if the primase activity can be maintained by UL52 alone. The region encompassed by residues 610-636 of HSV1 UL52 Swiss:P10236 is thought to contain a divalent metal cation binding motif. Indeed, this region contains several aspartate and glutamate residues that might be involved in divalent cation binding. The biological significance of UL52-UL8 interaction is not known. Yeast two-hybrid analysis together with immunoprecipitation experiments have shown that the HSV1 UL52 region between residues 366-914 is essential for this interaction, while the first 349 N-terminal residues are dispensable [2]. This family also includes protein UL70 from cytomegalovirus (CMV, a subgroup of the Herpesviridae) strains (e.g. Swiss:P17149), which, by analogy with UL52, is thought to have DNA primase activity. Indeed, CMV strains also possess a DNA . TRUNCATED at 1650 bytes (from Pfam) NF015240.5 PF03268.19 DUF267 25 25 360 domain Y Y N DUF267 domain-containing protein 0 EBI-EMBL Caenorhabditis protein of unknown function, DUF267 Caenorhabditis protein of unknown function, DUF267 NF015265.5 PF03294.19 Pox_Rap94 25 25 796 domain Y Y N RNA polymerase-associated transcription-specificity factor RAP94 GO:0003700 1565650,19759131 0 EBI-EMBL RNA polymerase-associated transcription specificity factor, Rap94 RNA polymerase-associated transcription-specificity factor RAP94 NF015283.5 PF03312.20 DUF272 25 25 124 domain Y Y N DUF272 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF272) Protein of unknown function (DUF272) This family of proteins is restricted to C.elegans and has no known function. The protein contains a ubiquitin fold. The GO annotation for the protein indicates that it has a function in nematode larval development. (from Pfam) NF015345.5 PF03380.19 DUF282 22.8 21.8 38 domain Y Y N DUF282 domain-containing protein 0 EBI-EMBL Caenorhabditis protein of unknown function, DUF282 Caenorhabditis protein of unknown function, DUF282 NF015381.5 PF03416.24 Peptidase_C54 25 25 276 domain Y Y N cysteine protease ATG4 GO:0019786 0 EBI-EMBL Peptidase family C54 cysteine protease ATG4 NF015401.5 PF03436.18 DUF281 25 25 55 domain Y Y N DUF281 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF281) Domain of unknown function (DUF281) This family of worm domain has no known function. The boundaries of the presumed domain are rather uncertain. (from Pfam) NF015518.5 PF03556.20 Cullin_binding 27.9 27.9 118 domain Y Y N cullin binding domain-containing protein 17597076,18206966,18826954 0 EBI-EMBL Cullin binding Cullin binding This domain binds to cullins and to Rbx-1, components of an E3 ubiquitin ligase complex for neddylation [1-3]. Neddylation is the process by which the C-terminal glycine of the ubiquitin-like protein Nedd8 is covalently linked to lysine residues in a protein through an isopeptide bond. The structure of this domain is composed entirely of alpha helices [1,2]. [1]. 17597076. Structural basis for the function of DCN-1 in protein Neddylation. Yang X, Zhou J, Sun L, Wei Z, Gao J, Gong W, Xu RM, Rao Z, Liu Y;. J Biol Chem. 2007;282:24490-24494. [2]. 18206966. Dcn1 functions as a scaffold-type E3 ligase for cullin neddylation. Kurz T, Chou YC, Willems AR, Meyer-Schaller N, Hecht ML, Tyers M, Peter M, Sicheri F;. Mol Cell. 2008;29:23-35. [3]. 18826954. SCCRO (DCUN1D1) is an essential component of the E3 complex for neddylation. Kim AY, Bommelje CC, Lee BE, Yonekawa Y, Choi L, Morris LG, Huang G, Kaufman A, Ryan RJ, Hao B, Ramanathan Y, Singh B;. J Biol Chem. 2008;283:33211-33220. (from Pfam) NF015593.5 PF03637.22 Mob1_phocein 27 27 170 domain Y Y N Mob1/phocein family protein 11251078,9436989 0 EBI-EMBL Mob1/phocein family Mob1/phocein family protein Mob1 is an essential Saccharomyces cerevisiae protein, identified from a two-hybrid screen, that binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Mob1 contains no known structural motifs; however MOB1 is a member of a conserved gene family and shares sequence similarity with a nonessential yeast gene, MOB2. Mob1 is a phosphoprotein in vivo and a substrate for the Mps1p kinase in vitro. Conditional alleles of MOB1 cause a late nuclear division arrest at restrictive temperature [1]. This family also includes phocein Swiss:Q9QYW3, a rat protein that by yeast two hybrid interacts with striatin [2]. [1]. 9436989. MOB1, an essential yeast gene required for completion of mitosis and maintenance of ploidy. Luca FC, Winey M;. Mol Biol Cell 1998;9:29-46. [2]. 11251078. Molecular cloning and characterization of phocein, a protein found from the Golgi complex to dendritic spines. Baillat G, Moqrich A, Castets F, Baude A, Bailly Y, Benmerah A, Monneron A;. Mol Biol Cell 2001;12:663-673. (from Pfam) NF015698.5 PF03754.18 At2g31720-like 24.4 24.4 113 domain Y Y N B3 domain-containing protein GO:0003677 29462363 0 EBI-EMBL B3 domain-containing protein At2g31720-like B3 domain-containing protein At2g31720-like This entry represents a group of uncharacterised plant proteins, including B3 domain-containing protein At2g31720 (also known as Protein AUXIN RESPONSE FACTOR 70) from Arabidopsis. These are DNA-binding proteins likely to be involved in stress response [1]. [1]. 29462363. A Gene Regulatory Network for Cellular Reprogramming in Plant Regeneration. Ikeuchi M, Shibata M, Rymen B, Iwase A, Bagman AM, Watt L, Coleman D, Favero DS, Takahashi T, Ahnert SE, Brady SM, Sugimoto K;. Plant Cell Physiol. 2018;59:765-777. (from Pfam) NF015719.5 PF03778.18 DUF321 25 10 23 domain Y Y N DUF321 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF321) Protein of unknown function (DUF321) This family may be related to the FARP (FMRFamide) family, Pfam:PF01581. (from Pfam) NF016106.5 PF04190.18 GET4 30 30 257 domain Y Y N Get4 family protein GO:0045048 20676083,21636303,21743475,22190685,24727835,25535373,28104892 0 EBI-EMBL Golgi to ER traffic protein 4 Get4 family protein In budding yeast, Get4 is part of the GET complex that inserts the tail-anchored (TA) proteins into the endoplasmic reticulum membrane [1,2]. In humans, Get4 is part the BAG6/BAT3 complex, maintains misfolded and hydrophobic patches-containing proteins in a soluble state and facilitates their proper delivery to the endoplasmic reticulum, or alternatively promotes their sorting to the proteasome where they undergo degradation [3,4,5,6]. The BAG6/BAT3 complex is involved in the post-translational delivery of tail-anchored/type II transmembrane proteins to the endoplasmic reticulum membrane [3,6,7]. [1]. 22190685. Interaction surface and topology of Get3-Get4-Get5 protein complex, involved in targeting tail-anchored proteins to endoplasmic reticulum. Chang YW, Lin TW, Li YC, Huang YS, Sun YJ, Hsiao CD;. J Biol Chem. 2012;287:4783-4789. [2]. 24727835. Crystal structure of ATP-bound Get3-Get4-Get5 complex reveals regulation of Get3 by Get4. Gristick HB, Rao M, Chartron JW, Rome ME, Shan SO, Clemons WM Jr;. Nat Struct Mol Biol. 2014;21:437-442. [3]. 20676083. A ribosome-associating factor chaperones tail-anchored membrane proteins. Mariappan M, Li X, Stefanovic S, Sharma A, Mateja A, Keenan RJ, Hegde RS;. Nature. 2010;466:1120-1124. [4]. 21636303. A ubiquitin ligase-associated chaperone holdase maintains polypeptides in soluble states for proteasome degradation. Wang Q, Liu Y, Soetandyo N, Baek K, Hegde R, Ye Y;. Mol Cell. 2011;42:758-770. [5]. 21743475. Protein targeting and degradation are coupled for elimination of mislocalized proteins. Hessa T, Sharma A, Mariappan M, Eshleman HD, Gutierrez E, Hegde RS;. Nature. 2011;475:39. TRUNCATED at 1650 bytes (from Pfam) NF016225.5 PF04318.17 DUF468 25 25 84 domain Y Y N DUF468 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF468) Protein of unknown function (DUF468) These conserved ORFs probably are probably not translated into protein [Personal communication, Val Wood]. (from Pfam) NF016237.5 PF04334.17 DUF478 25 25 68 domain Y Y N DUF478 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF478) Protein of unknown function (DUF478) This family contains uncharacterised protein encoded on Trypanosoma kinetoplast minicircles. (from Pfam) NF016273.5 PF04370.17 DUF508 25 25 149 domain Y Y N DUF508 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF508) Domain of unknown function (DUF508) This is a family of uncharacterised proteins from C. elegans. (from Pfam) NF016378.5 PF04489.18 DUF570 25 25 456 domain Y Y N DUF570 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF570) Protein of unknown function (DUF570) Protein of unknown function, found in herpesvirus and cytomegalovirus. (from Pfam) NF016393.5 PF04504.19 GeBP-like_DBD 29.5 29.5 94 domain Y Y N DNA-binding domain-containing protein GO:0006355 12028578,12535344,18162594,27031427,35890483 0 EBI-EMBL Glabrous-enhancer-binding protein-like family, DBD domain Glabrous-enhancer-binding protein-like family, DBD domain This entry represents the DNA binding domain (DBD) present in GLABROUS1 enhancer-binding protein (GeBP) and GeBP-like proteins, such us storekeeper and storekeeper-like (STKL) transcription factors. GeBP and GeBP-like proteins play a redundant role in cytokinin hormone pathway regulation [1,2,3]. Storekeeper was identified as a B-box motif binding factor that regulates expression of patatin, a storage protein in potato [4]. Storekeeper-like transcription factors STKL1 and STKL2 function as transcription factors in the glucose signalling pathway [5]. The overall predicted structure of this DNA binding domain (DBD) reveals a bundle of four helices, with helices alpha1 to alpha3 making up a single myb-type helix-turn-helix (HTH) domain. [1]. 12535344. GeBP, the first member of a new gene family in Arabidopsis, encodes a nuclear protein with DNA-binding activity and is regulated by KNAT1. Curaba J, Herzog M, Vachon G;. Plant J. 2003;33:305-317. [2]. 35890483. Genome-Wide Characterization and Expression Analysis of GeBP Family Genes in Soybean. Liu S, Liu Y, Liu C, Zhang F, Wei J, Li B;. Plants (Basel). 2022;11:1848. [3]. 18162594. GeBP and GeBP-like proteins are noncanonical leucine-zipper transcription factors that regulate cytokinin response in Arabidopsis. Chevalier F, Perazza D, Laporte F, Le Henanff G, Hornitschek P, Bonneville JM, Herzog M, Vachon G;. Plant Physiol. 2008;146:1142-1154. [4]. 12028578. Storekeeper defines a new class of plant-specific DNA-binding proteins and is a putative regulator of patatin expression. Zourelidou M, de Torres-Zabala M, Smith C, Bevan MW;. Plant J. 2002;30:489-497. [5]. 27031427. Regu. TRUNCATED at 1650 bytes (from Pfam) NF016399.5 PF04510.17 DUF577 27.6 27.6 173 domain Y Y N DUF577 domain-containing protein 25653662 0 EBI-EMBL Family of unknown function (DUF577) Family of unknown function (DUF577) This domain is found in Arabidopsis thaliana proteins, which are specifically expressed during meiosis [1]. Many of these members contain a repeated region. [1]. 25653662. Analysis of Arabidopsis floral transcriptome: detection of new florally expressed genes and expansion of Brassicaceae-specific gene families. Zhang L, Wang L, Yang Y, Cui J, Chang F, Wang Y, Ma H;. Front Plant Sci. 2015;5:802. (from Pfam) NF016406.5 PF04517.17 Microvir_lysis 25 25 40 domain Y Y N MraY-inhibiting host cell lysis protein E GO:0004857,GO:0019054 12100551 0 EBI-EMBL Microvirus lysis protein (E), C terminus MraY-inhibiting host cell lysis protein E E protein causes host cell lysis by inhibiting MraY, a peptidoglycan biosynthesis enzyme. This leads to cell wall failure at septation [1]. The N terminal transmembrane region matches the signal peptide model and must be omitted from the family. [1]. 12100551. The Escherichia coli FKBP-type PPIase SlyD is required for the stabilization of the E lysis protein of bacteriophage phiX174. Bernhardt TG, Roof WD, Young R;. Mol Microbiol 2002;45:99-108. (from Pfam) NF016411.5 PF04522.17 BBMV_Gp1_N 25 25 234 domain Y Y N broad bean mottle virus Gp1 domain-containing protein GO:0003723,GO:0003968,GO:0006351 0 EBI-EMBL Broad bean mottle virus, Gp1, N-terminal Broad bean mottle virus, Gp1, N-terminal This region represents the N terminus of Broad bean mottle virus, Gp1 (2a protein), and is always found N terminal to a predicted RNA-dependent RNA polymerase region (Pfam:PF00978). (from Pfam) NF016414.5 PF04526.18 DUF568 25 25 100 domain Y Y N DUF568 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF568) Protein of unknown function (DUF568) Family of uncharacterised plant proteins. (from Pfam) NF016420.5 PF04532.17 DUF587 25 25 227 domain Y Y N DUF587 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF587) Protein of unknown function (DUF587) This family consists of the N termini of some human herpesvirus U58 proteins, and some cytomegalovirus UL87 proteins. This region is always found N terminal to the Pfam family UL87 (Pfam:PF03043), which has no known function. (from Pfam) NF016434.5 PF04547.17 Anoctamin 28 28 460 domain Y Y N anoctamin 18724360 0 EBI-EMBL Calcium-activated chloride channel anoctamin The family carries eight putative transmembrane domains, and, although it has no similarity to other known channel proteins, it is clearly a calcium-activated ionic channel. It is expressed in various secretory epithelia, the retina and sensory neurons, and mediates receptor-activated chloride currents in diverse physiological processes [1]. [1]. 18724360. TMEM16A confers receptor-activated calcium-dependent chloride conductance. Yang YD, Cho H, Koo JY, Tak MH, Cho Y, Shim WS, Park SP, Lee J, Lee B, Kim BM, Raouf R, Shin YK, Oh U;. Nature, 2008; [Epub ahead of print] (from Pfam) NF016441.5 PF04554.18 Extensin_2 20.8 20.8 57 domain Y Y N extensin-like domain-containing protein GO:0005199,GO:0009664 0 EBI-EMBL Extensin-like region Extensin-like region NF016520.5 PF04641.17 Rtf2 27.4 27.4 258 domain Y Y N replication termination factor 2 family protein 19416828,9803414 0 EBI-EMBL Rtf2 RING-finger replication termination factor 2 family protein It is vital for effective cell-replication that replication is not stalled at any point by, for instance, damaged bases. Replication termination factor 2 (Rtf2) stabilizes the replication fork stalled at the site-specific replication barrier RTS1 by preventing replication restart until completion of DNA synthesis by a converging replication fork initiated at a flanking origin. The RTS1 element terminates replication forks that are moving in the cen2-distal direction while allowing forks moving in the cen2-proximal direction to pass through the region. Rtf2 contains a C2HC2 motif related to the C3HC4 RING-finger motif, and would appear to fold up, creating a RING finger-like structure but forming only one functional Zn2+ ion-binding site [1]. This domain is also found at the N-terminus of peptidyl-prolyl cis-trans isomerase 4, a divergent cyclophilin family [2]. [1]. 19416828. Schizosaccharomyces pombe Rtf2 mediates site-specific replication termination by inhibiting replication restart. Inagawa T, Yamada-Inagawa T, Eydmann T, Mian IS, Wang TS, Dalgaard JZ;. Proc Natl Acad Sci U S A. 2009;106:7927-7932. [2]. 9803414. A divergent multi-domain cyclophilin is highly conserved between parasitic and free-living nematode species and is important in larval muscle development. Page AP, Winter AD;. Mol Biochem Parasitol. 1998;95:215-227. (from Pfam) NF016521.5 PF04642.17 DUF601 24.1 24.1 327 domain Y Y N DUF601 domain-containing protein 0 EBI-EMBL Protein of unknown function, DUF601 Protein of unknown function, DUF601 This family represents a conserved region found in several uncharacterised plant proteins. (from Pfam) NF016525.5 PF04646.17 DUF604 25 25 256 domain Y Y N DUF604 domain-containing protein 0 EBI-EMBL Protein of unknown function, DUF604 Protein of unknown function, DUF604 This family includes a conserved region found in several uncharacterised plant proteins. (from Pfam) NF016622.5 PF04747.17 DUF612 22.6 22.6 511 domain Y Y N DUF612 domain-containing protein 0 EBI-EMBL Protein of unknown function, DUF612 Protein of unknown function, DUF612 This family includes several uncharacterised proteins from Caenorhabditis elegans. (from Pfam) NF016639.5 PF04764.17 DUF613 25 25 120 domain Y Y N DUF613 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF613) Protein of unknown function (DUF613) Family of chloroplast proteins of unknown function. Some members have two copies of the conserved region. (from Pfam) NF016651.5 PF04776.17 protein_MS5 25 25 119 domain Y Y N MS5 family protein 0 EBI-EMBL Protein MS5 MS5 family protein Proteins are known only from species of Brassicaceae. Protein MS5 is essential for pairing of homologues during early prophase stage of meiosis but not necessary for the initiation of DNA double-strand breaks. (from Pfam) NF016655.5 PF04781.17 DUF627 27.6 27.6 108 domain Y Y N DUF627 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF627) Protein of unknown function (DUF627) This family represents the N-terminal region of several plant proteins of unknown function. (from Pfam) NF016657.5 PF04783.17 DUF630 27 27 59 domain Y Y N DUF630 domain-containing protein 21348639 0 EBI-EMBL Protein of unknown function (DUF630) Protein of unknown function (DUF630) This region is sometimes found at the N-terminus of putative plant bZIP proteins. Its function is not known. Structural modelling suggests this domain may bind nucleic acids [1]. [1]. 21348639. Ab Initio Modeling Led Annotation Suggests Nucleic Acid Binding Function for Many DUFs. Rigden DJ;. OMICS 2011;0:0-0. (from Pfam) NF016660.5 PF04786.17 Baculo_DNA_bind 25 25 248 domain Y Y N DNA-binding protein 0 EBI-EMBL ssDNA binding protein DNA-binding protein Family of Baculovirus ssDNA binding proteins. (from Pfam) NF016692.5 PF04819.17 DUF716 25 25 138 domain Y Y N DUF716 domain-containing protein 0 EBI-EMBL Family of unknown function (DUF716) Family of unknown function (DUF716) This family is equally distributed in both metazoa and plants. Annotation associated with Swiss:Q9SLW7 suggest that it may be involved in response to viral attack in plants. However, no clear function has been assigned to this family. (from Pfam) NF016715.5 PF04842.17 DUF639 37.1 37.1 231 domain Y Y N DUF639 domain-containing protein 0 EBI-EMBL Plant protein of unknown function (DUF639) Plant protein of unknown function (DUF639) Plant protein of unknown function. (from Pfam) NF016788.5 PF04920.17 BNYVV_p31 25 25 126 domain Y Y N beet necrotic yellow vein virus protein p31 17412994 0 EBI-EMBL Beet necrotic yellow vein virus, p31 beet necrotic yellow vein virus protein p31 This is a family of hypothetical proteins known as p31, mostly from Beet necrotic yellow vein virus. P31, encoded by RNA4, is involved in efficient vector transmission, symptom severity and silencing suppression in roots [1]. [1]. 17412994. RNA4-encoded p31 of beet necrotic yellow vein virus is involved in efficient vector transmission, symptom severity and silencing suppression in roots. Rahim MD, Andika IB, Han C, Kondo H, Tamada T;. J Gen Virol. 2007;88:1611-1619. (from Pfam) NF016864.5 PF05003.17 DUF668 24 24 89 domain Y Y N DUF668 domain-containing protein GO:0045927 25062973 0 EBI-EMBL Protein of unknown function (DUF668) Protein of unknown function (DUF668) This entry represents the C-terminal domain of PSI proteins from Arabidopsis. This domain is found associated with Pfam:PF11961. PSI1 was identified as a gene that is co-expressed with the phytosulfokine (PSK) receptor genes PSKR1 and PSKR2 in Arabidopsis thaliana. PSI proteins are plant-specific and promote growth [1]. [1]. 25062973. The PSI family of nuclear proteins is required for growth in arabidopsis. Stuhrwohldt N, Hartmann J, Dahlke RI, Oecking C, Sauter M;. Plant Mol Biol. 2014;86:289-302. (from Pfam) NF016878.5 PF05018.18 CFA20_dom 24 24 185 domain Y Y N CFA20 domain-containing protein 20118210,24259666,24574454 0 EBI-EMBL CFA20 domain CFA20 domain This domain is characteristic of cilia- and flagella-associated protein 20 (CFA20). CFA20 is a cilium- and flagellum-specific protein that plays a role in axonemal structure organisation and motility [1,2]. In Chlamydomonas reinhardtii, it stabilises outer doublet microtubules (DMTs) of the axoneme and may work as a scaffold for intratubular proteins, such as tektin and PACRG, to produce the beak structures in DMT1 [2,3]. Other proteins contain a domain with homology to CFA20. WDR90/POC16 contains such a domain in its N terminus, followed by a large C-terminal domain with multiple WD40 repeats [2]. This domain is also present in the N terminus of uncharacterised protein C3orf67. [1]. 20118210. Bug22p, a conserved centrosomal/ciliary protein also present in higher plants, is required for an effective ciliary stroke in Paramecium. Laligne C, Klotz C, de Loubresse NG, Lemullois M, Hori M, Laurent FX, Papon JF, Louis B, Cohen J, Koll F;. Eukaryot Cell. 2010;9:645-655. [2]. 24574454. FAP20 is an inner junction protein of doublet microtubules essential for both the planar asymmetrical waveform and stability of flagella in Chlamydomonas. Yanagisawa HA, Mathis G, Oda T, Hirono M, Richey EA, Ishikawa H, Marshall WF, Kikkawa M, Qin H;. Mol Biol Cell. 2014;25:1472-1483. [3]. 24259666. The conserved ciliary protein Bug22 controls planar beating of Chlamydomonas flagella. Meng D, Cao M, Oda T, Pan J;. J Cell Sci. 2014;127:281-287. (from Pfam) NF016914.5 PF05056.17 DUF674 24.4 24.4 445 domain Y Y N DUF674 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF674) Protein of unknown function (DUF674) This family is found in Arabidopsis thaliana and contains several uncharacterised proteins. (from Pfam) NF016931.5 PF05075.19 DUF684 25 25 338 domain Y Y N DUF684 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF684) Protein of unknown function (DUF684) This family contains several uncharacterised proteins from Caenorhabditis elegans. The GO annotation suggests that the protein is involved in nematode larval development and has a positive regulation on growth rate. (from Pfam) NF016933.5 PF05077.17 DUF678 24.1 24.1 74 domain Y Y N DUF678 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF678) Protein of unknown function (DUF678) This family contains several poxvirus proteins of unknown function. (from Pfam) NF016934.5 PF05078.17 DUF679 25 25 163 domain Y Y N DUF679 domain-containing protein 20712629,22530652,30850817 0 EBI-EMBL Protein of unknown function (DUF679) Protein of unknown function (DUF679) This family includes members such as plant proteins AtDMPs 1-10 (Arabidopsis thaliana DUF679 domain membrane proteins 1 -10) [1]. The AtDMP proteins are predicted to have four transmembrane spans, with cytosolic amino- and carboxy-termini. DMP1 is a membrane protein that may be involved in membrane fission during breakdown of the ER and the tonoplast during leaf senescence and in membrane fusion during vacuole biogenesis in roots [2]. Several DMP proteins are expressed in senescing organs (DMP1, -3, -4) or tissues that will stall later in development (DMP1, -2, -4, -7). These expression patterns strongly suggest involvement of several DMPs in various programmed cell death processes, e.g. senescence, dehiscence and abscission [1]. AtDMP8 and AtDMP9 however, have been shown to facilitate gamete fusion during double fertilisation in flowering plants [3]. [1]. 20712629. Expression, localisation and phylogeny of a novel family of plant-specific membrane proteins. Kasaras A, Kunze R;. Plant Biol (Stuttg). 2010;12:140-152. [2]. 22530652. Arabidopsis senescence-associated protein DMP1 is involved in membrane remodeling of the ER and tonoplast. Kasaras A, Melzer M, Kunze R;. BMC Plant Biol. 2012;12:54. [3]. 30850817. Gamete fusion is facilitated by two sperm cell-expressed DUF679 membrane proteins. Cyprys P, Lindemeier M, Sprunck S;. Nat Plants. 2019;5:253-257. (from Pfam) NF016936.5 PF05080.17 DUF681 25 25 101 domain Y Y N DUF681 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF681) Protein of unknown function (DUF681) This family contains several uncharacterised beak and feather disease virus proteins. (from Pfam) NF016937.5 PF05081.17 AcMNPV_P18 25 25 157 domain Y Y N AcMNPV P18 family protein 0 EBI-EMBL Autographa californica nuclear polyhedrosis virus (AcMNPV), P18 AcMNPV P18 family protein This family is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), P18; it is a family of uncharacterised viral proteins. (from Pfam) NF017110.5 PF05266.19 DUF724 38.4 38.4 188 domain Y Y N DUF724 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF724) Protein of unknown function (DUF724) This family contains several uncharacterised proteins found in Arabidopsis thaliana and other plants. This region is often found associated with Agenet domains and may contain coiled-coil. (from Pfam) NF017111.5 PF05267.17 DUF725 22 22 121 domain Y Y N DUF725 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF725) Protein of unknown function (DUF725) This family contains several Drosophila proteins of unknown function. (from Pfam) NF017143.5 PF05300.16 MIC19_MIC25 33 33 168 domain Y Y N MIC19/MIC25 domain-containing protein GO:0005739,GO:0061617 21081504,22228767,27245231 0 EBI-EMBL MICOS complex subunit MIC19/MIC25 MICOS complex subunit MIC19/MIC25 MIC19 (also known as ChChd3) and MIC25 (also known as ChChd6) are components of the MICOS complex, a large protein complex of the mitochondrial inner membrane that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane [1,2,3]. MIC19 plays an important role in the maintenance of the MICOS complex stability and the mitochondrial cristae morphology [1]. [1]. 21081504. ChChd3, an inner mitochondrial membrane protein, is essential for maintaining crista integrity and mitochondrial function. Darshi M, Mendiola VL, Mackey MR, Murphy AN, Koller A, Perkins GA, Ellisman MH, Taylor SS;. J Biol Chem. 2011;286:2918-2932. [2]. 22228767. CHCM1/CHCHD6, novel mitochondrial protein linked to regulation of mitofilin and mitochondrial cristae morphology. An J, Shi J, He Q, Lui K, Liu Y, Huang Y, Sheikh MS;. J Biol Chem. 2012;287:7411-7426. [3]. 27245231. The MICOS complex of human mitochondria. Kozjak-Pavlovic V;. Cell Tissue Res. 2017;367:83-93. (from Pfam) NF017144.5 PF05301.16 Acetyltransf_16 27 27 173 domain Y Y N GNAT family N-acetyltransferase 2.3.1.- GO:0005874,GO:0019799,GO:0071929 12124626,17172875 0 EBI-EMBL GNAT acetyltransferase, Mec-17 GNAT family N-acetyltransferase Mec-17 is the protein product of one of the 18 genes required for the development and function of the touch receptor neuron for gentle touch. Mec-17 is specifically required for maintaining the differentiation of the touch receptor [1]. The family shares all the residue-motifs characteristic of Gcn5-related acetyl-transferases, though the exact unction is still unknown [2]. [1]. 12124626. Identification of genes expressed in C. elegans touch receptor neurons. Zhang Y, Ma C, Delohery T, Nasipak B, Foat BC, Bounoutas A, Bussemaker HJ, Kim SK, Chalfie M;. Nature. 2002;418:331-335. [2]. 17172875. Eukaryotic domain of unknown function DUF738 belongs to Gcn5-related N-acetyltransferase superfamily. Steczkiewicz K, Kinch L, Grishin NV, Rychlewski L, Ginalski K;. Cell Cycle. 2006;5:2927-2930. (from Pfam) NF017147.5 PF05304.17 DUF728 25 25 139 domain Y Y N DUF728 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF728) Protein of unknown function (DUF728) This family consists of several uncharacterised tobravirus proteins of unknown function. (from Pfam) NF017149.5 PF05306.16 DUF733 25 25 85 domain Y Y N DUF733 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF733) Protein of unknown function (DUF733) This family consists of several uncharacterised Drosophila melanogaster proteins of unknown function. (from Pfam) NF017166.5 PF05325.16 DUF730 32 32 122 domain Y Y N DUF730 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF730) Protein of unknown function (DUF730) This family consists of several uncharacterised Arabidopsis thaliana proteins of unknown function. (from Pfam) NF017171.5 PF05332.16 Vesi_VP2 27.7 27.7 113 domain Y Y N minor capsid protein VP2 family protein 30626974 0 EBI-EMBL Vesivirus VP2 protein minor capsid protein VP2 family protein This family consists of several Calicivirus VP2 proteins [1]. VP2 is a minor capsid protein encoded by all caliciviruses. forms a large portal-like assembly at a unique three-fold axis of symmetry, following receptor engagement. This assembly-which was not detected in undecorated virions-is formed of twelve copies of VP2, arranged with their hydrophobic N termini pointing away from the virion surface. Paper describing PDB structure 6gsi. [1]. 30626974. Calicivirus VP2 forms a portal-like assembly following receptor engagement. Conley MJ, McElwee M, Azmi L, Gabrielsen M, Byron O, Goodfellow IG, Bhella D;. Nature. 2019;565:377-381. (from Pfam) NF017176.5 PF05338.17 DUF717 27 27 55 domain Y Y N DUF717 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF717) Protein of unknown function (DUF717) This family consists of several herpesvirus proteins of unknown function. (from Pfam) NF017178.5 PF05340.17 DUF740 21.2 21.2 624 domain Y Y N DUF740 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF740) Protein of unknown function (DUF740) This family consists of several uncharacterised plant proteins of unknown function. (from Pfam) NF017278.5 PF05444.17 DUF753 24.7 24.7 79 domain Y Y N DUF753 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF753) Domain of unknown function (DUF753) This domain contains is found in many copies in a variety of uncharacterised fly proteins. This domain has a Ly6/uPAR/alpha-neurotoxin-like domain structure. (from Pfam) NF017325.5 PF05501.16 DUF755 29.1 29.1 122 domain Y Y N DUF755 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF755) Domain of unknown function (DUF755) This family is predominated by ORFs from Circoviridae. The function of this family remains to be determined. (from Pfam) NF017420.5 PF05603.17 Hikeshi-like_N 27 27 133 domain Y Y N Hikeshi-like domain-containing protein 24768994,25760597 0 EBI-EMBL Hikeshi-like, N-terminal domain Hikeshi-like, N-terminal domain This domain is found at the N-terminal end of Protein Hikeshi from humans and its orthologues OPI10 from other eukaryotes. Hikeshi is an specific nuclear import carrier for HSP70 proteins following heat-shock stress, which is required to protect cells from heat- shock damages. The N-terminal domain shows a jelly-roll/beta- sandwich fold with two layers of beta-sheets consisting of three and five and five antiparallel beta-strands [1]. [1]. 25760597. Structural and functional analysis of Hikeshi, a new nuclear transport receptor of Hsp70s. Song J, Kose S, Watanabe A, Son SY, Choi S, Hong H, Yamashita E, Park IY, Imamoto N, Lee SJ;. Acta Crystallogr D Biol Crystallogr. 2015;71:473-483. [2]. 24768994. The Schizosaccharomyces pombe Hikeshi/Opi10 protein has similar biochemical functions to its human homolog but acts in different physiological contexts. Oda Y, Kimura M, Kose S, Fasken MB, Corbett AH, Imamoto N;. FEBS Lett. 2014;588:1899-1905. (from Pfam) NF017421.5 PF05604.16 DUF776 25 25 180 domain Y Y N DUF776 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF776) Protein of unknown function (DUF776) This family consists of several highly related mouse and human proteins of unknown function. (from Pfam) NF017427.5 PF05611.16 DUF780 25 25 71 domain Y Y N DUF780 domain-containing protein 0 EBI-EMBL Caenorhabditis elegans protein of unknown function (DUF780) Caenorhabditis elegans protein of unknown function (DUF780) This family consists of several short C. elegans proteins of unknown function. (from Pfam) NF017439.5 PF05623.17 DUF789 25.5 25.5 296 domain Y Y N DUF789 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF789) Protein of unknown function (DUF789) This family consists of several plant proteins of unknown function. (from Pfam) NF017477.5 PF05663.16 DUF809 25 25 138 domain Y Y N DUF809 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF809) Protein of unknown function (DUF809) This family consists of several proteins of unknown function Raphanus sativus (Radish) and Brassica napus (Rape). (from Pfam) NF017480.5 PF05667.16 CCDC22_CC 39.2 39.2 477 domain Y Y N coiled-coil domain-containing protein 23563313,25355947 0 EBI-EMBL CCDC22 protein coiled-coil region CCDC22 protein coiled-coil region Human coiled-coil domain-containing protein 22 (CCDC22) is involved in regulation of NF-kappa-B signalling; the function may involve association with COMMD8 and a CUL1-dependent E3 ubiquitin ligase complex [1]. It is part of the COMMD/CCDC22/CCDC93 (CCC) complex, which interacts with the multisubunit WASH complex required for endosomal deposition of F-actin and cargo trafficking in conjunction with the retromer [2]. This entry also includes CCDC22 homologues from animals and plants. [1]. 23563313. CCDC22 deficiency in humans blunts activation of proinflammatory NF-kappaB signaling. Starokadomskyy P, Gluck N, Li H, Chen B, Wallis M, Maine GN, Mao X, Zaidi IW, Hein MY, McDonald FJ, Lenzner S, Zecha A, Ropers HH, Kuss AW, McGaughran J, Gecz J, Burstein E;. J Clin Invest. 2013;123:2244-2256. [2]. 25355947. COMMD1 is linked to the WASH complex and regulates endosomal trafficking of the copper transporter ATP7A. Phillips-Krawczak CA, Singla A, Starokadomskyy P, Deng Z, Osborne DG, Li H, Dick CJ, Gomez TS, Koenecke M, Zhang JS, Dai H, Sifuentes-Dominguez LF, Geng LN, Kaufmann SH, Hein MY, Wallis M, McGaughran J, Gecz J, Sluis Bv, Billadeau DD, Burstein E;. Mol Biol Cell. 2015;26:91-103. (from Pfam) NF017484.5 PF05672.16 MAP7 28.5 28.5 153 domain Y Y N MAP7/E-MAP-115 family protein GO:0000226,GO:0015630 8408219,9745708 0 EBI-EMBL MAP7 (E-MAP-115) family MAP7/E-MAP-115 family protein The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin [1]. The binding of this microtubule associated protein is nucleotide independent [2]. [1]. 9745708. The distribution of murine 115-kDa epithelial microtubule-associated protein (E-MAP-115) during embryogenesis and in adult organs suggests a role in epithelial polarization and differentiation. Fabre-Jonca N, Allaman JM, Radlgruber G, Meda P, Kiss JZ, French LE, Masson D;. Differentiation 1998;63:169-180. [2]. 8408219. Identification and molecular characterization of E-MAP-115, a novel microtubule-associated protein predominantly expressed in epithelial cells. Masson D, Kreis TE;. J Cell Biol 1993;123:357-371. (from Pfam) NF017664.5 PF05867.16 DUF851 26.3 26.3 241 domain Y Y N DUF851 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF851) Protein of unknown function (DUF851) NF017681.5 PF05887.16 Trypan_PARP 100 100 134 domain Y Y N procyclic acidic repetitive family protein GO:0016020 2342468 0 EBI-EMBL Procyclic acidic repetitive protein (PARP) procyclic acidic repetitive family protein This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated [1]. [1]. 2342468. Transcription of the procyclic acidic repetitive protein genes of Trypanosoma brucei. Clayton CE, Fueri JP, Itzhaki JE, Bellofatto V, Sherman DR, Wisdom GS, Vijayasarathy S, Mowatt MR;. Mol Cell Biol 1990;10:3036-3047. (from Pfam) NF017694.5 PF05904.16 DUF863 25 25 941 domain Y Y N DUF863 domain-containing protein 0 EBI-EMBL Plant protein of unknown function (DUF863) Plant protein of unknown function (DUF863) This family consists of a number of hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown. (from Pfam) NF017700.5 PF05912.16 DUF870 27.1 27.1 112 domain Y Y N DUF870 domain-containing protein 0 EBI-EMBL Caenorhabditis elegans protein of unknown function (DUF870) Caenorhabditis elegans protein of unknown function (DUF870) This family consists of a number of hypothetical proteins which seem to be specific to Caenorhabditis elegans. The function of this family is unknown. (from Pfam) NF017782.5 PF06001.18 RING_CBP-p300 25 25 40 domain Y Y N CREB-binding protein domain-containing protein 23934153 0 EBI-EMBL CREB-binding protein/p300, atypical RING domain CREB-binding protein/p300, atypical RING domain CBP (CREB-binding protein) and p300 (also known as CREBBP or KAT3A and EP300 or KAT3B, respectively) are two histone acetyltransferases (HATs) that associate with and acetylate transcriptional regulators and chromatin. The catalytic core of animal CBP-p300 contains a bromodomain, a CH2 region containing a discontinuous PHD domain interrupted by this RING domain, and a HAT domain. Bromodomain-RING-PHD forms a compact module in which the RING domain is juxtaposed with the HAT substrate-binding site. This RING domain contains only a single zinc ion-binding cluster instead of two; instead of a second zinc atom, a network of hydrophobic interactions stabilizes the domain. The RING domain has an inhibitory role. Disease mutations that disrupt RING attachment lead to upregulation of HAT activity. HAT regulation may require repositioning of the RING domain to facilitate access to an otherwise partially occluded HAT active site. Plant CBP-p300 type HATs lack a bromodomain whose role in the animal animal CBP-p300's is to bind acetylated histones; it has been suggested that these plant proteins may utilise a different domain or another bromodomain protein to perform this function [1]. This RING domain has also been referred to as DUF902. [1]. 23934153. Structure of the p300 catalytic core and implications for chromatin targeting and HAT regulation. Delvecchio M, Gaucher J, Aguilar-Gurrieri C, Ortega E, Panne D;. Nat Struct Mol Biol. 2013;20:1040-1046. (from Pfam) NF017792.5 PF06012.17 DUF908 34.7 34.7 358 domain Y Y N DUF908 domain-containing protein 0 EBI-EMBL Domain of Unknown Function (DUF908) Domain of Unknown Function (DUF908) NF017851.5 PF06075.17 DUF936 24 24 118 domain Y Y N DUF936 domain-containing protein 0 EBI-EMBL Plant protein of unknown function (DUF936) Plant protein of unknown function (DUF936) This entry consists of several hypothetical proteins from plants, whose function is unknown. According to structure predictions, this domain may adopt and OB-fold. (from Pfam) NF017891.5 PF06121.19 DUF959 25 25 192 domain Y Y N DUF959 domain-containing protein 9503365 0 EBI-EMBL Domain of Unknown Function (DUF959) Domain of Unknown Function (DUF959) This N-terminal domain is not expressed in the 'Short' isoform of Collagen A [1]. [1]. 9503365. Complete primary structure of two variant forms of human type XVIII collagen and tissue-specific differences in the expression of the corresponding transcripts. Saarela J, Ylikarppa R, Rehn M, Purmonen S, Pihlajaniemi T;. Matrix Biol 1998;16:319-328. (from Pfam) NF017905.5 PF06136.18 SOK 24.3 24.3 89 domain Y Y N SOK2 domain-containing protein 15186749,18156133,30737509,32004461 0 EBI-EMBL SOSEKI protein DIX-like domain SOSEKI protein DIX-like domain This entry represents a group of plant proteins, including protein SOSEKI1-5 from Arabidopsis thaliana and Physcomitrium patens. SOK1-5 integrate apical-basal and radial organismal axes to localise to polar cell edges and contain a DIX oligomerization domain that resembles that in the animal Dishevelled polarity regulator [1-4]. [1]. 15186749. A cluster of Arabidopsis genes with a coordinate response to an environmental stimulus. Finnegan EJ, Sheldon CC, Jardinaud F, Peacock WJ, Dennis ES;. Curr Biol. 2004;14:911-916. [2]. 18156133. The FLX gene of Arabidopsis is required for FRI-dependent activation of FLC expression. Andersson CR, Helliwell CA, Bagnall DJ, Hughes TP, Finnegan EJ, Peacock WJ, Dennis ES;. Plant Cell Physiol. 2008;49:191-200. [3]. 30737509. A SOSEKI-based coordinate system interprets global polarity cues in Arabidopsis. Yoshida S, van der Schuren A, van Dop M, van Galen L, Saiga S, Adibi M, Moller B, Ten Hove CA, Marhavy P, Smith R, Friml J, Weijers D;. Nat Plants. 2019;5:160-166. [4]. 32004461. DIX Domain Polymerization Drives Assembly of Plant Cell Polarity Complexes. van Dop M, Fiedler M, Mutte S, de Keijzer J, Olijslager L, Albrecht C, Liao CY, Janson ME, Bienz M, Weijers D;. Cell. 2020;180:427-439. (from Pfam) NF017960.5 PF06198.16 DUF999 25 25 143 domain Y Y N DUF999 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF999) Protein of unknown function (DUF999) Family of conserved Schizosaccharomyces pombe proteins with unknown function. (from Pfam) NF018026.5 PF06269.17 DUF1029 25 25 53 domain Y Y N DUF1029 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1029) Protein of unknown function (DUF1029) This family consists of several short Chordopoxvirus proteins of unknown function. (from Pfam) NF018027.5 PF06270.16 DUF1030 25 25 53 domain Y Y N DUF1030 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1030) Protein of unknown function (DUF1030) This family consists of several short Circovirus proteins of unknown function. (from Pfam) NF018078.5 PF06327.19 Adcy_cons_dom 21.1 21.1 98 domain Y Y N adenylate cyclase domain-containing protein GO:0004016,GO:0005886,GO:0006171 11264454,12940771,9417641 0 EBI-EMBL Adenylate cyclase, conserved domain Adenylate cyclase, conserved domain Adenylate cyclase (AC) enzyme uses ATP as its substrate to produce Cyclic AMP (cAMP), a ubiquitous signalling molecule that mediates many cellular processes by activating cAMP- dependent kinases and also inducing protein-protein interactions. Mammalian adenylate cyclase has nine closely related membrane-bound isoforms (AC1-9) showing significant sequence homology and sharing the same overall structure: two hydrophobic transmembrane domains, and two cytoplasmic domains that are responsible for the catalytic activity. These isoforms differ in both their tissue specificity and their regulation [1,2]. This entry represents a region of unknown function found in many of these isoforms. It is part of the N-terminal cytoplasmic domain but its presence is not necessary for catalytic activity [3]. [1]. 11264454. Regulation and role of adenylyl cyclase isoforms. Hanoune J, Defer N;. Annu Rev Pharmacol Toxicol. 2001;41:145-174. [2]. 12940771. Regulation and organization of adenylyl cyclases and cAMP. Cooper DM;. Biochem J. 2003;375:517-529. [3]. 9417641. Crystal structure of the catalytic domains of adenylyl cyclase in a complex with Gsalpha.GTPgammaS. Tesmer JJ, Sunahara RK, Gilman AG, Sprang SR;. Science. 1997;278:1907-1916. (from Pfam) NF018103.5 PF06358.16 BNYVV_TGB3 25 25 111 domain Y Y N beet necrotic yellow vein virus movement protein TGB3 10796018 0 EBI-EMBL Beet necrotic yellow vein virus, movement protein TGB3 beet necrotic yellow vein virus movement protein TGB3 This family is represented by Beet necrotic yellow vein virus movement protein TGB3 (also known as p15) which participates in the transport of viral RNA to the plasmodesmata [1]. [1]. 10796018. P42 movement protein of Beet necrotic yellow vein virus is targeted by the movement proteins P13 and P15 to punctate bodies associated with plasmodesmata. Erhardt M, Morant M, Ritzenthaler C, Stussi-Garaud C, Guilley H, Richards K, Jonard G, Bouzoubaa S, Gilmer D;. Mol Plant Microbe Interact. 2000;13:520-528. (from Pfam) NF018108.5 PF06364.17 DUF1068 25 25 165 domain Y Y N DUF1068 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1068) Protein of unknown function (DUF1068) This family consists of several hypothetical plant proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown. (from Pfam) NF018114.5 PF06370.16 DUF1069 25 25 206 domain Y Y N DUF1069 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1069) Protein of unknown function (DUF1069) This family consists of several Maize streak virus 21.7 kDa proteins. The function of this family is unknown. (from Pfam) NF018120.5 PF06376.17 AGP 25 25 36 domain Y Y N arabinogalactan peptide 11006345 0 EBI-EMBL Arabinogalactan peptide arabinogalactan peptide This entry represents the arabinogalactan peptide family found in plants [1]. [1]. 11006345. The classical arabinogalactan protein gene family of arabidopsis. Schultz CJ, Johnson KL, Currie G, Bacic A;. Plant Cell. 2000;12:1751-1768. (from Pfam) NF018124.5 PF06380.16 DUF1072 25 25 39 domain Y Y N DUF1072 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1072) Protein of unknown function (DUF1072) This family consists of several Barley yellow dwarf virus proteins of unknown function. (from Pfam) NF018131.5 PF06388.16 DUF1075 25 25 158 domain Y Y N DUF1075 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1075) Protein of unknown function (DUF1075) This family consists of several eukaryotic proteins of unknown function. (from Pfam) NF018186.5 PF06448.16 DUF1081 25 25 112 domain Y Y N DUF1081 domain-containing protein GO:0005319,GO:0006869 0 EBI-EMBL Domain of Unknown Function (DUF1081) Domain of Unknown Function (DUF1081) This region is found in Apolipophorin proteins. (from Pfam) NF018192.5 PF06454.16 THH1_TOM1-3_dom 25 25 273 domain Y Y N THH1/TOM1/TOM3 domain-containing protein 11836427,16847136,29649144,31412764 0 EBI-EMBL THH1/TOM1/TOM3 domain THH1/TOM1/TOM3 domain This domain is found in plant proteins including THH1/TOM1/TOM3 from Arabidopsis. TOM1 and TOM3 are transmembrane proteins necessary for the efficient multiplication of tobamoviruses [1]. THH1 supports tobamovirus multiplication, but to a lesser extent than TOM1 and TOM3 [2]. Members containing this domain are part of the GPCR superfamily and involved in stress tolerance [3,4]. [1]. 11836427. Complete inhibition of tobamovirus multiplication by simultaneous mutations in two homologous host genes. Yamanaka T, Imai T, Satoh R, Kawashima A, Takahashi M, Tomita K, Kubota K, Meshi T, Naito S, Ishikawa M;. J Virol. 2002;76:2491-2497. [2]. 16847136. Involvement of THH1, an Arabidopsis thaliana homologue of the TOM1 gene, in tobamovirus multiplication. Fujisaki K, Ravelo GB, Naito S, Ishikawa M;. J Gen Virol. 2006;87:2397-2401. [3]. 29649144. A Novel G-Protein-Coupled Receptors Gene from Upland Cotton Enhances Salt Stress Tolerance in Transgenic Arabidopsis. Lu P, Magwanga RO, Lu H, Kirungu JN, Wei Y, Dong Q, Wang X, Cai X, Zhou Z, Wang K, Liu F;. Genes (Basel). 2018; [Epub ahead of print]. [4]. 31412764. Genome-wide analysis of the cotton G-coupled receptor proteins (GPCR) and functional analysis of GTOM1, a novel cotton GPCR gene under drought and cold stress. Lu P, Magwanga RO, Kirungu JN, Dong Q, Cai X, Zhou Z, Wang X, Xu Y, Hou Y, Peng R, Wang K, Liu F;. BMC Genomics. 2019;20:651. (from Pfam) NF018199.5 PF06461.16 CHDII_SANT-like 28.8 28.8 138 domain Y Y N SANT-like domain-containing protein GO:0003677,GO:0006338 23128324 0 EBI-EMBL CHD subfamily II, SANT-like domain CHD subfamily II, SANT-like domain CHD proteins (name derived from the presence of a Chromodomain, SWI2/SNF2 ATPase/Helicase and a motif with sequence similarity to a DNA)binding domain) are ATP-dependent chromatin remodelers found in plant and animals. In eukaryotes, there are three subfamilies, I, II and III. This domain is found in members of subfamily II which play a role in repression of genes involved in developmental regulation, including Mi-2 from Drosophila melanogaster, CHD3/4/5 from animals and PICKLE (a CHD3/4-related protein) from Arabidopsis. Sequence analysis revealed that this domain has a considerable similarity to SANT domains suggesting that it fold into this type of domain and it is integral to the DNA binding domain of CHD remodelers in subfamily II [1]. [1]. 23128324. PICKLE is a CHD subfamily II ATP-dependent chromatin remodeling factor. Ho KK, Zhang H, Golden BL, Ogas J;. Biochim Biophys Acta. 2013;1829:199-210. (from Pfam) NF018203.5 PF06465.18 DUF1087 22.8 22.8 63 domain Y Y N DUF1087 domain-containing protein 23128324 0 EBI-EMBL CHD subfamily II, DUF1087 CHD subfamily II, DUF1087 This domain is found in chromatin remodelling factors (CHDs) from subfamily II [1] including CHD3/4/5 from animals and PICKLE. from Arabidopsis. The exact function is, as yet, unknown. [1]. 23128324. PICKLE is a CHD subfamily II ATP-dependent chromatin remodeling factor. Ho KK, Zhang H, Golden BL, Ogas J;. Biochim Biophys Acta. 2013;1829:199-210. (from Pfam) NF018207.5 PF06469.16 DUF1088 27 27 170 domain Y Y N DUF1088 domain-containing protein 31432443,31438473 0 EBI-EMBL Neurobeachin-like, DUF1088 Neurobeachin-like, DUF1088 This domain is found in the neurobeachins (NBEAs) and BEACH domain containing proteins (BDCPs). NBEAS are localised near Golgi apparatus and is involved in vesicular trafficking, intracellular transport, membrane dynamics, endosomal recycling, and receptor signalling. BDCPs are associated with lysosome size, apoptosis, autophagy, granule size, or synapse formation. Mutations in this domain have been related to autosomal recessively inherited lipopolysaccharide-responsive beige-like anchor (LRBA) protein deficiency, responsible for common variable immunodeficiency (CVID) and autoimmune lymphoproliferative syndrome (ALPS) [1]. NBEAs deficiency may induce spine loss with defects in synaptic efficacy and plasticity, being associated with autism spectrum disorder (ASD) and ASD-related syndromes [2]. [1]. 31432443. A Spectrum of Clinical Findings from ALPS to CVID: Several Novel LRBA Defects. Cagdas D, Halacli SO, Tan C, Lo B, Cetinkaya PG, Esenboga S, Karaatmaca B, Matthews H, Balci-Hayta B, Arikoglu T, Ezgu F, Aladag E, Saltik-Temizel IN, Demir H, Kuskonmaz B, Okur V, Gumruk F, Goker H, Cetinkaya D, Boztug K, Lenardo M, Sanal O, Tezcan I;. J Clin Immunol. 2019;39:726-738. [2]. 31438473. Autism Spectrum Disorder-Related Syndromes: Modeling with Drosophila and Rodents. Ueoka I, Pham HTN, Matsumoto K, Yamaguchi M;. Int J Mol Sci. 2019; [Epub ahead of print] (from Pfam) NF018215.5 PF06477.18 DUF1091 25 25 83 domain Y Y N DUF1091 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1091) Protein of unknown function (DUF1091) This is a family of uncharacterised proteins. Based on its distant similarity to Pfam:PF02221 and conserved pattern of cysteine residues it is possible that these domains are also lipid binding. (from Pfam) NF018230.5 PF06493.16 DUF1096 25 25 51 domain Y Y N DUF1096 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1096) Protein of unknown function (DUF1096) This family represents the N-terminal region of several proteins found in C. elegans. The family is often found with Pfam:PF02363. (from Pfam) NF018233.5 PF06497.16 Baculo_Ac102 27 27 99 domain Y Y N baculovirus Ac102 family protein 22592260,29540600,29618641 0 EBI-EMBL Baculovirus Ac102 baculovirus Ac102 family protein This family of baculovirus proteins is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV) Ac102. Nuclear actin is critical for AcMNPV progeny production, and Ac102 plays an essential role in actin translocation to the nucleus [1]. It plays a role in regulating nuclear actin polymerisation as well as the morphogenesis and spatial distribution of viral capsid structures in the host nucleus [2,3]. [1]. 22592260. Nuclear localization of actin requires AC102 in Autographa californica multiple nucleopolyhedrovirus-infected cells. Gandhi KM, Ohkawa T, Welch MD, Volkman LE;. J Gen Virol. 2012;93:1795-1803. [2]. 29540600. Baculovirus AC102 Is a Nucleocapsid Protein That Is Crucial for Nuclear Actin Polymerization and Nucleocapsid Morphogenesis. Hepp SE, Borgo GM, Ticau S, Ohkawa T, Welch MD;. J Virol. 2018; [Epub ahead of print]. [3]. 29618641. Ac102 Participates in Nuclear Actin Polymerization by Modulating BV/ODV-C42 Ubiquitination during Autographa californica Multiple Nucleopolyhedrovirus Infection. Zhang Y, Hu X, Mu J, Hu Y, Zhou Y, Zhao H, Wu C, Pei R, Chen J, Chen X, Wang Y;. J Virol. 2018; [Epub ahead of print] (from Pfam) NF018237.5 PF06503.16 DUF1101 25 25 360 domain Y Y N DUF1101 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1101) Protein of unknown function (DUF1101) This family consists of several hypothetical Fijivirus proteins of unknown function. (from Pfam) NF018274.5 PF06544.17 Prp3_C 27.6 27.6 138 domain Y Y N small nuclear ribonucleoprotein Prp3 domain-containing protein 26161500,26743623,26829225,26912367 0 EBI-EMBL Small nuclear ribonucleoprotein Prp3, C-terminal domain Small nuclear ribonucleoprotein Prp3, C-terminal domain This domain is found at the C-terminal end of U4/U6 and U4/U5/U6- small nuclear ribonucleoprotein Prp3, part of the tri-RNA complex that form the spliceosome. Prp3 plays a key role in the recognition of the snRNA duplex. This binding domain, highly conserved among eukaryotes, interacts with the 3' end of U6 snRNA. It adopts a ferredoxin-like fold, showing a five-stranded mixed beta-sheet with three alpha-helices, two of them running parallel to the beta-strands on one side of the sheet and one on the other. This fold is extended with a long beta-hairpin, an extra beta-strand, an helix and a final loop at the C terminus. It is located C-terminal to Pfam:PF08572 [1-4]. [1]. 26912367. Molecular architecture of the human U4/U6.U5 tri-snRNP. Agafonov DE, Kastner B, Dybkov O, Hofele RV, Liu WT, Urlaub H, Luhrmann R, Stark H;. Science. 2016;351:1416-1420. [2]. 26829225. Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 A resolution. Nguyen THD, Galej WP, Bai XC, Oubridge C, Newman AJ, Scheres SHW, Nagai K;. Nature. 2016;530:298-302. [3]. 26161500. A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing. Liu S, Mozaffari-Jovin S, Wollenhaupt J, Santos KF, Theuser M, Dunin-Horkawicz S, Fabrizio P, Bujnicki JM, Luhrmann R, Wahl MC;. Elife. 2015;4:e07320. [4]. 26743623. The 3.8 A structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis. Wan R, Yan C, Bai R, Wang L, Huang M, Wong CC, Shi Y;. Science. 2016;351:466-475. (from Pfam) NF018277.5 PF06547.17 DUF1117 25 25 113 domain Y Y N DUF1117 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1117) Protein of unknown function (DUF1117) This family represents the C-terminus of a number of hypothetical plant proteins. (from Pfam) NF018317.5 PF06592.18 DUF1138 34.8 34.8 73 domain Y Y N DUF1138 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1138) Protein of unknown function (DUF1138) This family consists of several hypothetical short plant proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown. (from Pfam) NF018331.5 PF06608.16 CFAP68 24 24 148 domain Y Y N Cilia- and flagella-associated protein 68 GO:0005634 37327785 0 EBI-EMBL Cilia- and flagella-associated protein 68 Cilia- and flagella-associated protein 68 This family represents the homologues of Cilia- and flagella-associated protein 68 (CFAP68). This protein is a microtubule inner protein (MIP) part of the doublet microtubules (DMTs). CFAP68 belongs to the axoneme core-MIPs and binds to the protofilament A09 of the sperm DMTs [1]. [1]. 37327785. Structural specializations of the sperm tail. Leung MR, Zeng J, Wang X, Roelofs MC, Huang W, Zenezini Chiozzi R, Hevler JF, Heck AJR, Dutcher SK, Brown A, Zhang R, Zeev-Ben-Mordehai T;. Cell. 2023;186:2880-2896. (from Pfam) NF018338.5 PF06615.16 Circovir2_Orf1 27.9 27.9 59 domain Y Y N circovirus 2 orf1 family protein 12954212 0 EBI-EMBL Circovirus 2, Orf1 circovirus 2 orf1 family protein This family consists of short Circovirus proteins of unknown function, including ORF1 (also known as Protein NS0) which may be involved in host modulation [1]. [1]. 12954212. The essential and nonessential transcription units for viral protein synthesis and DNA replication of porcine circovirus type 2. Cheung AK;. Virology. 2003;313:452-459. (from Pfam) NF018341.5 PF06618.16 DUF1148 25 25 114 domain Y Y N DUF1148 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1148) Protein of unknown function (DUF1148) This family consists of several Maize streak virus proteins of unknown function. (from Pfam) NF018348.5 PF06625.16 DUF1151 25 25 109 domain Y Y N DUF1151 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1151) Protein of unknown function (DUF1151) This family consists of several hypothetical eukaryotic proteins of unknown function. (from Pfam) NF018356.5 PF06633.16 DUF1155 25 25 42 domain Y Y N DUF1155 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1155) Protein of unknown function (DUF1155) This family consists of several Cucumber mosaic virus ORF IIB proteins. The function of this family is unknown. (from Pfam) NF018379.5 PF06663.18 CNK2_3_dom 27 27 212 domain Y Y N CNK2 domain-containing protein GO:0005737,GO:0009966,GO:0016020 10207009,14597674,22085542,22851176,32235845 0 EBI-EMBL Connector enhancer of kinase suppressor of ras 2/3 domain Connector enhancer of kinase suppressor of ras 2/3 domain This family represents a conserved region of unknown function within Connector enhancer of kinase suppressor of ras 2 (CNK2, also known MAGUIN) [1,2], Connector enhancer of kinase suppressor of ras 3 (CNK3) and CNK3/IPCEF1 fusion protein. This region is situated between the PDZ Pfam:PF00595 and PH Pfam:PF00169 domains in CNK2 and CNK3/IPCEF1, and after the PDZ domain in CNK3. All family members also contain an N-terminal Pfam:PF00536 domain. CNK2 is predominantly expressed in neural tissues, being critical for postsynaptic density morphology, implicated in X-linked intellectual disability (ID). CNK2 was first described as a regulator of Ras/MAPK signalling that lead to further studies concluding that it act as a scaffold for multiple signal cascades. It is able to direct the localisation of regulatory proteins within the cell and influences the behaviour of important regulatory molecules [2,3]. CNK3 regulates aldosterone-induced and epithelial sodium channel (ENaC)-mediated sodium transport through regulation of ENaC cell surface expression, acting as a scaffold protein that coordinates the assembly of an ENaC-regulatory complex (ERC) [4]. CNK3/IPCEF1 is required for hepatocyte growth factor (HGF)-dependent activation of Arf6 and HGF-stimulated cell migration [5]. [1]. 10207009. MAGUIN, a novel neuronal membrane-associated guanylate kinase-interacting protein. Yao I, Hata Y, Ide N, Hirao K, Deguchi M, Nishioka H, Mizoguchi A, Takai Y;. J Biol Chem 1999;274:11889-11896. [2]. 14597674. Human homologue of Drosophila CNK interacts with Ras effector proteins Raf and Rlf. Lanigan TM, Liu A, Huang YZ, Mei L, Margolis B, Guan KL;.. TRUNCATED at 1650 bytes (from Pfam) NF018395.5 PF06680.16 DUF1181 25 25 120 domain Y Y N DUF1181 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1181) Protein of unknown function (DUF1181) This family consists of several hypothetical proteins of around 120 residues in length which are found specifically in Trypanosoma brucei. The function of this family is unknown. (from Pfam) NF018396.5 PF06681.18 DUF1182 25 25 208 domain Y Y N DUF1182 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1182) Protein of unknown function (DUF1182) This family consists of several hypothetical proteins of around 360 residues in length and seems to be specific to Caenorhabditis elegans. The function of this family is unknown. It appears to carry seven TM regions. (from Pfam) NF018412.5 PF06697.17 DUF1191 25.8 25.8 183 domain Y Y N DUF1191 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1191) Protein of unknown function (DUF1191) This family contains hypothetical plant proteins of unknown function. (from Pfam) NF018421.5 PF06708.16 DUF1195 25 25 147 domain Y Y N DUF1195 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1195) Protein of unknown function (DUF1195) This family consists of several plant specific hypothetical proteins of around 160 residues in length. The function of this family is unknown. (from Pfam) NF018424.5 PF06712.16 DUF1199 25 25 52 domain Y Y N DUF1199 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1199) Protein of unknown function (DUF1199) This family consists of several hypothetical Feline immunodeficiency virus (FIV) proteins. Members of this family are typically around 67 residues long and are often annotated as ORF3 proteins. The function of this family is unknown. (from Pfam) NF018428.5 PF06716.16 MP_p6 22 22 54 domain Y Y N movement protein p6 15016890 0 EBI-EMBL Movement protein p6 movement protein p6 This entry represents the movement protein 6 (p6) from Beet yellows virus and related Closterovirus proteins. Movement proteins (MPs) encoded by many virus genera are specialised proteins essential for plant viral genomes or virions transport within and between cells. P6 is a small protein (6kDa) localised in the endoplasmic reticulum. It has a single-span N-terminal transmembrane domain and a C-terminal hydrophilic domain which faces the cytosol. It is involved, together with Hsp70h, CP, CPm, and P64, in cell to cell movement of the viral genome without any budding, being essential for this process. The mechanism of action of this protein is not clear. It is suggested that it also plays a role in virion formation [1]. [1]. 15016890. Movement protein of a closterovirus is a type III integral transmembrane protein localized to the endoplasmic reticulum. Peremyslov VV, Pan YW, Dolja VV;. J Virol. 2004;78:3704-3709. (from Pfam) NF018450.5 PF06740.17 MAP_Futsch 22 22 34 domain Y Y N microtubule associated protein Futsch domain-containing protein GO:0000226 10839355,10839356 0 EBI-EMBL Microtubule associated protein Futsch Microtubule associated protein Futsch The Drosophila protein Futsch has homology to MAP1B and controls synaptic growth at the Drosophila neuromuscular junction through the regulation of the synaptic microtubule cytoskeleton. Ftusch protein colocalises with microtubules and identifies cytoskeletal loops that traverse the lateral margin of select synaptic boutons. Futsch mutations disrupt synaptic microtubule organisation. The N- and C-terminal domains of Futsch are homologous to the vertebrate MAP1B microtubule-associated protein. The central domain of Futsch is highly repetitive and it is represented in this entry [1]. [1]. 10839356. Drosophila Futsch regulates synaptic microtubule organization and is necessary for synaptic growth. Roos J, Hummel T, Ng N, Klambt C, Davis GW;. Neuron. 2000;26:371-382. [2]. 10839355. Drosophila Futsch/22C10 is a MAP1B-like protein required for dendritic and axonal development. Hummel T, Krukkert K, Roos J, Davis G, Klambt C;. Neuron. 2000;26:357-370. (from Pfam) NF018469.5 PF06760.16 DUF1221 25 25 215 domain Y Y N DUF1221 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1221) Protein of unknown function (DUF1221) This is a family of plant proteins, most of which are hypothetical and of unknown function. All members contain the Pfam:PF00069 domain, suggesting that they may possess kinase activity. (from Pfam) NF018507.5 PF06802.16 DUF1231 25 25 340 domain Y Y N DUF1231 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1231) Protein of unknown function (DUF1231) This family consists of several Orthopoxvirus specific proteins predominantly of around 340 residues in length. This family contains both B17 and B15 proteins, the function of which are unknown. (from Pfam) NF018526.5 PF06822.17 DUF1235 25 25 261 domain Y Y N DUF1235 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1235) Protein of unknown function (DUF1235) This family contains a number of viral proteins of unknown function. (from Pfam) NF018542.5 PF06840.16 PDC10_C 27.3 27.3 90 domain Y Y N PDCD10/CCM3 family protein 24481819,24595293,26490252 0 EBI-EMBL Programmed cell death protein 10, C-terminal PDCD10/CCM3 family protein Programmed cell death 10 protein (PDCD10/CCM3) is part of the CCM complex and is required for neuronal migration [1]. Outside of this complex, it is crucial in vascularization and in angiogenesis as it functions in vessel permeability and stability [2]. PDCD10/CCM3 contains an N-terminal dimerisation domain and a C-terminal focal adhesion targeting-homology (FAT-H) domain (represented in this entry) [3]. [1]. 24595293. Ccm3, a gene associated with cerebral cavernous malformations, is required for neuronal migration. Louvi A, Nishimura S, Gunel M;. Development. 2014;141:1404-1415. [2]. 26490252. Downregulation of programmed cell death 10 is associated with tumor cell proliferation, hyperangiogenesis and peritumoral edema in human glioblastoma. Lambertz N, El Hindy N, Kreitschmann-Andermahr I, Stein KP, Dammann P, Oezkan N, Mueller O, Sure U, Zhu Y;. BMC Cancer. 2015;15:759. [3]. 24481819. Cerebral cavernous malformation proteins at a glance. Draheim KM, Fisher OS, Boggon TJ, Calderwood DA;. J Cell Sci. 2014;127:701-707. (from Pfam) NF018544.5 PF06842.17 DUF1242 25 25 35 domain Y Y N DUF1242 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1242) Protein of unknown function (DUF1242) This family consists of a number of eukaryotic proteins of around 72 residues in length. The function of this family is unknown. (from Pfam) NF018550.5 PF06851.16 DUF1247 25 25 149 domain Y Y N DUF1247 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1247) Protein of unknown function (DUF1247) This family contains a number of hypothetical viral proteins of unknown function approximately 200 residues long. (from Pfam) NF018566.5 PF06869.17 DUF1258 33.1 33.1 253 domain Y Y N DUF1258 domain-containing protein 24464998 0 EBI-EMBL Protein of unknown function (DUF1258) Protein of unknown function (DUF1258) This family represents a conserved region approximately 260 residues long within a number of hypothetical proteins of unknown function that seem to be specific to C. elegans. Note that this family contains a number of conserved cysteine and histidine residues.This family corresponds to the Mirage group of putative transposases and family members are relatively close homologs of Transposase_21 (Pfam:PF02992) proteins (1). [1]. 24464998. The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification. Majorek KA, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A, Nowotny M, Ginalski K, Bujnicki JM;. Nucleic Acids Res. 2014;42:4160-4179. (from Pfam) NF018576.5 PF06880.16 DUF1262 27 27 100 domain Y Y N DUF1262 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1262) Protein of unknown function (DUF1262) This family represents a conserved region within a number of proteins of unknown function that seem to be specific to Arabidopsis thaliana. Note that some family members contain more than one copy of this region. (from Pfam) NF018578.5 PF06882.17 DUF1263 27 27 57 domain Y Y N DUF1263 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1263) Protein of unknown function (DUF1263) This family represents a conserved region located towards the C-terminus of a number proteins of unknown function that seem to be specific to Oryza sativa. (from Pfam) NF018582.5 PF06887.19 DUF1265 25 25 47 domain Y Y N DUF1265 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1265) Protein of unknown function (DUF1265) This family represents a conserved region approximately 50 residues long within a number of proteins of unknown function that seem to be restricted to C. elegans. The GO annotation for this protein indicate that its a protein involved in nematode larval development and has a positive regulation on growth rate. (from Pfam) NF018607.5 PF06918.19 DUF1280 25 25 220 domain Y Y N DUF1280 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1280) Protein of unknown function (DUF1280) This family represents a conserved region approximately 200 residues long within a number of proteins of unknown function that seem to be specific to C. elegans. (from Pfam) NF018655.5 PF06972.16 GIP1_N 26.4 26.4 60 domain Y Y N GIP1 domain-containing protein 24484953,25387999 0 EBI-EMBL GBF-interacting protein 1 N-terminal GBF-interacting protein 1 N-terminal This entry represents the N-terminal domain of GBF1-interacting protein 1 (GIP1, AT3G13222) from Arabidopsis. GIP1 may act as a coactivator that regulates transcription factors involved in lateral organ development of plants, such as bZIP transcription factors and LBD18 [1,2]. [1]. 24484953. GIP1 may act as a coactivator that enhances transcriptional activity of LBD18 in Arabidopsis. Lee HW, Park JH, Park MY, Kim J;. J Plant Physiol. 2014;171:14-18. [2]. 25387999. GIP1 protein is a novel cofactor that regulates DNA-binding affinity of redox-regulated members of bZIP transcription factors involved in the early stages of Arabidopsis development. Shaikhali J;. Protoplasma. 2015;252:867-883. (from Pfam) NF018658.5 PF06975.16 DUF1299 25 25 47 domain Y Y N DUF1299 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1299) Protein of unknown function (DUF1299) This family represents a conserved region approximately 50 residues long within a number of proteins of unknown function that seem to be specific to Arabidopsis thaliana. Note that many family members contain multiple copies of this region. (from Pfam) NF018687.5 PF07011.16 Elf4 27 27 83 domain Y Y N Elf4 domain-containing protein 12214234,20357892 0 EBI-EMBL Early Flowering 4 domain Elf4 domain The Elf4 domain is named for the ELF4 (early flowering 4) gene product in the model plant Arabidopsis thaliana. The domain is rare or absent in prokaryotes. NF018689.5 PF07013.16 DUF1314 25 25 197 domain Y Y N DUF1314 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1314) Protein of unknown function (DUF1314) This family consists of several Alphaherpesvirus proteins of around 200 residues in length. The function of this family is unknown. (from Pfam) NF018702.5 PF07028.16 DUF1319 28.1 28.1 109 domain Y Y N DUF1319 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1319) Protein of unknown function (DUF1319) This family contains a number of viral proteins of unknown function approximately 200 residues long. Family members seem to be restricted to badnaviruses. (from Pfam) NF018710.5 PF07038.16 Circovir2_Orf4 25 25 59 domain Y Y N ferritin heavy chain-binding family protein GO:0052150 27030984 0 EBI-EMBL Circovirus 2, anti-apoptotic ORF4 ferritin heavy chain-binding family protein This family represents the anti-apoptotic ORF4 protein from Circovirus 2, which antagonises host cell apoptosis by interacting with host ferritin heavy chain (FHC). This protein physically binds host FHC, resulting in the reduction of FHC protein levels in host cells. The reduction of FHC concentration further inhibits the accumulation of reactive oxygen in host cells, leading to reduced apoptosis [1]. [1]. 27030984. The ORF4 protein of porcine circovirus type 2 antagonizes apoptosis by stabilizing the concentration of ferritin heavy chain through physical interaction. Lv Q, Guo K, Zhang G, Zhang Y;. J Gen Virol. 2016;97:1636-1646. (from Pfam) NF018720.5 PF07048.16 DUF1331 25 25 35 domain Y Y N DUF1331 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1331) Protein of unknown function (DUF1331) This family consists of several Circovirus proteins of around 35 residues in length. Members of this family are described as ORF-10 proteins and their function is unknown. (from Pfam) NF018725.5 PF07056.16 DUF1335 25 25 131 domain Y Y N DUF1335 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1335) Protein of unknown function (DUF1335) This family represents a conserved region approximately 130 residues long within a number of proteins of unknown function that seem to be specific to the white spot syndrome virus (WSSV). (from Pfam) NF018759.5 PF07092.17 TMEM106 24 24 141 domain Y Y N TM106 family protein 23136129,24357581,29131025,30456879,34347309 0 EBI-EMBL TM106 protein C-terminal domain TM106 protein C-terminal domain This family includes Transmembrane protein 106A/B/C, type II transmembrane proteins which have homology to the late embryogenesis abundant-2 (LEA-2) domain [5]. TMEM106A has been identified as a key factor to regulate macrophage activation and a tumour suppressor in gastric, renal cancer and non small-cell lung carcinoma (NSCLC) [1,2]. TMEM106B localises to late endosomes and lysosomes, and it is involved in dendrite morphogenesis and maintenance by regulating lysosomal trafficking via its interaction with MAP6 [3]. Its overexpression is associated with familial frontotemporal lobar degeneration [4]. It has also been identified as a protein required for productive SARS-CoV-2 [5]. Structural analysis of LEA-2 domains revealed that they have a long, conserved lipid-binding groove, implying that TMEM106B and its homologues Vac7 and Tag1 from yeast, may all be lipid transfer proteins in the lumen of late endocytic organelles [5]. [1]. 30456879. TMEM106A inhibits cell proliferation, migration, and induces apoptosis of lung cancer cells. Liu J, Zhu H;. J Cell Biochem. 2018; [Epub ahead of print]. [2]. 29131025. TMEM106a is a Novel Tumor Suppressor in Human Renal Cancer. Wu C, Xu J, Wang H, Zhang J, Zhong J, Zou X, Chen Y, Yang G, Zhong Y, Lai D, Li X, Tang A;. Kidney Blood Press Res. 2017;42:853-864. [3]. 24357581. The FTLD risk factor TMEM106B and MAP6 control dendritic trafficking of lysosomes. Schwenk BM, Lang CM, Hogl S, Tahirovic S, Orozco D, Rentzsch K, Lichtenthaler SF, Hoogenraad CC, Capell A, Haass C, Edbauer D;. EMBO J. 2014;33:450-467. [4]. 23136129. The frontotemporal lobar degeneration risk factor, TMEM106B, regula. TRUNCATED at 1650 bytes (from Pfam) NF018768.5 PF07101.16 DUF1363 24.2 24.2 124 domain Y Y N DUF1363 domain-containing protein 2720787,3405209,9763292 0 EBI-EMBL Protein of unknown function (DUF1363) Protein of unknown function (DUF1363) This family consists of several Trypanosoma brucei putative variant specific antigen proteins of around 80 residues in length. [1]. 9763292. Selection for activation of a new variant surface glycoprotein gene expression site in Trypanosoma brucei can result in deletion of the old one. Rudenko G, Chaves I, Dirks-Mulder A, Borst P;. Mol Biochem Parasitol 1998;95:97-109. [2]. 2720787. The genes and transcripts of an antigen gene expression site from T. brucei. Pays E, Tebabi P, Pays A, Coquelet H, Revelard P, Salmon D, Steinert M;. Cell 1989;57:835-845. [3]. 3405209. Putative genes of a variant-specific antigen gene transcription unit in Trypanosoma brucei. Alexandre S, Guyaux M, Murphy NB, Coquelet H, Pays A, Steinert M, Pays E;. Mol Cell Biol 1988;8:2367-2378. (from Pfam) NF018797.5 PF07134.16 AcMNPV_Orf18 25 25 327 domain Y Y N AcMNPV orf17 family protein 17573091 0 EBI-EMBL Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf18 AcMNPV orf17 family protein This family is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf18 (ac18) [1]; it is a family of uncharacterised viral proteins. [1]. 17573091. ac18 is not essential for the propagation of Autographa californica multiple nucleopolyhedrovirus. Wang Y, Wu W, Li Z, Yuan M, Feng G, Yu Q, Yang K, Pang Y;. Virology. 2007;367:71-81. (from Pfam) NF018800.5 PF07138.16 AcMNPV_AC11 27 27 334 domain Y Y N AcMNPV protein AC11 family protein 25320313 0 EBI-EMBL Baculovirus protein AC11 AcMNPV protein AC11 family protein This family of baculovirus proteins is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV) protein AC11 (Orf11). ac11 is an early gene essential for budded-virus production and occlusion-derived-virus envelopment [1]. [1]. 25320313. Autographa californica multiple nucleopolyhedrovirus ORF11 is essential for budded-virus production and occlusion-derived-virus envelopment. Tao XY, Choi JY, Kim WJ, An SB, Liu Q, Kim SE, Lee SH, Kim JH, Woo SD, Jin BR, Je YH;. J Virol. 2015;89:373-383. (from Pfam) NF018801.5 PF07139.16 SPATS2-like 25 25 309 domain Y Y N SPATS2 family protein 32118724,33037180,35077478 0 EBI-EMBL Spermatogenesis-associated serine-rich protein 2-like SPATS2 family protein This family includes spermatogenesis-associated serine-rich protein 2 (SPATS2) and SPATS2-like proteins from mammals. SPATS2 is involved in spermatogenesis and likely to be a cytoplasmic RNA-binding protein [1,2]. SPATS2 is highly expressed in hepatocellular carcinoma (HCC) and may function as an oncogene. It constitutes a novel diagnostic prognostic marker in liver cancer and a potential therapeutic target for the treatment of HCC [3]. [1]. 33037180. SPATS2, negatively regulated by miR-145-5p, promotes hepatocellular carcinoma progression through regulating cell cycle. Dong G, Zhang S, Shen S, Sun L, Wang X, Wang H, Wu J, Liu T, Wang C, Wang H, Lu T, Rao B, Ren Z;. Cell Death Dis. 2020;11:837. [2]. 35077478. SPATS2 is positively activated by long noncoding RNA SNHG5 via regulating DNMT3a expression to promote hepatocellular carcinoma progression. Yan J, Huang QY, Huang YJ, Wang CS, Liu PX;. PLoS One. 2022;17:e0262262. [3]. 32118724. Comprehensive evaluation of SPATS2 expression and its prognostic potential in liver cancer. Xing J, Tian Y, Ji W, Wang X;. Medicine (Baltimore). 2020;99:e19230. (from Pfam) NF018811.5 PF07150.16 DUF1390 24.7 24.7 226 domain Y Y N DUF1390 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1390) Protein of unknown function (DUF1390) This family consists of several Paramecium bursaria chlorella virus 1 (PBCV-1) proteins of around 250 residues in length. The function of this family is unknown. (from Pfam) NF018820.5 PF07159.17 CYRIA-B_Rac1-bd 23.1 23.1 301 domain Y Y N Rac1-binding domain-containing protein GO:0031267 30250061,31285585,31413787 0 EBI-EMBL CYRIA/CYRIB Rac1 binding domain CYRIA/CYRIB Rac1 binding domain This domain has been annotated as Rac1-binding domain [1, 2]. It can be found in human CYRIA/CYRIB and at the N terminus of CYFIP1/2 [3]. CYFIP proteins are known RAC1 effectors that stimulate actin polymerization [3]. In mice, CYRIB (also known as CYRI or FAM49B) negatively regulates RAC1-driven cytoskeletal remodelling and plays a role in restricting infection mediated by Mycobacterium tuberculosis and Listeria monocytogenes [3]. [1]. 31413787. CYRI/ Fam49 Proteins Represent a New Class of Rac1 Interactors. Whitelaw JA, Lilla S, Paul NR, Fort L, Zanivan S, Machesky LM;. Commun Integr Biol. 2019;12:112-118. [2]. 30250061. Fam49/CYRI interacts with Rac1 and locally suppresses protrusions. Fort L, Batista JM, Thomason PA, Spence HJ, Whitelaw JA, Tweedy L, Greaves J, Martin KJ, Anderson KI, Brown P, Lilla S, Neilson MP, Tafelmeyer P, Zanivan S, Ismail S, Bryant DM, Tomkinson NCO, Chamberlain LH, Mastick GS, Insall RH, Machesky LM;. Nat Cell Biol. 2018;20:1159-1171. [3]. 31285585. CYRI/FAM49B negatively regulates RAC1-driven cytoskeletal remodelling and protects against bacterial infection. Yuki KE, Marei H, Fiskin E, Eva MM, Gopal AA, Schwartzentruber JA, Majewski J, Cellier M, Mandl JN, Vidal SM, Malo D, Dikic I;. Nat Microbiol. 2019;4:1516-1531. (from Pfam) NF018821.5 PF07160.17 SKA1 29.6 29.6 237 domain Y Y N spindle and kinetochore-associated protein 1 GO:0007059,GO:0008017,GO:0051301 17093495,22483620,24413531 0 EBI-EMBL Spindle and kinetochore-associated protein 1 spindle and kinetochore-associated protein 1 Spindle and kinetochore-associated protein 1 (SKA1) is a component of the SKA1 complex (consists of Ska1, Ska2, and Ska3/Rama1), a microtubule-binding subcomplex of the outer kinetochore that is essential for proper chromosome segregation [1]. [1]. 17093495. Timely anaphase onset requires a novel spindle and kinetochore complex comprising Ska1 and Ska2. Hanisch A, Sillje HH, Nigg EA;. EMBO J. 2006;25:5504-5515. [2]. 22483620. Structural and functional organization of the Ska complex, a key component of the kinetochore-microtubule interface. Jeyaprakash AA, Santamaria A, Jayachandran U, Chan YW, Benda C, Nigg EA, Conti E;. Mol Cell. 2012;46:274-286. [3]. 24413531. Structural basis for microtubule recognition by the human kinetochore Ska complex. Abad MA, Medina B, Santamaria A, Zou J, Plasberg-Hill C, Madhumalar A, Jayachandran U, Redli PM, Rappsilber J, Nigg EA, Jeyaprakash AA;. Nat Commun. 2014;5:2964. (from Pfam) NF018854.5 PF07197.17 DUF1409 29.2 29.2 48 domain Y Y N DUF1409 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1409) Protein of unknown function (DUF1409) This family represents a short conserved region (approximately 50 residues long), sometimes repeated, within a number of hypothetical Oryza sativa proteins of unknown function. (from Pfam) NF018860.5 PF07203.16 DUF1412 25 25 53 domain Y Y N DUF1412 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1412) Protein of unknown function (DUF1412) This family consists of several Caenorhabditis elegans proteins of around 70-75 residues in length. The function of this family is unknown. (from Pfam) NF018903.5 PF07248.17 DUF1431 22 22 155 domain Y Y N DUF1431 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1431) Protein of unknown function (DUF1431) This family contains a number of Drosophila melanogaster proteins of unknown function. These contain several conserved cysteine residues. (from Pfam) NF018921.5 PF07270.16 DUF1438 25 25 151 domain Y Y N DUF1438 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1438) Protein of unknown function (DUF1438) This family consists of several hypothetical proteins of around 170 residues in length which appear to be mouse specific. The function of this family is unknown. (from Pfam) NF018994.5 PF07346.16 DUF1477 27 27 115 domain Y Y N DUF1477 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1477) Protein of unknown function (DUF1477) This family consists of several hypothetical Nucleopolyhedrovirus proteins of around 100 resides in length. The function of this family is unknown. (from Pfam) NF018997.5 PF07349.16 DUF1478 25 25 161 domain Y Y N DUF1478 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1478) Protein of unknown function (DUF1478) This family consists of several hypothetical Sapovirus proteins of around 165 residues in length. The function of this family is unknown. (from Pfam) NF019035.5 PF07389.17 Pox_B6 25 25 183 domain Y Y N orthopoxvirus family proten 0 EBI-EMBL Vaccinia B6 protein orthopoxvirus family proten This family consists of several Orthopoxvirus specific proteins, which include Vaccinia virus, B6 protein, of around 170 residues in length. The function of this family is unknown. (from Pfam) NF019049.5 PF07403.16 DUF1505 25.4 25.4 114 domain Y Y N DUF1505 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1505) Protein of unknown function (DUF1505) This family consists of several uncharacterised Caenorhabditis elegans proteins of around 115 resides in length. Members of this family contain 6 highly conserved cysteine residues. The function of this family is unknown. (from Pfam) NF019065.5 PF07420.16 DUF1509 24.9 24.9 384 domain Y Y N DUF1509 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1509) Protein of unknown function (DUF1509) This family consists of several uncharacterised viral proteins from the Marek's disease-like viruses. Members of this family are typically around 400 residues in length. The function of this family is unknown. (from Pfam) NF019112.5 PF07469.17 DUF1518 25 25 58 domain Y Y N DUF1518 domain-containing protein GO:0005634 21854393 0 EBI-EMBL Nuclear receptor coactivator, DUF1518 Nuclear receptor coactivator, DUF1518 This conserved domain of unknown function is usually found tandemly repeated in the nuclear receptor coactivator family (NCOA1/2/3, also known as the SRC/p160 nuclear receptor coactivator family, which are ligand-dependent transcription factors [1,2]. [1]. 21854393. Steroid receptor coactivator 2 modulates steroid-dependent male sexual behavior and neuroplasticity in Japanese quail (Coturnix japonica). Niessen NA, Balthazart J, Ball GF, Charlier TD;. J Neurochem. 2011;119:579-593. (from Pfam) NF019333.5 PF07713.18 DUF1604 25 25 84 domain Y Y N DUF1604 domain-containing protein GO:0006397 0 EBI-EMBL Protein of unknown function (DUF1604) Protein of unknown function (DUF1604) This family is found at the N-terminus of several eukaryotic RNA processing proteins (e.g Swiss:Q8N3B7). (from Pfam) NF019382.5 PF07762.19 DUF1618 24 24 133 domain Y Y N DUF1618 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1618) Protein of unknown function (DUF1618) The members of this family are mainly hypothetical proteins expressed by Oryza sativa. (from Pfam) NF019391.5 PF07773.16 TCTN_DUF1619 22 22 313 domain Y Y N tectonic domain-containing protein 22179047,27770015,29866362 0 EBI-EMBL Tectonic domain DUF1619 Tectonic domain DUF1619 This is a conserved domain found in tectonic proteins (TCTN1/2/3) which contains a Cys rich N-terminal region. Although its function is currently unknown (this domain is also known as DUF1619), studies in TCTN2 suggest that it is indispensable for normal functions [1,2]. These proteins form a complex required for hedgehog signalling transduction [3]. [1]. 29866362. Super-Resolution Imaging Reveals TCTN2 Depletion-Induced IFT88 Lumen Leakage and Ciliary Weakening. Weng RR, Yang TT, Huang CE, Chang CW, Wang WJ, Liao JC;. Biophys J. 2018;115:263-275. [2]. 27770015. Open Sesame: How Transition Fibers and the Transition Zone Control Ciliary Composition. Garcia-Gonzalo FR, Reiter JF;. Cold Spring Harb Perspect Biol. 2017; [Epub ahead of print]. [3]. 22179047. A ciliopathy complex at the transition zone protects the cilia as a privileged membrane domain. Chih B, Liu P, Chinn Y, Chalouni C, Komuves LG, Hass PE, Sandoval W, Peterson AS;. Nat Cell Biol. 2011;14:61-72. (from Pfam) NF019402.5 PF07785.16 DUF1623 25 25 90 domain Y Y N DUF1623 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1623) Protein of unknown function (DUF1623) The members of this family are all derived from relatively short hypothetical proteins thought to be expressed by various Nucleopolyhedroviruses. (from Pfam) NF019411.5 PF07794.16 DUF1633 26.4 26.4 854 domain Y Y N DUF1633 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1633) Protein of unknown function (DUF1633) This family contains sequences derived from a group of hypothetical proteins expressed by Arabidopsis thaliana. These sequences are highly similar and the region concerned is about 100 residues long. (from Pfam) NF019412.5 PF07795.16 DUF1635 27.2 27.2 223 domain Y Y N DUF1635 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1635) Protein of unknown function (DUF1635) The members of this family include sequences that are parts of hypothetical proteins expressed by plant species. The region in question is about 170 amino acids long. (from Pfam) NF019414.5 PF07797.19 DUF1639 22.2 22.2 50 domain Y Y N DUF1639 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1639) Protein of unknown function (DUF1639) This approximately 50 residue region is found in a number of sequences derived from hypothetical plant proteins. This region features a highly basic 5 amino-acid stretch towards its centre. (from Pfam) NF019417.5 PF07800.17 DUF1644 25 25 166 domain Y Y N DUF1644 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1644) Protein of unknown function (DUF1644) This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, and is probably a zinc-binding domain. (from Pfam) NF019433.5 PF07816.16 DUF1645 25 25 188 domain Y Y N DUF1645 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1645) Protein of unknown function (DUF1645) These sequences are derived from a number of hypothetical plant proteins. The region in question is approximately 270 amino acids long. Some members of this family are annotated as yeast pheromone receptor proteins AR781 but no literature was found to support this. (from Pfam) NF019470.5 PF07855.17 ATG101 26.5 26.5 158 domain Y Y N autophagy-related protein 101 GO:0006914 19287211,19597335,26389686 0 EBI-EMBL Autophagy-related protein 101 autophagy-related protein 101 Atg101 is a critical autophagy factor that functions together with ULK, Atg13 and FIP200 [1, 2]. Atg101 has been shown to be a HORMA (Hop1, Rev7 and MAD2) domain protein with an open conformation [3]. [1]. 19597335. Atg101, a novel mammalian autophagy protein interacting with Atg13. Hosokawa N, Sasaki T, Iemura S, Natsume T, Hara T, Mizushima N;. Autophagy. 2009;5:973-979. [2]. 19287211. A novel, human Atg13 binding protein, Atg101, interacts with ULK1 and is essential for macroautophagy. Mercer CA, Kaliappan A, Dennis PB;. Autophagy. 2009;5:649-662. [3]. 26389686. Open and closed HORMAs regulate autophagy initiation. Suzuki H, Kaizuka T, Mizushima N, Noda NN;. Autophagy. 2015;11:2123-2124. (from Pfam) NF019506.5 PF07891.17 DUF1666 25 25 246 domain Y Y N DUF1666 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1666) Protein of unknown function (DUF1666) These sequences are derived from hypothetical plant proteins of unknown function. The region in question is approximately 250 residues long. (from Pfam) NF019523.5 PF07909.16 DUF1663 25 25 514 domain Y Y N DUF1663 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1663) Protein of unknown function (DUF1663) The members of this family are hypothetical proteins expressed by Trypanosoma cruzi, a eukaryotic parasite that causes Chagas' disease in humans. This region is found as multiple copies per protein. (from Pfam) NF019545.5 PF07933.19 DUF1681 29.2 29.2 158 domain Y Y N DUF1681 domain-containing protein GO:0006897,GO:0016020 0 EBI-EMBL Protein of unknown function (DUF1681) Protein of unknown function (DUF1681) This family is composed of sequences derived from a number of hypothetical eukaryotic proteins of unknown function. (from Pfam) NF019558.5 PF07946.19 CCDC47 27.7 27.7 326 domain Y Y N PAT complex subunit CCDC47 family protein GO:0005509,GO:0005783,GO:0032469 12475939,25009997,30401460,32814900,32820719 0 EBI-EMBL PAT complex subunit CCDC47 PAT complex subunit CCDC47 family protein This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes [1]. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins [1]. CCDC47 (Swiss:Q96A33) is required to maintain the stability of Asterix [1,2]. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis [3]. It is also involved in the regulation of calcium ion homeostasis in the ER [4], being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway [5]. [1]. 32814900. An intramembrane chaperone complex facilitates membrane protein biogenesis. Chitwood PJ, Hegde RS;. Nature. 2020;584:630-634. [2]. 12475939. Different transmembrane domains associate with distinct endoplasmic reticulum components during membrane integration of a polytopic protein. Meacock SL, Lecomte FJ, Crawshaw SG, High S;. Mol Biol Cell. 2002;13:4114-4129. [3]. 32820719. An ER translocon for multi-pass membrane protein biogenesis. McGilvray PT, Anghel SA, Sundaram A, Zhong F, Trnka MJ, Fuller JR, Hu H, Burlingame AL, Keenan RJ;. Elife. 2020; [Epub ahead of print]. [4]. 30401460. Bi-allelic CCDC47 Variants Cause a Disorder Characterized b. TRUNCATED at 1650 bytes (from Pfam) NF019566.5 PF07954.16 DUF1689 25 25 148 domain Y Y N DUF1689 domain-containing protein 14562095 0 EBI-EMBL Protein of unknown function (DUF1689) Protein of unknown function (DUF1689) Family of fungal proteins with unknown function. A member of this family has been found to localise in the mitochondria [1]. [1]. 14562095. Global analysis of protein localization in budding yeast. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK;. Nature 2003;425:686-691. (from Pfam) NF019568.5 PF07956.16 DUF1690 29.7 29.7 139 domain Y Y N DUF1690 domain-containing protein 0 EBI-EMBL Protein of Unknown function (DUF1690) Protein of Unknown function (DUF1690) Family of uncharacterised fungal proteins. (from Pfam) NF019712.5 PF08101.16 Msb1-Mug8_dom 23.6 23.6 423 domain Y Y N Msb1/Mug8 domain-containing protein 12399379,16303567 0 EBI-EMBL Meiotically up-regulated protein Msb1/Mug8 domain Meiotically up-regulated protein Msb1/Mug8 domain This domain of unknown function is found in fungal proteins including Mug8 from Schizosaccharomyces pombe which may have a role in meiosis and septation [1]. Saccharomyces cerevisiae homologue MSB1 (swiss:P21339) may be involved in positive regulation of 1,3-beta-glucan synthesis and the Pkc1p-MAPK pathway [2]. [1]. 16303567. A large-scale screen in S. pombe identifies seven novel genes required for critical meiotic events. Martin-Castellanos C, Blanco M, Rozalen AE, Perez-Hidalgo L, Garcia AI, Conde F, Mata J, Ellermeier C, Davis L, San-Segundo P, Smith GR, Moreno S;. Curr Biol. 2005;15:2056-2062. [2]. 12399379. Dissection of upstream regulatory components of the Rho1p effector, 1,3-beta-glucan synthase, in Saccharomyces cerevisiae. Sekiya-Kawasaki M, Abe M, Saka A, Watanabe D, Kono K, Minemura-Asakawa M, Ishihara S, Watanabe T, Ohya Y;. Genetics. 2002;162:663-676. (from Pfam) NF019765.5 PF08155.16 NOGCT 27 27 54 domain Y Y N NOGCT domain-containing protein 15112237 0 EBI-EMBL NOGCT (NUC087) domain NOGCT (NUC087) domain This C terminal domain is found in the NOG subfamily of nucleolar GTP-binding proteins [1]. [1]. 15112237. Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire. Staub E, Fiziev P, Rosenthal A, Hinzmann B;. Bioessays 2004;26:567-581. (from Pfam) NF019830.5 PF08224.16 DUF1719 25 25 231 domain Y Y N DUF1719 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF1719) Domain of unknown function (DUF1719) This is a domain of unknown function. It may have a role in ATPase activation. (from Pfam) NF019897.5 PF08292.17 RNA_pol_Rbc25 25.1 25.1 121 domain Y Y N RNA polymerase III subunit Rbc25 domain-containing protein 15612920 0 EBI-EMBL RNA polymerase III subunit Rpc25 RNA polymerase III subunit Rpc25 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [1]. [1]. 15612920. Rpc25, a conserved RNA polymerase III subunit, is critical for transcription initiation. Zaros C, Thuriaux P;. Mol Microbiol 2005;55:104-114. (from Pfam) NF020017.5 PF08427.15 ARMH3_C 27 27 231 domain Y Y N helical domain-containing protein 31519766 0 EBI-EMBL Armadillo-like helical domain-containing protein 3, C-terminal Armadillo-like helical domain-containing protein 3, C-terminal This is the C-terminal domain of Armadillo-like helical domain- containing protein 3 (ARMH3), the previously uncharacterised peripheral Golgi protein C10orf76. ARMH3 interacts with and is involved in GBF1 recruitment, Golgi maintenance and protein secretion [1]. The function of this domain is unknown. [1]. 31519766. BioID Performed on Golgi Enriched Fractions Identify C10orf76 as a GBF1 Binding Protein Essential for Golgi Maintenance and Secretion. Chan CJ, Le R, Burns K, Ahmed K, Coyaud E, Laurent EMN, Raught B, Melancon P;. Mol Cell Proteomics. 2019;18:2285-2297. (from Pfam) NF020097.5 PF08508.15 DUF1746 22.3 22.3 116 domain Y Y N DUF1746 domain-containing protein 21504829,29355480 0 EBI-EMBL Fungal domain of unknown function (DUF1746) Fungal domain of unknown function (DUF1746) This is a fungal domain of unknown function. This domain can be found in DSC E3 ubiquitin ligase complex subunit 4 (Dsc4) from S. pombe, a component of the DSC E3 ubiquitin ligase complex required for the sre1 transcriptional activator proteolytic cleavage to release the soluble transcription factor from the membrane in low oxygen or sterol conditions. The complex plays also an important role in the multivesicular body (MVB) pathway and functions in a post-endoplasmic reticulum pathway for protein degradation [1]. This domain is also found in GLD1 from S. cerevisiae, also a component of the DSC E3 ubiquitin ligase complex involved in the targeting of the DSC complex to the Golgi apparatus and endosome membranes via the AP3 pathway to ubiquitinate Golgi/endosome membrane proteins [2]. [1]. 21504829. Yeast SREBP cleavage activation requires the Golgi Dsc E3 ligase complex. Stewart EV, Nwosu CC, Tong Z, Roguev A, Cummins TD, Kim DU, Hayles J, Park HO, Hoe KL, Powell DW, Krogan NJ, Espenshade PJ;. Mol Cell. 2011;42:160-171. [2]. 29355480. Sorting of a multi-subunit ubiquitin ligase complex in the endolysosome system. Yang X, Arines FM, Zhang W, Li M;. Elife. 2018; [Epub ahead of print] (from Pfam) NF020109.5 PF08520.15 Mitofissin 27 27 69 domain Y Y N mitofissin 37192628 0 EBI-EMBL Mitofissin mitofissin This is a family of fungal proteins identified as mitochondrial fission factors (mitofissin, also referred to as Atg44) which are essential for mitophagy. Mitofissin directly binds to lipid membranes to drive mitochondrial fission required for mitophagy [1]. [1]. 37192628. The mitochondrial intermembrane space protein mitofissin drives mitochondrial fission required for mitophagy. Fukuda T, Furukawa K, Maruyama T, Yamashita SI, Noshiro D, Song C, Ogasawara Y, Okuyama K, Alam JM, Hayatsu M, Saigusa T, Inoue K, Ikeda K, Takai A, Chen L, Lahiri V, Okada Y, Shibata S, Murata K, Klionsky DJ, Noda NN, Kanki T;. Mol Cell. 2023; [Epub ahead of print] (from Pfam) NF020138.5 PF08549.15 SWI-SNF_Ssr4_N 27 27 217 domain Y Y N SWI/SNF and RSC complexes subunit Ssr4 domain-containing protein GO:0006338 18622392,33263569 0 EBI-EMBL SWI/SNF and RSC complexes subunit Ssr4 N-terminal SWI/SNF and RSC complexes subunit Ssr4 N-terminal This entry represents the N-terminal domain of SWI/SNF and RSC complexes subunit Ssr4 from S. pombe, a essential member of the chromatin structure remodelling complex (RSC) and the SWI/SNF complex [1,2]. The structure of this domain revealed that it has a novel fold comprising an antiparallel beta-sheet of seven strands with alpha-helices on one side and random coil on the other [2]. It contains the highly conserved motif WxxxxxPxxGxxxxxxxxxxxxxxxDG. RSC is involved in transcription regulation and nucleosome positioning which controls, particularly, membrane and organelle development genes. The ATP-dependent chromatin remodelling complex SWI/SNF is required for the positive and negative regulation of gene expression of a large number of genes through the regulation of nucleosome remodelling [1]. [1]. 18622392. Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast. Monahan BJ, Villen J, Marguerat S, Bahler J, Gygi SP, Winston F;. Nat Struct Mol Biol. 2008;15:873-880. [2]. 33263569. The X-ray crystal structure of the N-terminal domain of Ssr4, a Schizosaccharomyces pombe chromatin-remodelling protein. Newman J, Nebl T, Van H, Peat TS;. Acta Crystallogr F Struct Biol Commun. 2020;76:583-589. (from Pfam) NF020147.5 PF08560.15 DUF1757 21 21 148 domain Y Y N DUF1757 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1757) Protein of unknown function (DUF1757) This family of proteins are about 150 amino acids in length and have no known function. (from Pfam) NF020161.5 PF08574.15 Iwr1 22 22 74 domain Y Y N transcription factor Iwr1 11805826,12663529,19679657 0 EBI-EMBL Transcription factor Iwr1 transcription factor Iwr1 Iwr1 is involved in transcription from polymerase II promoters; it interacts with with most of the polymerase II subunits [3]. Deletion of this protein results in hypersensitivity to the K1 killer toxin [1]. [1]. 12663529. A Saccharomyces cerevisiae genome-wide mutant screen for altered sensitivity to K1 killer toxin. Page N, Gerard-Vincent M, Menard P, Beaulieu M, Azuma M, Dijkgraaf GJ, Li H, Marcoux J, Nguyen T, Dowse T, Sdicu AM, Bussey H;. Genetics. 2003;163:875-894. [2]. 11805826. Functional organization of the yeast proteome by systematic analysis of protein complexes. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C,. Nature. 2002;415:141-147. [3]. 19679657. The yeast RNA polymerase II-associated factor Iwr1p is involved in the basal and regulated transcription of specific genes. Peiro-Chova L, Estruch F;. J Biol Chem. 2009;284:28958-28967. (from Pfam) NF020162.5 PF08576.15 DUF1764 27 27 100 domain Y Y N DUF1764 domain-containing protein 0 EBI-EMBL Eukaryotic protein of unknown function (DUF1764) Eukaryotic protein of unknown function (DUF1764) This is a family of eukaryotic proteins of unknown function. This family contains many hypothetical proteins. (from Pfam) NF020164.5 PF08578.15 DUF1765 25 25 125 domain Y Y N DUF1765 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1765) Protein of unknown function (DUF1765) This region represents a conserved region found in hypothetical proteins from fungi, mycetozoa and entamoebidae. (from Pfam) NF020173.5 PF08588.15 DUF1769 22 22 208 domain Y Y N DUF1769 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF1769) Protein of unknown function (DUF1769) Family of fungal protein with unknown function. (from Pfam) NF020174.5 PF08589.15 ATG43 25 25 98 domain Y Y N ATG43 family protein GO:0000423,GO:0140580 33138913 0 EBI-EMBL Autophagy receptor ATG43 ATG43 family protein This family represents the autophagy receptor ATG43 from fungi. It is a mitochondrial outer membrane protein which serves as a mitophagy receptor to promote the selective degradation of mitochondria. [1]. 33138913. Atg43 tethers isolation membranes to mitochondria to promote starvation-induced mitophagy in fission yeast. Fukuda T, Ebi Y, Saigusa T, Furukawa K, Yamashita SI, Inoue K, Kobayashi D, Yoshida Y, Kanki T;. Elife. 2020; [Epub ahead of print] (from Pfam) NF020301.5 PF08718.16 GLTP 25.6 25.6 147 domain Y Y N GLTP domain-containing protein GO:0005737,GO:0120009,GO:0120013 15329726,15504043,16169991,16309699,17105344 0 EBI-EMBL Glycolipid transfer protein (GLTP) Glycolipid transfer protein (GLTP) GLTP is a cytosolic protein that catalyses the intermembrane transfer of glycolipids [1][2]. [1]. 15504043. Glycolipid transfer protein mediated transfer of glycosphingolipids between membranes: a model for action based on kinetic and thermodynamic analyses. Rao CS, Lin X, Pike HM, Molotkovsky JG, Brown RE;. Biochemistry. 2004;43:13805-13815. [2]. 16309699. Structural evidence for adaptive ligand binding of glycolipid transfer protein. Airenne TT, Kidron H, Nymalm Y, Nylund M, West G, Mattjus P, Salminen TA;. J Mol Biol. 2006;355:224-236. [3]. 17105344. The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure. Malinina L, Malakhova ML, Kanack AT, Lu M, Abagyan R, Brown RE, Patel DJ;. PLoS Biol. 2006;4:e362. [4]. 15329726. Structural basis for glycosphingolipid transfer specificity. Malinina L, Malakhova ML, Teplov A, Brown RE, Patel DJ;. Nature. 2004;430:1048-1053. [5]. 16169991. Glycolipid transfer protein interaction with bilayer vesicles: modulation by changing lipid composition. Rao CS, Chung T, Pike HM, Brown RE;. Biophys J. 2005;89:4017-4028. (from Pfam) NF020500.5 PF08926.16 DUF1908 27.5 27.5 281 domain Y Y N DUF1908 domain-containing protein GO:0000287,GO:0004674,GO:0005524,GO:0006468 0 EBI-EMBL Domain of unknown function (DUF1908) Domain of unknown function (DUF1908) This domain is found in a set of hypothetical/structural eukaryotic proteins. (from Pfam) NF020521.5 PF08949.15 PRD1_P5_C 25 25 219 domain Y Y N phage spike protein domain-containing protein 10956048,15525981 0 EBI-EMBL Bacteriophage PRD1, spike protein P5, C-terminal Bacteriophage PRD1, spike protein P5, C-terminal This domain is found at the C-terminal of bacteriophage PRD1 spike protein P5. [1]. The spike structure of bacteriophage PRD1 is comprised of proteins P2, P5, and P31. P5 is an elongated multidomain trimer. This C-terminal domain appears to contain the residues responsible for the trimerization of the protein [1,2]. [1]. 15525981. Insights into assembly from structural analysis of bacteriophage PRD1. Abrescia NG, Cockburn JJ, Grimes JM, Sutton GC, Diprose JM, Butcher SJ, Fuller SD, San Martin C, Burnett RM, Stuart DI, Bamford DH, Bamford JK;. Nature. 2004;432:68-74. [2]. 10956048. Assembly of bacteriophage PRD1 spike complex: role of the multidomain protein P5. Caldentey J, Tuma R, Bamford DH;. Biochemistry. 2000;39:10566-10573. (from Pfam) NF020524.5 PF08952.16 DUF1866 23 23 146 domain Y Y N DUF1866 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF1866) Domain of unknown function (DUF1866) This domain, found in Synaptojanin, has no known function. (from Pfam) NF020552.5 PF08983.15 V1R_C 25 25 48 domain Y Y N vasopressin V1 receptor domain-containing protein 16511036,23830982 0 EBI-EMBL Vasopressin V1 receptor, C-terminal Vasopressin V1 receptor, C-terminal This is the conserved C-terminal domain of Vasopressin V1a/b receptors (V1R), which is involved in receptor trafficking and facilitates the interaction between the intracellular loops of the receptor, the G proteins and coupling to phospholipase C [1,2]. This domain is unstructured and may reflect its conformational plasticity that may be necessary for proper function of V1R [1]. [1]. 16511036. A C-terminal segment of the V1R vasopressin receptor is unstructured in the crystal structure of its chimera with the maltose-binding protein. Adikesavan NV, Mahmood SS, Stanley N, Xu Z, Wu N, Thibonnier M, Shoham M;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005;61:341-345. [2]. 23830982. Expression of arginine vasotocin receptors in the developing zebrafish CNS. Iwasaki K, Taguchi M, Bonkowsky JL, Kuwada JY;. Gene Expr Patterns. 2013;13:335-342. (from Pfam) NF020556.5 PF08987.15 DUF1892 27 27 109 domain Y Y N DUF1892 domain-containing protein 12717036 0 EBI-EMBL Protein of unknown function (DUF1892) Protein of unknown function (DUF1892) Members of this family, that are synthesised by Saccharomycetes, adopt a structure consisting of a four-stranded beta-sheet, with strand order beta2-beta1-beta4-beta3, and two alpha-helices, with an overall topology of beta-beta-alpha-beta-beta-alpha. They have no known function [1]. [1]. 12717036. A novel member of the split betaalphabeta fold: Solution structure of the hypothetical protein YML108W from Saccharomyces cerevisiae. Pineda-Lucena A, Liao JC, Cort JR, Yee A, Kennedy MA, Edwards AM, Arrowsmith CH;. Protein Sci. 2003;12:1136-1140. (from Pfam) NF020686.5 PF09122.15 DUF1930 27 27 68 domain Y Y N DUF1930 domain-containing protein 12952945 0 EBI-EMBL Domain of unknown function (DUF1930) Domain of unknown function (DUF1930) Members of this family are found in 3-mercaptopyruvate sulfurtransferase, and have no known function. They adopt a structure consisting of a four-stranded antiparallel beta-sheet and an alpha-helix, arranged in a beta(2)-alpha-beta(2) fashion, and bearing a remarkable structural similarity to the FK506-binding protein class of peptidylprolyl cis/trans-isomerase [1]. [1]. 12952945. The crystal structure of Leishmania major 3-mercaptopyruvate sulfurtransferase. A three-domain architecture with a serine protease-like triad at the active site. Alphey MS, Williams RA, Mottram JC, Coombs GH, Hunter WN;. J Biol Chem. 2003;278:48219-48227. (from Pfam) NF020712.5 PF09149.15 DUF1935 27 27 103 domain Y Y N DUF1935 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF1935) Domain of unknown function (DUF1935) Members of this family are found in various bacterial and eukaryotic hypothetical proteins, as well as in the cysteine protease calpain. Their exact function has not, as yet, been defined. (from Pfam) NF020722.5 PF09159.15 Ydc2-catalyt 23 23 258 domain Y Y N mitochondrial RNA-splicing protein MRS1 11726496,20064926,2834089 0 EBI-EMBL Mitochondrial resolvase Ydc2 / RNA splicing MRS1 mitochondrial RNA-splicing protein MRS1 Members of this family adopt a secondary structure consisting of two beta sheets and one alpha helix, arranged as a beta-alpha-beta motif. Each beta sheet has five strands, arranged in a 32145 order, with the second strand being antiparallel to the rest. Mitochondrial resolvase Ydc2 is capable of resolving Holliday junctions and cleaves DNA after 5'-CT-3' and 5'-TT-3' sequences [1]. This family also contains the mitochondrial RNA-splicing protein MRS1 which is involved in the excision of group I introns [2-3]. [1]. 11726496. Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2. Ceschini S, Keeley A, McAlister MS, Oram M, Phelan J, Pearl LH, Tsaneva IR, Barrett TE;. EMBO J. 2001;20:6601-6611. [2]. 20064926. Splicing of yeast aI5beta group I intron requires SUV3 to recycle MRS1 via mitochondrial degradosome-promoted decay of excised intron ribonucleoprotein (RNP). Turk EM, Caprara MG;. J Biol Chem. 2010;285:8585-8594. [3]. 2834089. Cloning of a nuclear gene MRS1 involved in the excision of a single group I intron (bI3) from the mitochondrial COB transcript in S. cerevisiae. Kreike J, Schulze M, Pillar T, Korte A, Rodel G;. Curr Genet. 1986;11:185-191. (from Pfam) NF020788.5 PF09227.15 Bubble 23 23 64 domain Y Y N DUF1962 domain-containing protein 14747700 0 EBI-EMBL Bubble protein Bubble protein Members of this family of fungal domains are functionally uncharacterised. They may act as toxins [1]. [1]. 14747700. Solving the structure of the bubble protein using the anomalous sulfur signal from single-crystal in-house Cu Kalpha diffraction data only. Olsen JG, Flensburg C, Olsen O, Bricogne G, Henriksen A;. Acta Crystallogr D Biol Crystallogr. 2004;60:250-255. (from Pfam) NF020971.5 PF09418.15 DUF2009 25 25 455 domain Y Y N DUF2009 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2009) Protein of unknown function (DUF2009) This is a eukaryotic family of proteins with unknown function. (from Pfam) NF020980.5 PF09427.15 DUF2014 27 27 263 domain Y Y N DUF2014 domain-containing protein GO:0032933,GO:0045944 15797383 0 EBI-EMBL Domain of unknown function (DUF2014) Domain of unknown function (DUF2014) This domain is found at the C terminal of a family of ER membrane bound transcription factors called sterol regulatory element binding proteins (SREBP). [1]. 15797383. SREBP pathway responds to sterols and functions as an oxygen sensor in fission yeast. Hughes AL, Todd BL, Espenshade PJ;. Cell. 2005;120:831-842. (from Pfam) NF020981.5 PF09428.15 DUF2011 24.5 24.5 89 domain Y Y N DUF2011 domain-containing protein 0 EBI-EMBL Fungal protein of unknown function (DUF2011) Fungal protein of unknown function (DUF2011) This is a family of fungal proteins whose function is unknown. (from Pfam) NF020986.5 PF09435.15 DUF2015 27 27 110 domain Y Y N DUF2015 domain-containing protein 0 EBI-EMBL Fungal protein of unknown function (DUF2015) Fungal protein of unknown function (DUF2015) This is a fungal family of uncharacterised proteins. (from Pfam) NF021044.5 PF09495.15 DUF2462 23 23 77 domain Y Y N DUF2462 domain-containing protein 15635413 0 EBI-EMBL Protein of unknown function (DUF2462) Protein of unknown function (DUF2462) This protein is highly conserved, but its function is unknown. It can be isolated from HeLa cell nucleoli and is found to be homologous with Leydig cell tumour protein whose function is unknown [1, supplementary Table I]. [1]. 15635413. Nucleolar proteome dynamics. Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M;. Nature. 2005;433:77-83. (from Pfam) NF021274.5 PF09741.14 DUF2045 25 25 231 domain Y Y N DUF2045 domain-containing protein 0 EBI-EMBL Uncharacterized conserved protein (DUF2045) Uncharacterized conserved protein (DUF2045) This entry is the conserved 250 residues of proteins of approximately 450 amino acids. It contains several highly conserved motifs including a CVxLxxxD motif.The function is unknown. (from Pfam) NF021278.5 PF09745.14 NSRP1_N 25 25 121 domain Y Y N NRP1 coiled-coil domain-containing protein GO:0000381 21296756,26797131 0 EBI-EMBL Nuclear speckle splicing regulatory protein 1, N-terminal Nuclear speckle splicing regulatory protein 1, N-terminal This domain is found at the N-terminal of Nuclear speckle splicing regulatory protein 1 (NRP1, also known as Nuclear speckle-related protein 70 and Coiled-coil domain-containing protein 55) and contains a coiled-coil domain that plays a critical role in NRP1 alternative splicing activity and self-oligomerization. NRP1 is a RNA-binding protein that mediates pre-mRNA alternative splicing regulation [1,2]. [1]. 21296756. NSrp70 is a novel nuclear speckle-related protein that modulates alternative pre-mRNA splicing in vivo. Kim YD, Lee JY, Oh KM, Araki M, Araki K, Yamamura K, Jun CD;. Nucleic Acids Res. 2011;39:4300-4314. [2]. 26797131. Nuclear Speckle-related Protein 70 Binds to Serine/Arginine-rich Splicing Factors 1 and 2 via an Arginine/Serine-like Region and Counteracts Their Alternative Splicing Activity. Kim CH, Kim YD, Choi EK, Kim HR, Na BR, Im SH, Jun CD;. J Biol Chem. 2016;291:6169-6181. (from Pfam) NF021280.5 PF09747.14 CCD97-like_C 27.1 27.1 197 domain Y Y N coiled-coil domain-containing protein 0 EBI-EMBL Coiled-coil domain containing protein 97-like, C-terminal Coiled-coil domain containing protein 97-like, C-terminal This domain is found at the C-terminal of CCD97. In some proteins, this domain is found as two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. (from Pfam) NF021333.5 PF09804.14 DENND11 27 27 283 domain Y Y N DENN domain-containing protein 17394467 0 EBI-EMBL DENN domain-containing protein 11 DENN domain-containing protein 11 DENN domain-containing protein 11 (also known as LCHN) is thought to play a role in neuritogenesis, as well as in neuronal recovery and/or restructuring in the hippocampus following transient cerebral ischemia [1]. [1]. 17394467. Isolation and characterization of LCHN: a novel factor induced by transient global ischemia in the adult rat hippocampus. Zhang G, Jung BP, Ho W, Jugloff DG, Cheung HH, Gurd JW, Wallace MC, Eubanks JH;. J Neurochem. 2007;101:263-273. (from Pfam) NF021656.5 PF10153.14 Efg1 25 25 113 domain Y Y N rRNA-processing protein Efg1 GO:0006364 12837249,16510898 0 EBI-EMBL rRNA-processing protein Efg1 rRNA-processing protein Efg1 Efg1 is involved in rRNA processing [1, 2]. [1]. 12837249. A panoramic view of yeast noncoding RNA processing. Peng WT, Robinson MD, Mnaimneh S, Krogan NJ, Cagney G, Morris Q, Davierwala AP, Grigull J, Yang X, Zhang W, Mitsakakis N, Ryan OW, Datta N, Jojic V, Pal C, Canadien V, Richards D, Beattie B, Wu LF, Altschuler SJ, Roweis S, Frey BJ, Emili A, Greenblatt JF,. Cell 2003;113:919-933. [2]. 16510898. Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Kastenmayer JP, Ni L, Chu A, Kitchen LE, Au WC, Yang H, Carter CD, Wheeler D, Davis RW, Boeke JD, Snyder MA, Basrai MA;. Genome Res. 2006;16:365-373. (from Pfam) NF021683.5 PF10180.14 WKF 25 25 63 domain Y Y N WKF domain-containing protein 30528433 0 EBI-EMBL WKF domain WKF domain This is the C-terminal conserved region of a family of proteins found from fungi to humans. The domain is named WKF after a conserved sequence motif. This domain has been shown to bind RNA [1]. This domain was previously known as DUF2373. [1]. 30528433. The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest. Trendel J, Schwarzl T, Horos R, Prakash A, Bateman A, Hentze MW, Krijgsveld J;. Cell. 2018; [Epub ahead of print] (from Pfam) NF021692.5 PF10189.14 Ints3_N 25 25 409 domain Y Y N integrator complex subunit 3 16239144,24630995 0 EBI-EMBL Integrator complex subunit 3 N-terminal integrator complex subunit 3 The Integrator complex is involved in small nuclear RNA (snRNA) U1 and U2 transcription, and in their 3'-box-dependent processing. This complex associates with the C-terminal domain of RNA polymerase II largest subunit and is recruited to the U1 and U2 snRNAs genes [1]. This entry represents the N-terminal domain of the Integrator complex subunit 3 (Ints3), also known as SOSS complex subunit A (SOSSA). It is a component of the sensor of single-stranded DNA complex (SOSS), which associates with single-stranded DNA, important for DNA repair and efficient homologous recombination [2]. This subunit serves as a central adaptor for SOSS complex assembly and stability, and facilitates the accumulation of the complex to the sites of DNA damage. This region acts as a scaffold for SOSSB1 and SOSSC interaction and it is not essential for ssDNA binding [2]. [1]. 16239144. Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Baillat D, Hakimi MA, Naar AM, Shilatifard A, Cooch N, Shiekhattar R;. Cell. 2005;123:265-276. [2]. 24630995. Structural basis of SOSS1 complex assembly and recognition of ssDNA. Ren W, Chen H, Sun Q, Tang X, Lim SC, Huang J, Song H;. Cell Rep. 2014;6:982-991. (from Pfam) NF021707.5 PF10209.14 DUF2340 25 25 120 domain Y Y N DUF2340 domain-containing protein 0 EBI-EMBL Uncharacterized conserved protein (DUF2340) Uncharacterized conserved protein (DUF2340) This is a family of small proteins of approximately 150 amino acids of unknown function. (from Pfam) NF021715.5 PF10217.14 DUF2039 27 27 89 domain Y Y N DUF2039 domain-containing protein 0 EBI-EMBL Uncharacterized conserved protein (DUF2039) Uncharacterized conserved protein (DUF2039) This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown. (from Pfam) NF021716.5 PF10218.14 SPRING1 22 22 131 domain Y Y N SPRING1 family protein GO:2000640 32111832 0 EBI-EMBL SREBP regulating gene protein SPRING1 family protein SPRING1 is a glycosylated Golgi-resident membrane protein involved in SREBP signaling and cholesterol metabolism. It modulates the proper localisation of SCAP (SREBP cleavage-activating protein) to the endoplasmic reticulum, thereby controlling the level of functional SCAP [1]. [1]. 32111832. Haploid genetic screens identify SPRING/C12ORF49 as a determinant of SREBP signaling and cholesterol metabolism. Loregger A, Raaben M, Nieuwenhuis J, Tan JME, Jae LT, van den Hengel LG, Hendrix S, van den Berg M, Scheij S, Song JY, Huijbers IJ, Kroese LJ, Ottenhoff R, van Weeghel M, van de Sluis B, Brummelkamp T, Zelcer N;. Nat Commun. 2020;11:1128. (from Pfam) NF021719.5 PF10222.14 DUF2152 29.4 29.4 593 domain Y Y N DUF2152 domain-containing protein 0 EBI-EMBL Uncharacterized conserved protein (DUF2152) Uncharacterized conserved protein (DUF2152) This is a family of proteins conserved from worms to humans. Its function is unknown. (from Pfam) NF021722.5 PF10225.14 NEMP 28.7 28.7 249 domain Y Y N NEMP family protein 19167377,25946333 0 EBI-EMBL NEMP family NEMP family protein This entry includes a group of nuclear envelope integral membrane proteins from animals and plants, including NEMP1 from Xenopus laevis. NEMP1 is a RanGTP-binding protein and is involved in eye development [1,2]. [1]. 19167377. Involvement of an inner nuclear membrane protein, Nemp1, in Xenopus neural development through an interaction with the chromatin protein BAF. Mamada H, Takahashi N, Taira M;. Dev Biol. 2009;327:497-507. [2]. 25946333. The Inner Nuclear Membrane Protein Nemp1 Is a New Type of RanGTP-Binding Protein in Eukaryotes. Shibano T, Mamada H, Hakuno F, Takahashi S, Taira M;. PLoS One. 2015;10:e0127271. (from Pfam) NF021735.5 PF10239.14 DUF2465 30.5 30.5 302 domain Y Y N DUF2465 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2465) Protein of unknown function (DUF2465) FAM98A and B proteins are found from worms to humans but their function is unknown. This entry is of a family of proteins that is rich in glycines. (from Pfam) NF021787.5 PF10293.14 DUF2405 24 24 156 domain Y Y N repeating beta-groove domain-containing protein 34415038,35015055,35491307 0 EBI-EMBL FMP27, sixth RBG unit FMP27, sixth RBG unit Fungal proteins FMP27 (also known as Hob1) and Hob2 (YPR117W) are tube-forming lipid transport proteins which bind to phosphatidylinositols and affects phosphatidylinositol-4,5-bisphosphate (PtdIns-4,5-P2) distribution [1,2,3]. They belong to the repeating beta-groove (RBG) superfamily together with VPS13, ATG2, SHIP164, Csf1/BLTP1 proteins, which are all conserved lipid transfer proteins containing long hydrophobic grooves [3]. They all share the same structure consisting of multiple repeating modules comprising five beta-sheets followed by a loop. This entry represents a RBG unit (the sixth) following Pfam:PF10344 (which covers the first five RBG units at the N-terminal). [1]. 34415038. The Hob proteins are novel and conserved lipid-binding proteins at ER-PM contact sites. Neuman SD, Jorgensen JR, Cavanagh AT, Smyth JT, Selegue JE, Emr SD, Bashirullah A;. J Cell Sci. 2022; [Epub ahead of print]. [2]. 35491307. A novel superfamily of bridge-like lipid transfer proteins. Neuman SD, Levine TP, Bashirullah A;. Trends Cell Biol. 2022;32:962-974. [3]. 35015055. Vps13-like proteins provide phosphatidylethanolamine for GPI anchor synthesis in the ER. Toulmay A, Whittle FB, Yang J, Bai X, Diarra J, Banerjee S, Levine TP, Golden A, Prinz WA;. J Cell Biol. 2022; [Epub ahead of print] (from Pfam) NF021789.5 PF10295.14 DUF2406 27 27 63 domain Y Y N DUF2406 domain-containing protein 0 EBI-EMBL Uncharacterised protein (DUF2406) Uncharacterised protein (DUF2406) This is a family of small proteins conserved in fungi. The function is not known. (from Pfam) NF021800.5 PF10309.14 NCBP3 28.9 28.9 59 domain Y Y N nuclear cap-binding protein subunit 3 GO:0000340,GO:0003729 26382858 0 EBI-EMBL Nuclear cap-binding protein subunit 3 nuclear cap-binding protein subunit 3 NCBP3 and NCBP1 form an alternative cap-binding complex in higher eukaryotes. NCBP3 binds mRNA, associates with components of the mRNA processing machinery and contributes to polyA RNA export [1]. [1]. 26382858. mRNA export through an additional cap-binding complex consisting of NCBP1 and NCBP3. Gebhardt A, Habjan M, Benda C, Meiler A, Haas DA, Hein MY, Mann A, Mann M, Habermann B, Pichlmair A;. Nat Commun. 2015;6:8192. (from Pfam) NF021801.5 PF10310.14 DUF5427 25.1 25.1 461 domain Y Y N maintenance of telomere capping protein 1 16702403,18845848 0 EBI-EMBL Family of unknown function (DUF5427) maintenance of telomere capping protein 1 This is a domain of unknown function. Family members found in Saccharomyces cerevisiae, are synthetic lethal with genes involved in maintenance of telomere capping [1, 2]. However, experimental evidence is yet to verify the exact function of family members and the domain. [1]. 16702403. Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes. Fleischer TC, Weaver CM, McAfee KJ, Jennings JL, Link AJ;. Genes Dev. 2006;20:1294-1307. [2]. 18845848. A genomewide suppressor and enhancer analysis of cdc13-1 reveals varied cellular processes influencing telomere capping in Saccharomyces cerevisiae. Addinall SG, Downey M, Yu M, Zubko MK, Dewar J, Leake A, Hallinan J, Shaw O, James K, Wilkinson DJ, Wipat A, Durocher D, Lydall D;. Genetics. 2008;180:2251-2266. (from Pfam) NF021805.5 PF10315.14 Aim19 29.5 29.5 119 domain Y Y N altered inheritance of mitochondria protein 19 0 EBI-EMBL Altered inheritance of mitochondria protein 19 altered inheritance of mitochondria protein 19 This is a family of conserved proteins found in fungi. The function is not known. (from Pfam) NF021821.5 PF10332.14 DUF2418 22.3 22.3 96 domain Y Y N DUF2418 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2418) Protein of unknown function (DUF2418) This is a conserved 100 residue central region of a family of proteins found in fungi. It carries a characteristic EYD sequence motif. The function is not known. (from Pfam) NF021825.5 PF10336.14 DUF2420 23 23 108 domain Y Y N DUF2420 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2420) Protein of unknown function (DUF2420) This is a family of proteins conserved in fungi. The function is not known. (from Pfam) NF021827.5 PF10338.14 YBL028C_N 28.2 28.2 44 domain Y Y N YBL028C ribosome biogenesis factor domain-containing protein 29245012,36423630,37129998 0 EBI-EMBL YBL028C ribosome biogenesis factor, N-terminal domain YBL028C ribosome biogenesis factor, N-terminal domain This entry represents a domain (previously known as DUF2423) found N-terminal in YBL028C ribosome biogenesis factor and related fungal protein [1-3]. This domain adopts an alpha-helix and makes extensive contacts with the ribosomal protein uL3 and rRNA. [1]. 29245012. Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes. Kater L, Thoms M, Barrio-Garcia C, Cheng J, Ismail S, Ahmed YL, Bange G, Kressler D, Berninghausen O, Sinning I, Hurt E, Beckmann R;. Cell. 2017;171:1599-1610. [2]. 36423630. Chromatin localization of nucleophosmin organizes ribosome biogenesis. Ugolini I, Bilokapic S, Ferrolino M, Teague J, Yan Y, Zhou X, Deshmukh A, White M, Kriwacki RW, Halic M;. Mol Cell. 2022;82:4443-4457. [3]. 37129998. Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis. Lau B, Huang Z, Kellner N, Niu S, Berninghausen O, Beckmann R, Hurt E, Cheng J;. EMBO Rep. 2023;24:e56910. (from Pfam) NF021840.5 PF10353.14 DUF2430 24.6 24.6 107 domain Y Y N DUF2430 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2430) Protein of unknown function (DUF2430) This is a family of short, 111 residue, proteins found in S. pombe. The function is not known. (from Pfam) NF021848.5 PF10361.14 DUF2434 25 25 294 domain Y Y N DUF2434 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2434) Protein of unknown function (DUF2434) This is a family of proteins conserved in fungi. The function is not known. (from Pfam) NF021929.5 PF10445.14 DUF2456 25 25 95 domain Y Y N DUF2456 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2456) Protein of unknown function (DUF2456) This is a family of uncharacterised proteins. (from Pfam) NF021930.5 PF10446.14 DUF2457 30 30 467 domain Y Y N DUF2457 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2457) Protein of unknown function (DUF2457) This is a family of uncharacterised proteins. (from Pfam) NF021937.5 PF10454.14 DUF2458 33.1 33.1 172 domain Y Y N DUF2458 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2458) Protein of unknown function (DUF2458) This a is family of uncharacterised proteins. (from Pfam) NF021957.5 PF10474.14 Syndetin_C 38.4 38.4 234 domain Y Y N syndetin domain-containing protein 25799061 0 EBI-EMBL Syndetin, C-terminal Syndetin, C-terminal The function of this domain is unknown but it is found at the C terminus of syndetin (VPS50), a unique component of the endosome-associated retrograde protein (EARP) complex. The EARP complex otherwise shares four of its five subunits with the Golgi-associated retrograde protein (GARP) complex. The EARP complex is localised to recycling to endosomes where it acts as a tethering complex for recycling of plasma membrane receptors [1]. [1]. 25799061. EARP is a multisubunit tethering complex involved in endocytic recycling. Schindler C, Chen Y, Pu J, Guo X, Bonifacino JS;. Nat Cell Biol. 2015;17:639-650. (from Pfam) NF022096.5 PF10629.14 CMI2B-like 21.6 21.6 67 domain Y Y N CMI2B domain-containing protein 36191189 0 EBI-EMBL Ciliary microtubule inner protein 2B-like Ciliary microtubule inner protein 2B-like This family represents a domain found in human Ciliary microtubule inner protein 2B (CMI2B) and similar proteins from eukaryotes. CMI2B is a microtubule inner proteins (MIP) that form part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating [1]. This domain is a tubulin-binding domain. Some proteins contain multiple copies of this domain. [1]. 36191189. SPACA9 is a lumenal protein of human ciliary singlet and doublet microtubules. Gui M, Croft JT, Zabeo D, Acharya V, Kollman JM, Burgoyne T, Hoog JL, Brown A;. Proc Natl Acad Sci U S A. 2022;119:e2207605119. (from Pfam) NF022097.5 PF10630.14 DUF2476 27 27 259 domain Y Y N DUF2476 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2476) Protein of unknown function (DUF2476) This is a family of proteins of unknown function. The family is rich in proline residues. (from Pfam) NF022270.5 PF10813.13 Herpesvir_UL11 21.2 21.2 32 domain Y Y N Epstein-Barr virus protein BBLF1 family protein 22740416 0 EBI-EMBL Herpesvirus UL11 homologue Epstein-Barr virus protein BBLF1 family protein This entry contains viral proteins that are involved in virion envelopment and egress. It includes Epstein-Barr virus (EBV) BBLF1 protein (also known as cytoplasmic envelopment protein 3), which is present in the tegument layer of EBV and is involved in virion maturation. BBLF1 also participates in viral entry at the fusion step probably by regulating the core fusion machinery. BBLF1 has been shown to localise to the trans-Golgi network along with gp350/220, a site where final envelopment of EBV particles takes place. BBLF1 shares 13 to 15% amino acid sequence identity with the herpes simplex virus 1 UL11 and cytomegalovirus UL99 tegument proteins, and like these it is a myristoylated and palmitoylated protein [1]. [1]. 22740416. Characterization and intracellular trafficking of Epstein-Barr virus BBLF1, a protein involved in virion maturation. Chiu YF, Sugden B, Chang PJ, Chen LW, Lin YJ, Lan YC, Lai CH, Liou JY, Liu ST, Hung CH;. J Virol. 2012;86:9647-9655. (from Pfam) NF022294.5 PF10838.13 DUF2677 27 27 166 domain Y Y N DUF2677 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2677) Protein of unknown function (DUF2677) Members in this family of proteins are annotated as UL121 however currently no function is known. (from Pfam) NF022295.5 PF10839.13 DUF2647 22.3 22.3 70 domain Y Y N DUF2647 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2647) Protein of unknown function (DUF2647) This eukaryotic family of proteins are annotated as ycf68 but have no known function. (from Pfam) NF022299.5 PF10843.13 RGI1 25 25 194 domain Y Y N respiratory growth induced protein 1 GO:0006112 20567505 0 EBI-EMBL Respiratory growth induced protein 1 respiratory growth induced protein 1 This family of fungal proteins includes RGI1, standing for respiratory growth induced 1. RGI1 is involved in aerobic energetic metabolism [1]. [1]. 20567505. Structural and functional study of YER067W, a new protein involved in yeast metabolism control and drug resistance. Domitrovic T, Kozlov G, Freire JC, Masuda CA, da Silva Almeida M, Montero-Lomeli M, Atella GC, Matta-Camacho E, Gehring K, Kurtenbach E;. PLoS One. 2010;5:e11163. (from Pfam) NF022302.5 PF10846.13 DUF2722 27.7 27.7 406 domain Y Y N DUF2722 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2722) Protein of unknown function (DUF2722) This eukaryotic family of proteins has no known function. (from Pfam) NF022309.5 PF10853.13 DUF2650 22.9 22.9 37 domain Y Y N DUF2650 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2650) Protein of unknown function (DUF2650) This family of proteins with unknown function appear to be restricted to Caenorhabditis elegans. (from Pfam) NF022312.5 PF10856.13 DUF2678 27.8 27.8 118 domain Y Y N DUF2678 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2678) Protein of unknown function (DUF2678) This family of proteins has no known function. (from Pfam) NF022313.5 PF10857.13 DUF2701 25 25 63 domain Y Y N DUF2701 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2701) Protein of unknown function (DUF2701) This viral family of proteins has no known function. (from Pfam) NF022319.5 PF10863.13 NOP19 25 25 140 domain Y Y N nucleolar protein 19 GO:0030686,GO:0042274 21941128 0 EBI-EMBL Nucleolar protein 19 nucleolar protein 19 Nucleolar protein 19 plays an essential role in 40S ribosomal subunit biogenesis [1]. [1]. 21941128. The nucleolar protein Nop19p interacts preferentially with Utp25p and Dhr2p and is essential for the production of the 40S ribosomal subunit in Saccharomyces cerevisiae. Choque E, Marcellin M, Burlet-Schiltz O, Gadal O, Dez C;. RNA Biol. 2011;8:1158-1172. (from Pfam) NF022322.5 PF10866.13 DUF2704 22 22 167 domain Y Y N DUF2704 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2704) Protein of unknown function (DUF2704) This viral family of proteins has no known function. (from Pfam) NF022326.5 PF10870.13 DUF2729 27 27 57 domain Y Y N DUF2729 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2729) Protein of unknown function (DUF2729) This viral family of proteins has no known function. (from Pfam) NF022329.5 PF10873.13 CYYR1 31 31 149 domain Y Y N cysteine and tyrosine-rich protein 1 12062809 0 EBI-EMBL Cysteine and tyrosine-rich protein 1 cysteine and tyrosine-rich protein 1 Members in this family of proteins are annotated as Cysteine and tyrosine-rich protein 1, however currently no function is known [1]. [1]. 12062809. Cysteine and tyrosine-rich 1 (CYYR1), a novel unpredicted gene on human chromosome 21 (21q21.2), encodes a cysteine and tyrosine-rich protein and defines a new family of highly conserved vertebrate-specific genes. Vitale L, Casadei R, Canaider S, Lenzi L, Strippoli P, D'Addabbo P, Giannone S, Carinci P, Zannotti M;. Gene. 2002;290:141-151. (from Pfam) NF022345.5 PF10890.13 Cyt_b-c1_8 24.3 24.3 72 domain Y Y N cytochrome b-c1 complex subunit 8 GO:0005743,GO:0045275,GO:0098803 7764624 0 EBI-EMBL Cytochrome b-c1 complex subunit 8 cytochrome b-c1 complex subunit 8 This entry represents subunit 8 of the Cytochrome b-c1 complex [1]. [1]. 7764624. Molecular identification of the ten subunits of cytochrome-c reductase from potato mitochondria. Braun HP, Kruft V, Schmitz UK;. Planta. 1994;193:99-106. (from Pfam) NF022346.5 PF10891.13 DUF2719 26 26 81 domain Y Y N DUF2719 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2719) Protein of unknown function (DUF2719) This family of proteins with unknown function appears to be restricted to Nucleopolyhedrovirus. (from Pfam) NF022360.5 PF10906.13 Mrx7 22.8 22.8 66 domain Y Y N MIOREX complex component 7 25683707 0 EBI-EMBL MIOREX complex component 7 MIOREX complex component 7 This entry includes budding yeast MIOREX complex component 7 (Mrx7), which associates with mitochondrial ribosome [1]. Its function is not clear. [1]. 25683707. Organization of Mitochondrial Gene Expression in Two Distinct Ribosome-Containing Assemblies. Kehrein K, Schilling R, Moller-Hergt BV, Wurm CA, Jakobs S, Lamkemeyer T, Langer T, Ott M;. Cell Rep. 2015; [Epub ahead of print] (from Pfam) NF022363.5 PF10909.13 DUF2682 33.3 33.3 88 domain Y Y N DUF2682 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2682) Protein of unknown function (DUF2682) This viral family of proteins has no known function. (from Pfam) NF022372.5 PF10918.13 DUF2718 25 25 129 domain Y Y N DUF2718 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2718) Protein of unknown function (DUF2718) This viral family of proteins has no known function. (from Pfam) NF022380.5 PF10927.13 DUF2738 23 23 236 domain Y Y N DUF2738 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2738) Protein of unknown function (DUF2738) This is a viral family of proteins with unknown function. (from Pfam) NF022390.5 PF10937.13 Kgd4-YMR31 22 22 116 domain Y Y N alpha-ketoglutarate dehydrogenase component 4 GO:0006103,GO:0045252 12392552,25165143,25838379,2693936,9445368 0 EBI-EMBL Alpha-ketoglutarate dehydrogenase component 4/YMR-31 ribosomal protein S36 This entry represents the alpha-ketoglutarate dehydrogenase component 4 (Kgd4, also referred to as Ymr31/MRPS36) which was originally identified as a subunit of the mitochondrial ribosome [1,2,3]. Through biochemical studies, it was shown that this protein co purifies with the oxoglutarate dehydrogenase complex (OGDC). Both mitochondrial ribosome 28S subunit and OGDC have a similar size and OGDC is highly abundant, being found to contaminate ribosomal preparations [4]. Kgd4 plays an evolutionarily conserved role in the organisation of mitochondrial alpha-KGDH complexes of fungi and animals which constitutes a molecular adaptor that is necessary to form a stable alpha-KGDH enzyme complex [4,5]. [1]. 2693936. Cloning and analysis of the nuclear genes for two mitochondrial ribosomal proteins in yeast. Matsushita Y, Kitakawa M, Isono K;. Mol Gen Genet. 1989;219:119-124. [2]. 9445368. Mitochondrial ribosomal proteins (MRPs) of yeast. Graack HR, Wittmann-Liebold B;. Biochem J 1998;329:433-448. [3]. 12392552. Tag-mediated isolation of yeast mitochondrial ribosome and mass spectrometric identification of its new components. Gan X, Kitakawa M, Yoshino KI, Oshiro N, Yonezawa K, Isono K;. Eur J Biochem 2002;269:5203-5214. [4]. 25838379. Ribosome. The structure of the human mitochondrial ribosome. Amunts A, Brown A, Toots J, Scheres SHW, Ramakrishnan V;. Science. 2015;348:95-98. [5]. 25165143. The novel component Kgd4 recruits the E3 subunit to the mitochondrial alpha-ketoglutarate dehydrogenase. Heublein M, Burguillos MA, Vogtle FN, Teixeira PF, Imhof A, Meisinger C, Ott M;. Mol Biol Cell. 2014;25:3342-3349. (from Pfam) NF022396.5 PF10943.13 DUF2632 25 25 233 domain Y Y N DUF2632 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2632) Protein of unknown function (DUF2632) This is a family of membrane proteins with unknown function. (from Pfam) NF022445.5 PF10992.13 Epiplasmin 30 30 83 domain Y Y N epiplasmin family protein 19493334 0 EBI-EMBL Epiplasmin protein epiplasmin family protein This entries covers epiplasmins, a multigene family in Paramecium. They make up a scale structure called the epiplasm under the cell membrane [1]. [1]. 19493334. Cross-study analysis of genomic data defines the ciliate multigenic epiplasmin family: strategies for functional analysis in Paramecium tetraurelia. Damaj R, Pomel S, Bricheux G, Coffe G, Vigues B, Ravet V, Bouchard P;. BMC Evol Biol. 2009;9:125. (from Pfam) NF022454.5 PF11001.13 DUF2841 31.3 31.3 124 domain Y Y N YDR124W-like helical bundle domain-containing protein 31945465 0 EBI-EMBL YDR124W-like, helical bundle domain YDR124W-like, helical bundle domain This entry represents mitochondrial proteins of unknown function found in yeast, such as YDR124W. Null mutant showed severe fragmentation of mitochondria and its expression is strongly induced by alpha factor. These proteins may have a role in maintenance of mitochondrial morphology [1]. This entry represents an helical bundle domain which seems to adopt a similar arrangement than the EIN3-like DNA-binding domain (Based on structural comparison, DALI server). [1]. 31945465. Predicting subcellular localization of proteins using protein-protein interaction data. Garapati HS, Male G, Mishra K;. Genomics. 2020;112:2361-2368. (from Pfam) NF022475.5 PF11022.13 ATP19 27 27 67 domain Y Y N ATP synthase subunit K family protein 9857174 0 EBI-EMBL ATP synthase subunit K ATP synthase subunit K family protein This entry represents ATP synthase subunit K (Atp19) from fungi. Atp19 is the subunit k of the mitochondrial F1F0 ATP synthase, which produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain [1]. [1]. 9857174. Yeast mitochondrial F1F0-ATP synthase exists as a dimer: identification of three dimer-specific subunits. Arnold I, Pfeiffer K, Neupert W, Stuart RA, Schagger H;. EMBO J. 1998;17:7170-7178. (from Pfam) NF022520.5 PF11069.13 CFAP298 27 27 97 domain Y Y N CFAP298 family protein GO:0003352 24094744,26904945 0 EBI-EMBL Cilia- and flagella-associated protein 298 CFAP298 family protein This is a eukaryotic family of proteins which includes a group of cilia- and flagella-associated protein, including Kur from zebrafish and C21orf59 from humans. Kur has been shown to play a dual role in cilia motility and polarization [1]. Primary ciliary dyskinesia (PCD) is caused when defects of motile cilia lead to chronic airway infections, male infertility, and situs abnormalities. Mutations in the C21orf59 gene cause ciliary dyskinesia, primary, 26 (CILD26) [2]. [1]. 26904945. c21orf59/kurly Controls Both Cilia Motility and Polarization. Jaffe KM, Grimes DT, Schottenfeld-Roames J, Werner ME, Ku TS, Kim SK, Pelliccia JL, Morante NF, Mitchell BJ, Burdine RD;. Cell Rep. 2016;14:1841-1849. [2]. 24094744. Zebrafish Ciliopathy Screen Plus Human Mutational Analysis Identifies C21orf59 and CCDC65 Defects as Causing Primary Ciliary Dyskinesia. Austin-Tse C, Halbritter J, Zariwala MA, Gilberti RM, Gee HY, Hellman N, Pathak N, Liu Y, Panizzi JR, Patel-King RS, Tritschler D, Bower R, O'Toole E, Porath JD, Hurd TW, Chaki M, Diaz KA, Kohl S, Lovric S, Hwang DY, Braun DA, Schueler M, Airik R, Otto EA, Leigh MW, Noone PG, Carson JL, Davis SD, Pittman JE, Ferkol TW, Atkinson JJ, Olivier KN, Sagel SD, Dell SD, Rosenfeld M, Milla CE, Loges NT, Omran H, Porter ME, King SM, Knowles MR, Drummond IA, Hildebrandt F;. Am J Hum Genet. 2013;93:672-686. (from Pfam) NF022547.5 PF11097.13 DUF2883 25 25 75 domain Y Y N DUF2883 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2883) Protein of unknown function (DUF2883) This family of proteins have no known function but appear to be restricted to phage. (from Pfam) NF022575.5 PF11125.13 Phage_MS2_lysis 25 25 54 domain Y Y N phage MS2 lysis protein family protein 2653958,2656650,498271 0 EBI-EMBL Bacteriophage MS2, lysis protein phage MS2 lysis protein family protein This entry represents putative lysis proteins from Bacteriophage MS2 and Bacteriophage BZ13. The bacteriophage MS2 lysin protein swiss:C0M1L5 was identified as an overlapping cistron in the bacteriophage MS2 RNA [1]. This proteins induces the formation of specific membrane adhesion sites between the inner and outer membranes, apparently leading to host cell lysis. Lysis may be performed via activation of host murein hydrolases [2,3]. [1]. 498271. Binding of mammalian ribosomes to MS2 phage RNA reveals an overlapping gene encoding a lysis function. Atkins JF, Steitz JA, Anderson CW, Model P;. Cell. 1979;18:247-256. [2]. 2656650. Specific localization of the lysis protein of bacteriophage MS2 in membrane adhesion sites of Escherichia coli. Walderich B, Holtje JV;. J Bacteriol. 1989;171:3331-3336. [3]. 2653958. Functioning of the cloned phage MS2 lysis protein in Escherichia coli impaired in murein synthesis. Ursinus-Wossner A, Holtje JV;. FEMS Microbiol Lett. 1989;48:75-79. (from Pfam) NF022585.5 PF11135.13 DUF2888 27 27 144 domain Y Y N DUF2888 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2888) Protein of unknown function (DUF2888) Some members in this family of proteins with unknown function are annotated as immediate early protein ICP-18 however this cannot be confirmed. (from Pfam) NF022595.5 PF11145.13 DUF2921 24 24 885 domain Y Y N DUF2921 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2921) Protein of unknown function (DUF2921) This eukaryotic family of proteins has no known function. (from Pfam) NF022624.5 PF11176.13 Tma16 22.7 22.7 146 domain Y Y N translation machinery-associated protein 16 14562095,16702403 0 EBI-EMBL Translation machinery-associated protein 16 translation machinery-associated protein 16 Proteins in this family localise to the nucleus [1, 2]. Their function is not clear. [1]. 14562095. Global analysis of protein localization in budding yeast. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK;. Nature 2003;425:686-691. [2]. 16702403. Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes. Fleischer TC, Weaver CM, McAfee KJ, Jennings JL, Link AJ;. Genes Dev. 2006;20:1294-1307. (from Pfam) NF022627.5 PF11179.13 DUF2967 25.3 25.3 961 domain Y Y N DUF2967 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2967) Protein of unknown function (DUF2967) This family of proteins with unknown function appears to be restricted to Drosophila. (from Pfam) NF022669.5 PF11223.13 DUF3020 25 25 49 domain Y Y N SPP41 domain-containing protein 22932476,8005438 0 EBI-EMBL SPP41, DUF3020 SPP41, DUF3020 This domain is found in the conserved fungal proteins SPP41 (suppressor of PrP4, there are four members, 1 to 4). In S. cerevisiae it is conserved towards the C-terminus of HMG domains. The function is not known. However, it has been shown that SPP41 is involved in negative regulation of expression of spliceosome components PRP4 and PRP3 and that it relocalizes to the cytosol in response to hypoxia [1,2]. [1]. 8005438. Extragenic suppressors of Saccharomyces cerevisiae prp4 mutations identify a negative regulator of PRP genes. Maddock JR, Weidenhammer EM, Adams CC, Lunz RL, Woolford JL Jr;. Genetics. 1994;136:833-847. [2]. 22932476. The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation. Dastidar RG, Hooda J, Shah A, Cao TM, Henke RM, Zhang L;. Cell Biosci. 2012;2:30. (from Pfam) NF022675.5 PF11229.13 Focadhesin 23 23 589 domain Y Y N focadhesin 22427331 0 EBI-EMBL Focadhesin focadhesin Focadhesin (FOCAD) is focal adhesion protein with potential tumour suppressor function in gliomas [1]. The structure prediction indicates that it consists in repetitive alpha hairpins that adopt an armadillo-like fold. [1]. 22427331. KIAA1797/FOCAD encodes a novel focal adhesion protein with tumour suppressor function in gliomas. Brockschmidt A, Trost D, Peterziel H, Zimmermann K, Ehrler M, Grassmann H, Pfenning PN, Waha A, Wohlleber D, Brockschmidt FF, Jugold M, Hoischen A, Kalla C, Waha A, Seifert G, Knolle PA, Latz E, Hans VH, Wick W, Pfeifer A, Angel P, Weber RG;. Brain. 2012;135:1027-1041. (from Pfam) NF022697.5 PF11252.13 DUF3051 27 27 189 domain Y Y N DUF3051 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3051) Protein of unknown function (DUF3051) This viral family of proteins has no known function. (from Pfam) NF022718.5 PF11274.13 DUF3074 27.5 27.5 185 domain Y Y N DUF3074 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3074) Protein of unknown function (DUF3074) This eukaryotic family of proteins has no known function but appears to be part of the START superfamily. (from Pfam) NF022735.5 PF11291.13 DUF3091 25 25 100 domain Y Y N DUF3091 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3091) Protein of unknown function (DUF3091) This eukaryotic family of proteins has no known function. (from Pfam) NF022765.5 PF11321.13 DUF3123 27 27 62 domain Y Y N DUF3123 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3123) Protein of unknown function (DUF3123) This eukaryotic family of proteins has no known function. (from Pfam) NF022770.5 PF11326.13 PANTS-like 27 27 80 domain Y Y N synaptic plasticity regulator family protein 35771867 0 EBI-EMBL Synaptic plasticity regulator PANTS-like synaptic plasticity regulator family protein This eukaryotic family of short proteins includes the mouse micropeptide known as Synaptic plasticity regulator PANTS (Plasticity-Associated Neural Transcript Short, C22orf39), which plays a role in synaptic plasticity [1]. [1]. 35771867. An Rtn4/Nogo-A-interacting micropeptide modulates synaptic plasticity with age. Kragness S, Clark Z, Mullin A, Guidry J, Earls LR;. PLoS One. 2022;17:e0269404. (from Pfam) NF022774.5 PF11330.13 30K_MP_C_Ter 25 25 242 domain Y Y N DTG domain-containing protein 27596536,30135122 0 EBI-EMBL C-Terminal of 30K viral movement proteins C-Terminal of 30K viral movement proteins This entry represents the C-terminal region found in viral movement proteins (MP) of the 30K type. This region has been suggested to be conserved in secondary structure in Ophioviruses Mps. It contains two parts, (i) a long segment with the potential to form an alpha-helix (alphaB), rich in charged residues, and (ii) a region highly variable in sequence downstream of alphaB. The C-terminal region corresponds to a protease domain which contains a strictly conserved DTG tripeptide also found in related aspartic retroviral proteases. This protease is required for autocleavage of the Movement Protein of ophioviruses in an N-terminal part that supports movement of viral particles through the plant, and this C-terminal part which retains protease activity [2]. Mutations in the aspartate residue in the core domain Pfam:PF17644 had an impact on cell to cell movement [1]. [1]. 27596536. Bioinformatic and mutational analysis of ophiovirus movement proteins, belonging to the 30K superfamily. Borniego MB, Karlin D, Pena EJ, Robles Luna G, Garcia ML;. Virology. 2016;498:172-180. [2]. 30135122. Citrus Psorosis Virus Movement Protein Contains an Aspartic Protease Required for Autocleavage and the Formation of Tubule-Like Structures at Plasmodesmata. Robles Luna G, Pena EJ, Borniego MB, Heinlein M, Garcia ML;. J Virol. 2018; [Epub ahead of print] (from Pfam) NF022806.5 PF11362.13 DUF3161 25 25 83 domain Y Y N DUF3161 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3161) Protein of unknown function (DUF3161) This eukaryotic family of proteins has no known function. (from Pfam) NF022809.5 PF11365.13 SOGA 31.1 31.1 94 domain Y Y N protein SOGA GO:0005615,GO:0010506 20813965 0 EBI-EMBL Protein SOGA protein SOGA The SOGA (suppressor of glucose by autophagy) family consists of proteins SOGA1, SOGA2, and SOGA3. SOGA1 regulates autophagy by playing a role in the reduction of glucose production in an adiponectin and insulin dependent manner [1]. [1]. 20813965. Adiponectin lowers glucose production by increasing SOGA. Cowherd RB, Asmar MM, Alderman JM, Alderman EA, Garland AL, Busby WH, Bodnar WM, Rusyn I, Medoff BD, Tisch R, Mayer-Davis E, Swenberg JA, Zeisel SH, Combs TP;. Am J Pathol. 2010;177:1936-1945. (from Pfam) NF022816.5 PF11374.13 DUF3176 27 27 105 domain Y Y N DUF3176 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3176) Protein of unknown function (DUF3176) This eukaryotic family of proteins has no known function. (from Pfam) NF022837.5 PF11395.13 bCoV_NS7B 25 25 43 domain Y Y N NS7B family protein GO:0016020 17037516,17079322,18632859 0 EBI-EMBL Betacoronavirus NS7B protein NS7B family protein This entry corresponds to Human SARS coronavirus (SARS-CoV) and similar betacoronaviruses NS7B protein (also known as accessory protein 7b, NS7B, ORF7b and 7b)[1]. It was found to be a structural component of SARS-CoV virions and an integral membrane protein. Its transmembrane domain is essential for Golgi compartment localization [2][3]. [1]. 17037516. Structure, expression, and intracellular localization of the SARS-CoV accessory proteins 7a and 7b. Pekosz A, Schaecher SR, Diamond MS, Fremont DH, Sims AC, Baric RS;. Adv Exp Med Biol. 2006;581:115-120. [2]. 18632859. The transmembrane domain of the severe acute respiratory syndrome coronavirus ORF7b protein is necessary and sufficient for its retention in the Golgi complex. Schaecher SR, Diamond MS, Pekosz A;. J Virol. 2008;82:9477-9491. [3]. 17079322. The ORF7b protein of severe acute respiratory syndrome coronavirus (SARS-CoV) is expressed in virus-infected cells and incorporated into SARS-CoV particles. Schaecher SR, Mackenzie JM, Pekosz A;. J Virol. 2007;81:718-731. (from Pfam) NF022882.5 PF11442.13 DUF2826 21 21 158 domain Y Y N DUF2826 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF2826) Protein of unknown function (DUF2826) This is a family of uncharacterised proteins that is highly conserved in Trypanosoma cruzi. (from Pfam) NF022926.5 PF11489.13 Aim21 27 27 718 domain Y Y N altered inheritance of mitochondria protein 21 16702403,19300474 0 EBI-EMBL Altered inheritance of mitochondria protein 21 altered inheritance of mitochondria protein 21 This is a family of proteins conserved in yeasts. Saccharomyces cerevisiae Aim21 may be involved in mitochondrial migration along actin filament [1]. It may also interact with ribosomes [2]. [1]. 19300474. Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. Hess DC, Myers CL, Huttenhower C, Hibbs MA, Hayes AP, Paw J, Clore JJ, Mendoza RM, Luis BS, Nislow C, Giaever G, Costanzo M, Troyanskaya OG, Caudy AA;. PLoS Genet. 2009;5:e1000407. [2]. 16702403. Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes. Fleischer TC, Weaver CM, McAfee KJ, Jennings JL, Link AJ;. Genes Dev. 2006;20:1294-1307. (from Pfam) NF023027.5 PF11595.13 DUF3245 26.4 26.4 148 domain Y Y N DUF3245 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3245) Protein of unknown function (DUF3245) This is a family of proteins conserved in fungi. The function is not known, and there is no S. cerevisiae member. (from Pfam) NF023028.5 PF11596.13 DUF3246 27.8 27.8 243 domain Y Y N DUF3246 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3246) Protein of unknown function (DUF3246) This is a small family of fungal proteins one of whose members, Swiss:A3LUS4 from Pichia stipitis is described as being an extremely serine rich protein-mucin-like protein. (from Pfam) NF023046.5 PF11615.13 Caf4 21 21 60 domain Y Y N CCR4-associated factor 4 GO:0000266,GO:0005739 11113136,16009724,16835275 0 EBI-EMBL CCR4-associated factor 4 CCR4-associated factor 4 Caf4 is a WD40 repeats containing protein involved in mitochondrial fission. It displays physical interactions with CCR4-NOT complex [1]. It has a paralogue, Mdv1. Both Caf4 and Mdv1 act as adapter proteins, binding to Fis1 on the mitochondrial outer membrane and recruiting the dynamin-like GTPase Dnm1 to form mitochondrial fission complexes [2]. However, Fis1 and Caf4, but not Mdv1, determine the polar localization of Dnm1 clusters on the mitochondrial surface [3]. [1]. 11113136. Characterization of CAF4 and CAF16 reveals a functional connection between the CCR4-NOT complex and a subset of SRB proteins of the RNA polymerase II holoenzyme. Liu HY, Chiang YC, Pan J, Chen J, Salvadore C, Audino DC, Badarinarayana V, Palaniswamy V, Anderson B, Denis CL;. J Biol Chem. 2001;276:7541-7548. [2]. 16009724. The WD40 protein Caf4p is a component of the mitochondrial fission machinery and recruits Dnm1p to mitochondria. Griffin EE, Graumann J, Chan DC;. J Cell Biol. 2005;170:237-248. [3]. 16835275. Fis1p and Caf4p, but not Mdv1p, determine the polar localization of Dnm1p clusters on the mitochondrial surface. Schauss AC, Bewersdorf J, Jakobs S;. J Cell Sci. 2006;119:3098-3106. (from Pfam) NF023061.5 PF11630.13 Anti-LPS-SCYG 25 25 100 domain Y Y N anti-lipopolysaccharide factor family protein 17092560,19490944,21195157 0 EBI-EMBL Anti-lipopolysaccharide factor/Scygonadin anti-lipopolysaccharide factor family protein Anti-lipopolysaccharide factor binds to bacterial LPS and may specifically inhibit the LPS-mediated activation of the hemolymph coagulation. It has a strong antibacterial effect, especially on the growth of Gram-negative bacteria [1,2]. This entry also includes the antibacterial protein Scygonadin, which has antibacterial activity against the Gram-positive bacterium Micrococcus luteus [3]. [1]. 19490944. Identification, cloning, characterization and recombinant expression of an anti-lipopolysaccharide factor from the hemocytes of Indian mud crab, Scylla serrata. Yedery RD, Reddy KV;. Fish Shellfish Immunol. 2009;27:275-284. [2]. 21195157. Antibacterial activity of a synthetic peptide that mimics the LPS binding domain of Indian mud crab, Scylla serrata anti-lipopolysaccharide factor (SsALF) also involved in the modulation of vaginal immune functions through NF-kB signaling. Sharma S, Yedery RD, Patgaonkar MS, Selvaakumar C, Reddy KV;. Microb Pathog. 2011;50:179-191. [3]. 17092560. A male-specific expression gene, encodes a novel anionic antimicrobial peptide, scygonadin, in Scylla serrata. Wang KJ, Huang WS, Yang M, Chen HY, Bo J, Li SJ, Wang GZ;. Mol Immunol. 2007;44:1961-1968. (from Pfam) NF023084.5 PF11654.13 NCE101 24 24 45 domain Y Y N non-classical export protein 1 GO:0009306 8655575 0 EBI-EMBL Non-classical export protein 1 non-classical export protein 1 This entry represents the non classical export protein 1 family. Family members are Involved in a novel pathway of export of proteins that lack a cleavable signal sequence [1]. [1]. 8655575. A new pathway for protein export in Saccharomyces cerevisiae. Cleves AE, Cooper DN, Barondes SH, Kelly RB;. J Cell Biol. 1996;133:1017-1026. (from Pfam) NF023106.5 PF11677.13 DUF3273 25 25 265 domain Y Y N DUF3273 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3273) Protein of unknown function (DUF3273) Some members in this family of proteins are annotated as multi-transmembrane proteins however this cannot be confirmed. Currently this family has no known function. (from Pfam) NF023124.5 PF11696.13 DUF3292 25.7 25.7 648 domain Y Y N DUF3292 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3292) Protein of unknown function (DUF3292) This eukaryotic family of proteins has no known function. (from Pfam) NF023130.5 PF11702.13 DUF3295 25.8 25.8 496 domain Y Y N DUF3295 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3295) Protein of unknown function (DUF3295) This family is conserved in fungi but the function is not known. (from Pfam) NF023196.5 PF11768.13 Frtz 26.2 26.2 548 domain Y Y N WD repeat-containing and planar cell polarity effector protein Fritz 15654087 0 EBI-EMBL WD repeat-containing and planar cell polarity effector protein Fritz WD repeat-containing and planar cell polarity effector protein Fritz Fritz is a probable effector of the planar cell polarity signaling pathway which regulates the septin cytoskeleton in both ciliogenesis and collective cell movements. In Drosophila melanogaster, fritz regulates both the location and the number of wing cell prehair initiation sites [1]. [1]. 15654087. The WD40 repeat protein fritz links cytoskeletal planar polarity to frizzled subcellular localization in the Drosophila epidermis. Collier S, Lee H, Burgess R, Adler P;. Genetics. 2005;169:2035-2045. (from Pfam) NF023199.5 PF11771.13 DUF3314 25 25 162 domain Y Y N DUF3314 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3314) Protein of unknown function (DUF3314) This small family contains human, mouse and fish members but the function is not known. (from Pfam) NF023207.5 PF11779.13 SPT_ssu-like 29.8 29.8 54 domain Y Y N serine palmitoyltransferase small subunit family protein 19416851 0 EBI-EMBL Small subunit of serine palmitoyltransferase-like serine palmitoyltransferase small subunit-like protein Serine palmitoyltransferase (SPT) catalyzes the first committed step in sphingolipid biosynthesis. In mammals, two small subunits of serine palmitoyltransferase, ssSPTa and ssSPTb, substantially enhance the activity of SPT, conferring full enzyme activity upon it [1]. The 2 ssSPT isoforms share a conserved hydrophobic central domain, which is predicted to reside in the membrane. [1]. 19416851. Identification of small subunits of mammalian serine palmitoyltransferase that confer distinct acyl-CoA substrate specificities. Han G, Gupta SD, Gable K, Niranjanakumari S, Moitra P, Eichler F, Brown RH Jr, Harmon JM, Dunn TM;. Proc Natl Acad Sci U S A. 2009;106:8186-8191. (from Pfam) NF023244.5 PF11816.13 DUF3337 35 35 171 domain Y Y N DUF3337 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF3337) Domain of unknown function (DUF3337) This family of proteins are functionally uncharacterised. This family is only found in eukaryotes. This presumed domain is typically between 285 to 342 amino acids in length. (from Pfam) NF023247.5 PF11819.13 CUPID 22.4 22.4 136 domain Y Y N CUPID domain-containing protein 30355448 0 EBI-EMBL Cytohesin Ubiquitin Protein Inducing Domain Cytohesin Ubiquitin Protein Inducing Domain C1ORF106 also known as INAVA (Innate Immune Activator), is identified as a risk factor for the chronic inflammatory bowel diseases (IBD). Mice lacking the protein show defects in intestinal barrier integrity at steady state and greater susceptibility to mucosal infection. INAVA carries CUPID (Cytohesin Ubiquitin Protein Inducing Domain). Three other human proteins contain CUPID: FRMD4A, FRMD4B, and CCDC120- proteins implicated in neurite outgrowth, and in human cancer, Alzheimer's, celiac, and heart disease. All appear to bind the ARF-GEF (guanine nucleotide-exchange factors) cytohesin family members, such as proteins (ARF 1-4), which regulate cell membrane and F-actin dynamics. INAVA-CUPID binds cytohesin 2 (also known as ARNO), targets the molecule to lateral membranes of epithelial monolayers, and enables ARNO to affect F-actin assembly that underlies cell-cell junctions and barrier function. In the case of inflammatory signalling, ARNO can coordinate CUPID function by binding and inhibiting CUPID activity of acting as an enhancer of TRAF6 dependent polyubiquitination. In other words, ARNO acts as a negative-regulator of inflammatory responses. In summary, INAVA-CUPID exhibits dual functions, coordinated directly by ARNO, that bridge epithelial barrier function with extracellular signals and inflammation [1]. [1]. 30355448. INAVA-ARNO complexes bridge mucosal barrier function with inflammatory signaling. Luong P, Hedl M, Yan J, Zuo T, Fu TM, Jiang X, Thiagarajah JR, Hansen SH, Lesser CF, Wu H, Abraham C, Lencer WI;. Elife. 2018; [Epub ahead of print] (from Pfam) NF023248.5 PF11820.13 DUF3339 25 25 67 domain Y Y N DUF3339 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3339) Protein of unknown function (DUF3339) This family of proteins are functionally uncharacterised. This family is found in eukaryotes. Proteins in this family are about 70 amino acids in length. (from Pfam) NF023250.5 PF11822.13 SANBR_BTB 26 26 97 domain Y Y N BTB domain domain-containing protein 33831416 0 EBI-EMBL SANT and BTB domain regulator of CSR, BTB domain SANT and BTB domain regulator of CSR, BTB domain Class switch recombination (CSR) is the process by which B cells switch production from IgM/IgD to other immunoglobulin isotypes in the immune response process. This entry represents the BTB domain found at the N-terminal half of the protein SANT and BTB domain regulator of class switch recombination (SANBR, previously known as KIAA1841). This domain is responsible for the negative regulation of CSR [1]. [1]. 33831416. The uncharacterized SANT and BTB domain-containing protein SANBR inhibits class switch recombination. Zheng S, Matthews AJ, Rahman N, Herrick-Reynolds K, Sible E, Choi JE, Wishnie A, Ng YK, Rhodes D, Elledge SJ, Vuong BQ;. J Biol Chem. 2021;296:100625. (from Pfam) NF023258.5 PF11830.13 DUF3350 25 25 63 domain Y Y N DUF3350 domain-containing protein 15971998 0 EBI-EMBL Domain of unknown function (DUF3350) Domain of unknown function (DUF3350) This domain is functionally uncharacterised and is found in eukaryotic proteins, such as TBC1 domain family members 1 and 4. This presumed domain is typically between 50 to 64 amino acids in length. TBC domain proteins may act as GTPase-activating proteins for RAB2A, RAB8A, RAB10 and RAB14 [1]. [1]. 15971998. AS160, the Akt substrate regulating GLUT4 translocation, has a functional Rab GTPase-activating protein domain. Miinea CP, Sano H, Kane S, Sano E, Fukuda M, Peranen J, Lane WS, Lienhard GE;. Biochem J. 2005;391:87-93. (from Pfam) NF023265.5 PF11837.13 INV_N 27.8 27.8 109 domain Y Y N beta-fructofuranosidase domain-containing protein GO:0004564,GO:0004575 27083698 0 EBI-EMBL Beta-fructofuranosidase, N-terminal domain Beta-fructofuranosidase, N-terminal domain This entry represents the N-terminal domain of beta-fructofuranosidase, which is involved in the hydrolysis of terminal non-reducing beta-D-fructofuranoside residues in beta-D-fructofuranosides [1]. [1]. 27083698. RhVI1 is a membrane-anchored vacuolar invertase highly expressed in Rosa hybrida L. petals. Farci D, Collu G, Kirkpatrick J, Esposito F, Piano D;. J Exp Bot. 2016;67:3303-3312. (from Pfam) NF023269.5 PF11841.13 ELMO_ARM 27 27 154 domain Y Y N helical domain-containing protein 23014990,30604775 0 EBI-EMBL ELMO, armadillo-like helical domain ELMO, armadillo-like helical domain This domain is found in eukaryotes and predominantly in ELMO (Elongation and Cell motility) proteins and corresponds to the armadillo repeats domain (ARR). It may play an important role in defining the functions of the ELMO family members and may be functionally linked to the ELMO domain in these proteins [1,2], being involved in protein-protein interactions. [1]. 23014990. ELMO domains, evolutionary and functional characterization of a novel GTPase-activating protein (GAP) domain for Arf protein family GTPases. East MP, Bowzard JB, Dacks JB, Kahn RA;. J Biol Chem. 2012;287:39538-39553. [2]. 30604775. Structure of BAI1/ELMO2 complex reveals an action mechanism of adhesion GPCRs via ELMO family scaffolds. Weng Z, Situ C, Lin L, Wu Z, Zhu J, Zhang R;. Nat Commun. 2019;10:51. (from Pfam) NF023279.5 PF11851.13 DUF3371 25.1 25.1 128 domain Y Y N DUF3371 domain-containing protein GO:0006355 0 EBI-EMBL Domain of unknown function (DUF3371) Domain of unknown function (DUF3371) This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 125 to 142 amino acids in length. (from Pfam) NF023289.5 PF11861.13 DUF3381 25 25 163 domain Y Y N ribosomal RNA methyltransferase Spb1 domain-containing protein 10556316,22195017 0 EBI-EMBL Ribosomal RNA methyltransferase Spb1, DUF3381 Ribosomal RNA methyltransferase Spb1, DUF3381 This domain is functionally uncharacterised and it is found in the central region of fungal SPB1 and mammalian homologue FTSJ3. This domain is found associated with Pfam:PF07780, Pfam:PF01728. SPB1 is an adoMet-dependent rRNA methyltransferase required for proper assembly of pre-ribosomal particles during the biogenesis of the 60S ribosomal subunit [1]. FTSJ3, SPB1 homologue in humans, is associated with NIP7 (involved in the biogenesis of 40S subunit) and functions in pre-rRNA processing [2]. [1]. 10556316. Spb1p is a putative methyltransferase required for 60S ribosomal subunit biogenesis in Saccharomyces cerevisiae. Kressler D, Rojo M, Linder P, Cruz J;. Nucleic Acids Res 1999;27:4598-4608. [2]. 22195017. The human nucleolar protein FTSJ3 associates with NIP7 and functions in pre-rRNA processing. Morello LG, Coltri PP, Quaresma AJ, Simabuco FM, Silva TC, Singh G, Nickerson JA, Oliveira CC, Moore MJ, Zanchin NI;. PLoS One. 2011;6:e29174. (from Pfam) NF023292.5 PF11864.13 DUF3384 28.1 28.1 473 domain Y Y N DUF3384 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF3384) Domain of unknown function (DUF3384) This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 422 to 486 amino acids in length. This domain is found associated with Pfam:PF02145. (from Pfam) NF023306.5 PF11878.13 DOCK_C-D_N 23.5 23.5 113 domain Y Y N DOCK-C subfamily domain-containing protein 12432077,25022758 0 EBI-EMBL Dedicator of cytokinesis C/D, N terminal Dedicator of cytokinesis C/D, N terminal This entry represents the N-terminal domain of the DOCK-C subfamily (DOCK 6, 7, 8) and DOCK-D subfamily (DOCK 9, 10, 11). DOCK family members are evolutionarily conserved guanine nucleotide exchange factors (GEFs) for Rho-family GTPases [1,2], required during several cellular processes, such as cell motility and phagocytosis. DOCK proteins are categorised into four subfamilies based on their sequence homology: DOCK-A (DOCK1/180, 2, 5), DOCK-B subfamily (DOCK3, 4), DOCK-C subfamily (DOCK6, 7, 8), DOCK-D subfamily (DOCK9, 10, 11) [1]. [1]. 12432077. Identification of an evolutionarily conserved superfamily of DOCK180-related proteins with guanine nucleotide exchange activity. Cote JF, Vuori K;. J Cell Sci. 2002;115:4901-4913. [2]. 25022758. Dock-family exchange factors in cell migration and disease. Gadea G, Blangy A;. Eur J Cell Biol. 2014;93:466-477. (from Pfam) NF023307.5 PF11879.13 DUF3399 25 25 76 domain Y Y N DUF3399 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF3399) Domain of unknown function (DUF3399) This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is about 100 amino acids in length. This domain is found associated with Pfam:PF02214, Pfam:PF00520. (from Pfam) NF023310.5 PF11882.13 DUF3402 25 25 454 domain Y Y N DUF3402 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF3402) Domain of unknown function (DUF3402) This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 350 to 473 amino acids in length. This domain is found associated with Pfam:PF07923. (from Pfam) NF023311.5 PF11883.13 DUF3403 28.9 28.9 45 domain Y Y N DUF3403 domain-containing protein GO:0004674 0 EBI-EMBL Domain of unknown function (DUF3403) Domain of unknown function (DUF3403) This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is about 50 amino acids in length. This domain is found associated with Pfam:PF00069, Pfam:PF08276, Pfam:PF00954, Pfam:PF01453. (from Pfam) NF023317.5 PF11889.13 Capsid_pestivir 27 27 56 domain Y Y N capsid protein C domain-containing protein GO:0003968,GO:0004197,GO:0004252,GO:0016817,GO:0017111,GO:0070008 0 EBI-EMBL Capsid protein C, pestivirus Capsid protein C, pestivirus This domain is found in the genome polyprotein from Pestivirus. It covers part of the capsid protein C region in the polyprotein. (from Pfam) NF023323.5 PF11895.13 Peroxidase_ext 25 25 79 domain Y Y N peroxidase extension domain-containing protein 0 EBI-EMBL Fungal peroxidase extension region fungal peroxidase extension region This region is found as an extension to a haem peroxidase domain in some fungi. This region is about 80 amino acids in length and forms an extended structure on the surface of the peroxidase domain Pfam:PF00141. (from Pfam) NF023328.5 PF11900.13 DUF3420 24.9 24.9 47 domain Y Y N DUF3420 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF3420) Domain of unknown function (DUF3420) This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 50 amino acids in length. This domain is found associated with Pfam:PF00023. (from Pfam) NF023333.5 PF11905.13 DUF3425 27.1 27.1 128 domain Y Y N DUF3425 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF3425) Domain of unknown function (DUF3425) This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 120 to 143 amino acids in length. (from Pfam) NF023339.5 PF11912.13 CfaA_B_C 28.6 28.6 206 domain Y Y N counting factor-associated protein A/B/C family protein 10444594 0 EBI-EMBL Counting factor-associated protein A/B/C counting factor-associated protein A/B/C family protein Developing Dictyostelium (Slime mold) cells form large aggregation streams that break up into groups of cells. Each group then becomes a fruiting body. Cells sense if there are too many cells in a stream by sensing the concentration of counting factor (CF), a protein complex secreted by the aggregating cells [1]. This entry includes counting factor-associated protein A/B/C from Slime mold. [1]. 10444594. A cell-counting factor regulating structure size in Dictyostelium. Brock DA, Gomer RH;. Genes Dev. 1999;13:1960-1969. (from Pfam) NF023346.5 PF11919.13 DUF3437 22.5 22.5 88 domain Y Y N DUF3437 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF3437) Domain of unknown function (DUF3437) This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 142 to 163 amino acids in length. (from Pfam) NF023353.5 PF11926.13 DUF3444 26.1 26.1 211 domain Y Y N DUF3444 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF3444) Domain of unknown function (DUF3444) This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 210 amino acids in length. This domain is found associated with Pfam:PF00226. This domain has two conserved sequence motifs: FSH and FSH. (from Pfam) NF023357.5 PF11931.13 SF3a60_Prp9_C 30.7 30.7 120 domain Y Y N zinc finger domain-containing protein GO:0000398,GO:0003723,GO:0005681 22314233 0 EBI-EMBL SF3a60/Prp9 C-terminal SF3a60/Prp9 C-terminal This domain corresponds to the C-terminal region of SF3a60 subunit (Prp9 in yeast counterpart) from the highly conserved heterotrimeric complex SF3a found in eukaryotes. It is essential for pre-mRNA splicing that functions in spliceosome assembly within the mature U2 snRNP (small ribonucleoprotein particle). This domain has two conserved sequence motifs: PIP and CEICG. It contains a zinc-finger domain of the C2H2-type which might be important for RNA binding and protein-protein interactions with components of the SF3b complex [1]. [1]. 22314233. Structure and assembly of the SF3a splicing factor complex of U2 snRNP. Lin PC, Xu RM;. EMBO J. 2012;31:1579-1590. (from Pfam) NF023360.5 PF11934.13 DUF3452 26.3 26.3 135 domain Y Y N DUF3452 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF3452) Domain of unknown function (DUF3452) This presumed domain is functionally uncharacterised. This domain is found in bacteria and eukaryotes. This domain is typically between 124 to 150 amino acids in length. This domain is found associated with Pfam:PF01858, Pfam:PF01857. This domain has a single completely conserved residue W that may be functionally important. (from Pfam) NF023361.5 PF11935.13 SYMPK_PTA1_N 25 25 229 domain Y Y N ARM/HEAT domain-containing protein 12819204,18042462,19450530,20861839 0 EBI-EMBL Symplekin/PTA1 N-terminal Symplekin/PTA1 N-terminal This is the N-terminal domain found in the symplekin protein from animals and PTA1 protein from budding yeasts and is typically between 239 to 261 amino acids in length. Symplekin is a scaffold protein that functions as a component of a multimolecular complex involved in histone mRNA 3'-end processing [1,2]. PTA1 is involved in pre-tRNA processing. PTA1 is a subunit of the cleavage and polyadenylation factor (CPF), which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB [3]. This domain has the ARM or HEAT fold, with seven pairs of antiparallel alpha-helices arranged in the shape of an arc. It is important for interaction with Ssu72 and stimulates Ssu72 C-terminal domain phosphatase activity in vitro [4]. [1]. 18042462. A genome-wide RNA interference screen reveals that variant histones are necessary for replication-dependent histone pre-mRNA processing. Wagner EJ, Burch BD, Godfrey AC, Salzler HR, Duronio RJ, Marzluff WF;. Mol Cell. 2007;28:692-699. [2]. 19450530. A core complex of CPSF73, CPSF100, and Symplekin may form two different cleavage factors for processing of poly(A) and histone mRNAs. Sullivan KD, Steiniger M, Marzluff WF;. Mol Cell. 2009;34:322-332. [3]. 12819204. Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3'-ends. Nedea E, He X, Kim M, Pootoolal J, Zhong G, Canadien V, Hughes T, Buratowski S, Moore CL, Greenblatt J;. J Biol Chem. 2003;278:33000-33010. [4]. 20861839. Crystal structure of the human sym. TRUNCATED at 1650 bytes (from Pfam) NF023387.5 PF11961.13 DUF3475 29.7 29.7 57 domain Y Y N DUF3475 domain-containing protein GO:0045927 25062973 0 EBI-EMBL Domain of unknown function (DUF3475) Domain of unknown function (DUF3475) This entry represents the N-terminal domain of PSI proteins from Arabidopsis. This domain is found associated with Pfam:PF05003. PSI1 was identified as a gene that is co-expressed with the phytosulfokine (PSK) receptor genes PSKR1 and PSKR2 in Arabidopsis thaliana. PSI proteins are plant-specific and promote growth [1]. [1]. 25062973. The PSI family of nuclear proteins is required for growth in arabidopsis. Stuhrwohldt N, Hartmann J, Dahlke RI, Oecking C, Sauter M;. Plant Mol Biol. 2014;86:289-302. (from Pfam) NF023389.5 PF11963.13 B-CoV_A_NSP1 25 25 355 domain Y Y N NSP1 domain-containing protein 25432065,30568804 0 EBI-EMBL Betacoronavirus, lineage A, NSP1 Betacoronavirus, lineage A, NSP1 This family the N-terminal region of the Betacoronavirus polyprotein which contains non-structural protein 1 (Nsp1) from Betacoronavirus lineage A. This protein is important for viral replication and pathogenesis [1,2]. It suppresses the host innate immune functions by inhibiting type I interferon expression and host antiviral signalling pathways. [1]. 25432065. Coronavirus nonstructural protein 1: Common and distinct functions in the regulation of host and viral gene expression. Narayanan K, Ramirez SI, Lokugamage KG, Makino S;. Virus Res. 2015;202:89-100. [2]. 30568804. Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains. Phan MVT, Ngo Tri T, Hong Anh P, Baker S, Kellam P, Cotten M;. Virus Evol. 2018;4:vey035. (from Pfam) NF023421.5 PF11995.13 DUF3490 25 25 161 domain Y Y N DUF3490 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF3490) Domain of unknown function (DUF3490) This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 160 amino acids in length. This domain is found associated with Pfam:PF00225. This domain is found associated with Pfam:PF00225. This domain has two conserved sequence motifs: EVE and ESA. (from Pfam) NF023429.5 PF12004.13 DAB2P_C 24.3 24.3 512 domain Y Y N GTPase-activating protein domain-containing protein 27565345 0 EBI-EMBL Disabled homolog 2-interacting protein, C-terminal domain Disabled homolog 2-interacting protein, C-terminal domain This domain is found at the C terminus of some GTPase-activating proteins (also known as GAP) found in animals, including Disabled homolog 2-interacting protein (DAB2P). This region is found associated with Pfam:PF00616 and Pfam:PF00168, and includes a coiled-coil domain that forms a parallel trimer in solution with one helical strand from each monomer [1]. [1]. 27565345. Phase Transition in Postsynaptic Densities Underlies Formation of Synaptic Complexes and Synaptic Plasticity. Zeng M, Shang Y, Araki Y, Guo T, Huganir RL, Zhang M;. Cell. 2016;166:1163-1175. (from Pfam) NF023436.5 PF12011.13 NPH-II 25 25 174 domain Y Y N RNA helicase NPH-II GO:0017111 8970979 0 EBI-EMBL RNA helicase NPH-II RNA helicase NPH-II RNA helicase NPH-II or I8 is found in Poxviridae. It is essential for viral replication and plays an important role during transcription of early mRNAs, presumably by preventing R-loop formation behind the elongating RNA polymerase. It acts as NTP-dependent helicase that catalyzes unidirectional unwinding of 3'tailed duplex RNAs. It might also play a role in the export of newly synthesized mRNA chains out of the core into the cytoplasm and is required for propagation of viral particles [1]. [1]. 8970979. Vaccinia virions lacking the RNA helicase nucleoside triphosphate phosphohydrolase II are defective in early transcription. Gross CH, Shuman S;. J Virol. 1996;70:8549-8557. (from Pfam) NF023440.5 PF12015.13 Bud3_N 25 25 182 domain Y Y N Bud3 domain-containing protein 7730410 0 EBI-EMBL Bud3, N-terminal Bud3, N-terminal This domain is found in the N-terminal of the yeast Bud3 protein. Bud3 is involved in bud-site selection in budding yeasts. This domain has a conserved ENL sequence motif [1]. [1]. 7730410. Role of Bud3p in producing the axial budding pattern of yeast. Chant J, Mischke M, Mitchell E, Herskowitz I, Pringle JR;. J Cell Biol. 1995;129:767-778. (from Pfam) NF023443.5 PF12018.13 FAP206 33 33 272 domain Y Y N DUF3508 domain-containing protein 25540426 0 EBI-EMBL Domain of unknown function Domain of unknown function This domain of about 280 residues is found in eukaryotes. There are two conserved sequence motifs: GFC and GLL. This family is also known as UPF0704. This domain is found FAP206 Swiss:Q23H79, a protein associated with cilia and flagella. In the ciliate Tetrahymena, the cilium has radial spokes, each of which is a macromolecular complex essential for motility. A triplet of three radial spokes, RS1, RS2, and RS3, is repeated every 96 nm along the doublet microtubule. Each spoke has a distinct base that docks to the doublet and is linked to different inner dynein arms. Knockout of the FAP206 gene results in slow cell motility and the 96-nm repeats lack RS2 and dynein c. FAP206 is probably part of the front prong and docks RS2 and dynein c to the microtubule [1]. [1]. 25540426. FAP206 is a microtubule-docking adapter for ciliary radial spoke 2 and dynein c. Vasudevan KK, Song K, Alford LM, Sale WS, Dymek EE, Smith EF, Hennessey T, Joachimiak E, Urbanska P, Wloga D, Dentler W, Nicastro D, Gaertig J;. Mol Biol Cell. 2015;26:696-710. (from Pfam) NF023447.5 PF12022.13 COG2_C 27.3 27.3 300 domain Y Y N COG complex component COG2 domain-containing protein 11980916,25541219,34061181 0 EBI-EMBL COG complex component, COG2, C-terminal COG complex component, COG2, C-terminal The COG complex comprises eight proteins (COG1-8) and plays critical roles in Golgi structure and function [1]. It is necessary for retrograde trafficking in the Golgi apparatus and for protein glycosylation [2]. COG complex, together with exocyst, Golgi-associated retrograde protein (GARP) and Dsl1 complexes, is a member of the CATHR (complexes associated with tethering containing helical rods) family sharing an evolutionary origin and structural features [3]. This domain represents the C-terminal of COG complex subunit 2 and consists of a conserved alpha-helical bundle. In Arabidopsis, COG2 forms a complex with FPP3/VETH1 and FPP2/VETH2 and ensures the correct secondary cell wall (SCW) deposition pattern by recruiting exocyst components to cortical microtubules in xylem cells during secondary cell wall deposition [2]. [1]. 11980916. Characterization of a mammalian Golgi-localized protein complex, COG, that is required for normal Golgi morphology and function. Ungar D, Oka T, Brittle EE, Vasile E, Lupashin VV, Chatterton JE, Heuser JE, Krieger M, Waters MG;. J Cell Biol 2002;157:405-415. [2]. 25541219. Novel coiled-coil proteins regulate exocyst association with cortical microtubules in xylem cells via the conserved oligomeric golgi-complex 2 protein. Oda Y, Iida Y, Nagashima Y, Sugiyama Y, Fukuda H;. Plant Cell Physiol. 2015;56:277-286. [3]. 34061181. Homology and Modular Evolution of CATCHR at the Origin of the Eukaryotic Endomembrane System. Santana-Molina C, Gutierrez F, Devos DP;. Genome Biol Evol. 2021; [Epub ahead of print] (from Pfam) NF023448.5 PF12023.13 DUF3511 25 25 45 domain Y Y N DUF3511 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF3511) Domain of unknown function (DUF3511) This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 50 amino acids in length. This domain has two completely conserved residues (Y and K) that may be functionally important. (from Pfam) NF023455.5 PF12030.13 DUF3517 25 25 406 domain Y Y N DUF3517 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF3517) Domain of unknown function (DUF3517) This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 340 amino acids in length. This domain is found associated with Pfam:PF00443. (from Pfam) NF023456.5 PF12031.13 BAF250_C 21.1 21.1 257 domain Y Y N SWI/SNF-like complex subunit BAF250/Osa 11124806,20086098 0 EBI-EMBL SWI/SNF-like complex subunit BAF250/Osa SWI/SNF-like complex subunit BAF250/Osa This entry represents the mammalian BAF250a/b and its homologue osa from fruit flies [1]. They are part of the SWI/SNF-like ATP-dependent chromatin remodelling complex that regulates gene expression through regulating nucleosome remodelling. In humans there are two BAF250 isoforms, BAF250a/ARID1a and BAF250b/ARID1b. BAF250a/b may be E3 ubiquitin ligases that target histone H2B [2]. [1]. 11124806. Osa-containing Brahma chromatin remodeling complexes are required for the repression of wingless target genes. Collins RT, Treisman JE;. Genes Dev. 2000;14:3140-3152. [2]. 20086098. Mammalian SWI/SNF--a subunit BAF250/ARID1 is an E3 ubiquitin ligase that targets histone H2B. Li XS, Trojer P, Matsumura T, Treisman JE, Tanese N;. Mol Cell Biol. 2010;30:1673-1688. (from Pfam) NF023460.5 PF12036.13 DUF3522 29.3 29.3 188 domain Y Y N DUF3522 domain-containing protein GO:0016020 21733186 0 EBI-EMBL Protein of unknown function (DUF3522) Protein of unknown function (DUF3522) This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 220 to 787 amino acids in length. This family belongs to the CREST superfamily [1], which are distant members of the GPCR superfamily. [1]. 21733186. CREST--a large and diverse superfamily of putative transmembrane hydrolases. Pei J, Millay DP, Olson EN, Grishin NV;. Biol Direct. 2011;6:37. (from Pfam) NF023461.5 PF12037.13 ATAD3_N 25 25 265 domain Y Y N AAA domain-containing protein 20154147,22664726 0 EBI-EMBL ATPase family AAA domain-containing protein 3, N-terminal ATPase family AAA domain-containing protein 3, N-terminal This is the conserved N-terminal domain of ATPase family AAA domain-containing protein 3 (ATAD3) which is involved in dimerisation [1] and interacts with the inner surface of the outer mitochondrial membrane [2]. This domain is found associated with the AAA ATPase domain (Pfam:PF00004). ATAD3 is essential for mitochondrial network organisation, mitochondrial metabolism and cell growth at organism and cellular level. It may also play an important role in mitochondrial protein synthesis. [1]. 22664726. ATAD3B is a human embryonic stem cell specific mitochondrial protein, re-expressed in cancer cells, that functions as dominant negative for the ubiquitous ATAD3A. Merle N, Feraud O, Gilquin B, Hubstenberger A, Kieffer-Jacquinot S, Assard N, Bennaceur-Griscelli A, Honnorat J, Baudier J;. Mitochondrion. 2012;12:441-448. [2]. 20154147. The AAA+ ATPase ATAD3A controls mitochondrial dynamics at the interface of the inner and outer membranes. Gilquin B, Taillebourg E, Cherradi N, Hubstenberger A, Gay O, Merle N, Assard N, Fauvarque MO, Tomohiro S, Kuge O, Baudier J;. Mol Cell Biol. 2010;30:1984-1996. (from Pfam) NF023463.5 PF12039.13 DUF3525 25 25 453 domain Y Y N DUF3525 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3525) Protein of unknown function (DUF3525) This family of proteins is functionally uncharacterised. This protein is found in viruses. Proteins in this family are about 360 amino acids in length. (from Pfam) NF023469.5 PF12045.13 DUF3528 29.5 29.5 126 domain Y Y N DUF3528 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3528) Protein of unknown function (DUF3528) This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 185 to 298 amino acids in length. This protein is found associated with Pfam:PF00046. (from Pfam) NF023477.5 PF12054.13 DUF3535 26.2 26.2 448 domain Y Y N DUF3535 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF3535) Domain of unknown function (DUF3535) This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 439 to 459 amino acids in length. This domain is found associated with Pfam:PF00271, Pfam:PF02985, Pfam:PF00176. This domain has two completely conserved residues (P and K) that may be functionally important. (from Pfam) NF023479.5 PF12056.13 DUF3537 25 25 391 domain Y Y N DUF3537 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3537) Protein of unknown function (DUF3537) This family of transmembrane proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 427 to 453 amino acids in length. (from Pfam) NF023484.5 PF12061.13 NB-LRR 28.7 28.7 295 domain Y Y N late blight resistance protein R1 12000683 0 EBI-EMBL Late blight resistance protein R1 late blight resistance protein R1 R1 is a gene for resistance to late blight, the most destructive disease in potato cultivation worldwide. The R1 gene belongs to the class of plant genes for pathogen resistance that have a leucine zipper motif, a putative nucleotide binding domain and a leucine-rich repeat domain [1]. This protein is found associated with Pfam:PF00931. [1]. 12000683. The R1 gene for potato resistance to late blight (Phytophthora infestans) belongs to the leucine zipper/NBS/LRR class of plant resistance genes. Ballvora A, Ercolano MR, Weiss J, Meksem K, Bormann CA, Oberhagemann P, Salamini F, Gebhardt C;. Plant J. 2002;30:361-371. (from Pfam) NF023486.5 PF12063.13 ATG1-like_MIT1 22.5 22.5 147 domain Y Y N MIT domain-containing protein GO:0004674 16887826,17204848,18936157,24793651 0 EBI-EMBL Atg1-like, MIT domain 1 Atg1-like, MIT domain 1 Members of this entry are serine/threonine-protein kinases and includes ATG1 from yeasts, Unc-51 from C. elegans and ULK1-2 from humans. ATG1 is required for vesicle formation in autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway [1,2]. Unc-51 is important for axonal elongation and axonal guidance [4] and ULK1-2 are involved in autophagy in response to starvation [3]. They consist of a kinase domain at the N-terminal (Pfam:PF00069) and two tandem microtubule interacting and transport (MIT) domains (tMIT) at the C-terminal. MIT domains are known to mediate protein-protein interactions. In ATG1, MIT domains mediate the interaction with ATG13 [1]. In ULK1-2, MIT domains control the regulatory function and localization of the proteins and also mediate interactions with additional autophagy proteins [3]. This is the C-terminal MIT domain (MIT2). [1]. 24793651. Structural basis of starvation-induced assembly of the autophagy initiation complex. Fujioka Y, Suzuki SW, Yamamoto H, Kondo-Kakuta C, Kimura Y, Hirano H, Akada R, Inagaki F, Ohsumi Y, Noda NN;. Nat Struct Mol Biol. 2014;21:513-521. [2]. 17204848. ATG genes involved in non-selective autophagy are conserved from yeast to man, but the selective Cvt and pexophagy pathways also require organism-specific genes. Meijer WH, van der Klei IJ, Veenhuis M, Kiel JA;. Autophagy. 2007;3:106-116. [3]. 18936157. Kinase-inactivated ULK proteins inhibit autophagy via their conserved C-terminal domains using an Atg13-independent mechanism. Chan EY, Longatti A, McKnight NC, Tooze SA;. Mol Cell Biol. 2009;29:157-171. [4]. 16887826. The autophagy-related kinase UNC-51 and its bind. TRUNCATED at 1650 bytes (from Pfam) NF023501.5 PF12078.13 DUF3557 26.2 26.2 154 domain Y Y N DUF3557 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF3557) Domain of unknown function (DUF3557) This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 150 amino acids in length. (from Pfam) NF023539.5 PF12117.13 NS1_C 25 25 121 domain Y Y N NS1 protein transactivation domain-containing protein 12050365,20097398,7799962,9847309 0 EBI-EMBL Parvovirus non-structural protein 1, C-terminal Parvovirus non-structural protein 1, C-terminal This domain is the transactivation domain of the Parvovirus NS1 protein, located immediately C-terminal to the helicase [1,2]. Parvovirus are some of the smallest viruses containing linear, non-segmented single-stranded DNA genomes, with an average genome size of 5000 nucleotides. They infect a wide range of invertebrates and vertebrates and are well known for causing enteric disease in mammals. Genomes contain two large ORFs: NS1 and VP1; other ORFs are found in some sub-types and different gene products can arise from splice variants and the use of different start codons [3]. NS1 protein is essential for viral life cycle stages, including DNA replication, trans-regulation of the two viral promoters and modulation of heterologous promoters. It exhibits DNA binding, endonuclease and helicase activities and is the major contributor to the toxic effect on host cells [4]. [1]. 7799962. Transcriptional activation by the parvoviral nonstructural protein NS-1 is mediated via a direct interaction with Sp1. Krady JK, Ward DC;. Mol Cell Biol. 1995;15:524-533. [2]. 9847309. A novel heterogeneous nuclear ribonucleoprotein-like protein interacts with NS1 of the minute virus of mice. Harris CE, Boden RA, Astell CR;. J Virol. 1999;73:72-80. [3]. 20097398. Determination and analysis of the full-length chicken parvovirus genome. Day JM, Zsak L;. Virology. 2010;399:59-64. [4]. 12050365. Parvovirus initiator protein NS1 and RPA coordinate replication fork progression in a reconstituted DNA replication system. Christensen J, Tattersall P;. J Virol. 2002;76:6518-6531. (from Pfam) NF023553.5 PF12131.13 DUF3586 25 25 75 domain Y Y N DUF3586 domain-containing protein GO:0004197 0 EBI-EMBL Protein of unknown function (DUF3586) Protein of unknown function (DUF3586) This domain is found in eukaryotes. This domain is about 80 amino acids in length and is found associated with Pfam:PF08246, and Pfam:PF00112. (from Pfam) NF023554.5 PF12132.13 DUF3587 25 25 201 domain Y Y N DUF3587 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3587) Protein of unknown function (DUF3587) This protein is found in viruses. Proteins in this family are typically between 209 and 248 amino acids in length. (from Pfam) NF023562.5 PF12140.13 SLED 25 25 112 domain Y Y N SLED domain-containing protein 24727478 0 EBI-EMBL SLED domain SLED domain The SLED (Scm-Like Embedded Domain) domain is a double-stranded DNA binding domain found in Scml2 which is a member of the Polycomb group of proteins involved in epigenetic gene silencing [1]. [1]. 24727478. Solution NMR structure of the DNA-binding domain from Scml2 (sex comb on midleg-like 2). Bezsonova I;. J Biol Chem. 2014;289:15739-15749. (from Pfam) NF023579.5 PF12157.13 DUF3591 25 25 444 domain Y Y N DUF3591 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3591) Protein of unknown function (DUF3591) This domain is found in eukaryotes and is typically between 445 to 462 amino acids in length. Most members are annotated as being transcription initiation factor TFIID subunit 1, and this region is the conserved central portion of these proteins. (from Pfam) NF023688.5 PF12267.13 DUF3614 25 25 173 domain Y Y N DUF3614 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3614) Protein of unknown function (DUF3614) This family of proteins is found in viruses. Proteins in this family are typically between 162 and 495 amino acids in length. (from Pfam) NF023694.5 PF12274.13 DUF3615 22 22 91 domain Y Y N DUF3615 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3615) Protein of unknown function (DUF3615) This domain family is found in bacteria and eukaryotes, and is typically between 86 and 97 amino acids in length. There is a conserved FAE sequence motif. There is a single completely conserved residue F that may be functionally important. (from Pfam) NF023705.5 PF12285.13 Astrovir_pp_1 25 25 171 domain Y Y N astroviridae polyprotein 1 family protein GO:0004252,GO:0070008 11799197 0 EBI-EMBL Astroviridae polyprotein 1 astroviridae polyprotein 1 family protein This family of proteins is found in non-structural polyprotein 1 A/AB from Astroviridae [1]. They are typically between 49 and 62 amino acids in length. There are two conserved sequence motifs: QPLDLS and EQQ. [1]. 11799197. Processing of nonstructural protein 1a of human astrovirus. Geigenmuller U, Chew T, Ginzton N, Matsui SM;. J Virol. 2002;76:2003-2008. (from Pfam) NF023722.5 PF12302.13 DUF3629 27.8 27.8 218 domain Y Y N DUF3629 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3629) Protein of unknown function (DUF3629) This family of proteins is found in eukaryotes. Proteins in this family are typically between 256 and 292 amino acids in length. (from Pfam) NF023748.5 PF12329.13 TMF_DNA_bd 35 35 74 domain Y Y N TMF DNA-binding domain-containing protein 1409643,15128430,18182439,9742951 0 EBI-EMBL TATA element modulatory factor 1 DNA binding TATA element modulatory factor 1 DNA binding This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures.[1]. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [3] and plant [4] cells. [1]. 9742951. Tyrosine phosphorylation of the TATA element modulatory factor by the FER nuclear tyrosine kinases. Schwartz Y, Ben-Dor I, Navon A, Motro B, Nir U;. FEBS Lett. 1998;434:339-345. [2]. 1409643. Cloning and chromosomal mapping of a human immunodeficiency virus 1 "TATA" element modulatory factor. Garcia JA, Ou SH, Wu F, Lusis AJ, Sparkes RS, Gaynor RB;. Proc Natl Acad Sci U S A. 1992;89:9372-9376. [3]. 15128430. TMF is a golgin that binds Rab6 and influences Golgi morphology. Fridmann-Sirkis Y, Siniossoglou S, Pelham HR;. BMC Cell Biol. 2004;5:18. [4]. 18182439. Localization and domain characterization of Arabidopsis golgin candidates. Latijnhouwers M, Gillespie T, Boevink P, Kriechbaumer V, Hawes C, Carvalho CM;. J Exp Bot. 2007;58:4373-4386. (from Pfam) NF023750.5 PF12331.13 Rad26-like_helical_rpts 29.9 29.9 215 domain Y Y N helical repeats-containing protein 28314775 0 EBI-EMBL Rad26-like, helical repeats Rad26-like, helical repeats This domain is found in Rad26 from Myceliophthora thermophila (Swiss:G2QDY6) and similar fungal proteins. Rad26 is a functional subunit of the Rad3-Rad26 complex that is responsible for bringing the kinase to sites of DNA damage. The central region of Rad26 is formed by five helical repeats forming an alpha-solenoid arrangement [1]. [1]. 28314775. Insights into Rad3 kinase recruitment from the crystal structure of the DNA damage checkpoint protein Rad26. Andersen KR;. J Biol Chem. 2017;292:8149-8157. (from Pfam) NF023755.5 PF12337.13 DUF3637 25 25 67 domain Y Y N DUF3637 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3637) Protein of unknown function (DUF3637) This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF00073, Pfam:PF08935. (from Pfam) NF023760.5 PF12342.13 DUF3640 25 25 26 domain Y Y N DUF3640 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3640) Protein of unknown function (DUF3640) This family of proteins is found in viruses. Proteins in this family are typically between 25 and 211 amino acids in length. (from Pfam) NF023774.5 PF12356.13 BIRC6 27 27 163 domain Y Y N IAP repeat-containing protein 6 GO:0004842,GO:0006915,GO:0032465 14765125,15200957,18329369 0 EBI-EMBL Baculoviral IAP repeat-containing protein 6 baculoviral IAP repeat-containing protein 6 BIRC6 is an anti-apoptotic protein which can regulate cell death by controlling caspases and by acting as an E3 ubiquitin-protein ligase [1]. [1]. 14765125. Nrdp1-mediated degradation of the gigantic IAP, BRUCE, is a novel pathway for triggering apoptosis. Qiu XB, Markant SL, Yuan J, Goldberg AL;. EMBO J. 2004;23:800-810. [2]. 15200957. Dual role of BRUCE as an antiapoptotic IAP and a chimeric E2/E3 ubiquitin ligase. Bartke T, Pohl C, Pyrowolakis G, Jentsch S;. Mol Cell. 2004;14:801-811. [3]. 18329369. Final stages of cytokinesis and midbody ring formation are controlled by BRUCE. Pohl C, Jentsch S;. Cell. 2008;132:832-845. (from Pfam) NF023793.5 PF12376.13 DUF3654 25 25 138 domain Y Y N DUF3654 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3654) Protein of unknown function (DUF3654) This family of proteins is found in eukaryotes. Proteins in this family are typically between 193 and 612 amino acids in length. (from Pfam) NF023796.5 PF12379.13 bCoV_NSP3_N 26.7 26.7 149 domain Y Y N NSP3a domain-containing protein 17728234,18367524,23943763,31776274 0 EBI-EMBL Betacoronavirus replicase NSP3, N-terminal Betacoronavirus replicase NSP3, N-terminal This domain family corresponds to the N-terminal domain of NSP3 (non-structural protein 3, also known as nsp3) found in Betacoronavirus, which is encoded on the replicase polyprotein. This family includes the NSP3a domain which has the ubiquitin-like 1 (UB1) and glutamic acid-rich acidic (AC) hypervariable domains [1]. NSP3a interacts with numerous other proteins involved in replication and transcription and may serve as a scaffolding protein for these processes. The N-terminal NSP3a domain interacts with N (nucleocapsid) protein to colocalise genomic RNA with the nascent replicase-transcriptase complex at the earliest stages of infection, essential for the virus [3]. The C-terminal Glu-rich subdomain is best described as a flexible tail attached to the globular UB1 subdomain [4]. The family is found in association with Pfam:PF08716, Pfam:PF01661, Pfam:PF05409, Pfam:PF06471, Pfam:PF08717, Pfam:PF06478, Pfam:PF09401, Pfam:PF06460, Pfam:PF08715, Pfam:PF08710. [1]. 18367524. Proteomics analysis unravels the functional repertoire of coronavirus nonstructural protein 3. Neuman BW, Joseph JS, Saikatendu KS, Serrano P, Chatterjee A, Johnson MA, Liao L, Klaus JP, Yates JR 3rd, Wuthrich K, Stevens RC, Buchmeier MJ, Kuhn P;. J Virol. 2008;82:5279-5294. [2]. 31776274. Nucleocapsid Protein Recruitment to Replication-Transcription Complexes Plays a Crucial Role in Coronaviral Life Cycle. Cong Y, Ulasli M, Schepers H, Mauthe M, V'kovski P, Kriegenburg F, Thiel V, de Haan CAM, Reggiori F;. J Virol. 2020; [Epub ahead of print]. [3]. 23943763. Severe acute respiratory syndrome coronavirus nonstructural proteins 3, 4, and 6 induce double-m. TRUNCATED at 1650 bytes (from Pfam) NF023811.5 PF12394.13 DUF3657 27 27 64 domain Y Y N protein FAM135 0 EBI-EMBL Protein FAM135 protein FAM135 This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF05057. (from Pfam) NF023841.5 PF12425.13 DUF3673 22.3 22.3 53 domain Y Y N DUF3673 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3673) Protein of unknown function (DUF3673) This domain family is found in eukaryotes, and is approximately 50 amino acids in length. (from Pfam) NF023844.5 PF12428.13 DUF3675 24.3 24.3 119 domain Y Y N DUF3675 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3675) Protein of unknown function (DUF3675) This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with Pfam:PF00097. There are two completely conserved residues (R and L) that may be functionally important. (from Pfam) NF023845.5 PF12429.13 DUF3676 25 25 230 domain Y Y N DUF3676 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3676) Protein of unknown function (DUF3676) This domain family is found in eukaryotes, and is approximately 230 amino acids in length. (from Pfam) NF023851.5 PF12435.13 DUF3678 23 23 35 domain Y Y N DUF3678 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3678) Protein of unknown function (DUF3678) This domain family is found in eukaryotes, and is approximately 40 amino acids in length. (from Pfam) NF023858.5 PF12442.13 DUF3681 24.3 24.3 96 domain Y Y N DUF3681 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3681) Protein of unknown function (DUF3681) This family of proteins is found in eukaryotes. Proteins in this family are typically between 112 and 212 amino acids in length. There is a single completely conserved residue G that may be functionally important. (from Pfam) NF023862.5 PF12446.13 DUF3682 25 25 129 domain Y Y N DUF3682 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3682) Protein of unknown function (DUF3682) This domain family is found in eukaryotes, and is typically between 125 and 136 amino acids in length. (from Pfam) NF023879.5 PF12463.13 DUF3689 27 27 315 domain Y Y N DUF3689 domain-containing protein GO:0006511,GO:0031464 0 EBI-EMBL Protein of unknown function (DUF3689) Protein of unknown function (DUF3689) This family of proteins is found in eukaryotes. Proteins in this family are typically between 399 and 797 amino acids in length. (from Pfam) NF023895.5 PF12479.13 DUF3698 25 25 107 domain Y Y N DUF3698 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3698) Protein of unknown function (DUF3698) This domain family is found in eukaryotes, and is typically between 89 and 105 amino acids in length. (from Pfam) NF023896.5 PF12480.13 GARIL_Rab2_bd 22 22 71 domain Y Y N Rab2B-binding domain-containing protein 26209634,28930687,29025071,34714330 0 EBI-EMBL Golgi associated RAB2 interactor protein-like, Rab2B-binding domain Golgi associated RAB2 interactor protein-like, Rab2B-binding domain This domain is found in Golgi associated RAB2 interactor proteins and it is likely a Rab2B-binding domain [1-3]. Some members included in this entry, such as GAR1A/B and GAR2, are RAB2B effector proteins required for accurate acrosome formation and normal male fertility [1,3]. GARI-L4 is a RAB2B effector protein required for the compacted Golgi morphology [2]. GARIL5 is a Rab2B effector protein which promotes cytosolic DNA-induced innate immune responses [4]. [1]. 29025071. The expression characteristics of FAM71D and its association with sperm motility. Ma Q, Li Y, Luo M, Guo H, Lin S, Chen J, Du Y, Jiang Z, Gui Y;. Hum Reprod. 2017;32:2178-2187. [2]. 26209634. Small GTPase Rab2B and Its Specific Binding Protein Golgi-associated Rab2B Interactor-like 4 (GARI-L4) Regulate Golgi Morphology. Aizawa M, Fukuda M;. J Biol Chem. 2015;290:22250-22261. [3]. 34714330. FAM71F1 binds to RAB2A and RAB2B and is essential for acrosome formation and male fertility in mice. Morohoshi A, Miyata H, Oyama Y, Oura S, Noda T, Ikawa M;. Development. 2021; [Epub ahead of print]. [4]. 28930687. The RAB2B-GARIL5 Complex Promotes Cytosolic DNA-Induced Innate Immune Responses. Takahama M, Fukuda M, Ohbayashi N, Kozaki T, Misawa T, Okamoto T, Matsuura Y, Akira S, Saitoh T;. Cell Rep. 2017;20:2944-2954. (from Pfam) NF023904.5 PF12488.13 DUF3704 21.9 21.9 27 domain Y Y N DUF3704 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3704) Protein of unknown function (DUF3704) This domain family is found in eukaryotes, and is approximately 30 amino acids in length. (from Pfam) NF023909.5 PF12494.13 DUF3695 27 27 101 domain Y Y N DUF3695 domain-containing protein 31199454 0 EBI-EMBL Protein of unknown function (DUF3695) Protein of unknown function (DUF3695) This family of proteins is found in eukaryotes. Proteins in this family are typically between 157 and 192 amino acids in length. There is a single completely conserved residue D that may be functionally important. The family includes Protein CFAP276 and homologues. CFAP276 has been suggested to be involved in intracellular Ca2 homeostasis [1]. [1]. 31199454. Mutations in C1orf194, encoding a calcium regulator, cause dominant Charcot-Marie-Tooth disease. Sun SC, Ma D, Li MY, Zhang RX, Huang C, Huang HJ, Xie YZ, Wang ZJ, Liu J, Cai DC, Liu CX, Yang Q, Bao FX, Gong XL, Li JR, Hui Z, Wei XF, Zhong JM, Zhou WJ, Shang X, Zhang C, Liu XG, Tang BS, Xiong F, Xu XM;. Brain. 2019;142:2215-2229. (from Pfam) NF023919.5 PF12505.13 DUF3712 24.1 24.1 125 domain Y Y N DUF3712 domain-containing protein 34347309 0 EBI-EMBL Protein of unknown function (DUF3712) Protein of unknown function (DUF3712) This domain family is found in fungi, and is approximately 130 amino acids in length. This domain showed a distant similarity to LEA-2 domains [1]. [1]. 34347309. TMEM106B in humans and Vac7 and Tag1 in yeast are predicted to be lipid transfer proteins. Levine TP;. Proteins. 2022;90:164-175. (from Pfam) NF023923.5 PF12509.13 DUF3715 28.5 28.5 150 domain Y Y N DUF3715 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3715) Protein of unknown function (DUF3715) This domain family is found in eukaryotes, and is approximately 170 amino acids in length. (from Pfam) NF023925.5 PF12511.13 DUF3716 22 22 59 domain Y Y N DUF3716 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3716) Protein of unknown function (DUF3716) This domain family is found in eukaryotes, and is approximately 60 amino acids in length. (from Pfam) NF023930.5 PF12516.13 DUF3719 23 23 66 domain Y Y N DUF3719 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3719) Protein of unknown function (DUF3719) This domain family is found in eukaryotes, and is approximately 70 amino acids in length. There is a conserved HLR sequence motif. There are two completely conserved residues (W and H) that may be functionally important. (from Pfam) NF023931.5 PF12517.13 DUF3720 25 25 99 domain Y Y N DUF3720 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3720) Protein of unknown function (DUF3720) This domain family is found in eukaryotes, and is approximately 100 amino acids in length. There are two completely conserved A residues that may be functionally important. (from Pfam) NF023935.5 PF12521.13 DUF3724 22 22 23 domain Y Y N DUF3724 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3724) Protein of unknown function (DUF3724) This domain family is found in viruses, and is approximately 20 amino acids in length. The family is found in association with Pfam:PF00073. There is a single completely conserved residue Y that may be functionally important. (from Pfam) NF023940.5 PF12526.13 DUF3729 25 25 115 domain Y Y N DUF3729 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3729) Protein of unknown function (DUF3729) This family of proteins is found in viruses. Proteins in this family are typically between 145 and 1707 amino acids in length. The family is found in association with Pfam:PF01443, Pfam:PF01661, Pfam:PF05417, Pfam:PF01660, Pfam:PF00978. There is a single completely conserved residue L that may be functionally important. (from Pfam) NF023944.5 PF12530.13 DUF3730 30.3 30.3 227 domain Y Y N DUF3730 domain-containing protein 16183838,22427331,31076735,31455787 0 EBI-EMBL Focadhesin/RST1, DUF3730 Focadhesin/RST1, DUF3730 This domain of unknown function is found in Focadhesin from animals and RST1 (RESURRECTION 1) from plants. Focadhesin (FOCAD) is a focal adhesion protein with potential tumour suppressor function in gliomas [1]. RST1 was originally identified in a genetic screen for factors involved in the biosynthesis of epicuticular waxes [2]. Later, RST1 and RST1 INTERACTING PROTEIN (RIPR) have been shown to act as cofactors of the cytoplasmic exosome and the Ski complex in plants [3]. It is involved in the suppression of siRNA-mediated silencing of transgenes and certain endogenous transcripts [4]. Structure predictions suggest that this is an alpha-helical domain with and armadillo-like fold. [1]. 22427331. KIAA1797/FOCAD encodes a novel focal adhesion protein with tumour suppressor function in gliomas. Brockschmidt A, Trost D, Peterziel H, Zimmermann K, Ehrler M, Grassmann H, Pfenning PN, Waha A, Wohlleber D, Brockschmidt FF, Jugold M, Hoischen A, Kalla C, Waha A, Seifert G, Knolle PA, Latz E, Hans VH, Wick W, Pfeifer A, Angel P, Weber RG;. Brain. 2012;135:1027-1041. [2]. 16183838. Mutation of the RESURRECTION1 locus of Arabidopsis reveals an association of cuticular wax with embryo development. Chen X, Goodwin SM, Liu X, Chen X, Bressan RA, Jenks MA;. Plant Physiol. 2005;139:909-919. [3]. 31455787. RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis. Lange H, Ndecky SYA, Gomez-Diaz C, Pflieger D, Butel N, Zumsteg J, Kuhn L, Piermaria C, Chicher J, Christie M, Karaaslan ES, Lang PLM, Weigel D, Vaucheret H, Hammann P, Gagliardi D;. Nat Commun. 2019;10:3871. [4]. 31076735. A genetics screen highlights emer. TRUNCATED at 1650 bytes (from Pfam) NF023954.5 PF12540.13 DUF3736 22.6 22.6 142 domain Y Y N DUF3736 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3736) Protein of unknown function (DUF3736) This domain family is found in eukaryotes, and is typically between 135 and 160 amino acids in length. (from Pfam) NF023966.5 PF12552.13 DUF3741 24 24 45 domain Y Y N DUF3741 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3741) Protein of unknown function (DUF3741) This domain family is found in eukaryotes, and is approximately 50 amino acids in length. (from Pfam) NF023976.5 PF12562.13 Pox_I6_C 23 23 37 domain Y Y N poxvirus telomere-binding protein I6 domain-containing protein 11581377 0 EBI-EMBL Poxvirus telomere-binding protein I6, C-terminal domain Poxvirus telomere-binding protein I6, C-terminal domain This domain is found at the C-terminal end of Telomere-binding protein I6 from poxvirus, I6 binds tightly and with great specificity to the hairpin form of the viral telomeric sequence. This protein is thought to play a role in the initiation of vaccinia virus genome replication and/or genome encapsidation [1]. The family is found in association with Pfam:PF04595. [1]. 11581377. Vaccinia virus telomeres: interaction with the viral I1, I6, and K4 proteins. DeMasi J, Du S, Lennon D, Traktman P;. J Virol 2001;75:10090-10105. (from Pfam) NF023986.5 PF12572.13 DUF3752 23.7 23.7 151 domain Y Y N DUF3752 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3752) Protein of unknown function (DUF3752) This domain family is found in eukaryotes, and is typically between 140 and 163 amino acids in length. (from Pfam) NF023993.5 PF12579.13 DUF3755 25 25 34 domain Y Y N DUF3755 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3755) Protein of unknown function (DUF3755) This domain family is found in eukaryotes, and is approximately 40 amino acids in length. There is a single completely conserved residue N that may be functionally important. (from Pfam) NF023995.5 PF12581.13 DUF3756 25 25 41 domain Y Y N DUF3756 domain-containing protein GO:0003968,GO:0004197,GO:0004252,GO:0016817,GO:0070008 0 EBI-EMBL Protein of unknown function (DUF3756) Protein of unknown function (DUF3756) This domain family is found in viruses, and is approximately 40 amino acids in length. (from Pfam) NF024000.5 PF12586.13 DUF3760 26.6 26.6 44 domain Y Y N DUF3760 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3760) Protein of unknown function (DUF3760) This domain family is found in eukaryotes, and is typically between 46 and 64 amino acids in length. (from Pfam) NF024005.5 PF12591.13 DUF3762 27 27 80 domain Y Y N DUF3762 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3762) Protein of unknown function (DUF3762) This domain family is found in viruses, and is approximately 80 amino acids in length. The family is found in association with Pfam:PF05533. (from Pfam) NF024017.5 PF12603.13 L_PA-C-like 22.6 22.6 200 domain Y Y N RNA-directed RNA polymerase L domain-containing protein GO:0003968 32313945 0 EBI-EMBL RNA-directed RNA polymerase L, PA-C-like domain RNA-directed RNA polymerase L, PA-C-like domain This domain is found in RNA-directed RNA polymerase L from from Bunyavirales. It has been described as the PA-C-like domain which forms a narrow and positively charged cleft with the thumb domain, where the 3' RNA is likely bound [1]. It is found in association with Pfam:PF04196. [1]. 32313945. Structural and functional characterization of the severe fever with thrombocytopenia syndrome virus L protein. Vogel D, Thorkelsson SR, Quemin ERJ, Meier K, Kouba T, Gogrefe N, Busch C, Reindl S, Gunther S, Cusack S, Grunewald K, Rosenthal M;. Nucleic Acids Res. 2020;48:5749-5765. (from Pfam) NF024020.5 PF12606.13 RELT 25 25 42 domain Y Y N RELT-like protein 11313261,19969290 0 EBI-EMBL Tumour necrosis factor receptor superfamily member 19 RELT-like protein This family of proteins is found in eukaryotes. Proteins in this family are typically between 49 and 288 amino acids in length. There are two completely conserved residues (K and Y) that may be functionally important. The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the 'guardians of the immune system' due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1. RELT is a TNF receptor family member that is expressed in hematological tissues and can stimulate the proliferation of T-cells, the p38 and JNK MAPK pathways, and serves as a substrate for the closely related kinases OSR1 and SPAK. Furthermore, family members include the homologues RELL1 and RELL2 (RELT-like protein 1 and 2 respectively). RELT, RELL1 and RELL2 bind to each other in vitro and co-localize with one another at the plasma membrane. Functional studies of the role of RELT, show that overexpression of RELT in epithelial cells induces cell death by promoting cell rounding and DNA fragmentation [2]. [1]. 11313261. RELT, a new member of the tumor necrosis factor receptor superfamily, is selectively expressed in hematopoietic tissues and activates transcription factor NF-kappaB. Sica GL, Zhu G, Tamada K, Liu D, Ni J, Chen L;. Blood. 2001;97:2702-2707. [2]. 19969290. RELT induces cellular death i. TRUNCATED at 1650 bytes (from Pfam) NF024032.5 PF12618.13 PHF20_AT-hook 25 25 105 domain Y Y N AT-hook domain-containing protein 22449972,22864287,24492612 0 EBI-EMBL PHD finger protein 20, AT-hook PHD finger protein 20, AT-hook PHD finger protein 20 (PHF20) is a Methyllysine-binding protein, component of the MOF histone acetyltransferase protein complex. It consists of tandem Tudor domains at the N-terminal, an AT hook, a C2H2-type zinc finger, and a plant homeodomain (PHD) finger [1-3]. This entry represents the AT-hook domain, a putative DNA-binding domain [1-3]. [1]. 22449972. Crystal structures of the Tudor domains of human PHF20 reveal novel structural variations on the Royal Family of proteins. Adams-Cioaba MA, Li Z, Tempel W, Guo Y, Bian C, Li Y, Lam R, Min J;. FEBS Lett. 2012;586:859-865. [2]. 24492612. Methyllysine reader plant homeodomain (PHD) finger protein 20-like 1 (PHF20L1) antagonizes DNA (cytosine-5) methyltransferase 1 (DNMT1) proteasomal degradation. Esteve PO, Terragni J, Deepti K, Chin HG, Dai N, Espejo A, Correa IR Jr, Bedford MT, Pradhan S;. J Biol Chem. 2014;289:8277-8287. [3]. 22864287. PHF20 is an effector protein of p53 double lysine methylation that stabilizes and activates p53. Cui G, Park S, Badeaux AI, Kim D, Lee J, Thompson JR, Yan F, Kaneko S, Yuan Z, Botuyan MV, Bedford MT, Cheng JQ, Mer G;. Nat Struct Mol Biol. 2012;19:916-924. (from Pfam) NF024034.5 PF12620.13 DUF3778 22.1 22.1 52 domain Y Y N DUF3778 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3778) Protein of unknown function (DUF3778) This domain family is found in eukaryotes, and is typically between 48 and 61 amino acids in length. There is a conserved LRF sequence motif. (from Pfam) NF024069.5 PF12656.12 G-patch_2 26 26 61 PfamEq Y Y N G patch domain-containing protein 15542821,16880513 0 EBI-EMBL G-patch domain G-patch domain Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ATP-dependent DExH-box splicing factor Prp2 [1]. As this interaction involves the G-patch sequence in Spp2 and is required for the recruitment of Prp2 to the spliceosome before the first catalytic step of splicing, it is proposed that Spp2 might be an accessory factor that confers spliceosome specificity on Prp2 [2]. [1]. 15542821. Interaction between a G-patch protein and a spliceosomal DEXD/H-box ATPase that is critical for splicing. Silverman EJ, Maeda A, Wei J, Smith P, Beggs JD, Lin RJ;. Mol Cell Biol. 2004;24:10101-10110. [2]. 16880513. Yeast ntr1/spp382 mediates prp43 function in postspliceosomes. Boon KL, Auchynnikava T, Edwalds-Gilbert G, Barrass JD, Droop AP, Dez C, Beggs JD;. Mol Cell Biol. 2006;26:6016-6023. (from Pfam) NF024127.5 PF12716.12 Apq12 25 25 54 domain Y Y N Apq12 family protein 15273328,17724120,20016074 0 EBI-EMBL Nuclear pore assembly and biogenesis Apq12 family protein This is a family of conserved fungal proteins involved in nuclear pore assembly [1]. Apq12 is an integral membrane protein of the nuclear envelope (NE) and endoplasmic reticulum. Its absence leads to a partial block in mRNA export and cold-sensitive defects in the growth and localisation of a subset of nucleoporins, particularly those asymmetrically localised to the cytoplasmic fibrils [2]. The defects in nuclear pore assembly appear to be due to defects in regulating membrane fluidity [3]. [1]. 15273328. The yeast Apq12 protein affects nucleocytoplasmic mRNA transport. Baker KE, Coller J, Parker R;. RNA. 2004;10:1352-1358. [2]. 17724120. The yeast integral membrane protein Apq12 potentially links membrane dynamics to assembly of nuclear pore complexes. Scarcelli JJ, Hodge CA, Cole CN;. J Cell Biol. 2007;178:799-812. [3]. 20016074. Integral membrane proteins Brr6 and Apq12 link assembly of the nuclear pore complex to lipid homeostasis in the endoplasmic reticulum. Hodg CA, Choudhary V, Wolyniak MJ, Scarcelli JJ, Schneiter R, Col CN;. J Cell Sci. 2010;123:141-151. (from Pfam) NF024131.5 PF12720.12 DUF3807 25 25 180 domain Y Y N DUF3807 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3807) Protein of unknown function (DUF3807) This is a family of conserved fungal proteins of unknown function. (from Pfam) NF024167.5 PF12757.12 Eisosome1 25 25 126 domain Y Y N eisosome protein 1 20526336 0 EBI-EMBL Eisosome protein 1 eisosome protein 1 Eisosome protein 1 is required for normal formation of eisosomes, large cytoplasmic protein assemblies that localize to specialised domains on plasma membrane and mark the site of endocytosis [1]. [1]. 20526336. A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking. Aguilar PS, Frohlich F, Rehman M, Shales M, Ulitsky I, Olivera-Couto A, Braberg H, Shamir R, Walter P, Mann M, Ejsing CS, Krogan NJ, Walther TC;. Nat Struct Mol Biol. 2010;17:901-908. (from Pfam) NF024250.5 PF12842.12 DUF3819 27 27 143 domain Y Y N DUF3819 domain-containing protein 11696541,24121232 0 EBI-EMBL CCR4-Not complex, Not1 subunit, domain of unknown function DUF3819 CCR4-Not complex, Not1 subunit, domain of unknown function DUF3819 This is an uncharacterised domain that is found on the CCR4-Not complex component Not1. Not1 is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID [1]. [1]. 11696541. Interaction between Not1p, a component of the Ccr4-not complex, a global regulator of transcription, and Dhh1p, a putative RNA helicase. Maillet L, Collart MA;. J Biol Chem 2002;277:2835-2842. [2]. 24121232. Structure and assembly of the NOT module of the human CCR4-NOT complex. Boland A, Chen Y, Raisch T, Jonas S, Kuzuoglu-Ozturk D, Wohlbold L, Weichenrieder O, Izaurralde E;. Nat Struct Mol Biol. 2013;20:1289-1297. (from Pfam) NF024283.5 PF12877.12 KIAA1549 24 24 676 PfamAutoEq Y Y N UPF0606 protein KIAA1549 18974108,19363522,19937730,30120214 0 EBI-EMBL UPF0606 protein KIAA1549 UPF0606 protein KIAA1549 This family contains KIAA1549 from human (Swiss:Q9HCM3) which has been implicated in pilocytic astrocytomas [1-3]. It has been found to be fused to BRAF gene in many cases of pilocytic astrocytomas. The fusion is due mainly to a tandem duplication of 2 Mb at 7q34 [1-2]. The BRAF protein is a well characterised oncoprotein. It is a serine/threonine protein kinase which is implicated in MAP/ERK signalling, a critical pathway for the regulation of cell division, differentiation and secretion [1-3]. More recently, KIAA1549 has been described to play a role in photoreceptor function [4]. [1]. 18974108. Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas. Jones DT, Kocialkowski S, Liu L, Pearson DM, Backlund LM, Ichimura K, Collins VP;. Cancer Res. 2008;68:8673-8677. [2]. 19363522. Oncogenic RAF1 rearrangement and a novel BRAF mutation as alternatives to KIAA1549:BRAF fusion in activating the MAPK pathway in pilocytic astrocytoma. Jones DT, Kocialkowski S, Liu L, Pearson DM, Ichimura K, Collins VP;. Oncogene. 2009;28:2119-2123. [3]. 19937730. MAPK pathway activation and the origins of pediatric low-grade astrocytomas. Tatevossian RG, Lawson AR, Forshew T, Hindley GF, Ellison DW, Sheer D;. J Cell Physiol. 2010;222:509-514. [4]. 30120214. Homozygous variants in KIAA1549, encoding a ciliary protein, are associated with autosomal recessive retinitis pigmentosa. de Bruijn SE, Verbakel SK, de Vrieze E, Kremer H, Cremers FPM, Hoyng CB, van den Born LI, Roosing S;. J Med Genet. 2018;55:705-712. (from Pfam) NF024357.5 PF12955.12 DUF3844 27 27 104 domain Y Y N DUF3844 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF3844) Domain of unknown function (DUF3844) This presumed domain is found in fungal species. It contains 8 largely conserved cysteine residues. This domain is found in proteins that are thought to be found in the endoplasmic reticulum. (from Pfam) NF024444.5 PF13044.11 Fusion_F0 25 25 436 domain Y Y N Isavirus-type fusion glycoprotein F0 16160182 0 EBI-EMBL Fusion glycoprotein F0, Isavirus fusion glycoprotein F0, Isavirus Fusion between viral and cellular membranes is mediated by viral membrane fusion glycoproteins. This entry represents fusion glycoprotein F0 from the infectious salmon anemia virus (ISAV). The precursor protein F0 is proteolytically cleaved to F1 and F2, which are held together by disulphide bridges [1]. [1]. 16160182. Characterization of the infectious salmon anemia virus fusion protein. Aspehaug V, Mikalsen AB, Snow M, Biering E, Villoing S;. J Virol. 2005;79:12544-12553. (from Pfam) NF024536.5 PF13136.11 DUF3984 22.1 22.1 330 domain Y Y N DUF3984 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF3984) Protein of unknown function (DUF3984) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 393 and 442 amino acids in length. (from Pfam) NF024563.5 PF13164.11 Diedel 21.3 21.3 76 domain Y Y N Diedel family protein 22442689,26739560 0 EBI-EMBL Diedel Diedel Diedel (die) was identified as an insect immune response protein. It is up-regulated after a septic injury and may act as a negative regulator of the JAK/STAT signalling pathway [1]. Its homologues can be found in Drosophila and Acyrtosiphon pisum. Interestingly, the orthologues of the die gene are present in the genome of insect DNA viruses of the Baculoviridae and Ascoviridae families. The viral homologues suppress the immune deficiency (IMD) pathway in Drosophila [2]. [1]. 22442689. Crystal structure of Diedel, a marker of the immune response of Drosophila melanogaster. Coste F, Kemp C, Bobezeau V, Hetru C, Kellenberger C, Imler JL, Roussel A;. PLoS One. 2012;7:e33416. [2]. 26739560. Cytokine Diedel and a viral homologue suppress the IMD pathway in Drosophila. Lamiable O, Kellenberger C, Kemp C, Troxler L, Pelte N, Boutros M, Marques JT, Daeffler L, Hoffmann JA, Roussel A, Imler JL;. Proc Natl Acad Sci U S A. 2016;113:698-703. (from Pfam) NF024648.5 PF13251.11 DUF4042 27 27 182 domain Y Y N DUF4042 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4042) Domain of unknown function (DUF4042) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 180 amino acids in length. (from Pfam) NF024651.5 PF13254.11 DUF4045 23.4 23.4 414 domain Y Y N DUF4045 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4045) Domain of unknown function (DUF4045) This presumed domain is functionally uncharacterised. This domain family is found in bacteria and eukaryotes, and is typically between 384 and 430 amino acids in length. (from Pfam) NF024654.5 PF13257.11 DUF4048 25 25 255 domain Y Y N DUF4048 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4048) Domain of unknown function (DUF4048) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 228 and 257 amino acids in length. (from Pfam) NF024667.5 PF13270.11 CCDC28 25.6 25.6 88 domain Y Y N coiled-coil domain-containing protein 23727834 0 EBI-EMBL Coiled-coil domain-containing protein 28 Coiled-coil domain-containing protein 28 This entry includes CCDC28A and CCDC28B. CCDC28B modulates mTORC2 complex assembly and function, possibly enhances AKT1 phosphorylation [1]. [1]. 23727834. The Bardet-Biedl syndrome-related protein CCDC28B modulates mTORC2 function and interacts with SIN1 to control cilia length independently of the mTOR complex. Cardenas-Rodriguez M, Irigoin F, Osborn DP, Gascue C, Katsanis N, Beales PL, Badano JL;. Hum Mol Genet. 2013;22:4031-4042. (from Pfam) NF024689.5 PF13293.11 DUF4074 22.3 22.3 63 domain Y Y N DUF4074 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4074) Domain of unknown function (DUF4074) This family is found at the C-terminal of Homeobox proteins in Metazoa. (from Pfam) NF024696.5 PF13300.11 DUF4078 25 25 86 domain Y Y N DUF4078 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4078) Domain of unknown function (DUF4078) This family is found from fungi to humans, but its exact function is not known. (from Pfam) NF024746.5 PF13352.11 DUF4100 27.9 27.9 232 domain Y Y N DUF4100 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF4100) Protein of unknown function (DUF4100) This is a family of uncharacterised proteins. Some members have an aspartic peptidase domain at the C-terminal (Pfam:PF13650). (from Pfam) NF024781.5 PF13389.11 DUF4107 27 27 167 domain Y Y N DUF4107 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF4107) Protein of unknown function (DUF4107) This family of putative proteins are found in Trichomonas vaginalis in large numbers. The function of this protein is unknown. (from Pfam) NF024814.5 PF13422.11 DUF4110 27 27 95 domain Y Y N DUF4110 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4110) Domain of unknown function (DUF4110) This is a family that is found predominantly at the C-terminus of Kelch-containing proteins. However, the exact function of this region is not known. (from Pfam) NF025148.5 PF13775.11 DUF4171 27 27 125 domain Y Y N DUF4171 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4171) Domain of unknown function (DUF4171) This short family is frequently found at the N-terminus of Homeobox proteins. (from Pfam) NF025191.5 PF13821.11 DUF4187 29 29 54 domain Y Y N DUF4187 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4187) Domain of unknown function (DUF4187) This family is found at the very C-terminus of proteins that carry a G-patch domain, Pfam:PF01585. The domain is short and cysteine-rich. (from Pfam) NF025206.5 PF13836.11 DUF4195 27 27 184 domain Y Y N DUF4195 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4195) Domain of unknown function (DUF4195) This family is found at the N-terminus of metazoan proteins that carry PHD-like zinc-finger domains. The function is not known. (from Pfam) NF025216.5 PF13846.11 DUF4196 25 25 112 domain Y Y N DUF4196 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4196) Domain of unknown function (DUF4196) This is a short region of ccdc82_homologues that is conserved from Schizo. pombe up to humans. The function is not known. (from Pfam) NF025267.5 PF13898.11 MINDY-3_4_CD 27 27 344 domain Y Y N deubiquitinating enzyme MINDY-3/4 domain-containing protein 27292798 0 EBI-EMBL Deubiquitinating enzyme MINDY-3/4, conserved domain Deubiquitinating enzyme MINDY-3/4, conserved domain Deubiquitinating enzymes (DUBs) remove ubiquitin (Ub) from Ub-conjugated substrates to regulate the functional outcome of ubiquitination. This entry includes MINDY-3/4. They belong to the MINDY (motif interacting with Ub-containing novel DUB) family (peptidase family C121), whose members are deubiquitinating enzymes releasing Lys48-linked ubiquitin [1]. This is a conserved domain found in deubiquitinating enzymes, MINDY-3 and MINDY-4. [1]. 27292798. MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes. Abdul Rehman SA, Kristariyanto YA, Choi SY, Nkosi PJ, Weidlich S, Labib K, Hofmann K, Kulathu Y;. Mol Cell. 2016;63:146-155. (from Pfam) NF025272.5 PF13904.11 CCDC34 35 35 169 domain Y Y N coiled-coil domain-containing protein 0 EBI-EMBL Coiled-coil domain-containing protein 34 Coiled-coil domain-containing protein 34 This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known. (from Pfam) NF025283.5 PF13915.11 DUF4210 21.2 21.2 73 domain Y Y N DUF4210 domain-containing protein 16169489 0 EBI-EMBL Domain of unknown function (DUF4210) Domain of unknown function (DUF4210) This short domain is found in fungi, plants and animals, and the proteins appear to be necessary for chromosome segregation during meiosis. [1]. 16169489. Novel genes required for meiotic chromosome segregation are identified by a high-throughput knockout screen in fission yeast. Gregan J, Rabitsch PK, Sakem B, Csutak O, Latypov V, Lehmann E, Kohli J, Nasmyth K;. Curr Biol. 2005;15:1663-1669. (from Pfam) NF025294.5 PF13926.11 DUF4211 27 27 137 domain Y Y N DUF4211 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4211) Domain of unknown function (DUF4211) NF025325.5 PF13959.11 DUF4217 27 27 52 domain Y Y N DUF4217 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4217) Domain of unknown function (DUF4217) This short domain is found at the C-terminus of many helicase proteins. (from Pfam) NF025375.5 PF14009.11 PADRE 29.6 29.6 184 domain Y Y N PADRE domain-containing protein 32547597 0 EBI-EMBL PADRE domain PADRE domain This entry represents the Pathogen and abiotic stress response, cadmium tolerance, disordered region-containing (PADRE) domain, which is specifically found in plants. PADRE typically occurs in small single-domain proteins with a bipartite architecture. PADRE contains conserved sequence motifs at the N-terminal, and its C-terminal includes an intrinsically disordered region with multiple phosphorylation sites. This domain is associated with plant defense upon diverse stress stimulus and has a role in disease resistance to fungi [1]. [1]. 32547597. Patterns of Sequence and Expression Diversification Associate Members of the PADRE Gene Family With Response to Fungal Pathogens. Didelon M, Khafif M, Godiard L, Barbacci A, Raffaele S;. Front Genet. 2020;11:491. (from Pfam) NF025648.5 PF14290.11 SDH5_plant 25 25 237 domain Y Y N succinate dehydrogenase subunit 5 GO:0006099,GO:0045273 15604729,30604579 0 EBI-EMBL Succinate dehydrogenase subunit 5, mitochondrial succinate dehydrogenase subunit 5 Complex II [succinate dehydrogenase (succinate-ubiquinone oxidoreductase); SDH] is the only enzyme shared by both the electron transport chain and the tricarboxylic acid (TCA) cycle in mitochondria. In plants, this complex is considered unusual because it has accessory subunits (SDH5-SDH8), in addition to the catalytic subunits of SDH found in all eukaryotes (SDH1- SDH4). This family represents the accessory complex II subunit Succinate dehydrogenase subunit 5 mitochondrial, from plants [1,2]. [1]. 15604729. Mitochondrial cytochrome c oxidase and succinate dehydrogenase complexes contain plant specific subunits. Millar AH, Eubel H, Jansch L, Kruft V, Heazlewood JL, Braun HP;. Plant Mol Biol. 2004;56:77-90. [2]. 30604579. Mitochondrial complex II of plants: subunit composition, assembly, and function in respiration and signaling. Huang S, Braun HP, Gawryluk RMR, Millar AH;. Plant J. 2019;98:405-417. (from Pfam) NF025649.5 PF14291.11 DUF4371 32.1 32.1 237 domain Y Y N DUF4371 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4371) Domain of unknown function (DUF4371) NF025667.5 PF14309.11 DUF4378 25.7 25.7 166 domain Y Y N DUF4378 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4378) Domain of unknown function (DUF4378) NF025926.5 PF14575.11 EphA2_TM 28.9 28.9 74 domain Y Y N ephrin type-A receptor 2 transmembrane domain-containing protein 20197042 0 EBI-EMBL Ephrin type-A receptor 2 transmembrane domain Ephrin type-A receptor 2 transmembrane domain Epha2_TM represents the left-handed dimer transmembrane domain of of EphA2 receptor. This domain oligomerises and is important for the active signalling process. [1]. 20197042. Left-handed dimer of EphA2 transmembrane domain: Helix packing diversity among receptor tyrosine kinases. Bocharov EV, Mayzel ML, Volynsky PE, Mineev KS, Tkach EN, Ermolyuk YS, Schulga AA, Efremov RG, Arseniev AS;. Biophys J. 2010;98:881-889. (from Pfam) NF025954.5 PF14603.11 hSH3 25.7 25.7 90 domain Y Y N SH3 domain-containing protein 15062083,20661443 0 EBI-EMBL Helically-extended SH3 domain helically-extended SH3 domain This domain is the 70 C-terminal residues of ADAP - Adhesion and de-granulation promoting adapter protein. It shows homology to SH3 domains; however, conserved residues of the fold are absent. It thus represents an altered SH3 domain fold. An N-terminal, amphipathic, helix makes extensive contacts to residues of the regular SH3 domain fold thereby creating a composite surface with unusual surface properties. The domain can no longer bind conventional proline-rich peptides [1]. There are key phosphorylation sites within the two hSH3 domains and it would appear that binding at these sites does not materially affect the folding of these regions although the equilibrium towards the unfolded state may be slightly altered [2]. The binding partners of the hSH3 domains are still unknown [2]. [1]. 15062083. Structure of a helically extended SH3 domain of the T cell adapter protein ADAP. Heuer K, Kofler M, Langdon G, Thiemke K, Freund C;. Structure. 2004;12:603-610. [2]. 20661443. Adhesion and degranulation promoting adapter protein (ADAP) is a central hub for phosphotyrosine-mediated interactions in T cells. Sylvester M, Kliche S, Lange S, Geithner S, Klemm C, Schlosser A, Grossmann A, Stelzl U, Schraven B, Krause E, Freund C;. PLoS One. 2010;5:e11708. (from Pfam) NF025961.5 PF14610.11 Psg1 30.1 30.1 186 domain Y Y N Psg1 family protein 28727280 0 EBI-EMBL Ykl077w/Psg1 (Pma1 Stabilization in Golgi) Psg1 family protein Ykl077w/Psg1 (Pma1 Stabilization in the Golgi) physically interacts with Exp1 (for ER eXport of Pma1). Psg1 can be found in the Golgi and coat protein I (COPI) vesicles but does not directly bind Pma1. Loss of Psg1 causes enhanced degradation of Pma1 in the vacuole. Psg1 is 392aa protein with a predicted signal sequence at its N-terminus and a single TMD near the C-terminus. The short cytosolic region bears 2 putative retrieval motifs KRR and KKxxKxx. It was previously shown to be cleaved by the Ca+ dependent serine protease, Kex2 [1]. [1]. 28727280. Two novel effectors of trafficking and maturation of the yeast plasma membrane H(+) -ATPase. Geva Y, Crissman J, Arakel EC, Gomez-Navarro N, Chuartzman SG, Stahmer KR, Schwappach B, Miller EA, Schuldiner M;. Traffic. 2017;18:672-682. (from Pfam) NF025964.5 PF14613.11 DUF4449 27 27 162 domain Y Y N DUF4449 domain-containing protein 20473289,25411845 0 EBI-EMBL Protein of unknown function (DUF4449) Protein of unknown function (DUF4449) This is a fungal DUF of unknown function [1]. A member of this family (Swiss:Q7SB48) designated HAM-13 is thought to associate with MAPKs and to be required for proper cell communication but it is also possible to be involved in other processes such as cell signalling or trafficking [2]. [1]. 20473289. Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe. Kim DU, Hayles J, Kim D, Wood V, Park HO, Won M, Yoo HS, Duhig T, Nam M, Palmer G, Han S, Jeffery L, Baek ST, Lee H, Shim YS, Lee M, Kim L, Heo KS, Noh EJ, Lee AR, Jang YJ, Chung KS, Choi SJ, Park JY, Park Y, Kim HM, Park SK, Park HJ, Kang EJ, Kim HB, Kang HS, Park HM, Kim K, Song K, Song KB, Nurse P, Hoe KL;. Nat Biotechnol. 2010;28:617-623. [2]. 25411845. Fungal communication requires the MAK-2 pathway elements STE-20 and RAS-2, the NRC-1 adapter STE-50 and the MAP kinase scaffold HAM-5. Dettmann A, Heilig Y, Valerius O, Ludwig S, Seiler S;. PLoS Genet. 2014;10:e1004762. (from Pfam) NF025967.5 PF14616.11 Rua1_C 27 27 122 domain Y Y N transcription regulator Rua1 domain-containing protein 11376151,17850255,20173069 0 EBI-EMBL Transcription regulator Rua1, C-terminal Transcription regulator Rua1, C-terminal This entry represents a domain that can be found at the C terminus f fungal proteins such as meiotic expression up-regulated protein 26 from Schizosaccharomyces pombe [1], Ecm8 from Saccharomyces cerevisiae and Rua1 from Ustilago maydis. Rua1 is a transcription factor and part of the gene cluster that mediates the biosynthesis of the glycolipid biosurfactant ustilagic acid (UA) [2,3]. [1]. 11376151. Comprehensive isolation of meiosis-specific genes identifies novel proteins and unusual non-coding transcripts in Schizosaccharomyces pombe. Watanabe T, Miyashita K, Saito TT, Yoneki T, Kakihara Y, Nabeshima K, Kishi YA, Shimoda C, Nojima H;. Nucleic Acids Res. 2001;29:2327-2337. [2]. 17850255. A biosynthetic gene cluster for a secreted cellobiose lipid with antifungal activity from Ustilago maydis. Teichmann B, Linne U, Hewald S, Marahiel MA, Bolker M;. Mol Microbiol. 2007;66:525-533. [3]. 20173069. Activation of the ustilagic acid biosynthesis gene cluster in Ustilago maydis by the C2H2 zinc finger transcription factor Rua1. Teichmann B, Liu L, Schink KO, Bolker M;. Appl Environ Microbiol. 2010;76:2633-2640. (from Pfam) NF025983.5 PF14632.11 SPT6_acidic 24.4 24.4 87 domain Y Y N SPT6 acidic N-terminal domain-containing protein 21094070,21844224,2201908 0 EBI-EMBL Acidic N-terminal SPT6 Acidic N-terminal SPT6 The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a transcription regulator, but the exact function of this acidic region is not certain. [1]. 21094070. Structure and biological importance of the Spn1-Spt6 interaction, and its regulatory role in nucleosome binding. McDonald SM, Close D, Xin H, Formosa T, Hill CP;. Mol Cell. 2010;40:725-735. [2]. 21844224. Spt6 is required for heterochromatic silencing in the fission yeast Schizosaccharomyces pombe. Kiely CM, Marguerat S, Garcia JF, Madhani HD, Bahler J, Winston F;. Mol Cell Biol. 2011;31:4193-4204. [3]. 2201908. SPT6, an essential gene that affects transcription in Saccharomyces cerevisiae, encodes a nuclear protein with an extremely acidic amino terminus. Swanson MS, Carlson M, Winston F;. Mol Cell Biol. 1990;10:4935-4941. (from Pfam) NF025995.5 PF14644.11 DUF4456 27.5 27.5 210 domain Y Y N DUF4456 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4456) Domain of unknown function (DUF4456) This domain family is found in bacteria and eukaryotes, and is approximately 210 amino acids in length. There is a single completely conserved residue E that may be functionally important. (from Pfam) NF026043.5 PF14692.11 DUF4462 25 25 28 domain Y Y N DUF4462 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4462) Domain of unknown function (DUF4462) This domain family is found in eukaryotes, and is approximately 30 amino acids in length. (from Pfam) NF026063.5 PF14713.11 DUF4464 27 27 230 domain Y Y N DUF4464 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4464) Domain of unknown function (DUF4464) This family of proteins is found in eukaryotes. Proteins in this family are typically between 224 and 241 amino acids in length. There is a conserved YID sequence motif. (from Pfam) NF026087.5 PF14737.11 DUF4470 25 25 97 domain Y Y N DUF4470 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4470) Domain of unknown function (DUF4470) This family is conserved from fungi to Metazoa and includes plants. The function is not known, but several members have zinc-finger domain, zf-MYND, Pfam:PF01753, at their very C-terminus. Others are also associated with DUF1279, Pfam:PF06916. (from Pfam) NF026090.5 PF14740.11 DUF4471 25 25 303 domain Y Y N DUF4471 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4471) Domain of unknown function (DUF4471) This family is conserved from fungi to Metazoa and includes plants. The function is not known, but several members have zinc-finger domain, zf-MYND, Pfam:PF01753, at their very C-terminus. Others are also associated with DUF1279, Pfam:PF06916. This domain is more C-terminal in many members to DUF4470, Pfam:PF14737. (from Pfam) NF026103.5 PF14753.11 FAM221 25 25 196 domain Y Y N FAM221A/B family protein 0 EBI-EMBL Protein FAM221A/B protein FAM221A/B This family of proteins is found in eukaryotes. Proteins in this family are typically between 99 and 305 amino acids in length. (from Pfam) NF026130.5 PF14780.11 NEPRO_N 24.9 24.9 185 domain Y Y N NEPRO protein domain-containing protein 19906856,26178919,31250547 0 EBI-EMBL Nucleolus and neural progenitor protein, N-terminal Nucleolus and neural progenitor protein, N-terminal This domain is found at the N-terminal of nucleolus and neural progenitor protein (NEPRO) which may play a role in cortex development as part of the Notch signalling pathway. Downstream of Notch may repress the expression of proneural genes and inhibit neuronal differentiation thereby maintaining neural progenitors [1]. NEPRO may also play a role in preimplentation embryo development [2]. NEPRO interacts with multiple protein subunits of RMRP and is implicated in Anauxetic dysplasia 3 [3]. NEPRO is likely the human orthologue of RMP1 subunit from yeast and they share a four-helix bundle domain structure. [1]. 19906856. Identification of Nepro, a gene required for the maintenance of neocortex neural progenitor cells downstream of Notch. Muroyama Y, Saito T;. Development. 2009;136:3889-3893. [2]. 26178919. Nepro is localized in the nucleolus and essential for preimplantation development in mice. Hashimoto M, Sato T, Muroyama Y, Fujimura L, Hatano M, Saito T;. Dev Growth Differ. 2015;57:529-538. [3]. 31250547. An emerging ribosomopathy affecting the skeleton due to biallelic variations in NEPRO. Narayanan DL, Shukla A, Kausthubham N, Bhavani GS, Shah H, Mortier G, Girisha KM;. Am J Med Genet A. 2019;179:1709-1717. (from Pfam) NF026150.5 PF14800.11 DUF4481 25 25 293 domain Y Y N DUF4481 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4481) Domain of unknown function (DUF4481) NF026168.5 PF14818.11 SOGA1-2-like_CC 26.6 26.6 54 domain Y Y N coiled-coil domain-containing protein 20813965,33587225 0 EBI-EMBL SOGA 1/2-like, coiled-coil SOGA 1/2-like, coiled-coil This entry represents a coiled-coil region found in microtubule cross-linking factors 1 and 2 (also known as SOGA1/2), which are members of the SOGA (suppressor of glucose by autophagy) family and in the uncharacterised human protein KIAA0408. SOGA1 regulates autophagy by playing a role in the reduction of glucose production in an adiponectin- and insulin-dependent manner [1]. SOGA1/2 are required for faithful chromosome segregation during mitosis [2]. These proteins contain long coiled-coils that dimerize and holds two N-terminal domains that bind to microtubules [2]. This region is found in association with Pfam:PF11365. [1]. 20813965. Adiponectin lowers glucose production by increasing SOGA. Cowherd RB, Asmar MM, Alderman JM, Alderman EA, Garland AL, Busby WH, Bodnar WM, Rusyn I, Medoff BD, Tisch R, Mayer-Davis E, Swenberg JA, Zeisel SH, Combs TP;. Am J Pathol. 2010;177:1936-1945. [2]. 33587225. SOGA1 and SOGA2/MTCL1 are CLASP-interacting proteins required for faithful chromosome segregation in human cells. Ferreira LT, Logarinho E, Macedo JC, Maia ARR, Maiato H;. Chromosome Res. 2021;29:159-173. (from Pfam) NF026175.5 PF14825.11 CFAP77 24 24 157 domain Y Y N CFAP77 family protein 15998802 0 EBI-EMBL Cilia- and flagella-associated protein 77 CFAP77 family protein This family of proteins is found in flagella [1]. Proteins in this family are typically between 203 and 326 amino acids in length. There is a single completely conserved residue N that may be functionally important. [1]. 15998802. Proteomic analysis of a eukaryotic cilium. Pazour GJ, Agrin N, Leszyk J, Witman GB;. J Cell Biol. 2005;170:103-113. (from Pfam) NF026181.5 PF14831.11 DUF4484 25.6 25.6 184 domain Y Y N DUF4484 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4484) Domain of unknown function (DUF4484) This domain is found, in a few members, a the the C-terminus of family Avl9, Pfam:PF09794. The function is not known. (from Pfam) NF026196.5 PF14846.11 DUF4485 24 24 83 domain Y Y N DUF4485 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4485) Domain of unknown function (DUF4485) This family is found in eukaryotes, and is approximately 90 amino acids in length. (from Pfam) NF026208.5 PF14858.11 CFAP54_N 27 27 540 domain Y Y N CFAP54 family protein 26224312 0 EBI-EMBL Cilia- and flagella-associated protein 54 CFAP54 family protein This domain family is found in eukaryotes, and is typically between 542 and 565 amino acids in length. This entry represents the N-terminal region of the cilia- and flagella-associated protein 54 which is required for assembly and function of cilia and flagella. [1]. 26224312. CFAP54 is required for proper ciliary motility and assembly of the central pair apparatus in mice. McKenzie CW, Craige B, Kroeger TV, Finn R, Wyatt TA, Sisson JH, Pavlik JA, Strittmatter L, Hendricks GM, Witman GB, Lee L;. Mol Biol Cell. 2015;26:3140-3149. (from Pfam) NF026242.5 PF14892.11 PIRC1_2 27 27 103 domain Y Y N microtubule wall 1/2 piercer family protein GO:0005879,GO:0035082 21159655,34715025 0 EBI-EMBL Piercer of microtubule wall 1/2 microtubule wall 1/2 piercer family protein This family of proteins is found in eukaryotes and includes Piercer of microtubule wall 1/2 proteins (PIRC1/2). In mice PIRC1 expression is induced by p53 may play a role in DNA damage response and has been shown to function at the initial step of left-right asymmetry specification of the visceral organs [1]. PIRC1/2 are microtubule inner proteins involved in the attachment of outer dynein arms (ODAs) to dynein-decorated doublet microtubules (DMTs) in cilia axoneme [2]. [1]. 21159655. Pierce1, a novel p53 target gene contributing to the ultraviolet-induced DNA damage response. Sung YH, Kim HJ, Devkota S, Roh J, Lee J, Rhee K, Bahk YY, Lee HW;. Cancer Res. 2010;70:10454-10463. [2]. 34715025. De novo identification of mammalian ciliary motility proteins using cryo-EM. Gui M, Farley H, Anujan P, Anderson JR, Maxwell DW, Whitchurch JB, Botsch JJ, Qiu T, Meleppattu S, Singh SK, Zhang Q, Thompson J, Lucas JS, Bingle CD, Norris DP, Roy S, Brown A;. Cell. 2021;184:5791-5806. (from Pfam) NF026256.5 PF14906.11 DUF4495 25 25 319 domain Y Y N DUF4495 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4495) Domain of unknown function (DUF4495) This domain family is found in eukaryotes, and is typically between 322 and 336 amino acids in length. There are two conserved sequence motifs: QMW and DLW. Proteins in this family vary in length from 793 to 1184 amino acids. (from Pfam) NF026274.5 PF14924.11 MAP10_N 21.5 21.5 144 domain Y Y N MAP10 domain-containing protein 23264731 0 EBI-EMBL Microtubule associated protein 10, N-terminal domain Microtubule associated protein 10, N-terminal domain This domain is found at the N-terminal of MAP10 (Microtubule associated protein 10, also known as MTR120/KIAA1383) from mammals. There are two completely conserved G residues that may be functionally important. It adopts a C2-like fold. MAP10 localises to stabilised MTs during interphase and to the mitotic apparatus during mitosis. It may promote microtubule stability and ensures normal progress of cytokinesis [1]. [1]. 23264731. MTR120/KIAA1383, a novel microtubule-associated protein, promotes microtubule stability and ensures cytokinesis. Fong KW, Leung JW, Li Y, Wang W, Feng L, Ma W, Liu D, Songyang Z, Chen J;. J Cell Sci. 2013;126:825-837. (from Pfam) NF026276.5 PF14926.11 CFAP300 27 27 246 domain Y Y N CFAP300 family protein 29727692,29727693 0 EBI-EMBL Cilia- and flagella-associated protein 300 CFAP300 family protein CFAP300 is a cilia- and flagella-associated protein that is essential for assembly of dynein arms. Mutations in the CFAP300 gene (C11orf70) cause defective cilia motility and primary ciliary dyskinesia [1,2]. [1]. 29727692. C11orf70 Mutations Disrupting the Intraflagellar Transport-Dependent Assembly of Multiple Axonemal Dyneins Cause Primary Ciliary Dyskinesia. Fassad MR, Shoemark A, le Borgne P, Koll F, Patel M, Dixon M, Hayward J, Richardson C, Frost E, Jenkins L, Cullup T, Chung EMK, Lemullois M, Aubusson-Fleury A, Hogg C, Mitchell DR, Tassin AM, Mitchison HM;. Am J Hum Genet. 2018;102:956-972. [2]. 29727693. Mutations in C11orf70 Cause Primary Ciliary Dyskinesia with Randomization of Left/Right Body Asymmetry Due to Defects of Outer and Inner Dynein Arms. Hoben IM, Hjeij R, Olbrich H, Dougherty GW, Nothe-Menchen T, Aprea I, Frank D, Pennekamp P, Dworniczak B, Wallmeier J, Raidt J, Nielsen KG, Philipsen MC, Santamaria F, Venditto L, Amirav I, Mussaffi H, Prenzel F, Wu K, Bakey Z, Schmidts M, Loges NT, Omran H;. Am J Hum Genet. 2018;102:973-984. (from Pfam) NF026287.5 PF14937.11 DUF4500 27 27 81 domain Y Y N DUF4500 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4500) Domain of unknown function (DUF4500) This family is found in eukaryotes. The function of this protein remains unknown. The gene which encodes for this protein is named chromosome 6 open reading frame 162 (C6orf162) and is found between the chromosomal positions 6q15-q16.1. It is thought that this protein may be an important part of membrane function. (from Pfam) NF026296.5 PF14946.11 DUF4501 29.6 29.6 179 domain Y Y N DUF4501 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4501) Domain of unknown function (DUF4501) This family of proteins is found in eukaryotes. Proteins in this family are typically between 167 and 308 amino acids in length. The exact function of this protein remains unknown, but it is thought to be a single-pass membrane protein. This family contains many highly conserved cysteine residues. (from Pfam) NF026300.5 PF14950.11 DUF4502 27 27 376 domain Y Y N DUF4502 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4502) Domain of unknown function (DUF4502) This family of proteins is found in eukaryotes. Proteins in this family are typically between 181 and 876 amino acids in length. (from Pfam) NF026301.5 PF14951.11 DUF4503 27 27 392 domain Y Y N DUF4503 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4503) Domain of unknown function (DUF4503) This family of proteins is found in eukaryotes. Proteins in this family are typically between 313 and 876 amino acids in length. (from Pfam) NF026303.5 PF14953.11 DUF4504 25 25 255 domain Y Y N DUF4504 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4504) Domain of unknown function (DUF4504) This family of proteins is found in eukaryotes. Proteins in this family are typically between 253 and 329 amino acids in length. There are two conserved sequence motifs: LLGYP and SFS. (from Pfam) NF026308.5 PF14958.11 PAAT-like 27 27 141 domain Y Y N PAAT domain-containing protein 25063848 0 EBI-EMBL ATPase PAAT-like ATPase PAAT-like This family is found in eukaryotes. It represents the ATPase protein associated with ABC transporters (PAAT) and related proteins. PAAT is formed of a nucleotide-binding domain (NBD)-like domain and a signal for intramitochondrial sorting. PAAT interacts with the mitochondrial inner membrane ABC proteins: ABCB7, ABCB8 and ABCB10. It is involved in maintenance of mitochondrial homeostasis and cell survival [1]. [1]. 25063848. PAAT, a novel ATPase and trans-regulator of mitochondrial ABC transporters, is critically involved in the maintenance of mitochondrial homeostasis. Yang X, Yang J, Li L, Sun L, Yi X, Han X, Si W, Yan R, Chen Z, Xie G, Li W, Shang Y, Liang J;. FASEB J. 2014;28:4821-4834. (from Pfam) NF026314.5 PF14964.11 INTS15 27 27 362 domain Y Y N integrator complex subunit 15 33973408 0 EBI-EMBL Integrator complex subunit 15 integrator complex subunit 15 Integrator complex subunit 15 (C7orf26) is likely a component of the Integrator (INT) complex, which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing [1]. [1]. 33973408. hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies. Drew K, Wallingford JB, Marcotte EM;. Mol Syst Biol. 2021;17:e10016. (from Pfam) NF026319.5 PF14969.11 DUF4508 27 27 97 domain Y Y N DUF4508 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4508) Domain of unknown function (DUF4508) This family of proteins is found in eukaryotes. Proteins in this family are typically between 117 and 253 amino acids in length. (from Pfam) NF026320.5 PF14970.11 TEDC1 27.4 27.4 169 domain Y Y N TEDC1 domain-containing protein 28796488,29459677 0 EBI-EMBL Tubulin epsilon and delta complex protein 1 Tubulin epsilon and delta complex protein 1 This family represents the tubulin epsilon and delta complex protein 1 (TEDC1). This complex is required for centriole maintenance and it is a component of several ciliary structures. It acts as a positive regulator of hedgehog signalling, which play key roles in embryonic development and in cancers [1]. Additionally, this protein may play a role in counteracting perturbation of actin filaments, such as after treatment with the actin depolymerising microbial metabolite Chivosazole F [2]. [1]. 29459677. A CRISPR-based screen for Hedgehog signaling provides insights into ciliary function and ciliopathies. Breslow DK, Hoogendoorn S, Kopp AR, Morgens DW, Vu BK, Kennedy MC, Han K, Li A, Hess GT, Bassik MC, Chen JK, Nachury MV;. Nat Genet. 2018;50:460-471. [2]. 28796488. Direct Interaction of Chivosazole F with Actin Elicits Cell Responses Similar to Latrunculin A but Distinct from Chondramide. Filipuzzi I, Thomas JR, Pries V, Estoppey D, Salcius M, Studer C, Schirle M, Hoepfner D;. ACS Chem Biol. 2017;12:2264-2269. (from Pfam) NF026325.5 PF14975.11 DUF4512 27 27 103 domain Y Y N DUF4512 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4512) Domain of unknown function (DUF4512) This family of proteins is found in eukaryotes. Proteins in this family are typically between 74 and 104 amino acids in length. There are two completely conserved residues (C and P) that may be functionally important. (from Pfam) NF026333.5 PF14983.11 SPMIP10-like 27 27 138 domain Y Y N microtubule inner protein 10 family protein 37327785 0 EBI-EMBL Sperm-associated microtubule inner protein 10 microtubule inner protein 10 family protein This family (previously DUF4513) represents homologs of Sperm-associated microtubule inner protein 10 (SPMIP10). SPMIP10 is a microtubule inner protein (MIP) part of the axonemal dynein-decorated doublet microtubules (DMTs). It plays a role in the stabilisation of the interacting protomers of TEKTL1 - a tektin-like molecule that forms a filament in the cleft between protofilaments A11 and A12 . In the EM structure of sperm DMTs, SPMIP10 cradles the inter-TEKTL1 interface while interacting with protofilaments A11 and A12 [1]. [1]. 37327785. Structural specializations of the sperm tail. Leung MR, Zeng J, Wang X, Roelofs MC, Huang W, Zenezini Chiozzi R, Hevler JF, Heck AJR, Dutcher SK, Brown A, Zhang R, Zeev-Ben-Mordehai T;. Cell. 2023;186:2880-2896. (from Pfam) NF026336.5 PF14986.11 DUF4514 27 27 60 domain Y Y N DUF4514 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4514) Domain of unknown function (DUF4514) This family of uncharacterised proteins are found in mammals. (from Pfam) NF026340.5 PF14990.11 DUF4516 27 27 46 domain Y Y N DUF4516 domain-containing protein GO:0034551 0 EBI-EMBL Domain of unknown function (DUF4516) Domain of unknown function (DUF4516) This family of proteins is found in eukaryotes. Proteins in this family are typically between 56 and 69 amino acids in length. (from Pfam) NF026356.5 PF15006.11 DUF4517 27 27 151 domain Y Y N DUF4517 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4517) Domain of unknown function (DUF4517) The function of this protein remains unknown. This family of proteins is found in eukaryotes and are typically between 160 and 182 amino acids in length. (from Pfam) NF026358.5 PF15008.11 DUF4518 27 27 271 domain Y Y N DUF4518 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4518) Domain of unknown function (DUF4518) The precise function of this protein family is unknown but it is thought to be involved in apoptosis regulation. (from Pfam) NF026366.5 PF15016.11 DUF4520 27 27 82 domain Y Y N DUF4520 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4520) Domain of unknown function (DUF4520) This family of proteins is found in eukaryotes. Proteins in this family are typically between 197 and 638 amino acids in length.This is the C-terminal domain of the member proteins. (from Pfam) NF026371.5 PF15021.11 SHLD1_C 27 27 120 domain Y Y N RINN3 domain-containing protein GO:2001032 29656893,30046110 0 EBI-EMBL Shieldin complex subunit 1, C-terminal domain Shieldin complex subunit 1, C-terminal domain SHLD1, also known as RINN3, is a component of the shieldin complex, a vertebrate-specific protein complex which functions as a downstream effector in the 53BP1 pathway, regulates NHEJ (non-homologous end joining) [1,2]. This entry represents a conserved helical domain found at the C-terminal of SHLD1. [1]. 29656893. DNA Repair Network Analysis Reveals Shieldin as a Key Regulator of NHEJ and PARP Inhibitor Sensitivity. Gupta R, Somyajit K, Narita T, Maskey E, Stanlie A, Kremer M, Typas D, Lammers M, Mailand N, Nussenzweig A, Lukas J, Choudhary C;. Cell. 2018;173:972-988. [2]. 30046110. 53BP1 cooperation with the REV7-shieldin complex underpins DNA structure-specific NHEJ. Ghezraoui H, Oliveira C, Becker JR, Bilham K, Moralli D, Anzilotti C, Fischer R, Deobagkar-Lele M, Sanchiz-Calvo M, Fueyo-Marcos E, Bonham S, Kessler BM, Rottenberg S, Cornall RJ, Green CM, Chapman JR;. Nature. 2018;560:122-127. (from Pfam) NF026372.5 PF15022.11 DUF4522 27 27 117 domain Y Y N DUF4522 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF4522) Protein of unknown function (DUF4522) This family of proteins is functionally uncharacterised. This family of proteins is found in mammals. In human this protein is known as C4orf36. (from Pfam) NF026373.5 PF15023.11 DUF4523 27 27 166 domain Y Y N DUF4523 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF4523) Protein of unknown function (DUF4523) This family of proteins is functionally uncharacterised. This family of proteins is found in mammals. (from Pfam) NF026375.5 PF15025.11 DUF4524_N 27 27 70 domain Y Y N DUF4524 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4524), N-terminal domain Domain of unknown function (DUF4524), N-terminal domain This entry represents a POLO box-like domain found in DUF4524 proteins. This family of proteins is found in eukaryotes. Proteins in this family are typically between 197 and 638 amino acids in length. This is the N-terminal domain of the member proteins. The human gene is from C5orf34. (from Pfam) NF026376.5 PF15027.11 DUF4525 27 27 137 domain Y Y N DUF4525 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4525) Domain of unknown function (DUF4525) This domain is found in eukaryotes. It is often found at the N-terminus of glycosyltransferase family 18 enzymes (Pfam:PF15024). It is also found in coiled-coil domain-containing protein 126. (from Pfam) NF026380.5 PF15031.11 DUF4528 27 27 126 domain Y Y N DUF4528 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4528) Domain of unknown function (DUF4528) This family of proteins is found in eukaryotes. Proteins in this family are typically between 95 and 154 amino acids in length. This family includes Human C15orf61. (from Pfam) NF026381.5 PF15032.11 DUF4529 27 27 406 domain Y Y N DUF4529 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF4529) Protein of unknown function (DUF4529) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. The proteins contain a conserved VLPPLK sequence motif. (from Pfam) NF026388.5 PF15039.11 DUF4530 28.1 28.1 113 domain Y Y N DUF4530 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4530) Domain of unknown function (DUF4530) This family of proteins is found in eukaryotes. Proteins in this family are typically around 140 amino acids in length. The human member of this family is C19orf69. (from Pfam) NF026390.5 PF15041.11 TKTI1 27 27 183 domain Y Y N tektin bundle interacting protein 1 family protein 34715025 0 EBI-EMBL Tektin bundle interacting protein 1 tektin bundle interacting protein 1 family protein This family includes Tektin bundle interacting protein 1 (TKTI1) which has been recently characterised as a microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating. It is located at the center of the tektin bundle where may function to recruit tektins or stabilize the bundle [1]. [1]. 34715025. De novo identification of mammalian ciliary motility proteins using cryo-EM. Gui M, Farley H, Anujan P, Anderson JR, Maxwell DW, Whitchurch JB, Botsch JJ, Qiu T, Meleppattu S, Singh SK, Zhang Q, Thompson J, Lucas JS, Bingle CD, Norris DP, Roy S, Brown A;. Cell. 2021;184:5791-5806. (from Pfam) NF026395.5 PF15046.11 DUF4532 27 27 279 domain Y Y N DUF4532 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF4532) Protein of unknown function (DUF4532) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. (from Pfam) NF026396.5 PF15047.11 DUF4533 28.6 28.6 225 domain Y Y N DUF4533 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF4533) Protein of unknown function (DUF4533) This family of proteins is functionally uncharacterised. This family of proteins is found in mammals. This family includes two human proteins: C12orf60 and C12orf69. (from Pfam) NF026398.5 PF15049.11 DUF4534 29.2 29.2 163 domain Y Y N DUF4534 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF4534) Protein of unknown function (DUF4534) This family of proteins is functionally uncharacterised. This family of proteins is found in mammals. Proteins in this family are typically between 170 and 190 amino acids in length. The protein includes the human integral membrane TMEM217 protein. (from Pfam) NF026403.5 PF15054.11 DUF4535 28.3 28.3 45 domain Y Y N DUF4535 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4535) Domain of unknown function (DUF4535) This family includes the uncharacterised protein C7orf73 that is found in eukaryotes. Members are generally less than 100 residues in length. Although the precise function of the domain is still unknown, members have a predicted N-terminal signal peptide sequence which suggests they are short secreted peptides. (from Pfam) NF026404.5 PF15055.11 DUF4536 27 27 47 domain Y Y N DUF4536 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4536) Domain of unknown function (DUF4536) This domain family is thought to be a transmembrane helix. It is found in eukaryotes, and is approximately 50 amino acids in length. In humans, it is located in the chromosomal position, C9orf123. The family contains the uncharacterised Sch. pombe protein TAM6 which is found in the mitochondrion. (from Pfam) NF026410.5 PF15061.11 DUF4538 27 27 57 domain Y Y N DUF4538 domain-containing protein GO:0016020,GO:0033617 0 EBI-EMBL Domain of unknown function (DUF4538) Domain of unknown function (DUF4538) This protein family is thought to be a transmembrane helix. Its function remains unknown. This family of proteins is found in eukaryotes. Proteins in this family are typically between 58 and 87 amino acids in length. (from Pfam) NF026421.5 PF15072.11 HROB 30.8 30.8 85 domain Y Y N OB-fold domain-containing protein GO:0000725 31467087,31575675 0 EBI-EMBL Homologous recombination OB-fold protein Homologous recombination OB-fold protein This family represents Homologous recombination OB-fold protein (HROB). During homologous recombination, HROB acts by recruiting the MCM8-MCM9 helicase complex to sites of DNA damage to promote DNA repair synthesis [1,2]. [1]. 31467087. Control of homologous recombination by the HROB-MCM8-MCM9 pathway. Hustedt N, Saito Y, Zimmermann M, Alvarez-Quilon A, Setiaputra D, Adam S, McEwan A, Yuan JY, Olivieri M, Zhao Y, Kanemaki MT, Jurisicova A, Durocher D;. Genes Dev. 2019;33:1397-1415. [2]. 31575675. Ways to unwind with HROB, a new player in homologous recombination. Saredi G, Rouse J;. Genes Dev. 2019;33:1293-1294. (from Pfam) NF026423.5 PF15074.11 CFAP90 32.6 32.6 92 domain Y Y N CFAP90 domain-containing protein 36191189,37327785 0 EBI-EMBL Cilia and flagella associated protein 90 Cilia and flagella associated protein 90 This family represents the homologues of Cilia and flagella associated protein 90 (CFAP90, also known as C5orf49). CFAP90 is a microtubule inner protein (MIP) part of the doublet microtubules (DMTs) in cilia and sperm axoneme [1,2]. It belongs to the core-MIPs and binds to protofilament B09 in the sperm DMTs. Members of this family contain a conserved KLHRDDR sequence motif. [1]. 36191189. SPACA9 is a lumenal protein of human ciliary singlet and doublet microtubules. Gui M, Croft JT, Zabeo D, Acharya V, Kollman JM, Burgoyne T, Hoog JL, Brown A;. Proc Natl Acad Sci U S A. 2022;119:e2207605119. [2]. 37327785. Structural specializations of the sperm tail. Leung MR, Zeng J, Wang X, Roelofs MC, Huang W, Zenezini Chiozzi R, Hevler JF, Heck AJR, Dutcher SK, Brown A, Zhang R, Zeev-Ben-Mordehai T;. Cell. 2023;186:2880-2896. (from Pfam) NF026424.5 PF15075.11 SPMAP1-like 27 27 134 domain Y Y N SPMAP1 domain-containing protein 37327785 0 EBI-EMBL Sperm microtubule associated protein 1 Sperm microtubule associated protein 1 This family (previously DUF4542) represents the homologs of Sperm microtubule associated protein 1 (SPMAP1 also known as C17orf98). These proteins contain a conserved IPPYN sequence motif. The EM structure of sperm DMTs shows that SPMAP1 interacts directly with the tubulin lattice at the A-tubule seam (between protofilaments A09/A10) where outer dense fibers (ODFs) are connected to dynein-decorated doublet microtubules (DMTs) [1]. [1]. 37327785. Structural specializations of the sperm tail. Leung MR, Zeng J, Wang X, Roelofs MC, Huang W, Zenezini Chiozzi R, Hevler JF, Heck AJR, Dutcher SK, Brown A, Zhang R, Zeev-Ben-Mordehai T;. Cell. 2023;186:2880-2896. (from Pfam) NF026425.5 PF15076.11 DUF4543 27 27 74 domain Y Y N DUF4543 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4543) Domain of unknown function (DUF4543) This family of proteins is found in eukaryotes. Proteins in this family are typically between and 90 amino acids in length. The human member of this family is C17orf67. (from Pfam) NF026426.5 PF15077.11 MAJIN 27 27 238 domain Y Y N membrane-anchored junction protein GO:0003677 26548954 0 EBI-EMBL Membrane-anchored junction protein membrane-anchored junction protein Membrane-anchored junction protein (MAJIN) is a meiosis-specific telomere-associated protein involved in meiotic telomere attachment to the nucleus inner membrane, a crucial step for homologous pairing and synapsis. It is a component of the MAJIN-TERB1-TERB2 complex, which promotes telomere cap exchange by mediating attachment of telomeric DNA to the inner nuclear membrane and replacement of the protective cap of telomeric chromosomes [1]. [1]. 26548954. MAJIN Links Telomeric DNA to the Nuclear Membrane by Exchanging Telomere Cap. Shibuya H, Hernandez-Hernandez A, Morimoto A, Negishi L, Hoog C, Watanabe Y;. Cell. 2015;163:1252-1266. (from Pfam) NF026427.5 PF15078.11 DUF4545 27 27 465 domain Y Y N DUF4545 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4545) Domain of unknown function (DUF4545) This family of proteins is found in eukaryotes. Proteins in this family are typically between and 417 amino acids in length. The human member of this family is C1orf141. (from Pfam) NF026429.5 PF15080.11 DUF4547 27 27 196 domain Y Y N DUF4547 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4547) Domain of unknown function (DUF4547) This family of proteins is found in eukaryotes. Proteins in this family are typically between 144 and 206 amino acids in length. The human member of this family is C3orf43. (from Pfam) NF026430.5 PF15081.11 DUF4548 27 27 167 domain Y Y N DUF4548 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4548) Domain of unknown function (DUF4548) This family of proteins is found in eukaryotes. Proteins in this family are typically between and 178 amino acids in length. The human member of this family is C1orf105. (from Pfam) NF026431.5 PF15082.11 DUF4549 27 27 142 domain Y Y N DUF4549 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4549) Domain of unknown function (DUF4549) This family of proteins is found in eukaryotes. Proteins in this family are typically between 143 and 1871 amino acids in length. The human member of this family is C6orf183. (from Pfam) NF026433.5 PF15084.11 DUF4550 27 27 95 domain Y Y N DUF4550 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4550) Domain of unknown function (DUF4550) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 100 amino acids in length. This domain contains an N-terminal HXE motif. (from Pfam) NF026436.5 PF15087.11 DUF4551 27 27 610 domain Y Y N DUF4551 domain-containing protein 0 EBI-EMBL Protein of unknown function (DUF4551) Protein of unknown function (DUF4551) This family of proteins is functionally uncharacterised. This family of proteins is found in metazoa. This family includes human protein C12orf56. (from Pfam) NF026438.5 PF15089.11 Redic1-like 27 27 425 domain Y Y N Redic1 family protein 37604834,37612290 0 EBI-EMBL Regulator of DNA class I crossover intermediates 1-like Redic1 family protein This family of proteins mainly found in vertebrates includes mouse Regulator of DNA class I crossover intermediates 1 (Redic1). Redic1 is involved in recombination, probably acting by stabilising recombination intermediates during meiotic crossover formation. It is required for normal germline development and fertility as well as for meiotic progression, complete chromosomal synapsis and crossover formation [1, 2]. This protein binds double-stranded DNA [1]. [1]. 37612290. A novel recombination protein C12ORF40/REDIC1 is required for meiotic crossover formation. Fan S, Wang Y, Jiang H, Jiang X, Zhou J, Jiao Y, Ye J, Xu Z, Wang Y, Xie X, Zhang H, Li Y, Liu W, Zhang X, Ma H, Shi B, Zhang Y, Zubair M, Shah W, Xu Z, Xu B, Shi Q;. Cell Discov. 2023;9:88. [2]. 37604834. Loss-of-function variants in human C12orf40 cause male infertility by blocking meiotic progression. Tu C, Wen J, Wang W, Zhu Q, Chen Y, Cheng J, Li Z, Meng L, Li Y, He W, Tan C, Xie C, Fu SM, Du J, Lu G, Lin G, Gou LT, Tan YQ;. Cell Discov. 2023;9:87. (from Pfam) NF026439.5 PF15090.11 DUF4553 27 27 479 domain Y Y N DUF4553 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4553) Domain of unknown function (DUF4553) This family of proteins is functionally uncharacterised. This family of proteins is found in vertebrates. This family includes the human protein C10orf12. (from Pfam) NF026440.5 PF15091.11 DUF4554 27 27 458 domain Y Y N DUF4554 domain-containing protein GO:0042138 0 EBI-EMBL Domain of unknown function (DUF4554) Domain of unknown function (DUF4554) This family of proteins is functionally uncharacterised. This family of proteins is found in some vertebrates. This family includes human protein C11orf80. (from Pfam) NF026443.5 PF15094.11 DUF4556 27 27 105 domain Y Y N DUF4556 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4556), Ig-like Domain of unknown function (DUF4556), Ig-like This entry represents a immunoglobulin-like domain found in a functionally uncharacterised protein family. This family of proteins is found in vertebrates and includes human protein C1orf127. (from Pfam) NF026450.5 PF15101.11 TERB2 27 27 207 domain Y Y N telomere-associated protein TERB2 26548954 0 EBI-EMBL Telomere-associated protein TERB2 telomere-associated protein TERB2 TERB2 is a meiosis-specific telomere-associated protein involved in meiotic telomere attachment to the nucleus inner membrane, a crucial step for homologous pairing and synapsis [1]. [1]. 26548954. MAJIN Links Telomeric DNA to the Nuclear Membrane by Exchanging Telomere Cap. Shibuya H, Hernandez-Hernandez A, Morimoto A, Negishi L, Hoog C, Watanabe Y;. Cell. 2015;163:1252-1266. (from Pfam) NF026453.5 PF15104.11 CFAP141 27 27 86 domain Y Y N CFAP141 family protein 34715025 0 EBI-EMBL Cilia- and flagella-associated protein 141 CFAP141 family protein This family includes Cilia- and flagella-associated protein 141 (CFAP141, also known as C1orf189 protein). Members of this family may be microtubule inner proteins (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating [1]. [1]. 34715025. De novo identification of mammalian ciliary motility proteins using cryo-EM. Gui M, Farley H, Anujan P, Anderson JR, Maxwell DW, Whitchurch JB, Botsch JJ, Qiu T, Meleppattu S, Singh SK, Zhang Q, Thompson J, Lucas JS, Bingle CD, Norris DP, Roy S, Brown A;. Cell. 2021;184:5791-5806. (from Pfam) NF026467.5 PF15118.11 DUF4560 27 27 64 domain Y Y N DUF4560 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4560) Domain of unknown function (DUF4560) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 66 and 78 amino acids in length. There are two conserved sequence motifs: FCK and RTL. (from Pfam) NF026472.5 PF15123.11 DUF4562 27 27 115 domain Y Y N DUF4562 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4562) Domain of unknown function (DUF4562) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. There is a conserved HRYQNPW sequence motif. This family includes the human protein C4orf45. (from Pfam) NF026473.5 PF15124.11 FANCD2OS 27 27 175 domain Y Y N FANCD2 opposite strand protein 0 EBI-EMBL FANCD2 opposite strand protein FANCD2 opposite strand protein This family of proteins of unknown function gets its name from its position in the mammalian genome: Fanconi anemia group D2 protein opposite strand transcript protein. (from Pfam) NF026478.5 PF15130.11 DUF4566 27 27 226 domain Y Y N DUF4566 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4566) Domain of unknown function (DUF4566) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. This family includes human protein C6orf62. (from Pfam) NF026479.5 PF15131.11 DUF4567 27 27 75 domain Y Y N DUF4567 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4567) Domain of unknown function (DUF4567) This family of proteins is functionally uncharacterised. This family of proteins is found in some mammals. (from Pfam) NF026480.5 PF15132.11 DUF4568 27 27 177 domain Y Y N DUF4568 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4568) Domain of unknown function (DUF4568) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. (from Pfam) NF026481.5 PF15133.11 TASL 27 27 300 domain Y Y N TASL family protein GO:0034121 31001245,32433612 0 EBI-EMBL TLR adaptor interacting with SLC15A4 on the lysosome TASL family protein In humans, TASL (TLR adaptor interacting with SLC15A4 on the lysosome) is encoded by CXorf21 that is associated with systemic lupus erythematosus [1]. It is an immune adaptor that is required for recruitment and activation of IRF5 by TLR7, TLR8 and TLR9, in mechanistic analogy to IRF3 and its three adaptors STING, MAVS and TRIF. TASL interacts with the endolysosomal transporter SLC15A4 forming the SLC15A4-TASL complex, which is required for endolysosomal TLR signalling. TASL contains a pLxIS motif that is important for its function [2]. [1]. 31001245. Lysosomal pH Is Regulated in a Sex Dependent Manner in Immune Cells Expressing CXorf21. Harris VM, Harley ITW, Kurien BT, Koelsch KA, Scofield RH;. Front Immunol. 2019;10:578. [2]. 32433612. TASL is the SLC15A4-associated adaptor for IRF5 activation by TLR7-9. Heinz LX, Lee J, Kapoor U, Kartnig F, Sedlyarov V, Papakostas K, Cesar-Razquin A, Essletzbichler P, Goldmann U, Stefanovic A, Bigenzahn JW, Scorzoni S, Pizzagalli MD, Bensimon A, Muller AC, King FJ, Li J, Girardi E, Mbow ML, Whitehurst CE, Rebsamen M, Superti-Furga G;. Nature. 2020;581:316-322. (from Pfam) NF026482.5 PF15134.11 CEP15-like 27 27 110 domain Y Y N CEP15 family protein 0 EBI-EMBL Centrosomal protein 15-like CEP15 family protein This family of animal proteins includes human Centrosomal protein 15 (CEP15), which may play a role in ciliary assembly. (from Pfam) NF026485.5 PF15137.11 CU062 27 27 218 domain Y Y N polycystin-1 Interacting protein-1 family protein 37681898 0 EBI-EMBL Polycystin-1 Interacting Protein-1 polycystin-1 Interacting protein-1 family protein This family includes the human protein Polycystin-1 Interacting Protein-1 (also known as C21orf62 or CU062), which is a small glycoprotein that can oligomerize with itself and interact with PC1 protein polycystin-1 (PC1). It may have a role in the identification of senescent mitochondria and their extrusion in extracellular vesicles [1]. [1]. 37681898. Polycystin-1 Interacting Protein-1 (CU062) Interacts with the Ectodomain of Polycystin-1 (PC1). Lea WA, Winklhofer T, Zelenchuk L, Sharma M, Rossol-Allison J, Fields TA, Reif G, Calvet JP, Bakeberg JL, Wallace DP, Ward CJ;. Cells. 2023;12:2166. (from Pfam) NF026487.5 PF15139.11 CFAP95 27 27 195 domain Y Y N CFAP95 family protein 0 EBI-EMBL Protein CFAP95 CFAP95 family protein This family includes Protein CFAP95, whose function is unknown, found in eukaryotes. Proteins in this family are typically between 160 and 220 amino acids in length. (from Pfam) NF026491.5 PF15143.11 DUF4575 27 27 129 domain Y Y N DUF4575 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4575) Domain of unknown function (DUF4575) This family of uncharacterised proteins is found in eukaryotes. (from Pfam) NF026492.5 PF15144.11 DUF4576 27 27 88 domain Y Y N DUF4576 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4576) Domain of unknown function (DUF4576) This family of uncharacterised proteins is found in eukaryotes. (from Pfam) NF026493.5 PF15145.11 DUF4577 27 27 128 domain Y Y N DUF4577 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4577) Domain of unknown function (DUF4577) The function of this family of proteins, has not, as yet, been determined. Members of this family are as yet uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically 128 amino acids in length. (from Pfam) NF026495.5 PF15147.11 DUF4578 27 27 126 domain Y Y N DUF4578 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4578) Domain of unknown function (DUF4578) This family of proteins is found in eukaryotes. Proteins in this family are typically between 44 and 137 amino acids in length. (from Pfam) NF026505.5 PF15158.11 TMEM249 25 25 184 domain Y Y N TMEM249 family protein 34225353 0 EBI-EMBL Cation channel sperm-associated auxiliary subunit TMEM249 TMEM249 family protein This family of proteins is found in eukaryotes and includes Cation channel sperm-associated auxiliary subunit TMEM249 from human (also known as C8orfK29). It is an auxiliary component of the CatSper complex, a complex involved in sperm cell hyperactivation [1]. TMEM249 contributes to the assembly of the CatSpermasome. [1]. 34225353. Structure of a mammalian sperm cation channel complex. Lin S, Ke M, Zhang Y, Yan Z, Wu J;. Nature. 2021;595:746-750. (from Pfam) NF026509.5 PF15162.11 SCRE 27 27 162 domain Y Y N protein SPO16 family protein GO:0007130 30746471,30949703 0 EBI-EMBL Protein SPO16 homolog protein SPO16 family protein This entry represents the Protein SPO16 homolog (SPO16, also known as Synaptonemal complex reinforcing element SCRE), including the mammalian orthologue of budding yeast Spo16. It plays a key role in reinforcing the integrity of the central element of the synaptonemal complex (SC), resulting in the SC stabilization which ensures the progression of meiotic prophase I in male and female germ cells [1. It promotes homologous recombination and crossing-over in meiotic prophase I via its association with SHOC1 [2]. It is also required for the localization of TEX11 and MSH4 to recombination intermediates [2]. [1]. 30949703. SCRE serves as a unique synaptonemal complex fastener and is essential for progression of meiosis prophase I in mice. Liu H, Huang T, Li M, Li M, Zhang C, Jiang J, Yu X, Yin Y, Zhang F, Lu G, Luo MC, Zhang LR, Li J, Liu K, Chen ZJ;. Nucleic Acids Res. 2019;47:5670-5683. [2]. 30746471. SPO16 binds SHOC1 to promote homologous recombination and crossing-over in meiotic prophase I. Zhang Q, Ji SY, Busayavalasa K, Yu C;. Sci Adv. 2019;5:eaau9780. (from Pfam) NF026513.5 PF15167.11 DUF4581 27 27 131 domain Y Y N DUF4581 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4581) Domain of unknown function (DUF4581) This family of proteins is found in eukaryotes. Proteins in this family are typically 131 amino acids in length. (from Pfam) NF026535.5 PF15189.11 MEIOC 27 27 166 domain Y Y N meiosis-specific coiled-coil domain-containing protein MEIOC GO:0051321 0 EBI-EMBL Meiosis-specific coiled-coil domain-containing protein MEIOC meiosis-specific coiled-coil domain-containing protein MEIOC This family of proteins is found in eukaryotes. In humans, it is encoded for on the chromosomal position C17orf104. (from Pfam) NF026577.5 PF15232.11 DUF4585 27 27 73 domain Y Y N DUF4585 domain-containing protein 19240791 0 EBI-EMBL Domain of unknown function (DUF4585) Domain of unknown function (DUF4585) The function of this protein domain family is yet to be characterised. It is putatively thought to lie in the C-terminal domain of the DNA nucleotide repair protein, Xeroderma pigmentosa complementation group A (XPA). The function of XPA is to bind to DNA and repair any mismatched base pairs. This domain family is often found in eukaryotes, and is approximately 70 amino acids in length. There is a conserved DPE sequence motif. In humans, this protein is encoded for in the chromosomal position, Chromosome 5 open reading frame 65. Mutations in the gene lead to myelodysplastic syndromes, where there is inefficient stem cell production in the bone marrow. This suggests that the protein may have a role in forming blood cells [1]. [1]. 19240791. Integrated genomic analysis implicates haploinsufficiency of multiple chromosome 5q31.2 genes in de novo myelodysplastic syndromes pathogenesis. Graubert TA, Payton MA, Shao J, Walgren RA, Monahan RS, Frater JL, Walshauser MA, Martin MG, Kasai Y, Walter MJ;. PLoS One. 2009;4:e4583. (from Pfam) NF026584.5 PF15239.11 CFAP96-like 27 27 296 domain Y Y N CFAP96 family protein 37327785 0 EBI-EMBL Cilia-and flagella-associated protein 96 CFAP96 family protein This family (previously DUF4586) represents Cilia- and flagella-associated protein 96 (CFAP96, also known as C4orf47). CFAP96 is an axonemal microtubule-associated protein (MAP). The EM structure of sperm DMTs shows that CFAP96 binds to tubulin and, similarly to other axonemal wedge-MAPs, binds deeper into the inter-protofilament cleft making extensive contacts with flanking protofilaments [1]. [1]. 37327785. Structural specializations of the sperm tail. Leung MR, Zeng J, Wang X, Roelofs MC, Huang W, Zenezini Chiozzi R, Hevler JF, Heck AJR, Dutcher SK, Brown A, Zhang R, Zeev-Ben-Mordehai T;. Cell. 2023;186:2880-2896. (from Pfam) NF026593.5 PF15248.11 DUF4587 27 27 76 domain Y Y N DUF4587 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4587) Domain of unknown function (DUF4587) This protein family is a domain of unknown function. The precise function of this protein domain remains to be elucidated. This domain family is found in eukaryotes, and is typically between 64 and 79 amino acids in length. There are two conserved sequence motifs: QNAQ and HHH. In humans, it is found in the position, chromosome 21 open reading frame 58. (from Pfam) NF026596.5 PF15251.11 TAPR1-like 27 27 249 domain Y Y N TAPR1 family protein 33660365,35776542 0 EBI-EMBL Telomere attrition and p53 response 1 protein-like TAPR1 family protein This entry represents the Telomere attrition and p53 response 1 protein (TAPR1) from eukaryotes, including TAPR1 from human (also known as C16orf72/HAPSTR1), which is a multistress-responsive protein that functions as a negative regulator of TP53/P53 in the cellular response to telomere erosion and probably also DNA damage. It may attenuate p53/TP53 activation through the E3 ubiquitin ligase HUWE1 which also promotes TAPR1's degradation [1,2]. This family also includes uncharacterised proteins from fungi, such as YJR056C from yeast. [1]. 33660365. A novel p53 regulator, C16ORF72/TAPR1, buffers against telomerase inhibition. Benslimane Y, Sanchez-Osuna M, Coulombe-Huntington J, Bertomeu T, Henry D, Huard C, Bonneil E, Thibault P, Tyers M, Harrington L;. Aging Cell. 2021;20:e13331. [2]. 35776542. C16orf72/HAPSTR1 is a molecular rheostat in an integrated network of stress response pathways. Amici DR, Ansel DJ, Metz KA, Smith RS, Phoumyvong CM, Gayatri S, Chamera T, Edwards SL, O'Hara BP, Srivastava S, Brockway S, Takagishi SR, Cho BK, Goo YA, Kelleher NL, Ben-Sahra I, Foltz DR, Li J, Mendillo ML;. Proc Natl Acad Sci U S A. 2022;119:e2111262119. (from Pfam) NF026597.5 PF15252.11 DUF4589 27 27 246 domain Y Y N DUF4589 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4589) Domain of unknown function (DUF4589) This protein family is a domain of unknown function. The precise function of the protein domain remains to be elucidated. This family of proteins is found in eukaryotes and are typically between 215 and 293 amino acids in length. The protein contains two conserved sequence motifs: SSS and KST. (from Pfam) NF026602.5 PF15257.11 DUF4590 27 27 114 domain Y Y N DUF4590 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4590) Domain of unknown function (DUF4590) This family of proteins remains to be characterised and is a domain of unknown function. This domain family is found in eukaryotes, and is approximately 120 amino acids in length. There are two conserved sequence motifs: CCE and PCY. In humans, the gene encoding this protein lies in the position, chromosome 1 open reading frame 173. (from Pfam) NF026607.5 PF15262.11 DUF4592 27 27 124 domain Y Y N DUF4592 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4592) Domain of unknown function (DUF4592) This protein family is a domain of unknown function, which lies to the N-terminus of the protein. This domain family is found in eukaryotes, and is typically between 114 and 130 amino acids in length. There are two completely conserved residues (L and A) that may be functionally important. In humans, the gene that encodes this protein lies in the position, chromosome 2 open reading frame 55. (from Pfam) NF026610.5 PF15266.11 DUF4594 27 27 177 domain Y Y N DUF4594 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4594) Domain of unknown function (DUF4594) This protein family is a domain of unknown function. The protein family is found in eukaryotes, and is typically between 170 and 183 amino acids in length.In humans, the gene encoding this protein lies in the position, chromosome 15 open reading frame 52. (from Pfam) NF026705.5 PF15363.11 BTBD8_C 27 27 46 domain Y Y N BTB/POZ domain-containing protein 29262337 0 EBI-EMBL BTB/POZ domain-containing protein 8, C-terminal BTB/POZ domain-containing protein 8, C-terminal This domain is found at the C terminus of BTB/POZ domain-containing protein 8 (BTBD8, also known as AP2-interacting clathrin-endocytosis protein). BTBD8 is involved in clathrin-mediated endocytosis at the synapse and plays a role in neuronal development and in synaptic vesicle recycling in mature neurons, a process required for normal synaptic transmission [1]. There is a conserved ELET sequence motif. There are two completely conserved residues (S and E) that may be functionally important. [1]. 29262337. APache Is an AP2-Interacting Protein Involved in Synaptic Vesicle Trafficking and Neuronal Development. Piccini A, Castroflorio E, Valente P, Guarnieri FC, Aprile D, Michetti C, Bramini M, Giansante G, Pinto B, Savardi A, Cesca F, Bachi A, Cattaneo A, Wren JD, Fassio A, Valtorta F, Benfenati F, Giovedi S;. Cell Rep. 2017;21:3596-3611. (from Pfam) NF026708.5 PF15366.11 DUF4597 26.5 26.5 63 domain Y Y N DUF4597 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4597) Domain of unknown function (DUF4597) This family of proteins is found in eukaryotes. Proteins in this family are typically between 63 and 76 amino acids in length. There is a conserved TPPTPT sequence motif. (from Pfam) NF026712.5 PF15370.11 NOPCHAP1 27 27 110 domain Y Y N NOP protein chaperone 1 family protein GO:0000492 33367824 0 EBI-EMBL NOP protein chaperone 1 NOP protein chaperone 1 family protein This entry includes NOPCHAP1 from animals and New4 from fission yeast. NOPCHAP1 is a client-loading PAQosome/R2TP complex cofactor that selects NOP58 to promote box C/D small nucleolar ribonucleoprotein (snoRNP) assembly [1]. The function of New4 is not clear. [1]. 33367824. NOPCHAP1 is a PAQosome cofactor that helps loading NOP58 on RUVBL1/2 during box C/D snoRNP biogenesis. Abel Y, Paiva ACF, Bizarro J, Chagot ME, Santo PE, Robert MC, Quinternet M, Vandermoere F, Sousa PMF, Fort P, Charpentier B, Manival X, Bandeiras TM, Bertrand E, Verheggen C;. Nucleic Acids Res. 2021;49:1094-1113. (from Pfam) NF026713.5 PF15371.11 DUF4599 34 34 88 domain Y Y N DUF4599 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4599) Domain of unknown function (DUF4599) The function of this family of eukaryotic proteins is not known. (from Pfam) NF026715.5 PF15373.11 SAXO5-like 27 27 438 domain Y Y N SAXO5 family protein 34031406,37327785 0 EBI-EMBL Stabilizer of axonemal microtubules 5 SAXO5 family protein This family (previously DUF4601) represents the homologues of Stabilizer of axonemal microtubules 5 (SAXO5, also known as C19orf45, TEX45). SAXO5 is a filamentous SAXO protein that binds along protofilament A04 with 96-nm periodicity [1]. A typical feature of SAXO proteins is the presence of Mn motif which forms a 5- to 6-residue helix flanked by a Tyr/Phe residue on one end and by a Ser/Thr on the other that binds the shoulder of the alpha-tubulin S9/S10 loop [2]. SAXO5 contains 11 Mn motifs and therefore has 96-nm periodicity, matching the external periodicity of the axoneme [1]. [1]. 37327785. Structural specializations of the sperm tail. Leung MR, Zeng J, Wang X, Roelofs MC, Huang W, Zenezini Chiozzi R, Hevler JF, Heck AJR, Dutcher SK, Brown A, Zhang R, Zeev-Ben-Mordehai T;. Cell. 2023;186:2880-2896. [2]. 34031406. Cryo-EM structure of cortical microtubules from human parasite Toxoplasma gondii identifies their microtubule inner proteins. Wang X, Fu Y, Beatty WL, Ma M, Brown A, Sibley LD, Zhang R;. Nat Commun. 2021;12:3065. (from Pfam) NF026717.5 PF15375.11 DUF4602 27 27 132 domain Y Y N DUF4602 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4602) Domain of unknown function (DUF4602) This family of proteins is found in eukaryotes. Proteins in this family are typically between 173 and 294 amino acids in length. This family includes Human C1orf131. (from Pfam) NF026718.5 PF15376.11 DUF4603 27 27 1297 domain Y Y N DUF4603 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4603) Domain of unknown function (DUF4603) This protein family is a domain of unknown function. In particular, this domain lies at the C-terminal end of a protein found in eukaryotes. (from Pfam) NF026719.5 PF15377.11 DUF4604 28 28 176 domain Y Y N DUF4604 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4604) Domain of unknown function (DUF4604) This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 141 and 174 amino acids in length and contain a conserved LSF sequence motif. (from Pfam) NF026720.5 PF15378.11 DUF4605 27 27 59 domain Y Y N DUF4605 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4605) Domain of unknown function (DUF4605) This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 82 and 137 amino acids in length. (from Pfam) NF026721.5 PF15379.11 DUF4606 27 27 103 domain Y Y N DUF4606 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4606) Domain of unknown function (DUF4606) This domain family is found in eukaryotes, and is approximately 100 amino acids in length. (from Pfam) NF026723.5 PF15382.11 DUF4609 27 27 68 domain Y Y N DUF4609 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4609) Domain of unknown function (DUF4609) This family of proteins is found in eukaryotes. Proteins in this family are typically between 70 and 139 amino acids in length. (from Pfam) NF026728.5 PF15387.11 DUF4611 32.1 32.1 96 domain Y Y N DUF4611 domain-containing protein GO:0000408 0 EBI-EMBL Domain of unknown function (DUF4611) Domain of unknown function (DUF4611) This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 100 amino acids in length. There is a conserved AKR sequence motif. (from Pfam) NF026730.5 PF15389.11 DUF4612 27 27 115 domain Y Y N DUF4612 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4612) Domain of unknown function (DUF4612) This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 109 and 323 amino acids in length. (from Pfam) NF026732.5 PF15391.11 DUF4614 25 25 180 domain Y Y N DUF4614 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4614) Domain of unknown function (DUF4614) This domain family is found in eukaryotes, and is approximately 180 amino acids in length. There is a conserved EALT sequence motif. (from Pfam) NF026734.5 PF15393.11 DUF4615 27 27 137 domain Y Y N DUF4615 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4615) Domain of unknown function (DUF4615) This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 161 and 229 amino acids in length. There is a single completely conserved residue F that may be functionally important. (from Pfam) NF026735.5 PF15394.11 DUF4616 27 27 524 domain Y Y N DUF4616 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4616) Domain of unknown function (DUF4616) This protein family is a domain of unknown function found at the C-terminal domain of the proteins. This protein family is found in eukaryotes. Proteins in this family are typically between 166 and 538 amino acids in length. (from Pfam) NF026736.5 PF15395.11 DUF4617 27 27 1085 domain Y Y N DUF4617 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4617) Domain of unknown function (DUF4617) This family of proteins is found in eukaryotes. Proteins in this family are typically between 702 and 1745 amino acids in length. (from Pfam) NF026738.5 PF15397.11 DUF4618 34.9 34.9 258 domain Y Y N DUF4618 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4618) Domain of unknown function (DUF4618) This family of proteins is found in eukaryotes. Proteins in this family are typically between 238 and 363 amino acids in length. There are two conserved sequence motifs: EYP and KCTPD. (from Pfam) NF026739.5 PF15398.11 DUF4619 31.7 31.7 296 domain Y Y N DUF4619 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4619) Domain of unknown function (DUF4619) This family of proteins is found in eukaryotes. Proteins in this family are typically between 128 and 299 amino acids in length. (from Pfam) NF026740.5 PF15399.11 DUF4620 27 27 113 domain Y Y N DUF4620 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4620) Domain of unknown function (DUF4620) NF026767.5 PF15429.11 DUF4628 26 26 269 domain Y Y N DUF4628 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4628) Domain of unknown function (DUF4628) This family of proteins is found in eukaryotes. Proteins in this family are typically between 152 and 673 amino acids in length. (from Pfam) NF026780.5 PF15442.11 DUF4629 27 27 150 domain Y Y N DUF4629 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4629) Domain of unknown function (DUF4629) This domain family is found in eukaryotes, and is approximately 150 amino acids in length. There are two conserved sequence motifs: MHML and LGKK. (from Pfam) NF026789.5 PF15451.11 DUF4632 27 27 71 domain Y Y N DUF4632 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4632) Domain of unknown function (DUF4632) This family of proteins is found in eukaryotes. Proteins in this family are typically between 59 and 190 amino acids in length. (from Pfam) NF026802.5 PF15464.11 DUF4633 27 27 113 domain Y Y N DUF4633 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4633) Domain of unknown function (DUF4633) This family of proteins is found in eukaryotes. Proteins in this family are typically between 94 and 123 amino acids in length. (from Pfam) NF026803.5 PF15465.11 DUF4634 27 27 131 domain Y Y N DUF4634 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4634) Domain of unknown function (DUF4634) This family of proteins is found in eukaryotes. Proteins in this family are typically between 98 and 133 amino acids in length. (from Pfam) NF026804.5 PF15466.11 DUF4635 27 27 134 domain Y Y N DUF4635 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4635) Domain of unknown function (DUF4635) This family of proteins is found in eukaryotes. Proteins in this family are typically between 120 and 154 amino acids in length. There are two conserved sequence motifs: LEQ and DLE. (from Pfam) NF026806.5 PF15468.11 DUF4636 27 27 243 domain Y Y N DUF4636 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4636) Domain of unknown function (DUF4636) This family of proteins is found in eukaryotes. Proteins in this family are typically between 196 and 244 amino acids in length. (from Pfam) NF026808.5 PF15470.11 DUF4637 27 27 164 domain Y Y N DUF4637 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4637) Domain of unknown function (DUF4637) This family of proteins is found in eukaryotes. Proteins in this family are typically between 142 and 178 amino acids in length. (from Pfam) NF026810.5 PF15472.11 DUF4638 27 27 262 domain Y Y N DUF4638 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4638) Domain of unknown function (DUF4638) This family of proteins is found in eukaryotes. Proteins in this family are typically between 240 and 272 amino acids in length. (from Pfam) NF026817.5 PF15479.11 DUF4639 27 27 580 domain Y Y N DUF4639 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4639) Domain of unknown function (DUF4639) This family of proteins is found in eukaryotes. Proteins in this family are typically between 161 and 601 amino acids in length. (from Pfam) NF026818.5 PF15480.11 DUF4640 26 26 292 domain Y Y N DUF4640 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4640) Domain of unknown function (DUF4640) This family of proteins is found in eukaryotes. Proteins in this family are typically between 99 and 306 amino acids in length. (from Pfam) NF026821.5 PF15483.11 DUF4641 27 27 443 domain Y Y N DUF4641 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4641) Domain of unknown function (DUF4641) This family of proteins is found in eukaryotes. Proteins in this family are typically between 201 and 519 amino acids in length. (from Pfam) NF026822.5 PF15484.11 DUF4642 27 27 159 domain Y Y N DUF4642 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4642) Domain of unknown function (DUF4642) This family of proteins is found in eukaryotes. Proteins in this family are typically between 115 and 196 amino acids in length. (from Pfam) NF026823.5 PF15485.11 DUF4643 27 27 270 domain Y Y N DUF4643 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4643) Domain of unknown function (DUF4643) This family of proteins is found in eukaryotes. Proteins in this family are typically between 254 and 462 amino acids in length. (from Pfam) NF026824.5 PF15486.11 DUF4644 27 27 161 domain Y Y N DUF4644 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4644) Domain of unknown function (DUF4644) This family of proteins is found in eukaryotes. Proteins in this family are typically between 143 and 191 amino acids in length. (from Pfam) NF026826.5 PF15488.11 DUF4645 27 27 294 domain Y Y N DUF4645 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4645) Domain of unknown function (DUF4645) This family of proteins is found in eukaryotes. Proteins in this family are typically between 200 and 298 amino acids in length. (from Pfam) NF026834.5 PF15496.11 DUF4646 23.4 23.4 126 domain Y Y N DUF4646 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4646) Domain of unknown function (DUF4646) This is a family of proteins largely from fungi. The function is not known. (from Pfam) NF026842.5 PF15504.11 DUF4647 27 27 457 domain Y Y N DUF4647 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4647) Domain of unknown function (DUF4647) This family of proteins is found in eukaryotes. Proteins in this family are typically between 282 and 480 amino acids in length. (from Pfam) NF026843.5 PF15505.11 Vexin 25 25 76 domain Y Y N vexin domain-containing protein 29518376 0 EBI-EMBL Vexin domain Vexin domain Proteins containing this domain include Xenopus laevis Vexin and its human homologue, C8orf46. Vexin is transiently expressed in differentiating progenitors in the developing central nervous system (CNS) and is required for neurogenesis in the neural plate and retina [1]. This entry corresponds to a presumed SH3 domain. [1]. 29518376. C8orf46 homolog encodes a novel protein Vexin that is required for neurogenesis in Xenopus laevis. Moore KB, Logan MA, Aldiri I, Roberts JM, Steele M, Vetter ML;. Dev Biol. 2018;437:27-40. (from Pfam) NF026847.5 PF15509.11 DUF4650 27 27 519 domain Y Y N DUF4650 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4650) Domain of unknown function (DUF4650) This family of vertebrate proteins lies to the C-terminus of Ubiquitin-specific peptidase-like protein family peptidase_C98, Pfam:PF15499. It might be acting as the exosite for the peptidase. (from Pfam) NF026884.5 PF15546.11 DUF4653 27 27 229 domain Y Y N DUF4653 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4653) Domain of unknown function (DUF4653) This family of proteins is found in eukaryotes. Proteins in this family are typically between 93 and 229 amino acids in length. (from Pfam) NF026886.5 PF15548.11 DUF4655 27 27 525 domain Y Y N DUF4655 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4655) Domain of unknown function (DUF4655) This family of proteins is found in eukaryotes. Proteins in this family are typically between 533 and 570 amino acids in length. (from Pfam) NF026889.5 PF15551.11 DUF4656 27 27 361 domain Y Y N DUF4656 domain-containing protein GO:0003334 0 EBI-EMBL Domain of unknown function (DUF4656) Domain of unknown function (DUF4656) This family of proteins is found in eukaryotes. Proteins in this family are typically between 286 and 398 amino acids in length. (from Pfam) NF026890.5 PF15552.11 DUF4657 27 27 296 domain Y Y N DUF4657 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4657) Domain of unknown function (DUF4657) This family of proteins is found in eukaryotes. Proteins in this family are typically between 305 and 370 amino acids in length. (from Pfam) NF026893.5 PF15555.11 DUF4658 27 27 123 domain Y Y N DUF4658 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4658) Domain of unknown function (DUF4658) This family of proteins is found in eukaryotes. Proteins in this family are typically between 129 and 161 amino acids in length. (from Pfam) NF026896.5 PF15558.11 DUF4659 27 27 374 domain Y Y N DUF4659 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4659) Domain of unknown function (DUF4659) This family of proteins is found in eukaryotes. Proteins in this family are typically between 427 and 674 amino acids in length. There are two completely conserved residues (D and I) that may be functionally important. (from Pfam) NF026897.5 PF15559.11 DUF4660 27 27 111 domain Y Y N DUF4660 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4660) Domain of unknown function (DUF4660) This family of proteins is found in eukaryotes. Proteins in this family are typically between 93 and 189 amino acids in length. (from Pfam) NF026914.5 PF15576.11 DUF4661 27 27 253 domain Y Y N DUF4661 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4661) Domain of unknown function (DUF4661) This family of proteins is found in eukaryotes. Proteins in this family are typically between 281 and 302 amino acids in length. (from Pfam) NF026916.5 PF15578.11 DUF4662 27 27 269 domain Y Y N DUF4662 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4662) Domain of unknown function (DUF4662) This family of proteins is found in eukaryotes. Proteins in this family are approximately 290 amino acids in length. (from Pfam) NF027004.5 PF15668.10 DUF4663 25 25 367 domain Y Y N DUF4663 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4663) Domain of unknown function (DUF4663) This family of proteins is found in eukaryotes. Proteins in this family are typically between 289 and 334 amino acids in length. There are two completely conserved residues (W and G) that may be functionally important. (from Pfam) NF027009.5 PF15673.10 Ciart 27 27 278 domain Y Y N circadian-associated transcriptional repressor GO:0000976,GO:0032922 24385426,24736997,24737000 0 EBI-EMBL Circadian-associated transcriptional repressor circadian-associated transcriptional repressor Circadian-associated transcriptional repressor (Ciart or Chrono) is a negative regulatory component of the circadian clock. It functions as a transcriptional repressor, modulating BMAL1-CLOCK activity. It also regulates metabolic pathways such as the glucocorticoid response triggered by behavioral stress [1, 2, 3]. [1]. 24385426. Gene model 129 (Gm129) encodes a novel transcriptional repressor that modulates circadian gene expression. Annayev Y, Adar S, Chiou YY, Lieb JD, Sancar A, Ye R;. J Biol Chem. 2014;289:5013-5024. [2]. 24736997. A novel protein, CHRONO, functions as a core component of the mammalian circadian clock. Goriki A, Hatanaka F, Myung J, Kim JK, Yoritaka T, Tanoue S, Abe T, Kiyonari H, Fujimoto K, Kato Y, Todo T, Matsubara A, Forger D, Takumi T;. PLoS Biol. 2014;12:e1001839. [3]. 24737000. Machine learning helps identify CHRONO as a circadian clock component. Anafi RC, Lee Y, Sato TK, Venkataraman A, Ramanathan C, Kavakli IH, Hughes ME, Baggs JE, Growe J, Liu AC, Kim J, Hogenesch JB;. PLoS Biol. 2014;12:e1001840. (from Pfam) NF027015.5 PF15679.10 DUF4665 27 27 99 domain Y Y N DUF4665 domain-containing protein GO:0042254 0 EBI-EMBL Domain of unknown function (DUF4665) Domain of unknown function (DUF4665) This family of proteins is found in eukaryotes. Proteins in this family are typically between 45 and 100 amino acids in length. (from Pfam) NF027033.5 PF15697.10 DUF4666 24 24 111 domain Y Y N DUF4666 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4666) Domain of unknown function (DUF4666) This family of proteins is found in plants. Proteins in this family are typically between 103 and 140 amino acids in length. There are two conserved sequence motifs: LQRS and FRR. (from Pfam) NF027036.5 PF15700.10 DUF4667 27 27 224 domain Y Y N DUF4667 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4667) Domain of unknown function (DUF4667) This family of proteins is found in fungi. Proteins in this family are typically between 172 and 313 amino acids in length. (from Pfam) NF027037.5 PF15701.10 DUF4668 27 27 162 domain Y Y N DUF4668 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4668) Domain of unknown function (DUF4668) This family of proteins is found in eukaryotes. Proteins in this family are typically between 142 and 211 amino acids in length. (from Pfam) NF027043.5 PF15707.10 MCCD1 27 27 90 domain Y Y N mitochondrial coiled-coil domain protein 1 14527716 0 EBI-EMBL Mitochondrial coiled-coil domain protein 1 mitochondrial coiled-coil domain protein 1 This is a family of uncharacterised proteins known as mitochondrial coiled-coil domain protein 1 [1]. [1]. 14527716. A novel gene encoding a coiled-coil mitochondrial protein located at the telomeric end of the human MHC Class III region. Semple JI, Ribas G, Hillyard G, Brown SE, Sanderson CM, Campbell RD;. Gene. 2003;314:41-54. (from Pfam) NF027045.5 PF15709.10 DUF4670 27 27 521 domain Y Y N DUF4670 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4670) Domain of unknown function (DUF4670) This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length. (from Pfam) NF027046.5 PF15710.10 Brme1 27 27 699 domain Y Y N Brme1 domain-containing protein GO:1990918 32460033,32463460 0 EBI-EMBL Break repair meiotic recombinase recruitment factor 1 Break repair meiotic recombinase recruitment factor 1 Brme1 (also known as Meiok21) is a component of meiotic recombination bridges involved in meiotic double-strand break repair [1,2]. The C-terminal domain of Brme1 physically interacts with the N-terminal domain of HSF2BP [1]. BRME1 facilitates the loading of RAD51 and DMC1 recombinases onto DSBs (DNA double-strand breaks) through interaction with MEILB2/HSF2BP and replacing ssDNA binding proteins [2]. Brme1 is highly expressed in mice testes and fetal ovaries. Knockout of Brme1 results in male mice infertility [1]. [1]. 32463460. MEIOK21: a new component of meiotic recombination bridges required for spermatogenesis. Shang Y, Huang T, Liu H, Liu Y, Liang H, Yu X, Li M, Zhai B, Yang X, Wei Y, Wang G, Chen Z, Wang S, Zhang L;. Nucleic Acids Res. 2020;48:6624-6639. [2]. 32460033. Meiosis-Specific C19orf57/4930432K21Rik/BRME1 Modulates Localization of RAD51 and DMC1 to DSBs in Mouse Meiotic Recombination. Takemoto K, Tani N, Takada-Horisawa Y, Fujimura S, Tanno N, Yamane M, Okamura K, Sugimoto M, Araki K, Ishiguro KI;. Cell Rep. 2020;31:107686. (from Pfam) NF027052.5 PF15716.10 DUF4672 27 27 204 domain Y Y N DUF4672 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4672) Domain of unknown function (DUF4672) This family of proteins is found in eukaryotes. Proteins in this family are typically between 165 and 199 amino acids in length. (from Pfam) NF027054.5 PF15718.10 MNR 27 27 964 domain Y Y N moonraker protein GO:0007099 26297806 0 EBI-EMBL Protein moonraker protein moonraker Protein moonraker is a centriolar satellite component involved in centriole duplication. It promotes centriole duplication by localizing WDR62 to the centrosome [1]. [1]. 26297806. Centriolar satellites assemble centrosomal microcephaly proteins to recruit CDK2 and promote centriole duplication. Kodani A, Yu TW, Johnson JR, Jayaraman D, Johnson TL, Al-Gazali L, Sztriha L, Partlow JN, Kim H, Krup AL, Dammermann A, Krogan NJ, Walsh CA, Reiter JF;. Elife. 2015; [Epub ahead of print] (from Pfam) NF027055.5 PF15719.10 DUF4674 28.6 28.6 190 domain Y Y N DUF4674 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4674) Domain of unknown function (DUF4674) This family of proteins is found in eukaryotes. Proteins in this family are typically between 126 and 221 amino acids in length. (from Pfam) NF027056.5 PF15720.10 DUF4675 27 27 198 domain Y Y N DUF4675 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4675) Domain of unknown function (DUF4675) This family of proteins is found in eukaryotes. Proteins in this family are approximately 190 amino acids in length. (from Pfam) NF027061.5 PF15725.10 RCDG1 27 27 83 domain Y Y N renal cancer differentiation gene 1 protein 25059753 0 EBI-EMBL Renal cancer differentiation gene 1 protein renal cancer differentiation gene 1 protein This family includes human protein C4orf46, also known as renal cancer differentiation gene 1 protein (RCDG1) [1]. [1]. 25059753. Expression and clinical significance of RCDG1 in renal cell carcinoma: a novel renal cancerassociated gene. Yu Z, Ni L, Chen D, Su Z, Yu W, Zhang Q, Wang Y, Li C, Gui Y, Lai Y;. Mol Med Rep. 2014;10:1583-1589. (from Pfam) NF027062.5 PF15726.10 DUF4677 27 27 198 domain Y Y N DUF4677 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4677) Domain of unknown function (DUF4677) This family of proteins is found in eukaryotes. Proteins in this family are typically between 157 and 195 amino acids in length. (from Pfam) NF027063.5 PF15727.10 DUF4678 27 27 381 domain Y Y N DUF4678 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4678) Domain of unknown function (DUF4678) This family of proteins is found in eukaryotes. Proteins in this family are typically between 318 and 395 amino acids in length. (from Pfam) NF027064.5 PF15728.10 DUF4679 27 27 399 domain Y Y N DUF4679 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4679) Domain of unknown function (DUF4679) This family of proteins is found in eukaryotes. Proteins in this family are typically between 213 and 412 amino acids in length. (from Pfam) NF027066.5 PF15730.10 DUF4680 27 27 144 domain Y Y N DUF4680 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4680) Domain of unknown function (DUF4680) This family of proteins is found in eukaryotes. Proteins in this family are typically between 65 and 178 amino acids in length. There are two conserved sequence motifs: VISRM and ENE. (from Pfam) NF027068.5 PF15732.10 DUF4681 27 27 125 domain Y Y N DUF4681 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4681) Domain of unknown function (DUF4681) This family of proteins is found in eukaryotes. Proteins in this family are typically between 101 and 127 amino acids in length. (from Pfam) NF027069.5 PF15733.10 DUF4682 27 27 121 domain Y Y N DUF4682 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4682) Domain of unknown function (DUF4682) This domain family is found in eukaryotes, and is typically between 152 and 183 amino acids in length. The family is found in association with Pfam:PF00566. There is a conserved NHLL sequence motif. (from Pfam) NF027071.5 PF15735.10 DUF4683 27 27 411 domain Y Y N DUF4683 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4683) Domain of unknown function (DUF4683) This domain family is found in eukaryotes, and is typically between 384 and 400 amino acids in length. (from Pfam) NF027072.5 PF15736.10 DUF4684 27.2 27.2 458 domain Y Y N DUF4684 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4684) Domain of unknown function (DUF4684) This family of proteins is found in eukaryotes. Proteins in this family are typically between 531 and 1277 amino acids in length. (from Pfam) NF027073.5 PF15737.10 DUF4685 27 27 117 domain Y Y N DUF4685 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4685) Domain of unknown function (DUF4685) This domain family is found in eukaryotes, and is typically between 106 and 131 amino acids in length. There are two conserved sequence motifs: SGE and VRF. (from Pfam) NF027083.5 PF15747.10 DUF4687 27 27 120 domain Y Y N DUF4687 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4687) Domain of unknown function (DUF4687) This family of proteins is found in eukaryotes. Proteins in this family are typically between 76 and 140 amino acids in length. (from Pfam) NF027088.5 PF15752.10 DUF4688 27 27 400 domain Y Y N DUF4688 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4688) Domain of unknown function (DUF4688) This family of proteins is found in eukaryotes. Proteins in this family are typically between 331 and 596 amino acids in length. (from Pfam) NF027091.5 PF15755.10 DUF4689 27 27 223 domain Y Y N DUF4689 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4689) Domain of unknown function (DUF4689) This family of proteins is found in eukaryotes. Proteins in this family are typically between 202 and 224 amino acids in length. (from Pfam) NF027098.5 PF15762.10 DUF4691 27 27 179 domain Y Y N DUF4691 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4691) Domain of unknown function (DUF4691) This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 317 amino acids in length. (from Pfam) NF027100.5 PF15764.10 DUF4693 27 27 285 domain Y Y N DUF4693 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4693) Domain of unknown function (DUF4693) This family of proteins is found in eukaryotes. Proteins in this family are typically between 238 and 436 amino acids in length. (from Pfam) NF027101.5 PF15765.10 DUF4694 27 27 156 domain Y Y N DUF4694 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4694) Domain of unknown function (DUF4694) This family of proteins is found in eukaryotes. Proteins in this family are typically between 154 and 217 amino acids in length. There is a conserved SSGY sequence motif. (from Pfam) NF027102.5 PF15766.10 DUF4695 27 27 105 domain Y Y N DUF4695 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4695) Domain of unknown function (DUF4695) This family of proteins is found in eukaryotes. Proteins in this family are typically between 109 and 206 amino acids in length. There is a conserved RFKTQP sequence motif. (from Pfam) NF027103.5 PF15767.10 ARMH4 25 25 583 domain Y Y N helical domain-containing protein 0 EBI-EMBL Armadillo-like helical domain-containing protein 4 Armadillo-like helical domain-containing protein 4 This family represents the Armadillo-like helical domain-containing protein 4, whose function is not clear. (from Pfam) NF027104.5 PF15768.10 CC190 27 27 270 domain Y Y N coiled-coil domain-containing protein 190 0 EBI-EMBL Coiled-coil domain-containing protein 190 coiled-coil domain-containing protein 190 This family of proteins is found in eukaryotes. Proteins in this family are typically between 234 and 297 amino acids in length. (from Pfam) NF027105.5 PF15769.10 DUF4698 28.6 28.6 481 domain Y Y N DUF4698 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4698) Domain of unknown function (DUF4698) This family of proteins is found in eukaryotes. Proteins in this family are typically between 464 and 550 amino acids in length. (from Pfam) NF027106.5 PF15770.10 DUF4699 27 27 310 domain Y Y N DUF4699 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4699) Domain of unknown function (DUF4699) This family of proteins is found in eukaryotes. Proteins in this family are typically between 303 and 319 amino acids in length. (from Pfam) NF027109.5 PF15773.10 DAAP1 27 27 505 domain Y Y N axonemal dynein regulator Daap1 GO:0070840 33263282 0 EBI-EMBL Dynein axonemal-associated protein 1 axonemal dynein regulator Daap1 Daap1 is a axonemal dynein regulator that interacts with outer dynein arm (ODA) subunits and is required for deployment of ODA to the axoneme [1]. [1]. 33263282. Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins. Lee C, Cox RM, Papoulas O, Horani A, Drew K, Devitt CC, Brody SL, Marcotte EM, Wallingford JB;. Elife. 2020; [Epub ahead of print] (from Pfam) NF027110.5 PF15774.10 DUF4702 27 27 395 domain Y Y N DUF4702 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4702) Domain of unknown function (DUF4702) This family of proteins is found in eukaryotes. Proteins in this family are typically between 346 and 637 amino acids in length. (from Pfam) NF027111.5 PF15775.10 DUF4703 27 27 186 domain Y Y N DUF4703 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4703) Domain of unknown function (DUF4703) This family of proteins is found in eukaryotes. Proteins in this family are typically between 149 and 210 amino acids in length. (from Pfam) NF027133.5 PF15797.10 DUF4706 27 27 108 domain Y Y N DUF4706 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4706) Domain of unknown function (DUF4706) This domain family is found in eukaryotes, and is approximately 110 amino acids in length. (from Pfam) NF027142.5 PF15806.10 DUF4707 27 27 433 domain Y Y N DUF4707 domain-containing protein GO:0043014,GO:0060271 0 EBI-EMBL Domain of unknown function (DUF4707) Domain of unknown function (DUF4707) This family of proteins is found in eukaryotes. The function is not known. (from Pfam) NF027149.5 PF15813.10 DUF4708 27 27 274 domain Y Y N DUF4708 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4708) Domain of unknown function (DUF4708) This family of proteins is found in eukaryotes. (from Pfam) NF027157.5 PF15821.10 DUF4709 27 27 110 domain Y Y N DUF4709 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4709) Domain of unknown function (DUF4709) This domain family is found in eukaryotes, and is approximately 110 amino acids in length. There is a conserved QQL sequence motif. (from Pfam) NF027164.5 PF15828.10 RDD1 27 27 77 domain Y Y N RDD1 family protein 32028983,35970996 0 EBI-EMBL Required for drug-induced death protein 1 RDD1 family protein This family of proteins is found in eukaryotes and includes Required for drug-induced death protein 1 (RDD1) which regulates drug efflux through modulation of ABCB1 localization and activity [1,2]. [1]. 32028983. Systematic functional identification of cancer multi-drug resistance genes. Lau MT, Ghazanfar S, Parkin A, Chou A, Rouaen JR, Littleboy JB, Nessem D, Khuong TM, Nevoltris D, Schofield P, Langley D, Christ D, Yang J, Pajic M, Neely GG;. Genome Biol. 2020;21:27. [2]. 35970996. Chemical genomics with pyrvinium identifies C1orf115 as a regulator of drug efflux. Masud SN, Chandrashekhar M, Aregger M, Tan G, Zhang X, Mero P, Pirman DA, Zaslaver O, Smolen GA, Lin ZY, Wong CJ, Boone C, Gingras AC, Montenegro-Burke JR, Moffat J;. Nat Chem Biol. 2022; [Epub ahead of print] (from Pfam) NF027165.5 PF15829.10 DUF4711 27 27 224 domain Y Y N DUF4711 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4711) Domain of unknown function (DUF4711) This family of proteins is found in eukaryotes. Proteins in this family are typically between 130 and 288 amino acids in length. (from Pfam) NF027166.5 PF15830.10 DUF4712 27 27 254 domain Y Y N DUF4712 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4712) Domain of unknown function (DUF4712) This family of proteins is found in eukaryotes. Proteins in this family are typically between 133 and 267 amino acids in length. (from Pfam) NF027167.5 PF15831.10 SMIM5_18_22 29.3 29.3 56 domain Y Y N small integral membrane protein 5/18/22 family protein 29765154 0 EBI-EMBL Small integral membrane protein 5/18/22 small integral membrane protein 5/18/22 family protein This entry represents a small family of single-pass membrane proteins described as small integral membrane proteins, including SMIM5/18/22 which have been described as variants of the Cancer-Associated Small Integral Membrane Open reading frame 1 (CASIMO1), a small open reading frame (sORF)-encode protein. CASIMO1 controls cell proliferation and interacts with squalene epoxidase (SQLE) modulating lipid droplet formation. CASIMO1 RNA is overexpressed predominantly in hormone receptor-positive breast tumors. Loss of CASIMO1 disturbs the organisation of the actin cytoskeleton, leads to inhibitions of cell motility, and stalls the cell cycle in the G0/G1 phase [1]. [1]. 29765154. The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation. Polycarpou-Schwarz M, Gross M, Mestdagh P, Schott J, Grund SE, Hildenbrand C, Rom J, Aulmann S, Sinn HP, Vandesompele J, Diederichs S;. Oncogene. 2018;37:4750-4768. (from Pfam) NF027169.5 PF15833.10 DUF4714 27 27 149 domain Y Y N DUF4714 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4714) Domain of unknown function (DUF4714) This family of proteins is found in eukaryotes. Proteins in this family are typically between 143 and 164 amino acids in length. (from Pfam) NF027171.5 PF15835.10 DUF4715 27 27 139 domain Y Y N DUF4715 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4715) Domain of unknown function (DUF4715) This family of proteins is found in eukaryotes. Proteins in this family are approximately 150 amino acids in length. The proteins are described as coiled-coil domain-containing protein ENSP00000299415-like. (from Pfam) NF027173.5 PF15837.10 DUF4716 27 27 60 domain Y Y N DUF4716 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4716) Domain of unknown function (DUF4716) This domain family is found in eukaryotes, and is approximately 60 amino acids in length. (from Pfam) NF027174.5 PF15838.10 LLCFC1 27 27 72 domain Y Y N LLLL/CFNLAS domain-containing protein GO:0007342 32393636 0 EBI-EMBL LLLL and CFNLAS motif-containing protein 1 LLLL and CFNLAS motif-containing protein 1 LLCFC1 (also known as SOF1) and its homologues can be found in eukaryotes. They have two conserved sequence motifs: LLLL and CFNLAS. LLCFC1 is a sperm protein required for sperm-oocyte fusion in mice [1]. [1]. 32393636. Sperm proteins SOF1, TMEM95, and SPACA6 are required for sperm-oocyte fusion in mice. Noda T, Lu Y, Fujihara Y, Oura S, Koyano T, Kobayashi S, Matzuk MM, Ikawa M;. Proc Natl Acad Sci U S A. 2020;117:11493-11502. (from Pfam) NF027178.5 PF15842.10 DUF4718 27 27 184 domain Y Y N DUF4718 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4718) Domain of unknown function (DUF4718) This family of proteins is found in eukaryotes. Proteins in this family are typically between 130 and 224 amino acids in length. (from Pfam) NF027179.5 PF15843.10 DUF4719 27 27 202 domain Y Y N DUF4719 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4719) Domain of unknown function (DUF4719) This family of proteins is found in eukaryotes. Proteins in this family are typically between 67 and 240 amino acids in length. (from Pfam) NF027182.5 PF15846.10 DUF4720 27 27 96 domain Y Y N DUF4720 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4720) Domain of unknown function (DUF4720) This family of proteins is found in vertebrates. Proteins in this family are typically between 101 and 117 amino acids in length. (from Pfam) NF027185.5 PF15849.10 DUF4722 27 27 167 domain Y Y N DUF4722 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4722) Domain of unknown function (DUF4722) This family of proteins is found in vertebrates. Proteins in this family are typically between 86 and 203 amino acids in length. (from Pfam) NF027186.5 PF15851.10 DUF4723 27 27 82 domain Y Y N DUF4723 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4723) Domain of unknown function (DUF4723) This domain is found in mammalian proteins. There are a number of conserved cysteines but it is unlikely to be a zinc-finger family. This entry includes PATE4 from mice. According to structure predictions (AlphaFold models and DALI server), this domain is structurally similar to members of the uPar/Lys6 domain superfamily. (from Pfam) NF027187.5 PF15852.10 DUF4724 27 27 93 domain Y Y N DUF4724 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4724) Domain of unknown function (DUF4724) This family of proteins is found in mammals. There is a conserved KVKPL sequence motif. (from Pfam) NF027189.5 PF15855.10 DUF4726 27 27 101 domain Y Y N DUF4726 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4726) Domain of unknown function (DUF4726) This family of proteins is found in vertebrates. Proteins in this family are typically between 40 and 110 amino acids in length. (from Pfam) NF027190.5 PF15856.10 DUF4727 27 27 216 domain Y Y N DUF4727 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4727) Domain of unknown function (DUF4727) This family of proteins is found in vertebrates. There are a number of conserved cysteines, but the domain is not a zinc-finger. (from Pfam) NF027199.5 PF15866.10 DUF4729 26 26 200 domain Y Y N DUF4729 domain-containing protein 36419248 0 EBI-EMBL Domain of unknown function (DUF4729) Domain of unknown function (DUF4729) This family of proteins is functionally uncharacterised. This family of proteins is found in insects. Proteins in this family are typically between 238 and 666 amino acids in length. This domain has been identified as structurally similar to TRAF-like domains (Pfam:PF03145) [1]. [1]. 36419248. DALI shines a light on remote homologs: One hundred discoveries. Holm L, Laiho A, Toronen P, Salgado M;. Protein Sci. 2023;32:e4519. (from Pfam) NF027206.5 PF15873.10 DUF4730 27 27 55 domain Y Y N DUF4730 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4730) Domain of unknown function (DUF4730) This family of proteins is found in eukaryotes. Proteins in this family are approximately 60 amino acids in length. (from Pfam) NF027208.5 PF15875.10 DUF4731 27 27 75 domain Y Y N DUF4731 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4731) Domain of unknown function (DUF4731) This family of proteins is found in eukaryotes. Proteins in this family are typically between 37 and 78 amino acids in length. (from Pfam) NF027209.5 PF15876.10 DUF4732 27 27 159 domain Y Y N DUF4732 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4732) Domain of unknown function (DUF4732) This family of proteins is found in eukaryotes. Proteins in this family are typically between 107 and 201 amino acids in length. (from Pfam) NF027211.5 PF15878.10 Frey 28.3 28.3 94 domain Y Y N Frey family protein 35960805,36050562 0 EBI-EMBL Protein Frey Frey family protein This family represents Frey proteins, which are key regulators for male fertility expressed transiently in round spermatids where it recruits IZUMO1 at the endoplasmic reticulum (ER) membrane and coordinates the oolemmal binding multimeric complex (IZUMO1 complex) assembly. Upon complete assembly of the IZUMO1 complex, its ER retention is released, facilitating IZUMO1 complex export to the acrosome [1,2]. Frey interacts with SPPL2C, which inhibits its intramembrane protease activity directly accessing the catalytic centre of an I-CLiP [1]. [1]. 35960805. C11orf94/Frey is a key regulator for male fertility by controlling Izumo1 complex assembly. Contreras W, Wiesehofer C, Schreier D, Leinung N, Peche P, Wennemuth G, Gentzel M, Schroder B, Mentrup T;. Sci Adv. 2022;8:eabo6049. [2]. 36050562. The vertebrate- and testis- specific transmembrane protein C11ORF94 plays a critical role in sperm-oocyte membrane binding. Hao H, Shi B, Zhang J, Dai A, Li W, Chen H, Ji W, Gong C, Zhang C, Li J, Chen L, Yao B, Hu P, Yang H, Brosius J, Lai S, Shi Q, Deng C;. Mol Biomed. 2022;3:27. (from Pfam) NF027214.5 PF15881.10 DUF4734 25 25 91 domain Y Y N DUF4734 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4734) Domain of unknown function (DUF4734) This domain family is found in species of Drosophila, and is approximately 90 amino acids in length. The family is found in association with Pfam:PF07707. (from Pfam) NF027216.5 PF15883.10 DUF4736 27 27 186 domain Y Y N DUF4736 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4736) Domain of unknown function (DUF4736) This family of proteins is functionally uncharacterised. This family of proteins is found in insects. Proteins in this family are typically between 186 and 228 amino acids in length. (from Pfam) NF027225.5 PF15893.10 DUF4739 27 27 235 domain Y Y N DUF4739 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4739) Domain of unknown function (DUF4739) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 138 and 167 amino acids in length. (from Pfam) NF027228.5 PF15897.10 DUF4741 27 27 169 domain Y Y N DUF4741 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4741) Domain of unknown function (DUF4741) NF027253.5 PF15923.10 DUF4745 34.8 34.8 133 domain Y Y N DUF4745 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4745) Domain of unknown function (DUF4745) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 180 amino acids in length. (from Pfam) NF027258.5 PF15928.10 DUF4746 27 27 297 domain Y Y N DUF4746 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4746) Domain of unknown function (DUF4746) This presumed domain is functionally uncharacterised. This domain is found in eukaryotes, and is typically between 247 and 324 amino acids in length. The family is found in association with Pfam:PF00085. (from Pfam) NF027262.5 PF15932.10 DUF4748 27 27 52 domain Y Y N DUF4748 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4748) Domain of unknown function (DUF4748) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 114 and 139 amino acids in length. (from Pfam) NF027266.5 PF15936.10 DUF4749 28.7 28.7 93 domain Y Y N DUF4749 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4749) Domain of unknown function (DUF4749) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 121 and 170 amino acids in length. It is usually found in association with Pfam:PF00595 (PDZ) and Pfam:PF00412 (LIM), and often contains the conserved Zasp-like motif (IPR006643). (from Pfam) NF027268.5 PF15938.10 DUF4750 27 27 54 domain Y Y N DUF4750 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4750) Domain of unknown function (DUF4750) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 76 and 92 amino acids in length. There are two completely conserved W residues that may be functionally important. (from Pfam) NF027279.5 PF15949.10 DUF4757 27 27 167 domain Y Y N DUF4757 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4757) Domain of unknown function (DUF4757) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 145 and 166 amino acids in length. The family is found in association with Pfam:PF00412. There are two completely conserved residues (W and L) that may be functionally important. (from Pfam) NF027291.5 PF15961.10 DUF4764 25 25 799 domain Y Y N DUF4764 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4764) Domain of unknown function (DUF4764) NF027303.5 PF15973.10 DUF4766 27 21 115 domain Y Y N DUF4766 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4766) Domain of unknown function (DUF4766) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 106 and 128 amino acids in length. There is a conserved KVI sequence motif. (from Pfam) NF027316.5 PF15989.10 DUF4768 27 27 88 domain Y Y N DUF4768 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4768) Domain of unknown function (DUF4768) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 116 and 180 amino acids in length. There is a conserved FFFGQY sequence motif. (from Pfam) NF027319.5 PF15992.10 DUF4769 23.9 23.9 256 domain Y Y N DUF4769 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4769) Domain of unknown function (DUF4769) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 291 and 501 amino acids in length. (from Pfam) NF027321.5 PF15994.10 DUF4770 27 27 181 domain Y Y N DUF4770 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4770) Domain of unknown function (DUF4770) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 169 and 182 amino acids in length. There is a single completely conserved residue L that may be functionally important. (from Pfam) NF027322.5 PF15995.10 DUF4771 27 27 160 domain Y Y N DUF4771 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4771) Domain of unknown function (DUF4771) This domain family is found in eukaryotes, and is approximately 160 amino acids in length. There is a conserved RYGK sequence motif. (from Pfam) NF027324.5 PF15997.10 DUF4772 27 27 112 domain Y Y N DUF4772 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4772) Domain of unknown function (DUF4772) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 107 and 124 amino acids in length. There is a single completely conserved residue V that may be functionally important. (from Pfam) NF027325.5 PF15998.10 DUF4773 27 27 118 domain Y Y N DUF4773 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4773) Domain of unknown function (DUF4773) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 120 amino acids in length. (from Pfam) NF027334.5 PF16007.10 DUF4777 34.4 34.4 66 domain Y Y N DUF4777 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4777) Domain of unknown function (DUF4777) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 70 amino acids in length. (from Pfam) NF027335.5 PF16008.10 DUF4778 27 27 284 domain Y Y N DUF4778 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4778) Domain of unknown function (DUF4778) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 321 and 791 amino acids in length. There is a single completely conserved residue P that may be functionally important. (from Pfam) NF027336.5 PF16009.10 DUF4779 27 27 160 domain Y Y N DUF4779 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4779) Domain of unknown function (DUF4779) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 234 and 351 amino acids in length. (from Pfam) NF027354.5 PF16027.10 DUF4786 27 27 169 domain Y Y N DUF4786 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4786) Domain of unknown function (DUF4786) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 209 and 353 amino acids in length. (from Pfam) NF027356.5 PF16029.10 DUF4787 27 27 63 domain Y Y N DUF4787 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4787) Domain of unknown function (DUF4787) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 70 amino acids in length. (from Pfam) NF027359.5 PF16032.10 DUF4788 27 27 229 domain Y Y N DUF4788 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4788) Domain of unknown function (DUF4788) This presumed domain is functionally uncharacterised. This domain is found in insects, and is approximately 230 amino acids in length. There is a single completely conserved residue D that may be functionally important. It adopts a C2-like fold. (from Pfam) NF027360.5 PF16033.10 DUF4789 27 27 101 domain Y Y N DUF4789 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4789) Domain of unknown function (DUF4789) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 87 and 100 amino acids in length. There is a conserved GPC sequence motif. There are two completely conserved C residues that may be functionally important. (from Pfam) NF027364.5 PF16037.10 DUF4790 31.5 31.5 93 domain Y Y N DUF4790 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4790) Domain of unknown function (DUF4790) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 134 and 191 amino acids in length. There is a single completely conserved residue C that may be functionally important. (from Pfam) NF027366.5 PF16039.10 DUF4791 27 27 163 domain Y Y N DUF4791 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4791) Domain of unknown function (DUF4791) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 189 and 203 amino acids in length. There are two conserved sequence motifs: PLPL and LGN. There is a single completely conserved residue N that may be functionally important. (from Pfam) NF027367.5 PF16040.10 APD1-4_N 27 27 71 domain Y Y N E3 ubiquitin-protein ligase APD1-4 domain-containing protein 22897245 0 EBI-EMBL E3 ubiquitin-protein ligase APD1-4, N-terminal E3 ubiquitin-protein ligase APD1-4, N-terminal This entry includes E3 ubiquitin-protein ligase APD1 to 4 from Arabidopsis. They are involved in pollen mitosis II (PMII) regulation during male gametogenesis [1]. This entry represents a functionally uncharacterised domain found towards the N-terminal of APD1-4 and in uncharacterised sequences, mainly from arthropods. [1]. 22897245. Four closely-related RING-type E3 ligases, APD1-4, are involved in pollen mitosis II regulation in Arabidopsis. Luo G, Gu H, Liu J, Qu LJ;. J Integr Plant Biol. 2012;54:814-827. (from Pfam) NF027368.5 PF16041.10 APD1-4_M 25 25 108 domain Y Y N E3 ubiquitin-protein ligase APD1-4 domain-containing protein 22897245 0 EBI-EMBL E3 ubiquitin-protein ligase APD1-4, middle domain E3 ubiquitin-protein ligase APD1-4, middle domain This entry includes E3 ubiquitin-protein ligase APD1 to 4 from Arabidopsis. They are involved in pollen mitosis II (PMII) regulation during male gametogenesis [1]. This entry represents a functionally uncharacterised domain found in the middle of APD1-4 and in uncharacterised sequences mainly from arthropods. There are two completely conserved C residues that may be functionally important. [1]. 22897245. Four closely-related RING-type E3 ligases, APD1-4, are involved in pollen mitosis II regulation in Arabidopsis. Luo G, Gu H, Liu J, Qu LJ;. J Integr Plant Biol. 2012;54:814-827. (from Pfam) NF027369.5 PF16042.10 DUF4794 25 25 75 domain Y Y N DUF4794 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4794) Domain of unknown function (DUF4794) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 74 and 92 amino acids in length. (from Pfam) NF027370.5 PF16043.10 DUF4795 34.8 34.8 208 domain Y Y N DUF4795 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4795) Domain of unknown function (DUF4795) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 285 and 978 amino acids in length. (from Pfam) NF027371.5 PF16044.10 DUF4796_C 28 28 152 domain Y Y N DUF4796 domain-containing protein 36419248 0 EBI-EMBL DUF4796 C-terminal DUF4796 C-terminal This domain is functionally uncharacterised and is found in eukaryotes. Proteins with this domain are typically between 194 and 289 amino acids in length. There is a single completely conserved residue C that may be functionally important. This domain has been identified as structurally similar to peptidase C97 domain (Pfam:PF05903) [1]. [1]. 36419248. DALI shines a light on remote homologs: One hundred discoveries. Holm L, Laiho A, Toronen P, Salgado M;. Protein Sci. 2023;32:e4519. (from Pfam) NF027378.5 PF16051.10 DUF4797 27 27 44 domain Y Y N DUF4797 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4797) Domain of unknown function (DUF4797) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. There is a conserved SGLPT sequence motif. There are two completely conserved residues (P and G) that may be functionally important. (from Pfam) NF027381.5 PF16055.10 DUF4798 27 27 100 domain Y Y N DUF4798 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4798) Domain of unknown function (DUF4798) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 80 and 365 amino acids in length. There is a single completely conserved residue H that may be functionally important. (from Pfam) NF027382.5 PF16056.10 DUF4799 27 27 375 domain Y Y N DUF4799 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4799) Domain of unknown function (DUF4799) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 362 and 1493 amino acids in length. (from Pfam) NF027383.5 PF16057.10 DUF4800 28.8 28.8 254 domain Y Y N DUF4800 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4800) Domain of unknown function (DUF4800) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 310 amino acids in length. The family is found in association with Pfam:PF02138, Pfam:PF00400. There is a conserved RDN sequence motif. (from Pfam) NF027385.5 PF16059.10 MGA_dom 27 27 51 domain Y Y N MAX gene-associated protein domain-containing protein 25516968 0 EBI-EMBL MGA, conserved domain MGA, conserved domain This domain can be found in the MAX gene-associated protein (Mga), which is a dual-specificity transcription factor that contains both a bHLHZip domain and a T-box domain and is able to bind to and regulate transcriptional targets through both E-box sites as well as T-box-binding elements (TBEs) [1]. [1]. 25516968. Mga is essential for the survival of pluripotent cells during peri-implantation development. Washkowitz AJ, Schall C, Zhang K, Wurst W, Floss T, Mager J, Papaioannou VE;. Development. 2015;142:31-40. (from Pfam) NF027386.5 PF16060.10 DUF4802 27 27 64 domain Y Y N DUF4802 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4802) Domain of unknown function (DUF4802) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 70 amino acids in length. There are two conserved sequence motifs: CRC and YFDC. (from Pfam) NF027387.5 PF16061.10 DUF4803 27 27 255 domain Y Y N DUF4803 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4803) Domain of unknown function (DUF4803) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 351 and 686 amino acids in length. There is a conserved RRY sequence motif. (from Pfam) NF027389.5 PF16063.10 DUF4805 27 27 265 domain Y Y N DUF4805 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4805) Domain of unknown function (DUF4805) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 244 and 363 amino acids in length. There is a conserved WEL sequence motif. (from Pfam) NF027390.5 PF16064.10 DUF4806 25 25 90 domain Y Y N DUF4806 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4806) Domain of unknown function (DUF4806) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 80 amino acids in length. (from Pfam) NF027392.5 PF16066.10 DUF4808 27 27 121 domain Y Y N DUF4808 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4808) Domain of unknown function (DUF4808) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 106 and 135 amino acids in length. (from Pfam) NF027397.5 PF16071.10 DUF4812 25 25 65 domain Y Y N DUF4812 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4812) Domain of unknown function (DUF4812) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with Pfam:PF03791, Pfam:PF03790. There are two completely conserved residues (H and I) that may be functionally important. (from Pfam) NF027412.5 PF16086.10 DUF4816 29.4 29.4 43 domain Y Y N DUF4816 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4816) Domain of unknown function (DUF4816) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 178 and 456 amino acids in length. There is a conserved WKP sequence motif. (from Pfam) NF027415.5 PF16089.10 DUF4818 25.6 25.6 116 domain Y Y N DUF4818 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4818) Domain of unknown function (DUF4818) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 176 and 214 amino acids in length. There is a single completely conserved residue W that may be functionally important. (from Pfam) NF027416.5 PF16090.10 DUF4819 27 27 85 domain Y Y N DUF4819 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4819) Domain of unknown function (DUF4819) This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 82 and 99 amino acids in length. (from Pfam) NF027417.5 PF16091.10 DUF4820 27 27 227 domain Y Y N DUF4820 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4820) Domain of unknown function (DUF4820) This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 320 and 483 amino acids in length. There are two conserved sequence motifs: WSLP and RPLPW. (from Pfam) NF027604.5 PF16279.10 DUF4927 29.8 29.8 89 domain Y Y N DUF4927 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF4927) Domain of unknown function (DUF4927) This family, around 80 residues, consists of uncharacterized and nuclear receptor coactivator 2 proteins and is mainly found in mammalia species. The specific function of this family is still unknown. (from Pfam) NF027739.5 PF16424.10 DUF5021 25 25 157 domain Y Y N DUF5021 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF5021) Domain of unknown function (DUF5021) This family consists of Prepilin-type cleavage/methylation N-terminal domain proteins around 200 residues in length and is mainly found in various Eubacterium species. The function of this family is unknown. (from Pfam) NF027741.5 PF16426.10 DUF5023 25 25 197 domain Y Y N DUF5023 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF5023) Domain of unknown function (DUF5023) This family consists of several uncharacterised proteins around 300 residues in length and is mainly found in various Eubacterium species. The function of this family is unknown. (from Pfam) NF028312.5 PF17002.10 DUF5089 36.1 36.1 193 domain Y Y N DUF5089 domain-containing protein 24259309 0 EBI-EMBL Domain of unknown function (DUF5089) Domain of unknown function (DUF5089) This is a family of microsporidial-specific proteins of unknown function. There is distant homology to synaptosomal-associated 25 family proteins. [1]. 24259309. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T;. Genome Biol Evol. 2013;5:2285-2303. (from Pfam) NF028316.5 PF17006.10 DUF5087 27 27 293 domain Y Y N DUF5087 domain-containing protein 24259309 0 EBI-EMBL Domain of unknown function (DUF5087) Domain of unknown function (DUF5087) This is a family of microsporidial sequences of unknown function. [1]. 24259309. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T;. Genome Biol Evol. 2013;5:2285-2303. (from Pfam) NF028318.5 PF17008.10 DUF5088 29.4 29.4 184 domain Y Y N DUF5088 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF5088) Domain of unknown function (DUF5088) This is a family of microsporidial sequences of unknown function. (from Pfam) NF028319.5 PF17009.10 DUF5090 27 27 187 domain Y Y N DUF5090 domain-containing protein 24259309 0 EBI-EMBL Domain of unknown function (DUF5090) Domain of unknown function (DUF5090) This is a microsporidial-specific family of proteins of unknown function. The family is likely to be of four transmembrane domains. [1]. 24259309. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T;. Genome Biol Evol. 2013;5:2285-2303. (from Pfam) NF028320.5 PF17010.10 DUF5092 27 27 145 domain Y Y N DUF5092 domain-containing protein 24259309 0 EBI-EMBL Domain of unknown function (DUF5092) Domain of unknown function (DUF5092) his is a family of microsporidial-specific sequences of unknown function. There is one transmembrane domain towards the C-terminus. [1]. 24259309. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T;. Genome Biol Evol. 2013;5:2285-2303. (from Pfam) NF028321.5 PF17011.10 DUF5093 27 27 131 domain Y Y N DUF5093 domain-containing protein 24259309 0 EBI-EMBL Domain of unknown function (DUF5093) Domain of unknown function (DUF5093) This is a family of microsporidial sequences that may be distantly related to RRP7, Pfam:PF12923, ribosomal-RNA-processing protein 7. [1]. 24259309. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T;. Genome Biol Evol. 2013;5:2285-2303. (from Pfam) NF028322.5 PF17012.10 DUF5091 27 27 147 domain Y Y N DUF5091 domain-containing protein 24259309 0 EBI-EMBL Domain of unknown function (DUF5091) Domain of unknown function (DUF5091) This is a family of microsporidial-specific sequences of unknown function. [1]. 24259309. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T;. Genome Biol Evol. 2013;5:2285-2303. (from Pfam) NF028325.5 PF17015.10 DUF5094 33.2 33.2 178 domain Y Y N DUF5094 domain-containing protein 24259309 0 EBI-EMBL Domain of unknown function (DUF5094) Domain of unknown function (DUF5094) This family of largely microsporidial-specific proteins is of unknown function. However there may be distant homology to family Csm1, Pfam:PF12539. [1]. 24259309. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T;. Genome Biol Evol. 2013;5:2285-2303. (from Pfam) NF028326.5 PF17016.10 DUF5095 27 27 229 domain Y Y N DUF5095 domain-containing protein 24259309 0 EBI-EMBL Domain of unknown function (DUF5095) Domain of unknown function (DUF5095) This is a family of microsporidial-specific sequences. The function is not known and there is no distant homology to any Pfam families so far. [1]. 24259309. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T;. Genome Biol Evol. 2013;5:2285-2303. (from Pfam) NF028329.5 PF17019.10 DUF5096 27 27 192 domain Y Y N DUF5096 domain-containing protein 24259309 0 EBI-EMBL Domain of unknown function (DUF5096) Domain of unknown function (DUF5096) This is a family of microsporidial sequences of unknown function. There is a well conserved Asp residue towards the C-terminus which may be functional. [1]. 24259309. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T;. Genome Biol Evol. 2013;5:2285-2303. (from Pfam) NF028330.5 PF17020.10 DUF5097 29.7 29.7 119 domain Y Y N DUF5097 domain-containing protein 24259309 0 EBI-EMBL Domain of unknown function (DUF5097) Domain of unknown function (DUF5097) This is a family of microsporidia-specific proteins of unknown function. There is the possibility of very distant homology to the WAC domain. [1]. 24259309. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T;. Genome Biol Evol. 2013;5:2285-2303. (from Pfam) NF028333.5 PF17023.10 DUF5098 27 27 462 domain Y Y N DUF5098 domain-containing protein 24259309 0 EBI-EMBL Domain of unknown function (DUF5098) Domain of unknown function (DUF5098) This is family of microsporidia-specific sequences with no known function. There is a very characteristic NPW sequence motif at the very C-terminus. [1]. 24259309. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T;. Genome Biol Evol. 2013;5:2285-2303. (from Pfam) NF028335.5 PF17025.10 DUF5099 27 27 108 domain Y Y N DUF5099 domain-containing protein 24259309 0 EBI-EMBL Domain of unknown function (DUF5099) Domain of unknown function (DUF5099) This is a family of microsporidia-specific sequences of unknown function. [1]. 24259309. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T;. Genome Biol Evol. 2013;5:2285-2303. (from Pfam) NF028339.5 PF17029.10 DUF5100 27 27 125 domain Y Y N DUF5100 domain-containing protein 24259309 0 EBI-EMBL Domain of unknown function (DUF5100) Domain of unknown function (DUF5100) This is a family of microsporidia-specific sequences of unknown function. [1]. 24259309. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T;. Genome Biol Evol. 2013;5:2285-2303. (from Pfam) NF028341.5 PF17031.10 DUF5101 27 27 99 domain Y Y N DUF5101 domain-containing protein 24259309 0 EBI-EMBL Domain of unknown function (DUF5101) Domain of unknown function (DUF5101) This is a family of short microsporidia-specific proteins of unknown function. [1]. 24259309. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T;. Genome Biol Evol. 2013;5:2285-2303. (from Pfam) NF028414.5 PF17104.10 DUF5102 30 30 292 domain Y Y N DUF5102 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF5102) Domain of unknown function (DUF5102) This is a family fungal sequences of no known function. (from Pfam) NF033127.1 ANT_3pp_AadA3 595.5 595.5 258 exception Y Y Y ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA3 aadA3 0 NCBIFAM ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA3 ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA3 NF033133.1 vanT-L-cat 750 750 366 exception Y Y Y serine racemase VanT-L catalytic subunit vanTr 0 NCBIFAM serine racemase VanT-L catalytic subunit serine racemase VanT-L catalytic subunit NF033150.1 AAC_6p_A49 410 410 184 exception Y Y Y aminoglycoside 6'-N-acetyltransferase AacA49 aacA49 2.3.1.82 GO:0047663 0 NCBIFAM aminoglycoside 6'-N-acetyltransferase AacA49 AAC(6')-Ia family aminoglycoside 6'-N-acetyltransferase AacA49 NF033151.0 AAC_6p_A10 400 400 178 exception Y Y Y AAC(6')-I family aminoglycoside 6'-N-acetyltransferase aacA10 2.3.1.82 GO:0047663 0 NCBIFAM AAC(6')-I family aminoglycoside 6'-N-acetyltransferase AAC(6')-I family aminoglycoside 6'-N-acetyltransferase NF033374.6 AAC_6p_Id 320 320 149 exception Y Y Y aminoglycoside N-acetyltransferase AAC(6')-Id aac(6')-Id 0 NCBIFAM aminoglycoside N-acetyltransferase AAC(6')-Id aminoglycoside N-acetyltransferase AAC(6')-Id The only known occurrence of this putative aminoglycoside resistance protein is in Klebsiella pneumoniae transposon TN4000. Its coding region was not marked in the original sequence report, accession X12618, but was recognized afterwards. NF033505.2 paceosortase 80 80 167 exception Y Y N pacearchaeosortase prtA GO:0004197,GO:0006605,GO:0016020,GO:0043687 0 NCBIFAM pacearchaeosortase pacearchaeosortase Members of this family, pacearchaeosortase, are archaeosortases from the uncultured (so far) Candidatus Pacearchaeota archaeon lineage and its close relatives. In most assemblies where pacearchaeosortase is found, only one protein can be found likely to make it the target for sorting and cleavage, and it is encoded by the adjacent gene. This dedicated arrangement suggests the adjacent gene encodes a critical surface protein, most likely one that helps form an S-layer. NF033506.0 PACE-CTERM-PROT 110 110 627 exception Y Y N putative S-layer protein 0 NCBIFAM putative S-layer protein putative S-layer protein Assembled genomes from the Candidatus Pacearchaeota archaeon group and its close relatives, so far all uncultured, have a single archaeosortase, called pacearchaseosortase. A search protein archaeosortase targets, with a C-terminal domain resembling other archaeosortase and exosortase sorting signal regions, found this family as the best candidate. It is nearly always encoded by a gene found adjacent to the pacearchaseosortase gene. This dedicated arrangement, a sorting enzyme encoded next to its only predicted sorting substrate, suggests that members of this family, called PACE-CTERM, may be an important and abundant surface protein, most likely the major S-layer protein. NF033670.1 polymyxin_MCR6 1235 1235 538 exception Y Y Y MCR-6 family phosphoethanolamine--lipid A transferase 0 NCBIFAM MCR-6 family phosphoethanolamine--lipid A transferase MCR-6 family phosphoethanolamine--lipid A transferase MCR-6 family phosphoethanolamine--lipid A transferases are nearly 90% identical to the MCR-1 and MCR-2 families, but are distinct enough that they are considered to have become mobilized by a distinct event. Therefore, MCR-6 is assigned to its own family. NF033895.2 blaCAM 535 535 241 exception Y Y Y CAM family subclass B1 metallo-beta-lactamase blaCAM 3.5.2.6 GO:0008800 30789204 0 NCBIFAM CAM family subclass B1 metallo-beta-lactamase CAM family subclass B1 metallo-beta-lactamase CAM (Central Alberta Metallo-beta-lactamase) is a subclass B1 metallo-beta-lactamase. As of mid-2019, a member of the family was sequenced only once, found in an integrative element of a Pseudomonas aeruginosa strain isolated in 2009 or earlier. NF033951.2 Cas12d 250 250 1180 equivalog Y Y N type V CRISPR-associated protein Cas12d/CasY cas12d casY 28005056,36648696 0 NCBIFAM type V CRISPR-associated protein Cas12d type V CRISPR-associated protein Cas12d/CasY NF036601.5 PF17492.7 D_CNTX 27 27 48 subfamily Y Y N delta-ctenitoxin 18619481,22069579,27077886 0 EBI-EMBL Delta Ctenitoxins delta-ctenitoxin This family includes peptides isolated from Phoneutria such as delta-ctenitoxins. Members of the CNTX-Pn1a family and its paralogs (delta-CNTX-Pn1b through delta-CNTX-Pn1e) of Phoneutria toxins have complex effects on sodium channels but their primary effect appears to be an inhibition of channel inactivation, a pharmacology similar to that of the delta-atracotoxins and delta-conotoxins. Orthologous toxins such as delta-CNTX-Pr1/PK1 and Pn2 are also family members, some of which act by blocking the calcium channels [1]. Delta-CNTX-Pn1a and delta-CNTX-PN2a are 48-amino-acid polypeptides, with 5 disulfide bridges [2]. The later has a complex pharmacology that results in inhibition of NaV channel inactivation and a hyperpolarizing shift in the channel activation potential [3]. [1]. 18619481. A rational nomenclature for naming peptide toxins from spiders and other venomous animals. King GF, Gentz MC, Escoubas P, Nicholson GM;. Toxicon. 2008;52:264-276. [2]. 27077886. delta-Ctenitoxin-Pn1a, a Peptide from Phoneutria nigriventer Spider Venom, Shows Antinociceptive Effect Involving Opioid and Cannabinoid Systems, in Rats. Emerich BL, Ferreira RC, Cordeiro MN, Borges MH, Pimenta AM, Figueiredo SG, Duarte ID, de Lima ME;. Toxins (Basel). 2016;8:106. [3]. 22069579. Spider-venom peptides as therapeutics. Saez NJ, Senff S, Jensen JE, Er SY, Herzig V, Rash LD, King GF;. Toxins (Basel). 2010;2:2851-2871. (from Pfam) NF036666.5 PF17554.7 DUF5466 25 25 57 domain Y Y N DUF5466 domain-containing protein 0 EBI-EMBL Family of unknown function (DUF5466) DUF5466 domain This is a family of unknown function found in Enterobacteria phage T7. (from Pfam) NF037146.5 PF17902.6 SH3_10 22.8 22.8 65 domain Y Y N SH3 domain-containing protein 21536047 0 EBI-EMBL SH3 domain SH3 domain This entry represents an SH3 domain. [1]. 21536047. Crystal structure of a rigid four-spectrin-repeat fragment of the human desmoplakin plakin domain. Choi HJ, Weis WI;. J Mol Biol. 2011;409:800-812. (from Pfam) NF037891.5 PF18738.6 HEPN_DZIP3 27 27 144 domain Y Y N DZIP3/ hRUL138 family HEPN domain-containing protein 23768067 0 EBI-EMBL DZIP3/ hRUL138-like HEPN DZIP3/ hRUL138 family HEPN domain DZIP3/ hRUL138-like HEPN nuclease. Fusion to TPR, Zn-ribbon, RING, Ankyrin, CARD, NACHT ATPase, DEATH and LRR in various animal lineages [1]. [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF038009.1 TatB_1 100 100 70 subfamily Y Y N twin-arginine translocation system-associated protein 0 NCBIFAM twin-arginine translocation system-associated protein This family is suggested by TCDB to be part of the twin-arginine translocation (TAT) system, but lacks detectable sequence similarity to subunits such as TatB. NF038103.1 blaGMB 580 580 270 exception Y Y Y GMB family subclass B1 metallo-beta-lactamase blaGMB 3.5.2.6 GO:0008800 0 NCBIFAM GMB family subclass B1 metallo-beta-lactamase NF038195.1 blaAAK 655 655 286 exception Y Y Y AAK family class A beta-lactamase blaAAK 3.5.2.6 GO:0008800 0 NCBIFAM AAK family class A beta-lactamase AAK is most closely related the SHV family of beta-lactamases, but is a distinct family. NF038275.1 Myrrnad 40 40 81 domain Y Y N MyrrNad domain-containing protein 28630471 0 NCBIFAM MyrrNad domain This HMM, the N-terminal domain counterpart to MyrrCad (NF033158), represents the N-terminal regions of a family of LRR-like repeat proteins. The coinage "MyrrCad", rendered without full capitalization because it is an acronym rather than an amino acid sequence motif, signifies "MYcoplasma Repeat-Rich protein C-terminal Anchor Domain." NF038311.1 FosU 295 295 137 exception Y Y Y FosU family fosfomycin resistance glutathione transferase fosU 2.5.1.18 0 NCBIFAM FosU family fosfomycin resistance glutathione transferase FosU was discovered as two closely related alleles for fosfomycin resistance from uncultured bacteria found in duck wastes. NF038374.1 omphalotin_tail 34 34 40 subfamily_domain Y Y N omphalotin biosynthesis suicide methyltransferase/RiPP precursor 28715095,32935693 0 NCBIFAM omphalotin family RiPP precursor domain This HMM describes a RiPP cyclopeptide precursor peptide region that appears as the tail region of certain self-sacrificing fungal methyltransferases . The founding member of the family is omphalotin A precursor region. NF038375.1 crocagin_RiPP 27 27 21 domain Y Y N crocagin A family RiPP precursor 28544148,32935693 0 NCBIFAM crocagin A family RiPP precursor NF038381.1 phage_DpoZ_2 350 350 754 exception Y Y N aminoadenine-incorporating DNA polymerase DpoZ dpoZ 33926956 0 NCBIFAM aminoadenine-incorporating DNA polymerase DpoZ NF039253.4 PF19182.5 DUF5864 25 25 136 subfamily Y Y N DUF5864 family protein 0 EBI-EMBL Family of unknown function (DUF5864) DUF5864 family protein This is a family of uncharacterised proteins of unknown function predominantly found in Mimiviridae. (from Pfam) NF039530.4 PF19064.5 DUF5760 27 27 86 domain Y N N Family of unknown function (DUF5760) 0 EBI-EMBL Family of unknown function (DUF5760) Family of unknown function (DUF5760) This is a family of uncharacterised proteins of unknown function found in Phycodnaviridae and Mimiviridae. (from Pfam) NF039531.4 PF19065.5 DUF5761 26.9 26.9 62 domain Y N N Family of unknown function (DUF5761) 0 EBI-EMBL Family of unknown function (DUF5761) Family of unknown function (DUF5761) This is a family of uncharacterised proteins of unknown function found in viruses. (from Pfam) NF039549.4 PF19150.5 DUF5832 26.7 26.7 81 domain Y Y N DUF5832 domain-containing protein 0 EBI-EMBL Family of unknown function (DUF5832) DUF5832 domain-containing protein This entry contains proteins of unknown function found predominantly in the Phycodnaviridae, Mimiviridae, Marseilleviridae and Iridoviridae virus families. (from Pfam) NF039853.4 PF19080.5 DUF5772 26.9 26.9 84 domain Y N N Family of unknown function (DUF5772) 0 EBI-EMBL Family of unknown function (DUF5772) Family of unknown function (DUF5772) This is a family of proteins of unknown function found in viruses which appears to contain transmembrane proteins inferred from homology. (from Pfam) NF040634.1 16S_A1408_NpmB 460 460 217 exception Y Y Y 16S rRNA (adenine(1408)-N(1))-methyltransferase NpmB npmB 2.1.1.180 34310216 0 NCBIFAM 16S rRNA (adenine(1408)-N(1))-methyltransferase NpmB NF040790.2 glucon_galact_dh 750 750 390 equivalog Y Y N bifunctional D-gluconate/D-galactonate dehydratase gad 4.2.1.140,4.2.1.39 GO:0008869,GO:0046177,GO:0047929 15509194,20023024 0 NCBIFAM bifunctional D-gluconate/D-galactonate dehydratase NF041072.1 FtrB_double_U 160 160 121 equivalog Y Y N FtrB family double-selenoprotein 35883471 0 NCBIFAM FtrB family double-selenoprotein NF041094.1 CheX_Thtogales 280 280 152 equivalog Y Y N CheY-P phosphatase CheX cheX GO:0006935,GO:0016787 15546616 0 NCBIFAM CheY-P phosphatase CheX NF041382.1 Trx_VPGUxxT_one 350 350 349 exception Y Y N VPGUxxT family thioredoxin-like (seleno)protein, type 1 35883471 0 NCBIFAM VPGUxxT family thioredoxin-like (seleno)protein, type 1 Type 1 members of the VPGUxxT family thioredoxin-like (seleno)protein have a single site where selenocysteine residues appear. NF041386.1 dihyfolred_HdrA_Halo 300 300 158 equivalog Y Y N dihydrofolate reductase HdrA hdrA 1.5.1.3 GO:0004146,GO:0046654 2509470,9493269 0 NCBIFAM dihydrofolate reductase HdrA NF041520.1 flexitail 40 40 107 domain Y Y N flexitail domain-containing putative surface protein 0 NCBIFAM flexitail putative surface-anchoring domain The flexitail domain is found several hundred proteins from metagenome-assembled genomes (MAGs) of Chloroflexi bacteria. As a rule, the flexitail domain, which averages about 110 amino acids in length, is located at the protein C-terminus, and is separated from other recognizable domains by stretches of low complexity sequences. This resembles the pattens seen for short, tripartite, C-terminal protein-sorting signals for surface-anchored proteins, such as PEP-CTERM, GlyGly-CTERM, or MYXO-CTERM, or the LPXTG signal in tripartite form as described by TIGR01167, or longer C-terminal sorting signals such as type IX secretion system (T9SS) signals. At the time of model creation, no example had yet appeared among the more than 200 million collected proteins from genomes of cultured prokaryotes in the RefSeq collection. This suggests that the flexitail domain may represent an adaptation to a lifestyle that has not been conducive to isolation in culture conditions known so far. NF041536.1 ArsM_DUF2284_UU 575 575 459 exception Y Y N arsenite methyltransferase/DUF2284 domain selenoprotein 0 NCBIFAM arsenite methyltransferase/DUF2284 domain selenoprotein Members of the seed alignment for this protein are selenoproteins with two selenocysteine-containing motifs. The first is in the N-terminal arsenite methyltransferase region, typically QUEGG, and the second is in a C-terminal DUF2284 domain, typically TUPSG. NF041627.1 NaLiK_antip_UmpA 490 490 243 equivalog Y Y N Na,Li,K/H(+) antiporter subunit UmpA umpA GO:0006813,GO:0006814,GO:0015297 28652569 0 NCBIFAM Na,Li,K/H(+) antiporter subunit UmpA NF041668.1 trim_DfrL 370 370 176 exception Y Y Y trimethoprim-resistant dihydrofolate reductase DfrL dfrL 1.5.1.3 GO:0004146 36935372 0 NCBIFAM trimethoprim-resistant dihydrofolate reductase DfrL NF041737.1 choice_anch_S 70 70 256 equivalog Y Y N choice-of-anchor S family protein coaS 0 NCBIFAM choice-of-anchor S family protein NF041739.1 ArtH_Nterm 55 55 61 subfamily_domain Y Y N archaeosortase H N-terminal-like domain-containing protein 0 NCBIFAM archaeosortase H N-terminal-like domain NF042500.3 PF20400.3 BAR_4 27 27 192 domain Y N N BAR-like domain 0 EBI-EMBL BAR-like domain BAR-like domain This entry represents a BAR-like domain found in a variety of fungal proteins. (from Pfam) NF042635.3 PF20206.3 Tra1_ring 27 27 1682 domain Y N N Tra1 HEAT repeat ring region 28767037,29146944,29559617,31069110 0 EBI-EMBL Tra1 HEAT repeat ring region Tra1 HEAT repeat ring region This entry represents part of the Tra1 protein composed of alpha solenoid repeats that form a ring region [1]. Paper describing PDB structure 5oej. [1]. 29146944. Structure of the transcription activator target Tra1 within the chromatin modifying complex SAGA. Sharov G, Voltz K, Durand A, Kolesnikova O, Papai G, Myasnikov AG, Dejaegere A, Ben Shem A, Schultz P;. Nat Commun. 2017;8:1556. Paper describing PDB structure 5ojs. [2]. 28767037. Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 at 3.7 angstrom resolution. Diaz-Santin LM, Lukoyanova N, Aciyan E, Cheung AC;. Elife. 2017; [Epub ahead of print]. Paper describing PDB structure 5y81. [3]. 29559617. Architecture of the Saccharomyces cerevisiae NuA4/TIP60 complex. Wang X, Ahmad S, Zhang Z, Cote J, Cai G;. Nat Commun. 2018;9:1147. Paper describing PDB structure 6ig9. [4]. 31069110. Architecture of Saccharomyces cerevisiae SAGA complex. Liu G, Zheng X, Guan H, Cao Y, Qu H, Kang J, Ren X, Lei J, Dong MQ, Li X, Li H;. Cell Discov. 2019;5:25. (from Pfam) NF042708.3 PF20294.3 KMPT-N 28.9 28.9 66 domain Y N N KTSC and Metallopeptidase N-terminal fusion domain 33466489 0 EBI-EMBL KTSC and Metallopeptidase N-terminal fusion domain KTSC and Metallopeptidase N-terminal fusion domain Uncharacterized alpha/beta domain N-terminally fused to diverse Metallopeptidase (MPTase) and the lysyl tRNA synthetase KTSC RNA-binding domain protein. Currently observed in only the jumbo phages [1]. [1]. 33466489. Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts. M Iyer L, Anantharaman V, Krishnan A, Burroughs AM, Aravind L;. Viruses. 2021; [Epub ahead of print] (from Pfam) NF042717.3 PF20318.3 DUF6613 24.3 24.3 200 domain Y Y N DUF6613 domain-containing protein 0 EBI-EMBL Family of unknown function (DUF6613) Family of unknown function (DUF6613) This family of proteins is functionally uncharacterised. However, the contain an N-terminal Pfam:PF07963 suggesting these may be pilin proteins. This family of proteins is found in bacteria. Proteins in this family are typically between 203 and 237 amino acids in length. (from Pfam) NF042747.3 PF20450.3 PPV_E1_DBD 25 25 140 domain Y Y N DNA-binding domain-containing protein GO:0003677 10949036,15289463 0 EBI-EMBL Papillomavirus E1, DNA-binding domain Papillomavirus E1, DNA-binding domain This is the DNA-binding domain (DBD) of Papillomavirus E1 protein, a DNA helicase that is required for initiation of viral DNA replication. This protein forms a complex with the E2 protein Pfam:PF00508 at the origin of replication (ori) [1,2]. This domain is found in the central region of E1 and binds DNA at specific sites of viral origin, and also binds cooperatively with E2-DBD. This domain comprises a five-stranded antiparallel beta-sheet flanked by alpha helices on each side [2]. This domain binds originally as a dimer in which each monomer binds to one half-site of the palindromic E1 binding site, and promotes the assembly of the hexameric helicase on the ori [2]. E1 has a domain architecture and function similar to SV40 T-antigen [1]. [1]. 15289463. The X-ray structure of the papillomavirus helicase in complex with its molecular matchmaker E2. Abbate EA, Berger JM, Botchan MR;. Genes Dev. 2004;18:1981-1996. [2]. 10949036. Crystal structure of the DNA binding domain of the replication initiation protein E1 from papillomavirus. Enemark EJ, Chen G, Vaughn DE, Stenlund A, Joshua-Tor L;. Mol Cell. 2000;6:149-158. (from Pfam) NF042878.3 PF20483.3 Flavi_NS5_thumb 25 25 164 domain Y Y N NS5 RNA-directed RNA polymerase thumb domain-containing protein 28345656,32313955,8269709 0 EBI-EMBL Flavivirus RNA-directed RNA polymerase, thumb domain Flavivirus RNA-directed RNA polymerase, thumb domain Flaviviruses produce a large polyprotein from the ssRNA genome, encoding structural proteins required for virus assembly and non-structural (NS1-5) proteins involved in replication of the viral genome [1,2,3]. This polyprotein is cleaved by viral and cellular proteases to produce mature viral proteins. NS5 is the largest mature viral protein and contains a N-terminal methyltransferase (MTase) domain separated by a short linker from the C-terminal RNA-directed RNA polymerase domain (RdRp) that adopts a characteristic right-handed fingers-palm-thumb fold and possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases [2,3]. This entry represents the thumb domain of NS5 RdRp. NS5 binds to a the stem loop A (SLA) at the 5' extremity of Flavivirus genome and regulates translation of the viral genome [3]. [1]. 8269709. Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Koonin EV, Dolja VV;. Crit Rev Biochem Mol Biol 1993;28:375-430. [2]. 28345656. Structure and function of the Zika virus full-length NS5 protein. Zhao B, Yi G, Du F, Chuang YC, Vaughan RC, Sankaran B, Kao CC, Li P;. Nat Commun. 2017;8:14762. [3]. 32313955. The flavivirus polymerase NS5 regulates translation of viral genomic RNA. Fajardo T, Sanford TJ, Mears HV, Jasper A, Storrie S, Mansur DS, Sweeney TR;. Nucleic Acids Res. 2020;48:5081-5093. (from Pfam) NF044280.2 PF20653.2 COG6_C 26.4 26.4 462 domain Y N N Conserved Oligomeric Golgi complex subunit 6, C-terminal 29335562,34061181 0 EBI-EMBL Conserved Oligomeric Golgi complex subunit 6, C-terminal Conserved Oligomeric Golgi complex subunit 6, C-terminal COG6 is a component of the peripheral membrane COG complex that is involved in intra-Golgi protein trafficking. COG is located at the cis-Golgi, regulates tethering of retrograde intra-Golgi vesicles and consists of one octamer comprising two tetramers (COG1-4 and COG5-8) [1]. COG subunits belong to the Complex Associated with Tethering Containing Helical Rods (CATCHRs) family which also includes subunits from the evolutionary related GARP (Golgi-Associated Retrograde Protein), exocyst and Dsl1 complexes. CATCHRs proteins share a structural fold consisting of alpha-helical bundles in tandem at the C-terminal and a coiled-coil region at the N-terminal [1]. This entry represents the alpha-helical bundle found at the C-terminal of COG6. [1]. 34061181. Homology and Modular Evolution of CATCHR at the Origin of the Eukaryotic Endomembrane System. Santana-Molina C, Gutierrez F, Devos DP;. Genome Biol Evol. 2021; [Epub ahead of print]. [2]. 29335562. Cryo-EM structure of the exocyst complex. Mei K, Li Y, Wang S, Shao G, Wang J, Ding Y, Luo G, Yue P, Liu JJ, Wang X, Dong MQ, Wang HW, Guo W;. Nat Struct Mol Biol. 2018;25:139-146. (from Pfam) NF044308.2 PF20764.2 DUF6837 22 22 73 domain Y Y N DUF6837 domain-containing protein 0 EBI-EMBL Domain of unknown function (DUF6837) DUF6837 domain This domain is found in proteins from tailed bacteriophages and eukaryotes, including 201phi2-1p060 from Pseudomonas phage 201phi2-1 Its function is unknown. (from Pfam) NF044320.2 PF20821.2 C1_PlyCB 30.5 30.5 65 domain Y N N Streptococcus virus C1, PlyCB 22807482,26978792,33756056 0 EBI-EMBL Streptococcus virus C1, PlyCB Streptococcus virus C1, PlyCB PlyCB is one of the two components of the potent endolysin PlyC, an enzyme specific for streptococcal species. PlyC consists of a single PlyCA catalytic subunit in complex with eight PlyCB molecules arranged in a planar octameric ring. One surface of the PlyCB octamer is quite planar, whereas the other is more convex in shape. The bacterial cell wall binding is achieved through a cleft on PlyCB, which interacts strongly with phosphatidylserine so that PlyC can cross the epithelial cell membrane [1-3]. Paper describing PDB structure 4f87. [1]. 22807482. X-ray crystal structure of the streptococcal specific phage lysin PlyC. McGowan S, Buckle AM, Mitchell MS, Hoopes JT, Gallagher DT, Heselpoth RD, Shen Y, Reboul CF, Law RH, Fischetti VA, Whisstock JC, Nelson DC;. Proc Natl Acad Sci U S A. 2012;109:12752-12757. Paper describing PDB structure 4zrz. [2]. 26978792. A bacteriophage endolysin that eliminates intracellular streptococci. Shen Y, Barros M, Vennemann T, Gallagher DT, Yin Y, Linden SB, Heselpoth RD, Spencer DJ, Donovan DM, Moult J, Fischetti VA, Heinrich F, Losche M, Nelson DC;. Elife. 2016; [Epub ahead of print]. Paper describing PDB structure 7kwt. [3]. 33756056. High avidity drives the interaction between the streptococcal C1 phage endolysin, PlyC, with the cell surface carbohydrates of Group A Streptococcus. Broendum SS, Williams DE, Hayes BK, Kraus F, Fodor J, Clifton BE, Geert Volbeda A, Codee JDC, Riley BT, Drinkwater N, Farrow KA, Tsyganov K, Heselpoth RD, Nelson DC, Jackson CJ, Buckle AM, McGowan S;. Mol Microbiol. 2021;116:397-415. (from Pfam) NF044612.2 PF20760.2 P23-45_gp39_N 30 30 94 domain Y Y N phage protein Gp35 domain-containing protein 24589779,29165680 0 EBI-EMBL Thermus phage P23-45 gp39, N-terminal domain Thermus phage P23-45 gp39, N-terminal domain This domain is found at the N terminus in the protein gp35 from Thermus phage P23-45 and similar sequences from tailed bacteriophages. This protein binds the host's DNA-dependent RNA polymerase (RNAP), inhibiting host gene transcription while allowing transcription of phage genes. Structural studies show this core domain of the protein binds to the RNA beta-flap domain. It consists of a central beta sheet and a N-terminal helix [1, 2]. Paper describing PDB structure 3wod. [1]. 24589779. Structural basis for promoter specificity switching of RNA polymerase by a phage factor. Tagami S, Sekine S, Minakhin L, Esyunina D, Akasaka R, Shirouzu M, Kulbachinskiy A, Severinov K, Yokoyama S;. Genes Dev. 2014;28:521-531. Paper describing PDB structure 5xj0. [2]. 29165680. A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation. Ooi WY, Murayama Y, Mekler V, Minakhin L, Severinov K, Yokoyama S, Sekine SI;. Nucleic Acids Res. 2018;46:431-441. (from Pfam) NF044613.2 PF20762.2 DUF6836 24.2 24.2 115 domain Y Y N DUF6836 family protein 0 EBI-EMBL Domain of unknown function (DUF6836) DUF6836 family protein This domain is predominantly found in proteins from bacteria, including CLOLEP_02462 from Clostridium leptum. The function of this protein is unknown. (from Pfam) NF044672.2 PF20977.2 GatF 33.4 33.4 150 domain Y N N Glutamyl-tRNA(Gln) amidotransferase subunit F 19417106,21799017,24692665 0 EBI-EMBL Glutamyl-tRNA(Gln) amidotransferase subunit F Glutamyl-tRNA(Gln) amidotransferase subunit F GatFAB is a trimeric tRNA-dependent amidotransferase (AdT) that allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in the mitochondria [1,2]. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). This family represents GatF (also known as GFT1), an essential subunit of the yeast tRNA-dependent amidotransferase [1]. GatF is a fungi-specific orthologue of the GatC subunit found in all other known heterotrimeric AdTs (GatCAB) [3]. GatF C-terminal encircles the GatA-GatB interface in the same manner as GatC to maintain GatA-GatB assembly, whereas the N-terminal region mediates additional hydrophobic and hydrophilic interactions with GatA [3], which may modulate GatA folding and stability [3]. [1]. 21799017. Characterization of Gtf1p, the connector subunit of yeast mitochondrial tRNA-dependent amidotransferase. Barros MH, Rak M, Paulela JA, Tzagoloff A;. J Biol Chem. 2011;286:32937-32947. [2]. 19417106. Yeast mitochondrial Gln-tRNA(Gln) is generated by a GatFAB-mediated transamidation pathway involving Arc1p-controlled subcellular sorting of cytosolic GluRS. Frechin M, Senger B, Braye M, Kern D, Martin RP, Becker HD;. Genes Dev. 2009;23:1119-1130. [3]. 24692665. Crystal structure of Saccharomyces cerevisiae mitochondrial GatFAB reveals a novel subunit assembly in tRNA-dependent amidotransferases. Araiso Y, Huot JL, Sekiguchi T, Frechin M, Fischer F, Enkler L, Senger B, Ishitani R, Becker HD, Nureki O;. Nucleic Acids Res. 2014;42:6052-6063. (from Pfam) NF044676.2 PF21005.2 MCEL_GT_OB 27 27 138 domain Y N N mRNA-capping enzyme catalytic subunit, GTase, OB fold 24607143 0 EBI-EMBL mRNA-capping enzyme catalytic subunit, GTase, OB fold mRNA-capping enzyme catalytic subunit, GTase, OB fold mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the methylation of the GpppN cap [1-3]. It consists of an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module and a C-terminal guanine-N7-methyltransferase (MTase) module (Pfam:PF03291). The N-terminal module comprises a TPase domain (Pfam:PF10640), followed by the GTase at the C-terminal, which consists of the nucleotidyltransferase (NTPase, Pfam:PF21004) and OB fold (represented in this entry) domains [1]. This domain contains an essential motif (RxxK) for GTase activity. [1]. 24607143. Crystal structure of vaccinia virus mRNA capping enzyme provides insights into the mechanism and evolution of the capping apparatus. Kyrieleis OJ, Chang J, de la Pena M, Shuman S, Cusack S;. Structure. 2014;22:452-465. (from Pfam) NF044798.2 PF21434.2 TerS_N 27 27 50 domain Y N N Phage G20C small terminase, N-terminal domain 32014998 0 EBI-EMBL Phage G20C small terminase, N-terminal domain Phage G20C small terminase, N-terminal domain This entry represents the N-terminal helix-turn-helix domain of the terminase small subunit (TerS) from Thermus phage G20c [1], which oligomerises into a nonamer that binds DNA, stimulates terminase large subunit (TerL) ATPase activity, and inhibits TerL nuclease activity [1]. Paper describing PDB structure 6v1i. [1]. 32014998. A thermophilic phage uses a small terminase protein with a fixed helix-turn-helix geometry. Hayes JA, Hilbert BJ, Gaubitz C, Stone NP, Kelch BA;. J Biol Chem. 2020;295:3783-3793. (from Pfam) NF044938.2 PF20907.2 Flav_NS3-hel_C 27 27 144 domain Y N N Flavivirus NS3 helicase, C-terminal helical domain 27399257,29165589,29633968 0 EBI-EMBL Flavivirus NS3 helicase, C-terminal helical domain Flavivirus NS3 helicase, C-terminal helical domain This domain is found at the C-terminal end of NS3 helicase (Non- structural protein 3-helicase, NS3-Hel) found in Flavivirus such as Zika virus (ZIKV) and Dengue virus type 1 (DENV-1). This protein binds RNA and unwinds dsRNA in the 3' to 5' direction. It consists of three domains. This entry represent the final domain, which is mostly alpha-helical [1,2]. A highly conserved R residue located in this domain was proven essential for the enzymatic activities of the protein [3]. [1]. 27399257. Structure of the NS3 helicase from Zika virus. Jain R, Coloma J, Garcia-Sastre A, Aggarwal AK;. Nat Struct Mol Biol. 2016;23:752-754. [2]. 29633968. Structural view of the helicase reveals that Zika virus uses a conserved mechanism for unwinding RNA. Li L, Wang J, Jia Z, Shaw N;. Acta Crystallogr F Struct Biol Commun. 2018;74:205-213. [3]. 29165589. NS3 helicase from dengue virus specifically recognizes viral RNA sequence to ensure optimal replication. Swarbrick CMD, Basavannacharya C, Chan KWK, Chan SA, Singh D, Wei N, Phoo WW, Luo D, Lescar J, Vasudevan SG;. Nucleic Acids Res. 2017;45:12904-12920. (from Pfam) NF044959.2 PF21004.2 MCEL_GT_NTPase 27 27 113 domain Y N N mRNA capping enzyme catalytic subunit, GTase, NTPase domain 17989694,24607143,8227060,8662635 0 EBI-EMBL mRNA capping enzyme catalytic subunit, GTase, NTPase domain mRNA capping enzyme catalytic subunit, GTase, NTPase domain mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the methylation of the GpppN cap [1-3]. It consists of an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module, and a C-terminal guanine-N7-methyltransferase (MTase) module (Pfam:PF03291) [4]. The N-terminal module comprises a TPase domain (Pfam:PF10640), followed by the GTase at the C-terminal, which consists of the nucleotidyltransferase (NTPase, this entry) and OB fold (Pfam:PF21005) domains [3,4]. The TPase and GTase modules stabilize their active conformations and their contacts also clamp the NTase and OB fold. [1]. 8227060. Identification of the vaccinia virus mRNA guanyltransferase active site lysine. Niles EG, Christen L;. J Biol Chem. 1993;268:24986-24989. [2]. 8662635. Domain structure of the vaccinia virus mRNA capping enzyme. Expression in Escherichia coli of a subdomain possessing the RNA 5'-triphosphatase and guanylyltransferase activities and a kinetic comparison to the full-size enzyme. Myette JR, Niles EG;. J Biol Chem. 1996;271:11936-11944. [3]. 17989694. Structural insights into the mechanism and evolution of the vaccinia virus mRNA cap N7 methyl-transferase. De la Pena M, Kyrieleis OJ, Cusack S;. EMBO J. 2007;26:4913-4925. [4]. 24607143. Crystal structure of vaccinia virus mRNA capping enzyme provides insights into the mechanism and evolution of the capping apparatus. Kyrieleis OJ, Chang J, de la Pena M, Shuman S, Cusack S;. Structure. 2014;22:4. TRUNCATED at 1650 bytes (from Pfam) NF045120.2 PF21659.2 Flavi_E_stem 27 27 95 domain Y N N Flavivirus envelope glycoprotein E, stem/anchor domain 14528291,23241927,23637405,23637416,25698059 0 EBI-EMBL Flavivirus envelope glycoprotein E, stem/anchor domain Flavivirus envelope glycoprotein E, stem/anchor domain This entry represents the stem/anchor domain found at the C-terminal of envelope glycoprotein E from Flavivirus. This domain comprises a stem region followed by two transmembrane anchor domains [1-5]. Paper describing PDB structure 1p58. [1]. 14528291. Visualization of membrane protein domains by cryo-electron microscopy of dengue virus. Zhang W, Chipman PR, Corver J, Johnson PR, Zhang Y, Mukhopadhyay S, Baker TS, Strauss JH, Rossmann MG, Kuhn RJ;. Nat Struct Biol. 2003;10:907-912. Paper describing PDB structure 3j27. [2]. 23241927. Cryo-EM structure of the mature dengue virus at 3.5-A resolution. Zhang X, Ge P, Yu X, Brannan JM, Bi G, Zhang Q, Schein S, Zhou ZH;. Nat Struct Mol Biol. 2013;20:105-110. Paper describing PDB structure 3j6s. [3]. 25698059. A highly potent human antibody neutralizes dengue virus serotype 3 by binding across three surface proteins. Fibriansah G, Tan JL, Smith SA, de Alwis R, Ng TS, Kostyuchenko VA, Jadi RS, Kukkaro P, de Silva AM, Crowe JE, Lok SM;. Nat Commun. 2015;6:6341. Paper describing PDB structure 3zko. [4]. 23637405. Structural changes in dengue virus when exposed to a temperature of 37 degrees C. Fibriansah G, Ng TS, Kostyuchenko VA, Lee J, Lee S, Wang J, Lok SM;. J Virol. 2013;87:7585-7592. Paper describing PDB structure 4b03. [5]. 23637416. Immature and mature dengue serotype 1 virus structures provide insight into the maturation process. Kostyuchenko VA, Zhang Q, Tan JL, Ng TS, Lok SM;. J Virol. 2013;87:7700-7707. (from Pfam) NF045121.2 PF21660.2 MCP_C 27 27 86 domain Y Y N coat protein domain-containing protein 19934032,28639939 0 EBI-EMBL Filamentous archaeal viruses coat protein, C-terminal Filamentous archaeal viruses coat protein, C-terminal This entry represents the C-terminal domain of a major coat protein from Acidianus filamentous virus 1 [1,2] which adopts a four-helix bundle fold. Paper describing PDB structure 3fbz. [1]. 19934032. Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage. Goulet A, Blangy S, Redder P, Prangishvili D, Felisberto-Rodrigues C, Forterre P, Campanacci V, Cambillau C;. Proc Natl Acad Sci U S A. 2009;106:21155-21160. Paper describing PDB structure 5w7g. [2]. 28639939. Model for a novel membrane envelope in a filamentous hyperthermophilic virus. Kasson P, DiMaio F, Yu X, Lucas-Staat S, Krupovic M, Schouten S, Prangishvili D, Egelman EH;. Elife. 2017; [Epub ahead of print] (from Pfam) NF045227.2 PF20837.2 P1 27 27 757 domain Y Y N major inner capsid protein P1 23891288,23891291,28287099 0 EBI-EMBL Major inner capsid protein P1 major inner capsid protein P1 Major inner capsid protein P1 forms the inner T=1 shell of Bacteriophage phi-6, a dodecahedral polymerase complex (PC) that contains the three viral dsRNA segments. The protein folds into a flattened trapezoid shape with a mostly alpha-helical fold. It was initially though to adopt a funnel-shaped pentameric assembly, but later research has shown dimers of different P1 chains are also present in the virus capsid [1-3]. Paper describing PDB structure 4btg. [1]. 23891288. Subunit folds and maturation pathway of a dsRNA virus capsid. Nemecek D, Boura E, Wu W, Cheng N, Plevka P, Qiao J, Mindich L, Heymann JB, Hurley JH, Steven AC;. Structure. 2013;21:1374-1383. Paper describing PDB structure 4btp. [2]. 23891291. Plate tectonics of virus shell assembly and reorganization in phage phi8, a distant relative of mammalian reoviruses. El Omari K, Sutton G, Ravantti JJ, Zhang H, Walter TS, Grimes JM, Bamford DH, Stuart DI, Mancini EJ;. Structure. 2013;21:1384-1395. Paper describing PDB structure 5muu. [3]. 28287099. Double-stranded RNA virus outer shell assembly by bona fide domain-swapping. Sun Z, El Omari K, Sun X, Ilca SL, Kotecha A, Stuart DI, Poranen MM, Huiskonen JT;. Nat Commun. 2017;8:14814. (from Pfam) NF045500.1 Omp28_seleno 200 200 377 equivalog_domain Y Y N Omp28-related selenoprotein 12030966,35883471 0 NCBIFAM Omp28-related selenoprotein Members of this family are selenoproteins distantly related to the Porphyromonas gingivalis protein named Omp28 (e.g. WP_012457262.1). A selenocysteine-containing motif UPYCP aligns to CLYCP in Omp28. Members have been found, so far, primarily in Candidatus Marinimicrobia species. Some members of this family have a long C-terminal extension. The function is unknown. NF045501.1 HUGP_GUXX-star 325 325 236 exception Y Y N HUGP/GUXX-star fusion selenoprotein hgfS uxx4 0 NCBIFAM HUGP/GUXX-star fusion selenoprotein The N-terminal region of proteins in this family is a variant form of C-GCAxxG-C-C domain with a selenocysteine-containing motif HUGP. The C-terminal domain ends with an easily missed tripeptide motif UXX-star, with star signifying that a stop codon follows the UXX motif. This unusual architecture appears to signify an uncommon fusion of two normally separate selenoproteins. We assign the gene symbol hgfS, for HUGP, GUXX Fusion Selenoproprotein. NF045528.1 heimosortase 130 130 199 equivalog Y Y N heimdallarchaeosortase artI 3.4.22.- GO:0004197,GO:0006605,GO:0016020,GO:0043687 22037399 0 NCBIFAM heimdallarchaeosortase Members of this family are heimdallarchaeosortase (archaeosortase ArtI), found so far exclusively in Candidatus Heimdallarchaeota archaea, a heterotrophic archaeal lineage observed in anaerobic sediments, considered the branch of the archaea most closely related to eukaryotes, with DNA sequence data so far available only from uncultured cells, primarily as metagenome-assembled genomes (MAGs). The archaeosortases in this family are variable in domain architecture, as about half have a long additional C-terminal domain. Members of this family show strongest homology to archaeosortase ArtA, and appear to be cleave sorting signals with a similar PGF-like signature motif (see model NF045529). NF045604.1 cas_Cas12e_CasX 200 200 886 equivalog Y Y N type V CRISPR RNA-guided endonuclease Cas12e/CasX GO:0004521 28005056,31248380 0 NCBIFAM type V CRISPR RNA-guided endonuclease Cas12e/CasX NF046170.1 PF22009.1 YLDV-IL18BP-like 27 27 104 domain Y N N Yaba-Like Disease Virus IL18BP 22927815 0 EBI-EMBL Yaba-Like Disease Virus IL18BP Yaba-Like Disease Virus IL18BP YLDV-IL18BP is unique among the diverse family of mammalian and poxvirus IL18BPs in that it uses a bivalent binding mode and a unique set of interacting residues for binding IL18 [1]. YLDV-IL18BP binds to the same surface of IL18 used by other IL18BPs, suggesting that all IL18BPs use a conserved inhibitory mechanism by blocking a putative receptor-binding site on IL18. This domain adopts a typical Ig-like fold. Paper describing PDB structure 4eee. [1]. 22927815. A unique bivalent binding and inhibition mechanism by the yatapoxvirus interleukin 18 binding protein. Krumm B, Meng X, Wang Z, Xiang Y, Deng J;. PLoS Pathog. 2012;8:e1002876. (from Pfam) NF046242.1 PF22325.1 CR4_N 27 27 80 domain Y N N Interferon-gamma receptor, N-terminal domain 18252829 0 EBI-EMBL Interferon-gamma receptor, N-terminal domain Interferon-gamma receptor, N-terminal domain This domain is found at the N-terminal end of Interferon-gamma receptor from Ectromelia virus (C4R) and simiral viral sequences. CR4 consists of two fibronectin type III domains (FBNIII) containing seven conserved beta-strands each: this entry and Pfam:PF07140 [1]. Paper describing PDB structure 3bes. [1]. 18252829. Structure and m echanism of IFN-gamma antagonism by an orthopoxvirus IFN-gamma-binding protein. Nuara AA, Walter LJ, Logsdon NJ, Yoon SI, Jones BC, Schriewer JM, Buller RM, Walter MR;. Proc Natl Acad Sci U S A. 2008;105:1861-1866. (from Pfam) NF046713.1 PF22246.1 NeqB_N 27 27 59 domain Y Y N NeqB domain-containing protein 26370083 0 EBI-EMBL NeqB N-terminal domain NeqB domain-containing protein This entry represents the N-terminal domain of the NeqB, a regulatory ATP synthase subunit [1]. Paper describing PDB structure 5bn3. [1]. 26370083. Structural Basis for a Unique ATP Synthase Core Complex from Nanoarcheaum equitans. Mohanty S, Jobichen C, Chichili VPR, Velazquez-Campoy A, Low BC, Hogue CWV, Sivaraman J;. J Biol Chem. 2015;290:27280-27296. (from Pfam) NF046791.1 PF22663.1 Rhv_5 27 27 216 domain Y N N Picornavirus coat protein 15299757,7773791,8382928,9083115,9253417 0 EBI-EMBL Picornavirus coat protein Picornavirus coat protein This domain is found in capsid proteins from picornavirus, such as enterovirus, rhinovirus and foot-and-mouth disease virus [1-5]. Paper describing PDB structure 1al2. [1]. 9253417. Structural studies of poliovirus mutants that overcome receptor defects. Wien MW, Curry S, Filman DJ, Hogle JM;. Nat Struct Biol. 1997;4:666-674. Paper describing PDB structure 1aym. [2]. 9083115. The refined structure of human rhinovirus 16 at 2.15 A resolution: implications for the viral life cycle. Hadfield AT, Lee Wm, Zhao R, Oliveira MA, Minor I, Rueckert RR, Rossmann MG;. Structure 1997;5:427-441. Paper describing PDB structure 1bbt. [3]. 8382928. Methods used in the structure determination of foot-and-mouth disease virus. Fry E, Acharya R, Stuart D;. Acta Crystallogr A. 1993;49:45-55. Paper describing PDB structure 1bev. [4]. 7773791. Implications for viral uncoating from the structure of bovine enterovirus. Smyth M, Tate J, Hoey E, Lyons C, Martin S, Stuart D;. Nat Struct Biol. 1995;2:224-231. Paper describing PDB structure 1cov. [5]. 15299757. Structure determination of coxsackievirus B3 to 3.5 A resolution. Muckelbauer JK, Kremer M, Minor I, Tong L, Zlotnick A, Johnson JE, Rossmann MG;. Acta Crystallogr D Biol Crystallogr. 1995;51:871-887. (from Pfam) NF047119.1 PF22169.1 AP205_coat 27 27 115 domain Y N N AP205 coat protein 27489348,27591890 0 EBI-EMBL AP205 coat protein AP205 coat protein AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence that is not similar to any other known single-stranded RNA phage protein. The AP205 coat protein forms a dimer which adopts the conserved Leviviridae coat protein core fold with exception of the N-terminal region. This coat protein has a similar structure that is circularly permuted compared to the other coat proteins [1]. Paper describing PDB structure 5fs4. [1]. 27591890. Structure of AP205 Coat Protein Reveals Circular Permutation in ssRNA Bacteriophages. Shishovs M, Rumnieks J, Diebolder C, Jaudzems K, Andreas LB, Stanek J, Kazaks A, Kotelovica S, Akopjana I, Pintacuda G, Koning RI, Tars K;. J Mol Biol. 2016;428:4267-4279. Paper describing PDB structure 5jzr. [2]. 27489348. Structure of fully protonated proteins by proton-detected magic-angle spinning NMR. Andreas LB, Jaudzems K, Stanek J, Lalli D, Bertarello A, Le Marchand T, Cala-De Paepe D, Kotelovica S, Akopjana I, Knott B, Wegner S, Engelke F, Lesage A, Emsley L, Tars K, Herrmann T, Pintacuda G;. Proc Natl Acad Sci U S A. 2016;113:9187-9192. (from Pfam) NF047161.1 PF22355.1 tRNA_int_end_N3 26 26 55 domain Y Y N tRNA-splicing endonuclease beta subunit domain-containing protein 19578064 0 EBI-EMBL tRNA-splicing endonuclease subunit NEQ261 N-terminal domain tRNA-splicing endonuclease beta subunit domain-containing protein This entry represents the N-terminal domain of the tRNA-splicing endonuclease structural (beta) subunit NEQ261 from Nanoarchaeum equitans [1]. Paper describing PDB structure 3iey. [1]. 19578064. Crystal structure and assembly of the functional Nanoarchaeum equitans tRNA splicing endonuclease. Mitchell M, Xue S, Erdman R, Randau L, Soll D, Li H;. Nucleic Acids Res. 2009;37:5793-5802. (from Pfam) NF047175.1 PF22387.1 PhiCb5_coat 27 27 89 domain Y N N Phage phiCb5, coat protein 19559027 0 EBI-EMBL Phage phiCb5, coat protein Phage phiCb5, coat protein This family includes Coat protein from Caulobacter phage phiCb5 (Swiss:D7RIC2), which consists of an N-terminal loop, a five -stranded beta-sheet and a C-terminal arm containing two helices. [1]. Paper describing PDB structure 2w4y. [1]. 19559027. The structure of bacteriophage phiCb5 reveals a role of the RNA genome and metal ions in particle stability and assembly. Plevka P, Kazaks A, Voronkova T, Kotelovica S, Dishlers A, Liljas L, Tars K;. J Mol Biol. 2009;391:635-647. (from Pfam) NF047338.1 gluta_UXX_star_3 97 97 70 exception Y Y N UXX-star (seleno)protein family 3 uxx3 0 NCBIFAM UXX-star (seleno)protein family 3 Members of this family are the third in a series glutaredoxin-like proteins, homologous to but distinct from a number of other families in which the last three amino acids are usually UXX but sometimes CXX. In this family, known so far only from uncultured bacteria, the final three amino acids are occassionally UXF but more often [S/T]XF. Note that selenoprotein families in which U replaces S or T instead of C are unusual. NF047647.1 UXPK-star_dom 35 35 34 domain Y Y N UXPK-star domain-containing selenoprotein 0 NCBIFAM UXPK-star domain The UXPK-star (Sec-Xaa-Pro-Lys-stop) domain occurs typically as the second selenocysteine-containing domain in a double (or triple) bacterial selenoprotein. NF047649.1 MTase_UXPK_star 460 460 283 exception Y Y N methyltransferase/UXPK-star double selenoprotein 0 NCBIFAM methyltransferase/UXPK-star double selenoprotein TIGR00058.1 TIGR00058 Hemerythrin 131.85 131.85 115 subfamily Y Y N hemerythrin family non-heme iron protein 0 JCVI hemerythrin family non-heme iron protein hemerythrin family non-heme iron protein This family includes oxygen carrier proteins of various oligomeric states from the vascular fluid (hemerythrin) and muscle (myohemerythrin) of some marine invertebrates. Each unit binds 2 non-heme Fe using 5 H, one E and one D. One member of this family,from the sandworm Nereis diversicolor, is an unusual (non-metallothionein) cadmium-binding protein. Homologous proteins, excluded from this narrowly defined family, are found in archaea and bacteria (see PF01814). TIGR00272.1 TIGR00272 DPH2 184.05 184.05 497 equivalog Y Y N diphthamide biosynthesis protein 2 GO:0017183 0 JCVI diphthamide biosynthesis protein 2 diphthamide biosynthesis protein 2 This protein has been shown in Saccharomyces cerevisiae to be one of several required for the modification of a particular histidine residue of translation elongation factor 2 to diphthamide. This modified site can then become the target for ADP-ribosylation by diphtheria toxin. TIGR00424.1 TIGR00424 APS_reduc 553.2 553.2 464 equivalog Y Y N 5'-adenylylsulfate reductase, thioredoxin-independent GO:0006790,GO:0016667 8917600 0 JCVI 5'-adenylylsulfate reductase, thioredoxin-independent 5'-adenylylsulfate reductase, thioredoxin-independent This enzyme, involved in the assimilation of inorganic sulfate, is closely related to the thioredoxin-dependent PAPS reductase of Bacteria (CysH) and Saccharomyces cerevisiae. However, it has its own C-terminal thioredoxin-like domain and is not thioredoxin-dependent. Also, it has a substrate preference for 5'-adenylylsulfate (APS) over 3'-phosphoadenylylsulfate (PAPS) so the pathway does not require an APS kinase (CysC) to convert APS to PAPS. Arabidopsis thaliana appears to have three isozymes, all able to complement E. coli CysH mutants (even in backgrounds lacking thioredoxin or APS kinase) but likely localized to different compartments in Arabidopsis. TIGR00469.1 TIGR00469 pheS_mito 258.35 258.35 451 equivalog Y Y N phenylalanine--tRNA ligase 6.1.1.20 GO:0004826,GO:0005739,GO:0006432 10329163,1924298 0 JCVI phenylalanine--tRNA ligase phenylalanine--tRNA ligase, mitochondrial type Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in Bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases. This HMM models the experimental example from Saccharomyces cerevisiae (designated MSF1) and its orthologs from other eukaryotic species. TIGR00495.1 TIGR00495 crvDNA_42K 430.05 430.05 383 hypoth_equivalog Y Y N ErbB3-binding protein EBP1 17024182,17690690,7556453 0 JCVI DNA-binding protein, 42 kDa ErbB3-binding protein EBP1 Proteins identified by this HMM have been identified in a number of species as a nuclear (but not nucleolar) protein with a cell cycle dependence. Various names given to members of this family have included cell cycle protein p38-2G4, DNA-binding protein GBP16, and proliferation-associated protein 1. This protein is closely related to methionine aminopeptidase, a cobalt-binding protein. TIGR00535.1 TIGR00535 SAM_DCase 233.15 233.15 334 equivalog Y Y N adenosylmethionine decarboxylase 4.1.1.50 GO:0004014,GO:0006597,GO:0008295 2266128 0 JCVI S-adenosylmethionine decarboxylase proenzyme S-adenosylmethionine decarboxylase proenzyme This enzyme is a key regulatory enzyme of the polyamine synthetic pathway. This protein is a pyruvoyl-dependent enzyme. The proenzyme is cleaved at a Ser residue that becomes a pyruvoyl group active site. TIGR00569.1 TIGR00569 ccl1 250.35 250.35 305 subfamily N N N cyclin ccl1 0 JCVI cyclin ccl1 cyclin ccl1 All proteins in this family for which functions are known are cyclins that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00570.1 TIGR00570 cdk7 160.2 160.2 309 equivalog Y Y N CDK-activating kinase assembly factor MAT1 GO:0000109,GO:0004693,GO:0005675,GO:0006289,GO:0006352 7553872 0 JCVI CDK-activating kinase assembly factor MAT1 CDK-activating kinase assembly factor MAT1 All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00578.1 TIGR00578 ku70 194.25 194.25 586 superfamily N N N ATP-dependent DNA helicase II, 70 kDa subunit (ku70) 0 JCVI ATP-dependent DNA helicase II, 70 kDa subunit (ku70) ATP-dependent DNA helicase II, 70 kDa subunit (ku70) Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast. TIGR00583.1 TIGR00583 mre11 434.6 434.6 405 equivalog Y Y N DNA repair protein (mre11) GO:0004519,GO:0006281,GO:0006303,GO:0008408,GO:0030870 0 JCVI DNA repair protein (mre11) DNA repair protein (mre11) All proteins in this family for which functions are known are subunits of a nuclease complex made up of multiple proteins including MRE11 and RAD50 homologs. The functions of this nuclease complex include recombinational repair and non-homolgous end joining. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The proteins in this family are distantly related to proteins in the SbcCD complex of bacteria. TIGR00584.1 TIGR00584 mug 402.6 402.6 328 subfamily N N N mismatch-specific thymine-DNA glycosylate (mug) 12711670,18587051 0 JCVI mismatch-specific thymine-DNA glycosylate (mug) mismatch-specific thymine-DNA glycosylate (mug) All proteins in this family for whcih functions are known are G-T or G-U mismatch glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Used 2pf model. TIGR00596.1 TIGR00596 rad1 806.65 806.65 813 subfamily Y Y N DNA repair protein, RAD1 family 0 JCVI DNA repair protein (rad1) DNA repair protein, RAD1 family All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologs of these genes, but the function of these Archaeal genes is not known, so we have set our cutoff to only pick up the eukaryotic genes. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit TIGR00597.1 TIGR00597 rad10 72.9 72.9 112 subfamily Y Y N nucleotide excision repair endonuclease ERCC1/Rad10 GO:0004520,GO:0006289 16076955,8479526,8621533 0 JCVI DNA repair protein rad10 nucleotide excision repair endonuclease ERCC1/Rad10 All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00598.1 TIGR00598 rad14 113.15 113.15 171 equivalog Y Y N XPA/Rad14 family DNA repair protein GO:0000109,GO:0000715,GO:0006289 1741034,1764072,2234061,8621533 0 JCVI DNA repair protein XPA/Rad14 family DNA repair protein All proteins in this family for which functions are known are used for the recognition of DNA damage as part of nucleotide excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00599.1 TIGR00599 rad18 175.05 175.05 397 equivalog Y Y N DNA repair protein rad18 GO:0003697,GO:0006301,GO:0006513,GO:0061630 0 JCVI DNA repair protein rad18 DNA repair protein rad18 All proteins in this family for which functions are known are involved in nucleotide excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00600.1 TIGR00600 rad2 1204.4 1204.4 1039 subfamily N N N DNA excision repair protein (rad2) 0 JCVI DNA excision repair protein (rad2) DNA excision repair protein (rad2) All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00601.1 TIGR00601 rad23 207.3 207.3 381 equivalog Y Y N UV excision repair protein Rad23 GO:0006289 0 JCVI UV excision repair protein Rad23 UV excision repair protein Rad23 All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00602.1 TIGR00602 rad24 482.55 482.55 640 subfamily N N N checkpoint protein rad24 0 JCVI checkpoint protein rad24 checkpoint protein rad24 All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00605.2 TIGR00605 rad4 400 400 683 subfamily Y Y N XPC/Rad4 family nucleotide excision DNA repair protein 0 JCVI DNA repair protein rad4 XPC/Rad4 family nucleotide excision DNA repair protein All proteins in this family for which functions are known are involved in targeting nucleotide excision repair to specific regions of the genome. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00606.1 TIGR00606 rad50 453.75 453.75 1311 subfamily Y Y N DNA repair protein Rad50 19308707,29374232 0 JCVI rad50 DNA repair protein Rad50 All proteins in this family for which functions are known are involved in recombination, recombinational repair, and/or non-homologous end joining. They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This model identifies eukaryotic but not archaeal Rad50 proteins. TIGR00607.1 TIGR00607 rad52 224.8 224.8 161 subfamily Y Y N DNA repair protein, RAD52 family 0 JCVI recombination protein rad52 DNA repair protein, RAD52 family All proteins in this family for which functions are known are involved in recombination and recombination repair. Their exact biochemical activity is not yet known. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00617.1 TIGR00617 rpa1 334.2 334.2 608 subfamily N N N replication factor-a protein 1 (rpa1) 0 JCVI replication factor-a protein 1 (rpa1) replication factor-a protein 1 (rpa1) All proteins in this family for which functions are known are part of a multiprotein complex made up of homologs of RPA1, RPA2 and RPA3 that bind ssDNA and function in the recognition of DNA damage for nucleotide excision repair This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00622.1 TIGR00622 ssl1 45.1 45.1 112 subfamily Y Y N TFIIH complex SSL1-like subunit 30798933 0 JCVI transcription factor ssl1 TFIIH complex SSL1-like subunit All proteins in this family for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00625.1 TIGR00625 tfb2 320.7 320.7 448 subfamily N N N transcription factor Tfb2 0 JCVI transcription factor Tfb2 transcription factor Tfb2 All proteins in this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00627.1 TIGR00627 tfb4 355.05 355.05 284 subfamily N N N transcription factor tfb4 0 JCVI transcription factor tfb4 transcription factor tfb4 All proteins in this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00699.1 TIGR00699 GABAtrns_euk 567.15 567.15 464 equivalog Y Y N 4-aminobutyrate--2-oxoglutarate transaminase 2.6.1.19 GO:0009448 0 JCVI 4-aminobutyrate aminotransferase 4-aminobutyrate--2-oxoglutarate transaminase This enzyme is a class III pyridoxal-phosphate-dependent aminotransferase. This model describes known eukaryotic examples of the enzyme. The degree of sequence difference between this set and known bacterial examples is greater than the distance between either set the most similar enzyme with distinct function, and so separate models are built for prokaryotic and eukaryotic sets. Alternate names include GABA transaminase, gamma-amino-N-butyrate transaminase, and beta-alanine--oxoglutarate aminotransferase. TIGR00727.1 TIGR00727 ISP4_OPT 438.7 438.7 681 equivalog Y Y N small oligopeptide transporter, OPT family GO:0035673 9043116,9643541 0 JCVI small oligopeptide transporter, OPT family small oligopeptide transporter, OPT family This HMM represents a family of transporters of small oligopeptides, demonstrated experimentally in three different species of yeast. A set of related proteins from the plant Arabidopsis thaliana forms an outgroup to the yeast set by neighbor joining analysis but is remarkably well conserved and is predicted here to have equivalent function. TIGR00798.1 TIGR00798 mtc 322.8 322.8 317 subfamily Y Y N sideroflexin family mitochondrial carrier protein 20737508,30442778 0 JCVI tricarboxylate carrier sideroflexin family mitochondrial carrier protein The MTC family consists of a limited number of homologues, all from eukaryotes. A single member of the family has been functionally characterized, the tricarboxylate carrier from rat liver mitochondria. The rat liver mitochondrial tricarboxylate carrier has been reported to transport citrate, cis-aconitate, threo-D-isocitrate, D- and L-tartrate, malate, succinate and phosphoenolpyruvate. It presumably functions by a proton symport mechanism. TIGR00799.1 TIGR00799 mtp 181.3 181.3 258 subfamily N N N Golgi 4-transmembrane spanning transporter 8661146 0 JCVI Golgi 4-transmembrane spanning transporter Golgi 4-transmembrane spanning transporter The proteins of the MET family have 4 TMS regions and are located in late endosomal or lysosomal membranes. Substrates of the mouse MTP transporter include thymidine, both nucleoside and nucleobase analogues, antibiotics, anthracyclines, ionophores and steroid hormones. MET transporters may be involved in the subcellular compartmentation of steroid hormones and other compounds.Drug sensitivity by mouse MET was regulated by compounds that inhibit lysosomal function, interface with intracellular cholesterol transport, or modulate the multidrug resistance phenotype of mammalian cells. Thus, MET family members may compartmentalize diverse hydrophobic molecules, thereby affecting cellular drug sensitivity,nucleoside/nucleobase availability and steroid hormone responses. TIGR00803.1 TIGR00803 nst 55.85 55.85 222 subfamily Y Y N solute carrier family 35 transporter 0 JCVI UDP-galactose transporter solute carrier family 35 transporter The 10-12 TMS Nucleotide Sugar Transporters (TC 2.A.7.10) Nucleotide-sugar transporters (NSTs) are found in the Golgi apparatus and the endoplasmic reticulum of eukaryotic cells. Members of the family have been sequenced from yeast, protozoans and animals. Animals such as C. elegans possess many of these transporters. Humans have at least two closely related isoforms of the UDP-galactose:UMP exchange transporter. NSTs generally appear to function by antiport mechanisms, exchanging a nucleotide-sugar for a nucleotide. Thus, CMP-sialic acid is exchanged for CMP; GDP-mannose is preferentially exchanged for GMP, and UDP-galactose and UDP-N-acetylglucosamine are exchanged for UMP (or possibly UDP). Other nucleotide sugars (e.g., GDP-fucose, UDP-xylose, UDP-glucose, UDP-N-acetylgalactosamine, etc.) may also be transported in exchange for various nucleotides, but their transporters have not been molecularly characterized. Each compound appears to be translocated by its own transport protein. Transport allows the compound, synthesized in the cytoplasm, to be exported to the lumen of the Golgi apparatus or the endoplasmic reticulum where it is used for the synthesis of glycoproteins and glycolipids. TIGR00805.1 TIGR00805 oat 280 280 639 subfamily Y Y N OAT family organic anion transporter 0 JCVI sodium-independent organic anion transporter OAT family organic anion transporter The Organo Anion Transporter (OAT) Family (TC 2.A.60) Proteins of the OAT family catalyze the Na+-independent facilitated transport of organic anions such as bromosulfobromophthalein and prostaglandins as well as conjugated and unconjugated bile acids (taurocholate and cholate, respectively). These transporters have been characterized in mammals, but homologues are present in C. elegans and A. thaliana. Some of the mammalian proteins exhibit a high degree of tissue specificity. For example, the rat OAT is found at high levels in liver and kidney and at lower levels in other tissues. These proteins possess 10-12 putative a-helical transmembrane spanners. They may catalyze electrogenic anion uniport or anion exchange. TIGR00806.1 TIGR00806 rfc 227.4 227.4 511 equivalog Y Y N reduced folate carrier GO:0008517,GO:0015884 0 JCVI reduced folate carrier reduced folate carrier The Reduced Folate Carrier (RFC) Family (TC 2.A.48) Members of the RFC family mediate the uptake of folate, reduce folate, derivatives of reduced folate and the drug, methotrexate. Proteins of the RFC family are so-far restricted to animals. RFC proteins possess 12 putative transmembrane a-helical spanners (TMSs) and evidence for a 12 TMS topology has been published for the human RFC. The RFC transporters appear to transport reduced folate by an energy-dependent, pH-dependent, Na+-independent mechanism. Folate:H+ symport, folate:OH- antiport and folate:anion antiport mechanisms have been proposed, but the energetic mechanism is not well defined. TIGR00811.1 TIGR00811 sit 1047.6 1047.6 548 subfamily N N N silicon transporter 0 JCVI silicon transporter silicon transporter Marine diatoms such as Cylindrotheca fusiformis encode at least six silicon transport protein homologues which exhibit similar size and topology. One characterized member of the family (Sit1) functions in the energy-dependent uptake of either Silicic acid [Si(OH)4] or Silicate [Si(OH)3O-] by a Na+ symport mechanism. The system is found in marine diatoms which make their "glass houses" out of silicon. TIGR00817.1 TIGR00817 tpt 317.9 317.9 302 subfamily N N N Tpt phosphate/phosphoenolpyruvate translocator 0 JCVI Tpt phosphate/phosphoenolpyruvate translocator Tpt phosphate/phosphoenolpyruvate translocator The 6-8 TMS Triose-phosphate Transporter (TPT) Family (TC 2.A.7.9) Functionally characterized members of the TPT family are derived from the inner envelope membranes of chloroplasts and nongreen plastids of plants. However, homologues are also present in yeast. Saccharomyces cerevisiae has three functionally uncharacterized TPT paralogues encoded within its genome. Under normal physiological conditions, chloroplast TPTs mediate a strict antiport of substrates, frequently exchanging an organic three carbon compound phosphate ester for inorganic phosphate (Pi). Normally, a triose-phosphate, 3-phosphoglycerate, or another phosphorylated C3 compound made in the chloroplast during photosynthesis, exits the organelle into the cytoplasm of the plant cell in exchange for Pi. However, experiments with reconstituted translocator in artificial membranes indicate that transport can also occur by a channel-like uniport mechanism with up to 10-fold higher transport rates. Channel opening may be induced by a membrane potential of large magnitude and/or by high substrate concentrations. Nongreen plastid and chloroplast carriers, such as those from maize endosperm and root membranes, mediate transport of C3 compounds phosphorylated at carbon atom 2, particularly phosphenolpyruvate, in exchange for Pi. These are the phosphoenolpyruvate:Pi antiporters (PPT). Glucose-6-P has also been shown to be a substrate of some plastid translocators (GPT). The three types of proteins (TPT, PPT and GPT) are divergent in sequence as well as substrate specificity, but their substrate specificities overlap. TIGR00820.1 TIGR00820 zip 231.15 231.15 324 subfamily N N N ZIP zinc/iron transport family 0 JCVI ZIP zinc/iron transport family ZIP zinc/iron transport family The Zinc (Zn2+)-Iron (Fe2+) Permease (ZIP) Family (TC 2.A.5) Members of the ZIP family consist of proteins with eight putative transmembrane spanners. They are derived from animals, plants and yeast. They comprise a diverse family, with several paralogues in any one organism (e.g., at least five in Caenorabditis elegans, at least five in Arabidopsis thaliana and two in Saccharomyces cervisiae. The two S. cerevisiae proteins, Zrt1 and Zrt2, both probably transport Zn2+ with high specificity, but Zrt1 transports Zn2+ with ten-fold higher affinity than Zrt2. Some members of the ZIP family have been shown to transport Zn2+ while others transport Fe2+, and at least one transports a range of metal ions. The energy source for transport has not been characterized, but these systems probably function as secondary carriers. TIGR00834.1 TIGR00834 ae 599.45 599.45 900 subfamily N N N anion exchange protein 0 JCVI anion exchange protein anion exchange protein The Anion Exchanger (AE) Family (TC 2.A.31) Characterized protein members of the AE family are found only in animals. They preferentially catalyze anion exchange (antiport) reactions, typically acting as HCO3-:Cl- antiporters, but also transporting a range of other inorganic and organic anions. Additionally, renal Na+:HCO3- cotransporters have been found to be members of the AE family. They catalyze the reabsorption of HCO3- in the renal proximal tubule. TIGR00840.1 TIGR00840 b_cpa1 251.25 251.25 559 equivalog Y Y N sodium/hydrogen exchanger 3 GO:0005886,GO:0006814,GO:0006883,GO:0006885,GO:0015385 0 JCVI sodium/hydrogen exchanger 3 sodium/hydrogen exchanger 3 The Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36) The CPA1 family is a large family of proteins derived from Gram-positive and Gram-negative bacteria, blue green bacteria, yeast, plants and animals. Transporters from eukaryotes have been functionally characterized, and all of these catalyze Na+:H+ exchange. Their primary physiological functions may be in (1) cytoplasmic pH regulation, extruding the H+ generated during metabolism, and (2) salt tolerance (in plants), due to Na+ uptake into vacuoles. This Hmm is specific for the eukaryotic members members of this family. TIGR00844.1 TIGR00844 c_cpa1 1236.05 1236.05 810 equivalog Y Y N sodium/hydrogen antiporter GO:0006814,GO:0015385,GO:1902600 0 JCVI sodium/hydrogen antiporter sodium/hydrogen antiporter The Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36) The CPA1 family is a large family of proteins derived from Gram-positive and Gram-negative bacteria, blue green bacteria, yeast, plants and animals. Transporters from eukaryotes have been functionally characterized, and all of these catalyze Na+:H+ exchange. Their primary physiological functions may be in (1) cytoplasmic pH regulation, extruding the H+ generated during metabolism, and (2) salt tolerance (in plants), due to Na+ uptake into vacuoles. This Hmm is specific for the fungal members of this family. TIGR00845.1 TIGR00845 caca 679.85 679.85 921 equivalog Y Y N sodium/calcium exchanger 1 GO:0005432,GO:0005886,GO:0006814,GO:0006816,GO:0006874,GO:0006883 0 JCVI sodium/calcium exchanger 1 sodium/calcium exchanger 1 The Ca2+:Cation Antiporter (CaCA) Family (TC 2.A.19) Proteins of the CaCA family are found ubiquitously, having been identified in animals, plants, yeast, archaea and widely divergent bacteria. All of the characterized animal proteins catalyze Ca2+:Na+ exchange although some also transport K+. The NCX1 plasma membrane protein exchanges 3 Na+ for 1 Ca2+. The E. coli ChaA protein catalyzes Ca2+:H+ antiport but may also catalyze Na+:H+ antiport. All remaining well-characterized members of the family catalyze Ca2+:H+ exchange. This Hmm is specific for the eukaryotic sodium ion/calcium ion exchangers of the Caca family TIGR00859.1 TIGR00859 ENaC 428 428 596 subfamily N N N sodium channel transporter 0 JCVI sodium channel transporter sodium channel transporter The Epithelial Na+ Channel (ENaC) Family (TC 1.A.06) The ENaC family consists of sodium channels from animals and has no recognizable homologues in other eukaryotes or bacteria. The vertebrate ENaC proteins from epithelial cells cluster tightly together on the phylogenetic tree: voltage-insensitive ENaC homologues are also found in the brain. Eleven sequenced C. elegans proteins, including the degenerins, are distantly related to the vertebrate proteins as well as to each other. At least some of these proteins form part of a mechano-transducing complex for touch sensitivity. Other members of the ENaC family, the acid-sensing ion channels, ASIC1-3, are homo- or hetero-oligomeric neuronal H+-gated channels that mediate pain sensation in response to tissue acidosis. The homologous Helix aspersa (FMRF-amide)-activated Na+ channel is the first peptide neurotransmitter-gated ionotropic receptor to be sequenced. Mammalian ENaC is important for the maintenance of Na+ balance and the regulation of blood pressure. Three homologous ENaC subunits, a, b and g, have been shown to assemble to form the highly Na+-selective channel. This Hmm is designed from the vertebrate members of the ENaC family. TIGR00862.1 TIGR00862 O-ClC 358.95 358.95 236 subfamily N N N intracellular chloride channel protein 0 JCVI intracellular chloride channel protein intracellular chloride channel protein The Organellar Chloride Channel (O-ClC) Family (TC 1.A.12) Proteins of the O-ClC family are voltage-sensitive chloride channels found in intracellular membranes but not the plasma membranes of animal cells. They are found in human nuclear membranes, and the bovine protein targets to the microsomes, but not the plasma membrane, when expressed in Xenopus laevis oocytes. These proteins are thought to function in the regulation of the membrane potential and in transepithelial ion absorption and secretion in the kidney. TIGR00863.1 TIGR00863 P2X 288 288 372 subfamily N N N cation transporter protein 0 JCVI cation transporter protein cation transporter protein ATP-gated Cation Channel (ACC) Family (TC 1.A.7) Members of the ACC family (also called P2X receptors) respond to ATP, a functional neurotransmitter released by exocytosis from many types of neurons. These channels, which function at neuron-neuron and neuron-smooth muscle junctions, may play roles in the control of blood pressure and pain sensation. They may also function in lymphocyte and platelet physiology. They are found only in animals. ACC channels are probably hetero- or homomultimers and transport small monovalent cations (Me+). Some also transport Ca2+; a few also transport small metabolites. TIGR00864.1 TIGR00864 PCC 1861.4 1861.4 2700 subfamily_domain Y Y N polycystin cation channel protein 0 JCVI polycystin cation channel protein polycystin cation channel protein The Polycystin Cation Channel (PCC) Family (TC 1.A.5) Polycystin is a huge protein of 4303aas. Its repeated leucine-rich (LRR) segment is found in many proteins. It contains 16 polycystic kidney disease (PKD) domains, one LDL-receptor class A domain, one C-type lectin family domain, and 16-18 putative TMSs in positions between residues 2200 and 4100. Polycystin-L has been shown to be a cation (Na+, K+ and Ca2+) channel that is activated by Ca2+. Two members of the PCC family (polycystin 1 and 2) are mutated in autosomal dominant polycystic kidney disease, and polycystin-L is deleted in mice with renal and retinal defects. Note: this model is restricted to the amino half because a full-length model is incompatible with the HMM software package. TIGR00865.1 TIGR00865 bcl-2 283.35 283.35 213 subfamily N N N apoptosis regulator 0 JCVI apoptosis regulator apoptosis regulator The Bcl-2 (Bcl-2) Family (TC 1.A.21) The Bcl-2 family consists of the apoptosis regulator, Bcl-X, and its homologues. Bcl-X is a dominant regulator of programmed cell death in mammalian cells. The long form (Bcl-X(L)) displays cell death repressor activity, but the short isoform (Bcl-X(S)) and the b-isoform (Bcl-Xb) promote cell death. Bcl-X(L), Bcl-X(S) and Bcl-Xb are three isoforms derived by alternative RNA splicing. Bcl-X(S) forms heterodimers with Bcl-2. Homologues of Bcl-X include the Bax (rat; 192 aas; spQ63690) and Bak (mouse; 208 aas; spO08734) proteins which also influence apoptosis. Using isolated mitochondria, recombinant Bax and Bak have been shown to induce Dy loss, swelling and cytochrome c release. All of these changes are dependent on Ca2+ and are prevented by cyclosporin A and bongkrekic acid, both of which are known to close permeability transition pores (megachannels). Coimmimoprecipitation studies revealed that Bax and Bak interact with VDAC to form permeability transition pores. Thus, even though they can form channels in artificial membranes at acidic pH, proapoptotic Bcl-2 family proteins (including Bax and Bak) probably induce the mitochondrial permeability transition and cytochrome c release by interacting with permeability transition pores, the most important component for pore fomation of which is VDAC. TIGR00867.1 TIGR00867 deg-1 598.45 598.45 611 subfamily Y Y N degenerin 12478294,7627559 0 JCVI degenerin degenerin The Epithelial Na+ Channel (ENaC) Family (TC 1.A.06) The ENaC family consists of sodium channels from animals and has no recognizable homologues in other eukaryotes or bacteria. The vertebrate ENaC proteins from epithelial cells cluster tightly together on the phylogenetic tree: voltage-insensitive ENaC homologues are also found in the brain. Eleven sequenced C. elegans proteins, including the degenerins, are distantly related to the vertebrate proteins as well as to each other. At least some of these proteins form part of a mechano-transducing complex for touch sensitivity. Other members of the ENaC family, the acid-sensing ion channels, ASIC1-3, are homo- or hetero-oligomeric neuronal H+-gated channels that mediate pain sensation in response to tissue acidosis. The homologous Helix aspersa (FMRF-amide)-activated Na+ channel is the first peptide neurotransmitter-gated ionotropic receptor to be sequenced. Mammalian ENaC is important for the maintenance of Na+ balance and the regulation of blood pressure. Three homologous ENaC subunits, a, b and g, have been shown to assemble to form the highly Na+-selective channel. This Hmm is designed from the invertebrate members of the ENaC family. TIGR00868.1 TIGR00868 hCaCC 900.85 900.85 863 subfamily N N N calcium-activated chloride channel protein 1 0 JCVI calcium-activated chloride channel protein 1 calcium-activated chloride channel protein 1 TIGR00869.1 TIGR00869 sec62 166.65 166.65 232 subfamily Y Y N translocation protein SEC62 2000150 0 JCVI protein translocation protein, Sec62 family translocation protein SEC62 Members of the NSCC2 family have been sequenced from various yeast, fungal and animals species including Saccharomyces cerevisiae, Drosophila melanogaster and Homo sapiens. These proteins are the Sec62 proteins, believed to be associated with the Sec61 and Sec63 constituents of the general protein secretary systems of yeast microsomes. They are also the non-selective cation (NS) channels of the mammalian cytoplasmic membrane. The yeast Sec62 protein has been shown to be essential for cell growth. The mammalian NS channel proteins has been implicated in platelet derived growth factor(PGDF) dependent single channel current in fibroblasts. These channels are essentially closed in serum deprived tissue-culture cells and are specifically opened by exposure to PDGF. These channels are reported to exhibit equal selectivity for Na+, K+ and Cs+ with low permeability to Ca2+, and no permeability to anions. TIGR00870.1 TIGR00870 trp 498.75 498.75 747 subfamily N N N transient-receptor-potential calcium channel protein 0 JCVI transient-receptor-potential calcium channel protein transient-receptor-potential calcium channel protein The Transient Receptor Potential Ca2+ Channel (TRP-CC) Family (TC. 1.A.4) The TRP-CC family has also been called the store-operated calcium channel (SOC) family. The prototypical members include the Drosophila retinal proteins TRP and TRPL (Montell and Rubin, 1989; Hardie and Minke, 1993). SOC members of the family mediate the entry of extracellular Ca2+ into cells in response to depletion of intracellular Ca2+ stores (Clapham, 1996) and agonist stimulated production of inositol-1,4,5 trisphosphate (IP3). One member of the TRP-CC family, mammalian Htrp3, has been shown to form a tight complex with the IP3 receptor (TC #1.A.3.2.1). This interaction is apparently required for IP3 to stimulate Ca2+ release via Htrp3. The vanilloid receptor subtype 1 (VR1), which is the receptor for capsaicin (the ?hot? ingredient in chili peppers) and serves as a heat-activated ion channel in the pain pathway (Caterina et al., 1997), is also a member of this family. The stretch-inhibitable non-selective cation channel (SIC) is identical to the vanilloid receptor throughout all of its first 700 residues, but it exhibits a different sequence in its last 100 residues. VR1 and SIC transport monovalent cations as well as Ca2+. VR1 is about 10x more permeable to Ca2+ than to monovalent ions. Ca2+ overload probably causes cell death after chronic exposure to capsaicin. (McCleskey and Gold, 1999). TIGR00887.1 TIGR00887 2A0109 610.3 610.3 502 equivalog Y Y N phosphate:H+ symporter GO:0006817 0 JCVI phosphate:H+ symporter phosphate:H+ symporter This HMM represents the phosphate uptake symporter subfamily of the major facilitator superfamily (PF00083). TIGR00892.1 TIGR00892 2A0113 586.1 586.1 455 subfamily Y Y N monocarboxylate transporter 0 JCVI monocarboxylate transporter monocarboxylate transporter TIGR00894.1 TIGR00894 2A0114euk 626.45 626.45 465 subfamily N N N Na(+)-dependent inorganic phosphate cotransporter 0 JCVI Na(+)-dependent inorganic phosphate cotransporter Na(+)-dependent inorganic phosphate cotransporter TIGR00898.1 TIGR00898 2A0119 550.75 550.75 506 subfamily N N N cation transport protein 0 JCVI cation transport protein cation transport protein TIGR00906.1 TIGR00906 2A0303 681.7 681.7 602 subfamily N N N cationic amino acid transport permease 0 JCVI cationic amino acid transport permease cationic amino acid transport permease TIGR00907.1 TIGR00907 2A0304 598.3 598.3 482 subfamily Y Y N amino acid permease 0 JCVI amino acid permease amino acid permease TIGR00911.1 TIGR00911 2A0308 701.8 701.8 505 subfamily N N N L-type amino acid transporter 0 JCVI L-type amino acid transporter L-type amino acid transporter TIGR00913.1 TIGR00913 2A0310 578.7 578.7 480 subfamily Y Y N amino acid permease GO:0006865,GO:0016020 0 JCVI amino acid permease (yeast) amino acid permease TIGR00917.1 TIGR00917 2A060601 1016.5 1016.5 1204 subfamily Y Y N NPC intracellular cholesterol transporter 1 14976318 0 JCVI Niemann-Pick C type protein family NPC intracellular cholesterol transporter 1 The model describes Niemann-Pick C type protein in eukaryotes. The defective protein has been associated with Niemann-Pick disease which is described in humans as autosomal recessive lipidosis. It is characterized by the lysosomal accumulation of unestrified cholesterol. It is an integral membrane protein, which indicates that this protein is most likely involved in cholesterol transport or acts as some component of cholesterol homeostasis. TIGR00918.1 TIGR00918 2A060602 1120.4 1120.4 1145 subfamily N N N transmembrane receptor Patched 0 JCVI transmembrane receptor Patched transmembrane receptor Patched TIGR00920.1 TIGR00920 2A060605 778.35 778.35 887 subfamily Y Y N hydroxymethylglutaryl-CoA reductase (NADPH) 1.1.1.34 0 JCVI 3-hydroxy-3-methylglutaryl-coenzyme A reductase hydroxymethylglutaryl-CoA reductase (NADPH) TIGR00926.1 TIGR00926 2A1704 821.6 821.6 671 subfamily Y Y N oligopeptide:H+ symporter 0 JCVI oligopeptide transporter, peptide:H+ symporter oligopeptide:H+ symporter TIGR00927.1 TIGR00927 2A1904 710.1 710.1 1209 subfamily N N N K+-dependent Na+/Ca+ exchanger 0 JCVI K+-dependent Na+/Ca+ exchanger K+-dependent Na+/Ca+ exchanger TIGR00930.1 TIGR00930 2a30 953.4 953.4 936 subfamily N N N K-Cl cotransporter 0 JCVI K-Cl cotransporter K-Cl cotransporter TIGR00934.2 TIGR00934 2a38euk 441.9 441.9 834 subfamily Y Y N TRK family potassium/sodium uptake transporter GO:0015079,GO:0016020 0 JCVI potassium uptake protein, Trk family TRK family potassium/sodium uptake transporter The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. TIGR00939.1 TIGR00939 2a57 297.5 297.5 439 subfamily N N N nucleoside Transporter 0 JCVI nucleoside Transporter nucleoside Transporter TIGR00951.1 TIGR00951 2A43 192.35 192.35 233 subfamily N N N lysosomal Cystine Transporter 0 JCVI lysosomal Cystine Transporter lysosomal Cystine Transporter TIGR00954.1 TIGR00954 3a01203 918.9 918.9 660 subfamily Y Y N peroxysomal long chain fatty acyl transporter 0 JCVI peroxysomal long chain fatty acyl transporter peroxysomal long chain fatty acyl transporter TIGR00955.1 TIGR00955 3a01204 736.35 736.35 617 subfamily Y Y N pigment precursor permease 0 JCVI pigment precursor permease pigment precursor permease TIGR00956.1 TIGR00956 3a01205 1959 1959 1394 subfamily N N N pleiotropic drug resistance family protein 0 JCVI pleiotropic drug resistance family protein pleiotropic drug resistance family protein TIGR00957.1 TIGR00957 MRP_assoc_pro 1470 1470 1522 equivalog Y Y N multi drug resistance-associated protein (MRP) GO:0006855,GO:0009410,GO:0042910 1360704 0 JCVI multi drug resistance-associated protein (MRP) multi drug resistance-associated protein (MRP) This model describes multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux, abrogated its function. The C-terminal domain seem to highly conserved. TIGR00958.1 TIGR00958 3a01208 874.6 874.6 711 subfamily N N N antigen peptide transporter 2 0 JCVI antigen peptide transporter 2 antigen peptide transporter 2 TIGR00980.1 TIGR00980 3a0801so1tim17 251.05 251.05 170 subfamily N N N mitochondrial import inner membrane translocase subunit tim17 0 JCVI mitochondrial import inner membrane translocase subunit tim17 mitochondrial import inner membrane translocase subunit tim17 TIGR00983.1 TIGR00983 3a0801s02tim23 181.7 181.7 149 subfamily N N N mitochondrial import inner membrane translocase subunit 0 JCVI mitochondrial import inner membrane translocase subunit mitochondrial import inner membrane translocase subunit TIGR00984.1 TIGR00984 3a0801s03tim44 552.35 552.35 376 subfamily N N N mitochondrial import inner membrane, translocase subunit 0 JCVI mitochondrial import inner membrane, translocase subunit mitochondrial import inner membrane, translocase subunit The mitochondrial protein translocase (MPT) family, which brings nuclearly encoded preproteins into mitochondria, is very complex with 19 currently identified protein constituents.These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tim proteins. TIGR00985.1 TIGR00985 3a0801s04tom 163.55 163.55 148 subfamily N N N mitochondrial import receptor subunit 0 JCVI mitochondrial import receptor subunit mitochondrial import receptor subunit TIGR00986.1 TIGR00986 3a0801s05tom22 193.2 193.2 145 subfamily N N N mitochondrial import receptor subunit 0 JCVI mitochondrial import receptor subunit mitochondrial import receptor subunit The mitochondrial protein translocase (MPT) family, which brings nuclearly encoded preproteins into mitochondria, is very complex with 19 currently identified protein constituents.These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tom22 proteins. TIGR00989.1 TIGR00989 3a0801s07tom40 271.85 271.85 161 subfamily N N N mitochondrial import receptor subunit 0 JCVI mitochondrial import receptor subunit mitochondrial import receptor subunit The mitochondrial protein translocase (MPT) family, which brings nuclearly encoded preproteins into mitochondria, is very complex with 19 currently identified protein constituents.These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tom40 proteins. TIGR00990.1 TIGR00990 3a0801s09 757.25 757.25 615 subfamily Y Y N mitochondrial import receptor subunit TOM70 11054285 0 JCVI mitochondrial precursor proteins import receptor mitochondrial import receptor subunit TOM70 TIGR00991.1 TIGR00991 3a0901s02IAP34 421.55 421.55 313 subfamily N N N GTP-binding protein 0 JCVI GTP-binding protein GTP-binding protein TIGR00993.1 TIGR00993 3a0901s04IAP86 660.7 660.7 763 subfamily_domain N N N chloroplast protein import component Toc86/159, G and M domains 10712545 0 JCVI chloroplast protein import component Toc86/159, G and M domains chloroplast protein import component Toc86/159, G and M domains The long precursor of the 86K protein originally described is proposed to have three domains. The N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, and not required for protein translocation. The other domains are designated G (GTPase) and M (membrane anchor); this family includes most of the G domain and all of M. TIGR00994.1 TIGR00994 3a0901s05TIC20 341.15 341.15 267 subfamily Y Y N Tic20 family chloroplast protein importer 0 JCVI chloroplast protein import component, Tic20 family Tic20 family chloroplast protein importer Two families of proteins are involved in the chloroplast envelope import appartus. They are the three proteins of the outer membrane (TOC) and four proteins in the inner membrane (TIC). This family is specific for the Tic20 protein. TIGR01040.1 TIGR01040 V-ATPase_V1_B 804.65 804.65 467 equivalog Y Y N V-type ATPase subunit B 7.1.2.2 GO:0008553,GO:0016471,GO:1902600 10224039 0 JCVI V-type ATPase, B subunit V-type ATPase subunit B This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase. TIGR01092.1 TIGR01092 P5CS 796.75 796.75 715 equivalog Y Y N delta l-pyrroline-5-carboxylate synthetase GO:0006561,GO:0017084 0 JCVI delta l-pyrroline-5-carboxylate synthetase delta l-pyrroline-5-carboxylate synthetase This protein contains a glutamate 5-kinase (ProB, EC 2.7.2.11) region followed by a gamma-glutamyl phosphate reductase (ProA, EC 1.2.1.41) region. TIGR01106.1 TIGR01106 ATPase-IIC_X-K 946.1 946.1 997 subfamily Y Y N Na,H/K antiporter P-type ATPase subunit alpha 11355008,9419228 0 JCVI Na,H/K antiporter P-type ATPase, alpha subunit Na,H/K antiporter P-type ATPase subunit alpha This model describes the P-type ATPases responsible for the exchange of either protons or sodium ions for potassium ions across the plasma membranes of eukaryotes. Unlike most other P-type ATPases, members of this subfamily require a beta subunit for activity. This model encompasses eukaryotes and consists of two functional types, a Na/K antiporter found widely distributed in eukaryotes and a H/K antiporter found only in vertebrates [1]. The Na+ or H+/K+ antiporter P-type ATPases have been characterized as Type IIC based on a published phylogenetic analysis [2]. Sequences from Blastocladiella emersonii (GP|6636502, GP|6636502 and PIR|T43025), C. elegans (GP|2315419, GP|6671808 and PIR|T31763) and Drosophila melanogaster (GP|7291424) score below trusted cutoff, apparently due to long branch length (excessive divergence from the last common ancestor) as evidenced by a phylogenetic tree. Experimental evidence is needed to determine whether these sequences represent ATPases with conserved function. Aside from fragments, other sequences between trusted and noise appear to be bacterial ATPases of unclear lineage, but most likely calcium pumps. TIGR01107.1 TIGR01107 Na_K_ATPase_bet 189.35 189.35 290 equivalog Y Y N sodium/potassium-exchanging ATPase subunit beta 7.2.2.13 GO:0005391,GO:0005890,GO:0006813,GO:0006814,GO:0030322 0 JCVI Na+/K+ ATPase, beta subunit sodium/potassium-exchanging ATPase subunit beta This model describes the Na+/K+ ATPase beta subunit in eukaryotes. Na+/K+ ATPase(also called Sodium-Potassium pump) is intimately associated with the plasma membrane. It couples the energy released by the hydrolysis of ATP to extrude 3 Na+ ions, with the concomitant uptake of 2K+ ions, against their ionic gradients. TIGR01126.1 TIGR01126 pdi_dom 107.2 107.2 105 equivalog_domain N N N protein disulfide-isomerase domain GO:0003756,GO:0006457 0 JCVI protein disulfide-isomerase domain protein disulfide-isomerase domain This HMM describes a domain of eukaryotic protein disulfide isomerases, generally found in two copies. The high cutoff for total score reflects the expectation of finding both copies. The domain is similar to thioredoxin but the redox-active disulfide region motif is APWCGHCK. TIGR01130.1 TIGR01130 ER_PDI_fam 344.25 344.25 476 subfamily Y Y N protein disulfide-isomerase 5.3.4.1 0 JCVI protein disulfide isomerase protein disulfide-isomerase This HMM represents eukaryotic protein disulfide isomerases retained in the endoplasmic reticulum (ER) and closely related forms. Some members have been assigned alternative or additional functions such as prolyl 4-hydroxylase and dolichyl-diphosphooligosaccharide-protein glycotransferase. Members of this family have at least two protein-disulfide domains, each similar to thioredoxin but with the redox-active disulfide in the motif PWCGHCK, and an ER retention signal at the extreme C-terminus (KDEL, HDEL, and similar motifs). TIGR01159.1 TIGR01159 DRP1 118.15 118.15 168 subfamily N N N density-regulated protein DRP1 9628587 0 JCVI density-regulated protein DRP1 density-regulated protein DRP1 This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs. TIGR01170.1 TIGR01170 rplA_mito 129.05 129.05 140 equivalog N N N ribosomal protein uL1, mitochondrial GO:0003735,GO:0005762,GO:0006412 0 JCVI ribosomal protein uL1, mitochondrial ribosomal protein uL1, mitochondrial This HMM represents the mitochondrial homolog of bacterial ribosomal protein L1. Unlike chloroplast L1, this form was not sufficiently similar to bacterial forms to include in a single bacterial/organellar L1 HMM. TIGR01219.1 TIGR01219 Pmev_kin_ERG8 376.95 376.95 456 equivalog Y Y N phosphomevalonate kinase 2.7.4.2 GO:0004631,GO:0016126,GO:0019287 11243736 0 JCVI phosphomevalonate kinase phosphomevalonate kinase This enzyme is part of the mevalonate pathway, one of two alternative pathways for the biosynthesis of IPP. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found - the animal type and this ERG8 type. This model represents plant and fungal forms of the ERG8 type of phosphomevalonate kinase. TIGR01223.1 TIGR01223 Pmev_kin_anim 188.15 188.15 185 equivalog Y Y N phosphomevalonate kinase 2.7.4.2 GO:0004631,GO:0005737,GO:0006695 11243736 0 JCVI phosphomevalonate kinase phosphomevalonate kinase This enzyme is part of the mevalonate pathway, one of two alternative pathways for the biosynthesis of IPP. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found. One is this type, found in animals. The other is the ERG8 type, found in plants and fungi (TIGR01219) and in Gram-positive bacteria (TIGR01220). TIGR01226.1 TIGR01226 phe_am_lyase 519.15 519.15 680 equivalog Y Y N phenylalanine ammonia-lyase 4.3.1.24 GO:0009698,GO:0016841 20577998 0 JCVI phenylalanine ammonia-lyase phenylalanine ammonia-lyase Members of this subfamily of MIO prosthetic group enzymes are phenylalanine ammonia-lyases. They are found, so far, in plants and fungi. From phenylalanine, this enzyme yields cinnaminic acid, a precursor of many important plant compounds. This protein shows extensive homology to histidine ammonia-lyase, the first enzyme of a histidine degradation pathway. Note that members of this family from plant species that synthesize taxol are actually phenylalanine aminomutase, and are covered by exception model TIGR04473. TIGR01257.1 TIGR01257 rim_protein 4012.85 4012.85 2272 equivalog Y Y N rim ABC transporter GO:0005524,GO:0006810,GO:0007601,GO:0016020,GO:0042626 0 JCVI rim ABC transporter rim ABC transporter This model describes the photoreceptor protein (rim protein) in eukaryotes. It is the member of ABC transporter superfamily. Rim protein is a membrane glycoprotein which is localized in the photoreceptor outer segment discs. Mutation/s in its genetic loci is implicated in the recessive Stargardt's disease. TIGR01264.1 TIGR01264 tyr_amTase_E 474.25 474.25 403 equivalog Y Y N tyrosine transaminase 2.6.1.5 GO:0004838,GO:0006559,GO:0006572 0 JCVI tyrosine aminotransferase tyrosine transaminase This HMM describes tyrosine aminotransferase as found in animals and Trypanosoma cruzi. It is the first enzyme of a pathway of tyrosine degradation via homogentisate. Several plant enzyme designated as probable tyrosine aminotransferases are very closely related to an experimentally demonstrated nicotianamine aminotransferase, an enzyme in a siderophore (iron uptake chelator) biosynthesis pathway. These plant sequences are excluded from the model seed and score between the trusted an noise cutoffs. TIGR01268.1 TIGR01268 Phe4hydrox_tetr 704.8 704.8 436 equivalog Y Y N phenylalanine 4-monooxygenase 1.14.16.1 GO:0004505,GO:0006559 0 JCVI phenylalanine-4-hydroxylase phenylalanine 4-monooxygenase This HMM describes the larger, tetrameric form of phenylalanine-4-hydroxylase, as found in metazoans. The enzyme irreversibly converts phenylalanine to tryosine and is known to be the rate-limiting step in phenylalanine catabolism in some systems. It is closely related to metazoan tyrosine 3-monooxygenase and tryptophan 5-monoxygenase, and more distantly to monomeric phenylalanine-4-hydroxylases of some Gram-negative bacteria. The member of this family from Drosophila has been described as having both phenylalanine-4-hydroxylase and tryptophan 5-monoxygenase activity (PMID:1371286). However, a Drosophila member of the tryptophan 5-monoxygenase clade has subsequently been discovered. TIGR01269.1 TIGR01269 Tyr_3_monoox 654.65 654.65 457 equivalog Y Y N tyrosine 3-monooxygenase 1.14.16.2 GO:0004511,GO:0006570 0 JCVI tyrosine 3-monooxygenase tyrosine 3-monooxygenase This HMM describes tyrosine 3-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tryptophan 5-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria. TIGR01270.1 TIGR01270 Trp_5_monoox 705.5 705.5 464 equivalog Y Y N tryptophan 5-monooxygenase 1.14.16.4 GO:0004510,GO:0006568 0 JCVI tryptophan 5-monooxygenase tryptophan 5-monooxygenase This HMM describes tryptophan 5-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tyrosine 3-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria. TIGR01271.1 TIGR01271 CFTR_protein 1761.2 1761.2 1490 equivalog Y Y N cystic fibrosis transmembrane conductor regulator (CFTR) 5.6.1.6 GO:0005260,GO:0030321 0 JCVI cystic fibrosis transmembrane conductor regulator (CFTR) cystic fibrosis transmembrane conductor regulator (CFTR) The model describes the cystis fibrosis transmembrane conductor regulator (CFTR) in eukaryotes. The principal role of this protein is chloride ion conductance. The protein is predicted to consist of 12 transmembrane domains. Mutations or lesions in the genetic loci have been linked to the aetiology of asthma, bronchiectasis, chronic obstructive pulmonary disease etc. Disease-causing mutations have been studied by 36Cl efflux assays in vitro cell cultures and electrophysiology, all of which point to the impairment of chloride channel stability and not the biosynthetic processing per se. TIGR01294.1 TIGR01294 P_lamban 72.85 72.85 52 equivalog Y Y N phospholamban pln GO:0008016,GO:0019855,GO:0042030 10198197,22463608 0 JCVI phospholamban phospholamban This HMM represents the short (52 residue) transmembrane phosphoprotein phospholamban. Phospholamban, in its unphosphorylated form, inhibits SERCA2, the cardiac sarcoplasmic reticulum Ca-ATPase. TIGR01299.1 TIGR01299 synapt_SV2 637.3 637.3 742 subfamily N N N synaptic vesicle protein SV2 10624962,1355409 0 JCVI synaptic vesicle protein SV2 synaptic vesicle protein SV2 This HMM describes a tightly conserved subfamily of the larger family of sugar (and other) transporters described by PFAM HMM PF00083. Members of this subfamily include closely related forms SV2A and SV2B of synaptic vesicle protein from vertebrates and a more distantly related homolog (below trusted cutoff) from Drosophila melanogaster. Members are predicted to have two sets of six transmembrane helices. TIGR01301.1 TIGR01301 GPH_sucrose 511 511 476 subfamily Y Y N sucrose/proton symporter 9847123 0 JCVI sucrose/H+ symporter sucrose/proton symporter This HMM represents sucrose/proton symporters, found in plants, from the Glycoside-Pentoside-Hexuronide (GPH)/cation symporter family. These proteins are predicted to have 12 transmembrane domains. Members may export sucrose (e.g. SUT1, SUT4) from green parts to the phloem for long-distance transport or import sucrose (e.g SUT2) to sucrose sinks such as the tap root of the carrot. TIGR01359.1 TIGR01359 UMP_CMP_kin_fam 207.6 207.6 185 subfamily N N N UMP-CMP kinase family 11306702 0 JCVI UMP-CMP kinase family UMP-CMP kinase family This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic. TIGR01360.1 TIGR01360 aden_kin_iso1 284.1 284.1 188 equivalog Y Y N adenylate kinase 2.7.4.3 GO:0004017,GO:0005524,GO:0005737,GO:0009151 0 JCVI adenylate kinase adenylate kinase Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351. TIGR01381.1 TIGR01381 E1_like_apg7 571.35 571.35 663 equivalog N N N E1-like protein-activating enzyme Gsa7p/Apg7p GO:0006497,GO:0061025 0 JCVI E1-like protein-activating enzyme Gsa7p/Apg7p E1-like protein-activating enzyme Gsa7p/Apg7p This HMM represents a family of eukaryotic proteins found in animals, plants, and yeasts, including Apg7p (YHR171W) from Saccharomyces cerevisiae and GSA7 from Pichia pastoris. Members are about 650 to 700 residues in length and include a central domain of about 150 residues shared with the ThiF/MoeB/HesA family of proteins. A low level of similarity to ubiquitin-activating enzyme E1 is described in a paper on peroxisome autophagy mediated by GSA7, and is the basis of the name ubiquitin activating enzyme E1-like protein. Members of the family appear to be involved in protein lipidation events analogous to ubiquitination and required for membrane fusion events during autophagy. TIGR01385.1 TIGR01385 TFSII 237.1 237.1 300 equivalog Y Y N transcription elongation factor S-II GO:0003711,GO:0006351 0 JCVI transcription elongation factor S-II transcription elongation factor S-II This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end. TIGR01423.1 TIGR01423 trypano_reduc 738.1 738.1 486 equivalog Y Y N trypanothione-disulfide reductase 1.8.1.12 GO:0015042,GO:0045454 0 JCVI trypanothione-disulfide reductase trypanothione-disulfide reductase Trypanothione, a glutathione-modified derivative of spermidine, is (in its reduced form) an important antioxidant found in trypanosomatids (Crithidia, Leishmania, Trypanosoma). This model describes trypanothione reductase, a possible antitrypanosomal drug target closely related to some forms of glutathione reductase. TIGR01425.1 TIGR01425 SRP54_euk 576.25 576.25 428 equivalog Y Y N signal recognition particle protein SRP54 GO:0003924,GO:0005786,GO:0006617 0 JCVI signal recognition particle protein SRP54 signal recognition particle protein SRP54 This HMM represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model. TIGR01429.1 TIGR01429 AMP_deaminase 726.3 726.3 611 equivalog Y Y N AMP deaminase 3.5.4.6 GO:0003876,GO:0032264 0 JCVI AMP deaminase AMP deaminase This HMM describes AMP deaminase, a large, well-conserved eukaryotic protein involved in energy metabolism. Most members of the family have an additional, poorly alignable region of 150 amino acids or more N-terminal to the region included in the HMM. TIGR01438.1 TIGR01438 TGR 475.85 475.85 485 subfamily N N N thioredoxin and glutathione reductase 11259642,8650234 0 JCVI thioredoxin and glutathione reductase thioredoxin and glutathione reductase This homodimeric, FAD-containing member of the pyridine nucleotide disulfide oxidoreductase family contains a C-terminal motif Cys-SeCys-Gly, where SeCys is selenocysteine encoded by TGA (in some sequence reports interpreted as a stop codon). In some members of this subfamily, Cys-SeCys-Gly is replaced by Cys-Cys-Gly. The reach of the selenium atom at the C-term arm of the protein is proposed to allow broad substrate specificity. TIGR01456.1 TIGR01456 CECR5 139.25 139.25 321 hypoth_equivalog Y Y N TIGR01456 family HAD-type hydrolase 0 JCVI HAD hydrolase, TIGR01456 family TIGR01456 family HAD-type hydrolase This hypothetical equivalog is a member of the Class IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this equivalog are all eukaryotes. One sequence (GP|13344995) is called "Cat Eye Syndrome critical region protein 5" (CECR5) [1]. This gene has been cloned from a pericentromere region of human chromosome 22 believed to be the location of the gene or genes responsible for Cat Eye Syndrome. This is one of a number of candidate genes. The Schizosaccharomyces pombe sequence (EGAD|138276) is annotated as "phosphatidyl synthase," however this is due entirely to a C-terminal region of the protein (outside the region of similarity of this HMM) which is highly homologous to a family of CDP-alcohol phosphatidyltransferases. (Thus, the annotation of GP|4226073 from C. elegans as similar to phosphatidyl synthase, is a mistake as this gene does not contain the C-terminal portion). The physical connection of the phosphatidyl synthase and the HAD-superfamily hydrolase domain in S. pombe may, however, be an important clue to the substrate for the hydrolases in this equivalog. TIGR01477.1 TIGR01477 RIFIN 176.95 176.95 356 paralog N N N variant surface antigen, rifin family 0 JCVI variant surface antigen, rifin family variant surface antigen, rifin family This HMM represents the rifin branch of the rifin/stevor family (PF02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of rifin sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 20 bits. TIGR01478.1 TIGR01478 STEVOR 166.65 166.65 308 paralog Y Y N STEVOR family variant surface protein 0 JCVI variant surface antigen, stevor family STEVOR family variant surface protein This HMM represents the stevor branch of the rifin/stevor family (PF02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits. TIGR01492.1 TIGR01492 CPW_WPC 35.6 35.6 62 domain Y Y N CPW-WPC domain-containing protein 0 JCVI Plasmodium falciparum CPW-WPC domain Plasmodium falciparum CPW-WPC domain This HMM represents a domain of about 61 residues in length with six well-conserved cysteine residues and six well-conserved aromatic sites. The domain can be found in tandem repeats, and is known so far only in Plasmodium falciparum. It is named for motifs of CPxxW and (less well conserved) WPC. TIGR01500.1 TIGR01500 sepiapter_red 206.55 206.55 255 equivalog Y Y N sepiapterin reductase (L-erythro-7,8-dihydrobiopterin forming) 1.1.1.153 GO:0004757,GO:0006729 11796169 0 JCVI sepiapterin reductase sepiapterin reductase (L-erythro-7,8-dihydrobiopterin forming) This HMM describes sepiapterin reductase, a member of the short chain dehydrogenase/reductase family. The enzyme catalyzes the last step in the biosynthesis of tetrahydrobiopterin. A similar enzyme in Bacillus cereus was isolated for its ability to convert benzil to (S)-benzoin, a property sepiapterin reductase also shares. Cutoff scores for this model are set such that benzil reductase scores between trusted and noise cutoffs. TIGR01519.1 TIGR01519 plasmod_dom_1 29.35 29.35 70 paralog_domain N N N Plasmodium falciparum uncharacterized domain 0 JCVI Plasmodium falciparum uncharacterized domain Plasmodium falciparum uncharacterized domain This HMM represents an uncharacterized domain present in roughly eight hypothetical proteins of the malaria parasite Plasmodium falciparum. TIGR01523.1 TIGR01523 ATPase-IID_K-Na 645.05 645.05 997 equivalog Y Y N potassium/sodium efflux P-type ATPase, fungal-type 7.2.2.- GO:0006812,GO:0016020,GO:0019829 11932440,1323458,9419228 0 JCVI potassium/sodium efflux P-type ATPase, fungal-type potassium/sodium efflux P-type ATPase, fungal-type Initially described as a calcium efflux ATPase [1], more recent work has shown that the S. pombe CTA3 gene is in fact a potassium ion efflux pump [2]. This HMM describes the clade of fungal P-type ATPases responsible for potassium and sodium efflux. The degree to which these pumps show preference for sodium or potassium varies. This group of ATPases has been classified by phylogentic analysis as type IID [3]. The Leishmania sequence (GP|3192903), which falls between trusted and noise in this model, may very well turn out to be an active potassium pump. TIGR01531.1 TIGR01531 glyc_debranch 1399.55 1399.55 1443 equivalog Y Y N glycogen debranching enzyme GO:0004133,GO:0005980 11375985,8136030 0 JCVI glycogen debranching enzyme glycogen debranching enzyme glycogen debranching enzyme possesses two different catalytic activities; oligo-1,4-->1,4-glucantransferase (EC 2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site directed mutagenesis studies in S. cerevisiae [1] indicate that the transferase and glucosidase activities are independent and located in different regions of the polypeptide chain. Proteins in this model belong to the larger alpha-amylase family. The model covers eukaryotic proteins with a seed composed of human, nematode and yeast sequences. Yeast seed sequence is well characterized. The model is quite rigorous; either query sequence yields large bit score or it fails to hit the model altogether. There doesn't appear to be any middle ground. TIGR01544.1 TIGR01544 HAD-SF-IE 256.95 256.95 283 hypoth_equivalog Y Y N HAD-IE family hydrolase 7966317 0 JCVI HAD hydrolase, family IE HAD-IE family hydrolase This HMM represents a small group of metazoan sequences. The sequences from mouse are annotated as Pyrimidine 5'-nucleotidases, aparrently in reference to HSPC233, the human homolog. However, no such annotation can currently be found for this gene. This group of sequences was found during searches for members of the haloacid dehalogenase (HAD) superfamily. All of the conserved catalytic motifs [1] are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches (IA, TIGR01493, TIGR01509, TIGR01549; IB, TIGR01488; IC, TIGR01494; ID, TIGR01658; IF TIGR01545) of that subfamily as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB. TIGR01557.1 TIGR01557 myb_SHAQKYF 29.3 29.3 57 subfamily_domain N N N myb-like DNA-binding domain, SHAQKYF class 10652136,7957104 0 JCVI myb-like DNA-binding domain, SHAQKYF class myb-like DNA-binding domain, SHAQKYF class This HMM describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model PF00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif. TIGR01565.1 TIGR01565 homeo_ZF_HD 57.45 57.45 58 subfamily_domain N N N homeobox domain, ZF-HD class 11289511 0 JCVI homeobox domain, ZF-HD class homeobox domain, ZF-HD class This HMM represents a class of homoebox domain that differs substantially from the typical homoebox domain described in Pfam HMM PF00046. It is found in both C4 and C3 plants. TIGR01566.1 TIGR01566 ZF_HD_prot_N 51.1 51.1 53 domain N N N ZF-HD homeobox protein Cys/His-rich dimerization domain 0 JCVI ZF-HD homeobox protein Cys/His-rich dimerization domain ZF-HD homeobox protein Cys/His-rich dimerization domain This HMM describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565. TIGR01568.1 TIGR01568 A_thal_3678 46.45 46.45 67 domain N N N uncharacterized plant-specific domain TIGR01568 0 JCVI uncharacterized plant-specific domain TIGR01568 uncharacterized plant-specific domain TIGR01568 This HMM describes an uncharacterized domain of about 70 residues found exclusively in plants, generally toward the C-terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana. Other regions of these proteins tend to consist largely of low-complexity sequence. TIGR01570.1 TIGR01570 A_thal_3588 109.55 109.55 161 subfamily_domain N N N uncharacterized plant-specific domain TIGR01570 0 JCVI uncharacterized plant-specific domain TIGR01570 uncharacterized plant-specific domain TIGR01570 This HMM represents a region of about 170 amino acids found at the C-terminus of a family of plant proteins. These proteins typically have additional highly divergent N-terminal regions rich in low complexity sequence. PSI-BLAST reveals no clear similarity to any characterized protein. At least 12 distinct members are found in Arabidopsis thaliana. TIGR01572.1 TIGR01572 A_thl_para_3677 104.2 104.2 265 paralog Y Y N TIGR01572 family protein 0 JCVI Arabidopsis paralogous family TIGR01572 TIGR01572 family protein This HMM describes a paralogous family of hypothetical proteins in Arabidopsis thaliana. No homologs are detected from other species. Length heterogeneity within the family is attributable partly to a 21-residue repeat present in from zero to three tandem copies. The central region of the repeat resembles the pattern [VIF][FY][QK]GX[LM]P[DEK]XXXDDAL. TIGR01589.1 TIGR01589 A_thal_3526 36.55 36.55 57 domain Y Y N TIGR01589 domain-containing protein 0 JCVI uncharacterized plant-specific domain TIGR01589 TIGR01589 domain This HMM represents an uncharacterized plant-specific domain 57 residues in length. It is found toward the N-terminus of most proteins that contain it. Examples include at least 10 proteins from Arabidopsis thaliana and at least one from Oryza sativa. TIGR01590.1 TIGR01590 yir-bir-cir_Pla 71.1 71.1 201 paralog N N N yir/bir/cir-family of variant antigens 11298455,11886633 0 JCVI yir/bir/cir-family of variant antigens yir/bir/cir-family of variant antigens This HMM represents a large paralogous family of variant antigens from several Plasmodium species (P. yoelii, P. berghei and P. chabaudi). The seed was generated from a list of ORF's in P. yoelii containing a paralagous domain as defined by an algorithm implemented at TIFR [1]. The list was aligned and reduced to six sequences approximating the most divergent clades present in the data set. The model only hits genes previously characterized as yir, bir, or cir genes above the trusted cutoff. In between trusted and noise is one gene from P. vivax (vir25) which has been characterized as a distant relative of the yir/bir/cir family [2]. The vir family [3] appears to be present in 600-1000 copies per haploid genome and is preferentially located in the sub-telomeric regions of the chromosomes. The genomic data for yoelii is consistent with this observation. It is not believed that there are any orthologs of this family in P. falciparum. TIGR01597.1 TIGR01597 PYST-B 175.5 175.5 256 paralog N N N Plasmodium yoelii subtelomeric family PYST-B 0 JCVI Plasmodium yoelii subtelomeric family PYST-B Plasmodium yoelii subtelomeric family PYST-B This model represents a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes [1]. There are no obvious homologs to these genes in any other organism. TIGR01599.1 TIGR01599 PYST-A 114.8 114.8 209 paralog N N N Plasmodium yoelii subtelomeric family PYST-A 0 JCVI Plasmodium yoelii subtelomeric family PYST-A Plasmodium yoelii subtelomeric family PYST-A This model represents a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes [1]. Members of this family are expressed in both the Sporozoite and Gametozoite life stages [1]. A single high-scoring gene was identified in the complete genome of P. falciparum [2] as well as a single gene from P. chaboudi from GenBank which were included in the seed. There are no obvious homologs to these genes in any non-Plasmodium organism. These observations suggest an expansion of this family in yoelii from a common Plasmodium ancestor gene (present in a single copy in falciparum). TIGR01601.1 TIGR01601 PYST-C1 54.75 54.75 82 paralog N N N Plasmodium yoelii subtelomeric domain PYST-C1 0 JCVI Plasmodium yoelii subtelomeric domain PYST-C1 Plasmodium yoelii subtelomeric domain PYST-C1 This model represents the N-terminal domain of a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes [1]. There are no obvious homologs to these genes in any other organism. The C-terminal portions of the genes which contain this domain are divergent and some contain other yoelii-specific paralogous domains such as PYST-C2 (TIGR01604). TIGR01602.1 TIGR01602 PY-rept-46 48.25 48.25 46 paralog_domain N N N Plasmodium yoelii repeat of length 46 0 JCVI Plasmodium yoelii repeat of length 46 Plasmodium yoelii repeat of length 46 This repeat is found in only 2 genes in Plasmodium yoelii, in each of these genes it is repeated 9 times. It is found in no other organism. TIGR01604.1 TIGR01604 PYST-C2 40.35 40.35 150 paralog_domain N N N Plasmodium yoelii subtelomeric domain PYST-C2 0 JCVI Plasmodium yoelii subtelomeric domain PYST-C2 Plasmodium yoelii subtelomeric domain PYST-C2 This model represents a domain of a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes [1]. There are no obvious homologs to these genes in any other organism. The genes found by this model often are associated with an N-terminal domain yoelii-specific domain such as PYST-C1 (TIGR01601). TIGR01605.1 TIGR01605 PYST-D 41.4 41.4 55 paralog N N N Plasmodium yoelii subtelomeric family PYST-D 0 JCVI Plasmodium yoelii subtelomeric family PYST-D Plasmodium yoelii subtelomeric family PYST-D This model represents a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes [1]. These genes are generally very short (ca. 50 residues). There are no obvious homologs to these genes in any other organism. TIGR01607.1 TIGR01607 PST-A 218.25 218.25 332 paralog N N N Plasmodium subtelomeric family 0 JCVI Plasmodium subtelomeric family Plasmodium subtelomeric family This model represents a paralogous family of genes in Plasmodium falciparum and Plasmodium yoelii [1,2] which are closely related to various phospholipases and lysophospholipases of plants as well as generally being related to the alpha/beta-fold superfamily of hydrolases. These genes are preferentially located in the subtelomeric regions of the chromosomes of both P. falciparum and P. yoelii [1,2]. TIGR01609.1 TIGR01609 PF_unchar_267 74.55 74.55 146 paralog_domain N N N Plasmodium falciparum uncharacterized protein TIGR01609 0 JCVI Plasmodium falciparum uncharacterized protein TIGR01609 Plasmodium falciparum uncharacterized protein TIGR01609 This HMM represents a family of at least four proteins in Plasmodium falciparum. An interesting feature is five perfectly conserved Trp residues. TIGR01612.1 TIGR01612 235kDa-fam 1615.85 1615.85 2756 paralog Y Y N rhoptry protein 10637585,11551627 0 JCVI rhoptry protein rhoptry protein This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite [1,2]. These proteins are found in P. falciparum, P. vivax and P. yoelii. TIGR01615.1 TIGR01615 A_thal_3542 80.05 80.05 131 domain N N N uncharacterized plant-specific domain TIGR01615 0 JCVI uncharacterized plant-specific domain TIGR01615 uncharacterized plant-specific domain TIGR01615 This HMM represents a domain found toward the C-terminus of a number of uncharacterized plant proteins. The domain is strongly conserved (greater than 30 % sequence identity between most pairs of members) but flanked by highly divergent regions including stretches of low-complexity sequence. TIGR01622.1 TIGR01622 SF-CC1 231.65 231.65 500 subfamily N N N splicing factor, CC1-like family GO:0008380 11704680,8227358,9578630 0 JCVI splicing factor, CC1-like family splicing factor, CC1-like family This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: PF00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR [4] and was included in the seed. TIGR01623.1 TIGR01623 put_zinc_LRP1 42 42 43 paralog_domain N N N putative zinc finger domain, LRP1 type 7647564 0 JCVI putative zinc finger domain, LRP1 type putative zinc finger domain, LRP1 type This HMM represents a putative zinc finger domain found in plants. Arabidopsis thaliana has at least 10 distinct members. Proteins containing this domain, including LRP1, generally share the same size, about 300 amino acids, and architecture. This 43-residue domain, and a more C-terminal companion domain of similar size, appear as tightly conserved islands of sequence similarity. The remainder consists largely of low-complexity sequence. Several animal proteins have regions with matching patterns of Cys, Gly, and His residues. These are not included in the model but score between trusted and noise cutoffs. TIGR01624.1 TIGR01624 LRP1_Cterm 36.4 36.4 50 paralog_domain N N N LRP1 C-terminal domain 7647564 0 JCVI LRP1 C-terminal domain LRP1 C-terminal domain This HMM represents a tightly conserved small domain found in LRP1 and related plant proteins. This family also contains a well-conserved putative zinc finger domain (TIGR01623). The rest of the sequence of most members consists of highly divergent, low-complexity sequence. TIGR01638.1 TIGR01638 Atha_cystat_rel 32.05 32.05 94 paralog_domain N N N Arabidopsis thaliana cystatin-related protein 0 JCVI Arabidopsis thaliana cystatin-related protein Arabidopsis thaliana cystatin-related protein This HMM represents a family similar in sequence and probably homologous to a large family of cysteine proteinase inhibitors, or cystatins, as described by Pfam HMM PF00031. Cystatins may help plants resist attack by insects. TIGR01640.1 TIGR01640 F_box_assoc_1 37.9 37.9 232 domain Y Y N F-box family protein GO:0016567 12169662 0 JCVI F-box protein interaction domain F-box protein interaction domain This HMM describes a large family of plant domains, with several hundred members in Arabidopsis thaliana. Most examples are found C-terminal to an F-box (PF00646), a 60 amino acid motif involved in ubiquitination of target proteins to mark them for degradation. Two-hybid experiments support the idea that most members are interchangeable F-box subunits of SCF E3 complexes. Some members have two copies of this domain. TIGR01642.1 TIGR01642 U2AF_lg 310.3 310.3 510 subfamily N N N U2 snRNP auxilliary factor, large subunit, splicing factor 16819553 0 JCVI U2 snRNP auxilliary factor, large subunit, splicing factor U2 snRNP auxilliary factor, large subunit, splicing factor These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (PF00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. TIGR01645.1 TIGR01645 half-pint 443.95 443.95 607 subfamily N N N poly-U binding splicing factor, half-pint family 10606266,10668799,11879639 0 JCVI poly-U binding splicing factor, half-pint family poly-U binding splicing factor, half-pint family The proteins represented by this model contain three RNA recognition motifs (rrm: PF00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors [1,2,3]. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA [2]. TIGR01648.1 TIGR01648 hnRNP-R-Q 317.85 317.85 577 subfamily N N N hnRNP-R, Q splicing factor family 10781591,11574476,9421497 0 JCVI hnRNP-R, Q splicing factor family hnRNP-R, Q splicing factor family Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R [1], Q [2] and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein)[3]. These proteins contain three RNA recognition domains (rrm: PF00076) and a somewhat variable C-terminal domain. TIGR01649.1 TIGR01649 hnRNP-L_PTB 287.4 287.4 493 subfamily N N N hnRNP-L/PTB/hephaestus splicing factor family 11804786,7542615 0 JCVI hnRNP-L/PTB/hephaestus splicing factor family hnRNP-L/PTB/hephaestus splicing factor family Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein [1]) and hnRNP-L [2]. These proteins contain four RNA recognition motifs (rrm: PF00067). TIGR01652.1 TIGR01652 ATPase-Plipid 431.25 431.25 1058 subfamily Y Y N phospholipid-translocating P-type ATPase 7.6.2.1 33320091,9099684 0 JCVI phospholipid-translocating P-type ATPase, flippase phospholipid-translocating P-type ATPase This model describes the P-type ATPase responsible for transporting phospholipids from one leaflet of bilayer membranes to the other [1]. These ATPases are found only in eukaryotes. TIGR01657.1 TIGR01657 P-ATPase-V 618.25 618.25 1055 hypoth_equivalog Y Y N ATP13A2 family polyamine export P-type ATPase 15381061,31996848,37080960,9419228 0 JCVI P-type ATPase of unknown pump specificity (type V) ATP13A2 family polyamine export P-type ATPase Members of this family of P-type APTases include Parkinson's disease-associated ATP13A2, recently reported to act as a lysosomal H+,K+-ATPase. Its disruption blocks polyamine export from the lysosome. TIGR01658.1 TIGR01658 EYA-cons_domain 195.3 195.3 274 equivalog_domain Y Y N EYA domain-containing protein 3.1.3.48 0 JCVI EYA conserved domain EYA conserved domain This domain is common to all eyes absent (EYA) homologs. Metazoan EYA's also contain a variable N-terminal domain consisting largely of low-complexity sequences. TIGR01659.1 TIGR01659 sex-lethal 486.2 486.2 346 subfamily Y Y N sex-lethal family splicing factor 10648226 0 JCVI sex-lethal family splicing factor sex-lethal family splicing factor This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species [1]. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). TIGR01661.1 TIGR01661 ELAV_HUD_SF 279.1 279.1 351 subfamily N N N ELAV/HuD family splicing factor 1655278,3144044 0 JCVI ELAV/HuD family splicing factor ELAV/HuD family splicing factor This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human [1]. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein [2]. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: PF00076). TIGR01663.1 TIGR01663 PNK-3'Pase 502.8 502.8 520 equivalog Y Y N bifunctional polynucleotide phosphatase/kinase 2.7.1.78,3.1.3.32 GO:0000012,GO:0046403,GO:0046404 10446192,10446193,32504494 0 JCVI polynucleotide kinase 3'-phosphatase bifunctional polynucleotide phosphatase/kinase This model represents the metazoan 5'-polynucleotide-kinase-3'-phosphatase, PNKP, which is believed to be involved in repair of oxidative DNA damage. Removal of 3' phosphates is essential for the further processing of the break by DNA polymerases [1,2]. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is replaced by a conserved arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Very close relatives of this domain are also found separate from the N- and C-terminal domains seen here, as in the 3'-phosphatase found in plants. The larger family of these domains is described by TIGR01664. Outside of the phosphatase domain is a P-loop ATP-binding motif associated with the kinase activity. The entry for the mouse homolog, GP|7108591, appears to be missing a large piece of sequence corresponding to the first conserved catalytic motif of the phosphatase domain as well as the conserved threonine of the second motif. Either this is a sequencing artifact or this may represent a pseudo- or non-functional gene. Note that the EC number for the kinase function is: 2.7.1.78 TIGR01664.1 TIGR01664 DNA-3'-Pase 107.65 107.65 167 equivalog_domain Y Y N DNA 3'-phosphatase GO:0000012,GO:0046403 10446192,10446193,11278717,11278831 0 JCVI DNA 3'-phosphatase DNA 3'-phosphatase This model represents a family of proteins and protein domains which catalyze the dephosphorylation of DNA 3'-phosphates. It is believed that this activity is important for the repair of single-strand breaks in DNA caused by radiation or oxidative damage. This domain is often (TIGR01663 [1,2]), but not always [3,4] linked to a DNA 5'-kinase domain. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is usually replaced by an arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Alternatively, there is an additional conserved aspartate downstream of the ususal site which may indicate slightly different fold in this region. TIGR01675.1 TIGR01675 plant-AP 264.3 264.3 229 equivalog Y Y N plant acid phosphatase 1639823,9193092,9747802,9758760 0 JCVI plant acid phosphatase plant acid phosphatase This model represents a family of acid phosphatase [1,2] from plants which are most closely related to the (so called) class B non-specific acid phosphatase OlpA (TIGR01533, which is believed to be a 5'-nucleotide phosphatase) and somewhat more distantly to another class B phosphatase, AphA (TIGR01672). Together these three clades define a subfamily (PF03767) which corresponds to the IIIB subfamily of the haloacid dehalogenase (HAD) superfamily of aspartate nucleophile hydrolases. TIGR01676.1 TIGR01676 GLDHase 458.25 458.25 541 equivalog Y Y N L-galactonolactone dehydrogenase 1.3.2.3 10050319 0 JCVI galactonolactone dehydrogenase L-galactonolactone dehydrogenase This HMM represents L-Galactono-gamma-lactone dehydrogenase (EC 1.3.2.3). This enzyme catalyzes the final step in ascorbic acid biosynthesis in higher plants. This protein is homologous to ascorbic acid biosynthesis enzymes of other species: L-gulono-gamma-lactone oxidase in rat and L-galactono-gamma-lactone oxidase in yeast. All three covalently bind the cofactor FAD. TIGR01677.1 TIGR01677 pln_FAD_oxido 383.1 383.1 560 subfamily Y Y N FAD-dependent oxidoreductase 1.-.-.- 0 JCVI plant-specific FAD-dependent oxidoreductase FAD-dependent oxidoreductase This HMM represents an uncharacterized plant-specific family of FAD-dependent oxidoreductases. At least seven distinct members are found in Arabidopsis thaliana. The family shows considerable sequence similarity to three different enzymes of ascorbic acid biosynthesis: L-galactono-1,4-lactone dehydrogenase (EC 1.3.2.3) from higher plants, D-arabinono-1,4-lactone oxidase (EC 1.1.3.37 from Saccharomyces cerevisiae, and L-gulonolactone oxidase (EC 1.1.3.8) from mouse, as well as to a bacterial sorbitol oxidase. The class of compound acted on by members of this family is unknown. TIGR01684.1 TIGR01684 viral_ppase 134 134 301 hypoth_equivalog N N N viral phosphatase 11601995,7966317 0 JCVI viral phosphatase viral phosphatase This model represents a family of viral proteins of unknown function. These proteins are members, however, of the IIIC (TIGR01681) subfamily of the haloacid dehalogenase (HAD) superfamily of aspartate nucleophile hydrolases. All characterized members of the III subfamilies (IIIA, TIGR01662; IIIB, PF03767) are phosphatases, including MDP-1, a member of subfamily IIIC (TIGR01681) [1]. No member of this subfamily is characterized with respect to particular function. All of the active site residues characteristic of HAD-superfamily phosphatases [2] are present in subfamily IIIC. These proteins also include an N-terminal domain (ca. 125 aas) that is unique (by HMM) to this clade. TIGR01739.1 TIGR01739 tegu_FGAM_synt 716.1 716.1 1206 hypoth_equivalog N N N herpesvirus tegument protein/v-FGAM-synthase 0 JCVI herpesvirus tegument protein/v-FGAM-synthase herpesvirus tegument protein/v-FGAM-synthase This HMM describes a family of large proteins of herpesvirues. The protein is described variably as tegument protein or phosphoribosylformylglycinamidine synthase (FGAM-synthase). Most of the length of the protein shows homology to eukaryotic FGAM-synthase. Functional characterizations were not verified during construction of this model. TIGR01756.1 TIGR01756 LDH_protist 486.25 486.25 313 equivalog Y Y N lactate dehydrogenase 1.1.1.27 10339579 0 JCVI lactate dehydrogenase lactate dehydrogenase This model represents a family of protist lactate dehydrogenases which have aparrently evolved from a recent protist malate dehydrogenase ancestor [1]. Lactate dehydrogenase converts the hydroxyl at C-2 of lactate to a carbonyl in the product, pyruvate. The preference of this enzyme for NAD or NADP has not been determined. A critical residue in malate dehydrogenase, arginine-91 (T. vaginalis numbering) has been mutated to a leucine, eliminating the positive charge which complemeted the carboxylate in malate which is absent in lactate. Several other more subtle changes are proposed to make the active site smaller to accomadate the less bulky lactate molecule. TIGR01757.1 TIGR01757 Malate-DH_plant 598.3 598.3 387 equivalog Y Y N malate dehydrogenase, NADP-dependent 1.1.1.82 10194350 0 JCVI malate dehydrogenase, NADP-dependent malate dehydrogenase, NADP-dependent This model represents the NADP-dependent malate dehydrogenase found in plants, mosses and green algae and localized to the chloroplast. Malate dehydrogenase converts oxaloacetate into malate, a critical step in the C4 cycle which allows circumvention of the effects of photorespiration. Malate is subsequenctly transported from the chloroplast to the cytoplasm (and then to the bundle sheath cells in C4 plants). The plant and moss enzymes are light regulated via cysteine disulfide bonds. The enzyme from Sorghum has been crystallized [1]. TIGR01758.1 TIGR01758 MDH_euk_cyt 470.4 470.4 324 equivalog Y Y N malate dehydrogenase, NAD-dependent 2775751 0 JCVI malate dehydrogenase, NAD-dependent malate dehydrogenase, NAD-dependent This model represents the NAD-dependent cytosolic malate dehydrogenase from eukaryotes. The enzyme from pig has been studied by X-ray crystallography [1] TIGR01880.1 TIGR01880 Ac-peptdase-euk 338.6 338.6 401 subfamily Y Y N N-acyl-aliphatic-L-amino acid amidohydrolase 3.5.1.14 0 JCVI N-acyl-L-amino-acid amidohydrolase N-acyl-aliphatic-L-amino acid amidohydrolase This model represents a family of eukaryotic N-acyl-L-amino-acid amidohydrolases active on fatty acid and acetyl amides of L-amino acids. TIGR01989.1 TIGR01989 COQ6 489.3 489.3 437 equivalog Y Y N ubiquinone biosynthesis monooxygenase COQ6 11583838,12721307 0 JCVI ubiquinone biosynthesis monooxygenase COQ6 ubiquinone biosynthesis monooxygenase COQ6 This model represents the monooxygenase responsible for the 4-hydroxylateion of the phenol ring in the aerobic biosynthesis of ubiquinone [1,2] TIGR02189.1 TIGR02189 GlrX-like_plant 93.8 93.8 99 paralog N N N glutaredoxin-like family 0 JCVI glutaredoxin-like family glutaredoxin-like family This family of glutaredoxin-like proteins is aparrently limited to plants. Multiple isoforms are found in A. thaliana and O.sativa. TIGR02238.1 TIGR02238 recomb_DMC1 447.7 447.7 314 equivalog Y Y N meiotic recombinase Dmc1 15164066 0 JCVI meiotic recombinase Dmc1 meiotic recombinase Dmc1 This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis. TIGR02239.1 TIGR02239 recomb_RAD51 478.05 478.05 316 equivalog Y Y N DNA repair protein RAD51 32663049,32938550,33433732 0 JCVI DNA repair protein RAD51 DNA repair protein RAD51 This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012). TIGR02245.1 TIGR02245 HAD_IIID1 192.25 192.25 195 hypoth_equivalog Y Y N HAD-IIID family hydrolase 10956028,11601995,7966317 0 JCVI HAD hydrolase, family IIID HAD-IIID family hydrolase This family of sequences appears to belong to the Haloacid Dehalogenase (HAD) superfamily of enzymes by virtue of the presence of three catalytic domains [1], in this case: LLVLD(ILV)D(YH)T, I(VMG)IWS, and (DN)(VC)K(PA)Lx{15-17}T(IL)(MH)(FV)DD(IL)(GRS)(RK)N. Since this family has no large "cap" domain [2] between motifs 1 and 2 or between 2 and 3, it is formally a "class III" HAD [3]. TIGR02250.1 TIGR02250 FCP1_euk 135.25 135.25 156 subfamily_domain Y Y N FCP1-like phosphatase 11601995,14701811,15170348,7966317 0 JCVI FCP1-like phosphatase, phosphatase domain FCP1-like phosphatase, phosphatase domain This model represents the phosphatase domain of the human RNA polymerase II subunit A C-terminal domain phosphatase (FCP1) and closely related phosphatases from eukaryotes including plants, fungi, and slime mold. This domain is a member of the haloacid dehalogenase (HAD) superfamily by virtue of a conserved set of three catalytic motifs and a conserved fold as predicted by PSIPRED. The third motif in this family is distinctive (hhhhDDppphW). This domain is classified as a "Class III" HAD, since there is no large "cap" domain found between motifs 1 and 2 or motifs 2 and 3. This domain is related to domains found in the human NLI interacting factor-like phosphatases, and together both are detected by the Pfam model PF03031. TIGR02251.1 TIGR02251 HIF-SF_euk 139.15 139.15 168 subfamily_domain N N N dullard-like phosphatase domain 11601995,12083771,15051889,7966317 0 JCVI dullard-like phosphatase domain dullard-like phosphatase domain This model represents the putative phosphatase domain of a family of eukaryotic proteins including "Dullard" [1], and the NLI interacting factor (NIF)-like phosphatases [2]. This domain is a member of the haloacid dehalogenase (HAD) superfamily by virtue of a conserved set of three catalytic motifs [3] and a conserved fold as predicted by PSIPRED. The third motif in this family is distinctive (hhhhDNxPxxa) and aparrently lacking the last aspartate. This domain is classified as a "Class III" HAD, since there is no large "cap" domain found between motifs 1 and 2 or motifs 2 and 3 [4]. This domain is related to domains found in FCP1-like phosphatases (TIGR02250), and together both are detected by the Pfam model PF03031. TIGR02340.1 TIGR02340 chap_CCT_alpha 800.2 800.2 536 equivalog Y Y N T-complex protein 1 subunit alpha 0 JCVI T-complex protein 1, alpha subunit T-complex protein 1 subunit alpha Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT alpha chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. TIGR02341.1 TIGR02341 chap_CCT_beta 522.15 522.15 519 equivalog Y Y N T-complex protein 1 subunit beta 0 JCVI T-complex protein 1, beta subunit T-complex protein 1 subunit beta Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT beta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. TIGR02342.1 TIGR02342 chap_CCT_delta 695.35 695.35 517 equivalog Y Y N T-complex protein 1 subunit delta 0 JCVI T-complex protein 1, delta subunit T-complex protein 1 subunit delta Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT delta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. TIGR02344.1 TIGR02344 chap_CCT_gamma 553.45 553.45 526 equivalog Y Y N T-complex protein 1 subunit gamma 0 JCVI T-complex protein 1, gamma subunit T-complex protein 1 subunit gamma Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT gamma chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. TIGR02345.1 TIGR02345 chap_CCT_eta 669.2 669.2 523 equivalog Y Y N T-complex protein 1 subunit eta 0 JCVI T-complex protein 1, eta subunit T-complex protein 1 subunit eta Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT eta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. TIGR02346.1 TIGR02346 chap_CCT_theta 455.9 455.9 531 equivalog Y Y N T-complex protein 1 subunit theta 0 JCVI T-complex protein 1, theta subunit T-complex protein 1 subunit theta Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT alpha chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. TIGR02347.1 TIGR02347 chap_CCT_zeta 587.15 587.15 531 equivalog Y Y N T-complex protein 1 subunit zeta 0 JCVI T-complex protein 1, zeta subunit T-complex protein 1 subunit zeta Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT zeta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. TIGR02411.1 TIGR02411 leuko_A4_hydro 761.7 761.7 600 equivalog Y Y N leukotriene-A(4) hydrolase/aminopeptidase 3.3.2.6,3.4.11.- 11601994,15339917 0 JCVI leukotriene A-4 hydrolase/aminopeptidase leukotriene-A(4) hydrolase/aminopeptidase Members of this family represent a distinctive subset within the zinc metallopeptidase family M1 (PF01433). The majority of the members of PF01433 are aminopeptidases, but the sequences in this family for which the function is known are leukotriene A-4 hydrolase. A dual epoxide hydrolase and aminopeptidase activity at the same active site is indicated. The physiological substrate for aminopeptidase activity is not known. TIGR02441.1 TIGR02441 fa_ox_alpha_mit 964.65 964.65 737 equivalog Y Y N fatty acid oxidation complex subunit alpha GO:0003857,GO:0004300,GO:0006635,GO:0016507 7881821,8135828,8253773 0 JCVI fatty acid oxidation complex, alpha subunit, mitochondrial fatty acid oxidation complex, alpha subunit, mitochondrial Members represent alpha subunit of mitochondrial multifunctional fatty acid degradation enzyme complex. Subunit activities include: enoyl-CoA hydratase (EC 4.2.1.17) & 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35). Some characterization in human (SP:P40939), pig (SP:Q29554), and rat (SP:Q64428). The beta subunit has activity: acetyl-CoA C-acyltransferase (EC 2.3.1.16). TIGR02468.1 TIGR02468 sucrsPsyn_pln 1143.95 1143.95 1051 equivalog Y Y N sucrose-phosphate synthase 2.4.1.14 15247374 0 JCVI sucrose phosphate synthase sucrose-phosphate synthase Members of this family are sucrose-phosphate synthases of plants. This enzyme is known to exist in multigene families in several species of both monocots and dicots. The N-terminal domain is the glucosyltransferase domain. Members of this family also have a variable linker region and a C-terminal domain that resembles sucrose phosphate phosphatase (SPP) (EC 3.1.3.24) (see TIGR01485), the next and final enzyme of sucrose biosynthesis. The SPP-like domain likely serves a binding and not a catalytic function, as the reported SPP is always encoded by a distinct protein. TIGR02540.1 TIGR02540 gpx7 207.3 207.3 153 equivalog Y Y N putative glutathione peroxidase Gpx7 1.11.1.9 0 JCVI putative glutathione peroxidase Gpx7 putative glutathione peroxidase Gpx7 This model represents one of several families of known and probable glutathione peroxidases. This family is restricted to animals and designated GPX7. TIGR02685.1 TIGR02685 pter_reduc_Leis 321.7 321.7 267 equivalog Y Y N pteridine reductase 1.5.1.33 16168672 0 JCVI pteridine reductase pteridine reductase Pteridine reductase is an enzyme used by trypanosomatids (including Trypanosoma cruzi and Leishmania major) to obtain reduced pteridines by salvage rather than biosynthetic pathways. Enzymes in T. cruzi described as pteridine reductase 1 (PTR1) and pteridine reductase 2 (PTR2) have different activity profiles. PTR1 is more active with with fully oxidized biopterin and folate than with reduced forms, while PTR2 reduces dihydrobiopterin and dihydrofolate but not oxidized pteridines. T. cruzi PTR1 and PTR2 are more similar to each other in sequence than either is to the pteridine reductase of Leishmania major, and all are included in this family. TIGR02766.1 TIGR02766 crypt_chrom_pln 603.85 603.85 480 subfamily Y Y N cryptochrome photoreceptor 11884681 0 JCVI cryptochrome, plant family cryptochrome photoreceptor At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light. TIGR02825.1 TIGR02825 B4_12hDH 579.85 579.85 327 equivalog Y Y N leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase 15007077,8576264 0 JCVI leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase Leukotriene B4 12-hydroxydehydrogenase is an NADP-dependent enzyme of arachidonic acid metabolism, responsible for converting leukotriene B4 to the much less active metabolite 12-oxo-leukotriene B4. The BRENDA database lists leukotriene B4 12-hydroxydehydrogenase as one of the synonyms of 2-alkenal reductase (EC 1.3.1.74), while 1.3.1.48 is 15-oxoprostaglandin 13-reductase. TIGR02969.1 TIGR02969 mam_aldehyde_ox 1912.3 1912.3 1330 subfamily Y Y N aldehyde oxidase 1.2.3.1 0 JCVI aldehyde oxidase aldehyde oxidase Members of this family are mammalian aldehyde oxidase (EC 1.2.3.1) isozymes, closely related to xanthine dehydrogenase/oxidase. TIGR03051.1 TIGR03051 PS_I_psaG_plant 104.55 104.55 89 equivalog Y Y N photosystem I reaction center subunit V psaG 0 JCVI photosystem I reaction center subunit V photosystem I reaction center subunit V TIGR03230.1 TIGR03230 lipo_lipase 822.75 822.75 442 equivalog Y Y N lipoprotein lipase 3.1.1.34 GO:0004465 8308035 0 JCVI lipoprotein lipase lipoprotein lipase Members of this protein family are lipoprotein lipase (EC 3.1.1.34), a eukaryotic triacylglycerol lipase active in plasma and similar to pancreatic and hepatic triacylglycerol lipases (EC 3.1.1.3). It is also called clearing factor. It cleaves chylomicron and VLDL triacylglycerols; it also has phospholipase A-1 activity. TIGR03376.1 TIGR03376 glycerol3P_DH 285.5 285.5 342 equivalog Y Y N glycerol-3-phosphate dehydrogenase (NAD(+)) 1.1.1.8 2500660,8196651 0 JCVI glycerol-3-phosphate dehydrogenase (NAD(+)) glycerol-3-phosphate dehydrogenase (NAD(+)) Members of this protein family are the eukaryotic enzyme, glycerol-3-phosphate dehydrogenase (NAD(+)) (EC 1.1.1.8). Enzymatic activity for 1.1.1.8 is defined as sn-glycerol 3-phosphate + NAD(+) = glycerone phosphate + NADH. Note the very similar reactions of enzymes defined as EC 1.1.1.94 and 1.1.99.5, assigned to families of proteins in the bacteria. TIGR03388.1 TIGR03388 ascorbase 614.8 614.8 542 equivalog Y Y N L-ascorbate oxidase 1.10.3.3 0 JCVI L-ascorbate oxidase L-ascorbate oxidase Members of this protein family are the copper-containing enzyme L-ascorbate oxidase (EC 1.10.3.3), also called ascorbase. This family is found in flowering plants, and shows greater sequence similarity to a family of laccases (EC 1.10.3.2) from plants than to other known ascorbate oxidases. TIGR03389.1 TIGR03389 laccase 558.9 558.9 539 equivalog Y Y N laccase 1.10.3.2 0 JCVI laccase laccase Members of this protein family include the copper-containing enzyme laccase (EC 1.10.3.2), often several from a single plant species, and additional, uncharacterized, closely related plant proteins termed laccase-like multicopper oxidases. This protein family shows considerable sequence similarity to the L-ascorbate oxidase (EC 1.10.3.3) family. Laccases are enzymes of rather broad specificity, and classification of all proteins scoring about the trusted cutoff of this model as laccases may be appropriate. TIGR03390.1 TIGR03390 ascorbOXfungal 445.35 445.35 538 equivalog Y Y N L-ascorbate oxidase 1.10.3.3 9858779 0 JCVI L-ascorbate oxidase L-ascorbate oxidase This model describes a family of fungal ascorbate oxidases, within a larger family of multicopper oxidases that also includes plant ascorbate oxidases (TIGR03388), plant laccases and laccase-like proteins (TIGR03389), and related proteins. The member from Acremonium sp. HI-25 is characterized. TIGR03400.1 TIGR03400 18S_RNA_Rcl1p 227.95 227.95 360 equivalog Y Y N 18S rRNA biogenesis protein RCL1 10790377 0 JCVI 18S rRNA biogenesis protein RCL1 18S rRNA biogenesis protein RCL1 Members of this strictly eukaryotic protein family are not RNA 3'-phosphate cyclase (6.5.1.4), but rather a homolog with a distinct function, found in the nucleolus and required for ribosomal RNA processing. Homo sapiens has both a member of this RCL (RNA terminal phosphate cyclase like) family and EC 6.5.1.4, while Saccharomyces has a member of this family only. TIGR03401.1 TIGR03401 cyanamide_fam 109.85 109.85 228 subfamily N N N HD domain protein, cyanamide hydratase family 2034671 0 JCVI HD domain protein, cyanamide hydratase family HD domain protein, cyanamide hydratase family Members of this protein family are known, so far, in the Ascomycota, a branch of the Fungi, and contain an HD domain (PF01966), found typically in various metal-dependent phosphohydrolases. The only characterized member of this family, from the soil fungus Myrothecium verrucaria, is cyanamide hydratase (EC 4.2.1.69), a zinc-containing homohexamer that adds water to the fertilizer cyanamide (NCNH2), a nitrile compound, to produce urea (NH2-CO-NH2). Homologs are likely to be nitrile hydratases. TIGR03430.1 TIGR03430 trp_dimet_allyl 740.75 740.75 419 equivalog Y Y N tryptophan dimethylallyltransferase 2.5.1.34 7488077 0 JCVI tryptophan dimethylallyltransferase tryptophan dimethylallyltransferase Members of this family are the enzyme tryptophan dimethylallyltransferase (EC 2.5.1.34), a distinct clade within a larger group of aromatic prenyltransferases that may act on on trp-containing cyclic dipeptides, or on tyrosine or other related substrates. Tryptophan dimethylallyltransferase and related enzymes typically are of fungal origin are involved in the biosynthesis of secondary metabolites such as ergot alkaloids. TIGR03443.1 TIGR03443 alpha_am_amid 1030.1 1030.1 1390 equivalog Y Y N L-aminoadipate-semialdehyde dehydrogenase 1.2.1.31 GO:0004043,GO:0009085 0 JCVI L-aminoadipate-semialdehyde dehydrogenase L-aminoadipate-semialdehyde dehydrogenase Members of this protein family are L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31), product of the LYS2 gene. It is also called alpha-aminoadipate reductase. In fungi, lysine is synthesized via aminoadipate. Currently, all members of this family are fungal. TIGR03575.1 TIGR03575 selen_PSTK_euk 382.35 382.35 340 equivalog Y Y N L-seryl-tRNA(Sec) kinase 2.7.1.164 GO:0016260,GO:0016773 15317934 0 JCVI L-seryl-tRNA(Sec) kinase L-seryl-tRNA(Sec) kinase Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity. TIGR04198.1 TIGR04198 paramyx_RNAcap 185 185 938 equivalog_domain Y Y N mRNA capping enzyme GO:0006370 19297608 0 JCVI mRNA capping enzyme mRNA capping enzyme This model represents a common C-terminal region shared by paramyxovirus-like RNA-dependent RNA polymerases (see Pfam model PF00946). Polymerase proteins described by these two models are often called L protein (large polymerase protein). Capping of mRNA requires RNA triphosphatase and guanylyl transferase activities, demonstrated for the rinderpest virus L protein and at least partially localized to the region of this model. TIGR04202.1 TIGR04202 capSnatchArena 40 40 61 signature N N N RNA endonuclease, cap-snatching 20862324 0 JCVI RNA endonuclease, cap-snatching RNA endonuclease, cap-snatching This HMM describes a shared signature region from an RNA endonuclease region associated with cap-snatching for mRNA production by RNA viruses. This domain usually is part of a multifunctional protein, the L protein responsible for RNA-dependent RNA polymerase activity. Cap-snatching is a viral alternative to synthesizing a eukaryotic-like mRNA cap itself. TIGR04210.1 TIGR04210 bunya_NSm 28 23 173 equivalog_domain N N N bunyavirus nonstructural protein NSm 0 JCVI bunyavirus nonstructural protein NSm bunyavirus nonstructural protein NSm This HMM describes a protein region that is cleaved from a bunyavirus polyprotein to become the nonstructural protein NSm (encoded by the M segment). It is flanked by glycoprotein GP2 and glycoprotein GP1. TIGR04230.1 TIGR04230 seadorna_VP11 75 75 175 equivalog N N N seadornavirus VP11 protein 10811934 0 JCVI seadornavirus VP11 protein seadornavirus VP11 protein This protein family occurs in the seadornavirus virus group, with designations VP11 in Banna virus, and VP12 in Kadipiro virus and Liao ning virus. The function has not been assigned. TIGR04231.1 TIGR04231 seadorna_VP5 80 80 505 equivalog N N N seadornavirus VP5 protein 10811934 0 JCVI seadornavirus VP5 protein seadornavirus VP5 protein This protein family occurs in the seadornavirus virus group, with designations VP5 in Banna virus, and VP6 in Kadipiro virus and Liao ning virus. The function is unassigned. TIGR04232.1 TIGR04232 seadorna_VP3 100 100 731 equivalog N N N seadornavirus VP3 protein 10811934 0 JCVI seadornavirus VP3 protein seadornavirus VP3 protein Members of this protein family are VP3 proteins in the seadornavirus group. Sequences show sequence similarity to methyltransferases. TIGR04233.1 TIGR04233 seadorna_VP8 75 75 291 equivalog N N N seadornavirus VP8 protein 10811934 0 JCVI seadornavirus VP8 protein seadornavirus VP8 protein This protein family occurs in the seadornavirus virus group, with designations VP8 in Banna virus, and VP9 in Kadipiro virus and Liao ning virus. The function has not been assigned. TIGR04234.1 TIGR04234 seadorna_RNAP 150 150 1144 equivalog Y Y N RNA-directed RNA polymerase 2.7.7.48 10811934 0 JCVI RNA-directed RNA polymerase RNA-directed RNA polymerase Members of this protein family are the seadornavirus VP1 protein, the RNA-directed RNA polymerase. TIGR04235.1 TIGR04235 seadorna_VP4 80 80 618 equivalog N N N seadornavirus VP4 protein 10811934 0 JCVI seadornavirus VP4 protein seadornavirus VP4 protein This protein family occurs in the seadornavirus virus group, with designation VP4 in Banna virus, Kadipiro virus, and Liao ning virus. Although this family has been suggested to resemble methyltransferases, members show apparent N-terminal sequence similarity to the outer capsid protein VP5 of the orbivirus group, such as bluetongue virus, which also belong to the Reoviridae. TIGR04236.1 TIGR04236 seadorna_VP2 125 125 953 equivalog N N N seadornavirus VP2 protein 10811934 0 JCVI seadornavirus VP2 protein seadornavirus VP2 protein This protein family occurs in the seadornavirus virus group, with the designation VP2 in Banna virus, Kadipiro virus, and Liao ning virus. TIGR04237.1 TIGR04237 seadorna_VP9 45 45 256 equivalog N N N seadornavirus/coltivirus VP9 protein 10811934 0 JCVI seadornavirus/coltivirus VP9 protein seadornavirus/coltivirus VP9 protein This model, broader than related Pfam model PF08978, describes proteins VP9 in Coltivirus, and proteins with various designations in the seadornavirus group: VP9 in Banna virus, VP10 in Liao ning virus, and VP11 in Kadipiro virus. TIGR04238.1 TIGR04238 seadorna_dsRNA 125 125 201 equivalog N N N seadornavirus double-stranded RNA-binding protein 10811934 0 JCVI seadornavirus double-stranded RNA-binding protein seadornavirus double-stranded RNA-binding protein This protein family occurs in the seadornavirus virus group, with an N-terminal domain for binding double-stranded RNA, is designated VP12 in Banna virus, VP8 in Kadipiro virus, and VP11 in Liao ning virus. TIGR04240.1 TIGR04240 flavi_E_stem 26 25.2 97 equivalog_domain N N N flavivirus envelope glycoprotein E, stem/anchor domain 21325407 0 JCVI flavivirus envelope glycoprotein E, stem/anchor domain flavivirus envelope glycoprotein E, stem/anchor domain This model describes the C-terminal domain, containing a stem region followed by two transmembrane anchor domains, of the envelope protein E. This protein is cleaved from the large flavivirus polyprotein, which yields three structural and seven nonstructural proteins. TIGR04241.1 TIGR04241 adenoE3CR1rpt 37 37 81 equivalog_domain Y Y N membrane glycoprotein E3 CR1-alpha 14573794 0 JCVI mastadenovirus E3 CR1-alpha-1 membrane glycoprotein E3 CR1-alpha This domain occurs only in the adenovirus E3 region CR1-alpha-1 protein. It may occur once, twice, or three times. TIGR04277.1 TIGR04277 squa_tetra_cyc 500 500 624 equivalog_domain Y Y N tetrahymanol synthase 4.2.1.123 GO:0016114,GO:0034073 0 JCVI tetrahymanol synthase tetrahymanol synthase This enzyme, also called squalene--tetrahymanol cyclase, occurs a small number of eukaryotes, some of them anaerobic. The pathway can occur under anaerobic conditions, and the product is thought to replace sterols, letting organisms with this compound build membrane suitable for performing phagocytosis. TIGR04278.1 TIGR04278 viperin 450 450 347 exception Y Y N antiviral radical SAM protein viperin RSAD2 GO:0005811,GO:0051539,GO:0051607,GO:1904047 18005724,29925952,32546482 0 JCVI antiviral radical SAM protein viperin antiviral radical SAM protein viperin Viperin (Virus Inhibitory Protein, ER-associated, Interferon-inducible) is a radical SAM enzyme found in human and other vertebrates. A recently identified antiviral activity is the conversion of cytidine triphosphate (CTP) to 3'-deoxy-3',4'-didehydro-CTP (ddhCTP), which serves as a chain terminator for viral RNA-dependent RNA polymerases. It previously was shown to be involved in modifying lipid chemistries in lipid droplets and membrane rafts, which also can affect viral life cycles. Viperin, product of the the RSAD2 gene, is both induced by interferon and demonstrably active in blocking replication by several types of virus. TIGR04309.1 TIGR04309 amanitin 35 35 33 subfamily Y Y N amanitin/phalloidin family toxin 0 JCVI amanitin/phalloidin family toxin amanitin/phalloidin family toxin Members of this family are ribosomally produced precursors of toxins produced by several mushrooms. These precursors undergo extensive post-translational modification to become amatoxins (e.g. alpha-amanitin) and phallotoxins (e.g. phalloidin). TIGR04473.1 TIGR04473 taxol_Phe_23mut 1250 1250 687 exception Y Y N phenylalanine aminomutase (L-beta-phenylalanine forming) 5.4.3.10 15494399 0 JCVI phenylalanine aminomutase (L-beta-phenylalanine forming) phenylalanine aminomutase (L-beta-phenylalanine forming) Members of this family are the phenylalanine aminomutase known from taxol biosynthesis. This enzyme has the MIO prosthetic group (4-methylideneimidazole-5-one), derived from an Ala-Ser-Gly motif. Other MIO enzymes include Phe, Tyr, and His ammonia-lyases. This model serves as an exception to overrule assignments by equivalog model TIGR01226 for phenylalanine ammonia-lyase. TIGR04532.1 TIGR04532 PT_fungal_PKS 168 168 329 subfamily_domain N N N polyketide product template domain GO:0030639 20479000 0 JCVI polyketide product template domain polyketide product template domain Sequences found by this model are the so-called product template (PT) domain of various fungal iterative type I polyketide synthases. This domain resembles PF14765, designated polyketide synthase dehydratase by Pfam, but members of that family are primarily bacterial, where type I PKS are predominantly modular, not iterative. The dehydratase active site residues well-conserved in PF14765 (His in the first hot dog domain, Asp in the second hot dog domain) seem well conserved in this family also. TIGR04556.1 TIGR04556 PKS_assoc 80 80 226 domain N N N polyketide synthase-associated domain 23139807 0 JCVI polyketide synthase-associated domain polyketide synthase-associated domain This model describes a rare domain found as the N-terminal region of a number of dinoflagellate-specific proteins that resemble type I polyketide synthases. NF041848.1 celb_epim_EpiA 800 800 405 equivalog Y Y N cellobiose 2-epimerase EpiA epiA GO:0005975,GO:0016853,GO:0047736 16842369,25704402 10 Cellvibrio genus 7 NCBIFAM cellobiose 2-epimerase EpiA NF023439.5 PF12014.13 Cyclin_D1_bind 22 22 156 domain Y Y N Cyclin D1-binding domain-containing protein 29279382 1032527 Pedosphaera parvula species 1 EBI-EMBL Cyclin D1 binding domain Cyclin D1 binding domain Ubiquitin-dependent proteolysis of cyclin D1 is associated with normal and tumour cell proliferation and survival. The best characterised member of this family is the SCF FBXO31 (Skp1-Cul1-Rbx1-FBXO31) ubiquitin ligase complex mediates genotoxic stress-induced cyclin D1 degradation [1]. FBXO31 possesses a unique substrate-binding beta barrel domain, whereas cyclin D1 binds to FBXO31 by tucking its free C-terminal carboxylate tail into an open cavity of the C-terminal FBXO31 beta-barrel. Biophysical and functional studies demonstrated that SCFFBXO31 is capable of recruiting and ubiquitinating cyclin D1 in a phosphorylation-independent manner. Paper describing PDB structure 5vzt. [1]. 29279382. Structural basis of the phosphorylation-independent recognition of cyclin D1 by the SCF(FBXO31) ubiquitin ligase. Li Y, Jin K, Bunker E, Zhang X, Luo X, Liu X, Hao B;. Proc Natl Acad Sci U S A. 2018;115:319-324. (from Pfam) NF021074.5 PF09528.15 Ehrlichia_rpt 27 9 36 repeat Y N N surface-exposed repeat protein 19420187 106178 canis group species group 8 EBI-EMBL Ehrlichia tandem repeat (Ehrlichia_rpt) surface-exposed repeat protein This entry represents 30 amino acid tandem repeat, found in a variable number of copies in an immunodominant outer membrane protein of Ehrlichia chaffeensis, a tick-borne obligate intracellular pathogen. These short tandem-repeats elicit a strong antibody response in the hosts [1]. [1]. 19420187. Major species-specific antibody epitopes of the Ehrlichia chaffeensis p120 and E. canis p140 orthologs in surface-exposed tandem repeat regions. Luo T, Zhang X, McBride JW;. Clin Vaccine Immunol. 2009;16:982-990. (from Pfam) NF022670.5 PF11224.13 DUF3023 22 22 129 domain Y Y N DUF3023 domain-containing protein 106178 canis group species group 184 EBI-EMBL Protein of unknown function (DUF3023) Protein of unknown function (DUF3023) This bacterial family of proteins with unknown function appear to be restricted to Alphaproteobacteria. (from Pfam) NF023452.5 PF12027.13 DUF3514 25 25 256 domain Y Y N DUF3514 domain-containing protein 106178 canis group species group 117 EBI-EMBL Protein of unknown function (DUF3514) Protein of unknown function (DUF3514) This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 368 to 823 amino acids in length. (from Pfam) NF033393.0 TRP47_fam_Nterm 75 75 105 subfamily_domain Y Y N TRP47 family tandem repeat effector 19273555,30408047 106178 canis group species group 50 NCBIFAM TRP47 family tandem repeat effector TRP47 family tandem repeat effector N-terminal domain This HMM describes a conserved N-terminal domain of a family of proteins found, so far, only in the genus Ehrlichia. The repeat region is followed by a long repeat region with a large content of acidic and serine residues, but other than in composition, the repeats themselves may be unrelated from one lineage to another. Characterized examples, such as TRP47 from Ehrlichia chaffeensis, are glycoproteins and are immunodominant antigens. NF042983.1 blaOXA-837_like 575 575 301 exception Y Y Y OXA-837 family class D beta-lactamase blaOXA 3.5.2.6 GO:0008800 31578249 106589 Cupriavidus genus 15 NCBIFAM OXA-837 family class D beta-lactamase The found member of this subfamily of class D beta-lactamases, OXA-837 from the emerging multidrug-resistant pathogen Cupriavidus gilardii, conferred reduced susceptibility to ampicillin, when expressed in test strain of Escherichia coli, but had no effect on amoxicillin-clavulanate in combination, cefotaxime, or carbapenems. NF004842.0 PRK06193 PRK06193.1-3 325 325 209 subfamily Y N N hypothetical protein 106633 Thioalkalivibrio genus 17 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein TIGR01310.1 TIGR01310 uL30_euk 254 254 236 subfamily N N N 60S ribosomal protein uL30 GO:0003735,GO:0006412,GO:0022625 106654 Acinetobacter nosocomialis species 1 JCVI 60S ribosomal protein uL30 60S ribosomal protein uL30 This HMM describes the eukaryotic 60S (cytosolic) ribosomal protein uL30 (previously L7) and paralogs that may or may not also be uL30. Human, Drosophila, and Arabidopsis all have both a typical L7 and an L7-related paralog. This family is designated subfamily rather than equivalog to reflect these uncharacterized paralogs. Members of this family average ~ 250 residues in length, somewhat longer than the archaeal L30P/L7E homolog (~ 155 residues) and much longer than the related bacterial/organellar form (~ 60 residues). NF009425.0 PRK12787 PRK12787.1-1 238 238 138 equivalog Y N N flagellar assembly regulator FliX 1073 Rhodopseudomonas genus 16 NCBI Protein Cluster (PRK) flagellar assembly regulator FliX flagellar assembly regulator FliX NF011295.0 PRK14708 PRK14708.1 1384 1384 888 subfamily Y N N flagellin 1073 Rhodopseudomonas genus 57 NCBI Protein Cluster (PRK) flagellin flagellin NF002512.0 PRK01903 PRK01903.2-3 231 231 146 equivalog Y N N ribonuclease P 1091 Chlorobium genus 2 NCBI Protein Cluster (PRK) ribonuclease P ribonuclease P NF002514.0 PRK01903 PRK01903.3-1 246 246 122 equivalog Y N N ribonuclease P 1100 Pelodictyon luteolum species 1 NCBI Protein Cluster (PRK) ribonuclease P ribonuclease P NF011370.0 PRK14789 PRK14789.1 248 248 194 equivalog Y N N lipoprotein signal peptidase 1107 Chloroflexus genus 13 NCBI Protein Cluster (PRK) lipoprotein signal peptidase lipoprotein signal peptidase NF000321.3 blaPEN-Bpc 580 580 295 exception Y Y Y PEN family class A beta-lactamase, Bpc-type blaPEN-bpc 3.5.2.6 GO:0008800 19075063,29983287,30006637 111527 pseudomallei group species group 61 NCBIFAM PenI family class A beta-lactamase PEN family class A beta-lactamase, Bpc-type Members of this family of chromosomal class A beta-lactamases from the Burkholderia pseudomallei complex (Bpc) include PenI from Burkholderia pseudomallei, PenJ from B. oklahomensis, PenK from B. mallei, and PenL from B. thailandensis. NF002335.0 PRK01294 PRK01294.1-3 637 637 344 equivalog Y Y N lipase secretion chaperone 111527 pseudomallei group species group 70 NCBI Protein Cluster (PRK) lipase chaperone lipase secretion chaperone NF005439.0 PRK07027 PRK07027.1-3 261 261 150 equivalog Y N N cobalamin biosynthesis protein CbiG 111527 pseudomallei group species group 63 NCBI Protein Cluster (PRK) cobalamin biosynthesis protein CbiG cobalamin biosynthesis protein CbiG NF005464.0 PRK07060 PRK07060.1-1 465 465 248 equivalog Y N N short chain dehydrogenase 111527 pseudomallei group species group 63 NCBI Protein Cluster (PRK) short chain dehydrogenase short chain dehydrogenase NF006115.0 PRK08264 PRK08264.1-1 454 454 237 equivalog Y Y N SDR family oxidoreductase 111527 pseudomallei group species group 24 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF008766.0 PRK11798 PRK11798.2-1 319 319 173 equivalog Y Y N ClpXP protease specificity-enhancing factor 111527 pseudomallei group species group 38 NCBI Protein Cluster (PRK) ClpXP protease specificity-enhancing factor ClpXP protease specificity-enhancing factor NF009465.0 PRK12826 PRK12826.1-1 526 526 277 equivalog Y Y N SDR family oxidoreductase 111527 pseudomallei group species group 53 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase SDR family oxidoreductase NF009865.0 PRK13328 PRK13328.1-1 487 487 256 equivalog Y Y N type III pantothenate kinase 2.7.1.33 111527 pseudomallei group species group 35 NCBI Protein Cluster (PRK) pantothenate kinase type III pantothenate kinase NF011283.0 PRK14693 PRK14693.1 686 686 552 equivalog Y N N hypothetical protein 111527 pseudomallei group species group 88 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF011311.0 PRK14722 PRK14722.1 777 777 374 equivalog Y N N flagellar biosynthesis regulator FlhF 111527 pseudomallei group species group 101 NCBI Protein Cluster (PRK) flagellar biosynthesis regulator FlhF flagellar biosynthesis regulator FlhF NF011808.0 PRK15278 PRK15278.1 328 328 261 equivalog Y N N type III secretion protein BopE 111527 pseudomallei group species group 58 NCBI Protein Cluster (PRK) type III secretion protein BopE type III secretion protein BopE NF038102.1 AAC_6p_III 305 305 156 exception Y Y Y tobramycin N-acetyltransferase AAC(6')-III aac(6')-III 2.3.1.82 32016409 111527 pseudomallei group species group 48 NCBIFAM tobramycin N-acetyltransferase AAC(6')-III AAC(6')-III is a family of aminoglycoside 6'-N-acetyltransferases, limited to and intrinsic in a number of Burkholderia species. In contrast to proteins designated AAC(6')-I and AAC(6')-II, members of this family do not affect resistance to either amikacin or gentamicin. Instead, they reduce sensitivity to tobramycin. NF040531.1 blaOXA-42_like 540 540 269 exception Y Y Y OXA-42 family class D beta-lactamase blaOXA 3.5.2.6 GO:0008800 12356787,15793160 111527 pseudomallei group species group 42 NCBIFAM OXA-42 family class D beta-lactamase Members of this family such as OXA-42 and OXA-43 were tested and did not show any ceftazidime or imipenem hydrolytic activity, and likewise failed to reduce susceptibility to those beta-lactams. However, hydrolysis was shown for ampicillin, oxacillin, piperacillin, and cephalothin. NF041330.1 BimD 200 200 121 equivalog Y Y N protein BimD bimD 17555434 111527 pseudomallei group species group 36 NCBIFAM protein BimD NF000842.0 PRK00071 PRK00071.2-1 167 167 191 equivalog Y Y N nicotinate-nucleotide adenylyltransferase 2.7.7.18 1117 Cyanobacteriota phylum 968 NCBI Protein Cluster (PRK) nicotinic acid mononucleotide adenylyltransferase nicotinate-nucleotide adenylyltransferase NF000935.0 PRK00092 PRK00092.3-3 187 187 153 equivalog Y Y N ribosome maturation factor RimP rimP 1117 Cyanobacteriota phylum 676 NCBI Protein Cluster (PRK) ribosome maturation protein RimP ribosome maturation factor RimP NF000951.0 PRK00095 PRK00095.2-1 391 391 559 equivalog Y Y N DNA mismatch repair endonuclease MutL mutL 1117 Cyanobacteriota phylum 914 NCBI Protein Cluster (PRK) DNA mismatch repair protein DNA mismatch repair endonuclease MutL NF001372.0 PRK00278 PRK00278.1-4 370 370 295 subfamily Y Y N indole-3-glycerol phosphate synthase TrpC trpC 4.1.1.48 1117 Cyanobacteriota phylum 1492 NCBI Protein Cluster (PRK) indole-3-glycerol-phosphate synthase indole-3-glycerol phosphate synthase TrpC NF001574.0 PRK00392 PRK00392.2-5 98 98 75 subfamily Y Y N DNA-directed RNA polymerase subunit omega 2.7.7.6 1117 Cyanobacteriota phylum 495 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit omega DNA-directed RNA polymerase subunit omega NF001778.0 PRK00513 PRK00513.2-4 315 315 266 equivalog Y Y N septum site-determining protein MinC minC 1117 Cyanobacteriota phylum 641 NCBI Protein Cluster (PRK) septum formation inhibitor septum site-determining protein MinC NF002108.0 PRK00951 PRK00951.1-3 328 328 205 equivalog Y Y N imidazoleglycerol-phosphate dehydratase HisB hisB 4.2.1.19 1117 Cyanobacteriota phylum 919 NCBI Protein Cluster (PRK) imidazoleglycerol-phosphate dehydratase imidazoleglycerol-phosphate dehydratase HisB NF002701.0 PRK02504 PRK02504.1 569 569 513 equivalog Y Y N NAD(P)H-quinone oxidoreductase subunit N 1117 Cyanobacteriota phylum 1013 NCBI Protein Cluster (PRK) NAD(P)H-quinone oxidoreductase subunit 2 NAD(P)H-quinone oxidoreductase subunit N NF002703.0 PRK02507 PRK02507.1-1 526 526 447 subfamily Y Y N proton extrusion protein PcxA pxcA 1117 Cyanobacteriota phylum 1008 NCBI Protein Cluster (PRK) proton extrusion protein PcxA proton extrusion protein PcxA NF002708.1 PRK02515 PRK02515.1 85 85 137 equivalog Y Y N photosystem II complex extrinsic protein PsbU psbU 1117 Cyanobacteriota phylum 807 NCBI Protein Cluster (PRK) photosystem II complex extrinsic protein precursor U photosystem II complex extrinsic protein PsbU Stabilizes and protects the oxygen-evolving complex of photosystem II against heat-induced inactivation NF002712.0 PRK02542 PRK02542.1 220 220 188 equivalog Y Y N photosystem I assembly protein Ycf4 1117 Cyanobacteriota phylum 836 NCBI Protein Cluster (PRK) photosystem I assembly protein Ycf4 photosystem I assembly protein Ycf4 Required for the assembly of photosystem I complex NF002713.0 PRK02546 PRK02546.1 827 827 533 subfamily Y Y N NAD(P)H-quinone oxidoreductase subunit 4 1117 Cyanobacteriota phylum 1181 NCBI Protein Cluster (PRK) NAD(P)H-quinone oxidoreductase subunit 4 NAD(P)H-quinone oxidoreductase subunit 4 NF002715.0 PRK02553 PRK02553.1 66 66 47 equivalog Y Y N photosystem II reaction center protein K 1117 Cyanobacteriota phylum 320 NCBI Protein Cluster (PRK) photosystem II reaction center protein K photosystem II reaction center protein K NF002724.0 PRK02597 PRK02597.1 1878 1878 1338 equivalog Y Y N DNA-directed RNA polymerase subunit beta' 1117 Cyanobacteriota phylum 971 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit beta' DNA-directed RNA polymerase subunit beta' DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates NF002725.1 PRK02603 PRK02603.1 143 143 173 equivalog Y Y N photosystem I assembly protein Ycf3 1117 Cyanobacteriota phylum 698 NCBI Protein Cluster (PRK) photosystem I assembly protein Ycf3 photosystem I assembly protein Ycf3 NF002726.0 PRK02610 PRK02610.1 391 391 374 equivalog Y Y N histidinol-phosphate transaminase 2.6.1.9 1117 Cyanobacteriota phylum 703 NCBI Protein Cluster (PRK) histidinol-phosphate aminotransferase histidinol-phosphate transaminase Catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis NF002729.0 PRK02625 PRK02625.1 1117 1117 626 equivalog Y Y N DNA-directed RNA polymerase subunit gamma 1117 Cyanobacteriota phylum 785 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit gamma DNA-directed RNA polymerase subunit gamma DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates NF002731.0 PRK02645 PRK02645.1 312 312 305 equivalog Y Y N NAD(+) kinase 2.7.1.23 1117 Cyanobacteriota phylum 861 NCBI Protein Cluster (PRK) inorganic polyphosphate/ATP-NAD kinase NAD(+) kinase Catalyzes the phosphorylation of NAD to NADP NF002732.0 PRK02649 PRK02649.1 348 348 305 equivalog Y Y N NAD(+) kinase 2.7.1.23 1117 Cyanobacteriota phylum 871 NCBI Protein Cluster (PRK) inorganic polyphosphate/ATP-NAD kinase NAD(+) kinase Catalyzes the phosphorylation of NAD to NADP NF002734.0 PRK02654 PRK02654.1 324 324 384 equivalog Y Y N membrane protein insertase YidC yidC 1117 Cyanobacteriota phylum 932 NCBI Protein Cluster (PRK) putative inner membrane protein translocase component YidC membrane protein insertase YidC NF002736.1 PRK02693 PRK02693.1 500 500 307 equivalog Y Y N cytochrome f petA 1421151,2842748,8856106 1117 Cyanobacteriota phylum 948 NCBI Protein Cluster (PRK) apocytochrome f cytochrome f Cytochrome f, with cytochrome b6, subunit IV, and the Rieske protein, makes up the large subunit of the cytochrome b6-f complex; cytochrome b6-f mediates electron transfer between photosystem II and photosystem I NF002740.0 PRK02724 PRK02724.1 135 135 117 equivalog Y Y N 30S ribosomal protein PSRP-3 1117 Cyanobacteriota phylum 554 NCBI Protein Cluster (PRK) hypothetical protein 30S ribosomal protein PSRP-3 NF002741.0 PRK02726 PRK02726.1 179 179 200 equivalog Y Y N molybdenum cofactor guanylyltransferase 2.7.7.77 1117 Cyanobacteriota phylum 775 NCBI Protein Cluster (PRK) molybdopterin-guanine dinucleotide biosynthesis protein A molybdenum cofactor guanylyltransferase NF002743.0 PRK02733 PRK02733.1 69 69 44 equivalog Y Y N photosystem I reaction center subunit IX psaJ 1117 Cyanobacteriota phylum 354 NCBI Protein Cluster (PRK) photosystem I reaction center subunit IX photosystem I reaction center subunit IX Enables the organization of the psaE and psaF subunits in the phosystem I complex NF002744.0 PRK02746 PRK02746.1 425 425 346 equivalog Y Y N 4-hydroxythreonine-4-phosphate dehydrogenase PdxA pdxA 1117 Cyanobacteriota phylum 1149 NCBI Protein Cluster (PRK) 4-hydroxythreonine-4-phosphate dehydrogenase 4-hydroxythreonine-4-phosphate dehydrogenase PdxA Catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate) NF002758.0 PRK02812 PRK02812.1 518 518 330 equivalog Y Y N ribose-phosphate pyrophosphokinase 1117 Cyanobacteriota phylum 873 NCBI Protein Cluster (PRK) ribose-phosphate pyrophosphokinase ribose-phosphate pyrophosphokinase Catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP NF003373.0 PRK04447 PRK04447.1-6 459 459 367 equivalog Y N N hypothetical protein 1117 Cyanobacteriota phylum 850 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004610.0 PRK05940 PRK05940.1 568 568 467 equivalog Y Y N anthranilate synthase component I 4.1.3.27 1117 Cyanobacteriota phylum 496 NCBI Protein Cluster (PRK) anthranilate synthase component I-like protein anthranilate synthase component I NF004611.0 PRK05942 PRK05942.1 628 628 394 equivalog Y Y N aspartate aminotransferase 1117 Cyanobacteriota phylum 785 NCBI Protein Cluster (PRK) aspartate aminotransferase aspartate aminotransferase Catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate NF004614.0 PRK05948 PRK05948.1 251 251 242 equivalog Y Y N precorrin-2 C(20)-methyltransferase 2.1.1.130 1117 Cyanobacteriota phylum 255 NCBI Protein Cluster (PRK) precorrin-2 methyltransferase precorrin-2 C(20)-methyltransferase Catalyzes the formation of precorrin-3 from precorrin-2 NF004615.0 PRK05949 PRK05949.1 530 530 327 subfamily Y N N RNA polymerase sigma factor 1117 Cyanobacteriota phylum 755 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF004618.0 PRK05952 PRK05952.1 455 455 384 equivalog Y Y N beta-ketoacyl-ACP synthase 2.3.1.179 1117 Cyanobacteriota phylum 789 NCBI Protein Cluster (PRK) 3-oxoacyl-(acyl carrier protein) synthase II beta-ketoacyl-ACP synthase NF004619.0 PRK05953 PRK05953.1 278 278 208 equivalog Y Y N precorrin-8X methylmutase 5.4.99.61 1117 Cyanobacteriota phylum 516 NCBI Protein Cluster (PRK) precorrin-8X methylmutase precorrin-8X methylmutase Catalyzes the interconversion of precorrin-8X and hydrogenobyrinate NF004620.0 PRK05954 PRK05954.1 264 264 205 equivalog Y N N precorrin-8X methylmutase 1117 Cyanobacteriota phylum 240 NCBI Protein Cluster (PRK) precorrin-8X methylmutase precorrin-8X methylmutase NF004744.0 PRK06076 PRK06076.1-5 542 542 372 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoH nuoH 1.6.5.9 1117 Cyanobacteriota phylum 814 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit H NADH-quinone oxidoreductase subunit NuoH NF005060.0 PRK06473 PRK06473.1 747 747 500 equivalog Y Y N NADH-quinone oxidoreductase subunit M 1117 Cyanobacteriota phylum 809 NCBI Protein Cluster (PRK) NAD(P)H-quinone oxidoreductase subunit D4 NADH-quinone oxidoreductase subunit M NF005163.0 PRK06638 PRK06638.1-3 174 174 203 equivalog Y Y N NADH-quinone oxidoreductase subunit J 1.6.5.9 1117 Cyanobacteriota phylum 839 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit J NADH-quinone oxidoreductase subunit J NF005606.0 PRK07352 PRK07352.1 137 137 175 equivalog Y Y N F0F1 ATP synthase subunit B 7.1.2.2 1117 Cyanobacteriota phylum 883 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit B F0F1 ATP synthase subunit B Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B is part of the membrane proton channel NF005607.0 PRK07353 PRK07353.1 131 131 155 equivalog Y Y N F0F1 ATP synthase subunit B' 7.1.2.2 1117 Cyanobacteriota phylum 757 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit B' F0F1 ATP synthase subunit B' Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B' is part of the membrane proton channel. NF005608.0 PRK07354 PRK07354.1 128 128 81 equivalog Y N N F0F1 ATP synthase subunit C 1117 Cyanobacteriota phylum 258 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit C F0F1 ATP synthase subunit C NF005612.0 PRK07364 PRK07364.1 487 487 415 equivalog Y Y N FAD-dependent hydroxylase 1117 Cyanobacteriota phylum 865 NCBI Protein Cluster (PRK) 2-octaprenyl-6-methoxyphenyl hydroxylase FAD-dependent hydroxylase NF005614.0 PRK07369 PRK07369.1 456 456 419 equivalog Y Y N dihydroorotase 3.5.2.3 1117 Cyanobacteriota phylum 906 NCBI Protein Cluster (PRK) dihydroorotase dihydroorotase NF005615.0 PRK07370 PRK07370.1 391 391 259 equivalog Y Y N enoyl-ACP reductase FabI fabI 1.3.1.9 1117 Cyanobacteriota phylum 840 NCBI Protein Cluster (PRK) enoyl-(acyl carrier protein) reductase enoyl-ACP reductase FabI NF005616.0 PRK07373 PRK07373.1 646 646 449 equivalog Y N N DNA polymerase III subunit alpha 1117 Cyanobacteriota phylum 630 NCBI Protein Cluster (PRK) DNA polymerase III subunit alpha DNA polymerase III subunit alpha NF005617.0 PRK07374 PRK07374.1 1653 1653 1170 equivalog Y Y N DNA polymerase III subunit alpha 1117 Cyanobacteriota phylum 391 NCBI Protein Cluster (PRK) DNA polymerase III subunit alpha DNA polymerase III subunit alpha Catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase NF005626.0 PRK07376 PRK07376.1 963 963 675 equivalog Y Y N NAD(P)H-quinone oxidoreductase subunit 5 1117 Cyanobacteriota phylum 1092 NCBI Protein Cluster (PRK) NAD(P)H-quinone oxidoreductase subunit F NAD(P)H-quinone oxidoreductase subunit 5 NF005633.0 PRK07390 PRK07390.1 676 676 613 subfamily Y Y N NAD(P)H-quinone oxidoreductase subunit F GO:0016491 1117 Cyanobacteriota phylum 1916 NCBI Protein Cluster (PRK) NAD(P)H-quinone oxidoreductase subunit F NAD(P)H-quinone oxidoreductase subunit F NF005635.0 PRK07394 PRK07394.1 287 287 348 equivalog Y N N hypothetical protein 1117 Cyanobacteriota phylum 1045 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005636.0 PRK07395 PRK07395.1 723 723 560 subfamily Y Y N L-aspartate oxidase 1117 Cyanobacteriota phylum 868 NCBI Protein Cluster (PRK) L-aspartate oxidase L-aspartate oxidase Catalyzes the formation of oxaloacetate from L-aspartate NF005638.0 PRK07399 PRK07399.1 230 230 317 subfamily Y N N DNA polymerase III subunit delta' 1117 Cyanobacteriota phylum 1189 NCBI Protein Cluster (PRK) DNA polymerase III subunit delta' DNA polymerase III subunit delta' NF005639.0 PRK07400 PRK07400.1 460 460 318 equivalog Y N N 30S ribosomal protein S1 1117 Cyanobacteriota phylum 884 NCBI Protein Cluster (PRK) 30S ribosomal protein S1 30S ribosomal protein S1 NF005640.0 PRK07402 PRK07402.1 219 219 200 equivalog Y Y N precorrin-6Y C5,15-methyltransferase subunit CbiT cbiT 1117 Cyanobacteriota phylum 711 NCBI Protein Cluster (PRK) precorrin-6B methylase precorrin-6Y C5,15-methyltransferase subunit CbiT Catalyzes the formation of precorrin-8x from precorrin-6y NF005641.0 PRK07403 PRK07403.1 616 616 337 equivalog Y Y N type I glyceraldehyde-3-phosphate dehydrogenase 1.2.1.- 11327708 1117 Cyanobacteriota phylum 696 NCBI Protein Cluster (PRK) glyceraldehyde-3-phosphate dehydrogenase type I glyceraldehyde-3-phosphate dehydrogenase NF005642.0 PRK07405 PRK07405.1 524 524 318 subfamily Y N N RNA polymerase sigma factor SigD 1117 Cyanobacteriota phylum 651 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigD RNA polymerase sigma factor SigD NF005643.0 PRK07406 PRK07406.1 500 500 397 equivalog Y Y N RNA polymerase sigma factor RpoD rpoD 1117 Cyanobacteriota phylum 798 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RpoD RNA polymerase sigma factor RpoD Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this is the primary sigma factor of bacteria NF005644.0 PRK07408 PRK07408.1 261 261 258 subfamily Y N N RNA polymerase sigma factor SigF 1117 Cyanobacteriota phylum 1110 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigF RNA polymerase sigma factor SigF NF005646.0 PRK07411 PRK07411.1 633 633 390 equivalog Y Y N molybdopterin-synthase adenylyltransferase MoeB moeB 1117 Cyanobacteriota phylum 851 NCBI Protein Cluster (PRK) hypothetical protein molybdopterin-synthase adenylyltransferase MoeB NF005647.0 PRK07413 PRK07413.1 426 426 382 equivalog Y Y N cob(I)yrinic acid a,c-diamide adenosyltransferase 2.5.1.17 1117 Cyanobacteriota phylum 713 NCBI Protein Cluster (PRK) hypothetical protein cob(I)yrinic acid a,c-diamide adenosyltransferase NF005649.0 PRK07415 PRK07415.1 583 583 394 equivalog Y Y N NAD(P)H-quinone oxidoreductase subunit H 1117 Cyanobacteriota phylum 882 NCBI Protein Cluster (PRK) NAD(P)H-quinone oxidoreductase subunit H NAD(P)H-quinone oxidoreductase subunit H NF005650.0 PRK07417 PRK07417.1 290 290 281 equivalog Y Y N prephenate/arogenate dehydrogenase 1117 Cyanobacteriota phylum 1070 NCBI Protein Cluster (PRK) arogenate dehydrogenase prephenate/arogenate dehydrogenase NF005651.0 PRK07418 PRK07418.1 942 942 617 subfamily Y Y N acetolactate synthase large subunit 1117 Cyanobacteriota phylum 1115 NCBI Protein Cluster (PRK) acetolactate synthase 3 catalytic subunit acetolactate synthase large subunit NF005653.0 PRK07424 PRK07424.1 336 336 414 equivalog Y Y N bifunctional sterol desaturase/short chain dehydrogenase 1117 Cyanobacteriota phylum 747 NCBI Protein Cluster (PRK) bifunctional sterol desaturase/short chain dehydrogenase bifunctional sterol desaturase/short chain dehydrogenase NF005669.0 PRK07451 PRK07451.1 122 122 116 equivalog Y Y N translation initiation factor 1117 Cyanobacteriota phylum 635 NCBI Protein Cluster (PRK) translation initiation factor Sui1 translation initiation factor NF005672.0 PRK07454 PRK07454.1 234 234 241 equivalog Y Y N SDR family oxidoreductase 1117 Cyanobacteriota phylum 953 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005673.0 PRK07455 PRK07455.1 232 232 213 equivalog Y Y N bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase 4.1.2.14,4.1.3.16 1117 Cyanobacteriota phylum 725 NCBI Protein Cluster (PRK) keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase NF005674.0 PRK07459 PRK07459.1 161 161 121 equivalog Y Y N single-stranded DNA-binding protein 1117 Cyanobacteriota phylum 769 NCBI Protein Cluster (PRK) single-stranded DNA-binding protein single-stranded DNA-binding protein NF005785.0 PRK07598 PRK07598.1 554 554 415 equivalog Y Y N RNA polymerase sigma factor SigC sigC 1117 Cyanobacteriota phylum 638 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigC RNA polymerase sigma factor SigC Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; the proteins in this cluster is involved expression of genes important stationary phase, nitrogen promoter recognition, and light/dark adaption NF006800.0 PRK09303 PRK09303.1 342 342 383 equivalog Y Y N histidine kinase 1117 Cyanobacteriota phylum 1018 NCBI Protein Cluster (PRK) adaptive-response sensory kinase histidine kinase NF006806.0 PRK09319 PRK09319.1 764 764 561 equivalog Y Y N bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II ribBA 3.5.4.25,4.1.99.12 GO:0003935,GO:0008686 1117 Cyanobacteriota phylum 1084 NCBI Protein Cluster (PRK) bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II/unknown domain fusion protein bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II NF007079.0 PRK09532 PRK09532.1 1525 1525 876 equivalog Y Y N DNA polymerase III subunit alpha 2.7.7.7 10734038,11170467,16219320,9689062 1117 Cyanobacteriota phylum 694 NCBI Protein Cluster (PRK) DNA polymerase III subunit alpha DNA polymerase III subunit alpha Main replicative polymerase NF007125.0 PRK09566 PRK09566.1 594 594 513 equivalog Y Y N ferredoxin--nitrite reductase 1.7.7.1 10542156,8490140 1117 Cyanobacteriota phylum 1023 NCBI Protein Cluster (PRK) ferredoxin-nitrite reductase ferredoxin--nitrite reductase Ferredoxin-dependent assimilatory nitrite reductase NF007143.0 PRK09585 PRK09585.2-2 533 533 382 equivalog Y Y N anhydro-N-acetylmuramic acid kinase 2.7.1.170 1117 Cyanobacteriota phylum 790 NCBI Protein Cluster (PRK) anhydro-N-acetylmuramic acid kinase anhydro-N-acetylmuramic acid kinase NF008170.0 PRK10917 PRK10917.2-4 975 975 826 equivalog Y Y N ATP-dependent DNA helicase RecG recG 3.6.4.12 1117 Cyanobacteriota phylum 1199 NCBI Protein Cluster (PRK) ATP-dependent DNA helicase RecG ATP-dependent DNA helicase RecG NF008697.0 PRK11713 PRK11713.4-1 234 234 250 equivalog Y Y N 16S rRNA (uracil(1498)-N(3))-methyltransferase 2.1.1.193 1117 Cyanobacteriota phylum 963 NCBI Protein Cluster (PRK) 16S ribosomal RNA methyltransferase RsmE 16S rRNA (uracil(1498)-N(3))-methyltransferase NF008824.0 PRK11874 PRK11874.1 39 39 31 equivalog Y Y N cytochrome b6-f complex subunit PetL petL 14526088 1117 Cyanobacteriota phylum 154 NCBI Protein Cluster (PRK) cytochrome b6-f complex subunit PetL cytochrome b6-f complex subunit PetL Cytochrome b6-f complex subunit 6; with PetG, PetM and PetN makes up the small subunit of the cytochrome b6-f complex; cytochrome b6-f mediates electron transfer between photosystem II and photosystem I NF008825.0 PRK11875 PRK11875.1 55 55 31 equivalog Y Y N photosystem II reaction center protein T 16355230 1117 Cyanobacteriota phylum 265 NCBI Protein Cluster (PRK) photosystem II reaction center protein T photosystem II reaction center protein T NF008932.0 PRK12289 PRK12289.1 483 483 363 equivalog Y Y N small ribosomal subunit biogenesis GTPase RsgA rsgA 3.6.1.- 1117 Cyanobacteriota phylum 811 NCBI Protein Cluster (PRK) GTPase RsgA small ribosomal subunit biogenesis GTPase RsgA EngC; RsgA; CpgA; circularly permuted GTPase; ribosome small subunit-dependent GTPase A; has the pattern G4-G1-G3 as opposed to other GTPases; interacts strongly with 30S ribosome which stimulates GTPase activity NF008940.0 PRK12292 PRK12292.2-3 450 450 404 equivalog Y Y N ATP phosphoribosyltransferase regulatory subunit 1117 Cyanobacteriota phylum 833 NCBI Protein Cluster (PRK) ATP phosphoribosyltransferase regulatory subunit ATP phosphoribosyltransferase regulatory subunit NF009035.0 PRK12367 PRK12367.1 266 266 249 equivalog Y N N short chain dehydrogenase 1117 Cyanobacteriota phylum 618 NCBI Protein Cluster (PRK) short chain dehydrogenase short chain dehydrogenase NF009141.0 PRK12494 PRK12494.1 175 175 175 equivalog Y Y N NAD(P)H-quinone oxidoreductase subunit J 1117 Cyanobacteriota phylum 932 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit J NAD(P)H-quinone oxidoreductase subunit J NF009172.0 PRK12519 PRK12519.1 222 222 194 subfamily Y N N RNA polymerase sigma factor 1117 Cyanobacteriota phylum 360 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009203.0 PRK12551 PRK12551.1 359 359 196 equivalog Y N N ATP-dependent Clp protease proteolytic subunit 1117 Cyanobacteriota phylum 185 NCBI Protein Cluster (PRK) ATP-dependent Clp protease proteolytic subunit ATP-dependent Clp protease proteolytic subunit NF009204.0 PRK12552 PRK12552.1 263 263 225 equivalog Y Y N ATP-dependent Clp protease proteolytic subunit 1117 Cyanobacteriota phylum 724 NCBI Protein Cluster (PRK) ATP-dependent Clp protease-like protein ATP-dependent Clp protease proteolytic subunit NF009212.0 PRK12561 PRK12561.1 645 645 531 subfamily Y Y N NAD(P)H-quinone oxidoreductase subunit 4 1117 Cyanobacteriota phylum 2401 NCBI Protein Cluster (PRK) NAD(P)H-quinone oxidoreductase subunit 4 NAD(P)H-quinone oxidoreductase subunit 4 NF009506.0 PRK12864 PRK12864.1 106 106 89 equivalog Y N N YciI-like protein 1117 Cyanobacteriota phylum 788 NCBI Protein Cluster (PRK) YciI-like protein YciI-like protein NF009514.0 PRK12873 PRK12873.1 246 246 297 equivalog Y Y N 4-hydroxybenzoate polyprenyltransferase 2.5.1.39 1117 Cyanobacteriota phylum 1098 NCBI Protein Cluster (PRK) prenyltransferase 4-hydroxybenzoate polyprenyltransferase NF009563.0 PRK13019 PRK13019.1-3 117 117 101 equivalog Y Y N ATP-dependent Clp protease adapter ClpS clpS 1117 Cyanobacteriota phylum 738 NCBI Protein Cluster (PRK) ATP-dependent Clp protease adaptor ATP-dependent Clp protease adapter ClpS NF009650.0 PRK13183 PRK13183.1 70 70 46 equivalog Y Y N photosystem II reaction center protein PsbN psbN 1117 Cyanobacteriota phylum 446 NCBI Protein Cluster (PRK) photosystem II reaction center protein N photosystem II reaction center protein PsbN NF009711.0 PRK13240 PRK13240.1 48 48 40 equivalog Y Y N photosystem II protein Y 15042356,9829828 1117 Cyanobacteriota phylum 465 NCBI Protein Cluster (PRK) photosystem II protein Y photosystem II protein Y NF009718.0 PRK13245 PRK13245.1 489 489 299 equivalog Y Y N heterocyst differentiation master regulator HetR hetR 15520378,17220221 1117 Cyanobacteriota phylum 441 NCBI Protein Cluster (PRK) heterocyst differentiation control protein heterocyst differentiation master regulator HetR Controls heterocyst differentiation; has protease DNA-binding activity NF009720.0 PRK13247 PRK13247.1 263 263 240 equivalog Y Y N 15,16-dihydrobiliverdin:ferredoxin oxidoreductase 1.3.7.2 1117 Cyanobacteriota phylum 469 NCBI Protein Cluster (PRK) dihydrobiliverdin:ferredoxin oxidoreductase 15,16-dihydrobiliverdin:ferredoxin oxidoreductase Catalyzes the reduction of biliverdin IX-alpha to 15,16-dihydrobiliverdin NF009723.0 PRK13250 PRK13250.1 327 327 248 equivalog Y Y N phycoerythrobilin:ferredoxin oxidoreductase 1.3.7.3 1117 Cyanobacteriota phylum 336 NCBI Protein Cluster (PRK) phycoerythrobilin:ferredoxin oxidoreductase phycoerythrobilin:ferredoxin oxidoreductase Catalyzes the reduction of 15,16-dihydrobiliverdin to (3Z)-phycoerythrobilin NF009871.0 PRK13331 PRK13331.1 251 251 253 equivalog Y Y N pantothenate kinase 2.7.1.33 1117 Cyanobacteriota phylum 864 NCBI Protein Cluster (PRK) pantothenate kinase pantothenate kinase NF009933.0 PRK13396 PRK13396.1 486 486 352 subfamily Y Y N 3-deoxy-7-phosphoheptulonate synthase 11847568,14337509,6129240,8157606,9387221 1117 Cyanobacteriota phylum 1028 NCBI Protein Cluster (PRK) 3-deoxy-7-phosphoheptulonate synthase 3-deoxy-7-phosphoheptulonate synthase Catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate; involved in carboxysome formation NF009946.0 PRK13410 PRK13410.1 1019 1019 669 equivalog Y Y N molecular chaperone DnaK dnaK 11157945,12763042,8658133,9609686 1117 Cyanobacteriota phylum 1056 NCBI Protein Cluster (PRK) molecular chaperone DnaK molecular chaperone DnaK Heat shock protein 70; assists in folding of nascent polypeptide chains; refolding of misfolded proteins; utilizes ATPase activity to help fold; co-chaperones are DnaJ and GrpE NF009947.0 PRK13411 PRK13411.1 1002 1002 662 equivalog Y Y N molecular chaperone DnaK dnaK 11157945,12763042,8658133,9609686 1117 Cyanobacteriota phylum 785 NCBI Protein Cluster (PRK) molecular chaperone DnaK molecular chaperone DnaK Heat shock protein 70; assists in folding of nascent polypeptide chains; refolding of misfolded proteins; utilizes ATPase activity to help fold; co-chaperones are DnaJ and GrpE NF010004.0 PRK13477 PRK13477.1 524 524 514 equivalog Y Y N bifunctional pantoate--beta-alanine ligase/(d)CMP kinase 2.7.4.25,6.3.2.1 1117 Cyanobacteriota phylum 1140 NCBI Protein Cluster (PRK) bifunctional pantoate ligase/cytidylate kinase bifunctional pantoate--beta-alanine ligase/(d)CMP kinase Catalyzes the formation of pantothenate from pantoate and beta-alanine and the formation of cytidine diphosphate from cytidine monophosphate NF010236.0 PRK13683 PRK13683.1 90 90 88 equivalog Y N N hypothetical protein 1117 Cyanobacteriota phylum 695 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010237.0 PRK13684 PRK13684.1 326 326 334 equivalog Y Y N photosynthesis system II assembly factor Ycf48 1117 Cyanobacteriota phylum 1019 NCBI Protein Cluster (PRK) Ycf48-like protein photosynthesis system II assembly factor Ycf48 NF010239.1 PRK13686 PRK13686.1 34 34 36 equivalog Y Y N photosystem II reaction center protein Ycf12/Psb30 psb30 GO:0009523,GO:0015979 17935689,17967798,21356599 1117 Cyanobacteriota phylum 425 NCBI Protein Cluster (PRK) hypothetical protein photosystem II reaction center protein Ycf12/Psb30 NF010527.0 PRK13922 PRK13922.6-2 289 289 249 equivalog Y Y N rod shape-determining protein MreC mreC 1117 Cyanobacteriota phylum 910 NCBI Protein Cluster (PRK) rod shape-determining protein MreC rod shape-determining protein MreC NF010537.0 PRK13925 PRK13925.1 252 252 200 equivalog Y Y N ribonuclease HII 3.1.26.4 1117 Cyanobacteriota phylum 943 NCBI Protein Cluster (PRK) ribonuclease HII ribonuclease HII RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids NF010551.0 PRK13945 PRK13945.1 348 348 282 equivalog Y Y N DNA-formamidopyrimidine glycosylase 3.2.2.23 1117 Cyanobacteriota phylum 1092 NCBI Protein Cluster (PRK) formamidopyrimidine-DNA glycosylase DNA-formamidopyrimidine glycosylase Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents; acts as DNA glycosylase that recognizes and removes damaged bases NF010702.0 PRK14102 PRK14102.1 115 115 108 equivalog Y Y N nitrogenase-stabilizing/protective protein NifW nifW 1117 Cyanobacteriota phylum 393 NCBI Protein Cluster (PRK) nitrogenase stabilizing/protective protein nitrogenase-stabilizing/protective protein NifW NF010886.0 PRK14293 PRK14293.1 522 522 374 equivalog Y Y N molecular chaperone DnaJ dnaJ 1117 Cyanobacteriota phylum 872 NCBI Protein Cluster (PRK) chaperone protein DnaJ molecular chaperone DnaJ Chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion NF010940.0 PRK14360 PRK14360.1 602 602 452 equivalog Y Y N bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU glmU 2.3.1.157,2.7.7.23 1117 Cyanobacteriota phylum 1111 NCBI Protein Cluster (PRK) bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU Catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis NF011149.0 PRK14559 PRK14559.1 374 374 642 equivalog Y Y N serine/threonine phosphatase 1117 Cyanobacteriota phylum 790 NCBI Protein Cluster (PRK) putative protein serine/threonine phosphatase serine/threonine phosphatase NF011212.0 PRK14619 PRK14619.1 377 377 309 equivalog Y Y N NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 1.1.1.94 1117 Cyanobacteriota phylum 860 NCBI Protein Cluster (PRK) NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NAD(P)H-dependent glycerol-3-phosphate dehydrogenase Catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate NF011406.0 PRK14831 PRK14831.1 375 375 256 subfamily Y N N undecaprenyl pyrophosphate synthase 1117 Cyanobacteriota phylum 1168 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate synthase undecaprenyl pyrophosphate synthase NF011493.0 PRK14901 PRK14901.1 540 540 447 equivalog Y Y N 16S rRNA (cytosine(967)-C(5))-methyltransferase 2.1.1.176 1117 Cyanobacteriota phylum 1055 NCBI Protein Cluster (PRK) 16S rRNA methyltransferase B 16S rRNA (cytosine(967)-C(5))-methyltransferase NF011510.0 PRK14948 PRK14948.1 593 593 640 equivalog Y Y N DNA polymerase III subunit gamma/tau 2.7.7.7 1117 Cyanobacteriota phylum 987 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunit gamma/tau Catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA NF013542.5 PF01383.26 CpcD 27 27 55 domain Y Y N phycobilisome linker polypeptide GO:0030089 8343609,9990029 1117 Cyanobacteriota phylum 4251 EBI-EMBL CpcD/allophycocyanin linker domain CpcD/allophycocyanin linker domain NF013564.5 PF01405.22 PsbT 22.4 22.4 29 PfamEq Y Y N photosystem II reaction center protein T GO:0009523,GO:0009539,GO:0015979,GO:0016020 8026459 1117 Cyanobacteriota phylum 311 EBI-EMBL Photosystem II reaction centre T protein photosystem II reaction center protein T The exact function of this protein is unknown. It probably consists of a single transmembrane spanning helix. The Swiss:P37256 protein, appears to be (i) a novel photosystem II subunit and (ii) required for maintaining optimal photosystem II activity under adverse growth conditions [1]. [1]. 8026459. The chloroplast ycf8 open reading frame encodes a photosystem II polypeptide which maintains photosynthetic activity under adverse growth conditions. Monod C, Takahashi Y, Goldschmidt-Clermont M, Rochaix JD;. EMBO J 1994;13:2747-2754. (from Pfam) NF014403.5 PF02341.20 RbcX 27 27 111 PfamEq Y Y N chaperonin family protein RbcX GO:0044183,GO:0110102 9171433,9642201 1117 Cyanobacteriota phylum 635 EBI-EMBL RbcX protein chaperonin family protein RbcX The RBCX protein has been identified as having a possible chaperone-like function [1]. The rbcX gene is juxtaposed to and cotranscribed with rbcL and rbcS encoding RuBisCO in Anabaena sp. CA [2]. RbcX has been shown to possess a chaperone-like function assisting correct folding of RuBisCO in E. coli expression studies and is needed for RuBisCO to reach its maximal activity [2]. [1]. 9642201. Evolution of cyanobacteria by exchange of genetic material among phyletically related strains. Rudi K, Skulberg OM, Jakobsen KS;. J Bacteriol 1998;180:3453-3461. [2]. 9171433. Maximum activity of recombinant ribulose 1,5-bisphosphate carboxylase/oxygenase of Anabaena sp. strain CA requires the product of the rbcX gene. Li LA, Tabita FR;. J Bacteriol 1997;179:3793-3796. (from Pfam) NF016374.5 PF04485.17 NblA 25 25 50 domain Y N N Phycobilisome degradation protein nblA 11532155 1117 Cyanobacteriota phylum 933 EBI-EMBL Phycobilisome degradation protein nblA Phycobilisome degradation protein nblA In the cyanobacterium Synechococcus PCC 7942 (Swiss:P35087) , nblA triggers degradation of light-harvesting phycobiliproteins in response to deprivation nutrients including nitrogen, phosphorus and sulphur. The mechanism of nblA function is not known, but it has been hypothesised that nblA may act by disrupting phycobilisome structure, activating a protease or tagging phycobiliproteins for proteolysis. Members of this family have also been identified in the chloroplasts of some red algae. [1]. 11532155. Convergence of two global transcriptional regulators on nitrogen induction of the stress-acclimation gene nblA in the cyanobacterium Synechococcus sp. PCC 7942. Luque I, Zabulon G, Contreras A, Houmard J;. Mol Microbiol 2001;41:937-947. (from Pfam) NF016712.5 PF04839.18 PSRP-3_Ycf65 25 25 48 PfamEq Y N N Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) GO:0003735,GO:0005840,GO:0006412 10874039 1117 Cyanobacteriota phylum 554 EBI-EMBL Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) This small acidic protein is found in 30S ribosomal subunit of cyanobacteria and plant plastids. In plants it has been named plastid-specific ribosomal protein 3 (PSRP-3), and in cyanobacteria it is named Ycf65. Plastid-specific ribosomal proteins may mediate the effects of nuclear factors on plastid translation. The acidic PSRPs are thought to contribute to protein-protein interactions in the 30S subunit, and are not thought to bind RNA [1]. [1]. 10874039. The plastid ribosomal proteins. Identification of all the proteins in the 30 S subunit of an organelle ribosome (chloroplast). Yamaguchi K, von Knoblauch K, Subramanian AR;. J Biol Chem 2000;275:28455-28465. (from Pfam) NF017258.5 PF05421.16 DUF751 27 27 60 PfamAutoEq Y Y N DUF751 domain-containing protein 1117 Cyanobacteriota phylum 653 EBI-EMBL Protein of unknown function (DUF751) DUF751 family protein This family contains several plant, cyanobacterial and algal proteins of unknown function. The family is exclusively found in phototrophic organisms and may therefore play a role in photosynthesis (personal obs:Moxon SJ). (from Pfam) NF017753.5 PF05969.16 PSII_Ycf12 24 24 33 PfamEq Y Y N photosystem II reaction center protein Ycf12/Psb30 psb30 GO:0009523,GO:0015979,GO:0016020 17935689,17967798 1117 Cyanobacteriota phylum 435 EBI-EMBL Photosystem II complex subunit Ycf12 photosystem II reaction center protein Ycf12/Psb30 Ycf12 has been identified as a core subunit in the photosystem II (PSII) complex [1-2]. PsbZ has been shown to be required for the association of PsbK and Ycf12 with PSII [2]. [1]. 17935689. Ycf12 is a core subunit in the photosystem II complex. Kashino Y, Takahashi T, Inoue-Kashino N, Ban A, Ikeda Y, Satoh K, Sugiura M;. Biochim Biophys Acta. 2007;1767:1269-1275. [2]. 17967798. Absence of the PsbZ subunit prevents association of PsbK and Ycf12 with the PSII complex in the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. Iwai M, Suzuki T, Dohmae N, Inoue Y, Ikeuchi M;. Plant Cell Physiol. 2007;48:1758-1763. (from Pfam) NF018223.5 PF06485.16 Tab2-like_N 25 25 103 subfamily Y Y N Tab2/Atab2 family RNA-binding protein GO:0003723 14633996,17139246,25725436 1117 Cyanobacteriota phylum 1781 EBI-EMBL RNA-binding protein Tab2/Atab2 N terminal DUF1092 family protein This is the N-terminal domain of proteins from photosynthetic organisms including plants and cyanobacteria, such as Tab2 proteins. Tab2 was first identified in Chlamydomonas reinhardtii as a RNA binding protein required for translation of the chloroplast PsaB photosystem I subunit [1]. Later, the Tab2 homologue (ATAB2) from Arabidopsis was found involved in the signalling pathway of light-controlled synthesis of photosystem proteins during early plant development [2], presumably functioning as an activator of translation with targets at PSI and PSII [3]. [1]. 14633996. Tab2 is a novel conserved RNA binding protein required for translation of the chloroplast psaB mRNA. Dauvillee D, Stampacchia O, Girard-Bascou J, Rochaix JD;. EMBO J. 2003;22:6378-6388. [2]. 17139246. ATAB2 is a novel factor in the signalling pathway of light-controlled synthesis of photosystem proteins. Barneche F, Winter V, Crevecoeur M, Rochaix JD;. EMBO J. 2006;25:5907-5918. [3]. 25725436. Large-scale genetic analysis of chloroplast biogenesis in maize. Belcher S, Williams-Carrier R, Stiffler N, Barkan A;. Biochim Biophys Acta. 2015;1847:1004-1016. (from Pfam) NF018505.5 PF06799.16 CGLD27-like 25 25 143 PfamAutoEq Y Y N CGLD27 family protein 23043051 1117 Cyanobacteriota phylum 922 EBI-EMBL Conserved in the green lineage and diatoms 27 CGLD27 family protein This family consist of proteins found in plants and algal chloroplasts, and in cyanobacteria. It includes CGLD27 (Conserved in the green lineage and diatoms 27), which has been described as one out of 14 Fe-responsive orthologues in Chlamydomonas and Arabidopsis, indicating that it is an important component of the iron deficiency response of the plant lineage [1]. [1]. 23043051. Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage. Urzica EI, Casero D, Yamasaki H, Hsieh SI, Adler LN, Karpowicz SJ, Blaby-Haas CE, Clarke SG, Loo JA, Pellegrini M, Merchant SS;. Plant Cell. 2012;24:3921-3948. (from Pfam) NF018650.5 PF06967.16 Mo-nitro_C 27 27 83 domain Y Y N Mo-dependent nitrogenase C-terminal domain-containing protein 7568132 1117 Cyanobacteriota phylum 2836 EBI-EMBL Mo-dependent nitrogenase C-terminus Mo-dependent nitrogenase C-terminus This family represents the C-terminus (approximately 80 residues) of a number of bacterial Mo-dependent nitrogenases. These are involved in nitrogen fixation in cyanobacteria [1]. Note that many family members are hypothetical proteins. [1]. 7568132. A second nitrogenase in vegetative cells of a heterocyst-forming cyanobacterium. Thiel T, Lyons EM, Erker JC, Ernst A;. Proc Natl Acad Sci U S A 1995;92:9358-9362. (from Pfam) NF018834.5 PF07176.16 DUF1400 23.4 23.4 127 domain Y Y N alpha/beta hydrolase 1117 Cyanobacteriota phylum 4737 EBI-EMBL Alpha/beta hydrolase of unknown function (DUF1400) alpha/beta hydrolase This family contains a number of hypothetical proteins of unknown function that seem to be specific to cyanobacteria. Members of this family have an alpha/beta hydrolase fold. (from Pfam) NF020424.5 PF08848.16 DUF1818 25 25 113 PfamAutoEq Y Y N DUF1818 family protein 1117 Cyanobacteriota phylum 1008 EBI-EMBL Domain of unknown function (DUF1818) DUF1818 family protein This presumed domain is found in a small family of cyanobacterial protein. These proteins are functionally uncharacterised. (from Pfam) NF020428.5 PF08853.16 DUF1823 25 25 113 PfamAutoEq Y Y N DUF1823 family protein 1117 Cyanobacteriota phylum 954 EBI-EMBL Domain of unknown function (DUF1823) DUF1823 family protein This presumed domain is functionally uncharacterised. (from Pfam) NF020429.5 PF08854.15 DUF1824 25 25 125 PfamAutoEq Y Y N DUF1824 family protein 1117 Cyanobacteriota phylum 867 EBI-EMBL Domain of unknown function (DUF1824) DUF1824 family protein This uncharacterised family of proteins are principally found in cyanobacteria. (from Pfam) NF020713.5 PF09150.15 Carot_N 25 25 151 domain Y Y N orange carotenoid protein N-terminal domain-containing protein GO:0016037,GO:0030089,GO:0031404 12517340 1117 Cyanobacteriota phylum 2219 EBI-EMBL Orange carotenoid protein, N-terminal Orange carotenoid protein, N-terminal Members of this family adopt an alpha-helical structure consisting of two four-helix bundles. They are predominantly found in prokaryotic orange carotenoid protein, and carotenoid binding proteins [1]. [1]. 12517340. The crystal structure of a cyanobacterial water-soluble carotenoid binding protein. Kerfeld CA, Sawaya MR, Brahmandam V, Cascio D, Ho KK, Trevithick-Sutton CC, Krogmann DW, Yeates TO;. Structure. 2003;11:55-65. (from Pfam) NF020910.5 PF09353.15 DUF1995 26 26 197 PfamAutoEq Y Y N DUF1995 family protein 1117 Cyanobacteriota phylum 1069 EBI-EMBL Domain of unknown function (DUF1995) DUF1995 family protein This family of proteins are functionally uncharacterised. (from Pfam) NF020924.5 PF09367.15 CpeS 23.3 23.3 170 domain Y Y N phycobiliprotein lyase GO:0017009 1117 Cyanobacteriota phylum 3381 EBI-EMBL CpeS-like protein phycobiliprotein lyase This family, that includes CpeS proteins, is functionally uncharacterised. (from Pfam) NF021714.5 PF10216.14 ChpXY 25 25 352 subfamily Y Y N CO2 hydration protein 11985719 1117 Cyanobacteriota phylum 1911 EBI-EMBL CO2 hydration protein (ChpXY) CO2 hydration protein This small family of proteins includes paralogues ChpX and ChpY in Synechococcus sp. PCC7942 and other cyanobacteria, associated with distinct NAD(P)H dehydrogenase complexes. These proteins collectively enable light-dependent CO2 hydration and CO2 uptake; loss of both blocks growth at low CO2 concentrations. (from Pfam) NF022129.5 PF10664.14 NdhM 27 27 107 PfamEq Y Y N NAD(P)H-quinone oxidoreductase subunit M ndhM GO:0016655 12460669,15548534,15608332,15910282 1117 Cyanobacteriota phylum 756 EBI-EMBL Cyanobacterial and plastid NDH-1 subunit M NAD(P)H-quinone oxidoreductase subunit M The proton-pumping NADH:ubiquinone oxidoreductase catalyses the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. It is the largest, most complex and least understood of the respiratory chain enzymes and is referred to as Complex I. The subunit composition of the enzyme varies between groups of organisms. Complex I originating from mammalian mitochondria contains 45 different proteins, whereas in bacteria, the corresponding complex NDH-1 consists of 14 different polypeptides. Homologues of these 14 proteins are found among subunits of the mitochondrial complex I, and therefore bacterial NDH-1 might be considered a model proton-pumping NADH dehydrogenase with a minimal set of subunits. Escherichia coli NDH-1 readily disintegrates into 3 sub-complexes: a water-soluble NADH dehydrogenase fragment (NuoE, -F, and -G),the connecting fragment (NuoB, -C, -D, and -I), and the membrane fragment (NuoA, -H, -J, -K, -L, -M, -N). In cyanobacteria and their descendants, the chloroplasts of green plants, the subunit composition of NDH-1 remains obscure. The genes for eleven subunits NdhA-NdhK, homologous to the NuoA-NuoD and NuoH-NuoN of the E. coli complex, have been found in the genome of Synechocystis sp. PCC 6803 which has a family of 6 ndhD genes and a family of 3 ndhF genes. Two reported multisubunit complexes, NDH-1L and NDH-1M, represent distinct NDH-1 complexes in the thylakoid membrane of Synechocystis 6803 -cyanobacterium. NDH-1L was shown to be essential for photoheterotrophic cell growth, whereas expression of NDH-1M was a prerequisite for CO2 uptake and played an important role . TRUNCATED at 1650 bytes (from Pfam) NF022178.5 PF10718.14 Ycf34 25 25 78 PfamEq Y Y N Ycf34 family protein 1117 Cyanobacteriota phylum 710 EBI-EMBL Hypothetical chloroplast protein Ycf34 Ycf34 family protein This family is of proteins annotated as hypothetical chloroplast protein YCF34. The function is not known. (from Pfam) NF022186.5 PF10726.14 DUF2518 25 25 145 PfamAutoEq Y Y N DUF2518 family protein 1117 Cyanobacteriota phylum 968 EBI-EMBL Protein of function (DUF2518) DUF2518 family protein This family is conserved in Cyanobacteria. Several members are annotated as the protein Ycf51. The function is not known. (from Pfam) NF022202.5 PF10742.14 DUF2555 25 25 55 PfamAutoEq Y Y N DUF2555 domain-containing protein 1117 Cyanobacteriota phylum 601 EBI-EMBL Protein of unknown function (DUF2555) Protein of unknown function (DUF2555) This family is conserved in Cyanobacteria. The function is not known. (from Pfam) NF022249.5 PF10792.14 DUF2605 25 25 96 PfamAutoEq Y Y N DUF2605 family protein 1117 Cyanobacteriota phylum 772 EBI-EMBL Protein of unknown function (DUF2605) DUF2605 family protein This family is conserved in Cyanobacteria. The function is not known. (from Pfam) NF022303.5 PF10847.13 DUF2656 28 28 141 PfamAutoEq Y Y N DUF2656 family protein 1117 Cyanobacteriota phylum 263 EBI-EMBL Protein of unknown function (DUF2656) DUF2656 family protein This bacterial family of proteins has no known function. (from Pfam) NF022613.5 PF11165.13 DUF2949 24.2 24.2 56 domain Y Y N DUF2949 domain-containing protein 1117 Cyanobacteriota phylum 1444 EBI-EMBL Protein of unknown function (DUF2949) Protein of unknown function (DUF2949) This family of proteins with unknown function appear to be restricted to Cyanobacteria. (from Pfam) NF022656.5 PF11210.13 DUF2996 27 27 120 PfamAutoEq Y Y N DUF2996 domain-containing protein 1117 Cyanobacteriota phylum 989 EBI-EMBL Protein of unknown function (DUF2996) Protein of unknown function (DUF2996) This family of proteins has no known function. (from Pfam) NF022708.5 PF11264.13 ThylakoidFormat 27 27 216 PfamEq Y Y N photosystem II biogenesis protein Psp29 GO:0010207,GO:0015979 15516501,16582010 1117 Cyanobacteriota phylum 980 EBI-EMBL Thylakoid formation protein photosystem II biogenesis protein Psp29 THF1 is localised to the outer plastid membrane and the stroma. THF1 has a role in sugar signalling [1]. THF1 is also thought to have a role in chloroplast and leaf development. THF1 has been shown to play a crucial role in vesicle-mediated thylakoid membrane biogenesis [2]. [1]. 16582010. The plastid protein THYLAKOID FORMATION1 and the plasma membrane G-protein GPA1 interact in a novel sugar-signaling mechanism in Arabidopsis. Huang J, Taylor JP, Chen JG, Uhrig JF, Schnell DJ, Nakagawa T, Korth KL, Jones AM;. Plant Cell. 2006;18:1226-1238. [2]. 15516501. Deletion of the chloroplast-localized Thylakoid formation1 gene product in Arabidopsis leads to deficient thylakoid formation and variegated leaves. Wang Q, Sullivan RW, Kight A, Henry RL, Huang J, Jones AM, Korth KL;. Plant Physiol. 2004;136:3594-3604. (from Pfam) NF022711.5 PF11267.13 DUF3067 25 25 98 PfamAutoEq Y Y N DUF3067 family protein 22592539 1117 Cyanobacteriota phylum 798 EBI-EMBL Domain of unknown function (DUF3067) DUF3067 family protein This family of proteins found in plants and cyanobacteria has no known function. The structure of this domain has been solved by NMR for the alr2454 protein [1]. The structure was determined to be a novel fold composed of four alpha helices and a sheet of three anti-parallel beta-strands. [1]. 22592539. Solution NMR structure of Alr2454 from Nostoc sp. PCC 7120, the first structural representative of Pfam domain family PF11267. Aramini JM, Petrey D, Lee DY, Janjua H, Xiao R, Acton TB, Everett JK, Montelione GT;. J Struct Funct Genomics. 2012;13:171-176. (from Pfam) NF022729.5 PF11285.13 DUF3086 24 24 277 PfamAutoEq Y Y N DUF3086 domain-containing protein 1117 Cyanobacteriota phylum 1100 EBI-EMBL Protein of unknown function (DUF3086) Protein of unknown function (DUF3086) This family of proteins with unknown function appears to be restricted to Cyanobacteria. (from Pfam) NF022762.5 PF11318.13 DUF3120 28.5 28.5 199 PfamAutoEq Y Y N DUF3120 domain-containing protein 1117 Cyanobacteriota phylum 1066 EBI-EMBL Protein of unknown function (DUF3120) Protein of unknown function (DUF3120) This family of proteins with unknown function appears to be restricted to Cyanobacteria. (from Pfam) NF022764.5 PF11320.13 DUF3122 25 25 134 domain Y Y N DUF3122 domain-containing protein 1117 Cyanobacteriota phylum 1099 EBI-EMBL Protein of unknown function (DUF3122) Protein of unknown function (DUF3122) This family of proteins with unknown function appear to be restricted to Cyanobacteria. (from Pfam) NF022776.5 PF11332.13 DUF3134 25 25 70 domain Y Y N DUF3134 family protein 1117 Cyanobacteriota phylum 914 EBI-EMBL Protein of unknown function (DUF3134) DUF3134 family protein This family of proteins with unknown function appears to be restricted to Cyanobacteria. (from Pfam) NF022785.5 PF11341.13 DUF3143 25 25 65 PfamAutoEq Y Y N DUF3143 domain-containing protein 1117 Cyanobacteriota phylum 756 EBI-EMBL Protein of unknown function (DUF3143) Protein of unknown function (DUF3143) This family of proteins has no known function. (from Pfam) NF022791.5 PF11347.13 CRR42-like 25 25 62 PfamAutoEq Y Y N NAD(P)H dehydrogenase assembly family protein GO:0010258 22274627 1117 Cyanobacteriota phylum 842 EBI-EMBL Protein CHLORORESPIRATORY REDUCTION 42-like NAD(P)H dehydrogenase assembly family protein This family includes includes Protein CHLORORESPIRATORY REDUCTION 42 (CRR42) from Arabidopsis thaliana, which is required for both formation and activity of the chloroplast NAD(P)H dehydrogenase (NDH) complex of the photosynthetic electron transport chain [1]. CRR42 functions in assembly or stabilization of the NDH complex and it is likely involved, together with CRR1 and CRR6 in the incorporation of NdhJ, NdhM, NdhK and NdhI into the NDH subcomplex A assembly intermediate (NAI500) to produce the complex NAI400 [1]. This family also includes uncharacterised proteins from cyanobacteria. [1]. 22274627. Multistep assembly of chloroplast NADH dehydrogenase-like subcomplex A requires several nucleus-encoded proteins, including CRR41 and CRR42, in Arabidopsis. Peng L, Fukao Y, Fujiwara M, Shikanai T;. Plant Cell. 2012;24:202-214. (from Pfam) NF022796.5 PF11352.13 DUF3155 22.1 22.1 88 PfamAutoEq Y Y N DUF3155 domain-containing protein 1117 Cyanobacteriota phylum 541 EBI-EMBL Protein of unknown function (DUF3155) Protein of unknown function (DUF3155) This family of proteins with unknown function appears to be restricted to Cyanobacteria. (from Pfam) NF022813.5 PF11371.13 DUF3172 25 25 139 PfamAutoEq Y Y N DUF3172 domain-containing protein 1117 Cyanobacteriota phylum 852 EBI-EMBL Protein of unknown function (DUF3172) Protein of unknown function (DUF3172) This family of proteins has no known function. (from Pfam) NF023054.5 PF11623.13 NdhS 27 27 52 PfamAutoEq Y Y N NAD(P)H dehydrogenase subunit NdhS GO:0009767 21035426,21505067,21785130,21880717,24225949,25630976 1117 Cyanobacteriota phylum 626 EBI-EMBL NAD(P)H dehydrogenase subunit S NAD(P)H dehydrogenase subunit NdhS This family is found in Bacteria and Streptophyta includes members such as NdhS (NAD(P)H-quinone oxidoreductase subunit S). NdhS, also known as CRR31 (chlororespiratory reduction 31), is a subunit of the chloroplast NADH dehydrogenase-like (NDH) complex [1]. It is also a subunit of the cyanobacterial NDH-1 complex [2] [3]. NAD(P)H-oxidizing subunits have not been found in chloroplasts or cyanobacteria, where ferredoxin is probably the electron donor. NdhS contributes to the formation of a ferredoxin binding site of NDH [1] and is necessary for high affinity binding of ferredoxin [4]. The cyanobacterial NDH-1 complex, also known as NADPH:plastoquinone oxidoreductase or type I NAD(P)H dehydrogenase, is involved in plastoquinone reduction and cyclic electron transfer (CET) around photosystem I. The chloroplast NDH is more similar to cyanobacterial NDH-1, which is believed to be the origin of chloroplast NDH, than to mitochondrial NADH dehydrogenase present in the same species [5] [6]. The NDH complexes of chloroplasts, however, contain many subunits that are absent from cyanobacterial NDH-1 complexes. [1]. 21505067. An Src homology 3 domain-like fold protein forms a ferredoxin binding site for the chloroplast NADH dehydrogenase-like complex in Arabidopsis. Yamamoto H, Peng L, Fukao Y, Shikanai T;. Plant Cell. 2011;23:1480-1493. [2]. 21880717. Identification of novel Ssl0352 protein (NdhS), essential for efficient operation of cyclic electron transport around photosystem I, in NADPH:plastoquinone oxidoreductase (NDH-1) complexes of Synechocystis sp. PCC 6803. Battchikova N, Wei L, Du L, Bersanini L, Aro EM, Ma W;. J Biol Chem.. TRUNCATED at 1650 bytes (from Pfam) NF023117.5 PF11688.13 DUF3285 25 25 44 PfamAutoEq Y Y N DUF3285 domain-containing protein 1117 Cyanobacteriota phylum 679 EBI-EMBL Protein of unknown function (DUF3285) Protein of unknown function (DUF3285) This family of proteins with unknown function appears to be restricted to Cyanobacteria. (from Pfam) NF023119.5 PF11691.13 DUF3288 25 25 89 PfamAutoEq Y Y N DUF3288 family protein 1117 Cyanobacteriota phylum 882 EBI-EMBL Protein of unknown function (DUF3288) DUF3288 family protein This family of proteins with unknown function appears to be restricted to Cyanobacteria. (from Pfam) NF023336.5 PF11909.13 NdhN 25 25 153 PfamEq Y Y N NAD(P)H-quinone oxidoreductase subunit N ndhN GO:0016020,GO:0016655 12460669,15548534 1117 Cyanobacteriota phylum 799 EBI-EMBL NADH-quinone oxidoreductase cyanobacterial subunit N NAD(P)H-quinone oxidoreductase subunit N The proton-pumping NADH:ubiquinone oxidoreductase catalyzes the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. It is the largest, most complex and least understood of the respiratory chain enzymes and is referred to as Complex I. The subunit composition of the enzyme varies between groups of organisms. Complex I originating from mammalian mitochondria contains 45 different proteins, whereas in bacteria, the corresponding complex NDH-1 consists of 14 different polypeptides. Homologues of these 14 proteins are found among subunits of the mitochondrial complex I, and therefore bacterial NDH-1 might be considered a model proton-pumping NADH dehydrogenase with a minimal set of subunits. Escherichia coli NDH-1 readily disintegrates into 3 subcomplexes: a water-soluble NADH dehydrogenase fragment (NuoE, -F, and -G),the connecting fragment (NuoB, -C, -D, and -I), and the membrane fragment (NuoA, -H, -J, -K, -L, -M, -N). In cyanobacteria and their descendants, the chloroplasts of green plants, the subunit composition of NDH-1 remains obscure. The genes for eleven subunits NdhA-NdhK, homologous to the NuoA-NuoD and NuoH-NuoN of the E. coli complex, have been found in the genome of Synechocystis sp. PCC 6803 which has a family of 6 ndhD genes and a family of 3 ndhF genes. Two reported multisubunit complexes, NDH-1L and NDH-1M, represent distinct NDH-1 complexes in the thylakoid membrane of Synechocystis 6803 -cyanobacterium. NDH-1L was shown to be essential for photoheterotrophic cell growth, whereas expression of NDH-1M was a prerequisite for CO2 uptake and played an important role in. TRUNCATED at 1650 bytes (from Pfam) NF023337.5 PF11910.13 NdhO 25 25 66 PfamEq Y Y N NAD(P)H-quinone oxidoreductase subunit O ndhO GO:0005886,GO:0016655 12460669,15548534,15608332 1117 Cyanobacteriota phylum 725 EBI-EMBL Cyanobacterial and plant NDH-1 subunit O NAD(P)H-quinone oxidoreductase subunit O The proton-pumping NADH:ubiquinone oxidoreductase catalyzes the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. It is the largest, most complex and least understood of the respiratory chain enzymes and is referred to as Complex I. The subunit composition of the enzyme varies between groups of organisms. Complex I originating from mammalian mitochondria contains 45 different proteins, whereas in bacteria, the corresponding complex NDH-1 consists of 14 different polypeptides. Homologues of these 14 proteins are found among subunits of the mitochondrial complex I, and therefore bacterial NDH-1 might be considered a model proton-pumping NADH dehydrogenase with a minimal set of subunits. Escherichia coli NDH-1 readily disintegrates into 3 subcomplexes: a water-soluble NADH dehydrogenase fragment (NuoE, -F, and -G),the connecting fragment (NuoB, -C, -D, and -I), and the membrane fragment (NuoA, -H, -J, -K, -L, -M, -N). In cyanobacteria and their descendants, the chloroplasts of green plants, the subunit composition of NDH-1 remains obscure. The genes for eleven subunits NdhA-NdhK, homologous to the NuoA-NuoD and NuoH-NuoN of the E. coli complex, have been found in the genome of Synechocystis sp. PCC 6803 which has a family of 6 ndhD genes and a family of 3 ndhF genes. Two reported multisubunit complexes, NDH-1L and NDH-1M, represent distinct NDH-1 complexes in the thylakoid membrane of Synechocystis 6803 -cyanobacterium. NDH-1L was shown to be essential for photoheterotrophic cell growth, whereas expression of NDH-1M was a prerequisite for CO2 uptake and played an important role i. TRUNCATED at 1650 bytes (from Pfam) NF023473.5 PF12049.13 DUF3531 25 25 143 PfamAutoEq Y Y N DUF3531 family protein 1117 Cyanobacteriota phylum 811 EBI-EMBL Protein of unknown function (DUF3531) DUF3531 family protein This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 149 to 199 amino acids in length. (from Pfam) NF023481.5 PF12058.13 PipX 25 25 86 PfamAutoEq Y Y N PII-interacting protein PipX family protein 20716687,24912181 1117 Cyanobacteriota phylum 655 EBI-EMBL PII-interacting protein X DUF3539 family protein This protein family includes PII-interacting protein X (PipX) from Synechococcus elongatus and similar proteins found in cyanobacteria. PipX modulates the expression of genes involved in nitrogen assimilation by interacting with the global nitrogen transcription factor NtcA and the signal transduction protein PII. It is involved in several regulatory pathways [1]. The crystal structure of this protein shows a tudor-like domain (TLD), formed by a highly bent beta-sheet that mediates the interactions with both PII and NtcA, and two C-terminal helices [2]. [1]. 24912181. PipX, the coactivator of NtcA, is a global regulator in cyanobacteria. Espinosa J, Rodriguez-Mateos F, Salinas P, Lanza VF, Dixon R, de la Cruz F, Contreras A;. Proc Natl Acad Sci U S A. 2014;111:E2423-E2430. [2]. 20716687. Structural basis for the regulation of NtcA-dependent transcription by proteins PipX and PII. Llacer JL, Espinosa J, Castells MA, Contreras A, Forchhammer K, Rubio V;. Proc Natl Acad Sci U S A. 2010;107:15397-15402. (from Pfam) NF023517.5 PF12095.13 CRR7 25 25 84 PfamEq Y Y N chlororespiratory reduction protein 7 16359395 1117 Cyanobacteriota phylum 867 EBI-EMBL Protein CHLORORESPIRATORY REDUCTION 7 chlororespiratory reduction protein 7 This entry includes protein from blue-green algae and plants, including CRR7 protein from Arabidopsis. CRR7 is part of the chloroplastic NAD(P)H dehydrogenase complex (NDH Complex) involved in respiration, photosystem I (PSI) cyclic electron transport and CO2 uptake [1]. It is essential for the stable formation of the NDH Complex [2]. [1]. 16359395. Identification of a novel protein, CRR7, required for the stabilization of the chloroplast NAD(P)H dehydrogenase complex in Arabidopsis. Kamruzzaman Munshi M, Kobayashi Y, Shikanai T;. Plant J. 2005;44:1036-1044. [2]. 20444231. Chloroplast stromal proteins, CRR6 and CRR7, are required for assembly of the NAD(P)H dehydrogenase subcomplex A in Arabidopsis. Peng L, Cai W, Shikanai T;. Plant J. 2010;63:203-211. (from Pfam) NF023868.5 PF12452.13 DUF3685 25 25 192 PfamAutoEq Y Y N DUF3685 domain-containing protein 1117 Cyanobacteriota phylum 1199 EBI-EMBL Protein of unknown function (DUF3685) Protein of unknown function (DUF3685) This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. There are two completely conserved residues (L and D) that may be functionally important. (from Pfam) NF023979.5 PF12565.13 DUF3747 25 25 175 domain Y Y N DUF3747 domain-containing protein 1117 Cyanobacteriota phylum 1055 EBI-EMBL Protein of unknown function (DUF3747) Protein of unknown function (DUF3747) This family of proteins is found in bacteria. Proteins in this family are typically between 215 and 413 amino acids in length. There is a conserved DSNGYS sequence motif. (from Pfam) NF025578.5 PF14217.11 DUF4327 27 27 67 subfamily Y Y N DUF4327 family protein 1117 Cyanobacteriota phylum 1108 EBI-EMBL Domain of unknown function (DUF4327) DUF4327 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. (from Pfam) NF025579.5 PF14218.11 COP23 27 27 138 domain Y Y N COP23 domain-containing protein 8818292 1117 Cyanobacteriota phylum 2727 EBI-EMBL Circadian oscillating protein COP23 Circadian oscillating protein COP23 This family includes the circadian oscillating protein COP23 from Cyanothece sp. (strain PCC 8801), Swiss:Q54702. The levels of this peripheral membrane protein display a circadian oscillation [1]. [1]. 8818292. Regulation and molecular structure of a circadian oscillating protein located in the cell membrane of the prokaryote Synechococcus RF-1. Chen HM, Chien CY, Huang TC;. Planta. 1996;199:520-527. (from Pfam) NF025593.5 PF14233.11 DUF4335 27 27 186 domain Y Y N DUF4335 domain-containing protein 1117 Cyanobacteriota phylum 2010 EBI-EMBL Domain of unknown function (DUF4335) Domain of unknown function (DUF4335) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 204 and 480 amino acids in length. There are two completely conserved residues (G and D) that may be functionally important. (from Pfam) NF027731.5 PF16416.10 GUN4_N 24.3 24.3 83 PfamEq Y Y N GUN4 N-terminal ARM-like repeat domain-containing protein 15909975 1117 Cyanobacteriota phylum 756 EBI-EMBL ARM-like repeat domain, GUN4-N terminal ARM-like repeat domain, GUN4-N terminal GUN4_N is the ARM-repeat like N-terminal domain of GUN4 proteins. It contains five helices arranged in an alternating antiparallel pattern that resembles ARM or HEAT repeats, though the functional importance of this poorly conserved domain in Gun4 is not currently known [1]. [1]. 15909975. Structural and biochemical characterization of Gun4 suggests a mechanism for its role in chlorophyll biosynthesis. Davison PA, Schubert HL, Reid JD, Iorg CD, Heroux A, Hill CP, Hunter CN;. Biochemistry. 2005;44:7603-7612. (from Pfam) NF033183.2 colliding_TM 90 90 188 subfamily_domain Y Y N low-complexity tail membrane protein 1117 Cyanobacteriota phylum 621 NCBIFAM low-complexity tail membrane protein low-complexity tail membrane protein Members of this family appear typically as an unusual gene pair with members of PF11998 (DUF3493). Strangely, members tend to have tail-to-tail overlapping regions, where the tail region from this protein is long, low-complexity, and typically rich in Asp, Glu, Asn, Gln, Ser, and Thr. These gene pairs occur broadly in Cyanobacteria. The function of this pair of convergently-transcribed overlapping proteins is unknown. The low-complexity region was trimmed from the seed alignment to build this HMM. NF033464.1 cyanoexo_CrtC 225 225 278 exception Y Y N cyanoexosortase C crtC GO:0004197,GO:0006605,GO:0016020,GO:0043687 22037399 1117 Cyanobacteriota phylum 81 NCBIFAM cyanoexosortase C cyanoexosortase C Cyanosortase C (CrtC) belongs to the exosortase/archaeosortase family of multiple membrane proteins that act as cysteine proteases, and probably as transpeptidases, analogous to (but unrelated to) the sortases. CrtC is known so far only in Cyanobacteria, and appears so far primarily in the lesser-studied genera: Leptolyngbya, Oscillatoriales, Scytonema, Alkalinema, Phormidesmis, etc. NF033769.1 after_VWA_1 45 45 90 domain Y Y N after-VIT domain-containing protein 1117 Cyanobacteriota phylum 513 NCBIFAM after-VIT domain-containing protein after-VIT domain The after-VIT domain is a bacterial surface protein C-terminal domain found on some proteins that have both the Vault protein Inter-alpha-Trypsin (VIT) domain and a von Willebrand factor type A domain. Note that some of after-VIT domain-containing proteins, such as members of TIGR03788, may have a known C-terminal sorting signal, such as LPXTG or PEP-CTERM, instead of the after-VIT domain. The after-VIT domain appears to be homologous to the myxo_SS_tail domain, some of whose member proteins are involved in adventurous gliding motility in Myxococcus xanthus, and it is similarly located. NF036462.5 PF17265.7 DUF5331 27 27 113 domain Y Y N DUF5331 domain-containing protein 1117 Cyanobacteriota phylum 1083 EBI-EMBL Family of unknown function (DUF5331) Family of unknown function (DUF5331) This bacterial family of unknown function can be found in Cyanobacteria. (from Pfam) NF036465.5 PF17275.7 DUF5340 27 27 70 domain Y Y N DUF5340 family protein 1117 Cyanobacteriota phylum 450 EBI-EMBL Family of unknown function (DUF5340) DUF5340 family protein This family of unknown function can be found in Cyanobacteria. (from Pfam) NF036689.5 PF18034.6 Bac_GH3_C 27 27 137 domain Y N N Bacterial Glycosyl hydrolase family 3 C-terminal domain 1117 Cyanobacteriota phylum 751 EBI-EMBL Bacterial Glycosyl hydrolase family 3 C-terminal domain Bacterial Glycosyl hydrolase family 3 C-terminal domain This is the C-terminal domain of the glycoside hydrolase family (Pfam:PF00933) (from Pfam) NF036701.5 PF18068.6 Npun_R1517 27 27 74 PfamEq Y Y N Npun_R1517 family heterocyst differentiation transcriptional regulator 19089958 1117 Cyanobacteriota phylum 253 EBI-EMBL Npun R1517 Npun_R1517 family heterocyst differentiation transcriptional regulator The founding member of this family, Npun_R1517 from Nostoc punctiforme PCC 73102, was shown to be a helix-turn-helix protein. The family is restricted to heterocyst-forming Cyanobacteria, and mutation of a family member affects heterocyst formation. NF037186.5 PF18087.6 RuBisCo_chap_C 25 25 138 domain Y Y N RuBisCO accumulation factor 1 26237510 1117 Cyanobacteriota phylum 816 EBI-EMBL Rubisco Assembly chaperone C-terminal domain RuBisCO accumulation factor 1 C-terminal domain This is the C-terminal domain, also known as the beta domain, of Rubsico Assembly Chaperone protein (Raf1). Raf1 is necessary for rubisco to catalyze the rate-limiting step of carbon fixation through carboxylating the five-carbon sugar substrate ribulose-1,5-bisphosphate. The beta domains primary function is dimerization, which is critical for Raf1 to achieve the necessary avidity for complex formation with RbcL (the large complex sub-unbit of Rubsico) assembly intermediates. The beta domain is also involved, to a small extent, in binding to RbcL with use of the lustiness near the beta domain's conserved top surface [1]. [1]. 26237510. Structure and mechanism of the Rubisco-assembly chaperone Raf1. Hauser T, Bhat JY, Milicic G, Wendler P, Hartl FU, Bracher A, Hayer-Hartl M;. Nat Struct Mol Biol. 2015;22:720-728. (from Pfam) NF037465.5 PF18578.6 Raf1_N 26.8 26.8 106 domain Y Y N RuBisCO accumulation factor 1 raf1 26237510 1117 Cyanobacteriota phylum 814 EBI-EMBL Rubisco accumulation factor 1 alpha helical domain RuBisCO accumulation factor 1 N-terminal domain This is the N-terminal alpha helical domain found in Rubisco accumulation factor1 (Raf1). Raf1 from Arabidopsis thaliana consists of an N-terminal alpha-domain, a flexible linker segment and a C-terminal beta-sheet domain that mediates dimerization. The alpha-domains mediate the majority of functionally important contacts with RbcL (Rubisco large subunits) by bracketing each RbcL dimer at the top and bottom. The alpha-domain alone is essentially inactive [1]. [1]. 26237510. Structure and mechanism of the Rubisco-assembly chaperone Raf1. Hauser T, Bhat JY, Milicic G, Wendler P, Hartl FU, Bracher A, Hayer-Hartl M;. Nat Struct Mol Biol. 2015;22:720-728. (from Pfam) NF037466.5 PF18579.6 Raf1_HTH 27.3 27.3 61 domain Y N N Rubisco accumulation factor 1 helix turn helix domain 26237510 1117 Cyanobacteriota phylum 811 EBI-EMBL Rubisco accumulation factor 1 helix turn helix domain Rubisco accumulation factor 1 helix turn helix domain This is helix turn helix domain found in alpha helical region of Rubisco accumulation factor1 (Raf1). Raf1 from Arabidopsis thaliana consists of an N-terminal alpha-domain, a flexible linker segment and a C-terminal beta-sheet domain that mediates dimerization. The alpha-domains mediate the majority of functionally important contacts with RbcL (Rubisco large subunits) by bracketing each RbcL dimer at the top and bottom. The alpha-domain alone is essentially inactive [1]. [1]. 26237510. Structure and mechanism of the Rubisco-assembly chaperone Raf1. Hauser T, Bhat JY, Milicic G, Wendler P, Hartl FU, Bracher A, Hayer-Hartl M;. Nat Struct Mol Biol. 2015;22:720-728. (from Pfam) NF037954.1 het_cyst_PatD 50 50 116 equivalog Y Y N heterocyst frequency control protein PatD patD 31405917 1117 Cyanobacteriota phylum 727 NCBIFAM heterocyst frequency control protein PatD NF037963.1 heterocyst_HetZ 550 550 366 equivalog Y Y N heterocyst differentiation protein HetZ hetZ 18045384,22389489,29440250,29676808 1117 Cyanobacteriota phylum 501 NCBIFAM heterocyst differentiation protein HetZ The HMM distinguishes HetZ itself, a heterocyst differentiation protein, from a closely related paralog. NF037964.1 HetZ_related 612 612 370 equivalog Y Y N HetZ-related protein 1117 Cyanobacteriota phylum 526 NCBIFAM HetZ-related protein Members of this cyanobacterial protein family are paralogs of the heterocyst differentiation protein HetZ and occur in largely the same set of genomes. NF037965.1 HetZ_rel_2 400 400 367 subfamily Y Y N HetZ-related protein 2 1117 Cyanobacteriota phylum 738 NCBIFAM HetZ-related protein 2 Members of this family are cyanobacterial proteins distantly related to heterocyst differentiation protein HetZ, which also has a much more closely related set of paralogs in heterocyst-forming species. NF037966.1 HetP_family 45 45 63 subfamily_domain Y Y N HetP family heterocyst commitment protein 27791130 1117 Cyanobacteriota phylum 736 NCBIFAM HetP family heterocyst commitment protein HetP and its paralogs occur in heterocyst-forming members of the Cyanobacteria, and play a role in commitment to development into heterocysts, which specialize in nitrogen fixation rather than photosynthesis. NF037993.1 cyano_chori_ly 175 175 176 equivalog Y Y N chorismate lyase 4.1.3.40 24337576 1117 Cyanobacteriota phylum 948 NCBIFAM cyanobacterial-type chorismate lyase This variant form of chorismate lyase is widespread in the cyanobacteria, including founding example sll1797 from Synechocystis sp. PCC6803. Previously, members of this family were named DUF98 domain-containing protein, as found by Pfam model PF01947. The product, 4-hydroxybenzoate, is next prenylated by slr0926, during plastoquinone biosynthesis. NF038024.1 CRR6_slr1097 125 125 151 equivalog Y Y N CRR6 family NdhI maturation factor 23725563 1117 Cyanobacteriota phylum 905 NCBIFAM CRR6 family NdhI maturation factor The protein Slr1097 and its functionally equivalent cyanobacterial homologs are required for proper maturation of NdhI, a subunit of NADPH dehydrogenase complexes, so that NDH-1 complexes can assemble properly. The related protein in the model plant species Arabidopsis thaliana is known as CRR6 (chlororespiratory reduction 6). NF038096.1 thylak_slr1796 140 140 157 equivalog Y Y N thylakoid membrane photosystem I accumulation factor 16287171,27382055 1117 Cyanobacteriota phylum 997 NCBIFAM thylakoid membrane photosystem I accumulation factor Members of this family, restricted to the Cyanobacteria and chloroplasts, show homology to thioredoxins. However, the core region of family protein alignment shows either one Cys residue or zero, suggesting family members may share the thioredoxin-like fold but lack redox capability. The founding member of the family, slr1796, was shown by proteomics to localize to the thylakoid membrane, consistent with taxonomic restriction to the Cyanobacteria. Targeted mutation of slr1796 shows a role in successful translation and insertion of photosystem I proteins into the thylakoid membrane. NF038295.1 EPS_HpsP 550 550 388 equivalog Y Y N hormogonium polysaccharide biosynthesis glycosyltransferase HpsP hpsP 32614458 1117 Cyanobacteriota phylum 655 NCBIFAM hormogonium polysaccharide biosynthesis glycosyltransferase HpsP NF038298.1 EPS_HpsO 575 575 388 equivalog Y Y N hormogonium polysaccharide biosynthesis glycosyltransferase HpsO hpsO 32614458 1117 Cyanobacteriota phylum 622 NCBIFAM hormogonium polysaccharide biosynthesis glycosyltransferase HpsO NF038299.1 EPS_HpsN 425 425 317 equivalog Y Y N hormogonium polysaccharide biosynthesis glycosyltransferase HpsN hpsN 32614458 1117 Cyanobacteriota phylum 601 NCBIFAM hormogonium polysaccharide biosynthesis glycosyltransferase HpsN NF038300.1 EPS_HpsL 640 640 534 equivalog Y Y N hormogonium polysaccharide biosynthesis protein HpsL hpsL 32614458 1117 Cyanobacteriota phylum 651 NCBIFAM hormogonium polysaccharide biosynthesis protein HpsL NF038301.1 EPS_HpsA 400 200 1503 equivalog Y Y N hormogonium polysaccharide biosynthesis protein HpsA hpsA 23279310 1117 Cyanobacteriota phylum 834 NCBIFAM hormogonium polysaccharide biosynthesis protein HpsA NF038302.1 EPS_HpsE 300 300 307 equivalog Y Y N hormogonium polysaccharide biosynthesis glycosyltransferase HpsE hpsE 23279310 1117 Cyanobacteriota phylum 1125 NCBIFAM hormogonium polysaccharide biosynthesis glycosyltransferase HpsE NF038307.1 EPS_acetyl_HpsU 305 305 178 equivalog Y Y N hormogonium polysaccharide biosynthesis acetyltransferase HpsU hpsU 32614458 1117 Cyanobacteriota phylum 599 NCBIFAM hormogonium polysaccharide biosynthesis acetyltransferase HpsU HpsU is related to the colanic acid biosynthesis acetyltransferase WcaF, which acts on a fucose residue in a disaccharide attached to a lipid carrier. NF038350.1 taxis_HmpF 200 200 553 equivalog Y Y N pilus motility taxis protein HmpF hmpF 28779543,33723073 1117 Cyanobacteriota phylum 828 NCBIFAM pilus motility taxis protein HmpF NF039784.4 PF20035.4 DUF6439 27 27 92 subfamily Y Y N DUF6439 family protein 1117 Cyanobacteriota phylum 822 EBI-EMBL Family of unknown function (DUF6439) DUF6439 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in cyanobacteria. Proteins in this family are typically between 87 and 98 amino acids in length. (from Pfam) NF040406.4 PF19959.4 EAD4 27 27 123 domain Y N N Effector-associated domain 4 32101166 1117 Cyanobacteriota phylum 747 EBI-EMBL Effector-associated domain 4 Effector-associated domain 4 Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling attenuates collinear transcription requirements. [1]. 32101166. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. Kaur G, Burroughs AM, Iyer LM, Aravind L;. Elife. 2020; [Epub ahead of print] (from Pfam) NF040430.4 PF20065.4 DUF6464 25 25 106 subfamily Y Y N DUF6464 family protein 1117 Cyanobacteriota phylum 1354 EBI-EMBL Family of unknown function (DUF6464) DUF6464 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 101 and 122 amino acids in length. (from Pfam) NF040946.1 PSII_PsbP 60 60 180 equivalog Y Y N photosystem II reaction center PsbP psbP 9039496 1117 Cyanobacteriota phylum 925 NCBIFAM photosystem II reaction center PsbP NF041358.1 GntT_guanitoxin 525 525 438 equivalog Y Y N guanitoxin biosynthesis MATE family efflux transporter GntT gntT 35583956 1117 Cyanobacteriota phylum 502 NCBIFAM guanitoxin biosynthesis MATE family efflux transporter GntT NF041521.1 HhoA_HhoB_HtrA 450 450 335 equivalog Y Y N HhoA/HhoB/HtrA family serine endopeptidase 3.4.21.- 23029195,25877158,27956128 1117 Cyanobacteriota phylum 2993 NCBIFAM HhoA/HhoB/HtrA family serine endopeptidase Members of this family include the paralogous serine proteases HhoA, HhoB, and HtrA of the model cyanobacterial isolate Synechocystis sp. PCC 6803. They resemble the paralogous trio of serine proteases DegQ, DegP, and DegS of Escherichia coli. NF041522.1 TPR_sll0314 225 225 275 equivalog Y Y N Sll0314/Alr1548 family TPR repeat-containing protein 24935866,25782455 1117 Cyanobacteriota phylum 810 NCBIFAM Sll0314/Alr1548 family TPR repeat-containing protein Members of this cyanobacterial family have signal peptides and are called periplasmic. The body of the protein contains regions of homology to tetratricopeptide repeats (TPR). Member protein Sll0314 was found to be upregulated as part of the iron deprivation stress regulon. NF041735.1 hist_kin_RppB 400 400 438 equivalog Y Y N two-component system sensor histidine kinase RppB rppB 2.7.13.3 GO:0000155 10894737,11849552 1117 Cyanobacteriota phylum 908 NCBIFAM two-component system sensor histidine kinase RppB NF042591.3 PF20522.3 DUF6737 27 27 57 subfamily Y Y N DUF6737 family protein 1117 Cyanobacteriota phylum 808 EBI-EMBL Domain of unknown function (DUF6737) DUF6737 family protein This presumed domain is functionally uncharacterised. This domain is approximately 57 amino acids in length. (from Pfam) NF042730.3 PF20384.3 DUF6679 23.9 23.9 103 subfamily Y Y N DUF6679 family protein 1117 Cyanobacteriota phylum 495 EBI-EMBL Family of unknown function (DUF6679) DUF6679 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. There is a conserved DQQRWIE sequence motif. (from Pfam) NF042767.3 PF20429.3 Tab2-like_C 28.2 28.2 151 subfamily Y Y N Tab2 family RNA-binding protein 14633996,17139246,25725436 1117 Cyanobacteriota phylum 1841 EBI-EMBL RNA-binding protein Tab2/Atab2, C-terminal domain RNA-binding protein Tab2/Atab2, C-terminal domain This is the C-terminal domain of Tab2 from plant and cyanobacteria. Tab2 was first identified in Chlamydomonas reinhardtii as a RNA binding protein required for translation of the chloroplast PsaB photosystem I subunit [1]. Later, the Tab2 homologue from Arabidopsis (Atab2) was found involved in the signalling pathway of light-controlled synthesis of photosystem proteins during early plant development, presumably functioning as an activator of translation with targets at PSI and PSII [2,3]. Directed mutagenesis experiments carried out in Chlamydomonas reinhardtii, Tab2 Swiss:Q7X8Y6, indicated the importance of a highly conserved C-terminal tripeptide WLL for normal psaB translation [1]. [1]. 14633996. Tab2 is a novel conserved RNA binding protein required for translation of the chloroplast psaB mRNA. Dauvillee D, Stampacchia O, Girard-Bascou J, Rochaix JD;. EMBO J. 2003;22:6378-6388. [2]. 25725436. Large-scale genetic analysis of chloroplast biogenesis in maize. Belcher S, Williams-Carrier R, Stiffler N, Barkan A;. Biochim Biophys Acta. 2015;1847:1004-1016. [3]. 17139246. ATAB2 is a novel factor in the signalling pathway of light-controlled synthesis of photosystem proteins. Barneche F, Winter V, Crevecoeur M, Rochaix JD;. EMBO J. 2006;25:5907-5918. (from Pfam) NF042828.3 PF20547.3 DUF6761 27 27 82 subfamily Y Y N DUF6761 family protein 1117 Cyanobacteriota phylum 631 EBI-EMBL Family of unknown function (DUF6761) DUF6761 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in cyanobacteria. Proteins in this family are approximately 80 amino acids in length. (from Pfam) NF044687.2 PF21053.2 BFA1_C 23.5 23.5 135 domain Y N N Biogenesis factor required for ATP synthase 1, C-terminal domain 30012777 1117 Cyanobacteriota phylum 1145 EBI-EMBL Biogenesis factor required for ATP synthase 1, C-terminal domain Biogenesis factor required for ATP synthase 1, C-terminal domain This domain is predominantly found at the C-terminal end of proteins from cyanobacteria and plants, including Biogenesis factor required for ATP synthase 1 (BFA1, Swiss:F4J1U2) from Arabidopsis thaliana. BFA1 promotes the assembly of the CF1 subcomplex of the chloroplast ATP synthase by specifically interacting with the gamma and beta subunits. This domain consists of ten beta-sheets and one alpha- helix forming a typical beta-barrel, which locates perpendicularly to Pfam:PF12204 [1]. [1]. 30012777. Nucleus-Encoded Protein BFA1 Promotes Efficient Assembly of the Chloroplast ATP Synthase Coupling Factor 1. Zhang L, Pu H, Duan Z, Li Y, Liu B, Zhang Q, Li W, Rochaix JD, Liu L, Peng L;. Plant Cell. 2018;30:1770-1788. (from Pfam) NF045036.2 PF21329.2 CYP38_PsbQ-like 27 27 117 domain Y N N Peptidyl-prolyl cis-trans isomerase CYP38-like, PsbQ-like domain 22706283 1117 Cyanobacteriota phylum 1103 EBI-EMBL Peptidyl-prolyl cis-trans isomerase CYP38-like, PsbQ-like domain Peptidyl-prolyl cis-trans isomerase CYP38-like, PsbQ-like domain Peptidyl-prolyl cis-trans isomerase CYP38 from Arabidopsis is required for the assembly and stabilization of PSII [1]. It consists of an N-terminal helical bundle and a C-terminal cyclophilin beta-barrel (Pfam:PF00160)[1]. This entry represents the N-terminal helical bundle found in Cyp37/38 from Arabidopsis and similar proteins from cyanobacteria. This domain establishes strong interactions with the C-terminal domain to avoid the access of the cyclophilin domain to other proteins [1]. Paper describing PDB structure 3rfy. [1]. 22706283. Crystal structure of Arabidopsis cyclophilin38 reveals a previously uncharacterized immunophilin fold and a possible autoinhibitory mechanism. Vasudevan D, Fu A, Luan S, Swaminathan K;. Plant Cell. 2012;24:2666-2674. (from Pfam) NF045180.2 PF20670.2 DUF6816 26.8 26.8 218 subfamily Y Y N DUF6816 family protein 1117 Cyanobacteriota phylum 1002 EBI-EMBL Domain of unknown function (DUF6816) DUF6816 family protein This presumed domain is functionally uncharacterised and it is found in bacterial (predominantly in cyanobacteria) and eukaryotic (mainly from plants) sequences. Structure prediction using AlphaFold resource, suggest that this domain may have a START-like (StAR-related lipid-transfer) fold consisting of an alpha/beta structure of a helix-grip fold, that forms cavities for hydrophobic substrates or ligands which may indicate a possible function for this domain. (from Pfam) NF045514.1 glycotran_HepC 140 140 220 equivalog Y Y N heterocyst development glycosyltransferase HepC hepC GO:0043158 9696774 1117 Cyanobacteriota phylum 469 NCBIFAM heterocyst development glycosyltransferase HepC NF045582.1 Npun_R2823_gen 250 250 299 subfamily Y Y N Npun_R2821/Npun_R2822 family protein 1117 Cyanobacteriota phylum 1770 NCBIFAM Npun_R2821/Npun_R2822 family protein This uncharacterized protein family occur in Cyanobacteria, almost perfectly matched to the presence of the cyanoexosortase CrtB (TIGR04156). Paralogs in Nostoc punctiforme include tandem-encoded proteins Npun_R2821, Npun_R2822, and Npun_R2823, plus a fourth, Npun_F3711. NF045585.1 rSAM_slr0320 775 775 511 equivalog Y Y N photosystem II high light acclimation radical SAM protein 33810453 1117 Cyanobacteriota phylum 1082 NCBIFAM photosystem II high light acclimation radical SAM protein NF045586.1 Npun_F0494_fam 65 65 118 equivalog Y Y N Npun_F0494 family protein 1117 Cyanobacteriota phylum 936 NCBIFAM Npun_F0494 family protein This uncharacterized protein is widespread in but restricted to Cyanobacteria. Most members are found encoded next to CobQ (TIGR00313). The central motif LRREVDGQGxxxxxRLTPLG is almost perfectly conserved. NF045587.1 T4P_biogen_EbsA 33 27.5 118 equivalog Y Y N type IV pilus biogenesis protein EbsA ebsA 33727363,39287971 1117 Cyanobacteriota phylum 712 NCBIFAM type IV pilus biogenesis protein EbsA EbsA (essential for biofilm self-suppression A), as characterized in Synechococcus elongatus, is a protein restricted to the cyanobacteria that plays a role in both type IV pilus formation and protein secretion across the outer membrane, two processes that rely on the same set of genes. NF045588.1 Cterm_S41_CtpA 625 625 401 exception Y Y N carboxyl-terminal processing protease CtpA ctpA 3.4.21.102 GO:0004252 35269663 1117 Cyanobacteriota phylum 793 NCBIFAM carboxyl-terminal processing protease CtpA Carboxyl-terminal processing protease A (CtpA) processes the photosystem II core complex protein D1 (PsbA). Paralogs CtpB and CtpC are also found broadly in Cyanobacteria. CtpC is essential and may have a general housekeeping role (see PMID:3526966). NF045589.1 Cterm_S41_CtpB 633 633 416 exception Y Y N carboxyl-terminal processing protease CtpB ctpB 3.4.21.102 GO:0004252 35269663 1117 Cyanobacteriota phylum 662 NCBIFAM carboxyl-terminal processing protease CtpB NF045590.1 Cterm_S41_CtpC 665 665 418 exception Y Y N carboxyl-terminal processing protease CtpC ctpC 3.4.21.102 GO:0004252 35269663 1117 Cyanobacteriota phylum 760 NCBIFAM carboxyl-terminal processing protease CtpC The serine protease CtpC (carboxyl-terminal processing protease A) is essential in Synechocystis sp. PCC 6803 and may have a general housekeeping function. Its paralog CtpA is required specifically to cleave the photosystem II core complex protein D1 (PsbA). NF045598.1 asr1405_asl0597 35 35 66 subfamily Y Y N Asr1405/Asl0597 family protein 12886952,20169071 1117 Cyanobacteriota phylum 957 NCBIFAM Asr1405/Asl0597 family protein Members of this family appear to be restricted to nitrogen-fixing cyanobacteria. Asr1405 from Anabaena sp. strain PCC 7120 was shown to be induced by nitrogen limitation, while its paralog asl0597 was not. NF045621.1 Npun_F0813_fam 210 210 221 hypoth_equivalog Y Y N Npun_F0813 family protein 20169071 1117 Cyanobacteriota phylum 479 NCBIFAM Npun_F0813 family protein of filamentous cyanobacteria Members of this family, including all1340 of Nostoc sp. PCC 7120 and Npun_F0813 of N. punctiforme, appear restricted to cyanobacteria that grow with a filamentous morphology. NF045622.1 Npun_F5560_fam 125 125 156 hypoth_equivalog Y Y N Npun_F5560 family protein 1117 Cyanobacteriota phylum 530 NCBIFAM Npun_F5560 family protein Members of this family, including Npun_F5560 from Nostoc punctiforme PCC 73102, appear only in the Cyanobacteria, and appear restricted to the subset of Cyanobacteria that grow in elongated fibers and form heterocysts for nitrogen fixation. This model describes full-length homologs of Npun_F5560, and currently excludes proteins lacking the N-terminal region, as from several species of Synechococcus. NF045624.1 filament_FraC 100 100 170 equivalog Y Y N filament integrity protein FraC fraC 20487302,25784700,38164507 1117 Cyanobacteriota phylum 553 NCBIFAM filament integrity protein FraC FraC, along with FraD and SepJ(FraG), is found at intercellular septa in heterocyst-forming filamentous cyanobacteria such as Nostoc punctiforme. NF045647.1 alr0857_fam 75 75 121 equivalog Y Y N alr0857 family protein 20169071 1117 Cyanobacteriota phylum 637 NCBIFAM alr0857 family protein NF045685.1 GGPPSynCrtE 460 460 293 equivalog Y Y N geranylgeranyl diphosphate synthase CrtE crtE 2.5.1.1 GO:0016740,GO:0033386 10412909,32523588 1117 Cyanobacteriota phylum 1008 NCBIFAM geranylgeranyl diphosphate synthase CrtE NF045686.1 PhytoSynCyanob 550 550 310 equivalog Y Y N 15-cis-phytoene synthase CrtB crtB 2.5.1.32 GO:0004311,GO:0016117,GO:0016767 1537409,8018713 1117 Cyanobacteriota phylum 610 NCBIFAM 15-cis-phytoene synthase CrtB NF045688.1 BCarotHydoxCrtR 475 475 297 equivalog Y Y N beta-carotene hydroxylase crtR GO:0016491 10431816 1117 Cyanobacteriota phylum 992 NCBIFAM beta-carotene hydroxylase NF045692.1 OglycostaseCruG 600 600 386 equivalog Y Y N 2'-O-glycosyltransferase CruG cruG 19304845 1117 Cyanobacteriota phylum 788 NCBIFAM 2'-O-glycosyltransferase CruG NF045693.1 GCarotHydoxCruF 400 400 310 equivalog Y Y N gamma-carotene 1'-hydroxylase CruF cruF 19304845 1117 Cyanobacteriota phylum 745 NCBIFAM gamma-carotene 1'-hydroxylase CruF NF045911.1 TCSHisKinNblS 1000 1000 621 equivalog Y Y N two-component system sensor histidine kinase NblS nblS 11948163,37925065 1117 Cyanobacteriota phylum 755 NCBIFAM two-component system sensor histidine kinase NblS NF045912.1 TransCoactPipX 125 125 85 equivalog Y Y N transcriptional coactivator PipX pipX 16796668,24912181 1117 Cyanobacteriota phylum 467 NCBIFAM transcriptional coactivator PipX NF045913.1 RegSipA 100 100 67 equivalog Y Y N regulatory protein SipA sipA 16451177,18004983 1117 Cyanobacteriota phylum 613 NCBIFAM regulatory protein SipA NF045914.1 RespRegNblR 300 300 228 equivalog Y Y N response regulator transcription factor NblR nblR GO:0000160,GO:0003677,GO:0006355 11532155,18391440,9724820 1117 Cyanobacteriota phylum 591 NCBIFAM response regulator transcription factor NblR NF045915.1 PhycobilmeDegNblB 300 300 214 equivalog Y Y N phycobilisome degradation protein NblB nblB 31820831,9882677 1117 Cyanobacteriota phylum 698 NCBIFAM phycobilisome degradation protein NblB NF045918.1 PhsystIBiosynBtpA 400 400 261 equivalog Y Y N photosystem I biogenesis protein BtpA btpA 9045660 1117 Cyanobacteriota phylum 664 NCBIFAM photosystem I biogenesis protein BtpA NF045929.1 FNRPetHCyano 600 600 411 equivalog Y Y N ferredoxin--NADP reductase petH 1.18.1.2 GO:0004324,GO:0022900 10651039,1554697,31015331,8890910 1117 Cyanobacteriota phylum 769 NCBIFAM ferredoxin--NADP reductase NF045930.1 Cytc6PetJCyano 135 135 110 equivalog Y Y N cytochrome c6 PetJ petJ GO:0005506,GO:0009055,GO:0015979 1967057,228936,9473522 1117 Cyanobacteriota phylum 1320 NCBIFAM cytochrome c6 PetJ NF045992.1 CircClkLdpA 450 450 360 equivalog Y Y N circadian clock protein LdpA ldpA GO:0007623,GO:0046872,GO:0051539 12562813,15775978 1117 Cyanobacteriota phylum 822 NCBIFAM circadian clock protein LdpA NF047018.1 PF23007.1 DnaA_N-like_STI 27 27 86 domain Y N N STICHEL, DnaA_N-like alpha-beta domain 12586888 1117 Cyanobacteriota phylum 949 EBI-EMBL STICHEL, DnaA_N-like alpha-beta domain STICHEL, DnaA_N-like alpha-beta domain This domain is found in protein STICHEL (STI) from Arabidopsis thaliana and related proteins mainly from plants. STICHEL acts as a key regulator of trichome branching through an endoreduplication-independent pathway [1]. The domain represented by this entry is predicted to adopt a globular alpha/beta structure with significant similarity to domains belonging to Ribosome-binding factor A, RbfA superfamily including ribosomal protein eS7. It has a significant sequence similarity to DnaA N-terminal domain. This domain is topologically very similar to KH type II domains but it lacks their characteristic KH-motif. [1]. 12586888. The Arabidopsis STICHEL gene is a regulator of trichome branch number and encodes a novel protein. Ilgenfritz H, Bouyer D, Schnittger A, Mathur J, Kirik V, Schwab B, Chua NH, Jurgens G, Hulskamp M;. Plant Physiol. 2003;131:643-655. (from Pfam) NF047378.1 photo_II_Psb35 40 40 46 equivalog Y Y N photosystem II assembly protein Psb35 psb35 GO:0019684 33258963 1117 Cyanobacteriota phylum 673 NCBIFAM photosystem II assembly protein Psb35 NF047379.1 photo_II_Psb32 160 160 207 equivalog Y Y N photosystem II repair protein Psb32 psb32 21653280 1117 Cyanobacteriota phylum 979 NCBIFAM photosystem II repair protein Psb32 Members of this family, distantly related to YgcG of Escherichia coli, are restricted to Cyanobacteria, where there are ascribed a role in photodamage repair. NF047380.1 photo_II_xxx 80 80 75 equivalog Y Y N photosystem II protein, Psb35-related 1117 Cyanobacteriota phylum 321 NCBIFAM photosystem II protein, Psb35-related This undescribed putative photosystem II protein is related to Psb35 and restricted to species that have photosystem II. NF047397.1 slr1339_fam 45 45 143 equivalog Y Y N salt stress protein, Slr1339 family GO:0009651 24643737 1117 Cyanobacteriota phylum 609 NCBIFAM salt stress protein, Slr1339 family Slr1339, the founding member of this strictly cyanobacterial protein family, was shown to be induced by extended salt stress, while its knockout was shown to increase salt sensitivity. NF047416.1 penta_HetL 260 260 218 equivalog Y Y N heterocyst differentiation pentapeptide repeat protein HetL hetL 12446638,18952182,32762845 1117 Cyanobacteriota phylum 271 NCBIFAM heterocyst differentiation pentapeptide repeat protein HetL HetL contributes to the differentiation of scattered individual cells in cyanobacterial filaments into nitrogen-fixing heterocysts. This HMM distinguishes HetL from paralogous pentapeptide repeat proteins that may be found in the same species. NF047598.1 ChaprRbcXCyano 170 170 111 equivalog Y Y N RuBisCO chaperone RbcX rcbX GO:0015977,GO:0044183,GO:0110102 17574029,19081849,20075914 1117 Cyanobacteriota phylum 541 NCBIFAM RuBisCO chaperone RbcX TIGR00403.1 TIGR00403 ndhI 302.35 302.35 183 equivalog Y Y N NAD(P)H-quinone oxidoreductase subunit I ndhI GO:0008753,GO:0030964 1117 Cyanobacteriota phylum 802 JCVI NADH-plastoquinone oxidoreductase, I subunit NAD(P)H-quinone oxidoreductase subunit I TIGR00788.1 TIGR00788 fbt 216.4 216.4 468 subfamily Y Y N folate/biopterin family MFS transporter fbt GO:0016020 1117 Cyanobacteriota phylum 819 JCVI folate/biopterin transporter folate/biopterin family MFS transporter The Folate-Biopterin Transporter (FBT) Family (TC 2.A.71) The only functionally characterized members of the family are from protozoa and include FT1, the major folate transporter in Leishmania, and BT1, the Leishmania biopterin/folate transporter. A related protein in Trypanosoma brucei, ESAGIO, shows weak folate/biopterin transport activity. TIGR00947.1 TIGR00947 2A73 366.4 366.4 425 equivalog Y Y N IctB family putative bicarbonate transporter 9688546 1117 Cyanobacteriota phylum 1069 JCVI putative bicarbonate transporter, IctB family putative bicarbonate transporter, IctB family This family of proteins is suggested to transport inorganic carbon (HCO3-), based on the phenotype of a mutant of IctB in Synechococcus sp. strain PCC 7942. Bicarbonate uptake is used by many photosynthetic organisms including cyanobacteria. These organisms are able to concentrate CO2/HCO3- against a greater than ten-fold concentration gradient. Cyanobacteria may have several such carriers operating with different efficiencies. Note that homology to various O-antigen ligases, with possible implications for mutant cell envelope structure, might allow alternatives to the interpretation of IctB as a bicarbonate transport protein. TIGR01335.1 TIGR01335 psaA 862.55 862.55 752 equivalog Y Y N photosystem I core protein PsaA psaA 1.97.1.12 GO:0009538,GO:0015979,GO:0016020,GO:0016168,GO:0046872 1117 Cyanobacteriota phylum 929 JCVI photosystem I core protein PsaA photosystem I core protein PsaA The core proteins of photosystem I are PsaA and PsaB, homologous integral membrane proteins that form a heterodimer. The heterodimer binds the electron-donating chlorophyll dimer P700, as well as chlorophyll, phylloquinone, and 4FE-4S electron acceptors. This model describes PsaA only. TIGR01337.1 TIGR01337 apcB 228.15 228.15 167 equivalog Y Y N allophycocyanin subunit beta apcB GO:0009055,GO:0015979,GO:0030089 10358042 1117 Cyanobacteriota phylum 1039 JCVI allophycocyanin, beta subunit allophycocyanin subunit beta The alpha and beta subunits of allophycocyanin form heterodimers, six of which associate into larger aggregates as part of the phycobilisome, a light-harvesting complex of phycobiliproteins and linker proteins. This model describes allophycocyanin beta subunit. Other, homologous phyobiliproteins include allophycocyanin alpha chain and the phycocyanin and phycoerythrin alpha and beta chains. TIGR01338.1 TIGR01338 phycocy_alpha 269.45 269.45 161 equivalog Y Y N phycocyanin subunit alpha cpcA GO:0009055,GO:0015979,GO:0030089 1117 Cyanobacteriota phylum 721 JCVI phycocyanin, alpha subunit phycocyanin subunit alpha This model describes the phycocyanin alpha subunit. Other, homologous phyobiliproteins of the phycobilisome include phycocyanin alpha chain and the allophycocyanin and phycoerythrin alpha and beta chains. This model excludes the closely related phycoerythrocyanin alpha subunit. TIGR01339.1 TIGR01339 phycocy_beta 279.3 279.3 171 equivalog Y Y N phycocyanin subunit beta GO:0015979,GO:0030089 1117 Cyanobacteriota phylum 786 JCVI phycocyanin, beta subunit phycocyanin subunit beta This model describes the phycocyanin beta subunit. Other, homologous phycobiliproteins of the phycobilisome include phycocyanin beta chain and the allophycocyanin and phycoerythrin alpha and beta chains. This model excludes the closely related phycoerythrocyanin beta subunit. TIGR01960.1 TIGR01960 ndhF3_CO2 588.7 588.7 606 subfamily Y N N NAD(P)H dehydrogenase, subunit NdhF3 family 10383770 1117 Cyanobacteriota phylum 1923 JCVI NAD(P)H dehydrogenase, subunit NdhF3 family NAD(P)H dehydrogenase, subunit NdhF3 family This family represents a subfamily of NAD(P)H dehydrogenase subunit 5, or ndhF. It is restricted to two paralogs in each completed cyanobacterial genome, in which several subtypes of ndhF are found. Included in this family is NdhF3, shown to play a role in high-affinity CO2 uptake in Synechococcus sp. PCC7002. In all cases, neighboring genes include a paralog of ndhD but do include other NAD(P)H dehydrogenase subunits. Instead, genes related to C02 uptake tend to be found nearby. TIGR01964.1 TIGR01964 chpXY 293.7 293.7 411 subfamily Y Y N CO2 hydration protein 11985719 1117 Cyanobacteriota phylum 1887 JCVI CO2 hydration protein CO2 hydration protein This small family of proteins includes paralogs ChpX and ChpY in Synechococcus sp. PCC7942 and other cyanobacteria, associated with distinct NAD(P)H dehydrogenase complexes. These proteins collectively enable light-dependent CO2 hydration and CO2 uptake; loss of both blocks growth at low CO2 concentrations. TIGR02028.1 TIGR02028 ChlP 505.3 505.3 398 equivalog Y Y N geranylgeranyl reductase chlP GO:0015995,GO:0045550 1117 Cyanobacteriota phylum 874 JCVI geranylgeranyl reductase geranylgeranyl reductase This HMM represents the reductase which acts reduces the geranylgeranyl group to the phytyl group in the side chain of chlorophyll. It is unclear whether the enzyme has a preference for acting before or after the attachment of the side chain to chlorophyllide a by chlorophyll synthase. This clade is restricted to plants and cyanobacteria to separate it from the homologues which act in the biosynthesis of bacteriochlorophyll. TIGR02042.1 TIGR02042 sir 731.5 731.5 581 equivalog Y Y N sulfite reductase, ferredoxin dependent sir 1.8.7.1 GO:0020037,GO:0050311,GO:0051539 8347657,8695637,9722674 1117 Cyanobacteriota phylum 1050 JCVI sulfite reductase, ferredoxin dependent sulfite reductase, ferredoxin dependent Distantly related to the iron-sulfur hemoprotein of sulfite reductase (NADPH) found in Proteobacteria and Eubacteria, sulfite reductase (ferredoxin) is a cyanobacterial and plant monomeric enzyme that also catalyzes the reduction of sulfite to sulfide [1,2,3]. TIGR02056.1 TIGR02056 ChlG 436.45 436.45 306 equivalog Y Y N chlorophyll synthase ChlG chlG 2.5.1.62 GO:0015995,GO:0016020,GO:0046408 12828371 1117 Cyanobacteriota phylum 986 JCVI chlorophyll synthase ChlG chlorophyll synthase ChlG This HMM represents the strictly cyanobacterial and plant-specific chlorophyll synthase ChlG. ChlG is the enzyme (esterase) which attaches the side chain moiety onto chlorophyllide a. Both geranylgeranyl and phytyl pyrophosphates are substrates to varying degrees in enzymes from different sources [1]. Thus, ChlG may act as the final or penultimate step in chlorophyll biosynthesis (along with the geranylgeranyl reductase, ChlP). TIGR02235.1 TIGR02235 menA_cyano-plnt 225 225 285 equivalog Y Y N 2-carboxy-1,4-naphthoquinone phytyltransferase menA 2.5.1.130 GO:0004659,GO:0016020,GO:0042372 3130097 1117 Cyanobacteriota phylum 1098 JCVI 1,4-dihydroxy-2-naphthoate phytyltransferase 2-carboxy-1,4-naphthoquinone phytyltransferase This family of phytyltransferases, found in plants and cyanobacteria, are involved in the biosythesis of phylloquinone (Vitamin K1). Phylloquinone is a critical component of photosystem I [1]. The closely related MenA enzyme from bacteria transfers a prenyl group (which only differs in the saturation of the isoprenyl groups) in the biosynthesis of menaquinone. Activity towards both substrates in certain organisms should be considered a possibility. TIGR02652.1 TIGR02652 TIGR02652 99.55 99.55 162 hypoth_equivalog Y Y N TIGR02652 family protein 1117 Cyanobacteriota phylum 581 JCVI TIGR02652 family protein TIGR02652 family protein Members of this family of conserved hypothetical proteins are found, so far, only in the Cyanobacteria. Members are about 170 amino acids long and share a motif CxxCx(14)CxxH near the amino end. TIGR02702.1 TIGR02702 SufR_cyano 178.8 178.8 208 equivalog Y Y N iron-sulfur cluster biosynthesis transcriptional regulator SufR sufR GO:0006355,GO:0016226,GO:0140110 14761990 1117 Cyanobacteriota phylum 936 JCVI iron-sulfur cluster biosynthesis transcriptional regulator SufR iron-sulfur cluster biosynthesis transcriptional regulator SufR All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus. TIGR02730.1 TIGR02730 carot_isom 586.9 586.9 493 equivalog Y Y N carotenoid isomerase crtH 5.2.1.13 GO:0016117,GO:0046608 11773533,15557094 1117 Cyanobacteriota phylum 1035 JCVI carotene isomerase carotenoid isomerase Members of this family, including sll0033 (crtH) of Synechocystis sp. PCC 6803, catalyze a cis-trans isomerization of carotenes to the all-trans lycopene, a reaction that can also occur non-enzymatically in light through photoisomerization. TIGR02731.1 TIGR02731 phytoene_desat 569.4 569.4 453 equivalog Y Y N 15-cis-phytoene desaturase pds 1.3.5.5 GO:0016117,GO:0016166 1117 Cyanobacteriota phylum 984 JCVI phytoene desaturase 15-cis-phytoene desaturase Plants and cyanobacteria (and, supposedly, Chlorobium tepidum) have a conserved pathway from two molecules geranylgeranyl-PP to one of all-trans-lycopene. Members of this family are the enzyme pytoene desaturase (also called phytoene dehydrogenase). This model does not include the region of the chloroplast transit peptide in plants. A closely related family, excluded by this model, is zeta-carotene desaturase, another enzyme in the same pathway. TIGR02732.1 TIGR02732 zeta_caro_desat 622.15 622.15 474 equivalog Y Y N 9,9'-di-cis-zeta-carotene desaturase zds 1.3.5.6 GO:0016117,GO:0016719 1117 Cyanobacteriota phylum 1034 JCVI 9,9'-di-cis-zeta-carotene desaturase 9,9'-di-cis-zeta-carotene desaturase Carotene 7,8-desaturase, also called zeta-carotene desaturase, catalyzes multiple steps in the pathway from geranylgeranyl-PP to all-trans-lycopene in plants and cyanobacteria. A similar enzyme and pathway is found in the green sulfur bacterium Chlorobium tepidum. TIGR02733.1 TIGR02733 desat_CrtD 549.7 549.7 492 equivalog Y Y N C-3',4' desaturase CrtD crtD GO:0016117,GO:0016491 15317766 1117 Cyanobacteriota phylum 1137 JCVI C-3',4' desaturase CrtD C-3',4' desaturase CrtD Members of this family are slr1293, a carotenoid biosynthesis protein which was shown to be the C-3',4' desaturase (CrtD) of myxoxanthophyll biosynthesis in Synechocystis sp. strain PCC 6803, and close homologs (presumed to be functionally equivalent) from other cyanobacteria, where myxoxanthophyll biosynthesis is either known or expected. This enzyme can act on neurosporene and so presumably catalyzes the first step that is committed to myxoxanthophyll. TIGR02749.1 TIGR02749 prenyl_cyano 383.2 383.2 322 equivalog Y Y N solanesyl diphosphate synthase sds GO:0010236,GO:0052923 12437513 1117 Cyanobacteriota phylum 899 JCVI solanesyl diphosphate synthase solanesyl diphosphate synthase Members of this family all are from cyanobacteria or plastid-containing eukaryotes. A member from Arabidopsis (where both plastoquinone and ubiquinone contain the C(45) prenyl moiety) was characterized by heterologous expression as a solanesyl diphosphate synthase. This family includes enzymes designated EC 2.5.1.85 (all-trans-nonaprenyl-diphosphate synthase [geranylgeranyl-diphosphate-specific) and EC 2.5.1.29 (geranylgeranyl diphosphate synthase). TIGR02997.1 TIGR02997 Sig70-cyanoRpoD 384.5 384.5 298 subfamily Y Y N RNA polymerase sigma factor, RpoD/SigA family GO:0003677,GO:0006352,GO:0016987 1117 Cyanobacteriota phylum 4665 JCVI RNA polymerase sigma factor, cyanobacterial RpoD-like family RNA polymerase sigma factor, RpoD/SigA family This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393). TIGR03039.1 TIGR03039 PS_II_CP47 630.8 630.8 504 equivalog Y Y N photosystem II chlorophyll-binding protein CP47 psbB GO:0009523,GO:0009772,GO:0015979,GO:0016020,GO:0016168,GO:0045156 1117 Cyanobacteriota phylum 883 JCVI photosystem II chlorophyll-binding protein CP47 photosystem II chlorophyll-binding protein CP47 TIGR03041.1 TIGR03041 PS_antenn_a_b 335 335 321 subfamily Y Y N chlorophyll a/b binding light-harvesting protein GO:0009765,GO:0016168 8986795 1117 Cyanobacteriota phylum 1732 JCVI chlorophyll a/b binding light-harvesting protein chlorophyll a/b binding light-harvesting protein This model represents a family of proteins from the Cyanobacteria, closely homologous to and yet distinct from PbsC, a chlorophyll a antenna protein of photosystem II. Members are not univerally present in Cyanobacteria, while the family has several members per genome in Prochlorococcus marinus, with seven members in a strain adapted to low light conditions. These antenna proteins may deliver light energy to photosystem I and/or photosystem II. TIGR03043.1 TIGR03043 PS_II_psbZ 39.95 39.95 58 equivalog Y Y N photosystem II reaction center protein PsbZ psbZ GO:0009523,GO:0009538 11402165,33495333 1117 Cyanobacteriota phylum 523 JCVI photosystem II core protein PsbZ photosystem II reaction center protein PsbZ PsbZ is a core protein of photosystem II in thylakoid-containing Cyanobacteria and plant chloroplasts. The original Chlamydomonas gene symbol, ycf9, is a synonym. PsbZ controls the interaction of the reaction center core with the light-harvesting antenna. TIGR03044.1 TIGR03044 PS_II_psb27 117.35 117.35 135 equivalog Y Y N photosystem II protein Psb27 psb27 GO:0009523,GO:0010206,GO:0010207 12069591,15308630,16897475 1117 Cyanobacteriota phylum 785 JCVI photosystem II protein Psb27 photosystem II protein Psb27 Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single HMM families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins. TIGR03047.1 TIGR03047 PS_II_psb28 61.1 61.1 109 equivalog Y Y N photosystem II reaction center protein Psb28 psb28 GO:0009523,GO:0009538 12069591 1117 Cyanobacteriota phylum 1070 JCVI photosystem II reaction center protein Psb28 photosystem II reaction center protein Psb28 Members of this protein family are the Psb28 protein of photosystem II. Two different protein families, apparently without homology between them, have been designated PsbW. Cyanobacterial proteins previously designated PsbW are members of the family described here. However, while members of the plant PsbW family are not found (so far) in Cyanobacteria, members of the present family do occur in plants. We therefore support the alternative designation that has emerged for this protein family, Psp28, rather than PsbW. TIGR03049.1 TIGR03049 PS_I_psaK 67.95 67.95 81 equivalog Y Y N photosystem I reaction center subunit PsaK psaK GO:0009522,GO:0009538,GO:0015979,GO:0042651 1117 Cyanobacteriota phylum 1191 JCVI photosystem I reaction center subunit PsaK photosystem I reaction center subunit PsaK Members of this protein family are the PsaK of the photosystem I reaction center. Photosystems I and II occur together in the same sets of organisms. Photosystem I uses light energy to transfer electrons from plastocyanin to ferredoxin, while photosystem II uses light energy to split water and releases molecular oxygen. TIGR03060.1 TIGR03060 PS_II_psb29 139.3 139.3 214 equivalog Y Y N photosystem II biogenesis protein Psp29 psb29 GO:0010207,GO:0015979 12069591,16155179,28808107 1117 Cyanobacteriota phylum 971 JCVI photosystem II biogenesis protein Psp29 photosystem II biogenesis protein Psp29 Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. Mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function. TIGR03279.1 TIGR03279 cyano_FeS_chp 574.7 574.7 433 hypoth_equivalog Y Y N TIGR03279 family radical SAM protein 1117 Cyanobacteriota phylum 1069 JCVI putative radical SAM enzyme, TIGR03279 family TIGR03279 family radical SAM protein Members of this protein family are predicted radical SAM enzymes of unknown function, apparently restricted to and universal across the Cyanobacteria. The high trusted cutoff score for this model, 700 bits, excludes homologs from other lineages. This exclusion seems justified because a significant number of sequence positions are simultaneously unique to and invariant across the Cyanobacteria, suggesting a specialized, conserved function, perhaps related to photosynthesis. A distantly related protein family, TIGR03278, universal in and restricted to archaeal methanogens, is the methyl coenzyme M reductase-arginine methyltransferase Mmp10. TIGR03678.1 TIGR03678 het_cyc_patell 39.6 39.6 34 subfamily_domain Y Y N microcyclamide/patellamide family RiPP 18245249 1117 Cyanobacteriota phylum 162 JCVI bacteriocin leader peptide, microcyclamide/patellamide family microcyclamide/patellamide family RiPP This model represents a conserved N-terminal region shared by microcyclamide and patellamide bacteriocins precursors. These RiPP (ribosomally translated, post-translationally modified peptide) precursors are associated with heterocyclization. Related precursors are found in family TIGR04446. TIGR03697.1 TIGR03697 NtcA_cyano 244.95 244.95 193 equivalog Y Y N global nitrogen regulator NtcA ntcA GO:0003677,GO:0003700,GO:0006355,GO:0006808 18805988,8366058 1117 Cyanobacteriota phylum 548 JCVI global nitrogen regulator NtcA global nitrogen regulator NtcA Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C. TIGR03985.1 TIGR03985 TIGR03985 60 60 249 hypoth_equivalog Y Y N TIGR03985 family CRISPR-associated protein 1117 Cyanobacteriota phylum 429 JCVI CRISPR-associated protein, TIGR03985 family TIGR03985 family CRISPR-associated protein Members of this protein family belong to CRISPR-associated (Cas) gene clusters. The majority of members are Cyanobacterial. TIGR04058.1 TIGR04058 AcACP_reductase 449.7 449.7 339 equivalog Y Y N long-chain acyl-[acyl-carrier-protein] reductase 1.2.1.80 GO:0016491,GO:0043447 20671186 1117 Cyanobacteriota phylum 859 JCVI long-chain fatty acyl-ACP reductase (aldehyde-forming) long-chain acyl-[acyl-carrier-protein] reductase This enzyme, found in cyanobacteria, reduces a long-chain (mainly C16 or C18) fatty acyl ACP ester to its corresponding fatty aldehyde, releasing the acyl carrier protein (ACP) [1]. NADPH or NADH is the reductant for this reaction. This enzyme may be distantly related to the short-chain dehydrogenase or reductase (SDR) family (PF00106). It performs the first step in a cyanobacterial-type pathway for alkane biosynthesis. TIGR04059.1 TIGR04059 Ald_deCOase 222.65 222.65 220 equivalog Y Y N aldehyde oxygenase (deformylating) 4.1.99.5 GO:0043447 20671186 1117 Cyanobacteriota phylum 876 JCVI long-chain fatty aldehyde decarbonylase aldehyde oxygenase (deformylating) This cyanobacterial family of fatty aldehyde decarbonylases acts on mainly C16 and C18 substrates to form hydrocarbons and carbon monoxide [1]. Note that the corresponding EC number (4.1.99.5) dating from 1989 refers to a nonorthologous Pisum sativum enzyme that acts on C18 and longer chains and attaches the overly narrow narrow name octadecanal decarbonylase. TIGR04156.1 TIGR04156 cyanoexo_CrtB 300 300 280 exception Y Y N cyanoexosortase B crtB 3.4.22.- GO:0004197,GO:0006605,GO:0016020,GO:0043687 22037399 1117 Cyanobacteriota phylum 605 JCVI cyanoexosortase B cyanoexosortase B This HMM describes a cyanobacterial-restricted form of exosortase, associated with a PEP-CTERM domain subclass described in model TIGR04155. This is one of two such cyanoexosortases, either of which is sufficient to accompany TIGR04155 family members. The other cyanoexosortase is TIGR03763 (crtA). TIGR04376.1 TIGR04376 TIGR04376 125 125 189 hypoth_equivalog Y Y N TIGR04376 family protein 1117 Cyanobacteriota phylum 733 JCVI TIGR04376 family protein TIGR04376 family protein Members of this protein family resemble TIGR04375 and, more distantly, to phage shock protein A (PspA). Members are restricted to the Cyanobacteria. TIGR04533.1 TIGR04533 cyanosortB_assc 65 65 221 hypoth_equivalog Y Y N cyanoexosortase B system-associated protein 1117 Cyanobacteriota phylum 609 JCVI cyanoexosortase B-associated protein cyanoexosortase B system-associated protein Members of this protein family are found exclusively in the Cyanobacteria, usually encoded next to a gene encoding cyanoexosortase B (TIGR04156). This relationship resembles the association of the unrelated protein family TIGR04153 with cyanoexosortase A (TIGR03763), and of most exosortases with EpsI. NF040408.4 PF19970.4 VMAP-M9 27 27 135 domain Y N N vWA-MoxR associated protein middle region (VMAP-M) 9 32101166 1125 Microcystis genus 60 EBI-EMBL vWA-MoxR associated protein middle region (VMAP-M) 9 vWA-MoxR associated protein middle region (VMAP-M) 9 Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. [1]. 32101166. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. Kaur G, Burroughs AM, Iyer LM, Aravind L;. Elife. 2020; [Epub ahead of print] (from Pfam) NF046676.1 PF22142.1 Hao_C 27 27 47 domain Y N N Hydroxylamine oxidoreductase, C-terminal domain 24302732,26249351,33798263 1127829 Candidatus Brocadiales order 12 EBI-EMBL Hydroxylamine oxidoreductase, C-terminal domain Hydroxylamine oxidoreductase, C-terminal domain This domain is found at the C-terminal end of Hydroxylamine oxidoreductase from Kuenenia stuttgartiensis (Hao, Swiss:Q1PX48) and similar bacterial sequences. This enzyme is responsible for the formation of NO from hydroxylamine in aerobic ammonium -oxidising bacteria. This domain shows a predominantly alpha -helical structure [1-3]. Paper describing PDB structure 4n4j. [1]. 24302732. Structural basis of biological NO generation by octaheme oxidoreductases. Maalcke WJ, Dietl A, Marritt SJ, Butt JN, Jetten MS, Keltjens JT, Barends TR, Kartal B;. J Biol Chem. 2014;289:1228-1242. Paper describing PDB structure 6t5e. [2]. 33798263. Purification of the key enzyme complexes of the anammox pathway from DEMON sludge. Akram M, Dietl A, Muller M, Barends TRM;. Biopolymers. 2021;112:e23428. [3]. 26249351. An unexpected reactivity of the P460 cofactor in hydroxylamine oxidoreductase. Dietl A, Maalcke W, Barends TR;. Acta Crystallogr D Biol Crystallogr. 2015;71:1708-1713. (from Pfam) NF003206.0 PRK04171 PRK04171.2-1 324 324 229 equivalog Y N N ribosome biogenesis protein 114380 Desulfurococcales order 14 NCBI Protein Cluster (PRK) ribosome biogenesis protein ribosome biogenesis protein NF003345.0 PRK04358 PRK04358.1-6 260 260 219 equivalog Y N N hypothetical protein 114380 Desulfurococcales order 12 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein TIGR04254.1 TIGR04254 OpituPEPCTERM_1 44 44 136 subfamily Y Y N putative globular PEP-CTERM protein 1148786 Geminisphaera colitermitum species 13 JCVI putative globular PEP-CTERM protein putative globular PEP-CTERM protein Representatives of this family include a 13-member paralogous family of proteins about 215 amino acids in length from the termite gut bacterium Opitutaceae bacterium TAV2, a member of the Verrucomicrobia. The signal peptide (N-terminal) and PEP-CTERM putative protein sorting signal (C-terminal) are not included in the seed alignment. Conserved residues such as an invariant Arg and a lack of conspicuous low-complexity sequence suggest a globular structure and possible enzymatic activity. Members average about thirty percent sequence identify overall, but over seventy percent in the PEP-CTERM region. The function of this family is unknown. NF040661.1 Osc7112_2153fam 50 50 75 equivalog Y Y N Osc7112_2153 family protein 1150 Oscillatoriales order 32 NCBIFAM Osc7112_2153 family protein This rare, small cyanobacterial protein, about 80 amino acids in length, has a signal peptide and a pair of invariant Cys residues that suggest disulfide bond formation. The protein regularly is found encoded just a few genes away from exosortase O (XrtO), but the significance of that finding is unclear. NF042906.1 Moor_cyan_RiPP 75 75 63 subfamily Y Y N cyanobactin class RiPP 1155738 Moorena genus 15 NCBIFAM cyanobactin class RiPP Members of this rather narrowly defined family are apparent RiPP (ribosomally synthesized and post-translationally modified peptide natural product) precursors, related in the leader peptide region at least to the family of microcyclamide/patellamide family RiPP precursors. Most members of this family have a PFAGDxxE motif at the C-terminus. Most members occur in the genus Moorena. NF001927.0 PRK00704 PRK00704.1-4 322 322 173 equivalog Y Y N photosystem I reaction center protein subunit XI 1161 Nostocales order 204 NCBI Protein Cluster (PRK) photosystem I reaction center protein subunit XI photosystem I reaction center protein subunit XI NF018815.5 PF07154.16 DUF1392 25 25 150 subfamily Y Y N DUF1392 family protein 1161 Nostocales order 658 EBI-EMBL Protein of unknown function (DUF1392) DUF1392 family protein This family consists of several hypothetical cyanobacterial proteins of around 150 residues in length which seem to be specific to Anabaena species. The function of this family is unknown. (from Pfam) NF039431.4 PF19958.4 EAD6 27 27 75 domain Y Y N EAD6 domain-containing conflict system protein 32101166,34061031 1161 Nostocales order 21 EBI-EMBL Effector-associated domain 6 effector-associated domain 6 Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating the EAD-EAD coupling approximates the advantages of collinear transcription. Profile-profile searches unify EAD6 with the Death superfamily of domains [2]. [1]. 32101166. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. Kaur G, Burroughs AM, Iyer LM, Aravind L;. Elife. 2020; [Epub ahead of print]. [2]. 34061031. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. Kaur G, Iyer LM, Burroughs AM, Aravind L;. Elife. 2021; [Epub ahead of print] (from Pfam) NF047415.1 heterocyst_PatS 30 30 13 equivalog Y Y N heterocyst-inhibiting signaling peptide PatS patS 28859320,29885033,32762845,33291589 1161 Nostocales order 7 NCBIFAM heterocyst-inhibiting signaling peptide PatS Reported examples of the cyanobacterial signaling PatS have lengths of 13 or 17 amino acids. PatS occurs in a subset of HetR-containing, heterocyst-forming species. The extreme shortness of this peptide, below 14 amino acids in length, means prokaryotic structural annotation (gene-finding) pipelines such as NCBI's PGAP may not report the feature. This HMM is provided for reference, but users should not that the absence of a reported feature in a genome does not guarantee that PatS in some form is not encoded. NF002920.0 PRK03537 PRK03537.2-1 470 470 314 equivalog Y Y N molybdate ABC transporter substrate-binding protein 1162 Nostocaceae family 81 NCBI Protein Cluster (PRK) molybdate ABC transporter periplasmic molybdate-binding protein molybdate ABC transporter substrate-binding protein NF016331.5 PF04435.23 SPK 22.1 22.1 104 domain Y Y N DUF545 domain-containing protein 1178825 Algibacter luteus species 1 EBI-EMBL Domain of unknown function (DUF545) Domain of unknown function (DUF545) Family of uncharacterised C. elegans proteins. The region represented by this family can is found to be repeated up to four time in some proteins. (from Pfam) NF022316.5 PF10860.13 DUF2661 23 23 113 domain Y Y N DUF2661 domain-containing protein 1181670 bacterium endosymbiont of Bathymodiolus sp. 5 South species 1 EBI-EMBL Protein of unknown function (DUF2661) Protein of unknown function (DUF2661) This viral family of proteins have no known function. (from Pfam) NF004686.0 PRK06030 PRK06030.1-1 148 148 151 equivalog Y N N hypothetical protein 118882 Brucellaceae family 109 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF000684.0 PRK00034 PRK00034.3-4 97 97 97 equivalog Y Y N Asp-tRNA(Asn) amidotransferase subunit GatC gatC 18279892 118883 Sulfolobaceae family 37 NCBI Protein Cluster (PRK) aspartyl/glutamyl-tRNA amidotransferase subunit C Asp-tRNA(Asn) amidotransferase subunit GatC NF000751.1 PRK00045 PRK00045.4-1 478 478 426 equivalog Y Y N glutamyl-tRNA reductase 1.2.1.70 118883 Sulfolobaceae family 12 NCBI Protein Cluster (PRK) glutamyl-tRNA reductase glutamyl-tRNA reductase NF000752.0 PRK00045 PRK00045.4-2 381 381 412 equivalog Y Y N glutamyl-tRNA reductase 1.2.1.70 118883 Sulfolobaceae family 47 NCBI Protein Cluster (PRK) glutamyl-tRNA reductase glutamyl-tRNA reductase NF001604.0 PRK00398 PRK00398.1-1 103 103 48 equivalog Y Y N DNA-directed RNA polymerase subunit P 2.7.7.6 118883 Sulfolobaceae family 23 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit P DNA-directed RNA polymerase subunit P NF001644.0 PRK00420 PRK00420.1-1 176 176 119 equivalog Y N N hypothetical protein 118883 Sulfolobaceae family 34 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF001665.0 PRK00431 PRK00431.2-1 315 315 177 equivalog Y Y N ADP-ribose-binding protein 118883 Sulfolobaceae family 13 NCBI Protein Cluster (PRK) RNase III inhibitor ADP-ribose-binding protein NF001668.0 PRK00431 PRK00431.2-4 278 278 220 equivalog Y Y N ADP-ribose-binding protein 118883 Sulfolobaceae family 28 NCBI Protein Cluster (PRK) RNase III inhibitor ADP-ribose-binding protein NF002209.0 PRK01099 PRK01099.1-4 93 93 87 equivalog Y Y N DNA-directed RNA polymerase subunit K 2.7.7.6 118883 Sulfolobaceae family 37 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit K DNA-directed RNA polymerase subunit K NF002220.0 PRK01115 PRK01115.1-3 284 284 246 subfamily Y Y N DNA polymerase sliding clamp 118883 Sulfolobaceae family 79 NCBI Protein Cluster (PRK) DNA polymerase sliding clamp DNA polymerase sliding clamp NF003070.0 PRK03995 PRK03995.1-1 352 352 237 equivalog Y Y N D-aminoacyl-tRNA deacylase 118883 Sulfolobaceae family 36 NCBI Protein Cluster (PRK) hypothetical protein D-aminoacyl-tRNA deacylase NF003202.0 PRK04169 PRK04169.1-6 353 353 254 equivalog Y Y N geranylgeranylglyceryl/heptaprenylglyceryl phosphate synthase 118883 Sulfolobaceae family 38 NCBI Protein Cluster (PRK) geranylgeranylglyceryl phosphate synthase-like protein geranylgeranylglyceryl/heptaprenylglyceryl phosphate synthase NF003203.0 PRK04171 PRK04171.1-1 310 310 223 equivalog Y N N ribosome biogenesis protein 118883 Sulfolobaceae family 37 NCBI Protein Cluster (PRK) ribosome biogenesis protein ribosome biogenesis protein NF003226.0 PRK04195 PRK04195.1-1 588 588 405 equivalog Y Y N replication factor C large subunit 118883 Sulfolobaceae family 45 NCBI Protein Cluster (PRK) replication factor C large subunit replication factor C large subunit NF003331.0 PRK04338 PRK04338.1-7 560 560 376 equivalog Y Y N tRNA (guanine(26)-N(2))-dimethyltransferase 2.1.1.216 118883 Sulfolobaceae family 37 NCBI Protein Cluster (PRK) N(2),N(2)-dimethylguanosine tRNA methyltransferase tRNA (guanine(26)-N(2))-dimethyltransferase NF003370.0 PRK04447 PRK04447.1-3 687 687 347 equivalog Y N N hypothetical protein 118883 Sulfolobaceae family 12 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004415.0 PRK05761 PRK05761.1-1 1289 1289 883 equivalog Y Y N DNA-directed DNA polymerase I 2.7.7.7 118883 Sulfolobaceae family 50 NCBI Protein Cluster (PRK) DNA polymerase I DNA-directed DNA polymerase I NF004433.0 PRK05771 PRK05771.3-2 1173 1173 701 equivalog Y Y N V-type ATP synthase subunit I 7.1.2.2 118883 Sulfolobaceae family 15 NCBI Protein Cluster (PRK) V-type ATP synthase subunit I V-type ATP synthase subunit I NF004435.0 PRK05771 PRK05771.3-4 1410 1410 701 equivalog Y Y N V-type ATP synthase subunit I 7.1.2.2 118883 Sulfolobaceae family 11 NCBI Protein Cluster (PRK) V-type ATP synthase subunit I V-type ATP synthase subunit I NF004726.0 PRK06073 PRK06073.1-1 150 150 129 equivalog Y N N NADH dehydrogenase subunit A 118883 Sulfolobaceae family 45 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit A NADH dehydrogenase subunit A NF004728.0 PRK06073 PRK06073.1-4 124 124 129 equivalog Y N N NADH dehydrogenase subunit A 118883 Sulfolobaceae family 46 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit A NADH dehydrogenase subunit A NF004734.0 PRK06074 PRK06074.2-1 169 169 164 equivalog Y Y N NADH-quinone oxidoreductase subunit C 1.6.5.9 118883 Sulfolobaceae family 47 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit C NADH-quinone oxidoreductase subunit C NF005048.0 PRK06461 PRK06461.1-1 230 230 148 equivalog Y N N single-stranded DNA-binding protein 118883 Sulfolobaceae family 9 NCBI Protein Cluster (PRK) single-stranded DNA-binding protein single-stranded DNA-binding protein NF005051.0 PRK06461 PRK06461.1-5 235 235 146 equivalog Y N N single-stranded DNA-binding protein 118883 Sulfolobaceae family 14 NCBI Protein Cluster (PRK) single-stranded DNA-binding protein single-stranded DNA-binding protein NF005327.0 PRK06853 PRK06853.2-1 242 242 194 equivalog Y Y N indolepyruvate oxidoreductase subunit beta 118883 Sulfolobaceae family 14 NCBI Protein Cluster (PRK) indolepyruvate oxidoreductase subunit beta indolepyruvate oxidoreductase subunit beta NF006348.0 PRK08575 PRK08575.1-1 386 386 328 equivalog Y N N 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 118883 Sulfolobaceae family 13 NCBI Protein Cluster (PRK) 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase NF006349.0 PRK08575 PRK08575.1-2 322 322 323 equivalog Y N N 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 118883 Sulfolobaceae family 53 NCBI Protein Cluster (PRK) 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase NF006401.0 PRK08651 PRK08651.1-4 381 381 376 equivalog Y N N succinyl-diaminopimelate desuccinylase 118883 Sulfolobaceae family 21 NCBI Protein Cluster (PRK) succinyl-diaminopimelate desuccinylase succinyl-diaminopimelate desuccinylase NF006812.0 PRK09334 PRK09334.1-2 171 171 109 equivalog Y Y N 30S ribosomal protein S25e 118883 Sulfolobaceae family 13 NCBI Protein Cluster (PRK) 30S ribosomal protein S25e 30S ribosomal protein S25e NF006814.0 PRK09334 PRK09334.1-4 128 128 110 equivalog Y Y N 30S ribosomal protein S25e 118883 Sulfolobaceae family 14 NCBI Protein Cluster (PRK) 30S ribosomal protein S25e 30S ribosomal protein S25e NF006906.0 PRK09400 PRK09400.1-1 95 95 62 equivalog Y N N preprotein translocase subunit SecE 118883 Sulfolobaceae family 25 NCBI Protein Cluster (PRK) preprotein translocase subunit SecE preprotein translocase subunit SecE NF007084.0 PRK09539 PRK09539.1-1 162 162 140 equivalog Y N N tRNA-splicing endonuclease subunit beta 118883 Sulfolobaceae family 10 NCBI Protein Cluster (PRK) tRNA-splicing endonuclease subunit beta tRNA-splicing endonuclease subunit beta NF007086.0 PRK09539 PRK09539.1-3 101 101 92 equivalog Y N N tRNA-splicing endonuclease subunit beta 118883 Sulfolobaceae family 8 NCBI Protein Cluster (PRK) tRNA-splicing endonuclease subunit beta tRNA-splicing endonuclease subunit beta NF007127.0 PRK09568 PRK09568.1 378 378 306 equivalog Y Y N DNA primase regulatory subunit PriL priL 118883 Sulfolobaceae family 20 NCBI Protein Cluster (PRK) DNA primase large subunit DNA primase regulatory subunit PriL NF009627.0 PRK13149 PRK13149.1-1 106 106 90 equivalog Y N N H/ACA RNA-protein complex component Gar1 118883 Sulfolobaceae family 25 NCBI Protein Cluster (PRK) H/ACA RNA-protein complex component Gar1 H/ACA RNA-protein complex component Gar1 NF009672.0 PRK13193 PRK13193.1 271 271 209 equivalog Y Y N pyroglutamyl-peptidase I 118883 Sulfolobaceae family 13 NCBI Protein Cluster (PRK) pyrrolidone-carboxylate peptidase pyroglutamyl-peptidase I NF009778.0 PRK13278 PRK13278.1-1 570 570 356 equivalog Y Y N formate--phosphoribosylaminoimidazolecarboxamide ligase 6.3.4.23 118883 Sulfolobaceae family 44 NCBI Protein Cluster (PRK) 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase formate--phosphoribosylaminoimidazolecarboxamide ligase NF010089.0 PRK13574 PRK13574.1 527 527 421 equivalog Y Y N anthranilate synthase component I 118883 Sulfolobaceae family 43 NCBI Protein Cluster (PRK) anthranilate synthase component I anthranilate synthase component I With component II catalyzes the formation of anthranilate and glutamate from chorismate and glutamine NF010091.0 PRK13576 PRK13576.1 263 263 216 equivalog Y Y N type I 3-dehydroquinate dehydratase 4.2.1.10 118883 Sulfolobaceae family 29 NCBI Protein Cluster (PRK) 3-dehydroquinate dehydratase type I 3-dehydroquinate dehydratase Catalyzes the dehydration of 3-dehydroquinate to form 3-dehydroshikimate in aromatic amino acid biosynthesis NF010113.0 PRK13586 PRK13586.1 238 238 232 equivalog Y Y N 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase hisA 118883 Sulfolobaceae family 46 NCBI Protein Cluster (PRK) 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase Catalyzes the formation of 5-(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino-l-(5-hosphoribosyl)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide NF010121.0 PRK13598 PRK13598.1 295 295 193 equivalog Y Y N imidazoleglycerol-phosphate dehydratase hisBd 4.2.1.19 9209067 118883 Sulfolobaceae family 41 NCBI Protein Cluster (PRK) imidazoleglycerol-phosphate dehydratase imidazoleglycerol-phosphate dehydratase Catalyzes the dehydration of D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate to 3-(imidazol-4-yl)-2-oxopropyl phosphate in histidine biosynthesis NF010251.0 PRK13696 PRK13696.1-3 101 101 84 equivalog Y N N hypothetical protein 118883 Sulfolobaceae family 26 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010326.0 PRK13763 PRK13763.1-1 247 247 186 equivalog Y N N putative RNA-processing protein 118883 Sulfolobaceae family 43 NCBI Protein Cluster (PRK) putative RNA-processing protein putative RNA-processing protein NF010342.0 PRK13768 PRK13768.1-5 414 414 255 equivalog Y N N GTPase 118883 Sulfolobaceae family 37 NCBI Protein Cluster (PRK) GTPase GTPase NF010840.0 PRK14246 PRK14246.1 425 425 257 equivalog Y N N phosphate ABC transporter ATP-binding protein 118883 Sulfolobaceae family 7 NCBI Protein Cluster (PRK) phosphate ABC transporter ATP-binding protein phosphate ABC transporter ATP-binding protein NF011067.0 PRK14497 PRK14497.1 536 536 546 equivalog Y N N putative molybdopterin biosynthesis protein MoeA/unknown domain fusion protein 118883 Sulfolobaceae family 50 NCBI Protein Cluster (PRK) putative molybdopterin biosynthesis protein MoeA/unknown domain fusion protein putative molybdopterin biosynthesis protein MoeA/unknown domain fusion protein NF011139.0 PRK14554 PRK14554.1-5 428 428 360 equivalog Y Y N pseudouridylate synthase 4.2.1.70 118883 Sulfolobaceae family 43 NCBI Protein Cluster (PRK) putative pseudouridylate synthase pseudouridylate synthase NF011144.0 PRK14555 PRK14555.2-2 281 281 149 equivalog Y Y N RNA-binding protein 118883 Sulfolobaceae family 6 NCBI Protein Cluster (PRK) hypothetical protein RNA-binding protein NF011150.0 PRK14560 PRK14560.1-1 217 217 155 equivalog Y N N putative RNA-binding protein 118883 Sulfolobaceae family 35 NCBI Protein Cluster (PRK) putative RNA-binding protein putative RNA-binding protein NF011156.0 PRK14562 PRK14562.1-1 308 308 200 equivalog Y N N haloacid dehalogenase superfamily protein 118883 Sulfolobaceae family 39 NCBI Protein Cluster (PRK) haloacid dehalogenase superfamily protein haloacid dehalogenase superfamily protein NF011479.0 PRK14889 PRK14889.1-2 264 264 145 equivalog Y N N VKOR family protein 118883 Sulfolobaceae family 5 NCBI Protein Cluster (PRK) VKOR family protein VKOR family protein NF011489.0 PRK14896 PRK14896.1-5 236 236 217 equivalog Y Y N 16S ribosomal RNA methyltransferase A 118883 Sulfolobaceae family 43 NCBI Protein Cluster (PRK) 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein 16S ribosomal RNA methyltransferase A NF011500.0 PRK14938 PRK14938.1 362 362 387 equivalog Y N N Ser-tRNA(Thr) hydrolase 118883 Sulfolobaceae family 50 NCBI Protein Cluster (PRK) Ser-tRNA(Thr) hydrolase Ser-tRNA(Thr) hydrolase NF011528.0 PRK14968 PRK14968.1-2 171 171 205 equivalog Y N N putative methyltransferase 118883 Sulfolobaceae family 47 NCBI Protein Cluster (PRK) putative methyltransferase putative methyltransferase NF011549.0 PRK14980 PRK14980.1 167 167 127 equivalog Y Y N DNA-directed RNA polymerase subunit G 2.7.7.6 118883 Sulfolobaceae family 22 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit G DNA-directed RNA polymerase subunit G NF011553.0 PRK14981 PRK14981.1-5 152 152 113 equivalog Y Y N DNA-directed RNA polymerase subunit F 2.7.7.6 118883 Sulfolobaceae family 28 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit F DNA-directed RNA polymerase subunit F NF014361.5 PF02294.23 7kD_DNA_binding 25 25 58 domain Y N N 7kD DNA-binding domain GO:0003677,GO:0004521 3130377 118883 Sulfolobaceae family 55 EBI-EMBL 7kD DNA-binding domain 7kD DNA-binding domain This family contains members of the hyper-thermophilic archaebacterium 7kD DNA-binding/endoribonuclease P2 family. There are five 7kD DNA-binding proteins, 7a-7e, found as monomers in the cell. Protein 7e shows the tightest DNA-binding ability. [1]. 3130377. Microsequence analysis of DNA-binding proteins 7a, 7b, and 7e from the archaebacterium Sulfolobus acidocaldarius. Choli T, Wittmann-Liebold B, Reinhardt R;. J Biol Chem 1988;263:7087-7093. (from Pfam) NF018036.5 PF06281.17 VP1_VP3 25 25 73 domain Y Y N VP1/VP3 family protein GO:0005198,GO:0016020 1926776 118883 Sulfolobaceae family 32 EBI-EMBL Structural protein VP1/VP3 VP1/VP3 family protein This family consists of Structural proteins VP1 and VP3 from Sulfolobus spindle-shape virus 1 (SSV1), two of the three structural proteins [1]. [1]. 1926776. Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobus shibatae. Palm P, Schleper C, Grampp B, Yeats S, McWilliam P, Reiter WD, Zillig W;. Virology 1991;185:242-250. (from Pfam) NF019723.5 PF08112.16 ATP-synt_E_2 25 25 56 PfamEq Y N N ATP synthase epsilon subunit GO:0015986,GO:0033178,GO:0042626 12231816 118883 Sulfolobaceae family 28 EBI-EMBL ATP synthase epsilon subunit ATP synthase epsilon subunit This family consists of epsilon subunits of the ATP synthase. The ATP synthase complex is composed of an oligomeric transmembrane sector (CF0), and a catalytic core (CF1). CF1 is composed of 5 subunits, of which the epsilon subunit functions as a potent inhibitor of ATPase activity in both soluble and bound CF1. Only when the epsilon inhibition is disabled is high ATPase activity detected in ATPase [1] [1]. 12231816. Aspects of Subunit Interactions in the Chloroplast ATP Synthase (II. Characterization of a Chloroplast Coupling Factor 1-Subunit III Complex from Spinach Thylakoids). Wetzel CM, McCarty RE;. Plant Physiol 1993;102:251-259. (from Pfam) NF020758.5 PF09196.15 DUF1953 25 25 63 domain Y Y N DUF1953 domain-containing protein 118883 Sulfolobaceae family 10 EBI-EMBL Domain of unknown function (DUF1953) Domain of unknown function (DUF1953) This domain is found in the Archaeal protein maltooligosyl trehalose synthase produced by Sulfolobus spp. Its function has not, as yet, been defined. (from Pfam) NF025573.5 PF14210.11 DUF4322 27 27 66 domain Y Y N DUF4322 domain-containing protein 118883 Sulfolobaceae family 195 EBI-EMBL Domain of unknown function (DUF4322) Domain of unknown function (DUF4322) This presumed domain is functionally uncharacterised. This domain family is found in archaea, and is approximately 60 amino acids in length. There is a conserved QTV sequence motif. (from Pfam) NF033588.1 transpos_ISC774 200 200 195 exception Y Y N IS6 family transposase GO:0004803 118883 Sulfolobaceae family 101 NCBIFAM IS6 family transposase IS6 family transposase ISC774 is an example of an outlier clade of IS6 family insertion sequences. Members so are appear restricted to the archaeal genus Sulfolobus. NF036387.5 PF17615.7 C166 36.7 36.7 171 PfamEq Y Y N C166 family protein 118883 Sulfolobaceae family 16 EBI-EMBL Family of unknown function C166 family protein Family members found in Fuselloviridae are predicted to play a role in virus function. (from Pfam) NF036677.5 PF17597.7 DUF5493 27 27 82 subfamily Y Y N DUF5493 family protein 118883 Sulfolobaceae family 15 EBI-EMBL Family of unknown function (DUF5493) DUF5493 family protein This is a family of unknown function found in viruses. (from Pfam) NF037597.5 PF17623.7 B277 27 27 277 PfamEq Y Y N B277 family protein 10430570 118883 Sulfolobaceae family 16 EBI-EMBL Domain of unknown function B277 family protein The founding member of this family, protein B277 from archaeal virus SSV1, is uncharacterized. NF037768.5 PF18249.6 Ca_bind_SSO6904 25 25 90 domain Y N N Calcium binding protein SSO6904 19768683 118883 Sulfolobaceae family 35 EBI-EMBL Calcium binding protein SSO6904 Calcium binding protein SSO6904 This domain is SSO6904 present in Sulfolobus solfataricus. SSO6904 is a calcium binding protein thought to have a weak affinity for other cations such as Mg2+ and Zn2+. The structure of SSO6904 is similar to that of saposin-fold proteins. Saposin proteins are membrane-interacting glycoproteins required for the hydrolysis of certain sphingolipids by specific lysosomal hydrolases [1]. [1]. 19768683. Solution structure and calcium binding of protein SSO6904 from the hyperthermophilic archaeon Sulfolobus solfataricus. Feng Y, Yao H, Wang J;. Proteins. 2010;78:474-479. (from Pfam) NF039523.4 PF19025.5 DUF5751 27 27 116 subfamily Y Y N DUF5751 family protein 118883 Sulfolobaceae family 53 EBI-EMBL Family of unknown function (DUF5751) DUF5751 family protein The function of this archaeal family is unknown. (from Pfam) NF040176.4 PF19021.5 Cmr7A 27 27 197 PfamEq Y Y N type III-B CRISPR system CMR subunit Cmr7 GO:0051607,GO:0099048 22227115 118883 Sulfolobaceae family 19 EBI-EMBL CRISPR system CMR subunit Cmr7 1 type III-B CRISPR system CMR subunit Cmr7 The CRISPR-Cas system is a prokaryotic defense mechanism against foreign genetic elements. The key elements of this defense system are the Cas proteins and the CRISPR RNA. In the CRISPR-Cas system, RNA is targeted by the CMR complex. In Sulfolobus solfataricus this complex is composed of seven CAS protein subunits (Cmr1-7) and carries a diverse "payload" of targeting crRNA. This entry represent the Cmr7 subunit of the CMR complex [1]. [1]. 22227115. Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity. Zhang J, Rouillon C, Kerou M, Reeks J, Brugger K, Graham S, Reimann J, Cannone G, Liu H, Albers SV, Naismith JH, Spagnolo L, White MF;. Mol Cell. 2012;45:303-313. (from Pfam) NF040581.1 cas_Crn1 125 125 178 equivalog Y Y N CRISPR-associated ring nuclease Crn1 crn1 30232454 118883 Sulfolobaceae family 67 NCBIFAM CRISPR-associated ring nuclease Crn1 Ring nucleases cleave second messengers such as cyclic oligoadenylate produced by type III CRISPR system effectors, in order to provide an off-switch for the regulation of CRISPR activity. This family of ring nuclease, which includes Sso2081 from Sulfolobus solfataricus, is designated Crn1. NF040595.1 HTH_Cbp1 140 140 135 equivalog Y Y N CRISPR DNA repeat-binding protein Cbp1 cbp1 12670964,22139923 118883 Sulfolobaceae family 41 NCBIFAM CRISPR DNA repeat-binding protein Cbp1 NF040787.1 S-lay_SlaA_Mtsph 170 170 1357 equivalog Y Y N S-layer protein SlaA slaA 19522740 118883 Sulfolobaceae family 31 NCBIFAM S-layer protein SlaA NF040866.1 AraD_Arch 650 650 372 equivalog Y Y N arabinonate dehydratase araD 4.2.1.5 GO:0019571,GO:0047675 16849334 118883 Sulfolobaceae family 23 NCBIFAM arabinonate dehydratase NF040935.1 helicase_Hel308 1200 1200 704 equivalog Y Y N ATP-dependent DNA helicase Hel308 hel308 3.6.4.12 GO:0003678,GO:0005524,GO:0006281 18056710,37409572 118883 Sulfolobaceae family 50 NCBIFAM ATP-dependent DNA helicase Hel308 NF040936.1 hexpp_archaea 400 400 275 equivalog Y Y N hexaprenyl pyrophosphate synthase gdS-2 2.5.1.82 GO:0008299,GO:0052922 11790729,16291686 118883 Sulfolobaceae family 40 NCBIFAM hexaprenyl pyrophosphate synthase NF040937.1 HerA_Thermprot 800 800 487 equivalog Y Y N DNA double-strand break repair helicase HerA herA 3.6.4.12 GO:0003678,GO:0006281,GO:0016887 22135300,25420454 118883 Sulfolobaceae family 50 NCBIFAM DNA double-strand break repair helicase HerA NF040951.1 CRSPR_nucase 600 600 322 equivalog Y Y N CRISPR system ring nuclease 4.6.1.- GO:0016829,GO:0051607 30232454 118883 Sulfolobaceae family 9 NCBIFAM CRISPR system ring nuclease NF040956.1 Arch_Xpf_endonucase 300 300 222 equivalog Y Y N 3'-flap repair endonuclease Xpf xpf GO:0004519,GO:0006281,GO:0006310 12675797 118883 Sulfolobaceae family 40 NCBIFAM 3'-flap repair endonuclease Xpf NF040957.1 Arch_PMK 500 500 316 equivalog Y Y N phosphomevalonate kinase 2.7.4.2 GO:0004631,GO:0010142,GO:0019287 23378249 118883 Sulfolobaceae family 38 NCBIFAM phosphomevalonate kinase NF041003.1 GGPP_syn 500 500 326 equivalog Y Y N geranylgeranyl diphosphate synthase gds 2.5.1.29 GO:0004311,GO:0033386,GO:0046872 8182085 118883 Sulfolobaceae family 48 NCBIFAM geranylgeranyl diphosphate synthase NF041005.1 cell_div_CdvB1_B2 350 350 212 equivalog Y Y N cell division protein CdvB1/B2 cdvB1/B2 GO:0051301 19008417,24399085 118883 Sulfolobaceae family 80 NCBIFAM cell division protein CdvB1/B2 NF041007.1 cell_div_CdvA 350 350 235 equivalog Y Y N cell division protein CdvA cdvA GO:0051301 18987308,21255729 118883 Sulfolobaceae family 42 NCBIFAM cell division protein CdvA NF041008.1 cell_div_CdvB 370 370 260 equivalog Y Y N cell division protein CdvB cdvB GO:0051301 18987308,19008417,21255729 118883 Sulfolobaceae family 34 NCBIFAM cell division protein CdvB NF041009.1 cell_div_CdvB3 170 170 164 equivalog Y Y N cell division protein CdvB3 cdvB3 GO:0051301 24399085 118883 Sulfolobaceae family 39 NCBIFAM cell division protein CdvB3 NF041010.1 glycosy_Agl16 575 575 352 equivalog Y Y N glycosylation protein Agl16 agl16 2.4.1.- GO:0006486,GO:0016757 23475978 118883 Sulfolobaceae family 10 NCBIFAM glycosylation protein Agl16 NF041016.1 trans_reg_ArnR 400 400 269 equivalog Y Y N HTH-type transcriptional activator ArnR arnR GO:0003700 23461567,27731916 118883 Sulfolobaceae family 31 NCBIFAM HTH-type transcriptional activator ArnR NF041017.1 DNA_import_CedB 700 700 590 equivalog Y Y N DNA import protein CedB cedB GO:0005524 26884154 118883 Sulfolobaceae family 49 NCBIFAM DNA import protein CedB NF041031.1 Mre11_Sulfo 500 500 374 equivalog Y Y N DNA double-strand break repair protein Mre11 mre11 GO:0006302,GO:0008408,GO:0045027 18294364 118883 Sulfolobaceae family 44 NCBIFAM DNA double-strand break repair protein Mre11 NF041033.1 NurA_Sulf 400 400 331 equivalog Y Y N DNA double-strand break repair nuclease NurA nurA GO:0004519,GO:0004527,GO:0006281 12052775,18194801,25447518 118883 Sulfolobaceae family 46 NCBIFAM DNA double-strand break repair nuclease NurA NF041034.1 Rad50_Sulf 1000 1000 872 equivalog Y Y N DNA double-strand break repair ATPase Rad50 rad50 GO:0005524,GO:0006302,GO:0016887 18294364 118883 Sulfolobaceae family 16 NCBIFAM DNA double-strand break repair ATPase Rad50 NF041073.1 S-lay_SlaA_Sulfolob 2300 2300 1462 equivalog Y Y N S-layer protein SlaA slaA GO:0030115 16391651,20936123 118883 Sulfolobaceae family 5 NCBIFAM S-layer protein SlaA NF041074.2 quin_ox_SoxA 110 110 154 equivalog Y Y N proton pump complex quinol oxidase subunit SoxA soxA 1.10.3.- GO:0004129,GO:0016682,GO:0042773 1372250,7984110,9079667 118883 Sulfolobaceae family 60 NCBIFAM proton pump complex quinol oxidase subunit SoxA NF041075.1 quin_ox_SoxB 700 700 468 equivalog Y Y N proton pump complex quinol oxidase subunit SoxB soxB 1.10.3.- GO:0004129,GO:0016682,GO:0042773 1372250,7984110,9079667 118883 Sulfolobaceae family 69 NCBIFAM proton pump complex quinol oxidase subunit SoxB NF041076.1 cyt_b_SoxC 740 740 542 equivalog Y Y N proton pump complex cytochrome B SoxC soxC GO:0009055,GO:0022904,GO:0046872 1372250,7984110,9079667 118883 Sulfolobaceae family 91 NCBIFAM proton pump complex cytochrome B SoxC NF041077.1 tRNAmeth_TrmJ_Sulfolob 350 350 229 equivalog Y Y N tRNA (cytidine-2'-O-)-methyltransferase TrmJ trmJ 2.1.1.- GO:0003723,GO:0008033,GO:0008173 24951554 118883 Sulfolobaceae family 41 NCBIFAM tRNA (cytidine-2'-O-)-methyltransferase TrmJ NF041084.1 trehalase_H1_Arch 820 820 570 equivalog Y Y N alpha,alpha-trehalase TreH1 treH1 3.2.1.28 GO:0004555,GO:0005993 29574614,29642287 118883 Sulfolobaceae family 104 NCBIFAM alpha,alpha-trehalase TreH1 NF041085.1 trehalase_H2_Arch 1000 1000 579 equivalog Y Y N alpha,alpha-trehalase TreH2 treH2 3.2.1.28 GO:0004555,GO:0005993 29574614 118883 Sulfolobaceae family 40 NCBIFAM alpha,alpha-trehalase TreH2 NF041173.1 Sug_nt_acttase_Thmprot 600 600 405 equivalog Y Y N bifunctional sugar-1-phosphate nucleotidylyltransferase/acetyltransferase spn 2.3.1.-,2.7.7.- GO:0003977,GO:0003983,GO:0006048,GO:0008879,GO:0019134,GO:0052630 15598657,20400541 118883 Sulfolobaceae family 44 NCBIFAM bifunctional sugar-1-phosphate nucleotidylyltransferase/acetyltransferase NF041176.1 GlyK_Thmprot 550 550 397 equivalog Y Y N glycerate 2-kinase 2.7.1.165 GO:0016310,GO:0043798 19690808 118883 Sulfolobaceae family 46 NCBIFAM glycerate 2-kinase NF041177.1 Cyp119_Thmprot 680 680 368 equivalog Y Y N cytochrome P450 Cyp119 cyp119 1.14.-.- GO:0005506,GO:0016705,GO:0020037 15219985 118883 Sulfolobaceae family 7 NCBIFAM cytochrome P450 Cyp119 NF041178.1 TQO_small_DoxA 300 300 165 equivalog Y Y N thiosulfate:quinone oxidoreductase small subunit doxA 1.8.5.2 GO:0043831,GO:0048038 15306018 118883 Sulfolobaceae family 24 NCBIFAM thiosulfate:quinone oxidoreductase small subunit NF041793.1 ORF56 50 50 39 equivalog Y Y N ORF56 family plasmid copy control protein GO:0003677,GO:0006355 11160922,19788170 118883 Sulfolobaceae family 4 NCBIFAM ORF56 family plasmid copy control protein NF041796.1 Ced_CedA 250 250 256 equivalog Y Y N DNA import protein CedA cedA GO:0009290 26884154,36750723 118883 Sulfolobaceae family 65 NCBIFAM DNA import protein CedA NF041798.1 Ced_CedA2 80 80 50 equivalog Y Y N Ced DNA import system-associated protein CedA2 cedA2 26884154,36750723 118883 Sulfolobaceae family 5 NCBIFAM Ced DNA import system-associated protein CedA2 NF045491.1 LysJ_Sulfobales 700 700 386 equivalog Y Y N [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase lysJ 2.6.1.118,2.6.1.124 GO:0008483,GO:0019878,GO:0042450 12042311,23434852 118883 Sulfolobaceae family 49 NCBIFAM [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase NF045555.1 Sul7d 100 100 61 equivalog Y Y N Sul7d family chromatin protein sul7d GO:0000785,GO:0003677 27853299,32518188 118883 Sulfolobaceae family 54 NCBIFAM Sul7d family chromatin protein NF045910.1 Sul7s 100 100 56 equivalog Y Y N winged-helix single-stranded DNA-binding protein Sul7s sul7s GO:0003697 35408816 118883 Sulfolobaceae family 16 NCBIFAM winged-helix single-stranded DNA-binding protein Sul7s Proteins of this family are highly conserved in Sulfolobaceae. Sul7s belongs to the winged helix DNA-binding superfamily protein. It consists of three alpha-helices, three beta-strands, and two short wings. It has been shown that Sul7s interacts with single-stranded via a large positively charged binding surface, presumably resulting in ssDNA deformation. NF046072.1 UpsX 550 550 641 equivalog Y Y N protein UpsX upsX 24106028 118883 Sulfolobaceae family 56 NCBIFAM protein UpsX Proteins of this family are encoded by the archaeal upsX gene on the UV-inducible pili operon (ups operon), which is involved in UV-induced pili assembly, cellular aggregation, and subsequent DNA exchange between cells. UspX is not structurally essential for UV-induced pili formation and cellular aggregation, but appears to be important for efficient DNA transfer. NF046073.1 UpsA 130 130 136 equivalog Y Y N pilin subunit UpsA upsA GO:0009289 24106028 118883 Sulfolobaceae family 34 NCBIFAM pilin subunit UpsA Proteins of this family are encoded by the archaeal upsA gene on the UV-inducible pili operon (ups operon), which is involved in UV-induced pili assembly, cellular aggregation, and subsequent DNA exchange between cells. UpsA and UpsB are major pilin subunits in the ups pili. NF046074.1 UpsB 70 70 126 equivalog Y Y N pilin subunit UpsB upsB GO:0009289 24106028 118883 Sulfolobaceae family 35 NCBIFAM pilin subunit UpsB Proteins of this family are encoded by the archaeal upsB gene on the UV-inducible pili operon (ups operon), which is involved in UV-induced pili assembly, cellular aggregation, and subsequent DNA exchange between cells. UpsA and UpsB are major pilin subunits in the ups pili. NF046258.1 PF22392.1 Cmr7b-like 26 26 184 domain Y N N Cmr7b-like, BtrG-like domain 22227115 118883 Sulfolobaceae family 16 EBI-EMBL Cmr7b-like, BtrG-like domain Cmr7b-like, BtrG-like domain This entry represents a BtrG-like domain present in Cmr7b protein from Sulfolobus solfataricus. Cmr7b is involved in the CRISPR/Cas pathway [1]. CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). Paper describing PDB structure 2xvo. [1]. 22227115. Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity. Zhang J, Rouillon C, Kerou M, Reeks J, Brugger K, Graham S, Reimann J, Cannone G, Liu H, Albers SV, Naismith JH, Spagnolo L, White MF;. Mol Cell. 2012;45:303-313. (from Pfam) NF046281.1 PF22445.1 Ssol_1539-like_2nd 27 27 45 domain Y N N Ssol_1539-like, second domain 26339031 118883 Sulfolobaceae family 24 EBI-EMBL Ssol_1539-like, second domain Ssol_1539-like, second domain This domain is found in Ssol_1539 from Saccharolobus solfataricus and similar archaeal sequences. Ssol_1539 is organised into two domains. The N-terminal domain contains two subdomains separated by a central helix. This entry represents the second subdomain, which shows an all-alpha configuration [1]. Paper describing PDB structure 5k5a. [1]. 26339031. Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages. Schumacher MA, Tonthat NK, Lee J, Rodriguez-Castaneda FA, Chinnam NB, Kalliomaa-Sanford AK, Ng IW, Barge MT, Shaw PL, Barilla D;. Science. 2015;349:1120-1124. (from Pfam) NF046389.1 PF22852.1 SoxE_N 27 27 48 domain Y N N Sulfocyanin, N-terminal 118883 Sulfolobaceae family 33 EBI-EMBL Sulfocyanin, N-terminal Sulfocyanin, N-terminal This domain is found at the N-terminal end of Sulfocyanin from Sulfolobus acidocaldarius (SoxE) and similar archaeal sequences. SoxE is a blue copper protein involved in in electron transfer reactions. This region is predicted to fold into an alpha-helix. (from Pfam) NF046529.1 PF21873.1 Thioredoxin_17 24.8 24.8 80 domain Y N N Thioredoxin-like domain 24306780 118883 Sulfolobaceae family 45 EBI-EMBL Thioredoxin-like domain Thioredoxin-like domain This entry represents an N-terminal thioredoxin domain, which is a non-canonical thioredoxin fold-containing structural unit present in Sso1120, a protein disulfide oxidoreductase (PDO) from the hyperthermophilic archaeon Sulfolobus solfataricus. This domain is composed of four beta-strands and three alpha-helices, with a well-defined disulfide bond between Cys24 and Cys45. The domain does not contain any active site but is part of the larger structure that comprises the C-terminal unit with the CTKC active site motif. The N-terminal domain shows unexpected similarity with the N-terminal domain of the alkyl hydroperoxide reductase F component from Salmonella typhimurium, and a possible involvement of this atypical PDO in a new antioxidant system of S. solfataricus has been proposed. Paper describing PDB structure 4mnn. [1]. 24306780. Sulfolobus solfataricus thiol redox puzzle: characterization of an atypical protein disulfide oxidoreductase. Limauro D, De Simone G, Pirone L, Bartolucci S, D'Ambrosio K, Pedone E;. Extremophiles. 2014;18:219-228. (from Pfam) NF046599.1 PF22139.1 XPD_arch 27 27 110 domain Y N N DNA repair helicase XPD, arch domain 18510925 118883 Sulfolobaceae family 18 EBI-EMBL DNA repair helicase XPD, arch domain DNA repair helicase XPD, arch domain This domain is found in DNA repair helicase XPD from Sulfurisphaera tokodaii (Swiss:Q971R4) and similar archaeal proteins. XPD, which functions as a 5'-3' DNA helicase, shows three major domains. This entry represents the central domain, called Arch domain, which folds into a mixed alpha/beta topology with a four-stranded antiparallel beta-sheet and four alpha -helices. The other two canonical motor domains are represented by Pfam:PF06733 at the N-terminal end and Pfam:PF13307 at the C-terminal end [1]. Paper describing PDB structure 2vl7. [1]. 18510925. Structure of the DNA repair helicase XPD. Liu H, Rudolf J, Johnson KA, McMahon SA, Oke M, Carter L, McRobbie AM, Brown SE, Naismith JH, White MF;. Cell. 2008;133:801-812. (from Pfam) NF046605.1 PF22165.1 SSO1393-like_WHD 26 26 59 domain Y N N SSO1393-like, winged-helix domain 30232454,30444997 118883 Sulfolobaceae family 15 EBI-EMBL SSO1393-like, winged-helix domain SSO1393-like, winged-helix domain This entry represents a WH-like domain present in SSO1393-like proteins. SSO1393 is an archaeal protein from Sulfolobus solfataricus (PDB:3qyf). This protein has been described as a component of the CRISPR system [1]. CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids) [1,2]. [1]. 30444997. If You'd Like to Stop a Type III CRISPR Ribonuclease, Then You Should Put a Ring (Nuclease) on It. Mo CY, Marraffini LA;. Mol Cell. 2018;72:608-609. [2]. 30232454. Ring nucleases deactivate type III CRISPR ribonucleases by degrading cyclic oligoadenylate. Athukoralage JS, Rouillon C, Graham S, Gruschow S, White MF;. Nature. 2018;562:277-280. (from Pfam) NF047083.1 PF22034.1 B129_C2H2-zf 27 27 22 domain Y N N Uncharacterized protein B-129, C2H2 zinc finger 118883 Sulfolobaceae family 35 EBI-EMBL Uncharacterized protein B-129, C2H2 zinc finger Uncharacterized protein B-129, C2H2 zinc finger This entry represents a C2H2 zinc finger found at the C-terminal of of poorly characterised viral proteins, including the uncharacterised protein B-129 from Sulfolobus spindle-shape virus 1 (SSV1). (from Pfam) NF047723.1 TransFacS4 120 120 90 equivalog Y Y N transcription factor S4 tfs4 GO:0003899,GO:0006351,GO:0051607 29203770,34535646 118883 Sulfolobaceae family 24 NCBIFAM transcription factor S4 NF047729.1 tRNAMtaseTaw21 400 400 250 equivalog Y Y N tRNA 4-demethylwyosine(37)-methyltransferase Taw21 taw21 2.1.1.- GO:0002939,GO:0008175 27852927 118883 Sulfolobaceae family 42 NCBIFAM tRNA 4-demethylwyosine(37)-methyltransferase Taw21 TIGR03154.1 TIGR03154 sulfolob_CbsA 468.4 468.4 465 equivalog Y Y N cytochrome b558/566 subunit A cbsA GO:0005886,GO:0016020,GO:0020037,GO:0022900 12887010 118883 Sulfolobaceae family 79 JCVI cytochrome b558/566, subunit A cytochrome b558/566 subunit A Members of this protein family are CbsA, one subunit of a highly glycosylated, heterodimeric, mono-heme cytochrome b558/566, found in Sulfolobus acidocaldarius and several other members of the Sulfolobales, a branch of the Crenarchaeota. TIGR03155.1 TIGR03155 sulfolob_CbsB 150.4 150.4 302 equivalog Y Y N cytochrome b558/566 subunit B cbsB 12887010 118883 Sulfolobaceae family 40 JCVI cytochrome b558/566, subunit B cytochrome b558/566 subunit B Members of this protein family are CbsB, one subunit of a highly glycosylated, heterodimeric, mono-heme cytochrome b558/566, found in Sulfolobus acidocaldarius and several other members of the Sulfolobales, a branch of the Crenarchaeota. TIGR03171.1 TIGR03171 soxL2 582.1 582.1 321 equivalog Y Y N Rieske iron-sulfur protein SoxL2 soxL2 15632423 118883 Sulfolobaceae family 41 JCVI Rieske iron-sulfur protein SoxL2 Rieske iron-sulfur protein SoxL2 This iron-sulfur protein is found in a contiguous genomic region with subunits of cytochrome b558/566 in several archaeal species, and appears to be part of a cytochrome bc1-analogous system. TIGR03876.1 TIGR03876 cas_csaX 222.5 222.5 281 equivalog Y Y N type I-A CRISPR-associated protein CsaX csaX 118883 Sulfolobaceae family 35 JCVI CRISPR type I-A/APERN-associated protein CsaX type I-A CRISPR-associated protein CsaX This family comprises a minor CRISPR-associated protein family. It occurs only in the context of the (strictly archaeal) Apern subtype of CRISPR/Cas system, and is further restricted to the Sulfolobales, including Metallosphaera sedula DSM 5348 and multiple species of the genus Sulfolobus. NF020197.5 PF08613.16 Cyclin 21 21 149 domain Y Y N cyclin GO:0000079,GO:0019901 10982385,8108735 118969 Legionellales order 19 EBI-EMBL Cyclin cyclin This family includes many different cyclin proteins. Members include the G1/S-specific cyclin pas1 [1], and the phosphate system cyclin PHO80/PHO85 [2]. [1]. 10982385. A pcl-like cyclin activates the Res2p-Cdc10p cell cycle "start" transcriptional factor complex in fission yeast. Tanaka K, Okayama H;. Mol Biol Cell. 2000;11:2845-2862. [2]. 8108735. Phosphorylation of the transcription factor PHO4 by a cyclin-CDK complex, PHO80-PHO85. Kaffman A, Herskowitz I, Tjian R, O'Shea EK;. Science. 1994;263:1153-1156. (from Pfam) NF021024.5 PF09475.15 Dot_icm_IcmQ 25 25 179 PfamEq Y Y N type IVB secretion system protein IcmQ icmQ 118969 Legionellales order 126 EBI-EMBL Dot/Icm secretion system protein (dot_icm_IcmQ) type IVB secretion system protein IcmQ Proteins in this entry are the IcmQ component of Dot/Icm secretion systems, as found in the obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the literature now seems to favour calling this the Dot/Icm system. This protein was shown to be essential for translocation. (from Pfam) NF024022.5 PF12608.13 T4bSS_IcmS 27 27 93 domain Y Y N type IV secretion IcmS family protein 21743810 118969 Legionellales order 86 EBI-EMBL Type IVb secretion, IcmS, effector-recruitment type IV secretion IcmS family protein This is a family of Gram-negative bacterial proteins involved in the Dot/Icm type IVb transport system. Members are small acidic cytoplasmic proteins required for Dot/Icm-dependent activities. Binary complexes of IcmW-IcmS and of IcmS-LvgA have been consistently reported, suggestive of the binary WXG100 system. The IcmW-IcmS complex may play a role in recruitment of effector proteins to the transport apparatus [1]. [1]. 21743810. Type IVB Secretion Systems of Legionella and Other Gram-Negative Bacteria. Nagai H, Kubori T;. Front Microbiol. 2011;2:136. (from Pfam) NF033882.1 T4SS_lipo_DotD 140 140 143 equivalog Y Y N type IVB secretion system lipoprotein DotD dotD 20949065 118969 Legionellales order 111 NCBIFAM type IVB secretion system lipoprotein DotD type IVB secretion system lipoprotein DotD Members of this family are the lipoprotein DotD from type IVB secretion systems, which are also called Dot/Icm secretion systems. DotD is is related to conjugal transfer protein TraH as that term is used in IncI1 plasmid transfer regions. NF033886.1 T4SS_DotA 500 300 790 equivalog Y Y N type IVB secretion system protein DotA dotA 118969 Legionellales order 172 NCBIFAM type IVB secretion system protein DotA type IVB secretion system protein DotA This HMM distinguishes DotA of type IVB secretion systems from TraY as the term is used in the conjugal transfer systems of IncI1 family plasmids. NF033900.0 T4SS_IcmE_DotG 750 450 1008 equivalog Y Y N type IVB secretion system protein DotG/IcmE dotG 25062693 118969 Legionellales order 161 NCBIFAM type IVB secretion system protein DotG/IcmE type IVB secretion system protein DotG/IcmE NF038218.1 IcmG_DotF_IVB 200 200 266 equivalog Y Y N type IVB secretion system protein IcmG/DotF icmG 15652976,23762385 118969 Legionellales order 115 NCBIFAM type IVB secretion system protein IcmG/DotF NF038219.1 IcmV_IVB 100 100 149 equivalog Y Y N type IVB secretion system protein IcmV icmV 15652976,28352254 118969 Legionellales order 129 NCBIFAM type IVB secretion system protein IcmV NF043023.1 T4SS_AnkH 600 600 467 equivalog Y Y N Dot/Icm T4SS effector AnkH/LegA3 ankH GO:0030255 18670632 118969 Legionellales order 130 NCBIFAM Dot/Icm T4SS effector AnkH/LegA3 NF045140.2 PF21727.2 DUF6863 27 27 123 domain Y N N Family of unknown function (DUF6863) 118969 Legionellales order 12 EBI-EMBL Family of unknown function (DUF6863) Family of unknown function (DUF6863) This entry represents an alpha helical bundle domain found at the N-terminus of a small group of putative bacterial toxins. The function of this domain is unknown. (from Pfam) TIGR02524.1 TIGR02524 dot_icm_DotB 463.3 463.3 358 equivalog Y Y N Dot/Icm type IV secretion system ATPase DotB dotB 15661013 118969 Legionellales order 117 JCVI Dot/Icm secretion system ATPase DotB Dot/Icm type IV secretion system ATPase DotB Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems. TIGR02527.1 TIGR02527 dot_icm_IcmQ 99.1 99.1 179 equivalog Y Y N Dot/Icm secretion system protein IcmQ icmQ 15661013 118969 Legionellales order 120 JCVI Dot/Icm secretion system protein IcmQ Dot/Icm secretion system protein IcmQ Members of this protein family are the IcmQ component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the literature now seems to favor calling this the Dot/Icm system. This protein was shown to be essential for translocation (PMID:15661013). NF001466.0 PRK00325 PRK00325.1-1 615 615 320 equivalog Y N N poly(beta-D-mannuronate) lyase 119060 Burkholderiaceae family 197 NCBI Protein Cluster (PRK) poly(beta-D-mannuronate) lyase poly(beta-D-mannuronate) lyase NF002502.0 PRK01842 PRK01842.1 188 188 150 equivalog Y N N hypothetical protein 119060 Burkholderiaceae family 1212 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002695.0 PRK02487 PRK02487.1-4 282 282 165 equivalog Y Y N heme-degrading domain-containing protein 119060 Burkholderiaceae family 617 NCBI Protein Cluster (PRK) hypothetical protein heme-degrading domain-containing protein NF002950.0 PRK03606 PRK03606.1-3 282 282 170 equivalog Y Y N ureidoglycolate lyase 4.3.2.3 119060 Burkholderiaceae family 909 NCBI Protein Cluster (PRK) ureidoglycolate hydrolase ureidoglycolate lyase NF003787.0 PRK05379 PRK05379.1-4 449 449 346 equivalog Y Y N bifunctional nicotinamide-nucleotide adenylyltransferase/Nudix hydroxylase 2.7.7.1,3.6.1.- 119060 Burkholderiaceae family 347 NCBI Protein Cluster (PRK) bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase bifunctional nicotinamide-nucleotide adenylyltransferase/Nudix hydroxylase NF003837.0 PRK05419 PRK05419.2-5 349 349 231 equivalog Y Y N protein-methionine-sulfoxide reductase heme-binding subunit MsrQ msrQ 119060 Burkholderiaceae family 1177 NCBI Protein Cluster (PRK) putative sulfite oxidase subunit YedZ protein-methionine-sulfoxide reductase heme-binding subunit MsrQ NF004990.0 PRK06370 PRK06370.1-1 842 842 459 equivalog Y Y N FAD-containing oxidoreductase 119060 Burkholderiaceae family 921 NCBI Protein Cluster (PRK) mercuric reductase FAD-containing oxidoreductase NF005401.0 PRK06948 PRK06948.1 906 906 604 subfamily Y N N ribonucleotide reductase-like protein 119060 Burkholderiaceae family 678 NCBI Protein Cluster (PRK) ribonucleotide reductase-like protein ribonucleotide reductase-like protein NF005405.0 PRK06955 PRK06955.1 312 312 300 equivalog Y Y N biotin--[acetyl-CoA-carboxylase] ligase 6.3.4.15 119060 Burkholderiaceae family 1282 NCBI Protein Cluster (PRK) biotin--protein ligase biotin--[acetyl-CoA-carboxylase] ligase NF005423.0 PRK07003 PRK07003.1 1260 1260 831 equivalog Y Y N DNA polymerase III subunit gamma/tau 2.7.7.7 119060 Burkholderiaceae family 1163 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunit gamma/tau Catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA NF005786.0 PRK07608 PRK07608.1-1 597 597 393 equivalog Y Y N UbiH/UbiF family hydroxylase 119060 Burkholderiaceae family 933 NCBI Protein Cluster (PRK) ubiquinone biosynthesis hydroxylase family protein UbiH/UbiF family hydroxylase NF005787.0 PRK07608 PRK07608.1-2 624 624 429 equivalog Y Y N UbiH/UbiF family hydroxylase 119060 Burkholderiaceae family 226 NCBI Protein Cluster (PRK) ubiquinone biosynthesis hydroxylase family protein UbiH/UbiF family hydroxylase NF005789.0 PRK07608 PRK07608.1-4 589 589 430 equivalog Y Y N UbiH/UbiF family hydroxylase 119060 Burkholderiaceae family 219 NCBI Protein Cluster (PRK) ubiquinone biosynthesis hydroxylase family protein UbiH/UbiF family hydroxylase NF006470.0 PRK08869 PRK08869.1-5 423 423 388 equivalog Y Y N flagellin 119060 Burkholderiaceae family 426 NCBI Protein Cluster (PRK) flagellin flagellin NF006680.0 PRK09229 PRK09229.1-1 810 810 460 equivalog Y Y N formimidoylglutamate deiminase 3.5.3.13 119060 Burkholderiaceae family 1348 NCBI Protein Cluster (PRK) N-formimino-L-glutamate deiminase formimidoylglutamate deiminase NF007140.0 PRK09585 PRK09585.1-4 605 605 382 equivalog Y Y N anhydro-N-acetylmuramic acid kinase 2.7.1.170 119060 Burkholderiaceae family 1176 NCBI Protein Cluster (PRK) anhydro-N-acetylmuramic acid kinase anhydro-N-acetylmuramic acid kinase NF007869.0 PRK10577 PRK10577.1-6 954 954 703 equivalog Y Y N Fe(3+)-hydroxamate ABC transporter permease FhuB fhuB 119060 Burkholderiaceae family 1270 NCBI Protein Cluster (PRK) iron-hydroxamate transporter permease subunit Fe(3+)-hydroxamate ABC transporter permease FhuB NF008326.0 PRK11114 PRK11114.1-5 1107 1107 782 equivalog Y Y N cellulose biosynthesis cyclic di-GMP-binding regulatory protein BcsB bcsB 119060 Burkholderiaceae family 1342 NCBI Protein Cluster (PRK) cellulose synthase regulator protein cellulose biosynthesis cyclic di-GMP-binding regulatory protein BcsB NF008327.0 PRK11114 PRK11114.2-1 1218 1218 845 equivalog Y Y N cellulose biosynthesis cyclic di-GMP-binding regulatory protein BcsB bcsB 119060 Burkholderiaceae family 584 NCBI Protein Cluster (PRK) cellulose synthase regulator protein cellulose biosynthesis cyclic di-GMP-binding regulatory protein BcsB NF008768.0 PRK11798 PRK11798.2-4 258 258 173 equivalog Y Y N ClpXP protease specificity-enhancing factor 119060 Burkholderiaceae family 660 NCBI Protein Cluster (PRK) ClpXP protease specificity-enhancing factor ClpXP protease specificity-enhancing factor NF009018.0 PRK12355 PRK12355.4-1 604 604 485 equivalog Y N N conjugal transfer mating pair stabilization protein TraN 119060 Burkholderiaceae family 38 NCBI Protein Cluster (PRK) conjugal transfer mating pair stabilization protein TraN conjugal transfer mating pair stabilization protein TraN NF009197.0 PRK12545 PRK12545.1 336 336 201 equivalog Y Y N RNA polymerase factor sigma-70 2.7.7.6 119060 Burkholderiaceae family 453 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase factor sigma-70 NF009337.1 PRK12697 PRK12697.1 380 380 215 equivalog Y Y N flagellar basal body L-ring protein FlgH flgH GO:0003774,GO:0009427,GO:0071973 119060 Burkholderiaceae family 584 NCBI Protein Cluster (PRK) flagellar basal body L-ring protein flagellar basal body L-ring protein FlgH Part of the basal body which consists of four rings L, P, S, and M mounted on a central rod NF009354.0 PRK12709 PRK12709.1 456 456 323 equivalog Y N N flagellar rod assembly protein/muramidase FlgJ flgJ 119060 Burkholderiaceae family 784 NCBI Protein Cluster (PRK) flagellar rod assembly protein/muramidase FlgJ flagellar assembly peptidoglycan hydrolase FlgJ NF009357.0 PRK12712 PRK12712.1 606 606 344 equivalog Y N N flagellar rod assembly protein/muramidase FlgJ flgJ 119060 Burkholderiaceae family 105 NCBI Protein Cluster (PRK) flagellar rod assembly protein/muramidase FlgJ flagellar assembly peptidoglycan hydrolase FlgJ NF009826.0 PRK13303 PRK13303.1-1 479 479 273 equivalog Y Y N aspartate dehydrogenase 1.4.1.21 119060 Burkholderiaceae family 766 NCBI Protein Cluster (PRK) L-aspartate dehydrogenase aspartate dehydrogenase NF009867.0 PRK13328 PRK13328.1-3 451 451 278 equivalog Y Y N type III pantothenate kinase 2.7.1.33 119060 Burkholderiaceae family 100 NCBI Protein Cluster (PRK) pantothenate kinase type III pantothenate kinase NF009868.0 PRK13328 PRK13328.1-4 388 388 268 equivalog Y Y N type III pantothenate kinase 2.7.1.33 119060 Burkholderiaceae family 1035 NCBI Protein Cluster (PRK) pantothenate kinase type III pantothenate kinase NF010067.0 PRK13547 PRK13547.1 374 374 272 equivalog Y Y N heme ABC transporter ATP-binding protein 119060 Burkholderiaceae family 811 NCBI Protein Cluster (PRK) hemin importer ATP-binding subunit heme ABC transporter ATP-binding protein NF010701.0 PRK14101 PRK14101.1 920 920 638 equivalog Y Y N bifunctional transcriptional regulator/glucokinase 2.7.1.2 119060 Burkholderiaceae family 764 NCBI Protein Cluster (PRK) bifunctional glucokinase/RpiR family transcriptional regulator bifunctional transcriptional regulator/glucokinase NF011982.0 PRK15446 PRK15446.1-3 684 684 377 equivalog Y Y N alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase 3.6.1.63 119060 Burkholderiaceae family 305 NCBI Protein Cluster (PRK) phosphonate metabolism protein PhnM alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase NF012230.0 LWXIA_domain 33 33 74 equivalog_domain Y Y N LWXIA domain-containing protein 119060 Burkholderiaceae family 1504 NCBIFAM LWXIA domain-containing protein LWXIA domain This domain occurs exclusively at the C-terminus of a set of long proteins (average length 4000 residues), and is separated form the rest of the protein sequence by a Pro and Ser-rich spacer region of poorly conserved, low-complexity sequence. This domain is named for its most conserved motif, LWxIA. Some but not all sequences in the seed alignment score well locally to the LysM domain model of PF01476, which may have a general peptidoglycan binding function. NF022516.5 PF11065.13 DUF2866 25 25 63 domain Y Y N DUF2866 domain-containing protein 119060 Burkholderiaceae family 734 EBI-EMBL Protein of unknown function (DUF2866) Protein of unknown function (DUF2866) This bacterial family of proteins have no known function. (from Pfam) NF022533.5 PF11082.13 DUF2880 25 25 79 PfamAutoEq Y Y N DUF2880 domain-containing protein 119060 Burkholderiaceae family 90 EBI-EMBL Protein of unknown function (DUF2880) Protein of unknown function (DUF2880) This bacterial family of proteins has no known function. (from Pfam) NF022618.5 PF11170.13 DUF2957 25 25 344 domain Y Y N DUF2957 domain-containing protein 119060 Burkholderiaceae family 3252 EBI-EMBL Protein of unknown function (DUF2957) Protein of unknown function (DUF2957) Some members annotate the proteins to be putative lipoproteins however this cannot be confirmed. Currently no function is known for this family of proteins. (from Pfam) NF022625.5 PF11177.13 DUF2964 24.2 24.2 62 subfamily Y Y N DUF2964 family protein 119060 Burkholderiaceae family 992 EBI-EMBL Protein of unknown function (DUF2964) DUF2964 family protein This family of proteins with unknown function appears to be restricted to Proteobacteria. (from Pfam) NF022672.5 PF11226.13 DUF3022 30.6 30.6 105 domain Y Y N DUF3022 domain-containing protein 119060 Burkholderiaceae family 1325 EBI-EMBL Protein of unknown function (DUF3022) Protein of unknown function (DUF3022) This family of proteins with unknown function appears to be restricted to Proteobacteria. (from Pfam) NF022888.5 PF11448.13 DUF3005 25 25 109 domain Y Y N DUF3005 domain-containing protein 119060 Burkholderiaceae family 1424 EBI-EMBL Protein of unknown function (DUF3005) Protein of unknown function (DUF3005) This is a bacterial family of uncharacterised proteins. (from Pfam) NF023239.5 PF11811.13 DUF3331 25 25 91 domain Y Y N DUF3331 domain-containing protein 119060 Burkholderiaceae family 3649 EBI-EMBL Domain of unknown function (DUF3331) Domain of unknown function (DUF3331) This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family vary in length from 96 to 160 amino acids. (from Pfam) NF023509.5 PF12087.13 DUF3564 25 25 120 subfamily Y Y N DUF3564 family protein 119060 Burkholderiaceae family 981 EBI-EMBL Protein of unknown function (DUF3564) DUF3564 family protein This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 118 to 142 amino acids in length. This protein has a conserved WSRE sequence motif. (from Pfam) NF024027.5 PF12613.13 FliC_D2 25 25 119 PfamEq Y N N Flagellin, D2 domain 26222657,9079894 119060 Burkholderiaceae family 615 EBI-EMBL Flagellin, D2 domain Flagellin, D2 domain This variable D2 domain is found in uncharacterised proteins from Betaproteobacteria, including Flagellin from Burkholderia pseudomallei (FliC). FliC assembles to form the flagellar filament that supports bacterial motility [1, 2]. The family is found in association with Pfam:PF00669, Pfam:PF00700. [1]. 9079894. Mutagenesis of Burkholderia pseudomallei with Tn5-OT182: isolation of motility mutants and molecular characterization of the flagellin structural gene. DeShazer D, Brett PJ, Carlyon R, Woods DE;. J Bacteriol. 1997;179:2116-2125. [2]. 26222657. Sequence- and Structure-Based Immunoreactive Epitope Discovery for Burkholderia pseudomallei Flagellin. Nithichanon A, Rinchai D, Gori A, Lassaux P, Peri C, Conchillio-Sole O, Ferrer-Navarro M, Gourlay LJ, Nardini M, Vila J, Daura X, Colombo G, Bolognesi M, Lertmemonkolchai G;. PLoS Negl Trop Dis. 2015;9:e0003917. (from Pfam) NF037717.5 PF18057.6 DUF5594 27 27 128 PfamEq Y Y N DUF5594 family protein 25495888 119060 Burkholderiaceae family 899 EBI-EMBL Domain of unknown function (DUF5594) DUF5594 family protein This domain was first discovered in BPSL1050, a highly immunoreactive protein found in Burkholderia pseudomallei. The domain's structure consists of three helical regions which pack onto an antiparallel beta sheet, formed by four strands. The beta sheet is solvent exposed on one side and packs tightly against the three helices on the other side, generating a network of hydrophobic and aromatic interactions that contribute to tight packing of the protein. Is is thought that the small loop L1, the main loop L2, and part of helix alpha-3 extending until Leu120 are the three main immunogenic sequences [1]. [1]. 25495888. Structure-based design of a B cell antigen from B. pseudomallei. Gaudesi D, Peri C, Quilici G, Gori A, Ferrer-Navarro M, Conchillo-Sole O, Thomas R, Nithichanon A, Lertmemongkolchai G, Titball R, Daura X, Colombo G, Musco G;. ACS Chem Biol. 2015;10:803-812. (from Pfam) NF038348.1 T2SS_HK 450 450 574 subfamily Y Y N histidine kinase 24866793 119060 Burkholderiaceae family 936 NCBIFAM histidine kinase NF040301.4 PF19476.4 DUF6013 32.6 32.6 184 subfamily Y Y N DUF6013 family protein 22765305,23055407 119060 Burkholderiaceae family 701 EBI-EMBL Family of unknown function (DUF6013) DUF6013 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001120) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the burkholderic acid biosynthetic gene cluster from Burkholderia thailandensis E264 and appears to be predominantly found in Burkholderiaceae [1,2] [1]. 23055407. Genomics-driven discovery of burkholderic acid, a noncanonical, cryptic polyketide from human pathogenic Burkholderia species. Franke J, Ishida K, Hertweck C;. Angew Chem Int Ed Engl. 2012;51:11611-11615. [2]. 22765305. Malleilactone, a polyketide synthase-derived virulence factor encoded by the cryptic secondary metabolome of Burkholderia pseudomallei group pathogens. Biggins JB, Ternei MA, Brady SF;. J Am Chem Soc. 2012;134:13192-13195. (from Pfam) NF041682.1 ant_diox_AndAa 650 650 406 equivalog Y Y N anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase andAa 1.18.1.3 GO:0008860,GO:0009056 13129960,22360670 119060 Burkholderiaceae family 1105 NCBIFAM anthranilate 1,2-dioxygenase system ferredoxin--NaD(+) reductase NF042427.1 lasso_burhizin 45 45 44 subfamily Y Y N burhizin family lasso peptide 23897438 119060 Burkholderiaceae family 45 NCBIFAM burhizin family lasso peptide NF042879.3 PF20484.3 DUF6723 27 27 73 subfamily Y Y N DUF6723 family protein 119060 Burkholderiaceae family 682 EBI-EMBL Family of unknown function (DUF6723) DUF6723 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 81 and 125 amino acids in length. (from Pfam) NF044522.2 PF21627.2 BTH_I2711-like 27 27 71 domain Y N N Uncharacterized protein BTH_I2711-like 119060 Burkholderiaceae family 218 EBI-EMBL Uncharacterized protein BTH_I2711-like Uncharacterized protein BTH_I2711-like This protein family represents a group of sequences mainly from Burkholderia, including the BTH_I2711 from Burkholderia thailandensis. This protein may adopt a fold consisting of two alpha-helices and two or three beta-sheets. (from Pfam) NF045537.1 phasin_PhaP7 200 200 141 equivalog Y Y N polyhydroxyalkanoate granule-associated phasin GO:0070088 22923598 119060 Burkholderiaceae family 61 NCBIFAM polyhydroxyalkanoate granule-associated phasin NF046013.1 surf_attach_Sap1 125 125 114 equivalog Y Y N surface attachment protein Sap1 sap1 33772012,36726566 119060 Burkholderiaceae family 477 NCBIFAM surface attachment protein Sap1 Surface attachment protein 1 (BP1026B_I0091), as described in the intracellular pathogen Burkholderia pseudomallei, is a virulence factor important for attachment to host cells. NF046014.1 sap1_reg_SapR 500 500 295 equivalog Y Y N sap1 transcriptional regulator SapR sapR GO:0003677,GO:0003700,GO:0006355 36726566 119060 Burkholderiaceae family 657 NCBIFAM sap1 transcriptional regulator SapR NF005329.0 PRK06853 PRK06853.2-4 267 267 175 equivalog Y Y N indolepyruvate oxidoreductase subunit beta 119484 Syntrophobacter fumaroxidans species 1 NCBI Protein Cluster (PRK) indolepyruvate oxidoreductase subunit beta indolepyruvate oxidoreductase subunit beta NF007147.0 PRK09585 PRK09585.3-1 822 822 393 equivalog Y Y N anhydro-N-acetylmuramic acid kinase 2.7.1.170 119977 Acidithiobacillus genus 12 NCBI Protein Cluster (PRK) anhydro-N-acetylmuramic acid kinase anhydro-N-acetylmuramic acid kinase NF010397.0 PRK13825 PRK13825.1-1 882 882 436 equivalog Y N N conjugal transfer protein TraB 119977 Acidithiobacillus genus 16 NCBI Protein Cluster (PRK) conjugal transfer protein TraB conjugal transfer protein TraB NF041615.1 Feoxidase_Iro 100 100 90 equivalog Y Y N iron oxidase iro 1.16.3.- GO:0009055,GO:0019646,GO:0046872 1317860 119977 Acidithiobacillus genus 31 NCBIFAM iron oxidase NF007037.0 PRK09496 PRK09496.2-4 445 445 454 equivalog Y Y N Trk system potassium transporter TrkA trkA 1202464 Dehalococcoidaceae family 21 NCBI Protein Cluster (PRK) potassium transporter peripheral membrane component Trk system potassium transporter TrkA NF010916.0 PRK14336 PRK14336.1 606 606 418 equivalog Y Y N tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB miaB 2.8.4.3 20472640 1202464 Dehalococcoidaceae family 30 NCBI Protein Cluster (PRK) (dimethylallyl)adenosine tRNA methylthiotransferase tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB NF010990.0 PRK14414 PRK14414.1 261 261 210 equivalog Y Y N glycerol-3-phosphate acyltransferase 1202464 Dehalococcoidaceae family 16 NCBI Protein Cluster (PRK) membrane protein glycerol-3-phosphate acyltransferase NF010993.0 PRK14417 PRK14417.1 249 249 232 equivalog Y N N membrane protein 1202464 Dehalococcoidaceae family 22 NCBI Protein Cluster (PRK) membrane protein membrane protein NF011072.0 PRK14502 PRK14502.1 762 762 694 equivalog Y Y N bifunctional mannosyl-3-phosphoglycerate synthase/mannosyl-3 phosphoglycerate phosphatase 3.1.3.85 15205409 1202464 Dehalococcoidaceae family 23 NCBI Protein Cluster (PRK) bifunctional mannosyl-3-phosphoglycerate synthase/mannosyl-3 phosphoglycerate phosphatase bifunctional mannosyl-3-phosphoglycerate synthase/mannosyl-3 phosphoglycerate phosphatase Catalyzes the hydrolysis of mannosyl-3-phosphoglycerate to form the osmolyte mannosylglycerate; functions in mannosylglycerate biosynthesis NF025889.5 PF14536.11 DUF4441 24 24 116 domain Y Y N DUF4441 domain-containing protein 120831 Dyadobacter genus 2 EBI-EMBL Domain of unknown function (DUF4441) Domain of unknown function (DUF4441) This family is largely made up of uncharacterised proteins from the Ciliophora. The function is not known. (from Pfam) NF011075.0 PRK14505 PRK14505.1 904 904 643 equivalog Y N N bifunctional photosynthetic reaction center subunit L/M 120961 Roseiflexus genus 4 NCBI Protein Cluster (PRK) bifunctional photosynthetic reaction center subunit L/M bifunctional photosynthetic reaction center subunit L/M NF026781.5 PF15443.11 DUF4630 25 25 155 domain Y Y N DUF4630 domain-containing protein 121620 Catellatospora methionotrophica species 1 EBI-EMBL Domain of unknown function (DUF4630) Domain of unknown function (DUF4630) This family of proteins is found in eukaryotes. Proteins in this family are typically between 124 and 286 amino acids in length. (from Pfam) NF001215.0 PRK00192 PRK00192.1-1 488 488 265 equivalog Y N N mannosyl-3-phosphoglycerate phosphatase 1218 Prochlorococcus genus 42 NCBI Protein Cluster (PRK) mannosyl-3-phosphoglycerate phosphatase mannosyl-3-phosphoglycerate phosphatase NF001925.0 PRK00704 PRK00704.1-1 366 366 199 equivalog Y Y N photosystem I reaction center protein subunit XI 1218 Prochlorococcus genus 36 NCBI Protein Cluster (PRK) photosystem I reaction center protein subunit XI photosystem I reaction center protein subunit XI NF001928.0 PRK00704 PRK00704.1-5 301 301 187 equivalog Y Y N photosystem I reaction center protein subunit XI 1218 Prochlorococcus genus 46 NCBI Protein Cluster (PRK) photosystem I reaction center protein subunit XI photosystem I reaction center protein subunit XI NF002717.0 PRK02561 PRK02561.1-1 153 153 97 exception Y Y N cytochrome b559 subunit beta, long form psbF 1218 Prochlorococcus genus 11 NCBI Protein Cluster (PRK) cytochrome b559 subunit beta cytochrome b559 subunit beta, long form Long forms of cytochrome b559 subunit beta (PsbF) are found in Prochlorococcus. NF002720.0 PRK02561 PRK02561.1-4 127 127 98 exception Y Y N cytochrome b559 subunit beta, long form psbF 1218 Prochlorococcus genus 23 NCBI Protein Cluster (PRK) cytochrome b559 subunit beta cytochrome b559 subunit beta, long form Long forms of cytochrome b559 subunit beta (PsbF) are found in Prochlorococcus. NF009562.0 PRK13019 PRK13019.1-2 160 160 95 equivalog Y Y N ATP-dependent Clp protease adapter ClpS clpS 1218 Prochlorococcus genus 47 NCBI Protein Cluster (PRK) ATP-dependent Clp protease adaptor ATP-dependent Clp protease adapter ClpS NF009719.0 PRK13246 PRK13246.1 290 290 236 equivalog Y Y N 15,16-dihydrobiliverdin:ferredoxin oxidoreductase 1.3.7.2 1218 Prochlorococcus genus 39 NCBI Protein Cluster (PRK) dihydrobiliverdin:ferredoxin oxidoreductase 15,16-dihydrobiliverdin:ferredoxin oxidoreductase Catalyzes the reduction of biliverdin IX-alpha to 15,16-dihydrobiliverdin NF009721.0 PRK13248 PRK13248.1 303 303 253 equivalog Y Y N phycoerythrobilin:ferredoxin oxidoreductase 1.3.7.3 1218 Prochlorococcus genus 40 NCBI Protein Cluster (PRK) phycoerythrobilin:ferredoxin oxidoreductase phycoerythrobilin:ferredoxin oxidoreductase Catalyzes the reduction of 15,16-dihydrobiliverdin to (3Z)-phycoerythrobilin NF009882.0 PRK13341 PRK13341.1-3 1197 1197 734 equivalog Y Y N AAA family ATPase 1218 Prochlorococcus genus 11 NCBI Protein Cluster (PRK) recombination factor protein RarA/unknown domain fusion protein AAA family ATPase NF010694.0 PRK14094 PRK14094.1 104 104 50 equivalog Y Y N photosystem II reaction center protein PsbM psbM 1218 Prochlorococcus genus 28 NCBI Protein Cluster (PRK) photosystem II reaction center protein M photosystem II reaction center protein PsbM NF011240.0 PRK14646 PRK14646.1 205 205 155 equivalog Y Y N ribosome maturation factor RimP rimP 1218 Prochlorococcus genus 42 NCBI Protein Cluster (PRK) hypothetical protein ribosome maturation factor RimP NF023678.5 PF12257.13 IML1 26.2 26.2 286 domain Y Y N vacuolar membrane-associated protein Iml1 domain-containing protein GO:0005096 21454883,21804352,21900499 1218 Prochlorococcus genus 11 EBI-EMBL Vacuolar membrane-associated protein Iml1, N-terminal domain vacuolar membrane-associated protein Iml1 Proteins in this family contain a DEP domain, which is a globular domain of about 80 residues. This entry includes vacuolar membrane-associated protein Iml1 and DEP domain-containing protein 5/DDB_G0279099. In Saccharomyces cerevisiae, Iml1 is a subunit of both the SEA (Seh1-associated) and Iml1 complexes (Iml1-Npr2-Npr3). SEA complex is associates dynamically with the vacuole and is involved in autophagy [1, 2]. Iml1 complex is required for non-nitrogen-starvation (NNS)-induced autophagy [3]. [1]. 21454883. A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Dokudovskaya S, Waharte F, Schlessinger A, Pieper U, Devos DP, Cristea IM, Williams R, Salamero J, Chait BT, Sali A, Field MC, Rout MP, Dargemont C;. Mol Cell Proteomics. 2011;10:M110. [2]. 21804352. A novel coatomer-related SEA complex dynamically associates with the vacuole in yeast and is implicated in the response to nitrogen starvation. Dokudovskaya S, Rout MP;. Autophagy. 2011;7:1392-1393. [3]. 21900499. Selective regulation of autophagy by the Iml1-Npr2-Npr3 complex in the absence of nitrogen starvation. Wu X, Tu BP;. Mol Biol Cell. 2011;22:4124-4133. (from Pfam) NF002916.0 PRK03537 PRK03537.1-2 359 359 244 equivalog Y Y N molybdate ABC transporter substrate-binding protein 122277 Pectobacterium genus 207 NCBI Protein Cluster (PRK) molybdate ABC transporter periplasmic molybdate-binding protein molybdate ABC transporter substrate-binding protein NF007717.0 PRK10410 PRK10410.2-1 241 241 141 equivalog Y Y N nitrous oxide-stimulated promoter family protein 122277 Pectobacterium genus 158 NCBI Protein Cluster (PRK) hypothetical protein nitrous oxide-stimulated promoter family protein NF000005.4 ble_BLMT 210 210 117 exception Y Y Y BLMT family bleomycin binding protein ble 1224 Pseudomonadota phylum 18 NCBIFAM BLMT family bleomycin binding protein BLMT family bleomycin binding protein This model describes the bleomycin resistance protein BLMT, which binds and sequesters bleomycin. NF000007.1 16S_rRNA_Rmt_D 500 500 247 exception Y Y Y RmtD family 16S rRNA (guanine(1405)-N(7))-methyltransferase 1224 Pseudomonadota phylum 4 NCBIFAM 16S rRNA (guanine(1405)-N(7))-methyltransferase RmtD RmtD family 16S rRNA (guanine(1405)-N(7))-methyltransferase NF000011.2 APH_6_Ic 500 500 280 exception Y Y Y aminoglycoside O-phosphotransferase APH(6)-Ic aph(6)-Ic 1224 Pseudomonadota phylum 35 NCBIFAM aminoglycoside O-phosphotransferase APH(6)-Ic aminoglycoside O-phosphotransferase APH(6)-Ic NF000067.2 SMR_qac_FL 205 205 110 exception Y Y Y quaternary ammonium compound efflux SMR transporter QacL qac 1224 Pseudomonadota phylum 54 NCBIFAM quaternary ammonium compound efflux SMR transporter QacL QacF/QacL family quaternary ammonium compound efflux SMR transporter NF000100.2 AAC_2p_IIa 510 510 238 exception Y Y Y kasugamycin N-acetyltransferase AAC(2')-IIa aac(2')-IIa 1224 Pseudomonadota phylum 5 NCBIFAM aminoglycoside 2'-N-acetyltransferase AAC(2')-IIa kasugamycin N-acetyltransferase AAC(2')-IIa NF000118.3 AAC_6p_A31 385 385 172 exception Y Y Y aminoglycoside N-acetyltransferase AAC(6')-31 aac(6')-31 1224 Pseudomonadota phylum 10 NCBIFAM aminoglycoside N-acetyltransferase AAC(6')-31 aminoglycoside N-acetyltransferase AAC(6')-31 NF000123.2 AAC_6p_A34 300 300 146 exception Y Y Y aminoglycoside 6'-N-acetyltransferase AacA34 aacA34 1224 Pseudomonadota phylum 1 NCBIFAM aminoglycoside 6'-N-acetyltransferase AacA34 aminoglycoside 6'-N-acetyltransferase AacA34 NF000148.1 SMR_qac_pB8 200 200 110 exception Y Y Y Qac-pB8 family quaternary ammonium compound efflux SMR transporter qac 1224 Pseudomonadota phylum 7 NCBIFAM quaternary ammonium compound efflux SMR transporter QacF Qac-pB8 family quaternary ammonium compound efflux SMR transporter NF000158.2 AAC_6p_Il 270 270 152 exception Y Y Y aminoglycoside N-acetyltransferase AAC(6')-Il aac(6')-Il 1224 Pseudomonadota phylum 12 NCBIFAM aminoglycoside N-acetyltransferase AAC(6')-Il aminoglycoside N-acetyltransferase AAC(6')-Il NF000219.1 FloR 700 700 404 exception Y Y Y chloramphenicol/florfenicol efflux MFS transporter FloR floR 1224 Pseudomonadota phylum 484 NCBIFAM chloramphenicol/florfenicol efflux MFS transporter FloR chloramphenicol/florfenicol efflux MFS transporter FloR NF000241.1 MPH_3 500 500 293 exception Y Y Y Mph(E)/Mph(G) family macrolide 2'-phosphotransferase mph 1224 Pseudomonadota phylum 159 NCBIFAM macrolide 2'-phosphotransferase Mph(E)/Mph(G) family macrolide 2'-phosphotransferase NF000255.1 macrolide_MphF 650 650 299 exception Y Y Y Mph(F) family macrolide 2'-phosphotransferase 1224 Pseudomonadota phylum 2 NCBIFAM macrolide 2'-phosphotransferase Mph(F) Mph(F) family macrolide 2'-phosphotransferase NF000259.2 blaNDM 580 580 270 exception Y Y Y NDM family subclass B1 metallo-beta-lactamase blaNDM 3.5.2.6 GO:0008800 19770275 1224 Pseudomonadota phylum 72 NCBIFAM NDM family subclass B1 metallo-beta-lactamase NDM family subclass B1 metallo-beta-lactamase NF000278.1 SMR_qac_G2 220 220 110 exception Y Y Y quaternary ammonium compound efflux SMR transporter QacG2 qacG2 1224 Pseudomonadota phylum 11 NCBIFAM quaternary ammonium compound efflux SMR transporter QacG2 quaternary ammonium compound efflux SMR transporter QacG2 NF000284.1 RTG 600 600 298 exception Y Y Y RTG family carbenicillin-hydrolyzing class A beta-lactamase blaRTG 3.5.2.6 GO:0008800 1224 Pseudomonadota phylum 13 NCBIFAM RTG family carbenicillin-hydrolyzing class A beta-lactamase RTG family carbenicillin-hydrolyzing class A beta-lactamase NF000287.1 SMB1_fam 400 400 280 exception Y Y Y SMB-1 family subclass B3 metallo-beta-lactamase blaSMB 3.5.2.6 GO:0008800 1224 Pseudomonadota phylum 10 NCBIFAM SMB-1 family subclass B3 metallo-beta-lactamase SMB-1 family subclass B3 metallo-beta-lactamase NF000331.2 trim_DfrB 137 137 78 exception Y Y Y trimethoprim-resistant dihydrofolate reductase DfrB dfrB 1.5.1.3 GO:0004146 36551425,37369703 1224 Pseudomonadota phylum 38 NCBIFAM trimethoprim-resistant dihydrofolate reductase DfrB trimethoprim-resistant dihydrofolate reductase DfrB NF000358.1 sat2 360 360 174 exception Y Y Y streptothricin N-acetyltransferase Sat2 sat2 1224 Pseudomonadota phylum 32 NCBIFAM streptothricin N-acetyltransferase Sat1 streptothricin N-acetyltransferase Sat2 NF000386.2 blaOXA-10_like 580 580 266 exception Y Y Y OXA-10 family class D beta-lactamase blaOXA 3.5.2.6 GO:0008658,GO:0008800 1224 Pseudomonadota phylum 60 NCBIFAM OXA-10 family class D beta-lactamase OXA-10 family class D beta-lactamase OXA-10 family class D beta-lactamases are integron-borne, observed frequently in Pseudomonas aeruginosa, are mobile and found elsewhere as well. Family members are typically narrow-spectrum, but OXA-14 and a number of other variants with the same G157D substitution hydrolyze ceftazidime. Members of the family show weak carbapenemase with potential for increased activity as in OXA-655. NF000390.2 blaVEB 670 670 299 exception Y Y Y VEB family extended-spectrum class A beta-lactamase blaVEB 3.5.2.6 GO:0008800 10049269,26926646 1224 Pseudomonadota phylum 36 NCBIFAM VEB family class A extended-spectrum beta-lactamase VEB family extended-spectrum class A beta-lactamase VEB signifies Vietnam Extended-spectrum Beta-lactamase. Members are highly conserved alleles of recently mobilized class A beta-lactamase that confers resistance to a number of clinically important cephalosporin-class beta-lactam antibiotics. Multiple alleles tested all were ESBL and all were inhibited by avibactam. NF000414.2 blaPME 650 650 309 exception Y Y Y PME family extended-spectrum class A beta-lactamase blaPME 3.5.2.6 GO:0008800 21402845 1224 Pseudomonadota phylum 4 NCBIFAM PME family class A beta-lactamase PME family extended-spectrum class A beta-lactamase NF000417.2 blaOXA-211_like 575 575 274 exception Y Y Y OXA-211 family carbapenem-hydrolyzing class D beta-lactamase blaOXA 3.5.2.6 GO:0008658,GO:0008800 1224 Pseudomonadota phylum 61 NCBIFAM OXA-211 family carbapenem-hydrolyzing class D beta-lactamase OXA-211 family carbapenem-hydrolyzing class D beta-lactamase NF000443.2 blaTMB 550 550 245 exception Y Y Y TMB family subclass B1 metallo-beta-lactamase blaTMB 3.5.2.6 GO:0008800 1224 Pseudomonadota phylum 2 NCBIFAM TMB family subclass B1 metallo-beta-lactamase TMB family subclass B1 metallo-beta-lactamase NF000467.1 FosG 240 240 132 exception Y Y Y FosG family fosfomycin resistance glutathione transferase 2.5.1.18 1224 Pseudomonadota phylum 4 NCBIFAM FosG family fosfomycin resistance glutathione transferase FosG family fosfomycin resistance glutathione transferase NF000480.2 PSE 580 580 288 exception Y Y Y PSE family carbenicillin-hydrolyzing class A beta-lactamase blaPSE 3.5.2.6 GO:0008800 1224 Pseudomonadota phylum 48 NCBIFAM PSE family carbenicillin-hydrolyzing class A beta-lactamase PSE family carbenicillin-hydrolyzing class A beta-lactamase NF000481.1 carbeni_gen 430 400 284 exception Y Y Y CARB/PSE/RTG family carbenicillin-hydrolyzing class A beta-lactamase blaCARB 3.5.2.6 GO:0008800 1224 Pseudomonadota phylum 375 NCBIFAM CARB/PSE/RTG family carbenicillin-hydrolyzing class A beta-lactamase CARB/PSE/RTG family carbenicillin-hydrolyzing class A beta-lactamase NF000496.1 Fos_GSH 190 190 131 equivalog Y Y Y fosfomycin resistance glutathione transferase fos 2.5.1.18 GO:0003824 1224 Pseudomonadota phylum 3910 NCBIFAM fosfomycin resistance glutathione transferase fosfomycin resistance glutathione transferase NF000509.1 efflux_CmlA 875 835 419 exception Y Y Y CmlA family chloramphenicol efflux MFS transporter GO:0016020,GO:0022857,GO:0042910,GO:0055085,GO:1990961 1224 Pseudomonadota phylum 125 NCBIFAM efflux_CmlA: CmlA family chloramphenicol efflux MFS transporter CmlA family chloramphenicol efflux MFS transporter NF000531.2 blaTEM 625 625 286 exception Y Y Y TEM family class A beta-lactamase blaTEM 3.5.2.6 GO:0008800 1224 Pseudomonadota phylum 415 NCBIFAM blaTEM: TEM family class A beta-lactamase TEM family class A beta-lactamase Members of this family are class A beta-lactamases from the narrowly defined family TEM. All full length beta-lactamases scoring above the trusted cutoff are proper members of the TEM family, and no true TEM is missed. NF000939.0 PRK00094 PRK00094.1-1 473 473 339 equivalog Y Y N NAD(P)H-dependent glycerol-3-phosphate dehydrogenase gpsA 1.1.1.94 GO:0006072,GO:0047952 1224 Pseudomonadota phylum 6208 NCBI Protein Cluster (PRK) NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NF000946.0 PRK00094 PRK00094.2-4 455 455 342 equivalog Y Y N NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 1.1.1.94 GO:0006072,GO:0009331,GO:0046168,GO:0047952,GO:0051287 1224 Pseudomonadota phylum 3889 NCBI Protein Cluster (PRK) NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NF000947.0 PRK00094 PRK00094.2-5 251 251 323 equivalog Y Y N NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 1.1.1.94 1224 Pseudomonadota phylum 108 NCBI Protein Cluster (PRK) NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NF000949.0 PRK00095 PRK00095.1-2 750 750 634 equivalog Y Y N DNA mismatch repair endonuclease MutL mutL GO:0005524,GO:0006298,GO:0016887,GO:0030983,GO:0032300 1224 Pseudomonadota phylum 12794 NCBI Protein Cluster (PRK) DNA mismatch repair protein DNA mismatch repair endonuclease MutL NF000952.0 PRK00095 PRK00095.2-2 840 840 623 subfamily Y Y N DNA mismatch repair endonuclease MutL mutL 1224 Pseudomonadota phylum 442 NCBI Protein Cluster (PRK) DNA mismatch repair protein DNA mismatch repair endonuclease MutL NF000988.0 PRK00103 PRK00103.2-2 199 199 156 equivalog Y Y N 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH rlmH 1224 Pseudomonadota phylum 2172 NCBI Protein Cluster (PRK) rRNA large subunit methyltransferase 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH NF000991.0 PRK00103 PRK00103.2-5 216 216 160 equivalog Y Y N 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH rlmH 1224 Pseudomonadota phylum 919 NCBI Protein Cluster (PRK) rRNA large subunit methyltransferase 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH NF001054.0 PRK00117 PRK00117.2-1 189 189 154 equivalog Y Y N recombination regulator RecX recX 1224 Pseudomonadota phylum 2549 NCBI Protein Cluster (PRK) recombination regulator RecX recombination regulator RecX NF001055.0 PRK00117 PRK00117.2-5 129 129 157 equivalog Y Y N recombination regulator RecX recX GO:0006282 1224 Pseudomonadota phylum 4560 NCBI Protein Cluster (PRK) recombination regulator RecX recombination regulator RecX NF001213.0 PRK00183 PRK00183.1 158 158 157 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 3832 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF001216.0 PRK00192 PRK00192.1-2 353 353 275 equivalog Y N N mannosyl-3-phosphoglycerate phosphatase 1224 Pseudomonadota phylum 50 NCBI Protein Cluster (PRK) mannosyl-3-phosphoglycerate phosphatase mannosyl-3-phosphoglycerate phosphatase NF001237.0 PRK00207 PRK00207.1 92 92 128 equivalog Y Y N sulfurtransferase complex subunit TusD tusD 2.8.1.- GO:0008033,GO:0016783 1224 Pseudomonadota phylum 9487 NCBI Protein Cluster (PRK) sulfur transfer complex subunit TusD sulfurtransferase complex subunit TusD The TusBCD complex is involved in sulfur related that results in thiouridation to U34 position in some tRNAs NF001240.0 PRK00216 PRK00216.1-1 378 378 251 equivalog Y Y N bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol methylase UbiE ubiE 2.1.1.163,2.1.1.201 GO:0008168 1224 Pseudomonadota phylum 10013 NCBI Protein Cluster (PRK) ubiquinone/menaquinone biosynthesis methyltransferase bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol methylase UbiE NF001246.0 PRK00218 PRK00218.1-2 181 181 207 equivalog Y Y N high frequency lysogenization protein HflD hflD 1224 Pseudomonadota phylum 8618 NCBI Protein Cluster (PRK) putative lysogenization regulator high frequency lysogenization protein HflD NF001266.0 PRK00228 PRK00228.1-1 198 198 187 equivalog Y Y N YqgE/AlgH family protein 25857636 1224 Pseudomonadota phylum 12359 NCBI Protein Cluster (PRK) hypothetical protein YqgE/AlgH family protein NF001278.0 PRK00235 PRK00235.1-5 252 252 246 equivalog Y Y N adenosylcobinamide-GDP ribazoletransferase 2.7.8.26 GO:0051073 1224 Pseudomonadota phylum 5093 NCBI Protein Cluster (PRK) cobalamin synthase adenosylcobinamide-GDP ribazoletransferase NF001325.0 PRK00259 PRK00259.1-3 180 180 177 equivalog Y Y N septation protein A GO:0016020 1224 Pseudomonadota phylum 8903 NCBI Protein Cluster (PRK) intracellular septation protein A septation protein A NF001397.0 PRK00281 PRK00281.3-4 363 363 281 equivalog Y Y N undecaprenyl-diphosphate phosphatase 3.6.1.27 1224 Pseudomonadota phylum 454 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate phosphatase undecaprenyl-diphosphate phosphatase NF001423.0 PRK00299 PRK00299.1 78 78 82 equivalog Y Y N sulfurtransferase TusA tusA 2.8.1.- GO:0002143,GO:0097163 1224 Pseudomonadota phylum 5852 NCBI Protein Cluster (PRK) sulfur transfer protein SirA sulfurtransferase TusA Transfers sulfur to TusBCD complex; involved in thiouridation of U34 position of some tRNAs NF001464.0 PRK00321 PRK00321.1-5 227 227 307 subfamily Y Y N recombination-associated protein RdgC rdgC 1224 Pseudomonadota phylum 16235 NCBI Protein Cluster (PRK) recombination associated protein recombination-associated protein RdgC NF001465.0 PRK00321 PRK00321.1-6 489 489 302 subfamily Y Y N recombination-associated protein RdgC rdgC 1224 Pseudomonadota phylum 719 NCBI Protein Cluster (PRK) recombination associated protein recombination-associated protein RdgC NF001469.0 PRK00325 PRK00325.1-4 366 366 360 equivalog Y Y N polysaccharide lyase 1224 Pseudomonadota phylum 449 NCBI Protein Cluster (PRK) poly(beta-D-mannuronate) lyase polysaccharide lyase NF001638.0 PRK00418 PRK00418.1 83 83 65 equivalog Y Y N DNA gyrase inhibitor YacG yacG GO:0006355,GO:0008270 12211008 1224 Pseudomonadota phylum 5893 NCBI Protein Cluster (PRK) DNA gyrase inhibitor DNA gyrase inhibitor YacG Inhibits supercoiling by DNA gyrase by binding to the GyrB subunit NF001784.0 PRK00517 PRK00517.2-1 244 244 290 equivalog Y Y N 50S ribosomal protein L11 methyltransferase GO:0006479,GO:0008276 1224 Pseudomonadota phylum 4175 NCBI Protein Cluster (PRK) ribosomal protein L11 methyltransferase 50S ribosomal protein L11 methyltransferase NF001901.0 PRK00654 PRK00654.1-5 649 649 502 equivalog Y Y N glycogen synthase GlgA glgA 2.4.1.21 GO:0004373 1224 Pseudomonadota phylum 3959 NCBI Protein Cluster (PRK) glycogen synthase glycogen synthase GlgA NF001935.0 PRK00714 PRK00714.1-2 259 259 183 equivalog Y Y N RNA pyrophosphohydrolase 3.6.1.- GO:0016787 1224 Pseudomonadota phylum 3168 NCBI Protein Cluster (PRK) RNA pyrophosphohydrolase RNA pyrophosphohydrolase NF001937.0 PRK00714 PRK00714.1-4 139 139 161 equivalog Y Y N RNA pyrophosphohydrolase 3.6.1.- GO:0016787 1224 Pseudomonadota phylum 10142 NCBI Protein Cluster (PRK) RNA pyrophosphohydrolase RNA pyrophosphohydrolase NF001962.0 PRK00736 PRK00736.1 72 72 69 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 1085 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF001974.0 PRK00756 PRK00756.1 295 295 197 subfamily Y N N acyltransferase NodA 1224 Pseudomonadota phylum 692 NCBI Protein Cluster (PRK) acyltransferase NodA acyltransferase NodA NF001978.0 PRK00767 PRK00767.1 118 118 197 equivalog Y Y N transcriptional regulator BetI betI GO:0003677 1224 Pseudomonadota phylum 11338 NCBI Protein Cluster (PRK) transcriptional regulator BetI transcriptional regulator BetI HTH-type; bet1; Repressor involved in choline regulation of the bet genes NF001994.1 PRK00790 PRK00790.1-5 100 100 96 equivalog Y Y N flagellar hook-basal body complex protein FliE fliE GO:0003774,GO:0005198,GO:0009288,GO:0071973 1224 Pseudomonadota phylum 1030 NCBI Protein Cluster (PRK) flagellar hook-basal body protein FliE flagellar hook-basal body complex protein FliE NF002009.0 PRK00810 PRK00810.1 117 117 117 equivalog Y Y N nitrogenase stabilizing/protective protein NifW nifW 1224 Pseudomonadota phylum 1102 NCBI Protein Cluster (PRK) nitrogenase stabilizing/protective protein nitrogenase stabilizing/protective protein NifW NF002058.0 PRK00888 PRK00888.1 101 101 111 equivalog Y Y N cell division protein FtsB ftsB 11972052,15165235 1224 Pseudomonadota phylum 7672 NCBI Protein Cluster (PRK) cell division protein FtsB cell division protein FtsB Forms a complex with FtsL and FtsQ; colocalizes to the septal region of the dividing cell NF002141.0 PRK00977 PRK00977.1-5 92 92 93 equivalog Y Y N exodeoxyribonuclease VII small subunit 3.1.11.6 GO:0006308,GO:0008855,GO:0009318 1224 Pseudomonadota phylum 2039 NCBI Protein Cluster (PRK) exodeoxyribonuclease VII small subunit exodeoxyribonuclease VII small subunit NF002153.0 PRK00984 PRK00984.1-2 413 413 353 equivalog Y Y N tRNA pseudouridine(13) synthase TruD truD 5.4.99.27 GO:0001522,GO:0003723,GO:0009451,GO:0009982 1224 Pseudomonadota phylum 5072 NCBI Protein Cluster (PRK) tRNA pseudouridine synthase D tRNA pseudouridine(13) synthase TruD NF002306.0 PRK01231 PRK01231.1 316 316 299 equivalog Y Y N NAD(+) kinase 2.7.1.23 GO:0003951,GO:0006741 1224 Pseudomonadota phylum 7933 NCBI Protein Cluster (PRK) inorganic polyphosphate/ATP-NAD kinase NAD(+) kinase Catalyzes the phosphorylation of NAD to NADP NF002334.0 PRK01294 PRK01294.1-2 285 285 336 equivalog Y Y N lipase secretion chaperone 1224 Pseudomonadota phylum 1672 NCBI Protein Cluster (PRK) lipase chaperone lipase secretion chaperone NF002341.0 PRK01305 PRK01305.1-1 252 252 247 equivalog Y Y N arginyltransferase 2.3.2.8 GO:0004057,GO:0016598 1224 Pseudomonadota phylum 11743 NCBI Protein Cluster (PRK) arginyl-tRNA-protein transferase arginyltransferase NF002348.0 PRK01310 PRK01310.1 115 115 106 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 2248 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002362.0 PRK01343 PRK01343.1 79 79 66 equivalog Y Y N DNA gyrase inhibitor YacG yacG GO:0006355,GO:0008270 1224 Pseudomonadota phylum 2462 NCBI Protein Cluster (PRK) zinc-binding protein DNA gyrase inhibitor YacG NF002386.0 PRK01402 PRK01402.1 346 346 335 equivalog Y Y N Hsp33 family molecular chaperone GO:0006457,GO:0051082 1224 Pseudomonadota phylum 3906 NCBI Protein Cluster (PRK) Hsp33-like chaperonin Hsp33 family molecular chaperone NF002401.0 PRK01441 PRK01441.1 317 317 207 equivalog Y Y N Maf-like protein GO:0047429 1224 Pseudomonadota phylum 2185 NCBI Protein Cluster (PRK) Maf-like protein Maf-like protein NF002453.0 PRK01636 PRK01636.1-1 172 172 134 equivalog Y Y N fluoride efflux transporter CrcB crcB 1224 Pseudomonadota phylum 138 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter CrcB NF002456.0 PRK01636 PRK01636.1-4 173 173 126 equivalog Y Y N fluoride efflux transporter CrcB crcB 1224 Pseudomonadota phylum 24 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter CrcB NF002490.0 PRK01777 PRK01777.1 75 75 96 equivalog Y Y N RnfH family protein 1224 Pseudomonadota phylum 12742 NCBI Protein Cluster (PRK) hypothetical protein RnfH family protein NF002494.0 PRK01821 PRK01821.1 124 124 133 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 2393 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002519.0 PRK01908 PRK01908.1 178 178 209 equivalog Y Y N electron transport complex subunit RsxG rsxG GO:0009055,GO:0010181,GO:0016020,GO:0022900 1224 Pseudomonadota phylum 9634 NCBI Protein Cluster (PRK) electron transport complex protein RnfG electron transport complex subunit RsxG NF002533.0 PRK02047 PRK02047.1 139 139 102 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 1298 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002535.0 PRK02079 PRK02079.1 101 101 92 equivalog Y Y N pyrroloquinoline quinone biosynthesis peptide chaperone PqqD pqqD GO:0018189,GO:0048038 1224 Pseudomonadota phylum 4057 NCBI Protein Cluster (PRK) pyrroloquinoline quinone biosynthesis protein PqqD pyrroloquinoline quinone biosynthesis peptide chaperone PqqD With PqqC converts a biosynthetic intermediate to pyrroloquinoline quinone NF002552.0 PRK02110 PRK02110.1 138 138 169 equivalog Y Y N disulfide bond formation protein B 1224 Pseudomonadota phylum 2382 NCBI Protein Cluster (PRK) disulfide bond formation protein B disulfide bond formation protein B Disulfide oxidoreductase; integral membrane protein; required for perioplasmic disulfide bond formation; oxidizes DsbA protein NF002563.0 PRK02186 PRK02186.1 625 625 890 subfamily Y N N argininosuccinate lyase 1224 Pseudomonadota phylum 1027 NCBI Protein Cluster (PRK) argininosuccinate lyase argininosuccinate lyase NF002576.0 PRK02227 PRK02227.1-5 297 297 236 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 43 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002592.0 PRK02250 PRK02250.1 158 158 167 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 1825 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002675.0 PRK02399 PRK02399.1-3 648 648 398 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 1073 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002837.0 PRK03059 PRK03059.1 1010 1010 857 equivalog Y Y N [protein-PII] uridylyltransferase 2.7.7.59 GO:0008152,GO:0008773 1224 Pseudomonadota phylum 4389 NCBI Protein Cluster (PRK) PII uridylyl-transferase [protein-PII] uridylyltransferase Uridylylates and de-uridylylates the small trimeric nitrogen regulatory protein PII NF002904.0 PRK03512 PRK03512.1 231 231 211 equivalog Y Y N thiamine phosphate synthase thiE 2.5.1.3 GO:0004789,GO:0009228 1224 Pseudomonadota phylum 12160 NCBI Protein Cluster (PRK) thiamine-phosphate pyrophosphorylase thiamine phosphate synthase NF002924.0 PRK03562 PRK03562.1 752 752 623 equivalog Y Y N glutathione-regulated potassium-efflux system protein KefC kefC GO:0006813,GO:0015503 1224 Pseudomonadota phylum 5938 NCBI Protein Cluster (PRK) glutathione-regulated potassium-efflux system protein KefC glutathione-regulated potassium-efflux system protein KefC Transport system that facilitates potassium efflux NF002935.0 PRK03578 PRK03578.1 198 198 176 equivalog Y Y N Fe-S protein assembly co-chaperone HscB hscB GO:0051087,GO:0051259,GO:0097428 1224 Pseudomonadota phylum 2930 NCBI Protein Cluster (PRK) co-chaperone HscB Fe-S protein assembly co-chaperone HscB J-type co-chaperone that regulates the ATPase and peptide-binding activity of Hsc66 chaperone NF002939.0 PRK03598 PRK03598.1 393 393 332 equivalog Y Y N secretion protein HlyD hlyD 1224 Pseudomonadota phylum 5187 NCBI Protein Cluster (PRK) putative efflux pump membrane fusion protein secretion protein HlyD NF002954.0 PRK03606 PRK03606.2-5 212 212 168 equivalog Y Y N ureidoglycolate lyase 4.3.2.3 1224 Pseudomonadota phylum 120 NCBI Protein Cluster (PRK) ureidoglycolate hydrolase ureidoglycolate lyase NF002975.0 PRK03661 PRK03661.1 212 212 164 equivalog Y Y N nicotinamide-nucleotide amidase pncC 3.5.1.42 1224 Pseudomonadota phylum 4339 NCBI Protein Cluster (PRK) hypothetical protein nicotinamide-nucleotide amidase NF002987.0 PRK03719 PRK03719.1 162 162 170 equivalog Y Y N serine protease inhibitor ecotin eco GO:0004867 2007606,24462575,7757004 1224 Pseudomonadota phylum 5106 NCBI Protein Cluster (PRK) ecotin serine protease inhibitor ecotin Serine protease inhibitor, inhibits trypsin and other proteases NF003011.0 PRK03837 PRK03837.1 260 260 241 subfamily Y Y N transcriptional regulator NanR nanR 1224 Pseudomonadota phylum 2966 NCBI Protein Cluster (PRK) transcriptional regulator NanR transcriptional regulator NanR Transcriptional repressor of the nan operon that encodes proteins involved in sialic acid utilization NF003030.0 PRK03910 PRK03910.1-3 429 429 338 equivalog Y Y N D-cysteine desulfhydrase 4.4.1.15 GO:0003824 1224 Pseudomonadota phylum 6099 NCBI Protein Cluster (PRK) D-cysteine desulfhydrase D-cysteine desulfhydrase NF003032.0 PRK03910 PRK03910.1-5 469 469 330 equivalog Y Y N D-cysteine desulfhydrase 4.4.1.15 1224 Pseudomonadota phylum 5576 NCBI Protein Cluster (PRK) D-cysteine desulfhydrase D-cysteine desulfhydrase NF003256.0 PRK04214 PRK04214.1 500 500 412 equivalog Y N N ribonuclease BN/unknown domain fusion protein 1224 Pseudomonadota phylum 1062 NCBI Protein Cluster (PRK) ribonuclease BN/unknown domain fusion protein ribonuclease BN/unknown domain fusion protein NF003316.0 PRK04325 PRK04325.1 80 80 74 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 509 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003404.0 PRK04750 PRK04750.1 667 667 529 equivalog Y Y N ubiquinone biosynthesis regulatory protein kinase UbiB ubiB GO:0006744 10960098,9422602 1224 Pseudomonadota phylum 16035 NCBI Protein Cluster (PRK) putative ubiquinone biosynthesis protein UbiB ubiquinone biosynthesis regulatory protein kinase UbiB NF003428.0 PRK04923 PRK04923.1 536 536 319 equivalog Y Y N ribose-phosphate diphosphokinase 2.7.6.1 1224 Pseudomonadota phylum 1205 NCBI Protein Cluster (PRK) ribose-phosphate pyrophosphokinase ribose-phosphate diphosphokinase Catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP NF003441.0 PRK04974 PRK04974.1 610 610 823 equivalog Y Y N glycerol-3-phosphate 1-O-acyltransferase PlsB plsB 2.3.1.15 GO:0004366,GO:0008654 16816185,6094487,6251087,6997313,7026564 1224 Pseudomonadota phylum 15849 NCBI Protein Cluster (PRK) glycerol-3-phosphate acyltransferase glycerol-3-phosphate 1-O-acyltransferase PlsB Catalyzes the formation of 1-acyl-sn-glycerol 3-phosphate by transfering the acyl moiety from acyl-CoA NF003451.0 PRK05022 PRK05022.1 476 476 512 equivalog Y Y N nitric oxide reductase transcriptional regulator NorR norR GO:0003700,GO:0006355 1224 Pseudomonadota phylum 14945 NCBI Protein Cluster (PRK) anaerobic nitric oxide reductase transcription regulator nitric oxide reductase transcriptional regulator NorR Required for the expression of anaerobic nitric oxide (NO) reductase; acts as a transcriptional activator for the norVW operon NF003456.0 PRK05057 PRK05057.1 195 195 173 equivalog Y Y N shikimate kinase AroK aroK 2.7.1.71 1309529,15299895,3026317 1224 Pseudomonadota phylum 5467 NCBI Protein Cluster (PRK) shikimate kinase I shikimate kinase AroK Type I enzyme similar to type II but differentially regulated; major shikimate kinase in fully repressed cells; catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis NF003468.0 PRK05093 PRK05093.1 522 522 405 subfamily Y Y N acetylornithine/succinyldiaminopimelate transaminase 2.6.1.11,2.6.1.17 10074354 1224 Pseudomonadota phylum 20670 NCBI Protein Cluster (PRK) bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein acetylornithine/succinyldiaminopimelate transaminase NF003473.0 PRK05105 PRK05105.1 236 236 331 equivalog Y Y N o-succinylbenzoate synthase menC 4.2.1.113 GO:0000287,GO:0009234,GO:0016836 1224 Pseudomonadota phylum 9364 NCBI Protein Cluster (PRK) O-succinylbenzoate synthase o-succinylbenzoate synthase Catalyzes the dehydration of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid to form O-succinylbenzoate NF003475.0 PRK05113 PRK05113.1 203 203 190 equivalog Y Y N electron transport complex subunit RsxB rsxB GO:0009055,GO:0022900,GO:0051536 1224 Pseudomonadota phylum 10336 NCBI Protein Cluster (PRK) electron transport complex protein RnfB electron transport complex subunit RsxB NF003496.0 PRK05166 PRK05166.1 540 540 373 equivalog Y Y N histidinol-phosphate transaminase 2.6.1.9 1224 Pseudomonadota phylum 457 NCBI Protein Cluster (PRK) histidinol-phosphate aminotransferase histidinol-phosphate transaminase Catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis NF003509.0 PRK05174 PRK05174.1 124 124 172 equivalog Y Y N bifunctional 3-hydroxydecanoyl-ACP dehydratase/trans-2-decenoyl-ACP isomerase fabA 4.2.1.59,5.3.3.14 GO:0006633,GO:0019171 1224 Pseudomonadota phylum 10310 NCBI Protein Cluster (PRK) 3-hydroxydecanoyl-(acyl carrier protein) dehydratase bifunctional 3-hydroxydecanoyl-ACP dehydratase/trans-2-decenoyl-ACP isomerase Catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP NF003640.0 PRK05277 PRK05277.1 350 350 471 equivalog Y Y N H(+)/Cl(-) exchange transporter ClcA clcA GO:0005247,GO:0005886,GO:0006821,GO:0055085 1224 Pseudomonadota phylum 7041 NCBI Protein Cluster (PRK) chloride channel protein H(+)/Cl(-) exchange transporter ClcA Acts as an electrical shunt for an outwardly-directed proton pump that is linked to amino acid decarboxylation NF003641.0 PRK05279 PRK05279.1 344 344 441 equivalog Y Y N amino-acid N-acetyltransferase argA 2.3.1.1 GO:0004042,GO:0006526 1224 Pseudomonadota phylum 13153 NCBI Protein Cluster (PRK) N-acetylglutamate synthase amino-acid N-acetyltransferase NF003656.0 PRK05287 PRK05287.1-4 213 213 252 equivalog Y Y N cell division protein ZapD zapD 1224 Pseudomonadota phylum 4441 NCBI Protein Cluster (PRK) hypothetical protein cell division protein ZapD NF003680.0 PRK05305 PRK05305.1-5 262 262 217 equivalog Y Y N phosphatidylserine decarboxylase 4.1.1.65 1224 Pseudomonadota phylum 1595 NCBI Protein Cluster (PRK) phosphatidylserine decarboxylase phosphatidylserine decarboxylase NF003706.0 PRK05324 PRK05324.1 170 170 336 subfamily Y Y N succinylglutamate desuccinylase 3.5.1.96 1224 Pseudomonadota phylum 16494 NCBI Protein Cluster (PRK) succinylglutamate desuccinylase succinylglutamate desuccinylase Catalyzes the formation of succinate and glutamate from N(2)-succinylglutamate in arginine catabolism NF003707.0 PRK05325 PRK05325.1-2 396 396 428 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 12706 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003708.0 PRK05325 PRK05325.1-3 466 466 423 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 12285 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003714.0 PRK05326 PRK05326.1-1 471 471 577 equivalog Y Y N potassium/proton antiporter GO:0006813,GO:0006884,GO:0016020,GO:0051139,GO:0055085 1224 Pseudomonadota phylum 10509 NCBI Protein Cluster (PRK) potassium/proton antiporter potassium/proton antiporter NF003743.0 PRK05340 PRK05340.1 134 134 242 equivalog Y Y N UDP-2,3-diacylglucosamine diphosphatase 3.6.1.54 GO:0009245,GO:0016462 1224 Pseudomonadota phylum 21585 NCBI Protein Cluster (PRK) UDP-2,3-diacylglucosamine hydrolase UDP-2,3-diacylglucosamine diphosphatase Catalyzes the formation of 2,3=diacylglucosamine 1-phosphate from UDP-2,3=diacylglucosamine NF003746.0 PRK05346 PRK05346.1-1 337 337 264 equivalog Y Y N Na(+)-translocating NADH-quinone reductase subunit C GO:0006814,GO:0016020,GO:0016655 1224 Pseudomonadota phylum 3241 NCBI Protein Cluster (PRK) Na(+)-translocating NADH-quinone reductase subunit C Na(+)-translocating NADH-quinone reductase subunit C NF003812.0 PRK05406 PRK05406.1-1 378 378 244 equivalog Y Y N 5-oxoprolinase subunit PxpA pxpA 3.5.2.9 GO:0003824,GO:0005975 28830929 1224 Pseudomonadota phylum 4281 NCBI Protein Cluster (PRK) LamB/YcsF family protein 5-oxoprolinase subunit PxpA NF003815.0 PRK05406 PRK05406.1-4 337 337 247 equivalog Y Y N 5-oxoprolinase subunit PxpA pxpA 3.5.2.9 GO:0003824,GO:0005975 28830929 1224 Pseudomonadota phylum 5518 NCBI Protein Cluster (PRK) LamB/YcsF family protein 5-oxoprolinase subunit PxpA NF003833.0 PRK05419 PRK05419.1-5 224 224 216 equivalog Y Y N protein-methionine-sulfoxide reductase heme-binding subunit MsrQ msrQ 1224 Pseudomonadota phylum 2832 NCBI Protein Cluster (PRK) putative sulfite oxidase subunit YedZ protein-methionine-sulfoxide reductase heme-binding subunit MsrQ NF003835.0 PRK05419 PRK05419.2-2 286 286 210 equivalog Y Y N protein-methionine-sulfoxide reductase heme-binding subunit MsrQ msrQ 1224 Pseudomonadota phylum 510 NCBI Protein Cluster (PRK) putative sulfite oxidase subunit YedZ protein-methionine-sulfoxide reductase heme-binding subunit MsrQ NF003938.0 PRK05447 PRK05447.1-1 515 515 398 equivalog Y Y N 1-deoxy-D-xylulose-5-phosphate reductoisomerase ispC 1.1.1.267 GO:0005515,GO:0008299,GO:0030604,GO:0046872,GO:0070402 25171339 1224 Pseudomonadota phylum 18627 NCBI Protein Cluster (PRK) 1-deoxy-D-xylulose 5-phosphate reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase NF003955.0 PRK05454 PRK05454.1-1 1037 1037 855 equivalog Y Y N glucans biosynthesis glucosyltransferase MdoH mdoH 2.4.1.- GO:0016758 1224 Pseudomonadota phylum 7653 NCBI Protein Cluster (PRK) glucosyltransferase MdoH glucans biosynthesis glucosyltransferase MdoH NF003959.0 PRK05454 PRK05454.2-2 550 550 599 equivalog Y Y N glucans biosynthesis glucosyltransferase MdoH mdoH 2.4.1.- 1224 Pseudomonadota phylum 815 NCBI Protein Cluster (PRK) glucosyltransferase MdoH glucans biosynthesis glucosyltransferase MdoH NF003960.0 PRK05454 PRK05454.2-3 829 829 659 equivalog Y Y N glucans biosynthesis glucosyltransferase MdoH mdoH 2.4.1.- 1224 Pseudomonadota phylum 601 NCBI Protein Cluster (PRK) glucosyltransferase MdoH glucans biosynthesis glucosyltransferase MdoH NF004144.0 PRK05621 PRK05621.1-1 372 372 287 equivalog Y Y N F0F1 ATP synthase subunit gamma atpG 7.1.2.2 GO:0015986,GO:0045261,GO:0046933 1224 Pseudomonadota phylum 10129 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit gamma F0F1 ATP synthase subunit gamma NF004163.0 PRK05627 PRK05627.1-6 315 315 313 equivalog Y Y N bifunctional riboflavin kinase/FAD synthetase ribF 2.7.1.26,2.7.7.2 GO:0003919 1224 Pseudomonadota phylum 15836 NCBI Protein Cluster (PRK) bifunctional riboflavin kinase/FMN adenylyltransferase bifunctional riboflavin kinase/FAD synthetase NF004206.0 PRK05656 PRK05656.1 688 688 392 subfamily Y Y N acetyl-CoA C-acetyltransferase 1224 Pseudomonadota phylum 4574 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA C-acetyltransferase Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A NF004207.0 PRK05657 PRK05657.1 394 394 329 equivalog Y Y N RNA polymerase sigma factor RpoS rpoS GO:0003677,GO:0003700,GO:0006352,GO:0006355,GO:0016987 29256853 1224 Pseudomonadota phylum 8239 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RpoS RNA polymerase sigma factor RpoS Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this sigma factor controls a regulon of genes required for protection against external stresses NF004212.0 PRK05665 PRK05665.1 309 309 241 equivalog Y Y N amidotransferase 1224 Pseudomonadota phylum 2110 NCBI Protein Cluster (PRK) amidotransferase amidotransferase NF004224.0 PRK05671 PRK05671.1 284 284 336 equivalog Y Y N aspartate-semialdehyde dehydrogenase 1.2.1.11 GO:0008652,GO:0016620,GO:0046983,GO:0051287 9084174 1224 Pseudomonadota phylum 10351 NCBI Protein Cluster (PRK) aspartate-semialdehyde dehydrogenase aspartate-semialdehyde dehydrogenase Catalyzes the formation of aspartate semialdehyde from aspartyl phosphate NF004238.1 PRK05682 PRK05682.1-1 400 400 414 equivalog Y Y N flagellar hook protein FlgE flgE 15687208,17593964 1224 Pseudomonadota phylum 12774 NCBI Protein Cluster (PRK) flagellar hook protein FlgE flagellar hook protein FlgE NF004270.2 PRK05687 PRK05687.2-1 180 180 223 equivalog Y Y N flagellar assembly protein FliH fliH GO:0003774,GO:0009288 1224 Pseudomonadota phylum 4797 NCBI Protein Cluster (PRK) flagellar assembly protein H flagellar assembly protein FliH NF004310.0 PRK05707 PRK05707.1 280 280 328 equivalog Y Y N DNA polymerase III subunit delta' 2.7.7.7 GO:0003677,GO:0003887,GO:0006260,GO:0008408,GO:0009360 1224 Pseudomonadota phylum 3806 NCBI Protein Cluster (PRK) DNA polymerase III subunit delta' DNA polymerase III subunit delta' Catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA NF004348.0 PRK05728 PRK05728.1-5 178 178 138 equivalog Y Y N DNA polymerase III subunit chi 2.7.7.7 1224 Pseudomonadota phylum 1013 NCBI Protein Cluster (PRK) DNA polymerase III subunit chi DNA polymerase III subunit chi NF004378.0 PRK05740 PRK05740.2-4 171 171 122 equivalog Y Y N preprotein translocase subunit SecE secE 1224 Pseudomonadota phylum 1260 NCBI Protein Cluster (PRK) preprotein translocase subunit SecE preprotein translocase subunit SecE NF004386.0 PRK05749 PRK05749.1-2 524 524 433 equivalog Y Y N lipid IV(A) 3-deoxy-D-manno-octulosonic acid transferase waaA 2.4.99.12 GO:0016740 1224 Pseudomonadota phylum 3527 NCBI Protein Cluster (PRK) 3-deoxy-D-manno-octulosonic-acid transferase lipid IV(A) 3-deoxy-D-manno-octulosonic acid transferase NF004388.0 PRK05749 PRK05749.1-4 438 438 425 equivalog Y Y N lipid IV(A) 3-deoxy-D-manno-octulosonic acid transferase waaA 2.4.99.12 GO:0016740 1224 Pseudomonadota phylum 16150 NCBI Protein Cluster (PRK) 3-deoxy-D-manno-octulosonic-acid transferase lipid IV(A) 3-deoxy-D-manno-octulosonic acid transferase NF004393.0 PRK05751 PRK05751.1-4 180 180 165 equivalog Y Y N protein-export chaperone SecB secB GO:0015031,GO:0051082,GO:0051262 1224 Pseudomonadota phylum 6283 NCBI Protein Cluster (PRK) preprotein translocase subunit SecB protein-export chaperone SecB NF004394.0 PRK05751 PRK05751.1-5 181 181 156 equivalog Y Y N protein-export chaperone SecB secB 1224 Pseudomonadota phylum 2838 NCBI Protein Cluster (PRK) preprotein translocase subunit SecB protein-export chaperone SecB NF004411.0 PRK05759 PRK05759.1-2 131 131 156 equivalog Y Y N F0F1 ATP synthase subunit B 7.1.2.2 GO:0015078,GO:0015986 1224 Pseudomonadota phylum 7952 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit B F0F1 ATP synthase subunit B NF004422.0 PRK05762 PRK05762.1-4 1103 1103 789 equivalog Y Y N DNA polymerase II 2.7.7.7 GO:0000166,GO:0003676,GO:0003887 1224 Pseudomonadota phylum 16233 NCBI Protein Cluster (PRK) DNA polymerase II DNA polymerase II NF004477.0 PRK05815 PRK05815.1-1 280 280 268 equivalog Y Y N F0F1 ATP synthase subunit A atpB 7.1.2.2 GO:0015078,GO:0015986,GO:0045263 1224 Pseudomonadota phylum 10238 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit A F0F1 ATP synthase subunit A NF004585.0 PRK05928 PRK05928.2-2 241 241 255 equivalog Y Y N uroporphyrinogen-III synthase 4.2.1.75 GO:0004852,GO:0006780 1224 Pseudomonadota phylum 1818 NCBI Protein Cluster (PRK) uroporphyrinogen-III synthase uroporphyrinogen-III synthase NF004595.0 PRK05932 PRK05932.1-2 513 513 484 equivalog Y Y N RNA polymerase factor sigma-54 2.7.7.6 GO:0001216,GO:0003677,GO:0006352,GO:0016987 1224 Pseudomonadota phylum 15991 NCBI Protein Cluster (PRK) RNA polymerase factor sigma-54 RNA polymerase factor sigma-54 NF004622.0 PRK05962 PRK05962.1 463 463 431 equivalog Y Y N amidase 1224 Pseudomonadota phylum 1406 NCBI Protein Cluster (PRK) amidase amidase NF004625.0 PRK05965 PRK05965.1 729 729 460 subfamily Y N N hypothetical protein 1224 Pseudomonadota phylum 3570 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004648.0 PRK05991 PRK05991.1 391 391 254 equivalog Y Y N precorrin-3B C(17)-methyltransferase 2.1.1.131 1224 Pseudomonadota phylum 1627 NCBI Protein Cluster (PRK) precorrin-3B C17-methyltransferase precorrin-3B C(17)-methyltransferase Catalyzes the formation of precorrin-4 from precorrin-3B and S-adenosyl-L-methionine NF004742.0 PRK06076 PRK06076.1-3 531 531 356 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoH nuoH 1.6.5.9 GO:0016020 1224 Pseudomonadota phylum 3283 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit H NADH-quinone oxidoreductase subunit NuoH NF004757.0 PRK06084 PRK06084.1 790 790 425 equivalog Y Y N bifunctional O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase 2.5.1.47 1224 Pseudomonadota phylum 1721 NCBI Protein Cluster (PRK) O-acetylhomoserine aminocarboxypropyltransferase bifunctional O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase NF004761.0 PRK06092 PRK06092.1 260 260 268 equivalog Y Y N aminodeoxychorismate lyase pabC 4.1.3.38 GO:0008696,GO:0030170,GO:0046656 8550484,9661666 1224 Pseudomonadota phylum 12598 NCBI Protein Cluster (PRK) 4-amino-4-deoxychorismate lyase aminodeoxychorismate lyase Catalyzes the formation of 4-aminobenzoate and pyruvate from 4-amino-4-deoxychorismate NF004773.0 PRK06113 PRK06113.1 367 367 255 equivalog Y Y N 7-alpha-hydroxysteroid dehydrogenase hdhA 1.1.1.159 1224 Pseudomonadota phylum 965 NCBI Protein Cluster (PRK) 7-alpha-hydroxysteroid dehydrogenase 7-alpha-hydroxysteroid dehydrogenase NF004774.0 PRK06114 PRK06114.1 360 360 262 equivalog Y Y N SDR family oxidoreductase GO:0016491 1224 Pseudomonadota phylum 2076 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF004797.0 PRK06145 PRK06145.1 850 850 499 equivalog Y N N acyl-CoA synthetase 1224 Pseudomonadota phylum 422 NCBI Protein Cluster (PRK) acyl-CoA synthetase acyl-CoA synthetase NF004809.0 PRK06156 PRK06156.1 438 438 573 equivalog Y Y N dipeptidase 3.4.13.- GO:0008270,GO:0016805 1224 Pseudomonadota phylum 4115 NCBI Protein Cluster (PRK) hypothetical protein dipeptidase NF004813.0 PRK06163 PRK06163.1 240 240 202 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 598 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004835.0 PRK06185 PRK06185.1-4 601 601 411 equivalog Y Y N FAD-dependent oxidoreductase 1224 Pseudomonadota phylum 1482 NCBI Protein Cluster (PRK) hypothetical protein FAD-dependent oxidoreductase NF004867.0 PRK06224 PRK06224.1-4 409 409 261 equivalog Y Y N citryl-CoA lyase 4.1.3.34 1224 Pseudomonadota phylum 501 NCBI Protein Cluster (PRK) citrate synthase citryl-CoA lyase NF004954.0 PRK06299 PRK06299.1-4 727 727 560 equivalog Y Y N 30S ribosomal protein S1 rpsA GO:0003723,GO:0003735,GO:0005840,GO:0006412 1224 Pseudomonadota phylum 10143 NCBI Protein Cluster (PRK) 30S ribosomal protein S1 30S ribosomal protein S1 NF004972.0 PRK06341 PRK06341.1 254 254 166 equivalog Y Y N single-stranded DNA-binding protein GO:0003697,GO:0006260 1224 Pseudomonadota phylum 2067 NCBI Protein Cluster (PRK) single-stranded DNA-binding protein single-stranded DNA-binding protein NF005067.0 PRK06484 PRK06484.1 713 713 524 equivalog Y N N short chain dehydrogenase 1224 Pseudomonadota phylum 143 NCBI Protein Cluster (PRK) short chain dehydrogenase short chain dehydrogenase NF005079.0 PRK06508 PRK06508.1 83 83 93 equivalog Y Y N acyl carrier protein 1224 Pseudomonadota phylum 969 NCBI Protein Cluster (PRK) acyl carrier protein acyl carrier protein NF005176.1 PRK06655 PRK06655.1-1 230 230 197 equivalog Y Y N flagellar hook assembly protein FlgD flgD 21604306 1224 Pseudomonadota phylum 4717 NCBI Protein Cluster (PRK) flagellar basal body rod modification protein flagellar hook assembly protein FlgD NF005272.0 PRK06777 PRK06777.1 725 725 421 equivalog Y Y N 4-aminobutyrate--2-oxoglutarate transaminase 2.6.1.19 GO:0009448,GO:0030170 1224 Pseudomonadota phylum 5162 NCBI Protein Cluster (PRK) 4-aminobutyrate aminotransferase 4-aminobutyrate--2-oxoglutarate transaminase Catalyzes the formation of succinate semialdehyde and glutamate from 4-aminobutanoate and 2-oxoglutarate NF005294.0 PRK06819 PRK06819.1 387 387 376 subfamily Y Y N FliC/FljB family flagellin GO:0005198 1224 Pseudomonadota phylum 3388 NCBI Protein Cluster (PRK) flagellin FliC/FljB family flagellin NF005295.0 PRK06820 PRK06820.1 690 690 440 equivalog Y Y N EscN/YscN/HrcN family type III secretion system ATPase 7.1.2.2 1224 Pseudomonadota phylum 285 NCBI Protein Cluster (PRK) type III secretion system ATPase EscN/YscN/HrcN family type III secretion system ATPase NF005296.0 PRK06823 PRK06823.1 438 438 315 equivalog Y Y N ornithine cyclodeaminase family protein 1224 Pseudomonadota phylum 983 NCBI Protein Cluster (PRK) ornithine cyclodeaminase ornithine cyclodeaminase family protein NF005402.0 PRK06949 PRK06949.1 358 358 260 equivalog Y Y N SDR family oxidoreductase 1224 Pseudomonadota phylum 1550 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005404.0 PRK06954 PRK06954.1 687 687 397 subfamily Y Y N acetyl-CoA C-acetyltransferase GO:0016747 1224 Pseudomonadota phylum 1787 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA C-acetyltransferase Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A NF005409.0 PRK06965 PRK06965.1 1035 1035 587 equivalog Y Y N acetolactate synthase 3 catalytic subunit GO:0003984,GO:0009082 1224 Pseudomonadota phylum 3082 NCBI Protein Cluster (PRK) acetolactate synthase 3 catalytic subunit acetolactate synthase 3 catalytic subunit NF005410.0 PRK06973 PRK06973.1 214 214 243 equivalog Y Y N nicotinate-nucleotide adenylyltransferase 2.7.7.18 1224 Pseudomonadota phylum 1703 NCBI Protein Cluster (PRK) nicotinic acid mononucleotide adenylyltransferase nicotinate-nucleotide adenylyltransferase NF005411.0 PRK06975 PRK06975.1 414 414 660 equivalog Y Y N fused uroporphyrinogen-III synthase HemD/membrane protein HemX hemDX 2.1.1.107,4.2.1.75 GO:0004852,GO:0033014 1224 Pseudomonadota phylum 1800 NCBI Protein Cluster (PRK) bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase fused uroporphyrinogen-III synthase HemD/membrane protein HemX Catalyzes the formation of uroporphyrinogen-III from hydroxymethylbilane and the formation of precorrin-2 from uroporphyrin III and S-adenosyl-L-methionine by two sequential methylation reactions; functions in tetrapyrrole and heme biosynthesis NF005422.0 PRK06997 PRK06997.1 440 440 262 equivalog Y Y N enoyl-ACP reductase FabI fabI GO:0004318,GO:0006633 1224 Pseudomonadota phylum 2426 NCBI Protein Cluster (PRK) enoyl-(acyl carrier protein) reductase enoyl-ACP reductase FabI NF005435.1 PRK07021 PRK07021.1 131 131 157 equivalog Y Y N flagellar basal body-associated protein FliL fliL GO:0006935,GO:0009425,GO:0071973 10439416,18284590,28717192 1224 Pseudomonadota phylum 3651 NCBI Protein Cluster (PRK) flagellar basal body-associated protein FliL flagellar basal body-associated protein FliL Interacts with the cytoplasmic MS ring of the basal body and may act to stabilize the MotAB complexes which surround the MS ring NF005443.0 PRK07030 PRK07030.1 729 729 451 equivalog Y Y N adenosylmethionine--8-amino-7-oxononanoate transaminase 2.6.1.62 GO:0004015,GO:0009102 1224 Pseudomonadota phylum 3649 NCBI Protein Cluster (PRK) adenosylmethionine--8-amino-7-oxononanoate transaminase adenosylmethionine--8-amino-7-oxononanoate transaminase Catalyzes the formation of S-adenosyl-4-methylthionine-2-oxobutanoate and 7,8-diaminononanoate from S-adenosyl-L-methionine and 8-amino-7-oxononanoate NF005444.0 PRK07033 PRK07033.1 520 520 438 equivalog Y Y N DotU family type VI secretion system protein 1224 Pseudomonadota phylum 3203 NCBI Protein Cluster (PRK) hypothetical protein DotU family type VI secretion system protein NF005448.0 PRK07037 PRK07037.1 190 190 186 equivalog Y Y N RNA polymerase factor sigma-70 2.7.7.6 GO:0003677,GO:0006352,GO:0016987 1224 Pseudomonadota phylum 2051 NCBI Protein Cluster (PRK) extracytoplasmic-function sigma-70 factor RNA polymerase factor sigma-70 NF005452.0 PRK07045 PRK07045.1 397 397 388 equivalog Y N N putative monooxygenase 1224 Pseudomonadota phylum 387 NCBI Protein Cluster (PRK) putative monooxygenase putative monooxygenase NF005459.0 PRK07054 PRK07054.1 475 475 476 equivalog Y Y N isochorismate synthase 5.4.4.2 1224 Pseudomonadota phylum 1255 NCBI Protein Cluster (PRK) salicylate biosynthesis isochorismate synthase isochorismate synthase NF005462.0 PRK07058 PRK07058.1 486 486 396 equivalog Y Y N acetate/propionate family kinase 1224 Pseudomonadota phylum 1337 NCBI Protein Cluster (PRK) acetate kinase acetate/propionate family kinase NF005465.0 PRK07060 PRK07060.1-2 331 331 241 equivalog Y N N short chain dehydrogenase 1224 Pseudomonadota phylum 442 NCBI Protein Cluster (PRK) short chain dehydrogenase short chain dehydrogenase NF005467.0 PRK07060 PRK07060.1-5 360 360 245 equivalog Y Y N SDR family oxidoreductase GO:0016491 1224 Pseudomonadota phylum 1151 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005469.0 PRK07063 PRK07063.1 306 306 260 equivalog Y Y N SDR family oxidoreductase GO:0016491 1224 Pseudomonadota phylum 3605 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005474.0 PRK07074 PRK07074.1 361 361 259 equivalog Y Y N SDR family oxidoreductase 1224 Pseudomonadota phylum 1300 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005476.0 PRK07077 PRK07077.1 215 215 243 equivalog Y Y N phosphorylase GO:0003824 1224 Pseudomonadota phylum 1790 NCBI Protein Cluster (PRK) hypothetical protein phosphorylase NF005525.0 PRK07178 PRK07178.1 768 768 471 equivalog Y Y N acetyl-CoA carboxylase biotin carboxylase subunit 6.4.1.2 GO:0005524 1224 Pseudomonadota phylum 2155 NCBI Protein Cluster (PRK) pyruvate carboxylase subunit A acetyl-CoA carboxylase biotin carboxylase subunit NF005535.1 PRK07196 PRK07196.1 715 715 434 equivalog Y Y N flagellar protein export ATPase FliI fliI 7.1.2.2 GO:0005524,GO:0016887,GO:0030254 1224 Pseudomonadota phylum 1507 NCBI Protein Cluster (PRK) flagellum-specific ATP synthase flagellar protein export ATPase FliI Involved in type III protein export during flagellum assembly NF005599.0 PRK07333 PRK07333.1 549 549 414 equivalog Y Y N ubiquinone biosynthesis hydroxylase GO:0006744,GO:0016709,GO:0071949 1224 Pseudomonadota phylum 3267 NCBI Protein Cluster (PRK) 2-octaprenyl-6-methoxyphenyl hydroxylase ubiquinone biosynthesis hydroxylase NF005675.0 PRK07468 PRK07468.1 350 350 262 equivalog Y Y N crotonase/enoyl-CoA hydratase family protein GO:0003824 1224 Pseudomonadota phylum 2362 NCBI Protein Cluster (PRK) enoyl-CoA hydratase crotonase/enoyl-CoA hydratase family protein NF005678.0 PRK07473 PRK07473.1 386 386 376 equivalog Y Y N M20/M25/M40 family metallo-hydrolase 1224 Pseudomonadota phylum 1464 NCBI Protein Cluster (PRK) carboxypeptidase M20/M25/M40 family metallo-hydrolase NF005695.0 PRK07503 PRK07503.1 666 666 403 equivalog Y Y N methionine gamma-lyase 4.4.1.11 GO:0018826,GO:0019346,GO:0030170 1224 Pseudomonadota phylum 2473 NCBI Protein Cluster (PRK) methionine gamma-lyase methionine gamma-lyase Catalyzes the formation of methanethiol and 2-ocobutanoate from L-methionine NF005716.0 PRK07531 PRK07531.1 592 592 495 equivalog Y Y N carnitine 3-dehydrogenase 1.1.1.108 1224 Pseudomonadota phylum 3070 NCBI Protein Cluster (PRK) bifunctional 3-hydroxyacyl-CoA dehydrogenase/thioesterase carnitine 3-dehydrogenase NF005723.0 PRK07539 PRK07539.1-3 226 226 158 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoE nuoE 1.6.5.9 GO:0016491 1224 Pseudomonadota phylum 2517 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit E NADH-quinone oxidoreductase subunit NuoE NF005724.0 PRK07539 PRK07539.1-4 280 280 240 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoE nuoE 1.6.5.9 1224 Pseudomonadota phylum 5636 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit E NADH-quinone oxidoreductase subunit NuoE NF005729.0 PRK07546 PRK07546.1-3 175 175 196 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 2536 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005788.0 PRK07608 PRK07608.1-3 478 478 388 equivalog Y Y N UbiH/UbiF family hydroxylase 1224 Pseudomonadota phylum 660 NCBI Protein Cluster (PRK) ubiquinone biosynthesis hydroxylase family protein UbiH/UbiF family hydroxylase NF005791.0 PRK07627 PRK07627.1 442 442 425 equivalog Y Y N dihydroorotase 3.5.2.3 1224 Pseudomonadota phylum 7657 NCBI Protein Cluster (PRK) dihydroorotase dihydroorotase NF005792.0 PRK07630 PRK07630.1 291 291 312 equivalog Y Y N CobD/CbiB family protein 1224 Pseudomonadota phylum 2681 NCBI Protein Cluster (PRK) CobD/CbiB family protein CobD/CbiB family protein NF005935.0 PRK07967 PRK07967.1 630 630 406 equivalog Y Y N beta-ketoacyl-ACP synthase I fabB 2.3.1.41 GO:0004315,GO:0006633 1224 Pseudomonadota phylum 14117 NCBI Protein Cluster (PRK) 3-oxoacyl-(acyl carrier protein) synthase I beta-ketoacyl-ACP synthase I NF005942.0 PRK07994 PRK07994.1 613 613 655 equivalog Y Y N DNA polymerase III subunit gamma/tau dnaX 2.7.7.7 GO:0003677,GO:0003887,GO:0005524,GO:0006260,GO:0009360 1224 Pseudomonadota phylum 33663 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunit gamma/tau NF005957.0 PRK08040 PRK08040.1 273 273 336 equivalog Y Y N aspartate-semialdehyde dehydrogenase 1.2.1.11 GO:0008652,GO:0016620,GO:0046983,GO:0051287 1224 Pseudomonadota phylum 11441 NCBI Protein Cluster (PRK) putative semialdehyde dehydrogenase aspartate-semialdehyde dehydrogenase NF005969.0 PRK08057 PRK08057.1-3 302 302 243 equivalog Y Y N cobalt-precorrin-6A reductase 1.3.1.106 GO:0009236,GO:0016994 1224 Pseudomonadota phylum 4547 NCBI Protein Cluster (PRK) cobalt-precorrin-6x reductase cobalt-precorrin-6A reductase NF005999.0 PRK08126 PRK08126.1 571 571 432 subfamily Y N N hypothetical protein 1224 Pseudomonadota phylum 1157 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006001.0 PRK08131 PRK08131.1 622 622 401 equivalog Y Y N 3-oxoadipyl-CoA thiolase 2.3.1.174 GO:0016746 1224 Pseudomonadota phylum 2068 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase 3-oxoadipyl-CoA thiolase NF006005.0 PRK08136 PRK08136.1 185 185 314 equivalog Y Y N DNA-binding protein YbiB ybiB 1224 Pseudomonadota phylum 8156 NCBI Protein Cluster (PRK) glycosyl transferase family protein DNA-binding protein YbiB NF006007.0 PRK08138 PRK08138.1 355 355 261 subfamily Y N N enoyl-CoA hydratase 1224 Pseudomonadota phylum 2344 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF006012.0 PRK08149 PRK08149.1 594 594 431 equivalog Y Y N type III secretion system ATPase SctN sctN 7.1.2.2 26520801 1224 Pseudomonadota phylum 1420 NCBI Protein Cluster (PRK) ATP synthase SpaL type III secretion system ATPase SctN The type III secretion system (T3SS) ATPase SctN (Secretion and Cellular Translocation N) includes proteins given lineage-specific designations YscN, EscN, PscN, Spa47, InvC, SsaN, CdsN, BsaS, HrcN, etc. The flagellar apparatus equivalent ATPase is FliI. NF006017.0 PRK08156 PRK08156.1 394 394 367 equivalog Y Y N EscU/YscU/HrcU family type III secretion system export apparatus switch protein 1224 Pseudomonadota phylum 1468 NCBI Protein Cluster (PRK) type III secretion system protein SpaS EscU/YscU/HrcU family type III secretion system export apparatus switch protein NF006033.0 PRK08175 PRK08175.1 647 647 407 equivalog Y Y N alanine transaminase alaC 2.6.1.2 GO:0003824,GO:0009058,GO:0030170 1224 Pseudomonadota phylum 6531 NCBI Protein Cluster (PRK) aminotransferase alanine transaminase NF006034.0 PRK08176 PRK08176.1 342 342 283 equivalog Y Y N pyridoxine/pyridoxal/pyridoxamine kinase pdxK thiJ 2.7.1.35 GO:0008478,GO:0009443 16740960 1224 Pseudomonadota phylum 3123 NCBI Protein Cluster (PRK) pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase pyridoxine/pyridoxal/pyridoxamine kinase Catalyzes the phosphorylation of three vitamin B6 precursors, pyridoxal, pyridoxine and pyridoxamine NF006035.0 PRK08177 PRK08177.1 251 251 228 equivalog Y Y N SDR family oxidoreductase GO:0016491 1224 Pseudomonadota phylum 3235 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006106.0 PRK08257 PRK08257.1-5 684 684 503 equivalog Y N N acetyl-CoA acetyltransferase 1224 Pseudomonadota phylum 816 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA acetyltransferase NF006447.0 PRK08769 PRK08769.1 348 348 319 equivalog Y Y N DNA polymerase III subunit delta' 2.7.7.7 1224 Pseudomonadota phylum 939 NCBI Protein Cluster (PRK) DNA polymerase III subunit delta' DNA polymerase III subunit delta' Catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA NF006456.0 PRK08815 PRK08815.1 464 464 376 equivalog Y Y N GTP cyclohydrolase II RibA ribA 3.5.4.25 1224 Pseudomonadota phylum 1178 NCBI Protein Cluster (PRK) GTP cyclohydrolase GTP cyclohydrolase II RibA NF006467.0 PRK08869 PRK08869.1-2 443 443 400 subfamily Y Y N flagellin 1224 Pseudomonadota phylum 1471 NCBI Protein Cluster (PRK) flagellin flagellin NF006487.0 PRK08905 PRK08905.1 281 281 290 equivalog Y Y N lysophospholipid acyltransferase family protein GO:0016740 1224 Pseudomonadota phylum 3458 NCBI Protein Cluster (PRK) lipid A biosynthesis lauroyl acyltransferase lysophospholipid acyltransferase family protein NF006509.0 PRK08945 PRK08945.1 269 269 248 equivalog Y Y N YciK family oxidoreductase GO:0016491 1224 Pseudomonadota phylum 10444 NCBI Protein Cluster (PRK) putative oxoacyl-(acyl carrier protein) reductase YciK family oxidoreductase NF006523.0 PRK08974 PRK08974.1 884 884 561 equivalog Y Y N long-chain-fatty-acid--CoA ligase FadD fadD 6.2.1.3 1224 Pseudomonadota phylum 6604 NCBI Protein Cluster (PRK) long-chain-fatty-acid--CoA ligase long-chain-fatty-acid--CoA ligase FadD Activates fatty acids by binding to coenzyme A NF006524.0 PRK08978 PRK08978.1 738 738 548 equivalog Y Y N acetolactate synthase 2 catalytic subunit ilvG 2.2.1.6 GO:0000287,GO:0003984,GO:0009082,GO:0030976,GO:0050660 9581571 1224 Pseudomonadota phylum 10654 NCBI Protein Cluster (PRK) acetolactate synthase 2 catalytic subunit acetolactate synthase 2 catalytic subunit NF006534.0 PRK09014 PRK09014.1 124 124 162 equivalog Y Y N transcription/translation regulatory transformer protein RfaH rfaH GO:0006355 23131843,26230837 1224 Pseudomonadota phylum 5537 NCBI Protein Cluster (PRK) transcriptional activator RfaH transcription/translation regulatory transformer protein RfaH NF006537.0 PRK09027 PRK09027.1 153 153 295 equivalog Y Y N cytidine deaminase cdd 3.5.4.5 GO:0004126,GO:0008270,GO:0009972 1224 Pseudomonadota phylum 7644 NCBI Protein Cluster (PRK) cytidine deaminase cytidine deaminase Reclaims exogenous and endogenous cytidine and 2'-deoxycytidine molecules for UMP synthesis NF006541.1 PRK09038 PRK09038.1 283 283 253 equivalog Y Y N flagellar motor protein MotD motD 15629949 1224 Pseudomonadota phylum 4178 NCBI Protein Cluster (PRK) flagellar motor protein MotD flagellar motor protein MotD Homologous to MotB; with MotC (a MotA homolog) forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine; either MotAB or MotCD is sufficient for swimming, but both are necessary for swarming motility NF006544.0 PRK09039 PRK09039.1-3 362 362 343 equivalog Y Y N peptidoglycan -binding protein 1224 Pseudomonadota phylum 2853 NCBI Protein Cluster (PRK) hypothetical protein peptidoglycan -binding protein NF006548.1 PRK09041 PRK09041.1 277 277 287 equivalog Y Y N flagellar motor protein MotB motB 19081534,21165649 1224 Pseudomonadota phylum 11183 NCBI Protein Cluster (PRK) flagellar motor protein MotB flagellar motor protein MotB NF006554.0 PRK09053 PRK09053.1 595 595 453 equivalog Y Y N 3-carboxy-cis,cis-muconate cycloisomerase 5.5.1.2 GO:0019619,GO:0047472 1224 Pseudomonadota phylum 8596 NCBI Protein Cluster (PRK) 3-carboxy-cis,cis-muconate cycloisomerase 3-carboxy-cis,cis-muconate cycloisomerase Catalyzes the cycloisomerization of cis,cis-muconate NF006564.0 PRK09071 PRK09071.1 257 257 335 equivalog Y Y N glycosyl transferase family protein 1224 Pseudomonadota phylum 8117 NCBI Protein Cluster (PRK) hypothetical protein glycosyl transferase family protein NF006565.0 PRK09072 PRK09072.1 238 238 265 equivalog Y Y N SDR family oxidoreductase GO:0016491 1224 Pseudomonadota phylum 5186 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006572.0 PRK09088 PRK09088.1 696 696 491 equivalog Y N N acyl-CoA synthetase 1224 Pseudomonadota phylum 508 NCBI Protein Cluster (PRK) acyl-CoA synthetase acyl-CoA synthetase NF006574.0 PRK09098 PRK09098.1 278 278 277 subfamily Y Y N HrpE/YscL family type III secretion apparatus protein 1224 Pseudomonadota phylum 619 NCBI Protein Cluster (PRK) type III secretion system protein HrpB HrpE/YscL family type III secretion apparatus protein NF006575.0 PRK09099 PRK09099.1 706 706 443 subfamily Y N N type III secretion system ATPase 1224 Pseudomonadota phylum 850 NCBI Protein Cluster (PRK) type III secretion system ATPase type III secretion system ATPase NF006576.0 PRK09101 PRK09101.1 346 346 376 equivalog Y Y N class Ia ribonucleoside-diphosphate reductase subunit beta nrdB 1.17.4.1 GO:0009263,GO:0016491 15158709,9748343 1224 Pseudomonadota phylum 5489 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit beta class Ia ribonucleoside-diphosphate reductase subunit beta NF006578.0 PRK09103 PRK09103.1 813 813 761 equivalog Y Y N class 1a ribonucleoside-diphosphate reductase subunit alpha nrdA GO:0004748,GO:0005524,GO:0006260 1224 Pseudomonadota phylum 8955 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit alpha class 1a ribonucleoside-diphosphate reductase subunit alpha NF006608.0 PRK09169 PRK09169.1-2 2775 0 2319 subfamily Y N N hypothetical protein 1224 Pseudomonadota phylum 976 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006620.0 PRK09188 PRK09188.1 490 490 365 equivalog Y N N serine/threonine protein kinase 1224 Pseudomonadota phylum 748 NCBI Protein Cluster (PRK) serine/threonine protein kinase serine/threonine protein kinase NF006682.0 PRK09229 PRK09229.1-3 637 637 454 equivalog Y Y N formimidoylglutamate deiminase 3.5.3.13 GO:0016810 1224 Pseudomonadota phylum 5099 NCBI Protein Cluster (PRK) N-formimino-L-glutamate deiminase formimidoylglutamate deiminase NF006723.0 PRK09261 PRK09261.1-1 568 568 351 equivalog Y Y N 3-deoxy-7-phosphoheptulonate synthase AroG aroG 2.5.1.54 GO:0003849,GO:0009073 1224 Pseudomonadota phylum 7832 NCBI Protein Cluster (PRK) phospho-2-dehydro-3-deoxyheptonate aldolase 3-deoxy-7-phosphoheptulonate synthase AroG NF006877.0 PRK09375 PRK09375.1-1 470 470 356 equivalog Y Y N quinolinate synthase NadA nadA 2.5.1.72 GO:0008987,GO:0009435,GO:0051539 1224 Pseudomonadota phylum 15208 NCBI Protein Cluster (PRK) quinolinate synthetase quinolinate synthase NadA NF006946.0 PRK09428 PRK09428.1 314 314 451 equivalog Y Y N CDP-diacylglycerol--serine O-phosphatidyltransferase pssA 2.7.8.8 GO:0008444,GO:0032049 1323044,2002065,4604873 1224 Pseudomonadota phylum 9326 NCBI Protein Cluster (PRK) phosphatidylserine synthase CDP-diacylglycerol--serine O-phosphatidyltransferase Catalyzes de novo synthesis of phosphatidylserine from CDP-diacylglycerol and L-serine which leads eventually to the production of phosphatidylethanolamine; bounds to the ribosome NF006947.1 PRK09429 PRK09429.1 272 272 256 equivalog Y Y N penicillin-insensitive murein endopeptidase mepA 3.4.-.- GO:0004252,GO:0006508,GO:0030288 15292190,2187143 1224 Pseudomonadota phylum 11690 NCBI Protein Cluster (PRK) penicillin-insensitive murein endopeptidase penicillin-insensitive murein endopeptidase D-alanyl-D-alanine endopeptidase; functions in hydrolyzing cell wall peptidoglycan NF006948.0 PRK09430 PRK09430.1 162 162 267 equivalog Y Y N co-chaperone DjlA djlA GO:0051087 11106641,12655402,8809778,9364917 1224 Pseudomonadota phylum 7311 NCBI Protein Cluster (PRK) Dna-J like membrane chaperone protein co-chaperone DjlA Functions as a co-chaperone with DnaK; involved in regulation of colanic acid capsule; J-like domain is cytoplasmic and can Functionally substitute for DnaJ; stimulates synthesis of colanic acid mucoid capsule through the RcsB/C signal transduction system NF006950.0 PRK09432 PRK09432.1 382 382 296 equivalog Y Y N methylenetetrahydrofolate reductase metF 1.5.1.20 GO:0004489,GO:0009086 10201405,10769117,15865426,6356036 1224 Pseudomonadota phylum 4803 NCBI Protein Cluster (PRK) 5,10-methylenetetrahydrofolate reductase methylenetetrahydrofolate reductase MTHFR; catalyzes NADH-linked reduction of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate using FAD as a cofactor NF006961.0 PRK09438 PRK09438.1 103 103 151 equivalog Y Y N dihydroneopterin triphosphate diphosphatase nudB 3.6.1.67 GO:0008828,GO:0019177,GO:0046656 1224 Pseudomonadota phylum 6827 NCBI Protein Cluster (PRK) dihydroneopterin triphosphate pyrophosphatase dihydroneopterin triphosphate diphosphatase Catalyzes the formation of dihydroneopterin phosphate from dihydroneopterin triphosphate NF006965.0 PRK09440 PRK09440.1-3 754 754 430 equivalog Y Y N valine--pyruvate transaminase 2.6.1.66 1224 Pseudomonadota phylum 725 NCBI Protein Cluster (PRK) valine--pyruvate transaminase valine--pyruvate transaminase NF006989.0 PRK09454 PRK09454.1 264 264 251 equivalog Y Y N glycerophosphodiester phosphodiesterase ugpQ 3.1.4.46 GO:0006629,GO:0008081 1851953 1224 Pseudomonadota phylum 8233 NCBI Protein Cluster (PRK) cytoplasmic glycerophosphodiester phosphodiesterase glycerophosphodiester phosphodiesterase NF006992.0 PRK09457 PRK09457.1 514 514 487 subfamily Y Y N succinylglutamate-semialdehyde dehydrogenase 1.2.1.71 15808744 1224 Pseudomonadota phylum 22206 NCBI Protein Cluster (PRK) succinylglutamic semialdehyde dehydrogenase succinylglutamate-semialdehyde dehydrogenase NF006999.0 PRK09462 PRK09462.1 146 146 148 equivalog Y Y N ferric iron uptake transcriptional regulator fur GO:0003700,GO:0006355 1868094,2015825,2823881 1224 Pseudomonadota phylum 8299 NCBI Protein Cluster (PRK) ferric uptake regulator ferric iron uptake transcriptional regulator Negatively regulates a number of operons that encode enzymes involved in iron transport; activated by manganese NF007005.1 PRK09468 PRK09468.1 331 331 237 equivalog Y Y N two-component system response regulator OmpR ompR GO:0000160,GO:0003677,GO:0006355 15979641,21345178,24813471,25893523,28861396,3533941,7932717,8989318,9016718 1224 Pseudomonadota phylum 5113 NCBI Protein Cluster (PRK) osmolarity response regulator two-component system response regulator OmpR Part of two-component system EnvZ/OmpR; regulates transcription of outer membrane porin genes ompC/F; under high osmolarity EnvZ functions as kinase/phosphotransferase and phosphorylates OmpR; the result is increased expression of ompC and repression of ompF; also functions in regulation of other genes; forms dimers upon phosphorylation; NF007006.0 PRK09469 PRK09469.1 845 845 469 equivalog Y Y N glutamate--ammonia ligase glnA 6.3.1.2 GO:0004356,GO:0006542,GO:0008152 1224 Pseudomonadota phylum 5354 NCBI Protein Cluster (PRK) glutamine synthetase glutamate--ammonia ligase NF007008.0 PRK09471 PRK09471.1 388 388 306 equivalog Y Y N oligopeptide ABC transporter permease OppB oppB 7.4.2.- GO:0016020,GO:0055085 31704256 1224 Pseudomonadota phylum 5017 NCBI Protein Cluster (PRK) oligopeptide transporter permease oligopeptide ABC transporter permease OppB NF007010.1 PRK09473 PRK09473.1 575 575 318 subfamily Y Y N oligopeptide ABC transporter ATP-binding protein OppD oppD 1224 Pseudomonadota phylum 4082 NCBI Protein Cluster (PRK) oligopeptide transporter ATP-binding component oligopeptide ABC transporter ATP-binding protein OppD NF007015.0 PRK09480 PRK09480.1 120 120 197 equivalog Y Y N nucleoid occlusion factor SlmA slmA GO:0003677,GO:0010974 28683122 1224 Pseudomonadota phylum 6693 NCBI Protein Cluster (PRK) division inhibitor protein nucleoid occlusion factor SlmA FtsZ binding protein; this protein is the first identified nucleoid occlusion factor which works along with the Min system to properly position the FtsZ ring assembly NF007019.0 PRK09484 PRK09484.1 208 208 187 equivalog Y Y N 3-deoxy-manno-octulosonate-8-phosphatase KdsC kdsC 3.1.3.45 GO:0016788 12639950,6246070 1224 Pseudomonadota phylum 4752 NCBI Protein Cluster (PRK) 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase 3-deoxy-manno-octulosonate-8-phosphatase KdsC Catalyzes hydrolysis of KDO 8-P to KDO and inorganic phosphate; functions in lipopolysaccharide biosynthesis NF007027.0 PRK09493 PRK09493.1 379 379 240 equivalog Y Y N glutamine ABC transporter ATP-binding protein GlnQ glnQ 7.4.2.1 GO:0003333,GO:0005524,GO:0015424 1224 Pseudomonadota phylum 2759 NCBI Protein Cluster (PRK) glutamine ABC transporter ATP-binding protein glutamine ABC transporter ATP-binding protein GlnQ NF007028.0 PRK09494 PRK09494.1 303 303 219 equivalog Y Y N glutamine ABC transporter permease GlnP glnP 7.4.2.1 GO:0016020,GO:0022857,GO:0043190,GO:0055085 3027504,6115851 1224 Pseudomonadota phylum 2050 NCBI Protein Cluster (PRK) glutamine ABC transporter permease protein glutamine ABC transporter permease GlnP NF007029.0 PRK09495 PRK09495.1 303 303 248 equivalog Y Y N glutamine ABC transporter substrate-binding protein GlnH glnH 7.4.2.1 GO:0015599,GO:0043190,GO:1903803 3027504,6115851 1224 Pseudomonadota phylum 2969 NCBI Protein Cluster (PRK) glutamine ABC transporter periplasmic protein glutamine ABC transporter substrate-binding protein GlnH NF007030.0 PRK09496 PRK09496.1-1 371 371 458 equivalog Y Y N Trk system potassium transporter TrkA trkA GO:0006813,GO:0015079,GO:0016020 1224 Pseudomonadota phylum 10041 NCBI Protein Cluster (PRK) potassium transporter peripheral membrane component Trk system potassium transporter TrkA NF007049.0 PRK09502 PRK09502.1 181 181 107 equivalog Y Y N iron-sulfur cluster assembly protein IscA iscA 14705938,14720122,15985427 1224 Pseudomonadota phylum 1721 NCBI Protein Cluster (PRK) iron-sulfur cluster assembly protein iron-sulfur cluster assembly protein IscA Forms iron-sulfur clusters of ferredoxin [2FE-2S]; binds iron in the presence of the thioredoxin reductase system NF007089.0 PRK09543 PRK09543.1 284 284 261 equivalog Y Y N zinc ABC transporter permease subunit ZnuB znuB 7.2.2.- GO:0042626,GO:0055085 9680209 1224 Pseudomonadota phylum 7605 NCBI Protein Cluster (PRK) high-affinity zinc transporter membrane component zinc ABC transporter permease subunit ZnuB NF007091.2 PRK09545 PRK09545.1 268 268 318 equivalog Y Y N zinc ABC transporter substrate-binding protein ZnuA znuA 7.2.2.- GO:0006829,GO:0046872 10496878,9680209 1224 Pseudomonadota phylum 9688 NCBI Protein Cluster (PRK) high-affinity zinc transporter periplasmic component zinc ABC transporter substrate-binding protein ZnuA NF007104.0 PRK09553 PRK09553.1 313 313 282 equivalog Y Y N taurine dioxygenase tauD 1.14.11.17 GO:0016491 10563813,11955067,12741810 1224 Pseudomonadota phylum 7114 NCBI Protein Cluster (PRK) taurine dioxygenase taurine dioxygenase NF007109.1 PRK09558 PRK09558.1 600 600 550 equivalog Y Y N bifunctional UDP-sugar hydrolase/5'-nucleotidase UshA ushA 3.1.3.5,3.6.1.45 GO:0000166,GO:0009166,GO:0016787,GO:0046872 10331872,18641143,23333297 1224 Pseudomonadota phylum 10155 NCBI Protein Cluster (PRK) bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor bifunctional UDP-sugar hydrolase/5'-nucleotidase UshA NF007130.1 PRK09575 PRK09575.1 445 445 435 equivalog Y Y N MATE family efflux transporter 1224 Pseudomonadota phylum 2206 NCBI Protein Cluster (PRK) multidrug efflux pump VmrA MATE family efflux transporter NF007131.0 PRK09577 PRK09577.1 1768 1768 1045 equivalog Y Y N multidrug efflux RND transporter permease subunit 1224 Pseudomonadota phylum 1808 NCBI Protein Cluster (PRK) multidrug efflux protein multidrug efflux RND transporter permease subunit NF007132.1 PRK09578 PRK09578.1 512 512 396 equivalog Y Y N MexX/AxyX family multidrug efflux RND transporter periplasmic adaptor subunit 1224 Pseudomonadota phylum 1114 NCBI Protein Cluster (PRK) periplasmic multidrug efflux lipoprotein precursor MexX/AxyX family multidrug efflux RND transporter periplasmic adaptor subunit NF007232.0 PRK09651 PRK09651.1 185 185 173 subfamily Y N N RNA polymerase sigma factor FecI 1224 Pseudomonadota phylum 5643 NCBI Protein Cluster (PRK) RNA polymerase sigma factor FecI RNA polymerase sigma factor FecI NF007256.0 PRK09705 PRK09705.1 312 312 393 subfamily Y Y N cyanate transporter GO:0022857,GO:0055085 3049588,8444806 1224 Pseudomonadota phylum 10133 NCBI Protein Cluster (PRK) putative cyanate transporter cyanate transporter MFS transporter family member induced in the presence of cyanate as part of a 3 gene operon NF007320.0 PRK09812 PRK09812.1 129 129 116 equivalog Y Y N type II toxin-antitoxin system ChpB family toxin 1224 Pseudomonadota phylum 843 NCBI Protein Cluster (PRK) toxin ChpB type II toxin-antitoxin system ChpB family toxin NF007339.0 PRK09834 PRK09834.1-1 299 299 271 equivalog Y Y N DNA-binding transcriptional regulator 1224 Pseudomonadota phylum 317 NCBI Protein Cluster (PRK) DNA-binding transcriptional activator MhpR DNA-binding transcriptional regulator NF007342.0 PRK09834 PRK09834.1-4 251 251 263 equivalog Y Y N DNA-binding transcriptional regulator 1224 Pseudomonadota phylum 356 NCBI Protein Cluster (PRK) DNA-binding transcriptional activator MhpR DNA-binding transcriptional regulator NF007345.0 PRK09835 PRK09835.1 423 423 482 subfamily Y Y N Cu(+)/Ag(+) sensor histidine kinase 2.7.13.3 1224 Pseudomonadota phylum 5127 NCBI Protein Cluster (PRK) sensor kinase CusS Cu(+)/Ag(+) sensor histidine kinase NF007392.0 PRK09918 PRK09918.1 183 183 236 subfamily Y Y N fimbria/pilus chaperone family protein GO:0061077 1224 Pseudomonadota phylum 3637 NCBI Protein Cluster (PRK) putative fimbrial chaperone protein fimbria/pilus chaperone family protein NF007394.0 PRK09920 PRK09920.1 315 315 219 equivalog Y Y N acetate CoA-transferase subunit alpha atoD 2.8.3.9 1224 Pseudomonadota phylum 1309 NCBI Protein Cluster (PRK) acetyl-CoA:acetoacetyl-CoA transferase subunit alpha acetate CoA-transferase subunit alpha NF007414.0 PRK09952 PRK09952.1 538 538 438 equivalog Y Y N shikimate transporter shiA GO:0016020,GO:0022857,GO:0055085 1224 Pseudomonadota phylum 4702 NCBI Protein Cluster (PRK) shikimate transporter shikimate transporter NF007429.0 PRK09974 PRK09974.1 125 125 114 equivalog Y Y N type II toxin-antitoxin system PrlF family antitoxin 1224 Pseudomonadota phylum 1235 NCBI Protein Cluster (PRK) putative regulator PrlF type II toxin-antitoxin system PrlF family antitoxin NF007442.0 PRK09990 PRK09990.1 301 301 256 equivalog Y Y N transcriptional regulator GlcC glcC GO:0003700,GO:0006355 1224 Pseudomonadota phylum 2113 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator GlcC transcriptional regulator GlcC NF007447.0 PRK10003 PRK10003.1 666 666 727 equivalog Y Y N ferric-rhodotorulic acid/ferric-coprogen receptor FhuE fhuE GO:0009279,GO:0015344,GO:0015891,GO:0038023 1224 Pseudomonadota phylum 7975 NCBI Protein Cluster (PRK) ferric-rhodotorulic acid outer membrane transporter ferric-rhodotorulic acid/ferric-coprogen receptor FhuE NF007454.0 PRK10019 PRK10019.1 195 195 283 subfamily Y Y N nickel/cobalt efflux transporter GO:0015099,GO:0035444 1224 Pseudomonadota phylum 8155 NCBI Protein Cluster (PRK) nickel/cobalt efflux protein RcnA nickel/cobalt efflux transporter NF007456.1 PRK10026 PRK10026.1 242 242 141 exception Y Y Y glutaredoxin-dependent arsenate reductase arsC 1.20.4.1 GO:0008794 7577935 1224 Pseudomonadota phylum 3875 NCBI Protein Cluster (PRK) arsenate reductase glutaredoxin-dependent arsenate reductase NF007474.0 PRK10060 PRK10060.1 782 782 663 equivalog Y Y N cyclic di-GMP phosphodiesterase pdeR 3.1.4.52 1224 Pseudomonadota phylum 5216 NCBI Protein Cluster (PRK) RNase II stability modulator cyclic di-GMP phosphodiesterase NF007489.0 PRK10083 PRK10083.1 376 376 339 equivalog Y Y N Zn-dependent oxidoreductase GO:0008270,GO:0016491 1224 Pseudomonadota phylum 5460 NCBI Protein Cluster (PRK) putative oxidoreductase Zn-dependent oxidoreductase NF007490.0 PRK10084 PRK10084.1 649 649 361 subfamily Y Y N dTDP-glucose 4,6-dehydratase 4.2.1.46 1224 Pseudomonadota phylum 9512 NCBI Protein Cluster (PRK) dTDP-glucose 4,6 dehydratase dTDP-glucose 4,6-dehydratase NAD(P) binding; catalyzes the formation of dTDP-4-dehydro-6-deoxy-D-glucose from dTDP-glucose NF007504.0 PRK10098 PRK10098.1 336 336 360 equivalog Y Y N malate/lactate/ureidoglycolate dehydrogenase GO:0016491 1224 Pseudomonadota phylum 6381 NCBI Protein Cluster (PRK) putative dehydrogenase malate/lactate/ureidoglycolate dehydrogenase NF007576.1 PRK10208 PRK10208.1 85 85 97 equivalog Y Y N acid-activated periplasmic chaperone HdeA hdeA 29016106,29138002 1224 Pseudomonadota phylum 567 NCBI Protein Cluster (PRK) acid-resistance protein acid-activated periplasmic chaperone HdeA HdeA is a periplasmic, ATP-independent chaperone that is activated at very low pH (2-3) and has many protein substrates. NF007582.0 PRK10217 PRK10217.1 698 698 355 equivalog Y Y N dTDP-glucose 4,6-dehydratase rffG 4.2.1.46 GO:0008460,GO:0009225 1224 Pseudomonadota phylum 3683 NCBI Protein Cluster (PRK) dTDP-glucose 4,6-dehydratase dTDP-glucose 4,6-dehydratase NF007677.0 PRK10352 PRK10352.1 433 433 314 equivalog Y Y N nickel ABC transporter permease subunit NikB nikB 7.2.2.- 1224 Pseudomonadota phylum 1743 NCBI Protein Cluster (PRK) nickel transporter permease NikB nickel ABC transporter permease subunit NikB With NikACDE is involved in nickel transport into the cell NF007682.0 PRK10357 PRK10357.1 181 181 202 equivalog Y Y N glutathione S-transferase 2.5.1.18 GO:0005515,GO:0006749 1224 Pseudomonadota phylum 2991 NCBI Protein Cluster (PRK) putative glutathione S-transferase glutathione S-transferase NF007691.0 PRK10369 PRK10369.1 394 394 573 subfamily Y Y N heme lyase NrfEFG subunit NrfE nrfE 1224 Pseudomonadota phylum 35035 NCBI Protein Cluster (PRK) heme lyase subunit NrfE heme lyase NrfEFG subunit NrfE With NrfF and NrfG catalyzes the insertion of heme into cytochrome c552 NF007702.0 PRK10387 PRK10387.1 133 133 215 equivalog Y Y N glutaredoxin 2 grxB GO:0004362,GO:0005515,GO:0006749 1224 Pseudomonadota phylum 5559 NCBI Protein Cluster (PRK) glutaredoxin 2 glutaredoxin 2 NF007738.0 PRK10417 PRK10417.1 335 335 277 equivalog Y Y N nickel ABC transporter permease subunit NikC nikC 7.2.2.- GO:0015099,GO:0016020,GO:0055085 1224 Pseudomonadota phylum 2030 NCBI Protein Cluster (PRK) nickel transporter permease NikC nickel ABC transporter permease subunit NikC With NikABDE is involved in nickel transport into the cell NF007785.0 PRK10476 PRK10476.1 376 376 347 equivalog Y Y N multidrug transporter subunit MdtN mdtN 11257026,8021163 1224 Pseudomonadota phylum 3839 NCBI Protein Cluster (PRK) multidrug resistance protein MdtN multidrug transporter subunit MdtN With MdtO and MdtP is involved in resistance to puromycin, acriflavine and tetraphenylarsonium chloride NF007820.0 PRK10529 PRK10529.1 325 325 225 equivalog Y Y N two-component system response regulator KdpE kdpE GO:0000160,GO:0003677,GO:0006355 1224 Pseudomonadota phylum 4943 NCBI Protein Cluster (PRK) DNA-binding transcriptional activator KdpE two-component system response regulator KdpE Response regulator in two-component regulatory system with KdpD; regulates the kdp operon involved in potassium transport NF007823.0 PRK10532 PRK10532.1 354 354 295 equivalog Y Y N threonine/homoserine exporter RhtA rhtA 1224 Pseudomonadota phylum 5701 NCBI Protein Cluster (PRK) threonine and homoserine efflux system threonine/homoserine exporter RhtA NF007826.0 PRK10535 PRK10535.1 966 966 648 equivalog Y Y N macrolide ABC transporter ATP-binding protein/permease MacB macB GO:0005524,GO:0022857,GO:1990195 28504659 1224 Pseudomonadota phylum 5263 NCBI Protein Cluster (PRK) macrolide transporter ATP-binding /permease protein macrolide ABC transporter ATP-binding protein/permease MacB With MacA is involved in the export of macrolide NF007828.0 PRK10537 PRK10537.1 425 425 403 equivalog Y Y N voltage-gated potassium channel protein kch 1224 Pseudomonadota phylum 1859 NCBI Protein Cluster (PRK) voltage-gated potassium channel voltage-gated potassium channel protein NF007829.0 PRK10538 PRK10538.1 411 411 248 equivalog Y Y N bifunctional NADP-dependent 3-hydroxy acid dehydrogenase/3-hydroxypropionate dehydrogenase YdfG ydfG 1.1.1.298,1.1.1.381 GO:0016491 1224 Pseudomonadota phylum 2867 NCBI Protein Cluster (PRK) malonic semialdehyde reductase bifunctional NADP-dependent 3-hydroxy acid dehydrogenase/3-hydroxypropionate dehydrogenase YdfG Catalyzes the formation of 3-hydroxypropionate from the toxic malonic semialdehyde, Catalyzes the formation of 2-aminomalonate-semialdehyde from L-serine; can also use 3-hydroxybutyrate, 3-hydroxy-isobutyrate, D-threonine, L-allo-threonine,D-serine NF007832.0 PRK10543 PRK10543.1 348 348 193 equivalog Y Y N superoxide dismutase [Fe] sodB 1.15.1.1 GO:0004784,GO:0006801,GO:0046872 1224 Pseudomonadota phylum 3701 NCBI Protein Cluster (PRK) superoxide dismutase superoxide dismutase [Fe] NF007835.0 PRK10547 PRK10547.1 793 793 670 equivalog Y Y N chemotaxis protein CheA cheA GO:0000155,GO:0000160,GO:0006935,GO:0016310 1224 Pseudomonadota phylum 9188 NCBI Protein Cluster (PRK) chemotaxis protein CheA chemotaxis protein CheA Chemotactic sensory histidine kinase in two-component regulatory system with CheB and CheY; sensory histidine kinase/signal sensing protein; CheA is the histidine kinase component NF007845.0 PRK10556 PRK10556.1-3 171 171 111 equivalog Y Y N DUF2002 family protein 1224 Pseudomonadota phylum 909 NCBI Protein Cluster (PRK) hypothetical protein DUF2002 family protein NF007849.0 PRK10558 PRK10558.1 393 393 256 equivalog Y Y N 2-dehydro-3-deoxyglucarate aldolase garL 4.1.2.20 GO:0008672,GO:0019394 1224 Pseudomonadota phylum 3123 NCBI Protein Cluster (PRK) alpha-dehydro-beta-deoxy-D-glucarate aldolase 2-dehydro-3-deoxyglucarate aldolase Cleaves 5-dehydro-4-deoxy-glucarate and 2-dehydro-3-deoxy-D-glucarate to 2-hydroxy-3-oxopropanoate and pyruvate NF007866.0 PRK10577 PRK10577.1-2 554 554 666 equivalog Y Y N Fe(3+)-hydroxamate ABC transporter permease FhuB fhuB GO:0016020,GO:0022857 1224 Pseudomonadota phylum 17569 NCBI Protein Cluster (PRK) iron-hydroxamate transporter permease subunit Fe(3+)-hydroxamate ABC transporter permease FhuB NF007903.0 PRK10612 PRK10612.1 260 260 167 equivalog Y Y N chemotaxis protein CheW cheW 1224 Pseudomonadota phylum 1488 NCBI Protein Cluster (PRK) purine-binding chemotaxis protein chemotaxis protein CheW NF007929.0 PRK10644 PRK10644.1 574 574 445 equivalog Y Y N arginine/agmatine antiporter adiC GO:0016020,GO:0022857,GO:0055085 1224 Pseudomonadota phylum 1770 NCBI Protein Cluster (PRK) arginine:agmatin antiporter arginine/agmatine antiporter NF007935.0 PRK10651 PRK10651.1 250 250 216 equivalog Y Y N two-component system response regulator NarL narL GO:0000160,GO:0003677,GO:0006355 1224 Pseudomonadota phylum 3865 NCBI Protein Cluster (PRK) transcriptional regulator NarL two-component system response regulator NarL phosphorylated by NarQ; activates transcription of nitrate and nitrite reductase genes and represses transcription of fumarate reductase NF007946.0 PRK10665 PRK10665.1 181 181 112 equivalog Y Y N P-II family nitrogen regulator glnK GO:0006808,GO:0030234 10760266,12218023,12366843,8293810,8843440 1224 Pseudomonadota phylum 3034 NCBI Protein Cluster (PRK) nitrogen regulatory protein P-II 2 P-II family nitrogen regulator NF007955.0 PRK10674 PRK10674.1 506 506 472 equivalog Y Y N deoxyribodipyrimidine photo-lyase phrB 4.1.99.3 1224 Pseudomonadota phylum 18115 NCBI Protein Cluster (PRK) deoxyribodipyrimidine photolyase deoxyribodipyrimidine photo-lyase UV-induced DNA repair; converts cyclobutane-type pyrimidine dimers created during exposure to UV ratiation to monomers; light dependent NF007958.0 PRK10677 PRK10677.1 253 253 256 equivalog Y Y N molybdate ABC transporter substrate-binding protein modA 7.3.2.- GO:0015689 1224 Pseudomonadota phylum 11047 NCBI Protein Cluster (PRK) molybdate transporter periplasmic protein molybdate ABC transporter substrate-binding protein NF007959.0 PRK10678 PRK10678.1 175 175 150 equivalog Y Y N molybdopterin synthase catalytic subunit MoaE moaE 2.8.1.12 GO:0006777 1224 Pseudomonadota phylum 10821 NCBI Protein Cluster (PRK) molybdopterin guanine dinucleotide biosynthesis protein MoaE molybdopterin synthase catalytic subunit MoaE Catalyzes the conversion of molybdopterin precursor Z into molybdopterin NF007961.0 PRK10681 PRK10681.1 244 244 252 equivalog Y Y N DNA-binding transcriptional repressor DeoR deoR GO:0003700,GO:0006355 1224 Pseudomonadota phylum 3328 NCBI Protein Cluster (PRK) DNA-binding transcriptional repressor DeoR DNA-binding transcriptional repressor DeoR NF007966.0 PRK10689 PRK10689.1 1329 1329 1148 equivalog Y Y N transcription-repair coupling factor mfd 3.6.1.- GO:0003676,GO:0003684,GO:0005524,GO:0006281 17239578 1224 Pseudomonadota phylum 24512 NCBI Protein Cluster (PRK) transcription-repair coupling factor transcription-repair coupling factor Mfd (mutation frequency decline) is a DNA-dependent ATPase that functions in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is closely related to the RecG and UvrB families. NF007970.0 PRK10694 PRK10694.1 162 162 133 equivalog Y Y N acyl-CoA thioester hydrolase YciA yciA 3.1.2.20 GO:0016790 18260643 1224 Pseudomonadota phylum 2850 NCBI Protein Cluster (PRK) acyl-CoA esterase acyl-CoA thioester hydrolase YciA NF007976.1 PRK10700 PRK10700.1 290 290 291 equivalog Y Y N 23S rRNA pseudouridine(2605) synthase RluB rluB 5.4.99.22 GO:0001522,GO:0003723,GO:0009982 24214967 1224 Pseudomonadota phylum 12803 NCBI Protein Cluster (PRK) 23S rRNA pseudouridylate synthase B 23S rRNA pseudouridine(2605) synthase RluB Catalyzes the synthesis of pseudouridine from U2605 in 23S ribosomal RNA NF007985.1 PRK10713 PRK10713.1 75 75 81 equivalog Y Y N class I ribonucleotide reductase maintenance protein YfaE yfaE GO:0051537 17880186 1224 Pseudomonadota phylum 4581 NCBI Protein Cluster (PRK) 2Fe-2S ferredoxin YfaE class I ribonucleotide reductase maintenance protein YfaE YfaE, classified as a ferredoxin because of its 2Fe-2S iron-sulfur cluster-binding structure, occurs in the neighborhood of class I ribonucleotide reductase subunit genes. It plays a role in the regeneration of the diferric-tyrosyl radical of the beta-subunit. NF008000.0 PRK10725 PRK10725.1 215 215 188 equivalog Y Y N fructose-1-phosphate/6-phosphogluconate phosphatase yqaB 3.1.3.- 16990279 1224 Pseudomonadota phylum 2602 NCBI Protein Cluster (PRK) fructose-1-P/6-phosphogluconate phosphatase fructose-1-phosphate/6-phosphogluconate phosphatase Catalyzes the dephosphorylation of fructose 1-phosphate, 6-phosphogluconate and p-nitrophenyl phosphate (pNPP) NF008009.0 PRK10738 PRK10738.1 138 138 134 equivalog Y Y N OsmC family protein 1224 Pseudomonadota phylum 9644 NCBI Protein Cluster (PRK) hypothetical protein OsmC family protein NF008011.0 PRK10740 PRK10740.1 379 379 308 equivalog Y Y N high-affinity branched-chain amino acid ABC transporter permease LivH livH 7.4.2.2 GO:0016020,GO:0022857,GO:0055085 14702302 1224 Pseudomonadota phylum 3722 NCBI Protein Cluster (PRK) branched-chain amino acid transporter permease subunit LivH high-affinity branched-chain amino acid ABC transporter permease LivH Part of the ABC transporter complexes LivFGHMJ and LivFGHMK involved in the high-affinity transport of branched-chain amino acids; LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for leucine, isoleucine, and valine NF008032.0 PRK10764 PRK10764.1 342 342 328 equivalog Y Y N dicarboxylate transporter/tellurite-resistance protein TehA tehA GO:0016020,GO:0055085 1224 Pseudomonadota phylum 4807 NCBI Protein Cluster (PRK) potassium-tellurite ethidium and proflavin transporter dicarboxylate transporter/tellurite-resistance protein TehA NF008063.0 PRK10797 PRK10797.1 375 375 302 subfamily Y Y N glutamate/aspartate ABC transporter substrate-binding protein 7.4.2.1 GO:0001522,GO:0003723,GO:0009451,GO:0009982 1224 Pseudomonadota phylum 6997 NCBI Protein Cluster (PRK) glutamate and aspartate transporter subunit glutamate/aspartate ABC transporter substrate-binding protein NF008070.2 PRK10807 PRK10807.1 525 525 542 equivalog Y Y N intermembrane transport protein PqiB pqiB 27795327 1224 Pseudomonadota phylum 7064 NCBI Protein Cluster (PRK) paraquat-inducible protein B intermembrane transport protein PqiB NF008072.0 PRK10809 PRK10809.1 190 190 194 equivalog Y Y N ribosomal protein S5-alanine N-acetyltransferase rimJ 2.3.1.267 GO:0008080 1224 Pseudomonadota phylum 3955 NCBI Protein Cluster (PRK) ribosomal-protein-S5-alanine N-acetyltransferase ribosomal protein S5-alanine N-acetyltransferase NF008095.0 PRK10837 PRK10837.1 281 281 290 subfamily Y Y N LysR family transcriptional regulator 1224 Pseudomonadota phylum 7441 NCBI Protein Cluster (PRK) putative DNA-binding transcriptional regulator LysR family transcriptional regulator NF008101.0 PRK10846 PRK10846.1 360 360 422 equivalog Y Y N bifunctional tetrahydrofolate synthase/dihydrofolate synthase folC 6.3.2.12,6.3.2.17 GO:0004326,GO:0005524,GO:0009396,GO:0016874 1224 Pseudomonadota phylum 24836 NCBI Protein Cluster (PRK) bifunctional folylpolyglutamate synthase/ dihydrofolate synthase bifunctional tetrahydrofolate synthase/dihydrofolate synthase NF008118.0 PRK10865 PRK10865.1 1417 1417 857 equivalog Y Y N ATP-dependent chaperone ClpB clpB GO:0005524,GO:0009408,GO:0016887,GO:0042026 1224 Pseudomonadota phylum 12659 NCBI Protein Cluster (PRK) protein disaggregation chaperone ATP-dependent chaperone ClpB NF008122.0 PRK10870 PRK10870.1 157 157 176 equivalog Y Y N transcriptional repressor MprA mprA 1224 Pseudomonadota phylum 1480 NCBI Protein Cluster (PRK) transcriptional repressor MprA transcriptional repressor MprA NF008137.0 PRK10885 PRK10885.1 451 451 409 equivalog Y Y N multifunctional CCA addition/repair protein 2.7.7.72,3.1.3.-,3.1.4.- GO:0001680,GO:0003723,GO:0004810,GO:0005524 15210699,3009457 1224 Pseudomonadota phylum 21372 NCBI Protein Cluster (PRK) multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase multifunctional CCA addition/repair protein Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template; phosphohydrolase activities include hydrolysis of pyrophosphate, 5'-nucleoside tri- and diphosphates, NADP, and 2'-AMP with the production of Pi, metal-dependent phosphodiesterase activity for 2',3'-cAMP, 2',3'-cGMP, and 2',3'-cCMP, and hydrolysis 2',3'-cyclic substrates with the formation of 2'-nucleotides and 3'-nucleotides; these phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases NF008140.0 PRK10888 PRK10888.1 412 412 323 equivalog Y Y N octaprenyl diphosphate synthase ispB 2.5.1.90 GO:0008299 1224 Pseudomonadota phylum 7913 NCBI Protein Cluster (PRK) octaprenyl diphosphate synthase octaprenyl diphosphate synthase NF008149.0 PRK10901 PRK10901.1 375 375 434 equivalog Y Y N 16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB rsmB 2.1.1.176 GO:0001510,GO:0003723,GO:0006355,GO:0006364,GO:0008649 1224 Pseudomonadota phylum 24499 NCBI Protein Cluster (PRK) 16S rRNA methyltransferase B 16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB Catalyzes the methylation of the C5 position of C967 of the 16S rRNA NF008163.0 PRK10917 PRK10917.1-1 796 796 692 equivalog Y Y N ATP-dependent DNA helicase RecG recG 3.6.4.12 GO:0003676,GO:0003678,GO:0005524,GO:0006281,GO:0006310 18242643 1224 Pseudomonadota phylum 25886 NCBI Protein Cluster (PRK) ATP-dependent DNA helicase RecG ATP-dependent DNA helicase RecG NF008166.0 PRK10917 PRK10917.1-4 864 864 705 equivalog Y Y N ATP-dependent DNA helicase RecG recG 3.6.4.12 GO:0003678,GO:0006281,GO:0006310 1224 Pseudomonadota phylum 24326 NCBI Protein Cluster (PRK) ATP-dependent DNA helicase RecG ATP-dependent DNA helicase RecG NF008175.0 PRK10922 PRK10922.1 788 788 497 equivalog Y Y N 4-hydroxy-3-polyprenylbenzoate decarboxylase ubiD 4.1.1.98 GO:0016831 1224 Pseudomonadota phylum 13132 NCBI Protein Cluster (PRK) 3-octaprenyl-4-hydroxybenzoate decarboxylase 4-hydroxy-3-polyprenylbenzoate decarboxylase Catalyzes the decarboxylation of 3-octaprenyl-4-hydroxy benzoate to 2-octaprenylphenol NF008176.1 PRK10923 PRK10923.1 620 620 469 equivalog Y Y N nitrogen regulation protein NR(I) glnG GO:0006355,GO:0043565 1224 Pseudomonadota phylum 10876 NCBI Protein Cluster (PRK) nitrogen regulation protein NR(I) nitrogen regulation protein NR(I) NF008192.1 PRK10946 PRK10946.1 783 783 534 equivalog Y Y N (2,3-dihydroxybenzoyl)adenylate synthase 6.2.1.71 GO:0008668,GO:0019290 20853905,27470582 1224 Pseudomonadota phylum 8317 NCBI Protein Cluster (PRK) enterobactin synthase subunit E (2,3-dihydroxybenzoyl)adenylate synthase Member of this family of (2,3-dihydroxybenzoyl)adenylate synthases include EntE from enterobactin biosynthesis in E. coli and Salmonella, but also NF008196.0 PRK10952 PRK10952.1 439 439 356 equivalog Y Y N glycine betaine/L-proline ABC transporter permease ProW proW GO:0016020,GO:0055085 2691838,33653345 1224 Pseudomonadota phylum 6660 NCBI Protein Cluster (PRK) glycine betaine transporter membrane protein glycine betaine/L-proline ABC transporter permease ProW With ProVX is involved in the high-affinity uptake of glycine betaine NF008197.0 PRK10953 PRK10953.1 838 838 601 equivalog Y Y N NADPH-dependent assimilatory sulfite reductase flavoprotein subunit cysJ 1.8.1.2 GO:0000103,GO:0004783,GO:0010181,GO:0019344,GO:0050660 1224 Pseudomonadota phylum 7447 NCBI Protein Cluster (PRK) sulfite reductase subunit alpha NADPH-dependent assimilatory sulfite reductase flavoprotein subunit Catalyzes the reduction of sulfite to sulfide in the biosynthesis of L-cysteine from sulfate; a flavoprotein with flavin reductase activity NF008205.1 PRK10965 PRK10965.1 525 525 529 equivalog Y Y N multicopper oxidase CueO cueO 1.16.3.1 GO:0005507,GO:0016491 21903583 1224 Pseudomonadota phylum 7546 NCBI Protein Cluster (PRK) multicopper oxidase multicopper oxidase CueO Laccase; copper-stimulated phenoloxidase and ferroxidase which may be involved in copper detoxification NF008206.2 PRK10966 PRK10966.1 450 450 380 equivalog Y Y N exonuclease subunit SbcD sbcD 3.1.11.- GO:0004527,GO:0006260,GO:0006310 1490631,1531222,9653124 1224 Pseudomonadota phylum 8042 NCBI Protein Cluster (PRK) exonuclease subunit SbcD exonuclease subunit SbcD With SbcC cleaves DNA hairpin structure, also has 5' single-strand endonuclease activity NF008216.0 PRK10983 PRK10983.1 305 305 370 equivalog Y Y N AI-2E family transporter YdiK ydiK 1224 Pseudomonadota phylum 4578 NCBI Protein Cluster (PRK) putative inner membrane protein AI-2E family transporter YdiK NF008221.0 PRK10992 PRK10992.1 254 254 220 equivalog Y Y N iron-sulfur cluster repair protein YtfE ytfE 1224 Pseudomonadota phylum 4309 NCBI Protein Cluster (PRK) iron-sulfur cluster repair di-iron protein iron-sulfur cluster repair protein YtfE NF008235.0 PRK11006 PRK11006.1 390 390 431 equivalog Y Y N phosphate regulon sensor histidine kinase PhoR phoR 2.7.13.3 GO:0000155,GO:0000160,GO:0004721,GO:0006355,GO:0016020,GO:0016310 27665757 1224 Pseudomonadota phylum 9804 NCBI Protein Cluster (PRK) phosphate regulon sensor protein phosphate regulon sensor histidine kinase PhoR Membrane-associated histidine protein kinase that phosphorylates phoB in response to environmental signals as part of the two-component phosphate regulatory system phoR/phoB NF008239.0 PRK11013 PRK11013.1 288 288 309 equivalog Y Y N LysR family transcriptional regulator GO:0003700,GO:0006355 1224 Pseudomonadota phylum 6074 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator LysR LysR family transcriptional regulator NF008249.0 PRK11025 PRK11025.1 378 378 317 equivalog Y Y N 23S rRNA pseudouridine(955/2504/2580) synthase RluC rluC 5.4.99.24 GO:0001522,GO:0003723,GO:0009982 1224 Pseudomonadota phylum 8970 NCBI Protein Cluster (PRK) 23S rRNA pseudouridylate synthase C 23S rRNA pseudouridine(955/2504/2580) synthase RluC Catalyzes the synthesis of pseudouridine from uracil U955, U2504, and U2580 in 23S rRNA NF008268.0 PRK11040 PRK11040.1 438 438 446 equivalog Y Y N metalloprotease PmbA pmbA 3.4.24.- GO:0006508,GO:0008237 1224 Pseudomonadota phylum 16992 NCBI Protein Cluster (PRK) peptidase PmbA metalloprotease PmbA Protease involved in proteolytic processing of the antibiotic Microcin B17 NF008271.1 PRK11045 PRK11045.1 155 155 188 equivalog Y Y N lipid IV(A) palmitoyltransferase PagP pagP 2.3.1.251 11013210,12357033,15272304,20826347,20853818 1224 Pseudomonadota phylum 4653 NCBI Protein Cluster (PRK) phospholipid:lipid A palmitoyltransferase lipid IV(A) palmitoyltransferase PagP Catalyzes the transfer of palmitate to lipid A NF008273.0 PRK11050 PRK11050.1 153 153 156 equivalog Y Y N manganese-binding transcriptional regulator MntR mntR GO:0003677,GO:0003700,GO:0006355,GO:0046914,GO:0046983 1224 Pseudomonadota phylum 3626 NCBI Protein Cluster (PRK) manganese transport regulator MntR manganese-binding transcriptional regulator MntR Transcriptional regulator that represses the manganese transporter MntH when manganese is present NF008280.0 PRK11058 PRK11058.1 441 441 426 equivalog Y Y N ribosome rescue GTPase HflX hflX 3.6.5.- GO:0005525 26458047,29930203 1224 Pseudomonadota phylum 13089 NCBI Protein Cluster (PRK) GTPase HflX ribosome rescue GTPase HflX Involved in modulation of proteins HflK and HflC; part of the hflA locus (high frequency of lysogenization) which governs the lysis-lysogeny decision of bacteriophage lambda by controlling stability of the phage cII protein NF008293.1 PRK11073 PRK11073.1 240 240 349 equivalog Y Y N nitrogen regulation protein NR(II) glnL GO:0000155,GO:0006355,GO:0007165,GO:0016310 1224 Pseudomonadota phylum 10971 NCBI Protein Cluster (PRK) nitrogen regulation protein NR(II) nitrogen regulation protein NR(II) NF008296.0 PRK11083 PRK11083.1 273 273 228 equivalog Y Y N two-component system response regulator CreB creB GO:0000160,GO:0003677,GO:0006355 1224 Pseudomonadota phylum 6786 NCBI Protein Cluster (PRK) DNA-binding response regulator CreB two-component system response regulator CreB Response regulator in two-component regulatory system with CreC; CreB protein is phosphorylated by sensor protein phospho-CreC; involved in catabolic regulation NF008305.0 PRK11097 PRK11097.1 299 299 378 equivalog Y Y N cellulose synthase complex periplasmic endoglucanase BcsZ bcsZ 3.2.1.4 GO:0004553,GO:0005975 21454578,27753193,27756305 1224 Pseudomonadota phylum 8880 NCBI Protein Cluster (PRK) endo-1,4-D-glucanase cellulose synthase complex periplasmic endoglucanase BcsZ BcsZ, a cellulase (i.e. beta-1,4-glucanase), is a periplasmic subunit of the Bcs macrocomplex that performs the biosynthesis and secretion of cellulose. Its presences improves cellulose synthesis and translation. NF008306.0 PRK11098 PRK11098.1 492 492 413 equivalog Y Y N peptide antibiotic transporter SbmA sbmA GO:0015833,GO:1904680 16621826,7768835 1224 Pseudomonadota phylum 5984 NCBI Protein Cluster (PRK) microcin B17 transporter peptide antibiotic transporter SbmA NF008319.0 PRK11109 PRK11109.1 302 302 376 equivalog Y Y N fused PTS fructose transporter subunit IIA/HPr protein fruB 1224 Pseudomonadota phylum 13535 NCBI Protein Cluster (PRK) bifunctional PTS system fructose-specific transporter subunit IIA/HPr protein fused PTS fructose transporter subunit IIA/HPr protein Phosphorylated by phospho-HPr which then transfers the phosphoryl group to the IIB component NF008320.0 PRK11111 PRK11111.1 216 216 215 equivalog Y Y N YchE family NAAT transporter GO:0016020 1224 Pseudomonadota phylum 2831 NCBI Protein Cluster (PRK) hypothetical protein YchE family NAAT transporter NF008321.0 PRK11112 PRK11112.1 328 328 257 equivalog Y Y N tRNA pseudouridine(65) synthase TruC truC 5.4.99.26 GO:0001522,GO:0009982 1224 Pseudomonadota phylum 7877 NCBI Protein Cluster (PRK) tRNA pseudouridine synthase C tRNA pseudouridine(65) synthase TruC Catalyzes formation of pseudouridine at position 65 in tRNA-Ile1 and tRNA-Asp NF008323.1 PRK11114 PRK11114.1-1 750 750 712 equivalog Y Y N cellulose biosynthesis cyclic di-GMP-binding regulatory protein BcsB bcsB 1224 Pseudomonadota phylum 11851 NCBI Protein Cluster (PRK) cellulose synthase regulator protein cellulose biosynthesis cyclic di-GMP-binding regulatory protein BcsB NF008330.0 PRK11114 PRK11114.2-4 945 945 761 subfamily Y Y N cellulose biosynthesis cyclic di-GMP-binding regulatory protein BcsB bcsB 1224 Pseudomonadota phylum 1032 NCBI Protein Cluster (PRK) cellulose synthase regulator protein cellulose biosynthesis cyclic di-GMP-binding regulatory protein BcsB NF008356.0 PRK11145 PRK11145.1 375 375 246 equivalog Y Y N pyruvate formate lyase 1-activating protein pflA 1.97.1.4 GO:0043365,GO:0051539 1224 Pseudomonadota phylum 3779 NCBI Protein Cluster (PRK) pyruvate formate lyase-activating enzyme 1 pyruvate formate lyase 1-activating protein Activates pyruvate formate-lyase 1 under anaerobic conditions NF008360.0 PRK11150 PRK11150.1 452 452 310 equivalog Y Y N ADP-glyceromanno-heptose 6-epimerase rfaD 5.1.3.20 GO:0005975,GO:0008712 1224 Pseudomonadota phylum 6050 NCBI Protein Cluster (PRK) ADP-L-glycero-D-mannoheptose-6-epimerase ADP-glyceromanno-heptose 6-epimerase Catalyzes the interconversion between ADP-D-glycero-beta-D-manno-heptose and ADP-L-glycero-beta-D-manno-heptose NF008365.0 PRK11161 PRK11161.1 228 228 250 subfamily Y Y N fumarate/nitrate reduction transcriptional regulator Fnr fnr GO:0003677,GO:0003700,GO:0006355 1224 Pseudomonadota phylum 9224 NCBI Protein Cluster (PRK) fumarate/nitrate reduction transcriptional regulator fumarate/nitrate reduction transcriptional regulator Fnr Global transcription factor that controls the expression of over 100 target genes in response to anoxia NF008368.0 PRK11166 PRK11166.1 257 257 217 equivalog Y Y N protein phosphatase CheZ cheZ 3.6.1.- GO:0003824,GO:0050920 1224 Pseudomonadota phylum 3894 NCBI Protein Cluster (PRK) chemotaxis regulator CheZ protein phosphatase CheZ Cytosolic phosphatase which functions in the chemotaxis signal transduction complex by controlling the level of phosphorylated CheY through dephosphorylation NF008377.0 PRK11172 PRK11172.1 327 327 267 equivalog Y Y N 2,5-didehydrogluconate reductase DkgB dkgB 1.1.1.346 GO:0047834 1224 Pseudomonadota phylum 12035 NCBI Protein Cluster (PRK) 2,5-diketo-D-gluconate reductase B 2,5-didehydrogluconate reductase DkgB Catalyzes the reduction of 2,5-didehydro-D-gluconic acid to 2-dehydro-L-gulonic acid NF008385.0 PRK11180 PRK11180.1 351 351 325 equivalog Y Y N 23S rRNA pseudouridine(1911/1915/1917) synthase RluD rluD 5.4.99.23 GO:0001522,GO:0003723,GO:0009451,GO:0009982 1224 Pseudomonadota phylum 10997 NCBI Protein Cluster (PRK) 23S rRNA pseudouridine synthase D 23S rRNA pseudouridine(1911/1915/1917) synthase RluD Catalyzes the synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA NF008390.0 PRK11188 PRK11188.1 269 269 209 equivalog Y Y N 23S rRNA (uridine(2552)-2'-O)-methyltransferase RlmE rlmE 2.1.1.166 GO:0001510,GO:0006364,GO:0016436 1224 Pseudomonadota phylum 6942 NCBI Protein Cluster (PRK) 23S rRNA methyltransferase J 23S rRNA (uridine(2552)-2'-O)-methyltransferase RlmE Catalyzes the methylation of U2552 in 23S rRNA NF008406.0 PRK11212 PRK11212.1 252 252 221 equivalog Y Y N 7-cyano-7-deazaguanine/7-aminomethyl-7-deazaguanine transporter GO:1990397 1224 Pseudomonadota phylum 6125 NCBI Protein Cluster (PRK) hypothetical protein 7-cyano-7-deazaguanine/7-aminomethyl-7-deazaguanine transporter NF008408.0 PRK11230 PRK11230.1 897 897 499 equivalog Y Y N glycolate oxidase subunit GlcD glcD 1.1.99.14 GO:0003973,GO:0009339,GO:0071949 1224 Pseudomonadota phylum 4496 NCBI Protein Cluster (PRK) glycolate oxidase subunit GlcD glycolate oxidase subunit GlcD NF008415.0 PRK11241 PRK11241.1 828 828 482 equivalog Y Y N NADP-dependent succinate-semialdehyde dehydrogenase gabD GO:0009013,GO:0009450 1224 Pseudomonadota phylum 8558 NCBI Protein Cluster (PRK) succinate-semialdehyde dehydrogenase I NADP-dependent succinate-semialdehyde dehydrogenase Catalyzes the formation of succinate from succinate semialdehyde; NADP dependent NF008424.0 PRK11253 PRK11253.1 378 378 308 equivalog Y Y N muramoyltetrapeptide carboxypeptidase ldcA 3.4.17.13 1224 Pseudomonadota phylum 5574 NCBI Protein Cluster (PRK) L,D-carboxypeptidase A muramoyltetrapeptide carboxypeptidase NF008427.0 PRK11263 PRK11263.1 281 281 409 equivalog Y Y N cardiolipin synthase ClsB clsB 2.7.8.- GO:0008808,GO:0032049 1224 Pseudomonadota phylum 10361 NCBI Protein Cluster (PRK) cardiolipin synthase 2 cardiolipin synthase ClsB NF008430.0 PRK11268 PRK11268.1 439 439 295 equivalog Y Y N phosphate ABC transporter permease PstA pstA 7.3.2.1 GO:0005886,GO:0035435 1224 Pseudomonadota phylum 3675 NCBI Protein Cluster (PRK) phosphate transporter permease subunit PtsA phosphate ABC transporter permease PstA Part of an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation NF008432.0 PRK11272 PRK11272.1 270 270 294 equivalog Y Y N drug/metabolite exporter YedA yedA GO:0016020 1224 Pseudomonadota phylum 7508 NCBI Protein Cluster (PRK) putative DMT superfamily transporter inner membrane protein drug/metabolite exporter YedA NF008435.0 PRK11275 PRK11275.1 502 502 319 equivalog Y Y N phosphate ABC transporter permease PstC pstC 7.3.2.1 GO:0006817,GO:0016020,GO:0055085 1224 Pseudomonadota phylum 2750 NCBI Protein Cluster (PRK) phosphate transporter permease subunit PstC phosphate ABC transporter permease PstC Part of an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation NF008437.0 PRK11280 PRK11280.1 99 99 179 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 5807 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF008441.0 PRK11285 PRK11285.1 378 378 333 equivalog Y Y N L-arabinose ABC transporter permease AraH araH 7.5.2.12 GO:0016020,GO:0022857,GO:0055085 1224 Pseudomonadota phylum 5491 NCBI Protein Cluster (PRK) L-arabinose transporter permease protein L-arabinose ABC transporter permease AraH Part of the ABC transporter complex AraFGH involved in the high affinity transport of arabinose NF008442.0 PRK11288 PRK11288.1 689 689 504 equivalog Y Y N L-arabinose ABC transporter ATP-binding protein AraG araG 7.5.2.12 GO:0005524,GO:0015612,GO:0016020,GO:0042882 1224 Pseudomonadota phylum 9577 NCBI Protein Cluster (PRK) L-arabinose transporter ATP-binding protein L-arabinose ABC transporter ATP-binding protein AraG NF008448.1 PRK11295 PRK11295.1 87 87 113 equivalog Y Y N YajD family HNH nuclease 1224 Pseudomonadota phylum 3649 NCBI Protein Cluster (PRK) hypothetical protein YajD family HNH nuclease NF008449.1 PRK11300 PRK11300.1 362 362 255 equivalog Y Y N high-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG livG GO:0005524 1224 Pseudomonadota phylum 4615 NCBI Protein Cluster (PRK) leucine/isoleucine/valine transporter ATP-binding subunit high-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG Part of the ABC transporter complexes LivFGHMJ and LivFGHMK involved in the high-affinity transport of branched-chain amino acids; LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for leucine, isoleucine, and valine NF008450.0 PRK11301 PRK11301.1 366 366 418 subfamily Y Y N high-affinity branched-chain amino acid ABC transporter permease LivM livM GO:0015658,GO:0016020,GO:0055085 1224 Pseudomonadota phylum 14226 NCBI Protein Cluster (PRK) leucine/isoleucine/valine transporter permease subunit high-affinity branched-chain amino acid ABC transporter permease LivM Part of the ABC transporter complexes LivFGHMJ and LivFGHMK involved in the high-affinity transport of branched-chain amino acids; LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for leucine, isoleucine, and valine NF008458.0 PRK11337 PRK11337.1 378 378 293 equivalog Y Y N MurR/RpiR family transcriptional regulator 1224 Pseudomonadota phylum 936 NCBI Protein Cluster (PRK) DNA-binding transcriptional repressor RpiR MurR/RpiR family transcriptional regulator NF008461.0 PRK11342 PRK11342.1 350 350 269 equivalog Y Y N 2-keto-4-pentenoate hydratase mhpD 4.2.1.80 GO:0008684,GO:0009056,GO:0030145 1224 Pseudomonadota phylum 3318 NCBI Protein Cluster (PRK) 2-keto-4-pentenoate hydratase 2-keto-4-pentenoate hydratase Catalyzes the formation of 2-keto-4-hydroxypentanoic acid from 2-hydroxypentadienoic acid NF008464.0 PRK11352 PRK11352.1 133 133 91 equivalog Y Y N formaldehyde-responsive transcriptional repressor FrmR frmR 26973631,27474740 1224 Pseudomonadota phylum 695 NCBI Protein Cluster (PRK) regulator protein FrmR formaldehyde-responsive transcriptional repressor FrmR Formaldehyde-induced negative regulator of the frmRAB operon NF008473.0 PRK11370 PRK11370.1 111 111 99 equivalog Y Y N YciI family protein 15779043 1224 Pseudomonadota phylum 8118 NCBI Protein Cluster (PRK) YciI-like protein YciI family protein YciI, a protein of unknown function named in E. coli and with homologs widely distributed in the Proteobacteria, is a homolog of the enzyme 5-chloro-2-hydroxyhydroquinone ( dehydrochlorinase (see PMID:23955343). NF008500.0 PRK11410 PRK11410.1 529 529 560 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 3697 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF008506.0 PRK11423 PRK11423.1 257 257 261 equivalog Y Y N methylmalonyl-CoA decarboxylase scpB 7.2.4.3 1224 Pseudomonadota phylum 1576 NCBI Protein Cluster (PRK) methylmalonyl-CoA decarboxylase methylmalonyl-CoA decarboxylase Catalyzes the formation of propanoyl-CoA from methylmalonyl-CoA NF008525.0 PRK11460 PRK11460.1 191 191 232 equivalog Y Y N esterase ypfH GO:0016787 1224 Pseudomonadota phylum 3804 NCBI Protein Cluster (PRK) putative hydrolase esterase NF008546.0 PRK11469 PRK11469.1 214 214 188 equivalog Y Y N manganese efflux pump MntP mntP 21908668,25774656 1224 Pseudomonadota phylum 3562 NCBI Protein Cluster (PRK) hypothetical protein manganese efflux pump MntP NF008547.0 PRK11470 PRK11470.1 227 227 205 equivalog Y Y N YebB family permuted papain-like enzyme 21799766 1224 Pseudomonadota phylum 1914 NCBI Protein Cluster (PRK) hypothetical protein YebB family permuted papain-like enzyme NF008558.0 PRK11498 PRK11498.1 992 992 872 equivalog Y Y N UDP-forming cellulose synthase catalytic subunit bcsA 2.4.1.12 GO:0006011,GO:0016020,GO:0016760,GO:0030244,GO:0035438 1224 Pseudomonadota phylum 10476 NCBI Protein Cluster (PRK) cellulose synthase catalytic subunit UDP-forming cellulose synthase catalytic subunit Polymerizes uridine 5'-diphosphate glucose to cellulose; acts with BcsB, BcsZ and BcsC in cellulose biosynthesis NF008586.0 PRK11551 PRK11551.1 410 410 406 equivalog Y Y N 3-(3-hydroxy-phenyl)propionate transporter MhpT mhpT GO:0016020,GO:0022857,GO:0055085 1224 Pseudomonadota phylum 6249 NCBI Protein Cluster (PRK) putative 3-hydroxyphenylpropionic transporter MhpT 3-(3-hydroxy-phenyl)propionate transporter MhpT NF008606.0 PRK11578 PRK11578.1 342 342 371 equivalog Y Y N macrolide transporter subunit MacA macA GO:0019898,GO:0022857,GO:1990195,GO:1990961 28504659 1224 Pseudomonadota phylum 5035 NCBI Protein Cluster (PRK) macrolide transporter subunit MacA macrolide transporter subunit MacA Confers macrolide resistance via active drug efflux NF008657.0 PRK11657 PRK11657.1 124 124 251 equivalog Y Y N thiol:disulfide interchange protein DsbG dsbG 1.8.4.- 1224 Pseudomonadota phylum 7933 NCBI Protein Cluster (PRK) disulfide isomerase/thiol-disulfide oxidase thiol:disulfide interchange protein DsbG NF008665.0 PRK11667 PRK11667.1-3 149 149 154 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 368 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF008668.0 PRK11669 PRK11669.1 294 294 316 equivalog Y Y N D-alanyl-D-alanine endopeptidase pbpG 3.4.21.- GO:0006508,GO:0009002 1224 Pseudomonadota phylum 9161 NCBI Protein Cluster (PRK) D-alanyl-D-alanine endopeptidase D-alanyl-D-alanine endopeptidase NF008675.0 PRK11688 PRK11688.1 107 107 156 equivalog Y Y N thioesterase family protein 1224 Pseudomonadota phylum 4284 NCBI Protein Cluster (PRK) hypothetical protein thioesterase family protein NF008689.0 PRK11712 PRK11712.1 594 594 489 equivalog Y Y N ribonuclease G rng 3.1.26.- GO:0003723,GO:0004540,GO:0006396 1224 Pseudomonadota phylum 11109 NCBI Protein Cluster (PRK) ribonuclease G ribonuclease G NF008727.0 PRK11730 PRK11730.1 870 870 717 equivalog Y Y N fatty acid oxidation complex subunit alpha FadB fadB GO:0006631,GO:0016491,GO:0070403 12535077,2191949,368024,6350283,7012144 1224 Pseudomonadota phylum 17690 NCBI Protein Cluster (PRK) multifunctional fatty acid oxidation complex subunit alpha fatty acid oxidation complex subunit alpha FadB NF008729.0 PRK11747 PRK11747.1 598 598 703 equivalog Y Y N ATP-dependent DNA helicase DinG dinG 3.6.4.12 GO:0003677,GO:0003678,GO:0005524,GO:0006139,GO:0016818 1224 Pseudomonadota phylum 16518 NCBI Protein Cluster (PRK) ATP-dependent DNA helicase DinG ATP-dependent DNA helicase DinG Helicase involved in DNA repair NF008736.0 PRK11762 PRK11762.1 169 169 186 equivalog Y Y N ADP compounds hydrolase NudE nudE 3.6.1.- GO:0016787 1224 Pseudomonadota phylum 7974 NCBI Protein Cluster (PRK) adenosine nucleotide hydrolase NudE ADP compounds hydrolase NudE NF008737.0 PRK11767 PRK11767.1 679 679 505 equivalog Y Y N SpoVR family protein 1224 Pseudomonadota phylum 13312 NCBI Protein Cluster (PRK) SpoVR family protein SpoVR family protein NF008755.0 PRK11788 PRK11788.1-3 430 430 388 equivalog Y Y N lipopolysaccharide assembly protein LapB lapB GO:0005515,GO:0008653 1224 Pseudomonadota phylum 3860 NCBI Protein Cluster (PRK) tetratricopeptide repeat protein lipopolysaccharide assembly protein LapB NF008757.0 PRK11788 PRK11788.1-5 363 363 388 equivalog Y Y N lipopolysaccharide assembly protein LapB lapB 1224 Pseudomonadota phylum 9327 NCBI Protein Cluster (PRK) tetratricopeptide repeat protein lipopolysaccharide assembly protein LapB NF008758.0 PRK11789 PRK11789.1 143 143 190 equivalog Y Y N 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD ampD 3.5.1.28 GO:0008745,GO:0009253 1224 Pseudomonadota phylum 18633 NCBI Protein Cluster (PRK) N-acetyl-anhydromuranmyl-L-alanine amidase 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD NF008767.0 PRK11798 PRK11798.2-2 182 182 131 equivalog Y Y N ClpXP protease specificity-enhancing factor 1224 Pseudomonadota phylum 245 NCBI Protein Cluster (PRK) ClpXP protease specificity-enhancing factor ClpXP protease specificity-enhancing factor NF008769.0 PRK11798 PRK11798.2-5 135 135 144 equivalog Y Y N ClpXP protease specificity-enhancing factor 1224 Pseudomonadota phylum 13329 NCBI Protein Cluster (PRK) ClpXP protease specificity-enhancing factor ClpXP protease specificity-enhancing factor NF008772.0 PRK11809 PRK11809.1 1750 1750 1318 equivalog Y Y N trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase putA GO:0003700,GO:0003842,GO:0004657,GO:0006355,GO:0006561,GO:0016620 15155740,15449943,15476410 1224 Pseudomonadota phylum 21797 NCBI Protein Cluster (PRK) trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase NF008816.0 PRK11860 PRK11860.1 943 943 662 equivalog Y Y N bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidylate kinase 2.5.1.19,2.7.4.14 1224 Pseudomonadota phylum 1610 NCBI Protein Cluster (PRK) bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidylate kinase Catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis; Catalyzes CMP phosphorylation NF008822.0 PRK11872 PRK11872.1 402 402 341 equivalog Y Y N anthranilate 1,2-dioxygenase electron transfer component AntC antC GO:0016491,GO:0051536 1224 Pseudomonadota phylum 2275 NCBI Protein Cluster (PRK) anthranilate dioxygenase reductase anthranilate 1,2-dioxygenase electron transfer component AntC NF008859.0 PRK11893 PRK11893.2-1 553 553 498 equivalog Y Y N methionine--tRNA ligase 6.1.1.10 1224 Pseudomonadota phylum 581 NCBI Protein Cluster (PRK) methionyl-tRNA synthetase methionine--tRNA ligase NF008867.0 PRK11902 PRK11902.1 656 656 419 equivalog Y Y N muropeptide transporter 1224 Pseudomonadota phylum 4667 NCBI Protein Cluster (PRK) muropeptide transporter muropeptide transporter NF008889.0 PRK11924 PRK11924.1-1 181 181 173 subfamily Y N N RNA polymerase sigma factor 1224 Pseudomonadota phylum 1578 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF008892.0 PRK11924 PRK11924.2-1 291 291 203 equivalog Y N N RNA polymerase sigma factor 1224 Pseudomonadota phylum 44 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF008923.0 PRK12284 PRK12284.1 597 597 431 equivalog Y Y N tryptophan--tRNA ligase 6.1.1.2 GO:0004830,GO:0006436 1224 Pseudomonadota phylum 6272 NCBI Protein Cluster (PRK) tryptophanyl-tRNA synthetase tryptophan--tRNA ligase Catalyzes a two-step reaction, first charging a tryptophan molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA NF008935.0 PRK12292 PRK12292.1-1 350 350 382 equivalog Y Y N ATP phosphoribosyltransferase regulatory subunit GO:0000105 1224 Pseudomonadota phylum 8682 NCBI Protein Cluster (PRK) ATP phosphoribosyltransferase regulatory subunit ATP phosphoribosyltransferase regulatory subunit NF008951.0 PRK12295 PRK12295.1-4 364 364 374 equivalog Y Y N ATP phosphoribosyltransferase regulatory subunit 1224 Pseudomonadota phylum 2006 NCBI Protein Cluster (PRK) ATP phosphoribosyltransferase regulatory subunit ATP phosphoribosyltransferase regulatory subunit NF008952.0 PRK12295 PRK12295.1-5 360 360 363 equivalog Y Y N ATP phosphoribosyltransferase regulatory subunit 1224 Pseudomonadota phylum 1783 NCBI Protein Cluster (PRK) ATP phosphoribosyltransferase regulatory subunit ATP phosphoribosyltransferase regulatory subunit NF008973.0 PRK12321 PRK12321.1 1235 1235 1105 equivalog Y Y N cobaltochelatase subunit CobN cobN 6.6.1.2 1224 Pseudomonadota phylum 4125 NCBI Protein Cluster (PRK) cobaltochelatase subunit CobN cobaltochelatase subunit CobN With CobST catalyzes the formation of cobyrinic acid a,c-diamide from hydrogenobyrinic acid a,c-diamide in an ATP-dependent manner; involved in porphyrin and chlorophyll metabolism; vitamin B12 metabolism NF009001.0 PRK12346 PRK12346.1 439 439 316 subfamily Y Y N transaldolase A 2.2.1.2 1224 Pseudomonadota phylum 13068 NCBI Protein Cluster (PRK) transaldolase A transaldolase A NF009019.0 PRK12355 PRK12355.4-2 518 518 550 equivalog Y N N conjugal transfer mating pair stabilization protein TraN 1224 Pseudomonadota phylum 81 NCBI Protein Cluster (PRK) conjugal transfer mating pair stabilization protein TraN conjugal transfer mating pair stabilization protein TraN NF009040.0 PRK12373 PRK12373.1 514 514 400 equivalog Y Y N NADH-quinone oxidoreductase subunit E 1.6.5.9 GO:0016491 1224 Pseudomonadota phylum 2456 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit E NADH-quinone oxidoreductase subunit E NF009047.0 PRK12381 PRK12381.1 630 630 406 subfamily Y Y N bifunctional succinylornithine transaminase/acetylornithine transaminase 1224 Pseudomonadota phylum 18504 NCBI Protein Cluster (PRK) bifunctional succinylornithine transaminase/acetylornithine transaminase bifunctional succinylornithine transaminase/acetylornithine transaminase Catalyzes the transamination of 2-N-succinylornithine and alpha-ketoglutarate into 2-N-succinylglutamate semialdehyde and glutamate; also functions as the catabolic acetylornithine aminotransferase catalyzing the formation of 2-N-acetylglutamate semialdehyde and glutamate from 2-N-acetylornithine and alpha-ketoglutarate NF009048.0 PRK12382 PRK12382.1 364 364 392 subfamily Y Y N arabinose transporter GO:0022857,GO:0055085 1224 Pseudomonadota phylum 11578 NCBI Protein Cluster (PRK) putative transporter arabinose transporter NF009059.0 PRK12393 PRK12393.1 543 543 460 equivalog Y Y N amidohydrolase family protein 1224 Pseudomonadota phylum 3167 NCBI Protein Cluster (PRK) amidohydrolase amidohydrolase family protein NF009068.0 PRK12403 PRK12403.1 817 817 460 equivalog Y Y N aspartate aminotransferase family protein GO:0008483 1224 Pseudomonadota phylum 1853 NCBI Protein Cluster (PRK) putative aminotransferase aspartate aminotransferase family protein NF009074.0 PRK12409 PRK12409.1 494 494 410 equivalog Y Y N D-amino acid dehydrogenase 1.4.99.- GO:0016491 1224 Pseudomonadota phylum 3618 NCBI Protein Cluster (PRK) D-amino acid dehydrogenase small subunit D-amino acid dehydrogenase NF009089.0 PRK12425 PRK12425.1 840 840 464 equivalog Y Y N class II fumarate hydratase 4.2.1.2 1224 Pseudomonadota phylum 2400 NCBI Protein Cluster (PRK) fumarate hydratase class II fumarate hydratase Fumarase C; reversibly converts (S)-malate to fumarate and water; functions in the TCA cycle NF009109.0 PRK12457 PRK12457.1 457 457 281 equivalog Y Y N 3-deoxy-8-phosphooctulonate synthase kdsA 2.5.1.55 GO:0008676 1224 Pseudomonadota phylum 7580 NCBI Protein Cluster (PRK) 2-dehydro-3-deoxyphosphooctonate aldolase 3-deoxy-8-phosphooctulonate synthase NF009122.0 PRK12474 PRK12474.1 835 835 518 subfamily Y N N hypothetical protein 1224 Pseudomonadota phylum 78 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF009133.0 PRK12486 PRK12486.1 410 410 369 equivalog Y Y N dimethylsulfoniopropionate demethylase 1224 Pseudomonadota phylum 936 NCBI Protein Cluster (PRK) putative dimethyl sulfoniopropionate demethylase dimethylsulfoniopropionate demethylase NF009135.0 PRK12488 PRK12488.1 850 850 549 subfamily Y Y N cation/acetate symporter 1224 Pseudomonadota phylum 8002 NCBI Protein Cluster (PRK) acetate permease cation/acetate symporter Member of the sodium:solute symporter family NF009173.0 PRK12520 PRK12520.1 255 255 191 equivalog Y N N RNA polymerase sigma factor 1224 Pseudomonadota phylum 612 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009176.0 PRK12524 PRK12524.1 264 264 196 equivalog Y Y N RNA polymerase sigma factor 1224 Pseudomonadota phylum 1327 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor Bacteria have multiple sigma factors which are active under specific conditions; the sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs Bacterial core RNA polymerase to specific promoter elements to initiate transcription NF009179.0 PRK12527 PRK12527.1 162 162 159 equivalog Y N N RNA polymerase sigma factor 1224 Pseudomonadota phylum 1225 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009180.0 PRK12528 PRK12528.1 184 184 165 subfamily Y N N RNA polymerase sigma factor 1224 Pseudomonadota phylum 10693 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009181.0 PRK12529 PRK12529.1 247 247 179 equivalog Y N N RNA polymerase sigma factor 1224 Pseudomonadota phylum 200 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009188.0 PRK12536 PRK12536.1 250 250 190 subfamily Y N N RNA polymerase sigma factor 1224 Pseudomonadota phylum 1385 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009189.0 PRK12537 PRK12537.1 261 261 182 equivalog Y N N RNA polymerase sigma factor 1224 Pseudomonadota phylum 1561 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009190.0 PRK12538 PRK12538.1 303 303 233 equivalog Y N N RNA polymerase sigma factor 1224 Pseudomonadota phylum 258 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009191.0 PRK12539 PRK12539.1 171 171 185 subfamily Y Y N sigma-70 family RNA polymerase sigma factor GO:0003677,GO:0006352,GO:0006355,GO:0016987 1224 Pseudomonadota phylum 2472 NCBI Protein Cluster (PRK) RNA polymerase sigma factor sigma-70 family RNA polymerase sigma factor NF009196.0 PRK12544 PRK12544.1 287 287 208 equivalog Y Y N RNA polymerase factor sigma-70 2.7.7.6 1224 Pseudomonadota phylum 621 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase factor sigma-70 NF009270.0 PRK12627 PRK12627.1 128 128 128 equivalog Y Y N FlgB family protein 1224 Pseudomonadota phylum 1222 NCBI Protein Cluster (PRK) flagellar basal body rod protein FlgB FlgB family protein NF009275.1 PRK12632 PRK12632.1 170 170 130 equivalog Y Y N flagellar basal body rod protein FlgC flgC 1224 Pseudomonadota phylum 1170 NCBI Protein Cluster (PRK) flagellar basal body rod protein FlgC flagellar basal body rod protein FlgC With FlgF and B makes up the proximal portion of the flagellar basal body rod NF009326.0 PRK12681 PRK12681.1 436 436 324 equivalog Y Y N HTH-type transcriptional regulator CysB cysB GO:0003700,GO:0006355 11038360,11918818,14663078,15255893,17010379 1224 Pseudomonadota phylum 6178 NCBI Protein Cluster (PRK) transcriptional regulator CysB HTH-type transcriptional regulator CysB NF009327.0 PRK12684 PRK12684.1 402 402 313 subfamily Y Y N CysB family HTH-type transcriptional regulator 1224 Pseudomonadota phylum 12131 NCBI Protein Cluster (PRK) transcriptional regulator CysB-like protein CysB family HTH-type transcriptional regulator NF009332.0 PRK12690 PRK12690.1 288 288 239 equivalog Y Y N flagellar hook-basal body complex protein 1224 Pseudomonadota phylum 1342 NCBI Protein Cluster (PRK) flagellar basal body rod protein FlgF flagellar hook-basal body complex protein With FlgB and C, makes up the proximal portion of the flagellar basal body rod; NF009365.1 PRK12722 PRK12722.1 216 216 170 equivalog Y Y N flagellar transcriptional regulator FlhC flhC GO:0003677,GO:0045893,GO:1902208 10586519,7961507,9287017 1224 Pseudomonadota phylum 5046 NCBI Protein Cluster (PRK) transcriptional activator FlhC flagellar transcriptional regulator FlhC With FlhD is involved in the activation of class 2 flagellar genes and as well as a number of other genetic systems NF009407.0 PRK12768 PRK12768.1 191 191 242 equivalog Y Y N sulfate transporter family protein 1224 Pseudomonadota phylum 3145 NCBI Protein Cluster (PRK) CysZ-like protein sulfate transporter family protein NF009432.1 PRK12791 PRK12791.1 153 153 126 equivalog Y Y N flagellar biosynthesis repressor FlbT flbT GO:0006402,GO:0048027,GO:1902209 17098908 1224 Pseudomonadota phylum 846 NCBI Protein Cluster (PRK) flagellar biosynthesis repressor FlbT flagellar biosynthesis repressor FlbT Post-transcriptional repressor of flagellum biosynthesis; promotes degradation of fljK mRNA NF009437.0 PRK12796 PRK12796.1 263 263 223 equivalog Y Y N EscR/YscR/HrcR family type III secretion system export apparatus protein 1224 Pseudomonadota phylum 1538 NCBI Protein Cluster (PRK) type III secretion system protein SpaP EscR/YscR/HrcR family type III secretion system export apparatus protein NF009453.0 PRK12813 PRK12813.1 264 264 223 equivalog Y N N flagellar basal body rod modification protein 1224 Pseudomonadota phylum 959 NCBI Protein Cluster (PRK) flagellar basal body rod modification protein flagellar basal body rod modification protein NF009477.0 PRK12843 PRK12843.1 758 758 578 equivalog Y Y N FAD-dependent oxidoreductase 1224 Pseudomonadota phylum 485 NCBI Protein Cluster (PRK) putative FAD-binding dehydrogenase FAD-dependent oxidoreductase NF009484.0 PRK12846 PRK12846.1-5 190 190 165 equivalog Y Y N peptide deformylase 3.5.1.88 GO:0042586 1224 Pseudomonadota phylum 2436 NCBI Protein Cluster (PRK) peptide deformylase peptide deformylase NF009501.0 PRK12861 PRK12861.1 1178 1178 764 subfamily Y Y N NADP-dependent malic enzyme 1224 Pseudomonadota phylum 5890 NCBI Protein Cluster (PRK) malic enzyme NADP-dependent malic enzyme NF009504.0 PRK12863 PRK12863.1-4 134 134 97 equivalog Y N N YciI-like protein 1224 Pseudomonadota phylum 440 NCBI Protein Cluster (PRK) YciI-like protein YciI-like protein NF009528.0 PRK12893 PRK12893.1-1 570 570 420 subfamily Y Y N Zn-dependent hydrolase 1224 Pseudomonadota phylum 1198 NCBI Protein Cluster (PRK) allantoate amidohydrolase Zn-dependent hydrolase NF009529.0 PRK12893 PRK12893.1-2 508 508 411 equivalog Y Y N Zn-dependent hydrolase 1224 Pseudomonadota phylum 575 NCBI Protein Cluster (PRK) allantoate amidohydrolase Zn-dependent hydrolase NF009530.0 PRK12893 PRK12893.1-4 551 551 423 subfamily Y Y N Zn-dependent hydrolase 1224 Pseudomonadota phylum 2229 NCBI Protein Cluster (PRK) allantoate amidohydrolase Zn-dependent hydrolase NF009531.0 PRK12893 PRK12893.1-5 486 486 421 equivalog Y Y N Zn-dependent hydrolase 1224 Pseudomonadota phylum 920 NCBI Protein Cluster (PRK) allantoate amidohydrolase Zn-dependent hydrolase NF009602.0 PRK13054 PRK13054.1 284 284 301 equivalog Y Y N lipid kinase YegS yegS 2.7.1.- GO:0001727,GO:0046872 1224 Pseudomonadota phylum 8648 NCBI Protein Cluster (PRK) lipid kinase lipid kinase YegS NF009639.0 PRK13168 PRK13168.1 458 458 446 equivalog Y Y N 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD rlmD 2.1.1.190 GO:0006396,GO:0008173 11779873,12907714,15016356,15181002,15766524,17085441 1224 Pseudomonadota phylum 24212 NCBI Protein Cluster (PRK) 23S rRNA m(5)U1939 methyltransferase 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD Catalyzes the methylation of U1939 in 23S ribomal RNA; binds an iron-sulfur cluster [4Fe-4S]; SAM-dependent NF009666.0 PRK13187 PRK13187.1 423 423 305 equivalog Y Y N UDP-3-O-acyl N-acetylglycosamine deacetylase 1224 Pseudomonadota phylum 593 NCBI Protein Cluster (PRK) UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase UDP-3-O-acyl N-acetylglycosamine deacetylase NF009690.0 PRK13211 PRK13211.1 481 481 477 equivalog Y Y N N-acetylglucosamine-binding protein GbpA gbpA 14983042,16341015 1224 Pseudomonadota phylum 4950 NCBI Protein Cluster (PRK) N-acetylglucosamine-binding protein A N-acetylglucosamine-binding protein GbpA Plays a role mediating bacterial attachment and colonization of zooplankton and/or intestinal epithelium NF009729.0 PRK13254 PRK13254.1-3 171 171 155 equivalog Y Y N cytochrome c maturation protein CcmE ccmE GO:0017003,GO:0017004,GO:0020037 1224 Pseudomonadota phylum 9922 NCBI Protein Cluster (PRK) cytochrome c-type biogenesis protein CcmE cytochrome c maturation protein CcmE NF009773.0 PRK13270 PRK13270.1 512 512 549 subfamily Y Y N alpha,alpha-trehalase TreF treF GO:0004555,GO:0005991 1224 Pseudomonadota phylum 14037 NCBI Protein Cluster (PRK) trehalase alpha,alpha-trehalase TreF Catalyzes the hydrolysis of trehalose to glucose NF009774.0 PRK13271 PRK13271.1 560 560 569 subfamily Y Y N alpha,alpha-trehalase TreA treA GO:0004555,GO:0005991 1224 Pseudomonadota phylum 13090 NCBI Protein Cluster (PRK) trehalase alpha,alpha-trehalase TreA Catalyzes the hydrolysis of trehalose to glucose NF009792.0 PRK13284 PRK13284.1 171 171 146 equivalog Y N N flagellar assembly protein FliW 1224 Pseudomonadota phylum 222 NCBI Protein Cluster (PRK) flagellar assembly protein FliW flagellar assembly protein FliW NF009827.0 PRK13303 PRK13303.1-2 226 226 267 equivalog Y Y N aspartate dehydrogenase 1.4.1.21 GO:0009435,GO:0033735 1224 Pseudomonadota phylum 3639 NCBI Protein Cluster (PRK) L-aspartate dehydrogenase aspartate dehydrogenase NF009858.0 PRK13322 PRK13322.1-3 379 379 243 equivalog Y Y N pantothenate kinase 2.7.1.33 1224 Pseudomonadota phylum 249 NCBI Protein Cluster (PRK) pantothenate kinase pantothenate kinase NF009859.0 PRK13322 PRK13322.1-4 379 379 249 equivalog Y Y N pantothenate kinase 2.7.1.33 GO:0004594 1224 Pseudomonadota phylum 2074 NCBI Protein Cluster (PRK) pantothenate kinase pantothenate kinase NF009879.0 PRK13340 PRK13340.1-4 434 434 406 subfamily Y Y N alanine racemase 5.1.1.1 1224 Pseudomonadota phylum 3429 NCBI Protein Cluster (PRK) alanine racemase alanine racemase NF009908.0 PRK13370 PRK13370.1-2 467 467 314 equivalog Y Y N 3-carboxyethylcatechol 2,3-dioxygenase 1.13.11.16 1224 Pseudomonadota phylum 731 NCBI Protein Cluster (PRK) 3-(2,3-dihydroxyphenyl)propionate dioxygenase 3-carboxyethylcatechol 2,3-dioxygenase NF009925.1 PRK13386 PRK13386.1 192 192 228 equivalog Y Y N flagellar assembly protein FliH fliH 15687208 1224 Pseudomonadota phylum 2018 NCBI Protein Cluster (PRK) flagellar assembly protein H flagellar assembly protein FliH Binds to and inhibits the function of flagella specific ATPase FliI NF009932.0 PRK13395 PRK13395.1 160 160 171 subfamily Y Y N ureidoglycolate lyase 4.3.2.3 1224 Pseudomonadota phylum 9542 NCBI Protein Cluster (PRK) ureidoglycolate hydrolase ureidoglycolate lyase NF009955.0 PRK13421 PRK13421.1 302 302 231 equivalog Y Y N F0F1 ATP synthase subunit A 1224 Pseudomonadota phylum 768 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit A F0F1 ATP synthase subunit A Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit A is part of the membrane proton channel F0 NF009972.0 PRK13435 PRK13435.1-3 119 119 146 subfamily Y Y N response regulator 1224 Pseudomonadota phylum 1019 NCBI Protein Cluster (PRK) response regulator response regulator NF009973.0 PRK13435 PRK13435.1-4 158 158 154 equivalog Y N N response regulator 1224 Pseudomonadota phylum 208 NCBI Protein Cluster (PRK) response regulator response regulator NF009981.0 PRK13447 PRK13447.1 160 160 151 equivalog Y Y N F0F1 ATP synthase subunit epsilon 7.1.2.2 1224 Pseudomonadota phylum 694 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit epsilon F0F1 ATP synthase subunit epsilon Produces ATP from ADP in the presence of a proton gradient across the membrane; the epsilon subunit is part of the catalytic core of the ATP synthase complex NF009988.0 PRK13454 PRK13454.1 186 186 181 equivalog Y Y N F0F1 ATP synthase subunit B' 1224 Pseudomonadota phylum 1501 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit B' F0F1 ATP synthase subunit B' Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B' is part of the membrane proton channel. NF009989.0 PRK13455 PRK13455.1 249 249 185 equivalog Y Y N F0F1 ATP synthase subunit B 1224 Pseudomonadota phylum 1417 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit B F0F1 ATP synthase subunit B Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B is part of the membrane proton channel NF010010.0 PRK13483 PRK13483.1 927 927 660 equivalog Y Y N ligand-gated channel protein 12065481,1406279,2174861 1224 Pseudomonadota phylum 2131 NCBI Protein Cluster (PRK) enterobactin receptor protein ligand-gated channel protein NF010014.0 PRK13489 PRK13489.1 290 290 238 equivalog Y Y N chemoreceptor glutamine deamidase CheD cheD 3.5.1.44 1224 Pseudomonadota phylum 1438 NCBI Protein Cluster (PRK) chemoreceptor glutamine deamidase CheD chemoreceptor glutamine deamidase CheD NF010038.0 PRK13513 PRK13513.1 942 942 659 equivalog Y Y N ligand-gated channel protein 16954402 1224 Pseudomonadota phylum 2861 NCBI Protein Cluster (PRK) putative outer membrane receptor ligand-gated channel protein NF010040.1 PRK13516 PRK13516.1 425 425 369 equivalog Y Y N YbdK family carboxylate-amine ligase 6.3.2.2 GO:0004357,GO:0042398 15211520 1224 Pseudomonadota phylum 5962 NCBI Protein Cluster (PRK) gamma-glutamyl:cysteine ligase YbdK family carboxylate-amine ligase This family of well-conserved proteins includes YbdK from E. coli K-12, which showed glutamate--cysteine ligase activity 500-fold slower than GshA from the same organism. Because the family is considered a putative glutamate--cysteine ligase by some, perhaps simply requiring a helper protein, it is also known as GCS2 (putative glutamate--cysteine ligase 2). NF010048.1 PRK13524 PRK13524.1 493 493 744 subfamily Y Y N FepA family TonB-dependent siderophore receptor GO:0009279,GO:0015344,GO:0015891 3015941,8419284 1224 Pseudomonadota phylum 15249 NCBI Protein Cluster (PRK) outer membrane receptor FepA FepA family TonB-dependent siderophore receptor FepA from Escherichia coli K-12, and PfeA from Pseudomonas aeruginosa, are both TonB-dependent receptors for the ferric-bound form of the siderophore enterobactin (enterochelin). NF010051.0 PRK13528 PRK13528.1 583 583 727 subfamily Y Y N FepA family TonB-dependent siderophore receptor GO:0015344,GO:0015891 1224 Pseudomonadota phylum 15156 NCBI Protein Cluster (PRK) outer membrane receptor FepA FepA family TonB-dependent siderophore receptor NF010059.0 PRK13536 PRK13536.1 549 549 342 equivalog Y Y N nodulation factor ABC transporter ATP-binding protein NodI nodI 1224 Pseudomonadota phylum 747 NCBI Protein Cluster (PRK) nodulation factor exporter subunit NodI nodulation factor ABC transporter ATP-binding protein NodI Involved in the export of lipooligosaccharides during nodulation NF010060.0 PRK13537 PRK13537.1 521 521 314 equivalog Y Y N nodulation factor ABC transporter ATP-binding protein NodI nodI 1224 Pseudomonadota phylum 1290 NCBI Protein Cluster (PRK) nodulation ABC transporter NodI nodulation factor ABC transporter ATP-binding protein NodI NF010061.0 PRK13538 PRK13538.1 195 195 211 equivalog Y Y N cytochrome c biogenesis heme-transporting ATPase CcmA ccmA 7.6.2.- GO:0005524,GO:0017004,GO:0022857 1224 Pseudomonadota phylum 13879 NCBI Protein Cluster (PRK) cytochrome c biogenesis protein CcmA cytochrome c biogenesis heme-transporting ATPase CcmA ATP-binding protein; required for proper cytochrome c maturation NF010231.0 PRK13682 PRK13682.2-1 82 82 57 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 181 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010240.0 PRK13687 PRK13687.1 99 99 85 subfamily Y N N hypothetical protein 1224 Pseudomonadota phylum 3081 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010253.0 PRK13699 PRK13699.1 244 244 226 subfamily Y Y N DNA methyltransferase 1224 Pseudomonadota phylum 5793 NCBI Protein Cluster (PRK) putative methylase DNA methyltransferase NF010297.0 PRK13737 PRK13737.1 298 298 330 equivalog Y Y N conjugal transfer pilus assembly protein TraU traU 7915817 1224 Pseudomonadota phylum 5398 NCBI Protein Cluster (PRK) conjugal transfer pilus assembly protein TraU conjugal transfer pilus assembly protein TraU NF010319.1 PRK13756 PRK13756.1 265 265 199 equivalog Y Y N tetracycline resistance transcriptional repressor TetR tetR 1224 Pseudomonadota phylum 1550 NCBI Protein Cluster (PRK) tetracycline repressor protein TetR tetracycline resistance transcriptional repressor TetR The seed for this HMM was rebuilt in 2019, with 17 member proteins all selected as neighbors of trusted tetracycline efflux MFS transporters. NF010393.0 PRK13821 PRK13821.1 576 576 323 equivalog Y Y N thymidylate synthase 2.1.1.45 1224 Pseudomonadota phylum 2485 NCBI Protein Cluster (PRK) thymidylate synthase thymidylate synthase NF010394.0 PRK13822 PRK13822.1 443 443 643 subfamily Y N N conjugal transfer coupling protein TraG 1224 Pseudomonadota phylum 2377 NCBI Protein Cluster (PRK) conjugal transfer coupling protein TraG conjugal transfer coupling protein TraG NF010401.0 PRK13825 PRK13825.1-5 500 500 407 equivalog Y N N conjugal transfer protein TraB 1224 Pseudomonadota phylum 7 NCBI Protein Cluster (PRK) conjugal transfer protein TraB conjugal transfer protein TraB NF010412.0 PRK13838 PRK13838.1 186 186 177 subfamily Y N N conjugal transfer pilin processing protease TraF 1224 Pseudomonadota phylum 1164 NCBI Protein Cluster (PRK) conjugal transfer pilin processing protease TraF conjugal transfer pilin processing protease TraF NF010430.0 PRK13856 PRK13856.1 344 344 241 equivalog Y N N two-component response regulator VirG 1224 Pseudomonadota phylum 221 NCBI Protein Cluster (PRK) two-component response regulator VirG two-component response regulator VirG NF010443.0 PRK13869 PRK13869.1 446 446 405 subfamily Y N N plasmid-partitioning protein RepA 1224 Pseudomonadota phylum 5316 NCBI Protein Cluster (PRK) plasmid-partitioning protein RepA plasmid-partitioning protein RepA NF010444.0 PRK13870 PRK13870.1 227 227 234 subfamily Y Y N transcriptional regulator TraR traR 1224 Pseudomonadota phylum 381 NCBI Protein Cluster (PRK) transcriptional regulator TraR transcriptional regulator TraR NF010456.0 PRK13883 PRK13883.1-2 319 319 160 equivalog Y N N conjugal transfer protein TrbH 1224 Pseudomonadota phylum 4 NCBI Protein Cluster (PRK) conjugal transfer protein TrbH conjugal transfer protein TrbH NF010457.0 PRK13883 PRK13883.1-4 160 160 137 subfamily Y N N conjugal transfer protein TrbH 1224 Pseudomonadota phylum 108 NCBI Protein Cluster (PRK) conjugal transfer protein TrbH conjugal transfer protein TrbH NF010474.0 PRK13899 PRK13899.1 74 74 97 equivalog Y N N type IV secretion system protein VirB3 virB3 1224 Pseudomonadota phylum 382 NCBI Protein Cluster (PRK) type IV secretion system protein VirB3 type IV secretion system protein VirB3 NF010475.0 PRK13900 PRK13900.1 389 389 333 equivalog Y N N type IV secretion system ATPase VirB11 1224 Pseudomonadota phylum 276 NCBI Protein Cluster (PRK) type IV secretion system ATPase VirB11 type IV secretion system ATPase VirB11 NF010533.0 PRK13922 PRK13922.9-5 384 384 345 equivalog Y Y N rod shape-determining protein MreC mreC 1224 Pseudomonadota phylum 1960 NCBI Protein Cluster (PRK) rod shape-determining protein MreC rod shape-determining protein MreC NF010541.0 PRK13931 PRK13931.1 422 422 261 equivalog Y Y N 5'/3'-nucleotidase SurE surE 3.1.3.6 1224 Pseudomonadota phylum 1574 NCBI Protein Cluster (PRK) stationary phase survival protein SurE 5'/3'-nucleotidase SurE NF010546.0 PRK13936 PRK13936.1 276 276 197 equivalog Y Y N phosphoheptose isomerase GO:0008968,GO:0097367,GO:1901135 1224 Pseudomonadota phylum 3852 NCBI Protein Cluster (PRK) phosphoheptose isomerase phosphoheptose isomerase NF010595.0 PRK13989 PRK13989.1 108 108 85 equivalog Y Y N cell division topological specificity factor MinE minE 1224 Pseudomonadota phylum 2010 NCBI Protein Cluster (PRK) cell division topological specificity factor MinE cell division topological specificity factor MinE works in conjunction with MinC and MinD to enable cell division at the midpoint of the long axis of the cell NF010603.0 PRK13999 PRK13999.1 320 320 201 equivalog Y Y N K(+)-transporting ATPase subunit C 1224 Pseudomonadota phylum 1048 NCBI Protein Cluster (PRK) potassium-transporting ATPase subunit C K(+)-transporting ATPase subunit C Component of the high-affinity ATP-driven potassium transport (or KDP)system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions; the C subunit may be involved in assembly of the KDP complex NF010616.0 PRK14013 PRK14013.2-2 606 606 365 equivalog Y N N hypothetical protein 1224 Pseudomonadota phylum 1032 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010650.0 PRK14049 PRK14049.1 904 904 729 equivalog Y N N ferrioxamine B receptor precursor protein 1224 Pseudomonadota phylum 460 NCBI Protein Cluster (PRK) ferrioxamine B receptor precursor protein ferrioxamine B receptor precursor protein NF010699.0 PRK14099 PRK14099.1 762 762 485 equivalog Y Y N glycogen synthase GlgA glgA 2.4.1.21 1224 Pseudomonadota phylum 730 NCBI Protein Cluster (PRK) glycogen synthase glycogen synthase GlgA NF010730.0 PRK14131 PRK14131.1 416 416 384 subfamily Y Y N N-acetylneuraminate epimerase 1224 Pseudomonadota phylum 2966 NCBI Protein Cluster (PRK) N-acetylneuraminic acid mutarotase N-acetylneuraminate epimerase NF010922.0 PRK14342 PRK14342.1 235 235 215 equivalog Y Y N lipoyl(octanoyl) transferase LipB lipB 2.3.1.181 GO:0009249,GO:0033819 1224 Pseudomonadota phylum 15732 NCBI Protein Cluster (PRK) lipoate-protein ligase B lipoyl(octanoyl) transferase LipB Catalyzes the transfer of the lipoyl/octanoyl moiety of lipoyl/octanoyl-ACP onto lipoate-dependent enzymes like pyruvate dehydrogenase and the glycine cleavage system H protein NF010923.0 PRK14343 PRK14343.1 298 298 237 equivalog Y Y N lipoyl(octanoyl) transferase LipB lipB 2.3.1.181 GO:0009249,GO:0033819 1224 Pseudomonadota phylum 2195 NCBI Protein Cluster (PRK) lipoate-protein ligase B lipoyl(octanoyl) transferase LipB Catalyzes the transfer of the lipoyl/octanoyl moiety of lipoyl/octanoyl-ACP onto lipoate-dependent enzymes like pyruvate dehydrogenase and the glycine cleavage system H protein NF010999.0 PRK14425 PRK14425.1 106 106 94 equivalog Y Y N acylphosphatase 1224 Pseudomonadota phylum 928 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011034.0 PRK14464 PRK14464.1 422 422 348 equivalog Y Y N RNA methyltransferase GO:0006364,GO:0008173 1224 Pseudomonadota phylum 2315 NCBI Protein Cluster (PRK) ribosomal RNA large subunit methyltransferase N RNA methyltransferase NF011077.0 PRK14507 PRK14507.1 2148 2148 1693 equivalog Y Y N malto-oligosyltrehalose synthase 2.4.1.25,5.4.99.15 1224 Pseudomonadota phylum 645 NCBI Protein Cluster (PRK) putative bifunctional 4-alpha-glucanotransferase/malto-oligosyltrehalose synthase malto-oligosyltrehalose synthase NF011177.0 PRK14582 PRK14582.1 923 923 671 equivalog Y Y N poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB pgaB 3.5.1.- 1224 Pseudomonadota phylum 4802 NCBI Protein Cluster (PRK) outer membrane N-deacetylase poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB NF011235.0 PRK14642 PRK14642.1 297 297 199 equivalog Y Y N ribosome maturation factor RimP rimP 1224 Pseudomonadota phylum 772 NCBI Protein Cluster (PRK) hypothetical protein ribosome maturation factor RimP NF011305.0 PRK14716 PRK14716.1-3 409 409 486 equivalog Y Y N glycosyl transferase family protein 1224 Pseudomonadota phylum 4664 NCBI Protein Cluster (PRK) bacteriophage N4 adsorption protein B glycosyl transferase family protein NF011323.0 PRK14736 PRK14736.1 145 145 133 subfamily Y N N F0F1 ATP synthase subunit epsilon 1224 Pseudomonadota phylum 241 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit epsilon F0F1 ATP synthase subunit epsilon NF011342.0 PRK14759 PRK14759.1 53 53 29 equivalog Y Y N K(+)-transporting ATPase subunit F 7.2.2.6 1224 Pseudomonadota phylum 443 NCBI Protein Cluster (PRK) potassium-transporting ATPase subunit F K(+)-transporting ATPase subunit F Component of the high-affinity ATP-driven potassium transport (or KDP)system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions NF011381.1 PRK14806 PRK14806.1 902 902 733 equivalog Y Y N bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyltransferase 1.3.1.12,2.5.1.19 GO:0008977,GO:0009073 1224 Pseudomonadota phylum 6290 NCBI Protein Cluster (PRK) bifunctional cyclohexadienyl dehydrogenase/ 3-phosphoshikimate 1-carboxyvinyltransferase bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyltransferase Catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate and the formation of tyrosine from arogenate and Catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis NF011458.0 PRK14876 PRK14876.1 603 603 931 equivalog Y Y N conjugal transfer mating pair stabilization protein TraN traN 1593622,16272376,9696748 1224 Pseudomonadota phylum 731 NCBI Protein Cluster (PRK) conjugal transfer mating pair stabilization protein TraN conjugal transfer mating pair stabilization protein TraN TrhN; involved in stabilizing mating pairs during plasmid conjugation; F plasmid TraN appears to recognize OmpA in the recipient cell NF011573.0 PRK14997 PRK14997.1 380 380 303 equivalog Y Y N LysR family transcriptional regulator 1224 Pseudomonadota phylum 4582 NCBI Protein Cluster (PRK) LysR family transcriptional regulator LysR family transcriptional regulator NF011576.0 PRK15000 PRK15000.1 301 301 200 subfamily Y Y N peroxiredoxin C 1.11.1.24 GO:0051920 1224 Pseudomonadota phylum 3430 NCBI Protein Cluster (PRK) peroxidase peroxiredoxin C NF011584.0 PRK15008 PRK15008.1 230 230 212 equivalog Y Y N HTH-type transcriptional regulator RutR rutR GO:0003677,GO:0045892 1224 Pseudomonadota phylum 2971 NCBI Protein Cluster (PRK) HTH-type transcriptional regulator RutR HTH-type transcriptional regulator RutR NF011607.0 PRK15033 PRK15033.1 524 524 389 subfamily Y Y N tricarballylate utilization 4Fe-4S protein TcuB tcuB 1224 Pseudomonadota phylum 4179 NCBI Protein Cluster (PRK) tricarballylate utilization protein B tricarballylate utilization 4Fe-4S protein TcuB NF011623.0 PRK15049 PRK15049.1 773 773 499 equivalog Y Y N L-asparagine permease ansP GO:0006865,GO:0016020 1224 Pseudomonadota phylum 3692 NCBI Protein Cluster (PRK) L-asparagine permease L-asparagine permease Involved in the transport of L-asparagine NF011630.0 PRK15056 PRK15056.1 393 393 274 equivalog Y Y N manganese/iron ABC transporter ATP-binding protein GO:0005524 1224 Pseudomonadota phylum 5655 NCBI Protein Cluster (PRK) manganese/iron transporter ATP-binding protein manganese/iron ABC transporter ATP-binding protein With SitACD is involved in the transport of manganese and iron NF011633.0 PRK15059 PRK15059.1 451 451 292 equivalog Y Y N 2-hydroxy-3-oxopropionate reductase glxR 1.1.1.60 GO:0008679,GO:0046487,GO:0051287 1224 Pseudomonadota phylum 2195 NCBI Protein Cluster (PRK) tartronate semialdehyde reductase 2-hydroxy-3-oxopropionate reductase NF011651.0 PRK15069 PRK15069.1 306 306 237 subfamily Y Y N histidine ABC transporter permease HisM hisM 1224 Pseudomonadota phylum 5366 NCBI Protein Cluster (PRK) histidine/lysine/arginine/ornithine ABC transporter permease HisM histidine ABC transporter permease HisM With HisJPQ is involved in transport of histidine, lysine, arginine and ornithine NF011658.0 PRK15078 PRK15078.1 333 333 380 subfamily Y Y N polysaccharide export protein 1224 Pseudomonadota phylum 8362 NCBI Protein Cluster (PRK) polysaccharide export protein Wza polysaccharide export protein NF011659.0 PRK15079 PRK15079.1 540 540 334 equivalog Y Y N murein tripeptide/oligopeptide ABC transporter ATP binding protein OppF oppF 7.4.2.- GO:0005524,GO:0015833 1224 Pseudomonadota phylum 4050 NCBI Protein Cluster (PRK) oligopeptide ABC transporter ATP-binding protein OppF murein tripeptide/oligopeptide ABC transporter ATP binding protein OppF With OppABCD is involved in the transport of oligopeptides; OppF and OppD are ATP-binding proteins NF011661.0 PRK15081 PRK15081.1 463 463 306 equivalog Y Y N glutathione ABC transporter permease GsiC gsiC 7.4.2.- GO:0016020,GO:0055085 1224 Pseudomonadota phylum 3740 NCBI Protein Cluster (PRK) glutathione ABC transporter permease GsiC glutathione ABC transporter permease GsiC With GsiABD is involved in the transport of glutathione into the cell NF011662.0 PRK15082 PRK15082.1 484 484 303 equivalog Y Y N glutathione ABC transporter permease GsiD gsiD 7.4.2.- GO:0016020,GO:0055085 1224 Pseudomonadota phylum 3839 NCBI Protein Cluster (PRK) glutathione ABC transporter permease GsiD glutathione ABC transporter permease GsiD With GsiABC is involved in the transport of glutathione into the cell NF011671.1 PRK15090 PRK15090.1 275 275 256 equivalog Y Y N DNA-binding transcriptional regulator KdgR kdgR GO:0003700,GO:0006355 1545709,4359651,8107132 1224 Pseudomonadota phylum 3464 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator KdgR DNA-binding transcriptional regulator KdgR Regulates the genes involved in 2-keto-3-deoxy gluconate transport and catabolism NF011686.0 PRK15106 PRK15106.1 311 311 289 subfamily Y Y N nucleoside-specific channel-forming protein Tsx tsx 1224 Pseudomonadota phylum 3463 NCBI Protein Cluster (PRK) nucleoside-specific channel-forming protein Tsx nucleoside-specific channel-forming protein Tsx Involved in the transfer of deoxyribo- and ribo-nucleotides across the outer membrane NF011687.0 PRK15107 PRK15107.1 318 318 224 equivalog Y Y N glutamate/aspartate ABC transporter permease GltK gltK 7.4.2.1 1224 Pseudomonadota phylum 2374 NCBI Protein Cluster (PRK) glutamate/aspartate transport system permease GltK glutamate/aspartate ABC transporter permease GltK With GltJLPS and GadC for glutamate and GltJLP, DctA and DcuAB for aspartate is involved in the transport of glutamate and aspartate NF011693.0 PRK15113 PRK15113.1 150 150 214 equivalog Y Y N glutathione transferase yfcF 2.5.1.18 GO:0006749 1224 Pseudomonadota phylum 5755 NCBI Protein Cluster (PRK) glutathione S-transferase glutathione transferase NF011694.0 PRK15114 PRK15114.1 280 280 246 equivalog Y Y N tRNA (cytosine(32)/uridine(32)-2'-O)-methyltransferase TrmJ trmJ 2.1.1.200 GO:0003723,GO:0006396,GO:0008173 1224 Pseudomonadota phylum 8501 NCBI Protein Cluster (PRK) tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ tRNA (cytosine(32)/uridine(32)-2'-O)-methyltransferase TrmJ Catalyzes the fromation of 2'O-methylated cytidine or 2'O-methylated uridine at position 32 in tRNA NF011714.0 PRK15135 PRK15135.1 319 319 228 subfamily Y Y N histidine ABC transporter permease HisQ hisQ GO:0003333,GO:0016020,GO:0022857,GO:0043190 1224 Pseudomonadota phylum 3914 NCBI Protein Cluster (PRK) histidine/lysine/arginine/ornithine ABC transporter permease HisQ histidine ABC transporter permease HisQ With HisJMP is involved in the transport of histidine/lysine/arginine/ornithine NF011854.0 PRK15326 PRK15326.1 96 96 80 equivalog Y Y N type III secretion system needle complex protein 1224 Pseudomonadota phylum 379 NCBI Protein Cluster (PRK) type III secretion system needle complex protein PrgI type III secretion system needle complex protein NF011857.0 PRK15329 PRK15329.1 99 99 138 equivalog Y Y N chaperone SicP sicP 1224 Pseudomonadota phylum 290 NCBI Protein Cluster (PRK) chaperone protein SicP chaperone SicP Type III secretion system chaperone NF011859.0 PRK15331 PRK15331.1 184 184 165 equivalog Y Y N type III secretion system translocator chaperone SicA sicA 1224 Pseudomonadota phylum 657 NCBI Protein Cluster (PRK) chaperone protein SicA type III secretion system translocator chaperone SicA NF011865.0 PRK15337 PRK15337.1 800 800 686 equivalog Y Y N EscV/YscV/HrcV family type III secretion system export apparatus protein 1224 Pseudomonadota phylum 1774 NCBI Protein Cluster (PRK) type III secretion system protein InvA EscV/YscV/HrcV family type III secretion system export apparatus protein NF011898.1 PRK15371 PRK15371.1 275 275 269 subfamily Y Y N YopJ/AvrA family T3SS effector serine/threonine acetyltransferase 25838979,31240408 1224 Pseudomonadota phylum 663 NCBI Protein Cluster (PRK) effector protein YopJ YopJ/AvrA family T3SS effector serine/threonine acetyltransferase NF011933.0 PRK15404 PRK15404.1 477 477 370 subfamily Y Y N high-affinity branched-chain amino acid ABC transporter substrate-binding protein 1224 Pseudomonadota phylum 8204 NCBI Protein Cluster (PRK) leucine ABC transporter subunit substrate-binding protein LivK high-affinity branched-chain amino acid ABC transporter substrate-binding protein With LivFGHM is involved in the high affinity leucine transport NF011935.0 PRK15406 PRK15406.1 433 433 302 equivalog Y Y N oligopeptide ABC transporter permease OppC oppC 7.4.2.- GO:0055085 1224 Pseudomonadota phylum 3106 NCBI Protein Cluster (PRK) oligopeptide ABC transporter permease OppC oligopeptide ABC transporter permease OppC With OppBCDF is involved in the transport of oligopeptides of up to 5 amino acids into the cell NF011942.0 PRK15413 PRK15413.1 594 594 512 equivalog Y Y N glutathione ABC transporter substrate-binding protein GsiB gsiB 7.4.2.- GO:0034634,GO:0034775,GO:0043190 30515393 1224 Pseudomonadota phylum 6456 NCBI Protein Cluster (PRK) glutathione ABC transporter substrate-binding protein GsiB glutathione ABC transporter substrate-binding protein GsiB With GsiACD is involved in the transport of glutathione into the cell NF011946.0 PRK15417 PRK15417.1 435 435 337 equivalog Y Y N integron integrase 1224 Pseudomonadota phylum 1890 NCBI Protein Cluster (PRK) integrase/recombinase integron integrase NF011963.0 PRK15434 PRK15434.1 146 146 159 subfamily Y Y N GDP-mannose mannosyl hydrolase 3.2.1.42 1224 Pseudomonadota phylum 4246 NCBI Protein Cluster (PRK) GDP-mannose mannosyl hydrolase NudD GDP-mannose mannosyl hydrolase Catalyzes the formation of GDP and D-mannose from GDP-D-mannose; also hydrolyzes GDP-glucose NF011967.0 PRK15439 PRK15439.1 586 586 510 equivalog Y Y N autoinducer 2 ABC transporter ATP-binding protein LsrA lsrA 7.6.2.- GO:0005524,GO:0016020,GO:0042626,GO:1905887 1224 Pseudomonadota phylum 4914 NCBI Protein Cluster (PRK) autoinducer 2 ABC transporter ATP-binding protein LsrA autoinducer 2 ABC transporter ATP-binding protein LsrA With LsrCDB is involved in the transport of autoindiuce 2 NF011968.0 PRK15440 PRK15440.1 393 393 395 equivalog Y Y N L-rhamnonate dehydratase rhmD 4.2.1.90 GO:0050032 1224 Pseudomonadota phylum 3507 NCBI Protein Cluster (PRK) L-rhamnonate dehydratase L-rhamnonate dehydratase Catalyzes the formation of 2-keto-3-deoxy-L-rhamnonate from L-rhamnonate NF011991.0 PRK15447 PRK15447.1 283 283 302 equivalog Y Y N U32 family peptidase GO:0006744 1224 Pseudomonadota phylum 12268 NCBI Protein Cluster (PRK) putative protease U32 family peptidase NF011999.0 PRK15455 PRK15455.1 576 576 644 equivalog Y Y N PrkA family serine protein kinase GO:0004672 1224 Pseudomonadota phylum 9743 NCBI Protein Cluster (PRK) PrkA family serine protein kinase PrkA family serine protein kinase NF012025.0 PRK15481 PRK15481.1 573 573 432 equivalog Y Y N transcriptional regulator PtsJ ptsJ GO:0003700,GO:0006355 1224 Pseudomonadota phylum 2843 NCBI Protein Cluster (PRK) transcriptional regulatory protein PtsJ transcriptional regulator PtsJ Regulator of the ptsHI/crr operon NF012033.0 PRK15489 PRK15489.1 537 537 703 equivalog Y Y N glycosyl transferase family protein 1224 Pseudomonadota phylum 4617 NCBI Protein Cluster (PRK) bacteriophage N4 adsorption protein B glycosyl transferase family protein NF012100.0 blaVIM 500 500 266 exception Y Y Y VIM family subclass B1 metallo-beta-lactamase blaVIM 3.5.2.6 GO:0008800 10390207 1224 Pseudomonadota phylum 62 NCBIFAM blaVIM: VIM family subclass B1 metallo-beta-lactamase VIM family subclass B1 metallo-beta-lactamase VIM (Verona integron-borne metallo-beta-lactamase) is a subclass B1 enzyme that hydrolyzes a broad array of beta-lactams, including ampicillin, carbenicillin, piperacillin, mezlocillin, cefotaxime, cefoxitin, ceftazidime, cefoperazone, cefepime, and carbapenems. NF012145.1 blaDIM_SIM_IMP 288 288 209 exception Y Y Y DIM/SIM/IMP family subclass B1 metallo-beta-lactamase blaDIM 3.5.2.6 GO:0008800 1224 Pseudomonadota phylum 199 NCBIFAM blaDIM_SIM_IMP: DIM/SIM/IMP family subclass B1 metallo-beta-lactamase DIM/SIM/IMP family subclass B1 metallo-beta-lactamase NF012147.1 blaIMP 460 460 245 exception Y Y Y IMP family subclass B1 metallo-beta-lactamase blaIMP 3.5.2.6 GO:0008800 1224 Pseudomonadota phylum 59 NCBIFAM blaIMP: IMP family subclass B1 metallo-beta-lactamase IMP family subclass B1 metallo-beta-lactamase NF012158.1 macrolide_MphE 640 640 294 exception Y Y Y Mph(E) family macrolide 2'-phosphotransferase 1224 Pseudomonadota phylum 87 NCBIFAM MPH_E: Mph(E) family macrolide 2'-phosphotransferase Mph(E) family macrolide 2'-phosphotransferase NF012165.0 AAC_6p_set_A 280 280 177 equivalog Y Y Y aminoglycoside 6'-N-acetyltransferase aac(6') 2.3.1.82 1224 Pseudomonadota phylum 385 NCBIFAM aac6_set_A: aminoglycoside 6'-N-acetyltransferase aminoglycoside 6'-N-acetyltransferase NF012182.0 exosortase_XrtQ 270 270 256 exception Y Y N exosortase Q xrtQ GO:0004197,GO:0006605,GO:0016020,GO:0043687 22037399 1224 Pseudomonadota phylum 400 NCBIFAM exosortase Q exosortase Q NF012190.1 tet_MFS_B 850 850 400 exception Y Y Y tetracycline efflux MFS transporter Tet(B) tet(B) GO:0008493,GO:0015904,GO:0016020,GO:0022857,GO:0055085 1224 Pseudomonadota phylum 195 NCBIFAM tetracycline efflux MFS transporter Tet(B) tetracycline efflux MFS transporter Tet(B) NF012192.0 tet_MFS_G 800 800 391 exception Y Y Y tetracycline efflux MFS transporter Tet(G) tet(G) GO:0008493,GO:0015904 1224 Pseudomonadota phylum 62 NCBIFAM tetracycline efflux MFS transporter Tet(G) tetracycline efflux MFS transporter Tet(G) NF012193.0 tet_MFS_A 840 840 394 exception Y Y Y tetracycline efflux MFS transporter Tet(A) tet(A) GO:0008493,GO:0015904 1224 Pseudomonadota phylum 387 NCBIFAM tetracycline efflux MFS transporter Tet(A) tetracycline efflux MFS transporter Tet(A) NF012203.0 cmlB1_MFS 900 900 407 exception Y Y Y chloramphenicol efflux MFS transporter CmlB1 cmlB1 1224 Pseudomonadota phylum 1 NCBIFAM chloramphenicol efflux MFS transporter CmlB1 chloramphenicol efflux MFS transporter CmlB1 NF012221.1 MARTX_Nterm 700 700 1910 equivalog_domain Y Y N MARTX multifunctional-autoprocessing repeats-in-toxin holotoxin RtxA rtxA 17464284,18591243,19620709 1224 Pseudomonadota phylum 2361 NCBIFAM MARTX multifunctional-autoprocessing repeats-in-toxin holotoxin RtxA MARTX multifunctional-autoprocessing repeats-in-toxin holotoxin N-terminal region This model describes the N-terminal 1900 amino acids of MARTX family multifunctional-autoprocessing repeats-in-toxin holotoxins, which contain both repeat regions that facilitate their entry into eukaryotic target cells, and multiple effector domains. NF012565.5 PF00345.25 PapD_N 23 23 126 domain Y Y N fimbria/pilus periplasmic chaperone GO:0030288,GO:0071555 2478891 1224 Pseudomonadota phylum 87583 EBI-EMBL Pili and flagellar-assembly chaperone, PapD N-terminal domain Pili and flagellar-assembly chaperone, PapD N-terminal domain C2 domain-like beta-sandwich fold. This domain is the n-terminal part of the PapD chaperone protein for pilus and flagellar assembly. [1]. 2478891. Crystal structure of chaperone protein PapD reveals an immunoglobulin fold. Holmgren A, Branden CI;. Nature 1989;342:248-251. (from Pfam) NF012635.5 PF00419.25 Fimbrial 25.6 25.6 151 domain Y Y N fimbrial protein GO:0007155,GO:0009289 1224 Pseudomonadota phylum 141445 EBI-EMBL Fimbrial protein fimbrial protein NF012786.5 PF00577.25 Usher 27.1 27.1 549 domain Y Y N fimbria/pilus outer membrane usher protein GO:0009297,GO:0015473,GO:0016020 18485872,19380723,7906046,7906265,7909802 1224 Pseudomonadota phylum 150739 EBI-EMBL Outer membrane usher protein fimbria/pilus outer membrane usher protein In Gram-negative bacteria the biogenesis of fimbriae (or pili) requires a two- component assembly and transport system which is composed of a periplasmic chaperone and an outer membrane protein which has been termed a molecular 'usher' [1-3]. The usher protein is rather large (from 86 to 100 Kd) and seems to be mainly composed of membrane-spanning beta-sheets, a structure reminiscent of porins. Although the degree of sequence similarity of these proteins is not very high they share a number of characteristics. One of these is the presence of two pairs of cysteines, the first one located in the N-terminal part and the second at the C-terminal extremity that are probably involved in disulphide bonds. The best conserved region is located in the central part of these proteins [4-5]. [1]. 7909802. Chaperone-assisted self-assembly of pili independent of cellular energy. Jacob-Dubuisson F, Striker R, Hultgren SJ;. J Biol Chem. 1994;269:12447-12455. [2]. 7906265. Permissive linker insertion sites in the outer membrane protein of 987P fimbriae of Escherichia coli. Schifferli DM, Alrutz MA;. J Bacteriol. 1994;176:1099-1110. [3]. 7906046. Structural and evolutionary relationships between two families of bacterial extracytoplasmic chaperone proteins which function cooperatively in fimbrial assembly. Van Rosmalen M, Saier MH Jr;. Res Microbiol. 1993;144:507-527. [4]. 19380723. Insights into pilus assembly and secretion from the structure and functional characterization of usher PapC. Huang Y, Smith BS, Chen LX, Baxter RH, Deisenhofer J;. Proc Natl Acad Sci U S A. 2009;106:7403-7407. [5]. 18485872. Fiber formation across the bacterial. TRUNCATED at 1650 bytes (from Pfam) NF012827.5 PF00620.32 RhoGAP 24.5 24.5 148 domain Y Y N RhoGAP domain-containing protein GO:0007165 8259209,8962058,9009196,9262406 1224 Pseudomonadota phylum 254 EBI-EMBL RhoGAP domain RhoGAP domain GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases. [1]. 8962058. Crystal structure of the breakpoint cluster region-homology domain from phosphoinositide 3-kinase p85 alpha subunit. Musacchio A, Cantley LC, Harrison SC;. Proc Natl Acad Sci U S A 1996;93:14373-14378. [2]. 9009196. The structure of the GTPase-activating domain from p50rhoGAP. Barrett T, Xiao B, Dodson EJ, Dodson G, Ludbrook SB, Nurmahomed K, Gamblin SJ, Musacchio A, Smerdon SJ, Eccleston JF;. Nature 1997;385:458-461. [3]. 9262406. Crystal structure of a small G protein in complex with the GTPase-activating protein rhoGAP. Rittinger K, Walker PA, Eccleston JF, Nurmahomed K, Owen D, Laue E, Gamblin SJ, Smerdon SJ;. Nature 1997;388:693-697. [4]. 8259209. Proteins regulating Ras and its relatives. Boguski MS, McCormick F;. Nature 1993;366:643-654. (from Pfam) NF013014.5 PF00816.26 Histone_HNS 25.6 25.6 38 domain Y Y N H-NS family nucleoid-associated regulatory protein GO:0003677,GO:0006355,GO:0030527 7875316 1224 Pseudomonadota phylum 28058 EBI-EMBL H-NS histone C-terminal domain H-NS family nucleoid-associated regulatory protein This entry represents the C-terminal DNA binding domain of H-NS histone protein. [1]. 7875316. Solution structure of the DNA binding domain of a nucleoid-associated protein, H-NS, from Escherichia coli. Shindo H, Iwaki T, Ieda R, Kurumizaka H, Ueguchi C, Mizuno T, Morikawa S, Nakamura H, Kuboniwa H;,. FEBS Lett 1995;360:125-131. (from Pfam) NF013329.5 PF01150.22 GDA1_CD39 24.9 24.9 423 domain Y N N GDA1/CD39 (nucleoside phosphatase) family GO:0016787 1224 Pseudomonadota phylum 374 EBI-EMBL GDA1/CD39 (nucleoside phosphatase) family GDA1/CD39 (nucleoside phosphatase) family NF013529.5 PF01369.25 Sec7 22 22 183 domain Y Y N Sec7 domain-containing protein GO:0005085,GO:0032012 8945478,9510256,9868368 1224 Pseudomonadota phylum 94 EBI-EMBL Sec7 domain Sec7 domain The Sec7 domain is a guanine-nucleotide-exchange-factor (GEF) for the Pfam:PF00025 family [2]. [1]. 9510256. Structure of the Sec7 domain of the Arf exchange factor ARNO. Cherfils J, Menetrey J, Mathieu M, Le Bras G, Robineau S, Beraud-Dufour S, Antonny B, Chardin P;. Nature 1998;392:101-105. [2]. 8945478. A human exchange factor for ARF contains Sec7- and pleckstrin- homology domains. Chardin P, Paris S, Antonny B, Robineau S, Beraud-Dufour S, Jackson CL, Chabre M. Nature 1996;384:481-484. [3]. 9868368. Triple association of CDC25-, Dbl- and Sec7-related domains in mammalian guanine-nucleotide-exchange factors. Abergel C, Chavrier P, Claverie JM;. Trends Biochem Sci 1998;23:472-473. (from Pfam) NF013785.5 PF01646.21 Herpes_UL24 27 27 177 domain Y N N Herpes virus proteins UL24 and UL76 23966401,9501052 1224 Pseudomonadota phylum 5 EBI-EMBL Herpes virus proteins UL24 and UL76 Herpes virus proteins UL24 and UL76 This family consists of various herpes virus proteins; the gene 20 product, U49 protein, UL24 and UL76 proteins and BXRF1. The UL24 gene (product of the 24th ORF) is not essential for virus replication, and mutants with lesions in UL24 show a reduced ability to replicate in tissue culture and have reduced thymidine kinase activity, as the UL24 gene overlaps with thymidine kinase [1]. The family of proteins is involved in viral production, latency, and reactivation. Protein UL76 presents as globular aggresomes in the nuclei of transiently transfected cells. Bioinformatic analyses predict that UL76 has a propensity for aggregation and targets cellular proteins implicated in protein folding and ubiquitin-proteasome systems. UL76 interacts with the VWA domain of S5a, the 26S proteasome non-ATPase regulatory subunit 4 (or PSMD4, or Rpn10), forming a complex in the late phase of infection [2]. [1]. 9501052. Importance of the herpes simplex virus UL24 gene for productive ganglionic infection in mice. Jacobson JG, Chen SH, Cook WJ, Kramer MF, Coen DM;. Virology 1998;242:161-169. [2]. 23966401. Human cytomegalovirus UL76 elicits novel aggresome formation via interaction with S5a of the ubiquitin proteasome system. Lin SR, Jiang MJ, Wang HH, Hu CH, Hsu MS, Hsi E, Duh CY, Wang SK;. J Virol. 2013;87:11562-11578. (from Pfam) NF014440.5 PF02382.20 RTX 26.8 26.8 311 PfamEq Y N N N-terminal domain in RTX protein GO:0005509,GO:0005576,GO:0015267 30405113,9628576 1224 Pseudomonadota phylum 1091 EBI-EMBL N-terminal domain in RTX protein N-terminal domain in RTX protein The RTX family of bacterial toxins are a group of cytolysins and cytotoxins that have RTX (Repeat in ToXin repeats) Pfam:PF00353. This is a hydrophobic pore-forming domain found at the N-terminal of these proteins [2]. [1]. 9628576. Complete nucleotide sequences of 93-kb and 3.3-kb plasmids of an enterohemorrhagic Escherichia coli O157:H7 derived from Sakai outbreak. Makino K, Ishii K, Yasunaga T, Hattori M, Yokoyama K, Yutsudo CH, Kubota Y, Yamaichi Y, Iida T, Yamamoto K, Honda T, Han CG, Ohtsubo E, Kasamatsu M, Hayashi T, Kuhara S, Shinagawa H;. DNA Res 1998;5:1-9. [2]. 30405113. Cytotoxic activity of Kingella kingae RtxA toxin depends on post-translational acylation of lysine residues and cholesterol binding. Osickova A, Balashova N, Masin J, Sulc M, Roderova J, Wald T, Brown AC, Koufos E, Chang EH, Giannakakis A, Lally ET, Osicka R;. Emerg Microbes Infect. 2018;7:178. (from Pfam) NF014551.5 PF02501.22 T2SSI 25 25 80 domain Y Y N type II secretion system protein GO:0015627,GO:0015628 14600218,15223057,19299134,8407845 1224 Pseudomonadota phylum 14164 EBI-EMBL Type II secretion system (T2SS), protein I type II secretion system protein The Type II secretion system, also called Secretion-dependent pathway (SDP), is responsible for the transport of proteins across the outer membrane first exported to the periplasm by the Sec or Tat translocon in Gram-negative (diderm) bacteria. As members of the T2SJ family, members of the T2SI family are pseudopilins containing prepilin signal sequences [1]. [1]. 8407845. Isolation and analysis of eight exe genes and their involvement in extracellular protein secretion and outer membrane assembly in Aeromonas hydrophila. Howard SP, Critch J, Bedi A;. J Bacteriol 1993;175:6695-6703. [2]. 15223057. The general secretory pathway: a general misnomer?. Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR;. Trends Microbiol. 2004;12:306-309. [3]. 14600218. Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella. Peabody CR, Chung YJ, Yen MR, Vidal-Ingigliardi D, Pugsley AP, Saier MH Jr;. Microbiology. 2003;149:3051-3072. [4]. 19299134. Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Desvaux M, Hebraud M, Talon R, Henderson IR;. Trends Microbiol. 2009;17:139-145. (from Pfam) NF014773.5 PF02753.22 PapD_C 22.8 22.8 63 domain Y N N Pili assembly chaperone PapD, C-terminal domain 2478891 1224 Pseudomonadota phylum 62987 EBI-EMBL Pili assembly chaperone PapD, C-terminal domain Pili assembly chaperone PapD, C-terminal domain Ig-like beta-sandwich fold. This domain is the C-terminal part of the pilus and flagellar-assembly chaperone protein PapD. [1]. 2478891. Crystal structure of chaperone protein PapD reveals an immunoglobulin fold. Holmgren A, Branden CI;. Nature 1989;342:248-251. (from Pfam) NF014915.5 PF02918.20 Pertussis_S2S3 27 27 109 domain Y N N Pertussis toxin, subunit 2 and 3, C-terminal domain GO:0005576 8637000 1224 Pseudomonadota phylum 146 EBI-EMBL Pertussis toxin, subunit 2 and 3, C-terminal domain Pertussis toxin, subunit 2 and 3, C-terminal domain NF014949.5 PF02953.20 zf-Tim10_DDP 22.3 22.3 64 domain Y Y N Tim10/DDP family zinc finger protein 11101512,8663351 1224 Pseudomonadota phylum 2 EBI-EMBL Tim10/DDP family zinc finger Tim10/DDP family zinc finger protein Putative zinc binding domain with four conserved cysteine residues. This domain is found in the human disease protein Swiss:O60220. Members of this family such as Tim9 and Tim10 are involved in mitochondrial protein import [1]. Members of this family seem to be localised to the mitochondrial intermembrane space [2]. [1]. 11101512. The role of the TIM8-13 complex in the import of Tim23 into mitochondria. Paschen SA, Rothbauer U, Kaldi K, Bauer MF, Neupert W, Brunner;. EMBO J 2000;19:6392-6400. [2]. 8663351. Mrs5p, an essential protein of the mitochondrial intermembrane space, affects protein import into yeast mitochondria. Jarosch E, Tuller G, Daum G, Waldherr M, Voskova A, Schweyen RJ;. J Biol Chem 1996;271:17219-17225. (from Pfam) NF014968.5 PF02974.19 Inh 25 25 97 domain Y Y N AprI/Inh family metalloprotease inhibitor 7752231 1224 Pseudomonadota phylum 6338 EBI-EMBL Protease inhibitor Inh AprI/Inh family metalloprotease inhibitor The Inh inhibitor is secreted into the periplasm where its presumed physiological function is to protect periplasmic proteins against the action of secreted proteases [1]. A range of proteases including A, B and C from E. chrysanthemi, alkaline protease from Pseudomonas aeruginosa and the 50 kDa protease from Serratia marcescens are inhibited. [1]. 7752231. Crystal structure of a complex between Serratia marcescens metallo-protease and an inhibitor from Erwinia chrysanthemi. Baumann U, Bauer M, Letoffe S, Delepelaire P, Wandersman C;. J Mol Biol 1995;248:653-661. (from Pfam) NF015342.5 PF03377.18 TAL_effector 28 13.1 34 repeat Y N N TAL effector repeat-containing protein 11106024,22223736 1224 Pseudomonadota phylum 4438 EBI-EMBL TAL effector repeat TAL effector repeat The proteins in this family bind to DNA. Each repeat binds to a base pair in a predictable way [2]. The structure shows that each repeat is composed of two alpha helices [2]. [1]. 11106024. Xanthomonas oryzae pv. oryzae avirulence genes contribute differently and specifically to pathogen aggressiveness. Bai J, Choi SH, Ponciano G, Leung H, Leach JE;. Mol Plant Microbe Interact 2000;13:1322-1329. [2]. 22223736. The crystal structure of TAL effector PthXo1 bound to its DNA target. Mak AN, Bradley P, Cernadas RA, Bogdanove AJ, Stoddard BL;. Science. 2012;335:716-719. (from Pfam) NF015386.5 PF03421.21 Acetyltransf_14 22.6 22.6 173 domain Y Y N YopJ family acetyltransferase 12433923,16728640,17116858,20430892,22802624 1224 Pseudomonadota phylum 1394 EBI-EMBL YopJ Serine/Threonine acetyltransferase YopJ family acetyltransferase The Yersinia effector YopJ inhibits the innate immune response by blocking MAP kinase and NFkappaB signaling pathways. YopJ is a serine/threonine acetyltransferase which regulates signalling pathways by blocking phosphorylation [1][2]. Specifically, YopJ has been shown to block phosphorylation of active site residues [3]. It has also been shown that YopJ acetyltransferase is activated by eukaryotic host cell inositol hexakisphosphate [4]. This family was previously incorrectly annotated in Pfam as being a peptidase family. [1]. 16728640. Yersinia YopJ acetylates and inhibits kinase activation by blocking phosphorylation. Mukherjee S, Keitany G, Li Y, Wang Y, Ball HL, Goldsmith EJ, Orth K;. Science. 2006;312:1211-1214. [2]. 12433923. Yersinia effector YopJ inhibits yeast MAPK signaling pathways by an evolutionarily conserved mechanism. Yoon S, Liu Z, Eyobo Y, Orth K;. J Biol Chem. 2003;278:2131-2135. [3]. 17116858. Acetylation of MEK2 and I kappa B kinase (IKK) activation loop residues by YopJ inhibits signaling. Mittal R, Peak-Chew SY, McMahon HT;. Proc Natl Acad Sci U S A. 2006;103:18574-18579. [4]. 20430892. The acetyltransferase activity of the bacterial toxin YopJ of Yersinia is activated by eukaryotic host cell inositol hexakisphosphate. Mittal R, Peak-Chew SY, Sade RS, Vallis Y, McMahon HT;. J Biol Chem. 2010; [Epub ahead of print]. [5]. 22802624. Serine/threonine acetylation of TGFbeta-activated kinase (TAK1) by Yersinia pestis YopJ inhibits innate immune signaling. Paquette N, Conlon J, Sweet C, Rus F, Wilson L, Pereira A, Rosadini CV, Goutagny N, Weber AN, Lane WS, Shaffer SA, Maniatis S, Fitzgerald KA, Stuart . TRUNCATED at 1650 bytes (from Pfam) NF015398.5 PF03433.18 EspA 23.4 23.4 180 PfamEq Y N N EspA-like secreted protein 10047555,10760148,9545230 1224 Pseudomonadota phylum 1004 EBI-EMBL EspA-like secreted protein EspA-like secreted protein EspA is the prototypical member of this family. EspA, together with EspB, EspD and Tir are exported by a type III secretion system. These proteins are essential for attaching and effacing lesion formation. EspA is a structural protein and a major component of a large, transiently expressed, filamentous surface organelle which forms a direct link between the bacterium and the host cell [1,2]. [1]. 9545230. A novel EspA-associated surface organelle of enteropathogenic Escherichia coli involved in protein translocation into epithelial cells. Knutton S, Rosenshine I, Pallen MJ, Nisan I, Neves BC, Bain C, Wolff C, Dougan G, Frankel G;. EMBO J 1998;17:2166-2176. [2]. 10760148. The type III protein translocation system of enteropathogenic Escherichia coli involves EspA-EspB protein interactions. Hartland EL, Daniell SJ, Delahay RM, Neves BC, Wallis T, Shaw RK, Hale C, Knutton S, Frankel G;. Mol Microbiol 2000;35:1483-1492. [3]. 10047555. Enteropathogenic Escherichia coli: cellular harassment. DeVinney R, Knoechel DG, Finlay BB;. Curr Opin Microbiol 1999;2:83-88. (from Pfam) NF015405.5 PF03440.19 APT 25 25 87 domain Y N N Aerolysin/Pertussis toxin (APT) domain 1224 Pseudomonadota phylum 1286 EBI-EMBL Aerolysin/Pertussis toxin (APT) domain Aerolysin/Pertussis toxin (APT) domain This family represents the N-terminal domain of aerolysin and pertussis toxin and has a type-C lectin like fold. (from Pfam) NF015464.5 PF03500.18 Cellsynth_D 23 23 110 PfamEq Y Y N cellulose biosynthesis protein BcsD bcsD GO:0030244 1224 Pseudomonadota phylum 2345 EBI-EMBL Cellulose synthase subunit D cellulose biosynthesis protein BcsD NF015482.5 PF03519.19 Invas_SpaK 25 25 78 PfamEq Y N N Invasion protein B family 1224 Pseudomonadota phylum 932 EBI-EMBL Invasion protein B family Invasion protein B family NF015499.5 PF03536.20 VRP3 25 25 240 PfamEq Y N N Salmonella virulence-associated 28kDa protein 1224 Pseudomonadota phylum 459 EBI-EMBL Salmonella virulence-associated 28kDa protein Salmonella virulence-associated 28kDa protein NF015611.5 PF03658.19 Ub-RnfH 23.7 23.7 83 PfamEq Y Y N RnfH family protein 16859499 1224 Pseudomonadota phylum 15913 EBI-EMBL RnfH family Ubiquitin RnfH family protein A member of the RnfH family of the ubiquitin superfamily. Members of this family strongly co-occur in two distinct gene neighborhood contexts. In one it is associated with a START domain protein, a membrane protein SmpA and the transfer mRNA binding protein SmpB. This association suggests a possible role in the SmpB-tmRNA-based tagging and degadation system of bacteria, which is interesting given that other members of the ubiquitin system are analogously involved in protein-tagging and degradation across eukaryotes and various prokaryotes. The second context in which the RnfH genes are present is in a membrane associated complex involved in transporting electrons for various reductive reactions such as nitrogen fixation [1]. [1]. 16859499. The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. Iyer LM, Burroughs AM, Aravind L;. Genome Biol. 2006;7:R60. (from Pfam) NF015782.5 PF03843.18 Slp 22.5 22.5 153 domain Y Y N Slp family lipoprotein GO:0019867 1224 Pseudomonadota phylum 8438 EBI-EMBL Outer membrane lipoprotein Slp family Slp family lipoprotein NF015827.5 PF03891.20 DUF333 25 25 47 domain Y Y N DUF333 domain-containing protein 1224 Pseudomonadota phylum 8093 EBI-EMBL Domain of unknown function (DUF333) Domain of unknown function (DUF333) This small domain of about 70 residues is found in a number of bacterial proteins. It is found at the N-terminus the of Swiss:O28332 protein. The proteins containing this domain are uncharacterised. (from Pfam) NF016161.5 PF04247.17 SirB 30.9 30.9 120 PfamEq Y Y N SirB2 family protein 10322010 1224 Pseudomonadota phylum 8858 EBI-EMBL Invasion gene expression up-regulator, SirB SirB2 family protein SirB up-regulates Salmonella typhimurium invasion gene transcription. It is, however, not essential for the expression of these genes. Its function is unknown [1]. [1]. 10322010. A HilA-independent pathway to Salmonella typhimurium invasion gene transcription. Rakeman JL, Bonifield HR, Miller SI;. J Bacteriol 1999;181:3096-3104. (from Pfam) NF016255.5 PF04352.18 ProQ 27 27 109 domain Y Y N ProQ/FINO family protein 10049386,10876242,21381725 1224 Pseudomonadota phylum 18097 EBI-EMBL ProQ/FINO family ProQ/FINO family protein This family includes ProQ, which is required for full activation of the osmoprotectant transporter, ProP, in Escherichia coli. This family includes several bacterial fertility inhibition (FINO) proteins. The conjugative transfer of F-like plasmids is repressed by FinO, an RNA binding protein. FinO interacts with the F-plasmid encoded traJ mRNA and its antisense RNA, FinP, stabilising FinP against endonucleolytic degradation and facilitating sense-antisense RNA recognition [2]. ProQ operates as an RNA-chaperone, binding RNA and bringing about both RNA strand-exchange and RNA duplexing. This suggests that in fact it does not regulate ProP transcription but rather regulates ProP translation through activity as an RNA-binding protein [3]. [1]. 10049386. Protein ProQ influences osmotic activation of compatible solute transporter ProP in Escherichia coli K-12. Kunte HJ, Crane RA, Culham DE, Richmond D, Wood JM;. J Bacteriol 1999;181:1537-1543. [2]. 10876242. Crystal structure of the bacterial conjugation repressor finO. Ghetu AF, Gubbins MJ, Frost LS, Glover JN;. Nat Struct Biol 2000;7:565-569. [3]. 21381725. ProQ is an RNA chaperone that controls ProP levels in Escherichia coli. Chaulk SG, Smith Frieday MN, Arthur DC, Culham DE, Edwards RA, Soo P, Frost LS, Keates RA, Glover JN, Wood JM;. Biochemistry. 2011;50:3095-3106. (from Pfam) NF016259.5 PF04356.17 DUF489 26 26 192 PfamAutoEq Y Y N DUF489 family protein 8969519 1224 Pseudomonadota phylum 9555 EBI-EMBL Protein of unknown function (DUF489) DUF489 family protein Protein of unknown function, cotranscribed with purB in Escherichia coli, but with function unrelated to purine biosynthesis [1]. [1]. 8969519. The purB gene of Escherichia coli K-12 is located in an operon. Green SM, Malik T, Giles IG, Drabble WT;. Microbiology 1996;142:3219-3230. (from Pfam) NF016264.5 PF04361.18 DUF494 22.6 22.6 153 subfamily Y Y N DUF494 family protein 1224 Pseudomonadota phylum 5321 EBI-EMBL Protein of unknown function (DUF494) DUF494 family protein Members of this family of uncharacterised proteins are often named Smg. (from Pfam) NF016275.5 PF04375.19 HemX 25.9 25.9 236 PfamEq Y Y N uroporphyrinogen-III C-methyltransferase 2.1.1.107 16079137,3062586 1224 Pseudomonadota phylum 22132 EBI-EMBL HemX, putative uroporphyrinogen-III C-methyltransferase uroporphyrinogen-III C-methyltransferase This is a family of bacterial putative uroporphyrinogen-III C-methyltransferase proteins. It forms one of the members of a complex of proteins involved in the biogenesis of the inner membrane in E.coli. Uroporphorphyrin-III C-methyltransferase (HemX) is a single spanning inner membrane protein that regulates the activity of NAD(P)H:glutamyl-tRNA reductase (HemA) in the tetrapyrrole biosynthesis pathway [1,2]. [1]. 3062586. Nucleotide sequence of the hemX gene, the third member of the Uro operon of Escherichia coli K12. Sasarman A, Echelard Y, Letowski J, Tardif D, Drolet M;. Nucleic Acids Res. 1988;16:11835. [2]. 16079137. Protein complexes of the Escherichia coli cell envelope. Stenberg F, Chovanec P, Maslen SL, Robinson CV, Ilag LL, von Heijne G, Daley DO;. J Biol Chem. 2005;280:34409-34419. (from Pfam) NF016298.5 PF04399.18 Glutaredoxin2_C 32.8 32.8 130 PfamEq Y N N Glutaredoxin 2, C terminal domain 11453697,11741965 1224 Pseudomonadota phylum 5687 EBI-EMBL Glutaredoxin 2, C terminal domain Glutaredoxin 2, C terminal domain Glutaredoxins are a multifunctional family of glutathione-dependent disulphide oxidoreductases. Unlike other glutaredoxins, glutaredoxin 2 (Grx2) cannot reduce ribonucleotide reductase. Grx2 has significantly higher catalytic activity in the reduction of mixed disulphides with glutathione (GSH) compared with other glutaredoxins. The active site residues (Cys9-Pro10-Tyr11-Cys12, in Escherichia coli Grx2, Swiss:P39811), which are found at the interface between the N- and C-terminal domains are identical to other glutaredoxins, but there is no other similarity between glutaredoxin 2 and other glutaredoxins. Grx2 is structurally similar to glutathione-S-transferases (GST), but there is no obvious sequence similarity. The inter-domain contacts are mainly hydrophobic, suggesting that the two domains are unlikely to be stable on their own. Both domains are needed for correct folding and activity of Grx2. It is thought that the primary function of Grx2 is to catalyse reversible glutathionylation of proteins with GSH in cellular redox regulation including the response to oxidative stress. [1]. 11453697. Solution structure of Escherichia coli glutaredoxin-2 shows similarity to mammalian glutathione-S-transferases. Xia B, Vlamis-Gardikas A, Holmgren A, Wright PE, Dyson HJ;. J Mol Biol 2001;310:907-918. [2]. 11741965. Characterization of Escherichia coli null mutants for glutaredoxin 2. Vlamis-Gardikas A, Potamitou A, Zarivach R, Hochman A, Holmgren A;. J Biol Chem 2002;277:10861-10868. (from Pfam) NF016344.5 PF04449.17 Fimbrial_CS1 21 21 133 subfamily Y Y N CS1 type fimbrial major subunit GO:0009289 10094617,10417651 1224 Pseudomonadota phylum 4679 EBI-EMBL CS1 type fimbrial major subunit CS1 type fimbrial major subunit Fimbriae, also known as pili, form filaments radiating from the surface of the bacterium to a length of 0.5-1.5 micrometres. They enable the cell to colonise host epithelia. This family constitutes the major subunits of CS1 like pili, including CS2 and CFA1 from Escherichia coli, and also the Cable type II pilin major subunit from Burkholderia cepacia [1]. The major subunit of CS1 pili is called CooA. Periplasmic CooA is mostly complexed with the assembly protein CooB. In addition, a small pool of CooA multimers, and CooA-CooD complexes exists, but the functional significance is unknown [1]. A member of this family has also been identified in Salmonella typhi and Salmonella enterica [2]. [1]. 10094617. New tools in an old trade: CS1 pilus morphogenesis. Sakellaris H, Scott JR;. Mol Microbiol 1998;30:681-687. [2]. 10417651. Multiple insertions of fimbrial operons correlate with the evolution of Salmonella serovars responsible for human disease. Folkesson A, Advani A, Sukupolvi S, Pfeifer JD, Normark S, Lofdahl S;. Mol Microbiol 1999;33:612-622. (from Pfam) NF016437.5 PF04550.17 Phage_holin_3_2 25 25 86 domain Y N N Phage holin family 2 GO:0044660 11459934 1224 Pseudomonadota phylum 1776 EBI-EMBL Phage holin family 2 Phage holin family 2 Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis. It is thought that the temporal precision of holin-mediated lysis may occur through the buildup of a holin oligomer which causes the lysis [1]. [1]. 11459934. Holins kill without warning. Grundling A, Manson MD, Young R;. Proc Natl Acad Sci U S A 2001;98:9348-9352. (from Pfam) NF016475.5 PF04591.17 DUF596 25 25 69 domain Y Y N DUF596 domain-containing protein 1224 Pseudomonadota phylum 1426 EBI-EMBL Protein of unknown function, DUF596 Protein of unknown function, DUF596 This family contains several uncharacterised proteins. (from Pfam) NF016997.5 PF05142.17 DUF702 20.6 20.6 151 domain Y Y N DUF702 domain-containing protein 1224 Pseudomonadota phylum 2 EBI-EMBL Domain of unknown function (DUF702) Domain of unknown function (DUF702) Members of this family are found in various putative zinc finger proteins. (from Pfam) NF017109.5 PF05265.18 DUF723 20.9 20.9 60 domain Y Y N DUF723 domain-containing protein 1224 Pseudomonadota phylum 246 EBI-EMBL Protein of unknown function (DUF723) Protein of unknown function (DUF723) This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA-binding. (from Pfam) NF017124.5 PF05280.16 FlhC 27 27 173 domain Y Y N FlhC family transcriptional regulator GO:0003677,GO:0045893,GO:1902208 11287152 1224 Pseudomonadota phylum 6635 EBI-EMBL Flagellar transcriptional activator (FlhC) FlhC family transcriptional regulator This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in E. coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [1]. [1]. 11287152. FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions. Pruss BM, Liu X, Hendrickson W, Matsumura P;. FEMS Microbiol Lett 2001;197:91-97. (from Pfam) NF017169.5 PF05328.17 CybS 27 27 133 PfamEq Y N N CybS, succinate dehydrogenase cytochrome B small subunit 10657297 1224 Pseudomonadota phylum 382 EBI-EMBL CybS, succinate dehydrogenase cytochrome B small subunit CybS, succinate dehydrogenase cytochrome B small subunit This family consists of several eukaryotic succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial precursor (CybS) proteins. SDHD encodes the small subunit (cybS) of cytochrome b in succinate-ubiquinone oxidoreductase (mitochondrial complex II). Mitochondrial complex II is involved in the Krebs cycle and in the aerobic electron transport chain. It contains four proteins. The catalytic core consists of a flavoprotein and an iron-sulfur protein; these proteins are anchored to the mitochondrial inner membrane by the large subunit of cytochrome b (cybL) and cybS, which together comprise the heme-protein cytochrome b. Mutations in the SDHD gene can lead to hereditary paraganglioma, characterised by the development of benign, vascularised tumours in the head and neck [1]. [1]. 10657297. Mutations in SDHD, a mitochondrial complex II gene, in hereditary paraganglioma. Baysal BE, Ferrell RE, Willett-Brozick JE, Lawrence EC, Myssiorek D, Bosch A, van der Mey A, Taschner PE, Rubinstein WS, Myers EN, Richard CW 3rd, Cornelisse CJ, Devilee P, Devlin B;. Science 2000;287:848-851. (from Pfam) NF017182.5 PF05344.16 DUF746 26.9 26.9 64 domain Y Y N DUF746 domain-containing protein 21348639 1224 Pseudomonadota phylum 691 EBI-EMBL Domain of Unknown Function (DUF746) Domain of Unknown Function (DUF746) This is a short conserved region found in some transposons. Structural modelling suggests this domain may bind nucleic acids [1]. [1]. 21348639. Ab Initio Modeling Led Annotation Suggests Nucleic Acid Binding Function for Many DUFs. Rigden DJ;. OMICS 2011;0:0-0. (from Pfam) NF017235.5 PF05398.16 PufQ 22.1 22.1 74 PfamEq Y Y N cytochrome PufQ pufQ GO:0015979,GO:0030494 10196154 1224 Pseudomonadota phylum 402 EBI-EMBL PufQ cytochrome subunit cytochrome PufQ This family consists of bacterial PufQ proteins. PufQ id required for bacteriochlorophyll biosynthesis serving a regulatory function in the formation of photosynthetic complexes [1]. [1]. 10196154. A new cytochrome subunit bound to the photosynthetic reaction center in the purple bacterium, Rhodovulum sulfidophilum. Masuda S, Yoshida M, Nagashima KV, Shimada K, Matsuura K;. J Biol Chem 1999;274:10795-10801. (from Pfam) NF017257.5 PF05420.16 BCSC_C 23.5 23.5 336 domain Y Y N cellulose synthase subunit BcsC-related outer membrane protein GO:0019867,GO:0030244 11260463 1224 Pseudomonadota phylum 24078 EBI-EMBL Cellulose synthase operon protein C C-terminus (BCSC_C) cellulose synthase subunit BcsC C-terminal domain This family contains the C-terminal regions of several bacterial cellulose synthase operon C (BCSC) proteins. BCSC is involved in cellulose synthesis although the exact function of this protein is unknown [1]. [1]. 11260463. The multicellular morphotypes of Salmonella typhimurium and Escherichia coli produce cellulose as the second component of the extracellular matrix. Zogaj X, Nimtz M, Rohde M, Bokranz W, Romling U;. Mol Microbiol 2001;39:1452-1463. (from Pfam) NF017281.5 PF05449.16 Phage_holin_3_7 25.4 25.4 80 domain Y Y N phage holin family protein 1224 Pseudomonadota phylum 6187 EBI-EMBL Putative 3TM holin, Phage_holin_3 phage holin family protein This is a family of putative proteobacterial phage three-transmembrane-domain holins. (from Pfam) NF017407.5 PF05589.16 DUF768 24.6 24.6 67 domain Y Y N DUF768 domain-containing protein 1224 Pseudomonadota phylum 78 EBI-EMBL Protein of unknown function (DUF768) Protein of unknown function (DUF768) This family consists of several uncharacterised hypothetical proteins from Rhizobium loti. (from Pfam) NF017465.5 PF05650.16 DUF802 22.6 22.6 53 PfamAutoEq Y Y N DUF802 domain-containing protein 1224 Pseudomonadota phylum 5882 EBI-EMBL Domain of unknown function (DUF802) Domain of unknown function (DUF802) This region is found as two or more repeats in a small number of hypothetical proteins. (from Pfam) NF017479.5 PF05666.16 Fels1 25 25 43 subfamily Y Y N YcgJ family protein 1224 Pseudomonadota phylum 1862 EBI-EMBL Fels-1 Prophage Protein-like YcgJ family protein Members of this family include AAL19841.1 from the Fels-1 prophage region of Salmonella typhimurium strain LT2 and YcgJ from Escherichia coli K-12. NF017589.5 PF05785.17 CNF1 25 25 286 domain Y Y N cytotoxic necrotizing factor Rho-activating domain-containing protein 11427886,12065482,12622819 1224 Pseudomonadota phylum 713 EBI-EMBL Rho-activating domain of cytotoxic necrotizing factor Rho-activating domain of cytotoxic necrotizing factor This family consists of several bacterial cytotoxic necrotizing factor proteins as well as related dermonecrotic toxin (DNT) from Bordetella species. Cytotoxic necrotizing factor 1 (CNF1) causes necrosis of rabbit skin and re-organisation of the actin cytoskeleton in cultured cells [1]. Bordetella dermonecrotic toxin (DNT) stimulates the assembly of actin stress fibres and focal adhesions by deamidating or polyaminating Gln63 of the small GTPase Rho. DNT is an A-B toxin which is composed of an N-terminal receptor-binding (B) domain and a C-terminal enzymatically active (A) domain [2]. [1]. 12622819. Expression of cnf1 by Escherichia coli J96 involves a large upstream DNA region including the hlyCABD operon, and is regulated by the RfaH protein. Landraud L, Gibert M, Popoff MR, Boquet P, Gauthier M;. Mol Microbiol 2003;47:1653-1667. [2]. 12065482. Identification of a receptor-binding domain of Bordetella dermonecrotic toxin. Matsuzawa T, Kashimoto T, Katahira J, Horiguchi Y;. Infect Immun 2002;70:3427-3432. [3]. 11427886. Structure of the Rho-activating domain of Escherichia coli cytotoxic necrotizing factor 1. Buetow L, Flatau G, Chiu K, Boquet P, Ghosh P;. Nat Struct Biol 2001;8:584-588. (from Pfam) NF017620.5 PF05819.16 NolX 26.1 26.1 436 subfamily Y Y N HrpF/NolX family T3SS translocon protein GO:0009877 11115117,11790754 1224 Pseudomonadota phylum 1080 EBI-EMBL NolX protein HrpF/NolX family T3SS translocon protein This family consists of Rhizobium NolX and Xanthomonas HrpF proteins. The interaction between the plant pathogen Xanthomonas campestris pv. vesicatoria and its host plants is controlled by hrp genes (hypersensitive reaction and pathogenicity), which encode a type III protein secretion system. Among type III-secreted proteins are avirulence proteins, effectors involved in the induction of plant defence reactions. HrpF is dispensable for protein secretion but required for AvrBs3 recognition in planta, is thought to function as a translocator of effector proteins into the host cell [1]. NolX, a soybean cultivar specificity protein, is secreted by a type III secretion system (TTSS) and shows homology to HrpF of the plant pathogen Xanthomonas campestris pv. vesicatoria. It is not known whether NolX functions at the bacterium-plant interface or acts inside the host cell. NolX is expressed in planta only during the early stages of nodule development [2]. [1]. 11115117. HrpB2 and HrpF from Xanthomonas are type III-secreted proteins and essential for pathogenicity and recognition by the host plant. Rossier O, Van den Ackerveken G, Bonas U;. Mol Microbiol 2000;38:828-838. [2]. 11790754. NolX of Sinorhizobium fredii USDA257, a type III-secreted protein involved in host range determination, Iis localized in the infection threads of cowpea (Vigna unguiculata [L.] Walp) and soybean (Glycine max [L.] Merr.) nodules. Krishnan HB;. J Bacteriol 2002;184:831-839. (from Pfam) NF017742.5 PF05957.18 DUF883 25.4 25.4 53 subfamily Y Y N DUF883 family protein 1224 Pseudomonadota phylum 9713 EBI-EMBL DUF883 N-terminal domain DUF883 family protein This family consists of several hypothetical bacterial proteins of unknown function. The N-terminal domain found in this entry is related to Pfam:PF05532. (from Pfam) NF017837.5 PF06059.17 DUF930 25 25 99 domain Y Y N DUF930 domain-containing protein 1224 Pseudomonadota phylum 4249 EBI-EMBL Domain of Unknown Function (DUF930) Domain of Unknown Function (DUF930) Family of bacterial proteins with undetermined function. All bacteria in this family are from the Rhizobiales order. (from Pfam) NF017866.5 PF06092.17 DUF943 25 25 151 subfamily Y Y N DUF943 family protein 1224 Pseudomonadota phylum 4286 EBI-EMBL Enterobacterial putative membrane protein (DUF943) DUF943 family protein This family consists of several hypothetical putative membrane proteins from Escherichia coli, Yersinia pestis and Salmonella typhi. (from Pfam) NF017982.5 PF06222.16 Phage_TAC_1 25 25 124 domain Y Y N phage tail assembly chaperone 23542344 1224 Pseudomonadota phylum 3168 EBI-EMBL Phage tail assembly chaperone phage tail assembly chaperone NF017990.5 PF06231.16 DUF1010 25 25 66 PfamAutoEq Y Y N DUF1010 domain-containing protein 1224 Pseudomonadota phylum 705 EBI-EMBL Protein of unknown function (DUF1010) Protein of unknown function (DUF1010) Family of plasmid encoded proteins with unknown function. (from Pfam) NF018110.5 PF06366.18 FlhE 25 25 106 PfamEq Y Y N flagellar protein FlhE 9387224 1224 Pseudomonadota phylum 3896 EBI-EMBL Flagellar protein FlhE flagellar protein FlhE This family consists of several Enterobacterial FlhE flagellar proteins. The exact function of this family is unknown [1]. [1]. 9387224. Flagellar flhA, flhB and flhE genes, organized in an operon, cluster upstream from the inv locus in Yersinia enterocolitica. Fauconnier A, Allaoui A, Campos A, Van Elsen A, Cornelis GR, Bollen A;. Microbiology 1997;143:3461-3471. (from Pfam) NF018151.5 PF06411.16 HdeA 22 22 91 subfamily Y Y N HdeA/HdeB family chaperone 10623550,17085547,9731767 1224 Pseudomonadota phylum 3731 EBI-EMBL HdeA/HdeB family HdeA/HdeB family chaperone HdeA (hns-dependent expression protein A) is a single domain alpha-helical protein localised in the periplasmic space. HdeA is involved in acid resistance essential for infectivity of enteric bacterial pathogens. Functional studies demonstrate that HdeA is activated by a dimer-to-monomer transition at acidic pH, leading to suppression of aggregation by acid-denatured proteins. The gene encoding HdeA was initially identified as part of an operon regulated by the nucleoid protein H-NS [1,2]. This family also contains HdeB [3]. [1]. 10623550. HDEA, a periplasmic protein that supports acid resistance in pathogenic enteric bacteria. Gajiwala KS, Burley SK;. J Mol Biol 2000;295:605-612. [2]. 9731767. Crystal structure of Escherichia coli HdeA. Yang F, Gustafson KR, Boyd MR, Wlodawer A;. Nat Struct Biol 1998;5:763-764. [3]. 17085547. Escherichia coli HdeB is an acid stress chaperone. Kern R, Malki A, Abdallah J, Tagourti J, Richarme G;. J Bacteriol. 2007;189:603-610. (from Pfam) NF018177.5 PF06438.17 HasA 26.3 26.3 206 domain Y Y N heme acquisition protein HasA 10360351 1224 Pseudomonadota phylum 1361 EBI-EMBL Heme-binding protein A (HasA) heme acquisition protein HasA Free iron is limited in vertebrate hosts, thus an alternative to siderophores has been developed by pathogenic bacteria to access host iron bound in protein complexes. HasA is a secreted hemophore that has the ability to obtain iron from hemoglobin. Once bound to HasA, the heme is shuttled to the receptor HasR, which releases the heme into the bacterium [1]. [1]. 10360351. The crystal structure of HasA, a hemophore secreted by Serratia marcescens. Arnoux P, Haser R, Izadi N, Lecroisey A, Delepierre M, Wandersman C, Czjzek M;. Nat Struct Biol 1999;6:516-520. (from Pfam) NF018181.5 PF06442.16 DHFR_2 25 25 78 PfamEq Y N N R67 dihydrofolate reductase GO:0004146,GO:0009410 7583655 1224 Pseudomonadota phylum 90 EBI-EMBL R67 dihydrofolate reductase R67 dihydrofolate reductase R67 dihydrofolate reductase is a plasmid encoded enzyme that provides resistance to the antibacterial drug trimethoprim. The R67 dihydrofolate reductase does not share significant similarity to the chromosomal encoded dihydrofolate reductase [1]. [1]. 7583655. A plasmid-encoded dihydrofolate reductase from trimethoprim-resistant bacteria has a novel D2-symmetric active site. Narayana N, Matthews DA, Howell EE, Nguyen-huu X;. Nat Struct Biol 1995;2:1018-1025. (from Pfam) NF018244.5 PF06511.16 T3SS_TC 25 25 355 subfamily Y Y N IpaD/SipD/SspD family type III secretion system needle tip protein 10971588,22423359,25353930 1224 Pseudomonadota phylum 2066 EBI-EMBL Type III secretion systems tip complex components IpaD/SipD/SspD family type III secretion system needle tip protein This family consists of several invasion plasmid antigen IpaD proteins found in Shigella [1] as well as homologues such as SipD from Salmonella and BipD from Burkholderia [2]. Gram-negative bacteria use type III secretion systems (T3SSs) as protein transport devices for injecting virulence effector proteins into eukaryotic cells during infection. T3SSs consist of a needle complex (NC) and a tip complex (TC). In Shigella the TC is composed of two proteins, each essential to host cell sensing: IpaD and IpaB. IpaD is hydrophilic and required for tip recruitment of the hydrophobic proteins IpaB and IpaC, which later form the pore in host cell membranes [3]. [1]. 10971588. Characterization of the interaction of IpaB and IpaD, proteins required for entry of Shigella flexneri into epithelial cells, with a lipid membrane. De Geyter C, Wattiez R, Sansonetti P, Falmagne P, Ruysschaert JM, Parsot C, Cabiaux V;. Eur J Biochem 2000;267:5769-5776. [2]. 22423359. Identification of the bile salt binding site on IpaD from Shigella flexneri and the influence of ligand binding on IpaD structure. Barta ML, Guragain M, Adam P, Dickenson NE, Patil M, Geisbrecht BV, Picking WL, Picking WD;. Proteins. 2012;80:935-945. [3]. 25353930. Three-dimensional electron microscopy reconstruction and cysteine-mediated crosslinking provide a model of the type III secretion system needle tip complex. Cheung M, Shen DK, Makino F, Kato T, Roehrich AD, Martinez-Argudo I, Walker ML, Murillo I, Liu X, Pain M, Brown J, Frazer G, Mantell J, Mina P, Todd T, Sessions RB, Namba K, Blocker AJ;. Mol Microbiol. 2015;95:31-50. (from Pfam) NF018260.5 PF06528.17 Phage_P2_GpE 23 23 37 domain Y Y N GpE family phage tail protein 12426340 1224 Pseudomonadota phylum 4782 EBI-EMBL Phage P2 GpE GpE family phage tail protein This family consists of several phage and bacterial proteins which are closely related to the GpE tail protein from Phage P2. [1]. 12426340. Programmed translational frameshift in the bacteriophage P2 FETUD tail gene operon. Christie GE, Temple LM, Bartlett BA, Goodwin TS;. J Bacteriol 2002;184:6522-6531. (from Pfam) NF018280.5 PF06551.17 DUF1120 21 21 116 domain Y Y N DUF1120 domain-containing protein 1224 Pseudomonadota phylum 10086 EBI-EMBL Protein of unknown function (DUF1120) Protein of unknown function (DUF1120) This family consists of several hypothetical bacterial proteins of unknown function. (from Pfam) NF018310.5 PF06585.16 JHBP 29.2 29.2 239 domain Y Y N JHBP domain-containing protein 12595713,18291417 1224 Pseudomonadota phylum 7 EBI-EMBL Haemolymph juvenile hormone binding protein (JHBP) Haemolymph juvenile hormone binding protein (JHBP) This family consists of several insect-specific haemolymph juvenile hormone binding proteins (JHBP). Juvenile hormone regulates embryogenesis, maintains the status quo of larval development and stimulates reproductive maturation in the adult insect. JH is transported from the sites of its synthesis to target tissues by a haemolymph carrier called juvenile hormone-binding protein (JHBP). JHBP protects the JH molecules from hydrolysis by non-specific esterases present in the insect haemolymph [1]. The crystal structure of the JHBP from Galleria mellonella shows an unusual fold consisting of a long alpha-helix wrapped in a much curved antiparallel beta-sheet. The folding pattern for this structure closely resembles that found in some tandem-repeat mammalian lipid-binding and bactericidal permeability-increasing proteins, with a similar organisation of the major cavity and a disulfide bond linking the long helix and the beta-sheet. It would appear that JHBP forms two cavities, only one of which, the one near the N- and C-termini, binds the hormone; binding induces a conformational change, of unknown significance [1]. This family now includes DUF233, Pfam:PF03027. [1]. 12595713. Crystallization and preliminary crystallographic studies of juvenile hormone-binding protein from Galleria mellonella haemolymph. Kolodziejczyk R, Kochman M, Bujacz G, Dobryszycki P, Ozyhar A, Jaskolski M;. Acta Crystallogr D Biol Crystallogr 2003;59:519-521. [2]. 18291417. Insect juvenile hormone binding protein shows ancestral fold present in human lipid-binding proteins. Kolodziejczyk R, Bujacz G, Jakob M, Ozyhar A, Jaskolski M, Kochman M;. J Mol Bio. TRUNCATED at 1650 bytes (from Pfam) NF018382.5 PF06667.17 PspB 25.6 25.6 73 PfamEq Y N N Phage shock protein B GO:0006355,GO:0009271 12562786,1712397 1224 Pseudomonadota phylum 4074 EBI-EMBL Phage shock protein B Phage shock protein B This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages [1]. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [2]. [1]. 1712397. Characterization and sequence of the Escherichia coli stress-induced psp operon. Brissette JL, Weiner L, Ripmaster TL, Model P;. J Mol Biol 1991;220:35-48. [2]. 12562786. Interactions between phage-shock proteins in Escherichia coli. Adams H, Teertstra W, Demmers J, Boesten R, Tommassen J;. J Bacteriol 2003;185:1174-1180. (from Pfam) NF018387.5 PF06672.16 DUF1175 27 27 226 PfamAutoEq Y Y N DUF1175 family protein 1224 Pseudomonadota phylum 2417 EBI-EMBL Protein of unknown function (DUF1175) DUF1175 family protein This family consists of several hypothetical bacterial proteins of around 210 residues in length. The function of this family is unknown. (from Pfam) NF018408.5 PF06693.16 DUF1190 22 22 159 domain Y Y N DUF1190 domain-containing protein 1224 Pseudomonadota phylum 8408 EBI-EMBL Protein of unknown function (DUF1190) Protein of unknown function (DUF1190) This family consists of several hypothetical Enterobacterial proteins of around 212 residues in length and is known as YjfM in Escherichia coli. The function of this family is unknown. (from Pfam) NF018458.5 PF06748.17 DUF1217 22.9 22.9 149 domain Y Y N DUF1217 domain-containing protein 1224 Pseudomonadota phylum 5931 EBI-EMBL Protein of unknown function (DUF1217) Protein of unknown function (DUF1217) This family represents a conserved region that is found within bacterial proteins, most of which are hypothetical. Some members contain multiple copies. (from Pfam) NF018509.5 PF06804.16 Lipoprotein_18 25 25 323 domain Y Y N outer membrane protein assembly factor BamC bamC 1885529 1224 Pseudomonadota phylum 15331 EBI-EMBL NlpB/DapX lipoprotein outer membrane protein assembly factor BamC This family consists of a number of bacterial lipoproteins often known as NlpB or DapX. This lipoprotein is detected in outer membrane vesicles in Escherichia coli and appears to be nonessential [1]. [1]. 1885529. A gene for a new lipoprotein in the dapA-purC interval of the Escherichia coli chromosome. Bouvier J, Pugsley AP, Stragier P;. J Bacteriol 1991;173:5523-5531. (from Pfam) NF018596.5 PF06903.17 VirK 23.7 23.7 98 PfamEq Y Y N VirK family protein 11434457 1224 Pseudomonadota phylum 1227 EBI-EMBL VirK protein VirK family protein This family consists of several bacterial VirK proteins of around 145 residues in length. The function of this family is unknown [1]. [1]. 11434457. Sequence characterization of the vir region of a nopaline type Ti plasmid, pTi-SAKURA. Hattori Y, Iwata K, Suzuki K, Uraji M, Ohta N, Katoh A, Yoshida K;. Genes Genet Syst 2001;76:121-130. (from Pfam) NF018693.5 PF07017.16 PagP 24 24 144 domain Y N N Antimicrobial peptide resistance and lipid A acylation protein PagP 12357033 1224 Pseudomonadota phylum 5164 EBI-EMBL Antimicrobial peptide resistance and lipid A acylation protein PagP Antimicrobial peptide resistance and lipid A acylation protein PagP This family consists of several bacterial antimicrobial peptide resistance and lipid A acylation (PagP) proteins. The bacterial outer membrane enzyme PagP transfers a palmitate chain from a phospholipid to lipid A. In a number of pathogenic Gram-negative bacteria, PagP confers resistance to certain cationic antimicrobial peptides produced during the host innate immune response. [1]. 12357033. Solution structure and dynamics of the outer membrane enzyme PagP by NMR. Hwang PM, Choy WY, Lo EI, Chen L, Forman-Kay JD, Raetz CR, Prive GG, Bishop RE, Kay LE;. Proc Natl Acad Sci U S A 2002;99:13560-13565. (from Pfam) NF018740.5 PF07072.16 ZapD 27 27 210 PfamAutoEq Y Y N cell division protein ZapD zapD GO:0051301 22505682 1224 Pseudomonadota phylum 8559 EBI-EMBL Cell division protein cell division protein ZapD Cell division protein ZapD enhances FtsZ-ring assembly. It directly interacts with FtsZ and promotes bundling of FtsZ protofilaments, with a reduction in FtsZ GTPase activity [1]. [1]. 22505682. Identification of ZapD as a cell division factor that promotes the assembly of FtsZ in Escherichia coli. Durand-Heredia J, Rivkin E, Fan G, Morales J, Janakiraman A;. J Bacteriol. 2012;194:3189-3198. (from Pfam) NF018741.5 PF07073.17 ROF 27.6 27.6 80 PfamEq Y Y N Rho-binding antiterminator 9723924 1224 Pseudomonadota phylum 4269 EBI-EMBL Modulator of Rho-dependent transcription termination (ROF) Rho-binding antiterminator This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo [1]. [1]. 9723924. An Escherichia coli gene (yaeO) suppresses temperature-sensitive mutations in essential genes by modulating Rho-dependent transcription termination. Pichoff S, Alibaud L, Guedant A, Castanie MP, Bouche JP;. Mol Microbiol 1998;29:859-869. (from Pfam) NF018762.5 PF07095.16 IgaA 25 25 702 PfamEq Y Y N IgaA/UmoB family intracellular growth attenuator GO:0016020 11553591,12524328 1224 Pseudomonadota phylum 6557 EBI-EMBL Intracellular growth attenuator protein IgaA IgaA/UmoB family intracellular growth attenuator This family consists of several bacterial intracellular growth attenuator (IgaA) proteins. IgaA is involved in negative control of bacterial proliferation within fibroblasts. IgaA is homologous to the E. coli YrfF and P. mirabilis UmoB proteins. Whereas the biological function of YrfF is currently unknown, UmoB has been shown elsewhere to act as a positive regulator of FlhDC, the master regulator of flagella and swarming. FlhDC has been shown to repress cell division during P. mirabilis swarming, suggesting that UmoB could repress cell division via FlhDC. This biological function, if maintained in S. enterica, could sustain a putative negative control of cell division and growth exerted by IgaA in intracellular bacteria [1]. [1]. 11553591. Salmonella enterica serovar Typhimurium response involved in attenuation of pathogen intracellular proliferation. Cano DA, Martinez-Moya M, Pucciarelli MG, Groisman EA, Casadesus J, Garcia-Del Portillo F;. Infect Immun 2001;69:6463-6474. [2]. 12524328. Regulation of capsule synthesis and cell motility in Salmonella enterica by the essential gene igaA. Cano DA, Dominguez-Bernal G, Tierrez A, Garcia-Del Portillo F, Casadesus J;. Genetics 2002;162:1513-1523. (from Pfam) NF018769.5 PF07102.17 YbcO 29.9 29.9 92 subfamily Y Y N nuclease domain-containing protein 27562564,29040665 1224 Pseudomonadota phylum 6035 EBI-EMBL Putative nuclease YbcO DUF1364 family protein This family includes YbcO (pdbe:3G27), a putative nuclease from E. coli [1]. Proteins in the entry have been predicted to have the His-Me finger nuclease domain and may act as a Recombinase that participates in DNA repair and replication [2]. [1]. 27562564. Classification of the treble clef zinc finger: noteworthy lessons for structure and function evolution. Kaur G, Subramanian S;. Sci Rep. 2016;6:32070. [2]. 29040665. Systematic classification of the His-Me finger superfamily. Jablonska J, Matelska D, Steczkiewicz K, Ginalski K;. Nucleic Acids Res. 2017;45:11479-11494. (from Pfam) NF018908.5 PF07254.17 Cpta_toxin 27.3 27.3 133 PfamEq Y Y N protein YgfX 22239607,22474332,23657679 1224 Pseudomonadota phylum 10382 EBI-EMBL Membrane-bound toxin component of toxin-antitoxin system protein YgfX CptA is a family of bacterial proteins named for the member of this family, YGFX_ECOLI, Swissprot:Q46824. YgfX was previously thought to be the toxic part of a toxin-antitoxin module [1] along with the antitoxin, Pfam:PF03937 Sdh5. However, studies have shown that, YgfX interferes with correct cell division and morphology. Furthermore, the function of YgfX-SdhE as a TA system could not be demonstrated in either E. coli or Serratia sp. ATCC 39006. YgfX is predicted to have a short N-terminal cytoplasmic domain followed by two transmembrane helices (TMHs) separated by a short periplasmic loop and finally, a larger C-terminal cytoplasmic domain. The TMHs of YgfX are required for activity, but the sequence of the cytoplasmic 13 N-terminal amino acids is not essential. Furthermore, the amino acids W34 and D117 are not required for localization but are necessary for YgfX multimerization, interaction with SdhE, and YgfX activity. It is proposed that the formation of YgfX multimeric membrane-bound proteins are required to enable the interaction with the cytoplasmic SDH assembly factor SdhE [2]. Another study has demonstrated that sdhEygfX (bicistronic operon) affects pig biosynthesis, directly or indirectly, at the level of transcription of the biosynthetic operon (pigA-O) [3]. It has also been suggested that, in addition to indirect transcriptional activation of pigA-O, YgfX might facilitate the formation of a terminal pig biosynthetic complex consisting of PigB and PigC [2]. [1]. 22239607. A novel membrane-bound toxin for cell division, CptA (YgfX), inhibits polymerization of cytoskeleton proteins, FtsZ and MreB, in Escherichia . TRUNCATED at 1650 bytes (from Pfam) NF018924.5 PF07273.17 DUF1439 25.9 25.9 152 PfamAutoEq Y Y N DUF1439 domain-containing protein 1224 Pseudomonadota phylum 6991 EBI-EMBL Protein of unknown function (DUF1439) Protein of unknown function (DUF1439) This family consists of several hypothetical bacterial proteins of around 190 residues in length. Several members of this family are annotated as being putative lipoproteins and are often known as YceB. The function of this family is unknown. (from Pfam) NF018941.5 PF07290.16 YqiJ_OB 25.4 25.4 64 domain Y Y N OB-fold-containig protein 1224 Pseudomonadota phylum 5259 EBI-EMBL Inner membrane protein YqiJ, OB-fold DUF1449 family protein This entry represents the OB-fold domain found in several bacterial proteins, including the inner membrane protein YqiJ from E. coli, whose function is not clear. (from Pfam) NF018967.5 PF07317.17 PilZN 23 23 107 domain Y Y N flagellar regulator YcgR PilZN domain-containing protein 16920715,20303158,20346719,31740493 1224 Pseudomonadota phylum 8254 EBI-EMBL Flagellar regulator YcgR, PilZN domain Flagellar regulator YcgR, PilZN domain This domain is found N terminal to Pfam:PF07238, therefore named PilZN. Proteins which contain PilZN (also known as YcgR) are know to interact with the flagellar switch-complex proteins FliG and FliM. This interaction results in a reduction of torque generation and induces CCW motor bias [3]. This domain exhibits a similar structur as PilZ domains comprising a beta-barrel fold but lack the C-terminal alpha-helix [4]. [1]. 16920715. The PilZ domain is a receptor for the second messenger c-di-GMP: the PilZ domain protein YcgR controls motility in enterobacteria. Ryjenkov DA, Simm R, Romling U, Gomelsky M;. J Biol Chem. 2006;281:30310-30314. [2]. 20303158. Second messenger-mediated adjustment of bacterial swimming velocity. Boehm A, Kaiser M, Li H, Spangler C, Kasper CA, Ackermann M, Kaever V, Sourjik V, Roth V, Jenal U;. Cell. 2010;141:107-116. [3]. 20346719. The c-di-GMP binding protein YcgR controls flagellar motor direction and speed to affect chemotaxis by a "backstop brake" mechanism. Paul K, Nieto V, Carlquist WC, Blair DF, Harshey RM;. Mol Cell. 2010;38:128-139. [4]. 31740493. Structural Conservation and Diversity of PilZ-Related Domains. Galperin MY, Chou SH;. J Bacteriol. 2020; [Epub ahead of print] (from Pfam) NF019008.5 PF07361.16 Cytochrom_B562 30 30 102 subfamily Y Y N cytochrome b562 GO:0005506,GO:0009055,GO:0020037,GO:0022900,GO:0042597 10393541 1224 Pseudomonadota phylum 4850 EBI-EMBL Cytochrome b562 cytochrome b562 This family contains the bacterial cytochrome b562. This forms a four-helix bundle that non-covalently binds a single heme prosthetic group. [1]. [1]. 10393541. The solution structure of oxidized Escherichia coli cytochrome b562. Arnesano F, Banci L, Bertini I, Faraone-Mennella J, Rosato A, Barker PD, Fersht AR;. Biochemistry 1999;38:8657-8670. (from Pfam) NF019016.5 PF07369.16 DUF1488 22 22 82 subfamily Y Y N DUF1488 family protein 1224 Pseudomonadota phylum 10369 EBI-EMBL Protein of unknown function (DUF1488) DUF1488 family protein This family consists of several hypothetical bacterial proteins of around 85 residues in length. The function of this family is unknown. (from Pfam) NF019041.5 PF07395.16 Mig-14 22 22 264 PfamEq Y N N Mig-14 12029036 1224 Pseudomonadota phylum 4568 EBI-EMBL Mig-14 Mig-14 This family contains a number of bacterial mig-14 proteins (approximately 270 residues long). In Salmonella, mig-14 contributes to resistance to antimicrobial peptides, although the mechanism is not fully understood [1]. [1]. 12029036. mig-14 is a Salmonella gene that plays a role in bacterial resistance to antimicrobial peptides. Brodsky IE, Ernst RK, Miller SI, Falkow S;. J Bacteriol 2002;184:3203-3213. (from Pfam) NF019064.5 PF07419.17 PilM 25 25 136 subfamily Y Y N type IV pilus biogenesis protein PilM pilM 11751821 1224 Pseudomonadota phylum 2461 EBI-EMBL PilM type IV pilus biogenesis protein PilM This family contains the bacterial protein PilM (approximately 150 residues long). PilM is an inner membrane protein that has been predicted to function as a component of the pilin transport apparatus and thin-pilus basal body [1]. [1]. 11751821. Genes required for plasmid R64 thin-pilus biogenesis: identification and localization of products of the pilK, pilM, pilO, pilP, pilR, and pilT genes. Sakai D, Komano T;. J Bacteriol 2002;184:444-451. (from Pfam) NF019078.5 PF07434.16 CblD 25 25 296 subfamily Y Y N CfaE/CblD family pilus tip adhesin 12686638 1224 Pseudomonadota phylum 3049 EBI-EMBL CblD like pilus biogenesis initiator CfaE/CblD family pilus tip adhesin Members of this family appear as the tip adhesin of fimbriae (pili), but also are required for fimbrial biogenesis and therefore are often refered to as pilus biogenesis initiator proteins. NF019081.5 PF07437.16 YfaZ 23 23 180 subfamily Y Y N YfaZ family outer membrane protein 1224 Pseudomonadota phylum 4982 EBI-EMBL YfaZ precursor YfaZ family outer membrane protein This family contains the precursor of the bacterial protein YfaZ (approximately 180 residues long). Many members of this family are hypothetical proteins. (from Pfam) NF019102.5 PF07459.16 CTX_RstB 26.2 26.2 92 domain Y N N CTX phage RstB protein 9220000 1224 Pseudomonadota phylum 666 EBI-EMBL CTX phage RstB protein CTX phage RstB protein This family contains a number of RstB proteins approximately 120 residues long, including RstB1 and RstB2, from the Vibrio cholerae phage CTX. Functional analyses indicate that rstB2 is required for integration of the CTXphi phage into the V. cholerae chromosome [1]. [1]. 9220000. Regulation, replication, and integration functions of the Vibrio cholerae CTXphi are encoded by region RS2. Waldor MK, Rubin EJ, Pearson GD, Kimsey H, Mekalanos JJ;. Mol Microbiol 1997;24:917-926. (from Pfam) NF019115.5 PF07472.16 PA-IIL 21 21 107 domain Y Y N fucose-binding lectin II 12415289 1224 Pseudomonadota phylum 1573 EBI-EMBL Fucose-binding lectin II (PA-IIL) fucose-binding lectin II In Pseudomonas aeruginosa the fucose-binding lectin II (PA-IIL) contributes to the pathogenic virulence of the bacterium. PA-IIL functions as a tetramer when binding fucose. Each monomer is comprised of a nine-stranded, antiparallel beta-sandwich arrangement and contains two calcium cations that mediate the binding of fucose in a recognition mode unique among carbohydrate-protein interactions [1]. [1]. 12415289. Structural basis for oligosaccharide-mediated adhesion of Pseudomonas aeruginosa in the lungs of cystic fibrosis patients. Mitchell E, Houles C, Sudakevitz D, Wimmerova M, Gautier C, Perez S, Wu AM, Gilboa-Garber N, Imberty A;. Nat Struct Biol 2002;9:918-921. (from Pfam) NF019129.5 PF07487.18 SopE_GEF 25 25 136 domain Y N N SopE GEF domain GO:0005085,GO:0030036,GO:0090630 12093730 1224 Pseudomonadota phylum 550 EBI-EMBL SopE GEF domain SopE GEF domain This family represents the C-terminal guanine nucleotide exchange factor (GEF) domain of SopE. Salmonella typhimurium employs a type III secretion system to inject bacterial toxins into the host cell cytosol. These toxins transiently activate Rho family GTP-binding protein-dependent signaling cascades to induce cytoskeletal rearrangements. SopE, can activate Cdc42, an essential component of the host cellular signaling cascade, in a Dbl-like fashion despite its lack of sequence similarity to Dbl-like proteins, the Rho-specific eukaryotic guanine nucleotide exchange factors [1]. [1]. 12093730. Structural basis for the reversible activation of a Rho protein by the bacterial toxin SopE. Buchwald G, Friebel A, Galan JE, Hardt WD, Wittinghofer A, Scheffzek K;. EMBO J 2002;21:3286-3295. (from Pfam) NF019152.5 PF07511.16 DUF1525 24.1 24.1 113 domain Y Y N DUF1525 domain-containing protein 1224 Pseudomonadota phylum 4244 EBI-EMBL Protein of unknown function (DUF1525) Protein of unknown function (DUF1525) NF019154.5 PF07515.16 TraI_2_C 27.3 27.3 126 domain Y Y N conjugal transfer nickase/helicase domain-containing protein 12426355 1224 Pseudomonadota phylum 8482 EBI-EMBL Putative conjugal transfer nickase/helicase TraI C-term Putative conjugal transfer nickase/helicase TraI C-term NF019293.5 PF07671.16 DUF1601 25 4 37 domain Y Y N DUF1601 domain-containing protein 1224 Pseudomonadota phylum 1065 EBI-EMBL Protein of unknown function (DUF1601) Protein of unknown function (DUF1601) This repeat is found in a small number of proteins and is apparently limited to Coxiella and related species. (from Pfam) NF019376.5 PF07756.17 DUF1612 30.1 30.1 127 domain Y Y N DUF1612 domain-containing protein 12271122,9163424 1224 Pseudomonadota phylum 3914 EBI-EMBL Protein of unknown function (DUF1612) Protein of unknown function (DUF1612) This family includes sequences of largely unknown function but which share a number of features in common. They are expressed by bacterial species, and in many cases these bacteria are known to associate symbiotically with plants. Moreover, the majority are coded for by plasmids, which in many cases are known to confer on the organism the ability to interact symbiotically with leguminous plants. An example of such a plasmid is NGR234, which encodes Y4CF, a protein of unknown function that is a member of this family [1]. Other members of this family are expressed by organisms with a documented genomic similarity to plant symbionts [2]. [1]. 9163424. Molecular basis of symbiosis between Rhizobium and legumes. Freiberg C, Fellay R, Bairoch A, Broughton WJ, Rosenthal A, Perret X;. Nature 1997;387:394-401. [2]. 12271122. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, Read TD, Dodson RJ, Umayam L, Brinkac LM, Beanan MJ, Daugherty SC, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Nelson WC, Ayodeji B, Kraul M, Shetty J, Malek J, Van Aken SE, Riedmuller S, Tettelin. Proc Natl Acad Sci U S A 2002;99:13148-13153. (from Pfam) NF019379.5 PF07759.17 DUF1615 25 25 319 PfamAutoEq Y Y N DUF1615 family protein 10976061 1224 Pseudomonadota phylum 11214 EBI-EMBL Protein of unknown function (DUF1615) DUF1615 family protein This is a family of proteins of unknown function expressed by various bacterial species. Some members of this family (e.g. Swiss:Q8Z8Z7, Swiss:Q8ZRF4) are thought to be lipoproteins. Another member of this family (Swiss:Q93SV8) is thought to be involved in photosynthesis [1]. Based on structure predictions (from AlphaFold and structural comparisons using DALI server), this family may have a lysozyme-like fold. [1]. 10976061. Molecular evidence for the early evolution of photosynthesis. Xiong J, Fischer WM, Inoue K, Nakahara M, Bauer CE;. Science 2000;289:1724-1730. (from Pfam) NF019389.5 PF07769.19 PsiF_repeat 21 21 34 subfamily Y Y N PsiF family protein 2160940 1224 Pseudomonadota phylum 6009 EBI-EMBL psiF repeat phosphate starvation-inducible protein PsiF repeat This region is approximately 35 residues long. It is found repeated in a number of putative phosphate starvation- inducible proteins expressed by various bacterial species. psiF (Swiss:Q7AH28) is known to be an example of such phosphate starvation-inducible proteins [1]. [1]. 2160940. Identification of phosphate starvation-inducible genes in Escherichia coli K-12 by DNA sequence analysis of psi::lacZ(Mu d1) transcriptional fusions. Metcalf WW, Steed PM, Wanner BL;. J Bacteriol 1990;172:3191-3200. (from Pfam) NF019437.5 PF07820.17 TraC 27.7 27.7 88 subfamily Y Y N TraC family protein 12591886 1224 Pseudomonadota phylum 1934 EBI-EMBL TraC-like protein TraC family protein The members of this family are sequences that are similar to TraC (Swiss:Q84HT8). The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli CFN42 that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42a, which is also known as plasmid pSym as it carries most of the genes required for nodulation and nitrogen fixation by the symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58 [1]. [1]. 12591886. Conjugative transfer of p42a from rhizobium etli CFN42, which is required for mobilization of the symbiotic plasmid, is regulated by quorum sensing. Tun-Garrido C, Bustos P, Gonzalez V, Brom S;. J Bacteriol 2003;185:1681-1692. (from Pfam) NF019484.5 PF07869.17 DUF1656 26.5 25.8 56 domain Y Y N DUF1656 domain-containing protein 23774757,29769716 1224 Pseudomonadota phylum 10976 EBI-EMBL Protein of unknown function (DUF1656) Protein of unknown function (DUF1656) This entry represents a putative component of efflux pumps that comprise MFP and FUSC proteins. Several members are in an operon with and have similar mutants phenotypes as an RND efflux pump and a fusaric acid resistance-like protein [1]. This system is involved in transporting diverse substrates including 4-hydroxybenzoate and octanoate [2]. [1]. 29769716. Mutant phenotypes for thousands of bacterial genes of unknown function. Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM;. Nature. 2018;557:503-509. [2]. 23774757. Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates. Skerker JM, Leon D, Price MN, Mar JS, Tarjan DR, Wetmore KM, Deutschbauer AM, Baumohl JK, Bauer S, Ibanez AB, Mitchell VD, Wu CH, Hu P, Hazen T, Arkin AP;. Mol Syst Biol. 2013;9:674. (from Pfam) NF019501.5 PF07886.16 BA14K 26 26 30 domain Y Y N BA14K family protein 9673296 1224 Pseudomonadota phylum 12562 EBI-EMBL BA14K-like protein BA14K family protein The sequences found in this family are similar to the BA14K proteins expressed by Brucella abortus (Swiss:Q44701) and by Brucella suis (Swiss:Q8FVU0). BA14K was found to be strongly immunoreactive; it induces both humoral and cellular responses in hosts throughout the infective process [1]. [1]. 9673296. Identification and characterization of a 14-kilodalton Brucella abortus protein reactive with antibodies from naturally and experimentally infected hosts and T lymphocytes from experimentally infected BALB/c mice. Chirhart-Gilleland RL, Kovach ME, Elzer PH, Jennings SR, Roop RM 2nd;. Infect Immun 1998;66:4000-4003. (from Pfam) NF019551.5 PF07939.16 DUF1685 21 21 60 domain Y Y N DUF1685 domain-containing protein 1224 Pseudomonadota phylum 3 EBI-EMBL Protein of unknown function (DUF1685) Protein of unknown function (DUF1685) The members of this family are hypothetical eukaryotic proteins of unknown function. The region in question is approximately 100 amino acid residues long. (from Pfam) NF019696.5 PF08085.16 Entericidin 23.3 23.3 20 domain Y Y N entericidin A/B family lipoprotein GO:0009636,GO:0016020 9677290 1224 Pseudomonadota phylum 8628 EBI-EMBL Entericidin EcnA/B family entericidin A/B family lipoprotein This family consists of the entericidin antidote/toxin peptides. The entericidin locus is activated in stationary phase under high osmolarity conditions by rho-S and simultaneously repressed by the osmoregulatory EnvZ/OmpR signal transduction pathway. The entericidin locus encodes tandem paralogous genes (ecnAB) and directs the synthesis of two small cell-envelope lipoproteins which can maintain plasmids in bacterial population by means of post-segregational killing [1]. [1]. 9677290. The entericidin locus of Escherichia coli and its implications for programmed bacterial cell death. Bishop RE, Leskiw BK, Hodges RS, Kay CM, Weiner JH;. J Mol Biol 1998;280:583-596. (from Pfam) NF019781.5 PF08173.16 YbgT_YccB 26.2 26.2 27 domain Y Y N cytochrome bd oxidase small subunit, CydX/CbdX family 9068659 1224 Pseudomonadota phylum 6137 EBI-EMBL Membrane bound YbgT-like protein cytochrome bd oxidase small subunit, CydX/CbdX family This family contains a set of membrane proteins, typically 33 amino acids long. The family has no known function, but the protein is found in the operon CydAB in E. coli. Members have a consensus motif (MWYFXW) which is rich in aromatic residues. The protein forms a single membrane-spanning helix. This family seems to be restricted to Proteobacteria [1]. [1]. 9068659. Characterization of the tol-pal and cyd region of Escherichia coli K-12: transcript analysis and identification of two new proteins encoded by the cyd operon. Muller MM, Webster RE;. J Bacteriol 1997;179:2077-2080. (from Pfam) NF019939.5 PF08339.15 RTX_C 30.2 30.2 132 domain Y N N RTX C-terminal domain 8800842 1224 Pseudomonadota phylum 805 EBI-EMBL RTX C-terminal domain RTX C-terminal domain This family describes the C-terminal region of various bacterial haemolysins and leukotoxins, which belong to the RTX family of toxins. These are produced by various Gram negative bacteria, such as E. coli (Swiss:P09983) and Actinobacillus pleuropneumoniae (Swiss:P15377). RTX toxins may interact with lipopolysaccharide (LPS) to functionally impair and eventually kill leukocytes [1]. This region is found in association with the RTX N-terminal domain (Pfam:PF02382) and multiple hemolysin-type calcium-binding repeats (Pfam:PF00353). [1]. 8800842. Biological effects of RTX toxins: the possible role of lipopolysaccharide. Czuprynski CJ, Welch RA;. Trends Microbiol 1995;3:480-483. (from Pfam) NF020057.5 PF08468.16 MTS_N 27.3 27.3 158 PfamEq Y N N Methyltransferase small domain N-terminal GO:0006364,GO:0008990 9873033 1224 Pseudomonadota phylum 14852 EBI-EMBL Methyltransferase small domain N-terminal Methyltransferase small domain N-terminal This domain is found to the N-terminus of the methyltransferase small domain (Pfam:PF05175) in bacterial proteins [1]. [1]. 9873033. Purification, cloning, and characterization of the 16 S RNA m2G1207 methyltransferase from Escherichia coli. Tscherne JS, Nurse K, Popienick P, Ofengand J;. J Biol Chem 1999;274:924-929. (from Pfam) NF020373.5 PF08794.15 FHBP_C 28.1 28.1 97 domain Y Y N factor H binding protein domain-containing protein 16407174,21543855,23133374,31442074,34125873 1224 Pseudomonadota phylum 2746 EBI-EMBL Factor H binding protein, C-terminal Factor H binding protein, C-terminal Factor H binding protein (also known as GNA1870) is a surface exposed lipoprotein in Neisseria meningitidis that is a potent antigen and a potential candidate for a vaccine against meningococcal disease [1-4]. The structure of the C-terminal domain consists of an anti-parallel beta barrel overlaid by a short alpha helical region [1,5]. This domain is highly similar to Transferrin-binding protein B beta barrel (Pfam:PF01298). [1]. 16407174. Solution structure of the immunodominant domain of protective antigen GNA1870 of Neisseria meningitidis. Cantini F, Savino S, Scarselli M, Masignani V, Pizza M, Romagnoli G, Swennen E, Veggi D, Banci L, Rappuoli R;. J Biol Chem. 2006;281:7220-7227. [2]. 34125873. Two human antibodies to a meningococcal serogroup B vaccine antigen enhance binding of complement Factor H by stabilizing the Factor H binding site. Sands NA, Beernink PT;. PLoS Pathog. 2021;17:e1009655. [3]. 23133374. Design and evaluation of meningococcal vaccines through structure-based modification of host and pathogen molecules. Johnson S, Tan L, van der Veen S, Caesar J, Goicoechea De Jorge E, Harding RJ, Bai X, Exley RM, Ward PN, Ruivo N, Trivedi K, Cumber E, Jones R, Newham L, Staunton D, Ufret-Vincenty R, Borrow R, Pickering MC, Lea SM, Tang CM;. PLoS Pathog. 2012;8:e1002981. [4]. 21543855. Structure of the uncomplexed Neisseria meningitidis factor H-binding protein fHbp (rLP2086). Cendron L, Veggi D, Girardi E, Zanotti G;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011;67:531-535. [5]. 31442074. Cocrystal structure of meningococcal factor H binding protein variant 3 reveals a new crossprotective epitope recogn. TRUNCATED at 1650 bytes (from Pfam) NF020395.5 PF08816.16 Ivy 21 21 117 subfamily Y Y N Ivy family c-type lysozyme inhibitor 17405861,23402825,26003922 1224 Pseudomonadota phylum 4872 EBI-EMBL Inhibitor of vertebrate lysozyme (Ivy) Ivy family c-type lysozyme inhibitor Ivy (Inhibitor of Vertebrate lysozyme) family inhibitors of vertebrate c-type lysozyme are periplasmic proteins that provide protection against lysozyme to Gram-negative pathogens. The protection can be demonstrated only if the outer membrane is compromised, as occurs in the presence of cationic antimicrobial peptide produced by host defenses. Overexpression of Ivy has been shown to have the chaperone-like function of helping to prevent aggregation of a certain proteins in the periplasm, a function that might also have physiological relevance. NF020474.5 PF08900.16 AcaB 27 27 215 domain Y Y N AcaB family transcriptional regulator 32807890 1224 Pseudomonadota phylum 5041 EBI-EMBL Transcriptional regulator AcaB AcaB family transcriptional regulator This family of proteins is found in the IncC family of broad-host-range plasmids which enables the spread of antibiotic resistance genes among human enteric pathogens. Recently, AcaB member has been characterised as a transcriptional regulator that plays a crucial role in the regulation of IncC conjugation. It is a DNA binding protein which binds upstream of the acaDB promoter to increase its transcription and, in turn, acaDB activates the transcription of IncC conjugation genes. Structurally, AcaB consists of two helical hairpins in tandem which assemble into an anti-parallel four-helix bundle to form a two-stranded antiparallel beta-sheet positioned parallel to the helices. This is structurally similar to bacterial transcription factors from the ribbon-helix-helix (RHH) superfamily [1]. [1]. 32807890. Comprehensive analysis of IncC plasmid conjugation identifies a crucial role for the transcriptional regulator AcaB. Hancock SJ, Phan MD, Luo Z, Lo AW, Peters KM, Nhu NTK, Forde BM, Whitfield J, Yang J, Strugnell RA, Paterson DL, Walsh TR, Kobe B, Beatson SA, Schembri MA;. Nat Microbiol. 2020; [Epub ahead of print] (from Pfam) NF020518.5 PF08946.15 Osmo_CC 24 24 46 PfamEq Y N N Osmosensory transporter coiled coil 14643666 1224 Pseudomonadota phylum 3671 EBI-EMBL Osmosensory transporter coiled coil Osmosensory transporter coiled coil The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function [1]. [1]. 14643666. Solution structure of the C-terminal antiparallel coiled-coil domain from Escherichia coli osmosensor ProP. Zoetewey DL, Tripet BP, Kutateladze TG, Overduin MJ, Wood JM, Hodges RS;. J Mol Biol. 2003;334:1063-1076. (from Pfam) NF020557.5 PF08988.15 T3SS_needle_E 22 22 67 PfamEq Y Y N EscE/YscE/SsaE family type III secretion system needle protein co-chaperone 16115870,18281060,22844497 1224 Pseudomonadota phylum 1028 EBI-EMBL Type III secretion system, cytoplasmic E component of needle EscE/YscE/SsaE family type III secretion system needle protein co-chaperone T3SS_needle_E is a family of proteins from the operon that builds and controls the needle of the injection system of type III secretion. The YscE protein, produced by the pathogen Yersinia, assumes a secondary structure composed of two anti-parallel alpha-helices separated by a flexible loop [1]. The family is cytoplasmic and may help to stabilise and prevent early polymerisation of the needle-protein F [2,3]. [1]. 16115870. The PscE-PscF-PscG complex controls type III secretion needle biogenesis in Pseudomonas aeruginosa. Quinaud M, Chabert J, Faudry E, Neumann E, Lemaire D, Pastor A, Elsen S, Dessen A, Attree I;. J Biol Chem. 2005;280:36293-36300. [2]. 18281060. Structural characterization of the Yersinia pestis type III secretion system needle protein YscF in complex with its heterodimeric chaperone YscE/YscG. Sun P, Tropea JE, Austin BP, Cherry S, Waugh DS;. J Mol Biol. 2008;377:819-830. [3]. 22844497. The Pseudomonas aeruginosa type III secretion system has an exotoxin S/T/Y independent pathogenic role during acute lung infection. Galle M, Jin S, Bogaert P, Haegman M, Vandenabeele P, Beyaert R;. PLoS One. 2012;7:e41547. (from Pfam) NF020613.5 PF09046.15 AvrPtoB-E3_ubiq 25 25 126 domain Y N N AvrPtoB E3 ubiquitin ligase 16373536 1224 Pseudomonadota phylum 167 EBI-EMBL AvrPtoB E3 ubiquitin ligase AvrPtoB E3 ubiquitin ligase The E3 ubiquitin ligase domain found in the bacterial protein AvrPtoB inhibits immunity-associated programmed cell death (PCD) when translocated into plant cells, probably by recruiting E2 enzymes and transferring ubiquitin molecules to cellular proteins involved in regulation of PCD and targeting them for degradation. The structure of this domain reveals a globular fold centred on a four-stranded beta-sheet that packs against two helices on one face and has three very extended loops connecting the elements of secondary structure, with remarkable homology to the RING-finger and U-box families of proteins involved in ubiquitin ligase complexes in eukaryotes [1]. [1]. 16373536. A bacterial inhibitor of host programmed cell death defenses is an E3 ubiquitin ligase. Janjusevic R, Abramovitch RB, Martin GB, Stebbins CE;. Science. 2006;311:222-226. (from Pfam) NF020644.5 PF09078.16 CheY-binding 24 24 63 PfamEq Y N N CheY binding 11134926 1224 Pseudomonadota phylum 10431 EBI-EMBL CheY binding CheY binding Members of this family adopt a secondary structure consisting of an open-face beta/alpha sandwich, with four antiparallel beta-strands and two alpha-helices. They bind to a corresponding domain on CheY, with subsequent phosphorylation of the CheY Asp57 residue, and activation of CheY, which then affects flagellar rotation [1]. [1]. 11134926. Further insights into the mechanism of function of the response regulator CheY from crystallographic studies of the CheY--CheA(124--257) complex. Gouet P, Chinardet N, Welch M, Guillet V, Cabantous S, Birck C, Mourey L, Samama JP;. Acta Crystallogr D Biol Crystallogr. 2001;57:44-51. (from Pfam) NF020684.5 PF09119.15 SicP-binding 25 25 84 domain Y Y N type III secretion system effector BopA family protein GO:0005615 11689946 1224 Pseudomonadota phylum 740 EBI-EMBL SicP binding type III secretion system effector BopA family protein Members of this family bind the chaperone SicP, which is required both to maintain the stability of SptP, as well as to ensure the eventual secretion of the protein. The domain is found in the Salmonella effector protein SptP, which interacts with SicP chaperone dimers mainly through four regions of its chaperone-binding domain. The structure of the SptP-SicP complex contains four molecules of SicP, aligned in a linear fashion and arranged in two sets of tightly bound homodimers that bind two SptP molecules. The SicP homodimers do not interact with each other, but are held together by a molecular interface formed between two SptP molecules. Each SptP molecule is wrapped around by three SicP chaperones (two chaperones from one homodimer and a third one from the opposite homodimer pair) [1]. [1]. 11689946. Maintenance of an unfolded polypeptide by a cognate chaperone in bacterial type III secretion. Stebbins CE, Galan JE;. Nature. 2001;414:77-81. (from Pfam) NF020707.5 PF09143.15 AvrPphF-ORF-2 25 25 175 domain Y Y N AvrPphF family type III effector 15341731 1224 Pseudomonadota phylum 504 EBI-EMBL AvrPphF-ORF-2 AvrPphF family type III effector Members of this family of plant pathogenic proteins adopt an elongated structure somewhat reminiscent of a mushroom that can be divided into 'stalk' and 'head' subdomains. The stalk subdomain is composed of the N-terminal helix (alpha1) and beta strands beta3-beta4. An antiparallel beta sheet (beta5, beta7-beta8) forms the base of the head subdomain that interacts with the stalk. A pair of twisted antiparallel beta sheets (beta1 and beta6; beta2 and beta9/9') supported by alpha2 form the dome of the head. The head subdomain possesses weak structural similarity with the catalytic portion of a number of ADP-ribosyltransferase toxins [1]. [1]. 15341731. Crystal structures of the type III effector protein AvrPphF and its chaperone reveal residues required for plant pathogenesis. Singer AU, Desveaux D, Betts L, Chang JH, Nimchuk Z, Grant SR, Dangl JL, Sondek J;. Structure. 2004;12:1669-1681. (from Pfam) NF020725.5 PF09163.16 Form-deh_trans 22.1 22.1 44 domain Y Y N formate dehydrogenase N subunit beta transmembrane domain-containing protein 11884747 1224 Pseudomonadota phylum 9851 EBI-EMBL Formate dehydrogenase N, transmembrane Formate dehydrogenase N, transmembrane Members of this family are predominantly found in the beta subunit of formate dehydrogenase, and consist of a single transmembrane helix. They act as a transmembrane anchor, and allow for conduction of electrons within the protein [1]. [1]. 11884747. Molecular basis of proton motive force generation: structure of formate dehydrogenase-N. Jormakka M, Tornroth S, Byrne B, Iwata S;. Science. 2002;295:1863-1868. (from Pfam) NF020929.5 PF09372.15 PRANC 25.8 25.8 97 domain Y Y N PRANC domain-containing protein 16025237 1224 Pseudomonadota phylum 241 EBI-EMBL PRANC domain PRANC domain This presumed domain is found at the C-terminus of a variety of Pox virus proteins. The PRANC (Pox proteins Repeats of ANkyrin - C terminal) domain is also found on its own in some proteins. The function of this domain is unknown, but it appears to be related to the F-box domain and may play a similar role. [1]. 16025237. F-box-like domains are present in most poxvirus ankyrin repeat proteins. Mercer AA, Fleming SB, Ueda N;. Virus Genes. 2005;31:127-133. (from Pfam). PRANC (Pox proteins Repeats of ANkyrin - C terminal) domain proteins occurring in bacteria tend to be found in endosymbionts or intracellular pathogens such as Wolbachia species Orientia tsutsugamushi. NF020948.5 PF09392.15 T3SS_needle_F 29.4 29.4 71 domain Y Y N EscF/YscF/HrpA family type III secretion system needle major subunit GO:0015031 16888041,18281060,22844497,23390616 1224 Pseudomonadota phylum 1920 EBI-EMBL Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF EscF/YscF/HrpA family type III secretion system needle major subunit Type III secretion systems are essential virulence determinants for many gram-negative bacterial pathogens. MxiH is an extracellular alpha helical needle that is required for translocation of effector proteins into host cells [1]. Once inside, the effector proteins subvert normal cell function to aid infection. The needle protein F, polymerises to form a shaft [2,3,4]. [1]. 16888041. Molecular model of a type III secretion system needle: Implications for host-cell sensing. Deane JE, Roversi P, Cordes FS, Johnson S, Kenjale R, Daniell S, Booy F, Picking WD, Picking WL, Blocker AJ, Lea SM;. Proc Natl Acad Sci U S A. 2006;103:12529-12533. [2]. 18281060. Structural characterization of the Yersinia pestis type III secretion system needle protein YscF in complex with its heterodimeric chaperone YscE/YscG. Sun P, Tropea JE, Austin BP, Cherry S, Waugh DS;. J Mol Biol. 2008;377:819-830. [3]. 22844497. The Pseudomonas aeruginosa type III secretion system has an exotoxin S/T/Y independent pathogenic role during acute lung infection. Galle M, Jin S, Bogaert P, Haegman M, Vandenabeele P, Beyaert R;. PLoS One. 2012;7:e41547. [4]. 23390616. Regulation of the Yersinia type III secretion system: traffic control. Dewoody RS, Merritt PM, Marketon MM;. Front Cell Infect Microbiol. 2013;3:4. (from Pfam) NF020955.5 PF09400.15 DUF2002 23 23 110 PfamAutoEq Y Y N DUF2002 family protein 1224 Pseudomonadota phylum 1121 EBI-EMBL Protein of unknown function (DUF2002) DUF2002 family protein This is a family of putative cytoplasmic proteins. The structure of these proteins form an antiparallel beta and sheet and contain some alpha helical regions. (from Pfam) NF021029.5 PF09480.15 PrgH 25.8 25.8 373 PfamEq Y Y N PrgH/EprH family type III secretion apparatus protein GO:0016020 15528446,7476203 1224 Pseudomonadota phylum 3668 EBI-EMBL Type III secretion system protein PrgH-EprH (PrgH) PrgH/EprH family type III secretion apparatus protein In Salmonella, the gene encoding this protein is part of a four-gene operon PrgHIJK, while in other organisms it is found in type III secretion operons. PrgH has been shown to be required for type III secretion and is a structural component of the needle complex, which is the core component of type III secretion systems. (from Pfam) NF021031.5 PF09482.15 OrgA_MxiK 25 25 181 PfamEq Y N N Bacterial type III secretion apparatus protein (OrgA_MxiK) 1224 Pseudomonadota phylum 1825 EBI-EMBL Bacterial type III secretion apparatus protein (OrgA_MxiK) Bacterial type III secretion apparatus protein (OrgA_MxiK) This protein is encoded by genes which are found in type III secretion operons, and has been shown to be essential for the invasion phenotype in Salmonella and a component of the secretion apparatus. The protein is known as OrgA in Salmonella due to its oxygen-dependent expression pattern in which low-oxygen levels up-regulate the gene. In Shigella the gene is called MxiK and has been shown to be essential for the proper assembly of the needle complex, which is the core component of type III secretion systems. (from Pfam) NF021035.5 PF09486.15 HrpB7 29.7 29.7 157 domain Y N N Bacterial type III secretion protein (HrpB7) 1224 Pseudomonadota phylum 958 EBI-EMBL Bacterial type III secretion protein (HrpB7) Bacterial type III secretion protein (HrpB7) This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow range of species including Xanthomonas, Burkholderia and Ralstonia. (from Pfam) NF021036.5 PF09487.15 HrpB2 26.5 26.5 114 domain Y N N Bacterial type III secretion protein (HrpB2) 1224 Pseudomonadota phylum 668 EBI-EMBL Bacterial type III secretion protein (HrpB2) Bacterial type III secretion protein (HrpB2) This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow group of species including Xanthomonas, Burkholderia and Ralstonia. (from Pfam) NF021051.5 PF09502.15 HrpB4 29 29 217 subfamily Y Y N type III secretion protein HrpB4 20720578 1224 Pseudomonadota phylum 1365 EBI-EMBL Bacterial type III secretion protein (HrpB4) type III secretion protein HrpB4 This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow range of species including Xanthomonas, Burkholderia and Ralstonia. (from Pfam) NF021139.5 PF09599.15 IpaC_SipC 25 25 334 PfamEq Y Y N IpaC/SipC family type III secretion system effector 17995960,25165162 1224 Pseudomonadota phylum 755 EBI-EMBL Salmonella-Shigella invasin protein C (IpaC_SipC) IpaC/SipC family type III secretion system effector This entry represents a family of proteins associated with bacterial type III secretion systems, which are injection machines for virulence factors into host cell cytoplasm. Characterized members of this protein family are known to be secreted and are described as invasins, including IpaC from Shigella flexneri and SipC from Salmonella typhimurium. Members may be referred to as invasins, pathogenicity island effectors, and cell invasion proteins. (from Pfam) NF021140.5 PF09600.15 Cyd_oper_YbgE 25.2 25.2 79 PfamEq Y Y N cyd operon YbgE family protein 1224 Pseudomonadota phylum 4365 EBI-EMBL Cyd operon protein YbgE (Cyd_oper_YbgE) cyd operon YbgE family protein This entry describes a small protein of unknown function, about 100 amino acids in length, essentially always found in an operon with CydAB, subunits of the cytochrome d terminal oxidase. It appears to be an integral membrane protein. It is found so far only in the Proteobacteria. (from Pfam) NF021212.5 PF09676.15 TraV 21 21 128 domain Y Y N TraV family lipoprotein 1224 Pseudomonadota phylum 7207 EBI-EMBL Type IV conjugative transfer system lipoprotein (TraV) TraV family lipoprotein This entry includes TraV, which is a component of conjugative type IV secretion system. TraV is an outer membrane lipoprotein that is believed to interact with the secretin TraK. The alignment contains three conserved cysteines in the N-terminal half. (from Pfam) NF021213.5 PF09677.15 TrbI_Ftype 27.4 27.4 106 domain Y Y N TrbI F-type domain-containing protein 1355084 1224 Pseudomonadota phylum 3949 EBI-EMBL Type-F conjugative transfer system protein (TrbI_Ftype) Type-F conjugative transfer system protein (TrbI_Ftype) This entry represents TrbI, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm. (from Pfam) NF021222.5 PF09686.15 Plasmid_RAQPRD 23.1 23.1 76 subfamily Y Y N RAQPRD family integrative conjugative element protein 1224 Pseudomonadota phylum 4406 EBI-EMBL Plasmid protein of unknown function (Plasmid_RAQPRD) RAQPRD family integrative conjugative element protein This entry identifies a family of proteins, which are about 100 amino acids in length, including a predicted signal sequence and a perfectly conserved motif RAQPRD towards the C terminus. Members are found in the Pseudomonas putida TOL plasmid pWW0 and in cryptic plasmid regions of Salmonella enterica subsp. enterica serovar Typhi and Pseudomonas syringae DC3000. The function of these proteins are unknown. (from Pfam) NF021383.5 PF09857.14 YjhX_toxin 27 27 85 domain Y Y N YjhX family toxin 21927020 1224 Pseudomonadota phylum 3255 EBI-EMBL Putative toxin of bacterial toxin-antitoxin pair YjhX family toxin YjhX_toxin is a putative toxin of a bacterial toxin-antitoxin pair, which is neutralised by the proteins YjhQ in family Pfam:PF00583. [1]. 21927020. Regulation of growth and death in Escherichia coli by toxin-antitoxin systems. Yamaguchi Y, Inouye M;. Nat Rev Microbiol. 2011;9:779-790. (from Pfam) NF021432.5 PF09909.14 DUF2138 22 22 560 PfamAutoEq Y Y N DUF2138 family protein 1224 Pseudomonadota phylum 4079 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2138) DUF2138 family protein This domain, found in various hypothetical prokaryotic proteins, has no known function. (from Pfam) NF021457.5 PF09938.14 DUF2170 27 27 137 PfamAutoEq Y Y N DUF2170 family protein 1224 Pseudomonadota phylum 4219 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2170) DUF2170 family protein This domain, found in various hypothetical prokaryotic proteins, has no known function. (from Pfam) NF021478.5 PF09961.14 DUF2195 25 25 117 PfamAutoEq Y Y N DUF2195 family protein 1224 Pseudomonadota phylum 513 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2195) DUF2195 family protein This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021499.5 PF09984.14 sCache_4 22.1 22.1 145 domain Y N N Single cache domain 4 1224 Pseudomonadota phylum 17465 EBI-EMBL Single cache domain 4 Single cache domain 4 Members of this family of domains are found in various BarA-like signal transduction histidine kinases, which are involved in the regulation of carbon metabolism via the csrA/csrB regulatory system. The role of this domain has not, as yet, been established. (from Pfam) NF021572.5 PF10062.14 DUF2300 25 25 127 PfamAutoEq Y Y N DUF2300 domain-containing protein 1224 Pseudomonadota phylum 4449 EBI-EMBL Predicted secreted protein (DUF2300) Predicted secreted protein (DUF2300) This domain, found in various bacterial hypothetical and putative signal peptide proteins, has no known function. (from Pfam) NF022024.5 PF10549.14 ORF11CD3 25 25 54 domain Y N N ORF11CD3 domain 11897024 1224 Pseudomonadota phylum 2620 EBI-EMBL ORF11CD3 domain ORF11CD3 domain This domain was identified by Iyer and colleagues [1]. [1]. 11897024. Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors. Iyer LM, Koonin EV, Aravind L;. Genome Biol 2002;3:RESEARCH0012. (from Pfam) NF022085.5 PF10617.14 DUF2474 26.6 26.6 39 PfamAutoEq Y Y N DUF2474 family protein 1224 Pseudomonadota phylum 5314 EBI-EMBL Protein of unknown function (DUF2474) DUF2474 family protein This family of short proteins has no known function. (from Pfam) NF022124.5 PF10658.14 DUF2484 25 25 76 subfamily Y Y N DUF2484 family protein 1224 Pseudomonadota phylum 2114 EBI-EMBL Protein of unknown function (DUF2484) DUF2484 family protein A role of this family in UDP-N-acetylenolpyruvoylglucosamine reductase, as MurB, could not be confirmed. (from Pfam) NF022144.5 PF10679.14 DUF2491 25 25 210 PfamAutoEq Y Y N DUF2491 family protein 1224 Pseudomonadota phylum 4166 EBI-EMBL Protein of unknown function (DUF2491) DUF2491 family protein This is a bacterial family of uncharacterised proteins. (from Pfam) NF022159.5 PF10696.14 DUF2501 21 21 78 PfamAutoEq Y Y N DUF2501 domain-containing protein 1224 Pseudomonadota phylum 3944 EBI-EMBL Protein of unknown function (DUF2501) Protein of unknown function (DUF2501) Members of this family are all Proteobacteria. Several are annotated as being YjjA or YjjA-like, but this protein is uncharacterised. (from Pfam) NF022181.5 PF10721.14 DUF2514 26 26 161 subfamily Y Y N DUF2514 family protein 1224 Pseudomonadota phylum 8557 EBI-EMBL Protein of unknown function (DUF2514) DUF2514 family protein This family is conserved in bacteria and some viruses. The function is not known. (from Pfam) NF022266.5 PF10809.13 DUF2732 25 25 75 subfamily Y Y N DUF2732 family protein 1224 Pseudomonadota phylum 4769 EBI-EMBL Protein of unknown function (DUF2732) DUF2732 family protein This family of proteins has no known function. (from Pfam) NF022361.5 PF10907.13 DUF2749 25.5 25.5 72 domain Y Y N DUF2749 domain-containing protein 1224 Pseudomonadota phylum 672 EBI-EMBL Protein of unknown function (DUF2749) Protein of unknown function (DUF2749) This bacterial family of proteins appear to come from the Trb operon however currently no function is known. (from Pfam) NF022398.5 PF10945.13 CBP_BcsR 25.2 25.2 41 domain Y Y N BcsR/BcsP family cellulose biosynthesis protein bcsR 26077867,29234007,33563593 1224 Pseudomonadota phylum 2640 EBI-EMBL Cellulose biosynthesis protein BcsR-like BcsR/BcsP domain BcsR (bacterial cellulose synthesis R, previously YhjR in Escherichia coli) is a small cytosolic protein essential for cellulose. It appears to form part of the Bcs macrocomplex that also includes membrane, periplasmic, and outer membrane components. BcsP, a much longer protein, share N-terminal homology with BcsR. NF022405.5 PF10952.13 DUF2753 28.7 28.7 140 PfamAutoEq Y Y N DUF2753 family protein 1224 Pseudomonadota phylum 770 EBI-EMBL Protein of unknown function (DUF2753) DUF2753 family protein This bacterial family of proteins has no known function. (from Pfam) NF022429.5 PF10976.13 DUF2790 27 27 56 domain Y Y N DUF2790 domain-containing protein 1224 Pseudomonadota phylum 8533 EBI-EMBL Protein of unknown function (DUF2790) Protein of unknown function (DUF2790) This family of proteins with unknown function appear to be restricted to Pseudomonadaceae. (from Pfam) NF022448.5 PF10995.13 CBP_BcsE 25 25 513 domain Y Y N BcsE family c-di-GMP-binding protein GO:0035438 24942809,26077867,29348238,32788377,33712813 1224 Pseudomonadota phylum 9085 EBI-EMBL Cellulose biosynthesis protein BcsE BcsE family c-di-GMP-binding protein This family of proteins includes members involved in cellulose biosynthesis such as BcsE proteins found in Salmonella typhimurium. Family members carry a GIL domain on the C-terminal. The GIL domain, for GGDEF I-site like domain, is a c-di-GMP binding domain on the BcsE proteins of enterobacteria. It is not essential for cellulose synthesis but is critical for maximal cellulose production. Cellulose production in enterobacteria is controlled by a two-tiered c-di-GMP-dependent system involving BcsE and the PilZ domain containing glycosyltransferase BcsA. The RxGD motif of the GIL domain is required for c-di-GMP binding [1-5]. [1]. 24942809. GIL, a new c-di-GMP-binding protein domain involved in regulation of cellulose synthesis in enterobacteria. Fang X, Ahmad I, Blanka A, Schottkowski M, Cimdins A, Galperin MY, Romling U, Gomelsky M;. Mol Microbiol. 2014;93:439-452. [2]. 26077867. Bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions. Romling U, Galperin MY;. Trends Microbiol. 2015;23:545-557. [3]. 32788377. Structure and Multitasking of the c-di-GMP-Sensing Cellulose Secretion Regulator BcsE. Zouhir S, Abidi W, Caleechurn M, Krasteva PV;. mBio. 2020; [Epub ahead of print]. [4]. 29348238. Phosphoethanolamine cellulose: A naturally produced chemically modified cellulose. Thongsomboon W, Serra DO, Possling A, Hadjineophytou C, Hengge R, Cegelski L;. Science. 2018;359:334-338. [5]. 33712813. Molecular organization of the E. coli cellulose synthase macrocomplex. Acheson JF, Ho R, Goularte NF, Cegelski L, Zimmer J;. Nat Struct Mol Biol. 2021;28:310-318. (from Pfam) NF022512.5 PF11060.13 DUF2861 25 25 267 subfamily Y Y N DUF2861 family protein 1224 Pseudomonadota phylum 2795 EBI-EMBL Protein of unknown function (DUF2861) DUF2861 family protein This bacterial family of proteins has no known function. (from Pfam) NF022523.5 PF11072.13 DUF2859 25 25 147 domain Y Y N DUF2859 domain-containing protein 1224 Pseudomonadota phylum 5454 EBI-EMBL Protein of unknown function (DUF2859) Protein of unknown function (DUF2859) This is a bacterial family of uncharacterised proteins. (from Pfam) NF022552.5 PF11102.13 YjbF 25.9 25.9 189 domain Y Y N YjbF family lipoprotein 16030220,17379715,21449614 1224 Pseudomonadota phylum 9174 EBI-EMBL Group 4 capsule polysaccharide lipoprotein gfcB, YjbF YjbF family lipoprotein This family includes lipoprotein GfcB (YmcC), involved in group 4 capsule polysaccharide formation [1]. YjbF is a family of Gram-negative bacterial outer-membrane lipoproteins, predicted to be a beta-barrel and possibly a porin that is one of four gene-products expressed from an operon, yjbEFGH, which is regulated by the Rcs phosphorelay in a RcsA-dependent manner, similar to that of other exopolysaccharide biosynthetic pathways. It is highly possible that the yjbEFGH operon encodes a system involved in EPS secretion since none of the products is predicted to have enzymic activity, the products are all secreted and YbjF and H are predicted to be beta-barrel lipoproteins similar to porins. It may be that the operon products play some role in biofilm formation and/or matrix production [1]. [1]. 16030220. Identification of an Escherichia coli operon required for formation of the O-antigen capsule. Peleg A, Shifrin Y, Ilan O, Nadler-Yona C, Nov S, Koby S, Baruch K, Altuvia S, Elgrably-Weiss M, Abe CM, Knutton S, Saper MA, Rosenshine I;. J Bacteriol. 2005;187:5259-5266. [2]. 17379715. The yjbEFGH locus in Escherichia coli K-12 is an operon encoding proteins involved in exopolysaccharide production. Ferrieres L, Aslam SN, Cooper RM, Clarke DJ;. Microbiology. 2007;153:1070-1080. [3]. 21449614. Crystal structure of E. coli group 4 capsule protein GfcC reveals a domain organization resembling Wza. Sathiyamoorthy K, Mills E, Franzmann TM, Rosenshine I, Saper MA;. Biochemistry 2011;0:0-0. (from Pfam) NF022584.5 PF11134.13 Phage_stabilise 25 25 469 PfamEq Y Y N packaged DNA stabilization protein GO:0019073 1853558 1224 Pseudomonadota phylum 4255 EBI-EMBL Phage stabilisation protein packaged DNA stabilization protein Members of this family are phage proteins that are probably involved with stabilising the condensed DNA within the capsid [1]. [1]. 1853558. Nucleotide sequence of the bacteriophage P22 genes required for DNA packaging. Eppler K, Wyckoff E, Goates J, Parr R, Casjens S;. Virology. 1991;183:519-538. (from Pfam) NF022628.5 PF11180.13 DUF2968 27 27 180 domain Y Y N DUF2968 domain-containing protein 1224 Pseudomonadota phylum 2911 EBI-EMBL Protein of unknown function (DUF2968) Protein of unknown function (DUF2968) This family of proteins has no known function. (from Pfam) NF022638.5 PF11190.13 DUF2976 28.2 28.2 87 domain Y Y N DUF2976 domain-containing protein 1224 Pseudomonadota phylum 3294 EBI-EMBL Protein of unknown function (DUF2976) Protein of unknown function (DUF2976) This family of proteins has no known function. Some members are annotated as membrane proteins however this cannot be confirmed. (from Pfam) NF022645.5 PF11198.13 DUF2857 36.8 36.8 174 PfamEq Y Y N STY4526/YPO1902 family pathogenicity island replication protein 18281395,22247511 1224 Pseudomonadota phylum 4453 EBI-EMBL Protein of unknown function (DUF2857) STY4526/YPO1902 family pathogenicity island replication protein Members of this family (DUF2857) cited as a conserved component of a mobile pathogenicity islands include STY4526 from Salmonella typhi SPI-7 element and YPO1902 from the high pathogenicity island (HPI) of Yersinia pestis. STY4526 was assigned to the replication region, rather than the pilus region or transfer region. NF022662.5 PF11216.13 DUF3012 25 25 32 PfamAutoEq Y Y N DUF3012 domain-containing protein 1224 Pseudomonadota phylum 1315 EBI-EMBL Protein of unknown function (DUF3012) Protein of unknown function (DUF3012) This family of proteins with unknown function is restricted to Gammaproteobacteria. (from Pfam) NF022699.5 PF11254.13 DUF3053 23.9 23.9 219 subfamily Y Y N DUF3053 family protein 1224 Pseudomonadota phylum 3238 EBI-EMBL Protein of unknown function (DUF3053) DUF3053 family protein Some members in this family of proteins are annotated as the membrane protein YiaF. No function is currently known. (from Pfam) NF022722.5 PF11278.13 DUF3079 27 27 51 PfamAutoEq Y Y N DUF3079 domain-containing protein 1224 Pseudomonadota phylum 2371 EBI-EMBL Protein of unknown function (DUF3079) Protein of unknown function (DUF3079) This family of proteins with unknown function appears to be restricted to Proteobacteria. (from Pfam) NF022763.5 PF11319.13 VasI 26.5 26.5 184 subfamily Y Y N type VI secretion system-associated protein TagO 18289922,22184413 1224 Pseudomonadota phylum 5223 EBI-EMBL Type VI secretion system VasI, EvfG, VC_A0118 type VI secretion system-associated protein TagO VasI is a family of Gram-negative proteins that form part of the pathogenicity apparatus for bacteria-to-bacteria attack. The exact function of this com[onent is not known [1,2]. [1]. 18289922. Type VI secretion: a beginner's guide. Bingle LE, Bailey CM, Pallen MJ;. Curr Opin Microbiol. 2008;11:3-8. [2]. 22184413. Hcp family proteins secreted via the type VI secretion system coordinately regulate Escherichia coli K1 interaction with human brain microvascular endothelial cells. Zhou Y, Tao J, Yu H, Ni J, Zeng L, Teng Q, Kim KS, Zhao GP, Guo X, Yao Y;. Infect Immun. 2012;80:1243-1251. (from Pfam) NF022780.5 PF11336.13 DUF3138 27.3 27.3 525 subfamily Y Y N DUF3138 family protein 1224 Pseudomonadota phylum 1894 EBI-EMBL Protein of unknown function (DUF3138) DUF3138 family protein This family of proteins with unknown function appear to be restricted to Proteobacteria. (from Pfam) NF022798.5 PF11354.13 DUF3156 23 23 161 PfamAutoEq Y Y N DUF3156 family protein 1224 Pseudomonadota phylum 3658 EBI-EMBL Protein of unknown function (DUF3156) DUF3156 family protein This family of proteins with unknown function appears to be restricted to Proteobacteria. (from Pfam) NF022802.5 PF11358.13 DUF3158 27 27 156 subfamily Y Y N DUF3158 family protein 1224 Pseudomonadota phylum 3076 EBI-EMBL Protein of unknown function (DUF3158) DUF3158 family protein Some members in this family of proteins are annotated as integrase regulator R however this cannot be confirmed. This family of proteins with unknown function appear to be restricted to Proteobacteria. (from Pfam) NF022836.5 PF11394.13 DUF2875 24.7 24.7 166 domain Y Y N DUF2875 family protein 1224 Pseudomonadota phylum 4036 EBI-EMBL Protein of unknown function (DUF2875) N-terminal domain Protein of unknown function (DUF2875) N-terminal domain This family of proteins with unknown function appear to be restricted to Proteobacteria. This family appears to be related to the thiolase domain suggesting it is an enzyme. (from Pfam) NF022866.5 PF11426.13 Tn7_TnsC_Int 24.3 24.3 47 PfamEq Y N N Tn7 transposition regulator TnsC 15257292 1224 Pseudomonadota phylum 939 EBI-EMBL Tn7 transposition regulator TnsC Tn7 transposition regulator TnsC TnsC is a molecular switch that regulates transposition and interacts with TnsA which is a component of the transposase. The two proteins interact via the residues 504-555 on TnsC. The TnsA/TnsC interaction is very important in Tn7 transposition [1]. [1]. 15257292. The carboxy-terminal portion of TnsC activates the Tn7 transposase through a specific interaction with TnsA. Ronning DR, Li Y, Perez ZN, Ross PD, Hickman AB, Craig NL, Dyda F;. EMBO J. 2004;23:2972-2981. (from Pfam) NF022884.5 PF11444.13 DUF2895 22.6 22.6 198 subfamily Y Y N DUF2895 family protein 1224 Pseudomonadota phylum 4689 EBI-EMBL Protein of unknown function (DUF2895) DUF2895 family protein This is a bacterial family of uncharacterised proteins. (from Pfam) NF022954.5 PF11519.13 DUF3222 25 25 75 PfamAutoEq Y Y N DUF3222 family protein 1224 Pseudomonadota phylum 29 EBI-EMBL Protein of unknown function (DUF3222) DUF3222 family protein This family of proteins with unknown function appears to be restricted to Rhodopseudomonas. (from Pfam) NF022960.5 PF11525.13 CopK 23.8 23.8 70 domain Y Y N CopK family periplasmic copper-binding protein GO:0046872 18533181 1224 Pseudomonadota phylum 391 EBI-EMBL Copper resistance protein K CopK family periplasmic copper-binding protein CopK is a periplasmic dimeric protein which is strongly up-regulated in the presence of copper, leading to a high periplasmic accumulation [1]. CopK has two different binding sites for Cu(I), each with a different affinity for the metal. Binding of the first Cu(I) ion induces a conformational change of CopK which involves dissociation of the dimeric apo-protein. Binding of a second Cu(I) further increases the plasticity of the protein. CopK has features that are common with functionally related proteins such as a structure consisting of an all-beta fold and a methionine-rich Cu(I) binding site [1]. [1]. 18533181. Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. Bersch B, Favier A, Schanda P, van Aelst S, Vallaeys T, Coves J, Mergeay M, Wattiez R;. J Mol Biol. 2008;380:386-403. (from Pfam) NF023024.5 PF11592.13 AvrPto 27 27 105 PfamEq Y N N Central core of the bacterial effector protein AvrPto 15242602 1224 Pseudomonadota phylum 120 EBI-EMBL Central core of the bacterial effector protein AvrPto Central core of the bacterial effector protein AvrPto This family of proteins represents the bacterial effector protein AvrPto from Pseudomonas syringae. This is the central core region of the protein which consists of a three-helix bundle motif. AvrPto is part of a type III secretion system from P.syringae which is involved in the bacterial speck disease of tomato. In resistant plants, AvrPto interacts with the host Pto kinase, which elicits an antibacterial defense response. In plants lacking resistance, the Pto kinase is not present and AvrPto acts as a virulence factor, promoting bacterial growth [1]. [1]. 15242602. The solution structure of type III effector protein AvrPto reveals conformational and dynamic features important for plant pathogenesis. Wulf J, Pascuzzi PE, Fahmy A, Martin GB, Nicholson LK;. Structure. 2004;12:1257-1268. (from Pfam) NF023080.5 PF11650.13 P22_Tail-4 21 21 159 PfamEq Y Y N packaged DNA stabilization gp4 family protein 16970964 1224 Pseudomonadota phylum 1639 EBI-EMBL P22 tail accessory factor packaged DNA stabilization gp4 family protein This tail accessory factor of the P22 virus is also referred to as gene product 4 (Gp4). The proteins structure consists of 60% alpha helices. Gp4 is the first tail accessory factor to be added to newly DNA-filled capsids during P22-morphogenesis. In solution, the protein acts as a monomer and has low structural stability. The interaction of gp4 with the portal protein involves the binding of two non-equivalent sets of six gp4 proteins [1]. Gp4 acts as a structural adaptor for gp10 and gp26, the other tail accessory factors [1]. [1]. 16970964. Binding-induced stabilization and assembly of the phage P22 tail accessory factor gp4. Olia AS, Al-Bassam J, Winn-Stapley DA, Joss L, Casjens SR, Cingolani G;. J Mol Biol. 2006;363:558-576. (from Pfam) NF023088.5 PF11658.13 CBP_BcsG 24.8 24.8 516 PfamEq Y Y N cellulose biosynthesis protein BcsG bcsG 26077867,29348224,29348238,30017920,32152228 1224 Pseudomonadota phylum 8930 EBI-EMBL Cellulose biosynthesis protein BcsG cellulose biosynthesis protein BcsG CBP_BcsG is a component of bacterial cellulose synthase complex that plays a role in biofilm formation in bacteria [1]. It is a Zn(2+)-dependent phosphoethanolamine transferase that catalyses transfer of phosphoethanolamine residues from membrane phosphatidylethanolamine to the glucosyl residues in the nascent cellulose chain [2-5]. [1]. 26077867. Bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions. Romling U, Galperin MY;. Trends Microbiol. 2015;23:545-557. [2]. 29348238. Phosphoethanolamine cellulose: A naturally produced chemically modified cellulose. Thongsomboon W, Serra DO, Possling A, Hadjineophytou C, Hengge R, Cegelski L;. Science. 2018;359:334-338. [3]. 29348224. A bacterial coat that is not pure cotton. Galperin MY, Shalaeva DN;. Science. 2018;359:276-277. [4]. 30017920. Structural and Functional Characterization of the BcsG Subunit of the Cellulose Synthase in Salmonella typhimurium. Sun L, Vella P, Schnell R, Polyakova A, Bourenkov G, Li F, Cimdins A, Schneider TR, Lindqvist Y, Galperin MY, Schneider G, Romling U;. J Mol Biol. 2018;430:3170-3189. [5]. 32152228. The Escherichia coli cellulose synthase subunit G (BcsG) is a Zn(2+)-dependent phosphoethanolamine transferase. Anderson AC, Burnett AJN, Hiscock L, Maly KE, Weadge JT;. J Biol Chem. 2020;295:6225-6235. (from Pfam) NF023090.5 PF11660.13 DUF3262 27 27 76 subfamily Y Y N DUF3262 family protein 1224 Pseudomonadota phylum 2907 EBI-EMBL Protein of unknown function (DUF3262) DUF3262 family protein This family of proteins with unknown function appears to be restricted to Proteobacteria. (from Pfam) NF023107.5 PF11678.13 DUF3274 21 21 286 domain Y Y N DUF3274 domain-containing protein 1224 Pseudomonadota phylum 5850 EBI-EMBL Protein of unknown function (DUF3274) Protein of unknown function (DUF3274) This bacterial family of proteins has no known function. (from Pfam) NF023108.5 PF11679.13 DUF3275 25 25 201 subfamily Y Y N DUF3275 family protein 1224 Pseudomonadota phylum 2094 EBI-EMBL Protein of unknown function (DUF3275) DUF3275 family protein This family of proteins with unknown function appear to be restricted to Proteobacteria. (from Pfam) NF023153.5 PF11725.13 AvrE_T3Es 24 24 1513 PfamEq Y Y N AvrE-family type 3 secretion system effector 17022173,23421848,27191168,9555912 1224 Pseudomonadota phylum 2047 EBI-EMBL AvrE-family Type-III effector proteins (T3Es) AvrE-family type 3 secretion system effector This family is secreted by gram-negative Gammaproteobacteria such as Pseudomonas syringae of tomato and the fire blight plant pathogen Erwinia amylovora, amongst others. It is an essential pathogenicity factor of approximately 198 kDa. Its injection into the host-plant is dependent upon the bacterial type III or Hrp secretion system [1]. The family is long and carries a number of predicted functional regions, including in Erwinia stewartii (Swiss:Q9FCY7) an ERMS or endoplasmic reticulum membrane retention signal at both the C- and the N-termini, a leucine-zipper motif from residues 539-560, and a nuclear localisation signal at 1358-1361. this conserved AvrE-family of effectors is among the few that are required for full virulence of many phytopathogenic pseudomonads, erwinias and pantoeas [2]. A double beta-propeller structure is found towards the N-terminus [3]. Furthermore, AvrE1, an AvrE-family T3E from Pseudomonas syringae pv. tomato strain DC3000, associates with specific PP2A B- subunit proteins from its susceptible host Arabidopsis. In a similar fashion, the WtsE (AvrE-family T3E from the maize pathogen Pantoea stewartii subsp. Stewartii) has been shown to target maize protein phosphatase 2A (PP2A) heterotrimeric enzyme complexes via direct interaction with B- regulatory subunits. Taken together, it has been indicated that that sub-component specific PP2A complexes are targeted by bacterial T3Es, including direct targeting by members of the widely conserved AvrE-family. Additionally, DspE, a type-III effector encoded by the broad-host-range bacterial soft-rot pathogen Pectobacterium carotovorum subsp. carotovorum (. TRUNCATED at 1650 bytes (from Pfam) NF023236.5 PF11808.13 PhoR 27.1 27.1 86 PfamAutoEq Y Y N phosphate regulon sensor protein PhoR GO:0000155,GO:0000160,GO:0004721 24563032 1224 Pseudomonadota phylum 15202 EBI-EMBL Phosphate regulon sensor protein PhoR phosphate regulon sensor protein PhoR This family is only found in bacteria. Family members include PhoR. A member of the two-component regulatory system PhoR/PhoB involved in the phosphate regulon genes expression. PhoR is the bifunctional histidine autokinase/phospho-PhoB phosphatase that donates a phosphoryl group to PhoB when environmental Pi is limiting and removes the phosphoryl group from phosphorylated PhoB (PhoB-P) when environmental Pi is abundant [1]. [1]. 24563032. The PhoU protein from Escherichia coli interacts with PhoR, PstB, and metals to form a phosphate-signaling complex at the membrane. Gardner SG, Johns KD, Tanner R, McCleary WR;. J Bacteriol. 2014;196:1741-1752. (from Pfam) NF023243.5 PF11815.13 DUF3336 25 25 138 PfamAutoEq Y Y N DUF3336 domain-containing protein GO:0004806,GO:0006629 1224 Pseudomonadota phylum 1940 EBI-EMBL Domain of unknown function (DUF3336) Domain of unknown function (DUF3336) This family of proteins are functionally uncharacterised. This family is found in bacteria and eukaryotes. This presumed domain is typically between 143 to 227 amino acids in length. (from Pfam) NF023290.5 PF11862.13 DUF3382 28.9 28.9 97 domain Y Y N DUF3382 domain-containing protein 1224 Pseudomonadota phylum 13935 EBI-EMBL Domain of unknown function (DUF3382) Domain of unknown function (DUF3382) This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 100 amino acids in length. This domain is found associated with Pfam:PF02653. (from Pfam) NF023293.5 PF11865.13 mTOR_dom 27.6 27.6 160 domain Y Y N mTOR domain-containing protein 12408816,27909983,29236692,31112131,31601708,32561715,34519269,36533617 1224 Pseudomonadota phylum 2 EBI-EMBL Serine/threonine-protein kinase mTOR domain Serine/threonine-protein kinase mTOR domain This entry represents a domain found in human serine/threonine-protein kinase mTOR and its homologues, a central regulator of cellular metabolism, growth and survival in response to hormones, growth factors, nutrients, energy and stress signals [1-5]. In Saccharomyces cerevisiae, the TOR proteins, TOR1 and TOR2, regulate growth in a rapamycin-sensitive manner [6]. This domain consists of HEAT repeats [7,8]. [1]. 31112131. GPCR signaling inhibits mTORC1 via PKA phosphorylation of Raptor. Jewell JL, Fu V, Hong AW, Yu FX, Meng D, Melick CH, Wang H, Lam WM, Yuan HX, Taylor SS, Guan KL;. Elife. 2019;8:e43038. [2]. 31601708. Structural basis for the docking of mTORC1 on the lysosomal surface. Rogala KB, Gu X, Kedir JF, Abu-Remaileh M, Bianchi LF, Bottino AMS, Dueholm R, Niehaus A, Overwijn D, Fils AP, Zhou SX, Leary D, Laqtom NN, Brignole EJ, Sabatini DM;. Science. 2019;366:468-475. [3]. 32561715. Leucine regulates autophagy via acetylation of the mTORC1 component raptor. Son SM, Park SJ, Stamatakou E, Vicinanza M, Menzies FM, Rubinsztein DC;. Nat Commun. 2020;11:3148. [4]. 34519269. Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace. Heimhalt M, Berndt A, Wagstaff J, Anandapadamanaban M, Perisic O, Maslen S, McLaughlin S, Yu CW, Masson GR, Boland A, Ni X, Yamashita K, Murshudov GN, Skehel M, Freund SM, Williams RL;. Elife. 2021;10:e68799. [5]. 29236692. Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40. Yang H, Jiang X, Li B, Yang HJ, Miller M, Yang A, Dhar A, Pavletich NP;. Nature. 2017;552:368-373. [6]. 12408816. Two TOR complexes, only one of which is rapamycin s. TRUNCATED at 1650 bytes (from Pfam) NF023312.5 PF11884.13 DUF3404 25 25 259 domain Y Y N DUF3404 domain-containing protein 1224 Pseudomonadota phylum 2735 EBI-EMBL Domain of unknown function (DUF3404) Domain of unknown function (DUF3404) This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 260 amino acids in length. This domain is found associated with Pfam:PF02518, Pfam:PF00512. (from Pfam) NF023320.5 PF11892.13 PpnN_C 25 25 121 PfamAutoEq Y Y N pyrimidine/purine nucleotide monophosphate nucleosidase domain-containing protein 27941785,31023582 1224 Pseudomonadota phylum 9482 EBI-EMBL Pyrimidine/purine nucleotide monophosphate nucleosidase, C-terminal Pyrimidine/purine nucleotide monophosphate nucleosidase, C-terminal This domain is found at the C-terminal end of Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase from Escherichia coli (PpnN, also known as YgdH) and similar proteins mainly found in gammaproteobacteria. PpnN is a nucleosidase that catalyses the hydrolysis of the N-glycosidic bond of diverse pyrimidine and purine nucleotide 5'-monophosphates. The binding of (p)ppGpp, an alarmone molecule that plays a role in the bacterial stringent response, gives rise to a large conformational change in the terminal region that leads to the exposure of the catalytic pocket. This domain shows a completely alpha-helical fold with an extension that wraps around the central domain [1, 2]. [1]. 31023582. (p)ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch. Zhang YE, Baerentsen RL, Fuhrer T, Sauer U, Gerdes K, Brodersen DE;. Mol Cell. 2019;74:1239-1249. [2]. 27941785. Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli. Sevin DC, Fuhrer T, Zamboni N, Sauer U;. Nat Methods. 2017;14:187-194. (from Pfam) NF023347.5 PF11920.13 DUF3438 25 25 286 subfamily Y Y N DUF3438 family protein 1224 Pseudomonadota phylum 6556 EBI-EMBL Protein of unknown function (DUF3438) DUF3438 family protein This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 276 to 307 amino acids in length. (from Pfam) NF023365.5 PF11939.13 NiFe-hyd_HybE 25 25 147 PfamEq Y Y N [NiFe]-hydrogenase assembly chaperone HybE hybE 19636963 1224 Pseudomonadota phylum 4452 EBI-EMBL [NiFe]-hydrogenase assembly, chaperone, HybE [NiFe]-hydrogenase assembly chaperone HybE Members of this family are chaperones for the assembly of [NiFe] hydrogenases, in the family of HybE, which is specific for hydrogenase-2 of Escherichia coli. Members often have an additional N-terminal rubredoxin domain [1]. [1]. 19636963. 1H, 13C and 15N resonance assignments of the chaperone HybE of hydrogenase-2 from Escherichia coli. Shao X, Lu J, Xia B, Jin C;. Biomol NMR Assign. 2009;3:129-131. (from Pfam) NF023416.5 PF11990.13 DUF3487 27.8 27.8 114 subfamily Y Y N DUF3487 family protein 1224 Pseudomonadota phylum 3920 EBI-EMBL Protein of unknown function (DUF3487) DUF3487 family protein This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 121 to 136 amino acids in length. This protein has a conserved RLN sequence motif. (from Pfam) NF023508.5 PF12086.13 DUF3563 26.9 26.9 61 domain Y Y N DUF3563 family protein 1224 Pseudomonadota phylum 1427 EBI-EMBL Protein of unknown function (DUF3563) DUF3563 family protein This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 50 amino acids in length. This protein has conserved AYL and DLE sequence motifs. (from Pfam) NF023513.5 PF12091.13 DUF3567 25 25 89 PfamEq Y Y N DUF3567 family protein 25786241 1224 Pseudomonadota phylum 1473 EBI-EMBL Protein of unknown function (DUF3567) DUF3567 family protein This family of proteins is functionally uncharacterised, but loss of member protein BTH_I0359 in a strain of Burkholderia pseudomallei conferred resistance to a contact-dependent growth inhibition (CDI) system. Members are about 90 amino acids in length. NF023523.5 PF12101.13 DUF3577 25 25 133 domain Y Y N DUF3577 domain-containing protein 1224 Pseudomonadota phylum 4280 EBI-EMBL Protein of unknown function (DUF3577) Protein of unknown function (DUF3577) This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 143 to 307 amino acids in length. (from Pfam) NF023592.5 PF12170.13 DNA_pol3_tau_5 28.8 28.8 142 domain Y Y N DNA polymerase III subunit gamma/tau C-terminal domain-containing protein GO:0003887 11078743,17355988,18344346 1224 Pseudomonadota phylum 29480 EBI-EMBL DNA polymerase III tau subunit V interacting with alpha DNA polymerase III tau subunit V interacting with alpha This domain family is found in bacteria, and is approximately 140 amino acids in length. The family is found in association with Pfam:PF00004. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. The extreme C-terminal region of this domain 5 is the part which interacts with the alpha subunit of the DNA polymerase III holoenzyme. [1]. 11078743. tau binds and organizes Escherichia coli replication through distinct domains. Partial proteolysis of terminally tagged tau to determine candidate domains and to assign domain V as the alpha binding domain. Gao D, McHenry CS;. J Biol Chem. 2001;276:4433-4440. [2]. 17355988. The unstructured C-terminus of the tau subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the alpha subunit. Jergic S, Ozawa K, Williams NK, Su XC, Scott DD, Hamdan SM, Crowther JA, Otting G, Dixon NE;. Nucleic Acids Res. 2007;35:2813-2824. [3]. 18344346. Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1. Dick GJ, Podell S, Johnson HA, Rivera-Espinoza Y, Bernier-Latmani R, McCarthy JK, Torpey JW, Clement BG, Gaasterland T, Tebo BM;. Appl Environ Microbiol. 2008;74:2646-2658. (from Pfam) NF023639.5 PF12218.13 End_N_terminal 26.3 26.3 67 domain Y N N N terminal extension of bacteriophage endosialidase 15608653 1224 Pseudomonadota phylum 614 EBI-EMBL N terminal extension of bacteriophage endosialidase N terminal extension of bacteriophage endosialidase This domain family is found in bacteria and viruses, and is approximately 70 amino acids in length. This domain is found in the bacteriophage protein endosialidase. The two N-terminal domains (this domain and the beta propeller) assemble in the compact 'cap' whereas the C-terminal domain forms an extended tail-like structure. The very N-terminal part of the 'cap' region (residues 246 to 312) holds the only alpha-helix of the protein and is presumably the residual part of the deleted N-terminal head-binding domain. The endosialidase protein complexes to form homotrimeric molecules. [1]. 15608653. Crystal structure of the polysialic acid-degrading endosialidase of bacteriophage K1F. Stummeyer K, Dickmanns A, Muhlenhoff M, Gerardy-Schahn R, Ficner R;. Nat Struct Mol Biol. 2005;12:90-96. (from Pfam) NF023642.5 PF12221.13 HflK_N 22 22 44 PfamEq Y Y N protease modulator HflK N-terminal domain-containing protein 8248183 1224 Pseudomonadota phylum 15460 EBI-EMBL Bacterial membrane protein N terminal Bacterial membrane protein N terminal This domain is found in bacteria. This domain is typically between 65 to 81 amino acids in length. This domain is found associated with Pfam:PF01145. This domain is the N terminal of the bacterial membrane protein HflK. HflK complexes with HflC to form a membrane protease which is modulated by the GTPase HflX. The N terminal domain of HflK is the membrane spanning region which anchors the protein in the bacterial membrane. [1]. 8248183. The Escherichia coli hflA locus encodes a putative GTP-binding protein and two membrane proteins, one of which contains a protease-like domain. Noble JA, Innis MA, Koonin EV, Rudd KE, Banuett F, Herskowitz I;. Proc Natl Acad Sci U S A. 1993;90:10866-10870. (from Pfam) NF023687.5 PF12266.13 DUF3613 25 25 66 PfamAutoEq Y Y N DUF3613 domain-containing protein 1224 Pseudomonadota phylum 4300 EBI-EMBL Protein of unknown function (DUF3613) Protein of unknown function (DUF3613) This family of proteins is found in bacteria. Proteins in this family are typically between 94 and 126 amino acids in length. (from Pfam) NF023689.5 PF12268.13 DUF3612 25 25 176 PfamAutoEq Y Y N DUF3612 domain-containing protein 1224 Pseudomonadota phylum 1531 EBI-EMBL Protein of unknown function (DUF3612) Protein of unknown function (DUF3612) This domain family is found in bacteria, and is approximately 180 amino acids in length. The family is found in association with Pfam:PF01381. (from Pfam) NF023712.5 PF12292.13 DUF3624 27 27 76 PfamAutoEq Y Y N DUF3624 family protein 1224 Pseudomonadota phylum 1396 EBI-EMBL Protein of unknown function (DUF3624) DUF3624 family protein This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved GRC sequence motif. (from Pfam) NF023861.5 PF12445.13 FliC 23.2 23.2 127 PfamEq Y N N Flagellin protein 8877129 1224 Pseudomonadota phylum 1755 EBI-EMBL Flagellin protein Flagellin protein This domain family is found in bacteria, and is typically between 125 and 147 amino acids in length. The family is found in association with Pfam:PF00669, Pfam:PF00700. There are two completely conserved G residues that may be functionally important. This family is the flagellin motor protein which confers motility to bacterial cells. [1]. 8877129. Mapping of the H7-serospecific domain of Escherichia coli flagellin. Kwang J, Wilson R, Yang S, He Y;. Clin Diagn Lab Immunol. 1996;3:523-526. (from Pfam) NF023893.5 PF12477.13 TraW_N 22.7 22.7 30 domain Y N N Sex factor F TraW protein N terminal 1355084 1224 Pseudomonadota phylum 2638 EBI-EMBL Sex factor F TraW protein N terminal Sex factor F TraW protein N terminal This domain family is found in bacteria, and is approximately 30 amino acids in length. There is a single completely conserved residue G that may be functionally important. The traW gene of the E. coli K-12 sex factor, F, encodes one of the numerous proteins required for conjugative transfer of this plasmid. [1]. 1355084. Characterization, localization, and sequence of F transfer region products: the pilus assembly gene product TraW and a new product, TrbI. Maneewannakul S, Maneewannakul K, Ippen-Ihler K;. J Bacteriol. 1992;174:5567-5574. (from Pfam) NF023898.5 PF12482.13 DUF3701 26.9 26.9 93 domain Y Y N phage integrase family protein 1224 Pseudomonadota phylum 4659 EBI-EMBL Phage integrase protein phage integrase family protein This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with Pfam:PF00589. (from Pfam) NF023967.5 PF12553.13 DUF3742 27.2 27.2 120 subfamily Y Y N DUF3742 family protein 1224 Pseudomonadota phylum 1780 EBI-EMBL Protein of unknown function (DUF3742) DUF3742 family protein This domain family is found in bacteria, and is approximately 50 amino acids in length. There is a single completely conserved residue Y that may be functionally important. (from Pfam) NF023977.5 PF12563.13 Hemolysin_N 22.5 22.5 192 domain Y Y N hemolysin N-terminal domain-containing protein 12479411 1224 Pseudomonadota phylum 1104 EBI-EMBL Hemolytic toxin N terminal Hemolytic toxin N terminal This domain family is found in bacteria, and is approximately 190 amino acids in length. The family is found in association with Pfam:PF07968, Pfam:PF00652. This family is a bacterial virulence factor - hemolysin - which forms pores in erythrocytes and causes them to lyse. [1]. 12479411. Purification, characterization and molecular cloning of Vibrio fluvialis hemolysin. Han JH, Lee JH, Choi YH, Park JH, Choi TJ, Kong IS;. Biochim Biophys Acta. 2002;1599:106-114. (from Pfam) NF023996.5 PF12582.13 DUF3757 23 23 125 domain Y Y N DUF3757 domain-containing protein 1224 Pseudomonadota phylum 1168 EBI-EMBL Protein of unknown function (DUF3757) Protein of unknown function (DUF3757) This family of proteins is found in bacteria. Proteins in this family are typically between 94 and 154 amino acids in length. (from Pfam) NF024029.5 PF12615.13 TraD_N 25 25 92 domain Y Y N TraD N-terminal domain-containing protein 2680768 1224 Pseudomonadota phylum 10966 EBI-EMBL F sex factor protein N terminal F sex factor protein N terminal This domain family is found in bacteria, and is typically between 96 and 107 amino acids in length. The family is found in association with Pfam:PF10412. TraD is a cytoplasmic membrane protein with possible DNA binding domains. It is part of the bacterial F sex factor complex. [1]. 2680768. Nucleotide sequence of the traD region in the Escherichia coli F sex factor. Jalajakumari MB, Manning PA;. Gene. 1989;81:195-202. (from Pfam) NF024202.5 PF12792.12 CSS-motif 23 23 209 domain Y Y N CSS-motif domain-containing protein 29514851 1224 Pseudomonadota phylum 41895 EBI-EMBL CSS motif domain associated with EAL CSS motif domain associated with EAL This domain, with its characteristic highly conserved CSS sequence motif, is found N-terminal to the EAL (Pfam:PF00563) domain in many cyclic diguanylate phosphodiesterases, such as PdeB/C/D/G/N from E. coli K-12 [1]. It has two highly conserved cysteine residues with potential disulfide bond formation, which might control the enzymatic activity of the cytoplasmic C-terminal EAL domain [1]. [1]. 29514851. Transmembrane redox control and proteolysis of PdeC, a novel type of c-di-GMP phosphodiesterase. Herbst S, Lorkowski M, Sarenko O, Nguyen TKL, Jaenicke T, Hengge R;. EMBO J. 2018; [Epub ahead of print] (from Pfam) NF024287.5 PF12883.12 DUF3828 26 14 125 domain Y Y N DUF3828 domain-containing protein 1224 Pseudomonadota phylum 8640 EBI-EMBL Protein of unknown function (DUF3828) Protein of unknown function (DUF3828) This is a family of bacterial proteins of unknown function. (from Pfam) NF024625.5 PF13227.11 DUF4035 22.1 22.1 55 domain Y Y N DUF4035 domain-containing protein 1224 Pseudomonadota phylum 2751 EBI-EMBL Protein of unknown function (DUF4035) Protein of unknown function (DUF4035) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 67 and 93 amino acids in length. (from Pfam) NF024679.5 PF13283.11 NfrA_C 25 25 173 domain Y Y N NfrA family protein 8226648,8226649 1224 Pseudomonadota phylum 6515 EBI-EMBL Bacteriophage N adsorption protein A C-term NfrA family protein The function of this domain is unknown but it is found at the C-terminus of bacteriophage N4 adsorption protein A, in association with an N-terminal region of TPR repeats. (from Pfam) NF024680.5 PF13284.11 DUF4072 24.6 24.6 46 PfamAutoEq Y Y N DUF4072 domain-containing protein 1224 Pseudomonadota phylum 1726 EBI-EMBL Domain of unknown function (DUF4072) Domain of unknown function (DUF4072) This short domain is normally found at the very N-terminus of Hyrdrolases Pfam:PF00702. (from Pfam) NF025003.5 PF13617.11 Lipoprotein_19 25.8 25.8 34 PfamEq Y Y N YnbE family lipoprotein 1224 Pseudomonadota phylum 4469 EBI-EMBL YnbE-like lipoprotein YnbE family lipoprotein This family includes lipoproteins similar to E. coli YnbE Swiss:P64448. Protein in this family are typically 60 amino acids in length and contain an N-terminal lipid attachment site, which has been included in the alignment to increase sensitivity. The specific function of these proteins is unknown. (from Pfam) NF025045.5 PF13663.11 DUF4148 27 27 62 domain Y Y N DUF4148 domain-containing protein 1224 Pseudomonadota phylum 23572 EBI-EMBL Domain of unknown function (DUF4148) Domain of unknown function (DUF4148) NF025098.5 PF13721.11 SecD-TM1 30.5 30.5 103 domain Y N N SecD export protein N-terminal TM region 16452406,8428584 1224 Pseudomonadota phylum 21391 EBI-EMBL SecD export protein N-terminal TM region SecD export protein N-terminal TM region This domain appears to be the fist transmembrane region of the SecD export protein. SecD is directly involved in protein secretion and important for the release of proteins that have been translocated across the cytoplasmic membrane. [1]. 16452406. Archaeal and bacterial SecD and SecF homologs exhibit striking structural and functional conservation. Hand NJ, Klein R, Laskewitz A, Pohlschroder M;. J Bacteriol. 2006;188:1251-1259. [2]. 8428584. SecD is involved in the release of translocated secretory proteins from the cytoplasmic membrane of Escherichia coli. Matsuyama S, Fujita Y, Mizushima S;. EMBO J. 1993;12:265-270. (from Pfam) NF025319.5 PF13953.11 PapC_C 27 27 66 domain Y Y N FimD/PapC C-terminal domain-containing protein 20118254 1224 Pseudomonadota phylum 128205 EBI-EMBL PapC C-terminal domain PapC C-terminal domain The PapC C-terminal domain is a structural domain found at the C-terminus of the E. coli PapC protein. Pili are assembled using the chaperone usher system. In E.coli this is composed of the chaperone PapD and the usher PapC. This domain represents the C-terminal domain from PapC and its homologues. This domain has a beta-sandwich structure similar to the plug domain of PapC [1]. [1]. 20118254. Structural homology between the C-terminal domain of the PapC usher and its plug. Ford B, Rego AT, Ragan TJ, Pinkner J, Dodson K, Driscoll PC, Hultgren S, Waksman G;. J Bacteriol. 2010;192:1824-1831. (from Pfam) NF025320.5 PF13954.11 PapC_N 27 27 146 domain Y Y N FimD/PapC N-terminal domain-containing protein GO:0005515 15920478 1224 Pseudomonadota phylum 119490 EBI-EMBL PapC N-terminal domain PapC N-terminal domain The PapC N-terminal domain is a structural domain found at the N-terminus of the E. coli PapC protein. Pili are assembled using the chaperone usher system. In E.coli this is composed of the chaperone PapD and the usher PapC. This domain represents the N-terminal domain from PapC and its homologues. This domain is involved in substrate binding [1]. [1]. 15920478. Structural basis of chaperone-subunit complex recognition by the type 1 pilus assembly platform FimD. Nishiyama M, Horst R, Eidam O, Herrmann T, Ignatov O, Vetsch M, Bettendorff P, Jelesarov I, Grutter MG, Wuthrich K, Glockshuber R, Capitani G;. EMBO J. 2005;24:2075-2086. (from Pfam) NF025621.5 PF14263.11 DUF4354 25.5 25.5 123 PfamAutoEq Y Y N DUF4354 family protein 1224 Pseudomonadota phylum 642 EBI-EMBL Domain of unknown function (DUF4354) DUF4354 family protein Several members of this family are annotated as being ATP/GTP-binding site motif A (P-loop) proteins, but this could not be confirmed. The one PDB:3NRF structure solved for this family exhibits an immunoglobin-like beta-sandwich fold. Crystal packing suggests that a tetramer is a significant oligomerisation state, and a disulfide bridge is formed between Cys 125 at the C-terminal end of the monomer, and Cys 69. (from Pfam) NF025706.5 PF14348.11 DUF4400 27 27 196 domain Y Y N DUF4400 domain-containing protein 1224 Pseudomonadota phylum 7849 EBI-EMBL Domain of unknown function (DUF4400) Domain of unknown function (DUF4400) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 209 and 249 amino acids in length. There is a single completely conserved residue P that may be functionally important. (from Pfam) NF025818.5 PF14463.11 E1-N 27 27 151 domain Y N N E1 N-terminal domain 16859499 1224 Pseudomonadota phylum 79 EBI-EMBL E1 N-terminal domain E1 N-terminal domain An uncharacterised alpha/beta domain fused to E1 proteins. This protein is usually present in gene neighbourhoods with genes encoding a JAB protein and a predicted metal-binding protein. In related E1 proteins, the E1-N domain is replaced by an E2/UBC superfamily domain [1]. [1]. 16859499. The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. Iyer LM, Burroughs AM, Aravind L;. Genome Biol. 2006;7:R60. (from Pfam) NF026068.5 PF14718.11 SLT_L 25 25 68 PfamEq Y N N Soluble lytic murein transglycosylase L domain GO:0004553,GO:0042597 10452894 1224 Pseudomonadota phylum 21471 EBI-EMBL Soluble lytic murein transglycosylase L domain Soluble lytic murein transglycosylase L domain Soluble lytic murein transglycosylase (SLT) consists of three domains, an N-terminal U domain, an L domain (linker domain) and a C-terminal domain (C). The L domain may be involved in the interaction of the enzyme with peptidoglycan [1]. [1]. 10452894. High resolution crystal structures of the Escherichia coli lytic transglycosylase Slt70 and its complex with a peptidoglycan fragment. van Asselt EJ, Thunnissen AM, Dijkstra BW;. J Mol Biol. 1999;291:877-898. (from Pfam) NF026143.5 PF14793.11 DUF4478 25 25 109 PfamAutoEq Y Y N pyrimidine/purine nucleosidase domain-containing protein 27941785 1224 Pseudomonadota phylum 9426 EBI-EMBL Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases This is an N-terminal domain found in pyrimidine/purine nucleotide 5'-monophosphate nucleosidases (PpnN) in bacteria. PpnN catalyzes the hydrolysis of the N-glycosidic bond of diverse pyrimidine and purine nucleotide 5'-monophosphates, to form ribose 5-phosphate and the corresponding free base. It can use AMP, GMP, IMP, CMP, dTMP and UMP as substrates [1]. It is found in association with Pfam:PF03641 and Pfam:PF11892. [1]. 27941785. Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli. Sevin DC, Fuhrer T, Zamboni N, Sauer U;. Nat Methods. 2017;14:187-194. (from Pfam) NF026184.5 PF14834.11 GST_C_4 30 30 117 PfamEq Y N N Glutathione S-transferase, C-terminal domain 9680481 1224 Pseudomonadota phylum 5774 EBI-EMBL Glutathione S-transferase, C-terminal domain Glutathione S-transferase, C-terminal domain GST conjugates reduced glutathione to a variety of targets including S-crystallin from squid, the eukaryotic elongation factor 1-gamma, the HSP26 family of stress-related proteins and auxin-regulated proteins in plants. Stringent starvation proteins in E. coli are also included in the alignment but are not known to have GST activity. The glutathione molecule binds in a cleft between N and C-terminal domains. The catalytically important residues are proposed to reside in the N-terminal domain [1]. [1]. 9680481. Three-dimensional structure of Escherichia coli glutathione S-transferase complexed with glutathione sulfonate: catalytic roles of Cys10 and His106. Nishida M, Harada S, Noguchi S, Satow Y, Inoue H, Takahashi K;. J Mol Biol 1998;281:135-147. (from Pfam) NF026209.5 PF14859.11 Colicin_M 27 27 281 subfamily Y Y N lipid II-degrading bacteriocin GO:0042742 16777846 1224 Pseudomonadota phylum 981 EBI-EMBL Colicin M lipid II-degrading bacteriocin Colicin M is a toxin produced by, and active against, Escherichia coli. It catalyses the hydrolysis of lipid I and lipid II peptidoglycan intermediates, therefore inhibiting peptidoglycan biosynthesis and leading to lysis of the bacterial cells [1]. [1]. 16777846. Colicin M exerts its bacteriolytic effect via enzymatic degradation of undecaprenyl phosphate-linked peptidoglycan precursors. El Ghachi M, Bouhss A, Barreteau H, Touze T, Auger G, Blanot D, Mengin-Lecreulx D;. J Biol Chem. 2006;281:22761-22772. (from Pfam) NF026233.5 PF14883.11 GHL13 27 27 324 domain Y Y N poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB 20556855,21954604,22295578 1224 Pseudomonadota phylum 11640 EBI-EMBL Hypothetical glycosyl hydrolase family 13 poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB GHL13 is a family of hypothetical glycoside hydrolases. [1]. 20556855. Gh101 family of glycoside hydrolases: subfamily structure and evolutionary connections with other families. Naumoff DG;. J Bioinform Comput Biol. 2010;8:437-451. [2]. 21954604. [Endo-alpha-1-4-polygalactosaminidases and their homologues: structure and evolution]. Naumov DG, Stepushchenko OO;. Mol Biol (Mosk). 2011;45:703-714. [3]. 22295578. [GHL1-GHL15: new families of hypothetical glycoside hydrolases]. Naumov DG;. Mol Biol (Mosk). 2011;45:1073-1083. (from Pfam) NF026278.5 PF14928.11 S_tail_recep_bd 23.8 23.8 93 PfamEq Y N N Short tail fibre protein receptor-binding domain GO:0046872 12888344 1224 Pseudomonadota phylum 91 EBI-EMBL Short tail fibre protein receptor-binding domain Short tail fibre protein receptor-binding domain This domain is a receptor binding domain found on bacteriophage short tail fibre proteins. It contains a zinc-binding site and a potential lipopolysaccharide-binding site [1]. [1]. 12888344. The structure of the receptor-binding domain of the bacteriophage T4 short tail fibre reveals a knitted trimeric metal-binding fold. Thomassen E, Gielen G, Schutz M, Schoehn G, Abrahams JP, Miller S, van Raaij MJ;. J Mol Biol 2003;331:361-373. (from Pfam) NF026742.5 PF15401.11 TAA-Trp-ring 25.8 17.3 66 domain Y N N Tryptophan-ring motif of head of Trimeric autotransporter adhesin 18397894,18948113,20862217,21557062 1224 Pseudomonadota phylum 546 EBI-EMBL Tryptophan-ring motif of head of Trimeric autotransporter adhesin Tryptophan-ring motif of head of Trimeric autotransporter adhesin TAA-head_Trp-ring is the tryptophan-ring motif of some Gram-negative Enterobacteriaceae. The Trp-ring folds into a beta-meander type on the top of the head domain of its trimeric autotransporter adhesin proteins. In conjunction with the GIN domain it is thought to be the region of the head that adheres to fibronectin. [1]. 18948113. Repetitive architecture of the Haemophilus influenzae Hia trimeric autotransporter. Meng G, St Geme JW 3rd, Waksman G;. J Mol Biol. 2008;384:824-836. [2]. 18397894. Domain annotation of trimeric autotransporter adhesins--daTAA. Szczesny P, Lupas A;. Bioinformatics. 2008;24:1251-1256. [3]. 20862217. Structure of a Burkholderia pseudomallei trimeric autotransporter adhesin head. Edwards TE, Phan I, Abendroth J, Dieterich SH, Masoudi A, Guo W, Hewitt SN, Kelley A, Leibly D, Brittnacher MJ, Staker BL, Miller SI, Van Voorhis WC, Myler PJ, Stewart LJ;. PLoS One. 2010; [Epub ahead of print]. [4]. 21557062. Structure and biology of trimeric autotransporter adhesins. Lyskowski A, Leo JC, Goldman A;. Adv Exp Med Biol. 2011;715:143-158. (from Pfam) NF026744.5 PF15403.11 HiaBD2 25 25 52 subfamily_domain Y Y N Hia/Hsf adhesin N-terminal domain-containing protein 18948113,20862217 1224 Pseudomonadota phylum 202 EBI-EMBL HiaBD2_N domain of Trimeric autotransporter adhesin (GIN) Hia/Hsf adhesin N-terminal domain HiaBD2_N may represent the GIN domain of the Head region of TAAs - trimeric autotransporter adhesins. Not all TAAs carry this domain; however, in those that do, the GIN in combination with the Trp-ring domain is necessary for adhesion to fibronectin in the host cell. [1]. 18948113. Repetitive architecture of the Haemophilus influenzae Hia trimeric autotransporter. Meng G, St Geme JW 3rd, Waksman G;. J Mol Biol. 2008;384:824-836. [2]. 20862217. Structure of a Burkholderia pseudomallei trimeric autotransporter adhesin head. Edwards TE, Phan I, Abendroth J, Dieterich SH, Masoudi A, Guo W, Hewitt SN, Kelley A, Leibly D, Brittnacher MJ, Staker BL, Miller SI, Van Voorhis WC, Myler PJ, Stewart LJ;. PLoS One. 2010; [Epub ahead of print] (from Pfam) NF026940.5 PF15602.11 Imm71 27 27 158 domain Y Y N Imm71 family immunity protein 22731697 1224 Pseudomonadota phylum 1769 EBI-EMBL Immunity protein 71 Imm71 family immunity protein A predicted immunity protein with a mostly alpha-helical fold and conserved arginine and phenylalanine residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Ntox48 family [1]. This domain is often fused to the Imm72 immunity domain. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF026994.5 PF15658.11 Latrotoxin_C 25 25 137 domain Y Y N latrotoxin-related protein 22731697 1224 Pseudomonadota phylum 522 EBI-EMBL Latrotoxin C-terminal domain Latrotoxin C-terminal domain A toxin domain present in arthropod alphaproteobacterial, gammaproteobacterial endosymbionts and also at the C-termini of the latrotoxins of the black widow spider. The domain is characterised by a conserved, hydrophobic helix and is predicted to associate with the cell membrane [1]. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam). Members of this family contain a domain related to the alpha-latrotoxin from the black widow spider, and are found regularly as large proteins in the Wolbachia bacterial endosymbionts of insects and other other arthropods. NF027197.5 PF15864.10 PglL_A 25 25 26 PfamEq Y Y N pilin glycosylation ligase domain-containing protein 16870136,23658772 1224 Pseudomonadota phylum 11825 EBI-EMBL Protein glycosylation ligase Protein glycosylation ligase PglL_A is a pilin glycosylation ligase domain found in Gram negative bacteria [1]. PglL protein O-oligosaccharyltransferases differ from the wider Wzy_C family, Pfam:PF04932, which contains both WaaL O-antigen ligases, in its substrate-specificity. PglL O-oligosaccharyltransferases (O-OTase) transfer oligosaccharide to serine or threonine in a protein. A further indication that the genes identified are PglL rather than WaaL homologues is that they are not located within lipopolysaccharide biosynthetic loci [2]. The specific pilin glycosylation ligases are a subset of the more general bacterial protein o-oligosaccharyltransferases [2]. [1]. 16870136. Pilin glycosylation in Neisseria meningitidis occurs by a similar pathway to wzy-dependent O-antigen biosynthesis in Escherichia coli. Power PM, Seib KL, Jennings MP;. Biochem Biophys Res Commun. 2006;347:904-908. [2]. 23658772. Identification of bacterial protein o-oligosaccharyltransferases and their glycoprotein substrates. Schulz BL, Jen FE, Power PM, Jones CE, Fox KL, Ku SC, Blanchfield JT, Jennings MP;. PLoS One. 2013;8:e62768. (from Pfam) NF027277.5 PF15947.10 DUF4755 27 27 129 PfamAutoEq Y Y N DUF4755 domain-containing protein 1224 Pseudomonadota phylum 838 EBI-EMBL Domain of unknown function (DUF4755) Domain of unknown function (DUF4755) This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length. (from Pfam) NF027406.5 PF16080.10 Phage_holin_2_3 28.8 28.8 56 subfamily Y Y N HP1 family phage holin 8710508,9068631 1224 Pseudomonadota phylum 3628 EBI-EMBL Bacteriophage holin family HP1 HP1 family phage holin Phage_holin_2_3 is a family of small hydrophobic phage proteins called holins with one transmembrane domain. Holins are produced by double-stranded DNA bacteriophages that use an endolysin-holin strategy to achieve lysis of their hosts. The endolysins are peptidoglycan-degrading enzymes that are usually accumulated in the cytosol until access to the cell wall substrate is provided by the holin membrane lesion 1,2]. [1]. 8710508. The complete nucleotide sequence of bacteriophage HP1 DNA. Esposito D, Fitzmaurice WP, Benjamin RC, Goodman SD, Waldman AS, Scocca JJ;. Nucleic Acids Res. 1996;24:2360-2368. [2]. 9068631. Cloning and characterization of bacteriophage-like DNA from Haemophilus somnus homologous to phages P2 and HP1. Pontarollo RA, Rioux CR, Potter AA;. J Bacteriol. 1997;179:1872-1879. (from Pfam) NF027408.5 PF16082.10 Phage_holin_2_4 30 30 77 PfamEq Y Y N holin 1224 Pseudomonadota phylum 980 EBI-EMBL Bacteriophage holin family, superfamily II-like holin, class II Phage_holin_2_4 is a family of small hydrophobic phage proteins called holins with one transmembrane domain. Holins are produced by double-stranded DNA bacteriophages that use an endolysin-holin strategy to achieve lysis of their hosts. The endolysins are peptidoglycan-degrading enzymes that are usually accumulated in the cytosol until access to the cell wall substrate is provided by the holin membrane lesion. (from Pfam) NF027432.5 PF16106.10 DUF4824 25 25 252 PfamAutoEq Y Y N DUF4824 family protein 1224 Pseudomonadota phylum 777 EBI-EMBL Domain of unknown function (DUF4824) DUF4824 family protein This family consists of several hypothetical lipoproteins around 270 residues in length and is mainly found in Pseudomonas species. The function of this family is unknown. (from Pfam) NF027570.5 PF16245.10 DUF4902 25 25 118 domain Y Y N DUF4902 domain-containing protein 24916958,29507087 1224 Pseudomonadota phylum 1200 EBI-EMBL Domain of unknown function (DUF4902) Domain of unknown function (DUF4902) This family of proteins mainly found in Proteobacteria includes RsaM from Burkholderia cenocepacia. RsaM is a transcriptional regulator involved in quorum sensing (QS). This protein folds into a unique domain with a five-stranded antiparallel beta-sheet that wraps around two alpha-helices [1,2]. [1]. 24916958. RsaM: a transcriptional regulator of Burkholderia spp. with novel fold. Michalska K, Chhor G, Clancy S, Jedrzejczak R, Babnigg G, Winans SC, Joachimiak A;. FEBS J. 2014;281:4293-4306. [2]. 29507087. Two rsaM Homologues Encode Central Regulatory Elements Modulating Quorum Sensing in Burkholderia thailandensis. Le Guillouzer S, Groleau MC, Deziel E;. J Bacteriol. 2018; [Epub ahead of print] (from Pfam) NF027577.5 PF16252.10 DUF4908 25 25 223 domain Y Y N DUF4908 domain-containing protein 1224 Pseudomonadota phylum 567 EBI-EMBL Domain of unknown function (DUF4908) Domain of unknown function (DUF4908) A small family of uncharacterized proteins around 260 residues in length and found in various Caulobacter and Brevundimonas species. The function of this family is unknown. (from Pfam) NF027614.5 PF16290.10 DUF4936 28.8 28.8 91 PfamAutoEq Y Y N DUF4936 family protein 1224 Pseudomonadota phylum 1197 EBI-EMBL Domain of unknown function (DUF4936) DUF4936 family protein This family consists of uncharacterized proteins around 100 residues in length and is mainly found in various Burkholderiales species, such as Herbaspirillum, Cupriavidus, Ralstonia and so on. The function of this family is unknown. (from Pfam) NF027655.5 PF16331.10 TolA_bind_tri 30.1 30.1 76 domain Y Y N YbgF trimerization domain-containing protein GO:0070206 20816983 1224 Pseudomonadota phylum 15672 EBI-EMBL TolA binding protein trimerisation TolA binding protein trimerisation This is the N-terminal domain of the YbgF protein. YbgF binds to TolA. This domain mediates trimerisation [1]. [1]. 20816983. TolA modulates the oligomeric status of YbgF in the bacterial periplasm. Krachler AM, Sharma A, Cauldwell A, Papadakos G, Kleanthous C;. J Mol Biol. 2010;403:270-285. (from Pfam) NF027692.5 PF16374.10 CIF 25 25 138 subfamily Y Y N cycle-inhibiting factor 22069713 1224 Pseudomonadota phylum 327 EBI-EMBL Cycle inhibiting factor (CIF) cycle-inhibiting factor Cycle inhibiting factors (Cif) are bacterial effectors that interfere with the eukarytoc cell cycle. CIF induce an irreversible cell cycle arrest upon injection into host cell. CIF blocks degradation of cyclin -dependent kinase inhibitors p21 and p27, inducing their accumulation in the cell. The x-ray crystal structure of Cif reveals it to be a divergent member of a superfamily of enzymes including cysteine proteases and acetyltransferases. [1]. 22069713. Cycle Inhibiting Factors (Cifs). Cyclomodulins That Usurp the Ubiquitin-Dependent Degradation Pathway of Host Cells. Taieb F, Nougayrede JP, Oswald E;. Toxins 2011;3:356-368; (from Pfam) NF027774.5 PF16459.10 Phage_TAC_13 28.8 28.8 98 domain Y Y N phage tail assembly chaperone family protein, TAC 23542344 1224 Pseudomonadota phylum 2326 EBI-EMBL Phage tail assembly chaperone, TAC phage tail assembly chaperone family protein, TAC This family represents the phage-tail assembly chaperone proteins from a small set of Siphoviridae from Gammaproteobacteria. TACs are required for the morphogenesis of all long-tailed phages. The proposed function for the TAC is to coat the tape-measure protein to prevent it from forming unproductive complexes or precipitating before the tail tube protein has been incorporated [1]. [1]. 23542344. A conserved spiral structure for highly diverged phage tail assembly chaperones. Pell LG, Cumby N, Clark TE, Tuite A, Battaile KP, Edwards AM, Chirgadze NY, Davidson AR, Maxwell KL;. J Mol Biol. 2013;425:2436-2449. (from Pfam) NF027838.5 PF16524.10 RisS_PPD 27.5 27.5 107 PfamEq Y N N Periplasmic domain of Sensor histidine kinase RisS 1224 Pseudomonadota phylum 2912 EBI-EMBL Periplasmic domain of Sensor histidine kinase RisS Periplasmic domain of Sensor histidine kinase RisS RisS_PPD is the periplasmic domain of the sensor histidine kinase RisS. It is purported to be the region of the kinase that senses the pH of the environs. (from Pfam) NF027849.5 PF16535.10 T3SSipB 31 31 155 PfamEq Y N N Type III cell invasion protein SipB 10051653,10972796,14662750,16159789,22321794,22975346,7608068,8801431 1224 Pseudomonadota phylum 1106 EBI-EMBL Type III cell invasion protein SipB Type III cell invasion protein SipB T3SSipB is a family of pathogenic Gram-negative bacterial proteins that invade human intestinal cells via the type III secretion system translocators. T3SSipB represents the coiled -coil region of the proteins and is shown to be homologous in activity to the pore-forming toxins of other Gram-negative pathogens, such as colicin Ia [1-8]. [1]. 8801431. Functional conservation of the Salmonella and Shigella effectors of entry into epithelial cells. Hermant D, Menard R, Arricau N, Parsot C, Popoff MY;. Mol Microbiol. 1995;17:781-789. [2]. 7608068. Homologs of the Shigella IpaB and IpaC invasins are required for Salmonella typhimurium entry into cultured epithelial cells. Kaniga K, Tucker S, Trollinger D, Galan JE;. J Bacteriol. 1995;177:3965-3971. [3]. 10051653. The Salmonella invasin SipB induces macrophage apoptosis by binding to caspase-1. Hersh D, Monack DM, Smith MR, Ghori N, Falkow S, Zychlinsky A;. Proc Natl Acad Sci U S A. 1999;96:2396-2401. [4]. 10972796. Membrane fusion activity of purified SipB, a Salmonella surface protein essential for mammalian cell invasion. Hayward RD, McGhie EJ, Koronakis V;. Mol Microbiol. 2000;37:727-739. [5]. 14662750. A Salmonella protein causes macrophage cell death by inducing autophagy. Hernandez LD, Pypaert M, Flavell RA, Galan JE;. J Cell Biol. 2003;163:1123-1131. [6]. 16159789. Multinucleated giant cell formation and apoptosis in infected host cells is mediated by Burkholderia pseudomallei type III secretion protein BipB. Suparak S, Kespichayawattana W, Haque A, Easton A, Damnin S, Lertmemongkolchai G, Bancroft GJ, Korbsrisate S;. J Bacteriol. 2005;187:6556-6560. [7]. 22975346. Membr. TRUNCATED at 1650 bytes (from Pfam) NF028005.5 PF16695.10 Tai4 27.1 27.1 92 subfamily Y Y N T6SS amidase immunity protein Tai4 family protein 23288853 1224 Pseudomonadota phylum 3227 EBI-EMBL Type VI secretion system (T6SS), amidase immunity protein T6SS amidase immunity protein Tai4 family protein Tai4 is a new form of autoimmunity protein for a type VI secretion system, T6SS. T6SS has roles in interspecies interactions, as well as higher order host-infection, by injecting effector proteins into the periplasmic compartment of the recipient cells of closely related species. Pseudomonas aeruginosa produces at least three effector proteins to other cells and thus has three specific cognate immunity proteins to protect itself. Tae4, or type VI amidase effector 4, in Enterobacter cloacae has a cognate Tai4 or type VI amidase immunity 4 protein [1]. The effector is Tae4, Pfam:PF14113. [1]. 23288853. Structure of the type VI effector-immunity complex (Tae4-Tai4) provides novel insights into the inhibition mechanism of the effector by its immunity protein. Zhang H, Zhang H, Gao ZQ, Wang WJ, Liu GF, Xu JH, Su XD, Dong YH;. J Biol Chem. 2013;288:5928-5939. (from Pfam) NF028096.5 PF16786.10 RecA_dep_nuc 26.9 26.9 103 subfamily Y Y N Ref family recombination enhancement nuclease 21193392 1224 Pseudomonadota phylum 3656 EBI-EMBL Recombination enhancement, RecA-dependent nuclease Ref family recombination enhancement nuclease REF is a family of P1-like phage RecA-dependent nucleases. It does not appear to act as a positive RecA regulator. It is a new kind of enzyme, a RecA-dependent nuclease [1]. [1]. 21193392. Creating directed double-strand breaks with the Ref protein: a novel RecA-dependent nuclease from bacteriophage P1. Gruenig MC, Lu D, Won SJ, Dulberger CL, Manlick AJ, Keck JL, Cox MM;. J Biol Chem. 2011;286:8240-8251. (from Pfam) NF028157.5 PF16847.10 AvrPtoB_bdg 27 27 91 domain Y N N Avirulence AvrPtoB, BAK1-binding domain 22169508 1224 Pseudomonadota phylum 151 EBI-EMBL Avirulence AvrPtoB, BAK1-binding domain Avirulence AvrPtoB, BAK1-binding domain AvrPtoB_bdg is a binding region on a family of bacterial plant pathogenic proteins. Type III effector proteins are injected into plants by bacteria when they are under attack, eg Pseudomonas syringae when attacking tomato. AvrPtoB is one such effector that suppresses the plants' PAMP-triggered innate immunity. PAMPs are pathogen/microbe-associated molecular patterns that are detected as non-self by a host. AvrPtoB suppresses this response by binding to BAK1, a kinase that acts with several pattern recognition receptors to activate defence signalling. AvrPtoB_bdg is the region of AvrPtoB that binds to BAK1 thereby preventing its kinase activity after the perception of flagellin [1]. [1]. 22169508. Structural analysis of Pseudomonas syringae AvrPtoB bound to host BAK1 reveals two similar kinase-interacting domains in a type III Effector. Cheng W, Munkvold KR, Gao H, Mathieu J, Schwizer S, Wang S, Yan YB, Wang J, Martin GB, Chai J;. Cell Host Microbe. 2011;10:616-626. (from Pfam) NF028247.5 PF16937.10 T3SS_HrpK1 30.9 30.9 251 domain Y Y N type III effector HrpK domain-containing protein 15629936 1224 Pseudomonadota phylum 1781 EBI-EMBL Type III secretion system translocator protein, HrpF Type III secretion system translocator protein, HrpF T3SS_HrpK1 is a family of putative Type III secretion system pore-forming bacterial proteins. These allow transfer of pathogenic material from bacterial cytoplasm into the plant host cytoplasm. (from Pfam) NF028270.5 PF16960.10 HpuA 29.7 29.7 251 PfamEq Y N N Haemoglobin-haptoglobin utilisation, porphyrin transporter 9157245 1224 Pseudomonadota phylum 766 EBI-EMBL Haemoglobin-haptoglobin utilisation, porphyrin transporter Haemoglobin-haptoglobin utilisation, porphyrin transporter HpuA is a family of Neisseria spp proteins from the hpuAB operon, which are putative porphyrin transporters. [1]. 9157245. Molecular characterization of hpuAB, the haemoglobin-haptoglobin-utilization operon of Neisseria meningitidis. Lewis LA, Gray E, Wang YP, Roe BA, Dyer DW;. Mol Microbiol. 1997;23:737-749. (from Pfam) NF028280.5 PF16970.10 FimA 30 30 145 domain Y N N Type-1 fimbrial protein, A GO:0007155 22411982 1224 Pseudomonadota phylum 7508 EBI-EMBL Type-1 fimbrial protein, A Type-1 fimbrial protein, A FimA is a family of Gram-negative fimbrial component A proteins that form part of the pili. There are usually up to 1000 copies of this subunit in one pilus that form a helically wound rod onto which the tip fibrillum (FimF.FimG, FimH) is attached. Pilus subunits are translocated from the cytoplasm to the periplasm via the general secretory pathway SecYEG [1]. [1]. 22411982. Chaperone-usher pathways: diversity and pilus assembly mechanism. Busch A, Waksman G;. Philos Trans R Soc Lond B Biol Sci. 2012;367:1112-1122. (from Pfam) NF028295.5 PF16985.10 DUF5086 27 27 137 PfamAutoEq Y Y N DUF5086 family protein 23295481 1224 Pseudomonadota phylum 312 EBI-EMBL Domain of unknown function (DUF5086) DUF5086 family protein This family includes uncharacterised proteins predominantly found in Proteobacteria, such as Swiss:Q9I380 from Pseudomonas aeruginosa. This protein folds into a five-stranded antiparallel beta -sheet sandwiched between two short alpha-helices [1]. [1]. 23295481. The AEROPATH project targeting Pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery. Moynie L, Schnell R, McMahon SA, Sandalova T, Boulkerou WA, Schmidberger JW, Alphey M, Cukier C, Duthie F, Kopec J, Liu H, Jacewicz A, Hunter WN, Naismith JH, Schneider G;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013;69:25-34. (from Pfam) NF028311.5 PF17001.10 T3SS_basalb_I 32.4 32.4 94 domain Y Y N EscI/YscI/HrpB family type III secretion system inner rod protein GO:0009306,GO:0030254 23390616 1224 Pseudomonadota phylum 1752 EBI-EMBL Type III secretion basal body protein I, YscI, HrpB, PscI EscI/YscI/HrpB family type III secretion system inner rod protein T3SS_basalb_I represents a family of Gram-negative type III secretion basal body proteins I. It is the inner rod protein of the secreted needle. YscI is suggested to form a rod that allows substrate passage across the inner membrane of the needle protein YscF through it [1]. [1]. 23390616. Regulation of the Yersinia type III secretion system: traffic control. Dewoody RS, Merritt PM, Marketon MM;. Front Cell Infect Microbiol. 2013;3:4. (from Pfam) NF028350.5 PF17040.10 CBP_CCPA 25 25 114 PfamEq Y N N Cellulose-complementing protein A 1224 Pseudomonadota phylum 63 EBI-EMBL Cellulose-complementing protein A Cellulose-complementing protein A This is a family of bacterial cellulose-complementing protein A proteins necessary for cellulose biosynthesis. Cellulose is necessary for biofilm formation in bacteria. (Roemling U. and Galperin M.Y. "Bacterial cellulose biosynthesis. Diversity of operons and subunits" (manuscript in preparation)). (from Pfam) NF028467.5 PF17158.9 MASE4 28.4 28.4 239 domain Y Y N MASE4 domain-containing protein 25361688,26148715 1224 Pseudomonadota phylum 13121 EBI-EMBL Membrane-associated sensor, integral membrane domain Membrane-associated sensor, integral membrane domain MASE4 (Membrane-Associated SEnsor) is an integral membrane sensor domain found in various GGDEF domain proteins, including a functional diguanylate cyclase DgcT (YcdT) and the enzymatically inactive CdgI (YeaI) of Escherichia coli [1]. In the Shiga toxin-producing enteroaggregative E. coli O104:H4, which caused the outbreak of the haemolytic uraemic syndrome in Germany in 2011, MASE4-containing diguanylate cyclase DgcX, UniProtKB:B7LBD9_ECO55, was highly expressed, ensuring strong biofilm formation [2]. [1]. 26148715. Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli. Hengge R, Galperin MY, Ghigo JM, Gomelsky M, Green J, Hughes KT, Jenal U, Landini P;. J Bacteriol. 2015;198:7-11. [2]. 25361688. Cyclic-di-GMP signalling and biofilm-related properties of the Shiga toxin-producing 2011 German outbreak Escherichia coli O104:H4. Richter AM, Povolotsky TL, Wieler LH, Hengge R;. EMBO Mol Med. 2014;6:1622-1637. (from Pfam) NF028497.5 PF17188.9 MucB_RseB_C 30.1 30.1 97 PfamEq Y Y N MucB/RseB C-terminal domain-containing protein 17496148,8412698,8606151 1224 Pseudomonadota phylum 13031 EBI-EMBL MucB/RseB C-terminal domain MucB/RseB C-terminal domain Members of this family are regulators of the anti-sigma E protein RseD. [1]. 8412698. Differentiation of Pseudomonas aeruginosa into the alginate-producing form: inactivation of mucB causes conversion to mucoidy. Martin DW, Schurr MJ, Mudd MH, Deretic V;. Mol Microbiol 1993;9:497-506. [2]. 8606151. Characterization of the genes coding for the putative sigma factor AlgU and its regulators MucA, MucB, MucC, and MucD in Azotobacter vinelandii and evaluation of their roles in alginate biosynthesis. Martinez-Salazar JM, Moreno S, Najera R, Boucher JC, Espin G, Soberon-Chavez G, Deretic V;. J Bacteriol 1996;178:1800-1808. [3]. 17496148. Crystal structure of RseB and a model of its binding mode to RseA. Kim DY, Jin KS, Kwon E, Ree M, Kim KK;. Proc Natl Acad Sci U S A. 2007;104:8779-8784. (from Pfam) NF033062.0 APH_3p_VI 525 525 259 exception Y Y Y APH(3')-VI family aminoglycoside O-phosphotransferase 1224 Pseudomonadota phylum 119 NCBIFAM APH(3')-VI family aminoglycoside O-phosphotransferase APH(3')-VI family aminoglycoside O-phosphotransferase NF033063.0 APH_3p_XV 550 550 263 exception Y Y Y aminoglycoside O-phosphotransferase APH(3')-XV aph(3')-XV 1224 Pseudomonadota phylum 11 NCBIFAM aminoglycoside O-phosphotransferase APH(3')-XV aminoglycoside O-phosphotransferase APH(3')-XV NF033074.0 AAC_6p_Ib 400 400 184 exception Y Y Y AAC(6')-Ib family aminoglycoside 6'-N-acetyltransferase aac(6')-Ib 1224 Pseudomonadota phylum 223 NCBIFAM AAC(6')-Ib family aminoglycoside 6'-N-acetyltransferase AAC(6')-Ib family aminoglycoside 6'-N-acetyltransferase NF033080.0 AAC_3_II 480 480 268 subfamily Y Y Y AAC(3)-II family aminoglycoside N-acetyltransferase 1224 Pseudomonadota phylum 240 NCBIFAM AAC(3)-II family aminoglycoside N-acetyltransferase AAC(3)-II family aminoglycoside N-acetyltransferase NF033087.1 bla_subclass_B2 240 240 221 equivalog Y Y Y subclass B2 metallo-beta-lactamase bla 3.5.2.6 GO:0008800 1224 Pseudomonadota phylum 641 NCBIFAM subclass B2 metallo-beta-lactamase subclass B2 metallo-beta-lactamase NF033136.1 SMR_qac_K 205 205 110 exception Y Y Y quaternary ammonium compound efflux SMR transporter QacK qacK GO:0016020 1224 Pseudomonadota phylum 11 NCBIFAM quaternary ammonium compound efflux SMR transporter QacM quaternary ammonium compound efflux SMR transporter QacK Members of this family are putative quaternary ammonium compound efflux SMR transporter that tend to occur in integrons, and that tend to occur in marine or wastewater environments rather than in known pathogens. NF033137.0 SMR_qac_int 188 188 109 equivalog Y Y Y Qac family quaternary ammonium compound efflux SMR transporter 1224 Pseudomonadota phylum 121 NCBIFAM Qac family quaternary ammonium compound efflux SMR transporter Qac family quaternary ammonium compound efflux SMR transporter This model describes a fairly narrow clade of quaternary ammonium compound (QAC) resistance proteins. The majority of these are found in integrons, along with various genes encoding additional forms of antimicrobial resistance. Qac is a member of a broader family of Small Multidrug Resistance (SMR) efflux proteins. NF033138.1 RND-peri-MexC 600 600 375 equivalog Y Y N MexC family multidrug efflux RND transporter periplasmic adaptor subunit 1224 Pseudomonadota phylum 750 NCBIFAM MexC family multidrug efflux RND transporter periplasmic adaptor subunit MexC family multidrug efflux RND transporter periplasmic adaptor subunit NF033391.2 lipid_A_LpxO 500 500 297 equivalog Y Y N lipid A hydroxylase LpxO lpxO GO:0018193 10903325,18254598,20593270,21764941,26578797 1224 Pseudomonadota phylum 4461 NCBIFAM lipid A hydroxylase LpxO lipid A hydroxylase LpxO Members of this family are LpxO, an enzyme that modifies one of the lipid chains in lipid A by hydroxylation, with resulting changes in resistance to the host immune response and to the antibiotic colistin. This family, as built, includes LpxO1 from Pseudomonas aeruginosa, but not its paralog LpxO2. NF033419.1 T6SS_TagK_dom 40 40 129 domain Y Y N TagK domain-containing protein 17660433 1224 Pseudomonadota phylum 1816 NCBIFAM TagK domain-containing protein TagK family protein C-terminal domain NF033463.1 polymyxin_MCR5 1250 1250 547 exception Y Y Y MCR-5 family phosphoethanolamine--lipid A transferase 28962028 1224 Pseudomonadota phylum 9 NCBIFAM MCR-5 family phosphoethanolamine--lipid A transferase MCR-5 family phosphoethanolamine--lipid A transferase NF033502.0 Sul4 600 600 277 exception Y Y Y sulfonamide-resistant dihydropteroate synthase Sul4 sul4 29246178 1224 Pseudomonadota phylum 5 NCBIFAM sulfonamide-resistant dihydropteroate synthase Sul4 sulfonamide-resistant dihydropteroate synthase Sul4 Sul4 is a dihydropteroate synthase that is insensitive to, and provides resistance to, the antibiotic sulfonamide. It appears to be mobilized, but was discovered through functional metagenomics, and has not yet been seen in a cultured bacterial isolate. NF033606.1 heat_AAA_ClpK 1900 1900 949 exception Y Y Y heat shock survival AAA family ATPase ClpK clpK 21085699,21617023,23201206,29263094,35011428 1224 Pseudomonadota phylum 1030 NCBIFAM heat shock survival AAA family ATPase ClpK heat shock survival AAA family ATPase ClpK ClpK, a Clp family AAA ATPase, was discovered as a plasmid-encoded determinant for survival of heat shock along with other putative heat shock proteins. ClpK requires the presence of ClpP to confer heat resistance. ClpK is about 65% identical to ClpG. Note that PMID:26974352 and PMID:29263094 discuss both ClpG itself and a member of this family (ClpK) that they call ClpG-GI. NF033614.1 APH_6_Ic_gen 460 460 278 exception Y Y Y APH(6)-I family aminoglycoside O-phosphotransferase 1224 Pseudomonadota phylum 57 NCBIFAM APH(6)-I family aminoglycoside O-phosphotransferase APH(6)-I family aminoglycoside O-phosphotransferase NF033619.1 perm_MlaE_1 315 315 253 exception Y Y N lipid asymmetry maintenance ABC transporter permease subunit MlaE mlaE GO:0043190 1224 Pseudomonadota phylum 10031 NCBIFAM lipid asymmetry maintenance ABC transporter permease subunit MlaE lipid asymmetry maintenance ABC transporter permease subunit MlaE NF033621.1 de_GSH_amidase 355 355 260 exception Y Y N deaminated glutathione amidase 28373563 1224 Pseudomonadota phylum 4397 NCBIFAM deaminated glutathione amidase deaminated glutathione amidase NF033626.2 blaBKC_GPC 575 575 297 exception Y Y Y BKC/GPC family carbapenem-hydrolyzing class A beta-lactamase bla 3.5.2.6 GO:0008800 1224 Pseudomonadota phylum 42 NCBIFAM BKC/GPC family carbapenem-hydrolyzing class A beta-lactamase BKC/GPC family carbapenem-hydrolyzing class A beta-lactamase The plasmid-borne founding member of the BKC/GPC family, BKC-1 (Brazilian Klebisiella Carbapenemase), is an unusual protein with a direct repeat of the sequence AGALLAVPAVSTLAAS near the N-terminus. Multiple homologs from Shinella (4) and Sinorhizobium (1) appear to be chromosomal and lack this insert. NF033665.1 PACE_efflu_PCE 165 165 130 exception Y Y N multidrug/biocide efflux PACE transporter 24277845,25670776 1224 Pseudomonadota phylum 4452 NCBIFAM multidrug/biocide efflux PACE transporter multidrug/biocide efflux PACE transporter PACE (proteobacterial antimicrobial compound efflux) transporters are single component proton-coupled efflux pumps that help confer resistance to a number of biocides and antibiotics. The family has also been named PCE (proteobacterial chlorhexidine efflux). Members of this subfamily of the PACE transporters, distinct from the AceI-like branch, include several whose expression is increased by exposure to chlorhexidine and/or help confer increased resistance to it. NF033677.1 biofilm_BapA_N 35 35 64 domain Y Y N BapA prefix-like domain-containing protein 16313619,21175701,28158695 1224 Pseudomonadota phylum 31639 NCBIFAM BapA prefix-like domain-containing protein BapA prefix-like domain Two largely unrelated repetitive proteins, both named biofilm-associated protein BapA (from Salmonella enterica and from Paracoccus denitrificans) share homology domains at the two ends. Both lack a typical signal peptide for translocation by Sec, and instead depend on type I secretion for export and for contribution to biofilm formation. The conserved prefix (i.e. N-terminal) domain is shared by a number of other large, repetitive proteins of Proteobacteria thought to be associated with adhesion or biofilm formation. NF033736.2 blaAFM 590 590 267 exception Y Y Y AFM family subclass B1 metallo-beta-lactamase blaAFM 3.5.2.6 GO:0008800 38759302 1224 Pseudomonadota phylum 5 NCBIFAM AFM family subclass B1 metallo-beta-lactamase AFM family subclass B1 metallo-beta-lactamase AFM (Alcaligenes faecalis metallo-beta-lactamase) is a subclass B1 metallo-beta-lactamase most closely related to the NDM family. The first three occurrences of the founding allele, AFM-1, have all been plasmid-borne, and from three different species. NF033773.1 tellur_TrgA 40 40 145 subfamily Y Y N TrgA family protein 22767205,9406390 1224 Pseudomonadota phylum 1313 NCBIFAM TrgA family protein TrgA family protein TrgA, a protein associated with tellurium resistance (but less critical to the phenotype than TrgB, encoded by the adjacent gene), is the founding member of a family of hydrophobic proteins, about 150 amino acids in length, probably embedded in the membrane, and possibly involved in transport. NF033786.1 phenyl_MerG 350 350 217 equivalog Y Y Y phenylmercury resistance protein MerG merG GO:0005515 23890172,9922233 1224 Pseudomonadota phylum 24 NCBIFAM phenylmercury resistance protein MerG phenylmercury resistance protein MerG MerG, a protein about 217 amino acids in length, with three Sel1-like repeats (which resemble tetratricopeptide repeats, TPR), occurs in mercury resistance loci and contributes to resistance to phenylmercury, apparently by reducing permeability to and uptake of the substance. NF033790.1 CnrY_NccY_antiS 35 35 95 subfamily Y Y N CnrY/NccY family anti-sigma factor 24727125,7961470,8380802 1224 Pseudomonadota phylum 48 NCBIFAM CnrY/NccY family anti-sigma factor CnrY/NccY family anti-sigma factor NF033807.0 CopL_fam 40 40 129 subfamily Y Y N CopL family metal-binding regulatory protein 15691931 1224 Pseudomonadota phylum 1468 NCBIFAM CopL family metal-binding regulatory protein CopL family metal-binding regulatory protein The founding member of this family was shown to be involved in the copper-responsive expression of a multicopper oxidase copA encoded downstream. The regulatory function likely involves copper-binding, but activity as a DNA-binding transcriptional regulator was not demonstrated directly. NF033814.1 copper_CopC 95 95 107 equivalog Y Y N copper homeostasis periplasmic binding protein CopC copC GO:0005507,GO:0006825,GO:0042597,GO:0046688 16637653,27010565 1224 Pseudomonadota phylum 8253 NCBIFAM copper homeostasis periplasmic binding protein CopC copper homeostasis periplasmic binding protein CopC NF033857.1 BPSL0067_fam 27 27 115 subfamily Y Y N BPSL0067 family protein 1224 Pseudomonadota phylum 1136 NCBIFAM BPSL0067 family protein BPSL0067 family protein null NF033867.1 blaPAU 640 640 293 exception Y Y Y PAU family class A beta-lactamase blaPAU 3.5.2.6 GO:0008800,GO:0030655,GO:0046677 30012438 1224 Pseudomonadota phylum 2 NCBIFAM PAU family class A beta-lactamase PAU family class A beta-lactamase PAU is first mentioned in PMID:30012438 has blaP on a plasmid of Pseudomonas aeruginosa strain PA1280. NF033890.1 DotM_IcmP_IVB 230 230 356 equivalog Y Y N type IVB secretion system coupling complex protein DotM/IcmP icmP 29410427 1224 Pseudomonadota phylum 158 NCBIFAM type IVB secretion system coupling complex protein DotM/IcmP type IVB secretion system coupling complex protein DotM/IcmP NF033899.1 T4SS_pilin_TrwL 100 100 103 exception Y Y N VirB2 family type IV secretion system major pilin TrwL trwL 18065487,20548954 1224 Pseudomonadota phylum 959 NCBIFAM VirB2 family type IV secretion system major pilin TrwL VirB2 family type IV secretion system major pilin TrwL TrwL is the major pilin of Trw type IV secretion system (T4SS) of Bartonella species. It is related to VirB2 of related T4SS and to the conjugal transfer protein TrbC. The Trw system is unusual for having duplications of certain subunits, and TrwL has divergent, tandem-duplicated copies, named in series TrwL1, TrwL2, etc. NF033901.1 L_lactate_LldD 550 550 377 exception Y Y N FMN-dependent L-lactate dehydrogenase LldD lldD GO:0004457,GO:0006089,GO:0010181 22574176,30066495,8407843 1224 Pseudomonadota phylum 9737 NCBIFAM FMN-dependent L-lactate dehydrogenase LldD FMN-dependent L-lactate dehydrogenase LldD LldD is an FMN-dependent L-lactate dehydrogenase. It occurs in E. coli, Salmonella, and as one of two L-lactate dehydrogenases in Pseudomonas aeruginosa. It is unrelated to the NAD-dependent enzyme. NF033943.0 RTX_toxin 1000 1000 930 subfamily Y Y N RTX family hemolysin GO:0005509,GO:0005576 16552030,19348784,23252494,27528275 1224 Pseudomonadota phylum 806 NCBIFAM RTX family hemolysin RTX family hemolysin RTX family toxin are secreted from the bacteria and inserted into the membranes of infected cells, causing host cell rupture. NF033950.0 Cas12c 250 250 1246 equivalog Y Y N type V CRISPR-associated protein Cas12c cas12c 1224 Pseudomonadota phylum 14 NCBIFAM type V CRISPR-associated protein Cas12c type V CRISPR-associated protein Cas12c NF035933.1 ESAT6_1 100 100 110 subfamily Y Y N pore-forming ESAT-6 family protein 1224 Pseudomonadota phylum 267 NCBIFAM pore-forming ESAT-6 family protein NF036336.5 PF17438.7 DUF5417 23.9 23.9 91 domain Y Y N DUF5417 domain-containing protein 1224 Pseudomonadota phylum 117 EBI-EMBL Family of unknown function (DUF5417) Family of unknown function (DUF5417) This is a family of unknown function found in Proteobacteria. (from Pfam) NF036352.5 PF17484.7 TbpB_A 25 25 136 domain Y Y N transferrin-binding N-lobe domain-containing protein 18186471,19716795,23836816,25800619 1224 Pseudomonadota phylum 2810 EBI-EMBL N-Lobe handle Tf-binding protein B N-Lobe handle Tf-binding protein B Bacterial lipoproteins represent a large group of specialized membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis, and cell adherence [1]. Pathogenic Gram-negative bacteria within the Neisseriaceae and Pasteurellaceae families rely on a specialized uptake system, characterized by an essential surface receptor complex that acquires iron from host transferrin (Tf) and transports the iron across the outer membrane. They have an iron uptake system composed of surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), that together function to extract iron from the host iron binding glycoprotein (Tf). TbpB is a bilobed (N and C lobe) lipid-anchored protein with each lobe consisting of an eight-stranded beta barrel flanked by a 'handle' domain made up of four (N lobe) or eight (C lobe) beta strands [2]. TbpB extends from the outer membrane surface by virtue of an N-terminal peptide region that is anchored to the outer membrane by fatty acyl chains on the N-terminal cysteine and is involved in the initial capture of iron-loaded Tf [3]. The 4-residue conserved LSAC motif found at the amino terminus of TbpB represents a prototypical lipobox, with the cysteine residue serving as the first amino acid in the mature protein which is subsequently modified by the addition of a diacyl glycerol. A second conserved motif of interest is located two amino acids downstream of the LSAC site. This region consists of four glycine residues in tan. TRUNCATED at 1650 bytes (from Pfam) NF036416.5 PF17271.7 Usher_TcfC 25 25 429 domain Y N N TcfC Usher-like barrel domain 1224 Pseudomonadota phylum 3766 EBI-EMBL TcfC Usher-like barrel domain TcfC Usher-like barrel domain This is the presumed beta barrel domain from the usher-like TcfC family of proteins. (from Pfam) NF036428.5 PF17311.7 DUF5358 25 25 160 subfamily Y Y N DUF5358 family protein 1224 Pseudomonadota phylum 612 EBI-EMBL Family of unknown function (DUF5358) DUF5358 family protein This family of unknown function is found in Proteobacteria. (from Pfam) NF036440.5 PF17336.7 DUF5368 25 25 112 domain Y Y N DUF5368 family protein 1224 Pseudomonadota phylum 676 EBI-EMBL Family of unknown function (DUF5368) DUF5368 family protein This is a family of unknown function found in Proteobacteria and predicted to contain 2 trans-membrane regions. (from Pfam) NF036461.5 PF17264.7 DUF5330 27.5 27.5 65 domain Y Y N DUF5330 domain-containing protein 1224 Pseudomonadota phylum 2478 EBI-EMBL Family of unknown function (DUF5330) Family of unknown function (DUF5330) This is a family of unknown function which is mostly found in Bacteria. (from Pfam) NF036554.5 PF17243.7 POTRA_TamA_1 26 26 74 domain Y Y N POTRA domain-containing protein 24056943,25101071 1224 Pseudomonadota phylum 18530 EBI-EMBL POTRA domain TamA domain 1 POTRA domain TamA domain 1 This family represents the POTRA domain found in the membrane insertase TamA. [1]. 24056943. The structural basis of autotransporter translocation by TamA. Gruss F, Zahringer F, Jakob RP, Burmann BM, Hiller S, Maier T;. Nat Struct Mol Biol. 2013;20:1318-1320. [2]. 25101071. A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution. Heinz E, Lithgow T;. Front Microbiol. 2014;5:370. (from Pfam) NF036562.5 PF17272.7 DUF5337 27 27 74 domain Y Y N DUF5337 family protein 1224 Pseudomonadota phylum 1354 EBI-EMBL Family of unknown function (DUF5337) DUF5337 family protein This family of unknown function is found in Rhodobacterales. Most members are predicted to have 2 trans-membrane regions. (from Pfam) NF036599.5 PF17483.7 TbpB_C 25 25 98 domain Y Y N transferrin-binding protein-like solute binding protein 18186471,19716795,25800619 1224 Pseudomonadota phylum 2793 EBI-EMBL C-lobe handle domain of Tf-binding protein B transferrin-binding protein-like solute binding protein Bacterial lipoproteins represent a large group of specialised membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis, and cell adherence [1]. Pathogenic Gram-negative bacteria within the Neisseriaceae and Pasteurellaceae families rely on a specialised uptake system, characterized by an essential surface receptor complex that acquires iron from host transferrin (Tf) and transports the iron across the outer membrane. They have an iron uptake system composed of surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), that together function to extract iron from the host iron binding glycoprotein (Tf). TbpB is a bilobed (N and C lobe) lipid-anchored protein with each lobe consisting of an eight-stranded beta barrel flanked by a 'handle' domain made up of four (N lobe) or eight (C lobe) beta strands [2]. TbpB extends from the outer membrane surface by virtue of an N-terminal peptide region that is anchored to the outer membrane by fatty acyl chains on the N-terminal cysteine and is involved in the initial capture of iron-loaded Tf [3]. This domain family is found in the handle domain of the C lobe (domain C) of TbpB proteins. It consists of a squashed six-stranded beta sheet flanked by two antiparallel beta strands and has no supporting alpha helix as in the N lobe [2]. [1]. 18186471. The solution structure of the outer membrane lipoprotein OmlA from Xanthomonas axonopodis pv. citri reveals a protein fold implicated in protein-p. TRUNCATED at 1650 bytes (from Pfam) NF036644.5 PF17434.7 DUF5413 31 31 133 domain Y Y N DUF5413 family protein 1224 Pseudomonadota phylum 427 EBI-EMBL Family of unknown function (DUF5413) DUF5413 family protein This is a family of unknown function found in Bradyrhizobiaceae. Family members contain 3 or 4 predicted trans-membrane regions. (from Pfam) NF036651.5 PF17470.7 Gp45_2 28 28 58 subfamily Y Y N protein GP45.2 9555879 1224 Pseudomonadota phylum 9 EBI-EMBL Phage gene product 45.2 protein GP45.2 This is a family of unknown function found in Myoviridae. [1]. 9555879. Divergence of a DNA replication gene cluster in the T4-related bacteriophage RB69. Yeh LS, Hsu T, Karam JD;. J Bacteriol. 1998;180:2005-2013. (from Pfam) NF036660.5 PF17524.7 CnrY 25 25 98 domain Y N N Anti-sigma factor CnrY 24727125,26131973 1224 Pseudomonadota phylum 49 EBI-EMBL Anti-sigma factor CnrY Anti-sigma factor CnrY This family is found in alpha and beta proteobacteria. Family members include anti-sigma factor CnrY from Cupriavidus metallidurans. Sigma factors are multi-domain sub-units of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. They also control a wide variety of adaptive responses such as morphological development and the management of stress. A recurring theme in sigma factor control is their sequestration by anti-sigma factors that occlude their RNAP-binding determinants [1]. CnrH, controls cobalt and nickel resistance in Cupriavidus metallidurans. CnrH is regulated by a complex of two transmembrane proteins: the periplasmic sensor CnrX and the anti-sigma CnrY. At rest, CnrH is sequestered by CnrY whose 45-residue-long cytosolic domain is one of the shortest anti-sigma domains. Upon Ni(II) or Co(II) ions detection by CnrX in the periplasm, CnrH is released between CnrH and the cytosolic domain of CnrY (CnrYc). The CnrH/CnrYC complex displays an unexpected structural similarity to the anti-sigma NepR in complex with its antagonist PhyR, whereas NepR shares no sequence similarity with CnrY. Crystal structure of CnrH/CnrY shows that CnrYC residues 3-19 are folded as a well-defined alpha-helix. The peptide further extends along the hydrophobic groove of sigma 2 with no canonical structure except for a short helical turn spanning residues 24-28. CnrY has a hydrophobic knob made of V4, W7 and L8 side chains protruding into sigma 4 hydrophobic pocket and contributing to the interface. In vivo in. TRUNCATED at 1650 bytes (from Pfam) NF036705.5 PF18081.6 FANC_SAP 23 23 51 domain Y N N Fanconi anemia-associated nuclease SAP domain 25319828 1224 Pseudomonadota phylum 7571 EBI-EMBL Fanconi anemia-associated nuclease SAP domain Fanconi anemia-associated nuclease SAP domain This domain is found in Fanconi-anemia-associated nuclease 1 (FAN1) present in Pseudomonas aeruginosa. FAN1 is a nuclease associated with Fanconi anemia (FA), an autosomal recessive genetic disorder caused by defects in FA genes responsible for processing DNA inter-strand cross-links (ICLs). The domain, known as the SAP domain, helps to augment the overall protein DNA interaction by interacting with the 3' and 5' ends of the template strand. Support of the pre-nick segment binding is crucial as multiple mutations in this domain resulted in hypersensitivity to a cross-linking agent in the SAP domain of Caenorhabditis elegans' FAN1. The helix-hairpin-helix of the SAP recognize three consecutive phosphate groups (C19, A20 and A21) at the 3' end of the template via the basic residues K116, K135 and K117 [1]. [1]. 25319828. Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5' flap DNA: basis of interstrand cross-link repair by FAN1. Gwon GH, Kim Y, Liu Y, Watson AT, Jo A, Etheridge TJ, Yuan F, Zhang Y, Kim Y, Carr AM, Cho Y;. Genes Dev. 2014;28:2276-2290. (from Pfam) NF036713.5 PF18113.6 Rbx_binding 22.1 22.1 71 domain Y N N Rubredoxin binding C-terminal domain 17636129 1224 Pseudomonadota phylum 14454 EBI-EMBL Rubredoxin binding C-terminal domain Rubredoxin binding C-terminal domain This is the C-terminal domain found in rubredoxin reductase (RdxR) present in Pseudomonas aeruginosa. RdxR are important in prokaryotes as they allow for the metabolism of inert n-alkanes and RdxR is also crucial for archaea and anaerobic bacteria in the response to oxidative stress. This domain is known to recognise and bind to rubredoxin [1]. [1]. 17636129. Crystal structure of the electron transfer complex rubredoxin rubredoxin reductase of Pseudomonas aeruginosa. Hagelueken G, Wiehlmann L, Adams TM, Kolmar H, Heinz DW, Tummler B, Schubert WD;. Proc Natl Acad Sci U S A. 2007;104:12276-12281. (from Pfam) NF036742.5 PF18225.6 AbfS_sensor 26 26 65 domain Y N N Sensor histidine kinase (AbfS) sensor domain 18922794 1224 Pseudomonadota phylum 182 EBI-EMBL Sensor histidine kinase (AbfS) sensor domain Sensor histidine kinase (AbfS) sensor domain This is the sensor domain of sensor histidine kinase (AbfS) present in Cellvibrio japonicus. AbfS forms part of the AbfR/S two-component system which is needed to to activate the expression of the suite of enzymes that remove the numerous side chains from xylan. The overall fold of the sensor domain is that of a classical Per Arndt Sim domain [1]. This domain binds xylotriose and xylobiose (Matilla et.al, FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 18922794. Regulation of the xylan-degrading apparatus of Cellvibrio japonicus by a novel two-component system. Emami K, Topakas E, Nagy T, Henshaw J, Jackson KA, Nelson KE, Mongodin EF, Murray JW, Lewis RJ, Gilbert HJ;. J Biol Chem. 2009;284:1086-1096. (from Pfam) NF037093.5 PF18715.6 Phage_spike 28.2 28.2 53 domain Y N N Phage spike trimer 21821878,22922659 1224 Pseudomonadota phylum 9249 EBI-EMBL Phage spike trimer Phage spike trimer Bacteriophages penetrate the host cell membrane using their tail to inject genetic material into the host [1]. In this penetration process, they use central spike domain located beneath their baseplate [2]. The spike domain folds as a trimeric iron-binding structure [1]. This entry contains three copies of the repeat unit. [1]. 21821878. The host-binding domain of the P2 phage tail spike reveals a trimeric iron-binding structure. Yamashita E, Nakagawa A, Takahashi J, Tsunoda K, Yamada S, Takeda S;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011;67:837-841. [2]. 22922659. Crystal structure of the C-terminal domain of Mu phage central spike and functions of bound calcium ion. Harada K, Yamashita E, Nakagawa A, Miyafusa T, Tsumoto K, Ueno T, Toyama Y, Takeda S;. Biochim Biophys Acta. 2013;1834:284-291. (from Pfam) NF037136.5 PF17841.6 Bep_C_terminal 29.5 29.5 97 domain Y Y N BID domain-containing protein 27889208 1224 Pseudomonadota phylum 4372 EBI-EMBL BID domain of Bartonella effector protein (Bep) BID domain of Bartonella effector protein (Bep) This entry is the BID (Bep intracellular delivery) domain located at the C-terminal of Bartonella effector proteins (Beps). It functions as a secretion signal in a subfamily of protein substrates of bacterial type IV secretion (T4S) systems. It mediates transfer of (1) relaxases and the attached DNA during bacterial conjugation, and (2) numerous Beps during protein transfer into host cells infected by pathogenic Bartonella species. Crystal structure of several representative BID domains show a conserved fold characterized by a compact, antiparallel four-helix bundle topped with a hook [1]. [1]. 27889208. The BID Domain of Type IV Secretion Substrates Forms a Conserved Four-Helix Bundle Topped with a Hook. Stanger FV, de Beer TA, Dranow DM, Schirmer T, Phan I, Dehio C;. Structure. 2017;25:203-211. (from Pfam) NF037176.5 PF18054.6 CEL_III_C 27 27 154 domain Y N N CEL-III C-terminal 15194688 1224 Pseudomonadota phylum 38 EBI-EMBL CEL-III C-terminal CEL-III C-terminal This is the C-terminal domain found in Cucumaria echinata CEL-III protein which is a lectin that exhibits both hemolytic and hemagglutinating activity. The domain is responsible for oligomerization and insertion of CEL-III into the erythrocyte membrane. The domain is composed of eight stranded beta sandwich and two alpha helices, the latter changes conformation upon binding to the cell surface carbohydrates [1]. [1]. 15194688. Crystal structure of the hemolytic lectin CEL-III isolated from the marine invertebrate Cucumaria echinata: implications of domain structure for its membrane pore-formation mechanism. Uchida T, Yamasaki T, Eto S, Sugawara H, Kurisu G, Nakagawa A, Kusunoki M, Hatakeyama T;. J Biol Chem. 2004;279:37133-37141. (from Pfam) NF037200.5 PF18125.6 RlmM_FDX 22.2 22.2 71 domain Y N N RlmM ferredoxin-like domain 22923526 1224 Pseudomonadota phylum 10713 EBI-EMBL RlmM ferredoxin-like domain RlmM ferredoxin-like domain This domain is found in Ribosomal methyltransferase RlmM (YdgE) present in E. coli. RlmM catalyzes the S-adenosyl methionine (AdoMet)-dependent 2'O methylation of C2498 in 23S ribosomal RNA. The domain is ferredoxin-like and forms part of the THUMP domain which binds RNA. THUMP domains typically have low sequence similarity [1]. [1]. 22923526. Crystal structure of RlmM, the 2'O-ribose methyltransferase for C2498 of Escherichia coli 23S rRNA. Punekar AS, Shepherd TR, Liljeruhm J, Forster AC, Selmer M;. Nucleic Acids Res. 2012;40:10507-10520. (from Pfam) NF037237.5 PF18412.6 Wza_C 25.8 25.8 30 domain Y N N Outer-membrane lipoprotein Wza C-terminal domain 17086202 1224 Pseudomonadota phylum 9750 EBI-EMBL Outer-membrane lipoprotein Wza C-terminal domain Outer-membrane lipoprotein Wza C-terminal domain This is the C-terminal domain found in Wza, an integral outer membrane lipoprotein, which is essential for group 1 capsule export in Escherichia coli. The domain is exposed on the cell surface and is suggested to mimic antimicrobial peptide pore formation [1]. [1]. 17086202. Wza the translocon for E. coli capsular polysaccharides defines a new class of membrane protein. Dong C, Beis K, Nesper J, Brunkan-Lamontagne AL, Clarke BR, Whitfield C, Naismith JH;. Nature. 2006;444:226-229. (from Pfam) NF037261.5 PF18518.6 TcA_RBD 32 32 132 domain Y N N TcA receptor binding domain 24572368 1224 Pseudomonadota phylum 1002 EBI-EMBL TcA receptor binding domain TcA receptor binding domain Tc toxin complexes are virulence factors of many bacteria such as the plague pathogen Yersinia pestis. Tc toxins are composed of TcA, TcB and TcC subunits. TcA forms a large bell-shaped pentameric structure and enters the membrane like a syringe, forming a translocation channel through which the cytotoxic domain is probably transported into the cytoplasm. TcA has four receptor-binding domains. This domain is one of 4 receptor binding domains found in TcA. All four domains have an immunoglobulin (Ig)-like beta-sandwich fold of two sheets with antiparallel beta-strands. The domains are structurally reminiscent of the receptor-binding domains of the diphtheria and anthrax toxins [1]. [1]. 24572368. Mechanism of Tc toxin action revealed in molecular detail. Meusch D, Gatsogiannis C, Efremov RG, Lang AE, Hofnagel O, Vetter IR, Aktories K, Raunser S;. Nature. 2014;508:61-65. (from Pfam) NF037366.5 PF18642.6 IMPa_helical 26.7 26.7 109 domain Y N N Immunomodulating metalloprotease helical domain 28096352 1224 Pseudomonadota phylum 3264 EBI-EMBL Immunomodulating metalloprotease helical domain Immunomodulating metalloprotease helical domain IMPa is an immunomodulator metalloprotease that belongs to the peptidase M60 family Pfam:PF13402. This entry represents the helical domain found at the N-terminal of the Ig domain [1]. [1]. 28096352. Recognition of protein-linked glycans as a determinant of peptidase activity. Noach I, Ficko-Blean E, Pluvinage B, Stuart C, Jenkins ML, Brochu D, Buenbrazo N, Wakarchuk W, Burke JE, Gilbert M, Boraston AB;. Proc Natl Acad Sci U S A. 2017;114:E679. (from Pfam) NF037384.5 PF18686.6 DUF5636 25 25 193 subfamily Y Y N LirA/MavJ family T4SS effector 1224 Pseudomonadota phylum 292 EBI-EMBL Family of unknown function (DUF5636) LirA/MavJ family T4SS effector This is a domain of unknown function mostly found in gammaproteobacteria. (from Pfam) NF037481.5 PF18650.6 IMPa_N_2 25 25 200 domain Y N N Immunomodulating metalloprotease N-terminal domain 22309196,28096352 1224 Pseudomonadota phylum 2458 EBI-EMBL Immunomodulating metalloprotease N-terminal domain Immunomodulating metalloprotease N-terminal domain PA0572 of P. aeruginosa is an inhibitor of PSGL-1, also known as an immunomodulating metalloprotease of P. aeruginosa (IMPa). IMPa prevents neutrophil extravasation and thereby protects P. aeruginosa from neutrophil attack [1]. It belongs to the peptidase M60 family Pfam:PF13402. This entry represents the N-terminal alpha/beta-fold domain [2]. [1]. 22309196. Identification of an immunomodulating metalloprotease of Pseudomonas aeruginosa (IMPa). Bardoel BW, Hartsink D, Vughs MM, de Haas CJ, van Strijp JA, van Kessel KP;. Cell Microbiol. 2012;14:902-913. [2]. 28096352. Recognition of protein-linked glycans as a determinant of peptidase activity. Noach I, Ficko-Blean E, Pluvinage B, Stuart C, Jenkins ML, Brochu D, Buenbrazo N, Wakarchuk W, Burke JE, Gilbert M, Boraston AB;. Proc Natl Acad Sci U S A. 2017;114:E679. (from Pfam) NF037682.5 PF17945.6 Crystall_4 30 30 90 domain Y N N Beta/Gamma crystallin 22483117 1224 Pseudomonadota phylum 742 EBI-EMBL Beta/Gamma crystallin Beta/Gamma crystallin This is the C-terminal domain found in mucin glycoproteins such as secreted protease of C1 esterase inhibitor from EHEC (StcE). This domain adopts a beta/gamma crystallin fold and has been shown to be dispensable for substrate binding. Furthermore, deletion analysis suggest that lack of the C-terminal resulted in impaired association with the cell surface [1]. [1]. 22483117. Structural insight into the bacterial mucinase StcE essential to adhesion and immune evasion during enterohemorrhagic E. coli infection. Yu AC, Worrall LJ, Strynadka NC;. Structure. 2012;20:707-717. (from Pfam) NF037905.5 PF18788.6 DarA_N 27 27 122 domain Y N N Defence against restriction A N-terminal 28559295 1224 Pseudomonadota phylum 2692 EBI-EMBL Defence against restriction A N-terminal Defence against restriction A N-terminal This is an alpha and beta fold domain [1]. It has a conserved aspartate, and an asparagine residue followed by a basic residue in a Nx+ motif [1]. This predicted structural domain is mainly found in polyvalent proteins of phages/prophages [1]. The P1 hdf protein, a solo version of the domain, and the Phage P1 DarA protein that contains this domain are components of the phage P1 head [1]. The domain might be involved in a counter-restriction activity [1]. [1]. 28559295. Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. Iyer LM, Burroughs AM, Anand S, de Souza RF, Aravind L;. J Bacteriol. 2017; [Epub ahead of print] (from Pfam) NF037915.5 PF18807.6 TTc_toxin_rep 29 25 45 domain Y N N Tripartite Tc toxins repeat 24572368 1224 Pseudomonadota phylum 2467 EBI-EMBL Tripartite Tc toxins repeat Tripartite Tc toxins repeat Tripartite Tc toxin complexes of bacterial pathogens perforate the host membrane and translocate toxic enzymes into the host cell. These structures undergo a transition between a prepore to a pore state [1] and they are mainly constituted by closed beta-layer repeats. This Pfam entry includes a single repeat unit. [1]. 24572368. Mechanism of Tc toxin action revealed in molecular detail. Meusch D, Gatsogiannis C, Efremov RG, Lang AE, Hofnagel O, Vetter IR, Aktories K, Raunser S;. Nature. 2014;508:61-65. (from Pfam) NF037929.5 PF18858.6 LPD39 27 27 198 domain Y N N Large polyvalent protein associated domain 39 28559295 1224 Pseudomonadota phylum 1378 EBI-EMBL Large polyvalent protein associated domain 39 Large polyvalent protein associated domain 39 This is a predicted enzymatic alpha-helical domain that is associated with polyvalent proteins of phages and prophages [1]. [1]. 28559295. Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. Iyer LM, Burroughs AM, Anand S, de Souza RF, Aravind L;. J Bacteriol. 2017; [Epub ahead of print] (from Pfam) NF037934.1 holdfast_HfaA 50 50 115 equivalog Y Y N holdfast anchoring protein HfaA hfaA 31061167 1224 Pseudomonadota phylum 455 NCBIFAM holdfast anchoring protein HfaA NF037969.1 SemiSWEET_3 100 100 97 subfamily Y Y N SemiSWEET transporter 29872447 1224 Pseudomonadota phylum 128 NCBIFAM SemiSWEET transporter The SWEET (Sugars Will Eventually be Exported Transporter) is a superfamily of sugar transporters found in both eukaryotes and prokaryotes. Eukaryotic SWEETs usually have seven transmembrane helices (TMHs), but most prokaryotic SWEETs (SemiSWEETs) have only three TMHs. Proteins of this family have 3 TMHs. NF038027.1 TssQ_fam 65 65 100 subfamily Y Y N TssQ family T6SS-associated lipoprotein 26459829 1224 Pseudomonadota phylum 1041 NCBIFAM TssQ family T6SS-associated lipoprotein The founding member of this protein family, TssQ (BB0812) from Bordetella bronchiseptica, is a lipoprotein, and possibly all other family members are as well. TssQ is encoded within a T6SS locus but its function remains unknown. NF038045.1 GEF_RalF 400 400 341 equivalog Y Y N T4SS guanine nucleotide exchange effector RalF ralF 1224 Pseudomonadota phylum 79 NCBIFAM T4SS guanine nucleotide exchange effector RalF RalF, a virulence factor secreted by type IV secretion systems (T4SS), is a guanine nucleotide exchange factor that acts on host cell ADP-ribosylation factors. NF038054.1 T3SS_SctI 39 39 76 equivalog Y Y N type III secretion system inner rod subunit SctI sctI 26520801 1224 Pseudomonadota phylum 1040 NCBIFAM type III secretion system inner rod subunit SctI This model describes protein SctI (Secretion and Cellular Translocation I), an inner rod protein in the basal body of the type III secretion system (T3SS) as found in many pathogenic bacteria. SctI has some sequence similarity to the needle filament protein SctF. Lineage-specific names for SctI in various bacteria include BsaK, PrgJ, and MxiI. NF038055.1 T3SS_SctB_pilot 37 37 313 subfamily Y Y N type III secretion system translocon subunit SctB sctB 26520801 1224 Pseudomonadota phylum 1618 NCBIFAM type III secretion system translocon subunit SctB One SctB and four SctE subunits, located at the tip of the type III secretion system (T3SS) injectosome, combine to form the translocon (translocator pore) in the membrane of targeted cells. Species-specific names for this highly variable component of T3SS include YopD, EspB, IpaC, SipC, etc. NF038071.1 lat_flg_LafA_2 365 365 284 exception Y Y N lateral flagellin LafA lafA 15170400,16428388,4010543 1224 Pseudomonadota phylum 907 NCBIFAM lateral flagellin LafA NF038104.1 lipo_NF038104 50 50 63 hypoth_equivalog Y Y N NF038104 family lipoprotein 1224 Pseudomonadota phylum 940 NCBIFAM NF038104 family lipoprotein This family of small lipoproteins of unknown function, about 68 amino acids long, occurs in genera that include Acinetobacter, Moraxella, Neisseria, and Psychrobacter. The N-terminal half, including the lipoprotein signal peptide, shows significant sequence similarity to the divisome-associated lipoprotein YraP, a three-fold longer protein, as found in Eschericia coli. NF038119.1 PEP_CTERM_MHFG 100 100 260 equivalog Y Y N MHFG family PEP-CTERM protein 1224 Pseudomonadota phylum 342 NCBIFAM MHFG family PEP-CTERM protein This PEP-CTERM protein, dependent on exosortase for processing and export, is named for a distinctive MHFG motif. NF038168.1 phazolicin_TOMM 33 33 54 subfamily Y Y N phazolicin family TOMM bacteriocin 31594941,32296456 1224 Pseudomonadota phylum 11 NCBIFAM phazolicin family TOMM bacteriocin Phazolicin is a ribosome-targeting thiazole/oxazole-modified microcin (TOMM), also called a linear azol(in)e-containing peptides (LAP). NF038235.1 retron_Ec48_2TM 65 65 219 equivalog Y Y N retron Ec48 family effector membrane protein 33157039 1224 Pseudomonadota phylum 564 NCBIFAM retron Ec48 family effector membrane protein NF038236.1 retron_eff_Se72 82 82 62 equivalog Y Y N retron Se72 family effector protein 33157039 1224 Pseudomonadota phylum 150 NCBIFAM retron Se72 family effector protein Members of this family are cold shock domain-containing proteins encoded adjacent to reverse transcriptases found in Se72-type retron systems, and considered effector proteins contributing to phage resistance. NF038241.1 RipB_Ich 340 340 175 equivalog Y Y N (R)-specific enoyl-CoA hydratase RipB/Ich ripB 24657929,32719152 1224 Pseudomonadota phylum 134 NCBIFAM (R)-specific enoyl-CoA hydratase RipB/Ich Second step in itaconate degradation. NF038252.1 cable_major 225 225 166 equivalog Y Y N cable pilus major pilin CblA cblA 7532166 1224 Pseudomonadota phylum 72 NCBIFAM cable pilus major pilin CblA NF038261.1 rhodoquin_RquA 175 175 218 equivalog Y Y N rhodoquinone biosynthesis methyltransferase RquA rquA 22194448,29697049,31121262 1224 Pseudomonadota phylum 517 NCBIFAM rhodoquinone biosynthesis methyltransferase RquA NF038263.1 prot_phos_SiaA 700 700 658 equivalog Y Y N biofilm regulation protein phosphatase SiaA siaA 3.1.3.16 19638175,26955366,32090355,33156827 1224 Pseudomonadota phylum 1124 NCBIFAM biofilm regulation protein phosphatase SiaA SiaB is a threonine kinase acting on SiaC; SiaA is the matching phosphatase. NF038264.1 kinase_SiaB 225 225 176 equivalog Y Y N biofilm regulation protein kinase SiaB siaB 2.7.1.- 32090355,33156827 1224 Pseudomonadota phylum 629 NCBIFAM biofilm regulation protein kinase SiaB NF038322.1 ImpA_fam_HExGH 250 250 885 subfamily Y Y N ImpA family metalloprotease 3.4.24.- 31527124 1224 Pseudomonadota phylum 3357 NCBIFAM ImpA family metalloprotease Members of this family are metalloproteases related to the ImpA from Pseudomonas aeruginosa (PA0572 in strain PAO1), a virulence factor that cleaves CD44 on the surface of human macrophages, inhibiting phagocytosis. Members of this family are distinguished by a strong motif, CGxGCSGNPxD, just a few residues upstream of the familiar metalloprotease motif HExxH (typically HELGH here) and completely lacking in more distant homologs of ImpA. NF038351.1 cyt_ox_assem_30 27.5 27.5 30 subfamily Y Y N cytochrome oxidase small assembly protein 1224 Pseudomonadota phylum 1782 NCBIFAM cytochrome oxidase small assembly protein Members of this family are small proteins, averaging about 40 amino acids in length as predicted, with a conserved core region just 30 amino acids long. The conserved region contains a highly hydrophobic probable transmembrane alpha helix. Members regularly are found encoded in the context of much larger cytochrome oxidase complex subunits, in members of the Burkholderiales such as Bordetella pertussis and Burkholderia sp. NF038368.1 P2_Rz1 27 27 85 equivalog Y Y N Rz1-like lysis system protein LysC lysC 17900620,27038077 1224 Pseudomonadota phylum 7007 NCBIFAM Rz1-like lysis system protein LysC LysC is an Rz1-like component of a phage lytic system, substantially overlapping although not fully embedded in the gene for the Rz-like LysB component. The phage lysis defect in the absence of a functional LysB/LysC system is appears in the presence of high concentrations of divalent cations. LysC is an Rz1-like component of a phage lytic system, substantially overlapping although not fully embedded in the gene for the Rz-like LysB component. NF038390.1 Nsidase_PpnN 450 450 450 equivalog Y Y N nucleotide 5'-monophosphate nucleosidase PpnN ppnN 3.2.2.10,3.2.2.4 31023582,31528633,33139383 1224 Pseudomonadota phylum 9274 NCBIFAM nucleotide 5'-monophosphate nucleosidase PpnN PpnN (pyrimidine/purine nucleotide 5'-monophosphate nucleosidase), widely conserved in gamma proteobacteria, plays a role in purine homeostasis. It can bind the the stringent response alarmones ppGpp and pppGpp and then, because of allosteric changes, have a much higher rate of cleavage of preferred substrate GMP. PpnN was previously known in E. coli as YgdH. NF039188.4 PF18918.5 DUF5669 25.9 25.9 76 subfamily Y Y N DUF5669 family protein 1224 Pseudomonadota phylum 2546 EBI-EMBL Family of unknown function (DUF5669) DUF5669 family protein This is a family of unknown function. Family members are mostly found in gammaproteobacteria. (from Pfam) NF039299.4 PF19357.4 DUF5934 27 27 172 domain Y Y N DUF5934 domain-containing protein 1224 Pseudomonadota phylum 11484 EBI-EMBL Family of unknown function (DUF5934) Family of unknown function (DUF5934) This presumed domain found in type IV secretion system proteins is functionally uncharacterised. This domain family is found in proteobacteria, and is approximately 170 amino acids in length. The family is found in association with Pfam:PF11130. There are two conserved sequence motifs: GWDL and QGEY. (from Pfam) NF039350.4 PF19602.4 DUF6107 27 27 106 subfamily Y Y N DUF6107 family protein 1224 Pseudomonadota phylum 678 EBI-EMBL Family of unknown function (DUF6107) DUF6107 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 105 and 125 amino acids in length. (from Pfam) NF039398.4 PF19793.4 DUF6277 32.8 32.8 117 subfamily Y Y N DUF6277 family protein 21291275 1224 Pseudomonadota phylum 102 EBI-EMBL Family of unknown function (DUF6277) DUF6277 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001096) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the FR901464 biosynthetic gene cluster from Pseudomonas sp. 2663 [1]. [1]. 21291275. Cloning and elucidation of the FR901464 gene cluster revealing a complex acyltransferase-less polyketide synthase using glycerate as starter units. Zhang F, He HY, Tang MC, Tang YM, Zhou Q, Tang GL;. J Am Chem Soc. 2011;133:2452-2462. (from Pfam) NF039434.4 PF19966.4 VMAP-M4 27 27 107 domain Y N N vWA-MoxR associated protein middle region (VMAP-M) 4 32101166 1224 Pseudomonadota phylum 13 EBI-EMBL vWA-MoxR associated protein middle region (VMAP-M) 4 vWA-MoxR associated protein middle region (VMAP-M) 4 Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. [1]. 32101166. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. Kaur G, Burroughs AM, Iyer LM, Aravind L;. Elife. 2020; [Epub ahead of print] (from Pfam) NF039439.4 PF19978.4 Inovirus_G7P_2 27 27 33 PfamEq Y Y N tail virion protein G7P-2 6945579 1224 Pseudomonadota phylum 95 EBI-EMBL Tail virion protein G7P tail virion protein G7P-2 Pfam models PF17091 and PF19978 describe two apparently unrelated small inovirus proteins with similar function, both designated G7P. This family is now called G7P-2. NF039461.4 PF20061.4 DUF6460 26.7 26.7 36 domain Y Y N DUF6460 domain-containing protein 1224 Pseudomonadota phylum 2690 EBI-EMBL Domain of unknown function (DUF6460) Domain of unknown function (DUF6460) This domain on unknown function is found at the C-terminal of uncharacterised proteins, found in Alphaproteobacteria. Proteins containing this domain are typically between 88 and 109 amino acids in length. There is a conserved motif GAxI/VVxP. Some members of this entry are likely integrases. (from Pfam) NF039597.4 PF19349.4 DUF5927 27 27 300 domain Y N N Family of unknown function (DUF5927) 1224 Pseudomonadota phylum 1672 EBI-EMBL Family of unknown function (DUF5927) Family of unknown function (DUF5927) This entry represents a presumed domain that is functionally uncharacterised. This domain family is primarily found in Rhodobacteria, and is approximately 300 amino acids in length. The family is found to the C-terminus of Pfam:PF02485 and so is likely to have a role in carbohydrate modification. (from Pfam) NF039651.4 PF19582.4 AdeT1_2 27 27 394 subfamily Y Y N putative solute-binding protein 21212056 1224 Pseudomonadota phylum 5446 EBI-EMBL Solute-binding protein AdeT 1/2 DUF6091 family protein This entry represents the Probable solute-binding protein AdeT1/2 from Acinetobacter baumannii. These proteins are involved in resistance to antibiotics by active efflux [1]. [1]. 21212056. Molecular cloning and functional characterization of two novel membrane fusion proteins in conferring antimicrobial resistance in Acinetobacter baumannii. Srinivasan VB, Rajamohan G, Pancholi P, Marcon M, Gebreyes WA;. J Antimicrob Chemother. 2011;66:499-504. (from Pfam) NF039656.4 PF19596.4 DUF6101 27 27 184 subfamily Y Y N DUF6101 family protein 1224 Pseudomonadota phylum 2699 EBI-EMBL Family of unknown function (DUF6101) DUF6101 family protein This family of proteins is functionally uncharacterised. This family of proteins is found primarily in Alphaproteobacteria. Proteins in this family are typically between 173 and 189 amino acids in length. (from Pfam) NF039666.4 PF19636.4 DUF6139 27 27 77 subfamily Y Y N DUF6139 family protein 1224 Pseudomonadota phylum 425 EBI-EMBL Family of unknown function (DUF6139) DUF6139 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. There are two conserved sequence motifs: EATN and KGYAI. (from Pfam) NF039725.4 PF19837.4 DUF6316 28.5 28.5 55 subfamily Y Y N DUF6316 family protein 1224 Pseudomonadota phylum 1488 EBI-EMBL Domain of unknown function (DUF6316) DUF6316 family protein This domain is found in bacterial proteins, functionally uncharacterised. It is approximately 50-70 amino acids in length and it has the conserved sequence TRExxxxGPF/Y. (from Pfam) NF039727.4 PF19849.4 DUF6324 27 27 60 subfamily Y Y N DUF6324 family protein 1224 Pseudomonadota phylum 1316 EBI-EMBL Family of unknown function (DUF6324) DUF6324 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There are two conserved sequence motifs: QIGPT and GMVR. (from Pfam) NF039754.4 PF19924.4 DUF6387 28.9 28.9 258 subfamily Y Y N DUF6387 family protein 17049458 1224 Pseudomonadota phylum 4150 EBI-EMBL Family of unknown function (DUF6387) DUF6387 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001055) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the yersiniabactin biosynthetic gene cluster from Escherichia coli [1]. This family appears to be predominantly found in proteobacteria. [1]. 17049458. Specific regions of genome plasticity and genetic diversity of the commensal Escherichia coli A0 34/86. Hejnova J, Pages D, Rusniok C, Glaser P, Sebo P, Buchrieser C;. Int J Med Microbiol. 2006;296:541-546. (from Pfam) NF039755.4 PF19930.4 DUF6393 26.9 26.9 96 subfamily Y Y N DUF6393 family protein 21609846 1224 Pseudomonadota phylum 152 EBI-EMBL Family of unknown function (DUF6393) DUF6393 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000385) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the lysobactin biosynthetic gene cluster from Lysobacter sp. ATCC 53042 [1]. [1]. 21609846. Identification and characterization of the lysobactin biosynthetic gene cluster reveals mechanistic insights into an unusual termination module architecture. Hou J, Robbel L, Marahiel MA;. Chem Biol. 2011;18:655-664. (from Pfam) NF039802.4 PF20121.4 DUF6511 28 28 69 domain Y Y N DUF6511 domain-containing protein 1224 Pseudomonadota phylum 1536 EBI-EMBL Family of unknown function (DUF6511) DUF6511 domain This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 87 and 141 amino acids in length. (from Pfam) NF039865.4 PF19114.5 EsV_1_7_cys 25 5 35 domain Y N N EsV-1-7 cysteine-rich motif 28049657,30644818 1224 Pseudomonadota phylum 183 EBI-EMBL EsV-1-7 cysteine-rich motif EsV-1-7 cysteine-rich motif The EsV-1-7 repeat is a cysteine-rich motif of unknown function. The motif was originally identified in the Ectocarpus "immediate upright" protein, which has an EsV-1-7 domain that contains five EsV-1-7 repeats [1]. The name is derived from the Ectocarpus virus EsV-1 protein EsV-1-7, which possesses six EsV-1-7 repeats. Ectocarpus has a large family of EsV-1-7 domain proteins with between one and 19 copies of the motif (C-X4-C-X16-C-X2-H-X12). In addition to brown algae, EsV-1-7 domain proteins have been found in eustigmatophytes, oomycetes, cryptophytes, two families of green algae (Coccomyxaceae and Selenastraceae) and also in viral genomes, such as Emiliania huxleyi virus PS401 and Pithovirus sibericum. Based on this unusual distribution, it has been proposed that EsV-1-7 domain genes have been exchanged between lineages by horizontal gene transfer during evolution [1,2]. [1]. 28049657. The Ectocarpus IMMEDIATE UPRIGHT gene encodes a member of a novel family of cysteine-rich proteins with an unusual distribution across the eukaryotes. Macaisne N, Liu F, Scornet D, Peters AF, Lipinska A, Perrineau MM, Henry A, Strittmatter M, Coelho SM, Cock JM;. Development. 2017;144:409-418. [2]. 30644818. Convergent recruitment of TALE homeodomain life cycle regulators to direct sporophyte development in land plants and brown algae. Arun A, Coelho SM, Peters AF, Bourdareau S, Peres L, Scornet D, Strittmatter M, Lipinska AP, Yao H, Godfroy O, Montecinos GJ, Avia K, Macaisne N, Troadec C, Bendahmane A, Cock JM;. Elife. 2019; [Epub ahead of print] (from Pfam) NF039920.4 PF19350.4 DUF5928 27 27 256 domain Y Y N DUF5928 domain-containing protein 1224 Pseudomonadota phylum 1690 EBI-EMBL Family of unknown function (DUF5928) Family of unknown function (DUF5928) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 260 amino acids in length. The family is found to the C-terminus of Pfam:PF02485 and so is likely to have a role in carbohydrate modification. (from Pfam) NF039962.4 PF19495.4 DUF6030 26.7 26.7 254 subfamily Y Y N DUF6030 family protein 9914965 1224 Pseudomonadota phylum 1456 EBI-EMBL Family of unknown function (DUF6030) DUF6030 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000762) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a protein from the exopolysaccharide biosynthetic gene cluster from Rhizobium leguminosarum bv. viciae and appears to be predominantly found in proteobacteria [1]. [1]. 9914965. [Structure-functional organization of exopolysaccharide biosynthetic genes in Rhizobium leguminosarum bv. viciae VF39]. Sadykov MR, Ivashina TV, Kanapin AA, Shliapnikov MG, Ksenzenko VN;. Mol Biol (Mosk). 1998;32:797-804. (from Pfam) NF040002.4 PF19624.4 DUF6129 23.6 23.6 53 subfamily Y Y N DUF6129 family protein 1224 Pseudomonadota phylum 454 EBI-EMBL Family of unknown function (DUF6129) DUF6129 family protein This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 50 amino acids in length. (from Pfam) NF040027.4 PF19723.4 DUF6216 27.3 27.3 270 subfamily Y Y N DUF6216 family protein 17049458 1224 Pseudomonadota phylum 2244 EBI-EMBL Family of unknown function (DUF6216) DUF6216 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001055) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the yersiniabactin biosynthetic gene cluster from Escherichia coli [1]. This family appears to be predominantly found in Proteobacteria. [1]. 17049458. Specific regions of genome plasticity and genetic diversity of the commensal Escherichia coli A0 34/86. Hejnova J, Pages D, Rusniok C, Glaser P, Sebo P, Buchrieser C;. Int J Med Microbiol. 2006;296:541-546. (from Pfam) NF040030.4 PF19742.4 DUF6231 35 35 145 subfamily Y Y N DUF6231 family protein 17506328,22615797 1224 Pseudomonadota phylum 3442 EBI-EMBL Family of unknown function (DUF6231) DUF6231 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000387) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the mangotoxin biosynthetic gene cluster from Pseudomonas syringae pv. syringae [1,2]. This family appears to be predominantly found in Proteobacteria. [1]. 17506328. A nonribosomal peptide synthetase gene (mgoA) of Pseudomonas syringae pv. syringae is involved in mangotoxin biosynthesis and is required for full virulence. Arrebola E, Cazorla FM, Romero D, Perez-Garcia A, de Vicente A;. Mol Plant Microbe Interact. 2007;20:500-509. [2]. 22615797. The mbo operon is specific and essential for biosynthesis of mangotoxin in Pseudomonas syringae. Carrion VJ, Arrebola E, Cazorla FM, Murillo J, de Vicente A;. PLoS One. 2012;7:e36709. (from Pfam) NF040085.4 PF19942.4 DUF6404 27.6 27.6 115 subfamily Y Y N DUF6404 family protein 17049458 1224 Pseudomonadota phylum 4397 EBI-EMBL Family of unknown function (DUF6404) DUF6404 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001055) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the yersiniabactin biosynthetic gene cluster from Escherichia coli [1]. This family appears to be predominantly found in Proteobacteria. [1]. 17049458. Specific regions of genome plasticity and genetic diversity of the commensal Escherichia coli A0 34/86. Hejnova J, Pages D, Rusniok C, Glaser P, Sebo P, Buchrieser C;. Int J Med Microbiol. 2006;296:541-546. (from Pfam) NF040106.4 PF20044.4 DUF6446 26.7 26.7 129 subfamily Y Y N DUF6446 family protein 1224 Pseudomonadota phylum 1652 EBI-EMBL Family of unknown function (DUF6446) DUF6446 family protein This family of proteins is functionally uncharacterised. This family of proteins is predominantly found in Rhodobacterales. Proteins in this family are typically between 160 and 175 amino acids in length. There are some conserved motifs: IDA/S, SSPxRxRACF and DG. Many members in this family are thought to be histidine kinases. (from Pfam) NF040324.4 PF19600.4 DUF6105 27 27 110 subfamily Y Y N DUF6105 family protein 1224 Pseudomonadota phylum 1218 EBI-EMBL Family of unknown function (DUF6105) DUF6105 family protein This family of putative integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. (from Pfam) NF040327.4 PF19606.4 DUF6111 24.1 24.1 87 subfamily Y Y N DUF6111 family protein 1224 Pseudomonadota phylum 1373 EBI-EMBL Family of unknown function (DUF6111) DUF6111 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 86 and 106 amino acids in length. (from Pfam) NF040338.4 PF19661.4 DUF6164 27 27 116 subfamily Y Y N DUF6164 family protein 1224 Pseudomonadota phylum 1600 EBI-EMBL Family of unknown function (DUF6164) DUF6164 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. (from Pfam) NF040344.4 PF19678.4 DUF6180 26.9 26.9 102 subfamily Y Y N DUF6180 family protein 21609846 1224 Pseudomonadota phylum 159 EBI-EMBL Family of unknown function (DUF6180) DUF6180 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000385) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the lysobactin biosynthetic gene cluster from Lysobacter sp. ATCC 53042 [1]. [1]. 21609846. Identification and characterization of the lysobactin biosynthetic gene cluster reveals mechanistic insights into an unusual termination module architecture. Hou J, Robbel L, Marahiel MA;. Chem Biol. 2011;18:655-664. (from Pfam) NF040369.4 PF19796.4 DUF6280 27 27 86 subfamily Y Y N DUF6280 family protein 1224 Pseudomonadota phylum 804 EBI-EMBL Family of unknown function (DUF6280) DUF6280 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in Alphaproteobacteria. Proteins in this family are approximately 110 amino acids in length. (from Pfam) NF040398.4 PF19925.4 DUF6388 25 25 107 subfamily Y Y N DUF6388 family protein 22615277,3759643 1224 Pseudomonadota phylum 2775 EBI-EMBL Family of unknown function (DUF6388) DUF6388 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001859) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular fosfomycin biosynthetic gene cluster from Pseudomonas syringae [1,2]. This family is predominantly found in proteobacteria. Some members of this family have been putatively identified as DNA repair proteins. [1]. 22615277. Different biosynthetic pathways to fosfomycin in Pseudomonas syringae and Streptomyces species. Kim SY, Ju KS, Metcalf WW, Evans BS, Kuzuyama T, van der Donk WA;. Antimicrob Agents Chemother. 2012;56:4175-4183. [2]. 3759643. Production of fosfomycin (phosphonomycin) by Pseudomonas syringae. Shoji J, Kato T, Hinoo H, Hattori T, Hirooka K, Matsumoto K, Tanimoto T, Kondo E;. J Antibiot (Tokyo). 1986;39:1011-1012. (from Pfam) NF040400.4 PF19933.4 DUF6396 28.2 28.2 108 domain Y Y N DUF6396 domain-containing protein 1224 Pseudomonadota phylum 5371 EBI-EMBL Domain of unknown function (DUF6396) DUF6396 domain This presumed domain of unknown function is found in uncharacterised proteins mainly from Proteobacteria, and is about 100 amino acids in length. It has the conserved sequences RxxRY and PLPPAxLPxWDG. (from Pfam) NF040436.4 PF20083.4 DUF6477 25 25 97 subfamily Y Y N DUF6477 family protein 1224 Pseudomonadota phylum 1724 EBI-EMBL Family of unknown function (DUF6477) DUF6477 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 96 and 116 amino acids in length. (from Pfam) NF040445.4 PF20107.4 DUF6497 24.3 24.3 116 subfamily Y Y N DUF6497 family protein 1224 Pseudomonadota phylum 1517 EBI-EMBL Family of unknown function (DUF6497) DUF6497 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 121 and 153 amino acids in length. (from Pfam) NF040448.4 PF20115.4 DUF6505 23.9 23.9 159 subfamily Y Y N DUF6505 family protein 1224 Pseudomonadota phylum 1847 EBI-EMBL Family of unknown function (DUF6505) DUF6505 family protein This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 100 amino acids in length. (from Pfam) NF040482.1 auto_BafA_Cterm 700 700 643 equivalog_domain Y Y N BafA family autotransporter bafA 32678094 1224 Pseudomonadota phylum 538 NCBIFAM BafA family autotransporter C-terminal domain BafA from both Bartonella henselae and Bartonella quintana, and possibly all Bartonella BafA, are mitogenic autotransporter virulence factors that help induce vasoproliferative lesions during infection. This HMM represents the more conserved C-terminal portion only, as the passenger region is more highly variable in length and sequence. NF040487.1 T3SS_CigR_fam 78 78 148 subfamily Y Y N anti-virulence regulator CigR family protein 29858228,30173754 1224 Pseudomonadota phylum 5699 NCBIFAM anti-virulence regulator CigR family protein Members of this family are full-length homologs of CigR, an inner membrane protein that appears to act as an anti-virulence factor. It was previously thought to be exported as a type III secretion system (T3SS) effector. A low-complexity, variable length repetitive region, rich in Gly, Pro, His, Lys, and Asn, separates a short, hydrophobic N-terminal domain from a longer, well-conserved C-terminal domain. A short stretch of that C-terminal domain, about 25 amino acids long, shows similarity to the C-terminal half of the domain described by Pfam model PF11776.10 (RcnB), but similarity between CigR and RcnB is not extensive. NF040527.2 blaOXA-5_like 574 574 267 exception Y Y Y OXA-5 family class D beta-lactamase blaOXA 3.5.2.6 GO:0008800 19721065 1224 Pseudomonadota phylum 7 NCBIFAM OXA-5 family class D beta-lactamase Members of this family occur typically in class 1 integrons. The founding member, OXA-5, hydrolyzes only a narrow spectrum of beta-lactams, namely narrow-spectrum penicillins, oxacillin, and cephalothin. NF040582.1 STY4528_fam 130 130 323 equivalog Y Y N STY4528 family pathogenicity island replication protein 15271940,22247511 1224 Pseudomonadota phylum 5618 NCBIFAM STY4528 family pathogenicity island replication protein The founding member of this family, STY4528 from Salmonella pathogenicity island 7 (SPI-7) of Salmonella typhi, belongs to the core set of proteins of SPI-7-related conjugative elements, and is assigned to the replication region. Members include a protein designated Api5 from the Yersinia pseudotuberculosis adhesion pathogenicity island (YAPI). NF040584.1 STY4534_fam 160 160 125 equivalog Y Y N STY4534 family ICE replication protein 22247511 1224 Pseudomonadota phylum 2554 NCBIFAM STY4534 family ICE replication protein Members of this family regularly are found near a TopB family topoisomerase, in mobile elements such as certain pathogenicity islands, in regions of those islands thought to be involved in replication. The founding member of the family is STY4534 in Salmonella pathogenicity island 7 (SPI-7), a core protein shared by members of SPI-7's subclass of integrative and conjugative element (ICE). NF040641.1 bifunc_ST_SDO 625 625 423 equivalog Y Y N bifunctional sulfur transferase/dioxygenase Blh blh 29472641 1224 Pseudomonadota phylum 1240 NCBIFAM bifunctional sulfur transferase/dioxygenase Blh NF040642.1 sulf_sens_BigR 155 155 95 equivalog Y Y N sulfite-sensing transcriptional repressor BigR bigR 29472641 1224 Pseudomonadota phylum 537 NCBIFAM sulfite-sensing transcriptional repressor BigR BigR (biofilm growth-associated repressor) is a winged-helix DNA-binding protein active as a transcriptional regulator for Blh, a bifunctional sulfur transferase/dioxygenase found in a number of plant-associated bacteria. Oxidative conditions that allow disulfide bond formation between the invariant residues Cys42 and Cys108 cause BigR to lose DNA-binding transcriptional repressor activity. NF040697.1 VPA1267_fam 90 90 143 equivalog Y Y N VPA1267 family protein 16672049 1224 Pseudomonadota phylum 687 NCBIFAM VPA1267 family protein Members of this family occur in mobile elements, as for VPA1267 found in pathogenicity island 6 of Vibrio parahaemolyticus RIMD2210633. NF040702.1 ileS_w_GNAT 1999 1999 1100 exception Y Y N isoleucine--tRNA ligase, N-acetyltransferase domain-containing ileS 6.1.1.5 GO:0004822,GO:0005737,GO:0006428,GO:0008080 1224 Pseudomonadota phylum 168 NCBIFAM isoleucine--tRNA ligase, N-acetyltransferase domain-containing This unusual form of isoleucine--tRNA ligase, found in at least six different species of Moraxella, has a GNAT-type N-acetyltransferase domain, about 170 amino acids long, inserted after position 270 of forms lacking the insert, such as that of Escherichia coli. NF040812.1 blaGMA 600 600 282 exception Y Y Y GMA family class A beta-lactamase blaGMA 3.5.2.6 GO:0008800 1224 Pseudomonadota phylum 3 NCBIFAM GMA family class A beta-lactamase NF040876.1 RHE_PE00001_fam 250 250 371 equivalog Y Y N RHE_PE00001 family protein 21217003 1224 Pseudomonadota phylum 3639 NCBIFAM RHE_PE00001 family protein RHE_PE00001, the founding member of this family, was shown to be essential for growth on rich medium, despite being encoded on a plasmid. Members of this family contain an apparent helix-turn-helix domain described by Pfam model PF11972, suggesting DNA-binding activity. NF040888.1 trans_reg_YafC 470 470 293 equivalog Y Y N DNA-binding transcriptional regulator YafC yafC GO:0003700,GO:0006355 30137486 1224 Pseudomonadota phylum 3254 NCBIFAM DNA-binding transcriptional regulator YafC NF041066.2 DpdI 150 150 239 equivalog Y Y N protein DpdI dpdI 26929322,30159947 1224 Pseudomonadota phylum 142 NCBIFAM protein DpdI NF041265.1 NadS 60 60 94 equivalog Y Y N NadS family protein nadS 22153074 1224 Pseudomonadota phylum 2655 NCBIFAM NadS family protein NF041281.1 TraA_gammapb 50 50 75 subfamily Y Y N TraA family conjugative transfer protein traA 21223599 1224 Pseudomonadota phylum 914 NCBIFAM TraA family conjugative transfer protein NF041282.1 TnpC_regulator 100 100 105 equivalog Y Y N Tn3 family transposase post-transcriptional regulator TnpC tnpC 10515920,22878084 1224 Pseudomonadota phylum 381 NCBIFAM Tn3 family transposase post-transcriptional regulator TnpC NF041289.1 KorA 100 100 91 subfamily Y Y N KorA family transcriptional regulator korA 7473715,7891554,8029323 1224 Pseudomonadota phylum 156 NCBIFAM KorA family transcriptional regulator NF041292.1 StbB 200 200 233 subfamily Y Y N StbB family protein stbB 21625564 1224 Pseudomonadota phylum 1349 NCBIFAM StbB family protein NF041295.1 dynobact_RiPP 40 40 48 equivalog Y Y N dynobactin A family peptide antibiotic dynB 36163500 1224 Pseudomonadota phylum 24 NCBIFAM dynobactin A family peptide antibiotic Members of this family are RiPP precursor peptides modified by radical SAM/SPASM enzyme maturases. The founding member of this family, from Photorhabdus australis, has the ten amino amino acids WNSNVHSYRF in the mature product called dynobactin A. This antibiotic targets BamA, involved in the insertion of beta-barrel proteins correctly into the outer membrane. NF041307.1 AvrBs1 400 400 435 subfamily Y Y N AvrBs1/Avra family type III secretion system effector avrBs1 GO:0030254 20573017,2979910 1224 Pseudomonadota phylum 75 NCBIFAM AvrBs1/Avra family type III secretion system effector NF041309.2 XopB 700 700 516 subfamily Y Y N XopB/HopD1 family type III secretion system effector xopB GO:0030254 22738163,27398933 1224 Pseudomonadota phylum 252 NCBIFAM XopB/HopD1 family type III secretion system effector NF041334.1 XopJ 400 400 349 equivalog Y Y N YopJ family type III secretion system effector XopJ xopJ GO:0030254 14645268,25739698 1224 Pseudomonadota phylum 127 NCBIFAM YopJ family type III secretion system effector XopJ NF041337.1 XopD 700 700 735 subfamily Y Y N Ulp1 family type III secretion system effector isopeptidase XopD xopD GO:0006508,GO:0019784,GO:0030254 23414755 1224 Pseudomonadota phylum 36 NCBIFAM Ulp1 family type III secretion system effector isopeptidase XopD NF041338.2 XopE 400 400 358 subfamily Y Y N XopE/AvrPphe family type III secretion system effector xopE GO:0030254 19849782 1224 Pseudomonadota phylum 285 NCBIFAM XopE/AvrPphe family type III secretion system effector NF041346.1 XopF2 600 600 546 subfamily Y Y N type III secretion system effector XopF2 xopF2 GO:0030254 19849782 1224 Pseudomonadota phylum 60 NCBIFAM type III secretion system effector XopF2 NF041347.1 XopG 150 150 201 subfamily Y Y N XopG/HopH/AvrPtoH family type III secretion system effector xopG GO:0030254 19849782,35150038 1224 Pseudomonadota phylum 366 NCBIFAM XopG/HopH/AvrPtoH family type III secretion system effector NF041348.1 XopH 500 500 368 equivalog Y Y N type III secretion system effector XopH xopH GO:0030254 19849782,29255246 1224 Pseudomonadota phylum 62 NCBIFAM type III secretion system effector XopH NF041353.1 XopO 300 300 218 subfamily Y Y N XopO/AvrRps4 family type III secretion system effector xopO GO:0030254 19849782,35616618 1224 Pseudomonadota phylum 52 NCBIFAM XopO/AvrRps4 family type III secretion system effector NF041354.1 XopP 800 800 715 equivalog Y Y N type III secretion system effector XopP xopP GO:0030254 19849782,25388636,35640532 1224 Pseudomonadota phylum 679 NCBIFAM type III secretion system effector XopP NF041355.1 XopQ 500 500 402 equivalog Y Y N type III secretion system effector XopQ xopQ GO:0030254 19849782,25079351,32654337 1224 Pseudomonadota phylum 420 NCBIFAM type III secretion system effector XopQ NF041357.1 XopU 1800 1800 984 equivalog Y Y N type III secretion system effector protein XopU xopU GO:0030254 19849782 1224 Pseudomonadota phylum 57 NCBIFAM type III secretion system effector protein XopU NF041375.1 XopV 220 220 261 subfamily Y Y N XopV/AopV family type III secretion system effector xopV GO:0030254 19849782,36233021 1224 Pseudomonadota phylum 234 NCBIFAM XopV/AopV family type III secretion system effector NF041381.1 XopAC 450 450 451 subfamily Y Y N XopAC/AvrAC family type III secretion system effector xopAC GO:0030254 17951377,19849782,23951354 1224 Pseudomonadota phylum 95 NCBIFAM XopAC/AvrAC family type III secretion system effector NF041399.1 XopAD 2000 2000 2133 subfamily Y Y N XopAD/skwp family type III secretion system effector xopAD GO:0030254 19849782 1224 Pseudomonadota phylum 1621 NCBIFAM XopAD/skwp family type III secretion system effector NF041401.1 XopAF 200 200 205 subfamily Y Y N XopAF/AvrXv3 family type III secretion system effector xopAF GO:0030254 10975648,19849782 1224 Pseudomonadota phylum 347 NCBIFAM XopAF/AvrXv3 family type III secretion system effector NF041402.1 XopAG 400 400 432 subfamily Y Y N XopAG/AvrGf1 family type III secretion system effector xopAG GO:0030254 19849782,27030294 1224 Pseudomonadota phylum 371 NCBIFAM XopAG/AvrGf1 family type III secretion system effector NF041404.1 XopAI 300 300 251 equivalog Y Y N type III secretion system effector XopAI xopAI GO:0030254 19849782,31615004 1224 Pseudomonadota phylum 49 NCBIFAM type III secretion system effector XopAI NF041406.1 XopAK 150 150 173 subfamily Y Y N XopAK family type III secretion system effector xopAK GO:0030254 19849782 1224 Pseudomonadota phylum 178 NCBIFAM XopAK family type III secretion system effector NF041407.1 XopAP 400 400 318 subfamily Y Y N XopAP family type III secretion system effector xopAP GO:0030254 26104875,35972796 1224 Pseudomonadota phylum 239 NCBIFAM XopAP family type III secretion system effector NF041408.1 XopAU 450 450 498 subfamily Y Y N XopAU family type III secretion system effector serine/threonine kinase xopAU 26104875,29377937 1224 Pseudomonadota phylum 242 NCBIFAM XopAU family type III secretion system effector serine/threonine kinase NF041412.1 XopC 1000 1000 828 subfamily Y Y N XopC/Rsp1239 family type III secretion system effector xopC GO:0030254 14645268,19849782,20121447 1224 Pseudomonadota phylum 53 NCBIFAM XopC/Rsp1239 family type III secretion system effector NF041432.1 MchS3 100 100 105 subfamily Y Y N MchS3 family protein mchS3 10471561,16569859,9783429 1224 Pseudomonadota phylum 288 NCBIFAM MchS3 family protein NF041434.1 UmoC 120 120 105 subfamily Y Y N UmoC family flagellar biogenesis regulator umoC 9723914 1224 Pseudomonadota phylum 197 NCBIFAM UmoC family flagellar biogenesis regulator NF041437.1 TfpZ 200 200 240 superfamily Y Y N TfpX/TfpZ family type IV pilin accessory protein tfpZ 15133094 1224 Pseudomonadota phylum 1463 NCBIFAM TfpX/TfpZ family type IV pilin accessory protein NF041440.1 hydrolase_YghX 460 460 292 exception Y Y N YghX family hydrolase yghX 3.-.-.- 30470963 1224 Pseudomonadota phylum 4895 NCBIFAM YghX family hydrolase YghX is a predicted hydrolase, homologous to dienelactone hydrolases, but its function is unknown. YghX is encoded intact in Escherichia coli O157:H7 str. Sakai, but is a frameshifted pseudogene in Escherichia coli K-12 MG1655, and consequently is used occasionally as a site for minimally disruptive genetic engineering. NF041455.1 DSF_Ax21 200 200 184 subfamily Y Y N diffusible signal factor-reguated Ax21 faimly protein 22204763,23688240 1224 Pseudomonadota phylum 741 NCBIFAM diffusible signal factor-reguated Ax21 faimly protein NF041466.1 factorH_bind 200 200 279 equivalog Y Y N factor H-binding protein 15608208,26057742,29847547 1224 Pseudomonadota phylum 433 NCBIFAM factor H-binding protein NF041487.1 copper_ox_MnxG 3100 3100 1894 equivalog Y Y N manganese-oxidizing multicopper oxidase MnxG mnxG GO:0005507 23124227,27084014 1224 Pseudomonadota phylum 1094 NCBIFAM manganese-oxidizing multicopper oxidase MnxG NF041494.1 MobH 200 200 340 equivalog Y Y N MobH family relaxase mobH 31584171 1224 Pseudomonadota phylum 8004 NCBIFAM MobH family relaxase NF041525.1 HrpD5 300 300 314 equivalog Y Y N HrpD5 family protein hrpD5 11410350,21615204 1224 Pseudomonadota phylum 696 NCBIFAM HrpD5 family protein NF041544.1 ParC 95 95 80 equivalog Y Y N ParC family partition-associated protein parC 15995187,27014233 1224 Pseudomonadota phylum 116 NCBIFAM ParC family partition-associated protein NF041577.1 nside_bi_sphtase 400 400 276 equivalog Y Y N 3',5'-nucleoside bisphosphate phosphatase 3.1.3.97 GO:0016311,GO:0097657 24401123 1224 Pseudomonadota phylum 3621 NCBIFAM 3',5'-nucleoside bisphosphate phosphatase NF041590.1 blaCAE 625 625 300 exception Y Y Y CAE family broad-spectrum class A beta-lactamase blaCAE 3.5.2.6 GO:0008800 36869066 1224 Pseudomonadota phylum 5 NCBIFAM CAE family broad-spectrum class A beta-lactamase CAE-1 (Comamonas aquatica enzyme, allele 1), expressed in a test strain of E. coli, conferred resistance to ampicillin, piperacillin, cefazolin, cefuroxime, and ceftriaxone. NF041599.1 reg_PtrA_PA2808 31 31 46 domain Y Y N co-regulatory protein PtrA N-terminal domain-containing protein 15469505 1224 Pseudomonadota phylum 2009 NCBIFAM co-regulatory protein PtrA N-terminal domain This HMM describes a shared N-terminal region of several families of proteins, some of which contain a C-terminal DUF2790 (PF10976) domain. The founding member of this family, PA2808 of Pseudomonas aeruginosa PAO1, was found to suppress expression of the type III secretion system (T3SS) via a protein-protein interaction with the T3SS transcriptional activator ExsA. It was named PtrA (Pseudomonas type III repressor A). Homologs are found broadly throughout the Pseudomonas genus. NF041602.1 VF_A0006_fam 65 65 89 subfamily Y Y N VF_A0006 family four-cysteine protein 1224 Pseudomonadota phylum 575 NCBIFAM VF_A0006 family four-cysteine protein Members of this family, including VF_A0006 of Vibrio fischeri, PSPA7_2531 of Pseudomonas aeruginosa, and BPSL3341 from Burkholderia pseudomallei, have an N-terminal signal peptide and four invariant Cys residues suggesting the formation of two disulfide bonds. The function is unknown. NF041631.1 KRQAASG_repeat 30 30 21 domain N N N KRQAASG repeat spurious translation 1224 Pseudomonadota phylum 634 NCBIFAM KRQAASG repeat spurious translation This AntiFam-like HMM describes spurious translations from an intergenic repeat common in Burkholderia. NF041636.1 slam_lipo 80 80 154 equivalog Y Y N Slam-dependent surface lipoprotein 28620585 1224 Pseudomonadota phylum 3239 NCBIFAM Slam-dependent surface lipoprotein NF041650.1 nod_mtase_NodS 300 300 190 equivalog Y Y N nodulation methyltransferase NodS nodS 2.1.1.- GO:0008757,GO:0009312 2134855,2134856,7772799 1224 Pseudomonadota phylum 518 NCBIFAM nodulation methyltransferase NodS NF041651.1 nodul_NodU 1000 1000 556 equivalog Y Y N nodulation protein NodU nodU 2.1.3.- GO:0016740 2134856,7559434 1224 Pseudomonadota phylum 669 NCBIFAM nodulation protein NodU NF041684.1 ant_diox_AndAc 750 750 418 equivalog Y Y N anthranilate 1,2-dioxygenase large subunit AndAc andAc 1.14.12.1 GO:0009056,GO:0018618 13129960,22360670 1224 Pseudomonadota phylum 714 NCBIFAM anthranilate 1,2-dioxygenase large subunit AndAc NF041685.1 ant_diox_AndAd 230 230 155 equivalog Y Y N anthranilate 1,2-dioxygenase small subunit AndAd andAd 1.14.12.1 GO:0009056,GO:0018618 13129960,22360670 1224 Pseudomonadota phylum 425 NCBIFAM anthranilate 1,2-dioxygenase small subunit AndAd NF041728.1 BPSL0761_fam 35 35 55 subfamily Y Y N BPSL0761 family protein 1224 Pseudomonadota phylum 1729 NCBIFAM BPSL0761 family protein Members of this family are found in Pseudomonas, Xanthomonas, and related genera. C-terminal regions are poorly conserved, variable in length, and not included in the seed alignment. NF041743.1 RdrA 600 600 742 equivalog Y Y N antiviral RADAR system adenosine triphosphatase RdrA rdrA GO:0051607 32855333 1224 Pseudomonadota phylum 498 NCBIFAM antiviral RADAR system adenosine triphosphatase RdrA Proteins of this family are the essential components of the anti-phage system RADAR (restriction by an adenosine deaminase acting on RNA). RADAR mediates RNA editing in response to phage infections. NF041744.1 RdrB 800 800 850 equivalog Y Y N antiviral RADAR system adenosine deaminase RdrB rdrB GO:0019239,GO:0051607 32855333 1224 Pseudomonadota phylum 555 NCBIFAM antiviral RADAR system adenosine deaminase RdrB Proteins of this family are adenosine deaminases, which are the essential components of the anti-phage system RADAR (restriction by an adenosine deaminase acting on RNA). RADAR mediates RNA editing in response to phage infections. NF041745.1 RdrD 230 230 227 equivalog Y Y N antiviral RADAR system accessory protein RdrD rdrD 32855333 1224 Pseudomonadota phylum 44 NCBIFAM antiviral RADAR system accessory protein RdrD Proteins of this family are accessory components of the anti-phage system RADAR (restriction by an adenosine deaminase acting on RNA). RADAR mediates RNA editing in response to phage infections. NF041760.1 PtuA 500 500 524 equivalog Y Y N retron Ec78 anti-phage system effector ATPase PtuA ptuA GO:0051607 1224 Pseudomonadota phylum 402 NCBIFAM retron Ec78 anti-phage system effector ATPase PtuA NF041814.1 Avs5 1000 1000 763 equivalog Y Y N AVAST type 5 anti-phage protein Avs5 avs5 32855333 1224 Pseudomonadota phylum 43 NCBIFAM AVAST type 5 anti-phage protein Avs5 NF041827.1 YtfQ_transport 510 510 320 equivalog Y Y N galactofuranose ABC transporter, galactofuranose-binding protein YtfQ ytfQ 7.5.2.9 GO:0042875,GO:0103116 30698741 1224 Pseudomonadota phylum 3635 NCBIFAM galactofuranose ABC transporter, galactofuranose-binding protein YtfQ NF041856.1 CrpP_rel_fam 35 35 54 subfamily Y Y N CrpP-related protein 29581123,34001507 1224 Pseudomonadota phylum 764 NCBIFAM CrpP-related protein Members of this uncharacterized protein family show sequence similarity, and apparently homology, to a family of integrative and conjugative element (ICE) proteins that has the founding member CrpP. Although CrpP, a protein about 65 aminos in length, was originally described as ciprofloxacin-inactivating enzyme that works by phosphorylation, that assertion has since been challenged. See BlastRule NBR016116 and HMM NF033696 for more information about CrpP and the family of proteins most closely related to it. NF041859.1 silencer_MvaTU 75 75 120 equivalog Y Y N histone-like nucleoid-structuring protein, MvaT/MvaU family GO:0003677,GO:0071824 22798496,26068099,30782629 1224 Pseudomonadota phylum 5673 NCBIFAM histone-like nucleoid-structuring protein, MvaT/MvaU family Paralogs MvaT and MvaU from Pseudomonas aeruginosa previously were viewed (or at least annotated) as transcription factors based on changes they mediated in the expression of various genes. However, like other histone-like nucleoid structuring proteins, MvaT, MvaU, and their homologs are considered to be xenogeneic silencers, part of a host cell defense against invasive DNA. Note that many secretion systems and virulence factors have xenogeneic origins, so modulation of the ability of these DNA-binding protein to inhibit transcription may become part of the regulatory networks of such systems. NF041861.1 YtfR_transport 850 850 492 equivalog Y Y N galactofuranose ABC transporter, ATP-binding protein YtfR ytfR 7.5.2.9 GO:0042875,GO:0103116 30698741 1224 Pseudomonadota phylum 4601 NCBIFAM galactofuranose ABC transporter, ATP-binding protein YtfR NF041886.1 Rmf_CrpP_fam 28 28 39 subfamily Y Y N Rmf/CrpP family protein 1224 Pseudomonadota phylum 3966 NCBIFAM Rmf/CrpP family protein This HMM describes a family of proteins about 60 amino acids in length with a near invariant CPY motif and with highly similar structures as predicted by AlphaFold. Members include Rmf (ribosome modulation factor), the integrative and conjugative element (ICE) protein CrpP, and a putative phage structural protein found encoded major and minor capsid proteins. AlphaFoldDB structures showing similar predicted folds include A0A0Q4SRM6, A0A5B7UVE0, and A0A6L9FUH1. NF041927.1 Xrt_dep_XDP1 125 125 242 equivalog Y Y N exosortase-dependent surface protein XDP1 xdp1 1224 Pseudomonadota phylum 647 NCBIFAM exosortase-dependent surface protein XDP1 All members of this family, here named XDP1 (exosortase-dependent surface protein 1), have an N-terminal signal peptide and a C-terminal sorting signal for recognition and cleavage by exosortase family intramembrane endopeptidases. The sorting signal is typically VPEP-CTERM, but variant forms of the motif, such as VSEP or VPLPA, do occur in the family. NF041931.2 MzaA 800 800 726 equivalog Y Y N MZA anti-phage system associated sigma-70 family RNA polymerase sigma factor MzaA mzaA GO:0003700,GO:0006355,GO:0016987,GO:0051607 32855333 1224 Pseudomonadota phylum 100 NCBIFAM MZA anti-phage system associated sigma-70 family RNA polymerase sigma factor MzaA Proteins of this family are sigma-70 family RNA polymerase sigma factors, which are associated with the MZA anti-phage system (MutL, Z1, and AIPR). The function of this protein in the MZA anti-phage system is not understood yet. NF041932.1 MzaB 850 850 480 equivalog Y Y N MZA anti-phage system associated ATPase MzaB mzaB GO:0051607 32855333 1224 Pseudomonadota phylum 146 NCBIFAM MZA anti-phage system associated ATPase MzaB Proteins of this family are components of the MZA anti-phage system (MutL, Z1, and AIPR). The function of this protein in the MZA anti-phage system is not understood yet. NF041935.1 MzaE 1050 1050 593 equivalog Y Y N MZA anti-phage system associated AIPR family protein MzaE mzaE GO:0051607 32855333 1224 Pseudomonadota phylum 150 NCBIFAM MZA anti-phage system associated AIPR family protein MzaE Proteins of this family are components of the MZA anti-phage system (MutL, Z1, and AIPR). The function of this protein in the MZA anti-phage system is not understood yet. NF042415.1 STY0301_fam 22 22 137 subfamily Y Y N STY0301 family protein 1224 Pseudomonadota phylum 2518 NCBIFAM STY0301 family protein Members of this highly divergent protein family average about 135 amino acids in length. Near-invariant residues or motifs include CP, GxP, LxP, CxY, and two additional Cys residues. The function is unknown. NF042419.1 Phyto_syn_CrtB 480 480 306 equivalog Y Y N 15-cis-phytoene synthase CrtB crtB 2.5.1.32 GO:0004311,GO:0016117,GO:0016767 9593819 1224 Pseudomonadota phylum 960 NCBIFAM 15-cis-phytoene synthase CrtB NF042422.1 oxyalk_red_OleD 580 580 329 equivalog Y Y N 2-alkyl-3-oxoalkanoate reductase oleD 1.1.1.412 GO:0003854,GO:0006694 21958090 1224 Pseudomonadota phylum 1006 NCBIFAM 2-alkyl-3-oxoalkanoate reductase NF042436.1 OxoIsoapKin_OiaK 700 700 451 equivalog Y Y N 3-oxo-isoapionate kinase OiaK oiaK 2.7.1.231 GO:0005975,GO:0016301 29867142 1224 Pseudomonadota phylum 247 NCBIFAM 3-oxo-isoapionate kinase OiaK NF042485.3 PF20336.3 DUF6631 27 27 157 subfamily Y Y N DUF6631 family protein 1224 Pseudomonadota phylum 1001 EBI-EMBL Family of unknown function (DUF6631) DUF6631 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 132 and 168 amino acids in length. (from Pfam) NF042517.3 PF20204.3 DUF6566 26.7 26.7 78 subfamily Y Y N DUF6566 family protein 1224 Pseudomonadota phylum 1072 EBI-EMBL Domain of unknown function (DUF6566) DUF6566 family protein This domain is found in functionally uncharacterised proteins from Burkholderiaceae. This domain is approximately 60 amino acids in length and it has a conserved tryptophan residue at the N-terminal, the conserved motifs PxW and AxRxxxE and an aspartate conserved residue at the C-terminal. Some members containing this domain are hypothetical transposases. (from Pfam) NF042541.3 PF20301.3 pNTSase1 25 25 161 hypoth_equivalog Y Y N nucleotide synthetase 32868406 1224 Pseudomonadota phylum 113 EBI-EMBL Predicted novel nucleotide synthetase nucleotide synthetase Conserved genome contexts in NAD+-derived nucleotide-activated effector systems predict a function as a previously-uncharacterised nucleotide synthetase [1]. [1]. 32868406. Identification of Uncharacterized Components of Prokaryotic Immune Systems and Their Diverse Eukaryotic Reformulations. Burroughs AM, Aravind L;. J Bacteriol. 2020; [Epub ahead of print] (from Pfam) NF042680.3 PF20361.3 DUF6656 27 27 182 subfamily Y Y N DUF6656 family protein 1224 Pseudomonadota phylum 744 EBI-EMBL Family of unknown function (DUF6656) DUF6656 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 200 amino acids in length. (from Pfam) NF042721.3 PF20339.3 DUF6634 27 27 157 subfamily Y Y N DUF6634 family protein 1224 Pseudomonadota phylum 1232 EBI-EMBL Family of unknown function (DUF6634) DUF6634 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 106 and 169 amino acids in length. (from Pfam) NF042736.3 PF20410.3 X-Tfes_XVIPCD 24.9 24.9 101 domain Y Y N XVIPCD domain-containing protein 15774874,25743609,34983846 1224 Pseudomonadota phylum 13164 EBI-EMBL X-Tfes, XVIPCD X-Tfes, XVIPCD This conserved domain is found in Xanthomonas VirD4 interacting proteins (XVIPs) and other type IV secretion system (T4SS) specialised in translocating effector proteins (toxic effector proteins, X-Tfes) into competing gram-negative species, leading to target cell death. This domain interacts with the central all-alpha domain of VirD4. Its structure shows two well ordered N-terminal antiparallel alpha-helices that pack against a carboxyl-terminal three-stranded antiparallel beta sheet [1-3]. [1]. 15774874. Identification of new protein-protein interactions involving the products of the chromosome- and plasmid-encoded type IV secretion loci of the phytopathogen Xanthomonas axonopodis pv. citri. Alegria MC, Souza DP, Andrade MO, Docena C, Khater L, Ramos CH, da Silva AC, Farah CS;. J Bacteriol. 2005;187:2315-2325. [2]. 25743609. Bacterial killing via a type IV secretion system. Souza DP, Oka GU, Alvarez-Martinez CE, Bisson-Filho AW, Dunger G, Hobeika L, Cavalcante NS, Alegria MC, Barbosa LR, Salinas RK, Guzzo CR, Farah CS;. Nat Commun. 2015;6:6453. [3]. 34983846. Structural basis for effector recognition by an antibacterial type IV secretion system. Oka GU, Souza DP, Cenens W, Matsuyama BY, Cardoso MVC, Oliveira LC, da Silva Lima F, Cuccovia IM, Guzzo CR, Salinas RK, Farah CS;. Proc Natl Acad Sci U S A. 2022; [Epub ahead of print] (from Pfam) NF042781.3 PF20477.3 DUF6719 27 27 78 subfamily Y Y N DUF6719 family protein 1224 Pseudomonadota phylum 806 EBI-EMBL Family of unknown function (DUF6719) DUF6719 family protein This family is functionally uncharacterised. This family of proteins is found in proteobacteria. Proteins in this family are typically 74 amino acids in length. (from Pfam) NF042787.3 PF20506.3 DUF6732 27 27 72 subfamily Y Y N DUF6732 family protein 1224 Pseudomonadota phylum 524 EBI-EMBL Family of unknown function (DUF6732) DUF6732 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 73 amino acids in length. (from Pfam) NF042924.1 SlmHylase 500 500 299 equivalog Y Y N 4-sulfomuconolactone hydrolase 3.1.1.92 GO:0102998 17660282 1224 Pseudomonadota phylum 7 NCBIFAM 4-sulfomuconolactone hydrolase NF042941.1 Retron_TIR_antiphage 600 600 464 equivalog Y Y N TIR domain-containing anti-phage reverse transcriptase GO:0051607 32855333 1224 Pseudomonadota phylum 221 NCBIFAM TIR domain-containing anti-phage reverse transcriptase Proteins of this family are anti-phage reverse transcriptases with a TIR domain in the C-terminal. NF042942.1 SIR2_antiphage 500 500 392 equivalog Y Y N SIR2 family anti-phage-associated protein 32855333 1224 Pseudomonadota phylum 240 NCBIFAM SIR2 family anti-phage-associated protein Proteins of this family are associated with an anti-phage system, which has been widely identified in bacterial and archaeal genomes. NF042943.1 HerA_antiphage 800 800 566 equivalog Y Y N anti-phage-associated helicase HerA herA GO:0005524,GO:0016887,GO:0051607 32855333 1224 Pseudomonadota phylum 184 NCBIFAM anti-phage-associated helicase HerA Helicase HerA of this protein family is associated with anti-phage activities. NF042953.1 Hhe_antiphage 2000 2000 1797 equivalog Y Y N DUF4011 domain-containing anti-phage protein Hhe hhe GO:0051607 32855333 1224 Pseudomonadota phylum 808 NCBIFAM DUF4011 domain-containing anti-phage protein Hhe Proteins of this family exhibited anti-phage activities. They contain a DUF4011 domain, a HEPN helicase region, and a Vsr endonuclease domain. NF042954.1 Upx_antiphage 1900 1900 1240 equivalog Y Y N anti-phage protein Upx upx GO:0051607 32855333 1224 Pseudomonadota phylum 62 NCBIFAM anti-phage protein Upx NF042956.1 IteS_antiphage 900 900 747 equivalog Y Y N S8 family anti-phage peptidase IteS iteS GO:0006508,GO:0008236,GO:0051607 32855333 1224 Pseudomonadota phylum 305 NCBIFAM S8 family anti-phage peptidase IteS Proteins of this family are the protease components of the IteAS anti-phage system, which consists of an ATPase (IteA) and a protease (IteS). NF042960.1 AcphenoCarb_ApcA 1250 1250 658 equivalog Y Y N acetophenone carboxylase subunit alpha apcA 6.4.1.8 GO:0005524,GO:0016787,GO:0016874 10941798,15687214,20047908 1224 Pseudomonadota phylum 6 NCBIFAM acetophenone carboxylase subunit alpha NF042969.1 AcxyGlmanDactase 500 500 323 equivalog Y Y N bifunctional acetylxylan esterase/glucomannan deacetylase AxeC2 axe2C 3.1.1.-,3.1.1.72 GO:0016798,GO:0045493,GO:0046555,GO:2000884 19338387 1224 Pseudomonadota phylum 90 NCBIFAM bifunctional acetylxylan esterase/glucomannan deacetylase AxeC2 NF042974.2 AcphenoCarb_ApcB 250 250 128 equivalog Y Y N acetophenone carboxylase subunit beta apcB 6.4.1.8 GO:0005524,GO:0016787,GO:0016874 12420173,20047908 1224 Pseudomonadota phylum 10 NCBIFAM acetophenone carboxylase subunit beta NF042975.2 AcphenoCarb_ApcC 1500 1500 733 equivalog Y Y N acetophenone carboxylase subunit gamma apcC 6.4.1.8 GO:0005524,GO:0016874 10941798,15687214,20047908 1224 Pseudomonadota phylum 5 NCBIFAM acetophenone carboxylase subunit gamma NF042976.1 AcphenoCarb_ApcD 1500 1500 685 equivalog Y Y N acetophenone carboxylase subunit delta apcD 6.4.1.8 GO:0005524,GO:0016874 10941798,15687214,20047908 1224 Pseudomonadota phylum 4 NCBIFAM acetophenone carboxylase subunit delta NF042977.1 AcphenoCarb_ApcE 450 450 293 equivalog Y Y N acetophenone carboxylase subunit epsilon apcE 6.4.1.8 GO:0005524,GO:0016874 10941798,15687214,20047908 1224 Pseudomonadota phylum 5 NCBIFAM acetophenone carboxylase subunit epsilon NF043014.1 DArabDhDalD 600 600 452 equivalog Y Y N D-arabinitol 4-dehydrogenase dalD 1.1.1.11 GO:0047813,GO:0051161 9639934 1224 Pseudomonadota phylum 4582 NCBIFAM D-arabinitol 4-dehydrogenase NF043017.1 DimsulpropLyDddP 600 600 443 equivalog Y Y N dimethylsulfonioproprionate lyase DddP dddP 4.4.1.3 GO:0042803,GO:0047869 19220400,20378650,25054772 1224 Pseudomonadota phylum 1195 NCBIFAM dimethylsulfonioproprionate lyase DddP NF043049.1 DimsulpropLyDddY 800 800 401 equivalog Y Y N dimethylsulfonioproprionate lyase DddY dddY 4.4.1.3 GO:0047869 21248856 1224 Pseudomonadota phylum 53 NCBIFAM dimethylsulfonioproprionate lyase DddY NF043076.1 PHA_gran_PhaM 38 38 52 subfamily_domain Y Y N PhaM family polyhydroxyalkanoate granule multifunctional regulatory protein 22023320,28389545 1224 Pseudomonadota phylum 4854 NCBIFAM polyhydroxyalkanoate granule regulatory protein PhaM N-terminal domain PhaM was identified in Ralstonia eutropha as a multifunctional protein, found as part of poly(3-hydroxybutyrate) granules, a type of polyhydroxyalkanoate (PHA) storage granule, able to bind the PHA synthase PhaC, but also shown to have DNA-binding activity. This domain occurs in PhaM, near the N-terminus, and in additional homologs, some no longer than the domain itself. NF044323.2 PF20829.2 Acr30-35_AcrF1 30.5 30.5 78 domain Y N N Anti-CRISPR protein Acr30-35/AcrF1 28340349,28574055,28985564 1224 Pseudomonadota phylum 11 EBI-EMBL Anti-CRISPR protein Acr30-35/AcrF1 Anti-CRISPR protein Acr30-35/AcrF1 Pseudomonas phages have diverse anti-CRISPR (Acr) proteins that subvert the immune systems in their hosts. These systems depend on a CRISPR RNA (crRNA)-guided surveillance complex (Csy) for the degradation of foreign DNA. This family represents AcrF1, which inhibits DNA recognition of the Csy complex by interfering with base pairing between the DNA target strand and crRNA spacer. AcrF1 can use different mechanisms to block target DNA recognition [1-3]. Paper describing PDB structure 5uz9. [1]. 28340349. Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex. Chowdhury S, Carter J, Rollins MF, Golden SM, Jackson RN, Hoffmann C, Nosaka L, Bondy-Denomy J, Maxwell KL, Davidson AR, Fischer ER, Lander GC, Wiedenheft B;. Cell. 2017;169:47-57. Paper describing PDB structure 5xlo. [2]. 28574055. Alternate binding modes of anti-CRISPR viral suppressors AcrF1/2 to Csy surveillance complex revealed by cryo-EM structures. Peng R, Xu Y, Zhu T, Li N, Qi J, Chai Y, Wu M, Zhang X, Shi Y, Wang P, Wang J, Gao N, Gao GF;. Cell Res. 2017;27:853-864. Paper describing PDB structure 6anv. [3]. 28985564. Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex. Guo TW, Bartesaghi A, Yang H, Falconieri V, Rao P, Merk A, Eng ET, Raczkowski AM, Fox T, Earl LA, Patel DJ, Subramaniam S;. Cell. 2017;171:414-426. (from Pfam) NF044327.2 PF20841.2 NtrZ 27.7 27.7 78 subfamily Y Y N NtrZ family periplasmic regulatory protein 34124942 1224 Pseudomonadota phylum 534 EBI-EMBL NtrZ NtrZ family periplasmic regulatory protein NtrZ (CCNA_03863) was described in Caulobacter crescentus as a periplasmic protein that regulates the ability of the histidine kinase NtrY to act as a phosphatase on NtrX. NF044354.2 PF20944.2 StcE_b-sandwich 27 27 75 domain Y N N Metalloprotease StcE, beta-sandwich domain 22483117 1224 Pseudomonadota phylum 2891 EBI-EMBL Metalloprotease StcE, beta-sandwich domain Metalloprotease StcE, beta-sandwich domain This domain is found in Metalloprotease StcE from Escherichia coli and similar proteins predominantly found in Gammaproteobacteria. StcE is a virulence factor that contributes to intimate adherence to host cells. This enzyme is organised into three distinct globular domains, IG, M and C, that are packed against each other to show an overall T-shape. This entry represents a region that is located within the domain IG. This region folds independently as a mixed, eight-stranded beta-sandwich and contains an additional beta-strand followed by a perpendicular arrangement of two alpha-helices in its N terminus. It is also known as the INS domain. This entry also covers a disordered region that has been described as D1 [1]. Paper describing PDB structure 3ujz. [1]. 22483117. Structural insight into the bacterial mucinase StcE essential to adhesion and immune evasion during enterohemorrhagic E. coli infection. Yu AC, Worrall LJ, Strynadka NC;. Structure. 2012;20:707-717. (from Pfam) NF044366.2 PF20983.2 ExoU_C 27 27 87 domain Y N N ExoU toxin, C-terminal domain 22496657,23166655,25505182 1224 Pseudomonadota phylum 623 EBI-EMBL ExoU toxin, C-terminal domain ExoU toxin, C-terminal domain This domain is found in the toxin ExoU from Pseudomonas aeruginosa, an effector of the type III secretion system of the bacteria. ExoU is a patatin-like phospholipase that binds to the host membranes and induces cytotoxic effects leading to rapid necrotic cell death. This protein shows four domains: a putative chaperone binding domain. a patatin-like domain (Pfam:PF01734), and two domains that form the membrane localization domain (MLD). This entry represents the C-terminal domain, which folds into a four-helical bundle with a conserved arginine exposed. This residue seems to be essential for localization [1-3]. [1]. 23166655. Structure of the type III secretion effector protein ExoU in complex with its chaperone SpcU. Halavaty AS, Borek D, Tyson GH, Veesenmeyer JL, Shuvalova L, Minasov G, Otwinowski Z, Hauser AR, Anderson WF;. PLoS One. 2012;7:e49388. [2]. 22496657. Structural basis of cytotoxicity mediated by the type III secretion toxin ExoU from Pseudomonas aeruginosa. Gendrin C, Contreras-Martel C, Bouillot S, Elsen S, Lemaire D, Skoufias DA, Huber P, Attree I, Dessen A;. PLoS Pathog. 2012;8:e1002637. [3]. 25505182. A novel phosphatidylinositol 4,5-bisphosphate binding domain mediates plasma membrane localization of ExoU and other patatin-like phospholipases. Tyson GH, Halavaty AS, Kim H, Geissler B, Agard M, Satchell KJ, Cho W, Anderson WF, Hauser AR;. J Biol Chem. 2015;290:2919-2937. (from Pfam) NF044371.2 PF20995.2 DUF2875_C 24.8 24.8 136 domain Y N N Protein of unknown function (DUF2875) C-terminal domain 1224 Pseudomonadota phylum 2905 EBI-EMBL Protein of unknown function (DUF2875) C-terminal domain Protein of unknown function (DUF2875) C-terminal domain This family of proteins with unknown function appear to be restricted to Proteobacteria. This family appears to be related to the thiolase domain suggesting it is an enzyme. (from Pfam) NF044404.2 PF21118.2 DosC_2nd 31 31 110 domain Y N N DosC CZB-like middle domain 26527135 1224 Pseudomonadota phylum 4811 EBI-EMBL DosC CZB-like middle domain DosC CZB-like middle domain This entry represents the middle (Mid) domain of DosC proteins an oxygen-regulated diguanylate cyclase [1]. Paper describing PDB structure 4zvc. [1]. 26527135. Structural analysis of an oxygen-regulated diguanylate cyclase. Tarnawski M, Barends TR, Schlichting I;. Acta Crystallogr D Biol Crystallogr. 2015;71:2158-2177. (from Pfam) NF044448.2 PF21332.2 AmiR_N 27 27 111 domain Y N N AmiR, N-terminal 10508151 1224 Pseudomonadota phylum 3670 EBI-EMBL AmiR, N-terminal AmiR, N-terminal This is the N-terminal domain of Aliphatic amidase regulator (AmiR) which acts as a transcriptional antitermination factor. It positively controls AmiE, the gene for aliphatic amidase [1]. Paper describing PDB structure 1qo0. [1]. 10508151. Crystal structure and induction mechanism of AmiC-AmiR: a ligand-regulated transcription antitermination complex. O'Hara BP, Norman RA, Wan PT, Roe SM, Barrett TE, Drew RE, Pearl LH;. EMBO J. 1999;18:5175-5186. (from Pfam) NF044484.2 PF21474.2 DNApolII_N 25 25 36 domain Y N N DNA polymerase II, N-terminal 20064374 1224 Pseudomonadota phylum 19646 EBI-EMBL DNA polymerase II, N-terminal DNA polymerase II, N-terminal This is the N-terminal domain of bacterial DNA polymerase II. This entry represents the OB fold [1]. Paper describing PDB structure 3k57. [1]. 20064374. Structural insight into translesion synthesis by DNA Pol II. Wang F, Yang W;. Cell. 2009;139:1279-1289. (from Pfam) NF044513.2 PF21593.2 DUF6853 27 27 120 domain Y N N Family of unknown function (DUF6853) 1224 Pseudomonadota phylum 81 EBI-EMBL Family of unknown function (DUF6853) Family of unknown function (DUF6853) This protein family includes NMB0500 from Neisseria meningitidis and similar bacterial uncharacterised proteins. NMB0500 has an all-alpha structure. Its function is unknown. (from Pfam) NF044555.2 PF21726.2 DUF6862 24.1 24.1 67 domain Y Y N DUF6862 domain-containing protein 1224 Pseudomonadota phylum 4843 EBI-EMBL Family of unknown function (DUF6862) DUF6862 domain This entry represents a small domain that is found in a variety of toxin proteins. The precise function of this domain is uncertain. It often follows Pfam:PF04829. (from Pfam) NF044645.2 PF20879.2 SidM_N 27 27 285 domain Y N N SidM, N-terminal domain 19942850,20064470,20176951,20616805,24530282 1224 Pseudomonadota phylum 30 EBI-EMBL SidM, N-terminal domain SidM, N-terminal domain This domain is found in the type IV virulence effector SidM/DrrA from Legionella pneumophila. This protein has dual GEF and GDF activity specifically toward Rab1, a key regulator for endoplasmic reticulum (ER)-to-Golgi vesicle trafficking. SidM consists of an N-terminal helical domain (this entry), a Rab1-activation domain (Pfam:PF20851), and a C- terminal phosphatidylinositol 4-phosphate-binding (P4M) domain (Pfam:PF14860). The N-terminal is mostly alpha-helical, but also shows a short two-stranded beta-sheet [1,3]. Paper describing PDB structure 2wwx. [1]. 19942850. Structural insights into the dual nucleotide exchange and GDI displacement activity of SidM/DrrA. Suh HY, Lee DW, Lee KH, Ku B, Choi SJ, Woo JS, Kim YG, Oh BH;. EMBO J. 2010;29:496-504. Paper describing PDB structure 3jz9. [2]. 20064470. RabGDI displacement by DrrA from Legionella is a consequence of its guanine nucleotide exchange activity. Schoebel S, Oesterlin LK, Blankenfeldt W, Goody RS, Itzen A;. Mol Cell. 2009;36:1060-1072. Paper describing PDB structure 3l0i. [3]. 20176951. Structural mechanism of host Rab1 activation by the bifunctional Legionella type IV effector SidM/DrrA. Zhu Y, Hu L, Zhou Y, Yao Q, Liu L, Shao F;. Proc Natl Acad Sci U S A. 2010;107:4699-4704. Paper describing PDB structure 3n6o. [4]. 20616805. High-affinity binding of phosphatidylinositol 4-phosphate by Legionella pneumophila DrrA. Schoebel S, Blankenfeldt W, Goody RS, Itzen A;. EMBO Rep. 2010;11:598-604. Paper describing PDB structure 4mxp. [5]. 24530282. Structural basis for PI(4)P-specific membrane recruitment of the Legionella pneumophila effector DrrA/SidM. Del Campo CM, Mi. TRUNCATED at 1650 bytes (from Pfam) NF044725.2 PF21197.2 PgaA_barrel 27 27 294 domain Y N N PgaA membrane beta barrel domain 26957546 1224 Pseudomonadota phylum 12321 EBI-EMBL PgaA membrane beta barrel domain PgaA membrane beta barrel domain The partially de-N-acetylated poly-beta-1,6-N-acetyl-d-glucosamine (dPNAG) polymer serves as an intercellular biofilm adhesin that plays an essential role for the development and maintenance of integrity of biofilms of diverse bacterial species. Translocation of dPNAG across the bacterial outer membrane is mediated by a tetratricopeptide repeat-containing outer membrane protein, PgaA [1]. This entry represents the PgaA membrane beta barrel domain [1]. Paper describing PDB structure 4y25. [1]. 26957546. Structural Basis for Translocation of a Biofilm-supporting Exopolysaccharide across the Bacterial Outer Membrane. Wang Y, Andole Pannuri A, Ni D, Zhou H, Cao X, Lu X, Romeo T, Huang Y;. J Biol Chem. 2016;291:10046-10057. (from Pfam) NF044767.2 PF21327.2 GspA_C39-like 27 27 97 domain Y N N GspA, peptidase C39-like domain 21378198,23385451 1224 Pseudomonadota phylum 5696 EBI-EMBL GspA, peptidase C39-like domain GspA, peptidase C39-like domain This entry represents a domain of the type II secretion system protein GspA from E. coli, which has a papain-like fold similar to that in peptidase C39 family [1,2]. Paper describing PDB structure 4g54. [1]. 23385451. Structure of a periplasmic domain of the EpsAB fusion protein of the Vibrio vulnificus type II secretion system. Martynowski D, Grochulski P, Howard PS;. Acta Crystallogr D Biol Crystallogr. 2013;69:142-149. [2]. 21378198. Involvement of the GspAB complex in assembly of the type II secretion system secretin of Aeromonas and Vibrio species. Strozen TG, Stanley H, Gu Y, Boyd J, Bagdasarian M, Sandkvist M, Howard SP;. J Bacteriol. 2011;193:2322-2331. (from Pfam) NF044793.2 PF21424.2 DTP-pb9_A-dom_C 27 27 32 domain Y N N Distal tail protein pb9, A domain C-terminal 24155371 1224 Pseudomonadota phylum 3 EBI-EMBL Distal tail protein pb9, A domain C-terminal Distal tail protein pb9, A domain C-terminal This entry includes phage distal tail proteins which form a hexameric ring located at the tail tube end, such as pb9 from bacteriophage T5 [1]. pb9 consists of two domains, A and B. Domain A adopts a split barrel fold and includes residues 1 to 82-172 to 205. This entry covers the C-terminal region of the A domain [1]. Paper describing PDB structure 4jmq. [1]. 24155371. Crystal structure of pb9, the distal tail protein of bacteriophage T5: a conserved structural motif among all siphophages. Flayhan A, Vellieux FM, Lurz R, Maury O, Contreras-Martel C, Girard E, Boulanger P, Breyton C;. J Virol. 2014;88:820-828. (from Pfam) NF044794.2 PF21425.2 DTP-pb9_A-dom_N 27 27 84 domain Y N N Distal tail protein pb9, A domain, N-terminal 24155371 1224 Pseudomonadota phylum 3 EBI-EMBL Distal tail protein pb9, A domain, N-terminal Distal tail protein pb9, A domain, N-terminal This entry includes phage distal tail proteins which form a hexameric ring located at the tail tube end, such as pb9 from bacteriophage T5 [1]. pb9 consists of two domains, A and B. Domain A adopts a split barrel fold and includes residues 1 to 82-172 to 205. This entry covers the N-terminal region of the A domain [1]. The C-terminal segment of the A domain is represented in Pfam:PF21424. Paper describing PDB structure 4jmq. [1]. 24155371. Crystal structure of pb9, the distal tail protein of bacteriophage T5: a conserved structural motif among all siphophages. Flayhan A, Vellieux FM, Lurz R, Maury O, Contreras-Martel C, Girard E, Boulanger P, Breyton C;. J Virol. 2014;88:820-828. (from Pfam) NF044797.2 PF21430.2 DTP-pb9_B-dom 27 27 85 domain Y N N Distal tail protein pb9, B domain 24155371 1224 Pseudomonadota phylum 5 EBI-EMBL Distal tail protein pb9, B domain Distal tail protein pb9, B domain This entry includes phage distal tail proteins which form a hexameric ring located at the tail tube end, such as pb9 from bacteriophage T5 [1]. pb9 consists of two domains, A and B. This entry represents domain B which adopts an OB fold and is inserted in domain A [1]. [1]. 24155371. Crystal structure of pb9, the distal tail protein of bacteriophage T5: a conserved structural motif among all siphophages. Flayhan A, Vellieux FM, Lurz R, Maury O, Contreras-Martel C, Girard E, Boulanger P, Breyton C;. J Virol. 2014;88:820-828. (from Pfam) NF044868.2 PF21775.2 PutA_1st 27 27 33 domain Y N N PutA, RHH domain 12514740,17001030,18586269,18767154 1224 Pseudomonadota phylum 16968 EBI-EMBL PutA, RHH domain PutA, RHH domain This domain is found in the Bifunctional protein PutA from Escherichia coli and similar sequences mainly found in proteobacteria. PutA is both a bifunctional proline catabolic enzyme that oxidises proline to glutamate for use as a carbon and nitrogen source and an autogenous transcriptional repressor of the put operon. This entry represents the N-terminal ribbon-helix-helix (RHH) domain, which consists of a beta-strand and two alpha-helices. This domain has a Lys at the end of the beta-strand that interacts directly with DNA bases through the major groove, contributing to transcriptional regulation [1,3]. Paper describing PDB structure 2ay0. [1]. 17001030. Crystal structures of the DNA-binding domain of Escherichia coli proline utilization A flavoprotein and analysis of the role of Lys9 in DNA recognition. Larson JD, Jenkins JL, Schuermann JP, Zhou Y, Becker DF, Tanner JJ;. Protein Sci. 2006;15:2630-2641. Paper describing PDB structure 2jxg. [2]. 18767154. Solution structure of the Pseudomonas putida protein PpPutA45 and its DNA complex. Halouska S, Zhou Y, Becker DF, Powers R;. Proteins. 2009;75:12-27. Paper describing PDB structure 2rbf. [3]. 18586269. Structural basis of the transcriptional regulation of the proline utilization regulon by multifunctional PutA. Zhou Y, Larson JD, Bottoms CA, Arturo EC, Henzl MT, Jenkins JL, Nix JC, Becker DF, Tanner JJ;. J Mol Biol. 2008;381:174-188. Paper describing PDB structure 4o8a. [4]. 12514740. Structure of the proline dehydrogenase domain of the multifunctional PutA flavoprotein. Lee YH, Nadaraia S, Gu D, Becker DF, Tanner JJ;. Nat Struct Biol. 2003;10:109-114. (from Pfam) NF044899.2 PF20707.2 bDLD2 25 25 93 domain Y N N Bacterial Death-like domain 2 32101166,34061031 1224 Pseudomonadota phylum 16 EBI-EMBL Bacterial Death-like domain 2 Bacterial Death-like domain 2 This bacterial adaptor domain of the Death-domain fold is involved in protein-protein interactions in biological conflict systems. bDLDs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP and iSTAND. Further copies of the same bDLD are fused to either effector or signal-transducing domains, or additional Effector-associated domains (EADs). bDLD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating the bDLD-bDLD coupling approximates the advantages of collinear transcription [1,2]. [1]. 32101166. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. Kaur G, Burroughs AM, Iyer LM, Aravind L;. Elife. 2020; [Epub ahead of print]. [2]. 34061031. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. Kaur G, Iyer LM, Burroughs AM, Aravind L;. Elife. 2021; [Epub ahead of print] (from Pfam) NF044995.2 PF21158.2 flgK_1st_1 24.2 24.2 81 domain Y N N Flagellar hook-associated protein 1, D2-like domain 25645451 1224 Pseudomonadota phylum 15427 EBI-EMBL Flagellar hook-associated protein 1, D2-like domain Flagellar hook-associated protein 1, D2-like domain This entry includes Flagellar hook-associated protein 1 (FlgK or HAP1), one of three HAPs that form the hook-filament junction and has structural similarity to flagellin. FlgK is required for normal flagellum assembly. Proteins in this entry have a multidomain fold comprising an elongated alpha-helical scaffold core, and depending on the bacterial species, a variable number of smaller domains [1]. This entry represents a beta-sandwich domain from FlgK proteins; Salmonella typhimurium FlgK (Swiss:P0A1J5) has one beta-sandwich domain, while FlgK from Burkholderia pseudomallei has two of them protruding from the alpha-helical core, referred to as D2 and D3 domains in [1], of which the first one, D2, is covered in this entry [1]. FlgK has cytotoxic effects suggesting an important role in pathogenesis and is highly immunogenic. Domains D2 and D3 from B. pseudomallei have been identified as epitopes with increased immunogenic potential for vaccine development. Paper describing PDB structure 4ut1. [1]. 25645451. From crystal structure to in silico epitope discovery in the Burkholderia pseudomallei flagellar hook-associated protein FlgK. Gourlay LJ, Thomas RJ, Peri C, Conchillo-Sole O, Ferrer-Navarro M, Nithichanon A, Vila J, Daura X, Lertmemongkolchai G, Titball R, Colombo G, Bolognesi M;. FEBS J. 2015;282:1319-1333. (from Pfam) NF045030.2 PF21304.2 T3S_SPI-1_N0 27 27 69 domain Y N N SPI-1 type 3 secretion system secretin, N0 domain 19396170,21385715,23633951,27974800,31427728 1224 Pseudomonadota phylum 4781 EBI-EMBL SPI-1 type 3 secretion system secretin, N0 domain SPI-1 type 3 secretion system secretin, N0 domain SPI-1 type 3 secretion system secretin forms a ring-shaped multimeric structure which is used to inject bacterial effector proteins into eukaryotic host cells [1-3]. It consists of several N-terminal short domains and a C-terminal secretin domain (Pfam:PF00263). This entry represents the N-terminal N0 domain. Paper describing PDB structure 2y9k. [1]. 21385715. Three-dimensional model of Salmonella's needle complex at subnanometer resolution. Schraidt O, Marlovits TC;. Science. 2011;331:1192-1195. Paper describing PDB structure 3gr5. [2]. 19396170. A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system. Spreter T, Yip CK, Sanowar S, Andre I, Kimbrough TG, Vuckovic M, Pfuetzner RA, Deng W, Yu AC, Finlay BB, Baker D, Miller SI, Strynadka NC;. Nat Struct Mol Biol. 2009;16:468-476. Paper describing PDB structure 3j1v. [3]. 23633951. A refined model of the prototypical Salmonella SPI-1 T3SS basal body reveals the molecular basis for its assembly. Bergeron JR, Worrall LJ, Sgourakis NG, DiMaio F, Pfuetzner RA, Felise HB, Vuckovic M, Yu AC, Miller SI, Baker D, Strynadka NC;. PLoS Pathog. 2013;9:e1003307. Paper describing PDB structure 5tcq. [4]. 27974800. Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body. Worrall LJ, Hong C, Vuckovic M, Deng W, Bergeron JRC, Majewski DD, Huang RK, Spreter T, Finlay BB, Yu Z, Strynadka NCJ;. Nature. 2016;540:597-601. Paper describing PDB structure 6pee. [5]. 31427728. T3S injectisome needle complex structures in four distinct states reveal the basis of membrane coupling and assembly. Hu J, Worrall LJ, Vuckovic M,. TRUNCATED at 1650 bytes (from Pfam) NF045065.2 PF21446.2 Gp34_trimer 27 27 116 domain Y N N Long-tail fiber proximal subunit, C-terminal, trimerization domain 28665339,31209305 1224 Pseudomonadota phylum 12378 EBI-EMBL Long-tail fiber proximal subunit, C-terminal, trimerization domain Long-tail fiber proximal subunit, C-terminal, trimerization domain The long tail fibers of bacteriophage T4 consist of rigid proximal and distal parts, connected by a hinge region. The proximal half- fiber is formed by a parallel homo-trimer of the Long-tail fiber proximal subunit Gp34. This entry represents a region of the C-terminal domain, which forms a long triple beta-helix made up of parallel beta-strands [1,2]. Paper describing PDB structure 4uxe. [1]. 28665339. Crystal Structure of the Carboxy-Terminal Region of the Bacteriophage T4 Proximal Long Tail Fiber Protein Gp34. Granell M, Namura M, Alvira S, Kanamaru S, van Raaij MJ;. Viruses. 2017; [Epub ahead of print]. Paper describing PDB structure 5yvq. [2]. 31209305. Phage tail fibre assembly proteins employ a modular structure to drive the correct folding of diverse fibres. North OI, Sakai K, Yamashita E, Nakagawa A, Iwazaki T, Buttner CR, Takeda S, Davidson AR;. Nat Microbiol. 2019;4:1645-1653. (from Pfam) NF045115.2 PF21641.2 NarE 27 27 120 domain Y N N NarE 1224 Pseudomonadota phylum 171 EBI-EMBL NarE NarE This is a group of short bacterial sequences that includes NarE from Neisseria meningitidis. NarE is a protein with predicted ADP-ribosyltransferase activity. It shows an alpha-beta structure. (from Pfam) NF045149.2 PF21765.2 A2MG_CUB 27 27 62 domain Y N N A2MG, CUB domain 25221932,26100869,26143919 1224 Pseudomonadota phylum 15866 EBI-EMBL A2MG, CUB domain A2MG, CUB domain This domain is found in a group of proteins predominantly found in proteobacteria, including Alpha-2-macroglobulin (A2MG) from Salmonella typhimurium, a protein that protects the bacterial cell from host peptidases. A2MG is composed of 13 domains, 12 of them folding as beta sandwiches. This entry represents the CUB (complement C1r/C1s, Uegf, Bmp1) domain, which is connected to the TED domain (Pfam:PF07678). Paper describing PDB structure 4rtd. [1]. 26143919. Structure of protease-cleaved Escherichia coli alpha-2-macroglobulin reveals a putative mechanism of conformational activation for protease entrapment. Fyfe CD, Grinter R, Josts I, Mosbahi K, Roszak AW, Cogdell RJ, Wall DM, Burchmore RJ, Byron O, Walker D;. Acta Crystallogr D Biol Crystallogr. 2015;71:1478-1486. Paper describing PDB structure 4u48. [2]. 25221932. Structure of a bacterial alpha2-macroglobulin reveals mimicry of eukaryotic innate immunity. Wong SG, Dessen A;. Nat Commun. 2014;5:4917. Paper describing PDB structure 4ziq. [3]. 26100869. Structural and functional insights into Escherichia coli alpha2-macroglobulin endopeptidase snap-trap inhibition. Garcia-Ferrer I, Arede P, Gomez-Blanco J, Luque D, Duquerroy S, Caston JR, Goulas T, Gomis-Ruth FX;. Proc Natl Acad Sci U S A. 2015;112:8290-8295. (from Pfam) NF045207.2 PF20745.2 TSP_Ig-like 27.9 27.9 86 domain Y N N Tailspike protein-like, Ig-like domain 18462681,27045683,28209973,29176754 1224 Pseudomonadota phylum 258 EBI-EMBL Tailspike protein-like, Ig-like domain Tailspike protein-like, Ig-like domain This domain is found in Tail spike protein (TSP) from Shigella phage Sf6 and similar sequences from tailed bacteriophages and bacterial prophages. It forms a beta-sandwich consisting of two antiparallel, three stranded beta-sheets. A short alpha helix is included in the connecting loop between the third and fourth strand. This domain is structurally homologous to viral coat proteins [1]. Paper describing PDB structure 2vbe. [1]. 18462681. An intersubunit active site between supercoiled parallel beta helices in the trimeric tailspike endorhamnosidase of Shigella flexneri Phage Sf6. Muller JJ, Barbirz S, Heinle K, Freiberg A, Seckler R, Heinemann U;. Structure. 2008;16:766-775. Paper describing PDB structure 4ru4. [2]. 29176754. The O-specific polysaccharide lyase from the phage LKA1 tailspike reduces Pseudomonas virulence. Olszak T, Shneider MM, Latka A, Maciejewska B, Browning C, Sycheva LV, Cornelissen A, Danis-Wlodarczyk K, Senchenkova SN, Shashkov AS, Gula G, Arabski M, Wasik S, Miroshnikov KA, Lavigne R, Leiman PG, Knirel YA, Drulis-Kawa Z;. Sci Rep. 2017;7:16302. Paper describing PDB structure 4urr. [3]. 27045683. Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein-Polysaccharide Interactions. Kang Y, Gohlke U, Engstrom O, Hamark C, Scheidt T, Kunstmann S, Heinemann U, Widmalm G, Santer M, Barbirz S;. J Am Chem Soc. 2016;138:9109-9118. Paper describing PDB structure 5js4. [4]. 28209973. Structural basis for fragmenting the exopolysaccharide of Acinetobacter baumannii by bacteriophage PhiAB6 tailspike protein. Lee IM, Tu IF, Yang FL, Ko TP, Liao JH, Lin NT, Wu CY, Ren CT, . TRUNCATED at 1650 bytes (from Pfam) NF045253.2 PF20937.2 FHBP_N 27.6 27.6 92 domain Y N N Factor H binding protein, N-terminal 21543855,23133374,31442074,34125873 1224 Pseudomonadota phylum 434 EBI-EMBL Factor H binding protein, N-terminal Factor H binding protein, N-terminal Factor H binding protein (also known as GNA1870) is a surface exposed lipoprotein in Neisseria meningitidis that is a potent antigen and a potential candidate for a vaccine against meningococcal disease [1,2,3]. The structure of the N-terminal domain consists of a more unusual taco-shaped beta-barrel fold characterised by higher intrinsic flexibility than the C-terminal one [4]. [1]. 34125873. Two human antibodies to a meningococcal serogroup B vaccine antigen enhance binding of complement Factor H by stabilizing the Factor H binding site. Sands NA, Beernink PT;. PLoS Pathog. 2021;17:e1009655. [2]. 23133374. Design and evaluation of meningococcal vaccines through structure-based modification of host and pathogen molecules. Johnson S, Tan L, van der Veen S, Caesar J, Goicoechea De Jorge E, Harding RJ, Bai X, Exley RM, Ward PN, Ruivo N, Trivedi K, Cumber E, Jones R, Newham L, Staunton D, Ufret-Vincenty R, Borrow R, Pickering MC, Lea SM, Tang CM;. PLoS Pathog. 2012;8:e1002981. [3]. 21543855. Structure of the uncomplexed Neisseria meningitidis factor H-binding protein fHbp (rLP2086). Cendron L, Veggi D, Girardi E, Zanotti G;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011;67:531-535. [4]. 31442074. Cocrystal structure of meningococcal factor H binding protein variant 3 reveals a new crossprotective epitope recognized by human mAb 1E6. Bianchi F, Veggi D, Santini L, Buricchi F, Bartolini E, Lo Surdo P, Martinelli M, Finco O, Masignani V, Bottomley MJ, Maione D, Cozzi R;. FASEB J. 2019;33:12099-12111. (from Pfam) NF045287.2 PF21085.2 CusS 24.1 24.1 160 domain Y N N CusS sensor domain 27583660 1224 Pseudomonadota phylum 13522 EBI-EMBL CusS sensor domain CusS sensor domain This entry represents a periplasmic sensor domain found in CusS from E. coli [1]. The overall structure of the domain shows a PAS like topology. Paper describing PDB structure 5ku5. [1]. 27583660. The Structure of the Periplasmic Sensor Domain of the Histidine Kinase CusS Shows Unusual Metal Ion Coordination at the Dimeric Interface. Affandi T, Issaian AV, McEvoy MM;. Biochemistry. 2016;55:5296-5306. (from Pfam) NF045304.2 PF21159.2 FlgK_2nd 24.7 24.7 116 domain Y N N Flagellar hook-associated protein 1, D3 domain 25645451 1224 Pseudomonadota phylum 1594 EBI-EMBL Flagellar hook-associated protein 1, D3 domain Flagellar hook-associated protein 1, D3 domain This entry includes Flagellar hook-associated protein 1 (FlgK or HAP1), one of three HAPs that form the hook-filament junction and has structural similarity to flagellin. FlgK has a multidomain fold comprising an elongated alpha-helical scaffold core, and depending on the bacterial species, a variable number of smaller domains [1]. FlgK from Burkholderia pseudomallei (the causing agent of melioidosis) has two beta-sandwich domains protruding from the large alpha-helical core, referred to as D2 and D3 domains in [1], which the second one (D3) is represented in this entry [1]. FlgK has cytotoxic effects suggesting an important role in pathogenesis and is highly immunogenic. Domains D2 and D3 have been identified as epitopes with increased immunogenic potential for vaccine development [1]. Paper describing PDB structure 4ut1. [1]. 25645451. From crystal structure to in silico epitope discovery in the Burkholderia pseudomallei flagellar hook-associated protein FlgK. Gourlay LJ, Thomas RJ, Peri C, Conchillo-Sole O, Ferrer-Navarro M, Nithichanon A, Vila J, Daura X, Lertmemongkolchai G, Titball R, Colombo G, Bolognesi M;. FEBS J. 2015;282:1319-1333. (from Pfam) NF045319.2 PF21214.2 SelB_WH_2nd_bact 27 27 59 domain Y N N Selenocysteine-specific elongation factor, winged helix domain 12145214,15665870,17537456 1224 Pseudomonadota phylum 15203 EBI-EMBL Selenocysteine-specific elongation factor, winged helix domain Selenocysteine-specific elongation factor, winged helix domain This domain is found in Selenocysteine-specific elongation factor from Escherichia coli (SelB) and similar bacterial sequences. SelB is a translation factor necessary for the incorporation of selenocysteine into proteins. The C-terminal region of this protein in bacteria shows four winged-helix (WH) domains arranged in tandem, which form two globular structures. This entry represents the second pair of WH domains (WH3 and 4). Each WH domain is an alpha-beta structure consisting of three alpha-helices and a twisted three- stranded antiparallel beta-sheet [1-3]. Paper describing PDB structure 1lva. [1]. 12145214. Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB. Selmer M, Su XD;. EMBO J. 2002;21:4145-4153. Paper describing PDB structure 1wsu. [2]. 15665870. Structural basis for mRNA recognition by elongation factor SelB. Yoshizawa S, Rasubala L, Ose T, Kohda D, Fourmy D, Maenaka K;. Nat Struct Mol Biol. 2005;12:198-203. Paper describing PDB structure 2pjp. [3]. 17537456. Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB. Soler N, Fourmy D, Yoshizawa S;. J Mol Biol. 2007;370:728-741. (from Pfam) NF045326.2 PF21239.2 RLMM_N 27 27 81 domain Y N N Ribosomal RNA large subunit methyltransferase M, N-terminal 22923526 1224 Pseudomonadota phylum 10779 EBI-EMBL Ribosomal RNA large subunit methyltransferase M, N-terminal Ribosomal RNA large subunit methyltransferase M, N-terminal This is the THUMP-like domain of Ribosomal RNA large subunit methyltransferase M (RLMM), adjacent the ferredoxin-like domain (Pfam:PF18125), which together constitutes the N-terminal domain [1]. RlmM specifically catalyses the 2'-O-methylation of nucleotide C2498 in the peptidyl transferase loop of 23S rRNA [1]. Paper describing PDB structure 4atn. [1]. 22923526. Crystal structure of RlmM, the 2'O-ribose methyltransferase for C2498 of Escherichia coli 23S rRNA. Punekar AS, Shepherd TR, Liljeruhm J, Forster AC, Selmer M;. Nucleic Acids Res. 2012;40:10507-10520. (from Pfam) NF045361.2 PF21393.2 Phage_pb10_N 27 27 59 domain Y Y N DUF5898 family protein 28165000 1224 Pseudomonadota phylum 4 EBI-EMBL Decoration protein pb10 N-terminal domain Decoration protein pb10 N-terminal domain Bacteriophage capsids constitute icosahedral shells of exceptional stability that protect the viral genome. Many capsids display on their surface decoration proteins whose structure and function remain largely unknown. The decoration protein pb10 of phage T5 binds at the centre of the 120 hexamers formed by the major capsid protein [1]. Pb10 consists of an N-terminal alpha-helical capsid-binding domain (this entry) and an Ig-like domain [1]. Paper describing PDB structure 5lxl. [1]. 28165000. High affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid. Vernhes E, Renouard M, Gilquin B, Cuniasse P, Durand D, England P, Hoos S, Huet A, Conway JF, Glukhov A, Ksenzenko V, Jacquet E, Nhiri N, Zinn-Justin S, Boulanger P;. Sci Rep. 2017;7:41662. (from Pfam) NF045384.2 PF21483.2 CdiA_helical 27 27 60 domain Y N N Toxin CdiA-like, helical domain 23236156 1224 Pseudomonadota phylum 653 EBI-EMBL Toxin CdiA-like, helical domain Toxin CdiA-like, helical domain This entry represents the helical domain of EC869 CdiA toxin, a toxin of the Contact-dependent growth inhibition (CDI) system [1]. EC869 appears to function as a Zn2+-dependent DNAse degrading the genome of target cells. Paper describing PDB structure 4g6u. [1]. 23236156. Structural basis of toxicity and immunity in contact-dependent growth inhibition (CDI) systems. Morse RP, Nikolakakis KC, Willett JL, Gerrick E, Low DA, Hayes CS, Goulding CW;. Proc Natl Acad Sci U S A. 2012;109:21480-21485. (from Pfam) NF045404.2 PF21560.2 Gp34_2nd 27 27 102 domain Y N N Long-tail fiber proximal subunit, C-terminal, second 28665339 1224 Pseudomonadota phylum 14 EBI-EMBL Long-tail fiber proximal subunit, C-terminal, second Long-tail fiber proximal subunit, C-terminal, second This domain is found at the C-terminal end of Long-tail fiber proximal subunit from Bacteriophage T4 (Gp34), an structural component of the proximal-half of the long-tail fiber. This protein adopts a trimeric configuration. This domain shows a core antiparallel beta-sheet [1]. Paper describing PDB structure 4uxe. [1]. 28665339. Crystal Structure of the Carboxy-Terminal Region of the Bacteriophage T4 Proximal Long Tail Fiber Protein Gp34. Granell M, Namura M, Alvira S, Kanamaru S, van Raaij MJ;. Viruses. 2017; [Epub ahead of print] (from Pfam) NF045423.2 PF21628.2 Gp10-like 27 27 98 PfamEq Y Y N capsid staple protein gp10 23840063 1224 Pseudomonadota phylum 742 EBI-EMBL Major coat protein-like capsid staple protein The founding member of this protein, gp10 of bacteriophage epsilon15, is called a capsid staple protein. In that virus, gp7 is the major capsid protein. NF045444.2 PF21735.2 RtxA_C 30 5 18 domain Y N N C-terminal repeat from RTX toxins 17646359,27058787 1224 Pseudomonadota phylum 2185 EBI-EMBL C-terminal repeat from RTX toxins C-terminal repeat from RTX toxins This entry represents a short repeat found near the C-terminus of some RTX toxins such as Swiss:Q9KS12 [1]. AlphaFold models suggest this repeat forms a beta solenoid structure. These repeats contain a GXGXD motif in each repeat which is similar to that found in the RTX calcium-binding nonapeptide repeat Pfam:PF00353. This suggests that these repeats may also be needed for translocation via the type I secretion system [1]. [1]. 17646359. MARTX, multifunctional autoprocessing repeats-in-toxin toxins. Satchell KJ;. Infect Immun. 2007;75:5079-5084. [2]. 27058787. Calcium-Driven Folding of RTX Domain beta-Rolls Ratchets Translocation of RTX Proteins through Type I Secretion Ducts. Bumba L, Masin J, Macek P, Wald T, Motlova L, Bibova I, Klimova N, Bednarova L, Veverka V, Kachala M, Svergun DI, Barinka C, Sebo P;. Mol Cell. 2016;62:47-62. (from Pfam) NF045488.1 tet_MFS_62 775 775 385 exception Y Y Y tetracycline efflux MFS transporter Tet(62) tet(62) GO:0008493,GO:0015904 33515651 1224 Pseudomonadota phylum 3 NCBIFAM tetracycline efflux MFS transporter Tet(62) NF045536.1 phasin_PhaP6 100 100 138 equivalog Y Y N polyhydroxyalkanoate granule-associated phasin GO:0070088 22923598,28425176 1224 Pseudomonadota phylum 562 NCBIFAM polyhydroxyalkanoate granule-associated phasin NF045540.1 scaf_prot_MCP1 475 475 652 exception Y Y N ClpP-like prohead protease/major capsid protein fusion protein 3.4.21.- GO:0004252,GO:0019082 1224 Pseudomonadota phylum 6543 NCBIFAM ClpP-like prohead protease/major capsid protein fusion protein Members of this family of phage proteins contain an N-terminal serine protease domain resembling ClpP (see PF00574), involved in phage head maturation, and a longer C-terminal major capsid protein domain. NF045570.1 HemSynCtaAAlphapr 550 550 380 equivalog Y Y N heme A synthase ctaA 1.17.99.9 GO:0006784,GO:0016653 15491161 1224 Pseudomonadota phylum 1724 NCBIFAM heme A synthase NF045609.1 EpsI_type_B 220 220 221 exception Y Y N exosortase-associated protein EpsI, B-type epsI 1224 Pseudomonadota phylum 886 NCBIFAM exosortase-associated protein EpsI, B-type NF045611.1 small_CydP 29.6 29.6 45 equivalog Y Y N cytochrome oxidase putative small subunit CydP cydP 35562951 1224 Pseudomonadota phylum 2190 NCBIFAM cytochrome oxidase putative small subunit CydP Members of this family are small proteins with a highly hydrophobic core region. Because they are invariably found in the context of larger subunits of cytochrome bd oxidases, they are presumed to be small subunit or assembly factor. NF045614.1 efflu_CzcI_Cupr 100 100 124 equivalog Y Y N cation efflux protein, CzcI family czcI 1459958,32117100,7766206 1224 Pseudomonadota phylum 539 NCBIFAM cation efflux protein, CzcI family This family(NF045614) and the related family NF045615 have very similar N-terminal regions but very different C-terminal regions. A founding member of this family was described the Cadmium/Zinc/Cobalt efflux system component CzcI NF045617.1 mostly_LP 43 43 119 subfamily Y Y N putative T6SS immunity periplasmic lipoprotein 31577948,32366874 1224 Pseudomonadota phylum 4456 NCBIFAM putative T6SS immunity periplasmic lipoprotein Members of this family, including SARI_02726 from Salmonella enterica subsp. arizonae and EC042_4532 from sequence type ST31 strains of enteroaggregative Escherichia coli, are associated with type VI secretion systems (T6SS), and suggested to be immunity proteins with periplasmic localization. A well-conserved lipoprotein-type signal peptide and two widely separated well-conserved or invariant Cys residues support an extracytoplasmic location. NF045619.1 adhes_GNV_Cterm 180 180 458 subfamily_domain Y Y N BapA/Bap/LapF family large adhesin 18024522,21557055,22083703,23042991,27812186 1224 Pseudomonadota phylum 12623 NCBIFAM BapA/Bap/LapF family large adhesin C-terminal domain This HMM describes a conserved C-terminal region shared by a number of large adhesins of Gram-negative genera such as Acinetobacter, Brucella, Citrobacter, Enterobacter, Pseudomonas, and Sphingomonas. Most members have repeat domains N-terminal to the region described here, including bacterial Ig-like domains. Notable members of the family include biofilm-associated protein BapA of Salmonella and biofilm-associated Ig-like repeat protein Bap of Acinetobacter baumannii. NF045640.1 AspGlyoxATaseBhcA 650 650 395 equivalog Y Y N L-aspartate--glyoxylate aminotransferase BhcA bhcA 2.6.1.35 GO:0009436,GO:0046296,GO:0047303 31723261 1224 Pseudomonadota phylum 1269 NCBIFAM L-aspartate--glyoxylate aminotransferase BhcA NF045641.2 BHydaspDhtseBhcB 550 550 312 equivalog Y Y N beta-hydroxyaspartate dehydratase BhcB bhcB 4.2.1.- GO:0009436,GO:0016836,GO:0046296 31723261 1224 Pseudomonadota phylum 1317 NCBIFAM beta-hydroxyaspartate dehydratase BhcB NF045642.2 HdxyAspAldBhcC 690 690 387 equivalog Y Y N 3-hydroxy-D-aspartate aldolase BhcC bhcC 4.1.3.41 GO:0009436,GO:0016833,GO:0046296 12835921,31723261 1224 Pseudomonadota phylum 1375 NCBIFAM 3-hydroxy-D-aspartate aldolase BhcC NF045643.1 ImmsucRedBhcD 500 500 321 equivalog Y Y N iminosuccinate reductase BhcD bhcD 1.4.1.- GO:0009436,GO:0016639,GO:0046296 31723261 1224 Pseudomonadota phylum 1309 NCBIFAM iminosuccinate reductase BhcD NF045644.1 TransRegBhcR 350 350 267 equivalog Y Y N HTH-type transcriptional regulator BhcR bhcR GO:0003677,GO:0006355 31723261 1224 Pseudomonadota phylum 1708 NCBIFAM HTH-type transcriptional regulator BhcR NF045657.1 MthfCyhylaseFchA 275 275 207 equivalog Y Y N methenyltetrahydrofolate cyclohydrolase fchA 3.5.4.9 GO:0004477,GO:0006730 10215859,35051495,7961516 1224 Pseudomonadota phylum 406 NCBIFAM methenyltetrahydrofolate cyclohydrolase NF045661.1 HdlasePehA 900 900 506 equivalog Y Y N phosphoric/sulfuric ester hydrolase PehA pehA 3.1.3.-,3.1.4.-,3.1.6.- GO:0008484 18793651,20133613,8824203 1224 Pseudomonadota phylum 303 NCBIFAM phosphoric/sulfuric ester hydrolase PehA NF045700.1 AHLLactAttM 390 390 257 equivalog Y Y N N-acyl homoserine lactonase AttM attM 3.1.1.81 GO:0102007 11930013 1224 Pseudomonadota phylum 884 NCBIFAM N-acyl homoserine lactonase AttM NF045763.1 PhenlGlyoxDHPadF 150 150 78 equivalog Y Y N NADH-dependent phenylglyoxylate dehydrogenase subunit delta padF 1.2.1.58 GO:0006558,GO:0047110 9490067 1224 Pseudomonadota phylum 66 NCBIFAM NADH-dependent phenylglyoxylate dehydrogenase subunit delta NF045766.1 PhenlGlyoxDHPadI 700 700 443 equivalog Y Y N NADH-dependent phenylglyoxylate dehydrogenase subunit beta padI 1.2.1.58 GO:0006558,GO:0047110 9490067 1224 Pseudomonadota phylum 85 NCBIFAM NADH-dependent phenylglyoxylate dehydrogenase subunit beta NF045802.1 MethMoxAlphaMmoY 700 700 389 equivalog Y Y N aromatic/alkene monooxygenase hydroxylase subunit beta mmoY 1.14.13.25 GO:0008152,GO:0015049 1845980,1904125,2505721,8255292 1224 Pseudomonadota phylum 67 NCBIFAM aromatic/alkene monooxygenase hydroxylase subunit beta NF045803.1 MethMoxFADbindMmoC 500 500 343 equivalog Y Y N aromatic/alkene monooxygenase hydroxylase FAD-binding subunit MmoC mmoC 1.14.13.25 GO:0015049,GO:0050660 1785954,1845980,2205538 1224 Pseudomonadota phylum 90 NCBIFAM aromatic/alkene monooxygenase hydroxylase FAD-binding subunit MmoC NF045804.1 MethMoxRegMmoB 245 245 136 equivalog Y Y N methane monooxygenase regulator MmoB mmoB GO:0004497,GO:0008152 10381404,1845980,1904125,2505721 1224 Pseudomonadota phylum 52 NCBIFAM methane monooxygenase regulator MmoB NF045805.1 MethMoxGammaMmoZ 230 230 162 equivalog Y Y N aromatic/alkene monooxygenase hydroxylase subunit gamma mmoZ 1.14.13.25 GO:0008152,GO:0015049 1845980,1904125,2505721,8255292 1224 Pseudomonadota phylum 65 NCBIFAM aromatic/alkene monooxygenase hydroxylase subunit gamma NF045839.1 blaOXA-18_like 540 540 269 exception Y Y Y OXA-18 family class D beta-lactamase blaOXA 3.5.2.6 17610599,9333046 1224 Pseudomonadota phylum 1 NCBIFAM OXA-18 family class D beta-lactamase NF045884.1 PhCholSynAgro 350 350 235 equivalog Y Y N phosphatidylcholine synthase pcsA 2.7.8.24 GO:0008654,GO:0050520 10858449,18978052,22333179 1224 Pseudomonadota phylum 1414 NCBIFAM phosphatidylcholine synthase NF045887.1 PhCholSynPs 300 300 235 equivalog Y Y N phosphatidylcholine synthase pcsA 2.7.8.24 GO:0008654,GO:0050520 12169604,14663079 1224 Pseudomonadota phylum 1172 NCBIFAM phosphatidylcholine synthase NF045919.1 HphnlacHdxRed 340 340 309 equivalog Y Y N p-hydroxyphenylacetate 3-hydroxylase reductase component 1.5.1.36 GO:0010181,GO:0036382 11683878,15451173,16042421 1224 Pseudomonadota phylum 1393 NCBIFAM p-hydroxyphenylacetate 3-hydroxylase reductase component NF045920.1 HphnlacHdxOX 650 650 384 equivalog Y Y N p-hydroxyphenylacetate 3-hydroxylase oxygenase component 1.14.14.9 GO:0016627,GO:0052881 11683878,15451173,16042421 1224 Pseudomonadota phylum 1080 NCBIFAM p-hydroxyphenylacetate 3-hydroxylase oxygenase component NF045923.1 SpheroidMoxCrtARhod 300 300 226 equivalog Y Y N spheroidene monooxygenase crtA 1.14.15.9 GO:0004311,GO:0016117 19136077,20851979 1224 Pseudomonadota phylum 493 NCBIFAM spheroidene monooxygenase NF045926.1 STM2901_fam 110 110 140 subfamily Y Y N STM2901 family protein 1224 Pseudomonadota phylum 3224 NCBIFAM STM2901 family protein The founding member of this family of uncharacterized proteins is STM2901, a putative cytoplasmic protein from many but not all forms of SPI-1 (Salmonella Pathogenicity Island 1). NF045988.1 HisKinRegBRhodob 570 570 462 equivalog Y Y N sensor histidine kinase RegB regB prrB 2.7.13.3 GO:0000155,GO:0005524 10358089,7751278,8550404 1224 Pseudomonadota phylum 1467 NCBIFAM sensor histidine kinase RegB NF045989.1 TransRegFnrLRhodb 300 300 245 equivalog Y Y N transcriptional regulator FnrL fnrL GO:0003677,GO:0003700 15351643,7592416,9393689 1224 Pseudomonadota phylum 1436 NCBIFAM transcriptional regulator FnrL NF046018.1 HisPtaseChptBrucRhz 240 240 211 equivalog Y Y N histidine phosphotransferase ChpT chpT 2.7.99.- GO:0000160,GO:0004672,GO:0018197,GO:0042803 26124143 1224 Pseudomonadota phylum 2615 NCBIFAM histidine phosphotransferase ChpT NF046059.1 NagB_SO3506 430 430 330 equivalog Y Y N glucosamine-6-phosphate deaminase NagB-II nagB-II 3.5.99.6 37145875 1224 Pseudomonadota phylum 604 NCBIFAM glucosamine-6-phosphate deaminase NagB-II NF046098.1 RSP_7527_fam 26 26 48 equivalog Y Y N RSP_7527 family protein 30456366,34830143,36555125 1224 Pseudomonadota phylum 781 NCBIFAM RSP_7527 family protein The hypothetical protein RSP_7527 from the facultative phototrophic alphaproteobacterium Rhodobacter sphaeroides is notable because a 67 nucleotide small structural RNA, UdsC (UTR-derived sRNA C), derives from the 3'-untranslated region of its mRNA. Homologs of RSP_7527 are found in about two percent of bacterial proteomes. NF046099.1 RSP_2647_MTase 600 600 391 equivalog Y Y N RSP_2647 family RNA methyltransferase 34830143,36555125 1224 Pseudomonadota phylum 1853 NCBIFAM RSP_2647 family RNA methyltransferase The hypothetical protein RSP_7527 from the facultative phototrophic alphaproteobacterium Rhodobacter sphaeroides is notable because a 67 nucleotide small structural RNA, UdsC (UTR-derived sRNA C), derives from the 3'-untranslated region of its mRNA. RSP_2647, an apparent RNA methyltransferase, is encoded immediately downstream from UdsC (despite the non-consecutive locus tag), and this juxtaposition is conserved across a large number of bacterial species. Further downstream, and also part of the conserved gene neighborhood, is a PIN-domain protein, likely to be a DNA-binding protein. NF046100.1 RSP_2648_fam_PIN 170 170 177 equivalog Y Y N RSP_2648 family PIN domain-containing protein 34830143,36555125 1224 Pseudomonadota phylum 1774 NCBIFAM RSP_2648 family PIN domain-containing protein The hypothetical protein RSP_7527 from the facultative phototrophic alphaproteobacterium Rhodobacter sphaeroides is notable because a 67 nucleotide small structural RNA, UdsC (UTR-derived sRNA C), derives from the 3'-untranslated region of its mRNA. Homologs of RSP_7527 are found in about two percent of bacterial proteomes. This HMM describes a neighboring PIN domain-containing protein that is regularly found in the same conserved gene neighborhood, along with an RNA methyltransferase. The whole system may be involved in stress responses. NF046101.1 PA3496_fam 22 22 54 subfamily Y Y N PA3496 family putative envelope integrity protein 24344868,32153524 1224 Pseudomonadota phylum 5177 NCBIFAM PA3496 family putative envelope integrity protein This poorly understood protein family consists of small and highly divergent proteins, about 65 amino long, making detection difficult, but is widely distributed in Gram-negative bacteria. PA3496 from Pseudomonas aeruginosa was shown to be upregulated somewhat in the presence of inulin or inulin-derived fructooligosaccharide. Moraxella catarrhalis strains in which MCR_0424 is knocked out by mutation have a severe defect in resistance to complement present in serum. The latter result suggests a role as a cell envelope integrity protein. This family appears related to Pfam family PF12065 (DUF3545), and probably should be considered as a related model from a broader clan. NF046141.1 PF21887.1 RhiE_B 27 27 120 domain Y N N RhiE branching domain 24048471 1224 Pseudomonadota phylum 106 EBI-EMBL RhiE branching domain RhiE branching domain This entry represents the RhiE branching domain, which is part of a non-canonical polyketide synthase (PKS) module found in the endofungal bacterium Burkholderia rhizoxinica. Unlike typical PKS modules, RhiE catalyzes a Michael-type acetyl addition to generate a branch in the carbon chain, expanding the biosynthetic scope of polyketide biosynthesis. The module consists of a ketosynthase domain, an acyl carrier protein domain, and a cryptic branching ('B') domain in between, featuring a double hot dog (DHD) fold that is structurally homologous to the product template domain of a fungal PKS. The RhiE B domain alone is not sufficient to catalyze the Michael addition, and mutagenesis experiments revealed a crucial role of the ketosynthase domain in branching the carbon chain. Paper describing PDB structure 4kc5. [1]. 24048471. Vinylogous chain branching catalysed by a dedicated polyketide synthase module. Bretschneider T, Heim JB, Heine D, Winkler R, Busch B, Kusebauch B, Stehle T, Zocher G, Hertweck C;. Nature. 2013;502:124-128. (from Pfam) NF046156.1 PF21955.1 CarG-like 28 28 144 subfamily Y Y N carbapenem self-resistance protein CarG family protein 24583229,9402024 1224 Pseudomonadota phylum 439 EBI-EMBL Carbapenem resistance protein CarG-like carbapenem self-resistance protein CarG family protein This entry represents the carbapenem resistance protein CarG from Serratia sp. and similar sequences mainly found in proteobacteria. CarG shows a unique beta-sandwich fold with short terminal alpha-helices, displaying close structural homology with bacterial inhibitors of invertebrate lysozyme (Pfam:PF16743) [1]. Paper describing PDB structure 4o7j. [1]. 24583229. Crystal structure of the carbapenem intrinsic resistance protein CarG. Tichy EM, Luisi BF, Salmond GP;. J Mol Biol. 2014;426:1958-1970. (from Pfam) NF046168.1 PF22003.1 MrkDrd 27 27 142 domain Y N N MrkD-like receptor binding domain 22988966 1224 Pseudomonadota phylum 8882 EBI-EMBL MrkD-like receptor binding domain MrkD-like receptor binding domain This entry represents the receptor binding domain of MrkD from Klebsiella pneumoniae and similar sequences [1]. MkrD is an adhesin protein that specifically interacts with type IV and/or V collagen [1]. Paper describing PDB structure 3u4k. [1]. 22988966. Crystal structure of the MrkD1P receptor binding domain of Klebsiella pneumoniae and identification of the human collagen V binding interface. Rego AT, Johnson JG, Gelbel S, Enguita FJ, Clegg S, Waksman G;. Mol Microbiol. 2012;86:882-893. (from Pfam) NF046233.1 PF22295.1 DUF6967 27 27 65 subfamily Y Y N DUF6967 family protein 1224 Pseudomonadota phylum 192 EBI-EMBL Family of unknown function (DUF6967) DUF6967 family protein This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. They are predicted to fold into a four-stranded beta-sheet meander and an alpha-helix. One face of this beta-sheet is enriched with conserved positively charged arginine and lysine residues. (from Pfam) NF046251.1 PF22356.1 MACPF_b-prism 26 26 150 domain Y N N MACPF/perforin-like, beta-prism domain 17717151 1224 Pseudomonadota phylum 45 EBI-EMBL MACPF/perforin-like, beta-prism domain MACPF/perforin-like, beta-prism domain This entry represents the C-terminal beta-prism domain of the MACPF/perforin-like protein from Photorhabdus luminescens [1]. This domain shows structural similarity to the Multivesicular body subunit 12B MABP domain DUF2464 (Pfam:PF10240). Paper describing PDB structure 2qp2. [1]. 17717151. A common fold mediates vertebrate defense and bacterial attack. Rosado CJ, Buckle AM, Law RH, Butcher RE, Kan WT, Bird CH, Ung K, Browne KA, Baran K, Bashtannyk-Puhalovich TA, Faux NG, Wong W, Porter CJ, Pike RN, Ellisdon AM, Pearce MC, Bottomley SP, Emsley J, Smith AI, Rossjohn J, Hartland EL, Voskoboinik I, Trapani. Science. 2007;317:1548-1551. (from Pfam) NF046305.1 PF22519.1 TorS_sen_N 27 27 87 domain Y N N TorS N-terminal sensor domain 19748340,22483119 1224 Pseudomonadota phylum 7342 EBI-EMBL TorS N-terminal sensor domain TorS N-terminal sensor domain TorS histidine kinase activates the TMAO reductase (Tor) pathway when sensing trimethylamine-N-oxide (TMAO) in the environment. This entry represents the N-terminal portion of the periplasmic sensor domains of TorS. Paper describing PDB structure 3i9w. [1]. 19748340. Structural analysis of sensor domains from the TMAO-responsive histidine kinase receptor TorS. Moore JO, Hendrickson WA;. Structure. 2009;17:1195-1204. Paper describing PDB structure 3o1h. [2]. 22483119. An asymmetry-to-symmetry switch in signal transmission by the histidine kinase receptor for TMAO. Moore JO, Hendrickson WA;. Structure. 2012;20:729-741. (from Pfam) NF046323.1 PF22587.1 DNApolII_insertion 27 27 61 domain Y N N DNA polymerase II, insertion domain 20064374 1224 Pseudomonadota phylum 16378 EBI-EMBL DNA polymerase II, insertion domain DNA polymerase II, insertion domain This is the insertion domain found in DNA polymerase II from E. coli, a member of family B of DNA polymerases [1]. Paper describing PDB structure 3k57. [1]. 20064374. Structural insight into translesion synthesis by DNA Pol II. Wang F, Yang W;. Cell. 2009;139:1279-1289. (from Pfam) NF046376.1 PF22791.1 DUF7011 27 27 48 domain Y Y N DUF7011 domain-containing protein 1224 Pseudomonadota phylum 1451 EBI-EMBL Domain of unknown function (DUF7011) Domain of unknown function (DUF7011) This domain of unknown function is found in a group of proteins predominantly from proteobacteria. It has a LxHDGK/RRL motif and a highly conserved W residue. (from Pfam) NF046464.1 PF21915.1 Sputnik_MCP_1st 27 27 289 domain Y Y N phage major capsid domain-containing protein 23091035 1224 Pseudomonadota phylum 2 EBI-EMBL Sputnik virophage major capsid protein 1st domain phage major capsid domain-containing protein This entry represents the first jelly roll domain in the sputnik virophage major capsid protein [1]. Sputnik is a dsDNA virus, referred to as a virophage, that is co-assembled with Mimivirus in the host amoeba. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double jelly-roll major capsid proteins creating pseudohexameric capsomer symmetry. Paper describing PDB structure 3j26. [1]. 23091035. Structure of Sputnik, a virophage, at 3.5-A resolution. Zhang X, Sun S, Xiang Y, Wong J, Klose T, Raoult D, Rossmann MG;. Proc Natl Acad Sci U S A. 2012;109:18431-18436. (from Pfam) NF046478.1 PF21987.1 YajR_YAM 26 26 56 domain Y N N YajR YAM domain 23950222,24952155 1224 Pseudomonadota phylum 8409 EBI-EMBL YajR YAM domain YajR YAM domain This entry represents the C-terminal domain of YajR, an Escherichia coli transporter that belongs to the major facilitator superfamily. This domain has been termed YAM domain, whose precise regulatory role is not yet known. It may sense environmental changes, such as pH and halogen ion variation [1,2]. Paper describing PDB structure 2ru9. [1]. 24952155. Atomic resolution structure of the E. coli YajR transporter YAM domain. Jiang D, Zhao Y, Fan J, Liu X, Wu Y, Feng W, Zhang XC;. Biochem Biophys Res Commun. 2014;450:929-935. Paper describing PDB structure 3wdo. [2]. 23950222. Structure of the YajR transporter suggests a transport mechanism based on the conserved motif A. Jiang D, Zhao Y, Wang X, Fan J, Heng J, Liu X, Feng W, Kang X, Huang B, Liu J, Zhang XC;. Proc Natl Acad Sci U S A. 2013;110:14664-14669. (from Pfam) NF046512.1 PF22118.1 MtrF-like_dom-III 27 27 143 domain Y N N Decaheme cytochrome c component MtrF-like domain III 21606337 1224 Pseudomonadota phylum 428 EBI-EMBL Decaheme cytochrome c component MtrF-like domain III Decaheme cytochrome c component MtrF-like domain III This entry includes the decaheme cytochrome c component MtrF from the MtrFDE complex, an homologue of MtrC. In Shewanella oneidensis, these proteins are located at bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits and allow the utilization of extracellular mineral forms of iron and manganese as respiratory electron acceptors [1]. Members of this entry consist of four domains: domain I and III containing seven antiparallel beta-strands in an extended Greek key topology; domains II and IV each bind five tightly packed hemes covalently attached to the Cys residues of the five CXXCH motifs in each domain and form the central core (Pfam:PF22113), flanked by domains I and III [1]. This entry represents domain III of MtrF and similar proteins [1]. [1]. 21606337. Structure of a bacterial cell surface decaheme electron conduit. Clarke TA, Edwards MJ, Gates AJ, Hall A, White GF, Bradley J, Reardon CL, Shi L, Beliaev AS, Marshall MJ, Wang Z, Watmough NJ, Fredrickson JK, Zachara JM, Butt JN, Richardson DJ;. Proc Natl Acad Sci U S A. 2011;108:9384-9389. (from Pfam) NF046542.1 PF21917.1 NMB0537_N 23.9 23.9 36 domain Y N N N-terminal region of NMB0537 1224 Pseudomonadota phylum 10254 EBI-EMBL N-terminal region of NMB0537 N-terminal region of NMB0537 This entry represents a pair of helices found at the N-terminus of some CBS domain proteins. A pair of these regions dimerise to form a four helical bundle. Proteins in this family have this region followed by two CBS domains and Pfam:PF03471. (from Pfam) NF046546.1 PF21930.1 Gp138_C 27 27 75 domain Y N N Gp138, beta helical trimerization domain 22325780 1224 Pseudomonadota phylum 1579 EBI-EMBL Gp138, beta helical trimerization domain Gp138, beta helical trimerization domain This domain is found in Gp138 from Escherichia phage phi92 (Swiss:I7HXF9) and similar sequences found in tailed bacteriophages and prophages from proteobacteria. Gp138 forms an spike-shaped trimer with three highly intertwined chains. Each polypeptide has an oligonucleotide/oligosaccharide-binding (OB-fold) domain (Pfam: PF18352) and a long beta-helical C-terminal domain (this entry), which initiates the contact with the host cell membrane. The trimeric beta-helix is composed of three antiparallel beta-sheets, which swap three C-terminal beta-strands with each other around the threefold axis [1]. Paper describing PDB structure 3pqh. [1]. 22325780. Phage pierces the host cell membrane with the iron-loaded spike. Browning C, Shneider MM, Bowman VD, Schwarzer D, Leiman PG;. Structure. 2012;20:326-339. (from Pfam) NF046549.1 PF21934.1 Yop-YscD_ppl_3rd 24.3 24.3 64 domain Y N N YscD/CdsD-like Bon-like domain 3 1860816,23908767 1224 Pseudomonadota phylum 4393 EBI-EMBL YscD/CdsD-like Bon-like domain 3 YscD/CdsD-like Bon-like domain 3 Yop-YscD-ppl is the periplasmic domain of Yop proteins like YscD from Proteobacteria. YscD forms part of the inner membrane component of the bacterial type III secretion injectosome apparatus [1,2]. This entry represents the third of three periplasmic BON domains. [1]. 1860816. Analysis of virC, an operon involved in the secretion of Yop proteins by Yersinia enterocolitica. Michiels T, Vanooteghem JC, Lambert de Rouvroit C, China B, Gustin A, Boudry P, Cornelis GR;. J Bacteriol 1991;173:4994-5009. [2]. 23908767. In situ structural analysis of the Yersinia enterocolitica injectisome. Kudryashev M, Stenta M, Schmelz S, Amstutz M, Wiesand U, Castano-Diez D, Degiacomi MT, Munnich S, Bleck CK, Kowal J, Diepold A, Heinz DW, Dal Peraro M, Cornelis GR, Stahlberg H;. Elife. 2013;2:e00792. (from Pfam) NF046554.1 PF21963.1 TcdA1_RBD_2 27 27 86 domain Y N N TcdA1, receptor binding domain 24572368,31663026 1224 Pseudomonadota phylum 368 EBI-EMBL TcdA1, receptor binding domain TcdA1, receptor binding domain This domain is found in TcdA1 from Photorhabdus luminescens and similar sequences from gammaproteobacteria. TcdA1 is one of the three subunits of the Tc toxins. TcdA1 acts as an injecting device responsible for translocating the actual toxic component into host cells. TcA has four receptor-binding domains. This domain is one of 4 receptor binding domains found in TcA. All four domains have an immunoglobulin (Ig)-like beta-sandwich fold of two sheets with antiparallel beta-strands [1,2]. Paper describing PDB structure 6rwa. [1]. 31663026. Common architecture of Tc toxins from human and insect pathogenic bacteria. Leidreiter F, Roderer D, Meusch D, Gatsogiannis C, Benz R, Raunser S;. Sci Adv. 2019;5:eaax6497. [2]. 24572368. Mechanism of Tc toxin action revealed in molecular detail. Meusch D, Gatsogiannis C, Efremov RG, Lang AE, Hofnagel O, Vetter IR, Aktories K, Raunser S;. Nature. 2014;508:61-65. (from Pfam) NF046579.1 PF22055.1 MvaT_DBD 27 27 37 domain Y N N Bacterial xenogeneic silencer MvaT, C-terminal domain 26068099 1224 Pseudomonadota phylum 5782 EBI-EMBL Bacterial xenogeneic silencer MvaT, C-terminal domain Bacterial xenogeneic silencer MvaT, C-terminal domain This is the C-terminal DNA-binding domain of bacterial xenogeneic silencer MvaT. This domain adopts an alpha/beta structure consisting of a three-stranded antiparallel beta-sheet and two short helices packed on one side [1]. It binds to AT-rich DNA at the minor groove. Paper describing PDB structure 2mxe. [1]. 26068099. A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT. Ding P, McFarland KA, Jin S, Tong G, Duan B, Yang A, Hughes TR, Liu J, Dove SL, Navarre WW, Xia B;. PLoS Pathog. 2015;11:e1004967. (from Pfam) NF046597.1 PF22137.1 T6SS_Tle1-like_C 34 34 353 domain Y N N T6SS, Phospholipase effector Tle1-like, C-terminal domain 25084336 1224 Pseudomonadota phylum 4616 EBI-EMBL T6SS, Phospholipase effector Tle1-like, C-terminal domain T6SS, Phospholipase effector Tle1-like, C-terminal domain This domain is found in the type VI secretion system (T6SS) Phospholipase effector Tle1 from Pseudomonas aeruginosa (Swiss:Q9HYV3), which hydrolyse membrane phospholipids. Tle1 is organised into two distinct parts, the phospholipase catalytic module (Pfam:PF09994) and the putative membrane-anchoring module (this entry), that can be divided into three independent domains: a three-helix bundle, a six-helix bundle and an alpha/beta mixed fold with a two-layer sandwich structure [1]. Paper describing PDB structure 4o5p. [1]. 25084336. Structure of the type VI secretion phospholipase effector Tle1 provides insight into its hydrolysis and membrane targeting. Hu H, Zhang H, Gao Z, Wang D, Liu G, Xu J, Lan K, Dong Y;. Acta Crystallogr D Biol Crystallogr. 2014;70:2175-2185. (from Pfam) NF046614.1 PF22186.1 HI1480 24.5 24.5 144 domain Y N N Hypothetical protein HI1480 15229888 1224 Pseudomonadota phylum 3 EBI-EMBL Hypothetical protein HI1480 Hypothetical protein HI1480 This entry represents the HI1480 protein from Haemophilus influenzae an apparent ORFan protein [1]. The protein HI1480 from Haemophilus influenzae has been structurally characterized. It exhibits a unique amino acid sequence, lacking homology with known proteins. HI1480 adopts a novel alpha+beta fold and forms dimers of tightly associated dimers. The dimerization is facilitated by intermolecular interactions mediated by an antiparallel beta-barrel involving both monomers, while tetramer formation is mediated by helical regions of the dimers. Notably, the helical region contains a four-helix bundle reminiscent of anticodon binding domains found in class I tRNA synthetases, suggesting a potential active centre or catalytic site. Gel mobility shift assays demonstrate HI1480's ability to bind both DNA and RNA molecules, with a preference for double-stranded DNA over single-stranded DNA and higher affinity for longer DNA fragments. Paper describing PDB structure 1mw5. [1]. 15229888. Novel structure and nucleotide binding properties of HI1480 from Haemophilus influenzae: a protein with no known sequence homologues. Lim K, Sarikaya E, Galkin A, Krajewski W, Pullalarevu S, Shin JH, Kelman Z, Howard A, Herzberg O;. Proteins. 2004;56:564-571. (from Pfam) NF046633.1 PF22310.1 NMB0315_dom_I 27 27 83 domain Y N N NMB0315-like, domain I 22046377 1224 Pseudomonadota phylum 4238 EBI-EMBL NMB0315-like, domain I NMB0315-like, domain I This entry represents the domain I of NMB0315, an outer membrane protein of Neisseria meningitidis serogroup B and a potential candidate for a broad-spectrum vaccine against meningococcal disease. This domain tightly associates with domain III, which blocks the active site and the substrate binding groove [1]. Paper describing PDB structure 3slu. [1]. 22046377. Crystal structure of outer membrane protein NMB0315 from Neisseria meningitidis. Wang X, Yang X, Yang C, Wu Z, Xu H, Shen Y;. PLoS One. 2011;6:e26845. (from Pfam) NF046685.1 PF22179.1 RickCE_cat 27 27 102 domain Y N N RickCE-like, catalytic domain 27425412,32393759 1224 Pseudomonadota phylum 237 EBI-EMBL RickCE-like, catalytic domain RickCE-like, catalytic domain This entry represents the catalytic domain of a subset of ubiquitin-like proteases from the CE clan, including RickCE from Rickettsia [1,2]. Paper describing PDB structure 5ham. [1]. 27425412. The Molecular Basis for Ubiquitin and Ubiquitin-like Specificities in Bacterial Effector Proteases. Pruneda JN, Durkin CH, Geurink PP, Ovaa H, Santhanam B, Holden DW, Komander D;. Mol Cell. 2016;63:261-276. Paper describing PDB structure 6ups. [2]. 32393759. A deubiquitylase with an unusually high-affinity ubiquitin-binding domain from the scrub typhus pathogen Orientia tsutsugamushi. Berk JM, Lim C, Ronau JA, Chaudhuri A, Chen H, Beckmann JF, Loria JP, Xiong Y, Hochstrasser M;. Nat Commun. 2020;11:2343. (from Pfam) NF046729.1 PF22303.1 OspG_kinase 27 27 152 domain Y N N Protein kinase OspG, kinase domain 24373767,24446487,24712300,24856362,29420175 1224 Pseudomonadota phylum 1430 EBI-EMBL Protein kinase OspG, kinase domain Protein kinase OspG, kinase domain This entry represents the kinase domain of protein kinase OspG which is involved in down-regulation of the host innate response induced by invasive bacteria [1-5]. OspG is a an effector kinase that binds host E2 ubiquitin-conjugating enzymes activated with ubiquitin, which enhances its kinase activity, playing a role to suppress the host inflammatory response during invasion and colonization [2,5]. Paper describing PDB structure 3zdu. [1]. 29420175. CDKL Family Kinases Have Evolved Distinct Structural Features and Ciliary Function. Canning P, Park K, Goncalves J, Li C, Howard CJ, Sharpe TD, Holt LJ, Pelletier L, Bullock AN, Leroux MR;. Cell Rep. 2018;22:885-894. Paper describing PDB structure 4bvu. [2]. 24446487. E2~Ub conjugates regulate the kinase activity of Shigella effector OspG during pathogenesis. Pruneda JN, Smith FD, Daurie A, Swaney DL, Villen J, Scott JD, Stadnyk AW, Le Trong I, Stenkamp RE, Klevit RE, Rohde JR, Brzovic PS;. EMBO J. 2014;33:437-449. Paper describing PDB structure 4lrj. [3]. 24373767. NleH defines a new family of bacterial effector kinases. Grishin AM, Cherney M, Anderson DH, Phanse S, Babu M, Cygler M;. Structure. 2014;22:250-259. Paper describing PDB structure 4o96. [4]. 24712300. Type III effector NleH2 from Escherichia coli O157:H7 str. Sakai features an atypical protein kinase domain. Halavaty AS, Anderson SM, Wawrzak Z, Kudritska M, Skarina T, Anderson WF, Savchenko A;. Biochemistry. 2014;53:2433-2435. Paper describing PDB structure 4q5e. [5]. 24856362. Structural basis for the inhibition of host protein ubiquitination by Shigella effector kinase OspG. Grishin AM, Condos TE, Barber KR, Camp. TRUNCATED at 1650 bytes (from Pfam) NF046873.1 PF22605.1 IBR_2 27 27 49 domain Y N N IBR domain 15236971,23708605,23770917,24058416,25161877 1224 Pseudomonadota phylum 7 EBI-EMBL IBR domain IBR domain This entry represents an IBR domain which is found to occur between pairs of ring fingers. Paper describing PDB structure 1wd2. [1]. 15236971. Structure of the C-terminal RING finger from a RING-IBR-RING/TRIAD motif reveals a novel zinc-binding domain distinct from a RING. Capili AD, Edghill EL, Wu K, Borden KL;. J Mol Biol. 2004;340:1117-1129. Paper describing PDB structure 2lwr. [2]. 23770917. A molecular explanation for the recessive nature of parkin-linked Parkinson's disease. Spratt DE, Martinez-Torres RJ, Noh YJ, Mercier P, Manczyk N, Barber KR, Aguirre JD, Burchell L, Purkiss A, Walden H, Shaw GS;. Nat Commun. 2013;4:1983. Paper describing PDB structure 2m6n. [3]. 23708605. Electron microscopy structure of human APC/C(CDH1)-EMI1 reveals multimodal mechanism of E3 ligase shutdown. Frye JJ, Brown NG, Petzold G, Watson ER, Grace CR, Nourse A, Jarvis MA, Kriwacki RW, Peters JM, Stark H, Schulman BA;. Nat Struct Mol Biol. 2013;20:827-835. Paper describing PDB structure 2m9y. [4]. 24058416. Structure of the HHARI catalytic domain shows glimpses of a HECT E3 ligase. Spratt DE, Mercier P, Shaw GS;. PLoS One. 2013;8:e74047. Paper describing PDB structure 2rt9. [5]. 25161877. The zinc-binding region (ZBR) fragment of Emi2 can inhibit APC/C by targeting its association with the coactivator Cdc20 and UBE2C-mediated ubiquitylation. Shoji S, Muto Y, Ikeda M, He F, Tsuda K, Ohsawa N, Akasaka R, Terada T, Wakiyama M, Shirouzu M, Yokoyama S;. FEBS Open Bio. 2014;4:689-703. (from Pfam) NF046917.1 PF22783.1 BapA_N 27 27 123 domain Y Y N BapA/Bap/LapF family prefix-like domain-containing protein 16313619,28158695 1224 Pseudomonadota phylum 32416 EBI-EMBL BapA, prefix-like domain BapA/Bap/LapF family prefix-like domain This entry represents the N-terminal domain of two largely unrelated repetitive proteins, both named Biofilm-associated protein BapA (from Salmonella enterica and from Paracoccus denitrificans), which share common domains at the two ends. The conserved prefix (N-terminal) domain is shared by a number of other large, repetitive proteins from proteobacteria and are thought to be associated with adhesion or biofilm formation [1,2]. [1]. 16313619. BapA, a large secreted protein required for biofilm formation and host colonization of Salmonella enterica serovar Enteritidis. Latasa C, Roux A, Toledo-Arana A, Ghigo JM, Gamazo C, Penades JR, Lasa I;. Mol Microbiol. 2005;58:1322-1339. [2]. 28158695. Biofilm formation by Paracoccus denitrificans requires a type I secretion system-dependent adhesin BapA. Yoshida K, Toyofuku M, Obana N, Nomura N;. FEMS Microbiol Lett. 2017; [Epub ahead of print] (from Pfam) NF046934.1 PF22828.1 HphA_N 22 22 110 domain Y N N HphA N-terminal heme-binding domain 34725337 1224 Pseudomonadota phylum 1777 EBI-EMBL HphA N-terminal heme-binding domain HphA N-terminal heme-binding domain HphA is a secreted hemophore that binds and acquires heme from hemoglobin. It consists of two domains: N-terminal heme binding domain (this entry) and C-terminal beta-barrel that is related to domains members of the Outer membrane beta-barrel superfamily. The N-terminal domain has a clamp-like structure consisting of six antiparallel beta-strands and an alpha-helix. Two histidines located on loops coordinate the heme [1]. [1]. 34725337. A Slam-dependent hemophore contributes to heme acquisition in the bacterial pathogen Acinetobacter baumannii. Bateman TJ, Shah M, Ho TP, Shin HE, Pan C, Harris G, Fegan JE, Islam EA, Ahn SK, Hooda Y, Gray-Owen SD, Chen W, Moraes TF;. Nat Commun. 2021;12:6270. (from Pfam) NF046982.1 PF22829.1 HphA_C 31 31 113 domain Y N N HphA C-terminal domain 34725337 1224 Pseudomonadota phylum 2001 EBI-EMBL HphA C-terminal domain HphA C-terminal domain HphA is a secreted hemophore that binds and acquires heme from hemoglobin. It consists of two domains: N-terminal heme binding domain and C-terminal beta-barrel (this entry) that is related to domains members of the Outer membrane beta-barrel superfamily [1]. [1]. 34725337. A Slam-dependent hemophore contributes to heme acquisition in the bacterial pathogen Acinetobacter baumannii. Bateman TJ, Shah M, Ho TP, Shin HE, Pan C, Harris G, Fegan JE, Islam EA, Ahn SK, Hooda Y, Gray-Owen SD, Chen W, Moraes TF;. Nat Commun. 2021;12:6270. (from Pfam) NF047035.1 PF21834.1 DUF6894 24.1 24.1 69 subfamily Y Y N DUF6894 family protein 1224 Pseudomonadota phylum 13170 EBI-EMBL Domain of unknown function (DUF6894) DUF6894 family protein This entry represents a small protein domain found in alpha proteobacteria. Its structure is composed of a four stranded sheet packed on one side by an alpha helix. The function of these proteins is unknown. (from Pfam) NF047056.1 PF21927.1 McpB_HAMP_2 27 27 49 domain Y N N Methyl-accepting chemotaxis protein McpB, second HAMP domain 20399181,23424282 1224 Pseudomonadota phylum 1677 EBI-EMBL Methyl-accepting chemotaxis protein McpB, second HAMP domain Methyl-accepting chemotaxis protein McpB, second HAMP domain This domain is found in Methyl-accepting chemotaxis protein McpB from Pseudomonas aeruginosa and similar sequences from proteobacteria. McpB, also known as Aerotaxis transducer Aer2, is a chemoreceptor that plays a critical role in the virulence and pathogenesis of the bacteria. This entry represents the second HAMP domain, which folds into a unique four-helix bundle that comparatively differs from the first and third HAMP domains of the same protein [1,2]. Paper describing PDB structure 3lnr. [1]. 20399181. Structure of concatenated HAMP domains provides a mechanism for signal transduction. Airola MV, Watts KJ, Bilwes AM, Crane BR;. Structure. 2010;18:436-448. Paper describing PDB structure 4i3m. [2]. 23424282. HAMP domain conformers that propagate opposite signals in bacterial chemoreceptors. Airola MV, Sukomon N, Samanta D, Borbat PP, Freed JH, Watts KJ, Crane BR;. PLoS Biol. 2013;11:e1001479. (from Pfam) NF047138.1 PF22258.1 DUF6949 28.7 28.7 99 subfamily Y Y N DUF6949 family protein 1224 Pseudomonadota phylum 1408 EBI-EMBL Family of unknown function (DUF6949) DUF6949 family protein This is a family of uncharacterised bacterial proteins. These proteins are enriched with hydrophobic residues and it is quite likely to be associated with the membrane. (from Pfam) NF047144.1 PF22276.1 SlmA-like_C 27 27 117 domain Y N N Tetracyclin repressor-like, C-terminal domain 21113127,23408580,23754405,27091999 1224 Pseudomonadota phylum 6707 EBI-EMBL Tetracyclin repressor-like, C-terminal domain Tetracyclin repressor-like, C-terminal domain This domain is found at the C-terminal end of Nucleoid occlusion factor SlmA from Escherichia coli and similar transcriptional repressors from proteobacteria. SlmA is required for the nucleoid occlusion (NO) phenomenon, which prevents Z-ring formation and cell division over the nucleoid. It is organised into two domains, a small N-terminal Pfam:PF00440 and a C-terminal domain (this entry). This domain shows an all-alpha configuration. This region mediates dimerisation [1]. Paper describing PDB structure 3nxc. [1]. 21113127. Molecular mechanism by which the nucleoid occlusion factor, SlmA, keeps cytokinesis in check. Tonthat NK, Arold ST, Pickering BF, Van Dyke MW, Liang S, Lu Y, Beuria TK, Margolin W, Schumacher MA;. EMBO J. 2011;30:154-164. Paper describing PDB structure 3vuq. [2]. 23408580. Structure and function of a TetR family transcriptional regulator, SbtR, from thermus thermophilus HB8. Agari Y, Sakamoto K, Yutani K, Kuramitsu S, Shinkai A;. Proteins. 2013;81:1166-1178. Paper describing PDB structure 4gck. [3]. 23754405. SlmA forms a higher-order structure on DNA that inhibits cytokinetic Z-ring formation over the nucleoid. Tonthat NK, Milam SL, Chinnam N, Whitfill T, Margolin W, Schumacher MA;. Proc Natl Acad Sci U S A. 2013;110:10586-10591. Paper describing PDB structure 5haw. [4]. 27091999. Structures of the nucleoid occlusion protein SlmA bound to DNA and the C-terminal domain of the cytoskeletal protein FtsZ. Schumacher MA, Zeng W;. Proc Natl Acad Sci U S A. 2016;113:4988-4993. (from Pfam) NF047190.1 PF22499.1 DUF6990 27 27 180 domain Y Y N DUF6990 domain-containing protein 1224 Pseudomonadota phylum 1005 EBI-EMBL Family of unknown function (DUF6990) DUF6990 domain This family of proteins is found in bacteria. Proteins in this family are typically between 185 and 199 amino acids in length. There are two semi-conserved sequence motifs: HLA and GFVPYI. (from Pfam) NF047241.1 PF22716.1 SNaCT11 27 27 164 domain Y N N Short NACHT-associated C-Terminal domain, family 11 37160116 1224 Pseudomonadota phylum 59 EBI-EMBL Short NACHT-associated C-Terminal domain, family 11 Short NACHT-associated C-Terminal domain, family 11 The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors [1]. [1]. 37160116. Bacterial NLR-related proteins protect against phage. Kibby EM, Conte AN, Burroughs AM, Nagy TA, Vargas JA, Whalen LA, Aravind L, Whiteley AT;. Cell. 2023;186:2410-2424. (from Pfam) NF047336.1 conj_memb_RcgA 325 325 537 subfamily Y Y N RcgA family putative transporter 36073816 1224 Pseudomonadota phylum 816 NCBIFAM RcgA family putative transporter RcgA (Rhizobial Conjugative Gene A), from a Rhizobium favelukesii plasmid, plays an essential role in a quorum sensing-dependent conjugative transfer system. It is thought to be a transporter that allows uptake of a quorum-signaling lactone. Its partner protein, RgcR, with an alpha/beta hydrolase domain, inhibits the transfer and may catabolize the signaling molecule. NF047384.1 BspC_dom 38 38 102 domain Y Y N BspC domain-containing protein 23950720 1224 Pseudomonadota phylum 1422 NCBIFAM BspC domain BspC from Brucella abortus and a number of closely related intracellular pathogens is a type VI secretion system (T4SS) effector, detected specifically by model NF047383. This model describes a core domain found in BspC and in more distant homologs from a much broader collection of bacterial species. NF047711.1 PutUtilRegPtrR 400 400 283 equivalog Y Y N putrescine utilization regulator PtrR ptrR GO:0003700,GO:0006355 35508583 1224 Pseudomonadota phylum 6455 NCBIFAM putrescine utilization regulator PtrR NF047825.1 T-richsensTspOAlph 180 180 152 equivalog Y Y N tryptophan-rich sensory protein TspO tspO crtK GO:0008289,GO:0033013,GO:0046906 10409680,10681549,23952237,25635101 1224 Pseudomonadota phylum 1387 NCBIFAM tryptophan-rich sensory protein TspO NF047835.1 UbiqAccUbiK 100 100 91 equivalog Y Y N ubiquinone biosynthesis accessory factor UbiK ubiK yqiC GO:0006744,GO:0042802 21554724,27777572,28559279 1224 Pseudomonadota phylum 4149 NCBIFAM ubiquinone biosynthesis accessory factor UbiK NF047836.1 UDPdiagluDHLpxI 400 400 275 equivalog Y Y N UDP-2,3-diacylglucosamine diphosphatase lpxI 3.6.1.54 GO:0008758,GO:0009245 20608695,23042606 1224 Pseudomonadota phylum 455 NCBIFAM UDP-2,3-diacylglucosamine diphosphatase TIGR00155.1 TIGR00155 pqiA_fam 260.35 260.35 403 subfamily Y Y N PqiA/YebS family transporter subunit 27795327 1224 Pseudomonadota phylum 14928 JCVI integral membrane protein, PqiA family PqiA/YebS family transporter subunit This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A. TIGR00402.1 TIGR00402 napF 102.2 102.2 149 equivalog Y Y N ferredoxin-type protein NapF napF GO:0051539 17074894 1224 Pseudomonadota phylum 6170 JCVI ferredoxin-type protein NapF ferredoxin-type protein NapF The gene codes for a ferredoxin-type cytosolic protein, NapF, of the periplasmic nitrate reductase system, as in Escherichia coli. NapF interacts with the catalytic subunit, NapA, and may be an accessory protein for NapA maturation. TIGR00540.1 TIGR00540 TPR_hemY_coli 142 142 385 hypoth_equivalog Y N N heme biosynthesis-associated TPR protein hemY GO:0016020,GO:0042168 1224 Pseudomonadota phylum 17426 JCVI heme biosynthesis-associated TPR protein heme biosynthesis-associated TPR protein Members of this protein family are uncharacterized tetratricopeptide repeat (TPR) proteins invariably found in heme biosynthesis gene clusters. The absence of any invariant residues other than Ala argues against this protein serving as an enzyme per se. The gene symbol hemY assigned in E. coli is unfortunate in that an unrelated protein, protoporphyrinogen oxidase (HemG in E. coli) is designated HemY in Bacillus subtilis. TIGR00548.1 TIGR00548 lolB 59.6 59.6 202 equivalog Y Y N lipoprotein insertase outer membrane protein LolB lolB GO:0009279,GO:0015031 19678842,9384574 1224 Pseudomonadota phylum 15291 JCVI outer membrane lipoprotein LolB lipoprotein insertase outer membrane protein LolB LolB, as found by this HMM, is known in the gamma and beta subdivisions of the Proteobacteria. It is a processed, lipid-modified outer membrane lipoprotein. It is required in E. coli for insertion of lipoproteins such the major outer lipoprotein (Lpp) into the outer membrane. Lpp is transferred to LolB from the carrier protein LolA in the periplasm. Previously, this protein was thought to play in role in 5-aminolevulinic acid synthesis and was designated HemM. TIGR00819.1 TIGR00819 ydaH 753.55 753.55 521 subfamily Y Y N AbgT family antimetabolite efflux transporter GO:0015558,GO:1902604 26443496 1224 Pseudomonadota phylum 2772 JCVI AbgT transporter family AbgT family antimetabolite efflux transporter The p-Aminobenzoyl-glutamate transporter family includes two transporters, the AbgT (YdaH) protein of E. coli and MtrF of Neisseria gonorrhoea. AbgT is apparently cryptic in wild type cells, but when expressed on a high copy number plasmid, or when expressed at higher levels due to mutation, it allows utilization of p-aminobenzoyl-glutamate as a source of p-aminobenzoate for p-aminobenzoate auxotrophs. p-Aminobenzoate is a constituent of and a precursor for the biosynthesis of folic acid. TIGR00895.1 TIGR00895 2A0115 418.55 418.55 398 subfamily Y Y N aromatic acid/H+ symport family MFS transporter GO:0016020,GO:0042908,GO:0042910 1224 Pseudomonadota phylum 6060 JCVI MFS transporter, aromatic acid:H+ symporter (AAHS) family aromatic acid/H+ symport family MFS transporter TIGR00988.1 TIGR00988 hip 119.95 119.95 94 equivalog Y Y N integration host factor subunit beta ihfB GO:0003677,GO:0005694,GO:0006310,GO:0006355,GO:0006417,GO:0075713 1224 Pseudomonadota phylum 9937 JCVI integration host factor, beta subunit integration host factor subunit beta This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU. TIGR00997.1 TIGR00997 ispZ 165.2 165.2 178 equivalog Y Y N septation protein IspZ ispZ GO:0000910,GO:0016020 8830250 1224 Pseudomonadota phylum 12411 JCVI intracellular septation protein A septation protein IspZ This partially characterized protein, whose absence can cause a cell division defect in an intracellularly replicating bacterium, is found only so far only in the Proteobacteria. TIGR00998.1 TIGR00998 8a0101 390.8 390.8 334 subfamily Y Y N EmrA/EmrK family multidrug efflux transporter periplasmic adaptor subunit GO:0042910,GO:1990961 1224 Pseudomonadota phylum 6690 JCVI efflux pump membrane protein EmrA/EmrK family multidrug efflux transporter periplasmic adaptor subunit TIGR01010.1 TIGR01010 BexC_CtrB_KpsE 437.5 437.5 362 subfamily Y N N polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family GO:0015161,GO:0015776 2082145 1224 Pseudomonadota phylum 798 JCVI polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family This family contains gamma proteobacterial proteins involved in capsule polysaccharide export. TIGR01013.1 TIGR01013 2a58 306.15 306.15 456 subfamily Y Y N sodium-dependent inorganic phosphate transporter 1224 Pseudomonadota phylum 6349 JCVI sodium-dependent inorganic phosphate (Pi) transporter sodium-dependent inorganic phosphate transporter TIGR01045.1 TIGR01045 RPE1 30 30 48 domain Y Y N palindromic element RPE1 domain-containing protein 11997347 1224 Pseudomonadota phylum 1771 JCVI rickettsial palindromic element RPE1 domain rickettsial palindromic element RPE1 domain This HMM describes protein translations of the first family described, RPE1, of Rickettsia palindromic elements (RPE). In Rickettsia conorii, 19 copies are found within protein coding regions, where they encode an insert relative to homologs from other species but do not disrupt the reading frame. Insertion is always in the same reading frame. This model finds RPE-encoded regions in several Rickettsial species and, so far, no where else. TIGR01074.1 TIGR01074 rep 951.45 951.45 668 equivalog Y Y N DNA helicase Rep rep 3.6.4.12 GO:0003677,GO:0003678,GO:0005524,GO:0006268 1224 Pseudomonadota phylum 12245 JCVI ATP-dependent DNA helicase Rep DNA helicase Rep Designed to identify rep members of the uvrD/rep subfamily. TIGR01075.1 TIGR01075 uvrD 1144.45 1144.45 715 equivalog Y Y N DNA helicase II uvrD 3.6.4.12 GO:0003678,GO:0005737,GO:0006268,GO:0006281 1224 Pseudomonadota phylum 9428 JCVI DNA helicase II DNA helicase UvrD Designed to identify uvrD members of the uvrD/rep subfamily. TIGR01096.1 TIGR01096 3A0103s03R 256.35 256.35 250 subfamily Y Y N lysine/arginine/ornithine ABC transporter substrate-binding protein GO:0030288,GO:0071705,GO:0140359 1224 Pseudomonadota phylum 20902 JCVI lysine-arginine-ornithine-binding periplasmic protein lysine/arginine/ornithine ABC transporter substrate-binding protein TIGR01190.1 TIGR01190 ccmB 156.2 156.2 211 equivalog Y Y N heme exporter protein CcmB ccmB 7.6.2.- GO:0015232,GO:0015886 1224 Pseudomonadota phylum 15767 JCVI heme exporter protein CcmB heme exporter protein CcmB This model describes the cyt c biogenesis protein encoded by ccmB in bacteria. Bacterial c-type cytochromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome C. TIGR01253.1 TIGR01253 thiP 395.1 395.1 519 equivalog Y Y N thiamine/thiamine pyrophosphate ABC transporter permease thiP GO:0015888,GO:0016020,GO:0030974,GO:0048502 9535878 1224 Pseudomonadota phylum 13366 JCVI thiamine/thiamine pyrophosphate ABC transporter, permease protein thiamine/thiamine pyrophosphate ABC transporter permease The model describes thiamine ABC transporter, permease protein in bacteria. The protein belongs to the larger ABC transport system. It consists of atleast three components: the inner mebrane permease; thiamine binding protein; an ATP-binding subunit. It has been experimentally demonstrated that the mutants in the various steps in the de novo synthesis of the thiamine and the biologically active form, namely thiamine pyrophosphate can be exogenously supplemented with thiamine, thiamine monophosphate (TMP) or thiamine pyrophosphate (TPP). TIGR01276.1 TIGR01276 thiB 317.15 317.15 324 equivalog Y Y N thiamine ABC transporter substrate binding subunit thiB GO:0015888,GO:0030288,GO:0030975,GO:0048502,GO:0055052 9535878 1224 Pseudomonadota phylum 12066 JCVI thiamin/thiamin pyrophosphate ABC transporter, thiamin/thiamin pyrophospate-binding protein thiamine ABC transporter substrate binding subunit This model finds the thiamine (and thiamine pyrophosphate) ABC transporter periplasmic binding protein ThiB in proteobacteria. Completed genomes having this protein (E. coli, Vibrio cholera, Haemophilus influenzae) also have the permease ThiP, described by TIGRFAMs equivalog model TIGR01253. TIGR01277.1 TIGR01277 thiQ 245.05 245.05 213 equivalog Y Y N thiamine ABC transporter ATP-binding protein thiQ 7.6.2.15 GO:0005524,GO:0015888,GO:0016020,GO:0030974,GO:0048502 1224 Pseudomonadota phylum 8199 JCVI thiamine ABC transporter, ATP-binding protein thiamine ABC transporter, ATP-binding protein This HMM describes the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several Proteobacteria. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found. TIGR01288.1 TIGR01288 nodI 424 424 303 equivalog Y Y N nodulation factor ABC transporter ATP-binding protein NodI nodI GO:0005524,GO:0016020,GO:0033231,GO:0043212 1224 Pseudomonadota phylum 1767 JCVI nodulation ABC transporter NodI nodulation factor ABC transporter ATP-binding protein NodI This protein is required for normal nodulation by nitrogen-fixing root nodule bacteria such as Mesorhizobium loti. It is a member of the family of ABC transporter ATP binding proteins and works with NodJ to export a nodulation signal molecule. This model does not recognize the highly divergent NodI from Azorhizobium caulinodans. TIGR01298.1 TIGR01298 RNaseT 246.2 246.2 200 equivalog Y Y N ribonuclease T rnt GO:0006364,GO:0016896,GO:0042780 9857048 1224 Pseudomonadota phylum 9419 JCVI ribonuclease T ribonuclease T This HMM describes ribonuclease T, an enzyme found so far only in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases. TIGR01387.1 TIGR01387 cztR_silR_copR 279.2 279.2 218 subfamily Y Y N heavy metal response regulator transcription factor GO:0003677,GO:0006355 1224 Pseudomonadota phylum 15224 JCVI heavy metal response regulator heavy metal response regulator transcription factor Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system. TIGR01419.1 TIGR01419 nitro_reg_IIA 138.7 138.7 145 equivalog Y Y N PTS IIA-like nitrogen regulatory protein PtsN ptsN GO:0006355,GO:0008982,GO:0009401 9537369 1224 Pseudomonadota phylum 8013 JCVI PTS IIA-like nitrogen-regulatory protein PtsN PTS IIA-like nitrogen regulatory protein PtsN This HMM describes a full-length protein of about 160 residues closely related to the fructose-specific phosphotransferase (PTS) system IIA component. It is a regulatory protein found only in species with a phosphoenolpyruvate-protein phosphotransferase (enzyme I of PTS systems) and an HPr-like phosphocarrier protein, but not all species have a IIC-like permease. Members of this family are found in Proteobacteria, Chlamydia, and the spirochete Treponema pallidum. TIGR01562.1 TIGR01562 FdhE 187.65 187.65 305 equivalog Y Y N formate dehydrogenase accessory protein FdhE fdhE 18716757,2170340 1224 Pseudomonadota phylum 10079 JCVI formate dehydrogenase accessory protein FdhE formate dehydrogenase accessory protein FdhE This HMM describes an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex [1]. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulfur clusters and cytochrome b556, it is likely to have something to do with the insertion of cofactors. TIGR01582.1 TIGR01582 FDH-beta 334.7 334.7 283 equivalog Y Y N formate dehydrogenase subunit beta fdxH 1.17.1.9 GO:0008863,GO:0015944,GO:0016020,GO:0051539 11884747 1224 Pseudomonadota phylum 9610 JCVI formate dehydrogenase, beta subunit formate dehydrogenase subunit beta This model represents the beta subunit of the gamma-proteobacterial formate dehydrogenase. This subunit contains four 4Fe-4S clusters and is involved in transmitting electrons from the alpha subunit (TIGR01553) at the periplasmic space to the gamma subunit which spans the cytoplasmic membrane [1]. In addition to the gamma proteobacteria, a sequence from Aquifex aolicus falls within the scope of this model. This appears to be the case for the alpha, gamma and epsilon (accessory protein TIGR01562) chains as well. TIGR01620.2 TIGR01620 hyp_HI0043 160 160 329 subfamily Y Y N TIGR01620 family protein 1224 Pseudomonadota phylum 16652 JCVI TIGR01620 family protein TIGR01620 family protein Members of this family of uncharacterized membrane proteins include YcjF from Escherichia coli. TIGR01666.1 TIGR01666 YCCS 470.75 470.75 705 hypoth_equivalog Y Y N YccS family putative transporter yccS GO:0016020 1224 Pseudomonadota phylum 16417 JCVI TIGR01666 family membrane protein YccS family putative transporter This model represents a clade of sequences from gamma and beta proteobacteria. These proteins are >700 amino acids long and many have been annotated as putative membrane proteins. The gene from Salmonella has been annotated as a putative efflux transporter. The gene from E. coli has the name yccS. TIGR01667.1 TIGR01667 YCCS_YHFK 467.8 467.8 701 subfamily Y Y N YccS/YhfK family putative transporter 11152613,11448883 1224 Pseudomonadota phylum 20581 JCVI integral membrane protein, YccS/YhfK family YccS/YhfK family putative transporter This model represents two clades of putative transmembrane proteins including the E. coli YccS and YhfK proteins. The YccS hypothetical equivalog (TIGR01666) is found in beta and gamma proteobacteria, while the smaller YhfK group is only found in E. coli, Salmonella and Yersinia. TMHMM [1,2] on the 19 hits to this model shows a consensus of 11 transmembrane helices separated into two clusters, an N-terminal cluster of 6 and a central cluster of 5. This would indicate two non-membrane domains one on each side of the membrane TIGR01690.1 TIGR01690 ICE_RAQPRD 60.85 60.85 96 hypoth_equivalog Y N N integrative conjugative element protein, RAQPRD family 1224 Pseudomonadota phylum 3990 JCVI integrative conjugative element protein, RAQPRD family integrative conjugative element protein, RAQPRD family This HMM represents a small family of proteins about 100 amino acids in length, including a predicted signal sequence and a perfectly conserved motif RAQPRD towards the C-terminus. Members are found in the Pseudomonas putida TOL plasmid pWW0 and in cryptic plasmid regions of Salmonella enterica subsp. enterica serovar Typhi and Pseudomonas syringae DC3000. The function is unknown. TIGR01705.1 TIGR01705 MTA_SAH-nuc-hyp 152.2 152.2 212 equivalog Y Y N 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase 3.2.2.16,3.2.2.9 24657441 1224 Pseudomonadota phylum 2872 JCVI putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase This model (TIGR01705 ) represents the enzyme 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase which acts on its two substrates at the same active site. Members of this family include the crystallized example from Brucella melitensis, while a related model, TIGR01704, represents the more common forms found in Escherichia coli, Mycobacterium, Staphylococcus aureus, Bacillus subtilis, etc. This enzyme is involved in the recycling of the components of S-adenosylmethionine after it has donated one of its two non-ribose sulfur ligands to an acceptor. In the case of 5'-methylthioadenosine this represents the first step of the methionine salvage pathway in bacteria. Enables the cleavage of the glycosidic bond in both 5'-methylthioadenosine and S-adenosylhomocysteine TIGR01707.1 TIGR01707 gspI 44.35 44.35 101 equivalog Y Y N type II secretion system minor pseudopilin GspI gspI GO:0015627,GO:0015628 30767847 1224 Pseudomonadota phylum 13735 JCVI type II secretion system protein I type II secretion system minor pseudopilin GspI This HMM represents GspI, one of two proteins highly conserved at their N-termini and described by PF02501 but easily separable phylogenetically. The other is GspJ. Both GspI and GspJ are proteins of the type II secretion pathway, or main terminal branch of the general secretion pathway. This pathway carries proteins across the outer membrane. Note that proteins of type II secretion are cryptic in E. coli K-12 - present but not yet demonstrated to act on any target. TIGR01708.2 TIGR01708 typeII_sec_gspH 80 80 169 equivalog Y Y N type II secretion system minor pseudopilin GspH gspH GO:0015627,GO:0015628 30767847 1224 Pseudomonadota phylum 8972 JCVI type II secretion system protein H type II secretion system minor pseudopilin GspH GspH is one of four minor pseudopilins of the type II secretion system (T2SS), previously called the main terminal branch of the general secretion pathway (hence the gene symbol). The T2SS system does not depend on cell-cell contact for its secretion (it has no injectosome) of its targets, which include pullulanase from Klebsiella oxytoca, exotoxin A from Pseudomonas aeruginosa, protease VesB from Vibrio cholerae, etc. TIGR01711.1 TIGR01711 gspJ 64.85 64.85 192 equivalog Y Y N type II secretion system minor pseudopilin GspJ gspJ GO:0015627,GO:0015628 30767847 1224 Pseudomonadota phylum 11248 JCVI type II secretion system protein J type II secretion system minor pseudopilin GspJ This HMM represents GspJ, one of two proteins highly conserved at their N-termini and described by PF02501 but easily separable phylogenetically. The other is GspI. Both GspI and GspJ are proteins of the type II secretion pathway (T2SS), previously called the main terminal branch of the General Secretion Pathway. TIGR01729.1 TIGR01729 taurine_ABC_bnd 304.25 304.25 300 equivalog Y Y N taurine ABC transporter substrate-binding protein tauA GO:0015411,GO:0015734,GO:0030977,GO:0042597,GO:0055052 8808933 1224 Pseudomonadota phylum 11277 JCVI taurine ABC transporter, periplasmic binding protein taurine ABC transporter substrate-binding protein This HMM identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulfonates, and sulfate esters import sulfur when sulfate levels are low. The most closely related proteins outside this family are putative aliphatic sulfonate binding proteins (TIGR01728). TIGR01738.1 TIGR01738 bioH 206.95 206.95 245 equivalog Y Y N pimeloyl-ACP methyl ester esterase BioH bioH 3.1.1.85 GO:0009102,GO:0052689 11904168,12732651 1224 Pseudomonadota phylum 11472 JCVI pimelyl-[acyl-carrier protein] methyl ester esterase pimeloyl-ACP methyl ester esterase BioH This CoA-binding enzyme is required for the production of pimeloyl-coenzyme A, the substrate of the BioF protein early in the biosynthesis of biotin. Its exact function is unknown, but is proposed in ref 2. This enzyme belongs to the alpha/beta hydrolase fold family (Pfam HMM PF00561). Members of this family are restricted to the Proteobacteria. TIGR01749.1 TIGR01749 fabA 238.15 238.15 169 equivalog Y Y N 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabA fabA 4.2.1.59 GO:0005737,GO:0006633,GO:0019171 8910376,9286984 1224 Pseudomonadota phylum 9915 JCVI beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabA 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabA This enzyme, FabA, shows overlapping substrate specificity with FabZ with regard to chain length in fatty acid biosynthesis. It is commonly designated 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.60) as if it were specific for that chain length, but its specificity is broader; it is active even in the initiation of fatty acid biosynthesis. This enzyme can also isomerize trans-2-decenoyl-ACP to cis-3-decenoyl-ACP to bypass reduction by FabI and instead allow biosynthesis of unsaturated fatty acids. FabA cannot elongate unsaturated fatty acids. TIGR01776.1 TIGR01776 TonB-tbp-lbp 468.8 468.8 946 subfamily Y Y N lactoferrin/transferrin family TonB-dependent receptor GO:0006810,GO:0019867,GO:0022857,GO:0038023 1224 Pseudomonadota phylum 2606 JCVI TonB-dependent lactoferrin and transferrin receptors lactoferrin/transferrin family TonB-dependent receptor This family of TonB-dependent receptors are responsible for import of iron from the mammalian iron carriers lactoferrin and transferrin across the outer membrane. These receptors are found only in bacteria which can infect mammals such as Moraxella, Mannheimia, Neisseria, Actinobacillus, Pasteurella, Haemophilus and Histophilus species. TIGR01854.1 TIGR01854 lipid_A_lpxH 190.35 190.35 231 equivalog Y Y N UDP-2,3-diacylglucosamine diphosphatase lpxH 3.6.1.54 GO:0005737,GO:0008758,GO:0009245,GO:0016462 12000771 1224 Pseudomonadota phylum 20676 JCVI UDP-2,3-diacylglucosamine diphosphatase UDP-2,3-diacylglucosamine diphosphatase This HMM represents LpxH, UDP-2,3-diacylglucosamine hydrolase, and essential enzyme in E. coli that catalyzes the fourth step in lipid A biosynthesis. Note that Pseudomonas aeruginosa has both a member of this family that shares this function and a more distant homolog, designated LpxH2, that does not. Many species that produce lipid A lack an lpxH gene in this family; some of those species have an lpxH2 gene instead, although for which the function is unknown. TIGR01955.1 TIGR01955 RfaH 144.5 144.5 159 equivalog Y Y N transcription/translation regulatory transformer protein RfaH rfaH GO:0006355 1584020,20132437,8987397 1224 Pseudomonadota phylum 5704 JCVI transcription elongation factor/antiterminator RfaH transcription/translation regulatory transformer protein RfaH This model represents the transcription elongation factor/antiterminator, RfaH [1]. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (PF00467) [2]. This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes. TIGR01984.1 TIGR01984 UbiH 392.2 392.2 382 equivalog Y Y N 2-octaprenyl-6-methoxyphenyl hydroxylase ubiH GO:0006744,GO:0008681 11583838 1224 Pseudomonadota phylum 16059 JCVI 2-polyprenyl-6-methoxyphenol 4-hydroxylase 2-octaprenyl-6-methoxyphenyl hydroxylase This HMM represents the FAD-dependent monoxygenase responsible for the second hydroxylation step in the aerobic ubiquinone bioynthetic pathway. The scope of this model is limited to the proteobacteria. This family is closely related to the UbiF hydroxylase which catalyzes the final hydroxylation step. The enzyme has also been named VisB due to a mutant VISible light sensitive phenotype. TIGR01985.1 TIGR01985 phasin_2 99.7 99.7 123 equivalog Y Y N phasin 12399487 1224 Pseudomonadota phylum 3507 JCVI phasin phasin This HMM represents a family of granule-associate proteins (phasins) which are part of the polyhydroxyalkanoate synthesis machinery. This family is based on a pair of characterized genes from Methylobacterium extorquens. Members of the seed for this model all contain the rest of the components believed to be essential for this system (see the "polyhydroxyalkanoic acid synthesis" property in the GenPropDB). Members of this family score below trusted to another phasin model, TIGR01841 and together may represent a subfamily or broader equivalog. TIGR01997.1 TIGR01997 sufA_proteo 136.2 136.2 107 equivalog Y Y N Fe-S cluster assembly scaffold SufA sufA GO:0016226,GO:0051536 1224 Pseudomonadota phylum 3087 JCVI FeS assembly scaffold SufA Fe-S cluster assembly scaffold SufA This HMM represents the SufA protein of the SUF system of iron-sulfur cluster biosynthesis. This system performs FeS biosynthesis even during oxidative stress and tends to be absent in obligate anaerobic and microaerophilic bacteria. TIGR02010.1 TIGR02010 IscR 207.55 207.55 135 equivalog Y Y N Fe-S cluster assembly transcriptional regulator IscR iscR GO:0003690,GO:0003700,GO:0006355 12732309 1224 Pseudomonadota phylum 5998 JCVI iron-sulfur cluster assembly transcription factor IscR Fe-S cluster assembly transcriptional regulator IscR This HMM describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system. TIGR02011.1 TIGR02011 IscA 150.6 150.6 105 equivalog Y Y N iron-sulfur cluster assembly protein IscA iscA GO:0016226,GO:0051536 11319236,11432781,16877383 1224 Pseudomonadota phylum 5095 JCVI iron-sulfur cluster assembly protein IscA iron-sulfur cluster assembly protein IscA This HMM represents the IscA component of the ISC system for iron-sulfur cluster assembly. The ISC system consists of IscRASU, HscAB and an Isc-specific ferredoxin [1]. IscA previously was believed to act as a scaffold [3] and now is seen as an iron donor protein. This clade is limited to the proteobacteria. TIGR02099.1 TIGR02099 TIGR02099 519.15 519.15 1260 equivalog Y Y N YhdP family protein 30087168,35226662 1224 Pseudomonadota phylum 30108 JCVI TIGR02099 family protein YhdP family protein This HMM describes a family of long proteins, over 1250 amino acids in length and present in the Proteobacteria. The degree of sequence similarity is low between sequences from different genera. Apparent membrane-spanning regions at the N-terminus and C-terminus suggest the protein is inserted into (or exported through) the membrane. Members of this family include YhdP from E. coli, shown to play a role in maintaining the outer membrane permeability barrier. TIGR02101.1 TIGR02101 IpaC_SipC 130.75 130.75 314 subfamily Y Y N IpaC/SipC family type III secretion system effector 7608068 1224 Pseudomonadota phylum 472 JCVI type III secretion target, IpaC/SipC family IpaC/SipC family type III secretion system effector This HMM represents a family of proteins associated with bacterial type III secretion systems, which are injection machines for virulence factors into host cell cytoplasm. Characterized members of this protein family are known to be secreted and are described as invasins, including IpaC from Shigella flexneri (SP:P18012) and SipC from Salmonella typhimurium (GB:AAA75170.1). Members may be referred to as invasins, pathogenicity island effectors, and cell invasion proteins. TIGR02105.1 TIGR02105 III_needle 41.7 41.7 72 equivalog Y Y N type III secretion system needle filament subunit SctF sctF GO:0030254,GO:0030257 14580388,26520801 1224 Pseudomonadota phylum 1259 JCVI type III secretion apparatus needle protein type III secretion system needle filament subunit SctF This model describes protein SctF, which makes up the injection apparatus needle filament of the type III secretion system (T3SS), which is found in many Gram-negative pathogenic bacteria. Unlike some other components of T3SS, SctF does not have a close homolog in flagellar systems. Lineage-specific names for SctT in various bacteria include YscF in Yersinia, and AscF, BsaL, BscF, EscF, PscF, and SsaG elsewhere. TIGR02161.1 TIGR02161 napC_nirT 310.6 310.6 185 subfamily Y N N periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family GO:0016020,GO:0019333,GO:0020037 8730872 1224 Pseudomonadota phylum 3515 JCVI periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family Nearly every member of this subfamily is NapC, a predicted membrane-anchored four-heme c-type cytochrome that forms one component of the periplasmic nitrate reductase along with NapA, NapB, NapD, NapE, and NapF subunits. A single known exception at this time is NirT, which is instead a component of a nitrite reductase. This family excludes TorC subunits of trimethylamine N-oxide (TMAO) reductases. TIGR02162.1 TIGR02162 torC 478.2 478.2 387 equivalog Y Y N pentaheme c-type cytochrome TorC torC GO:0005506,GO:0009055,GO:0009276,GO:0016020,GO:0020037 11056172 1224 Pseudomonadota phylum 2684 JCVI trimethylamine-N-oxide reductase c-type cytochrome TorC pentaheme c-type cytochrome TorC This family includes consists of TorC, a pentahemic c-type cytochrome subunit of periplasmic reductases for trimethylamine-N-oxide (TMAO). The N-terminal half is closely related to tetrahemic NapC (or NirT) subunits of periplasmic nitrate (or nitrite) reductases; some species have both TMAO and nitrate reductase complexes. TIGR02182.1 TIGR02182 GRXB 186.65 186.65 209 equivalog Y Y N GrxB family glutaredoxin GO:0005829,GO:0006790,GO:0015035,GO:0045454 11741965,14713336,15123823 1224 Pseudomonadota phylum 5085 JCVI glutaredoxin, GrxB family glutaredoxin, GrxB family Glutaredoxins are thioltransferases (disulfide reductases) which utilize glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system [1]. Glutaredoxins utilize the CXXC motif common to thioredoxins and are involved in multiple cellular processes including protection from redox stress, reduction of critical enzymes such as ribonucleotide reductase and the generation of reduced sulfur for iron sulfur cluster formation. Glutaredoxins are capable of reduction of mixed disulfides of glutathione as well as the formation of glutathione mixed disulfides. This model includes the highly abundant E. coli GrxB (Grx2) glutaredoxin which is notably longer than either GrxA or GrxC. Unlike the other two E. coli glutaredoxins, GrxB appears to be unable to reduce ribonucleotide reductase [2], and may have more to do with resistance to redox stress [3]. TIGR02186.1 TIGR02186 alph_Pro_TM 255.25 255.25 261 hypoth_equivalog Y Y N TIGR02186 family protein 1224 Pseudomonadota phylum 2036 JCVI conserved hypothetical protein TIGR02186 family protein This family consists of predicted transmembrane proteins of about 270 amino acids. Members are found, so far, only among the Alphaproteobacteria and only once in each genome. TIGR02211.1 TIGR02211 LolD_lipo_ex 307.75 307.75 221 equivalog Y Y N lipoprotein-releasing ABC transporter ATP-binding protein LolD lolD 7.6.2.- GO:0005524,GO:0042953,GO:0043190 12823819 1224 Pseudomonadota phylum 12151 JCVI lipoprotein releasing system, ATP-binding protein lipoprotein-releasing ABC transporter ATP-binding protein LolD This model represents LolD, a member of the ABC transporter family (PF00005). LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on whether the residue immediately following the new, modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. The top scoring proteins excluded by this model include homologs from the archaeal genus Methanosarcina. TIGR02216.1 TIGR02216 phage_TIGR02216 56.1 56.1 58 hypoth_equivalog Y Y N rcc01693 family protein 20532745,29124226 1224 Pseudomonadota phylum 2317 JCVI phage conserved hypothetical protein rcc01693 family phage/gene transfer agent protein This HMM describes a family of proteins found exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA. TIGR02223.1 TIGR02223 ftsN 107.65 107.65 299 equivalog Y Y N cell division protein FtsN ftsN GO:0000910,GO:0005515 12626683 1224 Pseudomonadota phylum 5464 JCVI cell division protein FtsN cell division protein FtsN FtsN is a poorly conserved protein active in cell division in a number of Proteobacteria. The N-terminal 30 residue region tends to by Lys/Arg-rich, and is followed by a membrane-spanning region. This is followed by an acidic low-complexity region of variable length and a well-conserved C-terminal domain of two tandem regions matched by Pfam model PF05036 (Sporulation related repeat), found in several cell division and sporulation proteins. The role of FtsN as a suppressor for other cell division mutations is poorly understood; it may involve cell wall hydrolysis. TIGR02256.1 TIGR02256 ICE_VC0181 127.6 127.6 131 hypoth_equivalog Y N N conserved hypothetical protein 14731283 1224 Pseudomonadota phylum 256 JCVI conserved hypothetical protein conserved hypothetical protein This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize. TIGR02279.1 TIGR02279 PaaC-3OHAcCoADH 669.4 669.4 503 equivalog Y Y N 3-hydroxyacyl-CoA dehydrogenase PaaH paaH GO:0008691,GO:0010124 11260461,9748275 1224 Pseudomonadota phylum 4407 JCVI 3-hydroxyacyl-CoA dehydrogenase PaaC 3-hydroxyacyl-CoA dehydrogenase PaaH This 3-hydroxyacyl-CoA dehydrogenase is involved in the degradation of phenylacetic acid, presumably in steps following the opening of the phenyl ring [1]. The sequences included in this model are all found in aparrent operons with other related genes such as paaA, paaB, paaD, paaE, paaF and paaN [2]. Some genomes contain these other genes without an apparent paaC in the same operon - possibly in these cases a different dehydrogenase involved in fatty acid degradation may fill in the needed activity. This enzyme has domains which are members of the PF02737 and PF00725 families. TIGR02292.1 TIGR02292 ygfB_yecA 33.8 33.8 179 subfamily Y Y N UPF0149 family protein 15317022 1224 Pseudomonadota phylum 18113 JCVI yecA family protein UPF0149 family protein This HMM originally was broader than Pfam model PF03695 (version PF03695.3), but because that model has broadened in scope and now includes additional proteins, the moniker UPF0149 can now be more broadly applied. This family includes two mutually very distant homologs in Escherichia coli K-12, YecA (for which this HMM was previously named) and YgfB. The crystal structure is known for the member from Haemophilus influenzae (Ygfb, HI0817). TIGR02296.1 TIGR02296 HpaC 205.95 205.95 154 equivalog Y Y N 4-hydroxyphenylacetate 3-monooxygenase, reductase component hpaC 1.14.14.9 GO:0016651,GO:0042537,GO:0051287 8077235 1224 Pseudomonadota phylum 2787 JCVI 4-hydroxyphenylacetate 3-monooxygenase, reductase component 4-hydroxyphenylacetate 3-monooxygenase, reductase component This model identifies the reductase component (HpaC) of 4-hydroxyphenylacetate 3-monooxygenase [1]. This enzyme catalyzes the first step (hydroxylation at the 3-position) in the degradation of 4-hydroxyphenylacetate to succinate and pyruvate. 4-hydroxyphenylacetate arises from the degradation of tyrosine. These reductases catalyze the reduction of free flavins by NADPH. The flavin is then utilized by the large subunit of the monooxygenase. TIGR02298.1 TIGR02298 HpaD_Fe 315.95 315.95 284 equivalog Y Y N 3,4-dihydroxyphenylacetate 2,3-dioxygenase hpaD 1.13.11.15 GO:0008152,GO:0008198,GO:0008687 2261999 1224 Pseudomonadota phylum 4795 JCVI 3,4-dihydroxyphenylacetate 2,3-dioxygenase 3,4-dihydroxyphenylacetate 2,3-dioxygenase This enzyme catalyzes the ring-opening step in the degradation of 4-hydroxyphenylacetate [1]. TIGR02329.1 TIGR02329 propionate_PrpR 499.2 499.2 526 equivalog Y Y N propionate catabolism operon regulatory protein PrpR prpR GO:0000156,GO:0000160,GO:0003677,GO:0005524,GO:0005737,GO:0006355,GO:0008134,GO:0019629,GO:0043565 1224 Pseudomonadota phylum 7454 JCVI propionate catabolism operon regulatory protein PrpR propionate catabolism operon regulatory protein PrpR At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR. TIGR02337.1 TIGR02337 HpaR 121.2 121.2 130 equivalog Y Y N homoprotocatechuate degradation operon regulator HpaR hpaR GO:0003677,GO:0003700,GO:0045892 1224 Pseudomonadota phylum 5638 JCVI homoprotocatechuate degradation operon regulator, HpaR homoprotocatechuate degradation operon regulator, HpaR This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (PF01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate. TIGR02381.1 TIGR02381 cspD 115.4 115.4 68 equivalog Y Y N cold shock domain-containing protein CspD cspD GO:0003676,GO:0005737,GO:0006355 11260474 1224 Pseudomonadota phylum 3607 JCVI cold shock domain protein CspD cold shock domain-containing protein CspD This HMM represents what appears to be a phylogenetically distinct clade, containing E. coli CspD (SP|P24245) and related proteobacterial proteins within the larger family of cold shock domain proteins described by Pfam HMM PF00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication [1]. TIGR02394.1 TIGR02394 rpoS_proteo 378.7 378.7 285 equivalog Y Y N RNA polymerase sigma factor RpoS rpoS GO:0003677,GO:0003700,GO:0006352,GO:0006355,GO:0016987 8475100 1224 Pseudomonadota phylum 8570 JCVI RNA polymerase sigma factor RpoS RNA polymerase sigma factor RpoS A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393). TIGR02409.1 TIGR02409 carnitine_bodg 414.75 414.75 366 equivalog Y Y N gamma-butyrobetaine dioxygenase 1.14.11.1 GO:0005506,GO:0008336,GO:0045329 8504802 1224 Pseudomonadota phylum 1921 JCVI gamma-butyrobetaine hydroxylase gamma-butyrobetaine dioxygenase Members of this protein family are gamma-butyrobetaine hydroxylase, both bacterial and eukarytotic. This enzyme catalyzes the last step in the conversion of lysine to carnitine. Carnitine can serve as a compatible solvent in bacteria and also participates in fatty acid metabolism. TIGR02419.1 TIGR02419 C4_traR_proteo 59.7 59.7 64 subfamily Y N N phage/conjugal plasmid C-4 type zinc finger protein, TraR family 1224 Pseudomonadota phylum 13060 JCVI phage/conjugal plasmid C-4 type zinc finger protein, TraR family phage/conjugal plasmid C-4 type zinc finger protein, TraR family Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA. TIGR02424.1 TIGR02424 TF_pcaQ 303.8 303.8 300 equivalog Y Y N pca operon transcription factor PcaQ pcaQ GO:0003677,GO:0019619,GO:0045893 15006791 1224 Pseudomonadota phylum 5353 JCVI pca operon transcription factor PcaQ pca operon transcription factor PcaQ Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria. TIGR02437.1 TIGR02437 FadB 933.55 933.55 714 equivalog Y Y N fatty acid oxidation complex subunit alpha FadB fadB GO:0003857,GO:0004165,GO:0004300,GO:0008692,GO:0009062,GO:0036125 1699931 1224 Pseudomonadota phylum 17209 JCVI fatty oxidation complex, alpha subunit FadB fatty acid oxidation complex subunit alpha FadB Members represent alpha subunit of multifunctional enzyme complex of the fatty acid degradation cycle. Activities include: enoyl-CoA hydratase (EC 4.2.1.17), dodecenoyl-CoA delta-isomerase activity (EC 5.3.3.8), 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35), 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A representative is E. coli FadB (SP:P21177). This model excludes the FadJ family represented by SP:P77399. TIGR02459.1 TIGR02459 CbtB 64.4 64.4 60 hypoth_equivalog Y N N cobalt transporter subunit CbtB (proposed) cbtB 1224 Pseudomonadota phylum 2487 JCVI cobalt transporter subunit CbtB (proposed) cobalt transporter subunit CbtB (proposed) This model represents a family of proteins which have been proposed [1] to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems. Evidence for this assignment includes 1) prediction of a single trans-membrane segment and a C-terminal histidine-rich motif likely to be a metal-binding site, 2) positional gene linkage with known B12 biosynthesis genes, 3) upstream proximity of B12 transcriptional regulatory sites, 4) the absence of other known cobalt import systems and 5) the obligate co-localization with a protein (CbtA) predicted to have five additional trans-membrane segments. TIGR02497.1 TIGR02497 yscI_hrpB_dom 23.45 23.45 39 equivalog_domain Y Y N type III secretion system inner rod subunit SctI sctI GO:0030254,GO:0030257 1224 Pseudomonadota phylum 1417 JCVI type III secretion apparatus protein, YscI/HrpB, C-terminal domain type III secretion system inner rod subunit SctI This model represents the conserved C-terminal domain of a protein conserved in across species in the bacterial type III secretion apparatus. This protein is designated YscI (Yop proteins translocation protein I) in Yersinia and HrpB (hypersensitivity response and pathogenicity protein B) in plant pathogens such as Pseudomonas syringae. TIGR02503.1 TIGR02503 type_III_SycN 84.55 84.55 120 equivalog Y Y N type III secretion chaperone SycN sycN GO:0009306 10094626 1224 Pseudomonadota phylum 575 JCVI type III secretion chaperone SycN type III secretion chaperone SycN Members of this protein family are part of the machinery of bacterial type III secretion in a number of bacteria that target animal cells. In the well-studied system from Yersinia, a complex of this protein (SycN) and YscB (PF07329) acts as a chaperone for the export of YopN (PMID:10094626). YopN then acts to control effector protein secretion, in response to calcium levels, so that secretion occurs only after contact with the targeted eukaryotic cell. TIGR02520.1 TIGR02520 pilus_B_mal_scr 287.65 287.65 513 equivalog Y Y N PilN family type IVB pilus formation outer membrane protein GO:0009297,GO:0009306,GO:0019867 9171405 1224 Pseudomonadota phylum 3429 JCVI type IVB pilus formation outer membrane protein, R64 PilN family type IVB pilus formation outer membrane protein, R64 PilN family Several related protein families encode outer membrane pore proteins for type II secretion, type III secretion, and type IV pilus formation. This protein family appears to encode a secretin for pilus formation, although it is quite different from PilQ. Members include the PilN lipoprotein of the plasmid R64 thin pilus, a type IV pilus. Scoring between the trusted and noise cutoffs are examples of bundle-forming pilus B (bfpB). TIGR02522.1 TIGR02522 pilus_cpaD 94.45 94.45 198 subfamily Y Y N CpaD family pilus assembly lipoprotein 10880436 1224 Pseudomonadota phylum 4309 JCVI pilus (Caulobacter type) biogenesis lipoprotein CpaD CpaD family pilus assembly lipoprotein This family consists of a pilus biogenesis protein, CpaD, from Caulobacter, and homologs in other bacteria, including three in the root nodule bacterium Bradyrhizobium japonicum. The molecular function is not known. TIGR02541.1 TIGR02541 flagell_FlgJ 193 193 294 equivalog Y Y N flagellar assembly peptidoglycan hydrolase FlgJ flgJ GO:0016798,GO:0044780 11554792,25248745,26871950 1224 Pseudomonadota phylum 16669 JCVI flagellar rod assembly protein/muramidase FlgJ flagellar assembly peptidoglycan hydrolase FlgJ Herlihey, et al. report "Surprisingly, FlgJ functions as neither a muramidase [lysozyme, 3.2.1.17] nor a lytic transglycosylases [4.2.2.n1/n2] but rather as a beta-N-acetylglucosaminidase [3.2.1.14]." For a clarification of the meaning of this statement, see figure 2 from PMID:18266855. TIGR02553.1 TIGR02553 SipD_IpaD_SspD 219.25 219.25 317 equivalog Y Y N type III secretion system needle tip protein SctA sctA 26520801,8748032 1224 Pseudomonadota phylum 416 JCVI type III effector protein IpaD/SipD/SspD type III secretion system needle tip protein SctA This model describes protein SctA, which makes up the injection apparatus needle tip of the type III secretion system (T3SS), found in many Gram-negative pathogenic bacteria. Lineage-specific names for needle tip protein in various bacteria include LcrV in Yersinia, and EspA, IpaD, SipD, SseB, and BipD elsewhere. TIGR02554.1 TIGR02554 PrgH 188.6 188.6 389 equivalog Y Y N PrgH/EprH family type III secretion apparatus protein GO:0030254,GO:0030257 15528446,7476203 1224 Pseudomonadota phylum 1706 JCVI type III secretion apparatus protein PrgH/EprH PrgH/EprH family type III secretion apparatus protein In Samonella, this gene is part of a four-gene operon PrgHIJK and in general is found in type III secretion operons. PrgH has been shown to be required for secretion [1], as well as being a structural component of the needle complex [2]. TIGR02555.1 TIGR02555 OrgA_MxiK 118.6 118.6 185 equivalog Y Y N type III secretion apparatus protein OrgA/MxiK GO:0030254,GO:0030257 10816487,12864857,8063389 1224 Pseudomonadota phylum 1058 JCVI type III secretion apparatus protein OrgA/MxiK type III secretion apparatus protein OrgA/MxiK This gene is found in type III secretion operons and has been shown to be essential for the invasion phenotype in Salmonella and a component of the secretion apparatus [1]. The protein is known as OrgA in Salmonella due to its oxygen-dependent expression pattern in which low-oxygen levels up-regulate the gene [2]. In Shigella the ghene is called MxiK and has been shown to be sessential for the proper assembly of the secretion needle complex [3]. TIGR02557.2 TIGR02557 HpaP 65 65 204 equivalog Y Y N type III secretion system protein SctP sctP 14657497,15773978,26520801,29345052 1224 Pseudomonadota phylum 1157 JCVI type III secretion protein HpaP type III secretion system protein SctP This model describes protein SctP (Secretion and Cellular Translocation P), a protein of type III secretion system (T3SS) that is found in many pathogenic bacteria. Lineage-specific names for SctP include HpaP in Ralstonia solanacearum, YscP in Yersinia, HrpP in Pseudomonas syringae, EscP in enteropathogenic Escherichia coli, etc. SctP is homologous to flagellar hook-length control protein FliK, and member protein YscP has been described as a molecular ruler, but it appears to have other functions as well. TIGR02558.1 TIGR02558 HrpB2 93.3 93.3 124 equivalog Y Y N type III secretion protein HrpB2 GO:0003824,GO:0030254,GO:0030257 1224 Pseudomonadota phylum 373 JCVI type III secretion protein HrpB2 type III secretion protein HrpB2 This family of genes is found in type III secretion operons in a narrow group of species including Xanthomonas, Burkholderia and Ralstonia. TIGR02559.1 TIGR02559 HrpB7 134.4 134.4 158 equivalog Y Y N type III secretion protein HrpB7 1224 Pseudomonadota phylum 413 JCVI type III secretion protein HrpB7 type III secretion protein HrpB7 This family of genes is found in type III secretion operons in a narrow range of species including Xanthomonas, Burkholderia and Ralstonia. TIGR02560.1 TIGR02560 HrpB4 167.45 167.45 220 equivalog Y Y N type III secretion protein HrpB4 1224 Pseudomonadota phylum 648 JCVI type III secretion protein HrpB4 type III secretion protein HrpB4 This family of genes are always found in type III secretion operons in a limited number of species including Burkholderia, Xanthomonas and Ralstonia. TIGR02561.1 TIGR02561 HrpB1_HrpK 123.85 123.85 183 equivalog Y Y N HrpB1 family type III secretion system apparatus protein 23934485 1224 Pseudomonadota phylum 479 JCVI type III secretion protein HrpB1/HrpK HrpB1 family type III secretion system apparatus protein This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia. TIGR02633.1 TIGR02633 xylG 723.65 723.65 500 equivalog Y Y N D-xylose ABC transporter ATP-binding protein xylG 7.5.2.10 GO:0005524,GO:0015614,GO:0015753,GO:0016020 1224 Pseudomonadota phylum 6950 JCVI D-xylose ABC transporter, ATP-binding protein D-xylose ABC transporter ATP-binding protein Several bacterial species have enzymes xylose isomerase and xylulokinase enzymes for xylose utilization. Members of this protein family are the ATP-binding cassette (ABC) subunit of the known or predicted high-affinity xylose ABC transporter for xylose import. These genes, which closely resemble other sugar transport ABC transporter genes, typically are encoded near xylose utilization enzymes and regulatory proteins. Note that this form of the transporter contains two copies of the ABC transporter domain (PF00005). TIGR02643.1 TIGR02643 T_phosphoryl 570.7 570.7 437 equivalog Y Y N thymidine phosphorylase deoA 2.4.2.4 GO:0006213,GO:0009032 1322661 1224 Pseudomonadota phylum 11741 JCVI thymidine phosphorylase thymidine phosphorylase Thymidine phosphorylase (alternate name: pyrimidine phosphorylase), EC 2.4.2.4, is the designation for the enzyme of E. coli and other Proteobacteria involved in (deoxy)nucleotide degradation. It often occurs in an operon with a deoxyribose-phosphate aldolase, phosphopentomutase and a purine nucleoside phosphorylase. In many other lineages, the corresponding enzyme is designated pyrimidine-nucleoside phosphorylase (EC 2.4.2.2); the naming convention imposed by this model represents standard literature practice. TIGR02647.1 TIGR02647 DNA 44.6 44.6 77 hypoth_equivalog Y Y N TIGR02647 family protein 1224 Pseudomonadota phylum 2537 JCVI TIGR02647 family protein TIGR02647 family protein Members of this family are found, so far, only in the Gammaproteobacteria. The function is unknown. The location on the chromosome usually is not far from housekeeping genes rather than in what is clearly, say, a prophage region. Some members have been annotated in public databases as DNA-binding protein inhibitor Id-2-related protein, putative transcriptional regulator, or hypothetical DNA binding protein. TIGR02658.1 TIGR02658 TTQ_MADH_Hv 454.45 454.45 358 equivalog Y Y N methylamine dehydrogenase (amicyanin) large subunit mauB 1.4.9.1 GO:0052876 1224 Pseudomonadota phylum 115 JCVI methylamine dehydrogenase (amicyanin) heavy chain methylamine dehydrogenase (amicyanin) large subunit This family consists of the heavy chain of methylamine dehydrogenase light chain, a periplasmic enzyme. The enzyme contains a tryptophan tryptophylquinone (TTQ) prothetic group derived from two Trp residues in the light subunity. The enzyme forms a complex with the type I blue copper protein amicyanin and a cytochrome. Electron transfer procedes from TQQ to the copper and then to the heme group of the cytochrome. TIGR02659.1 TIGR02659 TTQ_MADH_Lt 196.85 196.85 186 equivalog Y Y N methylamine dehydrogenase (amicyanin) small subunit mauA 1.4.9.1 GO:0030288,GO:0052876 15734739 1224 Pseudomonadota phylum 199 JCVI methylamine dehydrogenase (amicyanin) light chain methylamine dehydrogenase (amicyanin) small subunit This family consists of the light chain of methylamine dehydrogenase light chain, a periplasmic enzyme. This subunit contains a tryptophan tryptophylquinone (TTQ) prothetic group derived from Trp-114 and Trp-165 of the precursor, numbered according to the sequence from Paracoccus denitrificans. The enzyme forms a complex with the type I blue copper protein amicyanin and cytochrome. Electron transfer procedes from TQQ to the copper and then to the heme group of the cytochrome. TIGR02718.1 TIGR02718 sider_RhtX_FptX 356.15 356.15 390 subfamily Y Y N RhtX/FptX family siderophore transporter GO:0015343,GO:0015891 15126460 1224 Pseudomonadota phylum 1652 JCVI siderophore transporter, RhtX/FptX family RhtX/FptX family siderophore transporter RhtX from Sinorhizobium meliloti 2011 and FptX from Pseudomonas aeruginosa appear to be single polypeptide transporters, from the major facilitator family (see PF07690) for import of siderophores as a means to import iron. This function was suggested by proximity to siderophore biosynthesis genes and then confirmed by study of knockout and heterologous expression phenotypes. TIGR02742.1 TIGR02742 TrbC_Ftype 66.45 66.45 130 equivalog Y Y N type-F conjugative transfer system pilin assembly protein TrbC trbC 16138100,205063 1224 Pseudomonadota phylum 5996 JCVI type-F conjugative transfer system pilin assembly protein TrbC type-F conjugative transfer system pilin assembly protein TrbC This protein is an essential component of the F-type conjugative pilus assembly system for the transfer of plasmid DNA [1,2]. The N-terminal portion of these proteins are heterogeneous and are not covered by this model. TIGR02747.1 TIGR02747 TraV 44.75 44.75 145 equivalog Y Y N type IV conjugative transfer system lipoprotein TraV traV 11722740,12855161,16138100 1224 Pseudomonadota phylum 5465 JCVI type IV conjugative transfer system protein TraV type IV conjugative transfer system lipoprotein TraV The TraV protein is a component of conjugative type IV secretion systems. TraV is an outer membrane lipoprotein and is believed to interact with the secretin TraK [1,2,3]. The alignment contains three conserved cysteines in the N-terminal half. TIGR02767.1 TIGR02767 TraG-Ti 686.2 686.2 623 equivalog Y Y N Ti-type conjugative transfer system protein TraG traG GO:0016020 8763953 1224 Pseudomonadota phylum 2145 JCVI Ti-type conjugative transfer system protein TraG Ti-type conjugative transfer system protein TraG This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains [1]. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems. TIGR02793.1 TIGR02793 nikR 175.45 175.45 129 equivalog Y Y N nickel-responsive transcriptional regulator NikR nikR GO:0003677,GO:0005737,GO:0010045,GO:0016151 1224 Pseudomonadota phylum 1562 JCVI nickel-responsive transcriptional regulator NikR nickel-responsive transcriptional regulator NikR Three members of the seed for this model, from Escherichia coli, Pseudomonas putida, and Brucella melitensis, are found associated with a nickel ABC transporter operon that acts to import nickel for use as a cofactor in urease or hydrogenase. These proteins, with characterized nickel-binding and DNA-binding domains, act as nickel-responsive transcriptional regulators. In the larger family of full-length homologs, most others both lack proximity to the nickel ABC transporter operon and form a separate clade. Several of the homologs not within the scope of this model, but rather scoring between the trusted and noise cutoffs, have been shown to bind nickel, copper, or both, and to regulate genes in response to nickel. TIGR02797.1 TIGR02797 exbB 206.2 206.2 211 equivalog Y Y N tonB-system energizer ExbB exbB GO:0016020,GO:0022857,GO:0055085 12896813 1224 Pseudomonadota phylum 10082 JCVI tonB-system energizer ExbB tonB-system energizer ExbB This model describes ExbB proteins, part of the MotA/TolQ/ExbB protein family. The paired proteins MotA and MotB, TolQ and TolR, and ExbB and ExbD harness the proton-motive force to drive the flagellar motor, energize the Tol-Pal system, or energize TonB, respectively. Tol-Pal and TonB are both active at the outer membrane. Genomes may have many different TonB-dependent receptors, of which many of those characterized are involved in siderophore transport across the outer membrane. TIGR02799.1 TIGR02799 thio_ybgC 141.35 141.35 126 equivalog Y Y N tol-pal system-associated acyl-CoA thioesterase ybgC GO:0005737,GO:0047617 11959124 1224 Pseudomonadota phylum 15464 JCVI tol-pal system-associated acyl-CoA thioesterase tol-pal system-associated acyl-CoA thioesterase The tol-pal system consists of five critical genes. Inner membrane proteins TolQ and TolR convert protomotive force to energy that is transduced through TolA to an outer membrane complex of TolB and Pal. The system is known to be required to maintain outer membrane integrity. In a system with several homologous parts, ExbB and ExbD transduces energy through TonB to a variety of outer membrane proteins, many of which are siderophore receptors. The tol-pal system therefore may also be involved in transport. This family consists of a protein nearly always found in operons with the genes of the tol-pal system. The significance of this thioesterase to the tol-pal system is unclear, but either of two observations may be relevant. First, Pal, or peptidoglycan-associated lipoprotein, has a conserved N-terminal cleavage and acylation that makes it a lipoprotein. Second, the tol-pal system is implicated not only in the import of certain organics but also in the maintenance of outer membrane integrity (by an unknown mechanism). TIGR02803.1 TIGR02803 ExbD_1 152.95 152.95 122 equivalog Y Y N TonB system transport protein ExbD exbD GO:0015291,GO:0016020,GO:0055085 1224 Pseudomonadota phylum 6172 JCVI TonB system transport protein ExbD TonB system transport protein ExbD Members of this family are Gram-negative bacterial inner membrane proteins, generally designated ExbD, related to the TolR family modeled by TIGRFAMs TIGR02801. Members always are encoded next to a protein designated ExbB (TIGR02797), related to the TolQ family modeled by TIGRFAMs TIGR02796. ExbD and ExbB together form a proton channel through which they can harness the proton-motive force to energize TonB, which in turn energizes TonB-dependent receptors in the outer membrane. TonB-dependent receptors with known specificity tend to import siderophores or vitamin B12. A TonB system and Tol-Pal system often will co-exist in a single bacterial genome. TIGR02809.1 TIGR02809 phasin_3 65.85 65.85 110 equivalog Y Y N phasin family protein GO:0019752 1224 Pseudomonadota phylum 1025 JCVI phasin family protein phasin family protein Members of this protein family are encoded in polyhydroxyalkanoic acid storage system regions in Vibrio, Photobacterium profundum SS9, Acinetobacter sp., Aeromonas hydrophila, and several species of Vibrio. Members appear distantly related to the phasin family proteins modeled by TIGR01841 and TIGR01985. TIGR02843.1 TIGR02843 CyoB 1020.35 1020.35 646 equivalog Y Y N cytochrome o ubiquinol oxidase subunit I cyoB 7.1.1.3 GO:0009486,GO:0015990,GO:0016020 1224 Pseudomonadota phylum 16263 JCVI cytochrome o ubiquinol oxidase, subunit I cytochrome o ubiquinol oxidase subunit I Cytochrome o terminal oxidase complex is the component of the aerobic respiratory chain which reacts with oxygen, reducing it to water with the concomitant transport of 4 protons across the membrane. Also known as the cytochrome bo complex, cytochrome o ubiquinol oxidase contains four subunits, two heme b cofactors and a copper atom which is believed to be the oxygen active site. This complex is structurally related to the cytochrome caa3 oxidases which utilize cytochrome c as the reductant and contain heme a cofactors, as well as the intermediate form aa3 oxidases which also react directly with quinones as the reductant. TIGR02938.1 TIGR02938 nifL_nitrog 242.45 242.45 494 equivalog Y Y N nitrogen fixation negative regulator NifL nifL GO:0007165,GO:0009399 16417511 1224 Pseudomonadota phylum 988 JCVI nitrogen fixation negative regulator NifL nitrogen fixation negative regulator NifL NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes. TIGR02939.1 TIGR02939 RpoE_Sigma70 236.15 236.15 190 equivalog Y Y N RNA polymerase sigma factor RpoE rpoE GO:0003677,GO:0003700,GO:0006352,GO:0006355,GO:0016987 1224 Pseudomonadota phylum 6819 JCVI RNA polymerase sigma factor RpoE RNA polymerase sigma factor RpoE A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU. TIGR02973.1 TIGR02973 nitrate_rd_NapE 68.8 68.8 42 equivalog Y Y N periplasmic nitrate reductase, NapE protein napE GO:0008940,GO:0009325,GO:0042126 14663073 1224 Pseudomonadota phylum 1356 JCVI periplasmic nitrate reductase, NapE protein periplasmic nitrate reductase, NapE protein NapE, homologous to TorE (TIGR02972), is a membrane protein of unknown function that is part of the periplasmic nitrate reductase system; it may be part of the enzyme complex. The periplasmic nitrate reductase allows for nitrate respiration in anaerobic conditions. TIGR02974.1 TIGR02974 phageshock_pspF 443.55 443.55 336 equivalog Y Y N phage shock protein operon transcriptional activator pspF GO:0005737,GO:0006355,GO:0140110 15485810 1224 Pseudomonadota phylum 9896 JCVI psp operon transcriptional activator phage shock protein operon transcriptional activator Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH TIGR02976.1 TIGR02976 phageshock_pspB 51.7 51.7 75 equivalog Y Y N envelope stress response membrane protein PspB pspB GO:0009271 15485810,16468999 1224 Pseudomonadota phylum 3869 JCVI phage shock protein B envelope stress response membrane protein PspB This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response. TIGR02978.1 TIGR02978 phageshock_pspC 104 104 121 equivalog Y Y N envelope stress response membrane protein PspC pspC 16468999 1224 Pseudomonadota phylum 5157 JCVI phage shock protein C envelope stress response membrane protein PspC All members of this protein family are the phage shock protein PspC. These proteins contain a PspC domain, as do other members of the larger family of proteins described by Pfam model PF04024. The phage shock regulon is restricted to the Proteobacteria and somewhat sparsely distributed there. It is expressed, under positive control of a sigma-54-dependent transcription factor, PspF, which binds and is modulated by PspA. Stresses that induce the psp regulon include phage secretin overexpression, ethanol, heat shock, and protein export defects. TIGR03012.1 TIGR03012 sulf_tusD_dsrE 89.25 89.25 127 equivalog Y Y N sulfurtransferase complex subunit TusD tusD GO:0005737,GO:0008033,GO:0016783 16387657,9695921 1224 Pseudomonadota phylum 10117 JCVI sulfur relay protein TusD/DsrE sulfurtransferase complex subunit TusD The three proteins TusB, TusC, and TusD form a heterohexamer responsible for a sulfur relay reaction. In large numbers of proteobacterial species, this complex acts on a Cys-derived persulfide moiety, delivered by the cysteine desulfurase IscS to TusA, then to TusBCD. The activated sulfur group is then transferred to TusE (DsrC), then by MnmA (TrmU) for modification of an anticodon nucleotide in tRNAs for Glu, Lys, and Gln. The sulfur relay complex TusBCD is also found, under the designation DsrEFH, in phototrophic and chemotrophic sulfur bacteria, such as Chromatium vinosum. In these organisms, it seems the primary purpose is related to sulfur flux, such as oxidation from sulfide to molecular sulfur to sulfate. TIGR03014.2 TIGR03014 EpsL 275 275 385 equivalog Y Y N XrtB/PEP-CTERM-associated polysaccharide biosynthesis outer membrane protein EpsL epsL 12624205 1224 Pseudomonadota phylum 805 JCVI exopolysaccharide biosynthesis operon protein EpsL XrtB/PEP-CTERM-associated polysaccharide biosynthesis outer membrane protein EpsL EpsL was described originally as a component of the methanolan exopolysaccharide (EPS) biosynthesis operon in Methylobacillus sp. strain 12S, although no other information regarding its possible function was suggested. Homologs of this gene are found in several other exopolysaccharide operons in a small number of species. EpsL appears to be an outer membrane beta-barrel protein, likely with a role in transport of EPS components across the membrane. The majority of EPS loci with a member of this family, but not all, contain the exosortase XrtB, and those species all possess PEP-CTERM proteins that the EPS associates with or includes. XrtB was designated EpsH before it was recognized to be a protease involved in PEP-CTERM protein sorting and processing. These operons contain a subset of the methanolan operon genes by homology and synteny, including the epsH gene which is proposed to act as an "exosortase" directing proteins with a C-terminal tag (PEP-CTERM) to the exopolysaccharide layer [2]. Each of the genomes in which these genes and epsL are found also encode genes with these C-terminal tags. TIGR03017.1 TIGR03017 EpsF 422.75 422.75 444 equivalog Y Y N chain length determinant protein EpsF epsF 12624205 1224 Pseudomonadota phylum 1161 JCVI chain length determinant protein EpsF chain length determinant protein EpsF Sequences in this family of proteins are members of the chain length determinant family (PF02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S [1]. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein [2]. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer. TIGR03020.2 TIGR03020 EpsA 170 170 247 equivalog Y Y N XrtB/PEP-CTERM-associated transcriptional regulator EpsA epsA 12624205,16930487 1224 Pseudomonadota phylum 472 JCVI transcriptional regulator EpsA XrtB/PEP-CTERM-associated polysaccharide biosynthesis transcriptional regulator EpsA Proteins in this family include a C-terminal LuxR transcriptional regulator domain (PF00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type [1], or the associated PEP-CTERM-containing genes [2]. TIGR03028.1 TIGR03028 EpsE 262.65 262.65 239 equivalog Y Y N polysaccharide export protein EpsE epsE 12624205,8759852 1224 Pseudomonadota phylum 1017 JCVI polysaccharide export protein EpsE polysaccharide export protein EpsE Sequences in this family of proteins are members of a polysaccharide export protein family (PF02563) which includes the wza [1] protein from E.coli. This family of proteins are homologous to the EpsE protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S [2]. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein [2]. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer [3]. TIGR03029.1 TIGR03029 EpsG 313.8 313.8 274 equivalog Y Y N chain length determinant protein tyrosine kinase EpsG epsG 12624205 1224 Pseudomonadota phylum 775 JCVI chain length determinant protein tyrosine kinase EpsG chain length determinant protein tyrosine kinase EpsG The proteins in this family are homologs of the EpsG protein found in Methylobacillus strain 12S and are generally found in operons with other Eps homologs. The protein is believed to function as the protein tyrosine kinase component of the chain length regulator (along with the transmembrane component EpsF). TIGR03034.1 TIGR03034 TIGR03034 156.45 156.45 274 subfamily Y Y N YPO3983 family protein 1224 Pseudomonadota phylum 3200 JCVI conserved hypothetical protein YPO3983 family protein Members of this protein family have been found in several species of gammaproteobacteria, including Yersinia pestis and Y. pseudotuberculosis, Xylella fastidiosa, and Escherichia coli UTI89. As many as five members can be found in a single genome. The function is unknown. TIGR03074.1 TIGR03074 PQQ_membr_DH 832.65 832.65 783 subfamily Y Y N membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family 1.1.-.- GO:0016020,GO:0016491,GO:0048038 1224 Pseudomonadota phylum 30189 JCVI membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family This protein family has a phylogenetic distribution very similar to that coenzyme PQQ biosynthesis enzymes, as shown by partial phylogenetic profiling. Members of this family have several predicted transmembrane helices in the N-terminal region, and include the quinoprotein glucose dehydrogenase (EC 1.1.5.2) of Escherichia coli and the quinate/shikimate dehydrogenase of Acinetobacter sp. ADP1 (EC 1.1.99.25). Sequences closely related except for the absense of the N-terminal hydrophobic region, scoring in the gray zone between the trusted and noise cutoffs, include PQQ-dependent glycerol (EC 1.1.99.22) and and other polyol (sugar alcohol) dehydrogenases. TIGR03101.1 TIGR03101 hydr2_PEP 202.75 202.75 266 hypoth_equivalog Y Y N hydrolase 2, exosortase A system-associated 16930487 1224 Pseudomonadota phylum 983 JCVI exosortase A system-associated hydrolase 2 hydrolase 2, exosortase A system-associated This group of proteins are members of the alpha/beta hydrolase superfamily. These proteins are generally found in genomes containing the exosortase/PEP-CTERM protein expoert system [1], specifically the type 1 variant of this system described by the Genome Property GenProp0652. When found in this context they are invariably present in the vicinity of a second, relatively unrelated enzyme (ortholog 1, TIGR03100) of the same superfamily. TIGR03113.1 TIGR03113 exosort_XrtB 275 275 268 exception Y Y N exosortase B xrtB GO:0004197,GO:0006605,GO:0016020,GO:0043687 16930487 1224 Pseudomonadota phylum 983 JCVI exosortase B exosortase B The predicted protein-sorting transpeptidase that we call exosortase (see TIGR02602) has distinct subclasses that associated with different types of exopolysaccharide production loci. We designate this relatively uncommon proteobacterial type to be type 2. We propose the gene symbol xrtB. Most species encountered so far with xrtB also contain xrtA (TIGR03109). TIGR03186.1 TIGR03186 AKGDH_not_PDH 1408.3 1408.3 889 exception Y Y N alpha-ketoglutarate dehydrogenase mdeB GO:0016491 9190812 1224 Pseudomonadota phylum 3800 JCVI alpha-ketoglutarate dehydrogenase alpha-ketoglutarate dehydrogenase Several bacterial species have a paralog to homodimeric form of the pyruvate dehydrogenase E1 component (see model TIGR00759), often encoded next to L-methionine gamma-lyase gene (mdeA). The member from a strain of Pseudomonas putida was shown to act on alpha-ketobutyrate, which is produced by MdeA.This model serves as an exception model to TIGR00759, as other proteins hitting TIGR00759 should be identified as the pyruvate dehydrogenase E1 component. TIGR03193.1 TIGR03193 4hydroxCoAred 257.8 257.8 148 equivalog Y Y N 4-hydroxybenzoyl-CoA reductase subunit gamma hcrC 1.1.7.1 1224 Pseudomonadota phylum 80 JCVI 4-hydroxybenzoyl-CoA reductase, gamma subunit 4-hydroxybenzoyl-CoA reductase subunit gamma 4-hydroxybenzoyl-CoA reductase converts 4-hydroxybenzoyl-CoA to benzoyl-CoA, a common intermediate in the degradation of aromatic compounds. This protein family represents the gamma chain of this three-subunit enzyme. TIGR03195.1 TIGR03195 4hydrxCoA_B 404.55 404.55 321 equivalog Y Y N 4-hydroxybenzoyl-CoA reductase subunit beta hcrB 1.1.7.1 1224 Pseudomonadota phylum 108 JCVI 4-hydroxybenzoyl-CoA reductase, beta subunit 4-hydroxybenzoyl-CoA reductase subunit beta This model represents the second largest chain, beta, of the enzyme 4-hydroxybenzoyl-CoA reductase. In species capable of degrading various aromatic compounds by way of benzoyl-CoA, this enzyme can convert 4-hydroxybenzoyl-CoA to benzoyl-CoA. TIGR03204.1 TIGR03204 pimC_large 623.85 623.85 395 equivalog Y Y N pimeloyl-CoA dehydrogenase large subunit pimC 1.3.1.62 GO:0018515 15758219 1224 Pseudomonadota phylum 759 JCVI pimeloyl-CoA dehydrogenase, large subunit pimeloyl-CoA dehydrogenase large subunit Members of this protein family are the PimC proteins of species such as Rhodopseudomonas palustris and Bradyrhizobium japonicum. The pimFABCDE operon encodes proteins for the metabolism of straight chain dicarboxylates of seven to fourteen carbons. Especially relevant is pimeloyl-CoA, basis of the gene symbol, as it is a catabolite of benzoyl-CoA degradation, which occurs in Rhodopseudomonas palustris. TIGR03206.1 TIGR03206 benzo_BadH 431.2 431.2 250 equivalog Y Y N 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase badH 10781543 1224 Pseudomonadota phylum 512 JCVI 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase Members of this protein family are the enzyme 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase. The enzymatic properties were confirmed experimentally in Rhodopseudomonas palustris; the enzyme is homotetrameric, and not sensitive to oxygen. This enzyme is part of proposed pathway for degradation of benzoyl-CoA to 3-hydroxypimeloyl-CoA that differs from the analogous in Thauera aromatica. It also may occur in degradation of the non-aromatic compound cyclohexane-1-carboxylate. TIGR03207.1 TIGR03207 cyc_hxne_CoA_dh 575.35 575.35 372 equivalog Y Y N cyclohexanecarboxyl-CoA dehydrogenase aliB 1224 Pseudomonadota phylum 957 JCVI cyclohexanecarboxyl-CoA dehydrogenase cyclohexanecarboxyl-CoA dehydrogenase Cyclohex-1-ene-1carboxyl-CoA is an intermediate in the anaerobic degradation of benzoyl-CoA derived from varioius aromatic compounds, in Rhodopseudomonas palustris but not Thauera aromatica. The aliphatic compound cyclohexanecarboxylate, can be converted to the same intermediate in two steps. The first step is its ligation to coenzyme A. The second is the action of this enzyme, cyclohexanecarboxyl-CoA dehydrogenase. TIGR03208.1 TIGR03208 cyc_hxne_CoA_lg 792.3 792.3 538 equivalog Y Y N cyclohexanecarboxylate-CoA ligase aliA 1224 Pseudomonadota phylum 814 JCVI cyclohexanecarboxylate-CoA ligase cyclohexanecarboxylate-CoA ligase Members of this protein family are cyclohexanecarboxylate-CoA ligase. This enzyme prepares the aliphatic ring compound, cyclohexanecarboxylate, for dehydrogenation and then degradation by a pathway also used in benzoyl-CoA degradation in Rhodopseudomonas palustris. TIGR03210.1 TIGR03210 badI 467.6 467.6 256 equivalog Y Y N 2-ketocyclohexanecarboxyl-CoA hydrolase badI 9573182 1224 Pseudomonadota phylum 775 JCVI 2-ketocyclohexanecarboxyl-CoA hydrolase 2-ketocyclohexanecarboxyl-CoA hydrolase Members of this protein family are 2-ketocyclohexanecarboxyl-CoA hydrolase, a ring-opening enzyme that acts in catabolism of molecules such as benzoyl-CoA and cyclohexane carboxylate. It converts -ketocyclohexanecarboxyl-CoA to pimelyl-CoA. It is not sensitive to oxygen. TIGR03219.1 TIGR03219 salicylate_mono 446.35 446.35 414 equivalog Y Y N salicylate 1-monooxygenase salA 1.14.13.1 1224 Pseudomonadota phylum 762 JCVI salicylate 1-monooxygenase salicylate 1-monooxygenase Members of this protein family are salicylate 1-monooxygenase, also called salicylate hydroxylase. This enzyme converts salicylate to catechol, which is a common intermediate in the degradation of a number of aromatic compounds (phenol, toluene, benzoate, etc.). The gene for this protein may occur in catechol degradation genes, such as those of the meta-cleavage pathway. TIGR03227.1 TIGR03227 PhnS 395.3 395.3 360 equivalog Y Y N 2-aminoethylphosphonate ABC transporter substrate-binding protein phnS GO:0009897,GO:0030288,GO:0033223,GO:0033225,GO:0033226,GO:0055052 7592415 1224 Pseudomonadota phylum 2027 JCVI 2-aminoethylphosphonate ABC transporter, 2-aminoethylphosphonate binding protein 2-aminoethylphosphonate ABC transporter substrate-binding protein This ABC transporter periplasmic substrate binding protein component is found in a region of the salmonella typhimurium LT2 genome [1] responsible for the catabolism of 2-aminoethylphosphonate via the phnWX pathway (GenProp0238). The protein contains a match to PF01547 for the "Bacterial extracellular solute-binding protein" domain. TIGR03228.1 TIGR03228 anthran_1_2_A 671.9 671.9 438 equivalog Y Y N anthranilate 1,2-dioxygenase large subunit antA 1.14.12.1 GO:0006569,GO:0018618 11114907 1224 Pseudomonadota phylum 1980 JCVI anthranilate 1,2-dioxygenase, large subunit anthranilate 1,2-dioxygenase large subunit Anthranilate (2-aminobenzoate) is an intermediate of tryptophan (Trp) biosynthesis and degradation. Members of this family are the large subunit of anthranilate 1,2-dioxygenase, which acts in Trp degradation by converting anthranilate to catechol. Closely related paralogs typically are the benzoate 1,2-dioxygenase large subunit, among the larger set of ring-hydroxylating dioxygenases. TIGR03231.1 TIGR03231 anthran_1_2_B 213.5 213.5 155 equivalog Y Y N anthranilate 1,2-dioxygenase small subunit antB 1.14.12.1 GO:0006569,GO:0018618 11114907 1224 Pseudomonadota phylum 1278 JCVI anthranilate 1,2-dioxygenase, small subunit anthranilate 1,2-dioxygenase small subunit Anthranilate (2-aminobenzoate) is an intermediate of tryptophan (Trp) biosynthesis and degradation. Members of this family are the small subunit of anthranilate 1,2-dioxygenase, which acts in Trp degradation by converting anthranilate to catechol. Closely related paralogs typically are the benzoate 1,2-dioxygenase small subunit, among the larger set of ring-hydroxylating dioxygenases. TIGR03239.1 TIGR03239 GarL 406.75 406.75 249 equivalog Y Y N 2-dehydro-3-deoxyglucarate aldolase garL 4.1.2.20 GO:0008672,GO:0019394 10921867,9772162 1224 Pseudomonadota phylum 2970 JCVI 2-dehydro-3-deoxyglucarate aldolase 2-dehydro-3-deoxyglucarate aldolase In E. coli this enzyme (GarL, [1,2]) 2-dehydro-3-deoxyglucarate aldolase acts in the catabolism of several sugars including D-galactarate, D-glucarate and L-idarate. In fact, 5-dehydro-4-deoxy-D-glucarate aldolase is a synonym for this enzyme as it is unclear in the literature whether the enzyme acts on only one of these or, as seems likely, has no preference. (Despite the apparent large difference in substrate stucture indicated by their names, 2-DH-3DO- and 5-DH-4DO-glucarate differ only by the chirality of most central hydroxyl-bearing carbon and is alternately named 2-DH-3DO-galactarate.) The reported product of D-galactarate dehydratase (4.2.1.42) is the 5DH-4DO-glucarate isomer and this enzyme is found proximal to the aldolase in many genomes (GenProp0714) where no epimerase is known. Similarly, the product of D-glucarate dehydratase (4.2.1.40) is again the 5-DH-4DO isomer, so the provenance of the 2-DH-3DO-glucarate isomer for which this enzyme is named is unclear. TIGR03240.1 TIGR03240 arg_catab_astD 579.3 579.3 484 equivalog Y Y N succinylglutamate-semialdehyde dehydrogenase astD 1.2.1.71 GO:0006527,GO:0043824 1224 Pseudomonadota phylum 21861 JCVI succinylglutamate-semialdehyde dehydrogenase succinylglutamate-semialdehyde dehydrogenase Members of this protein family are succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71), the fourth enzyme in the arginine succinyltransferase (AST) pathway for arginine catabolism. TIGR03242.1 TIGR03242 arg_catab_astE 305.65 305.65 319 equivalog Y Y N succinylglutamate desuccinylase astE 3.5.1.96 GO:0006527,GO:0008270,GO:0009017 1224 Pseudomonadota phylum 13785 JCVI succinylglutamate desuccinylase succinylglutamate desuccinylase Members of this protein family are succinylglutamate desuccinylase, the fifth and final enzyme of the arginine succinyltransferase (AST) pathway for arginine catabolism. This model excludes the related protein aspartoacylase. TIGR03243.1 TIGR03243 arg_catab_AOST 284.35 284.35 335 subfamily Y N N arginine and ornithine succinyltransferase subunits 9393691 1224 Pseudomonadota phylum 19862 JCVI arginine and ornithine succinyltransferase subunits arginine and ornithine succinyltransferase subunits In many bacteria, the sole member of this protein family is arginine N-succinyltransferase (EC 2.3.1.109), the AstA protein of the arginine succinyltransferase (ast) pathway. However, in Pseudomonas aeruginosa and several other species, a tandem gene pair encodes alpha and beta subunits of a heterodimer that is designated arginine and ornithine succinyltransferase (AOST). TIGR03244.1 TIGR03244 arg_catab_AstA 391 391 336 equivalog Y Y N arginine N-succinyltransferase astA 2.3.1.109 GO:0006527,GO:0008791 9393691 1224 Pseudomonadota phylum 12529 JCVI arginine N-succinyltransferase arginine N-succinyltransferase In many bacteria, the arginine succinyltransferase (ast) pathway operon consists of five genes, including this protein, arginine N-succinyltransferase (EC 2.3.1.109). In a few species, such as Pseudomonas aeruginosa, the member of this family is encoded adjacent to a paralog, and the two polypeptides form a heterodimeric enzyme, active on both arginine and ornithine. In such species, this polypeptide may be treated as the beta subunit of an enzyme that may be named either arginine N-succinyltransferase (AST) or arginine and orthithine N-succinyltransferase (AOST). TIGR03245.1 TIGR03245 arg_AOST_alph 458.8 458.8 336 equivalog Y Y N arginine/ornithine succinyltransferase subunit alpha aruF 2.3.1.109 9393691 1224 Pseudomonadota phylum 2299 JCVI arginine/ornithine succinyltransferase, alpha subunit arginine/ornithine succinyltransferase subunit alpha In some bacteria, including Pseudomonas aeruginosa, the astB gene (arginine N-succinyltransferase) is replaced by tandem paralogs that form a heterodimer. This heterodimer from P. aeruginosa is characterized as arginine and ornithine N-2 succinyltransferase (AOST). Members of this protein family represent the less widespread paralog, designated AruI, or arginine/ornithine succinyltransferase, alpha subunit. TIGR03246.1 TIGR03246 arg_catab_astC 609.95 609.95 397 subfamily Y Y N acetylornithine/succinylornithine family transaminase astC GO:0006520,GO:0008483,GO:0030170 1224 Pseudomonadota phylum 20010 JCVI succinylornithine transaminase family acetylornithine/succinylornithine family transaminase Members of the seed alignment for this protein family are the enzyme succinylornithine transaminase (EC 2.6.1.81), which catalyzes the third of five steps in arginine succinyltransferase (AST) pathway, an ammonia-releasing pathway of arginine degradation. All seed alignment sequences are found within arginine succinyltransferase operons, and all proteins that score above 820.0 bits should function as succinylornithine transaminase. However, a number of sequences extremely closely related in sequence, found in different genomic contexts, are likely to act in different biological processes and may act on different substrates. This model is desigated subfamily rather than equivalog, pending further consideration, for this reason. TIGR03255.1 TIGR03255 PhnV 358.7 358.7 270 equivalog Y Y N 2-aminoethylphosphonate ABC transport system, membrane component PhnV phnV GO:0016020,GO:0033223,GO:0033225 1224 Pseudomonadota phylum 1561 JCVI 2-aminoethylphosphonate ABC transport system, membrane component PhnV 2-aminoethylphosphonate ABC transport system, membrane component PhnV This membrane component of an ABC transport system is found in Salmonella and Burkholderia lineages in the vicinity of enzymes for the breakdown of 2-aminoethylphosphonate. TIGR03258.1 TIGR03258 PhnT 499.15 499.15 359 equivalog Y Y N 2-aminoethylphosphonate ABC transport system ATP-binding subunit PhnT phnT GO:0005524,GO:0009898,GO:0033223,GO:0033225,GO:0055052 1224 Pseudomonadota phylum 2088 JCVI 2-aminoethylphosphonate ABC transport system, ATP-binding component PhnT 2-aminoethylphosphonate ABC transport system ATP-binding subunit PhnT This ATP-binding component of an ABC transport system is found in Salmonella and Burkholderia lineages in the vicinity of enzymes for the breakdown of 2-aminoethylphosphonate. TIGR03300.1 TIGR03300 assembly_YfgL 285.2 285.2 377 equivalog Y Y N outer membrane protein assembly factor BamB bamB GO:0005515,GO:0009279 17015657 1224 Pseudomonadota phylum 15651 JCVI outer membrane assembly lipoprotein YfgL outer membrane protein assembly factor BamB Members of this protein family are YfgL, a lipoprotein component of a complex that acts protein insertion into the bacterial outer membrane. Other members of this complex are NlpB, YfiO, and YaeT. This protein contains multiple copies of a repeat that, in other contexts, are associated with binding of the coenzyme PQQ. TIGR03329.1 TIGR03329 Phn_aa_oxid 632.8 632.8 460 hypoth_equivalog Y N N putative aminophosphonate oxidoreductase 1224 Pseudomonadota phylum 4950 JCVI putative aminophosphonate oxidoreductase putative aminophosphonate oxidoreductase This clade of sequences are members of the PF01266 family of FAD-dependent oxidoreductases. Characterized proteins within this family include glycerol-3-phosphate dehydrogenase (1.1.99.5), sarcosine oxidase beta subunit (1.5.3.1) and a number of deaminating amino acid oxidases (1.4.-.-). These genes have been consistently observed in a genomic context including genes for the import and catabolism of 2-aminoethylphosphonate (AEP). If the substrate of this oxidoreductase is AEP itself, then it is probably acting in the manner of a deaminating oxidase, resulting in the same product (phosphonoacetaldehyde) as the transaminase PhnW (TIGR02326), but releasing ammonia instead of coupling to pyruvate:alanine. Alternatively, it is reasonable to suppose that the various ABC cassette transporters which are also associated with these loci allow the import of phosphonates closely related to AEP which may not be substrates for PhnW. TIGR03339.1 TIGR03339 phn_lysR 341.1 341.1 279 subfamily Y N N aminoethylphosphonate catabolism associated LysR family transcriptional regulator GO:0003700,GO:0006355 1224 Pseudomonadota phylum 5369 JCVI aminoethylphosphonate catabolism associated LysR family transcriptional regulator aminoethylphosphonate catabolism associated LysR family transcriptional regulator This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (PF00126) and a periplasmic substrate-binding protein-like domain (PF03466). TIGR03340.1 TIGR03340 phn_DUF6 288.15 288.15 281 hypoth_equivalog Y N N phosphonate utilization associated putative membrane protein 1224 Pseudomonadota phylum 1531 JCVI phosphonate utilization associated putative membrane protein phosphonate utilization associated putative membrane protein This family of hydrophobic proteins has some homology to families of integral membrane proteins such as (PF00892) and may be a permease. It occurs in the vicinity of various types of operons for the catabolism of phosphonates in Vibrio, Pseudomonas, Polaromonas and Thiomicrospira. TIGR03343.1 TIGR03343 biphenyl_bphD 462.15 462.15 282 equivalog Y Y N 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase bphD GO:0009056,GO:0016823 9073078 1224 Pseudomonadota phylum 76 JCVI 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase Members of this family are 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase, or HOPD hydrolase, the BphD protein of biphenyl degradation. BphD acts on the product of ring meta-cleavage by BphC. Many species carrying bphC and bphD are capable of degrading polychlorinated biphenyls as well as biphenyl itself. TIGR03350.1 TIGR03350 type_VI_ompA 139.8 139.8 137 equivalog_domain Y Y N type VI secretion system protein TssL, long form tssL GO:0033103,GO:0033104 16763151,17660433,22371492 1224 Pseudomonadota phylum 8579 JCVI type VI secretion system peptidoglycan-associated domain type VI secretion system protein TssL C-terminal extension domain TssL of type VI secretion systems (T6SS) are related to IcmH/DotU of type IVb secretion systems (T4bSS). This model describes a domain found as the C-terminal region of long forms of TssL, a component of type VI secretion systems (T6SS), although other forms of TssL lack this domain. The domain shares homology with peptidoglycan-associating C-terminal regions of OmpA, MotB, Pal, and other proteins. TIGR03360.1 TIGR03360 VI_minor_1 124.2 124.2 187 equivalog Y Y N type VI secretion system-associated protein VasI vasI 17660433 1224 Pseudomonadota phylum 3698 JCVI type VI secretion-associated protein, VC_A0118 family type VI secretion system-associated protein VasI Members of this protein family, including VC_A0118 from Vibrio cholerae El Tor N16961, are restricted to a subset of bacteria with the type VI secretion system (T6SS), and are encoded among the type VI-associated pathogenicity islands. However, many species with type VI secretion lack a member of this family. This lack suggests that members of this family are accessory proteins, used in a lineage-specific manner in some versions of T6SS and not core to the apparatus. This HMM previously applied the designation TagO, but VasI appears standard. TIGR03368.1 TIGR03368 cellulose_yhjU 410.2 410.2 518 equivalog Y Y N cellulose biosynthesis protein BcsG bcsG 2.7.8.- GO:0030244 11929533,16930487,29348238 1224 Pseudomonadota phylum 8336 JCVI cellulose synthase operon protein YhjU cellulose biosynthesis protein BcsG This protein was identified by the partial phylogenetic profiling algorithm (PMID:16930487) as part of the system for cellulose biosynthesis in bacteria, and in fact is found in cellulose biosynthesis gene regions. The protein was designated YhjU in Salmonella enteritidis, where disruption of its gene disrupts cellulose biosynthesis and biofilm formation (PMID:11929533). TIGR03369.1 TIGR03369 cellulose_bcsE 244.65 244.65 322 equivalog Y Y N cellulose biosynthesis protein BcsE bcsE GO:0035438 11929533,16930487,29348238 1224 Pseudomonadota phylum 7968 JCVI cellulose biosynthesis protein BcsE cellulose biosynthesis protein BcsE This protein, called BcsE (bacterial cellulose synthase E) or YhjS, is required for cellulose biosynthesis in Salmonella enteritidis. Its role is this process across multiple bacterial species is implied by the partial phylogenetic profiling algorithm. Members are found in the vicinity of other cellulose biosynthesis genes. The model does not include a much less well-conserved N-terminal region about 150 amino acids in length for most members. Solano, et al. suggest this protein acts as a protease. TIGR03371.1 TIGR03371 cellulose_yhjQ 157.85 157.85 246 equivalog Y Y N cellulose biosynthesis protein BcsQ bcsQ GO:0090540 12382054,19400787,29234007 1224 Pseudomonadota phylum 7797 JCVI cellulose synthase operon protein YhjQ cellulose biosynthesis protein BcsQ BcsQ (bacterial cellulose synthesis protein Q), previously called YhjQ, forms a part of the Bcs macrocomplex. It is essential to cellulose biosynthesis and secretion in Escherichia coli. TIGR03384.1 TIGR03384 betaine_BetI 201.3 201.3 189 equivalog Y Y N choline-responsive transcriptional repressor BetI betI GO:0019285,GO:0045892 9141699 1224 Pseudomonadota phylum 9775 JCVI transcriptional repressor BetI choline-responsive transcriptional repressor BetI BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (PF00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme. TIGR03398.1 TIGR03398 plc_access_R 99.1 99.1 141 equivalog Y Y N phospholipase C accessory protein PlcR plcR 12410824 1224 Pseudomonadota phylum 744 JCVI phospholipase C accessory protein PlcR phospholipase C accessory protein PlcR The class of microbial phosphocholine-preferring phospholipase C enzymes described by model TIGR03396 has two members in Pseudomonas aeruginosa, one of which (PlcH) is hemolytic and can hydrolyzes sphingomyelin as well as phosphatidylcholine. This model describes PlcR, an accessory protein for PlcH with which it forms a heterodimer. The member of the family from P. aeruginosa, although not the members from various Burkholderia species, is encoded immediately downstream of phospholipase C. TIGR03418.1 TIGR03418 chol_sulf_TF 324.8 324.8 291 equivalog Y Y N choline sulfate utilization transcriptional regulator GO:0006355 1224 Pseudomonadota phylum 4119 JCVI putative choline sulfate-utilization transcription factor choline sulfate utilization transcriptional regulator Members of this protein family are transcription factors of the LysR family. Their genes nearly always are divergently transcribed from choline-sulfatase genes, implying regulation of that enzyme's expression. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate. TIGR03453.1 TIGR03453 partition_RepA 348.45 348.45 387 equivalog Y Y N plasmid partitioning protein RepA repA 11591666 1224 Pseudomonadota phylum 6771 JCVI plasmid partitioning protein RepA plasmid partitioning protein RepA Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error. TIGR03454.1 TIGR03454 partition_RepB 201.5 201.5 325 equivalog Y Y N plasmid partitioning protein RepB repB GO:0003677 1224 Pseudomonadota phylum 8206 JCVI plasmid partitioning protein RepB plasmid partitioning protein RepB Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently. TIGR03461.1 TIGR03461 pabC_Proteo 176.85 176.85 262 equivalog Y Y N aminodeoxychorismate lyase pabC 4.1.3.38 GO:0008696,GO:0030170,GO:0046656 1644759 1224 Pseudomonadota phylum 15930 JCVI aminodeoxychorismate lyase aminodeoxychorismate lyase Members of this protein family are aminodeoxychorismate lyase (ADC lyase), EC 4.1.3.38, the PabC protein of PABA biosynthesis. PABA (para-aminobenzoate) is a precursor of folate, needed for de novo purine biosynthesis. This enzyme is a pyridoxal-phosphate-binding protein in the class IV aminotransferase family (PF01063). TIGR03468.1 TIGR03468 HpnG 187.1 187.1 212 hypoth_equivalog Y N N hopanoid-associated phosphorylase hpnG 22221333,9714766 1224 Pseudomonadota phylum 2296 JCVI hopanoid-associated phosphorylase hopanoid-associated phosphorylase The sequences in this family are members of the PF01048 family of phosphorylases typically acting on nucleotide-sugar substrates. The genes of the family modeled here are generally in the same locus with genes involved in the biosynthesis and elaboration of hopene, the cyclization product of the polyisoprenoid squalene. This gene is adjacent to the genes PhnA-E and squalene-hopene cyclase (which would be HpnF) in Zymomonas mobilis and their association with hopene biosynthesis has been noted in the literature [1]. Extending the gene symbol sequence, we suggest the symbol HpnG for the product of this gene. Hopanoids are known to be components of the plasma membrane and to have polar sugar head groups in Z. mobilis and other species. TIGR03495.1 TIGR03495 phage_LysB 92.75 92.75 135 equivalog Y Y N Rz-like lysis system protein LysB lysB 17900620 1224 Pseudomonadota phylum 7866 JCVI phage lysis regulatory protein, LysB family Rz-like lysis system protein LysB Members of this protein family are Rz-like phage lysis system spanin subunits of the inner membrane (i-spanin). Members include the well-studied protein LysB (lysis protein B) of Enterobacteria phage P2. Similar systems, with components also termed Rz for the i-spanin and Rz1 for the o-spanin, are found in lambda-like and in T7-like phage, and share the property that the gene for the o-spanin is fully embedded or heavily overlapped by the gene for the i-spanin. The gene for this Rz-like phage lysis system protein may overlap extensively with the gene for the other spanin subunit, the Rz1-like protein in the outer membrane. TIGR03533.1 TIGR03533 L3_gln_methyl 229.7 229.7 284 equivalog Y Y N 50S ribosomal protein L3 N(5)-glutamine methyltransferase prmB 2.1.1.298 GO:0008276,GO:0008757,GO:0018364,GO:0042273 11847124 1224 Pseudomonadota phylum 17370 JCVI protein-(glutamine-N5) methyltransferase, ribosomal protein L3-specific 50S ribosomal protein L3 N(5)-glutamine methyltransferase Members of this protein family methylate ribosomal protein L3 on a glutamine side chain. This family is related to HemK, a protein-glutamine methyltranferase for peptide chain release factors. TIGR03541.1 TIGR03541 reg_near_HchA 215.6 215.6 232 equivalog Y Y N PA1136 family autoinducer-binding transcriptional regulator 21696459,28235098 1224 Pseudomonadota phylum 1403 JCVI LuxR family transcriptional regulatory, chaperone HchA-associated PA1136 family autoinducer-binding transcriptional regulator Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (PF03472) and transcriptional regulator (PF00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the glyoxalase III protein HchA (Hsp31), and are always encoded by the adjacent gene. TIGR03547.1 TIGR03547 muta_rot_YjhT 256.35 256.35 346 subfamily Y Y N YjhT family mutarotase 18063573 1224 Pseudomonadota phylum 3555 JCVI mutatrotase, YjhT family YjhT family mutarotase Members of this protein family contain multiple copies of the beta-propeller-forming Kelch repeat. All are full-length homologs to YjhT of Escherichia coli, which has been identified as a mutarotase for sialic acid. This protein improves bacterial ability to obtain host sialic acid, and thus serves as a virulence factor. Some bacteria carry what appears to be a cyclically permuted homolog of this protein. TIGR03610.1 TIGR03610 RutC 169.1 169.1 127 equivalog Y Y N pyrimidine utilization protein C rutC 16540542 1224 Pseudomonadota phylum 2604 JCVI pyrimidine utilization protein C pyrimidine utilization protein C This protein is observed in operons extremely similar to that characterized in E. coli K-12 [1] responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the endoribonuclease L-PSP family defined by PF01042. TIGR03611.1 TIGR03611 RutD 238.5 238.5 258 equivalog Y Y N pyrimidine utilization protein D rutD GO:0006212,GO:0016811 16540542 1224 Pseudomonadota phylum 5775 JCVI pyrimidine utilization protein D pyrimidine utilization protein D This protein is observed in operons extremely similar to that characterized in E. coli K-12 [1] responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the hydrolase, alpha/beta fold family defined by PF00067. TIGR03614.1 TIGR03614 RutB 377.95 377.95 226 equivalog Y Y N pyrimidine utilization protein B rutB GO:0016811 1224 Pseudomonadota phylum 4078 JCVI pyrimidine utilization protein B pyrimidine utilization protein B RN [1] RM PMID:16540542 RT A previously undescribed pathway for pyrimidine catabolism. RA Loh KD, Gyaneshwar P, Markenscoff Papadimitriou E, Fong R, Kim KS, Parales R, Zhou Z, Inwood W, Kustu S RL Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5114-9. Epub 2006 Mar 15. TIGR03615.1 TIGR03615 RutF 254.75 254.75 156 equivalog Y Y N NADH-dependent FMN reductase RutF rutF 1.5.1.42 GO:0008752 16540542 1224 Pseudomonadota phylum 2617 JCVI pyrimidine utilization flavin reductase protein F NADH-dependent FMN reductase RutF This protein is observed in operons extremely similar to that characterized in E. coli K-12 [1] responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the flavin reductase family defined by PF01613. Presumably, this protein recycles the flavin of the RutA luciferase-like oxidoreductase. TIGR03703.1 TIGR03703 plsB 618.5 618.5 799 equivalog Y Y N glycerol-3-phosphate 1-O-acyltransferase PlsB plsB 2.3.1.15 GO:0004366,GO:0005886,GO:0008654 16294310 1224 Pseudomonadota phylum 15811 JCVI glycerol-3-phosphate O-acyltransferase glycerol-3-phosphate 1-O-acyltransferase PlsB Members of this protein family are PlsB, glycerol-3-phosphate O-acyltransferase, present in E. coli and numerous related species. In many bacteria, PlsB is not found, and appears to be replaced by a two enzyme system for 1-acyl-glycerol-3-phosphate biosynthesis, the PlsX/Y system. TIGR03739.1 TIGR03739 PRTRC_D 214.8 214.8 320 hypoth_equivalog Y Y N PRTRC system protein D 1224 Pseudomonadota phylum 649 JCVI PRTRC system protein D PRTRC system protein D A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated PRTRC system protein D. The gray zone, between trusted and noise, includes proteins found in the same genomes as other proteins of the PRTRC systems, but not in the same contiguous gene region. TIGR03743.1 TIGR03743 SXT_TraD 366 366 636 subfamily Y Y N conjugative transfer system coupling protein TraD traD GO:0015074 12107144 1224 Pseudomonadota phylum 9109 JCVI conjugative coupling factor TraD, SXT/TOL subfamily conjugative transfer system coupling protein TraD These TraD proteins (sometimes called TraG) generally are found in conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains. This TraD subfamily is rather distantly related to the well-characterized TraD of the F plasmid. Members of this protein family are the putative conjugative coupling factor, TraD, as the term is used for the SXT and TOL plasmid systems. TIGR03744.1 TIGR03744 traC_PFL_4706 520.6 520.6 892 equivalog Y Y N conjugative transfer ATPase GO:0005524 1224 Pseudomonadota phylum 7633 JCVI conjugative transfer ATPase, PFL_4706 family conjugative transfer ATPase Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, VirB4 and TrsE. The granularity of this protein family definition is chosen so as to represent one distinctive clade and act as a marker through which to define and recognize the class of mobile element it serves. TIGR03745.1 TIGR03745 conj_TIGR03745 52.5 52.5 105 hypoth_equivalog Y Y N TIGR03745 family integrating conjugative element membrane protein GO:0005886 1224 Pseudomonadota phylum 3085 JCVI integrating conjugative element membrane protein, PFL_4702 family integrating conjugative element membrane protein Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in a region flanked by markers of conjugative transfer and/or transposition. TIGR03746.1 TIGR03746 conj_TIGR03746 137.25 137.25 202 equivalog Y Y N PFL_4703 family integrating conjugative element protein 1224 Pseudomonadota phylum 4089 JCVI integrating conjugative element protein, PFL_4703 family PFL_4703 family integrating conjugative element protein Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. TIGR03747.1 TIGR03747 conj_TIGR03747 138.5 138.5 233 hypoth_equivalog Y Y N TIGR03747 family integrating conjugative element membrane protein GO:0005886 1224 Pseudomonadota phylum 4708 JCVI integrating conjugative element membrane protein, PFL_4697 family integrating conjugative element membrane protein Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. TIGR03748.1 TIGR03748 conj_PilL 64.15 64.15 105 hypoth_equivalog_domain Y N N integrating conjugative element protein PilL, PFGI-1 class 14580391 1224 Pseudomonadota phylum 5023 JCVI integrating conjugative element protein PilL, PFGI-1 class integrating conjugative element protein PilL, PFGI-1 class This HMM describes the conserved N-terminal region of a variable length protein family associated with laterally transfered regions flanked by markers of conjugative plasmid integration and/or transposition. Most members of the family have the lipoprotein signal peptide motif. A member of the family from a pathogenicity island in Salmonella enterica serovar Dublin strain was designated PilL for nomenclature consistency with a neighboring gene for the pilin structural protein PilS. However, the species distribution of this protein family tracks much better with markers of conjugal transfer than with markers of PilS-like pilin structure. TIGR03749.1 TIGR03749 conj_TIGR03749 138.8 138.8 259 hypoth_equivalog Y Y N TIGR03749 family integrating conjugative element protein 1224 Pseudomonadota phylum 5794 JCVI integrating conjugative element protein, PFL_4704 family integrating conjugative element protein Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in a region flanked by markers of conjugative transfer and/or transposition. TIGR03750.1 TIGR03750 conj_TIGR03750 70.75 70.75 111 hypoth_equivalog Y Y N TIGR03750 family conjugal transfer protein 1224 Pseudomonadota phylum 3601 JCVI conjugative transfer region protein, TIGR03750 family TIGR03750 family conjugal transfer protein Members of this protein family are found occasionally on plasmids. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. TIGR03751.1 TIGR03751 conj_TIGR03751 77.7 77.7 124 hypoth_equivalog Y Y N TIGR03751 family conjugal transfer lipoprotein 1224 Pseudomonadota phylum 4222 JCVI conjugative transfer region lipoprotein, TIGR03751 family TIGR03751 family conjugal transfer lipoprotein Members of this protein family are found occasionally on plasmids. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. TIGR03752.1 TIGR03752 conj_TIGR03752 241 241 471 hypoth_equivalog Y Y N TIGR03752 family integrating conjugative element protein GO:0005886 1224 Pseudomonadota phylum 6141 JCVI integrating conjugative element protein, PFL_4705 family integrating conjugative element protein Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. TIGR03754.1 TIGR03754 conj_TOL_TraD 647.55 647.55 643 equivalog Y Y N type IV conjugative transfer system coupling protein TraD traD 1224 Pseudomonadota phylum 6163 JCVI conjugative coupling factor TraD, PFGI-1 class type IV conjugative transfer system coupling protein TraD Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion. TIGR03755.1 TIGR03755 conj_TIGR03755 270.45 270.45 419 equivalog Y Y N integrating conjugative element protein 1224 Pseudomonadota phylum 6333 JCVI integrating conjugative element protein, PFL_4711 family integrating conjugative element protein Members of this protein family are found in genomic regions associated with conjugative transfer and integrated TOL-like plasmids. The specific function is unknown. TIGR03756.1 TIGR03756 conj_TIGR03756 188.35 188.35 298 hypoth_equivalog Y Y N TIGR03756 family integrating conjugative element protein 1224 Pseudomonadota phylum 5861 JCVI integrating conjugative element protein, PFL_4710 family integrating conjugative element protein Members of this protein family are found in genomic regions associated with conjugative transfer and integrated TOL-like plasmids. The specific function is unknown. TIGR03757.1 TIGR03757 conj_TIGR03757 73.2 73.2 113 hypoth_equivalog Y Y N TIGR03757 family integrating conjugative element protein 1224 Pseudomonadota phylum 3823 JCVI integrating conjugative element protein, PFL_4709 family integrating conjugative element protein Members of this protein belong to extended genomic regions that appear to be spread by conjugative transfer. TIGR03758.1 TIGR03758 conj_TIGR03758 42.7 42.7 76 hypoth_equivalog Y Y N TIGR03758 family integrating conjugative element protein GO:0005886 1224 Pseudomonadota phylum 2671 JCVI integrating conjugative element protein, PFL_4701 family integrating conjugative element protein Members of this family of small, hydrophobic proteins are found occasionally on plasmids such as the Pseudomonas putida TOL (toluene catabolic) plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. TIGR03759.1 TIGR03759 conj_TIGR03759 126.4 126.4 200 hypoth_equivalog Y Y N TIGR03759 family integrating conjugative element protein 1224 Pseudomonadota phylum 5147 JCVI integrating conjugative element protein, PFL_4693 family integrating conjugative element protein Members of this protein family, such as model protein PFL_4693 from Pseudomonas fluorescens Pf-5, belong to extended genomic regions that appear to be spread by conjugative transfer. Most members have a predicted N-terminal signal sequence. The function is unknown. TIGR03760.1 TIGR03760 ICE_TraI_Pfluor 161.4 161.4 218 equivalog_domain Y N N integrating conjugative element relaxase, PFGI-1 class traI 1224 Pseudomonadota phylum 7491 JCVI integrating conjugative element relaxase, PFGI-1 class integrating conjugative element relaxase, PFGI-1 class Members of this protein family are the TraI putative relaxases required for transfer by a subclass of integrating conjugative elements (ICE) as found in Pseudomonas fluorescens Pf-5, and understood from study of two related ICE, SXT and R391. This model represents the N-terminal domain. Note that no homology is detected to the similarly named TraI relaxase of the F plasmid. TIGR03761.1 TIGR03761 ICE_PFL4669 110.7 110.7 216 equivalog Y Y N PFL_4669 family integrating conjugative element protein 19144133,34643711 1224 Pseudomonadota phylum 4450 JCVI integrating conjugative element protein, PFL_4669 family PFL_4669 family integrating conjugative element protein Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens. TIGR03764.1 TIGR03764 ICE_PFGI_1_parB 143.75 143.75 260 hypoth_equivalog_domain Y Y N ParB family protein 1224 Pseudomonadota phylum 5843 JCVI integrating conjugative element, PFGI_1 class, ParB family protein ParB family protein, PFGI_1 class integrating conjugative element Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5. TIGR03765.1 TIGR03765 ICE_PFL_4695 59.75 59.75 105 subfamily_domain Y Y N PFL_4695 family integrating conjugative element protein 1224 Pseudomonadota phylum 5081 JCVI integrating conjugative element protein, PFL_4695 family PFL_4695 family integrating conjugative element protein This model describes a protein family exemplified by PFL_4695 of Pseudomonas fluorescens Pf-5. Full-length proteins in this family show some architectural variety, but this model represents a conserved domain. Most or all member proteins belong to laterally transferred chromosomal islands called integrative conjugative elements, or ICE. TIGR03777.1 TIGR03777 RPE4 23.95 23.95 32 domain Y Y N palindromic element RPE4 domain-containing protein 11997347 1224 Pseudomonadota phylum 625 JCVI rickettsial palindromic element RPE4 domain rickettsial palindromic element RPE4 domain This HMM describes protein translations of a family, RPE4, of Rickettsia palindromic elements (RPE). The elements spread within a genome as selfish genetic elements, inserting into genes additional coding region that does not disrupt the reading frame. This model finds RPE-encoded regions in several Rickettsial species and, so far, no where else. TIGR03791.1 TIGR03791 TTQ_mauG 443.85 443.85 291 equivalog Y Y N tryptophan tryptophylquinone biosynthesis enzyme MauG mauG GO:0005509,GO:0016491,GO:0020037,GO:0030416 19196017 1224 Pseudomonadota phylum 63 JCVI tryptophan tryptophylquinone biosynthesis enzyme MauG tryptophan tryptophylquinone biosynthesis enzyme MauG Members of this protein family are the tryptophan tryptophylquinone biosynthesis (TTQ) enzyme MauG, as found in Methylobacterium extorquens and related species. This protein is required to complete the maturation of the TTQ cofactor in the methylamine dehydrogenase light (beta) chain. TIGR03808.1 TIGR03808 RR_plus_rpt_1 120 120 455 equivalog Y Y N TIGR03808 family TAT-translocated repetitive protein 1224 Pseudomonadota phylum 2625 JCVI twin-arg-translocated uncharacterized repeat protein TIGR03808 family TAT-translocated repetitive protein Members of this protein family have a Sec-independent twin-arginine tranlocation (TAT) signal sequence, which enables tranfer of proteins folded around prosthetic groups to cross the plasma membrane. These proteins have four copies of a repeat of about 23 amino acids that resembles the beta-helix repeat. Beta-helix refers to a structural motif in which successive beta strands wind around to stack parallel in a right-handed helix, as in AlgG and related enzymes of carbohydrate metabolism. The twin-arginine motif suggests that members of this protein family bind some unknown cofactor. TIGR03938.2 TIGR03938 deacetyl_PgaB 321.9 321.9 621 equivalog Y Y N poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB pgaB GO:0000271,GO:0019213 18359807 1224 Pseudomonadota phylum 11205 JCVI poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB Two well-characterized systems produce polysaccharide based on N-acetyl-D-glucosamine in straight chains with beta-1,6 linkages. These are encoded by the icaADBC operon in Staphylococcus species, where the system is designated polysaccharide intercellular adhesin (PIA), and the pgaABCD operon in Gram-negative bacteria such as E. coli. Both systems include a putative polysaccharide deacetylase. The PgaB protein, described here, contains an additional domain lacking from its Gram-positive counterpart IcaB (TIGR03933). Deacetylation by this protein appears necessary to allow export through the porin PgaA TIGR03939.1 TIGR03939 PGA_TPR_OMP 366.65 366.65 800 equivalog Y Y N poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA pgaA GO:0009279,GO:1901515 15090514 1224 Pseudomonadota phylum 11859 JCVI poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA Members of this protein family are the poly-beta-1,6 N-acetyl-D-glucosamine (PGA) export porin PgaA of Gram-negative bacteria. There is no counterpart in the poly-beta-1,6 N-acetyl-D-glucosamine biosynthesis systems of Gram-positive bacteria such as Staphylococcus epidermidis. The PGA polysaccharide adhesin is a critical determinant of biofilm formation. The conserved C-terminal domain of this outer membrane protein is preceded by a variable number of TPR repeats. TIGR03950.1 TIGR03950 sidero_Fe_reduc 137.9 137.9 223 hypoth_equivalog Y Y N siderophore ferric iron reductase GO:0008199,GO:0016491,GO:0033214,GO:0051537 1224 Pseudomonadota phylum 2855 JCVI siderophore ferric iron reductase, AHA_1954 family siderophore ferric iron reductase Members of this protein family are 2Fe-2S cluster binding proteins, found regularly in the context of siderophore transporters. Members are distantly related to FhuF from E. coli, a ferric iron reductase linked to removal of iron from hydroxamate-type siderophores (PMID:14756576). TIGR03981.2 TIGR03981 SAM_quin_mod 340 340 411 hypoth_equivalog Y Y N His-Xaa-Ser system-associated MauG-like protein 21478363 1224 Pseudomonadota phylum 160 JCVI His-Xaa-Ser system putative quinone modification maturase His-Xaa-Ser system-associated MauG-like protein This protein is related to MauG protein (see TIGR03791) involved in the tryptophan tryptophylquinone post-translational modification of methylamine dehydrogenase subunit beta. It occurs regularly with proteins of the His-Xaa-Ser system, which contains peptide-modifying radical SAM enzymes. Not all instances of the His-Xaa-Ser system include this protein. TIGR03982.2 TIGR03982 TIGR03982 40 40 118 hypoth_equivalog Y Y N TIGR03982 family His-Xaa-Ser system protein 21478363 1224 Pseudomonadota phylum 134 JCVI His-Xaa-Ser system protein, TIGR03982 family TIGR03982 family His-Xaa-Ser system protein Members of this rare protein family occur in the presence of TIGR03981 and TIGR03979, which in turn occur only in the context of radical SAM protein families TIGR03977 and TIGR03978. The function is unknown. TIGR03993.1 TIGR03993 hydrog_HybE 78.5 78.5 143 subfamily_domain Y Y N [NiFe]-hydrogenase assembly chaperone HybE hybE 19636963 1224 Pseudomonadota phylum 4064 JCVI [NiFe] hydrogenase assembly chaperone, HybE family [NiFe]-hydrogenase assembly chaperone HybE Members of this family are chaperones for the assembly of [NiFe] hydrogenases, in the family of HybE, which is specific for hydrogenase-2 of Escherichia coli. Members often have an additional N-terminal rubredoxin domain. TIGR04003.1 TIGR04003 rSAM_BssD 496.45 496.45 314 equivalog Y Y N [benzylsuccinate synthase]-activating enzyme bssD GO:0043687,GO:0046500,GO:0051539,GO:1904047 8706665,9632263 1224 Pseudomonadota phylum 17 JCVI [benzylsuccinate synthase]-activating enzyme [benzylsuccinate synthase]-activating enzyme Members of this radical SAM protein family are [benzylsuccinate synthase]-activating enzyme, a glycyl radical active site-creating enzyme related to [pyruvate formate-lyase]-activating enzyme and additional uncharacterized homologs activating additional glycyl radical-containing enzymes. TIGR04051.1 TIGR04051 rSAM_NirJ 515.45 515.45 354 equivalog Y Y N heme d1 biosynthesis radical SAM protein NirJ nirJ GO:0003824,GO:0006783,GO:0046500,GO:0051539,GO:1904047 1224 Pseudomonadota phylum 2580 JCVI heme d1 biosynthesis radical SAM protein NirJ heme d1 biosynthesis radical SAM protein NirJ Heme d1 occurs in the cytochrome cd1 subunit of nitrite reductase in species such as Pseudomonas stutzeri. NirJ is a radical SAM protein involved in its bioynthesis. In a number of species, distinct genes NirJ1 and NirJ2 are found in similar genomic regions; this model describe authentic NirJ from genomes with NirJ only. TIGR04061.1 TIGR04061 AZL_007950_fam 124.15 124.15 164 subfamily Y Y N putative natural product biosynthesis protein 1224 Pseudomonadota phylum 865 JCVI AZL_007950 family protein putative natural product biosynthesis protein This set of proteins includes PP_3335 from Pseudomonas putida, a protein of unknown function, and AZL_007950, a member of a putative biosynthetic cluster from Azospirillum sp. B510. TIGR04071.2 TIGR04071 methanobac_OB3b 24 24 29 subfamily Y Y N methanobactin mbnA 20961038,23682956,26984926 1224 Pseudomonadota phylum 69 JCVI methanobactin precursor, Mb-OB3b family MbnA family methanobactin Methanobactins are siderophore-like copper-chelating natural products (chalkophores) with considerable variety from species to species. The 11-residue methanobactin of Methylosinus trichosporium OB3b is derived from a ribosomally translated 30-residue precursor that is the founding member of this family. Genome mining identified a number of additional candidate methanobactins, designated MbnA, likewise in the neighborhood of genes for maturation proteins MbnB (TIGR04159) and MbnC (TIGR04160), starting with one from the rice endophyte Azospirillum sp. B510, which has not yet been shown to produce a methanobactin per se. In some species, copper acts as switch to control transcription, and a methanobactin-like domain, also recognized by this model, is found as a C-terminal suffix domain on an RNA polymerase sigma factor. TIGR04101.1 TIGR04101 CCGSCS 28 27.5 59 equivalog Y Y N CCGSCS motif protein 1224 Pseudomonadota phylum 181 JCVI CCGSCS motif protein CCGSCS motif protein This protein family, with average protein length about 58 residues, occurs in several marine bacteria, such as Shewanella benthica KT99, Marinobacter sp. ELB17, and Photobacterium profundum 3TCK. The striking feature is a C-terminal motif CCGSCS, which (perhaps coincidentally) resembles conserved core motif [LC]CGSC shared by two methanobactin precursors (see TIGR04071). There is no detectable conserved gene region for these proteins. TIGR04159.2 TIGR04159 methbact_MbnB 325 325 261 equivalog Y Y N methanobactin biosynthesis protein MbnB mbnB 20961038 1224 Pseudomonadota phylum 130 JCVI methanobactin biosynthesis cassette protein MbnB methanobactin biosynthesis protein MbnB The first characterized methanobactin is made from a ribosomal precursor in Methylosinus trichosporium OB3b. Two additional species noted early to have homologous precursor peptides (family TIGR04071) are Azospirillum sp. B510 and Gluconacetobacter sp. SXCC-1. This model originally described only the N-terminal domain of this methanobactin biosynthesis protein, MbnB, as founder sequences available at the time were not all full length. Following a rebuild, this HMM now describes full length proteins that occur always and only next to a methanobactin precursor. The model excludes related subfamilies of DUF692 family proteins rather are not encoded near any detectable ribosomally synthesized and post-translationally modified peptide (RiPP) precursor. TIGR04160.2 TIGR04160 methbact_MbnC 185 185 181 equivalog Y Y N methanobactin biosynthesis protein MbnC mbnC 20961038,23682956,34325792,35110668 1224 Pseudomonadota phylum 119 JCVI methanobactin biosynthesis cassette protein MbnC methanobactin biosynthesis protein MbnC Methanobactin is a copper-binding natural product, analogous in many wayts to siderophores produced for iron uptake, but produced as a RiPP (ribosomally synthesized and post-translationally modified peptide). The first characterized methanobactin was described in Methylosinus trichosporium OB3b. Additional early identified species with homologous precursor peptides (family TIGR04071) were Azospirillum sp. B510 and Gluconacetobacter sp. SXCC-1. This model describes a key protein methanobactin biosynthesis, MbnC, found in every known methanobactin biosynthesis system. MbnC belongs to a broader family described by TIGR04061, which includes additional protein of unknown function. TIGR04161.1 TIGR04161 VPEID-CTERM 33 33 31 equivalog_domain Y Y N VPEID-CTERM sorting domain-containing protein 22037399 1224 Pseudomonadota phylum 218 JCVI VPEID-CTERM protein sorting domain VPEID-CTERM protein-sorting domain Proteins belonging to this family are small, 80 to 120 residues, including a signal peptide, a central low-complexity region, and this roughly 31-amino acid extreme C-terminal region. Members occur paired with a variant form of exosortase. Species include Ruegeria sp., Phaeobacter gallaeciensis, Roseovarius nubinhibens ISM, and two in Methylobacter tundripaludum. TIGR04211.1 TIGR04211 SH3_and_anchor 65 65 198 equivalog Y Y N TIGR04211 family SH3 domain-containing protein 1224 Pseudomonadota phylum 7023 JCVI SH3 domain protein TIGR04211 family SH3 domain-containing protein Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region. TIGR04273.1 TIGR04273 Y_sulf_Ax21 250 250 186 equivalog Y Y N Ax21 family protein GO:0009372 22204763 1224 Pseudomonadota phylum 548 JCVI sulfation-dependent quorum factor, Ax21 family Ax21 family protein This family consists of proteins closely related to Ax21 (Activator of XA21-mediated immunity), a protein that is secreted by a type I secretion system (RaxABC), and that appears to be sulfated on an N-terminal region tryosine in a motif LSYN. Ax21 acts in a quorum-sensing system. Homologous peptide-mediated quorum-sensing systems appear to exist in other species, such as the emerging opportunistic pathogen Stenotrophomonas maltophilia. Intriguingly, the rice genome encodes a receptor (XA21) for this protein that triggers innate immunity. TIGR04300.1 TIGR04300 exosort_XrtM 125 125 150 exception Y Y N exosortase family protein XrtM xrtM GO:0004197,GO:0006605,GO:0016020,GO:0043687 22037399 1224 Pseudomonadota phylum 45 JCVI exosortase family protein XrtM exosortase family protein XrtM Members of this family, part of the larger exosortase/archaeosortase family, are known from five related cassettes of genes in Methylomonas methanica MC09, a gammaproteobacterial methanotroph. Each xrtM gene occurs near a large YD repeat (see TIGR01643) protein of 1500-2500 residues and a small, uncharacterized protein of about 200 residues. No PEP-CTERM-like recognition sequence has been identified, so this protein is designated as exosortase family, but not necessarily a functional exosortase. TIGR04301.1 TIGR04301 ODC_inducible 1310 1310 719 exception Y Y N ornithine decarboxylase SpeF speF 4.1.1.17 GO:0004586,GO:0006520 22247134 1224 Pseudomonadota phylum 5668 JCVI ornithine decarboxylase SpeF ornithine decarboxylase SpeF Members of this family are known or trusted examples of ornithine decarboxylase, all encoded in the immediate vicinity of an ornithine-putrescine antiporter. Decarboxylation of ornithine to putrescine, followed by exchange of a putrescine for a new ornithine, is a proton-motive cycle that can be induced by low pH and protect a bacterium against transient exposure to acidic conditions. TIGR04310.1 TIGR04310 pantocin_A_pre 35 35 29 subfamily Y Y N pantocin A family RiPP 21789243 1224 Pseudomonadota phylum 55 JCVI pantocin A family RiPP pantocin A family RiPP Members of this family are ribosomally-synthesized and posttranslationally-modified peptide (RiPP) precursors about 30 amino acids in length encoded in the vicinity of PaaA and PaaB homologs. Members include PaaP from Pantoea agglomerans, whose central tripeptide EEN appears to be the source of the mature product, pantocin A. Note, however, that the corresponding residues in Photobacterium sp. SKA34 and Photobacterium asymbiotica are EEK rather than EEN. This family, therefore, resembles the PQQ precursor PqqA as a peptide precursor of an extremely small mature product. TIGR04322.1 TIGR04322 rSAM_QueE_Ecoli 200 200 215 equivalog Y Y N 7-carboxy-7-deazaguanine synthase QueE queE 4.3.99.3 GO:0006400,GO:0051539,GO:1904047 1224 Pseudomonadota phylum 5650 JCVI putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE 7-carboxy-7-deazaguanine synthase QueE Members of this radical SAM domain protein family appear to be the E. coli form of the queuosine biosynthesis protein QueE. QueE is involved in making preQ0 (7-cyano-7-deazaquanine), a precursor of both the bacterial/eukaryotic modified tRNA base queuosine and the archaeal modified base archaeosine. Members occur in species that lack known forms of QueE but usually are not found in queuosine biosynthesis operons. Members of this family tend to form bi-directional best hit matches to members of known (TIGR03365) and putative (TIGR03963) QueE families from other lineages. TIGR04415.1 TIGR04415 O_hepto_targRPT 30 20 38 repeat Y N N strand-loop-strand repeat protein 11953358,22221153 1224 Pseudomonadota phylum 30902 JCVI autotransporter passenger strand-loop-strand repeat autotransporter passenger strand-loop-strand repeat This model describes two tandem copies of a strand-loop-strand repeat that occurs often in type V secretion system (T5SS). These repeats usually occur in the passenger domain of the classical monomeric autotransporter. Proteins with this repeat often are encoded next to a member of family TIGR04414, the Aah/TibC family O-heptosyltransferase, and may be glycosylated in regions with this repeat. TIGR04418.1 TIGR04418 PriB_gamma 72 72 96 exception Y Y N primosomal replication protein N priB GO:0003697,GO:0006260,GO:0030894 17588514,22938024 1224 Pseudomonadota phylum 5155 JCVI primosomal replication protein PriB primosomal replication protein N PriB binds single-stranded DNA at the primosome assembly site. This HMM describes a gamma-Proteobacterial form, usually encoded between rpsF (ribosomal protein S6) and rpsR (ribosomal protein S18). TIGR04431.1 TIGR04431 N6_acetyl_AAC6 260 260 184 equivalog Y Y N AacA4 family aminoglycoside N(6')-acetyltransferase 2.3.1.82 GO:0030647,GO:0047663 2841303 1224 Pseudomonadota phylum 443 JCVI aminoglycoside N(6')-acetyltransferase, AacA4 family AacA4 family aminoglycoside N(6')-acetyltransferase Members of this family are the aacA4 type of aminoglycoside N(6')-acetyltransferase (EC 2.3.1.82), an enzyme that modifies and inactivates aminoglycoside antibiotics such as kanamycin, neomycin, tobramycin, and amikacin. Members are regularly spread among pathogens into integron, transposon, and plasmid loci, with recombination often happening within the protein-coding region. Most of the region amino-terminal to the recombination site or sites was removed from this model. TIGR04438.1 TIGR04438 small_Trp_rich 36 36 76 hypoth_equivalog Y Y N TIGR04438 family Trp-rich protein 1224 Pseudomonadota phylum 1206 JCVI small Trp-rich protein TIGR04438 family Trp-rich protein Members of this bacterial protein family average 80 residues in length, and average nearly 6 Trp residues (two of which are invariant) in the first 45, which are strongly hydrophobic. Past this region, the protein is highly charged, with large numbers of Lys, Arg, Asp, and Glu residues. Members usually are divergently transcribed from a gene encoding a c-type cytochrome. TIGR04439.1 TIGR04439 histamin_N_OH 700 700 431 equivalog Y Y N putative histamine N-monooxygenase basC 15289555 1224 Pseudomonadota phylum 854 JCVI putative histamine N-monooxygenase putative histamine N-monooxygenase Members of this family are involved in synthesizing N-hydroxyhistamine as a precursor to acinetobactin, a siderophore found in Acinetobacter baumannii. Assuming histidine is first decarboxylated to histamine, then hydroxylated, members of this family are histamine N-monooxygenase. The putative histidine decarboxylase is found in the same biosynthetic cluster. TIGR04550.1 TIGR04550 sMetMonox_MmoD 80 80 64 equivalog Y Y N soluble methane monooxygenase-binding protein MmoD mmoD 11709550,15610020,23682956 1224 Pseudomonadota phylum 61 JCVI soluble methane monooxygenase-binding protein MmoD soluble methane monooxygenase-binding protein MmoD Members of this family are MmoD, a protein that binds the soluble (as opposed to the membrane-bound, copper-rich, particulate) methane monooxygenase and may regulate its activity. Recent work suggests that MmoD, together with methanobactin, acts a copper switch to regulate which enzyme form is produced. NF000012.1 trim_DfrI 400 400 191 exception Y Y Y trimethoprim-resistant dihydrofolate reductase DfrI dfrI 1.5.1.3 GO:0004146 1236 Gammaproteobacteria class 5 NCBIFAM trimethoprim-resistant dihydrofolate reductase DfrI trimethoprim-resistant dihydrofolate reductase DfrI NF000018.2 trim_DfrA10 400 400 187 exception Y Y Y trimethoprim-resistant dihydrofolate reductase DfrA10 dfrA10 1.5.1.3 GO:0004146 1236 Gammaproteobacteria class 3 NCBIFAM trimethoprim-resistant dihydrofolate reductase DfrA10 trimethoprim-resistant dihydrofolate reductase DfrA10 NF000039.1 trim_DfrA18 375 375 184 exception Y Y Y trimethoprim-resistant dihydrofolate reductase DfrA18 dfrA18 1.5.1.3 GO:0004146 1236 Gammaproteobacteria class 2 NCBIFAM trimethoprim-resistant dihydrofolate reductase Dfr18 trimethoprim-resistant dihydrofolate reductase DfrA18 DfrA18 is a dihydrofolate reductase that is insensitive to the antibiotic trimethoprim. Note that DfrA18 was originally described as Dfr18. Note also that one member of family DfrA19 was originally described in a publication as DfrA18, although the corresponding GenBank record was updated in 2003 to the name DfrA19. NF000040.3 Tn10_TetC 425 425 197 equivalog Y Y N tetracyline resistance-associated transcriptional repressor TetC tetC GO:0003677 15853893,9231897 1236 Gammaproteobacteria class 112 NCBIFAM putative tetracyline resistance transcriptional regulator TetC tetracyline resistance-associated transcriptional repressor TetC TetC, as found in composite transposon Tn10, is a transcriptional repressor of itself and of TetD, which is a transcriptional activator for some stress response proteins in the SoxS/MarA/Rob regulon in E. coli and which therefore contributes to antibiotic resistance. NF000041.1 trim_DfrA19 400 400 189 exception Y Y Y trimethoprim-resistant dihydrofolate reductase DfrA19 dfrA19 1.5.1.3 GO:0004146 1236 Gammaproteobacteria class 10 NCBIFAM DfrA18/DfrA19 family trimethoprim-resistant dihydrofolate reductase trimethoprim-resistant dihydrofolate reductase DfrA19 DfrA19 is a trimethoprim-resistant dihydrofolate reductase. Note that DfrA19 was first named in a publication as DfrA18, since the family now known as DfrA18 was previously named Dfr18. NF000050.2 AAC_6p_A29 250 250 131 exception Y Y Y aminoglycoside 6'-N-acetyltransferase AAC(6')-29 aac(6')-29 1236 Gammaproteobacteria class 35 NCBIFAM aminoglycoside 6'-N-acetyltransferase AAC(6')-29 aminoglycoside 6'-N-acetyltransferase AAC(6')-29 NF000053.2 trim_DfrA12 360 360 165 exception Y Y Y trimethoprim-resistant dihydrofolate reductase DfrA12 dfrA12 1.5.1.3 GO:0004146 1236 Gammaproteobacteria class 48 NCBIFAM trimethoprim-resistant dihydrofolate reductase DfrA12 trimethoprim-resistant dihydrofolate reductase DfrA12 NF000055.3 trim_DfrA12_A21 330 330 165 exception Y Y Y DfrA12/DfrA21 family trimethoprim-resistant dihydrofolate reductase dfrA 1.5.1.3 GO:0004146 1236 Gammaproteobacteria class 55 NCBIFAM DfrA13/DfrA21 family trimethoprim-resistant dihydrofolate reductase DfrA12/DfrA21 family trimethoprim-resistant dihydrofolate reductase Members of this family of trimethoprim-resistant dihydrofolate reductases include DfrA12, DfrA21, DfrA22, and DfrA33 (recently split from DfrA22). DfrA13, seen only once, differs from DfrA21 mostly by a double frameshift and is now thought to represent a sequencing artifact rather than natural variation. NF000056.3 penta_rpt_QnrS 460 460 218 exception Y Y Y QnrS family quinolone resistance pentapeptide repeat protein 1236 Gammaproteobacteria class 136 NCBIFAM QnrS family quinolone resistance pentapeptide repeat protein QnrS family quinolone resistance pentapeptide repeat protein NF000069.1 16S_rRNA_Rmt_E 525 525 273 exception Y Y Y RmtE family 16S rRNA (guanine(1405)-N(7))-methyltransferase GO:0046677 1236 Gammaproteobacteria class 5 NCBIFAM RmtE family 16S rRNA (guanine(1405)-N(7))-methyltransferase RmtE family 16S rRNA (guanine(1405)-N(7))-methyltransferase NF000071.4 penta_rpt_QnrA 450 450 218 exception Y Y Y QnrA family quinolone resistance pentapeptide repeat protein 1236 Gammaproteobacteria class 47 NCBIFAM QnrA family quinolone resistance pentapeptide repeat protein QnrA family quinolone resistance pentapeptide repeat protein NF000074.1 299782349_fosC 250 250 132 exception Y Y Y FosC2 family fosfomycin resistance glutathione transferase 2.5.1.18 1236 Gammaproteobacteria class 4 NCBIFAM FosC2 family fosfomycin resistance glutathione transferase FosC2 family fosfomycin resistance glutathione transferase NF000075.1 299782351_fosA 275 275 138 exception Y Y Y FosA3/FosA4 family fosfomycin resistance glutathione transferase fosA 2.5.1.18 1236 Gammaproteobacteria class 33 NCBIFAM FosA3/FosA4 family fosfomycin resistance glutathione transferase FosA3/FosA4 family fosfomycin resistance glutathione transferase NF000077.1 Erm42 600 600 303 exception Y Y Y 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(42) erm(42) 21371136 1236 Gammaproteobacteria class 28 NCBIFAM 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(42) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(42) Erm(42) is a type I Erm enzyme, that is, a monomethyltransferase. NF000113.1 16S_rRNA_Rmt_F 500 500 259 exception Y Y Y RmtF family 16S rRNA (guanine(1405)-N(7))-methyltransferase 1236 Gammaproteobacteria class 22 NCBIFAM RmtF family 16S rRNA (guanine(1405)-N(7))-methyltransferase RmtF family 16S rRNA (guanine(1405)-N(7))-methyltransferase NF000114.1 16S_rRNA_Rmt_G 500 500 264 exception Y Y Y RmtG family 16S rRNA (guanine(1405)-N(7))-methyltransferase 1236 Gammaproteobacteria class 2 NCBIFAM RmtG family 16S rRNA (guanine(1405)-N(7))-methyltransferase RmtG family 16S rRNA (guanine(1405)-N(7))-methyltransferase NF000124.1 fos-Vibrio 250 250 132 exception Y Y N FosG/FosC2-related fosfomycin resistance glutathione transferase fos 2.5.1.18 1236 Gammaproteobacteria class 69 NCBIFAM FosG/FosC2 family fosfomycin resistance glutathione transferase FosG/FosC2-related fosfomycin resistance glutathione transferase NF000127.2 trim_DfrA20 325 325 169 exception Y Y Y trimethoprim-resistant dihydrofolate reductase DfrA20 dfrA20 1.5.1.3 GO:0004146 1236 Gammaproteobacteria class 2 NCBIFAM trimethoprim-resistant dihydrofolate reductase DfrA20 trimethoprim-resistant dihydrofolate reductase DfrA20 NF000134.2 trim_DfrA23 375 375 186 exception Y Y Y trimethoprim-resistant dihydrofolate reductase DfrA23 dfrA23 1.5.1.3 GO:0004146 1236 Gammaproteobacteria class 4 NCBIFAM trimethoprim-resistant dihydrofolate reductase DfrA23 trimethoprim-resistant dihydrofolate reductase DfrA23 NF000135.2 AAC_6p_IIc 415 415 193 exception Y Y Y aminoglycoside N-acetyltransferase AAC(6')-IIc aac(6')-IIc 1236 Gammaproteobacteria class 9 NCBIFAM aminoglycoside N-acetyltransferase AAC(6')-IIc aminoglycoside N-acetyltransferase AAC(6')-IIc NF000150.1 16S_rRNA_Rmt_C 550 550 281 exception Y Y Y RmtC family 16S rRNA (guanine(1405)-N(7))-methyltransferase 1236 Gammaproteobacteria class 6 NCBIFAM RmtC family 16S rRNA (guanine(1405)-N(7))-methyltransferase RmtC family 16S rRNA (guanine(1405)-N(7))-methyltransferase NF000191.1 CMY2 800 800 381 exception Y Y Y CMY-2 family class C beta-lactamase blaCMY 3.5.2.6 GO:0008800 1236 Gammaproteobacteria class 462 NCBIFAM CMY family class C beta-lactamase CMY-2 family class C beta-lactamase NF000209.1 EreB 750 750 419 exception Y Y Y EreB family erythromycin esterase ere(B) GO:0046677 1236 Gammaproteobacteria class 2 NCBIFAM EreB family erythromycin esterase EreB family erythromycin esterase NF000221.4 FosA 250 250 137 exception Y Y Y FosA family fosfomycin resistance glutathione transferase 2.5.1.18 1236 Gammaproteobacteria class 1535 NCBIFAM glutathione transferase FosA FosA family fosfomycin resistance glutathione transferase NF000224.3 AAC_6p_Acine 225 225 146 exception Y Y Y AAC(6')-Ighjkrstuvwx family aminoglycoside N-acetyltransferase aac(6')-I GO:0008080 1236 Gammaproteobacteria class 84 NCBIFAM AAC(6')-Ighjkrstuvwx family aminoglycoside N-acetyltransferase AAC(6')-Ighjkrstuvwx family aminoglycoside N-acetyltransferase NF000239.3 MOX_CMY1_fam 770 770 383 exception Y Y Y CMY-1/MOX family class C beta-lactamase blaMOX 3.5.2.6 GO:0008800,GO:0030288 1236 Gammaproteobacteria class 180 NCBIFAM CMY-1/MOX family class C beta-lactamase CMY-1/MOX family class C beta-lactamase NF000254.1 macrolide_MphA 550 550 293 exception Y Y Y Mph(A) family macrolide 2'-phosphotransferase 1236 Gammaproteobacteria class 178 NCBIFAM macrolide 2'-phosphotransferase Mph(A) family macrolide 2'-phosphotransferase NF000298.2 blaTLA 640 640 309 exception Y Y Y TLA family extended-spectrum class A beta-lactamase blaTLA 3.5.2.6 GO:0008800 10722503 1236 Gammaproteobacteria class 4 NCBIFAM TLA family class A extended-spectrum beta-lactamase TLA family extended-spectrum class A beta-lactamase NF000323.2 blaFONA 600 600 295 exception Y Y Y FONA family class A beta-lactamase blaFONA 3.5.2.6 GO:0008800 1236 Gammaproteobacteria class 43 NCBIFAM FONA family class A beta-lactamase FONA family class A beta-lactamase NF000327.2 blaSCO 600 600 288 exception Y Y Y SCO family class A beta-lactamase blaSCO 3.5.2.6 GO:0008800 1236 Gammaproteobacteria class 4 NCBIFAM SCO family class A beta-lactamase SCO family class A beta-lactamase NF000383.2 blaLAP 600 600 285 exception Y Y Y LAP family class A beta-lactamase blaLAP 3.5.2.6 GO:0008800 1236 Gammaproteobacteria class 30 NCBIFAM LAP family class A beta-lactamase LAP family class A beta-lactamase NF000387.2 blaOXA-48_like 580 580 265 exception Y Y Y OXA-48 family class D beta-lactamase blaOXA 3.5.2.6 GO:0008658,GO:0008800 33753332 1236 Gammaproteobacteria class 81 NCBIFAM OXA-48 family class D beta-lactamase OXA-48 family class D beta-lactamase NF000388.2 blaOXA-1_like 580 580 276 exception Y Y Y OXA-1 family class D beta-lactamase blaOXA 3.5.2.6 GO:0008658,GO:0008800 1236 Gammaproteobacteria class 127 NCBIFAM OXA-1 family class D beta-lactamase OXA-1 family class D beta-lactamase NF000389.2 blaPER 650 650 308 exception Y Y Y PER family extended-spectrum class A beta-lactamase blaPER 3.5.2.6 GO:0008800 8517722 1236 Gammaproteobacteria class 26 NCBIFAM PER family class A extended-spectrum beta-lactamase PER family extended-spectrum class A beta-lactamase NF000396.3 blaGIM 525 525 250 exception Y Y Y GIM family subclass B1 metallo-beta-lactamase blaGIM 3.5.2.6 GO:0008800 23208706 1236 Gammaproteobacteria class 1 NCBIFAM GIM family subclass B1 metallo-beta-lactamase GIM family subclass B1 metallo-beta-lactamase NF000398.2 blaBEL 620 620 283 exception Y Y Y BEL family extended-spectrum class A beta-lactamase blaBEL 3.5.2.6 GO:0008800 1236 Gammaproteobacteria class 4 NCBIFAM BEL family class A extended-spectrum beta-lactamase BEL family extended-spectrum class A beta-lactamase NF000399.2 blaFOX 850 850 382 exception Y Y Y FOX family cephalosporin-hydrolyzing class C beta-lactamase blaFOX 3.5.2.6 GO:0008800,GO:0030288 1236 Gammaproteobacteria class 31 NCBIFAM FOX family cephalosporin-hydrolyzing class C beta-lactamase FOX family cephalosporin-hydrolyzing class C beta-lactamase NF000413.2 blaBKC 650 650 313 exception Y Y Y BKC family carbapenem-hydrolyzing class A beta-lactamase blaBKC 3.5.2.6 GO:0008800 1236 Gammaproteobacteria class 2 NCBIFAM BKC family carbapenem-hydrolyzing class A beta-lactamase BKC family carbapenem-hydrolyzing class A beta-lactamase NF000420.1 penta_rpt_QnrB 460 460 214 exception Y Y Y QnrB family quinolone resistance pentapeptide repeat protein 1236 Gammaproteobacteria class 153 NCBIFAM QnrB family quinolone resistance pentapeptide repeat protein QnrB family quinolone resistance pentapeptide repeat protein Members of this family are QnrB, a pentapeptide repeat protein that confers a reduced sensitivity to quinolone family antibiotics. The correct length for proteins in the QnrB family is 214, rather than 226, since translation from the more upstream candidate start codon would cause the coding region to overlap a conserved regulatory site. NF000421.1 penta_rpt_QnrVC 460 460 218 exception Y Y Y QnrVC family quinolone resistance pentapeptide repeat protein 1236 Gammaproteobacteria class 49 NCBIFAM QnrVC family quinolone resistance pentapeptide repeat protein QnrVC family quinolone resistance pentapeptide repeat protein NF000426.2 blaSIM 560 560 246 exception Y Y Y SIM family subclass B1 metallo-beta-lactamase blaSIM 3.5.2.6 GO:0008800 1236 Gammaproteobacteria class 2 NCBIFAM SIM family subclass B1 metallo-beta-lactamase SIM family subclass B1 metallo-beta-lactamase NF000431.1 AAC_6p_Ian 400 400 190 exception Y Y Y aminoglycoside N-acetyltransferase AAC(6')-Ian aac(6')-Ian GO:0008080 25576529,9371347 1236 Gammaproteobacteria class 12 NCBIFAM AAC6-Ian: aminoglycoside N-acetyltransferase AAC(6')-Ian aminoglycoside N-acetyltransferase AAC(6')-Ian NF000439.2 blaAIM 675 675 303 exception Y Y Y AIM family subclass B3 metallo-beta-lactamase blaAIM 3.5.2.6 GO:0008800 22985886 1236 Gammaproteobacteria class 12 NCBIFAM AIM family subclass B3 metallo-beta-lactamase AIM family subclass B3 metallo-beta-lactamase The founding member of this family, AIM-1, was shown to hydrolyze most beta-lactams other than aztreonam. NF000466.2 16S_rRNA_Rmt_gen 250 250 254 equivalog Y Y Y Rmt family 16S rRNA (guanine(1405)-N(7))-methyltransferase GO:0046677 1236 Gammaproteobacteria class 147 NCBIFAM Rmt family 16S rRNA (guanine(1405)-N(7))-methyltransferase Rmt family 16S rRNA (guanine(1405)-N(7))-methyltransferase NF000469.2 CAR_gen_B3 500 500 311 exception Y Y Y CAR family subclass B3 metallo-beta-lactamase blaCAR 3.5.2.6 GO:0008800 1236 Gammaproteobacteria class 168 NCBIFAM CAR family subclass B3 metallo-beta-lactamase CAR family subclass B3 metallo-beta-lactamase NF000494.1 FosF 280 280 132 exception Y Y Y fosfomycin resistance glutathione transferase FosF fosF 2.5.1.18 1236 Gammaproteobacteria class 2 NCBIFAM fosfomycin resistance glutathione transferase FosF fosfomycin resistance glutathione transferase FosF NF000495.1 FosK 280 280 132 exception Y Y Y fosfomycin resistance glutathione transferase FosK fosK 2.5.1.18 GO:0046872 1236 Gammaproteobacteria class 3 NCBIFAM fosfomycin resistance glutathione transferase FosK fosfomycin resistance glutathione transferase FosK NF000500.2 blaOXA-58_like 625 625 280 exception Y Y Y OXA-58 family carbapenem-hydrolyzing class D beta-lactamase blaOXA 3.5.2.6 GO:0008800 1236 Gammaproteobacteria class 9 NCBIFAM blaOXA-58_like: OXA-58 family carbapenem-hydrolyzing class D beta-lactamase OXA-58 family carbapenem-hydrolyzing class D beta-lactamase NF000518.2 blaVCC 625 625 284 exception Y Y Y VCC family carbapenem-hydrolyzing class A beta-lactamase blaVCC 3.5.2.6 GO:0008800 1236 Gammaproteobacteria class 2 NCBIFAM blaVCC: VCC family carbapenem-hydrolyzing class A beta-lactamase VCC family carbapenem-hydrolyzing class A beta-lactamase NF000538.0 classA_carba 410 410 254 equivalog Y Y Y carbapenem-hydrolyzing class A beta-lactamase bla 3.5.2.6 GO:0008800 1236 Gammaproteobacteria class 232 NCBIFAM classA_carba: carbapenem-hydrolyzing class A beta-lactamase carbapenem-hydrolyzing class A beta-lactamase NF000670.0 PRK00033 PRK00033.1-3 143 143 106 equivalog Y Y N ATP-dependent Clp protease adapter ClpS clpS GO:0006508 1236 Gammaproteobacteria class 2690 NCBI Protein Cluster (PRK) ATP-dependent Clp protease adaptor protein ClpS ATP-dependent Clp protease adapter ClpS NF000927.0 PRK00092 PRK00092.1-1 162 162 151 equivalog Y Y N ribosome maturation factor RimP rimP GO:0042274 1236 Gammaproteobacteria class 5359 NCBI Protein Cluster (PRK) ribosome maturation protein RimP ribosome maturation factor RimP NF000948.0 PRK00095 PRK00095.1-1 701 701 625 equivalog Y Y N DNA mismatch repair endonuclease MutL mutL GO:0005524,GO:0006298,GO:0016887,GO:0030983,GO:0032300 1236 Gammaproteobacteria class 13319 NCBI Protein Cluster (PRK) DNA mismatch repair protein DNA mismatch repair endonuclease MutL NF000984.0 PRK00103 PRK00103.1-1 242 242 156 equivalog Y Y N 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH rlmH 2.1.1.177 GO:0006364,GO:0008168 1236 Gammaproteobacteria class 3017 NCBI Protein Cluster (PRK) rRNA large subunit methyltransferase 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH NF001057.0 PRK00117 PRK00117.3-3 146 146 151 equivalog Y Y N recombination regulator RecX recX 1236 Gammaproteobacteria class 1421 NCBI Protein Cluster (PRK) recombination regulator RecX recombination regulator RecX NF001123.0 PRK00139 PRK00139.1-1 586 586 493 equivalog Y Y N UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase murE 6.3.2.13 GO:0005524,GO:0008360,GO:0009058,GO:0016881,GO:0051301 1236 Gammaproteobacteria class 10675 NCBI Protein Cluster (PRK) UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase NF001195.0 PRK00162 PRK00162.1 102 102 108 equivalog Y Y N thiosulfate sulfurtransferase GlpE glpE 2.8.1.1 GO:0004792 10735872,11092948,11709175 1236 Gammaproteobacteria class 5981 NCBI Protein Cluster (PRK) thiosulfate sulfurtransferase thiosulfate sulfurtransferase GlpE NF001214.0 PRK00187 PRK00187.1 449 449 464 equivalog Y Y N NorM family multidrug efflux MATE transporter GO:0015297,GO:0016020,GO:0042910,GO:0055085 1236 Gammaproteobacteria class 2895 NCBI Protein Cluster (PRK) multidrug efflux protein NorA NorM family multidrug efflux MATE transporter NF001218.0 PRK00192 PRK00192.1-5 362 362 275 equivalog Y N N mannosyl-3-phosphoglycerate phosphatase 1236 Gammaproteobacteria class 346 NCBI Protein Cluster (PRK) mannosyl-3-phosphoglycerate phosphatase mannosyl-3-phosphoglycerate phosphatase NF001248.0 PRK00218 PRK00218.1-4 225 225 207 equivalog Y Y N high frequency lysogenization protein HflD hflD 1236 Gammaproteobacteria class 4378 NCBI Protein Cluster (PRK) putative lysogenization regulator high frequency lysogenization protein HflD NF001250.0 PRK00218 PRK00218.1-6 262 262 205 equivalog Y Y N high frequency lysogenization protein HflD hflD 1236 Gammaproteobacteria class 1052 NCBI Protein Cluster (PRK) putative lysogenization regulator high frequency lysogenization protein HflD NF001324.0 PRK00259 PRK00259.1-2 187 187 181 equivalog Y Y N septation protein A 1236 Gammaproteobacteria class 4276 NCBI Protein Cluster (PRK) intracellular septation protein A septation protein A NF001327.0 PRK00259 PRK00259.1-5 327 327 197 equivalog Y Y N septation protein A 1236 Gammaproteobacteria class 1408 NCBI Protein Cluster (PRK) intracellular septation protein A septation protein A NF001366.0 PRK00275 PRK00275.1 1299 1299 895 equivalog Y Y N [protein-PII] uridylyltransferase 2.7.7.59 GO:0008152,GO:0008773 1236 Gammaproteobacteria class 3657 NCBI Protein Cluster (PRK) PII uridylyl-transferase [protein-PII] uridylyltransferase Uridylylates and de-uridylylates the small trimeric nitrogen regulatory protein PII NF001414.0 PRK00292 PRK00292.1-1 502 502 321 equivalog Y Y N glucokinase glk 2.7.1.2 GO:0004340,GO:0005524,GO:0005536,GO:0006096,GO:0051156 1236 Gammaproteobacteria class 2972 NCBI Protein Cluster (PRK) glucokinase glucokinase NF001420.0 PRK00294 PRK00294.1 169 169 173 equivalog Y Y N co-chaperone HscB hscB GO:0051087,GO:0051259 1236 Gammaproteobacteria class 1693 NCBI Protein Cluster (PRK) co-chaperone HscB co-chaperone HscB J-type co-chaperone that regulates the ATPase and peptide-binding activity of Hsc66 chaperone NF001441.0 PRK00304 PRK00304.1 126 126 75 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 828 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF001461.0 PRK00321 PRK00321.1-2 470 470 306 equivalog Y Y N recombination-associated protein RdgC rdgC 1236 Gammaproteobacteria class 1619 NCBI Protein Cluster (PRK) recombination associated protein recombination-associated protein RdgC NF001462.0 PRK00321 PRK00321.1-3 330 330 304 equivalog Y Y N recombination-associated protein RdgC rdgC GO:0006310 1236 Gammaproteobacteria class 8885 NCBI Protein Cluster (PRK) recombination associated protein recombination-associated protein RdgC NF001467.0 PRK00325 PRK00325.1-2 429 429 364 equivalog Y Y N mannuronate-specific alginate lyase 4.2.2.3 1236 Gammaproteobacteria class 2416 NCBI Protein Cluster (PRK) poly(beta-D-mannuronate) lyase mannuronate-specific alginate lyase NF001468.0 PRK00325 PRK00325.1-3 711 711 373 equivalog Y Y N mannuronate-specific alginate lyase 4.2.2.3 1236 Gammaproteobacteria class 1265 NCBI Protein Cluster (PRK) poly(beta-D-mannuronate) lyase mannuronate-specific alginate lyase NF001470.0 PRK00325 PRK00325.1-5 743 743 367 equivalog Y Y N mannuronate-specific alginate lyase 4.2.2.3 1236 Gammaproteobacteria class 357 NCBI Protein Cluster (PRK) poly(beta-D-mannuronate) lyase mannuronate-specific alginate lyase NF001486.0 PRK00341 PRK00341.1 120 120 91 equivalog Y Y N DUF493 domain-containing protein 1236 Gammaproteobacteria class 899 NCBI Protein Cluster (PRK) hypothetical protein DUF493 domain-containing protein NF001526.0 PRK00364 PRK00364.1-1 130 130 96 subfamily Y Y N co-chaperone GroES groES 1236 Gammaproteobacteria class 2145 NCBI Protein Cluster (PRK) co-chaperonin GroES co-chaperone GroES NF001557.0 PRK00378 PRK00378.1 341 341 334 equivalog Y Y N nucleoid-associated protein YejK yejK GO:0009295 1236 Gammaproteobacteria class 8719 NCBI Protein Cluster (PRK) nucleoid-associated protein NdpA nucleoid-associated protein YejK NF001659.0 PRK00430 PRK00430.1 99 99 98 equivalog Y Y N DNA-binding transcriptional regulator Fis fis 1986310 1236 Gammaproteobacteria class 2573 NCBI Protein Cluster (PRK) global DNA-binding transcriptional dual regulator Fis DNA-binding transcriptional regulator Fis Stimulates excision of phage lambda; affects Mu development; acts as an activator of rRNA and iRNA transcription NF001685.0 PRK00443 PRK00443.1-5 513 513 266 equivalog Y Y N glucosamine-6-phosphate deaminase nagB 3.5.99.6 GO:0004342,GO:0006044 1236 Gammaproteobacteria class 2065 NCBI Protein Cluster (PRK) glucosamine-6-phosphate deaminase glucosamine-6-phosphate deaminase NF001755.0 PRK00481 PRK00481.1-5 318 318 278 equivalog Y Y N Sir2 family NAD+-dependent deacetylase cobB 2.3.1.- GO:0070403 15019790,35325168 1236 Gammaproteobacteria class 5928 NCBI Protein Cluster (PRK) NAD-dependent deacetylase Sir2 family NAD+-dependent deacetylase NF001934.0 PRK00714 PRK00714.1-1 241 241 176 equivalog Y Y N RNA pyrophosphohydrolase rppH 3.6.1.- GO:0016787 1236 Gammaproteobacteria class 4268 NCBI Protein Cluster (PRK) RNA pyrophosphohydrolase RNA pyrophosphohydrolase NF002011.0 PRK00816 PRK00816.1 415 415 352 equivalog Y Y N electron transport complex subunit RsxD rsxD GO:0016020,GO:0022900,GO:0055085 10671439,12773378,9492268 1236 Gammaproteobacteria class 9641 NCBI Protein Cluster (PRK) electron transport complex protein RnfD electron transport complex subunit RsxD NF002012.0 PRK00819 PRK00819.1-1 233 233 184 equivalog Y Y N RNA 2'-phosphotransferase kptA 2.7.1.- 1236 Gammaproteobacteria class 1152 NCBI Protein Cluster (PRK) RNA 2'-phosphotransferase RNA 2'-phosphotransferase NF002024.0 PRK00846 PRK00846.1 90 90 78 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 286 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002072.0 PRK00913 PRK00913.1-1 826 826 502 equivalog Y Y N leucyl aminopeptidase pepA 3.4.11.1 GO:0006508,GO:0019538,GO:0030145,GO:0070006 1236 Gammaproteobacteria class 3516 NCBI Protein Cluster (PRK) multifunctional aminopeptidase A leucyl aminopeptidase NF002137.0 PRK00977 PRK00977.1-1 94 94 80 equivalog Y Y N exodeoxyribonuclease VII small subunit xseB 3.1.11.6 1236 Gammaproteobacteria class 2503 NCBI Protein Cluster (PRK) exodeoxyribonuclease VII small subunit exodeoxyribonuclease VII small subunit NF002155.0 PRK00984 PRK00984.1-4 445 445 349 equivalog Y Y N tRNA pseudouridine(13) synthase TruD truD 5.4.99.27 GO:0001522,GO:0003723,GO:0009982 1236 Gammaproteobacteria class 7254 NCBI Protein Cluster (PRK) tRNA pseudouridine synthase D tRNA pseudouridine(13) synthase TruD NF002340.1 PRK01297 PRK01297.1 564 564 372 equivalog Y Y N ATP-dependent RNA helicase RhlB rhlB 3.6.4.13 GO:0003676,GO:0003724,GO:0005524 1236 Gammaproteobacteria class 3947 NCBI Protein Cluster (PRK) ATP-dependent RNA helicase RhlB ATP-dependent RNA helicase RhlB Enables ATP-dependent unwinding of double stranded RNA as a component of the RNA degradosome, a multi-enzyme complex important in RNA processing and messenger RNA degradation NF002351.0 PRK01318 PRK01318.1-1 740 740 545 equivalog Y Y N membrane protein insertase YidC yidC GO:0016020,GO:0032977 1236 Gammaproteobacteria class 5526 NCBI Protein Cluster (PRK) membrane protein insertase membrane protein insertase YidC NF002448.0 PRK01614 PRK01614.1 83 83 85 equivalog Y Y N Sec-independent protein translocase subunit TatA tatA 1236 Gammaproteobacteria class 1377 NCBI Protein Cluster (PRK) twin arginine translocase protein A Sec-independent protein translocase subunit TatA NF002457.0 PRK01637 PRK01637.1 307 307 295 equivalog Y Y N virulence factor BrkB family protein 1236 Gammaproteobacteria class 5007 NCBI Protein Cluster (PRK) hypothetical protein virulence factor BrkB family protein NF002477.0 PRK01736 PRK01736.1 164 164 192 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 3310 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002484.0 PRK01747 PRK01747.1-5 878 878 672 equivalog Y Y N bifunctional tRNA (5-methylaminomethyl-2-thiouridine)(34)-methyltransferase MnmD/FAD-dependent 5-carboxymethylaminomethyl-2-thiouridine(34) oxidoreductase MnmC mnmC GO:0004808,GO:0008033 1236 Gammaproteobacteria class 14085 NCBI Protein Cluster (PRK) bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase bifunctional tRNA (5-methylaminomethyl-2-thiouridine)(34)-methyltransferase MnmD/FAD-dependent 5-carboxymethylaminomethyl-2-thiouridine(34) oxidoreductase MnmC NF002485.0 PRK01749 PRK01749.1 157 157 177 equivalog Y Y N disulfide bond formation protein DsbB dsbB 1.8.5.- GO:0006457,GO:0015035,GO:0016020 1236 Gammaproteobacteria class 5222 NCBI Protein Cluster (PRK) disulfide bond formation protein B disulfide bond formation protein DsbB Disulfide oxidoreductase; integral membrane protein; required for perioplasmic disulfide bond formation; oxidizes DsbA protein NF002487.0 PRK01759 PRK01759.1 890 890 862 equivalog Y Y N bifunctional uridylyltransferase/uridylyl-removing protein GlnD glnD 1236 Gammaproteobacteria class 9231 NCBI Protein Cluster (PRK) PII uridylyl-transferase bifunctional uridylyltransferase/uridylyl-removing protein GlnD NF002493.1 PRK01816 PRK01816.1 75 75 143 equivalog Y Y N terminus macrodomain insulation protein YfbV yfbV 22532809 1236 Gammaproteobacteria class 3634 NCBI Protein Cluster (PRK) hypothetical protein terminus macrodomain insulation protein YfbV YfbV was discovered to co-occur with the matS-binding replication terminus macrodomain (Ter) organizer protein MatP, and aid in defining the boundaries between Ter and rest of the chromosome. The system requires the presence of the Dam methylase. NF002500.0 PRK01833 PRK01833.1 115 115 74 equivalog Y Y N Sec-independent protein translocase subunit TatA tatA 1236 Gammaproteobacteria class 149 NCBI Protein Cluster (PRK) twin arginine translocase protein A Sec-independent protein translocase subunit TatA Part of system that translocates proteins with a conserved twin arginine motif across the inner membrane; capable of translocating folded substrates typically those with bound cofactors NF002525.0 PRK01966 PRK01966.1-1 457 457 364 equivalog Y Y N D-alanine--D-alanine ligase ddlA 6.3.2.4 GO:0008716 1236 Gammaproteobacteria class 6028 NCBI Protein Cluster (PRK) D-alanyl-alanine synthetase A D-alanine--D-alanine ligase NF002562.0 PRK02166 PRK02166.1 202 202 184 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 1724 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002755.0 PRK02797 PRK02797.1-4 543 543 357 equivalog Y Y N TDP-N-acetylfucosamine:lipid II N-acetylfucosaminyltransferase 2.4.1.325 1236 Gammaproteobacteria class 150 NCBI Protein Cluster (PRK) 4-alpha-L-fucosyltransferase TDP-N-acetylfucosamine:lipid II N-acetylfucosaminyltransferase NF002810.0 PRK02951 PRK02951.1-4 323 323 292 equivalog Y Y N DNA replication terminus site-binding protein 1236 Gammaproteobacteria class 292 NCBI Protein Cluster (PRK) DNA replication terminus site-binding protein DNA replication terminus site-binding protein NF002816.2 PRK02971 PRK02971.1-2 99 99 120 equivalog Y Y N 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnF arnF 1236 Gammaproteobacteria class 4285 NCBI Protein Cluster (PRK) 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnF 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnF NF002820.0 PRK02975 PRK02975.1 510 510 450 equivalog Y Y N ECA oligosaccharide polymerase wzyE GO:0009246,GO:0016020 16199561 1236 Gammaproteobacteria class 3860 NCBI Protein Cluster (PRK) putative common antigen polymerase ECA oligosaccharide polymerase ECA, enterobacterial common antigen, is widespread in bacteria such as Escherichia coli and Salmonella. It occurs glycerophosphatidyl-linked on the cell surface, and in a cyclized form in the periplasm. The pathway to ECA biosynthesis shares much with O-antigen biosynthesis, so the polymerase (this protein) and the flippase are named WzyE and WzxE, after the Wzy and Wzx proteins from O-antigen systems. However, WzyE is also known as WecF. NF002885.1 PRK03354 PRK03354.1 540 540 378 equivalog Y Y N crotonobetainyl-CoA dehydrogenase caiA 1.3.8.13 GO:0003995,GO:0009437,GO:0016627 8060125 1236 Gammaproteobacteria class 1193 NCBI Protein Cluster (PRK) crotonobetainyl-CoA dehydrogenase crotonobetainyl-CoA dehydrogenase Catalyzes the reduction of crotonobetainyl-CoA to gamma-butyrobetainyl-CoA NF002893.0 PRK03378 PRK03378.1 386 386 292 equivalog Y Y N NAD(+) kinase nadK 2.7.1.23 GO:0003951 1236 Gammaproteobacteria class 3945 NCBI Protein Cluster (PRK) inorganic polyphosphate/ATP-NAD kinase NAD(+) kinase Catalyzes the phosphorylation of NAD to NADP NF002894.0 PRK03379 PRK03379.1 234 234 266 equivalog Y Y N vitamin B12 ABC transporter substrate-binding protein BtuF btuF 7.6.2.- GO:0005524,GO:0031419 1236 Gammaproteobacteria class 6228 NCBI Protein Cluster (PRK) vitamin B12-transporter protein BtuF vitamin B12 ABC transporter substrate-binding protein BtuF NF002897.0 PRK03430 PRK03430.1 191 191 157 equivalog Y Y N DUF494 family protein 1236 Gammaproteobacteria class 2709 NCBI Protein Cluster (PRK) hypothetical protein DUF494 family protein NF002925.0 PRK03564 PRK03564.1 426 426 309 equivalog Y Y N formate dehydrogenase accessory protein FdhE fdhE 2170340,9274019 1236 Gammaproteobacteria class 3313 NCBI Protein Cluster (PRK) formate dehydrogenase accessory protein FdhE formate dehydrogenase accessory protein FdhE Required for the formation of active formate dehydrogenase NF002926.0 PRK03573 PRK03573.1 120 120 144 equivalog Y Y N transcriptional regulator SlyA slyA GO:0003700,GO:0006355 21550983,30510144,30837332 1236 Gammaproteobacteria class 2371 NCBI Protein Cluster (PRK) transcriptional regulator SlyA transcriptional regulator SlyA SlyA, a MarR family transcription factor, controls expression of many genes associated with virulence in species such as Salmonella. NF002946.0 PRK03601 PRK03601.1 240 240 275 equivalog Y Y N HTH-type transcriptional regulator HdfR hdfR GO:0003700,GO:0006355 1236 Gammaproteobacteria class 3246 NCBI Protein Cluster (PRK) transcriptional regulator HdfR HTH-type transcriptional regulator HdfR Negatively regulates the transcription of the flagellar master operon flhDC by binding to the upstream region of the operon NF002949.0 PRK03606 PRK03606.1-2 230 230 167 equivalog Y Y N ureidoglycolate lyase 4.3.2.3 1236 Gammaproteobacteria class 2359 NCBI Protein Cluster (PRK) ureidoglycolate hydrolase ureidoglycolate lyase NF002960.0 PRK03625 PRK03625.1 92 92 67 equivalog Y Y N twin-arginine translocase subunit TatE tatE 1236 Gammaproteobacteria class 1029 NCBI Protein Cluster (PRK) twin arginine translocase protein E twin-arginine translocase subunit TatE NF002973.0 PRK03659 PRK03659.1 804 804 602 equivalog Y Y N glutathione-regulated potassium-efflux system protein KefB kefB GO:0006813,GO:0015503 1236 Gammaproteobacteria class 5505 NCBI Protein Cluster (PRK) glutathione-regulated potassium-efflux system protein KefB glutathione-regulated potassium-efflux system protein KefB Transport system that facilitates potassium efflux NF002980.1 PRK03692 PRK03692.1 323 323 240 equivalog Y Y N lipopolysaccharide N-acetylmannosaminouronosyltransferase wecG 2.4.1.180 GO:0047241 3275612,36006410 1236 Gammaproteobacteria class 3343 NCBI Protein Cluster (PRK) putative UDP-N-acetyl-D-mannosaminuronic acid transferase lipopolysaccharide N-acetylmannosaminouronosyltransferase gene synonym:rffM, UDP-N-acetyl-D-mannosaminuronic acid transferase NF002981.0 PRK03695 PRK03695.1 281 281 253 equivalog Y Y N vitamin B12 ABC transporter ATP-binding protein BtuD btuD 7.6.2.8 GO:0005524,GO:0015889 1236 Gammaproteobacteria class 5916 NCBI Protein Cluster (PRK) vitamin B12-transporter ATPase vitamin B12 ABC transporter ATP-binding protein BtuD NF002982.0 PRK03699 PRK03699.1 221 221 395 equivalog Y Y N MFS transporter TsgA tsgA GO:0022857,GO:0055085 1236 Gammaproteobacteria class 4463 NCBI Protein Cluster (PRK) putative transporter MFS transporter TsgA NF002988.0 PRK03731 PRK03731.1 161 161 174 equivalog Y Y N shikimate kinase AroL aroL 2.7.1.71 GO:0004765,GO:0009073 1309529,15299895,3026317 1236 Gammaproteobacteria class 2724 NCBI Protein Cluster (PRK) shikimate kinase II shikimate kinase AroL Type II enzyme similar to type I but differentially regulated and with a lower Km; catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis NF002994.0 PRK03757 PRK03757.1 232 232 191 equivalog Y Y N YceI family protein 1236 Gammaproteobacteria class 6366 NCBI Protein Cluster (PRK) hypothetical protein YceI family protein NF002997.0 PRK03761 PRK03761.1 683 683 783 equivalog Y Y N LPS assembly protein LptD lptD GO:0015920,GO:0019867,GO:0043165 1236 Gammaproteobacteria class 8565 NCBI Protein Cluster (PRK) LPS assembly outer membrane complex protein LptD LPS assembly protein LptD NF003001.0 PRK03784 PRK03784.1 334 334 332 equivalog Y Y N vitamin B12 ABC transporter permease BtuC btuC 7.6.2.- GO:0005524,GO:0022857 1236 Gammaproteobacteria class 6229 NCBI Protein Cluster (PRK) vtamin B12-transporter permease vitamin B12 ABC transporter permease BtuC NF003004.0 PRK03814 PRK03814.1 84 84 86 equivalog Y Y N oxaloacetate decarboxylase subunit gamma 1236 Gammaproteobacteria class 535 NCBI Protein Cluster (PRK) oxaloacetate decarboxylase subunit gamma oxaloacetate decarboxylase subunit gamma NF003247.0 PRK04204 PRK04204.1-3 333 333 338 equivalog Y Y N RNA 3'-terminal phosphate cyclase rtcA 6.5.1.4 GO:0003963,GO:0006396 1236 Gammaproteobacteria class 2941 NCBI Protein Cluster (PRK) RNA 3'-terminal-phosphate cyclase RNA 3'-terminal phosphate cyclase NF003390.0 PRK04537 PRK04537.1 732 732 572 equivalog Y Y N ATP-dependent RNA helicase RhlB rhlB 3.6.4.13 1236 Gammaproteobacteria class 1280 NCBI Protein Cluster (PRK) ATP-dependent RNA helicase RhlB ATP-dependent RNA helicase RhlB Enables ATP-dependent unwinding of double stranded RNA as a component of the RNA degradosome, a multi-enzyme complex important in RNA processing and messenger RNA degradation NF003392.0 PRK04542 PRK04542.1 216 216 189 equivalog Y Y N elongation factor P-like protein YeiP yeiP GO:0003746,GO:0006414,GO:0043043 1236 Gammaproteobacteria class 3621 NCBI Protein Cluster (PRK) elongation factor P elongation factor P-like protein YeiP NF003396.0 PRK04598 PRK04598.1 121 121 81 equivalog Y Y N Sec-independent protein translocase subunit TatA tatA 1236 Gammaproteobacteria class 522 NCBI Protein Cluster (PRK) twin arginine translocase protein A Sec-independent protein translocase subunit TatA NF003419.0 PRK04837 PRK04837.1 588 588 424 equivalog Y Y N ATP-dependent RNA helicase RhlB rhlB 3.6.4.13 GO:0003676,GO:0003724,GO:0005524 1236 Gammaproteobacteria class 4898 NCBI Protein Cluster (PRK) ATP-dependent RNA helicase RhlB ATP-dependent RNA helicase RhlB Enables ATP-dependent unwinding of double stranded RNA as a component of the RNA degradosome, a multi-enzyme complex important in RNA processing and messenger RNA degradation NF003420.0 PRK04841 PRK04841.1 537 537 903 equivalog Y Y N HTH-type transcriptional regulator MalT malT GO:0003677,GO:0005515,GO:0006355 18610652 1236 Gammaproteobacteria class 8378 NCBI Protein Cluster (PRK) transcriptional regulator MalT HTH-type transcriptional regulator MalT Positively regulates the transcription of the maltose regulon whose gene products are responsible for uptake and catabolism of malto-oligosaccharides NF003421.0 PRK04860 PRK04860.1 175 175 170 equivalog Y Y N SprT family zinc-dependent metalloprotease 1236 Gammaproteobacteria class 7889 NCBI Protein Cluster (PRK) hypothetical protein SprT family zinc-dependent metalloprotease NF003422.0 PRK04863 PRK04863.1 699 699 1486 equivalog Y Y N chromosome partition protein MukB mukB GO:0003677,GO:0007059,GO:0030261 10545328,9688555 1236 Gammaproteobacteria class 14356 NCBI Protein Cluster (PRK) cell division protein MukB chromosome partition protein MukB SMC (structural maintenance of chromosomes) family of proteins; involved in chromosome condensatin and partitioning; forms a homodimer and the C-terminal is essential for DNA-binding activity while the purified N-terminal domain binds FtsZ NF003430.0 PRK04930 PRK04930.1 240 240 184 equivalog Y Y N glutathione-regulated potassium-efflux system ancillary protein KefG kefG GO:0006813 1236 Gammaproteobacteria class 2914 NCBI Protein Cluster (PRK) glutathione-regulated potassium-efflux system ancillary protein KefG glutathione-regulated potassium-efflux system ancillary protein KefG Required for KefB activity NF003431.1 PRK04940 PRK04940.1 240 240 180 equivalog Y Y N alpha/beta hydrolase YcfP ycfP 1236 Gammaproteobacteria class 2688 NCBI Protein Cluster (PRK) hypothetical protein alpha/beta hydrolase YcfP NF003432.0 PRK04946 PRK04946.1 128 128 181 equivalog Y Y N endonuclease SmrB smrB 1236 Gammaproteobacteria class 4702 NCBI Protein Cluster (PRK) hypothetical protein endonuclease SmrB NF003433.0 PRK04949 PRK04949.1 140 140 254 equivalog Y Y N sulfate transporter CysZ cysZ GO:0000103,GO:0005886,GO:0015116 1236 Gammaproteobacteria class 10435 NCBI Protein Cluster (PRK) putative sulfate transport protein CysZ sulfate transporter CysZ NF003434.0 PRK04950 PRK04950.1 127 127 205 equivalog Y Y N RNA chaperone ProQ proQ GO:0003723,GO:0010608,GO:0033592,GO:0034057 10049386 1236 Gammaproteobacteria class 4678 NCBI Protein Cluster (PRK) ProP expression regulator RNA chaperone ProQ NF003435.0 PRK04960 PRK04960.1 126 126 111 equivalog Y Y N universal stress protein UspB uspB 9829921 1236 Gammaproteobacteria class 1298 NCBI Protein Cluster (PRK) universal stress protein UspB universal stress protein UspB ppGpp-dependent, membrane associated, stress protein produced under conditions of nutrient deprivation, osmotic shock and oxidative stress NF003436.0 PRK04964 PRK04964.1 99 99 68 equivalog Y Y N YaeP family protein 1236 Gammaproteobacteria class 1280 NCBI Protein Cluster (PRK) hypothetical protein YaeP family protein NF003437.0 PRK04965 PRK04965.1 392 392 378 equivalog Y Y N NADH:flavorubredoxin reductase NorW norW 1.18.1.- GO:0016731 1236 Gammaproteobacteria class 7206 NCBI Protein Cluster (PRK) NADH:flavorubredoxin oxidoreductase NADH:flavorubredoxin reductase NorW NF003438.0 PRK04966 PRK04966.1 86 86 72 equivalog Y Y N YheU family protein 1236 Gammaproteobacteria class 2821 NCBI Protein Cluster (PRK) hypothetical protein YheU family protein NF003439.0 PRK04968 PRK04968.1 153 153 186 equivalog Y Y N SecY-interacting protein syd GO:0009898 1236 Gammaproteobacteria class 6456 NCBI Protein Cluster (PRK) SecY interacting protein Syd SecY-interacting protein NF003440.0 PRK04972 PRK04972.1 645 645 561 equivalog Y Y N aspartate:alanine antiporter GO:0006813,GO:0008324 1236 Gammaproteobacteria class 2584 NCBI Protein Cluster (PRK) putative transporter aspartate:alanine antiporter NF003442.0 PRK04976 PRK04976.1 132 132 211 equivalog Y Y N molecular chaperone TorD torD GO:0051259 1236 Gammaproteobacteria class 4067 NCBI Protein Cluster (PRK) chaperone protein TorD molecular chaperone TorD Involved in the biogenesis of torA; acts on torA before the insertion of the molybdenum cofactor and, as a result, probably favors a conformation of the apoenzyme that is competent for acquiring the cofactor NF003443.0 PRK04980 PRK04980.1 93 93 104 equivalog Y Y N N(4)-acetylcytidine aminohydrolase yqfB 15969587,31964920 1236 Gammaproteobacteria class 4019 NCBI Protein Cluster (PRK) hypothetical protein N(4)-acetylcytidine aminohydrolase NF003444.0 PRK04984 PRK04984.1 189 189 239 equivalog Y Y N fatty acid metabolism transcriptional regulator FadR fadR GO:0000062,GO:0003677,GO:0003700,GO:0006355,GO:0019217 1236 Gammaproteobacteria class 3549 NCBI Protein Cluster (PRK) fatty acid metabolism regulator fatty acid metabolism transcriptional regulator FadR Multifunctional regulator of fatty acid metabolism NF003445.0 PRK04987 PRK04987.1 143 143 130 equivalog Y Y N fumarate reductase subunit FrdC frdC 1.3.5.1 GO:0016020 1236 Gammaproteobacteria class 2580 NCBI Protein Cluster (PRK) fumarate reductase subunit C fumarate reductase subunit FrdC Part of four member fumarate reductase enzyme complex FrdABCD which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdCD are the membrane components which interact with quinone and are involved in electron transfer; the catalytic subunits are similar to succinate dehydrogenase SdhAB NF003447.0 PRK04998 PRK04998.1 86 86 88 equivalog Y Y N DUF493 family protein YbeD ybeD 15547281,25611823 1236 Gammaproteobacteria class 2038 NCBI Protein Cluster (PRK) hypothetical protein DUF493 family protein YbeD YbeD, a branch of the DUF493 family, regularly is found upstream of the lipBA gene pair, and is called structurally similar to allosteric regulatory domains, but a role affecting lipoic acid biosynthesis is not yet proven. NF003448.0 PRK05007 PRK05007.1 1255 1255 884 equivalog Y Y N bifunctional uridylyltransferase/uridylyl-removing protein GlnD glnD 2.7.7.59 GO:0008152,GO:0016779 1236 Gammaproteobacteria class 8160 NCBI Protein Cluster (PRK) PII uridylyl-transferase bifunctional uridylyltransferase/uridylyl-removing protein GlnD Catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein NF003449.0 PRK05014 PRK05014.1 189 189 172 equivalog Y Y N co-chaperone HscB hscB GO:0051087,GO:0097428 1236 Gammaproteobacteria class 4339 NCBI Protein Cluster (PRK) co-chaperone HscB co-chaperone HscB J-type co-chaperone that regulates the ATPase and peptide-binding activity of Hsc66 chaperone NF003450.0 PRK05015 PRK05015.1 437 437 429 equivalog Y Y N aminopeptidase PepB pepB 3.4.11.23 GO:0006508,GO:0019538,GO:0030145,GO:0070006 1236 Gammaproteobacteria class 9120 NCBI Protein Cluster (PRK) aminopeptidase B aminopeptidase PepB NF003455.0 PRK05054 PRK05054.1 542 542 645 equivalog Y Y N exoribonuclease II 3.1.13.1 GO:0003723,GO:0006401,GO:0008859 1236 Gammaproteobacteria class 10775 NCBI Protein Cluster (PRK) exoribonuclease II exoribonuclease II Involved in mRNA degradation; hydrolyzes single-stranded polyribonucleotides processively in the 3' to 5' direction NF003457.0 PRK05066 PRK05066.1 194 194 156 equivalog Y Y N transcriptional regulator ArgR argR 1236 Gammaproteobacteria class 2320 NCBI Protein Cluster (PRK) arginine repressor transcriptional regulator ArgR Regulates arginine biosynthesis when complexed with arginine by binding at site that overlap the promotors of the arginine biosynthesis genes NF003458.0 PRK05070 PRK05070.1 243 243 223 equivalog Y Y N DNA mismatch repair endonuclease MutH mutH GO:0004519,GO:0006304 1236 Gammaproteobacteria class 6533 NCBI Protein Cluster (PRK) DNA mismatch repair protein DNA mismatch repair endonuclease MutH Sequence-specific endonuclease that cleaves unmethylated GATC sequences during DNA repair NF003459.0 PRK05074 PRK05074.1 175 175 176 equivalog Y Y N inosine/xanthosine triphosphatase yjjX 3.6.1.- 16498616 1236 Gammaproteobacteria class 5083 NCBI Protein Cluster (PRK) inosine/xanthosine triphosphatase inosine/xanthosine triphosphatase NF003460.0 PRK05077 PRK05077.1 477 477 414 equivalog Y Y N esterase FrsA frsA GO:0016788 15169777 1236 Gammaproteobacteria class 5080 NCBI Protein Cluster (PRK) fermentation/respiration switch protein esterase FrsA NF003461.0 PRK05082 PRK05082.1 283 283 291 subfamily Y Y N N-acetylmannosamine kinase 2.7.1.60 1236 Gammaproteobacteria class 3883 NCBI Protein Cluster (PRK) N-acetylmannosamine kinase N-acetylmannosamine kinase Catalyzes the phosphorylation of the N-acetylmannosamine (ManNAc) liberated from N-acetyl-neuraminic acid by the nanA protein NF003466.1 PRK05090 PRK05090.1 138 138 93 exception Y Y N DUF167 family protein YggU yggU 12975589 1236 Gammaproteobacteria class 2621 NCBI Protein Cluster (PRK) hypothetical protein DUF167 family protein YggU The DUF167 (COG1872) family is uncharacterized, but distributed broadly from archaea to the bacterial model strain Escherichia coli K-12, where the family is represented by member protein YggU. This HMM represents the well-conserved YggU clade found within the DUF167 family. NF003469.0 PRK05094 PRK05094.1 103 103 107 equivalog Y Y N HI1450 family dsDNA-mimic protein 14747986,15883182 1236 Gammaproteobacteria class 2341 NCBI Protein Cluster (PRK) dsDNA-mimic protein HI1450 family dsDNA-mimic protein Members of this family of acidic proteins include HI1450 (from Haemophilus influenzae), which binds HU-alpha and therefore blocks its DNA binding, and YciU (from Escherichia coli). NF003471.0 PRK05097 PRK05097.1 186 186 150 equivalog Y Y N macrodomain Ter protein MatP matP GO:0006355,GO:0043565 1236 Gammaproteobacteria class 2550 NCBI Protein Cluster (PRK) Ter macrodomain organizer matS-binding protein macrodomain Ter protein MatP NF003472.0 PRK05101 PRK05101.1 499 499 382 equivalog Y Y N galactokinase galK 2.7.1.6 GO:0004335,GO:0005524,GO:0006012,GO:0046835 1236 Gammaproteobacteria class 9071 NCBI Protein Cluster (PRK) galactokinase galactokinase Catalyzes the formation of alpha-D-galactose 1-phosphate from D-galactose in galactose metabolism NF003474.0 PRK05111 PRK05111.1 460 460 383 equivalog Y Y N acetylornithine deacetylase argE 3.5.1.16 GO:0006526,GO:0019213 1236 Gammaproteobacteria class 10369 NCBI Protein Cluster (PRK) acetylornithine deacetylase acetylornithine deacetylase Catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine in arginine biosynthesis NF003476.0 PRK05114 PRK05114.1 72 72 60 equivalog Y Y N YoaH family protein 1236 Gammaproteobacteria class 1990 NCBI Protein Cluster (PRK) hypothetical protein YoaH family protein NF003500.0 PRK05170 PRK05170.1-4 203 203 147 equivalog Y Y N YcgN family cysteine cluster protein 1236 Gammaproteobacteria class 1176 NCBI Protein Cluster (PRK) hypothetical protein YcgN family cysteine cluster protein NF003502.0 PRK05170 PRK05170.1-6 250 250 149 equivalog Y Y N YcgN family cysteine cluster protein 1236 Gammaproteobacteria class 1394 NCBI Protein Cluster (PRK) hypothetical protein YcgN family cysteine cluster protein NF003503.0 PRK05170 PRK05170.2-1 232 232 145 equivalog Y Y N YcgN family cysteine cluster protein 1236 Gammaproteobacteria class 2217 NCBI Protein Cluster (PRK) hypothetical protein YcgN family cysteine cluster protein NF003505.0 PRK05170 PRK05170.2-3 206 206 164 equivalog Y Y N YcgN family cysteine cluster protein 1236 Gammaproteobacteria class 656 NCBI Protein Cluster (PRK) hypothetical protein YcgN family cysteine cluster protein NF003560.1 PRK05244 PRK05244.1-1 90 90 156 equivalog Y Y N Der GTPase-activating protein YihI yihI 20434458 1236 Gammaproteobacteria class 5324 NCBI Protein Cluster (PRK) Der GTPase activator Der GTPase-activating protein YihI NF003584.0 PRK05248 PRK05248.3-5 190 190 122 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 12 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003602.1 PRK05256 PRK05256.1 250 250 216 equivalog Y Y N chromosome partition protein MukE mukE GO:0007059,GO:0030261 10545099 1236 Gammaproteobacteria class 3253 NCBI Protein Cluster (PRK) condesin subunit E chromosome partition protein MukE Acts with MukB and MukF to condense the chromosome and allow for segregation during cell division NF003615.0 PRK05260 PRK05260.1 407 407 440 equivalog Y Y N chromosome partition protein MukF mukF GO:0005509,GO:0007059 1236 Gammaproteobacteria class 4582 NCBI Protein Cluster (PRK) condesin subunit F chromosome partition protein MukF Acts with MukB and MukE to condense the chromosome and allow for segregation during cell division NF003622.0 PRK05264 PRK05264.1 110 110 105 equivalog Y Y N met regulon transcriptional regulator MetJ metJ 1236 Gammaproteobacteria class 1670 NCBI Protein Cluster (PRK) transcriptional repressor protein MetJ met regulon transcriptional regulator MetJ NF003655.0 PRK05287 PRK05287.1-3 271 271 245 equivalog Y Y N cell division protein ZapD zapD 1236 Gammaproteobacteria class 4033 NCBI Protein Cluster (PRK) hypothetical protein cell division protein ZapD NF003721.0 PRK05329 PRK05329.1-4 403 403 428 equivalog Y Y N glycerol-3-phosphate dehydrogenase subunit GlpB glpB 1.1.5.3 1236 Gammaproteobacteria class 2860 NCBI Protein Cluster (PRK) anaerobic glycerol-3-phosphate dehydrogenase subunit B glycerol-3-phosphate dehydrogenase subunit GlpB NF003747.0 PRK05346 PRK05346.1-2 336 336 260 equivalog Y Y N Na(+)-translocating NADH-quinone reductase subunit C 1236 Gammaproteobacteria class 326 NCBI Protein Cluster (PRK) Na(+)-translocating NADH-quinone reductase subunit C Na(+)-translocating NADH-quinone reductase subunit C NF003831.0 PRK05419 PRK05419.1-2 226 226 212 equivalog Y Y N protein-methionine-sulfoxide reductase heme-binding subunit MsrQ msrQ 1236 Gammaproteobacteria class 6165 NCBI Protein Cluster (PRK) putative sulfite oxidase subunit YedZ protein-methionine-sulfoxide reductase heme-binding subunit MsrQ NF003841.0 PRK05421 PRK05421.1-3 223 223 261 equivalog Y Y N endonuclease/exonuclease/phosphatase family protein 1236 Gammaproteobacteria class 3783 NCBI Protein Cluster (PRK) hypothetical protein endonuclease/exonuclease/phosphatase family protein NF003883.0 PRK05428 PRK05428.2-1 252 252 189 equivalog Y Y N HPr kinase/phosphorylase-related protein 2.7.1.- 1236 Gammaproteobacteria class 10 NCBI Protein Cluster (PRK) HPr kinase/phosphorylase HPr kinase/phosphorylase-related protein This part-length close homolog of the HPr kinase/phosphorylase HprK appears restricted to the Coxiella genus. How its function may differ from full-length HPrK is unknown. NF003897.0 PRK05434 PRK05434.1-5 862 862 514 equivalog Y Y N 2,3-bisphosphoglycerate-independent phosphoglycerate mutase gpmM pgmI 5.4.2.12 GO:0004619,GO:0006007 1236 Gammaproteobacteria class 6372 NCBI Protein Cluster (PRK) phosphoglyceromutase 2,3-bisphosphoglycerate-independent phosphoglycerate mutase NF003954.0 PRK05452 PRK05452.1 711 711 479 equivalog Y Y N anaerobic nitric oxide reductase flavorubredoxin norV GO:0009055,GO:0010181,GO:0016966,GO:0046872 1236 Gammaproteobacteria class 5916 NCBI Protein Cluster (PRK) anaerobic nitric oxide reductase flavorubredoxin anaerobic nitric oxide reductase flavorubredoxin NF004065.0 PRK05580 PRK05580.1-1 858 858 731 equivalog Y Y N primosomal protein N' priA 3.6.1.- 1236 Gammaproteobacteria class 16106 NCBI Protein Cluster (PRK) primosome assembly protein PriA primosomal protein N' NF004190.0 PRK05645 PRK05645.1 377 377 295 equivalog Y Y N lysophospholipid acyltransferase 2.3.1.15 GO:0016740 1236 Gammaproteobacteria class 1919 NCBI Protein Cluster (PRK) lipid A biosynthesis lauroyl acyltransferase lysophospholipid acyltransferase NF004191.0 PRK05646 PRK05646.1 491 491 310 equivalog Y Y N lipid A biosynthesis lauroyl acyltransferase 1236 Gammaproteobacteria class 2458 NCBI Protein Cluster (PRK) lipid A biosynthesis lauroyl acyltransferase lipid A biosynthesis lauroyl acyltransferase Acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA NF004227.0 PRK05674 PRK05674.1 426 426 271 equivalog Y Y N gamma-carboxygeranoyl-CoA hydratase GO:0003824 1236 Gammaproteobacteria class 2734 NCBI Protein Cluster (PRK) gamma-carboxygeranoyl-CoA hydratase gamma-carboxygeranoyl-CoA hydratase Catalyzes the hydration of gamma-carboxygeranoyl-CoA to 3-hydroxy-gamma-carboxygeranoyl-CoA NF004229.0 PRK05677 PRK05677.1 879 879 563 subfamily Y N N long-chain-fatty-acid--CoA ligase 1236 Gammaproteobacteria class 5519 NCBI Protein Cluster (PRK) long-chain-fatty-acid--CoA ligase long-chain-fatty-acid--CoA ligase NF004267.1 PRK05687 PRK05687.1-3 293 293 266 equivalog Y Y N flagellar assembly protein FliH fliH GO:0003774,GO:0009288,GO:0071973 15170400 1236 Gammaproteobacteria class 1454 NCBI Protein Cluster (PRK) flagellar assembly protein H flagellar assembly protein FliH NF004269.1 PRK05687 PRK05687.1-5 279 279 249 equivalog Y Y N flagellar assembly protein FliH fliH GO:0003774,GO:0009288,GO:0071973 1236 Gammaproteobacteria class 2663 NCBI Protein Cluster (PRK) flagellar assembly protein H flagellar assembly protein FliH NF004285.1 PRK05696 PRK05696.1 179 179 171 equivalog Y Y N flagellar basal body-associated protein FliL fliL GO:0071973 1236 Gammaproteobacteria class 3479 NCBI Protein Cluster (PRK) flagellar basal body-associated protein FliL flagellar basal body-associated protein FliL Interacts with the cytoplasmic MS ring of the basal body and may act to stabilize the MotAB complexes which surround the MS ring NF004311.0 PRK05708 PRK05708.1 378 378 305 equivalog Y Y N putative 2-dehydropantoate 2-reductase GO:0008677,GO:0015940 1236 Gammaproteobacteria class 3432 NCBI Protein Cluster (PRK) 2-dehydropantoate 2-reductase putative 2-dehydropantoate 2-reductase NF004317.0 PRK05713 PRK05713.1 338 338 312 equivalog Y Y N iron-sulfur-binding ferredoxin reductase GO:0016491,GO:0051536 1236 Gammaproteobacteria class 3295 NCBI Protein Cluster (PRK) hypothetical protein iron-sulfur-binding ferredoxin reductase NF004319.0 PRK05715 PRK05715.1-1 101 101 100 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoK nuoK 1.6.5.9 GO:0016651,GO:0042773 1236 Gammaproteobacteria class 2222 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit K NADH-quinone oxidoreductase subunit NuoK NF004324.0 PRK05717 PRK05717.1 384 384 258 equivalog Y Y N SDR family oxidoreductase GO:0016491 1236 Gammaproteobacteria class 1785 NCBI Protein Cluster (PRK) oxidoreductase SDR family oxidoreductase NF004343.0 PRK05723 PRK05723.1 204 204 151 equivalog Y Y N flavodoxin GO:0010181 1236 Gammaproteobacteria class 2116 NCBI Protein Cluster (PRK) flavodoxin flavodoxin An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group NF004346.0 PRK05728 PRK05728.1-2 234 234 141 equivalog Y Y N DNA polymerase III subunit chi 2.7.7.7 1236 Gammaproteobacteria class 468 NCBI Protein Cluster (PRK) DNA polymerase III subunit chi DNA polymerase III subunit chi NF004350.0 PRK05731 PRK05731.1-1 441 441 325 equivalog Y Y N thiamine-phosphate kinase thiL 2.7.4.16 GO:0009030,GO:0009228 1236 Gammaproteobacteria class 5788 NCBI Protein Cluster (PRK) thiamine monophosphate kinase thiamine-phosphate kinase NF004356.0 PRK05732 PRK05732.1 384 384 395 equivalog Y Y N 2-octaprenyl-6-methoxyphenyl hydroxylase ubiH visB 1.14.13.- GO:0006744,GO:0008681,GO:0016709,GO:0071949 1236 Gammaproteobacteria class 18048 NCBI Protein Cluster (PRK) 2-octaprenyl-6-methoxyphenyl hydroxylase 2-octaprenyl-6-methoxyphenyl hydroxylase Catalyzes the formation of 2-octaprenyl-6-methoxy-1,4-benzoquinone from 2-octaprenyl-6-methoxyphenol NF004357.0 PRK05733 PRK05733.1 241 241 172 subfamily Y N N single-stranded DNA-binding protein 1236 Gammaproteobacteria class 2218 NCBI Protein Cluster (PRK) single-stranded DNA-binding protein single-stranded DNA-binding protein NF004358.0 PRK05738 PRK05738.1-1 134 134 100 equivalog Y Y N 50S ribosomal protein L23 rplW 1236 Gammaproteobacteria class 1386 NCBI Protein Cluster (PRK) 50S ribosomal protein L23 50S ribosomal protein L23 NF004372.0 PRK05740 PRK05740.1-2 134 134 123 equivalog Y Y N preprotein translocase subunit SecE secE 1236 Gammaproteobacteria class 2695 NCBI Protein Cluster (PRK) preprotein translocase subunit SecE preprotein translocase subunit SecE NF004373.0 PRK05740 PRK05740.1-3 154 154 150 equivalog Y Y N preprotein translocase subunit SecE secE 1236 Gammaproteobacteria class 617 NCBI Protein Cluster (PRK) preprotein translocase subunit SecE preprotein translocase subunit SecE NF004379.0 PRK05740 PRK05740.2-5 150 150 127 equivalog Y Y N preprotein translocase subunit SecE secE 1236 Gammaproteobacteria class 1096 NCBI Protein Cluster (PRK) preprotein translocase subunit SecE preprotein translocase subunit SecE NF004391.0 PRK05751 PRK05751.1-2 223 223 171 equivalog Y Y N protein-export chaperone SecB secB 1236 Gammaproteobacteria class 463 NCBI Protein Cluster (PRK) preprotein translocase subunit SecB protein-export chaperone SecB NF004395.0 PRK05752 PRK05752.1 380 380 255 equivalog Y Y N uroporphyrinogen-III synthase 4.2.1.75 GO:0004852,GO:0006780 1236 Gammaproteobacteria class 2747 NCBI Protein Cluster (PRK) uroporphyrinogen-III synthase uroporphyrinogen-III synthase Catalyzes the formation of uroporphyrinogen-III from hydroxymethylbilane NF004404.0 PRK05758 PRK05758.2-5 221 221 177 equivalog Y Y N F0F1 ATP synthase subunit delta atpH 7.1.2.2 GO:0015986,GO:0016020,GO:0046933 1236 Gammaproteobacteria class 3073 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit delta F0F1 ATP synthase subunit delta NF004413.0 PRK05759 PRK05759.1-4 197 197 156 equivalog Y Y N F0F1 ATP synthase subunit B atpF 7.1.2.2 GO:0015078,GO:0015986 1236 Gammaproteobacteria class 3067 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit B F0F1 ATP synthase subunit B NF004414.0 PRK05760 PRK05760.1 129 129 128 equivalog Y Y N F0F1 ATP synthase subunit I 7.1.2.2 1236 Gammaproteobacteria class 1466 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit I F0F1 ATP synthase subunit I Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit I associates with the membrane and may be involved with cation translocation NF004439.0 PRK05777 PRK05777.1-1 531 531 485 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoN nuoN 7.1.1.2 GO:0008137 1236 Gammaproteobacteria class 6145 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit N NADH-quinone oxidoreductase subunit NuoN NF004498.0 PRK05846 PRK05846.1-1 614 614 509 equivalog Y Y N NADH-quinone oxidoreductase subunit M nuoM 1.6.5.9 GO:0008137,GO:0042773 1236 Gammaproteobacteria class 6302 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit M NADH-quinone oxidoreductase subunit M NF004536.0 PRK05888 PRK05888.1-1 212 212 180 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoI nuoI 1.6.5.9 GO:0016020,GO:0016651,GO:0051539 1236 Gammaproteobacteria class 2964 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit I NADH-quinone oxidoreductase subunit NuoI NF004678.0 PRK06019 PRK06019.1-4 444 444 355 equivalog Y Y N 5-(carboxyamino)imidazole ribonucleotide synthase purK 6.3.4.18 GO:0004638,GO:0005524,GO:0006189,GO:0046872 1236 Gammaproteobacteria class 6446 NCBI Protein Cluster (PRK) phosphoribosylaminoimidazole carboxylase ATPase subunit 5-(carboxyamino)imidazole ribonucleotide synthase NF004740.0 PRK06076 PRK06076.1-1 399 399 325 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoH nuoH 1.6.5.9 1236 Gammaproteobacteria class 4198 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit H NADH-quinone oxidoreductase subunit NuoH NF004951.0 PRK06299 PRK06299.1-1 918 918 556 equivalog Y Y N 30S ribosomal protein S1 rpsA GO:0003723,GO:0003735,GO:0005840,GO:0006412 1236 Gammaproteobacteria class 5273 NCBI Protein Cluster (PRK) 30S ribosomal protein S1 30S ribosomal protein S1 NF005044.0 PRK06458 PRK06458.1-4 610 610 531 equivalog Y Y N hydrogenase 4 subunit F 1236 Gammaproteobacteria class 2341 NCBI Protein Cluster (PRK) hydrogenase 4 subunit F hydrogenase 4 subunit F NF005058.0 PRK06466 PRK06466.1 951 951 574 equivalog Y Y N acetolactate synthase 3 large subunit GO:0000287,GO:0003984,GO:0009082,GO:0030976,GO:0050660 1236 Gammaproteobacteria class 10955 NCBI Protein Cluster (PRK) acetolactate synthase 3 catalytic subunit acetolactate synthase 3 large subunit NF005066.0 PRK06483 PRK06483.1 249 249 239 equivalog Y Y N dihydromonapterin reductase folM 1.5.1.50 GO:0016491 1236 Gammaproteobacteria class 7022 NCBI Protein Cluster (PRK) dihydromonapterin reductase dihydromonapterin reductase NF005087.0 PRK06522 PRK06522.1-1 351 351 296 equivalog Y Y N 2-dehydropantoate 2-reductase panE 1.1.1.169 GO:0008677,GO:0015940 1236 Gammaproteobacteria class 6084 NCBI Protein Cluster (PRK) 2-dehydropantoate 2-reductase 2-dehydropantoate 2-reductase NF005162.0 PRK06638 PRK06638.1-1 157 157 184 equivalog Y Y N NADH-quinone oxidoreductase subunit J nuoJ 1.6.5.9 GO:0008137 1236 Gammaproteobacteria class 4218 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit J NADH-quinone oxidoreductase subunit J NF005271.0 PRK06774 PRK06774.1 340 340 191 equivalog Y Y N aminodeoxychorismate synthase component II 1236 Gammaproteobacteria class 3321 NCBI Protein Cluster (PRK) para-aminobenzoate synthase component II aminodeoxychorismate synthase component II Catalyzes the formation of 4-amino-4-deoxychorismate from chorismate and glutamine in para-aminobenzoate synthesis NF005284.0 PRK06801 PRK06801.1 406 406 286 equivalog Y Y N ketose 1,6-bisphosphate aldolase 1236 Gammaproteobacteria class 1187 NCBI Protein Cluster (PRK) hypothetical protein ketose 1,6-bisphosphate aldolase NF005286.1 PRK06803 PRK06803.1 467 467 402 equivalog Y Y N flagellar hook protein FlgE flgE 15170400,16428388 1236 Gammaproteobacteria class 1881 NCBI Protein Cluster (PRK) flagellar hook protein FlgE flagellar hook protein FlgE The hook connects flagellar basal body to the flagellar filament NF005338.0 PRK06856 PRK06856.1-4 162 162 136 equivalog Y Y N DNA polymerase III subunit psi 2.7.7.7 1236 Gammaproteobacteria class 220 NCBI Protein Cluster (PRK) DNA polymerase III subunit psi DNA polymerase III subunit psi NF005340.0 PRK06860 PRK06860.1 398 398 309 subfamily Y N N lipid A biosynthesis lauroyl acyltransferase 1236 Gammaproteobacteria class 11152 NCBI Protein Cluster (PRK) lipid A biosynthesis lauroyl acyltransferase lipid A biosynthesis lauroyl acyltransferase NF005364.0 PRK06882 PRK06882.1 1083 1083 574 equivalog Y Y N acetolactate synthase 3 large subunit 1236 Gammaproteobacteria class 566 NCBI Protein Cluster (PRK) acetolactate synthase 3 catalytic subunit acetolactate synthase 3 large subunit NF005367.0 PRK06895 PRK06895.1 265 265 190 equivalog Y Y N anthranilate synthase component II 1236 Gammaproteobacteria class 556 NCBI Protein Cluster (PRK) putative anthranilate synthase component II anthranilate synthase component II With component I catalyzes the formation of anthranilate and glutamate from chorismate and glutamine NF005369.0 PRK06904 PRK06904.1 809 809 474 equivalog Y Y N replicative DNA helicase 3.6.4.12 1236 Gammaproteobacteria class 431 NCBI Protein Cluster (PRK) replicative DNA helicase replicative DNA helicase Unwinds double stranded DNA NF005386.0 PRK06931 PRK06931.1 753 753 461 equivalog Y Y N diaminobutyrate--2-oxoglutarate transaminase 2.6.1.76 GO:0008483,GO:0009058,GO:0030170 1236 Gammaproteobacteria class 2965 NCBI Protein Cluster (PRK) diaminobutyrate--2-oxoglutarate aminotransferase diaminobutyrate--2-oxoglutarate transaminase Catalyzes the reversible formation of diaminobutyrate and 2-oxoglutarate from glutamate and L-aspartic beta-semialdehyde NF005387.0 PRK06932 PRK06932.1 492 492 314 equivalog Y Y N 2-hydroxyacid dehydrogenase 1236 Gammaproteobacteria class 767 NCBI Protein Cluster (PRK) glycerate dehydrogenase 2-hydroxyacid dehydrogenase NF005936.0 PRK07979 PRK07979.1 1080 1080 574 equivalog Y Y N acetolactate synthase 3 large subunit ilvI 2.2.1.6 GO:0000287,GO:0003984,GO:0009082,GO:0030976,GO:0050660 1236 Gammaproteobacteria class 4471 NCBI Protein Cluster (PRK) acetolactate synthase 3 catalytic subunit acetolactate synthase 3 large subunit NF005938.0 PRK07984 PRK07984.1 477 477 262 equivalog Y Y N enoyl-ACP reductase FabI fabI 1.3.1.9 1236 Gammaproteobacteria class 1473 NCBI Protein Cluster (PRK) enoyl-(acyl carrier protein) reductase enoyl-ACP reductase FabI NF005945.0 PRK08006 PRK08006.1 898 898 471 equivalog Y Y N replicative DNA helicase dnaB 3.6.4.12 1236 Gammaproteobacteria class 1812 NCBI Protein Cluster (PRK) replicative DNA helicase replicative DNA helicase Unwinds double stranded DNA NF005955.1 PRK08032 PRK08032.1 387 387 465 equivalog Y Y N flagellar filament capping protein FliD fliD GO:0007155,GO:0009288,GO:0009421 11118149 1236 Gammaproteobacteria class 5474 NCBI Protein Cluster (PRK) flagellar capping protein flagellar filament capping protein FliD Involved in flagellin assembly NF005959.0 PRK08043 PRK08043.1 886 886 719 equivalog Y Y N bifunctional acyl-ACP--phospholipid O-acyltransferase/long-chain-fatty-acid--ACP ligase aas 2.3.1.40,6.2.1.47 GO:0006631,GO:0008654,GO:0008779,GO:0008922 1236 Gammaproteobacteria class 7153 NCBI Protein Cluster (PRK) bifunctional acyl-[acyl carrier protein] synthetase/2-acylglycerophosphoethanolamine acyltransferase bifunctional acyl-ACP--phospholipid O-acyltransferase/long-chain-fatty-acid--ACP ligase NF005963.0 PRK08051 PRK08051.1 230 230 233 equivalog Y Y N NAD(P)H-flavin reductase fre 1.5.1.41 GO:0016491 1236 Gammaproteobacteria class 4365 NCBI Protein Cluster (PRK) FMN reductase NAD(P)H-flavin reductase NF005965.0 PRK08055 PRK08055.1 179 179 182 equivalog Y Y N chorismate mutase 5.4.99.5 GO:0046417 1236 Gammaproteobacteria class 1849 NCBI Protein Cluster (PRK) chorismate mutase chorismate mutase Catalyzes the interconversion of chorismate to prephenate NF005982.0 PRK08084 PRK08084.1 268 268 235 equivalog Y Y N DnaA inactivator Hda hda 1236 Gammaproteobacteria class 2040 NCBI Protein Cluster (PRK) DNA replication initiation factor DnaA inactivator Hda Controls initiation of DNA replication by inhibiting re-initiation of replication, promotes hydrolysis of DnaA-bound ATP NF005983.0 PRK08085 PRK08085.1 408 408 254 equivalog Y Y N gluconate 5-dehydrogenase idnO 1.1.1.69 1236 Gammaproteobacteria class 1271 NCBI Protein Cluster (PRK) gluconate 5-dehydrogenase gluconate 5-dehydrogenase Involved in the nonphosphorylative, ketogenic oxidation of glucose and oxidizes gluconate to 5-ketogluconate NF005984.0 PRK08087 PRK08087.1 264 264 215 subfamily Y Y N L-fuculose-phosphate aldolase 4.1.2.17 1236 Gammaproteobacteria class 2096 NCBI Protein Cluster (PRK) L-fuculose phosphate aldolase L-fuculose-phosphate aldolase Catalyzes the formation of glycerone phosphate and (S)-lactaldehyde from L-fuculose 1-phosphate NF005985.0 PRK08088 PRK08088.1 713 713 426 equivalog Y Y N 4-aminobutyrate--2-oxoglutarate transaminase gabT 2.6.1.19 GO:0009448,GO:0030170 1236 Gammaproteobacteria class 4757 NCBI Protein Cluster (PRK) 4-aminobutyrate aminotransferase 4-aminobutyrate--2-oxoglutarate transaminase Catalyzes the formation of succinate semialdehyde and glutamate from 4-aminobutanoate and 2-oxoglutarate NF005987.0 PRK08097 PRK08097.1 498 498 562 equivalog Y Y N NAD-dependent DNA ligase LigB ligB 6.5.1.2 GO:0003911,GO:0006260,GO:0006281 11812821 1236 Gammaproteobacteria class 12037 NCBI Protein Cluster (PRK) NAD-dependent DNA ligase LigB NAD-dependent DNA ligase LigB Catalyzes strand joining of nicked DNA in the presence of a divalent cation and NAD+ NF005989.0 PRK08105 PRK08105.1 160 160 149 equivalog Y Y N flavodoxin GO:0010181 1236 Gammaproteobacteria class 4077 NCBI Protein Cluster (PRK) flavodoxin flavodoxin An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group NF005990.0 PRK08114 PRK08114.1 634 634 395 equivalog Y Y N cystathionine beta-lyase metC 4.4.1.13 GO:0006520,GO:0019346,GO:0030170,GO:0047804 1236 Gammaproteobacteria class 5678 NCBI Protein Cluster (PRK) cystathionine beta-lyase cystathionine beta-lyase Catalyzes the formation of L-homocysteine from cystathionine NF005998.1 PRK08125 PRK08125.1 777 777 649 equivalog Y Y N bifunctional UDP-4-amino-4-deoxy-L-arabinose formyltransferase/UDP-glucuronic acid oxidase ArnA arnA 1.1.1.305,2.1.2.13 GO:0009058,GO:0016742 1236 Gammaproteobacteria class 8447 NCBI Protein Cluster (PRK) bifunctional UDP-glucuronic acid decarboxylase/UDP-4-amino-4-deoxy-L-arabinose formyltransferase bifunctional UDP-4-amino-4-deoxy-L-arabinose formyltransferase/UDP-glucuronic acid oxidase ArnA Catalyzes the decarboxylation of UDP-glucuronic acid to UDP-4-keto-arabinose and the addition of a formyl group to UDP-4-amino-4-deoxy-L-arabinose to form UDP-L-4-formamido-arabinose NF006434.0 PRK08722 PRK08722.1 759 759 414 equivalog Y Y N beta-ketoacyl-ACP synthase II fabF GO:0004315,GO:0006633 1236 Gammaproteobacteria class 2664 NCBI Protein Cluster (PRK) 3-oxoacyl-(acyl carrier protein) synthase II beta-ketoacyl-ACP synthase II NF006442.0 PRK08751 PRK08751.1 1023 1023 560 equivalog Y Y N long-chain fatty acid--CoA ligase 1236 Gammaproteobacteria class 976 NCBI Protein Cluster (PRK) putative long-chain fatty acyl CoA ligase long-chain fatty acid--CoA ligase NF006451.0 PRK08780 PRK08780.1 1265 1265 824 equivalog Y Y N DNA topoisomerase I 5.6.2.1 1236 Gammaproteobacteria class 1648 NCBI Protein Cluster (PRK) DNA topoisomerase I DNA topoisomerase I NF006458.0 PRK08840 PRK08840.1 884 884 464 equivalog Y Y N replicative DNA helicase 3.6.4.12 1236 Gammaproteobacteria class 1806 NCBI Protein Cluster (PRK) replicative DNA helicase replicative DNA helicase Unwinds double stranded DNA NF006461.0 PRK08850 PRK08850.1 633 633 405 equivalog Y Y N FAD-dependent 2-octaprenylphenol hydroxylase GO:0006744,GO:0016709 1236 Gammaproteobacteria class 2656 NCBI Protein Cluster (PRK) 2-octaprenyl-6-methoxyphenol hydroxylase FAD-dependent 2-octaprenylphenol hydroxylase Catalyzes the formation of 2-octaprenyl-6-methoxy-1,4-benzoquinone from 2-octaprenyl-6-methoxyphenol NF006462.0 PRK08857 PRK08857.1 345 345 193 equivalog Y Y N aminodeoxychorismate/anthranilate synthase component II 1236 Gammaproteobacteria class 3443 NCBI Protein Cluster (PRK) para-aminobenzoate synthase component II aminodeoxychorismate/anthranilate synthase component II NF006479.0 PRK08887 PRK08887.1 164 164 174 equivalog Y Y N nicotinate-nicotinamide nucleotide adenylyltransferase 2.7.7.18 1236 Gammaproteobacteria class 1251 NCBI Protein Cluster (PRK) nicotinic acid mononucleotide adenylyltransferase nicotinate-nicotinamide nucleotide adenylyltransferase NF006507.0 PRK08943 PRK08943.1 337 337 322 subfamily Y Y N lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase 1236 Gammaproteobacteria class 7190 NCBI Protein Cluster (PRK) lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase Transfers myristate or laurate, activated on ACP, to the lipid IVA moiety of (KDO)2-(lauroyl)-lipid IVA NF006510.0 PRK08947 PRK08947.1 519 519 387 equivalog Y Y N acetyl-CoA C-acyltransferase FadA fadA 2.3.1.16 GO:0003988,GO:0006631 2191949,368024,6350283,7012144 1236 Gammaproteobacteria class 9879 NCBI Protein Cluster (PRK) 3-ketoacyl-CoA thiolase acetyl-CoA C-acyltransferase FadA NF006511.0 PRK08951 PRK08951.1 173 173 190 subfamily Y N N malate synthase 1236 Gammaproteobacteria class 1059 NCBI Protein Cluster (PRK) malate synthase malate synthase NF006516.0 PRK08963 PRK08963.1 560 560 436 equivalog Y Y N acetyl-CoA C-acyltransferase FadI fadI 2.3.1.16 12270828,12535077 1236 Gammaproteobacteria class 8081 NCBI Protein Cluster (PRK) 3-ketoacyl-CoA thiolase acetyl-CoA C-acyltransferase FadI NF006525.0 PRK08979 PRK08979.1 1084 1084 572 equivalog Y Y N acetolactate synthase 3 large subunit 1236 Gammaproteobacteria class 5055 NCBI Protein Cluster (PRK) acetolactate synthase 3 catalytic subunit acetolactate synthase 3 large subunit NF006528.0 PRK08993 PRK08993.1 430 430 253 subfamily Y Y N 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD kduD 1.1.1.127 1236 Gammaproteobacteria class 4635 NCBI Protein Cluster (PRK) 2-deoxy-D-gluconate 3-dehydrogenase 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD NF006531.0 PRK09004 PRK09004.1 158 158 146 equivalog Y Y N FMN-binding protein MioC mioC GO:0010181 1236 Gammaproteobacteria class 5060 NCBI Protein Cluster (PRK) FMN-binding protein MioC FMN-binding protein MioC NF006532.0 PRK09009 PRK09009.1 330 330 235 equivalog Y Y N SDR family oxidoreductase GO:0016491 1236 Gammaproteobacteria class 2034 NCBI Protein Cluster (PRK) C factor cell-cell signaling protein SDR family oxidoreductase NF006533.0 PRK09010 PRK09010.1 260 260 177 subfamily Y Y N single-stranded DNA-binding protein 15576682 1236 Gammaproteobacteria class 4688 NCBI Protein Cluster (PRK) single-stranded DNA-binding protein single-stranded DNA-binding protein NF006536.0 PRK09019 PRK09019.1 142 142 108 equivalog Y Y N stress response translation initiation inhibitor YciH yciH 1236 Gammaproteobacteria class 4276 NCBI Protein Cluster (PRK) translation initiation factor Sui1 stress response translation initiation inhibitor YciH NF006539.0 PRK09029 PRK09029.1 494 494 458 equivalog Y Y N o-succinylbenzoate--CoA ligase menE 6.2.1.26 GO:0005524,GO:0008756,GO:0009234 1236 Gammaproteobacteria class 11122 NCBI Protein Cluster (PRK) O-succinylbenzoic acid--CoA ligase o-succinylbenzoate--CoA ligase NF006570.0 PRK09084 PRK09084.1 455 455 452 equivalog Y Y N lysine-sensitive aspartokinase 3 lysC 2.7.2.4 GO:0004072,GO:0009089 1236 Gammaproteobacteria class 8086 NCBI Protein Cluster (PRK) aspartate kinase III lysine-sensitive aspartokinase 3 NF006735.0 PRK09267 PRK09267.1-1 315 315 176 equivalog Y Y N flavodoxin FldA fldA 1236 Gammaproteobacteria class 1853 NCBI Protein Cluster (PRK) flavodoxin FldA flavodoxin FldA NF006736.0 PRK09267 PRK09267.1-2 202 202 161 equivalog Y Y N flavodoxin FldA fldA 1236 Gammaproteobacteria class 2215 NCBI Protein Cluster (PRK) flavodoxin FldA flavodoxin FldA NF006737.0 PRK09267 PRK09267.1-3 238 238 174 equivalog Y Y N flavodoxin FldA fldA 1236 Gammaproteobacteria class 2940 NCBI Protein Cluster (PRK) flavodoxin FldA flavodoxin FldA NF006745.0 PRK09270 PRK09270.1-4 228 228 246 equivalog Y Y N nucleoside/nucleotide kinase family protein 1236 Gammaproteobacteria class 2312 NCBI Protein Cluster (PRK) nucleoside triphosphate hydrolase domain-containing protein nucleoside/nucleotide kinase family protein NF006838.0 PRK09357 PRK09357.1-3 644 644 423 equivalog Y Y N dihydroorotase 3.5.2.3 GO:0004151,GO:0006221,GO:0046872 1236 Gammaproteobacteria class 3051 NCBI Protein Cluster (PRK) dihydroorotase dihydroorotase NF006846.0 PRK09358 PRK09358.1-1 459 459 333 equivalog Y Y N adenosine deaminase add 3.5.4.4 GO:0004000,GO:0009168 1236 Gammaproteobacteria class 7600 NCBI Protein Cluster (PRK) adenosine deaminase adenosine deaminase NF006919.0 PRK09410 PRK09410.1-1 702 702 465 equivalog Y Y N PTS ascorbate transporter subunit IIC ulaA 2.7.1.194 25686089 1236 Gammaproteobacteria class 3584 NCBI Protein Cluster (PRK) PTS system ascorbate-specific transporter subunit IIC PTS ascorbate transporter subunit IIC gene synonym: sgaT NF006928.0 PRK09413 PRK09413.1 229 229 121 subfamily Y N N IS2 repressor TnpA 1236 Gammaproteobacteria class 4236 NCBI Protein Cluster (PRK) IS2 repressor TnpA IS2 repressor TnpA NF006957.0 PRK09434 PRK09434.1 294 294 309 equivalog Y Y N aminoimidazole riboside kinase GO:0016301 12486071 1236 Gammaproteobacteria class 8133 NCBI Protein Cluster (PRK) aminoimidazole riboside kinase aminoimidazole riboside kinase Phosphorylates aminoimidazole ribotide (AIR) which forms 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) NF006966.0 PRK09440 PRK09440.1-4 640 640 417 equivalog Y Y N valine--pyruvate transaminase 2.6.1.66 1236 Gammaproteobacteria class 6527 NCBI Protein Cluster (PRK) valine--pyruvate transaminase valine--pyruvate transaminase NF006978.0 PRK09450 PRK09450.1-2 1035 1035 841 equivalog Y Y N class I adenylate cyclase 4.6.1.1 1236 Gammaproteobacteria class 6160 NCBI Protein Cluster (PRK) adenylate cyclase class I adenylate cyclase NF006983.0 PRK09450 PRK09450.2-3 1810 1810 949 equivalog Y Y N class I adenylate cyclase 4.6.1.1 GO:0004016,GO:0006171 1236 Gammaproteobacteria class 1998 NCBI Protein Cluster (PRK) adenylate cyclase class I adenylate cyclase NF006984.0 PRK09450 PRK09450.2-4 1300 1300 956 equivalog Y Y N class I adenylate cyclase 4.6.1.1 1236 Gammaproteobacteria class 148 NCBI Protein Cluster (PRK) adenylate cyclase class I adenylate cyclase NF006985.0 PRK09450 PRK09450.2-5 1866 1866 951 equivalog Y Y N class I adenylate cyclase 4.6.1.1 1236 Gammaproteobacteria class 501 NCBI Protein Cluster (PRK) adenylate cyclase class I adenylate cyclase NF006986.0 PRK09451 PRK09451.1 725 725 456 equivalog Y Y N bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU glmU GO:0000287,GO:0000902,GO:0003977,GO:0006048,GO:0009252,GO:0019134 11173485,11329257 1236 Gammaproteobacteria class 7742 NCBI Protein Cluster (PRK) bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU Catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis NF006987.0 PRK09452 PRK09452.1 482 482 378 equivalog Y Y N spermidine/putrescine ABC transporter ATP-binding protein PotA potA 7.6.2.- GO:0005524,GO:0015846,GO:0016020,GO:0022857,GO:0043190 10585849,7592703,8366082 1236 Gammaproteobacteria class 4962 NCBI Protein Cluster (PRK) putrescine/spermidine ABC transporter ATPase protein spermidine/putrescine ABC transporter ATP-binding protein PotA NF006990.0 PRK09455 PRK09455.1 368 368 319 equivalog Y Y N sigma-E factor regulatory protein RseB rseB 1236 Gammaproteobacteria class 3657 NCBI Protein Cluster (PRK) anti-sigma E factor sigma-E factor regulatory protein RseB Interacts with the C-terminal domain of RseA and stimulates RseA binding to sigmaE via the cytoplasmic RseA N-terminal domain which then sequesters sigmaE in the membrane thereby preventing sigmaE associated with core RNAP NF006993.0 PRK09458 PRK09458.1 90 90 75 equivalog Y Y N envelope stress response membrane protein PspB pspB GO:0009271 12562786,14594833,19775245,27698088 1236 Gammaproteobacteria class 2330 NCBI Protein Cluster (PRK) phage shock protein B envelope stress response membrane protein PspB DNA-binding transcriptional regulator; acts together with PspC to induce psp operon during infection with phage, exposure to ethanol or osmotic shock; forms a complex with PspA and C; PspC is required for PspAB binding NF007001.0 PRK09464 PRK09464.1 330 330 254 equivalog Y Y N pyruvate dehydrogenase complex transcriptional repressor PdhR pdhR 8262214 1236 Gammaproteobacteria class 2420 NCBI Protein Cluster (PRK) transcriptional regulator PdhR pyruvate dehydrogenase complex transcriptional repressor PdhR Activates lctPRD operon; autoregulates itself through repression of pdhR-aceEF-lpdA operon NF007002.0 PRK09465 PRK09465.1 495 495 460 equivalog Y Y N outer membrane channel protein TolC tolC GO:0015562,GO:0055085 10879525,25893523,9044294 1236 Gammaproteobacteria class 6013 NCBI Protein Cluster (PRK) outer membrane channel protein outer membrane channel protein TolC Trimeric outer membrane protein involved in efflux of hydrophobic/amphipathic molecules; functions with a number of efflux systems in the inner membrane to transport molecules out of the cell NF007004.0 PRK09467 PRK09467.1 415 415 440 equivalog Y Y N two-component system sensor histidine kinase EnvZ envZ 2.7.13.3 GO:0000155,GO:0007165,GO:0016020,GO:0016310 10426948,24813471,2824492,9409762,9817206 1236 Gammaproteobacteria class 5453 NCBI Protein Cluster (PRK) osmolarity sensor protein two-component system sensor histidine kinase EnvZ Membrane-localized osmosensor; histidine kinase; in high osmolarity EnvZ autophosphorylates itself and transfers phosphoryl group to OmpR NF007007.0 PRK09470 PRK09470.1 486 486 463 equivalog Y Y N envelope stress sensor histidine kinase CpxA cpxA 3.6.1.- GO:0000155,GO:0007165 15576781,15629938,3058985 1236 Gammaproteobacteria class 4523 NCBI Protein Cluster (PRK) two-component sensor protein envelope stress sensor histidine kinase CpxA Part of two-component CpxA/CpxR system; senses envelope stress; upregulates a number of periplasmic folding and trafficking factors NF007011.0 PRK09474 PRK09474.1 291 291 396 equivalog Y Y N maltose/maltodextrin ABC transporter substrate-binding protein MalE malE 7.5.2.1 GO:0008643,GO:0015144,GO:0055085 1420181,2002054,2155217,8226895 1236 Gammaproteobacteria class 5100 NCBI Protein Cluster (PRK) maltose ABC transporter periplasmic protein maltose/maltodextrin ABC transporter substrate-binding protein MalE Functions in the MalKFGE ABC transporter complex to transport maltose into the cell by using ATP hydrolysis NF007016.1 PRK09481 PRK09481.1 314 314 209 equivalog Y Y N stringent starvation protein SspA sspA GO:0005515,GO:0006749 12777805,12791143,8022275,8198564 1236 Gammaproteobacteria class 2751 NCBI Protein Cluster (PRK) stringent starvation protein A stringent starvation protein SspA NF007017.0 PRK09482 PRK09482.1 261 261 257 equivalog Y Y N flap endonuclease Xni xni 3.1.-.- GO:0003677,GO:0017108,GO:0033567 17567612,19000038,9592142 1236 Gammaproteobacteria class 7169 NCBI Protein Cluster (PRK) flap endonuclease-like protein flap endonuclease Xni NF007018.1 PRK09483 PRK09483.1 280 280 217 equivalog Y Y N UvrY/SirA/GacA family response regulator transcription factor uvrY GO:0000160,GO:0003677,GO:0006355 11022030 1236 Gammaproteobacteria class 4712 NCBI Protein Cluster (PRK) response regulator UvrY/SirA/GacA family response regulator transcription factor Part of a two-component system along with BarA that is needed for efficient switching between glycolytic and gluconeogenic carbon sources NF007021.0 PRK09487 PRK09487.1 180 180 129 equivalog Y Y N succinate dehydrogenase cytochrome b556 subunit sdhC cybA,dhsC 1.3.5.1 GO:0000104,GO:0006099,GO:0009055,GO:0016020,GO:0045273 1236 Gammaproteobacteria class 2002 NCBI Protein Cluster (PRK) succinate dehydrogenase cytochrome b556 large membrane subunit succinate dehydrogenase cytochrome b556 subunit NF007023.0 PRK09489 PRK09489.1 295 295 342 equivalog Y Y N 16S rRNA (guanine(1207)-N(2))-methyltransferase RsmC rsmC 2.1.1.172 GO:0003676,GO:0006364,GO:0008990 9873033 1236 Gammaproteobacteria class 7637 NCBI Protein Cluster (PRK) 16S ribosomal RNA m2G1207 methyltransferase 16S rRNA (guanine(1207)-N(2))-methyltransferase RsmC 16S rRNA M2G1207 methyltransferase; catalyzes the methylation of the N2 position of G1207 of the 16S rRNA NF007025.1 PRK09491 PRK09491.1 173 173 145 equivalog Y Y N ribosomal protein S18-alanine N-acetyltransferase rimI 2.3.1.266 GO:0006474,GO:0008080 2828880,6991870 1236 Gammaproteobacteria class 3027 NCBI Protein Cluster (PRK) ribosomal-protein-alanine N-acetyltransferase ribosomal protein S18-alanine N-acetyltransferase Alanine acetyltransferase that specifically acetylates ribosomal protein S18 NF007044.0 PRK09497 PRK09497.1 348 348 285 equivalog Y Y N spermidine/putrescine ABC transporter permease PotB potB 7.6.2.- GO:0016020,GO:0055085 10585849,7592703,8366082 1236 Gammaproteobacteria class 4212 NCBI Protein Cluster (PRK) spermidine/putrescine ABC transporter membrane protein spermidine/putrescine ABC transporter permease PotB NF007047.0 PRK09500 PRK09500.1 326 326 257 equivalog Y Y N spermidine/putrescine ABC transporter permease PotC potC 7.6.2.- GO:0055085 10585849,7592703,8366082 1236 Gammaproteobacteria class 3370 NCBI Protein Cluster (PRK) spermidine/putrescine ABC transporter membrane protein spermidine/putrescine ABC transporter permease PotC NF007051.0 PRK09505 PRK09505.1-1 864 864 686 equivalog Y Y N alpha-amylase 3.2.1.1 GO:0004556,GO:0009313,GO:0030980 1236 Gammaproteobacteria class 2261 NCBI Protein Cluster (PRK) alpha-amylase alpha-amylase NF007052.0 PRK09505 PRK09505.1-2 749 749 677 equivalog Y Y N alpha-amylase 3.2.1.1 GO:0004556 1236 Gammaproteobacteria class 8242 NCBI Protein Cluster (PRK) alpha-amylase alpha-amylase NF007059.0 PRK09505 PRK09505.2-4 865 865 683 equivalog Y Y N alpha-amylase 3.2.1.1 1236 Gammaproteobacteria class 7562 NCBI Protein Cluster (PRK) alpha-amylase alpha-amylase NF007060.0 PRK09505 PRK09505.2-5 790 790 690 equivalog Y Y N alpha-amylase 3.2.1.1 1236 Gammaproteobacteria class 8526 NCBI Protein Cluster (PRK) alpha-amylase alpha-amylase NF007061.0 PRK09506 PRK09506.1 1120 1120 825 equivalog Y Y N bifunctional glycosyl transferase/transpeptidase mrcB 2.4.99.28 GO:0008658,GO:0008955,GO:0009252,GO:0009274,GO:0046677 10037771,10217796,12057973,1885547 1236 Gammaproteobacteria class 5526 NCBI Protein Cluster (PRK) bifunctional glycosyl transferase/transpeptidase bifunctional glycosyl transferase/transpeptidase NF007063.1 PRK09508 PRK09508.1 262 262 307 equivalog Y Y N transcriptional regulator LeuO leuO GO:0003700,GO:0006355 10515950,26424466,3519576 1236 Gammaproteobacteria class 3595 NCBI Protein Cluster (PRK) leucine transcriptional activator transcriptional regulator LeuO Activator for leuABCD operon; member of LysR family of transcriptional Activators NF007064.0 PRK09509 PRK09509.1 447 447 300 equivalog Y Y N CDF family cation-efflux transporter FieF fieF GO:0006812,GO:0008324,GO:0016020,GO:0055085 15549269,16049012 1236 Gammaproteobacteria class 2971 NCBI Protein Cluster (PRK) ferrous iron efflux protein F CDF family cation-efflux transporter FieF FieF, a metal efflux transporter, is a member of the CDF (cation diffusion facilitator) family of transporters. NF007065.0 PRK09510 PRK09510.1 213 213 387 equivalog Y Y N cell envelope integrity protein TolA tolA GO:0016020,GO:0019534,GO:0043213 10404600,11418549,11703658,11994151,12670988,15866920 1236 Gammaproteobacteria class 9381 NCBI Protein Cluster (PRK) cell envelope integrity inner membrane protein TolA cell envelope integrity protein TolA Inner membrane component of 7 member Tol-Pal envelope-spanning complex; involved in maintaining cell envelope integrity; utilized by colicins and filamentous phages for import; interacts with TolB, Pal, and through TolB to various outer membrane porins NF007066.0 PRK09511 PRK09511.1 135 135 108 equivalog Y Y N nitrite reductase small subunit NirD nirD 11004182,1435259,2200672 1236 Gammaproteobacteria class 2774 NCBI Protein Cluster (PRK) nitrite reductase small subunit nitrite reductase small subunit NirD Involved in reducing nitrite to ammonium to detoxify nitrite accumulation in anaerobic nitrate-respiring cells and regenerate NAD+; bounds to NirB, the cytoplasmic subunit, whose expression is induced at high nitrate concentrations NF007068.0 PRK09513 PRK09513.1 432 432 312 equivalog Y Y N 1-phosphofructokinase fruK 2.7.1.56 GO:0008662,GO:0016773 1850730 1236 Gammaproteobacteria class 2358 NCBI Protein Cluster (PRK) 1-phosphofructokinase 1-phosphofructokinase Converts fructose-1-phosphate and ATP to fructose-1,6-bisphosphate and ADP; highly specific for fructose-1-phopshate NF007069.0 PRK09514 PRK09514.1 143 143 141 equivalog Y Y N Zn(2+)-responsive transcriptional regulator zntR GO:0003677,GO:0006355,GO:0008270 1236 Gammaproteobacteria class 3239 NCBI Protein Cluster (PRK) zinc-responsive transcriptional regulator Zn(2+)-responsive transcriptional regulator Mediates expression of the zinc export protein ZntA in response to high levels of zinc; member of MerR family of transcriptional regulators NF007075.0 PRK09526 PRK09526.1 340 340 358 subfamily Y Y N LacI family DNA-binding transcriptional regulator 1236 Gammaproteobacteria class 6197 NCBI Protein Cluster (PRK) lac repressor LacI family DNA-binding transcriptional regulator NF007090.0 PRK09544 PRK09544.1 306 306 251 equivalog Y Y N zinc ABC transporter ATP-binding protein ZnuC znuC 7.2.2.- GO:0005524,GO:0006829,GO:0015633 9680209 1236 Gammaproteobacteria class 7416 NCBI Protein Cluster (PRK) high-affinity zinc transporter ATPase zinc ABC transporter ATP-binding protein ZnuC NF007092.0 PRK09546 PRK09546.1 292 292 327 equivalog Y Y N zinc transporter ZntB zntB GO:0005385,GO:0005886,GO:0071577 1236 Gammaproteobacteria class 3189 NCBI Protein Cluster (PRK) zinc transporter zinc transporter ZntB NF007106.0 PRK09555 PRK09555.1 102 102 75 equivalog Y Y N ferrous iron transporter A feoA 1236 Gammaproteobacteria class 838 NCBI Protein Cluster (PRK) ferrous iron transport protein A ferrous iron transporter A NF007108.0 PRK09557 PRK09557.1 443 443 303 equivalog Y Y N fructokinase mak 2.7.1.4 1236 Gammaproteobacteria class 4627 NCBI Protein Cluster (PRK) fructokinase fructokinase NF007110.0 PRK09559 PRK09559.1 219 219 327 equivalog Y Y N tRNA-modifying protein YgfZ ygfZ GO:0005542,GO:0009451 1236 Gammaproteobacteria class 8836 NCBI Protein Cluster (PRK) putative global regulator tRNA-modifying protein YgfZ NF007133.0 PRK09579 PRK09579.1 1763 1763 1017 equivalog Y Y N multidrug efflux RND transporter permease subunit GO:0016020,GO:0022857,GO:0055085 1236 Gammaproteobacteria class 2489 NCBI Protein Cluster (PRK) multidrug efflux protein multidrug efflux RND transporter permease subunit NF007137.0 PRK09584 PRK09584.1 728 728 500 equivalog Y Y N dipeptide/tripeptide permease DtpA dtpA GO:0015833,GO:0016020,GO:0055085,GO:1904680 15175316,3037276,6090406 1236 Gammaproteobacteria class 3387 NCBI Protein Cluster (PRK) putative tripeptide transporter permease dipeptide/tripeptide permease DtpA NF007152.0 PRK09586 PRK09586.1 516 516 477 equivalog Y Y N PTS N-acetylmuramic acid transporter subunit IIBC murP 2.7.1.192 GO:0008982,GO:0009401,GO:0016020 15060041 1236 Gammaproteobacteria class 4784 NCBI Protein Cluster (PRK) PTS system N-acetylmuramic acid transporter subunits EIIBC PTS N-acetylmuramic acid transporter subunit IIBC Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF007198.0 PRK09619 PRK09619.1 267 267 218 equivalog Y Y N flagellar hook assembly protein FlgD flgD 1236 Gammaproteobacteria class 688 NCBI Protein Cluster (PRK) flagellar basal body rod modification protein flagellar hook assembly protein FlgD NF007239.0 PRK09674 PRK09674.1 371 371 257 equivalog Y Y N 2,3-dehydroadipyl-CoA hydratase PaaF paaF 4.2.1.17 20660314,9748275 1236 Gammaproteobacteria class 3746 NCBI Protein Cluster (PRK) enoyl-CoA hydratase-isomerase 2,3-dehydroadipyl-CoA hydratase PaaF NF007243.0 PRK09685 PRK09685.1 199 199 303 equivalog Y Y N transcriptional regulator FeaR feaR GO:0003700,GO:0006355,GO:0043565 1236 Gammaproteobacteria class 4724 NCBI Protein Cluster (PRK) DNA-binding transcriptional activator FeaR transcriptional regulator FeaR Activator of genes involved in phenylacetic acid catabolism NF007246.0 PRK09692 PRK09692.1 434 434 413 domain Y Y N integrase domain-containing protein GO:0003677,GO:0015074 1236 Gammaproteobacteria class 9003 NCBI Protein Cluster (PRK) integrase integrase domain-containing protein NF007251.0 PRK09698 PRK09698.1 253 253 304 equivalog Y Y N allose kinase alsK 2.7.1.55 GO:0019200,GO:0019316 1236 Gammaproteobacteria class 1954 NCBI Protein Cluster (PRK) D-allose kinase allose kinase NF007292.0 PRK09764 PRK09764.1 281 281 240 equivalog Y Y N GntR family transcriptional regulator 1236 Gammaproteobacteria class 1314 NCBI Protein Cluster (PRK) DNA-binding transcriptional repressor MngR GntR family transcriptional regulator NF007298.0 PRK09776 PRK09776.1 1135 1135 1111 equivalog Y Y N diguanylate cyclase 2.7.7.65 GO:0005515 1236 Gammaproteobacteria class 7476 NCBI Protein Cluster (PRK) putative diguanylate cyclase diguanylate cyclase NF007299.0 PRK09777 PRK09777.1 406 406 318 equivalog Y Y N Fe(3+) dicitrate ABC transporter permease subunit FecD fecD 7.2.2.- 10633096,12354617,12732308,16333751,16718597 1236 Gammaproteobacteria class 1497 NCBI Protein Cluster (PRK) iron-dicitrate transporter subunit FecD Fe(3+) dicitrate ABC transporter permease subunit FecD Part of the FecBCDE citrate-dependent iron (III) transport system NF007303.0 PRK09783 PRK09783.1 390 390 414 subfamily Y N N copper/silver efflux system membrane fusion protein CusB 1236 Gammaproteobacteria class 4495 NCBI Protein Cluster (PRK) copper/silver efflux system membrane fusion protein CusB copper/silver efflux system membrane fusion protein CusB NF007316.0 PRK09802 PRK09802.1 351 351 269 equivalog Y Y N DeoR family transcriptional regulator 1236 Gammaproteobacteria class 1685 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator AgaR DeoR family transcriptional regulator NF007330.0 PRK09818 PRK09818.1 277 277 183 equivalog Y Y N kinase inhibitor 1236 Gammaproteobacteria class 1099 NCBI Protein Cluster (PRK) putative kinase inhibitor kinase inhibitor NF007349.0 PRK09840 PRK09840.1 686 686 760 equivalog Y Y N catecholate siderophore receptor Fiu GO:0015344,GO:0015891 10411720,10806384,12949180,16718603,2407721,3072926 1236 Gammaproteobacteria class 6071 NCBI Protein Cluster (PRK) catecholate siderophore receptor Fiu catecholate siderophore receptor Fiu Porin involved in the uptake of iron complexed with catecholate siderophores (e.g. dihydroxybenzoylserine, dihydroxybenzoate) and beta lactam agents; Fiu interacts with TonB which provides the energy required for transport across the outer membrane; acts as a receptor for iron-siderophores and microcins E492, M, and H47; outer membrane protein NF007375.0 PRK09880 PRK09880.1 469 469 344 equivalog Y Y N L-idonate 5-dehydrogenase idnD 1.1.1.264 1236 Gammaproteobacteria class 1789 NCBI Protein Cluster (PRK) L-idonate 5-dehydrogenase L-idonate 5-dehydrogenase NF007376.0 PRK09881 PRK09881.1 434 434 298 equivalog Y Y N D,D-dipeptide ABC transporter permease ddpC 7.4.2.- GO:0016020,GO:0055085 1236 Gammaproteobacteria class 2130 NCBI Protein Cluster (PRK) D-ala-D-ala transporter subunit D,D-dipeptide ABC transporter permease NF007385.0 PRK09906 PRK09906.1 356 356 296 equivalog Y Y N DNA-binding transcriptional regulator HcaR hcaR 1236 Gammaproteobacteria class 1595 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator HcaR DNA-binding transcriptional regulator HcaR Activator of 3-phenylpropionic acid catabolism NF007387.0 PRK09908 PRK09908.1 212 212 159 equivalog Y Y N xanthine dehydrogenase iron sulfur-binding subunit XdhC xdhC 1.17.1.4 1236 Gammaproteobacteria class 944 NCBI Protein Cluster (PRK) xanthine dehydrogenase subunit XdhC xanthine dehydrogenase iron sulfur-binding subunit XdhC Iron-sulfur-binding subunit; with XdhA and XdhB participates in purine salvage NF007395.0 PRK09921 PRK09921.1 618 618 445 equivalog Y Y N D-serine transporter DsdX dsdX GO:0015128,GO:0016020,GO:0035429 3029015,3275618,7592420,9119199 1236 Gammaproteobacteria class 3354 NCBI Protein Cluster (PRK) permease DsdX D-serine transporter DsdX NF007404.0 PRK09936 PRK09936.1 344 344 296 equivalog Y Y N DUF4434 family protein 1236 Gammaproteobacteria class 1535 NCBI Protein Cluster (PRK) hypothetical protein DUF4434 family protein NF007408.0 PRK09943 PRK09943.1 211 211 185 equivalog Y Y N HTH-type transcriptional regulator PuuR puuR 1236 Gammaproteobacteria class 1398 NCBI Protein Cluster (PRK) DNA-binding transcriptional repressor PuuR HTH-type transcriptional regulator PuuR Regulates genes involved in putrescine degradation NF007412.0 PRK09950 PRK09950.1 647 647 536 equivalog Y Y N BCCT family transporter 16397293,7815937 1236 Gammaproteobacteria class 2674 NCBI Protein Cluster (PRK) putative transporter BCCT family transporter NF007413.0 PRK09951 PRK09951.1 349 349 222 subfamily Y N N hypothetical protein 1236 Gammaproteobacteria class 5263 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF007449.0 PRK10014 PRK10014.1 310 310 342 subfamily Y Y N Mal regulon transcriptional regulator MalI malI GO:0003677,GO:0006355 1236 Gammaproteobacteria class 5108 NCBI Protein Cluster (PRK) DNA-binding transcriptional repressor MalI Mal regulon transcriptional regulator MalI Regulates malXY which are involved in maltose-glucose transport NF007455.0 PRK10022 PRK10022.1 167 167 169 equivalog Y N N putative DNA-binding transcriptional regulator 1236 Gammaproteobacteria class 967 NCBI Protein Cluster (PRK) putative DNA-binding transcriptional regulator putative DNA-binding transcriptional regulator NF007463.0 PRK10040 PRK10040.1-2 93 93 58 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 135 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF007468.0 PRK10049 PRK10049.1 1043 1043 817 equivalog Y Y N poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA pgaA GO:1901515 15916613,16923806,16997959,17526692 1236 Gammaproteobacteria class 6648 NCBI Protein Cluster (PRK) outer membrane protein PgaA poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA Outer membrane protein essential for the synthesis of poly-beta-1,6-N-acetyl-D-glucosamine (PGA); adhesin required for biofilm formation; PgaA (HmsH) seems to translocate and/or dock PGA to the cell surface NF007491.0 PRK10086 PRK10086.1 316 316 313 equivalog Y Y N DNA-binding transcriptional regulator DsdC dsdC GO:0003700,GO:0006355 1236 Gammaproteobacteria class 4869 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator DsdC DNA-binding transcriptional regulator DsdC Regulates the synthesis and expression of the dsdXA operon and dadA gene NF007492.0 PRK10089 PRK10089.1-1 150 150 110 equivalog Y Y N tRNA-binding protein 1236 Gammaproteobacteria class 1281 NCBI Protein Cluster (PRK) tRNA-binding protein tRNA-binding protein NF007528.0 PRK10141 PRK10141.1 97 97 117 subfamily Y Y N metalloregulator ArsR/SmtB family transcription factor GO:0003700,GO:0006355 1236 Gammaproteobacteria class 9032 NCBI Protein Cluster (PRK) DNA-binding transcriptional repressor ArsR metalloregulator ArsR/SmtB family transcription factor NF007540.1 PRK10153 PRK10153.1 400 400 516 equivalog Y Y N lysine decarboxylation/transport transcriptional activator CadC cadC GO:0000160,GO:0003677,GO:0006355 16491024,24946151 1236 Gammaproteobacteria class 4777 NCBI Protein Cluster (PRK) DNA-binding transcriptional activator CadC lysine decarboxylation/transport transcriptional activator CadC CadC, a transcriptional activator of the cadAB operon, is membrane-associated, with a single transmembrane span. In response to acid stress and the presence of sufficient lysine, it undergoes a cleavage and then activates expression of the lysine decarboxylase CadA and the lysine-cadaverine antiporter CadB. NF007543.0 PRK10158 PRK10158.1 286 286 219 equivalog Y Y N bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA rluA 5.4.99.28,5.4.99.29 GO:0001522,GO:0003723,GO:0009451,GO:0009982 1236 Gammaproteobacteria class 5563 NCBI Protein Cluster (PRK) 23S rRNA/tRNA pseudouridine synthase A bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA Catalyzes the synthesis of pseudouridine from uracil-746 in 23S ribosomal RNA and from uracil-32 in the anticodon stem and loop of transfer RNAs NF007545.0 PRK10160 PRK10160.1 342 342 275 equivalog Y Y N taurine ABC transporter permease TauC tauC 7.2.2.- GO:0015411,GO:0016020,GO:0055085 1236 Gammaproteobacteria class 6274 NCBI Protein Cluster (PRK) taurine transporter subunit taurine ABC transporter permease TauC NF007553.0 PRK10173 PRK10173.1 425 425 413 equivalog Y Y N bifunctional glucose-1-phosphatase/inositol phosphatase agp 3.1.3.10,3.1.3.8 1236 Gammaproteobacteria class 5693 NCBI Protein Cluster (PRK) glucose-1-phosphatase/inositol phosphatase bifunctional glucose-1-phosphatase/inositol phosphatase NF007561.0 PRK10188 PRK10188.1 235 235 240 equivalog Y Y N transcriptional regulator SdiA sdiA GO:0003677,GO:0006355 1236 Gammaproteobacteria class 2463 NCBI Protein Cluster (PRK) DNA-binding transcriptional activator SdiA transcriptional regulator SdiA Regulates genes involved in cell division NF007571.0 PRK10202 PRK10202.1 146 146 149 equivalog Y Y N beta-galactosidase subunit beta 3.2.1.23 12868605,3939707,3939708,4124306 1236 Gammaproteobacteria class 2343 NCBI Protein Cluster (PRK) cryptic beta-D-galactosidase subunit beta beta-galactosidase subunit beta NF007581.0 PRK10216 PRK10216.1 314 314 319 equivalog Y Y N HTH-type transcriptional regulator YidZ yidZ GO:0003700,GO:0006355 1236 Gammaproteobacteria class 3917 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator YidZ HTH-type transcriptional regulator YidZ Involved in anaerobic NO protection NF007591.0 PRK10229 PRK10229.1 288 288 206 equivalog Y Y N threonine export protein RhtC rhtC GO:0006865 1236 Gammaproteobacteria class 2316 NCBI Protein Cluster (PRK) threonine efflux system threonine export protein RhtC NF007592.0 PRK10234 PRK10234.1 148 148 121 equivalog Y Y N transcriptional regulator GutM gutM 1236 Gammaproteobacteria class 1678 NCBI Protein Cluster (PRK) DNA-binding transcriptional activator GutM transcriptional regulator GutM Regulator for glucitol utilization NF007618.0 PRK10266 PRK10266.1 403 403 306 equivalog Y Y N curved DNA-binding protein cbpA GO:0006457,GO:0051082 1236 Gammaproteobacteria class 2759 NCBI Protein Cluster (PRK) curved DNA-binding protein CbpA curved DNA-binding protein Functional analog of DnaJ; co-chaperone with DnaK, molecular chaperone in an adaptive response to environmental stresses other than heat shock NF007623.0 PRK10279 PRK10279.1 272 272 301 equivalog Y Y N patatin-like phospholipase RssA rssA GO:0004622,GO:0006629 1236 Gammaproteobacteria class 3476 NCBI Protein Cluster (PRK) hypothetical protein patatin-like phospholipase RssA NF007624.0 PRK10280 PRK10280.1 944 944 681 equivalog Y Y N peptidyl-dipeptidase Dcp dcp 3.4.15.5 GO:0006508,GO:0008237 1236 Gammaproteobacteria class 9935 NCBI Protein Cluster (PRK) dipeptidyl carboxypeptidase II peptidyl-dipeptidase Dcp NF007644.0 PRK10314 PRK10314.1 171 171 153 equivalog Y Y N GNAT family N-acetyltransferase 2.3.1.- 1236 Gammaproteobacteria class 4044 NCBI Protein Cluster (PRK) putative acyltransferase GNAT family N-acetyltransferase NF007654.0 PRK10324 PRK10324.1 158 158 113 equivalog Y Y N ribosome-associated translation inhibitor RaiA raiA 1236 Gammaproteobacteria class 1109 NCBI Protein Cluster (PRK) translation inhibitor protein RaiA ribosome-associated translation inhibitor RaiA Associated with 30S ribosomal subunit; interferes with translation elongation NF007664.1 PRK10337 PRK10337.1 475 475 442 equivalog Y Y N quorum sensing histidine kinase QseC qseC 2.7.13.3 GO:0000155,GO:0007165 11929534,26426681,28396353,35464966 1236 Gammaproteobacteria class 6101 NCBI Protein Cluster (PRK) sensor protein QseC quorum sensing histidine kinase QseC NF007665.0 PRK10339 PRK10339.1 330 330 327 equivalog Y Y N transcriptional regulator EbgR ebgR 1236 Gammaproteobacteria class 2648 NCBI Protein Cluster (PRK) DNA-binding transcriptional repressor EbgR transcriptional regulator EbgR NF007672.0 PRK10347 PRK10347.1 181 181 200 equivalog Y Y N putative adenosine monophosphate-protein transferase Fic 1236 Gammaproteobacteria class 3648 NCBI Protein Cluster (PRK) cell filamentation protein Fic putative adenosine monophosphate-protein transferase Fic NF007673.0 PRK10348 PRK10348.1 148 148 133 equivalog Y Y N ribosome-associated heat shock protein Hsp15 hslR 1236 Gammaproteobacteria class 4542 NCBI Protein Cluster (PRK) ribosome-associated heat shock protein Hsp15 ribosome-associated heat shock protein Hsp15 NF007679.0 PRK10354 PRK10354.1 130 130 70 subfamily Y Y N RNA chaperone/antiterminator CspA cspA 1236 Gammaproteobacteria class 1134 NCBI Protein Cluster (PRK) RNA chaperone/anti-terminator RNA chaperone/antiterminator CspA NF007683.0 PRK10358 PRK10358.1 282 282 157 equivalog Y Y N tRNA (uridine(34)/cytosine(34)/5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase TrmL trmL 2.1.1.-,2.1.1.207 GO:0001510,GO:0008173 11763972,16848900,8265370 1236 Gammaproteobacteria class 2287 NCBI Protein Cluster (PRK) putative rRNA methylase tRNA (uridine(34)/cytosine(34)/5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase TrmL NF007685.0 PRK10360 PRK10360.1 258 258 196 equivalog Y Y N transcriptional regulator UhpA uhpA GO:0003677,GO:0006355 1236 Gammaproteobacteria class 2004 NCBI Protein Cluster (PRK) DNA-binding transcriptional activator UhpA transcriptional regulator UhpA Response regulator in two-component regulatory system wtih UhpB; phosphorylated UhpA is a positive activator uhpT, a hexose phosphates transporter NF007690.0 PRK10367 PRK10367.1 409 409 441 equivalog Y Y N MATE family efflux transporter DinF dinF GO:0015297,GO:0016020,GO:0042910,GO:0055085 1236 Gammaproteobacteria class 7788 NCBI Protein Cluster (PRK) DNA-damage-inducible SOS response protein MATE family efflux transporter DinF NF007696.0 PRK10377 PRK10377.1 165 165 121 equivalog Y Y N PTS glucitol/sorbitol transporter subunit IIA srlB gutB 2.7.1.198 1236 Gammaproteobacteria class 1392 NCBI Protein Cluster (PRK) PTS system glucitol/sorbitol-specific transporter subunit IIA PTS glucitol/sorbitol transporter subunit IIA Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF007698.0 PRK10380 PRK10380.1 61 61 63 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 804 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF007701.0 PRK10386 PRK10386.1 137 137 129 equivalog Y Y N curli production assembly/transport protein CsgE csgE 11823641,16420357,16522795,8817489,9383186 1236 Gammaproteobacteria class 1559 NCBI Protein Cluster (PRK) curli assembly protein CsgE curli production assembly/transport protein CsgE chaperone-like protein that participates in the polymerization of curlin (CsgA) subunits into curli; part of the curli secretion and assembly protein complex NF007704.0 PRK10396 PRK10396.1 149 149 221 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 4534 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF007711.0 PRK10408 PRK10408.1 124 124 112 equivalog Y Y N L-valine transporter subunit YgaH ygaH 17463081 1236 Gammaproteobacteria class 1555 NCBI Protein Cluster (PRK) putative L-valine exporter L-valine transporter subunit YgaH NF007715.0 PRK10410 PRK10410.1-3 179 179 132 equivalog Y Y N nitrous oxide-stimulated promoter family protein 1236 Gammaproteobacteria class 1264 NCBI Protein Cluster (PRK) hypothetical protein nitrous oxide-stimulated promoter family protein NF007721.0 PRK10413 PRK10413.1 115 115 87 equivalog Y Y N hydrogenase maturation factor HybG hybG 1236 Gammaproteobacteria class 706 NCBI Protein Cluster (PRK) hydrogenase 2 accessory protein HypG hydrogenase maturation factor HybG NF007740.0 PRK10420 PRK10420.1 918 918 551 equivalog Y Y N L-lactate permease lldP GO:0005886,GO:0015129,GO:0015727 1236 Gammaproteobacteria class 4176 NCBI Protein Cluster (PRK) L-lactate permease L-lactate permease gene synonym: lctP NF007741.0 PRK10421 PRK10421.1 311 311 262 equivalog Y Y N transcriptional regulator LldR lldR GO:0003700,GO:0006355 1236 Gammaproteobacteria class 3108 NCBI Protein Cluster (PRK) DNA-binding transcriptional repressor LldR transcriptional regulator LldR Represses the lctPRD operon NF007745.0 PRK10425 PRK10425.1 395 395 260 equivalog Y Y N 3'-5' ssDNA/RNA exonuclease TatD tatD 3.1.11.1 GO:0008408 1236 Gammaproteobacteria class 4393 NCBI Protein Cluster (PRK) DNase TatD 3'-5' ssDNA/RNA exonuclease TatD Magnesium dependent; involved in quality control of mutated Tat exported substrates; not involved in the Sec-independent protein export system NF007747.0 PRK10427 PRK10427.1 153 153 114 equivalog Y Y N PTS fructose-like transporter subunit IIB 2.7.1.- 1236 Gammaproteobacteria class 806 NCBI Protein Cluster (PRK) putative PTS system fructose-like transporter subunit EIIB PTS fructose-like transporter subunit IIB Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF007748.0 PRK10428 PRK10428.1 113 113 69 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 796 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF007752.0 PRK10433 PRK10433.1 212 212 228 equivalog Y Y N tRNA/rRNA methyltransferase 2.1.1.- 1236 Gammaproteobacteria class 4511 NCBI Protein Cluster (PRK) putative RNA methyltransferase tRNA/rRNA methyltransferase NF007753.0 PRK10434 PRK10434.1 312 312 257 equivalog Y Y N DNA-binding transcriptional repressor 1236 Gammaproteobacteria class 1473 NCBI Protein Cluster (PRK) DNA-bindng transcriptional repressor SrlR DNA-binding transcriptional repressor NF007754.0 PRK10435 PRK10435.1 585 585 443 equivalog Y Y N cadaverine/lysine antiporter cadB GO:0043872 14982633,16877381,16885318,17209032,8808945 1236 Gammaproteobacteria class 1691 NCBI Protein Cluster (PRK) lysine/cadaverine antiporter cadaverine/lysine antiporter Antiporter protein responsible for lysine import and cadaverine export; member of the lysine-dependent acid resistance system 4 (AR4) NF007762.0 PRK10444 PRK10444.1 368 368 250 equivalog Y Y N HAD-IIA family hydrolase 1236 Gammaproteobacteria class 1464 NCBI Protein Cluster (PRK) UMP phosphatase HAD-IIA family hydrolase NF007767.1 PRK10452 PRK10452.1 122 122 120 equivalog Y Y N multidrug/spermidine efflux SMR transporter subunit MdtJ mdtJ GO:0015606,GO:0015848,GO:0016020 1236 Gammaproteobacteria class 1949 NCBI Protein Cluster (PRK) multidrug efflux system protein MdtJ multidrug/spermidine efflux SMR transporter subunit MdtJ NF007770.0 PRK10456 PRK10456.1 521 521 344 equivalog Y Y N arginine N-succinyltransferase astA 2.3.1.109 GO:0006527,GO:0008791 1236 Gammaproteobacteria class 3594 NCBI Protein Cluster (PRK) arginine succinyltransferase arginine N-succinyltransferase NF007772.0 PRK10458 PRK10458.1 710 710 472 subfamily Y N N DNA cytosine methylase 1236 Gammaproteobacteria class 5751 NCBI Protein Cluster (PRK) DNA cytosine methylase DNA cytosine methylase NF007775.0 PRK10463 PRK10463.1 385 385 290 equivalog Y Y N hydrogenase nickel incorporation protein HypB hypB 3.6.5.- GO:0003924,GO:0016151,GO:0051604 1236 Gammaproteobacteria class 5677 NCBI Protein Cluster (PRK) hydrogenase nickel incorporation protein HypB hydrogenase nickel incorporation protein HypB GTP hydrolase involved in nickel liganding into hydrogenases NF007776.0 PRK10465 PRK10465.1 188 188 162 equivalog Y Y N hydrogenase-2 assembly chaperone hybE 1236 Gammaproteobacteria class 2188 NCBI Protein Cluster (PRK) hydrogenase 2-specific chaperone hydrogenase-2 assembly chaperone NF007777.0 PRK10466 PRK10466.1 190 190 164 equivalog Y Y N HyaD/HybD family hydrogenase maturation endopeptidase 3.4.23.- 1236 Gammaproteobacteria class 1817 NCBI Protein Cluster (PRK) hydrogenase 2 maturation endopeptidase HyaD/HybD family hydrogenase maturation endopeptidase NF007778.0 PRK10467 PRK10467.1 969 969 567 equivalog Y Y N hydrogenase 2 large subunit hybC GO:0008901 25368299 1236 Gammaproteobacteria class 2425 NCBI Protein Cluster (PRK) hydrogenase 2 large subunit hydrogenase 2 large subunit NF007779.0 PRK10468 PRK10468.1 659 659 372 equivalog Y Y N hydrogenase 2 small subunit hybO 25368299 1236 Gammaproteobacteria class 1520 NCBI Protein Cluster (PRK) hydrogenase 2 small subunit hydrogenase 2 small subunit NF007780.0 PRK10470 PRK10470.1 125 125 95 equivalog Y Y N ribosome hibernation promoting factor hpf GO:0044238 1236 Gammaproteobacteria class 1901 NCBI Protein Cluster (PRK) ribosome hibernation promoting factor HPF ribosome hibernation promoting factor NF007781.0 PRK10472 PRK10472.1 625 625 446 equivalog Y Y N gluconate transporter gntU GO:0015128,GO:0016020,GO:0035429 1236 Gammaproteobacteria class 2876 NCBI Protein Cluster (PRK) low affinity gluconate transporter gluconate transporter NF007782.0 PRK10473 PRK10473.1 417 417 394 subfamily Y Y N MdtL family multidrug efflux MFS transporter 1236 Gammaproteobacteria class 5846 NCBI Protein Cluster (PRK) multidrug efflux system protein MdtL MdtL family multidrug efflux MFS transporter MdtL, as found in E. coli K-12, is a multidrug efflux transporter from the major facilitator superfamily (MFS). NF007789.0 PRK10483 PRK10483.1 515 515 414 equivalog Y Y N tryptophan permease mtr GO:0005886,GO:0015173,GO:0015801 1236 Gammaproteobacteria class 5082 NCBI Protein Cluster (PRK) tryptophan permease tryptophan permease NF007791.0 PRK10486 PRK10486.1 135 135 96 equivalog Y Y N (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase lsrG 5.3.1.32 1236 Gammaproteobacteria class 1120 NCBI Protein Cluster (PRK) autoinducer-2 (AI-2) modifying protein LsrG (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase NF007794.0 PRK10494 PRK10494.1 205 205 259 equivalog Y Y N envelope biogenesis factor ElyC elyC 24391520 1236 Gammaproteobacteria class 5858 NCBI Protein Cluster (PRK) hypothetical protein envelope biogenesis factor ElyC NF007802.0 PRK10508 PRK10508.1 540 540 335 equivalog Y Y N luciferase-like monooxygenase GO:0016705 1236 Gammaproteobacteria class 4533 NCBI Protein Cluster (PRK) hypothetical protein luciferase-like monooxygenase NF007804.1 PRK10510 PRK10510.1 307 307 219 equivalog Y Y N OmpA family lipoprotein GO:0009279 1236 Gammaproteobacteria class 1954 NCBI Protein Cluster (PRK) putative outer membrane lipoprotein OmpA family lipoprotein NF007816.0 PRK10525 PRK10525.1 511 511 318 equivalog Y Y N cytochrome o ubiquinol oxidase subunit II cyoA 7.1.1.- GO:0004129,GO:0022900 1236 Gammaproteobacteria class 2262 NCBI Protein Cluster (PRK) cytochrome o ubiquinol oxidase subunit II cytochrome o ubiquinol oxidase subunit II NF007817.0 PRK10526 PRK10526.1 481 481 286 equivalog Y Y N acyl-CoA thioesterase II tesB 3.1.2.20 1236 Gammaproteobacteria class 2577 NCBI Protein Cluster (PRK) acyl-CoA thioesterase II acyl-CoA thioesterase II NF007819.1 PRK10528 PRK10528.1 270 270 210 equivalog Y Y N multifunctional acyl-CoA thioesterase I/protease I/lysophospholipase L1 tesA 3.1.1.5,3.1.2.14,3.1.2.2 GO:0006629,GO:0016298 1236 Gammaproteobacteria class 3186 NCBI Protein Cluster (PRK) multifunctional acyl-CoA thioesterase I and protease I and lysophospholipase L1 multifunctional acyl-CoA thioesterase I/protease I/lysophospholipase L1 gene synonym: apeA NF007821.0 PRK10530 PRK10530.1 274 274 272 equivalog Y Y N pyridoxal phosphatase 3.1.3.74 GO:0016787 1236 Gammaproteobacteria class 4714 NCBI Protein Cluster (PRK) pyridoxal phosphate (PLP) phosphatase pyridoxal phosphatase NF007822.0 PRK10531 PRK10531.1 436 436 430 equivalog Y Y N putative acyl-CoA thioester hydrolase GO:0030599,GO:0042545 1236 Gammaproteobacteria class 4074 NCBI Protein Cluster (PRK) acyl-CoA thioesterase putative acyl-CoA thioester hydrolase NF007833.0 PRK10545 PRK10545.1 367 367 289 equivalog Y Y N excinuclease Cho cho 3.1.25.- 1236 Gammaproteobacteria class 3889 NCBI Protein Cluster (PRK) nucleotide excision repair endonuclease excinuclease Cho 3' incision activity; acts with UvrC NF007838.0 PRK10550 PRK10550.1 395 395 312 equivalog Y Y N tRNA dihydrouridine(16) synthase DusC dusC 1.3.1.- GO:0002943,GO:0017150,GO:0050660 1236 Gammaproteobacteria class 7422 NCBI Protein Cluster (PRK) tRNA-dihydrouridine synthase C tRNA dihydrouridine(16) synthase DusC NF007844.0 PRK10556 PRK10556.1-2 204 204 116 equivalog Y Y N DUF2002 family protein 1236 Gammaproteobacteria class 746 NCBI Protein Cluster (PRK) hypothetical protein DUF2002 family protein NF007846.0 PRK10556 PRK10556.1-4 222 222 114 equivalog Y Y N DUF2002 family protein 1236 Gammaproteobacteria class 579 NCBI Protein Cluster (PRK) hypothetical protein DUF2002 family protein NF007855.0 PRK10564 PRK10564.1 295 295 303 equivalog Y Y N maltose operon protein MalM malM GO:0008643,GO:0042597 1236 Gammaproteobacteria class 3781 NCBI Protein Cluster (PRK) maltose regulon periplasmic protein maltose operon protein MalM NF007859.0 PRK10569 PRK10569.1 225 225 191 equivalog Y Y N NADPH-dependent FMN reductase ssuE 1.5.1.38 GO:0008752,GO:0046306 1236 Gammaproteobacteria class 3998 NCBI Protein Cluster (PRK) NAD(P)H-dependent FMN reductase NADPH-dependent FMN reductase NF007860.0 PRK10572 PRK10572.1 208 208 292 equivalog Y Y N arabinose operon transcriptional regulator AraC araC GO:0003700,GO:0006355,GO:0043565 1236 Gammaproteobacteria class 3006 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator AraC arabinose operon transcriptional regulator AraC Positive and negative regulator; regulates the araBAD and araFGH operons and other genes involved in the transport and catabolism of L-arabinose NF007862.0 PRK10574 PRK10574.1 138 138 145 equivalog Y Y N prepilin peptidase-dependent pilin ppdD 1236 Gammaproteobacteria class 3291 NCBI Protein Cluster (PRK) putative major pilin subunit prepilin peptidase-dependent pilin NF007877.0 PRK10581 PRK10581.1 321 321 299 equivalog Y Y N (2E,6E)-farnesyl diphosphate synthase ispA 2.5.1.10 GO:0008299 1236 Gammaproteobacteria class 9062 NCBI Protein Cluster (PRK) geranyltranstransferase (2E,6E)-farnesyl diphosphate synthase NF007878.0 PRK10582 PRK10582.1 144 144 109 equivalog Y Y N cytochrome o ubiquinol oxidase subunit IV 7.1.1.- 1236 Gammaproteobacteria class 1302 NCBI Protein Cluster (PRK) cytochrome o ubiquinol oxidase subunit IV cytochrome o ubiquinol oxidase subunit IV NF007894.1 PRK10598 PRK10598.1 186 186 186 equivalog Y Y N lipoprotein 1236 Gammaproteobacteria class 2644 NCBI Protein Cluster (PRK) lipoprotein lipoprotein NF007897.0 PRK10602 PRK10602.1 157 157 237 equivalog Y Y N murein tripeptide amidase MpaA mpaA GO:0004181,GO:0006508,GO:0008270 1236 Gammaproteobacteria class 4453 NCBI Protein Cluster (PRK) murein peptide amidase A murein tripeptide amidase MpaA NF007898.0 PRK10604 PRK10604.1 478 478 433 equivalog Y Y N two-component system sensor histidine kinase RstB rstB 2.7.13.3 GO:0000155,GO:0007165,GO:0016020,GO:0016310 1236 Gammaproteobacteria class 5064 NCBI Protein Cluster (PRK) sensor protein RstB two-component system sensor histidine kinase RstB NF007921.0 PRK10636 PRK10636.1 917 917 638 equivalog Y Y N ABC transporter ATP-binding protein GO:0005524 1236 Gammaproteobacteria class 8978 NCBI Protein Cluster (PRK) putative ABC transporter ATP-binding protein ABC transporter ATP-binding protein NF007930.0 PRK10645 PRK10645.1 145 145 114 equivalog Y Y N divalent cation tolerance protein CutA cutA 12949080,7623666 1236 Gammaproteobacteria class 1380 NCBI Protein Cluster (PRK) divalent-cation tolerance protein CutA divalent cation tolerance protein CutA Copper binding protein required for copper tolerance; involved in resistance toward heavy metals NF007933.0 PRK10649 PRK10649.1 404 404 577 subfamily Y Y N phosphoethanolamine transferase CptA cptA 1236 Gammaproteobacteria class 4415 NCBI Protein Cluster (PRK) hypothetical protein phosphoethanolamine transferase CptA NF007934.1 PRK10650 PRK10650.1 103 103 109 equivalog Y Y N multidrug/spermidine efflux SMR transporter subunit MdtI mdtI 1236 Gammaproteobacteria class 1891 NCBI Protein Cluster (PRK) multidrug efflux system protein MdtI multidrug/spermidine efflux SMR transporter subunit MdtI NF007937.0 PRK10654 PRK10654.1 513 513 455 equivalog Y Y N anaerobic C4-dicarboxylate transporter DcuC dcuC GO:0015556,GO:0015740 1236 Gammaproteobacteria class 4418 NCBI Protein Cluster (PRK) C4-dicarboxylate transporter DcuC anaerobic C4-dicarboxylate transporter DcuC Functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate NF007944.0 PRK10663 PRK10663.1 340 340 204 equivalog Y Y N cytochrome o ubiquinol oxidase subunit III 7.1.1.- GO:0004129,GO:0022904 1236 Gammaproteobacteria class 2146 NCBI Protein Cluster (PRK) cytochrome o ubiquinol oxidase subunit III cytochrome o ubiquinol oxidase subunit III NF007945.0 PRK10664 PRK10664.1 157 157 90 equivalog Y Y N nucleoid-associated protein HU-beta hupB 20010798 1236 Gammaproteobacteria class 1034 NCBI Protein Cluster (PRK) transcriptional regulator HU subunit beta nucleoid-associated protein HU-beta Histone-like DNA-binding protein NF007960.0 PRK10680 PRK10680.1 509 509 411 equivalog Y Y N molybdopterin molybdotransferase MoeA moeA 2.10.1.1 GO:0006777,GO:0032324 17198377 1236 Gammaproteobacteria class 10835 NCBI Protein Cluster (PRK) molybdopterin biosynthesis protein MoeA molybdopterin molybdotransferase MoeA Involved in the formation of active molybdenum cofactor and the chelation of molybdenum NF007965.0 PRK10687 PRK10687.1 206 206 119 equivalog Y Y N purine nucleoside phosphoramidase hinT 3.9.1.- 1236 Gammaproteobacteria class 2354 NCBI Protein Cluster (PRK) purine nucleoside phosphoramidase purine nucleoside phosphoramidase NF007967.0 PRK10691 PRK10691.1 201 201 219 equivalog Y Y N fumarylacetoacetate hydrolase family protein GO:0003824 1236 Gammaproteobacteria class 6930 NCBI Protein Cluster (PRK) hypothetical protein fumarylacetoacetate hydrolase family protein NF007971.0 PRK10695 PRK10695.1 824 824 875 equivalog Y Y N YdbH family protein 34781743 1236 Gammaproteobacteria class 10756 NCBI Protein Cluster (PRK) hypothetical protein YdbH family protein NF007977.0 PRK10701 PRK10701.1 330 330 241 equivalog Y Y N two-component system response regulator RstA rstA GO:0000160,GO:0003677,GO:0006355 1236 Gammaproteobacteria class 2851 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator RstA two-component system response regulator RstA Response regulator in two-component regulatory system with RstB NF007978.0 PRK10702 PRK10702.1 405 405 211 equivalog Y Y N endonuclease III nth 4.2.99.18 GO:0003906,GO:0006284 1236 Gammaproteobacteria class 4473 NCBI Protein Cluster (PRK) endonuclease III endonuclease III DNA-(apurinic or apyrimidinic site) lyase; has apurinic or apyrimidinic endonuclease activity and DNA N-glycosylase activity; removed damaged DNA at cytosines, thymines and guanines NF007979.0 PRK10703 PRK10703.1 501 501 341 equivalog Y Y N HTH-type transcriptional repressor PurR purR GO:0003677,GO:0006355 1236 Gammaproteobacteria class 2189 NCBI Protein Cluster (PRK) DNA-binding transcriptional repressor PurR HTH-type transcriptional repressor PurR Binds to the purF operator and coregulates other genes for de novo purine nucleotide synthesis; is involved in regulation of purB, purC, purEK, purHD, purL, purMN and guaBA expression; Binds hypoxanthine and guanine as inducers NF007984.0 PRK10712 PRK10712.1 793 793 563 equivalog Y Y N PTS fructose transporter subunit IIBC fruA 2.7.1.- GO:0008982,GO:0009401,GO:0022877 1236 Gammaproteobacteria class 8234 NCBI Protein Cluster (PRK) PTS system fructose-specific transporter subunits IIBC PTS fructose transporter subunit IIBC Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF007986.1 PRK10714 PRK10714.1 529 529 316 equivalog Y Y N undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase arnC 2.4.2.53 GO:0016780 1236 Gammaproteobacteria class 4071 NCBI Protein Cluster (PRK) undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase Catalyzes the transfer of 4-deoxy-4-formamido-L-arabinose from UDP to undecaprenyl phosphate NF008003.0 PRK10729 PRK10729.1 248 248 210 equivalog Y Y N ADP-ribose diphosphatase nudF 3.6.1.13 GO:0016787,GO:0046872 1236 Gammaproteobacteria class 5171 NCBI Protein Cluster (PRK) ADP-ribose pyrophosphatase NudF ADP-ribose diphosphatase NF008004.0 PRK10733 PRK10733.1 1008 1008 644 equivalog Y Y N ATP-dependent zinc metalloprotease FtsH ftsH 3.4.24.- GO:0004176,GO:0004222,GO:0006508 12037319,12176385 1236 Gammaproteobacteria class 5960 NCBI Protein Cluster (PRK) ATP-dependent metalloprotease ATP-dependent zinc metalloprotease FtsH NF008008.0 PRK10737 PRK10737.1 174 174 196 equivalog Y Y N peptidylprolyl isomerase slyD 5.2.1.8 GO:0003755 1236 Gammaproteobacteria class 3791 NCBI Protein Cluster (PRK) FKBP-type peptidyl-prolyl cis-trans isomerase peptidylprolyl isomerase NF008010.0 PRK10739 PRK10739.1 215 215 197 equivalog Y Y N YhgN family NAAT transporter GO:0016020 1236 Gammaproteobacteria class 2586 NCBI Protein Cluster (PRK) putative antibiotic transporter YhgN family NAAT transporter NF008015.0 PRK10745 PRK10745.1 883 883 622 equivalog Y Y N low affinity potassium transporter Kup kup GO:0015079,GO:0016020 1236 Gammaproteobacteria class 3282 NCBI Protein Cluster (PRK) potassium transport protein Kup low affinity potassium transporter Kup NF008018.0 PRK10748 PRK10748.1 225 225 238 equivalog Y Y N 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB yigB 3.1.3.104 16990279 1236 Gammaproteobacteria class 4951 NCBI Protein Cluster (PRK) flavin mononucleotide phosphatase 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB NF008021.0 PRK10751 PRK10751.1 204 204 174 equivalog Y Y N molybdopterin-guanine dinucleotide biosynthesis protein MobB mobB GO:0005525,GO:0006777 12682065 1236 Gammaproteobacteria class 5285 NCBI Protein Cluster (PRK) molybdopterin-guanine dinucleotide biosynthesis protein B molybdopterin-guanine dinucleotide biosynthesis protein MobB NF008023.0 PRK10753 PRK10753.1 162 162 90 equivalog Y Y N nucleoid-associated protein HU-alpha hupA 20010798 1236 Gammaproteobacteria class 485 NCBI Protein Cluster (PRK) transcriptional regulator HU subunit alpha nucleoid-associated protein HU-alpha Histone-like DNA-binding protein NF008026.0 PRK10756 PRK10756.1 241 241 157 equivalog Y Y N protein CreA creA 18375564 1236 Gammaproteobacteria class 1728 NCBI Protein Cluster (PRK) hypothetical protein protein CreA NF008027.1 PRK10757 PRK10757.1 332 332 267 equivalog Y Y N inositol-1-monophosphatase suhB 3.1.3.25 GO:0008934,GO:0046854 10747806,32871103 1236 Gammaproteobacteria class 3841 NCBI Protein Cluster (PRK) inositol monophosphatase inositol-1-monophosphatase gene synonym: ssyA, Nus factor SuhB NF008028.1 PRK10759 PRK10759.1 117 117 106 equivalog Y Y N YfiM family lipoprotein 1236 Gammaproteobacteria class 2288 NCBI Protein Cluster (PRK) lipoprotein YfiM family lipoprotein NF008029.0 PRK10760 PRK10760.1 449 449 359 equivalog Y Y N lytic murein transglycosylase B mltB 4.2.2.- 1236 Gammaproteobacteria class 4192 NCBI Protein Cluster (PRK) murein hydrolase B lytic murein transglycosylase B Membrane-bound lytic murein transglycosylase B; catalyzes the cleavage of the glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycan NF008031.0 PRK10763 PRK10763.1 369 369 290 equivalog Y Y N phospholipase A pldA GO:0004620,GO:0006629 1236 Gammaproteobacteria class 2320 NCBI Protein Cluster (PRK) phospholipase A phospholipase A NF008034.0 PRK10766 PRK10766.1 275 275 231 equivalog Y Y N two-component system response regulator TorR torR 1236 Gammaproteobacteria class 1702 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator TorR two-component system response regulator TorR Response regulator in two-component regulatory system with TorS; involved in regulation of trimethylamine N-oxide reductase genes NF008038.0 PRK10770 PRK10770.1 394 394 431 equivalog Y Y N peptidylprolyl isomerase SurA surA GO:0003755,GO:0006457,GO:0030288,GO:0042277,GO:0043165,GO:0050821,GO:0051082,GO:0060274 1236 Gammaproteobacteria class 6554 NCBI Protein Cluster (PRK) peptidyl-prolyl cis-trans isomerase SurA peptidylprolyl isomerase SurA NF008039.0 PRK10771 PRK10771.1 298 298 234 equivalog Y Y N thiamine ABC transporter ATP-binding protein ThiQ thiQ 7.6.2.- 1236 Gammaproteobacteria class 4888 NCBI Protein Cluster (PRK) thiamine transporter ATP-binding subunit thiamine ABC transporter ATP-binding protein ThiQ NF008041.0 PRK10773 PRK10773.1 551 551 453 equivalog Y Y N UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase murF 6.3.2.10 GO:0005524,GO:0009058,GO:0047480,GO:0071555 1236 Gammaproteobacteria class 7276 NCBI Protein Cluster (PRK) UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase NF008042.0 PRK10774 PRK10774.1 493 493 405 equivalog Y Y N cell division protein FtsW ftsW GO:0051301 1236 Gammaproteobacteria class 4164 NCBI Protein Cluster (PRK) cell division protein FtsW cell division protein FtsW Integral membrane protein involved in stabilizing FstZ ring during cell division NF008044.0 PRK10776 PRK10776.1 148 148 130 equivalog Y Y N 8-oxo-dGTP diphosphatase MutT mutT 3.6.1.55 GO:0006281,GO:0008413 1236 Gammaproteobacteria class 3565 NCBI Protein Cluster (PRK) nucleoside triphosphate pyrophosphohydrolase 8-oxo-dGTP diphosphatase MutT NF008045.0 PRK10778 PRK10778.1 289 289 151 equivalog Y Y N RNA polymerase-binding protein DksA dksA 22904284 1236 Gammaproteobacteria class 764 NCBI Protein Cluster (PRK) RNA polymerase-binding transcription factor RNA polymerase-binding protein DksA NF008046.0 PRK10779 PRK10779.1 477 477 450 equivalog Y Y N sigma E protease regulator RseP rseP 3.4.24.- GO:0004222,GO:0005515,GO:0006508,GO:0016020 1236 Gammaproteobacteria class 9723 NCBI Protein Cluster (PRK) zinc metallopeptidase RseP sigma E protease regulator RseP Catalyzes the cleavage of RseA which activates the sigmaE-mediated stress response NF008051.0 PRK10785 PRK10785.1 568 568 607 equivalog Y Y N maltodextrin glucosidase malZ 3.2.1.20 GO:0004558,GO:0005975 1236 Gammaproteobacteria class 8972 NCBI Protein Cluster (PRK) maltodextrin glucosidase maltodextrin glucosidase NF008052.0 PRK10786 PRK10786.1 500 500 367 equivalog Y Y N bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD ribD GO:0008270,GO:0008703,GO:0008835,GO:0050661 1236 Gammaproteobacteria class 7509 NCBI Protein Cluster (PRK) bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD Riboflavin biosynthesis protein which catalyzes the deamination and reduction steps in the riboflavin biosynthesis pathway; catalyzes the formation of 5-amino-6-(5-phosphoribosylamino)uracil from 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine and the formation of 5-amino-6-(5-phosphoribosylamino)uracil from 5-amino-6-(5-phosphoribitylamino)uracil NF008054.0 PRK10788 PRK10788.1 493 493 626 equivalog Y Y N peptidylprolyl isomerase ppiD 5.2.1.8 GO:0003755 1236 Gammaproteobacteria class 8775 NCBI Protein Cluster (PRK) periplasmic folding chaperone peptidylprolyl isomerase NF008060.0 PRK10794 PRK10794.1 590 590 370 equivalog Y Y N peptidoglycan glycosyltransferase MrdB mrdB rodA 2.4.99.28 2644207,27643381 1236 Gammaproteobacteria class 1677 NCBI Protein Cluster (PRK) cell wall shape-determining protein peptidoglycan glycosyltransferase MrdB rod shape-determining protein RodA NF008069.0 PRK10805 PRK10805.1 440 440 285 equivalog Y Y N formate transporter FocA focA 1236 Gammaproteobacteria class 2235 NCBI Protein Cluster (PRK) formate transporter formate transporter FocA NF008071.1 PRK10808 PRK10808.1 277 277 358 equivalog Y Y N porin OmpA ompA GO:0015288 1370823,16079137,323051,330500,7517935 1236 Gammaproteobacteria class 5306 NCBI Protein Cluster (PRK) outer membrane protein A porin OmpA Involved in diffusion of nonspecific small solutes across the outer membrane; is known to play a role as a phage receptor, a mediator of F-factor dependent conjugation, and in maintaining the structural shape of the outer membrane NF008074.0 PRK10811 PRK10811.1 908 908 1068 equivalog Y Y N ribonuclease E rne 3.1.26.12 GO:0003723,GO:0006396,GO:0008995 1236 Gammaproteobacteria class 25322 NCBI Protein Cluster (PRK) ribonuclease E ribonuclease E NF008076.0 PRK10814 PRK10814.1 473 473 399 exception Y Y N lipoprotein-releasing ABC transporter permease subunit LolC lolC GO:0016020,GO:0042953 1236 Gammaproteobacteria class 5259 NCBI Protein Cluster (PRK) outer membrane-specific lipoprotein transporter subunit LolC lipoprotein-releasing ABC transporter permease subunit LolC NF008079.0 PRK10818 PRK10818.1 508 508 270 equivalog Y Y N septum site-determining protein MinD minD 1236 Gammaproteobacteria class 1469 NCBI Protein Cluster (PRK) cell division inhibitor MinD septum site-determining protein MinD ATPase; with MinC inhibits cell division by blocking formation of the polar Z ring septums NF008085.0 PRK10820 PRK10820.1 576 576 520 equivalog Y Y N transcriptional regulator TyrR tyrR GO:0006355,GO:0008134 1236 Gammaproteobacteria class 5870 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator TyrR transcriptional regulator TyrR Regulates genes involved in the biosynthesis and transport of aromatic amino acids NF008086.0 PRK10824 PRK10824.1 205 205 115 equivalog Y Y N Grx4 family monothiol glutaredoxin GO:0016491 1236 Gammaproteobacteria class 2031 NCBI Protein Cluster (PRK) glutaredoxin-4 Grx4 family monothiol glutaredoxin NF008088.0 PRK10828 PRK10828.1 183 183 183 equivalog Y Y N NAD(P)H nitroreductase GO:0016491 1236 Gammaproteobacteria class 6664 NCBI Protein Cluster (PRK) putative oxidoreductase NAD(P)H nitroreductase NF008090.0 PRK10832 PRK10832.1 304 304 182 equivalog Y Y N CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase pgsA 2.7.8.5 1236 Gammaproteobacteria class 1219 NCBI Protein Cluster (PRK) phosphatidylglycerophosphate synthetase CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase NF008091.0 PRK10833 PRK10833.1 412 412 618 equivalog Y Y N outer membrane assembly protein AsmA asmA 1236 Gammaproteobacteria class 8521 NCBI Protein Cluster (PRK) putative assembly protein outer membrane assembly protein AsmA NF008097.0 PRK10839 PRK10839.1 275 275 232 equivalog Y Y N 16S rRNA pseudouridine(516) synthase RsuA rsuA 5.4.99.19 1236 Gammaproteobacteria class 5794 NCBI Protein Cluster (PRK) 16S rRNA pseudouridylate synthase A 16S rRNA pseudouridine(516) synthase RsuA Catalyzes the synthesis pseudouridine from uracil-516 in 16S ribosomal RNA NF008104.0 PRK10850 PRK10850.1 153 153 85 equivalog Y Y N phosphocarrier protein Hpr ptsH 1236 Gammaproteobacteria class 531 NCBI Protein Cluster (PRK) PTS system phosphohistidinoprotein-hexose phosphotransferase subunit Hpr phosphocarrier protein Hpr NF008109.0 PRK10856 PRK10856.1 208 208 334 equivalog Y Y N cytoskeleton protein RodZ rodZ GO:0003677,GO:0008360,GO:0016020 1236 Gammaproteobacteria class 6704 NCBI Protein Cluster (PRK) cytoskeletal protein RodZ cytoskeleton protein RodZ NF008110.0 PRK10857 PRK10857.1 275 275 164 equivalog Y Y N Fe-S cluster assembly transcriptional regulator IscR iscR 1236 Gammaproteobacteria class 1228 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator IscR Fe-S cluster assembly transcriptional regulator IscR Regulates the expression of the iscRSUA operon NF008111.0 PRK10858 PRK10858.1 202 202 112 equivalog Y Y N nitrogen regulatory protein P-II glnB 10760266,12218023,12366843,8293810,8843440 1236 Gammaproteobacteria class 1191 NCBI Protein Cluster (PRK) nitrogen regulatory protein P-II 1 nitrogen regulatory protein P-II Indirectly regulates nitrogen metabolism; at high nitrogen levels P-II prevents the phosphorylation of NR-I, the transcriptional activator of the glutamine synthetase gene (glnA); at low nitrogen levels P-II is uridylylated to form PII-UMP and interacts with an adenylyltransferase (GlnE) that activates GlnA NF008114.0 PRK10861 PRK10861.1 277 277 324 equivalog Y Y N signal peptidase I lepB 3.4.21.89 GO:0004252,GO:0006465 1236 Gammaproteobacteria class 3367 NCBI Protein Cluster (PRK) signal peptidase I signal peptidase I NF008117.0 PRK10864 PRK10864.1 267 267 344 equivalog Y Y N tRNA/rRNA methyltransferase 2.1.1.- GO:0003723,GO:0006396,GO:0008173 1236 Gammaproteobacteria class 4028 NCBI Protein Cluster (PRK) putative methyltransferase tRNA/rRNA methyltransferase NF008123.1 PRK10871 PRK10871.1 311 311 365 equivalog Y Y N murein hydrolase activator NlpD nlpD 15513925,8132457 1236 Gammaproteobacteria class 4997 NCBI Protein Cluster (PRK) lipoprotein NlpD murein hydrolase activator NlpD Outer membrane lipoprotein involved in stationary-phase cell survival NF008124.0 PRK10872 PRK10872.1 728 728 744 equivalog Y Y N GTP diphosphokinase relA 2.7.6.5 GO:0015969 1236 Gammaproteobacteria class 9107 NCBI Protein Cluster (PRK) (p)ppGpp synthetase I/GTP pyrophosphokinase GTP diphosphokinase (p)ppGpp synthetase; catalyzes the formation of pppGpp and ppGpp from ATP and GTP or GDP NF008127.0 PRK10875 PRK10875.1 671 671 619 equivalog Y Y N exodeoxyribonuclease V subunit alpha recD GO:0004386,GO:0006302,GO:0006310,GO:0008854,GO:0009338 1236 Gammaproteobacteria class 10372 NCBI Protein Cluster (PRK) exonuclease V subunit alpha exodeoxyribonuclease V subunit alpha Helicase/nuclease; with RecBC catalyzes the exonucleolytic cleavage of DNA; RecD has 5' to 3' helicase activity NF008129.0 PRK10877 PRK10877.1 215 215 237 equivalog Y Y N bifunctional protein-disulfide isomerase/oxidoreductase DsbC dsbC 5.3.4.1 GO:0042597 10391895,10841975,7536035,7830566,8168498,8645242 1236 Gammaproteobacteria class 5596 NCBI Protein Cluster (PRK) protein disulfide isomerase II DsbC bifunctional protein-disulfide isomerase/oxidoreductase DsbC NF008132.0 PRK10880 PRK10880.1 427 427 351 equivalog Y Y N A/G-specific adenine glycosylase mutY 3.2.2.31 GO:0006281,GO:0019104 1236 Gammaproteobacteria class 13956 NCBI Protein Cluster (PRK) adenine DNA glycosylase A/G-specific adenine glycosylase NF008133.1 PRK10881 PRK10881.1 450 450 377 equivalog Y Y N Ni/Fe-hydrogenase cytochrome b subunit hybB 1.12.99.6 10224080,11506918,8021226,9738917 1236 Gammaproteobacteria class 1858 NCBI Protein Cluster (PRK) putative hydrogenase 2 b cytochrome subunit Ni/Fe-hydrogenase cytochrome b subunit Cytochrome b subunit of the hydrogenase 2 enzyme, composed of HybA, B, C, and O subunits NF008134.0 PRK10882 PRK10882.1 263 263 329 equivalog Y Y N hydrogenase 2 operon protein HybA hybA 1.12.99.6 25368299 1236 Gammaproteobacteria class 2372 NCBI Protein Cluster (PRK) hydrogenase 2 protein HybA hydrogenase 2 operon protein HybA Fe-S ferrodoxin type component; participates in the periplasmic electron-transferring activity of hydrogenase 2 NF008141.0 PRK10892 PRK10892.1 505 505 328 equivalog Y Y N arabinose-5-phosphate isomerase KdsD kdsD 5.3.1.13 GO:0016853,GO:0097367,GO:1901135 1236 Gammaproteobacteria class 3005 NCBI Protein Cluster (PRK) D-arabinose 5-phosphate isomerase arabinose-5-phosphate isomerase KdsD NF008144.0 PRK10895 PRK10895.1 381 381 241 equivalog Y Y N LPS export ABC transporter ATP-binding protein lptB 7.5.2.5 GO:0005524,GO:0043190,GO:0055085 1236 Gammaproteobacteria class 4616 NCBI Protein Cluster (PRK) lipopolysaccharide ABC transporter ATP-binding protein LPS export ABC transporter ATP-binding protein NF008145.0 PRK10896 PRK10896.1 221 221 161 equivalog Y Y N PTS IIA-like nitrogen regulatory protein PtsN ptsN 1236 Gammaproteobacteria class 1276 NCBI Protein Cluster (PRK) PTS system sugar transporter subunit IIA PTS IIA-like nitrogen regulatory protein PtsN Involved in nitrogen metabolism; protein IIA is phosphorylated by enzyme I(Ntr) NF008146.0 PRK10897 PRK10897.1 119 119 90 equivalog Y Y N PTS phosphocarrier protein NPr npr 1236 Gammaproteobacteria class 874 NCBI Protein Cluster (PRK) phosphohistidinoprotein-hexose phosphotransferase component of N-regulated PTS system (Npr) PTS phosphocarrier protein NPr NF008147.1 PRK10898 PRK10898.1 408 408 352 equivalog Y Y N outer membrane-stress sensor serine endopeptidase DegS degS 3.4.21.107 GO:0004252,GO:0006508 1236 Gammaproteobacteria class 3990 NCBI Protein Cluster (PRK) serine endoprotease outer membrane-stress sensor serine endopeptidase DegS NF008150.0 PRK10902 PRK10902.1 215 215 271 equivalog Y Y N FKBP-type peptidyl-prolyl cis-trans isomerase fkpA 5.2.1.8 GO:0003755,GO:0006457 1236 Gammaproteobacteria class 4461 NCBI Protein Cluster (PRK) FKBP-type peptidyl-prolyl cis-trans isomerase FKBP-type peptidyl-prolyl cis-trans isomerase NF008154.0 PRK10906 PRK10906.1 331 331 252 equivalog Y Y N DeoR/GlpR family transcriptional regulator 1236 Gammaproteobacteria class 4009 NCBI Protein Cluster (PRK) DNA-binding transcriptional repressor GlpR DeoR/GlpR family transcriptional regulator NF008159.0 PRK10911 PRK10911.1 927 927 680 equivalog Y Y N oligopeptidase A prlC 3.4.24.70 GO:0004222,GO:0006508 1236 Gammaproteobacteria class 15798 NCBI Protein Cluster (PRK) oligopeptidase A oligopeptidase A NF008162.0 PRK10916 PRK10916.1 569 569 348 equivalog Y Y N ADP-heptose--LPS heptosyltransferase RfaF rfaF GO:0009103,GO:0016757 1236 Gammaproteobacteria class 4170 NCBI Protein Cluster (PRK) ADP-heptose:LPS heptosyltransferase II ADP-heptose--LPS heptosyltransferase RfaF Catalyzes the transfer of the second heptose to the heptosyl-KDO2 moiety of the lipopolysaccharide inner core NF008172.0 PRK10919 PRK10919.1 1168 1168 673 equivalog Y Y N DNA helicase Rep rep 3.6.4.12 GO:0003678,GO:0006268 1236 Gammaproteobacteria class 6236 NCBI Protein Cluster (PRK) ATP-dependent DNA helicase Rep DNA helicase Rep Single-stranded DNA-dependent ATPase; initiates unwinding at a nick in the DNA; involved in DNA replication NF008173.0 PRK10920 PRK10920.1 313 313 390 equivalog Y Y N uroporphyrinogen-III C-methyltransferase hemX 2.1.1.107 1236 Gammaproteobacteria class 5779 NCBI Protein Cluster (PRK) putative uroporphyrinogen III C-methyltransferase uroporphyrinogen-III C-methyltransferase NF008177.0 PRK10925 PRK10925.1 363 363 206 equivalog Y Y N superoxide dismutase [Mn] sodA 1.15.1.1 GO:0004784,GO:0006801 1236 Gammaproteobacteria class 2162 NCBI Protein Cluster (PRK) superoxide dismutase superoxide dismutase [Mn] NF008180.0 PRK10929 PRK10929.1 809 809 1109 equivalog Y Y N miniconductance mechanosensitive channel MscM mscM GO:0016020,GO:0055085 1236 Gammaproteobacteria class 6764 NCBI Protein Cluster (PRK) putative mechanosensitive channel protein miniconductance mechanosensitive channel MscM NF008184.0 PRK10935 PRK10935.1 553 553 565 equivalog Y Y N nitrate/nitrite two-component system sensor histidine kinase NarQ narQ 2.7.13.3 GO:0000155,GO:0000160,GO:0016020,GO:0046983 1236 Gammaproteobacteria class 6501 NCBI Protein Cluster (PRK) nitrate/nitrite sensor protein NarQ nitrate/nitrite two-component system sensor histidine kinase NarQ NF008186.0 PRK10938 PRK10938.1 459 459 490 equivalog Y Y N molybdate ABC transporter ATP-binding protein ModF modF GO:0005524 1236 Gammaproteobacteria class 9569 NCBI Protein Cluster (PRK) putative molybdenum transport ATP-binding protein ModF molybdate ABC transporter ATP-binding protein ModF NF008195.0 PRK10949 PRK10949.1 746 746 618 equivalog Y Y N signal peptide peptidase SppA sppA 3.4.21.- GO:0006465,GO:0008233 3522590,6378913,7018496,7020700,7040383 1236 Gammaproteobacteria class 6143 NCBI Protein Cluster (PRK) protease 4 signal peptide peptidase SppA NF008202.0 PRK10959 PRK10959.1 287 287 212 equivalog Y Y N outer membrane protein OmpW ompW GO:0019867 1236 Gammaproteobacteria class 3638 NCBI Protein Cluster (PRK) outer membrane protein W outer membrane protein OmpW NF008203.0 PRK10963 PRK10963.1 254 254 234 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 2706 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF008204.0 PRK10964 PRK10964.1 437 437 322 equivalog Y Y N lipopolysaccharide heptosyltransferase RfaC rfaC 2.4.-.- GO:0008920,GO:0009244 1236 Gammaproteobacteria class 6191 NCBI Protein Cluster (PRK) ADP-heptose:LPS heptosyl transferase I lipopolysaccharide heptosyltransferase RfaC NF008208.0 PRK10971 PRK10971.1 415 415 277 equivalog Y Y N sulfate/thiosulfate ABC transporter permease CysT cysT 7.3.2.- GO:0015419,GO:0016020,GO:0055085,GO:1902358 1236 Gammaproteobacteria class 2555 NCBI Protein Cluster (PRK) sulfate/thiosulfate transporter subunit sulfate/thiosulfate ABC transporter permease CysT NF008209.0 PRK10972 PRK10972.1 96 96 109 equivalog Y Y N cell division protein ZapA zapA 12368265 1236 Gammaproteobacteria class 934 NCBI Protein Cluster (PRK) Z-ring-associated protein cell division protein ZapA This protein is cell division protein ZapA (Z-ring associated protein A). NF008212.0 PRK10975 PRK10975.1 219 219 232 equivalog Y Y N dTDP-4-amino-4,6-dideoxy-D-galactose acyltransferase rffC wecD 2.3.1.210 GO:0008080 1236 Gammaproteobacteria class 4544 NCBI Protein Cluster (PRK) TDP-fucosamine acetyltransferase dTDP-4-amino-4,6-dideoxy-D-galactose acyltransferase null NF008217.0 PRK10984 PRK10984.1 117 117 133 equivalog Y Y N sigma factor-binding protein Crl crl GO:0045893 1236 Gammaproteobacteria class 2631 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator Crl sigma factor-binding protein Crl NF008219.0 PRK10987 PRK10987.1 238 238 285 equivalog Y Y N beta-lactamase regulator AmpE ampE 1236 Gammaproteobacteria class 4100 NCBI Protein Cluster (PRK) regulatory protein AmpE beta-lactamase regulator AmpE Involved in regulation of beta-lactamase; putative signaling protein NF008230.0 PRK10997 PRK10997.1 500 500 487 equivalog Y Y N ATPase RavA stimulator ViaA viaA 1236 Gammaproteobacteria class 6848 NCBI Protein Cluster (PRK) hypothetical protein ATPase RavA stimulator ViaA Stimulates the ATPase activity of RavA NF008231.0 PRK10998 PRK10998.1 261 261 296 equivalog Y Y N maltose ABC transporter permease MalG malG 7.5.2.1 GO:0016020,GO:0055085 1236 Gammaproteobacteria class 2940 NCBI Protein Cluster (PRK) maltose transporter permease maltose ABC transporter permease MalG Functions in the MalKFGE ABC transporter complex to transport maltose into the cell by using ATP hydrolysis NF008232.0 PRK10999 PRK10999.1 392 392 520 equivalog Y Y N maltose ABC transporter permease MalF malF 7.5.2.1 GO:0043190,GO:0055085 1236 Gammaproteobacteria class 6728 NCBI Protein Cluster (PRK) maltose transporter membrane protein maltose ABC transporter permease MalF Functions in the MalKFGE ABC transporter complex to transport maltose into the cell by using ATP hydrolysis NF008233.0 PRK11000 PRK11000.1 568 568 369 equivalog Y Y N maltose/maltodextrin ABC transporter ATP-binding protein MalK malK 7.5.2.1 GO:0005524,GO:0008643,GO:0043190,GO:0055085,GO:0140359 1236 Gammaproteobacteria class 2820 NCBI Protein Cluster (PRK) maltose/maltodextrin transporter ATP-binding protein maltose/maltodextrin ABC transporter ATP-binding protein MalK Functions in the MalKFGE ABC transporter complex to transport maltose into the cell by using ATP hydrolysis NF008234.1 PRK11001 PRK11001.1 149 149 170 subfamily Y Y N MltR family transcriptional regulator 1236 Gammaproteobacteria class 2443 NCBI Protein Cluster (PRK) mannitol repressor protein MltR family transcriptional regulator NF008240.0 PRK11014 PRK11014.1 182 182 141 equivalog Y Y N nitric oxide-sensing transcriptional repressor NsrR nsrR 1236 Gammaproteobacteria class 1385 NCBI Protein Cluster (PRK) transcriptional repressor NsrR nitric oxide-sensing transcriptional repressor NsrR Negatively regulates the transcription of genes upregulated by nitrosative stress NF008244.0 PRK11020 PRK11020.1 110 110 120 equivalog Y Y N YibL family ribosome-associated protein 17337586,25456817 1236 Gammaproteobacteria class 2236 NCBI Protein Cluster (PRK) hypothetical protein YibL family ribosome-associated protein NF008245.0 PRK11021 PRK11021.1 284 284 419 equivalog Y Y N L-methionine/branched-chain amino acid transporter yjeH GO:0016020,GO:0022857,GO:0055085 10931886 1236 Gammaproteobacteria class 7230 NCBI Protein Cluster (PRK) putative transporter L-methionine/branched-chain amino acid transporter NF008246.0 PRK11022 PRK11022.1 541 541 326 equivalog Y Y N dipeptide ABC transporter ATP-binding protein dppD 7.4.2.- GO:0000166,GO:0005524,GO:0015833 1236 Gammaproteobacteria class 2804 NCBI Protein Cluster (PRK) dipeptide transporter ATP-binding subunit dipeptide ABC transporter ATP-binding protein NF008247.1 PRK11023 PRK11023.1 184 184 192 equivalog Y Y N division/outer membrane stress-associated lipid-binding lipoprotein dolP GO:0006970 28708841,33315009 1236 Gammaproteobacteria class 2932 NCBI Protein Cluster (PRK) outer membrane lipoprotein division/outer membrane stress-associated lipid-binding lipoprotein NF008248.0 PRK11024 PRK11024.1 162 162 142 equivalog Y Y N colicin uptake protein TolR tolR 1236 Gammaproteobacteria class 1206 NCBI Protein Cluster (PRK) colicin uptake protein TolR colicin uptake protein TolR Membrane spanning protein in TolA-TolQ-TolR complex; involved in the tonB-independent uptake of group A colicins NF008252.0 PRK11027 PRK11027.1-2 135 135 119 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 1362 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF008255.0 PRK11027 PRK11027.2-2 184 184 124 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 77 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF008260.0 PRK11031 PRK11031.1 624 624 496 equivalog Y Y N guanosine-5'-triphosphate,3'-diphosphate diphosphatase gppA 3.6.1.40 GO:0008894,GO:0015974 1236 Gammaproteobacteria class 6055 NCBI Protein Cluster (PRK) guanosine pentaphosphate phosphohydrolase guanosine-5'-triphosphate,3'-diphosphate diphosphatase Catalyzes the conversion of guanosine 5'-triphosphate,3'-diphosphate (pppGpp) to guanosine 5'-diphosphate,3'-diphosphate (ppGpp); pppGpp and ppGpp control the stringent response during amino acid starvation NF008261.0 PRK11032 PRK11032.1 183 183 160 equivalog Y Y N zinc ribbon-containing protein 1236 Gammaproteobacteria class 2104 NCBI Protein Cluster (PRK) hypothetical protein zinc ribbon-containing protein NF008262.1 PRK11033 PRK11033.1 1005 1005 731 equivalog Y Y N zinc/cadmium/mercury/lead-transporting ATPase 7.2.2.12,7.2.2.21 GO:0006812,GO:0019829 11412123 1236 Gammaproteobacteria class 13015 NCBI Protein Cluster (PRK) zinc/cadmium/mercury/lead-transporting ATPase zinc/cadmium/mercury/lead-transporting ATPase NF008263.0 PRK11034 PRK11034.1 1350 1350 758 equivalog Y Y N ATP-dependent Clp protease ATP-binding subunit ClpA clpA 3.4.21.92 GO:0005524,GO:0016887,GO:0043335 1236 Gammaproteobacteria class 4656 NCBI Protein Cluster (PRK) ATP-dependent Clp protease ATP-binding subunit ATP-dependent Clp protease ATP-binding subunit ClpA ATPase and specificity subunit of the ClpA-ClpP ATP dependent serine protease; directs protease to specific substrates NF008264.0 PRK11036 PRK11036.1 366 366 261 equivalog Y Y N tRNA uridine 5-oxyacetic acid(34) methyltransferase CmoM cmoM 2.1.1.- 1236 Gammaproteobacteria class 4046 NCBI Protein Cluster (PRK) putative S-adenosyl-L-methionine-dependent methyltransferase tRNA uridine 5-oxyacetic acid(34) methyltransferase CmoM NF008265.0 PRK11037 PRK11037.1 105 105 83 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 2022 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF008266.1 PRK11038 PRK11038.1 76 76 46 equivalog Y Y N pleiotropic regulatory protein RsmS rsmS 30872786 1236 Gammaproteobacteria class 2519 NCBI Protein Cluster (PRK) hypothetical protein pleiotropic regulatory protein RsmS RsmS (rsmB suppressor), previously called YbaM in Escherichia coli, and DUF2496 more broadly, belongs to a regulatory system that also includes rsmB (regulation of secondary metabolite B), a regulatory RNA. This pleiotropic system found in a number of species, including phytopathogens such as Pectobacterium atrosepticum, regulates the production of factors such as antibiotics, quorum sensing molecules, and plant cell wall degrading enzymes. NF008267.0 PRK11039 PRK11039.1 195 195 141 equivalog Y Y N DUF1249 family protein 1236 Gammaproteobacteria class 1612 NCBI Protein Cluster (PRK) putative dehydrogenase DUF1249 family protein NF008269.0 PRK11041 PRK11041.1 436 436 342 equivalog Y Y N DNA-binding transcriptional regulator CytR cytR GO:0003677,GO:0006355 1236 Gammaproteobacteria class 2904 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator CytR DNA-binding transcriptional regulator CytR Negatively controls the transcription initiation of genes such as deoCABD, udp, and cdd encoding catabolizing enzymes and nupC, nupG, and tsx encoding transporting and pore-forming proteins NF008274.0 PRK11052 PRK11052.1 806 806 695 equivalog Y Y N 4-alpha-glucanotransferase malQ 2.4.1.25 GO:0004134,GO:0005975 1236 Gammaproteobacteria class 10617 NCBI Protein Cluster (PRK) 4-alpha-glucanotransferase 4-alpha-glucanotransferase Amylomaltase; acts to release glucose from maltodextrins NF008276.0 PRK11054 PRK11054.1 543 543 684 equivalog Y Y N DNA helicase IV helD 3.6.4.12 GO:0003677,GO:0003678,GO:0005524 1236 Gammaproteobacteria class 10160 NCBI Protein Cluster (PRK) DNA helicase IV DNA helicase IV Catalyzes the ATP-dependent unwinding of duplex DNA in the 3' to 5' direction with respect to the bound single strand NF008278.0 PRK11056 PRK11056.1 127 127 120 equivalog Y Y N YijD family membrane protein 1236 Gammaproteobacteria class 2157 NCBI Protein Cluster (PRK) hypothetical protein YijD family membrane protein NF008279.0 PRK11057 PRK11057.1 1015 1015 608 equivalog Y Y N ATP-dependent DNA helicase RecQ recQ 3.6.4.12 GO:0003678,GO:0006310 1236 Gammaproteobacteria class 5542 NCBI Protein Cluster (PRK) ATP-dependent DNA helicase RecQ ATP-dependent DNA helicase RecQ Functions in blocking illegitimate recombination, enhancing topoisomerase activity, initiating SOS signaling and clearing blocked replication forks; component of the RecF recombinational pathway NF008281.1 PRK11059 PRK11059.1 663 663 633 equivalog Y Y N RNase E specificity factor CsrD csrD 1236 Gammaproteobacteria class 6418 NCBI Protein Cluster (PRK) regulatory protein CsrD RNase E specificity factor CsrD Regulates the degradation of the small RNAs CsrB and CsrC NF008282.0 PRK11060 PRK11060.1 205 205 162 equivalog Y Y N rod shape-determining protein MreD mreD 1236 Gammaproteobacteria class 1576 NCBI Protein Cluster (PRK) rod shape-determining protein MreD rod shape-determining protein MreD Part of cell wall structural complex MreBCD; transmembrane component NF008283.0 PRK11061 PRK11061.1 583 583 748 equivalog Y Y N phosphoenolpyruvate--protein phosphotransferase ptsP 2.7.3.9 1236 Gammaproteobacteria class 11001 NCBI Protein Cluster (PRK) fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain phosphoenolpyruvate--protein phosphotransferase NF008287.0 PRK11067 PRK11067.1 1181 1181 802 subfamily Y Y N outer membrane protein assembly factor BamA bamA 1236 Gammaproteobacteria class 5912 NCBI Protein Cluster (PRK) outer membrane protein assembly factor YaeT outer membrane protein assembly factor BamA Part of a complex with YfgL, YfiO, and NlpB involved in outer membrane protein biosynthesis; involved in the assembly of outer membrane proteins NF008288.0 PRK11068 PRK11068.1 226 226 165 equivalog Y Y N phosphatidylglycerophosphatase A pgpA GO:0006629,GO:0008962 1236 Gammaproteobacteria class 2621 NCBI Protein Cluster (PRK) phosphatidylglycerophosphatase A phosphatidylglycerophosphatase A Hydrolyzes phosphatidylglycerophosphate to produce phosphatidylglycerol and phosphate NF008289.0 PRK11069 PRK11069.1 1470 1470 1122 equivalog Y Y N exodeoxyribonuclease V subunit gamma recC GO:0008854,GO:0009338 1236 Gammaproteobacteria class 12587 NCBI Protein Cluster (PRK) exonuclease V subunit gamma exodeoxyribonuclease V subunit gamma Catalyzes ATP-dependent exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'-direction to yield 5'-phosphooligonucleotides; component of the RecBCD (Exo V) helicase/nuclease complex that is essential for recombination NF008290.0 PRK11070 PRK11070.1 900 900 577 equivalog Y Y N single-stranded-DNA-specific exonuclease RecJ recJ 3.1.11.6 GO:0006281,GO:0006310,GO:0008409 1236 Gammaproteobacteria class 8002 NCBI Protein Cluster (PRK) ssDNA exonuclease RecJ single-stranded-DNA-specific exonuclease RecJ 5'-3' single-stranded-DNA-specific exonuclease NF008291.0 PRK11071 PRK11071.1 252 252 193 equivalog Y Y N esterase YqiA yqiA 1236 Gammaproteobacteria class 3311 NCBI Protein Cluster (PRK) esterase YqiA esterase YqiA NF008294.1 PRK11074 PRK11074.1 345 345 300 equivalog Y Y N DNA-binding transcriptional activator PunR punR GO:0003700,GO:0006355 34413462 1236 Gammaproteobacteria class 4818 NCBI Protein Cluster (PRK) putative DNA-binding transcriptional regulator DNA-binding transcriptional activator PunR NF008299.0 PRK11087 PRK11087.1 249 249 238 equivalog Y Y N oxidative stress defense protein 1236 Gammaproteobacteria class 3718 NCBI Protein Cluster (PRK) oxidative stress defense protein oxidative stress defense protein NF008300.0 PRK11088 PRK11088.1 303 303 272 equivalog Y Y N 23S rRNA (guanine(745)-N(1))-methyltransferase rlmA 2.1.1.187 GO:0008168 1236 Gammaproteobacteria class 7654 NCBI Protein Cluster (PRK) 23S rRNA methyltransferase A 23S rRNA (guanine(745)-N(1))-methyltransferase Catalyzes the methylation of the N1 position of G745 of 23S rRNA; required for translation and cell growth NF008301.0 PRK11089 PRK11089.1 647 647 477 equivalog Y Y N PTS glucose transporter subunit IIBC ptsG 2.7.1.199 GO:0008982,GO:0009401,GO:0055056,GO:1904659 1236 Gammaproteobacteria class 3550 NCBI Protein Cluster (PRK) PTS system glucose-specific transporter subunits IIBC PTS glucose transporter subunit IIBC Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF008302.0 PRK11091 PRK11091.1 838 838 779 equivalog Y Y N aerobic respiration two-component sensor histidine kinase ArcB arcB 2.7.13.3 GO:0000155,GO:0000160,GO:0006355,GO:0016020,GO:0016310 1236 Gammaproteobacteria class 7226 NCBI Protein Cluster (PRK) aerobic respiration control sensor protein ArcB aerobic respiration two-component sensor histidine kinase ArcB Sensory histidine kinase in two-component regulatory system with ArcA; regulates the expression of many genes in response to respiratory growth conditions including anaerobic repression of the arc modulon NF008303.0 PRK11092 PRK11092.1 947 947 702 equivalog Y Y N bifunctional GTP diphosphokinase/guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase spoT 2.7.6.5,3.1.7.2 GO:0008728,GO:0008893,GO:0015969 1236 Gammaproteobacteria class 7090 NCBI Protein Cluster (PRK) bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase bifunctional GTP diphosphokinase/guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase NF008317.0 PRK11106 PRK11106.1 378 378 231 equivalog Y Y N 7-cyano-7-deazaguanine synthase QueC queC 6.3.4.20 14660578,16199558,9367855 1236 Gammaproteobacteria class 5660 NCBI Protein Cluster (PRK) queuosine biosynthesis protein QueC 7-cyano-7-deazaguanine synthase QueC Catalyzes the transformation of GTP to 7-cyano-7-deazaguanine (preQ0), as one of the early reactions of quenosine biosynthesis NF008318.0 PRK11107 PRK11107.1 890 890 920 equivalog Y Y N two-component sensor histidine kinase BarA barA 2.7.13.3 GO:0000155,GO:0000160,GO:0016020,GO:0016310 1236 Gammaproteobacteria class 9451 NCBI Protein Cluster (PRK) hybrid sensory histidine kinase BarA two-component sensor histidine kinase BarA NF008322.0 PRK11113 PRK11113.1 527 527 477 equivalog Y Y N serine-type D-Ala-D-Ala carboxypeptidase dacB 3.4.16.4,3.4.21.- GO:0004185,GO:0006508 1236 Gammaproteobacteria class 7197 NCBI Protein Cluster (PRK) D-alanyl-D-alanine carboxypeptidase/endopeptidase serine-type D-Ala-D-Ala carboxypeptidase NF008325.0 PRK11114 PRK11114.1-3 922 922 766 equivalog Y Y N cellulose biosynthesis cyclic di-GMP-binding regulatory protein BcsB bcsB 1236 Gammaproteobacteria class 7869 NCBI Protein Cluster (PRK) cellulose synthase regulator protein cellulose biosynthesis cyclic di-GMP-binding regulatory protein BcsB NF008332.0 PRK11115 PRK11115.1 342 342 239 equivalog Y Y N phosphate signaling complex protein PhoU phoU GO:0030643 24563032 1236 Gammaproteobacteria class 2232 NCBI Protein Cluster (PRK) transcriptional regulator PhoU phosphate signaling complex protein PhoU NF008335.0 PRK11121 PRK11121.1 199 199 154 equivalog Y Y N anaerobic ribonucleoside-triphosphate reductase-activating protein nrdG 1.97.1.- GO:0043365,GO:0051539 1236 Gammaproteobacteria class 5618 NCBI Protein Cluster (PRK) anaerobic ribonucleotide reductase-activating protein anaerobic ribonucleoside-triphosphate reductase-activating protein NF008336.0 PRK11122 PRK11122.1 248 248 222 equivalog Y Y N arginine ABC transporter permease ArtM artM 7.4.2.1 GO:0016020,GO:0022857,GO:0043190,GO:0071705 1236 Gammaproteobacteria class 3687 NCBI Protein Cluster (PRK) arginine transporter permease subunit ArtM arginine ABC transporter permease ArtM With ArtPQJI acts to transport arginine across the inner membrane NF008337.0 PRK11123 PRK11123.1 277 277 238 equivalog Y Y N arginine ABC transporter permease ArtQ artQ 7.4.2.1 GO:0016020,GO:0022857,GO:0043190,GO:0055085,GO:0071705 8801422 1236 Gammaproteobacteria class 3814 NCBI Protein Cluster (PRK) arginine transporter permease subunit ArtQ arginine ABC transporter permease ArtQ With ArtPMJI transports arginine across the inner membrane NF008338.0 PRK11124 PRK11124.1 369 369 242 equivalog Y Y N arginine ABC transporter ATP-binding protein ArtP artP 7.4.2.1 GO:0003333,GO:0005524,GO:0015424,GO:0043190 8801422 1236 Gammaproteobacteria class 3086 NCBI Protein Cluster (PRK) arginine transporter ATP-binding subunit arginine ABC transporter ATP-binding protein ArtP With ArtMQJI transports arginine across the inner membrane NF008340.0 PRK11126 PRK11126.1 261 261 255 equivalog Y Y N 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase menH 4.2.99.20 GO:0009234,GO:0070205 1236 Gammaproteobacteria class 9108 NCBI Protein Cluster (PRK) 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase Catalyzes the formation of (1 R,6 R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate in menaquinone biosynthesis NF008346.0 PRK11128 PRK11128.1 259 259 383 equivalog Y Y N 3-phenylpropionate MFS transporter 15044727,16397293,9603882 1236 Gammaproteobacteria class 7487 NCBI Protein Cluster (PRK) putative 3-phenylpropionic acid transporter 3-phenylpropionate MFS transporter Transporter of 3-phenylpropionate across the inner membrane; member of the major facilitator superfamily of transporters NF008347.0 PRK11130 PRK11130.1 94 94 81 equivalog Y Y N molybdopterin synthase sulfur carrier subunit moaD 2.8.1.12 GO:0006777 1236 Gammaproteobacteria class 3655 NCBI Protein Cluster (PRK) molybdopterin synthase small subunit molybdopterin synthase sulfur carrier subunit Catalyzes the conversion of molybdopterin precursor Z into molybdopterin NF008349.0 PRK11132 PRK11132.1 397 397 273 equivalog Y Y N serine O-acetyltransferase cysE 2.3.1.30 GO:0006535,GO:0009001 1236 Gammaproteobacteria class 2688 NCBI Protein Cluster (PRK) serine acetyltransferase serine O-acetyltransferase Catalyzes the O-acetylation of serine NF008350.0 PRK11133 PRK11133.1 413 413 324 equivalog Y Y N phosphoserine phosphatase serB 3.1.3.3 GO:0006564,GO:0036424 1236 Gammaproteobacteria class 4520 NCBI Protein Cluster (PRK) phosphoserine phosphatase phosphoserine phosphatase NF008351.0 PRK11138 PRK11138.1 423 423 394 equivalog Y Y N outer membrane protein assembly factor BamB bamB GO:0005515 1236 Gammaproteobacteria class 5577 NCBI Protein Cluster (PRK) outer membrane biogenesis protein BamB outer membrane protein assembly factor BamB NF008355.0 PRK11144 PRK11144.1 434 434 353 equivalog Y Y N molybdenum ABC transporter ATP-binding protein ModC modC 7.3.2.5 GO:0005524,GO:0015098,GO:0015689,GO:0016020 1236 Gammaproteobacteria class 7024 NCBI Protein Cluster (PRK) molybdate transporter ATP-binding protein molybdenum ABC transporter ATP-binding protein ModC NF008357.0 PRK11146 PRK11146.1 439 439 414 exception Y Y N lipoprotein-releasing ABC transporter permease subunit LolE lolE GO:0042953 1236 Gammaproteobacteria class 7444 NCBI Protein Cluster (PRK) outer membrane-specific lipoprotein transporter subunit LolE lipoprotein-releasing ABC transporter permease subunit LolE NF008358.0 PRK11147 PRK11147.1 936 936 635 equivalog Y Y N ABC transporter ATP-binding protein GO:0005524 1236 Gammaproteobacteria class 9033 NCBI Protein Cluster (PRK) ABC transporter ATPase component ABC transporter ATP-binding protein NF008361.0 PRK11151 PRK11151.1 329 329 305 equivalog Y Y N DNA-binding transcriptional regulator OxyR oxyR GO:0003700,GO:0006355 1236 Gammaproteobacteria class 3681 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator OxyR DNA-binding transcriptional regulator OxyR Activates the expression of a regulon of hydrogen peroxide-inducible genes such as katG, gor, ahpC, ahpF, oxyS, dps, fur and grxA NF008362.0 PRK11152 PRK11152.1 68 68 85 equivalog Y Y N acetolactate synthase 2 small subunit ilvM 2.2.1.6 9581571 1236 Gammaproteobacteria class 2483 NCBI Protein Cluster (PRK) acetolactate synthase 2 regulatory subunit acetolactate synthase 2 small subunit NF008363.0 PRK11154 PRK11154.1 869 869 708 equivalog Y Y N fatty acid oxidation complex subunit alpha FadJ fadJ 1.1.1.35,4.2.1.17,5.1.2.3 GO:0003857,GO:0006635,GO:0008692,GO:0016491,GO:0051287 12270828,12535077 1236 Gammaproteobacteria class 13773 NCBI Protein Cluster (PRK) multifunctional fatty acid oxidation complex subunit alpha fatty acid oxidation complex subunit alpha FadJ NF008364.0 PRK11160 PRK11160.1 630 630 575 equivalog Y Y N heme ABC transporter ATP-binding protein/permease CydC cydC 7.4.2.- GO:0005524,GO:0016020,GO:0042626,GO:0045454,GO:0140359 15470119,16040611,37095238 1236 Gammaproteobacteria class 12069 NCBI Protein Cluster (PRK) cysteine/glutathione ABC transporter membrane/ATP-binding component heme ABC transporter ATP-binding protein/permease CydC NF008366.0 PRK11162 PRK11162.1 242 242 366 equivalog Y Y N murein transglycosylase A mltA 4.2.2.- GO:0004553,GO:0009254,GO:0019867 1236 Gammaproteobacteria class 5279 NCBI Protein Cluster (PRK) murein transglycosylase A murein transglycosylase A Membrane-bound, lytic; catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine residues NF008370.0 PRK11169 PRK11169.1 233 233 164 equivalog Y Y N leucine-responsive transcriptional regulator Lrp lrp 21642464,22484176 1236 Gammaproteobacteria class 1529 NCBI Protein Cluster (PRK) leucine-responsive transcriptional regulator leucine-responsive transcriptional regulator Lrp Mediates a global response to leucine; acts as a regulator for several genes involved in the high-affinity branched-chain amino acid transport system NF008371.0 PRK11170 PRK11170.1 483 483 382 equivalog Y Y N N-acetylglucosamine-6-phosphate deacetylase nagA 3.5.1.25 GO:0006044,GO:0008448 1236 Gammaproteobacteria class 6109 NCBI Protein Cluster (PRK) N-acetylglucosamine-6-phosphate deacetylase N-acetylglucosamine-6-phosphate deacetylase Catalyzes the formation of glucosamine 6-phosphate from N-acetylglucosamine 6-phosphate NF008378.0 PRK11173 PRK11173.1 334 334 238 equivalog Y Y N two-component system response regulator ArcA arcA 1236 Gammaproteobacteria class 2338 NCBI Protein Cluster (PRK) two-component response regulator two-component system response regulator ArcA NF008379.0 PRK11174 PRK11174.1 684 684 588 equivalog Y Y N heme ABC transporter permease/ATP-binding protein CydD cydD 7.4.2.- GO:0005524,GO:0016020,GO:0140359 15470119,16040611,37095238 1236 Gammaproteobacteria class 11141 NCBI Protein Cluster (PRK) cysteine/glutathione ABC transporter membrane/ATP-binding component heme ABC transporter permease/ATP-binding protein CydD The CydCD ABC transporter exports cysteine and glutathione into the periplasm in order to maintain redox balance NF008380.0 PRK11175 PRK11175.1 227 227 313 equivalog Y Y N universal stress protein UspE uspE 1236 Gammaproteobacteria class 5063 NCBI Protein Cluster (PRK) universal stress protein UspE universal stress protein UspE With UspC and UspD is involved in resistance to UV irradiation NF008381.0 PRK11176 PRK11176.1 867 867 582 equivalog Y Y N lipid A ABC transporter ATP-binding protein/permease MsbA msbA 7.5.2.5 GO:0005524,GO:0016020,GO:0034040,GO:0055085,GO:0140359 1236 Gammaproteobacteria class 5019 NCBI Protein Cluster (PRK) lipid transporter ATP-binding/permease protein lipid A ABC transporter ATP-binding protein/permease MsbA Involved in the transport of lipid A across the inner membrane NF008382.0 PRK11177 PRK11177.1 824 824 575 equivalog Y Y N phosphoenolpyruvate-protein phosphotransferase PtsI ptsI 2.7.3.9 1236 Gammaproteobacteria class 4225 NCBI Protein Cluster (PRK) phosphoenolpyruvate-protein phosphotransferase phosphoenolpyruvate-protein phosphotransferase PtsI Phosphotransferase system, enzyme I; transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein; part of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) NF008384.0 PRK11179 PRK11179.1 227 227 153 equivalog Y Y N transcriptional regulator AsnC asnC GO:0043565 1236 Gammaproteobacteria class 1941 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator AsnC transcriptional regulator AsnC Transcriptional repressor of asnA which codes for aspartate-ammonia ligase NF008386.0 PRK11181 PRK11181.1 366 366 244 equivalog Y Y N 23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB rlmB 2.1.1.185 GO:0003723,GO:0006396,GO:0008173 1236 Gammaproteobacteria class 5353 NCBI Protein Cluster (PRK) 23S rRNA (guanosine-2'-O-)-methyltransferase 23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB Catalyzes the methylation of the ribose of G2251 in 23S rRNA NF008388.0 PRK11186 PRK11186.1 880 880 671 equivalog Y Y N carboxy terminal-processing peptidase prc 3.4.21.102 GO:0005515,GO:0006508,GO:0008236 1236 Gammaproteobacteria class 8568 NCBI Protein Cluster (PRK) carboxy-terminal protease carboxy terminal-processing peptidase NF008389.0 PRK11187 PRK11187.1 185 185 182 equivalog Y Y N replication initiation negative regulator SeqA seqA GO:0003677,GO:0032297 1236 Gammaproteobacteria class 4106 NCBI Protein Cluster (PRK) replication initiation regulator SeqA replication initiation negative regulator SeqA Negative modulator of the initiation of chromosome replication NF008391.2 PRK11189 PRK11189.1 250 250 297 equivalog Y Y N lipoprotein NlpI nlpI GO:0005515 35418955 1236 Gammaproteobacteria class 4603 NCBI Protein Cluster (PRK) lipoprotein NlpI lipoprotein NlpI NF008392.0 PRK11190 PRK11190.1 268 268 192 equivalog Y Y N Fe-S biogenesis protein NfuA nfuA GO:0016226,GO:0051539,GO:0051604 1236 Gammaproteobacteria class 2743 NCBI Protein Cluster (PRK) Fe/S biogenesis protein NfuA Fe-S biogenesis protein NfuA NF008393.0 PRK11191 PRK11191.1 82 82 134 equivalog Y Y N ribonuclease E inhibitor RraB rraB 1236 Gammaproteobacteria class 3580 NCBI Protein Cluster (PRK) RNase E inhibitor protein ribonuclease E inhibitor RraB NF008394.0 PRK11192 PRK11192.1 507 507 441 equivalog Y Y N ATP-dependent RNA helicase SrmB srmB 3.6.4.13 GO:0000027,GO:0003724 1236 Gammaproteobacteria class 5649 NCBI Protein Cluster (PRK) ATP-dependent RNA helicase SrmB ATP-dependent RNA helicase SrmB Facilitates an early step in the assembly of the 50S subunit of the ribosome NF008395.0 PRK11193 PRK11193.1 192 192 173 equivalog Y Y N 23S rRNA accumulation protein YceD yceD 1236 Gammaproteobacteria class 3355 NCBI Protein Cluster (PRK) hypothetical protein 23S rRNA accumulation protein YceD NF008396.0 PRK11194 PRK11194.1 633 633 379 equivalog Y Y N bifunctional tRNA (adenosine(37)-C2)-methyltransferase TrmG/ribosomal RNA large subunit methyltransferase RlmN 2.1.1.-,2.1.1.192 1236 Gammaproteobacteria class 4112 NCBI Protein Cluster (PRK) ribosomal RNA large subunit methyltransferase N bifunctional tRNA (adenosine(37)-C2)-methyltransferase TrmG/ribosomal RNA large subunit methyltransferase RlmN NF008401.0 PRK11200 PRK11200.1 84 84 87 equivalog Y Y N GrxA family glutaredoxin 1236 Gammaproteobacteria class 2884 NCBI Protein Cluster (PRK) glutaredoxin 1 GrxA family glutaredoxin NF008402.0 PRK11202 PRK11202.1 151 151 211 equivalog Y Y N HTH-type transcriptional repressor FabR fabR GO:0003677 1236 Gammaproteobacteria class 4052 NCBI Protein Cluster (PRK) DNA-binding transcriptional repressor FabR HTH-type transcriptional repressor FabR Negatively controls the expression of fabA and fabB, genes involved in the unsaturated fatty acid biosynthesis NF008407.0 PRK11228 PRK11228.1 396 396 330 equivalog Y Y N iron-dicitrate ABC transporter permease FecC fecC 7.2.2.- 1236 Gammaproteobacteria class 1662 NCBI Protein Cluster (PRK) iron-dicitrate transporter permease subunit iron-dicitrate ABC transporter permease FecC Part of the FecBCDE citrate-dependent iron (III) transport system NF008409.0 PRK11231 PRK11231.1 375 375 255 equivalog Y Y N Fe(3+) dicitrate ABC transporter ATP-binding protein FecE fecE 7.2.2.- GO:0005524 1236 Gammaproteobacteria class 2245 NCBI Protein Cluster (PRK) iron-dicitrate transporter ATP-binding subunit Fe(3+) dicitrate ABC transporter ATP-binding protein FecE Part of the FecBCDE citrate-dependent iron (III) transport system NF008411.1 PRK11234 PRK11234.1 1170 1170 723 equivalog Y Y N cyclic di-3',5'-guanylate-activated glycosyltransferase NrfB nrfB 34903052 1236 Gammaproteobacteria class 2330 NCBI Protein Cluster (PRK) bacteriophage N4 adsorption protein B cyclic di-3',5'-guanylate-activated glycosyltransferase NrfB NF008414.0 PRK11240 PRK11240.1 1121 1121 774 equivalog Y Y N peptidoglycan glycosyltransferase PbpC pbpC 2.4.99.28 GO:0008658,GO:0008955,GO:0009252 10542235 1236 Gammaproteobacteria class 10992 NCBI Protein Cluster (PRK) penicillin-binding protein 1C peptidoglycan glycosyltransferase PbpC penicillin-binding protein 1C NF008418.0 PRK11245 PRK11245.1 152 152 121 equivalog Y Y N dihydroneopterin triphosphate 2'-epimerase folX 5.1.99.7 GO:0004150,GO:0006760 1236 Gammaproteobacteria class 2917 NCBI Protein Cluster (PRK) D-erythro-7,8-dihydroneopterin triphosphate 2'-epimerase dihydroneopterin triphosphate 2'-epimerase Catalyzes the formation of dihydromonapterin triphosphate from dihydroneopterin triphosphate NF008420.0 PRK11247 PRK11247.1 395 395 257 equivalog Y Y N aliphatic sulfonates ABC transporter ATP-binding protein ssuB 7.6.2.- GO:0005524 1236 Gammaproteobacteria class 5277 NCBI Protein Cluster (PRK) aliphatic sulfonates transport ATP-binding subunit aliphatic sulfonates ABC transporter ATP-binding protein Part of the ABC type transport system SsuABC for aliphatic sulfonates NF008421.0 PRK11248 PRK11248.1 357 357 255 equivalog Y Y N taurine ABC transporter ATP-binding subunit tauB GO:0005524,GO:0015411,GO:0016020 1236 Gammaproteobacteria class 5161 NCBI Protein Cluster (PRK) taurine transporter ATP-binding subunit taurine ABC transporter ATP-binding subunit NF008423.0 PRK11251 PRK11251.1 65 65 112 equivalog Y Y N osmotically-inducible lipoprotein OsmE osmE GO:0019867 1236 Gammaproteobacteria class 2110 NCBI Protein Cluster (PRK) DNA-binding transcriptional activator OsmE osmotically-inducible lipoprotein OsmE NF008426.0 PRK11260 PRK11260.1 312 312 266 equivalog Y Y N cystine ABC transporter substrate-binding protein tcyJ GO:0015276,GO:0016020 1236 Gammaproteobacteria class 3894 NCBI Protein Cluster (PRK) cystine transporter subunit cystine ABC transporter substrate-binding protein NF008428.0 PRK11264 PRK11264.1 406 406 250 equivalog Y Y N L-cystine ABC transporter ATP-binding protein TcyN tcyN 7.4.2.- GO:0003333,GO:0005524,GO:0015424 1236 Gammaproteobacteria class 4075 NCBI Protein Cluster (PRK) putative amino-acid ABC transporter ATP-binding protein YecC L-cystine ABC transporter ATP-binding protein TcyN NF008429.0 PRK11267 PRK11267.1 216 216 141 equivalog Y Y N TonB system transport protein ExbD exbD GO:0022857,GO:0055085 1236 Gammaproteobacteria class 2177 NCBI Protein Cluster (PRK) biopolymer transport protein ExbD TonB system transport protein ExbD Membrane spanning protein in TonB-ExbB-ExbD complex; involved in the tonB-independent energy-dependent transport iron-siderophore complexes and vitamin B12 into the cell NF008433.0 PRK11273 PRK11273.1 748 748 452 equivalog Y Y N glycerol-3-phosphate transporter glpT GO:0015169,GO:0015794,GO:0016020 1236 Gammaproteobacteria class 5233 NCBI Protein Cluster (PRK) sn-glycerol-3-phosphate transporter glycerol-3-phosphate transporter Catalyzes the uptake of glycerol-3-phosphate into the cell with the simultaneous export of inorganic phosphate from the cell NF008436.0 PRK11278 PRK11278.1 749 749 448 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoF nuoF 1.6.5.9 GO:0008137,GO:0051539 1236 Gammaproteobacteria class 4514 NCBI Protein Cluster (PRK) NADH dehydrogenase I subunit F NADH-quinone oxidoreductase subunit NuoF NF008438.0 PRK11281 PRK11281.1 991 991 1113 equivalog Y Y N mechanosensitive channel MscK mscK GO:0016020,GO:0055085 1236 Gammaproteobacteria class 11384 NCBI Protein Cluster (PRK) hypothetical protein mechanosensitive channel MscK NF008451.0 PRK11302 PRK11302.1 296 296 286 subfamily Y Y N transcriptional regulator HexR hexR GO:0003700,GO:0006355 1236 Gammaproteobacteria class 5963 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator HexR transcriptional regulator HexR Represses the expression of the zwf, eda, glp and gap NF008452.0 PRK11303 PRK11303.1 385 385 332 equivalog Y Y N catabolite repressor/activator cra GO:0003677,GO:0006355,GO:0009750 1236 Gammaproteobacteria class 6472 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator FruR catabolite repressor/activator Binds D-fructose as an inducer; involved in regulation of operons for central pathways of carbon metabolism NF008485.2 PRK11388 PRK11388.1 551 551 643 equivalog Y Y N dihydroxyacetone kinase operon transcriptional regulator DhaR dhaR GO:0005524,GO:0006355,GO:0008134,GO:0043565 15616579,7635824 1236 Gammaproteobacteria class 5221 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator DhaR dihydroxyacetone kinase operon transcriptional regulator DhaR Positively regulates the dhaKLM operon from a sigma-70 promoter NF008487.1 PRK11394 PRK11394.1 284 284 206 equivalog Y Y N 23S rRNA pseudouridine(2457) synthase RluE rluE 5.4.99.20 GO:0001522,GO:0009982 1236 Gammaproteobacteria class 4616 NCBI Protein Cluster (PRK) 23S rRNA pseudouridine synthase E 23S rRNA pseudouridine(2457) synthase RluE Catalyzes the synthesis of pseudouridine from U2457 in 23S ribosomal RNA NF008499.0 PRK11409 PRK11409.1 121 121 83 equivalog Y Y N YoeB-YefM toxin-antitoxin system antitoxin YefM yefM 1236 Gammaproteobacteria class 388 NCBI Protein Cluster (PRK) antitoxin YefM YoeB-YefM toxin-antitoxin system antitoxin YefM NF008513.0 PRK11432 PRK11432.1 496 496 351 equivalog Y Y N ferric ABC transporter ATP-binding protein fbpC GO:0005524,GO:0016020,GO:0022857,GO:0043190,GO:0055085 1236 Gammaproteobacteria class 2119 NCBI Protein Cluster (PRK) ferric transporter ATP-binding subunit ferric ABC transporter ATP-binding protein afuC, part of the ABC transporter complex FbpABC involved in Fe(3+) ions import NF008520.0 PRK11447 PRK11447.1 858 858 1157 equivalog Y Y N cellulose synthase complex outer membrane protein BcsC bcsC GO:0005515,GO:0019867,GO:0030244 1236 Gammaproteobacteria class 12050 NCBI Protein Cluster (PRK) cellulose synthase subunit BcsC cellulose synthase complex outer membrane protein BcsC NF008553.0 PRK11480 PRK11480.1 490 490 320 equivalog Y Y N taurine ABC transporter substrate-binding protein tauA 7.2.2.- GO:0015411,GO:0042597,GO:0043190,GO:0055085 1236 Gammaproteobacteria class 3370 NCBI Protein Cluster (PRK) taurine transporter substrate binding subunit taurine ABC transporter substrate-binding protein NF008561.0 PRK11507 PRK11507.1 95 95 70 equivalog Y Y N ribosome-associated protein YbcJ ybcJ 12837795,17337586 1236 Gammaproteobacteria class 1342 NCBI Protein Cluster (PRK) ribosome-associated protein ribosome-associated protein YbcJ YbcJ has an S4-like RNA binding domain, and was identified in Escherichia coli as a ribosome-associated protein by weak association with the 50S ribosome subunit and copurification with other ribosome-associated proteins or assembly factors such as CsdA, SrmB, RluB, and RluC. NF008571.0 PRK11523 PRK11523.1 396 396 258 equivalog Y Y N transcriptional regulator ExuR exuR 1236 Gammaproteobacteria class 1583 NCBI Protein Cluster (PRK) DNA-binding transcriptional repressor ExuR transcriptional regulator ExuR Regulates the exuT, uxaCA and uxuRAB operons which encode genes involved in hexuronate utilization. NF008578.0 PRK11537 PRK11537.1 361 361 318 equivalog Y Y N GTPase yjiA 3.6.5.- 1236 Gammaproteobacteria class 6862 NCBI Protein Cluster (PRK) putative GTP-binding protein YjiA GTPase NF008585.0 PRK11548 PRK11548.1 93 93 113 equivalog Y Y N outer membrane protein assembly factor BamE bamE 1236 Gammaproteobacteria class 2213 NCBI Protein Cluster (PRK) outer membrane biogenesis protein BamE outer membrane protein assembly factor BamE NF008595.0 PRK11562 PRK11562.1 293 293 268 equivalog Y Y N nitrite transporter NirC nirC GO:0022857,GO:0055085 1236 Gammaproteobacteria class 2589 NCBI Protein Cluster (PRK) nitrite transporter NirC nitrite transporter NirC Member of the FNT family of formate and nitrite transporters NF008604.1 PRK11573 PRK11573.1 475 475 428 equivalog Y N N hypothetical protein yfjD 1236 Gammaproteobacteria class 6198 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF008614.0 PRK11593 PRK11593.1 184 184 119 equivalog Y Y N bifunctional dihydroneopterin aldolase/7,8-dihydroneopterin epimerase folB 4.1.2.25,5.1.99.8 GO:0004150,GO:0006760 1236 Gammaproteobacteria class 2097 NCBI Protein Cluster (PRK) bifunctional dihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimerase bifunctional dihydroneopterin aldolase/7,8-dihydroneopterin epimerase Catalyzes the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin and can also catalyze the epimerization of carbon 2' of dihydroneopterin and dihydromonapterin NF008619.0 PRK11598 PRK11598.1 660 660 546 equivalog Y Y N phosphoethanolamine transferase EptA eptA GO:0016772 1236 Gammaproteobacteria class 6078 NCBI Protein Cluster (PRK) putative metal dependent hydrolase phosphoethanolamine transferase EptA NF008625.0 PRK11613 PRK11613.1 455 455 282 equivalog Y Y N dihydropteroate synthase folP 2.5.1.15 GO:0004156 1236 Gammaproteobacteria class 3377 NCBI Protein Cluster (PRK) dihydropteroate synthase dihydropteroate synthase Catalyzes the formation of dihydropteroate from 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate and 4-aminobenzoate NF008631.0 PRK11619 PRK11619.1 536 536 644 equivalog Y Y N murein transglycosylase sltY 4.2.2.- GO:0000270,GO:0004553,GO:0008933,GO:0016020,GO:0042597 1236 Gammaproteobacteria class 8049 NCBI Protein Cluster (PRK) lytic murein transglycosylase murein transglycosylase Catalyzes the cleavage of the glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine residues in peptidoglycan NF008638.0 PRK11628 PRK11628.1 137 137 105 equivalog Y Y N transcriptional regulator BolA bolA 1236 Gammaproteobacteria class 1685 NCBI Protein Cluster (PRK) transcriptional regulator BolA transcriptional regulator BolA Positive transcriptional regulator of several genes involved in oxidative stress, acid stress, heat shock, osmotic shock, and carbon-starvation stress NF008641.0 PRK11633 PRK11633.1 150 150 228 equivalog Y Y N cell division protein DedD dedD GO:0030428,GO:0032506,GO:0042834 1236 Gammaproteobacteria class 4815 NCBI Protein Cluster (PRK) cell division protein DedD cell division protein DedD NF008644.1 PRK11637 PRK11637.1 270 270 385 equivalog Y Y N murein hydrolase activator EnvC envC 32284369 1236 Gammaproteobacteria class 4970 NCBI Protein Cluster (PRK) AmiB activator murein hydrolase activator EnvC NF008646.0 PRK11639 PRK11639.1 167 167 171 equivalog Y Y N zinc uptake transcriptional repressor Zur zur GO:0003700,GO:0006355 1236 Gammaproteobacteria class 2589 NCBI Protein Cluster (PRK) zinc uptake transcriptional repressor zinc uptake transcriptional repressor Zur Negative regulator; uses Zn(2+) as a cofactor to bind the operator of the repressed genes znuACB NF008647.0 PRK11640 PRK11640.1 267 267 191 equivalog Y Y N transcriptional regulator GO:0003677 1236 Gammaproteobacteria class 2117 NCBI Protein Cluster (PRK) putative transcriptional regulator transcriptional regulator NF008648.0 PRK11642 PRK11642.1 982 982 813 equivalog Y Y N ribonuclease R rnr 3.1.13.1 GO:0004540,GO:0016070 1236 Gammaproteobacteria class 13719 NCBI Protein Cluster (PRK) exoribonuclease R ribonuclease R NF008649.0 PRK11644 PRK11644.1 408 408 499 equivalog Y Y N signal transduction histidine-protein kinase/phosphatase UhpB uhpB 2.7.13.3 GO:0000155,GO:0000160 1236 Gammaproteobacteria class 6251 NCBI Protein Cluster (PRK) sensory histidine kinase UhpB signal transduction histidine-protein kinase/phosphatase UhpB Member of the two-component regulatory system UhpB/UhpA involved in the regulation of the uptake of hexose ph NF008650.1 PRK11646 PRK11646.1 469 469 400 equivalog Y Y N multidrug efflux MFS transporter MdtH mdtH GO:0022857,GO:0055085 1236 Gammaproteobacteria class 4132 NCBI Protein Cluster (PRK) multidrug resistance protein MdtH multidrug efflux MFS transporter MdtH NF008652.0 PRK11649 PRK11649.1 341 341 439 equivalog Y Y N murein DD-endopeptidase MepM mepM 3.4.24.- GO:0042834 1236 Gammaproteobacteria class 4432 NCBI Protein Cluster (PRK) putative peptidase murein DD-endopeptidase MepM NF008654.0 PRK11652 PRK11652.1 479 479 397 equivalog Y Y N multidrug efflux MFS transporter EmrD emrD GO:0016020,GO:0042908,GO:0042910 1236 Gammaproteobacteria class 5199 NCBI Protein Cluster (PRK) multidrug resistance protein D multidrug efflux MFS transporter EmrD NF008658.2 PRK11658 PRK11658.1 631 631 379 equivalog Y Y N UDP-4-amino-4-deoxy-L-arabinose aminotransferase arnB 2.6.1.87 GO:0008483 1236 Gammaproteobacteria class 6285 NCBI Protein Cluster (PRK) UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase UDP-4-amino-4-deoxy-L-arabinose aminotransferase Catalyzes the conversion of UDP-4-keto-arabinose to UDP-4-amino-4-deoxy-L-arabinose NF008659.0 PRK11659 PRK11659.1 184 184 188 equivalog Y Y N cytochrome c nitrite reductase pentaheme subunit nrfB 1.7.2.2 GO:0008152,GO:0042597 1236 Gammaproteobacteria class 2958 NCBI Protein Cluster (PRK) cytochrome c nitrite reductase pentaheme subunit cytochrome c nitrite reductase pentaheme subunit Part of nitrite reductase complex; NrfB is active at high nitrate conditions; NrfA, B, C, and D are essential for the formate-dependent nitrite reduction to ammonia NF008661.1 PRK11663 PRK11663.1 564 564 439 subfamily Y Y N MFS transporter family glucose-6-phosphate receptor UhpC uhpC GO:0022857,GO:0055085 12654000 1236 Gammaproteobacteria class 6663 NCBI Protein Cluster (PRK) regulatory protein UhpC MFS transporter family glucose-6-phosphate receptor UhpC NF008662.0 PRK11664 PRK11664.1 1053 1053 813 equivalog Y Y N ATP-dependent helicase HrpB hrpB 3.6.4.13 GO:0004386,GO:0005524 1236 Gammaproteobacteria class 13523 NCBI Protein Cluster (PRK) ATP-dependent RNA helicase HrpB ATP-dependent helicase HrpB NF008670.0 PRK11671 PRK11671.1 375 375 359 equivalog Y Y N membrane-bound lytic murein transglycosylase MltC mltC 4.2.2.- GO:0000270,GO:0008933,GO:0016020 1236 Gammaproteobacteria class 5127 NCBI Protein Cluster (PRK) murein transglycosylase C membrane-bound lytic murein transglycosylase MltC Murein hydrolase C; membrane-bound; lytic; catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine residues NF008671.0 PRK11675 PRK11675.1 62 62 95 equivalog Y Y N LexA regulated protein ybfE 1236 Gammaproteobacteria class 1611 NCBI Protein Cluster (PRK) LexA regulated protein LexA regulated protein NF008672.1 PRK11677 PRK11677.1 150 150 133 equivalog Y Y N Z-ring associated protein ZapG zapG 33895137 1236 Gammaproteobacteria class 1590 NCBI Protein Cluster (PRK) hypothetical protein Z-ring associated protein ZapG NF008673.0 PRK11678 PRK11678.1 331 331 450 equivalog Y Y N molecular chaperone yegD GO:0005524,GO:0016887 1236 Gammaproteobacteria class 10272 NCBI Protein Cluster (PRK) putative chaperone molecular chaperone NF008674.1 PRK11679 PRK11679.1 371 371 345 equivalog Y Y N outer membrane protein assembly factor BamC bamC 1236 Gammaproteobacteria class 4003 NCBI Protein Cluster (PRK) lipoprotein outer membrane protein assembly factor BamC NF008677.0 PRK11697 PRK11697.1 246 246 238 equivalog Y Y N two-component system response regulator BtsR btsR yehT 15522865,22685278,24659770,28469239 1236 Gammaproteobacteria class 4280 NCBI Protein Cluster (PRK) putative two-component response-regulatory protein YehT two-component system response regulator BtsR null NF008685.0 PRK11702 PRK11702.1 115 115 108 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 2998 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF008690.0 PRK11713 PRK11713.1-1 342 342 243 equivalog Y Y N 16S rRNA (uracil(1498)-N(3))-methyltransferase rsmE 2.1.1.193 GO:0006364,GO:0008168 1236 Gammaproteobacteria class 5745 NCBI Protein Cluster (PRK) 16S ribosomal RNA methyltransferase RsmE 16S rRNA (uracil(1498)-N(3))-methyltransferase NF008723.0 PRK11718 PRK11718.1 139 139 161 equivalog Y Y N sigma D regulator rsd GO:0006355 1236 Gammaproteobacteria class 5416 NCBI Protein Cluster (PRK) anti-RNA polymerase sigma 70 factor sigma D regulator NF008728.0 PRK11742 PRK11742.1 840 840 598 equivalog Y Y N NADH-quinone oxidoreductase subunit C/D nuoC 1.6.5.9 GO:0030964,GO:0048038,GO:0050136,GO:0051287 1236 Gammaproteobacteria class 6689 NCBI Protein Cluster (PRK) bifunctional NADH:ubiquinone oxidoreductase subunit C/D NADH-quinone oxidoreductase subunit C/D NF008732.0 PRK11753 PRK11753.1 266 266 214 equivalog Y Y N cAMP-activated global transcriptional regulator CRP crp GO:0003700,GO:0006355 11124031,21345179,26305456,28620358,29991587 1236 Gammaproteobacteria class 4375 NCBI Protein Cluster (PRK) DNA-binding transcriptional dual regulator Crp cAMP-activated global transcriptional regulator CRP cAMP receptor protein; complexes with cyclic AMP and binds to specific DNA sites near the promoter to regulate the transcription of several catabolite-sensitive operons NF008733.0 PRK11756 PRK11756.1 280 280 269 equivalog Y Y N exodeoxyribonuclease III xthA 3.1.11.2 GO:0003677,GO:0004519,GO:0006281,GO:0008311 1236 Gammaproteobacteria class 10311 NCBI Protein Cluster (PRK) exonuclease III exodeoxyribonuclease III Removes the damaged DNA at cytosines and guanines by cleaving on the 3' side of the AP site by a beta-elimination reaction NF008739.0 PRK11770 PRK11770.1-1 213 213 148 equivalog Y Y N YccF domain-containing protein 1236 Gammaproteobacteria class 1624 NCBI Protein Cluster (PRK) hypothetical protein YccF domain-containing protein NF008743.0 PRK11773 PRK11773.1 965 965 720 equivalog Y Y N DNA helicase II uvrD mutU,recL 3.6.4.12 GO:0003677,GO:0003678,GO:0005524,GO:0006268,GO:0016787 1236 Gammaproteobacteria class 13761 NCBI Protein Cluster (PRK) DNA-dependent helicase II DNA helicase II Unwinds DNA duplexes with 3' to 5' polarity with respect to the bound strand and initiates unwinding most effectively when a single-stranded region is present; involved in the post-incision events of nucleotide excision repair and methyl-directed mismatch repair. NF008753.0 PRK11788 PRK11788.1-1 395 395 389 equivalog Y Y N lipopolysaccharide assembly protein LapB lapB GO:0005515,GO:0008653 1236 Gammaproteobacteria class 5219 NCBI Protein Cluster (PRK) tetratricopeptide repeat protein lipopolysaccharide assembly protein LapB NF008756.0 PRK11788 PRK11788.1-4 474 474 389 equivalog Y Y N lipopolysaccharide assembly protein LapB lapB 1236 Gammaproteobacteria class 5114 NCBI Protein Cluster (PRK) tetratricopeptide repeat protein lipopolysaccharide assembly protein LapB NF008762.0 PRK11798 PRK11798.1-1 202 202 170 equivalog Y Y N ClpXP protease specificity-enhancing factor sspB 1236 Gammaproteobacteria class 2794 NCBI Protein Cluster (PRK) ClpXP protease specificity-enhancing factor ClpXP protease specificity-enhancing factor NF008763.0 PRK11798 PRK11798.1-2 162 162 156 equivalog Y Y N ClpXP protease specificity-enhancing factor 1236 Gammaproteobacteria class 5937 NCBI Protein Cluster (PRK) ClpXP protease specificity-enhancing factor ClpXP protease specificity-enhancing factor NF008764.0 PRK11798 PRK11798.1-4 191 191 143 equivalog Y Y N ClpXP protease specificity-enhancing factor 1236 Gammaproteobacteria class 2039 NCBI Protein Cluster (PRK) ClpXP protease specificity-enhancing factor ClpXP protease specificity-enhancing factor NF008849.0 PRK11886 PRK11886.1-4 474 474 320 equivalog Y Y N bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA birA 6.3.4.15 GO:0004077,GO:0036211 1236 Gammaproteobacteria class 3532 NCBI Protein Cluster (PRK) bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA NF008890.0 PRK11924 PRK11924.1-3 284 284 205 equivalog Y N N RNA polymerase sigma factor 1236 Gammaproteobacteria class 227 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF008898.0 PRK11933 PRK11933.1 588 588 480 equivalog Y Y N 16S rRNA (cytosine(1407)-C(5))-methyltransferase RsmF rsmF 2.1.1.178 GO:0001510,GO:0003723,GO:0008649 16678201 1236 Gammaproteobacteria class 10978 NCBI Protein Cluster (PRK) rRNA (cytosine-C(5)-)-methyltransferase RsmF 16S rRNA (cytosine(1407)-C(5))-methyltransferase RsmF Catalyzes the methylation of the C5 position of C1407 of the 16S rRNA NF008930.0 PRK12287 PRK12287.1 318 318 344 subfamily Y Y N AI-2E family transporter 1236 Gammaproteobacteria class 5745 NCBI Protein Cluster (PRK) pheromone autoinducer 2 transporter AI-2E family transporter NF008931.0 PRK12288 PRK12288.1 360 360 347 equivalog Y Y N small ribosomal subunit biogenesis GTPase RsgA rsgA 3.6.1.- GO:0003924,GO:0005525 15466596 1236 Gammaproteobacteria class 9119 NCBI Protein Cluster (PRK) GTPase RsgA small ribosomal subunit biogenesis GTPase RsgA EngC; RsgA; CpgA; circularly permuted GTPase; ribosome small subunit-dependent GTPase A; has the pattern G4-G1-G3 as opposed to other GTPases; interacts strongly with 30S ribosome which stimulates GTPase activity NF008937.0 PRK12292 PRK12292.1-4 693 693 395 equivalog Y Y N ATP phosphoribosyltransferase regulatory subunit GO:0000105 1236 Gammaproteobacteria class 1827 NCBI Protein Cluster (PRK) ATP phosphoribosyltransferase regulatory subunit ATP phosphoribosyltransferase regulatory subunit NF008964.0 PRK12308 PRK12308.1 657 657 624 equivalog Y Y N argininosuccinate lyase argH 4.3.2.1 GO:0004056,GO:0042450 1236 Gammaproteobacteria class 8051 NCBI Protein Cluster (PRK) bifunctional argininosuccinate lyase/N-acetylglutamate synthase argininosuccinate lyase Catalyzes the formation of arginine from (N-L-arginino)succinate and the formation of N-acetylglutamate from glutamate and acetyl-CoA NF009002.0 PRK12347 PRK12347.1 386 386 231 subfamily Y Y N L-ribulose-5-phosphate 4-epimerase 5.1.3.4 10769139,11741871,2251150,4879898,9548961 1236 Gammaproteobacteria class 5438 NCBI Protein Cluster (PRK) L-ribulose-5-phosphate 4-epimerase L-ribulose-5-phosphate 4-epimerase Catalyzes the isomerization of L-ribulose 5-phosphate to D-xylulose 5-phosphate in the anaerobic catabolism of L-ascorbate; links the arabinose metabolic pathway to the pentose phosphate pathway and allows the bacteria to use arabinose as an energy source NF009016.0 PRK12355 PRK12355.3-2 648 648 626 equivalog Y Y N type-F conjugative transfer system mating-pair stabilization protein TraN traN 1236 Gammaproteobacteria class 1019 NCBI Protein Cluster (PRK) conjugal transfer mating pair stabilization protein TraN type-F conjugative transfer system mating-pair stabilization protein TraN NF009017.0 PRK12355 PRK12355.3-3 796 796 576 subfamily Y Y N type-F conjugative transfer system mating-pair stabilization protein TraN traN 1236 Gammaproteobacteria class 196 NCBI Protein Cluster (PRK) conjugal transfer mating pair stabilization protein TraN type-F conjugative transfer system mating-pair stabilization protein TraN NF009023.0 PRK12359 PRK12359.1 215 215 172 equivalog Y Y N flavodoxin FldB fldB GO:0009055,GO:0010181 1236 Gammaproteobacteria class 4119 NCBI Protein Cluster (PRK) flavodoxin FldB flavodoxin FldB An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group NF009027.0 PRK12363 PRK12363.1 572 572 703 equivalog Y Y N phosphoglycerol transferase I 2.7.8.20 1236 Gammaproteobacteria class 997 NCBI Protein Cluster (PRK) phosphoglycerol transferase I phosphoglycerol transferase I Catalyzes the transfer of phosphoglycerol to the glucan backbone NF009046.0 PRK12380 PRK12380.1 113 113 113 subfamily Y Y N hydrogenase/urease nickel incorporation protein 1236 Gammaproteobacteria class 2819 NCBI Protein Cluster (PRK) hydrogenase nickel incorporation protein HybF hydrogenase/urease nickel incorporation protein Plays a role in hydrogenase/urease nickel cofactor insertion NF009051.0 PRK12385 PRK12385.1 333 333 244 equivalog Y Y N succinate dehydrogenase/fumarate reductase iron-sulfur subunit GO:0006099,GO:0009055,GO:0016491,GO:0051536 1236 Gammaproteobacteria class 3176 NCBI Protein Cluster (PRK) fumarate reductase iron-sulfur subunit succinate dehydrogenase/fumarate reductase iron-sulfur subunit NF009072.1 PRK12407 PRK12407.1 323 323 220 equivalog Y Y N flagellar basal body L-ring protein FlgH flgH GO:0003774,GO:0009427,GO:0071973 15687208,7921252 1236 Gammaproteobacteria class 635 NCBI Protein Cluster (PRK) flagellar basal body L-ring protein flagellar basal body L-ring protein FlgH Part of the basal body which consists of four rings L, P, S, and M mounted on a central rod NF009099.0 PRK12440 PRK12440.1 693 693 397 equivalog Y Y N acetate/propionate family kinase 1236 Gammaproteobacteria class 1133 NCBI Protein Cluster (PRK) acetate kinase acetate/propionate family kinase NF009132.0 PRK12485 PRK12485.1 693 693 369 equivalog Y Y N bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II ribBA 3.5.4.25 1236 Gammaproteobacteria class 1387 NCBI Protein Cluster (PRK) bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II Bifunctional enzyme DHBP synthase/GTP cyclohydrolase II-like protein; functions in riboflavin synthesis NF009139.0 PRK12492 PRK12492.1 1018 1018 562 equivalog Y Y N long-chain-fatty-acid--CoA ligase 6.2.1.3 21042406 1236 Gammaproteobacteria class 2824 NCBI Protein Cluster (PRK) long-chain-fatty-acid--CoA ligase long-chain-fatty-acid--CoA ligase This family includes both FadD1 and FadD2 from Pseudomonas aeruginosa. NF009175.0 PRK12523 PRK12523.1 271 271 172 equivalog Y Y N RNA polymerase sigma factor 1236 Gammaproteobacteria class 1584 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor Bacteria have multiple sigma factors which are active under specific conditions; the sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs Bacterial core RNA polymerase to specific promoter elements to initiate transcription NF009178.0 PRK12526 PRK12526.1 301 301 211 equivalog Y N N RNA polymerase sigma factor 1236 Gammaproteobacteria class 504 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009213.0 PRK12562 PRK12562.1 559 559 334 subfamily Y Y N ornithine carbamoyltransferase 1236 Gammaproteobacteria class 4960 NCBI Protein Cluster (PRK) ornithine carbamoyltransferase subunit F ornithine carbamoyltransferase NF009296.0 PRK12653 PRK12653.1 306 306 220 subfamily Y Y N fructose-6-phosphate aldolase 4.1.2.- 11120740,12051943 1236 Gammaproteobacteria class 5424 NCBI Protein Cluster (PRK) fructose-6-phosphate aldolase fructose-6-phosphate aldolase NF009313.0 PRK12674 PRK12674.1-1 151 151 140 equivalog Y Y N Na+/H+ antiporter subunit G 1236 Gammaproteobacteria class 950 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit G Na+/H+ antiporter subunit G NF009324.0 PRK12679 PRK12679.1 491 491 316 equivalog Y Y N HTH-type transcriptional regulator Cbl cbl GO:0003700,GO:0006355 11038360,11918818,14663078,15255893,17010379,3032953,3094306,8529872,9309218 1236 Gammaproteobacteria class 2839 NCBI Protein Cluster (PRK) transcriptional regulator Cbl HTH-type transcriptional regulator Cbl DNA-binding transcriptional activator for the ssuEADCB and tauABCD operons NF009328.0 PRK12685 PRK12685.1 169 169 116 equivalog Y N N flagellar basal body rod protein FlgB 1236 Gammaproteobacteria class 305 NCBI Protein Cluster (PRK) flagellar basal body rod protein FlgB flagellar basal body rod protein FlgB NF009361.0 PRK12717 PRK12717.1 407 407 524 equivalog Y Y N flagellar hook-associated protein 3 GO:0005198,GO:0044781 1236 Gammaproteobacteria class 2350 NCBI Protein Cluster (PRK) flagellar hook-associated protein FlgL flagellar hook-associated protein 3 With FlgK acts as a hook filament junction protein to join the flagellar filament to the hook NF009391.0 PRK12750 PRK12750.1 148 148 170 equivalog Y Y N CpxP family protein 1236 Gammaproteobacteria class 1121 NCBI Protein Cluster (PRK) periplasmic repressor CpxP CpxP family protein NF009505.0 PRK12863 PRK12863.1-6 171 171 100 equivalog Y N N YciI-like protein 1236 Gammaproteobacteria class 378 NCBI Protein Cluster (PRK) YciI-like protein YciI-like protein NF009545.0 PRK12933 PRK12933.1 728 728 604 equivalog Y Y N protein translocase subunit SecD secD 1236 Gammaproteobacteria class 2747 NCBI Protein Cluster (PRK) preprotein translocase subunit SecD protein translocase subunit SecD Part of the preprotein secretory system; when complexed with proteins SecF and YajC, SecDFYajC stimulates the proton motive force-driven protein translocation, and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane NF009638.0 PRK13165 PRK13165.1 186 186 161 equivalog Y Y N cytochrome c maturation protein CcmE ccmE GO:0005886,GO:0017004,GO:0020037 12486054,15465823,16373344,16824107,17419738 1236 Gammaproteobacteria class 4223 NCBI Protein Cluster (PRK) cytochrome c-type biogenesis protein CcmE cytochrome c maturation protein CcmE CycJ; periplasmic heme chaperone that binds heme transiently via a histidine residue and delivers it to newly synthesized and exported c-type cytochromes; requires the ATP hydrolysis activity of the CcmA protein in order to transfer the heme to the apocytochrome; part of the cytochrome c maturation system; periplasmic protein anchored to the inner membrane NF009696.0 PRK13222 PRK13222.1-3 359 359 223 equivalog Y Y N N-acetylmuramic acid 6-phosphate phosphatase MupP mupP GO:0016791 28351914 1236 Gammaproteobacteria class 2038 NCBI Protein Cluster (PRK) phosphoglycolate phosphatase N-acetylmuramic acid 6-phosphate phosphatase MupP This enzyme belongs to a cell wall recycling pathway that lacks MurQ and that bypasses the step sensitive to the antibiotic fosfomycin. NF009698.0 PRK13223 PRK13223.1 466 466 272 equivalog Y Y N phosphoglycolate phosphatase 3.1.3.18 GO:0005975,GO:0008967 1236 Gammaproteobacteria class 1698 NCBI Protein Cluster (PRK) phosphoglycolate phosphatase phosphoglycolate phosphatase Catalyzes the dephosphorylation of 2-phosphoglycolate to form glycolate and phosphate NF009753.0 PRK13261 PRK13261.1-5 287 287 166 equivalog Y Y N urease accessory protein UreE ureE 1236 Gammaproteobacteria class 1521 NCBI Protein Cluster (PRK) urease accessory protein UreE urease accessory protein UreE NF009775.0 PRK13272 PRK13272.1 941 941 558 equivalog Y Y N alpha,alpha-trehalase TreA treA 3.2.1.28 1236 Gammaproteobacteria class 944 NCBI Protein Cluster (PRK) trehalase alpha,alpha-trehalase TreA Catalyzes the hydrolysis of trehalose to glucose NF009784.2 PRK13279 PRK13279.1 567 567 539 equivalog Y Y N lipid IV(A) 4-amino-4-deoxy-L-arabinosyltransferase arnT 2.4.2.43 GO:0000030,GO:0006493,GO:0016020,GO:0016763 1236 Gammaproteobacteria class 10413 NCBI Protein Cluster (PRK) 4-amino-4-deoxy-L-arabinose transferase lipid IV(A) 4-amino-4-deoxy-L-arabinosyltransferase Catalyzes the addition of 4-amino-4-deoxy-L-arabinose to lipid A NF009835.0 PRK13310 PRK13310.1 380 380 303 equivalog Y Y N N-acetylglucosamine kinase nagK 2.7.1.59 GO:0045127 1236 Gammaproteobacteria class 5676 NCBI Protein Cluster (PRK) N-acetyl-D-glucosamine kinase N-acetylglucosamine kinase Catalyzes the formation of N-acetyl-D-glucosamine-6-phosphate from N-acetyl-D-glucosamine NF009857.0 PRK13322 PRK13322.1-2 378 378 249 equivalog Y Y N pantothenate kinase 2.7.1.33 1236 Gammaproteobacteria class 1429 NCBI Protein Cluster (PRK) pantothenate kinase pantothenate kinase NF009860.0 PRK13322 PRK13322.1-5 288 288 248 equivalog Y Y N pantothenate kinase 2.7.1.33 1236 Gammaproteobacteria class 29 NCBI Protein Cluster (PRK) pantothenate kinase pantothenate kinase NF009866.0 PRK13328 PRK13328.1-2 360 360 266 equivalog Y Y N type III pantothenate kinase 2.7.1.33 1236 Gammaproteobacteria class 13 NCBI Protein Cluster (PRK) pantothenate kinase type III pantothenate kinase NF009923.0 PRK13384 PRK13384.1 507 507 327 equivalog Y Y N porphobilinogen synthase hemB 4.2.1.24 GO:0004655,GO:0033014 1236 Gammaproteobacteria class 3475 NCBI Protein Cluster (PRK) delta-aminolevulinic acid dehydratase porphobilinogen synthase Catalyzes the formation of porphobilinogen from 5-aminolevulinate NF010020.0 PRK13498 PRK13498.1 236 236 168 equivalog Y Y N chemoreceptor glutamine deamidase CheD cheD 3.5.1.44 1236 Gammaproteobacteria class 486 NCBI Protein Cluster (PRK) chemoreceptor glutamine deamidase CheD chemoreceptor glutamine deamidase CheD Catalyzes the conversion of glutamine residues to glutamate on methyl-accepting chemotaxis receptors NF010034.0 PRK13509 PRK13509.1 244 244 251 equivalog Y Y N HTH-type transcriptional regulator UlaR ulaR GO:0003700,GO:0006355 1236 Gammaproteobacteria class 1815 NCBI Protein Cluster (PRK) transcriptional repressor UlaR HTH-type transcriptional regulator UlaR Negative regulator of ulaG and ulaABCDEF NF010058.0 PRK13535 PRK13535.1 539 539 339 equivalog Y Y N erythrose-4-phosphate dehydrogenase epd 1.2.1.72 GO:0042823,GO:0048001,GO:0051287 1236 Gammaproteobacteria class 4747 NCBI Protein Cluster (PRK) erythrose 4-phosphate dehydrogenase erythrose-4-phosphate dehydrogenase NF010133.0 PRK13607 PRK13607.1 339 339 443 equivalog Y Y N Xaa-Pro dipeptidase pepQ 3.4.13.9 1236 Gammaproteobacteria class 8927 NCBI Protein Cluster (PRK) proline dipeptidase Xaa-Pro dipeptidase NF010149.0 PRK13626 PRK13626.1 476 476 552 equivalog Y Y N HTH-type transcriptional regulator SgrR sgrR 1236 Gammaproteobacteria class 6447 NCBI Protein Cluster (PRK) transcriptional regulator SgrR HTH-type transcriptional regulator SgrR Activates sgrS under glucose-phosphate stress conditions NF010213.0 PRK13677 PRK13677.1 150 150 128 equivalog Y Y N DUF3461 family protein 1236 Gammaproteobacteria class 1468 NCBI Protein Cluster (PRK) hypothetical protein DUF3461 family protein NF010230.0 PRK13682 PRK13682.1-5 89 89 53 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 258 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010242.0 PRK13689 PRK13689.1 90 90 75 equivalog Y N N hypothetical protein 1236 Gammaproteobacteria class 1828 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010256.0 PRK13702 PRK13702.1 87 87 85 subfamily Y Y N replication regulatory protein RepA repA 1236 Gammaproteobacteria class 1249 NCBI Protein Cluster (PRK) replication protein replication regulatory protein RepA NF010259.0 PRK13705 PRK13705.1 725 725 388 equivalog Y Y N plasmid-partitioning protein SopA sopA 1236 Gammaproteobacteria class 703 NCBI Protein Cluster (PRK) plasmid-partitioning protein SopA plasmid-partitioning protein SopA NF010264.0 PRK13710 PRK13710.1 100 100 72 equivalog Y Y N type II toxin-antitoxin system antitoxin CcdA ccdA 1236 Gammaproteobacteria class 671 NCBI Protein Cluster (PRK) plasmid maintenance protein CcdA type II toxin-antitoxin system antitoxin CcdA NF010295.2 PRK13735 PRK13735.1 600 600 922 equivalog Y Y N conjugal transfer mating-pair stabilization protein TraG traG 17259615,7915817 1236 Gammaproteobacteria class 8330 NCBI Protein Cluster (PRK) conjugal transfer mating pair stabilization protein TraG conjugal transfer mating-pair stabilization protein TraG TraG, as the term is used for conjugal transfer regions of F-like plasmids, is a mating pair stabilization protein. Note that the term TraG has other meanings for proteins from other classes of plasmid conjugal transfer system. NF010313.0 PRK13750 PRK13750.1 478 478 287 subfamily Y N N replication protein 1236 Gammaproteobacteria class 3677 NCBI Protein Cluster (PRK) replication protein replication protein NF010363.0 PRK13791 PRK13791.1 127 127 113 equivalog Y Y N c-type lysozyme inhibitor 16937244,18369469 1236 Gammaproteobacteria class 276 NCBI Protein Cluster (PRK) lysozyme inhibitor c-type lysozyme inhibitor Periplasmic lysozyme inhibitor of c-type lysozyme NF010643.0 PRK14040 PRK14040.1 892 892 595 subfamily Y Y N oxaloacetate decarboxylase subunit alpha 4.1.1.112 1236 Gammaproteobacteria class 12209 NCBI Protein Cluster (PRK) oxaloacetate decarboxylase oxaloacetate decarboxylase subunit alpha Catalyzes the formation of pyruvate from oxaloacetate NF010653.0 PRK14052 PRK14052.1 364 364 387 equivalog Y Y N VopS family T3SS effector adenosine monophosphate-protein transferase 1236 Gammaproteobacteria class 670 NCBI Protein Cluster (PRK) effector protein VopS family T3SS effector adenosine monophosphate-protein transferase null NF010711.0 PRK14113 PRK14113.1 240 240 152 equivalog Y N N urease accessory protein UreE 1236 Gammaproteobacteria class 126 NCBI Protein Cluster (PRK) urease accessory protein UreE urease accessory protein UreE NF010745.0 PRK14147 PRK14147.1 184 184 172 equivalog Y Y N nucleotide exchange factor GrpE grpE 1236 Gammaproteobacteria class 793 NCBI Protein Cluster (PRK) heat shock protein GrpE nucleotide exchange factor GrpE With DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins NF010749.0 PRK14151 PRK14151.1 231 231 188 equivalog Y Y N nucleotide exchange factor GrpE grpE 1236 Gammaproteobacteria class 1822 NCBI Protein Cluster (PRK) heat shock protein GrpE nucleotide exchange factor GrpE With DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins NF010790.0 PRK14194 PRK14194.1 508 508 301 equivalog Y Y N bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD folD 1236 Gammaproteobacteria class 922 NCBI Protein Cluster (PRK) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD Catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate NF010796.0 PRK14200 PRK14200.1 144 144 127 equivalog Y Y N fluoride efflux transporter CrcB crcB 1236 Gammaproteobacteria class 761 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter CrcB NF011000.0 PRK14426 PRK14426.1 89 89 92 equivalog Y Y N acylphosphatase yccX 3.6.1.7 GO:0003998 1236 Gammaproteobacteria class 4527 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011022.0 PRK14451 PRK14451.1 91 91 91 equivalog Y Y N acylphosphatase 1236 Gammaproteobacteria class 1554 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011086.0 PRK14511 PRK14511.1-3 1411 1411 924 equivalog Y Y N malto-oligosyltrehalose synthase 5.4.99.15 GO:0005975 1236 Gammaproteobacteria class 4220 NCBI Protein Cluster (PRK) maltooligosyl trehalose synthase malto-oligosyltrehalose synthase NF011162.1 PRK14563 PRK14563.1 40 40 47 equivalog Y Y N ribosome modulation factor rmf GO:0043022,GO:0141014 12473202 1236 Gammaproteobacteria class 2608 NCBI Protein Cluster (PRK) ribosome modulation factor ribosome modulation factor NF011285.0 PRK14696 PRK14696.1 1278 1278 757 equivalog Y Y N primary-amine oxidase tynA 1.4.3.21 GO:0005507,GO:0008131,GO:0009308,GO:0048038 1236 Gammaproteobacteria class 5885 NCBI Protein Cluster (PRK) tyramine oxidase primary-amine oxidase Members of this family, such as TynA of E. coli K-12, and primary-amine oxidases, and act on a wide range of primary amines, of which tyramine is one. NF011333.0 PRK14749 PRK14749.1 57 57 30 equivalog Y Y N cytochrome bd-II oxidase subunit CbdX cbdX 1236 Gammaproteobacteria class 126 NCBI Protein Cluster (PRK) hypothetical protein cytochrome bd-II oxidase subunit CbdX NF011366.0 PRK14785 PRK14785.1 256 256 198 subfamily Y N N lipoprotein signal peptidase 1236 Gammaproteobacteria class 332 NCBI Protein Cluster (PRK) lipoprotein signal peptidase lipoprotein signal peptidase NF011427.0 PRK14854 PRK14854.1 558 558 383 subfamily Y N N pH-dependent sodium/proton antiporter 1236 Gammaproteobacteria class 108 NCBI Protein Cluster (PRK) pH-dependent sodium/proton antiporter pH-dependent sodium/proton antiporter NF011433.1 PRK14864 PRK14864.1 100 100 98 equivalog Y Y N biofilm peroxide resistance protein BsmA bsmA 19833773 1236 Gammaproteobacteria class 1930 NCBI Protein Cluster (PRK) putative biofilm stress and motility protein A bioflm peroxide resistance protein BsmA NF011561.0 PRK14985 PRK14985.1 1273 1273 800 equivalog Y Y N maltodextrin phosphorylase malP 2.4.1.1 GO:0005975,GO:0008184,GO:0030170 1236 Gammaproteobacteria class 6965 NCBI Protein Cluster (PRK) maltodextrin phosphorylase maltodextrin phosphorylase NF011563.0 PRK14987 PRK14987.1 433 433 331 equivalog Y Y N gluconate operon transcriptional repressor GntR gntR GO:0003677,GO:0003700,GO:0006355 1236 Gammaproteobacteria class 3200 NCBI Protein Cluster (PRK) gluconate operon transcriptional regulator gluconate operon transcriptional repressor GntR NF011564.0 PRK14988 PRK14988.1 189 189 225 equivalog Y Y N GMP/IMP nucleotidase yrfG 3.1.3.5 1236 Gammaproteobacteria class 8032 NCBI Protein Cluster (PRK) GMP/IMP nucleotidase GMP/IMP nucleotidase NF011569.0 PRK14993 PRK14993.1 416 416 244 equivalog Y Y N tetrathionate reductase subunit TtrB ttrB 10231485 1236 Gammaproteobacteria class 1032 NCBI Protein Cluster (PRK) tetrathionate reductase subunit B tetrathionate reductase subunit TtrB NF011571.1 PRK14995 PRK14995.1 701 701 493 subfamily Y Y N SmvA family efflux MFS transporter 7926834 1236 Gammaproteobacteria class 4090 NCBI Protein Cluster (PRK) methyl viologen resistance protein SmvA SmvA family efflux MFS transporter NF011572.0 PRK14996 PRK14996.1 144 144 192 equivalog Y Y N TetR family transcriptional regulator GO:0003677 1236 Gammaproteobacteria class 2381 NCBI Protein Cluster (PRK) TetR family transcriptional regulator TetR family transcriptional regulator NF011574.0 PRK14998 PRK14998.1 147 147 73 equivalog Y Y N cold shock-like protein CspD cspD 1236 Gammaproteobacteria class 700 NCBI Protein Cluster (PRK) cold shock-like protein CspD cold shock-like protein CspD NF011592.0 PRK15017 PRK15017.1 1271 1271 663 equivalog Y Y N cytochrome o ubiquinol oxidase subunit I cyoB 7.1.1.- GO:0004129 1236 Gammaproteobacteria class 2357 NCBI Protein Cluster (PRK) cytochrome o ubiquinol oxidase subunit I cytochrome o ubiquinol oxidase subunit I NF011597.0 PRK15022 PRK15022.1 154 154 167 equivalog Y Y N non-heme ferritin-like protein 1236 Gammaproteobacteria class 1507 NCBI Protein Cluster (PRK) ferritin-like protein non-heme ferritin-like protein NF011606.0 PRK15032 PRK15032.1 455 455 390 equivalog Y Y N pentaheme c-type cytochrome TorC torC GO:0009055,GO:0016020,GO:0020037 1236 Gammaproteobacteria class 2105 NCBI Protein Cluster (PRK) trimethylamine N-oxide reductase cytochrome c-type subunit pentaheme c-type cytochrome TorC With TorA forms the inducible trimethylamine N-oxide reductase which transfers electrons from menaquinones first to TorC then to TorA NF011611.0 PRK15037 PRK15037.1 603 603 486 subfamily Y Y N fructuronate reductase 1.1.1.57 GO:0016491 1236 Gammaproteobacteria class 16063 NCBI Protein Cluster (PRK) D-mannonate oxidoreductase fructuronate reductase Catalyzes the reduction of D-fructuronate to D-mannonate NF011612.1 PRK15038 PRK15038.1 500 500 322 equivalog Y Y N autoinducer 2 ABC transporter permease LsrD lsrD 7.6.2.- 1236 Gammaproteobacteria class 2809 NCBI Protein Cluster (PRK) autoinducer 2 import system permease LsrD autoinducer 2 ABC transporter permease LsrD With IsrABC is involved with autoinducer 2 import NF011613.0 PRK15039 PRK15039.1 138 138 90 equivalog Y Y N Ni(II)/Co(II)-binding transcriptional repressor RcnR rcnR 18505253,21040754 1236 Gammaproteobacteria class 483 NCBI Protein Cluster (PRK) transcriptional repressor RcnR to maintain nickel and cobalt homeostasis Ni(II)/Co(II)-binding transcriptional repressor RcnR DNA-binding; binds the RcnA promotor NF011632.3 PRK15058 PRK15058.1 130 130 127 equivalog Y Y N cytochrome b562 cybC GO:0005506,GO:0009055,GO:0022900,GO:0042597 3178744,8499452 1236 Gammaproteobacteria class 2016 NCBI Protein Cluster (PRK) cytochrome b562 cytochrome b562 NF011655.0 PRK15074 PRK15074.1 367 367 434 subfamily Y Y N inosine/guanosine kinase 1236 Gammaproteobacteria class 5209 NCBI Protein Cluster (PRK) inosine/guanosine kinase inosine/guanosine kinase NF011664.0 PRK15084 PRK15084.1 145 145 135 subfamily Y Y N formate hydrogenlyase maturation protein HycH hycH 1236 Gammaproteobacteria class 3075 NCBI Protein Cluster (PRK) formate hydrogenlyase maturation protein HycH formate hydrogenlyase maturation protein HycH Required for the maturation of the formate hydrogenlyase complex NF011669.0 PRK15087 PRK15087.1 270 270 219 equivalog Y Y N PAQR family membrane homeostatis protein TrhA trhA GO:0019835 35285724,37345585,38054739,7495855 1236 Gammaproteobacteria class 3449 NCBI Protein Cluster (PRK) hemolysin PAQR family membrane homeostatis protein TrhA TrhA (transmembrane homeostasis protein A), a plasma membrane protein found in both Escherichia coli and Bacillus subtilis, belongs to the PAQR family, named for eukaryotic Progestin and AdipoQ Receptors. PAQR family proteins in bacteria originally were named for a family member from Bacillus cereus that was named hemolysin III. NF011670.1 PRK15088 PRK15088.1 400 400 323 equivalog Y Y N PTS mannose transporter subunit IIAB manX 2.7.1.191 GO:0008982,GO:0009401 1236 Gammaproteobacteria class 3226 NCBI Protein Cluster (PRK) PTS system mannose-specific transporter subunits IIAB PTS mannose transporter subunit IIAB Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF011675.0 PRK15094 PRK15094.1 379 379 292 equivalog Y Y N CNNM family magnesium/cobalt transport protein CorC corC GO:0050660 1779764 1236 Gammaproteobacteria class 3043 NCBI Protein Cluster (PRK) magnesium/cobalt efflux protein CorC CNNM family magnesium/cobalt transport protein CorC Involved in the transport of magnesium and cobalt ions. CorC(YbeX) belongs to the Cyclin M Mg2+ Exporter (CNNM) family, and was characterized as belonging to a set of three proteins, at least one of which must be present for CorA to function. NF011676.0 PRK15095 PRK15095.1 125 125 156 equivalog Y Y N FKBP-type peptidyl-prolyl cis-trans isomerase fkpB 5.2.1.8 GO:0003755 1236 Gammaproteobacteria class 5639 NCBI Protein Cluster (PRK) FKBP-type peptidyl-prolyl cis-trans isomerase FKBP-type peptidyl-prolyl cis-trans isomerase NF011677.0 PRK15097 PRK15097.1 968 968 522 equivalog Y Y N cytochrome ubiquinol oxidase subunit I cydA 7.1.1.- GO:0009055,GO:0019646,GO:0070069 1236 Gammaproteobacteria class 2888 NCBI Protein Cluster (PRK) cytochrome d terminal oxidase subunit 1 cytochrome ubiquinol oxidase subunit I NF011680.0 PRK15100 PRK15100.1 300 300 222 equivalog Y Y N cystine ABC transporter permease tcyL 7.4.2.- 1236 Gammaproteobacteria class 2385 NCBI Protein Cluster (PRK) amino acid ABC transporter permease cystine ABC transporter permease NF011681.0 PRK15101 PRK15101.1 765 765 961 equivalog Y Y N pitrilysin ptrA 3.4.24.55 GO:0004222,GO:0006508,GO:0046872 1236 Gammaproteobacteria class 9260 NCBI Protein Cluster (PRK) protease3 pitrilysin NF011685.0 PRK15105 PRK15105.1 737 737 588 subfamily Y Y N peptidoglycan glycosyltransferase FtsI ftsI 3.4.16.4 GO:0005886,GO:0008658,GO:0008955,GO:0009252,GO:0051301 1236 Gammaproteobacteria class 5547 NCBI Protein Cluster (PRK) peptidoglycan synthase FtsI peptidoglycan glycosyltransferase FtsI Penicillin-binding protein 3; transpeptidase involved in septal peptidoglycan synthesis NF011689.0 PRK15109 PRK15109.1 560 560 547 equivalog Y Y N ABC transporter substrate-binding protein SapA sapA GO:0043190,GO:0055085 20551214,27803167 1236 Gammaproteobacteria class 6090 NCBI Protein Cluster (PRK) antimicrobial peptide ABC transporter periplasmic binding protein SapA ABC transporter substrate-binding protein SapA While SapA, recognized by homology as an ABC transporter periplasmic binding protein, is encoded in the same operon as the putrescine export ABC transporter SapBCDF, it appears not to function in putrescine export when tested experimentally in E. coli, and its function is unknown. NF011691.0 PRK15111 PRK15111.1 379 379 296 equivalog Y Y N putrescine export ABC transporter permease SapC sapC GO:0016020,GO:0055085 20551214,27803167 1236 Gammaproteobacteria class 2517 NCBI Protein Cluster (PRK) antimicrobial peptide ABC transporter permease SapC putrescine export ABC transporter permease SapC NF011697.0 PRK15117 PRK15117.1 195 195 211 equivalog Y Y N phospholipid-binding protein MlaC mlaC 1236 Gammaproteobacteria class 3048 NCBI Protein Cluster (PRK) ABC transporter periplasmic binding protein MlaC phospholipid-binding protein MlaC NF011698.0 PRK15118 PRK15118.1 202 202 144 equivalog Y Y N universal stress protein UspA uspA 1236 Gammaproteobacteria class 1180 NCBI Protein Cluster (PRK) universal stress global response regulator UspA universal stress protein UspA Involved in resistance to DNA-damaging agents NF011703.0 PRK15123 PRK15123.1 170 170 268 equivalog Y Y N lipopolysaccharide core heptose(I) kinase RfaP rfaP 2.7.1.- GO:0009103,GO:0016301 1236 Gammaproteobacteria class 4924 NCBI Protein Cluster (PRK) lipopolysaccharide core heptose(I) kinase RfaP lipopolysaccharide core heptose(I) kinase RfaP Catalyzes the phosphorylation of heptose I in the lipopolysaccharide core NF011708.0 PRK15129 PRK15129.1 343 343 321 equivalog Y Y N L-Ala-D/L-Glu epimerase ycjG 5.1.1.20 GO:0009063,GO:0016855 1236 Gammaproteobacteria class 7106 NCBI Protein Cluster (PRK) L-Ala-D/L-Glu epimerase L-Ala-D/L-Glu epimerase NF011713.0 PRK15134 PRK15134.1 834 834 529 equivalog Y Y N microcin C ABC transporter ATP-binding protein YejF yejF GO:0000166,GO:0005524,GO:0006810 1236 Gammaproteobacteria class 6757 NCBI Protein Cluster (PRK) microcin C ABC transporter ATP-binding protein YejF microcin C ABC transporter ATP-binding protein YejF YejABEF is involved in resistance to microcin C NF011716.0 PRK15137 PRK15137.1 372 372 235 equivalog Y Y N deoxyribonuclease I endA 3.1.21.1 GO:0004518 1236 Gammaproteobacteria class 3153 NCBI Protein Cluster (PRK) DNA-specific endonuclease I deoxyribonuclease I NF011717.0 PRK15138 PRK15138.1 645 645 387 equivalog Y Y N alcohol dehydrogenase yqhD 1.1.1.2 GO:0046872,GO:1990362 1236 Gammaproteobacteria class 4107 NCBI Protein Cluster (PRK) aldehyde reductase alcohol dehydrogenase NF011758.0 PRK15211 PRK15211.1 248 248 230 equivalog Y Y N fimbrial chaperone 1236 Gammaproteobacteria class 661 NCBI Protein Cluster (PRK) fimbrial chaperone protein PefD fimbrial chaperone NF011760.0 PRK15213 PRK15213.1 752 752 796 equivalog Y Y N PefC/AfrB family outer membrane usher protein pefC 8100983 1236 Gammaproteobacteria class 1984 NCBI Protein Cluster (PRK) fimbrial outer membrane usher protein PefC PefC/AfrB family outer membrane usher protein Involved in the export and assembly of fimbriae subunit PetA NF011781.0 PRK15245 PRK15245.1 305 305 241 equivalog Y Y N type III secretion system effector phosphothreonine lyase 1236 Gammaproteobacteria class 214 NCBI Protein Cluster (PRK) type III effector phosphothreonine lyase type III secretion system effector phosphothreonine lyase NF011812.0 PRK15284 PRK15284.1 972 972 881 subfamily Y Y N outer membrane usher protein GO:0005515,GO:0009297,GO:0015473,GO:0016020 1236 Gammaproteobacteria class 8112 NCBI Protein Cluster (PRK) putative fimbrial outer membrane usher protein StfC outer membrane usher protein NF011896.0 PRK15369 PRK15369.1 242 242 211 equivalog Y Y N two component system response regulator 1236 Gammaproteobacteria class 458 NCBI Protein Cluster (PRK) two component system sensor kinase SsrB two component system response regulator NF011922.0 PRK15393 PRK15393.1 152 152 182 equivalog Y Y N NUDIX hydrolase YfcD yfcD GO:0016817 1236 Gammaproteobacteria class 2113 NCBI Protein Cluster (PRK) NUDIX hydrolase YfcD NUDIX hydrolase YfcD NF011923.2 PRK15394 PRK15394.1 382 382 294 equivalog Y Y N 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase arnD 3.5.1.n3 GO:0016810 1236 Gammaproteobacteria class 5727 NCBI Protein Cluster (PRK) 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase Catalyzes the formation of 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol from 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol NF011926.0 PRK15397 PRK15397.1 335 335 239 subfamily Y Y N nicotinamide riboside transporter PnuC pnuC 1236 Gammaproteobacteria class 4503 NCBI Protein Cluster (PRK) nicotinamide riboside transporter PnuC nicotinamide riboside transporter PnuC NF011928.0 PRK15399 PRK15399.1 968 968 713 subfamily Y Y N lysine decarboxylase LdcC ldcC 4.1.1.18 1236 Gammaproteobacteria class 7479 NCBI Protein Cluster (PRK) lysine decarboxylase LdcC lysine decarboxylase LdcC Constitutive; catalyzes the formation of cadaverine from lysine NF011929.0 PRK15400 PRK15400.1 1056 1056 714 subfamily Y Y N lysine decarboxylase cadA 4.1.1.18 1236 Gammaproteobacteria class 7354 NCBI Protein Cluster (PRK) lysine decarboxylase CadA lysine decarboxylase Acid-inducible; catalyzes the formation of cadaverine from lysine NF011931.1 PRK15402 PRK15402.1 439 439 401 subfamily Y Y N MdfA family multidrug efflux MFS transporter 1236 Gammaproteobacteria class 4983 NCBI Protein Cluster (PRK) multidrug efflux system translocase MdfA MdfA family multidrug efflux MFS transporter NF011947.0 PRK15418 PRK15418.1 486 486 319 equivalog Y Y N transcriptional regulator LsrR lsrR 1236 Gammaproteobacteria class 2038 NCBI Protein Cluster (PRK) transcriptional regulator LsrR transcriptional regulator LsrR Regulates the transcription of lsr genes; involved in autoinducer 2 uptake, biofilm formation and stress responses NF011950.0 PRK15421 PRK15421.1 382 382 317 equivalog Y Y N HTH-type transcriptional regulator MetR metR GO:0003700,GO:0006355 1236 Gammaproteobacteria class 3082 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator MetR HTH-type transcriptional regulator MetR NF011953.0 PRK15424 PRK15424.1 703 703 538 equivalog Y Y N propionate catabolism operon regulatory protein PrpR prpR 1236 Gammaproteobacteria class 4439 NCBI Protein Cluster (PRK) propionate catabolism operon regulatory protein PrpR propionate catabolism operon regulatory protein PrpR Sigma-54 dependent activator family protein; activates the prpBCDE operon NF011961.0 PRK15432 PRK15432.1 388 388 344 equivalog Y Y N autoinducer 2 ABC transporter permease LsrC lsrC 7.6.2.- GO:0022857,GO:0055085 1236 Gammaproteobacteria class 3425 NCBI Protein Cluster (PRK) autoinducer 2 ABC transporter permease LsrC autoinducer 2 ABC transporter permease LsrC With LsrADB is involved in the transport of autoindiuce 2 NF011995.0 PRK15451 PRK15451.1 285 285 247 equivalog Y Y N carboxy-S-adenosyl-L-methionine synthase CmoA cmoA 2.1.3.- 1236 Gammaproteobacteria class 7753 NCBI Protein Cluster (PRK) tRNA cmo(5)U34 methyltransferase carboxy-S-adenosyl-L-methionine synthase CmoA NF012000.0 PRK15456 PRK15456.1 189 189 142 equivalog Y Y N universal stress protein UspG uspG 1236 Gammaproteobacteria class 794 NCBI Protein Cluster (PRK) universal stress protein UspG universal stress protein UspG Interacts with GroEL; is induced by starvation, heat shock and toxic agents NF012002.0 PRK15458 PRK15458.1 707 707 428 equivalog Y Y N tagatose-bisphosphate aldolase subunit KbaZ kbaZ 4.1.2.40 1236 Gammaproteobacteria class 3367 NCBI Protein Cluster (PRK) tagatose 6-phosphate aldolase subunit KbaZ tagatose-bisphosphate aldolase subunit KbaZ NF012009.0 PRK15465 PRK15465.1 622 622 453 equivalog Y Y N aminodeoxychorismate synthase component 1 pabB GO:0009396 1236 Gammaproteobacteria class 8089 NCBI Protein Cluster (PRK) aminodeoxychorismate synthase subunit I aminodeoxychorismate synthase component 1 Aminodeoxychorismate synthase subunit PabB; with PabA catalyzes the formation of 4-amino-4-deoxychorismate from chorismate and glutamine in para-aminobenzoate synthesis NF012023.0 PRK15479 PRK15479.1 337 337 224 equivalog Y Y N transcriptional regulator TctD tctD 1236 Gammaproteobacteria class 1122 NCBI Protein Cluster (PRK) transcriptional regulatory protein TctD transcriptional regulator TctD Transcriptional activator of tricarboxylate transport system genes NF012024.0 PRK15480 PRK15480.1 588 588 292 equivalog Y Y N glucose-1-phosphate thymidylyltransferase RfbA rfbA 2.7.7.24 GO:0000271,GO:0008879 1236 Gammaproteobacteria class 2082 NCBI Protein Cluster (PRK) glucose-1-phosphate thymidylyltransferase RfbA glucose-1-phosphate thymidylyltransferase RfbA Catalyzes the formation of dTDP-glucose from dTTP and glucose 1-phosphate NF012103.0 blaGES 625 625 287 exception Y Y Y GES family class A beta-lactamase blaGES 3.5.2.6 GO:0008800 17704567,19738007 1236 Gammaproteobacteria class 37 NCBIFAM blaGES: GES family class A beta-lactamase GES family class A beta-lactamase At amino acid position 165 of most GES (Guiana extended-spectrum) sequences, referred to as position 170 in a standard numbering scheme used across all class A beta-lactamases, Gly occurs in extended-spectrum enzymes (ESBL) that lack carbapenemase activity, while replacement with Ser confers carbapenemase activity. NF012141.0 blaKPC 625 625 293 exception Y Y Y KPC family carbapenem-hydrolyzing class A beta-lactamase blaKPC 3.5.2.6 GO:0008800 1236 Gammaproteobacteria class 156 NCBIFAM blaKPC: KPC family carbapenem-hydrolyzing class A beta-lactamase KPC family carbapenem-hydrolyzing class A beta-lactamase NF012148.0 blaKHM-HMB 450 450 238 exception Y Y Y KHM/HMB family subclass B1 metallo-beta-lactamase blaKHM 3.5.2.6 GO:0008800 1236 Gammaproteobacteria class 10 NCBIFAM blaKHM: KHM family subclass B1 metallo-beta-lactamase KHM/HMB family subclass B1 metallo-beta-lactamase This family is named for KHM-1 (Kyorin Health Science metallo-beta-lactamase 1) and HMB-1 (Hamburg Metallo-Beta-lactamase 1). NF012152.0 penta_rpt_QnrC 500 500 221 exception Y Y Y QnrC family quinolone resistance pentapeptide repeat protein 1236 Gammaproteobacteria class 14 NCBIFAM qnrC: QnrC family quinolone resistance pentapeptide repeat protein QnrC family quinolone resistance pentapeptide repeat protein NF012159.0 polymyxin_MCR2 1200 1200 538 exception Y Y Y MCR-2 family phosphoethanolamine--lipid A transferase 1236 Gammaproteobacteria class 4 NCBIFAM polymyxin_MCR2: MCR-2 family phosphoethanolamine--lipid A transferase MCR-2 family phosphoethanolamine--lipid A transferase NF012163.2 BaeS_SmeS 500 500 457 equivalog Y Y N sensor histidine kinase efflux regulator BaeS baeS 2.7.13.3 GO:0000155,GO:0007165,GO:0016020,GO:0016310 1236 Gammaproteobacteria class 6524 NCBIFAM BaeS_SmeS: sensor histidine kinase efflux regulator BaeS sensor histidine kinase efflux regulator BaeS NF012172.1 FOX-MOX 700 700 382 exception Y Y Y FOX/MOX family class C beta-lactamase ampC 3.5.2.6 GO:0008800,GO:0030288 1236 Gammaproteobacteria class 588 NCBIFAM FOX-MOX: FOX/MOX family class C beta-lactamase FOX/MOX family class C beta-lactamase NF012173.1 CMY2-MIR-ACT-EC 680 680 380 exception Y Y Y CMY2/MIR/ACT/EC family class C beta-lactamase ampC 3.5.2.6 GO:0008800,GO:0030288 1236 Gammaproteobacteria class 3095 NCBIFAM CMY2-MIR-ACT-EC: CMY2/MIR/ACT/EC family class c beta-lactamase CMY2/MIR/ACT/EC family class C beta-lactamase NF012179.0 CptA 900 900 556 domain Y Y N phosphoethanolamine transferase CptA cptA 1236 Gammaproteobacteria class 3931 NCBIFAM phosphoethanolamine transferase CptA phosphoethanolamine transferase CptA NF012186.0 tet_MFS_D 775 775 394 exception Y Y Y tetracycline efflux MFS transporter Tet(D) tet(D) GO:0008493,GO:0015904 1236 Gammaproteobacteria class 88 NCBIFAM tetracycline efflux MFS transporter Tet(D) tetracycline efflux MFS transporter Tet(D) NF012187.0 tet_MFS_E 820 820 405 exception Y Y Y tetracycline efflux MFS transporter Tet(E) tet(E) GO:0008493,GO:0015904 1236 Gammaproteobacteria class 18 NCBIFAM tetracycline efflux MFS transporter Tet(E) tetracycline efflux MFS transporter Tet(E) NF012202.0 ble_MBL 250 250 121 exception Y Y Y bleomycin binding protein Ble-MBL ble 1236 Gammaproteobacteria class 55 NCBIFAM bleomycin binding protein Ble-MBL bleomycin binding protein Ble-MBL This bleomycin resistance protein, which binds bleomycin and confers resistance by sequestration, occurs in the context of the metallo-beta-lactamase NDM-1, and therefore was described as ble(MBL). NF012225.0 blaSFH_gen 440 440 252 exception Y Y Y SFH-related subclass B2 metallo-beta-lactamase bla 3.5.2.6 GO:0008800 1236 Gammaproteobacteria class 16 NCBIFAM SFH-related subclass B2 metallo-beta-lactamase SFH-related subclass B2 metallo-beta-lactamase NF012249.5 PF00019.25 TGF_beta 27 27 104 domain Y Y N TGF-beta family protein GO:0008083 1631557,8570652,9187648 1236 Gammaproteobacteria class 5 EBI-EMBL Transforming growth factor beta like domain Transforming growth factor beta like domain NF012261.5 PF00031.26 Cystatin 22.2 22.2 92 domain Y Y N cystatin domain-containing protein GO:0004869 1236 Gammaproteobacteria class 1280 EBI-EMBL Cystatin domain cystatin domain Very diverse family. Attempts to define separate sub-families failed. Typically, either the N-terminal or C-terminal end is very divergent. But splitting into two domains would make very short families. All members except Swiss:Q03196 and Swiss:Q10993 are found. Pfam:PF00666 are related to this family but have not been included. (from Pfam) NF012405.5 PF00178.27 Ets 26.9 26.9 81 domain Y Y N ETS domain-containing protein GO:0003700,GO:0006355,GO:0043565 9644975 1236 Gammaproteobacteria class 19 EBI-EMBL Ets-domain Ets-domain NF013016.5 PF00818.22 Ice_nucleation 20.8 20.8 15 repeat Y N N Ice nucleation protein repeat GO:0009279 1236 Gammaproteobacteria class 994 EBI-EMBL Ice nucleation protein repeat Ice nucleation protein repeat NF013211.5 PF01024.24 Colicin 23.4 23.4 185 domain Y Y N colicin-like pore-forming protein GO:0016020,GO:0019835,GO:0031640,GO:0050829,GO:0140911 1373773 1236 Gammaproteobacteria class 4127 EBI-EMBL Colicin pore forming domain colicin-like pore-forming domain NF013503.5 PF01340.25 MetJ 25 25 97 PfamEq Y N N Met Apo-repressor, MetJ GO:0003700,GO:0006355,GO:0006555 2677753,8092669 1236 Gammaproteobacteria class 1676 EBI-EMBL Met Apo-repressor, MetJ Met Apo-repressor, MetJ NF013536.5 PF01376.23 Enterotoxin_b 25 25 102 domain Y N N Heat-labile enterotoxin beta chain GO:0005576 8478941 1236 Gammaproteobacteria class 76 EBI-EMBL Heat-labile enterotoxin beta chain Heat-labile enterotoxin beta chain NF014142.5 PF02048.21 Enterotoxin_ST 21.1 21.1 54 subfamily Y Y N ST-I family heat-stable enterotoxin GO:0005615,GO:0090729 15049831 1236 Gammaproteobacteria class 123 EBI-EMBL Heat-stable enterotoxin ST ST-I family heat-stable enterotoxin This family consists of the heat stable enterotoxin ST from Escherichia coli. ST is a small peptide of 18 or 19 amino acid residues produced by enterotoxigenic E. coli and is one of the causes of acute diarrhoea in infants and travellers in developing countries. ST triggers a biological response by binding to a membrane-associated guanylyl cyclase C which is located on intestinal epithelial cell membranes [1]. [1]. 15049831. Structural features of Escherichia coli heat-stable enterotoxin that activates membrane-associated guanylyl cyclase. Sato T, Shimonishi Y;. J Pept Res 2004;63:200-206. (from Pfam) NF014444.5 PF02387.20 IncFII_repA 22.9 22.9 275 domain Y Y N RepA family replication protein GO:0006276 3041379 1236 Gammaproteobacteria class 7916 EBI-EMBL IncFII RepA protein family RepA family replication protein This protein is plasmid encoded and found to be essential for plasmid replication [1]. [1]. 3041379. RepA protein- and oriR-dependent initiation of R1 plasmid replication: identification of a rho-dependent transcription terminator required for cis-action of repA protein. Masai H, Arai K;. Nucleic Acids Res 1988;16:6493-6514. (from Pfam) NF014506.5 PF02453.22 Reticulon 31.8 31.8 157 domain Y Y N reticulon family protein 12832288,9693037 1236 Gammaproteobacteria class 2 EBI-EMBL Reticulon reticulon family protein Reticulon, also know as neuroendocrine-specific protein (NSP), is a protein of unknown function which associates with the endoplasmic reticulum. This family represents the C-terminal domain of the three reticulon isoforms and their homologues. [1]. 9693037. cDNA cloning, genomic organization, and expression of the human RTN2 gene, a member of a gene family encoding reticulons. Roebroek AJ, Contreras B, Pauli IG, Van de Ven WJ;. Genomics 1998;51:98-106. [2]. 12832288. A reticular rhapsody: phylogenic evolution and nomenclature of the RTN/Nogo gene family. Oertle T, Klinger M, Stuermer CA, Schwab ME;. FASEB J. 2003;17:1238-1247. (from Pfam) NF015067.5 PF03081.20 Exo70_C 24.1 24.1 372 domain Y Y N exocyst complex component EXO70 GO:0000145,GO:0005546,GO:0006887 10207081,10588647,16359701,29335562,8978675,9405631 1236 Gammaproteobacteria class 2 EBI-EMBL Exo70 exocyst complex subunit C-terminal exocyst complex component EXO70 The Exo70 protein is a subunit of the exocyst complex [1-7], first identified in yeast, it is evolutionarily conserved. It mediates the tethering of post-Golgi secretory vesicles to the plasma membrane and promotes the assembly of the SNARE complex for membrane fusion [1,2,3,4]. It also plays a role in cell polarisation, primary ciliogenesis, cytokinesis, pathogen invasion, tumourigenesis and metastasis [6]. It is a member of the the Complex Associated with Tethering Containing Helical Rods (CATCHRs) family which also includes Conserved Oligomeric Golgi complex (COG) and Golgi-Associated Retrograde Protein complex (GARP) and DSL1 complexes, all evolutionarily related and share structural features consisting of alpha-helical bundles at the C-terminus and coiled-coil region at the N-terminus [5,6]. Exo70 interacts with phospholipids and Rho3 GTPase [4,5,7]. This interaction mediates one of the three known functions of Rho3 in cell polarity: vesicle docking and fusion with the plasma membrane (the other two functions are regulation of actin polarity and transport of exocytic vesicle from the mother cell to the bud) [3]. This is the C-terminal domain of Exo70, which consists of alpha-helical bundles involved in binding the small GTPase Rho3 and it is important for localization to the plasma membrane as it directly interacts with phosphatidylinositol 4,5-biphosphate The interaction with phospholipids is essential for the membrane association of the exocyst complex [5,6,7]. [1]. 8978675. The Exocyst is a multiprotein complex required for exocytosis in Saccharomyces cerevisiae. TerBush DR, Maurice T, Roth D, Novick P;. EMBO J 199. TRUNCATED at 1650 bytes (from Pfam) NF015301.5 PF03333.18 PapB 29.4 29.4 91 subfamily Y Y N PapB/FocB family fimbrial expression transcriptional regulator GO:0006355 10747013 1236 Gammaproteobacteria class 2461 EBI-EMBL Adhesin biosynthesis transcription regulatory protein PapB/FocB family fimbrial expression transcriptional regulator This family includes PapB, DaaA, FanA, FanB, and AfaA. [1]. 10747013. Regulatory cross-talk between adhesin operons in Escherichia coli: inhibition of type 1 fimbriae expression by the PapB protein. Xia Y, Gally D, Forsman-Semb K, Uhlin BE;. EMBO J 2000;19:1450-1457. (from Pfam) NF015315.5 PF03348.20 Serinc 24 24 434 PfamEq Y Y N serine incorporator domain-containing protein GO:0016020 10559794,10637174,16120614 1236 Gammaproteobacteria class 2 EBI-EMBL Serine incorporator (Serinc) Serine incorporator (Serinc) This is a family of eukaryotic membrane proteins which incorporate serine into membranes and facilitate the synthesis of the serine-derived lipids phosphatidylserine and sphingolipid [3]. Members of this family contain 11 transmembrane domains and form intracellular complexes with key enzymes involved in serine and sphingolipid biosynthesis [3]. [1]. 10559794. The human TDE gene homologue: localization to 20q13.1-13.3 and variable expression in human tumor cell lines and tissue. Bossolasco M, Lebel M, Lemieux N, Mes-Masson AM;. Mol Carcinog 1999;26:189-200. [2]. 10637174. Identification of a ubiquitous family of membrane proteins and their expression in mouse brain. Grossman TR, Luque JM, Nelson N;. J Exp Biol 2000;203:447-457. [3]. 16120614. Serinc, an activity-regulated protein family, incorporates serine into membrane lipid synthesis. Inuzuka M, Hayakawa M, Ingi T;. J Biol Chem. 2005;280:35776-35783. (from Pfam) NF015365.5 PF03400.18 DDE_Tnp_IS1 24.1 24.1 131 subfamily Y Y N IS1 family transposase GO:0003677,GO:0004803,GO:0006313 11274106 1236 Gammaproteobacteria class 34862 EBI-EMBL IS1 transposase IS1 family transposase Transposase proteins are necessary for efficient DNA transposition. This family represents bacterial IS1 transposases. [1]. 11274106. Involvement of H-NS in transpositional recombination mediated by IS1. Shiga Y, Sekine Y, Kano Y, Ohtsubo E;. J Bacteriol 2001;183:2476-2484. (from Pfam) NF015489.5 PF03526.18 Microcin 25 25 55 subfamily Y Y N colicin E1 family microcin immunity protein GO:0015643,GO:0030153 1236 Gammaproteobacteria class 1217 EBI-EMBL Colicin E1 (microcin) immunity protein colicin E1 family microcin immunity protein NF015507.5 PF03545.18 YopE 25 25 70 domain Y N N Yersinia virulence determinant (YopE) 1236 Gammaproteobacteria class 1470 EBI-EMBL Yersinia virulence determinant (YopE) Yersinia virulence determinant (YopE) NF015560.5 PF03603.18 DNA_III_psi 22.2 22.2 127 PfamEq Y Y N DNA polymerase III subunit psi 2.7.7.7 GO:0003887,GO:0006260,GO:0008408 1236 Gammaproteobacteria class 5284 EBI-EMBL DNA polymerase III psi subunit DNA polymerase III subunit psi NF015646.5 PF03701.19 UPF0181 23.5 23.5 50 PfamEq Y Y N YoaH family protein 1236 Gammaproteobacteria class 2059 EBI-EMBL Uncharacterised protein family (UPF0181) YoaH family protein This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH Swiss:P76260. (from Pfam) NF015750.5 PF03811.18 Zn_Tnp_IS1 26.1 26.1 35 domain Y Y N IS1 family transposase GO:0006313 1236 Gammaproteobacteria class 25034 EBI-EMBL InsA N-terminal domain IS1 family transposase N-terminal domain This appears to be a short zinc binding domain found in IS1 InsA family protein. It is found at the N-terminus of the protein and may be a DNA-binding domain. (from Pfam) NF015784.5 PF03846.19 SulA 23.1 23.1 91 domain Y Y N SulA-like leucine-rich domain-containing protein GO:0009432,GO:0051782 12808143 1236 Gammaproteobacteria class 6128 EBI-EMBL Cell division inhibitor SulA Cell division inhibitor SulA High-scoring members of this family are the cell division inhibitor SulA. A stretch of 89 residues in the conserved portion of the seed alignment contains 21 consensus Leu sites, suggesting that some low-scoring members of this family may exceed the model's cutoff because of non-specific hits rather than true homology. NF015795.5 PF03857.18 Colicin_im 25.8 25.8 138 PfamEq Y Y N colicin immunity protein Cui cui GO:0015643,GO:0030153 11590016 1236 Gammaproteobacteria class 656 EBI-EMBL Colicin immunity protein colicin immunity protein Cui Colicin immunity proteins are plasmid-encoded proteins necessary for protecting the cell against colicins. Colicins are toxins released by bacteria during times of stress [1]. [1]. 11590016. Immunity proteins: enzyme inhibitors that avoid the active site. Kleanthous C, Walker D;. Trends Biochem Sci 2001;26:624-631. (from Pfam) NF015811.5 PF03873.18 RseA_C 23 23 55 domain Y Y N anti sigma-E factor RseA C-terminal domain-containing protein 9159523 1236 Gammaproteobacteria class 6596 EBI-EMBL Anti sigma-E protein RseA, C-terminal domain Anti sigma-E protein RseA, C-terminal domain Sigma-E is important for the induction of proteins involved in heat shock response. RseA binds sigma-E via its N-terminal domain, sequestering sigma-E and preventing transcription from heat-shock promoters [1]. The C-terminal domain is located in the periplasm, and may interact with other protein that signal periplasmic stress. [1]. 9159523. The sigmaE-mediated response to extracytoplasmic stress in Escherichia coli is transduced by RseA and RseB, two negative regulators of sigmaE. De Las Penas A, Connolly L, Gross CA;. Mol Microbiol 1997;24:373-385. (from Pfam) NF015819.5 PF03882.19 KicB 22.1 22.1 115 PfamEq Y N N MukF winged-helix domain 15902272,7513784 1236 Gammaproteobacteria class 4579 EBI-EMBL MukF winged-helix domain MukF winged-helix domain The kicA and kicB genes are found upstream of mukB. It has been suggested that the kicB gene encodes a killing factor and the kicA gene codes for a protein that suppresses the killing function of the kicB gene product [1]. It was also demonstrated that KicA and KicB can function as a post-segregational killing system, when the genes are transferred from the E. coli chromosome onto a plasmid [1]. [1]. 7513784. New killing system controlled by two genes located immediately upstream of the mukB gene in Escherichia coli. Feng J, Yamanaka K, Niki H, Ogura T, Hiraga S;. Mol Gen Genet 1994;243:136-147. [2]. 15902272. The MukF subunit of Escherichia coli condensin: architecture and functional relationship to kleisins. Fennell-Fezzie R, Gradia SD, Akey D, Berger JM;. EMBO J. 2005;24:1921-1930. (from Pfam) NF015860.5 PF03925.18 SeqA 25.5 25.5 111 PfamEq Y N N SeqA protein C-terminal domain GO:0003677 11442835,11457824,7553853,9736699 1236 Gammaproteobacteria class 4439 EBI-EMBL SeqA protein C-terminal domain SeqA protein C-terminal domain The binding of SeqA protein to hemimethylated GATC sequences is important in the negative modulation of chromosomal initiation at oriC, and in the formation of SeqA foci necessary for Escherichia coli chromosome segregation [3]. SeqA tetramers are able to aggregate or multimerise in a reversible, concentration-dependent manner [3]. Apart from its function in the control of DNA replication, SeqA may also be a specific transcription factor [4]. [1]. 9736699. High-affinity binding of hemimethylated oriC by Escherichia coli membranes is mediated by a multiprotein system that includes SeqA and a newly identified factor, SeqB. Shakibai N, Ishidate K, Reshetnyak E, Gunji S, Kohiyama M, Rothfield L;. Proc Natl Acad Sci U S A 1998;95:11117-11121. [2]. 7553853. E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration. Slater S, Wold S, Lu M, Boye E, Skarstad K, Kleckner N;. Cell 1995;82:927-936. [3]. 11457824. SeqA protein aggregation is necessary for SeqA function. Lee H, Kang S, Bae SH, Choi BS, Hwang DS;. J Biol Chem 2001;276:34600-34606. [4]. 11442835. SeqA, the Escherichia coli origin sequestration protein, is also a specific transcription factor. Slominska M, Wegrzyn A, Konopa G, Skarstad K, Wegrzyn G;. Mol Microbiol 2001;40:1371-1379. (from Pfam) NF016091.5 PF04175.17 DUF406 25 25 91 subfamily Y Y N DUF406 family protein 19927321 1236 Gammaproteobacteria class 4027 EBI-EMBL Protein of unknown function (DUF406) DUF406 family protein Members of this family appear to be found only in gamma proteobacteria. The function of this protein family is undetermined. Solution of the structures of the two members of this family investigated bear some resemblance to that of the single domain enzyme pterin-4a-carbinolamine dehydratase, PDC. Although the residues of PCDs involved in binding of metabolite are not conserved in the two structures under study, they do correspond to a surface-region structurally aligned with residues that are highly conserved, eg Glu 89, suggesting that this region is also involved in binding of a ligand, thereby possibly constituting a catalytic site of a yet uncharacterised enzyme specific for gamma proteobacteria. [1]. 19927321. Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175. Singarapu KK, Mills JL, Xiao R, Acton T, Punta M, Fischer M, Honig B, Rost B, Montelione GT, Szyperski T;. Proteins. 2010;78:779-784. (from Pfam) NF016132.5 PF04217.18 DUF412 23.6 23.6 141 PfamAutoEq Y Y N DUF412 family protein 22532809 1236 Gammaproteobacteria class 3722 EBI-EMBL Protein of unknown function, DUF412 DUF412 family protein This family consists of bacterial proteins, including yfbV from E. coli. YfbV is a membrane protien involved in insulating the chromosome from the TerR macrodomain [1]. [1]. 22532809. Long-range chromosome organization in E. coli: a site-specific system isolates the Ter macrodomain. Thiel A, Valens M, Vallet-Gely I, Espeli O, Boccard F;. PLoS Genet. 2012;8:e1002672. (from Pfam) NF016134.5 PF04219.17 DUF413 25 25 90 PfamEq Y Y N DUF413 domain-containing protein maoP 27627105 1236 Gammaproteobacteria class 3065 EBI-EMBL Protein of unknown function, DUF macrodomain Ori organization protein MaoP NF016135.5 PF04220.17 YihI 25 25 155 PfamEq Y Y N GTPase-activating protein GO:0005096 20434458 1236 Gammaproteobacteria class 5462 EBI-EMBL Der GTPase activator (YihI) GTPase-activating protein YihI activates the GTPase activity of Der, a 50S ribosomal subunit stability factor [1]. The stimulation is specific to Der as YihI does not stimulate the GTPase activity of Era or ObgE. The interaction of YihI with Der requires only the C-terminal 78 amino acids of YihI [1]. A yihI deletion mutant is viable and shows a shorter lag period, but the same post-lag growth rate as a wild-type strain. yihI is expressed during the lag period. Overexpression of yihI inhibits cell growth and biogenesis of the 50S ribosomal subunit [1]. YihI is an unusual, highly hydrophilic protein with an uneven distribution of charged residues, resulting in an N-terminal region with high pI and a C-terminal region with low pI [1]. [1]. 20434458. A bacterial GAP-like protein, YihI, regulating the GTPase of Der, an essential GTP-binding protein in Escherichia coli. Hwang J, Inouye M;. J Mol Biol. 2010;399:759-772. (from Pfam) NF016181.5 PF04269.17 DUF440 27 27 101 PfamAutoEq Y Y N DUF440 family protein 1236 Gammaproteobacteria class 2626 EBI-EMBL Protein of unknown function, DUF440 DUF440 family protein This family consists of uncharacterised bacterial proteins. (from Pfam) NF016198.5 PF04288.18 MukE 25 25 229 PfamEq Y Y N chromosome partition protein MukE GO:0005737,GO:0007059,GO:0030261 10545099 1236 Gammaproteobacteria class 3589 EBI-EMBL MukE-like family chromosome partition protein MukE Bacterial protein involved in chromosome partitioning, MukE [1]. 10545099. Complex formation of MukB, MukE and MukF proteins involved in chromosome partitioning in Escherichia coli. Yamazoe M, Onogi T, Sunako Y, Niki H, Yamanaka K, Ichimura T, Hiraga S;. EMBO J 1999;18:5873-5884. (from Pfam) NF016222.5 PF04315.17 EpmC 23.8 23.8 162 PfamEq Y Y N elongation factor P hydroxylase 22706199,23671590 1236 Gammaproteobacteria class 8284 EBI-EMBL Elongation factor P hydroxylase elongation factor P hydroxylase This family catalyses the final step in the elongation factor P modification pathway. It hydroxylates Lys-34 of elongation factor P [1]. Members of this family have a conserved HEXXH motif, suggesting they are putative peptidases of zincin fold [2]. [1]. 22706199. Lys34 of translation elongation factor EF-P is hydroxylated by YfcM. Peil L, Starosta AL, Virumae K, Atkinson GC, Tenson T, Remme J, Wilson DN;. Nat Chem Biol. 2012;8:695-697. [2]. 23671590. CLCAs - A Family of Metalloproteases of Intriguing Phylogenetic Distribution and with Cases of Substituted Catalytic Sites. Lenart A, Dudkiewicz M, Grynberg M, Pawlowski K;. PLoS One. 2013;8:e62272. (from Pfam) NF016256.5 PF04353.18 Rsd_AlgQ 35 35 150 PfamEq Y Y N Rsd/AlgQ family anti-sigma factor GO:0006355,GO:0016989 11591686 1236 Gammaproteobacteria class 5769 EBI-EMBL Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ Rsd/AlgQ family anti-sigma factor This family includes bacterial transcriptional regulators that are thought to act through an interaction with the conserved region 4 of the sigma(70) subunit of RNA polymerase. The Pseudomonas aeruginosa homologue, AlgQ, positively regulates virulence gene expression and is associated with the mucoid phenotype observed in Pseudomonas aeruginosa isolates from cystic fibrosis patients. [1]. 11591686. Bacterial two-hybrid analysis of interactions between region 4 of the sigma(70) subunit of RNA polymerase and the transcriptional regulators Rsd from Escherichia coli and AlgQ from Pseudomonas aeruginosa. Dove SL, Hochschild A;. J Bacteriol 2001;183:6413-6421. (from Pfam) NF016287.5 PF04387.19 PTPLA 27 27 162 domain Y Y N protein tyrosine phosphatase-like domain-containing protein 10644438,11054553 1236 Gammaproteobacteria class 10 EBI-EMBL Protein tyrosine phosphatase-like protein, PTPLA Protein tyrosine phosphatase-like protein, PTPLA This family includes the mammalian protein tyrosine phosphatase-like protein, PTPLA. A significant variation of PTPLA from other protein tyrosine phosphatases is the presence of proline instead of catalytic arginine at the active site. It is thought that PTPLA proteins have a role in the development, differentiation, and maintenance of a number of tissue types [1]. [1]. 10644438. Molecular cloning, chromosomal mapping, and developmental expression of a novel protein tyrosine phosphatase-like gene. Uwanogho DA, Hardcastle Z, Balogh P, Mirza G, Thornburg KL, Ragoussis J, Sharpe PT;. Genomics 1999;62:406-416. [2]. 11054553. Human protein tyrosine phosphatase-like gene: expression profile, genomic structure, and mutation analysis in families with ARVD. Li D, Gonzalez O, Bachinski LL, Roberts R;. Gene 2000;256:237-243. (from Pfam) NF016666.5 PF04792.17 LcrV 25 25 323 domain Y Y N virulence-associated V antigen GO:0005576 7730287,9642196 1236 Gammaproteobacteria class 1780 EBI-EMBL V antigen (LcrV) protein virulence-associated V antigen Yersinia pestis, the aetiologic agent of plague, secretes a set of environmentally regulated, plasmid pCD1-encoded virulence proteins termed Yops and V antigen (LcrV) by a type III secretion mechanism. LcrV is a multifunctional protein that has been shown to act at the level of secretion control by binding the Ysc inner-gate protein LcrG and to modulate the host immune response by altering cytokine production. LcrV is also necessary for full induction of low-calcium response (LCR) stimulon virulence gene transcription. Family members are not confined to Yersinia pestis [1,2]. [1]. 9642196. The V antigen of Yersinia pestis regulates Yop vectorial targeting as well as Yop secretion through effects on YopB and LcrG. Nilles ML, Fields KA, Straley SC;. J Bacteriol 1998;180:3410-3420. [2]. 7730287. Differential effects of deletions in lcrV on secretion of V antigen, regulation of the low-Ca2+ response, and virulence of Yersinia pestis. Skrzypek E, Straley SC;. J Bacteriol 1995;177:2530-2542. (from Pfam) NF016748.5 PF04877.17 Harpin 25.1 25.1 311 PfamEq Y N N HrpZ 11134504,12650449 1236 Gammaproteobacteria class 818 EBI-EMBL HrpZ HrpZ HrpZ from the plant pathogen Pseudomonas syringae binds to lipid bilayers and forms a cation-conducting pore in vivo. This pore-forming activity may allow nutrient release or delivery of virulence factors during bacterial colonisation of host plants [1]. The family of hairpinN proteins, Harpin, has been merged into this family. HrpN is a virulence determinant which elicits lesion formation in Arabidopsis and tobacco and triggers systemic resistance in Arabidopsis [2]. [1]. 11134504. HrpZ(Psph) from the plant pathogen Pseudomonas syringae pv. phaseolicola binds to lipid bilayers and forms an ion-conducting pore in vitro. Lee J, Klusener B, Tsiamis G, Stevens C, Neyt C, Tampakaki AP, Panopoulos NJ, Noller J, Weiler EW, Cornelis GR, Mansfield JW, Nurnberger T;. Proc Natl Acad Sci U S A 2001;98:289-294. [2]. 12650449. Erwinia carotovora subsp. carotovora and Erwinia-derived elicitors HrpN and PehA trigger distinct but interacting defense responses and cell death in Arabidopsis. Kariola T, Palomaki TA, Brader G, Palva ET;. Mol Plant Microbe Interact 2003;16:179-187. (from Pfam) NF016821.5 PF04957.17 RMF 27.9 27.9 54 PfamEq Y Y N ribosome modulation factor 2181444,8440252 1236 Gammaproteobacteria class 2488 EBI-EMBL Ribosome modulation factor ribosome modulation factor This protein associates with 70s ribosomes and converts them to a dimeric form (100S ribosomes) which appear during the transition from the exponential growth phase to the stationary phase of Escherichia coli cells. [1]. 2181444. Structure and probable genetic location of a ribosome modulation factor associated with 100S ribosomes in stationary-phase Escherichia coli cells. Wada A, Yamazaki Y, Fujita N, Ishihama A;. Proc Natl Acad Sci U S A 1990;87:2657-2661. [2]. 8440252. Regulation of the Escherichia coli rmf gene encoding the ribosome modulation factor: growth phase- and growth rate-dependent control. Yamagishi M, Matsushima H, Wada A, Sakagami M, Fujita N, Ishihama A;. EMBO J 1993;12:625-630. (from Pfam) NF016835.5 PF04971.17 Phage_holin_2_1 26 26 64 PfamEq Y Y N phage holin GO:0001907,GO:0019835,GO:0140911 17827300,8467992 1236 Gammaproteobacteria class 5165 EBI-EMBL Bacteriophage P21 holin S membrane-depolarizing phage holin The pinholin type of holin produces a membrane hold just large enough to cause a membrane depolarization that triggers release of Sec-secreted endolysin from the inner membrane, activating the enzyme. This holin mechanism differs from that of holins that actually disrupt membrane enough to provide endolysin access to the cell wall. NF016926.5 PF05068.17 MtlR 25.2 25.2 165 subfamily Y Y N MltR family transcriptional regulator 8300537 1236 Gammaproteobacteria class 4308 EBI-EMBL Mannitol repressor MltR family transcriptional regulator The mannitol operon of Escherichia coli, encoding the mannitol-specific enzyme II of the phosphotransferase system (MtlA) and mannitol phosphate dehydrogenase (MtlD) contains an additional downstream open reading frame which encodes the mannitol repressor (MtlR). [1]. 8300537. The mannitol repressor (MtlR) of Escherichia coli. Figge RM, Ramseier TM, Saier MH Jr;. J Bacteriol 1994;176:840-847. (from Pfam) NF017018.5 PF05166.18 YcgL 25 25 73 PfamEq Y Y N YcgL domain-containing protein 17221885 1236 Gammaproteobacteria class 7745 EBI-EMBL YcgL domain YcgL domain This family of proteins formerly called DUF709 includes the E. coli gene ycgL. Homologues of YcgL are found in gammaproteobacteria. The structure of this protein shows a novel alpha/beta/alpha sandwich structure [1]. [1]. 17221885. NMR structure of YcgL, a conserved protein from Escherichia coli representing the DUF709 family, with a novel alpha/beta/alpha sandwich fold. Minailiuc OM, Vavelyuk O, Gandhi S, Hung MN, Cygler M, Ekiel I;. Proteins. 2007;66:1004-1007. (from Pfam) NF017162.5 PF05321.16 HHA 25 25 57 subfamily Y Y N Hha/YmoA family nucleoid-associated regulatory protein 11790731,18001134,23515315 1236 Gammaproteobacteria class 4077 EBI-EMBL Haemolysin expression modulating protein Hha/YmoA family nucleoid-associated regulatory protein This family consists of haemolysin expression modulating protein (HHA) homologues. YmoA and Hha are highly similar bacterial proteins downregulating gene expression in Yersinia enterocolitica and Escherichia coli, respectively. (from Pfam) NF017300.5 PF05472.16 Ter 22 22 296 subfamily Y Y N DNA replication terminus site-binding protein GO:0003677,GO:0005737,GO:0006274 2687269 1236 Gammaproteobacteria class 8433 EBI-EMBL DNA replication terminus site-binding protein (Ter protein) DNA replication terminus site-binding protein This family contains several bacterial Ter proteins. The Ter protein specifically binds to DNA replication terminus sites on the host and plasmid genome and then blocks progress of the DNA replication fork [1]. [1]. 2687269. Purification of a DNA replication terminus (ter) site-binding protein in Escherichia coli and identification of the structural gene. Hidaka M, Kobayashi T, Takenaka S, Takeya H, Horiuchi T;. J Biol Chem 1989;264:21031-21037. (from Pfam) NF017337.5 PF05513.16 TraA 21.6 21.6 118 domain Y Y N type IV conjugative transfer system pilin TraA GO:0005576 12399504 1236 Gammaproteobacteria class 3660 EBI-EMBL TraA type IV conjugative transfer system pilin TraA Conjugative transfer of a bacteriocin plasmid, pPD1, of Enterococcus faecalis is induced in response to a peptide sex pheromone, cPD1, secreted from plasmid-free recipient cells. cPD1 is taken up by a pPD1 donor cell and binds to an intracellular receptor, TraA. Once a recipient cell acquires pPD1, it starts to produce an inhibitor of cPD1, termed iPD1, which functions as a TraA antagonist and blocks self-induction in donor cells. TraA transduces the signal of cPD1 to the mating response [1]. [1]. 12399504. Functional analysis of TraA, the sex pheromone receptor encoded by pPD1, in a promoter region essential for the mating response in Enterococcus faecalis. Horii T, Nagasawa H, Nakayama J;. J Bacteriol 2002;184:6343-6350. (from Pfam) NF017644.5 PF05844.17 YopD 25 25 297 subfamily Y Y N YopD family type III secretion system translocon subunit 8418066 1236 Gammaproteobacteria class 1036 EBI-EMBL YopD protein YopD family type III secretion system translocon subunit This family consists of several bacterial YopD like proteins. Virulent Yersinia species harbour a common plasmid that encodes essential virulence determinants (Yersinia outer proteins [Yops]), which are regulated by the extracellular stimuli Ca2+ and temperature. YopD is thought to be a possible transmembrane protein and contains an amphipathic alpha-helix in its carboxy terminus [1]. [1]. 8418066. YopB and YopD constitute a novel class of Yersinia Yop proteins. Hakansson S, Bergman T, Vanooteghem JC, Cornelis G, Wolf-Watz H;. Infect Immun 1993;61:71-80. (from Pfam) NF017708.5 PF05920.16 Homeobox_KN 24 24 40 domain Y Y N homeobox domain-containing protein GO:0003677,GO:0006355 17429685,17665086,19734295,21557080,8537382,9336443 1236 Gammaproteobacteria class 9 EBI-EMBL Homeobox KN domain Homeobox KN domain This is a homeobox transcription factor KN domain conserved from fungi to human and plants. They were first identified as TALE homeobox genes in eukaryotes, (including KNOX and MEIS genes) [1,2,3]. They have been recently classified [4,5,6]. [1]. 17429685. Expression patterns of class I KNOX and YABBY genes in Ruscus aculeatus (Asparagaceae) with implications for phylloclade homology. Hirayama Y, Yamada T, Oya Y, Ito M, Kato M, Imaichi R;. Dev Genes Evol. 2007;217:363-372. [2]. 8537382. A novel homeobox protein which recognizes a TGT core and functionally interferes with a retinoid-responsive motif. Bertolino E, Reimund B, Wildt-Perinic D, Clerc RG;. J Biol Chem. 1995;270:31178-31188. [3]. 9336443. Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals. Burglin TR;. Nucleic Acids Res 1997;25:4173-4180. [4]. 17665086. Comprehensive analysis of animal TALE homeobox genes: new conserved motifs and cases of accelerated evolution. Mukherjee K, Burglin TR;. J Mol Evol. 2007;65:137-153. [5]. 19734295. A comprehensive classification and evolutionary analysis of plant homeobox genes. Mukherjee K, Brocchieri L, Burglin TR;. Mol Biol Evol. 2009;26:2775-2794. [6]. 21557080. Homeodomain subtypes and functional diversity. Burglin TR;. Subcell Biochem. 2011;52:95-122. (from Pfam) NF017712.5 PF05925.17 IpgD 22 22 580 PfamEq Y Y N inositol phosphate phosphatase SopB GO:0016791 12356723 1236 Gammaproteobacteria class 1143 EBI-EMBL Enterobacterial virulence protein IpgD inositol phosphate phosphatase SopB This family consists of several enterobacterial IpgD like virulence factor proteins. In the Gram-negative pathogen Shigella flexneri, the virulence factor IpgD is translocated directly into eukaryotic cells and acts as a potent inositol 4-phosphatase that specifically dephosphorylates phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P(2)] into phosphatidylinositol 5-monophosphate [PtdIns(5)P] that then accumulates. Transformation of PtdIns(4,5)P(2) into PtdIns(5)P by IpgD is responsible for dramatic morphological changes of the host cell, leading to a decrease in membrane tether force associated with membrane blebbing and actin filament remodelling [1]. [1]. 12356723. Conversion of PtdIns(4,5)P(2) into PtdIns(5)P by the S.flexneri effector IpgD reorganizes host cell morphology. Niebuhr K, Giuriato S, Pedron T, Philpott DJ, Gaits F, Sable J, Sheetz MP, Parsot C, Sansonetti PJ, Payrastre B;. EMBO J 2002;21:5069-5078. (from Pfam) NF017732.5 PF05946.17 TcpA 25 25 130 subfamily Y Y N type IV pilus major pilin GO:0009289,GO:0043230 12540588 1236 Gammaproteobacteria class 320 EBI-EMBL Toxin-coregulated pilus subunit TcpA type IV pilus major pilin This family consists of toxin-coregulated pilus subunit (TcpA) proteins from Vibrio cholerae and related sequences. The major virulence factors of toxigenic Vibrio cholerae are cholera toxin (CT), which is encoded by a lysogenic bacteriophage (CTXPhi), and toxin-coregulated pilus (TCP), an essential colonisation factor which is also the receptor for CTXPhi. The genes for the biosynthesis of TCP are part of a larger genetic element known as the TCP pathogenicity island [1]. [1]. 12540588. Pathogenic potential of environmental Vibrio cholerae strains carrying genetic variants of the toxin-coregulated pilus pathogenicity island. Faruque SM, Kamruzzaman M, Meraj IM, Chowdhury N, Nair GB, Sack RB, Colwell RR, Sack DA;. Infect Immun 2003;71:1020-1025. (from Pfam) NF017840.5 PF06062.16 UPF0231 25 25 121 PfamEq Y Y N YacL family protein 1236 Gammaproteobacteria class 4294 EBI-EMBL Uncharacterised protein family (UPF0231) YacL family protein Family of uncharacterised Proteobacteria proteins. (from Pfam) NF017890.5 PF06120.16 Phage_HK97_TLTM 24 24 295 domain Y Y N phage tail tape measure protein 1236 Gammaproteobacteria class 14424 EBI-EMBL Tail length tape measure protein phage tail tape measure protein, HK97-type This family consists of the tail length tape measure protein from bacteriophage HK97 and related sequences from Escherichia coli O157:H7. (from Pfam) NF017909.5 PF06141.16 Phage_tail_U 25 25 130 PfamEq Y Y N phage tail terminator protein gpU 19426744 1236 Gammaproteobacteria class 5265 EBI-EMBL Phage minor tail protein U phage tail terminator protein Members of this family are hexameric tail tube terminator proteins of phage lambda or of related phage or prophage such as the Gifsy-1 and Gifsy-2 prophage of Salmonella. NF017914.5 PF06147.16 DUF968 27.6 27.6 171 domain Y Y N DUF968 domain-containing protein 1236 Gammaproteobacteria class 22512 EBI-EMBL Protein of unknown function (DUF968) Protein of unknown function (DUF968) Family of uncharacterised prophage proteins found in Gammaproteobacteria. These may be HNH-nucleases, as there are several conserved cysteines and histidines. (from Pfam) NF017921.5 PF06154.16 CbeA_antitoxin 27 27 101 domain Y Y N type IV toxin-antitoxin system YeeU family antitoxin GO:0051495 14594833,22515815 1236 Gammaproteobacteria class 11326 EBI-EMBL CbeA_antitoxin, type IV, cytoskeleton bundling-enhancing factor A type IV toxin-antitoxin system YeeU family antitoxin CbeA_antitoxin is a family of cognate antitoxins to the CbtA toxins that act by inhibiting the polymerisation of cytoskeletal proteins, see Pfam:PF06755. These are classified as a type IV toxin-antitoxin system [1]. The family includes three proteins from E. coli YagB, YeeU and YfjZ, which act not by forming a complex with CbtA but through acting as antagonists to the CbtA toxicity, by stabilising the CbtA target proteins. For example, YeeU binds directly to both MreB and FtsZ and enhances the bundling of their filaments in vitro. YeeU is also able to neutralise the toxicity caused by other MreB and FtsZ inhibitors, such as A22 [S-(3, 4-dichlorobenzyl)isothiourea] for MreB, and SulA and DicB for FtsZ [2]. Thus CbeA, for cytoskeleton bundling-enhancing factor A, is proposed as a general name for all of these antitoxin proteins. [1]. 14594833. A novel family of Escherichia coli toxin-antitoxin gene pairs. Brown JM, Shaw KJ;. J Bacteriol. 2003;185:6600-6608. [2]. 22515815. YeeU enhances the bundling of cytoskeletal polymers of MreB and FtsZ, antagonizing the CbtA (YeeV) toxicity in Escherichia coli. Masuda H, Tan Q, Awano N, Wu KP, Inouye M;. Mol Microbiol. 2012;84:979-989. (from Pfam) NF017942.5 PF06178.18 KdgM 22 22 222 domain Y Y N oligogalacturonate-specific porin KdgM family protein 11773048 1236 Gammaproteobacteria class 8684 EBI-EMBL Oligogalacturonate-specific porin protein (KdgM) oligogalacturonate-specific porin KdgM family protein This family consists of several bacterial proteins which are homologous to the oligogalacturonate-specific porin protein KdgM (Swiss:Q934G3) from Erwinia chrysanthemi. The phytopathogenic Gram-negative bacteria Erwinia chrysanthemi secretes pectinases, which are able to degrade the pectic polymers of plant cell walls, and uses the degradation products as a carbon source for growth. KdgM is a major outer membrane protein, whose synthesis is strongly induced in the presence of pectic derivatives. KdgM behaves like a voltage-dependent porin that is slightly selective for anions and that exhibits fast block in the presence of trigalacturonate. In contrast to most porins, KdgM seems to be monomeric [1]. [1]. 11773048. The oligogalacturonate-specific porin KdgM of Erwinia chrysanthemi belongs to a new porin family. Blot N, Berrier C, Hugouvieux-Cotte-Pattat N, Ghazi A, Condemine G;. J Biol Chem 2002;277:7936-7944. (from Pfam) NF017947.5 PF06183.18 DinI 24.2 24.2 63 domain Y Y N DinI-like family protein 11152126,12626715 1236 Gammaproteobacteria class 10828 EBI-EMBL DinI-like family DinI-like family protein This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity [1]. The structure of DinI is known [2]. [1]. 12626715. An NMR study on the interaction of Escherichia coli DinI with RecA-ssDNA complexes. Yoshimasu M, Aihara H, Ito Y, Rajesh S, Ishibe S, Mikawa T, Yokoyama S, Shibata T;. Nucleic Acids Res 2003;31:1735-1743. [2]. 11152126. Solution structure of DinI provides insight into its mode of RecA inactivation. Ramirez BE, Voloshin ON, Camerini-Otero RD, Bax A;. Protein Sci 2000;9:2161-2169. (from Pfam) NF017949.5 PF06185.17 YecM 25 25 180 PfamEq Y Y N VOC family protein 12660999 1236 Gammaproteobacteria class 7432 EBI-EMBL YecM protein VOC family protein This family consists of several bacterial YecM proteins of unknown function. [1]. 12660999. Conserved protein YecM from Escherichia coli shows structural homology to metal-binding isomerases and oxygenases. Zhang RG, Duke N, Laskowski R, Evdokimova E, Skarina T, Edwards A, Joachimiak A, Savchenko A;. Proteins 2003;51:311-314. (from Pfam) NF017965.5 PF06203.19 CCT 28.4 28.4 44 domain Y Y N CCT domain-containing protein GO:0005515 10926537 1236 Gammaproteobacteria class 2 EBI-EMBL CCT motif CCT motif This short motif is found in a number of plant proteins. It is rich in basic amino acids and has been called a CCT motif after Co, Col and Toc1 [1]. The CCT motif is about 45 amino acids long and contains a putative nuclear localisation signal within the second half of the CCT motif [1]. Toc1 mutants have been identified in this region. [1]. 10926537. Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. Strayer C, Oyama T, Schultz TF, Raman R, Somers DE, Mas P, Panda S, Kreps JA, Kay SA;. Science 2000;289:768-771. (from Pfam) NF018010.5 PF06251.16 Caps_syn_GfcC_C 20 20 90 domain Y Y N capsule biosynthesis GfcC family protein 10200953,16030220,17250770,21449614 1236 Gammaproteobacteria class 8765 EBI-EMBL Capsule biosynthesis GfcC C-terminal capsule biosynthesis GfcC family protein Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organisation of genes responsible for capsule assembly, the assembly pathway and regulation [1]. This family plays a role in group 4 capsule biosynthesis [2]. These proteins have a beta-grasp fold [3]. Two beta-grasp domains, D2 and D3, are arranged in tandem. There is a C-terminal amphipathic helix which packs against D3. A helical hairpin insert in D2 binds to D3 and constrains its position, a conserved arginine residue at the end of this hairpin is essential for structural integrity [4]. This is the C-terminal domain which covers D3 and D4 domains [4]. [1]. 10200953. Structure, assembly and regulation of expression of capsules in Escherichia coli. Whitfield C, Roberts IS;. Mol Microbiol. 1999;31:1307-1319. [2]. 16030220. Identification of an Escherichia coli operon required for formation of the O-antigen capsule. Peleg A, Shifrin Y, Ilan O, Nadler-Yona C, Nov S, Koby S, Baruch K, Altuvia S, Elgrably-Weiss M, Abe CM, Knutton S, Saper MA, Rosenshine I;. J Bacteriol. 2005;187:5259-5266. [3]. 17250770. A novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands. Burroughs AM, Balaji S, Iyer LM, Aravind L;. Biol Direct. 2007;2:4-4. [4]. 21449614. Crystal structure of E. coli group 4 capsule protein GfcC reveals a domain organization resembling Wza. Sathiyamoorthy K, Mills E, Franzmann TM, Rosenshine I, Saper MA;. Biochemistry 2011;0:0-0. (from Pfam) NF018023.5 PF06266.17 HrpF 22.8 22.8 74 PfamEq Y N N HrpF protein 9721291 1236 Gammaproteobacteria class 348 EBI-EMBL HrpF protein HrpF protein The species Pseudomonas syringae encompasses plant pathogens with differing host specificities and corresponding pathovar designations. P. syringae requires the Hrp (type III protein secretion) system, encoded by a 25-kb cluster of hrp and hrc genes, in order to elicit the hypersensitive response (HR) in nonhosts or to be pathogenic in hosts. The exact function of HrpF is unknown but the protein is needed for pathogenicity [1]. [1]. 9721291. Characterization of the hrpC and hrpRS operons of Pseudomonas syringae pathovars syringae, tomato, and glycinea and analysis of the ability of hrpF, hrpG, hrcC, hrpT, and hrpV mutants to elicit the hypersensitive response and disease in plants. Deng WL, Preston G, Collmer A, Chang CJ, Huang HC;. J Bacteriol 1998;180:4523-4531. (from Pfam) NF018042.5 PF06288.18 DUF1040 27 27 86 PfamAutoEq Y Y N DUF1040 family protein 9868784 1236 Gammaproteobacteria class 2138 EBI-EMBL Protein of unknown function (DUF1040) DUF1040 family protein This family consists of several bacterial YihD proteins of unknown function [1]. [1]. 9868784. Small genes/gene-products in Escherichia coli K-12. Wasinger VC, Humphery-Smith I;. FEMS Microbiol Lett 1998;169:375-382. (from Pfam) NF018056.5 PF06303.17 MatP 27 27 84 PfamEq Y N N MatP N-terminal domain 18984159 1236 Gammaproteobacteria class 2646 EBI-EMBL MatP N-terminal domain MatP N-terminal domain This family, many of whose members are YcbG, organises the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. Organisation of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. MatS sites are the main targets in the E. coli chromosome of YcbG or MatP (macrodomain Ter protein). MatP accumulates in the cell as a discrete focus that co-localises with the Ter macrodomain. The effects of MatP inactivation reveal its role as the main organiser of the Ter macrodomain: in the absence of MatP, DNA is less compacted, the mobility of markers is increased, and segregation of the Ter macrodomain occurs early in the cell cycle. A specific organisational system is required in the Terminus region for bacterial chromosome management during the cell cycle. This entry represents the N-terminal domain of MatP. [1]. 18984159. The MatP/matS site-specific system organizes the terminus region of the E. coli chromosome into a macrodomain. Mercier R, Petit MA, Schbath S, Robin S, El Karoui M, Boccard F, Espeli O;. Cell. 2008;135:475-485. (from Pfam) NF018148.5 PF06406.16 StbA_N 24.6 24.6 158 domain Y Y N plasmid segregation protein ParM domain-containing protein parM 16500678,1706707,19748346,20106979 1236 Gammaproteobacteria class 5985 EBI-EMBL Plasmid segregation protein ParM, N-terminal plasmid segregation protein ParM This entry consists of several bacterial ParM/StbA plasmid stability proteins [1-3]. ParM is involved in the control of plasmid partition and required for the accurate segregation of the plasmid, which forms filaments to drive partition. This protein is an actin homologue and consists of two domains (I and II) with the same conformation [2-4]. This is the N-terminal domain. [1]. 1706707. Transcription of the stability operon of IncFII plasmid NR1. Min YN, Tabuchi A, Womble DD, Rownd RH;. J Bacteriol 1991;173:2378-2384. [2]. 16500678. Crystal structure of an archaeal actin homolog. Roeben A, Kofler C, Nagy I, Nickell S, Hartl FU, Bracher A;. J Mol Biol. 2006;358:145-156. [3]. 20106979. Structure and filament dynamics of the pSK41 actin-like ParM protein: implications for plasmid DNA segregation. Popp D, Xu W, Narita A, Brzoska AJ, Skurray RA, Firth N, Goshdastider U, Maeda Y, Robinson RC, Schumacher MA;. J Biol Chem. 2010;285:10130-10140. [4]. 19748346. Structural polymorphism of the ParM filament and dynamic instability. Galkin VE, Orlova A, Rivera C, Mullins RD, Egelman EH;. Structure. 2009;17:1253-1264. (from Pfam) NF018179.5 PF06440.16 DNA_pol3_theta 34.6 34.6 70 domain Y Y N DNA polymerase III subunit theta GO:0003677,GO:0003887,GO:0006260 10794414,12667053 1236 Gammaproteobacteria class 5332 EBI-EMBL DNA polymerase III, theta subunit DNA polymerase III subunit theta DNA polymerase III (EC 2.7.7.7) is comprised of three tightly associated subunits, alpha, epsilon and theta. This family contains the theta subunit. The structure of the theta subunit shows that the N-terminal two thirds is comprised of three helices while the C-terminal third is disordered [1]. The function of the theta subunit is poorly understood, but the interaction of the theta subunit with the epsilon subunit is thought to enhance the 3' to 5' exonucleolytic proofreading activity of epsilon [2]. [1]. 10794414. NMR solution structure of the theta subunit of DNA polymerase III from Escherichia coli. Keniry MA, Berthon HA, Yang JY, Miles CS, Dixon NE;. Protein Sci 2000;9:721-733. [2]. 12667053. Elucidation of the epsilon-theta subunit interface of Escherichia coli DNA polymerase III by NMR spectroscopy. DeRose EF, Darden T, Harvey S, Gabel S, Perrino FW, Schaaper RM, London RE;. Biochemistry 2003;42:3635-3644. (from Pfam) NF018212.5 PF06474.17 MLTD_N 24.8 24.8 34 domain Y Y N lytic transglycosylase domain-containing protein 7548026,8692991 1236 Gammaproteobacteria class 2738 EBI-EMBL MltD lipid attachment motif MltD lipid attachment motif This short motif is a lipid attachment site. (from Pfam) NF018258.5 PF06526.17 DUF1107 25 25 63 domain Y Y N DUF1107 family protein 1236 Gammaproteobacteria class 1694 EBI-EMBL Protein of unknown function (DUF1107) DUF1107 family protein This family consists of several short, hypothetical bacterial proteins of unknown function. (from Pfam) NF018333.5 PF06610.18 AlaE 25 25 141 PfamEq Y Y N L-alanine exporter AlaE alaE GO:0016020,GO:0034639 21531828 1236 Gammaproteobacteria class 2905 EBI-EMBL L-alanine exporter L-alanine exporter AlaE AlaE is a family of Gram-negative amino-acid transporters. It is not entirely clear why bacteria export metabolites but recent studies have shown that many excrete alanine. AlaE is likely to be the exporter protein for L-alanine. UniProtKB:A8ANM6, UniProt:G4R961 and UniProt:H5SVY7 are classified as putative alanine exporters [1]. [1]. 21531828. Inducible L-alanine exporter encoded by the novel gene ygaW (alaE) in Escherichia coli. Hori H, Yoneyama H, Tobe R, Ando T, Isogai E, Katsumata R;. Appl Environ Microbiol. 2011;77:4027-4034. (from Pfam) NF018334.5 PF06611.17 DUF1145 21 21 58 domain Y Y N DUF1145 domain-containing protein 1236 Gammaproteobacteria class 4256 EBI-EMBL Protein of unknown function (DUF1145) Protein of unknown function (DUF1145) This family consists of several hypothetical bacterial proteins of unknown function. (from Pfam) NF018369.5 PF06649.17 DUF1161 25 25 52 domain Y Y N DUF1161 domain-containing protein 1236 Gammaproteobacteria class 5605 EBI-EMBL Protein of unknown function (DUF1161) Protein of unknown function (DUF1161) This family consists of several short, hypothetical bacterial proteins of unknown function. (from Pfam) NF018468.5 PF06758.18 Olduvai 23 23 68 domain Y N N Olduvai domain 19850849 1236 Gammaproteobacteria class 3 EBI-EMBL Olduvai domain Olduvai domain This domain formerly known as DUF1220 or NBPF domain has been renamed as the Olduvai domain. It is found highly duplicated in the human lineage. [1]. 19850849. DUF1220 Domains, Cognitive Disease, and Human Brain Evolution. Dumas L, Sikela JM;. Cold Spring Harb Symp Quant Biol. 2009; [Epub ahead of print] (from Pfam) NF018492.5 PF06786.17 UPF0253 27 27 65 PfamEq Y Y N YaeP family protein 1236 Gammaproteobacteria class 1415 EBI-EMBL Uncharacterised protein family (UPF0253) YaeP family protein NF018496.5 PF06790.16 UPF0259 31.4 31.4 248 PfamEq Y Y N YciC family protein 1236 Gammaproteobacteria class 5278 EBI-EMBL Uncharacterised protein family (UPF0259) YciC family protein NF018500.5 PF06794.17 UPF0270 25.6 25.6 69 PfamEq Y Y N YheU family protein 1236 Gammaproteobacteria class 5030 EBI-EMBL Uncharacterised protein family (UPF0270) YheU family protein NF018521.5 PF06817.19 RVT_thumb 27.6 27.6 66 domain Y N N Reverse transcriptase thumb domain GO:0003964,GO:0006278 1377403 1236 Gammaproteobacteria class 2 EBI-EMBL Reverse transcriptase thumb domain Reverse transcriptase thumb domain This domain is known as the thumb domain. It is composed of a four helix bundle [1]. [1]. 1377403. Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Kohlstaedt LA, Wang J, Friedman JM, Rice PA, Steitz TA;. Science 1992;256:1783-1790. (from Pfam) NF018538.5 PF06836.17 DUF1240 24.3 24.3 95 domain Y Y N DUF1240 domain-containing protein 1236 Gammaproteobacteria class 2626 EBI-EMBL Protein of unknown function (DUF1240) Protein of unknown function (DUF1240) This family consists of a number of hypothetical putative membrane proteins which seem to be specific to Photorhabdus and Yersinia species. The function of this family is unknown. (from Pfam) NF018552.5 PF06853.17 DUF1249 25 25 116 PfamAutoEq Y Y N DUF1249 domain-containing protein 1236 Gammaproteobacteria class 6547 EBI-EMBL Protein of unknown function (DUF1249) Protein of unknown function (DUF1249) This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown. (from Pfam) NF018592.5 PF06899.16 WzyE 25 25 447 subfamily Y Y N WzyE family oligosaccharide polymerase GO:0009246,GO:0016020 11673418 1236 Gammaproteobacteria class 4499 EBI-EMBL WzyE protein, O-antigen assembly polymerase WzyE family oligosaccharide polymerase This family consists of several WzyE proteins which appear to be specific to Enterobacteria. Members of this family are described as putative ECA polymerases this has been found to be incorrect [1]. The function of this family is unknown. The family is a transmembrane family with up to 11 TM regions, and is necessary for the assembly of O-antigen lipopolysaccharide. [1]. 11673418. Identification of the structural gene for the TDP-Fuc4NAc:lipid II Fuc4NAc transferase involved in synthesis of enterobacterial common antigen in Escherichia coli K-12. Rahman A, Barr K, Rick PD;. J Bacteriol 2001;183:6509-6516. (from Pfam) NF018664.5 PF06984.18 MRP-L47 27 27 87 PfamEq Y N N Mitochondrial 39-S ribosomal protein L47 (MRP-L47) GO:0003735,GO:0005761,GO:0006412 9445368 1236 Gammaproteobacteria class 10 EBI-EMBL Mitochondrial 39-S ribosomal protein L47 (MRP-L47) Mitochondrial 39-S ribosomal protein L47 (MRP-L47) This family represents the N-terminal region (approximately 8 residues) of the eukaryotic mitochondrial 39-S ribosomal protein L47 (MRP-L47). Mitochondrial ribosomal proteins (MRPs) are the counterparts of the cytoplasmic ribosomal proteins, in that they fulfil similar functions in protein biosynthesis. However, they are distinct in number, features and primary structure [1]. [1]. 9445368. Mitochondrial ribosomal proteins (MRPs) of yeast. Graack HR, Wittmann-Liebold B;. Biochem J 1998;329:433-448. (from Pfam) NF018698.5 PF07023.17 DUF1315 25 25 82 PfamAutoEq Y Y N DUF1315 family protein 1236 Gammaproteobacteria class 5983 EBI-EMBL Protein of unknown function (DUF1315) DUF1315 family protein This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown. (from Pfam) NF018726.5 PF07057.16 TraI_C 27 27 154 domain Y Y N conjugative transfer relaxase/helicase TraI domain-containing protein GO:0003677,GO:0003678,GO:0005524,GO:0016818 11054423,19136009,28457609 1236 Gammaproteobacteria class 16491 EBI-EMBL DNA helicase TraI, C-terminal conjugative transfer relaxase/helicase TraI This entry represents the C-terminal domain of the bacterial DNA helicase TraI (EC:3.6.1.-). TraI is a bifunctional protein that catalyses the unwinding of duplex DNA as well as acts as a sequence-specific DNA trans-esterase, providing the site- and strand-specific nick required to initiate DNA transfer [1]. This domain is essential for conjugative DNA transfer [2]. [1]. 11054423. F plasmid conjugative DNA transfer: the TraI helicase activity is essential for DNA strand transfer. Matson SW, Sampson JK, Byrd DR;. J Biol Chem 2001;276:2372-2379. [2]. 19136009. A novel fold in the TraI relaxase-helicase c-terminal domain is essential for conjugative DNA transfer. Guogas LM, Kennedy SA, Lee JH, Redinbo MR;. J Mol Biol. 2009;386:554-568. [3]. 28457609. Cryo-EM Structure of a Relaxase Reveals the Molecular Basis of DNA Unwinding during Bacterial Conjugation. Ilangovan A, Kay CWM, Roier S, El Mkami H, Salvadori E, Zechner EL, Zanetti G, Waksman G;. Cell. 2017;169:708-721. (from Pfam) NF018758.5 PF07091.16 FmrO 27 27 255 PfamEq Y N N Ribosomal RNA methyltransferase (FmrO) 2013410,8486289 1236 Gammaproteobacteria class 348 EBI-EMBL Ribosomal RNA methyltransferase (FmrO) Ribosomal RNA methyltransferase (FmrO) This family consists of several bacterial ribosomal RNA methyltransferase (aminoglycoside-resistance methyltransferase) proteins [1,2]. [1]. 8486289. Analysis of the self-defense gene (fmrO) of a fortimicin A (astromicin) producer, Micromonospora olivasterospora: comparison with other aminoglycoside-resistance-encoding genes. Ohta T, Hasegawa M;. Gene 1993;127:63-69. [2]. 2013410. Cloning and characterization of gentamicin-resistance genes from Micromonospora purpurea and Micromonospora rosea. Kelemen GH, Cundliffe E, Financsek I;. Gene 1991;98:53-60. (from Pfam) NF018782.5 PF07117.16 DUF1373 25.7 25.7 212 domain Y Y N DUF1373 domain-containing protein 1236 Gammaproteobacteria class 2 EBI-EMBL Protein of unknown function (DUF1373) Protein of unknown function (DUF1373) This family consists of several hypothetical proteins which seem to be specific to Oryzias latipes (Japanese ricefish). Members of this family are typically around 200 residues in length. The function of this family is unknown. (from Pfam) NF018790.5 PF07126.17 ZapC_C 27 27 81 PfamEq Y Y N cell division protein ZapC domain-containing protein GO:0051301 21216997,26619764,26655719 1236 Gammaproteobacteria class 4466 EBI-EMBL Cell-division protein ZapC, C-terminal Cell-division protein ZapC, C-terminal ZapC is one of four FtsZ-binding components of the Z ring in bacteria. Formation of the Z ring on the cytoplasmic surface of the membrane is the starting process for assembly of the cell-division apparatus. It binds directly to the Z ring, and although it is not essential for absolute cell division it contributes to it by enhancing the interactions between the FtsZ protofilaments (or polymers) which aggregate to form the ring conformation in the Z ring [1]. This is the C-terminal domain which contains a pocket with a hydrophobic centre surrounded by conserved basic residues, critical for FtsZ binding [2,3]. [1]. 21216997. Identification of Escherichia coli ZapC (YcbW) as a component of the division apparatus that binds and bundles FtsZ polymers. Hale CA, Shiomi D, Liu B, Bernhardt TG, Margolin W, Niki H, de Boer PA;. J Bacteriol. 2011;193:1393-1404. [2]. 26655719. Structural and Functional Analyses Reveal Insights into the Molecular Properties of the Escherichia coli Z Ring Stabilizing Protein, ZapC. Schumacher MA, Zeng W, Huang KH, Tchorzewski L, Janakiraman A;. J Biol Chem. 2016;291:2485-2498. [3]. 26619764. Crystal structure of the Z-ring associated cell division protein ZapC from Escherichia coli. Ortiz C, Kureisaite-Ciziene D, Schmitz F, McLaughlin SH, Vicente M, Lowe J;. FEBS Lett. 2015;589:3822-3828. (from Pfam) NF018792.5 PF07128.17 DUF1380 26 26 137 domain Y Y N DUF1380 family protein 1236 Gammaproteobacteria class 5217 EBI-EMBL Protein of unknown function (DUF1380) DUF1380 family protein This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be specific to Enterobacteria. The function of this family is unknown. (from Pfam) NF018794.5 PF07130.17 YebG 27.5 27.5 74 PfamEq Y Y N YebG family protein 10474193 1236 Gammaproteobacteria class 5274 EBI-EMBL YebG protein YebG family protein This family consists of several bacterial YebG proteins of around 75 residues in length. The exact function of this protein is unknown but it is thought to be involved in the SOS response. The induction of the yebG gene occurs as cell enter into the stationary growth phase and is dependent on is dependent on cyclic AMP and H-NS [1]. [1]. 10474193. Identification of genetic factors altering the SOS induction of DNA damage-inducible yebG gene in Escherichia coli. Oh TJ, Kim IG;. FEMS Microbiol Lett 1999;177:271-277. (from Pfam) NF018809.5 PF07148.17 MalM 26 26 134 subfamily Y Y N MalM family protein GO:0008643,GO:0042597 1730061 1236 Gammaproteobacteria class 7755 EBI-EMBL Maltose operon periplasmic protein precursor (MalM) MalM family protein This family consists of several maltose operon periplasmic protein precursor (MalM) sequences. The function of this family is unknown [1]. [1]. 1730061. Completion of the nucleotide sequence of the 'maltose B' region in Salmonella typhimurium: the high conservation of the malM gene suggests a selected physiological role for its product. Schneider E, Francoz E, Dassa E;. Biochim Biophys Acta 1992;1129:223-227. (from Pfam) NF018865.5 PF07208.16 DUF1414 25 25 44 PfamAutoEq Y Y N DUF1414 domain-containing protein 1236 Gammaproteobacteria class 2115 EBI-EMBL Protein of unknown function (DUF1414) Protein of unknown function (DUF1414) This family consists of several hypothetical bacterial proteins of around 70 residues in length. Members of this family are often referred to as YejL. The function of this family is unknown. (from Pfam) NF018872.5 PF07216.17 LcrG 24.1 24.1 91 PfamEq Y N N LcrG protein 9484897 1236 Gammaproteobacteria class 396 EBI-EMBL LcrG protein LcrG protein This family consists of several bacterial LcrG proteins. Yersiniae are equipped with the Yop virulon, an apparatus that allows extracellular bacteria to deliver toxic Yop proteins inside the host cell cytosol in order to sabotage the communication networks of the host cell or even to cause cell death. LcrG is a component of the Yop virulon involved in the regulation of secretion of the Yops [1]. [1]. 9484897. Heparin interferes with translocation of Yop proteins into HeLa cells and binds to LcrG, a regulatory component of the Yersinia Yop apparatus. Boyd AP, Sory MP, Iriarte M, Cornelis GR;. Mol Microbiol 1998;27:425-436. (from Pfam) NF018882.5 PF07226.16 DUF1422 23.2 23.2 114 PfamAutoEq Y Y N DUF1422 family protein 1236 Gammaproteobacteria class 2280 EBI-EMBL Protein of unknown function (DUF1422) DUF1422 family protein This family consists of several hypothetical bacterial proteins of around 120 residues in length. The function of this family is unknown. (from Pfam) NF018929.5 PF07278.16 DUF1441 35.1 35.1 147 subfamily Y Y N DUF1441 family protein 1236 Gammaproteobacteria class 2800 EBI-EMBL Protein of unknown function (DUF1441) DUF1441 family protein This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown. However, it appears to be distantly related to other HTH families so may act as a transcriptional regulator. (from Pfam) NF019004.5 PF07356.17 DUF1481 25 25 186 PfamAutoEq Y Y N DUF1481 domain-containing protein 1236 Gammaproteobacteria class 4594 EBI-EMBL Protein of unknown function (DUF1481) Protein of unknown function (DUF1481) This family consists of several hypothetical bacterial proteins of around 230 residues in length. Members of this family are often referred to as YjaH and are found in the Orders Vibrionales and Enterobacteriales. The function of this family is unknown. (from Pfam) NF019006.5 PF07358.16 DUF1482 25 25 57 subfamily Y Y N DUF1482 family protein 1236 Gammaproteobacteria class 3490 EBI-EMBL Protein of unknown function (DUF1482) DUF1482 family protein This family consists of several Enterobacterial proteins of around 60 residues in length. The function of this family is unknown. (from Pfam) NF019029.5 PF07383.17 DUF1496 20.2 20.2 53 PfamAutoEq Y Y N DUF1496 domain-containing protein 1236 Gammaproteobacteria class 3866 EBI-EMBL Protein of unknown function (DUF1496) Protein of unknown function (DUF1496) This family consists of several bacterial proteins of around 90 residues in length. Members of this family seem to be found exclusively in the Orders Vibrionales and Enterobacteriales. The function of this family is unknown. (from Pfam) NF019062.5 PF07417.17 Crl 27 27 128 PfamEq Y Y N Crl family RNA polymerase assembly factor GO:0045893 1357528,27180360 1236 Gammaproteobacteria class 2696 EBI-EMBL Sigma factor-binding transcriptional regulator Crl Crl family RNA polymerase assembly factor This family contains the bacterial Sigma factor-binding protein Crl (approximately 130 residues long). This is a transcriptional regulator of the csgA curlin subunit gene for curli fibres that are found on the surface of certain bacteria [1]. These proteins bind to the sigma-S subunit of RNA polymerase, activating expression of sigma-S-regulated genes. It was initially suggested that Crl affects transcription initiation in vitro by other sigmas, such as sigma-70 and sigma-32. However, it is now established that Crl binds specifically to the alternative sigma factor S/RpoS and favors its association with the core RNAP (RNA polymerase), thereby increasing its activity, which in turn regulates general stress response that protects many Gram-negative bacteria from several harmful environmental conditions. Furthermore, sigma S factor/RpoS plays important roles in biofilm formation and virulence of the food-borne pathogen Salmonella enterica serovar Typhimurium [2]. [1]. 1357528. The Crl protein activates cryptic genes for curli formation and fibronectin binding in Escherichia coli HB101. Arnqvist A, Olsen A, Pfeifer J, Russell DG, Normark S;. Mol Microbiol 1992;6:2443-2452. [2]. 27180360. Recent advances in the characterization of Crl, the unconventional activator of the stress sigma factor sigmaS/RpoS. Cavaliere P, Norel F;. Biomol Concepts. 2016;7:197-204. (from Pfam) NF019089.5 PF07445.17 PriC 23.3 23.3 174 PfamEq Y Y N primosomal replication protein PriC priC 10613856 1236 Gammaproteobacteria class 6426 EBI-EMBL Primosomal replication protein priC primosomal replication protein PriC This family contains the bacterial primosomal replication protein priC. In Escherichia coli, this function in the assembly of the primosome [1]. [1]. 10613856. Role of PriA in replication fork reactivation in Escherichia coli. Sandler SJ, Marians KJ;. J Bacteriol 2000;182:9-13. (from Pfam) NF019445.5 PF07828.17 PA-IL 22.5 22.5 121 PfamEq Y Y N LecA/PA-IL family lectin 1429650 1236 Gammaproteobacteria class 608 EBI-EMBL PA-IL-like protein LecA/PA-IL family lectin The members of this family are similar to the galactophilic lectin-1 expressed by P. aeruginosa ((PA-IL, Swiss:Q05097). Lectins recognising specific carbohydrates found on the surface of host cells are known to be involved in the initiation of infections by this organism. The protein is thought to be organised into an extensive network of beta-sheets, as is the case with many other lectins [1]. [1]. 1429650. Analysis of the amino acid sequence of the Pseudomonas aeruginosa galactophilic PA-I lectin. Avichezer D, Katcoff DJ, Garber NC, Gilboa-Garber N;. J Biol Chem 1992;267:23023-23027. (from Pfam) NF019482.5 PF07867.16 DUF1654 27 27 70 domain Y Y N DUF1654 domain-containing protein 1236 Gammaproteobacteria class 4025 EBI-EMBL Protein of unknown function (DUF1654) Protein of unknown function (DUF1654) This family consists of proteins from the Pseudomonadaceae. (from Pfam) NF019596.5 PF07984.17 NTP_transf_7 27 27 321 PfamEq Y N N Nucleotidyltransferase GO:1990817 19833706 1236 Gammaproteobacteria class 5 EBI-EMBL Nucleotidyltransferase Nucleotidyltransferase This family contains many hypothetical proteins. It also includes four nematode prion-like proteins. This domain has been identified as part of the nucleotidyltransferase superfamily [1]. [1]. 19833706. Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. Kuchta K, Knizewski L, Wyrwicz LS, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2009; [Epub ahead of print] (from Pfam) NF019660.5 PF08048.17 RepA1_leader 25 25 25 PfamEq Y N N Tap RepA1 leader peptide 1447133 1236 Gammaproteobacteria class 549 EBI-EMBL Tap RepA1 leader peptide Tap RepA1 leader peptide This family consists of the RepA1 leader peptides. The frequency of replication of IncFII plasmid NR1 during the cell division cycle is regulated by the control of the synthesis of the plasmid-specific replication initiation protein (RepA1). When RepA1 is synthesised, it binds to the plasmid replication origin (ori) and effects the assembly of a replication complex composed of host proteins that mediate the replication of the plasmid [1]. The tap gene encodes a 24-amino acids protein. The translation of tap is required for translation of repA. [1]. 1447133. Expression of the repA1 gene of IncFII plasmid NR1 is translationally coupled to expression of an overlapping leader peptide. Wu R, Wang X, Womble DD, Rownd RH;. J Bacteriol 1992;174:7620-7628. (from Pfam) NF019877.5 PF08272.16 Topo_Zn_Ribbon 25 25 41 PfamEq Y N N Topoisomerase I zinc-ribbon-like GO:0003677,GO:0003917,GO:0006265 10873443 1236 Gammaproteobacteria class 14669 EBI-EMBL Topoisomerase I zinc-ribbon-like Topoisomerase I zinc-ribbon-like Some Proteobacteria topoisomerase I contain two zinc-ribbon-like domains at the C-terminus that structurally homologous to Pfam:PF01396. However, this domain no longer bind zinc. Indeed, only one of the four cysteine residues remains [1]. [1]. 10873443. C-terminal domains of Escherichia coli topoisomerase I belong to the zinc-ribbon superfamily. Grishin NV;. J Mol Biol 2000;299:1165-1177. (from Pfam) NF020114.5 PF08525.16 OapA_N 20.7 20.7 28 domain Y Y N OapA N-terminal domain-containing protein 8559074,8830271 1236 Gammaproteobacteria class 9951 EBI-EMBL Opacity-associated protein A N-terminal motif Opacity-associated protein A N-terminal motif This family includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonisation, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [1,2]. This motif occurs at the N-terminus of these proteins. It contains a conserved histidine followed by a run of hydrophobic residues. [1]. 8559074. Identification and characterization of a cell envelope protein of Haemophilus influenzae contributing to phase variation in colony opacity and nasopharyngeal colonization. Weiser JN, Chong ST, Greenberg D, Fong W;. Mol Microbiol 1995;17:555-564. [2]. 8830271. Phenotypic switching of Haemophilus influenzae. Moxon ER, Gewurz BE, Richards JC, Inzana T, Jennings MP, Hood DW;. Mol Microbiol 1996;19:1149-1150. (from Pfam) NF020266.5 PF08682.15 DUF1780 27 27 208 PfamAutoEq Y Y N DUF1780 domain-containing protein 22638584 1236 Gammaproteobacteria class 969 EBI-EMBL Putative endonuclease, protein of unknown function (DUF1780) DUF1780 family protein This is a family of uncharacterised proteins. The structure of a hypothetical protein from Pseudomonas aeruginosa has shown it to adopt an alpha/beta fold, placing it in the Endonuclease superfamily/clan of restriction endonucleases. [1]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF020355.5 PF08775.15 ParB 25 25 126 domain Y Y N ParB family protein 16306995 1236 Gammaproteobacteria class 3162 EBI-EMBL ParB family ParB family protein ParB is a component of the par system which mediates accurate DNA partition during cell division. It recognises A-box and B-box DNA motifs. ParB forms an asymmetric dimer with 2 extended helix-turn-helix (HTH) motifs that bind to A-boxes. The HTH motifs emanate from a beta sheet coiled coil DNA binding module [1]. Both DNA binding elements are free to rotate around a flexible linker, this enables them to bind to complex arrays of A- and B-box elements on adjacent DNA arms of the looped partition site [1]. [1]. 16306995. Structures of ParB bound to DNA reveal mechanism of partition complex formation. Schumacher MA, Funnell BE;. Nature. 2005;438:516-519. (from Pfam) NF020383.5 PF08804.15 gp32 26.8 26.8 208 domain Y N N gp32 DNA binding protein like GO:0003697 7630406 1236 Gammaproteobacteria class 748 EBI-EMBL gp32 DNA binding protein like gp32 DNA binding protein like gp32 is a single stranded (ss) DNA binding protein in bacteriophage T4 that is essential for DNA replication, recombination and repair. The ssDNA binding cleft of gp32 comprises regions from three structural subdomains [1]. [1]. 7630406. Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA. Shamoo Y, Friedman AM, Parsons MR, Konigsberg WH, Steitz TA;. Nature. 1995;376:362-366. (from Pfam) NF020465.5 PF08891.16 YfcL 25 25 83 PfamEq Y Y N YfcL family protein 1236 Gammaproteobacteria class 3086 EBI-EMBL YfcL protein YfcL family protein This family of proteins are functionally uncharacterised. THey are related to the short YfcL protein from E. coli. (from Pfam) NF020578.5 PF09009.15 Exotox-A_cataly 25.9 25.9 177 domain Y N N Exotoxin A catalytic GO:0047286 8692916 1236 Gammaproteobacteria class 974 EBI-EMBL Exotoxin A catalytic Exotoxin A catalytic Members of this family, which are found in prokaryotic exotoxin A, catalyse the transfer of ADP ribose from nicotinamide adenine dinucleotide (NAD) to elongation factor-2 in eukaryotic cells, with subsequent inhibition of protein synthesis [1]. [1]. 8692916. Crystal structure of the catalytic domain of Pseudomonas exotoxin A complexed with a nicotinamide adenine dinucleotide analog: implications for the activation process and for ADP ribosylation. Li M, Dyda F, Benhar I, Pastan I, Davies DR;. Proc Natl Acad Sci U S A. 1996;93:6902-6906. (from Pfam) NF020582.5 PF09013.15 YopH_N 25 25 123 domain Y N N YopH, N-terminal GO:0004725,GO:0006470 11375498 1236 Gammaproteobacteria class 181 EBI-EMBL YopH, N-terminal YopH, N-terminal The N-terminal domain of YopH is a compact structure composed of four alpha-helices and two beta-hairpins. Helices alpha-1 and alpha-3 are parallel to each other and antiparallel to helices alpha-2 and alpha-4. This domain targets YopH for secretion from the bacterium and translocation into eukaryotic cells, and has phosphotyrosyl peptide-binding activity, allowing for recognition of p130Cas and paxillin [1]. [1]. 11375498. Structure of the N-terminal domain of Yersinia pestis YopH at 2.0 A resolution. Evdokimov AG, Tropea JE, Routzahn KM, Copeland TD, Waugh DS;. Acta Crystallogr D Biol Crystallogr. 2001;57:793-799. (from Pfam) NF020593.5 PF09025.15 T3SS_needle_reg 25 25 145 domain Y Y N YopR/YscH family type III secretion effector GO:0030254,GO:0030257 15930010,19968786 1236 Gammaproteobacteria class 1128 EBI-EMBL YopR, type III needle-polymerisation regulator YopR/YscH family type III secretion effector The YopR core domain, predominantly found in the Gammaproteobacteria virulence factor YopR, is composed of five alpha-helices, four of which are arranged in an antiparallel bundle. Little is known about this domain, though it may contribute to the virulence of the protein YopR [1]. YopR controls the selective access of early (YscF, YscI and YscP) substrates to the type III secretion machines of yersiniae and other Gammaproteobacteriae. YopR is a mobile regulatory component thought to function as a checkpoints probing the completion of discrete intermediary stages in the assembly of the type III injection pathway. The location of secreted YopR (into the medium) is directly controlling the secretion of YscF, the polymerised needle protein Pfam:PF09392, thereby impacting the assembly of type III machines [2]. [1]. 15930010. Crystal structure of the protease-resistant core domain of Yersinia pestis virulence factor YopR. Schubot FD, Cherry S, Austin BP, Tropea JE, Waugh DS;. Protein Sci. 2005;14:1679-1683. [2]. 19968786. YopR impacts type III needle polymerization in Yersinia species. Blaylock B, Berube BJ, Schneewind O;. Mol Microbiol. 2010;75:221-229. (from Pfam) NF020641.5 PF09075.15 STb_secrete 25 25 48 PfamEq Y N N Heat-stable enterotoxin B, secretory 8528070 1236 Gammaproteobacteria class 32 EBI-EMBL Heat-stable enterotoxin B, secretory Heat-stable enterotoxin B, secretory Members of this family assume a helical secondary structure, with two alpha helices forming a disulphide crosslinked alpha-helical hairpin. The disulphide bonds are crucial for the toxic activity of the protein, and are required for maintenance of the tertiary structure, and subsequent interaction with the particulate form of guanylate cyclase, increasing cyclic GMP levels within the host intestinal epithelial cells [1]. [1]. 8528070. The structure of Escherichia coli heat-stable enterotoxin b by nuclear magnetic resonance and circular dichroism. Sukumar M, Rizo J, Wall M, Dreyfus LA, Kupersztoch YM, Gierasch LM;. Protein Sci. 1995;4:1718-1729. (from Pfam) NF020666.5 PF09101.16 Exotox-A_bind 20.5 20.5 274 domain Y Y N exotoxin A binding domain-containing protein 11734000 1236 Gammaproteobacteria class 1222 EBI-EMBL Exotoxin A binding Exotoxin A binding Members of this family are found in Pseudomonas aeruginosa exotoxin A, and are responsible for binding of the toxin to the alpha-2-macroglobulin receptor, with subsequent internalisation into endosomes. The domain adopts a thirteen-strand antiparallel beta jelly roll topology, which belongs to the Concanavalin A-like lectins/glucanases fold superfamily [1]. [1]. 11734000. Refined crystallographic structure of Pseudomonas aeruginosa exotoxin A and its implications for the molecular mechanism of toxicity. Wedekind JE, Trame CB, Dorywalska M, Koehl P, Raschke TM, McKee M, FitzGerald D, Collier RJ, McKay DB;. J Mol Biol. 2001;314:823-837. (from Pfam) NF020667.5 PF09102.15 Exotox-A_target 25 25 142 PfamEq Y N N Exotoxin A, targeting 11734000 1236 Gammaproteobacteria class 968 EBI-EMBL Exotoxin A, targeting Exotoxin A, targeting Members of this family are found in Pseudomonas aeruginosa exotoxin A, and are responsible for transmembrane targeting of the toxin, as well as transmembrane translocation of the catalytic domain into the cytoplasmic compartment. A furin cleavage site is present within the domain: cleavage generates a 37 kDa carboxy-terminal fragment, which includes the enzymatic domain, which is then is translocated into the cytoplasm. The domain adopts a helical structure, with six alpha-helices forming a bundle [1]. [1]. 11734000. Refined crystallographic structure of Pseudomonas aeruginosa exotoxin A and its implications for the molecular mechanism of toxicity. Wedekind JE, Trame CB, Dorywalska M, Koehl P, Raschke TM, McKee M, FitzGerald D, Collier RJ, McKay DB;. J Mol Biol. 2001;314:823-837. (from Pfam) NF020783.5 PF09222.15 Fim-adh_lectin 25 25 171 PfamEq Y N N Fimbrial adhesin F17-AG, lectin domain GO:0009289,GO:0044406 12864853 1236 Gammaproteobacteria class 148 EBI-EMBL Fimbrial adhesin F17-AG, lectin domain Fimbrial adhesin F17-AG, lectin domain Members of this family are carbohydrate-specific lectin domains found in bacterial fimbrial adhesins. They adopt a compact, elongated structure consisting of a beta-sandwich with two major sheets: one consisting of five long strands in mixed orientations, and a front sheet with four antiparallel strands, forming an immunoglobin-like fold [1]. [1]. 12864853. The fimbrial adhesin F17-G of enterotoxigenic Escherichia coli has an immunoglobulin-like lectin domain that binds N-acetylglucosamine. Buts L, Bouckaert J, De Genst E, Loris R, Oscarson S, Lahmann M, Messens J, Brosens E, Wyns L, De Greve H;. Mol Microbiol. 2003;49:705-715. (from Pfam) NF020825.5 PF09264.16 Sial-lect-inser 25.8 25.8 198 PfamEq Y N N Vibrio cholerae sialidase, lectin insertion GO:0033691 15226294 1236 Gammaproteobacteria class 323 EBI-EMBL Vibrio cholerae sialidase, lectin insertion Vibrio cholerae sialidase, lectin insertion Members of this family are predominantly found in Vibrio cholerae sialidase, and adopt a beta sandwich structure consisting of 12-14 strands arranged in two beta-sheets. They bind to lectins with high affinity helping to target the protein to sialic acid-rich environments, thereby enhancing the catalytic efficiency of the enzyme [1]. [1]. 15226294. Sialic acid recognition by Vibrio cholerae neuraminidase. Moustafa I, Connaris H, Taylor M, Zaitsev V, Wilson JC, Kiefel MJ, von Itzstein M, Taylor G;. J Biol Chem. 2004;279:40819-40826. (from Pfam) NF021026.5 PF09477.15 Type_III_YscG 32.1 32.1 116 PfamEq Y Y N YscG family type III secretion protein 16115870,18281060 1236 Gammaproteobacteria class 613 EBI-EMBL Bacterial type II secretion system chaperone protein (type_III_yscG) YscG family type III secretion protein YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designated Yops (Yersinia outer proteins), in Yersinia. This entry consists of YscG from Yersinia and functionally equivalent type III secretion proteins in other species: e.g. AscG in Aeromonas and LscG in Photorhabdus luminescens. (from Pfam) NF021047.5 PF09498.15 DUF2388 25 25 70 domain Y Y N DUF2388 domain-containing protein 1236 Gammaproteobacteria class 8258 EBI-EMBL Protein of unknown function (DUF2388) Protein of unknown function (DUF2388) This family consists of small hypothetical proteins, about 100 amino acids in length. The family includes five members (three in tandem) in Pseudomonas aeruginosa PAO1 and in Pseudomonas putida (strain KT2440), four in Pseudomonas syringae DC3000, and single members in several other Proteobacteria. The function is unknown. (from Pfam) NF021072.5 PF09526.15 DUF2387 25.9 25.9 72 PfamAutoEq Y Y N YheV family putative metal-binding protein 1236 Gammaproteobacteria class 5261 EBI-EMBL Probable metal-binding protein (DUF2387) YheV family putative metal-binding protein Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria. (from Pfam) NF021115.5 PF09574.15 DUF2374 27 27 42 PfamEq Y Y N TIGR02808 family protein 1236 Gammaproteobacteria class 517 EBI-EMBL Protein of unknown function (Duf2374) TIGR02808 family protein This very small protein (about 46 amino acids) consists largely of a single predicted membrane-spanning region. It is found in Photobacterium profundum SS9 and in three species of Vibrio, always near periplasmic nitrate reductase genes, but far from the periplasmic nitrate reductase genes in Aeromonas hydrophila ATCC 7966. (from Pfam) NF021123.5 PF09583.15 Phageshock_PspG 25 25 64 domain Y Y N envelope stress response protein PspG 15485810,19555453 1236 Gammaproteobacteria class 2098 EBI-EMBL Phage shock protein G (Phageshock_PspG) envelope stress response protein PspG This protein was previously designated as YjbO in Escherichia coli. It is found only in genomes that have the phage shock operon (psp), but it is only rarely encoded near other psp genes. The psp regulon is upregulated in response to a number of stress conditions, including ethanol, expression of the filamentous phage secretin protein IV and other secretins and heat shock. (from Pfam) NF021132.5 PF09592.15 DUF2031 27 27 227 PfamAutoEq Y Y N DUF2031 domain-containing protein 12368865 1236 Gammaproteobacteria class 3 EBI-EMBL Protein of unknown function (DUF2031) Protein of unknown function (DUF2031) This protein is expressed in Plasmodium; its function is unknown. It may be the product of gene family pyst-b [1]. [1]. 12368865. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, Shallom SJ, van Aken SE, Riedmuller SB, Feldblyum TV, Cho JK, Quackenbush J, Sedegah M, Shoa. Nature. 2002;419:512-519. (from Pfam) NF021160.5 PF09621.15 LcrR 21.2 21.2 138 PfamEq Y N N Type III secretion system regulator (LcrR) 1236 Gammaproteobacteria class 1114 EBI-EMBL Type III secretion system regulator (LcrR) Type III secretion system regulator (LcrR) This family of proteins are encoded within type III secretion operons and have been characterised in Yersinia as a regulator of the Low-Calcium Response (LCR). (from Pfam) NF021171.5 PF09632.15 Rac1 25 25 297 domain Y N N Rac1-binding domain 16959567 1236 Gammaproteobacteria class 55 EBI-EMBL Rac1-binding domain Rac1-binding domain The Rac1-binding domain is the C-terminal portion of YpkA from Yersinia. It is an all-helical molecule consisting of two distinct subdomains connected by a linker. the N-terminal end, residues 434-615, consists of six helices organised into two three-helix bundles packed against each other. This region is involved with binding to GTPases. The C-terminal end, residues 705-732. is a novel and elongated fold consisting of four helices clustered into two pairs, and this fold carries the helix implicated in actin activation. Rac1-binding domain mimics host guanidine nucleotide dissociation inhibitors (GDIs) of the Rho GTPases, thereby inhibiting nucleotide exchange in Rac1 and causing cytoskeletal disruption in the host [1]. It is usually found downstream of Pfam:PF00069. [1]. 16959567. Yersinia virulence depends on mimicry of host Rho-family nucleotide dissociation inhibitors. Prehna G, Ivanov MI, Bliska JB, Stebbins CE;. Cell. 2006;126:869-880. (from Pfam) NF021173.5 PF09634.15 DUF2025 25 25 105 PfamAutoEq Y Y N DUF2025 family protein 1236 Gammaproteobacteria class 1463 EBI-EMBL Protein of unknown function (DUF2025) DUF2025 family protein This protein is produced from gene PA1123 in Pseudomonas. It contains three alpha helices and six beta strands and is thought to be monomeric. It appears to be present in the biofilm layer and may be a lipoprotein. (from Pfam) NF021231.5 PF09695.15 YtfJ_HI0045 24 24 160 domain Y Y N YtfJ family protein 1236 Gammaproteobacteria class 6584 EBI-EMBL Bacterial protein of unknown function (YtfJ_HI0045) YtfJ family protein These are sequences from gamma proteobacteria that are related to the E. coli protein, YtfJ. (from Pfam) NF021358.5 PF09829.14 DUF2057 24.2 24.2 192 domain Y Y N DUF2057 family protein 1236 Gammaproteobacteria class 11835 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2057) DUF2057 family protein This domain, found in various prokaryotic proteins, has no known function. (from Pfam) NF021647.5 PF10144.14 SMP_2 28.9 28.9 159 domain Y Y N AhpA/YtjB family protein 10699510 1236 Gammaproteobacteria class 6993 EBI-EMBL Bacterial virulence factor haemolysin AhpA/YtjB family protein Members of this family of bacterial proteins are membrane proteins that effect the expression of haemolysin under anaerobic conditions [1]. [1]. 10699510. Cloning and characterisation of the Pasteurella multocida ahpA gene responsible for a haemolytic phenotype in Escherichia coli. Cox AJ, Hunt ML, Ruffolo CG, Adler B;. Vet Microbiol. 2000;72:135-152. (from Pfam) NF022023.5 PF10548.14 P22_AR_C 22.4 22.4 73 domain Y Y N P22AR C-terminal domain-containing protein 11897024 1236 Gammaproteobacteria class 4577 EBI-EMBL P22AR C-terminal domain P22AR C-terminal domain This domain was identified by Iyer and colleagues [1]. It is found associated with Pfam:PF10547. [1]. 11897024. Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors. Iyer LM, Koonin EV, Aravind L;. Genome Biol 2002;3:RESEARCH0012. (from Pfam) NF022029.5 PF10554.14 Phage_ASH 26 26 107 domain Y Y N ash family protein 11897024 1236 Gammaproteobacteria class 11065 EBI-EMBL Ash protein family ash family protein This family was identified by Iyer and colleagues [1]. It includes the Ash protein from bacteriophage P4. [1]. 11897024. Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors. Iyer LM, Koonin EV, Aravind L;. Genome Biol 2002;3:RESEARCH0012. (from Pfam) NF022092.5 PF10625.14 UspB 28.6 28.6 107 PfamEq Y N N Universal stress protein B (UspB) 9829921 1236 Gammaproteobacteria class 1348 EBI-EMBL Universal stress protein B (UspB) Universal stress protein B (UspB) UspB in Escherichia coli is a 14kDa protein which is predicted to be an integral membrane protein. Overexpression of UspB results in cell death in stationary phase, and mutants of uspB are sensitive to ethanol exposure during stationary phase [1]. [1]. 9829921. uspB, a new sigmaS-regulated gene in Escherichia coli which is required for stationary-phase resistance to ethanol. Farewell A, Kvint K, Nystrom T;. J Bacteriol. 1998;180:6140-6147. (from Pfam) NF022153.5 PF10689.14 DUF2496 25 25 43 PfamAutoEq Y Y N DUF2496 domain-containing protein 1236 Gammaproteobacteria class 3044 EBI-EMBL Protein of unknown function (DUF2496) Protein of unknown function (DUF2496) This family consists of proteins from Gammaproteobacteria spp. Many members are annotated as being like the E coli protein YbaM. (from Pfam) NF022156.5 PF10692.14 DUF2498 25 25 79 PfamAutoEq Y Y N DUF2498 family protein 1236 Gammaproteobacteria class 2193 EBI-EMBL Protein of unknown function (DUF2498) DUF2498 family protein Members of this family are Gammaproteobacteria. Many are annotated as like E coli protein YciN. The function is not known. (from Pfam) NF022183.5 PF10723.14 RepB-RCR_reg 21 21 81 domain Y Y N RepB family protein GO:0006276 9409148 1236 Gammaproteobacteria class 2357 EBI-EMBL Replication regulatory protein RepB plasmid replication regulatory protein RepB family protein This family includes the plasmid rolling circle replication regulatory protein RepB and additional homologs. NF022185.5 PF10725.14 DUF2517 25 25 61 PfamAutoEq Y Y N DUF2517 family protein 1236 Gammaproteobacteria class 1395 EBI-EMBL Protein of unknown function (DUF2517) DUF2517 family protein This family is conserved in Proteobacteria. Several members are annotated as being protein YbfA. The function is not known. (from Pfam) NF022284.5 PF10828.13 DUF2570 26.6 26.6 108 domain Y Y N DUF2570 family protein 1236 Gammaproteobacteria class 912 EBI-EMBL Protein of unknown function (DUF2570) DUF2570 family protein This is a family of proteins with unknown function. (from Pfam) NF022288.5 PF10832.13 YhfG 22.6 22.6 54 PfamAutoEq Y Y N YhfG family protein 27657533 1236 Gammaproteobacteria class 2596 EBI-EMBL YhfG DUF2559 family protein This protein family includes proteins predominantly found in Gammaproteobacteria, such as YhfG from Escherichia coli. YhfG is a FicA antitoxin homologue (also known as antitoxin EcFicA) that interacts with EcFiT and forms a complex with it. YhfG shows a unique conformation, forming two parallel alpha- helices linked by a 10-residues loop. The structure of the complex shows a highly conserved extended ligand-binding pocket [1]. [1]. 27657533. Crystal Structure of the Escherichia coli Fic Toxin-Like Protein in Complex with Its Cognate Antitoxin. Stanger FV, Harms A, Dehio C, Schirmer T;. PLoS One. 2016;11:e0163654. (from Pfam) NF022297.5 PF10841.13 DUF2644 22 22 59 domain Y Y N DUF2644 domain-containing protein 1236 Gammaproteobacteria class 419 EBI-EMBL Protein of unknown function (DUF2644) Protein of unknown function (DUF2644) This family of proteins with unknown function appear to be restricted to Pasteurellaceae. (from Pfam) NF022381.5 PF10928.13 DUF2810 25 25 53 PfamAutoEq Y Y N DUF2810 domain-containing protein 1236 Gammaproteobacteria class 2296 EBI-EMBL Protein of unknown function (DUF2810) Protein of unknown function (DUF2810) This is a bacterial family of uncharacterised proteins. (from Pfam) NF022393.5 PF10940.13 SpeFL 25 25 40 PfamAutoEq Y Y N leader peptide SpeFL speFL 32094585 1236 Gammaproteobacteria class 369 EBI-EMBL Leader peptide SpeFL leader peptide SpeFL SpeFL is a small protein (arrest peptide) encoded upstream of inducible ornithine carboxylase gene (speF) that controls expression of downstream genes (speF and patE) by nascent chain-translational arrest and transcriptional attenuation. Ornithine capture by a translating ribosome controls bacterial polyamine synthesis, inducing the expression of ornithine decarboxylase SpeF4, in a mechanism involving ribosome stalling and transcription antitermination [1] [1]. 32094585. Ornithine capture by a translating ribosome controls bacterial polyamine synthesis. Herrero Del Valle A, Seip B, Cervera-Marzal I, Sacheau G, Seefeldt AC, Innis CA;. Nat Microbiol. 2020;5:554-561. (from Pfam) NF022417.5 PF10964.13 DUF2766 27 27 79 PfamAutoEq Y Y N DUF2766 family protein 1236 Gammaproteobacteria class 781 EBI-EMBL Protein of unknown function (DUF2766) DUF2766 family protein This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. (from Pfam) NF022433.5 PF10980.13 DUF2787 27 27 126 domain Y Y N DUF2787 family protein 18300248 1236 Gammaproteobacteria class 7150 EBI-EMBL Protein of unknown function (DUF2787) DUF2787 family protein This bacterial family of proteins has no known function. The conserved hypothetical protein VC1805 from Vibrio cholerae belongs to this group. It adopts a monomeric assembly, showing an unusual topology with a flat seven-stranded anti-parallel beta-sheet and two helices located on the same side of the sheet. It has some structural homology with the human protein p32 and binds to the complement protein C1q, which suggests a possible role in the adherence of the bacteria to the intestinal wall [1]. [1]. 18300248. Crystal structure of VC1805, a conserved hypothetical protein from a Vibrio cholerae pathogenicity island, reveals homology to human p32. Sheikh MA, Potter JA, Johnson KA, Sim RB, Boyd EF, Taylor GL;. Proteins. 2008;71:1563-1571. (from Pfam) NF022551.5 PF11101.13 DUF2884 30.6 30.6 228 domain Y Y N DUF2884 family protein 1236 Gammaproteobacteria class 8204 EBI-EMBL Protein of unknown function (DUF2884) DUF2884 family protein Some members in this bacterial family of proteins are annotated as YggN which currently has no known function. (from Pfam) NF022570.5 PF11120.13 CBP_BcsF 23 23 60 PfamEq Y Y N cellulose biosynthesis protein BcsF bcsF 26077867,32788377 1236 Gammaproteobacteria class 1259 EBI-EMBL Cellulose biosynthesis protein BcsF cellulose biosynthesis protein BcsF CBP_BcsF is a family of bacterial cellulose biosynthesis proteins. Cellulose is necessary for biofilm formation in bacteria [1,2]. [1]. 26077867. Bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions. Romling U, Galperin MY;. Trends Microbiol. 2015;23:545-557. [2]. 32788377. Structure and Multitasking of the c-di-GMP-Sensing Cellulose Secretion Regulator BcsE. Zouhir S, Abidi W, Caleechurn M, Krasteva PV;. mBio. 2020; [Epub ahead of print] (from Pfam) NF022590.5 PF11140.13 DUF2913 23 23 207 subfamily Y Y N DUF2913 family protein 1236 Gammaproteobacteria class 6481 EBI-EMBL Protein of unknown function (DUF2913) DUF2913 family protein This family of proteins with unknown function appear to be restricted to Gammaproteobacteria. (from Pfam) NF022593.5 PF11143.13 DUF2919 27.2 27.2 146 PfamAutoEq Y Y N DUF2919 family protein 1236 Gammaproteobacteria class 5281 EBI-EMBL Protein of unknown function (DUF2919) DUF2919 family protein This bacterial family of proteins has no known function. Some members are annotated as YfeZ however this cannot be confirmed. (from Pfam) NF022621.5 PF11173.13 DUF2960 27 27 79 PfamAutoEq Y Y N DUF2960 family protein 1236 Gammaproteobacteria class 999 EBI-EMBL Protein of unknown function (DUF2960) DUF2960 family protein This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. (from Pfam) NF022658.5 PF11212.13 DUF2999 25 25 82 PfamAutoEq Y Y N DUF2999 family protein 1236 Gammaproteobacteria class 837 EBI-EMBL Protein of unknown function (DUF2999) DUF2999 family protein This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. (from Pfam) NF022713.5 PF11269.13 DUF3069 25 25 119 PfamAutoEq Y Y N DUF3069 domain-containing protein 1236 Gammaproteobacteria class 834 EBI-EMBL Protein of unknown function (DUF3069) Protein of unknown function (DUF3069) This family of proteins with unknown function appear to be restricted to Gammaproteobacteria. (from Pfam) NF022737.5 PF11293.13 DUF3094 27.1 27.1 55 PfamAutoEq Y Y N DUF3094 family protein 1236 Gammaproteobacteria class 1064 EBI-EMBL Protein of unknown function (DUF3094) DUF3094 family protein This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. (from Pfam) NF022886.5 PF11446.13 DUF2897 25.2 25.2 54 PfamAutoEq Y Y N DUF2897 family protein 1236 Gammaproteobacteria class 2818 EBI-EMBL Protein of unknown function (DUF2897) DUF2897 family protein This is a bacterial family of uncharacterised proteins. (from Pfam) NF022901.5 PF11462.13 DUF3203 25.4 25.4 74 PfamAutoEq Y Y N DUF3203 family protein 1236 Gammaproteobacteria class 1262 EBI-EMBL Protein of unknown function (DUF3203) DUF3203 family protein This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. (from Pfam) NF022910.5 PF11471.13 Sugarporin_N 25.7 25.7 31 domain Y Y N carbohydrate porin 10027967 1236 Gammaproteobacteria class 9086 EBI-EMBL Maltoporin periplasmic N-terminal extension carbohydrate porin This domain would appear to be the periplasmic, N-terminal extension of the outer membrane maltoporins, Pfam:PF02264, LamB. [1]. 10027967. The gene bglH present in the bgl operon of Escherichia coli, responsible for uptake and fermentation of beta-glucosides encodes for a carbohydrate-specific outer membrane porin. Andersen C, Rak B, Benz R;. Mol Microbiol. 1999;31:499-510. (from Pfam) NF022990.5 PF11557.13 Omp_AT 22.5 22.5 327 domain Y Y N Solitary outer membrane autotransporter beta-barrel domain 22073138 1236 Gammaproteobacteria class 1974 EBI-EMBL Solitary outer membrane autotransporter beta-barrel domain Solitary outer membrane autotransporter beta-barrel domain Omp_AT is a family of Gram-negative Gamma-proteobacteria outer membrane autotransporter beta-barrel proteins. Secondary structure prediction indicates a beta-barrel domain of 12 beta-strands. with an N terminal helix running along the central barrel axis perpendicular to the 12 antiparallel strands that form the barrel. Autotransporter translocation units defined by a beta-barrel of 12 to 14 antiparallel strands with an N terminal helix perpendicular to the barrel [1]. [1]. 22073138. Protein domain of unknown function 3233 is a translocation domain of autotransporter secretory mechanism in gamma proteobacteria. Prakash A, Yogeeshwari S, Sircar S, Agrawal S;. PLoS One. 2011;6:e25570. (from Pfam) NF023039.5 PF11607.13 DUF3247 25 25 92 PfamAutoEq Y Y N DUF3247 family protein 17546661 1236 Gammaproteobacteria class 781 EBI-EMBL Protein of unknown function (DUF3247) DUF3247 family protein This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris. The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions [1]. [1]. 17546661. XC5848, an ORFan protein from Xanthomonas campestris, adopts a novel variant of Sm-like motif. Chin KH, Ruan SK, Wang AH, Chou SH;. Proteins. 2007;68:1006-1010. (from Pfam) NF023086.5 PF11656.13 DUF3811 23.5 23.5 88 PfamEq Y Y N DUF3811 domain-containing protein yjbD 1236 Gammaproteobacteria class 1406 EBI-EMBL YjbD family (DUF3811) DUF3811 family protein This is a family of proteobacteria proteins of unknown function. This family is unrelated to Pfam:PF03960 which contains a set of transcription factors that are also named YjbD. (from Pfam) NF023115.5 PF11686.13 DUF3283 25.8 25.8 61 PfamAutoEq Y Y N DUF3283 family protein 1236 Gammaproteobacteria class 945 EBI-EMBL Protein of unknown function (DUF3283) DUF3283 family protein This family of proteins with unknown function appears to be restricted to Proteobacteria. (from Pfam) NF023210.5 PF11782.13 DUF3319 25 25 89 PfamAutoEq Y Y N DUF3319 domain-containing protein 1236 Gammaproteobacteria class 867 EBI-EMBL Protein of unknown function (DUF3319) Protein of unknown function (DUF3319) This is a family of short bacterial proteins, a few of which are annotated as being minor tail protein. Otherwise the function is unknown. (from Pfam) NF023254.5 PF11826.13 RctB_central 27 27 329 PfamAutoEq Y Y N replication initiator protein RctB domain-containing protein 28031373 1236 Gammaproteobacteria class 1268 EBI-EMBL Vibrionales, replication initiator protein RctB, central region Vibrionales, replication initiator protein RctB, central region This region is found in the replication initiator protein RctB from Vibrio cholerae (Swiss:Q9KNG2) and similar sequences predominantly found in Vibrionales. RctB mediates oriCII-based replication and other regulatory processes. This protein is organised into four domains and adopts a dimeric configuration. This entry represents the two central domains, one consisting of a seven-stranded beta- sheet that forms the interface of the dimer by forming a swapped configuration with the same domain of the other monomer. It seems to be involved in DNA binding [1]. [1]. 28031373. The replication initiator of the cholera pathogen's second chromosome shows structural similarity to plasmid initiators. Orlova N, Gerding M, Ivashkiv O, Olinares PDB, Chait BT, Waldor MK, Jeruzalmi D;. Nucleic Acids Res. 2017;45:3724-3737. (from Pfam) NF023297.5 PF11869.13 DUF3389 25 25 75 PfamAutoEq Y Y N DUF3389 family protein 1236 Gammaproteobacteria class 1049 EBI-EMBL Protein of unknown function (DUF3389) DUF3389 family protein This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length. (from Pfam) NF023370.5 PF11944.13 DUF3461 27.4 27.4 125 PfamAutoEq Y Y N DUF3461 family protein 1236 Gammaproteobacteria class 1827 EBI-EMBL Protein of unknown function (DUF3461) DUF3461 family protein This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 130 amino acids in length. This protein has two conserved sequence motifs: KFK and HLE. (from Pfam) NF023533.5 PF12111.13 PNPase_C 25 25 37 PfamEq Y N N Polyribonucleotide phosphorylase C terminal 19327365 1236 Gammaproteobacteria class 11461 EBI-EMBL Polyribonucleotide phosphorylase C terminal Polyribonucleotide phosphorylase C terminal PNPase regulates the expression of small non-coding RNAs that control expression of outer-membrane proteins. The enzyme also affects complex processes, such as the tissue-invasive virulence of Salmonella enterica and the regulation of a virulence-factor secretion system in Yersinia. In Escherichia coli, PNPase is involved in the quality control of ribosomal RNA precursors and is required for growth following cold shock. This family contains the C terminal protomer domain of the PNPase core. The function of the C terminal protomer is to catalyse phosphorolysis through its two active sites. [1] [1]. 19327365. Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly. Nurmohamed S, Vaidialingam B, Callaghan AJ, Luisi BF;. J Mol Biol. 2009;389:17-33. (from Pfam) NF023544.5 PF12122.13 Rhomboid_N 26.2 26.2 86 PfamEq Y N N Cytoplasmic N-terminal domain of rhomboid serine protease GO:0004252,GO:0016020 22963263 1236 Gammaproteobacteria class 6673 EBI-EMBL Cytoplasmic N-terminal domain of rhomboid serine protease Cytoplasmic N-terminal domain of rhomboid serine protease Rhomboid_N is the N-terminal cytoplasmic domain of the rhomboid intra-membraneous serine protease, otherwise known as Peptidase_S54, Pfam:PF01694. This N-terminal domain has similarity to other GlnB-like domains, some of which appear to have a binding role, eg to peptidoglycan. It is not clear exactly what the function of this domain is in the protease, but its presence is critical for maintaining a catalytically competent state for the protein [1]. [1]. 22963263. Activity-based protein profiling of the Escherichia coli GlpG rhomboid protein delineates the catalytic core. Sherratt AR, Blais DR, Ghasriani H, Pezacki JP, Goto NK;. Biochemistry. 2012;51:7794-7803. (from Pfam) NF023590.5 PF12168.13 DNA_pol3_tau_4 25 25 82 PfamEq Y N N DNA polymerase III subunits tau domain IV DnaB-binding 17355988 1236 Gammaproteobacteria class 9681 EBI-EMBL DNA polymerase III subunits tau domain IV DnaB-binding DNA polymerase III subunits tau domain IV DnaB-binding This domain family is found in bacteria, and is approximately 80 amino acids in length. The family is found in association with Pfam:PF00004. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. [1]. 17355988. The unstructured C-terminus of the tau subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the alpha subunit. Jergic S, Ozawa K, Williams NK, Su XC, Scott DD, Hamdan SM, Crowther JA, Otting G, Dixon NE;. Nucleic Acids Res. 2007;35:2813-2824. (from Pfam) NF023616.5 PF12195.13 End_beta_barrel 35 35 83 domain Y N N Beta barrel domain of bacteriophage endosialidase 15608653 1236 Gammaproteobacteria class 566 EBI-EMBL Beta barrel domain of bacteriophage endosialidase Beta barrel domain of bacteriophage endosialidase This domain family is found in bacteria and viruses, and is approximately 80 amino acids in length.This domain is the beta barrel domain of bacteriophage endosialidase which represents the one of the two sialic acid binding sites of the enzyme. The domain is nested in the beta propeller domain of the endosialidase enzyme. The endosialidase protein complexes to form homotrimeric molecules. [1]. 15608653. Crystal structure of the polysialic acid-degrading endosialidase of bacteriophage K1F. Stummeyer K, Dickmanns A, Muhlenhoff M, Gerardy-Schahn R, Ficner R;. Nat Struct Mol Biol. 2005;12:90-96. (from Pfam) NF023638.5 PF12217.13 End_beta_propel 24 24 367 domain Y Y N endosialidase catalytic beta-propeller domain-containing protein GO:0016996 15608653 1236 Gammaproteobacteria class 849 EBI-EMBL Catalytic beta propeller domain of bacteriophage endosialidase Catalytic beta propeller domain of bacteriophage endosialidase This domain family is found in bacteria and viruses, and is typically between 443 and 460 amino acids in length. This domain is the highly conserved beta propeller of bacteriophage endosialidase which represents the catalytically active part of the enzymes. This core domain forms stable SDS-resistant trimers. There is a nested beta barrel domain in this domain (Pfam:PF12195). The endosialidase protein complexes to form a homotrimeric molecule. [1]. 15608653. Crystal structure of the polysialic acid-degrading endosialidase of bacteriophage K1F. Stummeyer K, Dickmanns A, Muhlenhoff M, Gerardy-Schahn R, Ficner R;. Nat Struct Mol Biol. 2005;12:90-96. (from Pfam) NF023640.5 PF12219.13 End_tail_spike 25 25 160 domain Y N N Catalytic domain of bacteriophage endosialidase 15608653 1236 Gammaproteobacteria class 594 EBI-EMBL Catalytic domain of bacteriophage endosialidase Catalytic domain of bacteriophage endosialidase This domain family is found in bacteria and viruses, and is approximately 160 amino acids in length. There are two conserved sequence motifs: VSR and YGA. This domain is the C terminal domain of the bacteriophage protein endosialidase. The endosialidase protein forms homotrimeric molecules and this domain complexes into a tail-spike stalk. The stalk region folds in a triple beta-helix that is interrupted by a small triple beta-prism domain. The tail-spike is a multifunctional protein device used by the phage to fulfill the following functions: (i) to adsorb to the bacterial polySia capsule (ii) to de-polymerise the capsule to gain access to the outer bacterial membrane, and finally (iii) to mediate tight adhesion to the membrane, a prerequisite for the initiation of the infection cycle. [1]. 15608653. Crystal structure of the polysialic acid-degrading endosialidase of bacteriophage K1F. Stummeyer K, Dickmanns A, Muhlenhoff M, Gerardy-Schahn R, Ficner R;. Nat Struct Mol Biol. 2005;12:90-96. (from Pfam) NF023710.5 PF12290.13 DUF3802 26 26 111 PfamAutoEq Y Y N DUF3802 family protein 1236 Gammaproteobacteria class 1046 EBI-EMBL Protein of unknown function (DUF3802) DUF3802 family protein This family of proteins is found in bacteria. Proteins in this family are typically between 114 and 143 amino acids in length. There is a conserved KNLFD sequence motif. (from Pfam) NF023821.5 PF12404.13 DUF3663 25 25 77 PfamEq Y N N Peptidase GO:0005737,GO:0006508,GO:0030145,GO:0070006 1236 Gammaproteobacteria class 9078 EBI-EMBL Peptidase Peptidase This domain family is found in bacteria, and is approximately 80 amino acids in length. The family is found in association with Pfam:PF00883. There is a conserved WAF sequence motif. (from Pfam) NF023865.5 PF12449.13 DUF3684 27 27 1098 PfamAutoEq Y Y N DUF3684 domain-containing protein 1236 Gammaproteobacteria class 2 EBI-EMBL Protein of unknown function (DUF3684) Protein of unknown function (DUF3684) This domain family is found in eukaryotes, and is typically between 1072 and 1090 amino acids in length. (from Pfam) NF023878.5 PF12462.13 Helicase_IV_N 24.5 24.5 163 PfamEq Y N N DNA helicase IV / RNA helicase N terminal 2542273 1236 Gammaproteobacteria class 11096 EBI-EMBL DNA helicase IV / RNA helicase N terminal DNA helicase IV / RNA helicase N terminal This domain family is found in bacteria, and is approximately 170 amino acids in length. This family is found in bacterial DNA helicase IV, at the N-terminus of Pfam:PF00580. [1]. 2542273. The molecular cloning of the gene encoding the Escherichia coli 75-kDa helicase and the determination of its nucleotide sequence and gentic map position. Wood ER, Matson SW;. J Biol Chem. 1989;264:8297-8303. (from Pfam) NF023902.5 PF12486.13 VasL 27.3 27.3 147 domain Y Y N VasL domain-containing protein 16826484,22184413 1236 Gammaproteobacteria class 8687 EBI-EMBL Type VI secretion system, EvfB, or VasL Type VI secretion system, EvfB, or VasL EvfB or VasL is a domain found on many Gram-negative proteins with an ImpA_N domain at the N-terminus. These proteins are expressed from the pathogenicity locus that forms the bacterial type VI secretion system. The exact function of VasL is not known. One E.coli member is annotated as being EvfB, though the E.coli equivalent of ImpA would be expected to be EvfG. It is possible that in many bacteria what is a single protein in one species, eg E.coli, is a fusion of two genes in others, which would explain an ImpA at the N-terminus and a VasL at the C-terminus. [1]. 16826484. Identification and characterization of Escherichia coli RS218-derived islands in the pathogenesis of E. coli meningitis. Xie Y, Kolisnychenko V, Paul-Satyaseela M, Elliott S, Parthasarathy G, Yao Y, Plunkett G 3rd, Blattner FR, Kim KS;. J Infect Dis. 2006;194:358-364. [2]. 22184413. Hcp family proteins secreted via the type VI secretion system coordinately regulate Escherichia coli K1 interaction with human brain microvascular endothelial cells. Zhou Y, Tao J, Yu H, Ni J, Zeng L, Teng Q, Kim KS, Zhao GP, Guo X, Yao Y;. Infect Immun. 2012;80:1243-1251. (from Pfam) NF023934.5 PF12520.13 DUF3723 22 22 508 domain Y Y N DUF3723 domain-containing protein 1236 Gammaproteobacteria class 4 EBI-EMBL Protein of unknown function (DUF3723) Protein of unknown function (DUF3723) This family of proteins is found in eukaryotes. Proteins in this family are typically between 374 and 1069 amino acids in length. There is a conserved LGF sequence motif. (from Pfam) NF024006.5 PF12592.13 ATPase_RavA_C 27 27 55 PfamAutoEq Y Y N ATPase RavA domain-containing protein GO:0042626 21148420,31992852 1236 Gammaproteobacteria class 7171 EBI-EMBL ATPase, RavA, C-terminal ATPase, RavA, C-terminal This domain is found at the C-terminal of bacterial regulatory ATPase RavA (Regulatory ATPase variant A) [1,2] and is the second subdomain that forms the discontinuous triple helical domain [1]. RavA forms an hexamer in which the triple helical domain mediates the lateral interactions between neighbouring RavA monomers [2]. [1]. 21148420. Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity. El Bakkouri M, Gutsche I, Kanjee U, Zhao B, Yu M, Goret G, Schoehn G, Burmeister WP, Houry WA;. Proc Natl Acad Sci U S A. 2010;107:22499-22504. [2]. 31992852. Structural insights into ATP hydrolysis by the MoxR ATPase RavA and the LdcI-RavA cage-like complex. Jessop M, Arragain B, Miras R, Fraudeau A, Huard K, Bacia-Verloop M, Catty P, Felix J, Malet H, Gutsche I;. Commun Biol. 2020;3:46. (from Pfam) NF024018.5 PF12604.13 gp37_C 22.5 22.5 95 domain Y Y N tail fiber protein 11029414 1236 Gammaproteobacteria class 4383 EBI-EMBL Tail fibre protein gp37 C terminal domain phage tail fiber domain This domain family is found in bacteria and viruses, and is typically between 49 and 166 amino acids in length. The family is found in association with Pfam:PF03906. In T-even phages, gp37 and gp38 are components of the tail fibre that are critical for phage-host interaction. [1]. 11029414. Characterization of the distal tail fiber locus and determination of the receptor for phage AR1, which specifically infects Escherichia coli O157:H7. Yu SL, Ko KL, Chen CS, Chang YC, Syu WJ;. J Bacteriol. 2000;182:5962-5968. (from Pfam) NF024028.5 PF12614.13 RRF_GI 26.8 26.8 126 PfamEq Y Y N ribosome recycling factor family protein 17293419 1236 Gammaproteobacteria class 1593 EBI-EMBL Ribosome recycling factor ribosome recycling factor family protein This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 130 amino acids in length. There are two conserved sequence motifs: LPS and LKR. Overproduction of ribosome recycling factor (RRF) reduces tna operon expression and increases the rate of cleavage of TnaC-tRNA(2)(Pro), relieving the growth inhibition associated with plasmid-mediated tnaC overexpression. [1]. 17293419. Ribosome recycling factor and release factor 3 action promotes TnaC-peptidyl-tRNA Dropoff and relieves ribosome stalling during tryptophan induction of tna operon expression in Escherichia coli. Gong M, Cruz-Vera LR, Yanofsky C;. J Bacteriol. 2007;189:3147-3155. (from Pfam) NF024204.5 PF12794.12 MscS_TM 28 28 339 domain Y N N Mechanosensitive ion channel inner membrane domain 1 10202137,12080120,16079835 1236 Gammaproteobacteria class 20853 EBI-EMBL Mechanosensitive ion channel inner membrane domain 1 Mechanosensitive ion channel inner membrane domain 1 The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this domain is one of the inner membrane domains. [1]. 10202137. Protection of Escherichia coli cells against extreme turgor by activation of MscS and MscL mechanosensitive channels: identification of genes required for MscS activity. Levina N, Totemeyer S, Stokes NR, Louis P, Jones MA, Booth IR;. EMBO J. 1999;18:1730-1737. [2]. 12080120. Purification of the small mechanosensitive channel of Escherichia coli (MscS): the subunit structure, conduction, and gating characteristics in liposomes. Sukharev S;. Biophys J. 2002;83:290-298. [3]. 16079835. A possible unifying principle for mechanosensation. Kung C;. Nature. 2005;436:647-654. (from Pfam) NF024205.5 PF12795.12 MscS_porin 34.4 30.5 238 domain Y N N Mechanosensitive ion channel porin domain 10202137,12080120,16079835 1236 Gammaproteobacteria class 18913 EBI-EMBL Mechanosensitive ion channel porin domain Mechanosensitive ion channel porin domain The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this MscS_porin is towards the N-terminal of the molecules. The high concentration of negative charges at the extracellular entrance of the pore helps select the cations for efflux. [1]. 10202137. Protection of Escherichia coli cells against extreme turgor by activation of MscS and MscL mechanosensitive channels: identification of genes required for MscS activity. Levina N, Totemeyer S, Stokes NR, Louis P, Jones MA, Booth IR;. EMBO J. 1999;18:1730-1737. [2]. 12080120. Purification of the small mechanosensitive channel of Escherichia coli (MscS): the subunit structure, conduction, and gating characteristics in liposomes. Sukharev S;. Biophys J. 2002;83:290-298. [3]. 16079835. A possible unifying principle for mechanosensation. Kung C;. Nature. 2005;436:647-654. (from Pfam) NF024662.5 PF13265.11 DUF4056 23.6 23.6 266 PfamAutoEq Y Y N DUF4056 domain-containing protein 1236 Gammaproteobacteria class 4048 EBI-EMBL Protein of unknown function (DUF4056) Protein of unknown function (DUF4056) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 355 and 380 amino acids in length. (from Pfam) NF024718.5 PF13322.11 DUF4092 22.2 22.2 176 PfamAutoEq Y Y N DUF4092 domain-containing protein 1236 Gammaproteobacteria class 4647 EBI-EMBL Domain of unknown function (DUF4092) Domain of unknown function (DUF4092) This family is found in Proteobacteria. The function is not known. (from Pfam) NF025036.5 PF13652.11 QSregVF 23.8 23.8 112 PfamEq Y Y N PA3611 family quorum-sensing-regulated virulence factor 24174223 1236 Gammaproteobacteria class 1478 EBI-EMBL Putative quorum-sensing-regulated virulence factor PA3611 family quorum-sensing-regulated virulence factor This is a family of short ~14 kDa proteins from Psuedomonas. The structure of UniProtKB:Q9HY15 a secreted protein has been solved and deposited as PDB:3npd. It comprises one structural domain with five beta-strands and five alpha-helices. Various comparative structural prediction methods plus its genomic location point to the protein forming a functional dimer with its adjacent genomic partner, UniProtKB:Q9HY14, in Pfam:PF12843. Together these might be regulated by the other product from the PotABCD operon, namely the putrescine-binding periplasmic protein UniProtKB:Q9HY16. which has been implicated in quorum-sensing. QSregVF is certainly up-regulated in quorum-sensing, and is predicted to be a virulence factor [1]. [1]. 24174223. Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family. Das D, Chiu HJ, Farr CL, Grant JC, Jaroszewski L, Knuth MW, Miller MD, Tien HJ, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Proteins. 2014;82:1086-1092. (from Pfam) NF025127.5 PF13752.11 DUF4165 25 25 121 domain Y Y N DUF4165 domain-containing protein 1236 Gammaproteobacteria class 2946 EBI-EMBL Domain of unknown function (DUF4165) Domain of unknown function (DUF4165) NF025225.5 PF13856.11 Gifsy-2 24.1 24.1 99 domain Y N N ATP-binding sugar transporter from pro-phage 1236 Gammaproteobacteria class 1265 EBI-EMBL ATP-binding sugar transporter from pro-phage ATP-binding sugar transporter from pro-phage Members of this short family are putative ATP-binding sugar transporter-like protein. (from Pfam) NF025323.5 PF13957.11 YafO_toxin 25 25 101 domain Y Y N type II toxin-antitoxin system YafO family toxin 19617347,19837801 1236 Gammaproteobacteria class 2410 EBI-EMBL Toxin YafO, type II toxin-antitoxin system type II toxin-antitoxin system YafO family toxin YafO is a toxin which inhibits protein synthesis. It acts as a ribosome-dependent mRNA interferase. It forms part of a type II toxin-antitoxin system, where the YafN protein acts as an antitoxin [1,2]. This domain forms complexes with yafN antitoxins containing Pfam:PF02604. [1]. 19617347. Characterization of YafO, an Escherichia coli toxin. Zhang Y, Yamaguchi Y, Inouye M;. J Biol Chem. 2009;284:25522-25531. [2]. 19837801. An SOS-regulated type 2 toxin-antitoxin system. Singletary LA, Gibson JL, Tanner EJ, McKenzie GJ, Lee PL, Gonzalez C, Rosenberg SM;. J Bacteriol. 2009;191:7456-7465. (from Pfam) NF025327.5 PF13961.11 DUF4219 27 27 27 domain Y Y N DUF4219 domain-containing protein 1236 Gammaproteobacteria class 8 EBI-EMBL Domain of unknown function (DUF4219) Domain of unknown function (DUF4219) This domain is very short and is found at the N-terminal of many Gag-pol polyprotein and related proteins. There is a highly conserved YxxWxxxM sequence motif. (from Pfam) NF025344.5 PF13978.11 DUF4223 27 27 54 PfamAutoEq Y Y N DUF4223 family protein 1236 Gammaproteobacteria class 784 EBI-EMBL Protein of unknown function (DUF4223) DUF4223 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. These proteins are likely to be lipoproteins (attachment site currently included in alignment). (from Pfam) NF025354.5 PF13988.11 DUF4225 25.9 25.9 165 domain Y Y N DUF4225 domain-containing protein 1236 Gammaproteobacteria class 5532 EBI-EMBL Protein of unknown function (DUF4225) Protein of unknown function (DUF4225) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 182 and 282 amino acids in length. (from Pfam) NF025358.5 PF13992.11 YecR 27 27 73 PfamEq Y Y N YecR family lipoprotein yecR 1236 Gammaproteobacteria class 2186 EBI-EMBL YecR-like lipoprotein YecR family lipoprotein YecR family lipoproteins, named for the founding member in E. coli, average about 110 amino acids in length. In addition to one invariant Cys residue in the lipoprotein signal peptide, four other conserved Cys residues are found, suggesting disulfide bond formation. The function is unknown. NF025367.5 PF14001.11 YdfZ 27 27 64 PfamEq Y Y N putative selenium delivery protein YdfZ 12084818 1236 Gammaproteobacteria class 942 EBI-EMBL YdfZ protein putative selenium delivery protein YdfZ This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved YDRNRN sequence motif. The E. coli protein has been shown to bind selenium [1]. This protein shows structural similarity to the KOW motif. [1]. 12084818. Direct detection of potential selenium delivery proteins by using an Escherichia coli strain unable to incorporate selenium from selenite into proteins. Lacourciere GM, Levine RL, Stadtman TC;. Proc Natl Acad Sci U S A. 2002;99:9150-9153. (from Pfam) NF025368.5 PF14002.11 YniB 27 27 166 PfamEq Y Y N YniB family protein 9495751 1236 Gammaproteobacteria class 2825 EBI-EMBL YniB-like protein YniB family protein The YniB-like protein family includes the E. coli YniB protein Swiss:P76208 which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 180 amino acids in length. This family of proteins are integral membrane proteins. (from Pfam) NF025782.5 PF14426.11 Imm2 35.7 35.7 60 PfamEq Y Y N Imm2 family immunity protein imm2 21890906 1236 Gammaproteobacteria class 169 EBI-EMBL Immunity protein Imm2 Imm2 family immunity protein A predicted Immunity protein, with a mostly all-alpha fold, present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene [1]. [1]. 21890906. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Iyer LM, Zhang D, Rogozin IB, Aravind L;. Nucleic Acids Res. 2011; [Epub ahead of print] (from Pfam) NF026135.5 PF14785.11 MalF_P2 34.4 34.4 164 PfamEq Y N N Maltose transport system permease protein MalF P2 domain 18033289,21825153 1236 Gammaproteobacteria class 6624 EBI-EMBL Maltose transport system permease protein MalF P2 domain Maltose transport system permease protein MalF P2 domain This is the second periplasmic domain (P2 domain) of the maltose transport system permease protein MalF [1-2]. [1]. 21825153. Snapshots of the maltose transporter during ATP hydrolysis. Oldham ML, Chen J;. Proc Natl Acad Sci U S A. 2011;108:15152-15156. [2]. 18033289. Crystal structure of a catalytic intermediate of the maltose transporter. Oldham ML, Khare D, Quiocho FA, Davidson AL, Chen J;. Nature. 2007;450:515-521. (from Pfam) NF026868.5 PF15530.11 Ntox25 25 25 168 domain Y Y N polymorphic toxin type 25 domain-containing protein 21085179,22731697,33646095,35558562 1236 Gammaproteobacteria class 1378 EBI-EMBL Bacterial toxin 25 polymorphic toxin type 25 domain This domain family, predicted to have RNase activity, is found in a group of toxins mainly found in Enterobacterales. It shows a conserved FGPY motif and a histidine residue and is predicted to have a mostly all-beta fold. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 5 secretion system [1]. Some members of this family are annotated as CdiA, a member of a contact-dependent growth inhibition system (CDI) that show diverse functions implicated in bacterial competition, including the dissipation of the proton motive force (PMF) and the degradation of DNA or RNA [2-4]. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. [2]. 33646095. Escherichia coli EC93 deploys two plasmid-encoded class I contact-dependent growth inhibition systems for antagonistic bacterial interactions. Waneskog M, Halvorsen T, Filek K, Xu F, Hammarlof DL, Hayes CS, Braaten BA, Low DA, Poole SJ, Koskiniemi S;. Microb Genom. 2021; [Epub ahead of print]. [3]. 35558562. Functional and Structural Diversity of Bacterial Contact-Dependent Growth Inhibition Effectors. Cuthbert BJ, Hayes CS, Goulding CW;. Front Mol Biosci. 2022;9:866854. [4]. 21085179. A widespread family of polymorphic contact-dependent toxin delivery systems in bacteria. Aoki SK, Diner EJ, de Roodenbeke CT, Burgess BR, Poole SJ, Braaten BA, Jones AM, Webb JS, Hayes CS, Cotter PA, Low DA;. Nature. 2010;468:439-442. (from Pfam) NF026876.5 PF15538.11 Ntox46 25 25 157 domain Y Y N polymorphic toxin type 46 domain-containing protein 22731697 1236 Gammaproteobacteria class 725 EBI-EMBL Bacterial toxin 46 polymorphic toxin type 46 domain A predicted toxin domain found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold with a conserved glutamine residue and a [KR]STxxPxxDxx[ST] motif. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 6 secretion system [1]. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF026944.5 PF15606.11 Ntox34 25 25 80 domain Y Y N polymorphic toxin type 34 domain-containing protein 22731697 1236 Gammaproteobacteria class 3431 EBI-EMBL Bacterial toxin 34 polymorphic toxin type 34 domain (predicted RNase) A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-alpha helical fold and conserved lysine and cysteine residues, and GNxxD and WxCxH motifs. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 6 secretion system [1]. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF027260.5 PF15930.10 YdiH 27 27 62 PfamEq Y Y N YdiH family protein 9680201 1236 Gammaproteobacteria class 431 EBI-EMBL Domain of unknown function YdiH family protein YdiH is a family of proteins found in bacteria. Proteins in this family are typically between 62 and 80 amino acids in length. The function is not known. (from Pfam) NF027271.5 PF15941.10 FidL_like 27 27 87 subfamily Y Y N FidL-like protein 1236 Gammaproteobacteria class 1104 EBI-EMBL FidL-like putative membrane protein FidL-like protein FidL-like is a family of bacterial proteins that are purported to be membrane proteins. (from Pfam) NF027410.5 PF16084.10 LydB 28 28 147 PfamEq Y N N LydA-holin antagonist 8576044 1236 Gammaproteobacteria class 311 EBI-EMBL LydA-holin antagonist LydA-holin antagonist LydB is a family of proteins that are antagonistic to the lysing action of holin LydA [1]. [1]. 8576044. Three functions of bacteriophage P1 involved in cell lysis. Schmidt C, Velleman M, Arber W;. J Bacteriol. 1996;178:1099-1104. (from Pfam) NF027411.5 PF16085.10 Phage_holin_3_5 27 27 113 domain Y Y N phage holin family protein 11069649 1236 Gammaproteobacteria class 1908 EBI-EMBL Bacteriophage holin Hol, superfamily III phage holin family protein Phage_holin_6_2 is a family of holins classified as 1.E.20 in the TC database. The hol gene (PRF9) product (117 aas) of Pseudomonas aeruginosa PAO1 exhibits a hydrophobicity profile similar to holins of P2 and phiCTX phages with two peaks of hydrophobicity that might correspond to either one or two TMSs. Hol functions in conjunction with the lytic enzyme, Lys, a glycosyl hydrolase that breaks-up the murein in the bacterial cell-wall, causing lysis of the cell and hence entry of phage particles [1]. Several members are annotated as pyocin R2_PP when encoded on the chromosome. [1]. 11069649. The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage. Nakayama K, Takashima K, Ishihara H, Shinomiya T, Kageyama M, Kanaya S, Ohnishi M, Murata T, Mori H, Hayashi T;. Mol Microbiol. 2000;38:213-231. (from Pfam) NF027654.5 PF16330.10 MukB_hinge 27 27 167 PfamEq Y N N MukB hinge domain 19853611 1236 Gammaproteobacteria class 14080 EBI-EMBL MukB hinge domain MukB hinge domain The hinge domain of chromosome partition protein MukB is responsible for dimerisation and is also involved in protein-DNA interactions and conformational flexibility [1]. [1]. 19853611. The crystal structure of the hinge domain of the Escherichia coli structural maintenance of chromosomes protein MukB. Li Y, Schoeffler AJ, Berger JM, Oakley MG;. J Mol Biol. 2010;395:11-19. (from Pfam) NF027676.5 PF16358.10 RcsF 29 29 110 PfamEq Y Y N Rcs stress response system protein RcsF rcsF GO:0009279,GO:0035556 21454485,21471196 1236 Gammaproteobacteria class 2256 EBI-EMBL RcsF lipoprotein Rcs stress response system protein RcsF The RcsF lipoprotein is a component of the Rcs signaling system. It activates the Rcs system by transmitting signals from the cell suface to the histidine kinase RcsC [1-2]. [1]. 21471196. A disulfide bridge network within the soluble periplasmic domain determines structure and function of the outer membrane protein RCSF. Rogov VV, Rogova NY, Bernhard F, Lohr F, Dotsch V;. J Biol Chem. 2011;286:18775-18783. [2]. 21454485. Crystal structure of the outer membrane protein RcsF, a new substrate for the periplasmic protein-disulfide isomerase DsbC. Leverrier P, Declercq JP, Denoncin K, Vertommen D, Hiniker A, Cho SH, Collet JF;. J Biol Chem. 2011;286:16734-16742. (from Pfam) NF027680.5 PF16362.10 YaiA 30 30 63 PfamEq Y N N YaiA protein 1236 Gammaproteobacteria class 813 EBI-EMBL YaiA protein YaiA protein This family of proteins is found in Enterobacteriaceae, where they are immediately downstream of a Shikimate kinase. (from Pfam) NF027767.5 PF16452.10 Phage_CI_C 27 27 101 domain Y N N Bacteriophage CI repressor C-terminal domain GO:0051259 16507359 1236 Gammaproteobacteria class 6534 EBI-EMBL Bacteriophage CI repressor C-terminal domain Bacteriophage CI repressor C-terminal domain The C-terminal domain of the CI repressor functions in oligomer formation [1]. [1]. 16507359. The structural basis of cooperative regulation at an alternate genetic switch. Pinkett HW, Shearwin KE, Stayrook S, Dodd IB, Burr T, Hochschild A, Egan JB, Lewis M;. Mol Cell. 2006;21:605-615. (from Pfam) NF027832.5 PF16518.10 GrlR 26.8 26.8 110 domain Y Y N GrlR family regulatory protein 17511515,24092262 1236 Gammaproteobacteria class 274 EBI-EMBL T3SS negative regulator,GrlR GrlR family regulatory protein GrlR is a family of protobacterial type III secretion system negative regulators. Structurally, GrlR consists of a typical beta-barrel fold with eight beta-strands containing an internal hydrophobic cavity and a plug-like loop on one side of the barrel. Strong hydrophobic interactions between the two beta-barrels maintain its dimeric architecture. A unique surface-exposed EDED (Glu-Asp-Glu-Asp) motif is identified to be critical for GrlA-GrlR interaction and for the repressive activity of GrlR [1]. The locus of enterocyte effacement (LEE) is essential for virulence of enterohaemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC). It encodes some 20 genes including an overall regulator ler and two others, GrlR and GrlA, that form the type three secretion system for infection. GrlR comlexes with GrlA to repress expression of ler [2]. GrlA is found in family Pfam:PF00462. [1]. 17511515. Structure of GrlR and the implication of its EDED motif in mediating the regulation of type III secretion system in EHEC. Jobichen C, Li M, Yerushalmi G, Tan YW, Mok YK, Rosenshine I, Leung KY, Sivaraman J;. PLoS Pathog. 2007;3:e69. [2]. 24092262. Structure of GrlR-GrlA complex that prevents GrlA activation of virulence genes. Padavannil A, Jobichen C, Mills E, Velazquez-Campoy A, Li M, Leung KY, Mok YK, Rosenshine I, Sivaraman J;. Nat Commun. 2013;4:2546. (from Pfam) NF027841.5 PF16527.10 CpxA_peri 23.5 23.5 134 PfamEq Y N N Two-component sensor protein CpxA, periplasmic domain 22760860 1236 Gammaproteobacteria class 4033 EBI-EMBL Two-component sensor protein CpxA, periplasmic domain Two-component sensor protein CpxA, periplasmic domain CpxA_peri is the periplasmic domain-family of the Gram-negative Gammaproteobacteria two-component signalling system, Cpx. It represents the recognition-site for sensing specific envelope stress signals. The fold that the domain-core of CpxA_peri conforms to is a PAS fold. The domain senses the environmental change and triggers a signal transduction to the cytoplasmic domain. As well as the PAS-core, there is a C-terminal tail that is necessary for ligand-sensing and binding to CpxP, a CpxA-associated and a regulatory protein [1]. This domain recognises KCl and RbCl (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 22760860. The crystal structure of the periplasmic domain of Vibrio parahaemolyticus CpxA. Kwon E, Kim DY, Ngo TD, Gross CA, Gross JD, Kim KK;. Protein Sci. 2012;21:1334-1343. (from Pfam) NF027846.5 PF16532.10 Phage_tail_NK 27 27 175 PfamEq Y Y N tail needle knob protein 21705802,23951045 1236 Gammaproteobacteria class 1635 EBI-EMBL Sf6-type phage tail needle knob or tip of some Caudovirales tail needle knob protein Phage_tail_NK is the globular tip protein of some tailed bacteriophages. Tailed bacteriophage virions deliver DNA to susceptible cells after adsorbing to specific receptors on the surface of the bacteria. In the Gram-negative bacteria these receptors are surface proteins or polysaccharides. In the phage Sf6-type needle, this distal tip folds into a knob with a TNF-like fold, similar to the fibre knobs of bacteriophage PRD1 and Adenovirus. It contains three bound L-glutamate molecules that are bind tightly in the crevices between the trimers of this trimeric tip [1,2]. [1]. 21705802. Atomic structure of bacteriophage Sf6 tail needle knob. Bhardwaj A, Molineux IJ, Casjens SR, Cingolani G;. J Biol Chem. 2011;286:30867-30877. [2]. 23951045. The tip of the tail needle affects the rate of DNA delivery by bacteriophage P22. Leavitt JC, Gogokhia L, Gilcrease EB, Bhardwaj A, Cingolani G, Casjens SR;. PLoS One. 2013;8:e70936. (from Pfam) NF027863.5 PF16549.10 T2SSS_2 25 25 104 PfamEq Y Y N type II secretion system pilot lipoprotein GspS-beta gspS2 23326233 1236 Gammaproteobacteria class 1464 EBI-EMBL Type II secretion system (T2SS) pilotin, S protein type II secretion system pilot lipoprotein GspS-beta GspS-beta is the lipoprotein that replaces GspS as the pilot protein (pilotin) that, in some types of type II secretion system (T2SS), helps the secretin to assemble into a pore in the outer membrane. NF028003.5 PF16693.10 Yop-YscD_ppl_1st 24 24 62 domain Y Y N EscD/YscD/HrpQ family type III secretion system periplasmic domain-containing protein 1860816,23908767,26914207 1236 Gammaproteobacteria class 1684 EBI-EMBL YscD/CdsD-like Bon-like domain 1 YscD/CdsD-like Bon-like domain 1 Yop-YscD-ppl is the periplasmic domain of Yop proteins like YscD from Proteobacteria. YscD forms part of the inner membrane component of the bacterial type III secretion injectosome apparatus [1,2]. This entry represents the first of three periplasmic BON domains [3]. [1]. 1860816. Analysis of virC, an operon involved in the secretion of Yop proteins by Yersinia enterocolitica. Michiels T, Vanooteghem JC, Lambert de Rouvroit C, China B, Gustin A, Boudry P, Cornelis GR;. J Bacteriol 1991;173:4994-5009. Paper describing PDB structure 4alz. [2]. 23908767. In situ structural analysis of the Yersinia enterocolitica injectisome. Kudryashev M, Stenta M, Schmelz S, Amstutz M, Wiesand U, Castano-Diez D, Degiacomi MT, Munnich S, Bleck CK, Kowal J, Diepold A, Heinz DW, Dal Peraro M, Cornelis GR, Stahlberg H;. Elife. 2013;2:e00792. Paper describing PDB structure 4qo6. [3]. 26914207. The extended structure of the periplasmic region of CdsD, a structural protein of the type III secretion system of Chlamydia trachomatis. Merilainen G, Koski MK, Wierenga RK;. Protein Sci. 2016;25:987-998. (from Pfam) NF028020.5 PF16710.10 CTXphi_pIII-N1 27 27 111 subfamily_domain Y Y N minor coat protein pIII 22942280 1236 Gammaproteobacteria class 93 EBI-EMBL N-terminal N1 domain of Vibrio phage CTXphi pIII phage minor coat protein pIII The minor coat protein pIII was described in CTXphi, a filamentous phage from Vibrio cholerae that transforms the host bacterium into a pathogen. NF028060.5 PF16750.10 HK_sensor 30.5 30.5 110 domain Y Y N histidine kinase sensor domain-containing protein 1236 Gammaproteobacteria class 6024 EBI-EMBL Sensor domain of 2-component histidine kinase Sensor domain of 2-component histidine kinase HK_sensor is the sensor domain found at the N-terminus of the integral membrane two-component system sensor histidine kinase proteins in bacteria. (from Pfam) NF028077.5 PF16767.10 KinB_sensor 27 27 122 domain Y Y N KinB sensor domain-containing domain 12372152,9218420 1236 Gammaproteobacteria class 3093 EBI-EMBL Sensor domain of alginate biosynthesis sensor protein KinB Sensor domain of alginate biosynthesis sensor protein KinB KinB_sensor is the N-terminal sensor domain of histidine kinase from Pseudomonas species. The domain is the extracellular sensing domain, and is four helical bundle [1,2]. It recognises inorganic phosphate Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 12372152. Histidine protein kinases: key signal transducers outside the animal kingdom. Wolanin PM, Thomason PA, Stock JB;. Genome Biol. 2002;3:REVIEWS3013. [2]. 9218420. Identification of the histidine protein kinase KinB in Pseudomonas aeruginosa and its phosphorylation of the alginate regulator algB. Ma S, Wozniak DJ, Ohman DE;. J Biol Chem. 1997;2:17952-60. (from Pfam) NF028116.5 PF16806.10 ExsD 27 27 79 subfamily Y Y N T3SS regulon anti-activator ExsD domain-containing protein 19235906 1236 Gammaproteobacteria class 1126 EBI-EMBL Antiactivator protein ExsD N-terminal domain T3SS regulon anti-activator ExsD family protein The antiactivator protein ExsD represses the transcriptional activator ExsA. ExsA activates expression of type III secretion system genes. Repression of ExsA by ExsD is relieved by the secretion chaperone ExsC [1]. Paper describing PDB structure 3fd9. [1]. 19235906. Structural evidence suggests that antiactivator ExsD from Pseudomonas aeruginosa is a DNA binding protein. Bernhards RC, Jing X, Vogelaar NJ, Robinson H, Schubot FD;. Protein Sci. 2009;18:503-513. (from Pfam) NF028134.5 PF16824.10 CBM_26 26.6 26.6 125 domain Y Y N alginate biosynthesis protein AlgX 23779107 1236 Gammaproteobacteria class 2679 EBI-EMBL C-terminal carbohydrate-binding module alginate biosynthesis protein AlgX CBM_26 is a family of bacterial carbohydrate-binding modules frequently found at the C-terminus of enzymes. The combination is not unusual as the CBMs function to bring the relevant polysaccharide into close proximity to the active site [1]. [1]. 23779107. Structural and functional characterization of Pseudomonas aeruginosa AlgX: role of AlgX in alginate acetylation. Riley LM, Weadge JT, Baker P, Robinson H, Codee JD, Tipton PA, Ohman DE, Howell PL;. J Biol Chem. 2013;288:22299-22314. (from Pfam) NF028251.5 PF16941.10 CymA 27 27 341 PfamEq Y N N Putative cyclodextrin porin GO:0098657 1236 Gammaproteobacteria class 404 EBI-EMBL Putative cyclodextrin porin Putative cyclodextrin porin NF028266.5 PF16956.10 Porin_7 26.6 26.6 287 domain Y Y N putative porin 1236 Gammaproteobacteria class 3469 EBI-EMBL Putative general bacterial porin putative porin NF028274.5 PF16964.10 TadF 27.3 27.3 178 subfamily Y Y N tight adherence pilus pseudopilin TadF tadF 16980493 1236 Gammaproteobacteria class 2021 EBI-EMBL Putative tight adherence pilin protein F tight adherence pilus pseudopilin TadF Members of this family resemble TadF, a pseudopilin encoded as part of the tight adherence (tad) loci in species such as Actinobacillus actinomycetemcomitans and Vibrio fischeri. NF028276.5 PF16966.10 Porin_8 25 25 372 PfamEq Y Y N carbohydrate porin 1236 Gammaproteobacteria class 5545 EBI-EMBL Porin-like glycoporin RafY carbohydrate porin This is a family of Gram-negative Gammaproteobacteria putative raffinose-like porins. (from Pfam) NF028281.5 PF16971.10 RcpB 21 21 169 PfamEq Y N N Rough colony protein B, tight adherence - tad - subunit 17435791,18055598 1236 Gammaproteobacteria class 157 EBI-EMBL Rough colony protein B, tight adherence - tad - subunit Rough colony protein B, tight adherence - tad - subunit RcpB is part of the Tad operon of proteins [1]. The Tad (tight adherence) macromolecular transport system, present in many bacterial and archaeal species, represents an ancient and major new subtype of type II secretion. The three Rcp proteins (RcpA, RcpB, and RcpC) and TadD, a putative lipoprotein, are localised to the bacterial outer membrane [2]. [1]. 17435791. The tad locus: postcards from the widespread colonization island. Tomich M, Planet PJ, Figurski DH;. Nat Rev Microbiol. 2007;5:363-375. [2]. 18055598. Outer membrane components of the Tad (tight adherence) secreton of Aggregatibacter actinomycetemcomitans. Clock SA, Planet PJ, Perez BA, Figurski DH;. J Bacteriol. 2008;190:980-990. (from Pfam) NF028400.5 PF17090.10 Ytca 28.8 28.8 62 PfamEq Y Y N YtcA family lipoprotein 1236 Gammaproteobacteria class 2095 EBI-EMBL YtcA family YtcA family lipoprotein Members of this family resemble the uncharacterized apparent lipoprotein YtcA of Escherichia coli. NF028466.5 PF17157.9 GAPES4 27 27 98 PfamEq Y N N Gammaproteobacterial periplasmic sensor domain 16980588,22672726,23131828,26148715 1236 Gammaproteobacteria class 6767 EBI-EMBL Gammaproteobacterial periplasmic sensor domain Gammaproteobacterial periplasmic sensor domain GAPES4 (GAmmaproteobacterial PEriplasmic Sensor) domain is a periplasmic sensor domain found in various GGDEF- and EAL-containing proteins. In Escherichia coli, GAPES4 forms the N-terminal domain of the regulatory protein CsrD (YhdA) [1], which contains enzymatically inactive GGDEF and EAL domains and controls CsrD) that controls the degradation of two non-coding RNAs, CsrB and CsrC [2,3]. In Vibrio cholerae, GAPES4-containing protein MshH (Q9KUW1_VIBCH) inhibits biofilm formation, apparently acting through the glucose-specific enzyme IIA (Q9KTD8, Pfam:PF00358) [4]. [1]. 26148715. Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli. Hengge R, Galperin MY, Ghigo JM, Gomelsky M, Green J, Hughes KT, Jenal U, Landini P;. J Bacteriol. 2015;198:7-11. [2]. 16980588. Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E. Suzuki K, Babitzke P, Kushner SR, Romeo T;. Genes Dev. 2006;20:2605-2617. [3]. 22672726. Post-transcriptional regulation on a global scale: form and function of Csr/Rsm systems. Romeo T, Vakulskas CA, Babitzke P;. Environ Microbiol. 2013;15:313-324. [4]. 23131828. Glucose-specific enzyme IIA has unique binding partners in the vibrio cholerae biofilm. Pickering BS, Smith DR, Watnick PI;. MBio. 2012;3:e00228-e00212. (from Pfam) NF028485.5 PF17176.9 tRNA_bind_3 27 27 119 domain Y Y N tRNA-binding protein 19322199 1236 Gammaproteobacteria class 12370 EBI-EMBL tRNA-binding domain tRNA-binding domain This domain, found at the C-terminus of tRNA(Met) cytidine acyltransferase, may be involved in tRNA-binding [1]. This family represents the tRNA-binding domain proteins not captured by Pfam:PF13725. [1]. 19322199. RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon. Chimnaronk S, Suzuki T, Manita T, Ikeuchi Y, Yao M, Suzuki T, Tanaka I;. EMBO J. 2009;28:1362-1373. (from Pfam) NF028487.5 PF17178.9 MASE5 25.2 25.2 192 PfamEq Y Y N membrane-associated sensor domain-containing protein 26148715 1236 Gammaproteobacteria class 3349 EBI-EMBL Membrane-associated sensor Membrane-associated sensor MASE5 is a family of bacterial membrane-associated sensor domains. It is an integral membrane sensor domain found in various GGDEF domain proteins, including a diguanylate cyclase DgcY (EcSMS35_1716) from multidrug-resistant environmental isolate Escherichia coli SMS-3-5 [1]. [1]. 26148715. Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli. Hengge R, Galperin MY, Ghigo JM, Gomelsky M, Green J, Hughes KT, Jenal U, Landini P;. J Bacteriol. 2015;198:7-11. (from Pfam) NF028501.5 PF17192.9 MukF_M 25.2 25.2 161 PfamEq Y N N MukF middle domain 15902272,7513784 1236 Gammaproteobacteria class 4690 EBI-EMBL MukF middle domain MukF middle domain The kicA and kicB genes are found upstream of mukB. It has been suggested that the kicB gene encodes a killing factor and the kicA gene codes for a protein that suppresses the killing function of the kicB gene product [1]. It was also demonstrated that KicA and KicB can function as a post-segregational killing system, when the genes are transferred from the E. coli chromosome onto a plasmid [1]. [1]. 7513784. New killing system controlled by two genes located immediately upstream of the mukB gene in Escherichia coli. Feng J, Yamanaka K, Niki H, Ogura T, Hiraga S;. Mol Gen Genet 1994;243:136-147. [2]. 15902272. The MukF subunit of Escherichia coli condensin: architecture and functional relationship to kleisins. Fennell-Fezzie R, Gradia SD, Akey D, Berger JM;. EMBO J. 2005;24:1921-1930. (from Pfam) NF028502.5 PF17193.9 MukF_C 27 27 158 PfamEq Y N N MukF C-terminal domain 1236 Gammaproteobacteria class 4590 EBI-EMBL MukF C-terminal domain MukF C-terminal domain This presumed domain is found at the C-terminus of the MukF protein. (from Pfam) NF028515.5 PF17206.8 SeqA_N 23 23 36 PfamEq Y N N SeqA protein N-terminal domain 11442835,11457824,19304745,7553853,9736699 1236 Gammaproteobacteria class 4441 EBI-EMBL SeqA protein N-terminal domain SeqA protein N-terminal domain The binding of SeqA protein to hemimethylated GATC sequences is important in the negative modulation of chromosomal initiation at oriC, and in the formation of SeqA foci necessary for Escherichia coli chromosome segregation [3]. SeqA tetramers are able to aggregate or multimerise in a reversible, concentration-dependent manner [3]. Apart from its function in the control of DNA replication, SeqA may also be a specific transcription factor [4]. This short domain mediates dimerisation [5]. [1]. 9736699. High-affinity binding of hemimethylated oriC by Escherichia coli membranes is mediated by a multiprotein system that includes SeqA and a newly identified factor, SeqB. Shakibai N, Ishidate K, Reshetnyak E, Gunji S, Kohiyama M, Rothfield L;. Proc Natl Acad Sci U S A 1998;95:11117-11121. [2]. 7553853. E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration. Slater S, Wold S, Lu M, Boye E, Skarstad K, Kleckner N;. Cell 1995;82:927-936. [3]. 11457824. SeqA protein aggregation is necessary for SeqA function. Lee H, Kang S, Bae SH, Choi BS, Hwang DS;. J Biol Chem 2001;276:34600-34606. [4]. 11442835. SeqA, the Escherichia coli origin sequestration protein, is also a specific transcription factor. Slominska M, Wegrzyn A, Konopa G, Skarstad K, Wegrzyn G;. Mol Microbiol 2001;40:1371-1379. [5]. 19304745. Structural insights into the cooperative binding of SeqA to a tandem GATC repeat. Chung YS, Brendler T, Austin S, Guarne A;. Nucleic Acids Res. 2009;37:3143-3152. (from Pfam) NF028535.0 ANT_4p_II 350 350 251 subfamily Y Y Y ANT(4')-II family aminoglycoside nucleotidyltransferase ant(4') 1236 Gammaproteobacteria class 7 NCBIFAM ANT(4')-II family aminoglycoside nucleotidyltransferase ANT(4')-II family aminoglycoside nucleotidyltransferase NF028538.0 PAP2_lipid_A 275 275 234 equivalog Y Y N PAP2 family lipid A phosphatase 1236 Gammaproteobacteria class 436 NCBIFAM PAP2 family lipid A phosphatase PAP2 family lipid A phosphatase All members of the seed alignment for this family belong to the PAP2 superfamily and therefore share homology with the lipid A 1-phosphatase LpxE of Helicobacter pylori. LpxE removes one of two KDO sugar phosphates from lipid A, making it possible for a phosphoethanolamine--lipid A transferase to add the modifying group that increases resistance to colistin. All members of the seed alignment for this model are encoded close to the gene for a phosphoethanolamine--lipid A transferase, such as MCR-1. NF033069.2 acnA_upstr_60 50 50 60 domain N N N acnA regulatory region 60-length spurious protein 1236 Gammaproteobacteria class 7 NCBIFAM acnA regulatory region 60-length spurious protein acnA regulatory region 60-length spurious protein This HMM describes an apparently spurious protein translation from the region upstream of the aconitase A gene acnA in Escherichia coli str. K-12 substr. MG1655, positions 1335595-1335774, and in related strains. Evidence against its expression as a real protein include a putative TTG start codon, the lack of good RBS, non-conservative substitutions where found, the absence of credible homologs in any species besides E. coli, and a DNA region in Salmonella enterica LT2 in which one third of the translation is present, but the other two thirds are missing. NF033077.0 AAC_6p_A30 255 255 129 exception Y Y Y aminoglycoside 6'-N-acetyltransferase AAC(6')-30 aacA30 2.3.1.82 GO:0047663 1236 Gammaproteobacteria class 5 NCBIFAM AacA30 family aminoglycoside 6'-N-acetyltransferase aminoglycoside 6'-N-acetyltransferase AAC(6')-30 This family is known both as AAC(6')-30 and as AacA30. NF033130.1 AAC_6p_A48 300 300 147 exception Y Y Y AacA48 family aminoglycoside 6'-N-acetyltransferase 2.3.1.82 GO:0047663 1236 Gammaproteobacteria class 2 NCBIFAM AacA48 family aminoglycoside 6'-N-acetyltransferase aminoglycoside 6'-N-acetyltransferase AAC(6')-Iag NF033153.2 phage_ICD_like 25 25 48 subfamily_domain Y Y N host cell division inhibitor Icd-like protein 8491703 1236 Gammaproteobacteria class 12855 NCBIFAM host cell division inhibitor Icd-like protein host cell division inhibitor Icd domain Icd from temperate phage P1 inhibits cell division in its host. Homologous sequence is found in many other proteins, often as the C-terminal region of what appears to be a much larger protein. Putative phage proteins that contain this domain may be designated "host cell division inhibitor Icd-like protein". See PMID: 8491703 for a description of Icd. Many proteins with this domain also have the Ash domain described by PF10554, which also occurs in phage. NF033154.1 endonuc_SmrA 180 180 189 equivalog Y Y N DNA endonuclease SmrA smrA 1236 Gammaproteobacteria class 5977 NCBIFAM DNA endonuclease SmrA DNA endonuclease SmrA YdaL is a small endonuclease with homology to the C-terminal domain found in the endonuclease MutS2, but not found in the related mismatch repair protein MutS. The biological role of this endonuclease is not yet known. As one of two Small MutS2-Related proteins in E. coli, This protein was designated SmrA by Gui, et al. (PMID:21276852). The term SMR is much better known for describing a large family of Small Multidrug Resistance (SMR) efflux transporters, but in that context is used with three capital letters. NF033159.0 blaPAC 850 850 380 exception Y Y Y PAC family class C beta-lactamase blaPAC 3.5.2.6 GO:0008800 1236 Gammaproteobacteria class 3 NCBIFAM PAC family class C beta-lactamase PAC family class C beta-lactamase NF033209.1 16S_rRNA_Rmt_B 525 525 251 exception Y Y Y RmtB family 16S rRNA (guanine(1405)-N(7))-methyltransferase GO:0046677 1236 Gammaproteobacteria class 16 NCBIFAM RmtB family 16S rRNA (guanine(1405)-N(7))-methyltransferase RmtB family 16S rRNA (guanine(1405)-N(7))-methyltransferase NF033213.1 matur_PanM 68 68 130 equivalog Y Y N aspartate 1-decarboxylase autocleavage activator PanM panM GO:0008080,GO:0015940,GO:0031638 22497218,22782525,22940551,25910242 1236 Gammaproteobacteria class 2940 NCBIFAM aspartate 1-decarboxylase autocleavage activator PanM aspartate 1-decarboxylase autocleavage activator PanM Members of this family, called PanM (or PanZ), although related to the GNAT family N-acetyltransferases, have a different function. Then enzyme PanD, aspartate 1-decarboxylase, has an active site modified Ser residue, created by cleavage of a precursor form. PanM promotes the maturation of the CoA biosynthesis enzyme PanD, but also inhibits its activity in the presence of CoA. Figure 6 in PMID:26276430 identifies residues considered critical to interaction with PanD; seed alignment sequences and cutoff scores were chosen to separate proposed PanM from functionally distinct relatives. NF033408.5 polymyxin_MCR3 1225 1225 540 exception Y Y Y MCR-3 family phosphoethanolamine--lipid A transferase mcr-3 GO:0008484,GO:0016020 28655818 1236 Gammaproteobacteria class 63 NCBIFAM MCR-3 family phosphoethanolamine--lipid A transferase MCR-3 family phosphoethanolamine--lipid A transferase This model was originally narrowly defined to describe only mobilized phosphoethanolamine--lipid A transferases of the MCR-3 family, while excluding the broader set of chromosomal enzymes intrinsic to many members of the genus Aeromonas. It is now somewhat broader to accomodate published allele designations. Related proteins will be named as "MCR-3-related," not "MCR-3 family," if they have qualifying hits only to the broader model NF033409 and not to this narrower model. NF033409.0 poly_MCR3_broad 1075 1075 535 equivalog Y Y Y MCR-3-related phosphoethanolamine--lipid A transferase 28655818 1236 Gammaproteobacteria class 318 NCBIFAM MCR-3 family phosphoethanolamine--lipid A transferase MCR-3-related phosphoethanolamine--lipid A transferase The plasmid-borne colistin resistance gene mcr-3, which encodes a phosphoethanolamine--lipid A transferase, appears to have originated from a chromosomally encoded enzyme widespread in the genus Aeromonas. This family (NF033409) includes both mobilized enzymes (ASF81896.1 and its closest homologs) and enzymes intrinsic to Aeromonas. A narrower family, polymyxin_MCR3 (NF033408), describes only the mobilized forms. Proteins with qualifying hits only to this model, and not to the more narrowly focused model NF033408, are named "MCR3-related" rather than "MCR-3 family" to show the distinction. Any protein that is a member of this family and not NF033408, that now is carried on a mobile element, is potentially of scientic interest. NF033411.1 small_mem_YnhF 30 30 29 hypoth_equivalog Y Y N YnhF family membrane protein 21050835,21778229 1236 Gammaproteobacteria class 868 NCBIFAM YnhF family membrane protein YnhF family membrane protein Members of this protein family, are small membrane proteins, about 29 amino acids in length. YnhF from E. coli was shown to have an intact fMet residue at the N-terminus and to be chloroform-soluble. The previously generated narrow cluster PRK14756 includes some members of this family. NF033420.0 T6SS_PAAR_dom 124 124 94 equivalog_domain Y Y N type VI secretion system PAAR protein 23925114,27352036 1236 Gammaproteobacteria class 1785 NCBIFAM type VI secretion system PAAR protein type VI secretion system PAAR domain The PAAR domain is widespread, but this model represents a narrow clade that may occur in type VI secretion systems (T6SS), either free-standing or fused to a long extension. Effector domains of T6SS may be separate proteins, or may be fused to on of the tube or spike proteins: VgrG (spike), Hcp (tube), or this PAAR family (spike tip). Members of this family that have long extensions are likely to be T6SS effectors. NF033439.1 small_mem_YoeI 33 33 20 equivalog Y Y N membrane protein YoeI yoeI 19121005 1236 Gammaproteobacteria class 120 NCBIFAM membrane protein YoeI membrane protein YoeI YoeI, a hydrophobic protein of only 20 amino acids, is found in at least these genera: Escherichia, Salmonella, Citrobacter, Enterobacter, and Klebsiella. It is known to be expressed in E. coli. NF033462.1 polymyxin_MCR4 1225 1225 541 exception Y Y Y MCR-4 family phosphoethanolamine--lipid A transferase 28797329 1236 Gammaproteobacteria class 8 NCBIFAM MCR-4 family phosphoethanolamine--lipid A transferase MCR-4 family phosphoethanolamine--lipid A transferase NF033511.1 metallo_CpaA 750 750 575 exception Y Y N metalloendopeptidase CpaA cpaA 28982978 1236 Gammaproteobacteria class 477 NCBIFAM metalloendopeptidase CpaA metalloendopeptidase CpaA NF033512.1 T2SS_chap_CpaB 90 90 206 equivalog Y Y N metalloprotease secretion chaperone CpaB cpaB 1236 Gammaproteobacteria class 396 NCBIFAM metalloprotease secretion chaperone CpaB metalloprotease secretion chaperone CpaB The cpaA and cpaB gene pair, as described in the genus Acinetobacter, consists of a metalloendopeptidase virulence factor, CpaA, and a tightly binding membrane-bound chaperone, CpaB, important for its secretion by a type II secretion system (T2SS). CpaA, in at least some Acinetobacter, is the most heavily secreted T2SS effector, and behaves as a virulence factor that cleaves factor V in blood and alters coagulation. NF033650.1 ANR_neg_reg 32 32 54 subfamily Y Y N ANR family transcriptional regulator 24875828 1236 Gammaproteobacteria class 2775 NCBIFAM ANR family transcriptional regulator ANR family transcriptional regulator ANR family transcriptional regulators include the AggR-activated regulator Aar. The name ANR (AraC Negative Regulators) refers to an effect on, rather than homology to, certain AraC family transcriptional regulators. NF033785.1 sulfur_OscA 85 85 60 equivalog Y Y N sulfur starvation response protein OscA oscA 19118350 1236 Gammaproteobacteria class 534 NCBIFAM sulfur starvation response protein OscA sulfur starvation response protein OscA OscA (organosulfur compound A) is a small protein, about 60 amino acids in length, in the DUF2292 family. As characterized in Pseudomonas corrugata, OscA is required during sulfur starvation for obtaining it from organosulfur compounds. The pathway is required to remediate oxidative stress from chromate, so oscA was discovered by the loss of high resistance to chromate in Pseudomonas corrugata 28 when the gene is insertionally inactivated. The oscA gene tends to be found near sulfate transporter genes. NF033868.0 trim_DfrA36 360 360 170 exception Y Y Y trimethoprim-resistant dihydrofolate reductase DfrA36 dfrA36 1.5.1.3 GO:0004146,GO:0046654,GO:0050661 31068437,31217307 1236 Gammaproteobacteria class 12 NCBIFAM trimethoprim-resistant dihydrofolate reductase DfrA36 trimethoprim-resistant dihydrofolate reductase DfrA36 NF033883.1 conj_TraQ_IncI1 80 80 175 equivalog Y Y N conjugal transfer protein TraQ traQ 25477379 1236 Gammaproteobacteria class 843 NCBIFAM conjugal transfer protein TraQ conjugal transfer protein TraQ NF033884.1 conj_TraO_IncI1 225 225 381 equivalog Y Y N conjugal transfer protein TraO traO 25477379 1236 Gammaproteobacteria class 1635 NCBIFAM conjugal transfer protein TraO conjugal transfer protein TraO TraO, involved in the conjugal transfer of plasmids such as IncI1 plasmids, shares homology with IcmE of type IVB secretion systems. NF033885.1 conj_TraP_IncI1 135 135 217 equivalog Y Y N conjugal transfer protein TraP traP 25477379 1236 Gammaproteobacteria class 974 NCBIFAM conjugal transfer protein TraP conjugal transfer protein TraP Members of this family are the conjugal transfer protein TraP, as the term is used for the member protein from IncI1 plasmids and for their homologs. Note that the same terminology may be applied to unrelated proteins from other forms of conjugal transfer system. NF033887.1 conj_TraX 100 100 163 equivalog Y Y N conjugal transfer protein TraX traX 1236 Gammaproteobacteria class 1049 NCBIFAM conjugal transfer protein TraX conjugal transfer protein TraX NF033888.1 conj_TraW 100 100 380 equivalog Y Y N conjugal transfer protein TraW traW 25477379 1236 Gammaproteobacteria class 1893 NCBIFAM conjugal transfer protein TraW conjugal transfer protein TraW Members of this family are the TraW protein of conjugal plasmid transfer systems, as the term is used for certain transfer systems, including that of IncI1 family plasmids. Note that an unrelated protein, also designated TraW, participates in the assembly of F-pilin subunits, involved in transfer of F-plasmids. NF033891.1 surf_exc_IncI1 100 100 210 exception Y Y N plasmid IncI1-type surface exclusion protein ExcA excA 23201046,25477379,7991676 1236 Gammaproteobacteria class 1302 NCBIFAM plasmid IncI1-type surface exclusion protein ExcA plasmid IncI1-type surface exclusion protein ExcA The surface exclusion protein ExcA, as found in R64 and other IncI1 family plasmids, is not required for plasmid transfer. Instead, it is required for blocking transfer of closely related plasmids into the host cell. NF033906.1 ExsE_fam 35 35 77 subfamily Y Y N T3SS regulon translocated regulator ExsE family protein 15911752,20536183 1236 Gammaproteobacteria class 311 NCBIFAM T3SS regulon translocated regulator ExsE family protein T3SS regulon translocated regulator ExsE family protein ExsE, through protein-protein interaction, serves in a regulatory cascade that modulates the role of ExsA, a transcriptional activator of Pseudomonas aeruginosa's type III secretion system (T3SS) regulon. ExsE itself is a substrate for translocation (i.e. removal) by the T3SS system, providing feedback that modulates expression of secretion system genes. Homologs found in multiple species of Aeromonas and Photorhabdus may be functionally equivalent. Note that VP1702 from Vibrio parahaemolyticus, given the same gene symbol and ascribed an equivalent function, appears unrelated in sequence. NF035942.1 T3SS_eff_HopBF1 200 200 200 equivalog Y Y N T3SS effector protein kinase HopBF1 hopBF1 2.7.11.- 31522888 1236 Gammaproteobacteria class 68 NCBIFAM T3SS effector protein kinase HopBF1 HopBF1, found in plant pathogens such as Pseudomonas syringae and in the human pathogen Ewingella americana, it a type III secretion system effector that acts as a protein kinase. It phosphorylates the eukaryotic chaperone HSP90 on a serine residue, inhibiting its ATPase activity. The inhibition interferes with the proper folding of client proteins of HSP90 that are important to resistance to bacterial infection. NF035945.1 Zn_serralysin 500 500 462 subfamily Y Y N serralysin family metalloprotease 3.4.24.40 GO:0004222,GO:0005615,GO:0006508,GO:0046872 24654978,8797082 1236 Gammaproteobacteria class 3885 NCBIFAM serralysin family metalloprotease NF036332.5 PF17414.7 MatP_C 24 24 60 domain Y N N MatP C-terminal ribbon-helix-helix domain 18984159 1236 Gammaproteobacteria class 2622 EBI-EMBL MatP C-terminal ribbon-helix-helix domain MatP C-terminal ribbon-helix-helix domain This family, many of whose members are YcbG, organises the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. Organisation of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. MatS sites are the main targets in the E. coli chromosome of YcbG or MatP (macrodomain Ter protein). MatP accumulates in the cell as a discrete focus that co-localises with the Ter macrodomain. The effects of MatP inactivation reveal its role as the main organiser of the Ter macrodomain: in the absence of MatP, DNA is less compacted, the mobility of markers is increased, and segregation of the Ter macrodomain occurs early in the cell cycle. A specific organisational system is required in the Terminus region for bacterial chromosome management during the cell cycle. This entry represents the C-terminal ribbon-helix-helix domain. [1]. 18984159. The MatP/matS site-specific system organizes the terminus region of the E. coli chromosome into a macrodomain. Mercier R, Petit MA, Schbath S, Robin S, El Karoui M, Boccard F, Espeli O;. Cell. 2008;135:475-485. (from Pfam) NF036359.5 PF17519.7 DUF5444 25 25 62 domain Y Y N DUF5444 family protein 1236 Gammaproteobacteria class 147 EBI-EMBL Family of unknown function (DUF5444) DUF5444 family protein This is a family of unknown function found in Enterobacterales. (from Pfam) NF036365.5 PF17547.7 DUF5462 25 25 157 domain Y Y N DUF5462 family protein 1236 Gammaproteobacteria class 709 EBI-EMBL Family of unknown function (DUF5462) DUF5462 family protein This is a family of unknown function found in Gammaproteobacteria. (from Pfam) NF036529.5 PF17969.6 Ldt_C 26.8 26.8 67 domain Y N N L,D-transpeptidase C-terminal domain 23832002 1236 Gammaproteobacteria class 14876 EBI-EMBL L,D-transpeptidase C-terminal domain L,D-transpeptidase C-terminal domain This is the C-terminal domain found in d-transpeptidases (Ldt) homologues from E.coli. Three of these enzymes (YbiS, ErfK, YcfS) have been shown to cross-link Braun's lipoprotein to the peptidoglycan (PG), while the other two (YnhG, YcbB) form direct meso-diaminopimelate (DAP-DAP, or 3-3) cross-links within the PG. Family members include erfK (ldtA), ybiS (ldtB), ycfS (ldtC), and ynhG (ldtE). [1]. 23832002. Phenotypic analysis of Eschericia coli mutants lacking L,D-transpeptidases. Sanders AN, Pavelka MS;. Microbiology. 2013;159:1842-1852. (from Pfam) NF036530.5 PF17970.6 bMG1 26.4 26.4 105 domain Y N N Bacterial Alpha-2-macroglobulin MG1 domain 25221932 1236 Gammaproteobacteria class 17136 EBI-EMBL Bacterial Alpha-2-macroglobulin MG1 domain Bacterial Alpha-2-macroglobulin MG1 domain Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. However, A2M-like proteins were identified in pathogenically invasive bacteria and species that colonize higher eukaryotes. Bacterial A2Ms are located in the periplasm where they are believed to provide protection to the cell by trapping external proteases through a covalent interaction with an activated thioester. This domain is found on the N-terminal region in A2Ms in bacteria. Structure analysis of Salmonella enterica ser A2Ms (SA-A2Ms) show that they are composed of 13 domains, all of which fold as variants of beta sandwiches with the exception of the TED, which consists of 14 alpha helices. Most of the beta sandwich domains appear to serve a structural role and are referred to as the macroglobulin-like (MG) domains. This is the MG1 domain which is the farthest from the body of the structure. It is normally anchored to the inner membrane in vivo and connected to MG2 by a flexible linker [1]. [1]. 25221932. Structure of a bacterial alpha2-macroglobulin reveals mimicry of eukaryotic innate immunity. Wong SG, Dessen A;. Nat Commun. 2014;5:4917. (from Pfam) NF036568.5 PF17320.7 DUF5363 25.8 25.8 54 domain Y Y N DUF5363 family protein 1236 Gammaproteobacteria class 770 EBI-EMBL Family of unknown function (DUF5363) DUF5363 family protein This is a family of unknown function found in Gammaproteobacteri. (from Pfam) NF036589.5 PF17426.7 Putative_G5P 25 25 108 domain Y Y N DNA-binding protein 1236 Gammaproteobacteria class 533 EBI-EMBL Putative Gamma DNA binding protein G5P DNA-binding protein This domain family is found in Gammaproteobacterial proteins. Members of the family are predicted to be G5P DNA binding proteins. Homologous proteins are found in Pfam:PF02303 (from Pfam) NF036593.5 PF17457.7 DUF5420 26 26 184 domain Y Y N DUF5420 family protein 1236 Gammaproteobacteria class 256 EBI-EMBL Family of unknown function (DUF5420) DUF5420 family protein This is a domain of unknown function found in Gammaproteobacteria such as Haemophilus influenzae. (from Pfam) NF036758.5 PF18284.6 DNA_meth_N 25 25 57 domain Y N N DNA methylase N-terminal domain 1236 Gammaproteobacteria class 6040 EBI-EMBL DNA methylase N-terminal domain DNA methylase N-terminal domain This is the N-terminal domain of DNA methylase (Pfam:PF00145). Family members include Modification methylase EcoRII (EC:2.1.1.37) and DNA-cytosine methyltransferase. (from Pfam) NF036865.5 PF18390.6 GlgX_C 25.8 25.8 85 domain Y N N Glycogen debranching enzyme C-terminal domain 20187119 1236 Gammaproteobacteria class 8118 EBI-EMBL Glycogen debranching enzyme C-terminal domain Glycogen debranching enzyme C-terminal domain This is the C-terminal domain of the glycogen debranching enzyme GlgX. GlgX hydrolyzes alpha-1,6-glycosidic linkages of phosphorylase-limit dextrin containing only three or four glucose subunits produced by glycogen phosphorylase. Sequence analysis suggests that GlgX is a debranching enzyme belonging to the glycoside hydrolase GH-13 family in the CAZy database [1]. [1]. 20187119. Structural rationale for the short branched substrate specificity of the glycogen debranching enzyme GlgX. Song HN, Jung TY, Park JT, Park BC, Myung PK, Boos W, Woo EJ, Park KH;. Proteins. 2010;78:1847-1855. (from Pfam) NF036912.5 PF18629.6 DUF5629 26.6 26.6 98 domain Y Y N DUF5629 family protein 25972860 1236 Gammaproteobacteria class 2092 EBI-EMBL Family of unknown function (DUF5629) DUF5629 family protein This is a domain of unknown function found in hypothetical proteins from Pseudomonas aeruginosa [1]. [1]. 25972860. Dissection of the cis-2-decenoic acid signaling network in Pseudomonas aeruginosa using microarray technique. Rahmani-Badi A, Sepehr S, Fallahi H, Heidari-Keshel S;. Front Microbiol. 2015;6:383. (from Pfam) NF036932.5 PF17516.7 ProQ_C 23.3 23.3 51 domain Y N N ProQ C-terminal domain 1236 Gammaproteobacteria class 4424 EBI-EMBL ProQ C-terminal domain ProQ C-terminal domain This domain is found at the C-terminus of many ProQ proteins. (from Pfam) NF037215.5 PF18340.6 TraI_2B 26.7 26.7 79 domain Y N N DNA relaxase TraI 2B/2B-like domain 28457609 1236 Gammaproteobacteria class 14949 EBI-EMBL DNA relaxase TraI 2B/2B-like domain DNA relaxase TraI 2B/2B-like domain This is the 2B and 2B-like sub-domain found in TraI (EC:5.99.1.2) a relaxase of F-family plasmids. It contains four domains; a trans-esterase domain that executes the nicking and covalent attachment of the T-strand to the relaxase, a vestigial helicase domain (carrying the 2B/2B-like sub-domain) that operates as an ssDNA-binding domain, an active 5' to 3' helicase domain, and a C-terminal domain that functions as a recruitment platform for relaxosome components. The 2B sub-domains in TraI are formed by residues 625-773 in the vestigial helicase domain and residues 1255-1397 in the active helicase domain. The 2B/2B-like sub-domain interacts with ssDNA where it contributes to the surface area where ssDNA bind. In other words the ssDNA-binding site is located in a groove between the 2B and 2B-like parts of the sub-domain. The sub-domain parts appear to act as clamps holding the ssDNA in place, resulting in the ssDNA being completely surrounded by protein. In previous studies, the 2B/2B-like sub-domain of the TraI vestigial helicase domain has been identified as translocation signal A (TSA) since it contains sequences essential for the recruitment of TraI to the T4S system. Thus, the 2B/2B-like sub-domain plays two major roles in relaxase function: (1) interacting with the DNA and possibly promoting high processivity and (2) mediating recruitment of the relaxosome to the T4S system [1]. [1]. 28457609. Cryo-EM Structure of a Relaxase Reveals the Molecular Basis of DNA Unwinding during Bacterial Conjugation. Ilangovan A, Kay CWM, Roier S, El Mkami H, Salvadori E, Zechner EL, Zanetti G, Waksman G;. Cell. 2017;169:708-721. (from Pfam) NF037239.5 PF18415.6 HKR_ArcB_TM 27.3 27.3 75 domain Y N N Histidine kinase receptor ArcB trans-membrane domain 20498088 1236 Gammaproteobacteria class 7797 EBI-EMBL Histidine kinase receptor ArcB trans-membrane domain Histidine kinase receptor ArcB trans-membrane domain Histidine kinase receptors (HKRs) are part of a two-component system, in which an HKR in the bacterial inner membrane transmits a signal to a response regulator located in the cytoplasm. This is a trans-membrane domain (TM) found in ArcB (class 2, aerobic respiratory control sensor). ArcB has two TM helices connected by a short periplasmic loop. TM domain structures suggests a loose helical packing which provides an inherent flexibility in the TM domains and that this is perhaps essential to the mechanism of signal transduction across the membrane [1]. [1]. 20498088. Membrane domain structures of three classes of histidine kinase receptors by cell-free expression and rapid NMR analysis. Maslennikov I, Klammt C, Hwang E, Kefala G, Okamura M, Esquivies L, Mors K, Glaubitz C, Kwiatkowski W, Jeon YH, Choe S;. Proc Natl Acad Sci U S A. 2010;107:10902-10907. (from Pfam) NF037379.5 PF18668.6 Tail_spike_N 25 25 70 domain Y N N Tail spike TSP1/Gp66 receptor binding N-terminal domain 24671238,28513100 1236 Gammaproteobacteria class 4335 EBI-EMBL Tail spike TSP1/Gp66 receptor binding N-terminal domain Tail spike TSP1/Gp66 receptor binding N-terminal domain Bacteriophages recognize and bind to their hosts with the help of receptor-binding proteins (RBPs) that emanate from the phage particle in the form of fibers or tailspikes. RBPs of podovirus G7C tailspikes gp63.1 and gp66 are essential for infection of its natural host bacterium E. coli 4s. Gp63.1 and gp66 form a stable complex, in which the N-terminal part of gp66 serves as an attachment site for gp63.1 and anchors the gp63.1-gp66 complex to the G7C tail. The two N-terminal domains show 70% sequence identity to the N-terminal region of the CBA120 phage tailspike 1 (orf210, TSP1) [1]. The N-terminal domain of TSP1 is the virion head binding domain that interfaces with the phage baseplate. The N-terminal domain can be further divided into two subdomains, each beginning with a alpha-helix followed by an anti-parallel beta-sandwich. Subdomain two folds similarly to the chitin binding domain of Chitinase from Bacillus circulans [2]. [1]. 28513100. Function of bacteriophage G7C esterase tailspike in host cell adsorption. Prokhorov NS, Riccio C, Zdorovenko EL, Shneider MM, Browning C, Knirel YA, Leiman PG, Letarov AV;. Mol Microbiol. 2017;105:385-398. [2]. 24671238. Crystal structure of ORF210 from E. coli O157:H1 phage CBA120 (TSP1), a putative tailspike protein. Chen C, Bales P, Greenfield J, Heselpoth RD, Nelson DC, Herzberg O;. PLoS One. 2014;9:e93156. (from Pfam) NF037436.5 PF18493.6 DUF5617 26.3 26.3 90 domain Y Y N DUF5617 domain-containing protein 27986836 1236 Gammaproteobacteria class 264 EBI-EMBL Domain of unknown function (DUF5617) Domain of unknown function (DUF5617) This domain of unknown function is found at the C-terminal end of proteins mainly from Legionella, including lpg0944 from Legionella pneumophila (Swiss:Q5ZWY9), which is thought to be an effector of the Icm/Dot translocation system from this bacteria. This domain folds into an all-alpha structure [1]. [1]. 27986836. Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila. Urbanus ML, Quaile AT, Stogios PJ, Morar M, Rao C, Di Leo R, Evdokimova E, Lam M, Oatway C, Cuff ME, Osipiuk J, Michalska K, Nocek BP, Taipale M, Savchenko A, Ensminger AW;. Mol Syst Biol. 2016;12:893. (from Pfam) NF037684.5 PF17948.6 DnaT 25 25 69 domain Y Y N DnaT-like ssDNA-binding domain-containing protein 25053836,25265331 1236 Gammaproteobacteria class 10196 EBI-EMBL DnaT DNA-binding domain DnaT-like ssDNA-binding domain This domain is found in E.coli primosomal protein 1 (Pp1). PP1 domain (residues 84-153) in Swiss:P0A8J2 can bind to different types of ssDNA, which is fundamental for its physiological substrate bindings. Functional analysis indicate that both N- and C- terminals are essential to having the cooperative effect in binding ssDNA. The ssDNA bound complex displays a spiral filament assembly that is adopted by many proteins that are involved in DNA replication, such as DnaA, RecA and PriB. This domain is similar to Pfam:PF08585 except that it contains an extra loop at the N-terminus (84-99). Structural analysis indicate that this extra loop might be essential for the stabilisation of the three-helix bundle [1]. [1]. 25265331. Structure and mechanism of the primosome protein DnaT-functional structures for homotrimerization, dissociation of ssDNA from the PriB.ssDNA complex, and formation of the DnaT.ssDNA complex. Fujiyama S, Abe Y, Tani J, Urabe M, Sato K, Aramaki T, Katayama T, Ueda T;. FEBS J. 2014;281:5356-5370. [2]. 25053836. Crystal structure of DnaT84-153-dT10 ssDNA complex reveals a novel single-stranded DNA binding mode. Liu Z, Chen P, Wang X, Cai G, Niu L, Teng M, Li X;. Nucleic Acids Res. 2014;42:9470-9483. (from Pfam) NF037779.5 PF18285.6 LuxT_C 25 25 87 domain Y N N Tetracycline repressor LuxT C-terminal domain 22130678 1236 Gammaproteobacteria class 1251 EBI-EMBL Tetracycline repressor LuxT C-terminal domain Tetracycline repressor LuxT C-terminal domain This is the C-terminal domain of LuxT. LuxT is a tetracycline repressor family regulator identified in Vibrio alginolyticus which may play a role in the fine-tuning of the virulence via quorum sensing (QS) [1]. [1]. 22130678. Characterization of a new quorum sensing regulator luxT and its roles in the extracellular protease production, motility, and virulence in fish pathogen Vibrio alginolyticus. Liu H, Gu D, Cao X, Liu Q, Wang Q, Zhang Y;. Arch Microbiol. 2012;194:439-452. (from Pfam) NF037780.5 PF18286.6 T3SS_ExsE 27 27 46 domain Y N N Type III secretion system ExsE 20536183 1236 Gammaproteobacteria class 297 EBI-EMBL Type III secretion system ExsE Type III secretion system ExsE This domain is found in ExsE present in Pseudomonas aeruginosa. ExsE forms part of the ExsACDE signaling cascade which acts as an important regulatory switch that ensures timely expression of the Type III secretion system (T3SS) and so plays a critical role in facilitating infection. Prior to host-cell contact, the T3SS is inactive and ExsE and Type III Secretion Chaperone (ExsC) form a stable complex. ExsC forms a compact homodimer and ExsE wraps around one face of this dimer [1]. [1]. 20536183. Analysis of the crystal structure of the ExsC.ExsE complex reveals distinctive binding interactions of the Pseudomonas aeruginosa type III secretion chaperone ExsC with ExsE and ExsD. Vogelaar NJ, Jing X, Robinson HH, Schubot FD;. Biochemistry. 2010;49:5870-5879. (from Pfam) NF037815.5 PF18429.6 DUF5609 25 25 65 domain Y Y N DUF5609 domain-containing protein 1236 Gammaproteobacteria class 4593 EBI-EMBL Domain of unknown function (DUF5609) Domain of unknown function (DUF5609) This is a probable HAD-like (haloalkanoate dehalogenase) domain found in bacterial phosphoserine phosphatases. (from Pfam) NF037835.5 PF18494.6 Pullulanase_Ins 27.4 27.4 74 domain Y N N Pullulanase Ins domain 24375572,26688215 1236 Gammaproteobacteria class 6383 EBI-EMBL Pullulanase Ins domain Pullulanase Ins domain Pullulanases (pullulan 6-glucanohydrolase, EC 3.2.1.41) are debranching enzymes that are able to hydrolyze the alpha-1,6-glycosidic linkage in pullulan, starch, amylopectin, and related oligosaccharides. Type I pullulanases specifically cleave the alpha-1,6-glycosidic linkages in pullulan and branched oligosaccharides to produce maltotriose and linear oligosaccharides, respectively [1]. Structural analysis of Klebsiella lipoprotein pullulanase (PulA) illustrates that the catalytic core is composed of two major regions: the TIM-barrel domain A and beta-sandwich fold domain C. PulA contains an extra domain, a highly mobile Ins subdomain of unknown function which is inserted into the catalytic TIM-barrel domain A of Klebsiella pullulanases. The Ins subdomain is rich in helical and loop secondary structure. A disulfide bond between Cys491 and Cys506 and two Ca2+ ions presumably stabilizes this domain.This insertion is also found in pullulanases from other Gram-negative genera that have a functional T2SS, such as Vibrio, Aeromonas, and Photorhabdus. Functional analysis indicate that this domain is required for PulA secretion via the T2SS [2]. [1]. 24375572. Functional and structural studies of pullulanase from Anoxybacillus sp. LM18-11. Xu J, Ren F, Huang CH, Zheng Y, Zhen J, Sun H, Ko TP, He M, Chen CC, Chan HC, Guo RT, Song H, Ma Y;. Proteins. 2014;82:1685-1693. [2]. 26688215. Structural Basis of Pullulanase Membrane Binding and Secretion Revealed by X-Ray Crystallography, Molecular Dynamics and Biochemical Analysis. East A, Mechaly AE, Huysmans GHM, Bernarde C, Tello-Manigne D, Nadeau N, Pugsley AP, Buschiazzo A, Alza. TRUNCATED at 1650 bytes (from Pfam) NF037861.5 PF18607.6 HTH_54 32.3 32.3 92 domain Y N N ParA helix turn helix domain 19461582 1236 Gammaproteobacteria class 1498 EBI-EMBL ParA helix turn helix domain ParA helix turn helix domain The accurate segregation of DNA is essential for the faithful inheritance of genetic information. Segregation of the prototypical P1 plasmid par system requires two proteins, ParA and ParB, and a centromere. When bound to ATP, ParA mediates segregation by interacting with centromere-bound ParB, but when bound to ADP, ParA fulfills a different function: DNA-binding transcription autoregulation. ParA consists of an elongated N-terminal alpha-helix which mediates dimerization, a winged-HTH and a Walker-box containing C-domain. This entry describes the N-terminal alpha helix domain combined with the winged HTH region [1]. [1]. 19461582. Structural basis for ADP-mediated transcriptional regulation by P1 and P7 ParA. Dunham TD, Xu W, Funnell BE, Schumacher MA;. EMBO J. 2009;28:1792-1802. (from Pfam) NF037877.5 PF18673.6 IrmA 25 25 109 subfamily Y Y N IrmA family protein 26980835 1236 Gammaproteobacteria class 1905 EBI-EMBL interleukin receptor mimic protein A IrmA family protein The E. coli interleukin [IL] receptor mimic protein A (IrmA), is a small (13 kDa) Uropathogenic E. coli (UPEC) protein that was originally identified in a large reverse genetic screen as a broadly protective vaccine antigen. It has a fibronectin III (FNIII)-like fold that forms a domain-swapped dimer with structural mimicry to the binding domain of the IL-2 receptor (IL-2R), the IL-4 receptor (IL-4R) and, to a lesser extent, the IL-10 receptor (IL-10R). IrmA binds to all three cytokines, with the greatest affinity observed for IL-4. It is suggested that IrmA may contribute to manipulation of the innate immune response during UPEC infection [1]. [1]. 26980835. Molecular and Structural Characterization of a Novel Escherichia coli Interleukin Receptor Mimic Protein. Moriel DG, Heras B, Paxman JJ, Lo AW, Tan L, Sullivan MJ, Dando SJ, Beatson SA, Ulett GC, Schembri MA;. MBio. 2016;7:e02046. (from Pfam) NF037974.1 SslE_AcfD_Zn_LP 800 800 1403 subfamily Y Y N SslE/AcfD family lipoprotein zinc metalloprotease 22451516,25789808,28212863,29891541 1236 Gammaproteobacteria class 4486 NCBIFAM SslE/AcfD family lipoprotein zinc metalloprotease Members of this family are surface lipoprotein zinc metalloproteases, from the family that includes accessory colonization factor AcfD from Vibrio cholerae, SslE (YghJ ) from E. coli (Secreted and Surface-associated Lipoprotein from E. coli), and VPA1376 from Vibrio parahaemolyticus. Each is about 1500 amino acids long, and SslE is a known substrate of a type II secretion system (T2SS). SslE is known to have mucinase activity. NF037978.1 T2SS_GspB 100 100 179 equivalog Y Y N type II secretion system assembly factor GspB gspB 25025769,30767847 1236 Gammaproteobacteria class 1564 NCBIFAM type II secretion system assembly factor GspB GspB (general secretory pathway B) occurs in type II secretion systems (T2SS) and is viewed as an accessory protein, a factor involved in the assembly process rather than integral to the completed T2SS apparatus. NF038004.1 darobactin_RiPP 45 45 45 equivalog Y Y N darobactin family peptide antibiotic darA 31747680 1236 Gammaproteobacteria class 111 NCBIFAM darobactin family peptide antibiotic Darobactin, discovered in the genus Photorhabdus, is a peptide antibiotic, made from a ribosomally translated precursor, and modified by the radical SAM/SPASM peptide maturase DarE. Darobactin A is the founding member of a new class of antibiotic that appears to target BamA, a component of the outer membrane beta-barrel assembly machine. It is seven amino acids long, Trp1-Asn2-Trp3-Ser4-Lys5-Ser6-Phe7, with two crosslinks, one from Trp1 to Trp3, the other from Trp3 to Lys5. Homologs of the darobactin A precursor are encoded in various strains of Photorhabdus, Yersinia, and Vibrio. NF038005.1 rSAM_mat_DarE 650 650 432 equivalog Y Y N darobactin maturation radical SAM/SPASM protein DarE darE 31747680 1236 Gammaproteobacteria class 220 NCBIFAM darobactin maturation radical SAM/SPASM protein DarE The radical SAM/SPASM protein DarE is a maturase for the ribosomally translated, post-translationally modified peptide natural product (RiPP) darobactin, including forms A, B, C, D, and E. The mature form is just seven amino acids long, with two cross-links, a Trp1-Trp3 linkage and a Trp3-Lys5 (or Arg5) linkage. NF038008.1 ABC_perm_DarB 700 700 777 equivalog Y Y N darobactin export ABC transporter permease subunit darB 31747680 1236 Gammaproteobacteria class 354 NCBIFAM darobactin export ABC transporter permease subunit NF038106.1 gamma_NF038106 50 50 93 equivalog Y Y N PA4642 family protein 1236 Gammaproteobacteria class 2501 NCBIFAM PA4642 family protein Member of this family are small (about 95 amino acids), uncharacterized, and apparently restricted to the Gammaproteobacteria. Members include PA4642 from Pseudomonas aeruginosa PAO1. NF038111.1 rhom_dep_M36 1700 1700 1315 equivalog Y Y N rhombosortase-dependent M36 family metallopeptidase 22194940,30352106 1236 Gammaproteobacteria class 269 NCBIFAM rhombosortase-dependent M36 family metallopeptidase Members of this bacterial protein family have an M36 family metallopeptidase domain, like fungalysin (see PF02128), and a C-terminal GlyGly-CTERM domain, recognized and cleaved by rhombosortase. NF038115.1 SVAGG 150 150 407 subfamily Y Y N SVAGG family GlyGly-CTERM protein GO:0031240 22194940,30352106 1236 Gammaproteobacteria class 113 NCBIFAM SVAGG family GlyGly-CTERM protein The SVAGG (Shewanella/Vibrio/Aeromonas GlyGly-CTERM protein) family (defined and named here) averages about 420 amino acids in length. Member proteins have a C-terminal GlyGly-CTERM sorting signal, which implies cleavage by rhombosortase, export by a type II secretion system (T2SS), and covalent attachment to the outer membrane. NF038177.1 epimerase_AlgG 700 700 519 equivalog Y Y N mannuronan 5-epimerase AlgG algG 5.1.3.37 8144447,8830682 1236 Gammaproteobacteria class 2660 NCBIFAM mannuronan 5-epimerase AlgG NF038178.1 AlgP_Nterm 100 100 132 equivalog_domain Y Y N AlgP family protein 32634088 1236 Gammaproteobacteria class 5384 NCBIFAM AlgP family protein N-terminal domain This HMM describes the conserved N-terminal domain of a protein that has extensive lysine-rich repeats in the C-terminal half, typically PAAK, and is called histone-like for that reason. Some reports have called AlgP (also called AlgR3) a regulator of alginate biosynthesis, responsible for a mucoid phenotype in Pseudomonas aeruginosa, but recent work casts doubt on the specificity of the connection to alginate. NF038184.1 blaVMB 500 500 242 exception Y Y Y VMB family subclass B1 metallo-beta-lactamase blaVMB 3.5.2.6 GO:0008800 32293144 1236 Gammaproteobacteria class 5 NCBIFAM VMB family subclass B1 metallo-beta-lactamase NF038187.1 FadE_coli 1300 1300 816 exception Y Y N acyl-CoA dehydrogenase FadE fadE 1.3.8.7,1.3.8.8 GO:0003995,GO:0033539,GO:0050660 10206693,12057976 1236 Gammaproteobacteria class 9810 NCBIFAM acyl-CoA dehydrogenase FadE This HMM describes a narrow clade of medium-chain and long-chain acyl-CoA dehydrogenases that includes YafH from Escherichia coli K-12 and Salmonella enterica LT2 (also called FadF), now called FadE. NF038217.2 blaOXA-427_like 600 600 264 exception Y Y Y OXA-427 family carbapenem-hydrolyzing class D beta-lactamase blaOXA 3.5.2.6 GO:0008800 28859446,29311088,36995982 1236 Gammaproteobacteria class 11 NCBIFAM OXA-427 family carbapenem-hydrolyzing class D beta-lactamase NF038222.1 IcmW_IVB 100 100 139 equivalog Y Y N type IVB secretion system protein IcmW icmW 15661013,29203674 1236 Gammaproteobacteria class 120 NCBIFAM type IVB secretion system protein IcmW NF038239.1 T6SS_TssL_short 180 180 207 exception Y Y N type VI secretion system protein TssL, short form tssL 27600410,29458124,33020223 1236 Gammaproteobacteria class 4318 NCBIFAM type VI secretion system protein TssL, short form TssL is a type VI secretion system (T6SS) protein, related to IcmH/DotU of type IVb secretion systems (T4bSS). Some forms have a OmpA-related C-terminal extension domain, likely to mediated interaction with peptidoglycan, but this form, also called SciP, lacks that extension. NF038255.1 exopoly_VpsD 300 300 381 equivalog Y Y N VpsD family glycosyltransferase 20466768 1236 Gammaproteobacteria class 360 NCBIFAM VpsD family glycosyltransferase Member of this family include VpsD (VC0920), involved in the biosynthesis of Vibrio polysaccharide, an exopolysaccharide component of biofilm matrix. NF038257.2 exopoly_VpsP 125 125 213 subfamily Y Y N VpsP family polysaccharide biosynthesis protein 20466768 1236 Gammaproteobacteria class 644 NCBIFAM VpsP family polysaccharide biosynthesis protein Vps genes contribute to biofilm formation by directing biosynthesis of the exopolysaccharide VPS (Vibrio polysaccharide), a major component of the biofilm matrix. The specific function of VpsP is not known. NF039252.4 PF19180.5 DUF5862 33.3 33.3 68 domain Y N N Family of unknown function (DUF5862) 1236 Gammaproteobacteria class 258 EBI-EMBL Family of unknown function (DUF5862) Family of unknown function (DUF5862) This is a family of uncharacterised proteins of unknown function predominantly found in Ascoviridae. This family also includes uncharacterised proteins found in Bacteria. (from Pfam) NF039327.4 PF19491.4 DUF6026 26.6 26.6 51 subfamily Y Y N DUF6026 family protein 26507104 1236 Gammaproteobacteria class 882 EBI-EMBL Family of unknown function (DUF6026) DUF6026 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001285) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). This family includes a protein from the pseudopyronine A biosynthetic gene cluster from Pseudomonas putida and appears to be predominantly found in Pseudomonas [1]. [1]. 26507104. Biosynthetic Origin of the Antibiotic Pseudopyronines A and B in Pseudomonas putida BW11M1. Bauer JS, Ghequire MG, Nett M, Josten M, Sahl HG, De Mot R, Gross H;. Chembiochem. 2015;16:2491-2497. (from Pfam) NF039365.4 PF19667.4 DUF6170 27 27 100 subfamily Y Y N DUF6170 family protein 1236 Gammaproteobacteria class 516 EBI-EMBL Family of unknown function (DUF6170) DUF6170 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 84 and 107 amino acids in length. (from Pfam) NF039388.4 PF19759.4 DUF6246 27 27 185 subfamily Y Y N DUF6246 family protein 1236 Gammaproteobacteria class 4712 EBI-EMBL Family of unknown function (DUF6246) DUF6246 family protein This family of proteins found in bacteria and viruses is functionally uncharacterised. Proteins in this family are typically between 205 and 235 amino acids in length. (from Pfam) NF039418.4 PF19894.4 DUF6367 25 25 142 subfamily Y Y N DUF6367 family protein 15324808 1236 Gammaproteobacteria class 604 EBI-EMBL Family of unknown function (DUF6367) DUF6367 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001053) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the tubulysin A biosynthetic gene cluster from Archangium disciforme [1]. [1]. 15324808. Identification and analysis of the core biosynthetic machinery of tubulysin, a potent cytotoxin with potential anticancer activity. Sandmann A, Sasse F, Muller R;. Chem Biol. 2004;11:1071-1079. (from Pfam) NF039622.4 PF19456.4 MobI 26.6 26.6 116 subfamily Y Y N conjugative transfer protein MobI(A/C) mobI 18539733,19396961,24567731,28878309,32848007 1236 Gammaproteobacteria class 2089 EBI-EMBL MobI protein conjugative transfer protein MobI(A/C) Members of this family are the mobility protein MobI as found in incompatibility group C (IncC) or A (IncA) plasmids, hence the designation MobI(A/C). MobI(A/C) has also been known as Vcrx001. NF039664.4 PF19619.4 DUF6124 27 27 63 subfamily Y Y N DUF6124 family protein 1236 Gammaproteobacteria class 21994 EBI-EMBL Family of unknown function (DUF6124) DUF6124 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 85 and 119 amino acids in length. (from Pfam) NF039674.4 PF19657.4 DUF6160 27 27 96 subfamily Y Y N DUF6160 family protein 1236 Gammaproteobacteria class 6537 EBI-EMBL Family of unknown function (DUF6160) DUF6160 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 153 and 460 amino acids in length. (from Pfam) NF040077.4 PF19929.4 DUF6392 25.9 25.9 151 subfamily Y Y N DUF6392 family protein 1236 Gammaproteobacteria class 4305 EBI-EMBL Family of unknown function (DUF6392) DUF6392 family protein This family of proteins is functionally uncharacterised and it is predominantly found in Proteobacteria. Proteins in this family are typically between 55 and 170 amino acids in length. Proteins in this family are likely to be related to pyocin immunity protein. (from Pfam) NF040110.4 PF20051.4 DUF6453 25 25 291 subfamily Y Y N DUF6453 family protein 1236 Gammaproteobacteria class 2815 EBI-EMBL Family of unknown function (DUF6453) DUF6453 family protein This family of uncharacterised proteins is mainly found in phages. It may represent structural phage proteins. There are several conserved motifs: FxxI, GxxxxP and FSxxxxP, and also 7 additional conserved Glycine residues. (from Pfam) NF040300.4 PF19475.4 DUF6012 25 25 200 subfamily Y Y N DUF6012 family protein 15033239,16581203 1236 Gammaproteobacteria class 1290 EBI-EMBL Family of unknown function (DUF6012) DUF6012 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000128) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein encoded by the pyoluteorin biosynthetic gene cluster from Pseudomonas sp. M18 [1,2] [1]. 15033239. Identification and characterization of pltZ, a gene involved in the repression of pyoluteorin biosynthesis in Pseudomonas sp. M18. Huang X, Zhu D, Ge Y, Hu H, Zhang X, Xu Y;. FEMS Microbiol Lett. 2004;232:197-202. [2]. 16581203. Identification and characterization of a putative ABC transporter PltHIJKN required for pyoluteorin production in Pseudomonas sp. M18. Huang X, Yan A, Zhang X, Xu Y;. Gene. 2006;376:68-78. (from Pfam) NF040304.4 PF19485.4 DUF6021 29 29 61 subfamily Y Y N DUF6021 family protein 17254952 1236 Gammaproteobacteria class 1044 EBI-EMBL Family of unknown function (DUF6021) DUF6021 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000399) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This family includes a protein from the orfamide A biosynthetic gene cluster from Pseudomonas protegens Pf-5 and appears to be predominantly found in Pseudomonadaceae [1]. [1]. 17254952. The genomisotopic approach: a systematic method to isolate products of orphan biosynthetic gene clusters. Gross H, Stockwell VO, Henkels MD, Nowak-Thompson B, Loper JE, Gerwick WH;. Chem Biol. 2007;14:53-63. (from Pfam) NF040409.4 PF19983.4 DUF6419 27 27 71 subfamily Y Y N DUF6419 family natural product biosynthesis protein 25140825 1236 Gammaproteobacteria class 166 EBI-EMBL Family of unknown function (DUF6419) DUF6419 family natural product biosynthesis protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000299) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the alterochromide A biosynthetic gene cluster from Pseudoalteromonas piscicida JCM 20779 [1]. [1]. 25140825. Targeted capture and heterologous expression of the Pseudoalteromonas alterochromide gene cluster in Escherichia coli represents a promising natural product exploratory platform. Ross AC, Gulland LE, Dorrestein PC, Moore BS;. ACS Synth Biol. 2015;4:414-420. (from Pfam) NF040532.1 blaOXA-9_like 575 575 274 exception Y Y Y OXA-9 family oxacillin-hydrolyzing class D beta-lactamase blaOXA 3.5.2.6 GO:0008800 8382826,9620445 1236 Gammaproteobacteria class 9 NCBIFAM OXA-9 family oxacillin-hydrolyzing class D beta-lactamase NF040574.1 T3SS_ATP_VscN2 750 750 420 exception Y Y N type III secretion system ATPase VscN2 vscN2 18347050,34481262 1236 Gammaproteobacteria class 151 NCBIFAM type III secretion system ATPase VscN2 NF040580.1 MBL_fold_Vmh 430 430 286 equivalog Y Y N Vmh family MBL fold metallo-hydrolase 34228542 1236 Gammaproteobacteria class 3253 NCBIFAM Vmh family MBL fold metallo-hydrolase Members of this family are zinc-binding enzymes with a metallo-beta-lactamase fold. The founding member, Vmh from Vibrio vulnificus (AAO08273.1), was described as having actual beta-lactamase activity. Because the search for beta-lactamases in known and potential pathogens has been so intense for so long, the potential zinc-binding motifs differ so greatly from those of the well-characterized metallo-beta-lactamases, and reports of beta-lactamase activity have not been widespread throughout this family, the question of whether the beta-lactamase activity seen for Vmh is essential or incidental is not yet answered. NF040643.1 S6_alt_immun 30 30 78 equivalog Y Y N pyocin S6 family toxin immunity protein 26860427 1236 Gammaproteobacteria class 956 NCBIFAM pyocin S6 family toxin immunity protein All members of the seed alignment for this family are found in the genus Pseudomonas, always adjacent or close to proteins with the killing domain (see PF09000) of 16S rRNA-cleaving colicin E3 and pyocin S6 family toxins. This family is unrelated to that of PF03513, a well-characterized family of immunity protein for ribosome inactivating toxins in the family of colicin E3, pyocin S6, but is called an immunity protein for the same family of toxins by Dingemans, et al., (2016) in pyocin S6-encoding strain P. aeruginosa CF_PA39. In most strains with a toxin from family PF09000, an immunity protein is found either from this family, or from PF03513, but only occasionally from both. NF040703.1 cyclopro_CfaB 650 650 393 exception Y Y N C17 cyclopropane fatty acid synthase CfaB cfaB 16391080 1236 Gammaproteobacteria class 2410 NCBIFAM C17 cyclopropane fatty acid synthase CfaB NF040717.1 BcsR_only 46 46 42 exception Y Y N cellulose biosynthesis protein BcsR bcsR 26077867,29234007 1236 Gammaproteobacteria class 1400 NCBIFAM cellulose biosynthesis protein BcsR BcsR (bacterial cellulose synthesis R, previously YhjR in Escherichia coli) is a small cytosolic protein essential for cellulose. It appears to form part of the Bcs macrocomplex that also includes membrane, periplasmic, and outer membrane components. BcsR shares homology with the N-terminal domain of BcsP, a longer protein with variable and repetitive C-terminal regions, found in beta-proteobacteria. See PF10945 for an HMM that describes the shared region. NF040760.1 AgaE 500 500 292 equivalog Y Y N PTS N-acetylgalactosamine transporter subunit IID agaE 10931310 1236 Gammaproteobacteria class 1529 NCBIFAM PTS N-acetylgalactosamine transporter subunit IID NF040805.1 blaOXA-732_like 585 585 261 exception Y Y Y OXA-732 family class D beta-lactamase blaOXA 3.5.2.6 GO:0008800 35231657 1236 Gammaproteobacteria class 2 NCBIFAM OXA-732 family class D beta-lactamase This first two beta-lactamases in this family to receive allele numbers, OXA-732 and OXA-1011, are integron-encoded enzymes. Transfer of the element containing OXA-1011 (which also encodes a GES-7 enzyme) contributes to resistance to carbapenems, suggesting that this enzyme acts as a carbapenemase. Note that some GES enzymes are carbapenemases, but GES-7 is reported to be an extended spectrum beta-lactamase and not a carbapenemase. NF040857.1 condensinMksB 750 750 412 equivalog Y Y N Mks condensin complex protein MksB mksB 35072315 1236 Gammaproteobacteria class 1936 NCBIFAM Mks condensin complex protein MksB NF040859.1 condensinMksF 1900 1900 926 equivalog Y Y N Mks condensin complex protein MksF mksF 35072315 1236 Gammaproteobacteria class 2836 NCBIFAM Mks condensin complex protein MksF NF040881.1 PTS_reg_TmaR 170 170 103 equivalog Y Y N PTS system regulator TmaR tmaR 33376208 1236 Gammaproteobacteria class 806 NCBIFAM PTS system regulator TmaR NF040884.1 acetylneur_anom 160 160 155 equivalog Y Y N N-acetylneuraminate anomerase nanQ GO:0006974 33895133 1236 Gammaproteobacteria class 2489 NCBIFAM N-acetylneuraminate anomerase NF040887.1 trans_reg_YciT 300 300 246 equivalog Y Y N DNA-binding transcriptional regulator YciT GO:0003700,GO:0006355 34428301 1236 Gammaproteobacteria class 2923 NCBIFAM DNA-binding transcriptional regulator YciT Involved in osmolarity control regulation NF040977.1 RepA_IncFII_LM 70 70 266 equivalog Y Y N plasmid replication initiator RepA repA GO:0006276 7543895 1236 Gammaproteobacteria class 9697 NCBIFAM plasmid replication initiator RepA Members of this family are the plasmid replication initiator protein RepA, as the term is used in IncFII (see TIGR03474) and IncL/M plasmids. Other RepA proteins may have no readily detectable homology. NF041161.1 blaHMB 500 500 238 exception Y Y Y HMB family subclass B1 metallo-beta-lactamase blaHMB GO:0008800 28065891,31211681 1236 Gammaproteobacteria class 2 NCBIFAM HMB family subclass B1 metallo-beta-lactamase NF041189.1 blaKBL 600 600 286 exception Y Y Y KBL family class A beta-lactamase blaKBL 3.5.2.6 GO:0008800 35862995 1236 Gammaproteobacteria class 1 NCBIFAM KBL family class A beta-lactamase KBL-1, the founding member of the KBL (Kathmandu beta-lactamase) family of class A beta-lactamases, appears to be mobilized, and appears active only against penicillins. NF041275.1 MurL_Xanthmoales 700 700 447 equivalog Y Y N UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-L-glutamate epimerase murL 5.1.1.23 GO:0009252,GO:0016855 28294606,34114638 1236 Gammaproteobacteria class 1458 NCBIFAM UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-L-glutamate epimerase NF041290.1 StbA_2 100 100 123 equivalog Y Y N plasmid stabilization protein StbA stbA 21625564 1236 Gammaproteobacteria class 361 NCBIFAM plasmid stabilization protein StbA NF041291.1 StbC 100 100 122 equivalog Y Y N plasmid stabilization protein StbC stbC 21625564 1236 Gammaproteobacteria class 122 NCBIFAM plasmid stabilization protein StbC NF041403.1 XopAH 220 220 288 subfamily Y Y N XopAH/AvrB family type III secretion system effector xopAH GO:0030254 15016364,19849782,23252460 1236 Gammaproteobacteria class 175 NCBIFAM XopAH/AvrB family type III secretion system effector NF041429.1 EexR 200 200 142 subfamily Y Y N EexR/EexS family entry exclusion protein eex 17307849 1236 Gammaproteobacteria class 232 NCBIFAM EexR/EexS family entry exclusion protein NF041447.1 TrbC_conju 800 800 685 equivalog Y Y N F-type conjugative transfer protein TrbC trbC 1848841,1917882,8014987 1236 Gammaproteobacteria class 1865 NCBIFAM F-type conjugative transfer protein TrbC NF041471.1 phage_reg_YmfL 90 90 143 equivalog Y Y N YmfL family putative regulatory protein 1236 Gammaproteobacteria class 6394 NCBIFAM YmfL family putative phage regulatory protein Members of this family are homologs of the e14 prophage region protein YmfL from Escherichia coli K-12. Distant homology to phage regulatory protein CII, as described by Pfam model PF06892, suggests a similar function. NF041472.1 toxin_DinQ 30 30 22 equivalog Y Y N damage-inducible type I toxin DinQ dinQ 23408903,27651528,31582786 1236 Gammaproteobacteria class 248 NCBIFAM damage-inducible type I toxin DinQ Members of this family include DinQ as seen in Escherichia coli K-12 and a family of closely related DinQ-like type I toxins termed DqlA. See model NF041473 for the more distantly related DqlB type I toxins. NF041473.1 DinQ_rel 35 35 31 equivalog Y Y N DinQ-like type I toxin DqlB dqlB 27651528 1236 Gammaproteobacteria class 337 NCBIFAM DinQ-like type I toxin DqlB NF041477.1 YnaM_YnfT_fam 35 35 34 subfamily Y Y N YnaM/YnfT family protein 29645342 1236 Gammaproteobacteria class 311 NCBIFAM YnaM/YnfT family protein This uncharacterized protein family is named for two identical proteins found in prophage regions of Escherichia coli K-12, YnaM (Rac prophage) and YnfT (Qin prophage). NF041490.1 trans_reg_SutA 145 145 109 equivalog Y Y N transcriptional regulator SutA sutA 26787849 1236 Gammaproteobacteria class 1004 NCBIFAM transcriptional regulator SutA NF041512.1 PA2817_fam 70 70 136 subfamily Y Y N PA2817 family protein 1236 Gammaproteobacteria class 1778 NCBIFAM PA2817 family protein This family is named for uncharacterized protein PA2817 from Pseudomonas aeruginosa. Many members of the family have been annotated previously with the name dehydrogenase, but no source for that annotation, nor homology to any characterized enzyme or solved crystal structure, could be found as this HMM was built. NF041532.1 HprT 50 50 52 equivalog Y Y N HrpT family type III secretion system protein hrpT 1236 Gammaproteobacteria class 619 NCBIFAM HrpT family type III secretion system protein NF041550.1 CesT_sub 120 120 143 subfamily Y Y N type III secretion system chaperone 1236 Gammaproteobacteria class 399 NCBIFAM type III secretion system chaperone NF041583.1 SOS_SulA_aeru 150 150 157 exception Y Y N SOS-induced cell division inhibitor SulA sulA GO:0005515,GO:0009432,GO:0051782 12808143,22432817 1236 Gammaproteobacteria class 1785 NCBIFAM SOS-induced cell division inhibitor SulA, Pseudomonas type SulA, as found in Pseudomonas aeruginosa, is a cell division inhibitor induced by the SOS response. It interacts with FtsZ to halt cell division. SulA proteins, like FtsZ, differ greatly by lineage; SulA of Escherichia coli is architecturally somewhat different and is described by a different model, TIGR00623. NF041596.1 fum_diaprop_lig_DdaG 700 700 390 equivalog Y Y N fumarate--(S)-2,3-diaminopropanoate ligase ddaG 6.3.2.46 GO:0016874,GO:0017000 19807062 1236 Gammaproteobacteria class 17 NCBIFAM fumarate--(S)-2,3-diaminopropanoate ligase NF041600.1 cyt_ox_CcoM 40 40 34 equivalog Y Y N cytochrome c oxidase subunit CcoM ccoM 26814183 1236 Gammaproteobacteria class 901 NCBIFAM cytochrome c oxidase subunit CcoM NF041601.1 PA5502_lipo 285 285 237 equivalog Y Y N PA5502 family lipoprotein 1236 Gammaproteobacteria class 2023 NCBIFAM PA5502 family lipoprotein NF041609.1 esterase_EstP 1000 1000 642 equivalog Y Y N esterase EstP estP 3.1.1.1 GO:0006629,GO:0016298,GO:0052689 20931591 1236 Gammaproteobacteria class 2746 NCBIFAM esterase EstP NF041613.1 fdxn_Azotob 195 195 107 equivalog_domain Y Y N 2Fe-2S ferredoxin GO:0046872,GO:0051537 10439076 1236 Gammaproteobacteria class 33 NCBIFAM 2Fe-2S ferredoxin NF041632.1 blaKHM 480 480 237 exception Y Y Y KHM family subclass B1 metallo-beta-lactamase blaKHM 3.5.2.6 GO:0008800 18765691 1236 Gammaproteobacteria class 9 NCBIFAM KHM family subclass B1 metallo-beta-lactamase NF041672.1 ADPriboarghdlase 490 490 361 equivalog Y Y N ADP-ribosylarginine hydrolase Tri1 tri1 3.2.2.19 GO:0003875 30343895 1236 Gammaproteobacteria class 1074 NCBIFAM ADP-ribosylarginine hydrolase Tri1 NF041676.1 FecA_OM_dicitr 1100 1100 773 equivalog Y Y N TonB-dependent Fe(3+) dicitrate receptor FecA fecA 19118371,7729419 1236 Gammaproteobacteria class 5398 NCBIFAM TonB-dependent Fe(3+) dicitrate receptor FecA NF041729.1 PA1414_fam 28 28 43 equivalog Y Y N PA1414 family protein 1236 Gammaproteobacteria class 630 NCBIFAM PA1414 family protein This HMM represents a corrected (shorter) length for PA1414 from the representative strain Pseudomonas aeruginosa PAO1, and its homologs from other strains and species. The function of this small protein is unknown. NF041788.1 anti-phage_ZorB1 400 400 243 equivalog Y Y N type I Zorya anti-phage system protein ZorB1 zorB1 GO:0051607 29371424 1236 Gammaproteobacteria class 416 NCBIFAM type I Zorya anti-phage system protein ZorB1 NF041789.2 anti-phage_ZorC 490 490 551 equivalog Y Y N type I Zorya anti-phage system protein ZorC zorC GO:0051607 29371424 1236 Gammaproteobacteria class 607 NCBIFAM type I Zorya anti-phage system protein ZorC NF041790.1 anti-phage_ZorD 1500 1500 1035 equivalog Y Y N type I Zorya anti-phage system protein ZorD zorD GO:0051607 29371424 1236 Gammaproteobacteria class 745 NCBIFAM type I Zorya anti-phage system protein ZorD NF041791.1 anti-phage_ZorE 600 600 358 equivalog Y Y N type II Zorya anti-phage system protein ZorE zorE GO:0051607 29371424 1236 Gammaproteobacteria class 185 NCBIFAM type II Zorya anti-phage system protein ZorE NF041794.1 1_anti-phage_ZorA1 750 750 729 equivalog Y Y N type I Zorya anti-phage system protein ZorA1 zorA1 1236 Gammaproteobacteria class 618 NCBIFAM type I Zorya anti-phage system protein ZorA1 NF041830.1 RR_TF_ErdR 390 390 213 exception Y Y N response regulator transcription factor ErdR erdR 20093290,20549193,28510688 1236 Gammaproteobacteria class 1298 NCBIFAM response regulator transcription factor ErdR ErdR, a broadly acting response regulator transcription factor, with founding member PA3604 in Pseudomonas aeruginosa, has been implicated in the regulation of ethanol oxidation and biofilm-specific antibiotic resistance. NF041847.1 transduc_aer2_vibrio 1200 1200 804 equivalog Y Y N aerotaxis transducer Aer2 aer2 GO:0004888,GO:0006935,GO:0007165 29719085,36420630 1236 Gammaproteobacteria class 338 NCBIFAM aerotaxis transducer Aer2 NF041862.1 YtfT_transport 535 535 339 equivalog Y Y N galactofuranose ABC transporter, ATP-binding protein YtfT ytfT 7.5.2.9 GO:0042875,GO:0103116 30698741 1236 Gammaproteobacteria class 3140 NCBIFAM galactofuranose ABC transporter, ATP-binding protein YtfT NF041882.1 PA3371_fam 50 50 60 equivalog Y Y N PA3371 family protein 1236 Gammaproteobacteria class 1102 NCBIFAM PA3371 family protein This family resembles the DUF1328 family (see PF07043). It differs in having a C-terminal extension with a nearly invariant motif GRRIKRDPVLR, and in having a less hydrophobic central region. The average length is 60 amino acids. a less extremely hydrophoib NF041888.1 ABC_SBP_YdcS 725 725 379 equivalog Y Y N putative ABC transporter substrate-binding protein YdcS ydcS 18640095 1236 Gammaproteobacteria class 4290 NCBIFAM putative ABC transporter substrate-binding protein YdcS YdcS is identified as putative ABC transporter by homology and by arrangement in an operon with ABC transporter permease and ATP-binding cassette proteins. Dai and Reusch report that YdcS doubles as a poly-3-hydroxybutyrate (PHB) synthase in the periplasm of Escherichia coli. The type of PHB produced in E. coli, and reduced 30 percent by mutation of ydcS, consists of short polymers (60,000 units) that many bacteria synthesize and deposit in storage granules. NF041933.1 MzaC 1500 1500 806 equivalog Y Y N MZA anti-phage system associated Z1 domain-containing protein MzaC mzaC GO:0051607 32855333 1236 Gammaproteobacteria class 158 NCBIFAM MZA anti-phage system associated Z1 domain-containing protein MzaC Proteins of this family are components of the MZA anti-phage system (MutL, Z1, and AIPR). The function of this protein in the MZA anti-phage system is not understood yet. NF041934.1 MzaD 420 420 326 equivalog Y Y N MZA anti-phage system associated PD-(D/E)XK motif protein MzaD mzaD GO:0051607 32855333 1236 Gammaproteobacteria class 132 NCBIFAM MZA anti-phage system associated PD-(D/E)XK motif protein MzaD Proteins of this family are components of the MZA anti-phage system (MutL, Z1, and AIPR). The function of this protein in the MZA anti-phage system is not understood yet. NF041950.1 CBU_0585_fam 35 35 43 equivalog Y Y N CBU_0585 family protein 23133385 1236 Gammaproteobacteria class 161 NCBIFAM CBU_0585 family protein Two founding members of this family, Cbu_0585 from Coxiella burnetii and lpg0581 from Legionella pneumophila, were listed as potential type IV secretion system (T4SS) virulence effectors because of their homology to each other but absence from a number of related bacteria that lack T4SS. However, while subsequent analysis identified other effectors based on similar observations, no claim was made for this pair and their homologs. NF042435.1 DhshikDhtase_QuiC 1200 1200 635 equivalog Y Y N 3-dehydroshikimate dehydratase QuiC quiC 4.2.1.118 GO:0019631,GO:0019633,GO:0046565 27706847 1236 Gammaproteobacteria class 2877 NCBIFAM 3-dehydroshikimate dehydratase QuiC NF042499.3 PF20396.3 DUF6689 27 27 275 subfamily Y Y N DUF6689 family protein 1236 Gammaproteobacteria class 339 EBI-EMBL Family of unknown function (DUF6689) DUF6689 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in gamma proteobacteria. Proteins in this family are typically between 273 and 287 amino acids in length. (from Pfam) NF042513.3 PF20192.3 DUF6555 30.5 30.5 74 subfamily Y Y N DUF6555 family protein 1236 Gammaproteobacteria class 1973 EBI-EMBL Family of unknown function (DUF6555) DUF6555 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in Proteobacteria. Proteins in this family are typically between 76 and 94 amino acids in length. (from Pfam) NF042618.3 PF20616.3 Caps_syn_GfcC_N 22.1 22.1 129 domain Y Y N capsule biosynthesis GfcC D2 domain-containing protein 10200953,16030220,17250770,21449614 1236 Gammaproteobacteria class 7372 EBI-EMBL Capsule biosynthesis GfcC, N-terminal capsule biosynthesis GfcC D2 domain-containing protein Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organisation of genes responsible for capsule assembly, the assembly pathway and regulation [1]. This family plays a role in group 4 capsule biosynthesis [2]. These proteins have a beta-grasp fold [3]. Two beta-grasp domains, D2 and D3, are arranged in tandem. There is a C-terminal amphipathic helix which packs against D3. A helical hairpin insert in D2 binds to D3 and constrains its position, a conserved arginine residue at the end of this hairpin is essential for structural integrity [4]. This entry represents D2 domain found at the N-terminal [4]. [1]. 10200953. Structure, assembly and regulation of expression of capsules in Escherichia coli. Whitfield C, Roberts IS;. Mol Microbiol. 1999;31:1307-1319. [2]. 16030220. Identification of an Escherichia coli operon required for formation of the O-antigen capsule. Peleg A, Shifrin Y, Ilan O, Nadler-Yona C, Nov S, Koby S, Baruch K, Altuvia S, Elgrably-Weiss M, Abe CM, Knutton S, Saper MA, Rosenshine I;. J Bacteriol. 2005;187:5259-5266. [3]. 17250770. A novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands. Burroughs AM, Balaji S, Iyer LM, Aravind L;. Biol Direct. 2007;2:4-4. [4]. 21449614. Crystal structure of E. coli group 4 capsule protein GfcC reveals a domain organization resembling Wza. Sathiyamoorthy K, Mills E, Franzmann TM, Rosenshine I, Saper MA;. Biochemistry 2011;0:0-0. (from Pfam) NF042702.3 PF20265.3 LARA_dom 27.4 27.4 104 domain Y Y N regulatory ATPase RavA LARA domain-containing protein 21148420,31992852 1236 Gammaproteobacteria class 6622 EBI-EMBL ATPase, RavA, LARA domain regulatory ATPase RavA LARA domain-containing protein This is the LARA (LdcI Associating domain of RavA) domain of bacterial regulatory ATPase RavA (Regulatory ATPase variant A) [1,2]. It adopts an unique fold which consists of a compact antiparallel beta-barrel- like structure formed by six beta-strands and one alpha-helix [1,2]. This domain mediates the interaction between RavA and LdcI (inducible lysine decarboxylase) which form a cage-like complex proposed to assist assembly of specific respiratory complexes in E. coli [2]. [1]. 21148420. Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity. El Bakkouri M, Gutsche I, Kanjee U, Zhao B, Yu M, Goret G, Schoehn G, Burmeister WP, Houry WA;. Proc Natl Acad Sci U S A. 2010;107:22499-22504. [2]. 31992852. Structural insights into ATP hydrolysis by the MoxR ATPase RavA and the LdcI-RavA cage-like complex. Jessop M, Arragain B, Miras R, Fraudeau A, Huard K, Bacia-Verloop M, Catty P, Felix J, Malet H, Gutsche I;. Commun Biol. 2020;3:46. (from Pfam) NF042891.3 PF20535.3 DUF6750 27 27 128 subfamily Y Y N DUF6750 family protein 1236 Gammaproteobacteria class 916 EBI-EMBL Family of unknown function (DUF6750) DUF6750 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in proteobacteria. Proteins in this family are approximately 130 amino acids in length. (from Pfam) NF042946.1 3PPDioc_HcaE 830 830 450 equivalog Y Y N 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha hcaE 1.14.12.19 GO:0008695,GO:0019380 9603882 1236 Gammaproteobacteria class 1473 NCBIFAM 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha NF042947.1 3PPDioc_HcaF 230 230 172 equivalog Y Y N 3-phenylpropionate/cinnamic acid dioxygenase subunit beta hcaF 1.14.12.19 GO:0008695,GO:0019380 9603882 1236 Gammaproteobacteria class 968 NCBIFAM 3-phenylpropionate/cinnamic acid dioxygenase subunit beta NF042948.2 3PPDioc_HcaC 150 150 105 equivalog Y Y N 3-phenylpropionate/cinnamic acid dioxygenase ferredoxin subunit hcaC GO:0008695,GO:0019380 18286376,9603882 1236 Gammaproteobacteria class 618 NCBIFAM 3-phenylpropionate/cinnamic acid dioxygenase ferredoxin subunit NF042949.2 3PPDioc_HcaD 450 450 386 equivalog Y Y N 3-phenylpropionate/cinnamic acid dioxygenase ferredoxin--NAD(+) reductase subunit hcaD 1.18.1.3 GO:0008695,GO:0008860,GO:0019380 9603882 1236 Gammaproteobacteria class 2303 NCBIFAM 3-phenylpropionate/cinnamic acid dioxygenase ferredoxin--NAD(+) reductase subunit NF042950.1 3PPDhyd_Dh_HcaB 450 450 269 equivalog Y Y N 3-phenylpropionate-dihydrodiol/cinnamic acid-dihydrodiol dehydrogenase hcaB 1.3.1.87 GO:0018498,GO:0019380 9603882 1236 Gammaproteobacteria class 1135 NCBIFAM 3-phenylpropionate-dihydrodiol/cinnamic acid-dihydrodiol dehydrogenase 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate dehydrogenase NF042955.1 Ppl_antiphage 1000 1000 882 equivalog Y Y N anti-phage protein Ppl ppl GO:0051607 32855333 1236 Gammaproteobacteria class 223 NCBIFAM anti-phage protein Ppl Proteins of this family exhibited anti-phage activities. They contain a histidinol phosphatase and an ATPase regions. NF043000.1 carsnrspmd_synth 800 800 405 equivalog Y Y N carboxynorspermidine synthase 1.5.1.43 GO:0006596,GO:0102143 19196710,1955861 1236 Gammaproteobacteria class 1139 NCBIFAM carboxynorspermidine synthase NF044303.2 PF20749.2 DUF6833 26 26 57 domain Y N N Domain of unknown function (DUF6833) 1236 Gammaproteobacteria class 4 EBI-EMBL Domain of unknown function (DUF6833) Domain of unknown function (DUF6833) This presumed domain predominantly is found in sequences from tailed bacteriophages and proteobacterial prophages, including Pseudomonas phage LUZ7. Its function is unknown. (from Pfam) NF044318.2 PF20812.2 PM2_P3 27 27 61 domain Y N N Bacteriophage PM2, Viral membrane protein P3 18775333 1236 Gammaproteobacteria class 49 EBI-EMBL Bacteriophage PM2, Viral membrane protein P3 Bacteriophage PM2, Viral membrane protein P3 Viral membrane protein P3 assemblies into dimers. Each P3 subunit comprise a core of two perpendicular alpha helices, and subunits are bound together by a parallel two-stranded beta sheet. 120 asymmetric dimers form a layer below the outer capsid shell in an almost planar structure. This protein family is found in Bacteriophage PM2 and similar PRD1-adenovirus [1]. Paper describing PDB structure 2w0c. [1]. 18775333. Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2. Abrescia NG, Grimes JM, Kivela HM, Assenberg R, Sutton GC, Butcher SJ, Bamford JK, Bamford DH, Stuart DI;. Mol Cell. 2008;31:749-761. (from Pfam) NF044330.2 PF20849.2 TelK_muzzle 27 27 118 domain Y N N Protelomerase, muzzle domain 17889664 1236 Gammaproteobacteria class 581 EBI-EMBL Protelomerase, muzzle domain Protelomerase, muzzle domain This domain is found in Protelomerase from Klebsiella phage phiKO2 (TelK) and similar proteins from tailed bacteriophages and bacterial prophages mainly from Gammaproteobacteria. TelK is a hairpin telomere resolvase with DNA cleavage-rejoining activity that resolves the catenated circular dimer produced from the bidirectional replication of a chromosome. The core of the TelK monomer consists of an N-terminal domain and a catalytic domain connected by a long alpha- helical linker. However, there are two extensions of the protein: a C-terminal DNA binding domain named the stirrup (Pfam:PF20818) and an N-terminal domain. The latter has an insertion termed the muzzle (this entry), which folds into two long alpha-helices. This protruding element is packed against the DNA-binding catalytic and N-terminal domains of the opposite subunit in each dimer [1]. Paper describing PDB structure 2v6e. [1]. 17889664. An interlocked dimer of the protelomerase TelK distorts DNA structure for the formation of hairpin telomeres. Aihara H, Huang WM, Ellenberger T;. Mol Cell. 2007;27:901-913. (from Pfam) NF044338.2 PF20876.2 VipE 27 27 125 domain Y N N Effector protein VipE 1236 Gammaproteobacteria class 51 EBI-EMBL Effector protein VipE Effector protein VipE Legionella pneumophila use the Icm/Dot type IVB secretion system to deliver into the host cell effectors that inhibit phagosome maturation and modulate host vesicle trafficking pathways. VipE is one of those effectors. This entry represents the N-terminal domain that adopts an alpha-helical fold. (from Pfam) NF044342.2 PF20898.2 P_T4SS_TraN 27 27 59 domain Y N N P-type Type IV secretion system, TraN 12855161,17244707,19946264,23511972 1236 Gammaproteobacteria class 129 EBI-EMBL P-type Type IV secretion system, TraN P-type Type IV secretion system, TraN TraN, a subunit of the P-type Type IV secretion system (T4SS) encoded by the conjugative plasmid pKM101 from Escherichia coli, is the homologue of the F-type T4SS protein VirB7 (Pfam:PF17413). This protein forms spokes radially crossing the entire assembly of the T4SS in the periphery of the outer membrane complex. It forms a complex with TraO (the homologue of VirB9) that surrounds the inner ring formed by TraF (VirB10 homologue) [1-4]. Paper describing PDB structure 2ofq. [1]. 17244707. NMR structure of a complex between the VirB9/VirB7 interaction domains of the pKM101 type IV secretion system. Bayliss R, Harris R, Coutte L, Monier A, Fronzes R, Christie PJ, Driscoll PC, Waksman G;. Proc Natl Acad Sci U S A. 2007;104:1673-1678. Paper describing PDB structure 3jqo. [2]. 19946264. Structure of the outer membrane complex of a type IV secretion system. Chandran V, Fronzes R, Duquerroy S, Cronin N, Navaza J, Waksman G;. Nature. 2009;462:1011-1015. Paper describing PDB structure 3zbi. [3]. 23511972. Structure of a bacterial type IV secretion core complex at subnanometre resolution. Rivera-Calzada A, Fronzes R, Savva CG, Chandran V, Lian PW, Laeremans T, Pardon E, Steyaert J, Remaut H, Waksman G, Orlova EV;. EMBO J. 2013;32:1195-1204. [4]. 12855161. F factor conjugation is a true type IV secretion system. Lawley TD, Klimke WA, Gubbins MJ, Frost LS;. FEMS Microbiol Lett. 2003;224:1-15. (from Pfam) NF044344.2 PF20905.2 ExsD_C 27 27 61 domain Y N N Antiactivator protein ExsD C-terminal domain 19235906 1236 Gammaproteobacteria class 892 EBI-EMBL Antiactivator protein ExsD C-terminal domain Antiactivator protein ExsD C-terminal domain The antiactivator protein ExsD represses the transcriptional activator ExsA. ExsA activates expression of type III secretion system genes. Repression of ExsA by ExsD is relieved by the secretion chaperone ExsC [1]. [1]. 19235906. Structural evidence suggests that antiactivator ExsD from Pseudomonas aeruginosa is a DNA binding protein. Bernhards RC, Jing X, Vogelaar NJ, Robinson H, Schubot FD;. Protein Sci. 2009;18:503-513. (from Pfam) NF044430.2 PF21216.2 PepQ_N 27 27 152 domain Y N N Xaa-Pro dipeptidase, N-terminal domain 20000741,23545636,25354344,26418828,32515491 1236 Gammaproteobacteria class 8899 EBI-EMBL Xaa-Pro dipeptidase, N-terminal domain Xaa-Pro dipeptidase, N-terminal domain This domain is found in Xaa-Pro dipeptidase from Escherichia coli (PepQ), a metalloprotease that catalyse the cleavage of Xaa-Pro dipeptides. This protein is organised into N-terminal (this entry) and C-terminal (usually Pfam:PF00557) domains and adopts a dimeric configuration. This domain shows an alpha-beta structure with four helices, one pair flanking each side of the six-stranded mixed beta-sheet [1-5]. Paper describing PDB structure 3l24. [1]. 20000741. Structural insights into the dual activities of the nerve agent degrading organophosphate anhydrolase/prolidase. Vyas NK, Nickitenko A, Rastogi VK, Shah SS, Quiocho FA;. Biochemistry. 2010;49:547-559. Paper describing PDB structure 3rva. [2]. 23545636. Organophosphorus acid anhydrolase from Alteromonas macleodii: structural study and functional relationship to prolidases. Stepankova A, Duskova J, Skalova T, Hasek J, Koval' T, Ostergaard LH, Dohnalek J;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013;69:346-354. Paper describing PDB structure 4qr8. [3]. 25354344. Structural basis of substrate selectivity of E. coli prolidase. Weaver J, Watts T, Li P, Rye HS;. PLoS One. 2014;9:e111531. Paper describing PDB structure 4zwo. [4]. 26418828. Engineering the Organophosphorus Acid Anhydrolase Enzyme for Increased Catalytic Efficiency and Broadened Stereospecificity on Russian VX. Daczkowski CM, Pegan SD, Harvey SP;. Biochemistry. 2015;54:6423-6433. Paper describing PDB structure 6ah7. [5]. 32515491. Repurposing a bacterial prolidase for organophosphorus hydrolysis: Reshaped catalytic cavity switches substrate selectivity. Yang J, Xiao YZ, Li R, Liu Y, Long LJ;. Biote. TRUNCATED at 1650 bytes (from Pfam) NF044441.2 PF21293.2 RNAseD_HRDC_C 25 25 66 domain Y N N Ribonuclease D, C-terminal HRDC domain 16004870 1236 Gammaproteobacteria class 9759 EBI-EMBL Ribonuclease D, C-terminal HRDC domain Ribonuclease D, C-terminal HRDC domain Ribonuclease D is a bacterial 3'-5' exonuclease that acts on tRNA. It contributes to the 3' maturation of several stable RNAs [1]. It consists of a catalytic domain (Pfam:PF01612) and two alpha- helical domains at the C-terminal that closely resemble the HRDC domain seen in RecQ-family helicases. This is the second HRDC domain from RNAse D. The first one is included in Pfam:PF00570. Paper describing PDB structure 1yt3. [1]. 16004870. Crystal structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing. Zuo Y, Wang Y, Malhotra A;. Structure. 2005;13:973-984. (from Pfam) NF044586.2 PF20661.2 SutA-RBD 29.3 29.3 35 domain Y N N SutA RNAP-binding domain 35859063 1236 Gammaproteobacteria class 3614 EBI-EMBL SutA RNAP-binding domain SutA RNAP-binding domain This domain (previously known as DUF6813) is found in the transcriptional regulator SutA from Pseudomonas aeruginosa and similar proteins mainly from Gammaproteobacteria. In Pseudomonas aeruginosa, SutA adapts bacteria to hypoxia and nutrition-limited environment during chronic infection by increasing transcriptional activity of an RNA polymerase (RNAP) holoenzyme. SutA interacts directly with RNAP holoenzyme and the RNAP-beta protrusion is its primary anchor site. This domain comprises an alpha-helix and a beta-strand and is responsible for interaction with RNAP-beta protrusion [1]. It contains a conserved FLxxGG sequence motif that appears to be located near the C-terminal helix cap. The SutA-RBD alpha-helix binds to a hydrophobic groove on RNAP-beta protrusion [1]. [1]. 35859063. Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding. He D, You L, Wu X, Shi J, Wen A, Yan Z, Mu W, Fang C, Feng Y, Zhang Y;. Nat Commun. 2022;13:4204. (from Pfam) NF044624.2 PF20793.2 VopS_N 27 27 141 domain Y N N Adenosine monophosphate-protein transferase VopS, N-terminal domain 19039103,20410310 1236 Gammaproteobacteria class 683 EBI-EMBL Adenosine monophosphate-protein transferase VopS, N-terminal domain Adenosine monophosphate-protein transferase VopS, N-terminal domain This domain is found at the N-terminal end of VopS from Vibrio parahaemolyticus. VopS is an adenylyltransferase involved in virulence by provoking the disruption of Rho GTPase signaling and the inhibition of actin assembly in infected cells. This domain is required for full activity of VopS. It consists of nine alpha helices [1, 2]. [1]. 19039103. AMPylation of Rho GTPases by Vibrio VopS disrupts effector binding and downstream signaling. Yarbrough ML, Li Y, Kinch LN, Grishin NV, Ball HL, Orth K;. Science. 2009;323:269-272. [2]. 20410310. Kinetic and structural insights into the mechanism of AMPylation by VopS Fic domain. Luong P, Kinch LN, Brautigam CA, Grishin NV, Tomchick DR, Orth K;. J Biol Chem. 2010;285:20155-20163. (from Pfam) NF044633.2 PF20818.2 TelK_stirrup 27 27 92 domain Y N N Protelomerase, stirrup domain 17889664 1236 Gammaproteobacteria class 641 EBI-EMBL Protelomerase, stirrup domain Protelomerase, stirrup domain This domain is found in Protelomerase from Klebsiella phage phiKO2 (TelK) and similar proteins from tailed bacteriophages and bacterial prophages mainly from Gammaproteobacteria. TelK is a hairpin telomere resolvase with DNA cleavage-rejoining activity that resolves the catenated circular dimer produced from the bidirectional replication of a chromosome. The core of the TelK monomer consists of an N-terminal domain and a catalytic domain connected by a long alpha- helical linker. However, there are two extensions of the protein: a C-terminal DNA binding domain named the stirrup (this entry) and a N-terminal core binding domain. This domain, which shows alpha- helical and beta-hairpin segments, binds to DNA using the winged helix-turn-helix motif and contacts the DNA flanking the cleavage site, extending the DNA binding interface. It is essential for the orientation and extent of DNA bending and for the refolding of cleaved DNA strands into hairpins [1]. Paper describing PDB structure 2v6e. [1]. 17889664. An interlocked dimer of the protelomerase TelK distorts DNA structure for the formation of hairpin telomeres. Aihara H, Huang WM, Ellenberger T;. Mol Cell. 2007;27:901-913. (from Pfam) NF044809.2 PF21500.2 HolB_lid 27.1 27.1 40 domain Y N N DNA polymerase III subunit delta', AAA+ ATPase lid domain 11525729,9363942 1236 Gammaproteobacteria class 5425 EBI-EMBL DNA polymerase III subunit delta', AAA+ ATPase lid domain DNA polymerase III subunit delta', AAA+ ATPase lid domain DNA polymerase III subunit delta' is part of the beta sliding clamp loading complex, which hydrolyses ATP to load the beta clamp onto primed DNA to form the DNA replication pre-initiation complex [1,2]. It consists of three domains, of which the N-terminal domain contains a nonfunctional nucleotide binding site. This entry represents the lid domain (or domain 2 in [1]). Paper describing PDB structure 1a5t. [1]. 9363942. Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III. Guenther B, Onrust R, Sali A, O'Donnell M, Kuriyan J;. Cell. 1997;91:335-345. Paper describing PDB structure 1jr3. [2]. 11525729. Crystal structure of the processivity clamp loader gamma (gamma) complex of E. coli DNA polymerase III. Jeruzalmi D, O'Donnell M, Kuriyan J;. Cell. 2001;106:429-441. (from Pfam) NF044850.2 PF21689.2 TorS_sensor_domain 27 27 131 domain Y N N Sensor protein TorS, sensor domain 19748340,22483119 1236 Gammaproteobacteria class 6541 EBI-EMBL Sensor protein TorS, sensor domain Sensor protein TorS, sensor domain This domain is found in Sensor protein TorS from Escherichia coli and similar proteins predominantly found in proteobacteria. TorS is a sensor histidine kinase that forms a complex with TorT, and TorR, to form the trimethylamine-N-oxide (TMAO) reductase (Tor) pathway, which plays a role in the regulation of this terminal electron receptor in anaerobic respiration. This domain folds into a four-helical bundle [1-3]. Paper describing PDB structure 3i9w. [1]. 19748340. Structural analysis of sensor domains from the TMAO-responsive histidine kinase receptor TorS. Moore JO, Hendrickson WA;. Structure. 2009;17:1195-1204. Paper describing PDB structure 3o1h. [2]. 22483119. An asymmetry-to-symmetry switch in signal transmission by the histidine kinase receptor for TMAO. Moore JO, Hendrickson WA;. Structure. 2012;20:729-741. (from Pfam) NF044895.2 PF20684.2 Fung_rhodopsin 27 27 237 domain Y N N Fungal rhodopsin domain 1236 Gammaproteobacteria class 5 EBI-EMBL Fungal rhodopsin domain Fungal rhodopsin domain This domain is found in a wide range of fungi. It can form a large multigene family in many species. As with other rhodopsin-like proteins this domain contains 7 transmembrane helices that form an integral membrane domain. (from Pfam) NF044904.2 PF20759.2 DUF6835 27 27 64 domain Y N N Domain of unknown function (DUF6835) 1236 Gammaproteobacteria class 34 EBI-EMBL Domain of unknown function (DUF6835) Domain of unknown function (DUF6835) This domain of unknown function is found in proteins from bacteria, including the product of the gene SO_2669 from Shewanella oneidensis. Its structure has been solved and shows 16 alpha helices (Swiss:Q8EDS4). (from Pfam) NF044936.2 PF20904.2 ExsD_M 27 27 66 domain Y N N Antiactivator protein ExsD helical hairpin domain 19235906 1236 Gammaproteobacteria class 691 EBI-EMBL Antiactivator protein ExsD helical hairpin domain Antiactivator protein ExsD helical hairpin domain The antiactivator protein ExsD represses the transcriptional activator ExsA. ExsA activates expression of type III secretion system genes. Repression of ExsA by ExsD is relieved by the secretion chaperone ExsC [1]. [1]. 19235906. Structural evidence suggests that antiactivator ExsD from Pseudomonas aeruginosa is a DNA binding protein. Bernhards RC, Jing X, Vogelaar NJ, Robinson H, Schubot FD;. Protein Sci. 2009;18:503-513. (from Pfam) NF044953.2 PF20982.2 CSS_CxxC 27.3 27.3 132 domain Y N N CSS_CxxC domain 35311563 1236 Gammaproteobacteria class 1821 EBI-EMBL CSS_CxxC domain CSS_CxxC domain This is a periplasmic sensor domain found at the N-terminal of c-di-GMP phosphodiesterases, which is a variation of the CSS motif sensor Pfam:PF12792 [1]. This domain, apart of the CSS motif, has an additional conserved CxxC motif, which presumably broaden its redox-sensing palette. It has been found in Shewanella spp. and other members of Altermonadales, Vibrionales and in some acidobacteria [1]. [1]. 35311563. Comparative Genomics of Cyclic di-GMP Metabolism and Chemosensory Pathways in Shewanella algae Strains: Novel Bacterial Sensory Domains and Functional Insights into Lifestyle Regulation. Martin-Rodriguez AJ, Higdon SM, Thorell K, Tellgren-Roth C, Sjoling A, Galperin MY, Krell T, Romling U;. mSystems. 2022; [Epub ahead of print] (from Pfam) NF044973.2 PF21083.2 ZapC_N 27 27 88 domain Y N N Cell-division protein ZapC, N-terminal 21216997,26619764,26655719 1236 Gammaproteobacteria class 4444 EBI-EMBL Cell-division protein ZapC, N-terminal Cell-division protein ZapC, N-terminal ZapC is one of four FtsZ-binding components of the Z ring in bacteria. Formation of the Z ring on the cytoplasmic surface of the membrane is the starting process for assembly of the cell-division apparatus. It binds directly to the Z ring, and although it is not essential for absolute cell division it contributes to it by enhancing the interactions between the FtsZ protofilaments (or polymers) which aggregate to form the ring conformation in the Z ring [1]. This entry represents the N-terminal alpha/beta region which contains a pocket, termed the N-domain pocket, lined with residues important for ZapC function as an FtsZ bundler [2,3]. [1]. 21216997. Identification of Escherichia coli ZapC (YcbW) as a component of the division apparatus that binds and bundles FtsZ polymers. Hale CA, Shiomi D, Liu B, Bernhardt TG, Margolin W, Niki H, de Boer PA;. J Bacteriol. 2011;193:1393-1404. [2]. 26655719. Structural and Functional Analyses Reveal Insights into the Molecular Properties of the Escherichia coli Z Ring Stabilizing Protein, ZapC. Schumacher MA, Zeng W, Huang KH, Tchorzewski L, Janakiraman A;. J Biol Chem. 2016;291:2485-2498. [3]. 26619764. Crystal structure of the Z-ring associated cell division protein ZapC from Escherichia coli. Ortiz C, Kureisaite-Ciziene D, Schmitz F, McLaughlin SH, Vicente M, Lowe J;. FEBS Lett. 2015;589:3822-3828. (from Pfam) NF044993.2 PF21155.2 VpsT-like_REC 27 27 124 domain Y N N VpsT-like, receiver domain 20150502,28758290 1236 Gammaproteobacteria class 4647 EBI-EMBL VpsT-like, receiver domain VpsT-like, receiver domain This domain is found at the N-terminal end of the transcriptional regulator VC_A0952 from Vibrio cholerae (VpsT), in CsgD from Salmonella typhimurium and other proteins predominantly found in proteobacteria. VpsT inversely regulates biofilm formation and motility. Like CsgD, it is organised into two domains: an N-terminal regulatory receiver domain (REC, this entry) and a C-terminal helix-turn-helix domain (Pfam:PF00196). This domain shows five alpha- helices and five beta-strands, with the beta-strands stabilising as a parallel beta-sheet surrounded by the alpha-helices [1,2]. Paper describing PDB structure 3kln. [1]. 20150502. Vibrio cholerae VpsT regulates matrix production and motility by directly sensing cyclic di-GMP. Krasteva PV, Fong JC, Shikuma NJ, Beyhan S, Navarro MV, Yildiz FH, Sondermann H;. Science. 2010;327:866-868. Paper describing PDB structure 5xp0. [2]. 28758290. Crystal structure of master biofilm regulator CsgD regulatory domain reveals an atypical receiver domain. Wen Y, Ouyang Z, Devreese B, He W, Shao Y, Lu W, Zheng F;. Protein Sci. 2017;26:2073-2082. (from Pfam) NF045007.2 PF21213.2 PriA-like_WH 27 27 63 domain Y N N Primosomal protein N'-like, winged helix 24379377,30201718 1236 Gammaproteobacteria class 8599 EBI-EMBL Primosomal protein N'-like, winged helix Primosomal protein N'-like, winged helix This domain is found in Primosomal protein N' from Escherichia coli (PriA) and similar proteins predominantly found in Proteobacteria. PriA is a DNA helicase involved in the restart of stalled replication forks, which are lethal in bacteria if left unrepaired. This protein shows a modular arrangement in which its central helicase core is surrounded by several DNA-binding elements, including a circularly permuted winged helix (WH) domain (this entry), which is located towards the N-terminal of the protein and can bind DNA in isolation [1,2]. Paper describing PDB structure 4nl4. [1]. 24379377. Structural mechanisms of PriA-mediated DNA replication restart. Bhattacharyya B, George NP, Thurmes TM, Zhou R, Jani N, Wessel SR, Sandler SJ, Ha T, Keck JL;. Proc Natl Acad Sci U S A. 2014;111:1373-1378. Paper describing PDB structure 6dgd. [2]. 30201718. Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase. Windgassen TA, Leroux M, Satyshur KA, Sandler SJ, Keck JL;. Proc Natl Acad Sci U S A. 2018;115:E9075. (from Pfam) NF045050.2 PF21372.2 TOP1_ZnF 27 27 45 domain Y N N Topoisomerase I, zinc finger 26490962 1236 Gammaproteobacteria class 14691 EBI-EMBL Topoisomerase I, zinc finger Topoisomerase I, zinc finger This entry represents a zinc ribbon domain found at the C-terminal of topoisomerase I from bacteria (it corresponds to D6 described in [1]. Topoisomerase I has an essential function in preventing hypernegative supercoiling of DNA. The C-terminal domains bind ssDNA to recognise the accumulation of negative supercoils in duplex DNA [1]. Paper describing PDB structure 4rul. [1]. 26490962. Structural basis for suppression of hypernegative DNA supercoiling by E. coli topoisomerase I. Tan K, Zhou Q, Cheng B, Zhang Z, Joachimiak A, Tse-Dinh YC;. Nucleic Acids Res. 2015;43:11031-11046. (from Pfam) NF045081.2 PF21510.2 PirA-like 27 27 95 domain Y N N PirA-like 26261348 1236 Gammaproteobacteria class 117 EBI-EMBL PirA-like PirA-like This family includes PirA from Vibrio parahaemolyticus. PirA is a plasmid-encoded homolog of a Photorhabdus insect-related (Pir) protein. It folds into an eight-stranded antiparallel beta-barrel with jelly-roll topology [1]. Paper describing PDB structure 3x0t. [1]. 26261348. The opportunistic marine pathogen Vibrio parahaemolyticus becomes virulent by acquiring a plasmid that expresses a deadly toxin. Lee CT, Chen IT, Yang YT, Ko TP, Huang YT, Huang JY, Huang MF, Lin SJ, Chen CY, Lin SS, Lightner DV, Wang HC, Wang AH, Wang HC, Hor LI, Lo CF;. Proc Natl Acad Sci U S A. 2015;112:10798-10803. (from Pfam) NF045094.2 PF21562.2 Gp63_3rd_G7C 27 27 66 domain Y N N G7C, Tail fiber protein, domain 3 28513100 1236 Gammaproteobacteria class 204 EBI-EMBL G7C, Tail fiber protein, domain 3 G7C, Tail fiber protein, domain 3 This domain is found in Tail fiber protein from Escherichia virus G7C (Gp63) and similar proteins from tailed bacteriophages and bacterial prophages. Gp63 is a receptor-binding proteins (RBP) that emanate from the phage particle in the form of fibres for the virus to recognise and bind to their host. It deacetylates surface polysaccharides of E. coli leaving the backbone of the polysaccharide intact. This entry represents domain 3 of Ggp63, which shows structural similarity to a small domain that connects the sialidase domain with the N-terminal particle-binding domain in phage tailspikes with sialidase activity (Pfam:PF12218). It shows two beta-helical rungs capped by an N-terminal alpha-helix oriented perpendicular to the rungs' axis [1]. Paper describing PDB structure 4qnl. [1]. 28513100. Function of bacteriophage G7C esterase tailspike in host cell adsorption. Prokhorov NS, Riccio C, Zdorovenko EL, Shneider MM, Browning C, Knirel YA, Leiman PG, Letarov AV;. Mol Microbiol. 2017;105:385-398. (from Pfam) NF045220.2 PF20792.2 VCD 27 27 240 domain Y N N VopL C-terminal dimerization domain 21873984,21873985,24120140 1236 Gammaproteobacteria class 397 EBI-EMBL VopL C-terminal dimerization domain VopL C-terminal dimerization domain The VopL C-terminal dimerization domain (VCD) is found in Vibrio parahaemolyticus protein L (VopL), an actin nucleation factor that induces stress fibres when injected into eukaryotic host cells. VCD shows a mainly alpha-helical fold, forms a U-shaped dimer and interacts with the pointed end of the actin nucleus, contributing to the nucleation activity directly [1-3]. Paper describing PDB structure 3ryl. [1]. 21873985. Mechanism of actin filament nucleation by Vibrio VopL and implications for tandem W domain nucleation. Namgoong S, Boczkowska M, Glista MJ, Winkelman JD, Rebowski G, Kovar DR, Dominguez R;. Nat Struct Mol Biol. 2011;18:1060-1067. Paper describing PDB structure 3seo. [2]. 21873984. Mechanism of actin filament nucleation by the bacterial effector VopL. Yu B, Cheng HC, Brautigam CA, Tomchick DR, Rosen MK;. Nat Struct Mol Biol. 2011;18:1068-1074. Paper describing PDB structure 4m63. [3]. 24120140. The bacterial effector VopL organizes actin into filament-like structures. Zahm JA, Padrick SB, Chen Z, Pak CW, Yunus AA, Henry L, Tomchick DR, Chen Z, Rosen MK;. Cell. 2013;155:423-434. (from Pfam) NF045237.2 PF20872.2 MalF_N_TM 24.3 24.3 48 domain Y N N MalF, N-terminal region, transmembrane helices 18033289,19250913,24145421 1236 Gammaproteobacteria class 5978 EBI-EMBL MalF, N-terminal region, transmembrane helices MalF, N-terminal region, transmembrane helices MalF is a component of the maltose uptake system found in Proteobacteria, an ATP-binding cassette (ABC) transporter. This protein is composed of eight transmembrane (TM) helices and folds in a way its concave surface faces the similar assembly of MalG to enclose the maltose. This entry represents the first TM helices of this structure, which are located N-terminal to the large periplasmic loop (P2, Pfam:PF14785) [1]. Paper describing PDB structure 2r6g. [1]. 18033289. Crystal structure of a catalytic intermediate of the maltose transporter. Oldham ML, Khare D, Quiocho FA, Davidson AL, Chen J;. Nature. 2007;450:515-521. Paper describing PDB structure 3fh6. [2]. 19250913. Alternating access in maltose transporter mediated by rigid-body rotations. Khare D, Oldham ML, Orelle C, Davidson AL, Chen J;. Mol Cell. 2009;33:528-536. [3]. 24145421. Structural basis for substrate specificity in the Escherichia coli maltose transport system. Oldham ML, Chen S, Chen J;. Proc Natl Acad Sci U S A. 2013;110:18132-18137. (from Pfam) NF045244.2 PF20889.2 TsiV3 28.4 28.4 90 domain Y N N Antitoxin TsiV3 24348240,24699653,24751834 1236 Gammaproteobacteria class 192 EBI-EMBL Antitoxin TsiV3 Antitoxin TsiV3 Antitoxin TsiV3, also known as TsaB, is a immmunity protein from Vibrio cholerae that inhibits the activity of toxin VgrG3, a protein found in the spike of the type VI secretion system (T6SS) syringe- like complex. TsiV3 folds into a three-helix bundle and adopts a dimeric assembly to bind the deep active-site groove of the catalytic domain in the C-terminal region of VgrG3, modifying the conformation and preventing substrate binding [1-3]. Paper describing PDB structure 4noo. [1]. 24699653. Molecular mechanism for self-protection against the type VI secretion system in Vibrio cholerae. Yang X, Xu M, Wang Y, Xia P, Wang S, Ye B, Tong L, Jiang T, Fan Z;. Acta Crystallogr D Biol Crystallogr. 2014;70:1094-1103. Paper describing PDB structure 4nso. [2]. 24751834. Structural basis for recognition of the type VI spike protein VgrG3 by a cognate immunity protein. Zhang J, Zhang H, Gao Z, Hu H, Dong C, Dong YH;. FEBS Lett. 2014;588:1891-1898. [3]. 24348240. Dual expression profile of type VI secretion system immunity genes protects pandemic Vibrio cholerae. Miyata ST, Unterweger D, Rudko SP, Pukatzki S;. PLoS Pathog. 2013;9:e1003752. (from Pfam) NF045298.2 PF21130.2 YgfZ_barrel 27.2 27.2 68 domain Y N N YgfZ, beta-barrel domain 15489424,16359333 1236 Gammaproteobacteria class 9835 EBI-EMBL YgfZ, beta-barrel domain YgfZ, beta-barrel domain YgfZ is a folate-binding protein involved in regulating the level of ATP-dnaA and in the modification of some tRNAs [1,2]. It consists of a folate-binding domain at the N-terminal (Pfam:PF01571) and a six-stranded antiparallel beta-barrel at the C-terminal, represented in this entry, with identical topology found at the C-terminal of elongation factors Tu and eEF-1alpha and in the gamma subunit of the initiation factor eIF2 [1]. Paper describing PDB structure 1nrk. [1]. 15489424. Crystal structure of the YgfZ protein from Escherichia coli suggests a folate-dependent regulatory role in one-carbon metabolism. Teplyakov A, Obmolova G, Sarikaya E, Pullalarevu S, Krajewski W, Galkin A, Howard AJ, Herzberg O, Gilliland GL;. J Bacteriol. 2004;186:7134-7140. [2]. 16359333. Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation. Ote T, Hashimoto M, Ikeuchi Y, Su'etsugu M, Suzuki T, Katayama T, Kato J;. Mol Microbiol. 2006;59:265-275. (from Pfam) NF045302.2 PF21150.2 YebU_pre-PUA_dom 27 27 77 domain Y N N Ribosomal RNA small subunit methyltransferase F, pre-PUA domain 16793063 1236 Gammaproteobacteria class 10986 EBI-EMBL Ribosomal RNA small subunit methyltransferase F, pre-PUA domain Ribosomal RNA small subunit methyltransferase F, pre-PUA domain This domain is found in Ribosomal RNA small subunit methyltransferase F from Escherichia coli (YebU) and similar proteins mainly from proteobacteria. YebU requires S-adenosyl-l-methionine (SAM) to specifically methylate the cytosine at position 1407 of assembled 30 S rRNA subunits. This proteins is organized into two distinct structural domains: the N-terminal MTase domain (catalytic domain), which can be divided in Pfam:PF17125 and Pfam:PF01189, and the C-terminal, also consisting of two subdomains. This entry represents the first of these subdomains, which is found N-terminal to the PUA- like domain (Pfam:PF13636). The pre-PUA domain has six beta-strands that form a central sheet in an anti-parallel fashion, and three alpha-helices packing against the edges of the sheet [1]. Paper describing PDB structure 2frx. [1]. 16793063. The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain. Hallberg BM, Ericsson UB, Johnson KA, Andersen NM, Douthwaite S, Nordlund P, Beuscher AE 4th, Erlandsen H;. J Mol Biol. 2006;360:774-787. (from Pfam) NF045372.2 PF21444.2 CofB_pilin_dom 27 27 234 domain Y N N CofB, pilin domain 26324721,26876601 1236 Gammaproteobacteria class 414 EBI-EMBL CofB, pilin domain CofB, pilin domain This domain is found in CofB from Escherichia coli and in similar proteins predominantly from proteobacteria. CofB is a minor pilin, required for assembly of Type IV pili. This entry represents the pilin domain, which is located in the N-terminal region of the protein. It shows a canonical T4b pilin fold seen in the major pilins, with an alpha-helical backbone and a five-stranded anti- parallel beta-sheet [1,2]. Paper describing PDB structure 4qs4. [1]. 26324721. Crystal Structure of the Minor Pilin CofB, the Initiator of CFA/III Pilus Assembly in Enterotoxigenic Escherichia coli. Kolappan S, Ng D, Yang G, Harn T, Craig L;. J Biol Chem. 2015;290:25805-25818. Paper describing PDB structure 5ax6. [2]. 26876601. Homo-trimeric Structure of the Type IVb Minor Pilin CofB Suggests Mechanism of CFA/III Pilus Assembly in Human Enterotoxigenic Escherichia coli. Kawahara K, Oki H, Fukakusa S, Yoshida T, Imai T, Maruno T, Kobayashi Y, Motooka D, Iida T, Ohkubo T, Nakamura S;. J Mol Biol. 2016;428:1209-1226. (from Pfam) NF045505.1 RR_RssB_Pseudo 700 700 394 equivalog Y Y N two-component system response regulator RssB rssB GO:0000160 37328957 1236 Gammaproteobacteria class 1583 NCBIFAM two-component system response regulator RssB NF045506.1 antisigant_RssC_Pseudo 250 250 159 equivalog Y Y N anti-sigma factor antagonist RssC rssC GO:0043856 37328957 1236 Gammaproteobacteria class 723 NCBIFAM anti-sigma factor antagonist RssC NF045613.1 PA1571_fam 35 35 52 equivalog Y Y N PA1571 family protein 30720421 1236 Gammaproteobacteria class 1556 NCBIFAM PA1571 family protein The small protein BAL062_00718 of Acinetobacter baumanii was identified by transposon mutagenesis as a likely mediator of reduced sensitivity to colistin. BAL062_00718 is homologous to PA1571 of Pseudomonas aeruginosa. NF045658.1 DiMArgaseDdah 450 450 254 equivalog Y Y N dimethylargininase ddaH 3.5.3.18 GO:0000052,GO:0006525,GO:0016403 10510241,16634643 1236 Gammaproteobacteria class 320 NCBIFAM dimethylargininase NF045673.1 c-di-GMPRcptLapD 1020 1020 647 equivalog Y Y N cyclic di-GMP receptor LapD lapD GO:0007165 16622054,25182848 1236 Gammaproteobacteria class 3471 NCBIFAM cyclic di-GMP receptor LapD NF045674.1 CystProtLapG 320 320 221 equivalog Y Y N cysteine protease LapG lapG 19602146,22707708 1236 Gammaproteobacteria class 2635 NCBIFAM cysteine protease LapG NF045675.1 PhdiestaseDibA 980 980 623 equivalog Y Y N phosphodiesterase DibA dibA 37927230 1236 Gammaproteobacteria class 2795 NCBIFAM phosphodiesterase DibA NF045786.1 OlefBLtnSynXan 900 900 544 equivalog Y Y N olefin beta-lactone synthetase oleC 6.1.3.1 GO:0005524,GO:0016874 20823539,21266575,27238740 1236 Gammaproteobacteria class 1359 NCBIFAM olefin beta-lactone synthetase NF045789.1 OmpVVibrio 400 400 259 equivalog Y Y N outer membrane protein OmpV ompV 3031428 1236 Gammaproteobacteria class 629 NCBIFAM outer membrane protein OmpV NF045904.1 RND-peri-MexE 714 714 390 equivalog Y Y Y multidrug efflux RND transporter periplasmic adaptor subunit MexE mexE 10515918,9044268 1236 Gammaproteobacteria class 2320 NCBIFAM multidrug efflux RND transporter periplasmic adaptor subunit MexE NF045949.1 PrtAdtaseSelOPseudom 850 850 487 equivalog Y Y N protein adenylyltransferase SelO selO 2.7.7.- GO:0000287,GO:0070733 30270044 1236 Gammaproteobacteria class 3788 NCBIFAM protein adenylyltransferase SelO NF046057.1 bifunc_MtlD 800 800 683 equivalog Y Y N bifunctional mannitol-1-phosphate dehydrogenase/phosphatase mtlD 1.1.1.17,3.1.3.22 GO:0008926,GO:0019593,GO:0050084 23414076,29575790,35363566 1236 Gammaproteobacteria class 1861 NCBIFAM bifunctional mannitol-1-phosphate dehydrogenase/phosphatase In response to the high salt that results from desiccation, the bifunctional enzyme mannitol-1-phosphate dehydrogenase/phosphatase, called MtlD, becomes activated through dimerization and then synthesizes mannitol, a compatible solute, from fructose-6-phosphate. The first step, reduction of D-fructose 6-phosphate to D-mannitol 1-phosphate, is catalyzed by the mannitol-1-phosphate 5-dehydrogenase domain, located in the C-terminal portion of the protein. The N-terminal mannitol-1-phosphatase domain belongs to the HAD (haloacid dehalogenase-like enzyme) family of hydrolases. NF046088.1 anchor_EppA 90 90 58 equivalog Y Y N EPS-associated small membrane protein EppA eppA 34985979 1236 Gammaproteobacteria class 103 NCBIFAM EPS-associated small membrane protein EppA EppA (EPS Pea-dependent phenotypes A) is a small protein required for the nearby "pea" operon for exopolysaccharide biosynthesis to be able to cause a pea-like wrinkled colony morphology. The C-terminal domain of this 58-amino acid protein has a high degree of sequence similarity with the VPLPA-CTERM, which has the cognate sorting enzyme exosortase D, but EppA appears not to be associated with any exosortase family protein. NF046105.1 TransRegNosR 1000 1000 680 equivalog Y Y N transcriptional regulator NosR nosR GO:0003677,GO:0010181,GO:0045893 1644760,3049543 1236 Gammaproteobacteria class 1806 NCBIFAM transcriptional regulator NosR NF046136.1 PF21868.1 GbpA_D3 27 27 97 domain Y N N GlcNAc-binding protein A, third domain 22253590 1236 Gammaproteobacteria class 4287 EBI-EMBL GlcNAc-binding protein A, third domain GlcNAc-binding protein A, third domain This domain is found in GlcNAc-binding protein A from Vibrio cholerae (GbpA), which is thought to promote attachment to both epithelial cell surfaces and marine chitin. GbpA shows four domains. This entry represents the third domain D3, which bind to the surface of the bacteria. It shows distant structural similarity to bacterial surface proteins, adopting an immunoglobulin fold [1]. Paper describing PDB structure 2xwx. [1]. 22253590. The Vibrio cholerae colonization factor GbpA possesses a modular structure that governs binding to different host surfaces. Wong E, Vaaje-Kolstad G, Ghosh A, Hurtado-Guerrero R, Konarev PV, Ibrahim AF, Svergun DI, Eijsink VG, Chatterjee NS, van Aalten DM;. PLoS Pathog. 2012;8:e1002373. (from Pfam) NF046148.1 PF21937.1 Yop-YscD_ppl_2nd 27 27 67 domain Y N N YscD/CdsD-like Bon-like domain 2 1860816,23908767 1236 Gammaproteobacteria class 2206 EBI-EMBL YscD/CdsD-like Bon-like domain 2 YscD/CdsD-like Bon-like domain 2 Yop-YscD-ppl is the periplasmic domain of Yop proteins like YscD from Proteobacteria. YscD forms part of the inner membrane component of the bacterial type III secretion injectosome apparatus [1,2]. This entry represents the second of three periplasmic BON domains. [1]. 1860816. Analysis of virC, an operon involved in the secretion of Yop proteins by Yersinia enterocolitica. Michiels T, Vanooteghem JC, Lambert de Rouvroit C, China B, Gustin A, Boudry P, Cornelis GR;. J Bacteriol 1991;173:4994-5009. [2]. 23908767. In situ structural analysis of the Yersinia enterocolitica injectisome. Kudryashev M, Stenta M, Schmelz S, Amstutz M, Wiesand U, Castano-Diez D, Degiacomi MT, Munnich S, Bleck CK, Kowal J, Diepold A, Heinz DW, Dal Peraro M, Cornelis GR, Stahlberg H;. Elife. 2013;2:e00792. (from Pfam) NF046204.1 PF22182.1 DUF6945 28 28 83 domain Y Y N DUF6945 domain-containing protein 1236 Gammaproteobacteria class 493 EBI-EMBL Domain of unknown function (DUF6945) DUF6945 domain This entry represents a WH-like domain (PDB:4ro3) found at the N-terminal of an uncharacterised protein from Vibrio cholerae (Swiss:M1RHE3), whose function is unknown. This domain is also found in phage proteins. (from Pfam) NF046239.1 PF22318.1 DUF6971 27 27 89 subfamily Y Y N DUF6971 family protein 1236 Gammaproteobacteria class 176 EBI-EMBL Domain of unknown function (DUF6971) DUF6971 family protein This is a domain of unknown function found at the N-terminal end. (from Pfam) NF046358.1 PF22710.1 SNaCT1 27 27 184 domain Y N N Short NACHT-associated C-Terminal domain, family 1 37160116 1236 Gammaproteobacteria class 35 EBI-EMBL Short NACHT-associated C-Terminal domain, family 1 Short NACHT-associated C-Terminal domain, family 1 The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors [1]. [1]. 37160116. Bacterial NLR-related proteins protect against phage. Kibby EM, Conte AN, Burroughs AM, Nagy TA, Vargas JA, Whalen LA, Aravind L, Whiteley AT;. Cell. 2023;186:2410-2424. (from Pfam) NF046390.1 PF22853.1 TelK_N 28 28 75 domain Y N N Protelomerase TelK-like N-terminal domain 17889664 1236 Gammaproteobacteria class 567 EBI-EMBL Protelomerase TelK-like N-terminal domain Protelomerase TelK-like N-terminal domain This entry represents the N-terminal domain of protelomerase TelK from Klebsiella phage phiKO2 and similar proteins from tailed bacteriophages and bacterial prophages. TelK is a hairpin telomere resolvase with DNA cleavage-rejoining activity that resolves the catenated circular dimer produced from the bidirectional replication of a chromosome. The core of the TelK monomer consists of an N-terminal domain and a catalytic domain connected by a long alpha- helical linker. However, there are two extensions of the protein: a C-terminal DNA binding domain named the stirrup (Pfam:PF20818) and an N-terminal domain containing an insertion, called the muzzle domain (Pfam:PF20849) [1]. [1]. 17889664. An interlocked dimer of the protelomerase TelK distorts DNA structure for the formation of hairpin telomeres. Aihara H, Huang WM, Ellenberger T;. Mol Cell. 2007;27:901-913. (from Pfam) NF046502.1 PF22079.1 HopBA1 27 27 193 domain Y N N Type III effector protein HopBA1 28137883 1236 Gammaproteobacteria class 79 EBI-EMBL Type III effector protein HopBA1 Type III effector protein HopBA1 HopBA1 is a type III effector protein that triggers an RBA1-dependent cell-death response. It folds into an alpha/beta structure that consists of a central mixed beta-sheet packed on both sides with alpha helices [1]. HopBA1 is structurally similar to proteins members of EreA/ChaN-like superfamily. It contains a psi-loop between strands 5 and 6. Paper describing PDB structure 5t09. [1]. 28137883. TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death in Arabidopsis. Nishimura MT, Anderson RG, Cherkis KA, Law TF, Liu QL, Machius M, Nimchuk ZL, Yang L, Chung EH, El Kasmi F, Hyunh M, Osborne Nishimura E, Sondek JE, Dangl JL;. Proc Natl Acad Sci U S A. 2017;114:E2053. (from Pfam) NF046670.1 PF22454.1 PQQ_syn_pqqF_N_2 27 27 147 domain Y N N PQQ synthase PqqF, N-terminal lobe domain 2 27231346 1236 Gammaproteobacteria class 7510 EBI-EMBL PQQ synthase PqqF, N-terminal lobe domain 2 PQQ synthase PqqF, N-terminal lobe domain 2 This entry represents domain 2 from the N-terminal lobe of PQQ synthase PqqF, a protein required for coenzyme pyrroloquinoline quinone (PQQ) biosynthesis. It consists of four structurally similar domains organised in N-terminal (domain 1 represented in Pfam: PF00675 and domain 2) and C-terminal (domain 3 and domain 4) lobes [1]. Paper describing PDB structure 5cio. [1]. 27231346. Crystal Structure and Function of PqqF Protein in the Pyrroloquinoline Quinone Biosynthetic Pathway. Wei Q, Ran T, Ma C, He J, Xu D, Wang W;. J Biol Chem. 2016;291:15575-15587. (from Pfam) NF046889.1 PF22678.1 Cytochrom_c_NrfB-like 27 27 89 domain Y N N Cytochrome c-type protein NrfB-like 11095707,16156654,17521287,24670637,32289252 1236 Gammaproteobacteria class 5440 EBI-EMBL Cytochrome c-type protein NrfB-like Cytochrome c-type protein NrfB-like This entry includes Cytochrome c-type protein NrfB and similar proteins, which plays a role in nitrite reduction. These proteins contain several copies of the CXXCH haem-binding motif [1-5]. Paper describing PDB structure 1eys. [1]. 11095707. Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum, thermostability and electron transfer. Nogi T, Fathir I, Kobayashi M, Nozawa T, Miki K;. Proc Natl Acad Sci U S A 2000;97:13561-13566. Paper describing PDB structure 2czs. [2]. 16156654. Structural and biochemical characterization of DHC2, a novel diheme cytochrome c from Geobacter sulfurreducens. Heitmann D, Einsle O;. Biochemistry. 2005;44:12411-12419. Paper describing PDB structure 2ozy. [3]. 17521287. The crystal structure of the pentahaem c-type cytochrome NrfB and characterization of its solution-state interaction with the pentahaem nitrite reductase NrfA. Clarke TA, Cole JA, Richardson DJ, Hemmings AM;. Biochem J. 2007;406:19-30. Paper describing PDB structure 3wmm. [4]. 24670637. Structure of the LH1-RC complex from Thermochromatium tepidum at 3.0 A. Niwa S, Yu LJ, Takeda K, Hirano Y, Kawakami T, Wang-Otomo ZY, Miki K;. Nature. 2014;508:228-232. Paper describing PDB structure 6r2q. [5]. 32289252. The Crystal Structure of a Biological Insulated Transmembrane Molecular Wire. Edwards MJ, White GF, Butt JN, Richardson DJ, Clarke TA;. Cell. 2020;181:665-673. (from Pfam) NF046953.1 PF22909.1 Caulimovir_coat_dom 27 27 113 domain Y N N Caulimovirus coat protein, conserved domain 1236 Gammaproteobacteria class 5 EBI-EMBL Caulimovirus coat protein, conserved domain Caulimovirus coat protein, conserved domain This is a conserved domain found in Cauliflower mosaic virus coat protein. Caulimoviruses are encapsidated plant viruses that contain circular double-stranded DNA. The viral coat proteins contain a fairly hydrophilic N-terminal region and a highly-basic C-terminal domain, which may be involved in DNA-binding. This domain may adopt an all-helical structure. (from Pfam) NF047068.1 PF21988.1 G7C_GBD 27 27 152 domain Y N N Podovirus tailspike protein Galactose-binding domain-like 28513100 1236 Gammaproteobacteria class 187 EBI-EMBL Podovirus tailspike protein Galactose-binding domain-like Podovirus tailspike protein Galactose-binding domain-like This entry represents the Tailspike Galactose-binding domain-like domain, also known as domain 5 (d5) of the tailspike receptor-binding protein (RBP) gp63.1 of bacteriophage G7C. This domain is structurally similar to carbohydrate-binding modules (CBMs) and is involved in substrate binding. Specifically, gp63.1 deacetylates surface polysaccharides of E. coli 4s using the esterase domain located within d5, while other domains mediate the interaction between gp63.1 and gp66 to form a stable complex. CBMs, including d5, are non-catalytic domains found in multidomain polysaccharide depolymerases where they play a role in substrate binding and determine the substrate specificity of the entire enzyme [1]. Paper describing PDB structure 4qnl. [1]. 28513100. Function of bacteriophage G7C esterase tailspike in host cell adsorption. Prokhorov NS, Riccio C, Zdorovenko EL, Shneider MM, Browning C, Knirel YA, Leiman PG, Letarov AV;. Mol Microbiol. 2017;105:385-398. (from Pfam) NF047101.1 PF22111.1 MtrC-MtrF_N 27.7 27.7 126 domain Y N N Decaheme cytochrome c component MtrC/MtrF N-terminal domain 21606337,26126857,32289252,34556577 1236 Gammaproteobacteria class 926 EBI-EMBL Decaheme cytochrome c component MtrC/MtrF N-terminal domain Decaheme cytochrome c component MtrC/MtrF N-terminal domain This entry represents the N-terminal domain of the decaheme cytochrome c component MtrC from the MtrCAB complex and its homologue MtrF, which is part of the MtrFDE complex. In Shewanella oneidensis, these proteins are at bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits and allow the utilization of extracellular mineral forms of iron and manganese as respiratory electron acceptors [1-4]. MtrC/MtrF consist of four domains: domain I and III containing seven antiparallel beta-strands in an extended Greek key topology; domains II and IV each bind five tightly packed hemes covalently attached to the Cys residues of the five CXXCH motifs in each domain and form the central core, flanked by domains I and III [1-4]. This entry represents domain I (N-terminal) of MtrC/MtrF. Paper describing PDB structure 3pmq. [1]. 21606337. Structure of a bacterial cell surface decaheme electron conduit. Clarke TA, Edwards MJ, Gates AJ, Hall A, White GF, Bradley J, Reardon CL, Shi L, Beliaev AS, Marshall MJ, Wang Z, Watmough NJ, Fredrickson JK, Zachara JM, Butt JN, Richardson DJ;. Proc Natl Acad Sci U S A. 2011;108:9384-9389. Paper describing PDB structure 4lm8. [2]. 26126857. Redox Linked Flavin Sites in Extracellular Decaheme Proteins Involved in Microbe-Mineral Electron Transfer. Edwards MJ, White GF, Norman M, Tome-Fernandez A, Ainsworth E, Shi L, Fredrickson JK, Zachara JM, Butt JN, Richardson DJ, Clarke TA;. Sci Rep. 2015;5:11677. Paper describing PDB structure 6qyc. [3]. 32289252. The Crystal Structure of a Biological Insulated Transmembrane Molecular Wire. Edwards MJ, White GF, Butt JN, Richardson DJ,. TRUNCATED at 1650 bytes (from Pfam) NF047158.1 PF22348.1 ColA_N 27 27 47 domain Y N N Colicin-A N-terminal domain 19627502,22493500 1236 Gammaproteobacteria class 201 EBI-EMBL Colicin-A N-terminal domain Colicin-A N-terminal domain This entry represents the N-terminal translocation domain of colicin A, an endonuclease active on both single- and double-stranded DNA but with undefined specificity [1,2]. This domain interacts directly with TolAIII (C-terminal domain of TolA) which facilitates translocation through the cell envelope to reach their cytotoxic site of action [2]. Paper describing PDB structure 3iax. [1]. 19627502. The crystal structure of the TolB box of colicin A in complex with TolB reveals important differences in the recruitment of the common TolB translocation portal used by group A colicins. Zhang Y, Li C, Vankemmelbeke MN, Bardelang P, Paoli M, Penfold CN, James R;. Mol Microbiol. 2010;75:623-636. Paper describing PDB structure 3qdr. [2]. 22493500. Structural evidence that colicin A protein binds to a novel binding site of TolA protein in Escherichia coli periplasm. Li C, Zhang Y, Vankemmelbeke M, Hecht O, Aleanizy FS, Macdonald C, Moore GR, James R, Penfold CN;. J Biol Chem. 2012;287:19048-19057. (from Pfam) NF047185.1 PF22470.1 Histone_HNS_N 24.5 24.5 79 domain Y N N H-NS histone-like proteins, N-terminal domain 12460581,12592399,14607110,20798056,26085102 1236 Gammaproteobacteria class 9393 EBI-EMBL H-NS histone-like proteins, N-terminal domain H-NS histone-like proteins, N-terminal domain This entry corresponds to the N-terminal oligomerisation domain of H-NS histone-like proteins. Paper describing PDB structure 1lr1. [1]. 12460581. H-NS oligomerization domain structure reveals the mechanism for high order self-association of the intact protein. Esposito D, Petrovic A, Harris R, Ono S, Eccleston JF, Mbabaali A, Haq I, Higgins CF, Hinton JC, Driscoll PC, Ladbury JE;. J Mol Biol. 2002;324:841-850. Paper describing PDB structure 1ni8. [2]. 12592399. The H-NS dimerization domain defines a new fold contributing to DNA recognition. Bloch V, Yang Y, Margeat E, Chavanieu A, Auge MT, Robert B, Arold S, Rimsky S, Kochoyan M;. Nat Struct Biol. 2003;10:212-218. Paper describing PDB structure 1ov9. [3]. 14607110. Crystal structure of the N-terminal dimerisation domain of VicH, the H-NS-like protein of Vibrio cholerae. Cerdan R, Bloch V, Yang Y, Bertin P, Dumas C, Rimsky S, Kochoyan M, Arold ST;. J Mol Biol. 2003;334:179-185. Paper describing PDB structure 2mw2. [4]. 26085102. A Three-protein Charge Zipper Stabilizes a Complex Modulating Bacterial Gene Silencing. Cordeiro TN, Garcia J, Bernado P, Millet O, Pons M;. J Biol Chem. 2015;290:21200-21212. Paper describing PDB structure 3nr7. [5]. 20798056. H-NS forms a superhelical protein scaffold for DNA condensation. Arold ST, Leonard PG, Parkinson GN, Ladbury JE;. Proc Natl Acad Sci U S A. 2010;107:15728-15732. (from Pfam) NF047242.1 PF22719.1 SNaCT12 27 27 174 domain Y Y N SNaCT domain-containing protein 37160116 1236 Gammaproteobacteria class 8 EBI-EMBL Short NACHT-associated C-Terminal domain, family 12 SNaCT domain-containing protein The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors [1]. [1]. 37160116. Bacterial NLR-related proteins protect against phage. Kibby EM, Conte AN, Burroughs AM, Nagy TA, Vargas JA, Whalen LA, Aravind L, Whiteley AT;. Cell. 2023;186:2410-2424. (from Pfam) NF047285.1 PF22870.1 YibX 27 27 80 domain Y N N Protein YibX 30837344 1236 Gammaproteobacteria class 14 EBI-EMBL Protein YibX Protein YibX This protein family includes Protein YibX from Escherichia coli, the product of a small open reading frame (smORF) that is encoded antisense to the waaL gene [1]. [1]. 30837344. Identifying Small Proteins by Ribosome Profiling with Stalled Initiation Complexes. Weaver J, Mohammad F, Buskirk AR, Storz G;. mBio. 2019;10:e02819-e02818. (from Pfam) NF047437.1 VC2662_fam 140 140 187 equivalog Y Y N VC2662 family protein 38206049 1236 Gammaproteobacteria class 884 NCBIFAM VC2662 family protein NF047789.1 AgBindSilE 200 200 143 equivalog Y Y N silver-binding protein SilE silE GO:0046872 27085056,34396382,9930866 1236 Gammaproteobacteria class 447 NCBIFAM silver-binding protein SilE SilE acts as a periplasmic molecular sponge for silver ions, reported to bind optimally 6 Ag(+) ions, and reportedly as many as 38. It shares about 48% sequence identity with periplasmic copper-binding protein PcoE, which can bind silver as well as copper. NF047790.1 tRNAmsioHdxaseMiaE 320 320 251 equivalog Y Y N tRNA isopentenyl-2-thiomethyl-A-37 hydroxylase MiaE miaE 1.14.99.69 GO:0004497,GO:0006400,GO:0045301,GO:0046872 8253666 1236 Gammaproteobacteria class 5977 NCBIFAM tRNA isopentenyl-2-thiomethyl-A-37 hydroxylase MiaE NF047791.1 RNaseRnm 375 375 275 equivalog Y Y N RNase RNM rnm trpH,yciV 3.1.3.97 GO:0004534,GO:0006364,GO:0035312,GO:0097657 25871919,32343306 1236 Gammaproteobacteria class 7411 NCBIFAM RNase RNM 5'-3' exoribonuclease NF047866.1 TF_DicD_YjdC 240 240 191 equivalog Y Y N division control transcriptional repressor DicD dicD yjdC GO:0003700 35835781 1236 Gammaproteobacteria class 2127 NCBIFAM division control transcriptional repressor DicD DicD (previously YjdC), is a DNA-binding transcription repressor of the division control locus dicABC. TIGR00156.1 TIGR00156 TIGR00156 108.15 108.15 128 subfamily Y Y N YgiW/YdeI family stress tolerance OB fold protein 15178340,19767429,19919618,22990488,33106344 1236 Gammaproteobacteria class 3871 JCVI TIGR00156 family protein YgiW/YdeI family stress tolerance OB fold protein This HMM describes certain OB fold proteins involved in stress tolerance, including YgiW and YdeI , both of which are found in both Escherichia coli and Salmonella enterica, as well as more broadly. TIGR00201.1 TIGR00201 comF 233.55 233.55 190 subfamily Y Y N ComF family protein 1236 Gammaproteobacteria class 1317 JCVI comF family protein ComF family protein This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis. TIGR00438.1 TIGR00438 rrmJ 300.15 300.15 188 equivalog Y Y N 23S rRNA (uridine(2552)-2'-O)-methyltransferase rrmJ 2.1.1.166 GO:0006364,GO:0016436 1236 Gammaproteobacteria class 1302 JCVI ribosomal RNA large subunit methyltransferase J 23S rRNA (uridine(2552)-2'-O)-methyltransferase Methylates the 23S rRNA. Previously known as cell division protein ftsJ.// Trusted cutoff too high? [SS 10/1/04] TIGR00664.1 TIGR00664 DNA_III_psi 150.55 150.55 131 equivalog Y Y N DNA polymerase III subunit psi holD 2.7.7.7 GO:0003887,GO:0006260,GO:0008408,GO:0009360 9722585 1236 Gammaproteobacteria class 1458 JCVI DNA polymerase III, psi subunit DNA polymerase III subunit psi This small subunit of the DNA polymerase III holoenzyme in E. coli and related species appearsto have a narrow taxonomic distribution. It is not found so far outside the gamma subdivision proteobacteria. TIGR00743.1 TIGR00743 TIGR00743 71.45 71.45 95 superfamily Y Y N DUF406 family protein 19927321 1236 Gammaproteobacteria class 2748 JCVI conserved hypothetical protein DUF406 family protein The family of proteins containing YfcZ and YiiS from Escherichia coli K-12, VPA0419 from Vibrio parahaemolyticus, and HI0400 and HI0636 in Haemophilus influenzae, was named DUF406 by Pfam model PF04175. The function remains unknown as of 2017. Members appear restricted to the gamma Proteobacteria. TIGR00752.1 TIGR00752 slp 88.45 88.45 182 superfamily Y Y N Slp family lipoprotein GO:0019867 8022277 1236 Gammaproteobacteria class 6627 JCVI outer membrane lipoprotein, Slp family Slp family lipoprotein Slp superfamily members are present in the Gram-negative gamma proteobacteria Escherichia coli, which also contains a close paralog, Haemophilus influenzae and Pasteurella multocida and Vibrio cholera. The known members of the family to date share a motif LX[GA]C near the N-terminus, which is compatible with the possibility that the protein is modified into a lipoprotein with Cys as the new N-terminus. Slp from Escherichia coli is known to be a lipoprotein of the outer membrane and to be expressed in response to carbon starvation. TIGR00774.1 TIGR00774 NhaB 826.1 826.1 515 equivalog Y Y N Na(+)/H(+) antiporter NhaB nhaB GO:0006814,GO:0015385,GO:0016020 1236 Gammaproteobacteria class 6222 JCVI Na+/H+ antiporter NhaB Na(+)/H(+) antiporter NhaB These proteins are members of the NhaB Na+:H+ Antiporter (NhaB) Family (TC 2.A.34). The only characterised member of this family is the Escherichia coli NhaB protein, which has 12 GES predicted transmembrane regions, and catalyses sodium/proton exchange. Unlike NhaA this activity is not pH dependent. TIGR00794.1 TIGR00794 kup 539.6 539.6 688 equivalog Y Y N potassium uptake protein kup GO:0006813,GO:0015079,GO:0016020 1236 Gammaproteobacteria class 3003 JCVI potassium uptake protein potassium uptake protein Proteins of the KUP family include the KUP (TrkD) protein of E. coli, a partially sequenced ORF from Lactococcus lactis, high affinity K+ uptake systems (Hak1) of the yeast Debaryomyces occidentalis as well as the fungus, Neurospora crassa, and several homologues in plants. While the E. coli KUP protein is assumed to be a secondary transporter, and uptake is blocked by protonophores such as CCCP (but not arsenate), the energy coupling mechanism has not been defined. However, the N. crassa protein has been shown to be a K+:H+ symporter, establishing that the KUP family consists of secondary carriers. The plant high affinity (20mM) K+ transporter can complement K+ uptake defects in E. coli. TIGR00816.1 TIGR00816 tdt 237.25 237.25 320 subfamily Y Y N tellurite-resistance/dicarboxylate transporter tdt GO:0016020 1236 Gammaproteobacteria class 3589 JCVI C4-dicarboxylate transporter/malic acid transport protein tellurite-resistance/dicarboxylate transporter The Tellurite-Resistance/Dicarboxylate Transporter (TDT) Family (TC 2.A.16) Two members of the TDT family have been functionally characterized. One is the TehA protein of E. coli which has been implicated in resistance to tellurite; the other is the Mae1 protein of S. pombe which functions in the uptake of malate and other dicarboxylates by a proton symport mechanism. These proteins exhibit 10 putative transmembrane a-helical spanners (TMSs). TIGR01086.1 TIGR01086 fucA 400.25 400.25 214 equivalog Y Y N L-fuculose-phosphate aldolase fucA 4.1.2.17 GO:0006004,GO:0008270,GO:0008738 1236 Gammaproteobacteria class 1083 JCVI L-fuculose phosphate aldolase L-fuculose-phosphate aldolase Members of this family are L-fuculose phosphate aldolase from various Proteobacteria, encoded in fucose utilization operons. Homologs in other bacteria given similar annotation but scoring below the trusted cutoff may share extensive sequence similarity but are not experimenally characterized and are not found in apparent fucose utilization operons; we consider their annotation as L-fuculose phosphate aldolase to be tenuous. This model has been narrowed in scope from the previous version. TIGR01160.1 TIGR01160 SUI1_MOF2 143.9 143.9 110 equivalog Y Y N translation initiation factor SUI1 GO:0003743,GO:0006413 10376878 1236 Gammaproteobacteria class 10 JCVI translation initiation factor SUI1 translation initiation factor SUI1 Alternate name: MOF2. A similar protein family (see TIGRFAMs model TIGR01158) is found in prokaryotes. The human proteins complements a yeast SUI1 mutatation. TIGR01355.1 TIGR01355 cyt_deam_dimer 275 275 283 equivalog Y Y N cytidine deaminase cdd 3.5.4.5 GO:0004126,GO:0008270,GO:0008655,GO:0009972 10493793 1236 Gammaproteobacteria class 5910 JCVI cytidine deaminase cytidine deaminase This homodimeric zinc metalloprotein is found in Arabidopis and some Proteobacteria. A related, homotetrameric form with a much smaller subunit is found most bacteria and in animals. Both types may act on deoxycytidine as well as cytidine. TIGR01532.1 TIGR01532 E4PD_g-proteo 530.55 530.55 325 equivalog Y Y N erythrose-4-phosphate dehydrogenase epd 1.2.1.72 GO:0005737,GO:0042823,GO:0048001,GO:0051287 7751290 1236 Gammaproteobacteria class 6702 JCVI erythrose-4-phosphate dehydrogenase erythrose-4-phosphate dehydrogenase This HMM represents the small clade of dehydrogenases in gamma-proteobacteria which utilize NAD+ to oxidize erythrose-4-phosphate (E4P) to 4-phospho-erythronate, a precursor for the de novo synthesis of pyridoxine via 4-hydroxythreonine and D-1-deoxyxylulose [1]. This enzyme activity appears to have evolved from glyceraldehyde-3-phosphate dehydrogenase, whose substrate differs only in the lack of one carbon relative to E4P. Accordingly, this model is very close to the corresponding models for GAPDH, and those sequences which hit above trusted here invariably hit between trusted and noise to the GAPDH model (TIGR01534). Similarly, it may be found that there are species outside of the gamma proteobacteria which synthesize pyridoxine and have more than one aparrent GAPDH gene of which one may have E4PD activity - this may necessitate a readjustment of these models. Alternatively, some of the GAPDH enzymes may prove to be bifunctional in certain species. TIGR01626.1 TIGR01626 ytfJ_HI0045 151.1 151.1 184 hypoth_equivalog Y Y N YtfJ family protein 1236 Gammaproteobacteria class 6100 JCVI conserved hypothetical protein YtfJ-family, TIGR01626 YtfJ family protein This model represents sequences from gamma proteobacteria that are related to the E. coli protein, YtfJ. TIGR01699.1 TIGR01699 XAPA 370.9 370.9 248 equivalog Y Y N xanthosine phosphorylase xapA GO:0004731,GO:0005737,GO:0055086 7559336 1236 Gammaproteobacteria class 2657 JCVI xanthosine phosphorylase xanthosine phosphorylase This model represents a small clade of purine nucleotide phosphorylases found in certain gamma proteobacteria. The gene is part of an operon for the degradation of xanthosine and is induced by xanthosine [1]. The enzyme is also capable of acting on inosine and guanosine (but not adenosine) in a manner similar to those other phosphorylases to which it is closely related (TIGR01698, TIGR01700). TIGR01713.1 TIGR01713 typeII_sec_gspC 101.6 101.6 259 equivalog Y Y N type II secretion system protein GspC gspC GO:0015627,GO:0015628 30767847 1236 Gammaproteobacteria class 7581 JCVI type II secretion system protein C type II secretion system protein GspC This HMM represents GspC of type II secretion systems (T2SS). The gene symbol reflects the outdated description of T2SS as the main terminal branch of the General Secretion Pathway. Lineage-specific synonyms include EpsC in Vibrio vulnificus and ExeC in Aeromonas hydrophila. TIGR01772.1 TIGR01772 MDH_euk_gproteo 273.05 273.05 313 equivalog Y Y N malate dehydrogenase mdh 1.1.1.37 GO:0006099,GO:0030060 11021970 1236 Gammaproteobacteria class 4469 JCVI malate dehydrogenase, NAD-dependent malate dehydrogenase This model represents the NAD-dependent malate dehydrogenase found in eukaryotes and certain gamma proteobacteria. The enzyme is involved in the citric acid cycle as well as the glyoxalate cycle. Several isoforms exidt in eukaryotes. In S. cereviseae, for example, there are cytoplasmic, mitochondrial and peroxisomal forms. Although malate dehydrogenases have in some cases been mistaken for lactate dehydrogenases due to the similarity of these two substrates and the apparent ease with which evolution can toggle these activities, critical residues have been identified [1] which can discriminate between the two activities. At the time of the creation of this model no hits above the trusted cutoff contained critical residues typical of lactate dehydrogenases. TIGR01779.1 TIGR01779 TonB-B12 599.7 599.7 614 equivalog Y Y N TonB-dependent vitamin B12 receptor btuB GO:0015420,GO:0015889,GO:0019867,GO:0031419 3882670 1236 Gammaproteobacteria class 9429 JCVI TonB-dependent vitamin B12 receptor TonB-dependent vitamin B12 receptor This model represents the TonB-dependent outer membrane receptor found in gamma proteobacteria responsible for translocating the cobalt-containing vitamin B12 (cobalamin) [1]. TIGR01797.1 TIGR01797 CM_P_1 73.7 73.7 83 equivalog_domain Y Y N chorismate mutase 5.4.99.5 GO:0004106,GO:0005737,GO:0009094,GO:0009095 1236 Gammaproteobacteria class 6255 JCVI chorismate mutase chorismate mutase This model represents the chorismate mutase domain of the gamma and beta proteobacterial "P-protein" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain. TIGR01799.1 TIGR01799 CM_T 95.9 95.9 83 equivalog_domain Y Y N chorismate mutase tyrA 5.4.99.5 GO:0004106,GO:0005737,GO:0006571,GO:0009095 1236 Gammaproteobacteria class 7022 JCVI chorismate mutase chorismate mutase This model represents the chorismate mutase domain of the gamma proteobacterial "T-protein" which consists of an N-terminal chorismate mutase domain and a C-terminal prephenate dehydrogenase domain. TIGR01833.1 TIGR01833 HMG-CoA-S_euk 286.2 286.2 457 equivalog Y Y N hydroxymethylglutaryl-CoA synthase 2.3.3.10 20346956 1236 Gammaproteobacteria class 2 JCVI hydroxymethylglutaryl-CoA synthase hydroxymethylglutaryl-CoA synthase Hydroxymethylglutaryl(HMG)-CoA synthase is the first step of isopentenyl pyrophosphate (IPP) biosynthesis via the mevalonate pathway. This pathway is found mainly in eukaryotes, but also in archaea and some bacteria. This model is specific for eukaryotes. TIGR01839.1 TIGR01839 PHA_synth_II 855.4 855.4 560 subfamily Y Y N class II poly(R)-hydroxyalkanoic acid synthase phaC GO:0016746,GO:0042619 11418564 1236 Gammaproteobacteria class 4451 JCVI poly(R)-hydroxyalkanoic acid synthase, class II class II poly(R)-hydroxyalkanoic acid synthase This HMM represents the class II subfamily of poly(R)-hydroxyalkanoate synthases, which polymerizes hydroxyacyl-CoAs, typically with six to fourteen carbons in the hydroxyacyl backbone into aliphatic esters termed poly(R)-hydroxyalkanoic acids. These polymers accumulate as carbon and energy storage inclusions in many species and can amount to 90 percent of the dry weight of cell. TIGR02036.1 TIGR02036 dsdC 352.4 352.4 302 equivalog Y Y N DNA-binding transcriptional regulator DsdC dsdC GO:0003677,GO:0003700,GO:0005737,GO:0006355,GO:0009063 1236 Gammaproteobacteria class 4028 JCVI D-serine deaminase transcriptional activator DNA-binding transcriptional regulator DsdC This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea. TIGR02038.1 TIGR02038 protease_degS 422.95 422.95 351 equivalog Y Y N outer membrane-stress sensor serine endopeptidase DegS degS 3.4.21.107 GO:0008236,GO:0030288,GO:0045152 11442831,12679025 1236 Gammaproteobacteria class 4243 JCVI periplasmic serine peptidase DegS outer membrane-stress sensor serine endopeptidase DegS This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E). TIGR02043.1 TIGR02043 ZntR 167.95 167.95 131 equivalog Y Y N Zn(2+)-responsive transcriptional regulator zntR GO:0003677,GO:0006351,GO:0008270 10048032,12958362 1236 Gammaproteobacteria class 2949 JCVI Zn(II)-responsive transcriptional regulator Zn(2+)-responsive transcriptional regulator This HMM represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system [1]. This protein is a member of the MerR family of transcriptional activators (PF00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix [1]. TIGR02062.1 TIGR02062 RNase_B 641.9 641.9 646 equivalog Y Y N exoribonuclease II rnb 3.1.13.1 GO:0003723,GO:0006401,GO:0008859 1236 Gammaproteobacteria class 10698 JCVI exoribonuclease II exoribonuclease II This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing. TIGR02077.1 TIGR02077 thr_lead_pep 22.95 22.95 23 equivalog Y Y N thr operon leader peptide thrL GO:0009088,GO:0031554,GO:0031556 1236 Gammaproteobacteria class 438 JCVI thr operon leader peptide thr operon leader peptide This family consists of examples of the threonine biosynthesis (thr) operon leader peptide, also called the thr operon attenuator. The small gene for this peptide is often missed in genome annotation. It should be looked for in genomes of the proteobacteria, immediately upstream of genes for threonine biosynthesis, typically aspartokinase I/homoserine dehydrogenase, homoserine kinase, and threonine synthase. Transcription of the rest of the Thr operon is attenuated (mostly turned off) unless the ribosome pauses during a stretch of the leader sequence rich in both Ile (made from Thr) and in Thr itself because of the scarcity of those amino acids at the time. The leader peptide itself, once made, may have no role other than to be degraded. Similar systems exist for some other amino acid biosynthetic operons, such as Trp. TIGR02110.1 TIGR02110 PQQ_syn_pqqF 320 320 697 equivalog Y Y N pyrroloquinoline quinone biosynthesis protein PqqF pqqF 3.4.24.- GO:0004222,GO:0006508,GO:0008270,GO:0018189 8526497 1236 Gammaproteobacteria class 10214 JCVI coenzyme PQQ biosynthesis protein PqqF pyrroloquinoline quinone biosynthesis protein PqqF In a subset of species that make coenzyme PQQ (pyrrolo-quinoline-quinone), this probable peptidase is found in the PQQ biosynthesis region and is thought to act as a protease on PqqA (TIGR02107), a probable peptide precursor of the coenzyme. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases. TIGR02112.1 TIGR02112 cyd_oper_ybgE 89.55 89.55 93 equivalog Y Y N cyd operon protein YbgE ybgE 9068659 1236 Gammaproteobacteria class 2546 JCVI cyd operon protein YbgE cyd operon protein YbgE This HMM describes a small protein of unknown function, about 100 amino acids in length, essentially always found in an operon with CydAB, subunits of the cytochrome d terminal oxidase. It appears to be an integral membrane protein. It is found so far only in the Proteobacteria. TIGR02164.1 TIGR02164 torA 1465 1465 824 equivalog Y Y N trimethylamine-N-oxide reductase TorA torA 1.7.2.3 GO:0009055,GO:0009061,GO:0030151,GO:0050626 1236 Gammaproteobacteria class 4963 JCVI trimethylamine-N-oxide reductase TorA trimethylamine-N-oxide reductase TorA This very narrowly defined family represents TorA, part of a family of related molybdoenzymes that include biotin sulfoxide reductases, dimethyl sulfoxide reductases, and at least two different subfamilies of trimethylamine-N-oxide reductases. A single enzyme from the larger family may have more than one activity. TorA typically is located in the periplasm, has a Tat (twin-arginine translocation)-dependent signal sequence, and is encoded in a torCAD operon. TIGR02178.1 TIGR02178 yeiP 264.05 264.05 186 equivalog Y Y N elongation factor P-like protein YeiP yeiP GO:0003746,GO:0006414 1236 Gammaproteobacteria class 2635 JCVI elongation factor P-like protein YeiP elongation factor P-like protein YeiP This HMM represents the family of Escherichia coli protein YeiP, a close homolog of elongation factor P (TIGR00038) and probably itself a translation factor. Member of this family are found only in some Gammaproteobacteria, including E. coli and Vibrio cholerae. TIGR02183.1 TIGR02183 GRXA 106.5 106.5 86 equivalog Y Y N GrxA family glutaredoxin GO:0009055,GO:0015035,GO:0045454 14713336,15123823 1236 Gammaproteobacteria class 2277 JCVI glutaredoxin, GrxA family glutaredoxin, GrxA family Glutaredoxins are thioltransferases (disulfide reductases) which utilize glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system [1]. Glutaredoxins utilize the CXXC motif common to thioredoxins and are involved in multiple cellular processes including protection from redox stress, reduction of critical enzymes such as ribonucleotide reductase and the generation of reduced sulfur for iron sulfur cluster formation. Glutaredoxins are capable of reduction of mixed disulfides of glutathione as well as the formation of glutathione mixed disulfides. This model includes the E. coli glyutaredoxin GrxA which appears to have primary responsibility for the reduction of ribonucleotide reductase [2]. TIGR02205.1 TIGR02205 septum_zipA 119.65 119.65 284 equivalog Y Y N cell division protein ZipA zipA GO:0000917,GO:0005515,GO:0016020 30478085,31390865 1236 Gammaproteobacteria class 14857 JCVI cell division protein ZipA cell division protein ZipA This HMM represents the full length of bacterial cell division protein ZipA. The N-terminal hydrophobic stretch is an uncleaved signal-anchor sequence. This is followed by an unconserved, variable length, low complexity region, and then a conserved C-terminal region of about 140 amino acids (see PF04354) that interacts with the tubulin-like cell division protein FtsZ. TIGR02207.1 TIGR02207 lipid_A_htrB 297.8 297.8 303 subfamily Y Y N LpxL/LpxP family Kdo(2)-lipid IV(A) lauroyl/palmitoleoyl acyltransferase lpxL 2.3.1.- GO:0009245,GO:0016020,GO:0016746 11830594 1236 Gammaproteobacteria class 18183 JCVI lipid A biosynthesis lauroyl (or palmitoleoyl) acyltransferase LpxL/LpxP family Kdo(2)-lipid IV(A) lauroyl/palmitoleoyl acyltransferase Members of this family include LpxL (EC 2.3.1.241) and LpxP (EC 2.3.1.242). TIGR02208.1 TIGR02208 lipid_A_msbB 336.05 336.05 305 equivalog Y Y N lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase lpxM msbB 2.3.1.243 GO:0009103,GO:0009276,GO:0016020,GO:0016747 1236 Gammaproteobacteria class 6978 JCVI lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase This family consists of LpxM (MsbB) in E. coli and closely related proteins in other species. LpxM is homologous to HtrB (TIGR02207) and acts immediately after it in the biosynthesis of KDO-2 lipid A (also called Re LPS and Re endotoxin). These two enzymes act after creation of KDO-2 lipid IV-A by addition of the KDO sugars. LpxM is lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase, an enzyme characterized in Escherichia coli and involved in biosynthesis of the form of lipid A found in that species and some closely related species. TIGR02213.1 TIGR02213 lolE_release 540.35 540.35 411 exception Y Y N lipoprotein-releasing ABC transporter permease subunit LolE lolE GO:0016020,GO:0042953,GO:0044874 12823819,20888319 1236 Gammaproteobacteria class 6216 JCVI lipoprotein releasing system, transmembrane protein LolE lipoprotein-releasing ABC transporter permease subunit LolE This protein is part of an unusual ABC transporter complex that releases lipoproteins from the periplasmic side of the bacterial inner membrane, rather than transport any substrate across the inner membrane. In some species, the permease-like transmembrane protein is represented by two paralogs, LolC and LolE, both in the LolCDE complex. This family consists of LolE, as found in E. coli and related species. TIGR02248.1 TIGR02248 mutH_TIGR 229.9 229.9 217 equivalog Y Y N DNA mismatch repair endonuclease MutH mutH GO:0003677,GO:0004519,GO:0006304 1236 Gammaproteobacteria class 6483 JCVI DNA mismatch repair endonuclease MutH DNA mismatch repair endonuclease MutH This family consists exclusively of MutH, an endonuclease in some Proteobacteria that is activated by MutS1 and MutL for methylation-directed mismatch repair. TIGR02287.1 TIGR02287 PaaY 319.6 319.6 192 equivalog Y Y N phenylacetic acid degradation protein PaaY paaY 3.1.2.- GO:0010124 11260461,22398448,24983528 1236 Gammaproteobacteria class 2973 JCVI phenylacetic acid degradation protein PaaY phenylacetic acid degradation protein PaaY Members of this family are located next to other genes organized into apparent operons for phenylacetic acid degradation [1]. PaaY is located near the end of these gene clusters and often next to PaaX, a transcriptional regulator. TIGR02297.1 TIGR02297 HpaA 274.65 274.65 287 equivalog Y Y N 4-hydroxyphenylacetate catabolism regulatory protein HpaA hpaA GO:0003700,GO:0006355,GO:0043565 8550403 1236 Gammaproteobacteria class 3073 JCVI 4-hydroxyphenylacetate catabolism regulatory protein HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (PF02311) and the helix-turn-helix DNA-binding domain (PF00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway [1]. TIGR02310.1 TIGR02310 HpaB-2 885.2 885.2 519 equivalog Y Y N 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component hpaB 1.14.14.9 GO:0010124,GO:0016712,GO:0050660 1236 Gammaproteobacteria class 2504 JCVI 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component This gene for this monooxygenase is found within apparent operons for the degradation of 4-hydroxyphenylacetic acid in Shigella, Photorhabdus and Pasteurella. The family modelled by this HMM is narrowly limited to gammaproteobacteria to exclude other aromatic hydroxylases involved in various secondary metabolic pathways. Generally, this enzyme acts with the assistance of a small flavin reductase domain protein (HpaC) to provide the cycle the flavin reductant for the reaction. This family of sequences is a member of a larger subfamily of monooxygenases (PF03241). TIGR02314.1 TIGR02314 ABC_MetN 499.7 499.7 343 equivalog Y Y N methionine ABC transporter ATP-binding protein MetN metN 7.4.2.11 GO:0005524,GO:0009276,GO:0033232,GO:0048473 12169620,25678706 1236 Gammaproteobacteria class 4999 JCVI D-methionine ABC transporter, ATP-binding protein methionine ABC transporter ATP-binding protein MetN Members of this family are largely restricted to the gamma-proteobacteria. TIGR02355.1 TIGR02355 moeB 376.55 376.55 240 equivalog Y Y N molybdopterin-synthase adenylyltransferase MoeB moeB 2.7.7.80 GO:0006777,GO:0008641 12234097 1236 Gammaproteobacteria class 8061 JCVI molybdopterin synthase sulfurylase MoeB molybdopterin-synthase adenylyltransferase MoeB This model describes the molybdopterin biosynthesis protein MoeB in E. coli and related species. The enzyme covalently modifies the molybdopterin synthase MoaD by sulfurylation. This enzyme is closely related to ThiF, a thiamine biosynthesis enzyme that modifies ThiS by an analogous adenylation. Both MoeB and ThiF belong to the HesA/MoeB/ThiF family (PF00899). TIGR02380.1 TIGR02380 ECA_wecA 326.05 326.05 346 exception Y Y N UDP-N-acetylglucosamine--undecaprenyl-phosphate N-acetylglucosaminephosphotransferase wecA 2.7.8.33 GO:0000287,GO:0009103,GO:0009246,GO:0009276,GO:0016020,GO:0016780,GO:0030145,GO:0036380 11700352 1236 Gammaproteobacteria class 6818 JCVI undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphatetransferase UDP-N-acetylglucosamine--undecaprenyl-phosphate N-acetylglucosaminephosphotransferase Members of this family are the WecA enzyme of enterobacterial common antigen biosynthesis, UDP-N-acetylglucosamine--undecaprenyl-phosphate N-acetylglucosaminephosphotransferase. This family represents one narrow clade, and closely related sequences outside this clade may represent enzymes that catalyze the same specific reaction, but in the context of different pathways. The Bacillus subtilis teichoic acid biosynthesis enzyme TagO is one such functionally equivalent enzyme that is outside the scope of this model. TIGR02405.1 TIGR02405 trehalos_R_Ecol 357.35 357.35 311 equivalog Y Y N trehalose operon repressor TreR treR GO:0003677,GO:0005991,GO:0006355,GO:0045892 9865945 1236 Gammaproteobacteria class 4727 JCVI trehalose operon repressor trehalose operon repressor TreR TetR belongs to the LacI family and represses trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate, which TetR binds, and then is hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and should not be confused with the GntR family transcriptional regulator TreR of Bacillus subtilis. TIGR02417.1 TIGR02417 fruct_sucro_rep 389.55 389.55 327 subfamily Y N N D-fructose-responsive transcription factor GO:0003677,GO:0006355,GO:0009750 1805309,8412665 1236 Gammaproteobacteria class 8024 JCVI D-fructose-responsive transcription factor D-fructose-responsive transcription factor Members of this family belong the lacI helix-turn-helix family (PF00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer. TIGR02440.1 TIGR02440 FadJ 968.45 968.45 699 equivalog Y Y N fatty acid oxidation complex subunit alpha FadJ fadJ GO:0003857,GO:0004300,GO:0008692,GO:0009062,GO:0051287 12535077 1236 Gammaproteobacteria class 13442 JCVI fatty oxidation complex, alpha subunit FadJ fatty acid oxidation complex subunit alpha FadJ Members represent alpha subunit of multifunctional enzyme complex of the fatty acid degradation cycle. Plays a minor role in aerobic beta-oxidation of fatty acids. FadJI complex is necessary for anaerobic growth on short-chain acids with nitrate as an electron acceptor. Activities include: enoyl-CoA hydratase (EC 4.2.1.17),3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35), 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A representative is E. coli FadJ (aka YfcX) (SP:P77399). This model excludes the FadB of TIGR02437 equivalog hmm. TIGR02443.1 TIGR02443 TIGR02443 49.45 49.45 59 equivalog Y Y N YheV family putative zinc ribbon protein 1236 Gammaproteobacteria class 4883 JCVI conserved hypothetical protein YheV family putative zinc ribbon protein Members of this family of proteins are small, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria. TIGR02445.1 TIGR02445 fadA 591 591 385 equivalog Y Y N acetyl-CoA C-acyltransferase FadA fadA 2.3.1.16 GO:0003988,GO:0005737,GO:0006631,GO:0016042 2191949 1236 Gammaproteobacteria class 9651 JCVI acetyl-CoA C-acyltransferase FadA acetyl-CoA C-acyltransferase FadA This subunit of the FadBA complex has acetyl-CoA C-acyltransferase (EC 2.3.1.16) activity, and is also known as beta-ketothiolase and fatty oxidation complex, beta subunit. This protein is almost always located adjacent to FadB (TIGR02437). The FadBA complex is the major complex active for beta-oxidation of fatty acids in E. coli. TIGR02446.1 TIGR02446 FadI 711.55 711.55 430 equivalog Y Y N acetyl-CoA C-acyltransferase FadI fadI 2.3.1.16 GO:0003988,GO:0005737,GO:0006631,GO:0016042 12535077 1236 Gammaproteobacteria class 7652 JCVI acetyl-CoA C-acyltransferase FadI acetyl-CoA C-acyltransferase FadI This subunit of the FadJI complex has acetyl-CoA C-acyltransferase (EC 2.3.1.16) activity, and is also known as beta-ketothiolase and fatty oxidation complex, beta subunit, and YfcY. This protein is almost always located adjacent to FadJ (TIGR02440). The FadJI complex is needed for anaerobic beta-oxidation of short-chain fatty acids in E. coli. TIGR02448.1 TIGR02448 TIGR02448 53.85 53.85 101 subfamily_domain Y N N conserverd hypothetical protein 1236 Gammaproteobacteria class 7336 JCVI conserverd hypothetical protein conserverd hypothetical protein This family consists of small hypothetical proteins, about 100 amino acids in length. The family includes five members (three in tandem) in Pseudomonas aeruginosa PAO1, and also in Pseudomonas putida KT2440, four in Pseudomonas syringae DC3000, and single members in several other Proteobacteria. The function is unknown. TIGR02449.1 TIGR02449 TIGR02449 55.4 55.4 65 hypoth_equivalog Y Y N TIGR02449 family protein 1236 Gammaproteobacteria class 1958 JCVI TIGR02449 family protein TIGR02449 family protein Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown. TIGR02501.1 TIGR02501 type_III_yscE 38.25 38.25 67 equivalog Y Y N EscE/YscE/SsaE family type III secretion system needle protein co-chaperone 23524615 1236 Gammaproteobacteria class 702 JCVI type III secretion system protein, YseE family EscE/YscE/SsaE family type III secretion system needle protein co-chaperone Members of this family are found exclusively in type III secretion appparatus gene clusters in bacteria. Those bacteria with a protein from this family tend to target animal cells, as does Yersinia pestis. This protein is small (about 70 amino acids) and not well characterized. TIGR02502.1 TIGR02502 type_III_YscX 99.2 99.2 121 equivalog Y Y N YscX family type III secretion protein 9882687 1236 Gammaproteobacteria class 468 JCVI type III secretion protein, YscX family type III secretion protein, YscX family Members of this family are encoded within bacterial type III secretion gene clusters. Among all species with type III secretion, those with this protein are found among those that target animal rather than plant cells. The member of this family in Yersinia was shown by mutation to be required for type III secretion of Yops effector proteins and therefore is believe to be part of the secretion machinery. TIGR02508.1 TIGR02508 type_III_yscG 97.15 97.15 116 equivalog Y Y N YscG family type III secretion system chaperone 11035761 1236 Gammaproteobacteria class 571 JCVI type III secretion protein, YscG family YscG family type III secretion system chaperone YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc. TIGR02509.1 TIGR02509 type_III_yopR 114 114 131 equivalog Y Y N YopR family T3SS polymerization control protein GO:0030254,GO:0030257 10209737,19968786,24119189,8709853 1236 Gammaproteobacteria class 1042 JCVI type III secretion effector, YopR family YopR family T3SS polymerization control protein Members of this family are type III secretion system effectors, named differently in different species and designated YopR (Yersinia outer protein R), encoded by the YscH (Yersinia secretion H) gene. This Yops protein is unusual in that it is released to extracellularly rather than injected directly into the target cell as are most Yops. TIGR02513.1 TIGR02513 type_III_yscB 90.05 90.05 140 equivalog Y Y N YscB family type III secretion system chaperone GO:0030254 15701523 1236 Gammaproteobacteria class 692 JCVI type III secretion system chaperone, YscB family YscB family type III secretion system chaperone Members of this family include YscB of Yersinia and functionally equivalent (but differently named) proteins from type III secretion systems of other pathogens that affect animal cells. YscB acts, along with SycN (TIGR02503), as a chaperone for YopN, a key part of a complex that regulates type III secretion so it responds to contact with the eukaryotic target cell. TIGR02514.1 TIGR02514 type_III_yscP 76.5 76.5 129 equivalog_domain Y Y N type III secretion system needle length determinant 14657497,19055526,20643949 1236 Gammaproteobacteria class 3308 JCVI type III secretion system needle length determinant type III secretion system needle length determinant Members of this family include YscP of the Yersinia type III secretion system and equivalent proteins in other animal pathogen bacterial type III secretion systems. The model describes the conserved C-terminal region. N-terminal regions are poorly conserved and variable in length with some low-complexity sequence. TIGR02525.1 TIGR02525 plasmid_TraJ 368.3 368.3 372 equivalog Y Y N plasmid transfer ATPase TraJ traJ 1236 Gammaproteobacteria class 1153 JCVI plasmid transfer ATPase TraJ plasmid transfer ATPase TraJ Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524). TIGR02567.1 TIGR02567 YscW 58.2 58.2 124 equivalog Y Y N YscW family type III secretion system pilotin 15292137 1236 Gammaproteobacteria class 1029 JCVI type III secretion system chaperone YscW YscW family type III secretion system pilotin YscW (Yop secretion W) is the founding member of this family of lipoproteins that act as chaperones for type III secretion systems (T3SS). YsW has been characterized as a pilotin, that is chaperone for the outer membrane pore component, or secretin, YscC (TIGR02516). YscW localizes to the outer membrane and appears to guide the oligomerization and proper localization of YscC. TIGR02572.1 TIGR02572 LcrR 139.5 139.5 139 equivalog Y Y N LcrR family type III secretion system chaperone 12654835,1695896 1236 Gammaproteobacteria class 812 JCVI type III secretion system regulator LcrR LcrR family type III secretion system chaperone LcrR (low calcium response R), along with CesD2, AcrR, PcrR, VcrR, and SseE, represent a family type III secretion systems (T3SS) chaperones. TIGR02573.1 TIGR02573 LcrG_PcrG 90.8 90.8 90 equivalog Y Y N LcrG family type III secretion system chaperone 11443094,14565848 1236 Gammaproteobacteria class 335 JCVI type III secretion protein LcrG LcrG family type III secretion system chaperone LcrG, the founding member of this family, is found in type III secretion operons, along with LcrR, H and V. As with PcrG in Pseudomonas, the protein is believed to make a 1:1 complex with LcrV (PcrV). Mutants of LcrG cause premature secretion of effector proteins into the medium. TIGR02616.1 TIGR02616 tnaC_leader 23.55 23.55 22 equivalog Y Y N tryptophanase leader peptide tnaC GO:0006569,GO:0031554,GO:0031556 9045840 1236 Gammaproteobacteria class 329 JCVI tryptophanase leader peptide tryptophanase leader peptide Members of this family are the apparent leader peptides of tryptophanase operons in Esherichia coli, Vibrio cholerae, Photobacterium profundum, Haemophilus influenzae type b, and related species. All members of the seed alignment are examples ORFs upstream of tryptophanase, with a start codon, a conserved single Trp residue, and several other conserved residues. It is suggested (Konan KV and Yanofsky C) that the nascent peptide interacts with the ribosome once (if) the ribosome reaches the stop codon. Note that this model describes a much broader set (and shorter protein region) than Pfam model PF08053. TIGR02617.1 TIGR02617 tnaA_trp_ase 825.8 825.8 467 equivalog Y Y N tryptophanase tnaA 4.1.99.1 GO:0006568,GO:0009034 25253268 1236 Gammaproteobacteria class 2154 JCVI tryptophanase tryptophanase Members of this family belong to the beta-eliminating lyase family (PF01212) and act as tryptophanase (L-tryptophan indole-lyase). The tryptophanases of this family, as a rule, are found with a tryptophanase leader peptide (TnaC) encoded upstream. Both tryptophanases (4.1.99.1) and tyrosine phenol-lyases (EC 4.1.99.2) are found between trusted and noise cutoffs, but this model captures nearly all tryptophanases for which the leader peptide gene tnaC can be found upstream. TIGR02628.1 TIGR02628 fuculo_kin_coli 470.9 470.9 465 equivalog Y Y N L-fuculokinase fucK 2.7.1.51 GO:0008737,GO:0042355 1236 Gammaproteobacteria class 4304 JCVI L-fuculokinase L-fuculokinase Members of this family are L-fuculokinase, from the clade that includes the L-fuculokinase of Escherichia coli. This enzyme catalyzes the second step in fucose catabolism. This family belongs to FGGY family of carbohydrate kinases (PF02782, PF00370). It is encoded by the kinase (K) gene of the fucose (fuc) operon. TIGR02642.1 TIGR02642 phage_xxxx 101.4 101.4 267 hypoth_equivalog Y Y N TIGR02642 family protein 1236 Gammaproteobacteria class 885 JCVI uncharacterized phage protein TIGR02642 family phage protein This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q. TIGR02721.1 TIGR02721 ycfN_thiK 299.45 299.45 256 equivalog Y Y N thiamine kinase thiK 2.7.1.89 GO:0009228,GO:0016310,GO:0019165 15150256 1236 Gammaproteobacteria class 2804 JCVI thiamine kinase thiamine kinase Members of this family are the ycfN gene product of Escherichia coli, now identified as the salvage enzyme thiamine kinase (thiK), and additional proteobacterial homologs taken to be orthologs with equivalent function. TIGR02738.1 TIGR02738 TrbB 132 132 153 equivalog Y Y N type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB trbB 16138100,16321931 1236 Gammaproteobacteria class 3048 JCVI type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold, contains a conserved pair of cysteines and has been shown to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect [1]. The protein is believed to be involved in pilin assembly [2]. The protein is closely related to TraF (TIGR02739) which is somewhat longer, lacks the cysteine motif and is apparently not functional as a disulfide bond isomerase. TIGR02739.1 TIGR02739 TraF 204.6 204.6 256 equivalog Y Y N type-F conjugative transfer system pilin assembly protein TraF traF 16138100,16321931,3042757 1236 Gammaproteobacteria class 3721 JCVI type-F conjugative transfer system pilin assembly protein TraF type-F conjugative transfer system pilin assembly protein TraF This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold and has been shown to be localized to the periplasm [1]. Unlike the related protein TrbB (TIGR02738), TraF does not contain a conserved pair of cysteines and has been shown not to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect [2]. The protein is believed to be involved in pilin assembly [3]. Even more closely related than TrbB is a clade of genes (TIGR02740) which do contain the CXXC motif, but it is unclear whether these genes are involved in type-F conjugation systems per se. TIGR02744.1 TIGR02744 TrbI_Ftype 83.65 83.65 112 equivalog Y Y N type-F conjugative transfer system protein TrbI trbI 1355084,16138100 1236 Gammaproteobacteria class 2556 JCVI type-F conjugative transfer system protein TrbI type-F conjugative transfer system protein TrbI This protein is an essential component of the F-type conjugative transfer sytem for plasmid DNA transfer and has been shown to be localized to the periplasm [1,2]. TIGR02750.1 TIGR02750 TraN_Ftype 422.45 422.45 572 equivalog Y Y N type-F conjugative transfer system mating-pair stabilization protein TraN traN 12855161,1593622,16138100 1236 Gammaproteobacteria class 5632 JCVI type-F conjugative transfer system mating-pair stabilization protein TraN type-F conjugative transfer system mating-pair stabilization protein TraN TraN is a large cysteine-rich outer membrane protein involved in the mating-pair stabilization (adhesin) component of the F-type conjugative plamid transfer system. TraN is believed to interact with the core type IV secretion system apparatus through the TraV protein [1,2,3]. TIGR02756.1 TIGR02756 TraK_Ftype 124 124 232 equivalog Y Y N type-F conjugative transfer system secretin TraK traK 11722740,12855161,16138100 1236 Gammaproteobacteria class 3610 JCVI type-F conjugative transfer system secretin TraK type-F conjugative transfer system secretin TraK The TraK protein is predicted to interact with the TraV and TraB proteins as part of the scaffold which extends from the inner membrane, through the periplasm to the cell envelope and through which the F-type conjugative pilus passes. TraK is homologous to the P-type IV secretion system protein TrbG, the Ti-type protein VirB9 and the I-type TraN protein. The protein is related to the secretin family especially the HrcC subgroup of the type III secretion system. The protein is hypothesized to oligomerize to form a ring structure akin to other secretins [1,2,3]. TIGR02759.1 TIGR02759 TraD_Ftype 521.35 521.35 566 equivalog Y Y N type IV conjugative transfer system coupling protein TraD traD 15466052,16138100 1236 Gammaproteobacteria class 10367 JCVI type IV conjugative transfer system coupling protein TraD type IV conjugative transfer system coupling protein TraD The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM) [1,2]. TIGR02760.1 TIGR02760 TraI_TIGR 929.85 929.85 1960 equivalog Y Y N conjugative transfer relaxase/helicase TraI traI 15629940 1236 Gammaproteobacteria class 11947 JCVI conjugative transfer relaxase protein TraI conjugative transfer relaxase/helicase TraI This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein [1]. TIGR02761.1 TIGR02761 TraE_TIGR 109.05 109.05 181 equivalog Y Y N type IV conjugative transfer system protein TraE traE 16138100 1236 Gammaproteobacteria class 3075 JCVI type IV conjugative transfer system protein TraE type IV conjugative transfer system protein TraE TraE is a component of type IV secretion systems involved in conjugative transfer of plasmid DNA [1]. The function of the TraE protein is unknown. TIGR02808.1 TIGR02808 short_TIGR02808 40 40 42 hypoth_equivalog Y Y N TIGR02808 family protein 1236 Gammaproteobacteria class 513 JCVI TIGR02808 family protein TIGR02808 family protein This very small protein (about 46 amino acids) consists largely of a single predicted membrane-spanning region. It is found in Photobacterium profundum SS9 and in three species of Vibrio, always near periplasmic nitrate reductase genes, but far from the periplasmic nitrate reductase genes in Aeromonas hydrophila ATCC7966. TIGR02812.1 TIGR02812 fadR_gamma 249.2 249.2 235 equivalog Y Y N fatty acid metabolism transcriptional regulator FadR fadR GO:0000062,GO:0003677,GO:0003700,GO:0006355,GO:0019217 16027119 1236 Gammaproteobacteria class 3436 JCVI fatty acid metabolism transcriptional regulator FadR fatty acid metabolism transcriptional regulator FadR Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function. TIGR02955.1 TIGR02955 TMAO_TorT 310 310 295 equivalog Y Y N TMAO reductase system periplasmic protein TorT torT 8576063 1236 Gammaproteobacteria class 4030 JCVI TMAO reductase system periplasmic protein TorT TMAO reductase system periplasmic protein TorT Members of this family are the periplasmic protein TorT which, together with the the TorS/TorR histidine kinase/response regulator system, regulates expression of the torCAD operon for trimethylamine N-oxide reductase (TMAO reductase). It appears to bind an inducer for TMAO reductase, and shows homology to a periplasmic D-ribose binding protein. TIGR02956.1 TIGR02956 TMAO_torS 676.5 676.5 967 equivalog Y Y N TMAO reductase system sensor histidine kinase/response regulator TorS torS 2.7.13.3 GO:0000155,GO:0000160,GO:0004673,GO:0016020 16221580,8809780 1236 Gammaproteobacteria class 6786 JCVI TMAO reductase sytem sensor TorS TMAO reductase system sensor histidine kinase/response regulator TorS This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (PF02518), HAMP (PF00672), phosphoacceptor (PF00512), and phosphotransfer (PF01627) domains and a response regulator receiver domain (PF00072). TIGR02972.1 TIGR02972 TMAO_torE 77.75 77.75 49 equivalog Y Y N trimethylamine N-oxide reductase system protein TorE torE 1.7.2.3 GO:0009061 1236 Gammaproteobacteria class 346 JCVI trimethylamine N-oxide reductase system, TorE protein trimethylamine N-oxide reductase system protein TorE Members of this small, apparent transmembrane protein are designated TorE and occur in operons for the trimethylamine N-oxide (TMAO) reductase system. Members are closely related to the NapE protein of the related periplasmic nitrate reductase system. It may be that TorE is an integral membrane subunit of a complex with the reductase TorA. TIGR02975.1 TIGR02975 phageshock_pspG 53.7 53.7 64 equivalog Y Y N envelope stress response protein PspG pspG 15485810 1236 Gammaproteobacteria class 1999 JCVI phage shock protein G envelope stress response protein PspG This protein previously was designated yjbO in E. coli. It is found only in genomes that have the phage shock operon (psp), but only rarely is encoded near other psp genes. The psp regulon is upregulated in response to a number of stress conditions, including ethanol, expression of the filamentous phage secretin protein IV and other secretins, and heat shock. TIGR02998.1 TIGR02998 RraA_entero 241.25 241.25 161 equivalog Y Y N ribonuclease E activity regulator RraA rraA GO:0008428,GO:0051252 12837779,13678585,14499605 1236 Gammaproteobacteria class 2957 JCVI regulator of ribonuclease activity A ribonuclease E activity regulator RraA This family includes a number of closely related sequences from certain enterobacteria. The E. coli member of this family has been characterized as a regulator of RNase E [1] and its crystal structure has been analyzed [2]. The broader subfamily which includes this equivalog, TIGR01935, was initially classified as a "hypothetical equivalog" with the name "regulator of ribonuclease activity A" based on the same evidence for this model. It now appears that, considering the second group of enterobacterial sequences within TIGR01935, the functional assignment is unsupported. THIS PROTEIN IS _NOT_ MenG, AKA S-adenosylmethionine: 2-demethylmenaquinone methyltransferase (EC 2.1.-.-). See the references characterizing this as a case of transitive annotation error [2,3]. TIGR03050.1 TIGR03050 PS_I_psaK_plant 105.3 105.3 83 equivalog Y Y N photosystem I reaction center PsaK psaK 1236 Gammaproteobacteria class 2 JCVI photosystem I reaction center PsaK photosystem I reaction center PsaK This protein family is based on a model that separates the photosystem I PsaK subunit of chloroplasts from chloroplast PsaG protein and from Cyanobacterial PsaK, both of which show sequence similarity. TIGR03145.1 TIGR03145 cyt_nit_nrfE 927.3 927.3 631 subfamily Y Y N heme lyase NrfEFG subunit NrfE nrfE 1236 Gammaproteobacteria class 1617 JCVI cytochrome c nitrate reductase biogenesis protein NrfE heme lyase NrfEFG subunit NrfE Members of this protein family closely resemble the CcmF protein of the CcmABCDEFGH system, or system I, for c-type cytochrome biogenesis (GenProp0678). Members are found, as a rule, next to closely related paralogs of CcmG and CcmH and always located near other genes associated with the cytochrome c nitrite reductase enzyme complex. As a rule, members are found in species that also encode bona fide members of the CcmF, CcmG, and CcmH families. TIGR03146.1 TIGR03146 cyt_nit_nrfB 166.6 166.6 145 equivalog Y Y N cytochrome c nitrite reductase pentaheme subunit nrfB 1.7.2.2 GO:0008152,GO:0020037,GO:0042597 1236 Gammaproteobacteria class 2729 JCVI cytochrome c nitrite reductase, pentaheme subunit cytochrome c nitrite reductase pentaheme subunit Members of this protein family contain five copies of the CXXCH heme-binding motif, and are the NrfB component of the multisubunit enzyme, cytochrome c nitrite reductase. TIGR03147.1 TIGR03147 cyt_nit_nrfF 159.2 159.2 126 exception Y Y N heme lyase NrfEFG subunit NrfF nrfF 1236 Gammaproteobacteria class 3650 JCVI cytochrome c nitrite reductase, accessory protein NrfF heme lyase NrfEFG subunit NrfF TIGR03148.1 TIGR03148 cyt_nit_nrfD 347.6 347.6 316 equivalog Y Y N cytochrome c nitrite reductase subunit NrfD nrfD 1.7.2.2 8057835 1236 Gammaproteobacteria class 4574 JCVI cytochrome c nitrite reductase, NrfD subunit cytochrome c nitrite reductase subunit NrfD Members of this protein family are NrfD, a highly hydrophobic protein encoded in the nrf operon, which encodes cytochrome c nitrite reductase. This multiple heme-containing enzyme can reduce nitrite to ammonia. Members belong to a broader PFAM protein family, PF03916, which also contains an NrfD-related subunit of polysulphide reductase. TIGR03149.1 TIGR03149 cyt_nit_nrfC 377.6 377.6 225 equivalog Y Y N cytochrome c nitrite reductase Fe-S protein nrfC 1.7.2.2 8057835 1236 Gammaproteobacteria class 2388 JCVI cytochrome c nitrite reductase, Fe-S protein cytochrome c nitrite reductase Fe-S protein Members of this protein family are the Fe-S protein, NrfC, of a cytochrome c nitrite reductase system for which the pentaheme cytochrome c protein, NrfB (family TIGR03146) is an unambiguous marker. Members of this protein family show similarity to other ferredoxin-like proteins, including a subunit of a polysulfide reductase. TIGR03152.1 TIGR03152 cyto_c552_HCOOH 692.5 692.5 441 exception Y Y N ammonia-forming nitrite reductase cytochrome c552 subunit nrfA 1.7.2.2 GO:0005509,GO:0008152,GO:0020037,GO:0042279,GO:0042597 1236 Gammaproteobacteria class 4551 JCVI formate-dependent cytochrome c nitrite reductase, c552 subunit ammonia-forming nitrite reductase cytochrome c552 subunit Members of this protein family are cytochrome c552, a component of cytochrome c nitrite reductase, which is known more formally as nitrite reductase (cytochrome; ammonia-forming) (EC 1.7.2.2). Nitrate can be reduced by several enzymes. EC 1.7.2.2 reduces nitrite all the way to ammonia, rather than to ammonium hydroxide (nitrite reductase (NAD(P)H), EC 1.7.1.4) or nitric oxide (nitrite reductase (NO-forming), EC 1.7.2.1). Some examples of EC 1.7.2.2 occur in a seven gene system that enables formate-dependent nitrite reduction, but is also found in simpler contexts. Members of this protein family, however, belong to the formate-dependent system. TIGR03307.1 TIGR03307 PhnP 272.25 272.25 249 equivalog Y Y N phosphonate metabolism protein PhnP phnP 3.1.4.55 GO:0008081,GO:0019700 21341651,21830807 1236 Gammaproteobacteria class 5896 JCVI phosphonate metabolism protein PhnP phosphonate metabolism protein PhnP The phosphonate metabolism protein PhnP is a phosphoribosyl cyclic phosphodiesterase that occurs only in genomic contexts that contain a C-P lyase system, although it is not found with all such systems. PhnP is a member of the metallo-beta-lactamase superfamily (PF00753). TIGR03312.1 TIGR03312 Se_sel_red_FAD 241.5 241.5 257 hypoth_equivalog Y Y N molybdopterin-dependent oxidoreductase FAD-binding subunit ygfM 12480890 1236 Gammaproteobacteria class 1448 JCVI probable selenate reductase, FAD-binding subunit molybdopterin-dependent oxidoreductase FAD-binding subunit This protein is suggested by Bebien, et al., to be the FAD-binding subunit of a molydbopterin-containing selenate reductase. Our comparative genomics suggests it to be a subunit of a selenium-dependent molybdenum hydroxylase for an unknown substrate. TIGR03313.1 TIGR03313 Se_sel_red_Mo 1101.9 1101.9 951 hypoth_equivalog Y Y N molybdopterin-dependent oxidoreductase Mo/Fe-S-binding subunit 10986234,12480890 1236 Gammaproteobacteria class 2730 JCVI probable selenate reductase, molybdenum-binding subunit molybdopterin-dependent oxidoreductase Mo/Fe-S-binding subunit Our comparative genomics suggests this protein family to be a subunit of a selenium-dependent molybdenum hydroxylase, although the substrate is not specified. This protein is suggested by Bebien, et al., to be the molybdenum-binding subunit of a molydbopterin-containing selenate reductase. Xi, et al, however, show that mutation of this gene in E. coli conferred sensitivity to adenine, suggesting a defect in purine interconversion. This finding, plus homology of nearby genes in a 23-gene purine catabolism region in E. coli to xanthine dehydrogase subunits suggests xanthine dehydrogenase activity. TIGR03318.1 TIGR03318 YdfZ_fam 49.7 49.7 65 hypoth_equivalog Y Y N putative selenium delivery protein YdfZ ydfZ 12084818 1236 Gammaproteobacteria class 903 JCVI putative selenium-binding protein YdfZ putative selenium delivery protein YdfZ This small protein has a very limited distribution, being found so far only among some gamma-Proteobacteria. The member from Escherichia coli was shown to bind selenium in the absence of a working SelD-dependent selenium incorporation system. Note that while the E. coli member contains a single Cys residue, a likely selenium binding site, some other members of this protein family contain two Cys residues or none. TIGR03337.1 TIGR03337 phnR 296.75 296.75 231 equivalog Y Y N phosphonate utilization transcriptional regulator PhnR phnR GO:0003700,GO:0006355 7592415 1236 Gammaproteobacteria class 1846 JCVI phosphonate utilization transcriptional regulator PhnR phosphonate utilization transcriptional regulator PhnR This family of proteins are members of the GntR family (PF00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella [1], Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii. TIGR03341.1 TIGR03341 YhgI_GntY 269.35 269.35 190 equivalog Y Y N Fe-S biogenesis protein NfuA nfuA GO:0016226,GO:0051539,GO:0051604 16677314,18339628,9871335 1236 Gammaproteobacteria class 4913 JCVI IscR-regulated protein YhgI Fe-S biogenesis protein NfuA IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization. TIGR03391.1 TIGR03391 FeS_syn_CsdE 136.4 136.4 139 equivalog Y Y N cysteine desulfurase sulfur acceptor subunit CsdE csdE 2.8.1.7 GO:0016226,GO:0031071 15901727 1236 Gammaproteobacteria class 4938 JCVI cysteine desulfurase, sulfur acceptor subunit CsdE cysteine desulfurase sulfur acceptor subunit CsdE Members of this protein family are CsdE, formerly called YgdK. This protein, found as a paralog to SufE in Escherichia coli, Yersinia pestis, Photorhabdus luminescens, and related species, works together and physically interacts with CsdA (a paralog of SufS). CsdA has cysteine desulfurase activity that is enhanced by this protein (CsdE), in which Cys-61 (numbered as in E. coli) is a sulfur acceptor site. This gene pair, although involved in Fe-S cluster biosynthesis, is not found next to other such genes as are its paralogs from the SUF or ISC systems. TIGR03392.1 TIGR03392 FeS_syn_CsdA 493.6 493.6 398 equivalog Y Y N cysteine desulfurase CsdA csdA 2.8.1.7 GO:0016226,GO:0031071 15901727 1236 Gammaproteobacteria class 8344 JCVI cysteine desulfurase, catalytic subunit CsdA cysteine desulfurase CsdA Members of this protein family are CsdA. This protein, found in Escherichia coli, Yersinia pestis, Photorhabdus luminescens, and related species, and related to SufS, works together with and physically interacts with CsdE (a paralog of SufE). CsdA has cysteine desulfurase activity that is enhanced by CsdE, a sulfur acceptor protein. This gene pair, although involved in Fe-S cluster biosynthesis, is not found next to other such genes as are its paralogs from the SUF or ISC systems. TIGR03474.1 TIGR03474 incFII_RepA 446.9 446.9 275 equivalog Y Y N incFII family plasmid replication initiator RepA repA GO:0006276 1236 Gammaproteobacteria class 3779 JCVI incFII family plasmid replication initiator RepA incFII family plasmid replication initiator RepA Members of this protein are the plasmid replication initiator RepA of incFII (plasmid incompatibility group F-II) plasmids. R1 and R100 are plasmids in this group. Immediately upstream of repA is found tap, a leader peptide of about 24 amino acids, often not assigned as a gene in annotated plasmid sequences. Note that other, non-homologous plasmid replication proteins share the gene symbol (repA) and similar names (plasmid replication protein RepA). TIGR03475.1 TIGR03475 tap_IncFII_lead 35.05 35.05 25 equivalog Y Y N RepA leader peptide Tap tap GO:0006276,GO:0031556 1378398 1236 Gammaproteobacteria class 509 JCVI RepA leader peptide Tap RepA leader peptide Tap This protein is a translated leader peptide that actis in the regulation of the expression of the plasmid replication protein RepA in incF2 group plasmids. TIGR03536.1 TIGR03536 DapD_gpp 518.45 518.45 341 equivalog Y Y N 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase dapD 2.3.1.117 GO:0008666 1236 Gammaproteobacteria class 4382 JCVI 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (DapD) is involved in the succinylated branch of the "lysine biosynthesis via diaminopimelate (DAP)" pathway (GenProp0125). This model represents a clade of DapD sequences most closely related to the actinobacterial DapD family represented by the TIGR03535 model. All of the genes evaluated for the seed of this model are found in genomes where the downstream desuccinylase is present, but known DapD genes are absent. Additionally, many of the genes identified by this model are found proximal to genes involved in this lysine biosynthesis pathway. TIGR03613.1 TIGR03613 RutR 368 368 202 equivalog Y Y N pyrimidine utilization regulatory protein R rutR 16540542 1236 Gammaproteobacteria class 555 JCVI pyrimidine utilization regulatory protein R pyrimidine utilization regulatory protein R This protein is observed in operons extremely similar to that characterized in E. coli K-12 [1] responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model PF00440 and the C-terminal model PF08362 (YcdC-like protein, C-terminal region). TIGR03616.1 TIGR03616 RutG 758.65 758.65 429 equivalog Y Y N pyrimidine utilization transport protein G rutG GO:0006864,GO:0015218,GO:0016020 1236 Gammaproteobacteria class 4033 JCVI pyrimidine utilization transport protein G pyrimidine utilization transport protein G This protein is observed in operons extremely similar to that characterized in E. coli K-12 [1] responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the uracil-xanthine permease family defined by TIGR00801. As well as the The Nucleobase:Cation Symporter-2 (NCS2) Family (TC 2.A.40). TIGR03702.1 TIGR03702 lip_kinase_YegS 387.45 387.45 295 equivalog Y Y N lipid kinase YegS yegS GO:0001727,GO:0046872 17351295,17393457 1236 Gammaproteobacteria class 6960 JCVI lipid kinase YegS lipid kinase YegS Members of this protein family are designated YegS, an apparent lipid kinase family in the Proteobacteria. Bakali, et al. report phosphatidylglycerol kinase activity for the member from Escherichia coli, but refrain from calling that activity synonymous with its biological role. Note that a broader, subfamily-type model (TIGR00147), includes this family but also multiple paralogs in some species and varied functions. TIGR04110.1 TIGR04110 heme_HutZ 225 225 168 equivalog Y Y N heme utilization protein HutZ hutZ GO:0020037,GO:0042167 1236 Gammaproteobacteria class 1430 JCVI heme utilization protein HutZ heme utilization protein HutZ Members of this family are heme utilization proteins, typically designated HutZ. They are members of the PPOX family (PF01243) and, except for the lack of an N-terminal extension, are closely related to one form of heme oxidase (1.14.99.3), HugZ (TIGR04109). Members typically are found in a three-gene operon with radical SAM enzyme HutW and a protein of unknown function, HutX. TIGR04239.1 TIGR04239 rhombo_GlpG 250 250 271 equivalog Y Y N rhomboid family intramembrane serine protease GlpG glpG 3.4.21.105 GO:0004252,GO:0005886,GO:0019538 19919105,39136457 1236 Gammaproteobacteria class 6106 JCVI rhomboid family protease GlpG rhomboid family intramembrane serine protease GlpG GlpG in E. coli is a rhomboid family intramembrane serine protease that has been extensively characterized as a proxy for rhomboid family proteases in animals. It efficiently cleaves eukaryote-derived model substrates. This multiple membrane-spanning protein excludes inappropriate substrates from access to its cleavage site, and shows activity against truncated versions, but not full-length versions, of the E. coli multidrug transporter MdfA. This finding suggests a housekeeping function in removing faulty proteins. In contrast, several eukaryotic rhomboid family proteases release peptide hormones for signaling functions, and the Shewanella and Vibrio protein rhombosortase appears to be part of a protein-sorting system, cleaving a C-terminal anchoring helix domain. TIGR04298.1 TIGR04298 his_histam_anti 750 750 429 equivalog Y Y N histidine-histamine antiporter hdcC GO:0070907 22247134 1236 Gammaproteobacteria class 146 JCVI histidine-histamine antiporter histidine-histamine antiporter Members of this protein family are antiporters that exchange histidine with histamine, product of histidine decarboxylation. A system consisting of this protein, and a histidine decarboxylase encoded by an adjacent gene, creates decarboxylation/antiport proton-motive cycle that provides a transient resistance to acidic conditions. TIGR04365.1 TIGR04365 spare_glycyl 170 170 126 equivalog Y Y N autonomous glycyl radical cofactor GrcA grcA GO:0003824 11444864 1236 Gammaproteobacteria class 1929 JCVI autonomous glycyl radical cofactor GrcA autonomous glycyl radical cofactor GrcA This small protein, previously designated YfiD in E. coli, is closely homologous to pyruvate formate_lyase (PFL) in a region surrounding the stable glycyl radical that is prepared by the action of pyruvate formate-lyase activase, a radical SAM enzyme. When damage at the site of this radical breaks the main chain of PFL, this protein acts as a spare part that reintroduces the needed stable glycyl radical. Cutoffs for this model are set to exclude a set of closely related phage proteins that appear to have a corresponding function. TIGR04412.1 TIGR04412 T2SS_GspM_XcpZ 60 60 126 equivalog Y Y N type II secretion system protein GspM gspM 1236 Gammaproteobacteria class 414 JCVI type II secretion system protein M type II secretion system protein GspM, XcpZ type Members of this family are a variant form of the type II secretion system (T2SS) protein M, GspM, as found in several species of Pseudomonas. Members, including XcpZ, are short relative to most members of Pfam family PF04612 (as of release 26.0) and are not recognized by that HMM. TIGR04496.1 TIGR04496 rSAM_XyeB 450 450 385 equivalog Y Y N cyclophane-forming radical SAM/SPASM peptide maturase XyeB xyeB 32807886,38047390 1236 Gammaproteobacteria class 133 JCVI radical SAM/SPASM domain peptide maturase, XyeB family cyclophane-forming radical SAM/SPASM peptide maturase XyeB Members of this family are radical SAM/SPASM domain enzymes designated XyeB (Xenorhabdus, Yersinia, and Erwinia B),associated with maturation of the XyeA family of GG-motif containing RiPP (Ribosomally synthesized, Post-translationally modified Peptide) natural products, identified bioinformatically by TIGRFAMs and subsequently characterized by Nguyen, et al. The enzyme crosslinks side chains of the first and third residues in motifs of three, one of them Trp or Phe, to form strained aromatic cyclophane moieties. Peptide natural products with these three-residue strained cyclophanes may be called triceptides. Note that members of this family may be given species-specific names, e.g. XncB in Xenorhabdus nematophila. TIGR04510.1 TIGR04510 mod_pep_cyc 400 400 814 subfamily Y Y N putative peptide modification system cyclase 1236 Gammaproteobacteria class 1275 JCVI putative peptide modification system cyclase putative peptide modification system cyclase Members of this family show homology to mononucleotidyl cyclases and to tetratricopeptide repeat (TPR) proteins. Members occur in next to two other markers of ribosomal peptide modification systems. One is a dehydrogenase related to SagB proteins from thiazole/oxazole modification systems. The other is the putative precursor, related to the nitrile hydratase-related leader peptide (NHLP) and nitrile hydratase alpha subunit families. These systems occur in many species of Xanthomonas and Stenotrophomonas, among others. NF000004.1 vanH-D 550 550 323 exception Y Y Y D-lactate dehydrogenase VanH-D vanH-D 1.1.1.28 GO:0016616,GO:0051287 1239 Bacillota phylum 17 NCBIFAM D-lactate dehydrogenase VanH-D D-lactate dehydrogenase VanH-D NF000076.3 APH_2pp_Ie_IVa 600 600 301 exception Y Y Y APH(2'')-Ie/IVa family aminoglycoside O-phosphotransferase aph(2'') 1239 Bacillota phylum 3 NCBIFAM APH(2'')-Ie/IVa family aminoglycoside O-phosphotransferase APH(2'')-Ie/IVa family aminoglycoside O-phosphotransferase NF000090.1 trans_reg_VanU 150 150 75 equivalog Y Y Y glycopeptide resistance transcriptional regulator VanU vanU 1239 Bacillota phylum 2 NCBIFAM glycopeptide resistance transcriptional regulator VanU glycopeptide resistance transcriptional regulator VanU NF000111.1 stregram_VatD 400 400 209 exception Y Y Y streptogramin A O-acetyltransferase Vat(D) vat(D) GO:0016740 1239 Bacillota phylum 5 NCBIFAM streptogramin A O-acetyltransferase Vat(D) streptogramin A O-acetyltransferase Vat(D) NF000144.1 D_ala_D_lac_VanF 750 750 343 exception Y Y Y D-alanine--(R)-lactate ligase VanF vanF 6.1.2.1 GO:0005737,GO:0008716,GO:0046872 1239 Bacillota phylum 4 NCBIFAM D-alanine--(R)-lactate ligase VanF D-alanine--(R)-lactate ligase VanF NF000149.1 vanXY_G 500 500 254 exception Y Y Y D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase VanXY-G vanXY GO:0006508 1239 Bacillota phylum 4 NCBIFAM D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase VanXY-G D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase VanXY-G NF000326.1 blaR1_generic 400 400 585 equivalog Y Y Y BlaR1 family beta-lactam sensor/signal transducer GO:0008658 1239 Bacillota phylum 2667 NCBIFAM BlaR1 family beta-lactam sensor/signal transducer BlaR1 family beta-lactam sensor/signal transducer NF000380.1 vanXY 250 250 179 equivalog Y Y Y D,D-carboxypeptidase/D,D-dipeptidase VanXY vanXY 1239 Bacillota phylum 91 NCBIFAM D,D-carboxypeptidase/D,D-dipeptidase VanXY D,D-carboxypeptidase/D,D-dipeptidase VanXY NF000404.1 vanR-D 500 500 232 exception Y Y Y vancomycin resistance response regulator transcription factor VanR-D vanR-D 1239 Bacillota phylum 20 NCBIFAM VanD-type vancomycin resistance DNA-binding response regulator VanR vancomycin resistance response regulator transcription factor VanR-D Members of this family are the response regulator VanR of VanD-type vancomycin resistance systems. NF000448.2 blaACI 640 640 284 exception Y Y Y ACI family class A beta-lactamase blaACI 3.5.2.6 GO:0008800 1239 Bacillota phylum 16 NCBIFAM ACI family class A beta-lactamase ACI family class A beta-lactamase NF000471.1 vanY_of_D 625 625 354 exception Y Y Y transpeptidase-like D-Ala-D-Ala carboxypeptidase VanY-D vanY-D GO:0006508 1239 Bacillota phylum 24 NCBIFAM transpeptidase-like D-Ala-D-Ala carboxypeptidase VanY-D transpeptidase-like D-Ala-D-Ala carboxypeptidase VanY-D NF000778.0 PRK00052 PRK00052.3-4 334 334 252 equivalog Y Y N prolipoprotein diacylglyceryl transferase 2.4.99.- 1239 Bacillota phylum 729 NCBI Protein Cluster (PRK) prolipoprotein diacylglyceryl transferase prolipoprotein diacylglyceryl transferase NF001072.0 PRK00118 PRK00118.2-2 97 97 111 equivalog Y Y N putative DNA-binding protein 1239 Bacillota phylum 736 NCBI Protein Cluster (PRK) putative DNA-binding protein putative DNA-binding protein NF001663.0 PRK00431 PRK00431.1-4 285 285 180 equivalog Y Y N ADP-ribose-binding protein 1239 Bacillota phylum 255 NCBI Protein Cluster (PRK) RNase III inhibitor ADP-ribose-binding protein NF001680.0 PRK00441 PRK00441.1 184 184 150 equivalog Y Y N arginine repressor 1239 Bacillota phylum 646 NCBI Protein Cluster (PRK) arginine repressor arginine repressor Regulates arginine biosynthesis when complexed with arginine by binding at site that overlap the promotors of the arginine biosynthesis genes NF002001.0 PRK00802 PRK00802.1-1 272 272 202 equivalog Y Y N DNA-3-methyladenine glycosylase 3.2.2.- 1239 Bacillota phylum 1363 NCBI Protein Cluster (PRK) 3-methyladenine DNA glycosylase DNA-3-methyladenine glycosylase NF002054.0 PRK00886 PRK00886.1-3 330 330 241 equivalog Y Y N 2-phosphosulfolactate phosphatase family protein 1239 Bacillota phylum 53 NCBI Protein Cluster (PRK) 2-phosphosulfolactate phosphatase 2-phosphosulfolactate phosphatase family protein This bacterial enzyme is related to archaeal 2-phosphosulfolactate phosphatase, involved in biosynthesis of coenzyme M, a cofactor involved in methanogenesis in the archaea. It may differ in function. NF002107.0 PRK00951 PRK00951.1-2 267 267 194 equivalog Y Y N imidazoleglycerol-phosphate dehydratase HisB hisB 4.2.1.19 GO:0000105,GO:0004424 1239 Bacillota phylum 3673 NCBI Protein Cluster (PRK) imidazoleglycerol-phosphate dehydratase imidazoleglycerol-phosphate dehydratase HisB NF002112.0 PRK00951 PRK00951.2-2 315 315 194 equivalog Y Y N imidazoleglycerol-phosphate dehydratase HisB hisB 4.2.1.19 1239 Bacillota phylum 123 NCBI Protein Cluster (PRK) imidazoleglycerol-phosphate dehydratase imidazoleglycerol-phosphate dehydratase HisB NF002495.0 PRK01827 PRK01827.1-1 327 327 279 equivalog Y Y N thymidylate synthase 2.1.1.45 1239 Bacillota phylum 2725 NCBI Protein Cluster (PRK) thymidylate synthase thymidylate synthase NF002653.0 PRK02318 PRK02318.2-6 404 404 387 equivalog Y Y N mannitol-1-phosphate 5-dehydrogenase 1.1.1.17 1239 Bacillota phylum 74 NCBI Protein Cluster (PRK) mannitol-1-phosphate 5-dehydrogenase mannitol-1-phosphate 5-dehydrogenase NF002803.0 PRK02944 PRK02944.1 377 377 255 equivalog Y Y N YidC family membrane integrase SpoIIIJ spoIIIJ 1239 Bacillota phylum 1456 NCBI Protein Cluster (PRK) OxaA-like protein precursor YidC family membrane integrase SpoIIIJ NF002867.0 PRK03174 PRK03174.1 100 100 59 equivalog Y Y N small acid-soluble spore protein H 1239 Bacillota phylum 739 NCBI Protein Cluster (PRK) acid-soluble spore protein H small acid-soluble spore protein H SASP H; spore coat; expressed in forespore compartment NF003413.0 PRK04778 PRK04778.1-7 556 556 564 equivalog Y Y N septation ring formation regulator EzrA ezrA 1239 Bacillota phylum 3190 NCBI Protein Cluster (PRK) septation ring formation regulator EzrA septation ring formation regulator EzrA NF003518.0 PRK05182 PRK05182.2-4 523 523 312 equivalog Y Y N DNA-directed RNA polymerase subunit alpha 2.7.7.6 1239 Bacillota phylum 656 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit alpha DNA-directed RNA polymerase subunit alpha NF003990.0 PRK05472 PRK05472.1-4 233 233 214 equivalog Y Y N redox-sensing transcriptional repressor Rex GO:0045892,GO:0051775 1239 Bacillota phylum 2274 NCBI Protein Cluster (PRK) redox-sensing transcriptional repressor Rex redox-sensing transcriptional repressor Rex NF004045.0 PRK05562 PRK05562.1 181 181 225 equivalog Y Y N NAD(P)-dependent oxidoreductase 1239 Bacillota phylum 593 NCBI Protein Cluster (PRK) precorrin-2 dehydrogenase NAD(P)-dependent oxidoreductase NF004049.0 PRK05568 PRK05568.1 206 206 142 equivalog Y N N flavodoxin 1239 Bacillota phylum 248 NCBI Protein Cluster (PRK) flavodoxin flavodoxin NF004050.0 PRK05569 PRK05569.1 136 136 141 subfamily Y N N flavodoxin 1239 Bacillota phylum 410 NCBI Protein Cluster (PRK) flavodoxin flavodoxin NF004059.0 PRK05576 PRK05576.1-2 274 274 236 equivalog Y Y N cobalt-factor II C(20)-methyltransferase 2.1.1.151 1239 Bacillota phylum 586 NCBI Protein Cluster (PRK) cobalt-precorrin-2 C(20)-methyltransferase cobalt-factor II C(20)-methyltransferase NF004078.0 PRK05583 PRK05583.1 77 77 104 equivalog Y N N ribosomal protein L7Ae family protein 1239 Bacillota phylum 493 NCBI Protein Cluster (PRK) ribosomal protein L7Ae family protein ribosomal protein L7Ae family protein NF004086.0 PRK05588 PRK05588.1 321 321 255 equivalog Y Y N histidinol phosphate phosphatase 1239 Bacillota phylum 555 NCBI Protein Cluster (PRK) histidinol-phosphatase histidinol phosphate phosphatase NF004088.0 PRK05590 PRK05590.1 140 140 166 equivalog Y N N hypothetical protein 1239 Bacillota phylum 1512 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004486.0 PRK05815 PRK05815.3-4 272 272 224 equivalog Y Y N F0F1 ATP synthase subunit A 7.1.2.2 1239 Bacillota phylum 913 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit A F0F1 ATP synthase subunit A NF004880.0 PRK06241 PRK06241.2-1 972 972 837 equivalog Y Y N phosphoenolpyruvate synthase 2.7.9.2 1239 Bacillota phylum 40 NCBI Protein Cluster (PRK) phosphoenolpyruvate synthase phosphoenolpyruvate synthase NF004882.0 PRK06241 PRK06241.2-3 850 850 827 equivalog Y Y N phosphoenolpyruvate synthase 2.7.9.2 1239 Bacillota phylum 230 NCBI Protein Cluster (PRK) phosphoenolpyruvate synthase phosphoenolpyruvate synthase NF004975.0 PRK06348 PRK06348.1 549 549 384 equivalog Y Y N pyridoxal phosphate-dependent aminotransferase 2.6.1.- 1239 Bacillota phylum 952 NCBI Protein Cluster (PRK) aspartate aminotransferase pyridoxal phosphate-dependent aminotransferase NF005168.0 PRK06638 PRK06638.2-3 154 154 172 equivalog Y Y N NADH-quinone oxidoreductase subunit J 1.6.5.9 1239 Bacillota phylum 1462 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit J NADH-quinone oxidoreductase subunit J NF005264.0 PRK06769 PRK06769.1 217 217 175 equivalog Y Y N HAD-IIIA family hydrolase 1239 Bacillota phylum 1260 NCBI Protein Cluster (PRK) hypothetical protein HAD-IIIA family hydrolase NF005290.0 PRK06813 PRK06813.1 286 286 346 equivalog Y Y N homoserine dehydrogenase 1.1.1.3 1239 Bacillota phylum 886 NCBI Protein Cluster (PRK) homoserine dehydrogenase homoserine dehydrogenase Catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine NF005307.0 PRK06839 PRK06839.1 748 748 496 equivalog Y Y N o-succinylbenzoate--CoA ligase 6.2.1.26 1239 Bacillota phylum 442 NCBI Protein Cluster (PRK) acyl-CoA synthetase o-succinylbenzoate--CoA ligase NF005379.0 PRK06922 PRK06922.1 602 602 677 equivalog Y Y N class I SAM-dependent methyltransferase 2.1.1.- 1239 Bacillota phylum 1314 NCBI Protein Cluster (PRK) hypothetical protein class I SAM-dependent methyltransferase NF005382.1 PRK06925 PRK06925.1 264 264 225 equivalog Y Y N flagellar motor protein MotS motS 15306009,16095621 1239 Bacillota phylum 1044 NCBI Protein Cluster (PRK) flagellar motor protein MotS flagellar motor protein MotS NF005383.1 PRK06926 PRK06926.1 394 394 271 equivalog Y Y N flagellar motor protein MotP motP 15306009,16095621 1239 Bacillota phylum 859 NCBI Protein Cluster (PRK) flagellar motor protein MotP flagellar motor protein MotP Homolog of MotA, appears to be involved in motility on surfaces and under different ionic conditions; with MotS (a MotB homolog) forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine. NF005483.0 PRK07088 PRK07088.1 1214 1214 764 equivalog Y Y N ribonucleoside-diphosphate reductase subunit alpha 1239 Bacillota phylum 743 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit alpha ribonucleoside-diphosphate reductase subunit alpha NF005542.0 PRK07205 PRK07205.1 602 602 444 subfamily Y Y N M20 family metallopeptidase 1239 Bacillota phylum 2448 NCBI Protein Cluster (PRK) hypothetical protein M20 family metallopeptidase NF005575.0 PRK07260 PRK07260.1 335 335 263 equivalog Y Y N enoyl-CoA hydratase 4.2.1.17 1239 Bacillota phylum 1293 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF005576.0 PRK07261 PRK07261.1 224 224 171 equivalog Y Y N DNA topology modulation protein 1239 Bacillota phylum 1250 NCBI Protein Cluster (PRK) topology modulation protein DNA topology modulation protein NF005815.0 PRK07681 PRK07681.1 545 545 399 equivalog Y Y N LL-diaminopimelate aminotransferase 2.6.1.83 1239 Bacillota phylum 1448 NCBI Protein Cluster (PRK) aspartate aminotransferase LL-diaminopimelate aminotransferase NF005817.0 PRK07683 PRK07683.1 575 575 387 equivalog Y Y N aminotransferase A GO:0003824,GO:0009058 1239 Bacillota phylum 2826 NCBI Protein Cluster (PRK) aminotransferase A aminotransferase A NF005837.0 PRK07742 PRK07742.1 409 409 299 equivalog Y Y N phosphate butyryltransferase yqiS 2.3.1.19 GO:0019605,GO:0050182 1239 Bacillota phylum 2162 NCBI Protein Cluster (PRK) phosphate butyryltransferase phosphate butyryltransferase Catalyzes the synthesis of butanoylphosphate from butanoyl-CoA and inorganic phosphate NF005838.0 PRK07748 PRK07748.1 169 169 207 equivalog Y Y N 3'-5' exonuclease KapD kapD 27188294 1239 Bacillota phylum 1118 NCBI Protein Cluster (PRK) sporulation inhibitor KapD 3'-5' exonuclease KapD Inhibitor of the KinA pathway of sporulation NF006160.0 PRK08304 PRK08304.1 402 402 337 subfamily Y Y N stage V sporulation protein AD 1239 Bacillota phylum 7669 NCBI Protein Cluster (PRK) stage V sporulation protein AD stage V sporulation protein AD NF006174.0 PRK08311 PRK08311.2-2 319 319 252 equivalog Y Y N RNA polymerase sigma factor SigI sigI 1239 Bacillota phylum 83 NCBI Protein Cluster (PRK) putative RNA polymerase sigma factor SigI RNA polymerase sigma factor SigI NF006175.0 PRK08311 PRK08311.2-3 244 244 244 subfamily Y Y N RNA polymerase sigma factor SigI sigI 1239 Bacillota phylum 221 NCBI Protein Cluster (PRK) putative RNA polymerase sigma factor SigI RNA polymerase sigma factor SigI NF006176.0 PRK08311 PRK08311.2-4 260 260 249 equivalog Y Y N RNA polymerase sigma factor SigI sigI 1239 Bacillota phylum 270 NCBI Protein Cluster (PRK) putative RNA polymerase sigma factor SigI RNA polymerase sigma factor SigI NF006839.0 PRK09357 PRK09357.1-4 576 576 422 equivalog Y Y N dihydroorotase 3.5.2.3 GO:0004151,GO:0006221,GO:0046872 1239 Bacillota phylum 3322 NCBI Protein Cluster (PRK) dihydroorotase dihydroorotase NF006856.0 PRK09358 PRK09358.3-3 510 510 316 equivalog Y Y N adenosine deaminase 3.5.4.4 1239 Bacillota phylum 24 NCBI Protein Cluster (PRK) adenosine deaminase adenosine deaminase NF006930.0 PRK09415 PRK09415.1 198 198 179 subfamily Y N N RNA polymerase factor sigma C 1239 Bacillota phylum 1939 NCBI Protein Cluster (PRK) RNA polymerase factor sigma C RNA polymerase factor sigma C NF007325.0 PRK09814 PRK09814.1-4 491 491 337 equivalog Y Y N sugar transferase 1239 Bacillota phylum 113 NCBI Protein Cluster (PRK) beta-1,6-galactofuranosyltransferase sugar transferase NF008691.0 PRK11713 PRK11713.1-4 279 279 252 equivalog Y Y N 16S rRNA (uracil(1498)-N(3))-methyltransferase 2.1.1.193 GO:0006364,GO:0008168 1239 Bacillota phylum 8037 NCBI Protein Cluster (PRK) 16S ribosomal RNA methyltransferase RsmE 16S rRNA (uracil(1498)-N(3))-methyltransferase NF008936.0 PRK12292 PRK12292.1-3 492 492 406 equivalog Y Y N ATP phosphoribosyltransferase regulatory subunit 1239 Bacillota phylum 431 NCBI Protein Cluster (PRK) ATP phosphoribosyltransferase regulatory subunit ATP phosphoribosyltransferase regulatory subunit NF009004.0 PRK12349 PRK12349.1 508 508 372 equivalog Y Y N citrate synthase mmgD 1239 Bacillota phylum 1548 NCBI Protein Cluster (PRK) citrate synthase 3 citrate synthase Forms citrate from oxaloacetate and acetyl-CoA; functions in TCA cycle, glyoxylate cycle and respiration NF009024.0 PRK12360 PRK12360.1 387 387 281 equivalog Y Y N 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 1.17.7.4 1239 Bacillota phylum 619 NCBI Protein Cluster (PRK) 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 4-hydroxy-3-methylbut-2-enyl diphosphate reductase Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP); functions in the nonmevalonate isoprenoid biosynthesis pathway NF009174.0 PRK12522 PRK12522.1 217 217 175 equivalog Y Y N RNA polymerase sigma factor 1239 Bacillota phylum 317 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor Bacteria have multiple sigma factors which are active under specific conditions; the sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs Bacterial core RNA polymerase to specific promoter elements to initiate transcription NF009200.0 PRK12548 PRK12548.1 432 432 289 subfamily Y Y N shikimate dehydrogenase 1.1.1.25 1239 Bacillota phylum 929 NCBI Protein Cluster (PRK) shikimate 5-dehydrogenase shikimate dehydrogenase Catalyzes the conversion of shikimate to 3-dehydroshikimate NF009403.0 PRK12767 PRK12767.1-2 286 286 342 equivalog Y N N carbamoyl phosphate synthase-like protein 1239 Bacillota phylum 110 NCBI Protein Cluster (PRK) carbamoyl phosphate synthase-like protein carbamoyl phosphate synthase-like protein NF009798.0 PRK13285 PRK13285.2-1 208 208 159 equivalog Y N N flagellar assembly protein FliW 1239 Bacillota phylum 77 NCBI Protein Cluster (PRK) flagellar assembly protein FliW flagellar assembly protein FliW NF009926.0 PRK13387 PRK13387.1 316 316 317 equivalog Y Y N 1,4-dihydroxy-2-naphthoate polyprenyltransferase menA 2.5.1.74 GO:0004659 1239 Bacillota phylum 2553 NCBI Protein Cluster (PRK) 1,4-dihydroxy-2-naphthoate octaprenyltransferase 1,4-dihydroxy-2-naphthoate polyprenyltransferase Catalyzes the formation of dimethylmenaquinone from 1,4-dihydroxy-2-naphthoate and octaprenyl diphosphate NF010118.0 PRK13592 PRK13592.1 443 443 299 equivalog Y N N prenyltransferase 1239 Bacillota phylum 149 NCBI Protein Cluster (PRK) prenyltransferase prenyltransferase NF010158.0 PRK13637 PRK13637.1 390 390 287 equivalog Y Y N energy-coupling factor transporter ATPase 3.6.3.- GO:0055085 1239 Bacillota phylum 2395 NCBI Protein Cluster (PRK) cobalt transporter ATP-binding subunit energy-coupling factor transporter ATPase NF010222.0 PRK13678 PRK13678.2-5 87 87 96 equivalog Y N N hypothetical protein 1239 Bacillota phylum 754 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010543.0 PRK13933 PRK13933.1 280 280 253 equivalog Y N N stationary phase survival protein SurE 3.1.3.6 1239 Bacillota phylum 350 NCBI Protein Cluster (PRK) stationary phase survival protein SurE stationary phase survival protein SurE NF010576.0 PRK13969 PRK13969.1 556 556 335 equivalog Y Y N proline racemase 5.1.1.4 1239 Bacillota phylum 247 NCBI Protein Cluster (PRK) proline racemase proline racemase NF010600.0 PRK13995 PRK13995.1 311 311 210 equivalog Y Y N K(+)-transporting ATPase subunit C 7.2.2.6 1239 Bacillota phylum 265 NCBI Protein Cluster (PRK) potassium-transporting ATPase subunit C K(+)-transporting ATPase subunit C Component of the high-affinity ATP-driven potassium transport (or KDP)system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions; the C subunit may be involved in assembly of the KDP complex NF010757.0 PRK14160 PRK14160.1 184 184 211 equivalog Y Y N nucleotide exchange factor GrpE grpE 1239 Bacillota phylum 752 NCBI Protein Cluster (PRK) heat shock protein GrpE nucleotide exchange factor GrpE With DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins NF010828.0 PRK14232 PRK14232.1 118 118 120 equivalog Y Y N fluoride efflux transporter CrcB crcB 1239 Bacillota phylum 110 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter CrcB NF010870.0 PRK14277 PRK14277.1 587 587 387 equivalog Y N N chaperone protein DnaJ 1239 Bacillota phylum 99 NCBI Protein Cluster (PRK) chaperone protein DnaJ chaperone protein DnaJ NF011069.0 PRK14499 PRK14499.1 457 457 308 equivalog Y Y N cyclic pyranopterin monophosphate synthase MoaC/MOSC-domain-containing protein 4.6.1.17 1239 Bacillota phylum 54 NCBI Protein Cluster (PRK) molybdenum cofactor biosynthesis protein MoaC/MOSC-domain-containing protein cyclic pyranopterin monophosphate synthase MoaC/MOSC-domain-containing protein NF011083.0 PRK14510 PRK14510.1-2 1322 1322 1186 equivalog Y Y N bifunctional glycogen debranching protein GlgX/4-alpha-glucanotransferase 2.4.1.25,3.2.1.196 1239 Bacillota phylum 75 NCBI Protein Cluster (PRK) putative bifunctional 4-alpha-glucanotransferase/glycogen debranching enzyme bifunctional glycogen debranching protein GlgX/4-alpha-glucanotransferase NF011124.0 PRK14553 PRK14553.1-4 186 186 114 equivalog Y Y N ribosomal-processing cysteine protease Prp 1239 Bacillota phylum 100 NCBI Protein Cluster (PRK) hypothetical protein ribosomal-processing cysteine protease Prp NF011126.0 PRK14553 PRK14553.1-6 135 135 112 equivalog Y Y N ribosomal-processing cysteine protease Prp 1239 Bacillota phylum 1643 NCBI Protein Cluster (PRK) hypothetical protein ribosomal-processing cysteine protease Prp NF011286.0 PRK14697 PRK14697.1 260 260 233 equivalog Y N N bifunctional 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/phosphatase 1239 Bacillota phylum 649 NCBI Protein Cluster (PRK) bifunctional 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/phosphatase bifunctional 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/phosphatase NF011542.0 PRK14975 PRK14975.2-2 1061 1061 802 equivalog Y Y N bifunctional 3'-5' exonuclease/DNA polymerase 1239 Bacillota phylum 137 NCBI Protein Cluster (PRK) bifunctional 3'-5' exonuclease/DNA polymerase bifunctional 3'-5' exonuclease/DNA polymerase NF012168.1 BlaI_of_BCL 180 180 121 exception Y Y N penicillinase repressor BlaI blaI 1239 Bacillota phylum 375 NCBIFAM BlaI_of_BCL: penicillinase repressor BlaI penicillinase repressor BlaI NF012215.1 D_ala_D_lac_VanD 700 700 343 exception Y Y Y D-alanine--(R)-lactate ligase VanD vanD 6.1.2.1 1239 Bacillota phylum 19 NCBIFAM D-alanine--(R)-lactate ligase VanD D-alanine--(R)-lactate ligase VanD NF012216.1 D_ala_D_lac_VanB 750 750 342 exception Y Y Y D-alanine--(R)-lactate ligase VanB vanB 6.1.2.1 GO:0005737,GO:0008716,GO:0046872 1239 Bacillota phylum 33 NCBIFAM D-alanine--(R)-lactate ligase VanB D-alanine--(R)-lactate ligase VanB NF013850.5 PF01721.23 Bacteriocin_II 24.5 24.5 34 domain Y Y N leucocin A/sakacin P family class II bacteriocin GO:0005576,GO:0042742 9398233,9611809 1239 Bacillota phylum 489 EBI-EMBL Class II bacteriocin leucocin A/sakacin P family class II bacteriocin The bacteriocins are small peptides that inhibit the growth of various bacteria. Bacteriocins of lactic acid bacteria may inhibit their target cells by permeabilising the cell membrane [1]. [1]. 9611809. Sequence and structural relationships of leucocins A-, B- and C-TA33a from Leuconostoc mesenteroides TA33a. Papathanasopoulos MA, Dykes GA, Revol-Junelles AM, Delfour A, von Holy A, Hastings JW;. Microbiology 1998;144:1343-1348. [2]. 9398233. Three-dimensional structure of leucocin A in trifluoroethanol and dodecylphosphocholine micelles: spatial location of residues critical for biological activity in type IIa bacteriocins from lactic acid bacteria. Fregeau Gallagher NL, Sailer M, Niemczura WP, Nakashima TT, Stiles ME, Vederas JC;. Biochemistry 1997;36:15062-15072. (from Pfam) NF014742.5 PF02721.19 DUF223 21 21 95 domain Y Y N DUF223 domain-containing protein 1239 Bacillota phylum 18 EBI-EMBL Domain of unknown function DUF223 Domain of unknown function DUF223 NF015469.5 PF03505.19 Clenterotox 25 25 197 domain Y Y N enterotoxin GO:0005576 21839091,25020226 1239 Bacillota phylum 65 EBI-EMBL Clostridium enterotoxin enterotoxin NF016890.5 PF05031.17 NEAT 32.8 32.8 119 domain Y Y N NEAT domain-containing protein 25153520,25862688 1239 Bacillota phylum 17665 EBI-EMBL Iron Transport-associated domain Iron Transport-associated domain NEAT domains are heme and/or hemoprotein-binding modules highly conserved in secondary structure [1]. They have roles in hemoprotein binding, heme extraction and heme transfer [2] [1]. 25153520. Molecular and evolutionary analysis of NEAr-iron Transporter (NEAT) domains. Honsa ES, Maresso AW, Highlander SK;. PLoS One. 2014;9:e104794. [2]. 25862688. Recent developments in understanding the iron acquisition strategies of gram positive pathogens. Sheldon JR, Heinrichs DE;. FEMS Microbiol Rev. 2015;39:592-630. (from Pfam) NF017406.5 PF05588.16 Botulinum_HA-17 21 21 146 domain Y N N Clostridium botulinum HA-17 domain 8631890 1239 Bacillota phylum 399 EBI-EMBL Clostridium botulinum HA-17 domain Clostridium botulinum HA-17 domain This family consists of several Clostridium botulinum hemagglutinin (HA) subcomponents. Clostridium botulinum type D strain 4947 produces two different sizes of progenitor toxins (M and L) as intact forms without proteolytic processing. The M toxin is composed of neurotoxin (NT) and nontoxic-nonhemagglutinin (NTNHA), whereas the L toxin is composed of the M toxin and hemagglutinin (HA) subcomponents (HA-70, HA-17, and HA-33) [1]. [1]. 8631890. Genetic characterization of Clostridium botulinum type A containing silent type B neurotoxin gene sequences. Hutson RA, Zhou Y, Collins MD, Johnson EA, Hatheway CL, Sugiyama H;. J Biol Chem 1996;271:10786-10792. (from Pfam) NF017894.5 PF06124.16 DUF960 25 25 94 subfamily Y Y N DUF960 family protein 1239 Bacillota phylum 3940 EBI-EMBL Staphylococcal protein of unknown function (DUF960) DUF960 family protein This family consists of several hypothetical proteins from several species of Staphylococcus. The function of this family is unknown. (from Pfam) NF018296.5 PF06570.16 DUF1129 29.1 29.1 207 PfamAutoEq Y Y N DUF1129 family protein 1239 Bacillota phylum 5966 EBI-EMBL Protein of unknown function (DUF1129) DUF1129 family protein This family consists of several hypothetical bacterial proteins of unknown function. (from Pfam) NF018703.5 PF07029.16 CryBP1 25 25 180 domain Y N N CryBP1 protein 7730255,9209052 1239 Bacillota phylum 180 EBI-EMBL CryBP1 protein CryBP1 protein This family consists of several CryBP1 like proteins from Bacillus thuringiensis and Paenibacillus popilliae. Members of this family are thought to be involved in the overall toxicity of the bacteria to their hosts [1,2]. [1]. 7730255. Transcriptional regulation of the cryIVD gene operon from Bacillus thuringiensis subsp. israelensis. Dervyn E, Poncet S, Klier A, Rapoport G;. J Bacteriol 1995;177:2283-2291. [2]. 9209052. Cloning and analysis of the first cry gene from Bacillus popilliae. Zhang J, Hodgman TC, Krieger L, Schnetter W, Schairer HU;. J Bacteriol 1997;179:4336-4341. (from Pfam) NF019798.5 PF08191.16 LRR_adjacent 21.8 5.7 57 domain Y Y N Ig-like domain-containing protein 11575932,12526809,15003459 1239 Bacillota phylum 9747 EBI-EMBL LRR adjacent LRR adjacent These are small, all beta strand domains, structurally described for the protein Internalin (InlA) and related proteins InlB, InlE, InlH from the pathogenic bacterium Listeria monocytogenes. Their function appears to be mainly structural: They are fused to the C-terminal end of leucine-rich repeats (LRR), significantly stabilising the LRR, and forming a common rigid entity with the LRR. They are themselves not involved in protein-protein-interactions but help to present the adjacent LRR-domain for this purpose. These domains belong to the family of Ig-like domains in that they consist of two sandwiched beta sheets that follow the classical connectivity of Ig-domains. The beta strands in one of the sheets is, however, much smaller than in most standard Ig-like domains, making it somewhat of an outlier [1],[2] [3]. [1]. 11575932. Internalins from the human pathogen Listeria monocytogenes combine three distinct folds into a contiguous internalin domain. Schubert WD, Gobel G, Diepholz M, Darji A, Kloer D, Hain T, Chakraborty T, Wehland J, Domann E, Heinz DW;. J Mol Biol 2001;312:783-794. [2]. 12526809. Structure of internalin, a major invasion protein of Listeria monocytogenes, in complex with its human receptor E-cadherin. Schubert WD, Urbanke C, Ziehm T, Beier V, Machner MP, Domann E, Wehland J, Chakraborty T, Heinz DW;. Cell 2002;111:825-836. [3]. 15003459. Folding and stability of the leucine-rich repeat domain of internalin B from Listeri monocytogenes. Freiberg A, Machner MP, Pfeil W, Schubert WD, Heinz DW, Seckler R;. J Mol Biol 2004;337:453-461. (from Pfam) NF020435.5 PF08860.15 DUF1827 23.4 23.4 92 subfamily Y Y N DUF1827 family protein 1239 Bacillota phylum 1484 EBI-EMBL Domain of unknown function (DUF1827) DUF1827 family protein This presumed domain has no known function. (from Pfam) NF020540.5 PF08970.15 Sda 22.6 22.6 45 domain Y Y N sporulation histidine kinase inhibitor Sda sda 15023339 1239 Bacillota phylum 3795 EBI-EMBL Sporulation inhibitor A sporulation histidine kinase inhibitor Sda Members of this protein family contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilised by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A) [1]. [1]. 15023339. Structure and mechanism of action of Sda, an inhibitor of the histidine kinases that regulate initiation of sporulation in Bacillus subtilis. Rowland SL, Burkholder WF, Cunningham KA, Maciejewski MW, Grossman AD, King GF;. Mol Cell. 2004;13:689-701. (from Pfam) NF020773.5 PF09211.15 DUF1958 24 24 63 PfamAutoEq Y Y N DUF1958 domain-containing protein 1239 Bacillota phylum 2771 EBI-EMBL Domain of unknown function (DUF1958) Domain of unknown function (DUF1958) Members of this functionally uncharacterised family are found in prokaryotic penicillin-binding protein 4. (from Pfam) NF021142.5 PF09602.15 PhaP_Bmeg 28.3 28.3 168 PfamEq Y N N Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg) 1239 Bacillota phylum 646 EBI-EMBL Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg) Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg) This entry describes a protein found in polyhydroxyalkanoic acid (PHA) gene regions and incorporated into PHA inclusions in Bacillus cereus and Bacillus megaterium. The role of the protein may include amino acid storage. (from Pfam) NF021181.5 PF09642.15 YonK 25 25 60 PfamEq Y Y N YonK family protein 10376821 1239 Bacillota phylum 272 EBI-EMBL YonK protein YonK family protein YonK protein is expressed by the bacterial prophage SPbetaC [1]. It is a 63 residue protein that associates into a homo-octamer in the form of a beta-stranded barrel with four outer helical features at points of the compass. Its function is unknown. [1]. 10376821. Nucleotide sequence of the Bacillus subtilis temperate bacteriophage SPbetac2. Lazarevic V, Dusterhoft A, Soldo B, Hilbert H, Mauel C, Karamata D;. Microbiology. 1999;145:1055-1067. (from Pfam) NF021644.5 PF10141.14 ssDNA-exonuc_C 26.4 26.4 202 PfamEq Y Y N single-stranded-DNA-specific exonuclease C-terminal domain-containing protein 1239 Bacillota phylum 15978 EBI-EMBL Single-strand DNA-specific exonuclease, C terminal domain Single-strand DNA-specific exonuclease, C terminal domain Members of this set of prokaryotic domains are found in a set of single-strand DNA-specific exonucleases, including RecJ. Their exact function has not, as yet, been determined. (from Pfam) NF021854.5 PF10368.14 YkyA 28.8 28.8 186 domain Y Y N YkyA family protein 16684363 1239 Bacillota phylum 4996 EBI-EMBL Putative cell-wall binding lipoprotein YkyA family protein YkyA is a family of proteins containing a lipoprotein signal and a hydrolase domain. It is similar to cell wall binding proteins and might also be recognisable by a host immune defence system. It is thus likely to belong to pathways important for pathogenicity [1]. [1]. 16684363. Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228. Wei W, Cao Z, Zhu YL, Wang X, Ding G, Xu H, Jia P, Qu D, Danchin A, Li Y;. BMC Genomics. 2006;7:112. (from Pfam) NF022308.5 PF10852.13 DUF2651 25 25 73 domain Y Y N DUF2651 family protein 1239 Bacillota phylum 1562 EBI-EMBL Protein of unknown function (DUF2651) DUF2651 family protein This family of proteins with unknown function appears to be restricted to Bacillus spp. (from Pfam) NF022566.5 PF11116.13 DUF2624 24.7 24.7 83 PfamAutoEq Y Y N DUF2624 family protein 1239 Bacillota phylum 1478 EBI-EMBL Protein of unknown function (DUF2624) DUF2624 family protein This family is conserved in the Bacillaceae family. Several members are named as YqfT. The function is not known. (from Pfam) NF022755.5 PF11311.13 DUF3114 25 25 266 domain Y Y N DUF3114 domain-containing protein 1239 Bacillota phylum 2847 EBI-EMBL Protein of unknown function (DUF3114) Protein of unknown function (DUF3114) Some members in this family of proteins with unknown function are annotated as cytosolic proteins. This cannot be confirmed. (from Pfam) NF022811.5 PF11368.13 DUF3169 31.6 31.6 250 PfamAutoEq Y Y N DUF3169 family protein 1239 Bacillota phylum 4605 EBI-EMBL Protein of unknown function (DUF3169) DUF3169 family protein Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function. (from Pfam) NF023063.5 PF11632.13 LcnG-beta 29.4 29.4 61 subfamily Y Y N lactococcin G-beta family bacteriocin 18187052 1239 Bacillota phylum 20 EBI-EMBL Lactococcin G-beta lactococcin G-beta family bacteriocin This family of proteins is LcnG-beta, which with LcnG-alpha constitute the two-peptide bacteriocin lactococcin G (LcnG). This family of proteins represents the N terminal domain which has an alpha-helical structure and is amphiphilic. Both peptides have a GxxxG motif which they use for interaction through a helix-helix structure [1]. [1]. 18187052. Three-dimensional structure of the two peptides that constitute the two-peptide bacteriocin lactococcin G. Rogne P, Fimland G, Nissen-Meyer J, Kristiansen PE;. Biochim Biophys Acta. 2008;1784:543-554. (from Pfam) NF023105.5 PF11676.13 DUF3272 25 25 61 PfamAutoEq Y Y N DUF3272 family protein 1239 Bacillota phylum 532 EBI-EMBL Protein of unknown function (DUF3272) DUF3272 family protein This family of proteins with unknown function appears to be restricted to Streptococcus. (from Pfam) NF023200.5 PF11772.13 EpuA 27 27 46 PfamEq Y Y N DNA-directed RNA polymerase subunit beta 2.7.7.6 2359120 1239 Bacillota phylum 3834 EBI-EMBL DNA-directed RNA polymerase subunit beta DNA-directed RNA polymerase subunit beta This short 60-residue long bacterial family is the beta subunit of the DNA-directed RNA polymerase, likely to be EC:2.7.7.6. It is membrane-bound and is referred to by the name EpuA. [1]. 2359120. Genetic and structural characterization of endA. A membrane-bound nuclease required for transformation of Streptococcus pneumoniae. Puyet A, Greenberg B, Lacks SA;. J Mol Biol. 1990;213:727-738. (from Pfam) NF023296.5 PF11868.13 DUF3388 25 25 190 PfamAutoEq Y Y N DUF3388 domain-containing protein 1239 Bacillota phylum 2787 EBI-EMBL Protein of unknown function (DUF3388) Protein of unknown function (DUF3388) This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 261 to 275 amino acids in length. This protein is found associated with Pfam:PF01842. (from Pfam) NF024068.5 PF12655.12 DUF3787 25 25 52 PfamAutoEq Y Y N DUF3787 domain-containing protein 1239 Bacillota phylum 523 EBI-EMBL Domain of unknown function (DUF3787) Domain of unknown function (DUF3787) This family of proteins is functionally uncharacterised. This family of proteins is found in Clostridia. Proteins in this family are approximately 60 amino acids in length. There is a conserved TAAW sequence motif that may be functionally important. (from Pfam) NF024089.5 PF12677.12 DUF3797 25.1 25.1 48 PfamAutoEq Y Y N DUF3797 domain-containing protein 1239 Bacillota phylum 530 EBI-EMBL Domain of unknown function (DUF3797) Domain of unknown function (DUF3797) This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif. (from Pfam) NF024198.5 PF12788.12 YmaF 27 27 97 subfamily Y Y N YmaF family protein 1239 Bacillota phylum 2788 EBI-EMBL YmaF family YmaF family protein This family of proteins is named after the B. subtilis YmaF protein. It contains 6 conserved HXH motifs that are predicted to be involved in metal-binding, but the specific function is unknown. NF024365.5 PF12963.12 DUF3852 25 25 107 domain Y Y N DUF3852 family protein 20532204 1239 Bacillota phylum 658 EBI-EMBL Protein of unknown function (DUF3852) DUF3852 family protein A family of uncharacterized proteins found by clustering human gut metagenomic sequences [1]. This domain frequently seen with DUF3848. [1]. 20532204. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. Ellrott K, Jaroszewski L, Weizhong L, Wooley J, Godzik, A. PLoS Computational Biology, 2010 (from Pfam) NF024448.5 PF13048.11 DUF3908 22.9 22.8 134 PfamAutoEq Y Y N DUF3908 family protein 1239 Bacillota phylum 446 EBI-EMBL Protein of unknown function (DUF3908) DUF3908 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 140 amino acids in length. There is a single completely conserved residue Y that may be functionally important. (from Pfam) NF024457.5 PF13057.11 DUF3919 25 25 232 domain Y Y N DUF3919 family protein 1239 Bacillota phylum 1132 EBI-EMBL Protein of unknown function (DUF3919) DUF3919 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 251 and 262 amino acids in length. There is a conserved YLNG sequence motif. (from Pfam) NF024613.5 PF13215.11 DUF4023 25 25 38 PfamAutoEq Y Y N DUF4023 family protein 1239 Bacillota phylum 987 EBI-EMBL Protein of unknown function (DUF4023) DUF4023 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There is a conserved KLP sequence motif. (from Pfam) NF024652.5 PF13255.11 DUF4046 22.8 22.8 90 domain Y Y N DUF4046 domain-containing protein 1239 Bacillota phylum 952 EBI-EMBL Protein of unknown function (DUF4046) Protein of unknown function (DUF4046) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 64 and 331 amino acids in length. (from Pfam) NF025163.5 PF13790.11 SR1P 26 26 37 domain Y Y N GapA-binding peptide SR1P 17020585,20444087 1239 Bacillota phylum 1759 EBI-EMBL SR1 protein GapA-binding peptide SR1P This family of proteins is encoded by the dual function SR1 RNA. SR1 is a sRNA which regulates arginine metabolism [1], it also encodes a short protein that binds to glyceraldehyde-3-phosphate dehydrogenase (GapA) and stabilises the gapA operon mRNAs [2]. [1]. 17020585. The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism. Heidrich N, Chinali A, Gerth U, Brantl S;. Mol Microbiol. 2006;62:520-536. [2]. 20444087. A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon. Gimpel M, Heidrich N, Mader U, Krugel H, Brantl S;. Mol Microbiol. 2010;76:990-1009. (from Pfam) NF025370.5 PF14004.11 DUF4227 27 27 71 PfamAutoEq Y Y N DUF4227 family protein 1239 Bacillota phylum 1983 EBI-EMBL Protein of unknown function (DUF4227) DUF4227 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. (from Pfam) NF025372.5 PF14006.11 YqzL 27 27 44 PfamEq Y Y N YqzL family protein 1239 Bacillota phylum 1950 EBI-EMBL YqzL-like protein YqzL family protein The YqzL-like protein family includes the B. subtilis YqzL protein Swiss:C0H452 which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. (from Pfam) NF025404.5 PF14038.11 YqzE 27 27 54 PfamEq Y Y N YqzE family protein 18628959 1239 Bacillota phylum 2072 EBI-EMBL YqzE-like protein YqzE family protein The YqzE-like protein family includes the B. subtilis YqzE protein Swiss:O32020, which is functionally uncharacterised. It is a part of the ComG operon, which is regulated by the competence transcription factor ComK [1]. This family of proteins is found in bacteria. Proteins in this family are typically between 49 and 66 amino acids in length. [1]. 18628959. Genome holography: deciphering function-form motifs from gene expression data. Madi A, Friedman Y, Roth D, Regev T, Bransburg-Zabary S, Ben Jacob E;. PLoS One. 2008;3:e2708. (from Pfam) NF025411.5 PF14045.11 YIEGIA 27 27 282 domain Y Y N YIEGIA domain-containing protein 8759874 1239 Bacillota phylum 2453 EBI-EMBL YIEGIA protein YIEGIA protein This family includes the B. subtilis YphB protein Swiss:P50742, which is functionally uncharacterised. Its expression is regulated by the sporulation transcription factor sigma-F, however it is not essential for sporulation or germination [1]. This is not a homologue of E. coli YphB, which belongs to Pfam:PF01263. This family of proteins is found in bacteria. Proteins in this family are typically between 276 and 300 amino acids in length and contain a conserved YIEGIA motif. [1]. 8759874. Identification of additional genes under the control of the transcription factor sigma F of Bacillus subtilis. Decatur A, Losick R;. J Bacteriol. 1996;178:5039-5041. (from Pfam) NF025450.5 PF14084.11 DUF4264 27 27 52 PfamAutoEq Y Y N DUF4264 family protein 1239 Bacillota phylum 1121 EBI-EMBL Protein of unknown function (DUF4264) DUF4264 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. (from Pfam) NF025508.5 PF14143.11 YrhC 27 27 72 PfamEq Y Y N YrhC family protein 17056751 1239 Bacillota phylum 1360 EBI-EMBL YrhC-like protein YrhC family protein The YrhC-like protein family includes the B. subtilis YrhC protein Swiss:O05395 which is functionally uncharacterised. YrhC is on the same operon as the MccA and MccB genes, which are involved in the conversion of methionine to cysteine. Expression of this operon is repressed in the presence of sulphate or cysteine [1]. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. [1]. 17056751. Conversion of methionine to cysteine in Bacillus subtilis and its regulation. Hullo MF, Auger S, Soutourina O, Barzu O, Yvon M, Danchin A, Martin-Verstraete I;. J Bacteriol. 2007;189:187-197. (from Pfam) NF025517.5 PF14152.11 YfhE 27 27 36 PfamEq Y Y N YfhE family protein 11532142 1239 Bacillota phylum 1202 EBI-EMBL YfhE-like protein YfhE family protein The YfhE-like protein family includes the B. subtilis YfhE protein Swiss:O31573, which is functionally uncharacterised. Its expression may be regulated by the sigma factor sigma-B, which regulates the expression of stress-response proteins [1]. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There is a conserved QEV sequence motif. [1]. 11532142. Genome-wide analysis of the general stress response in Bacillus subtilis. Price CW, Fawcett P, Ceremonie H, Su N, Murphy CK, Youngman P;. Mol Microbiol. 2001;41:757-774. (from Pfam) NF025537.5 PF14173.11 ComGG 25 25 95 PfamEq Y Y N competence type IV pilus minor pilin ComGG comGG 9422590 1239 Bacillota phylum 1781 EBI-EMBL ComG operon protein 7 competence type IV pilus minor pilin ComGG This family is required for DNA-binding during transformation of competent bacterial cells [1]. [1]. 9422590. All seven comG open reading frames are required for DNA binding during transformation of competent Bacillus subtilis. Chung YS, Dubnau D;. J Bacteriol. 1998;180:41-45. (from Pfam) NF025564.5 PF14201.11 DUF4318 27 27 75 domain Y Y N DUF4318 domain-containing protein 1239 Bacillota phylum 783 EBI-EMBL Domain of unknown function (DUF4318) Domain of unknown function (DUF4318) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. There is a single completely conserved residue F that may be functionally important. (from Pfam) NF026229.5 PF14879.11 DUF4489 27 27 151 domain Y Y N DUF4489 domain-containing protein 1239 Bacillota phylum 732 EBI-EMBL Domain of unknown function (DUF4489) Domain of unknown function (DUF4489) NF026770.5 PF15432.11 Sec-ASP3 27 27 126 domain Y Y N accessory Sec system protein Asp3 GO:0015031 18621893,21531800 1239 Bacillota phylum 2830 EBI-EMBL Accessory Sec secretory system ASP3 accessory Sec system protein Asp3 Sec-ASP3 is family of bacterial proteins involved in the Sec secretory system. The family forms part of the accessory SecA2/SecY2 system specifically required to export GspB, a serine-rich repeat cell-wall glycoprotein adhesin encoded upstream in the same operon. [1]. 18621893. Characterization of the accessory Sec system of Staphylococcus aureus. Siboo IR, Chaffin DO, Rubens CE, Sullam PM;. J Bacteriol. 2008;190:6188-6196. [2]. 21531800. Asp2 and Asp3 interact directly with GspB, the export substrate of the Streptococcus gordonii accessory Sec System. Yen YT, Seepersaud R, Bensing BA, Sullam PM;. J Bacteriol. 2011;193:3165-3174. (from Pfam) NF026935.5 PF15597.11 Imm59 26.9 26.9 100 subfamily Y Y N Imm59 family immunity protein 22731697 1239 Bacillota phylum 884 EBI-EMBL Immunity protein 59 Imm59 family immunity protein A predicted immunity protein with an alpha+beta fold and a conserved [DE]R motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Ntox13 or Ntox40 families [1]. In some proteins this domain is fused to the Imm38, Pfam:PF15599 immunity domain. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF027310.5 PF15980.10 ComGF 27 27 100 domain Y Y N competence type IV pilus minor pilin ComGF 9723928 1239 Bacillota phylum 7662 EBI-EMBL Putative Competence protein ComGF competence type IV pilus minor pilin ComGF ComGF is a family of putative bacterial competence proteins. [1]. 9723928. Cell surface localization and processing of the ComG proteins, required for DNA binding during transformation of Bacillus subtilis. Chung YS, Breidt F, Dubnau D;. Mol Microbiol. 1998;29:905-913. (from Pfam) NF027395.5 PF16069.10 DUF4811 27 27 155 domain Y Y N DUF4811 domain-containing protein 1239 Bacillota phylum 3246 EBI-EMBL Domain of unknown function (DUF4811) Domain of unknown function (DUF4811) This family of proteins is found in bacteria. Proteins in this family are typically between 188 and 241 amino acids in length. There is a single completely conserved residue Y that may be functionally important. (from Pfam) NF027486.5 PF16160.10 DUF4866 25 25 247 PfamAutoEq Y Y N DUF4866 family protein 1239 Bacillota phylum 784 EBI-EMBL Domain of unknown function (DUF4866) DUF4866 family protein This family consists of uncharacterized proteins around 250 residues in length and is mainly found in various human gut Firmicute species and abundant in human gut metagenomic datasets. The function of this family is unknown. (from Pfam) NF027740.5 PF16425.10 DUF5022 25 25 287 domain Y Y N DUF5022 domain-containing protein 1239 Bacillota phylum 10 EBI-EMBL Domain of unknown function (DUF5022) Domain of unknown function (DUF5022) This family consists of several uncharacterized proteins around 350 in length and is mainly found in various Firmicutes species. The function of this family is unknown. (from Pfam) NF027744.5 PF16429.10 DUF5026 25 25 82 domain Y Y N DUF5026 domain-containing protein 1239 Bacillota phylum 77 EBI-EMBL Domain of unknown function (DUF5026) Domain of unknown function (DUF5026) This family consists of several uncharacterized proteins around 100 residues in length and is mainly found in various Clostridiales species. The function of this family is unknown. (from Pfam) NF027756.5 PF16441.10 DUF5038 25 25 144 PfamAutoEq Y Y N DUF5038 domain-containing protein 1239 Bacillota phylum 111 EBI-EMBL Domain of unknown function (DUF5038) Domain of unknown function (DUF5038) This family consists of several uncharacterized proteins around 200 residues in length and is mainly found in various Clostridiales species. The function of this family is unknown. (from Pfam) NF027762.5 PF16447.10 DUF5044 25 25 178 domain Y Y N DUF5044 domain-containing protein 1239 Bacillota phylum 122 EBI-EMBL Domain of unknown function (DUF5044) Domain of unknown function (DUF5044) This family consists of several uncharacterized proteins around 220 residues in length and is mainly found in various Clostridiales species. The function of this family is unknown. (from Pfam) NF027884.5 PF16570.10 GramPos_pilinD3 27.2 27.2 162 PfamEq Y N N Gram-positive pilin backbone subunit 3, Cna-B-like domain 20559564,21760959 1239 Bacillota phylum 777 EBI-EMBL Gram-positive pilin backbone subunit 3, Cna-B-like domain Gram-positive pilin backbone subunit 3, Cna-B-like domain GramPos_pilinD3 is one of the major backbone units of Gram-positive pili, such as those from S.pneumoniae [1]. There are three major pilin subunits that form the polymeric backbone of the pilin from S. pneumoniae, constructed of three transthyretin-like, CnaB, domains along with a crucial N-terminal domain, D1. The three Cna-B like domains are stabilised by internal Lys-Asn isopeptdie bonds, Gram-positive pili are formed from a single chain of covalently linked subunit proteins (pilins), usually comprising an adhesin at the distal tip, a major pilin that forms the polymer shaft and a minor pilin that mediates cell wall anchoring at the base [2]. [1]. 20559564. Supramolecular organization of the repetitive backbone unit of the Streptococcus pneumoniae pilus. Spraggon G, Koesema E, Scarselli M, Malito E, Biagini M, Norais N, Emolo C, Barocchi MA, Giusti F, Hilleringmann M, Rappuoli R, Lesley S, Covacci A, Masignani V, Ferlenghi I;. PLoS One. 2010;5:e10919. [2]. 21760959. Structure of the full-length major pilin from Streptococcus pneumoniae: implications for isopeptide bond formation in gram-positive bacterial pili. Paterson NG, Baker EN;. PLoS One. 2011;6:e22095. (from Pfam) NF028117.5 PF16807.10 DUF5072 27 27 118 PfamAutoEq Y Y N DUF5072 family protein 1239 Bacillota phylum 243 EBI-EMBL Domain of unknown function (DUF5072) DUF5072 family protein NF028244.5 PF16934.10 Mersacidin 27 27 69 subfamily Y Y N mersacidin family lantibiotic GO:0050830 10818347,12562773 1239 Bacillota phylum 699 EBI-EMBL Two-component Enterococcus faecalis cytolysin (EFC) mersacidin family lantibiotic Mersacidin is a cytolysin, a lantibiotic produced by Gram-positive bacteria, The cytolysin is a 'pseudohaemolysin' which produces haemolysis on blood agar plates, but not in broth culture [1]. Mersacidin is one of the type B lantibiotics (lanthionine-containing antibiotics) that contain post-translationally modified amino acids and cyclic ring structures. Mersacidin attacks the cell wall precursor lipid II, thereby inhibiting cell-wall synthesis [2]. [1]. 10818347. Ab initio structure determination of the lantibiotic mersacidin. Schneider TR, Karcher J, Pohl E, Lubini P, Sheldrick GM;. Acta Crystallogr D Biol Crystallogr. 2000;56:705-713. [2]. 12562773. NMR study of mersacidin and lipid II interaction in dodecylphosphocholine micelles. Conformational changes are a key to antimicrobial activity. Hsu ST, Breukink E, Bierbaum G, Sahl HG, de Kruijff B, Kaptein R, van Nuland NA, Bonvin AM;. J Biol Chem. 2003;278:13110-13117. (from Pfam) NF033073.1 LPXTG_double 48 48 66 subfamily_domain Y Y N doubled motif LPXTG anchor domain-containing protein 1239 Bacillota phylum 753 NCBIFAM doubled motif LPXTG anchor domain-containing protein doubled motif LPXTG anchor domain This unusual LPXTG-type C-terminal protein sorting domain occurs largely in the genus Clostridium and typically is separated from the main body of the protein by a glycine-rich linker sequence. In this domain, the classical sortase cleavage motif, LPXTG, has the consensus sequence VPLAxLPKTG. Much of this motif, the sequence VPLAxLP, is repeated an average 20 amino acids upstream within this domain. This unusual structure of a sortase recognition site-containing domain suggest a specialized form of interaction with its cognate sortase. NF033091.0 HK_VanS_ACDEFG 400 400 293 equivalog Y Y Y vancomycin resistance histidine kinase VanS vanS 1239 Bacillota phylum 740 NCBIFAM vancomycin resistance histidine kinase VanS vancomycin resistance histidine kinase VanS NF033120.0 vanR_FM 460 460 231 exception Y Y Y vancomycin resistance response regulator transcription factor, VanR-F/VanR-M family vanR 1239 Bacillota phylum 224 NCBIFAM VanR-FM family DNA-binding response regulator vancomycin resistance response regulator transcription factor, VanR-F/VanR-M family Members of this family include the response regulator transcription factor VanR of both the VanF and VanM type glycopeptide (namely vancomycin) resistance systems. Members also include putative VanR proteins encoded near putative VanY-like carboxypeptidases in systems that seem to lack other key proteins of complete glycopeptide resistance systems, such as a D-alanine--(R)-lactate ligase. In these systems, the members of this family may respond to vancomycin, but achieve something other than conferring full resistance. NF033123.1 vanW-G 600 600 273 exception Y Y Y glycopeptide resistance accessory protein VanW-G vanW-G 1239 Bacillota phylum 3 NCBIFAM glycopeptide resistance accessory protein VanW-G glycopeptide resistance accessory protein VanW-G Members of this family are the accessory protein VanW of VanG-type vancomycin resistance systems. NF033417.1 glycocin_F_RiPP 40 40 68 subfamily Y Y N glycocin F family RiPP peptide gccF 21251913 1239 Bacillota phylum 12 NCBIFAM glycocin F family RiPP peptide glycocin F family RiPP peptide Glycocin F, from Lactobacillus plantarum strain KW30, represents one of the rarer known classes of ribosomally translated, post-translationally modified peptide (RiPP) antibiotics. Members of the family are glycosylated, which is uncommon among RiPP natural products. NF033457.1 elgicin_lanti 40 40 64 subfamily Y Y N elgicin/penisin family lantibiotic 22443157,26574006 1239 Bacillota phylum 26 NCBIFAM elgicin/penisin family lantibiotic elgicin/penisin family lantibiotic The HMM describes the elgicin family of lanthipeptides active as bacteriocins. The leader domain occurs in additional proteins that lack homology in the core region, although sharing richness in Cys residues there. NF033675.1 NTTRR-F1 70 70 155 subfamily_domain Y Y N NTTRR-F1 domain 1239 Bacillota phylum 3077 NCBIFAM NTTRR-F1 domain NTTRR-F1 domain NTTRR-F1 (N-terminal To Repetitive Region - Firmicutes 1) is a homology domain found strictly as the N-terminal non-repetitive region of otherwise highly repetitive proteins of various Firmicutes. The repetitive region that follows typically is collagen-like, with every third residue a glycine. NF033863.1 immun_TipC_fam 30 30 198 subfamily Y Y N TipC family immunity protein 30194969 1239 Bacillota phylum 1459 NCBIFAM TipC family immunity protein TipC family immunity protein This family is named for founding member TipC1 (previously TipC), an immunity protein for the toxin TelC, which is a type VII secretion system (T7SS) effector lipid II phosphatase. NF035934.1 ESAT6_2 100 100 96 subfamily Y Y N pore-forming ESAT-6 family protein 1239 Bacillota phylum 148 NCBIFAM pore-forming ESAT-6 family protein NF035952.1 WxPxxD_TM 70 70 234 subfamily Y Y N WxPxxD family membrane protein 1239 Bacillota phylum 329 NCBIFAM WxPxxD family membrane protein This uncommon, extremely hydrophobic protein of about 240 amino acids occurs sporadically in members of the Firmicutes, including the Listeria, Bacillus, Anoxybacillus, and Terribacillus genera. The protein is named for its most distinctive motif. The function is unknown, but the size and hydrophobicity suggests a transport-related function. NF036301.5 PF17279.7 DUF5344 27 27 87 domain Y Y N DUF5344 family protein 22733768 1239 Bacillota phylum 2061 EBI-EMBL Family of unknown function (DUF5344) DUF5344 family protein This is a Bacterial family of unknown function. Family members are predicted to belong to Type VII secretion (T7S) system. There is a conserved YxxxD/E sequence. It is a general secretion signal that is present in all known mycobacterial T7S substrates or substrate complexes [1]. [1]. 22733768. General secretion signal for the mycobacterial type VII secretion pathway. Daleke MH, Ummels R, Bawono P, Heringa J, Vandenbroucke-Grauls CM, Luirink J, Bitter W;. Proc Natl Acad Sci U S A. 2012;109:11342-11347. (from Pfam) NF036338.5 PF17443.7 pXO2-72 25 25 62 domain Y N N Uncharacterized protein pXO2-72 1239 Bacillota phylum 420 EBI-EMBL Uncharacterized protein pXO2-72 Uncharacterized protein pXO2-72 This is a family of unknown function found in Bacilli. (from Pfam) NF036441.5 PF17340.7 DUF5370 25 25 63 domain Y Y N DUF5370 family protein 1239 Bacillota phylum 475 EBI-EMBL Family of unknown function (DUF5370) DUF5370 family protein This is a family of unknown function found in Bacillaceae. (from Pfam) NF036573.5 PF17369.7 DUF5391 25.7 25.7 135 domain Y Y N DUF5391 family protein 1239 Bacillota phylum 817 EBI-EMBL Family of unknown function (DUF5391) DUF5391 family protein This is a family of unknown function found in Bacilli. Family members are predicted to have 4 trans-membrane regions. (from Pfam) NF036612.5 PF17312.7 Helveticin_J 25.5 25.5 314 subfamily Y Y N helveticin J family class III bacteriocin GO:0042742 11472525,2228964,24031346 1239 Bacillota phylum 755 EBI-EMBL Bacteriocin helveticin-J helveticin J family class III bacteriocin Bacteriocins are biologically active proteins or protein complexes that display a bactericidal mode of action towards closely related species [1]. Bacteriocins produced by lactic acid bacteria are grouped into different classes. Class III of bacteriocins includes large heat liable proteins [2]. Lactobacillus helveticus 481 produces a 37-kDa bacteriocin called helveticin J which is a representative for Class III bacteriocins [3]. [1]. 24031346. Bacteriocins from Lactobacillus plantarum - production, genetic organization and mode of action: producao, organizacao genetica e modo de acao. Todorov SD;. Braz J Microbiol. 2009;40:209-221. [2]. 11472525. Partial characterization of a bacteriocin produced by Lactobacillus helveticus. Bonade A, Murelli F, Vescovo M, Scolari G;. Lett Appl Microbiol. 2001;33:153-158. [3]. 2228964. Cloning, expression, and nucleotide sequence of the Lactobacillus helveticus 481 gene encoding the bacteriocin helveticin J. Joerger MC, Klaenhammer TR;. J Bacteriol. 1990;172:6339-6347. (from Pfam) NF036947.5 PF17573.7 GA-like 25 10 50 domain Y Y N albumin-binding GA domain-containing protein 7589548,9086265 1239 Bacillota phylum 588 EBI-EMBL GA-like domain GA-like domain This domain is found in bacterial cell surface proteins. It is related to the GA domain that forms a three helix bundle. (from Pfam) NF036961.5 PF17630.7 DUF5511 27 27 69 domain Y Y N DUF5511 family protein 1239 Bacillota phylum 97 EBI-EMBL Family of unknown function (DUF5511) DUF5511 family protein This is a family of unknown function found in Bacillus. (from Pfam) NF037022.5 PF18002.6 T6_Ig_like 25 25 145 domain Y N N T6 antigen Ig like domain 24778112 1239 Bacillota phylum 267 EBI-EMBL T6 antigen Ig like domain T6 antigen Ig like domain This is the N-terminal immunoglobulin-like domain. Family members carrying this domain include Trypsin-resistant surface T6 protein found in Streptococcus pyogenes [1]. [1]. 24778112. Structural conservation, variability, and immunogenicity of the T6 backbone pilin of serotype M6 Streptococcus pyogenes. Young PG, Moreland NJ, Loh JM, Bell A, Atatoa Carr P, Proft T, Baker EN;. Infect Immun. 2014;82:2949-2957. (from Pfam) NF037293.5 PF18208.6 NES_C_h 26.6 26.6 109 domain Y N N Nicking enzyme C-terminal middle helical domain 23359708 1239 Bacillota phylum 3252 EBI-EMBL Nicking enzyme C-terminal middle helical domain Nicking enzyme C-terminal middle helical domain This domain is found in nicking enzyme in S. aureus. NES initiates and terminates the transfer of plasmids that variously confer resistance to a range of drugs, including vancomycin and gentamicin. This domain is found in the C-terminal region of NES. The C-terminal region is required for conjugation and significantly impacts the catalytic activity of the N-terminal relaxase [1]. [1]. 23359708. Molecular basis of antibiotic multiresistance transfer in Staphylococcus aureus. Edwards JS, Betts L, Frazier ML, Pollet RM, Kwong SM, Walton WG, Ballentine WK 3rd, Huang JJ, Habibi S, Del Campo M, Meier JL, Dervan PB, Firth N, Redinbo MR;. Proc Natl Acad Sci U S A. 2013;110:2804-2809. (from Pfam) NF037303.5 PF18259.6 CBM65_1 25 25 113 domain Y N N Carbohydrate binding module 65 domain 1 23229556 1239 Bacillota phylum 377 EBI-EMBL Carbohydrate binding module 65 domain 1 Carbohydrate binding module 65 domain 1 This domain is found in the non-catalytic carbohydrate binding module 65B (CMB65B) present in Eubacterium cellulosolvens. CBMs are present in plant cell wall degrading enzymes and are responsible for targeting, which enhances catalysis. CBM65s display higher affinity for oligosaccharides, such as cellohexaose, and particularly polysaccharides than cellotetraose, which fully occupies the core component of the substrate binding cleft. The concave surface presented by beta-sheet 2 comprises the beta-glucan binding site in CBM65s. C6 of all the backbone glucose moieties makes extensive hydrophobic interactions with the surface tryptophans of CBM65s. Three out of the four surface Trp are highly conserved. The conserved metal ion site typical of CBMs is absent in this CBM65 family [1]. [1]. 23229556. Understanding how noncatalytic carbohydrate binding modules can display specificity for xyloglucan. Luis AS, Venditto I, Temple MJ, Rogowski A, Basle A, Xue J, Knox JP, Prates JA, Ferreira LM, Fontes CM, Najmudin S, Gilbert HJ;. J Biol Chem. 2013;288:4799-4809. (from Pfam) NF037347.5 PF18438.6 Glyco_hydro_38 28.4 28.4 111 domain Y N N Glycosyl hydrolases family 38 C-terminal domain 1 20140249 1239 Bacillota phylum 6236 EBI-EMBL Glycosyl hydrolases family 38 C-terminal domain 1 Glycosyl hydrolases family 38 C-terminal domain 1 The enzymatic hydrolysis of alpha-mannosides is catalyzed by glycoside hydrolases (GH), termed alpha-mannosidases. Streptococcal (Sp) GH38 alpha-mannosidase active on N-glycans and possibly O-glycans. SpGH38 structure can be considered as five domains: an N-terminal alpha/beta-domain, a three-helix bundle and three predominantly beta-sheet domains. This is the first of the three beta-sheet domains found in GH38, termed Beta-1. Structural analysis indicate that the beta-1 domain bows outward from the protein core, is involved in dimer interactions whilst also forming a lid 'above' and somewhat into the active centre of its dimer [1]. [1]. 20140249. Structure and kinetic investigation of Streptococcus pyogenes family GH38 alpha-mannosidase. Suits MD, Zhu Y, Taylor EJ, Walton J, Zechel DL, Gilbert HJ, Davies GJ;. PLoS One. 2010;5:e9006. (from Pfam) NF037351.5 PF18449.6 Endotoxin_C2 30.7 30.7 63 domain Y Y N toxin Cry1Ac domain D-VI-related protein 25139047 1239 Bacillota phylum 3252 EBI-EMBL Delta endotoxin toxin Cry1Ac D-VI-related domain This is domain (D-VI) can be found in Bacillus thuringiensis (Bt) insecticidal protein Cry1Ac. Full length structural analysis reveal that Cry1Ac contains seven distinct domains (DI-DVII): the three canonical toxin core domains (D-I through D-III) and four protoxin domains (D-IV through D-VII). Cry1Ac is sickle-shaped with the toxic core as handle and the protoxin domains as the blade. Domains IV and VI are alpha-bundles that resemble structural/interaction domains such as spectrin [PDB ID: 1CUN] or bacterial fibrinogen-binding complement inhibitor [1]. [1]. 25139047. Structure of the full-length insecticidal protein Cry1Ac reveals intriguing details of toxin packaging into in vivo formed crystals. Evdokimov AG, Moshiri F, Sturman EJ, Rydel TJ, Zheng M, Seale JW, Franklin S;. Protein Sci. 2014;23:1491-1497. (from Pfam) NF037393.5 PF18705.6 DUF5643 34 34 115 domain Y Y N DUF5643 domain-containing protein 1239 Bacillota phylum 8426 EBI-EMBL Family of unknown function (DUF5643) Family of unknown function (DUF5643) This is an immunoglobulin-like domain found in bacteria. (from Pfam) NF037438.5 PF18496.6 ColG_sub 27.8 27.8 117 domain Y N N Collagenase G catalytic helper subdomain 21947205,23703618 1239 Bacillota phylum 4258 EBI-EMBL Collagenase G catalytic helper subdomain Collagenase G catalytic helper subdomain This is the catalytic helper subdomain found in collagenase G from Clostridium histolyticum. This domain is indispensable for proper folding and full peptidase activity [1, 2]. [1]. 23703618. Structural basis for activity regulation and substrate preference of clostridial collagenases G, H, and T. Eckhard U, Schonauer E, Brandstetter H;. J Biol Chem. 2013;288:20184-20194. [2]. 21947205. Structure of collagenase G reveals a chew-and-digest mechanism of bacterial collagenolysis. Eckhard U, Schonauer E, Nuss D, Brandstetter H;. Nat Struct Mol Biol. 2011;18:1109-1114. (from Pfam) NF037487.5 PF18683.6 ChiW_Ig_like 27 27 106 domain Y N N Chitinase W immunoglobulin-like domain 27907169 1239 Bacillota phylum 131 EBI-EMBL Chitinase W immunoglobulin-like domain Chitinase W immunoglobulin-like domain This is an immunoglobulin like domain found in ChiW, a chitinase with high activity towards various chitins. ChiW has a multi-modular architecture composed of six domains to function efficiently on the cell surface: a right-handed beta-helix domain (carbohydrate-binding module family 54, CBM-54), a Gly-Ser-rich loop, 1st immunoglobulin-like (Ig-like) fold domain, 1st beta/alpha-barrel catalytic domain (glycoside hydrolase family 18, GH-18), 2nd Ig-like fold domain and 2nd beta/alpha-barrel catalytic domain (GH-18) [1]. [1]. 27907169. Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery. Itoh T, Hibi T, Suzuki F, Sugimoto I, Fujiwara A, Inaka K, Tanaka H, Ohta K, Fujii Y, Taketo A, Kimoto H;. PLoS One. 2016;11:e0167310. (from Pfam) NF037575.5 PF17528.7 HdcB 30.4 30.4 174 PfamEq Y Y N histidine decarboxylase maturation protein HdcB hdcB GO:0006547 21208300 1239 Bacillota phylum 52 EBI-EMBL Histidine decarboxylase maturation protein HdcB histidine decarboxylase maturation protein HdcB HdcB performs a cleavage and modification of the pyruvoyl-dependent histidine decarboxylase HdcA, generating the pyruvoyl prosthetic group. NF037691.5 PF17965.6 MucBP_2 23.4 23.4 74 domain Y Y N mucin-binding protein 19758995 1239 Bacillota phylum 13004 EBI-EMBL Mucin binding domain Mucin binding domain This domain is found in bacterial cell surface proteins that interact with mucins. The archetypal member of this family is the Mub-R5 B1 domain [1]. This domain has a beta-grasp fold [1]. [1]. 19758995. Crystal structure of a mucus-binding protein repeat reveals an unexpected functional immunoglobulin binding activity. MacKenzie DA, Tailford LE, Hemmings AM, Juge N;. J Biol Chem. 2009;284:32444-32453. (from Pfam) NF037758.5 PF18220.6 BspA_v 25 25 150 domain Y N N Adhesin BspA variable domain 27311712 1239 Bacillota phylum 988 EBI-EMBL Adhesin BspA variable domain Adhesin BspA variable domain This domain is found in BspA protein present in Streptococcus agalactiae. BspA is an antigen I/II family polypeptide that confers adhesion linked to pathogenesis in group B Streptococcus. This domain is referred to as the variable domain (BspA-V). BspA-V is responsible for binding to scavenger receptor gp340. BspA-V adopts a fold that is distinct from those of other AgI/II family polypeptide variable domains [1]. [1]. 27311712. Structural and Functional Analysis of Cell Wall-anchored Polypeptide Adhesin BspA in Streptococcus agalactiae. Rego S, Heal TJ, Pidwill GR, Till M, Robson A, Lamont RJ, Sessions RB, Jenkinson HF, Race PR, Nobbs AH;. J Biol Chem. 2016;291:15985-16000. (from Pfam) NF037932.1 ocin_sys_WGxF 40 40 59 subfamily Y Y N bacteriocin-like WGxF protein 1239 Bacillota phylum 206 NCBIFAM bacteriocin-like WGxF protein Members of this protein family of hydrophobic proteins about 60 amino acids long are found various members of the Firmicutes in three-gene contexts that suggest a role as a bacteriocin or an immunity protein. The protein is named for its most striking sequence feature, a nearly invariant WGxF motif. The two conserved neighboring families are TIGR01654-like (e.g. WP_149116529.1) and TIGR03608-like (e.g. WP_149116530.1). Built to rescue LMOF2365_14255 during structural annotation change regression. NF037937.1 septum_RefZ 180 180 195 equivalog Y Y N forespore capture DNA-binding protein RefZ refZ 22730127,30092000,31160399 1239 Bacillota phylum 1895 NCBIFAM forespore capture DNA-binding protein RefZ RefZ (regulator of FtsZ), a DNA-binding protein in the family of TetR/AcrR family transcriptional regulators, participates in septum placement and in chromosome capture during the asymmetrical cell division in endospore formation. The five nearly palindromic DNA motifs (RBMs) to which RefZ binds affect chromosomal localization, not transcription, so RefZ is not considered a transcription factor. NF038035.1 lactGalph_entA 37 37 35 subfamily Y Y N lactococcin G-alpha/enterocin 1071A family bacteriocin 1512201,15718027,18187052 1239 Bacillota phylum 18 NCBIFAM lactococcin G-alpha/enterocin 1071A family bacteriocin NF038107.1 rSAM_NF038107 600 600 444 equivalog Y Y N Cys-every-fifth radical SAM/SPASM peptide maturase CefB 21478363 1239 Bacillota phylum 19 NCBIFAM Cys-every-fifth radical SAM/SPASM peptide maturase CefB Members of this family are radical SAM/SPASM domain proteins, most of which perform post-translational modification on RiPP peptide precursors or enzyme subunits. Target residues for modification often are Cys residues. Members of family NF038108, with a Cys Every Fifth position (CefA) over most of the short length of that family, are the putative target RiPP proteins. NF038169.1 lachnocin 40 40 42 equivalog Y Y N lachnocin family radical SAM-modified peptide 31059252 1239 Bacillota phylum 20 NCBIFAM lachnocin family radical SAM-modified peptide NF038170.1 lachnocin_rSAM 550 550 440 equivalog Y Y N lachnocin radical SAM maturase 31059252 1239 Bacillota phylum 20 NCBIFAM lachnocin radical SAM maturase NF038185.1 KdpD_non_kinase 550 550 373 exception Y Y N KdpD-like non-kinase potassium sensor kdpDN 1239 Bacillota phylum 910 NCBIFAM KdpD-like non-kinase potassium sensor Members of this family contain the N-terminal sensor region, but lack the C-terminal histidine kinase region, of the sensor histidine kinase KdpD found broadly in species such as Escherichia coli, Mycobacterium tuberculosis, Clostridium acetobutylicum, and Staphylococcus aureus. Members are found in Bacillus anthracis and related species. KdpDN resembles contains the N-terminal sensor region of KdpD but lacks the C-terminal histidine kinase region. NF038246.1 bile_salt_MFS 400 400 408 equivalog Y Y N conjugated bile salt MFS transporter 11739773 1239 Bacillota phylum 524 NCBIFAM conjugated bile salt MFS transporter Members of this family are MFS transporters found regularly in the vicinity of bile acid hydrolases in Gram-positive bacteria such as Lactobacillus acidophilus and Enterococcus cecorum, and presumed to be bile salt MFS transporters, or transporter subunits. NF038292.1 SagF_ScfC 70 70 225 equivalog Y Y N SagF family protein 19286651,31591169 1239 Bacillota phylum 219 NCBIFAM SagF family protein This protein of unknown function SagF is encoded by the extended locus that includes the key proteins of streptolysin S biosynthesis. Because it is encoded just upstream of genes for ABC transporter permease and ATPase components of an ABC transporter, one group calls the protein a probable ABC transporter substrate-binding protein, designated ScfC (subcutaneous fitness C). However, the protein lacks any readily detected homology to any other ABC transporter substrate-binding protein. Additional members of the family are found in other loci producing RiPP class peptide natural products related to streptolysin S, such clostridiolysin S. NF038293.1 permease_SagG 450 450 370 equivalog Y Y N SagG family ABC transporter permease subunit 19286651 1239 Bacillota phylum 242 NCBIFAM SagG family ABC transporter permease subunit Members of this family are ABC transporter permease subunits, typically found in extended loci for the production of bacterial cytotoxins such as streptolysin S and clostridiolysin S. NF038323.1 DISARM_DrmE 250 250 785 equivalog Y Y N DISARM system-associated protein DrmE drmE 29085076 1239 Bacillota phylum 87 NCBIFAM DISARM system-associated protein DrmE DrmE appears as an fifth component in a subset of class II DISARM phage defense systems. Its role in DISARM is unknown. NF039304.4 PF19393.4 DUF5968 25 25 150 domain Y N N Family of unknown function (DUF5968) 1239 Bacillota phylum 252 EBI-EMBL Family of unknown function (DUF5968) Family of unknown function (DUF5968) This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000566) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide). (from Pfam) NF039328.4 PF19499.4 DUF6034 27 27 481 subfamily Y Y N DUF6034 family protein 1239 Bacillota phylum 1012 EBI-EMBL Family of unknown function (DUF6034) DUF6034 family protein This family of proteins is functionally uncharacterised. This family of proteins is mainly found in Clostridia. Proteins in this family are typically between 466 and 533 amino acids in length. (from Pfam) NF039537.4 PF19092.5 DUF5780 28.2 28.2 109 domain Y Y N DUF5780 domain-containing protein 1239 Bacillota phylum 440 EBI-EMBL Family of unknown function (DUF5780) Family of unknown function (DUF5780) This entry adopts a Greek-key beta sandwich topology, with long loops in some of the members. While a structure is known, the function of this domain is yet to be determined. (from Pfam) NF039550.4 PF19151.5 Sublancin 26.9 26.9 57 subfamily Y Y N sublancin family glycopeptide 21196935,24405370,9722542 1239 Bacillota phylum 31 EBI-EMBL Sublancin sublancin family glycopeptide This family represents sublancin, a small bacteriocin active against Gram-positive bacteria. This family appears to be restricted to Bacilli. Sublancin was thought to be a lantibiotic but was later shown to be an S-linked glycopeptide [1,2]. Glycosylation is essential for its antimicrobial activity. Sublancin is biosynthesised as a precursor peptide bearing an N-terminal leader peptide, and a C-terminal core peptide that is converted into the mature peptide [1]. Sublancin comprises two alpha helices and a well-defined inter-helical loop [3]. Sublancin inhibits B.cereus spore outgrowth, after the germination stage, approximately 1000-fold better than it inhibits exponential growth of the same cells and inhibits B.subtilis strain ATCC6633 and B. megaterium strain 14581 [2]. [1]. 21196935. Sublancin is not a lantibiotic but an S-linked glycopeptide. Oman TJ, Boettcher JM, Wang H, Okalibe XN, van der Donk WA;. Nat Chem Biol. 2011;7:78-80. [2]. 9722542. Identification and characterization of the structural and transporter genes for, and the chemical and biological properties of, sublancin 168, a novel lantibiotic produced by Bacillus subtilis 168. Paik SH, Chakicherla A, Hansen JN;. J Biol Chem. 1998;273:23134-23142. [3]. 24405370. NMR structure of the S-linked glycopeptide sublancin 168. Garcia De Gonzalo CV, Zhu L, Oman TJ, van der Donk WA;. ACS Chem Biol. 2014;9:796-801. (from Pfam) NF039668.4 PF19640.4 DUF6143 27 27 182 subfamily Y Y N DUF6143 family protein 1239 Bacillota phylum 792 EBI-EMBL Family of unknown function (DUF6143) DUF6143 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 173 and 198 amino acids in length. (from Pfam) NF039973.4 PF19535.4 DUF6060 26.5 26.5 171 domain Y N N Family of unknown function (DUF6060) 23688303,25879325 1239 Bacillota phylum 172 EBI-EMBL Family of unknown function (DUF6060) Family of unknown function (DUF6060) This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001035) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide), polyketide and other (Aminocoumarin). This family includes a protein from the pneumocandin B0 biosynthetic gene cluster from Glarea lozoyensis ATCC 20868 and appear to be predominantly found in fungi [1,2]. [1]. 23688303. Genomics-driven discovery of the pneumocandin biosynthetic gene cluster in the fungus Glarea lozoyensis. Chen L, Yue Q, Zhang X, Xiang M, Wang C, Li S, Che Y, Ortiz-Lopez FJ, Bills GF, Liu X, An Z;. BMC Genomics. 2013;14:339. [2]. 25879325. Genetic Manipulation of the Pneumocandin Biosynthetic Pathway for Generation of Analogues and Evaluation of Their Antifungal Activity. Li Y, Chen L, Yue Q, Liu X, An Z, Bills GF;. ACS Chem Biol. 2015;10:1702-1710. (from Pfam) NF039998.4 PF19615.4 DUF6120 27 27 92 subfamily Y Y N DUF6120 family protein 1239 Bacillota phylum 440 EBI-EMBL Family of unknown function (DUF6120) DUF6120 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 125 and 138 amino acids in length. There is a conserved MGK sequence motif. (from Pfam) NF040034.4 PF19753.4 DUF6240 26.6 26.6 276 domain Y Y N DUF6240 domain-containing protein 1239 Bacillota phylum 597 EBI-EMBL Family of unknown function (DUF6240) Family of unknown function (DUF6240) This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 969 and 1090 amino acids in length. Some members of this family are thought to be related to the Flagellar hook-length control protein FliK. (from Pfam) NF040037.4 PF19767.4 DUF6254 39.5 39.5 36 subfamily Y Y N DUF6254 family protein 1239 Bacillota phylum 944 EBI-EMBL Family of unknown function (DUF6254) DUF6254 family protein This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 39 and 59 amino acids in length. This family contains a highly conserved sequence HGKV/IKS/T. (from Pfam) NF040283.4 PF19401.4 DUF5976 25 25 50 domain Y N N Family of unknown function (DUF5976) 1239 Bacillota phylum 62 EBI-EMBL Family of unknown function (DUF5976) Family of unknown function (DUF5976) This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000624) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide). (from Pfam) NF040336.4 PF19651.4 DUF6154 27 27 79 subfamily Y Y N DUF6154 family protein 1239 Bacillota phylum 679 EBI-EMBL Family of unknown function (DUF6154) DUF6154 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. (from Pfam) NF040512.1 histam_anti_2 725 725 477 exception Y Y N histidine-histamine antiporter hdcC GO:0070907 1239 Bacillota phylum 87 NCBIFAM histidine-histamine antiporter Members of this histidine-histamine antiporter found in Firmicutes such as Lentilactobacillus parabuchneri and Clostridium thermobutyricum are more closely related to antiporters of different substrates than they are to TIGR04298 family histidine-histamine antiporters such as found in Haemophilus influenzae. Members of the seed alignment were selected with help from proximity to the hdcB gene. NF040513.1 antiport_TyrP 630 630 465 equivalog Y Y N tyrosine-tyramine antiporter tyrP GO:0070908 16513749,21255297,21415114 1239 Bacillota phylum 497 NCBIFAM tyrosine-tyramine antiporter NF040628.1 GT-D_rel 75 75 223 domain Y Y N GT-D fold domain-containing glycosyltransferase 1239 Bacillota phylum 1191 NCBIFAM GT-D fold domain This HMM describes a domain related to the GT-D fold glycotransferase domain described in Pfam model PF08759. The two families share the strong motif R[VIL]GDGE, and full-length homology, but only about 16 percent identity overall. As characterized sequences included in PF08759 include glycosyltransferase proteins or domains, members of this family are proposed also to be glycosyltransferases and to share the GT-D fold of PF08759. NF040793.1 sarcosine_GrdG 780 780 428 exception Y Y N sarcosine reductase complex component B subunit alpha grdG 1.21.4.3 24926057 1239 Bacillota phylum 177 NCBIFAM sarcosine reductase complex component B subunit alpha NF040837.1 BMC_EutD_Gpos 315 315 205 exception Y Y N ethanolamine utilization phosphate acetyltransferase EutD eutD 2.3.1.8 23144756,33850044 1239 Bacillota phylum 622 NCBIFAM ethanolamine utilization phosphate acetyltransferase EutD, CD1920-type Members of this family of bacterial microcompartment (BMC) enzymes for ethanolamine utilization are thought to have the same phosphate acetyltransferase activity (EC 2.3.1.8) as EutD of Salmonella and E. coli, but lacking sequence similarity and instead being related to PduL, phosphate propanoyltransferase (EC 2.3.1.222) of propanediol utilization BMC enzymes. Examples discussed in the literature, such as Lmo1182 from Listeria monocytogenes and CD1920 from Clostridium difficile, are called EutD despite the lack of homology. NF040908.1 CPC_1213_fam 33 33 42 subfamily Y Y N CPC_1213 family protein 1239 Bacillota phylum 334 NCBIFAM CPC_1213 family protein NF040982.1 ComGD 70 70 139 equivalog Y Y N competence type IV pilus minor pilin ComGD comGD 35004361 1239 Bacillota phylum 6142 NCBIFAM competence type IV pilus minor pilin ComGD NF041000.1 ATPase_ComGA 300 300 267 equivalog Y Y N competence type IV pilus ATPase ComGA comGA 9422590 1239 Bacillota phylum 8664 NCBIFAM competence type IV pilus ATPase ComGA NF041427.1 TrsD 200 200 201 subfamily Y Y N TrsD/TraD family conjugative transfer protein trsD 7687249,8293996 1239 Bacillota phylum 492 NCBIFAM TrsD/TraD family conjugative transfer protein NF041545.1 GrdB_like_no_Se 175 175 171 equivalog Y Y N GrdB-related putative oxidoreductase 1239 Bacillota phylum 841 NCBIFAM GrdB-related putative oxidoreductase Members of this family are not selenoproteins, but are homologs to the N-terminal domain of GrdB, a selenoprotein subunit in the glycine reductase complex. Members of this family are found in a different context, not near other glycine reductase subunits. NF042414.1 CLC_0170_fam 30 30 56 subfamily Y Y N CLC_0170 family protein 1239 Bacillota phylum 856 NCBIFAM CLC_0170 family protein Members of this family, named after Clostridium botulinum protein CLC_0170, are found in endospore-forming Gram-positive species, average about 65 amino acids in length, and contain extensively hydrophobic regions. The family is highly divergent, as making the seed alignment for the family non-redundant to below 45 percent pairwise identity between any pair of proteins still left over 90 different sequences. NF042420.1 Hsp18_Clos 195 195 147 equivalog Y Y N heat shock protein Hsp18 hsp18 8501044 1239 Bacillota phylum 243 NCBIFAM heat shock protein Hsp18 NF042548.3 PF20324.3 DUF6619 27 27 102 domain Y Y N DUF6619 domain-containing protein 1239 Bacillota phylum 93 EBI-EMBL Family of unknown function (DUF6619) Family of unknown function (DUF6619) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 100 amino acids in length. (from Pfam) NF042597.3 PF20548.3 DUF6762 27 27 132 subfamily Y Y N DUF6762 family protein 1239 Bacillota phylum 478 EBI-EMBL Family of unknown function (DUF6762) DUF6762 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in Firmicutes bacteria. Proteins in this family are approximately 135 amino acids in length. (from Pfam) NF042678.3 PF20353.3 DUF6648 27 27 182 subfamily Y Y N DUF6648 family protein 1239 Bacillota phylum 383 EBI-EMBL Family of unknown function (DUF6648) DUF6648 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 180 amino acids in length. (from Pfam) NF042807.3 PF20596.3 pAdhesive_11 24.3 24.3 112 domain Y Y N adhesive domain-containing protein 1239 Bacillota phylum 354 EBI-EMBL Putative adhesive domain (group 11) Putative adhesive domain (group 11) This domain is found N-terminal to repeating stalk domains in Firmicutes and Actinobacteria surface proteins. The structure model resembles a receptor binding domain in cattle suggesting protein binding function. The structure model also resembles partly a galactose binding Yersinia pestis antigen. (from Pfam) NF044480.2 PF21454.2 MSP1_barrel 27.8 27.8 112 domain Y N N Major structural protein 1, jelly-roll domain 26814179 1239 Bacillota phylum 27 EBI-EMBL Major structural protein 1, jelly-roll domain Major structural protein 1, jelly-roll domain This entry represents a beta barrel domain found towards the N-terminal of phage Tuc2009 receptor binding protein (RBP) which forms the head domain, involved in carbohydrate recognition [1]. Paper describing PDB structure 5e7f. [1]. 26814179. The Atomic Structure of the Phage Tuc2009 Baseplate Tripod Suggests that Host Recognition Involves Two Different Carbohydrate Binding Modules. Legrand P, Collins B, Blangy S, Murphy J, Spinelli S, Gutierrez C, Richet N, Kellenberger C, Desmyter A, Mahony J, van Sinderen D, Cambillau C;. mBio. 2016;7:e01781-e01715. (from Pfam) NF044486.2 PF21480.2 PlyCA_N 27 27 187 domain Y N N PlyCA, N-terminal domain 22807482 1239 Bacillota phylum 10 EBI-EMBL PlyCA, N-terminal domain PlyCA, N-terminal domain This domain is found at the N-terminal end of PlyCA from Streptococcus virus C1, the catalytic subunit of the potent lysin PlyC that is specific for streptococcal species. PlyCA contains three distinct domains. This domain, which folds into a loose bundle of alpha- helices, is considered as a putative glycosyl hydrolase (GyH) domain, as it has similarity to class IV family 19 chitinases [1]. Paper describing PDB structure 4f88. [1]. 22807482. X-ray crystal structure of the streptococcal specific phage lysin PlyC. McGowan S, Buckle AM, Mitchell MS, Hoopes JT, Gallagher DT, Heselpoth RD, Shen Y, Reboul CF, Law RH, Fischetti VA, Whisstock JC, Nelson DC;. Proc Natl Acad Sci U S A. 2012;109:12752-12757. (from Pfam) NF044523.2 PF21629.2 Bleomycin_resist_prot_dom 27 27 63 domain Y N N Bleomycin resistance protein domain 1239 Bacillota phylum 72 EBI-EMBL Bleomycin resistance protein domain Bleomycin resistance protein domain This domain is found in Bleomycin resistance protein from Lachnoclostridium phytofermentans (Cphy_0674) and similar bacterial sequences. It is found usually associated with Pfam:PF12833. It shows an alpha-beta structure. (from Pfam) NF044622.2 PF20787.2 SPP1_GP23-1 27 27 47 domain Y N N SPP1 phage GP23.1 20665904 1239 Bacillota phylum 71 EBI-EMBL SPP1 phage GP23.1 SPP1 phage GP23.1 Gp23.1 from Bacillus subtilis SPP1 phage adopts a hexamer assembly and is likely to function as a chaperone [1]. This family of highly conserved sequences is predominantly found in phages with long non-contractile tails and in bacterial prophages. Paper describing PDB structure 2xf5. [1]. 20665904. Crystal structure of Bacillus subtilis SPP1 phage gp23.1, a putative chaperone. Veesler D, Blangy S, Lichiere J, Ortiz-Lombardia M, Tavares P, Campanacci V, Cambillau C;. Protein Sci. 2010;19:1812-1816. (from Pfam) NF044819.2 PF21540.2 Choline_bind_4 27 10 21 repeat Y N N choline-binding repeat-containing protein 1239 Bacillota phylum 2979 EBI-EMBL Choline-binding repeat choline-binding repeat 4 This entry represents probable choline-binding cell wall repeats. (from Pfam) NF044978.2 PF21106.2 YtxK_like 24.3 24.3 81 domain Y N N YtxK N-terminal helical domain 1239 Bacillota phylum 4906 EBI-EMBL YtxK N-terminal helical domain YtxK N-terminal helical domain This entry represents the N-terminal helical domain found in the B. subtilis YtxK protein (Swiss:P37876), which is a restriction-modification system methylation subunit. (from Pfam) NF045099.2 PF21574.2 Cas9_PI_C 27 27 63 domain Y N N CRISPR-associated endonuclease Cas9, C-terminal domain 26317473,34107040 1239 Bacillota phylum 262 EBI-EMBL CRISPR-associated endonuclease Cas9, C-terminal domain CRISPR-associated endonuclease Cas9, C-terminal domain This domain is found at the C-terminal end of CRISPR-associated endonuclease Cas9 from Staphylococcus aureus (Cas9). This protein adopts a bilobed architecture consisting of a REC lobe and a NUC lobe connected by an arginine-rich bridge helix and a linker loop. The C-terminal region, known as the PI domain, can be divided into a Topoisomerase-homology (TOPO) domain (Pfam:PF18070) and a C- terminal domain (this entry). This domain forms a twisted six- stranded anti-parallel beta-sheet [1,2]. Paper describing PDB structure 7el1. [1]. 34107040. Structural basis of Staphylococcus aureus Cas9 inhibition by AcrIIA14. Liu H, Zhu Y, Lu Z, Huang Z;. Nucleic Acids Res. 2021;49:6587-6595. [2]. 26317473. Crystal Structure of Staphylococcus aureus Cas9. Nishimasu H, Cong L, Yan WX, Ran FA, Zetsche B, Li Y, Kurabayashi A, Ishitani R, Zhang F, Nureki O;. Cell. 2015;162:1113-1126. (from Pfam) NF045367.2 PF21426.2 GBS104-like_Ig 27.6 27.6 127 domain Y N N Tip pilin GBS104-like, Ig-like domain 20152157,23695252,28252635,32653644 1239 Bacillota phylum 3942 EBI-EMBL Tip pilin GBS104-like, Ig-like domain Tip pilin GBS104-like, Ig-like domain This is a Ig-like domain found in Streptococcus agalactiae tip pilin GBS104 and similar proteins [1-4]. Paper describing PDB structure 2ww8. [1]. 20152157. Structural basis of host cell recognition by the pilus adhesin from Streptococcus pneumoniae. Izore T, Contreras-Martel C, El Mortaji L, Manzano C, Terrasse R, Vernet T, Di Guilmi AM, Dessen A;. Structure. 2010;18:106-115. Paper describing PDB structure 3txa. [2]. 23695252. Structure of Streptococcus agalactiae tip pilin GBS104: a model for GBS pili assembly and host interactions. Krishnan V, Dwivedi P, Kim BJ, Samal A, Macon K, Ma X, Mishra A, Doran KS, Ton-That H, Narayana SV;. Acta Crystallogr D Biol Crystallogr. 2013;69:1073-1089. Paper describing PDB structure 5mkc. [3]. 28252635. Autocatalytic association of proteins by covalent bond formation: a Bio Molecular Welding toolbox derived from a bacterial adhesin. Bonnet J, Cartannaz J, Tourcier G, Contreras-Martel C, Kleman JP, Morlot C, Vernet T, Di Guilmi AM;. Sci Rep. 2017;7:43564. Paper describing PDB structure 6m3y. [4]. 32653644. Crystal structure of lactobacillar SpaC reveals an atypical five-domain pilus tip adhesin: Exposing its substrate-binding and assembly in SpaCBA pili. Kant A, Palva A, von Ossowski I, Krishnan V;. J Struct Biol. 2020;211:107571. (from Pfam) NF045467.1 Opp4A 650 650 556 equivalog Y Y N oligopeptide ABC transporter substrate-binding protein opp4A GO:0043190,GO:0140359 17496096,7997159 1239 Bacillota phylum 2735 NCBIFAM oligopeptide ABC transporter substrate-binding protein NF045468.1 Opp5A_nikA 600 600 488 equivalog Y Y N nickel ABC transporter substrate-binding protein nikA GO:0043190,GO:0140359 17496096,20662775 1239 Bacillota phylum 2568 NCBIFAM nickel ABC transporter substrate-binding protein NF045475.1 Opp3C 450 450 328 equivalog Y Y N oligopeptide ABC transporter permease opp3C GO:0043190,GO:0140359 17496096 1239 Bacillota phylum 2866 NCBIFAM oligopeptide ABC transporter permease NF045593.1 bilirub_TF_BilQ 125 125 135 equivalog Y Y N bilirubin utilization transcriptional regulator BilQ bilQ GO:0003700,GO:0006355 38172624 1239 Bacillota phylum 344 NCBIFAM bilirubin utilization transcriptional regulator BilQ BilQ, a MarR family transcriptional regulator, occurs regularly in operons with the bilirubin reductase BilR. NF046067.1 SigPepSipWBacil 190 190 189 equivalog Y Y N signal peptidase I SipW sipW 3.4.21.89 GO:0004252,GO:0006465 10559173,16430695,22328672 1239 Bacillota phylum 1795 NCBIFAM signal peptidase I SipW NF046359.1 PF22712.1 SNaCT7 27 27 160 domain Y N N Short NACHT-associated C-Terminal domain, family 7 37160116 1239 Bacillota phylum 102 EBI-EMBL Short NACHT-associated C-Terminal domain, family 7 Short NACHT-associated C-Terminal domain, family 7 The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors [1]. [1]. 37160116. Bacterial NLR-related proteins protect against phage. Kibby EM, Conte AN, Burroughs AM, Nagy TA, Vargas JA, Whalen LA, Aravind L, Whiteley AT;. Cell. 2023;186:2410-2424. (from Pfam) NF046383.1 PF22823.1 MrpR_C_cat 27 27 213 domain Y N N MrpR, C-terminal catalytic domain 37602373 1239 Bacillota phylum 641 EBI-EMBL MrpR, C-terminal catalytic domain MrpR, C-terminal catalytic domain This family includes the MrpR protein from Bacillus subtilis (also known as YopR), the master repressor of the lytic cycle of the temperate phage SPbeta. MrpR, a DNA-binding protein that has lost its recombinase function, shows a tyrosine recombinase fold with an N-terminal all-alpha domain (Pfam:PF22822) and a C-terminal catalytic domain (this entry) [1]. [1]. 37602373. Structural and functional characterization of MrpR, the master repressor of the Bacillus subtilis prophage SPbeta. Kohm K, Jalomo-Khayrova E, Kruger A, Basu S, Steinchen W, Bange G, Frunzke J, Hertel R, Commichau FM, Czech L;. Nucleic Acids Res. 2023; [Epub ahead of print] (from Pfam) NF046624.1 PF22268.1 DUF6954 27 27 58 subfamily Y Y N DUF6954 family protein 1239 Bacillota phylum 245 EBI-EMBL Family of unknown function (DUF6954) DUF6954 family protein This is a family of uncharacterised bacterial proteins. They are enriched in hydrophobic residues and are likely associated with the membrane. (from Pfam) NF046736.1 PF22340.1 TubZ_C_3 27 27 88 domain Y N N Tubulin-like protein TubZ, C-terminal domain 22538818 1239 Bacillota phylum 111 EBI-EMBL Tubulin-like protein TubZ, C-terminal domain Tubulin-like protein TubZ, C-terminal domain This domain is found at the C-terminal end of Tubulin-like protein TubZ from Clostridium botulinum C phage and similar sequences found in tailed bacteriophages and prophages mainly from Clostridium bacteria. TubZ is a tubulin-like, filament forming GTPase. This protein adopts a tubulin/FtsZ protein family fold organised into two domains, a canonical N-terminal GTP-binding domain, and a C-terminal GTPase domain (this entry) [1]. Paper describing PDB structure 3v3t. [1]. 22538818. Tubulin homolog TubZ in a phage-encoded partition system. Oliva MA, Martin-Galiano AJ, Sakaguchi Y, Andreu JM;. Proc Natl Acad Sci U S A. 2012;109:7711-7716. (from Pfam) NF046933.1 PF22820.1 TcaA_3rd_4th 27 27 73 domain Y Y N TcaA 3rd/4th domain-containing protein 37401629 1239 Bacillota phylum 8651 EBI-EMBL TcaA protein 3rd/4th domain TcaA protein 3rd/4th domain This entry represents the third and fourth domains of the TcaA protein that adopt an Ig-like fold. [1]. 37401629. Extensive remodelling of the cell wall during the development of Staphylococcus aureus bacteraemia. Douglas EJA, Palk N, Brignoli T, Altwiley D, Boura M, Laabei M, Recker M, Cheung GCY, Liu R, Hseih RC, Otto M, O'Brien E, McLoughlin RM, Massey RC;. Elife. 2023;12:RP87026. (from Pfam) NF047110.1 PF22145.1 GtfA_EBD 27.9 27.9 97 domain Y N N GtfA extended beta-sheet domain 24936067,26884191 1239 Bacillota phylum 3768 EBI-EMBL GtfA extended beta-sheet domain GtfA extended beta-sheet domain This entry represents the extended beta-sheet domain (EBD, also known as DUF1975) of UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase GtfA subunit [1,2]. GtfA is the core enzyme of the OGT complex, which also includes the co-activator GtfB, to glycosylate the serine-rich repeat (SRR) of adhesin PsrP in Streptococcus pneumoniae, a protein involved in the infection and pathogenesis [1,2]. The function of this domain is not clear. [1]. 26884191. Mechanism of a cytosolic O-glycosyltransferase essential for the synthesis of a bacterial adhesion protein. Chen Y, Seepersaud R, Bensing BA, Sullam PM, Rapoport TA;. Proc Natl Acad Sci U S A. 2016;113:E1190-E1199. [2]. 24936067. Structure of a novel O-linked N-acetyl-D-glucosamine (O-GlcNAc) transferase, GtfA, reveals insights into the glycosylation of pneumococcal serine-rich repeat adhesins. Shi WW, Jiang YL, Zhu F, Yang YH, Shao QY, Yang HB, Ren YM, Wu H, Chen Y, Zhou CZ;. J Biol Chem. 2014;289:20898-20907. (from Pfam) NF047135.1 PF22251.1 PFF1_TM 32.3 32.3 300 domain Y N N Vacuolar membrane protease, transmembrane domain 23679341,35175277 1239 Bacillota phylum 39 EBI-EMBL Vacuolar membrane protease, transmembrane domain Vacuolar membrane protease, transmembrane domain This entry includes fungal vacuolar membrane proteases, such as PFF1 from yeast, which may be involved in vacuolar sorting and osmoregulation [1]. It is the homologue of human ERMP1 [2]. According to AlphaFold structure prediction, these proteins consist of a M28 peptidase domain (Pfam:PF04389) at the N-terminal, a central transmembrane domain (TM) and a C-terminal domain with an elongated beta-sandwich-like fold (Pfam:PF22250), similar to the Mu homology domain (MHD) (Pfam:PF00928). This entry represents the TM domain of PFF1 and fungal its homologues. [1]. 23679341. Characterization of an M28 metalloprotease family member residing in the yeast vacuole. Hecht KA, Wytiaz VA, Ast T, Schuldiner M, Brodsky JL;. FEMS Yeast Res. 2013;13:471-484. [2]. 35175277. A lysosomal biogenesis map reveals the cargo spectrum of yeast vacuolar protein targeting pathways. Eising S, Esch B, Walte M, Vargas Duarte P, Walter S, Ungermann C, Bohnert M, Frohlich F;. J Cell Biol. 2022;221:e202107148. (from Pfam) NF047209.1 PF22568.1 Tet_C_40 27 27 129 domain Y N N Tetracyclin repressor-like, C-terminal domain 1239 Bacillota phylum 147 EBI-EMBL Tetracyclin repressor-like, C-terminal domain Tetracyclin repressor-like, C-terminal domain This domain is found at the C-terminal end of Transcriptional regulator Swiss:Q8DWD0 from Streptococcus mutans and similar sequences from firmicutes. It is normally found associated with Pfam:PF00440. This domain shows an all-alpha configuration. (from Pfam) NF047265.1 PF22813.1 TcaA_2nd 26 26 103 domain Y Y N TcaA second domain-containing protein 37401629 1239 Bacillota phylum 7643 EBI-EMBL TcaA protein second domain TcaA protein second domain This entry represents the second domain of the TcaA protein. [1]. 37401629. Extensive remodelling of the cell wall during the development of Staphylococcus aureus bacteraemia. Douglas EJA, Palk N, Brignoli T, Altwiley D, Boura M, Laabei M, Recker M, Cheung GCY, Liu R, Hseih RC, Otto M, O'Brien E, McLoughlin RM, Massey RC;. Elife. 2023;12:RP87026. (from Pfam) NF047340.1 Athe_2463_dom 36 36 177 domain Y Y N Athe_2463 domain-containing protein 29588665 1239 Bacillota phylum 279 NCBIFAM Athe_2463 domain This domain is taxonomically restricted to the Bacillota, which have no outer membrane. It occurs with the first 300 amino acids of proteins that typically range in length from 450 to 2000 amino acids. The founding member of this family, Athe_2463 from Caldicellulosiruptor bescii, becomes highly abundant during grown on the five-carbon sugar xylose or on xylan, a beta-1,4 xylose polymer. NF047357.1 antiterm_GlcT 320 320 272 equivalog Y Y N glucose PTS transporter transcription antiterminator GlcT glcT 10974121,14527945,22750856 1239 Bacillota phylum 3266 NCBIFAM glucose PTS transporter transcription antiterminator GlcT NF047400.1 MazE_PemI_antitoxin 50 50 68 equivalog Y Y N type II toxin-antitoxin system PemI/MazE family antitoxin mazE pemI GO:0110001 26305399,33095389 1239 Bacillota phylum 1051 NCBIFAM type II toxin-antitoxin system PemI/MazE family antitoxin TIGR00394.1 TIGR00394 lac_pts_IIC 614.4 614.4 412 equivalog Y Y N lactose-specific PTS transporter subunit EIIC 2.7.1.207 GO:0009401,GO:0015155,GO:0016020,GO:0019197 11947593,1400164,2125052,2125053,7737179 1239 Bacillota phylum 3225 JCVI PTS system, lactose-specific IIC component lactose-specific PTS transporter subunit EIIC This family of proteins models the IIC domain of the phosphotransferase system (PTS) for lactose. The IIC domain catalyzes the transfer of a phosphoryl group from the IIB domain to lactose. When the IIC component and IIB components are in the same polypeptide chain they are designated IIBC. TIGR01231.1 TIGR01231 lacC 409.55 409.55 310 equivalog Y Y N tagatose-6-phosphate kinase lacC 2.7.1.144 GO:0009024,GO:0019512 1239 Bacillota phylum 3351 JCVI tagatose-6-phosphate kinase tagatose-6-phosphate kinase This enzyme is part of the tagatose-6-phosphate pathway of lactose degradation. TIGR01295.2 TIGR01295 PedC_BrcD 120 120 152 equivalog Y Y N PedC/BrcD family bacteriocin maturation disulfide isomerase GO:0030152 26147827 1239 Bacillota phylum 85 JCVI putative bacteriocin transport accessory protein PedC/BrcD family bacteriocin maturation disulfide isomerase This HMM describes a small family of thioredoxin-like proteins that aid in the export of various class II bacteriocins, which are ribosomally-synthesized, non-lantibiotic bacterial peptide antibiotics, in proper formations with correct disulfide bond patterns. Seed members of this family are found in operons for pediocin PA-1 from Pediococcus acidilactici (PedC) and brochocin-C from Brochothrix campestris (BrcD). TIGR01734.1 TIGR01734 D-ala-DACP-lig 559.85 559.85 504 equivalog Y Y N D-alanine--poly(phosphoribitol) ligase subunit DltA dltA 6.1.1.13 GO:0005524,GO:0019350,GO:0047473 7797557 1239 Bacillota phylum 7850 JCVI D-alanine--poly(phosphoribitol) ligase, subunit 1 D-alanine--poly(phosphoribitol) ligase subunit DltA This model represents the enzyme (also called D-alanine-D-alanyl carrier protein ligase) which activates D-alanine as an adenylate via the reaction D-ala + ATP -> D-ala-AMP + PPi, and further catalyzes the condensation of the amino acid adenylate with the D-alanyl carrier protein (D-ala-ACP). The D-alanine is then further transferred to teichoic acid in the biosynthesis of lipoteichoic acid (LTA) and wall teichoic acid (WTA) in gram positive bacteria, both polysacchatides [1]. TIGR02526.1 TIGR02526 eut_PduT 250.3 250.3 182 equivalog Y Y N ethanolamine utilization microcompartment shell protein GO:0046336 33850044 1239 Bacillota phylum 112 JCVI PduT-like ethanolamine utilization protein Lmo1185 family ethanolamine utilization microcompartment shell protein Members of this family, such as Lmo1185 from Listeria monocytogenes, are trimeric shell proteins encoded in ethanolamine utilization microcompartment operons. This family is closely related to the PduT protein encoded in propane-diol operons. TIGR02785.1 TIGR02785 addA_Gpos 707.65 707.65 1234 equivalog Y Y N helicase-exonuclease AddAB subunit AddA addA 3.6.4.12 GO:0000724,GO:0003678,GO:0006302,GO:0016818 15547262 1239 Bacillota phylum 24499 JCVI helicase-exonuclease AddAB, AddA subunit helicase-exonuclease AddAB subunit AddA AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species. TIGR02829.1 TIGR02829 spore_III_AE 247.45 247.45 381 equivalog Y Y N stage III sporulation protein AE spoIIIAE GO:0030436 16311624 1239 Bacillota phylum 4294 JCVI stage III sporulation protein AE stage III sporulation protein AE A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AE. TIGR02833.1 TIGR02833 spore_III_AB 146.5 146.5 170 equivalog Y Y N stage III sporulation protein SpoIIIAB spoIIIAB GO:0030436 16311624 1239 Bacillota phylum 3126 JCVI stage III sporulation protein AB stage III sporulation protein SpoIIIAB A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage III sporulation protein AB. TIGR02834.1 TIGR02834 spo_ytxC 206.95 206.95 276 equivalog Y Y N putative sporulation protein YtxC ytxC GO:0030436 16311624 1239 Bacillota phylum 2011 JCVI putative sporulation protein YtxC putative sporulation protein YtxC This uncharacterized protein is part of a panel of proteins conserved in all known endospore-forming Firmicutes (low-GC Gram-positive bacteria), including Carboxydothermus hydrogenoformans, and nowhere else. TIGR02835.1 TIGR02835 spore_sigmaE 348.6 348.6 234 equivalog Y Y N RNA polymerase sporulation sigma factor SigE sigE GO:0003677,GO:0003700,GO:0006352,GO:0006355,GO:0016987 1239 Bacillota phylum 3357 JCVI RNA polymerase sigma-E factor RNA polymerase sporulation sigma factor SigE Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active. TIGR02845.1 TIGR02845 spore_V_AD 411.8 411.8 327 equivalog Y Y N stage V sporulation protein AD spoVAD GO:0030436 16077113 1239 Bacillota phylum 6483 JCVI stage V sporulation protein AD stage V sporulation protein AD Bacillus and Clostridium species contain about 10 % dipicolinic acid (pyridine-2,6-dicarboxylic acid) by weight. This protein family, SpoVAD, belongs to the spoVA operon that is suggested to act in the transport of dipicolinic acid (DPA) from the mother cell, where DPA is synthesized, to the forespore, a process essential to sporulation. Members of this protein family are found, so far, in exactly those species believed capable of endospore formation. TIGR02848.1 TIGR02848 spore_III_AC 56.65 56.65 64 equivalog Y Y N stage III sporulation protein AC spoIIIAC GO:0030436 16311624 1239 Bacillota phylum 2224 JCVI stage III sporulation protein AC stage III sporulation protein AC Members of this protein family are designated SpoIIIAC, part of the spoIIIA operon of sporulation genes whose mutant phenotype is linked to sporulation stage III. Members of this family are encoded by the genome of a species if and only if that species is capable of endospore formation, as in Bacillus subtilis. The molecular function of this small, probable integral membrane protein is unknown. TIGR02871.1 TIGR02871 spore_ylbJ 304.65 304.65 363 equivalog Y Y N sporulation integral membrane protein YlbJ ylbJ GO:0016020,GO:0030436 12662922 1239 Bacillota phylum 4782 JCVI sporulation integral membrane protein YlbJ sporulation integral membrane protein YlbJ Members of this protein family are found exclusively in Firmicutes (low-GC Gram-positive bacterial) and are known from studies in Bacillus subtilis to be part of the sigma-E regulon. Mutation leads to a sporulation defect, confirming that members of this protein family, YlbJ, are sporulation proteins. This protein appears to be universal among endospore-forming bacteria, but is encoded by a pair ORFs distant from eash other in Symbiobacterium thermophilum IAM14863. TIGR02874.1 TIGR02874 spore_ytfJ 116.3 116.3 125 equivalog Y Y N GerW family sporulation protein ytfJ GO:0030436 12480901,23921501,25790435 1239 Bacillota phylum 4179 JCVI sporulation protein YtfJ GerW family sporulation protein Members of this protein family, exemplified by YtfJ of Bacillus subtilis (now renamed GerW), are encoded by bacterial genomes if and only if the species is capable of endospore formation. YtfJ was confirmed in spores of Bacillus subtilis; it appears to be expressed in the forespore under control of SigF (see PMID:12480901). TIGR02876.1 TIGR02876 spore_yqfD 256.7 256.7 382 equivalog Y Y N sporulation protein YqfD yqfD GO:0030436 14523133 1239 Bacillota phylum 5044 JCVI sporulation protein YqfD sporulation protein YqfD YqfD is part of the sigma-E regulon in the sporulation program of endospore-forming Gram-positive bacteria. Mutation results in a sporulation defect in Bacillus subtilis. Members are found in all currently known endospore-forming bacteria, including the genera Bacillus, Symbiobacterium, Carboxydothermus, Clostridium, and Thermoanaerobacter. TIGR02896.1 TIGR02896 spore_III_AF 61.3 61.3 106 equivalog Y Y N stage III sporulation protein AF spoIIIAF GO:0016020,GO:0030436 1239 Bacillota phylum 4103 JCVI stage III sporulation protein AF stage III sporulation protein AF This family represents the stage III sporulation protein AF of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of this protein is poorly conserved, so only the N-terminal region, which includes two predicted transmembrane domains, is included in the seed alignment. TIGR02903.1 TIGR02903 spore_lon_C 678.8 678.8 615 equivalog Y Y N Lon family ATP-dependent protease lonC GO:0004252,GO:0006508,GO:0016887,GO:0030436 1239 Bacillota phylum 1217 JCVI ATP-dependent protease, Lon family ATP-dependent protease, Lon family Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC. TIGR02906.1 TIGR02906 spore_CotS 172.7 172.7 314 subfamily Y Y N CotS family spore coat protein GO:0030436 9603889 1239 Bacillota phylum 4792 JCVI spore coat protein, CotS family CotS family spore coat protein Members of this family include the spore coat proteins CotS and YtaA from Bacillus subtilis and, from other endospore-forming bacteria, homologs that are more closely related to these two than to the spore coat proteins YutH and YsxE. The CotS family is more broadly distributed than YutH or YsxE, but still is not universal among spore-formers. TIGR02907.1 TIGR02907 spore_VI_D 169.85 169.85 344 equivalog Y Y N stage VI sporulation protein D spoVID GO:0030436 11325931 1239 Bacillota phylum 1956 JCVI stage VI sporulation protein D stage VI sporulation protein D SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation. TIGR02918.1 TIGR02918 TIGR02918 574.6 574.6 500 equivalog Y Y N accessory Sec system glycosyltransferase GtfA gtfA GO:0016757 15901716 1239 Bacillota phylum 3335 JCVI accessory Sec system glycosylation protein GtfA accessory Sec system glycosyltransferase GtfA Members of this protein family are found only in Gram-positive bacteria of the Firmicutes lineage, including several species of Staphylococcus, Streptococcus, and Lactobacillus. Members are associated with glycosylation of serine-rich glycoproteins exported by the accessory Sec system. TIGR02950.1 TIGR02950 SigM_subfam 147.95 147.95 159 subfamily Y N N RNA polymerase sigma factor, SigM family GO:0003677,GO:0003700,GO:0006352,GO:0006355,GO:0016987 10216858,12775685 1239 Bacillota phylum 1846 JCVI RNA polymerase sigma factor, SigM family RNA polymerase sigma factor, SigM family This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors [1,2]. TIGR02954.1 TIGR02954 Sig70_famx3 188.5 188.5 170 hypoth_equivalog Y N N RNA polymerase sigma-70 factor, TIGR02954 family 1239 Bacillota phylum 1442 JCVI RNA polymerase sigma-70 factor, TIGR02954 family RNA polymerase sigma-70 factor, TIGR02954 family This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species. TIGR03065.1 TIGR03065 srtB_sig_QVPTGV 21.35 21.35 32 subfamily_domain Y Y N QVPTGV class sortase B protein-sorting domain-containing protein 15317792 1239 Bacillota phylum 264 JCVI sortase B signal domain, QVPTGV class QVPTGV class sortase B protein-sorting domain This model represents a boutique (unusual) sorting signal, recognized by a member of the sortase SrtB family rather than by the housekeeping sortase, SrtA. TIGR03110.1 TIGR03110 exosort_Gpos 102.75 102.75 187 exception Y Y N exosortase family protein XrtG xrtG GO:0004197,GO:0006605,GO:0016020,GO:0043687 22037399 1239 Bacillota phylum 494 JCVI exosortase family protein XrtG exosortase family protein XrtG Members of this protein family are found in a modest number of non-pathogenic Gram-positive bacteria, including three species of Lactococcus and three paralogs in Clostridium acetobutylicum. This protein appears related to the conserved core region of a family of proposed transpeptidases, exosortase (previously EpsH), thought to act on PEP-CTERM proteins. Members of the seed alignment include all exosortase proposed active site residues. However, in contrast to canonical exosortase (TIGR02602) and archaeal (TIGR03762), and cyanobacterial (TIGR03763) variants, this family has not yet been matched to a cognate PEP-CTERM-like sorting signal. This protein is assigned the gene symbol XrtG (eXosoRTase family protein of Gram-positives). TIGR03112.1 TIGR03112 6_pyr_pter_rel 69.35 69.35 113 hypoth_equivalog_domain Y N N 6-pyruvoyl tetrahydropterin synthase-related domain 22037399 1239 Bacillota phylum 498 JCVI 6-pyruvoyl tetrahydropterin synthase-related domain 6-pyruvoyl tetrahydropterin synthase-related domain Members of this family are small proteins, or small domains of larger proteins, that occur in certain Firmicutes in the same regions as members of families TIGR03110 and TIGR03111. Members of TIGR03110 resemble exosortase, a proposed protein sorting transpeptidase (see TIGR02602). TIGR03111 represents a small clade among the group 2 glycosyltransferases. Members of the current protein family resemble eukaryotic known and prokaryotic predicted 6-pyruvoyl tetrahydropterin synthases. TIGR03602.1 TIGR03602 streptolysinS 39.95 39.95 56 subfamily Y Y N streptolysin S family TOMM toxin GO:0019835 18375757,21822292,25381594 1239 Bacillota phylum 75 JCVI bacteriocin protoxin, streptolysin S family streptolysin S family TOMM toxin Members of this family are bacteriocin and/or hemolysin precursors. These small, ribosomally produced polypeptide precursors are extensively processed post-translationally. This family belongs to a class of heterocycle-containing bacteriocins, including streptolysin S from Streptococcus pyogenes, and related bacteriocins from Streptococcus iniae and Clostridium botulinum. Streptolysin S is hemolytic. Bacteriocin genes in general are small and highly diverse, with odd sequence composition, and are easily missed by many gene-finding programs. TIGR03603.1 TIGR03603 cyclo_dehy_ocin 187.65 187.65 319 subfamily Y N N thiazole/oxazole-forming peptide maturase, SagC family component GO:0016882,GO:0030152 18375757,22522320 1239 Bacillota phylum 253 JCVI thiazole/oxazole-forming peptide maturase, SagC family component thiazole/oxazole-forming peptide maturase, SagC family component Members of this protein family include enzymes related to SagC, a protein involved in thiazole/oxazole cyclodehydration modifications during biosynthesis of streptolysin S in Streptococcus pyogenes from the protoxin polypeptide (product of the sagA gene). Recent evidence suggests that the YcaO/SagD-like component, not this component, performs an ATP-dependent cyclodehydration. This protein family serves as a marker for widely distributed prokaryotic systems for making a general class of heterocycle-containing bacteriocins. Note that this model does not find all possible examples of bacteriocin biosynthesis cyclodehydratases, an in particular misses the E. coli plasmid protein McbB of microcin B17 biosynthesis. TIGR03608.1 TIGR03608 L_ocin_972_ABC 254.85 254.85 206 subfamily Y Y N putative bacteriocin export ABC transporter GO:0005524,GO:0006810,GO:0042626 1239 Bacillota phylum 3076 JCVI putative bacteriocin export ABC transporter, lactococcin 972 group putative bacteriocin export ABC transporter A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins. TIGR03651.1 TIGR03651 circ_ocin_uber 30.7 30.7 73 subfamily Y Y N circular bacteriocin, circularin A/uberolysin family 18034824 1239 Bacillota phylum 505 JCVI circular bacteriocin, circularin A/uberolysin family circular bacteriocin, circularin A/uberolysin family Circular bacteriocins are antibiotic proteins made by ribosomal translation of a precursor molecular, followed by cleavage and circularization. Members of this subclass of the circular bacteriocins include circularin A from Clostridium beijerinckii, bacteriocin AS-48 from Enterococcus faecalis, uberolysin from Streptococcus uberis, and carnocyclin A from Carnobacterium maltaromaticum. The mature circularized peptides average about 70 amino acids in size. TIGR03659.1 TIGR03659 IsdE 298.65 298.65 292 equivalog Y Y N heme ABC transporter substrate-binding protein IsdE isdE GO:0015886,GO:0016020,GO:0020037 17666394,17929943,18676371,18715872 1239 Bacillota phylum 3246 JCVI heme ABC transporter, heme-binding protein isdE heme ABC transporter substrate-binding protein IsdE This family of ABC substrate-binding proteins is observed primarily in close proximity with proteins localized to the cell wall and bearing the NEAT (NEAr Transporter, PF05031) heme-binding domain [1,2]. IsdE has been shown to bind heme and is involved in the process of scavenging heme for the purpose of obtaining iron [3,4]. TIGR03711.1 TIGR03711 acc_sec_asp3 67.25 67.25 135 equivalog Y Y N accessory Sec system protein Asp3 asp3 GO:0006886 18621893 1239 Bacillota phylum 2705 JCVI accessory Sec system protein Asp3 accessory Sec system protein Asp3 This protein is designated Asp3 because, along with SecY2, SecA2, and other proteins it is part of the accessory Sec system. The system is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus. This protein family is assigned to transport rather than glycosylation function, but the specific molecular role is unknown. TIGR03712.1 TIGR03712 acc_sec_asp2 210.75 210.75 511 equivalog Y Y N accessory Sec system protein Asp2 asp2 GO:0006886 18621893 1239 Bacillota phylum 3577 JCVI accessory Sec system protein Asp2 accessory Sec system protein Asp2 This protein is designated Asp2 because, along with SecY2, SecA2, and other proteins it is part of the accessory secretory protein system. The system is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus. This protein family is assigned to transport rather than glycosylation function, but the specific molecular role is unknown. TIGR03729.1 TIGR03729 acc_ester 148.25 148.25 239 subfamily Y N N putative phosphoesterase 1239 Bacillota phylum 3792 JCVI putative phosphoesterase putative phosphoesterase Members of this protein family belong to the larger family PF00149 (calcineurin-like phosphoesterase), a family largely defined by small motifs of metal-chelating residues. The subfamily in this model shows a good but imperfect co-occurrence in species with domain TIGR03715 that defines a novel class of signal peptide typical of the accessory secretory system. TIGR03811.1 TIGR03811 tyr_de_CO2_Ent 905.3 905.3 608 equivalog Y Y N tyrosine decarboxylase tdc 4.1.1.25 GO:0004837,GO:0006572 12089039 1239 Bacillota phylum 851 JCVI tyrosine decarboxylase tyrosine decarboxylase This model represents tyrosine decarboxylases in the family of the Enterococcus faecalis enzyme Tdc. These enzymes often are encoded next to tyrosine/tyramine antiporter, together comprising a system in which tyrosine decarboxylation can protect against exposure to acid conditions. This clade differs from the archaeal tyrosine decarboxylases associated with methanofuran biosynthesis. TIGR04002.1 TIGR04002 TIGR04002 120 120 151 hypoth_equivalog Y Y N TIGR04002 family protein 1239 Bacillota phylum 504 JCVI TIGR04002 family protein TIGR04002 family protein TIGR04002 family proteins, a division within DUF1393 ( PF07155), occur strictly as part of a tandem gene pair with an uncharacterized radical SAM protein. TIGR04067.1 TIGR04067 oc_CLOSPO_01332 45 45 59 equivalog Y Y N Apre_1838 family putative sactipeptide bacteriocin GO:0030152 21478363 1239 Bacillota phylum 47 JCVI putative bacteriocin precursor, CLOSPO_01332 family Apre_1838 family putative sactipeptide bacteriocin Members of this protein family are Cys-rich putative bacteriocin precursor peptides found in a few strains of Clostridium and Anaerococcus. This family is related to the family of CLI_3235 (TIGR04065). Members of both families are found next to radical SAM protein/SPASM enzymes related to the sulfur-to-alpha-carbon (sacti)peptide maturase RumMC involved in ruminococcin C biosynthesis. TIGR04069.1 TIGR04069 ocin_ACP_rel 70 70 77 hypoth_equivalog Y Y N peptide maturation system acyl carrier-related protein GO:0030152 21478363 1239 Bacillota phylum 134 JCVI peptide maturation system acyl carrier-related protein peptide maturation system acyl carrier-related protein Both PSI-BLAST and large numbers of noise-level HMM hits show a relationship between this family and the phosphopantetheine attachment site domain modeled by PF00550. That domain includes acyl carrier proteins (ACP) and features an essentially invariant serine residue that is the attachment site for the phosphopantetheine prosthetic group. In this family, the corresponding residue is not Ser and is not conserved. Members are found in genomic contexts associated with a small Cys-rich peptide and a radical SAM protein we predict modifies the peptide. TIGR04087.1 TIGR04087 YqxM_for_SipW 80 80 186 equivalog Y Y N amyloid fiber anchoring/assembly protein TapA tapA GO:0097311 21477127 1239 Bacillota phylum 1119 JCVI YqxM protein amyloid fiber anchoring/assembly protein TapA Members of this protein, including the partially characterized YqxM of Bacillus subtilis, are always found adjacent to a variant form, SipW, of signal peptidase, and are targets for this signal peptide, as is the biofilm protein constituent TasA. The function may always be associated with biofilm formation. In one instance, this protein is fused with the SipW signal peptidase. TIGR04090.1 TIGR04090 exp_by_SipW_IV 60 55 241 subfamily Y Y N BsaA family SipW-dependent biofilm matrix protein 32737303 1239 Bacillota phylum 956 JCVI alternate signal-mediated exported protein, CPF_0494 family BsaA family SipW-dependent biofilm matrix protein Members of this largely Clostridial protein family contain the cognate signal peptide domain, modeled by TIGR04088, for the variant SipW form of the signal peptidase I family, which in Bacillus subtilis was to secrete proteins found as the biofilm matrix material. Members of this Clostridial family include CPF_0494, adjacent to SipW homolog CPF_0493, and CPE0515 from Clostridium perfringens, recently shown to be a matrix protein of extracellular polymeric substance and given the name BsaA. TIGR04094.1 TIGR04094 adjacent_YSIRK 200 200 383 equivalog Y Y N YSIRK-targeted surface antigen transcriptional regulator 31641092 1239 Bacillota phylum 1075 JCVI YSIRK-targeted surface antigen transcriptional regulator YSIRK-targeted surface antigen transcriptional regulator Bacteria whose genomes encode only one protein with the YSIRK variant form of signal peptide (TIGR01168) were examined for conserved genes near that one tagged protein. This protein is found adjacent to at various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK proteins include Streptococcal protective antigen (see PMID:19865839) and proteins with the Rib/alpha/Esp surface antigen repeat (see TIGR02331). The last quarter of this protein has an AraC family helix-turn-helix (HTH)transcriptional regulator domain. Members of this family include SezV, described as a positive regulator for the FSIRK-containing M-like virulence factor SzM of Streptococcus equi. TIGR04118.1 TIGR04118 Cxxx_AC3_0185 35 35 46 subfamily Y Y N AC3_0185 family rSAM-modified Cys-rich RiPP 21478363 1239 Bacillota phylum 18 JCVI modification target Cys-rich peptide, AC3_0185 family AC3_0185 family rSAM-modified Cys-rich RiPP Radical SAM enzyme family TIGR04115 is paired with a number of short peptides with multiple tandem repeats of Cys-Xaa-Xaa-Xaa (see TIGR04114). This family represent a peptide family with a TIGR04114-like region, although the repeat region is relatively short in this group. TIGR04145.2 TIGR04145 Firmicu_CTERM 50 50 191 equivalog_domain Y Y N Firmicu-CTERM sorting domain-containing protein 22037399 1239 Bacillota phylum 757 JCVI Firmicu-CTERM domain Firmicu-CTERM protein-sorting domain This C-terminal domain is found only in the Firmicutes, where its presence is sporadically distributed. Proteins with this domain are most conserved in the C-terminal region, where the pattern of ending with a transmembrane domain resembles both the LPXTG (sortase target) and PEP-CTERM (exosortase target) domain structures. However, members occur exclusively in the presence of an exosortase-like protein XrtG (TIGR03110), a putative glycosyltransferase (TIGR03111), and a 6-pyruvoyl tetrahydropterin synthase-related protein (TIGR03112). TIGR04224.1 TIGR04224 ser_adhes_Nterm 25 25 50 equivalog_domain Y Y N accessory Sec-dependent serine-rich glycoprotein adhesin 11854202,20562303,21531800,26833566 1239 Bacillota phylum 4684 JCVI serine-rich repeat adhesion glycoprotein serine-rich repeat glycoprotein adhesin accessory Sec interaction domain This HMM describes a definitive conserved N-terminal domain shared by Streptococcal serine-rich adhesion glycoproteins. These highly repetitive proteins may exceed 4000 amino acids in length, consisting largely of long regions in which every second amino acid is Ser. Members of this family, if sequenced completely and assigned the correct start site, begin with a KxYKxGKxW motif region (see TIGR03715) and end with an LPXTG motif region (see TIGR01167). Members are exported by the accessory secretory system (SecA2 and SecY2). They are highly variable among the Streptococci and may help determine host ranges for pathogenesis. TIGR04383.1 TIGR04383 acidic_w_LPXTA 50 50 320 equivalog Y Y N processed acidic surface protein GO:0009297,GO:0010339 1239 Bacillota phylum 1741 JCVI processed acidic surface protein processed acidic surface protein Members of this family are acidic surface proteins with an N-terminal signal peptide and a variant C-terminal sortase recognition sequence, LPXTA rather than LPXTG. The N-terminal region past the signal peptide is repeated a second or third time in many members of this family. Members occur in Firmicutes, encoded next to a dedicated sortase related to SrtC that assembles pilins, suggesting that this protein serves a structural rather than enzymatic role. Processing by the neighboring sortase may result in polymerization as well as surface attachment. NF003635.0 PRK05270 PRK05270.2-5 905 905 499 subfamily Y Y N UDP-glucose--hexose-1-phosphate uridylyltransferase 2.7.7.12 1243 Leuconostoc genus 111 NCBI Protein Cluster (PRK) galactose-1-phosphate uridylyltransferase UDP-glucose--hexose-1-phosphate uridylyltransferase NF007323.0 PRK09814 PRK09814.1-2 529 529 327 equivalog Y N N beta-1,6-galactofuranosyltransferase 1243 Leuconostoc genus 135 NCBI Protein Cluster (PRK) beta-1,6-galactofuranosyltransferase beta-1,6-galactofuranosyltransferase NF035936.1 agg_sub_LPXTH 100 100 281 equivalog Y Y N serine-rich aggregation substance UasX uasX 25013139 1243 Leuconostoc genus 520 NCBIFAM serine-rich aggregation substance UasX Members of this protein family are repetitive, serine-rich surface proteins of the Firmicutes, found primarily in the genus Leuconostoc. The variant form of sortase signal, LPXTH, is replaced by LPXTG in members from some lineages, such as Weissella oryzae, and therefore recognizable. Some members of this family have the KxYKxGKxW type signal peptide as seen in the glycoprotein adhesin GspB, a substrate of the accessory Sec system for secretion. WOSG25_050600 from Weissella oryzae SG25 is identified in a publication as an unnamed aggregation substance, a conclusion supported by the sorting signals and composition reported here. We assign the gene symbol uasX (unnamed aggregation substance X) based on our evaluation of the family. NF037262.5 PF18522.6 DUF5620 25 25 120 domain Y Y N DUF5620 domain-containing protein 27298375 1263 Ruminococcus genus 326 EBI-EMBL Domain of unknown function (DUF5620) DUF5620 domain This is a domain of unknown function predicted to be a carbohydrate binding module [1]. [1]. 27298375. Complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition. Venditto I, Luis AS, Rydahl M, Schuckel J, Fernandes VO, Vidal-Melgosa S, Bule P, Goyal A, Pires VM, Dourado CG, Ferreira LM, Coutinho PM, Henrissat B, Knox JP, Basle A, Najmudin S, Gilbert HJ, Willats WG, Fontes CM;. Proc Natl Acad Sci U S A. 2016;113:7136-7141. (from Pfam) NF037764.5 PF18244.6 CttA_N 25 25 71 domain Y Y N cellulose-binding protein CttA-related protein 23580648 1263 Ruminococcus genus 105 EBI-EMBL Cellulose-binding protein CttA N-terminal domain cellulose-binding protein CttA N-terminal-like domain This is the N-terminal domain of cellulose-binding protein CttA present in Ruminococcus flavefaciens. CttA mediates attachment of the bacterial substrate via two carbohydrate-binding modules. The domain is known as the X-module and lacks a true hydrophobic core. Unlike the X-modules in other types of CohE-XDoc complexes it does not contribute to the binding surface. This X-module appears to serve as an extended spacer, which separates the cellulose-binding modules at the N terminus of CttA and the bacterial cell wall. The domain does not share structural similarity with other known X-modules from cellulolytic bacteria but does show similarity to G5-1 module of StrH from S. pneumoniae [1]. [1]. 23580648. Atypical cohesin-dockerin complex responsible for cell surface attachment of cellulosomal components: binding fidelity, promiscuity, and structural buttresses. Salama-Alber O, Jobby MK, Chitayat S, Smith SP, White BA, Shimon LJ, Lamed R, Frolow F, Bayer EA;. J Biol Chem. 2013;288:16827-16838. (from Pfam) NF047212.1 PF22579.1 Cbm74 27 27 64 domain Y N N Carbohydrate binding module-like 27298375 1263 Ruminococcus genus 76 EBI-EMBL Carbohydrate binding module-like Carbohydrate binding module-like This entry represents a Carbohydrate binding module from Ruminococcus flavefaciens (Cbm74-rfgh5) and similar sequences predominantly from clostridia. This domain adopts a beta- sandwich fold typical of carbohydrate binding modules (CBMs) [1]. Paper describing PDB structure 5aos. [1]. 27298375. Complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition. Venditto I, Luis AS, Rydahl M, Schuckel J, Fernandes VO, Vidal-Melgosa S, Bule P, Goyal A, Pires VM, Dourado CG, Ferreira LM, Coutinho PM, Henrissat B, Knox JP, Basle A, Najmudin S, Gilbert HJ, Willats WG, Fontes CM;. Proc Natl Acad Sci U S A. 2016;113:7136-7141. (from Pfam) NF005847.0 PRK07764 PRK07764.2-3 1670 1670 1078 equivalog Y Y N DNA polymerase III subunit gamma and tau 2.7.7.7 1268 Micrococcaceae family 27 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunit gamma and tau NF045769.1 TransActPmfR 800 800 470 equivalog_domain Y Y N transcciptional activator PmfR pmfR GO:0003700,GO:0019608,GO:0045893 15838033,17293530 1268 Micrococcaceae family 21 NCBIFAM transcciptional activator PmfR NF046106.1 ResusProRpf 180 180 258 equivalog Y Y N resuscitation-promoting factor Rpf rpf GO:0016787 12410820,16359320,20016836 1268 Micrococcaceae family 171 NCBIFAM resuscitation-promoting factor Rpf NF000063.1 Fos_BSH_Sepi 300 300 142 exception Y Y Y FosB family fosfomycin resistance bacillithiol transferase 1279 Staphylococcus genus 47 NCBIFAM FosB family fosfomycin resistance thiol transferase FosB family fosfomycin resistance bacillithiol transferase NF000186.1 BlaI_of_MRSA 250 250 126 exception Y Y Y penicillinase repressor BlaI blaI GO:0045892 1279 Staphylococcus genus 142 NCBIFAM penicillinase repressor BlaI penicillinase repressor BlaI NF000257.1 MupA 1900 1900 1024 exception Y Y Y mupirocin-resistant isoleucine--tRNA ligase MupA mupA 6.1.1.5 1279 Staphylococcus genus 49 NCBIFAM mupirocin-resistant isoleucine--tRNA ligase MupA mupirocin-resistant isoleucine--tRNA ligase MupA NF000340.1 fusB 375 375 213 exception Y Y Y FusB family fusidic acid resistance EF-G-binding protein 1279 Staphylococcus genus 8 NCBIFAM fusidic acid resistance protein FusB FusB family fusidic acid resistance EF-G-binding protein NF000407.1 MECC_PBP 1500 1500 665 exception Y Y Y PBP2a family beta-lactam-resistant peptidoglycan transpeptidase MecC mecC GO:0008658,GO:0046677 1279 Staphylococcus genus 5 NCBIFAM PBP2a family beta-lactam-resistant peptidoglycan transpeptidase MecC PBP2a family beta-lactam-resistant peptidoglycan transpeptidase MecC NF000460.1 fusD 450 450 213 exception Y Y Y FusD family fusidic acid resistance EF-G-binding protein 1279 Staphylococcus genus 17 NCBIFAM FusD family fusidic acid resistance EF-G-binding protein FusD family fusidic acid resistance EF-G-binding protein NF000503.1 fusF 435 400 214 exception Y Y Y fusidic acid resistance EF-G-binding protein FusF fusF 1279 Staphylococcus genus 20 NCBIFAM fusF: fusidic acid resistance EF-G-binding protein FusF fusidic acid resistance EF-G-binding protein FusF NF002583.0 PRK02234 PRK02234.1-4 330 330 208 equivalog Y Y N Holliday junction resolvase RecU recU 3.1.21.10 23356868 1279 Staphylococcus genus 416 NCBI Protein Cluster (PRK) Holliday junction-specific endonuclease Holliday junction resolvase RecU NF002642.0 PRK02315 PRK02315.1-3 383 383 239 equivalog Y Y N adaptor protein MecA mecA 1279 Staphylococcus genus 447 NCBI Protein Cluster (PRK) adaptor protein adaptor protein MecA NF003647.0 PRK05286 PRK05286.1-5 619 619 354 equivalog Y Y N quinone-dependent dihydroorotate dehydrogenase 1.3.5.2 1279 Staphylococcus genus 687 NCBI Protein Cluster (PRK) dihydroorotate dehydrogenase 2 quinone-dependent dihydroorotate dehydrogenase NF004753.0 PRK06080 PRK06080.1-5 555 555 312 equivalog Y Y N 1,4-dihydroxy-2-naphthoate polyprenyltransferase 2.5.1.74 1279 Staphylococcus genus 612 NCBI Protein Cluster (PRK) 1,4-dihydroxy-2-naphthoate octaprenyltransferase 1,4-dihydroxy-2-naphthoate polyprenyltransferase NF005106.0 PRK06545 PRK06545.1-4 569 569 363 equivalog Y Y N prephenate dehydrogenase 1.3.1.12 1279 Staphylococcus genus 960 NCBI Protein Cluster (PRK) prephenate dehydrogenase prephenate dehydrogenase NF006360.0 PRK08581 PRK08581.1-2 605 605 709 equivalog Y Y N amidase domain-containing protein 1279 Staphylococcus genus 1421 NCBI Protein Cluster (PRK) N-acetylmuramoyl-L-alanine amidase amidase domain-containing protein NF009127.0 PRK12480 PRK12480.1 579 579 330 equivalog Y Y N D-lactate dehydrogenase 1.1.1.28 1279 Staphylococcus genus 530 NCBI Protein Cluster (PRK) D-lactate dehydrogenase D-lactate dehydrogenase NF009237.0 PRK12587 PRK12587.1 158 158 118 equivalog Y Y N Na+/H+ antiporter subunit G1 1279 Staphylococcus genus 296 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit G Na+/H+ antiporter subunit G1 NF009291.0 PRK12651 PRK12651.1-1 228 228 159 equivalog Y Y N Na+/H+ antiporter subunit E 1279 Staphylococcus genus 371 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit E Na+/H+ antiporter subunit E NF010078.0 PRK13562 PRK13562.1 96 96 84 equivalog Y Y N ACT domain-containing protein 1279 Staphylococcus genus 149 NCBI Protein Cluster (PRK) acetolactate synthase 1 regulatory subunit ACT domain-containing protein NF010123.0 PRK13600 PRK13600.1 104 104 84 equivalog Y N N putative ribosomal protein L7Ae-like 1279 Staphylococcus genus 306 NCBI Protein Cluster (PRK) putative ribosomal protein L7Ae-like putative ribosomal protein L7Ae-like NF010166.0 PRK13646 PRK13646.1 458 458 286 equivalog Y Y N energy-coupling factor transporter ATPase 3.6.3.- 1279 Staphylococcus genus 629 NCBI Protein Cluster (PRK) cobalt transporter ATP-binding subunit energy-coupling factor transporter ATPase NF010195.0 PRK13673 PRK13673.1-2 189 189 129 equivalog Y N N hypothetical protein 1279 Staphylococcus genus 285 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010212.0 PRK13676 PRK13676.1-5 177 177 114 equivalog Y Y N YlbF/YmcA family competence regulator 1279 Staphylococcus genus 208 NCBI Protein Cluster (PRK) hypothetical protein YlbF/YmcA family competence regulator NF010343.0 PRK13770 PRK13770.1 647 647 416 equivalog Y Y N histidinol dehydrogenase hisD 1.1.1.23 1279 Staphylococcus genus 858 NCBI Protein Cluster (PRK) histidinol dehydrogenase histidinol dehydrogenase Catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis NF010585.0 PRK13978 PRK13978.1 365 365 228 equivalog Y Y N ribose 5-phosphate isomerase A 1279 Staphylococcus genus 504 NCBI Protein Cluster (PRK) ribose-5-phosphate isomerase A ribose 5-phosphate isomerase A Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway NF010604.0 PRK14000 PRK14000.1 342 342 185 equivalog Y Y N K(+)-transporting ATPase subunit C 1279 Staphylococcus genus 31 NCBI Protein Cluster (PRK) potassium-transporting ATPase subunit C K(+)-transporting ATPase subunit C Component of the high-affinity ATP-driven potassium transport (or KDP)system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions; the C subunit may be involved in assembly of the KDP complex NF010609.0 PRK14010 PRK14010.1 1323 1323 673 equivalog Y Y N K(+)-transporting ATPase subunit B 7.2.2.6 1279 Staphylococcus genus 157 NCBI Protein Cluster (PRK) potassium-transporting ATPase subunit B K(+)-transporting ATPase subunit B Component of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions NF010671.0 PRK14068 PRK14068.1 95 95 76 equivalog Y Y N exodeoxyribonuclease VII small subunit 1279 Staphylococcus genus 253 NCBI Protein Cluster (PRK) exodeoxyribonuclease VII small subunit exodeoxyribonuclease VII small subunit Catalyzes the bidirectional exonucleolytic cleavage of DNA NF010797.0 PRK14201 PRK14201.1 119 119 121 equivalog Y Y N fluoride efflux transporter CrcB crcB 1279 Staphylococcus genus 510 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter CrcB NF011189.0 PRK14595 PRK14595.1 232 232 162 equivalog Y Y N peptide deformylase 3.5.1.88 15382235 1279 Staphylococcus genus 429 NCBI Protein Cluster (PRK) peptide deformylase peptide deformylase Cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins NF011336.0 PRK14752 PRK14752.1-1 65 65 25 equivalog Y Y N delta-lysin family phenol-soluble modulin 1279 Staphylococcus genus 10 NCBI Protein Cluster (PRK) delta-hemolysin delta-lysin family phenol-soluble modulin NF011338.0 PRK14752 PRK14752.1-4 68 68 26 equivalog Y Y N delta-lysin family phenol-soluble modulin 1279 Staphylococcus genus 30 NCBI Protein Cluster (PRK) delta-hemolysin delta-lysin family phenol-soluble modulin NF014293.5 PF02216.21 B 27 27 53 domain Y Y N B domain-containing protein GO:0019865 1390743 1279 Staphylococcus genus 4099 EBI-EMBL B domain B domain This family contains the B domain of Staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G. [1]. 1390743. Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures. Gouda H, Torigoe H, Saito A, Sato M, Arata Y, Shimada I;. Biochemistry 1992;31:9665-9672. (from Pfam) NF016186.5 PF04276.17 DUF443 26.2 26.2 202 subfamily Y Y N DUF443 family protein 1279 Staphylococcus genus 6857 EBI-EMBL Protein of unknown function (DUF443) DUF443 family protein Family of uncharacterised proteins. (from Pfam) NF016396.5 PF04507.17 DUF576 27 27 225 domain Y Y N Csa1 family protein 23895222 1279 Staphylococcus genus 13576 EBI-EMBL Csa1 family Csa1 family protein This family contains several uncharacterised staphylococcal proteins. These proteins have been called conserved staphylococcal antigens (Csa) [1]. [1]. 23895222. Mining the bacterial unknown proteome: identification and characterization of a novel family of highly conserved protective antigens in Staphylococcus aureus. Schluepen C, Malito E, Marongiu A, Schirle M, McWhinnie E, Lo Surdo P, Biancucci M, Falugi F, Nardi-Dei V, Marchi S, Fontana MR, Lombardi B, De Falco MG, Rinaudo CD, Spraggon G, Nissum M, Bagnoli F, Grandi G, Bottomley MJ, Liberatori S;. Biochem J. 2013;455:273-284. (from Pfam) NF017210.5 PF05372.16 Delta_lysin 25 25 25 PfamEq Y Y N delta-lysin family phenol-soluble modulin GO:0005576,GO:0019836 12206677 1279 Staphylococcus genus 104 EBI-EMBL Delta lysin family delta-lysin family phenol-soluble modulin Delta-lysin is a 26 amino acid, hemolytic peptide toxin secreted by Staphylococcus aureus. It is thought that delta-toxin forms an amphipathic helix upon binding to lipid bilayers [1]. The precise mode of action of delta-lysis is unclear. [1]. 12206677. Mechanism and kinetics of delta-lysin interaction with phospholipid vesicles. Pokorny A, Birkbeck TH, Almeida PF;. Biochemistry 2002;41:11044-11056. (from Pfam). Members of this family are produced with retention of the N-formyl-methionine at the N-terminus. NF017308.5 PF05480.16 PSMbeta 25 25 43 subfamily Y Y N beta-class phenol-soluble modulin 27525453,3134553,8975897 1279 Staphylococcus genus 984 EBI-EMBL Phenol-soluble modulin beta protein beta-class phenol-soluble modulin This family consists of several different short Staphylococcal proteins known as the phenol-soluble modulin beta proteins. The family contains SLUSH A, B and C proteins as well as haemolysin and gonococcal growth inhibitor. Some strains of the coagulase-negative Staphylococcus lugdunensis produce a synergistic hemolytic activity (SLUSH), phenotypically similar to the delta-hemolysin of S. aureus [1]. Gonococcal growth inhibitor from Staphylococcus act on the cytoplasmic membrane of the gonococcal cell causing cytoplasmic leakage and, eventually, death [2]. [1]. 8975897. Synergistic hemolytic activity of Staphylococcus lugdunensis is mediated by three peptides encoded by a non-agr genetic locus. Donvito B, Etienne J, Denoroy L, Greenland T, Benito Y, Vandenesch F;. Infect Immun 1997;65:95-100. [2]. 3134553. Site of action of a gonococcal growth inhibitor produced by Staphylococcus haemolyticus. Frenette M, Beaudet R, Bisaillon JG, Portelance V;. J Med Microbiol 1988;26:199-204. Paper describing PDB structure 5kgz. [3]. 27525453. Solution Structures of Phenol-Soluble Modulins alpha1, alpha3, and beta2, Virulence Factors from Staphylococcus aureus. Towle KM, Lohans CT, Miskolzie M, Acedo JZ, van Belkum MJ, Vederas JC;. Biochemistry. 2016;55:4798-4806. (from Pfam) NF017887.5 PF06116.17 RinB 27 27 51 domain Y N N Transcriptional activator RinB GO:0006355 8432703 1279 Staphylococcus genus 2191 EBI-EMBL Transcriptional activator RinB Transcriptional activator RinB This family consists of several Staphylococcus aureus bacteriophage RinB proteins and related sequences from their host. The int gene of staphylococcal bacteriophage phi 11 is the only viral gene responsible for the integrative recombination of phi 11. rinA and rinB, are both required to activate expression of the int gene [1]. [1]. 8432703. Cloning, sequencing, and genetic characterization of regulatory genes, rinA and rinB, required for the activation of staphylococcal phage phi 11 int expression. Ye ZH, Lee CY;. J Bacteriol 1993;175:1095-1102. (from Pfam) NF018019.5 PF06260.17 DUF1024 27 27 82 subfamily Y Y N DUF1024 family protein 1279 Staphylococcus genus 2363 EBI-EMBL Protein of unknown function (DUF1024) DUF1024 family protein This family consists of several hypothetical Staphylococcus aureus and Staphylococcus aureus phage phi proteins. The function of this family is unknown. (from Pfam) NF018263.5 PF06531.16 DUF1108 25 25 84 subfamily Y Y N DUF1108 family protein 1279 Staphylococcus genus 1647 EBI-EMBL Protein of unknown function (DUF1108) DUF1108 family protein This family consists of several bacterial proteins from Staphylococcus aureus as well as a number of phage proteins. The function of this family is unknown. (from Pfam) NF018593.5 PF06900.16 DUF1270 27 27 53 subfamily Y Y N DUF1270 family protein 1279 Staphylococcus genus 875 EBI-EMBL Protein of unknown function (DUF1270) DUF1270 family protein This family consists of several hypothetical Staphylococcus aureus and phage proteins of 53 residues in length. The function of this family is unknown. (from Pfam) NF018793.5 PF07129.16 DUF1381 25 25 44 domain Y Y N DUF1381 domain-containing protein 1279 Staphylococcus genus 2558 EBI-EMBL Protein of unknown function (DUF1381) Protein of unknown function (DUF1381) This family consists of several hypothetical Staphylococcus aureus and Staphylococcus aureus bacteriophage proteins of around 65 residues in length. The function of this family is unknown. (from Pfam) NF018990.5 PF07342.16 DUF1474 25 25 97 subfamily Y Y N DUF1474 family protein 1279 Staphylococcus genus 1272 EBI-EMBL Protein of unknown function (DUF1474) DUF1474 family protein This family consists of several bacterial proteins of around 100 residues in length. Members of this family seem to be found exclusively in Staphylococcus aureus. The function of this family is unknown. (from Pfam) NF019082.5 PF07438.16 DUF1514 25 25 62 domain Y Y N DUF1514 family protein 21348639 1279 Staphylococcus genus 705 EBI-EMBL Protein of unknown function (DUF1514) DUF1514 family protein This family consists of several Staphylococcus aureus and related bacteriophage proteins of around 65 residues in length. The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids [1]. [1]. 21348639. Ab Initio Modeling Led Annotation Suggests Nucleic Acid Binding Function for Many DUFs. Rigden DJ;. OMICS 2011;0:0-0. (from Pfam) NF019388.5 PF07768.16 PVL_ORF50 27 27 116 subfamily Y Y N SA1788 family PVL leukocidin-associated protein 10524952,12044378 1279 Staphylococcus genus 2933 EBI-EMBL PVL ORF-50-like family SA1788 family PVL leukocidin-associated protein Members of this family may appear in staphylococcal genomes in prophage regions that also encode virulence factors such as Panton-Valentine leukocidin (PVL). NF020591.5 PF09022.15 Staphostatin_A 24.1 24.1 105 subfamily Y Y N staphostatin A 14621990 1279 Staphylococcus genus 400 EBI-EMBL Staphostatin A staphostatin A The staphostatin A polypeptide chain folds into a slightly deformed, eight-stranded beta-barrel, with strands beta-4 through beta-8 forming an antiparallel sheet while the N-terminus forms a a psi-loop motif. Members of this family constitute a class of cysteine protease inhibitors distinct in the fold and the mechanism of action from any known inhibitors of these enzymes [1]. [1]. 14621990. A novel class of cysteine protease inhibitors: solution structure of staphostatin A from Staphylococcus aureus. Dubin G, Krajewski M, Popowicz G, Stec-Niemczyk J, Bochtler M, Potempa J, Dubin A, Holak TA;. Biochemistry. 2003;42:13449-13456. (from Pfam) NF022121.5 PF10655.14 DUF2482 25 25 97 subfamily Y Y N DUF2482 family protein 1279 Staphylococcus genus 663 EBI-EMBL Hypothetical protein of unknown function (DUF2482) DUF2482 family protein All the members of this very small, very short family are derived from bacteriophages, of the SA bacteriophages 11, Mu50B, system, and from the Staphylococcal_phi-Mu50B-like_prophages subsystem. All members are hypothetical proteins. (from Pfam) NF022614.5 PF11166.13 DUF2951 26.7 26.7 98 subfamily Y Y N DUF2951 family protein 1279 Staphylococcus genus 987 EBI-EMBL Protein of unknown function (DUF2951) DUF2951 family protein This family of proteins has no known function. It has a highly conserved sequence. (from Pfam) NF023052.5 PF11621.13 Sbi-IV 25 25 69 domain Y Y N C3-binding domain-containing protein 18550524 1279 Staphylococcus genus 833 EBI-EMBL C3 binding domain 4 of IgG-bind protein SBI C3 binding domain 4 of IgG-bind protein SBI This family of proteins represents Sbi domain IV which binds the central complement protein C3. Sbi-IV interacts with Sbi-III to induce a consumption of complement via alternative pathway activation [1]. When not interacting with Sbi-III, Sbi-IV inhibits the alternative pathway without complement consumption. The structure of Sbi-IV consists of a three-helix bundle fold [1]. [1]. 18550524. Structure-function analysis of the C3 binding region of Staphylococcus aureus immune subversion protein Sbi. Upadhyay A, Burman JD, Clark EA, Leung E, Isenman DE, van den Elsen JM, Bagby S;. J Biol Chem. 2008;283:22113-22120. (from Pfam) NF027553.5 PF16228.10 DUF4887 30.2 30.2 176 PfamAutoEq Y Y N DUF4887 domain-containing protein 1279 Staphylococcus genus 858 EBI-EMBL Domain of unknown function (DUF4887) Domain of unknown function (DUF4887) This family consists of uncharacterised proteins around 210 residues in length and is mainly found in various Staphylococcus species. The function of this family is unknown. (from Pfam) NF027874.5 PF16560.10 SAPI 25 25 213 domain Y N N Putative mobile pathogenicity island 17369699,20634809 1279 Staphylococcus genus 1241 EBI-EMBL Putative mobile pathogenicity island Putative mobile pathogenicity island SAPI is a family of putative Gram-positive mobile pathogenicity island proteins. SAPIs are responsible for many superantigen-related diseases in humans as they carry two or more superantigens [1,2]. [1]. 17369699. The SaPIs: mobile pathogenicity islands of Staphylococcus. Novick RP, Subedi A;. Chem Immunol Allergy. 2007;93:42-57. [2]. 20634809. The phage-related chromosomal islands of Gram-positive bacteria. Novick RP, Christie GE, Penades JR;. Nat Rev Microbiol. 2010;8:541-551. (from Pfam) NF028192.5 PF16882.10 DUF5079 27 27 241 subfamily Y Y N DUF5079 family protein 1279 Staphylococcus genus 1911 EBI-EMBL Domain of unknown function (DUF5079) DUF5079 family protein This protein is believed to be involved in the type VII secretion system. (from Pfam) NF028193.5 PF16883.10 DUF5080 27 27 204 subfamily Y Y N DUF5080 family protein 1279 Staphylococcus genus 798 EBI-EMBL Domain of unknown function (DUF5080) DUF5080 family protein This protein is believed to be involved in the type VII secretion system. (from Pfam) NF028200.5 PF16890.10 DUF5083 27 27 157 PfamAutoEq Y Y N DUF5083 family protein 1279 Staphylococcus genus 164 EBI-EMBL Domain of unknown function (DUF5083) DUF5083 family protein This protein is believed to be involved in the type VII secretion system. (from Pfam) NF028204.5 PF16894.10 DUF5084 27 27 130 PfamAutoEq Y Y N DUF5084 family protein 1279 Staphylococcus genus 205 EBI-EMBL Domain of unknown function (DUF5084) DUF5084 family protein This protein is believed to be involved in the type VII secretion system. (from Pfam) NF033108.1 sensor_BlaR1 1200 1200 585 exception Y Y Y beta-lactam sensor/signal transducer BlaR1 blaR1 1279 Staphylococcus genus 686 NCBIFAM beta-lactam sensor/signal transducer BlaR1 beta-lactam sensor/signal transducer BlaR1 NF033109.1 sensor_MecR1 1200 1200 585 exception Y Y Y beta-lactam sensor/signal transducer MecR1 mecR1 GO:0008658 1279 Staphylococcus genus 98 NCBIFAM beta-lactam sensor/signal transducer MecR1 beta-lactam sensor/signal transducer MecR1 Three proteins of the Mec locus for methicillin resistance are the methicillin-insensitive transpeptidase MecA, the repressor MecI, and this protein, called MecR1, which is a beta-lactam sensor and signal transducer. MecR1 and BlaR1 are full-length homologs of each other and of additional proteins that tend be found in the context of a BlaI-like penicillinase repressor and a beta-lactamase. This model hits only MecR1 itself. NF033386.1 blaARL 620 620 282 exception Y Y Y ARL family class A beta-lactamase blaARL 3.5.2.6 GO:0008800 28497118 1279 Staphylococcus genus 16 NCBIFAM ARL family class A beta-lactamase ARL family class A beta-lactamase BlaARL, discovered in Staphylococcus arlettae, joins blaZ as a penicillin-hydrolyzing beta-lactamase in the genus Staphylococcus. NF033392.1 PSM_delta 37.5 37.5 23 equivalog Y Y N PSM-delta family phenol-soluble modulin 1279 Staphylococcus genus 6 NCBIFAM PSM-delta family phenol-soluble modulin PSM-delta family phenol-soluble modulin Members of this family are phenol-soluble modulins (short peptides, usually cytolysins) with an intact N-formyl-methionine at the N-terminus. NF033427.2 PSM_alpha_Shaem 33 30 20 equivalog Y Y N alpha family phenol-soluble modulin 28596942 1279 Staphylococcus genus 5 NCBIFAM alpha family phenol-soluble modulin alpha family phenol-soluble modulin This family is based on an alpha family Staphylococcus haemolyticus phenol-soluble modulin, somewhat similar to delta-lysin. NF033428.5 PSM_epsilo 33 33 21 equivalog Y Y N epsilon family phenol-soluble modulin 24372362 1279 Staphylococcus genus 35 NCBIFAM epsilon family phenol-soluble modulin epsilon family phenol-soluble modulin Members of this family epsilon-family phenol-soluble modulins. Species with members include Staphylococcus epidermidis, Staphylococcus capitis, Staphylococcus lugdunensis, Staphylococcus pseudintermedius, and Staphylococcus schleiferi. NF033583.1 staphy_B_SbnC 700 700 584 exception Y Y N staphyloferrin B biosynthesis protein SbnC sbnC 1279 Staphylococcus genus 690 NCBIFAM staphyloferrin B biosynthesis protein SbnC staphyloferrin B biosynthesis protein SbnC SbnC, related to siderophore biosynthesis protein IucA and IucC, is encoded in Staphylococcus aureus in the sbnABCDEFGHI locus responsible for the biosynthesis of staphyloferrin B, a carboxylate-type siderophore. SbnC is found in many species of Staphylococcus. NF033586.1 staphy_B_SbnF 900 900 577 exception Y Y N staphyloferrin B biosynthesis protein SbnF sbnF 29483190 1279 Staphylococcus genus 755 NCBIFAM staphyloferrin B biosynthesis protein SbnF staphyloferrin B biosynthesis protein SbnF NF033589.0 staphy_B_SbnI 350 350 254 equivalog Y Y N bifunctional transcriptional regulator/O-phospho-L-serine synthase SbnI sbnI 26534960,29483190 1279 Staphylococcus genus 294 NCBIFAM bifunctional transcriptional regulator/O-phospho-L-serine synthase SbnI bifunctional transcriptional regulator/O-phospho-L-serine synthase SbnI SbnI is a bifunctional protein involved in staphyloferrin B (staphylobactin) biosynthesis in Staphylococcus aureus and other members of the genus. It is a bifunctional protein. The N-terminal region is heme-binding, and loses the ability to bind DNA when heme is bound. Under low iron conditions, the biosynthesis operon for staphyloferrin B, a carboxylate-type siderophore, is derepressed. The C-terminal domain is a kinase that acts on free serine, producing O-phospho-L-serine, which is used as one of the precursors of staphyloferrin B. NF033598.2 elast_bind_EbpS 300 300 498 equivalog Y Y N elastin-binding protein EbpS ebpS 11684686,24787448,8663124 1279 Staphylococcus genus 1559 NCBIFAM elastin-binding protein EbpS elastin-binding protein EbpS The elastin-binding protein EbpS is an adhesin described in Staphylococcus aureus, with orthologs found in many additional staphylococcal species. EbpS is a membrane protein that lacks an N-terminal signal peptide region, has extensive regions low-complexity sequence rich in Asn and Gln, and has a C-terminal LysM domain. NF033599.1 His_racem_CntK 300 300 271 equivalog Y Y N histidine racemase CntK cntK 27230378 1279 Staphylococcus genus 583 NCBIFAM histidine racemase CntK histidine racemase CntK CntK (cobalt and nickel transport system protein K) is a histidine racemase that performs the first step in the biosynthesis of staphylopine, a metallophore involved in the import of multiple divalent cations. It was first characterized in Staphylococcus aureus. NF033600.0 staphylopine_DH 675 675 424 equivalog Y Y N staphylopine biosynthesis dehydrogenase cntM 27230378 1279 Staphylococcus genus 798 NCBIFAM staphylopine biosynthesis dehydrogenase staphylopine biosynthesis dehydrogenase NF033601.2 Sta_opine_CntL 350 350 255 equivalog Y Y N staphylopine biosynthesis enzyme CntL cntL 27230378 1279 Staphylococcus genus 557 NCBIFAM staphylopine biosynthesis enzyme CntL staphylopine biosynthesis enzyme CntL CntL (cobalt and nickel transporter L) is an enzyme involved in biosynthesis of staphylopine, a metallophore involved in the import of zinc, cobalt, nickel, and other divalent cations. CntL transfers aminobutyrate from S-adenoyslmethionine, and is sometimes misannotated as a SAM-dependent methyltransferase. The staphylopine biosynthesis pathway was first characterized in Staphylococcus aureus. NF033869.1 viru_reg_Rsp 400 400 701 equivalog Y Y N AraC family transcriptional regulator Rsp rsp GO:0003700,GO:0006355,GO:0043565 26712209,30028663 1279 Staphylococcus genus 1617 NCBIFAM AraC family transcriptional regulator Rsp AraC family transcriptional regulator Rsp Rsp (repressor of surface proteins), as described in Staphylococcus aureus, is a large protein with an AraC-like helix-turn-helix DNA-binding domain. Regulatory targets include the accessory gene regulator (agr) operon, which in turn regulates a large number of virulence factors. NF037543.5 PF17412.7 VraX 25 25 55 PfamEq Y Y N C1q-binding complement inhibitor VraX vraX 26251622,26322035 1279 Staphylococcus genus 231 EBI-EMBL Family of unknown function C1q-binding complement inhibitor VraX This domain family is found in VraX proteins from Staphylococcus aureus. The vraX gene belongs to the vra operon together with the vraA gene encoding for a long chain fatty acid-CoA ligase, which is up-regulated in the VISA (vancomycin-intermediate S. aureus) [1]. The gene product, a 55-amino acids protein,is upregulated in the stress response to cell wall-active antibiotics and other surface-interactive molecules. VraX harbors a putative phosphorylation site, and could therefore be involved in regulatory processes within the cell. However, no exact function has been demonstrated [2]. [1]. 26322035. Quantitative proteomic view associated with resistance to clinically important antibiotics in Gram-positive bacteria: a systematic review. Lee CR, Lee JH, Park KS, Jeong BC, Lee SH;. Front Microbiol. 2015;6:828. [2]. 26251622. Impact of space flight on bacterial virulence and antibiotic susceptibility. Taylor PW;. Infect Drug Resist. 2015;8:249-262. (from Pfam) NF038207.1 glyco_res_GraF 34 34 44 equivalog Y Y N glycopeptide resistance-associated protein GraF graF 16048954,23554199 1279 Staphylococcus genus 229 NCBIFAM glycopeptide resistance-associated protein GraF GraF was discovered as a small stress protein expressed at higher levels in glycopeptide (vancomycin, teicoplanin)-intermediate strains of Staphylococcus aureus. Overexperssion leads to a thicker cell wall, and reduced sensitivities to glycopeptides and oxacillin. NF039681.4 PF19693.4 PSMdelta 25 25 22 domain Y N N Phenol-soluble modulin delta protein 15272403 1279 Staphylococcus genus 25 EBI-EMBL Phenol-soluble modulin delta protein Phenol-soluble modulin delta protein This entry represents the phenol-soluble modulin delta peptide found in staphylococcal species. [1]. 15272403. Activity of Staphylococcus epidermidis phenol-soluble modulin peptides expressed in Staphylococcus carnosus. Otto M, O'Mahoney DS, Guina T, Klebanoff SJ;. J Infect Dis. 2004;190:748-755. (from Pfam) NF040679.1 halocin_of_epi 200 200 243 equivalog Y Y N halocin C8 precursor-like protein 18658263 1279 Staphylococcus genus 128 NCBIFAM halocin C8 precursor-like protein Members of this family are bacterial (mostly staphylococcal) homologs of the archaeal bacteriocin halocin C8 precursor. Members average about 245 amino acids in length, with the 76 amino acid Cys-rich mature peptide region at the C-terminus. Cutoff scores are set fairly high because this HMM is designed to identify full-length members of the family such as WP_002493350.1 from Staphylococcus epidermidis. NF040844.1 Lac_Quin_Ox_NO 915 915 489 exception Y Y N L-lactate dehydrogenase (quinone) lqo 1.1.5.- 22919585,26851155 1279 Staphylococcus genus 829 NCBIFAM L-lactate dehydrogenase (quinone), SACOL2623 family Members of this family, found primarily in the genus Streptococcus, were shown to be L-lactate dehydrogenase (quinone) (Lqo) although they have generally been misannotated as malate dehydrogenase (quinone). Staphylococcus can survive nitrous oxide exposure from host defense through a response in which L-lactate is excreted in large amounts. Lqo acts in L-lactate consumption after its reuptake. NF040846.1 SAS049_fam 55 55 47 equivalog Y Y N SAS049 family protein 23554199,34061833 1279 Staphylococcus genus 174 NCBIFAM SAS049 family protein This family of small proteins, about 59 amino acids in length, includes SAS049 from Staphylococcus aureus, SE1307 from Staphylococcus epidermidis, and closely related proteins from other staphylococcal species. The N-terminal region appears highly similar to Rv0909 from Mycobacterium tuberculosis, which appears to be the antitoxin member of a novel class of type 2 toxin-antitoxin system (see PF14013). NF040879.1 SAR1012_fam 40 40 36 equivalog Y Y N SAR1012 family small protein 23554199,34061833 1279 Staphylococcus genus 109 NCBIFAM SAR1012 family small protein This small protein of unknown function is encoded in multiple species of Staphylococcus. It has been demonstrated by mass spectroscopy to be expressed with an unmodified N-terminal fMet residue. NF041710.1 UDPacetylman_taseTarA 350 350 247 equivalog Y Y N N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase TarA tarA 2.4.1.187 GO:0019350,GO:0047244 18215769,21035733 1279 Staphylococcus genus 662 NCBIFAM N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase TarA NF041711.1 TagprimaseTarB 500 500 362 equivalog Y Y N teichoic acid glycerol-phosphate primase TarB tarB 2.7.8.44 GO:0019350,GO:0047355 18215769,21035733 1279 Staphylococcus genus 948 NCBIFAM teichoic acid glycerol-phosphate primase TarB NF041768.1 acyl_LnsB_CPBP 240 240 241 equivalog Y Y N CPBP family lipoprotein N-acylation protein LnsB lnsB 32723923 1279 Staphylococcus genus 611 NCBIFAM CPBP family lipoprotein N-acylation protein LnsB The founding member of this family, YP_501220.1 from Staphylococus aureus, was assigned a role in a two-protein system for the N-acylation of lipoproteins. It belongs to the CPBP family of Rce1-like glutamic-type intramembrane proteases, which includes the type II CAAX prenyl proteases in eukaryotes and the myxosortases in prokaryotes. However, the typical active site-containing motif, EExxxR, is disrupted in most members of this family, suggesting a loss of endopeptidase activity. The partner protein in this system, LnsA, belongs to the NlpC/P60 superfamily. NF041769.1 acyl_LnsA 225 225 183 equivalog Y Y N lipoprotein N-acylation protein LnsA lnsA 32723923 1279 Staphylococcus genus 454 NCBIFAM lipoprotein N-acylation protein LnsA NF041852.1 trans_reg_HypR 180 180 139 equivalog Y Y N redox-sensitive transcriptional regulator HypR hypR 29237286 1279 Staphylococcus genus 529 NCBIFAM redox-sensitive transcriptional regulator HypR NF046015.1 HisKinAgrCStaph 500 500 414 equivalog Y Y N quorum-sensing sensor histidine kinase AgrC agrC 2.7.13.3 16622233,24858185,9197262,9632266 1279 Staphylococcus genus 2284 NCBIFAM quorum-sensing sensor histidine kinase AgrC NF046766.1 PF22538.1 HexPS-like 28.9 28.9 106 domain Y N N Hexaprenyl diphosphate synthase, small subunit 21068379,27457559 1279 Staphylococcus genus 258 EBI-EMBL Hexaprenyl diphosphate synthase, small subunit Hexaprenyl diphosphate synthase, small subunit This entry represents a group of bacterial sequences, including the small subunit of the Hexaprenyl diphosphate synthase from Micrococcus luteus (HexPS or HexA), a trans-prenyltransferase that catalyses consecutive head-to-tail condensations of three molecules of isopentenyl diphosphates on a farnesyl diphosphate to form an hexaprenyl diphosphate. HexPS is directly involved in the control of the product chain length. It is composed of mostly antiparallel alpha-helices joined by connecting loops [1]. Paper describing PDB structure 3aqb. [1]. 21068379. Crystal structure of heterodimeric hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 reveals that the small subunit is directly involved in the product chain length regulation. Sasaki D, Fujihashi M, Okuyama N, Kobayashi Y, Noike M, Koyama T, Miki K;. J Biol Chem. 2011;286:3729-3740. Paper describing PDB structure 5h9d. [2]. 27457559. Structure, Function, and Inhibition of Staphylococcus aureus Heptaprenyl Diphosphate Synthase. Desai J, Liu YL, Wei H, Liu W, Ko TP, Guo RT, Oldfield E;. ChemMedChem. 2016;11:1915-1923. (from Pfam) NF047349.1 4PPT_AusB 225 225 205 equivalog Y Y N aureusimine biosynthesis 4'-phosphopantetheinyl transferase AusB ausB 2.7.8.- GO:0016780 23302043 1279 Staphylococcus genus 326 NCBIFAM aureusimine biosynthesis 4'-phosphopantetheinyl transferase AusB NF047350.1 aureusi_NRPS 2500 2500 2373 equivalog Y Y N aureusimine non-ribosomal peptide synthetase AusA ausA 23302043 1279 Staphylococcus genus 2258 NCBIFAM aureusimine non-ribosomal peptide synthetase AusA Aureusimines, named for their production by Staphylococcus aureus, are cyclic dipeptide pyrazinone natural products, produced by the non-ribosomal peptide synthetase (NRPS) AusA and the 4'-phosphopantetheinyl transferase AusB. Aureusimines are suggested to contribute to the virulence of Staphylococcus aureus. NF047351.1 lipase_YSIRK_Sa 650 650 704 exception Y Y N YSIRK-targeted triacylglycerol lipase lip 3.1.1.3 GO:0005509,GO:0016298 17582438,38750133,9654065 1279 Staphylococcus genus 3815 NCBIFAM YSIRK-targeted triacylglycerol lipase Members of this staphylococcal lipase family have an N-terminal YSIRK-type signal peptide that is known for targeting sortase-dependent (LPXTG motif-containing) cell wall proteins to the cross-wall of growing and dividing cells. However, YSIRK also occurs on proteins that associate with the cell surface through other means. The YSIRK region is followed by a long, variable length low-complexity region rich in Ser, Thr, Asn, Asp, Glu, and Gln, followed by the lipase domain. Genes for member of this family in Staphylococcus aureus may be given as lip1 (e.g. YP_501455.1) and lip2 (YP_498890.1), or gehA and gehB. Members of this family in Staphylococcus aureus are considered virulence factors. NF047365.1 TscA 90 90 63 equivalog Y Y N type II toxin-antitoxin system antitoxin TscA tscA GO:0110001 31375497 1279 Staphylococcus genus 476 NCBIFAM type II toxin-antitoxin system antitoxin TscA NF047366.1 TscT 100 100 100 equivalog Y Y N type II toxin-antitoxin system toxin TscT tscT GO:0090729,GO:0110001 31375497 1279 Staphylococcus genus 1020 NCBIFAM type II toxin-antitoxin system toxin TscT NF047369.1 antitoxin_TsaA 100 100 84 equivalog Y Y N type II toxin-antitoxin system antitoxin TsaA tsaA GO:0110001 31375497 1279 Staphylococcus genus 229 NCBIFAM type II toxin-antitoxin system antitoxin TsaA NF047370.1 toxin_TsaT 80 80 60 equivalog Y Y N type II toxin-antitoxin system toxin TsaT tsaT GO:0090729,GO:0110001 31375497 1279 Staphylococcus genus 179 NCBIFAM type II toxin-antitoxin system toxin TsaT NF047418.1 teichoic_AuxB 300 300 345 equivalog Y Y N lipoteichoic acid stability factor AuxB auxB 33503451 1279 Staphylococcus genus 1002 NCBIFAM lipoteichoic acid stability factor AuxB AuxB, an apparent membrane protein found in methicillin-resistant Staphylococcus aureus (MRSA), contributes to lipoteichoic acid (LTA) stability and therefore to a beta-lactam resistance phenotype that depends primarily on the cell wall biosynthesis enzyme PBP2a encoded by mecA. NF047427.1 phage_activ_RinB 25 25 39 equivalog Y Y N transcriptional activator RinB rinB 31402174,8432703 1279 Staphylococcus genus 2299 NCBIFAM phage transcriptional activator RinB NF047455.1 TF_Staph_AryK 850 850 759 equivalog Y Y N transcriptional regulator AryK aryK 24512075 1279 Staphylococcus genus 995 NCBIFAM transcriptional regulator AryK AryK is a AraC/XylS family transcriptional regulator in the genus Streptococcus. In S. aureus, AryK affects virulance factor gene expression and toxin production. Orthologs in other staphylococcal species may be quite difference in sequence, and their role is not well characterized. NF047536.1 Cu_chaper_CsoZ 77 77 66 equivalog Y Y N putative copper chaperone CsoZ csoZ 21812885 1279 Staphylococcus genus 357 NCBIFAM putative copper chaperone CsoZ NF047564.1 PSM_export_PmtD 220 220 242 equivalog Y Y N phenol-soluble modulin export ABC transporter permease subunit PmtD pmtD 23396209 1279 Staphylococcus genus 656 NCBIFAM phenol-soluble modulin export ABC transporter permease subunit PmtD NF047566.1 SE1626_fam 70 70 55 equivalog Y Y N SE1626 family protein 1279 Staphylococcus genus 271 NCBIFAM SE1626 family protein Members of this family average about 59 amino acids in length, are restricted to the genus Staphylococcus, and are encoded close to the pmtABCD genes that encode an export system for phenol-soluble modulins. The function is unknown. Similar proteins are found in the genus Mammaliicoccus, scoring between the trusted and noise cutoffs of this model. NF047567.1 SAOUHSC_02157 45 45 31 equivalog Y Y N Trp-rich small protein 1279 Staphylococcus genus 110 NCBIFAM Trp-rich small protein, SAOUHSC_02157 family Members of this family are restricted to the genus Staphylococcus and usually are encoded near the pmtABCD genes for the subunits of an ABC transporter that exports phenol-soluble modulins. Peptides in this family average just 32 amino acids in length, and generally hydrophobic, but typically contain four Trp residues, an unusually large number for such a small protein. The function is unknown. NF047572.1 lant_immun_BsaG 75 75 229 subfamily Y Y N BsaG family lantibiotic immunity ABC transporter permease subunit 20023032 1279 Staphylococcus genus 165 NCBIFAM BsaG family lantibiotic immunity ABC transporter permease subunit Bsa (bacteriocin of S. aureus) is a lantibiotic related to epidermin. BsaG is an apparent immunity protein to Bsa and probably to other lantibiotics closely related to Bsa. NF047573.1 opine_perm_CntC 440 440 271 exception Y Y N staphylopine uptake ABC transporter permease subunit CntC cntC opp1C 23279021,29431891 1279 Staphylococcus genus 973 NCBIFAM staphylopine uptake ABC transporter permease subunit CntC Staphylopine is an opine class metallophore, similar to pseudopaline, yersinopine, and the plant metallophore nicotianamine. It can chelate metals such as zinc, copper, nickel, and cobalt after export by an MFS transporter, and then be reimported with its bound metal by the ABC transporter CntABCDF. This family consists of permease subunits closely related to CntC of Staphylococcus aureus. NF047575.1 opine_bind_CntA 800 800 535 exception Y Y N staphylopine-dependent metal ABC transporter substrate-binding lipoprotein cntA 1279 Staphylococcus genus 1389 NCBIFAM staphylopine-dependent metal ABC transporter substrate-binding lipoprotein CntA from Staphylococcus aureus, the founding member of this family, binds the holo-staphylopine, that is, the metallophore with a chelated metal. The tailoring of staphylopine-like metallophores likely differs some among the species in which the CntABCDE ABC transporter is present. Metals that can chelated and then imported include zinc, nickel, and copper. Members of this family belong to a broader family (see TIGR02294) that also includes NikA from Escherichia coli. NF047576.1 opine_ATP_CntF 385 385 264 equivalog Y Y N staphylopine uptake ABC transporter ATP-binding protein CntF cntF 27230378,29089427 1279 Staphylococcus genus 960 NCBIFAM staphylopine uptake ABC transporter ATP-binding protein CntF NF047694.1 TnucaseNucIStaph 250 250 175 equivalog Y Y N thermonuclease NucI nucI 3.1.31.1 GO:0003676,GO:0016894 1408843,8045422 1279 Staphylococcus genus 617 NCBIFAM thermonuclease NucI NF047829.1 epilancin_ElxI1 45 45 72 equivalog Y Y N epilancin biosynthesis-related protein ElxI1 elxI1 21802007 1279 Staphylococcus genus 246 NCBIFAM epilancin biosynthesis-related protein ElxI1 TIGR00941.1 TIGR00941 2a6301s03 161.2 161.2 104 subfamily Y N N multicomponent Na+:H+ antiporter, MnhC subunit mnhC GO:0051139,GO:0098662,GO:1902600 1279 Staphylococcus genus 162 JCVI multicomponent Na+:H+ antiporter, MnhC subunit multicomponent Na+:H+ antiporter, MnhC subunit TIGR01889.1 TIGR01889 Staph_reg_Sar 62.6 62.6 109 paralog_domain Y N N staphylococcal accessory regulator family GO:0006355 1279 Staphylococcus genus 3114 JCVI staphylococcal accessory regulator family staphylococcal accessory regulator family This HMM represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by Pfam HMM PF01047. TIGR03068.1 TIGR03068 srtB_sig_NPQTN 24.5 24.5 33 domain Y Y N NPQTN class sortase B protein-sorting domain-containing protein 14762051 1279 Staphylococcus genus 322 JCVI sortase B signal domain, NPQTN class NPQTN class sortase B protein-sorting domain This model represents one of the boutique (rare) sortase signals, recognized by sortase B (SrtB) rather than by the housekeeping-type SrtA class sortase. This sequence, beginning NPQTN, shows little similarity to several other SrtB substrates. TIGR03932.1 TIGR03932 PIA_icaD 69.05 69.05 88 equivalog Y Y N intracellular adhesion protein IcaD icaD GO:0000271,GO:0005886,GO:0008375 9660830 1279 Staphylococcus genus 260 JCVI intracellular adhesion protein D intracellular adhesion protein IcaD Members of this protein family are IcaD (intracellular adhesion protein D), which with catalytic subunit IcaA forms an N-acetylglucosaminyltransferase. In the absence of IcaC, this enzyme forms N-acetylglucosamine oligomers up to 20 in length. TIGR04263.1 TIGR04263 SasC_Mrp_aggreg 60 60 366 subfamily_domain Y Y N SasC/FmtB family protein GO:0098609 10896508,19851500 1279 Staphylococcus genus 6397 JCVI SasC/Mrp/FmtB intercellular aggregation domain SasC/FmtB intercellular aggregation domain This domain, about 375 amino acids long on average, occurs only in Staphylococcus and Streptococcus. It occurs as a non-repetitive N-terminal domain of LPXTG-anchored surface proteins, including SasC, Mrp, and FmtB. This region in SasC was shown to be involved in cell aggregation and biofilm formation, which may explain the methicillin resistance seen for Mrp and FmtB. TIGR04264.1 TIGR04264 hyperosmo_Ebh 250 250 2354 equivalog_domain Y Y N hyperosmolarity resistance protein Ebh ebh GO:0006972 18334223,18639517 1279 Staphylococcus genus 6337 JCVI hyperosmolarity resistance protein Ebh hyperosmolarity resistance protein Ebh Staphylococcal protein Ebh (extracellular matrix-binding protein homolog) is a giant protein, sometimes over 10,000 amino acids long as reported. This model describes a non-repetitive amino-terminal domain of about 2400 amino acids. NF000131.1 MATE_multi_MepA 850 850 451 equivalog Y Y Y multidrug efflux MATE transporter MepA mepA 15855508 1280 Staphylococcus aureus species 430 NCBIFAM multidrug efflux MATE transporter MepA multidrug efflux MATE transporter MepA MepA, a MATE family efflux transporter, was previously known as SvrA (staphylococcal virulence regulator A). MepA (multidrug export protein A), as described originally in Staphylococcus aureus, is a MATE transporter shown to be over-expressed after culturing in the presence of tigecycline, owing to mutation of its repressor MepR, and then to be one of several factors contributing to elevated tigecycline resistance. NF000535.3 MSCRAMM_SdrC 1700 1700 963 exception Y Y N MSCRAMM family adhesin SdrC sdrC GO:0007155 1280 Staphylococcus aureus species 2422 NCBIFAM MSCRAMM_SdrC: MSCRAMM family adhesin SdrC MSCRAMM family adhesin SdrC Features of this protein family include a YSIRK-type signal peptide at the N-terminus and a variable-length C-terminal region of Ser-Asp (SD) repeats followed by an LPXTG motif for surface immobilization by sortase. NF005157.0 PRK06635 PRK06635.2-1 832 832 401 equivalog Y Y N aspartate kinase 2.7.2.4 1280 Staphylococcus aureus species 443 NCBI Protein Cluster (PRK) aspartate kinase aspartate kinase NF006359.0 PRK08581 PRK08581.1-1 798 798 619 equivalog Y Y N amidase domain-containing protein 1280 Staphylococcus aureus species 454 NCBI Protein Cluster (PRK) N-acetylmuramoyl-L-alanine amidase amidase domain-containing protein NF009591.0 PRK13032 PRK13032.1 303 303 149 equivalog Y Y N chemotaxis-inhibiting protein CHIPS 14993252,16213522 1280 Staphylococcus aureus species 85 NCBI Protein Cluster (PRK) chemotaxis-inhibiting protein CHIPS chemotaxis-inhibiting protein CHIPS Specifically inhibits the activation of neutrophils and monocytes by binding to the formylated peptide receptor and the C5a receptor; blocks neutrophil migration towards the infection site and hinders the establishment of the initial defense against the infection NF009592.0 PRK13033 PRK13033.1 225 225 133 equivalog Y Y N FPRL1 inhibitory protein FLIPr 17114475,23740955 1280 Staphylococcus aureus species 175 NCBI Protein Cluster (PRK) formyl peptide receptor-like 1 inhibitory protein FPRL1 inhibitory protein FLIPr FPRL1 inhibitory protein (FLIPr); secreted protein that blocks the formyl peptide receptor-like 1 (FPRL1) found in neutrophils, monocytes, B cells, and NK cells; inhibits the binding of chemoattractants (such as formylated peptides) to FPRL1, which initiates the phagocyte mobilization towards the infection site. Some authors refer to the branch of the family that includes WP_000739558.1 as FLIPr-like rather than FLIPr, but it appears that no Staphylococcus aureus genome encodes both FLIPr and FLIPr-like. NF009593.0 PRK13035 PRK13035.1 284 284 234 equivalog Y Y N superantigen-like protein SSL5 10899837,11544350,11812213,12082105,12930353,15049778,15213171,16322743,17132726,17303163,17314375 1280 Staphylococcus aureus species 328 NCBI Protein Cluster (PRK) superantigen-like protein 5 superantigen-like protein SSL5 NF009594.0 PRK13036 PRK13036.1 369 369 227 equivalog Y Y N superantigen-like protein SSL11 10899837,11544350,11812213,12082105,12930353,15049778,15213171,16322743,17132726,17303163,17314375 1280 Staphylococcus aureus species 231 NCBI Protein Cluster (PRK) superantigen-like protein superantigen-like protein SSL11 NF009595.0 PRK13037 PRK13037.1 396 396 226 equivalog Y Y N superantigen-like protein SSL1 10899837,11544350,11812213,12082105,12930353,15049778,15213171,16322743,17132726,17303163,17314375 1280 Staphylococcus aureus species 280 NCBI Protein Cluster (PRK) superantigen-like protein superantigen-like protein SSL1 NF009596.0 PRK13038 PRK13038.1 405 405 227 equivalog Y Y N superantigen-like protein SSL10 10899837,11544350,11812213,12082105,12930353,15049778,15213171,16322743,17132726,17303163,17314375 1280 Staphylococcus aureus species 302 NCBI Protein Cluster (PRK) superantigen-like protein superantigen-like protein SSL10 NF009597.0 PRK13039 PRK13039.1 459 459 232 equivalog Y Y N superantigen-like protein SSL8 10899837,11544350,11812213,12082105,12930353,15049778,15213171,16322743,17132726,17303163,17314375 1280 Staphylococcus aureus species 220 NCBI Protein Cluster (PRK) superantigen-like protein superantigen-like protein SSL8 NF009598.0 PRK13040 PRK13040.1 423 423 231 equivalog Y Y N superantigen-like protein SSL6 10899837,11544350,11812213,12082105,12930353,15049778,15213171,16322743,17132726,17303163,17314375 1280 Staphylococcus aureus species 98 NCBI Protein Cluster (PRK) superantigen-like protein superantigen-like protein SSL6 NF009599.0 PRK13041 PRK13041.1 418 418 231 equivalog Y Y N superantigen-like protein SSL2 10899837,11544350,11812213,12082105,12930353,15049778,15213171,16322743,17132726,17303163,17314375 1280 Staphylococcus aureus species 269 NCBI Protein Cluster (PRK) superantigen-like protein superantigen-like protein SSL2 NF009600.0 PRK13042 PRK13042.1 485 485 291 equivalog Y Y N superantigen-like protein SSL4 10899837,11544350,11812213,12082105,12930353,15049778,15213171,16322743,17132726,17303163,17314375 1280 Staphylococcus aureus species 660 NCBI Protein Cluster (PRK) superantigen-like protein superantigen-like protein SSL4 NF009601.0 PRK13043 PRK13043.1 465 465 241 equivalog Y Y N superantigen-like protein SSL14 10899837,11544350,11812213,12082105,12930353,15049778,15213171,16322743,17132726,17303163,17314375 1280 Staphylococcus aureus species 304 NCBI Protein Cluster (PRK) superantigen-like protein superantigen-like protein SSL14 NF009837.0 PRK13312 PRK13312.1 215 215 107 equivalog Y Y N staphylobilin-forming heme oxygenase IsdG isdG 1.14.99.48 1280 Staphylococcus aureus species 97 NCBI Protein Cluster (PRK) heme-degrading monooxygenase IsdG staphylobilin-forming heme oxygenase IsdG NF009838.2 PRK13313 PRK13313.1 200 200 108 equivalog Y Y N staphylobilin-forming heme oxygenase IsdI isdI 1.14.99.48 1280 Staphylococcus aureus species 83 NCBI Protein Cluster (PRK) heme-degrading monooxygenase IsdI staphylobilin-forming heme oxygenase IsdI NF009873.0 PRK13335 PRK13335.1 537 537 356 equivalog Y Y N superantigen-like protein SSL3 10899837,11544350,11812213,12082105,12930353,15049778,15213171,16322743,17132726,17303163,17314375 1280 Staphylococcus aureus species 467 NCBI Protein Cluster (PRK) superantigen-like protein superantigen-like protein SSL3 NF009886.0 PRK13345 PRK13345.1 432 432 232 equivalog Y Y N superantigen-like protein SSL9 10899837,11544350,11812213,12082105,12930353,15049778,15213171,16322743,17132726,17303163,17314375 1280 Staphylococcus aureus species 285 NCBI Protein Cluster (PRK) superantigen-like protein superantigen-like protein SSL9 NF009887.0 PRK13346 PRK13346.1 313 313 231 equivalog Y Y N superantigen-like protein SSL7 10899837,11544350,11812213,12082105,12930353,15049778,15213171,16322743,17132726,17303163,17314375 1280 Staphylococcus aureus species 304 NCBI Protein Cluster (PRK) superantigen-like protein 7 superantigen-like protein SSL7 NF009889.0 PRK13349 PRK13349.1 428 428 241 equivalog Y Y N superantigen-like protein SSL13 10899837,11544350,11812213,12082105,12930353,15049778,15213171,16322743,17132726,17303163,17314375 1280 Staphylococcus aureus species 321 NCBI Protein Cluster (PRK) superantigen-like protein superantigen-like protein SSL13 NF009890.0 PRK13350 PRK13350.1 339 339 238 equivalog Y Y N superantigen-like protein SSL12 10899837,11544350,11812213,12082105,12930353,15049778,15213171,16322743,17132726,17303163,17314375 1280 Staphylococcus aureus species 331 NCBI Protein Cluster (PRK) superantigen-like protein superantigen-like protein SSL12 NF010602.0 PRK13998 PRK13998.1 378 378 186 equivalog Y Y N K(+)-transporting ATPase subunit C 1280 Staphylococcus aureus species 168 NCBI Protein Cluster (PRK) potassium-transporting ATPase subunit C K(+)-transporting ATPase subunit C Component of the high-affinity ATP-driven potassium transport (or KDP)system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions; the C subunit may be involved in assembly of the KDP complex NF012176.0 tet_MFS_38 925 925 450 exception Y Y Y tetracycline efflux MFS transporter Tet(38) tet(38) GO:0008493,GO:0015904 1280 Staphylococcus aureus species 260 NCBIFAM tetracycline efflux MFS transporter Tet(38) tetracycline efflux MFS transporter Tet(38) NF012181.0 MSCRAMM_SdrD 2500 2500 1379 exception Y Y N MSCRAMM family adhesin SdrD sdrD GO:0007155 26924733 1280 Staphylococcus aureus species 2521 NCBIFAM MSCRAMM family adhesin SdrD MSCRAMM family adhesin SdrD Features of this protein family include a YSIRK-type signal peptide at the N-terminus and a variable-length C-terminal region of Ser-Asp (SD) repeats followed by an LPXTG motif for surface immobilization by sortase. NF015339.5 PF03373.19 Octapeptide 17.5 3.9 8 repeat Y N N Octapeptide repeat GO:0019865 1280 Staphylococcus aureus species 2393 EBI-EMBL Octapeptide repeat Octapeptide repeat This octapeptide repeat is found in several bacterial proteins. The function of this repeat is unknown. (from Pfam) NF015598.5 PF03642.18 MAP 24.3 24.3 88 domain Y Y N MAP domain-containing protein 7545162 1280 Staphylococcus aureus species 2422 EBI-EMBL MAP domain MAP domain This presumed 110 amino acid residue domain is found in multiple copies in MAP (MHC class II analogue protein) Swiss:Q9Z4J2 [1]. The protein has been found in a wide range of extracellular matrix proteins [1]. [1]. 7545162. Staphylococcus aureus expresses a major histocompatibility complex class II analog. Jonsson K, McDevitt D, McGavin MH, Patti JM, Hook M;. J Biol Chem 1995;270:21457-21460. (from Pfam) NF015955.5 PF04022.17 Staphylcoagulse 19.7 19.7 27 repeat Y N N staphylocoagulase repeat-containing protein 1280 Staphylococcus aureus species 1642 EBI-EMBL Staphylocoagulase repeat staphylocoagulase repeat NF017956.5 PF06194.16 Phage_Orf51 27 27 80 subfamily Y Y N SAV1978 family virulence-associated passenger protein 17078814 1280 Staphylococcus aureus species 2493 EBI-EMBL Phage Conserved Open Reading Frame 51 SAV1978 family virulence-associated passenger protein Members of this family occur as phage-borne pathogenicity island proteins appearing in the genus Staphylococcus. A contribution to virulence was shown in a nematode infection model. NF020592.5 PF09023.15 Staphostatin_B 25 25 105 PfamEq Y Y N cysteine protease inhibitor staphostatin B 15644332 1280 Staphylococcus aureus species 158 EBI-EMBL Staphostatin B cysteine protease inhibitor staphostatin B Staphostatin B inhibits the cysteine protease Staphopain B, produced by Staphylococcus aureus, by blocking the active site of the enzyme. The domain adopts an eight-stranded mixed beta-barrel structure, with a deviation from the up-down topology of canonical beta-barrels in the amino-terminal part of the molecule [1]. [1]. 15644332. A comparison of staphostatin B with standard mechanism serine protease inhibitors. Filipek R, Potempa J, Bochtler M;. J Biol Chem. 2005;280:14669-14674. (from Pfam) NF020761.5 PF09199.15 SSL_OB 27 27 84 domain Y N N Staphylococcal superantigen-like OB-fold domain 12082105,15213171,17848512,17996251,18045383,20133685,21217642,22949551 1280 Staphylococcus aureus species 4264 EBI-EMBL Staphylococcal superantigen-like OB-fold domain Staphylococcal superantigen-like OB-fold domain This OB-fold domain folds into a five-stranded beta-barrel [1]. Members of this family are found in various staphylococcal toxins described as staphylococcal superantigen-like (SSL) proteins that are related to the staphylococcal enterotoxins (SEs) or superantigens. These SSL proteins of which 11 have so far been characterised have a typical SE tertiary structure consisting of a distinct oligonucleotide/oligosaccharide binding (OB-fold), this domain, linked to a beta-grasp domain, family Stap_Strp_tox_C, Pfam:PF02876. SSLs do not bind to T-cell receptors or major histocompatibility complex class II molecules and do not stimulate T cells. SSLs target components of innate immunity, such as complement, Fc receptors, and myeloid cells 2,3,4,5,6,7,8]. SSL protein 7 (SSL7) is the best characterised of the SSLs and binds complement factor C5 and IgA with high affinity and inhibits the end stage of complement activation and IgA binding to FcalphaR [8]. [1]. 12082105. The Three-dimensional structure of a superantigen-like protein, SET3, from a pathogenicity island of the Staphylococcus aureus genome. Arcus VL, Langley R, Proft T, Fraser JD, Baker EN;. J Biol Chem. 2002;277:32274-32281. [2]. 15213171. Structural relationships and cellular tropism of staphylococcal superantigen-like proteins. Al-Shangiti AM, Naylor CE, Nair SP, Briggs DC, Henderson B, Chain BM;. Infect Immun. 2004;72:4261-4270. [3]. 17848512. Structural basis for evasion of IgA immunity by Staphylococcus aureus revealed in the complex of SSL7 with Fc of human IgA1. Ramsland PA, Willoughby N, Trist HM, Farrugia W, Hogarth PM, Fraser JD, Wines BD;. Proc Natl Acad Sci U. TRUNCATED at 1650 bytes (from Pfam) NF022754.5 PF11310.13 DUF3113 25 25 60 subfamily Y Y N DUF3113 family protein 1280 Staphylococcus aureus species 643 EBI-EMBL Protein of unknown function (DUF3113) DUF3113 family protein This family of proteins has no known function. It has a highly conserved sequence. (from Pfam) NF022874.5 PF11434.13 CHIPS 25 25 91 PfamEq Y N N Chemotaxis-inhibiting protein CHIPS 16213522 1280 Staphylococcus aureus species 119 EBI-EMBL Chemotaxis-inhibiting protein CHIPS Chemotaxis-inhibiting protein CHIPS The chemotaxis inhibitory protein, CHIPS, is an excreted virulence factor which acts by binding to C5a and formylated peptide receptor (FPR), blocking phagocyte responses. A fragment of CHIPS, which contains residues 31-121 comprises of an alpha helix packed onto a four stranded anti-parallel beta-sheet. Most of the conserved residues of CHIPS are present in the alpha-helix [1]. [1]. 16213522. The structure of the C5a receptor-blocking domain of chemotaxis inhibitory protein of Staphylococcus aureus is related to a group of immune evasive molecules. Haas PJ, de Haas CJ, Poppelier MJ, van Kessel KP, van Strijp JA, Dijkstra K, Scheek RM, Fan H, Kruijtzer JA, Liskamp RM, Kemmink J;. J Mol Biol. 2005;353:859-872. (from Pfam) NF022980.5 PF11546.13 CompInhib_SCIN 23 23 114 domain Y Y N complement inhibitor SCIN family protein 17709514 1280 Staphylococcus aureus species 629 EBI-EMBL Staphylococcal complement inhibitor SCIN complement inhibitor SCIN family protein SCIN is released by Staphylococcus aureus to counteract the host immune defense. The protein binds to and inhibits C3 convertases on the bacterial surface, reducing phagocytosis and blocking downstream effector functions by C3b deposition on its surface [1]. An 18 residue stretch 31-48 is crucial for SCIN activity [1]. [1]. 17709514. Staphylococcal complement inhibitor: structure and active sites. Rooijakkers SH, Milder FJ, Bardoel BW, Ruyken M, van Strijp JA, Gros P;. J Immunol. 2007;179:2989-2998. (from Pfam) NF023620.5 PF12199.13 efb-c 27 27 65 domain Y Y N fibrinogen-binding protein GO:0001848,GO:0005615 17351618 1280 Staphylococcus aureus species 476 EBI-EMBL Extracellular fibrinogen binding protein C terminal fibrinogen-binding protein This domain family is found in bacteria, and is approximately 70 amino acids in length. There is a conserved VLK sequence motif. It is the C terminal domain of bacterial extracellular fibrinogen binding protein. It contains a helical motif involved in complement regulation. This motif binds to complement and changes its conformation to a form which cannot activate downstream components of the complement cascade. [1]. 17351618. A structural basis for complement inhibition by Staphylococcus aureus. Hammel M, Sfyroera G, Ricklin D, Magotti P, Lambris JD, Geisbrecht BV;. Nat Immunol. 2007;8:430-437. (from Pfam) NF026147.5 PF14797.11 SEEEED 28.7 28.7 113 domain Y Y N serine-rich SEEEED domain-containing protein 1280 Staphylococcus aureus species 1 EBI-EMBL Serine-rich region of AP3B1, clathrin-adaptor complex Serine-rich region of AP3B1, clathrin-adaptor complex This short low-complexity, highly serine-rich region lies on clathrin-adaptor complex 3 beta-1 subunit proteins, between family Adaptin_N, Pfam:PF01602 and a C-terminal domain, AP3B1_C,Pfam:PF14796. (from Pfam) NF027430.5 PF16104.10 FPRL1_inhibitor 27 27 105 domain Y N N Formyl peptide receptor-like 1 inhibitory protein 17114475 1280 Staphylococcus aureus species 236 EBI-EMBL Formyl peptide receptor-like 1 inhibitory protein Formyl peptide receptor-like 1 inhibitory protein This family consists of several formyl peptide receptor-like 1 inhibitory proteins from Staphylococcus aureus. These are secreted proteins that block the formyl peptide receptor-like 1 found in neutrophils, monocytes, B cells, and NK cells; and inhibit the binding of chemoattractants (such as formylated peptides) to FPRL1, which initiate phagocyte mobilization towards the infection site [1]. [1]. 17114475. A new staphylococcal anti-inflammatory protein that antagonizes the formyl peptide receptor-like 1. Prat C, Bestebroer J, de Haas CJ, van Strijp JA, van Kessel KP;. J Immunol. 2006 Dec 1;177(11):8017-26. (from Pfam) NF027554.5 PF16229.10 DUF4888 25 25 141 PfamAutoEq Y Y N DUF4888 domain-containing protein 1280 Staphylococcus aureus species 555 EBI-EMBL Domain of unknown function (DUF4888) Domain of unknown function (DUF4888) This family consists of uncharacterized proteins around 190 residues in length and is mainly found in various Staphylococcus species. The function of this family is unknown. (from Pfam) NF027578.5 PF16253.10 DUF4909 25 25 127 PfamAutoEq Y Y N DUF4909 domain-containing protein 22492855 1280 Staphylococcus aureus species 270 EBI-EMBL Domain of unknown function (DUF4909) Domain of unknown function (DUF4909) This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length. Several members are associated with vancomycin virulence in Staph. aureus in some way [1]. These proteins are all lipoproteins, carrying the characteristic prokaryotic membrane-attachment site at their N-termini. [1]. 22492855. Serine/threonine phosphatase Stp1 contributes to reduced susceptibility to vancomycin and virulence in Staphylococcus aureus. Cameron DR, Ward DV, Kostoulias X, Howden BP, Moellering RC Jr, Eliopoulos GM, Peleg AY;. J Infect Dis. 2012;205:1677-1687. (from Pfam) NF028032.5 PF16722.10 SAPIS-gp6 27.4 27.4 72 PfamEq Y Y N capsid morphogenesis B protein 21821042 1280 Staphylococcus aureus species 95 EBI-EMBL Pathogenicity island protein gp6 in Staphylococcus capsid morphogenesis B protein SAPIS-gp6 is a family of proteins produced from the pathogenicity island SAPI1 in pathogenic Staphylococcus aureus. This is a mobile genetic element that carries genes for several superantigen toxins. SAPIS-gp6 is a dimeric protein produced from the pathogenicity island with a helix-loop-helix motif similar to that of bacteriophage scaffolding proteins. It is thought to determine the size of the capsids of distribution of the SAPI1 genome as it acts as an internal scaffolding protein during capsid size determination [1]. [1]. 21821042. The Staphylococcus aureus pathogenicity island 1 protein gp6 functions as an internal scaffold during capsid size determination. Dearborn AD, Spilman MS, Damle PK, Chang JR, Monroe EB, Saad JS, Christie GE, Dokland T;. J Mol Biol. 2011;412:710-722. (from Pfam) NF028252.5 PF16942.10 CclA_1 25 25 103 subfamily Y Y N putative cyclic bacteriocin 1280 Staphylococcus aureus species 63 EBI-EMBL Putative cyclic bacteriocin putative cyclic bacteriocin This is a family of short proteins from Gram- putatively from the carnocylcin A family of bacteriocins. (from Pfam) NF028373.5 PF17063.10 PSMalpha 23 23 21 subfamily Y Y N alpha family phenol-soluble modulin 17994102 1280 Staphylococcus aureus species 89 EBI-EMBL Phenol-soluble modulin alpha peptide family alpha family phenol-soluble modulin This family includes various Phenol-soluble modulin proteins from S. Aureus. Psma4 is a methicillin-resistant Staphylococcus aureus (MRSA) protein that may recruit, activate and induce the lysis of human neutrophils. It stimulates the secretion of IL-8 and also has haemolytic activity during MRSA infection [1]. [1]. 17994102. Identification of novel cytolytic peptides as key virulence determinants for community-associated MRSA. Wang R, Braughton KR, Kretschmer D, Bach TH, Queck SY, Li M, Kennedy AD, Dorward DW, Klebanoff SJ, Peschel A, DeLeo FR, Otto M;. Nat Med. 2007;13:1510-1514. (from Pfam) NF033425.2 PSM_alpha_1_2 30 30 21 equivalog Y Y N alpha-1/alpha-2 family phenol-soluble modulin 1280 Staphylococcus aureus species 65 NCBIFAM alpha-1/alpha-2 family phenol-soluble modulin alpha-1/alpha-2 family phenol-soluble modulin Members of this family are extremely short proteins, about 21 amino acids long, that are known to retain an N-formyl-methionine (fMet) at the N-terminus. These proteins, phenol-soluble modulins of the alpha class, including alpha-1 and alpha-2 from Staphylococcus aureus, are exported by an ABC transporter, and affect the state of the host immune system in a number of ways. NF033426.1 PSM_alpha_3 33 33 22 equivalog Y Y N alpha-3 family phenol-soluble modulin 24008753 1280 Staphylococcus aureus species 20 NCBIFAM alpha-3 family phenol-soluble modulin alpha-3 family phenol-soluble modulin NF033609.2 MSCRAMM_ClfA 1150 1150 934 exception Y Y N MSCRAMM family adhesin clumping factor ClfA clfA GO:0007155 1280 Staphylococcus aureus species 4513 NCBIFAM MSCRAMM family adhesin clumping factor ClfA MSCRAMM family adhesin clumping factor ClfA Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif. NF033750.1 vWF_bind_Staph 700 700 509 exception Y Y N von Willebrand factor binding protein Vwb vwb 12101292,28182324 1280 Staphylococcus aureus species 658 NCBIFAM von Willebrand factor binding protein Vwb von Willebrand factor binding protein Vwb The von Willebrand factor binding protein Vwb, like its paralog staphylocoagulase, is a coagulase and a virulence factor. It induces clotting, not by being an enzyme, but by activating prothrombin to generate fibrin. NF033845.1 MSCRAMM_ClfB 999 999 871 exception Y Y N MSCRAMM family adhesin clumping factor ClfB clfB GO:0007155 21543319,22719251 1280 Staphylococcus aureus species 5304 NCBIFAM MSCRAMM family adhesin clumping factor ClfB MSCRAMM family adhesin clumping factor ClfB Clumping factor B is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif. NF035921.1 staph_coagu 400 400 520 equivalog Y Y N staphylocoagulase coa 22222316 1280 Staphylococcus aureus species 1493 NCBIFAM staphylocoagulase Staphylocoagulase, like its paralog von Willebrand factor binding protein Vwb, is a coagulase and a virulence factor. It induces clotting, not by being an enzyme, but by activating prothrombin to generate fibrin. Past residue 485, the protein consists of a variable number of 27 amino acid tandem repeats (see PF04022). This HMM omits coverage of a portion of the repetitive C-terminal region. Staphylocoagulase, like its paralog von Willebrand factor binding protein Vwb, is a coagulase and a virulence factor. It induces clotting, not by being an enzyme, but by activating host prothrombin to generate fibrin. NF040802.1 Fos_BSH_FosY 305 305 140 exception Y Y Y fosfomycin resistance bacillithiol transferase FosY fosY 35332834 1280 Staphylococcus aureus species 3 NCBIFAM fosfomycin resistance bacillithiol transferase FosY NF041467.1 caps_synth_Cap8I 770 770 463 equivalog Y Y N type 8 capsular polysaccharide synthesis protein Cap8I cap8I 15608208 1280 Staphylococcus aureus species 199 NCBIFAM type 8 capsular polysaccharide synthesis protein Cap8I NF041712.1 techglyph_taseTarF 550 550 388 equivalog Y Y N teichoic acid glycerol-phosphate transferase TarF tarF 2.7.8.45 GO:0019350 18215769,21035733 1280 Staphylococcus aureus species 344 NCBIFAM teichoic acid glycerol-phosphate transferase TarF NF041713.1 Tar_polymTarL 1000 1000 562 equivalog Y Y N teichoic acid ribitol-phosphate polymerase TarL tarL 2.7.8.14 GO:0019350,GO:0047355,GO:0047356 18215769,21035733 1280 Staphylococcus aureus species 1086 NCBIFAM teichoic acid ribitol-phosphate polymerase TarL NF044927.2 PF20861.2 Isd_H_B_linker 27 27 63 domain Y N N Iron-regulated surface determinant protein H/B, linker domain 23132864,24425866,26057669,29109153 1280 Staphylococcus aureus species 1849 EBI-EMBL Iron-regulated surface determinant protein H/B, linker domain Iron-regulated surface determinant protein H/B, linker domain The bacterial pathogen Staphylococcus aureus uses two closely related receptors located on its surface, IsdH and IsdB, to capture from haemoglobin (Hb) the iron it needs to grow. Both proteins show conserved near iron transporter (NEAT) domains (Pfam:PF05031) that function synergistically. These domains, essential for the arrest of iron, are appropriately positioned by an alpha-helical linker domain (this entry), which does not interact itself with the heme group. In IsdH, this linker domain forms a three-helix bundle structure that is essential for efficient heme capture [1-4]. Paper describing PDB structure 2lhr. [1]. 23132864. Staphylococcus aureus uses a novel multidomain receptor to break apart human hemoglobin and steal its heme. Spirig T, Malmirchegini GR, Zhang J, Robson SA, Sjodt M, Liu M, Krishna Kumar K, Dickson CF, Gell DA, Lei B, Loo JA, Clubb RT;. J Biol Chem. 2013;288:1065-1078. Paper describing PDB structure 4ij2. [2]. 24425866. Structure of the hemoglobin-IsdH complex reveals the molecular basis of iron capture by Staphylococcus aureus. Dickson CF, Kumar KK, Jacques DA, Malmirchegini GR, Spirig T, Mackay JP, Clubb RT, Guss JM, Gell DA;. J Biol Chem. 2014;289:6728-6738. Paper describing PDB structure 4xs0. [3]. 26057669. The structure of haemoglobin bound to the haemoglobin receptor IsdH from Staphylococcus aureus shows disruption of the native alpha-globin haem pocket. Dickson CF, Jacques DA, Clubb RT, Guss JM, Gell DA;. Acta Crystallogr D Biol Crystallogr. 2015;71:1295-1306. Paper describing PDB structure 5vmm. [4]. 29109153. Structure-function analyses reveal key features in Staphylococcus aureus IsdB-as. TRUNCATED at 1650 bytes (from Pfam) NF046255.1 PF22386.1 PPI 27 27 63 domain Y N N Protease propeptides/inhibitors 1280 Staphylococcus aureus species 161 EBI-EMBL Protease propeptides/inhibitors Protease propeptides/inhibitors This entry represents the propeptide domain found at the N-terminal of peptidases belonging to MEROPS family S8A, subtilisins. This propeptide is removed by proteolytic cleavage, which activates the enzyme. (from Pfam) NF046650.1 PF22377.1 TarS_C2 27 27 78 domain Y N N TarS C-terminal domain 2 27973583 1280 Staphylococcus aureus species 470 EBI-EMBL TarS C-terminal domain 2 TarS C-terminal domain 2 This entry represents the C-terminal domain 2 (C2) of TarS from Staphylococcus aureus [1], the enzyme responsible for polyribitol phosphate beta-O-GlcNAcylation of wall teichoic acid polymers [1], a process that has been shown to be specifically responsible for methicillin resistance. This domain is involved in formation of extensive trimerization interface [1]. [1]. 27973583. Structure and Mechanism of Staphylococcus aureus TarS, the Wall Teichoic Acid beta-glycosyltransferase Involved in Methicillin Resistance. Sobhanifar S, Worrall LJ, King DT, Wasney GA, Baumann L, Gale RT, Nosella M, Brown ED, Withers SG, Strynadka NC;. PLoS Pathog. 2016;12:e1006067. (from Pfam) TIGR00942.1 TIGR00942 2a6301s05 212.25 212.25 144 subfamily Y N N multicomponent Na+:H+ antiporter mnhC GO:0015297,GO:0016020,GO:1902600 1280 Staphylococcus aureus species 119 JCVI multicomponent Na+:H+ antiporter multicomponent Na+:H+ antiporter TIGR01742.1 TIGR01742 SA_tandem_lipo 160.45 160.45 255 subfamily Y Y N tandem-type lipoprotein 23895222,26083414 1280 Staphylococcus aureus species 10803 JCVI Staphylococcus tandem lipoproteins tandem-type lipoprotein Members of this family are predicted lipoproteins (mostly), found in Staphylococcus aureus in several different tandem clusters in pathogenicity islands. Members are also found, clustered, in Staphylococcus epidermidis. Nguyen, et al. (PMID:26083414) discuss a cluster, SAUSA300_0410 to SAUSA300_0419, and name the first of these lpl1. TIGR03657.1 TIGR03657 IsdB 1231.5 1231.5 644 equivalog Y Y N heme uptake protein IsdB isdB GO:0015232,GO:0015886,GO:0020037 17229211,18467329,18676371 1280 Staphylococcus aureus species 743 JCVI heme uptake protein IsdB heme uptake protein IsdB Isd proteins are iron-regulated surface proteins found in Bacillus, Staphylococcus and Listeria species and are responsible for heme scavenging from hemoproteins [1]. The IsdB protein is only observed in Staphylococcus and consists of an N-terminal hydrophobic signal sequence, a pair of tandem NEAT (NEAr Transporter, PF05031) domains which confers the ability to bind heme [2] and a C-terminal sortase processing signal which targets the protein to the cell wall. IsdB is believed to make a direct contact with methemoglobin facilitating transfer of heme to IsdB [3]. The heme is then transferred to other cell wall-bound NEAT domain proteins such as IsdA and IsdC. TIGR03658.1 TIGR03658 IsdH_HarA 1400.25 1400.25 895 equivalog Y Y N haptoglobin-binding heme uptake protein HarA harA GO:0020037 16762363,17041047,18676371 1280 Staphylococcus aureus species 801 JCVI haptoglobin-binding heme uptake protein HarA haptoglobin-binding heme uptake protein HarA HarA is a heme-binding NEAT-domain (NEAr Transporter, PF05031) protein which has been shown to bind to the haptoglobin-hemoglobin complex in order to extract heme from it. HarA has also been reported to bind hemoglobin directly [2]. HarA (also known as IsdH) contains three NEAT domains as well as a sortase A C-terminal signal for localization to the cell wall. The heme bound at the third of these NEAT domains has been shown to be transferred to the IsdA protein also localized at the cell wall, presumably through an additional specific protein-protein interaction [3]. Haptoglobin is a hemoglobin carrier protein involved in scavenging hemoglobin in the blood following red blood cell lysis and targetting it to the liver. NF021257.5 PF09724.14 Dcc1 22.9 22.9 319 domain Y Y N Dcc1 family protein GO:0007064,GO:0031390 11389843,12930902,15964801 1282 Staphylococcus epidermidis species 2 EBI-EMBL Sister chromatid cohesion protein Dcc1 Dcc1 family protein Sister chromatid cohesion protein Dcc1 is a component of the Ctf18-RFC complex. This complex is required for the efficient establishment of chromosome cohesion during S-phase and for loading the replication clamp Pol30/PCNA, which functions in DNA replication and repair [1,2]. Ctf18-RFC loads PCNA onto DNA in an ATP-dependent manner. It may also have PCNA-unloading activity [3]. [1]. 11389843. Identification of RFC(Ctf18p, Ctf8p, Dcc1p): an alternative RFC complex required for sister chromatid cohesion in S. cerevisiae. Mayer ML, Gygi SP, Aebersold R, Hieter P;. Mol Cell. 2001;7:959-970. [2]. 12930902. The alternative Ctf18-Dcc1-Ctf8-replication factor C complex required for sister chromatid cohesion loads proliferating cell nuclear antigen onto DNA. Bermudez VP, Maniwa Y, Tappin I, Ozato K, Yokomori K, Hurwitz J;. Proc Natl Acad Sci U S A. 2003;100:10237-10242. [3]. 15964801. Replication protein A-directed unloading of PCNA by the Ctf18 cohesion establishment complex. Bylund GO, Burgers PM;. Mol Cell Biol. 2005;25:5445-5455. (from Pfam) NF045479.1 FRAT_87_prot 50 50 86 subfamily Y Y N FRAT-87 protein 128827 Erysipelotrichaceae family 106 NCBIFAM FRAT-87 protein FRAT-87 is a rare protein family whose founding members were a Faecalibaculum rodentium Array of Tandem proteins, all six exactly 87 amino acids in length, aligning without gaps, but with pairwise identities as low as 46 percent. Similar sets of paralogs are found in other species such as Ileibacterium valens and Allobaculum mucilyticum. AlphaFold makes a high-confidence prediction with four anti-parallel alpha-helices (e.g. A0A1Q9YAZ8). The function is unknown. NF047272.1 PF22832.1 PsaO_TMD 27 27 91 domain Y N N PsaO transmembrane domain 36951548 1292 Staphylococcus warneri species 1 EBI-EMBL PsaO transmembrane domain PsaO transmembrane domain PsaO is one of the nine membrane-embedded subunits of photosystem I. This entry represents the transmembrane domain that was shown to consists of three transmembrane helices arranged in an L-shape [1]. [1]. 36951548. The photosystem I supercomplex from a primordial green alga Ostreococcus tauri harbors three light-harvesting complex trimers. Ishii A, Shan J, Sheng X, Kim E, Watanabe A, Yokono M, Noda C, Song C, Murata K, Liu Z, Minagawa J;. Elife. 2023;12:e84488. (from Pfam) TIGR03059.1 TIGR03059 psaOeuk 107.85 107.85 82 equivalog Y Y N photosystem I protein PsaO psaO 11801243,15169790 1292 Staphylococcus warneri species 1 JCVI photosystem I protein PsaO photosystem I protein PsaO Members of this family are the PsaO protein of photosystem I. This protein is found in chloroplasts but not in Cyanobacteria. NF022451.5 PF10998.13 DUF2838 25.2 25.2 111 domain Y Y N DUF2838 domain-containing protein 1293 Staphylococcus gallinarum species 1 EBI-EMBL Protein of unknown function (DUF2838) Protein of unknown function (DUF2838) This bacterial family of proteins has no known function. (from Pfam) NF003789.0 PRK05379 PRK05379.2-1 355 355 312 equivalog Y N N bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase 1298 Deinococcus genus 58 NCBI Protein Cluster (PRK) bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase NF008943.0 PRK12292 PRK12292.3-1 690 690 403 equivalog Y Y N ATP phosphoribosyltransferase regulatory subunit 1298 Deinococcus genus 24 NCBI Protein Cluster (PRK) ATP phosphoribosyltransferase regulatory subunit ATP phosphoribosyltransferase regulatory subunit NF009675.0 PRK13196 PRK13196.1 308 308 219 equivalog Y Y N pyroglutamyl-peptidase I 1298 Deinococcus genus 90 NCBI Protein Cluster (PRK) pyrrolidone-carboxylate peptidase pyroglutamyl-peptidase I NF010735.0 PRK14137 PRK14137.1 294 294 197 equivalog Y Y N recombination regulator RecX recX 1298 Deinococcus genus 10 NCBI Protein Cluster (PRK) recombination regulator RecX recombination regulator RecX Binds RecA and inhibits RecA-mediated DNA strand exchange and ATP hydrolysis and coprotease activities NF010941.0 PRK14361 PRK14361.1 272 272 194 equivalog Y N N Maf-like protein 1298 Deinococcus genus 100 NCBI Protein Cluster (PRK) Maf-like protein Maf-like protein NF011294.0 PRK14706 PRK14706.1 1284 1284 642 equivalog Y Y N 1,4-alpha-glucan branching enzyme 2.4.1.18 1298 Deinococcus genus 86 NCBI Protein Cluster (PRK) glycogen branching enzyme 1,4-alpha-glucan branching enzyme Catalyzes the transfer of a segment of a 1,4-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain NF041652.1 Nud_hyd_Dein 200 200 152 equivalog Y Y N Nudix hydrolase 3.6.1.69 GO:0016787,GO:0046872 23481913 1298 Deinococcus genus 86 NCBIFAM Nudix hydrolase NF041674.1 RNA-bind_Rsr 900 900 531 equivalog Y Y N RNA-binding protein Rsr rsr GO:0003723,GO:0046872 10766734,17392270 1298 Deinococcus genus 41 NCBIFAM RNA-binding protein Rsr NF000993.0 PRK00104 PRK00104.1-2 268 268 237 equivalog Y Y N segregation/condensation protein A 1300 Streptococcaceae family 1406 NCBI Protein Cluster (PRK) segregation and condensation protein A segregation/condensation protein A NF001315.0 PRK00258 PRK00258.2-4 413 413 284 equivalog Y Y N shikimate dehydrogenase 1.1.1.25 1300 Streptococcaceae family 1588 NCBI Protein Cluster (PRK) shikimate 5-dehydrogenase shikimate dehydrogenase NF002580.0 PRK02234 PRK02234.1-1 300 300 202 equivalog Y Y N Holliday junction resolvase RecU recU 3.1.21.10 1300 Streptococcaceae family 954 NCBI Protein Cluster (PRK) Holliday junction-specific endonuclease Holliday junction resolvase RecU NF002609.0 PRK02260 PRK02260.3-2 275 275 158 equivalog Y Y N S-ribosylhomocysteine lyase 4.4.1.21 1300 Streptococcaceae family 67 NCBI Protein Cluster (PRK) S-ribosylhomocysteinase S-ribosylhomocysteine lyase NF002685.0 PRK02436 PRK02436.1 178 178 245 equivalog Y Y N site-specific tyrosine recombinase XerD xerD 1300 Streptococcaceae family 1664 NCBI Protein Cluster (PRK) site-specific tyrosine recombinase XerD-like protein site-specific tyrosine recombinase XerD Site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation NF002687.0 PRK02463 PRK02463.1 425 425 307 equivalog Y Y N membrane protein insertase YidC yidC 1300 Streptococcaceae family 1315 NCBI Protein Cluster (PRK) OxaA-like protein precursor membrane protein insertase YidC NF003783.0 PRK05371 PRK05371.1-4 988 988 758 equivalog Y Y N Xaa-Pro dipeptidyl-peptidase 3.4.14.11 GO:0006508,GO:0008239 1300 Streptococcaceae family 3135 NCBI Protein Cluster (PRK) x-prolyl-dipeptidyl aminopeptidase Xaa-Pro dipeptidyl-peptidase NF004068.0 PRK05580 PRK05580.1-5 1249 1249 795 equivalog Y Y N primosomal protein N' 3.6.1.- GO:0003677,GO:0003678,GO:0005524,GO:0006260,GO:0032508 1300 Streptococcaceae family 2949 NCBI Protein Cluster (PRK) primosome assembly protein PriA primosomal protein N' NF004158.0 PRK05627 PRK05627.1-1 396 396 304 equivalog Y Y N bifunctional riboflavin kinase/FAD synthetase 2.7.1.26,2.7.7.2 GO:0003919 28790457 1300 Streptococcaceae family 1836 NCBI Protein Cluster (PRK) bifunctional riboflavin kinase/FMN adenylyltransferase bifunctional riboflavin kinase/FAD synthetase NF005105.0 PRK06545 PRK06545.1-3 524 524 367 equivalog Y Y N prephenate dehydrogenase 1.3.1.12 1300 Streptococcaceae family 1726 NCBI Protein Cluster (PRK) prephenate dehydrogenase prephenate dehydrogenase NF005577.0 PRK07269 PRK07269.1 620 620 364 equivalog Y Y N cystathionine gamma-synthase 2.5.1.48 12725939 1300 Streptococcaceae family 1533 NCBI Protein Cluster (PRK) cystathionine gamma-synthase cystathionine gamma-synthase Catalyzes the formation of cystathionine from L-cysteine and O-succinyl-L-homoserine NF005579.0 PRK07274 PRK07274.1 169 169 131 equivalog Y Y N single-stranded DNA-binding protein 1300 Streptococcaceae family 937 NCBI Protein Cluster (PRK) single-stranded DNA-binding protein single-stranded DNA-binding protein NF005581.0 PRK07276 PRK07276.1 263 263 291 equivalog Y Y N DNA polymerase III subunit delta' 2.7.7.7 GO:0003887,GO:0006260,GO:0008408 1300 Streptococcaceae family 1892 NCBI Protein Cluster (PRK) DNA polymerase III subunit delta' DNA polymerase III subunit delta' Catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA. NF005582.0 PRK07279 PRK07279.1 1279 1279 1033 equivalog Y Y N DNA polymerase III subunit alpha 2.7.7.7 GO:0003676,GO:0006260,GO:0008408 1300 Streptococcaceae family 3443 NCBI Protein Cluster (PRK) DNA polymerase III DnaE DNA polymerase III subunit alpha Catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time. Proposed to be responsible for the synthesis of the lagging strand. In the low GC gram positive bacteria this enzyme is less processive and more error prone than its counterpart in other bacteria. NF005583.0 PRK07281 PRK07281.1 445 445 286 equivalog Y Y N methionyl aminopeptidase 11371525 1300 Streptococcaceae family 971 NCBI Protein Cluster (PRK) methionine aminopeptidase methionyl aminopeptidase NF005584.0 PRK07282 PRK07282.1 970 970 566 equivalog Y Y N acetolactate synthase large subunit 1300 Streptococcaceae family 1354 NCBI Protein Cluster (PRK) acetolactate synthase catalytic subunit acetolactate synthase large subunit NF009996.0 PRK13466 PRK13466.1 110 110 66 equivalog Y Y N F0F1 ATP synthase subunit C 1300 Streptococcaceae family 42 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit C F0F1 ATP synthase subunit C Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit C is part of the membrane proton channel F0 NF010561.0 PRK13956 PRK13956.1 223 223 147 equivalog Y Y N dUTP diphosphatase 3.6.1.23 1300 Streptococcaceae family 1057 NCBI Protein Cluster (PRK) deoxyuridine 5'-triphosphate nucleotidohydrolase dUTP diphosphatase Catalyzes the formation of dUMP from dUTP NF010715.0 PRK14117 PRK14117.1 421 421 230 equivalog Y Y N phosphoglycerate mutase 5.4.2.12 1300 Streptococcaceae family 501 NCBI Protein Cluster (PRK) phosphoglyceromutase phosphoglycerate mutase Catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate NF020503.5 PF08930.15 DUF1912 25 25 84 PfamAutoEq Y Y N DUF1912 family protein 1300 Streptococcaceae family 631 EBI-EMBL Domain of unknown function (DUF1912) DUF1912 family protein This domain has no known function. It is found in various Streptococcal proteins. (from Pfam) NF022808.5 PF11364.13 DUF3165 25 25 81 PfamAutoEq Y Y N DUF3165 family protein 1300 Streptococcaceae family 644 EBI-EMBL Protein of unknown function (DUF3165) DUF3165 family protein Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function. (from Pfam) NF023103.5 PF11674.13 DUF3270 25 25 86 PfamAutoEq Y Y N DUF3270 family protein 1300 Streptococcaceae family 923 EBI-EMBL Protein of unknown function (DUF3270) DUF3270 family protein This family of proteins with unknown function appears to be restricted to Streptococcus. (from Pfam) NF023201.5 PF11773.13 ComGE 25 25 82 PfamEq Y Y N competence system putative prepilin ComGE comGE 23825953 1300 Streptococcaceae family 1168 EBI-EMBL Competence system putative prepilin ComGE competence system putative prepilin ComGE Members of this family are ComGE (protein E of the comG locus), as found in multiple species of Streptococcus. The protein is suggested to be a prepilin. Note that Pfam annotation for this family that described pseudopilin PulG, as found in Gram-negative type II secretion, apparently was intended for an unrelated pseudopilin. NF023392.5 PF11966.13 SSURE 25 10 149 domain Y Y N SSURE domain-containing protein 15703481,30030946 1300 Streptococcaceae family 4115 EBI-EMBL SSURE domain SSURE domain Streptococcal surface repeat domain - SSURE - is a protein fragment found to bind to extracellular matrix protein fibronectin but not to collagen or submaxillary mucin in Streptococci. Anti-SSURE antibodies recognised the corresponding protein on the surface of streptococcal cells. The full-length proteins are thus fibronectin-binding surface adhesins. The structure was predicted to be composed of two subdomains [1]. [1]. 15703481. Sequence analysis and characterization of a novel fibronectin-binding repeat domain from the surface of Streptococcus pneumoniae. Bumbaca D, Littlejohn JE, Nayakanti H, Rigden DJ, Galperin MY, Jedrzejas MJ;. OMICS. 2004;8:341-356. [2]. 30030946. The Streptococcus agalactiae cell wall-anchored protein PbsP mediates adhesion to and invasion of epithelial cells by exploiting the host vitronectin/alphav integrin axis. De Gaetano GV, Pietrocola G, Romeo L, Galbo R, Lentini G, Giardina M, Biondo C, Midiri A, Mancuso G, Venza M, Venza I, Firon A, Trieu-Cuot P, Teti G, Speziale P, Beninati C;. Mol Microbiol. 2018; [Epub ahead of print] (from Pfam) NF024665.5 PF13268.11 DUF4059 25 25 72 PfamAutoEq Y Y N DUF4059 family protein 1300 Streptococcaceae family 485 EBI-EMBL Protein of unknown function (DUF4059) DUF4059 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved DKT sequence motif. (from Pfam) NF026845.5 PF15507.11 DUF4649 27 27 69 subfamily Y Y N DUF4649 family protein 1300 Streptococcaceae family 976 EBI-EMBL Domain of unknown function (DUF4649) DUF4649 family protein This family of Firmicute sequences has members that are annotated as ribose-phosphate pyrophosphokinase; however there is no evidence for this attribution. Member proteins are all shorter than 100 residues in length. (from Pfam) NF037300.5 PF18255.7 SAM_DrpA 26.2 26.2 62 domain Y N N DNA processing protein A sterile alpha motif domain 22904190 1300 Streptococcaceae family 1909 EBI-EMBL DNA processing protein A sterile alpha motif domain DNA processing protein A sterile alpha motif domain This is the N-terminal domain found in DNA processing protein A (DprA) present in Streptococcus pneumoniae. DprA has recently been discovered to be a transformation-dedicated RecA loader. Transformation is believed to play a major role in genetic plasticity. This domain is known as the sterile alpha motif (SAM) domain. DprAs are able to form a type of dimer through SAM-SAM interactions, also known as N/N interactions [1]. [1]. 22904190. Structure-function analysis of pneumococcal DprA protein reveals that dimerization is crucial for loading RecA recombinase onto DNA during transformation. Quevillon-Cheruel S, Campo N, Mirouze N, Mortier-Barriere I, Brooks MA, Boudes M, Durand D, Soulet AL, Lisboa J, Noirot P, Martin B, van Tilbeurgh H, Noirot-Gros MF, Claverys JP, Polard P;. Proc Natl Acad Sci U S A. 2012;109:E2466-E2475. (from Pfam) NF038251.1 AdcR_fam_Zn_TF 175 175 143 equivalog Y Y N zinc-dependent MarR family transcriptional regulator GO:0003700,GO:0006355,GO:0008270 22085181,32393509 1300 Streptococcaceae family 800 NCBIFAM zinc-dependent MarR family transcriptional regulator This HMM represents one of several unusual clades within the MarR family transcription factors that bind Zn(2+) and regulate the response to zinc abundance or scarcity. Members include AdcR (adhesin competence regulator), which regulates expression of the high affinity zinc uptake transporter AdcABC and various other proteins. NF045553.1 AquGlycerPorinGla 400 400 290 equivalog Y Y N aquaglyceroporin Gla gla GO:0006071,GO:0015267 11320116 1300 Streptococcaceae family 991 NCBIFAM aquaglyceroporin Gla NF045635.1 isoglutsynth_MurT 800 800 447 equivalog Y Y N lipid II isoglutaminyl synthase subunit MurT murT 6.3.5.13 GO:0009252,GO:0016881,GO:0140282 24044435,30093673 1300 Streptococcaceae family 2220 NCBIFAM lipid II isoglutaminyl synthase subunit MurT NF045636.1 isoglutsynth_GatD 400 400 258 equivalog Y Y N lipid II isoglutaminyl synthase subunit GatD gatD 6.3.5.13 GO:0004359,GO:0009252,GO:0140282 30093673 1300 Streptococcaceae family 1726 NCBIFAM lipid II isoglutaminyl synthase subunit GatD TIGR02774.1 TIGR02774 rexB_recomb 718.35 718.35 1076 equivalog Y Y N ATP-dependent nuclease subunit B rexB GO:0000724,GO:0004518 1300 Streptococcaceae family 3930 JCVI ATP-dependent nuclease subunit B ATP-dependent nuclease subunit B DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RecAB) in other. The AddA protein is conserved between the firmicutes and the alphaproteobacteria, while the partner protein is not. The partner may be designated AddB, as in Bacillus and in alphaproteobacteria, or RexB as in Streptococcus and Lactococcus. Note, however, that RexB proteins lack an N-terminal GxxGxGK[ST] ATP-binding motif found in Bacillus subtilis and related species, and this difference may be important; this model represents specifically RexB proteins as found in Streptococcus and Lactococcus. TIGR04079.1 TIGR04079 phero_cyc_pep 35 20 23 subfamily Y Y N KxxxW-cyclized peptide pheromone GO:0005576 17921293 1300 Streptococcaceae family 25 JCVI KxxxW-cyclized secreted peptide KxxxW-cyclized peptide pheromone Members of this family are short precursor peptides in which the mature form undergoes a cyclization between a Lys and a Trp four residues away. The modification enzyme appears to be an adjacent encoded radical SAM protein. Genomes encoding this system include Streptococcus thermophilus LMD-9 and Lactococcus lactis subsp. cremoris MG1363, among others. TIGR04080.1 TIGR04080 rSAM_pep_cyc 500 500 440 equivalog Y Y N KxxxW cyclic peptide radical SAM maturase kwcM GO:0031179,GO:0046500,GO:0051539,GO:1904047 17921293,28893989 1300 Streptococcaceae family 114 JCVI KxxxW cyclic peptide radical SAM maturase KxxxW cyclic peptide radical SAM maturase Members of this family are radical SAM/SPASM domain enzymes that cyclize a cognate peptide, described by family TIGR04079, by introducing a Lys-to-Trp crosslink. Genomes with the complete system include Streptococcus thermophilus LMD-9 and Lactococcus lactis subsp. cremoris MG1363, among others. The gene symbol assigned is kwcM, for KxxxW Cyclic peptide Maturase. Individual members of this family have been named StrB, SuiB, and AgaB. This protein, a peptide-modifying radical SAM/SPASM domain protein, cyclizes KxxxW-containing RiPP precursor peptides by creating a Lys-to-Trp crosslink. NF000474.1 tet_ABC_46_A 1250 1250 574 exception Y Y Y tetracycline efflux ABC transporter Tet(46) subunit A tetA(46) GO:0005524,GO:0008493,GO:0015904,GO:0016020,GO:0016887 1301 Streptococcus genus 108 NCBIFAM tetracycline efflux ABC transporter Tet(46) subunit A tetracycline efflux ABC transporter Tet(46) subunit A NF000475.1 tet_ABC_46_B 1250 1250 578 exception Y Y Y tetracycline efflux ABC transporter Tet(46) subunit B tetB(46) GO:0008493,GO:0015904 1301 Streptococcus genus 118 NCBIFAM tetracycline efflux ABC transporter Tet(46) subunit B tetracycline efflux ABC transporter Tet(46) subunit B NF000997.0 PRK00106 PRK00106.1 937 937 535 equivalog Y Y N ribonuclease Y 1301 Streptococcus genus 1132 NCBI Protein Cluster (PRK) hypothetical protein ribonuclease Y NF001137.0 PRK00142 PRK00142.1-5 641 641 328 equivalog Y Y N rhodanese-related sulfurtransferase 1301 Streptococcus genus 1048 NCBI Protein Cluster (PRK) putative rhodanese-related sulfurtransferase rhodanese-related sulfurtransferase NF001528.0 PRK00364 PRK00364.1-4 119 119 95 equivalog Y Y N co-chaperone GroES groES 1301 Streptococcus genus 644 NCBI Protein Cluster (PRK) co-chaperonin GroES co-chaperone GroES NF001546.0 PRK00373 PRK00373.1-5 334 334 207 equivalog Y Y N V-type ATP synthase subunit D 7.1.2.2 1301 Streptococcus genus 286 NCBI Protein Cluster (PRK) V-type ATP synthase subunit D V-type ATP synthase subunit D NF002361.0 PRK01326 PRK01326.1 428 428 336 equivalog Y Y N peptidylprolyl isomerase PrsA prsA 5.2.1.8 1301 Streptococcus genus 1263 NCBI Protein Cluster (PRK) foldase protein PrsA peptidylprolyl isomerase PrsA Cis/trans isomerase of peptidylprolyl NF002607.0 PRK02260 PRK02260.2-5 290 290 160 equivalog Y Y N S-ribosylhomocysteine lyase 4.4.1.21 1301 Streptococcus genus 677 NCBI Protein Cluster (PRK) S-ribosylhomocysteinase S-ribosylhomocysteine lyase NF002622.0 PRK02289 PRK02289.1 103 103 60 equivalog Y Y N 4-oxalocrotonate tautomerase 5.3.2.6 1301 Streptococcus genus 344 NCBI Protein Cluster (PRK) 4-oxalocrotonate tautomerase 4-oxalocrotonate tautomerase NF002631.0 PRK02302 PRK02302.1 103 103 90 equivalog Y N N hypothetical protein 1301 Streptococcus genus 658 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002643.0 PRK02315 PRK02315.1-4 324 324 248 equivalog Y Y N adaptor protein MecA mecA 1301 Streptococcus genus 1133 NCBI Protein Cluster (PRK) adaptor protein adaptor protein MecA NF003407.0 PRK04778 PRK04778.1-1 913 913 574 equivalog Y Y N septation ring formation regulator EzrA ezrA 1301 Streptococcus genus 503 NCBI Protein Cluster (PRK) septation ring formation regulator EzrA septation ring formation regulator EzrA NF003628.0 PRK05270 PRK05270.1-1 1021 1021 493 equivalog Y Y N UDP-glucose--hexose-1-phosphate uridylyltransferase 2.7.7.12 1301 Streptococcus genus 837 NCBI Protein Cluster (PRK) galactose-1-phosphate uridylyltransferase UDP-glucose--hexose-1-phosphate uridylyltransferase NF003988.0 PRK05472 PRK05472.1-1 321 321 214 equivalog Y Y N redox-sensing transcriptional repressor Rex 1301 Streptococcus genus 683 NCBI Protein Cluster (PRK) redox-sensing transcriptional repressor Rex redox-sensing transcriptional repressor Rex NF004427.0 PRK05771 PRK05771.1-1 942 942 668 equivalog Y Y N V-type ATP synthase subunit I 7.1.2.2 1301 Streptococcus genus 483 NCBI Protein Cluster (PRK) V-type ATP synthase subunit I V-type ATP synthase subunit I NF005100.0 PRK06531 PRK06531.1 129 129 121 equivalog Y Y N preprotein translocase subunit YajC yajC 1301 Streptococcus genus 515 NCBI Protein Cluster (PRK) preprotein translocase subunit YajC preprotein translocase subunit YajC NF005211.0 PRK06687 PRK06687.1 703 703 419 equivalog Y Y N TRZ/ATZ family protein 1301 Streptococcus genus 877 NCBI Protein Cluster (PRK) chlorohydrolase TRZ/ATZ family protein NF005254.0 PRK06762 PRK06762.2-1 198 198 165 equivalog Y N N hypothetical protein 1301 Streptococcus genus 85 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005569.0 PRK07246 PRK07246.1 794 794 820 equivalog Y Y N bifunctional DnaQ family exonuclease/ATP-dependent helicase GO:0003677,GO:0003887,GO:0004386,GO:0005524,GO:0006139,GO:0006260,GO:0008408 1301 Streptococcus genus 3071 NCBI Protein Cluster (PRK) bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon bifunctional DnaQ family exonuclease/ATP-dependent helicase NF005570.0 PRK07247 PRK07247.1 226 226 195 equivalog Y Y N 3'-5' exonuclease 1301 Streptococcus genus 1057 NCBI Protein Cluster (PRK) DNA polymerase III subunit epsilon 3'-5' exonuclease NF005573.0 PRK07252 PRK07252.1 183 183 120 equivalog Y Y N S1 RNA-binding domain-containing protein 1301 Streptococcus genus 584 NCBI Protein Cluster (PRK) hypothetical protein S1 RNA-binding domain-containing protein NF006971.0 PRK09441 PRK09441.1-4 781 781 484 equivalog Y Y N alpha-amylase 3.2.1.1 GO:0004556,GO:0005975 1301 Streptococcus genus 1811 NCBI Protein Cluster (PRK) cytoplasmic alpha-amylase alpha-amylase NF007322.0 PRK09814 PRK09814.1-1 580 580 336 equivalog Y Y N sugar transferase 1301 Streptococcus genus 297 NCBI Protein Cluster (PRK) beta-1,6-galactofuranosyltransferase sugar transferase NF008871.0 PRK11907 PRK11907.1 1266 1266 814 equivalog Y Y N bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase 1301 Streptococcus genus 939 NCBI Protein Cluster (PRK) bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precursor protein bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase Functions during ribonucleic acid degradation; 2',3'-cyclic nucleotides are first converted to 3'-nucleotide and then cleaved to yield a ribonucleotide and a phosphate NF009105.0 PRK12450 PRK12450.1 526 526 309 subfamily Y N N foldase protein PrsA 1301 Streptococcus genus 211 NCBI Protein Cluster (PRK) foldase protein PrsA foldase protein PrsA NF009231.0 PRK12581 PRK12581.1 954 954 468 equivalog Y N N oxaloacetate decarboxylase 1301 Streptococcus genus 181 NCBI Protein Cluster (PRK) oxaloacetate decarboxylase oxaloacetate decarboxylase NF009552.0 PRK12997 PRK12997.1-4 921 921 477 equivalog Y Y N PTS sugar transporter subunit IIC 1301 Streptococcus genus 318 NCBI Protein Cluster (PRK) PTS system ascorbate-specific transporter subunit IIC PTS sugar transporter subunit IIC NF009640.0 PRK13169 PRK13169.1-1 134 134 105 equivalog Y Y N DNA replication initiation control protein YabA yabA 1301 Streptococcus genus 287 NCBI Protein Cluster (PRK) DNA replication intiation control protein YabA DNA replication initiation control protein YabA NF009759.0 PRK13261 PRK13261.2-5 290 290 150 equivalog Y Y N urease accessory protein UreE ureE 1301 Streptococcus genus 26 NCBI Protein Cluster (PRK) urease accessory protein UreE urease accessory protein UreE NF009997.0 PRK13467 PRK13467.1 98 98 66 equivalog Y Y N F0F1 ATP synthase subunit C 7.1.2.2 1301 Streptococcus genus 217 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit C F0F1 ATP synthase subunit C Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit C is part of the membrane proton channel F0 NF010209.0 PRK13676 PRK13676.1-1 130 130 113 equivalog Y Y N YlbF/YmcA family competence regulator 1301 Streptococcus genus 821 NCBI Protein Cluster (PRK) hypothetical protein YlbF/YmcA family competence regulator NF010347.0 PRK13775 PRK13775.1 381 381 331 equivalog Y N N formimidoylglutamase 1301 Streptococcus genus 338 NCBI Protein Cluster (PRK) formimidoylglutamase formimidoylglutamase Catalyzes the formation of glutamate and formamide from N-formimidoyl-L-glutamate NF010817.0 PRK14221 PRK14221.1 103 103 124 equivalog Y Y N fluoride efflux transporter CrcB crcB 1301 Streptococcus genus 554 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter CrcB NF010825.0 PRK14229 PRK14229.1 101 101 109 equivalog Y Y N fluoride efflux transporter CrcB crcB 1301 Streptococcus genus 545 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter CrcB NF011122.0 PRK14553 PRK14553.1-1 166 166 108 equivalog Y Y N ribosomal-processing cysteine protease Prp 1301 Streptococcus genus 70 NCBI Protein Cluster (PRK) hypothetical protein ribosomal-processing cysteine protease Prp NF011416.0 PRK14843 PRK14843.1 429 429 347 equivalog Y Y N dihydrolipoamide acetyltransferase GO:0006086,GO:0016746,GO:0045254 1301 Streptococcus genus 2069 NCBI Protein Cluster (PRK) dihydrolipoamide acetyltransferase dihydrolipoamide acetyltransferase NF014913.5 PF02916.20 DNA_PPF 25 25 116 domain Y Y N LCP family protein GO:0006260 10535734 1301 Streptococcus genus 2269 EBI-EMBL DNA polymerase processivity factor LCP family protein NF018771.5 PF07104.16 DUF1366 23 23 117 domain Y Y N DUF1366 domain-containing protein 1301 Streptococcus genus 1086 EBI-EMBL Protein of unknown function (DUF1366) Protein of unknown function (DUF1366) This family consists of several hypothetical Streptococcus thermophilus bacteriophage proteins of around 130 residues in length. One of the sequences in this family, from phage Sfi11 (Swiss:O80186) is known as Gp149. The function of this family is unknown. (from Pfam) NF019629.5 PF08017.16 Fibrinogen_BP 50 50 425 PfamEq Y N N Fibrinogen binding protein 15383464 1301 Streptococcus genus 658 EBI-EMBL Fibrinogen binding protein Fibrinogen binding protein Proteins in this family bind to fibrinogen. Members of this family includes the fibrinogen receptor, FbsA, (Swiss:Q8GIU3) which mediates platelet aggregation [1]. [1]. 15383464. FbsA, a fibrinogen-binding protein from Streptococcus agalactiae, mediates platelet aggregation. Pietrocola G, Schubert A, Visai L, Torti M, Fitzgerald JR, Foster TJ, Reinscheid DJ, Speziale P;. Blood 2004; [Epub ahead of print] (from Pfam) NF020408.5 PF08829.15 AlphaC_N 25 25 106 domain Y Y N ACP N-terminal domain-containing protein 12427097,15753100,18048918,9371832 1301 Streptococcus genus 656 EBI-EMBL Alpha C protein N terminal Alpha C protein N terminal The alpha C protein (ACP) is found in Streptococcus and acts as an invasin which plays a role in the internalisation and translocation of the organism across human epithelial surfaces. Group B Streptococcus is the leading cause of diseases including bacterial pneumonia, sepsis and meningitis. The N terminal of ACP is associated with virulence and forms a beta sandwich and a three helix bundle [1] [2] [3]. ACP consists of an N-terminal domain (170 amino acids) followed by a variable number of tandem repeats (82 amino acids each) and a C-terminal domain (45 amino acids) containing an LPXTG peptidoglycan-anchoring motif. This entry is the N-terminal domain of ACP (NtACP). NtACP can be further divided into two structurally distinct domains, D1 and D2. D1, the more distal (amino-terminal) portion, consists of a beta sandwich with strong structural homology to fibronectin's integrin-binding region (FnIII10). D2 consists of three antiparallel alpha helix coils containing a portion of the glycosaminoglycan (GAG)-binding domain adjacent to the repeat region. NtACP binds to heparin and GAGs only when it is covalently associated with the adjacent repeat region. NtACP's D1 region contains a K144- T145-D146 (KTD) motif, located within a loop region that is structurally analogous to the loop containing the RGD integrin-binding motif in FnIII10. Single mutation within the KTD motif (D146A), present in the D1 domain, reduces NtACP binding to a1b integrion. The a1b1-integrin is one of four collagen-binding I-domain-containing integrins. Structural analysis of the D1 domain, in particular the region containing the putative integrin-binding . TRUNCATED at 1650 bytes (from Pfam) NF026851.5 PF15513.11 DUF4651 22 22 61 PfamAutoEq Y Y N DUF4651 domain-containing protein 1301 Streptococcus genus 995 EBI-EMBL Domain of unknown function (DUF4651) Domain of unknown function (DUF4651) family of short, secreted proteins specific to the Streptococcus genus, with distant homologs, not recognized by this HMM, found in other cocci. In all sequenced genomes, proteins from this family appear in a conserved genomic context with an thioredoxin, tRNA synthase and tRNA binding protein, but the functional implication of this is unclear (from Pfam) NF027957.5 PF16645.10 PHtD_u1 28.4 28.4 56 domain Y N N Unstructured region on Pneumococcal histidine triad protein 24312273 1301 Streptococcus genus 5963 EBI-EMBL Unstructured region on Pneumococcal histidine triad protein Unstructured region on Pneumococcal histidine triad protein PHtD_u1 is a natively unstructured region on Pneumococcal histidine triad proteins of higher eukaryotes lying between the first two Strep_his_triad domains so far identified, Pfam:PF04270. The function is not known but it does not carry the characteristic histidine triad. [1]. 24312273. New insights into histidine triad proteins: solution structure of a Streptococcus pneumoniae PhtD domain and zinc transfer to AdcAII. Bersch B, Bougault C, Roux L, Favier A, Vernet T, Durmort C;. PLoS One. 2013;8:e81168. (from Pfam) NF028028.5 PF16718.10 IFS 30 30 164 PfamEq Y Y N NAD glycohydrolase toxin immunity factor ifs 21300288 1301 Streptococcus genus 269 EBI-EMBL Immunity factor for SPN NAD glycohydrolase SPN toxin immunity factor IFS Immunity factor for SPN (IFS) binds to and inhibits the SPN toxin [1]. [1]. 21300288. Structural basis of Streptococcus pyogenes immunity to its NAD+ glycohydrolase toxin. Smith CL, Ghosh J, Elam JS, Pinkner JS, Hultgren SJ, Caparon MG, Ellenberger T;. Structure. 2011;19:192-202. (from Pfam) NF028306.5 PF16996.10 Asp4 27.7 27.7 55 PfamEq Y Y N accessory secretory system protein Asp4 asp4 23000954 1301 Streptococcus genus 149 EBI-EMBL Accessory secretory protein Sec Asp4 accessory secretory system protein Asp4 Asp4 and Asp5 are putative accessory components of the SecY2 channel of the SecA2-SecY2 mediated export system, but they are not present in all SecA2-SecY2 systems. This family of Asp4 is found in Firmicutes [1]. [1]. 23000954. Emerging themes in SecA2-mediated protein export. Feltcher ME, Braunstein M;. Nat Rev Microbiol. 2012;10:779-789. (from Pfam) NF028310.5 PF17000.10 Asp5 25 25 71 PfamEq Y N N Accessory secretory protein Sec, Asp5 23000954 1301 Streptococcus genus 283 EBI-EMBL Accessory secretory protein Sec, Asp5 Accessory secretory protein Sec, Asp5 Asp4 and Asp5 are putative accessory components of the SecY2 channel of the SecA2-SecY2 mediated export system, but they are not present in all SecA2-SecY2 systems. This family of Asp5 is found in Firmicutes [1]. [1]. 23000954. Emerging themes in SecA2-mediated protein export. Feltcher ME, Braunstein M;. Nat Rev Microbiol. 2012;10:779-789. (from Pfam) NF033093.1 HK_VicK 680 680 448 exception Y Y N cell wall metabolism sensor histidine kinase VicK vicK 2.7.13.3 1301 Streptococcus genus 1246 NCBIFAM cell wall metabolism sensor histidine kinase VicK cell wall metabolism sensor histidine kinase VicK This model describes the protein VicK (or WalK) as found in Streptococcus pneumoniae, This protein is shorter than the WalK of Staphylococcus aureus, although apparently is functionally similar. Compare to model NF033092 (HK_WalK). VicK is a sensor histidine kinase involved in regulating cell wall metabolism. Its two component system partner is the response regulatory VicR. NF033214.1 ComC_Streptocco 50 50 41 equivalog Y Y N competence-stimulating peptide ComC comC 7479953 1301 Streptococcus genus 205 NCBIFAM competence-stimulating peptide ComC competence-stimulating peptide ComC Members of this family are ComC, a secreted peptide that stimulates competence for natural transformation in Streptococcus. ComC peptides fall within the broader family of PF03047, a homology family of pheromone/bacteriocin precursors that is also restricted to Streptococcus. The PF03047 HMM runs only a few residues past the GlyGly precursor peptide cleavage site, and thus does not distinguish ComC from other pheromone precursors, such as BlpC. NF033777.1 M_group_A_cterm 400 400 218 equivalog_domain Y Y N M protein emm 2670192 1301 Streptococcus genus 412 NCBIFAM M protein M protein C-terminal domain M protein (emm) is an important virulence protein and serology-defining surface antigen of Streptococcus pyogenes (group A Streptococcus). M protein has an amino-terminal YSIRK-type signal sequence (associated with cross-wall targeting in dividing cells), and a C-terminal LPXTG domain for processing by sortase and covalent attachment to the Gram-positive cell wall. Past the signal peptide, M protein has a hypervariable region, but this HMM describes only the well-conserved region C-terminal to the hypervariable region. It discriminates M protein from two related proteins, Enn and Mrp. NF033797.0 phero_SHP2_SHP3 38 38 23 subfamily Y Y N SHP2/SHP3 family peptide pheromone 21829369,29555699 1301 Streptococcus genus 71 NCBIFAM SHP2/SHP3 family peptide pheromone SHP2/SHP3 family peptide pheromone NF033804.1 Streccoc_I_II 1500 1200 1551 equivalog Y Y N antigen I/II family LPXTG-anchored adhesin 19609934,20138058,20231452 1301 Streptococcus genus 531 NCBIFAM antigen I/II family LPXTG-anchored adhesin antigen I/II family LPXTG-anchored adhesin Members of the antigen I/II family are adhesins with a glucan-binding domain, two types of repetitive regions, an isopeptide bond-forming domain associated with shear resistance, and a C-terminal LPXTG motif for anchoring to the cell wall. They occur in oral Streptococci, and tend to be major cell surface adhesins. Members of this family include SspA and SspB from Streptococcus gordonii, antigen I/II from S. mutans, etc. NF033840.1 PspC_relate_1 850 650 967 equivalog Y Y N PspC-related protein choline-binding protein 1 11891047 1301 Streptococcus genus 127 NCBIFAM PspC-related protein choline-binding protein 1 PspC-related protein choline-binding protein 1 Members of this family share C-terminal homology to the choline-binding form of the pneumococcal surface antigen PspC, but not to its allelic LPXTG-anchored forms because they lack the choline-binding repeat region. Members of this family should not be confused with PspC itself, whose identity and function reflect regions N-terminal to the choline-binding region. See Iannelli, et al. (PMID: 11891047) for information about the different allelic forms of PspC. NF035941.1 GBS_alph_likeN 250 250 225 equivalog_domain Y Y N alpha-like surface protein 10944228,25540270,8702550 1301 Streptococcus genus 637 NCBIFAM alpha-like surface protein N-terminal domain Most Group B Streptococcus (GBS) have a member of a mosaic family of repetitive surface protein. The founding member is the alpha C protein (bca), but other named members with complete sequences include Alp2, Alp3, and Rib. This HMM describes the shared, non-repetitive N-terminal region, including a YSIRK-like signal peptide region. NF036654.5 PF17480.7 AlphaC_N2 25 25 71 domain Y Y N ACP C-terminal domain-containing protein 15753100,17259175,18048918 1301 Streptococcus genus 647 EBI-EMBL AlphaC N-terminal domain 2 AlphaC N-terminal domain 2 This is the second domain on the N-terminal region found on the alpha C protein (ACP). ACP is found in Streptococcus and acts as an invasin which plays a role in the internalisation and translocation of the organism across human epithelial surfaces [1]. Group B Streptococcus is the leading cause of diseases including bacterial pneumonia, sepsis and meningitis. ACP consists of an N-terminal domain (NtACP; 170 amino acids) followed by a variable number of tandem repeats (82 amino acids each) and a C-terminal domain (45 amino acids) containing an LPXTG peptidoglycan-anchoring motif. The NtACP, contains two structural domains, D1 and D2. D1, the more distal (amino-terminal) portion Pfam:PF08829 and consists of a beta sandwich with strong structural homology to fibronectin's integrin-binding region (FnIII10). This entry, D2 (connects distally to Domain 1 and proximally to the repeat region) [1] consists of three antiparallel alpha helix coils [2]. It is suggested that the GAG-binding region of ACP may extend from Domain 2 into the repeat region [3]. [1]. 15753100. Crystal structure of the N-terminal domain of the group B streptococcus alpha C protein. Auperin TC, Bolduc GR, Baron MJ, Heroux A, Filman DJ, Madoff LC, Hogle JM;. J Biol Chem. 2005;280:18245-18252. [2]. 18048918. The group B streptococcal alpha C protein binds alpha1beta1-integrin through a novel KTD motif that promotes internalization of GBS within human epithelial cells. Bolduc GR, Madoff LC;. Microbiology. 2007;153:4039-4049. [3]. 17259175. Identification of a glycosaminoglycan binding region of the alpha C protein that mediates entry of group B Streptococci in. TRUNCATED at 1650 bytes (from Pfam) NF036840.5 PF17890.6 WW_like 37.8 37.8 53 domain Y N N Peptidoglycan hydrolase LytB WW-like domain 25002590 1301 Streptococcus genus 1356 EBI-EMBL Peptidoglycan hydrolase LytB WW-like domain Peptidoglycan hydrolase LytB WW-like domain Structural analysis revealed that the catalytic domain of LytB consists of three structurally independent modules: SH3b, WW domain-like, and the glycoside hydrolase family 73 (GH73). This entry is the WW like domain found in endo-beta-N-acetylglucosaminidase LytB from Streptococcus pneumoniae. Functional analysis show that the deletion of both SH3b and WW modules almost completely abolished the activity of LytB. Furthermore, it was shown that the SH3b and WW modules are indispensable for LytB in cell separation [1]. [1]. 25002590. Structure of pneumococcal peptidoglycan hydrolase LytB reveals insights into the bacterial cell wall remodeling and pathogenesis. Bai XH, Chen HJ, Jiang YL, Wen Z, Huang Y, Cheng W, Li Q, Qi L, Zhang JR, Chen Y, Zhou CZ;. J Biol Chem. 2014;289:23403-23416. (from Pfam) NF036852.5 PF18342.6 LytB_SH3 25.8 25.8 67 domain Y N N Endo-beta-N-acetylglucosaminidase LytB SH3 domain 25002590 1301 Streptococcus genus 1355 EBI-EMBL Endo-beta-N-acetylglucosaminidase LytB SH3 domain Endo-beta-N-acetylglucosaminidase LytB SH3 domain This domain has can be found in endo-beta-N-acetylglucosaminidase LytB (EC 3.2.1.96) of S. pneumoniae and other gram positive bacteria. This domain adopts an SH3-like structure. [1]. 25002590. Structure of pneumococcal peptidoglycan hydrolase LytB reveals insights into the bacterial cell wall remodeling and pathogenesis. Bai XH, Chen HJ, Jiang YL, Wen Z, Huang Y, Cheng W, Li Q, Qi L, Zhang JR, Chen Y, Zhou CZ;. J Biol Chem. 2014;289:23403-23416. (from Pfam) NF037071.5 PF18229.6 GcnA_N 27 27 79 domain Y N N N-acetyl-beta-D-glucosaminidase N-terminal domain 18237743 1301 Streptococcus genus 1517 EBI-EMBL N-acetyl-beta-D-glucosaminidase N-terminal domain N-acetyl-beta-D-glucosaminidase N-terminal domain This is the N-terminal domain found in N-acetyl-beta-D-glucosaminidase (GcnA) present in Streptococcus gordonii. GcnA is a family 20 glycosidase that cleaves N-acetyl-beta-D-glucosamine and N-acetyl-beta-D-galactosamine from 4-methylumbelliferylated substrates. Similar N-terminal domains have been observed in all family 20 glycosidases although the number of beta-sheet strands may vary from five [1]. [1]. 18237743. Structure of N-acetyl-beta-D-glucosaminidase (GcnA) from the endocarditis pathogen Streptococcus gordonii and its complex with the mechanism-based inhibitor NAG-thiazoline. Langley DB, Harty DW, Jacques NA, Hunter N, Guss JM, Collyer CA;. J Mol Biol. 2008;377:104-116. (from Pfam) NF037869.5 PF18627.6 PgdA_N 26 26 218 domain Y N N Peptidoglycan GlcNAc deacetylase N-terminal domain 16221761 1301 Streptococcus genus 1763 EBI-EMBL Peptidoglycan GlcNAc deacetylase N-terminal domain Peptidoglycan GlcNAc deacetylase N-terminal domain This is the N-terminal and middle domain found in Streptococcus pneumoniae peptidoglycan GlcNAc deacetylase (SpPgdA). PgdA protects the Gram-positive bacterial cell wall from host lysozymes by deacetylating peptidoglycan GlcNAc residues. It is a member of the family 4 carbohydrate esterases (CE-4) [1]. [1]. 16221761. Structure and metal-dependent mechanism of peptidoglycan deacetylase, a streptococcal virulence factor. Blair DE, Schuttelkopf AW, MacRae JI, van Aalten DM;. Proc Natl Acad Sci U S A. 2005;102:15429-15434. (from Pfam) NF038244.1 pheromon_TrpTrp 29 29 32 equivalog Y Y N quorum-sensing system DWW-type pheromone 20969646 1301 Streptococcus genus 43 NCBIFAM quorum-sensing system DWW-type pheromone Members of this family are pheromone precursor peptides about 31 amino acids in length, including a signal peptide. The active pheromone is derived from the C-terminal few residues, containing a nearly invariant DWW motif. Member proteins are found encoded near Rgg-type quorum-sensing transcriptional regulators. NF038253.1 GBS_IgA_bnd_BAC 1700 1300 1127 equivalog Y Y N IgA Fc-binding protein BAC bac 17004655,26047354 1301 Streptococcus genus 95 NCBIFAM IgA Fc-binding protein BAC The IgA Fc-region binding protein of Streptococcus agalactiae (group B streptococcus) is a surface-anchored virulence factor with a YSIRK-type signal sequence at the N-terminus and an LPXTG sorting signal near the C-terminus. It is also called beta-antigen. NF038271.1 strep_PBP2X 1050 1050 750 exception Y Y N penicillin-binding protein PBP2X pbp2X GO:0008658 1301 Streptococcus genus 2743 NCBIFAM penicillin-binding protein PBP2X NF038272.1 strep_PBP1A 1075 1075 658 exception Y Y N penicillin-binding protein PBP1A pbp1a GO:0008658 16316661,23449828 1301 Streptococcus genus 2405 NCBIFAM streptococcal penicillin-binding protein PBP1A PBP1a is a bifunctional enzyme of cell wall biosynthesis, performing both polymerization of GlcNAc–MurNAc chains (glycosyltransfer, GT) and peptide cross-linking (transpeptidation, TP). NF038273.1 strep_PBP3 490 490 407 exception Y Y N D-alanyl-D-alanine carboxypeptidase PBP3 pbp3 3.4.16.4 15009891,15596446 1301 Streptococcus genus 2374 NCBIFAM streptococcal D-alanyl-D-alanine carboxypeptidase PBP3 PBP3 (penicillin-binding protein 3) is the lone D-alanyl-D-alanine carboxypeptidase in Streptococcus pneumoniae. The gene is known as pbp3 or dacA. NF038274.1 strep_PBP1B 1225 1225 745 exception Y Y N penicillin-binding protein PBP1B pbp1b 16751607,17676039 1301 Streptococcus genus 2534 NCBIFAM streptococcal penicillin-binding protein PBP1B NF038276.1 strep_PBP2A 1100 1100 716 exception Y Y N penicillin-binding protein PBP2A pbp2a GO:0008658 29487215 1301 Streptococcus genus 2426 NCBIFAM streptococcal penicillin-binding protein PBP2A NF038278.1 strep_PBP2B 975 975 678 exception Y Y N penicillin-binding protein PBP2B pbp2b GO:0008658,GO:0009252,GO:0071972 2798106 1301 Streptococcus genus 2531 NCBIFAM streptococcal penicillin-binding protein PBP2B NF038279.1 TF_CBS_SpxR 600 600 427 exception Y Y N CBS-HotDog domain-containing transcription factor SpxR spxR 18179423 1301 Streptococcus genus 1023 NCBIFAM CBS-HotDog domain-containing transcription factor SpxR SpxR from Streptococcus pneumoniae, like its full-length homolog YtoI from Listeria monocytogenes, is a transcriptional regulator with an N-terminal DNA-binding domain, and with CBS and HotDog domains. SpxR regulates the pyruvate oxidase SpxB. NF038388.1 sigmaX_act_ComW 55 55 73 equivalog Y Y N sigma(X)-activator ComW comW 15458414,27353650,31160340 1301 Streptococcus genus 319 NCBIFAM sigma(X)-activator ComW The pneumococcal DNA-binding protein ComW, critical for natural transformation, interacts with the sigma factor that is a master regulator for competence, sigma(X). NF040483.1 serum_opaci_fac 150 150 342 subfamily_domain Y Y N serum opacification factor 10216862,28374173,7822031 1301 Streptococcus genus 901 NCBIFAM serum opacification domain Serum opacity factors are virulence proteins from Streptococcus pyogenes and related bacterial pathogens. The opacification domain binds to apoA-I and apoA-II of HDL, and apparently in non-enzymatic fashion causes HDL to release the lipid it was carrying. That lipid then coalesces in serum, forming droplets that opacify mammalian serum. This HMM represents a region within the described opacification domain from which poorly conserved regions and sequences recognized as von Willebrand factor type A domain have been removed. NF040528.1 SP_0198_lipo 100 100 144 equivalog Y Y N SP_0198 family lipoprotein 1301 Streptococcus genus 916 NCBIFAM SP_0198 family lipoprotein Members of this family, found only in Streptococcus, are lipoproteins with a lipoprotein signal peptide, a Ser-rich low-complexity region, and a C-terminal DUF3642 (PF12182) domain. NF040549.1 Nt5e_LPXTG 1050 1050 731 exception Y Y N cell surface ecto-5'-nucleotidase Nt5e nt5e 22685551,24446521 1301 Streptococcus genus 1208 NCBIFAM cell surface ecto-5'-nucleotidase Nt5e Members of this family, found in Streptococcus sanguinis and related species, are LPXTG-anchored cell surface proteins. By hydrolyzing pro-inflammatory extracellular ATP in the host, it may blunt immune responses and contribute to virulence. Nt5e has also been called adenosine synthase AdsA. NF040663.1 salivaricin_M 60 60 57 equivalog Y Y N salivaricin M family lantibiotic slmA 22038965,26744310 1301 Streptococcus genus 125 NCBIFAM salivaricin M family lantibiotic Members of this family are type A2 lantibiotic precursors in the family of founding members EGX30806.1, called salivaricin M, from Streptococcus salivarius strain M18 (previously strain Mia), a commensal strain of the oral microbiome, and ALO23661.1, called salivaricin E. Salivaricin M affects the caries-causing oral pathogen Streptococcus mutans. NF040665.1 relax_SAG1250 575 575 606 exception Y Y N SAG1250 family conjugative relaxase 31039174 1301 Streptococcus genus 1020 NCBIFAM SAG1250 family conjugative relaxase NF040666.1 Tn5252_Orf10 110 110 114 equivalog Y Y N SAG1252 family conjugative relaxosome accessory protein 26870017,31039174 1301 Streptococcus genus 539 NCBIFAM SAG1252 family conjugative relaxosome accessory protein SAG1252, a member of the Tn5252 ORF10 family, occurs in mobile elements from a class associated with the movement of bacteriocins and antibiotic resistance proteins in Streptococcus. This HMM excludes related MobC proteins, such as the adjacent SAG1251, a homolog over the short length of these small proteins except for a small central region recognized by Pfam model PF05713 (MobC). NF040896.1 SP_0009_fam 33 33 32 equivalog Y Y N SP_0009 family protein 1301 Streptococcus genus 364 NCBIFAM SP_0009 family protein NF040904.1 PhrA_Strep 40 40 56 subfamily Y Y N PhrA family quorum-sensing system peptide 25869931,31572692 1301 Streptococcus genus 218 NCBIFAM PhrA family quorum-sensing system peptide NF041193.1 lipo_SP0191 75 75 190 subfamily Y Y N SP0191 family lipoprotein 1301 Streptococcus genus 898 NCBIFAM SP0191 family lipoprotein NF041194.1 LD_carboxy_LdcB 275 275 180 exception Y Y N LD-carboxypeptidase LdcB/DacB ldcB 24909784,25060741 1301 Streptococcus genus 1607 NCBIFAM LD-carboxypeptidase LdcB/DacB NF041436.1 Wzy_Strepto 450 450 395 subfamily Y Y N oligosaccharide repeat unit polymerase Wzy wzy 10085014,15845517,9748469 1301 Streptococcus genus 41 NCBIFAM oligosaccharide repeat unit polymerase Wzy NF041488.1 caps_synth_Cps4B 400 400 243 equivalog Y Y N capsular polysaccharide biosynthesis protein Cps4B cps4B 19616007 1301 Streptococcus genus 1300 NCBIFAM capsular polysaccharide biosynthesis protein Cps4B NF041534.1 rodZ_Strepcoccus 375 375 275 equivalog Y Y N cytoskeleton protein RodZ rodZ 36001060 1301 Streptococcus genus 765 NCBIFAM cytoskeleton protein RodZ NF041574.1 antitoxPezT_Strep 470 470 251 equivalog Y Y N type II toxin-antitoxin system toxin PezT pezT GO:0005524 17488720 1301 Streptococcus genus 1051 NCBIFAM type II toxin-antitoxin system toxin PezT NF041629.1 anti_IS1548_end 40 40 27 domain N N N IS1548 end spurious translation-containing protein 1301 Streptococcus genus 116 NCBIFAM IS1548 end spurious translation NF041849.1 trans_regNmlR 175 175 117 equivalog Y Y N stress response transcriptional regulator NmlR nmlR GO:0003700,GO:0006355 18190263,20525825,36349475 1301 Streptococcus genus 435 NCBIFAM stress response transcriptional regulator NmlR NF042514.3 PF20193.3 DUF6556 28.1 28.1 113 subfamily Y Y N DUF6556 family protein 1301 Streptococcus genus 1418 EBI-EMBL Family of unknown function (DUF6556) DUF6556 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in Firmicutes. Proteins in this family are typically between 130 and 155 amino acids in length. Some members are predicted histone acetyltransferases. (from Pfam) NF042932.1 BlpZ_fam 50 50 82 equivalog Y Y N immunity protein BlpZ blpZ 17704229,30910792 1301 Streptococcus genus 369 NCBIFAM immunity protein BlpZ BlpZ, also called PncQ, is an putative membrane protein, apparently an immunity protein, encoded within the larger BLP (Bacteriocin-Like Peptide) locus, in Streptococcus pneumoniae and related species that produces bacteriocins such as BlpE, BlpI, BlpK, BlpN, etc., plus various immunity proteins. Some members of this family, including AAK74703.1 from Streptococcus pneumoniae TIGR4, appear to be disrupted, overlapping a normally intergenic BOX element at the C-terminus. NF044531.2 PF21642.2 SP_0191-like 27 27 132 domain Y N N SP_0191-like 1301 Streptococcus genus 922 EBI-EMBL SP_0191-like SP_0191-like This group of proteins predominantly found in firmicutes includes Lipoprotein from Streptococcus pneumoniae (SP_0191), which shows a two-layered alpha-beta structure. Its specific function is unknown. (from Pfam) NF045208.2 PF20746.2 EndoS_Ig-like 27 27 124 domain Y N N Endo-beta-N-acetylglucosaminidase F2, Ig-like domain 24753590,29760474,30937380 1301 Streptococcus genus 437 EBI-EMBL Endo-beta-N-acetylglucosaminidase F2, Ig-like domain Endo-beta-N-acetylglucosaminidase F2, Ig-like domain This domain is found in Endo-beta-N-acetylglucosaminidase F2 (EndoS) from Streptococcus pyogenes (Swiss:Q48RM3) and similar sequences predominantly found in Firmicutes. EndoS is an immunomodulatory enzyme secreted by the bacteria to remove carbohydrates from IgG antibodies in a highly specific manner, which gives the pathogen a survival advantage over its host. This protein is composed of five distinct protein domains. The domain located at the base of the V-shaped EndoS structure (this entry), also named hybrid Ig domain, is composed of two subdomains. The smaller one is inserted within the loop that connects the LRR domain to the second and third beta strands of the larger subdomain. The latter is a typical Ig domain structurally similar to the interleukin-4 receptor [1,2,3]. Paper describing PDB structure 4nuy. [1]. 24753590. Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies. Trastoy B, Lomino JV, Pierce BG, Carter LG, Gunther S, Giddens JP, Snyder GA, Weiss TM, Weng Z, Wang LX, Sundberg EJ;. Proc Natl Acad Sci U S A. 2014;111:6714-6719. Paper describing PDB structure 6e58. [2]. 30937380. Molecular Basis of Broad Spectrum N-Glycan Specificity and Processing of Therapeutic IgG Monoclonal Antibodies by Endoglycosidase S2. Klontz EH, Trastoy B, Deredge D, Fields JK, Li C, Orwenyo J, Marina A, Beadenkopf R, Gunther S, Flores J, Wintrode PL, Wang LX, Guerin ME, Sundberg EJ;. ACS Cent Sci. 2019;5:524-538. Paper describing PDB structure 6en3. [3]. 29760474. Structural basis for the recognition of complex-type N-glycans by Endoglycosidase S. Trastoy B, Klont. TRUNCATED at 1650 bytes (from Pfam) NF045691.1 ABCF_VgaF 975 975 459 exception Y Y Y ABC-F type ribosomal protection protein Vga(F) vga(F) srpA 34493269 1301 Streptococcus genus 188 NCBIFAM ABC-F type ribosomal protection protein Vga(F) Members of this ABC-F type ribosomal protection protein family were first reported as Vga(F) and reported to confer resistance to pleuromutilin. A more recent report (doi.org/10.1016/j.eng.2020.12.015) uses the name SrpA (S. suis ribosome protective ABC-F family protein), and reports resistance to streptogramin A, pleuromutilins, and lincosamides. Multiple sequence alignment of family members suggests that multiple instances of homologous recombination have occurred in the family. NF045820.1 PgAcgDacpgdA_Strep 800 800 463 equivalog Y Y N peptidoglycan-N-acetylglucosamine deacetylase PgdA pgdA 3.5.1.104 GO:0005975,GO:0042545,GO:0050119 10781617,12438406,16221761 1301 Streptococcus genus 595 NCBIFAM peptidoglycan-N-acetylglucosamine deacetylase PgdA NF046102.1 CellCycRegCcrZ 400 400 260 equivalog Y Y N cell cycle regulator CcrZ ccrZ 2.7.1.15,2.7.1.229 GO:0004747,GO:0006270,GO:0016773,GO:0019200,GO:0051726 34373624 1301 Streptococcus genus 627 NCBIFAM cell cycle regulator CcrZ NF046104.1 PptglHdxlasePcsB 450 450 400 equivalog Y Y N peptidoglycan hydrolase PcsB pcsB 3.2.1.- GO:0016787 14651645,15306019,24804636 1301 Streptococcus genus 1325 NCBIFAM peptidoglycan hydrolase PcsB NF046254.1 PF22382.1 EndoS_helical 26 26 64 domain Y N N Endo-beta-N-acetylglucosaminidase, helical bundle 24753590,29760474 1301 Streptococcus genus 357 EBI-EMBL Endo-beta-N-acetylglucosaminidase, helical bundle Endo-beta-N-acetylglucosaminidase, helical bundle This entry represents a three-helix bundle domain of EndoS from Streptococcus pyogenes and similar bacterial proteins. EndoS is involved in immune evasion mechanisms and possesses a specific endoglycosidase activity that targets IgG antibodies [1,2]. Paper describing PDB structure 4nuy. [1]. 24753590. Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies. Trastoy B, Lomino JV, Pierce BG, Carter LG, Gunther S, Giddens JP, Snyder GA, Weiss TM, Weng Z, Wang LX, Sundberg EJ;. Proc Natl Acad Sci U S A. 2014;111:6714-6719. Paper describing PDB structure 6en3. [2]. 29760474. Structural basis for the recognition of complex-type N-glycans by Endoglycosidase S. Trastoy B, Klontz E, Orwenyo J, Marina A, Wang LX, Sundberg EJ, Guerin ME;. Nat Commun. 2018;9:1874. (from Pfam) NF046600.1 PF22143.1 ScpA_C 27 27 91 domain Y N N C5a peptidase, fibronectin type III domain 16344483,19152799,33897974 1301 Streptococcus genus 872 EBI-EMBL C5a peptidase, fibronectin type III domain C5a peptidase, fibronectin type III domain This domain is found at the C-terminal end of C5a peptidase from Streptococcus pyogenes (ScpA) and similar sequences from firmicutes. ScpA is a multidomain cell-envelope subtilase that cleaves complement component C5a. This protein consists of a catalytic domain (Pfam:PF00082) with an inserted PA domain (Pfam:PF02225) and and three tandemly arranged fibronectin type III domains (Fn1-Fn3). This entry represents the last FN domain [1-3]. Paper describing PDB structure 1xf1. [1]. 16344483. Structure of the streptococcal cell wall C5a peptidase. Brown CK, Gu ZY, Matsuka YV, Purushothaman SS, Winter LA, Cleary PP, Olmsted SB, Ohlendorf DH, Earhart CA;. Proc Natl Acad Sci U S A. 2005;102:18391-18396. Paper describing PDB structure 3eif. [2]. 19152799. Model for substrate interactions in C5a peptidase from Streptococcus pyogenes: A 1.9 A crystal structure of the active form of ScpA. Kagawa TF, O'Connell MR, Mouat P, Paoli M, O'Toole PW, Cooney JC;. J Mol Biol. 2009;386:754-772. Paper describing PDB structure 7bj3. [3]. 33897974. Enzyme kinetic and binding studies identify determinants of specificity for the immunomodulatory enzyme ScpA, a C5a inactivating bacterial protease. Tecza M, Kagawa TF, Jain M, Cooney JC;. Comput Struct Biotechnol J. 2021;19:2356-2365. (from Pfam) NF047220.1 PF22610.1 CovS-like_HAMP 27.4 27.4 57 domain Y N N Histidine kinase, HAMP domain 21397188,22244755,23468592,24568954,24680785,24681325 1301 Streptococcus genus 1266 EBI-EMBL Histidine kinase, HAMP domain Histidine kinase, HAMP domain This domain is found at the N-terminal end of the histidine kinase SMU_1516 from Streptococcus mutans (CovS) and similar proteins mainly found in bacilli. CovS plays a role in the regulation of acid production and tolerance conducive to dental caries, including proton expulsion. This protein has one transmembrane domain before a HAMP signal transducer domain (this entry), a PAS sensor domain (Pfam:PF00989), a DHp domain (Pfam:PF00512) and a CA domain (Pfam:PF02518). This domain shows two alpha- helices that form a parallel four-helical coiled-coil when the protein dimerises [6]. Paper describing PDB structure 2l7h. [1]. 21397188. The mechanisms of HAMP-mediated signaling in transmembrane receptors. Ferris HU, Dunin-Horkawicz S, Mondejar LG, Hulko M, Hantke K, Martin J, Schultz JE, Zeth K, Lupas AN, Coles M;. Structure. 2011;19:378-385. Paper describing PDB structure 2lfr. [2]. 22244755. Mechanism of regulation of receptor histidine kinases. Ferris HU, Dunin-Horkawicz S, Hornig N, Hulko M, Martin J, Schultz JE, Zeth K, Lupas AN, Coles M;. Structure. 2012;20:56-66. Paper describing PDB structure 3zx6. [3]. 24680785. Axial helix rotation as a mechanism for signal regulation inferred from the crystallographic analysis of the E. coli serine chemoreceptor. Ferris HU, Zeth K, Hulko M, Dunin-Horkawicz S, Lupas AN;. J Struct Biol. 2014;186:349-356. Paper describing PDB structure 4cq4. [4]. 24568954. A soluble mutant of the transmembrane receptor Af1503 features strong changes in coiled-coil periodicity. Hartmann MD, Dunin-Horkawicz S, Hulko M, Martin J, Coles M, Lupas AN;. J Struct Biol. 2014;186:357-366. Paper describing PDB stru. TRUNCATED at 1650 bytes (from Pfam) NF047589.1 GlcsyltransPgfM1Strep 1400 1400 955 equivalog Y Y N glycosyltransferase PgfM1 pgfM1 29549320,37972006 1301 Streptococcus genus 380 NCBIFAM glycosyltransferase PgfM1 NF047591.1 transregBrpAStrep 450 450 336 equivalog Y Y N biofilm formation/cell division transcriptional regulator BrpA brpA 11872468,16585759 1301 Streptococcus genus 1307 NCBIFAM biofilm formation/cell division transcriptional regulator BrpA TIGR02708.1 TIGR02708 L_lactate_ox 645.5 645.5 367 equivalog Y Y N L-lactate oxidase lctO 10508058,12919327 1301 Streptococcus genus 569 JCVI L-lactate oxidase L-lactate oxidase Members of this protein oxidize L-lactate to pyruvate, reducing molecular oxygen to hydrogen peroxide. The enzyme is known in Aerococcus viridans, Streptococcus iniae, and some strains of Streptococcus pyogenes where it appears to contribute to virulence. TIGR04227.1 TIGR04227 zmp_18_rpt 50 20 18 repeat Y N N zinc metalloproteinase 18-residue repeat-containing protein 23033471 1301 Streptococcus genus 359 JCVI zinc metalloproteinase 18-residue repeat zinc metalloproteinase 18-residue repeat This model describes a short (18-amino acid) tandem repeat that occurs variable numbers of times in zinc metalloproteinase C (ZmpC) homologs in various species of Streptococcus, such as S. sanguinis, S. gordonii, S, mitis, and S. oralis, but notably not S. pneumoniae. This repeat occurs, oddly, as an interruption in a region of tandem repeats of another type. TIGR04307.1 TIGR04307 ProTailRpt 40 10 23 repeat Y N N proline-rich tandem repeat surface protein 1301 Streptococcus genus 44 JCVI proline-rich tail region repeat proline-rich tandem repeat This HMM describes a proline-rich tandem repeat of about 24 residues found in C-terminal regions of Gram-positive surface proteins with LPXTG sequences for processing and cell surface attachment by sortase. NF046094.1 SSU0593_fam 80 80 109 subfamily Y Y N SSU0592/SSU0593 family protein 26110524 1307 Streptococcus suis species 229 NCBIFAM SSU0592/SSU0593 family protein Members of this family appear restricted to Streptococcus suis, but several tandem copies are found, e.g. SSU0592, SSU0593, and SSU0594. The N-terminal region, with an apparent signal peptide or signal-anchor sequence, is well conserved, but the rest shows variability. NF037999.1 mutacin 115 115 63 equivalog Y Y N lantibiotic mutacin mutA 10919773,9596742 1309 Streptococcus mutans species 5 NCBIFAM lantibiotic mutacin Mutacins are lantibiotics in the epidermin/gallidermin/nisin family, found in the biofilm-forming dental caries pathogen Streptococcus mutans. Named members of the family include mutacin I and mutacin 1140. This HMM separates the mutacins (MutA) from paralog MutA' encoded nearby, which lacks mutacin activity. NF038000.1 mutacin_prime 110 110 64 exception Y Y N mutacin-like lanthipeptide mutA' 1309 Streptococcus mutans species 7 NCBIFAM mutacin-like lanthipeptide MutA', a paralog of the nisin-like lantibiotic mutacin precursor MutA, is a lanthipeptide of unknown function, encoded in Streptococcus mutans within the same region. It is not required for mutacin function. NF047590.1 GlcsyltransPgfM2Strep 1500 1500 884 equivalog Y Y N glycosyltransferase PgfM2 pgfM2 29549320,37972006 1309 Streptococcus mutans species 156 NCBIFAM glycosyltransferase PgfM2 NF044667.2 PF20959.2 BibA_N 27 27 48 domain Y N N BibA adhesin stalk domain 32744258 1311 Streptococcus agalactiae species 402 EBI-EMBL BibA adhesin stalk domain BibA adhesin stalk domain BibA, a group B streptococcus (GBS) surface protein, has been shown to protect the pathogen from phagocytic killing by sequestering a complement inhibitor: C4b-binding protein (C4BP) [1]. This entry represents a three helical repeated domain in this protein. Paper describing PDB structure 6poo. [1]. 32744258. Novel structure of the N-terminal helical domain of BibA, a group B streptococcus immunogenic bacterial adhesin. Manne K, Chattopadhyay D, Agarwal V, Blom AM, Khare B, Chakravarthy S, Chang C, Ton-That H, Narayana SVL;. Acta Crystallogr D Struct Biol. 2020;76:759-770. (from Pfam) NF016920.5 PF05062.17 RICH 23.2 23.2 82 domain Y Y N RICH domain-containing protein 1313 Streptococcus pneumoniae species 4944 EBI-EMBL RICH domain RICH domain This presumed domain is about 85 residues in length and very rich in charged residues, hence the name RICH (Rich In CHarged residues). It is found in secreted proteins such as PspC Swiss:Q9KK19, SpsA Swiss:O33742 and IgA FC receptor Swiss:P27951 from Streptococcus agalactiae. This domain could be involved in bacterial adherence or cell wall binding. (from Pfam) NF033215.1 BlpC_Streptocco 70 70 51 equivalog Y Y N quorum-sensing system pheromone BlpC blpC 1313 Streptococcus pneumoniae species 103 NCBIFAM quorum-sensing system pheromone BlpC quorum-sensing system pheromone BlpC Members of this family are BlpC, a peptide pheromone that stimulates production of BLP (bacteriocin-like peptides) family class II bacteriocins. BlpC peptides fall within the broader family of PF03047, a homology family of pheromone/bacteriocin precursors that is also restricted to Streptococcus. The PF03047 HMM runs only a few residues past the GlyGly precursor peptide cleavage site, and thus does not distinguish BlpC from other pheromone precursors, such as ComC. NF033771.1 colonize_BriC 120 120 60 equivalog Y Y N biofilm-regulating peptide BriC briC 30308062 1313 Streptococcus pneumoniae species 84 NCBIFAM biofilm-regulating peptide BriC biofilm-regulating peptide BriC BriC (Biofilm-Regulating peptide Induced by Competence), as characterized in Streptococcus pneumoniae, is a cell-cell communication peptide, or peptide pheromone, that is induced by expression of ComE (a master regulator of competence). BriC contributes to biofilm formation, and to colonization in a mouse mole. NF033772.1 pheromone_VP1 85 85 65 equivalog Y Y N peptide pheromone VP1 28557053 1313 Streptococcus pneumoniae species 73 NCBIFAM peptide pheromone VP1 peptide pheromone VP1 VP1 (virulence peptide 1), as characterized in Streptococcus pneumoniae (a.k.a. pneumococcus), is part of a large panel of secreted regulatory peptides with paralogous leader domains, typically ending with the cleavage site GlyGly, but with highly variable core regions. VP1, along with other pneumococcal peptide pheromones such as BriC, participate to cell-cell communication to regulate pathogenic processes such as biofilm formation. NF033838.0 PspC_subgroup_1 700 500 684 exception Y Y N pneumococcal surface protein PspC, choline-binding form pspC 11891047,30323030 1313 Streptococcus pneumoniae species 2539 NCBIFAM pneumococcal surface protein PspC, choline-binding form pneumococcal surface protein PspC, choline-binding form The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A. The other form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. NF033839.1 PspC_subgroup_2 500 225 557 exception Y Y N pneumococcal surface protein PspC, LPXTG-anchored form pspC 11891047,30323030 1313 Streptococcus pneumoniae species 604 NCBIFAM pneumococcal surface protein PspC, LPXTG-anchored form pneumococcal surface protein PspC, LPXTG-anchored form The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A. NF033930.1 pneumo_PspA 850 500 659 exception Y Y N pneumococcal surface protein A pspA 10456922,30323030 1313 Streptococcus pneumoniae species 1697 NCBIFAM pneumococcal surface protein A pneumococcal surface protein A The pneumococcal surface protein proteins, found in Streptococcus pneumoniae, are repetitive, with patterns of localized high sequence identity across pairs of proteins given different specific names that recombination may be presumed. This protein, PspA, has an N-terminal region that lacks a cross-wall-targeting YSIRK type extended signal peptide, in contrast to the closely related choline-binding protein CbpA which has a similar C-terminus but a YSIRK-containing region at the N-terminus. NF038031.1 PavB_Nterm 225 225 128 equivalog_domain Y Y N PavB family fibronectin-binding SSURE repeat adhesin 28657670 1313 Streptococcus pneumoniae species 1134 NCBIFAM PavB family adhesin N-terminal domain This HMM describes the portion of PavB from Streptococcus pneumoniae, and closely related proteins from Streptococcus mitis and Streptococcus pseudopneumoniae, N-terminal to the repetitive region with variable numbers of SSURE (Streptococcal Surface REpeats) regions (see PF11966), which bind fibronectin. The PavB region is notable, in part, for its rare variant, WSIRR, of the YSIRK motif signal peptide. Full-length versions of proteins from this family have a C-terminal LPXTG-containing region for sortase-mediated anchoring to the cell wall. NF040533.1 endo_SpGH101 2900 2900 1962 exception Y Y N SpGH101 family endo-alpha-N-acetylgalactosaminidase 3.2.1.97 GO:0033926 19788271,20556855 1313 Streptococcus pneumoniae species 1302 NCBIFAM SpGH101 family endo-alpha-N-acetylgalactosaminidase Members of this family are streptococcal surface proteins with a complex (and somewhat variable) architecture that includes a crosswall-targeting N-terminal YSIRK domain, a C-terminal cell wall-anchoring LPXTG domain, and a central endo-alpha-N-acetylgalactosaminidase that removes an O-linked disaccharide from host glycoproteins. NF042929.1 immun_PncF_fam 45 45 36 subfamily Y Y N PncF family bacteriocin immunity protein 17704229,30915281 1313 Streptococcus pneumoniae species 146 NCBIFAM PncF family bacteriocin immunity protein NF046017.1 ZmpA 3000 3000 2052 exception Y Y N zinc metalloprotease A zmpA GO:0004222,GO:0006508,GO:0008236,GO:0008270 28028839,31481387 1313 Streptococcus pneumoniae species 313 NCBIFAM zinc metalloprotease A NF046019.1 ZmpB 3000 3000 1969 exception Y Y N zinc metalloprotease B zmpB GO:0004222,GO:0006508,GO:0008270 31481387 1313 Streptococcus pneumoniae species 67 NCBIFAM zinc metalloprotease B NF046021.1 ZmpC 3000 3000 2181 exception Y Y N zinc metalloprotease C zmpC GO:0004222,GO:0006508,GO:0008270 31481387 1313 Streptococcus pneumoniae species 53 NCBIFAM zinc metalloprotease C NF046024.1 ZmpD 3000 3000 1812 exception Y Y N zinc metalloprotease D zmpD GO:0004222,GO:0006508,GO:0008270 31481387 1313 Streptococcus pneumoniae species 274 NCBIFAM zinc metalloprotease D NF003362.0 PRK04439 PRK04439.1-1 481 481 406 equivalog Y Y N methionine adenosyltransferase 2.5.1.6 1314 Streptococcus pyogenes species 99 NCBI Protein Cluster (PRK) S-adenosylmethionine synthetase methionine adenosyltransferase NF005053.0 PRK06462 PRK06462.1-3 322 322 274 equivalog Y N N asparagine synthetase A 1314 Streptococcus pyogenes species 101 NCBI Protein Cluster (PRK) asparagine synthetase A asparagine synthetase A NF014429.5 PF02370.21 M 20.8 15.6 21 domain Y N N M protein repeat 8830235 1314 Streptococcus pyogenes species 830 EBI-EMBL M protein repeat M protein repeat This short repeat is found in multiple copies in bacterial M proteins. The M proteins bind to IgA and are closely associated with virulence. The M protein has been postulated to be a major group A Streptococcal (GAS) virulence factor because of its contribution to the bacterial resistance to opsonophagocytosis [1]. [1]. 8830235. M-related protein (Mrp) contributes to group A streptococcal resistance to phagocytosis by human granulocytes. Podbielski A, Schnitzler N, Beyhs P, Boyle MD;. Mol Microbiol 1996;19:429-441. (from Pfam) NF015447.5 PF03482.18 SIC 25 25 30 repeat Y N N lysis inhibitor SIC family protein 10426317 1314 Streptococcus pyogenes species 153 EBI-EMBL sic protein repeat lysis inhibitor SIC repeat Serotype M1 group A Streptococcus strains cause epidemic waves of human infections. This 30 aa repeat occurs in the sic protein, an extracellular protein (streptococcal inhibitor of complement) that inhibits human complement [1]. [1]. 10426317. Rapid selection of complement-inhibiting protein variants in group A Streptococcus epidemic waves. Hoe NP, Nakashima K, Lukomski S, Grigsby D, Liu M, Kordari P, Dou SJ, Pan X, Vuopio-Varkila J, Salmelinna S, McGeer A, Low DE, Schwartz B, Schuchat A, Naidich S, De Lorenzo D, Fu YX, Musser JM;. Nat Med 1999;5:924-929. (from Pfam) NF023529.5 PF12107.13 VEK-30 20.8 20.8 17 PfamEq Y N N Plasminogen (Pg) ligand in fibrinolytic pathway 16964966 1314 Streptococcus pyogenes species 138 EBI-EMBL Plasminogen (Pg) ligand in fibrinolytic pathway Plasminogen (Pg) ligand in fibrinolytic pathway Pg is an important mediator of angiostatin production in the fibrinolytic pathway. Pg is made up of five subunit kringle molecules (Pg-K1 to Pg-K5), of which the first three make the protein angiostatin. VEK-30 is a domain of the group A streptococcal protein PAM. It binds to Pg-K2 of angiostatin and activates the molecule to mediate its anti-angiogenic effects. VEK-30 binds to angiostatin via a C terminal lysine with argininyl and glutamyl side chain residues known as a 'through space isostere'. [1] [1]. 16964966. X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group A streptococcal surface protein PAM. Cnudde SE, Prorok M, Castellino FJ, Geiger JH;. Biochemistry. 2006;45:11052-11060. (from Pfam) NF033395.0 fibronec_SfbI 800 500 593 exception Y Y N fibronectin-binding protein PrtF1/SfbI prtF1 17371855 1314 Streptococcus pyogenes species 528 NCBIFAM fibronectin-binding protein SfbI fibronectin-binding protein PrtF1/SfbI PrtF1/SfbI is a fibronectin-binding protein a C-terminal region LPXTG region that mediates processing by sortase and covalent attachment to the cell wall. Near the N-terminus is a TED domain, which includes a Cys residue that forms a covalent thioester bond. NF033396.0 pilus_ancill_1 600 600 737 equivalog Y Y N pilus ancillary protein 1 18928376 1314 Streptococcus pyogenes species 206 NCBIFAM pilus ancillary protein 1 pilus ancillary protein 1 NF033798.1 biofilm_StcA 50 50 89 subfamily Y Y N StcA family protein 29555699 1314 Streptococcus pyogenes species 72 NCBIFAM StcA family protein StcA family protein StcA (streptococcal charged A protein), as described in Streptococcus pyogenes, is a small, positively charged, secreted protein that participates in a quorum-sensing system, and promotes biofilm formation. Related proteins are found in several other Streptococcus spp. NF033913.1 fibronec_FbpA 400 400 384 exception Y Y N LPXTG-anchored fibronectin-binding protein FbpA fbpA 28808160 1314 Streptococcus pyogenes species 286 NCBIFAM LPXTG-anchored fibronectin-binding protein FbpA LPXTG-anchored fibronectin-binding protein FbpA FbpA, a fibronectin-binding protein described in Streptococcus pyogenes, has a YSIRK-type (crosswall-targeting) signal peptide and a C-terminal LPXTG motif for covalent attachment to the cell wall. It is unrelated to the PavA-like protein from Streptococcus gordonii (see BlastRule NBR009716) that was given the identical name, so the phase LPXTG-anchored is added to the protein name for clarity. NF038329.2 gly_rich_SclB 325 250 442 equivalog Y Y N LPXTG-anchored collagen-like adhesin Scl2/SclB slc2 11158359,11179350,11976327,22245789,23989154 1314 Streptococcus pyogenes species 1563 NCBIFAM LPXTG-anchored collagen-like adhesin Scl2/SclB SclB (or Scl2 - streptococcal collagen-like protein 2) is an LPXTG-anchored surface-anchored adhesin with a variable-length region of triple helix-forming collagen-like Gly-Xaa-Xaa repeats. NF038330.1 adhesin_SclA 400 220 405 exception Y Y N LPXTG-anchored collagen-like adhesin Scl1/SclA scl1 11035747,11976327,21159159 1314 Streptococcus pyogenes species 910 NCBIFAM LPXTG-anchored collagen-like adhesin Scl1/SclA Scl1 (streptococcal collagen-like protein 1), also called SclA, is an LPXTG-anchored surface-anchored adhesin with a variable-length region of triple helix-forming collagen-like Gly-Xaa-Xaa repeats. NF043072.1 GAS_sig_Nterm 44 44 33 subfamily_domain Y Y N SpoV family signaling peptide 33722844,34835447 1314 Streptococcus pyogenes species 319 NCBIFAM SpoV family signaling peptide N-terminal domain Members of this family include SpyM3_0132 from Streptococcus pyogenes MGAS315, named SpoV (streptococcal peptide controlling virulence), and tandem proteins Spy0169 and SPy0170. The N-terminal region is well conserved among members of this family, while C-terminal regions may be unrelated. The family appears restricted to Streptococcus pyogenes (Group A Streptotoccus). NF000355.4 ribo_prot_ABC_F 380 350 499 equivalog Y Y N ribosomal protection-like ABC-F family protein abc-f GO:0003677,GO:0005524,GO:0016887 18535149,24687494 131567 cellular organisms no rank 45369 NCBIFAM ABC-F type ribosomal protection protein ribosomal protection-like ABC-F family protein NF000584.1 PRK00009 PRK00009.1 815 815 898 equivalog Y Y N phosphoenolpyruvate carboxylase ppc 4.1.1.31 GO:0006099,GO:0008964,GO:0015977 131567 cellular organisms no rank 40795 NCBI Protein Cluster (PRK) phosphoenolpyruvate carboxylase phosphoenolpyruvate carboxylase NF000586.1 PRK00011 PRK00011.1 335 335 404 subfamily Y Y N serine hydroxymethyltransferase 2.1.2.1 GO:0004372,GO:0019264 12913008 131567 cellular organisms no rank 95320 NCBI Protein Cluster (PRK) serine hydroxymethyltransferase serine hydroxymethyltransferase NF000592.1 PRK00013 PRK00013.1 397 397 524 subfamily Y Y N chaperonin GroEL groEL 131567 cellular organisms no rank 75402 NCBI Protein Cluster (PRK) chaperonin GroEL chaperonin GroEL NF000642.1 PRK00024 PRK00024.1 180 180 212 equivalog Y Y N DNA repair protein RadC radC GO:0003677,GO:0006281 131567 cellular organisms no rank 41700 NCBI Protein Cluster (PRK) hypothetical protein DNA repair protein RadC NF000658.1 PRK00029 PRK00029.1 431 431 462 subfamily Y Y N YdiU family protein 131567 cellular organisms no rank 47709 NCBI Protein Cluster (PRK) hypothetical protein YdiU family protein NF000711.0 PRK00039 PRK00039.2-1 163 163 161 equivalog Y Y N crossover junction endodeoxyribonuclease RuvC ruvC 3.1.21.10 GO:0006310,GO:0008821 131567 cellular organisms no rank 10247 NCBI Protein Cluster (PRK) Holliday junction resolvase crossover junction endodeoxyribonuclease RuvC NF000756.0 PRK00047 PRK00047.1 498 498 502 subfamily Y Y N glycerol kinase GlpK glpK 2.7.1.30 15383715 131567 cellular organisms no rank 72247 NCBI Protein Cluster (PRK) glycerol kinase glycerol kinase GlpK NF000766.0 PRK00049 PRK00049.1 449 449 396 subfamily Y Y N elongation factor Tu 12963376,14622294,15147200 131567 cellular organisms no rank 60918 NCBI Protein Cluster (PRK) elongation factor Tu elongation factor Tu EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts NF000768.0 PRK00051 PRK00051.1 126 126 131 equivalog Y Y N phosphoribosyl-AMP cyclohydrolase hisI 3.5.4.19 GO:0000105,GO:0004635 16042384,9931020 131567 cellular organisms no rank 55747 NCBI Protein Cluster (PRK) phosphoribosyl-AMP cyclohydrolase phosphoribosyl-AMP cyclohydrolase Functions in histidine biosynthesis from PRPP; converts 1-(5-phosphoribosyl)-AMP to 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxyamide during the histidine biosynthesis pathway; binds zinc and magnesium; forms homodimers NF000796.0 PRK00054 PRK00054.1-1 224 224 254 equivalog Y Y N dihydroorotate dehydrogenase electron transfer subunit 131567 cellular organisms no rank 725 NCBI Protein Cluster (PRK) dihydroorotate dehydrogenase electron transfer subunit dihydroorotate dehydrogenase electron transfer subunit NF000801.0 PRK00055 PRK00055.1-3 252 252 307 equivalog Y Y N ribonuclease Z 3.1.26.11 GO:0016891,GO:0042780 131567 cellular organisms no rank 25921 NCBI Protein Cluster (PRK) ribonuclease Z ribonuclease Z NF000818.0 PRK00062 PRK00062.1 398 398 429 subfamily Y Y N glutamate-1-semialdehyde 2,1-aminomutase 5.4.3.8 9144156 131567 cellular organisms no rank 64225 NCBI Protein Cluster (PRK) glutamate-1-semialdehyde aminotransferase glutamate-1-semialdehyde 2,1-aminomutase Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway NF000824.0 PRK00066 PRK00066.1 339 339 316 subfamily Y Y N L-lactate dehydrogenase 1.1.1.27 131567 cellular organisms no rank 14865 NCBI Protein Cluster (PRK) L-lactate dehydrogenase L-lactate dehydrogenase NF000848.0 PRK00074 PRK00074.1 423 423 512 equivalog Y Y N glutamine-hydrolyzing GMP synthase guaA 6.3.5.2 GO:0003922,GO:0005524,GO:0006177,GO:0016462 8208731,8548458 131567 cellular organisms no rank 69077 NCBI Protein Cluster (PRK) GMP synthase glutamine-hydrolyzing GMP synthase Contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway NF000849.0 PRK00075 PRK00075.1-1 348 348 366 equivalog Y Y N cobalt-precorrin-5B (C(1))-methyltransferase 2.1.1.195 GO:0008168,GO:0009236 131567 cellular organisms no rank 13266 NCBI Protein Cluster (PRK) cobalt-precorrin-6A synthase cobalt-precorrin-5B (C(1))-methyltransferase NF000868.0 PRK00080 PRK00080.1 282 282 330 equivalog Y Y N Holliday junction branch migration DNA helicase RuvB ruvB 3.6.4.12 GO:0003677,GO:0005524,GO:0006281,GO:0006310,GO:0009378 12054856,8433990 131567 cellular organisms no rank 55712 NCBI Protein Cluster (PRK) Holliday junction DNA helicase RuvB Holliday junction DNA helicase RuvB Promotes strand exchange during homologous recombination; RuvAB complex promotes branch migration; RuvABC complex scans the DNA during branch migration and resolves Holliday junctions at consensus sequences; forms hexameric rings around opposite DNA arms; requires ATP for branch migration and orientation of RuvAB complex determines direction of migration NF000940.0 PRK00094 PRK00094.1-2 202 202 330 subfamily Y Y N NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 1.1.1.94 131567 cellular organisms no rank 63493 NCBI Protein Cluster (PRK) NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NF000942.0 PRK00094 PRK00094.1-4 257 257 334 subfamily Y Y N NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 1.1.1.94 GO:0006072,GO:0016616,GO:0047952 131567 cellular organisms no rank 63654 NCBI Protein Cluster (PRK) NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NF000985.0 PRK00103 PRK00103.1-3 172 172 159 equivalog Y Y N 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH rlmH 2.1.1.177 GO:0006364,GO:0008168 131567 cellular organisms no rank 11603 NCBI Protein Cluster (PRK) rRNA large subunit methyltransferase 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH NF000990.0 PRK00103 PRK00103.2-4 207 207 157 equivalog Y Y N 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH rlmH GO:0006364,GO:0008168 131567 cellular organisms no rank 4130 NCBI Protein Cluster (PRK) rRNA large subunit methyltransferase 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH NF000996.0 PRK00105 PRK00105.1 306 306 350 subfamily Y Y N nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase 2.4.2.21 131567 cellular organisms no rank 56272 NCBI Protein Cluster (PRK) nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide and 5,6-dimethylbenzimidazole NF001080.0 PRK00121 PRK00121.2-2 132 132 224 equivalog Y Y N tRNA (guanosine(46)-N7)-methyltransferase TrmB trmB 2.1.1.33 GO:0006400,GO:0008176 131567 cellular organisms no rank 17899 NCBI Protein Cluster (PRK) tRNA (guanine-N(7)-)-methyltransferase tRNA (guanosine(46)-N7)-methyltransferase TrmB NF001097.0 PRK00129 PRK00129.1 114 114 209 equivalog Y Y N uracil phosphoribosyltransferase upp 2.4.2.9 GO:0004845,GO:0009116 131567 cellular organisms no rank 40315 NCBI Protein Cluster (PRK) uracil phosphoribosyltransferase uracil phosphoribosyltransferase NF001100.0 PRK00133 PRK00133.1 587 587 676 equivalog Y Y N methionine--tRNA ligase metG 6.1.1.10 GO:0000166,GO:0004825,GO:0005524,GO:0006431 10600385,11243794,15388861,16155581,16189106 131567 cellular organisms no rank 35486 NCBI Protein Cluster (PRK) methionyl-tRNA synthetase methionine--tRNA ligase MetRS; adds methionine to tRNA(Met) with cleavage of ATP to AMP and diphosphate; some MetRS enzymes form dimers depending on a C-terminal domain that is also found in other proteins such as Trbp111 in Aquifex aeolicus and the cold-shock protein CsaA from Bacillus subtilis while others do not; four subfamilies exist based on sequence motifs and zinc content NF001126.0 PRK00139 PRK00139.1-4 373 373 486 equivalog Y Y N UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase 6.3.2.13 GO:0005524,GO:0008360,GO:0009058,GO:0016874,GO:0051301 131567 cellular organisms no rank 80838 NCBI Protein Cluster (PRK) UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase NF001138.1 PRK00143 PRK00143.1 284 284 345 equivalog Y Y N tRNA 2-thiouridine(34) synthase MnmA mnmA 2.8.1.13 GO:0008033,GO:0016740,GO:0016783 3298234 131567 cellular organisms no rank 73930 NCBI Protein Cluster (PRK) tRNA-specific 2-thiouridylase MnmA tRNA 2-thiouridine(34) synthase MnmA Catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs NF001140.0 PRK00147 PRK00147.1 324 324 346 equivalog Y Y N tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA queA 2.4.99.17 GO:0016740,GO:0016853 12731872 131567 cellular organisms no rank 54420 NCBI Protein Cluster (PRK) S-adenosylmethionine:tRNA ribosyltransferase-isomerase tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step NF001159.1 PRK00150 PRK00150.1-3 125 125 167 subfamily Y Y N peptide deformylase 3.5.1.88 131567 cellular organisms no rank 84833 NCBI Protein Cluster (PRK) peptide deformylase peptide deformylase NF001183.0 PRK00155 PRK00155.1-3 166 166 237 subfamily Y Y N D-ribitol-5-phosphate cytidylyltransferase 2.7.7.40 131567 cellular organisms no rank 5653 NCBI Protein Cluster (PRK) 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase D-ribitol-5-phosphate cytidylyltransferase NF001199.0 PRK00164 PRK00164.2-1 231 231 308 equivalog Y Y N GTP 3',8-cyclase MoaA moaA 4.1.99.22 131567 cellular organisms no rank 6809 NCBI Protein Cluster (PRK) molybdenum cofactor biosynthesis protein A GTP 3',8-cyclase MoaA NF001208.0 PRK00174 PRK00174.1 657 657 649 subfamily Y Y N acetate--CoA ligase 6.2.1.1 10735852,12627952,17497934 131567 cellular organisms no rank 77435 NCBI Protein Cluster (PRK) acetyl-CoA synthetase acetate--CoA ligase Catalyzes the conversion of acetate and CoA to acetyl-CoA NF001209.0 PRK00175 PRK00175.1 331 331 381 equivalog Y Y N homoserine O-acetyltransferase 2.3.1.31 GO:0009058,GO:0016747 9209059 131567 cellular organisms no rank 31090 NCBI Protein Cluster (PRK) homoserine O-acetyltransferase homoserine O-acetyltransferase Catalyzes the formation of O-acetyl -L-homoserine from L-homoserine and acetyl-CoA NF001220.0 PRK00194 PRK00194.1 74 74 90 equivalog Y Y N ACT domain-containing protein 131567 cellular organisms no rank 5473 NCBI Protein Cluster (PRK) hypothetical protein ACT domain-containing protein NF001221.0 PRK00197 PRK00197.1 289 289 418 equivalog Y Y N glutamate-5-semialdehyde dehydrogenase 1.2.1.41 GO:0004350,GO:0006561,GO:0016620 10330610 131567 cellular organisms no rank 74029 NCBI Protein Cluster (PRK) gamma-glutamyl phosphate reductase glutamate-5-semialdehyde dehydrogenase Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway NF001243.0 PRK00216 PRK00216.1-4 235 235 237 equivalog Y Y N demethylmenaquinone methyltransferase 2.1.1.163 GO:0008168,GO:0009234 131567 cellular organisms no rank 5112 NCBI Protein Cluster (PRK) ubiquinone/menaquinone biosynthesis methyltransferase demethylmenaquinone methyltransferase NF001244.0 PRK00216 PRK00216.1-5 216 216 236 equivalog Y Y N bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol methylase UbiE ubiE 2.1.1.163,2.1.1.201 GO:0042372,GO:0052624 131567 cellular organisms no rank 29983 NCBI Protein Cluster (PRK) ubiquinone/menaquinone biosynthesis methyltransferase bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol methylase UbiE NF001299.0 PRK00241 PRK00241.1 158 158 263 equivalog Y Y N NAD(+) diphosphatase nudC 3.6.1.22 GO:0000210,GO:0016787 7829480 131567 cellular organisms no rank 42539 NCBI Protein Cluster (PRK) NADH pyrophosphatase NAD(+) diphosphatase NF001314.0 PRK00258 PRK00258.2-2 248 248 290 equivalog Y Y N shikimate dehydrogenase 1.1.1.25 131567 cellular organisms no rank 2381 NCBI Protein Cluster (PRK) shikimate 5-dehydrogenase shikimate dehydrogenase NF001319.0 PRK00258 PRK00258.3-3 252 252 279 equivalog Y Y N shikimate dehydrogenase 1.1.1.25 GO:0004764,GO:0019632 131567 cellular organisms no rank 14530 NCBI Protein Cluster (PRK) shikimate 5-dehydrogenase shikimate dehydrogenase NF001322.0 PRK00258 PRK00258.3-6 285 285 272 equivalog Y Y N shikimate dehydrogenase 1.1.1.25 131567 cellular organisms no rank 25 NCBI Protein Cluster (PRK) shikimate 5-dehydrogenase shikimate dehydrogenase NF001368.0 PRK00277 PRK00277.1 249 249 203 subfamily Y Y N ATP-dependent Clp protease proteolytic subunit GO:0004252,GO:0006508 11447171,12101312,12270812,12511518,15317791,15385462,9678574 131567 cellular organisms no rank 61381 NCBI Protein Cluster (PRK) ATP-dependent Clp protease proteolytic subunit ATP-dependent Clp protease proteolytic subunit Hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates NF001370.0 PRK00278 PRK00278.1-2 348 348 266 equivalog Y Y N indole-3-glycerol phosphate synthase TrpC trpC 4.1.1.48 GO:0004425,GO:0006568 131567 cellular organisms no rank 15330 NCBI Protein Cluster (PRK) indole-3-glycerol-phosphate synthase indole-3-glycerol phosphate synthase TrpC NF001373.0 PRK00278 PRK00278.1-6 317 317 263 equivalog Y Y N indole-3-glycerol phosphate synthase TrpC trpC 4.1.1.48 GO:0004425,GO:0006568 131567 cellular organisms no rank 20448 NCBI Protein Cluster (PRK) indole-3-glycerol-phosphate synthase indole-3-glycerol phosphate synthase TrpC NF001376.0 PRK00278 PRK00278.2-3 284 284 255 equivalog Y Y N indole-3-glycerol phosphate synthase TrpC trpC 4.1.1.48 131567 cellular organisms no rank 273 NCBI Protein Cluster (PRK) indole-3-glycerol-phosphate synthase indole-3-glycerol phosphate synthase TrpC NF001377.0 PRK00278 PRK00278.2-4 260 260 259 equivalog Y Y N indole-3-glycerol phosphate synthase TrpC trpC 4.1.1.48 GO:0004425,GO:0006568 131567 cellular organisms no rank 58374 NCBI Protein Cluster (PRK) indole-3-glycerol-phosphate synthase indole-3-glycerol phosphate synthase TrpC NF001380.0 PRK00279 PRK00279.1-2 251 251 216 equivalog Y Y N adenylate kinase 2.7.4.3 GO:0005524,GO:0006139,GO:0016776,GO:0019205 131567 cellular organisms no rank 29577 NCBI Protein Cluster (PRK) adenylate kinase adenylate kinase NF001381.0 PRK00279 PRK00279.1-3 187 187 188 equivalog Y Y N adenylate kinase 2.7.4.3 GO:0005524,GO:0006139,GO:0019205 131567 cellular organisms no rank 50272 NCBI Protein Cluster (PRK) adenylate kinase adenylate kinase NF001386.0 PRK00279 PRK00279.2-4 256 256 220 equivalog Y Y N adenylate kinase 2.7.4.3 131567 cellular organisms no rank 68 NCBI Protein Cluster (PRK) adenylate kinase adenylate kinase NF001389.0 PRK00281 PRK00281.1-2 262 262 272 equivalog Y Y N undecaprenyl-diphosphate phosphatase 3.6.1.27 GO:0016020,GO:0016311,GO:0050380 131567 cellular organisms no rank 23696 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate phosphatase undecaprenyl-diphosphate phosphatase NF001390.0 PRK00281 PRK00281.1-4 260 260 272 equivalog Y Y N undecaprenyl-diphosphate phosphatase 3.6.1.27 GO:0016020,GO:0016311,GO:0050380 131567 cellular organisms no rank 29962 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate phosphatase undecaprenyl-diphosphate phosphatase NF001413.0 PRK00290 PRK00290.1 648 648 625 equivalog Y Y N molecular chaperone DnaK dnaK GO:0005524,GO:0006457,GO:0016887 12763042,25058675,8658133,9609686 131567 cellular organisms no rank 72481 NCBI Protein Cluster (PRK) molecular chaperone DnaK molecular chaperone DnaK Heat shock protein 70; assists in folding of nascent polypeptide chains; refolding of misfolded proteins; utilizes ATPase activity to help fold; co-chaperones are DnaJ and GrpE NF001452.0 PRK00311 PRK00311.1 272 272 267 subfamily Y Y N 3-methyl-2-oxobutanoate hydroxymethyltransferase 2.1.2.11 12842039 131567 cellular organisms no rank 56033 NCBI Protein Cluster (PRK) 3-methyl-2-oxobutanoate hydroxymethyltransferase 3-methyl-2-oxobutanoate hydroxymethyltransferase NF001453.0 PRK00312 PRK00312.1 188 188 217 equivalog Y Y N protein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 GO:0004719,GO:0036211 11080641 131567 cellular organisms no rank 29011 NCBI Protein Cluster (PRK) protein-L-isoaspartate O-methyltransferase protein-L-isoaspartate(D-aspartate) O-methyltransferase Catalyzes the methyl esterification of L-isoaspartyl residues that are formed in damaged proteins NF001454.0 PRK00315 PRK00315.1 178 178 193 equivalog Y Y N potassium-transporting ATPase subunit KdpC kdpC 7.2.2.6 GO:0006813,GO:0008556,GO:0016020 11248697 131567 cellular organisms no rank 29728 NCBI Protein Cluster (PRK) potassium-transporting ATPase subunit C potassium-transporting ATPase subunit KdpC Component of the high-affinity ATP-driven potassium transport (or KDP)system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions NF001484.0 PRK00331 PRK00331.1 381 381 601 subfamily Y Y N isomerizing glutamine--fructose-6-phosphate transaminase 2.6.1.16 7476196 131567 cellular organisms no rank 88565 NCBI Protein Cluster (PRK) glucosamine--fructose-6-phosphate aminotransferase isomerizing glutamine--fructose-6-phosphate transaminase Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source NF001490.0 PRK00346 PRK00346.1-4 233 233 254 equivalog Y Y N 5'/3'-nucleotidase SurE surE 3.1.3.6 GO:0008252 131567 cellular organisms no rank 31918 NCBI Protein Cluster (PRK) 5'(3')-nucleotidase/polyphosphatase 5'/3'-nucleotidase SurE NF001503.0 PRK00349 PRK00349.1 1147 1147 943 equivalog Y Y N excinuclease ABC subunit UvrA uvrA 3.1.25.- GO:0003677,GO:0005524,GO:0006289,GO:0016887 15358371,20455546 131567 cellular organisms no rank 88236 NCBI Protein Cluster (PRK) excinuclease ABC subunit A excinuclease ABC subunit UvrA The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 uvrA and 2 uvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by uvrB, the uvrA molecules dissociate NF001567.0 PRK00389 PRK00389.1 300 300 359 subfamily Y Y N glycine cleavage system aminomethyltransferase GcvT gcvT 2.1.2.10 14995075 131567 cellular organisms no rank 64033 NCBI Protein Cluster (PRK) glycine cleavage system aminomethyltransferase T glycine cleavage system aminomethyltransferase GcvT Catalyzes the transfer of a methylene carbon from the methylamine-loaded GcvH protein to tetrahydrofolate, causing the release of ammonia and the generation of reduced GcvH protein NF001591.0 PRK00393 PRK00393.1 148 148 199 subfamily Y Y N GTP cyclohydrolase II RibA ribA 3.5.4.25 11301327 131567 cellular organisms no rank 60466 NCBI Protein Cluster (PRK) GTP cyclohydrolase II GTP cyclohydrolase II RibA Catalyzes the conversion of GTP to formate and 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine and diphosphate NF001611.0 PRK00400 PRK00400.1-3 99 99 108 equivalog Y Y N phosphoribosyl-ATP diphosphatase 3.6.1.31 GO:0000105,GO:0004636 131567 cellular organisms no rank 13787 NCBI Protein Cluster (PRK) phosphoribosyl-ATP pyrophosphatase phosphoribosyl-ATP diphosphatase NF001614.1 PRK00402 PRK00402.1 385 385 415 subfamily Y Y N aconitase/3-isopropylmalate dehydratase large subunit family protein 4.2.1.33 11328601 131567 cellular organisms no rank 13863 NCBI Protein Cluster (PRK) 3-isopropylmalate dehydratase large subunit aconitase/3-isopropylmalate dehydratase large subunit family protein NF001616.1 PRK00405 PRK00405.1 896 896 1096 equivalog Y Y N DNA-directed RNA polymerase subunit beta 2.7.7.6 GO:0003677,GO:0003899,GO:0006351,GO:0032549 16524917,6266829 131567 cellular organisms no rank 64706 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit beta DNA-directed RNA polymerase subunit beta DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates NF001617.0 PRK00407 PRK00407.1 126 126 139 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 534 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF001624.0 PRK00411 PRK00411.1-2 354 354 374 subfamily Y Y N ORC1-type DNA replication protein 131567 cellular organisms no rank 1097 NCBI Protein Cluster (PRK) cell division control protein 6 ORC1-type DNA replication protein NF001662.0 PRK00431 PRK00431.1-3 215 215 185 equivalog Y Y N [protein ADP-ribosylglutamate] hydrolase 131567 cellular organisms no rank 112 NCBI Protein Cluster (PRK) RNase III inhibitor [protein ADP-ribosylglutamate] hydrolase NF001664.0 PRK00431 PRK00431.1-6 200 200 173 equivalog Y Y N O-acetyl-ADP-ribose deacetylase 3.1.1.106 19141481,21257746,26481419 131567 cellular organisms no rank 25094 NCBI Protein Cluster (PRK) RNase III inhibitor O-acetyl-ADP-ribose deacetylase NF001696.0 PRK00451 PRK00451.1 364 364 447 equivalog Y Y N aminomethyl-transferring glycine dehydrogenase subunit GcvPA gcvPA 1.4.4.2 GO:0004375,GO:0006546 131567 cellular organisms no rank 27642 NCBI Protein Cluster (PRK) glycine dehydrogenase subunit 1 aminomethyl-transferring glycine dehydrogenase subunit GcvPA NF001750.0 PRK00476 PRK00476.1 443 443 590 equivalog Y Y N aspartate--tRNA ligase aspS 6.1.1.12 GO:0000166,GO:0004812,GO:0005524,GO:0006418,GO:0016874 131567 cellular organisms no rank 75681 NCBI Protein Cluster (PRK) aspartyl-tRNA synthetase aspartate--tRNA ligase Catalyzes a two-step reaction, first charging an aspartate molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; contains discriminating and non-discriminating subtypes NF001752.0 PRK00481 PRK00481.1-1 221 221 242 equivalog Y Y N NAD-dependent protein deacylase 2.3.1.286 GO:0034979,GO:0051287,GO:0070403 131567 cellular organisms no rank 11106 NCBI Protein Cluster (PRK) NAD-dependent deacetylase NAD-dependent protein deacylase NF001753.0 PRK00481 PRK00481.1-3 243 243 252 subfamily Y Y N NAD-dependent protein deacylase 2.3.1.286 131567 cellular organisms no rank 12840 NCBI Protein Cluster (PRK) NAD-dependent deacetylase NAD-dependent protein deacylase NF001756.1 PRK00484 PRK00484.1 468 468 488 subfamily Y Y N lysine--tRNA ligase 6.1.1.6 14536069,15314242 131567 cellular organisms no rank 64316 NCBI Protein Cluster (PRK) lysyl-tRNA synthetase lysine--tRNA ligase Class II; LysRS2; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri, LysRS2 charges both tRNA molecules for lysine that exist in this organism and in addition can charge the tRNAPyl with lysine in the presence of LysRS1 NF001770.0 PRK00509 PRK00509.1 334 334 401 equivalog Y Y N argininosuccinate synthase 6.3.4.5 GO:0004055,GO:0005524,GO:0006526 131567 cellular organisms no rank 38931 NCBI Protein Cluster (PRK) argininosuccinate synthase argininosuccinate synthase Catalyzes the formation of arginosuccinate from citrulline and aspartate in arginine biosynthesis NF001810.0 PRK00529 PRK00529.1 161 161 187 subfamily Y Y N elongation factor P 131567 cellular organisms no rank 40518 NCBI Protein Cluster (PRK) elongation factor P elongation factor P Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA NF001824.0 PRK00558 PRK00558.1-5 451 451 652 equivalog Y Y N excinuclease ABC subunit UvrC uvrC 3.1.25.- GO:0003677,GO:0005515,GO:0006289,GO:0009380,GO:0009381 131567 cellular organisms no rank 54340 NCBI Protein Cluster (PRK) excinuclease ABC subunit C excinuclease ABC subunit UvrC NF001843.0 PRK00567 PRK00567.1-4 142 142 135 equivalog Y Y N large-conductance mechanosensitive channel protein MscL mscL GO:0008381,GO:0034220 131567 cellular organisms no rank 19534 NCBI Protein Cluster (PRK) large-conductance mechanosensitive channel large-conductance mechanosensitive channel protein MscL NF001862.0 PRK00601 PRK00601.1 103 103 150 equivalog Y Y N dUTP diphosphatase dut 3.6.1.23 GO:0000287,GO:0004170,GO:0006226,GO:0046081 131567 cellular organisms no rank 43138 NCBI Protein Cluster (PRK) deoxyuridine 5'-triphosphate nucleotidohydrolase dUTP diphosphatase NF001884.0 PRK00630 PRK00630.1 119 119 148 subfamily Y N N nickel responsive regulator 131567 cellular organisms no rank 2437 NCBI Protein Cluster (PRK) nickel responsive regulator nickel responsive regulator NF001908.0 PRK00668 PRK00668.1 155 155 141 equivalog Y Y N nucleoside-diphosphate kinase ndk 2.7.4.6 GO:0004550 131567 cellular organisms no rank 37782 NCBI Protein Cluster (PRK) mulitfunctional nucleoside diphosphate kinase/apyrimidinic endonuclease/3'- nucleoside-diphosphate kinase NF001911.0 PRK00685 PRK00685.1 144 144 228 equivalog Y Y N metal-dependent hydrolase 131567 cellular organisms no rank 17272 NCBI Protein Cluster (PRK) metal-dependent hydrolase metal-dependent hydrolase NF001913.0 PRK00696 PRK00696.1 370 370 388 equivalog Y Y N ADP-forming succinate--CoA ligase subunit beta sucC 6.2.1.5 GO:0003824,GO:0005524,GO:0006099,GO:0046872 131567 cellular organisms no rank 46615 NCBI Protein Cluster (PRK) succinyl-CoA synthetase subunit beta ADP-forming succinate--CoA ligase subunit beta NF001923.0 PRK00701 PRK00701.1 430 430 439 subfamily Y Y N Mn(2+) uptake NRAMP transporter MntH mntH 10712688 131567 cellular organisms no rank 33051 NCBI Protein Cluster (PRK) manganese transport protein MntH Mn(2+) uptake NRAMP transporter MntH NF001924.0 PRK00702 PRK00702.1 192 192 223 equivalog Y Y N ribose-5-phosphate isomerase RpiA rpiA 5.3.1.6 GO:0004751,GO:0009052 131567 cellular organisms no rank 32393 NCBI Protein Cluster (PRK) ribose-5-phosphate isomerase A ribose-5-phosphate isomerase RpiA Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway NF001943.0 PRK00724 PRK00724.1-2 269 269 274 equivalog Y Y N formate dehydrogenase accessory sulfurtransferase FdhD fdhD GO:0016783 131567 cellular organisms no rank 16426 NCBI Protein Cluster (PRK) formate dehydrogenase accessory protein formate dehydrogenase accessory sulfurtransferase FdhD NF001950.0 PRK00733 PRK00733.1-1 826 826 807 equivalog Y Y N sodium-translocating pyrophosphatase 3.6.1.1 131567 cellular organisms no rank 807 NCBI Protein Cluster (PRK) membrane-bound proton-translocating pyrophosphatase sodium-translocating pyrophosphatase NF001951.0 PRK00733 PRK00733.1-2 859 859 691 equivalog Y Y N sodium-translocating pyrophosphatase 3.6.1.1 GO:0009678,GO:1902600 131567 cellular organisms no rank 9088 NCBI Protein Cluster (PRK) membrane-bound proton-translocating pyrophosphatase sodium-translocating pyrophosphatase NF001953.0 PRK00733 PRK00733.2-1 783 783 697 equivalog Y Y N sodium-translocating pyrophosphatase 3.6.1.1 131567 cellular organisms no rank 4434 NCBI Protein Cluster (PRK) membrane-bound proton-translocating pyrophosphatase sodium-translocating pyrophosphatase NF001954.0 PRK00733 PRK00733.2-2 894 894 723 equivalog Y Y N sodium-translocating pyrophosphatase 3.6.1.1 131567 cellular organisms no rank 2735 NCBI Protein Cluster (PRK) membrane-bound proton-translocating pyrophosphatase sodium-translocating pyrophosphatase NF001959.0 PRK00733 PRK00733.3-4 975 975 674 equivalog Y Y N sodium-translocating pyrophosphatase 3.6.1.1 131567 cellular organisms no rank 257 NCBI Protein Cluster (PRK) membrane-bound proton-translocating pyrophosphatase sodium-translocating pyrophosphatase NF001960.0 PRK00733 PRK00733.3-5 546 546 673 equivalog Y Y N sodium-translocating pyrophosphatase 3.6.1.1 131567 cellular organisms no rank 28497 NCBI Protein Cluster (PRK) membrane-bound proton-translocating pyrophosphatase sodium-translocating pyrophosphatase NF001965.0 PRK00742 PRK00742.1 293 293 357 subfamily Y Y N chemotaxis-specific protein-glutamate methyltransferase CheB cheB 3.1.1.61 GO:0000156,GO:0000160,GO:0006935,GO:0008984 131567 cellular organisms no rank 40375 NCBI Protein Cluster (PRK) chemotaxis-specific methylesterase chemotaxis-specific protein-glutamate methyltransferase CheB Regulates chemotaxis by demethylation of methyl-accepting chemotaxis proteins NF001975.0 PRK00758 PRK00758.1 198 198 185 equivalog Y Y N GMP synthase subunit A 6.3.5.2 131567 cellular organisms no rank 1224 NCBI Protein Cluster (PRK) GMP synthase subunit A GMP synthase subunit A NF001980.1 PRK00770 PRK00770.1 450 450 350 equivalog Y Y N homospermidine biosynthesis protein 2.5.1.- 29923645,37532583 131567 cellular organisms no rank 590 NCBI Protein Cluster (PRK) deoxyhypusine synthase-like protein homospermidine biosynthesis protein Members of this strictly bacterial protein family resemble the enzyme deoxyhypusine synthase, which performs a post-translational modification known only in archaea and eukaryotes on a translation initiation factor found only there. The function of this family is in homospermidine biosynthesis. A related protein from Thermus thermophilus produces the sym-homospermidine precursor 1,9-bis(guanidino)-5-aza-nonane synthase. NF001985.0 PRK00777 PRK00777.1 104 104 157 subfamily Y Y N pantetheine-phosphate adenylyltransferase 2.7.7.3 131567 cellular organisms no rank 1429 NCBI Protein Cluster (PRK) phosphopantetheine adenylyltransferase pantetheine-phosphate adenylyltransferase Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-CoA NF001986.0 PRK00779 PRK00779.1 306 306 307 subfamily Y Y N ornithine carbamoyltransferase 2.1.3.3 131567 cellular organisms no rank 52462 NCBI Protein Cluster (PRK) ornithine carbamoyltransferase ornithine carbamoyltransferase Catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation NF001987.0 PRK00782 PRK00782.1 295 295 267 equivalog Y Y N MEMO1 family protein 131567 cellular organisms no rank 576 NCBI Protein Cluster (PRK) hypothetical protein MEMO1 family protein NF001989.1 PRK00784 PRK00784.1 273 273 480 equivalog Y Y N cobyric acid synthase GO:0003824,GO:0009236 131567 cellular organisms no rank 51341 NCBI Protein Cluster (PRK) cobyric acid synthase cobyric acid synthase Catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide NF002000.0 PRK00801 PRK00801.1 273 273 201 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 231 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002003.0 PRK00802 PRK00802.1-3 182 182 203 equivalog Y Y N DNA-3-methyladenine glycosylase 3.2.2.- GO:0003905,GO:0006284 131567 cellular organisms no rank 21354 NCBI Protein Cluster (PRK) 3-methyladenine DNA glycosylase DNA-3-methyladenine glycosylase NF002010.0 PRK00811 PRK00811.1 260 260 287 equivalog Y Y N polyamine aminopropyltransferase speE 2.5.1.16 131567 cellular organisms no rank 16379 NCBI Protein Cluster (PRK) spermidine synthase polyamine aminopropyltransferase NF002013.0 PRK00819 PRK00819.1-2 231 231 183 equivalog Y Y N RNA 2'-phosphotransferase 2.7.1.- 131567 cellular organisms no rank 276 NCBI Protein Cluster (PRK) RNA 2'-phosphotransferase RNA 2'-phosphotransferase NF002016.0 PRK00823 PRK00823.1-1 133 133 113 equivalog Y Y N 4a-hydroxytetrahydrobiopterin dehydratase 4.2.1.96 GO:0006729,GO:0008124 131567 cellular organisms no rank 3937 NCBI Protein Cluster (PRK) pterin-4-alpha-carbinolamine dehydratase 4a-hydroxytetrahydrobiopterin dehydratase NF002017.0 PRK00823 PRK00823.1-2 80 80 94 equivalog Y Y N 4a-hydroxytetrahydrobiopterin dehydratase 4.2.1.96 GO:0006729,GO:0008124 131567 cellular organisms no rank 20176 NCBI Protein Cluster (PRK) pterin-4-alpha-carbinolamine dehydratase 4a-hydroxytetrahydrobiopterin dehydratase NF002018.0 PRK00823 PRK00823.1-3 108 108 98 equivalog Y Y N 4a-hydroxytetrahydrobiopterin dehydratase 4.2.1.96 GO:0006729,GO:0008124 131567 cellular organisms no rank 8914 NCBI Protein Cluster (PRK) pterin-4-alpha-carbinolamine dehydratase 4a-hydroxytetrahydrobiopterin dehydratase NF002032.1 PRK00856 PRK00856.1 263 263 297 equivalog Y Y N aspartate carbamoyltransferase catalytic subunit 2.1.3.2 GO:0004070,GO:0006207,GO:0006520,GO:0016597 131567 cellular organisms no rank 58837 NCBI Protein Cluster (PRK) aspartate carbamoyltransferase catalytic subunit aspartate carbamoyltransferase catalytic subunit NF002043.0 PRK00870 PRK00870.1 265 265 302 subfamily Y Y N haloalkane dehalogenase 3.8.1.5 GO:0003824 131567 cellular organisms no rank 5071 NCBI Protein Cluster (PRK) haloalkane dehalogenase haloalkane dehalogenase NF002048.0 PRK00876 PRK00876.1 313 313 330 subfamily Y Y N NAD(+) synthase 6.3.1.5 131567 cellular organisms no rank 1721 NCBI Protein Cluster (PRK) NAD synthetase NAD(+) synthase Catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP NF002049.0 PRK00881 PRK00881.1 402 402 510 equivalog Y Y N bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase purH 2.1.2.3,3.5.4.10 GO:0003824,GO:0003937,GO:0004643,GO:0006164,GO:0006189 131567 cellular organisms no rank 75677 NCBI Protein Cluster (PRK) bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase NF002057.0 PRK00886 PRK00886.1-6 235 235 228 equivalog Y Y N 2-phosphosulfolactate phosphatase family protein 131567 cellular organisms no rank 24 NCBI Protein Cluster (PRK) 2-phosphosulfolactate phosphatase 2-phosphosulfolactate phosphatase family protein This bacterial enzyme is related to archaeal 2-phosphosulfolactate phosphatase, involved in biosynthesis of coenzyme M, a cofactor involved in methanogenesis in the archaea. It may differ in function. NF002060.0 PRK00892 PRK00892.1 207 207 345 subfamily Y Y N UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase 2.3.1.191 GO:0009245,GO:0016410 131567 cellular organisms no rank 42546 NCBI Protein Cluster (PRK) UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase Adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis NF002068.0 PRK00911 PRK00911.1 644 644 559 subfamily Y Y N dihydroxy-acid dehydratase 4.2.1.9 131567 cellular organisms no rank 38409 NCBI Protein Cluster (PRK) dihydroxy-acid dehydratase dihydroxy-acid dehydratase NF002073.0 PRK00913 PRK00913.1-2 432 432 505 equivalog Y Y N leucyl aminopeptidase 3.4.11.1 GO:0006508,GO:0030145,GO:0070006 131567 cellular organisms no rank 37610 NCBI Protein Cluster (PRK) multifunctional aminopeptidase A leucyl aminopeptidase NF002074.0 PRK00913 PRK00913.1-4 415 415 496 equivalog Y Y N leucyl aminopeptidase 3.4.11.1 GO:0019538,GO:0070006 131567 cellular organisms no rank 30586 NCBI Protein Cluster (PRK) multifunctional aminopeptidase A leucyl aminopeptidase NF002083.0 PRK00913 PRK00913.3-5 468 468 492 equivalog Y Y N leucyl aminopeptidase 3.4.11.1 GO:0006508,GO:0070006 131567 cellular organisms no rank 10910 NCBI Protein Cluster (PRK) multifunctional aminopeptidase A leucyl aminopeptidase NF002085.0 PRK00915 PRK00915.1-2 517 517 504 subfamily Y Y N 2-isopropylmalate synthase 2.3.3.13 131567 cellular organisms no rank 3599 NCBI Protein Cluster (PRK) 2-isopropylmalate synthase 2-isopropylmalate synthase NF002086.0 PRK00915 PRK00915.1-3 532 532 516 equivalog Y Y N 2-isopropylmalate synthase 2.3.3.13 GO:0003852,GO:0009098,GO:0019752 131567 cellular organisms no rank 35235 NCBI Protein Cluster (PRK) 2-isopropylmalate synthase 2-isopropylmalate synthase NF002088.0 PRK00915 PRK00915.1-5 697 697 514 equivalog Y Y N 2-isopropylmalate synthase 2.3.3.13 GO:0003852,GO:0009098 131567 cellular organisms no rank 7535 NCBI Protein Cluster (PRK) 2-isopropylmalate synthase 2-isopropylmalate synthase NF002096.0 PRK00939 PRK00939.1 98 98 102 subfamily Y Y N stress response translation initiation inhibitor YciH yciH 131567 cellular organisms no rank 848 NCBI Protein Cluster (PRK) translation initiation factor Sui1 stress response translation initiation inhibitor YciH NF002111.0 PRK00951 PRK00951.2-1 231 231 194 equivalog Y Y N imidazoleglycerol-phosphate dehydratase HisB hisB 4.2.1.19 GO:0000105,GO:0004424 131567 cellular organisms no rank 50311 NCBI Protein Cluster (PRK) imidazoleglycerol-phosphate dehydratase imidazoleglycerol-phosphate dehydratase HisB NF002114.0 PRK00951 PRK00951.2-4 189 189 190 equivalog Y Y N imidazoleglycerol-phosphate dehydratase HisB hisB 4.2.1.19 131567 cellular organisms no rank 46307 NCBI Protein Cluster (PRK) imidazoleglycerol-phosphate dehydratase imidazoleglycerol-phosphate dehydratase HisB NF002116.0 PRK00951 PRK00951.2-6 269 269 197 equivalog Y Y N imidazoleglycerol-phosphate dehydratase HisB hisB 4.2.1.19 131567 cellular organisms no rank 3295 NCBI Protein Cluster (PRK) imidazoleglycerol-phosphate dehydratase imidazoleglycerol-phosphate dehydratase HisB NF002138.0 PRK00977 PRK00977.1-2 77 77 77 equivalog Y Y N exodeoxyribonuclease VII small subunit 3.1.11.6 131567 cellular organisms no rank 1995 NCBI Protein Cluster (PRK) exodeoxyribonuclease VII small subunit exodeoxyribonuclease VII small subunit NF002139.0 PRK00977 PRK00977.1-3 68 68 84 equivalog Y Y N exodeoxyribonuclease VII small subunit 3.1.11.6 GO:0006308,GO:0008855 131567 cellular organisms no rank 18913 NCBI Protein Cluster (PRK) exodeoxyribonuclease VII small subunit exodeoxyribonuclease VII small subunit NF002140.0 PRK00977 PRK00977.1-4 71 71 81 equivalog Y Y N exodeoxyribonuclease VII small subunit 3.1.11.6 GO:0006308,GO:0008855,GO:0009318 131567 cellular organisms no rank 9195 NCBI Protein Cluster (PRK) exodeoxyribonuclease VII small subunit exodeoxyribonuclease VII small subunit NF002142.0 PRK00979 PRK00979.1-1 287 287 306 subfamily Y Y N tetrahydromethanopterin S-methyltransferase subunit H 7.2.1.4 131567 cellular organisms no rank 111 NCBI Protein Cluster (PRK) tetrahydromethanopterin S-methyltransferase subunit H tetrahydromethanopterin S-methyltransferase subunit H NF002145.0 PRK00979 PRK00979.1-4 392 392 312 equivalog Y Y N tetrahydromethanopterin S-methyltransferase subunit H 7.2.1.4 131567 cellular organisms no rank 58 NCBI Protein Cluster (PRK) tetrahydromethanopterin S-methyltransferase subunit H tetrahydromethanopterin S-methyltransferase subunit H NF002160.0 PRK00984 PRK00984.2-5 428 428 395 equivalog Y Y N tRNA pseudouridine(13) synthase TruD truD 5.4.99.27 131567 cellular organisms no rank 40 NCBI Protein Cluster (PRK) tRNA pseudouridine synthase D tRNA pseudouridine(13) synthase TruD NF002169.0 PRK01002 PRK01002.1 111 111 141 subfamily Y N N nickel responsive regulator 131567 cellular organisms no rank 3680 NCBI Protein Cluster (PRK) nickel responsive regulator nickel responsive regulator NF002204.1 PRK01077 PRK01077.1 254 254 420 equivalog Y Y N cobyrinate a,c-diamide synthase GO:0042242 131567 cellular organisms no rank 45476 NCBI Protein Cluster (PRK) cobyrinic acid a,c-diamide synthase cobyrinate a,c-diamide synthase Responsible for the amidation of carboxylic groups at position A and C of cobyrinic acid or hydrogenobrynic acid NF002211.1 PRK01103 PRK01103.1 212 212 274 equivalog Y Y N bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase mutM 3.2.2.23,4.2.99.18 GO:0003676,GO:0003684,GO:0003906,GO:0006281,GO:0006284,GO:0008270,GO:0008534,GO:0016799,GO:0019104 131567 cellular organisms no rank 58533 NCBI Protein Cluster (PRK) formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents; acts as DNA glycosylase that recognizes and removes damaged bases NF002217.0 PRK01112 PRK01112.1 320 320 228 equivalog Y Y N 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase 5.4.2.11 131567 cellular organisms no rank 230 NCBI Protein Cluster (PRK) phosphoglyceromutase 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase NF002223.0 PRK01117 PRK01117.1 402 402 430 equivalog Y Y N adenylosuccinate synthase 6.3.4.4 GO:0004019,GO:0005525,GO:0006164 131567 cellular organisms no rank 60094 NCBI Protein Cluster (PRK) adenylosuccinate synthetase adenylosuccinate synthase Catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis NF002232.0 PRK01143 PRK01143.1 162 162 164 equivalog Y Y N 50S ribosomal protein L11 131567 cellular organisms no rank 1138 NCBI Protein Cluster (PRK) 50S ribosomal protein L11P 50S ribosomal protein L11 Binds directly to 23S ribosomal RNA NF002242.0 PRK01151 PRK01151.1 72 72 67 equivalog Y Y N 30S ribosomal protein S17e 131567 cellular organisms no rank 952 NCBI Protein Cluster (PRK) 30S ribosomal protein S17e 30S ribosomal protein S17e NF002243.0 PRK01153 PRK01153.1 127 127 175 subfamily Y Y N nicotinamide-nucleotide adenylyltransferase 2.7.7.1 131567 cellular organisms no rank 1422 NCBI Protein Cluster (PRK) nicotinamide-nucleotide adenylyltransferase nicotinamide-nucleotide adenylyltransferase Catalyzes the formation of NAD+ from nicotinamide ribonucleotide and ATP NF002245.0 PRK01158 PRK01158.1 198 198 233 equivalog Y N N phosphoglycolate phosphatase 3.1.3.18 131567 cellular organisms no rank 557 NCBI Protein Cluster (PRK) phosphoglycolate phosphatase phosphoglycolate phosphatase NF002270.0 PRK01202 PRK01202.1 117 117 129 subfamily Y Y N glycine cleavage system protein GcvH gcvH 131567 cellular organisms no rank 45610 NCBI Protein Cluster (PRK) glycine cleavage system protein H glycine cleavage system protein GcvH Part of multienzyme complex composed of H, L, P, and T proteins which catalyzes oxidation of glycine to yield carbon dioxide, ammonia, 5,10-CH2-H4folate and a reduced pyridine nucleotide; protein H is involved in transfer of methylamine group from the P to T protein; covalently bound to a lipoyl cofactor NF002281.0 PRK01209 PRK01209.2-5 273 273 311 equivalog Y Y N cobalamin biosynthesis protein 131567 cellular organisms no rank 800 NCBI Protein Cluster (PRK) cobalamin biosynthesis protein cobalamin biosynthesis protein NF002288.1 PRK01212 PRK01212.1-4 194 194 303 equivalog Y Y N homoserine kinase 2.7.1.39 GO:0004413,GO:0005524,GO:0006566 131567 cellular organisms no rank 16681 NCBI Protein Cluster (PRK) homoserine kinase homoserine kinase NF002290.1 PRK01213 PRK01213.1 648 648 723 equivalog Y Y N phosphoribosylformylglycinamidine synthase subunit PurL purL 6.3.5.3 GO:0004642,GO:0006189 131567 cellular organisms no rank 41841 NCBI Protein Cluster (PRK) phosphoribosylformylglycinamidine synthase II phosphoribosylformylglycinamidine synthase subunit PurL With PurQ and PurS catalyzes the conversion of formylglycinamide ribonucleotide, ATP, and glutamine to formylglycinamidine ribonucleotide, ADP, and glutamate in the fourth step of the purine biosynthetic pathway NF002302.0 PRK01222 PRK01222.2-2 172 172 193 equivalog Y Y N phosphoribosylanthranilate isomerase 5.3.1.24 131567 cellular organisms no rank 22 NCBI Protein Cluster (PRK) N-(5'-phosphoribosyl)anthranilate isomerase phosphoribosylanthranilate isomerase NF002305.0 PRK01229 PRK01229.1 183 183 210 equivalog Y Y N N-glycosylase/DNA lyase 131567 cellular organisms no rank 509 NCBI Protein Cluster (PRK) N-glycosylase/DNA lyase N-glycosylase/DNA lyase NF002317.0 PRK01250 PRK01250.1 200 200 176 equivalog Y Y N inorganic diphosphatase ppa 3.6.1.1 GO:0004427,GO:0006796 17009951 131567 cellular organisms no rank 14970 NCBI Protein Cluster (PRK) inorganic pyrophosphatase inorganic diphosphatase NF002325.0 PRK01278 PRK01278.1 372 372 395 subfamily Y Y N acetylornithine transaminase 2.6.1.11 131567 cellular organisms no rank 69610 NCBI Protein Cluster (PRK) acetylornithine transaminase protein acetylornithine transaminase Catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine in the arginine biosynthetic pathway NF002360.0 PRK01322 PRK01322.1 226 226 243 equivalog Y Y N 6-carboxyhexanoate--CoA ligase 6.2.1.14 131567 cellular organisms no rank 2580 NCBI Protein Cluster (PRK) 6-carboxyhexanoate--CoA ligase 6-carboxyhexanoate--CoA ligase Catalyzes the formation of pimeloyl-CoA from pimelate and coenzyme A NF002378.0 PRK01372 PRK01372.1 243 243 305 subfamily Y Y N D-alanine--D-alanine ligase 6.3.2.4 GO:0005524,GO:0008716,GO:0046872 1993184,7939684 131567 cellular organisms no rank 56723 NCBI Protein Cluster (PRK) D-alanine--D-alanine ligase D-alanine--D-alanine ligase Catalyzes the formation of D-alanyl-D-alanine from two D-alanines in peptidoglycan synthesis NF002436.0 PRK01584 PRK01584.1 529 529 595 equivalog Y Y N alanine--tRNA ligase 6.1.1.7 131567 cellular organisms no rank 636 NCBI Protein Cluster (PRK) alanyl-tRNA synthetase alanine--tRNA ligase Catalyzes a two-step reaction, first charging an alanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA NF002447.0 PRK01611 PRK01611.3-4 460 460 613 equivalog Y Y N arginine--tRNA ligase 6.1.1.19 131567 cellular organisms no rank 389 NCBI Protein Cluster (PRK) arginyl-tRNA synthetase arginine--tRNA ligase NF002458.0 PRK01641 PRK01641.1 167 167 202 subfamily Y Y N 3-isopropylmalate dehydratase small subunit 131567 cellular organisms no rank 55055 NCBI Protein Cluster (PRK) isopropylmalate isomerase small subunit 3-isopropylmalate dehydratase small subunit NF002497.0 PRK01827 PRK01827.1-3 327 327 264 equivalog Y Y N thymidylate synthase 2.1.1.45 GO:0004799,GO:0006231 131567 cellular organisms no rank 33507 NCBI Protein Cluster (PRK) thymidylate synthase thymidylate synthase NF002499.0 PRK01827 PRK01827.1-5 405 405 264 equivalog Y Y N thymidylate synthase thyA 2.1.1.45 GO:0004799,GO:0006231 131567 cellular organisms no rank 30013 NCBI Protein Cluster (PRK) thymidylate synthase thymidylate synthase NF002537.0 PRK02090 PRK02090.1 154 154 244 equivalog Y Y N phosphoadenylyl-sulfate reductase 1.8.4.8 GO:0003824,GO:0004604,GO:0019379 131567 cellular organisms no rank 44935 NCBI Protein Cluster (PRK) phosphoadenosine phosphosulfate reductase phosphoadenylyl-sulfate reductase Catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite NF002550.0 PRK02106 PRK02106.1 605 605 563 subfamily Y Y N choline dehydrogenase 1.1.99.1 GO:0016614,GO:0050660 10094709 131567 cellular organisms no rank 33456 NCBI Protein Cluster (PRK) choline dehydrogenase choline dehydrogenase Catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine NF002554.0 PRK02114 PRK02114.1 297 297 297 subfamily Y Y N formylmethanofuran--tetrahydromethanopterin N-formyltransferase 2.3.1.101 131567 cellular organisms no rank 2387 NCBI Protein Cluster (PRK) formylmethanofuran--tetrahydromethanopterin formyltransferase formylmethanofuran--tetrahydromethanopterin N-formyltransferase Catalyzes the transfer of a formyl group from formylmethanofuran to tetrahydromethanopterin tetrahydromethanopterin NF002560.0 PRK02135 PRK02135.1 183 183 200 equivalog Y Y N tRNA (pseudouridine(54)-N(1))-methyltransferase TrmY trmY 131567 cellular organisms no rank 1828 NCBI Protein Cluster (PRK) hypothetical protein tRNA (pseudouridine(54)-N(1))-methyltransferase TrmY NF002573.0 PRK02227 PRK02227.1-1 341 341 236 equivalog Y Y N (5-formylfuran-3-yl)methyl phosphate synthase 4.2.3.153 131567 cellular organisms no rank 1705 NCBI Protein Cluster (PRK) hypothetical protein (5-formylfuran-3-yl)methyl phosphate synthase NF002575.0 PRK02227 PRK02227.1-3 304 304 233 equivalog Y Y N (5-formylfuran-3-yl)methyl phosphate synthase 4.2.3.153 131567 cellular organisms no rank 428 NCBI Protein Cluster (PRK) hypothetical protein (5-formylfuran-3-yl)methyl phosphate synthase NF002586.0 PRK02237 PRK02237.1 114 114 109 equivalog Y Y N YnfA family protein GO:0016020 131567 cellular organisms no rank 23330 NCBI Protein Cluster (PRK) hypothetical protein YnfA family protein NF002598.0 PRK02253 PRK02253.1 130 130 167 equivalog Y Y N deoxyuridine 5'-triphosphate nucleotidohydrolase 131567 cellular organisms no rank 791 NCBI Protein Cluster (PRK) deoxyuridine 5'-triphosphate nucleotidohydrolase deoxyuridine 5'-triphosphate nucleotidohydrolase NF002600.0 PRK02256 PRK02256.1 529 529 463 equivalog Y Y N aminopeptidase 3.4.11.- GO:0004177,GO:0006508,GO:0008270 131567 cellular organisms no rank 6297 NCBI Protein Cluster (PRK) putative aminopeptidase 1 aminopeptidase NF002612.0 PRK02261 PRK02261.1 110 110 148 equivalog Y Y N methylaspartate mutase subunit S glmS 5.4.99.1 GO:0050097 7880251 131567 cellular organisms no rank 1350 NCBI Protein Cluster (PRK) methylaspartate mutase subunit S methylaspartate mutase subunit S Methylaspartate mutase (also called glutamate mutase) is a cob(II)alamin-dependent enzyme that interconverts methylaspartate and L-glutamate. GlmS is the sigma subunit. NF002614.0 PRK02265 PRK02265.1 150 150 246 subfamily Y Y N acetoacetate decarboxylase 4.1.1.4 GO:0016829 131567 cellular organisms no rank 5723 NCBI Protein Cluster (PRK) acetoacetate decarboxylase acetoacetate decarboxylase NF002616.0 PRK02268 PRK02268.1-2 139 139 148 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 3415 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002627.0 PRK02290 PRK02290.1-5 392 392 330 equivalog Y Y N 3-dehydroquinate synthase II 1.4.1.24 131567 cellular organisms no rank 235 NCBI Protein Cluster (PRK) 3-dehydroquinate synthase 3-dehydroquinate synthase II NF002633.0 PRK02304 PRK02304.1-2 224 224 172 equivalog Y Y N adenine phosphoribosyltransferase 2.4.2.7 GO:0003999,GO:0006168,GO:0009116 131567 cellular organisms no rank 8059 NCBI Protein Cluster (PRK) adenine phosphoribosyltransferase adenine phosphoribosyltransferase NF002634.0 PRK02304 PRK02304.1-3 170 170 182 equivalog Y Y N adenine phosphoribosyltransferase 2.4.2.7 GO:0003999,GO:0006168,GO:0009116 131567 cellular organisms no rank 39788 NCBI Protein Cluster (PRK) adenine phosphoribosyltransferase adenine phosphoribosyltransferase NF002635.0 PRK02304 PRK02304.1-4 146 146 188 subfamily Y Y N adenine phosphoribosyltransferase 2.4.2.7 131567 cellular organisms no rank 1236 NCBI Protein Cluster (PRK) adenine phosphoribosyltransferase adenine phosphoribosyltransferase NF002636.0 PRK02304 PRK02304.1-5 125 125 176 equivalog Y Y N adenine phosphoribosyltransferase 2.4.2.7 GO:0003999,GO:0009116 131567 cellular organisms no rank 43508 NCBI Protein Cluster (PRK) adenine phosphoribosyltransferase adenine phosphoribosyltransferase NF002669.0 PRK02391 PRK02391.1 341 341 298 equivalog Y Y N zinc metalloprotease HtpX htpX 3.4.24.- GO:0004222,GO:0006508 131567 cellular organisms no rank 5909 NCBI Protein Cluster (PRK) heat shock protein HtpX zinc metalloprotease HtpX NF002670.0 PRK02395 PRK02395.1-1 324 324 292 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 520 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002671.0 PRK02395 PRK02395.1-3 258 258 262 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 548 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002674.0 PRK02399 PRK02399.1-2 335 335 410 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 9496 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002677.0 PRK02406 PRK02406.1 256 256 357 equivalog Y Y N DNA polymerase IV dinB 2.7.7.7 GO:0003684,GO:0003887,GO:0006281 15276832,15629916,16107880,16166552,16199565,16379496 131567 cellular organisms no rank 80475 NCBI Protein Cluster (PRK) DNA polymerase IV DNA polymerase IV Involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function NF002688.0 PRK02471 PRK02471.1 425 425 756 equivalog Y Y N bifunctional glutamate--cysteine ligase GshA/glutathione synthetase GshB gshAB 6.3.2.2,6.3.2.3 GO:0004357,GO:0005524,GO:0006750,GO:0046872 131567 cellular organisms no rank 5829 NCBI Protein Cluster (PRK) bifunctional glutamate--cysteine ligase/glutathione synthetase bifunctional glutamate--cysteine ligase GshA/glutathione synthetase GshB Synthesizes glutathione from L-glutamate and L-cysteine via gamma-L-glutamyl-L-cysteine NF002699.1 PRK02492 PRK02492.1 500 500 338 equivalog Y Y N 1,9-bis(guanidino)-5-aza-nonane synthase 37532583 131567 cellular organisms no rank 1434 NCBI Protein Cluster (PRK) deoxyhypusine synthase-like protein 1,9-bis(guanidino)-5-aza-nonane synthase Members of this family include the 1,9-bis(guanidino)-5-aza-nonane synthase protein TTHA1570 from Thermus thermophilus. This family previous was annotated as deoxyhypusine synthase (dhs), but member proteins are bacterial, whereas that function is a post-translational modification that does not occur in bacteria. 1,9-bis(guanidino)-5-aza-nonane is the immediate precursor of sym-homospermidine. NF002747.0 PRK02759 PRK02759.1 187 187 208 equivalog Y Y N bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE hisIE 3.5.4.19,3.6.1.31 GO:0000105,GO:0004635,GO:0004636 3062174,3528746 131567 cellular organisms no rank 25707 NCBI Protein Cluster (PRK) bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE Catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribosyl)-ATP and the subsequent formation of 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-AMP in histidine biosynthesis NF002759.0 PRK02813 PRK02813.1 356 356 430 equivalog Y Y N M18 family aminopeptidase GO:0004177,GO:0006508,GO:0008270 131567 cellular organisms no rank 23635 NCBI Protein Cluster (PRK) putative aminopeptidase 2 M18 family aminopeptidase NF002773.0 PRK02866 PRK02866.1 150 150 147 subfamily Y Y N cyanase 4.2.1.104 6336748 131567 cellular organisms no rank 10333 NCBI Protein Cluster (PRK) cyanate hydratase cyanase Catalyzes the reaction of cyanate and bicarbonate to produce ammonia and carbon dioxide NF002780.0 PRK02898 PRK02898.1 84 84 104 equivalog Y Y N energy-coupling factor ABC transporter substrate-binding protein GO:0006824,GO:0009236,GO:0015087,GO:0016020 131567 cellular organisms no rank 5479 NCBI Protein Cluster (PRK) cobalt transport protein CbiN energy-coupling factor ABC transporter substrate-binding protein NF002794.0 PRK02925 PRK02925.1 387 387 459 equivalog Y Y N glucuronate isomerase uxaC 5.3.1.12 GO:0006064,GO:0008880 12945057 131567 cellular organisms no rank 29314 NCBI Protein Cluster (PRK) glucuronate isomerase glucuronate isomerase Catalyzes the interconversion of D-glucuronate to D-fructuronate or D-galacturonate to D-tagaturonate; functions in glucuronic and galacturonic metabolism NF002795.0 PRK02929 PRK02929.1 622 622 499 equivalog Y Y N L-arabinose isomerase araA 5.3.1.4 GO:0005996,GO:0008733 131567 cellular organisms no rank 19825 NCBI Protein Cluster (PRK) L-arabinose isomerase L-arabinose isomerase Catalyzes the formation of L-ribulose from L-arabinose in L-arabinose catabolism NF002805.0 PRK02947 PRK02947.1 135 135 247 subfamily Y Y N sugar isomerase domain-containing protein GO:0097367,GO:1901135 131567 cellular organisms no rank 15242 NCBI Protein Cluster (PRK) hypothetical protein sugar isomerase domain-containing protein NF002806.0 PRK02948 PRK02948.1 304 304 381 subfamily Y Y N IscS subfamily cysteine desulfurase GO:0003824 131567 cellular organisms no rank 24356 NCBI Protein Cluster (PRK) cysteine desulfurase IscS subfamily cysteine desulfurase NF002815.0 PRK02967 PRK02967.1 83 83 139 equivalog Y Y N nickel-responsive transcriptional regulator NikR nikR GO:0003677,GO:0006355,GO:0010045,GO:0016151 131567 cellular organisms no rank 6584 NCBI Protein Cluster (PRK) nickel responsive regulator nickel-responsive transcriptional regulator NikR Inhibits transcription at high concentrations of nickel NF002826.0 PRK03001 PRK03001.1 369 369 285 equivalog Y Y N zinc metalloprotease HtpX htpX 3.4.24.- GO:0004222,GO:0006508 131567 cellular organisms no rank 8257 NCBI Protein Cluster (PRK) M48 family peptidase zinc metalloprotease HtpX NF002841.0 PRK03080 PRK03080.1-2 477 477 389 equivalog Y Y N phosphoserine transaminase 2.6.1.52 GO:0004648,GO:0006564 131567 cellular organisms no rank 9392 NCBI Protein Cluster (PRK) phosphoserine aminotransferase phosphoserine transaminase NF002872.1 PRK03202 PRK03202.1 253 253 323 subfamily Y Y N ATP-dependent 6-phosphofructokinase 2.7.1.11 GO:0006002 131567 cellular organisms no rank 44565 NCBI Protein Cluster (PRK) 6-phosphofructokinase ATP-dependent 6-phosphofructokinase Catalyzes the formation of D-fructose 1,6-bisphosphate from D-fructose 6-phosphate in glycolysis NF002874.0 PRK03244 PRK03244.1 457 457 399 equivalog Y Y N acetylornithine transaminase 2.6.1.11 GO:0006525,GO:0008483,GO:0030170 131567 cellular organisms no rank 18650 NCBI Protein Cluster (PRK) acetylornithine aminotransferase acetylornithine transaminase Catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine in the arginine biosynthetic pathway NF002898.0 PRK03437 PRK03437.1 393 393 347 equivalog Y Y N 3-isopropylmalate dehydrogenase 1.1.1.85 GO:0000287,GO:0003862,GO:0009098,GO:0051287 15663922,9111927 131567 cellular organisms no rank 16666 NCBI Protein Cluster (PRK) 3-isopropylmalate dehydrogenase 3-isopropylmalate dehydrogenase Catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis NF002937.0 PRK03584 PRK03584.1 639 639 657 subfamily Y Y N acetoacetate--CoA ligase 6.2.1.16 131567 cellular organisms no rank 33156 NCBI Protein Cluster (PRK) acetoacetyl-CoA synthetase acetoacetate--CoA ligase NF002938.0 PRK03592 PRK03592.1 241 241 298 equivalog Y Y N haloalkane dehalogenase 3.8.1.5 GO:0018786 131567 cellular organisms no rank 5115 NCBI Protein Cluster (PRK) haloalkane dehalogenase haloalkane dehalogenase Catalyzes the cleavage of carbon-halogen bonds in aliphatic compounds forming a primary alcohol and a halide NF002947.1 PRK03604 PRK03604.1 285 285 301 equivalog Y Y N bifunctional molybdenum cofactor biosynthesis protein MoaC/MoaB moaCB 4.6.1.17 GO:0006777 131567 cellular organisms no rank 4393 NCBI Protein Cluster (PRK) bifunctional molybdenum cofactor biosynthesis protein MoaC/MogA bifunctional molybdenum cofactor biosynthesis protein MoaC/MoaB NF002957.0 PRK03619 PRK03619.1 212 212 222 equivalog Y Y N phosphoribosylformylglycinamidine synthase subunit PurQ purQ 3.5.1.2,6.3.5.3 GO:0004642,GO:0006189 131567 cellular organisms no rank 30086 NCBI Protein Cluster (PRK) phosphoribosylformylglycinamidine synthase I phosphoribosylformylglycinamidine synthase subunit PurQ With PurL and PurS catalyzes the conversion of formylglycinamide ribonucleotide, ATP, and glutamine to formylglycinamidine ribonucleotide, ADP, and glutamate in the fourth step of the purine biosynthetic pathway NF002995.0 PRK03759 PRK03759.1 127 127 185 equivalog Y Y N isopentenyl-diphosphate Delta-isomerase idi 5.3.3.2 GO:0004452,GO:0008299 131567 cellular organisms no rank 20784 NCBI Protein Cluster (PRK) isopentenyl-diphosphate delta-isomerase isopentenyl-diphosphate Delta-isomerase NF002999.0 PRK03767 PRK03767.1 141 141 200 equivalog Y Y N NAD(P)H:quinone oxidoreductase wrbA 1.6.5.2 GO:0003955,GO:0010181 9694845 131567 cellular organisms no rank 27414 NCBI Protein Cluster (PRK) NAD(P)H:quinone oxidoreductase NAD(P)H:quinone oxidoreductase Catalyzes the transfer of electrons from NADH to ubiquinone NF003006.0 PRK03817 PRK03817.1 443 443 352 equivalog Y Y N galactokinase 2.7.1.6 131567 cellular organisms no rank 118 NCBI Protein Cluster (PRK) galactokinase galactokinase Catalyzes the formation of alpha-D-galactose 1-phosphate from D-galactose in galactose metabolism NF003008.0 PRK03824 PRK03824.1 125 125 135 equivalog Y Y N hydrogenase nickel incorporation protein HypA hypA 131567 cellular organisms no rank 121 NCBI Protein Cluster (PRK) hydrogenase nickel incorporation protein hydrogenase nickel incorporation protein HypA Plays a role in hydrogenase nickel cofactor insertion NF003012.0 PRK03839 PRK03839.1 152 152 180 equivalog Y N N putative kinase 131567 cellular organisms no rank 161 NCBI Protein Cluster (PRK) putative kinase putative kinase NF003013.0 PRK03846 PRK03846.1 163 163 202 subfamily Y Y N adenylyl-sulfate kinase 2.7.1.25 131567 cellular organisms no rank 40749 NCBI Protein Cluster (PRK) adenylylsulfate kinase adenylyl-sulfate kinase Converts ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate NF003025.0 PRK03902 PRK03902.1 138 138 142 equivalog Y Y N transcriptional regulator MntR mntR GO:0003677,GO:0003700,GO:0006355 131567 cellular organisms no rank 2641 NCBI Protein Cluster (PRK) manganese transport transcriptional regulator transcriptional regulator MntR Involved in manganese homeostasis; activates the transcription of the mntABCD operon NF003037.0 PRK03932 PRK03932.1 414 414 451 equivalog Y Y N asparagine--tRNA ligase asnS 6.1.1.22 GO:0004816,GO:0005524,GO:0006421 131567 cellular organisms no rank 28618 NCBI Protein Cluster (PRK) asparaginyl-tRNA synthetase asparagine--tRNA ligase Catalyzes a two-step reaction, first charging an asparagine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA NF003046.0 PRK03955 PRK03955.1 163 163 132 equivalog Y Y N DUF126 domain-containing protein 131567 cellular organisms no rank 515 NCBI Protein Cluster (PRK) hypothetical protein DUF126 domain-containing protein NF003058.0 PRK03976 PRK03976.1 87 87 91 equivalog Y Y N 50S ribosomal protein L37ae 15184028 131567 cellular organisms no rank 713 NCBI Protein Cluster (PRK) 50S ribosomal protein L37Ae 50S ribosomal protein L37ae structural models have indicated that the folded zinc-finger motif interacts mainly with domain III of 23S rRNA, whereas the amino-terminal region of L37 interacts primarily with domain II NF003068.0 PRK03991 PRK03991.1 484 484 613 equivalog Y Y N threonine--tRNA ligase 6.1.1.3 131567 cellular organisms no rank 778 NCBI Protein Cluster (PRK) threonyl-tRNA synthetase threonine--tRNA ligase Catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr); Catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA NF003075.0 PRK03996 PRK03996.1 219 219 248 subfamily Y Y N archaeal proteasome endopeptidase complex subunit alpha 3.4.25.1 131567 cellular organisms no rank 1837 NCBI Protein Cluster (PRK) proteasome subunit alpha archaeal proteasome endopeptidase complex subunit alpha NF003076.0 PRK03999 PRK03999.1 138 138 129 equivalog Y Y N translation initiation factor IF-5A 131567 cellular organisms no rank 1082 NCBI Protein Cluster (PRK) translation initiation factor IF-5A translation initiation factor IF-5A aIF-5A; promotes the formation of the first peptide bond NF003080.0 PRK04007 PRK04007.1 95 95 74 equivalog Y Y N 30S ribosomal protein S28e 14627742,14627743 131567 cellular organisms no rank 597 NCBI Protein Cluster (PRK) 30S ribosomal protein S28e 30S ribosomal protein S28e NF003089.1 PRK04016 PRK04016.1 79 79 61 equivalog Y Y N DNA-directed RNA polymerase subunit N 2.7.7.6 131567 cellular organisms no rank 868 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit N DNA-directed RNA polymerase subunit N DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates NF003099.0 PRK04019 PRK04019.2-2 341 341 293 equivalog Y Y N 50S ribosomal protein L10 131567 cellular organisms no rank 48 NCBI Protein Cluster (PRK) acidic ribosomal protein P0 50S ribosomal protein L10 NF003104.0 PRK04024 PRK04024.1 489 489 412 equivalog Y Y N 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 5.4.2.12 131567 cellular organisms no rank 628 NCBI Protein Cluster (PRK) cofactor-independent phosphoglycerate mutase 2,3-bisphosphoglycerate-independent phosphoglycerate mutase Catalyzes the interconversion of 3-phosphoglycerate and 2-phosphoglycerate; this enzyme does not require the cofactor 2,3-bisphosphoglycerate as a phosphate donor NF003106.0 PRK04027 PRK04027.1 225 225 195 equivalog Y Y N 30S ribosomal protein S7 131567 cellular organisms no rank 1170 NCBI Protein Cluster (PRK) 30S ribosomal protein S7P 30S ribosomal protein S7 Binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit NF003107.0 PRK04028 PRK04028.1 456 456 630 equivalog Y Y N Glu-tRNA(Gln) amidotransferase subunit GatE gatE 6.3.5.- 131567 cellular organisms no rank 1607 NCBI Protein Cluster (PRK) glutamyl-tRNA(Gln) amidotransferase subunit E Glu-tRNA(Gln) amidotransferase subunit GatE Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase NF003115.0 PRK04034 PRK04034.1 126 126 130 equivalog Y Y N 30S ribosomal protein S8 131567 cellular organisms no rank 942 NCBI Protein Cluster (PRK) 30S ribosomal protein S8P 30S ribosomal protein S8 Binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit NF003122.0 PRK04040 PRK04040.1 155 155 189 equivalog Y Y N adenylate kinase 2.7.4.3 131567 cellular organisms no rank 608 NCBI Protein Cluster (PRK) adenylate kinase adenylate kinase NF003125.0 PRK04044 PRK04044.1 252 252 213 equivalog Y Y N 30S ribosomal protein S5 131567 cellular organisms no rank 1094 NCBI Protein Cluster (PRK) 30S ribosomal protein S5P 30S ribosomal protein S5 Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body; contacts S4 and S8; with S4 and S12 plays a role in translational accuracy; mutations in this gene result in spectinomycin resistance NF003139.0 PRK04051 PRK04051.1 138 138 179 equivalog Y Y N 30S ribosomal protein S4 131567 cellular organisms no rank 1151 NCBI Protein Cluster (PRK) 30S ribosomal protein S4P 30S ribosomal protein S4 Primary rRNA binding protein; nucleates 30S assembly; involved in translational accuracy with proteins S5 and S12; interacts with protein S5; involved in autogeneously regulating ribosomal proteins by binding to pseudoknot structures in the polycistronic mRNA; interacts with transcription complex and functions similar to protein NusA in antitermination NF003140.0 PRK04053 PRK04053.1 159 159 157 equivalog Y Y N 30S ribosomal protein S13 131567 cellular organisms no rank 1163 NCBI Protein Cluster (PRK) 30S ribosomal protein S13P 30S ribosomal protein S13 Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA; makes contact with the large subunit via RNA-protein interactions and via protein-protein interactions with L5; contacts P-site tRNA NF003156.0 PRK04128 PRK04128.1 285 285 231 equivalog Y Y N 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase hisA 5.3.1.16 131567 cellular organisms no rank 69 NCBI Protein Cluster (PRK) 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase Catalyzes the formation of 5-(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino-l-(5-phosphoribosyl)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide NF003163.0 PRK04143 PRK04143.1 272 272 265 equivalog Y Y N protein-ADP-ribose hydrolase 131567 cellular organisms no rank 4426 NCBI Protein Cluster (PRK) hypothetical protein protein-ADP-ribose hydrolase NF003166.0 PRK04149 PRK04149.1 387 387 393 subfamily Y Y N sulfate adenylyltransferase 2.7.7.4 15065853,9627961 131567 cellular organisms no rank 8289 NCBI Protein Cluster (PRK) sulfate adenylyltransferase sulfate adenylyltransferase NF003167.0 PRK04151 PRK04151.1 150 150 199 equivalog Y Y N IMP cyclohydrolase 3.5.4.10 11844782 131567 cellular organisms no rank 942 NCBI Protein Cluster (PRK) IMP cyclohydrolase IMP cyclohydrolase Catalyzes the formation of inosine monophosphate from 5-formylamidoimidazole-4-carboxamide in purine biosynthesis NF003191.0 PRK04164 PRK04164.1-2 179 179 200 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 938 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003195.0 PRK04165 PRK04165.1 306 306 450 equivalog Y Y N acetyl-CoA decarbonylase/synthase complex subunit gamma acsC 131567 cellular organisms no rank 1078 NCBI Protein Cluster (PRK) acetyl-CoA decarbonylase/synthase complex subunit gamma acetyl-CoA decarbonylase/synthase complex subunit gamma AcsC is the corrinoid iron-sulfur protein large subunit. NF003196.0 PRK04168 PRK04168.1 355 355 338 equivalog Y Y N tungstate ABC transporter substrate-binding protein WtpA wtpA 131567 cellular organisms no rank 419 NCBI Protein Cluster (PRK) molybdate ABC transporter periplasmic substrate-binding protein tungstate ABC transporter substrate-binding protein WtpA NF003198.0 PRK04169 PRK04169.1-2 247 247 249 equivalog Y Y N geranylgeranylglyceryl/heptaprenylglyceryl phosphate synthase GO:0006650,GO:0047294 131567 cellular organisms no rank 3071 NCBI Protein Cluster (PRK) geranylgeranylglyceryl phosphate synthase-like protein geranylgeranylglyceryl/heptaprenylglyceryl phosphate synthase NF003199.0 PRK04169 PRK04169.1-3 169 169 233 equivalog Y Y N heptaprenylglyceryl phosphate synthase 2.5.1.n9 131567 cellular organisms no rank 5921 NCBI Protein Cluster (PRK) geranylgeranylglyceryl phosphate synthase-like protein heptaprenylglyceryl phosphate synthase NF003210.0 PRK04172 PRK04172.1 350 350 496 equivalog Y Y N phenylalanine--tRNA ligase subunit alpha 6.1.1.20 131567 cellular organisms no rank 1904 NCBI Protein Cluster (PRK) phenylalanyl-tRNA synthetase subunit alpha phenylalanine--tRNA ligase subunit alpha Catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a heterotetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 2 subfamily NF003211.1 PRK04173 PRK04173.1 312 312 454 equivalog Y Y N glycine--tRNA ligase 6.1.1.14 GO:0000166,GO:0004820,GO:0005524,GO:0006426 131567 cellular organisms no rank 27065 NCBI Protein Cluster (PRK) glycyl-tRNA synthetase glycine--tRNA ligase Catalyzes a two-step reaction, first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA NF003214.0 PRK04179 PRK04179.1 71 71 62 equivalog Y Y N 50S ribosomal protein L37e 131567 cellular organisms no rank 804 NCBI Protein Cluster (PRK) 50S ribosomal protein L37e 50S ribosomal protein L37e NF003215.0 PRK04180 PRK04180.1 395 395 298 equivalog Y Y N pyridoxal 5'-phosphate synthase lyase subunit PdxS pdxS GO:0003824,GO:0042823 131567 cellular organisms no rank 19884 NCBI Protein Cluster (PRK) pyridoxal biosynthesis lyase PdxS pyridoxal 5'-phosphate synthase lyase subunit PdxS PdxST is involved in the biosynthesis of pyridoxal 5'-phosphate; PdxT catalyzes the hydrolysis of glutamine to glutamate and ammonia; PdxS utilizes the ammonia to synthesize pyridoxal 5'-phosphate NF003217.0 PRK04183 PRK04183.1 310 310 420 equivalog Y Y N Glu-tRNA(Gln) amidotransferase subunit GatD gatD 6.3.5.- 131567 cellular organisms no rank 1553 NCBI Protein Cluster (PRK) glutamyl-tRNA(Gln) amidotransferase subunit D Glu-tRNA(Gln) amidotransferase subunit GatD Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase NF003218.0 PRK04184 PRK04184.1 274 274 539 equivalog Y Y N DNA topoisomerase VI subunit B 5.6.2.2 131567 cellular organisms no rank 1523 NCBI Protein Cluster (PRK) DNA topoisomerase VI subunit B DNA topoisomerase VI subunit B NF003219.0 PRK04191 PRK04191.1 147 147 229 equivalog Y Y N 30S ribosomal protein S3 131567 cellular organisms no rank 1254 NCBI Protein Cluster (PRK) 30S ribosomal protein S3P 30S ribosomal protein S3 Forms a complex with S10 and S14; binds the lower part of the 30S subunit head and the mRNA in the complete ribosome to position it for translation NF003220.0 PRK04192 PRK04192.1 470 470 588 subfamily Y Y N V-type ATP synthase subunit A 7.1.2.2 131567 cellular organisms no rank 11032 NCBI Protein Cluster (PRK) V-type ATP synthase subunit A V-type ATP synthase subunit A NF003235.0 PRK04196 PRK04196.1 349 349 462 subfamily Y Y N V-type ATP synthase subunit B 131567 cellular organisms no rank 8127 NCBI Protein Cluster (PRK) V-type ATP synthase subunit B V-type ATP synthase subunit B NF003239.0 PRK04199 PRK04199.1-4 91 91 172 equivalog Y Y N 50S ribosomal protein L16 131567 cellular organisms no rank 1156 NCBI Protein Cluster (PRK) 50S ribosomal protein L10e 50S ribosomal protein L16 NF003242.0 PRK04200 PRK04200.1 426 426 395 equivalog Y Y N cofactor-independent phosphoglycerate mutase 5.4.2.12 131567 cellular organisms no rank 3433 NCBI Protein Cluster (PRK) cofactor-independent phosphoglycerate mutase cofactor-independent phosphoglycerate mutase Catalyzes the interconversion of 3-phosphoglycerate and 2-phosphoglycerate; this enzyme does not require the cofactor 2,3-bisphosphoglycerate as a phosphate donor; BPG-independent PGAM; aPGAM NF003243.0 PRK04201 PRK04201.1 252 252 266 equivalog Y Y N zinc transporter ZupT zupT 131567 cellular organisms no rank 6203 NCBI Protein Cluster (PRK) zinc transporter ZupT zinc transporter ZupT NF003244.0 PRK04203 PRK04203.1 203 203 216 equivalog Y Y N 50S ribosomal protein L1 15659579 131567 cellular organisms no rank 1154 NCBI Protein Cluster (PRK) 50S ribosomal protein L1P 50S ribosomal protein L1 NF003246.0 PRK04204 PRK04204.1-2 352 352 342 equivalog Y Y N RNA 3'-terminal phosphate cyclase rtcA 6.5.1.4 GO:0003963,GO:0006396 131567 cellular organisms no rank 5721 NCBI Protein Cluster (PRK) RNA 3'-terminal-phosphate cyclase RNA 3'-terminal phosphate cyclase NF003251.0 PRK04207 PRK04207.1 185 185 343 equivalog Y Y N type II glyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 131567 cellular organisms no rank 2348 NCBI Protein Cluster (PRK) glyceraldehyde-3-phosphate dehydrogenase type II glyceraldehyde-3-phosphate dehydrogenase Catalyzes the formation of 3-phospho-D-glycerol phosphate from D-glyceraldehyde 3-phosphate in glycolysis NF003252.0 PRK04208 PRK04208.1 438 438 468 subfamily Y Y N ribulose-bisphosphate carboxylase large subunit 4.1.1.39 10049390,12730164,15375115,2118521,8245022 131567 cellular organisms no rank 4548 NCBI Protein Cluster (PRK) ribulose bisophosphate carboxylase ribulose-bisphosphate carboxylase large subunit Type III RuBisCO; involved in carbon fixation NF003253.0 PRK04210 PRK04210.1 504 504 612 equivalog Y Y N phosphoenolpyruvate carboxykinase (GTP) 4.1.1.32 GO:0004611,GO:0005525,GO:0006094,GO:0017076 131567 cellular organisms no rank 24176 NCBI Protein Cluster (PRK) phosphoenolpyruvate carboxykinase phosphoenolpyruvate carboxykinase (GTP) Catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using GTP NF003254.0 PRK04211 PRK04211.1 196 196 146 equivalog Y Y N 30S ribosomal protein S12 131567 cellular organisms no rank 622 NCBI Protein Cluster (PRK) 30S ribosomal protein S12P 30S ribosomal protein S12 Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone; located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side; mutations in the S12 gene confer streptomycin resistance NF003258.0 PRK04219 PRK04219.1 166 166 178 equivalog Y Y N 50S ribosomal protein L5 131567 cellular organisms no rank 1200 NCBI Protein Cluster (PRK) 50S ribosomal protein L5P 50S ribosomal protein L5 Part of 50S and 5S/L5/L18/L25 subcomplex; contacts 5S rRNA and P site tRNA; forms a bridge to the 30S subunit in the ribosome by binding to S13 NF003259.0 PRK04220 PRK04220.1 343 343 306 equivalog Y Y N 2-phosphoglycerate kinase 131567 cellular organisms no rank 305 NCBI Protein Cluster (PRK) 2-phosphoglycerate kinase 2-phosphoglycerate kinase Catalyzes the formation of 2-phospho-D-glyceroyl phosphate from ATP and 2-phospho-D-glycerate NF003269.0 PRK04243 PRK04243.1 178 178 196 equivalog Y Y N 50S ribosomal protein L15e 131567 cellular organisms no rank 1154 NCBI Protein Cluster (PRK) 50S ribosomal protein L15e 50S ribosomal protein L15e NF003270.0 PRK04247 PRK04247.1 216 216 250 equivalog Y Y N endonuclease NucS nucS GO:0000014,GO:0003677 19609302,22431731 131567 cellular organisms no rank 1137 NCBI Protein Cluster (PRK) hypothetical protein endonuclease NucS NF003274.0 PRK04262 PRK04262.1 244 244 347 equivalog Y Y N hydroxymethylglutaryl-CoA synthase 2.3.3.10 131567 cellular organisms no rank 928 NCBI Protein Cluster (PRK) hypothetical protein hydroxymethylglutaryl-CoA synthase NF003276.0 PRK04266 PRK04266.1-2 113 113 222 equivalog Y Y N fibrillarin-like rRNA/tRNA 2'-O-methyltransferase 131567 cellular organisms no rank 1400 NCBI Protein Cluster (PRK) fibrillarin fibrillarin-like rRNA/tRNA 2'-O-methyltransferase NF003280.0 PRK04270 PRK04270.1 242 242 323 equivalog Y Y N RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5 5.4.99.- 131567 cellular organisms no rank 1464 NCBI Protein Cluster (PRK) H/ACA RNA-protein complex component Cbf5p RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5 NF003288.0 PRK04286 PRK04286.1-2 409 409 303 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 48 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003295.0 PRK04293 PRK04293.1 368 368 337 equivalog Y Y N adenylosuccinate synthetase 131567 cellular organisms no rank 643 NCBI Protein Cluster (PRK) adenylosuccinate synthetase adenylosuccinate synthetase Catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis NF003296.0 PRK04296 PRK04296.1-1 183 183 195 equivalog Y Y N thymidine kinase 2.7.1.21 GO:0004797,GO:0005524 131567 cellular organisms no rank 9405 NCBI Protein Cluster (PRK) thymidine kinase thymidine kinase NF003302.0 PRK04302 PRK04302.1 132 132 223 subfamily Y Y N triose-phosphate isomerase 5.3.1.1 15342242 131567 cellular organisms no rank 2409 NCBI Protein Cluster (PRK) triosephosphate isomerase triose-phosphate isomerase NF003313.0 PRK04319 PRK04319.1 729 729 574 equivalog Y Y N acetate--CoA ligase acsA 6.2.1.1 131567 cellular organisms no rank 8966 NCBI Protein Cluster (PRK) acetyl-CoA synthetase acetate--CoA ligase Catalyzes the conversion of acetate and CoA to acetyl-CoA NF003314.0 PRK04322 PRK04322.1 126 126 117 equivalog Y Y N peptidyl-tRNA hydrolase Pth2 pth2 3.1.1.29 15766258,16251366 131567 cellular organisms no rank 1253 NCBI Protein Cluster (PRK) peptidyl-tRNA hydrolase peptidyl-tRNA hydrolase Pth2 Pth2 is an archaeal type of peptidyl-tRNA hydrolase. It does not show a relationship to the bacterial type, Pth1, described by TIGR00447. NF003317.0 PRK04326 PRK04326.1 406 406 340 equivalog Y Y N methionine synthase 2.1.1.13 131567 cellular organisms no rank 697 NCBI Protein Cluster (PRK) methionine synthase methionine synthase NF003333.0 PRK04342 PRK04342.1-2 465 465 367 equivalog Y Y N DNA topoisomerase IV subunit A 5.6.2.2 131567 cellular organisms no rank 166 NCBI Protein Cluster (PRK) DNA topoisomerase VI subunit A DNA topoisomerase IV subunit A NF003335.0 PRK04342 PRK04342.1-4 424 424 373 equivalog Y N N DNA topoisomerase VI subunit A 131567 cellular organisms no rank 77 NCBI Protein Cluster (PRK) DNA topoisomerase VI subunit A DNA topoisomerase VI subunit A NF003338.0 PRK04350 PRK04350.1 434 434 502 subfamily Y Y N thymidine phosphorylase 2.4.2.4 131567 cellular organisms no rank 4186 NCBI Protein Cluster (PRK) thymidine phosphorylase thymidine phosphorylase Catalyzes the formation of thymine and 2-deoxy-alpha-D-ribose 1-phosphate from thymidine NF003346.0 PRK04366 PRK04366.1 441 441 487 equivalog Y Y N aminomethyl-transferring glycine dehydrogenase subunit GcvPB gcvPB 1.4.4.2 GO:0004375,GO:0006546 131567 cellular organisms no rank 65403 NCBI Protein Cluster (PRK) glycine dehydrogenase subunit 2 aminomethyl-transferring glycine dehydrogenase subunit GcvPB NF003349.0 PRK04375 PRK04375.1-2 246 246 318 equivalog Y Y N heme o synthase 2.5.1.141 GO:0008495,GO:0016020,GO:0048034 131567 cellular organisms no rank 35217 NCBI Protein Cluster (PRK) protoheme IX farnesyltransferase heme o synthase NF003363.0 PRK04439 PRK04439.1-2 557 557 403 equivalog Y Y N methionine adenosyltransferase 2.5.1.6 131567 cellular organisms no rank 180 NCBI Protein Cluster (PRK) S-adenosylmethionine synthetase methionine adenosyltransferase NF003366.0 PRK04439 PRK04439.1-5 435 435 395 subfamily Y Y N methionine adenosyltransferase 2.5.1.6 131567 cellular organisms no rank 1541 NCBI Protein Cluster (PRK) S-adenosylmethionine synthetase methionine adenosyltransferase NF003367.0 PRK04443 PRK04443.1 363 363 349 equivalog Y Y N [LysW]-lysine hydrolase 131567 cellular organisms no rank 1023 NCBI Protein Cluster (PRK) acetyl-lysine deacetylase [LysW]-lysine hydrolase NF003372.0 PRK04447 PRK04447.1-5 306 306 350 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 1479 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003376.0 PRK04452 PRK04452.1-2 280 280 313 subfamily Y Y N acetyl-CoA decarbonylase/synthase complex subunit delta 131567 cellular organisms no rank 784 NCBI Protein Cluster (PRK) acetyl-CoA decarbonylase/synthase complex subunit delta acetyl-CoA decarbonylase/synthase complex subunit delta NF003379.0 PRK04456 PRK04456.1 372 372 464 domain Y N N acetyl-CoA decarbonylase/synthase complex subunit beta 131567 cellular organisms no rank 1259 NCBI Protein Cluster (PRK) acetyl-CoA decarbonylase/synthase complex subunit beta acetyl-CoA decarbonylase/synthase complex subunit beta NF003381.0 PRK04460 PRK04460.1 105 105 139 equivalog Y Y N nickel-responsive transcriptional regulator NikR nikR GO:0003677,GO:0006355,GO:0010045,GO:0016151 131567 cellular organisms no rank 6177 NCBI Protein Cluster (PRK) nickel responsive regulator nickel-responsive transcriptional regulator NikR Inhibits transcription at high concentrations of nickel NF003384.0 PRK04523 PRK04523.1 288 288 336 equivalog Y Y N N-acetylornithine carbamoyltransferase 2.1.3.9 GO:0016597,GO:0042450,GO:0043857 15731101 131567 cellular organisms no rank 3783 NCBI Protein Cluster (PRK) N-acetylornithine carbamoyltransferase N-acetylornithine carbamoyltransferase Catalyzes the conversion of N-acetylornithine to N-acetylcitrulline in an alternative arginine biosynthesis pathway NF003417.0 PRK04813 PRK04813.1 476 0 505 subfamily Y Y N D-alanine--poly(phosphoribitol) ligase subunit DltA dltA 6.1.1.13 131567 cellular organisms no rank 152511 NCBI Protein Cluster (PRK) D-alanine--poly(phosphoribitol) ligase subunit 1 D-alanine--poly(phosphoribitol) ligase subunit DltA Transfers D-alanine to the D-alanyl carrier protein during the incorporation of D-alanine into lipoteichoic acid NF003454.1 PRK05035 PRK05035.1 345 345 556 equivalog Y Y N electron transport complex subunit RsxC rsxC GO:0009055,GO:0016020,GO:0051539 131567 cellular organisms no rank 42401 NCBI Protein Cluster (PRK) electron transport complex protein RnfC electron transport complex subunit RsxC NF003478.0 PRK05124 PRK05124.1 590 590 475 equivalog Y Y N sulfate adenylyltransferase subunit CysN cysN 2.7.7.4 GO:0003924,GO:0005525,GO:0006790 131567 cellular organisms no rank 27585 NCBI Protein Cluster (PRK) sulfate adenylyltransferase subunit 1 sulfate adenylyltransferase subunit CysN With CysD catalyzes the formation of adenylylsulfate from sulfate and ATP NF003483.0 PRK05159 PRK05159.1 353 353 438 equivalog Y Y N aspartate--tRNA(Asn) ligase aspS 6.1.1.23 GO:0000166,GO:0003676,GO:0004815,GO:0005524,GO:0006422 131567 cellular organisms no rank 12666 NCBI Protein Cluster (PRK) aspartyl-tRNA synthetase aspartate--tRNA(Asn) ligase Catalyzes a two-step reaction, first charging an aspartate molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; contains discriminating and non-discriminating subtypes NF003543.0 PRK05198 PRK05198.1 242 242 273 equivalog Y Y N 3-deoxy-8-phosphooctulonate synthase kdsA 2.5.1.55 GO:0008676,GO:0009058 131567 cellular organisms no rank 32947 NCBI Protein Cluster (PRK) 2-dehydro-3-deoxyphosphooctonate aldolase 3-deoxy-8-phosphooctulonate synthase Catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis NF003549.0 PRK05205 PRK05205.1-5 138 138 182 equivalog Y Y N bifunctional pyr operon transcriptional regulator/uracil phosphoribosyltransferase PyrR pyrR 2.4.2.9 GO:0009116 131567 cellular organisms no rank 24568 NCBI Protein Cluster (PRK) bifunctional pyrimidine regulatory protein PyrR uracil phosphoribosyltransferase bifunctional pyr operon transcriptional regulator/uracil phosphoribosyltransferase PyrR NF003555.1 PRK05218 PRK05218.1 371 371 614 equivalog Y Y N molecular chaperone HtpG htpG GO:0005524,GO:0006457,GO:0016887,GO:0051082 131567 cellular organisms no rank 54004 NCBI Protein Cluster (PRK) heat shock protein 90 molecular chaperone HtpG NF003556.0 PRK05222 PRK05222.1 541 541 750 equivalog Y Y N 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase metE 2.1.1.14 GO:0003871,GO:0008270,GO:0008652,GO:0009086 131567 cellular organisms no rank 51845 NCBI Protein Cluster (PRK) 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine NF003559.0 PRK05234 PRK05234.1 84 84 145 equivalog Y Y N methylglyoxal synthase 4.2.3.3 GO:0008929,GO:0019242 131567 cellular organisms no rank 17471 NCBI Protein Cluster (PRK) methylglyoxal synthase methylglyoxal synthase Catalyzes the formation of methylglyoxal from glycerone phosphate NF003587.0 PRK05253 PRK05253.1 195 195 301 subfamily Y Y N sulfate adenylyltransferase subunit CysD cysD 2.7.7.4 131567 cellular organisms no rank 41555 NCBI Protein Cluster (PRK) sulfate adenylyltransferase subunit 2 sulfate adenylyltransferase subunit CysD With CysN catalyzes the formation of adenylylsulfate from sulfate and ATP NF003588.0 PRK05254 PRK05254.1-1 143 143 225 equivalog Y Y N uracil-DNA glycosylase 3.2.2.27 GO:0004844,GO:0006284 131567 cellular organisms no rank 61541 NCBI Protein Cluster (PRK) uracil-DNA glycosylase uracil-DNA glycosylase NF003589.0 PRK05254 PRK05254.1-2 223 223 227 equivalog Y Y N uracil-DNA glycosylase ung 3.2.2.27 GO:0004844,GO:0006284,GO:0016799 131567 cellular organisms no rank 47580 NCBI Protein Cluster (PRK) uracil-DNA glycosylase uracil-DNA glycosylase NF003591.1 PRK05254 PRK05254.1-4 237 237 208 equivalog Y Y N uracil-DNA glycosylase 3.2.2.27 GO:0004844,GO:0006281,GO:0006284 131567 cellular organisms no rank 42233 NCBI Protein Cluster (PRK) uracil-DNA glycosylase uracil-DNA glycosylase NF003592.0 PRK05254 PRK05254.1-5 162 162 225 equivalog Y Y N uracil-DNA glycosylase 3.2.2.27 GO:0004844,GO:0006284 131567 cellular organisms no rank 62001 NCBI Protein Cluster (PRK) uracil-DNA glycosylase uracil-DNA glycosylase NF003645.0 PRK05286 PRK05286.1-2 366 366 359 equivalog Y Y N quinone-dependent dihydroorotate dehydrogenase 1.3.5.2 GO:0004152,GO:0006207,GO:0016020 131567 cellular organisms no rank 42027 NCBI Protein Cluster (PRK) dihydroorotate dehydrogenase 2 quinone-dependent dihydroorotate dehydrogenase NF003648.0 PRK05286 PRK05286.2-1 433 433 360 equivalog Y Y N quinone-dependent dihydroorotate dehydrogenase 1.3.5.2 GO:0004152,GO:0006207,GO:0016020 131567 cellular organisms no rank 13306 NCBI Protein Cluster (PRK) dihydroorotate dehydrogenase 2 quinone-dependent dihydroorotate dehydrogenase NF003652.0 PRK05286 PRK05286.2-5 267 267 353 equivalog Y Y N quinone-dependent dihydroorotate dehydrogenase 1.3.5.2 GO:0004152,GO:0006222,GO:0016020 131567 cellular organisms no rank 55346 NCBI Protein Cluster (PRK) dihydroorotate dehydrogenase 2 quinone-dependent dihydroorotate dehydrogenase NF003658.0 PRK05290 PRK05290.1 367 367 546 equivalog Y Y N hydroxylamine reductase hcp priS 1.7.99.1 GO:0016661,GO:0051536 131567 cellular organisms no rank 21340 NCBI Protein Cluster (PRK) hybrid cluster protein hydroxylamine reductase Has hydroxylamine reductase activity, catalyzes the reduction of hydroxylamine to ammonia and water NF003671.0 PRK05294 PRK05294.1 599 599 1058 equivalog Y Y N carbamoyl-phosphate synthase large subunit carB 6.3.5.5 GO:0005524,GO:0008152,GO:0046872 10089390,11729189,15322282,4358555,5339592,9174345 131567 cellular organisms no rank 92041 NCBI Protein Cluster (PRK) carbamoyl phosphate synthase large subunit carbamoyl-phosphate synthase large subunit NF003673.1 PRK05298 PRK05298.1 743 743 653 equivalog Y Y N excinuclease ABC subunit UvrB uvrB 3.1.25.- GO:0003677,GO:0005515,GO:0005524,GO:0006289,GO:0009380,GO:0016787,GO:0016887 131567 cellular organisms no rank 75762 NCBI Protein Cluster (PRK) excinuclease ABC subunit B excinuclease ABC subunit UvrB The UvrABC repair system catalyzes the recognition and processing of DNA lesions. The beta-hairpin of the Uvr-B subunit is inserted between the strands, where it probes for the presence of a lesion NF003683.0 PRK05305 PRK05305.2-3 244 244 204 equivalog Y Y N phosphatidylserine decarboxylase 4.1.1.65 131567 cellular organisms no rank 3667 NCBI Protein Cluster (PRK) phosphatidylserine decarboxylase phosphatidylserine decarboxylase NF003685.0 PRK05305 PRK05305.2-5 183 183 198 equivalog Y Y N phosphatidylserine decarboxylase 4.1.1.65 131567 cellular organisms no rank 11741 NCBI Protein Cluster (PRK) phosphatidylserine decarboxylase phosphatidylserine decarboxylase NF003698.1 PRK05309 PRK05309.1 111 111 120 equivalog Y Y N 30S ribosomal protein S11 rpsK GO:0003735,GO:0005840,GO:0006412 12937172,2459389,3191988,7007074 131567 cellular organisms no rank 18021 NCBI Protein Cluster (PRK) 30S ribosomal protein S11 30S ribosomal protein S11 Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA; forms part of the Shine-Dalgarno cleft in the 70S ribosome; interacts with S7 and S18 and IF-3 NF003700.0 PRK05313 PRK05313.1 440 440 452 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 10778 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003704.0 PRK05321 PRK05321.1 379 379 398 subfamily Y Y N nicotinate phosphoribosyltransferase 6.3.4.21 131567 cellular organisms no rank 22762 NCBI Protein Cluster (PRK) nicotinate phosphoribosyltransferase nicotinate phosphoribosyltransferase Catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate NF003705.0 PRK05322 PRK05322.1 385 385 388 equivalog Y Y N galactokinase 2.7.1.6 GO:0004335,GO:0005524,GO:0006012,GO:0046835 131567 cellular organisms no rank 14978 NCBI Protein Cluster (PRK) galactokinase galactokinase Catalyzes the formation of alpha-D-galactose 1-phosphate from D-galactose in galactose metabolism NF003715.0 PRK05326 PRK05326.1-2 309 309 595 equivalog Y Y N potassium/proton antiporter 131567 cellular organisms no rank 29111 NCBI Protein Cluster (PRK) potassium/proton antiporter potassium/proton antiporter NF003716.0 PRK05326 PRK05326.1-3 355 355 499 equivalog Y Y N potassium/proton antiporter GO:0006813,GO:0008324,GO:0016020 131567 cellular organisms no rank 28932 NCBI Protein Cluster (PRK) potassium/proton antiporter potassium/proton antiporter NF003740.0 PRK05337 PRK05337.1 207 207 340 equivalog Y Y N beta-N-acetylhexosaminidase nagZ 3.2.1.52 GO:0004553,GO:0005975 131567 cellular organisms no rank 33601 NCBI Protein Cluster (PRK) beta-hexosaminidase beta-N-acetylhexosaminidase Hydrolyzes the terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides NF003763.0 PRK05354 PRK05354.1 369 369 636 equivalog Y Y N biosynthetic arginine decarboxylase speA 4.1.1.19 GO:0006527,GO:0008792 12634339,15583399 131567 cellular organisms no rank 15787 NCBI Protein Cluster (PRK) arginine decarboxylase biosynthetic arginine decarboxylase Catalyzes the formation of agmatine from arginine in putrescine and spermidine biosynthesis NF003768.0 PRK05365 PRK05365.1 152 152 200 equivalog Y Y N malonic semialdehyde reductase 1.1.1.298 GO:0016491 131567 cellular organisms no rank 17795 NCBI Protein Cluster (PRK) malonic semialdehyde reductase malonic semialdehyde reductase NF003780.0 PRK05371 PRK05371.1-1 642 642 594 subfamily Y Y N Xaa-Pro dipeptidyl-peptidase 3.4.14.11 131567 cellular organisms no rank 10035 NCBI Protein Cluster (PRK) x-prolyl-dipeptidyl aminopeptidase Xaa-Pro dipeptidyl-peptidase NF003792.0 PRK05380 PRK05380.1 308 308 534 equivalog Y Y N CTP synthase 6.3.4.2 GO:0003883,GO:0006221,GO:0006241 15157079 131567 cellular organisms no rank 60367 NCBI Protein Cluster (PRK) CTP synthetase CTP synthase Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen NF003793.1 PRK05382 PRK05382.1 321 321 344 equivalog Y Y N chorismate synthase aroC 4.2.3.5 GO:0004107,GO:0009073 11279147,12595729,14705034,8885411 131567 cellular organisms no rank 69799 NCBI Protein Cluster (PRK) chorismate synthase chorismate synthase Catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis NF003802.0 PRK05388 PRK05388.1 351 351 400 equivalog Y Y N bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ argJ 2.3.1.1,2.3.1.35 GO:0004358,GO:0006526 131567 cellular organisms no rank 53955 NCBI Protein Cluster (PRK) bifunctional ornithine acetyltransferase/N-acetylglutamate synthase protein bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ Bifunctional arginine biosynthesis protein ArgJ; functions at the 1st and 5th steps in arginine biosynthesis; involved in synthesis of acetylglutamate from glutamate and acetyl-CoA and ornithine by transacetylation between acetylornithine and glutmate NF003805.0 PRK05395 PRK05395.1-2 146 146 147 subfamily Y Y N type II 3-dehydroquinate dehydratase 4.2.1.10 131567 cellular organisms no rank 51197 NCBI Protein Cluster (PRK) 3-dehydroquinate dehydratase type II 3-dehydroquinate dehydratase NF003806.0 PRK05395 PRK05395.1-3 171 171 149 subfamily Y Y N type II 3-dehydroquinate dehydratase 4.2.1.10 131567 cellular organisms no rank 44579 NCBI Protein Cluster (PRK) 3-dehydroquinate dehydratase type II 3-dehydroquinate dehydratase NF003807.0 PRK05395 PRK05395.1-4 130 130 148 subfamily Y Y N type II 3-dehydroquinate dehydratase 4.2.1.10 131567 cellular organisms no rank 52121 NCBI Protein Cluster (PRK) 3-dehydroquinate dehydratase type II 3-dehydroquinate dehydratase NF003808.0 PRK05396 PRK05396.1 380 380 341 equivalog Y Y N L-threonine 3-dehydrogenase tdh 1.1.1.103 GO:0006567,GO:0008743 131567 cellular organisms no rank 19789 NCBI Protein Cluster (PRK) L-threonine 3-dehydrogenase L-threonine 3-dehydrogenase NF003810.1 PRK05399 PRK05399.1 480 480 793 equivalog Y Y N DNA mismatch repair protein MutS mutS GO:0005524,GO:0006298,GO:0030983 131567 cellular organisms no rank 73854 NCBI Protein Cluster (PRK) DNA mismatch repair protein MutS DNA mismatch repair protein MutS Performs the mismatch recognition step during the DNA repair process NF003811.1 PRK05402 PRK05402.1 741 741 619 equivalog Y Y N 1,4-alpha-glucan branching protein GlgB glgB 2.4.1.18 GO:0003844,GO:0004553,GO:0005975,GO:0005978,GO:0043169 17005418 131567 cellular organisms no rank 65795 NCBI Protein Cluster (PRK) glycogen branching enzyme 1,4-alpha-glucan branching protein GlgB Catalyzes the transfer of a segment of a 1,4-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain NF003814.0 PRK05406 PRK05406.1-3 226 226 256 subfamily Y Y N 5-oxoprolinase subunit PxpA pxpA 3.5.2.9 GO:0003824,GO:0005975 28830929 131567 cellular organisms no rank 51429 NCBI Protein Cluster (PRK) LamB/YcsF family protein 5-oxoprolinase subunit PxpA NF003816.0 PRK05406 PRK05406.1-5 213 213 246 subfamily Y Y N 5-oxoprolinase subunit PxpA pxpA 3.5.2.9 28830929 131567 cellular organisms no rank 48711 NCBI Protein Cluster (PRK) LamB/YcsF family protein 5-oxoprolinase subunit PxpA NF003820.1 PRK05414 PRK05414.1 603 603 538 equivalog Y Y N urocanate hydratase 4.2.1.49 GO:0016153 131567 cellular organisms no rank 49145 NCBI Protein Cluster (PRK) urocanate hydratase urocanate hydratase Catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism NF003838.0 PRK05420 PRK05420.1 256 256 231 equivalog Y Y N aquaporin Z aqpZ GO:0006833,GO:0015250 131567 cellular organisms no rank 15836 NCBI Protein Cluster (PRK) aquaporin Z aquaporin Z Porin involved in osmoregulation allowing water to move into and out of the cell in response to osmotic pressure NF003877.0 PRK05427 PRK05427.1 283 283 308 equivalog Y Y N manganese-dependent inorganic pyrophosphatase 3.6.1.1 GO:0004427 131567 cellular organisms no rank 16314 NCBI Protein Cluster (PRK) putative manganese-dependent inorganic pyrophosphatase manganese-dependent inorganic pyrophosphatase Catalyzes the hydrolysis of pyrophosphate to phosphate NF003915.0 PRK05441 PRK05441.1 168 168 300 subfamily Y Y N N-acetylmuramic acid 6-phosphate etherase 4.2.1.126 15983044,16452451 131567 cellular organisms no rank 43174 NCBI Protein Cluster (PRK) N-acetylmuramic acid-6-phosphate etherase N-acetylmuramic acid 6-phosphate etherase Catalyzes the cleavage of the lactyl ether moiety of N-acetylmuramic acid-6-phosphate (MurNAc-6-P) to form N-acetylglucosamine-6-phosphate (GlcNAc-6-P) and lactate; involved in MurNAc dissimilation pathway NF003917.0 PRK05443 PRK05443.1-1 470 470 689 subfamily Y Y N RNA degradosome polyphosphate kinase 2.7.4.1 131567 cellular organisms no rank 58126 NCBI Protein Cluster (PRK) polyphosphate kinase RNA degradosome polyphosphate kinase NF003918.0 PRK05443 PRK05443.1-2 691 691 697 subfamily Y Y N RNA degradosome polyphosphate kinase 2.7.4.1 131567 cellular organisms no rank 43493 NCBI Protein Cluster (PRK) polyphosphate kinase RNA degradosome polyphosphate kinase NF003921.0 PRK05443 PRK05443.2-2 701 701 707 subfamily Y Y N RNA degradosome polyphosphate kinase 2.7.4.1 131567 cellular organisms no rank 50876 NCBI Protein Cluster (PRK) polyphosphate kinase RNA degradosome polyphosphate kinase NF003925.0 PRK05443 PRK05443.3-3 707 707 688 equivalog Y Y N RNA degradosome polyphosphate kinase 2.7.4.1 131567 cellular organisms no rank 895 NCBI Protein Cluster (PRK) polyphosphate kinase RNA degradosome polyphosphate kinase NF003927.0 PRK05443 PRK05443.3-6 1042 1042 717 equivalog Y Y N RNA degradosome polyphosphate kinase 2.7.4.1 131567 cellular organisms no rank 246 NCBI Protein Cluster (PRK) polyphosphate kinase RNA degradosome polyphosphate kinase NF003952.0 PRK05450 PRK05450.1-5 193 193 250 subfamily Y Y N 3-deoxy-manno-octulosonate cytidylyltransferase kdsB 2.7.7.38 131567 cellular organisms no rank 41421 NCBI Protein Cluster (PRK) 3-deoxy-manno-octulosonate cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase NF004005.0 PRK05476 PRK05476.2-3 275 275 418 equivalog Y Y N adenosylhomocysteinase 3.13.2.1 GO:0004013 131567 cellular organisms no rank 43775 NCBI Protein Cluster (PRK) S-adenosyl-L-homocysteine hydrolase adenosylhomocysteinase NF004012.0 PRK05477 PRK05477.1-2 338 338 481 equivalog Y Y N Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB gatB GO:0016884 131567 cellular organisms no rank 58717 NCBI Protein Cluster (PRK) aspartyl/glutamyl-tRNA amidotransferase subunit B Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB NF004014.0 PRK05477 PRK05477.1-4 414 414 475 equivalog Y Y N Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB gatB GO:0016884 131567 cellular organisms no rank 57747 NCBI Protein Cluster (PRK) aspartyl/glutamyl-tRNA amidotransferase subunit B Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB NF004016.0 PRK05478 PRK05478.1 510 510 468 subfamily Y Y N 3-isopropylmalate dehydratase large subunit 4.2.1.33 131567 cellular organisms no rank 63635 NCBI Protein Cluster (PRK) isopropylmalate isomerase large subunit 3-isopropylmalate dehydratase large subunit NF004017.0 PRK05479 PRK05479.1 336 336 337 equivalog Y Y N ketol-acid reductoisomerase ilvC 1.1.1.86 131567 cellular organisms no rank 39773 NCBI Protein Cluster (PRK) ketol-acid reductoisomerase ketol-acid reductoisomerase NF004018.0 PRK05480 PRK05480.1 180 180 210 equivalog Y Y N uridine kinase udk 2.7.1.48 GO:0004849 131567 cellular organisms no rank 14924 NCBI Protein Cluster (PRK) uridine/cytidine kinase uridine kinase NF004019.1 PRK05481 PRK05481.1 203 203 286 subfamily Y Y N lipoyl synthase 2.8.1.8 131567 cellular organisms no rank 50471 NCBI Protein Cluster (PRK) lipoyl synthase lipoyl synthase Catalyzes the radical-mediated insertion of two sulfur atoms into an acyl carrier protein (ACP) bound to an octanoyl group to produce a lipoyl group NF004036.0 PRK05508 PRK05508.1 179 179 121 equivalog Y Y N methionine-R-sulfoxide reductase 1.8.4.12 131567 cellular organisms no rank 2661 NCBI Protein Cluster (PRK) methionine sulfoxide reductase B methionine-R-sulfoxide reductase NF004041.0 PRK05541 PRK05541.1 127 127 176 subfamily Y Y N adenylyl-sulfate kinase 2.7.1.25 131567 cellular organisms no rank 2880 NCBI Protein Cluster (PRK) adenylylsulfate kinase adenylyl-sulfate kinase Converts ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate NF004042.0 PRK05550 PRK05550.1 330 330 293 equivalog Y Y N bifunctional methionine sulfoxide reductase B/A protein 1.8.4.11,1.8.4.12 131567 cellular organisms no rank 2118 NCBI Protein Cluster (PRK) bifunctional methionine sulfoxide reductase B/A protein bifunctional methionine sulfoxide reductase B/A protein NF004043.1 PRK05560 PRK05560.1 902 902 798 equivalog Y Y N DNA gyrase subunit A gyrA 5.6.2.2 GO:0003677,GO:0003916,GO:0003918,GO:0005524,GO:0006259,GO:0006265 131567 cellular organisms no rank 81912 NCBI Protein Cluster (PRK) DNA gyrase subunit A DNA gyrase subunit A Negatively supercoils closed circular double-stranded DNA NF004044.1 PRK05561 PRK05561.1 654 654 738 subfamily Y Y N DNA topoisomerase (ATP-hydrolyzing) 5.6.2.2 GO:0003677,GO:0003918,GO:0005524,GO:0006265 131567 cellular organisms no rank 142174 NCBI Protein Cluster (PRK) DNA topoisomerase IV subunit A DNA topoisomerase (ATP-hydrolyzing) This HMM identifies type II DNA topoisomerases such as ParC (DNA topoisomerase IV subunit A) and GyrA (DNA gyrase subunit A). NF004051.0 PRK05571 PRK05571.1 135 135 149 subfamily Y N N ribose-5-phosphate isomerase B 131567 cellular organisms no rank 42582 NCBI Protein Cluster (PRK) ribose-5-phosphate isomerase B ribose-5-phosphate isomerase B NF004064.0 PRK05578 PRK05578.1 74 74 130 equivalog Y Y N cytidine deaminase 3.5.4.5 GO:0004126,GO:0008270,GO:0009972 131567 cellular organisms no rank 37832 NCBI Protein Cluster (PRK) cytidine deaminase cytidine deaminase Reclaims exogenous and endogenous cytidine and 2'-deoxycytidine molecules for UMP synthesis NF004076.0 PRK05581 PRK05581.1-4 165 165 221 subfamily Y Y N ribulose-phosphate 3-epimerase 5.1.3.1 131567 cellular organisms no rank 67323 NCBI Protein Cluster (PRK) ribulose-phosphate 3-epimerase ribulose-phosphate 3-epimerase NF004123.1 PRK05610 PRK05610.1 74 74 72 equivalog Y Y N 30S ribosomal protein S17 rpsQ GO:0003735,GO:0005840,GO:0006412 10561594,8251502,8608120 131567 cellular organisms no rank 25851 NCBI Protein Cluster (PRK) 30S ribosomal protein S17 30S ribosomal protein S17 Primary binding protein; helps mediate assembly; involved in translation fidelity NF004160.0 PRK05627 PRK05627.1-3 295 295 325 equivalog Y Y N bifunctional riboflavin kinase/FAD synthetase 2.7.1.26,2.7.7.2 GO:0003919 131567 cellular organisms no rank 48238 NCBI Protein Cluster (PRK) bifunctional riboflavin kinase/FMN adenylyltransferase bifunctional riboflavin kinase/FAD synthetase NF004171.0 PRK05639 PRK05639.1 639 639 457 equivalog Y Y N acetyl ornithine aminotransferase family protein 131567 cellular organisms no rank 52 NCBI Protein Cluster (PRK) 4-aminobutyrate aminotransferase acetyl ornithine aminotransferase family protein NF004189.0 PRK05644 PRK05644.1 740 740 641 subfamily Y Y N DNA gyrase subunit B GO:0003677,GO:0003918,GO:0005524,GO:0006265 131567 cellular organisms no rank 88981 NCBI Protein Cluster (PRK) DNA gyrase subunit B DNA gyrase subunit B Negatively supercoils closed circular double-stranded DNA NF004198.0 PRK05653 PRK05653.1-3 296 296 248 equivalog Y Y N 3-oxoacyl-ACP reductase FabG fabG 1.1.1.100 GO:0004316,GO:0006633,GO:0051287 131567 cellular organisms no rank 10078 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase 3-oxoacyl-ACP reductase FabG NF004202.0 PRK05653 PRK05653.2-2 333 333 259 equivalog Y Y N 3-oxoacyl-ACP reductase FabG fabG 1.1.1.100 GO:0016491 131567 cellular organisms no rank 2384 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase 3-oxoacyl-ACP reductase FabG NF004226.0 PRK05673 PRK05673.1 1002 1002 1146 equivalog Y Y N DNA polymerase III subunit alpha dnaE 2.7.7.7 GO:0003676,GO:0006260,GO:0008408 131567 cellular organisms no rank 82662 NCBI Protein Cluster (PRK) DNA polymerase III subunit alpha DNA polymerase III subunit alpha Catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase NF004230.0 PRK05678 PRK05678.1 336 336 291 equivalog Y Y N succinate--CoA ligase subunit alpha sucD 6.2.1.5 GO:0003824 131567 cellular organisms no rank 42209 NCBI Protein Cluster (PRK) succinyl-CoA synthetase subunit alpha succinate--CoA ligase subunit alpha Catalyzes the only substrate-level phosphorylation in the TCA cycle NF004281.0 PRK05690 PRK05690.1 266 266 250 subfamily Y Y N molybdopterin-synthase adenylyltransferase MoeB moeB GO:0008641 131567 cellular organisms no rank 49628 NCBI Protein Cluster (PRK) molybdopterin biosynthesis protein MoeB molybdopterin-synthase adenylyltransferase MoeB ATP-dependent adenylate transferase, transfers adenyl moiety to the MoeD subunit of molybdopterin synthase NF004282.0 PRK05691 PRK05691.1 4090 0 4334 subfamily Y Y N non-ribosomal peptide synthase/polyketide synthase GO:0008610,GO:0031177 131567 cellular organisms no rank 30425 NCBI Protein Cluster (PRK) peptide synthase non-ribosomal peptide synthase/polyketide synthase Catalyzes the specific recognition and activation of amino acids during peptide synthesis; involved in the biosynthesis of the peptide chain of pyoverdines NF004283.0 PRK05692 PRK05692.1 246 246 300 subfamily Y Y N hydroxymethylglutaryl-CoA lyase 4.1.3.4 GO:0004419 131567 cellular organisms no rank 51015 NCBI Protein Cluster (PRK) hydroxymethylglutaryl-CoA lyase hydroxymethylglutaryl-CoA lyase Catalyzes the formation of acetoacetate and acetyl-CoA from 3-hydroxy-3-methylglutaryl-CoA NF004320.0 PRK05715 PRK05715.1-2 57 57 99 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoK nuoK 1.6.5.9 GO:0016651,GO:0042773 131567 cellular organisms no rank 27276 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit K NADH-quinone oxidoreductase subunit NuoK NF004321.0 PRK05715 PRK05715.1-3 91 91 101 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoK nuoK 1.6.5.9 131567 cellular organisms no rank 13717 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit K NADH-quinone oxidoreductase subunit NuoK NF004322.0 PRK05715 PRK05715.1-4 128 128 104 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoK nuoK 1.6.5.9 GO:0016651,GO:0042773 131567 cellular organisms no rank 1746 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit K NADH-quinone oxidoreductase subunit NuoK NF004323.0 PRK05715 PRK05715.1-5 89 89 102 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoK nuoK 1.6.5.9 GO:0016651,GO:0042773 131567 cellular organisms no rank 13873 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit K NADH-quinone oxidoreductase subunit NuoK NF004326.0 PRK05720 PRK05720.1 271 271 358 subfamily Y Y N s-methyl-5-thioribose-1-phosphate isomerase 5.3.1.23 11545674,12022921,14551435,15102328 131567 cellular organisms no rank 33343 NCBI Protein Cluster (PRK) methylthioribose-1-phosphate isomerase s-methyl-5-thioribose-1-phosphate isomerase Isomerizes methylthioribose-1-phosphate into methylthioribulose-1-phosphate; involved in methionine salvage pathway NF004397.1 PRK05755 PRK05755.1 720 720 889 equivalog Y Y N DNA polymerase I polA 2.7.7.7 GO:0003676,GO:0003677,GO:0003887,GO:0006261,GO:0008408 131567 cellular organisms no rank 95029 NCBI Protein Cluster (PRK) DNA polymerase I DNA polymerase I Has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair NF004424.0 PRK05766 PRK05766.1 54 54 54 equivalog Y Y N 30S ribosomal protein S14 131567 cellular organisms no rank 841 NCBI Protein Cluster (PRK) 30S ribosomal protein S14P 30S ribosomal protein S14 Located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the archaeal forms appear to contain the zinc-binding motif NF004426.0 PRK05769 PRK05769.1 552 552 441 equivalog Y Y N acetyl ornithine aminotransferase family protein 131567 cellular organisms no rank 1059 NCBI Protein Cluster (PRK) 4-aminobutyrate aminotransferase acetyl ornithine aminotransferase family protein NF004457.0 PRK05787 PRK05787.1-5 302 302 252 equivalog Y Y N cobalt-precorrin-7 (C(5))-methyltransferase 2.1.1.289 131567 cellular organisms no rank 656 NCBI Protein Cluster (PRK) cobalt-precorrin-6Y C(5)-methyltransferase cobalt-precorrin-7 (C(5))-methyltransferase NF004474.0 PRK05808 PRK05808.1 408 408 283 subfamily Y Y N 3-hydroxybutyryl-CoA dehydrogenase 1.1.1.157 GO:0006631 131567 cellular organisms no rank 17721 NCBI Protein Cluster (PRK) 3-hydroxybutyryl-CoA dehydrogenase 3-hydroxybutyryl-CoA dehydrogenase Converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA NF004481.0 PRK05815 PRK05815.2-3 227 227 225 equivalog Y Y N F0F1 ATP synthase subunit A 7.1.2.2 GO:0015078,GO:0015986,GO:0045263 131567 cellular organisms no rank 2293 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit A F0F1 ATP synthase subunit A NF004490.0 PRK05820 PRK05820.1 269 269 439 equivalog Y Y N thymidine phosphorylase 2.4.2.4 GO:0006206 8349569 131567 cellular organisms no rank 44107 NCBI Protein Cluster (PRK) thymidine phosphorylase thymidine phosphorylase NF004491.0 PRK05826 PRK05826.1 432 432 477 subfamily Y Y N pyruvate kinase 2.7.1.40 131567 cellular organisms no rank 75210 NCBI Protein Cluster (PRK) pyruvate kinase pyruvate kinase Catalyzes the formation of phosphoenolpyruvate from pyruvate NF004508.0 PRK05849 PRK05849.1 501 501 789 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 1926 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004513.0 PRK05854 PRK05854.1 282 282 314 subfamily Y Y N SDR family oxidoreductase GO:0016491 131567 cellular organisms no rank 14181 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF004531.0 PRK05878 PRK05878.1 456 456 534 equivalog Y Y N pyruvate, phosphate dikinase 2.7.9.1 131567 cellular organisms no rank 32391 NCBI Protein Cluster (PRK) pyruvate phosphate dikinase pyruvate, phosphate dikinase NF004559.0 PRK05899 PRK05899.2-5 488 488 627 equivalog Y Y N transketolase 2.2.1.1 131567 cellular organisms no rank 5651 NCBI Protein Cluster (PRK) transketolase transketolase NF004609.0 PRK05939 PRK05939.1 555 555 412 equivalog Y Y N cystathionine gamma-synthase family protein 131567 cellular organisms no rank 1910 NCBI Protein Cluster (PRK) hypothetical protein cystathionine gamma-synthase family protein NF004616.0 PRK05950 PRK05950.1 228 228 238 subfamily Y Y N succinate dehydrogenase iron-sulfur subunit sdhB 1.3.5.1 12560550 131567 cellular organisms no rank 28478 NCBI Protein Cluster (PRK) succinate dehydrogenase iron-sulfur subunit succinate dehydrogenase iron-sulfur subunit NF004617.0 PRK05951 PRK05951.1 239 239 306 equivalog Y N N prenyltransferase 131567 cellular organisms no rank 79 NCBI Protein Cluster (PRK) prenyltransferase prenyltransferase NF004624.0 PRK05964 PRK05964.1 494 494 427 equivalog Y Y N adenosylmethionine--8-amino-7-oxononanoate transaminase 2.6.1.62 GO:0004015,GO:0009102 131567 cellular organisms no rank 50548 NCBI Protein Cluster (PRK) adenosylmethionine--8-amino-7-oxononanoate transaminase adenosylmethionine--8-amino-7-oxononanoate transaminase Catalyzes the formation of S-adenosyl-4-methylthionine-2-oxobutanoate and 7,8-diaminononanoate from S-adenosyl-L-methionine and 8-amino-7-oxononanoate NF004630.0 PRK05974 PRK05974.1 75 75 83 equivalog Y Y N phosphoribosylformylglycinamidine synthase subunit PurS purS 6.3.5.3 10784038,12211007,15301532 131567 cellular organisms no rank 18738 NCBI Protein Cluster (PRK) phosphoribosylformylglycinamidine synthase subunit PurS phosphoribosylformylglycinamidine synthase subunit PurS With PurL and PurQ catalyzes the conversion of formylglycinamide ribonucleotide, ATP, and glutamine to formylglycinamidine ribonucleotide, ADP, and glutamate in the fourth step of the purine biosynthetic pathway NF004637.0 PRK05986 PRK05986.1 185 185 197 subfamily Y Y N cob(I)yrinic acid a,c-diamide adenosyltransferase 2.5.1.17 131567 cellular organisms no rank 29590 NCBI Protein Cluster (PRK) cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase cob(I)yrinic acid a,c-diamide adenosyltransferase Catalyzes the formation of adenosylcobalamide from cobinamide and the formation of coenzyme B12 from cob(I)alamin NF004646.0 PRK05989 PRK05989.2-4 1468 1468 1277 equivalog Y Y N cobaltochelatase subunit CobN cobN 6.6.1.2 131567 cellular organisms no rank 239 NCBI Protein Cluster (PRK) cobaltochelatase subunit CobN cobaltochelatase subunit CobN NF004675.0 PRK06019 PRK06019.1-1 375 375 375 equivalog Y Y N 5-(carboxyamino)imidazole ribonucleotide synthase purK 6.3.4.18 GO:0004638,GO:0005524,GO:0006189,GO:0046872 131567 cellular organisms no rank 22133 NCBI Protein Cluster (PRK) phosphoribosylaminoimidazole carboxylase ATPase subunit 5-(carboxyamino)imidazole ribonucleotide synthase NF004676.0 PRK06019 PRK06019.1-2 387 387 363 equivalog Y Y N 5-(carboxyamino)imidazole ribonucleotide synthase 6.3.4.18 131567 cellular organisms no rank 28104 NCBI Protein Cluster (PRK) phosphoribosylaminoimidazole carboxylase ATPase subunit 5-(carboxyamino)imidazole ribonucleotide synthase NF004679.0 PRK06019 PRK06019.1-5 326 326 376 equivalog Y Y N 5-(carboxyamino)imidazole ribonucleotide synthase 6.3.4.18 GO:0004638,GO:0005524,GO:0006189,GO:0046872 131567 cellular organisms no rank 59596 NCBI Protein Cluster (PRK) phosphoribosylaminoimidazole carboxylase ATPase subunit 5-(carboxyamino)imidazole ribonucleotide synthase NF004680.0 PRK06019 PRK06019.1-6 327 327 405 equivalog Y Y N 5-(carboxyamino)imidazole ribonucleotide synthase 6.3.4.18 GO:0004638,GO:0005524,GO:0006189,GO:0046872 131567 cellular organisms no rank 15939 NCBI Protein Cluster (PRK) phosphoribosylaminoimidazole carboxylase ATPase subunit 5-(carboxyamino)imidazole ribonucleotide synthase NF004684.0 PRK06027 PRK06027.1 223 223 286 subfamily Y Y N formyltetrahydrofolate deformylase 3.5.1.10 7868604,8226647 131567 cellular organisms no rank 50038 NCBI Protein Cluster (PRK) formyltetrahydrofolate deformylase formyltetrahydrofolate deformylase Produces formate from formyl-tetrahydrofolate which is the major source of formate for PurT in de novo purine nucleotide biosynthesis; has a role in one-carbon metabolism; forms a homohexamer; activated by methionine and inhibited by glycine NF004685.0 PRK06029 PRK06029.1 188 188 187 subfamily Y Y N UbiX family flavin prenyltransferase 2.5.1.129 GO:0003824 131567 cellular organisms no rank 27542 NCBI Protein Cluster (PRK) 3-octaprenyl-4-hydroxybenzoate carboxy-lyase UbiX family flavin prenyltransferase UbiX partners with UbiD for decarboxylation of the 3-octaprenyl-4-hydroxybenzoate precursor during ubiquinone biosynthesis, but the role of UbiX is as a flavin prenyltransferase that provides a cofactor UbiD requires. NF004711.0 PRK06049 PRK06049.1 130 130 156 equivalog Y Y N 50S ribosomal protein L30 131567 cellular organisms no rank 1202 NCBI Protein Cluster (PRK) 50S ribosomal protein L30P 50S ribosomal protein L30 L30 binds domain II of the 23S rRNA and the 5S rRNA NF004718.0 PRK06062 PRK06062.1 472 472 454 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 14065 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004720.0 PRK06064 PRK06064.1 420 420 389 subfamily Y Y N thiolase domain-containing protein 131567 cellular organisms no rank 1986 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase thiolase domain-containing protein NF004721.0 PRK06065 PRK06065.1 455 455 393 equivalog Y Y N thiolase domain-containing protein 131567 cellular organisms no rank 81 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase thiolase domain-containing protein NF004723.0 PRK06067 PRK06067.1 194 194 243 subfamily Y N N flagellar accessory protein FlaH 131567 cellular organisms no rank 222 NCBI Protein Cluster (PRK) flagellar accessory protein FlaH flagellar accessory protein FlaH NF004724.0 PRK06069 PRK06069.1 826 826 577 subfamily Y Y N succinate dehydrogenase/fumarate reductase flavoprotein subunit 1.3.5.- 131567 cellular organisms no rank 136 NCBI Protein Cluster (PRK) succinate dehydrogenase flavoprotein subunit succinate dehydrogenase/fumarate reductase flavoprotein subunit NF004737.0 PRK06074 PRK06074.2-4 144 144 150 equivalog Y Y N NADH-quinone oxidoreductase subunit C 1.6.5.9 131567 cellular organisms no rank 30 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit C NADH-quinone oxidoreductase subunit C NF004739.1 PRK06075 PRK06075.1 360 360 384 equivalog Y Y N NADH-quinone oxidoreductase subunit D 7.1.1.- GO:0016651,GO:0048038,GO:0051287 131567 cellular organisms no rank 41583 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit D NADH-quinone oxidoreductase subunit D NF004741.0 PRK06076 PRK06076.1-2 305 305 337 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoH nuoH 1.6.5.9 GO:0016020 131567 cellular organisms no rank 35188 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit H NADH-quinone oxidoreductase subunit NuoH NF004751.0 PRK06080 PRK06080.1-3 264 264 296 equivalog Y Y N 1,4-dihydroxy-2-naphthoate polyprenyltransferase 2.5.1.74 GO:0009234,GO:0016020,GO:0046428 30978223 131567 cellular organisms no rank 13680 NCBI Protein Cluster (PRK) 1,4-dihydroxy-2-naphthoate octaprenyltransferase 1,4-dihydroxy-2-naphthoate octaprenyltransferase NF004780.0 PRK06126 PRK06126.1 445 445 552 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 4987 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004790.0 PRK06136 PRK06136.1 198 198 250 subfamily Y Y N uroporphyrinogen-III C-methyltransferase 2.1.1.107 7959054 131567 cellular organisms no rank 96086 NCBI Protein Cluster (PRK) uroporphyrin-III C-methyltransferase uroporphyrinogen-III C-methyltransferase NF004799.0 PRK06148 PRK06148.1 1128 1128 1015 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 1831 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004801.0 PRK06151 PRK06151.1 416 416 491 subfamily Y Y N chlorohydrolase family protein GO:0016787 131567 cellular organisms no rank 3114 NCBI Protein Cluster (PRK) N-ethylammeline chlorohydrolase chlorohydrolase family protein NF004804.0 PRK06153 PRK06153.1-3 340 340 401 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 1600 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004805.0 PRK06153 PRK06153.1-4 352 352 392 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 1617 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004807.0 PRK06154 PRK06154.1 607 607 565 equivalog Y Y N thiamine pyrophosphate-requiring protein 131567 cellular organisms no rank 990 NCBI Protein Cluster (PRK) hypothetical protein thiamine pyrophosphate-requiring protein NF004810.0 PRK06157 PRK06157.1 403 403 400 equivalog Y Y N acetyl-CoA acetyltransferase GO:0016740 131567 cellular organisms no rank 1746 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA acetyltransferase NF004811.0 PRK06158 PRK06158.1 421 421 384 subfamily Y Y N acetyl-CoA acetyltransferase GO:0016747 131567 cellular organisms no rank 3840 NCBI Protein Cluster (PRK) thiolase acetyl-CoA acetyltransferase NF004818.0 PRK06172 PRK06172.1 336 336 253 equivalog Y Y N SDR family oxidoreductase GO:0016491 131567 cellular organisms no rank 3360 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF004825.0 PRK06181 PRK06181.1 215 215 268 equivalog Y Y N SDR family oxidoreductase GO:0016491 131567 cellular organisms no rank 6991 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF004826.0 PRK06182 PRK06182.1 305 305 274 subfamily Y Y N oxidoreductase GO:0016491 131567 cellular organisms no rank 5319 NCBI Protein Cluster (PRK) short chain dehydrogenase oxidoreductase NF004837.0 PRK06187 PRK06187.1 476 476 531 subfamily Y Y N long-chain-fatty-acid--CoA ligase 6.2.1.3 131567 cellular organisms no rank 81590 NCBI Protein Cluster (PRK) long-chain-fatty-acid--CoA ligase long-chain-fatty-acid--CoA ligase Activates fatty acids by binding to coenzyme A NF004845.0 PRK06196 PRK06196.1 414 414 320 subfamily Y Y N oxidoreductase GO:0016491 131567 cellular organisms no rank 8440 NCBI Protein Cluster (PRK) oxidoreductase oxidoreductase NF004846.0 PRK06197 PRK06197.1 268 268 306 subfamily Y Y N oxidoreductase GO:0016491 131567 cellular organisms no rank 29386 NCBI Protein Cluster (PRK) short chain dehydrogenase oxidoreductase NF004850.0 PRK06201 PRK06201.1 231 231 222 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 6501 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004861.0 PRK06217 PRK06217.1 203 203 183 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 2895 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004862.0 PRK06222 PRK06222.1 220 220 281 subfamily Y Y N sulfide/dihydroorotate dehydrogenase-like FAD/NAD-binding protein 131567 cellular organisms no rank 8052 NCBI Protein Cluster (PRK) ferredoxin-NADP(+) reductase subunit alpha sulfide/dihydroorotate dehydrogenase-like FAD/NAD-binding protein NF004863.0 PRK06223 PRK06223.1 283 283 313 subfamily Y Y N malate dehydrogenase 1.1.1.37 15597737,9245810 131567 cellular organisms no rank 26447 NCBI Protein Cluster (PRK) malate dehydrogenase malate dehydrogenase Catalyzes the oxidation of malate to oxaloacetate NF004866.0 PRK06224 PRK06224.1-3 245 245 275 subfamily Y Y N citryl-CoA lyase 4.1.3.34 131567 cellular organisms no rank 277 NCBI Protein Cluster (PRK) citrate synthase citryl-CoA lyase NF004868.0 PRK06224 PRK06224.1-5 193 193 260 subfamily Y Y N citryl-CoA lyase 4.1.3.34 131567 cellular organisms no rank 4299 NCBI Protein Cluster (PRK) citrate synthase citryl-CoA lyase NF004869.0 PRK06224 PRK06224.1-6 212 212 263 subfamily Y Y N citryl-CoA lyase 4.1.3.34 131567 cellular organisms no rank 443 NCBI Protein Cluster (PRK) citrate synthase citryl-CoA lyase NF004870.0 PRK06225 PRK06225.1 351 351 380 equivalog Y Y N pyridoxal phosphate-dependent aminotransferase 131567 cellular organisms no rank 617 NCBI Protein Cluster (PRK) aspartate aminotransferase pyridoxal phosphate-dependent aminotransferase NF004871.0 PRK06228 PRK06228.1 135 135 133 equivalog Y Y N F0F1 ATP synthase subunit epsilon 7.1.2.2 131567 cellular organisms no rank 876 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit epsilon F0F1 ATP synthase subunit epsilon Produces ATP from ADP in the presence of a proton gradient across the membrane; the epsilon subunit is part of the catalytic core of the ATP synthase complex NF004877.0 PRK06241 PRK06241.1-2 866 866 869 subfamily Y Y N phosphoenolpyruvate synthase 2.7.9.2 131567 cellular organisms no rank 11058 NCBI Protein Cluster (PRK) phosphoenolpyruvate synthase phosphoenolpyruvate synthase NF004878.0 PRK06241 PRK06241.1-3 945 945 891 subfamily Y Y N phosphoenolpyruvate synthase 2.7.9.2 131567 cellular organisms no rank 6467 NCBI Protein Cluster (PRK) phosphoenolpyruvate synthase phosphoenolpyruvate synthase NF004884.0 PRK06245 PRK06245.1 209 209 340 equivalog Y Y N 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase subunit CofG cofG 131567 cellular organisms no rank 16681 NCBI Protein Cluster (PRK) FO synthase subunit 1 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase subunit CofG 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase subunit 1; catalyzes radical-mediated transfer of hydroxybenzyl group from 4-hydroxyphenylpyruvate (HPP) to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione to form 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO); functions in F420 biosynthesis along with cofH NF004885.0 PRK06246 PRK06246.1 276 276 279 equivalog Y Y N fumarate hydratase 4.2.1.2 GO:0016829 131567 cellular organisms no rank 7877 NCBI Protein Cluster (PRK) fumarate hydratase fumarate hydratase Catalyzes the reversible hydration of fumaric acid to yield I-malic acid NF004889.0 PRK06252 PRK06252.1 244 244 340 subfamily Y N N methylcobalamin:coenzyme M methyltransferase 131567 cellular organisms no rank 1511 NCBI Protein Cluster (PRK) methylcobalamin:coenzyme M methyltransferase methylcobalamin:coenzyme M methyltransferase NF004902.0 PRK06265 PRK06265.1-1 219 219 213 equivalog Y Y N cobalt transporter CbiM cbiM 131567 cellular organisms no rank 456 NCBI Protein Cluster (PRK) cobalt transport protein CbiM cobalt transporter CbiM NF004905.0 PRK06265 PRK06265.1-5 173 173 205 equivalog Y Y N cobalt transporter CbiM cbiM 131567 cellular organisms no rank 1843 NCBI Protein Cluster (PRK) cobalt transport protein CbiM cobalt transporter CbiM NF004912.0 PRK06270 PRK06270.1 373 373 343 equivalog Y Y N homoserine dehydrogenase 1.1.1.3 GO:0004412,GO:0006520 131567 cellular organisms no rank 2732 NCBI Protein Cluster (PRK) homoserine dehydrogenase homoserine dehydrogenase Catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine NF004937.0 PRK06290 PRK06290.1 585 585 410 equivalog Y Y N LL-diaminopimelate aminotransferase 2.6.1.83 131567 cellular organisms no rank 1046 NCBI Protein Cluster (PRK) aspartate aminotransferase LL-diaminopimelate aminotransferase NF004938.0 PRK06291 PRK06291.1 528 528 468 equivalog Y Y N aspartate kinase 2.7.2.4 131567 cellular organisms no rank 464 NCBI Protein Cluster (PRK) aspartate kinase aspartate kinase Catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP NF004943.0 PRK06292 PRK06292.2-1 432 432 456 equivalog Y Y N dihydrolipoyl dehydrogenase 1.8.1.4 131567 cellular organisms no rank 199 NCBI Protein Cluster (PRK) dihydrolipoamide dehydrogenase dihydrolipoyl dehydrogenase NF004976.0 PRK06349 PRK06349.1 205 205 430 subfamily Y Y N homoserine dehydrogenase 1.1.1.3 GO:0004412,GO:0006520,GO:0050661 25945586 131567 cellular organisms no rank 57626 NCBI Protein Cluster (PRK) homoserine dehydrogenase homoserine dehydrogenase Catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine NF004978.0 PRK06354 PRK06354.1 462 462 590 subfamily Y Y N pyruvate kinase 2.7.1.40 131567 cellular organisms no rank 63818 NCBI Protein Cluster (PRK) pyruvate kinase pyruvate kinase Catalyzes the formation of phosphoenolpyruvate from pyruvate NF004981.0 PRK06361 PRK06361.1 117 117 217 equivalog Y Y N histidinol phosphate phosphatase domain-containing protein 131567 cellular organisms no rank 858 NCBI Protein Cluster (PRK) hypothetical protein histidinol phosphate phosphatase domain-containing protein NF004982.0 PRK06365 PRK06365.1 695 695 430 equivalog Y Y N thiolase domain-containing protein 131567 cellular organisms no rank 25 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase thiolase domain-containing protein NF004996.0 PRK06381 PRK06381.1 266 266 319 equivalog Y N N threonine synthase 131567 cellular organisms no rank 264 NCBI Protein Cluster (PRK) threonine synthase threonine synthase NF005012.1 PRK06411 PRK06411.1 116 116 166 subfamily Y Y N NADH-quinone oxidoreductase subunit NuoB nuoB 1.6.5.9 GO:0008137,GO:0048038,GO:0051536 131567 cellular organisms no rank 39393 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit B NADH-quinone oxidoreductase subunit NuoB NF005024.0 PRK06433 PRK06433.1-4 101 101 89 equivalog Y N N NADH dehydrogenase subunit J 131567 cellular organisms no rank 437 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit J NADH dehydrogenase subunit J NF005033.0 PRK06445 PRK06445.1 511 511 395 equivalog Y Y N acetyl-CoA C-acetyltransferase 2.3.1.9 131567 cellular organisms no rank 90 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA C-acetyltransferase Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A NF005034.0 PRK06446 PRK06446.1 369 369 436 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 1294 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005035.0 PRK06450 PRK06450.1 301 301 338 equivalog Y N N threonine synthase 4.2.3.1 131567 cellular organisms no rank 91 NCBI Protein Cluster (PRK) threonine synthase threonine synthase NF005036.0 PRK06451 PRK06451.1 484 484 412 equivalog Y Y N NADP-dependent isocitrate dehydrogenase 131567 cellular organisms no rank 329 NCBI Protein Cluster (PRK) isocitrate dehydrogenase NADP-dependent isocitrate dehydrogenase Catalyzes the formation of 2-oxoglutarate from isocitrate NF005052.0 PRK06462 PRK06462.1-1 368 368 353 equivalog Y N N asparagine synthetase A 131567 cellular organisms no rank 1571 NCBI Protein Cluster (PRK) asparagine synthetase A asparagine synthetase A NF005054.0 PRK06462 PRK06462.1-4 309 309 318 equivalog Y N N asparagine synthetase A 131567 cellular organisms no rank 325 NCBI Protein Cluster (PRK) asparagine synthetase A asparagine synthetase A NF005057.0 PRK06464 PRK06464.1 598 598 798 equivalog Y Y N phosphoenolpyruvate synthase ppsA 2.7.9.2 GO:0005524,GO:0006090,GO:0008986,GO:0016310,GO:0016772 131567 cellular organisms no rank 31655 NCBI Protein Cluster (PRK) phosphoenolpyruvate synthase phosphoenolpyruvate synthase Catalyzes the formation of phosphoenolpyruvate from pyruvate NF005089.0 PRK06522 PRK06522.1-4 223 223 326 subfamily Y Y N 2-dehydropantoate 2-reductase 1.1.1.169 131567 cellular organisms no rank 11458 NCBI Protein Cluster (PRK) 2-dehydropantoate 2-reductase 2-dehydropantoate 2-reductase NF005091.0 PRK06522 PRK06522.2-2 252 252 302 equivalog Y Y N 2-dehydropantoate 2-reductase 1.1.1.169 131567 cellular organisms no rank 6718 NCBI Protein Cluster (PRK) 2-dehydropantoate 2-reductase 2-dehydropantoate 2-reductase NF005097.0 PRK06525 PRK06525.1 430 430 480 equivalog Y Y N hydrogenase 4 subunit D GO:0008137 131567 cellular organisms no rank 1827 NCBI Protein Cluster (PRK) hydrogenase 4 subunit D hydrogenase 4 subunit D NF005121.0 PRK06555 PRK06555.1 395 395 404 equivalog Y Y N pyrophosphate--fructose-6-phosphate 1-phosphotransferase 2.7.1.90 GO:0006002 131567 cellular organisms no rank 2382 NCBI Protein Cluster (PRK) pyrophosphate--fructose-6-phosphate 1-phosphotransferase pyrophosphate--fructose-6-phosphate 1-phosphotransferase Catalyzes the formation of fructose 1,6-bisphosphate from fructose 6-phosphate and diphosphate NF005141.0 PRK06590 PRK06590.1 556 556 615 equivalog Y Y N NADH-quinone oxidoreductase subunit L nuoL 7.1.1.2 GO:0008137,GO:0042773 8566820 131567 cellular organisms no rank 53112 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit L NADH-quinone oxidoreductase subunit L NF005146.0 PRK06606 PRK06606.1 279 279 307 equivalog Y Y N branched-chain amino acid transaminase 2.6.1.42 GO:0004084,GO:0009081 131567 cellular organisms no rank 23327 NCBI Protein Cluster (PRK) branched-chain amino acid aminotransferase branched-chain amino acid transaminase Catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids NF005159.0 PRK06635 PRK06635.2-3 379 379 406 equivalog Y Y N aspartate kinase 2.7.2.4 131567 cellular organisms no rank 597 NCBI Protein Cluster (PRK) aspartate kinase aspartate kinase NF005214.0 PRK06701 PRK06701.1 413 413 293 subfamily Y Y N SDR family oxidoreductase GO:0016491 131567 cellular organisms no rank 13330 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005292.0 PRK06815 PRK06815.1 371 371 320 equivalog Y Y N threonine/serine dehydratase 131567 cellular organisms no rank 1192 NCBI Protein Cluster (PRK) hypothetical protein threonine/serine dehydratase NF005306.0 PRK06837 PRK06837.1 376 376 427 subfamily Y Y N ArgE/DapE family deacylase 3.4.-.- 131567 cellular organisms no rank 4593 NCBI Protein Cluster (PRK) acetylornithine deacetylase ArgE/DapE family deacylase NF005308.0 PRK06840 PRK06840.1 315 315 339 equivalog Y Y N 3-oxoacyl-ACP synthase 131567 cellular organisms no rank 1724 NCBI Protein Cluster (PRK) hypothetical protein 3-oxoacyl-ACP synthase NF005314.0 PRK06848 PRK06848.1 131 131 139 equivalog Y Y N cytidine deaminase 3.5.4.5 131567 cellular organisms no rank 968 NCBI Protein Cluster (PRK) hypothetical protein cytidine deaminase NF005316.0 PRK06850 PRK06850.1 536 536 505 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 3470 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005321.0 PRK06852 PRK06852.1 420 420 308 equivalog Y N N aldolase 131567 cellular organisms no rank 455 NCBI Protein Cluster (PRK) aldolase aldolase NF005325.0 PRK06853 PRK06853.1-5 230 230 192 equivalog Y Y N indolepyruvate oxidoreductase subunit beta 131567 cellular organisms no rank 1638 NCBI Protein Cluster (PRK) indolepyruvate oxidoreductase subunit beta indolepyruvate oxidoreductase subunit beta NF005326.0 PRK06853 PRK06853.1-6 348 348 202 equivalog Y Y N indolepyruvate oxidoreductase subunit beta 131567 cellular organisms no rank 92 NCBI Protein Cluster (PRK) indolepyruvate oxidoreductase subunit beta indolepyruvate oxidoreductase subunit beta NF005331.0 PRK06854 PRK06854.1-2 557 557 563 equivalog Y Y N adenylyl-sulfate reductase subunit alpha 1.8.99.2 131567 cellular organisms no rank 1374 NCBI Protein Cluster (PRK) adenylylsulfate reductase subunit alpha adenylyl-sulfate reductase subunit alpha NF005334.0 PRK06855 PRK06855.1 443 443 434 equivalog Y Y N pyridoxal phosphate-dependent aminotransferase 2.6.1.- 131567 cellular organisms no rank 728 NCBI Protein Cluster (PRK) aminotransferase pyridoxal phosphate-dependent aminotransferase NF005393.0 PRK06938 PRK06938.1 671 671 469 subfamily Y Y N diaminobutyrate--2-oxoglutarate transaminase 2.6.1.76 131567 cellular organisms no rank 4654 NCBI Protein Cluster (PRK) diaminobutyrate--2-oxoglutarate aminotransferase diaminobutyrate--2-oxoglutarate transaminase Catalyzes the reversible formation of diaminobutyrate and 2-oxoglutarate from glutamate and L-aspartic beta-semialdehyde NF005394.0 PRK06939 PRK06939.1 460 460 397 equivalog Y Y N glycine C-acetyltransferase 2.3.1.29 GO:0008890,GO:0009058,GO:0030170 131567 cellular organisms no rank 32208 NCBI Protein Cluster (PRK) 2-amino-3-ketobutyrate coenzyme A ligase glycine C-acetyltransferase Catalyzes the formation of 2-amino-3-oxobutanoate from acetyl-CoA and glycine NF005395.0 PRK06940 PRK06940.1 280 280 276 subfamily Y Y N SDR family oxidoreductase GO:0016491 131567 cellular organisms no rank 3709 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005403.0 PRK06953 PRK06953.1 254 254 222 equivalog Y Y N SDR family oxidoreductase GO:0016491 131567 cellular organisms no rank 2142 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005425.0 PRK07006 PRK07006.1 490 490 416 equivalog Y Y N NADP-dependent isocitrate dehydrogenase icd GO:0000287,GO:0004450,GO:0006099,GO:0051287 131567 cellular organisms no rank 20813 NCBI Protein Cluster (PRK) isocitrate dehydrogenase NADP-dependent isocitrate dehydrogenase NF005442.0 PRK07028 PRK07028.1 593 593 430 equivalog Y N N bifunctional hexulose-6-phosphate synthase/ribonuclease regulator 131567 cellular organisms no rank 286 NCBI Protein Cluster (PRK) bifunctional hexulose-6-phosphate synthase/ribonuclease regulator bifunctional hexulose-6-phosphate synthase/ribonuclease regulator NF005454.0 PRK07048 PRK07048.1 452 452 324 equivalog Y Y N threo-3-hydroxy-L-aspartate ammonia-lyase 4.3.1.16 GO:0003677,GO:0006352,GO:0006355,GO:0016987 131567 cellular organisms no rank 8122 NCBI Protein Cluster (PRK) serine/threonine dehydratase threo-3-hydroxy-L-aspartate ammonia-lyase NF005457.0 PRK07051 PRK07051.1 87 87 80 equivalog Y Y N acetyl-CoA carboxylase GO:0003989,GO:0006633,GO:0009317 131567 cellular organisms no rank 7899 NCBI Protein Cluster (PRK) hypothetical protein acetyl-CoA carboxylase NF005491.0 PRK07105 PRK07105.1 231 231 286 equivalog Y Y N pyridoxamine kinase 2.7.1.35 GO:0008478,GO:0009443 131567 cellular organisms no rank 7494 NCBI Protein Cluster (PRK) pyridoxamine kinase pyridoxamine kinase NF005495.0 PRK07109 PRK07109.1 264 264 334 subfamily Y Y N SDR family oxidoreductase GO:0016491 131567 cellular organisms no rank 14626 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005499.0 PRK07114 PRK07114.1 275 275 223 equivalog Y Y N bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase 4.1.2.14,4.1.3.16 GO:0016829 131567 cellular organisms no rank 2945 NCBI Protein Cluster (PRK) keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase Catalyzes the formation of pyruvate and glyoxylate from 4-hydroxy-2-oxoglutarate; or pyruvate and D-glyceraldehyde 3-phosphate from 2-dehydro-3-deoxy-D-glyconate 6-phosphate NF005501.0 PRK07116 PRK07116.1 198 198 161 subfamily Y Y N flavodoxin GO:0010181 131567 cellular organisms no rank 2636 NCBI Protein Cluster (PRK) flavodoxin flavodoxin NF005507.0 PRK07119 PRK07119.1 399 399 352 subfamily Y Y N 3-methyl-2-oxobutanoate dehydrogenase subunit VorB vorB 131567 cellular organisms no rank 4367 NCBI Protein Cluster (PRK) 2-ketoisovalerate ferredoxin reductase 3-methyl-2-oxobutanoate dehydrogenase subunit VorB NF005543.0 PRK07206 PRK07206.1 302 302 416 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 4177 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005544.0 PRK07207 PRK07207.1 965 965 965 equivalog Y Y N ribonucleoside-diphosphate reductase subunit alpha GO:0004748,GO:0005524,GO:0006260 131567 cellular organisms no rank 10549 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit alpha ribonucleoside-diphosphate reductase subunit alpha NF005545.0 PRK07208 PRK07208.1-1 451 451 504 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 2423 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005546.0 PRK07208 PRK07208.1-2 418 418 527 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 2049 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005548.0 PRK07208 PRK07208.1-4 389 389 488 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 3865 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005549.0 PRK07208 PRK07208.1-5 587 587 534 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 1086 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005550.0 PRK07209 PRK07209.1 309 309 383 equivalog Y Y N ribonucleotide-diphosphate reductase subunit beta 1.17.4.1 GO:0009263,GO:0016491 131567 cellular organisms no rank 8625 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit beta ribonucleotide-diphosphate reductase subunit beta NF005552.0 PRK07213 PRK07213.1 294 294 382 equivalog Y N N chlorohydrolase 131567 cellular organisms no rank 498 NCBI Protein Cluster (PRK) chlorohydrolase chlorohydrolase NF005555.0 PRK07220 PRK07220.1 635 635 740 equivalog Y Y N DNA topoisomerase I 131567 cellular organisms no rank 1540 NCBI Protein Cluster (PRK) DNA topoisomerase I DNA topoisomerase I NF005556.0 PRK07226 PRK07226.1 241 241 267 subfamily Y Y N 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase GO:0004332 131567 cellular organisms no rank 3867 NCBI Protein Cluster (PRK) fructose-bisphosphate aldolase 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase NF005557.0 PRK07228 PRK07228.1 522 522 445 equivalog Y Y N 5'-deoxyadenosine deaminase 131567 cellular organisms no rank 1725 NCBI Protein Cluster (PRK) N-ethylammeline chlorohydrolase 5'-deoxyadenosine deaminase NF005558.0 PRK07229 PRK07229.1 612 612 647 equivalog Y Y N aconitate hydratase 4.2.1.3 131567 cellular organisms no rank 13030 NCBI Protein Cluster (PRK) aconitate hydratase aconitate hydratase Catalyzes the conversion of citrate to isocitrate NF005559.1 PRK07231 PRK07231.1 215 215 249 subfamily Y Y N glucose 1-dehydrogenase 1.1.1.47 GO:0016491 131567 cellular organisms no rank 332440 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase glucose 1-dehydrogenase NF005560.0 PRK07233 PRK07233.1 252 252 435 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 3433 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005565.0 PRK07235 PRK07235.1 545 545 506 subfamily Y Y N amidase 3.5.1.4 131567 cellular organisms no rank 3688 NCBI Protein Cluster (PRK) amidase amidase NF005566.0 PRK07236 PRK07236.1 333 333 386 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 3872 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005574.0 PRK07259 PRK07259.1 269 269 304 equivalog Y Y N dihydroorotate dehydrogenase 1.3.1.14 GO:0004152,GO:0006221 11188687,12732650,8021180,9032071 131567 cellular organisms no rank 20114 NCBI Protein Cluster (PRK) dihydroorotate dehydrogenase 1B dihydroorotate dehydrogenase NF005589.0 PRK07314 PRK07314.1 387 387 413 subfamily Y Y N beta-ketoacyl-ACP synthase II 2.3.1.179 131567 cellular organisms no rank 109229 NCBI Protein Cluster (PRK) 3-oxoacyl-(acyl carrier protein) synthase II beta-ketoacyl-ACP synthase II NF005592.0 PRK07322 PRK07322.1 143 143 180 subfamily Y N N adenine phosphoribosyltransferase 131567 cellular organisms no rank 2167 NCBI Protein Cluster (PRK) adenine phosphoribosyltransferase adenine phosphoribosyltransferase NF005598.0 PRK07331 PRK07331.1 401 401 323 equivalog Y Y N cobalt transporter CbiM cbiM 131567 cellular organisms no rank 1266 NCBI Protein Cluster (PRK) cobalt transport protein CbiM cobalt transporter CbiM NF005609.0 PRK07360 PRK07360.1 426 426 374 equivalog Y Y N 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase subunit CofH cofH 131567 cellular organisms no rank 12950 NCBI Protein Cluster (PRK) FO synthase subunit 2 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase subunit CofH 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase subunit 2; catalyzes radical-mediated transfer of hydroxybenzyl group from 4-hydroxyphenylpyruvate (HPP) to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione to form 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO); functions in F420 biosynthesis along with cofG NF005621.0 PRK07375 PRK07375.1-6 126 126 120 equivalog Y N N putative monovalent cation/H+ antiporter subunit C 131567 cellular organisms no rank 970 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit C putative monovalent cation/H+ antiporter subunit C NF005623.0 PRK07375 PRK07375.2-2 81 81 93 equivalog Y N N putative monovalent cation/H+ antiporter subunit C 131567 cellular organisms no rank 71 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit C putative monovalent cation/H+ antiporter subunit C NF005624.0 PRK07375 PRK07375.2-3 95 95 105 equivalog Y Y N cation:proton antiporter subunit C 131567 cellular organisms no rank 1380 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit C cation:proton antiporter subunit C NF005655.0 PRK07429 PRK07429.1 236 236 326 subfamily Y Y N phosphoribulokinase 2.7.1.19 131567 cellular organisms no rank 1756 NCBI Protein Cluster (PRK) phosphoribulokinase phosphoribulokinase Catalyzes a reaction in which the CO2 acceptor molecule, RuBP, is generated via the phosphorylation of ribulose 5-phosphate with ATP NF005679.0 PRK07475 PRK07475.1 231 231 246 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 3376 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005681.0 PRK07478 PRK07478.1 267 267 254 subfamily Y Y N SDR family oxidoreductase GO:0016491 131567 cellular organisms no rank 5745 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005712.0 PRK07524 PRK07524.1 500 500 536 subfamily Y Y N 5-guanidino-2-oxopentanoate decarboxylase 4.1.1.75 131567 cellular organisms no rank 9379 NCBI Protein Cluster (PRK) hypothetical protein 5-guanidino-2-oxopentanoate decarboxylase NF005713.0 PRK07525 PRK07525.1 620 620 592 subfamily Y Y N sulfoacetaldehyde acetyltransferase 2.3.3.15 131567 cellular organisms no rank 4006 NCBI Protein Cluster (PRK) sulfoacetaldehyde acetyltransferase sulfoacetaldehyde acetyltransferase Catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source NF005719.0 PRK07535 PRK07535.1 259 259 268 domain Y N N methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase 131567 cellular organisms no rank 7940 NCBI Protein Cluster (PRK) methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase NF005722.0 PRK07539 PRK07539.1-2 141 141 157 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoE nuoE 1.6.5.9 GO:0016491 131567 cellular organisms no rank 7263 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit E NADH-quinone oxidoreductase subunit NuoE NF005751.0 PRK07575 PRK07575.1 529 529 440 equivalog Y Y N dihydroorotase 131567 cellular organisms no rank 835 NCBI Protein Cluster (PRK) dihydroorotase dihydroorotase NF005757.0 PRK07581 PRK07581.1 332 332 339 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 4620 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005762.0 PRK07589 PRK07589.1 302 302 350 subfamily Y Y N ornithine cyclodeaminase 4.3.1.12 131567 cellular organisms no rank 9051 NCBI Protein Cluster (PRK) ornithine cyclodeaminase ornithine cyclodeaminase Catalyzes the formation of L-proline from L-ornithine NF005840.0 PRK07757 PRK07757.1 154 154 153 equivalog Y Y N N-acetyltransferase GO:0006526,GO:0008080 131567 cellular organisms no rank 3137 NCBI Protein Cluster (PRK) acetyltransferase N-acetyltransferase NF005861.0 PRK07791 PRK07791.1 373 373 300 subfamily Y Y N SDR family oxidoreductase GO:0016491 131567 cellular organisms no rank 11040 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005866.0 PRK07803 PRK07803.1 819 819 631 equivalog Y Y N fumarate reductase/succinate dehydrogenase flavoprotein subunit GO:0016491 131567 cellular organisms no rank 8868 NCBI Protein Cluster (PRK) succinate dehydrogenase flavoprotein subunit fumarate reductase/succinate dehydrogenase flavoprotein subunit Part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol NF005871.0 PRK07811 PRK07811.1 513 513 389 equivalog Y Y N cystathionine gamma-synthase 2.5.1.48 GO:0019346,GO:0030170 19428471 131567 cellular organisms no rank 21083 NCBI Protein Cluster (PRK) cystathionine gamma-synthase cystathionine gamma-synthase Catalyzes the formation of cystathionine from L-cysteine and O-succinyl-L-homoserine NF005875.0 PRK07819 PRK07819.1 319 319 287 subfamily Y Y N 3-hydroxybutyryl-CoA dehydrogenase GO:0006631,GO:0016491,GO:0070403 131567 cellular organisms no rank 27941 NCBI Protein Cluster (PRK) 3-hydroxybutyryl-CoA dehydrogenase 3-hydroxybutyryl-CoA dehydrogenase NF005876.0 PRK07823 PRK07823.1 306 306 267 equivalog Y Y N S-methyl-5'-thioadenosine phosphorylase 2.4.2.28 GO:0009116,GO:0017061 22225784 131567 cellular organisms no rank 9264 NCBI Protein Cluster (PRK) 5'-methylthioadenosine phosphorylase S-methyl-5'-thioadenosine phosphorylase Catalyzes the reversible phosphorolysis of 5'-deoxy-5'- methylthioadenosine (MTA) to adenine and 5-methylthio-D-ribose-1- phosphate NF005913.0 PRK07906 PRK07906.1 382 382 442 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 21917 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005914.0 PRK07907 PRK07907.1 300 300 456 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 38948 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005928.0 PRK07945 PRK07945.1 250 250 337 equivalog Y Y N PHP domain-containing protein GO:0003824 131567 cellular organisms no rank 12783 NCBI Protein Cluster (PRK) hypothetical protein PHP domain-containing protein NF005932.1 PRK07956 PRK07956.1 369 369 664 equivalog Y Y N NAD-dependent DNA ligase LigA ligA 6.5.1.2 GO:0003677,GO:0003911,GO:0006260,GO:0006281 131567 cellular organisms no rank 101672 NCBI Protein Cluster (PRK) NAD-dependent DNA ligase LigA NAD-dependent DNA ligase LigA Catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction; essential for DNA replication and repair of damaged DNA NF006010.0 PRK08142 PRK08142.1 462 462 388 subfamily Y Y N thiolase domain-containing protein 131567 cellular organisms no rank 2106 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase thiolase domain-containing protein NF006043.0 PRK08186 PRK08186.1 487 487 600 subfamily Y Y N allophanate hydrolase 3.5.1.54 131567 cellular organisms no rank 21640 NCBI Protein Cluster (PRK) allophanate hydrolase allophanate hydrolase NF006045.0 PRK08190 PRK08190.1 282 282 467 subfamily Y Y N bifunctional enoyl-CoA hydratase/phosphate acetyltransferase GO:0016746 131567 cellular organisms no rank 13012 NCBI Protein Cluster (PRK) bifunctional enoyl-CoA hydratase/phosphate acetyltransferase bifunctional enoyl-CoA hydratase/phosphate acetyltransferase NF006049.0 PRK08195 PRK08195.1 229 229 344 subfamily Y N N 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase, 131567 cellular organisms no rank 19791 NCBI Protein Cluster (PRK) 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase, 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase, NF006050.0 PRK08197 PRK08197.1 303 303 406 equivalog Y Y N threonine synthase 4.2.3.1 131567 cellular organisms no rank 6262 NCBI Protein Cluster (PRK) threonine synthase threonine synthase Catalyzes the formation of L-threonine from O-phospho-L-homoserine NF006053.0 PRK08201 PRK08201.1 441 441 458 equivalog Y Y N dipeptidase 3.4.13.- GO:0016787 131567 cellular organisms no rank 18662 NCBI Protein Cluster (PRK) hypothetical protein dipeptidase NF006054.0 PRK08202 PRK08202.1 218 218 274 equivalog Y Y N purine-nucleoside phosphorylase 2.4.2.1 GO:0004731,GO:0009116 131567 cellular organisms no rank 34300 NCBI Protein Cluster (PRK) purine nucleoside phosphorylase purine-nucleoside phosphorylase Catalyzes the formation of a purine and ribose phosphate from a purine nucleoside NF006056.0 PRK08204 PRK08204.1 391 391 449 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 8689 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006070.0 PRK08213 PRK08213.1 279 279 259 subfamily Y N N gluconate 5-dehydrogenase 131567 cellular organisms no rank 4625 NCBI Protein Cluster (PRK) gluconate 5-dehydrogenase gluconate 5-dehydrogenase NF006088.0 PRK08238 PRK08238.1 351 351 482 equivalog Y Y N UbiA family prenyltransferase GO:0016765 131567 cellular organisms no rank 6321 NCBI Protein Cluster (PRK) hypothetical protein UbiA family prenyltransferase NF006108.0 PRK08259 PRK08259.1 273 273 256 equivalog Y Y N crotonase/enoyl-CoA hydratase family protein GO:0003824 131567 cellular organisms no rank 9854 NCBI Protein Cluster (PRK) enoyl-CoA hydratase crotonase/enoyl-CoA hydratase family protein NF006126.0 PRK08270 PRK08270.1 548 548 684 equivalog Y Y N ribonucleoside triphosphate reductase 1.17.4.2 GO:0006260,GO:0008998 131567 cellular organisms no rank 7186 NCBI Protein Cluster (PRK) anaerobic ribonucleoside triphosphate reductase ribonucleoside triphosphate reductase Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates NF006127.0 PRK08271 PRK08271.1 545 545 631 equivalog Y Y N anaerobic ribonucleoside-triphosphate reductase 1.17.4.2 131567 cellular organisms no rank 1932 NCBI Protein Cluster (PRK) anaerobic ribonucleoside triphosphate reductase anaerobic ribonucleoside-triphosphate reductase Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates NF006128.0 PRK08272 PRK08272.1 257 257 308 subfamily Y Y N crotonase/enoyl-CoA hydratase family protein 131567 cellular organisms no rank 3310 NCBI Protein Cluster (PRK) enoyl-CoA hydratase crotonase/enoyl-CoA hydratase family protein NF006130.0 PRK08274 PRK08274.1 369 369 467 equivalog Y Y N FAD-dependent tricarballylate dehydrogenase TcuA tcuA 131567 cellular organisms no rank 8491 NCBI Protein Cluster (PRK) tricarballylate dehydrogenase FAD-dependent tricarballylate dehydrogenase TcuA Catalyzes the oxidation of tricarballylate to cis-aconitate; FAD-dependent; required for the utilization of tricarballylate as a carbon and energy source by S. enterica NF006132.0 PRK08277 PRK08277.1 281 281 280 subfamily Y N N D-mannonate oxidoreductase 1.1.1.131 131567 cellular organisms no rank 7955 NCBI Protein Cluster (PRK) D-mannonate oxidoreductase D-mannonate oxidoreductase NF006133.0 PRK08278 PRK08278.1 250 250 278 subfamily Y Y N SDR family oxidoreductase 131567 cellular organisms no rank 10916 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006143.0 PRK08293 PRK08293.1 312 312 291 equivalog Y Y N 3-hydroxyacyl-CoA dehydrogenase 1.1.1.35 GO:0006631,GO:0016616 131567 cellular organisms no rank 5442 NCBI Protein Cluster (PRK) 3-hydroxybutyryl-CoA dehydrogenase 3-hydroxyacyl-CoA dehydrogenase NF006153.0 PRK08296 PRK08296.1-5 578 578 608 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 983 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006157.0 PRK08300 PRK08300.1 166 166 303 subfamily Y N N acetaldehyde dehydrogenase 1.2.1.10 131567 cellular organisms no rank 19624 NCBI Protein Cluster (PRK) acetaldehyde dehydrogenase acetaldehyde dehydrogenase NF006180.0 PRK08313 PRK08313.1 514 514 389 subfamily Y Y N thiolase domain-containing protein 131567 cellular organisms no rank 6462 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase thiolase domain-containing protein NF006181.0 PRK08314 PRK08314.1 705 705 563 subfamily Y Y N long-chain-fatty-acid--CoA ligase 131567 cellular organisms no rank 4166 NCBI Protein Cluster (PRK) long-chain-fatty-acid--CoA ligase long-chain-fatty-acid--CoA ligase NF006182.0 PRK08316 PRK08316.1 663 663 523 subfamily Y Y N fatty acyl-CoA synthetase 131567 cellular organisms no rank 10439 NCBI Protein Cluster (PRK) acyl-CoA synthetase fatty acyl-CoA synthetase NF006183.0 PRK08318 PRK08318.1 335 335 422 equivalog Y Y N NAD-dependent dihydropyrimidine dehydrogenase subunit PreA preA 1.3.1.1 GO:0006210,GO:0006212,GO:0017113 131567 cellular organisms no rank 12017 NCBI Protein Cluster (PRK) dihydropyrimidine dehydrogenase subunit B NAD-dependent dihydropyrimidine dehydrogenase subunit PreA NADH-dependent; catalyzes the conversion of pyrimidines to 5,6-dihydro compounds in pyrimidine degradation NF006184.0 PRK08319 PRK08319.1 180 180 224 equivalog Y Y N energy-coupling factor ABC transporter permease GO:0000041,GO:0016020,GO:0043190 131567 cellular organisms no rank 6894 NCBI Protein Cluster (PRK) cobalt transport protein CbiM energy-coupling factor ABC transporter permease NF006185.0 PRK08320 PRK08320.1 363 363 292 subfamily Y Y N branched-chain amino acid aminotransferase 2.6.1.42 12670965 131567 cellular organisms no rank 2957 NCBI Protein Cluster (PRK) branched-chain amino acid aminotransferase branched-chain amino acid aminotransferase Catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids NF006186.0 PRK08321 PRK08321.1 378 378 302 equivalog Y Y N 1,4-dihydroxy-2-naphthoyl-CoA synthase 4.1.3.36 GO:0008935,GO:0009234 131567 cellular organisms no rank 11162 NCBI Protein Cluster (PRK) naphthoate synthase 1,4-dihydroxy-2-naphthoyl-CoA synthase Catalyzes the formation of 1,4-dihydroxy-2-naphthoate from O-succinylbenzoyl-CoA NF006187.0 PRK08322 PRK08322.1 509 509 548 equivalog Y Y N acetolactate synthase large subunit 2.2.1.6 GO:0000287,GO:0003824,GO:0030976 10972805 131567 cellular organisms no rank 11489 NCBI Protein Cluster (PRK) acetolactate synthase acetolactate synthase large subunit NF006195.0 PRK08324 PRK08324.2-3 931 931 678 equivalog Y Y N bifunctional aldolase/short-chain dehydrogenase 131567 cellular organisms no rank 221 NCBI Protein Cluster (PRK) short chain dehydrogenase short-chain dehydrogenase NF006198.0 PRK08326 PRK08326.1-1 274 274 308 subfamily Y Y N R2-like ligand-binding oxidase 131567 cellular organisms no rank 50 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit beta R2-like ligand-binding oxidase NF006199.0 PRK08326 PRK08326.1-2 286 286 324 equivalog Y Y N R2-like ligand-binding oxidase 131567 cellular organisms no rank 1619 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit beta R2-like ligand-binding oxidase NF006200.0 PRK08326 PRK08326.1-3 194 194 321 equivalog Y Y N R2-like ligand-binding oxidase 131567 cellular organisms no rank 2386 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit beta R2-like ligand-binding oxidase NF006203.0 PRK08327 PRK08327.1 456 456 571 equivalog Y Y N thiamine pyrophosphate-requiring protein GO:0030976 131567 cellular organisms no rank 2607 NCBI Protein Cluster (PRK) acetolactate synthase catalytic subunit thiamine pyrophosphate-requiring protein NF006219.0 PRK08344 PRK08344.1 108 108 161 equivalog Y N N V-type ATP synthase subunit K 131567 cellular organisms no rank 124 NCBI Protein Cluster (PRK) V-type ATP synthase subunit K V-type ATP synthase subunit K NF006221.0 PRK08348 PRK08348.1 124 124 136 subfamily Y N N NADH-plastoquinone oxidoreductase subunit 131567 cellular organisms no rank 183 NCBI Protein Cluster (PRK) NADH-plastoquinone oxidoreductase subunit NADH-plastoquinone oxidoreductase subunit NF006225.0 PRK08354 PRK08354.1 288 288 318 equivalog Y N N putative aminotransferase 131567 cellular organisms no rank 122 NCBI Protein Cluster (PRK) putative aminotransferase putative aminotransferase NF006228.0 PRK08360 PRK08360.1 608 608 443 equivalog Y Y N aspartate aminotransferase family protein 131567 cellular organisms no rank 130 NCBI Protein Cluster (PRK) 4-aminobutyrate aminotransferase aspartate aminotransferase family protein NF006240.0 PRK08376 PRK08376.1 662 662 521 subfamily Y N N putative monovalent cation/H+ antiporter subunit D 131567 cellular organisms no rank 217 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit D putative monovalent cation/H+ antiporter subunit D NF006242.0 PRK08378 PRK08378.1 98 98 85 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 139 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006248.0 PRK08386 PRK08386.1 92 92 151 subfamily Y N N putative monovalent cation/H+ antiporter subunit B 131567 cellular organisms no rank 523 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit B putative monovalent cation/H+ antiporter subunit B NF006321.0 PRK08534 PRK08534.1 225 225 181 equivalog Y Y N pyruvate ferredoxin oxidoreductase subunit gamma 131567 cellular organisms no rank 567 NCBI Protein Cluster (PRK) pyruvate ferredoxin oxidoreductase subunit gamma pyruvate ferredoxin oxidoreductase subunit gamma Catalyzes the ferredoxin-dependent oxidative decarboxylation of pyruvate to form acetyl-CoA NF006323.0 PRK08537 PRK08537.1 235 235 181 equivalog Y Y N 2-oxoacid:ferredoxin oxidoreductase subunit gamma 131567 cellular organisms no rank 326 NCBI Protein Cluster (PRK) 2-oxoglutarate ferredoxin oxidoreductase subunit gamma 2-oxoacid:ferredoxin oxidoreductase subunit gamma NF006326.0 PRK08554 PRK08554.1 354 354 446 equivalog Y N N peptidase 131567 cellular organisms no rank 50 NCBI Protein Cluster (PRK) peptidase peptidase NF006330.0 PRK08560 PRK08560.1 220 220 342 equivalog Y Y N tyrosine--tRNA ligase 6.1.1.1 131567 cellular organisms no rank 1446 NCBI Protein Cluster (PRK) tyrosyl-tRNA synthetase tyrosine--tRNA ligase Catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr) NF006331.0 PRK08561 PRK08561.1 154 154 152 equivalog Y Y N 30S ribosomal protein S15 131567 cellular organisms no rank 1159 NCBI Protein Cluster (PRK) 30S ribosomal protein S15P 30S ribosomal protein S15 Primary rRNA binding protein; helps nucleate assembly of 30S; binds directly to the 16S rRNA and an intersubunit bridge to the 23S rRNA; autoregulates translation through interactions with the mRNA leader sequence NF006332.0 PRK08562 PRK08562.1 120 120 132 equivalog Y Y N 50S ribosomal protein L32e 131567 cellular organisms no rank 1211 NCBI Protein Cluster (PRK) 50S ribosomal protein L32e 50S ribosomal protein L32e Contacts helix 25 of domain II of the 23S rRNA NF006341.0 PRK08568 PRK08568.1-5 300 300 464 equivalog Y Y N preprotein translocase subunit SecY secY 131567 cellular organisms no rank 1345 NCBI Protein Cluster (PRK) preprotein translocase subunit SecY preprotein translocase subunit SecY NF006342.0 PRK08569 PRK08569.1 143 143 193 equivalog Y Y N 50S ribosomal protein L18 131567 cellular organisms no rank 1166 NCBI Protein Cluster (PRK) 50S ribosomal protein L18P 50S ribosomal protein L18 Binds 5S rRNA along with protein L5 and L25 NF006343.0 PRK08570 PRK08570.1 131 131 150 equivalog Y Y N 50S ribosomal protein L19e 15184028 131567 cellular organisms no rank 1139 NCBI Protein Cluster (PRK) 50S ribosomal protein L19e 50S ribosomal protein L19e NF006344.0 PRK08571 PRK08571.1 168 168 132 equivalog Y Y N 50S ribosomal protein L14 131567 cellular organisms no rank 857 NCBI Protein Cluster (PRK) 50S ribosomal protein L14P 50S ribosomal protein L14 Binds to the 23S rRNA between the centers for peptidyl transferase and GTPase NF006345.0 PRK08572 PRK08572.1 120 120 111 equivalog Y Y N 30S ribosomal protein S17 131567 cellular organisms no rank 993 NCBI Protein Cluster (PRK) 30S ribosomal protein S17P 30S ribosomal protein S17 Primary binding protein; helps mediate assembly; involved in translation fidelity NF006367.0 PRK08591 PRK08591.1 597 597 451 subfamily Y Y N acetyl-CoA carboxylase biotin carboxylase subunit 6.4.1.2 GO:0005524,GO:0046872 131567 cellular organisms no rank 92975 NCBI Protein Cluster (PRK) acetyl-CoA carboxylase biotin carboxylase subunit acetyl-CoA carboxylase biotin carboxylase subunit Catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA NF006375.0 PRK08609 PRK08609.1 426 426 571 equivalog Y Y N DNA polymerase/3'-5' exonuclease PolX polX GO:0003677,GO:0003887,GO:0006281 131567 cellular organisms no rank 13003 NCBI Protein Cluster (PRK) hypothetical protein DNA polymerase/3'-5' exonuclease PolX NF006395.0 PRK08644 PRK08644.1 159 159 215 equivalog Y Y N sulfur carrier protein ThiS adenylyltransferase ThiF thiF 131567 cellular organisms no rank 4028 NCBI Protein Cluster (PRK) thiamine biosynthesis protein ThiF sulfur carrier protein ThiS adenylyltransferase ThiF Catalyzes the adenylation of ThiS which is involved in the formation of 5-methyl-4-(beta-hydroxyethyl)thiazole phosphate NF006404.0 PRK08652 PRK08652.1-2 348 348 332 equivalog Y N N acetylornithine deacetylase 131567 cellular organisms no rank 11 NCBI Protein Cluster (PRK) acetylornithine deacetylase acetylornithine deacetylase NF006406.0 PRK08654 PRK08654.1 739 739 499 equivalog Y Y N acetyl-CoA carboxylase biotin carboxylase subunit 131567 cellular organisms no rank 536 NCBI Protein Cluster (PRK) pyruvate carboxylase subunit A acetyl-CoA carboxylase biotin carboxylase subunit NF006409.0 PRK08655 PRK08655.1-3 310 310 290 equivalog Y Y N prephenate dehydrogenase 1.3.1.12 131567 cellular organisms no rank 34 NCBI Protein Cluster (PRK) prephenate dehydrogenase prephenate dehydrogenase NF006412.0 PRK08659 PRK08659.1 411 411 378 equivalog Y Y N 2-oxoacid:acceptor oxidoreductase subunit alpha 131567 cellular organisms no rank 4545 NCBI Protein Cluster (PRK) 2-oxoglutarate ferredoxin oxidoreductase subunit alpha 2-oxoacid:acceptor oxidoreductase subunit alpha NF006413.0 PRK08660 PRK08660.1 203 203 184 equivalog Y Y N aldolase 131567 cellular organisms no rank 272 NCBI Protein Cluster (PRK) L-fuculose phosphate aldolase aldolase NF006415.0 PRK08662 PRK08662.1 243 243 381 equivalog Y Y N nicotinate phosphoribosyltransferase 6.3.4.21 15753098 131567 cellular organisms no rank 1462 NCBI Protein Cluster (PRK) nicotinate phosphoribosyltransferase nicotinate phosphoribosyltransferase Catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate NF006416.0 PRK08664 PRK08664.1 232 232 350 subfamily Y Y N aspartate-semialdehyde dehydrogenase 1.2.1.11 1348268 131567 cellular organisms no rank 5416 NCBI Protein Cluster (PRK) aspartate-semialdehyde dehydrogenase aspartate-semialdehyde dehydrogenase Catalyzes the formation of aspartate semialdehyde from aspartyl phosphate NF006417.0 PRK08665 PRK08665.1 961 961 759 equivalog Y Y N vitamin B12-dependent ribonucleotide reductase 1.17.4.1 131567 cellular organisms no rank 963 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit alpha vitamin B12-dependent ribonucleotide reductase Catalyzes the reduction of ribonucleotides to deoxyribonucleotides; the rate-limiting step in dNTP synthesis NF006418.0 PRK08667 PRK08667.1 794 794 644 equivalog Y N N hydrogenase membrane subunit 131567 cellular organisms no rank 87 NCBI Protein Cluster (PRK) hydrogenase membrane subunit hydrogenase membrane subunit NF006419.0 PRK08668 PRK08668.1 617 617 613 equivalog Y N N NADH dehydrogenase subunit M 131567 cellular organisms no rank 175 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit M NADH dehydrogenase subunit M NF006421.0 PRK08673 PRK08673.1 335 335 338 subfamily Y Y N 3-deoxy-7-phosphoheptulonate synthase 2.5.1.54 11847568,14337509,6129240,9387221 131567 cellular organisms no rank 18162 NCBI Protein Cluster (PRK) 3-deoxy-7-phosphoheptulonate synthase 3-deoxy-7-phosphoheptulonate synthase Catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate NF006423.0 PRK08674 PRK08674.1-2 254 254 317 equivalog Y Y N bifunctional phosphoglucose/phosphomannose isomerase 5.3.1.9 131567 cellular organisms no rank 243 NCBI Protein Cluster (PRK) bifunctional phosphoglucose/phosphomannose isomerase bifunctional phosphoglucose/phosphomannose isomerase NF006426.0 PRK08674 PRK08674.1-6 295 295 354 subfamily Y Y N bifunctional phosphoglucose/phosphomannose isomerase 5.3.1.9 131567 cellular organisms no rank 348 NCBI Protein Cluster (PRK) bifunctional phosphoglucose/phosphomannose isomerase bifunctional phosphoglucose/phosphomannose isomerase NF006427.0 PRK08676 PRK08676.1 511 511 486 equivalog Y N N hydrogenase membrane subunit 131567 cellular organisms no rank 82 NCBI Protein Cluster (PRK) hydrogenase membrane subunit hydrogenase membrane subunit NF006560.0 PRK09061 PRK09061.1 340 340 517 subfamily Y Y N amidohydrolase family protein 131567 cellular organisms no rank 2752 NCBI Protein Cluster (PRK) D-glutamate deacylase amidohydrolase family protein NF006577.0 PRK09102 PRK09102.1 620 620 604 equivalog Y Y N ribonucleoside-diphosphate reductase subunit alpha 1.17.4.1 GO:0004748,GO:0006260 131567 cellular organisms no rank 5200 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit alpha ribonucleoside-diphosphate reductase subunit alpha NF006579.0 PRK09104 PRK09104.1 327 327 465 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 24888 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006588.0 PRK09120 PRK09120.1 276 276 276 equivalog Y Y N p-hydroxycinnamoyl CoA hydratase/lyase 4.1.2.61 GO:0003824 131567 cellular organisms no rank 3148 NCBI Protein Cluster (PRK) p-hydroxycinnamoyl CoA hydratase/lyase p-hydroxycinnamoyl CoA hydratase/lyase Catalyzes the conversion of feruloyl-CoA to vanillin and acetyl-CoA NF006597.0 PRK09134 PRK09134.1 281 281 261 equivalog Y Y N SDR family oxidoreductase GO:0016491 131567 cellular organisms no rank 7650 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006599.0 PRK09136 PRK09136.1 223 223 247 equivalog Y Y N S-methyl-5'-thioinosine phosphorylase 2.4.2.44 131567 cellular organisms no rank 13802 NCBI Protein Cluster (PRK) 5'-methylthioadenosine phosphorylase S-methyl-5'-thioinosine phosphorylase NF006619.0 PRK09186 PRK09186.1 255 255 256 equivalog Y Y N oxidoreductase GO:0016491 131567 cellular organisms no rank 1519 NCBI Protein Cluster (PRK) flagellin modification protein A oxidoreductase NF006629.0 PRK09198 PRK09198.1 405 405 465 equivalog Y Y N nicotinate phosphoribosyltransferase 6.3.4.21 GO:0004514,GO:0009435 131567 cellular organisms no rank 8180 NCBI Protein Cluster (PRK) putative nicotinate phosphoribosyltransferase nicotinate phosphoribosyltransferase NF006667.0 PRK09212 PRK09212.1 321 321 327 subfamily Y Y N pyruvate dehydrogenase complex E1 component subunit beta GO:0004739,GO:0006086 131567 cellular organisms no rank 35711 NCBI Protein Cluster (PRK) pyruvate dehydrogenase subunit beta pyruvate dehydrogenase complex E1 component subunit beta NF006679.0 PRK09228 PRK09228.1 351 351 433 subfamily Y Y N guanine deaminase 3.5.4.3 131567 cellular organisms no rank 23584 NCBI Protein Cluster (PRK) guanine deaminase guanine deaminase Catalyzes the deamination of guanine NF006690.0 PRK09238 PRK09238.1 782 782 852 equivalog Y Y N bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase 4.2.1.3,4.2.1.99 GO:0003994,GO:0006099,GO:0051539 131567 cellular organisms no rank 27310 NCBI Protein Cluster (PRK) bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase Catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate NF006695.0 PRK09243 PRK09243.1-2 469 469 480 equivalog Y Y N nicotinate phosphoribosyltransferase 6.3.4.21 GO:0004516,GO:0009435 131567 cellular organisms no rank 18079 NCBI Protein Cluster (PRK) nicotinate phosphoribosyltransferase nicotinate phosphoribosyltransferase NF006696.0 PRK09243 PRK09243.1-3 503 503 451 equivalog Y Y N nicotinate phosphoribosyltransferase 6.3.4.21 GO:0004514,GO:0009435 131567 cellular organisms no rank 4113 NCBI Protein Cluster (PRK) nicotinate phosphoribosyltransferase nicotinate phosphoribosyltransferase NF006731.0 PRK09262 PRK09262.1 179 179 229 equivalog Y Y N 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase GO:0047443 131567 cellular organisms no rank 12010 NCBI Protein Cluster (PRK) hypothetical protein 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase NF006733.0 PRK09264 PRK09264.1 438 438 425 subfamily Y Y N diaminobutyrate--2-oxoglutarate transaminase 2.6.1.76 131567 cellular organisms no rank 16375 NCBI Protein Cluster (PRK) diaminobutyrate--2-oxoglutarate aminotransferase diaminobutyrate--2-oxoglutarate transaminase Catalyzes the reversible formation of diaminobutyrate and 2-oxoglutarate from glutamate and L-aspartic beta-semialdehyde NF006755.0 PRK09275 PRK09275.1 321 321 530 equivalog Y Y N bifunctional aspartate transaminase/aspartate 4-decarboxylase 2.6.1.1,4.1.1.12 GO:0030170 131567 cellular organisms no rank 7339 NCBI Protein Cluster (PRK) aspartate aminotransferase bifunctional aspartate transaminase/aspartate 4-decarboxylase NF006756.0 PRK09276 PRK09276.1 507 507 387 subfamily Y Y N LL-diaminopimelate aminotransferase 2.6.1.83 131567 cellular organisms no rank 2078 NCBI Protein Cluster (PRK) LL-diaminopimelate aminotransferase LL-diaminopimelate aminotransferase Catalyzes the formation of LL-diaminopimelate from tetrahydrodipicolinate; involved in lysine and peptidoglycan synthesis NF006757.0 PRK09277 PRK09277.1 686 686 888 subfamily Y Y N aconitate hydratase AcnA acnA 4.2.1.3,4.2.1.99 131567 cellular organisms no rank 79710 NCBI Protein Cluster (PRK) aconitate hydratase aconitate hydratase AcnA Catalyzes the conversion of citrate to isocitrate NF006761.0 PRK09282 PRK09282.1 402 402 591 domain Y Y N pyruvate carboxylase subunit B 6.4.1.1 GO:0003824 131567 cellular organisms no rank 55739 NCBI Protein Cluster (PRK) pyruvate carboxylase subunit B pyruvate carboxylase subunit B Catalyzes the formation of oxaloacetate from pyruvate NF006762.1 PRK09283 PRK09283.1 297 297 327 equivalog Y Y N porphobilinogen synthase hemB 4.2.1.24 GO:0003824,GO:0004655,GO:0033014,GO:0046872 131567 cellular organisms no rank 61014 NCBI Protein Cluster (PRK) delta-aminolevulinic acid dehydratase porphobilinogen synthase Catalyzes the formation of porphobilinogen from 5-aminolevulinate NF006763.1 PRK09284 PRK09284.1 650 650 564 equivalog Y Y N phosphomethylpyrimidine synthase ThiC thiC 4.1.99.17 GO:0009228,GO:0051536 131567 cellular organisms no rank 51704 NCBI Protein Cluster (PRK) thiamine biosynthesis protein ThiC phosphomethylpyrimidine synthase ThiC Catalyzes the formation of 4-amino-2-methyl-5-phosphomethylpyrimidine from 5-amino-1-(5-phospho-D-ribosyl)imidazole and S-adenosyl-L-methionine in thiamine biosynthesis NF006764.0 PRK09285 PRK09285.1 446 446 456 equivalog Y Y N adenylosuccinate lyase purB 4.3.2.2 GO:0004018,GO:0006188,GO:0009152 131567 cellular organisms no rank 29805 NCBI Protein Cluster (PRK) adenylosuccinate lyase adenylosuccinate lyase NF006766.0 PRK09288 PRK09288.1 339 339 396 equivalog Y Y N formate-dependent phosphoribosylglycinamide formyltransferase purT 2.1.2.- GO:0000287,GO:0004644,GO:0005524,GO:0009152 131567 cellular organisms no rank 29007 NCBI Protein Cluster (PRK) phosphoribosylglycinamide formyltransferase 2 formate-dependent phosphoribosylglycinamide formyltransferase Non-folate utilizing enzyme, catalyzes the production of beta-formyl glycinamide ribonucleotide from formate, ATP, and beta-GAR and a side reaction producing acetyl phosphate and ADP from acetate and ATP; involved in de novo purine biosynthesis NF006767.1 PRK09289 PRK09289.1 155 155 192 equivalog Y Y N riboflavin synthase 2.5.1.9 131567 cellular organisms no rank 64123 NCBI Protein Cluster (PRK) riboflavin synthase subunit alpha riboflavin synthase NF006769.0 PRK09290 PRK09290.1-3 452 452 417 subfamily Y Y N allantoate amidohydrolase 131567 cellular organisms no rank 21620 NCBI Protein Cluster (PRK) allantoate amidohydrolase allantoate amidohydrolase NF006771.0 PRK09290 PRK09290.1-5 399 399 413 subfamily Y Y N allantoate amidohydrolase 131567 cellular organisms no rank 38576 NCBI Protein Cluster (PRK) allantoate amidohydrolase allantoate amidohydrolase NF006776.0 PRK09291 PRK09291.1 265 265 257 equivalog Y Y N SDR family oxidoreductase GO:0016491 131567 cellular organisms no rank 3208 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006798.0 PRK09301 PRK09301.1 110 110 105 equivalog Y Y N circadian clock protein KaiB kaiB 131567 cellular organisms no rank 742 NCBI Protein Cluster (PRK) circadian clock protein KaiB circadian clock protein KaiB Decreases the phosphorylation of KaiC, a component of the main circadian regulator in cyanobacteria NF006799.0 PRK09302 PRK09302.1 408 408 515 equivalog Y Y N circadian clock protein KaiC kaiC 2.7.11.1 15377674 131567 cellular organisms no rank 2992 NCBI Protein Cluster (PRK) circadian clock protein KaiC circadian clock protein KaiC Acts as a promotor non-specific transcription repressor NF006803.0 PRK09311 PRK09311.1 569 569 417 equivalog Y Y N bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II 3.5.4.25,4.1.99.12 GO:0003935,GO:0008686 131567 cellular organisms no rank 23937 NCBI Protein Cluster (PRK) bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II Bifunctional enzyme DHBP synthase/GTP cyclohydrolase II; functions in riboflavin synthesis; converts GTP to 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine; converts ribulose 5-phopshate to 3,4-dihydroxy-2-butanone 4-phosphate NF006805.0 PRK09318 PRK09318.1 486 486 387 equivalog Y Y N bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II 131567 cellular organisms no rank 93 NCBI Protein Cluster (PRK) bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II Bifunctional enzyme DHBP synthase/GTP cyclohydrolase II; functions in riboflavin synthesis; converts GTP to 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine; converts ribulose 5-phopshate to 3,4-dihydroxy-2-butanone 4-phosphate NF006811.0 PRK09333 PRK09333.1 156 156 150 equivalog Y Y N 30S ribosomal protein S19e 131567 cellular organisms no rank 1162 NCBI Protein Cluster (PRK) 30S ribosomal protein S19e 30S ribosomal protein S19e NF006820.0 PRK09344 PRK09344.1-2 636 636 529 subfamily Y Y N phosphoenolpyruvate carboxykinase 4.1.1.49 131567 cellular organisms no rank 33447 NCBI Protein Cluster (PRK) phosphoenolpyruvate carboxykinase phosphoenolpyruvate carboxykinase NF006821.0 PRK09344 PRK09344.1-3 369 369 525 subfamily Y Y N phosphoenolpyruvate carboxykinase 4.1.1.49 131567 cellular organisms no rank 34213 NCBI Protein Cluster (PRK) phosphoenolpyruvate carboxykinase phosphoenolpyruvate carboxykinase NF006825.1 PRK09347 PRK09347.1-2 174 174 179 subfamily Y Y N GTP cyclohydrolase I FolE folE 3.5.4.16 131567 cellular organisms no rank 43220 NCBI Protein Cluster (PRK) GTP cyclohydrolase I GTP cyclohydrolase I FolE NF006826.0 PRK09347 PRK09347.1-3 162 162 189 subfamily Y Y N GTP cyclohydrolase I FolE folE 3.5.4.16 131567 cellular organisms no rank 48710 NCBI Protein Cluster (PRK) GTP cyclohydrolase I GTP cyclohydrolase I FolE NF006827.1 PRK09348 PRK09348.1 369 369 276 equivalog Y Y N glycine--tRNA ligase subunit alpha 6.1.1.14 GO:0000166,GO:0004820,GO:0005524,GO:0006426 131567 cellular organisms no rank 29306 NCBI Protein Cluster (PRK) glycyl-tRNA synthetase subunit alpha glycine--tRNA ligase subunit alpha Glycine--tRNA ligase alpha chain; GlyRS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA NF006830.0 PRK09355 PRK09355.1 221 221 267 equivalog Y Y N hydroxyethylthiazole kinase thiM 2.7.1.50 GO:0004417,GO:0009228 10891066,26960569 131567 cellular organisms no rank 32011 NCBI Protein Cluster (PRK) hydroxyethylthiazole kinase hydroxyethylthiazole kinase Catalyzes the formation of 4-methyl-5-(2-phosphoethyl)-thiazole and ADP from 4-methyl-5-(2-hydroxyethyl)-thiazole and ATP NF006850.0 PRK09358 PRK09358.1-6 419 419 334 equivalog Y Y N adenosine deaminase 3.5.4.4 GO:0000034,GO:0006146 131567 cellular organisms no rank 19846 NCBI Protein Cluster (PRK) adenosine deaminase adenosine deaminase NF006870.0 PRK09364 PRK09364.1 162 162 161 subfamily Y Y N cyclic pyranopterin monophosphate synthase MoaC moaC 4.6.1.17 10903949 131567 cellular organisms no rank 46145 NCBI Protein Cluster (PRK) molybdenum cofactor biosynthesis protein MoaC cyclic pyranopterin monophosphate synthase MoaC Along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis NF006871.0 PRK09367 PRK09367.1 524 524 505 subfamily Y Y N histidine ammonia-lyase 4.3.1.3 131567 cellular organisms no rank 51067 NCBI Protein Cluster (PRK) histidine ammonia-lyase histidine ammonia-lyase Catalyzes the degradation of histidine to urocanate and ammmonia NF006873.0 PRK09369 PRK09369.1 297 297 419 subfamily Y Y N UDP-N-acetylglucosamine 1-carboxyvinyltransferase 2.5.1.7 GO:0016765 131567 cellular organisms no rank 79060 NCBI Protein Cluster (PRK) UDP-N-acetylglucosamine 1-carboxyvinyltransferase UDP-N-acetylglucosamine 1-carboxyvinyltransferase Adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation NF006874.0 PRK09371 PRK09371.1 100 100 71 subfamily Y Y N gas vesicle structural protein GvpA gvpA 10894744,1864501,3448465,8002589,8423144 131567 cellular organisms no rank 1699 NCBI Protein Cluster (PRK) gas vesicle synthesis protein GvpA gas vesicle structural protein GvpA There are 14 genes on the gvp gene cluster in halophilic archaea. The product of gvpA is a structural component of gas vesicles, which provide buoyancy to cells and promote flotation. It has been reported that the products of gvpAO and gvpFGJKLM represent the minimal set required for gas vesicle formation in halophilic archaea. There are 14 genes on the gvp gene cluster in halophilic archaea. The product of gvpA is a structural component of gas vesicles, which provide buoyancy to cells and promote flotation. It has been reported that the products of gvpAO and gvpFGJKLM represent the minimal set required for gas vesicle formation in halophilic archaea. NF006878.0 PRK09375 PRK09375.1-2 294 294 306 equivalog Y Y N quinolinate synthase NadA nadA 2.5.1.72 GO:0008987,GO:0009435,GO:0051539 131567 cellular organisms no rank 36504 NCBI Protein Cluster (PRK) quinolinate synthetase quinolinate synthase NadA NF006879.0 PRK09375 PRK09375.1-4 374 374 336 equivalog Y Y N quinolinate synthase NadA nadA 2.5.1.72 GO:0008987,GO:0009435,GO:0051539 131567 cellular organisms no rank 12045 NCBI Protein Cluster (PRK) quinolinate synthetase quinolinate synthase NadA NF006883.0 PRK09375 PRK09375.2-4 357 357 366 equivalog Y Y N quinolinate synthase NadA nadA 2.5.1.72 131567 cellular organisms no rank 15994 NCBI Protein Cluster (PRK) quinolinate synthetase quinolinate synthase NadA NF006886.1 PRK09376 PRK09376.1 315 315 413 equivalog Y Y N transcription termination factor Rho rho 3.6.4.- GO:0003723,GO:0005524,GO:0006353,GO:0008186 131567 cellular organisms no rank 57998 NCBI Protein Cluster (PRK) transcription termination factor Rho transcription termination factor Rho NF006916.0 PRK09407 PRK09407.1 521 521 526 equivalog Y Y N succinic semialdehyde dehydrogenase 1.2.1.79 131567 cellular organisms no rank 13976 NCBI Protein Cluster (PRK) succinic semialdehyde dehydrogenase succinic semialdehyde dehydrogenase NF006929.0 PRK09414 PRK09414.1 536 536 445 equivalog Y Y N NADP-specific glutamate dehydrogenase gdhA 1.4.1.4 GO:0006520,GO:0016639 131567 cellular organisms no rank 38462 NCBI Protein Cluster (PRK) glutamate dehydrogenase NADP-specific glutamate dehydrogenase NF006941.0 PRK09423 PRK09423.1 336 336 367 subfamily Y Y N glycerol dehydrogenase 1.1.1.6 GO:0016614 131567 cellular organisms no rank 14995 NCBI Protein Cluster (PRK) glycerol dehydrogenase glycerol dehydrogenase NF006942.0 PRK09424 PRK09424.1 383 383 510 equivalog Y Y N Re/Si-specific NAD(P)(+) transhydrogenase subunit alpha 7.1.1.1 GO:1902600 1633824,1932078,3525165 131567 cellular organisms no rank 33985 NCBI Protein Cluster (PRK) NAD(P) transhydrogenase subunit alpha Re/Si-specific NAD(P)(+) transhydrogenase subunit alpha Involved in catalyzing the transfer of hydride ion equivalents between NAD and NADP; stereospecific (AB-specific); functions as a proton pump by translocating protons from cytoplasm to periplasm NF006944.0 PRK09426 PRK09426.1 876 876 721 equivalog Y Y N methylmalonyl-CoA mutase scpA 5.4.99.2 GO:0004494,GO:0031419,GO:0046872 10769117,8098211 131567 cellular organisms no rank 30258 NCBI Protein Cluster (PRK) methylmalonyl-CoA mutase methylmalonyl-CoA mutase NF006958.0 PRK09435 PRK09435.1 329 329 333 equivalog Y Y N methylmalonyl Co-A mutase-associated GTPase MeaB meaB 3.6.5.- GO:0003924,GO:0005525 131567 cellular organisms no rank 23158 NCBI Protein Cluster (PRK) membrane ATPase/protein kinase methylmalonyl Co-A mutase-associated GTPase MeaB NF006960.0 PRK09437 PRK09437.1 140 140 156 equivalog Y Y N thioredoxin-dependent thiol peroxidase bcp 1.11.1.24 GO:0016209,GO:0016491 131567 cellular organisms no rank 33867 NCBI Protein Cluster (PRK) thioredoxin-dependent thiol peroxidase thioredoxin-dependent thiol peroxidase NF006970.0 PRK09441 PRK09441.1-3 516 516 466 equivalog Y Y N alpha-amylase 3.2.1.1 131567 cellular organisms no rank 1151 NCBI Protein Cluster (PRK) cytoplasmic alpha-amylase alpha-amylase NF007031.0 PRK09496 PRK09496.1-2 289 289 458 equivalog Y Y N Trk system potassium transporter TrkA trkA GO:0005886,GO:0006813,GO:0015079 131567 cellular organisms no rank 17339 NCBI Protein Cluster (PRK) potassium transporter peripheral membrane component Trk system potassium transporter TrkA NF007032.0 PRK09496 PRK09496.1-4 309 309 457 equivalog Y Y N Trk system potassium transporter TrkA trkA GO:0005886,GO:0006813,GO:0015079 131567 cellular organisms no rank 14929 NCBI Protein Cluster (PRK) potassium transporter peripheral membrane component Trk system potassium transporter TrkA NF007034.0 PRK09496 PRK09496.2-1 344 344 445 subfamily Y Y N Trk system potassium transporter TrkA trkA 131567 cellular organisms no rank 1323 NCBI Protein Cluster (PRK) potassium transporter peripheral membrane component Trk system potassium transporter TrkA NF007036.0 PRK09496 PRK09496.2-3 407 407 448 subfamily Y Y N Trk system potassium transporter TrkA trkA 131567 cellular organisms no rank 155 NCBI Protein Cluster (PRK) potassium transporter peripheral membrane component Trk system potassium transporter TrkA NF007039.0 PRK09496 PRK09496.3-2 293 293 446 equivalog Y Y N Trk system potassium transporter TrkA trkA GO:0006813,GO:0015079 131567 cellular organisms no rank 20748 NCBI Protein Cluster (PRK) potassium transporter peripheral membrane component Trk system potassium transporter TrkA NF007041.0 PRK09496 PRK09496.3-4 386 386 450 equivalog Y Y N Trk system potassium transporter TrkA trkA 131567 cellular organisms no rank 3244 NCBI Protein Cluster (PRK) potassium transporter peripheral membrane component Trk system potassium transporter TrkA NF007078.0 PRK09529 PRK09529.1 809 809 710 subfamily Y N N bifunctional acetyl-CoA decarbonylase/synthase complex subunit alpha/beta 131567 cellular organisms no rank 924 NCBI Protein Cluster (PRK) bifunctional acetyl-CoA decarbonylase/synthase complex subunit alpha/beta bifunctional acetyl-CoA decarbonylase/synthase complex subunit alpha/beta NF007113.1 PRK09562 PRK09562.1 208 208 251 equivalog Y Y N nucleoside triphosphate pyrophosphohydrolase mazG 3.6.1.9 12218018,16390452 131567 cellular organisms no rank 42264 NCBI Protein Cluster (PRK) nucleoside triphosphate pyrophosphohydrolase nucleoside triphosphate pyrophosphohydrolase NF007161.0 PRK09599 PRK09599.1 271 271 302 subfamily Y Y N NADP-dependent phosphogluconate dehydrogenase 1.1.1.44 15231785 131567 cellular organisms no rank 27064 NCBI Protein Cluster (PRK) 6-phosphogluconate dehydrogenase-like protein NADP-dependent phosphogluconate dehydrogenase NF007180.0 PRK09612 PRK09612.1 265 265 238 equivalog Y Y N 50S ribosomal protein L2 131567 cellular organisms no rank 1091 NCBI Protein Cluster (PRK) 50S ribosomal protein L2P 50S ribosomal protein L2 One of the primary rRNA-binding proteins; required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation NF007186.0 PRK09614 PRK09614.1-5 237 237 328 equivalog Y Y N ribonucleotide-diphosphate reductase subunit beta 1.17.4.1 GO:0009263,GO:0016491 131567 cellular organisms no rank 10899 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit beta ribonucleotide-diphosphate reductase subunit beta NF007233.1 PRK09653 PRK09653.1 310 310 319 subfamily Y Y N phosphotransacetylase 16272400 131567 cellular organisms no rank 48068 NCBI Protein Cluster (PRK) phosphotransacetylase phosphotransacetylase NF007277.0 PRK09736 PRK09736.1 338 338 353 equivalog Y Y N 5-methylcytosine-specific restriction endonuclease system specificity protein McrC mcrC 3.1.21.- GO:0009307 131567 cellular organisms no rank 2673 NCBI Protein Cluster (PRK) 5-methylcytosine-specific restriction enzyme subunit McrC 5-methylcytosine-specific restriction endonuclease system specificity protein McrC McrC protein together with McrB forms the McrBC restriction system; recognizes N4- and C5-methylcytosine (and 5-hydroxy-methylcytosines); appears to act against 5-methylcytosine preceded by a purine residue; MrcC modulates the specificty of McrB and has DNA cleavage activity NF007479.0 PRK10069 PRK10069.1 145 145 185 subfamily Y Y N 3-phenylpropionate/cinnamic acid dioxygenase subunit beta 1.14.12.19 GO:0019380 131567 cellular organisms no rank 4303 NCBI Protein Cluster (PRK) 3-phenylpropionate dioxygenase subunit beta 3-phenylpropionate/cinnamic acid dioxygenase subunit beta NF007494.0 PRK10089 PRK10089.1-3 109 109 112 equivalog Y Y N tRNA-binding protein GO:0000049 131567 cellular organisms no rank 15535 NCBI Protein Cluster (PRK) tRNA-binding protein tRNA-binding protein NF007495.0 PRK10089 PRK10089.1-4 117 117 113 equivalog Y Y N tRNA-binding protein GO:0000049 131567 cellular organisms no rank 15300 NCBI Protein Cluster (PRK) tRNA-binding protein tRNA-binding protein NF007695.0 PRK10376 PRK10376.1 280 280 290 subfamily Y Y N oxidoreductase 131567 cellular organisms no rank 21017 NCBI Protein Cluster (PRK) putative oxidoreductase oxidoreductase NF007739.0 PRK10419 PRK10419.1 354 0 268 subfamily Y Y N nickel ABC transporter ATP-binding protein NikE nikE 131567 cellular organisms no rank 142253 NCBI Protein Cluster (PRK) nickel transporter ATP-binding protein NikE nickel ABC transporter ATP-binding protein NikE NF007764.0 PRK10446 PRK10446.1 331 331 300 equivalog Y Y N 30S ribosomal protein S6--L-glutamate ligase rimK 6.3.2.- GO:0005524,GO:0036211,GO:0046872 131567 cellular organisms no rank 12108 NCBI Protein Cluster (PRK) ribosomal protein S6 modification protein 30S ribosomal protein S6--L-glutamate ligase Responsible for the addition of glutamate residues to the C-terminus of ribosomal protein S6 NF007914.0 PRK10628 PRK10628.1 233 233 262 equivalog Y Y N 4,5-DOPA dioxygenase extradiol ygiD 1.13.11.29 17145952 131567 cellular organisms no rank 12072 NCBI Protein Cluster (PRK) LigB family dioxygenase 4,5-DOPA dioxygenase extradiol NF007940.0 PRK10658 PRK10658.1 606 606 771 equivalog Y Y N alpha-xylosidase yicI 3.2.1.177 GO:0004553,GO:0005975 15294295,15501829,16510986 131567 cellular organisms no rank 17510 NCBI Protein Cluster (PRK) putative alpha-glucosidase alpha-xylosidase Catalyzes the transfer of alpha-xylosyl residue NF007956.0 PRK10675 PRK10675.1 394 394 338 subfamily Y Y N UDP-glucose 4-epimerase 5.1.3.2 131567 cellular organisms no rank 33496 NCBI Protein Cluster (PRK) UDP-galactose-4-epimerase UDP-glucose 4-epimerase NF008035.0 PRK10767 PRK10767.1 338 338 374 subfamily Y Y N molecular chaperone DnaJ dnaJ 131567 cellular organisms no rank 67433 NCBI Protein Cluster (PRK) chaperone protein DnaJ molecular chaperone DnaJ Chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion NF008058.0 PRK10792 PRK10792.1 355 355 285 equivalog Y Y N bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD folD 1.5.1.5,3.5.4.9 GO:0004488 131567 cellular organisms no rank 29632 NCBI Protein Cluster (PRK) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD Catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate NF008168.0 PRK10917 PRK10917.2-2 718 718 795 equivalog Y Y N ATP-dependent DNA helicase RecG recG 3.6.4.12 GO:0003676,GO:0003678,GO:0005524,GO:0006281,GO:0006310 131567 cellular organisms no rank 65875 NCBI Protein Cluster (PRK) ATP-dependent DNA helicase RecG ATP-dependent DNA helicase RecG NF008183.0 PRK10933 PRK10933.1 535 535 551 subfamily Y Y N alpha,alpha-phosphotrehalase 3.2.1.93 GO:0003824 131567 cellular organisms no rank 51422 NCBI Protein Cluster (PRK) trehalose-6-phosphate hydrolase alpha,alpha-phosphotrehalase NF008277.0 PRK11055 PRK11055.1 240 240 349 subfamily Y Y N galactose-1-epimerase 5.1.3.3 GO:0005975,GO:0016853,GO:0030246 131567 cellular organisms no rank 50139 NCBI Protein Cluster (PRK) galactose-1-epimerase galactose-1-epimerase Mutarotase; catalyzes the conversion of beta-galactose to the alpha-anomer; links the metabolism of lactose and galactose NF008369.0 PRK11168 PRK11168.1 278 278 401 equivalog Y Y N anaerobic glycerol-3-phosphate dehydrogenase subunit C 1.1.5.3 131567 cellular organisms no rank 7401 NCBI Protein Cluster (PRK) sn-glycerol-3-phosphate dehydrogenase subunit C anaerobic glycerol-3-phosphate dehydrogenase subunit C Catalyzes the conversion of glycerol 3-phosphate to dihydroxyacetone using fumarate or nitrate as electron acceptor NF008425.0 PRK11259 PRK11259.1 257 257 377 equivalog Y Y N N-methyl-L-tryptophan oxidase solA 1.5.3.2 GO:0050131 10220347,18186483 131567 cellular organisms no rank 16574 NCBI Protein Cluster (PRK) N-methyltryptophan oxidase N-methyl-L-tryptophan oxidase Catalyzes the demethylation of N-methyl-L-tryptophan forming L-tryptophan and formaldehyde; FAD-binding; can also catalyze the demethylation of other N-methyl amino acids NF008453.0 PRK11308 PRK11308.1 408 0 334 subfamily Y Y N dipeptide ABC transporter ATP-binding protein 7.4.2.- GO:0005524,GO:0015833 131567 cellular organisms no rank 203723 NCBI Protein Cluster (PRK) dipeptide transporter ATP-binding subunit dipeptide ABC transporter ATP-binding protein NF008512.0 PRK11431 PRK11431.1 126 126 105 equivalog Y Y N quaternary ammonium compound efflux SMR transporter SugE sugE GO:0016020,GO:0022857 11948170 131567 cellular organisms no rank 8569 NCBI Protein Cluster (PRK) multidrug efflux system protein quaternary ammonium compound efflux SMR transporter SugE Member of the SMR family of proton-dependent drug efflux transporters; quaternary ammonium compound efflux pump; confers resistance to cetylpyridinium, cetyldimethylethyl ammonium and cetrimide cations NF008521.0 PRK11448 PRK11448.1 729 729 1123 equivalog Y Y N type I restriction-modification system endonuclease hsdR 3.1.21.3 131567 cellular organisms no rank 5402 NCBI Protein Cluster (PRK) type I restriction enzyme EcoKI subunit R type I restriction-modification system endonuclease NF008528.1 PRK11463 PRK11463.1-2 40 40 109 subfamily Y Y N FxsA family membrane protein fxsA 10497017 131567 cellular organisms no rank 30813 NCBI Protein Cluster (PRK) phage T7 F exclusion suppressor FxsA FxsA family membrane protein Members of this family are predicted membrane proteins homologous to FxsA, named for a phenomenon in Escherichia coli in which overexpression counteracts the ability of F plasmid to cause exclusion of phage T7. The most generally relevant function for members of this family remains unknown. NF008559.0 PRK11504 PRK11504.1 651 651 648 subfamily Y Y N primary-amine oxidase 1.4.3.21 131567 cellular organisms no rank 7308 NCBI Protein Cluster (PRK) tyramine oxidase primary-amine oxidase NF008573.0 PRK11525 PRK11525.1 242 242 288 equivalog Y Y N DNA damage-inducible protein D dinD 131567 cellular organisms no rank 3558 NCBI Protein Cluster (PRK) DNA-damage-inducible protein D DNA damage-inducible protein D NF008629.1 PRK11617 PRK11617.1 230 230 218 equivalog Y Y N deoxyribonuclease V nfi 3.1.21.7 GO:0004519,GO:0006281 131567 cellular organisms no rank 8435 NCBI Protein Cluster (PRK) endonuclease V deoxyribonuclease V cleaves DNA at apurinic or apyrimidinic sites NF008653.0 PRK11650 PRK11650.1 432 432 357 subfamily Y Y N sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC ugpC GO:0005524,GO:0140359 131567 cellular organisms no rank 127109 NCBI Protein Cluster (PRK) glycerol-3-phosphate transporter ATP-binding subunit sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC Part of the UgpABCE glycerol-3-phosphate uptake system NF008726.1 PRK11728 PRK11728.1 299 299 389 equivalog Y Y N L-2-hydroxyglutarate oxidase lhgO 1.1.3.- GO:0016491 131567 cellular organisms no rank 22639 NCBI Protein Cluster (PRK) hydroxyglutarate oxidase L-2-hydroxyglutarate oxidase Catalyzes the formation of 2-ketoglutarate from 2-hydroxyglutarate NF008730.0 PRK11750 PRK11750.1 1047 1047 1490 equivalog Y Y N glutamate synthase large subunit gltB 1.4.1.13 GO:0003824,GO:0006537,GO:0008152,GO:0015930,GO:0016491 131567 cellular organisms no rank 75830 NCBI Protein Cluster (PRK) glutamate synthase subunit alpha glutamate synthase large subunit Catalyzes the formation of glutamate from glutamine and alpha-ketoglutarate NF008805.1 PRK11824 PRK11824.1 471 471 683 equivalog Y Y N polyribonucleotide nucleotidyltransferase 2.7.7.8 GO:0003723,GO:0004654,GO:0006396,GO:0006402 131567 cellular organisms no rank 67586 NCBI Protein Cluster (PRK) polynucleotide phosphorylase/polyadenylase polyribonucleotide nucleotidyltransferase NF008808.1 PRK11830 PRK11830.1 204 204 243 equivalog Y Y N 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase 2.3.1.117 GO:0016740 131567 cellular organisms no rank 23775 NCBI Protein Cluster (PRK) 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase Catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway NF008818.0 PRK11864 PRK11864.1 405 405 300 subfamily Y Y N 3-methyl-2-oxobutanoate dehydrogenase subunit beta 131567 cellular organisms no rank 242 NCBI Protein Cluster (PRK) 2-ketoisovalerate ferredoxin oxidoreductase subunit beta 3-methyl-2-oxobutanoate dehydrogenase subunit beta NF008819.1 PRK11865 PRK11865.1 405 405 300 equivalog Y Y N pyruvate synthase subunit PorB porB 1.2.7.1 GO:0019164 8380721,8620891,9108258 131567 cellular organisms no rank 552 NCBI Protein Cluster (PRK) pyruvate ferredoxin oxidoreductase subunit beta pyruvate synthase subunit PorB Catalyzes the formation of acetyl-CoA from pyruvate and coenzyme A NF008820.0 PRK11866 PRK11866.1 402 402 287 equivalog Y N N 2-oxoacid ferredoxin oxidoreductase subunit beta 131567 cellular organisms no rank 44 NCBI Protein Cluster (PRK) 2-oxoacid ferredoxin oxidoreductase subunit beta 2-oxoacid ferredoxin oxidoreductase subunit beta NF008821.0 PRK11869 PRK11869.1 438 438 286 equivalog Y N N 2-oxoacid ferredoxin oxidoreductase subunit beta 131567 cellular organisms no rank 184 NCBI Protein Cluster (PRK) 2-oxoacid ferredoxin oxidoreductase subunit beta 2-oxoacid ferredoxin oxidoreductase subunit beta NF008823.0 PRK11873 PRK11873.1 263 263 272 subfamily Y Y N arsenite methyltransferase arsM 16452170 131567 cellular organisms no rank 5461 NCBI Protein Cluster (PRK) arsenite S-adenosylmethyltransferase arsenite methyltransferase Catalyzes the formation of a number of methylated intermediates from arsenite and SAM producing trimethylarsine NF008864.0 PRK11895 PRK11895.1 119 119 164 equivalog Y Y N acetolactate synthase small subunit ilvN 2.2.1.6 GO:0009082,GO:1990610 10430574,11097879,12183585,14702326,16111681,16458324 131567 cellular organisms no rank 29148 NCBI Protein Cluster (PRK) acetolactate synthase 3 regulatory subunit acetolactate synthase small subunit NF008865.0 PRK11898 PRK11898.1 219 219 284 equivalog Y Y N prephenate dehydratase pheA 4.2.1.51 GO:0004664,GO:0009094 15753077 131567 cellular organisms no rank 41164 NCBI Protein Cluster (PRK) prephenate dehydratase prephenate dehydratase Catalyzes the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis NF008873.0 PRK11909 PRK11909.1 225 225 230 equivalog Y Y N cobalt transporter CbiM cbiM 131567 cellular organisms no rank 1663 NCBI Protein Cluster (PRK) cobalt transport protein CbiM cobalt transporter CbiM NF008887.0 PRK11921 PRK11921.1 635 635 396 equivalog Y Y N anaerobic nitric oxide reductase flavorubredoxin 131567 cellular organisms no rank 756 NCBI Protein Cluster (PRK) metallo-beta-lactamase/flavodoxin domain-containing protein anaerobic nitric oxide reductase flavorubredoxin NF008909.0 PRK12273 PRK12273.1 510 510 474 subfamily Y Y N aspartate ammonia-lyase 4.3.1.1 GO:0006099,GO:0016829 131567 cellular organisms no rank 86413 NCBI Protein Cluster (PRK) aspartate ammonia-lyase aspartate ammonia-lyase Catalyzes the formation of fumarate from aspartate NF008913.0 PRK12276 PRK12276.1 253 253 248 equivalog Y Y N hydrogen peroxide-dependent heme synthase hemQ 1.3.98.5 GO:0004601,GO:0006785 20543190,27936663,27982566 131567 cellular organisms no rank 5216 NCBI Protein Cluster (PRK) putative heme peroxidase hydrogen peroxide-dependent heme synthase, Bacillota family This enzyme, also called coproheme III oxidative decarboxylase, occurs in a heme biosynthesis pathway in Gram-positive bacteria. NF008957.0 PRK12300 PRK12300.1 677 677 946 subfamily Y Y N leucine--tRNA ligase 6.1.1.4 15388951 131567 cellular organisms no rank 1243 NCBI Protein Cluster (PRK) leucyl-tRNA synthetase leucine--tRNA ligase LeuRS; class-I aminoacyl-tRNA synthetase; charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA; due to the large number of codons that tRNA(Leu) recognizes, the leucyl-tRNA synthetase does not recognize the anticodon loop of the tRNA, but instead recognition is dependent on a conserved discriminator base A37 and a long arm; an editing domain hydrolyzes misformed products; in Methanothermobacter thermautotrophicus this enzyme associates with prolyl-tRNA synthetase NF008967.0 PRK12313 PRK12313.1 577 577 633 equivalog Y Y N 1,4-alpha-glucan branching protein GlgB glgB GO:0003844,GO:0004553,GO:0005975,GO:0005978,GO:0043169 131567 cellular organisms no rank 69114 NCBI Protein Cluster (PRK) glycogen branching enzyme 1,4-alpha-glucan branching protein GlgB Catalyzes the transfer of a segment of a 1,4-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain NF008969.0 PRK12317 PRK12317.1 502 502 426 subfamily Y Y N elongation factor 1-alpha 131567 cellular organisms no rank 1425 NCBI Protein Cluster (PRK) elongation factor 1-alpha elongation factor 1-alpha EF-1-alpha; EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-1-alpha-GDP leaves the ribosome and GDP/GTP exchange is promoted by EF-1-beta NF008977.0 PRK12324 PRK12324.1-2 234 234 297 equivalog Y Y N decaprenyl-phosphate phosphoribosyltransferase 2.4.2.45 GO:0016765 131567 cellular organisms no rank 1958 NCBI Protein Cluster (PRK) phosphoribose diphosphate:decaprenyl-phosphate phosphoribosyltransferase decaprenyl-phosphate phosphoribosyltransferase NF008978.0 PRK12324 PRK12324.1-4 207 207 322 equivalog Y Y N decaprenyl-phosphate phosphoribosyltransferase 2.4.2.45 GO:0016765 131567 cellular organisms no rank 8653 NCBI Protein Cluster (PRK) phosphoribose diphosphate:decaprenyl-phosphate phosphoribosyltransferase decaprenyl-phosphate phosphoribosyltransferase NF008985.0 PRK12331 PRK12331.1 718 718 465 equivalog Y Y N oxaloacetate decarboxylase subunit alpha 4.1.1.112 GO:0003824 131567 cellular organisms no rank 3311 NCBI Protein Cluster (PRK) oxaloacetate decarboxylase oxaloacetate decarboxylase subunit alpha Catalyzes the formation of pyruvate from oxaloacetate NF008999.0 PRK12343 PRK12343.1 171 171 156 equivalog Y Y N cyclic pyranopterin monophosphate synthase MoaC moaC 4.6.1.17 131567 cellular organisms no rank 1463 NCBI Protein Cluster (PRK) putative molybdenum cofactor biosynthesis protein MoaC cyclic pyranopterin monophosphate synthase MoaC NF009005.0 PRK12350 PRK12350.1 332 332 366 subfamily Y Y N citrate synthase 2.3.3.16 131567 cellular organisms no rank 15521 NCBI Protein Cluster (PRK) citrate synthase 2 citrate synthase Forms citrate from oxaloacetate and acetyl-CoA; functions in TCA cycle, glyoxylate cycle and respiration NF009007.0 PRK12352 PRK12352.1 266 266 316 subfamily Y Y N carbamate kinase 2.7.2.2 131567 cellular organisms no rank 17290 NCBI Protein Cluster (PRK) putative carbamate kinase carbamate kinase NF009008.0 PRK12354 PRK12354.1 361 361 308 subfamily Y Y N carbamate kinase 2.7.2.2 131567 cellular organisms no rank 11495 NCBI Protein Cluster (PRK) carbamate kinase carbamate kinase Reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP NF009052.0 PRK12386 PRK12386.1 256 256 255 equivalog Y Y N succinate dehydrogenase/fumarate reductase iron-sulfur subunit 131567 cellular organisms no rank 7338 NCBI Protein Cluster (PRK) fumarate reductase iron-sulfur subunit succinate dehydrogenase/fumarate reductase iron-sulfur subunit NF009057.0 PRK12391 PRK12391.1 366 366 441 equivalog Y Y N TrpB-like pyridoxal phosphate-dependent enzyme GO:0000162,GO:0004834,GO:0006568,GO:0030170 131567 cellular organisms no rank 8201 NCBI Protein Cluster (PRK) tryptophan synthase subunit beta TrpB-like pyridoxal phosphate-dependent enzyme NF009064.0 PRK12398 PRK12398.1 207 207 165 equivalog Y N N pyruvoyl-dependent arginine decarboxylase 131567 cellular organisms no rank 116 NCBI Protein Cluster (PRK) pyruvoyl-dependent arginine decarboxylase pyruvoyl-dependent arginine decarboxylase NF009070.0 PRK12405 PRK12405.1 184 184 231 subfamily Y Y N electron transport complex subunit RsxE rsxE 131567 cellular organisms no rank 18478 NCBI Protein Cluster (PRK) electron transport complex RsxE subunit electron transport complex subunit RsxE NF009116.0 PRK12466 PRK12466.1 531 531 472 subfamily Y Y N 3-isopropylmalate dehydratase large subunit 131567 cellular organisms no rank 63429 NCBI Protein Cluster (PRK) isopropylmalate isomerase large subunit 3-isopropylmalate dehydratase large subunit NF009131.0 PRK12484 PRK12484.1 330 330 455 equivalog Y Y N nicotinate phosphoribosyltransferase 6.3.4.21 131567 cellular organisms no rank 37331 NCBI Protein Cluster (PRK) nicotinate phosphoribosyltransferase nicotinate phosphoribosyltransferase Catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate NF009159.0 PRK12504 PRK12504.1 141 141 178 equivalog Y Y N DUF4040 domain-containing protein 131567 cellular organisms no rank 1627 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit B DUF4040 domain-containing protein NF009162.0 PRK12508 PRK12508.1 120 120 139 equivalog Y Y N Na(+)/H(+) antiporter subunit B 131567 cellular organisms no rank 1130 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit B Na(+)/H(+) antiporter subunit B Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF009205.0 PRK12553 PRK12553.1 228 228 211 subfamily Y Y N ATP-dependent Clp protease proteolytic subunit GO:0004176,GO:0006508 131567 cellular organisms no rank 68914 NCBI Protein Cluster (PRK) ATP-dependent Clp protease proteolytic subunit ATP-dependent Clp protease proteolytic subunit NF009206.0 PRK12555 PRK12555.1 342 342 340 subfamily Y Y N chemotaxis-specific protein-glutamate methyltransferase CheB cheB 3.1.1.61 131567 cellular organisms no rank 22932 NCBI Protein Cluster (PRK) chemotaxis-specific methylesterase chemotaxis-specific protein-glutamate methyltransferase CheB Regulates chemotaxis by demethylation of methyl-accepting chemotaxis proteins NF009208.0 PRK12557 PRK12557.1 258 258 342 subfamily Y Y N H(2)-dependent methylenetetrahydromethanopterin dehydrogenase-related protein 131567 cellular organisms no rank 98 NCBI Protein Cluster (PRK) H(2)-dependent methylenetetrahydromethanopterin dehydrogenase-related protein H(2)-dependent methylenetetrahydromethanopterin dehydrogenase-related protein NF009211.0 PRK12560 PRK12560.1 188 188 187 equivalog Y N N adenine phosphoribosyltransferase 131567 cellular organisms no rank 262 NCBI Protein Cluster (PRK) adenine phosphoribosyltransferase adenine phosphoribosyltransferase NF009214.0 PRK12563 PRK12563.1 413 413 317 equivalog Y Y N sulfate adenylyltransferase subunit CysD cysD 2.7.7.4 GO:0000103,GO:0004781 15184554 131567 cellular organisms no rank 36346 NCBI Protein Cluster (PRK) sulfate adenylyltransferase subunit 2 sulfate adenylyltransferase subunit CysD With CysN catalyzes the formation of adenylylsulfate from sulfate and ATP NF009222.0 PRK12570 PRK12570.1 255 255 307 subfamily Y Y N N-acetylmuramic acid 6-phosphate etherase 4.2.1.126 131567 cellular organisms no rank 39001 NCBI Protein Cluster (PRK) N-acetylmuramic acid-6-phosphate etherase N-acetylmuramic acid 6-phosphate etherase Catalyzes the cleavage of the lactyl ether moiety of N-acetylmuramic acid-6-phosphate (MurNAc-6-P) to form N-acetylglucosamine-6-phosphate (GlcNAc-6-P) and lactate; involved in MurNAc dissimilation pathway NF009233.0 PRK12583 PRK12583.1 832 832 558 subfamily Y Y N fatty acid CoA ligase family protein 131567 cellular organisms no rank 11430 NCBI Protein Cluster (PRK) acyl-CoA synthetase fatty acid CoA ligase family protein NF009239.0 PRK12595 PRK12595.1 279 279 360 equivalog Y Y N bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase GO:0003824,GO:0009073,GO:0046417 11847568,14337509,15869469,7496534 131567 cellular organisms no rank 18210 NCBI Protein Cluster (PRK) bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase Catalyzes the formation of 3-deoxy-D-aribino-hept-2-ulosonate 7-phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate and the formation of prephenate from chorismate NF009242.0 PRK12599 PRK12599.1-1 89 89 86 equivalog Y N N putative monovalent cation/H+ antiporter subunit F 131567 cellular organisms no rank 142 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit F putative monovalent cation/H+ antiporter subunit F NF009251.0 PRK12607 PRK12607.1 371 371 315 equivalog Y Y N phosphoribosylaminoimidazolesuccinocarboxamide synthase 6.3.2.6 GO:0004639,GO:0006164 131567 cellular organisms no rank 7697 NCBI Protein Cluster (PRK) phosphoribosylaminoimidazole-succinocarboxamide synthase phosphoribosylaminoimidazolesuccinocarboxamide synthase Catalyzes the formation of (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate and L-aspartate in purine biosynthesis; SAICAR synthase NF009310.0 PRK12668 PRK12668.1 564 564 584 equivalog Y Y N Na(+)/H(+) antiporter subunit D 131567 cellular organisms no rank 2492 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit D Na(+)/H(+) antiporter subunit D Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF009312.0 PRK12672 PRK12672.1 122 122 122 subfamily Y N N putative monovalent cation/H+ antiporter subunit G 131567 cellular organisms no rank 192 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit G putative monovalent cation/H+ antiporter subunit G NF009314.0 PRK12674 PRK12674.1-2 102 102 116 subfamily Y Y N Na+/H+ antiporter subunit G 131567 cellular organisms no rank 13182 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit G Na+/H+ antiporter subunit G NF009372.0 PRK12735 PRK12735.1 479 479 396 subfamily Y Y N elongation factor Tu GO:0003746,GO:0003924,GO:0005525,GO:0006414 12963376,14622294,15147200 131567 cellular organisms no rank 59765 NCBI Protein Cluster (PRK) elongation factor Tu elongation factor Tu EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts NF009373.0 PRK12736 PRK12736.1 452 452 394 subfamily Y Y N elongation factor Tu 14602655 131567 cellular organisms no rank 60255 NCBI Protein Cluster (PRK) elongation factor Tu elongation factor Tu EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts NF009379.0 PRK12740 PRK12740.1-3 513 513 674 equivalog Y Y N elongation factor G GO:0003924,GO:0005525 131567 cellular organisms no rank 32610 NCBI Protein Cluster (PRK) elongation factor G elongation factor G NF009381.0 PRK12740 PRK12740.1-5 583 583 692 subfamily Y Y N elongation factor G fusA 131567 cellular organisms no rank 93343 NCBI Protein Cluster (PRK) elongation factor G elongation factor G NF009402.0 PRK12767 PRK12767.1-1 218 218 329 equivalog Y N N carbamoyl phosphate synthase-like protein 131567 cellular organisms no rank 682 NCBI Protein Cluster (PRK) carbamoyl phosphate synthase-like protein carbamoyl phosphate synthase-like protein NF009404.0 PRK12767 PRK12767.1-3 316 316 344 equivalog Y N N carbamoyl phosphate synthase-like protein 131567 cellular organisms no rank 649 NCBI Protein Cluster (PRK) carbamoyl phosphate synthase-like protein carbamoyl phosphate synthase-like protein NF009409.0 PRK12770 PRK12770.1 343 343 360 subfamily Y N N putative glutamate synthase subunit beta 131567 cellular organisms no rank 249 NCBI Protein Cluster (PRK) putative glutamate synthase subunit beta putative glutamate synthase subunit beta NF009410.0 PRK12771 PRK12771.1 516 516 566 subfamily Y Y N NAD(P)-binding protein 131567 cellular organisms no rank 4876 NCBI Protein Cluster (PRK) putative glutamate synthase (NADPH) small subunit NAD(P)-binding protein NF009455.0 PRK12815 PRK12815.1 752 752 1068 equivalog Y Y N carbamoyl phosphate synthase large subunit 131567 cellular organisms no rank 87787 NCBI Protein Cluster (PRK) carbamoyl phosphate synthase large subunit carbamoyl phosphate synthase large subunit NF009464.0 PRK12824 PRK12824.1 269 269 245 subfamily Y Y N 3-oxoacyl-ACP reductase 1.1.1.36 131567 cellular organisms no rank 24587 NCBI Protein Cluster (PRK) acetoacetyl-CoA reductase 3-oxoacyl-ACP reductase NF009466.0 PRK12826 PRK12826.1-2 222 222 248 subfamily Y Y N 3-oxoacyl-ACP reductase FabG fabG 1.1.1.100 GO:0016491 131567 cellular organisms no rank 142698 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase 3-oxoacyl-ACP reductase FabG NF009475.0 PRK12838 PRK12838.1 221 221 359 equivalog Y Y N carbamoyl phosphate synthase small subunit GO:0004088,GO:0006541 131567 cellular organisms no rank 72697 NCBI Protein Cluster (PRK) carbamoyl phosphate synthase small subunit carbamoyl phosphate synthase small subunit NF009487.0 PRK12849 PRK12849.1 352 352 543 subfamily Y Y N chaperonin GroEL groEL 131567 cellular organisms no rank 75919 NCBI Protein Cluster (PRK) chaperonin GroEL chaperonin GroEL NF009488.0 PRK12850 PRK12850.1 475 475 544 subfamily Y Y N chaperonin GroEL groEL 131567 cellular organisms no rank 74676 NCBI Protein Cluster (PRK) chaperonin GroEL chaperonin GroEL NF009489.0 PRK12851 PRK12851.1 464 464 541 subfamily Y Y N chaperonin GroEL groEL 131567 cellular organisms no rank 74712 NCBI Protein Cluster (PRK) chaperonin GroEL chaperonin GroEL NF009497.0 PRK12857 PRK12857.1 423 423 284 equivalog Y Y N class II fructose-1,6-bisphosphate aldolase 4.1.2.13 131567 cellular organisms no rank 303 NCBI Protein Cluster (PRK) fructose-1,6-bisphosphate aldolase class II fructose-1,6-bisphosphate aldolase Catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate NF009516.0 PRK12875 PRK12875.1 205 205 292 equivalog Y Y N prenyltransferase 131567 cellular organisms no rank 705 NCBI Protein Cluster (PRK) prenyltransferase prenyltransferase NF009520.0 PRK12881 PRK12881.1 905 905 893 subfamily Y Y N aconitate hydratase AcnA acnA 4.2.1.3 131567 cellular organisms no rank 78826 NCBI Protein Cluster (PRK) aconitate hydratase aconitate hydratase AcnA Catalyzes the conversion of citrate to isocitrate NF009523.0 PRK12884 PRK12884.1 269 269 279 equivalog Y N N prenyltransferase 131567 cellular organisms no rank 305 NCBI Protein Cluster (PRK) prenyltransferase prenyltransferase NF009544.0 PRK12928 PRK12928.1 210 210 300 subfamily Y Y N lipoyl synthase 2.8.1.8 131567 cellular organisms no rank 50432 NCBI Protein Cluster (PRK) lipoyl synthase lipoyl synthase Catalyzes the radical-mediated insertion of two sulfur atoms into an acyl carrier protein (ACP) bound to an octanoyl group to produce a lipoyl group NF009566.0 PRK13020 PRK13020.1 180 180 206 equivalog Y Y N riboflavin synthase subunit alpha 131567 cellular organisms no rank 35884 NCBI Protein Cluster (PRK) riboflavin synthase subunit alpha riboflavin synthase subunit alpha NF009668.0 PRK13189 PRK13189.1 211 211 224 equivalog Y Y N peroxiredoxin 1.11.1.24 GO:0008379,GO:0051920,GO:0098869 131567 cellular organisms no rank 12772 NCBI Protein Cluster (PRK) peroxiredoxin peroxiredoxin Alkyl hydroperoxidase; catalyze the reduction of hydrogen peroxide to water and the reduction of alkyl hydroperoxides to the corresponding alcohols NF009669.0 PRK13190 PRK13190.1 261 261 203 equivalog Y N N putative peroxiredoxin 131567 cellular organisms no rank 153 NCBI Protein Cluster (PRK) putative peroxiredoxin putative peroxiredoxin NF009671.0 PRK13192 PRK13192.1 243 243 231 subfamily Y N N bifunctional urease subunit gamma/beta 131567 cellular organisms no rank 8035 NCBI Protein Cluster (PRK) bifunctional urease subunit gamma/beta bifunctional urease subunit gamma/beta NF009673.0 PRK13194 PRK13194.1 274 274 208 equivalog Y Y N pyroglutamyl-peptidase I 3.4.19.3 131567 cellular organisms no rank 15 NCBI Protein Cluster (PRK) pyrrolidone-carboxylate peptidase pyroglutamyl-peptidase I NF009676.0 PRK13197 PRK13197.1 199 199 215 subfamily Y Y N pyroglutamyl-peptidase I 3.4.19.3 131567 cellular organisms no rank 16897 NCBI Protein Cluster (PRK) pyrrolidone-carboxylate peptidase pyroglutamyl-peptidase I NF009682.0 PRK13203 PRK13203.1 129 129 104 equivalog Y Y N urease subunit beta 3.5.1.5 GO:0035550,GO:0043419 10913107,11101668,14981304,17101645,17578575 131567 cellular organisms no rank 24916 NCBI Protein Cluster (PRK) urease subunit beta urease subunit beta Catalyzes the hydrolysis of urea into ammonia and carbon dioxide; the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa NF009686.0 PRK13207 PRK13207.1 354 354 569 subfamily Y Y N urease subunit alpha 3.5.1.5 10075427,10639468,10844692,10913107,11101668,11373617,11500473,17101645,17578575 131567 cellular organisms no rank 44876 NCBI Protein Cluster (PRK) urease subunit alpha urease subunit alpha Catalyzes the hydrolysis of urea into ammonia and carbon dioxide; the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa NF009687.0 PRK13208 PRK13208.1 738 738 801 equivalog Y Y N valine--tRNA ligase 6.1.1.9 131567 cellular organisms no rank 11183 NCBI Protein Cluster (PRK) valyl-tRNA synthetase valine--tRNA ligase ValRS; converts valine ATP and tRNA(Val) to AMP PPi and valyl-tRNA(Val); class-I aminoacyl-tRNA synthetase type 1 subfamily; has a posttransfer editing process to hydrolyze mischarged Thr-tRNA(Val) which is done by the editing domain NF009701.0 PRK13230 PRK13230.1 350 350 291 subfamily Y N N nitrogenase reductase-like protein 131567 cellular organisms no rank 72 NCBI Protein Cluster (PRK) nitrogenase reductase-like protein nitrogenase reductase-like protein NF009709.0 PRK13238 PRK13238.1 285 285 463 subfamily Y Y N tryptophanase 4.1.99.1 131567 cellular organisms no rank 10158 NCBI Protein Cluster (PRK) tryptophanase/L-cysteine desulfhydrase, PLP-dependent tryptophanase NF009712.0 PRK13241 PRK13241.1 123 123 100 equivalog Y Y N urease subunit gamma 3.5.1.5 GO:0009039,GO:0016151,GO:0043419 131567 cellular organisms no rank 19460 NCBI Protein Cluster (PRK) urease subunit gamma urease subunit gamma Catalyzes the hydrolysis of urea into ammonia and carbon dioxide; the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa NF009714.1 PRK13243 PRK13243.1 455 455 332 equivalog Y Y N glyoxylate reductase gyaR 1.1.1.26 GO:0047964 11532010 131567 cellular organisms no rank 166 NCBI Protein Cluster (PRK) glyoxylate reductase glyoxylate reductase NF009752.0 PRK13261 PRK13261.1-2 162 162 169 equivalog Y Y N urease accessory protein UreE ureE 131567 cellular organisms no rank 610 NCBI Protein Cluster (PRK) urease accessory protein UreE urease accessory protein UreE NF009802.0 PRK13286 PRK13286.1 427 427 345 equivalog Y Y N aliphatic amidase GO:0004040,GO:0008152 131567 cellular organisms no rank 3612 NCBI Protein Cluster (PRK) acylamide amidohydrolase aliphatic amidase NF009806.0 PRK13290 PRK13290.1 128 128 130 subfamily Y Y N ectoine synthase GO:0019491,GO:0033990 131567 cellular organisms no rank 10112 NCBI Protein Cluster (PRK) L-ectoine synthase ectoine synthase NF009809.0 PRK13293 PRK13293.1 274 274 253 equivalog Y Y N coenzyme F420-0:L-glutamate ligase 6.3.2.31 131567 cellular organisms no rank 1107 NCBI Protein Cluster (PRK) F420-0--gamma-glutamyl ligase coenzyme F420-0:L-glutamate ligase Catalyzes the addition of gamma linked glutamate to 7,8-didemethyl-8-hydroxy-5-deazariboflavin NF009825.0 PRK13302 PRK13302.1 253 253 271 equivalog Y Y N aspartate dehydrogenase 131567 cellular organisms no rank 1343 NCBI Protein Cluster (PRK) putative L-aspartate dehydrogenase aspartate dehydrogenase Catalyzes the formation of L-aspartate to iminoaspartate in NAD(+) biosynthesis NF009828.0 PRK13303 PRK13303.1-3 177 177 263 subfamily Y Y N aspartate dehydrogenase 1.4.1.21 131567 cellular organisms no rank 6623 NCBI Protein Cluster (PRK) L-aspartate dehydrogenase aspartate dehydrogenase NF009829.0 PRK13303 PRK13303.1-4 184 184 245 subfamily Y Y N aspartate dehydrogenase 1.4.1.21 131567 cellular organisms no rank 1802 NCBI Protein Cluster (PRK) L-aspartate dehydrogenase aspartate dehydrogenase NF009830.0 PRK13304 PRK13304.1 267 267 265 equivalog Y Y N aspartate dehydrogenase 1.4.1.21 131567 cellular organisms no rank 507 NCBI Protein Cluster (PRK) L-aspartate dehydrogenase aspartate dehydrogenase Catalyzes the formation of L-aspartate to iminoaspartate in NAD(+) biosynthesis NF009855.0 PRK13321 PRK13321.1 233 233 256 equivalog Y Y N type III pantothenate kinase 2.7.1.33 131567 cellular organisms no rank 18689 NCBI Protein Cluster (PRK) pantothenate kinase type III pantothenate kinase Catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP NF009884.0 PRK13343 PRK13343.1 554 554 507 equivalog Y Y N F0F1 ATP synthase subunit alpha 7.1.2.2 GO:0005524,GO:0015986,GO:0045261,GO:0046933 131567 cellular organisms no rank 51664 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit alpha F0F1 ATP synthase subunit alpha Produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit NF009895.0 PRK13352 PRK13352.1 410 410 430 equivalog Y Y N phosphomethylpyrimidine synthase ThiC thiC 4.1.99.17 GO:0009228,GO:0051536 131567 cellular organisms no rank 58432 NCBI Protein Cluster (PRK) thiamine biosynthesis protein ThiC phosphomethylpyrimidine synthase ThiC Catalyzes the formation of 4-amino-2-methyl-5-phosphomethylpyrimidine from 5-amino-1-(5-phospho-D-ribosyl)imidazole and S-adenosyl-L-methionine in thiamine biosynthesis NF009897.0 PRK13357 PRK13357.1 307 307 358 equivalog Y Y N branched-chain amino acid aminotransferase 2.6.1.42 GO:0004084,GO:0009081 131567 cellular organisms no rank 43201 NCBI Protein Cluster (PRK) branched-chain amino acid aminotransferase branched-chain amino acid aminotransferase Catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids NF009905.0 PRK13368 PRK13368.1 255 255 243 subfamily Y Y N 3-deoxy-manno-octulosonate cytidylyltransferase 2.7.7.38 131567 cellular organisms no rank 26557 NCBI Protein Cluster (PRK) 3-deoxy-manno-octulosonate cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase CMP-2-keto-3-deoxyoctulosonic acid synthetase; catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS NF009940.0 PRK13403 PRK13403.1 406 406 335 equivalog Y Y N ketol-acid reductoisomerase 131567 cellular organisms no rank 33766 NCBI Protein Cluster (PRK) ketol-acid reductoisomerase ketol-acid reductoisomerase NF009990.0 PRK13456 PRK13456.1 158 158 188 equivalog Y N N DNA protection protein DPS 131567 cellular organisms no rank 373 NCBI Protein Cluster (PRK) DNA protection protein DPS DNA protection protein DPS NF009998.0 PRK13468 PRK13468.1 116 116 88 equivalog Y Y N F0F1 ATP synthase subunit C 7.1.2.2 131567 cellular organisms no rank 1470 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit C F0F1 ATP synthase subunit C Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit C is part of the membrane proton channel F0 NF010002.0 PRK13475 PRK13475.1 489 489 459 equivalog Y Y N ribulose-bisphosphate carboxylase 4.1.1.39 131567 cellular organisms no rank 661 NCBI Protein Cluster (PRK) ribulose bisphosphate carboxylase ribulose-bisphosphate carboxylase Catalyzes the carboxylation of D-ribulose 1,5-bisphosphate in carbon dioxide fixation NF010030.0 PRK13505 PRK13505.1 652 652 557 equivalog Y Y N formate--tetrahydrofolate ligase 6.3.4.3 GO:0004329,GO:0005524 131567 cellular organisms no rank 34916 NCBI Protein Cluster (PRK) formate--tetrahydrofolate ligase formate--tetrahydrofolate ligase Catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate NF010039.0 PRK13515 PRK13515.1 371 371 378 equivalog Y Y N carboxylate-amine ligase GO:0004357,GO:0042398 131567 cellular organisms no rank 5809 NCBI Protein Cluster (PRK) carboxylate-amine ligase carboxylate-amine ligase ATP-dependent carboxylate-amine ligase NF010052.0 PRK13529 PRK13529.1 326 326 564 subfamily Y Y N oxaloacetate-decarboxylating malate dehydrogenase maeA 1.1.1.38 131567 cellular organisms no rank 23967 NCBI Protein Cluster (PRK) malate dehydrogenase oxaloacetate-decarboxylating malate dehydrogenase malic enzyme; oxaloacetate-decarboxylating; NAD-dependent; catalyzes the formation of pyruvate form malate NF010068.0 PRK13548 PRK13548.1 261 261 261 equivalog Y Y N heme ABC transporter ATP-binding protein GO:0005524 131567 cellular organisms no rank 27306 NCBI Protein Cluster (PRK) hemin importer ATP-binding subunit heme ABC transporter ATP-binding protein With HmuTU is involved in the transport of hemin NF010112.0 PRK13585 PRK13585.1 243 243 241 equivalog Y Y N 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase hisA 131567 cellular organisms no rank 9307 NCBI Protein Cluster (PRK) 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase Catalyzes the formation of 5-(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino-l-(5-hosphoribosyl)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide NF010120.0 PRK13596 PRK13596.1 389 389 433 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoF nuoF GO:0008137,GO:0010181,GO:0051287,GO:0051539 131567 cellular organisms no rank 35428 NCBI Protein Cluster (PRK) NADH dehydrogenase I subunit F NADH-quinone oxidoreductase subunit NuoF NF010147.0 PRK13623 PRK13623.1 117 117 115 equivalog Y Y N iron-sulfur cluster insertion protein ErpA erpA GO:0016226,GO:0051536 22363723 131567 cellular organisms no rank 14188 NCBI Protein Cluster (PRK) iron-sulfur cluster insertion protein ErpA iron-sulfur cluster insertion protein ErpA NF010151.0 PRK13628 PRK13628.1 308 308 407 equivalog Y Y N serine/threonine transporter SstT sstT GO:0015293,GO:0015826,GO:0016020,GO:0032329 131567 cellular organisms no rank 16074 NCBI Protein Cluster (PRK) serine/threonine transporter SstT serine/threonine transporter SstT Involved in the import of serine and threonine coupled with the import of sodium NF010167.0 PRK13648 PRK13648.1 241 0 269 subfamily Y Y N energy-coupling factor transporter ATPase GO:0005524,GO:0015833 131567 cellular organisms no rank 33792 NCBI Protein Cluster (PRK) cobalt transporter ATP-binding subunit energy-coupling factor transporter ATPase NF010184.0 PRK13663 PRK13663.1 631 631 494 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 6936 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010229.0 PRK13682 PRK13682.1-4 52 52 53 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 8464 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010248.0 PRK13695 PRK13695.1 156 156 180 equivalog Y Y N NTPase 14503925,15777481 131567 cellular organisms no rank 456 NCBI Protein Cluster (PRK) putative NTPase NTPase NF010322.0 PRK13759 PRK13759.1 481 481 486 equivalog Y Y N arylsulfatase 3.1.6.1 GO:0008484 18408004 131567 cellular organisms no rank 2470 NCBI Protein Cluster (PRK) arylsulfatase arylsulfatase NF010324.0 PRK13761 PRK13761.1 227 227 252 subfamily Y Y N phosphopantothenate/pantothenate synthetase 19666462,22940806 131567 cellular organisms no rank 1385 NCBI Protein Cluster (PRK) hypothetical protein phosphopantothenate/pantothenate synthetase Members of this family are found in the archaea, and replace the pantothenate synthetase of bacteria, pantoate--beta-alanine ligase (AMP-forming) (EC 6.3.2.1). Members may be pantoate--beta-alanine ligase (ADP-forming) (EC 6.3.2.44) or 4-phosphopantoate--beta-alanine ligase (EC 6.3.2.36). NF010335.0 PRK13764 PRK13764.1 340 340 613 equivalog Y N N ATPase 131567 cellular organisms no rank 1479 NCBI Protein Cluster (PRK) ATPase ATPase NF010386.0 PRK13813 PRK13813.1 208 208 216 equivalog Y N N orotidine 5'-phosphate decarboxylase 4.1.1.23 131567 cellular organisms no rank 1259 NCBI Protein Cluster (PRK) orotidine 5'-phosphate decarboxylase orotidine-5'-phosphate decarboxylase Type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide NF010392.0 PRK13820 PRK13820.1 512 512 395 equivalog Y Y N argininosuccinate synthase 6.3.4.5 131567 cellular organisms no rank 1125 NCBI Protein Cluster (PRK) argininosuccinate synthase argininosuccinate synthase Catalyzes the formation of arginosuccinate from citrulline and aspartate in arginine biosynthesis NF010480.0 PRK13905 PRK13905.1 259 259 303 equivalog Y Y N UDP-N-acetylmuramate dehydrogenase murB 1.3.1.98 GO:0008762,GO:0071949 131567 cellular organisms no rank 28312 NCBI Protein Cluster (PRK) UDP-N-acetylenolpyruvoylglucosamine reductase UDP-N-acetylmuramate dehydrogenase NF010557.0 PRK13952 PRK13952.1 159 159 142 equivalog Y Y N large conductance mechanosensitive channel protein MscL mscL GO:0008381,GO:0016020,GO:0034220 131567 cellular organisms no rank 12224 NCBI Protein Cluster (PRK) large-conductance mechanosensitive channel large conductance mechanosensitive channel protein MscL Channel that opens in response to pressure or hypoosmotic shock NF010568.0 PRK13961 PRK13961.1 251 251 297 equivalog Y Y N phosphoribosylaminoimidazolesuccinocarboxamide synthase 6.3.2.6 GO:0004639,GO:0006164 131567 cellular organisms no rank 32177 NCBI Protein Cluster (PRK) phosphoribosylaminoimidazole-succinocarboxamide synthase phosphoribosylaminoimidazolesuccinocarboxamide synthase Catalyzes the formation of (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate and L-aspartate in purine biosynthesis; SAICAR synthase NF010584.0 PRK13977 PRK13977.1 567 567 577 equivalog Y Y N oleate hydratase 4.2.1.53 GO:0006631,GO:0050151,GO:0071949 8188369 131567 cellular organisms no rank 14603 NCBI Protein Cluster (PRK) myosin-cross-reactive antigen oleate hydratase NF010587.0 PRK13980 PRK13980.1 255 255 267 equivalog Y Y N NAD+ synthase 6.3.1.5 GO:0008795,GO:0009435 131567 cellular organisms no rank 5252 NCBI Protein Cluster (PRK) NAD synthetase NAD+ synthase Catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP NF010588.0 PRK13981 PRK13981.1 479 479 546 equivalog Y Y N NAD+ synthase 6.3.5.1 GO:0003952,GO:0005524,GO:0009435 131567 cellular organisms no rank 30832 NCBI Protein Cluster (PRK) NAD synthetase NAD+ synthase Catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP NF010589.0 PRK13983 PRK13983.1 333 333 409 equivalog Y Y N M20 family metallo-hydrolase 131567 cellular organisms no rank 894 NCBI Protein Cluster (PRK) diaminopimelate aminotransferase M20 family metallo-hydrolase NF010612.0 PRK14013 PRK14013.1-2 386 386 307 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 191 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010613.0 PRK14013 PRK14013.1-3 385 385 362 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 11258 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010619.0 PRK14013 PRK14013.2-5 387 387 329 subfamily Y N N hypothetical protein 131567 cellular organisms no rank 5152 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010620.0 PRK14013 PRK14013.2-6 437 437 346 equivalog Y N N hypothetical protein 131567 cellular organisms no rank 2692 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010624.0 PRK14017 PRK14017.1 311 311 382 equivalog Y Y N galactonate dehydratase dgoD 4.2.1.6 GO:0008869,GO:0009063 131567 cellular organisms no rank 14939 NCBI Protein Cluster (PRK) galactonate dehydratase galactonate dehydratase NF010635.0 PRK14032 PRK14032.1 426 426 448 subfamily Y Y N citrate synthase 131567 cellular organisms no rank 5349 NCBI Protein Cluster (PRK) citrate synthase citrate synthase Forms citrate from oxaloacetate and acetyl-CoA; functions in TCA cycle, glyoxylate cycle and respiration NF010644.0 PRK14041 PRK14041.1 734 734 467 equivalog Y Y N pyruvate carboxylase subunit B 6.4.1.1 131567 cellular organisms no rank 92 NCBI Protein Cluster (PRK) oxaloacetate decarboxylase pyruvate carboxylase subunit B NF010659.0 PRK14058 PRK14058.1-1 223 223 267 equivalog Y Y N [LysW]-aminoadipate kinase 131567 cellular organisms no rank 1703 NCBI Protein Cluster (PRK) acetylglutamate/acetylaminoadipate kinase [LysW]-aminoadipate kinase NF010661.0 PRK14058 PRK14058.1-3 251 251 283 equivalog Y Y N acetylglutamate/acetylaminoadipate kinase 131567 cellular organisms no rank 863 NCBI Protein Cluster (PRK) acetylglutamate/acetylaminoadipate kinase acetylglutamate/acetylaminoadipate kinase NF010662.0 PRK14058 PRK14058.1-4 194 194 264 equivalog Y Y N [LysW]-aminoadipate/[LysW]-glutamate kinase 131567 cellular organisms no rank 217 NCBI Protein Cluster (PRK) acetylglutamate/acetylaminoadipate kinase [LysW]-aminoadipate/[LysW]-glutamate kinase NF010696.0 PRK14096 PRK14096.1 671 671 528 equivalog Y Y N glucose-6-phosphate isomerase 5.3.1.9 131567 cellular organisms no rank 1593 NCBI Protein Cluster (PRK) glucose-6-phosphate isomerase glucose-6-phosphate isomerase Functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family NF010713.0 PRK14115 PRK14115.1 305 305 248 equivalog Y Y N 2,3-diphosphoglycerate-dependent phosphoglycerate mutase gpmA 5.4.2.11 GO:0004619,GO:0006096 131567 cellular organisms no rank 25843 NCBI Protein Cluster (PRK) phosphoglyceromutase 2,3-diphosphoglycerate-dependent phosphoglycerate mutase Catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate; 2,3-diphosphoglycerate-dependent NF010718.0 PRK14120 PRK14120.1 366 366 249 equivalog Y Y N phosphoglyceromutase 5.4.2.11 GO:0004619,GO:0006096 131567 cellular organisms no rank 11767 NCBI Protein Cluster (PRK) phosphoglyceromutase phosphoglyceromutase Catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate NF010738.0 PRK14140 PRK14140.1 137 137 191 equivalog Y Y N nucleotide exchange factor GrpE grpE GO:0000774,GO:0006457,GO:0042803,GO:0051087 9103205 131567 cellular organisms no rank 30285 NCBI Protein Cluster (PRK) heat shock protein GrpE nucleotide exchange factor GrpE With DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins NF010748.0 PRK14150 PRK14150.1 152 152 198 equivalog Y Y N nucleotide exchange factor GrpE grpE GO:0000774,GO:0006457,GO:0042803,GO:0051087 131567 cellular organisms no rank 13606 NCBI Protein Cluster (PRK) heat shock protein GrpE nucleotide exchange factor GrpE With DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins NF010783.0 PRK14186 PRK14186.1 333 333 297 equivalog Y Y N bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD folD GO:0004488 131567 cellular organisms no rank 33677 NCBI Protein Cluster (PRK) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD Catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate NF010925.0 PRK14345 PRK14345.1 155 155 236 equivalog Y Y N lipoyl(octanoyl) transferase LipB lipB 2.3.1.181 GO:0009249,GO:0033819 131567 cellular organisms no rank 31503 NCBI Protein Cluster (PRK) lipoate-protein ligase B lipoyl(octanoyl) transferase LipB Catalyzes the transfer of the lipoyl/octanoyl moiety of lipoyl/octanoyl-ACP onto lipoate-dependent enzymes like pyruvate dehydrogenase and the glycine cleavage system H protein NF011007.0 PRK14433 PRK14433.1 100 100 88 equivalog Y Y N acylphosphatase 131567 cellular organisms no rank 202 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011009.0 PRK14435 PRK14435.1 119 119 90 equivalog Y Y N acylphosphatase 3.6.1.7 131567 cellular organisms no rank 15 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011010.0 PRK14436 PRK14436.1 117 117 91 equivalog Y Y N acylphosphatase 131567 cellular organisms no rank 90 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011011.0 PRK14438 PRK14438.1 109 109 91 equivalog Y Y N acylphosphatase 3.6.1.7 131567 cellular organisms no rank 72 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011012.0 PRK14440 PRK14440.1 103 103 90 equivalog Y Y N acylphosphatase 131567 cellular organisms no rank 43 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011013.0 PRK14441 PRK14441.1 114 114 93 equivalog Y Y N acylphosphatase 131567 cellular organisms no rank 78 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011016.0 PRK14444 PRK14444.1 103 103 92 equivalog Y Y N acylphosphatase 131567 cellular organisms no rank 981 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011020.0 PRK14449 PRK14449.1 103 103 90 equivalog Y Y N acylphosphatase 131567 cellular organisms no rank 33 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011063.0 PRK14494 PRK14494.1-2 258 258 227 equivalog Y N N putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein protein 131567 cellular organisms no rank 27 NCBI Protein Cluster (PRK) putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein protein putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein protein NF011068.0 PRK14498 PRK14498.1 534 534 647 equivalog Y Y N molybdopterin biosynthesis protein GO:0032324 131567 cellular organisms no rank 3897 NCBI Protein Cluster (PRK) putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein molybdopterin biosynthesis protein NF011071.0 PRK14501 PRK14501.1 634 634 729 equivalog Y Y N bifunctional alpha,alpha-trehalose-phosphate synthase (UDP-forming)/trehalose-phosphatase GO:0003824,GO:0005992 131567 cellular organisms no rank 3632 NCBI Protein Cluster (PRK) putative bifunctional trehalose-6-phosphate synthase/HAD hydrolase subfamily IIB bifunctional alpha,alpha-trehalose-phosphate synthase (UDP-forming)/trehalose-phosphatase NF011079.0 PRK14508 PRK14508.1-2 555 555 506 subfamily Y Y N 4-alpha-glucanotransferase 2.4.1.25 131567 cellular organisms no rank 2613 NCBI Protein Cluster (PRK) 4-alpha-glucanotransferase 4-alpha-glucanotransferase NF011080.0 PRK14508 PRK14508.1-3 477 477 496 subfamily Y Y N 4-alpha-glucanotransferase 2.4.1.25 131567 cellular organisms no rank 14551 NCBI Protein Cluster (PRK) 4-alpha-glucanotransferase 4-alpha-glucanotransferase NF011099.0 PRK14526 PRK14526.1 223 223 211 equivalog Y N N adenylate kinase 131567 cellular organisms no rank 182 NCBI Protein Cluster (PRK) adenylate kinase adenylate kinase NF011100.0 PRK14527 PRK14527.1 154 154 191 equivalog Y Y N adenylate kinase 2.7.4.3 131567 cellular organisms no rank 45435 NCBI Protein Cluster (PRK) adenylate kinase adenylate kinase NF011101.0 PRK14528 PRK14528.1 195 195 187 equivalog Y Y N adenylate kinase 2.7.4.3 131567 cellular organisms no rank 8031 NCBI Protein Cluster (PRK) adenylate kinase adenylate kinase NF011105.0 PRK14532 PRK14532.1 162 162 189 equivalog Y Y N adenylate kinase 2.7.4.3 131567 cellular organisms no rank 21431 NCBI Protein Cluster (PRK) adenylate kinase adenylate kinase NF011118.0 PRK14548 PRK14548.1 82 82 84 equivalog Y Y N 50S ribosomal protein L23 131567 cellular organisms no rank 1049 NCBI Protein Cluster (PRK) 50S ribosomal protein L23P 50S ribosomal protein L23 Binds third domain of 23S rRNA and protein L29; part of exit tunnel NF011201.0 PRK14607 PRK14607.1 670 670 534 equivalog Y Y N bifunctional anthranilate synthase component II/anthranilate phosphoribosyltransferase 2.4.2.18,4.1.3.27 131567 cellular organisms no rank 625 NCBI Protein Cluster (PRK) bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase bifunctional anthranilate synthase component II/anthranilate phosphoribosyltransferase Bifunctional anthranilate synthase II/anthranilate phosphoribosyltransferase; TrpD; forms a heterotetramer with Trp E and the complex catalyzes the formation of anthranilate from chorismate and glutamine; also catalyzes the formation of N-(5-phospho-D-ribosyl)-anthranilate from athranilate and 5-phospho-alpha-D-ribose 1-diphosphate; functions in tryptophan biosynthesis NF011314.0 PRK14725 PRK14725.1 642 642 614 equivalog Y Y N pyruvate kinase 131567 cellular organisms no rank 1707 NCBI Protein Cluster (PRK) pyruvate kinase pyruvate kinase NF011430.0 PRK14861 PRK14861.1 62 62 61 subfamily Y N N twin arginine translocase protein A 131567 cellular organisms no rank 9799 NCBI Protein Cluster (PRK) twin arginine translocase protein A twin arginine translocase protein A NF011442.0 PRK14869 PRK14869.1-4 400 400 543 equivalog Y Y N putative manganese-dependent inorganic diphosphatase 3.6.1.1 131567 cellular organisms no rank 3559 NCBI Protein Cluster (PRK) putative manganese-dependent inorganic pyrophosphatase putative manganese-dependent inorganic diphosphatase NF011443.0 PRK14869 PRK14869.1-5 335 335 546 equivalog Y Y N putative manganese-dependent inorganic diphosphatase 3.6.1.1 GO:0016462 131567 cellular organisms no rank 4648 NCBI Protein Cluster (PRK) putative manganese-dependent inorganic pyrophosphatase putative manganese-dependent inorganic diphosphatase NF011456.0 PRK14874 PRK14874.1 223 223 346 equivalog Y Y N aspartate-semialdehyde dehydrogenase 1.2.1.11 GO:0004073,GO:0008652,GO:0016620,GO:0051287 12071715,12493825,15288787,7910936,8100567,8934665,8936306 131567 cellular organisms no rank 63566 NCBI Protein Cluster (PRK) aspartate-semialdehyde dehydrogenase aspartate-semialdehyde dehydrogenase Catalyzes the formation of aspartate semialdehyde from aspartyl phosphate NF011465.1 PRK14886 PRK14886.1-1 40 40 162 equivalog Y Y N KEOPS complex subunit Cgi121 cgi121 131567 cellular organisms no rank 1332 NCBI Protein Cluster (PRK) KEOPS complex Cgi121-like subunit KEOPS complex subunit Cgi121 NF011501.0 PRK14939 PRK14939.1 796 796 803 subfamily Y Y N DNA gyrase subunit B 131567 cellular organisms no rank 62733 NCBI Protein Cluster (PRK) DNA gyrase subunit B DNA gyrase subunit B Negatively supercoils closed circular double-stranded DNA NF011539.0 PRK14975 PRK14975.1-3 640 640 628 equivalog Y Y N bifunctional 3'-5' exonuclease/DNA polymerase 131567 cellular organisms no rank 195 NCBI Protein Cluster (PRK) bifunctional 3'-5' exonuclease/DNA polymerase bifunctional 3'-5' exonuclease/DNA polymerase NF011635.0 PRK15061 PRK15061.1 981 981 725 subfamily Y Y N catalase/peroxidase 1.11.1.21 131567 cellular organisms no rank 50760 NCBI Protein Cluster (PRK) catalase/hydroperoxidase HPI(I) catalase/peroxidase NF011645.0 PRK15063 PRK15063.1 562 562 430 equivalog Y Y N isocitrate lyase aceA 4.1.3.1 GO:0004451,GO:0019752 131567 cellular organisms no rank 21746 NCBI Protein Cluster (PRK) isocitrate lyase isocitrate lyase Catalyzes the reversible formation of glyoxylate and succinate from isocitrate; glyoxylate bypass pathway NF011648.0 PRK15066 PRK15066.1 225 225 257 subfamily Y Y N ABC transporter permease GO:0055085 131567 cellular organisms no rank 17019 NCBI Protein Cluster (PRK) inner membrane transport permease ABC transporter permease NF011657.0 PRK15076 PRK15076.1 486 486 432 subfamily Y Y N alpha-galactosidase melA 3.2.1.22 131567 cellular organisms no rank 13808 NCBI Protein Cluster (PRK) alpha-galactosidase alpha-galactosidase Catalyzes the hydrolysis of terminal non-reducing alpha-D-galactose residues in alpha-D-galactosides NF011936.0 PRK15407 PRK15407.1 423 423 440 equivalog Y Y N lipopolysaccharide biosynthesis protein RfbH rfbH GO:0003824 131567 cellular organisms no rank 6258 NCBI Protein Cluster (PRK) lipopolysaccharide biosynthesis protein RfbH lipopolysaccharide biosynthesis protein RfbH NF011975.0 PRK15443 PRK15443.2-2 196 196 139 subfamily Y Y N diol dehydratase small subunit 131567 cellular organisms no rank 143 NCBI Protein Cluster (PRK) propanediol dehydratase small subunit diol dehydratase small subunit NF011984.0 PRK15446 PRK15446.1-5 260 260 379 equivalog Y Y N alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase 3.6.1.63 GO:0016810,GO:0019700 131567 cellular organisms no rank 16362 NCBI Protein Cluster (PRK) phosphonate metabolism protein PhnM alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase NF011987.0 PRK15446 PRK15446.2-3 253 253 395 subfamily Y Y N alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase 3.6.1.63 131567 cellular organisms no rank 15745 NCBI Protein Cluster (PRK) phosphonate metabolism protein PhnM alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase NF011990.0 PRK15446 PRK15446.2-6 233 233 390 subfamily Y Y N alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase 3.6.1.63 131567 cellular organisms no rank 17738 NCBI Protein Cluster (PRK) phosphonate metabolism protein PhnM alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase NF012200.0 choice_anch_D 45 25 108 domain Y Y N choice-of-anchor D domain-containing protein 131567 cellular organisms no rank 10360 NCBIFAM choice-of-anchor D domain choice-of-anchor D domain This HMM describes a repeat domain just over 100 amino acids long and usually found in tandem copies. Members appear to be extracellular proteins that have some C-terminal anchoring domain, such as type IX secrection (T9SS) or PEP-CTERM. NF012211.1 tand_rpt_95 90 30 98 domain Y Y N tandem-95 repeat protein 131567 cellular organisms no rank 39584 NCBIFAM tandem-95 repeat protein tandem-95 repeat This 95-amino acid repeat occurs in tandem in proteins that may be several thousand amino acids long. NF012234.5 PF00004.34 AAA 21.2 21.2 131 domain Y Y N AAA family ATPase GO:0005524,GO:0016887 7646486,9927482 131567 cellular organisms no rank 1395785 EBI-EMBL ATPase family associated with various cellular activities (AAA) AAA family ATPase AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2]. [1]. 7646486. A 200-amino acid ATPase module in search of a basic function. Confalonieri F, Duguet M;. Bioessays 1995;17:639-650. A large extension of the family. [2]. 9927482. AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Neuwald AF, Aravind L, Spouge JL, Koonin EV;. Genome Res 1999;9:27-43. (from Pfam) NF012235.5 PF00005.32 ABC_tran 25 25 137 domain Y Y N ATP-binding cassette domain-containing protein GO:0005524 1864505,1977073,2229036,9872322 131567 cellular organisms no rank 6293178 EBI-EMBL ABC transporter ATP-binding cassette domain-containing protein ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain Pfam:PF00664. These four domains may belong to a single polypeptide as in Swiss:P13569, or belong in different polypeptide chains. [1]. 1864505. Homology between proteins controlling Streptomyces fradiae tylosin resistance and ATP-binding transport. Rosteck PR Jr, Reynolds PA, Hershberger CL;. Gene 1991;102:27-32. [2]. 1977073. Structure and function of haemolysin B,P-glycoprotein and other members of a novel family of membrane translocators. Blight MA, Holland IB;. Mol Microbiol 1990;4:873-880. [3]. 2229036. Binding protein-dependent transport systems. Higgins CF, Hyde SC, Mimmack MM, Gileadi U, Gill DR, Gallagher MP;. J Bioenerg Biomembr 1990;22:571-592. [4]. 9872322. Crystal structure of the ATP-binding subunit of an ABC transporter. Hung LW, Wang IX, Nikaido K, Liu PQ, Ames GF, Kim SH;. Nature 1998;396:703-707. (from Pfam) NF012236.5 PF00006.30 ATP-synt_ab 29.5 29.5 213 domain Y N N ATP synthase alpha/beta family, nucleotide-binding domain GO:0005524 8065448,9261073 131567 cellular organisms no rank 224989 EBI-EMBL ATP synthase alpha/beta family, nucleotide-binding domain ATP synthase alpha/beta family, nucleotide-binding domain This entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho. [1]. 8065448. Structure at 2.8 A resolution of F1-ATPase from bovine heart mitochondria. Abrahams JP, Leslie AG, Lutter R, Walker JE;. Nature 1994;370:621-628. [2]. 9261073. The crystal structure of the nucleotide-free alpha 3 beta 3 subcomplex of F1-ATPase from the thermophilic Bacillus PS3 is a symmetric trimer. Shirakihara Y, Leslie AG, Abrahams JP, Walker JE, Ueda T, Sekimoto Y, Kambara M, Saika K, Kagawa Y, Yoshida M;. Structure 1997;5:825-836. (from Pfam) NF012239.5 PF00009.32 GTP_EFTU 26.5 26.5 188 domain Y Y N GTP-binding protein GO:0003924,GO:0005525 9311785 131567 cellular organisms no rank 658827 EBI-EMBL Elongation factor Tu GTP binding domain elongation factor Tu-like GTP-binding domain This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains. Cryoelectron microscopy structure. [1]. 9311785. Visualization of elongation factor Tu on the Escherichia coli ribosome. Stark H, Rodnina MV, Rinke-Appel J, Brimacombe R, Wintermeyer W, van Heel M;. Nature 1997;389:403-406. (from Pfam) NF012240.5 PF00010.31 HLH 20.7 20.7 53 domain Y Y N helix-loop-helix domain-containing protein GO:0046983 7553065 131567 cellular organisms no rank 45 EBI-EMBL Helix-loop-helix DNA-binding domain Helix-loop-helix DNA-binding domain NF012241.5 PF00011.26 HSP20 20.8 20.8 102 domain Y Y N Hsp20 family protein 24265841,9707123 131567 cellular organisms no rank 96256 EBI-EMBL Hsp20/alpha crystallin family Hsp20 family protein Not only do small heat-shock-proteins occur in eukaryotes and prokaryotes but they have also now been shown to occur in cyanobacterial phages as well as their bacterial hosts [2]. [1]. 9707123. Crystal structure of a small heat-shock protein. Kim KK, Kim R, Kim SH. Nature 1998;394:595-599. [2]. 24265841. Analysis and phylogeny of small heat shock proteins from marine viruses and their cyanobacteria host. Maaroufi H, Tanguay RM;. PLoS One. 2013;8:e81207. (from Pfam) NF012242.5 PF00012.25 HSP70 20.6 20.6 599 domain Y Y N Hsp70 family protein GO:0005524,GO:0140662 9476895 131567 cellular organisms no rank 216686 EBI-EMBL Hsp70 protein Hsp70 family protein Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region. [1]. 9476895. The Hsp70 and Hsp60 chaperone machines. Bukau B, Horwich AL;. Cell 1998;92:351-366. (from Pfam) NF012243.5 PF00013.34 KH_1 21.5 21.5 66 domain Y Y N KH domain-containing protein GO:0003723 8036511,8612276 131567 cellular organisms no rank 93836 EBI-EMBL KH domain KH domain KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. [1]. 8036511. Conserved structures and diversity of functions of RNA-binding proteins. Burd CG, Dreyfuss G;. Science 1994;265:615-621. [2]. 8612276. Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome. Musco G, Stier G, Joseph C, Castiglione Morelli MA, Nilges M, Gibson TJ, Pastore A;. Cell 1996;85:237-245. (from Pfam) NF012244.5 PF00014.28 Kunitz_BPTI 21 21 53 domain Y Y N BPTI/Kunitz-type proteinase inhibitor domain-containing protein GO:0004867 10716178,7925983 131567 cellular organisms no rank 249 EBI-EMBL Kunitz/Bovine pancreatic trypsin inhibitor domain BPTI/Kunitz-type proteinase inhibitor domain Indicative of a protease inhibitor, usually a serine protease inhibitor. Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure. Certain family members are similar to the tick anticoagulant peptide (TAP, Swiss:P17726). This is a highly selective inhibitor of factor Xa in the blood coagulation pathways [1]. TAP molecules are highly dipolar [2], and are arranged to form a twisted two- stranded antiparallel beta-sheet followed by an alpha helix [1]. [1]. 7925983. NMR solution structure of the recombinant tick anticoagulant protein (rTAP), a factor Xa inhibitor from the tick Ornithodoros moubata. Antuch W, Guntert P, Billeter M, Hawthorne T, Grossenbacher H, Wuthrich K;. FEBS Lett 1994;352:251-257. [2]. 10716178. Structure of tick anticoagulant peptide at 1.6 A resolution complexed with bovine pancreatic trypsin inhibitor. St Charles R, Padmanabhan K, Arni RV, Padmanabhan KP, Tulinsky A;. Protein Sci 2000;9:265-272. (from Pfam) NF012245.5 PF00015.26 MCPsignal 34.6 34.6 172 domain Y Y N methyl-accepting chemotaxis protein GO:0007165,GO:0016020 1601874 131567 cellular organisms no rank 770442 EBI-EMBL Methyl-accepting chemotaxis protein (MCP) signalling domain methyl-accepting chemotaxis protein signalling domain This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs. [1]. 1601874. Sequence and characterization of Bacillus subtilis CheW. Hanlon DW, Marquez-Magana LM, Carpenter PB, Chamberlin MJ, Ordal GW;. J Biol Chem 1992;267:12055-12060. (from Pfam) NF012246.5 PF00016.25 RuBisCO_large 30.1 30.1 299 domain Y Y N RuBisCO large subunit C-terminal-like domain-containing protein GO:0000287,GO:0016984 9034362 131567 cellular organisms no rank 15796 EBI-EMBL Ribulose bisphosphate carboxylase large chain, catalytic domain RuBisCO large subunit C-terminal-like domain Most proteins in this family are the ribulose-bisphosphate carboxylase (EC 4.1.1.39) large subunit, but the family also includes 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (EC 5.3.2.5). NF012252.5 PF00022.24 Actin 27 27 410 domain Y N N Actin 8413665,8548558 131567 cellular organisms no rank 22664 EBI-EMBL Actin Actin NF012253.5 PF00023.35 Ank 21.1 14.7 33 repeat Y N N ankyrin repeat protein GO:0005515 12456646,14731966,2141669 131567 cellular organisms no rank 135330 EBI-EMBL Ankyrin repeat ankyrin repeat Ankyrins are multifunctional adaptors that link specific proteins to the membrane-associated, spectrin- actin cytoskeleton. This repeat-domain is a 'membrane-binding' domain of up to 24 repeated units, and it mediates most of the protein's binding activities. Repeats 13-24 are especially active, with known sites of interaction for the Na/K ATPase, Cl/HCO(3) anion exchanger, voltage-gated sodium channel, clathrin heavy chain and L1 family cell adhesion molecules. The ANK repeats are found to form a contiguous spiral stack such that ion transporters like the anion exchanger associate in a large central cavity formed by the ANK repeat spiral, while clathrin and cell adhesion molecules associate with specific regions outside this cavity [2][3]. [1]. 2141669. Hereditary spherocytosis associated with deletion of human erythrocyte ankyrin gene on chromosome 8. Lux SE, John KM, Bennett V;. Nature 1990;345:736-739. [2]. 12456646. Crystal structure of a 12 ANK repeat stack from human ankyrinR. Michaely P, Tomchick DR, Machius M, Anderson RG;. EMBO J. 2002;21:6387-6396. [3]. 14731966. The ANK repeat: a ubiquitous motif involved in macromolecular recognition. Michaely P, Bennett V;. Trends Cell Biol. 1992;2:127-129. (from Pfam) NF012254.5 PF00024.31 PAN_1 21.4 21.4 76 domain Y Y N PAN domain-containing protein 10561497 131567 cellular organisms no rank 5695 EBI-EMBL PAN domain PAN domain The PAN domain [1] contains a conserved core of three disulphide bridges. In some members of the family there is an additional fourth disulphide bridge the links the N and C termini of the domain. The domain is found in diverse proteins, in some they mediate protein-protein interactions, in others they mediate protein-carbohydrate interactions. [1]. 10561497. The PAN module: the N-terminal domains of plasminogen and hepatocyte growth factor are homologous with the apple domains of the prekallikrein family and with a novel domain found in numerous nematode proteins. Tordai H, Banyai L, Patthy L;. FEBS Lett 1999;461:63-67. (from Pfam) NF012255.5 PF00025.26 Arf 22.3 22.3 174 domain Y Y N ADP-ribosylation factor-like protein GO:0003924,GO:0005525 1899243,7759471,7770914,7990966 131567 cellular organisms no rank 43461 EBI-EMBL ADP-ribosylation factor family ADP-ribosylation factor family Pfam combines a number of different Prosite families together 3D Structure reference. [1]. 7990966. Structure of the human ADP-ribosylation factor 1 complexed with GDP. Amor JC, Harrison DH, Kahn RA, Ringe D;. Nature 1994;372:704-708. Mini review. [2]. 7759471. Structure and function of ARF proteins: Activators of cholera toxin and critical components of intracellular vesicular transport processes. Moss J, Vaughan M;. J. Biol. Chem. 1995;270:12327-12330. [3]. 7770914. Arf proteins: the membrane traffic police?. Boman AL, Kahn RA;. Trends Biochem Sci 1995;20:147-150. [4]. 1899243. Human ADP-ribosylation factors. A functionally conserved family of GTP-binding proteins. Kahn RA, Kern FG, Clark J, Gelmann EP, Rulka C;. J Biol Chem 1991;266:2606-2614. (from Pfam) NF012257.5 PF00027.34 cNMP_binding 27.5 27.5 89 domain Y Y N cyclic nucleotide-binding domain-containing protein 7513422 131567 cellular organisms no rank 368112 EBI-EMBL Cyclic nucleotide-binding domain Cyclic nucleotide-binding domain This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 7513422. Cyclic nucleotide-gated channels: an expanding new family of ion channels. Yau KW;. Proc Natl Acad Sci USA 1994;91:3481-3483. (from Pfam) NF012258.5 PF00028.22 Cadherin 28.8 28.8 93 domain Y Y N cadherin domain-containing protein GO:0005509,GO:0007156,GO:0016020 131567 cellular organisms no rank 9828 EBI-EMBL Cadherin domain cadherin domain NF012260.5 PF00030.24 Crystall 25 25 82 domain Y Y N beta/gamma crystallin-related protein 131567 cellular organisms no rank 3133 EBI-EMBL Beta/Gamma crystallin beta/gamma crystallin-related protein The alignment comprises two Greek key motifs since the similarity between them is very low. (from Pfam) NF012262.5 PF00032.22 Cytochrom_B_C 20.7 18.9 102 PfamEq Y N N Cytochrome b(C-terminal)/b6/petD GO:0009055,GO:0016020,GO:0016491 9565029 131567 cellular organisms no rank 24237 EBI-EMBL Cytochrome b(C-terminal)/b6/petD Cytochrome b(C-terminal)/b6/petD NF012263.5 PF00033.24 Cytochrome_B 27.2 27.2 189 domain Y N N Cytochrome b/b6/petB GO:0009055,GO:0016020,GO:0016491 131567 cellular organisms no rank 46619 EBI-EMBL Cytochrome b/b6/petB Cytochrome b/b6/petB NF012264.5 PF00034.26 Cytochrom_C 21.3 21.3 90 domain Y Y N c-type cytochrome GO:0009055,GO:0020037 131567 cellular organisms no rank 370375 EBI-EMBL Cytochrome c c-type cytochrome The Pfam entry does not include all Prosite members. The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, Pfam:PF06181, has now been merged into this family. (from Pfam) NF012265.5 PF00035.31 dsrm 23 21 66 domain Y Y N putative dsRNA-binding protein 8036511 131567 cellular organisms no rank 55901 EBI-EMBL Double-stranded RNA binding motif double-stranded RNA binding motif Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localisation of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA. [1]. 8036511. Conserved structures and diversity of functions of RNA-binding proteins. Burd CG, Dreyfuss G;. Science 1994;265:615-621. (from Pfam) NF012266.5 PF00036.37 EF-hand_1 25.4 25.4 29 repeat Y N N EF-hand domain-containing protein GO:0005509 1602495,1618836,2401372,7743133 131567 cellular organisms no rank 8281 EBI-EMBL EF hand EF hand The EF-hands can be divided into two classes: signalling proteins and buffering/transport proteins. The first group is the largest and includes the most well-known members of the family such as calmodulin, troponin C and S100B. These proteins typically undergo a calcium-dependent conformational change which opens a target binding site. The latter group is represented by calbindin D9k and do not undergo calcium dependent conformational changes. [1]. 1602495. Evolution of EF-hand calcium-modulated proteins. II. Domains of several subfamilies have diverse evolutionary histories. Nakayama S, Moncrief ND, Kretsinger RH;. J Mol Evol 1992;34:416-448. [2]. 1618836. Comparison of terbium (III) luminescence enhancement in mutants of EF hand calcium binding proteins. Hogue CW, MacManus JP, Banville D, Szabo AG;. J Biol Chem 1992;267:13340-13347. [3]. 2401372. EF-hand motifs in inositol phospholipid-specific phospholipase C. Bairoch A, Cox JA;. FEBS Lett 1990;269:454-456. [4]. 7743133. The evolving model of calmodulin structure, function and activation. Finn BE, Forsen S;. Structure 1995;3:7-11. (from Pfam) NF012267.5 PF00037.32 Fer4 21.1 21.1 24 domain Y Y N 4Fe-4S binding protein 131567 cellular organisms no rank 504106 EBI-EMBL 4Fe-4S binding domain 4Fe-4S binding domain Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. (from Pfam) NF012271.5 PF00041.26 fn3 25 25 84 domain Y Y N fibronectin type III domain-containing protein GO:0005515 2169613,2992939,7528812 131567 cellular organisms no rank 143907 EBI-EMBL Fibronectin type III domain Fibronectin type III domain NF012272.5 PF00042.27 Globin 22 22 117 domain Y Y N globin domain-containing protein GO:0020037 2448639,3656444,6292840,9108146 131567 cellular organisms no rank 60028 EBI-EMBL Globin globin domain NF012273.5 PF00043.30 GST_C 20.7 20.7 93 domain Y Y N glutathione binding-like protein 11897031,9680481 131567 cellular organisms no rank 259087 EBI-EMBL Glutathione S-transferase, C-terminal domain glutathione S-transferase-like protein C-terminal domain Members of this family include glutathione S-transferases, glutathione-dependent disulfide bond oxidoreductases, and some proteins not known to interact with glutathione, although most of the latter set score only a little above cutoffs for the model. NF012274.5 PF00044.29 Gp_dh_N 31.7 31.7 101 domain Y Y N glyceraldehyde 3-phosphate dehydrogenase NAD-binding domain-containing protein GO:0051287 7578111 131567 cellular organisms no rank 112265 EBI-EMBL Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. N-terminal domain is a Rossmann NAD(P) binding fold. [1]. 7578111. Crystal structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Leishmania mexicana: implications for structure-based drug design and a new position for the inorganic phosphate binding site. Kim H, Feil IK, Verlinde CL, Petra PH, Hol WG;. Biochemistry 1995;34:14975-14986. (from Pfam) NF012275.5 PF00045.24 Hemopexin 21.3 21.3 45 domain Y Y N hemopexin repeat-containing protein 8969305 131567 cellular organisms no rank 1601 EBI-EMBL Hemopexin hemopexin repeat Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metallopeptidases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metallopeptidases (TIMPs). [1]. 8969305. The helping hand of collagenase-3 (MMP-13): 2.7 A crystal structure of its C-terminal haemopexin-like domain. Gomis-Ruth FX, Gohlke U, Betz M, Knauper V, Murphy G, Lopez-Otin C, Bode W. J Mol Biol 1996;264:556-566. (from Pfam) NF012277.5 PF00047.30 ig 21.8 21.8 81 domain Y N N Immunoglobulin domain 3289571,7932691,8574878 131567 cellular organisms no rank 640 EBI-EMBL Immunoglobulin domain Immunoglobulin domain Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions. [1]. 8574878. Cell adhesion molecules 1: immunoglobulin superfamily. Bruemmendorf T, Rathjen FG;. Protein Profile 1995;2:963-1085. [2]. 7932691. The immunoglobulin fold. Bork P, Holm L, Sander C;. J Mol Biol 1994;242:309-320. [3]. 3289571. The immunoglobulin superfamily--domains for cell surface recognition. Williams AF, Barclay AN;. Annu Rev Immunol 1988;6:381-405. (from Pfam) NF012280.5 PF00050.26 Kazal_1 21 21 49 domain Y N N Kazal-type serine protease inhibitor domain GO:0005515 131567 cellular organisms no rank 1977 EBI-EMBL Kazal-type serine protease inhibitor domain Kazal-type serine protease inhibitor domain Usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors. Kazal domains often occur in tandem arrays. Small alpha+beta fold containing three disulphides. Alignment also includes a single domain from transporters in the OATP/PGT family Swiss:P46721. (from Pfam) NF012282.5 PF00052.23 Laminin_B 22.4 22.4 136 domain Y Y N laminin B domain-containing protein 1975589 131567 cellular organisms no rank 260 EBI-EMBL Laminin B (Domain IV) Laminin B (Domain IV) NF012284.5 PF00054.29 Laminin_G_1 24 24 131 domain Y N N Laminin G domain 1975589,9480764 131567 cellular organisms no rank 1897 EBI-EMBL Laminin G domain Laminin G domain NF012286.5 PF00056.28 Ldh_1_N 27 27 141 domain Y Y N lactate/malate family dehydrogenase GO:0016491 10075524,12029364 131567 cellular organisms no rank 73309 EBI-EMBL lactate/malate dehydrogenase, NAD binding domain lactate/malate family dehydrogenase, NAD binding domain L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. N-terminus (this family) is a Rossmann NAD-binding fold. C-terminus is an unusual alpha+beta fold. [1]. 10075524. Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD. Chapman AD, Cortes A, Dafforn TR, Clarke AR, Brady RL;. J Mol Biol 1999;285:703-712. [2]. 12029364. Molecular evolution within the L-malate and L-lactate dehydrogenase super-family. Madern D;. J Mol Evol 2002;54:825-840. (from Pfam) NF012289.5 PF00059.26 Lectin_C 22.6 22.6 107 domain Y Y N lectin-like protein 10368295 131567 cellular organisms no rank 2509 EBI-EMBL Lectin C-type domain Lectin C-type domain This family includes both long and short form C-type [1]. 10368295. Crystal structure of the trimeric alpha-helical coiled-coil and the three lectin domains of human lung surfactant protein D. Hakansson K, Lim NK, Hoppe HJ, Reid KB;. Structure Fold Des 1999;7:255-264. (from Pfam) NF012290.5 PF00060.31 Lig_chan 30.8 30.8 146 PfamEq Y N N Ligand-gated ion channel GO:0015276,GO:0016020 7878472 131567 cellular organisms no rank 3204 EBI-EMBL Ligand-gated ion channel Ligand-gated ion channel This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors. [1]. 7878472. Synaptic desensitization of NMDA receptors by calcineurin. Tong G, Shepherd D, Jahr CE;. Science 1995;267:1510-1512. (from Pfam) NF012296.5 PF00067.27 p450 22.8 22.8 462 subfamily Y Y N cytochrome P450 GO:0004497,GO:0005506,GO:0016705,GO:0020037 11178272,2037557,3304150,7549871,7678494,8405421 131567 cellular organisms no rank 403775 EBI-EMBL Cytochrome P450 cytochrome P450 Cytochrome P450s are haem-thiolate proteins [6] involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyse regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures [6]. [1]. 7549871. A three-dimensional model of aromatase cytochrome P450. Graham-Lorence S, Amarneh B, White RE, Peterson JA, Simpson ER;. Protein Sci 1995;4:1065-1080. [2]. 8405421. Molecular evolution of P450 superfamily and P450-containing monooxygenase systems. Degtyarenko KN, Archakov AI;. FEBS Lett 1993;332:1-8. [3]. 7678494. The P450 superfamily: update on new sequences, gene mapping, accession numbers, early trivial names of enzymes, and nomenclature. Nelson DR, Kamataki T, Waxman DJ, Guengerich FP, Estabrook RW, Fe. TRUNCATED at 1650 bytes (from Pfam) NF012298.5 PF00069.30 Pkinase 31.7 31.7 263 domain Y Y N protein kinase domain-containing protein GO:0004672,GO:0005524,GO:0006468 1956325,7768349,9020587 131567 cellular organisms no rank 680993 EBI-EMBL Protein kinase domain protein kinase domain NF012299.5 PF00070.32 Pyr_redox 22 22 82 domain Y Y N NAD-binding protein 8805537 131567 cellular organisms no rank 1051550 EBI-EMBL Pyridine nucleotide-disulphide oxidoreductase NAD-binding protein This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain. [1]. 8805537. Protein-protein interactions in the pyruvate dehydrogenase multienzyme complex: dihydrolipoamide dehydrogenase complexed with the binding domain of dihydrolipoamide acetyltransferase. Mande SS, Sarfaty S, Allen MD, Perham RN, Hol WG;. Structure 1996;4:277-286. (from Pfam) NF012300.5 PF00071.27 Ras 21.6 21.6 162 domain Y N N Ras family GO:0003924,GO:0005525 11387043 131567 cellular organisms no rank 101963 EBI-EMBL Ras family Ras family Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1]. [1]. 11387043. The Rab GTPase family. Stenmark H, Olkkonen VM;. Genome Biol 2001;2:REVIEWS3007. (from Pfam) NF012301.5 PF00072.29 Response_reg 30.2 30.2 111 domain Y Y N response regulator GO:0000160 7699720 131567 cellular organisms no rank 3168479 EBI-EMBL Response regulator receiver domain response regulator receiver domain This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain. [1]. 7699720. Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution. Pao GM, Saier MH;. J Mol Evol 1995;40:136-154. (from Pfam) NF012304.5 PF00075.29 RNase_H 25.8 25.8 141 domain Y Y N RNase H family protein GO:0003676,GO:0004523 131567 cellular organisms no rank 81058 EBI-EMBL RNase H RNase H family protein RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. (from Pfam) NF012305.5 PF00076.27 RRM_1 20.7 20.7 70 domain Y N N RNA recognition motif GO:0003676,GO:0003723 8290338 131567 cellular organisms no rank 17643 EBI-EMBL RNA recognition motif RNA recognition motif The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. [1]. 8290338. Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Birney E., Kumar S., Krainer A.R. Nucleic Acid Res 1993;21:5803-5816. (from Pfam) NF012306.5 PF00077.25 RVP 20.7 20.7 101 domain Y N N Retroviral aspartyl protease 131567 cellular organisms no rank 4646 EBI-EMBL Retroviral aspartyl protease Retroviral aspartyl protease Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (Pfam:PF00026). (from Pfam) NF012307.5 PF00078.32 RVT_1 29.6 29.6 205 domain Y Y N reverse transcriptase domain-containing protein 1698615 131567 cellular organisms no rank 117667 EBI-EMBL Reverse transcriptase (RNA-dependent DNA polymerase) Reverse transcriptase (RNA-dependent DNA polymerase) A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. [1]. 1698615. Origin and evolution of retroelements based upon their reverse transcriptase sequences. Xiong Y, Eickbush TH;. EMBO J 1990;9:3353-3362. (from Pfam) NF012308.5 PF00079.25 Serpin 27 27 370 domain Y Y N serpin family protein 8787534 131567 cellular organisms no rank 15456 EBI-EMBL Serpin (serine protease inhibitor) serpin family protein Structure is a multi-domain fold containing a bundle of helices and a beta sandwich. [1]. 8787534. The structural puzzle of how serpin serine proteinase inhibitors work. Wright HT;. Bioessays 1996;18:453-464. (from Pfam) NF012309.5 PF00080.25 Sod_Cu 28.9 28.9 133 domain Y Y N superoxide dismutase family protein GO:0006801,GO:0046872 131567 cellular organisms no rank 28280 EBI-EMBL Copper/zinc superoxide dismutase (SODC) superoxide dismutase family protein superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene cause familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Structure is an eight-stranded beta sandwich, similar to the immunoglobulin fold. (from Pfam) NF012310.5 PF00081.27 Sod_Fe_N 27 27 82 domain Y N N Iron/manganese superoxide dismutases, alpha-hairpin domain GO:0004784,GO:0006801,GO:0046872 9878438 131567 cellular organisms no rank 65204 EBI-EMBL Iron/manganese superoxide dismutases, alpha-hairpin domain Iron/manganese superoxide dismutases, alpha-hairpin domain superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. N-terminal domain is a long alpha antiparallel hairpin. A small fragment of YTRE_LEPBI matches well - sequencing error? [1]. 9878438. Refined crystal structure of a superoxide dismutase from the hyperthermophilic archaeon Sulfolobus acidocaldarius at 2.2 A resolution. Knapp S, Kardinahl S, Hellgren N, Tibbelin G, Schafer G, Ladenstein R;. J Mol Biol 1999;285:689-702. (from Pfam) NF012311.5 PF00082.27 Peptidase_S8 21.8 21.8 288 domain Y Y N S8 family serine peptidase GO:0006508,GO:0008236 131567 cellular organisms no rank 381015 EBI-EMBL Subtilase family S8 family serine peptidase Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see Pfam:PF00089). Structure is an alpha/beta fold containing a 7-stranded parallel beta sheet, order 2314567. (from Pfam) NF012312.5 PF00083.29 Sugar_tr 22.3 22.3 452 domain Y Y N MFS transporter GO:0016020,GO:0022857,GO:0055085 131567 cellular organisms no rank 1507127 EBI-EMBL Sugar (and other) transporter MFS transporter NF012314.5 PF00085.25 Thioredoxin 23.5 23.5 103 domain Y Y N thioredoxin domain-containing protein 131567 cellular organisms no rank 378803 EBI-EMBL Thioredoxin Thioredoxin Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise. (from Pfam) NF012318.5 PF00089.31 Trypsin 20.6 20.6 220 domain Y Y N trypsin-like serine protease 3.4.21.- GO:0004252,GO:0006508 3112942,7845208 131567 cellular organisms no rank 352881 EBI-EMBL Trypsin trypsin-like serine protease NF012320.5 PF00091.30 Tubulin 33 33 190 domain Y N N Tubulin/FtsZ family, GTPase domain GO:0003924,GO:0005525 9144213,9428769,9428770,9628483 131567 cellular organisms no rank 61538 EBI-EMBL Tubulin/FtsZ family, GTPase domain Tubulin/FtsZ family, GTPase domain This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ and tubulin are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules. [1]. 9428769. Structure of the alphabeta tubulin dimer by electron crystallography. Nogales E, Wolf SG, Downing KH;. Nature 1998;391:199-203. [2]. 9628483. Tubulin and FtsZ form a distinct family of GTPases. Nogales E, Downing KH, Amos LA, Lowe J;. Nat Struct Biol 1998;5:451-458. [3]. 9428770. Crystal structure of the bacterial cell-division protein FtsZ [see comments]. Lowe J, Amos LA;. Nature 1998;391:203-206. [4]. 9144213. An essential cell division gene of Drosophila, absent from Saccharomyces, encodes an unusual protein with tubulin-like and myosin-like peptide motifs. Miklos GL, Yamamoto M, Burns RG, Maleszka R;. Proc Natl Acad Sci U S A. 1997;94:5189-5194. (from Pfam) NF012321.5 PF00092.33 VWA 23.8 23.8 174 domain Y Y N VWA domain-containing protein 1659389 131567 cellular organisms no rank 220797 EBI-EMBL von Willebrand factor type A domain von Willebrand factor type A domain NF012323.5 PF00094.30 VWD 22.9 22.9 156 domain Y Y N VWD domain-containing protein 30642920,7687569 131567 cellular organisms no rank 1315 EBI-EMBL von Willebrand factor type D domain VWD domain VWD signifies von Willebrand factor type D domain. Von Willebrand factor (vWF) is found in animals, but homologs to domain in vWF can be found elsewhere. NF012325.5 PF00096.31 zf-C2H2 25.2 15.8 23 domain Y Y N C2H2-type zinc finger protein 12683994,9171100 131567 cellular organisms no rank 1064 EBI-EMBL Zinc finger, C2H2 type C2H2-type zinc finger domain The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter [2]. [1]. 9171100. Variations of the C2H2 zinc finger motif in the yeast genome and classification of yeast zinc finger proteins. Boehm S, Frishman D, Mewes HW;. Nucleic Acids Res 1997;25:2464-2469. [2]. 12683994. Assessment by molecular dynamics simulations of the structural determinants of DNA-binding specificity for transcription factor Sp1. Marco E, Garcia-Nieto R, Gago F;. J Mol Biol 2003;328:9-32. (from Pfam) NF012330.5 PF00102.32 Y_phosphatase 20.9 20.9 234 domain Y Y N protein-tyrosine phosphatase family protein GO:0004725,GO:0006470 9491886 131567 cellular organisms no rank 16798 EBI-EMBL Protein-tyrosine phosphatase protein-tyrosine phosphatase family protein NF012334.5 PF00106.30 adh_short 26.6 25 195 subfamily Y Y N SDR family NAD(P)-dependent oxidoreductase 10387002,9735295 131567 cellular organisms no rank 2831556 EBI-EMBL short chain dehydrogenase SDR family NAD(P)-dependent oxidoreductase This family contains a wide variety of dehydrogenases. [1]. 9735295. The refined crystal structure of Drosophila lebanonensis alcohol dehydrogenase at 1.9 A resolution. Benach J, Atrian S, Gonzalez-Duarte R, Ladenstein R;. J Mol Biol 1998;282:383-399. [2]. 10387002. Structure of tropinone reductase-II complexed with NADP+ and pseudotropine at 1.9 A resolution: implication for stereospecific substrate binding and catalysis. Yamashita A, Kato H, Wakatsuki S, Tomizaki T, Nakatsu T, Nakajima K, Hashimoto T, Yamada Y, Oda J;. Biochemistry 1999;38:7630-7637. (from Pfam) NF012335.5 PF00107.31 ADH_zinc_N 31.8 31.8 129 domain Y Y N zinc-binding dehydrogenase 131567 cellular organisms no rank 1058159 EBI-EMBL Zinc-binding dehydrogenase zinc-binding dehydrogenase NF012336.5 PF00108.28 Thiolase_N 26.4 26.4 260 domain Y N N Thiolase, N-terminal domain GO:0016747 9402066 131567 cellular organisms no rank 559557 EBI-EMBL Thiolase, N-terminal domain Thiolase, N-terminal domain Thiolase is reported to be structurally related to beta-ketoacyl synthase (Pfam:PF00109), and also chalcone synthase. [1]. 9402066. The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: implications for substrate binding and reaction mechanism. Mathieu M, Modis Y, Zeelen JP, Engel CK, Abagyan RA, Ahlberg A, Rasmussen B, Lamzin VS, Kunau WH, Wierenga RK;. J Mol Biol 1997;273:714-728. (from Pfam) NF012337.5 PF00109.31 ketoacyl-synt 20.8 20.8 252 domain Y Y N beta-ketoacyl synthase N-terminal-like domain-containing protein 9482715 131567 cellular organisms no rank 693445 EBI-EMBL Beta-ketoacyl synthase, N-terminal domain beta-ketoacyl synthase N-terminal-like domain The structure of beta-ketoacyl synthase is similar to that of the thiolase family (Pfam:PF00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains. The N-terminal domain contains most of the structures involved in dimer formation and also the active site cysteine [1]. [1]. 9482715. Crystal structure of beta-ketoacyl-acyl carrier protein synthase II from E.coli reveals the molecular architecture of condensing enzymes. Huang W, Jia J, Edwards P, Dehesh K, Schneider G, Lindqvist Y;. EMBO J 1998;17:1183-1191. (from Pfam) NF012339.5 PF00111.32 Fer2 21 21 77 domain Y Y N 2Fe-2S iron-sulfur cluster-binding protein GO:0051536 131567 cellular organisms no rank 486049 EBI-EMBL 2Fe-2S iron-sulfur cluster binding domain 2Fe-2S iron-sulfur cluster-binding domain NF012340.5 PF00112.28 Peptidase_C1 20.7 20.7 220 domain Y Y N C1 family peptidase GO:0006508,GO:0008234 11440158,7548082 131567 cellular organisms no rank 23943 EBI-EMBL Papain family cysteine protease C1 family peptidase NF012341.5 PF00113.27 Enolase_C 21.5 21.5 296 domain Y N N Enolase, C-terminal TIM barrel domain 131567 cellular organisms no rank 66499 EBI-EMBL Enolase, C-terminal TIM barrel domain Enolase, C-terminal TIM barrel domain NF012343.5 PF00115.25 COX1 34.8 34.8 436 domain Y Y N cbb3-type cytochrome c oxidase subunit I GO:0004129,GO:0009060,GO:0016020,GO:0020037 31489376,8013452,8049679,8638158 131567 cellular organisms no rank 149052 EBI-EMBL Cytochrome C and Quinol oxidase polypeptide I cbb3-type cytochrome c oxidase subunit I Cytochrome c oxidase (E.C:7.1.1.9) is a key enzyme in aerobic metabolism. Proton pumping haem-copper oxidases represent the terminal, energy-transfer enzymes of respiratory chains in prokaryotes and eukaryotes. The CuB-haem a3 (or haem o) binuclear centre, associated with the largest subunit I of cytochrome c and ubiquinol oxidases (E.C:1.10.3.11), is directly involved in the coupling between dioxygen reduction and proton pumping [1,2,3,4]. Some terminal oxidases generate a transmembrane proton gradient across the plasma membrane (prokaryotes) or the mitochondrial inner membrane (eukaryotes). The enzyme complex consists of 3-4 subunits (prokaryotes) up to 13 polypeptides (mammals) of which only the catalytic subunit (equivalent to mammalian subunit I (COXI) is found in all haem-copper respiratory oxidases. The presence of a bimetallic centre (formed by a high-spin haem and copper B) as well as a low-spin haem, both ligated to six conserved histidine residues near the outer side of four transmembrane spans within CO I is common to all family members [2,3]. [1]. 8638158. The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A. Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S;. Science 1996;272:1136-1144. [2]. 8013452. Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen. Castresana J, Lubben M, Saraste M, Higgins DG;. EMBO J. 1994;13:2516-2525. [3]. 31489376. Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo-electron microscopy. Gopalasingam CC, Johnson RM, Chiduza GN, Tosha T, Yamamot. TRUNCATED at 1650 bytes (from Pfam) NF012344.5 PF00116.25 COX2 22 22 120 domain Y N N Cytochrome C oxidase subunit II, periplasmic domain GO:0004129,GO:0005507,GO:0016020 8638158 131567 cellular organisms no rank 77197 EBI-EMBL Cytochrome C oxidase subunit II, periplasmic domain Cytochrome C oxidase subunit II, periplasmic domain NF012345.5 PF00117.33 GATase 22.8 22.8 190 domain Y Y N glutamine amidotransferase-related protein 131567 cellular organisms no rank 529671 EBI-EMBL Glutamine amidotransferase class-I glutamine amidotransferase-related protein NF012346.5 PF00118.29 Cpn60_TCP1 34.3 34.3 490 domain Y Y N TCP-1/cpn60 chaperonin family protein GO:0005524 10802661,29018216 131567 cellular organisms no rank 85427 EBI-EMBL TCP-1/cpn60 chaperonin family TCP-1/cpn60 chaperonin family protein This family includes members from the HSP60 chaperone family and the TCP-1 (T-complex protein) family. (from Pfam) NF012347.5 PF00119.25 ATP-synt_A 33.9 33.9 217 PfamEq Y Y N F0F1 ATP synthase subunit A 7.1.2.2 GO:0015078,GO:0015986,GO:0045263 131567 cellular organisms no rank 51685 EBI-EMBL ATP synthase A chain F0F1 ATP synthase subunit A NF012348.5 PF00120.29 Gln-synt_C 24 24 344 domain Y N N Glutamine synthetase, catalytic domain GO:0004356,GO:0008152 131567 cellular organisms no rank 163186 EBI-EMBL Glutamine synthetase, catalytic domain Glutamine synthetase, catalytic domain NF012349.5 PF00121.23 TIM 20.1 20.1 245 domain Y Y N triose-phosphate isomerase GO:0004807 12023819,12206759,12509510,2005961,2204417 131567 cellular organisms no rank 74419 EBI-EMBL Triosephosphate isomerase triose-phosphate isomerase Triosephosphate isomerase (EC:5.3.1.1) (TIM) [1] is the glycolytic enzyme that catalyses the reversible interconversion of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. TIM plays an important role in several metabolic pathways and is essential for efficient energy production, present in eukaryotes and prokaryotes. TIM is a dimer of identical subunits, each of which is made up of about 250 amino-acid residues. A glutamic acid residue is involved in the catalytic mechanism [2,3]. The tertiary structure of TIM has eight beta/alpha motifs folded into a barrel structure [4]. The sequence around the active site residue is perfectly conserved in all known TIM's. Deficiencies in TIM are associated with haemolytic anaemia coupled with a progressive, severe neurological disorder [5]. [1]. 2204417. Structure of yeast triosephosphate isomerase at 1.9-A resolution. Lolis E, Alber T, Davenport RC, Rose D, Hartman FC, Petsko GA;. Biochemistry. 1990;29:6609-6618. [2]. 2005961. Enzyme catalysis: not different, just better. Knowles JR;. Nature. 1991;350:121-124. [3]. 12509510. Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution. Jogl G, Rozovsky S, McDermott AE, Tong L;. Proc Natl Acad Sci U S A. 2003;100:50-55. [4]. 12206759. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. Nagano N, Orengo CA, Thornton JM;. J Mol Biol. 2002;321:741-765. [5]. 12023819. Triosephosphate isomerase deficiency: a neurodegenerative misfolding disease. Olah J, Orosz F, Keseru GM, . TRUNCATED at 1650 bytes (from Pfam) NF012350.5 PF00122.25 E1-E2_ATPase 28.1 28.1 181 domain Y N N E1-E2 ATPase 131567 cellular organisms no rank 516204 EBI-EMBL E1-E2 ATPase E1-E2 ATPase NF012353.5 PF00125.29 Histone 26.4 26.4 122 domain Y N N Core histone H2A/H2B/H3/H4 GO:0003677 9305837 131567 cellular organisms no rank 1369 EBI-EMBL Core histone H2A/H2B/H3/H4 Core histone H2A/H2B/H3/H4 NF012354.5 PF00126.32 HTH_1 26.6 26.6 60 domain Y Y N LysR family transcriptional regulator GO:0003700,GO:0006355 9309218 131567 cellular organisms no rank 2146886 EBI-EMBL Bacterial regulatory helix-turn-helix protein, lysR family LysR family transcriptional regulator NF012355.5 PF00127.25 Copper-bind 21.2 21.2 99 domain Y Y N plastocyanin/azurin family copper-binding protein GO:0005507,GO:0009055 131567 cellular organisms no rank 49138 EBI-EMBL Copper binding proteins, plastocyanin/azurin family plastocyanin/azurin family copper-binding domain NF012356.5 PF00128.29 Alpha-amylase 22 22 347 domain Y Y N alpha-amylase family glycosyl hydrolase GO:0003824,GO:0005975 8107092,9600843 131567 cellular organisms no rank 591306 EBI-EMBL Alpha amylase, catalytic domain alpha-amylase catalytic domain Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain. [1]. 8107092. Refined molecular structure of pig pancreatic alpha-amylase at 2.1 A resolution. Larson SB, Greenwood A, Cascio D, Day J, McPherson A;. J Mol Biol 1994;235:1560-1584. [2]. 9600843. Crystal structure of yellow meal worm alpha-amylase at 1.64 A resolution. Strobl S, Maskos K, Betz M, Wiegand G, Huber R, Gomis-Ruth FX, Glockshuber R;. J Mol Biol 1998;278:617-628. (from Pfam) NF012360.5 PF00132.29 Hexapep 27 27 36 repeat Y N N transferase-like hexapeptide repeat-containing protein 7481807 131567 cellular organisms no rank 475017 EBI-EMBL Bacterial transferase hexapeptide (six repeats) transferase-like hexapeptide repeats NF012361.5 PF00133.27 tRNA-synt_1 22.7 22.7 414 domain Y Y N class I tRNA ligase family protein GO:0000166,GO:0004812,GO:0005524,GO:0006418 10446055,10673435,10811626,11114335,11243794 131567 cellular organisms no rank 436492 EBI-EMBL tRNA synthetases class I (I, L, M and V) class I tRNA ligase family protein Other tRNA synthetase sub-families are too dissimilar to be included. Paper describing PDB structure 1a8h. [1]. 10673435. The 2.0 A crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules. Sugiura I, Nureki O, Ugaji-Yoshikawa Y, Kuwabara S, Shimada A, Tateno M, Lorber B, Giege R, Moras D, Yokoyama S, Konno M;. Structure. 2000;8:197-208. Paper describing PDB structure 1f4l. [2]. 11243794. How methionyl-tRNA synthetase creates its amino acid recognition pocket upon L-methionine binding. Serre L, Verdon G, Choinowski T, Hervouet N, Risler JL, Zelwer C;. J Mol Biol. 2001;306:863-876. Paper describing PDB structure 1ffy. [3]. 10446055. Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin. Silvian LF, Wang J, Steitz TA;. Science. 1999;285:1074-1077. Paper describing PDB structure 1gax. [4]. 11114335. Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase. Fukai S, Nureki O, Sekine S, Shimada A, Tao J, Vassylyev DG, Yokoyama S;. Cell 2000;103:793-803. Paper describing PDB structure 1h3n. [5]. 10811626. The 2 A crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue. Cusack S, Yaremchuk A, Tukalo M;. EMBO J. 2000;19:2351-2361. (from Pfam) NF012362.5 PF00134.28 Cyclin_N 23 23 127 domain Y N N Cyclin, N-terminal domain 2001396,8152925,8591034,8756328 131567 cellular organisms no rank 37 EBI-EMBL Cyclin, N-terminal domain Cyclin, N-terminal domain Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins [4]. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain. The cyclins include an internal duplication, which is related to that found in TFIIB and the RB protein. [1]. 8152925. Evidence for a protein domain superfamily shared by the cyclins, TFIIB and RB/p107. Gibson TJ, Thompson JD, Blocker A, Kouzarides T;. Nucleic Acids Res 1994;22:946-952. [2]. 8591034. The crystal structure of cyclin A. Brown NR, Noble MEM, Endicott JA, Garman EF, Wakatsuki S, Mitchell E, Rasmussen B, Hunt T, Johnson LN;. Structure. 1995;3:1235-1247. Complex of cyclin and cyclin dependent kinase. [3]. 8756328. Structural basis of cyclin-dependant kinase activation by phosphorylation. Russo AA, Jeffrey PD, Pavletich NP;. Nat Struct Biol. 1996;3:696-700. [4]. 2001396. Isolation and characterization of a human cDNA encoding uracil-DNA glycosylase. Muller SJ, Caradonna S;. Biochim Biophys Acta 1991;1088:197-207. (from Pfam) NF012363.5 PF00135.33 COesterase 27 27 515 domain Y Y N carboxylesterase family protein 131567 cellular organisms no rank 176739 EBI-EMBL Carboxylesterase family carboxylesterase family protein NF012364.5 PF00136.26 DNA_pol_B 23 23 453 domain Y Y N DNA polymerase domain-containing protein GO:0000166,GO:0003677 8679562,9757117 131567 cellular organisms no rank 25751 EBI-EMBL DNA polymerase family B DNA polymerase family B This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities. [1]. 8679562. Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions. Wang J, Yu P, Lin TC, Konigsberg WH, Steitz TA;. Biochemistry 1996;35:8110-8119. [2]. 9757117. Crystallization and preliminary diffraction analysis of a hyperthermostable DNA polymerase from a Thermococcus archaeon. Zhou M, Mao C, Rodriguez AC, Kiefer JR, Kucera RB, Beese LS;. Acta Crystallogr D Biol Crystallogr 1998;54:994-995. (from Pfam) NF012365.5 PF00137.26 ATP-synt_C 24 24 60 domain Y N N ATP synthase subunit C GO:0015078,GO:0033177,GO:1902600 15629643,20610387,33065002,36631659 131567 cellular organisms no rank 28388 EBI-EMBL ATP synthase subunit C ATP synthase subunit C This domain is found in the subunit c of ATP synthases and similar sequences from all cellular organisms. It forms two alpha-helices [1-4]. [1]. 20610387. Crystal structure of the Mg.ADP-inhibited state of the yeast F1c10-ATP synthase. Dautant A, Velours J, Giraud MF;. J Biol Chem. 2010;285:29502-29510. [2]. 36631659. Changes within the central stalk of E. coli F(1)F(o) ATP synthase observed after addition of ATP. Sobti M, Zeng YC, Walshe JL, Brown SHJ, Ishmukhametov R, Stewart AG;. Commun Biol. 2023;6:26. [3]. 33065002. Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly. Wang L, Wu D, Robinson CV, Wu H, Fu TM;. Mol Cell. 2020;80:501-511. [4]. 15629643. A structural model of the vacuolar ATPase from transmission electron microscopy. Wilkens S, Zhang Z, Zheng Y;. Micron. 2005;36:109-126. (from Pfam) NF012366.5 PF00139.25 Lectin_legB 26.3 26.3 250 domain Y N N Legume lectin domain GO:0030246 131567 cellular organisms no rank 2419 EBI-EMBL Legume lectin domain Legume lectin domain NF012368.5 PF00141.28 peroxidase 27 27 237 subfamily Y Y N peroxidase family protein GO:0004601,GO:0006979,GO:0020037 131567 cellular organisms no rank 53553 EBI-EMBL Peroxidase peroxidase family protein This family includes various types of peroxidase, catalase, and ligninase. NF012369.5 PF00142.23 Fer4_NifH 25 25 271 domain Y N N 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family GO:0005524,GO:0016491 131567 cellular organisms no rank 110462 EBI-EMBL 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family NF012371.5 PF00144.29 Beta-lactamase 27 27 329 domain Y Y N serine hydrolase 131567 cellular organisms no rank 527836 EBI-EMBL Beta-lactamase serine hydrolase This model finds serine hydrolases of many sorts, including class C beta-lactamases. Despite the name given by Pfam as a short-hand for this HMM, members proteins should be assumed to be something other than a beta-lactamase if RefSeq or PGAP uses this HMM for naming. True beta-lactamases are named by more specific HMMs. NF012372.5 PF00145.22 DNA_methylase 22 22 324 domain Y Y N DNA cytosine methyltransferase GO:0008168 131567 cellular organisms no rank 142894 EBI-EMBL C-5 cytosine-specific DNA methylase DNA cytosine methyltransferase NF012373.5 PF00146.26 NADHdh 27 27 298 domain Y Y N NADH-quinone oxidoreductase subunit H 1.6.5.9 GO:0016020 7690854 131567 cellular organisms no rank 60435 EBI-EMBL NADH dehydrogenase NADH-quinone oxidoreductase subunit H NF012375.5 PF00148.24 Oxidored_nitro 28.6 28.6 399 domain Y Y N nitrogenase component 1 GO:0016491 11913144,16123301 131567 cellular organisms no rank 41865 EBI-EMBL Nitrogenase component 1 type Oxidoreductase nitrogenase component 1 NF012376.5 PF00149.33 Metallophos 21.5 21.5 191 domain Y Y N metallophosphoesterase GO:0016787 9685491 131567 cellular organisms no rank 807428 EBI-EMBL Calcineurin-like phosphoesterase metallophosphoesterase This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or yeast MRE11 Swiss:P32829. The most conserved regions in this superfamily centre around the metal chelating residues. [1]. 9685491. Phosphoesterase domains associated with DNA polymerases of diverse origins. Aravind L, Koonin EV;. Nucleic Acids Res 1998;26:3746-3752. (from Pfam) NF012377.5 PF00150.23 Cellulase 23.5 23.5 272 domain Y Y N cellulase family glycosylhydrolase GO:0000272,GO:0004553 131567 cellular organisms no rank 107470 EBI-EMBL Cellulase (glycosyl hydrolase family 5) cellulase family glycosylhydrolase NF012378.5 PF00151.24 Lipase 27 27 336 PfamEq Y N N Lipase GO:0004806,GO:0016298 9822688 131567 cellular organisms no rank 249 EBI-EMBL Lipase Lipase NF012379.5 PF00152.25 tRNA-synt_2 25 25 308 domain Y Y N amino acid--tRNA ligase-related protein GO:0000166,GO:0004812,GO:0005524,GO:0043039 131567 cellular organisms no rank 206367 EBI-EMBL tRNA synthetases class II (D, K and N) amino acid--tRNA ligase-related protein Members of this family contain a domain found in class II ligases of amino acids to tRNA for protein translation, but also in related proteins such as the EF-P-lysine lysyltransferase EpmA. NF012381.5 PF00154.26 RecA 27 27 262 domain Y N N recA bacterial DNA recombination protein GO:0003697,GO:0005524,GO:0006281 7022448 131567 cellular organisms no rank 55159 EBI-EMBL recA bacterial DNA recombination protein recA bacterial DNA recombination protein RecA is a DNA-dependent ATPase and functions in DNA repair systems. RecA protein catalyses an ATP-dependent DNA strand-exchange reaction that is the central step in the repair of dsDNA breaks by homologous recombination [1]. [1]. 7022448. recA protein of Escherichia coli promotes branch migration, a kinetically distinct phase of DNA strand exchange. Cox MM, Lehman IR;. Proc Natl Acad Sci U S A. 1981;78:3433-3437. (from Pfam) NF012382.5 PF00155.26 Aminotran_1_2 19.7 19.7 361 subfamily Y Y N aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme GO:0009058,GO:0030170 10029535,10417420 131567 cellular organisms no rank 1754814 EBI-EMBL Aminotransferase class I and II aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme NF012383.5 PF00156.32 Pribosyltran 26.3 26.3 158 domain Y Y N phosphoribosyltransferase family protein GO:0009116 17143579 131567 cellular organisms no rank 443014 EBI-EMBL Phosphoribosyl transferase domain phosphoribosyltransferase domain This family includes a range of diverse phosphoribosyl transferase enzymes. This family includes: Adenine phosphoribosyl-transferase EC:2.4.2.7, Swiss:P07672. Hypoxanthine-guanine-xanthine phosphoribosyl-transferase Swiss:P51900. Hypoxanthine phosphoribosyl-transferase EC:2.4.2.8 Swiss:P36766. Ribose-phosphate pyrophosphokinase i EC:2.7.6.1 Swiss:P09329. Amidophosphoribosyltransferase EC:2.4.2.14 Swiss:P00496. Orotate phosphoribosyl-transferase EC:2.4.2.10 Swiss:P11172. Uracil phosphoribosyl-transferase EC:2.4.2.9 Swiss:P25532. Xanthine-guanine phosphoribosyl-transferase EC:2.4.2.22 Swiss:P00501. In Arabidopsis, At the very N-terminus of this domain is the P-Loop NTPase domain [1]. [1]. 17143579. Functional characterization of a gene encoding a dual domain for uridine kinase and uracil phosphoribosyltransferase in Arabidopsis thaliana. Islam MR, Kim H, Kang SW, Kim JS, Jeong YM, Hwang HJ, Lee SY, Woo JC, Kim SG;. Plant Mol Biol. 2007;63:465-477. (from Pfam) NF012385.5 PF00158.31 Sigma54_activat 20.2 20.2 168 domain Y Y N sigma 54-interacting transcriptional regulator GO:0005524,GO:0006355,GO:0008134 11544185,12618438 131567 cellular organisms no rank 703857 EBI-EMBL Sigma-54 interaction domain Sigma-54 interaction domain NF012387.5 PF00160.26 Pro_isomerase 21.7 21.7 159 domain Y Y N peptidylprolyl isomerase 5.2.1.8 GO:0000413,GO:0003755 15998457 131567 cellular organisms no rank 128101 EBI-EMBL Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD peptidylprolyl isomerase The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function [1]. [1]. 15998457. The cyclophilins. Wang P, Heitman J;. Genome Biol 2005;6:226. (from Pfam) NF012389.5 PF00162.24 PGK 27 27 379 PfamEq Y Y N phosphoglycerate kinase pgk GO:0004618,GO:0006096 131567 cellular organisms no rank 70711 EBI-EMBL Phosphoglycerate kinase phosphoglycerate kinase NF012390.5 PF00163.24 Ribosomal_S4 23 23 95 PfamEq Y N N Ribosomal protein S4/S9 N-terminal domain GO:0019843 9707415 131567 cellular organisms no rank 36160 EBI-EMBL Ribosomal protein S4/S9 N-terminal domain Ribosomal protein S4/S9 N-terminal domain This family includes small ribosomal subunit S9 from prokaryotes and S16 from metazoans. This domain is predicted to bind to ribosomal RNA [1]. This domain is composed of four helices in the known structure. However the domain is discontinuous in sequence and the alignment for this family contains only the first three helices. [1]. 9707415. The crystal structure of ribosomal protein S4 reveals a two-domain molecule with an extensive RNA-binding surface: one domain shows structural homology to the ETS DNA-binding motif. Davies C, Gerstner RB, Draper DE, Ramakrishnan V, White SW;. EMBO J 1998;17:4545-4558. (from Pfam) NF012391.5 PF00164.30 Ribosom_S12_S23 22.3 22.3 114 PfamEq Y N N Ribosomal protein S12/S23 GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 16464 EBI-EMBL Ribosomal protein S12/S23 Ribosomal protein S12/S23 This protein is known as S12 in bacteria and archaea and S23 in eukaryotes. (from Pfam) NF012392.5 PF00165.28 HTH_AraC 26.6 26.6 42 domain Y Y N AraC family transcriptional regulator GO:0003700,GO:0006355,GO:0043565 9600836,9600837 131567 cellular organisms no rank 1059886 EBI-EMBL Bacterial regulatory helix-turn-helix proteins, AraC family AraC family transcriptional regulator In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (Pfam:PF00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerisation domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilised when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added [1-2]. [1]. 9600836. Apo-AraC actively seeks to loop. Seabold RR, Schleif RF;. J Mol Biol 1998;278:529-538. [2]. 9600837. Arm-domain interactions in AraC. Saviola B, Seabold R, Schleif RF;. J Mol Biol 1998;278:539-548. (from Pfam) NF012393.5 PF00166.26 Cpn10 21.1 21.1 93 domain Y N N Chaperonin 10 Kd subunit GO:0005524,GO:0006457,GO:0044183 9244309 131567 cellular organisms no rank 38348 EBI-EMBL Chaperonin 10 Kd subunit Chaperonin 10 Kd subunit This family contains GroES and Gp31-like chaperonins. Gp31 is a functional co-chaperonin that is required for the folding and assembly of Gp23, a major capsid protein, during phage morphogenesis [1]. [1]. 9244309. Structural adaptations in the specialized bacteriophage T4 co-chaperonin Gp31 expand the size of the Anfinsen cage. Hunt JF, van der Vies SM, Henry L, Deisenhofer J;. Cell 1997;90:361-371. (from Pfam) NF012395.5 PF00168.35 C2 22 9.6 104 domain Y N N C2 domain 8771209 131567 cellular organisms no rank 221 EBI-EMBL C2 domain C2 domain NF012398.5 PF00171.27 Aldedh 23 23 461 subfamily Y Y N aldehyde dehydrogenase family protein GO:0016491 9195888 131567 cellular organisms no rank 1147006 EBI-EMBL Aldehyde dehydrogenase family aldehyde dehydrogenase family protein This family of dehydrogenases act on aldehyde substrates. Members use NADP as a cofactor. The family includes the following members: The prototypical members are the aldehyde dehydrogenases Swiss:P00352 EC:1.2.1.3. Succinate-semialdehyde dehydrogenase Swiss:P25526 EC:1.2.1.16. Lactaldehyde dehydrogenase Swiss:P25553 EC:1.2.1.22. Benzaldehyde dehydrogenase Swiss:P43503 EC:1.2.1.28. Methylmalonate-semialdehyde dehydrogenase Swiss:Q02252 EC:1.2.1.27. Glyceraldehyde-3-phosphate dehydrogenase Swiss:P81406 EC:1.2.1.9. Delta-1-pyrroline-5-carboxylate dehydrogenase Swiss:P30038 EC: 1.5.1.12. Acetaldehyde dehydrogenase Swiss:P17547 EC:1.2.1.10. Glutamate-5-semialdehyde dehydrogenase Swiss:P07004 EC:1.2.1.41. This family also includes omega crystallin Swiss:P30842 an eye lens protein from squid and octopus that has little aldehyde dehydrogenase activity. [1]. 9195888. Structure of mitochondrial aldehyde dehydrogenase: the genetic component of ethanol aversion. Steinmetz CG, Xie P, Weiner H, Hurley TD;. Structure 1997;5:701-711. (from Pfam) NF012400.5 PF00173.33 Cyt-b5 23.7 23.7 74 domain Y Y N cytochrome b5 domain-containing protein 12537557,8774719,9705155 131567 cellular organisms no rank 4360 EBI-EMBL Cytochrome b5-like Heme/Steroid binding domain Cytochrome b5-like Heme/Steroid binding domain This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors such as Swiss:O00264 [1,2]. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases. [1]. 9705155. Cloning and tissue expression of two putative steroid membrane receptors. Gerdes D, Wehling M, Leube B, Falkenstein E;. Biol Chem 1998;379:907-911. [2]. 8774719. Purification and partial sequencing of high-affinity progesterone-binding site(s) from porcine liver membranes. Meyer C, Schmid R, Scriba PC, Wehling M;. Eur J Biochem 1996;239:726-731. [3]. 12537557. Membrane-bound progesterone receptors contain a cytochrome b5-like ligand-binding domain. Mifsud W, Bateman A;. Genome Biol 2002;3:0-0. (from Pfam) NF012401.5 PF00174.24 Oxidored_molyb 24 24 169 domain Y Y N molybdopterin-dependent oxidoreductase 9428520 131567 cellular organisms no rank 128121 EBI-EMBL Oxidoreductase molybdopterin binding domain Oxidoreductase molybdopterin binding domain This domain is found in a variety of oxidoreductases. This domain binds to a molybdopterin cofactor. Xanthine dehydrogenases, that also bind molybdopterin, have essentially no similarity. [1]. 9428520. Molecular basis of sulfite oxidase deficiency from the structure of sulfite oxidase. Kisker C, Schindelin H, Pacheco A, Wehbi WA, Garrett RM, Rajagopalan KV, Enemark JH, Rees DC;. Cell 1997;91:973-983. (from Pfam) NF012402.5 PF00175.26 NAD_binding_1 22 22 109 domain Y N N Oxidoreductase NAD-binding domain GO:0016491 1748631 131567 cellular organisms no rank 371681 EBI-EMBL Oxidoreductase NAD-binding domain Oxidoreductase NAD-binding domain Xanthine dehydrogenases, that also bind FAD/NAD, have essentially no similarity. [1]. 1748631. The sequence of squash NADH:nitrate reductase and its relationship to the sequences of other flavoprotein oxidoreductases. A family of flavoprotein pyridine nucleotide cytochrome reductases. Hyde GE, Crawford NM, Campbell W;. J Biol Chem 1991;266:23542-23547. (from Pfam) NF012403.5 PF00176.28 SNF2-rel_dom 24.9 24.9 290 domain Y Y N SNF2-related protein GO:0005524,GO:0140658 14729263,21549307,7651832 131567 cellular organisms no rank 188482 EBI-EMBL SNF2-related domain SNF2-related domain This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1)[1,2,3]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. [1]. 7651832. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Eisen JA, Sweder KS, Hanawalt PC;. Nucleic Acids Res. 1995;23:2715-2723. [2]. 14729263. The SNF2 domain protein family in higher vertebrates displays dynamic expression patterns in Xenopus laevis embryos. Linder B, Cabot RA, Schwickert T, Rupp RA;. Gene. 2004;326:59-66. [3]. 21549307. Maintenance of silent chromatin through replication requires SWI/SNF-like chromatin remodeler SMARCAD1. Rowbotham SP, Barki L, Neves-Costa A, Santos F, Dean W, Hawkes N, Choudhary P, Will WR, Webster J, Oxley D, Green CM, Varga-Weisz P, Mermoud JE;. Mol Cell. 2011;42:285-296. (from Pfam) NF012404.5 PF00177.26 Ribosomal_S7 24 24 149 PfamEq Y N N Ribosomal protein S7p/S5e 9331418 131567 cellular organisms no rank 25137 EBI-EMBL Ribosomal protein S7p/S5e Ribosomal protein S7p/S5e This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. [1]. 9331418. The structure of ribosomal protein S7 at 1.9 A resolution reveals a beta-hairpin motif that binds double-stranded nucleic acids. Wimberly BT, White SW, Ramakrishnan V;. Structure 1997;5:1187-1198. (from Pfam) NF012406.5 PF00179.31 UQ_con 27 27 140 domain Y Y N ubiquitin-conjugating enzyme E2 1321826,18276160,8268156,9048545,9241264,9253709 131567 cellular organisms no rank 376 EBI-EMBL Ubiquitin-conjugating enzyme ubiquitin-conjugating enzyme E2 Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5]. [1]. 1321826. Three-dimensional structure of a ubiquitin-conjugating enzyme (E2). Cook WJ, Jeffrey LC, Sullivan ML, Vierstra RD;. J Biol Chem 1992;267:15116-15121. [2]. 8268156. Tertiary structures of class I ubiquitin-conjugating enzymes are highly conserved: crystal structure of yeast Ubc4. Cook WJ, Jeffrey LC, Xu Y, Chau V;. Biochemistry 1993;32:13809-13817. [3]. 9048545. Crystal structure of a class I ubiquitin conjugating enzyme (Ubc7) from Saccharomyces cerevisiae at 2.9 angstroms resolution. Cook WJ, Martin PD, Edwards BF, Yamazaki RK, Chau V;. Biochemistry 1997;36:1621-1627. [4]. 9241264. TSG101 may be the prototype of a class of dominant negative ubiquitin regulators. Koonin EV, Abagyan RA;. Nat Genet 1997;16:330-331. [5]. 9253709. The breast cancer gene product TSG101: a regulator of ubiquitination?. Ponting CP, Cai YD, Bork P. J Mol Med 1997;75:467-469. [6]. 18276160. Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation. Burroughs AM, Jaffee M, Iyer LM, Aravind L;. J Struct Biol. 2008;162:205-218. (from Pfam) NF012407.5 PF00180.25 Iso_dh 27 27 348 subfamily Y Y N isocitrate/isopropylmalate family dehydrogenase GO:0016616 131567 cellular organisms no rank 150085 EBI-EMBL Isocitrate/isopropylmalate dehydrogenase isocitrate/isopropylmalate family dehydrogenase NF012408.5 PF00181.28 Ribosomal_L2 27.5 27.5 77 PfamEq Y N N Ribosomal Proteins L2, RNA binding domain GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 35726 EBI-EMBL Ribosomal Proteins L2, RNA binding domain Ribosomal Proteins L2, RNA binding domain NF012410.5 PF00183.23 HSP90 24.4 24.4 518 domain Y N N Hsp90 protein GO:0005524,GO:0006457,GO:0016887,GO:0051082,GO:0140662 9187656 131567 cellular organisms no rank 60839 EBI-EMBL Hsp90 protein Hsp90 protein NF012412.5 PF00185.29 OTCace 29.4 29.4 157 domain Y N N Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain GO:0006520,GO:0016597,GO:0016743 10318893 131567 cellular organisms no rank 141657 EBI-EMBL Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain NF012413.5 PF00186.24 DHFR_1 25 25 159 subfamily Y Y N dihydrofolate reductase 1.5.1.3 GO:0004146,GO:0046654 131567 cellular organisms no rank 59807 EBI-EMBL Dihydrofolate reductase dihydrofolate reductase NF012415.5 PF00188.31 CAP 21.1 21.1 117 domain Y Y N CAP domain-containing protein 12625841,12759345,18824526,9067611 131567 cellular organisms no rank 95993 EBI-EMBL Cysteine-rich secretory protein family CAP domain The CAP domain, named for cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins, is found in both eukaryotes and prokaryotes. NF012416.5 PF00189.25 Ribosomal_S3_C 34.1 34.1 83 PfamEq Y N N Ribosomal protein S3, C-terminal domain GO:0003735,GO:0006412 8036511 131567 cellular organisms no rank 33427 EBI-EMBL Ribosomal protein S3, C-terminal domain Ribosomal protein S3, C-terminal domain This family contains a central domain Pfam:PF00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer. [1]. 8036511. Conserved structures and diversity of functions of RNA-binding proteins. Burd CG, Dreyfuss G;. Science 1994;265:615-621. (from Pfam) NF012417.5 PF00190.27 Cupin_1 22 22 151 domain Y Y N cupin domain-containing protein GO:0045735 9573603 131567 cellular organisms no rank 93985 EBI-EMBL Cupin Cupin This family represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant. [1]. 9573603. Cupins: a new superfamily of functionally diverse proteins that include germins and plant storage proteins. Dunwell JM;. Biotechnol Genet Eng Rev 1998;15:1-32. (from Pfam) NF012422.5 PF00196.24 GerE 23.5 23.5 57 domain Y Y N LuxR C-terminal-related transcriptional regulator GO:0006355 131567 cellular organisms no rank 1181874 EBI-EMBL Bacterial regulatory proteins, luxR family LuxR C-terminal-related transcriptional regulator NF012424.5 PF00198.28 2-oxoacid_dh 23 23 232 domain Y Y N 2-oxo acid dehydrogenase subunit E2 GO:0016746 8487300 131567 cellular organisms no rank 231011 EBI-EMBL 2-oxoacid dehydrogenases acyltransferase (catalytic domain) 2-oxo acid dehydrogenase subunit E2 These proteins contain one to three copies of a lipoyl binding domain followed by the catalytic domain. [1]. 8487300. Refined crystal structure of the catalytic domain of dihysrolipoyl transacetylase (E2P) from azotobacter vineelandii at 2.6 angstroms resolution. Mattevi A, Obmolova G, Kalk KH, Westphal AH, De Kok A, Hol WG;. J Mol Biol 1993;230:1183-1199. (from Pfam) NF012425.5 PF00199.24 Catalase 25 25 383 domain Y Y N catalase 1.11.1.6 GO:0004096,GO:0020037 131567 cellular organisms no rank 115481 EBI-EMBL Catalase catalase NF012427.5 PF00201.23 UDPGT 19.5 19.5 499 domain Y N N UDP-glucoronosyl and UDP-glucosyl transferase 131567 cellular organisms no rank 76174 EBI-EMBL UDP-glucoronosyl and UDP-glucosyl transferase UDP-glucoronosyl and UDP-glucosyl transferase NF012428.5 PF00202.26 Aminotran_3 30.5 30.5 403 subfamily Y Y N aminotransferase class III-fold pyridoxal phosphate-dependent enzyme GO:0008483,GO:0030170 9514741 131567 cellular organisms no rank 556413 EBI-EMBL Aminotransferase class-III aminotransferase class III-fold pyridoxal phosphate-dependent enzyme NF012429.5 PF00203.26 Ribosomal_S19 27 27 81 PfamEq Y Y N ribosomal protein S19 family protein GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 19300 EBI-EMBL Ribosomal protein S19 ribosomal protein S19 family protein NF012430.5 PF00204.30 DNA_gyraseB 27 27 173 domain Y N N DNA gyrase B GO:0003677,GO:0003918,GO:0005524,GO:0006265 10575351,10734094,1646964,9230303,9657678,9817206 131567 cellular organisms no rank 129199 EBI-EMBL DNA gyrase B DNA gyrase B This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119. [1]. 1646964. Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Wigley DB, Davies GJ, Dodson EJ, Maxwell A, Dodson G;. Nature 1991;351:624-629. [2]. 10734094. Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center. Brino L, Urzhumtsev A, Mousli M, Bronner C, Mitschler A, Oudet P, Moras D. J Biol Chem 2000;275:9468-9475. [3]. 10575351. Isoleucine 10 is essential for DNA gyrase B function in Escherichia coli. Brino L, Bronner C, Oudet P, Mousli M. Biochimie 1999;81:973-980. [4]. 9817206. NMR structure of the histidine kinase domain of the E. coli osmosensor EnvZ. Tanaka T, Saha SK, Tomomori C, Ishima R, Liu D, Tong KI, Park H, Dutta R, Qin L, Swindells MB, Yamazaki T, Ono AM, Kainosho M, Inouye M, Ikura M. Nature 1998;396:88-92. [5]. 9657678. Identification of a residue involved in transition-state stabilization in the ATPase reaction of DNA gyrase. Smith CV, Maxwell A. Biochemistry 1998;37:9658-9667. [6]. 9230303. Identification and structural characterization of the ATP/ADP-binding site in the Hsp90 molecular chaperone. Prodromou C, Roe SM, O'Brien R, Ladbury JE, Piper PW, Pearl LH. Cell 1997;90:65-75. (from Pfam) NF012431.5 PF00205.27 TPP_enzyme_M 30.4 30.4 137 domain Y N N Thiamine pyrophosphate enzyme, central domain GO:0000287,GO:0030976 8604141 131567 cellular organisms no rank 337976 EBI-EMBL Thiamine pyrophosphate enzyme, central domain Thiamine pyrophosphate enzyme, central domain The central domain of TPP enzymes contains a 2-fold Rossman fold. [1]. 8604141. Crystal structure of the thiamin diphosphate-dependent enzyme pyruvate decarboxylase from the yeast Saccharomyces cerevisiae at 2.3 A resolution. Arjunan P, Umland T, Dyda F, Swaminathan S, Furey W, Sax M, Farrenkopf B, Gao Y, Zhang D, Jordan F;. J Mol Biol 1996;256:590-600. (from Pfam) NF012432.5 PF00206.25 Lyase_1 27 27 312 domain Y Y N lyase family protein 131567 cellular organisms no rank 298435 EBI-EMBL Lyase lyase family protein Members of this family include fumarate hydratase, L-aspartate ammonia-lyase, argininosuccinate lyase, and adenylosuccinate lyase. All are classified as lyases, meaning these enzymes break a bond by an eliminating reaction that does not involve hydrolysis or oxidation. NF012433.5 PF00207.27 A2M 21 21 92 domain Y Y N alpha-2-macroglobulin family protein GO:0004866 10625650,10825534,11106161,11387479 131567 cellular organisms no rank 58120 EBI-EMBL Alpha-2-macroglobulin family alpha-2-macroglobulin family protein This family includes the C-terminal region of the alpha-2-macroglobulin family. [1]. 10625650. NMR solution structure of the receptor binding domain of human alpha(2)-macroglobulin. Huang W, Dolmer K, Liao X, Gettins PG;. J Biol Chem 2000;275:1089-1094. [2]. 11106161. Structure of a rat alpha 1-macroglobulin receptor-binding domain dimer. Xiao T, DeCamp DL, Spran SR;. Protein Sci 2000;9:1889-1897. [3]. 11387479. Structure of complement receptor 2 in complex with its C3d ligand. Szakonyi G, Guthridge JM, Li D, Young K, Holers VM, Chen XS;. Science 2001;292:1725-1728. [4]. 10825534. Structure at 1.44 A resolution of an N-terminally truncated form of the rat serum complement C3d fragment. Zanotti G, Bassetto A, Battistutta R, Folli C, Arcidiaco P, Stoppini M, Berni R;. Biochim Biophys Acta 2000;1478:232-238. (from Pfam) NF012434.5 PF00208.26 ELFV_dehydrog 23.4 23.4 241 domain Y N N Glutamate/Leucine/Phenylalanine/Valine dehydrogenase GO:0006520,GO:0016491 8591046 131567 cellular organisms no rank 107957 EBI-EMBL Glutamate/Leucine/Phenylalanine/Valine dehydrogenase Glutamate/Leucine/Phenylalanine/Valine dehydrogenase NF012435.5 PF00209.23 SNF 27 27 524 domain Y N N Sodium:neurotransmitter symporter family GO:0016020 131567 cellular organisms no rank 58267 EBI-EMBL Sodium:neurotransmitter symporter family Sodium:neurotransmitter symporter family These are twelve xTM-containing region transporters. (from Pfam) NF012436.5 PF00210.29 Ferritin 24.5 24.5 142 domain Y Y N ferritin-like domain-containing protein GO:0008199 131567 cellular organisms no rank 116485 EBI-EMBL Ferritin-like domain ferritin-like domain This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins. (from Pfam) NF012437.5 PF00211.25 Guanylate_cyc 21.9 21.9 183 domain Y Y N adenylate/guanylate cyclase domain-containing protein GO:0009190,GO:0035556 131567 cellular organisms no rank 145994 EBI-EMBL Adenylate and Guanylate cyclase catalytic domain Adenylate and Guanylate cyclase catalytic domain NF012439.5 PF00213.23 OSCP 22.3 22.3 172 PfamEq Y Y N F0F1 ATP synthase subunit delta 7.1.2.2 GO:0015986,GO:0046933 9468613 131567 cellular organisms no rank 56716 EBI-EMBL ATP synthase delta (OSCP) subunit F0F1 ATP synthase subunit delta The ATP D subunit from E. coli is the same as the OSCP subunit which is this family. The ATP D subunit from metazoa are found in family Pfam:PF00401. [1]. 9468613. Structure and arrangement of the delta subunit in the E. coli ATP synthase (ECF1F0). Wilkens S, Rodgers A, Ogilvie I, Capaldi RA;. Biophys Chem 1997;68:95-102. (from Pfam) NF012441.5 PF00215.29 OMPdecase 27 27 221 subfamily Y Y N orotidine 5'-phosphate decarboxylase / HUMPS family protein 4.1.1.23 GO:0004590,GO:0006207 131567 cellular organisms no rank 90130 EBI-EMBL Orotidine 5'-phosphate decarboxylase / HUMPS family orotidine 5'-phosphate decarboxylase / HUMPS family protein This family includes Orotidine 5'-phosphate decarboxylase enzymes EC:4.1.1.23 that are involved in the final step of pyrimidine biosynthesis. The family also includes enzymes such as hexulose-6-phosphate synthase. This family appears to be distantly related to Pfam:PF00834. (from Pfam) NF012442.5 PF00216.26 Bac_DNA_binding 22.4 22.4 90 domain Y Y N HU family DNA-binding protein GO:0003677,GO:0030527 7500343 131567 cellular organisms no rank 96783 EBI-EMBL Bacterial DNA-binding protein HU family DNA-binding protein NF012444.5 PF00218.26 IGPS 27 27 254 PfamEq Y N N Indole-3-glycerol phosphate synthase GO:0004425 131567 cellular organisms no rank 76205 EBI-EMBL Indole-3-glycerol phosphate synthase Indole-3-glycerol phosphate synthase NF012447.5 PF00221.24 Lyase_aromatic 27.3 27.3 466 domain Y Y N aromatic amino acid lyase 10220322,16793524,7925471 131567 cellular organisms no rank 81767 EBI-EMBL Aromatic amino acid lyase aromatic amino acid lyase This family includes proteins with phenylalanine ammonia-lyase, EC:4.3.1.24, histidine ammonia-lyase, EC:4.3.1.3, and tyrosine aminomutase, EC:5.4.3.6, activities [1-3]. [1]. 7925471. Structural and catalytic properties of the four phenylalanine ammonia-lyase isoenzymes from parsley (Petroselinum crispum Nym.). Appert C, Logemann E, Hahlbrock K, Schmid J, Amrhein N;. Eur J Biochem. 1994;225:491-499. [2]. 10220322. Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile. Schwede TF, Retey J, Schulz GE;. Biochemistry. 1999;38:5355-5361. [3]. 16793524. Molecular and biochemical studies of chondramide formation-highly cytotoxic natural products from Chondromyces crocatus Cm c5. Rachid S, Krug D, Kunze B, Kochems I, Scharfe M, Zabriskie TM, Blocker H, Muller R;. Chem Biol. 2006;13:667-681. (from Pfam) NF012449.5 PF00224.26 PK 30 30 328 subfamily Y Y N pyruvate kinase GO:0000287,GO:0004743,GO:0006096,GO:0030955 11960989,12798932,29748232,9308890 131567 cellular organisms no rank 83880 EBI-EMBL Pyruvate kinase, barrel domain pyruvate kinase, barrel domain This is the barrel domain of pyruvate kinases. This domain represents the beta/alpha barrel and the small beta-barrel domain inserted within it. The active site is found in a cleft between the two domains [1,2,3,4]. [1]. 9308890. Ligand-induced domain movement in pyruvate kinase: structure of the enzyme from rabbit muscle with Mg2+, K+, and L-phospholactate at 2.7 A resolution. Larsen TM, Benning MM, Wesenberg GE, Rayment I, Reed GH;. Arch Biochem Biophys 1997;345:199-206. [2]. 12798932. Pyruvate kinase: current status of regulatory and functional properties. Munoz ME, Ponce E;. Comp Biochem Physiol B Biochem Mol Biol. 2003;135:197-218. [3]. 11960989. Structure and function of human erythrocyte pyruvate kinase. Molecular basis of nonspherocytic hemolytic anemia. Valentini G, Chiarelli LR, Fortin R, Dolzan M, Galizzi A, Abraham DJ, Wang C, Bianchi P, Zanella A, Mattevi A;. J Biol Chem. 2002;277:23807-23814. [4]. 29748232. An allostatic mechanism for M2 pyruvate kinase as an amino-acid sensor. Yuan M, McNae IW, Chen Y, Blackburn EA, Wear MA, Michels PAM, Fothergill-Gilmore LA, Hupp T, Walkinshaw MD;. Biochem J. 2018;475:1821-1837. (from Pfam) NF012451.5 PF00226.36 DnaJ 27.8 27.8 63 domain Y Y N DnaJ domain-containing protein 8016869,8764403,9271376,9644977 131567 cellular organisms no rank 194407 EBI-EMBL DnaJ domain DnaJ domain DnaJ domains (J-domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction. DnaJ-domain is therefore part of a chaperone (protein folding) system. The T-antigens, although not in Prosite are confirmed as DnaJ containing domains from literature [2]. [1]. 8016869. DnaJ-like proteins: molecular chaperones and specific regulators of Hsp70. Cyr DM, Langer T, Douglas MG;. Trends Biochem Sci 1994;19:176-181. [2]. 9271376. Inactivation of pRB-related proteins p130 and p107 mediated by the J domain of simian virus 40 large T antigen. Stubdal H, Zalvide J, Campbell KS, Schweitzer C, Roberts TM, DeCaprio JA;. Mol Cell Biol 1997;17:4979-4990. The structure of the DnaJ domain by NMR. [3]. 8764403. NMR structure of the J-domain and the Gly/Phe-rich region of the Escherichia coli DnaJ chaperone. Pellecchia M, Szyperski T, Wall D, Georgopoulos C, Wuthrich K;. J Mol Biol 1996;260:236-250. [4]. 9644977. The J-domain family and the recruitment of chaperone power. Kelley WL;. Trends Biochem Sci 1998;23:222-227. (from Pfam) NF012452.5 PF00227.31 Proteasome 22.4 22.4 189 domain Y N N Proteasome subunit GO:0005839,GO:0051603 18389302 131567 cellular organisms no rank 53719 EBI-EMBL Proteasome subunit Proteasome subunit The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologues vary greatly in complexity: from HslV (heat shock locus v), which is encoded by 1 gene in bacteria, to the eukaryotic 20S proteasome, which is encoded by more than 14 genes [1]. Recently evidence of two novel groups of bacterial proteasomes was proposed. The first is Anbu, which is sparsely distributed among cyanobacteria and proteobacteria [1]. The second is call beta-proteobacteria proteasome homologue (BPH) [1]. [1]. 18389302. Rethinking proteasome evolution: two novel bacterial proteasomes. Valas RE, Bourne PE;. J Mol Evol. 2008;66:494-504. (from Pfam) NF012455.5 PF00230.25 MIP 25 25 222 domain Y Y N aquaporin GO:0015267,GO:0016020,GO:0055085 9655351 131567 cellular organisms no rank 82676 EBI-EMBL Major intrinsic protein aquaporin MIP (Major Intrinsic Protein) family proteins exhibit essentially two distinct types of channel properties: (1) specific water transport by the aquaporins, and (2) small neutral solutes transport, such as glycerol by the glycerol facilitators [1]. [1]. 9655351. Prediction of functional residues in water channels and related proteins. Froger A, Tallur B, Thomas D, Delamarche C;. Protein Sci 1998;7:1458-1468. (from Pfam) NF012456.5 PF00231.24 ATP-synt 39.9 39.9 285 PfamEq Y Y N F0F1 ATP synthase subunit gamma 7.1.2.2 GO:0015986,GO:0045261,GO:0046933 8065448 131567 cellular organisms no rank 54502 EBI-EMBL ATP synthase F0F1 ATP synthase subunit gamma NF012457.5 PF00232.23 Glyco_hydro_1 22.6 22.6 453 subfamily Y Y N family 1 glycosylhydrolase GO:0004553,GO:0005975 131567 cellular organisms no rank 173406 EBI-EMBL Glycosyl hydrolase family 1 glycosyl hydrolase family protein NF012462.5 PF00237.24 Ribosomal_L22 28 28 104 domain Y Y N uL22 family ribosomal protein GO:0003735,GO:0005840,GO:0006412 9862810 131567 cellular organisms no rank 26626 EBI-EMBL Ribosomal protein L22p/L17e uL22 family ribosomal protein This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. [1]. 9862810. The crystal structure of ribosomal protein L22 from Thermus thermophilus: insights into the mechanism of erythromycin resistance. Unge J, berg A, Al-Kharadaghi S, Nikulin A, Nikonov S, Davydova N, Nevskaya N, Garber M, Liljas A;. Structure 1998;6:1577-1586. (from Pfam) NF012463.5 PF00238.24 Ribosomal_L14 23.6 23.6 122 PfamEq Y Y N uL14 family ribosomal protein GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 17788 EBI-EMBL Ribosomal protein L14p/L23e uL14 family ribosomal protein NF012464.5 PF00239.26 Resolvase 23.3 23.3 145 domain Y Y N recombinase family protein GO:0000150,GO:0003677,GO:0006310 7628011 131567 cellular organisms no rank 279509 EBI-EMBL Resolvase, N terminal domain Resolvase, N terminal domain The N-terminal domain of the resolvase family (this family) contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase - see Pfam:PF02796. [1]. 7628011. Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site. Yang W, Steitz TA;. Cell 1995;82:193-207. (from Pfam) NF012465.5 PF00240.28 ubiquitin 25.4 21.2 72 domain Y Y N ubiquitin-like protein GO:0005515 12826399,3041007,8107144,9654451,9857030 131567 cellular organisms no rank 1128 EBI-EMBL Ubiquitin family ubiquitin-like protein This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5]. [1]. 3041007. Structure of ubiquitin refined at 1.8 A resolution. Vijay-Kumar S, Bugg CE, Cook WJ;. J Mol Biol 1987;194:531-544. [2]. 8107144. Structure of tetraubiquitin shows how multiubiquitin chains can be formed. Cook WJ, Jeffrey LC, Kasperek E, Pickart CM;. J Mol Biol 1994;236:601-609. [3]. 9654451. Structure determination of the small ubiquitin-related modifier SUMO-1. Bayer P, Arndt A, Metzger S, Mahajan R, Melchior F, Jaenicke R, Becker J;. J Mol Biol 1998;280:275-286. [4]. 9857030. Crystal structure of the human ubiquitin-like protein NEDD8 and interactions with ubiquitin pathway enzymes. Whitby FG, Xia G, Pickart CM, Hill CP;. J Biol Chem 1998;273:34983-34991. [5]. 12826399. A potential proteasome-interacting motif within the ubiquitin-like domain of parkin and other proteins. Upadhya SC, Hegde AN;. Trends Biochem Sci 2003;28:280-283. (from Pfam) NF012466.5 PF00241.25 Cofilin_ADF 22.4 22.4 125 domain Y N N Cofilin/tropomyosin-type actin-binding protein GO:0003779 9145106,9145107,9214506,9275236 131567 cellular organisms no rank 796 EBI-EMBL Cofilin/tropomyosin-type actin-binding protein Cofilin/tropomyosin-type actin-binding protein Severs actin filaments and binds to actin monomers. [1]. 9145106. Structure determination of yeast cofilin. Fedorov AA, Lappalainen P, Fedorov EV, Drubin DG, Almo SC;. Nat Struct Biol 1997;4:366-369. [2]. 9145107. Crystal structure of the actin-binding protein actophorin from Acanthamoeba. Leonard SA, Gittis AG, Petrella EC, Pollard TD, Lattman EE;. Nat Struct Biol 1997;4:369-373. [3]. 9275236. F-actin and G-actin binding are uncoupled by mutation of conserved tyrosine residues in maize actin depolymerizing factor. Jiang CJ, Weeds AG, Khan S, Hussey PJ;. Proc Natl Acad Sci U S A 1997;94:9973-9978. [4]. 9214506. Cofilin promotes rapid actin filament turnover in vivo. Lappalainen P, Drubin DG;. Nature 1997;388:78-82. (from Pfam) NF012469.5 PF00244.25 14-3-3 33.2 33.2 223 subfamily Y Y N 14-3-3 family protein 12184815,7603573,7603574,8601312,8684458,8798343,9280296 131567 cellular organisms no rank 24 EBI-EMBL 14-3-3 protein 14-3-3 family protein NF012470.5 PF00245.25 Alk_phosphatase 24.4 24.4 423 domain Y Y N alkaline phosphatase 3.1.3.1 GO:0016791 131567 cellular organisms no rank 43987 EBI-EMBL Alkaline phosphatase alkaline phosphatase NF012471.5 PF00246.29 Peptidase_M14 21.6 21.6 286 domain Y Y N M14 family zinc carboxypeptidase GO:0004181,GO:0006508,GO:0008270 131567 cellular organisms no rank 101237 EBI-EMBL Zinc carboxypeptidase M14 family zinc carboxypeptidase NF012472.5 PF00248.26 Aldo_ket_red 24 24 291 subfamily Y Y N aldo/keto reductase 10884227,8234324 131567 cellular organisms no rank 671190 EBI-EMBL Aldo/keto reductase family aldo/keto reductase This family includes a number of K+ ion channel beta chain regulatory domains - these are reported to have oxidoreductase activity [2]. [1]. 8234324. Refined 1.8 A structure of human aldose reductase complexed with the potent inhibitor zopolrestat. Wilson DK, Tarle I, Petrash JM, Quiocho FA;. Proc Natl Acad Sci U S A 1993;90:9847-9851. [2]. 10884227. Structure of the cytoplasmic beta subunit-T1 assembly of voltage-dependent K+ channels. Gulbis JM, Zhou M, Mann S, MacKinnon R;. Science 2000;289:123-127. (from Pfam) NF012473.5 PF00249.36 Myb_DNA-binding 24.4 24.4 46 domain Y Y N Myb-like DNA-binding domain-containing protein 8882580 131567 cellular organisms no rank 442 EBI-EMBL Myb-like DNA-binding domain Myb-like DNA-binding domain This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family [1]. A sub-family of Myb-like DNA binding domains. [1]. 8882580. The SANT domain: a putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB. Aasland R, Stewart AF, Gibson T;. Trends Biochem Sci 1996;21:87-88. (from Pfam) NF012475.5 PF00251.25 Glyco_hydro_32N 22.1 22.1 307 domain Y N N Glycosyl hydrolases family 32 N-terminal domain 14973124 131567 cellular organisms no rank 83517 EBI-EMBL Glycosyl hydrolases family 32 N-terminal domain Glycosyl hydrolases family 32 N-terminal domain This domain corresponds to the N-terminal domain of glycosyl hydrolase family 32 which forms a five bladed beta propeller structure [1]. [1]. 14973124. The three-dimensional structure of invertase (beta-fructosidase) from Thermotoga maritima reveals a bimodular arrangement and an evolutionary relationship between retaining and inverting glycosidases. Alberto F, Bignon C, Sulzenbacher G, Henrissat B, Czjzek M;. J Biol Chem 2004;279:18903-18910. (from Pfam) NF012476.5 PF00252.23 Ribosomal_L16 27.9 27.9 132 PfamEq Y Y N ribosomal protein L16 GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 24326 EBI-EMBL Ribosomal protein L16p/L10e ribosomal protein L16 NF012477.5 PF00253.26 Ribosomal_S14 27 27 54 domain Y N N Ribosomal protein S14p/S29e GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 31544 EBI-EMBL Ribosomal protein S14p/S29e Ribosomal protein S14p/S29e This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes. (from Pfam) NF012478.5 PF00254.33 FKBP_C 21.1 21.1 94 domain Y Y N FKBP-type peptidyl-prolyl cis-trans isomerase 5.2.1.8 GO:0003755 131567 cellular organisms no rank 195014 EBI-EMBL FKBP-type peptidyl-prolyl cis-trans isomerase FKBP-type peptidyl-prolyl cis-trans isomerase NF012479.5 PF00255.24 GSHPx 27 27 108 domain Y N N Glutathione peroxidase GO:0004602,GO:0006979 131567 cellular organisms no rank 67573 EBI-EMBL Glutathione peroxidase Glutathione peroxidase NF012481.5 PF00258.30 Flavodoxin_1 25 25 143 domain Y Y N flavodoxin domain-containing protein GO:0010181 131567 cellular organisms no rank 158915 EBI-EMBL Flavodoxin Flavodoxin NF012483.5 PF00261.25 Tropomyosin 38.6 38.6 242 PfamEq Y Y N tropomyosin 11563548,23904035,3606587,6993480 131567 cellular organisms no rank 270 EBI-EMBL Tropomyosin tropomyosin Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites [1]. The protein is best known for its role in regulating the interaction between actin and myosin in muscle contraction, but is also involved in the organisation and dynamics of the cytoskeleton in non-muscle cells [2]. There are multiple cell-specific isoforms, expressed by alternative promoters and alternative RNA processing of at least four genes [3]. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region [4]. [1]. 6993480. The amino acid sequence of rabbit cardiac tropomyosin. Lewis WG, Smillie LB;. J Biol Chem. 1980;255:6854-6859. [2]. 23904035. Cytoskeletal tropomyosins: choreographers of actin filament functional diversity. Vindin H, Gunning P;. J Muscle Res Cell Motil. 2013;34:261-274. [3]. 11563548. Vertebrate tropomyosin: distribution, properties and function. Perry SV;. J Muscle Res Cell Motil. 2001;22:5-49. [4]. 3606587. Genetic origin of diversity of human cytoskeletal tropomyosins. MacLeod AR;. Bioessays. 1987;6:208-212. (from Pfam) NF012486.5 PF00264.25 Tyrosinase 22.6 22.6 214 domain Y Y N tyrosinase family protein GO:0016491 2585484 131567 cellular organisms no rank 13351 EBI-EMBL Common central domain of tyrosinase tyrosinase family protein This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to Pfam:PF00372. [1]. 2585484. Crystal structure of hexameric haemocyanin from Panulirus interruptus refined at 3.2 A resolution. Volbeda A, Hol WG;. J Mol Biol 1989;209:249-279. (from Pfam) NF012487.5 PF00265.23 TK 20.6 20.6 176 PfamEq Y N N Thymidine kinase GO:0004797,GO:0005524 131567 cellular organisms no rank 35526 EBI-EMBL Thymidine kinase Thymidine kinase NF012488.5 PF00266.24 Aminotran_5 21.5 21.5 371 subfamily Y Y N aminotransferase class V-fold PLP-dependent enzyme 131567 cellular organisms no rank 871008 EBI-EMBL Aminotransferase class-V aminotransferase class V-fold PLP-dependent enzyme This domain is found in amino transferases, and other enzymes including cysteine desulphurase EC:4.4.1.-. (from Pfam) NF012490.5 PF00268.26 Ribonuc_red_sm 33.6 33.6 281 domain Y Y N ribonucleotide-diphosphate reductase subunit beta GO:0009263 8331655 131567 cellular organisms no rank 56474 EBI-EMBL Ribonucleotide reductase, small chain ribonucleotide-diphosphate reductase subunit beta NF012492.5 PF00270.34 DEAD 26 24.1 167 domain Y Y N DEAD/DEAH box helicase GO:0003676,GO:0005524 10322435,9862990 131567 cellular organisms no rank 1438171 EBI-EMBL DEAD/DEAH box helicase DEAD/DEAH box helicase Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. [1]. 10322435. Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families. de la Cruz J, Kressler D, Linder P;. Trends Biochem Sci 1999;24:192-198. [2]. 9862990. The DEAD box RNA helicase family in Arabidopsis thaliana. Aubourg S, Kreis M, Lecharny A;. Nucleic Acids Res 1999;27:628-636. (from Pfam) NF012493.5 PF00271.36 Helicase_C 23.5 23.5 110 domain Y Y N helicase-related protein 131567 cellular organisms no rank 1404456 EBI-EMBL Helicase conserved C-terminal domain helicase C-terminal domain The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. (from Pfam) NF012496.5 PF00274.24 Glycolytic 22.2 22.2 349 PfamEq Y Y N class I fructose-bisphosphate aldolase 4.1.2.13 GO:0004332,GO:0006096 131567 cellular organisms no rank 14119 EBI-EMBL Fructose-bisphosphate aldolase class-I class I fructose-bisphosphate aldolase NF012497.5 PF00275.25 EPSP_synthase 22.8 22.8 417 domain Y N N EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) GO:0016765 131567 cellular organisms no rank 174336 EBI-EMBL EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) NF012498.5 PF00276.25 Ribosomal_L23 30.8 30.8 86 PfamEq Y Y N 50S ribosomal protein L23 rplW GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 28773 EBI-EMBL Ribosomal protein L23 50S ribosomal protein L23 NF012499.5 PF00277.23 SAA 30.8 30.8 102 PfamEq Y N N Serum amyloid A protein GO:0005576 30165816,30852808,7504491,8188253 131567 cellular organisms no rank 125 EBI-EMBL Serum amyloid A protein Serum amyloid A protein The serum amyloid A (SAA) proteins comprise a family of vertebrate amphipathic alpha-helical apolipoproteins that associate predominantly with high density lipoproteins (HDL) [1,2]. They play a role in the mobilisation of cholesterol for tissue repair and regeneration [3]. The synthesis of these proteins is greatly increased (as much as a 1000 fold) in inflammation, being a major acute phase reactant together with C-reactive protein. They act as cytokine-like proteins that are involved in cell-cell communication and in inflammatory, immunologic, neoplastic and protective pathways [4]. Prolonged elevation of plasma SAA levels, as in chronic inflammation, results in a pathological condition, called amyloidosis, which is characterised by the highly insoluble accumulation of SAA in several tissues. During chronic inflammation, SAA association with HDL can change its protein and lipid composition which abrogates the HDL anti-atherogenic properties, contributing to a pro-atherogenic state [3,4]. [1]. 7504491. Serum amyloid A (SAA): an acute phase protein and apolipoprotein. Malle E, Steinmetz A, Raynes JG;. Atherosclerosis. 1993;102:131-146. [2]. 8188253. Evolution of the serum amyloid A (SAA) protein superfamily. Uhlar CM, Burgess CJ, Sharp PM, Whitehead AS;. Genomics. 1994;19:228-235. [3]. 30852808. Serum amyloid A levels are associated with polymorphic variants in the serum amyloid A 1 and 2 genes. Griffiths K, Maxwell AP, McCarter RV, Nicol P, Hogg RE, Harbinson M, McKay GJ;. Ir J Med Sci. 2019;188:1175-1183. [4]. 30165816. Serum amyloid A - a review. Sack GH Jr;. Mol Med. 2018;24:46. (from Pfam) NF012500.5 PF00278.27 Orn_DAP_Arg_deC 23 23 95 domain Y N N Pyridoxal-dependent decarboxylase, C-terminal sheet domain GO:0003824 10378276 131567 cellular organisms no rank 149423 EBI-EMBL Pyridoxal-dependent decarboxylase, C-terminal sheet domain Pyridoxal-dependent decarboxylase, C-terminal sheet domain These pyridoxal-dependent decarboxylases act on ornithine, lysine, arginine and related substrates. [1]. 10378276. Structure of mammalian ornithine decarboxylase at 1.6 A resolution: stereochemical implications of PLP-dependent amino acid decarboxylases. Kern AD, Oliveira MA, Coffino P, Hackert ML;. Structure Fold Des 1999;7:567-581. (from Pfam) NF012502.5 PF00281.24 Ribosomal_L5 34.9 34.9 57 PfamEq Y Y N 50S ribosomal protein L5 rplE 131567 cellular organisms no rank 33216 EBI-EMBL Ribosomal protein L5 50S ribosomal protein L5 NF012503.5 PF00282.24 Pyridoxal_deC 27 27 375 domain Y Y N pyridoxal-dependent decarboxylase GO:0016830,GO:0019752,GO:0030170 7940675 131567 cellular organisms no rank 106840 EBI-EMBL Pyridoxal-dependent decarboxylase conserved domain pyridoxal-dependent decarboxylase NF012506.5 PF00285.26 Citrate_synt 27 27 357 domain Y Y N citrate/2-methylcitrate synthase GO:0046912 27656296 131567 cellular organisms no rank 118886 EBI-EMBL Citrate synthase, C-terminal domain Citrate synthase, C-terminal domain This is the long, C-terminal part of the enzyme. (from Pfam) NF012509.5 PF00288.31 GHMP_kinases_N 22.3 22.3 65 domain Y N N GHMP kinases N terminal domain GO:0005524 131567 cellular organisms no rank 214557 EBI-EMBL GHMP kinases N terminal domain GHMP kinases N terminal domain This family includes homoserine kinases, galactokinases and mevalonate kinases. (from Pfam) NF012510.5 PF00289.27 Biotin_carb_N 25.5 24.5 110 domain Y Y N biotin carboxylase N-terminal domain-containing protein 20443544,25383525,7915138 131567 cellular organisms no rank 229295 EBI-EMBL Biotin carboxylase, N-terminal domain Biotin carboxylase, N-terminal domain This domain is structurally related to the PreATP-grasp domain. The family contains the N-terminus of biotin carboxylase enzymes [1,3], and propionyl-CoA carboxylase A chain [2]. [1]. 7915138. Three-dimensional structure of the biotin carboxylase subunit. of acetyl-CoA carboxylase. Waldrop GL, Rayment I, Holden HM;. Biochemistry 1994;33:10249-10256. [2]. 25383525. Structure and function of a single-chain, multi-domain long-chain acyl-CoA carboxylase. Tran TH, Hsiao YS, Jo J, Chou CY, Dietrich LE, Walz T, Tong L;. Nature. 2015;518:120-124. [3]. 20443544. Structural impact of human and Escherichia coli biotin carboxyl carrier proteins on biotin attachment. Healy S, McDonald MK, Wu X, Yue WW, Kochan G, Oppermann U, Gravel RA;. Biochemistry. 2010;49:4687-4694. (from Pfam) NF012511.5 PF00290.25 Trp_syntA 27 27 259 domain Y Y N tryptophan synthase subunit alpha 4.2.1.20 GO:0004834,GO:0006568 3053720,9535826 131567 cellular organisms no rank 73184 EBI-EMBL Tryptophan synthase alpha chain tryptophan synthase subunit alpha NF012512.5 PF00291.30 PALP 35 35 295 subfamily Y Y N pyridoxal-phosphate dependent enzyme 131567 cellular organisms no rank 589710 EBI-EMBL Pyridoxal-phosphate dependent enzyme pyridoxal-phosphate dependent enzyme Members of this family are all pyridoxal-phosphate dependent enzymes. This family includes: serine dehydratase EC:4.2.1.13 P20132, threonine dehydratase EC:4.2.1.16 Swiss:P04968, tryptophan synthase beta chain EC:4.2.1.20 Swiss:P00932, threonine synthase EC:4.2.99.2 Swiss:P04990, cysteine synthase EC:4.2.99.8 P11096, cystathionine beta-synthase EC:4.2.1.22 Swiss:P35520, 1-aminocyclopropane-1-carboxylate deaminase EC:4.1.99.4 Swiss:P76316. (from Pfam) NF012513.5 PF00292.23 PAX 22 22 125 domain Y N N 'Paired box' domain GO:0003677,GO:0006355 9297966 131567 cellular organisms no rank 1438 EBI-EMBL 'Paired box' domain 'Paired box' domain NF012514.5 PF00293.33 NUDIX 21.1 21.1 134 domain Y Y N NUDIX domain-containing protein GO:0016787 131567 cellular organisms no rank 835072 EBI-EMBL NUDIX domain NUDIX domain NF012515.5 PF00294.29 PfkB 25.8 25.8 302 subfamily Y Y N PfkB family carbohydrate kinase 9519409 131567 cellular organisms no rank 594484 EBI-EMBL pfkB family carbohydrate kinase PfkB family carbohydrate kinase This family includes a variety of carbohydrate and pyrimidine kinases. [1]. 9519409. Identification and characterization of an operon in Salmonella typhimurium involved in thiamine biosynthesis. Petersen LA, Downs DM;. J Bacteriol 1997;179:4894-4900. (from Pfam) NF012516.5 PF00295.22 Glyco_hydro_28 22.9 22.9 324 domain Y Y N glycosyl hydrolase family 28 protein GO:0004650,GO:0005975 9115442 131567 cellular organisms no rank 38276 EBI-EMBL Glycosyl hydrolases family 28 glycosyl hydrolase family 28 domain Glycosyl hydrolase family 28 includes polygalacturonase EC:3.2.1.15 as well as rhamnogalacturonase A(RGase A), EC:3.2.1.-. These enzymes is important in cell wall metabolism. NF012517.5 PF00296.25 Bac_luciferase 27.9 27.9 314 subfamily Y Y N LLM class flavin-dependent oxidoreductase GO:0016705 131567 cellular organisms no rank 649537 EBI-EMBL Luciferase-like monooxygenase LLM class flavin-dependent oxidoreductase NF012518.5 PF00297.27 Ribosomal_L3 22.8 22.8 369 PfamEq Y Y N 50S ribosomal protein L3 rplC GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 37876 EBI-EMBL Ribosomal protein L3 50S ribosomal protein L3 NF012519.5 PF00298.24 Ribosomal_L11 21.4 21.4 69 PfamEq Y N N Ribosomal protein L11, RNA binding domain GO:0003735,GO:0005840,GO:0006412 8989327,9398519 131567 cellular organisms no rank 28957 EBI-EMBL Ribosomal protein L11, RNA binding domain Ribosomal protein L11, RNA binding domain NF012521.5 PF00300.27 His_Phos_1 21.7 21.7 194 domain Y Y N histidine phosphatase family protein 18092946 131567 cellular organisms no rank 375565 EBI-EMBL Histidine phosphatase superfamily (branch 1) histidine phosphatase family protein The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle. Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue. Structure and sequence analyses show that different families contribute different additional residues to the 'phosphate pocket' and, more surprisingly, differ in the position, in sequence and in three dimensions, of a catalytically essential acidic residue. The superfamily may be divided into two main branches. The larger branch 1 contains a wide variety of catalytic functions, the best known being fructose 2,6-bisphosphatase (found in a bifunctional protein with 2-phosphofructokinase) and cofactor-dependent phosphoglycerate mutase. The latter is an unusual example of a mutase activity in the superfamily: the vast majority of members appear to be phosphatases. The bacterial regulatory protein phosphatase SixA is also in branch 1 and has a minimal, and possible ancestral-like structure, lacking the large domain insertions that contribute to binding of small molecules in branch 1 members. [1]. 18092946. The histidine phosphatase superfamily: structure and function. Rigden DJ;. Biochem J. 2008;409:333-348. (from Pfam) NF012522.5 PF00301.25 Rubredoxin 23 23 47 domain Y Y N rubredoxin GO:0005506 131567 cellular organisms no rank 30948 EBI-EMBL Rubredoxin rubredoxin NF012523.5 PF00302.23 CAT 23.5 23.5 205 subfamily Y Y N CatA-like O-acetyltransferase 131567 cellular organisms no rank 14693 EBI-EMBL Chloramphenicol acetyltransferase CatA-like O-acetyltransferase This family contains both true examples of the CatA-like family of chloramphenicol acetyltransferase, involved in antibiotic resistance, and additional full-length homologs of unknown function, some below 25 percent identical. Note that the PGAP annotation pipeline has HMMs assigned higher precedence levels to annotate all trusted CatA family enzymes involved in resistance to chloramphenicol, so any that PGAP uses this HMM to name is unlikely to be a chloramphenicol resistance protein. NF012524.5 PF00303.24 Thymidylat_synt 24.3 24.3 266 PfamEq Y Y N thymidylate synthase 12029065,15046578,17890305 131567 cellular organisms no rank 58096 EBI-EMBL Thymidylate synthase thymidylate synthase This is a family of proteins that are flavin-dependent thymidylate synthases. [1]. 12029065. An alternative flavin-dependent mechanism for thymidylate synthesis. Myllykallio H, Lipowski G, Leduc D, Filee J, Forterre P, Liebl U;. Science. 2002;297:105-107. [2]. 15046578. Two distinct pathways for thymidylate (dTMP) synthesis in (hyper)thermophilic Bacteria and Archaea. Leduc D, Graziani S, Meslet-Cladiere L, Sodolescu A, Liebl U, Myllykallio H;. Biochem Soc Trans. 2004;32:231-235. [3]. 17890305. Flavin-dependent thymidylate synthase ThyX activity: implications for the folate cycle in bacteria. Leduc D, Escartin F, Nijhout HF, Reed MC, Liebl U, Skouloubris S, Myllykallio H;. J Bacteriol. 2007;189:8537-8545. (from Pfam) NF012527.5 PF00306.32 ATP-synt_ab_C 27 27 126 domain Y N N ATP synthase alpha/beta chain, C terminal domain GO:0015986 8065448 131567 cellular organisms no rank 52131 EBI-EMBL ATP synthase alpha/beta chain, C terminal domain ATP synthase alpha/beta chain, C terminal domain NF012529.5 PF00308.23 Bac_DnaA 23 23 180 domain Y Y N DnaA ATPase domain-containing protein 12234917 131567 cellular organisms no rank 135466 EBI-EMBL Bacterial DnaA ATPAse domain Bacterial DnaA ATPAse domain This entry represents the ATPAse domain of DnaA and similar proteins. [1]. 12234917. The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation. Erzberger JP, Pirruccello MM, Berger JM;. EMBO J. 2002;21:4763-4773. (from Pfam) NF012531.5 PF00310.26 GATase_2 19.9 19.9 420 domain Y N N Glutamine amidotransferases class-II 11967268 131567 cellular organisms no rank 89089 EBI-EMBL Glutamine amidotransferases class-II Glutamine amidotransferases class-II NF012532.5 PF00311.22 PEPcase 22.4 22.4 919 PfamEq Y Y N phosphoenolpyruvate carboxylase 4.1.1.31 GO:0006099,GO:0008964,GO:0015977 131567 cellular organisms no rank 57308 EBI-EMBL Phosphoenolpyruvate carboxylase phosphoenolpyruvate carboxylase NF012533.5 PF00312.27 Ribosomal_S15 31 31 81 PfamEq Y Y N 30S ribosomal protein S15 GO:0003735,GO:0005840,GO:0006412 9562554 131567 cellular organisms no rank 28333 EBI-EMBL Ribosomal protein S15 30S ribosomal protein S15 NF012534.5 PF00313.27 CSD 27 27 66 domain Y Y N cold shock domain-containing protein GO:0003676 8197194 131567 cellular organisms no rank 119280 EBI-EMBL 'Cold-shock' DNA-binding domain 'Cold-shock' DNA-binding domain NF012535.5 PF00314.22 Thaumatin 27.4 27.4 209 domain Y Y N thaumatin family protein 21324123 131567 cellular organisms no rank 1602 EBI-EMBL Thaumatin family thaumatin family protein NF012536.5 PF00316.25 FBPase 34.8 34.8 191 PfamEq Y N N Fructose-1-6-bisphosphatase, N-terminal domain 10089399 131567 cellular organisms no rank 26556 EBI-EMBL Fructose-1-6-bisphosphatase, N-terminal domain Fructose-1-6-bisphosphatase, N-terminal domain This family represents the N-terminus of this protein family. [1]. 10089399. Structure of rabbit liver fructose 1,6-bisphosphatase at 2.3 A resolution. Weeks CM, Roszak AW, Erman M, Kaiser R, Jornvall H, Ghosh D;. Acta Crystallogr D Biol Crystallogr 1999;55:93-102. (from Pfam) NF012537.5 PF00317.26 Ribonuc_red_lgN 28 28 77 domain Y Y N ribonucleotide reductase N-terminal alpha domain-containing protein GO:0004748,GO:0005524,GO:0006260 8052308 131567 cellular organisms no rank 90262 EBI-EMBL Ribonucleotide reductase, all-alpha domain Ribonucleotide reductase, all-alpha domain NF012538.5 PF00318.25 Ribosomal_S2 26.1 26.1 216 PfamEq Y Y N 30S ribosomal protein S2 GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 47070 EBI-EMBL Ribosomal protein S2 30S ribosomal protein S2 NF012544.5 PF00324.26 AA_permease 24.6 24.6 470 subfamily Y N N Amino acid permease GO:0016020,GO:0055085 131567 cellular organisms no rank 558304 EBI-EMBL Amino acid permease Amino acid permease NF012545.5 PF00325.25 Crp 21 21 32 domain Y N N Bacterial regulatory proteins, crp family GO:0003677,GO:0006355 131567 cellular organisms no rank 82179 EBI-EMBL Bacterial regulatory proteins, crp family Bacterial regulatory proteins, crp family NF012546.5 PF00326.26 Peptidase_S9 22.6 22.6 213 domain Y Y N prolyl oligopeptidase family serine peptidase GO:0006508,GO:0008236 131567 cellular organisms no rank 634956 EBI-EMBL Prolyl oligopeptidase family prolyl oligopeptidase family serine peptidase NF012547.5 PF00327.25 Ribosomal_L30 23 23 51 PfamEq Y Y N uL30 family ribosomal protein 131567 cellular organisms no rank 22587 EBI-EMBL Ribosomal protein L30p/L7e uL30 family ribosomal protein This family includes prokaryotic L30 and eukaryotic L7. (from Pfam) NF012549.5 PF00329.24 Complex1_30kDa 22.5 22.5 124 domain Y Y N NADH-quinone oxidoreductase subunit C 1.6.5.9 GO:0008137 131567 cellular organisms no rank 70052 EBI-EMBL Respiratory-chain NADH dehydrogenase, 30 Kd subunit NADH-quinone oxidoreductase subunit C NF012550.5 PF00330.25 Aconitase 28.7 28.7 463 domain Y Y N aconitase family protein 131567 cellular organisms no rank 211399 EBI-EMBL Aconitase family (aconitate hydratase) aconitase family protein Members of this family include aconitase (aconitate hydratase), 3-isopropylmalate dehydratase, and homoaconitase. NF012551.5 PF00331.25 Glyco_hydro_10 22.1 22.1 311 domain Y Y N endo-1,4-beta-xylanase GO:0004553,GO:0005975 131567 cellular organisms no rank 42379 EBI-EMBL Glycosyl hydrolase family 10 endo-1,4-beta-xylanase NF012552.5 PF00332.23 Glyco_hydro_17 28.2 28.2 306 domain Y Y N glycosyl hydrolase family 17 protein GO:0004553,GO:0005975 131567 cellular organisms no rank 4215 EBI-EMBL Glycosyl hydrolases family 17 glycosyl hydrolase 17 domain NF012553.5 PF00333.25 Ribosomal_S5 27.1 27.1 65 PfamEq Y N N Ribosomal protein S5, N-terminal domain GO:0003723,GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 29166 EBI-EMBL Ribosomal protein S5, N-terminal domain Ribosomal protein S5, N-terminal domain NF012554.5 PF00334.24 NDK 27 27 135 domain Y Y N nucleoside-diphosphate kinase 17330300,8263923 131567 cellular organisms no rank 41444 EBI-EMBL Nucleoside diphosphate kinase nucleoside-diphosphate kinase NF012558.5 PF00338.27 Ribosomal_S10 21.2 21.2 98 subfamily Y Y N 30S ribosomal protein S10 10938081,11279123 131567 cellular organisms no rank 12117 EBI-EMBL Ribosomal protein S10p/S20e 30S ribosomal protein S10 This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes. (from Pfam) NF012562.5 PF00342.24 PGI 22 22 486 PfamEq Y N N Phosphoglucose isomerase GO:0004347,GO:0006094,GO:0006096 833853 131567 cellular organisms no rank 84477 EBI-EMBL Phosphoglucose isomerase Phosphoglucose isomerase Phosphoglucose isomerase catalyses the interconversion of glucose-6-phosphate and fructose-6-phosphate. [1]. 833853. Crystallographic structure analysis of glucose 6-phosphate isomerase at 3-5 A resolution. Shaw PJ, Muirhead H. J Mol Biol 1977;109:475-485. (from Pfam) NF012563.5 PF00343.25 Phosphorylase 27 27 713 domain Y Y N glycogen/starch/alpha-glucan phosphorylase GO:0005975,GO:0008184 1304390 131567 cellular organisms no rank 76024 EBI-EMBL Carbohydrate phosphorylase glycogen/starch/alpha-glucan phosphorylase The members of this family catalyse the formation of glucose 1-phosphate from one of the following polyglucoses; glycogen, starch, glucan or maltodextrin. [1]. 1304390. Control of phosphorylase b conformation by a modified cofactor: crystallographic studies on R-state glycogen phosphorylase reconstituted with pyridoxal 5'-diphosphate. Leonidas DD, Oikonomakos NG, Papageorgiou AC, Acharya KR, Barford D, Johnson LN;. Protein Sci 1992;1:1112-1122. (from Pfam) NF012564.5 PF00344.25 SecY 32.2 32.2 306 domain Y N N SecY GO:0015031,GO:0016020 131567 cellular organisms no rank 51611 EBI-EMBL SecY SecY NF012566.5 PF00346.24 Complex1_49kDa 24 24 271 domain Y N N Respiratory-chain NADH dehydrogenase, 49 Kd subunit GO:0016651,GO:0048038,GO:0051287 131567 cellular organisms no rank 64068 EBI-EMBL Respiratory-chain NADH dehydrogenase, 49 Kd subunit Respiratory-chain NADH dehydrogenase, 49 Kd subunit NF012567.5 PF00347.28 Ribosomal_L6 27 27 80 PfamEq Y Y N 50S ribosomal protein L6 rplF GO:0003735,GO:0005840,GO:0006412,GO:0019843 8262035,9642068 131567 cellular organisms no rank 40741 EBI-EMBL Ribosomal protein L6 50S ribosomal protein L6 NF012568.5 PF00348.22 polyprenyl_synt 27 27 251 domain Y Y N polyprenyl synthetase family protein GO:0008299 131567 cellular organisms no rank 180790 EBI-EMBL Polyprenyl synthetase polyprenyl synthetase family protein NF012570.5 PF00350.28 Dynamin_N 27 27 168 domain Y Y N dynamin family protein 2144893,8939066 131567 cellular organisms no rank 73077 EBI-EMBL Dynamin family dynamin family protein NF012572.5 PF00352.26 TBP 22.9 22.9 85 domain Y N N Transcription factor TFIID (or TATA-binding protein, TBP) GO:0003677,GO:0006352 1436073,2197561,2374612,8598932 131567 cellular organisms no rank 2053 EBI-EMBL Transcription factor TFIID (or TATA-binding protein, TBP) Transcription factor TFIID (or TATA-binding protein, TBP) NF012573.5 PF00353.24 HemolysinCabind 23 7 36 repeat Y N N RTX calcium-binding repeat protein GO:0005509 1735728,2303029,8253063 131567 cellular organisms no rank 184999 EBI-EMBL RTX calcium-binding nonapeptide repeat (4 copies) RTX calcium-binding nonapeptide repeat (4 copies) NF012574.5 PF00354.23 Pentaxin 25 25 194 domain Y N N Pentaxin family 7772283,7881902,8114934 131567 cellular organisms no rank 1294 EBI-EMBL Pentaxin family Pentaxin family Pentaxins are also known as pentraxins. [1]. 7772283. Structure and function of the pentraxins. Gewurz H, Zhang XH, Lint TF;. Curr Opin Immunol 1995;7:54-64. [2]. 7881902. Comparative analyses of pentraxins: implications for protomer assembly and ligand binding. Srinivasan N, White HE, Emsley J, Wood SP, Pepys MB, Blundell TL;. Structure 1994;2:1017-1027. [3]. 8114934. Structure of pentameric human serum amyloid P component. Emsley J, White HE, O'Hara BP, Oliva G, Srinivasan N, Tickle IJ, Blundell TL, Pepys MB, Wood SP;. Nature 1994;367:338-345. (from Pfam) NF012575.5 PF00355.31 Rieske 20.3 20.3 88 domain Y Y N Rieske 2Fe-2S domain-containing protein GO:0051537 1961737,19862563,8386158,8736555 131567 cellular organisms no rank 319735 EBI-EMBL Rieske [2Fe-2S] domain Rieske 2Fe-2S domain The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilises the protein [4]. [1]. 8736555. Structure of a water soluble fragment of the 'Rieske' iron- sulfur protein of the bovine heart mitochondrial cytochrome bc1 complex determined by MAD phasing at 1.5 A resolution. Iwata S, Saynovits M, Link TA, Michel H. Structure 1996;4:567-579. [2]. 1961737. Functional analysis in yeast of cDNA coding for the mitochondrial Rieske iron-sulfur protein of higher plants. Huang JT, Struck F, Matzinger DF, Levings CS;. Proc Natl Acad Sci U S A 1991;88:10716-10720. [3]. 8386158. The mitochondrial targeting presequence of the Rieske iron-sulfur protein is processed in a single step after insertion into the cytochrome bc1 complex in mammals and retained as a subunit in the complex. Brandt U, Yu L, Yu CA, Trumpower BL;. J Biol Chem 1993;268:8387-8390. [4]. 19862563. Role of a novel disulfide bridge within the all-beta fold of soluble Rieske proteins. Botelho HM, Leal SS, Veith A, Prosinecki V, Bauer C, Frohlich R, Kletzin A, Gomes CM;. J Biol Inorg Chem. 2010;15:271-281. (from Pfam) NF012579.5 PF00359.27 PTS_EIIA_2 27 27 144 domain Y Y N PTS sugar transporter subunit IIA 131567 cellular organisms no rank 208150 EBI-EMBL Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 PTS sugar transporter subunit IIA NF012581.5 PF00361.25 Proton_antipo_M 21.5 21.5 294 domain Y Y N proton-conducting transporter membrane subunit 1470679,24142251 131567 cellular organisms no rank 330764 EBI-EMBL Proton-conducting membrane transporter proton-conducting transporter membrane subunit Members of this family include multiple membrane-spanning proteins associated with proton translocation. These include NADH ubiquinone oxidoreductase subunits NuoL, NuoN, and NuoM, hydrogenase components HyfB, HyfD, and HyfF, as well as subunits of carbon monoxide dehydrogenase, F420 dehydrogenase, etc, as well as Na+/H+ antiporter subunits. NF012582.5 PF00362.23 Integrin_beta 24.8 24.8 248 domain Y N N Integrin beta chain VWA domain 10087915 131567 cellular organisms no rank 337 EBI-EMBL Integrin beta chain VWA domain Integrin beta chain VWA domain Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer [1]. This domain corresponds to the integrin beta VWA domain. [1]. 10087915. Integrin alpha- and beta 4-subunit-domain homologues in cyanobacterial proteins. May AP, Ponting CP;. Trends Biochem Sci 1999;24:12-13. (from Pfam) NF012584.5 PF00364.27 Biotin_lipoyl 22.1 22.1 73 domain Y Y N biotin/lipoyl-containing protein 131567 cellular organisms no rank 509755 EBI-EMBL Biotin-requiring enzyme biotin/lipoyl-binding domain This family covers two Prosite entries, the conserved lysine residue binds biotin in one group and lipoic acid in the other. Note that the HMM does not currently recognise the Glycine cleavage system H proteins. (from Pfam) NF012585.5 PF00365.25 PFK 30.9 30.9 277 domain Y Y N 6-phosphofructokinase 2.7.1.11 GO:0006096 131567 cellular organisms no rank 65746 EBI-EMBL Phosphofructokinase 6-phosphofructokinase NF012586.5 PF00366.25 Ribosomal_S17 25.9 25.9 68 PfamEq Y Y N 30S ribosomal protein S17 rpsQ GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 27159 EBI-EMBL Ribosomal protein S17 30S ribosomal protein S17 NF012588.5 PF00368.23 HMG-CoA_red 27 27 368 PfamEq Y N N Hydroxymethylglutaryl-coenzyme A reductase GO:0004420,GO:0015936 15535874,7792601 131567 cellular organisms no rank 21122 EBI-EMBL Hydroxymethylglutaryl-coenzyme A reductase Hydroxymethylglutaryl-coenzyme A reductase The HMG-CoA reductases catalyse the conversion of HMG-CoA to mevalonate, which is the rate-limiting step in the synthesis of isoprenoids like cholesterol. Probably because of the critical role of this enzyme in cholesterol homeostasis, mammalian HMG-CoA reductase is heavily regulated at the transcriptional, translational, and post-translational levels [2]. [1]. 7792601. Crystal structure of Pseudomonas mevalonii HMG-CoA reductase at 3.0 angstrom resolution. Lawrence CM, Rodwell VW, Stauffacher CV;. Science 1995;268:1758-1762. [2]. 15535874. The 3-hydroxy-3-methylglutaryl coenzyme-A (HMG-CoA) reductases. Friesen JA, Rodwell VW;. Genome Biol 2004;5:248. (from Pfam) NF012589.5 PF00370.26 FGGY_N 28.8 28.8 245 domain Y Y N FGGY family carbohydrate kinase GO:0005975,GO:0016301 8430315,9843423 131567 cellular organisms no rank 302024 EBI-EMBL FGGY family of carbohydrate kinases, N-terminal domain FGGY family of carbohydrate kinases, N-terminal domain This domain adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain. [1]. 8430315. Structure of the regulatory complex of Escherichia coli IIIGlc with glycerol kinase. Hurley JH, Faber HR, Worthylake D, Meadow ND, Roseman S, Pettigrew DW, Remington SJ;. Science. 1993;259:673-677. [2]. 9843423. Crystal structure of a complex of Escherichia coli glycerol kinase and an allosteric effector fructose 1,6-bisphosphate. Ormo M, Bystrom CE, Remington SJ;. Biochemistry 1998;37:16565-16572. (from Pfam) NF012592.5 PF00374.24 NiFeSe_Hases 25.8 25.8 508 domain Y Y N nickel-dependent hydrogenase large subunit GO:0016151 131567 cellular organisms no rank 40025 EBI-EMBL Nickel-dependent hydrogenase nickel-dependent hydrogenase large subunit NF012593.5 PF00375.23 SDF 27.9 27.9 387 subfamily Y Y N cation:dicarboxylate symporter family transporter GO:0015293,GO:0016020 131567 cellular organisms no rank 169311 EBI-EMBL Sodium:dicarboxylate symporter family cation:dicarboxylate symporter family transporter NF012594.5 PF00376.28 MerR 28.2 28.2 38 domain Y Y N MerR family DNA-binding transcriptional regulator GO:0003677,GO:0006355 131567 cellular organisms no rank 510257 EBI-EMBL MerR family regulatory protein MerR family DNA-binding transcriptional regulator NF012596.5 PF00378.25 ECH_1 27 27 251 domain Y Y N enoyl-CoA hydratase-related protein GO:0003824 131567 cellular organisms no rank 699005 EBI-EMBL Enoyl-CoA hydratase/isomerase enoyl-CoA hydratase-related protein This family contains a diverse set of enzymes including: enoyl-CoA hydratase, napthoate synthase, carnitate racemase, 3-hydroxybutyryl-CoA dehydratase and dodecanoyl-CoA delta-isomerase. (from Pfam) NF012598.5 PF00380.24 Ribosomal_S9 22.5 22.5 121 PfamEq Y Y N 30S ribosomal protein S9 rpsI GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 34263 EBI-EMBL Ribosomal protein S9/S16 30S ribosomal protein S9 This family includes small ribosomal subunit S9 from prokaryotes and S16 from eukaryotes. (from Pfam) NF012599.5 PF00381.24 PTS-HPr 23 23 81 domain Y Y N HPr family phosphocarrier protein 8226757 131567 cellular organisms no rank 94156 EBI-EMBL PTS HPr component phosphorylation site HPr family phosphocarrier protein NF012601.5 PF00383.28 dCMP_cyt_deam_1 25 25 102 domain Y N N Cytidine and deoxycytidylate deaminase zinc-binding region 8203015 131567 cellular organisms no rank 269990 EBI-EMBL Cytidine and deoxycytidylate deaminase zinc-binding region Cytidine and deoxycytidylate deaminase zinc-binding region NF012602.5 PF00384.27 Molybdopterin 24 24 353 domain Y Y N molybdopterin-dependent oxidoreductase GO:0016491 8890912 131567 cellular organisms no rank 447546 EBI-EMBL Molybdopterin oxidoreductase molybdopterin-dependent oxidoreductase NF012603.5 PF00385.29 Chromo 25.1 25.1 53 domain Y N N Chromo (CHRromatin Organisation MOdifier) domain 131567 cellular organisms no rank 112 EBI-EMBL Chromo (CHRromatin Organisation MOdifier) domain Chromo (CHRromatin Organisation MOdifier) domain NF012604.5 PF00386.26 C1q 23.7 23.7 127 domain Y Y N C1q-like domain-containing protein 131567 cellular organisms no rank 1536 EBI-EMBL C1q domain C1q domain C1q is a subunit of the C1 enzyme complex that activates the serum complement system. (from Pfam) NF012606.5 PF00388.24 PI-PLC-X 23.1 23.1 144 PfamEq Y Y N phosphatidylinositol-specific phospholipase C domain-containing protein 131567 cellular organisms no rank 9293 EBI-EMBL Phosphatidylinositol-specific phospholipase C, X domain phosphatidylinositol-specific phospholipase C domain-containing protein This associates with Pfam:PF00387 to form a single structural unit. (from Pfam) NF012607.5 PF00389.35 2-Hacid_dh 24.6 24.6 134 domain Y N N D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain GO:0016616,GO:0051287 9126843 131567 cellular organisms no rank 328950 EBI-EMBL D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain This family represents the largest portion of the catalytic domain of 2-hydroxyacid dehydrogenases as the NAD binding domain is inserted within the structural domain. [1]. 9126843. Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution. Dengler U, Niefind K, Kiess M, Schomburg D;. J Mol Biol 1997;267:640-660. (from Pfam) NF012608.5 PF00390.24 malic 23.1 23.1 182 domain Y N N Malic enzyme, N-terminal domain GO:0004471 131567 cellular organisms no rank 103347 EBI-EMBL Malic enzyme, N-terminal domain Malic enzyme, N-terminal domain NF012609.5 PF00391.28 PEP-utilizers 23.1 23.1 72 domain Y Y N PEP-utilizing enzyme GO:0016310,GO:0016772 8610096 131567 cellular organisms no rank 220252 EBI-EMBL PEP-utilising enzyme, mobile domain PEP-utilizing enzyme swiveling domain This domain is a "swivelling" beta/beta/alpha domain which is thought to be mobile in all proteins known to contain it. [1]. 8610096. Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites. Herzberg O, Chen CC, Kapadia G, McGuire M, Carroll LJ, Noh SJ, Dunaway-Mariano D;. Proc Natl Acad Sci U S A 1996;93:2652-2657. (from Pfam) NF012610.5 PF00392.26 GntR 27 27 64 domain Y Y N GntR family transcriptional regulator GO:0003700,GO:0006355 11756427,12867439,15247334,16672238,16925557,16936034 131567 cellular organisms no rank 1251881 EBI-EMBL Bacterial regulatory proteins, gntR family GntR family transcriptional regulator This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR [1-2][4][5]. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships [3]. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor [5]. [1]. 12867439. PlmA, a new member of the GntR family, has plasmid maintenance functions in Anabaena sp. strain PCC 7120. Lee MH, Scherer M, Rigali S, Golden JW;. J Bacteriol 2003;185:4315-4325. [2]. 11756427. Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies. Rigali S, Derouaux A, Giannotta F, Dusart J;. J Biol Chem 2002;277:12507-12515. [3]. 15247334. Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships. Rigali S, Schlicht M, Hoskisson P, Nothaft H, Merzbacher M, Joris B, Titgemeyer F;. Nucleic Acids Res 2004;32:3418-3426. [4]. 16936034. A new GntR family transcriptional regulator in streptomyces coelicolor is required for morphogenesis and antibiotic production and controls transcription of an ABC transporter in response to carbon source. Hillerich B, Westpheling J;. J Bacteriol. 2006;188:7477-7487. [5]. 16925557. The sugar phosphotransfer. TRUNCATED at 1650 bytes (from Pfam) NF012611.5 PF00393.24 6PGD 27 27 290 domain Y N N 6-phosphogluconate dehydrogenase, C-terminal domain GO:0004616,GO:0006098 131567 cellular organisms no rank 71486 EBI-EMBL 6-phosphogluconate dehydrogenase, C-terminal domain 6-phosphogluconate dehydrogenase, C-terminal domain This family represents the C-terminal all-alpha domain of 6-phosphogluconate dehydrogenase. The domain contains two structural repeats of 5 helices each. (from Pfam) NF012612.5 PF00394.27 Cu-oxidase 21 21 157 domain Y N N Multicopper oxidase 1548698,2404764 131567 cellular organisms no rank 66240 EBI-EMBL Multicopper oxidase Multicopper oxidase Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain. [1]. 2404764. The blue oxidases, ascorbate oxidase, laccase and ceruloplasmin. Modelling and structural relationships. Messerschmidt A, Huber R;. Eur J Biochem 1990;187:341-352. [2]. 1548698. Refined crystal structure of ascorbate oxidase at 1.9 A resolution. Messerschmidt A, Ladenstein R, Huber R, Bolognesi M, Avigliano L, Petruzzelli R, Rossi A, Finazzi-Agro A;. J Mol Biol 1992;224:179-205. (from Pfam) NF012616.5 PF00398.25 RrnaAD 24 24 263 domain Y Y N rRNA adenine N-6-methyltransferase family protein 9187657 131567 cellular organisms no rank 148268 EBI-EMBL Ribosomal RNA adenine dimethylase rRNA adenine N-6-methyltransferase family protein NF012618.5 PF00400.37 WD40 27 12.1 39 repeat Y N N WD40 repeat-containing protein GO:0005515 8090199 131567 cellular organisms no rank 103855 EBI-EMBL WD domain, G-beta repeat WD40 repeat NF012621.5 PF00403.31 HMA 24.8 24.8 62 domain Y Y N cation transporter GO:0046872 10404590 131567 cellular organisms no rank 266522 EBI-EMBL Heavy-metal-associated domain Heavy-metal-associated domain NF012622.5 PF00404.23 Dockerin_1 22.9 22.9 57 domain Y Y N dockerin type I domain-containing protein GO:0000272,GO:0004553 10390637,10898940 131567 cellular organisms no rank 28306 EBI-EMBL Dockerin type I domain dockerin type I domain The dockerin repeat is the binding partner of the cohesin domain Pfam:PF00963. The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome [1]. The dockerin repeats, each bearing homology to the EF-hand calcium-binding loop bind calcium [2]. This family contains two copies of the repeat. [1]. 10390637. The cellulosome concept as an efficient microbial strategy for the degradation of insoluble polysaccharides [In Process Citation]. Shoham Y, Lamed R, Bayer EA;. Trends Microbiol 1999;7:275-281. [2]. 10898940. Secondary structure and calcium-induced folding of the Clostridium thermocellum dockerin domain determined by NMR spectroscopy. Lytle BL, Volkman BF, Westler WM, Wu JH;. Arch Biochem Biophys 2000;379:237-244. (from Pfam) NF012624.5 PF00406.27 ADK 26.8 26.8 151 PfamEq Y Y N nucleoside monophosphate kinase 9715904 131567 cellular organisms no rank 58757 EBI-EMBL Adenylate kinase nucleoside monophosphate kinase NF012626.5 PF00408.25 PGM_PMM_IV 23.1 23.1 68 domain Y N N Phosphoglucomutase/phosphomannomutase, C-terminal domain GO:0016868 1532581 131567 cellular organisms no rank 202476 EBI-EMBL Phosphoglucomutase/phosphomannomutase, C-terminal domain Phosphoglucomutase/phosphomannomutase, C-terminal domain NF012627.5 PF00410.24 Ribosomal_S8 24 24 126 PfamEq Y Y N 30S ribosomal protein S8 rpsH GO:0003735,GO:0005840,GO:0006412 8805594 131567 cellular organisms no rank 28427 EBI-EMBL Ribosomal protein S8 30S ribosomal protein S8 NF012628.5 PF00411.24 Ribosomal_S11 25.1 25.1 110 PfamEq Y Y N 30S ribosomal protein S11 rpsK GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 19365 EBI-EMBL Ribosomal protein S11 30S ribosomal protein S11 NF012629.5 PF00412.27 LIM 22.9 22.9 58 domain Y Y N LIM domain-containing protein 7664053 131567 cellular organisms no rank 113 EBI-EMBL LIM domain LIM domain This family represents two copies of the LIM structural domain. [1]. 7664053. Structure of the carboxy-terminal Lim domain from the cysteine rich protein Crp. Perez-Alvarado GC, Miles C, Michelsen JW, Louis HA, Winge DR, Beckerle MC, Summers MF;. Nat Struct Biol 1994;1:388-398. (from Pfam) NF012630.5 PF00413.29 Peptidase_M10 24 24 159 domain Y Y N matrixin family metalloprotease 3.4.24.- GO:0004222,GO:0006508,GO:0008270,GO:0031012 7656014,7674922 131567 cellular organisms no rank 27460 EBI-EMBL Matrixin matrixin family metalloprotease The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. [1]. 7674922. Evolutionary families of metallopeptidases. Rawlings ND, Barrett AJ;. Meth Enzymol 1995;248:183-228. [2]. 7656014. The NMR structure of the inhibited catalytic domain of human stromelysin-1. Gooley PR, O'Connell JF, Marcy AI, Cuca GC, Salowe SP, Bush BL, Hermes JD, Esser CK, Hagmann WK, Springer JP, et al;. Nat Struct Biol 1994;1:111-118. (from Pfam) NF012632.5 PF00415.23 RCC1 21.7 21.7 50 repeat Y N N RCC1 family seven-bladed propeller repeat protein 9510255 131567 cellular organisms no rank 17086 EBI-EMBL Regulator of chromosome condensation (RCC1) repeat RCC1 family seven-bladed propeller repeat NF012633.5 PF00416.27 Ribosomal_S13 31 31 128 PfamEq Y Y N 30S ribosomal protein S13 rpsM GO:0003723,GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 27698 EBI-EMBL Ribosomal protein S13/S18 30S ribosomal protein S13 This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes. (from Pfam) NF012636.5 PF00420.29 Oxidored_q2 26.1 26.1 95 domain Y Y N NADH-quinone oxidoreductase subunit K 1.6.5.9 131567 cellular organisms no rank 57973 EBI-EMBL NADH-ubiquinone/plastoquinone oxidoreductase chain 4L NADH-quinone oxidoreductase subunit K NF012639.5 PF00424.23 REV 22 22 94 domain Y N N REV protein (anti-repression trans-activator protein) GO:0003700,GO:0006355,GO:0042025 131567 cellular organisms no rank 26 EBI-EMBL REV protein (anti-repression trans-activator protein) REV protein (anti-repression trans-activator protein) NF012640.5 PF00425.23 Chorismate_bind 27 27 257 domain Y Y N chorismate-binding protein 11371633,11450855 131567 cellular organisms no rank 238318 EBI-EMBL chorismate binding enzyme chorismate-binding protein This family includes the catalytic regions of the chorismate binding enzymes anthranilate synthase, isochorismate synthase, aminodeoxychorismate synthase and para-aminobenzoate synthase. [1]. 11371633. The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan. Spraggon G, Kim C, Nguyen-Huu X, Yee MC, Yanofsky C, Mills SE;. Proc Natl Acad Sci U S A 2001;98:6021-6026. [2]. 11450855. A metabolic node in action: chorismate-utilizing enzymes in microorganisms. Dosselaere F, Vanderleyden J;. Crit Rev Microbiol 2001;27:75-131. (from Pfam) NF012643.5 PF00428.24 Ribosomal_60s 28.1 28.1 88 domain Y N N 60s Acidic ribosomal protein 8722011 131567 cellular organisms no rank 1281 EBI-EMBL 60s Acidic ribosomal protein 60s Acidic ribosomal protein This family includes archaebacterial L12, eukaryotic P0, P1 and P2. [1]. 8722011. Proteins P1, P2, and P0, components of the eukaryotic ribosome stalk. New structural and functional aspects. Remacha M, Jimenez-Diaz A, Santos C, Briones E, Zambrano R, Rodriguez Gabriel MA, Guarinos E, Ballesta JP;. Biochem Cell Biol 1995;73:959-968. (from Pfam) NF012645.5 PF00430.23 ATP-synt_B 28 28 132 domain Y N N ATP synthase B/B' CF(0) GO:0015078,GO:0015986,GO:0045263 131567 cellular organisms no rank 60415 EBI-EMBL ATP synthase B/B' CF(0) ATP synthase B/B' CF(0) Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in Pfam:PF00006 (from Pfam) NF012646.5 PF00431.25 CUB 21.4 21.4 110 domain Y Y N CUB domain-containing protein 8510165,9334740 131567 cellular organisms no rank 1995 EBI-EMBL CUB domain CUB domain NF012647.5 PF00432.26 Prenyltrans 26.5 6 44 domain Y Y N prenyltransferase/squalene oxidase repeat-containing protein GO:0003824 8016864,9295270 131567 cellular organisms no rank 37319 EBI-EMBL Prenyltransferase and squalene oxidase repeat Prenyltransferase and squalene oxidase repeat NF012651.5 PF00436.30 SSB 26 26 104 domain Y Y N single-stranded DNA-binding protein GO:0003697 9033597,9192620,9271227 131567 cellular organisms no rank 138182 EBI-EMBL Single-strand binding protein family single-stranded DNA-binding protein This family includes single stranded binding proteins and also the primosomal replication protein N (PriB). PriB forms a complex with PriA, PriC and ssDNA. [1]. 9192620. Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution. Raghunathan S, Ricard CS, Lohman TM, Waksman G;. Proc Natl Acad Sci U S A 1997;94:6652-6657. [2]. 9033597. Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 A resolution. Yang C, Curth U, Urbanke C, Kang C;. Nat Struct Biol 1997;4:153-157. [3]. 9271227. A common core for binding single-stranded DNA: structural comparison of the single-stranded DNA-binding proteins (SSB) from E. coli and human mitochondria. Webster G, Genschel J, Curth U, Urbanke C, Kang C, Hilgenfeld R;. FEBS Lett 1997;411:313-316. (from Pfam) NF012652.5 PF00437.25 T2SSE 24.9 24.9 269 subfamily Y Y N ATPase, T2SS/T4P/T4SS family 11566978,8102361 131567 cellular organisms no rank 263041 EBI-EMBL Type II/IV secretion system protein ATPase, T2SS/T4P/T4SS family Members of this family include ATPases of type 2 secretion systems (T2SS), type 4 pilin (T4P, often involved in twitching motility), and type 4 secretion systems. NF012653.5 PF00438.25 S-AdoMet_synt_N 33.1 33.1 99 domain Y Y N S-adenosylmethionine synthetase N-terminal domain-containing protein GO:0004478,GO:0006556 8611562 131567 cellular organisms no rank 66184 EBI-EMBL S-adenosylmethionine synthetase, N-terminal domain S-adenosylmethionine synthetase, N-terminal domain The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold. [1]. 8611562. Structure and function of S-adenosylmethionine synthetase: crystal structures of S-adenosylmethionine synthetase with ADP, BrADP, and PPi at 28 angstroms resolution. Takusagawa F, Kamitori S, Markham GD;. Biochemistry 1996;35:2586-2596. (from Pfam) NF012655.5 PF00440.28 TetR_N 24 24 47 domain Y Y N TetR family transcriptional regulator GO:0003677 131567 cellular organisms no rank 2123998 EBI-EMBL Bacterial regulatory proteins, tetR family TetR family transcriptional regulator NF012656.5 PF00441.29 Acyl-CoA_dh_1 22.4 22.4 150 domain Y Y N acyl-CoA dehydrogenase family protein GO:0016627 11514662,7857927,8356049 131567 cellular organisms no rank 936494 EBI-EMBL Acyl-CoA dehydrogenase, C-terminal domain acyl-CoA dehydrogenase C-terminal domain C-terminal domain of Acyl-CoA dehydrogenase is an all-alpha, four helical up-and-down bundle. [1]. 7857927. Three-dimensional structure of butyryl-CoA dehydrogenase from Megasphaera elsdenii. Djordjevic S, Pace CP, Stankovich MT, Kim JJ;. Biochemistry. 1995;34:2163-2171. [2]. 8356049. Crystal structures of medium-chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate. Kim JJ, Wang M, Paschke R;. Proc Natl Acad Sci U S A 1993;90:7523-7527. [3]. 11514662. Sequence-structure analysis of FAD-containing proteins. Dym O, Eisenberg D;. Protein Sci 2001;10:1712-1728. (from Pfam) NF012662.5 PF00448.27 SRP54 22.7 22.7 196 domain Y N N SRP54-type protein, GTPase domain GO:0005525,GO:0006614 9002525 131567 cellular organisms no rank 180297 EBI-EMBL SRP54-type protein, GTPase domain SRP54-type protein, GTPase domain This family includes relatives of the G-domain of the SRP54 family of proteins. [1]. 9002525. Crystal structure of the NG domain from the signal-recognition particle receptor FtsY. Montoya G, Svensson C, Luirink J, Sinning I;. Nature 1997;385:365-368. (from Pfam) NF012663.5 PF00449.25 Urease_alpha 23 23 121 domain Y N N Urease alpha-subunit, N-terminal domain 7754395 131567 cellular organisms no rank 45766 EBI-EMBL Urease alpha-subunit, N-terminal domain Urease alpha-subunit, N-terminal domain The N-terminal domain is a composite domain and plays a major trimer stabilising role by contacting the catalytic domain of the symmetry related alpha-subunit. [1]. 7754395. The crystal structure of urease from Klebsiella aerogenes. Jabri E, Carr MB, Hausinger RP, Karplus PA;. Science 1995;268:998-1004. (from Pfam) NF012664.5 PF00450.27 Peptidase_S10 21.9 21.9 420 domain Y Y N S10 family serine carboxypeptidase-like protein GO:0004185,GO:0006508 131567 cellular organisms no rank 18378 EBI-EMBL Serine carboxypeptidase S10 family serine carboxypeptidase-like protein Characterized members of S10 family of hydrolases are primarily eukaryotic, including mostly serine carboxypeptidases (EC 3.4.16.-), but also littorine synthase (EC 2.3.1.185), hydroxynitrile lyase, and anthocyanin 7-O-glucoside acyltransferase, and other serine carboxypeptidase-like acyltransferases. NF012669.5 PF00455.27 DeoRC 31.8 31.8 160 domain Y N N DeoR C terminal sensor domain 16376935,18844374 131567 cellular organisms no rank 182332 EBI-EMBL DeoR C terminal sensor domain DeoR C terminal sensor domain The sensor domains of the DeoR are catalytically inactive versions of the ISOCOT fold, but retain the substrate binding site [1]. DeorC senses diverse sugar derivatives such as deoxyribose nucleoside (DeoR), tagatose phosphate (LacR), galactosamine (AgaR), myo-inositol (Bacillus IolR) and L-ascorbate (UlaR) [1,2]. It can also bind L-ascorbate 6-phosphate, agrocinopines, sn-glycerol 3-phosphate, and sulfoquinovose (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 16376935. Diversification of catalytic activities and ligand interactions in the protein fold shared by the sugar isomerases, eIF2B, DeoR transcription factors, acyl-CoA transferases and methenyltetrahydrofolate synthetase. Anantharaman V, Aravind L;. J Mol Biol. 2006;356:823-842. [2]. 18844374. Quaternary structural transitions in the DeoR-type repressor UlaR control transcriptional readout from the L-ascorbate utilization regulon in Escherichia coli. Garces F, Fernandez FJ, Gomez AM, Perez-Luque R, Campos E, Prohens R, Aguilar J, Baldoma L, Coll M, Badia J, Vega MC;. Biochemistry. 2008;47:11424-11433. (from Pfam) NF012670.5 PF00456.26 Transketolase_N 22 22 334 domain Y N N Transketolase, thiamine diphosphate binding domain 1628611,8176731 131567 cellular organisms no rank 223400 EBI-EMBL Transketolase, thiamine diphosphate binding domain Transketolase, thiamine diphosphate binding domain This family includes transketolase enzymes EC:2.2.1.1. and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit Swiss:P37941 EC:1.2.4.4. Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis. [1]. 8176731. Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 A resolution. Nikkola M, Lindqvist Y, Schneider G;. J Mol Biol 1994;238:387-404. [2]. 1628611. Three-dimensional structure of transketolase, a thiamine diphosphate dependent enzyme, at 2.5 A resolution. Lindqvist Y, Schneider G, Ermler U, Sundstrom M;. EMBO J 1992;11:2373-2379. (from Pfam) NF012671.5 PF00457.23 Glyco_hydro_11 27 27 178 domain Y Y N glycoside hydrolase family 11 protein 131567 cellular organisms no rank 7068 EBI-EMBL Glycosyl hydrolases family 11 glycoside hydrolase family 11 protein NF012673.5 PF00459.30 Inositol_P 27 27 271 subfamily Y Y N inositol monophosphatase family protein 7947723 131567 cellular organisms no rank 177746 EBI-EMBL Inositol monophosphatase family inositol monophosphatase family protein NF012675.5 PF00462.29 Glutaredoxin 22.9 22.9 60 domain Y Y N glutaredoxin domain-containing protein GO:0015035 131567 cellular organisms no rank 125306 EBI-EMBL Glutaredoxin Glutaredoxin NF012676.5 PF00463.26 ICL 26 26 526 domain Y N N Isocitrate lyase family GO:0004451,GO:0019752 131567 cellular organisms no rank 61213 EBI-EMBL Isocitrate lyase family Isocitrate lyase family NF012677.5 PF00464.24 SHMT 27 27 399 domain Y N N Serine hydroxymethyltransferase 131567 cellular organisms no rank 99971 EBI-EMBL Serine hydroxymethyltransferase Serine hydroxymethyltransferase NF012678.5 PF00465.24 Fe-ADH 26.8 26.8 363 subfamily Y Y N iron-containing alcohol dehydrogenase 1.1.1.1 GO:0016491,GO:0046872 131567 cellular organisms no rank 279433 EBI-EMBL Iron-containing alcohol dehydrogenase iron-containing alcohol dehydrogenase NF012679.5 PF00466.25 Ribosomal_L10 22.8 22.8 100 PfamEq Y Y N 50S ribosomal protein L10 rplJ GO:0042254 131567 cellular organisms no rank 40201 EBI-EMBL Ribosomal protein L10 50S ribosomal protein L10 NF012680.5 PF00467.34 KOW 22.3 22.3 32 domain Y Y N KOW motif-containing protein 8987397 131567 cellular organisms no rank 54747 EBI-EMBL KOW motif KOW motif This family has been extended to coincide with ref [1]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG. [1]. 8987397. KOW: a novel motif linking a bacterial transcription factor with ribosomal proteins. Kyrpides NC, Woese CR, Ouzounis CA;. Trends Biochem Sci 1996;21:425-426. (from Pfam) NF012686.5 PF00474.22 SSF 22.8 22.8 406 subfamily Y Y N sodium:solute symporter family transporter GO:0016020,GO:0022857,GO:0055085 131567 cellular organisms no rank 239374 EBI-EMBL Sodium:solute symporter family sodium:solute symporter family transporter This family includes Swiss:P33413 which is not in the Prosite entry. Membership of this family is supported by a significant blast score. (from Pfam) NF012687.5 PF00475.23 IGPD 27 27 144 PfamEq Y N N Imidazoleglycerol-phosphate dehydratase GO:0000105,GO:0004424 131567 cellular organisms no rank 53209 EBI-EMBL Imidazoleglycerol-phosphate dehydratase Imidazoleglycerol-phosphate dehydratase NF012688.5 PF00476.25 DNA_pol_A 34.3 34.3 381 subfamily_domain Y Y N DNA polymerase GO:0003677,GO:0003887,GO:0006260 131567 cellular organisms no rank 126289 EBI-EMBL DNA polymerase family A DNA polymerase NF012689.5 PF00477.22 LEA_5 40 40 109 domain Y Y N KGG domain-containing protein 131567 cellular organisms no rank 84 EBI-EMBL Small hydrophilic plant seed protein Small hydrophilic plant seed protein This model identifies repetitive plant seed proteins, but also highly similar repetitive bacterial proteins. Sample repeats include GGQTRKEQLGHEGYSEMG from a corn ate embryogenesis abundant protein, GGETRKEQLGPEGYSALG from reported bacterial protein such as WP_209616755.1. The repeat is similar to one described in Pfam model PF10685. NF012690.5 PF00478.30 IMPDH 25.6 25.6 345 domain Y Y N IMP dehydrogenase 1.1.1.205 GO:0003824 10200156,9271497 131567 cellular organisms no rank 156632 EBI-EMBL IMP dehydrogenase / GMP reductase domain IMP dehydrogenase / GMP reductase domain This family is involved in biosynthesis of guanosine nucleotide. Members of this family contain a TIM barrel structure. In the inosine monophosphate dehydrogenases 2 CBS domains Pfam:PF00571 are inserted in the TIM barrel [2]. This family is a member of the common phosphate binding site TIM barrel family. [1]. 9271497. Crystal structure of Tritrichomonas foetus inosine-5'-monophosphate dehydrogenase and the enzyme-product complex. Whitby FG, Luecke H, Kuhn P, Somoza JR, Huete-Perez JA, Phillips JD, Hill CP, Fletterick RJ, Wang CC;. Biochemistry 1997;36:10666-10674. [2]. 10200156. Characteristics and crystal structure of bacterial inosine-5'-monophosphate dehydrogenase. Zhang R, Evans G, Rotella FJ, Westbrook EM, Beno D, Huberman E, Joachimiak A, Collart FR;. Biochemistry 1999;38:4691-4700. (from Pfam) NF012692.5 PF00480.25 ROK 22.9 22.9 294 subfamily Y Y N ROK family protein 131567 cellular organisms no rank 381538 EBI-EMBL ROK family ROK family protein This family, known as ROK (Repressor, ORF, Kinase) includes the xylose operon repressor, xylR, from Bacillus subtilis, Lactobacillus pentosus and Staphylococcus xylosus; N-acetylglucosamine repressor, nagC, from Escherichia coli; glucokinase from Streptomyces coelicolor; fructokinase from from Pediococcus pentosaceus, Streptococcus mutans and Zymomonas mobilis; allokinase and mlc from E. coli; and E. coli hypothetical proteins yajF and yhcI and the corresponding Haemophilus influenzae proteins. The repressor proteins (xylR and nagC) from this family possess an N-terminal region not present in the sugar kinases and which contains an helix-turn-helix DNA-binding motif. (from Pfam) NF012693.5 PF00481.26 PP2C 20.3 20.3 255 domain Y N N Protein phosphatase 2C GO:0016791 9003755 131567 cellular organisms no rank 63238 EBI-EMBL Protein phosphatase 2C Protein phosphatase 2C Protein phosphatase 2C is a Mn++ or Mg++ dependent protein serine/threonine phosphatase. [1]. 9003755. Crystal structure of the protein serine/threonine phosphatase 2C at 2.0 A resolution. Das AK, Helps NR, Cohen PT, Barford D;. EMBO J 1996;15:6798-6809. (from Pfam) NF012694.5 PF00482.28 T2SSF 25.2 25.2 125 domain Y Y N type II secretion system F family protein 11266368,14600218,15223057,19299134 131567 cellular organisms no rank 219268 EBI-EMBL Type II secretion system (T2SS), protein F type II secretion system F family protein The original family covered both the regions found by the current model. The splitting of the family has allowed the related FlaJ_arch (archaeal FlaJ family) to be merged with it. Proteins with this domain in form a platform for the machiney of the Type II secretion system, as well as the Type 4 pili and the archaeal flagella [1]. This domain seems to show some similarity to PF00664 but this may just be due to similarities in the TM helices (personal obs: C Yeats). [1]. 11266368. An inner membrane platform in the type II secretion machinery of Gram-negative bacteria. Py B, Loiseau L, Barras F;. EMBO Rep 2001;2:244-248. [2]. 15223057. The general secretory pathway: a general misnomer?. Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR;. Trends Microbiol. 2004;12:306-309. [3]. 14600218. Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella. Peabody CR, Chung YJ, Yen MR, Vidal-Ingigliardi D, Pugsley AP, Saier MH Jr;. Microbiology. 2003;149:3051-3072. [4]. 19299134. Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Desvaux M, Hebraud M, Talon R, Henderson IR;. Trends Microbiol. 2009;17:139-145. (from Pfam) NF012695.5 PF00483.28 NTP_transferase 21.2 21.2 245 domain Y Y N sugar phosphate nucleotidyltransferase GO:0009058,GO:0016779 9507048 131567 cellular organisms no rank 464822 EBI-EMBL Nucleotidyl transferase sugar phosphate nucleotidyltransferase This family includes a wide range of enzymes which transfer nucleotides onto phosphosugars. [1]. 9507048. Domain organisation in phosphomannose isomerases (types I and II). Jensen SO, Reeves PR;. Biochim Biophys Acta 1998;1382:5-7. (from Pfam) NF012696.5 PF00484.24 Pro_CA 25.7 25.7 156 domain Y Y N carbonic anhydrase GO:0004089,GO:0008270 10747009,1740425 131567 cellular organisms no rank 101064 EBI-EMBL Carbonic anhydrase carbonic anhydrase This family includes carbonic anhydrases as well as a family of non-functional homologues related to YbcF. (from Pfam) NF012697.5 PF00485.23 PRK 22 22 196 domain Y N N Phosphoribulokinase / Uridine kinase family GO:0005524,GO:0016301 1328157,17143579,8366067,9548738 131567 cellular organisms no rank 78467 EBI-EMBL Phosphoribulokinase / Uridine kinase family Phosphoribulokinase / Uridine kinase family This family matches three types of P-loop containing kinases: phosphoribulokinases [1], uridine kinases [2] and bacterial pantothenate kinases(CoaA) [3]. Arabidopsis and other organisms have a dual uridine kinase/uracil phosphoribosyltransferase protein where the N-terminal region consists of a UK domain and the C-terminal region of a UPRT domain [4]. [1]. 9548738. The crystal structure of phosphoribulokinase from Rhodobacter sphaeroides reveals a fold similar to that of adenylate kinase. Harrison DH, Runquist JA, Holub A, Miziorko HM;. Biochemistry 1998;37:5074-5085. [2]. 8366067. Location of the udk gene on the physical map of Escherichia coli. Neuhard J, Tarpo L;. J Bacteriol. 1993;175:5742-5743. [3]. 1328157. Cloning, sequencing, and expression of the pantothenate kinase (coaA) gene of Escherichia coli. Song WJ, Jackowski S;. J Bacteriol. 1992;174:6411-6417. [4]. 17143579. Functional characterization of a gene encoding a dual domain for uridine kinase and uracil phosphoribosyltransferase in Arabidopsis thaliana. Islam MR, Kim H, Kang SW, Kim JS, Jeong YM, Hwang HJ, Lee SY, Woo JC, Kim SG;. Plant Mol Biol. 2007;63:465-477. (from Pfam) NF012699.5 PF00487.29 FA_desaturase 29.7 29.7 253 domain Y Y N fatty acid desaturase 1.14.19.- GO:0006629 2006187,2118597,2570068,26098317,32470559,8861937 131567 cellular organisms no rank 151397 EBI-EMBL Fatty acid desaturase fatty acid desaturase Fatty acid desaturases are enzymes that catalyse the insertion of a double bond at the delta position of fatty acids. There seem to be two distinct families of fatty acid desaturases which do not seem to be evolutionary related: Family 1 composed of Stearoyl-CoA desaturases (SCD) [1,2] and Family 2 composed of Bacterial fatty acid desaturases, Plant stearoyl-acyl-carrier-protein desaturase [3] and Cyanobacterial DesA [4]. Members of this entry are ER integral membrane proteins that share the same mushroom-shaped fold consisting of four transmembrane helices (TM1-TM4) which anchor them to the membrane, capped by a cytosolic domain containing a unique 9-10 histidine- coordinating di metal (di-iron) catalytic centre [5,6]. The structure of mouse stearoyl-CoA desaturase (SDC) revealed that TM2 and TM4 are longer than TM1 and TM3 and protrude into the cytosolic domain, providing three of the nine histidine residues that coordinate the two metal ions, while the other histidine residues are provided by the soluble domain in this enzyme [5]. [1]. 8861937. Crystal structure of delta9 stearoyl-acyl carrier protein desaturase from castor seed and its relationship to other di-iron proteins. Lindqvist Y, Huang W, Schneider G, Shanklin J;. EMBO J 1996;15:4081-4092. [2]. 2570068. Differentiation-induced gene expression in 3T3-L1 preadipocytes. A second differentially expressed gene encoding stearoyl-CoA desaturase. Kaestner KH, Ntambi JM, Kelly TJ Jr, Lane MD;. J Biol Chem. 1989;264:14755-14761. [3]. 2006187. Stearoyl-acyl-carrier-protein desaturase from higher plants is structurally unrelated to the animal and fungal homologs. Shanklin . TRUNCATED at 1650 bytes (from Pfam) NF012700.5 PF00488.26 MutS_V 30.2 30.2 188 domain Y Y N MutS-related protein GO:0005524,GO:0006298,GO:0030983 11048710,8036718,8510668,9722634 131567 cellular organisms no rank 138966 EBI-EMBL MutS domain V MutS domain V This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with Pfam:PF01624, Pfam:PF05188, Pfam:PF05192 and Pfam:PF05190. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [2]. The aligned region corresponds with domain V of Thermus aquaticus MutS as characterised in [4], which contains a Walker A motif, and is structurally similar to the ATPase domain of ABC transporters. [1]. 9722634. Domain organization and functional analysis of Thermus thermophilus MutS protein [published erratum appears in Nucleic Acids Res 1998 Oct 15;26(20):following 4789]. Tachiki H, Kato R, Masui R, Hasegawa K, Itakura H, Fukuyama K, Kuramitsu S;. Nucleic Acids Res 1998;26:4153-4159. [2]. 8036718. Colon cancer and DNA repair: have mismatches met their match?. Jiricny J;. Trends Genet 1994;10:164-168. [3]. 8510668. The yeast gene MSH3 defines a new class of eukaryotic MutS homologues. New L, Liu K, Crouse GF;. Mol Gen Genet 1993;239:97-108. [4]. 11048710. Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Obmolova G, Ban C, Hsieh P, Yang W;. Nature 2000;407:703-710. (from Pfam) NF012702.5 PF00490.26 ALAD 24.6 24.6 317 PfamEq Y N N Delta-aminolevulinic acid dehydratase GO:0004655,GO:0033014,GO:0046872 131567 cellular organisms no rank 61716 EBI-EMBL Delta-aminolevulinic acid dehydratase Delta-aminolevulinic acid dehydratase NF012703.5 PF00491.26 Arginase 22 22 280 domain Y Y N arginase family protein GO:0046872 131567 cellular organisms no rank 121647 EBI-EMBL Arginase family arginase family protein NF012704.5 PF00493.28 MCM 23.3 23.3 224 domain Y N N MCM P-loop domain GO:0003677,GO:0005524,GO:0032508 8332451 131567 cellular organisms no rank 112449 EBI-EMBL MCM P-loop domain MCM P-loop domain NF012705.5 PF00494.24 SQS_PSY 26 26 263 domain Y Y N squalene/phytoene synthase family protein GO:0009058 131567 cellular organisms no rank 72629 EBI-EMBL Squalene/phytoene synthase squalene/phytoene synthase family protein NF012706.5 PF00496.27 SBP_bac_5 32.4 32.4 368 domain Y Y N ABC transporter substrate-binding protein 131567 cellular organisms no rank 675422 EBI-EMBL Bacterial extracellular solute-binding proteins, family 5 Middle ABC transporter substrate-binding protein The borders of this family are based on the PDBSum definitions of the domain edges for Swiss:P06202. (from Pfam) NF012707.5 PF00497.25 SBP_bac_3 26.4 26.4 132 domain Y Y N transporter substrate-binding domain-containing protein 34424339 131567 cellular organisms no rank 568470 EBI-EMBL Bacterial extracellular solute-binding proteins, family 3 Bacterial extracellular solute-binding proteins, family 3 This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. This domain recognises Nicotinate, quidalnate, pyridine-2,5-dicarboxylate and salicylate [1]. [1]. 34424339. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. Matilla MA, Velando F, Martin-Mora D, Monteagudo-Cascales E, Krell T;. FEMS Microbiol Rev. 2022;46:fuab043. (from Pfam) NF012708.5 PF00498.31 FHA 20.7 20.7 67 domain Y Y N FHA domain-containing protein GO:0005515 10518219,12564991,7482699 131567 cellular organisms no rank 181286 EBI-EMBL FHA domain FHA domain The FHA (Forkhead-associated) domain is a phosphopeptide binding motif [2]. [1]. 7482699. The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors. Hofmann K, Bucher, P;. Trends Biochem Sci 1995;20:347-349. [2]. 10518219. The FHA domain is a modular phosphopeptide recognition motif. Durocher D, Henckel J, Fersht AR, Jackson SP;. Mol Cell. 1999;4:387-394. [3]. 12564991. Bacterial FHA domains: neglected players in the phospho-threonine signalling game?. Pallen M, Chaudhuri R, Khan A;. Trends Microbiol 2002;10:556-563. (from Pfam) NF012709.5 PF00499.25 Oxidored_q3 33.2 33.2 146 PfamEq Y Y N NADH-quinone oxidoreductase subunit J 1.6.5.9 GO:0008137 131567 cellular organisms no rank 48469 EBI-EMBL NADH-ubiquinone/plastoquinone oxidoreductase chain 6 NADH-quinone oxidoreductase subunit J NF012711.5 PF00501.33 AMP-binding 29.9 29.9 384 domain Y Y N AMP-binding protein 8805533 131567 cellular organisms no rank 1728666 EBI-EMBL AMP-binding enzyme AMP-binding protein NF012717.5 PF00507.24 Oxidored_q4 23.3 23.3 99 PfamEq Y Y N NADH-quinone oxidoreductase subunit A ndhC 1.6.5.9 GO:0008137 30573545 131567 cellular organisms no rank 31332 EBI-EMBL NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 NAD(P)H-quinone oxidoreductase subunit 3 NF012720.5 PF00510.23 COX3 23.8 23.8 258 domain Y Y N cytochrome c oxidase subunit 3 GO:0004129,GO:0016020 8638158 131567 cellular organisms no rank 71433 EBI-EMBL Cytochrome c oxidase subunit III cytochrome c oxidase subunit 3 NF012722.5 PF00512.30 HisKA 26.9 26.9 66 domain Y Y N histidine kinase dimerization/phospho-acceptor domain-containing protein GO:0000155,GO:0007165 18361456,9989504 131567 cellular organisms no rank 2062531 EBI-EMBL His Kinase A (phospho-acceptor) domain His Kinase A (phospho-acceptor) domain Dimerisation and phospho-acceptor domain of histidine kinases. [1]. 9989504. Structure of CheA, a signal-transducing histidine kinase. Bilwes AM, Alex LA, Crane BR, Simon MI;. Cell 1999;96:131-141. [2]. 18361456. Crystal structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source. Li Y, Bahti P, Shaw N, Song G, Chen S, Zhang X, Zhang M, Cheng C, Yin J, Zhu JY, Zhang H, Che D, Xu H, Abbas A, Wang BC, Liu ZJ;. Proteins 2008;71:2109-13. (from Pfam) NF012724.5 PF00514.28 Arm 20.6 20.3 41 domain Y N N Armadillo/beta-catenin-like repeat GO:0005515 2261639,8259518,8259519,8573337,9298899,9309175 131567 cellular organisms no rank 1419 EBI-EMBL Armadillo/beta-catenin-like repeat Armadillo/beta-catenin-like repeat Approx. 40 amino acid repeat. Tandem repeats form super-helix of helices that is proposed to mediate interaction of beta-catenin with its ligands. CAUTION: This family does not contain all known armadillo repeats. [1]. 9298899. Three-dimensional structure of the armadillo repeat region of beta-catenin. Huber AH, Nelson WJ, Weis WI;. Cell 1997;90:871-882. [2]. 8573337. Signal transduction of beta-catenin. Gumbiner BM;. Curr Opin Cell Biol 1995;7:634-640. [3]. 9309175. Armadillo and dTCF: a marriage made in the nucleus. Cavallo R, Rubenstein D, Peifer M;. Curr Opin Genet Dev 1997;7:459-466. [4]. 8259519. Association of the APC tumor suppressor protein with catenins. Su LK, Vogelstein B, Kinzler KW;. Science 1993;262:1734-1737. [5]. 8259518. Association of the APC gene product with beta-catenin. Rubinfeld B, Souza B, Albert I, Muller O, Chamberlain SH, Masiarz FR, Munemitsu S, Polakis P;. Science 1993;262:1731-1734. [6]. 2261639. The segment polarity gene armadillo encodes a functionally modular protein that is the Drosophila homolog of human plakoglobin. Peifer M, Wieschaus E;. Cell 1990;63:1167-1176. (from Pfam) NF012725.5 PF00515.33 TPR_1 27.8 27.8 34 repeat Y N N tetratricopeptide repeat protein GO:0005515 7667876,9482716 131567 cellular organisms no rank 132814 EBI-EMBL Tetratricopeptide repeat tetratricopeptide repeat NF012730.5 PF00520.36 Ion_trans 25 25 241 domain Y Y N ion transporter GO:0006811,GO:0016020,GO:0055085 131567 cellular organisms no rank 59888 EBI-EMBL Ion transport protein ion transporter This family contains sodium, potassium and calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. (from Pfam) NF012731.5 PF00521.25 DNA_topoisoIV 31 31 432 domain Y Y N DNA gyrase subunit A GO:0003677,GO:0003918,GO:0005524,GO:0006265 131567 cellular organisms no rank 158608 EBI-EMBL DNA gyrase/topoisomerase IV, subunit A DNA gyrase subunit A NF012738.5 PF00528.27 BPD_transp_1 26.4 26.4 184 domain Y Y N ABC transporter permease subunit GO:0016020,GO:0055085 131567 cellular organisms no rank 3297006 EBI-EMBL Binding-protein-dependent transport system inner membrane component ABC transporter permease subunit The alignments cover the most conserved region of the proteins, which is thought to be located in a cytoplasmic loop between two transmembrane domains. The members of this family have a variable number of transmembrane helices. (from Pfam) NF012743.5 PF00533.31 BRCT 21.3 21.3 78 domain Y Y N BRCT domain-containing protein 11573086,14534301,15133503,15501676,8673121 131567 cellular organisms no rank 115734 EBI-EMBL BRCA1 C Terminus (BRCT) domain BRCA1 C Terminus (BRCT) domain The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs [2]. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilised head-to-tail BRCT-BRCT oligomerisation mode [3]. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants [5]. Original discovery of duplicated domain in BRCA1. [1]. 8673121. BRCA1 protein products ...Functional motifs... Koonin EV, Altschul SF, Bork P;. Nature Genet 1996;13:266-268. Extension of BRCT superfamily. [2]. 15501676. Interactions between BRCT repeats and phosphoproteins: tangled up in two. Glover JN, Williams RS, Lee MS;. Trends Biochem Sci. 2004;29:579-585. [3]. 11573086. Crystal structure of the BRCT repeat region from the breast cancer-associated protein BRCA1. Williams RS, Green R, Glover JN;. Nat Struct Biol. 2001;8:838-842. [4]. 15133503. Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1. Williams RS, Lee MS, Hau DD, Glover JN;. Nat Struct Mol Biol. 2004;11:519-525. [5]. 14534301. Detection of protein folding defects caused by BRCA1-BRCT truncation and missense mutations. Williams. TRUNCATED at 1650 bytes (from Pfam) NF012744.5 PF00534.25 Glycos_transf_1 26.4 26.4 172 domain Y Y N glycosyltransferase 2.4.-.- GO:0016757 131567 cellular organisms no rank 1095871 EBI-EMBL Glycosyl transferases group 1 glycosyltransferase Mutations in this domain of Swiss:P37287 lead to disease (Paroxysmal Nocturnal haemoglobinuria). Members of this family transfer activated sugars to a variety of substrates, including glycogen, Fructose-6-phosphate and lipopolysaccharides. Members of this family transfer UDP, ADP, GDP or CMP linked sugars. The eukaryotic glycogen synthases may be distant members of this family. (from Pfam) NF012745.5 PF00535.31 Glycos_transf_2 23.3 23.3 168 domain Y Y N glycosyltransferase 2.4.-.- 131567 cellular organisms no rank 1241884 EBI-EMBL Glycosyl transferase family 2 glycosyltransferase Diverse family, transferring sugar from UDP-glucose, UDP-N-acetyl- galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids. (from Pfam) NF012752.5 PF00542.24 Ribosomal_L12 25.9 25.9 67 PfamEq Y Y N ribosomal protein L7/L12 GO:0003735,GO:0006412 3309338 131567 cellular organisms no rank 40170 EBI-EMBL Ribosomal protein L7/L12 C-terminal domain Ribosomal protein L7/L12 C-terminal domain NF012753.5 PF00543.27 P-II 25 25 102 domain Y Y N P-II family nitrogen regulator GO:0006808,GO:0030234 16754965,7866749 131567 cellular organisms no rank 49609 EBI-EMBL Nitrogen regulatory protein P-II P-II family nitrogen regulator P-II modulates the activity of glutamine synthetase. It is a tetrameric protein encoded by the glnB gene, a component of the adenylation cascade involved in the regulation of GS activity [1,2]. [1]. 7866749. Structure of the Escherichia coli signal transducing protein P-II. Cheah E, Carr PD, Suffolk PM, Vasudevan SG, Dixon NE, Ollis DL;. Structure 1994;2:981-990. [2]. 16754965. Structure of the PII signal transduction protein of Neisseria meningitidis at 1.85 A resolution. Nichols CE, Sainsbury S, Berrow NS, Alderton D, Saunders NJ, Stammers DK, Owens RJ;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006;62:494-497. (from Pfam) NF012755.5 PF00545.25 Ribonuclease 24 24 98 domain Y Y N ribonuclease domain-containing protein GO:0003723,GO:0004521 8110767 131567 cellular organisms no rank 21547 EBI-EMBL ribonuclease ribonuclease This enzyme hydrolyses RNA and oligoribonucleotides. [1]. 8110767. Subsite binding in an RNase: structure of a barnase- tetranucleotide complex at 1.76-A resolution. Buckle AM, Fersht AR;. Biochemistry 1994;33:1644-1653. (from Pfam) NF012756.5 PF00547.23 Urease_gamma 23.9 23.9 99 domain Y Y N urease subunit gamma 3.5.1.5 GO:0016151,GO:0043419 7754395 131567 cellular organisms no rank 25624 EBI-EMBL Urease, gamma subunit urease subunit gamma Urease is a nickel-binding enzyme that catalyses the hydrolysis of urea to carbon dioxide and ammonia. [1]. 7754395. The crystal structure of urease from Klebsiella aerogenes. Jabri E, Carr MB, Hausinger RP, Karplus PA;. Science 1995;268:998-1004. (from Pfam) NF012758.5 PF00549.24 Ligase_CoA 24.5 24.5 128 domain Y N N CoA-ligase GO:0003824 8144675 131567 cellular organisms no rank 104047 EBI-EMBL CoA-ligase CoA-ligase This family includes the CoA ligases Succinyl-CoA synthetase alpha and beta chains, malate CoA ligase and ATP-citrate lyase. Some members of the family utilise ATP others use GTP. [1]. 8144675. The crystal structure of succinyl-CoA synthetase from Escherichia coli at 2.5-A resolution. Wolodko WT, Fraser ME, James MN, Bridger WA;. J Biol Chem 1994;269:10883-10890. (from Pfam) NF012759.5 PF00550.30 PP-binding 20.8 20.8 67 domain Y Y N phosphopantetheine-binding protein 131567 cellular organisms no rank 931267 EBI-EMBL Phosphopantetheine attachment site phosphopantetheine attachment domain A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Swiss:P19828 has the attachment serine replaced by an alanine. (from Pfam) NF012760.5 PF00551.24 Formyl_trans_N 26.1 26.1 181 domain Y Y N formyltransferase family protein GO:0009058,GO:0016742 1522592 131567 cellular organisms no rank 239584 EBI-EMBL Formyl transferase formyltransferase-like domain Many but not all members of this family are formyltransferases or deformylases, including hosphoribosylglycinamide formyltransferase 1 (EC 2.1.2.2), methionyl-tRNA formyltransferase (EC 2.1.2.9), and formyltetrahydrofolate deformylase (EC 3.5.1.1). NF012762.5 PF00553.24 CBM_2 24 24 101 domain Y Y N cellulose binding domain-containing protein GO:0004553,GO:0005975,GO:0030246 7766609 131567 cellular organisms no rank 109673 EBI-EMBL Cellulose binding domain Cellulose binding domain Two tryptophan residues are involved in cellulose binding. Cellulose binding domain found in bacteria. [1]. 7766609. Solution structure of a cellulose-binding domain from Cellulomonas fimi by nuclear magnetic resonance spectroscopy. Xu GY, Ong E, Gilkes NR, Kilburn DG, Muhandiram DR, Harris-Brandts M, Carver JP, Kay LE, Harvey TS;. Biochemistry 1995;34:6993-7009. (from Pfam) NF012766.5 PF00557.29 Peptidase_M24 23 23 208 domain Y Y N M24 family metallopeptidase 18579787,7674922,8471602 131567 cellular organisms no rank 344501 EBI-EMBL Metallopeptidase family M24 M24 family metallopeptidase This family contains metallopeptidases. It also contains non-peptidase homologues such as the N terminal domain of Spt16 which is a histone H3-H4 binding module [3]. The structure of a representative of this family. [1]. 8471602. Structure of the cobalt-dependent methionine aminopeptidase from Escherichia coli: a new type of proteolytic enzyme. Roderick SL, Matthews BW. Biochemistry 1993;32:3907-3912. -!- Members of this family are metallopeptidases. They belong to family M24 in the classification of Rawlings and Barrett. [2]. 7674922. Evolutionary families of metallopeptidases. Rawlings ND, Barrett AJ;. Meth Enzymol 1995;248:183-228. [3]. 18579787. The FACT Spt16 "peptidase" domain is a histone H3-H4 binding module. Stuwe T, Hothorn M, Lejeune E, Rybin V, Bortfeld M, Scheffzek K, Ladurner AG;. Proc Natl Acad Sci U S A. 2008;105:8884-8889. (from Pfam) NF012769.5 PF00560.38 LRR_1 20.6 9.3 23 repeat Y N N leucine-rich repeat protein GO:0005515 7817399,8264799 131567 cellular organisms no rank 39176 EBI-EMBL Leucine Rich Repeat leucine-rich repeat CAUTION: This Pfam may not find all Leucine Rich Repeats in a protein. Leucine Rich Repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. These repeats are usually involved in protein-protein interactions. Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains. Review of LRR proteins. [1]. 7817399. The leucine-rich repeat: a versatile binding motif. Kobe B, Deisenhofer J;. Trends Biochem Sci 1994;19:415-421. 3D Structure of LRR from Porcine Ribonuclease Inhibitor. [2]. 8264799. Crystal structure of porcine ribonuclease inhibitor, a protein with leucine-rich repeats. Kobe B, Deisenhofer J;. Nature 1993;366:751-756. (from Pfam) NF012770.5 PF00561.25 Abhydrolase_1 25.8 25.8 245 subfamily Y Y N alpha/beta fold hydrolase 1409539 131567 cellular organisms no rank 1945894 EBI-EMBL alpha/beta hydrolase fold alpha/beta fold hydrolase This catalytic domain is found in a very wide range of enzymes. [1]. 1409539. The alpha/beta hydrolase fold. Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J, Sussman JL, Verschueren KHG, Goldman A;. Protein Eng 1992;5:197-211. (from Pfam) NF012771.5 PF00562.33 RNA_pol_Rpb2_6 23.4 23.4 373 PfamEq Y N N RNA polymerase Rpb2, domain 6 GO:0003677,GO:0003899,GO:0006351 11313498 131567 cellular organisms no rank 67239 EBI-EMBL RNA polymerase Rpb2, domain 6 RNA polymerase Rpb2, domain 6 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII). [1]. 11313498. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Cramer P, Bushnell DA, Kornberg RD;. Science 2001;292:1863-1876. (from Pfam) NF012774.5 PF00565.22 SNase 21 21 107 domain Y Y N thermonuclease family protein 9003410,9041650 131567 cellular organisms no rank 56425 EBI-EMBL Staphylococcal nuclease homologue thermonuclease family protein Present in all three domains of cellular life. Four copies in the transcriptional coactivator p100: these, however, appear to lack the active site residues of Staphylococcal nuclease. Positions 14 (Asp-21), 34 (Arg-35), 39 (Asp-40), 42 (Glu-43) and 110 (Arg-87) [SNase numbering in parentheses] are thought to be involved in substrate-binding and catalysis. [1]. 9041650. P100, a transcriptional coactivator, is a human homologue of staphylococcal nuclease. Ponting CP;. Protein Sci 1997;6:459-463. [2]. 9003410. The human EBNA-2 coactivator p100: multidomain organization and relationship to the staphylococcal nuclease fold and to the tudor protein involved in Drosophila melanogaster development. Callebaut I, Mornon JP;. Biochem J 1997;321:125-132. (from Pfam) NF012779.5 PF00570.28 HRDC 23.8 23.8 68 domain Y Y N HRDC domain-containing protein GO:0003676 10647186,15990871,17085080,9397680 131567 cellular organisms no rank 130565 EBI-EMBL HRDC domain HRDC domain The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains [4]. [1]. 9397680. A putative nucleic acid-binding domain in Bloom's and Werner's syndrome helicases. Morozov V, Mushegian AR, Koonin EV, Bork P;. Trends Biochem Sci 1997;22:417-418. [2]. 15990871. The HRDC domain of BLM is required for the dissolution of double Holliday junctions. Wu L, Chan KL, Ralf C, Bernstein DA, Garcia PL, Bohr VA, Vindigni A, Janscak P, Keck JL, Hickson ID;. EMBO J. 2005;24:2679-2687. [3]. 10647186. The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins. Liu Z, Macias MJ, Bottomley MJ, Stier G, Linge JP, Nilges M, Bork P, Sattler M;. Structure. 1999;7:1557-1566. [4]. 17085080. Three tandem HRDC domains have synergistic effect on the RecQ functions in Deinococcus radiodurans. Huang L, Hua X, Lu H, Gao G, Tian B, Shen B, Hua Y;. DNA Repair (Amst). 2006; [Epub ahead of print] (from Pfam) NF012780.5 PF00571.33 CBS 24 16.5 57 domain Y Y N CBS domain-containing protein 10200156,11524006,14722609,14722619,9020585,9106071 131567 cellular organisms no rank 703392 EBI-EMBL CBS domain CBS domain CBS domains are small intracellular modules that pair together to form a stable globular domain [2]. This family represents a single CBS domain. Pairs of these domains have been termed a Bateman domain [6]. CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet [5]. CBS domains are found attached to a wide range of other protein domains suggesting that CBS domains may play a regulatory role making proteins sensitive to adenosyl carrying ligands. The region containing the CBS domains in Cystathionine-beta synthase is involved in regulation by S-AdoMet [4]. CBS domain pairs from AMPK bind AMP or ATP [5]. The CBS domains from IMPDH and the chloride channel CLC2 bind ATP [5]. Discovery and naming of the CBS domain. [1]. 9020585. The structure of a domain common to archaebacteria and the homocystinuria disease protein. Bateman A;. Trends Biochem Sci 1997;22:12-13. 3D Structure found as a sub-domain in TIM barrel of inosine-monophosphate dehydrogenase. [2]. 10200156. Characteristics and crystal structure of bacterial inosine-5'-monophosphate dehydrogenase. Zhang R, Evans G, Rotella FJ, Westbrook EM, Beno D, Huberman E, Joachimiak A, Collart FR;. Biochemistry 1999;38:4691-4700. Discovery of CBS domain. [3]. 9106071. CBS domains in ClC chloride channels implicated in myotonia and nephrolithiasis (kidney stones). Ponting CP;. J Mol Med 1997;75:160-163. [4]. 11524006. Regulation of human cystathionine beta-synthase by S-adenosyl-L-methionine: evidence for two catalytically active conformations involving an autoinhibitory domain in the C-terminal region. Janosik M, Kery V, Gaustadnes M, Macl. TRUNCATED at 1650 bytes (from Pfam) NF012781.5 PF00572.23 Ribosomal_L13 27 27 119 PfamEq Y Y N uL13 family ribosomal protein GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 32954 EBI-EMBL Ribosomal protein L13 uL13 family ribosomal protein NF012782.5 PF00573.27 Ribosomal_L4 25.8 25.8 190 PfamEq Y Y N 50S ribosomal protein L4 rplD GO:0003735,GO:0005840,GO:0006412 9838082 131567 cellular organisms no rank 41046 EBI-EMBL Ribosomal protein L4/L1 family 50S ribosomal protein L4 This family includes Ribosomal L4/L1 from eukaryotes and archaebacteria and L4 from eubacteria. L4 from yeast has been shown to bind rRNA [1]. [1]. 9838082. Yeast ribosomal proteins L4, L17, L20, and L25 exhibit different binding characteristics for the yeast 35S precursor rRNA. Yeh LC, Lee JC;. Biochim Biophys Acta 1998;1443:139-148. (from Pfam) NF012783.5 PF00574.28 CLP_protease 20.2 20.2 182 domain Y Y N ATP-dependent Clp protease proteolytic subunit 9390554 131567 cellular organisms no rank 136645 EBI-EMBL Clp protease ATP-dependent Clp protease proteolytic subunit The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. Swiss:P48254 has lost all of these active site residues and is therefore inactive. Swiss:P42379 contains two large insertions, Swiss:P42380 contains one large insertion. [1]. 9390554. The structure of ClpP at 2.3 angstroms resolution suggests a model for ATP-dependent proteolysis. Wang J, Hartling JA, Flanagan JM;. Cell 1997;91:447-456. (from Pfam) NF012784.5 PF00575.28 S1 22 22 74 domain Y Y N S1 RNA-binding domain-containing protein GO:0003676 9008164 131567 cellular organisms no rank 371860 EBI-EMBL S1 RNA binding domain S1 RNA binding domain The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Structure and an extension of S1 family. [1]. 9008164. The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG;. Cell 1997;88:235-242. (from Pfam) NF012785.5 PF00576.26 Transthyretin 25.3 25.3 109 domain Y Y N hydroxyisourate hydrolase 3.5.2.17 16098976,16462750,16952372,8428915 131567 cellular organisms no rank 30877 EBI-EMBL HIUase/Transthyretin family hydroxyisourate hydrolase This family includes transthyretin that is a thyroid hormone-binding protein that transports thyroxine from the bloodstream to the brain. However, most of the sequences listed in this family do not bind thyroid hormones. They are actually enzymes of the purine catabolism that catalyse the conversion of 5-hydroxyisourate (HIU) to OHCU [2,3]. HIU hydrolysis is the original function of the family and is conserved from bacteria to mammals; transthyretins arose by gene duplications in the vertebrate lineage [4]. HIUases are distinguished in the alignment from the conserved C-terminal YRGS sequence. [1]. 8428915. The x-ray crystal structure refinements of normal human transthyretin and the amyloidogenic Val-30-->Met variant to 1.7-A resolution. Hamilton JA, Steinrauf LK, Braden BC, Liepnieks J, Benson MD, Holmgren G, Sandgren O, Steen L;. J Biol Chem 1993;268:2416-2424. [2]. 16462750. Completing the uric acid degradation pathway through phylogenetic comparison of whole genomes. Ramazzina I, Folli C, Secchi A, Berni R, Percudani R;. Nat Chem Biol. 2006;2:144-148. [3]. 16098976. Transthyretin-related proteins function to facilitate the hydrolysis of 5-hydroxyisourate, the end product of the uricase reaction. Lee Y, Lee DH, Kho CW, Lee AY, Jang M, Cho S, Lee CH, Lee JS, Myung PK, Park BC, Park SG;. FEBS Lett. 2005;579:4769-4774. [4]. 16952372. Structure of zebra fish HIUase: insights into evolution of an enzyme to a hormone transporter. Zanotti G, Cendron L, Ramazzina I, Folli C, Percudani R, Berni R;. J Mol Biol. 2006;363:1-9. (from Pfam) NF012787.5 PF00578.26 AhpC-TSA 26 26 124 domain Y Y N redoxin domain-containing protein GO:0016209,GO:0016491 8041738 131567 cellular organisms no rank 530678 EBI-EMBL AhpC/TSA family AhpC/TSA family This family contains proteins related to alkyl hydroperoxide reductase (AhpC) and thiol specific antioxidant (TSA). [1]. 8041738. Cloning and sequencing of thiol-specific antioxidant from mammalian brain: alkyl hydroperoxide reductase and thiol-specific antioxidant define a large family of antioxidant enzymes. Chae HZ, Robison K, Poole LB, Church G, Storz G, Rhee SG;. Proc Natl Acad Sci U S A 1994;91:7017-7021. (from Pfam) NF012788.5 PF00579.30 tRNA-synt_1b 21.1 21.1 292 domain Y N N tRNA synthetases class I (W and Y) GO:0000166,GO:0004812,GO:0005524,GO:0006418 7743129 131567 cellular organisms no rank 169459 EBI-EMBL tRNA synthetases class I (W and Y) tRNA synthetases class I (W and Y) NF012789.5 PF00580.26 UvrD-helicase 23 23 271 domain Y Y N UvrD-helicase domain-containing protein GO:0005524 9288744 131567 cellular organisms no rank 472603 EBI-EMBL UvrD/REP helicase N-terminal domain UvrD/REP helicase N-terminal domain The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family. Structure of Swiss:P09980. [1]. 9288744. Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP. Korolev S, Hsieh J, Gauss GH, Lohman TM, Waksman G;. Cell 1997;90:635-647. (from Pfam) NF012790.5 PF00581.25 Rhodanese 22.2 22.2 102 domain Y Y N rhodanese-like domain-containing protein 8702871 131567 cellular organisms no rank 444129 EBI-EMBL Rhodanese-like domain rhodanese-like domain Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases. Crystal structure. [1]. 8702871. Active site structural features for chemically modified forms of rhodanese. Gliubich F, Gazerro M, Zanotti G, Delbono S, Bombieri G, Berni R;. J Biol Chem 1996;271:21054-21061. (from Pfam) NF012791.5 PF00582.31 Usp 24 24 141 domain Y Y N universal stress protein 11738040,8152377,9860944 131567 cellular organisms no rank 373408 EBI-EMBL Universal stress protein family universal stress protein The universal stress protein UspA Swiss:P28242 [1] is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA [3] reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP [2], though UspA lacks ATP-binding activity. [1]. 8152377. Expression and role of the universal stress protein, UspA, of Escherichia coli during growth arrest. Nystrom T, Neidhardt FC;. Mol Microbiol 1994;11:537-544. [2]. 9860944. Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. Zarembinski TI, Hung LW, Mueller-Dieckmann HJ, Kim KK, Yokota H, Kim R, Kim SH;. Proc Natl Acad Sci U S A 1998;95:15189-15193. [3]. 11738040. Structure of the universal stress protein of Haemophilus influenzae. Sousa MC, McKay DB;. Structure (Camb) 2001;9:1135-1141. (from Pfam) NF012792.5 PF00583.30 Acetyltransf_1 20.7 20.7 116 subfamily Y Y N GNAT family N-acetyltransferase 2.3.1.- GO:0016747 11893502,9175471 131567 cellular organisms no rank 2508979 EBI-EMBL Acetyltransferase (GNAT) family GNAT family N-acetyltransferase This family contains proteins with N-acetyltransferase functions such as Elp3-related proteins. [1]. 9175471. GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein. Neuwald AF, Landsman D;. Trends Biochem Sci 1997;22:154-155. [2]. 11893502. A second catalytic domain in the Elp3 histone acetyltransferases: a candidate for histone demethylase activity?. Chinenov Y;. Trends Biochem Sci 2002;27:115-117. (from Pfam) NF012793.5 PF00584.25 SecE 22.7 22.7 55 PfamEq Y Y N preprotein translocase subunit SecE GO:0006605,GO:0006886,GO:0016020 9393849 131567 cellular organisms no rank 36622 EBI-EMBL SecE/Sec61-gamma subunits of protein translocation complex preprotein translocase subunit SecE SecE is part of the SecYEG complex in bacteria which translocates proteins from the cytoplasm. In eukaryotes the complex, made from Sec61-gamma and Sec61-alpha translocates protein from the cytoplasm to the ER. Archaea have a similar complex. [1]. 9393849. Protein translocation in the three domains of life: variations on a theme. Pohlschroder M, Prinz WA, Hartmann E, Beckwith J;. Cell 1997;91:563-566. (from Pfam) NF012795.5 PF00586.29 AIRS 24 15 112 domain Y Y N AIR synthase related protein 10508786 131567 cellular organisms no rank 237128 EBI-EMBL AIR synthase related protein, N-terminal domain AIR synthase related protein, N-terminal domain This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain [1]. [1]. 10508786. X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 A resolution. Li C, Kappock TJ, Stubbe J, Weaver TM, Ealick SE;. Structure Fold Des 1999;7:1155-1166. (from Pfam) NF012796.5 PF00587.30 tRNA-synt_2b 29.3 29.3 179 domain Y Y N aminoacyl--tRNA ligase-related protein GO:0000166,GO:0004812,GO:0005524,GO:0006418 10447505,7552701 131567 cellular organisms no rank 336652 EBI-EMBL tRNA synthetase class II core domain (G, H, P, S and T) aminoacyl--tRNA ligase class II core domain (G, H, P, S and T) This HMM finds multiple types of aminoacyl--tRNA ligase, such as those for Thr, Pro, His, and Ser in Escherichia coli. Because equivalog-level HMMs exist to identify full-length members of the tRNA ligase families, any protein receiving annotation from this HMM is most likely to be either a partial sequence or a tRNA ligase-related protein involved in some process other than protein translation on the ribosome. NF012797.5 PF00588.24 SpoU_methylase 29.7 29.7 142 domain Y Y N TrmH family RNA methyltransferase GO:0003723,GO:0006396,GO:0008173 8265370,9321663 131567 cellular organisms no rank 267517 EBI-EMBL SpoU rRNA Methylase family TrmH family RNA methyltransferase This family of proteins probably use S-AdoMet. [1]. 8265370. SpoU protein of Escherichia coli belongs to a new family of putative rRNA methylases. Koonin EV, Rudd KE;. Nucleic Acids Res 1993;21:5519-5519. [2]. 9321663. The spoU gene of escherichia coli , the fourth gene of the spoT operon, is essential for tRNA (Gm18) 2 ' - O -methyltransferase activity. Persson BC, Jager G, Gustafsson C;. Nucleic Acids Res 1997;25:4093-4097. (from Pfam) NF012798.5 PF00589.27 Phage_integrase 27.1 27.1 172 domain Y Y N tyrosine-type recombinase/integrase GO:0003677,GO:0006310,GO:0015074 9082984,9288963 131567 cellular organisms no rank 922475 EBI-EMBL Phage integrase family tyrosine-type recombinase/integrase Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase (Swiss:P06956) are Arg-173, His-289, Arg-292 and Tyr-324. [1]. 9082984. Flexibility in DNA recombination: structure of the lambda integrase catalytic core. Kwon HJ, Tirumalai R, Landy A, Ellenberger T;. Science 1997;276:126-131. [2]. 9288963. Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Guo F, Gopaul DN, van Duyne GD;. Nature 1997;389:40-46. (from Pfam) NF012799.5 PF00590.25 TP_methylase 27.8 27.8 212 domain Y Y N SAM-dependent methyltransferase GO:0008168 131567 cellular organisms no rank 354718 EBI-EMBL Tetrapyrrole (Corrin/Porphyrin) Methylases SAM-dependent methyltransferase This family uses S-AdoMet in the methylation of diverse substrates. This family includes a related group of bacterial proteins of unknown function, including Swiss:P45528. This family includes the methylase Dipthine synthase. (from Pfam) NF012800.5 PF00591.26 Glycos_transf_3 27 27 253 domain Y N N Glycosyl transferase family, a/b domain GO:0016757 2199449 131567 cellular organisms no rank 125426 EBI-EMBL Glycosyl transferase family, a/b domain Glycosyl transferase family, a/b domain This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate. [1]. 2199449. Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 A resolution. Walter MR, Cook WJ, Cole LB, Short SA, Koszalka GW, Krenitsky TA, Ealick SE;. J Biol Chem 1990;265:14016-14022. (from Pfam) NF012801.5 PF00593.29 TonB_dep_Rec_b-barrel 27 27 436 subfamily Y Y N TonB-dependent receptor domain-containing protein 9886293 131567 cellular organisms no rank 1111325 EBI-EMBL TonB dependent receptor-like, beta-barrel TonB-dependent receptor This entry represents the beta-barrel domain of TonB-dependent receptors, such as BtuB, CirA, FatA, FcuT, FecA, FepA, among others [1]. [1]. 9886293. Crystal structure of the outer membrane active transporter FepA from Escherichia coli. Buchanan SK, Smith BS, Venkatramani L, Xia D, Esser L, Palnitkar M, Chakraborty R, van der Helm D, Deisenhofer J;. Nat Struct Biol 1999;6:56-63. (from Pfam) NF012803.5 PF00595.29 PDZ 23.2 23.2 81 domain Y Y N PDZ domain-containing protein GO:0005515 19738200,8674113,9041651,9204764 131567 cellular organisms no rank 296251 EBI-EMBL PDZ domain PDZ domain PDZ domains are found in diverse signaling proteins. Review article. [1]. 9204764. PDZ domains: targeting signalling molecules to sub-membranous sites. Ponting CP, Phillips C, Davies KE, Blake DJ. Bioessays 1997;19:469-479. [2]. 8674113. Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Doyle DA, Lee A, Lewis J, Kim E, Sheng M, MacKinnon R;. Cell. 1996;85:1067-1076. Extension of PDZ family. [3]. 9041651. Evidence for PDZ domains in bacteria, yeast, and plants. Ponting CP;. Protein Sci 1997;6:464-468. [4]. 19738200. Rapid evolution of functional complexity in a domain family. Ernst A, Sazinsky SL, Hui S, Currell B, Dharsee M, Seshagiri S, Bader GD, Sidhu SS;. Sci Signal. 2009;2:ra50. (from Pfam) NF012804.5 PF00596.26 Aldolase_II 22.2 22.2 183 domain Y Y N class II aldolase/adducin family protein 8515438,8676381 131567 cellular organisms no rank 158551 EBI-EMBL Class II Aldolase and Adducin N-terminal domain Class II Aldolase and Adducin N-terminal domain This family includes class II aldolases and adducins which have not been ascribed any enzymatic function. [1]. 8515438. The spatial structure of the class II L-fuculose-1-phosphate aldolase from Escherichia coli. Dreyer MK, Schulz GE;. J Mol Biol 1993;231:549-553. [2]. 8676381. Catalytic mechanism of the metal-dependent fuculose aldolase from Escherichia coli as derived from the structure. Dreyer MK, Schulz GE;. J Mol Biol 1996;259:458-466. (from Pfam) NF012821.5 PF00614.27 PLDc 21.9 21.9 28 domain Y N N Phospholipase D Active site motif GO:0003824 10074947,8051126,8732763,8755242,9242915 131567 cellular organisms no rank 113219 EBI-EMBL Phospholipase D Active site motif Phospholipase D Active site motif Phosphatidylcholine-hydrolysing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, and/or asparagine residues which may contribute to the active site. aspartic acid. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not been achieved. [1]. 8732763. A novel family of phospholipase D homologues that includes phospholipid synthases and putative endonucleases: identification of duplicated repeats and potential active site residues. Ponting CP, Kerr ID;. Protein Sci 1996;5:914-922. [2]. 8755242. A duplicated catalytic motif in a new superfamily of phosphohydrolases and phospholipid synthases that includes poxvirus envelope proteins. Koonin EV;. Trends Biochem Sci 1996;21:242-243. [3]. 8051126. Cloning and expression of phosphatidylcholine-hydrolyzing phospholipase D from Ricinus communis L. Wang X, Xu L, Zheng L;. J Biol Chem 1994;269:20312-20317. [4]. 9242915. Regulation of eukaryotic phosphatidylinositol-specific phosp. TRUNCATED at 1650 bytes (from Pfam) NF012830.5 PF00623.25 RNA_pol_Rpb1_2 25.3 25.3 166 PfamEq Y N N RNA polymerase Rpb1, domain 2 GO:0003677,GO:0003899,GO:0006351 11313498,8910400 131567 cellular organisms no rank 66707 EBI-EMBL RNA polymerase Rpb1, domain 2 RNA polymerase Rpb1, domain 2 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2]. [1]. 8910400. Structural modules of the large subunits of RNA polymerase. Introducing archaebacterial and chloroplast split sites in the beta and beta' subunits of Escherichia coli RNA polymerase. Severinov K, Mustaev A, Kukarin A, Muzzin O, Bass I, Darst SA, Goldfarb A;. J Biol Chem 1996;271:27969-27974. [2]. 11313498. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Cramer P, Bushnell DA, Kornberg RD;. Science 2001;292:1863-1876. (from Pfam) NF012832.5 PF00625.26 Guanylate_kin 25.2 25.2 182 domain Y N N Guanylate kinase 1314905 131567 cellular organisms no rank 59224 EBI-EMBL Guanylate kinase Guanylate kinase NF012837.5 PF00630.24 Filamin 26.9 26.9 93 domain Y Y N filamin/ABP280 repeat domain-containing protein 9164464 131567 cellular organisms no rank 148 EBI-EMBL Filamin/ABP280 repeat Filamin/ABP280 repeat NF012840.5 PF00633.28 HHH 24 24 30 domain Y N N Helix-hairpin-helix motif GO:0003677 10908318,12832627,18439896,8692686,8832889 131567 cellular organisms no rank 196833 EBI-EMBL Helix-hairpin-helix motif Helix-hairpin-helix motif The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA [2]. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [5]. [1]. 8692686. The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. Doherty AJ, Serpell LC, Ponting CP;. Nucleic Acids Res 1996;24:2488-2497. [2]. 8832889. Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction. Rafferty JB, Sedelnikova SE, Hargreaves D, Artymiuk PJ, Baker PJ, Sharples GJ, Mahdi AA, Lloyd RG, Rice DW;. Science 1996;274:415-421. [3]. 12832627. An evolutionary analysis of the helix-hairpin-helix superfamily of DNA repair glycosylases. Denver DR, Swenson SL, Lynch M;. Mol Biol Evol 2003;20:1603-1611. [4]. 10908318. Common fold in helix-hairpin-helix proteins. Shao X, Grishin NV;. Nucleic Acids Res 2000;28:2643-2650. [5]. 18439896. Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates. Witte G, Hartung S, Buttner K, Hopfner KP;. Mol Cell. 2008;30:167-178. (from Pfam) NF012843.5 PF00636.31 Ribonuclease_3 27 27 102 domain Y Y N ribonuclease III domain-containing protein GO:0004525,GO:0006396 26748718 131567 cellular organisms no rank 66175 EBI-EMBL Ribonuclease III domain Ribonuclease III domain NF012846.5 PF00639.26 Rotamase 21.7 21.7 97 domain Y Y N peptidylprolyl isomerase 5.2.1.8 GO:0003755 131567 cellular organisms no rank 133367 EBI-EMBL PPIC-type PPIASE domain PPIC-type PPIASE domain Rotamases increase the rate of protein folding by catalysing the interconversion of cis-proline and trans-proline. (from Pfam) NF012848.5 PF00641.23 zf-RanBP 27 17 30 domain Y Y N zinc finger protein 18611384 131567 cellular organisms no rank 203 EBI-EMBL Zn-finger in Ran binding protein and others zinc finger protein NF012850.5 PF00643.29 zf-B_box 24.1 24.1 42 domain Y Y N B-box zinc finger protein GO:0008270 131567 cellular organisms no rank 583 EBI-EMBL B-box zinc finger B-box zinc finger protein NF012855.5 PF00648.26 Peptidase_C2 23.8 23.8 297 domain Y Y N C2 family cysteine protease GO:0004198,GO:0006508 131567 cellular organisms no rank 2509 EBI-EMBL Calpain family cysteine protease calpain-like cysteine protease domain NF012859.5 PF00652.27 Ricin_B_lectin 29 29 126 domain Y Y N ricin-type beta-trefoil lectin domain protein 131567 cellular organisms no rank 170587 EBI-EMBL Ricin-type beta-trefoil lectin domain Ricin-type beta-trefoil lectin domain NF012861.5 PF00654.25 Voltage_CLC 24.8 24.8 346 domain Y Y N chloride channel protein GO:0005247,GO:0006821,GO:0016020,GO:0055085 11182894,8857733,9252364 131567 cellular organisms no rank 109623 EBI-EMBL Voltage gated chloride channel chloride channel protein This family of ion channels contains 10 or 12 transmembrane helices. Each protein forms a single pore. It has been shown that some members of this family form homodimers. In terms of primary structure, they are unrelated to known cation channels or other types of anion channels. Three ClC subfamilies are found in animals. ClC-1 (Swiss:P35523) is involved in setting and restoring the resting membrane potential of skeletal muscle, while other channels play important parts in solute concentration mechanisms in the kidney [3]. These proteins contain two Pfam:PF00571 domains. [1]. 9252364. Reconstitution of functional voltage-gated chloride channels from complementary fragments of CLC-1. Schmidt-Rose T, Jentsch TJ;. J Biol Chem 1997;272:20515-20521. [2]. 8857733. Mutations in the human skeletal muscle chloride channel gene (CLCN1) associated with dominant and recessive myotonia congenita. Zhang J, George AL Jr, Griggs RC, Fouad GT, Roberts J, Kwiecinski H, Connolly AM, Ptacek LJ;. Neurology 1996;47:993-998. [3]. 11182894. ClC chloride channels. Mindell JA, Maduke M;. Genome Biol 2001;2:REVIEWS3003. (from Pfam) NF012862.5 PF00656.27 Peptidase_C14 21.4 21.4 233 domain Y Y N caspase family protein GO:0004197,GO:0006508 8035875 131567 cellular organisms no rank 68265 EBI-EMBL Caspase domain Caspase domain NF012863.5 PF00657.27 Lipase_GDSL 23.6 23.6 208 domain Y Y N SGNH/GDSL hydrolase family protein GO:0016788 10801485,7610479 131567 cellular organisms no rank 324171 EBI-EMBL GDSL-like Lipase/Acylhydrolase SGNH/GDSL hydrolase family protein NF012868.5 PF00662.25 Proton_antipo_N 24.5 24.5 51 domain Y N N NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus 1470679 131567 cellular organisms no rank 120694 EBI-EMBL NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus This sub-family represents an amino terminal extension of Pfam:PF00361. Only NADH-Ubiquinone chain 5 and eubacterial chain L are in this family. This sub-family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane. [1]. 1470679. The NADH:ubiquinone oxidoreductase (complex I) of respiratory chains. Walker JE;. Q Rev Biophys 1992;25:253-324. (from Pfam) NF012869.5 PF00664.28 ABC_membrane 28 21.7 274 domain Y Y N ABC transporter transmembrane domain-containing protein GO:0005524,GO:0016020,GO:0042626,GO:0055085,GO:0140359 131567 cellular organisms no rank 916549 EBI-EMBL ABC transporter transmembrane region ABC transporter transmembrane region This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (Pfam:PF00005) have two such regions. (from Pfam) NF012870.5 PF00665.31 rve 32.6 32.6 102 domain Y Y N DDE-type integrase/transposase/recombinase GO:0015074 7801124 131567 cellular organisms no rank 357341 EBI-EMBL Integrase core domain DDE-type integrase/transposase/recombinase Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain Pfam:PF02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain Pfam:PF00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site [1]. [1]. 7801124. Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases [see comments]. Dyda F, Hickman AB, Jenkins TM, Engelman A, Craigie R, Davies DR;. Science 1994;266:1981-1986. (from Pfam) NF012872.5 PF00667.25 FAD_binding_1 32.3 32.3 222 domain Y N N FAD binding domain GO:0016491 7589518,7657631,8078947,9237990 131567 cellular organisms no rank 48033 EBI-EMBL FAD binding domain FAD binding domain This domain is found in sulfite reductase, NADPH cytochrome P450 reductase, Nitric oxide synthase and methionine synthase reductase. [1]. 7657631. The flavin reductase activity of the flavoprotein component of sulfite reductase from Escherichia coli. A new model for the protein structure. Eschenbrenner M, Coves J, Fontecave M;. J Biol Chem 1995;270:20550-20555. [2]. 7589518. NADPH-sulfite reductase flavoprotein from Escherichia coli: contribution to the flavin content and subunit interaction. Eschenbrenner M, Coves J, Fontecave M;. FEBS Lett 1995;374:82-84. [3]. 8078947. Dissection of NADPH-cytochrome P450 oxidoreductase into distinct functional domains. Smith GC, Tew DG, Wolf CR;. Proc Natl Acad Sci U S A 1994;91:8710-8714. [4]. 9237990. Three-dimensional structure of NADPH-cytochrome P450 reductase: prototype for FMN- and FAD-containing enzymes. Wang M, Roberts DL, Paschke R, Shea TM, Masters BS, Kim JJ;. Proc Natl Acad Sci U S A 1997;94:8411-8416. (from Pfam) NF012873.5 PF00668.25 Condensation 30.6 30.6 456 domain Y Y N condensation domain-containing protein GO:0003824 9712910 131567 cellular organisms no rank 530698 EBI-EMBL Condensation domain condensation domain This domain is found in many multi-domain enzymes which synthesise peptide antibiotics. This domain catalyses a condensation reaction to form peptide bonds in non- ribosomal peptide biosynthesis. It is usually found to the carboxy side of a phosphopantetheine binding domain (Pfam:PF00550). It has been shown that mutations in the HHXXXDG motif abolish activity suggesting this is part of the active site [1]. [1]. 9712910. Peptide bond formation in nonribosomal peptide biosynthesis. Catalytic role of the condensation domain. Stachelhaus T, Mootz HD, Bergendahl V, Marahiel MA;. J Biol Chem 1998;273:22773-22781. (from Pfam) NF012875.5 PF00670.26 AdoHcyase_NAD 27 27 162 domain Y N N S-adenosyl-L-homocysteine hydrolase, NAD binding domain 131567 cellular organisms no rank 58618 EBI-EMBL S-adenosyl-L-homocysteine hydrolase, NAD binding domain S-adenosyl-L-homocysteine hydrolase, NAD binding domain NF012876.5 PF00672.30 HAMP 25 15 53 domain Y Y N HAMP domain-containing protein GO:0007165,GO:0016020 10418137 131567 cellular organisms no rank 1306151 EBI-EMBL HAMP domain HAMP domain NF012877.5 PF00673.26 Ribosomal_L5_C 27.8 27.8 94 PfamEq Y N N ribosomal L5P family C-terminus 131567 cellular organisms no rank 33062 EBI-EMBL ribosomal L5P family C-terminus ribosomal L5P family C-terminus This region is found associated with Pfam:PF00281. (from Pfam) NF012879.5 PF00675.25 Peptidase_M16 22.3 22.3 149 domain Y Y N insulinase family protein 131567 cellular organisms no rank 217064 EBI-EMBL Insulinase (Peptidase family M16) insulinase family protein NF012880.5 PF00676.25 E1_dh 22 22 300 domain Y Y N thiamine pyrophosphate-dependent enzyme GO:0016624 131567 cellular organisms no rank 274915 EBI-EMBL Dehydrogenase E1 component thiamine pyrophosphate-dependent enzyme This family uses thiamine pyrophosphate as a cofactor. This family includes pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase and 2-oxoisovalerate dehydrogenase. (from Pfam) NF012881.5 PF00677.22 Lum_binding 27 27 86 domain Y N N Lumazine binding domain 131567 cellular organisms no rank 64805 EBI-EMBL Lumazine binding domain Lumazine binding domain This domain binds to derivatives of lumazine in some proteins. Some proteins have lost the residues involved in binding lumazine. (from Pfam) NF012882.5 PF00679.29 EFG_C 27.9 27.9 89 domain Y N N Elongation factor G C-terminus 131567 cellular organisms no rank 234248 EBI-EMBL Elongation factor G C-terminus Elongation factor G C-terminus This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold. (from Pfam) NF012883.5 PF00680.25 RdRP_1 23.9 23.9 450 domain Y N N Viral RNA-dependent RNA polymerase GO:0003723,GO:0003968,GO:0006351 15306852,29439438,31138817,32438371,34580920 131567 cellular organisms no rank 2076 EBI-EMBL Viral RNA-dependent RNA polymerase Viral RNA-dependent RNA polymerase This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases [1,2,3,4]. Remdesivir, a recent treatment approved for Covid-19 disease, directly interacts with this region of the RdRp (NSP12) from SARS-CoV-2 and explains its mechanism of action via delayed-chain termination [5]. [1]. 29439438. RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution. Venkataraman S, Prasad BVLS, Selvarajan R;. Viruses. 2018; [Epub ahead of print]. [2]. 15306852. Structural basis for proteolysis-dependent activation of the poliovirus RNA-dependent RNA polymerase. Thompson AA, Peersen OB;. EMBO J. 2004;23:3462-3471. [3]. 31138817. Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors. Kirchdoerfer RN, Ward AB;. Nat Commun. 2019;10:2342. [4]. 32438371. Structure of replicating SARS-CoV-2 polymerase. Hillen HS, Kokic G, Farnung L, Dienemann C, Tegunov D, Cramer P;. Nature. 2020;584:154-156. [5]. 34580920. Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic. Lubin JH, Zardecki C, Dolan EM, Lu C, Shen Z, Dutta S, Westbrook JD, Hudson BP, Goodsell DS, Williams JK, Voigt M, Sarma V, Xie L, Venkatachalam T, Arnold S, Alfaro Alvarado LH, Catalfano K, Khan A, McCarthy E, Staggers S, Tinsley B, Trudeau A, Singh J, Whitmore L, Zheng H, Benedek M. TRUNCATED at 1650 bytes (from Pfam) NF012885.5 PF00682.24 HMGL-like 29 29 260 domain Y N N HMGL-like GO:0003824 131567 cellular organisms no rank 260838 EBI-EMBL HMGL-like HMGL-like This family contains a diverse set of enzymes. These include various aldolases and a region of pyruvate carboxylase. (from Pfam) NF012887.5 PF00684.24 DnaJ_CXXCXGXG 32.7 32.7 65 domain Y Y N zinc finger domain-containing protein GO:0031072,GO:0051082 10891270,14656432 131567 cellular organisms no rank 70529 EBI-EMBL DnaJ central domain DnaJ central domain The central cysteine-rich (CR) domain of DnaJ proteins contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DNAJ cysteine rich domain and various hydrophobic peptides has been found [1]. [1]. 10891270. Solution Structure of the Cysteine-rich Domain of the Escherichia coli Chaperone Protein DnaJ. Martinez-Yamout M, Legge GB, Zhang O, Wright PE, Dyson HJ;. J Mol Biol 2000;300:805-818. [2]. 14656432. The crystal structure of the yeast Hsp40 Ydj1 complexed with its peptide substrate. Li J, Qian X, Sha B;. Structure. 2003;11:1475-1483. (from Pfam) NF012888.5 PF00685.32 Sulfotransfer_1 22 22 255 domain Y Y N sulfotransferase domain-containing protein GO:0015016,GO:0016787 9360604 131567 cellular organisms no rank 53200 EBI-EMBL Sulfotransferase domain Sulfotransferase domain NF012889.5 PF00686.24 CBM_20 23.3 23.3 97 domain Y Y N carbohydrate-binding module family 20 domain-containing protein GO:2001070 10348915,8955113 131567 cellular organisms no rank 15525 EBI-EMBL Starch binding domain Starch binding domain NF012890.5 PF00687.26 Ribosomal_L1 32.2 32.2 198 PfamEq Y N N Ribosomal protein L1p/L10e family 131567 cellular organisms no rank 41376 EBI-EMBL Ribosomal protein L1p/L10e family Ribosomal protein L1p/L10e family This family includes prokaryotic L1 and eukaryotic L10. (from Pfam) NF012891.5 PF00688.23 TGFb_propeptide 25.8 25.8 242 PfamEq Y N N TGF-beta propeptide 8617200,9150447 131567 cellular organisms no rank 452 EBI-EMBL TGF-beta propeptide TGF-beta propeptide This propeptide is known as latency associated peptide (LAP) in TGF-beta. LAP is a homodimer which is disulfide linked to TGF-beta binding protein. [1]. 8617200. Association of the small latent transforming growth factor-beta with an eight cysteine repeat of its binding protein LTBP-1. Saharinen J, Taipale J, Keski-Oja J;. EMBO J 1996;15:245-253. [2]. 9150447. Latent transforming growth factor-beta: structural features and mechanisms of activation. Munger JS, Harpel JG, Gleizes PE, Mazzieri R, Nunes I, Rifkin DB;. Kidney Int 1997;51:1376-1382. (from Pfam) NF012892.5 PF00689.26 Cation_ATPase_C 27.3 27.3 175 domain Y Y N cation transporting ATPase C-terminal domain-containing protein 131567 cellular organisms no rank 122670 EBI-EMBL Cation transporting ATPase, C-terminus Cation transporting ATPase, C-terminus Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport. This family represents 5 transmembrane helices. (from Pfam) NF012893.5 PF00690.31 Cation_ATPase_N 20.4 20.4 69 domain Y Y N cation-transporting P-type ATPase 131567 cellular organisms no rank 119078 EBI-EMBL Cation transporter/ATPase, N-terminus cation-transporting P-type ATPase Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport. (from Pfam) NF012895.5 PF00692.24 dUTPase 22 22 129 domain Y N N dUTPase 1311056,8805593 131567 cellular organisms no rank 68161 EBI-EMBL dUTPase dUTPase dUTPase hydrolyses dUTP to dUMP and pyrophosphate. [1]. 1311056. Crystal structure of a dUTPase. Cedergren-Zeppezauer ES, Larsson G, Nyman PO, Dauter Z, Wilson KS;. Nature 1992;355:740-743. [2]. 8805593. Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits. Mol CD, Harris JM, McIntosh EM, Tainer JA;. Structure 1996;4:1077-1092. (from Pfam) NF012897.5 PF00694.24 Aconitase_C 22.8 22.8 131 domain Y N N Aconitase C-terminal domain 7675781 131567 cellular organisms no rank 164165 EBI-EMBL Aconitase C-terminal domain Aconitase C-terminal domain Members of this family usually also match to Pfam:PF00330. This domain undergoes conformational change in the enzyme mechanism [1]. [1]. 7675781. Steric and conformational features of the aconitase mechanism. Lauble H, Stout CD;. Proteins 1995;22:1-11. (from Pfam) NF012899.5 PF00696.33 AA_kinase 24.9 24.9 234 domain Y N N Amino acid kinase family 10860751 131567 cellular organisms no rank 320309 EBI-EMBL Amino acid kinase family Amino acid kinase family This family includes kinases that phosphorylate a variety of amino acid substrates, as well as uridylate kinase and carbamate kinase. This family includes: Aspartokinase EC:2.7.2.4, Swiss:P00561. Acetylglutamate kinase EC:2.7.2.8, Swiss:Q07905. Glutamate 5-kinase EC:2.7.2.11, Swiss:P07005. Uridylate kinase EC:2.7.4.-, Swiss:P29464. Carbamate kinase EC:2.7.2.2, Swiss:O96432. [1]. 10860751. The 1.5 A resolution crystal structure of the carbamate kinase-like carbamoyl phosphate synthetase from the hyperthermophilic Archaeon pyrococcus furiosus, bound to ADP, confirms that this thermostable enzyme is a carbamate kinase, and provides insight in. Ramon-Maiques S, Marina A, Uriarte M, Fita I, Rubio V;. J Mol Biol 2000;299:463-476. (from Pfam) NF012900.5 PF00697.27 PRAI 22.7 22.7 193 PfamEq Y N N N-(5'phosphoribosyl)anthranilate (PRA) isomerase GO:0004640,GO:0006568 1738159 131567 cellular organisms no rank 67130 EBI-EMBL N-(5'phosphoribosyl)anthranilate (PRA) isomerase N-(5'phosphoribosyl)anthranilate (PRA) isomerase NF012901.5 PF00698.26 Acyl_transf_1 32.7 32.7 319 domain Y Y N acyltransferase domain-containing protein 7768883 131567 cellular organisms no rank 325825 EBI-EMBL Acyl transferase domain Acyl transferase domain NF012902.5 PF00699.25 Urease_beta 25 25 98 domain Y Y N urease subunit beta 3.5.1.5 GO:0035550,GO:0043419 7754395 131567 cellular organisms no rank 33079 EBI-EMBL Urease beta subunit urease subunit beta This subunit is known as alpha in Heliobacter. [1]. 7754395. The crystal structure of urease from Klebsiella aerogenes. Jabri E, Carr MB, Hausinger RP, Karplus PA;. Science 1995;268:998-1004. (from Pfam) NF012904.5 PF00701.27 DHDPS 22.1 22.1 289 subfamily Y Y N dihydrodipicolinate synthase family protein GO:0016829 7853400,8081752 131567 cellular organisms no rank 225418 EBI-EMBL Dihydrodipicolinate synthetase family dihydrodipicolinate synthase family protein This family has a TIM barrel structure. [1]. 7853400. The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 A resolution. Mirwaldt C, Korndorfer I, Huber R;. J Mol Biol 1995;246:227-239. [1]. 8081752. The three-dimensional structure of N-acetylneuraminate lyase from Escherichia coli. Izard T, Lawrence MC, Malby RL, Lilley GG, Colman PM;. Structure 1994;2:361-369. (from Pfam) NF012905.5 PF00702.31 Hydrolase 26.4 26.4 191 domain Y Y N HAD family hydrolase 20485265,8702766 131567 cellular organisms no rank 1465355 EBI-EMBL haloacid dehalogenase-like hydrolase HAD family hydrolase This family is structurally different from the alpha/beta hydrolase family (Pfam:PF00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of Swiss:P24069. The rest of the fold is composed of the core alpha/beta domain [1]. Those members with the characteristic DxD triad at the N-terminus are probably phosphatidylglycerolphosphate (PGP) phosphatases involved in cardiolipin biosynthesis in the mitochondria [2]. [1]. 8702766. Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold. Hisano T, Hata Y, Fujii T, Liu JQ, Kurihara T, Esaki N, Soda K;. J Biol Chem 1996;271:20322-20330. [2]. 20485265. A mitochondrial phosphatase required for cardiolipin biosynthesis: the PGP phosphatase Gep4. Osman C, Haag M, Wieland FT, Brugger B, Langer T;. EMBO J. 2010;29:1976-1987 (from Pfam) NF012906.5 PF00703.26 Glyco_hydro_2 23 23 109 domain Y N N Glycosyl hydrolases family 2 GO:0004553,GO:0005975 8008071 131567 cellular organisms no rank 185746 EBI-EMBL Glycosyl hydrolases family 2 Glycosyl hydrolases family 2 This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities. [1]. 8008071. Three-dimensional structure of beta-galactosidase from E. coli. Jacobson RH, Zhang XJ, DuBose RF, Matthews BW;. Nature. 1994;369:761-766. (from Pfam) NF012907.5 PF00704.33 Glyco_hydro_18 29.6 29.6 317 domain Y Y N glycosyl hydrolase family 18 protein GO:0005975 7704527 131567 cellular organisms no rank 127043 EBI-EMBL Glycosyl hydrolases family 18 glycosyl hydrolase family 18 NF012908.5 PF00705.23 PCNA_N 20.3 20.3 127 domain Y N N Proliferating cell nuclear antigen, N-terminal domain GO:0003677,GO:0006275 8001157 131567 cellular organisms no rank 1617 EBI-EMBL Proliferating cell nuclear antigen, N-terminal domain Proliferating cell nuclear antigen, N-terminal domain N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA. [1]. 8001157. Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Krishna TS, Kong XP, Gary S, Burgers PM, Kuriyan J;. Cell 1994;79:1233-1243. (from Pfam) NF012911.5 PF00708.23 Acylphosphatase 22.5 22.5 85 domain Y Y N acylphosphatase 3.6.1.7 131567 cellular organisms no rank 69795 EBI-EMBL Acylphosphatase acylphosphatase NF012912.5 PF00709.26 Adenylsucc_synt 27 27 416 PfamEq Y Y N adenylosuccinate synthetase 6.3.4.4 GO:0000166,GO:0004019,GO:0006164 131567 cellular organisms no rank 68078 EBI-EMBL Adenylosuccinate synthetase adenylosuccinate synthetase NF012913.5 PF00710.25 Asparaginase 22.5 22.5 193 domain Y Y N asparaginase domain-containing protein 3.5.1.1 131567 cellular organisms no rank 72480 EBI-EMBL Asparaginase, N-terminal Asparaginase, N-terminal This is the N-terminal domain of this enzyme. (from Pfam) NF012915.5 PF00712.24 DNA_pol3_beta 24.4 24.4 120 PfamEq Y N N DNA polymerase III beta subunit, N-terminal domain GO:0003677,GO:0003887,GO:0006260,GO:0008408,GO:0009360 1349852 131567 cellular organisms no rank 63287 EBI-EMBL DNA polymerase III beta subunit, N-terminal domain DNA polymerase III beta subunit, N-terminal domain A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold. [1]. 1349852. Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. Kong XP, Onrust R, O'Donnell M, Kuriyan J;. Cell 1992;69:425-437. (from Pfam) NF012920.5 PF00717.28 Peptidase_S24 23.3 23.3 116 domain Y Y N S24 family peptidase 10892750 131567 cellular organisms no rank 180656 EBI-EMBL Peptidase S24-like S24 family peptidase NF012922.5 PF00719.24 Pyrophosphatase 23.5 23.5 153 domain Y Y N inorganic diphosphatase GO:0000287,GO:0004427,GO:0005737,GO:0006796 131567 cellular organisms no rank 36656 EBI-EMBL Inorganic pyrophosphatase inorganic diphosphatase NF012925.5 PF00722.27 Glyco_hydro_16 22 22 175 domain Y Y N family 16 glycosylhydrolase GO:0004553,GO:0005975 131567 cellular organisms no rank 63425 EBI-EMBL Glycosyl hydrolases family 16 glycosyl hydrolase family protein NF012926.5 PF00723.26 Glyco_hydro_15 22 22 427 domain Y Y N glycoside hydrolase family 15 protein 131567 cellular organisms no rank 73558 EBI-EMBL Glycosyl hydrolases family 15 glycoside hydrolase family 15 domain In higher organisms this family is represented by phosphorylase kinase subunits. (from Pfam) NF012927.5 PF00724.25 Oxidored_FMN 27 27 342 domain Y N N NADH:flavin oxidoreductase / NADH oxidase family GO:0010181,GO:0016491 131567 cellular organisms no rank 280400 EBI-EMBL NADH:flavin oxidoreductase / NADH oxidase family NADH:flavin oxidoreductase / NADH oxidase family NF012928.5 PF00725.27 3HCDH 22.1 22.1 97 domain Y Y N 3-hydroxyacyl-CoA dehydrogenase family protein GO:0006631,GO:0016491,GO:0016616 3479790 131567 cellular organisms no rank 252701 EBI-EMBL 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain This family also includes lambda crystallin. Some proteins include two copies of this domain. [1]. 3479790. Structure of L-3-hydroxyacyl-coenzyme A dehydrogenase: preliminary chain tracing at 2.8-A resolution. Birktoft JJ, Holden HM, Hamlin R, Xuong NH, Banaszak LJ;. Proc Natl Acad Sci U S A 1987;84:8262-8266. (from Pfam) NF012931.5 PF00728.27 Glyco_hydro_20 22.3 22.3 348 domain Y Y N family 20 glycosylhydrolase GO:0004553,GO:0005975 8673609 131567 cellular organisms no rank 101346 EBI-EMBL Glycosyl hydrolase family 20, catalytic domain Glycosyl hydrolase family 20, catalytic domain This domain has a TIM barrel fold. [1]. 8673609. Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay-Sachs disease. Tews I, Perrakis A, Oppenheim A, Dauter Z, Wilson KS, Vorgias CE;. Nat Struct Biol 1996;3:638-648. (from Pfam) NF012933.5 PF00730.30 HhH-GPD 26.2 26.2 108 domain Y N N HhH-GPD superfamily base excision DNA repair protein GO:0006284 10499592,10706276 131567 cellular organisms no rank 215218 EBI-EMBL HhH-GPD superfamily base excision DNA repair protein HhH-GPD superfamily base excision DNA repair protein This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate [2]. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases such as Swiss:P53397. The methyl-CPG binding protein MBD4 Swiss:Q9Z2D7 also contains a related domain [1] that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family. [1]. 10499592. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Hendrich B, Hardeland U, Ng HH, Jiricny J, Bird A;. Nature 1999;401:301-304. [2]. 10706276. Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. Bruner SD, Norman DP, Verdine GL;. Nature 2000;403:859-866. (from Pfam) NF012934.5 PF00731.25 AIRC 30 30 148 domain Y Y N AIR carboxylase family protein GO:0006189 10574791 131567 cellular organisms no rank 65184 EBI-EMBL AIR carboxylase AIR carboxylase family protein Members of this family catalyse the decarboxylation of 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (AIR). This family catalyse the sixth step of de novo purine biosynthesis. Some members of this family contain two copies of this domain. [1]. 10574791. Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway. Mathews II, Kappock TJ, Stubbe J, Ealick SE;. Structure Fold Des 1999;7:1395-1406. (from Pfam) NF012935.5 PF00732.24 GMC_oxred_N 23 23 218 domain Y Y N GMC family oxidoreductase N-terminal domain-containing protein GO:0016614,GO:0050660 131567 cellular organisms no rank 201058 EBI-EMBL GMC oxidoreductase GMC oxidoreductase This family of proteins bind FAD as a cofactor. (from Pfam) NF012936.5 PF00733.26 Asn_synthase 21 21 354 domain Y Y N asparagine synthase-related protein GO:0004066,GO:0006529 131567 cellular organisms no rank 179726 EBI-EMBL Asparagine synthase asparagine synthase-related protein Most members of this family are asparagine synthase, which catalyzes conversion of aspartate to asparagine. Exceptions that score well against the HMM include isopeptide bond formation proteins for lasso peptide biosynthesis. But note that many additional proteins, such as the 7-cyano-7-deazaguanine synthase QueC, hit with scores barely above the model's cutoff scores to N-terminal regions about 60 amino acids long, whereas the full length of the model is 355. NF012938.5 PF00735.23 Septin 26.2 26.2 280 PfamEq Y N N Septin GO:0005525 12665577,14611653 131567 cellular organisms no rank 2816 EBI-EMBL Septin Septin Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerise to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis [2]. [1]. 12665577. Molecular dissection of a yeast septin: distinct domains are required for septin interaction, localization, and function. Casamayor A, Snyder M;. Mol Cell Biol 2003;23:2762-2777. [2]. 14611653. The septins. Kinoshita M;. Genome Biol 2003;4:236. (from Pfam) NF012939.5 PF00736.24 EF1_GNE 20.8 20.8 88 PfamEq Y N N EF-1 guanine nucleotide exchange domain GO:0003746,GO:0006414 10368288 131567 cellular organisms no rank 1124 EBI-EMBL EF-1 guanine nucleotide exchange domain EF-1 guanine nucleotide exchange domain This family is the guanine nucleotide exchange domain of EF-1 beta and EF-1 delta chains. [1]. 10368288. The solution structure of the guanine nucleotide exchange domain of human elongation factor 1beta reveals a striking resemblance to that of EF-Ts from Escherichia coli. Perez JM, Siegal G, Kriek J, H rd K, Dijk J, Canters GW, Moller W;. Structure Fold Des 1999;7:217-226. (from Pfam) NF012944.5 PF00741.23 Gas_vesicle 25 25 39 PfamEq Y Y N gas vesicle protein GvpJ gvpJ GO:0005198,GO:0012506 15126480 131567 cellular organisms no rank 23587 EBI-EMBL Gas vesicle protein gas vesicle protein GvpJ This family includes gas vesicle proteins such as GvpJ [1]. [1]. 15126480. Complexity of gas vesicle biogenesis in Halobacterium sp. strain NRC-1: identification of five new proteins. Shukla HD, DasSarma S;. J Bacteriol. 2004;186:3182-3186. (from Pfam) NF012945.5 PF00742.24 Homoserine_dh 22.9 22.9 173 domain Y N N Homoserine dehydrogenase GO:0006520 131567 cellular organisms no rank 93359 EBI-EMBL Homoserine dehydrogenase Homoserine dehydrogenase NF012946.5 PF00743.24 FMO-like 22 22 532 domain Y N N Flavin-binding monooxygenase-like GO:0004499,GO:0050660,GO:0050661 9538688 131567 cellular organisms no rank 165145 EBI-EMBL Flavin-binding monooxygenase-like Flavin-binding monooxygenase-like This family includes FMO proteins, cyclohexanone mono-oxygenase and a number of different mono-oxygenases. [1]. 9538688. A hydrophobic sequence motif common to N-hydroxylating enzymes. Stehr M, Diekmann H, Smau L, Seth O, Ghisla S, Singh M, Macheroux P;. Trends Biochem Sci 1998;23:56-57. (from Pfam) NF012947.5 PF00745.25 GlutR_dimer 22.9 22.9 99 PfamEq Y N N Glutamyl-tRNAGlu reductase, dimerisation domain GO:0008883,GO:0033014,GO:0050661 3075378 131567 cellular organisms no rank 50785 EBI-EMBL Glutamyl-tRNAGlu reductase, dimerisation domain Glutamyl-tRNAGlu reductase, dimerisation domain NF012951.5 PF00749.26 tRNA-synt_1c 23.4 23.4 314 domain Y Y N glutamate--tRNA ligase family protein GO:0004812,GO:0005524,GO:0043039 9562563 131567 cellular organisms no rank 173641 EBI-EMBL tRNA synthetases class I (E and Q), catalytic domain tRNA synthetases class I (E and Q), catalytic domain Members of this family include glutamate--tRNA ligases and tRNA glutamyl-Q(34) synthetase, both of which bind a tRNA and attach a glutamate residue, although at different sites on tRNA molecules, the latter at the anticodon site. It would be misleading to call the latter a glutamate--tRNA ligase, as the reaction is for base modification, rather than charging the tRNA with an amino acid destined for use in translation. NF012952.5 PF00750.24 tRNA-synt_1d 23.3 23.3 349 PfamEq Y Y N arginine--tRNA ligase argS 6.1.1.19 131567 cellular organisms no rank 90411 EBI-EMBL tRNA synthetases class I (R) arginine--tRNA ligase Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only arginyl tRNA synthetase. (from Pfam) NF012954.5 PF00752.22 XPG_N 22 22 101 PfamEq Y N N XPG N-terminal domain GO:0004518 9612080 131567 cellular organisms no rank 1482 EBI-EMBL XPG N-terminal domain XPG N-terminal domain NF012955.5 PF00753.32 Lactamase_B 22.7 21.9 196 domain Y Y N MBL fold metallo-hydrolase 7588620,9108146 131567 cellular organisms no rank 927814 EBI-EMBL Metallo-beta-lactamase superfamily MBL fold metallo-hydrolase NF012956.5 PF00754.30 F5_F8_type_C 28.2 28.2 127 domain Y Y N discoidin domain-containing protein 9684896 131567 cellular organisms no rank 185525 EBI-EMBL F5/8 type C domain F5/8 type C domain This domain is also known as the discoidin (DS) domain family [1]. Extension of family to prokaryotes. [1]. 9684896. The discoidin domain family revisited: new members from prokaryotes and a homology-based fold prediction. Baumgartner S, Hofmann K, Chiquet-Ehrismann R, Bucher P;. Protein Sci 1998;7:1626-1631. (from Pfam) NF012958.5 PF00756.25 Esterase 22 22 251 domain Y Y N alpha/beta hydrolase-fold protein 19653299,29352107 131567 cellular organisms no rank 309487 EBI-EMBL Putative esterase alpha/beta hydrolase-fold protein Members of this family alpha/beta hydrolase-fold proteins. Known members include hydrolases such as S-formylglutathione hydrolase (called esterase D in human) and the three paralogous mycolyltransferases of the Ag85 complex in Mycobacterium tuberculosis. NF012961.5 PF00759.24 Glyco_hydro_9 27.7 27.7 444 domain Y Y N glycoside hydrolase family 9 protein GO:0004553,GO:0005975 131567 cellular organisms no rank 27666 EBI-EMBL Glycosyl hydrolase family 9 glycoside hydrolase family 9 protein NF012964.5 PF00762.24 Ferrochelatase 27 27 317 PfamEq Y Y N ferrochelatase 4.98.1.1 GO:0004325,GO:0006783 131567 cellular organisms no rank 70112 EBI-EMBL Ferrochelatase ferrochelatase NF012965.5 PF00763.28 THF_DHG_CYH 32.8 32.8 115 domain Y Y N tetrahydrofolate dehydrogenase/cyclohydrolase catalytic domain-containing protein GO:0004488 9519408 131567 cellular organisms no rank 77937 EBI-EMBL Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain NF012966.5 PF00764.24 Arginosuc_synth 27 27 162 domain Y Y N argininosuccinate synthase domain-containing protein GO:0004055,GO:0005524,GO:0006526 7731953 131567 cellular organisms no rank 63012 EBI-EMBL Arginosuccinate synthase N-terminal HUP domain Arginosuccinate synthase N-terminal HUP domain This entry represents the N-terminal domain of the Arginosuccinate synthase enzyme. This domain is part of the HUP superfamily. (from Pfam) NF012968.5 PF00766.24 ETF_alpha 27 27 81 domain Y Y N FAD-binding protein 8962055 131567 cellular organisms no rank 87784 EBI-EMBL Electron transfer flavoprotein FAD-binding domain electron transfer flavoprotein FAD-binding domain This domain found at the C-terminus of electron transfer flavoprotein alpha chain and binds to FAD [1]. The fold consists of a five-stranded parallel beta sheet as the core of the domain, flanked by alternating helices. A small part of this domain is donated by the beta chain [1]. [1]. 8962055. Three-dimensional structure of human electron transfer flavoprotein to 2.1-A resolution. Roberts DL, Frerman FE, Kim JJ;. Proc Natl Acad Sci U S A 1996;93:14355-14360. (from Pfam) NF012975.5 PF00773.24 RNB 29.3 29.3 326 domain Y Y N RNB domain-containing ribonuclease GO:0003723,GO:0004540 16806266 131567 cellular organisms no rank 107493 EBI-EMBL RNB domain RNB domain This domain is the catalytic domain of ribonuclease II [1]. [1]. 16806266. Characterization of the functional domains of Escherichia coli RNase II. Amblar M, Barbas A, Fialho AM, Arraiano CM;. J Mol Biol. 2006;360:921-933. (from Pfam) NF012976.5 PF00775.26 Dioxygenase_C 27.3 27.3 182 domain Y N N Dioxygenase GO:0003824,GO:0008152,GO:0008199 131567 cellular organisms no rank 83073 EBI-EMBL Dioxygenase Dioxygenase NF012977.5 PF00777.23 Glyco_transf_29 23 23 272 PfamEq Y Y N glycosyltransferase family 29 protein 2.4.-.- GO:0006486,GO:0008373 9334165 131567 cellular organisms no rank 1547 EBI-EMBL Glycosyltransferase family 29 (sialyltransferase) glycosyltransferase family 29 protein Members of this family belong to glycosyltransferase family 29 [1]. [1]. 9334165. A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Campbell JA, Davies GJ, Bulone V, Henrissat B;. Biochem J 1997;326:929-939. (from Pfam) NF012981.5 PF00781.29 DAGK_cat 23.6 20.8 125 domain Y Y N diacylglycerol kinase family protein GO:0016301 17351295,2156169,2159661,2175712,8626538 131567 cellular organisms no rank 132926 EBI-EMBL Diacylglycerol kinase catalytic domain Diacylglycerol kinase catalytic domain Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family [5]. [1]. 2156169. Porcine diacylglycerol kinase sequence has zinc finger and E-F hand motifs. Sakane F, Yamada K, Kanoh H, Yokoyama C, Tanabe T;. Nature 1990;344:345-348. [2]. 8626538. Molecular cloning of a novel diacylglycerol kinase isozyme with a pleckstrin homology domain and a C-terminal tail similar to those of the EPH family of protein-tyrosine kinases. Sakane F, Imai S, Kai M, Wada I, Kanoh H;. J Biol Chem 1996;271:8394-8401. [3]. 2175712. Purification, cDNA-cloning and expression of human diacylglycerol kinase. Schaap D, de Widt J, van der Wal J, Vandekerckhove J, van Damme J, Gussow D, Ploegh HL, van Blitterswijk WJ, van der Bend RL;. FEBS Lett 1990;275:151-158. [4]. 2159661. Diacylglycerol kinase: a key modulator of signal transduction?. Kanoh H, Yamada K, Sakane F;. Trends Biochem Sci 1990;15:47-50. [5]. 17351295. Crystal structure of YegS, a homologue to the mammalian diacylglycerol kinases, reveals a novel regulatory metal binding site. Bakali HM, Herman MD, Johnson KA, Kelly AA, Wieslander A, Hallberg BM, Nordlund P;. J Biol Chem. 2007;282:19644-19652. (from Pfam) NF012982.5 PF00782.25 DSPc 33.5 33.5 133 domain Y Y N dual specificity protein phosphatase family protein GO:0008138,GO:0016311 8650541,8987394 131567 cellular organisms no rank 19768 EBI-EMBL Dual specificity phosphatase, catalytic domain Dual specificity phosphatase, catalytic domain Ser/Thr and Tyr protein phosphatases. The enzyme's tertiary fold is highly similar to that of tyrosine-specific phosphatases, except for a "recognition" region [2]. [1]. 8987394. Structure and function of the protein tyrosine phosphatases. Fauman EB, Saper MA;. Trends Biochem Sci 1996;21:413-417. [2]. 8650541. Crystal structure of the dual specificity protein phosphatase VHR. Yuvaniyama J, Denu JM, Dixon JE, Saper MA;. Science 1996;272:1328-1331. (from Pfam) NF012989.5 PF00791.25 ZU5 21 21 97 domain Y N N ZU5 domain 9126742,9126743 131567 cellular organisms no rank 169 EBI-EMBL ZU5 domain ZU5 domain Domain present in ZO-1 and Unc5-like netrin receptors Domain of unknown function. [1]. 9126743. The mouse rostral cerebellar malformation gene encodes an UNC-5-like protein. Ackerman SL, Kozak LP, Przyborski SA, Rund LA, Boyer BB, Knowles BB;. Nature 1997;386:838-842. [2]. 9126742. Vertebrate homologues of C. elegans UNC-5 are candidate netrin receptors. Leonardo ED, Hinck L, Masu M, Keino-Masu K, Ackerman SL, Tessier-Lavigne M;. Nature 1997;386:833-838. (from Pfam) NF012991.5 PF00793.25 DAHP_synth_1 25.5 25.5 270 domain Y N N DAHP synthetase I family GO:0009058 10425687 131567 cellular organisms no rank 108831 EBI-EMBL DAHP synthetase I family DAHP synthetase I family Members of this family catalyse the first step in aromatic amino acid biosynthesis from chorismate. E-coli has three related synthetases, which are inhibited by different aromatic amino acids. This family also includes KDSA which has very similar catalytic activity but is involved in the first step of liposaccharide biosynthesis. The enzyme is also part of the shikimate pathway, EC:2.5.1.54. [1]. 10425687. Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli. Shumilin IA, Kretsinger RH, Bauerle RH;. Structure Fold Des 1999;7:865-875. (from Pfam) NF012993.5 PF00795.27 CN_hydrolase 23.2 23.2 256 domain Y Y N nitrilase-related carbon-nitrogen hydrolase GO:0008152 11380987,7987228 131567 cellular organisms no rank 350030 EBI-EMBL Carbon-nitrogen hydrolase nitrilase-related carbon-nitrogen hydrolase This family contains hydrolases that break carbon-nitrogen bonds [1]. The family includes: Nitrilase EC:3.5.5.1 Swiss:Q42965, Aliphatic amidase EC:3.5.1.4 Swiss:Q01360, Biotidinase EC:3.5.1.12 Swiss:P43251, Beta-ureidopropionase EC:3.5.1.6 Swiss:Q03248. Nitrilase-related proteins generally have a conserved E-K-C catalytic triad, and are multimeric alpha-beta-beta-alpha sandwich proteins [2]. [1]. 7987228. A new family of carbon-nitrogen hydrolases. Bork P, Koonin EV;. Protein Sci 1994;3:1344-1346. [2]. 11380987. The nitrilase superfamily: classification, structure and function. Pace HC, Brenner C;. Genome Biol 2001;2:REVIEWS0001. (from Pfam) NF012995.5 PF00797.22 Acetyltransf_2 22.8 22.8 240 domain Y Y N arylamine N-acetyltransferase GO:0016407 131567 cellular organisms no rank 39538 EBI-EMBL N-acetyltransferase arylamine N-acetyltransferase Arylamine N-acetyltransferase (NAT) is a cytosolic enzyme of approximately 30kDa. It facilitates the transfer of an acetyl group from Acetyl Coenzyme A on to a wide range of arylamine, N-hydroxyarylamines and hydrazines. Acetylation of these compounds generally results in inactivation. NAT is found in many species from Mycobacteria (M. tuberculosis, M. smegmatis etc) to man. It was the first enzyme to be observed to have polymorphic activity amongst human individuals. NAT is responsible for the inactivation of Isoniazid (a drug used to treat Tuberculosis) in humans. The NAT protein has also been shown to be involved in the breakdown of folic acid. (from Pfam) NF012998.5 PF00800.23 PDT 25.2 25.2 181 domain Y Y N prephenate dehydratase domain-containing protein GO:0004664,GO:0009094 18171624,9497350 131567 cellular organisms no rank 64171 EBI-EMBL Prephenate dehydratase Prephenate dehydratase This protein is involved in Phenylalanine biosynthesis. This protein catalyses the decarboxylation of prephenate to phenylpyruvate. (from Pfam) NF012999.5 PF00801.25 PKD 23.5 23.5 80 domain Y Y N PKD domain-containing protein 7736581,9889186 131567 cellular organisms no rank 90916 EBI-EMBL PKD domain PKD domain This domain was first identified in the Polycystic kidney disease protein PKD1. This domain has been predicted to contain an Ig-like fold [1]. [1]. 7736581. Polycystic kidney disease: the complete structure of the PKD1 gene and its protein. The International Polycystic Kidney Disease Consortium;. Cell. 1995;81:289-298. [2]. 9889186. The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease. Bycroft M, Bateman A, Clarke J, Hamill SJ, Sandford R, Thomas RL, Chothia C;. EMBO J 1999;18:297-305. (from Pfam) NF013003.5 PF00805.27 Pentapeptide 20.2 15 40 domain Y Y N pentapeptide repeat-containing protein 7592418,9654141,9655353 131567 cellular organisms no rank 155742 EBI-EMBL Pentapeptide repeats (8 copies) Pentapeptide repeats (8 copies) These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK [1]. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix [2]. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid. [1]. 7592418. The hglK gene is required for localization of heterocyst-specific glycolipids in the cyanobacterium Anabaena sp. strain PCC 7120. Black K, Buikema WJ, Haselkorn R;. J Bacteriol 1995;177:6440-6448. [2]. 9655353. Structure and distribution of pentapeptide repeats in bacteria. Bateman A, Murzin A, Teichmann SA;. Protein Sci 1998;7:1477-1480. [3]. 9654141. Characterisation of an Arabidopsis cDNA encoding a thylakoid lumen protein related to a novel 'pentapeptide repeat' family of proteins. Kieselbach T, Mant A, Robinson C, Schroder WP;. FEBS Lett 1998;428:241-244. (from Pfam) NF013006.5 PF00808.28 CBFD_NFYB_HMF 21.4 21.4 65 domain Y Y N histone-like protein GO:0003677 9032065 131567 cellular organisms no rank 1499 EBI-EMBL Histone-like transcription factor (CBF/NF-Y) and archaeal histone histone-like protein This family includes archaebacterial histones and histone like transcription factors from eukaryotes. [1]. 9032065. Histone-like transcription factors in eukaryotes. Burley SK, Xie X, Clark KL, Shu F;. Curr Opin Struct Biol 1997;7:94-102. (from Pfam) NF013007.5 PF00809.27 Pterin_bind 25.5 25.5 244 domain Y Y N dihydropteroate synthase 2.5.1.15 10997901,9187658 131567 cellular organisms no rank 174498 EBI-EMBL Pterin binding enzyme dihydropteroate synthase This family includes a variety of pterin binding enzymes that all adopt a TIM barrel fold. The family includes dihydropteroate synthase EC:2.5.1.15 as well as a group methyltransferase enzymes including methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) Swiss:Q46389 that catalyses a key step in the Wood-Ljungdahl pathway of carbon dioxide fixation. It transfers the N5-methyl group from methyltetrahydrofolate (CH3-H4folate) to a cob(I)amide centre in another protein, the corrinoid iron-sulfur protein. MeTr is a member of a family of proteins that includes methionine synthase and methanogenic enzymes that activate the methyl group of methyltetra-hydromethano(or -sarcino)pterin [2]. [1]. 9187658. Crystal structure of the anti-bacterial sulfonamide drug target dihydropteroate synthase. Achari A, Somers DO, Champness JN, Bryant PK, Rosemond J, Stammers DK. Nat Struct Biol 1997;4:490-497. This paper shows similarity by sequence of DHPS and MetH enzymes. [2]. 10997901. Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase. Doukov T, Seravalli J, Stezowski JJ, Ragsdale SW;. Structure Fold Des 2000;8:817-830. (from Pfam) NF013012.5 PF00814.30 TsaD 24.8 24.8 264 domain Y N N tRNA N6-adenosine threonylcarbamoyltransferase 23471679,26798630 131567 cellular organisms no rank 152701 EBI-EMBL tRNA N6-adenosine threonylcarbamoyltransferase tRNA N6-adenosine threonylcarbamoyltransferase This domain can be found in Kae1/Qri7/YgjD, products of COG0533 that belong to a small group of 60 proteins that are present in all three domains of life. COG0533 proteins are suggest to play a role in a post translational modification of certain tRNAs. For example, YgjD along with YeaZ, YjeE, and YrdC have been deemed necessary and sufficient for the tRNA modification [1]. This modification involves the formation of N6-threonyl carbamoyl adenosine (t6A) at position 37 in the anti-codon stem loop which is critical for translational speed and accuracy [2]. Structural analysis indicate that YeaZ lacks resemblance to any known protease active site. Together with the absence of a putative zinc-binding motif. Thus the likelyhood of it being a protease, as previously thought, has been negated [1]. EC:2.3.1.234 [1]. 23471679. Crystal structure of the dimer of two essential Salmonella typhimurium proteins, YgjD & YeaZ and calorimetric evidence for the formation of a ternary YgjD-YeaZ-YjeE complex. Nichols CE, Lamb HK, Thompson P, El Omari K, Lockyer M, Charles I, Hawkins AR, Stammers DK;. Protein Sci. 2013;22:628-640. [2]. 26798630. Global translational impacts of the loss of the tRNA modification t(6)A in yeast. Thiaville PC, Legendre R, Rojas-Benitez D, Baudin-Baillieu A, Hatin I, Chalancon G, Glavic A, Namy O, de Crecy-Lagard V;. Microb Cell. 2016;3:29-45. (from Pfam) NF013013.5 PF00815.25 Histidinol_dh 27 27 411 domain Y Y N histidinol dehydrogenase 1.1.1.23 GO:0016616,GO:0046872,GO:0051287 131567 cellular organisms no rank 89186 EBI-EMBL Histidinol dehydrogenase histidinol dehydrogenase NF013015.5 PF00817.25 IMS 23.2 23.2 148 domain Y N N impB/mucB/samB family GO:0006281 131567 cellular organisms no rank 189245 EBI-EMBL impB/mucB/samB family impB/mucB/samB family These proteins are involved in UV protection (Swiss). (from Pfam) NF013019.5 PF00821.23 PEPCK_GTP 23.8 23.8 357 PfamEq Y Y N phosphoenolpyruvate carboxykinase domain-containing protein 4.1.1.32 GO:0004611,GO:0006094 131567 cellular organisms no rank 24723 EBI-EMBL Phosphoenolpyruvate carboxykinase C-terminal P-loop domain phosphoenolpyruvate carboxykinase (GTP) Catalyses the formation of phosphoenolpyruvate by decarboxylation of oxaloacetate. (from Pfam) NF013022.5 PF00825.23 Ribonuclease_P 22.3 22.3 109 PfamEq Y Y N ribonuclease P protein component GO:0000049,GO:0004526,GO:0008033 131567 cellular organisms no rank 49571 EBI-EMBL Ribonuclease P ribonuclease P protein component NF013023.5 PF00827.22 Ribosomal_L15e 27 27 191 PfamEq Y N N Ribosomal L15 GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 1166 EBI-EMBL Ribosomal L15 Ribosomal L15 NF013024.5 PF00828.24 Ribosomal_L27A 22.5 22.5 123 PfamEq Y Y N uL15 family ribosomal protein 11154066,23636399,23695244 131567 cellular organisms no rank 38785 EBI-EMBL Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A uL15 family ribosomal protein This family includes higher eukaryotic ribosomal 60S L27A, archaeal 50S L18e, prokaryotic 50S L15, fungal mitochondrial L10, plant L27A, mitochondrial L15 and chloroplast L18-3 proteins. [1]. 11154066. Identification of the 50S ribosomal proteins from the Eubacterium Thermus thermophilus. Katsani KR, Tsiboli P, Anagnostopoulos K, Urlaub H, Choli-Papadopoulou T;. Biol Chem. 2000;381:1079-1087. [2]. 23636399. Structures of the human and Drosophila 80S ribosome. Anger AM, Armache JP, Berninghausen O, Habeck M, Subklewe M, Wilson DN, Beckmann R;. Nature. 2013;497:80-85. [3]. 23695244. Revisiting the Haloarcula marismortui 50S ribosomal subunit model. Gabdulkhakov A, Nikonov S, Garber M;. Acta Crystallogr D Biol Crystallogr. 2013;69:997-1004. (from Pfam) NF013027.5 PF00831.28 Ribosomal_L29 24.5 24.5 57 PfamEq Y Y N 50S ribosomal protein L29 GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 24535 EBI-EMBL Ribosomal L29 protein 50S ribosomal protein L29 NF013028.5 PF00832.25 Ribosomal_L39 21.6 21.6 42 PfamEq Y N N Ribosomal L39 protein GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 665 EBI-EMBL Ribosomal L39 protein Ribosomal L39 protein NF013029.5 PF00833.23 Ribosomal_S17e 22.8 22.8 122 PfamEq Y N N Ribosomal S17 GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 1047 EBI-EMBL Ribosomal S17 Ribosomal S17 NF013030.5 PF00834.24 Ribul_P_3_epim 21.1 21.1 198 domain Y N N Ribulose-phosphate 3 epimerase family GO:0005975,GO:0016857 131567 cellular organisms no rank 72500 EBI-EMBL Ribulose-phosphate 3 epimerase family Ribulose-phosphate 3 epimerase family This enzyme catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate. (from Pfam) NF013033.5 PF00837.22 T4_deiodinase 27 27 237 domain Y Y N deiodinase-like protein GO:0004800 16131321 131567 cellular organisms no rank 520 EBI-EMBL Iodothyronine deiodinase deiodinase-like protein Iodothyronine deiodinase converts thyroxine (T4) to 3,5,3'-triiodothyronine (T3). [1]. 16131321. Cellular and structural biology of the deiodinases. Bianco AC, Larsen PR;. Thyroid. 2005;15:777-786. (from Pfam) NF013034.5 PF00838.23 TCTP 24.3 24.3 164 PfamEq Y N N Translationally controlled tumour protein 131567 cellular organisms no rank 146 EBI-EMBL Translationally controlled tumour protein Translationally controlled tumour protein NF013038.5 PF00842.26 Ala_racemase_C 25 25 127 domain Y Y N alanine racemase C-terminal domain-containing protein 9063881 131567 cellular organisms no rank 107141 EBI-EMBL Alanine racemase, C-terminal domain Alanine racemase, C-terminal domain NF013043.5 PF00847.25 AP2 33.3 33.3 54 domain Y Y N AP2 domain-containing protein GO:0003700,GO:0006355 16040597,7756828,7773013,7919989,9192694 131567 cellular organisms no rank 701 EBI-EMBL AP2 domain AP2 domain This 60 amino acid residue domain can bind to DNA [2] and is found in transcription factor proteins. Initial discovery of this family. [1]. 7919989. Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Jofuku KD, den Boer BG, Van Montagu M, Okamuro JK;. Plant Cell. 1994;6:1211-1225. Evidence that this domain is DNA binding. [2]. 7756828. Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Ohme-takagi M, Shinshi H;. Plant Cell 1995;7:173-182. [3]. 7773013. The APETALA2 domain is related to a novel type of DNA binding domain. Weigel D;. Plant Cell 1995;7:388-389. [4]. 16040597. Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Balaji S, Babu MM, Iyer LM, Aravind L;. Nucleic Acids Res. 2005;33:3994-4006. [5]. 9192694. The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis. Okamuro JK, Caster B, Villarroel R, Van Montagu M, Jofuku KD;. Proc Natl Acad Sci U S A. 1997;94:7076-7081. (from Pfam) NF013044.5 PF00848.24 Ring_hydroxyl_A 24.9 24.9 208 domain Y Y N SRPBCC family protein GO:0005506,GO:0008152,GO:0051537 18922149 131567 cellular organisms no rank 79619 EBI-EMBL Ring hydroxylating alpha subunit (catalytic domain) SRPBCC family protein This family is the catalytic domain of aromatic-ring- hydroxylating dioxygenase systems. The active site contains a non-heme ferrous ion coordinated by three ligands. (from Pfam) NF013045.5 PF00849.27 PseudoU_synth_2 26.8 26.8 152 domain Y Y N pseudouridine synthase GO:0001522,GO:0003723,GO:0009451,GO:0009982 7493321 131567 cellular organisms no rank 394956 EBI-EMBL RNA pseudouridylate synthase pseudouridine synthase Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD Swiss:P33643, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA [1]. [1]. 7493321. A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for psi 746 in 23S RNA is also specific for psi 32 in tRNA(phe). Wrzesinski J, Nurse K, Bakin A, Lane BG, Ofengand J;. RNA 1995;1:437-448. (from Pfam) NF013046.5 PF00850.24 Hist_deacetyl 27.9 27.9 298 domain Y N N Histone deacetylase domain 9278492 131567 cellular organisms no rank 77807 EBI-EMBL Histone deacetylase domain Histone deacetylase domain Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1]. [1]. 9278492. Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are members of an ancient protein superfamily. Leipe DD, Landsman D;. Nucleic Acids Res 1997;25:3693-3697. (from Pfam) NF013048.5 PF00852.24 Glyco_transf_10 23.9 23.9 182 domain Y Y N glycosyltransferase family 10 domain-containing protein GO:0006486,GO:0008417,GO:0016020 17251184,9334165,9451017 131567 cellular organisms no rank 6947 EBI-EMBL Glycosyltransferase family 10 (fucosyltransferase) C-term glycosyltransferase family 10 (fucosyltransferase) C-terminal domain This is the C-terminal domain of a family of fucosyltransferases. This enzyme transfers fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage [1]. This family is known as glycosyltransferase family 10 [2]. The C-terminal domain is the likely binding-region for ADP (manuscript in publication). [1]. 9451017. Conserved structural features in eukaryotic and prokaryotic fucosyltransferases. Breton C, Oriol R, Imberty A;. Glycobiology 1998;8:87-94. [2]. 9334165. A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Campbell JA, Davies GJ, Bulone V, Henrissat B;. Biochem J 1997;326:929-939. [3]. 17251184. Structure and mechanism of Helicobacter pylori fucosyltransferase. A basis for lipopolysaccharide variation and inhibitor design. Sun HY, Lin SW, Ko TP, Pan JF, Liu CL, Lin CN, Wang AH, Lin CH;. J Biol Chem. 2007;282:9973-9982. (from Pfam) NF013050.5 PF00854.26 PTR2 27 27 392 domain Y N N POT family GO:0016020,GO:0022857,GO:0055085 7817396 131567 cellular organisms no rank 69853 EBI-EMBL POT family POT family The POT (proton-dependent oligopeptide transport) family all appear to be proton dependent transporters [1]. [1]. 7817396. The POT family of transport proteins. Paulsen IT, Skurray RA;. Trends Biochem Sci 1994;19:404-404. (from Pfam) NF013052.5 PF00856.33 SET 22.4 22.4 105 domain Y Y N SET domain-containing protein-lysine N-methyltransferase GO:0005515 12389037,12575990,8725238,9537414,9632640 131567 cellular organisms no rank 14972 EBI-EMBL SET domain SET domain SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases) [2]. A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction [3]. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure [5]. [1]. 8725238. The Drosophila ash1 gene product, which is localized at specific sites on polytene chromosomes, contains a SET domain and a PHD finger. Tripoulas N, LaJeunesse D, Gildea J, Shearn A;. Genetics 1996;143:913-928. [2]. 9537414. Association of SET domain and myotubularin-related proteins modulates growth control. Cui X, De Vivo I, Slany R, Miyamoto A, Firestein R, Cleary ML;. Nat Genet 1998;18:331-337. [3]. 9632640. The PR domain of the Rb-binding zinc finger protein RIZ1 is a protein binding interface and is related to the SET domain functioning in chromatin-mediated gene expression. Huang S, Shao G, Liu L;. J Biol Chem 1998;273:15933-15939. [4]. 12389037. Structure of the SET domain histone lysine methyltransferase Clr4. Min J, Zhang X, Cheng X, Grewal SI, Xu RM;. Nat Struct Biol 2002;0:0-0. [5]. 12575990. Structure of SET domain proteins: a new twist o. TRUNCATED at 1650 bytes (from Pfam) NF013053.5 PF00857.25 Isochorismatase 27 27 175 subfamily Y Y N isochorismatase family protein 1381445 131567 cellular organisms no rank 275859 EBI-EMBL Isochorismatase family isochorismatase family protein This family are hydrolase enzymes. [1]. 1381445. Crystal structure analysis, refinement and enzymatic reaction mechanism of N-carbamoylsarcosine amidohydrolase from Arthrobacter sp. at 2.0 A resolution. Romao MJ, Turk D, Gomis-Ruth FX, Huber R, Schumacher G, Mollering H, Russmann L;. J Mol Biol 1992;226:1111-1130. (from Pfam) NF013056.5 PF00860.25 Xan_ur_permease 27 27 389 subfamily Y Y N solute carrier family 23 protein GO:0016020,GO:0022857,GO:0055085 10331392,10395795 131567 cellular organisms no rank 215459 EBI-EMBL Permease family solute carrier family 23 protein This family includes permeases for diverse substrates such as xanthine Swiss:P42086, uracil Swiss:P39766 and vitamin C Swiss:Q9UGH3. However many members of this family are functionally uncharacterised and may transport other substrates. Members of this family have ten predicted transmembrane helices. (from Pfam) NF013057.5 PF00861.27 Ribosomal_L18p 27.8 27.8 116 PfamEq Y Y N 50S ribosomal protein L18 GO:0003735,GO:0005840,GO:0006412 333392,354687 131567 cellular organisms no rank 32579 EBI-EMBL Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast 50S ribosomal protein L18 This family includes the large subunit ribosomal proteins from bacteria, archaea, the mitochondria and the chloroplast. It does not include the 60S L18 or L5 proteins from Metazoa. (from Pfam) NF013062.5 PF00866.23 Ring_hydroxyl_B 27 27 144 domain Y Y N aromatic-ring-hydroxylating dioxygenase subunit beta GO:0008152 9634695 131567 cellular organisms no rank 23525 EBI-EMBL Ring hydroxylating beta subunit aromatic-ring-hydroxylating dioxygenase subunit beta This subunit has a similar structure to NTF-2 and scytalone dehydratase. [1]. 9634695. Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1, 2-dioxygenase. Kauppi B, Lee K, Carredano E, Parales RE, Gibson DT, Eklund H, Ramaswamy S;. Structure 1998;6:571-586. (from Pfam) NF013063.5 PF00867.23 XPG_I 24.9 24.9 89 PfamEq Y N N XPG I-region GO:0004518 9612080 131567 cellular organisms no rank 1482 EBI-EMBL XPG I-region XPG I-region NF013067.5 PF00871.22 Acetate_kinase 22 22 392 domain Y N N Acetokinase family GO:0016301,GO:0016310,GO:0016774 131567 cellular organisms no rank 78816 EBI-EMBL Acetokinase family Acetokinase family This family includes acetate kinase, butyrate kinase and 2-methylpropanoate kinase. (from Pfam) NF013068.5 PF00872.23 Transposase_mut 21 21 379 domain Y Y N transposase GO:0003677,GO:0004803,GO:0006313 131567 cellular organisms no rank 94559 EBI-EMBL Transposase, Mutator family transposase NF013069.5 PF00873.24 ACR_tran 28 28 1021 subfamily Y Y N efflux RND transporter permease subunit GO:0016020,GO:0022857,GO:0055085 12374972 131567 cellular organisms no rank 560113 EBI-EMBL AcrB/AcrD/AcrF family efflux RND transporter permease subunit Members of this family are integral membrane proteins. Some are involved in drug resistance. AcrB cooperates with a membrane fusion protein, AcrA, and an outer membrane channel TolC. The structure shows the AcrB forms a homotrimer [1]. [1]. 12374972. Crystal structure of bacterial multidrug efflux transporter AcrB. Murakami S, Nakashima R, Yamashita E, Yamaguchi A;. Nature 2002;419:587-593. (from Pfam) NF013071.5 PF00875.23 DNA_photolyase 26.6 26.6 164 domain Y Y N deoxyribodipyrimidine photo-lyase 4.1.99.3 9360600 131567 cellular organisms no rank 80724 EBI-EMBL DNA photolyase deoxyribodipyrimidine photo-lyase This domain binds a light harvesting cofactor. [1]. 9360600. Crystal structure of DNA photolyase from Anacystis nidulans. Tamada T, Kitadokoro K, Higuchi Y, Inaka K, Yasui A, de Ruiter PE, Eker AP, Miki K. Nat Struct Biol 1997;4:887-891. (from Pfam) NF013073.5 PF00877.24 NLPC_P60 23 23 105 domain Y Y N NlpC/P60 family protein 12620121 131567 cellular organisms no rank 303340 EBI-EMBL NlpC/P60 family NlpC/P60 catalytic domain Most members of the NlpC/P60 family are lipoprotein-hydrolyzing enzymes, cleaving the D-gamma-glutamyl-meso-diaminopimelate linkage or N-acetylmuramate-l-alanine linkage. The family includes transglutaminases, papain-like cysteine peptidases, and arylamine acetyltransferases. NF013077.5 PF00881.29 Nitroreductase 23.5 23.5 167 domain Y Y N nitroreductase family protein 17331467,8846223 131567 cellular organisms no rank 309479 EBI-EMBL Nitroreductase family nitroreductase family protein The nitroreductase family comprises a group of FMN- or FAD-dependent and NAD(P)H-dependent enzymes able to metabolize nitrosubstituted compounds. [1]. 8846223. Crystal structure of NADH oxidase from Thermus thermophilus. Hecht HJ, Erdmann H, Park HJ, Sprinzl M, Schmid RD. Nat Struct Biol 1995;2:1109-1114. [2]. 17331467. In silico identification of a new group of specific bacterial and fungal nitroreductases-like proteins. de Oliveira IM, Henriques JA, Bonatto D;. Biochem Biophys Res Commun. 2007;355:919-925. (from Pfam) NF013078.5 PF00882.23 Zn_dep_PLPC 26.8 26.8 167 domain Y Y N zinc dependent phospholipase C family protein 131567 cellular organisms no rank 23776 EBI-EMBL Zinc dependent phospholipase C zinc dependent phospholipase C family protein NF013079.5 PF00883.26 Peptidase_M17 25 25 310 domain Y N N Cytosol aminopeptidase family, catalytic domain GO:0006508,GO:0046872,GO:0070006 2395881 131567 cellular organisms no rank 92046 EBI-EMBL Cytosol aminopeptidase family, catalytic domain Cytosol aminopeptidase family, catalytic domain The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine aminopeptidase. [1]. 2395881. Molecular structure of leucine aminopeptidase at 2.7-A resolution. Burley SK, David PR, Taylor A, Lipscomb WN;. Proc Natl Acad Sci U S A 1990;87:6878-6882. (from Pfam) NF013080.5 PF00884.28 Sulfatase 25 25 301 domain Y Y N sulfatase-like hydrolase/transferase GO:0008484 9521684 131567 cellular organisms no rank 414485 EBI-EMBL Sulfatase sulfatase-like hydrolase/transferase NF013081.5 PF00885.24 DMRL_synthase 26.7 26.7 139 PfamEq Y Y N 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 GO:0009349 16923880,17854827,20195542 131567 cellular organisms no rank 50000 EBI-EMBL 6,7-dimethyl-8-ribityllumazine synthase 6,7-dimethyl-8-ribityllumazine synthase This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example Swiss:O28856. The family contains a number of different subsets including a family of proteins comprising archaeal lumazine and riboflavin synthases, type I lumazine synthases, and the eubacterial type II lumazine synthases [1]. It has been established that lumazine synthase catalyses the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. The type I lumazine synthases area active in pentameric or icosahedral quaternary assemblies, whereas the type II are decameric [2]. Brucella, a bacterial genus that causes brucellosis, and other Rhizobiales have an atypical riboflavin metabolic pathway. Brucella spp code for both a type-I and a type-II lumazine synthase, and it has been shown that at least one of these two has to be present in order for Brucella to be viable, showing that in the case of Brucella flavin metabolism is implicated in bacterial virulence [3]. [1]. 16923880. Evolution of vitamin B2 biosynthesis: 6,7-dimethyl-8-ribityllumazine synthases of Brucella. Zylberman V, Klinke S, Haase I, Bacher A, Fischer M, Goldbaum FA;. J Bacteriol. 2006;188:6135-6142. [2]. 17854827. Structural and kinetic properties of lumazine synthase isoenzymes in the order Rhizobiales. Klinke S, Zylberman V, Bonomi HR, Haase I, Guimaraes BG, Braden BC, Bacher A, Fischer M, Goldbaum FA;. J Mol Biol. 2007;373:664-680. [3]. 20195542. An atypical riboflavin pat. TRUNCATED at 1650 bytes (from Pfam) NF013083.5 PF00887.24 ACBP 28.3 28.3 76 PfamEq Y Y N acyl-CoA-binding protein GO:0000062 131567 cellular organisms no rank 6047 EBI-EMBL Acyl CoA binding protein acyl-CoA-binding protein NF013086.5 PF00890.29 FAD_binding_2 20.4 20.4 414 domain Y Y N FAD-binding protein 8061609 131567 cellular organisms no rank 1512735 EBI-EMBL FAD binding domain FAD binding domain This family includes members that bind FAD. This family includes the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase. [1]. 8061609. Structure of glutathione reductase from Escherichia coli at 1.86 A resolution: comparison with the enzyme from human erythrocytes. Mittl PR, Schulz GE. Protein Sci 1994;3:799-809. (from Pfam) NF013087.5 PF00891.23 Methyltransf_2 22.3 22.3 210 domain Y Y N methyltransferase GO:0008171 8434913 131567 cellular organisms no rank 113198 EBI-EMBL O-methyltransferase domain SAM-dependent O-methyltransferase domain This family includes a range of O-methyltransferases. These enzymes utilise S-adenosyl methionine. [1]. 8434913. Purification of a 40-kilodalton methyltransferase active in the aflatoxin biosynthetic pathway. Keller NP, Dischinger HC, Bhatnagar D, Cleveland TE, Ullah AH;. Appl Environ Microbiol 1993;59:479-484. (from Pfam) NF013088.5 PF00892.25 EamA 27.2 27.2 136 domain Y Y N EamA family transporter GO:0016020 131567 cellular organisms no rank 875058 EBI-EMBL EamA-like transporter family EamA family transporter This family includes many hypothetical membrane proteins of unknown function. Many of the proteins contain two copies of the aligned region. The family used to be known as DUF6. Members of this family usually carry 5+5 transmembrane domains, and this domain attempts to model five of these. (from Pfam) NF013089.5 PF00893.24 Multi_Drug_Res 23.7 23.7 93 subfamily Y Y N SMR family transporter GO:0016020,GO:0022857 1314803,2602117,7896833 131567 cellular organisms no rank 93969 EBI-EMBL Small Multidrug Resistance protein SMR family transporter Members of this family belong to the SMR (Small Multidrug Resistance) family of transporters, many known to be involved in the efflux of various biocides, antibiotics, and other toxic substrates. NF013094.5 PF00899.26 ThiF 28.1 28.1 238 domain Y Y N ThiF family adenylyltransferase GO:0008641 11713534,15660128,18662542 131567 cellular organisms no rank 170225 EBI-EMBL ThiF family ThiF family adenylyltransferase This domain is found in ubiquitin activating E1 family and members of the bacterial ThiF/MoeB/HesA family. It is repeated in Ubiquitin-activating enzyme E1 [1-3]. [1]. 11713534. Mechanism of ubiquitin activation revealed by the structure of a bacterial MoeB-MoaD complex. Lake MW, Wuebbens MM, Rajagopalan KV, Schindelin H;. Nature. 2001;414:325-329. [2]. 15660128. Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1. Lois LM, Lima CD;. EMBO J. 2005;24:439-451. [3]. 18662542. Structural insights into E1-catalyzed ubiquitin activation and transfer to conjugating enzymes. Lee I, Schindelin H;. Cell. 2008;134:268-278. (from Pfam) NF013095.5 PF00900.25 Ribosomal_S4e 25 25 75 PfamEq Y N N Ribosomal family S4e 131567 cellular organisms no rank 1255 EBI-EMBL Ribosomal family S4e Ribosomal family S4e NF013097.5 PF00902.23 TatC 25.1 25.1 208 PfamEq Y Y N twin-arginine translocase subunit TatC GO:0016020 12163163 131567 cellular organisms no rank 58782 EBI-EMBL Sec-independent protein translocase protein (TatC) twin-arginine translocase subunit TatC The bacterial Tat system has a remarkable ability to transport folded proteins even enzyme complexes across the cytoplasmic membrane. It is structurally and mechanistically similar to the Delta pH-driven thylakoidal protein import pathway. A functional Tat system or Delta pH-dependent pathway requires three integral membrane proteins: TatA/Tha4, TatB/Hcf106 and TatC/cpTatC. The TatC protein is essential for the function of both pathways. It might be involved in twin-arginine signal peptide recognition, protein translocation and proton translocation. Sequence analysis predicts that TatC contains six transmembrane helices (TMHs), and experimental data confirmed that N- and C-termini of TatC or cpTatC are exposed to the cytoplasmic or stromal face of the membrane. The cytoplasmic N-terminus and the first cytoplasmic loop region of the Escherichia coli TatC protein are essential for protein export. At least two TatC molecules co-exist within each Tat translocon [1]. [1]. 12163163. Topology determination and functional analysis of the Escherichia coli TatC protein. Gouffi K, Santini CL, Wu LF;. FEBS Lett 2002;525:65-70. (from Pfam) NF013098.5 PF00903.30 Glyoxalase 20.6 20.6 121 domain Y Y N VOC family protein 7481800,8504803 131567 cellular organisms no rank 965797 EBI-EMBL Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily VOC family protein NF013103.5 PF00908.22 dTDP_sugar_isom 27 27 168 domain Y Y N dTDP-4-dehydrorhamnose 3,5-epimerase family protein GO:0008830 131567 cellular organisms no rank 76702 EBI-EMBL dTDP-4-dehydrorhamnose 3,5-epimerase dTDP-4-dehydrorhamnose 3,5-epimerase family protein This family catalyse the isomerisation of dTDP-4-dehydro-6-deoxy -D-glucose with dTDP-4-dehydro-6-deoxy-L-mannose. The EC number of this enzyme is 5.1.3.13. (from Pfam) NF013104.5 PF00909.26 Ammonium_transp 23.2 23.2 399 domain Y N N Ammonium Transporter Family GO:0008519,GO:0016020,GO:0072488 8062822,9433124 131567 cellular organisms no rank 90427 EBI-EMBL Ammonium Transporter Family Ammonium Transporter Family NF013105.5 PF00910.27 RNA_helicase 21.5 21.5 105 domain Y N N RNA helicase GO:0003723,GO:0003724 2546125 131567 cellular organisms no rank 19358 EBI-EMBL RNA helicase RNA helicase This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses. [1]. 2546125. Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Gorbalenya AE, Koonin EV, Donchenko AP, Blinov VM;. Nucleic Acids Res 1989;17:4713-4730. (from Pfam) NF013109.5 PF00916.25 Sulfate_transp 23.2 23.2 380 domain Y Y N SulP family inorganic anion transporter GO:0015116,GO:0016020,GO:1902358 131567 cellular organisms no rank 166733 EBI-EMBL Sulfate permease family SulP family inorganic anion transporter This family of integral membrane proteins are known as the Sulfate Permease (SulP) family. SulP is a large family found in all domains of life. Although sulfate is a commonly transported ion there are many other activities in this family. See the TCDB description for a comprehensive summary. (from Pfam) NF013112.5 PF00919.25 UPF0004 27 27 98 domain Y N N Uncharacterized protein family UPF0004 GO:0035596,GO:0051539 11313137,11882645 131567 cellular organisms no rank 148414 EBI-EMBL Uncharacterized protein family UPF0004 Uncharacterized protein family UPF0004 This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins [1,2]. This domain is a nearly always found in conjunction with Pfam:PF04055 and Pfam:PF01938 although its function is uncertain. [1]. 11313137. TRAM, a predicted RNA-binding domain, common to tRNA uracil methylation and adenine thiolation enzymes. Anantharaman V, Koonin EV, Aravind L;. FEMS Microbiol Lett 2001;197:215-221. [2]. 11882645. Enzymatic modification of tRNAs: MiaB is an iron-sulfur protein. Pierrel F, Bjork GR, Fontecave M, Atta M;. J Biol Chem 2002;277:13367-13370. (from Pfam) NF013113.5 PF00920.26 ILVD_EDD 27 27 516 domain Y Y N dihydroxy-acid dehydratase 4.2.1.9 GO:0003824,GO:0016836 131567 cellular organisms no rank 153527 EBI-EMBL Dehydratase family dihydroxy-acid dehydratase NF013116.5 PF00923.24 TAL_FSA 27 27 285 domain Y Y N transaldolase family protein GO:0005975 10869557,11298760,11705376,25267444,26131847 131567 cellular organisms no rank 84400 EBI-EMBL Transaldolase/Fructose-6-phosphate aldolase transaldolase family protein Transaldolase (TAL) is an enzyme of the pentose phosphate pathway (PPP) found almost ubiquitously in the three domains of life (Archaea, Bacteria, and Eukarya). TAL shares a high degree of structural similarity and sequence identity with fructose-6-phosphate aldolase (FSA). They both belong to the class I aldolase family[4]. Their protein structures have been revealed[5]. [1]. 11705376. Snapshots of catalysis: the structure of fructose-1,6-(bis)phosphate aldolase covalently bound to the substrate dihydroxyacetone phosphate. Choi KH, Shi J, Hopkins CE, Tolan DR, Allen KN;. Biochemistry 2001;40:13868-13875. [2]. 11298760. Identification of catalytically important residues in the active site of Escherichia coli transaldolase. Schorken U, Thorell S, Schurmann M, Jia J, Sprenger GA, Schneider G;. Eur J Biochem 2001;268:2408-2415. [3]. 10869557. The three-dimensional structure of human transaldolase. Thorell S, Gergely P Jr, Banki K, Perl A, Schneider G. FEBS Lett 2000;475:205-208. [4]. 26131847. Converting Transaldolase into Aldolase through Swapping of the Multifunctional Acid-Base Catalyst: Common and Divergent Catalytic Principles in F6P Aldolase and Transaldolase. Sautner V, Friedrich MM, Lehwess-Litzmann A, Tittmann K;. Biochemistry. 2015;54:4475-4486. [5]. 25267444. Sweet siblings with different faces: the mechanisms of FBP and F6P aldolase, transaldolase, transketolase and phosphoketolase revisited in light of recent structural data. Tittmann K;. Bioorg Chem. 2014;57:263-280. (from Pfam) NF013117.5 PF00924.23 MS_channel_2nd 20.2 20.2 68 domain Y Y N mechanosensitive ion channel domain-containing protein GO:0016020,GO:0055085 11159397,11275684,11296222,23012406,23074248,23339071,34376558 131567 cellular organisms no rank 260702 EBI-EMBL Mechanosensitive ion channel, beta-domain Mechanosensitive ion channel, beta-domain This entry includes small conductance mechanosensitive channels (MscS), which assembles to a homoheptameric complex [1-6]. Each monomer consists of a N-terminal transmembrane region and a large cytoplasmic segment composed of a five-stranded antiparallel beta-sheet (middle/second) domain and a C-terminal alpha/beta-domain [4-7]. This is the beta domain which adopts a SH3-like barrel structure. [1]. 11296222. Structural and functional differences between two homologous mechanosensitive channels of Methanococcus jannaschii. Kloda A, Martinac B;. EMBO J 2001;20:1888-1896. [2]. 11159397. Molecular identification of a mechanosensitive channel in archaea. Kloda A, Martinac B;. Biophys J 2001;80:229-240. [3]. 11275684. Mechanosensitive channels in prokaryotes. Martinac B;. Cell Physiol Biochem 2001;11:61-76. [4]. 34376558. Mechanosensitive channel gating by delipidation. Flegler VJ, Rasmussen A, Borbil K, Boten L, Chen HA, Deinlein H, Halang J, Hellmanzik K, Loffler J, Schmidt V, Makbul C, Kraft C, Hedrich R, Rasmussen T, Bottcher B;. Proc Natl Acad Sci U S A. 2021; [Epub ahead of print]. [5]. 23012406. Conformational state of the MscS mechanosensitive channel in solution revealed by pulsed electron-electron double resonance (PELDOR) spectroscopy. Pliotas C, Ward R, Branigan E, Rasmussen A, Hagelueken G, Huang H, Black SS, Booth IR, Schiemann O, Naismith JH;. Proc Natl Acad Sci U S A. 2012;109:E2675-E2682. [6]. 23339071. Open and shut: crystal structures of the dodecylmaltoside solubilized mechanosensitive channel of small conductance from Escherichia coli and Helicobacter pylori at 4.4 A and 4.1 A resolutions. Lai JY, Poon YS, K. TRUNCATED at 1650 bytes (from Pfam) NF013118.5 PF00925.25 GTP_cyclohydro2 23.3 23.3 165 domain Y N N GTP cyclohydrolase II 8320220 131567 cellular organisms no rank 90954 EBI-EMBL GTP cyclohydrolase II GTP cyclohydrolase II GTP cyclohydrolase II catalyses the first committed step in the biosynthesis of riboflavin. [1]. 8320220. Biosynthesis of riboflavin: cloning, sequencing, mapping, and expression of the gene coding for GTP cyclohydrolase II in Escherichia coli. Richter G, Ritz H, Katzenmeier G, Volk R, Kohnle A, Lottspeich F, Allendorf D, Bacher A;. J Bacteriol 1993;175:4045-4051. (from Pfam) NF013119.5 PF00926.24 DHBP_synthase 26.4 26.4 191 domain Y Y N 3,4-dihydroxy-2-butanone-4-phosphate synthase GO:0008686 9211332 131567 cellular organisms no rank 74139 EBI-EMBL 3,4-dihydroxy-2-butanone 4-phosphate synthase 3,4-dihydroxy-2-butanone-4-phosphate synthase 3,4-Dihydroxy-2-butanone 4-phosphate is biosynthesised from ribulose 5-phosphate and serves as the biosynthetic precursor for the xylene ring of riboflavin. Sometimes found as a bifunctional enzyme with Pfam:PF00925. [1]. 9211332. Biosynthesis of riboflavin: 3,4-dihydroxy-2-butanone -4-phosphate synthase. Richter G, Krieger C, Volk R, Kis K, Ritz H, Gotze E, Bacher A;. Methods Enzymol 1997;280:374-382. (from Pfam) NF013122.5 PF00929.29 RNase_T 24 24 164 domain Y Y N exonuclease domain-containing protein GO:0004527 8506149 131567 cellular organisms no rank 278792 EBI-EMBL Exonuclease RNase T-like exonuclease domain This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.; [1]. 8506149. RNase T shares conserved sequence motifs with DNA proofreading exonucleases. Koonin EV, Deutscher MP;. Nucleic Acids Res 1993;21:2521-2522. (from Pfam) NF013123.5 PF00930.26 DPPIV_N 22 22 354 domain Y Y N DPP IV N-terminal domain-containing protein GO:0006508 131567 cellular organisms no rank 63549 EBI-EMBL Dipeptidyl peptidase IV (DPP IV) N-terminal region Dipeptidyl peptidase IV (DPP IV) N-terminal region This family is an alignment of the region to the N-terminal side of the active site. The Prosite motif does not correspond to this Pfam entry. (from Pfam) NF013124.5 PF00931.27 NB-ARC 23.5 23.5 248 domain Y Y N NB-ARC domain-containing protein GO:0043531 9545207 131567 cellular organisms no rank 164924 EBI-EMBL NB-ARC domain NB-ARC domain NF013125.5 PF00932.24 LTD 34.3 34.3 109 domain Y Y N lamin tail domain-containing protein 15611647 131567 cellular organisms no rank 51777 EBI-EMBL Lamin Tail Domain Lamin Tail Domain The lamin-tail domain (LTD), which has an immunoglobulin (Ig) fold, is found in Nuclear Lamins, Chlo1887 from Chloroflexus, and several bacterial proteins where it occurs with membrane associated hydrolases of the metallo-beta-lactamase,synaptojanin, and calcineurin-like phosphoesterase superfamilies [1]. [1]. 15611647. Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. Mans BJ, Anantharaman V, Aravind L, Koonin EV;. Cell Cycle. 2004;3:1612-1637. (from Pfam) NF013126.5 PF00933.26 Glyco_hydro_3 27 27 316 domain Y Y N glycoside hydrolase family 3 N-terminal domain-containing protein GO:0004553,GO:0005975 10368285 131567 cellular organisms no rank 270849 EBI-EMBL Glycosyl hydrolase family 3 N terminal domain Glycosyl hydrolase family 3 N terminal domain NF013128.5 PF00935.24 Ribosomal_L44 25 25 76 PfamEq Y N N Ribosomal protein L44 GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 850 EBI-EMBL Ribosomal protein L44 Ribosomal protein L44 NF013132.5 PF00939.24 Na_sulph_symp 27 27 472 domain Y Y N anion permease GO:0016020,GO:0022857,GO:0055085 131567 cellular organisms no rank 117350 EBI-EMBL Sodium:sulfate symporter transmembrane region anion permease There are also some members in this family that do not match the Prosite motif, and belong to the subfamily SODIT1. (from Pfam) NF013133.5 PF00940.24 RNA_pol 22 22 448 domain Y Y N DNA-directed RNA polymerase 2.7.7.6 GO:0003677,GO:0003899,GO:0006351 131567 cellular organisms no rank 1220 EBI-EMBL DNA-dependent RNA polymerase phage T7/mitochondrial-type DNA-directed RNA polymerase Members of this family are small, single chain-type RNA polymerases as found in mitochondria and in phage T7. NF013134.5 PF00941.26 FAD_binding_5 27 27 170 domain Y Y N FAD binding domain-containing protein GO:0016491 10430865 131567 cellular organisms no rank 126879 EBI-EMBL FAD binding domain in molybdopterin dehydrogenase FAD binding domain in molybdopterin dehydrogenase NF013135.5 PF00942.23 CBM_3 22.4 22.4 83 domain Y Y N cellulose binding domain-containing protein GO:0005975,GO:0030248 1490597,8918451 131567 cellular organisms no rank 14627 EBI-EMBL Cellulose binding domain Cellulose binding domain NF013143.5 PF00950.22 ABC-3 20.1 20.1 258 domain Y Y N metal ABC transporter permease GO:0005886,GO:0042626,GO:0043190,GO:0055085 131567 cellular organisms no rank 158036 EBI-EMBL ABC 3 transport family metal ABC transporter permease NF013146.5 PF00953.26 Glycos_transf_4 27 27 160 domain Y N N Glycosyl transferase family 4 GO:0016020,GO:0016780 7734839 131567 cellular organisms no rank 119969 EBI-EMBL Glycosyl transferase family 4 Glycosyl transferase family 4 NF013151.5 PF00958.27 GMP_synt_C 27 27 92 PfamEq Y N N GMP synthase C terminal domain GO:0003922,GO:0005524,GO:0006164,GO:0006177 8548458 131567 cellular organisms no rank 70270 EBI-EMBL GMP synthase C terminal domain GMP synthase C terminal domain GMP synthetase is a glutamine amidotransferase from the de novo purine biosynthetic pathway. This family is the C-terminal domain specific to the GMP synthases Swiss:P49915 EC:6.3.5.2. In prokaryotes this domain mediates dimerisation. Eukaryotic GMP synthases are monomers. This domain in eukaryotes includes several large insertions that may form globular domains. [1]. 8548458. The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families. Tesmer JJ, Klem TJ, Deras ML, Davisson VJ, Smith JL;. Nat Struct Biol 1996;3:74-86. (from Pfam) NF013154.5 PF00961.24 LAGLIDADG_1 23.1 23.1 102 domain Y Y N LAGLIDADG family homing endonuclease GO:0004519 9187655,9254693,9358175 131567 cellular organisms no rank 312 EBI-EMBL LAGLIDADG endonuclease LAGLIDADG family homing endonuclease NF013155.5 PF00962.27 A_deaminase 27 27 330 domain Y N N Adenosine deaminase GO:0019239 1925539 131567 cellular organisms no rank 86006 EBI-EMBL Adenosine deaminase Adenosine deaminase NF013156.5 PF00963.23 Cohesin 24.1 24.1 139 domain Y Y N cohesin domain-containing protein GO:0000272,GO:0030246 9083107 131567 cellular organisms no rank 8201 EBI-EMBL Cohesin domain cohesin domain Cohesin domains interact with a complementary domain, termed the dockerin domain. The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome [1]. [1]. 9083107. A cohesin domain from Clostridium thermocellum: the crystal structure provides new insights into cellulosome assembly. Shimon LJ, Bayer EA, Morag E, Lamed R, Yaron S, Shoham Y, Frolow F;. Structure 1997;5:381-390. (from Pfam) NF013158.5 PF00965.22 TIMP 23.1 23.1 183 domain Y N N Tissue inhibitor of metalloproteinase GO:0008191 7918391 131567 cellular organisms no rank 582 EBI-EMBL Tissue inhibitor of metalloproteinase Tissue inhibitor of metalloproteinase Members of this family are common in extracellular regions of vertebrate species NMR structure. [1]. 7918391. Solution structure of the active domain of tissue inhibitor of metalloproteinases-2. A new member of the OB fold protein family. Williamson RA, Martorell G, Carr MD, Murphy G, Docherty AJ, Freedman RB, Feeney J;. Biochemistry 1994;33:11745-11759. (from Pfam) NF013161.5 PF00970.29 FAD_binding_6 21.1 21.1 99 domain Y Y N FAD-binding oxidoreductase 1748631,7812715 131567 cellular organisms no rank 247267 EBI-EMBL Oxidoreductase FAD-binding domain oxidoreductase FAD-binding domain NF013166.5 PF00975.25 Thioesterase 26.4 26.4 226 domain Y Y N thioesterase domain-containing protein GO:0009058 9560421 131567 cellular organisms no rank 331719 EBI-EMBL Thioesterase domain thioesterase domain Peptide synthetases are involved in the non-ribosomal synthesis of peptide antibiotics. Next to the operons encoding these enzymes, in almost all cases, are genes that encode proteins that have similarity to the type II fatty acid thioesterases of vertebrates. There are also modules within the peptide synthetases that also share this similarity. With respect to antibiotic production, thioesterases are required for the addition of the last amino acid to the peptide antibiotic, thereby forming a cyclic antibiotic. Thioesterases (non-integrated) have molecular masses of 25-29 kDa. [1]. 9560421. Genetic evidence for a role of thioesterase domains, integrated in or associated with peptide synthetases, in non-ribosomal peptide biosynthesis in Bacillus subtilis. Schneider A, Marahiel MA;. Arch Microbiol 1998;169:404-410. (from Pfam) NF013168.5 PF00977.26 His_biosynth 23.6 23.6 228 domain Y Y N HisA/HisF-related TIM barrel protein GO:0000105 11054297,8028028,9332345 131567 cellular organisms no rank 162366 EBI-EMBL Histidine biosynthesis protein HisA/HisF-related TIM barrel protein Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalysed by eight enzymes. The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold. In some archaeal HisA proteins the TIM barrel is composed of two tandem repeats of a half barrel e.g. Swiss:P05325 [2]. This family belong to the common phosphate binding site TIM barrel family [3]. [1]. 9332345. Paralogous histidine biosynthetic genes: evolutionary analysis of the Saccharomyces cerevisiae HIS6 and HIS7 genes. Fani R, Tamburini E, Mori E, Lazcano A, Lio P, Barberio C, Casalone E, Cavalieri D, Perito B, Polsinelli M,. Gene 1997;197:9-17. [2]. 8028028. The evolution of the histidine biosynthetic genes in prokaryotes: a common ancestor for the hisA and hisF genes. Fani R, Lio P, Chiarelli I, Bazzicalupo M;. J Mol Evol 1994;38:489-495. [3]. 11054297. Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways. Copley RR, Bork P;. J Mol Biol 2000;303:627-641. (from Pfam) NF013173.5 PF00982.26 Glyco_transf_20 32.5 32.5 473 domain Y Y N trehalose-6-phosphate synthase GO:0003824,GO:0005992 8045430,9334165 131567 cellular organisms no rank 41130 EBI-EMBL Glycosyltransferase family 20 trehalose-6-phosphate synthase Members of this family belong to glycosyl transferase family 20 [1]. OtsA (Trehalose-6-phosphate synthase) is homologous to regions in the subunits of yeast trehalose-6-phosphate synthase/phosphate complex, [2]. [1]. 9334165. A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Campbell JA, Davies GJ, Bulone V, Henrissat B;. Biochem J 1997;326:929-939. [2]. 8045430. Analysis of the otsBA operon for osmoregulatory trehalose synthesis in Escherichia coli and homology of the OtsA and OtsB proteins to the yeast trehalose-6-phosphate synthase/phosphatase complex. Kaasen I, McDougall J, Strom AR;. Gene 1994;145:9-15. (from Pfam) NF013175.5 PF00984.24 UDPG_MGDP_dh 25.4 25.4 94 domain Y N N UDP-glucose/GDP-mannose dehydrogenase family, central domain GO:0016616,GO:0051287 2470755,9013585 131567 cellular organisms no rank 170353 EBI-EMBL UDP-glucose/GDP-mannose dehydrogenase family, central domain UDP-glucose/GDP-mannose dehydrogenase family, central domain The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [2]. [1]. 2470755. Purification and characterization of guanosine diphospho-D-mannose dehydrogenase. A key enzyme in the biosynthesis of alginate by Pseudomonas aeruginosa. Roychoudhury S, May TB, Gill JF, Singh SK, Feingold DS, Chakrabarty AM;. J Biol Chem 1989;264:9380-9385. [2]. 9013585. Properties and kinetic analysis of UDP-glucose dehydrogenase from group A streptococci. Irreversible inhibition by UDP-chloroacetol. Campbell RE, Sala RF, van de Rijn I, Tanner ME;. J Biol Chem 1997;272:3416-3422. (from Pfam) NF013177.5 PF00986.26 DNA_gyraseB_C 29.8 29.8 63 domain Y N N DNA gyrase B subunit, carboxyl terminus GO:0003677,GO:0003918,GO:0005524,GO:0006265 7770916 131567 cellular organisms no rank 121435 EBI-EMBL DNA gyrase B subunit, carboxyl terminus DNA gyrase B subunit, carboxyl terminus The amino terminus of eukaryotic and prokaryotic DNA topoisomerase II are similar, but they have a different carboxyl terminus. The amino-terminal portion of the DNA gyrase B protein is thought to catalyse the ATP-dependent super-coiling of DNA. See Pfam:PF00204. The carboxyl-terminal end supports the complexation with the DNA gyrase A protein and the ATP-independent relaxation. This family also contains Topoisomerase IV. This is a bacterial enzyme that is closely related to DNA gyrase, [1]. [1]. 7770916. The mechanisms of DNA topoisomerases. Roca J;. Trends Biochem Sci 1995;20:156-160. (from Pfam) NF013178.5 PF00988.27 CPSase_sm_chain 27 27 126 domain Y Y N carbamoyl-phosphate synthase domain-containing protein 1972379 131567 cellular organisms no rank 73595 EBI-EMBL Carbamoyl-phosphate synthase small chain, CPSase domain Carbamoyl-phosphate synthase small chain, CPSase domain The carbamoyl-phosphate synthase domain is in the amino terminus of protein. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines [1]. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See Pfam:PF00289. The small chain has a GATase domain in the carboxyl terminus. See Pfam:PF00117. [1]. 1972379. Mammalian carbamyl phosphate synthetase (CPS). DNA sequence and evolution of the CPS domain of the Syrian hamster multifunctional protein CAD. Simmer JP, Kelly RE, Rinker AG Jr, Scully JL, Evans DR;. Biol Chem 1990;265:10395-10402. (from Pfam) NF013179.5 PF00989.30 PAS 22.6 22.6 113 domain Y Y N PAS domain-containing protein GO:0006355 15009198,7756254,9301332,9382818 131567 cellular organisms no rank 996669 EBI-EMBL PAS fold PAS fold The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 9301332. PAS domain S-boxes in archaea, bacteria and sensors for oxygen and redox. Zhulin IB, Taylor BL, Dixon R;. Trends Biochem Sci 1997;22:331-333. [2]. 7756254. 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore. Borgstahl GE, Williams DR, Getzoff ED;. Biochemistry 1995;34:6278-6287. [3]. 9382818. PAS: a multifunctional domain family comes to light. Ponting CP, Aravind L;. Curr Biol 1997;7:674-677. [4]. 15009198. The PAS fold: a redefination of the PAS domain based upon structural prediction. Hefti MH, Francoijs KJ, de Vries SC, Dixon R, Vervoort J;. Eur J Biochem 2004;271:1198-1208. (from Pfam) NF013183.5 PF00994.29 MoCF_biosynth 26.6 26.6 144 domain Y Y N molybdopterin-binding protein 11325967 131567 cellular organisms no rank 236554 EBI-EMBL Probable molybdopterin binding domain molybdopterin-binding domain This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerisation [1]. [1]. 11325967. X-ray crystal structure of the trimeric N-terminal domain of gephyrin. Sola M, Kneussel M, Heck IS, Betz H, Weissenhorn W;. J Biol Chem 2001;276:25294-25301. (from Pfam) NF013185.5 PF00996.23 GDI 23 23 436 PfamEq Y N N GDP dissociation inhibitor GO:0005092,GO:0007264 8609986 131567 cellular organisms no rank 294 EBI-EMBL GDP dissociation inhibitor GDP dissociation inhibitor NF013188.5 PF00999.26 Na_H_Exchanger 26.2 26.2 375 domain Y Y N cation:proton antiporter GO:0006812,GO:0015297,GO:0016020,GO:0055085,GO:1902600 9278382,9507001,9537504 131567 cellular organisms no rank 316437 EBI-EMBL Sodium/hydrogen exchanger family cation:proton antiporter Na/H antiporters are key transporters in maintaining the pH of actively metabolising cells. The molecular mechanisms of antiport are unclear. These antiporters contain 10-12 transmembrane regions (M) at the amino-terminus and a large cytoplasmic region at the carboxyl terminus. The transmembrane regions M3-M12 share identity with other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the region that is involved in the transport of sodium and hydrogen ions. The cytoplasmic region has little similarity throughout the family. [1]. 9537504. Comparative molecular analysis of Na+/H+ exchangers: a unified model for Na+/H+ antiport?. Dibrov P, Fliegel L;. FEBS Lett 1998;424:1-5. [2]. 9278382. Na+/H+ exchangers of mammalian cells. Orlowski J, Grinstein S;. J Biol Chem 1997;272:22373-22376. [3]. 9507001. Identification of a mitochondrial Na+/H+ exchanger. Numata M, Petrecca K, Lake N, Orlowski J;. J Biol Chem 1998;273:6951-6959. (from Pfam) NF013189.5 PF01000.31 RNA_pol_A_bac 33.9 33.9 119 PfamEq Y N N RNA polymerase Rpb3/RpoA insert domain GO:0003899,GO:0006351,GO:0046983 7613089,9050843,9657722 131567 cellular organisms no rank 36331 EBI-EMBL RNA polymerase Rpb3/RpoA insert domain RNA polymerase Rpb3/RpoA insert domain Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal [1]. 9657722. Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain. Zhang G, Darst SA;. Science 1998;281:262-266. [2]. 7613089. The Escherichia coli RNA polymerase alpha subunit: structure and function. Ebright RH, Busby S;. Curr Opin Genet Dev 1995;5:197-203. [3]. 9050843. The two alpha subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element. Murakami K, Kimura M, Owens JT, Meares CF, Ishihama A;. Proc Natl Acad Sci USA 1997;94:1709-1714. (from Pfam) NF013197.5 PF01008.22 IF-2B 22.4 22.4 280 domain Y N N Initiation factor 2 subunit family GO:0008152 15215245,9520434 131567 cellular organisms no rank 36768 EBI-EMBL Initiation factor 2 subunit family Initiation factor 2 subunit family This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes, initiation factor 2B subunits 1 and 2 from archaebacteria and some proteins of unknown function from prokaryotes. Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit. Members of this family have also been characterised as 5-methylthioribose- 1-phosphate isomerases, an enzyme of the methionine salvage pathway. The crystal structure of Ypr118w, a non-essential, low-copy number gene product from Saccharomyces cerevisiae, reveals a dimeric protein with two domains and a putative active site cleft [2]. [1]. 9520434. Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families. Kyrpides NC, Woese CR;. Proc Natl Acad Sci U S A 1998;95:3726-3730. [2]. 15215245. Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits. Bumann M, Djafarzadeh S, Oberholzer AE, Bigler P, Altmann M, Trachsel H, Baumann U;. J Biol Chem 2004; [Epub ahead of print] (from Pfam) NF013198.5 PF01010.24 Proton_antipo_C 26.8 26.8 243 PfamEq Y N N NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus 1470679 131567 cellular organisms no rank 2543 EBI-EMBL NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus This sub-family represents a carboxyl terminal extension of Pfam:PF00361. It includes subunit 5 from chloroplasts, and bacterial subunit L. This sub-family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane. This family is largely a few TM regions of the F subunit of NADH-Ubiquinone oxidoreductase from plants. The TMs form part of the anti-porter subunit. [1]. 1470679. The NADH:ubiquinone oxidoreductase (complex I) of respiratory chains. Walker JE;. Q Rev Biophys 1992;25:253-324. (from Pfam) NF013199.5 PF01011.26 PQQ 20.3 20.1 38 repeat Y N N PQQ-binding-like beta-propeller repeat protein 7735834,8676383 131567 cellular organisms no rank 110982 EBI-EMBL PQQ enzyme repeat PQQ enzyme repeat The family represent a single repeat of a beta propeller. This propeller has been found in several enzymes which utilise pyrrolo-quinoline quinone as a prosthetic group. [1]. 7735834. The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 A. Ghosh M, Anthony C, Harlos K, Goodwin MG, Blake C;. Structure 1995;3:177-187. [2]. 8676383. Determination of the gene sequence and the three-dimensional structure at 2.4 angstroms resolution of methanol dehydrogenase from Methylophilus W3A1. Xia Z, Dai W, Zhang Y, White SA, Boyd GD, Mathews FS;. J Mol Biol 1996;259:480-501. (from Pfam) NF013200.5 PF01012.26 ETF 26.7 26.7 181 domain Y N N Electron transfer flavoprotein domain 8962055 131567 cellular organisms no rank 154061 EBI-EMBL Electron transfer flavoprotein domain Electron transfer flavoprotein domain This family includes the homologous domain shared between the alpha and beta subunits of the electron transfer flavoprotein [1]. [1]. 8962055. Three-dimensional structure of human electron transfer flavoprotein to 2.1-A resolution. Roberts DL, Frerman FE, Kim JJ;. Proc Natl Acad Sci U S A 1996;93:14355-14360. (from Pfam) NF013201.5 PF01014.23 Uricase 25 25 140 domain Y N N Uricase 9360612 131567 cellular organisms no rank 12129 EBI-EMBL Uricase Uricase NF013202.5 PF01015.23 Ribosomal_S3Ae 29.3 29.3 191 PfamEq Y N N Ribosomal S3Ae family GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 1200 EBI-EMBL Ribosomal S3Ae family Ribosomal S3Ae family NF013206.5 PF01019.26 G_glu_transpept 27 27 512 domain Y Y N gamma-glutamyltransferase 2.3.2.2 131567 cellular organisms no rank 133098 EBI-EMBL Gamma-glutamyltranspeptidase gamma-glutamyltransferase NF013207.5 PF01020.22 Ribosomal_L40e 23 23 50 PfamEq Y N N Ribosomal L40e family GO:0003735,GO:0005840,GO:0006412 3129699,7488009 131567 cellular organisms no rank 681 EBI-EMBL Ribosomal L40e family Ribosomal L40e family Bovine L40 has been identified as a secondary RNA binding protein [1]. L40 is fused to a ubiquitin protein [2]. [1]. 3129699. RNA binding proteins of the large subunit of bovine mitochondrial ribosomes. Piatyszek MA, Denslow ND, O'Brien TW;. Nucleic Acids Res 1988;16:2565-2583. [2]. 7488009. The carboxyl extensions of two rat ubiquitin fusion proteins are ribosomal proteins S27a and L40. Chan YL, Suzuki K, Wool IG;. Biochem Biophys Res Commun 1995;215:682-690. (from Pfam) NF013209.5 PF01022.25 HTH_5 22 22 47 domain Y Y N ArsR family transcriptional regulator GO:0003700,GO:0006355 9466913 131567 cellular organisms no rank 530187 EBI-EMBL Bacterial regulatory protein, arsR family ArsR family transcriptional regulator Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition. [1]. 9466913. Crystal structure of the cyanobacterial metallothionein repressor SmtB: a model for metalloregulatory proteins. Cook WJ, Kar SR, Taylor KB, Hall LM;. J Mol Biol 1998;275:337-346. (from Pfam) NF013212.5 PF01025.24 GrpE 25.8 25.8 165 PfamEq Y Y N nucleotide exchange factor GrpE grpE GO:0000774,GO:0006457,GO:0042803,GO:0051087 9103205 131567 cellular organisms no rank 70276 EBI-EMBL GrpE nucleotide exchange factor GrpE NF013213.5 PF01026.26 TatD_DNase 27 27 253 subfamily Y Y N TatD family hydrolase GO:0016788 10747959,9144792 131567 cellular organisms no rank 141070 EBI-EMBL TatD related DNase TatD family hydrolase This family of proteins are related to a large superfamily of metalloenzymes [1]. TatD, a member of this family has been shown experimentally to be a DNase enzyme. [1]. 9144792. An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Holm L, Sander C;. Proteins 1997;28:72-82. [2]. 10747959. TatD is a cytoplasmic protein with DNase activity. No requirement for TatD family proteins in sec-independent protein export. Wexler M, Sargent F, Jack RL, Stanley NR, Bogsch EG, Robinson C, Berks BC, Palmer T;. J Biol Chem 2000;275:16717-16722. (from Pfam) NF013215.5 PF01028.25 Topoisom_I 23.7 23.7 228 PfamEq Y N N Eukaryotic DNA topoisomerase I, catalytic core GO:0003677,GO:0003917,GO:0006265 7770916,9488644 131567 cellular organisms no rank 22218 EBI-EMBL Eukaryotic DNA topoisomerase I, catalytic core Eukaryotic DNA topoisomerase I, catalytic core Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination [2]. [1]. 7770916. The mechanisms of DNA topoisomerases. Roca J;. Trends Biochem Sci 1995;20:156-160. [2]. 9488644. Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol WG;. Science 1998;279:1504-1513. (from Pfam) NF013216.5 PF01029.23 NusB 23.1 23.1 133 domain Y Y N transcription antitermination factor NusB GO:0003723,GO:0006355 9670024 131567 cellular organisms no rank 118976 EBI-EMBL NusB family transcription antitermination factor NusB The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination. NMR structure. [1]. 9670024. Solution structure of the antitermination protein NusB of Escherichia coli: a novel all-helical fold for an RNA-binding protein. Huenges M, Rolz C, Gschwind R, Peteranderl R, Berglechner F, Richter G, Bacher A, Kessler H,Gemmecker G;. EMBO J 1998;17:4092-4100. (from Pfam) NF013219.5 PF01032.23 FecCD 26.5 26.5 311 subfamily Y Y N iron chelate uptake ABC transporter family permease subunit GO:0016020,GO:0022857 2651410 131567 cellular organisms no rank 413320 EBI-EMBL FecCD transport family iron chelate uptake ABC transporter family permease subunit This is a sub-family of bacterial binding protein-dependent transport systems family. This Pfam entry contains the inner components of this multicomponent transport system. [1]. 2651410. Nucleotide sequences of the fecBCDE genes and locations of the proteins suggest a periplasmic-binding-protein-dependent transport mechanism for iron(III) dicitrate in Escherichia coli. Staudenmaier H, Van Hove B, Yaraghi Z, Braun V;. J Bacteriol 1989;171:2626-2633. (from Pfam) NF013222.5 PF01035.25 DNA_binding_1 27 27 81 domain Y Y N MGMT family protein GO:0003824,GO:0006281 8156986 131567 cellular organisms no rank 171550 EBI-EMBL 6-O-methylguanine DNA methyltransferase, DNA binding domain 6-O-methylguanine DNA methyltransferase, DNA binding domain This is the C-terminal DNA-binding domain of 6-O-methylguanine-DNA methyltransferases [1]. [1]. 8156986. Crystal structure of a suicidal DNA repair protein: the Ada O6-methylguanine-DNA methyltransferase from E. coli. Moore MH, Gulbis JM, Dodson EJ, Demple B, Moody PC;. EMBO J 1994;13:1495-1501. (from Pfam) NF013223.5 PF01036.23 Bac_rhodopsin 24.6 24.6 224 domain Y Y N bacteriorhodopsin GO:0006811,GO:0016020 2468194,2591367,8676377 131567 cellular organisms no rank 4247 EBI-EMBL Bacteriorhodopsin-like protein bacteriorhodopsin The bacterial opsins are retinal-binding proteins that provide light- dependent ion transport and sensory functions to a family of halophilic bacteria [2,3]. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, the last of which contains the attachment point for retinal (a conserved lysine). This family also includes distantly related proteins that do not contain the retinal binding lysine and so cannot function as opsins. Some fungal examples are: Swiss:O74870, Swiss:P25619, Swiss:P38079, Swiss:Q12117. [1]. 8676377. Electron-crystallographic refinement of the structure of bacteriorhodopsin. Grigorieff N, Ceska TA, Downing KH, Baldwin JM, Henderson R;. J Mol Biol 1996;259:393-421. [2]. 2468194. Two pumps, one principle: light-driven ion transport in halobacteria. Oesterhelt D, Tittor J;. Trends Biochem Sci. 1989;14:57-61. [3]. 2591367. Primary structure of sensory rhodopsin I, a prokaryotic photoreceptor. Blanck A, Oesterhelt D, Ferrando E, Schegk ES, Lottspeich F;. EMBO J. 1989;8:3963-3971. (from Pfam) NF013224.5 PF01037.26 AsnC_trans_reg 25 25 73 domain Y Y N Lrp/AsnC ligand binding domain-containing protein 17374605,7770911 131567 cellular organisms no rank 282828 EBI-EMBL Lrp/AsnC ligand binding domain Lrp/AsnC ligand binding domain The l-leucine-responsive regulatory protein (Lrp/AsnC) family is a family of similar bacterial transcription regulatory proteins. The family is named after two E. coli proteins involved in regulating amino acid metabolism. This entry corresponds to the usually C-terminal regulatory ligand binding domain. Structurally this domain has a dimeric alpha/beta barrel fold [2]. This domain binds almost exclusively amino acids but also 4-hydroxyphenylpyruvate and kynurenine (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 7770911. The eubacterial transcriptional activator Lrp is present in the archaeon Pyrococcus furiosus. Kyrpides NC, Ouzounis CA;. Trends Biochem Sci 1995;20:140-141. [2]. 17374605. The structure and transcriptional analysis of a global regulator from Neisseria meningitidis. Ren J, Sainsbury S, Combs SE, Capper RG, Jordan PW, Berrow NS, Stammers DK, Saunders NJ, Owens RJ;. J Biol Chem. 2007;282:14655-14664. (from Pfam) NF013225.5 PF01039.27 Carboxyl_trans 22.3 22.3 493 domain Y Y N carboxyl transferase domain-containing protein 12663926,8102604,8366018 131567 cellular organisms no rank 248573 EBI-EMBL Carboxyl transferase domain Carboxyl transferase domain All of the members in this family are biotin dependent carboxylases. The carboxyl transferase domain carries out the following reaction; transcarboxylation from biotin to an acceptor molecule. There are two recognised types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxoacid as the acceptor molecule of carbon dioxide. All of the members in this family utilise acyl-CoA as the acceptor molecule. [1]. 8366018. Primary structure of the monomer of the 12S subunit of transcarboxylase as deduced from DNA and characterization of the product expressed in Escherichia coli. Thornton CG, Kumar GK, Haase FC, Phillips NF, Woo SB, Park VM, Magner WJ, Shenoy BC, Wood HG, Samols D;. J Bacteriol 1993;175:5301-5308. [2]. 8102604. Molecular evolution of biotin-dependent carboxylases. Toh H, Kondo H, Tanabe T;. Eur J Biochem 1993;215:687-696. [3]. 12663926. Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase. Zhang H, Yang Z, Shen Y, Tong L;. Science 2003;299:2064-2067. (from Pfam) NF013226.5 PF01040.23 UbiA 34.2 34.2 250 domain Y Y N UbiA family prenyltransferase GO:0016020,GO:0016765 131567 cellular organisms no rank 194313 EBI-EMBL UbiA prenyltransferase family UbiA family prenyltransferase NF013227.5 PF01041.22 DegT_DnrJ_EryC1 19.8 19.8 360 domain Y Y N DegT/DnrJ/EryC1/StrS family aminotransferase 9238101 131567 cellular organisms no rank 659404 EBI-EMBL DegT/DnrJ/EryC1/StrS aminotransferase family DegT/DnrJ/EryC1/StrS family aminotransferase The members of this family are probably all pyridoxal-phosphate-dependent aminotransferase enzymes with a variety of molecular functions. The family includes StsA Swiss:P72454, StsC Swiss:P77952 and StsS [1]. The aminotransferase activity was demonstrated for purified StsC protein as the L-glutamine:scyllo-inosose aminotransferase EC:2.6.1.50, which catalyses the first amino transfer in the biosynthesis of the streptidine subunit of streptomycin [1]. [1]. 9238101. Identification of stsC, the gene encoding the L-glutamine:scyllo-inosose aminotransferase from streptomycin-producing Streptomycetes. Ahlert J, Distler J, Mansouri K, Piepersberg W;. Arch Microbiol 1997;168:102-113. (from Pfam) NF013228.5 PF01042.26 Ribonuc_L-PSP 27.3 27.3 121 domain Y Y N Rid family hydrolase 10368157,10400702,14729707,19899170,22094463,8530410 131567 cellular organisms no rank 246331 EBI-EMBL Endoribonuclease L-PSP Rid family hydrolase The YjgF/YER057c/UK114 family, including a member protein that has been called endoribonuclease L-PSP (perchloric acid-soluble protein), is now called the RidA family, or more generally the Rid family, with subfamilies RidA and Rid1 through Rid7. YjgF from Salmonella enterica deaminates the toxic metabolite 2-amino acrylate and so was renamed RidA (reactive intermediate imine deaminase A). This HMM hits proteins that are members of multiple Rid subfamilies. NF013231.5 PF01047.27 MarR 24.6 24.6 59 domain Y Y N MarR family transcriptional regulator GO:0003700,GO:0006355 11473263,9068629 131567 cellular organisms no rank 889662 EBI-EMBL MarR family MarR family transcriptional regulator The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds [1]. The structure of MarR is known [2] and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif. [1]. 9068629. The Salmonella typhimurium mar locus: molecular and genetic analyses and assessment of its role in virulence. Sulavik MC, Dazer M, Miller PF;. J Bacteriol 1997;179:1857-1866. [2]. 11473263. The crystal structure of MarR, a regulator of multiple antibiotic resistance, at 2.3 A resolution. Alekshun MN, Levy SB, Mealy TR, Seaton BA, Head JF;. Nat Struct Biol 2001;8:710-714. (from Pfam) NF013232.5 PF01048.25 PNP_UDP_1 25.1 25.1 233 domain Y N N Phosphorylase superfamily GO:0003824,GO:0009116 7920254,9351810 131567 cellular organisms no rank 204513 EBI-EMBL Phosphorylase superfamily Phosphorylase superfamily Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase) [1]. 7920254. Unexpected sequence similarity between nucleosidases and phosphoribosyltransferases of different specificity. Mushegian AR, Koonin EV;. Protein Sci 1994;3:1081-1088. [2]. 9351810. The crystal structure of Escherichia coli purine nucleoside phosphorylase: a comparison with the human enzyme reveals a conserved topology. Mao C, Cook WJ, Zhou M, Koszalka GW, Krenitsky TA, Ealick SE;. Structure 1997;5:1373-1383. (from Pfam) NF013234.5 PF01050.23 MannoseP_isomer 23.6 23.6 116 domain Y N N Mannose-6-phosphate isomerase C-terminal GO:0005976,GO:0016779 9507048 131567 cellular organisms no rank 58348 EBI-EMBL Mannose-6-phosphate isomerase C-terminal Mannose-6-phosphate isomerase C-terminal All of the members of this Pfam entry belong to family 2 of the mannose-6-phosphate isomerases. The type II phosphomannose isomerases are bifunctional enzymes. This Pfam entry covers the isomerase domain. The guanosine diphospho-D-mannose pyrophosphorylase domain is in another Pfam entry, see Pfam:PF00483. [1]. 9507048. Domain organisation in phosphomannose isomerases (types I and II). Jensen SO, Reeves PR;. Biochim Biophys Acta 1998;1382:5-7. (from Pfam) NF013237.5 PF01053.25 Cys_Met_Meta_PP 27 27 381 domain Y Y N PLP-dependent transferase GO:0019346,GO:0030170 8831789,9843488 131567 cellular organisms no rank 405955 EBI-EMBL Cys/Met metabolism PLP-dependent enzyme PLP-dependent transferase This family includes enzymes involved in cysteine and methionine metabolism. The following are members: Cystathionine gamma-lyase, Cystathionine gamma-synthase, Cystathionine beta-lyase, Methionine gamma-lyase, OAH/OAS sulfhydrylase, O-succinylhomoserine sulfhydrylase All of these members participate is slightly different reactions. All these enzymes use PLP (pyridoxal-5'-phosphate) as a cofactor. [1]. 8831789. Crystal structure of the pyridoxal-5'-phosphate dependent cystathionine beta-lyase from Escherichia coli at 1.83 A. Clausen T, Huber R, Laber B, Pohlenz HD, Messerschmidt A;. J Mol Biol 1996;262:202-224. [2]. 9843488. Crystal structure of Escherichia coli cystathionine gamma-synthase at 1.5 A resolution. Clausen T, Huber R, Prade L, Wahl MC, Messerschmidt A;. EMBO J 1998;17:6827-6838. (from Pfam) NF013239.5 PF01055.31 Glyco_hydro_31_2nd 23.5 23.5 328 domain Y Y N TIM-barrel domain-containing protein GO:0004553,GO:0005975 1747104,9649738 131567 cellular organisms no rank 115561 EBI-EMBL Glycosyl hydrolases family 31 TIM-barrel domain Glycosyl hydrolases family 31 TIM-barrel domain Glycosyl hydrolases are key enzymes of carbohydrate metabolism. Family 31 comprises of enzymes that are, or similar to, alpha- galactosidases. This entry corresponds to the second domain of family 31 enzymes and adopts a TIM-barrel fold. [1]. 1747104. A classification of glycosyl hydrolases based on amino acid sequence similarities. Henrissat B;. Biochem J 1991;280:309-316. [2]. 9649738. Glycosidase families. Henrissat B. Biochem Soc Trans 1998;26:153-156. (from Pfam) NF013241.5 PF01057.22 Parvo_NS1 20 18 271 domain Y N N Parvovirus non-structural protein NS1 GO:0019079 8372437,9454701 131567 cellular organisms no rank 1156 EBI-EMBL Parvovirus non-structural protein NS1 Parvovirus non-structural protein NS1 This family also contains the NS2 protein. Parvoviruses encode two non-structural proteins, NS1 and NS2. The mRNA for NS2 contains the coding sequence for the first 87 amino acids of NS1, then by an alternative splicing mechanism mRNA from a different reading frame, encoding the last 78 amino acids, makes up the full length of the NS2 mRNA [2]. NS1, is the major non-structural protein. It is essential for DNA replication. It is an 83-kDa nuclear phosphoprotein. It has DNA helicase and ATPase activity [1]. [1]. 8372437. Nuclear targeting of the parvoviral replicator molecule NS1: evidence for self-association prior to nuclear transport. Nuesch JP, Tattersall P;. Virology 1993;196:637-651. [2]. 9454701. Nonstructural protein-2 and the replication of canine parvovirus. Wang D, Yuan W, Davis I, Parrish CR;. Virology 1998;240:273-281. (from Pfam) NF013242.5 PF01058.27 Oxidored_q6 27 27 128 domain Y N N NADH ubiquinone oxidoreductase, 20 Kd subunit GO:0051536 1470679,1577158,8459836 131567 cellular organisms no rank 67277 EBI-EMBL NADH ubiquinone oxidoreductase, 20 Kd subunit NADH ubiquinone oxidoreductase, 20 Kd subunit NF013243.5 PF01059.22 Oxidored_q5_N 22.7 22.7 110 PfamEq Y N N NADH-ubiquinone oxidoreductase chain 4, amino terminus 1470679 131567 cellular organisms no rank 9577 EBI-EMBL NADH-ubiquinone oxidoreductase chain 4, amino terminus NADH-ubiquinone oxidoreductase chain 4, amino terminus NF013245.5 PF01061.29 ABC2_membrane 26.9 26.9 211 domain Y Y N ABC transporter permease GO:0016020,GO:0140359 1303751 131567 cellular organisms no rank 462048 EBI-EMBL ABC-2 type transporter ABC transporter permease NF013247.5 PF01063.24 Aminotran_4 28.5 28.5 223 domain Y Y N aminotransferase class IV GO:0003824 7626635,9163511 131567 cellular organisms no rank 186674 EBI-EMBL Amino-transferase class IV aminotransferase class IV The D-amino acid transferases (D-AAT) are required by bacteria to catalyse the synthesis of D-glutamic acid and D-alanine, which are essential constituents of bacterial cell wall and are the building block for other D-amino acids. Despite the difference in the structure of the substrates, D-AATs and L-ATTs have strong similarity. Crystal structure. [1]. 7626635. Crystal structure of a D-amino acid aminotransferase: how the protein controls stereoselectivity. Sugio S, Petsko GA, Manning JM, Soda K, Ringe D;. Biochemistry 1995;34:9661-9669. [2]. 9163511. Three-dimensional structure of Escherichia coli branched-chain amino acid aminotransferase at 2.5 A resolution. Okada K, Hirotsu K, Sato M, Hayashi H, Kagamiyama H;. J Biochem 1997;121:637-641. (from Pfam) NF013250.5 PF01066.26 CDP-OH_P_transf 22 22 152 domain Y Y N CDP-alcohol phosphatidyltransferase family protein GO:0008654,GO:0016020,GO:0016780 8917447 131567 cellular organisms no rank 184394 EBI-EMBL CDP-alcohol phosphatidyltransferase CDP-alcohol phosphatidyltransferase family protein All of these members have the ability to catalyse the displacement of CMP from a CDP-alcohol by a second alcohol with formation of a phosphodiester bond and concomitant breaking of a phosphoride anhydride bond. [1]. 8917447. Two-dimensional 1H-NMR of transmembrane peptides from Escherichia coli phosphatidylglycerophosphate synthase in micelles. Morein S, Trouard TP, Hauksson JB, Rilfors L, Arvidson G, Lindblom G;. Eur J Biochem 1996;241:489-497. (from Pfam) NF013252.5 PF01068.26 DNA_ligase_A_M 26.2 26.2 204 domain Y N N ATP dependent DNA ligase domain GO:0003910,GO:0005524,GO:0006281,GO:0006310 10222208,8653795,9363683 131567 cellular organisms no rank 118935 EBI-EMBL ATP dependent DNA ligase domain ATP dependent DNA ligase domain This domain belongs to a more diverse superfamily, including Pfam:PF01331 and Pfam:PF01653 [3]. [1]. 8653795. Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Subramanya HS, Doherty AJ, Ashford SR, Wigley DB;. Cell 1996;85:607-615. [2]. 9363683. Mammalian DNA ligases. Tomkinson AE, Levin DS;. Bioessays 1997;19:893-901. [3]. 10222208. Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. Aravind L, Koonin EV;. J Mol Biol 1999;287:1023-1040. (from Pfam) NF013253.5 PF01070.23 FMN_dh 24.9 24.9 350 domain Y Y N alpha-hydroxy-acid oxidizing protein GO:0016491 2329585,2681790 131567 cellular organisms no rank 207496 EBI-EMBL FMN-dependent dehydrogenase alpha-hydroxy-acid oxidizing protein NF013254.5 PF01071.24 GARS_A 27 27 194 domain Y N N Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain 2687276,9843369 131567 cellular organisms no rank 119157 EBI-EMBL Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the ATP-grasp domain of biotin carboxylase/carbamoyl phosphate synthetase (see Pfam:PF02786). [1]. 2687276. Nucleotide sequence analysis of genes purH and purD involved in the de novo purine nucleotide biosynthesis of Escherichia coli. Aiba A, Mizobuchi K;. J Biol Chem 1989;264:21239-21246. [2]. 9843369. X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli. Wang W, Kappock TJ, Stubbe J, Ealick SE;. Biochemistry 1998;37:15647-15662. (from Pfam) NF013255.5 PF01073.24 3Beta_HSD 22 22 280 domain Y N N 3-beta hydroxysteroid dehydrogenase/isomerase family GO:0003854,GO:0006694,GO:0016616 1562516 131567 cellular organisms no rank 807045 EBI-EMBL 3-beta hydroxysteroid dehydrogenase/isomerase family 3-beta hydroxysteroid dehydrogenase/isomerase family The enzyme 3 beta-hydroxysteroid dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD) catalyses the oxidation and isomerisation of 5-ene-3 beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid precursors into the corresponding 4-ene-ketosteroids necessary for the formation of all classes of steroid hormones. [1]. 1562516. Structure and tissue-specific expression of 3 beta-hydroxysteroid dehydrogenase/5-ene-4-ene isomerase genes in human and rat classical and peripheral steroidogenic tissues. Labrie F, Simard J, Luu-The V, Pelletier G, Belanger A, Lachance Y, Zhao HF, Labrie C, Breton N, de Launoit Y, et al. J Steroid Biochem Mol Biol 1992;41:421-435. (from Pfam) NF013256.5 PF01074.27 Glyco_hydro_38N 25 25 270 domain Y N N Glycosyl hydrolases family 38 N-terminal domain GO:0004559,GO:0006013 9649738 131567 cellular organisms no rank 56638 EBI-EMBL Glycosyl hydrolases family 38 N-terminal domain Glycosyl hydrolases family 38 N-terminal domain Glycosyl hydrolases are key enzymes of carbohydrate metabolism. [1]. 9649738. Glycosidase families. Henrissat B. Biochem Soc Trans 1998;26:153-156. (from Pfam) NF013257.5 PF01075.22 Glyco_transf_9 22 22 247 domain Y Y N glycosyltransferase family 9 protein GO:0016757 9334165,9446588 131567 cellular organisms no rank 137994 EBI-EMBL Glycosyltransferase family 9 (heptosyltransferase) glycosyltransferase family 9 protein Members of this family belong to glycosyltransferase family 9 [1]. Lipopolysaccharide is a major component of the outer leaflet of the outer membrane in Gram-negative bacteria. It is composed of three domains; lipid A, Core oligosaccharide and the O-antigen. All of these enzymes transfer heptose to the lipopolysaccharide core. [1]. 9334165. A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Campbell JA, Davies GJ, Bulone V, Henrissat B;. Biochem J 1997;326:929-939. [2]. 9446588. Enzymatic synthesis of lipopolysaccharide in Escherichia coli. Purification and properties of heptosyltransferase I. Kadrmas JL, Raetz CR;. J Biol Chem 1998;273:2799-2807. (from Pfam) NF013258.5 PF01076.24 Mob_Pre 25.5 25.5 196 domain Y Y N plasmid recombination protein GO:0003677,GO:0006310 2768188,28739894 131567 cellular organisms no rank 23195 EBI-EMBL Plasmid recombination enzyme plasmid recombination protein With some plasmids, recombination can occur in a site specific manner that is independent of RecA. In such cases, the recombination event requires another protein called Pre. Pre is a plasmid recombination enzyme. This protein is also known as Mob (conjugative mobilisation). This family is also known as Mob-V. One of the family members, MobM, is encoded by a promiscuous plasmid actively involved in the spread of antibiotic resistance. Homologs of MobM are found in many plasmids and other mobile genetic elements of pathogenic bacteria, including S. aureus. MobM is a metal-dependent nuclease that uses histidine nitrogen for the nucleophilic attack on the scissile phosphate. Furthermore, in contrast to other DNA-processing enzymes, MobM is a histidine relaxase, a DNA-breaking and -joining enzyme, that operates through a phosphorus-nitrogen protein-DNA adduct for cell-to-cell DNA transfer. Mutational analysis indicate that the H(N/D)(Q/E)R N-terminal motif of MobM plays a crucial role in the cleavage and generation of stable DNA-protein adducts [2]. [1]. 2768188. Region of the streptococcal plasmid pMV158 required for conjugative mobilization. Priebe SD, Lacks SA;. J Bacteriol 1989;171:4778-4784. [2]. 28739894. Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance. Pluta R, Boer DR, Lorenzo-Diaz F, Russi S, Gomez H, Fernandez-Lopez C, Perez-Luque R, Orozco M, Espinosa M, Coll M;. Proc Natl Acad Sci U S A. 2017;114:E6526. (from Pfam) NF013259.5 PF01077.27 NIR_SIR 27 27 158 domain Y N N Nitrite and sulphite reductase 4Fe-4S domain GO:0016491,GO:0020037,GO:0051536 7569952,9315849 131567 cellular organisms no rank 144274 EBI-EMBL Nitrite and sulphite reductase 4Fe-4S domain Nitrite and sulphite reductase 4Fe-4S domain Sulphite and nitrite reductases are vital in the biosynthetic assimilation of sulphur and nitrogen, respectfully. They are also both important for the dissimilation of oxidised anions for energy transduction. [1]. 7569952. Sulfite reductase structure at 1.6 A: evolution and catalysis for reduction of inorganic anions. Crane BR, Siegel LM, Getzoff ED;. Science 1995;270:59-67. [2]. 9315849. Probing the catalytic mechanism of sulfite reductase by X-ray crystallography: structures of the Escherichia coli hemoprotein in complex with substrates, inhibitors, intermediates, and products. Crane BR, Siegel LM, Getzoff ED;. Biochemistry 1997;36:12120-12137. (from Pfam) NF013260.5 PF01078.26 Mg_chelatase 20.3 20.3 207 domain Y Y N ATP-binding protein GO:0005524 9359397,9457877 131567 cellular organisms no rank 181178 EBI-EMBL Magnesium chelatase, subunit ChlI ATP-binding protein Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa. [1]. 9359397. Mechanism and regulation of Mg-chelatase. Walker CJ, Willows RD;. Biochem J 1997;327:321-333. [2]. 9457877. Reconstitution of an active magnesium chelatase enzyme complex from the bchI, -D, and -H gene products of the green sulfur bacterium Chlorobium vibrioforme expressed in Escherichia coli. Petersen BL, Jensen PE, Gibson LC, Stummann BM, Hunter CN, Henningsen KW;. J Bacteriol 1998;180:699-704. (from Pfam) NF013261.5 PF01079.25 Hint 29.7 29.7 213 domain Y N N Hint module GO:0016540 9335337 131567 cellular organisms no rank 2131 EBI-EMBL Hint module Hint module This is an alignment of the Hint module in the Hedgehog proteins. It does not include any Inteins which also possess the Hint module. [1]. 9335337. Crystal structure of a Hedgehog autoprocessing domain: homology between Hedgehog and self-splicing proteins. Hall TM, Porter JA, Young KE, Koonin EV, Beachy PA, Leahy DJ;. Cell 1997;91:85-97. (from Pfam) NF013263.5 PF01081.24 Aldolase 27.8 27.8 196 domain Y N N KDPG and KHG aldolase GO:0016829 131567 cellular organisms no rank 82404 EBI-EMBL KDPG and KHG aldolase KDPG and KHG aldolase This family includes the following members: 4-hydroxy-2-oxoglutarate aldolase (KHG-aldolase) Phospho-2-dehydro-3-deoxygluconate aldolase (KDPG-aldolase) (from Pfam) NF013269.5 PF01087.27 GalP_UDP_transf 22.1 22.1 184 domain Y N N Galactose-1-phosphate uridyl transferase, N-terminal domain GO:0006012,GO:0008108 7669762 131567 cellular organisms no rank 45792 EBI-EMBL Galactose-1-phosphate uridyl transferase, N-terminal domain Galactose-1-phosphate uridyl transferase, N-terminal domain SCOP reports fold duplication with C-terminal domain. Both involved in Zn and Fe binding. [1]. 7669762. Three-dimensional structure of galactose-1-phosphate uridylyltransferase from Escherichia coli at 1.8 A resolution. Wedekind JE, Frey PA, Rayment I;. Biochemistry 1995;34:11049-11061. (from Pfam) NF013271.5 PF01090.24 Ribosomal_S19e 29.4 29.4 137 PfamEq Y Y N 40S ribosomal protein S19 GO:0003735,GO:0005840,GO:0006412 16289379,17726054,8367309 131567 cellular organisms no rank 1187 EBI-EMBL Ribosomal protein S19e 40S ribosomal protein S19 NF013273.5 PF01092.24 Ribosomal_S6e 26 26 125 PfamEq Y Y N S6e family ribosomal protein GO:0003735,GO:0005840,GO:0006412 26155016 131567 cellular organisms no rank 1243 EBI-EMBL Ribosomal protein S6e S6e family ribosomal protein NF013275.5 PF01094.33 ANF_receptor 25.4 25.4 353 domain Y N N Receptor family ligand binding region 8011339 131567 cellular organisms no rank 202243 EBI-EMBL Receptor family ligand binding region Receptor family ligand binding region This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure. [1]. 8011339. Mutational analysis of the glycine-binding site of the NMDA receptor: structural similarity with bacterial amino acid-binding proteins. Kuryatov A, Laube B, Betz H, Kuhse J;. Neuron 1994;12:1291-1300. (from Pfam) NF013276.5 PF01095.24 Pectinesterase 27 27 298 subfamily_domain Y Y N pectinesterase family protein GO:0030599,GO:0042545 131567 cellular organisms no rank 27306 EBI-EMBL Pectinesterase pectinesterase family protein NF013277.5 PF01096.23 TFIIS_C 21 21 39 domain Y N N Transcription factor S-II (TFIIS) GO:0003676,GO:0006351,GO:0008270 131567 cellular organisms no rank 1935 EBI-EMBL Transcription factor S-II (TFIIS) Transcription factor S-II (TFIIS) NF013285.5 PF01105.29 EMP24_GP25L 25.9 25.9 182 domain Y Y N emp24/gp25L/p24 family protein 12049664,9472029 131567 cellular organisms no rank 33 EBI-EMBL emp24/gp25L/p24 family/GOLD emp24/gp25L/p24 family protein Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains. This domain corresponds closely to the beta-strand rich GOLD domain described in [2]. The GOLD domain is always found combined with lipid- or membrane-association domains [2]. [1]. 9472029. gp25L/emp24/p24 protein family members of the cis-Golgi network bind both COP I and II coatomer. Dominguez M, Dejgaard K, Fullekrug J, Dahan S, Fazel A, Paccaud JP, Thomas DY, Bergeron JJ, Nilsson T;. J Cell Biol 1998;140:751-765. [2]. 12049664. The GOLD domain, a novel protein module involved in Golgi function and secretion. Anantharaman V, Aravind L;. Genome Biol 2002;3:research0023. (from Pfam) NF013286.5 PF01106.22 NifU 27 27 67 domain Y Y N NifU family protein GO:0005506,GO:0016226,GO:0051536 8048161 131567 cellular organisms no rank 36477 EBI-EMBL NifU-like domain NifU-like domain This is an alignment of the carboxy-terminal domain. This is the only common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown [1]. [1]. 8048161. The modular structure of NifU proteins. Ouzounis C, Bork P, Sander C;. Trends Biochem Sci 1994;19:199-200. (from Pfam) NF013292.5 PF01112.23 Asparaginase_2 27 27 309 domain Y Y N isoaspartyl peptidase/L-asparaginase GO:0016787 131567 cellular organisms no rank 31681 EBI-EMBL Asparaginase isoaspartyl peptidase/L-asparaginase NF013293.5 PF01113.25 DapB_N 25.6 20.8 124 domain Y N N Dihydrodipicolinate reductase, N-terminus GO:0008839,GO:0009089 7893645,8873595,9398235 131567 cellular organisms no rank 92445 EBI-EMBL Dihydrodipicolinate reductase, N-terminus Dihydrodipicolinate reductase, N-terminus Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The N-terminal domain of DapB binds the dinucleotide NADPH. [1]. 8873595. Interaction of pyridine nucleotide substrates with Escherichia coli dihydrodipicolinate reductase: thermodynamic and structural analysis of binary complexes. Reddy SG, Scapin G, Blanchard JS;. Biochemistry 1996;35:13294-13302. [2]. 9398235. Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase in complex with NADH and the inhibitor 2,6-pyridinedicarboxylate. Scapin G, Reddy SG, Zheng R, Blanchard JS;. Biochemistry 1997;36:15081-15088. [3]. 7893645. Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase. Scapin G, Blanchard JS, Sacchettini JC;. Biochemistry 1995;34:3502-3512. (from Pfam) NF013296.5 PF01116.25 F_bP_aldolase 25.5 25.5 277 domain Y Y N class II fructose-bisphosphate aldolase 4.1.2.13 GO:0005975,GO:0008270,GO:0016832 8836102 131567 cellular organisms no rank 87504 EBI-EMBL Fructose-bisphosphate aldolase class-II class II fructose-bisphosphate aldolase NF013298.5 PF01118.29 Semialdhyde_dh 26 26 121 domain Y N N Semialdehyde dehydrogenase, NAD binding domain GO:0016620,GO:0051287 10369777 131567 cellular organisms no rank 181441 EBI-EMBL Semialdehyde dehydrogenase, NAD binding domain Semialdehyde dehydrogenase, NAD binding domain This Pfam entry contains the following members: N-acetyl-glutamine semialdehyde dehydrogenase (AgrC) Aspartate-semialdehyde dehydrogenase [1]. 10369777. Structure of aspartate-beta-semialdehyde dehydrogenase from Escherichia coli, a key enzyme in the aspartate family of amino acid biosynthesis. Hadfield A, Kryger G, Ouyang J, Petsko GA, Ringe D, Viola R;. J Mol Biol 1999;289:991-1002. (from Pfam) NF013299.5 PF01119.24 DNA_mis_repair 26 26 119 PfamEq Y N N DNA mismatch repair protein, C-terminal domain GO:0005524,GO:0006298,GO:0030983 131567 cellular organisms no rank 73193 EBI-EMBL DNA mismatch repair protein, C-terminal domain DNA mismatch repair protein, C-terminal domain This family represents the C-terminal domain of the mutL/hexB/PMS1 family. This domain has a ribosomal S5 domain 2-like fold. (from Pfam) NF013300.5 PF01120.22 Alpha_L_fucos 25.2 25.2 345 domain Y Y N alpha-L-fucosidase GO:0004560,GO:0005975 131567 cellular organisms no rank 61837 EBI-EMBL Alpha-L-fucosidase alpha-L-fucosidase NF013301.5 PF01121.25 CoaE 27 27 180 PfamEq Y Y N dephospho-CoA kinase 2.7.1.24 GO:0004140,GO:0005524,GO:0015937 131567 cellular organisms no rank 77157 EBI-EMBL Dephospho-CoA kinase dephospho-CoA kinase This family catalyses the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form Coenzyme A EC:2.7.1.24. This enzyme uses ATP in its reaction. (from Pfam) NF013307.5 PF01127.27 Sdh_cyt 25.8 25.8 122 domain Y N N Succinate dehydrogenase/Fumarate reductase transmembrane subunit GO:0016627 10586875 131567 cellular organisms no rank 54925 EBI-EMBL Succinate dehydrogenase/Fumarate reductase transmembrane subunit Succinate dehydrogenase/Fumarate reductase transmembrane subunit This family includes a transmembrane protein from both the Succinate dehydrogenase and Fumarate reductase complexes. [1]. 10586875. Structure of fumarate reductase from Wolinella succinogenes at 2.2 A resolution. Lancaster CR, Kroger A, Auer M, Michel H;. Nature 1999;402:377-385. (from Pfam) NF013308.5 PF01128.24 IspD 27 27 221 domain Y Y N 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase GO:0070567 10518523 131567 cellular organisms no rank 148191 EBI-EMBL 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase Members of this family are enzymes which catalyse the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from cytidine triphosphate and 2-C-methyl-D-erythritol 4-phosphate (MEP) [1]. [1]. 10518523. Cytidine 5'-triphosphate-dependent biosynthesis of isoprenoids: YgbP protein of Escherichia coli catalyzes the formation of 4-diphosphocytidyl-2-C-methylerythritol. Rohdich F, Wungsintaweekul J, Fellermeier M, Sagner S, Herz S, Kis K, Eisenreich W, Bacher A, Zenk MH;. Proc Natl Acad Sci U S A. 1999;96:11758-11763. (from Pfam) NF013309.5 PF01129.23 ART 22.3 22.3 222 domain Y Y N ADP-ribosyltransferase domain-containing protein GO:0106274 131567 cellular organisms no rank 4400 EBI-EMBL NAD:arginine ADP-ribosyltransferase NAD:arginine ADP-ribosyltransferase NF013311.5 PF01131.25 Topoisom_bac 35.1 35.1 411 domain Y Y N DNA topoisomerase 5.6.2.- GO:0003677,GO:0003916,GO:0006265 8114910 131567 cellular organisms no rank 171053 EBI-EMBL DNA topoisomerase DNA topoisomerase This HMM identifies a region shared by DNA topoisomerases of different types, including ATP-independent (type I) topoisomerases such as TopA and TopB, and ATP-dependent reverse gyrases. NF013312.5 PF01132.25 EFP 27 27 54 domain Y N N Elongation factor P (EF-P) OB domain GO:0003746,GO:0006414 131567 cellular organisms no rank 41440 EBI-EMBL Elongation factor P (EF-P) OB domain Elongation factor P (EF-P) OB domain NF013314.5 PF01134.27 GIDA 22.1 19.1 391 domain Y Y N FAD-dependent oxidoreductase 131567 cellular organisms no rank 481216 EBI-EMBL Glucose inhibited division protein A FAD-dependent oxidoreductase NF013315.5 PF01135.24 PCMT 20.3 20.3 210 domain Y N N Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) 131567 cellular organisms no rank 362824 EBI-EMBL Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) NF013316.5 PF01136.24 Peptidase_U32 22.4 22.4 233 domain Y Y N U32 family peptidase 131567 cellular organisms no rank 101798 EBI-EMBL Peptidase family U32 U32 family peptidase NF013317.5 PF01137.26 RTC 27 27 221 PfamEq Y Y N RNA 3'-terminal phosphate cyclase 10673421 131567 cellular organisms no rank 7656 EBI-EMBL RNA 3'-terminal phosphate cyclase RNA 3'-terminal phosphate cyclase RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate [1]. The structure of RTC demonstrates that RTCs are comprised two domain. The larger domain contains an insert domain of approximately 100 amino acids [1]. [1]. 10673421. Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology. Palm GJ, Billy E, Filipowicz W, Wlodawer A;. Structure Fold Des 2000;8:13-23. (from Pfam) NF013318.5 PF01138.26 RNase_PH 25.5 25.5 130 domain Y N N 3' exoribonuclease family, domain 1 9390555 131567 cellular organisms no rank 108244 EBI-EMBL 3' exoribonuclease family, domain 1 3' exoribonuclease family, domain 1 This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components, Swiss:P46948 Swiss:Q12277 and Swiss:P25359 contain a copy of this domain [1]. Swiss:Q10205, a hypothetical protein from S. pombe appears to belong to an uncharacterised subfamily. This subfamily is found in both eukaryotes and archaebacteria. [1]. 9390555. The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases. Mitchell P, Petfalski E, Shevchenko A, Mann M, Tollervey D;. Cell 1997;91:457-466. (from Pfam) NF013319.5 PF01139.22 RtcB 27 27 426 domain Y Y N RtcB family protein GO:0006396,GO:0008452 21224389,21311021,21757685 131567 cellular organisms no rank 48155 EBI-EMBL tRNA-splicing ligase RtcB RtcB family protein This family of RNA ligases (EC:6.5.1.3) join 2',3'-cyclic phosphate and 5'-OH ends. They catalyse the splicing of tRNA and may also participate in tRNA repair and recovery from stress-induced RNA damage [1-3]. [1]. 21757685. RtcB, a novel RNA ligase, can catalyze tRNA splicing and HAC1 mRNA splicing in vivo. Tanaka N, Meineke B, Shuman S;. J Biol Chem. 2011;286:30253-30257. [2]. 21224389. RtcB is the RNA ligase component of an Escherichia coli RNA repair operon. Tanaka N, Shuman S;. J Biol Chem. 2011;286:7727-7731. [3]. 21311021. HSPC117 is the essential subunit of a human tRNA splicing ligase complex. Popow J, Englert M, Weitzer S, Schleiffer A, Mierzwa B, Mechtler K, Trowitzsch S, Will CL, Luhrmann R, Soll D, Martinez J;. Science. 2011;331:760-764. (from Pfam) NF013322.5 PF01142.23 TruD 27 27 412 PfamEq Y Y N tRNA pseudouridine(13) synthase TruD truD 5.4.99.27 GO:0001522,GO:0003723,GO:0009451,GO:0009982 12756329,15135053 131567 cellular organisms no rank 24028 EBI-EMBL tRNA pseudouridine synthase D (TruD) tRNA pseudouridine(13) synthase TruD TruD is responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs [1]. The structure of TruD reveals an overall V-shaped molecule which contains an RNA-binding cleft [2]. [1]. 12756329. A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. Kaya Y, Ofengand J;. RNA 2003;9:711-721. [2]. 15135053. X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold. Ericsson UB, Nordlund P, Hallberg BM;. FEBS Lett 2004;565:59-64. (from Pfam) NF013323.5 PF01144.28 CoA_trans 23 23 217 domain Y Y N CoA-transferase 2.8.3.- GO:0008410 9083111 131567 cellular organisms no rank 165310 EBI-EMBL Coenzyme A transferase CoA-transferase NF013324.5 PF01145.30 Band_7 23.6 23.6 176 domain Y Y N SPFH domain-containing protein 10542406,18267007 131567 cellular organisms no rank 225619 EBI-EMBL SPFH domain / Band 7 family SPFH domain This family has been called SPFH [1], Band 7 or PHB domain. Recent phylogenetic analysis has shown this domain to be a slipin or Stomatin-like integral membrane domain conserved from protozoa to mammals. [1]. 10542406. The SPFH domain: implicated in regulating targeted protein turnover in stomatins and other membrane-associated proteins. Tavernarakis N, Driscoll M, Kyrpides NC;. Trends Biochem Sci 1999;24:425-427. [2]. 18267007. Slipins: ancient origin, duplication and diversification of the stomatin protein family. Green JB, Young JP;. BMC Evol Biol. 2008;8:44. (from Pfam) NF013327.5 PF01148.25 CTP_transf_1 24 24 264 domain Y Y N phosphatidate cytidylyltransferase 2.7.7.41 131567 cellular organisms no rank 80008 EBI-EMBL Cytidylyltransferase family phosphatidate cytidylyltransferase The members of this family are integral membrane protein cytidylyltransferases. The family includes phosphatidate cytidylyltransferase EC:2.7.7.41 as well as Sec59 from yeast. Sec59 is a dolichol kinase EC:2.7.1.108. (from Pfam) NF013328.5 PF01149.29 Fapy_DNA_glyco 25.5 25.5 117 domain Y Y N DNA-formamidopyrimidine glycosylase family protein GO:0003906,GO:0006284,GO:0008270,GO:0019104 11912217 131567 cellular organisms no rank 117144 EBI-EMBL Formamidopyrimidine-DNA glycosylase N-terminal domain Formamidopyrimidine-DNA glycosylase N-terminal domain Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidised purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges [1]. [1]. 11912217. Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA. Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz E, Kycia JH, Grollman AP, Shoham G;. J Biol Chem 2002;277:19811-19816. (from Pfam) NF013331.5 PF01152.26 Bac_globin 21 21 121 domain Y N N Bacterial-like globin GO:0019825 131567 cellular organisms no rank 48335 EBI-EMBL Bacterial-like globin Bacterial-like globin This family of heme binding proteins are found mainly in bacteria. However they can also be found in some protozoa and plants as well. (from Pfam) NF013333.5 PF01154.22 HMG_CoA_synt_N 25 25 174 PfamEq Y N N Hydroxymethylglutaryl-coenzyme A synthase N terminal GO:0008299 2865259 131567 cellular organisms no rank 12776 EBI-EMBL Hydroxymethylglutaryl-coenzyme A synthase N terminal Hydroxymethylglutaryl-coenzyme A synthase N terminal NF013334.5 PF01155.24 HypA 28.9 28.9 112 domain Y Y N hydrogenase/urease maturation nickel metallochaperone HypA GO:0016151,GO:0051604 19621959 131567 cellular organisms no rank 18666 EBI-EMBL Hydrogenase/urease nickel incorporation, metallochaperone, hypA hydrogenase/urease maturation nickel metallochaperone HypA HypA is a metallochaperone that binds nickel to bring it safely to its target. The targets for Hypa are the nickel-containing enzymes [Ni,Fe]-hydrogenase and urease. The nickel coordinates with four nitrogens within the protein. The four conserved cysteines towards the C-terminus bind one zinc moiety probably to stabilise the protein fold [1]. [1]. 19621959. Structure of a nickel chaperone, HypA, from Helicobacter pylori reveals two distinct metal binding sites. Xia W, Li H, Sze KH, Sun H;. J Am Chem Soc. 2009;131:10031-10040. (from Pfam) NF013335.5 PF01156.24 IU_nuc_hydro 34.2 34.2 297 domain Y Y N nucleoside hydrolase GO:0016799 8634238 131567 cellular organisms no rank 85151 EBI-EMBL Inosine-uridine preferring nucleoside hydrolase nucleoside hydrolase NF013336.5 PF01157.23 Ribosomal_L21e 27 27 101 PfamEq Y N N Ribosomal protein L21e GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 1084 EBI-EMBL Ribosomal protein L21e Ribosomal protein L21e NF013340.5 PF01161.25 PBP 24 24 135 domain Y N N Phosphatidylethanolamine-binding protein 9782050,9782057 131567 cellular organisms no rank 51853 EBI-EMBL Phosphatidylethanolamine-binding protein Phosphatidylethanolamine-binding protein NF013341.5 PF01163.27 RIO1 22 22 187 domain Y Y N RIO1 family regulatory kinase/ATPase 12021457,12612080,12690111,16008568 131567 cellular organisms no rank 45274 EBI-EMBL RIO1 family RIO1 family regulatory kinase/ATPase This is a family of atypical serine kinases which are found in archaea, bacteria and eukaryotes. Activity of Rio1 is vital in Saccharomyces cerevisiae for the processing of ribosomal RNA, as well as for proper cell cycle progression and chromosome maintenance. The structure of RIO1 has been determined [4]. [1]. 12021457. Lipopolysaccharide phosphorylating enzymes encoded in the genomes of Gram-negative bacteria are related to the eukaryotic protein kinases. Krupa A, Srinivasan N;. Protein Sci 2002;11:1580-1584. [2]. 12612080. Late cytoplasmic maturation of the small ribosomal subunit requires RIO proteins in Saccharomyces cerevisiae. Vanrobays E, Gelugne JP, Gleizes PE, Caizergues-Ferrer M;. Mol Cell Biol 2003;23:2083-2095. [3]. 12690111. Rio2p: An evolutionarily conserved, low-abundant protein kinase essential for processing of 20S Pre-rRNA in Saccharomyces cerevisiae. Geerlings TH, Faber AW, Bister M, Vos JC, Raue HA;. 0;0:0-0. [4]. 16008568. Structure and activity of the atypical serine kinase Rio1. Laronde-Leblanc N, Guszczynski T, Copeland T, Wlodawer A;. FEBS J 2005;272:3698-3713. (from Pfam) NF013345.5 PF01168.25 Ala_racemase_N 24.1 24.1 220 domain Y Y N alanine racemase 5.1.1.1 9063881 131567 cellular organisms no rank 296332 EBI-EMBL Alanine racemase, N-terminal domain Alanine racemase, N-terminal domain NF013346.5 PF01169.24 UPF0016 27 27 75 PfamEq Y Y N TMEM165/GDT1 family protein 24955841 131567 cellular organisms no rank 22802 EBI-EMBL Uncharacterized protein family UPF0016 TMEM165/GDT1 family protein This family contains integral membrane proteins of unknown function. Most members of the family contain two copies of a region that contains an EXGD motif. Each of these regions contains three predicted transmembrane regions. It has been suggested that these proteins are calcium transporters [1]. [1]. 24955841. Molecular evolution of a novel family of putative calcium transporters. Demaegd D, Colinet AS, Deschamps A, Morsomme P;. PLoS One. 2014;9:e100851. (from Pfam) NF013347.5 PF01170.23 UPF0020 22.3 22.3 197 domain Y N N RMKL-like, methyltransferase domain 11295541,16343540,17010378,22362734 131567 cellular organisms no rank 165053 EBI-EMBL RMKL-like, methyltransferase domain RMKL-like, methyltransferase domain This domain is the methyltransferase domain found in ribosomal RNA large subunit methyltransferase K/L from Escherichia coli (RmlKL), tRNA (guanine(10)-N2)-dimethyltransferase from Methanocaldococcus jannaschii and similar proteins, which have a THUMP domain at the N-terminal [1-4]. [1]. 11295541. THUMP - a predicted RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases. Aravind L, Koonin EV;. Trends Biochem Sci 2001;26:215-217. [2]. 16343540. Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain. Waterman DG, Ortiz-Lombardia M, Fogg MJ, Koonin EV, Antson AA;. J Mol Biol. 2006;356:97-110. [3]. 17010378. Identification of Escherichia coli m2G methyltransferases: I. the ycbY gene encodes a methyltransferase specific for G2445 of the 23 S rRNA. Lesnyak DV, Sergiev PV, Bogdanov AA, Dontsova OA;. J Mol Biol. 2006;364:20-25. [4]. 22362734. Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA. Wang KT, Desmolaize B, Nan J, Zhang XW, Li LF, Douthwaite S, Su XD;. Nucleic Acids Res. 2012;40:5138-5148. (from Pfam) NF013348.5 PF01171.25 ATP_bind_3 27 27 182 domain Y Y N ATP-binding protein 7731953 131567 cellular organisms no rank 131779 EBI-EMBL PP-loop family ATP-binding protein This family of proteins belongs to the PP-loop superfamily [1]. [1]. 7731953. A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity. Bork P, Koonin EV;. Proteins 1994;20:347-355. (from Pfam) NF013349.5 PF01172.23 SBDS 24.6 24.6 88 PfamEq Y N N Shwachman-Bodian-Diamond syndrome (SBDS) protein 12496757,15701631,15701634,17353896 131567 cellular organisms no rank 1262 EBI-EMBL Shwachman-Bodian-Diamond syndrome (SBDS) protein Shwachman-Bodian-Diamond syndrome (SBDS) protein This family is highly conserved in species ranging from archaea to vertebrates and plants. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. It is characterised by bone marrow failure and leukemia predisposition. Members of this family play a role in RNA metabolism [2] [3]. In yeast these proteins have been shown to be critical for the release and recycling of the nucleolar shuttling factor Tif6 from pre-60S ribosomes, a key step in 60S maturation and translational activation of ribosomes [4]. This data links defective late 60S subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition [4]. [1]. 12496757. Mutations in SBDS are associated with Shwachman-Diamond syndrome. Boocock GR, Morrison JA, Popovic M, Richards N, Ellis L, Durie PR, Rommens JM;. Nat Genet 2003;33:97-101. [2]. 15701634. The SHWACHMAN-Bodian-diamond syndromeprotein family is involved in RNA metabolism. Savchenko A, Krogan N, Cort JR, Evdokimova E, Lew JM, Yee AA, Sanchez-Pulido L, Andrade MA, Bochkarev A, Watson JD, Kennedy MA, Greenblatt J, Hughes T, Arrowsmith CH, Rommens JM, Edwards AM;. J Biol Chem 2005; [Epub ahead of print]. [3]. 15701631. Structural and mutational analysis of the SBDS protein family: insight into the leukemia-associated shwachman-diamond syndrome. Shammas C, Menne TF, Hilcenko C, Michell SR, Goyenechea B, Boocock GR, Durie PR, Rommens JM, Warre. TRUNCATED at 1650 bytes (from Pfam) NF013350.5 PF01174.24 SNO 27 27 188 domain Y N N SNO glutamine amidotransferase family GO:0004359,GO:0042819,GO:0042823 9159529,9791124 131567 cellular organisms no rank 38268 EBI-EMBL SNO glutamine amidotransferase family SNO glutamine amidotransferase family This family and its amidotransferase domain was first described in [1]. It is predicted that members of this family are involved in the pyridoxine biosynthetic pathway, based on the proximity and co-regulation of the corresponding genes and physical interaction between the members of Pfam:PF01174 and Pfam:PF01680 [2]. [1]. 9159529. Sequence analysis of an exceptionally conserved operon suggests enzymes for a new link between histidine and purine biosynthesis. Galperin MY, Koonin EV;. Mol Microbiol 1997;24:443-445. [2]. 9791124. The highly conserved, coregulated SNO and SNZ gene families in Saccharomyces cerevisiae respond to nutrient limitation. Padilla PA, Fuge EK, Crawford ME, Errett A, Werner-Washburne M;. J Bacteriol 1998;180:5718-5726. (from Pfam) NF013351.5 PF01175.23 Urocanase 23.2 23.2 209 PfamEq Y N N Urocanase Rossmann-like domain 131567 cellular organisms no rank 50119 EBI-EMBL Urocanase Rossmann-like domain Urocanase Rossmann-like domain NF013352.5 PF01176.24 eIF-1a 30.2 30.2 64 PfamEq Y N N Translation initiation factor 1A / IF-1 GO:0003723,GO:0003743,GO:0006413 9419357 131567 cellular organisms no rank 14796 EBI-EMBL Translation initiation factor 1A / IF-1 Translation initiation factor 1A / IF-1 This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1. [1]. 9419357. Universally conserved translation initiation factors. Kyrpides NC, Woese CR;. Proc Natl Acad Sci U S A 1998;95:224-228. (from Pfam) NF013353.5 PF01177.27 Asp_Glu_race 31 31 211 domain Y Y N aspartate/glutamate racemase family protein GO:0008152,GO:0036361 18576402,20677745 131567 cellular organisms no rank 157770 EBI-EMBL Asp/Glu/Hydantoin racemase aspartate/glutamate racemase family protein This family contains aspartate racemase, maleate isomerases EC:5.2.1.1 [1], glutamate racemase, hydantoin racemase and arylmalonate decarboxylase EC:4.1.1.76 [2]. [1]. 20677745. A Covalent Succinylcysteine-like Intermediate in the Enzyme-Catalyzed Transformation of Maleate to Fumarate by Maleate Isomerase. Fisch F, Fleites CM, Delenne M, Baudendistel N, Hauer B, Turkenburg JP, Hart S, Bruce NC, Grogan G;. J Am Chem Soc. 2010;132:11455-11457. [2]. 18576402. Structure and mechanism of an unusual malonate decarboxylase and related racemases. Okrasa K, Levy C, Hauer B, Baudendistel N, Leys D, Micklefield J;. Chemistry. 2008;14:6609-6613. (from Pfam) NF013354.5 PF01179.25 Cu_amine_oxid 27 27 407 PfamEq Y N N Copper amine oxidase, enzyme domain GO:0005507,GO:0008131,GO:0009308,GO:0048038 8591028 131567 cellular organisms no rank 17410 EBI-EMBL Copper amine oxidase, enzyme domain Copper amine oxidase, enzyme domain Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme. [1]. 8591028. Crystal structure of a quinoenzyme: copper amine oxidase of Escherichia coli at 2 A resolution. Parsons MR, Convery MA, Wilmot CM, Yadav KD, Blakeley V, Corner AS, Phillips SE, McPherson MJ, Knowles PF;. Structure 1995;3:1171-1184. (from Pfam) NF013355.5 PF01180.26 DHO_dh 27 27 291 domain Y N N Dihydroorotate dehydrogenase GO:0005737,GO:0016627 9655329 131567 cellular organisms no rank 106401 EBI-EMBL Dihydroorotate dehydrogenase Dihydroorotate dehydrogenase NF013357.5 PF01183.25 Glyco_hydro_25 27 27 180 domain Y Y N GH25 family lysozyme GO:0003796,GO:0009253,GO:0016998 19595298,33711051 131567 cellular organisms no rank 79414 EBI-EMBL Glycosyl hydrolases family 25 GH25 family lysozyme NF013358.5 PF01184.24 Gpr1_Fun34_YaaH 25 25 207 subfamily Y Y N GPR1/FUN34/YaaH family transporter GO:0016020 14968426 131567 cellular organisms no rank 13481 EBI-EMBL GPR1/FUN34/yaaH family GPR1/FUN34/YaaH family transporter The Ady2 protein in (Swiss:P25613) is required for acetate in Saccharomyces cerevisiae, and is probably an acetate transporter. A homologue in Yarrowia lipolytica (GPR1) has a role in acetic acid sensitivity. [1]. 14968426. Ady2p is essential for the acetate permease activity in the yeast Saccharomyces cerevisiae. Paiva S, Devaux F, Barbosa S, Jacq C, Casal M;. Yeast 2004;21:201-210. (from Pfam) NF013360.5 PF01186.22 Lysyl_oxidase 20.4 20.4 204 domain Y Y N lysyl oxidase family protein GO:0005507,GO:0016641 131567 cellular organisms no rank 3596 EBI-EMBL Lysyl oxidase lysyl oxidase family protein NF013361.5 PF01187.23 MIF 22 22 114 subfamily Y Y N phenylpyruvate tautomerase MIF-related protein 8643551 131567 cellular organisms no rank 2091 EBI-EMBL Macrophage migration inhibitory factor (MIF) phenylpyruvate tautomerase MIF-related protein Members of this family include eukaryotic MIF (macrophage migration inhibitory factor), which has phenylpyruvate tautomerase and other (e.g. L-dopachrome isomerase) enzymatic activities, but also prokaryotic homologs with unknown function. NF013362.5 PF01189.22 Methyltr_RsmB-F 27 27 199 domain Y N N 16S rRNA methyltransferase RsmB/F GO:0008168 14997580,20558545 131567 cellular organisms no rank 125549 EBI-EMBL 16S rRNA methyltransferase RsmB/F 16S rRNA methyltransferase RsmB/F This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme [1,2]. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) position of cytosine 2870 (m5C2870) in 25S rRNA [1,2]. [1]. 14997580. Crystal structure of human p120 homologue protein PH1374 from Pyrococcus horikoshii. Ishikawa I, Sakai N, Tamura T, Yao M, Watanabe N, Tanaka I;. Proteins. 2004;54:814-816. [2]. 20558545. Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus. Demirci H, Larsen LH, Hansen T, Rasmussen A, Cadambi A, Gregory ST, Kirpekar F, Jogl G;. RNA. 2010;16:1584-1596. (from Pfam) NF013364.5 PF01191.24 RNA_pol_Rpb5_C 23.5 23.5 73 PfamEq Y Y N DNA-directed RNA polymerase subunit RpoH/Rpb5 C-terminal domain-containing protein GO:0003677,GO:0003899,GO:0006351 10784442 131567 cellular organisms no rank 1039 EBI-EMBL RNA polymerase Rpb5, C-terminal domain RNA polymerase Rpb5, C-terminal domain The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain. [1]. 10784442. Architecture of RNA polymerase II and implications for the transcription mechanism. Cramer P, Bushnell DA, Fu J, Gnatt AL, Maier-Davis B, Thompson NE, Burgess RR, Edwards AM, David PR, Kornberg RD;. Science 2000;288:640-649. (from Pfam) NF013365.5 PF01192.27 RNA_pol_Rpb6 26 26 53 PfamEq Y Y N DNA-directed RNA polymerase subunit omega 2.7.7.6 GO:0003677,GO:0003899,GO:0006351 11158566,16908155 131567 cellular organisms no rank 28388 EBI-EMBL RNA polymerase Rpb6 DNA-directed RNA polymerase subunit omega Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit. Rpb6 and omega are structurally conserved and both function in polymerase assembly [1]. [1]. 11158566. Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly. Minakhin L, Bhagat S, Brunning A, Campbell EA, Darst SA, Ebright RH, Severinov K;. Proc Natl Acad Sci U S A 2001;98:892-897. [2]. 16908155. The evolving story of the omega subunit of bacterial RNA polymerase. Mathew R, Chatterji D;. Trends Microbiol. 2006;14:450-455. (from Pfam) NF013366.5 PF01193.29 RNA_pol_L 24 24 74 PfamEq Y N N RNA polymerase Rpb3/Rpb11 dimerisation domain GO:0003899,GO:0006351 7613089,9050843,9657722 131567 cellular organisms no rank 37588 EBI-EMBL RNA polymerase Rpb3/Rpb11 dimerisation domain RNA polymerase Rpb3/Rpb11 dimerisation domain The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. [1]. 9657722. Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain. Zhang G, Darst SA;. Science 1998;281:262-266. [2]. 7613089. The Escherichia coli RNA polymerase alpha subunit: structure and function. Ebright RH, Busby S;. Curr Opin Genet Dev 1995;5:197-203. [3]. 9050843. The two alpha subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element. Murakami K, Kimura M, Owens JT, Meares CF, Ishihama A;. Proc Natl Acad Sci USA 1997;94:1709-1714. (from Pfam) NF013367.5 PF01194.22 RNA_pol_N 26.9 26.9 58 PfamEq Y N N RNA polymerases N / 8 kDa subunit GO:0003677,GO:0003899,GO:0006351 131567 cellular organisms no rank 878 EBI-EMBL RNA polymerases N / 8 kDa subunit RNA polymerases N / 8 kDa subunit NF013369.5 PF01196.24 Ribosomal_L17 27 27 97 domain Y Y N L17 family ribosomal protein GO:0003735,GO:0005840,GO:0006412 10717392,16272117 131567 cellular organisms no rank 37994 EBI-EMBL Ribosomal protein L17 L17 family ribosomal protein NF013371.5 PF01198.24 Ribosomal_L31e 25 25 82 PfamEq Y N N 60S ribosomal protein L31 GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 1054 EBI-EMBL Ribosomal protein L31e 60S ribosomal protein L31 NF013372.5 PF01199.23 Ribosomal_L34e 27 27 94 PfamEq Y N N Ribosomal protein L34e GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 311 EBI-EMBL Ribosomal protein L34e Ribosomal protein L34e NF013373.5 PF01200.23 Ribosomal_S28e 25 25 64 PfamEq Y N N Ribosomal protein S28e GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 609 EBI-EMBL Ribosomal protein S28e Ribosomal protein S28e NF013374.5 PF01201.27 Ribosomal_S8e 30.2 30.2 133 PfamEq Y N N Ribosomal protein S8e 131567 cellular organisms no rank 1187 EBI-EMBL Ribosomal protein S8e Ribosomal protein S8e NF013375.5 PF01202.27 SKI 22.1 22.1 159 domain Y Y N shikimate kinase 131567 cellular organisms no rank 100690 EBI-EMBL Shikimate kinase shikimate kinase NF013377.5 PF01204.23 Trehalase 21 21 512 domain Y Y N trehalase family glycosidase GO:0004555,GO:0005991 12782117 131567 cellular organisms no rank 39904 EBI-EMBL Trehalase trehalase family glycosidase Trehalase (EC:3.2.1.28) is known to recycle trehalose to glucose. Trehalose is a physiological hallmark of heat-shock response in yeast and protects of proteins and membranes against a variety of stresses. This family is found in conjunction with Pfam:PF07492 in fungi. [1]. 12782117. Biochemical and genomic regulation of the trehalose cycle in yeast: review of observations and canonical model analysis. Voit EO;. J Theor Biol 2003;223:55-78. (from Pfam) NF013378.5 PF01205.24 UPF0029 27 27 107 PfamEq Y Y N YigZ family protein 131567 cellular organisms no rank 57407 EBI-EMBL Uncharacterized protein family UPF0029 YigZ family protein NF013379.5 PF01206.22 TusA 28.6 28.6 70 domain Y Y N sulfurtransferase TusA family protein 16387657 131567 cellular organisms no rank 61696 EBI-EMBL Sulfurtransferase TusA sulfurtransferase TusA family protein This family includes the TusA sulfurtransferases [1]. [1]. 16387657. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T;. Mol Cell. 2006;21:97-108. (from Pfam) NF013380.5 PF01207.22 Dus 20.4 20.4 311 domain Y Y N tRNA-dihydrouridine synthase GO:0008033,GO:0017150,GO:0050660 12003496 131567 cellular organisms no rank 209849 EBI-EMBL Dihydrouridine synthase (Dus) tRNA-dihydrouridine synthase Members of this family catalyse the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 (Swiss:Q9HGN6) from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 (Swiss:P53720) acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD [1]. Some family members may be targeted to the mitochondria and even have a role in mitochondria [1]. [1]. 12003496. A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA. Xing F, Martzen MR, Phizicky EM;. RNA 2002;8:370-381. (from Pfam) NF013381.5 PF01208.22 URO-D 23.9 23.9 346 domain Y Y N uroporphyrinogen decarboxylase family protein GO:0004853,GO:0006779 17122346,8224882 131567 cellular organisms no rank 76511 EBI-EMBL Uroporphyrinogen decarboxylase (URO-D) uroporphyrinogen decarboxylase family protein NF013382.5 PF01209.23 Ubie_methyltran 20.1 20.1 233 domain Y Y N class I SAM-dependent methyltransferase 2.1.1.- GO:0008168 131567 cellular organisms no rank 707185 EBI-EMBL ubiE/COQ5 methyltransferase family methyltransferase NF013383.5 PF01210.28 NAD_Gly3P_dh_N 23.1 23.1 158 domain Y N N NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus GO:0016616,GO:0046168,GO:0051287 10801498,12032156 131567 cellular organisms no rank 120249 EBI-EMBL NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyses the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the N-terminal NAD-binding domain [2]. [1]. 12032156. Kinetic regulation of the mitochondrial glycerol-3-phosphate dehydrogenase by the external NADH dehydrogenase in Saccharomyces cerevisiae. Pahlman IL, Larsson C, Averet N, Bunoust O, Boubekeur S, Gustafsson L, Rigoulet M;. J Biol Chem 2002;277:27991-27995. [2]. 10801498. A potential target enzyme for trypanocidal drugs revealed by the crystal structure of NAD-dependent glycerol-3-phosphate dehydrogenase from Leishmania mexicana. Suresh S, Turley S, Opperdoes FR, Michels PA, Hol WG;. Structure Fold Des 2000;8:541-552. (from Pfam) NF013384.5 PF01212.26 Beta_elim_lyase 27 27 288 domain Y Y N beta-eliminating lyase-related protein GO:0006520,GO:0016829 9551100 131567 cellular organisms no rank 281439 EBI-EMBL Beta-eliminating lyase beta-eliminating lyase-related protein NF013391.5 PF01219.24 DAGK_prokar 22.3 22.3 102 PfamEq Y Y N diacylglycerol kinase 2.7.1.107 GO:0008654,GO:0016020,GO:0016301 131567 cellular organisms no rank 34364 EBI-EMBL Prokaryotic diacylglycerol kinase diacylglycerol kinase NF013392.5 PF01220.24 DHquinase_II 23.3 23.3 138 domain Y Y N type II 3-dehydroquinate dehydratase 4.2.1.10 GO:0003855 131567 cellular organisms no rank 53347 EBI-EMBL Dehydroquinase class II type II 3-dehydroquinate dehydratase NF013394.5 PF01222.22 ERG4_ERG24 27 27 432 PfamEq Y N N Ergosterol biosynthesis ERG4/ERG24 family GO:0016020,GO:0016126,GO:0016628 131567 cellular organisms no rank 1402 EBI-EMBL Ergosterol biosynthesis ERG4/ERG24 family Ergosterol biosynthesis ERG4/ERG24 family NF013395.5 PF01223.28 Endonuclease_NS 23 23 223 domain Y Y N DNA/RNA non-specific endonuclease GO:0003676,GO:0016787,GO:0046872 7664065 131567 cellular organisms no rank 37132 EBI-EMBL DNA/RNA non-specific endonuclease DNA/RNA non-specific endonuclease NF013396.5 PF01225.30 Mur_ligase 21 21 95 domain Y Y N Mur ligase domain-containing protein GO:0009058,GO:0016881 9218784 131567 cellular organisms no rank 255199 EBI-EMBL Mur ligase family, catalytic domain Mur ligase family, catalytic domain This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC (Swiss:P17952), MurD (Swiss:P14900), MurE (Swiss:P22188), MurF (Swiss:P11880), Mpl (Swiss:P37773) and FolC (Swiss:P08192). MurC, MurD, Mure and MurF catalyse consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesised by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine. This family also includes Folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate. [1]. 9218784. Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli. Bertrand JA, Auger G, Fanchon E, Martin L, Blanot D, van Heijenoort J, Dideberg O;. EMBO J 1997;16:3416-3425. (from Pfam) NF013397.5 PF01226.22 Form_Nir_trans 34.6 34.6 240 domain Y Y N formate/nitrite transporter family protein GO:0016020,GO:0022857,GO:0055085 22407320 131567 cellular organisms no rank 47646 EBI-EMBL Formate/nitrite transporter formate/nitrite transporter family protein Proteins in this entry belong to the Formate-Nitrite Transporter (FNT) family and includes the nitrite transport protein NirC and formate channel FocA [1,2]. They have a pentameric architecture with structural similarity to aquaporins and glyceroporins [1]. Proteins in this family transport the structurally related compounds, formate and nitrite. [1]. 22407320. Identification and characterization of a bacterial hydrosulphide ion channel. Czyzewski BK, Wang DN;. Nature. 2012;483:494-497. (from Pfam) NF013398.5 PF01227.27 GTP_cyclohydroI 27 27 179 domain Y Y N GTP cyclohydrolase I 3.5.4.16 7663943 131567 cellular organisms no rank 52685 EBI-EMBL GTP cyclohydrolase I GTP cyclohydrolase I This family includes GTP cyclohydrolase enzymes and a family of related bacterial proteins including Swiss:Q46920. [1]. 7663943. Atomic structure of GTP cyclohydrolase I. Nar H, Huber R, Meining W, Schmid C, Weinkauf S, Bacher A;. Structure 1995;3:459-466. (from Pfam) NF013400.5 PF01229.22 Glyco_hydro_39 26 26 472 domain Y Y N GH39 family glycosyl hydrolase GO:0004553,GO:0005975 131567 cellular organisms no rank 16248 EBI-EMBL Glycosyl hydrolases family 39 GH39 family glycosyl hydrolase NF013401.5 PF01230.28 HIT 21.5 21.5 98 domain Y Y N HIT domain-containing protein GO:0003824 8643579,9323207 131567 cellular organisms no rank 120799 EBI-EMBL HIT domain HIT domain NF013402.5 PF01231.23 IDO 26 26 412 PfamEq Y N N Indoleamine 2,3-dioxygenase GO:0020037 131567 cellular organisms no rank 759 EBI-EMBL Indoleamine 2,3-dioxygenase Indoleamine 2,3-dioxygenase NF013406.5 PF01235.22 Na_Ala_symp 24 24 392 domain Y Y N alanine:cation symporter family protein GO:0005283,GO:0006814,GO:0006865,GO:0015655,GO:0016020,GO:0032328 131567 cellular organisms no rank 87984 EBI-EMBL Sodium:alanine symporter family alanine:cation symporter family protein NF013411.5 PF01242.24 PTPS 22.4 22.4 121 domain Y Y N 6-carboxytetrahydropterin synthase 8137809 131567 cellular organisms no rank 49782 EBI-EMBL 6-pyruvoyl tetrahydropterin synthase 6-carboxytetrahydropterin synthase 6-Pyruvoyl tetrahydrobiopterin synthase catalyses the conversion of dihydroneopterin triphosphate to 6-pyruvoyl tetrahydropterin, the second of three enzymatic steps in the synthesis of tetrahydrobiopterin from GTP. The functional enzyme is a hexamer of identical subunits [1]. [1]. 8137809. Three-dimensional structure of 6-pyruvoyl tetrahydropterin synthase, an enzyme involved in tetrahydrobiopterin biosynthesis. Nar H, Huber R, Heizmann CW, Thony B, Burgisser D;. EMBO J 1994;13:1255-1262. (from Pfam) NF013412.5 PF01243.25 Putative_PNPOx 21 21 88 domain Y Y N pyridoxamine 5'-phosphate oxidase family protein 26327315 131567 cellular organisms no rank 318169 EBI-EMBL Pyridoxamine 5'-phosphate oxidase pyridoxamine 5'-phosphate oxidase family protein Family of domains with putative PNPOx function. Family members were predicted to encode pyridoxamine 5'-phosphate oxidase, based on sequence similarity. However, there is no experimental data to validate the predicted activity and purified proteins, such as Swiss:Q06199 and its paralogs, do not possess this activity, nor do they bind to flavin mononucleotide (FMN). To date, the only time functional oxidase activity has been experimentally demonstrated is when the sequences contain both Pfam:PF01243 and Pfam:PF10590. Moreover, some of the family members that contain both domains have been shown to be involved in phenazine biosynthesis. While some molecular function has been experimentally validated for the proteins containing both domains, the role performed by each domain on its own is unknown [1]. [1]. 26327315. Experimental Evidence for a Revision in the Annotation of Putative Pyridoxamine 5'-Phosphate Oxidases P(N/M)P from Fungi. Domitrovic T, Raymundo DP, da Silva TF, Palhano FL;. PLoS One. 2015;10:e0136761. (from Pfam) NF013413.5 PF01244.26 Peptidase_M19 26 26 319 domain Y Y N membrane dipeptidase 3.4.13.- GO:0006508,GO:0070573 131567 cellular organisms no rank 65004 EBI-EMBL Membrane dipeptidase (Peptidase family M19) membrane dipeptidase NF013415.5 PF01246.25 Ribosomal_L24e 27 27 66 PfamEq Y N N Ribosomal protein L24e 131567 cellular organisms no rank 1014 EBI-EMBL Ribosomal protein L24e Ribosomal protein L24e NF013416.5 PF01247.23 Ribosomal_L35Ae 27 27 95 PfamEq Y Y N 50S ribosomal protein L35ae GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 125 EBI-EMBL Ribosomal protein L35Ae 50S ribosomal protein L35ae NF013417.5 PF01248.31 Ribosomal_L7Ae 22.1 22.1 95 domain Y Y N ribosomal L7Ae/L30e/S12e/Gadd45 family protein 9151207 131567 cellular organisms no rank 13211 EBI-EMBL Ribosomal protein L7Ae/L30e/S12e/Gadd45 family ribosomal L7Ae/L30e/S12e/Gadd45 family protein This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118 [1]. [1]. 9151207. Cell cycle and apoptosis: possible roles of Gadd45 and MyD118 proteins inferred from their homology to ribosomal proteins. Koonin EV;. J Mol Med 1997;75:236-238. (from Pfam) NF013422.5 PF01253.27 SUI1 25.5 25.5 77 PfamEq Y N N Translation initiation factor SUI1 GO:0003743,GO:0006413 131567 cellular organisms no rank 16798 EBI-EMBL Translation initiation factor SUI1 Translation initiation factor SUI1 NF013424.5 PF01255.24 Prenyltransf 27 27 219 domain Y Y N undecaprenyl diphosphate synthase family protein GO:0016765 9677368 131567 cellular organisms no rank 79808 EBI-EMBL Putative undecaprenyl diphosphate synthase undecaprenyl diphosphate synthase family protein Previously known as uncharacterized protein family UPF0015, a single member of this family Swiss:O82827 has been identified as an undecaprenyl diphosphate synthase [1]. [1]. 9677368. Molecular cloning, expression, and purification of undecaprenyl diphosphate synthase. No sequence similarity between E- and Z-prenyl diphosphate synthases. Shimizu N, Koyama T, Ogura K;. J Biol Chem 1998;273:19476-19481. (from Pfam) NF013425.5 PF01256.22 Carb_kinase 27 27 242 domain Y Y N NAD(P)H-hydrate dehydratase GO:0016836,GO:0052855 131567 cellular organisms no rank 113894 EBI-EMBL Carbohydrate kinase NAD(P)H-hydrate dehydratase This family is related to Pfam:PF02110 and Pfam:PF00294 implying that it also is a carbohydrate kinase. (personal obs Yeats C). (from Pfam) NF013426.5 PF01257.24 2Fe-2S_thioredx 24.8 24.8 145 domain Y Y N NAD(P)H-dependent oxidoreductase subunit E 12089152 131567 cellular organisms no rank 68264 EBI-EMBL Thioredoxin-like [2Fe-2S] ferredoxin NAD(P)H-dependent oxidoreductase subunit E NF013427.5 PF01258.22 zf-dskA_traR 24.9 24.9 36 domain Y Y N TraR/DksA C4-type zinc finger protein GO:0008270 131567 cellular organisms no rank 82483 EBI-EMBL Prokaryotic dksA/traR C4-type zinc finger TraR/DksA C4-type zinc finger protein NF013428.5 PF01259.23 SAICAR_synt 19.7 19.7 233 PfamEq Y Y N phosphoribosylaminoimidazolesuccinocarboxamide synthase 131567 cellular organisms no rank 64343 EBI-EMBL SAICAR synthetase phosphoribosylaminoimidazolesuccinocarboxamide synthase Also known as Phosphoribosylaminoimidazole-succinocarboxamide synthase. (from Pfam) NF013429.5 PF01261.29 AP_endonuc_2 31.1 31.1 249 domain Y Y N TIM barrel protein 11497462 131567 cellular organisms no rank 452995 EBI-EMBL Xylose isomerase-like TIM barrel TIM barrel protein This TIM alpha/beta barrel structure is found in xylose isomerase (Swiss:P19148) and in endonuclease IV (Swiss:P12638, EC:3.1.21.2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae [1]. [1]. 11497462. Investigation of myo-inositol catabolism in Rhizobium leguminosarum bv. viciae and its effect on nodulation competitiveness. Fry J, Wood M, Poole PS;. Mol Plant Microbe Interact 2001;14:1016-1025. (from Pfam) NF013430.5 PF01262.26 AlaDh_PNT_C 23 23 214 domain Y N N Alanine dehydrogenase/PNT, C-terminal domain 11354603 131567 cellular organisms no rank 198302 EBI-EMBL Alanine dehydrogenase/PNT, C-terminal domain Alanine dehydrogenase/PNT, C-terminal domain This family now also contains the lysine 2-oxoglutarate reductases. [1]. 11354603. Lysine metabolism in higher plants. Azevedo RA, Lea PJ;. Amino Acids 2001;20:261-279. (from Pfam) NF013431.5 PF01263.25 Aldose_epim 27 27 299 domain Y N N Aldose 1-epimerase GO:0005975,GO:0016853 131567 cellular organisms no rank 147296 EBI-EMBL Aldose 1-epimerase Aldose 1-epimerase NF013432.5 PF01264.26 Chorismate_synt 27 27 327 PfamEq Y Y N chorismate synthase 4.2.3.5 GO:0004107,GO:0009073 131567 cellular organisms no rank 74342 EBI-EMBL Chorismate synthase chorismate synthase NF013434.5 PF01266.29 DAO 27.9 27.9 353 subfamily Y Y N FAD-dependent oxidoreductase GO:0016491 9153426 131567 cellular organisms no rank 1232198 EBI-EMBL FAD dependent oxidoreductase FAD-dependent oxidoreductase This family includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase EC:1.1.99.5, Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1. [1]. 9153426. Active site plasticity in D-amino acid oxidase: a crystallographic analysis. Todone F, Vanoni MA, Mozzarelli A, Bolognesi M, Coda A, Curti B, Mattevi A;. Biochemistry 1997;36:5853-5860. (from Pfam) NF013436.5 PF01268.24 FTHFS 27 27 556 PfamEq Y Y N formate--tetrahydrofolate ligase 6.3.4.3 GO:0004329,GO:0005524 131567 cellular organisms no rank 38650 EBI-EMBL Formate--tetrahydrofolate ligase formate--tetrahydrofolate ligase NF013437.5 PF01269.22 Fibrillarin 27 27 227 domain Y Y N fibrillarin-like rRNA/tRNA 2'-O-methyltransferase GO:0003723,GO:0006364,GO:0008168 14975761,17617422,21270896 131567 cellular organisms no rank 1820 EBI-EMBL Fibrillarin fibrillarin-like rRNA/tRNA 2'-O-methyltransferase NF013442.5 PF01274.27 MS_TIM-barrel 26.4 26.4 248 domain Y N N Malate synthase, TIM barrel domain GO:0004474,GO:0006097 10715138,12930982,15637152,18714089 131567 cellular organisms no rank 61680 EBI-EMBL Malate synthase, TIM barrel domain Malate synthase, TIM barrel domain Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been identified two isoforms, A and G (MSA and MSG, respectively) that differ in size and is attributed to an inserted alpha/beta domain in MSG that may have regulatory function [1,2]. In malate synthases, the TIM beta/alpha-barrel fold and the C-terminal domain are well conserved and the cleft between them forms the active site [1,2,3,4]. MSA and MSG consist of an N-terminal alpha-helical clasp domain, a central TIM barrel domain and a C-terminal helical plug domain. This is the TIM barrel domain of malate synthases. [1]. 10715138. Crystal structure of Escherichia coli malate synthase G complexed with magnesium and glyoxylate at 2.0 A resolution: mechanistic implications. Howard BR, Endrizzi JA, Remington SJ;. Biochemistry 2000;39:3156-3168. [2]. 18714089. Atomic resolution structures of Escherichia coli and Bacillus anthracis malate synthase A: comparison with isoform G and implications for structure-based drug discovery. Lohman JR, Olson AC, Remington SJ;. Protein Sci. 2008;17:1935-1945. [3]. 12930982. Structure of the Escherichia coli malate synthase G:pyruvate:acetyl-coenzyme A abortive ternary complex at 1.95 A resolution. Anstrom DM, Kallio K, Remington SJ;. Protein Sci. 2003;12:1822-1832. [4]. 15637152. Solution NMR-derived global fold of a monomeric 82-kDa enzyme. Tugarinov V, Choy WY, Orekhov VY, Kay LE;. Proc Natl Acad Sci U S A. 2005;102:622-627. (from Pfam) NF013444.5 PF01276.25 OKR_DC_1 27 27 417 domain Y N N Orn/Lys/Arg decarboxylase, major domain GO:0003824 7563080 131567 cellular organisms no rank 73015 EBI-EMBL Orn/Lys/Arg decarboxylase, major domain Orn/Lys/Arg decarboxylase, major domain NF013448.5 PF01280.25 Ribosomal_L19e 25 25 144 PfamEq Y Y N 50S ribosomal protein L19e GO:0003735,GO:0005840,GO:0006412 10476961,24524803 131567 cellular organisms no rank 1191 EBI-EMBL Ribosomal protein L19e 50S ribosomal protein L19e NF013450.5 PF01282.24 Ribosomal_S24e 25 25 79 PfamEq Y N N Ribosomal protein S24e GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 1159 EBI-EMBL Ribosomal protein S24e Ribosomal protein S24e NF013451.5 PF01283.24 Ribosomal_S26e 27 27 108 PfamEq Y N N Ribosomal protein S26e GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 127 EBI-EMBL Ribosomal protein S26e Ribosomal protein S26e NF013455.5 PF01287.25 eIF-5a 24.2 24.2 69 PfamEq Y N N Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold GO:0003723,GO:0003746,GO:0043022,GO:0045901,GO:0045905 19424157,9753699 131567 cellular organisms no rank 566 EBI-EMBL Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold eIF5A, previously thought to be an initiation factor, has been shown to be required for peptide chain elongation in yeast [1]. [1]. 9753699. Structure of translation initiation factor 5A from Pyrobaculum aerophilum at 1.75 A resolution. Peat TS, Newman J, Waldo GS, Berendzen J, Terwilliger TC;. Structure 1998;6:1207-1214. [2]. 19424157. Hypusine-containing protein eIF5A promotes translation elongation. Saini P, Eyler DE, Green R, Dever TE;. Nature. 2009;459:118-121. (from Pfam) NF013456.5 PF01288.25 HPPK 25.7 25.7 116 domain Y Y N 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase GO:0003848,GO:0009396 131567 cellular organisms no rank 76838 EBI-EMBL 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase NF013460.5 PF01292.25 Ni_hydr_CYTB 30.1 30.1 179 domain Y Y N cytochrome b/b6 domain-containing protein GO:0009055,GO:0016020 131567 cellular organisms no rank 127259 EBI-EMBL Prokaryotic cytochrome b561 Prokaryotic cytochrome b561 This family includes cytochrome b561 and related proteins, in addition to the nickel-dependent hydrogenases b-type cytochrome subunit. Cytochrome b561 is a secretory vesicle-specific electron transport protein. It is an integral membrane protein, that binds two heme groups non-covalently. This is a prokaryotic family. Members of the 'eukaryotic cytochrome b561' family can be found in Pfam: PF03188. (from Pfam) NF013461.5 PF01293.25 PEPCK_ATP 26.5 26.5 465 domain Y Y N phosphoenolpyruvate carboxykinase (ATP) 4.1.1.49 GO:0004612,GO:0005524,GO:0006094 8599762 131567 cellular organisms no rank 39983 EBI-EMBL Phosphoenolpyruvate carboxykinase phosphoenolpyruvate carboxykinase (ATP) NF013462.5 PF01294.23 Ribosomal_L13e 24.9 24.9 180 PfamEq Y Y N ribosomal protein L13e GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 108 EBI-EMBL Ribosomal protein L13e ribosomal protein L13e Members of this family are the ribosomal large subunit L13, as the term is used in eukaryotics and archaea (eL13). This protein is unrelated to the bacterial ribosomal protein L13. NF013465.5 PF01297.22 ZnuA 29 29 263 subfamily Y Y N metal ABC transporter solute-binding protein, Zn/Mn family GO:0046872 10404217,21338480,24128931 131567 cellular organisms no rank 128515 EBI-EMBL Zinc-uptake complex component A periplasmic metal ABC transporter solute-binding protein, Zn/Mn family ZnuA includes periplasmic solute binding proteins such as TroA that interacts with an ATP-binding cassette transport system in Treponema pallidum [1]. ZnuA is part of the bacterial zinc-uptake complex ZnuABC, whose components are the following families, ZinT, Pfam:PF09223, Pfam:PF00950, Pfam:PF00005, all of which are regulated by the transcription-regulator family FUR, Pfam:PF01475. ZinT acts as a Zn2+-buffering protein that delivers Zn2+ to ZnuA (TroA), a high-affinity zinc-uptake protein. In Gram-negative bacteria the ZnuABC transporter system ensures an adequate import of zinc in Zn2+-poor environments, such as those encountered by pathogens within the infected host [2,3]. [1]. 10404217. Treponema pallidum TroA is a periplasmic zinc-binding protein with a helical backbone. Lee YH, Deka RK, Norgard MV, Radolf JD, Hasemann CA;. Nat Struct Biol 1999;6:628-633. [2]. 21338480. Role of ZnuABC and ZinT in Escherichia coli O157:H7 zinc acquisition and interaction with epithelial cells. Gabbianelli R, Scotti R, Ammendola S, Petrarca P, Nicolini L, Battistoni A;. BMC Microbiol. 2011;11:36. [3]. 24128931. The Salmonella enterica ZinT structure, zinc affinity and interaction with the high-affinity uptake protein ZnuA provide insight into the management of periplasmic zinc. Ilari A, Alaleona F, Tria G, Petrarca P, Battistoni A, Zamparelli C, Verzili D, Falconi M, Chiancone E;. Biochim Biophys Acta. 2014;1840:535-544. (from Pfam) NF013468.5 PF01300.23 Sua5_yciO_yrdC 25.1 25.1 178 domain Y Y N Sua5/YciO/YrdC/YwlC family protein GO:0003725 11206077,19287007,19884342,20309016 131567 cellular organisms no rank 135431 EBI-EMBL Telomere recombination Sua5/YciO/YrdC/YwlC family protein This domain has been shown to bind preferentially to dsRNA [1]. The domain is found in SUA5 Swiss:P32579 as well as HypF and YrdC Swiss:P45748. It has also been shown to be required for telomere recombniation in yeast. [1]. 11206077. The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding. Teplova M, Tereshko V, Sanishvili R, Joachimiak A, Bushueva T, Anderson WF, Egli M;. Protein Sci 2000;9:2557-2566. [2]. 19287007. The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F, Williamson JR, Schimmel P, Swairjo MA, de Crecy-Lagard V;. Nucleic Acids Res. 2009;37:2894-2909. [3]. 19884342. The Sua5 protein is essential for normal translational regulation in yeast. Lin CA, Ellis SR, True HL;. Mol Cell Biol. 2010;30:354-363. [4]. 20309016. Sua5p is required for telomere recombination in Saccharomyces cerevisiae. Meng FL, Chen XF, Hu Y, Tang HB, Dang W, Zhou JQ;. Cell Res. 2010;20:495-498. (from Pfam) NF013469.5 PF01301.24 Glyco_hydro_35 27 27 319 domain Y Y N beta-galactosidase 3.2.1.23 131567 cellular organisms no rank 38054 EBI-EMBL Glycosyl hydrolases family 35 beta-galactosidase NF013473.5 PF01306.24 LacY_symp 24 24 413 domain Y Y N MFS transporter GO:0005351,GO:0008643,GO:0016020 8438231 131567 cellular organisms no rank 48374 EBI-EMBL LacY proton/sugar symporter MFS transporter This family is closely related to the sugar transporter family. [1]. 8438231. A major superfamily of transmembrane facilitators that catalyse uniport, symport and antiport. Marger MD, Saier MH Jr;. Trends Biochem Sci 1993;18:13-20. (from Pfam) NF013481.5 PF01314.23 AFOR_C 27 27 385 domain Y Y N aldehyde ferredoxin oxidoreductase C-terminal domain-containing protein GO:0009055,GO:0016491,GO:0016625,GO:0051536 7878465 131567 cellular organisms no rank 12420 EBI-EMBL Aldehyde ferredoxin oxidoreductase, domains 2 & 3 Aldehyde ferredoxin oxidoreductase, domains 2 & 3 Aldehyde ferredoxin oxidoreductase (AOR) catalyses the reversible oxidation of aldehydes to their corresponding carboxylic acids with their accompanying reduction of the redox protein ferredoxin. This family is composed of two structural domains that bind the tungsten cofactor via DXXGL(C/D) motifs. In addition to maintaining specific binding interactions with the cofactor, another role for domains 2 and 3 may be to regulate substrate access to AOR [1]. [1]. 7878465. Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase. Chan MK, Mukund S, Kletzin A, Adams MW, Rees DC;. Science 1995;267:1463-1469. (from Pfam) NF013482.5 PF01315.27 Ald_Xan_dh_C 31.3 31.3 110 domain Y N N Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain 10430865,7502041 131567 cellular organisms no rank 152452 EBI-EMBL Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain NF013486.5 PF01321.23 Creatinase_N 22 22 128 domain Y Y N aminopeptidase P family N-terminal domain-containing protein GO:0016787 15005612,1696320 131567 cellular organisms no rank 145185 EBI-EMBL Creatinase/Prolidase N-terminal domain Creatinase/Prolidase N-terminal domain This family includes the N-terminal non-catalytic domains from creatinase and prolidase. The exact function of this domain is uncertain. [1]. 1696320. Enzymatic mechanism of creatine amidinohydrolase as deduced from crystal structures. Coll M, Knof SH, Ohga Y, Messerschmidt A, Huber R, Moellering H, Russmann L, Schumacher G;. J Mol Biol 1990;214:597-610. [2]. 15005612. Structure of the prolidase from Pyrococcus furiosus. Maher MJ, Ghosh M, Grunden AM, Menon AL, Adams MW, Freeman HC, Guss JM;. Biochemistry. 2004;43:2771-2783. (from Pfam) NF013488.5 PF01323.25 DSBA 25.6 25.6 191 domain Y Y N DsbA family protein GO:0015035 8002605,8226631,8765742,9149147,9882667 131567 cellular organisms no rank 206079 EBI-EMBL DSBA-like thioredoxin domain DSBA-like thioredoxin domain This family contains a diverse set of proteins with a thioredoxin-like structure Pfam:PF00085. This family also includes 2-hydroxychromene-2-carboxylate (HCCA) isomerase enzymes catalyse one step in prokaryotic polyaromatic hydrocarbon (PAH) catabolic pathways [2,3,4]. This family also contains members with functions other than HCCA isomerisation, such as Kappa family GSTs (e.g. Swiss:P24473), whose similarity to HCCA isomerases was not previously recognised. The sequence Swiss:O07298 has been annotated as a dioxygenase but is almost certainly an HCCA isomerase enzyme. Similarly, the sequence Swiss:Q9ZI67 has been annotated as a dehydrogenase, but is most probably also an HCCA isomerase enzyme. In addition, the Rhizobium leguminosarum Swiss:Q52782 protein has been annotated as a putative glycerol-3-phosphate transfer protein, but is also most likely to be an HCCA isomerase enzyme (see [5]). [1]. 9149147. Structure of TcpG, the DsbA protein folding catalyst from Vibrio cholerae. Hu SH, Peek JA, Rattigan E, Taylor RK, Martin JL;. J Mol Biol 1997;268:137-146. [2]. 8226631. Metabolism of dibenzothiophene and naphthalene in Pseudomonas strains: complete DNA sequence of an upper naphthalene catabolic pathway. Denome SA, Stanley DC, Olson ES, Young KD;. J Bacteriol 1993;175:6890-6901. [3]. 8002605. Organization and evolution of naphthalene catabolic pathways: sequence of the DNA encoding 2-hydroxychromene-2-carboxylate isomerase and trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from the NAH7 plasmid. Eaton RW;. J Bacteriol 1994;176:7757-7762. [4]. 9882667. The phn genes of Burkholderia sp. strain RP007 constitute a dive. TRUNCATED at 1650 bytes (from Pfam) NF013490.5 PF01325.24 Fe_dep_repress 26 26 60 domain Y N N Iron dependent repressor, N-terminal DNA binding domain GO:0003677 7568230,7743135 131567 cellular organisms no rank 57334 EBI-EMBL Iron dependent repressor, N-terminal DNA binding domain Iron dependent repressor, N-terminal DNA binding domain This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif. [1]. 7568230. Structures of the apo- and the metal ion-activated forms of the diphtheria tox repressor from Corynebacterium diphtheriae. Schiering N, Tao X, Zeng H, Murphy JR, Petsko GA, Ringe D;. Proc Natl Acad Sci USA 1995;92:9843-9850. [2]. 7743135. Three-dimensional structure of the diphtheria toxin repressor in complex with divalent cation co-repressors. Qiu X, Verlinde CL, Zhang S, Schmitt MP, Holmes RK, Hol WG;. Structure 1995;3:87-100. (from Pfam) NF013491.5 PF01326.24 PPDK_N 27 27 328 domain Y Y N PEP/pyruvate-binding domain-containing protein GO:0005524,GO:0016301,GO:0016310 18052212 131567 cellular organisms no rank 109759 EBI-EMBL Pyruvate phosphate dikinase, AMP/ATP-binding domain Pyruvate phosphate dikinase, AMP/ATP-binding domain This enzyme catalyses the reversible conversion of ATP to AMP, pyrophosphate and phosphoenolpyruvate (PEP). The N-terminal domain has been shown to be the AMP/ATP-binding domain [1]. [1]. 18052212. Swiveling domain mechanism in pyruvate phosphate dikinase. Lim K, Read RJ, Chen CC, Tempczyk A, Wei M, Ye D, Wu C, Dunaway-Mariano D, Herzberg O;. Biochemistry. 2007;46:14845-14853. (from Pfam) NF013492.5 PF01327.26 Pep_deformylase 22.8 22.8 156 domain Y Y N peptide deformylase GO:0042586 8845003,9665852 131567 cellular organisms no rank 107951 EBI-EMBL Polypeptide deformylase peptide deformylase NF013494.5 PF01329.24 Pterin_4a 26 26 91 domain Y Y N 4a-hydroxytetrahydrobiopterin dehydratase 4.2.1.96 GO:0006729,GO:0008124 8897596 131567 cellular organisms no rank 38844 EBI-EMBL Pterin 4 alpha carbinolamine dehydratase 4a-hydroxytetrahydrobiopterin dehydratase Pterin 4 alpha carbinolamine dehydratase is also known as DCoH (dimerisation cofactor of hepatocyte nuclear factor 1-alpha). [1]. 8897596. High-resolution structures of the bifunctional enzyme and transcriptional coactivator DCoH and its complex with a product analogue. Cronk JD, Endrizzi JA, Alber T;. Protein Sci 1996;5:1963-1972. (from Pfam) NF013495.5 PF01330.26 RuvA_N 23.6 23.6 61 domain Y Y N OB-fold domain-containing protein GO:0005524,GO:0006281,GO:0006310,GO:0009378 8832889 131567 cellular organisms no rank 57820 EBI-EMBL RuvA N terminal domain RuvA N terminal domain The N terminal domain of RuvA has an OB-fold structure. This domain forms the RuvA tetramer contacts [1]. [1]. 8832889. Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction. Rafferty JB, Sedelnikova SE, Hargreaves D, Artymiuk PJ, Baker PJ, Sharples GJ, Mahdi AA, Lloyd RG, Rice DW;. Science 1996;274:415-421. (from Pfam) NF013499.5 PF01336.30 tRNA_anti-codon 27 27 75 domain Y Y N OB-fold nucleic acid binding domain-containing protein GO:0003676 10829230,2047877,7760808,8990123 131567 cellular organisms no rank 417665 EBI-EMBL OB-fold nucleic acid binding domain OB-fold nucleic acid binding domain This family contains OB-fold domains that bind to nucleic acids [4]. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See Pfam:PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family [2,3]. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain. [1]. 2047877. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D;. Science 1991;252:1682-1689. [2]. 7760808. Rpa4, a homolog of the 34-kilodalton subunit of the replication protein A complex. Keshav KF, Chen C, Dutta A;. Mol Cell Biol 1995;15:3119-3128. [3]. 8990123. Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Bochkarev A, Pfuetzner RA, Edwards AM, Frappier L;. Nature 1997;385:176-181. [4]. 10829230. Protein fold recognition using sequence profiles and its application in structural genomics. Koonin EV, Wolf YI, Aravind L;. Adv Protein Chem 2000;54:245-275. (from Pfam) NF013500.5 PF01337.23 Barstar 22.1 22.1 81 domain Y Y N barstar family protein 8043575 131567 cellular organisms no rank 29431 EBI-EMBL Barstar (barnase inhibitor) barstar family protein NF013502.5 PF01339.22 CheB_methylest 24 24 174 domain Y Y N chemotaxis protein CheB GO:0000156,GO:0000160,GO:0005737,GO:0006935,GO:0008984 7608974 131567 cellular organisms no rank 82434 EBI-EMBL CheB methylesterase chemotaxis protein CheB NF013506.5 PF01343.23 Peptidase_S49 24.9 24.9 154 domain Y Y N S49 family peptidase GO:0006508,GO:0008233 131567 cellular organisms no rank 93844 EBI-EMBL Peptidase family S49 S49 family peptidase NF013507.5 PF01344.30 Kelch_1 20.1 20 46 repeat Y N N kelch repeat protein GO:0005515 15475350,2002850,8126718 131567 cellular organisms no rank 23959 EBI-EMBL Kelch motif kelch motif The kelch motif was initially discovered in Kelch (Swiss:Q04652). In this protein there are six copies of the motif. It has been shown that Swiss:Q04652 is related to Galactose Oxidase [1] for which a structure has been solved [2]. The kelch motif forms a beta sheet. Several of these sheets associate to form a beta propeller structure as found in Pfam:PF00064, Pfam:PF00400 and Pfam:PF00415. [1]. 8126718. Drosophila kelch motif is derived from a common enzyme fold. Bork P, Doolittle RF;. J Mol Biol 1994;236:1277-1282. [2]. 2002850. Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase. Ito N, Phillips SE, Stevens C, Ogel ZB, McPherson MJ, Keen JN, Yadav KD, Knowles PF;. Nature 1991;350:87-90. [3]. 15475350. Crystal structure of the Kelch domain of human Keap1. Li X, Zhang D, Hannink M, Beamer LJ;. J Biol Chem 2004;279:54750-54758. (from Pfam) NF013508.5 PF01345.23 DUF11 24.6 24.6 114 repeat Y N N DUF11 domain-containing protein 31189768 131567 cellular organisms no rank 69665 EBI-EMBL Domain of unknown function DUF11 Domain of unknown function DUF11 A domain of unknown function found in multiple copies in several archaebacterial proteins. Conserved N-terminal lysine and C-terminal asparagine with central asp/glu suggests that many of these domain may contain an isopeptide bond. In Methanothermobacter sp. CaT2, a DUF11-containing repeat hypothetical protein encoded by MTCT_1020 plays a key role as a membrane-bound adhesion protein in the aggregation of CaT2. DUF11-containing repeat domains are not involved in aggregation, but may be important for stabilizing the surface cell wall structures of CaT2 [1]. [1]. 31189768. An Aggregation-defective Mutant of Methanothermobacter sp. CaT2 Reveals Unique Protein-dependent Aggregation. Sumikawa K, Kosaka T, Mayahara N, Matsutani M, Udo K, Yamada M;. Microbes Environ. 2019;34:244-251. (from Pfam) NF013510.5 PF01347.27 Vitellogenin_N 24 24 590 domain Y N N Lipoprotein amino terminal region GO:0005319,GO:0006869 9687371 131567 cellular organisms no rank 374 EBI-EMBL Lipoprotein amino terminal region Lipoprotein amino terminal region This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100. These proteins are all involved in lipid transport [1]. This family contains the LV1n chain from lipovitellin, that contains two structural domains. [1]. 9687371. The structural basis of lipid interactions in lipovitellin, a soluble lipoprotein. Anderson TA, Levitt DG, Banaszak LJ. Structure 1998;6:895-909. (from Pfam) NF013511.5 PF01348.26 Intron_maturas2 20.8 11.5 140 domain Y Y N group II intron reverse transcriptase/maturase GO:0006397 8029012,8255751,9362497 131567 cellular organisms no rank 6351 EBI-EMBL Type II intron maturase group II intron reverse transcriptase/maturase Group II introns use intron-encoded reverse transcriptase, maturase and DNA endonuclease activities for site-specific insertion into DNA [2]. Although this type of intron is self splicing in vitro they require a maturase protein for splicing in vivo. It has been shown that a specific region of the aI2 intron is needed for the maturase function [1]. This region was found to be conserved in group II introns and called domain X [3]. [1]. 8029012. Splicing defective mutants of the COXI gene of yeast mitochondrial DNA: initial definition of the maturase domain of the group II intron aI2. Moran JV, Mecklenburg KL, Sass P, Belcher SM, Mahnke D, Lewin A, Perlman P;. Nucleic Acids Res 1994;22:2057-2064. [2]. 9362497. Group II intron endonucleases use both RNA and protein subunits for recognition of specific sequences in double-stranded DNA. Guo H, Zimmerly S, Perlman PS, Lambowitz AM;. EMBO J 1997;16:6835-6848. [3]. 8255751. Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Mohr G, Perlman PS, Lambowitz AM;. Nucleic Acids Res 1993;21:4991-4997. (from Pfam) NF013514.5 PF01351.23 RNase_HII 25.8 25.8 199 domain Y N N Ribonuclease HII GO:0004523 9241229 131567 cellular organisms no rank 82302 EBI-EMBL Ribonuclease HII Ribonuclease HII NF013517.5 PF01355.22 HIPIP 22 22 66 domain Y Y N high-potential iron-sulfur protein GO:0009055,GO:0019646 11095707,1917989 131567 cellular organisms no rank 4705 EBI-EMBL High potential iron-sulfur protein high-potential iron-sulfur protein NF013522.5 PF01361.26 Tautomerase 22 22 60 domain Y Y N tautomerase family protein GO:0008152,GO:0016853 7966298 131567 cellular organisms no rank 49107 EBI-EMBL Tautomerase enzyme tautomerase family protein This family includes the enzyme 4-oxalocrotonate tautomerase Swiss:Q01468 that catalyses the ketonisation of 2-hydroxymuconate to 2-oxo-3-hexenedioate. [1]. 7966298. Preliminary crystallographic analysis of 4-oxalocrotonate tautomerase reveals the oligomeric structure of the enzyme. Roper DI, Subramanya HS, Shingler V, Wigley DB;. J Mol Biol 1994;243:799-801. (from Pfam) NF013524.5 PF01364.23 Peptidase_C25 23 23 374 domain Y Y N C25 family cysteine peptidase GO:0006508,GO:0008234 131567 cellular organisms no rank 9967 EBI-EMBL Peptidase family C25 C25 family cysteine peptidase domain NF013527.5 PF01367.25 5_3_exonuc 40 40 97 domain Y Y N 5'-3' exonuclease H3TH domain-containing protein GO:0003677,GO:0003824 8657312,8717047 131567 cellular organisms no rank 128537 EBI-EMBL 5'-3' exonuclease, C-terminal SAM fold 5'-3' exonuclease, C-terminal SAM fold NF013528.5 PF01368.25 DHH 28.1 28.1 125 domain Y Y N DHH family phosphoesterase 9478130 131567 cellular organisms no rank 152642 EBI-EMBL DHH family DHH family phosphoesterase It is predicted that this family of proteins all perform a phosphoesterase function. It included the single stranded DNA exonuclease RecJ. [1]. 9478130. A novel family of predicted phosphoesterases includes Drosophila prune protein and bacterial RecJ exonuclease. Aravind L, Koonin EV;. Trends Biochem Sci 1998;23:17-19. (from Pfam) NF013530.5 PF01370.26 Epimerase 20.9 20.9 240 domain Y Y N NAD-dependent epimerase/dehydratase family protein GO:0003824 9174344 131567 cellular organisms no rank 2438199 EBI-EMBL NAD dependent epimerase/dehydratase family NAD-dependent epimerase/dehydratase family protein This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions. [1]. 9174344. Structural analysis of UDP-sugar binding to UDP-galactose 4-epimerase from Escherichia coli. Thoden JB, Hegeman AD, Wesenberg G, Chapeau MC, Frey PA, Holden HM;. Biochemistry 1997;36:6294-6304. (from Pfam) NF013533.5 PF01373.22 Glyco_hydro_14 27 27 402 domain Y Y N family 14 glycosylhydrolase GO:0000272,GO:0016161 131567 cellular organisms no rank 1201 EBI-EMBL Glycosyl hydrolase family 14 glycosyl hydrolase family protein This family are beta amylases. (from Pfam) NF013534.5 PF01374.23 Glyco_hydro_46 27 27 210 domain Y Y N chitosanase GO:0005576,GO:0005975,GO:0016977 131567 cellular organisms no rank 10594 EBI-EMBL Glycosyl hydrolase family 46 chitosanase This family are chitosanase enzymes. (from Pfam) NF013538.5 PF01379.25 Porphobil_deam 22.1 22.1 207 PfamEq Y N N Porphobilinogen deaminase, dipyromethane cofactor binding domain GO:0004418,GO:0033014 131567 cellular organisms no rank 70231 EBI-EMBL Porphobilinogen deaminase, dipyromethane cofactor binding domain Porphobilinogen deaminase, dipyromethane cofactor binding domain NF013539.5 PF01380.27 SIS 25 25 131 domain Y Y N SIS domain-containing protein GO:0097367,GO:1901135 10203754,9739095 131567 cellular organisms no rank 383176 EBI-EMBL SIS domain SIS domain SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars. Presumably the SIS domains bind to the end-product of the pathway. Structure of SIS domain. [1]. 9739095. Involvement of the C terminus in intramolecular nitrogen channeling in glucosamine 6-phosphate synthase: evidence from a 1.6 A crystal structure of the isomerase domain. Teplyakov A, Obmolova G, Badet-Denisot MA, Badet B, Polikarpov I;. Structure 1998;6:1047-1055. [2]. 10203754. The SIS domain: a phosphosugar-binding domain. Bateman A;. Trends Biochem Sci 1999;24:94-95. (from Pfam) NF013540.5 PF01381.27 HTH_3 23 23 55 domain Y Y N helix-turn-helix domain-containing protein 20196080 131567 cellular organisms no rank 1388844 EBI-EMBL Helix-turn-helix Helix-turn-helix This large family of DNA binding helix-turn helix proteins includes Cro Swiss:P03036 and CI Swiss:P03034. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteristic of the whole family [1]. [1]. 20196080. The crystal structure of NGO0477 from Neisseria gonorrhoeae reveals a novel protein fold incorporating a helix-turn-helix motif. Ren J, Sainsbury S, Nettleship JE, Saunders NJ, Owens RJ;. Proteins. 2010;78:1798-1802. (from Pfam) NF013543.5 PF01384.25 PHO4 33.7 33.7 350 domain Y Y N inorganic phosphate transporter GO:0006817,GO:0016020 7732001 131567 cellular organisms no rank 77946 EBI-EMBL Phosphate transporter family inorganic phosphate transporter This family includes PHO-4 from Neurospora crassa which is a is a Na(+)-phosphate symporter [1]. This family also contains the leukaemia virus receptor Swiss:Q08344. [1]. 7732001. Repressible cation-phosphate symporters in Neurospora crassa. Versaw WK, Metzenberg RL;. Proc Natl Acad Sci U S A 1995;92:3884-3887. (from Pfam) NF013544.5 PF01385.24 OrfB_IS605 30.5 30.5 120 domain Y Y N transposase 2553665,7557457,8386127 131567 cellular organisms no rank 144226 EBI-EMBL Probable transposase transposase This family includes IS891 [1], IS1136 [2] and IS1341 [3]. DUF1225, Pfam:PF06774, has now been merged into this family. [1]. 2553665. Characterization of an insertion sequence (IS891) of novel structure from the cyanobacterium Anabaena sp. strain M-131. Bancroft I, Wolk CP;. J Bacteriol 1989;171:5949-5954. [2]. 8386127. IS1136, an insertion element in the erythromycin gene cluster of Saccharopolyspora erythraea. Donadio S, Staver MJ;. Gene 1993;126:147-151. Sequence of IS1341. [3]. 7557457. A novel insertion sequence (IS)-like element of the thermophilic bacterium PS3 promotes expression of the alanine carrier protein-encoding gene. Murai N, Kamata H, Nagashima Y, Yagisawa H, Hirata H;. gene 1995;163:103-107. (from Pfam) NF013555.5 PF01396.24 zf-C4_Topoisom 32 7.5 39 domain Y Y N topoisomerase DNA-binding C4 zinc finger domain-containing protein GO:0003677,GO:0003916,GO:0005694,GO:0006265 2846526,9792804 131567 cellular organisms no rank 78635 EBI-EMBL Topoisomerase DNA binding C4 zinc finger Topoisomerase DNA binding C4 zinc finger NF013557.5 PF01398.26 JAB 22.5 22.5 117 PfamEq Y N N JAB1/Mov34/MPN/PAD-1 ubiquitin protease GO:0005515,GO:0008233,GO:0008237 10369758,12183636,16859499,17506697,20838651,22970855,9150866,9605331,9644972 131567 cellular organisms no rank 3183 EBI-EMBL JAB1/Mov34/MPN/PAD-1 ubiquitin protease JAB1/Mov34/MPN/PAD-1 ubiquitin protease Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain [3] and PAD-1-like domain [4], JABP1 domain [5] or JAMM domain [7]. These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signalling and protein turnover pathways in eukaryotes [7]. Versions of the domain in prokaryotic cognates of the ubiquitin-modification pathway are shown to have a similar role, and the archael protein from Haloferax volcanii is found to cleave ubiquitin-like small archaeal modifier proteins (SAMP1/2) from protein conjugates [8,9]. [1]. 9605331. Homologues of 26S proteasome subunits are regulators of transcription and translation. Aravind L, Ponting CP;. Protein Sci 1998;7:1250-1254. [2]. 9150866. Conservation and diversity in the structure of translation initiation factor EIF3 from humans and yeast. Hershey JW, Asano K, Naranda T, Vornlocher HP, Hanachi P, Merrick WC;. Biochimie 1996;78:903-907. [3]. 9644972. The PCI domain: a common theme in three multiprotein complexes. Hofmann K, Bucher P;. Trends Biochem Sci 1998;23:204-205. [4]. 10369758. Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. Ponting CP, Aravind L, Schultz J, Bork P, Koonin EV;. J Mol Biol 1999;289:729-745. [5]. 20838651. A global census of fission yeast deubiquitinating enzyme localization and interaction networks reveals distinct compartmentalization profiles and overlapping functions in endocytosis and polarity. Kouranti. TRUNCATED at 1650 bytes (from Pfam) NF013558.5 PF01399.32 PCI 22 22 84 domain Y Y N PCI domain-containing protein 17761670,9605331,9644972 131567 cellular organisms no rank 306 EBI-EMBL PCI domain PCI domain This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) [1]. [1]. 9644972. The PCI domain: a common theme in three multiprotein complexes. Hofmann K, Bucher P;. Trends Biochem Sci 1998;23:204-205. [2]. 9605331. Homologues of 26S proteasome subunits are regulators of transcription and translation. Aravind L, Ponting CP;. Protein Sci 1998;7:1250-1254. [3]. 17761670. Isolation of the Schizosaccharomyces pombe proteasome subunit Rpn7 and a structure-function study of the PCI domain. Sha Z, Yen HC, Scheel H, Suo J, Hofmann K, Chang EC;. J Biol Chem. 2007; [Epub ahead of print] (from Pfam) NF013559.5 PF01400.29 Astacin 22.5 22.5 189 domain Y Y N M12 family metallopeptidase GO:0004222,GO:0006508 7674922 131567 cellular organisms no rank 7216 EBI-EMBL Astacin (Peptidase family M12A) M12 family metallopeptidase The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family contain two conserved disulphide bridges, these are joined 1-4 and 2-3. Members of this family have an amino terminal propeptide which is cleaved to give the active protease domain. All other linked domains are found to the carboxyl terminus of this domain. This family includes: Astacin Swiss:P07584, a digestive enzyme from Crayfish. Meprin, Swiss:Q16819, a multiple domain membrane component that is constructed from a homologous alpha and beta chain. Proteins involved in morphogenesis such as Swiss:P13497, and Tolloid from drosophila Swiss:P25723. [1]. 7674922. Evolutionary families of metallopeptidases. Rawlings ND, Barrett AJ;. Meth Enzymol 1995;248:183-228. (from Pfam) NF013561.5 PF01402.26 RHH_1 20.5 20.5 39 domain Y Y N ribbon-helix-helix protein, CopG family GO:0006355 9714164,9857196 131567 cellular organisms no rank 51427 EBI-EMBL Ribbon-helix-helix protein, copG family ribbon-helix-helix protein, CopG family The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement [2]. The helix-turn-helix-like structure is involved in dimerisation and not DNA binding as might have been expected [2]. [1]. 9714164. Structural features of the plasmid pMV158-encoded transcriptional repressor CopG, a protein sharing similarities with both helix-turn-helix and beta-sheet DNA binding proteins. Acebo P, Garcia de Lacoba M, Rivas G, Andreu JM, Espinosa M, del Solar G. Proteins 1998;32:248-261. [2]. 9857196. The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator. Gomis-R th FX, Sol M, Acebo P, Parraga A, Guasch A, Eritja R, Gonzalez A, Espinosa M, del Solar G, Coll M. EMBO J 1998;17:7404-7415. (from Pfam) NF013565.5 PF01406.24 tRNA-synt_1e 27 27 301 domain Y N N tRNA synthetases class I (C) catalytic domain 131567 cellular organisms no rank 155619 EBI-EMBL tRNA synthetases class I (C) catalytic domain tRNA synthetases class I (C) catalytic domain This family includes only cysteinyl tRNA synthetases. (from Pfam) NF013567.5 PF01408.27 GFO_IDH_MocA 24 24 120 domain Y Y N Gfo/Idh/MocA family oxidoreductase GO:0000166,GO:0016491 8994968 131567 cellular organisms no rank 609691 EBI-EMBL Oxidoreductase family, NAD-binding Rossmann fold Gfo/Idh/MocA family oxidoreductase This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot. [1]. 8994968. The structure of glucose-fructose oxidoreductase from Zymomonas mobilis: an osmoprotective periplasmic enzyme containing non-dissociable NADP. Kingston RL, Scopes RK, Baker EN;. Structure 1996;4:1413-1428. (from Pfam) NF013568.5 PF01409.25 tRNA-synt_2d 19.8 19.8 246 domain Y N N tRNA synthetases class II core domain (F) GO:0000049,GO:0004812,GO:0005524,GO:0043039 131567 cellular organisms no rank 76423 EBI-EMBL tRNA synthetases class II core domain (F) tRNA synthetases class II core domain (F) Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only phenylalanyl-tRNA synthetases. This is the core catalytic domain. (from Pfam) NF013570.5 PF01411.24 tRNA-synt_2c 30.3 30.3 552 domain Y Y N alanine--tRNA ligase-related protein GO:0000166,GO:0004813,GO:0005524,GO:0006419 131567 cellular organisms no rank 112787 EBI-EMBL tRNA synthetases class II (A) alanine--tRNA ligase-related protein Proteins belonging to this family include alanine--tRNA ligases and related smaller proteins such as alanyl-tRNA editing proteins. NF013575.5 PF01416.25 PseudoU_synth_1 23.3 23.3 108 PfamEq Y N N tRNA pseudouridine synthase GO:0001522,GO:0003723,GO:0009451,GO:0009982 9585540 131567 cellular organisms no rank 78656 EBI-EMBL tRNA pseudouridine synthase tRNA pseudouridine synthase Involved in the formation of pseudouridine at the anticodon stem and loop of transfer-RNAs Pseudouridine is an isomer of uridine (5-(beta-D-ribofuranosyl) uracil, and id the most abundant modified nucleoside found in all cellular RNAs. The TruA-like proteins also exhibit a conserved sequence with a strictly conserved aspartic acid, likely involved in catalysis. [1]. 9585540. Transfer RNA-pseudouridine synthetase Pus1 of Saccaromyces cerevisiae contains one atom of zinc essential for its native conformation and tRNA recognition. Arluison V, Hountondji C, Robert B, Grosjean H;. Biochemistry 1998;37:7268-7276. (from Pfam) NF013578.5 PF01419.22 Jacalin 22 22 136 domain Y Y N jacalin-like lectin 8673603 131567 cellular organisms no rank 3464 EBI-EMBL Jacalin-like lectin domain jacalin-like lectin domain Proteins containing this domain are lectins. It is found in 1 to 6 copies in these proteins. The domain is also found in the animal prostatic spermine-binding protein (Swiss:P15501). [1]. 8673603. A novel mode of carbohydrate recognition in jacalin, a Moraceae plant lectin with a beta-prism fold. Sankaranarayanan R, Sekar K, Banerjee R, Sharma V, Surolia A, Vijayan M;. Nat Struct Biol 1996;3:596-603. (from Pfam) NF013579.5 PF01420.24 Methylase_S 22 22 168 domain Y Y N restriction endonuclease subunit S 3.1.21.- GO:0003677,GO:0006304 8336674,9837717 131567 cellular organisms no rank 173497 EBI-EMBL Type I restriction modification DNA specificity domain Type I restriction modification DNA specificity domain This domain is also known as the target recognition domain (TRD). Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity subunit (this family), two modification (M) subunits and two restriction (R) subunits [2]. [1]. 8336674. Biology of DNA restriction. Bickle TA, Kruger DH;. Microbiol Rev 1993;57:434-450. [2]. 9837717. The DNA recognition subunit of the type IB restriction-modification enzyme EcoAI tolerates circular permutions of its polypeptide chain. Janscak P, Bickle TA;. J Mol Biol 1998;284:937-948. (from Pfam) NF013582.5 PF01423.27 LSM 23.4 23.4 66 domain Y Y N LSM domain-containing protein 10025403,10428970,10677490,10809669,12438310,7744013 131567 cellular organisms no rank 1498 EBI-EMBL LSM domain LSM domain The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings. [1]. 7744013. snRNP Sm proteins share two evolutionarily conserved sequence motifs which are involved in Sm protein-protein interactions. Hermann H, Fabrizio P, Raker VA, Foulaki K, Hornig H, Brahms H, Luhrmann R. EMBO J 1995;14:2076-2088. [2]. 10025403. Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. Kambach C, Walke S, Young R, Avis JM, de la Fortelle E, Raker VA, Luhrmann R, Li J, Nagai K;. Cell 1999;96:375-387. [3]. 10428970. Characterization of Sm-like proteins in yeast and their association with U6 snRNA. Mayes AE, Verdone L, Legrain P, Beggs JD;. EMBO J 1999;18:4321-4331. [4]. 10677490. Host factor Hfq of Escherichia coli stimulates elongation of poly(A) tails by poly(A) polymerase I. Hajnsdorf E, Regnier P;. Proc Natl Acad Sci U S A 2000;97:1501-1505. [5]. 10809669. Hfq (. TRUNCATED at 1650 bytes (from Pfam) NF013583.5 PF01424.27 R3H 26.8 26.8 60 domain Y Y N R3H domain-containing nucleic acid-binding protein GO:0003676 9787637 131567 cellular organisms no rank 27271 EBI-EMBL R3H domain R3H domain Most bacterial proteins with this domain (R3H) at the C-terminus have a KH domain at the N-terminus plus additional regions of homology, and may be referred to as JAG (spoIIIJ Associated Gene), after proteins described in Bacillus subtilis and Streptococcus pneumoniae. The S. pneumoniae protein, a phosphoprotein, is also called RNA-binding cell elongation regulator EloR. NF013584.5 PF01425.26 Amidase 27 27 445 domain Y Y N amidase family protein 131567 cellular organisms no rank 309536 EBI-EMBL Amidase amidase family protein NF013586.5 PF01427.22 Peptidase_M15 27 27 199 domain Y Y N M15 family metallopeptidase GO:0006508,GO:0008237,GO:0016805 9702193 131567 cellular organisms no rank 33612 EBI-EMBL D-ala-D-ala dipeptidase M15 family metallopeptidase NF013587.5 PF01428.21 zf-AN1 27.9 27.9 40 domain Y Y N AN1-type zinc finger domain-containing protein GO:0008270 8390387 131567 cellular organisms no rank 962 EBI-EMBL AN1-like Zinc finger AN1-like Zinc finger Zinc finger at the C-terminus of An1 Swiss:Q91889, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues. [1]. 8390387. Two related localized mRNAs from Xenopus laevis encode ubiquitin-like fusion proteins. Linnen JM, Bailey CP, Weeks DL;. Gene 1993;128:181-188. (from Pfam) NF013590.5 PF01431.26 Peptidase_M13 24.5 24.5 205 domain Y Y N M13-type metalloendopeptidase 3.4.24.- GO:0004222,GO:0006508 7674922 131567 cellular organisms no rank 49165 EBI-EMBL Peptidase family M13 M13-type metalloendopeptidase domain Mammalian enzymes are typically type-II membrane anchored enzymes which are known, or believed to activate or inactivate oligopeptide (pro)-hormones such as opioid peptides. The family also contains a bacterial member believed to be involved with milk protein cleavage. [1]. 7674922. Evolutionary families of metallopeptidases. Rawlings ND, Barrett AJ;. Meth Enzymol 1995;248:183-228. (from Pfam) NF013591.5 PF01432.25 Peptidase_M3 27 27 457 domain Y Y N M3 family metallopeptidase GO:0004222,GO:0006508 7674922 131567 cellular organisms no rank 148962 EBI-EMBL Peptidase family M3 M3 family metallopeptidase domain This is the Thimet oligopeptidase family, large family of mammalian and bacterial oligopeptidases that cleave medium sized peptides. The group also contains mitochondrial intermediate peptidase which is encoded by nuclear DNA but functions within the mitochondria to remove the leader sequence. [1]. 7674922. Evolutionary families of metallopeptidases. Rawlings ND, Barrett AJ;. Meth Enzymol 1995;248:183-228. (from Pfam) NF013592.5 PF01433.25 Peptidase_M1 27.7 27.7 218 domain Y Y N M1 family aminopeptidase GO:0008237,GO:0008270 7674922 131567 cellular organisms no rank 194548 EBI-EMBL Peptidase family M1 domain M1 family aminopeptidase domain The M1 family metalloproteases in this family are zinc-dependent enzymes with aminopeptidase activity. NF013594.5 PF01435.23 Peptidase_M48 20.3 20.3 186 domain Y Y N M48 family metalloprotease 3.4.24.- GO:0004222,GO:0006508 23539602,23539603 131567 cellular organisms no rank 243194 EBI-EMBL Peptidase family M48 M48 family metalloprotease Peptidase_M48 is the largely extracellular catalytic region of CAAX prenyl protease homologues such as Human FACE-1 protease. These are metallopeptidases, with the characteristic HExxH motif giving the two histidine-zinc-ligands and an adjacent glutamate on the next helix being the third. The whole molecule folds to form a deep groove/cleft into which the substrate can fit [1,2]. [1]. 23539602. Structure of the integral membrane protein CAAX protease Ste24p. Pryor EE Jr, Horanyi PS, Clark KM, Fedoriw N, Connelly SM, Koszelak-Rosenblum M, Zhu G, Malkowski MG, Wiener MC, Dumont ME;. Science. 2013;339:1600-1604. [2]. 23539603. The structural basis of ZMPSTE24-dependent laminopathies. Quigley A, Dong YY, Pike AC, Dong L, Shrestha L, Berridge G, Stansfeld PJ, Sansom MS, Edwards AM, Bountra C, von Delft F, Bullock AN, Burgess-Brown NA, Carpenter EP;. Science. 2013;339:1604-1607. (from Pfam) NF013595.5 PF01436.26 NHL 20 20 28 repeat Y N N NHL repeat protein GO:0005515 1894599,7778269,9868369 131567 cellular organisms no rank 35531 EBI-EMBL NHL repeat NHL repeat The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat Pfam:PF00400. The repeats have a catalytic activity in Swiss:P10731, proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats [2]. Swiss:Q13049 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats [3]. [1]. 9868369. A novel repeat domain that is often associated with RING finger and B-box motifs. Slack FJ, Ruvkun G;. Trends Biochem Sci 1998;23:474-475. [2]. 1894599. The membrane-bound bifunctional peptidylglycine alpha-amidating monooxygenase protein. Exploration of its domain structure through limited proteolysis. Husten EJ, Eipper BA;. J Biol Chem 1991;266:17004-17010. [3]. 7778269. Identification of a novel human zinc finger protein that specifically interacts with the activation domain of lentiviral Tat proteins. Fridell RA, Harding LS, Bogerd HP, Cullen BR;. Virology 1995;209:347-357. (from Pfam) NF013601.5 PF01443.23 Viral_helicase1 21 21 228 domain Y N N Viral (Superfamily 1) RNA helicase GO:0005524 10217401,10982322,8057461,8269709 131567 cellular organisms no rank 83993 EBI-EMBL Viral (Superfamily 1) RNA helicase Viral (Superfamily 1) RNA helicase Helicase activity for this family has been demonstrated [1] and NTPase activity [2]. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [3]. This family is discussed pages 388-391. [1]. 8269709. Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Koonin EV, Dolja VV;. Crit Rev Biochem Mol Biol 1993;28:375-430. [2]. 10217401. RNA helicase activity of Semliki Forest virus replicase protein NSP2. Gomez de Cedron M, Ehsani N, Mikkola ML, Garcia JA, Kaariainen L;. FEBS Lett 1999;448:19-22. [3]. 8057461. ATPase and GTPase activities associated with Semliki Forest virus nonstructural protein nsP2. Rikkonen M, Peranen J, Kaariainen L;. J Virol 1994;68:5804-5810. [4]. 10982322. Helicase and capping enzyme active site mutations in brome mosaic virus protein 1a cause defects in template recruitment, negative-strand RNA synthesis, and viral RNA capping. Ahola T, den Boon JA, Ahlquist P;. J Virol 2000;74:8803-8811. (from Pfam) NF013604.5 PF01447.23 Peptidase_M4 22.4 22.4 145 domain Y N N Thermolysin metallopeptidase, catalytic domain GO:0004222 7674922,9753696 131567 cellular organisms no rank 70858 EBI-EMBL Thermolysin metallopeptidase, catalytic domain Thermolysin metallopeptidase, catalytic domain NF013606.5 PF01450.24 IlvC 29.1 29.1 144 PfamEq Y N N Acetohydroxy acid isomeroreductase, catalytic domain GO:0004455,GO:0009082 9218783 131567 cellular organisms no rank 52360 EBI-EMBL Acetohydroxy acid isomeroreductase, catalytic domain Acetohydroxy acid isomeroreductase, catalytic domain Acetohydroxy acid isomeroreductase catalyses the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine. [1]. 9218783. The crystal structure of plant acetohydroxy acid isomeroreductase complexed with NADPH, two magnesium ions and a herbicidal transition state analog determined at 1.65 A resolution. Biou V, Dumas R, Cohen-Addad C, Douce R, Job D, Pebay-Peyroula E;. EMBO J 1997;16:3405-3415. (from Pfam) NF013607.5 PF01451.26 LMWPc 23.2 23.2 144 domain Y N N Low molecular weight phosphotyrosine protein phosphatase 8052313 131567 cellular organisms no rank 148206 EBI-EMBL Low molecular weight phosphotyrosine protein phosphatase Low molecular weight phosphotyrosine protein phosphatase NF013611.5 PF01455.23 HupF_HypC 28.5 28.5 65 domain Y Y N HypC/HybG/HupF family hydrogenase formation chaperone 131567 cellular organisms no rank 19544 EBI-EMBL HupF/HypC family HypC/HybG/HupF family hydrogenase formation chaperone NF013613.5 PF01457.21 Peptidase_M8 21 21 529 domain Y Y N leishmanolysin-related zinc metalloendopeptidase GO:0004222,GO:0006508,GO:0007155,GO:0016020 7674922 131567 cellular organisms no rank 1077 EBI-EMBL Leishmanolysin leishmanolysin-related zinc metalloendopeptidase Members of this family, called M8 by MEROPS, have the typical HExxH motif of metalloendopeptidases and share homology with leishmanolysin, from a eukaryotic parasite. NF013614.5 PF01458.22 SUFBD 27 27 218 domain Y Y N SufD family Fe-S cluster assembly protein GO:0016226 15278785,16221578,17350000,17350958,20857974,26472926 131567 cellular organisms no rank 106725 EBI-EMBL SUF system FeS cluster assembly, SufBD SufD family Fe-S cluster assembly protein Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] [1]. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA [2]. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. SufA is homologous to IscA [3], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. This entry represents SufB and SufD proteins, which are homologous, and form part of the SufBCD complex in . TRUNCATED at 1650 bytes (from Pfam) NF013621.5 PF01467.31 CTP_transf_like 21 21 133 domain Y N N Cytidylyltransferase-like GO:0003824,GO:0009058 10208837 131567 cellular organisms no rank 225341 EBI-EMBL Cytidylyltransferase-like Cytidylyltransferase-like This family includes: Cholinephosphate cytidylyltransferase Swiss:P49585; glycerol-3-phosphate cytidylyltransferase Swiss:P27623. It also includes putative adenylyltransferases, and FAD synthases. [1]. 10208837. CTP:Phosphocholine Cytidylyltransferase: Insights into Regulatory Mechanisms and Novel Functions. Clement JM, Kent C;. Biochem Biophys Res Commun 1999;257:643-650. (from Pfam) NF013624.5 PF01470.22 Peptidase_C15 22.7 22.7 204 domain Y N N Pyroglutamyl peptidase 10196127 131567 cellular organisms no rank 22173 EBI-EMBL Pyroglutamyl peptidase Pyroglutamyl peptidase NF013625.5 PF01471.23 PG_binding_1 23 23 57 domain Y Y N peptidoglycan-binding protein 1683402,17697255,7121588,7656014 131567 cellular organisms no rank 258267 EBI-EMBL Putative peptidoglycan binding domain Putative peptidoglycan binding domain This domain is composed of three alpha helices [1]. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [2]. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins [3]. The domain is found to bind peptidoglycan experimentally [4]. This paper gives the crystal structure for this domain. However no function is given for this domain. [1]. 7121588. Structure of a Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase at 2.5 A resolution. Dideberg O, Charlier P, Dive G, Joris B, Frere JM, Ghuysen JM;. Nature 1982;299:469-470. [2]. 1683402. Cloning, expression, sequence analysis and biochemical characterization of an autolytic amidase of Bacillus subtilis 168 trpC2. Foster SJ;. J Gen Microbiol 1991;137:1987-1998. [3]. 7656014. The NMR structure of the inhibited catalytic domain of human stromelysin-1. Gooley PR, O'Connell JF, Marcy AI, Cuca GC, Salowe SP, Bush BL, Hermes JD, Esser CK, Hagmann WK, Springer JP, et al;. Nat Struct Biol 1994;1:111-118. [4]. 17697255. Muralytic activity and modular structure of the endolysins of Pseudomonas aeruginosa bacteriophages phiKZ and EL. Briers Y, Volckaert G, Cornelissen A, Lagaert S, Michiels CW, Hertveldt K, Lavigne R;. Mol Microbiol. 2007;65:1334-1344. (from Pfam) NF013626.5 PF01472.25 PUA 24.8 24.8 74 domain Y Y N PUA domain-containing protein GO:0003723 10093218 131567 cellular organisms no rank 56566 EBI-EMBL PUA domain PUA domain The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes [1]. It is predicted that the PUA domain is an RNA binding domain. [1]. 10093218. Novel predicted RNA-binding domains associated with the translation machinery. Aravind L, Koonin EV;. J Mol Evol 1999;48:291-302. (from Pfam) NF013629.5 PF01475.24 FUR 23.1 23.1 121 domain Y Y N transcriptional repressor GO:0003700,GO:0006355 9784364 131567 cellular organisms no rank 123248 EBI-EMBL Ferric uptake regulator family transcriptional repressor This family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes. This family is also known as the FUR family. [1]. 9784364. Binding of the fur (ferric uptake regulator) repressor of Escherichia coli to arrays of the GATAAT sequence. Escolar L, Perez-Martin J, de Lorenzo V;. J Mol Biol 1998;283:537-547. (from Pfam) NF013631.5 PF01477.28 PLAT 23 23 117 domain Y Y N PLAT/LH2 domain-containing protein GO:0005515 131567 cellular organisms no rank 1074 EBI-EMBL PLAT/LH2 domain PLAT/LH2 domain This domain is found in a variety of membrane or lipid associated proteins. It is called the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain. The known structure of pancreatic lipase shows this domain binds to procolipase Pfam:PF01114, which mediates membrane association. So it appears possible that this domain mediates membrane attachment via other protein binding partners. The structure of this domain is known for many members of the family and is composed of a beta sandwich. (from Pfam) NF013632.5 PF01478.23 Peptidase_A24 26.5 26.5 104 domain Y Y N prepilin peptidase 3.4.23.43 GO:0004190,GO:0016020 10625704,12813086 131567 cellular organisms no rank 97308 EBI-EMBL Type IV leader peptidase family prepilin peptidase Peptidase A24, or the prepilin peptidase as it is also known, processes the N-terminus of the prepilins [1]. The processing is essential for the correct formation of the pseudopili of type IV bacterial protein secretion. The enzyme is found across eubacteria and archaea [2]. [1]. 10625704. The type 4 prepilin peptidases comprise a novel family of aspartic acid proteases. LaPointe CF, Taylor RK;. J Biol Chem 2000;275:1502-1510. [2]. 12813086. Archaeal homolog of bacterial type IV prepilin signal peptidases with broad substrate specificity. Albers SV, Szabo Z, Driessen AJ;. J Bacteriol 2003;185:3918-3925. (from Pfam) NF013633.5 PF01479.30 S4 22.8 22.8 48 domain Y Y N S4 domain-containing protein GO:0003723 10093218,9707415 131567 cellular organisms no rank 376559 EBI-EMBL S4 domain S4 domain The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA. [1]. 10093218. Novel predicted RNA-binding domains associated with the translation machinery. Aravind L, Koonin EV;. J Mol Evol 1999;48:291-302. [2]. 9707415. The crystal structure of ribosomal protein S4 reveals a two-domain molecule with an extensive RNA-binding surface: one domain shows structural homology to the ETS DNA-binding motif. Davies C, Gerstner RB, Draper DE, Ramakrishnan V, White SW;. EMBO J 1998;17:4545-4558. (from Pfam) NF013636.5 PF01483.25 P_proprotein 21 21 86 domain Y Y N proprotein convertase P-domain-containing protein GO:0004252,GO:0006508 8194519,9556596 131567 cellular organisms no rank 41414 EBI-EMBL Proprotein convertase P-domain Proprotein convertase P-domain A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain. [1]. 8194519. A C-terminal domain conserved in precursor processing proteases is required for intramolecular N-terminal maturation of pro-Kex2 protease. Gluschankof P, Fuller RS;. EMBO J 1994;13:2280-2288. [2]. 9556596. Regulatory roles of the P domain of the subtilisin-like prohormone convertases. Zhou A, Martin S, Lipkind G, LaMendola J, Steiner DF;. J Biol Chem 1998;273:11107-11114. (from Pfam) NF013638.5 PF01485.26 IBR 24.3 24.3 65 domain Y Y N IBR domain-containing protein GO:0008270 10366851,10422847,12446796,15152079,15236971 131567 cellular organisms no rank 21 EBI-EMBL IBR domain, a half RING-finger domain IBR domain, a half RING-finger domain The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (Pfam:PF00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain [2]. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organisms. RBR family members play roles in protein quality control and can indirectly regulate transcription [3]. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease [3][4]. Discovery of IBR domain. [1]. 10366851. A novel transactivation domain in parkin. Morett E, Bork P;. Trends Biochem Sci 1999;24:229-231. [2]. 10422847. TRIADs: a new class of proteins with a novel cysteine-rich signature. van der Reijden BA, Erpelinck-Verschueren CA, Lowenberg B, Jansen JH;. Protein Sci 1999;8:1557-1561. [3]. 15152079. Parkin and relatives: the RBR family of ubiquitin ligases. Marin I, Lucas JI, Gradilla AC, Ferrus A;. Physiol Genomics 2004;17:253-263. [4]. 12446796. Comparative genomics of the RBR family, including the Parkinson's disease-related gene parkin and the genes of the ariadne subfamily. Marin I, Ferrus A;. Mol Biol Evol 2002;19:2039-2050. [5]. 15236971. Structure of the C-terminal RING finger from a RING-IBR-RING/TRIAD motif reveals a novel zinc-binding domain distinct from a RING. Capili AD, Edghill EL, Wu K, Borden KL;. J Mol Biol. 2004;340:1117-1129. (from Pfam) NF013640.5 PF01487.20 DHquinase_I 22.2 22.2 230 PfamEq Y Y N type I 3-dehydroquinate dehydratase 4.2.1.10 GO:0003855 10360352,7556173 131567 cellular organisms no rank 17614 EBI-EMBL Type I 3-dehydroquinase type I 3-dehydroquinate dehydratase Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase.) Catalyses the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate giving dehydroshikimate. Dehydroquinase functions in the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Type II 3-dehydroquinase catalyses the trans-dehydration of 3-dehydroshikimate see Pfam:PF01220. [1]. 10360352. The two types of 3-dehydroquinase have distinct structures but catalyze the same overall reaction. Gourley DG, Shrive AK, Polikarpov I, Krell T, Coggins JR, Hawkins AR, Isaacs NW, Sawyer L;. Nat Struct Biol 1999;6:521-525. Discusses the pentafunctional AROM multi-domain protein, which possesses a Type I 3-dehydroquinase enzyme. The AROM protein catalyses steps two to six in the shikimate pathway in many microbial eukaryotes. [2]. 7556173. The molecular biology of multidomain proteins. Selected examples. Hawkins AR, Lamb HK;. Eur J Biochem 1995;232:7-18. (from Pfam) NF013641.5 PF01488.25 Shikimate_DH 24.3 24.3 138 domain Y N N Shikimate / quinate 5-dehydrogenase 7556173 131567 cellular organisms no rank 213338 EBI-EMBL Shikimate / quinate 5-dehydrogenase Shikimate / quinate 5-dehydrogenase This family contains both shikimate and quinate dehydrogenases. Shikimate 5-dehydrogenase catalyses the conversion of shikimate to 5-dehydroshikimate. This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Quinate 5-dehydrogenase catalyses the conversion of quinate to 5-dehydroquinate. This reaction is part of the quinate pathway where quinic acid is exploited as a source of carbon in prokaryotes and microbial eukaryotes. Both the shikimate and quinate pathways share two common pathway metabolites 3-dehydroquinate and dehydroshikimate. Discusses the pentafunctional AROM multi-domain protein, which possesses a shikimate 5-dehydrogenase enzyme. The AROM protein catalyses steps two to six in the shikimate pathway in many microbial eukaryotes. [1]. 7556173. The molecular biology of multidomain proteins. Selected examples. Hawkins AR, Lamb HK;. Eur J Biochem 1995;232:7-18. (from Pfam) NF013645.5 PF01493.24 GXGXG 32.5 32.5 190 domain Y N N GXGXG motif GO:0016491 9818358 131567 cellular organisms no rank 93659 EBI-EMBL GXGXG motif GXGXG motif This domain is found in glutamate synthase, tungsten formylmethanofuran dehydrogenase subunit c (FwdC) and molybdenum formylmethanofuran dehydrogenase subunit c (FmdC). A repeated G-XX-G-XXX-G motif is seen in the alignment. [1]. 9818358. The formylmethanofuran dehydrogenase isoenzymes in Methanobacterium wolfei and Methanobacterium thermoautotrophicum: induction of the molybdenum isoenzyme by molybdate and constitutive synthesis of the tungsten isoenzyme. Hochheimer A, Hedderich R, Thauer RK;. Arch Microbiol 1998;170:389-393. (from Pfam) NF013646.5 PF01494.24 FAD_binding_3 22 22 349 domain Y Y N FAD-dependent monooxygenase GO:0071949 1409567 131567 cellular organisms no rank 929163 EBI-EMBL FAD binding domain FAD binding domain This domain is involved in FAD binding in a number of enzymes. [1]. 1409567. Crystal structure of the reduced form of p-hydroxybenzoate hydroxylase refined at 2.3A resolution. Schreuder HA, van der Laan JM, Swarte MB, Kalk KH, Hol WG, Drenth J;. Proteins 1992;14:178-190. (from Pfam) NF013647.5 PF01496.24 V_ATPase_I 30.7 30.7 815 domain Y Y N V-type ATPase 116kDa subunit family protein GO:0015078,GO:0033179,GO:0046961,GO:1902600 10224039,10340849 131567 cellular organisms no rank 12299 EBI-EMBL V-type ATPase 116kDa subunit family V-type ATPase 116kDa subunit family protein This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes [1]. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal [1,2]. It has roles in proton transport and assembly of the V-type ATPase complex [1,2]. This subunit is encoded by two homologous gene in yeast VPH1 and STV1 [2]. Mini-review. [1]. 10224039. Structure and properties of the vacuolar (H+)-ATPases. Forgac M;. J Biol Chem 1999;274:12951-12954. [2]. 10340849. Structure and properties of the clathrin-coated vesicle and yeast vacuolar V-ATPases. Forgac M;. J Bioenerg Biomembr 1999;31:57-65. (from Pfam) NF013648.5 PF01497.23 Peripla_BP_2 27.5 27.5 235 domain Y Y N ABC transporter substrate-binding protein 12475936,14514690,2651410 131567 cellular organisms no rank 355305 EBI-EMBL Periplasmic binding protein ABC transporter substrate-binding protein This is sensor domain found in bacterial periplasmic binding proteins, several of which are involved in iron and cobalamin transport [1,2,3]. Among its ligands are siderophores bacillibactin, enterobactin and iron(III)-hydroxamates (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1 https://doi.org/10.1093/femsre/fuab043). [1]. 2651410. Nucleotide sequences of the fecBCDE genes and locations of the proteins suggest a periplasmic-binding-protein-dependent transport mechanism for iron(III) dicitrate in Escherichia coli. Staudenmaier H, Van Hove B, Yaraghi Z, Braun V;. J Bacteriol 1989;171:2626-2633. [2]. 12475936. The structure of Escherichia coli BtuF and binding to its cognate ATP binding cassette transporter. Borths EL, Locher KP, Lee AT, Rees DC;. Proc Natl Acad Sci U S A. 2002;99:16642-16647. [3]. 14514690. The role of FhuD2 in iron(III)-hydroxamate transport in Staphylococcus aureus. Demonstration that FhuD2 binds iron(III)-hydroxamates but with minimal conformational change and implication of mutations on transport. Sebulsky MT, Shilton BH, Speziali CD, Heinrichs DE;. J Biol Chem. 2003;278:49890-49900. (from Pfam) NF013652.5 PF01501.25 Glyco_transf_8 24.3 24.3 253 domain Y Y N glycosyltransferase GO:0016757 15564529 131567 cellular organisms no rank 52460 EBI-EMBL Glycosyl transferase family 8 glycosyltransferase This family includes enzymes that transfer sugar residues to donor molecules. Members of this family are involved in lipopolysaccharide biosynthesis and glycogen synthesis. This family includes Lipopolysaccharide galactosyltransferase Swiss:P27128, lipopolysaccharide glucosyltransferase 1 Swiss:P27129, and glycogenin glucosyltransferase Swiss:P46976. (from Pfam) NF013653.5 PF01502.23 PRA-CH 27 27 74 domain Y Y N phosphoribosyl-AMP cyclohydrolase GO:0000105,GO:0004635 9931020 131567 cellular organisms no rank 58804 EBI-EMBL Phosphoribosyl-AMP cyclohydrolase phosphoribosyl-AMP cyclohydrolase This enzyme catalyses the third step in the histidine biosynthetic pathway. It requires Zn ions for activity. [1]. 9931020. N1-(5'-phosphoribosyl)adenosine-5'-monophosphate cyclohydrolase: purification and characterization of a unique metalloenzyme. D'Ordine RL, Klem TJ, Davisson VJ;. Biochemistry 1999;38:1537-1546. (from Pfam) NF013654.5 PF01503.22 PRA-PH 21.3 21.3 86 domain Y N N Phosphoribosyl-ATP pyrophosphohydrolase 3528746,379004 131567 cellular organisms no rank 91291 EBI-EMBL Phosphoribosyl-ATP pyrophosphohydrolase Phosphoribosyl-ATP pyrophosphohydrolase This enzyme catalyses the second step in the histidine biosynthetic pathway. [1]. 379004. The product of the his4 gene cluster in Saccharomyces cerevisiae. A trifunctional polypeptide. Keesey JK Jr, Bigelis R, Fink GR;. J Biol Chem 1979;254:7427-7433. [2]. 3528746. Primary and secondary structural homologies between the HIS4 gene product of Saccharomyces cerevisiae and the hisIE and hisD gene products of Escherichia coli and Salmonella typhimurium. Bruni CB, Carlomagno MS, Formisano S, Paolella G;. Mol Gen Genet 1986;203:389-396. (from Pfam) NF013658.5 PF01507.24 PAPS_reduct 22.5 22.5 175 domain Y Y N phosphoadenosine phosphosulfate reductase family protein GO:0003824 2250719,7588765,9261082 131567 cellular organisms no rank 124506 EBI-EMBL Phosphoadenosine phosphosulfate reductase family phosphoadenosine phosphosulfate reductase family protein This domain is found in phosphoadenosine phosphosulfate (PAPS) reductase enzymes or PAPS sulfotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases [1]. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) [1,2]. It is also found in NodP nodulation protein P from Rhizobium which has ATP sulfurylase activity (sulfate adenylate transferase) [3]. [1]. 9261082. Crystal structure of phosphoadenylyl sulphate (PAPS) reductase: a new family of adenine nucleotide alpha hydrolases. Savage H, Montoya G, Svensson C, Schwenn JD, Sinning I;. Structure 1997;5:895-906. [2]. 7588765. Reaction mechanism of thioredoxin: 3'-phospho-adenylylsulfate reductase investigated by site-directed mutagenesis. Berendt U, Haverkamp T, Prior A, Schwenn JD;. Eur J Biochem 1995;233:347-356. [3]. 2250719. ATP sulphurylase activity of the nodP and nodQ gene products of Rhizobium meliloti. Schwedock J, Long SR;. Nature 1990;348:644-647. (from Pfam) NF013660.5 PF01509.23 TruB_N 27.3 27.3 149 PfamEq Y N N TruB family pseudouridylate synthase (N terminal domain) GO:0006396 7489483,9472021 131567 cellular organisms no rank 74930 EBI-EMBL TruB family pseudouridylate synthase (N terminal domain) TruB family pseudouridylate synthase (N terminal domain) Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA [2]. [1]. 7489483. Purification, cloning, and properties of the tRNA psi 55 synthase from Escherichia coli. Nurse K, Wrzesinski J, Bakin A, Lane BG, Ofengand J;. RNA 1995;1:102-112. [2]. 9472021. The box H + ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. Lafontaine DLJ, Bousquet-Antonelli C, Henry Y, Caizergues-Ferrer M, Tollervey D;. Genes Dev 1998;12:527-537. (from Pfam) NF013661.5 PF01510.30 Amidase_2 26 26 131 domain Y Y N N-acetylmuramoyl-L-alanine amidase 3.5.1.28 GO:0008745,GO:0009253 1677905,3070348,8171031 131567 cellular organisms no rank 173855 EBI-EMBL N-acetylmuramoyl-L-alanine amidase N-acetylmuramoyl-L-alanine amidase This family includes zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity EC:3.5.1.28. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala). The structure is known for the bacteriophage T7 structure and shows that two of the conserved histidines are zinc binding. This reference shows that the amino terminal region of Swiss:P14892 is required for bacteriolytic activity. [1]. 3070348. Cloning, sequencing and expression of a Bacillus bacteriolytic enzyme in Escherichia coli. Potvin C, Leclerc D, Tremblay G, Asselin A, Bellemare G;. Mol Gen Genet 1988;214:241-248. [2]. 1677905. Sequence analysis of a Staphylococcus aureus gene encoding a peptidoglycan hydrolase activity. Wang X, Wilkinson BJ, Jayaswal RK;. Gene 1991;102:105-109. [3]. 8171031. The structure of bacteriophage T7 lysozyme, a zinc amidase and an inhibitor of T7 RNA polymerase. Cheng X, Zhang X, Pflugrath JW, Studier FW;. Proc Natl Acad Sci U S A 1994;91:4034-4038. (from Pfam) NF013662.5 PF01512.22 Complex1_51K 31.2 31.2 150 domain Y N N Respiratory-chain NADH dehydrogenase 51 Kd subunit 131567 cellular organisms no rank 121905 EBI-EMBL Respiratory-chain NADH dehydrogenase 51 Kd subunit Respiratory-chain NADH dehydrogenase 51 Kd subunit NF013663.5 PF01513.26 NAD_kinase 25.5 25.5 130 domain Y Y N NAD(+)/NADH kinase GO:0003951,GO:0006741 131567 cellular organisms no rank 83503 EBI-EMBL ATP-NAD kinase N-terminal domain ATP-NAD kinase N-terminal domain Members of this family include ATP-NAD kinases EC:2.7.1.23, which catalyses the phosphorylation of NAD to NADP utilising ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus. Also includes NADH kinases EC:2.7.1.86. (from Pfam) NF013665.5 PF01515.24 PTA_PTB 24 24 319 subfamily Y Y N phosphate acyltransferase GO:0016746 131567 cellular organisms no rank 108015 EBI-EMBL Phosphate acetyl/butaryl transferase phosphate acyltransferase This family contains phosphate acetyltransferases (EC 2.3.1.8) but also several other related enzymes such as phosphate butyryltransferase (EC 2.3.1.19). NF013670.5 PF01520.23 Amidase_3 27 27 174 domain Y Y N N-acetylmuramoyl-L-alanine amidase 3.5.1.28 GO:0008745,GO:0009253 1495475 131567 cellular organisms no rank 144070 EBI-EMBL N-acetylmuramoyl-L-alanine amidase N-acetylmuramoyl-L-alanine amidase This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls. Characterisation of Swiss:P37134. [1]. 1495475. Genetic structure, isolation and characterization of a Bacillus licheniformis cell wall hydrolase. Kuroda A, Sugimoto Y, Funahashi T, Sekiguchi J;. Mol Gen Genet 1992;234:129-137. (from Pfam) NF013671.5 PF01521.25 Fe-S_biosyn 26.3 26.3 110 domain Y Y N iron-sulfur cluster biosynthesis family protein 10217509,11941510,12207230 131567 cellular organisms no rank 66616 EBI-EMBL Iron-sulphur cluster biosynthesis iron-sulfur cluster biosynthesis family protein This family is involved in iron-sulphur cluster biosynthesis [3]. Its members include proteins that are involved in nitrogen fixation such as the HesB and HesB-like proteins [1] [2]. [1]. 10217509. Organization and expression of nitrogen-fixation genes in the aerobic nitrogen-fixing unicellular cyanobacterium Synechococcus sp. strain RF-1. Huang TC, Lin RF, Chu MK, Chen HM;. Microbiology 1999;145:743-753. [2]. 12207230. The Rhizobium etli gene iscN is highly expressed in bacteroids and required for nitrogen fixation. Dombrecht B, Tesfay MZ, Verreth C, Heusdens C, Napoles MC, Vanderleyden J, Michiels J;. Mol Genet Genomics 2002;267:820-828. [3]. 11941510. Iron-sulfur cluster biosynthesis: characterization of Schizosaccharomyces pombe Isa1. Wu G, Mansy SS, Hemann C, Hille R, Surerus KK, Cowan JA;. J Biol Inorg Chem 2002;7:526-532. (from Pfam) NF013672.5 PF01522.26 Polysacc_deac_1 23.1 23.1 124 domain Y Y N polysaccharide deacetylase family protein GO:0005975,GO:0016810 8170399,9133736,9163424 131567 cellular organisms no rank 331421 EBI-EMBL Polysaccharide deacetylase polysaccharide deacetylase family protein This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase [1]. It also includes chitin deacetylase from yeast [2], and endoxylanases which hydrolyses glucosidic bonds in xylan [3]. [1]. 9163424. Molecular basis of symbiosis between Rhizobium and legumes. Freiberg C, Fellay R, Bairoch A, Broughton WJ, Rosenthal A, Perret X;. Nature 1997;387:394-401. [2]. 9133736. Cloning and expression of two chitin deacetylase genes of Saccharomyces cerevisiae. C. Mishra, C. E. Semino, K. J. McCreath, H. de la Vega, B. J. Jones, C. A. Specht & P. W. Robbins;. Yeast 1996;13:327-336. [3]. 8170399. Evidence for a general role for high-affinity non-catalytic cellulose binding domains in microbial plant cell wall hydrolases. S. J. Millward-Sadler, D. M. Poole, B. Henrissat, G. P. Hazlewood, J. H. Clarke & H. J. Gilbert;. Mol Microbiol 1994;11:375-382. (from Pfam) NF013673.5 PF01523.21 PmbA_TldD_1st 20.9 20.9 65 domain Y Y N PmbA/TldA family metallopeptidase GO:0006508,GO:0008237 12029038,22950735,28943336 131567 cellular organisms no rank 91547 EBI-EMBL PmbA/TldA metallopeptidase domain 1 PmbA/TldA family metallopeptidase This entry represents a group of metalloproteases. The tertiary structure of the Escherichia coli TdlD/TdlE complex has been solved, and shows that the TdlD subunit is the active peptidase, binding a single zinc ion at an HEXXXH motif in which the glutamic acid is a substrate-binding residue and the two histidines are zinc ligands. The third zinc ligand is a cysteine, C-terminal to the HEXXXH motif. The TldE (also known as PmbA) by itself has no catalytic activity, does not bind zinc, and does not carry the HEXXXH motif [1]. TldD and TldE were originally identified as regulators of DNA gyrase. Later, they are shown to be metalloproteases involved in CcdA degradation [2-3]. [1]. 28943336. The Origins of Specificity in the Microcin-Processing Protease TldD/E. Ghilarov D, Serebryakova M, Stevenson CEM, Hearnshaw SJ, Volkov DS, Maxwell A, Lawson DM, Severinov K;. Structure. 2017;25:1549-1561. [2]. 22950735. An archaeal protein evolutionarily conserved in prokaryotes is a zinc-dependent metalloprotease. Hu Y, Peng N, Han W, Mei Y, Chen Z, Feng X, Liang YX, She Q;. Biosci Rep. 2012;32:609-618. [3]. 12029038. The highly conserved TldD and TldE proteins of Escherichia coli are involved in microcin B17 processing and in CcdA degradation. Allali N, Afif H, Couturier M, Van Melderen L;. J Bacteriol. 2002;184:3224-3231. (from Pfam) NF013677.5 PF01527.25 HTH_Tnp_1 24.1 24.1 75 domain Y Y N transposase GO:0003677,GO:0004803,GO:0006313 8917074,8973350,9180700 131567 cellular organisms no rank 222634 EBI-EMBL Transposase transposase Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family. [1]. 9180700. Genetic organization and transposition properties of IS511. D. A. Mullin, D. L. Zies, A. H. Mullin, N. Caballera & B. Ely;. Mol Gen Genet 1997;254:456-463. [2]. 8973350. The use of an improved transposon mutagenesis system for DNA sequencing leads to the characterization of a new insertion sequence of Streptomyces lividans 66. J. Fischer, H. Maier, P. Viell & J. Altenbuchner;. Gene 1996;180:81-89. [3]. 8917074. Identification and nucleotide sequence of Rhizobium meliloti insertion sequence ISRm6, a small transposable element that belongs to the IS3 family. S. Zekri & N. Toro;. Gene 1996;175:43-48. (from Pfam) NF013681.5 PF01531.21 Glyco_transf_11 23.9 23.9 298 domain Y Y N alpha-1,2-fucosyltransferase GO:0005975,GO:0008107,GO:0016020 131567 cellular organisms no rank 8607 EBI-EMBL Glycosyl transferase family 11 alpha-1,2-fucosyltransferase This family contains several fucosyl transferase enzymes. (from Pfam) NF013682.5 PF01532.25 Glyco_hydro_47 22.9 22.9 455 domain Y Y N glycoside hydrolase family 47 protein GO:0004571,GO:0005509,GO:0016020 131567 cellular organisms no rank 1009 EBI-EMBL Glycosyl hydrolase family 47 glycoside hydrolase family 47 protein Members of this family are alpha-mannosidases that catalyse the hydrolysis of the terminal 1,2-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide Man(9)(GlcNAc)(2). (from Pfam) NF013685.5 PF01535.25 PPR 25 9.3 31 repeat Y N N pentatricopeptide repeat protein 10664580,7664742,8039510 131567 cellular organisms no rank 4490 EBI-EMBL PPR repeat pentatricopeptide repeat This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 Swiss:P32522 that may be involved in RNA stabilisation [1]. This domain occurs in crp1 that is involved in RNA processing [2]. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR [3]. [1]. 7664742. The product of the nuclear gene PET309 is required for translation of mature mRNA and stability or production of intron-containing RNAs derived from the mitochondrial COX1 locus of Saccharomyces cerevisiae. Manthey GM, McEwen JE;. EMBO J 1995;14:4031-4043. [2]. 8039510. A nuclear mutation in maize blocks the processing and translation of several chloroplast mRNAs and provides evidence for the differential translation of alternative mRNA forms. Barkan A, Walker M, Nolasco M, Johnson D;. EMBO J 1994;13:3170-3181. [3]. 10664580. The PPR motif - a TPR-related motif prevalent in plant organellar proteins. Small ID, Peeters I;. Trends Biochem Sci 2000;25:45-47. (from Pfam) NF013691.5 PF01541.29 GIY-YIG 22.6 22.6 78 domain Y Y N GIY-YIG nuclease family protein 10219084,12379841,1631169,16646971,9973609 131567 cellular organisms no rank 165126 EBI-EMBL GIY-YIG catalytic domain GIY-YIG catalytic domain This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices [4]. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site. [1]. 1631169. Identification of a family of bacteriophage T4 genes encoding proteins similar to those present in group I introns of fungi and phage. Sharma M, Ellis RL, Hinton DM;. Proc Natl Acad Sci U S A 1992;89:6658-6662. [2]. 9973609. Conserved domains in DNA repair proteins and evolution of repair systems. Aravind L, Walker DR, Koonin EV;. Nucleic Acids Res 1999;27:1223-1242. [3]. 10219084. Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings. Kowalski JC, Belfort M, Stapleton MA, Holpert M, Dansereau JT, Pietrokovski S, Baxter SM, Derbyshire V;. Nucleic Acids Res 1999;27:2115-2125. [4]. 12379841. Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI. Van Roey P, Meehan L, Kowalski JC, Belfort M, Derbyshire V;. Nat Struct Biol 2002;9:806-811. [5]. 16646971. Phylogenomic analysis of the GIY-YIG nuclease superfamily. Dunin-Horkawicz S, Feder M, Bujnicki JM;. BMC Genomics. 2006;7:98. (from Pfam) NF013694.5 PF01544.23 CorA 27 27 292 domain Y Y N CorA family divalent cation transporter GO:0016020,GO:0055085 12142406,16598263,17619822,23425532,9775386,9786860 131567 cellular organisms no rank 113177 EBI-EMBL CorA-like Mg2+ transporter protein CorA family divalent cation transporter The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli. CorA is virtually ubiquitous in the Bacteria and Archaea [1,2,4-6]. There are also eukaryotic relatives of this protein, like the plasma membrane magnesium transporter ALR2 from yeast (Swiss:P43553). This entry also includes related proteins such as the zinc transporter ZntB [6]. [1]. 9775386. The CorA magnesium transporter gene family. Kehres DG, Lawyer CH, Maguire ME;. Microb Comp Genomics 1998;3:151-169. [2]. 9786860. The CorA Mg2+ transport protein of Salmonella typhimurium. Mutagenesis of conserved residues in the third membrane domain identifies a Mg2+ pore. Smith RL, Szegedy MA, Kucharski LM, Walker C, Wiet RM, Redpath A, Kaczmarek MT, Maguire ME;. J Biol Chem 1998;273:28663-28669. [3]. 12142406. ZntB is a novel Zn2+ transporter in Salmonella enterica serovar Typhimurium. Worlock AJ, Smith RL;. J Bacteriol. 2002;184:4369-4373. [4]. 17619822. The CorA family: structure and function revisited. Niegowski D, Eshaghi S;. Cell Mol Life Sci. 2007;64:2564-2574. [5]. 23425532. Exploring the structure and function of Thermotoga maritima CorA reveals the mechanism of gating and ion selectivity in Co2+/Mg2+ transport. Nordin N, Guskov A, Phua T, Sahaf N, Xia Y, Lu S, Eshaghi H, Eshaghi S;. Biochem J. 2013;451:365-374. [6]. 16598263. Crystal structure of the CorA Mg2+ transporter. Lunin VV, Dobrovetsky E, Khutoreskaya G, Zhang R, Joachimiak A, Doyle DA, Bochkarev A, Maguire ME, Edwards AM, Koth CM;. Nature. 2006;440:833-837. (from Pfam) NF013695.5 PF01545.26 Cation_efflux 26.6 26.6 198 domain Y Y N cation transporter GO:0006812,GO:0008324,GO:0016020,GO:0055085 8829543,9696746 131567 cellular organisms no rank 207402 EBI-EMBL Cation efflux family cation transporter Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells. [1]. 9696746. Molecular characterization of a chromosomal determinant conferring resistance to zinc and cobalt ions in Staphylococcus aureus. Xiong A, Jayaswal RK;. J Bacteriol 1998;180:4024-4029. [2]. 8829543. Cloning and sequence analysis of czc genes in Alcaligenes sp. strain CT14. Kunito T, Kusano T, Oyaizu H, Senoo K, Kanazawa S, Matsumoto S;. Biosci Biotechnol Biochem 1996;60:699-704. (from Pfam) NF013696.5 PF01546.33 Peptidase_M20 24.6 24.6 206 subfamily Y Y N M20/M25/M40 family metallo-hydrolase GO:0016787 7674922 131567 cellular organisms no rank 766344 EBI-EMBL Peptidase family M20/M25/M40 M20/M25/M40 family metallo-hydrolase This family includes a range of zinc metallopeptidases belonging to several families in the peptidase classification [1]. Family M20 are Glutamate carboxypeptidases. Peptidase family M25 contains X-His dipeptidases. [1]. 7674922. Evolutionary families of metallopeptidases. Rawlings ND, Barrett AJ;. Meth Enzymol 1995;248:183-228. (from Pfam) NF013697.5 PF01547.30 SBP_bac_1 26 26 307 subfamily Y Y N extracellular solute-binding protein 2002054,8336670,9360608,9651355 131567 cellular organisms no rank 1028311 EBI-EMBL Bacterial extracellular solute-binding protein extracellular solute-binding protein This family also includes the bacterial extracellular solute-binding protein family POTD/POTF. [1]. 2002054. The 2.3-A resolution structure of the maltose- or maltodextrin-binding protein, a primary receptor of bacterial active transport and chemotaxis. Spurlino JC, Lu GY, Quiocho FA;. J Biol Chem 1991;266:5202-5219. [2]. 9360608. Structure of Haemophilus influenzae Fe(+3)-binding protein reveals convergent evolution within a superfamily. Bruns CM, Nowalk AJ, Arvai AS, McTigue MA, Vaughan KG, Mietzner TA, McRee DE;. Nat Struct Biol 1997;4:919-924. [3]. 9651355. Crystal structure and mutational analysis of the Escherichia coli putrescine receptor. Structural basis for substrate specificity. Vassylyev DG, Tomitori H, Kashiwagi K, Morikawa K, Igarashi K;. J Biol Chem 1998;273:17604-17609. [4]. 8336670. Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Tam R, Saier MH Jr;. Microbiol Rev 1993;57:320-346. (from Pfam) NF013698.5 PF01548.22 DEDD_Tnp_IS110 29 29 155 domain Y Y N transposase GO:0003677,GO:0004803,GO:0006313 1324903,2403542 131567 cellular organisms no rank 144180 EBI-EMBL Transposase transposase Transposase proteins are necessary for efficient DNA transposition. This family includes an amino-terminal region of the pilin gene inverting protein (PIVML) and of members of the IS111A/IS1328/IS1533 family of transposases. The C-terminus is represented by family Pfam:PF02371. [1]. 1324903. A Coxiella burnetti repeated DNA element resembling a bacterial insertion sequence. Hoover TA, Vodkin MH, Williams JC;. J Bacteriol 1992;174:5540-5548. [2]. 2403542. Sequence analysis of the inversion region containing the pilin genes of Moraxella bovis. Fulks KA, Marrs CF, Stevens SP, Green MR;. J Bacteriol 1990;172:310-316. (from Pfam) NF013700.5 PF01551.27 Peptidase_M23 28.7 28.7 96 domain Y Y N peptidoglycan DD-metalloendopeptidase family protein 131567 cellular organisms no rank 401165 EBI-EMBL Peptidase family M23 peptidoglycan DD-metalloendopeptidase family protein Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown. (from Pfam) NF013703.5 PF01554.23 MatE 24.9 24.9 161 domain Y Y N MATE family efflux transporter GO:0015297,GO:0016020,GO:0042910,GO:0055085 131567 cellular organisms no rank 365156 EBI-EMBL MatE MATE family efflux transporter MATE (Multi Antimicrobial Extrusion), 2.A.66.1 in Transporter Classification Database, is a widely distributed transporter family that includes both human proteins and bacterial antibiotic resistance efflux transporters. NF013704.5 PF01555.23 N6_N4_Mtase 26.7 26.7 221 domain Y Y N DNA methyltransferase GO:0003677,GO:0008170 131567 cellular organisms no rank 153549 EBI-EMBL DNA methylase DNA methyltransferase Members of this family are DNA methylases. The family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases. (from Pfam) NF013705.5 PF01556.23 DnaJ_C 26.6 26.6 152 domain Y Y N DnaJ C-terminal domain-containing protein 14656432,22011374,9644977 131567 cellular organisms no rank 112759 EBI-EMBL DnaJ C terminal domain DnaJ C terminal domain This family consists of the C terminal region of the DnaJ protein. It is always found associated with Pfam:PF00226 and Pfam:PF00684. DnaJ is a chaperone associated with the Hsp70 heat-shock system involved in protein folding and renaturation after stress. The two C-terminal domains CTDI and CTDII, both incorporated in this family are necessary for maintaining the J-domains in their specific relative positions [2]. Structural analysis of PDB:1nlt shows that PF00684 is nested within this DnaJ C-terminal region [3]. [1]. 9644977. The J-domain family and the recruitment of chaperone power. Kelley WL;. Trends Biochem Sci 1998;23:222-227. [2]. 22011374. Central domain deletions affect the SAXS solution structure and function of yeast Hsp40 proteins Sis1 and Ydj1. Silva JC, Borges JC, Cyr DM, Ramos CH, Torriani IL;. BMC Struct Biol. 2011;11:40. [3]. 14656432. The crystal structure of the yeast Hsp40 Ydj1 complexed with its peptide substrate. Li J, Qian X, Sha B;. Structure. 2003;11:1475-1483. (from Pfam) NF013706.5 PF01557.23 FAA_hydrolase 23.9 23.9 214 domain Y Y N fumarylacetoacetate hydrolase family protein GO:0003824 7568087,7737515,8223600,8510667,8550403,9101289,9492273 131567 cellular organisms no rank 275796 EBI-EMBL Fumarylacetoacetate (FAA) hydrolase family fumarylacetoacetate hydrolase family protein This family consists of fumarylacetoacetate (FAA) hydrolase, or fumarylacetoacetate hydrolase (FAH) and it also includes HHDD isomerase/OPET decarboxylase from E. coli strain W. FAA is the last enzyme in the tyrosine catabolic pathway, it hydrolyses fumarylacetoacetate into fumarate and acetoacetate which then join the citric acid cycle [1]. Mutations in FAA cause type I tyrosinemia in humans this is an inherited disorder mainly affecting the liver leading to liver cirrhosis, hepatocellular carcinoma, renal tubular damages and neurologic crises amongst other symptoms [1]. The enzymatic defect causes the toxic accumulation of phenylalanine/tyrosine catabolites [3]. The E. coli W enzyme HHDD isomerase/OPET decarboxylase contains two copies of this domain and functions in fourth and fifth steps of the homoprotocatechuate pathway; here it decarboxylates OPET to HHDD and isomerises this to OHED. The final products of this pathway are pyruvic acid and succinic semialdehyde. This family also includes various hydratases and 4-oxalocrotonate decarboxylases which are involved in the bacterial meta-cleavage pathways for degradation of aromatic compounds. 2-hydroxypentadienoic acid hydratase encoded by mhpD in E. coli Swiss:P77608 is involved in the phenylpropionic acid pathway of E. coli and catalyses the conversion of 2-hydroxy pentadienoate to 4-hydroxy-2-keto-pentanoate and uses a Mn2+ co-factor [5]. OHED hydratase encoded by hpcG in E. coli Swiss:P42270 is involved in the homoprotocatechuic acid (HPC) catabolism [6]. XylI in P. putida Swiss:P49155 is a 4-Oxalocrotonate decarboxylase [7]. [1]. 9101289. Mutations in th. TRUNCATED at 1650 bytes (from Pfam) NF013707.5 PF01558.23 POR 27.4 27.4 173 domain Y Y N 2-oxoacid:acceptor oxidoreductase family protein GO:0016903 8415612,8550425 131567 cellular organisms no rank 108603 EBI-EMBL Pyruvate ferredoxin/flavodoxin oxidoreductase 2-oxoacid:acceptor oxidoreductase family protein This family includes a region of the large protein pyruvate-flavodoxin oxidoreductase and the whole pyruvate ferredoxin oxidoreductase gamma subunit protein. It is not known whether the gamma subunit has a catalytic or regulatory role. Pyruvate oxidoreductase (POR) catalyses the final step in the fermentation of carbohydrates in anaerobic microorganisms [1]. This involves the oxidative decarboxylation of pyruvate with the participation of thiamine followed by the transfer of an acetyl moiety to coenzyme A for the synthesis of acetyl-CoA [1]. The family also includes pyruvate flavodoxin oxidoreductase as encoded by the nifJ gene in cyanobacterium which is required for growth on molecular nitrogen when iron is limited [2]. [1]. 8550425. Molecular and phylogenetic characterization of pyruvate and 2-ketoisovalerate ferredoxin oxidoreductases from Pyrococcus furiosus and pyruvate ferredoxin oxidoreductase from Thermotoga maritima. Kletzin A, Adams MW;. J Bacteriol 1996;178:248-257. [2]. 8415612. Growth of the cyanobacterium Anabaena on molecular nitrogen: NifJ is required when iron is limited. Bauer CC, Scappino L, Haselkorn R;. Proc Natl Acad Sci U S A 1993;90:8812-8816. (from Pfam) NF013713.5 PF01564.22 Spermine_synth 22.9 22.9 186 domain Y N N Spermine/spermidine synthase domain 131567 cellular organisms no rank 73976 EBI-EMBL Spermine/spermidine synthase domain Spermine/spermidine synthase domain Spermine and spermidine are polyamines. This family includes spermidine synthase that catalyses the fifth (last) step in the biosynthesis of spermidine from arginine, and spermine synthase. (from Pfam) NF013714.5 PF01565.28 FAD_binding_4 26.4 26.4 139 domain Y Y N FAD-binding protein GO:0050660 8805513,9261083 131567 cellular organisms no rank 473496 EBI-EMBL FAD binding domain FAD binding domain This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 [1]. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyses the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan [2]. [1]. 9261083. Crystal structures and inhibitor binding in the octameric flavoenzyme vanillyl-alcohol oxidase: the shape of the active-site cavity controls substrate specificity. Mattevi A, Fraaije MW, Mozzarelli A, Olivi L, Coda A, van Berkel WJ;. Structure 1997;5:907-920. [2]. 8805513. The structure of the substrate-free form of MurB, an essential enzyme for the synthesis of bacterial cell walls. Benson TE, Walsh CT, Hogle JM;. Structure 1996;4:47-54. (from Pfam) NF013715.5 PF01566.23 Nramp 29.8 29.8 357 domain Y Y N divalent metal cation transporter GO:0016020 24968120,25326704,30714568,7479731,8928221,9360964,9632246,9719491 131567 cellular organisms no rank 80907 EBI-EMBL Natural resistance-associated macrophage protein-like divalent metal cation transporter The natural resistance-associated macrophage protein (NRAMP) family consists of animal NRAMP1, NRAMP2, yeast proteins Smf1 and Smf2 and bacterial homologues [6-8]. The NRAMP family includes functional related proteins defined by a conserved hydrophobic core of ten transmembrane domains [5]. These membrane proteins are divalent cation transporters which have a high degree of sequence conservation, particularly, the residues contributing to ion interaction are stongly conserved (DPNG and MPH motifs) [6,7]. NRAMP1 is an integral membrane protein expressed exclusively in cells of the immune system and is recruited to the membrane of a phagosome upon phagocytosis, where it plays an essential role in host defense against pathogens [1-6]. Mutations in NRAMP1 may genetically predispose an individual to susceptibility to diseases including leprosy and tuberculosis [1]. NRAMP2 (DMT1) is a multiple divalent cation transporter broadly expressed in the duodenum, kidney, brain, testis and placenta. It transports Fe2+, Mn2+ and Cd+2, whereas Zn2+ is a poor substrate. Ca+2 and Mg+2 are not transported, which is important because their high concentrations in duodenum, where NRAMP2 is expressed at high levels, would interfere with the absorption of Fe2+ [6]. It is the major transferrin-independent iron uptake system in mammals [1,6]. NRAMP related members of this family have substrate specificity for Mn2+ and/or Mg2+, such as the yeast proteins Smf1 and Smf2 [3] and a group of bacterial transporters (NrmT, for Nramp-related magnesium transporter) [8]. [1]. 9719491. Macrophage NRAMP1 and its role in resistance to microbial infections. Govoni. TRUNCATED at 1650 bytes (from Pfam) NF013717.5 PF01568.26 Molydop_binding 26.8 26.8 110 domain Y Y N molybdopterin dinucleotide binding domain-containing protein GO:0016491,GO:0043546 8890912,9818358 131567 cellular organisms no rank 394793 EBI-EMBL Molydopterin dinucleotide binding domain Molydopterin dinucleotide binding domain This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor [1]. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [2]. [1]. 9818358. The formylmethanofuran dehydrogenase isoenzymes in Methanobacterium wolfei and Methanobacterium thermoautotrophicum: induction of the molybdenum isoenzyme by molybdate and constitutive synthesis of the tungsten isoenzyme. Hochheimer A, Hedderich R, Thauer RK;. Arch Microbiol 1998;170:389-393. [2]. 8890912. Crystal structure of dimethyl sulfoxide reductase from Rhodobacter capsulatus at 1.88 A resolution. Schneider F, Lowe J, Huber R, Schindelin H, Kisker C, Knablein J;. J Mol Biol 1996;263:53-69. (from Pfam) NF013718.5 PF01569.26 PAP2 27.2 27.2 130 domain Y Y N phosphatase PAP2 family protein 8552646,9041652,9260289 131567 cellular organisms no rank 270788 EBI-EMBL PAP2 superfamily phosphatase PAP2 domain This family includes the enzyme type 2 phosphatidic acid phosphatase (PAP2), Glucose-6-phosphatase EC:3.1.3.9, Phosphatidylglycerophosphatase B EC:3.1.3.27 and bacterial acid phosphatase EC:3.1.3.2. The family also includes a variety of haloperoxidases [1,2] that function by oxidising halides in the presence of hydrogen peroxide to form the corresponding hypohalous acids. [1]. 9041652. Identification of a novel phosphatase sequence motif. Stukey J, Carman GM;. Protein Sci 1997;6:469-472. [2]. 9260289. An unexpected structural relationship between integral membrane phosphatases and soluble haloperoxidases. Neuwald AF;. Protein Sci 1997;6:1764-1767. [3]. 8552646. X-ray structure of a vanadium-containing enzyme: chloroperoxidase from the fungus Curvularia inaequalis. Messerschmidt A, Wever R;. Proc Natl Acad Sci U S A 1996;93:392-396. (from Pfam) NF013720.5 PF01571.26 GCV_T 25.6 25.6 255 domain Y N N Aminomethyltransferase folate-binding domain 9047339 131567 cellular organisms no rank 183901 EBI-EMBL Aminomethyltransferase folate-binding domain Aminomethyltransferase folate-binding domain This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. [1]. 9047339. Cloning, and molecular characterization of the GCV1 gene encoding the glycine cleavage T-protein from Saccharomyces cerevisiae. McNeil JB, Zhang F, Taylor BV, Sinclair DA, Pearlman RE, Bognar AL;. Gene 1997;186:13-20. (from Pfam) NF013722.5 PF01575.24 MaoC_dehydratas 27 27 123 domain Y Y N MaoC/PaaZ C-terminal domain-containing protein 8647101,9457873 131567 cellular organisms no rank 193512 EBI-EMBL MaoC like domain MaoC like domain The maoC gene is part of a operon with maoA which is involved in the synthesis of monoamine oxidase [1]. The MaoC protein is found to share similarity with a wide variety of enzymes; estradiol 17 beta-dehydrogenase 4, peroxisomal hydratase-dehydrogenase-epimerase, fatty acid synthase beta subunit. Several bacterial proteins that are composed solely of this domain have (R)-specific enoyl-CoA hydratase activity [2]. This domain is also present in the NodN nodulation protein N. [1]. 8647101. A monoamine-regulated Klebsiella aerogenes operon containing the monoamine oxidase structural gene (maoA) and the maoC gene. Sugino H, Sasaki M, Azakami H, Yamashita M, Murooka Y. J Bacteriol 1992;174:2485-2492. [2]. 9457873. Expression and characterization of (R)-specific enoyl coenzyme A hydratase involved in polyhydroxyalkanoate biosynthesis by Aeromonas caviae. Fukui T, Shiomi N, Doi Y;. J Bacteriol. 1998;180:667-673. (from Pfam) NF013725.5 PF01578.25 Cytochrom_C_asm 29.9 29.9 212 domain Y Y N cytochrome c biogenesis protein CcsA ccsA GO:0017004,GO:0020037 20382024,21958041,22723177,7529870,7635817,7665469,9043133 131567 cellular organisms no rank 125078 EBI-EMBL Cytochrome C assembly protein cytochrome c biogenesis protein CcsA This family consists of various proteins involved in cytochrome c assembly from mitochondria and bacteria; CycK from Rhizobium[3], CcmC from E. coli and Paracoccus denitrificans [2,1] and orf240 from wheat mitochondria [4]. The members of this family are probably integral membrane proteins with six predicted transmembrane helices. It has been proposed that members of this family comprise a membrane component of an ABC (ATP binding cassette) transporter complex. It is also proposed that this transporter is necessary for transport of some component needed for cytochrome c assembly. One member CycK contains a putative heme-binding motif [3], orf240 also contains a putative heme-binding motif and is a proposed ABC transporter with c-type heme as its proposed substrate [4]. However it seems unlikely that all members of this family transport heme nor c-type apocytochromes because CcmC in the putative CcmABC transporter transports neither [1]. CcmF forms a working module with CcmH and CcmI, CcmFHI, and itself is unlikely to bind haem directly [5]. [1]. 9043133. The Paracoccus denitrificans ccmA, B and C genes: cloning and sequencing, and analysis of the potential of their products to form a haem or apo-c-type cytochrome transporter. Page D, Pearce DA, Norris HA, Ferguson SJ;. Microbiology 1997;143:563-576. [2]. 7635817. Escherichia coli genes required for cytochrome c maturation. Thony-Meyer L, Fischer F, Kunzler P, Ritz D, Hennecke H;. J Bacteriol 1995;177:4321-4326. [3]. 7665469. Characterization of the cycHJKL genes involved in cytochrome c biogenesis and symbiotic nitrogen fixation in Rhizobium leguminosarum. Delgado MJ, Yeo. TRUNCATED at 1650 bytes (from Pfam) NF013727.5 PF01580.23 FtsK_SpoIIIE 24 24 221 domain Y Y N FtsK/SpoIIIE domain-containing protein GO:0000166,GO:0003677,GO:0005524 7592387,8160014 131567 cellular organisms no rank 239417 EBI-EMBL FtsK/SpoIIIE family FtsK/SpoIIIE family FtsK has extensive sequence similarity to wide variety of proteins from prokaryotes and plasmids [1], termed the FtsK/SpoIIIE family. This domain contains a putative ATP binding P-loop motif. It is found in the FtsK cell division protein from E. coli Swiss:P46889 and the stage III sporulation protein E SpoIIIE Swiss:P21458 which has roles in regulation of prespore specific gene expression in B. subtilis. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification [1]. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer [1]. [1]. 7592387. A new Escherichia coli cell division gene, ftsK. Begg KJ, Dewar SJ, Donachie WD;. J Bacteriol 1995;177:6211-6222. [2]. 8160014. Bacillus subtilis spoIIIE protein required for DNA segregation during asymmetric cell division. Wu LJ ,Errington J;. Science 1994;264:572-575. (from Pfam) NF013729.5 PF01582.25 TIR 21.3 21.3 179 domain Y Y N toll/interleukin-1 receptor domain-containing protein GO:0005515,GO:0007165 12186654,9013863,9237759 131567 cellular organisms no rank 16524 EBI-EMBL TIR domain TIR domain The Toll/interleukin-1 receptor (TIR) homology domain is an intracellular signalling domain found in MyD88, interleukin 1 receptor and the Toll receptor. It contains three highly-conserved regions, and mediates protein-protein interactions between the Toll-like receptors (TLRs) and signal-transduction components. TIR-like motifs are also found in plant proteins thought to be involved in resistance to disease. When activated, TIR domains recruit cytoplasmic adaptor proteins MyD88 (Swiss:Q99836) and TOLLIP (Toll interacting protein, Swiss:Q9H0E2). In turn, these associate with various kinases to set off signalling cascades [3]. [1]. 9013863. The cloning and characterization of human MyD88: a member of an IL-1 receptor related family. Bonnert TP, Garka KE, Parnet P, Sonoda G, Testa JR, Sims JE;. FEBS Lett 1997;402:81-84. [2]. 9237759. A human homologue of the Drosophila Toll protein signals activation of adaptive immunity [see comments]. Medzhitov R, Preston-Hurlburt P, Janeway CA Jr;. Nature 1997;388:394-397. [3]. 12186654. Toll-like receptors: a family of pattern-recognition receptors in mammals. Armant MA, Fenton MJ;. Genome Biol 2002;3:REVIEWS3011. (from Pfam) NF013730.5 PF01583.25 APS_kinase 21.1 20.7 152 domain Y Y N adenylyl-sulfate kinase 2.7.1.25 9786849 131567 cellular organisms no rank 67430 EBI-EMBL Adenylylsulphate kinase adenylyl-sulfate kinase Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif. [1]. 9786849. Adenosine 5'-phosphosulfate kinase from Penicillium chrysogenum. site- directed mutagenesis at putative phosphoryl-accepting and ATP P-loop residues. MacRae IJ, Rose AB, Segel IH;. J Biol Chem 1998;273:28583-28589. (from Pfam) NF013731.5 PF01584.24 CheW 23.5 23.5 138 domain Y Y N chemotaxis protein CheW GO:0006935,GO:0007165 9989504 131567 cellular organisms no rank 199427 EBI-EMBL CheW-like domain CheW-like domain CheW proteins are part of the chemotaxis signaling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and other related proteins that are involved in chemotaxis. The CheW-like regulatory domain in CheA [1] binds to CheW, suggesting that these domains can interact with each other. [1]. 9989504. Structure of CheA, a signal-transducing histidine kinase. Bilwes AM, Alex LA, Crane BR, Simon MI;. Cell 1999;96:131-141. (from Pfam) NF013734.5 PF01588.25 tRNA_bind 27 27 96 domain Y N N Putative tRNA binding domain GO:0000049 8895587,9162081 131567 cellular organisms no rank 184068 EBI-EMBL Putative tRNA binding domain Putative tRNA binding domain This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1) [2], human tyrosyl-tRNA synthetase [1], and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases [2]. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme [2]. This domain may perform a common function in tRNA aminoacylation [1]. [1]. 9162081. Human tyrosyl-tRNA synthetase shares amino acid sequence homology with a putative cytokine. Kleeman TA, Wei D, Simpson KL, First EA;. J Biol Chem 1997;272:14420-14425. [2]. 8895587. The yeast protein Arc1p binds to tRNA and functions as a cofactor for the methionyl-and glutamyl-tRNA synthetases. Simos G, Segref A, Fasiolo F, Hellmuth K, Shevchenko A, Mann M, Hurt EC;. EMBO J 1996;15:5437-5448. (from Pfam) NF013736.5 PF01590.31 GAF 22.4 22.4 133 domain Y Y N GAF domain-containing protein GO:0005515 1404379,20004158,20298248,9433123 131567 cellular organisms no rank 730543 EBI-EMBL GAF domain GAF domain This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalysed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). Discovery and naming of the GAF domain. [1]. 9433123. The GAF domain: an evolutionary link between diverse phototransducing proteins. Aravind L, Ponting CP;. Trends Biochem Sci 1997;22:458-459. [2]. 20004158. Cyclic nucleotide binding GAF domains from phosphodiesterases: structural and mechanistic insights. Heikaus CC, Pandit J, Klevit RE;. Structure. 2009;17:. TRUNCATED at 1650 bytes (from Pfam) NF013738.5 PF01592.21 NifU_N 22 22 127 domain Y Y N iron-sulfur cluster assembly scaffold protein GO:0005506,GO:0016226,GO:0051536 12970193,8875867 131567 cellular organisms no rank 43596 EBI-EMBL NifU-like N terminal domain NifU-like N terminal domain This domain is found in NifU in combination with Pfam:PF01106. This domain is found on isolated in several bacterial species such as Swiss:O53156. The nif genes are responsible for nitrogen fixation. However this domain is found in bacteria that do not fix nitrogen, so it may have a broader significance in the cell than nitrogen fixation. These proteins appear to be scaffold proteins for iron-sulfur clusters [2]. [1]. 8875867. A modular domain of NifU, a nitrogen fixation cluster protein, is highly conserved in evolution. Hwang DM, Dempsey A, Tan KT, Liew CC;. J Mol Evol 1996;43:536-540. [2]. 12970193. Components involved in assembly and dislocation of iron-sulfur clusters on the scaffold protein Isu1p. Muhlenhoff U, Gerber J, Richhardt N, Lill R;. EMBO J 2003;22:4815-4825. (from Pfam) NF013739.5 PF01593.29 Amino_oxidase 19.8 19.8 443 domain Y Y N FAD-dependent oxidoreductase GO:0016491 7770050,9162023,9598979 131567 cellular organisms no rank 477202 EBI-EMBL Flavin containing amine oxidoreductase FAD-dependent oxidoreductase This family consists of various amine oxidases, including maze polyamine oxidase (PAO) [1] and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene dehydrogenases and related enzymes. In vertebrates MAO plays an important role regulating the intracellular levels of amines via there oxidation; these include various neurotransmitters, neurotoxins and trace amines [2]. In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium [3]. PAOs in plants, bacteria and protozoa oxidase spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines [1]. Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid binding proteins and antibacterial glycoproteins. [1]. 9598979. Maize polyamine oxidase: primary structure from protein and cDNA sequencing. Tavladoraki P, Schinina ME, Cecconi F, Agostino SD, Manera F, Rea G, Mariottini P, Federico R, Angelini R;. FEBS Lett 1998;426:62-66. [2]. 9162023. A key amino acid responsible for substrate selectivity of monoamine oxidase A and B. Tsugeno Y, Ito A;. J Biol Chem 1997;272:14033-14036. [3]. 7770050. Cloning, sequencing and heterologous expression of the monoamine oxidase gene from Aspergillus niger. Schilling B, Lerch K;. Mol Gen Genet 1995;247:430-438. (from Pfam) NF013740.5 PF01594.21 AI-2E_transport 34.3 34.3 327 subfamily Y Y N AI-2E family transporter 16385049,20559013 131567 cellular organisms no rank 223324 EBI-EMBL AI-2E family transporter AI-2E family transporter This family includes four different proteins from E. coli alone. One of them, YdgG or TqsA, has been shown to mediate transport of the quorum-sensing signal autoinducer 2 (AI-2). It is not clear if TqsA enhances secretion of AI-2 or inhibits AI-2 uptake. By altering the intracellular concentration of AI-2, TqsA affects gene expression in biofilms and biofilm formation [1]. TsqA belongs to the AI-2 exporter (AI-2E) superfamily [2]. [1]. 16385049. YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport. Herzberg M, Kaye IK, Peti W, Wood TK;. J Bacteriol. 2006;188:587-598. [2]. 20559013. The autoinducer-2 exporter superfamily. Rettner RE, Saier MH Jr;. J Mol Microbiol Biotechnol. 2010;18:195-205. (from Pfam) NF013741.5 PF01595.25 CNNM 28.4 28.4 181 domain Y Y N CNNM domain-containing protein 15498024,22399287,27856537,27899452,34188059 131567 cellular organisms no rank 172997 EBI-EMBL Cyclin M transmembrane N-terminal domain Cyclin M transmembrane N-terminal domain This transmembrane domain is found in metal transporter proteins such as cyclin M 1/2 (CNNM). CNNMs are integral membrane proteins that are conserved from bacteria to humans. CNNM family members influence metal ion homeostasis through mechanisms that may not involve direct membrane transport of the ions. Structurally, CNNMs are complex proteins that contain an extracellular N-terminal domain preceding a transmembrane domain, a 'Bateman module', which consists of two cystathionine- beta-synthase (CBS) domains Pfam:PF00571, and a C-terminal cNMP (cyclic nucleotide monophosphate) binding domain [1, 2, 3, 4]. This entry describes the CNNM transmembrane domain which contains four hydrophobic regions and forms a dimer through hydrophobic contacts between TM2 and TM3, in which each chain is composed of three transmembrane helices (TM1-3), a pair of short helices exposed on the intracellular side, and a juxtamembrane (JM) helix that forms a belt-like structure [2,5]. The homodimer adopts an inward-facing conformation with a negatively charged cavity containing a conserved pi-helical turn in TM3 that coordinates a Mg2 ion [5]. [1]. 15498024. Manganese toxicity and Saccharomyces cerevisiae Mam3p, a member of the ACDP (ancient conserved domain protein) family. Yang M, Jensen LT, Gardner AJ, Culotta VC;. Biochem J. 2005;386:479-487. [2]. 22399287. Membrane topology and intracellular processing of cyclin M2 (CNNM2). de Baaij JH, Stuiver M, Meij IC, Lainez S, Kopplin K, Venselaar H, Muller D, Bindels RJ, Hoenderop JG;. J Biol Chem. 2012;287:13644-13655. [3]. 27856537. Phosphocysteine in the PRL-CNNM pathway mediates magnesium homeostasi. TRUNCATED at 1650 bytes (from Pfam) NF013742.5 PF01596.22 Methyltransf_3 22 22 204 domain Y N N O-methyltransferase GO:0008171 8936303 131567 cellular organisms no rank 87756 EBI-EMBL O-methyltransferase O-methyltransferase Members of this family are O-methyltransferases. The family includes catechol o-methyltransferase Swiss:P21964, caffeoyl-CoA O-methyltransferase Swiss:Q43095 and a family of bacterial O-methyltransferases that may be involved in antibiotic production [1]. [1]. 8936303. Two multifunctional peptide synthetases and an O-methyltransferase are involved in the biosynthesis of the DNA-binding antibiotic and antitumour agent saframycin Mx1 from Myxococcus xanthus. Pospiech A, Bietenhader J, Schupp T;. Microbiology 1996;142:741-746. (from Pfam) NF013743.5 PF01597.24 GCV_H 22.2 22.2 122 domain Y N N Glycine cleavage H-protein 8197146 131567 cellular organisms no rank 55566 EBI-EMBL Glycine cleavage H-protein Glycine cleavage H-protein This is a family of glycine cleavage H-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. A lipoyl group is attached to a completely conserved lysine residue. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. [1]. 8197146. X-ray structure determination at 2.6-A resolution of a lipoate- containing protein: the H-protein of the glycine decarboxylase complex from pea leaves. Pares S, Cohen-Addad C, Sieker L, Neuburger M, Douce R;. Proc Natl Acad Sci U S A 1994;91:4850-4853. (from Pfam) NF013744.5 PF01599.24 Ribosomal_S27 22.3 22.3 44 PfamEq Y N N Ribosomal protein S27a GO:0003735,GO:0005840,GO:0006412 2538753,2538756,9305777 131567 cellular organisms no rank 806 EBI-EMBL Ribosomal protein S27a Ribosomal protein S27a This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesised as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis [3]. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [2]. [1]. 9305777. Characterization and expression of two chicken cDNAs encoding ubiquitin fused to ribosomal proteins of 52 and 80 amino acids. Mezquita J, Pau M, Mezquita C;. Gene 1997;195:313-319. [2]. 2538756. Identification of the long ubiquitin extension as ribosomal protein S27a. Redman KL, Rechsteiner M;. Nature 1989;338:438-440. [3]. 2538753. The tails of ubiquitin precursors are ribosomal proteins whose fusion to ubiquitin facilitates ribosome biogenesis. Finley D, Bartel B, Varshavsky A;. Nature 1989;338:394-401. (from Pfam) NF013747.5 PF01602.25 Adaptin_N 37 37 524 domain Y N N Adaptin N terminal region GO:0006886,GO:0016192,GO:0030117 2495531,9261055 131567 cellular organisms no rank 305 EBI-EMBL Adaptin N terminal region Adaptin N terminal region This family consists of the N terminal region of various alpha, beta and gamma subunits of the AP-1, AP-2 and AP-3 adaptor protein complexes. The adaptor protein (AP) complexes are involved in the formation of clathrin-coated pits and vesicles [1]. The N-terminal region of the various adaptor proteins (APs) is constant by comparison to the C-terminal which is variable within members of the AP-2 family[2]; and it has been proposed that this constant region interacts with another uniform component of the coated vesicles [2]. [1]. 9261055. Linking cargo to vesicle formation: receptor tail interactions with coat proteins. Kirchhausen T, Bonifacino JS, Riezman H;. Curr Opin Cell Biol 1997;9:488-495. [2]. 2495531. Structural and functional division into two domains of the large (100- to 115-kDa)chains of the clathrin-associated protein complex AP-2. RAKirchhausen T, Nathanson KL, Matsui W, Vaisberg A, Chow EP, Burne C, Keen JH, Davis AE;. Proc Natl Acad Sci U S A 1989;86:2612-2616. (from Pfam) NF013750.5 PF01607.29 CBM_14 22.1 22.1 53 domain Y Y N chitin-binding domain-containing protein GO:0005576,GO:0008061 8621536,9256413,9651363 131567 cellular organisms no rank 864 EBI-EMBL Chitin binding Peritrophin-A domain Chitin binding Peritrophin-A domain This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include [1-3]. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains [1]. [1]. 9651363. A type I peritrophic matrix protein from the malaria vector Anopheles gambiae binds to chitin. Cloning, expression, and characterization. Shen Z, Jacobs-Lorena M;. J Biol Chem 1998;273:17665-17670. [2]. 8621536. Characterization of a major peritrophic membrane protein, peritrophin-44, from the larvae of Lucilia cuprina. cDNA and deduced amino acid sequences. Elvin CM, Vuocolo T, Pearson RD, East IJ, Riding GA, Eisemann CH, Tellam RL;. J Biol Chem 1996;271:8925-8935. [3]. 9256413. Antibody-mediated inhibition of the growth of larvae from an insect causing cutaneous myiasis in a mammalian host. Casu R, Eisemann C, Pearson R, Riding G, East I, Donaldson A, Cadogan L, Tellam R;. Proc Natl Acad Sci U S A 1997;94:8939-8944. (from Pfam) NF013752.5 PF01609.26 DDE_Tnp_1 23 23 200 domain Y Y N transposase GO:0003677,GO:0004803,GO:0006313 10207011,1650732,1963949,2542093,6268937,6281654,8335077 131567 cellular organisms no rank 443643 EBI-EMBL Transposase DDE domain transposase Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction [3]. This family contains transposases for IS4 Swiss:P03835 [1], IS421 Swiss:P11901 [2], IS5377 Swiss:Q45620, IS427 [4], IS402 [5], IS1355 Swiss:O69604, IS5, which was original isolated in bacteriophage lambda [6]. [1]. 6268937. The sequence of IS4. Klaer R, Kuhn S, Tillmann E, Fritz HJ, Starlinger P;. Mol Gen Genet 1981;181:169-175. [2]. 2542093. IS421, a new insertion sequence in Escherichia coli. Sato S, Nakada Y, Shiratsuchi A;. FEBS Lett 1989;249:21-26. [3]. 8335077. Identification and analysis of the gas vesicle gene cluster on an unstable plasmid of Halobacterium halobium. DasSarma S;. Plasmid 1993;29:1-9. [4]. 10207011. The three-dimensional structure of a Tn5 transposase-related protein determined to 2.9-A resolution. Davies DR, Braam LM, Reznikoff WS, Rayment I;. J Biol Chem 1999;274:11904-11913. [5]. 1963949. Nucleotide sequence analysis of IS427 and its target sites in Agrobacterium tumefaciens T37. De Meirsman C, Van Soom C, Verreth C, Van Gool A, Vanderleyden J;. Plasmid 1990;24:227-234. [6]. 1650732. Nucleotide sequence of IS402 from Pseudomonas cepacia. Ferrante AA, Lessie TG;. Gene 1991;102:143-144. [7]. 6281654. Structural analysis of insertion sequence IS5. Kroger M, Hobom G;. Nature 1982;297:159-162. (from Pfam) NF013753.5 PF01610.22 DDE_Tnp_ISL3 23 23 240 domain Y Y N transposase 1325060,1660454,8093238,8196545 131567 cellular organisms no rank 108980 EBI-EMBL Transposase transposase Transposase proteins are necessary for efficient DNA transposition. Contains transposases for IS204 (Swiss:Q50911) [1], IS1001 (Swiss:Q06126) [2], IS1096 (Swiss:Q50440) [3] and IS1165 Swiss:Q48788 [4]. [1]. 8196545. Isolation and characterization of IS31831, a transposable element from Corynebacterium glutamicum. Vertes AA, Inui M, Kobayashi M, Kurusu Y, Yukawa H;. Mol Microbiol 1994;11:739-746. [2]. 8093238. Characterization of IS1001, an insertion sequence element of Bordetella parapertussis. van der Zee A, Agterberg C, van Agterveld M, Peeters M, Mooi FR;. J Bacteriol 1993;175:141-147. [3]. 1660454. A novel transposon trap for mycobacteria: isolation and characterization of IS1096. Cirillo JD, Barletta RG, Bloom BR, Jacobs WR Jr;. J Bacteriol 1991;173:7772-7780. [4]. 1325060. Isolation and characterization of IS1165, an insertion sequence of Leuconostoc mesenteroides subsp. cremoris and other lactic acid bacteria. Johansen E, Kibenich A;. Plasmid 1992;27:200-206. (from Pfam) NF013755.5 PF01612.25 DNA_pol_A_exo1 23.6 23.6 173 domain Y N N 3'-5' exonuclease GO:0003676,GO:0006139,GO:0008408 3883192,9224595,9288107,9396823,9697700 131567 cellular organisms no rank 118489 EBI-EMBL 3'-5' exonuclease 3'-5' exonuclease This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction [4,5]. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homologue of the WRN protein [3]. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome. [1]. 3883192. Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Ollis DL, Brick P, Hamlin R, Xuong NG, Steitz TA;. Nature 1985;313:762-766. [2]. 9396823. The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains. Moser MJ, Holley WR, Chatterjee A, Mian IS;. Nucleic Acids Res 1997;25:5110-5118. [3]. 9697700. Replication focus-forming activity 1 and the Werner syndrome gene product. Yan H, Chen CY, Kobayashi R, Newport J;. Nat Genet 1998;19:375-378. [4]. 9288107. The Werner syndrome protein is a DNA helicase. Gray MD, Shen JC, Kamath-Loeb AS, Blank A, Sopher BL, Martin GM, Oshima J, Loeb LA;. Nat Genet 1997;17:100-103. [5]. 9224595. DNA helicase activity in Werner's syndrome gene product s. TRUNCATED at 1650 bytes (from Pfam) NF013756.5 PF01613.23 Flavin_Reduct 27 27 153 domain Y Y N flavin reductase GO:0010181 7665509,9287340 131567 cellular organisms no rank 191291 EBI-EMBL Flavin reductase like domain Flavin reductase like domain This is a flavin reductase family consisting of enzymes known to be flavin reductases as well as various oxidoreductase and monooxygenase components. VlmR is a flavin reductase that functions in a two-component enzyme system to provide isobutylamine N-hydroxylase with reduced flavin and may be involved in the synthesis of valanimycin [1]. SnaC is a flavin reductase that provides reduced flavin for the oxidation of pristinamycin IIB to pristinamycin IIA as catalysed by SnaA, SnaB heterodimer [2]. This flavin reductase region characterised by enzymes of the family is present in the C-terminus of potential FMN proteins from Synechocystis sp. suggesting it is a flavin reductase domain [1]. [1]. 7665509. Cloning and analysis of structural genes from Streptomyces pristinaespiralis encoding enzymes involved in the conversion of pristinamycin IIB to pristinamycin IIA (PIIA): PIIA synthase and NADH:riboflavin 5'-phosphate oxidoreductase. Blanc V, Lagneaux D, Didier P, Gil P, Lacroix P, Crouzet J;. J Bacteriol 1995;177:5206-5214. [2]. 9287340. An NADPH:FAD oxidoreductase from the valanimycin producer, Streptomyces viridifaciens. Cloning, analysis, and overexpression. Parry RJ, Li W;. J Biol Chem 1997;272:23303-23311. (from Pfam) NF013757.5 PF01614.23 IclR 24 24 128 domain Y Y N IclR family transcriptional regulator C-terminal domain-containing protein 1995429,3225846 131567 cellular organisms no rank 300855 EBI-EMBL Bacterial transcriptional regulator Bacterial transcriptional regulator This family of bacterial transcriptional regulators includes the glycerol operon regulatory protein and acetate operon repressor both of which are members of the iclR family. These proteins have a Helix-Turn-Helix motif at the N-terminus. However this family covers the C-terminal region that binds to regulatory substrates including Glyoxylate, allantoin/ate, indole, aromatic hydrocarbons, sugar acids, succinic semialdehyde, benzoate derivatives, ascorbic acid, glycerol-3-phosphate, glyceraldehyde-3-phosphate and pyruvate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 1995429. Primary structure of the intergenic region between aceK and iclR in the Escherichia coli chromosome. Galinier A, Bleicher F, Negre D, Perriere G, Duclos B, Cozzone AJ, Cortay JC;. Gene 1991;97:149-150. [2]. 3225846. Structure and regulation of controlling sequences for the Streptomyces coelicolor glycerol operon. Smith CP, Chater KF;. J Mol Biol 1988;204:569-580. (from Pfam) NF013760.5 PF01618.21 MotA_ExbB 22.9 22.9 127 domain Y Y N MotA/TolQ/ExbB proton channel family protein 10348868,9811664 131567 cellular organisms no rank 144276 EBI-EMBL MotA/TolQ/ExbB proton channel family MotA/TolQ/ExbB proton channel family protein This family groups together integral membrane proteins that appear to be involved translocation of proteins across a membrane. These proteins are probably proton channels. MotA is an essential component of the flageller motor that uses a proton gradient to generate rotational motion in the flageller [1]. ExbB is part of the TonB-dependent transduction complex. The TonB complex uses the proton gradient across the inner bacterial membrane to transport large molecules across the outer bacterial membrane. [1]. 10348868. Function of proline residues of MotA in torque generation by the flagellar motor of Escherichia coli. Braun TF, Poulson S, Gully JB, Empey JC, Van Way S, Putnam A, Blair DF;. J Bacteriol 1999;181:3542-3551. [2]. 9811664. Interactions in the TonB-dependent energy transduction complex: ExbB and ExbD form homomultimers. Higgs PI, Myers PS, Postle K;. J Bacteriol 1998;180:6031-6038. (from Pfam) NF013761.5 PF01619.23 Pro_dh 27 27 278 PfamEq Y Y N proline dehydrogenase family protein 7966312 131567 cellular organisms no rank 81354 EBI-EMBL Proline dehydrogenase proline dehydrogenase family protein NF013765.5 PF01624.25 MutS_I 20.6 20.6 113 PfamEq Y N N MutS domain I GO:0005524,GO:0006298,GO:0030983 11048710,8036718,8510668,9722634 131567 cellular organisms no rank 75578 EBI-EMBL MutS domain I MutS domain I This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with Pfam:PF00488, Pfam:PF05188, Pfam:PF05192 and Pfam:PF05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [2]. The aligned region corresponds with globular domain I, which is involved in DNA binding, in Thermus aquaticus MutS as characterised in [4]. [1]. 9722634. Domain organization and functional analysis of Thermus thermophilus MutS protein [published erratum appears in Nucleic Acids Res 1998 Oct 15;26(20):following 4789]. Tachiki H, Kato R, Masui R, Hasegawa K, Itakura H, Fukuyama K, Kuramitsu S;. Nucleic Acids Res 1998;26:4153-4159. [2]. 8036718. Colon cancer and DNA repair: have mismatches met their match?. Jiricny J;. Trends Genet 1994;10:164-168. [3]. 8510668. The yeast gene MSH3 defines a new class of eukaryotic MutS homologues. New L, Liu K, Crouse GF;. Mol Gen Genet 1993;239:97-108. [4]. 11048710. Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Obmolova G, Ban C, Hsieh P, Yang W;. Nature 2000;407:703-710. (from Pfam) NF013766.5 PF01625.26 PMSR 23.7 23.7 153 domain Y Y N peptide-methionine (S)-S-oxide reductase 1.8.4.11 GO:0008113 8700890,8755589 131567 cellular organisms no rank 106929 EBI-EMBL Peptide methionine sulfoxide reductase peptide-methionine (S)-S-oxide reductase This enzyme repairs damaged proteins. Methionine sulfoxide in proteins is reduced to methionine. [1]. 8755589. Peptide methionine sulfoxide reductase contributes to the maintenance of adhesins in three major pathogens. Wizemann TM, Moskovitz J, Pearce BJ, Cundell D, Arvidson CG, So M, Weissbach H, Brot N, Masure HR;. Proc Natl Acad Sci USA 1996;93:7985-7990. [2]. 8700890. Cloning the expression of a mammalian gene involved in the reduction of methionine sulfoxide residues in proteins. Moskovitz J, Weissbach H, Brot N;. Proc Natl Acad Sci U S A 1996;93:2095-2099. (from Pfam) NF013767.5 PF01627.28 Hpt 24.6 24.6 84 domain Y Y N Hpt domain-containing protein GO:0000160 12582120,9054511 131567 cellular organisms no rank 264447 EBI-EMBL Hpt domain Hpt domain The histidine-containing phosphotransfer (HPt) domain is a novel protein module with an active histidine residue that mediates phosphotransfer reactions in the two-component signaling systems. A multistep phosphorelay involving the HPt domain has been suggested for these signaling pathways. The crystal structure of the HPt domain of the anaerobic sensor kinase ArcB has been determined [1]. The domain consists of six alpha helices containing a four-helix bundle-folding. The pattern of sequence similarity of the HPt domains of ArcB and components in other signaling systems can be interpreted in light of the three-dimensional structure and supports the conclusion that the HPt domains have a common structural motif both in prokaryotes and eukaryotes. In S. cerevisiae ypd1p this domain has been shown to contain a binding surface for Ssk1p (response regulator receiver domain containing protein Pfam:PF00072) [2]. [1]. 9054511. Insights into multistep phosphorelay from the crystal structure of the C-terminal HPt domain of ArcB. Kato M, Mizuno T, Shimizu T, Hakoshima T;. Cell 1997;88:717-723. [2]. 12582120. Ssk1p response regulator binding surface on histidine- containing phosphotransfer protein ypd1p. Porter SW, Xu Q, West AH;. Eukaryot Cell 2003;2:27-33. (from Pfam) NF013768.5 PF01628.26 HrcA 22.2 22.2 215 PfamEq Y N N HrcA protein C terminal domain GO:0003677,GO:0006355 8576042,8606155 131567 cellular organisms no rank 37843 EBI-EMBL HrcA protein C terminal domain HrcA protein C terminal domain HrcA is found to negatively regulate the transcription of heat shock genes [1,2]. HrcA contains an amino terminal helix-turn-helix domain, however this corresponds to the carboxy terminal domain. [1]. 8576042. hrcA, the first gene of the Bacillus subtilis dnaK operon encodes a negative regulator of class I heat shock genes. Schulz A, Schumann W;. J Bacteriol 1996;178:1088-1093. [2]. 8606155. Identification of a Caulobacter crescentus operon encoding hrcA, involved in negatively regulating heat-inducible transcription, and the chaperone gene grpE. Roberts RC, Toochinda C, Avedissian M, Baldini RL, Gomes SL, Shapiro L;. J Bacteriol 1996;178:1829-1841. (from Pfam) NF013772.5 PF01633.25 Choline_kinase 23 23 211 domain Y N N Choline/ethanolamine kinase 9506987 131567 cellular organisms no rank 55193 EBI-EMBL Choline/ethanolamine kinase Choline/ethanolamine kinase Choline kinase catalyses the committed step in the synthesis of phosphatidylcholine by the CDP-choline pathway [1]. This alignment covers the protein kinase portion of the protein. The divergence of this family makes it very difficult to create a model that specifically predicts choline/ethanolamine kinases only. However if [add Pfam ID here for Choline_kinase_C] is also present then it is definitely a member of this family. [1]. 9506987. Expression, purification, and characterization of choline kinase, product of the CKI gene from Saccharomyces cerevisiae. Kim KH, Voelker DR, Flocco MT, Carman GM;. J Biol Chem 1998;273:6844-6852. (from Pfam) NF013773.5 PF01634.23 HisG 25.5 25.5 158 PfamEq Y N N ATP phosphoribosyltransferase GO:0000105,GO:0003879,GO:0005737 131567 cellular organisms no rank 50926 EBI-EMBL ATP phosphoribosyltransferase ATP phosphoribosyltransferase NF013775.5 PF01636.28 APH 23.2 23.2 239 domain Y Y N phosphotransferase 2163618,2167474 131567 cellular organisms no rank 546242 EBI-EMBL Phosphotransferase enzyme family phosphotransferase This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides they include: aminoglycoside 3'-phosphotransferase or kanamycin kinase / neomycin-kanamycin phosphotransferase and streptomycin 3''-kinase or streptomycin 3''-phosphotransferase. The aminoglycoside phosphotransferases inactivate aminoglycoside antibiotics via phosphorylation [2]. This family also includes homoserine kinase. This family is related to fructosamine kinase Pfam:PF03881. [1]. 2163618. Cloning of aminoglycoside phosphotransferase (APH) gene from antibiotic- producing strain of Bacillus circulans into a high-expression vector, pKK223-3. Purification, properties and location of the enzyme [published erratum appears in Biochem J 1991 Feb 1. Sarwar M, Akhtar M;. Biochem J 1990;268:671-677. [2]. 2167474. PCR cloning of a streptomycin phosphotransferase (aphE) gene from Streptomyces griseus ATCC 12475. Trower MK, Clark KG;. Nucleic Acids Res 1990;18:4615-4615. (from Pfam) NF013776.5 PF01637.23 ATPase_2 33.2 33.2 225 domain Y Y N ATP-binding protein GO:0005524 9045616 131567 cellular organisms no rank 17131 EBI-EMBL ATPase domain predominantly from Archaea ATP-binding protein This family contain a conserved P-loop motif that is involved in binding ATP. There are eukaryote members as well as archaeal members in this family. [1]. 9045616. Evidence for a family of archaeal ATPases. Koonin EV;. Science 1997;275:1489-1490. (from Pfam) NF013777.5 PF01638.22 HxlR 20.8 20.8 91 domain Y Y N winged helix-turn-helix transcriptional regulator 15978081 131567 cellular organisms no rank 297230 EBI-EMBL HxlR-like helix-turn-helix winged helix-turn-helix transcriptional regulator HxlR, a member of this family, is a DNA-binding protein that acts as a positive regulator of the formaldehyde-inducible hxlAB operon in Bacillus subtilis. [1]. 15978081. HxlR, a member of the DUF24 protein family, is a DNA-binding protein that acts as a positive regulator of the formaldehyde-inducible hxlAB operon in Bacillus subtilis. Yurimoto H, Hirai R, Matsuno N, Yasueda H, Kato N, Sakai Y;. Mol Microbiol 2005;57:511-519. (from Pfam) NF013780.5 PF01641.24 SelR 24.9 24.9 121 domain Y Y N peptide-methionine (R)-S-oxide reductase 1.8.4.12 GO:0033743 10608886,11929995 131567 cellular organisms no rank 79906 EBI-EMBL SelR domain SelR domain Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterised with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidised methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR , evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain Pfam:PF01625. The domain has two conserved cysteine and histidines. The domain binds both selenium and zinc [2]. The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family [1]. This family has methionine-R-sulfoxide reductase activity [2]. [1]. 10608886. Novel selenoproteins identified in silico and in vivo by using a conserved RNA structural motif. Lescure A, Gautheret D, Carbon P, Krol A;. J Biol Chem 1999;274:38147-38154. [2]. 11929995. Selenoprotein R is a zinc-containing stereo-specific methionine sulfoxide reductase. Kryukov GV, Kumar RA, Koc A, Sun Z, Gladyshev VN;. Proc Natl Aca. TRUNCATED at 1650 bytes (from Pfam) NF013781.5 PF01642.27 MM_CoA_mutase 22.1 22.1 512 subfamily_domain Y Y N methylmalonyl-CoA mutase family protein GO:0016866,GO:0031419 8805541 131567 cellular organisms no rank 102246 EBI-EMBL Methylmalonyl-CoA mutase methylmalonyl-CoA mutase family protein The enzyme methylmalonyl-CoA mutase is a member of a class of enzymes that uses coenzyme B12 (adenosylcobalamin) as a cofactor. The enzyme induces the formation of an adenosyl radical from the cofactor. This radical then initiates a free-radical rearrangement of its substrate, succinyl-CoA, to methylmalonyl-CoA [1]. [1]. 8805541. How coenzyme B12 radicals are generated: the crystal structure of methylmalonyl-coenzyme A mutase at 2 A resolution. Mancia F, Keep NH, Nakagawa A, Leadlay PF, McSweeney S, Rasmussen B, Bosecke P, Diat O, Evans PR;. Structure 1996;4:339-350. (from Pfam) NF013782.5 PF01643.22 Acyl-ACP_TE 23.7 23.7 131 domain Y Y N acyl-ACP thioesterase domain-containing protein GO:0006633,GO:0016790 15531590,1621095,7479856 131567 cellular organisms no rank 38290 EBI-EMBL Acyl-ACP thioesterase N-terminal domain thioesterase This family consists of various acyl-acyl carrier protein (ACP) thioesterases (TE) these terminate fatty acyl group extension via hydrolysing an acyl group on a fatty acid [1]. These proteins are usually composed of a pair of tandem HotDog domains. This entry represents the N-terminal one of the pair. [1]. 7479856. Modification of the substrate specificity of an acyl-acyl carrier protein thioesterase by protein engineering. Yuan L, Voelker TA, Hawkins DJ;. Proc Natl Acad Sci U S A 1995;92:10639-10643. [2]. 1621095. Fatty acid biosynthesis redirected to medium chains in transgenic oilseed plants. Voelker TA, Worrell AC, Anderson L, Bleibaum J, Fan C, Hawkins DJ, Radke SE, Davies HM;. Science 1992;257:72-74. [3]. 15531590. A structural model of the plant acyl-acyl carrier protein thioesterase FatB comprised of two helix/4-stranded sheet domains: The N-terminal domain containing residues that affect specificity, the C-terminal domain containing catalytic residues. Mayer KM, Shanklin J;. J Biol Chem 2004; [Epub ahead of print] (from Pfam) NF013784.5 PF01645.22 Glu_synthase 20.4 20.4 369 domain Y Y N glutamate synthase-related protein GO:0006537,GO:0015930,GO:0016638 8923741 131567 cellular organisms no rank 187788 EBI-EMBL Conserved region in glutamate synthase glutamate synthase-related protein This family represents a region of the glutamate synthase protein. This region is expressed as a separate subunit in the glutamate synthase alpha subunit from archaebacteria, or part of a large multidomain enzyme in other organisms. The aligned region of these proteins contains a putative FMN binding site and Fe-S cluster. [1]. 8923741. Sequence of the GLT1 gene from Saccharomyces cerevisiae reveals the domain structure of yeast glutamate synthase. Filetici P, Martegani MP, Valenzuela L, Gonzalez A, Ballario P;. Yeast 1996;12:1359-1366. (from Pfam) NF013786.5 PF01648.25 ACPS 25 25 111 domain Y Y N 4'-phosphopantetheinyl transferase superfamily protein GO:0000287,GO:0008897 10581256,7559576,8939709 131567 cellular organisms no rank 140159 EBI-EMBL 4'-phosphopantetheinyl transferase superfamily 4'-phosphopantetheinyl transferase superfamily protein Members of this family transfers the 4'-phosphopantetheine (4'-PP) moiety from coenzyme A (CoA) to the invariant serine of Pfam:PF00550. This post-translational modification renders holo-ACP capable of acyl group activation via thioesterification of the cysteamine thiol of 4'-PP [1]. This superfamily consists of two subtypes: The ACPS type such as Swiss:P24224 and the Sfp type such as Swiss:P39135. The structure of the Sfp type is known [3], which shows the active site accommodates a magnesium ion. The most highly conserved regions of the alignment are involved in binding the magnesium ion. [1]. 7559576. Cloning, overproduction, and characterization of the Escherichia coli holo-acyl carrier protein synthase. Lambalot RH, Walsh CT;. J Biol Chem 1995;270:24658-24661. [2]. 8939709. A new enzyme superfamily - the phosphopantetheinyl transferases. Lambalot RH, Gehring AM, Flugel RS, Zuber P, LaCelle M, Marahiel MA, Reid R, Khosla C, Walsh CT;. Chem Biol 1996;3:923-936. [3]. 10581256. Crystal structure of the surfactin synthetase-activating enzyme sfp: a prototype of the 4'-phosphopantetheinyl transferase superfamily [In Process Citation]. Reuter K, Mofid MR, Marahiel MA, Ficner R;. EMBO J 1999;18:6823-6831. (from Pfam) NF013788.5 PF01650.23 Peptidase_C13 22.8 22.8 258 domain Y Y N C13 family peptidase GO:0006508,GO:0008233 10682836,15105025,9065484 131567 cellular organisms no rank 8655 EBI-EMBL Peptidase C13 family C13 family peptidase Members of this family are asparaginyl peptidases [1]. The blood fluke parasite Schistosoma mansoni has at least five Clan CA cysteine peptidases in its digestive tract including cathepsins B (2 isoforms), C, F and L. All have been recombinantly expressed as active enzymes, albeit in various stages of activation [2]. In addition, a Clan CD peptidase, termed asparaginyl endopeptidase or 'legumain' has been identified. This has formerly been characterised as a 'haemoglobinase', but this term is probably incorrect [2]. Two cDNAs have been described for Schistosoma mansoni legumain; one encodes an active enzyme whereas the active site cysteine residue encoded by the second cDNA is substituted by an asparagine residue. Both forms have been recombinantly expressed [3]. [1]. 9065484. Cloning, isolation, and characterization of mammalian legumain, an asparaginyl endopeptidase. Chen JM, Dando PM, Rawlings ND, Brown MA, Young NE, Stevens RA, Hewitt E, Watts C, Barrett AJ;. J Biol Chem 1997;272:8090-8098. [2]. 15105025. Blood 'n' guts: an update on schistosome digestive peptidases. Caffrey CR, McKerrow JH, Salter JP, Sajid M;. Trends Parasitol 2004;20:241-248. [3]. 10682836. Identification of a cDNA encoding an active asparaginyl endopeptidase of Schistosoma mansoni and its expression in Pichia pastoris. Caffrey CR, Mathieu MA, Gaffney AM, Salter JP, Sajid M, Lucas KD, Franklin C, Bogyo M, McKerrow JH;. FEBS Lett 2000;466:244-248. (from Pfam) NF013790.5 PF01653.23 DNA_ligase_aden 27 27 253 domain Y N N NAD-dependent DNA ligase adenylation domain GO:0003911 10368271,10698952,11368162 131567 cellular organisms no rank 114814 EBI-EMBL NAD-dependent DNA ligase adenylation domain NAD-dependent DNA ligase adenylation domain DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor [1]. This domain is the catalytic adenylation domain. The NAD+ group is covalently attached to this domain at the lysine in the KXDG motif of this domain. This enzyme- adenylate intermediate is an important feature of the proposed catalytic mechanism [1]. [1]. 10698952. Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications. Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW;. EMBO J 2000;19:1119-1129. [2]. 11368162. Mutational analyses of Aquifex pyrophilus DNA ligase define essential domains for self-adenylation and DNA binding activity. Lim JH, Choi J, Kim W, Ahn BY, Han YS;. Arch Biochem Biophys 2001;388:253-260. [3]. 10368271. Structure of the adenylation domain of an NAD+-dependent DNA ligase. Singleton MR, Hakansson K, Timson DJ, Wigley DB;. Structure Fold Des 1999;7:35-42. (from Pfam) NF013791.5 PF01654.22 Cyt_bd_oxida_I 26.2 26.2 418 domain Y Y N cytochrome ubiquinol oxidase subunit I 1.10.3.- GO:0009055,GO:0019646,GO:0070069 9274021 131567 cellular organisms no rank 87271 EBI-EMBL Cytochrome bd terminal oxidase subunit I cytochrome ubiquinol oxidase subunit I This family are the alternative oxidases found in many bacteria which oxidise ubiquinol and reduce oxygen as part of the electron transport chain. This family is the subunit I of the oxidase E. coli has two copies of the oxidase, bo and bd', both of which are represented here In some nitrogen fixing bacteria, e.g. Klebsiella pneumoniae this oxidase is responsible for removing oxygen in microaerobic conditions, making the oxidase required for nitrogen fixation. This subunit binds a single b-haem, through ligands at His186 and Met393 (using SW:P11026 numbering). In addition His19 is a ligand for the haem b found in subunit II [1]. 9274021. The Klebsiella pneumoniae cytochrome bd' terminal oxidase complex and its role in microaerobic nitrogen fixation. Juty NS, Moshiri F, Merrick M, Anthony C, Hill S;. Microbiology 1997;143:2673-2683. (from Pfam) NF013792.5 PF01655.23 Ribosomal_L32e 25 25 108 domain Y Y N eL32 family ribosomal protein GO:0003735,GO:0005840,GO:0006412 2462715,29557065 131567 cellular organisms no rank 1236 EBI-EMBL Ribosomal protein L32 eL32 family ribosomal protein This family includes ribosomal protein L32 from eukaryotes and archaebacteria. (from Pfam) NF013793.5 PF01656.28 CbiA 25.4 25.4 125 domain Y N N CobQ/CobB/MinD/ParA nucleotide binding domain 10966576,2149583,7635831,8501034,9742225,9742226 131567 cellular organisms no rank 663664 EBI-EMBL CobQ/CobB/MinD/ParA nucleotide binding domain CobQ/CobB/MinD/ParA nucleotide binding domain This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA Swiss:P29946 and CbiP Swiss:Q05597 from S.typhimurium [4], and CobQ Swiss:Q52686 from R. capsulatus [3]. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [4]. The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family [6]. [1]. 9742225. Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon. Raux E, Lanois A, Warren MJ, Rambach A, Thermes C;. Biochem J 1998;335:159-166. [2]. 9742226. Cobalamin (vitamin B12) biosynthesis: functional characterization of the Bacillus megaterium cbi genes required to convert uroporphyrinogen III into cobyrinic acid a,c-diamide. Raux E, Lanois A, Rambach A, Warren MJ, Thermes C;. Biochem J 1998;335:167-173. [3]. 7635831. Identification and sequence analysis of genes involved in late steps in cobalamin (vitamin B12) synthesis in Rhodobacter capsulatus. Pollich M, Klug G;. J Bacteriol 1995;177:4481-4487. [4]. 8501034. Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM;. J Bacteriol 1993;175:3303-3316. [5]. 10966576. The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of AT. TRUNCATED at 1650 bytes (from Pfam) NF013795.5 PF01658.22 Inos-1-P_synth 27 27 107 domain Y N N Myo-inositol-1-phosphate synthase 7975896 131567 cellular organisms no rank 23809 EBI-EMBL Myo-inositol-1-phosphate synthase Myo-inositol-1-phosphate synthase This is a family of myo-inositol-1-phosphate synthases. Inositol-1-phosphate catalyses the conversion of glucose-6- phosphate to inositol-1-phosphate, which is then dephosphorylated to inositol [1]. Inositol phosphates play an important role in signal transduction. [1]. 7975896. Comparison of INO1 gene sequences and products in Candida albicans and Saccharomyces cerevisiae. Klig LS, Zobel PA, Devry CG, Losberger C;. Yeast 1994;10:789-800. (from Pfam) NF013798.5 PF01661.26 Macro 22 22 118 domain Y Y N macro domain-containing protein 12842467,16912299,16959969,18172500,18983849 131567 cellular organisms no rank 50360 EBI-EMBL Macro domain Macro domain The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent [1]: in certain cases it is believed to bind non-covalently [2]; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein [3]. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein [4]. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site [5]. [1]. 16959969. Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we. TRUNCATED at 1650 bytes (from Pfam) NF013799.5 PF01663.27 Phosphodiest 23 23 342 domain Y Y N alkaline phosphatase family protein 7730366,7982964,8617788,9344668 131567 cellular organisms no rank 204540 EBI-EMBL Type I phosphodiesterase / nucleotide pyrophosphatase alkaline phosphatase family protein This family consists of phosphodiesterases, including human plasma-cell membrane glycoprotein PC-1 / alkaline phosphodiesterase i / nucleotide pyrophosphatase (nppase). These enzymes catalyse the cleavage of phosphodiester and phosphosulfate bonds in NAD, deoxynucleotides and nucleotide sugars [1]. Also in this family is ATX an autotaxin, tumour cell motility-stimulating protein which exhibits type I phosphodiesterases activity [4]. The alignment encompasses the active site [3,4]. Also present with in this family is 60-kDa Ca2+-ATPase form F. odoratum [2]. [1]. 9344668. Molecular cloning and chromosomal localization of PD-Ibeta (PDNP3), a new member of the human phosphodiesterase I genes. Jin-Hua P, Goding JW, Nakamura H, Sano K;. Genomics 1997;45:412-415. [2]. 8617788. Cloning and expression of the unique Ca2+-ATPase from Flavobacterium odoratum. Peiffer WE, Desrosiers MG, Menick DR;. J Biol Chem 1996;271:5095-5100. [3]. 7730366. Affinity purification and cDNA cloning of rat neural differentiation and tumor cell surface antigen gp130RB13-6 reveals relationship to human and murine PC-1. Deissler H, Lottspeich F, Rajewsky MF;. J Biol Chem 1995;270:9849-9855. [4]. 7982964. cDNA cloning of the human tumor motility-stimulating protein, autotaxin, reveals a homology with phosphodiesterases. Murata J, Lee HY, Clair T, Krutzsch HC, Arestad AA, Sobel ME, Liotta LA, Stracke ML;. J Biol Chem 1994;269:30479-30484. (from Pfam) NF013803.5 PF01667.22 Ribosomal_S27e 24.5 24.5 55 PfamEq Y N N Ribosomal protein S27 GO:0003735,GO:0005840,GO:0006412 8441676 131567 cellular organisms no rank 914 EBI-EMBL Ribosomal protein S27 Ribosomal protein S27 NF013806.5 PF01670.22 Glyco_hydro_12 27 27 207 domain Y Y N GH12 family glycosyl hydrolase domain-containing protein GO:0000272,GO:0008810 9440876 131567 cellular organisms no rank 9481 EBI-EMBL Glycosyl hydrolase family 12 GH12 family glycosyl hydrolase domain NF013810.5 PF01674.23 Lipase_2 20.3 20.3 219 domain Y N N Lipase (class 2) GO:0016042,GO:0016787 1320940 131567 cellular organisms no rank 35610 EBI-EMBL Lipase (class 2) Lipase (class 2) This family consists of hypothetical C. elegans proteins and lipases. Lipases or triacylglycerol acylhydrolases hydrolyse ester bonds in triacylglycerol giving diacylglycerol, monoacylglycerol, glycerol and free fatty acids [1]. Swiss:P37957 is a extracellular lipase from B. subtilis 168 [1]. [1]. 1320940. Cloning, nucleotide sequence and expression in Escherichia coli of a lipase gene from Bacillus subtilis 168. Dartois V, Baulard A, Schanck K, Colson C;. Biochim Biophys Acta 1992;1131:253-260. (from Pfam) NF013811.5 PF01676.23 Metalloenzyme 24.3 24.3 252 domain Y N N Metalloenzyme superfamily GO:0003824,GO:0046872 10082381 131567 cellular organisms no rank 115271 EBI-EMBL Metalloenzyme superfamily Metalloenzyme superfamily This family includes phosphopentomutase Swiss:P07651 and 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, Swiss:P37689. This family is also related to Pfam:PF00245 [1]. The alignment contains the most conserved residues that are probably involved in metal binding and catalysis. [1]. 10082381. A superfamily of metalloenzymes unifies phosphopentomutase and cofactor- independent phosphoglycerate mutase with alkaline phosphatases and sulfatases. Galperin MY, Bairoch A, Koonin EV;. Protein Sci 1998;7:1829-1835. (from Pfam) NF013813.5 PF01678.24 DAP_epimerase 34.7 34.7 121 PfamEq Y N N Diaminopimelate epimerase GO:0008837,GO:0009089 9843410 131567 cellular organisms no rank 72373 EBI-EMBL Diaminopimelate epimerase Diaminopimelate epimerase Diaminopimelate epimerase contains two domains of the same alpha/beta fold, both contained in this family. [1]. 9843410. Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase. Cirilli M, Zheng R, Scapin G, Blanchard JS;. Biochemistry 1998;37:16452-16458. (from Pfam) NF013815.5 PF01680.22 SOR_SNZ 27 27 207 PfamEq Y N N SOR/SNZ family 10430950,10438537,8955308 131567 cellular organisms no rank 20024 EBI-EMBL SOR/SNZ family SOR/SNZ family Members of this family are enzymes involved in a new pathway of pyridoxine/pyridoxal 5-phosphate biosynthesis [1]. This family was formerly known as UPF0019. [1]. 8955308. A stationary-phase gene in Saccharomyces cerevisiae is a member of a novel, highly conserved gene family. Braun EL, Fuge EK, Padilla PA, Werner-Washburne M;. J Bacteriol 1996;178:6865-6872. [2]. 10430950. A highly conserved sequence is a novel gene involved in de novo vitamin B6 biosynthesis. Ehrenshaft M, Bilski P, Li MY, Chignell CF, Daub ME;. Proc Natl Acad Sci U S A 1999;96:9374-9378. [3]. 10438537. The extremely conserved pyroA gene of Aspergillus nidulans is required for pyridoxine synthesis and is required indirectly for resistance to photosensitizers. Osmani AH, May GS, Osmani SA;. J Biol Chem 1999;274:23565-23569. (from Pfam) NF013821.5 PF01687.22 Flavokinase 19.6 19.6 124 domain Y Y N riboflavin kinase 15468322,9473052 131567 cellular organisms no rank 72288 EBI-EMBL Riboflavin kinase riboflavin kinase This family represents the C-terminal region of the bifunctional riboflavin biosynthesis protein known as RibC in Bacillus subtilis. The RibC protein from Bacillus subtilis has both flavokinase and flavin adenine dinucleotide synthetase (FAD-synthetase) activities. RibC plays an essential role in the flavin metabolism [1]. This domain is thought to have kinase activity [2]. [1]. 9473052. Regulation of riboflavin biosynthesis in Bacillus subtilis is affected by the activity of the flavokinase/flavin adenine dinucleotide synthetase encoded by ribC. Mack M, van Loon AP, Hohmann HP;. J Bacteriol 1998;180:950-955. [2]. 15468322. Crystal structure of flavin binding to FAD synthetase of Thermotoga maritima. Wang W, Kim R, Yokota H, Kim SH;. Proteins 2005;58:246-248. (from Pfam) NF013826.5 PF01693.21 Cauli_VI 21 21 44 PfamEq Y Y N viroplasmin family protein 2402462,8372449 131567 cellular organisms no rank 10269 EBI-EMBL Caulimovirus viroplasmin viroplasmin family protein This family consists of various caulimovirus viroplasmin proteins. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms [2]. Inclusions are the site of viral assembly, DNA synthesis and accumulation [2]. Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner [1]. [1]. 8372449. Identification of domains within gene VI of cauliflower mosaic virus that influence systemic infection of Nicotiana bigelovii in a light- dependent manner. Wintermantel WM, Anderson EJ, Schoelz JE;. Virology 1993;196:789-798. [2]. 2402462. DNA sequence of gene VI of cauliflower mosaic virus strain PV147. Volovitch M, Modjtahedi N, Chouikh Y, Yot P;. Nucleic Acids Res 1990;18:5297-5297. (from Pfam) NF013827.5 PF01694.27 Rhomboid 22.6 22.6 143 subfamily Y Y N rhomboid family intramembrane serine protease 3.4.21.105 GO:0004252,GO:0016020 11672525,12620104,15684070,15753289,2110920 131567 cellular organisms no rank 132211 EBI-EMBL Rhomboid family rhomboid family intramembrane serine protease This family contains integral membrane proteins that are related to Drosophila rhomboid protein Swiss:P20350. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease [2][3][4] (EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite [5]. [1]. 2110920. rhomboid, a gene required for dorsoventral axis establishment and peripheral nervous system development in Drosophila melanogaster. Bier E, Jan LY, Jan YN;. Genes Dev 1990;4:190-203. [2]. 11672525. Drosophila rhomboid-1 defines a family of putative intramembrane serine proteases. Urban S, Lee JR, Freeman M;. Cell 2001;107:173-182. [3]. 12620104. The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers. Koonin EV, Makarova KS, Rogozin IB, Davidovic L, Letellier MC, Pellegrini L;. Genome Biol 2003;4:R19. [4]. 15684070. Reconstitution of intramembrane proteolysis in vitro reveals that pure rhomboid is sufficient for catalysis and specificity. Urban S, Wolfe MS;. Proc Natl Acad Sci U S A. 2005;102:1883-1888. [5]. 15753289. A spatially localized rhomboid protease cleaves cell surface adhesins essential for invasion by Toxoplasma. Brossier F, Jewett TJ, Sibley LD, Urban S;. Proc Natl Acad Sci U S A. 2005;102:4146-4151. (from Pfam) NF013828.5 PF01695.22 IstB_IS21 24.1 24.1 238 domain Y Y N ATP-binding protein GO:0005524 7698671,9141667 131567 cellular organisms no rank 174486 EBI-EMBL IstB-like ATP binding protein ATP-binding protein This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences [1]. The function of this protein is unknown, but it may perform a transposase function [2]. [1]. 7698671. Characterization and sequence of a novel insertion sequence, IS1162, from Pseudomonas fluorescens. Solinas F, Marconi AM, Ruzzi M, Zennaro E;. Gene 1995;155:77-82. [2]. 9141667. Characterization of IS1474, an insertion sequence of the IS21 family isolated from Pseudomonas alcaligenes NCIB 9867. Yeo CC, Poh CL;. FEMS Microbiol Lett 1997;149:257-263. (from Pfam) NF013829.5 PF01696.22 Adeno_E1B_55K 24.5 24.5 387 PfamEq Y N N Adenovirus EB1 55K protein / large t-antigen 10207064 131567 cellular organisms no rank 160 EBI-EMBL Adenovirus EB1 55K protein / large t-antigen Adenovirus EB1 55K protein / large t-antigen This family consists of adenovirus E1B 55K protein or large t-antigen. E1B 55K binds p53 the tumour suppressor protein converting it from a transcriptional activator which responds to damaged DNA in to an unregulated repressor of genes with a p53 binding site [1]. This protects the virus against p53 induced host antiviral responses and prevents apoptosis as induced by the adenovirus E1A protein [1]. The E1B region of adenovirus encodes two proteins E1B 55K the large t-antigen as found in this family and E1B 19K Pfam:PF01691 the small t-antigen which is not found in this family; both of these proteins inhibit E1A induced apoptosis. This family shows distant similarities to the pectate lyase superfamily. [1]. 10207064. Corepressor required for adenovirus E1B 55,000-molecular-weight protein repression of basal transcription. Martin ME, Berk AJ;. Mol Cell Biol 1999;19:3403-3414. (from Pfam) NF013830.5 PF01697.32 Glyco_transf_92 23 23 249 domain Y Y N glycosyltransferase family 92 protein 2.4.-.- 19858195,19959475,22629278 131567 cellular organisms no rank 7680 EBI-EMBL Glycosyltransferase family 92 glycosyltransferase family 92 protein Members of this family act as galactosyltransferases, belonging to glycosyltransferase family 92 [1,2,3]. The aligned region contains several conserved cysteine residues and several charged residues that may be catalytic residues. This is supported by the inclusion of this family in the GT-A glycosyl transferase superfamily. [1]. 19858195. Molecular basis for galactosylation of core fucose residues in invertebrates: identification of caenorhabditis elegans N-glycan core alpha1,6-fucoside beta1,4-galactosyltransferase GALT-1 as a member of a novel glycosyltransferase family. Titz A, Butschi A, Henrissat B, Fan YY, Hennet T, Razzazi-Fazeli E, Hengartner MO, Wilson IB, Kunzler M, Aebi M;. J Biol Chem. 2009;284:36223-36233. [2]. 19959475. Molecular cloning of pigeon UDP-galactose beta-D-galactoside alpha1,4-galactosyltransferase and UDP-galactose beta-D-galactoside and.. Suzuki N, Yamamoto K;. J Biol Chem. 2010;285:5178-5187. [3]. 22629278. Plant Glycosyltransferases Beyond CAZy: A Perspective on DUF Families. Hansen SF, Harholt J, Oikawa A, Scheller HV;. Front Plant Sci. 2012;3:59. (from Pfam) NF013832.5 PF01699.29 Na_Ca_ex 24.9 22 151 domain Y N N Sodium/calcium exchanger protein GO:0016020,GO:0055085 1700476,8798769 131567 cellular organisms no rank 68436 EBI-EMBL Sodium/calcium exchanger protein Sodium/calcium exchanger protein This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells [2]. Ca2+ is moved into or out of the cytosol depending on Na+ concentration [2]. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3 [1] see Swiss:Q01728, Swiss:P48768 and Swiss:P70549 respectively. [1]. 8798769. Cloning of a third mammalian Na+-Ca2+ exchanger, NCX3. Nicoll DA, Quednau BD, Qui Z, Xia YR, Lusis AJ, Philipson KD;. J Biol Chem 1996;271:24914-24921. [2]. 1700476. Molecular cloning and functional expression of the cardiac sarcolemmal Na(+)-Ca2+ exchanger. Nicoll DA, Longoni S, Philipson KD;. Science 1990;250:562-565. (from Pfam) NF013835.5 PF01702.23 TGT 26.3 26.3 357 PfamEq Y N N Queuine tRNA-ribosyltransferase GO:0006400,GO:0016763 8323579,8654383 131567 cellular organisms no rank 59001 EBI-EMBL Queuine tRNA-ribosyltransferase Queuine tRNA-ribosyltransferase This is a family of queuine tRNA-ribosyltransferases EC:2.4.2.29, also known as tRNA-guanine transglycosylase and guanine insertion enzyme. Queuine tRNA-ribosyltransferase modifies tRNAs for asparagine, aspartic acid, histidine and tyrosine with queuine. It catalyses the exchange of guanine-34 at the wobble position with 7-aminomethyl-7-deazaguanine, and the addition of a cyclopentenediol moiety to 7-aminomethyl-7-deazaguanine-34 tRNA; giving a hypermodified base queuine in the wobble position [1,2]. The aligned region contains a zinc binding motif C-x-C-x2-C-x29-H, and important tRNA and 7-aminomethyl-7deazaguanine binding residues [1]. [1]. 8654383. Crystal structure of tRNA-guanine transglycosylase: RNA modification by base exchange. Romier C, Reuter K, Suck D, Ficner R;. EMBO J 1996;15:2850-2857. [2]. 8323579. tRNA-guanine transglycosylase from Escherichia coli. Overexpression, purification and quaternary structure. Garcia GA, Koch KA, Chong S;. J Mol Biol 1993;231:489-497. (from Pfam) NF013842.5 PF01710.21 HTH_Tnp_IS630 21.3 21.3 119 domain Y Y N IS630 transposase-related protein 9305771 131567 cellular organisms no rank 12503 EBI-EMBL Transposase IS630 transposase-related protein Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily [1]. [1]. 9305771. Three insertion sequences from the cyanobacterium Synechocystis PCC6803 support the occurrence of horizontal DNA transfer among bacteria. Cassier-Chauvat C, Poncelet M, Chauvat F;. Gene 1997;195:257-266. (from Pfam) NF013843.5 PF01712.24 dNK 27 27 203 domain Y Y N deoxynucleoside kinase 8692979,9079672 131567 cellular organisms no rank 25318 EBI-EMBL Deoxynucleoside kinase deoxynucleoside kinase This family consists of various deoxynucleoside kinases cytidine EC:2.7.1.74, guanosine EC:2.7.1.113, adenosine EC:2.7.1.76 and thymidine kinase EC:2.7.1.21 (which also phosphorylates deoxyuridine and deoxycytosine.) These enzymes catalyse the production of deoxynucleotide 5'-monophosphate from a deoxynucleoside. Using ATP and yielding ADP in the process. [1]. 9079672. Cloning of the cDNA and chromosome localization of the gene for human thymidine kinase 2. Johansson M, Karlsson A;. J Biol Chem 1997;272:8454-8458. [2]. 8692979. Cloning and expression of human deoxyguanosine kinase cDNA. Johansson M, Karlsson A;. Proc Natl Acad Sci U S A 1996;93:7258-7262. (from Pfam) NF013847.5 PF01717.23 Meth_synt_2 21 21 324 domain Y N N Cobalamin-independent synthase, Catalytic domain GO:0003871,GO:0008270,GO:0009086 15326182,9636232 131567 cellular organisms no rank 102211 EBI-EMBL Cobalamin-independent synthase, Catalytic domain Cobalamin-independent synthase, Catalytic domain This is a family of vitamin-B12 independent methionine synthases or 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferases, EC:2.1.1.14 from bacteria and plants. Plants are the only higher eukaryotes that have the required enzymes for methionine synthesis [1]. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to homocysteine [1]. The aligned region makes up the carboxy region of the approximately 750 amino acid protein except in some hypothetical archaeal proteins present in the family, where this region corresponds to the entire length. This domain contains the catalytic residues of the enzyme [2]. [1]. 9636232. The specific features of methionine biosynthesis and metabolism in plants. Ravanel S, Gakiere B, Job D, Douce R;. Proc Natl Acad Sci U S A 1998;95:7805-7812. [2]. 15326182. Crystal structures of cobalamin-independent methionine synthase complexed with zinc, homocysteine, and methyltetrahydrofolate. Ferrer JL, Ravanel S, Robert M, Dumas R;. J Biol Chem 2004;279:44235-44238. (from Pfam) NF013851.5 PF01722.23 BolA 25.7 25.7 76 domain Y Y N BolA/IbaG family iron-sulfur metabolism protein 10361282,2684651 131567 cellular organisms no rank 34681 EBI-EMBL BolA-like protein BolA/IbaG family iron-sulfur metabolism protein This family consist of the morphoprotein BolA from E. coli and its various homologues. In E. coli over expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division [1]. The expression of BolA is growth rate regulated and is induced during the transition into the the stationary phase [1]. BolA is also induced by stress during early stages of growth [1] and may have a general role in stress response. It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5 [2,1]. [1]. 10361282. The stationary-phase morphogene bolA from Escherichia coli is induced by stress during early stages of growth. Santos JM, Freire P, Vicente M, Arraiano CM;. Mol Microbiol 1999;32:789-798. [2]. 2684651. Induction of a growth-phase-dependent promoter triggers transcription of bolA, an Escherichia coli morphogene. Aldea M, Garrido T, Hernandez-Chico C, Vicente M, Kushner SR;. EMBO J 1989;8:3923-3931. (from Pfam) NF013854.5 PF01725.21 Ham1p_like 22.5 22.5 186 PfamEq Y Y N non-canonical purine NTP pyrophosphatase GO:0009143,GO:0047429 8789257 131567 cellular organisms no rank 73199 EBI-EMBL Ham1 family non-canonical purine NTP pyrophosphatase This family consists of the HAM1 protein Swiss:P47119 and hypothetical archaeal bacterial and C. elegans proteins. HAM1 controls 6-N-hydroxylaminopurine (HAP) sensitivity and mutagenesis in S. cerevisiae Swiss:P47119 [1]. The HAM1 protein protects the cell from HAP, either on the level of deoxynucleoside triphosphate or the DNA level by a yet unidentified set of reactions [1]. [1]. 8789257. HAM1, the gene controlling 6-N-hydroxylaminopurine sensitivity and mutagenesis in the yeast Saccharomyces cerevisiae. Noskov VN, Staak K, Shcherbakova PV, Kozmin SG, Negishi K, Ono BC, Hayatsu H, Pavlov YI;. Yeast 1996;12:17-29. (from Pfam) NF013855.5 PF01726.21 LexA_DNA_bind 23.7 23.7 65 domain Y N N LexA DNA binding domain GO:0004252,GO:0006508 8076591 131567 cellular organisms no rank 49624 EBI-EMBL LexA DNA binding domain LexA DNA binding domain This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif [1]. This domain is found associated with Pfam:PF00717 the auto-proteolytic domain of LexA EC:3.4.21.88. [1]. 8076591. Solution structure of the LexA repressor DNA binding domain determined by 1H NMR spectroscopy. Fogh RH, Ottleben G, Ruterjans H, Schnarr M, Boelens R, Kaptein R;. EMBO J 1994;13:3936-3944. (from Pfam) NF013856.5 PF01728.24 FtsJ 24.1 22.2 181 domain Y Y N SAM-dependent methyltransferase GO:0008168 10983982,8385698 131567 cellular organisms no rank 201558 EBI-EMBL FtsJ-like methyltransferase SAM-dependent methyltransferase This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesised that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping [2]. [1]. 10983982. RNA methylation under heat shock control. Bugl H, Fauman EB, Staker BL, Zheng F, Kushner SR, Saper MA, Bardwell JC, Jakob U;. Mol Cell 2000;6:349-360. [2]. 8385698. Computer-assisted identification of a putative methyltransferase domain in NS5 protein of flaviviruses and lambda 2 protein of reovirus. Koonin EV;. J Gen Virol 1993;74:733-740. (from Pfam) NF013857.5 PF01729.24 QRPTase_C 23.1 23.1 169 domain Y N N Quinolinate phosphoribosyl transferase, C-terminal domain GO:0004514,GO:0009435 8561507,9016724 131567 cellular organisms no rank 71467 EBI-EMBL Quinolinate phosphoribosyl transferase, C-terminal domain Quinolinate phosphoribosyl transferase, C-terminal domain Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase EC:2.4.2.19 is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [1,2]. The QA substrate is bound between the C-terminal domain of one subunit, and the N-terminal domain of the other. The C-terminal domain has a 7 beta-stranded TIM barrel-like fold. [1]. 9016724. A new function for a common fold: the crystal structure of quinolinic acid phosphoribosyltransferase. Eads JC, Ozturk D, Wexler TB, Grubmeyer C, Sacchettini JC;. Structure 1997;5:47-58. [2]. 8561507. The sequencing expression, purification, and steady-state kinetic analysis of quinolinate phosphoribosyl transferase from Escherichia coli. Bhatia R, Calvo KC;. Arch Biochem Biophys 1996;325:270-278. (from Pfam) NF013858.5 PF01730.21 UreF 23.3 23.3 151 domain Y Y N urease accessory UreF family protein GO:0008152,GO:0016151 8550495,8808930 131567 cellular organisms no rank 39983 EBI-EMBL UreF urease accessory UreF family protein This family consists of the Urease accessory protein UreF. The urease enzyme (urea amidohydrolase) hydrolyses urea into ammonia and carbamic acid [2]. UreF is proposed to modulate the activation process of urease by eliminating the binding of nickel irons to noncarbamylated protein [1]. [1]. 8808930. Purification and activation properties of UreD-UreF-urease apoprotein complexes. Moncrief MB, Hausinger RP;. J Bacteriol 1996;178:5417-5421. [2]. 8550495. Organization of Ureaplasma urealyticum urease gene cluster and expression in a suppressor strain of Escherichia coli. Neyrolles O, Ferris S, Behbahani N, Montagnier L, Blanchard A;. J Bacteriol 1996;178:647-655. (from Pfam) NF013859.5 PF01731.25 Arylesterase 21.3 21.3 86 PfamEq Y N N Arylesterase GO:0004064 8661009,9032442 131567 cellular organisms no rank 5923 EBI-EMBL Arylesterase Arylesterase This family consists of arylesterases (Also known as serum paraoxonase) EC:3.1.1.2. These enzymes hydrolyse organophosphorus esters such as paraoxon and are found in the liver and blood. They confer resistance to organophosphate toxicity [1]. Human arylesterase (PON1) Swiss:P27169 is associated with HDL and may protect against LDL oxidation [2]. [1]. 9032442. Purification and characterization of paraoxon hydrolase from rat liver. Rodrigo L, Gil F, Hernandez AF, Marina A, Vazquez J, Pla A;. Biochem J 1997;321:595-601. [2]. 8661009. The human serum paraoxonase/arylesterase gene (PON1) is one member of a multigene family. Primo-Parmo SL, Sorenson RC, Teiber J, La Du BN;. Genomics 1996;33:498-507. (from Pfam) NF013862.5 PF01734.27 Patatin 27.7 27.7 191 domain Y Y N patatin-like phospholipase family protein GO:0006629 3371664,7808402 131567 cellular organisms no rank 185520 EBI-EMBL Patatin-like phospholipase patatin-like phospholipase family protein This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers [2]. Patatin is a storage protein but it also has the enzymatic activity of lipid acyl hydrolase, catalysing the cleavage of fatty acids from membrane lipids [2]. Members of this family have been found also in vertebrates. [1]. 7808402. Solanum brevidens possesses a non-sucrose-inducible patatin gene. Banfalvi Z, Kostyal Z, Barta E;. Mol Gen Genet 1994;245:517-522. [2]. 3371664. Molecular characterization of the patatin multigene family of potato. Mignery GA, Pikaard CS, Park WD;. Gene 1988;62:27-44. (from Pfam) NF013865.5 PF01737.22 Ycf9 22.3 22.3 58 PfamEq Y N N YCF9 GO:0009523,GO:0009539,GO:0015979,GO:0042549 131567 cellular organisms no rank 527 EBI-EMBL YCF9 YCF9 This family consists of the hypothetical protein product of the YCF9 gene from chloroplasts and cyanobacteria. These proteins have no known function. (from Pfam) NF013866.5 PF01738.23 DLH 21 21 217 domain Y Y N dienelactone hydrolase family protein GO:0016787 2380986 131567 cellular organisms no rank 380135 EBI-EMBL Dienelactone hydrolase family dienelactone hydrolase family protein NF013867.5 PF01739.23 CheR 27 27 195 domain Y Y N CheR family methyltransferase 9115443 131567 cellular organisms no rank 80693 EBI-EMBL CheR methyltransferase, SAM binding domain CheR family methyltransferase SAM binding domain CheR proteins are part of the chemotaxis signaling mechanism in bacteria. CheR methylates the chemotaxis receptor at specific glutamate residues. CheR is an S-adenosylmethionine- dependent methyltransferase - the C-terminal domain (this one) binds SAM. [1]. 9115443. Crystal structure of the chemotaxis receptor methyltransferase CheR suggests a conserved structural motif for binding S-adenosylmethionine. Djordjevic S, Stock AM;. Structure 1997;5:545-558. (from Pfam) NF013868.5 PF01740.26 STAS 22.6 22.6 106 domain Y Y N STAS domain-containing protein 10662676,9560229 131567 cellular organisms no rank 321899 EBI-EMBL STAS domain STAS domain The STAS (after Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C terminal region of Sulphate transporters and bacterial antisigma factor antagonists. It has been suggested that this domain may have a general NTP binding function [2]. [1]. 9560229. Solution structure of SpoIIAA, a phosphorylatable component of the system that regulates transcription factor sigmaF of Bacillus subtilis. Kovacs H, Comfort D, Lord M, Campbell ID, Yudkin MD;. Proc Natl Acad Sci U S A 1998;95:5067-5071. [2]. 10662676. The STAS domain - a link between anion transporters and antisigma-factor antagonists. Aravind L, Koonin EV;. CurrBiol 2000;10:53-55. (from Pfam) NF013869.5 PF01741.23 MscL 27.4 27.4 123 PfamEq Y Y N MscL family protein 9856938 131567 cellular organisms no rank 49534 EBI-EMBL Large-conductance mechanosensitive channel, MscL MscL family protein NF013871.5 PF01743.25 PolyA_pol 23 23 126 domain Y N N Poly A polymerase head domain GO:0003723,GO:0006396,GO:0016779 1438224 131567 cellular organisms no rank 109293 EBI-EMBL Poly A polymerase head domain Poly A polymerase head domain This family includes nucleic acid independent RNA polymerases, such as Poly(A) polymerase, which adds the poly (A) tail to mRNA EC:2.7.7.19. This family also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA EC:2.7.7.25. This family is part of the nucleotidyltransferase superfamily. [1]. 1438224. Identification of the gene for an Escherichia coli poly(A) polymerase. Cao GJ, Sarkar N;. Proc Natl Acad Sci U S A 1992;89:10380-10384. (from Pfam) NF013875.5 PF01747.22 ATP-sulfurylase 24.3 24.3 212 domain Y N N ATP-sulfurylase GO:0004781 8522184,9671738 131567 cellular organisms no rank 13237 EBI-EMBL ATP-sulfurylase ATP-sulfurylase This domain is the catalytic domain of ATP-sulfurylase or sulfate adenylyltransferase EC:2.7.7.4 some of which are part of a bifunctional polypeptide chain associated with adenosyl phosphosulphate (APS) kinase Pfam:PF01583. Both enzymes are required for PAPS (phosphoadenosine-phosphosulfate) synthesis from inorganic sulphate [2]. ATP sulfurylase catalyses the synthesis of adenosine-phosphosulfate APS from ATP and inorganic sulphate [1]. [1]. 9671738. A member of a family of sulfate-activating enzymes causes murine brachymorphism [published erratum appears in Proc Natl Acad Sci U S A 1998 Sep 29;95(20):12071]. Kurima K, Warman ML, Krishnan S, Domowicz M, Krueger RC Jr, Deyrup A, Schwartz NB;. Proc Natl Acad Sci U S A 1998;95:8681-8685. [2]. 8522184. A multifunctional Urechis caupo protein, PAPS synthetase, has both ATP sulfurylase and APS kinase activities. Rosenthal E, Leustek T;. Gene 1995;165:243-248. (from Pfam) NF013877.5 PF01750.23 HycI 23 23 130 domain Y N N Hydrogenase maturation protease GO:0008047,GO:0008233 7851435 131567 cellular organisms no rank 25427 EBI-EMBL Hydrogenase maturation protease Hydrogenase maturation protease The family consists of hydrogenase maturation proteases. In E. coli HypI the hydrogenase maturation protease is involved in processing of HypE the large subunit of hydrogenases 3, by cleavage of its C-terminal [1]. [1]. 7851435. Characterisation of a protease from Escherichia coli involved in hydrogenase maturation. Rossmann R, Maier T, Lottspeich F, Bock A;. Eur J Biochem 1995;227:545-550. (from Pfam) NF013878.5 PF01751.27 Toprim 23.1 23.1 96 domain Y Y N toprim domain-containing protein 8294018,9121560,9224947,9722641 131567 cellular organisms no rank 439630 EBI-EMBL Toprim domain toprim domain This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins [1]. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity [1]. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesises the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division [2]. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases [4]. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks. [1]. 9722641. Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Aravind L, Leipe DD, Koonin EV;. Nucleic Acids Res 1998;26:4205-4213. [2]. 9224947. Cloning and analysis of the dnaG gene encoding Pseudomonas putida DNA primase. Szafranski P, Smith CL, Cantor CR;. Biochim Biophys Acta 1997;1352:243-248. [3]. 8294018. The Haemophilus influenzae dnaG sequence and conserved bacterial primase motifs. Versalovic J, Lupski JR;. Gene 1993;136:281-286. [4]. 9121560. An atypical topoisomerase II from Archaea with implications for meiotic recombination. Bergerat A, de Massy B, Gadelle D, Varoutas PC, Nicolas A, Forterre P;. Nature 1997;386:414-417. (from Pfam) NF013884.5 PF01757.27 Acyl_transf_3 31 31 326 domain Y Y N acyltransferase family protein GO:0016747 16118202,16980385,21844299,32350117 131567 cellular organisms no rank 374591 EBI-EMBL Acyltransferase family acyltransferase family protein This family includes a range of acyltransferase enzymes. This domain is found in a wide range of acyltransferase enzymes, including, mainly, bacterial proteins which catalyse the transfer of acyl groups, other than amino-acyl, from one compound to another, such as Glucans biosynthesis protein C (OPGC) or protein OatA from Listeria monocytogenes serovar 1/2a and Staphylococcus aureus, an integral membrane protein which is responsible for O-acetylation at the C6-hydroxyl group of N-acetylmuramyl residues, forming the corresponding N,6-O-diacetylmuramic acid of the peptidoglycan, a modification that determines lysozyme resistance [1,2]. This domain is also present in eukaryotic proteins, namely O-acyltransferase like protein (OACYL) from mouse and RHY1 (Regulator of hypoxia-inducible factor 1) [3] and NRF6 (Nose resistant to fluoxetine protein 6) from Caenorhabditis elegans [4]. [1]. 21844299. OatA, a peptidoglycan O-acetyltransferase involved in Listeria monocytogenes immune escape, is critical for virulence. Aubry C, Goulard C, Nahori MA, Cayet N, Decalf J, Sachse M, Boneca IG, Cossart P, Dussurget O;. J Infect Dis. 2011;204:731-740. [2]. 32350117. Structural basis for the O-acetyltransferase function of the extracytoplasmic domain of OatA from Staphylococcus aureus. Jones CS, Sychantha D, Howell PL, Clarke AJ;. J Biol Chem. 2020;295:8204-8213. [3]. 16980385. The Caenorhabditis elegans rhy-1 gene inhibits HIF-1 hypoxia-inducible factor activity in a negative feedback loop that does not include vhl-1. Shen C, Shao Z, Powell-Coffman JA;. Genetics. 2006;174:1205-1214. [4]. 16118202. Fluoxetine-resistance genes in Caenorhabditi. TRUNCATED at 1650 bytes (from Pfam) NF013885.5 PF01758.21 SBF 24.3 24.3 191 domain Y N N Sodium Bile acid symporter family GO:0016020 1961729,9234670 131567 cellular organisms no rank 133611 EBI-EMBL Sodium Bile acid symporter family Sodium Bile acid symporter family This family consists of Na+/bile acid co-transporters. These transmembrane proteins function in the liver in the uptake of bile acids from portal blood plasma a process mediated by the co-transport of Na+ [2]. Also in the family is ARC3 from S. cerevisiae Swiss:Q06598 this is a putative transmembrane protein involved in resistance to arsenic compounds [1]. [1]. 9234670. Isolation of three contiguous genes, ACR1, ACR2 and ACR3, involved in resistance to arsenic compounds in the yeast Saccharomyces cerevisiae. Bobrowicz P, Wysocki R, Owsianik G, Goffeau A, Ulaszewski S;. Yeast 1997;13:819-828. [2]. 1961729. Functional expression cloning and characterization of the hepatocyte Na+/bile acid cotransport system. Hagenbuch B, Stieger B, Foguet M, Lubbert H, Meier PJ;. Proc Natl Acad Sci U S A 1991;88:10629-10633. (from Pfam) NF013887.5 PF01761.25 DHQ_synthase 24.2 24.2 261 domain Y N N 3-dehydroquinate synthase 7556173,9613570 131567 cellular organisms no rank 91711 EBI-EMBL 3-dehydroquinate synthase 3-dehydroquinate synthase The 3-dehydroquinate synthase EC:4.6.1.3 domain is present in isolation in various bacterial 3-dehydroquinate synthases and also present as a domain in the pentafunctional AROM polypeptide Swiss:P07547 [2]. 3-dehydroquinate (DHQ) synthase catalyses the formation of dehydroquinate (DHQ) and orthophosphate from 3-deoxy-D-arabino heptulosonic 7 phosphate [1]. This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. [1]. 9613570. Cloning and characterisation of the Neisseria gonorrhoeae aroB gene. Barten R, Meyer TF;. Mol Gen Genet 1998;258:34-44. Discusses the pentafunctional AROM multi-domain protein, which possesses a shikimate 5-dehydrogenase enzyme. The AROM protein catalyses steps two to six in the shikimate pathway in many microbial eukaryotes. [2]. 7556173. The molecular biology of multidomain proteins. Selected examples. Hawkins AR, Lamb HK;. Eur J Biochem 1995;232:7-18. (from Pfam) NF013890.5 PF01764.30 Lipase_3 22 22 140 domain Y Y N lipase family protein GO:0006629 131567 cellular organisms no rank 28435 EBI-EMBL Lipase (class 3) lipase family protein NF013895.5 PF01769.21 MgtE 27.6 27.6 125 domain Y Y N magnesium transporter GO:0006812,GO:0008324 7665526,7868596 131567 cellular organisms no rank 54916 EBI-EMBL Divalent cation transporter magnesium transporter This region is the integral membrane part of the eubacterial MgtE family of magnesium transporters. Related regions are found also in archaebacterial and eukaryotic proteins. All the archaebacterial and eukaryotic examples have two copies of the region. This suggests that the eubacterial examples may act as dimers. Members of this family probably transport Mg2+ or other divalent cations into the cell. The alignment contains two highly conserved aspartates that may be involved in cation binding (Bateman A unpubl.) [1]. 7868596. Cloning and characterization of MgtE, a putative new class of Mg2+ transporter from Bacillus firmus OF4. Smith RL, Thompson LJ, Maguire ME;. J Bacteriol 1995;177:1233-1238. [2]. 7665526. Cloning of the mgtE Mg2+ transporter from Providencia stuartii and the distribution of mgtE in gram-negative and gram-positive bacteria. Townsend DE, Esenwine AJ, George J 3rd, Bross D, Maguire ME, Smith RL;. J Bacteriol 1995;177:5350-5354. (from Pfam) NF013899.5 PF01774.22 UreD 27 27 201 PfamEq Y Y N urease accessory protein UreD GO:0008152,GO:0016151 7909161,8550495,9209019 131567 cellular organisms no rank 43221 EBI-EMBL UreD urease accessory protein urease accessory protein UreD UreD is a urease accessory protein. Urease Pfam:PF00449 hydrolyses urea into ammonia and carbamic acid [2]. UreD is involved in activation of the urease enzyme via the UreD-UreF-UreG-urease complex [1] and is required for urease nickel metallocenter assembly [3]. See also UreF Pfam:PF01730, UreG Pfam:PF01495. [1]. 9209019. Characterization of UreG, identification of a UreD-UreF-UreG complex, and evidence suggesting that a nucleotide-binding site in UreG is required for in vivo metallocenter assembly of Klebsiella aerogenes urease. Moncrief MB, Hausinger RP;. J Bacteriol 1997;179:4081-4086. [2]. 8550495. Organization of Ureaplasma urealyticum urease gene cluster and expression in a suppressor strain of Escherichia coli. Neyrolles O, Ferris S, Behbahani N, Montagnier L, Blanchard A;. J Bacteriol 1996;178:647-655. [3]. 7909161. In vitro activation of urease apoprotein and role of UreD as a chaperone required for nickel metallocenter assembly. Park IS, Carr MB, Hausinger RP;. Proc Natl Acad Sci U S A 1994;91:3233-3237. (from Pfam) NF013900.5 PF01775.22 Ribosomal_L18A 22.9 22.9 59 PfamEq Y N N Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A GO:0003735,GO:0005840,GO:0006412 1711982 131567 cellular organisms no rank 932 EBI-EMBL Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A This family includes: archaeal 50S ribosomal protein L18Ae, often referred to as L20e or LX; fungal 60S ribosomal protein L20; and higher eukaryote 60S ribosomal protein L18A. [1]. 1711982. A small basic ribosomal protein from the extreme thermophilic archaebacterium Sulfolobus solfataricus that has no equivalent in Escherichia coli. Ramirez C, Louie KA, Matheson AT;. FEBS Lett 1991;284:39-41. (from Pfam) NF013901.5 PF01776.22 Ribosomal_L22e 23.6 23.6 110 domain Y Y N 60S ribosomal protein L22 GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 8 EBI-EMBL Ribosomal L22e protein family 60S ribosomal protein L22 NF013905.5 PF01780.24 Ribosomal_L37ae 21.9 21.9 85 PfamEq Y N N Ribosomal L37ae protein family GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 1094 EBI-EMBL Ribosomal L37ae protein family Ribosomal L37ae protein family This ribosomal protein is found in archaebacteria and eukaryotes. It contains four conserved cysteine residues that may bind to zinc. (from Pfam) NF013906.5 PF01781.23 Ribosomal_L38e 27 27 68 PfamEq Y N N Ribosomal L38e protein family GO:0003735,GO:0005840,GO:0006412 1840484 131567 cellular organisms no rank 20 EBI-EMBL Ribosomal L38e protein family Ribosomal L38e protein family NF013907.5 PF01782.23 RimM 23.5 23.5 84 PfamEq Y N N RimM N-terminal domain GO:0006364 12429060,9422595 131567 cellular organisms no rank 59403 EBI-EMBL RimM N-terminal domain RimM N-terminal domain The RimM protein is essential for efficient processing of 16S rRNA [1]. The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes [1]. This N-terminal domain is found associated with a PRC-barrel domain [2]. [1]. 9422595. RimM and RbfA are essential for efficient processing of 16S rRNA in Escherichia coli. Bylund GO, Wipemo LC, Lundberg LA, Wikstrom PM;. J Bacteriol 1998;180:73-82. [2]. 12429060. The PRC-barrel: a widespread, conserved domain shared by photosynthetic reaction center subunits and proteins of RNA metabolism. Anantharaman V, Aravind L;. Genome Biol 2002;3:RESEARCH0061. (from Pfam) NF013909.5 PF01784.23 DUF34_NIF3 23.4 23.4 244 PfamEq Y Y N Nif3-like dinuclear metal center hexameric protein 11124544,23825549,34572495,8663102 131567 cellular organisms no rank 69484 EBI-EMBL Duf34/NIF3 (NGG1p interacting factor 3) Nif3-like dinuclear metal center hexameric protein This family includes the DUF34/metal-binding protein/NIF3 proteins, which are widely distributed across superkingdoms. They were previously annotated as GTP cyclohydrolase 1 type 2 [3] and, recently, through a comprehensive literature review and integrative bioinformatic analyses it was revealed that annotations for these members were misleading as they were based on a single set of in vitro results examining the NIF3 homolog of Helicobacter pylori [3]. Actually, they have varied phenotypes with the unifying functional role as metal-binding proteins [4]. This entry contains several NIF3 (NGG1p interacting factor 3) protein homologues. NIF3 interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex, the exact function of this interaction is unknown [1,2]. [1]. 8663102. Transcriptional activation by yeast PDR1p is inhibited by its association with NGG1p/ADA3p. Martens JA, Genereaux J, Saleh A, Brandl CJ;. J Biol Chem 1996;271:15884-15890. [2]. 11124544. Isolation and characterization of a novel human gene, NIF3L1, and its mouse ortholog, Nif3l1, highly conserved from bacteria to mammals. Tascou S, Uedelhoven J, Dixkens C, Nayernia K, Engel W, Burfeind P;. Cytogenet Cell Genet 2000;90:330-336. [3]. 23825549. Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori. Choi HP, Juarez S, Ciordia S, Fernandez M, Bargiela R, Albar JP, Mazumdar V, Anton BP, Kasif S, Ferrer M, Steffen M;. PLoS One. 2013;8:e66605. [4]. 34572495. Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase. Reed CJ, Hutinet G, de Crecy-Lagard V;. Bi. TRUNCATED at 1650 bytes (from Pfam) NF013914.5 PF01789.21 PsbP 23.5 23.5 155 domain Y Y N PsbP-related protein GO:0005509,GO:0009523,GO:0009654,GO:0015979,GO:0019898 20698571,22414666,8910540,9039496 131567 cellular organisms no rank 2336 EBI-EMBL PsbP PsbP-related protein While most members of this family PsbP are from photosystem II, those proteins are easily named by other annotation rules. This family also includes proteins from non-photosynthetic lineages such as Treponema, Micromonospora, and Methanobacterium, so proteins named only by this model are designated PsbP-related protein. NF013916.5 PF01791.14 DeoC 23.8 23.8 229 domain Y N N DeoC/LacD family aldolase GO:0016829 1655695,1730028 131567 cellular organisms no rank 88642 EBI-EMBL DeoC/LacD family aldolase DeoC/LacD family aldolase This family includes diverse aldolase enzymes. This family includes the enzyme deoxyribose-phosphate aldolase EC:4.1.2.4, which is involved in nucleotide metabolism. The family also includes a group of related bacterial proteins of unknown function, see examples Swiss:Q57843 and Swiss:P76143. The family also includes tagatose 1,6-diphosphate aldolase (EC:4.1.2.40) is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation [2]. [1]. 1730028. Deoxyribose 5-phosphate aldolase of Bacillus cereus: purification and properties. Sgarrella F, Del Corso A, Tozzi MG, Camici M;. Biochim Biophys Acta 1992;1118:130-133. [2]. 1655695. Lactose metabolism by Staphylococcus aureus: characterization of lacABCD, the structural genes of the tagatose 6-phosphate pathway. Rosey EL, Oskouian B, Stewart GC;. J Bacteriol 1991;173:5992-5998. (from Pfam) NF013918.5 PF01794.24 Ferric_reduct 28 28 121 domain Y Y N ferric reductase-like transmembrane domain-containing protein 1318579,3600768,3600769,8321236 131567 cellular organisms no rank 52863 EBI-EMBL Ferric reductase like transmembrane component Ferric reductase like transmembrane component This family includes a common region in the transmembrane proteins mammalian cytochrome B-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress. This may be a family of flavocytochromes capable of moving electrons across the plasma membrane [1]. The Frp1 protein Swiss:Q04800 from S. pombe is a ferric reductase component and is required for cell surface ferric reductase activity, mutants in frp1 are deficient in ferric iron uptake [1]. Cytochrome B-245 heavy chain Swiss:P04839 is a FAD-dependent dehydrogenase it is also has electron transferase activity which reduces molecular oxygen to superoxide anion, a precursor in the production of microbicidal oxidants [2]. Mutations in the sequence of cytochrome B-245 heavy chain (gp91-phox) lead to the X-linked chronic granulomatous disease. The bacteriocidal ability of phagocytic cells is reduced and is characterised by the absence of a functional plasma membrane associated NADPH oxidase [3]. The chronic granulomatous disease gene codes for the beta chain of cytochrome B-245 and cytochrome B-245 is missing from patients with the disease [4]. [1]. 8321236. The fission yeast ferric reductase gene frp1+ is required for ferric iron uptake and encodes a protein that is homologous to the gp91-phox subunit of the human NADPH phagocyte oxidoreductase. Roman DG, Dancis A, Anderson GJ, Klausner RD;. Mol Cell Biol 1993;13:4342-4350. [2]. 1318579. Cytochrome b558: the flavin-binding component of the phagocyte NADPH oxidase. Rotrosen D, Yeung CL, Leto TL, Malech HL, Kwong CH;. Science 1992;256:1459-1462. [3]. 3600768. . TRUNCATED at 1650 bytes (from Pfam) NF013919.5 PF01795.24 Methyltransf_5 27 27 309 domain Y Y N 16S rRNA (cytosine(1402)-N(4))-methyltransferase mraW 2.1.1.199 GO:0008168 10572301 131567 cellular organisms no rank 73258 EBI-EMBL MraW methylase family 16S rRNA (cytosine(1402)-N(4))-methyltransferase Members of this family are probably SAM dependent methyltransferases based on Swiss:P18595 [1]. This family appears to be related to Pfam:PF01596. [1]. 10572301. mraW, an essential gene at the dcw cluster of Escherichia coli codes for a cytoplasmic protein with methyltransferase activity. Carrion M, Gomez MJ, Merchante-Schubert R, Dongarra S, Ayala JA;. Biochimie 1999;81:879-888. (from Pfam) NF013920.5 PF01796.22 OB_aCoA_assoc 27.1 27.1 65 domain Y Y N OB-fold domain-containing protein 20944206,23793631 131567 cellular organisms no rank 59632 EBI-EMBL DUF35 OB-fold domain, acyl-CoA-associated DUF35 OB-fold domain, acyl-CoA-associated The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain and a C-terminal OB fold domain represented in this entry. OB-folds are frequently found to bind nucleic acids suggesting this domain might bind to DNA or RNA (Topsan http://www.topsan.org/). Genomic context shows it to be adjacent to acyl-CoA transferase (http:/www.microbesonline.org/). [1]. 20944206. The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role. Krishna SS, Aravind L, Bakolitsa C, Caruthers J, Carlton D, Miller MD, Abdubek P, Astakhova T, Axelrod HL, Chiu HJ, Clayton T, Deller MC, Duan L, Feuerhelm J, Grant JC, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:1160-1166. [2]. 23793631. Haloarchaeal-type beta-ketothiolases involved in Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) synthesis in Haloferax mediterranei. Hou J, Feng B, Han J, Liu H, Zhao D, Zhou J, Xiang H;. Appl Environ Microbiol. 2013;79:5104-5111. (from Pfam) NF013921.5 PF01797.21 Y1_Tnp 23 23 121 domain Y Y N transposase GO:0003677,GO:0004803,GO:0006313 16209952,9245800 131567 cellular organisms no rank 89631 EBI-EMBL Transposase IS200 like transposase Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS200 from E. coli. [1]. 9245800. The Clostridium perfringens enterotoxin gene is on a transposable element in type A human food poisoning strains. Brynestad S, Synstad B, Granum PE;. Microbiology 1997;143:2109-2115. [2]. 16209952. Active site sharing and subterminal hairpin recognition in a new class of DNA transposases. Ronning DR, Guynet C, Ton-Hoang B, Perez ZN, Ghirlando R, Chandler M, Dyda F;. Mol Cell. 2005;20:143-154. (from Pfam) NF013922.5 PF01798.23 Nop 25.4 17.1 228 PfamEq Y N N snoRNA binding domain, fibrillarin 20864039,8604353,9372940,9632712 131567 cellular organisms no rank 1582 EBI-EMBL snoRNA binding domain, fibrillarin snoRNA binding domain, fibrillarin This family consists of various Pre RNA processing ribonucleoproteins. The function of the aligned region is unknown however it may be a common RNA or snoRNA or Nop1p binding domain. Nop5p (Nop58p) Swiss:Q12499 from yeast is the protein component of a ribonucleoprotein required for pre-18s rRNA processing and is suggested to function with Nop1p in a snoRNA complex [1]. Nop56p Swiss:O00567 and Nop5p interact with Nop1p and are required for ribosome biogenesis [2]. Prp31p Swiss:p49704 is required for pre-mRNA splicing in S. cerevisiae [3]. Fibrillarin, or Nop, is the catalytic subunit responsible for the methyl transfer reaction of the site-specific 2'-O-methylation of ribosomal and spliceosomal RNA [4]. [1]. 9632712. Nop5p is a small nucleolar ribonucleoprotein component required for pre- 18 S rRNA processing in yeast. Wu P, Brockenbrough JS, Metcalfe AC, Chen S, Aris JP;. J Biol Chem 1998;273:16453-16463. [2]. 9372940. Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis. Gautier T, Berges T, Tollervey D, Hurt E;. Mol Cell Biol 1997;17:7088-7098. [3]. 8604353. The PRP31 gene encodes a novel protein required for pre-mRNA splicing in Saccharomyces cerevisiae. Weidenhammer EM, Singh M, Ruiz-Noriega M, Woolford JL Jr;. Nucleic Acids Res. 1996;24:1164-1170. [4]. 20864039. Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle. Xue S, Wang R, Yang F, Terns RM, Terns MP, Zhang X, Maxwell ES, Li H;. Mol Cell. 2010;39:939-949. (from Pfam) NF013923.5 PF01799.25 Fer2_2 30.3 30.3 75 domain Y Y N 2Fe-2S iron-sulfur cluster-binding protein GO:0016491,GO:0046872 7502041 131567 cellular organisms no rank 161734 EBI-EMBL [2Fe-2S] binding domain 2Fe-2S iron-sulfur cluster-binding domain NF013927.5 PF01804.23 Penicil_amidase 21.3 21.3 675 domain Y Y N penicillin acylase family protein GO:0016787,GO:0017000 7816145,9292993 131567 cellular organisms no rank 78929 EBI-EMBL Penicillin amidase penicillin acylase family protein Penicillin amidase or penicillin acylase EC:3.5.1.11 catalyses the hydrolysis of benzylpenicillin to phenylacetic acid and 6-aminopenicillanic acid (6-APA) a key intermediate in the the synthesis of penicillins [1]. Also in the family is cephalosporin acylase Swiss:P07662 and Swiss:P29958 aculeacin A acylase which are involved in the synthesis of related peptide antibiotics. [1]. 9292993. Molecular cloning and analysis of the gene encoding the thermostable penicillin G acylase from Alcaligenes faecalis. Verhaert RM, Riemens AM, van der Laan JM, van Duin J, Quax WJ;. Appl Environ Microbiol 1997;63:3412-3418. [2]. 7816145. Penicillin acylase has a single-amino-acid catalytic centre. Duggleby HJ, Tolley SP, Hill CP, Dodson EJ, Dodson G, Moody PC;. Nature 1995;373:264-268. (from Pfam) NF013930.5 PF01807.25 zf-CHC2 24.9 24.9 98 domain Y Y N CHC2 zinc finger domain-containing protein GO:0003677,GO:0003896,GO:0006260,GO:0008270 10745010 131567 cellular organisms no rank 103156 EBI-EMBL CHC2 zinc finger CHC2 zinc finger This domain is principally involved in DNA binding in DNA primases. [1]. 10745010. Structure of the zinc-binding domain of Bacillus stearothermophilus DNA primase. Pan H, Wigley DB;. Structure Fold Des 2000;8:231-239. (from Pfam) NF013931.5 PF01808.23 AICARFT_IMPCHas 25 25 311 PfamEq Y N N AICARFT/IMPCHase bienzyme GO:0003937,GO:0004643,GO:0006164 21890906,8567683,9332377 131567 cellular organisms no rank 82378 EBI-EMBL AICARFT/IMPCHase bienzyme AICARFT/IMPCHase bienzyme This is a family of bifunctional enzymes catalysing the last two steps in de novo purine biosynthesis. The bifunctional enzyme is found in both prokaryotes and eukaryotes. The second last step is catalysed by 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase EC:2.1.2.3 (AICARFT), this enzyme catalyses the formylation of AICAR with 10-formyl-tetrahydrofolate to yield FAICAR and tetrahydrofolate [1]. This is catalysed by a pair of C-terminal deaminase fold domains in the protein [3], where the active site is formed by the dimeric interface of two monomeric units [3]. The last step is catalysed by the N-terminal IMP (Inosine monophosphate) cyclohydrolase domain EC:3.5.4.10 (IMPCHase), cyclizing FAICAR (5-formylaminoimidazole-4-carboxamide ribonucleotide) to IMP [1]. [1]. 9332377. Molecular cloning and expression of a rat cDNA encoding 5- aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase [published erratum appears in Gene 1998 Feb 27;208(2):337]. Akira T, Komatsu M, Nango R, Tomooka A, Konaka K, Yamauchi M, Kitamura Y, Nomura S, Tsukamoto I;. Gene 1997;197:289-293. [2]. 8567683. The human purH gene product, 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase. Cloning, sequencing, expression, purification, kinetic analysis, and domain mapping. Rayl EA, Moroson BA, Beardsley GP;. J Biol Chem 1996;271:2225-2233. [3]. 21890906. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Iyer LM, Zhang D, Rogozin IB, Aravind L;. Nucleic Acids Res. 2011; [Epub ahead of prin. TRUNCATED at 1650 bytes (from Pfam) NF013932.5 PF01809.23 YidD 27 27 67 PfamEq Y Y N membrane protein insertion efficiency factor YidD yidD 21803992 131567 cellular organisms no rank 48837 EBI-EMBL Putative membrane protein insertion efficiency factor membrane protein insertion efficiency factor YidD This family consists of membrane insertion efficiency factor proteins. They contain three conserved cysteine residues. Family members such as YidD may be involved in insertion of integral membrane proteins into the membrane by assisting YidC (membrane protein insertase). Some members of the yidD family have been previously thought to posses alpha-hemolysin activity, however no sufficient evidence was found to corroborate this idea. Secondary structure prediction indicated the presence of three alpha-helices in YidD. None of the three alpha-helices appeared sufficiently hydrophobic to serve as a transmembrane, suggesting a cytoplasmic localization for YidD. However, a closer examination of the alpha-helical wheel projection of the predicted first alpha-helix in YidD suggested an amphipathic structure in its N-terminal region which might be involved in membrane targeting [1]. [1]. 21803992. Role for Escherichia coli YidD in membrane protein insertion. Yu Z, Laven M, Klepsch M, de Gier JW, Bitter W, van Ulsen P, Luirink J;. J Bacteriol. 2011;193:5242-5251. (from Pfam) NF013933.5 PF01810.23 LysE 25.6 25.6 193 subfamily Y Y N LysE family transporter GO:0006865,GO:0016020 10322417,8971704 131567 cellular organisms no rank 311709 EBI-EMBL LysE type translocator LysE family transporter This family consists of various hypothetical proteins and an l-lysine exporter LysE Swiss:P94633 from Corynebacterium glutamicum which is proposed to be the first of a novel family of translocators [1]. LysE exports l-lysine from the cell into the surrounding medium and is predicted to span the membrane six times [1]. The physiological function of the exporter is to excrete excess l-Lysine as a result of natural flux imbalances or peptide hydrolysis; and also after artificial deregulation of l-Lysine biosynthesis as used by the biotechnology. industry for the production of l-lysine [1]. [1]. 8971704. A new type of transporter with a new type of cellular function: L- lysine export from Corynebacterium glutamicum. Vrljic M, Sahm H, Eggeling L;. Mol Microbiol 1996;22:815-826. [2]. 10322417. A new family of amino-acid-efflux proteins. Aleshin VV, Zakataeva NP, Livshits VA;. Trends Biochem Sci 1999;24:133-135. (from Pfam) NF013934.5 PF01812.25 5-FTHF_cyc-lig 27 27 186 PfamEq Y Y N 5-formyltetrahydrofolate cyclo-ligase 8034591,8522195 131567 cellular organisms no rank 80307 EBI-EMBL 5-formyltetrahydrofolate cyclo-ligase family 5-formyltetrahydrofolate cyclo-ligase 5-formyltetrahydrofolate cyclo-ligase or methenyl-THF synthetase EC:6.3.3.2 catalyses the interchange of 5-formyltetrahydrofolate (5-FTHF) to 5-10-methenyltetrahydrofolate, this requires ATP and Mg2+ [1]. 5-FTHF is used in chemotherapy where it is clinically known as Leucovorin [2]. [1]. 8522195. Cloning and characterization of the human 5,10-methenyltetrahydrofolate synthetase-encoding cDNA. Dayan A, Bertrand R, Beauchemin M, Chahla D, Mamo A, Filion M, Skup D, Massie B, Jolivet J;. Gene 1995;165:307-311. [2]. 8034591. Primary structure and tetrahydropteroylglutamate binding site of rabbit liver cytosolic 5,10-methenyltetrahydrofolate synthetase. Maras B, Stover P, Valiante S, Barra D, Schirch V;. J Biol Chem 1994;269:18429-18433. (from Pfam) NF013935.5 PF01813.22 ATP-synt_D 25.7 25.7 196 domain Y Y N V-type ATP synthase subunit D GO:0042626,GO:0046961 7831318,8702544 131567 cellular organisms no rank 8552 EBI-EMBL ATP synthase subunit D V-type ATP synthase subunit D This is a family of subunit D form various ATP synthases including V-type H+ transporting and Na+ dependent. Subunit D is suggested to be an integral part of the catalytic sector of the V-ATPase [2]. [1]. 8702544. Subunit structure and organization of the genes of the A1A0 ATPase from the Archaeon Methanosarcina mazei Go1. Wilms R, Freiberg C, Wegerle E, Meier I, Mayer F, Muller V;. J Biol Chem 1996;271:18843-18852. [2]. 7831318. A bovine cDNA and a yeast gene (VMA8) encoding the subunit D of the vacuolar H(+)-ATPase. Nelson H, Mandiyan S, Nelson N;. Proc Natl Acad Sci U S A 1995;92:497-501. (from Pfam) NF013936.5 PF01814.28 Hemerythrin 25.3 25.3 127 domain Y Y N hemerythrin domain-containing protein 11513618,12625841,678527,9188702 131567 cellular organisms no rank 125501 EBI-EMBL Hemerythrin HHE cation binding domain Hemerythrin HHE cation binding domain Iteration of the HHE family ([2]) found it to be related to Hemerythrin. It also demonstrated that what has been described as a single domain ([1]) in fact consists of two cation binding domains. Members of this family occur all across nature and are involved in a variety of processes. For instance, in Nereis diversicolor Swiss:P80255 binds Cadmium so as to protect the organism from toxicity ([3]). However Hemerythrin is classically described as Oxygen-binding through two attached Fe2+ ions. And the bacterial Swiss:Q7WX96 is a regulator of response to NO, which suggests yet another set-up for its metal ligands ([4]). In Staphylococcus aureus P72360 has been noted to be important when the organism switches to living in environments with low oxygen concentrations ([4]); perhaps this protein acts as an oxygen store or scavenger. This domain can bind oxygen (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043) [1]. 678527. Structure of methemerythrin at 2.8-Angstrom resolution: computer graphics fit of an averaged electron density map. Stenkamp RE, Sieker LC, Jensen LH, McQueen JE Jr;. Biochemistry 1978;17:2499-2504. [2]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. [3]. 9188702. Structures of wild-type chloromet and L103N hydroxomet Themiste zostericola myohemerythrins at 1.8 A resolution. Martins LJ, Hill CP, Ellis WR Jr;. Biochemistry 1997;36:7044-7049. [4]. 11513618. The srhSR gene pair from Staphylococcus aureus: genomic and proteomic approaches to the . TRUNCATED at 1650 bytes (from Pfam) NF013938.5 PF01816.22 LRV 21.6 21.6 26 repeat Y N N variant-type leucine-rich repeat protein 8946850 131567 cellular organisms no rank 4469 EBI-EMBL Leucine rich repeat variant variant-type leucine-rich repeat The function of this repeat is unknown. It has an unusual structure of two helices. One is an alpha helix, the other is the much rarer 3-10 helix. [1]. 8946850. A leucine-rich repeat variant with a novel repetitive protein structural motif. Peters JW, Stowell MH, Rees DC;. Nat Struct Biol 1996;3:991-994. (from Pfam) NF013939.5 PF01817.26 CM_2 27 27 80 domain Y Y N chorismate mutase 5.4.99.5 GO:0046417 7971967,9497350,9642265 131567 cellular organisms no rank 88806 EBI-EMBL Chorismate mutase type II chorismate mutase Chorismate mutase EC:5.4.99.5 catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine [2,3]. [1]. 7971967. The crystal structure of allosteric chorismate mutase at 2.2-A resolution. Xue Y, Lipscomb WN, Graf R, Schnappauf G, Braus G;. Proc Natl Acad Sci U S A 1994;91:10814-10818. [2]. 9642265. Tyrosine and tryptophan act through the same binding site at the dimer interface of yeast chorismate mutase. Schnappauf G, Krappmann S, Braus GH;. J Biol Chem 1998;273:17012-17017. [3]. 9497350. Chorismate mutase-prephenate dehydratase from Escherichia coli. Study of catalytic and regulatory domains using genetically engineered proteins. Zhang S, Pohnert G, Kongsaeree P, Wilson DB, Clardy J, Ganem B;. J Biol Chem 1998;273:6248-6253. (from Pfam) NF013942.5 PF01820.26 Dala_Dala_lig_N 34.6 34.6 121 domain Y N N D-ala D-ala ligase N-terminus 10908650,12499203,9054558 131567 cellular organisms no rank 88972 EBI-EMBL D-ala D-ala ligase N-terminus D-ala D-ala ligase N-terminus This family represents the N-terminal region of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4 which is thought to be involved in substrate binding [2]. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF) [3]. This domain is structurally related to the PreATP-grasp domain. [1]. 9054558. D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant. Fan C, Park IS, Walsh CT, Knox JR;. Biochemistry 1997;36:2531-2538. [2]. 10908650. The molecular basis of vancomycin resistance in clinically relevant Enterococci: crystal structure of D-alanyl-D-lactate ligase (VanA). Roper DI, Huyton T, Vagin A, Dodson G;. Proc Natl Acad Sci U S A 2000;97:8921-8925. [3]. 12499203. Roles of Mycobacterium smegmatis D-alanine:D-alanine ligase and D-alanine racemase in the mechanisms of action of and resistance to the peptidoglycan inhibitor D-cycloserine. Feng Z, Barletta RG;. Antimicrob Agents Chemother 2003;47:283-291. (from Pfam) NF013945.5 PF01823.24 MACPF 21.5 21.5 214 domain Y Y N MAC/perforin domain-containing protein 17717151,17872444 131567 cellular organisms no rank 2203 EBI-EMBL MAC/Perforin domain MAC/perforin domain The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (Pfam:PF01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold [1]. [1]. 17717151. A common fold mediates vertebrate defense and bacterial attack. Rosado CJ, Buckle AM, Law RH, Butcher RE, Kan WT, Bird CH, Ung K, Browne KA, Baran K, Bashtannyk-Puhalovich TA, Faux NG, Wong W, Porter CJ, Pike RN, Ellisdon AM, Pearce MC, Bottomley SP, Emsley J, Smith AI, Ros. TRUNCATED at 1650 bytes (from Pfam) NF013950.5 PF01828.23 Peptidase_A4 22.3 22.3 206 subfamily Y Y N G1 family glutamic endopeptidase GO:0006508,GO:0070007 21122090 131567 cellular organisms no rank 2234 EBI-EMBL Peptidase A4 family G1 family glutamic endopeptidase NF013955.5 PF01833.29 TIG 20.9 19.7 84 domain Y Y N IPT/TIG domain-containing protein 10222208,10390613 131567 cellular organisms no rank 30409 EBI-EMBL IPT/TIG domain IPT/TIG domain This family consists of a domain that has an immunoglobulin like fold. These domains are found in cell surface receptors such as Met and Ron as well as in intracellular transcription factors where it is involved in DNA binding. CAUTION: This family does not currently recognise a significant number of members. [1]. 10390613. Domains in plexins: links to integrins and transcription factors. Bork P, Doerks T, Springer TA, Snel B;. Trends Biochem Sci 1999;24:261-263. [2]. 10222208. Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. Aravind L, Koonin EV;. J Mol Biol 1999;287:1023-1040. (from Pfam) NF013957.5 PF01835.24 MG2 32.8 32.8 96 domain Y Y N MG2 domain-containing protein GO:0004866 16177781,22290936,25221932 131567 cellular organisms no rank 58263 EBI-EMBL MG2 domain MG2 domain This is the MG2 (macroglobulin) domain of alpha-2-macroglobulin in eukaryotes [1]. Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. However, A2M-like proteins were identified in pathogenically invasive bacteria and species that colonize higher eukaryotes. This domain is found in eukaryotic and bacterial proteins. In human A2Ms, this domain is termed macroglobulin-like (MG) domain 2 and in Salmonella enterica ser A2Ms, this is domain 4 [2] [3]. [1]. 16177781. Structures of complement component C3 provide insights into the function and evolution of immunity. Janssen BJ, Huizinga EG, Raaijmakers HC, Roos A, Daha MR, Nilsson-Ekdahl K, Nilsson B, Gros P;. Nature. 2005;437:505-511. [2]. 25221932. Structure of a bacterial alpha2-macroglobulin reveals mimicry of eukaryotic innate immunity. Wong SG, Dessen A;. Nat Commun. 2014;5:4917. [3]. 22290936. The crystal structure of human alpha2-macroglobulin reveals a unique molecular cage. Marrero A, Duquerroy S, Trapani S, Goulas T, Guevara T, Andersen GR, Navaza J, Sottrup-Jensen L, Gomis-Ruth FX;. Angew Chem Int Ed Engl. 2012;51:3340-3344. (from Pfam) NF013958.5 PF01837.21 HcyBio 26.2 26.2 349 domain Y Y N homocysteine biosynthesis protein 25315403 131567 cellular organisms no rank 2477 EBI-EMBL Homocysteine biosynthesis enzyme, sulfur-incorporation homocysteine biosynthesis protein This presumed domain is about is about 360 residues long. The function of this domain is unknown. It is found in some proteins that have two C-terminal CBS Pfam:PF00571 domains. There are also proteins that contain two inserted Fe4S domains near the C-terminal end of the domain. The protein Swiss:O26943 has been misannotated as an inosine monophosphate dehydrogenase based on the similarity to the CBS domains. Based on genetic analyses in the methanogen Methanosarcina acetivorans, this family is a key component of the metabolic network for sulfide assimilation and trafficking in methanogens. It is essential to a novel, O-acetylhomoserine sulfhydrylase-independent pathway for homocysteine biosynthesis, and may catalyse sulfur incorporation into the side chain of an as yet unidentified amino acid precursor [1]. The DUF39-CBS and DUF39-ferredoxin architectures repeatedly occur together in the genomes of methanogenic Archaea, suggesting they may be of diverged function. This is consistent with a phylogenetic reconstruction of the DUF39 family, which clearly distinguishes the CBS-associated and ferredoxin-associated DUF39s [1]. [1]. 25315403. Novel proteins for homocysteine biosynthesis in anaerobic microorganisms. Rauch BJ, Gustafson A, Perona JJ;. Mol Microbiol. 2014;94:1330-1342. (from Pfam) NF013959.5 PF01839.28 FG-GAP 22.1 22.1 37 repeat Y N N FG-GAP repeat protein 7929213,8990162 131567 cellular organisms no rank 55496 EBI-EMBL FG-GAP repeat FG-GAP repeat This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure [1]. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat [1]. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding [2]. A putative Ca2+ binding motif is found in some of the repeats. [1]. 8990162. Folding of the N-terminal, ligand-binding region of integrin alpha- subunits into a beta-propeller domain. Springer TA;. Proc Natl Acad Sci U S A 1997;94:65-72. [2]. 7929213. Integrin-mediated cell adhesion: the extracellular face. Loftus JC, Smith JW, Ginsberg MH;. J Biol Chem 1994;269:25235-25238. (from Pfam) NF013961.5 PF01841.24 Transglut_core 23 23 108 domain Y Y N transglutaminase domain-containing protein 10452618,7913750,9791169 131567 cellular organisms no rank 203673 EBI-EMBL Transglutaminase-like superfamily Transglutaminase-like superfamily This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterised transglutaminase, the human blood clotting factor XIIIa' [1]. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase [2], it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease. [3] [1]. 7913750. Three-dimensional structure of a transglutaminase: human blood coagulation factor XIII. Yee VC, Pedersen LC, Le Trong I, Bishop PD, Stenkamp RE, Teller DC;. Proc Natl Acad Sci USA 1994;91:7296-7300. [2]. 9791169. Molecular analysis of Methanobacterium phage psiM2. Pfister P, Wasserfallen A, Stettler R, Leisinger T;. Mol Microbiol 1998;30:233-244. [3]. 10452618. A superfamily of archaeal, bacterial, and eukaryotic proteins homologous to animal transglutaminases [In Process Citation]. Makarova KS, Aravind L, Koonin EV;. Protein Sci 1999;8:1714-1719. (from Pfam) NF013962.5 PF01842.30 ACT 27 27 66 domain Y Y N ACT domain-containing protein 10222208,7719856 131567 cellular organisms no rank 297848 EBI-EMBL ACT domain ACT domain This family of domains generally have a regulatory role. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. The ACT domain is found in: D-3-phosphoglycerate dehydrogenase EC:1.1.1.95 Swiss:P08328, which is inhibited by serine [1]. Aspartokinase EC:2.7.2.4 Swiss:P53553, which is regulated by lysine. Acetolactate synthase small regulatory subunit Swiss:P00894, which is inhibited by valine. Phenylalanine-4-hydroxylase EC:1.14.16.1 Swiss:P00439, which is regulated by phenylalanine. Prephenate dehydrogenase EC:4.2.1.51 Swiss:P21203. formyltetrahydrofolate deformylase EC:3.5.1.10, Swiss:P37051, which is activated by methionine and inhibited by glycine. GTP pyrophosphokinase EC:2.7.6.5 Swiss:P11585 [1]. 7719856. The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase. Schuller DJ, Grant GA, Banaszak LJ;. Nat Struct Biol 1995;2:69-76. Definition of the domain. [2]. 10222208. Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. Aravind L, Koonin EV;. J Mol Biol 1999;287:1023-1040. (from Pfam) NF013964.5 PF01844.28 HNH 21.4 21.4 47 domain Y Y N HNH endonuclease GO:0003676,GO:0004519,GO:0008270 27131500,7817395,7920259,9358175 131567 cellular organisms no rank 191574 EBI-EMBL HNH endonuclease HNH endonuclease His-Asn-His (HNH) proteins are a very common family of small nucleic acid-binding proteins that are generally associated with endonuclease activity [4]. Named family as HNH. [1]. 7817395. Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns. Shub DA, Goodrich-Blair H, Eddy SR;. Trends Biochem Sci 1994;19:402-404. Extended HNH family. [2]. 9358175. Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family. Dalgaard JZ, Klar AJ, Moser MJ, Holley WR, Chatterjee A, Mian IS;. Nucleic Acids Res 1997;25:4626-4638. Named family as EX1HH-HX3H. [3]. 7920259. Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family. Gorbalenya AE;. Protein Sci 1994;3:1117-1120. [4]. 27131500. Biochemical characterization of a thermostable HNH endonuclease from deep-sea thermophilic bacteriophage GVE2. Zhang L, Huang Y, Xu D, Yang L, Qian K, Chang G, Gong Y, Zhou X, Ma K;. Appl Microbiol Biotechnol. 2016;100:8003-8012. (from Pfam) NF013969.5 PF01849.23 NAC 21.3 21.3 57 domain Y Y N NAC domain-containing protein 10413400 131567 cellular organisms no rank 1270 EBI-EMBL NAC domain NAC domain NF013970.5 PF01850.26 PIN 23.6 23.6 120 domain Y Y N PIN domain-containing protein 10413400,11137022,15864262,15993073 131567 cellular organisms no rank 170478 EBI-EMBL PIN domain PIN domain NF013974.5 PF01855.24 POR_N 27 27 231 domain Y N N Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg GO:0016491 10048931,8415612,8550425 131567 cellular organisms no rank 86788 EBI-EMBL Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg This family includes the N terminal structural domain of the pyruvate ferredoxin oxidoreductase. This domain binds thiamine diphosphate, and along with domains II and IV, is involved in inter subunit contacts [3]. The family also includes pyruvate flavodoxin oxidoreductase as encoded by the nifJ gene in cyanobacterium which is required for growth on molecular nitrogen when iron is limited [2]. [1]. 8550425. Molecular and phylogenetic characterization of pyruvate and 2-ketoisovalerate ferredoxin oxidoreductases from Pyrococcus furiosus and pyruvate ferredoxin oxidoreductase from Thermotoga maritima. Kletzin A, Adams MW;. J Bacteriol 1996;178:248-257. [2]. 8415612. Growth of the cyanobacterium Anabaena on molecular nitrogen: NifJ is required when iron is limited. Bauer CC, Scappino L, Haselkorn R;. Proc Natl Acad Sci U S A 1993;90:8812-8816. [3]. 10048931. Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate. Chabriere E, Charon MH, Volbeda A, Pieulle L, Hatchikian EC, Fontecilla-Camps JC;. Nat Struct Biol 1999;6:182-190. (from Pfam) NF013978.5 PF01861.21 BpsA_C 27 27 243 domain Y Y N bis-aminopropyl spermidine synthase family protein 24610711 131567 cellular organisms no rank 3223 EBI-EMBL Branched-chain polyamine synthase A C-terminal domain bis-aminopropyl spermidine synthase-like domain This domain is found in the C terminus of N(4)-bis(aminopropyl)spermidine synthase (EC:2.5.1.128, also known as Branched-chain polyamine synthase A, BpsA) from hyperthermophiles [1] and in uncharacterised proteins from bacteria and archaea. [1]. 24610711. Identification of a novel aminopropyltransferase involved in the synthesis of branched-chain polyamines in hyperthermophiles. Okada K, Hidese R, Fukuda W, Niitsu M, Takao K, Horai Y, Umezawa N, Higuchi T, Oshima T, Yoshikawa Y, Imanaka T, Fujiwara S;. J Bacteriol. 2014;196:1866-1876. (from Pfam) NF013979.5 PF01862.21 PvlArgDC 22.7 22.7 161 domain Y Y N pyruvoyl-dependent arginine decarboxylase GO:0006527,GO:0008792 12623016 131567 cellular organisms no rank 2244 EBI-EMBL Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) pyruvoyl-dependent arginine decarboxylase Methanococcus jannaschii contains homologues of most genes required for spermidine polyamine biosynthesis. Yet genomes from neither this organism nor any other euryarchaeon have orthologues of the pyridoxal 5'-phosphate- dependent ornithine or arginine decarboxylase genes, required to produce putrescine. Instead,these organisms have a new class of arginine decarboxylase (PvlArgDC) formed by the self-cleavage of a proenzyme into a 5-kDa subunit and a 12-kDa subunit that contains a reactive pyruvoyl group. Although this extremely thermostable enzyme has no significant sequence similarity to previously characterised proteins, conserved active site residues are similar to those of the pyruvoyl-dependent histidine decarboxylase enzyme, and its subunits form a similar (alpha-beta)(3) complex. Homologues of PvlArgDC are found in several bacterial genomes, including those of Chlamydia spp., which have no agmatine ureohydrolase enzyme to convert agmatine (decarboxylated arginine) into putrescine. In these intracellular pathogens, PvlArgDC may function analogously to pyruvoyl-dependent histidine decarboxylase; the cells are proposed to import arginine and export agmatine, increasing the pH and affecting the host cell's metabolism. Phylogenetic analysis of Pvl- ArgDC proteins suggests that this gene has been recruited from the euryarchaeal polyamine biosynthetic pathway to function as a degradative enzyme in bacteria [1]. [1]. 12623016. Pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii: crystal structures of the self-cleaved and S53A proenzyme forms. Tolbert WD, Graham DE, White RH, Ealick SE;. Structure. 2003;. TRUNCATED at 1650 bytes (from Pfam) NF013980.5 PF01863.22 YgjP-like 26 26 207 domain Y Y N YgjP-like metallopeptidase domain-containing protein 23733187,25802851,26257768,27941785 131567 cellular organisms no rank 68637 EBI-EMBL YgjP-like, metallopeptidase domain YgjP-like, metallopeptidase domain This is a conserved domain containing the catalytic zinc-metallopeptidase (HExxH) catalytic motif. Proteins containing this domain are found in some archaebacteria, as well as Helicobacter pylori. The proteins are 190-240 amino acids long, with the C terminus being the most conserved region, containing three conserved histidines [1,2,3,4]. This domain is found in YgjP from E. coli [4], a predicted metal-dependent hydrolase that hydrolyses UTP to UMP and diphosphate in vitro; and in MJ0123 from Methanocaldococcus jannaschii (also referred to as projannalysin) [3]. [1]. 25802851. MALDI-TOF MS and CD spectral analysis for identification and structure prediction of a purified, novel, organic solvent stable, fibrinolytic metalloprotease from Bacillus cereus B80. Saxena R, Singh R;. Biomed Res Int. 2015;2015:527015. [2]. 26257768. Remote homology and the functions of metagenomic dark matter. Lobb B, Kurtz DA, Moreno-Hagelsieb G, Doxey AC;. Front Genet. 2015;6:234. [3]. 23733187. A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral membrane metallopeptidases. Lopez-Pelegrin M, Cerda-Costa N, Martinez-Jimenez F, Cintas-Pedrola A, Canals A, Peinado JR, Marti-Renom MA, Lopez-Otin C, Arolas JL, Gomis-Ruth FX;. J Biol Chem. 2013;288:21279-21294. [4]. 27941785. Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli. Sevin DC, Fuhrer T, Zamboni N, Sauer U;. Nat Methods. 2017;14:187-194. (from Pfam) NF013981.5 PF01864.22 CarS-like 22 22 175 PfamEq Y Y N CDP-archaeol synthase 25219966 131567 cellular organisms no rank 6595 EBI-EMBL CDP-archaeol synthase CDP-archaeol synthase CDP-archaeol synthase functions in the archaeal lipid biosynthetic pathway. It catalyses the transfer of the nucleotide to its specific archaeal lipid substrate, leading to the formation of a CDP-activated precursor (CDP-archaeol) to which polar head groups are attached [1]. Bacterial members of this family are uncharacterized. [1]. 25219966. Identification of CDP-archaeol synthase, a missing link of ether lipid biosynthesis in Archaea. Jain S, Caforio A, Fodran P, Lolkema JS, Minnaard AJ, Driessen AJ;. Chem Biol. 2014;21:1392-1401. (from Pfam) NF013982.5 PF01865.21 PhoU_div 24.4 24.4 214 PfamAutoEq Y Y N DUF47 family protein 8013901 131567 cellular organisms no rank 21567 EBI-EMBL Protein of unknown function DUF47 DUF47 family protein This family includes prokaryotic proteins of unknown function, as well as a protein annotated as the pit accessory protein from Sinorhizobium meliloti Swiss:O30498. However, the function of this protein is also unknown (Pit stands for Phosphate transport). It is probably distantly related to Pfam:PF01895 (personal obs:Yeats C). [1]. 8013901. Second site mutations specifically suppress the Fix- phenotype of Rhizobium meliloti ndvF mutations on alfalfa: identification of a conditional ndvF-dependent mucoid colony phenotype. Oresnik IJ, Charles TC, Finan TM;. Genetics 1994;136:1233-1243. (from Pfam) NF013983.5 PF01866.22 Diphthamide_syn 33.2 33.2 302 PfamEq Y Y N diphthamide synthesis protein GO:0017183,GO:0090560 23169644,8406038,8603384 131567 cellular organisms no rank 1442 EBI-EMBL Putative diphthamide synthesis protein diphthamide synthesis protein Diphthamide_syn, diphthamide synthase, catalyses the last amidation step of diphthamide biosynthesis using ammonium and ATP. Swiss:Q16439 is a candidate tumour suppressor gene [1]. DPH2 from yeast Swiss:P32461 [2], which confers resistance to diphtheria toxin has been found to be involved in diphthamide synthesis. Diphtheria toxin inhibits eukaryotic protein synthesis by ADP-ribosylating diphthamide, a post-translationally modified histidine residue present in EF2. Diphthamide synthase is evolutionarily conserved in eukaryotes. Diphthamide is a post-translationally modified histidine residue found on archaeal and eukaryotic translation elongation factor 2 (eEF-2) [3]. [1]. 8603384. A cDNA from the ovarian cancer critical region of deletion on chromosome 17p13.3. Phillips NJ, Zeigler MR, Deaven LL;. Cancer Lett 1996;102:85-90. [2]. 8406038. Diphthamide synthesis in Saccharomyces cerevisiae: structure of the DPH2 gene. Mattheakis LC, Sor F, Collier RJ;. Gene 1993;132:149-154. [3]. 23169644. Chemogenomic approach identified yeast YLR143W as diphthamide synthetase. Su X, Lin Z, Chen W, Jiang H, Zhang S, Lin H;. Proc Natl Acad Sci U S A. 2012;109:19983-19987. (from Pfam) NF013984.5 PF01867.21 Cas_Cas1 22.3 22.3 283 domain Y Y N CRISPR-associated endonuclease Cas1 3.1.-.- GO:0003676,GO:0004519,GO:0043571,GO:0046872,GO:0051607 16079334,16292354 131567 cellular organisms no rank 38882 EBI-EMBL CRISPR associated protein Cas1 CRISPR-associated endonuclease Cas1 Clustered regularly interspaced short palindromic repeats (CRISPRs) are a family of DNA direct repeats found in many prokaryotic genomes. This family of proteins corresponds to Cas1, a CRISPR-associated protein. Cas1 may be involved in linking DNA segments to CRISPR [2]. [1]. 16292354. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. Haft DH, Selengut J, Mongodin EF, Nelson KE;. PLoS Comput Biol. 2005;1:e60. [2]. 16079334. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Bolotin A, Quinquis B, Sorokin A, Ehrlich SD;. Microbiology. 2005;151:2551-2561. (from Pfam) NF013986.5 PF01869.25 BcrAD_BadFG 31.5 31.5 271 domain Y Y N BadF/BadG/BcrA/BcrD ATPase family protein 8365476,9177244,9746358 131567 cellular organisms no rank 77953 EBI-EMBL BadF/BadG/BcrA/BcrD ATPase family BadF/BadG/BcrA/BcrD ATPase family protein This family includes the BadF Swiss:O07462 and BadG Swiss:O07463 proteins that are two subunits of Benzoyl-CoA reductase, that may be involved in ATP hydrolysis. The family also includes an activase subunit from the enzyme 2-hydroxyglutaryl-CoA dehydratase Swiss:P11568. The protein Swiss:O66634 contains two copies of this region suggesting that the family may structurally dimerise. This family appears to be related to Pfam:PF00370. [1]. 8365476. Identification of the gene encoding the activator of (R)-2- hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans by gene expression in Escherichia coli. Bendrat K, Muller U, Klees AG, Buckel W;. FEBS Lett 1993;329:329-331. [2]. 9746358. Genes coding for the benzoyl-CoA pathway of anaerobic aromatic metabolism in the bacterium Thauera aromatica. Breese K, Boll M, Alt-Morbe J, Schagger H, Fuchs G;. Eur J Biochem 1998;256:148-154. [3]. 9177244. A cluster of bacterial genes for anaerobic benzene ring biodegradation. Egland PG, Pelletier DA, Dispensa M, Gibson J, Harwood CS;. Proc Natl Acad Sci U S A 1997;94:6484-6489. (from Pfam) NF013987.5 PF01870.23 Hjc 21.1 21.1 93 domain Y N N Archaeal holliday junction resolvase (hjc) 10430863 131567 cellular organisms no rank 2245 EBI-EMBL Archaeal holliday junction resolvase (hjc) Archaeal holliday junction resolvase (hjc) This family of archaebacterial proteins are holliday junction resolvases (hjc gene) [1]. The Holliday junction is an essential intermediate of homologous recombination. This protein is the archaeal equivalent of RuvC but is not sequence similar. [1]. 10430863. A Holliday junction resolvase from Pyrococcus furiosus: functional similarity to Escherichia coli RuvC provides evidence for conserved mechanism of homologous recombination in Bacteria, Eukarya, and Archaea. Komori K, Sakae S, Shinagawa H, Morikawa K, Ishino Y;. Proc Natl Acad Sci U S A 1999;96:8873-8878. (from Pfam) NF013988.5 PF01871.22 AMMECR1 25 25 168 PfamEq Y Y N AMMECR1 domain-containing protein 10049589,10828604 131567 cellular organisms no rank 7397 EBI-EMBL AMMECR1 AMMECR1 This family consists of several AMMECR1 as well as several uncharacterised proteins. The contiguous gene deletion syndrome AMME is characterised by Alport syndrome, midface hypoplasia, mental retardation and elliptocytosis and is caused by a deletion in Xq22.3, comprising several genes including COL4A5, FACL4 and AMMECR1 [1]. This family contains sequences from several eukaryotic species as well as archaebacteria and it has been suggested that the AMMECR1 protein may have a basic cellular function, potentially in either the transcription, replication, repair or translation machinery [2]. [1]. 10828604. Identification and characterization of mouse orthologs of the AMMECR1 and FACL4 genes deleted in AMME syndrome: orthology of Xq22.3 and MmuXF1-F3. Vitelli F, Meloni I, Fineschi S, Favara F, Tiziana Storlazzi C, Rocchi M, Renieri A;. Cytogenet Cell Genet 2000;88:259-263. [2]. 10049589. Identification and characterization of a highly conserved protein absent in the Alport syndrome (A), mental retardation (M), midface hypoplasia (M), and elliptocytosis (E) contiguous gene deletion syndrome (AMME). Vitelli F, Piccini M, Caroli F, Franco B, Malandrini A, Pober B, Jonsson J, Sorrentino V, Renieri A;. Genomics 1999;55:335-340. (from Pfam) NF013989.5 PF01872.22 RibD_C 24.1 24.1 197 domain Y Y N dihydrofolate reductase family protein GO:0008703 131567 cellular organisms no rank 254466 EBI-EMBL RibD C-terminal domain RibD C-terminal domain The function of this domain is not known, but it is thought to be involved in riboflavin biosynthesis. This domain is found in the C terminus of RibD/RibG Swiss:P25539, in combination with Pfam:PF00383, as well as in isolation in some archaebacterial proteins Swiss:P95872. This family appears to be related to Pfam:PF00186. (from Pfam) NF013991.5 PF01874.21 CitG 27 27 284 domain Y Y N triphosphoribosyl-dephospho-CoA synthase 2.4.2.52 GO:0005524,GO:0016310,GO:0046917 10924139,11042274,7830578 131567 cellular organisms no rank 29269 EBI-EMBL ATP:dephospho-CoA triphosphoribosyl transferase triphosphoribosyl-dephospho-CoA synthase The citG gene is found in a gene cluster with citrate lyase subunits [1]. The function of the CitG protein was elucidated as ATP:dephospho-CoA triphosphoribosyl transferase [2-3]. [1]. 7830578. Klebsiella pneumoniae genes for citrate lyase and citrate lyase ligase: localization, sequencing, and expression. Bott M, Dimroth P;. Mol Microbiol 1994;14:347-356. [2]. 10924139. Biosynthesis of the prosthetic group of citrate lyase. Schneider K, Dimroth P, Bott M;. Biochemistry 2000;39:9438-9450. [3]. 11042274. Identification of triphosphoribosyl-dephospho-CoA as precursor of the citrate lyase prosthetic group. Schneider K, Dimroth P, Bott M;. FEBS Lett 2000;483:165-168. (from Pfam) NF013992.5 PF01875.22 Memo 27 27 269 domain Y Y N MEMO1 family protein 15156151 131567 cellular organisms no rank 6258 EBI-EMBL Memo-like protein MEMO1 family protein This family contains members from all branches of life. The molecular function of this protein is unknown, but Memo (mediator of ErbB2-driven cell motility) a human protein is included in this family [1]. It has been suggested that Memo controls cell migration by relaying extracellular chemotactic signals to the microtubule cytoskeleton [1]. [1]. 15156151. Memo mediates ErbB2-driven cell motility. Marone R, Hess D, Dankort D, Muller WJ, Hynes NE, Badache A;. Nat Cell Biol. 2004;6:515-522. (from Pfam) NF013993.5 PF01876.21 RNase_P_p30 35 35 214 domain Y Y N RNase P subunit p30 family protein GO:0004526,GO:0008033 15613537,9037013 131567 cellular organisms no rank 1285 EBI-EMBL RNase P subunit p30 RNase P subunit p30 family protein This protein is part of the RNase P complex that is involved in tRNA maturation [1]. [1]. 9037013. Characterization of two scleroderma autoimmune antigens that copurify with human ribonuclease P. Eder PS, Kekuda R, Stolc V, Altman S;. Proc Natl Acad Sci U S A 1997;94:1101-1106. [2]. 15613537. 3D models of yeast RNase P/MRP proteins Rpp1p and Pop3p. Dlakic M;. RNA 2005;11:123-127. (from Pfam) NF013995.5 PF01878.23 EVE 23 23 145 domain Y Y N EVE domain-containing protein 16511295,19191354,19237743 131567 cellular organisms no rank 27971 EBI-EMBL EVE domain EVE domain This domain was formerly known as DUF55. Crystal structures have shown that this domain is part of the PUA superfamily. This domain has been named EVE and is thought to be RNA-binding [3]. [1]. 16511295. Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major. Arakaki T, Le Trong I, Phizicky E, Quartley E, DeTitta G, Luft J, Lauricella A, Anderson L, Kalyuzhniy O, Worthey E, Myler PJ, Kim D, Baker D, Hol WG, Merritt EA;. Acta Crystallograph Sect F Struct Biol Cryst Commun. 2006;62:175-179. [2]. 19237743. Determining the DUF55-domain structure of human thymocyte nuclear protein 1 from crystals partially twinned by tetartohedry. Yu F, Song A, Xu C, Sun L, Li J, Tang L, Yu M, Yeates TO, Hu H, He J;. Acta Crystallogr D Biol Crystallogr. 2009;65:212-219. [3]. 19191354. Structural genomics reveals EVE as a new ASCH/PUA-related domain. Bertonati C, Punta M, Fischer M, Yachdav G, Forouhar F, Zhou W, Kuzin AP, Seetharaman J, Abashidze M, Ramelot TA, Kennedy MA, Cort JR, Belachew A, Hunt JF, Tong L, Montelione GT, Rost B;. Proteins. 2009;75:760-773. (from Pfam) NF013996.5 PF01880.23 Desulfoferrodox 22.2 22.2 98 domain Y Y N desulfoferrodoxin family protein GO:0005506,GO:0016491 2174880,8647238 131567 cellular organisms no rank 5937 EBI-EMBL Desulfoferrodoxin desulfoferrodoxin family protein Desulfoferrodoxins contains two types of iron: an Fe-S4 site very similar to that found in desulforedoxin from Desulfovibrio gigas and an octahedral coordinated high-spin ferrous site most probably with nitrogen/oxygen-containing ligands. Due to this rather unusual combination of active centres, this novel protein is named desulfoferrodoxin [1]. [1]. 2174880. Purification and characterization of desulfoferrodoxin. A novel protein from Desulfovibrio desulfuricans (ATCC 27774) and from Desulfovibrio vulgaris (strain Hildenborough) that contains a distorted rubredoxin center and a mononuclear ferrous center. Moura I, Tavares P, Moura JJ, Ravi N, Huynh BH, Liu MY, LeGall J;. J Biol Chem 1990;265:21596-21602. [2]. 8647238. Primary structure of desulfoferrodoxin from Desulfovibrio desulfuricans ATCC 27774, a new class of non-heme iron proteins. Devreese B, Tavares P, Lampreia J, Van Damme N, Le Gall J, Moura JJ, Van Beeumen J, Moura I;. FEBS Lett 1996;385:138-142. (from Pfam) NF013997.5 PF01881.21 Cas_Cas6_C 23 23 125 domain Y Y N CRISPR-associated endoribonuclease Cas6 GO:0016788 16292354,18157154,18703739,24150936 131567 cellular organisms no rank 6507 EBI-EMBL CRISPR associated protein Cas6, C-terminal CRISPR-associated endoribonuclease Cas6 This group of families is one of several protein families that are always found associated with prokaryotic CRISPRs, themselves a family of clustered regularly interspaced short palindromic repeats, DNA repeats found in nearly half of all bacterial and archaeal genomes. These DNA repeat regions have a remarkably regular structure: unique sequences of constant size, called spacers, sit between each pair of repeats [1]. It has been shown that the CRISPRs are virus-derived sequences acquired by the host to enable them to resist viral infection. The Cas proteins from the host use the CRISPRs to mediate an antiviral response. After transcription of the CRISPR, a complex of Cas proteins termed Cascade cleaves a CRISPR RNA precursor in each repeat and retains the cleavage products containing the virus-derived sequence. Assisted by the helicase Cas3, these mature CRISPR RNAs then serve as small guide RNAs that enable Cascade to interfere with virus proliferation [2]. Cas5 contains an endonuclease motif, whose inactivation leads to loss of resistance, even in the presence of phage-derived spacers [3]. In Type I and III CRISPR/Cas systems, the Cas6 family of endoribonucleases generates functional CRISPR-derived RNAs by site-specific cleavage of repeat sequences in precursor transcripts. The structure of Cas6 [4] showed it adopts a tandem ferredoxin/RRM fold. This entry represents the C-terminal domain. [1]. 16292354. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. Haft DH, Selengut J, Mongodin EF, Nelson KE;. PLoS Comput Biol. 2005;1:e60. [2]. 18703739. Small CRIS. TRUNCATED at 1650 bytes (from Pfam) NF013998.5 PF01882.23 DUF58 23.3 23.3 86 domain Y Y N DUF58 domain-containing protein 14594835 131567 cellular organisms no rank 130250 EBI-EMBL Protein of unknown function DUF58 Protein of unknown function DUF58 This family of prokaryotic proteins have no known function. Swiss:P71138 a protein of unknown function in the family has been misannotated as alpha-dextrin 6-glucanohydrolase. [1]. 14594835. Slr2013 is a novel protein regulating functional assembly of photosystem II in Synechocystis sp. strain PCC 6803. Kufryk GI, Vermaas WF;. J Bacteriol. 2003;185:6615-6623. (from Pfam) NF013999.5 PF01883.24 FeS_assembly_P 23.5 23.5 73 domain Y Y N iron-sulfur cluster assembly protein 16199668,19817716,27517714,9600981,9748275 131567 cellular organisms no rank 102309 EBI-EMBL Iron-sulfur cluster assembly protein iron-sulfur cluster assembly protein This family has an alpha/beta topology, with 13 conserved hydrophobic residues at its core and a putative active site containing a highly conserved cysteine [1]. Members of this family are involved in a range of physiological functions. The family includes PaaJ (PhaH) Swiss:O84984 from Pseudomonas putida. PaaJ forms a complex with PaaG (PhaF) Swiss:O84982, PaaI (PhaG) Swiss:O84983 and PaaK (PhaI) Swiss:O84985, which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid [2]. It also includes PaaD Swiss:P76080 from Escherichia coli, a member of a multicomponent oxygenase involved in phenylacetyl-CoA hydroxylation [3]. Furthermore, several members of this family are shown to be involved in iron-sulfur (FeS) cluster assembly. Iron-sulfur (FeS) clusters are inorganic co-factors that are are able to transfer electrons and act as catalysts [4]. They are involved in diverse cellular processes including cellular respiration, DNA replication and repair, antibiotic resistance, and dinitrogen fixation [5]. The biogenesis of such clusters from elemental iron and sulfur is an enzymatic process that requires a set of specialised proteins. Proteins containing this domain include the chloroplast protein HCF101 (high chlorophyll fluorescence 101), Swiss:Q6STH5, which has been described as an essential and specific factor for assembly of [4Fe-4S]-cluster-containing protein complexes such as the membrane complex Photosystem I (PSI) and the heterodimeric FTR (ferredoxin-thioredoxin reductase) complex [4] and is involved in the assembly of [4Fe-4S] clusters and their transfer to apoproteins [4]. The mature HCF101 protein contains this do. TRUNCATED at 1650 bytes (from Pfam) NF014000.5 PF01884.22 PcrB 23.9 23.9 226 PfamEq Y Y N geranylgeranylglyceryl/heptaprenylglyceryl phosphate synthase GO:0016765 11732904,12801917,8238912 131567 cellular organisms no rank 10623 EBI-EMBL PcrB family geranylgeranylglyceryl/heptaprenylglyceryl phosphate synthase This family contains proteins that are related to PcrB Swiss:Q53726. The function of these proteins is unknown. (from Pfam) NF014001.5 PF01885.21 PTS_2-RNA 26 26 177 domain Y Y N RNA 2'-phosphotransferase 2.7.1.- GO:0003950,GO:0016740 9915792 131567 cellular organisms no rank 18424 EBI-EMBL RNA 2'-phosphotransferase, Tpt1 / KptA family RNA 2'-phosphotransferase Tpt1 catalyses the last step of tRNA splicing in yeast. It transfers the splice junction 2'-phosphate from ligated tRNA to NAD, to produce ADP-ribose 1"-2"-cyclic phosphate. This is presumed to be followed by a transesterification step to release the RNA. The first step of this reaction is similar to that catalysed by some bacterial toxins. E. coli KptA and mouse Tpt1 are likely to use the same reaction mechanism [1]. [1]. 9915792. Transient ADP-ribosylation of a 2'-phosphate implicated in its removal from ligated tRNA during splicing in yeast. Spinelli SL, Kierzek R, Turner DH, Phizicky EM;. J Biol Chem 1999;274:2637-2644. (from Pfam) NF014003.5 PF01887.21 SAM_HAT_N 26.3 26.3 145 PfamEq Y Y N SAM-dependent chlorinase/fluorinase 17910070,18675376 131567 cellular organisms no rank 15948 EBI-EMBL SAM hydroxide adenosyltransferase N-terminal domain SAM hydroxide adenosyltransferase N-terminal domain This is a family of proteins, previously known as DUF62, found in archaebacteria and bacteria. The structure of proteins in this family is similar to that of a bacterial fluorinating enzyme [1]. S-adenosyl-l-methionine hydroxide adenosyltransferases utilises a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion [2]. This family used to be known as DUF62. [1]. 17910070. Crystal structure of a conserved protein of unknown function (MJ1651) from Methanococcus jannaschii. Rao KN, Burley SK, Swaminathan S;. Proteins. 2008;70:572-577. [2]. 18675376. The fluorinase, the chlorinase and the duf-62 enzymes. Deng H, O'Hagan D;. Curr Opin Chem Biol. 2008;12:582-592. (from Pfam) NF014004.5 PF01888.22 CbiD 25 25 254 PfamEq Y Y N cobalt-precorrin-5B (C(1))-methyltransferase 2.1.1.195 GO:0008168,GO:0009236 9742225 131567 cellular organisms no rank 23993 EBI-EMBL CbiD cobalt-precorrin-5B (C(1))-methyltransferase CbiD is essential for cobalamin biosynthesis in both S. typhimurium and B. megaterium, no functional role has been ascribed to the protein. The CbiD protein has a putative S-AdoMet binding site. It is possible that CbiD might have the same role as CobF in undertaking the C-1 methylation and deacylation reactions required during the ring contraction process [1]. [1]. 9742225. Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon. Raux E, Lanois A, Warren MJ, Rambach A, Thermes C;. Biochem J 1998;335:159-166. (from Pfam) NF014005.5 PF01889.22 DUF63 25 25 269 subfamily Y Y N DUF63 family protein 131567 cellular organisms no rank 1939 EBI-EMBL Membrane protein of unknown function DUF63 DUF63 family protein Proteins found in Archaebacteria of unknown function. These proteins are probably transmembrane proteins. (from Pfam) NF014006.5 PF01890.21 CbiG_C 27 27 117 PfamEq Y Y N cobalamin biosynthesis protein GO:0009236 16936030,9742225 131567 cellular organisms no rank 33605 EBI-EMBL Cobalamin synthesis G C-terminus cobalamin biosynthesis protein Members of this family are involved in cobalamin synthesis. The gene encoded by Swiss:P72862 has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process [1]. Within the cobalamin synthesis pathway CbiG catalyses the both the opening of the lactone ring and the extrusion of the two-carbon fragment of cobalt-precorrin-5A from C-20 and its associated methyl group (deacylation) to give cobalt-precorrin-5B [2]. This family is the C-terminal region, and the mid- and N-termival parts are conserved independently in other families. [1]. 9742225. Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon. Raux E, Lanois A, Warren MJ, Rambach A, Thermes C;. Biochem J 1998;335:159-166. [2]. 16936030. Fine-tuning our knowledge of the anaerobic route to cobalamin (vitamin B12). Roessner CA, Scott AI;. J Bacteriol. 2006;188:7331-7334. (from Pfam) NF014007.5 PF01891.21 CbiM 23.1 23.1 205 domain Y Y N energy-coupling factor ABC transporter permease GO:0000041,GO:0016020 16352848,18174128,8501034 131567 cellular organisms no rank 32254 EBI-EMBL Cobalt uptake substrate-specific transmembrane region energy-coupling factor ABC transporter permease This family of proteins forms part of the cobalt-transport complex in prokaryotes, CbiMNQO. CbiMNQO and NikMNQO are the most widespread groups of microbial transporters for cobalt and nickel ions and are unusual uptake systems as they consist of eg two transmembrane components (CbiM and CbiQ), a small membrane-bound component (CbiN) and an ATP-binding protein (CbiO) but no extracytoplasmic solute-binding protein. Similar components constitute the nickel transporters with some variability in the small membrane-bound component, either NikN or NikL, which are not similar to CbiN at the sequence level. CbiM is the substrate-specific component of the complex and is a seven-transmembrane protein [2]. The CbiMNQO and NikMNQO systems form part of the coenzyme B12 biosynthesis pathway [3]. The NikM protein is Pfam:PF10670. [1]. 8501034. Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM;. J Bacteriol 1993;175:3303-3316. [2]. 16352848. Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters. Rodionov DA, Hebbeln P, Gelfand MS, Eitinger T;. J Bacteriol. 2006;188:317-327. [3]. 18174128. The complete coenzyme B12 biosynthesis gene cluster of Lactobacillus reuteri CRL1098. Santos F, Vera JL, van der Heijden R, Valdez G, de Vos WM, Sesma F, Hugenholtz J;. Microbiology. 2008;154:81-93. (from Pfam) NF014008.5 PF01893.21 UPF0058 25 25 87 subfamily Y Y N UPF0058 family protein 131567 cellular organisms no rank 1620 EBI-EMBL Uncharacterised protein family UPF0058 UPF0058 family protein This archaebacterial protein has no known function. (from Pfam) NF014009.5 PF01894.22 UPF0047 27 27 117 domain Y Y N YjbQ family protein 131567 cellular organisms no rank 35878 EBI-EMBL Uncharacterised protein family UPF0047 YjbQ family protein This family has no known function. The alignment contains a conserved aspartate and histidine that may be functionally important. (from Pfam) NF014010.5 PF01895.24 PhoU 23.5 23.5 89 domain Y Y N PhoU domain-containing protein 15716271 131567 cellular organisms no rank 76545 EBI-EMBL PhoU domain PhoU domain This family contains phosphate regulatory proteins including PhoU. PhoU proteins are known to play a role in the regulation of phosphate uptake. The PhoU domain is composed of a three helix bundle [1]. The PhoU protein contains two copies of this domain. The domain binds to an iron cluster via its conserved E/DXXXD motif. [1]. 15716271. Crystal structure of a PhoU protein homologue: a new class of metalloprotein containing multinuclear iron clusters. Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH;. J Biol Chem. 2005;280:15960-15966. (from Pfam) NF014011.5 PF01896.24 DNA_primase_S 26.8 26.8 163 domain Y Y N DNA primase small subunit domain-containing protein GO:0003896,GO:0006269 11836407,16027112,2023935 131567 cellular organisms no rank 33457 EBI-EMBL DNA primase small subunit DNA primase small subunit DNA primase synthesises the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. DNA primase is a heterodimer of large and small subunits. This family also includes baculovirus late expression factor 1 or LEF-1 proteins. Baculovirus LEF-1 is a DNA primase enzyme [1]. The family also contains many bacterial DNA primases. [1]. 2023935. Mutations in conserved yeast DNA primase domains impair DNA replication in vivo. Francesconi S, Longhese MP, Piseri A, Santocanale C, Lucchini G, Plevani P;. Proc Natl Acad Sci U S A 1991;88:3877-3881. [2]. 11836407. Baculovirus replication factor LEF-1 is a DNA primase. Mikhailov VS, Rohrmann GF;. J Virol 2002;76:2287-2297. [3]. 16027112. Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Iyer LM, Koonin EV, Leipe DD, Aravind L;. Nucleic Acids Res. 2005;33:3875-3896. (from Pfam) NF014012.5 PF01899.21 MNHE 27 27 145 domain Y Y N Na+/H+ antiporter subunit E GO:0006812,GO:0008324,GO:0016020 9680201,9852009 131567 cellular organisms no rank 32793 EBI-EMBL Na+/H+ ion antiporter subunit Na+/H+ antiporter subunit E Subunit of a Na+/H+ Prokaryotic antiporter complex ([1],[2]). [1]. 9852009. A putative multisubunit Na+/H+ antiporter from Staphylococcus aureus. Hiramatsu T, Kodama K, Kuroda T, Mizushima T, Tsuchiya T;. J Bacteriol 1998;180:6642-6648. [2]. 9680201. The pha gene cluster of Rhizobium meliloti involved in pH adaptation and symbiosis encodes a novel type of K+ efflux system. Putnoky P, Kereszt A, Nakamura T, Endre G, Grosskopf E, Kiss P, Kondorosi A;. Mol Microbiol 1998;28:1091-1101. (from Pfam) NF014013.5 PF01900.24 RNase_P_Rpp14 23 23 104 domain Y Y N Rpp14/Pop5 family protein GO:0001682,GO:0004540,GO:0008033,GO:0030677 10024167,16829535,28715256,30262633 131567 cellular organisms no rank 1177 EBI-EMBL Rpp14/Pop5 family Rpp14/Pop5 family protein tRNA processing enzyme ribonuclease P (RNase P) is a ubiquitous ribozyme that catalyzes a Mg2-dependent hydrolysis to remove the 5'-leader sequence of precursor tRNA (pre-tRNA). Archaeal and eukaryotic RNase P consist of a single RNA and archaeal RNase P has four or five proteins, while eukaryotic RNase P consists of 9 or 10 proteins [1]. Human RNase P is composed of a singular protein Pop1 and three subcomplexes, the Rpp20-Rpp25 heterodimer, Pop5-Rpp14- (Rpp30)2-Rpp40 heteropentamer, and Rpp21-Rpp29-Rpp38 heterotrimer. This family includes Rnp2 (also known as Pop5) from archaea [4] and Pop5/Rpp14 from eukaryotes [2,3]. [1]. 10024167. Rpp14 and Rpp29, two protein subunits of human ribonuclease P. Jarrous N, Eder PS, Wesolowski D, Altman S;. RNA 1999;5:153-157. [2]. 30262633. Structural insight into precursor tRNA processing by yeast ribonuclease P. Lan P, Tan M, Zhang Y, Niu S, Chen J, Shi S, Qiu S, Wang X, Peng X, Cai G, Cheng H, Wu J, Li G, Lei M;. Science. 2018; [Epub ahead of print]. [3]. 28715256. Structural basis for activation of an archaeal ribonuclease P RNA by protein cofactors. Kimura M;. Biosci Biotechnol Biochem. 2017;81:1670-1680. [4]. 16829535. Characterization of the archaeal ribonuclease P proteins from Pyrococcus horikoshii OT3. Terada A, Honda T, Fukuhara H, Hada K, Kimura M;. J Biochem. 2006;140:293-298. (from Pfam) NF014014.5 PF01901.21 O_anti_polymase 24.2 24.2 335 domain Y N N Putative O-antigen polymerase 20418877,29886169,7517391 131567 cellular organisms no rank 1149 EBI-EMBL Putative O-antigen polymerase Putative O-antigen polymerase Archaebacterial proteins of unknown function. Members of this family may be transmembrane proteins. These are potentially O-antigen assembly enzymes, with up to 11 transmembrane regions. (from Pfam) NF014015.5 PF01902.22 Diphthami_syn_2 23.2 23.2 219 domain Y N N Diphthamide synthase 23169644 131567 cellular organisms no rank 13053 EBI-EMBL Diphthamide synthase Diphthamide synthase Diphthamide_syn, diphthamide synthase, catalyses the last amidation step of diphthamide biosynthesis using ammonium and ATP. Diphthamide synthase is evolutionarily conserved in eukaryotes. Diphthamide is a post-translationally modified histidine residue found on archaeal and eukaryotic translation elongation factor 2 (eEF-2) [1]. In some members of this family e.g. Swiss:Q12429, this domain is associated with Pfam:PF01042. The enzyme classification is EC:6.3.1.14. [1]. 23169644. Chemogenomic approach identified yeast YLR143W as diphthamide synthetase. Su X, Lin Z, Chen W, Jiang H, Zhang S, Lin H;. Proc Natl Acad Sci U S A. 2012;109:19983-19987. (from Pfam) NF014016.5 PF01903.22 CbiX 22 22 106 domain Y Y N CbiX/SirB N-terminal domain-containing protein GO:0016829 9742225 131567 cellular organisms no rank 56113 EBI-EMBL CbiX CbiX The function of CbiX is uncertain, however it is found in cobalamin biosynthesis operons and so may have a related function. Some CbiX proteins contain a striking histidine-rich region at their C-terminus, which suggests that it might be involved in metal chelation [1]. [1]. 9742225. Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon. Raux E, Lanois A, Warren MJ, Rambach A, Thermes C;. Biochem J 1998;335:159-166. (from Pfam) NF014017.5 PF01904.23 DUF72 25.3 25.3 217 domain Y Y N DUF72 domain-containing protein 131567 cellular organisms no rank 65953 EBI-EMBL Protein of unknown function DUF72 Protein of unknown function DUF72 The function of this family is unknown. (from Pfam) NF014018.5 PF01905.21 DevR 23.8 18.8 270 domain Y N N CRISPR-associated negative auto-regulator DevR/Csa2 16292354,18157154,18703739,7693658 131567 cellular organisms no rank 2541 EBI-EMBL CRISPR-associated negative auto-regulator DevR/Csa2 CRISPR-associated negative auto-regulator DevR/Csa2 This group of families is one of several protein families that are always found associated with prokaryotic CRISPRs, themselves a family of clustered regularly interspaced short palindromic repeats, DNA repeats found in nearly half of all bacterial and archaeal genomes. These DNA repeat regions have a remarkably regular structure: unique sequences of constant size, called spacers, sit between each pair of repeats [2]. It has been shown that the CRISPRs are virus-derived sequences acquired by the host to enable them to resist viral infection. The Cas proteins from the host use the CRISPRs to mediate an antiviral response. After transcription of the CRISPR, a complex of Cas proteins termed Cascade cleaves a CRISPR RNA precursor in each repeat and retains the cleavage products containing the virus-derived sequence. Assisted by the helicase Cas3, these mature CRISPR RNAs then serve as small guide RNAs that enable Cascade to interfere with virus proliferation [3]. Cas5 contains an endonuclease motif, whose inactivation leads to loss of resistance, even in the presence of phage-derived spacers [4]. This family used to be known as DUF73. DevR appears to be negative auto-regulator within the system [2]. [1]. 7693658. devRS, an autoregulated and essential genetic locus for fruiting body development in Myxococcus xanthus. Thony-Meyer L, Kaiser D;. J Bacteriol. 1993;175:7450-7462. [2]. 16292354. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. Haft DH, Selengut J, Mongodin EF, Nelson KE;. PLoS Comput Biol. 2005;1:e60. [3]. 18703739. Small CRISPR RNAs guide antiviral. TRUNCATED at 1650 bytes (from Pfam) NF014019.5 PF01906.22 YbjQ_1 23 23 103 domain Y Y N heavy metal-binding domain-containing protein 131567 cellular organisms no rank 27502 EBI-EMBL Putative heavy-metal-binding heavy metal-binding domain-containing protein From comparative structural analysis, this family is likely to be a heavy-metal binding domain. The domain oligomerises as a pentamer. The domain is about 100 amino acids long and is found in prokaryotes. (from Pfam) NF014020.5 PF01907.24 Ribosomal_L37e 27.6 27.6 53 PfamEq Y N N Ribosomal protein L37e GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 819 EBI-EMBL Ribosomal protein L37e Ribosomal protein L37e This family includes ribosomal protein L37 from eukaryotes and archaebacteria. The family contains many conserved cysteines and histidines suggesting that this protein may bind to zinc. (from Pfam) NF014021.5 PF01909.28 NTP_transf_2 21 21 93 domain Y Y N nucleotidyltransferase domain-containing protein GO:0016779 7482698 131567 cellular organisms no rank 124728 EBI-EMBL Nucleotidyltransferase domain Nucleotidyltransferase domain Members of this family belong to a large family of nucleotidyltransferases [1]. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug. [1]. 7482698. DNA polymerase beta belongs to an ancient nucleotidyltransferase superfamily. Holm L, Sander C;. Trends Biochem Sci 1995;20:345-347. (from Pfam) NF014022.5 PF01910.22 Thiamine_BP 24.9 24.9 92 domain Y Y N thiamine-binding protein 12866058,20471400 131567 cellular organisms no rank 22191 EBI-EMBL Thiamine-binding protein thiamine-binding protein The crystal structure of two of these members shows that this domain has a ferredoxin like fold and is likely to exists as at least homodimers. Sulphate ions are are located at the dimer interfaces, which are thought to confer additional stability. Although the function of this domain remains to be identified, its structure suggests a role in protein-protein interactions possibly regulated by the binding of small-molecule ligands [1]. Solution of the structure of the hyperthermophilic anaerobic Thermotoga maritima sequence, UniProtKB:Q9WYV6, shows that this has a beta-alpha-beta-beta-alpha-beta ferredoxin-like fold and assembles as a homotetramer. It was possible to identify a pocket in each monmer that bound an unidentified ligand. It was also found that it bound charged thiamine though not hydroxymethyl pyrimidine. It is proposed that it is transporting charged thiamine around the cytoplasm. Under oxidative conditions this bacterium is under stress, and the transcriiptional unit within which this protein is expressed is up-regulated in these conditions, suggesting that the chelation of cytoplasmic thaimine is part of the response mechanism to such oxidatvie stress, which is mediated by this family [2]. [1]. 12866058. Crystal structures of MTH1187 and its yeast ortholog YBL001c. Tao X, Khayat R, Christendat D, Savchenko A, Xu X, Goldsmith-Fischman S, Honig B, Edwards A, Arrowsmith CH, Tong L;. Proteins 2003;52:478-480. [2]. 20471400. TM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin-binding protein involved in response of the cell to oxidative conditions. Dermoun Z, Foulon A, Miller MD, Harrin. TRUNCATED at 1650 bytes (from Pfam) NF014024.5 PF01913.23 FTR 27 27 142 domain Y N N Formylmethanofuran-tetrahydromethanopterin formyltransferase GO:0006730,GO:0016740 9195883 131567 cellular organisms no rank 2417 EBI-EMBL Formylmethanofuran-tetrahydromethanopterin formyltransferase Formylmethanofuran-tetrahydromethanopterin formyltransferase This enzyme EC:2.3.1.101 is involved in archaebacteria in the formation of methane from carbon dioxide. N-terminal distal lobe of alpha+beta ferredoxin-like fold. SCOP reports fold duplication with C-terminal proximal lobe. [1]. 9195883. Formylmethanofuran: tetrahydromethanopterin formyltransferase from Methanopyrus kandleri - new insights into salt-dependence and thermostability. Ermler U, Merckel M, Thauer R, Shima S;. Structure 1997;5:635-646. (from Pfam) NF014025.5 PF01914.22 MarC 23.9 23.9 203 subfamily Y Y N MarC family protein GO:0016020 17954692 131567 cellular organisms no rank 45919 EBI-EMBL MarC family integral membrane protein MarC family protein Integral membrane protein family that includes the protein MarC. MarC was thought to be a multiple antibiotic resistance protein. Nevertheless, a study has shown that MarC is not involved in multiple antibiotic resistance [1]. The function of this family is unclear. [1]. 17954692. The marC gene of Escherichia coli is not involved in multiple antibiotic resistance. McDermott PF, McMurry LM, Podglajen I, Dzink-Fox JL, Schneiders T, Draper MP, Levy SB;. Antimicrob Agents Chemother. 2008;52:382-383. (from Pfam) NF014026.5 PF01915.27 Glyco_hydro_3_C 31 31 200 domain Y Y N glycoside hydrolase family 3 C-terminal domain-containing protein GO:0004553,GO:0005975 10368285 131567 cellular organisms no rank 182273 EBI-EMBL Glycosyl hydrolase family 3 C-terminal domain Glycosyl hydrolase family 3 C-terminal domain This domain is involved in catalysis and may be involved in binding beta-glucan [1]. This domain is found associated with Pfam:PF00933. [1]. 10368285. Three-dimensional structure of a barley beta-D-glucan exohydrolase, a family 3 glycosyl hydrolase. Varghese JN, Hrmova M, Fincher GB;. Structure Fold Des 1999;7:179-190. (from Pfam) NF014027.5 PF01916.22 DS 27 27 288 domain Y Y N deoxyhypusine synthase family protein GO:0008612 9493264 131567 cellular organisms no rank 7808 EBI-EMBL Deoxyhypusine synthase deoxyhypusine synthase family protein Eukaryotic initiation factor 5A (eIF-5A) contains an unusual amino acid, hypusine [N epsilon-(4-aminobutyl-2-hydroxy)lysine]. The first step in the post-translational formation of hypusine is catalysed by the enzyme deoxyhypusine synthase (DS) EC:1.1.1.249. The modified version of eIF-5A, and DS, are required for eukaryotic cell proliferation [1]. [1]. 9493264. Crystal structure of the NAD complex of human deoxyhypusine synthase: an enzyme with a ball-and-chain mechanism for blocking the active site. Liao DI, Wolff EC, Park MH, Davies DR;. Structure 1998;6:23-32. (from Pfam) NF014028.5 PF01917.21 Arch_flagellin 29.5 29.5 162 subfamily Y N N Archaebacterial flagellin GO:0005198,GO:0097588 10632878,11250034,14622420,15170402,16983194,3417656 131567 cellular organisms no rank 4175 EBI-EMBL Archaebacterial flagellin archaellin (archaeal flagellin) Archaeal motility occurs by the rotation of flagella that show similarity to bacterial type IV pili, including the multiflagellin nature of the flagellar filament, N-terminal sequence similarities, as well as the presence of homologous proteins in the two systems [2,3]. Similar to type IV pilins, archaeal flagellins are initially synthesised with a short leader peptide that is cleaved by a membrane-located peptidase [3,4]. The enzyme responsible for the removal of the this leader peptide is FlaK [4]. Archaeal flagella are composed of a number of distinct flagellin proteins, specified by genes in two separate operons (A and B) [6]. [1]. 3417656. Halobacterial flagellins are encoded by a multigene family. Characterization of five flagellin genes. Gerl L, Sumper M;. J Biol Chem 1988;263:13246-13251. [2]. 16983194. Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications. Ng SY, Chaban B, Jarrell KF;. J Mol Microbiol Biotechnol. 2006;11:167-191. [3]. 11250034. The archaeal flagellum: a different kind of prokaryotic motility structure. Thomas NA, Bardy SL, Jarrell KF;. FEMS Microbiol Rev 2001;25:147-174. [4]. 15170402. Recent advances in the structure and assembly of the archaeal flagellum. Bardy SL, Ng SY, Jarrell KF;. J Mol Microbiol Biotechnol. 2004;7:41-51. [5]. 14622420. Cleavage of preflagellins by an aspartic acid signal peptidase is essential for flagellation in the archaeon Methanococcus voltae. Bardy SL, Jarrell KF;. Mol Microbiol. 2003;50:1339-1347. [6]. 10632878. Role of flagellins from A and B loci in flagella formation of Halobacterium salinarum. Tarasov VY,. TRUNCATED at 1650 bytes (from Pfam) NF014029.5 PF01918.26 Alba 25 25 66 domain Y N N Alba GO:0003676 10320587,10869069,11935028,14519199 131567 cellular organisms no rank 687 EBI-EMBL Alba Alba Alba is a novel chromosomal protein that coats archaeal DNA without compacting it. [1]. 14519199. The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism. Aravind L, Iyer LM, Anantharaman V;. Genome Biol 2003;4:R64. [2]. 11935028. The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. Bell SD, Botting CH, Wardleworth BN, Jackson SP, White MF;. Science 2002;296:148-151. [3]. 10869069. An abundant DNA binding protein from the hyperthermophilic archaeon Sulfolobus shibatae affects DNA supercoiling in a temperature-dependent fashion. Xue H, Guo R, Wen Y, Liu D, Huang L;. J Bacteriol 2000;182:3929-3933. [4]. 10320587. Identification of the gene encoding archeal-specific DNA-binding proteins of the Sac10b family. Forterre P, Confalonieri F, Knapp S;. Mol Microbiol 1999;32:669-670. (from Pfam) NF014030.5 PF01920.25 Prefoldin_2 27.6 27.6 106 PfamEq Y Y N prefoldin subunit GO:0006457,GO:0016272,GO:0051082 1748305,7828874,9463374 131567 cellular organisms no rank 1215 EBI-EMBL Prefoldin subunit prefoldin subunit This family includes prefoldin subunits that are not detected by Pfam:PF02996. [1]. 1748305. Primary structure of the embryo-expressed gene KE2 from the mouse H-2K region. Ha H, Abe K, Artzt K;. Gene 1991;107:345-346. [2]. 7828874. YKE2, a yeast nuclear gene encoding a protein showing homology to mouse KE2 and containing a putative leucine-zipper motif. Shang HS, Wong SM, Tan HM, Wu M;. Gene 1994;151:197-201. [3]. 9463374. A novel protein complex promoting formation of functional alpha- and gamma-tubulin. Geissler S, Siegers K, Schiebel E;. EMBO J 1998;17:952-966. (from Pfam) NF014031.5 PF01921.23 tRNA-synt_1f 27 27 360 PfamEq Y N N tRNA synthetases class I (K) GO:0000166,GO:0004824,GO:0005524,GO:0005737,GO:0006430 9353192 131567 cellular organisms no rank 28672 EBI-EMBL tRNA synthetases class I (K) tRNA synthetases class I (K) This family includes only lysyl tRNA synthetases from prokaryotes. [1]. 9353192. A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. Ibba M, Morgan S, Curnow AW, Pridmore DR, Vothknecht UC, Gardner W, Lin W, Woese CR, Soll D;. Science 1997;278:1119-1122. (from Pfam) NF014033.5 PF01923.23 Cob_adeno_trans 24 24 171 domain Y N N Cobalamin adenosyltransferase 10464203,11160088 131567 cellular organisms no rank 50914 EBI-EMBL Cobalamin adenosyltransferase Cobalamin adenosyltransferase Cobalamin adenosyltransferase This family contains the gene products of PduO and EutT which are both cobalamin adenosyltransferases. PduO is a protein with ATP:cob(I)alamin adenosyltransferase activity. The main role of this protein is the conversion of inactive cobalamins to AdoCbl for 1,2-propanediol degradation [1].The EutT enzyme appears to be an adenosyl transferase, converting CNB12 to AdoB12 [2]. [1]. 11160088. Functional genomic, biochemical, and genetic characterization of the Salmonella pduO gene, an ATP:cob(I)alamin adenosyltransferase gene. Johnson CL, Pechonick E, Park SD, Havemann GD, Leal NA, Bobik TA;. J Bacteriol 2001;183:1577-1584. [2]. 10464203. The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. Kofoid E, Rappleye C, Stojiljkovic I, Roth J;. J Bacteriol 1999;181:5317-5329. (from Pfam) NF014034.5 PF01924.21 HypD 25 25 351 PfamEq Y N N Hydrogenase formation hypA family GO:0046872 8326860 131567 cellular organisms no rank 24303 EBI-EMBL Hydrogenase formation hypA family Hydrogenase formation hypA family HypD is involved in hydrogenase formation. It contains many possible metal binding residues, which may bind to nickel. Transposon Tn5 insertions into hypD resulted in R. leguminosarum mutants that lacked any hydrogenase activity in symbiosis with peas [1]. [1]. 8326860. Molecular analysis of a microaerobically induced operon required for hydrogenase synthesis in Rhizobium leguminosarum biovar viciae. Rey L, Murillo J, Hernando Y, Hidalgo E, Cabrera E, Imperial J, Ruiz-Argueso T;. Mol Microbiol 1993;8:471-481. (from Pfam) NF014035.5 PF01925.24 TauE 32.6 32.6 237 subfamily Y Y N TSUP family transporter GO:0016020 17768248,18506422 131567 cellular organisms no rank 274895 EBI-EMBL Sulfite exporter TauE/SafE TSUP family transporter This is a family of integral membrane proteins where the alignment appears to contain two duplicated modules of three transmembrane helices. The proteins are involved in the transport of anions across the cytoplasmic membrane [1] during taurine metabolism as an exporter of sulfoacetate [2]. This family used to be known as DUF81. [1]. 17768248. The DUF81 protein TauE in Cupriavidus necator H16, a sulfite exporter in the metabolism of C2 sulfonates. Weinitschke S, Denger K, Cook AM, Smits TH;. Microbiology. 2007;153:3055-3060. [2]. 18506422. Sulfoacetate released during the assimilation of taurine-nitrogen by Neptuniibacter caesariensis: purification of sulfoacetaldehyde dehydrogenase. Krejcik Z, Denger K, Weinitschke S, Hollemeyer K, Paces V, Cook AM, Smits TH;. Arch Microbiol. 2008;190:159-168. (from Pfam) NF014036.5 PF01926.28 MMR_HSR1 21.9 21.9 113 domain Y Y N GTPase GO:0005525 16803892,19109926,19181811,19824612,8180467 131567 cellular organisms no rank 930143 EBI-EMBL 50S ribosome-binding GTPase GTPase This HMM identifies the P-loop-containing domain of large numbers of GTPases with ribosome-associated functions, including many involved in ribosome maturation (Der, Era, etc), ribosome rescue (HflX), and protein translation (InfB, Tuf, PrfC). NF014037.5 PF01927.21 Mut7-C 23.3 23.3 146 domain Y Y N Mut7-C RNAse domain-containing protein 11917006,16859499 131567 cellular organisms no rank 12814 EBI-EMBL Mut7-C RNAse domain Mut7-C RNAse domain RNAse domain of the PIN fold [1] with an inserted Zinc Ribbon at the C terminus [2]. [1]. 11917006. Comparative genomics and evolution of proteins involved in RNA metabolism. Anantharaman V, Koonin EV, Aravind L;. Nucleic Acids Res. 2002;30:1427-1464. [2]. 16859499. The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. Iyer LM, Burroughs AM, Aravind L;. Genome Biol. 2006;7:R60. (from Pfam) NF014038.5 PF01928.26 CYTH 23.2 23.2 179 domain Y Y N CYTH domain-containing protein 12456267,16511301,16905149,9642185 131567 cellular organisms no rank 72520 EBI-EMBL CYTH domain CYTH domain These sequences are functionally identified as members of the adenylate cyclase family, which catalyses the conversion of ATP to 3',5'-cyclic AMP and pyrophosphate. Six distinct non-homologous classes of AC have been identified. The structure of three classes of adenylyl cyclases have been solved [3]. [1]. 9642185. Aeromonas hydrophila adenylyl cyclase 2: a new class of adenylyl cyclases with thermophilic properties and sequence similarities to proteins from hyperthermophilic archaebacteria. Sismeiro O, Trotot P, Biville F, Vivares C, Danchin A;. J Bacteriol 1998;180:3339-3344. [2]. 12456267. The catalytic domains of thiamine triphosphatase and CyaB-like adenylyl cyclase define a novel superfamily of domains that bind organic phosphates. Iyer LM, Aravind L;. BMC Genomics 2002;3:33-33. [3]. 16905149. Structure of the class IV adenylyl cyclase reveals a novel fold. Gallagher DT, Smith NN, Kim SK, Heroux A, Robinson H, Reddy PT;. J Mol Biol. 2006;362:114-122. [4]. 16511301. Crystallization of the class IV adenylyl cyclase from Yersinia pestis. Smith N, Kim SK, Reddy PT, Gallagher DT;. Acta Crystallograph Sect F Struct Biol Cryst Commun. 2006;62:200-204. (from Pfam) NF014040.5 PF01930.22 Cas_Cas4 22.7 22.7 160 domain Y Y N Dna2/Cas4 domain-containing protein 15972856 131567 cellular organisms no rank 16494 EBI-EMBL Domain of unknown function DUF83 Domain of unknown function DUF83 This domain has no known function. The domain contains three conserved cysteines at its C terminus. [1]. 15972856. Identification of novel restriction endonuclease-like fold families among hypothetical proteins. Kinch LN, Ginalski K, Rychlewski L, Grishin NV;. Nucleic Acids Res. 2005;33:3598-3605. (from Pfam) NF014041.5 PF01931.23 NTPase_I-T 25 25 162 PfamAutoEq Y Y N DUF84 family protein 16216582,16498616 131567 cellular organisms no rank 8976 EBI-EMBL Protein of unknown function DUF84 DUF84 family protein NTPase_I-T is a family of NTPases with supreme activity against ITP and XTP. Active site analysis and structure comparison of YjjX strongly suggested that it is an NTP binding protein with nucleoside triphosphatase activity. YjjX exhibits a mixed alpha-beta fold [1,2]. [1]. 16498616. Crystal structure of VC0702 at 2.0 A: conserved hypothetical protein from Vibrio cholerae. Ni S, Forouhar F, Bussiere DE, Robinson H, Kennedy MA;. Proteins. 2006;63:733-741. [2]. 16216582. Identification of an ITPase/XTPase in Escherichia coli by structural and biochemical analysis. Zheng J, Singh VK, Jia Z;. Structure. 2005;13:1511-1520. (from Pfam) NF014042.5 PF01933.23 CofD 30 30 290 domain Y Y N 2-phospho-L-lactate transferase CofD family protein GO:0043743 11888293,18252724 131567 cellular organisms no rank 44320 EBI-EMBL 2-phospho-L-lactate transferase CofD 2-phospho-L-lactate transferase CofD family protein This entry contains 2-phospho-L-lactate transferase (CofD), phosphoenolpyruvate transferase and related sequences. CofD catalyses the fourth step in the biosynthesis of coenzyme F420, which is the transfer of the 2-phospholactate moiety from lactyl (2)diphospho-(5') guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) with the formation of the L-lactyl phosphodiester of 7,8-didemethyl- 8-hydroxy-5-deazariboflavin (F420-0) and GMP. F420 is a flavin derivative found in methanogens, Mycobacteria, and several other lineages. This enzyme is characterised so far in Methanocaldococcus jannaschii (Methanococcus jannaschii) [1] but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. CofD monomer contains 12 beta- strands, seven of them form a Rossmann fold, and 13 alpha-helices [2]. [1]. 11888293. Characterization of the 2-phospho-L-lactate transferase enzyme involved in coenzyme F(420) biosynthesis in Methanococcus jannaschii. Graupner M, Xu H, White RH;. Biochemistry. 2002;41:3754-3761. [2]. 18252724. Molecular insights into the biosynthesis of the F420 coenzyme. Forouhar F, Abashidze M, Xu H, Grochowski LL, Seetharaman J, Hussain M, Kuzin A, Chen Y, Zhou W, Xiao R, Acton TB, Montelione GT, Galinier A, White RH, Tong L;. J Biol Chem. 2008;283:11832-11840. (from Pfam) NF014043.5 PF01934.22 HepT-like 23.5 23.5 120 domain Y Y N HepT-like ribonuclease domain-containing protein GO:0004540,GO:0110001 26112399,29555683,33045733 131567 cellular organisms no rank 26877 EBI-EMBL Ribonuclease HepT-like Ribonuclease HepT-like This family includes the toxic component HepT of a type II toxin-antitoxin (TA) system, which has RNase activity. These proteins contain a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain and are neutralised through tri-AMPylation by the cognate antitoxin MntA, containing a MNT (minimal nucleotidyltransferase) domain [1, 2, 3]. HepT-MnA form an heterooctamer (at a 2:6 ratio), a rare organisation for this kind of TA systems. HepT dimerises and enables the formation of a deep cleft at the HEPN-domain interface, containing the RX4-6H motif (where X is any amino acid and the residue immediately after the conserved R is typically a polar amino acid) as the active site that functions as an RNA-cleaving RNase. This type II TA system regulates cell motility and confers plasmid stability [2]. Due to the prevalence of these HEPN/MNT modules in bacteria and archaea, it has been suggested that these TA systems may also play a role in the environmental adaptation to extreme habitats [3]. [1]. 26112399. Identification and characterization of a HEPN-MNT family type II toxin-antitoxin in Shewanella oneidensis. Yao J, Guo Y, Zeng Z, Liu X, Shi F, Wang X;. Microb Biotechnol. 2015;8:961-973. [2]. 29555683. Structure-function analyses reveal the molecular architecture and neutralization mechanism of a bacterial HEPN-MNT toxin-antitoxin system. Jia X, Yao J, Gao Z, Liu G, Dong YH, Wang X, Zhang H;. J Biol Chem. 2018;293:6812-6823. [3]. 33045733. Novel polyadenylylation-dependent neutralization mechanism of the HEPN/MNT toxin/antitoxin system. Yao J, Zhen X, Tang K, Liu T, Xu X, Chen Z, Guo Y, Liu X, Wood TK, Ouyang S, Wang . TRUNCATED at 1650 bytes (from Pfam) NF014044.5 PF01935.22 DUF87 23.2 23.2 220 domain Y Y N helicase HerA domain-containing protein 14990749,25420454,25880130 131567 cellular organisms no rank 128074 EBI-EMBL Helicase HerA, central domain Helicase HerA, central domain This entry represents the central domain found in archaeal proteins such as DNA double-strand break repair helicase HerA (EC:3.6.4.12). HerA is a helicase which is able to utilise either 3' or 5' single-stranded DNA extensions for loading and subsequent DNA duplex unwinding [1]. It forms a complex with NurA nuclease, this complex has the 5'-3' DNA end resection activity and is essential for cell viability in the crenarchaeon Sulfolobus islandicus [2]. This domain includes the the central RecA-like catalytic core and a flanking four-helix bundle [3]. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands. [1]. 14990749. A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea. Constantinesco F, Forterre P, Koonin EV, Aravind L, Elie C;. Nucleic Acids Res. 2004;32:1439-1447. [2]. 25880130. Efficient 5'-3' DNA end resection by HerA and NurA is essential for cell viability in the crenarchaeon Sulfolobus islandicus. Huang Q, Liu L, Liu J, Ni J, She Q, Shen Y;. BMC Mol Biol. 2015;16:2. [3]. 25420454. Structure of the hexameric HerA ATPase reveals a mechanism of translocation-coupled DNA-end processing in archaea. Rzechorzek NJ, Blackwood JK, Bray SM, Maman JD, Pellegrini L, Robinson NP;. Nat Commun. 2014;5:5506. (from Pfam) NF014045.5 PF01936.23 NYN 24.2 24.2 145 domain Y Y N NYN domain-containing protein GO:0004540 17114934 131567 cellular organisms no rank 63183 EBI-EMBL NYN domain NYN domain These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions. Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs. [1]. 17114934. The NYN Domains: Novel Predicted RNAses with a PIN Domain-Like Fold. Anantharaman V, Aravind L;. RNA Biol. 2006; [Epub ahead of print] (from Pfam) NF014046.5 PF01937.24 ARMT1-like_dom 25 25 311 domain Y Y N ARMT1-like domain-containing protein 27322068 131567 cellular organisms no rank 8372 EBI-EMBL Damage-control phosphatase ARMT1-like domain DUF89 family protein This domain is widely distributed in all domains of life and occur in stand-alone form and as C-terminal fusions to pantothenate kinase (PanK) in plants and animals. They are metal-dependent phosphatases involved in metabolic damage-control processes termed "damage pre-emption" or "housecleaning". S.cerevisiae Damage-control phosphatase YMR027W and the human orthologue Damage-control phosphatase ARMT1 (also known as C6orf211) are involved in response to DNA damage, a damage pre-emption function. Crystal structure of Damage-control phosphatase At2g17340 from Arabidopsis revealed a novel protein fold and several conserved residues coordinating a metal ion (probably Mg2+), which exhibits a high degree of conservation, suggesting that the metal-binding site is central for the function [1]. [1]. 27322068. A family of metal-dependent phosphatases implicated in metabolite damage-control. Huang L, Khusnutdinova A, Nocek B, Brown G, Xu X, Cui H, Petit P, Flick R, Zallot R, Balmant K, Ziemak MJ, Shanklin J, de Crecy-Lagard V, Fiehn O, Gregory JF 3rd, Joachimiak A, Savchenko A, Yakunin AF, Hanson AD;. Nat Chem Biol. 2016;12:621-627. (from Pfam) NF014047.5 PF01938.25 TRAM 21 21 61 domain Y Y N TRAM domain-containing protein 11313137 131567 cellular organisms no rank 145406 EBI-EMBL TRAM domain TRAM domain This small domain has no known function. However it may perform a nucleic acid binding role (Bateman A. unpublished observation). [1]. 11313137. TRAM, a predicted RNA-binding domain, common to tRNA uracil methylation and adenine thiolation enzymes. Anantharaman V, Koonin EV, Aravind L;. FEMS Microbiol Lett 2001;197:215-221. (from Pfam) NF014048.5 PF01939.21 NucS_C 24 24 124 PfamAutoEq Y Y N endonuclease NucS domain-containing protein GO:0004519 19609302,22431731 131567 cellular organisms no rank 16976 EBI-EMBL Endonuclease NucS C-terminal domain Endonuclease NucS C-terminal domain Endonuclease NucS cleaves both 3' and 5' ssDNA extremities of branched DNA structures and it binds to ssDNA [1,2]. This entry represents the C-terminal domain of NucS. [1]. 22431731. Modulation of the Pyrococcus abyssi NucS endonuclease activity by replication clamp at functional and structural levels. Creze C, Ligabue A, Laurent S, Lestini R, Laptenok SP, Khun J, Vos MH, Czjzek M, Myllykallio H, Flament D;. J Biol Chem. 2012;287:15648-15660. [2]. 19609302. Structure and function of a novel endonuclease acting on branched DNA substrates. Ren B, Kuhn J, Meslet-Cladiere L, Briffotaux J, Norais C, Lavigne R, Flament D, Ladenstein R, Myllykallio H;. EMBO J. 2009;28:2479-2489. (from Pfam) NF014049.5 PF01940.21 DUF92 27.5 27.5 251 PfamAutoEq Y Y N DUF92 domain-containing protein GO:0016020 26452599 131567 cellular organisms no rank 6168 EBI-EMBL Integral membrane protein DUF92 Integral membrane protein DUF92 Members of this family have several predicted transmembrane helices. One member of the family has been characterised as protein PGR (AtPGR). PGR is suggested to be a potential glucose-responsive regulator in carbohydrate metabolism in plants. This entry also includes protein VTE6, which is a Pphytyl-phosphate kinase catalysing the conversion of phytyl-monophosphate to phytyl-diphosphate [1]. [1]. 26452599. Remobilization of Phytol from Chlorophyll Degradation Is Essential for Tocopherol Synthesis and Growth of Arabidopsis. Vom Dorp K, Holzl G, Plohmann C, Eisenhut M, Abraham M, Weber AP, Hanson AD, Dormann P;. Plant Cell. 2015;27:2846-2859. (from Pfam) NF014050.5 PF01941.24 AdoMet_Synthase 27 27 395 domain Y Y N methionine adenosyltransferase 11872742 131567 cellular organisms no rank 2978 EBI-EMBL S-adenosylmethionine synthetase (AdoMet synthetase) methionine adenosyltransferase This family consists of several archaebacterial S-adenosylmethionine synthetase C(AdoMet synthetase or MAT) (EC 2.5.1.6). S-Adenosylmethionine (AdoMet) occupies a central role in the metabolism of all cells. The biological roles of AdoMet include acting as the primary methyl group donor, as a precursor to the polyamines, and as a progenitor of a 5'-deoxyadenosyl radical. S-Adenosylmethionine synthetase catalyses the only known route of AdoMet biosynthesis. The synthetic process occurs in a unique reaction in which the complete triphosphate chain is displaced from ATP and a sulfonium ion formed. MATs from various organisms contain ~400-amino acid polypeptide chains [1]. [1]. 11872742. Enzymatic properties of S-adenosylmethionine synthetase from the archaeon Methanococcus jannaschii. Lu ZJ, Markham GD;. J Biol Chem 2002;277:16624-16631. (from Pfam) NF014051.5 PF01943.22 Polysacc_synt 28.2 28.2 274 domain Y Y N oligosaccharide flippase family protein GO:0016020 1744050,7517390,8118055 131567 cellular organisms no rank 205488 EBI-EMBL Polysaccharide biosynthesis protein oligosaccharide flippase family protein Members of this family are integral membrane proteins [1]. Many members of the family are implicated in production of polysaccharide. The family includes RfbX part of the O antigen biosynthesis operon [2]. The family includes SpoVB from Bacillus subtilis Swiss:Q00758, which is involved in spore cortex biosynthesis [3]. [1]. 8118055. Analysis of the Rhizobium meliloti genes exoU, exoV, exoW, exoT, and exoI involved in exopolysaccharide biosynthesis and nodule invasion: exoU and exoW probably encode glucosyltransferases. Becker A, Kleickmann A, Kuster H, Keller M, Arnold W, Puhler A;. Mol Plant Microbe Interact. 1993;6:735-744. [2]. 7517390. Genetic analysis of the O-specific lipopolysaccharide biosynthesis region (rfb) of Escherichia coli K-12 W3110: identification of genes that confer group 6 specificity to Shigella flexneri serotypes Y and 4a. Yao Z, Valvano MA;. J Bacteriol 1994;176:4133-4143. [3]. 1744050. Cloning, characterization, and expression of the spoVB gene of Bacillus subtilis. Popham DL, Stragier P;. J Bacteriol 1991;173:7942-7949. (from Pfam) NF014052.5 PF01944.22 SpoIIM 26.9 26.9 163 domain Y Y N stage II sporulation protein M 17376078 131567 cellular organisms no rank 33753 EBI-EMBL Stage II sporulation protein M stage II sporulation protein M SpoIIM is on e of four stage II sporulation proteins that is necessary for the forespore inside the mother-cell to be properly internalised through the breakdown of peptidoglycans trapped between the membranes of the septum separating the forespore and the mother-cell. The four proteins working in sequence are SpoIIB, Pfam:PF05036, SpoIIM, SpoIIP, Pfam:PF07454, and finally SpoIID, Pfam:PF08486. D, M and P are in a complex with each other and the complex assembles in a hierarchical manner such that M, which serves as a membrane anchor, recruits P to the septum and P, in turn, recruits D to the septum [1]. [1]. 17376078. Engulfment during sporulation in Bacillus subtilis is governed by a multi-protein complex containing tandemly acting autolysins. Chastanet A, Losick R;. Mol Microbiol. 2007;64:139-152. (from Pfam) NF014053.5 PF01946.22 Thi4 26.2 26.2 235 domain Y N N Thi4 family 7961415 131567 cellular organisms no rank 124582 EBI-EMBL Thi4 family Thi4 family This family includes Swiss:P32318 a putative thiamine biosynthetic enzyme. [1]. 7961415. Cloning, nucleotide sequence, and regulation of Schizosaccharomyces pombe thi4, a thiamine biosynthetic gene. Zurlinden A, Schweingruber ME;. J Bacteriol 1994;176:6631-6635. (from Pfam) NF014054.5 PF01947.21 Rv2949c-like 22 22 149 PfamAutoEq Y Y N chorismate pyruvate-lyase family protein 16210318,20437231,24337576 131567 cellular organisms no rank 4960 EBI-EMBL Chorismate pyruvate-lyase Rv2949c-like chorismate pyruvate-lyase family protein This domain is found in chorismate pyruvate-lyases (EC:4.1.3.40, also known as 4-HB synthase and p-hydroxybenzoic acid synthase) such as those found in Mycobacterium tuberculosis where it removes the pyruvyl group from chorismate to provide 4-hydroxybenzoate (4HB) [1]. The chorismate pyruvate-lyase encoded by sll1797 in cyanobacteria Synechocystis sp. , has been shown to catalyse the initial and essential step in plastoquinone biosynthesis [2]. In E. coli, the chorismate lyase (UbiC) catalyses the conversion of chorismate to p-hydroxybenzoate and pyruvate in the biosynthesis of ubiquinone as well [3]. [1]. 16210318. p-Hydroxybenzoic acid synthesis in Mycobacterium tuberculosis. Stadthagen G, Kordulakova J, Griffin R, Constant P, Bottova I, Barilone N, Gicquel B, Daffe M, Jackson M;. J Biol Chem. 2005;280:40699-40706. [2]. 24337576. Chorismate pyruvate-lyase and 4-hydroxy-3-solanesylbenzoate decarboxylase are required for plastoquinone biosynthesis in the cyanobacterium Synechocystis sp. PCC6803. Pfaff C, Glindemann N, Gruber J, Frentzen M, Sadre R;. J Biol Chem. 2014;289:2675-2686. [3]. 20437231. Functional analysis of genes for benzoate metabolism in the albicidin biosynthetic region of Xanthomonas albilineans. Hashimi SM, Birch RG;. Appl Microbiol Biotechnol. 2010;87:1475-1485. (from Pfam) NF014055.5 PF01948.23 PyrI 25 25 93 PfamEq Y Y N aspartate carbamoyltransferase regulatory subunit 10651286,364472 131567 cellular organisms no rank 7013 EBI-EMBL Aspartate carbamoyltransferase regulatory chain, allosteric domain Aspartate carbamoyltransferase regulatory chain, allosteric domain The regulatory chain is involved in allosteric regulation of aspartate carbamoyltransferase. The N-terminal domain has ferredoxin-like fold, and provides the regulatory chain dimerisation interface. [1]. 364472. Three-dimensional structures of aspartate carbamoyltransferase from Escherichia coli and of its complex with cytidine triphosphate. Monaco HL, Crawford JL, Lipscomb WN;. Proc Natl Acad Sci U S A 1978;75:5276-5280. [2]. 10651286. Insights into the mechanisms of catalysis and heterotropic regulation of Escherichia coli aspartate transcarbamoylase based upon a structure of the enzyme complexed with the bisubstrate analogue N-phosphonacetyl-L-aspartate at 2.1 A. Jin L, Stec B, Lipscomb WN, Kantrowitz ER;. Proteins 1999;37:729-742. (from Pfam) NF014056.5 PF01949.21 DUF99 32.7 32.7 182 PfamAutoEq Y Y N DUF99 family protein 24464998 131567 cellular organisms no rank 1736 EBI-EMBL Protein of unknown function DUF99 DUF99 family protein This family includes uncharacterised archaebacterial proteins. Sequence and structure analysis to identify RNase H-like superfamily members, has clustered this family in endonuclease Clade V, thus suggesting endonuclease activity of these proteins [1]. [1]. 24464998. The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification. Majorek KA, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A, Nowotny M, Ginalski K, Bujnicki JM;. Nucleic Acids Res. 2014;42:4160-4179. (from Pfam) NF014057.5 PF01950.21 FBPase_3 25 25 361 PfamEq Y Y N fructose 1,6-bisphosphatase 15274916 131567 cellular organisms no rank 1280 EBI-EMBL Fructose-1,6-bisphosphatase fructose 1,6-bisphosphatase This is a family of bacterial and archaeal fructose-1,6-bisphosphatases (FBPases). FBPase catalyses the hydrolysis of D-fructose-1,6-bisphosphate (FBP) to D-fructose-6-phosphate (F6P) and orthophosphate and is an essential regulatory enzyme in the glyconeogenic pathway. [1]. 15274916. The first crystal structure of the novel class of fructose-1,6-bisphosphatase present in thermophilic archaea. Nishimasu H, Fushinobu S, Shoun H, Wakagi T;. Structure (Camb) 2004;12:949-959. (from Pfam) NF014058.5 PF01951.21 Archease 25 25 136 PfamEq Y Y N archease 15162483,15281131,17470432 131567 cellular organisms no rank 4536 EBI-EMBL Archease protein family (MTH1598/TM1083) archease This archease family of proteins [1], has two SHS2 domains [2], with one inserted into another. It is predicted to be an enzyme [2]. It is predicted to act as a chaperone in DNA/RNA metabolism [1]. [1]. 15162483. Predicted role for the archease protein family based on structural and sequence analysis of TM1083 and MTH1598, two proteins structurally characterized through structural genomics efforts. Canaves JM;. Proteins. 2004;56:19-27. [2]. 15281131. The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies. Anantharaman V, Aravind L;. Proteins. 2004;56:795-807. [3]. 17470432. Archease from Pyrococcus abyssi improves substrate specificity and solubility of a tRNA m5C methyltransferase. Auxilien S, El Khadali F, Rasmussen A, Douthwaite S, Grosjean H;. J Biol Chem. 2007;282:18711-18721. (from Pfam) NF014059.5 PF01954.21 AF2212-like 21.6 21.6 59 domain Y Y N antitoxin AF2212-like protein 15718296,19493340 131567 cellular organisms no rank 966 EBI-EMBL AF2212-like antitoxin AF2212-like protein This family includes short bacterial and archaebacterial proteins thought to be antitoxin components of the a type II toxin-antitoxin (TA) system. This entry includes AF2212 from Archaeoglobus fulgidus which has sequence similarity with the AbrB superfamily of DNA-binding proteins, identified as antitoxins [1,2]. The secondary structure of AF2212 revealed at least three beta-strands that are most conserved in other AbrB superfamily members [2]. [1]. 15718296. Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Pandey DP, Gerdes K;. Nucleic Acids Res. 2005;33:966-976. [2]. 19493340. Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Makarova KS, Wolf YI, Koonin EV;. Biol Direct. 2009;4:19. (from Pfam) NF014060.5 PF01955.23 CbiZ 27 27 191 domain Y Y N adenosylcobinamide amidohydrolase 14990804 131567 cellular organisms no rank 11220 EBI-EMBL Adenosylcobinamide amidohydrolase adenosylcobinamide amidohydrolase This prokaryotic protein family includes CbiZ which converts adenosylcobinamide (AdoCbi) to adenosylcobyric acid (AdoCby), an intermediate of the de novo coenzyme B12 biosynthetic route [1]. [1]. 14990804. CbiZ, an amidohydrolase enzyme required for salvaging the coenzyme B12 precursor cobinamide in archaea. Woodson JD, Escalante-Semerena JC;. Proc Natl Acad Sci U S A 2004;101:3591-3596. (from Pfam) NF014061.5 PF01956.21 EMC3_TMCO1 27.1 27.1 169 domain Y Y N EMC3/TMCO1 family protein GO:0016020 19325107,26256539,27212239 131567 cellular organisms no rank 1379 EBI-EMBL Integral membrane protein EMC3/TMCO1-like EMC3/TMCO1 family protein This entry represents a group of eukaryotic and archaeal proteins. Eukaryotic members include EMC3, a subunit of the ER membrane protein complex (EMC) required for protein folding [1], and TMCO1, a ER calcium load-activated calcium channel [2]. Archaeal members may function as insertases of the archaeal plasma membrane [3]. [1]. 19325107. Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum. Jonikas MC, Collins SR, Denic V, Oh E, Quan EM, Schmid V, Weibezahn J, Schwappach B, Walter P, Weissman JS, Schuldiner M;. Science. 2009;323:1693-1697. [2]. 27212239. TMCO1 Is an ER Ca(2+) Load-Activated Ca(2+) Channel. Wang QC, Zheng Q, Tan H, Zhang B, Li X, Yang Y, Yu J, Liu Y, Chai H, Wang X, Sun Z, Wang JQ, Zhu S, Wang F, Yang M, Guo C, Wang H, Zheng Q, Li Y, Chen Q, Zhou A, Tang TS;. Cell. 2016;165:1454-1466. [3]. 26256539. A YidC-like Protein in the Archaeal Plasma Membrane. Borowska MT, Dominik PK, Anghel SA, Kossiakoff AA, Keenan RJ;. Structure. 2015;23:1715-1724. (from Pfam) NF014062.5 PF01957.23 NfeD 29.1 29.1 91 domain Y Y N NfeD family protein 20012272 131567 cellular organisms no rank 61222 EBI-EMBL NfeD-like C-terminal, partner-binding NfeD family protein NfeD-like proteins are widely distributed throughout prokaryotes and are frequently associated with genes encoding stomatin-like proteins (slipins). There appear to be three major groups: an ancestral group with only an N-terminal serine protease domain and this C-terminal beta sheet-rich domain which is structurally very similar to the OB-fold domain, associated with its neighbouring slipin cluster; a second major group with an additional middle, membrane-spanning domain, associated in some species with eoslipin and in others with yqfA; a final 'artificial' group which unites truncated forms lacking the protease region and associated with their ancestral gene partner, either yqfA or eoslipin. This NefD, C-terminal, domain appears to be the major one for relating to the associated protein. NfeD homologues are clearly reliant on their conserved gene neighbour which is assumed to be necessary for function, either through direct physical interaction or by functioning in the same pathway, possibly involve with lipid-rafts [1]. [1]. 20012272. The NfeD Protein Family and Its Conserved Gene Neighbours Throughout Prokaryotes: Functional Implications for Stomatin-Like Proteins. Green JB, Lower RP, Young JP;. J Mol Evol. 2009;69:657-667. (from Pfam) NF014063.5 PF01958.23 Asp_DH_C 27 27 89 domain Y Y N aspartate dehydrogenase domain-containing protein GO:0009435,GO:0033735 12496312 131567 cellular organisms no rank 10786 EBI-EMBL Aspartate dehydrogenase, C-terminal Aspartate dehydrogenase, C-terminal This entry represents the C-terminal domain of aspartate dehydrogenases that belong to a unique class of amino acid dehydrogenases. The structure of Thermotoga maritima TM1643 has been found to contain an N-terminal Rossmann fold domain (which binds the NAD(P)+ cofactor) and a C-terminal alpha/beta domain [1]. Enzymatic characterisation of TM1643 revealed that it possesses NAD or NADP-dependent dehydrogenase activity toward L-aspartate but no aspartate oxidase activity [1]. Members of this group share some structural similarity to several other NAD(P)+-dependent oxidoreductases, including inositol 1-phosphate synthase, dihydrodipicolinate reductase, and ASA-DH [1]. It has been proposed that in Thermotoga maritima, TM1643 catalyses the first reaction of de novo biosynthesis of NAD from aspartate, and it produces iminoaspartate required for this pathway. [1]. 12496312. Aspartate dehydrogenase, a novel enzyme identified from structural and functional studies of TM1643. Yang Z, Savchenko A, Yakunin A, Zhang R, Edwards A, Arrowsmith C, Tong L;. J Biol Chem. 2003;278:8804-8808. (from Pfam) NF014064.5 PF01959.21 DHQS 22.2 22.2 344 domain Y Y N 3-dehydroquinate synthase II GO:0003856,GO:0009073,GO:0016491 15182204,17010158 131567 cellular organisms no rank 3981 EBI-EMBL 3-dehydroquinate synthase II 3-dehydroquinate synthase II This family includes members of 3-dehydroquinate synthase II (EC:1.4.1.24), encoded by aroB genes in M. maripaludis which is widely distributed in methanogens. In M. jannaschii, proteins ADTH synthase (AroA) and DHQ synthase II (AroB) are required to convert 6-deoxy-5-ketofructose-1-phosphate (DKFP) and aspartate semialdehyde to 3-dehydroquinate (DHQ) in vitro [1, 2]. [1]. 17010158. Biochemical and genetic characterization of an early step in a novel pathway for the biosynthesis of aromatic amino acids and p-aminobenzoic acid in the archaeon Methanococcus maripaludis. Porat I, Sieprawska-Lupa M, Teng Q, Bohanon FJ, White RH, Whitman WB;. Mol Microbiol. 2006;62:1117-1131. [2]. 15182204. L-Aspartate semialdehyde and a 6-deoxy-5-ketohexose 1-phosphate are the precursors to the aromatic amino acids in Methanocaldococcus jannaschii. White RH;. Biochemistry. 2004;43:7618-7627. (from Pfam) NF014065.5 PF01960.23 ArgJ 32 32 377 PfamEq Y Y N bifunctional ornithine acetyltransferase/N-acetylglutamate synthase GO:0004358,GO:0006526 8473852 131567 cellular organisms no rank 56042 EBI-EMBL ArgJ family bifunctional ornithine acetyltransferase/N-acetylglutamate synthase Members of the ArgJ family catalyse the first EC:2.3.1.1 and fifth steps EC:2.3.1.35 in arginine biosynthesis. [1]. 8473852. Primary structure, partial purification and regulation of key enzymes of the acetyl cycle of arginine biosynthesis in Bacillus stearothermophilus: dual function of ornithine acetyltransferase. Sakanyan V, Charlier D, Legrain C, Kochikyan A, Mett I, Pierard A, Glansdorff N;. J Gen Microbiol 1993;139:393-402. (from Pfam) NF014066.5 PF01963.22 TraB_PrgY_gumN 26.8 26.8 263 domain Y Y N TraB/GumN family protein 22726442,23673329 131567 cellular organisms no rank 36546 EBI-EMBL TraB/PrgY/gumN family TraB/GumN family protein This entry includes Tiki1/2 from humans, TraB/PrgY from the gut flora Enterococcusfaecalis and gumN from the plant pathogen Xanthomonas. Tiki1 is homologous to TraB/PrgY. They have a pair of widely spaced GX2H motifs and a conserved glutamate. From the structural study, this group of proteins have been identified as an ancient metalloprotease clan with a common protein architecture (cobbled from the folds of the EreA/ChaN/PMT group) that mediates proteolytic activities [2]. Tiki1 is a membrane-associated protease that inhibits Wnt via the cleavage of its amino terminus, diminishing Wnt's binding to receptors [1,2]. TraB/PrgY is an inhibitor peptide that may act as a protease to inactivate the mating pheromone [2]. [1]. 23673329. The TIKI/TraB/PrgY family: a common protease fold for cell signaling from bacteria to metazoa?. Bazan JF, Macdonald BT, He X;. Dev Cell. 2013;25:225-227. [2]. 22726442. Tiki1 is required for head formation via Wnt cleavage-oxidation and inactivation. Zhang X, Abreu JG, Yokota C, MacDonald BT, Singh S, Coburn KL, Cheong SM, Zhang MM, Ye QZ, Hang HC, Steen H, He X;. Cell. 2012;149:1565-1577. (from Pfam) NF014067.5 PF01964.23 ThiC_Rad_SAM 25 25 420 PfamEq Y Y N phosphomethylpyrimidine synthase ThiC 4.1.99.17 GO:0009228,GO:0051536 10382260,18953358,8432721 131567 cellular organisms no rank 60918 EBI-EMBL Radical SAM ThiC family phosphomethylpyrimidine synthase ThiC ThiC is found within the thiamine biosynthesis operon. ThiC is involved in pyrimidine biosynthesis [1]. ThiC participates in the formation of 4-Amino-5-hydroxymethyl-2-methylpyrimidine from AIR, an intermediate in the de novo pyrimidine biosynthesis. Thic is a member of the radical SAM superfamily [3]. [1]. 8432721. Structural genes for thiamine biosynthetic enzymes (thiCEFGH) in Escherichia coli K-12. Vander Horn PB, Backstrom AD, Stewart V, Begley TP;. J Bacteriol 1993;175:982-992. [2]. 10382260. Thiamin biosynthesis in prokaryotes. Begley TP, Downs DM, Ealick SE, McLafferty FW, Van Loon AP, Taylor S, Campobasso N, Chiu HJ, Kinsland C, Reddick JJ, Xi J;. Arch Microbiol 1999;171:293-300. [3]. 18953358. Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily. Chatterjee A, Li Y, Zhang Y, Grove TL, Lee M, Krebs C, Booker SJ, Begley TP, Ealick SE;. Nat Chem Biol. 2008;4:758-765. (from Pfam) NF014068.5 PF01965.29 DJ-1_PfpI 26.6 26.6 165 domain Y Y N DJ-1/PfpI family protein 15784968,8626329 131567 cellular organisms no rank 416354 EBI-EMBL DJ-1/PfpI family DJ-1/PfpI family protein The family includes the protease PfpI Swiss:Q51732 [1]. This domain is also found in transcriptional regulators such as Swiss:Q9RJG8. [1]. 8626329. Sequence, expression in Escherichia coli, and analysis of the gene encoding a novel intracellular protease (PfpI) from the hyperthermophilic archaeon Pyrococcus furiosus. Halio SB, Blumentals II, Short SA, Merrill BM, Kelly RM;. J Bacteriol 1996;178:2605-2612. [2]. 15784968. AdpA, a central transcriptional regulator in the A-factor regulatory cascade that leads to morphological development and secondary metabolism in Streptomyces griseus. Ohnishi Y, Yamazaki H, Kato JY, Tomono A, Horinouchi S;. Biosci Biotechnol Biochem. 2005;69:431-439. (from Pfam) NF014069.5 PF01966.27 HD 22 22 116 domain Y Y N HD domain-containing protein 9868367 131567 cellular organisms no rank 615968 EBI-EMBL HD domain HD domain HD domains are metal dependent phosphohydrolases. [1]. 9868367. The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Aravind L, Koonin EV;. Trends Biochem Sci 1998;23:469-472. (from Pfam) NF014070.5 PF01967.26 MoaC 27 27 136 domain Y Y N cyclic pyranopterin monophosphate synthase MoaC GO:0006777 10411269 131567 cellular organisms no rank 51271 EBI-EMBL MoaC family cyclic pyranopterin monophosphate synthase MoaC Members of this family are involved in molybdenum cofactor biosynthesis. However their molecular function is not known. [1]. 10411269. Characterization of a molybdenum cofactor biosynthetic gene cluster in Rhodobacter capsulatus which is specific for the biogenesis of dimethylsulfoxide reductase. Solomon PS, Shaw AL, Lane I, Hanson GR, Palmer T, McEwan AG;. Microbiology 1999;145:1421-1429. (from Pfam) NF014071.5 PF01968.23 Hydantoinase_A 22.9 22.9 291 domain Y Y N hydantoinase/oxoprolinase family protein GO:0016787 8943290 131567 cellular organisms no rank 69383 EBI-EMBL Hydantoinase/oxoprolinase hydantoinase/oxoprolinase family protein This family includes the enzymes hydantoinase and oxoprolinase EC:3.5.2.9. Both reactions involve the hydrolysis of 5-membered rings via hydrolysis of their internal imide bonds [1]. [1]. 8943290. The amino acid sequence of rat kidney 5-oxo-L-prolinase determined by cDNA cloning [published erratum appears in J Biol Chem 1997 Feb 14;272(7):4646]. Ye GJ, Breslow EB, Meister A, Guo-jie GE;. J Biol Chem 1996;271:32293-32300. (from Pfam) NF014072.5 PF01969.22 Ni_insertion 22.1 22.1 375 subfamily Y Y N nickel insertion protein larC 4.99.1.12 24710389,27114550 131567 cellular organisms no rank 15328 EBI-EMBL Nickel insertion protein pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel chelatase The nickel insertion protein LarC (pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel chelatase) seems to be split into two subunits in some species. NF014073.5 PF01970.21 TctA 28.9 28.9 423 domain Y Y N tripartite tricarboxylate transporter permease 14499931,6141166 131567 cellular organisms no rank 64539 EBI-EMBL Tripartite tricarboxylate transporter TctA family tripartite tricarboxylate transporter permease This family, formerly known as DUF112, is a family of bacterial and archaeal tripartite tricarboxylate transporters of the extracytoplasmic solute binding receptor-dependent transporter group of families, distinct from the ABC and TRAP-T families [1]. TctA is part of the tripartite TctABC system which, as characterised in S. typhimurium [2], is a secondary carrier that depends for activity on the extracytoplasmic tricarboxylate-binding receptor TctC as well as two integral membrane proteins, TctA and TctB. complete three-component systems are found only in bacteria. TctA is a large transmembrane protein with up to 12 predicted membrane spanning regions in bacteria and up to 11 such in archaea, with the N-terminal within the cytoplasm. TctA is thought to be a permease, and in most other bacteria functions without TctB and TctC molecules [1]. [1]. 14499931. The tripartite tricarboxylate transporter (TTT) family. Winnen B, Hvorup RN, Saier MH Jr;. Res Microbiol. 2003;154:457-465. [2]. 6141166. Tricarboxylate-binding proteins of Salmonella typhimurium. Purification, crystallization, and physical properties. Sweet GD, Kay CM, Kay WW;. J Biol Chem. 1984;259:1586-1592. (from Pfam) NF014074.5 PF01972.21 SDH_sah 20 20 286 domain Y Y N SDH family Clp fold serine proteinase 3.4.21.- GO:0004252,GO:0016020 15752073 131567 cellular organisms no rank 50763 EBI-EMBL Serine dehydrogenase proteinase SDH family Clp fold serine proteinase domain This family of archaebacterial proteins, formerly known as DUF114, has been found to be a serine dehydrogenase proteinase distantly related to ClpP proteinases that belong to the serine proteinase superfamily. The family has a catalytic triad of Ser, Asp, His residues, which shows an altered residue ordering compared with the ClpP proteinases but similar to that of the carboxypeptidase clan [1]. [1]. 15752073. Identification and analysis of a new family of bacterial serine proteinases. Pandit SB, Srinivasan N;. In Silico Biol. 2004;4:563-572. (from Pfam) NF014075.5 PF01973.23 MptE-like 34.6 34.6 171 domain Y Y N 6-hydroxymethylpterin diphosphokinase MptE-like protein 22931285 131567 cellular organisms no rank 33764 EBI-EMBL 6-hydroxymethylpterin diphosphokinase MptE-like 6-hydroxymethylpterin diphosphokinase MptE-like protein This domain can be found in a group of proteins, including archaeal 6-hydroxymethylpterin diphosphokinase (6-HMDPK), known as MptE, which catalyses the formation of 6-hydroxymethyl-7,8-dihydropterin diphosphate (6-HMDP) from 6-HMD and ATP [1]. 6-HMDP is the precursor of the pterin containing moiety of the essential C1-carriers tetrahydrofolate and tetrahydromethanopterin. This entry also includes a number of uncharacterised proteins from bacteria. [1]. 22931285. Comparative genomics guided discovery of two missing archaeal enzyme families involved in the biosynthesis of the pterin moiety of tetrahydromethanopterin and tetrahydrofolate. de Crecy-Lagard V, Phillips G, Grochowski LL, El Yacoubi B, Jenney F, Adams MW, Murzin AG, White RH;. ACS Chem Biol. 2012;7:1807-1816. (from Pfam) NF014076.5 PF01974.22 tRNA_int_endo 27 27 85 domain Y N N tRNA intron endonuclease, catalytic C-terminal domain GO:0000213,GO:0006388 22638584,9200602,9535656 131567 cellular organisms no rank 1528 EBI-EMBL tRNA intron endonuclease, catalytic C-terminal domain tRNA intron endonuclease, catalytic C-terminal domain Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9. [1]. 9200602. Properties of H. volcanii tRNA intron endonuclease reveal a relationship between the archaeal and eucaryal tRNA intron processing systems. Kleman-Leyer K, Armbruster DW, Daniels CJ;. Cell 1997;89:839-847. [2]. 9535656. Crystal structure and evolution of a transfer RNA splicing enzyme. Li H, Trotta CR, Abelson J;. Science 1998;280:279-284. [3]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF014077.5 PF01975.22 SurE 22.1 22.1 189 domain Y Y N 5'/3'-nucleotidase SurE GO:0016787 1423722,7928962 131567 cellular organisms no rank 45425 EBI-EMBL Survival protein SurE 5'/3'-nucleotidase SurE E. coli cells with the surE gene disrupted are found to survive poorly in stationary phase [1]. It is suggested that SurE may be involved in stress response. Yeast also contains a member of the family Swiss:P38254. Swiss:P30887 can complement a mutation in acid phosphatase, suggesting that members of this family could be phosphatases. [1]. 7928962. A new gene involved in stationary-phase survival located at 59 minutes on the Escherichia coli chromosome. Li C, Ichikawa JK, Ravetto JJ, Kuo HC, Fu JC, Clarke S;. J Bacteriol 1994;176:6015-6022. [2]. 1423722. Complementation of Saccharomyces cerevisiae acid phosphatase mutation by a genomic sequence from the yeast Yarrowia lipolytica identifies a new phosphatase. Treton BY, Le Dall MT, Gaillardin CM;. Curr Genet 1992;22:345-355. (from Pfam) NF014078.5 PF01976.22 DUF116 25 25 155 domain Y Y N DUF116 domain-containing protein 25583072 131567 cellular organisms no rank 2942 EBI-EMBL Protein of unknown function DUF116 Protein of unknown function DUF116 This archaebacterial protein has no known function. The protein contains seven conserved cysteines containing a CxxCxxC motif and may also be an integral membrane protein [1]. [1]. 25583072. Comparative genomic analysis of evolutionarily conserved but functionally uncharacterized membrane proteins in archaea: Prediction of novel components of secretion, membrane remodeling and glycosylation systems. Makarova KS, Galperin MY, Koonin EV;. Biochimie. 2015;118:302-312. (from Pfam) NF014079.5 PF01977.21 UbiD 23.3 23.3 206 domain Y Y N UbiD family decarboxylase domain-containing protein 4.1.1.- GO:0016831 23671667,25862228,26083754,28057757,28857436,782527 131567 cellular organisms no rank 51988 EBI-EMBL 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain This family has been characterised as 3-octaprenyl-4- hydroxybenzoate carboxy-lyase enzymes [1]. This enzyme catalyses the third reaction in ubiquinone biosynthesis. For optimal activity the carboxy-lase was shown to require Mn2+ [1]. This entry represents the central RIFT-related domain. [1]. 782527. Membrane-associated reactions in ubiquinone biosynthesis in Escherichia coli. 3-Octaprenyl-4-hydroxybenzoate carboxy-lyase. Leppik RA, Young IG, Gibson F;. Biochim Biophys Acta 1976;436:800-810. [2]. 23671667. Structural insights into the UbiD protein family from the crystal structure of PA0254 from Pseudomonas aeruginosa. Jacewicz A, Izumi A, Brunner K, Schnell R, Schneider G;. PLoS One. 2013;8:e63161. [3]. 25862228. Structure and Mechanism of Ferulic Acid Decarboxylase (FDC1) from Saccharomyces cerevisiae. Bhuiya MW, Lee SG, Jez JM, Yu O;. Appl Environ Microbiol. 2015;81:4216-4223. [4]. 26083754. New cofactor supports alpha,beta-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition. Payne KA, White MD, Fisher K, Khara B, Bailey SS, Parker D, Rattray NJ, Trivedi DK, Goodacre R, Beveridge R, Barran P, Rigby SE, Scrutton NS, Hay S, Leys D;. Nature. 2015;522:497-501. [5]. 28057757. Oxidative Maturation and Structural Characterization of Prenylated FMN Binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis. Marshall SA, Fisher K, Ni Cheallaigh A, White MD, Payne KA, Parker DA, Rigby SE, Leys D;. J Biol Chem. 2017;292:4623-4637. [6]. 28857436. Regioselective para-Carboxylation of Catechols with a Prenylated Flavin Dependent Decarboxylase. Payer SE, Marshall SA, Barland N, Sheng X, Reiter T, Dordic. TRUNCATED at 1650 bytes (from Pfam) NF014080.5 PF01978.24 TrmB 25.6 25.6 68 domain Y Y N helix-turn-helix domain-containing protein 12426307,8594196 131567 cellular organisms no rank 73291 EBI-EMBL Sugar-specific transcriptional regulator TrmB Sugar-specific transcriptional regulator TrmB One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter [2] in Thermococcus litoralis. [1]. 8594196. Genetics of a novel starch utilisation pathway present in Klebsiella oxytoca. Fiedler G, Pajatsch M, Bock A;. J Mol Biol 1996;256:279-291. [2]. 12426307. TrmB, a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter from the hyperthermophilic archaeon Thermococcus litoralis. Lee SJ, Engelmann A, Horlacher R, Qu Q, Vierke G, Hebbeln C, Thomm M, Boos W;. J Biol Chem 2003;278:983-990. (from Pfam) NF014081.5 PF01979.25 Amidohydro_1 25 25 345 domain Y Y N amidohydrolase family protein GO:0016787 7754395,8550522,8590465,9144792,9878395 131567 cellular organisms no rank 842033 EBI-EMBL Amidohydrolase family amidohydrolase family protein This family of enzymes are a a large metal dependent hydrolase superfamily [1]. The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilisation as a purine and also as a nitrogen source [2]. This family also includes dihydroorotase and N-acetylglucosamine-6-phosphate deacetylases, EC:3.5.1.25 These enzymes catalyse the reaction N-acetyl-D-glucosamine 6-phosphate + H2O D-glucosamine 6-phosphate + acetate. This family includes the catalytic domain of urease alpha subunit [3]. Dihydroorotases (EC:3.5.2.3) are also included [4-5]. [1]. 9144792. An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Holm L, Sander C;. Proteins 1997;28:72-82. [2]. 8550522. Role of adenine deaminase in purine salvage and nitrogen metabolism and characterization of the ade gene in Bacillus subtilis. Nygaard P, Duckert P, Saxild HH;. J Bacteriol 1996;178:846-853. [3]. 7754395. The crystal structure of urease from Klebsiella aerogenes. Jabri E, Carr MB, Hausinger RP, Karplus PA;. Science 1995;268:998-1004. [4]. 9878395. Novel organization and sequences of five genes encoding all six enzymes for de novo pyrimidine biosynthesis in Trypanosoma cruzi. Gao G, Nara T, Nakajima-Shimada J, Aoki T;. J Mol Biol 1999;285:149-161. [5]. 8590465. As in Saccharomyces cerevisiae, aspartate transcarbamoylase is assembled on a multifunctional protein including a dihydroorotase-like cryptic domain in Schizosaccharomyces pombe. Lollier M, Jaquet L, Nedeva T, Lacroute F, Potier S, Souciet JL;. Curr Genet 1995;28:138-149. (from Pfam) NF014082.5 PF01980.21 TrmO 26.8 26.8 116 subfamily Y Y N TrmO family methyltransferase 2.1.1.- 25063302,27913733 131567 cellular organisms no rank 32211 EBI-EMBL tRNA-methyltransferase O TrmO family methyltransferase This family includes members such as TrmO (tRNA-methyltransferase O) also known as YaeB, which contains a single-sheeted beta-barrel structure. TrmO is an AdoMet-dependent methyltransferase responsible for m6t6A formation [1]. Its human homolog, is responsible for formation of m6t6A37 in cytoplasmic tRNASer. Lack of TrmO decreases attenuation activity of the thr operon, indicating that N6 methylation of m6t6A37 ensures efficient decoding of ACY codons [2]. In bacteria and eukaryotes, TrmO has a C-terminal domain containing the conserved DPRxxY motif. Where the Asp194 and Arg196 in this motif of E. coli TrmO are necessary for N6-methylation. However, no archaeal YaeB has a C-terminal domain containing the DPRxxY motif that is conserved in bacterial and mammalian TrmO homologs [1]. [1]. 25063302. Discovery of the beta-barrel-type RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs. Kimura S, Miyauchi K, Ikeuchi Y, Thiaville PC, Crecy-Lagard Vd, Suzuki T;. Nucleic Acids Res. 2014;42:9350-9365. [2]. 27913733. Identification of 2-methylthio cyclic N6-threonylcarbamoyladenosine (ms2ct6A) as a novel RNA modification at position 37 of tRNAs. Kang BI, Miyauchi K, Matuszewski M, D'Almeida GS, Rubio MAT, Alfonzo JD, Inoue K, Sakaguchi Y, Suzuki T, Sochacka E, Suzuki T;. Nucleic Acids Res. 2017;45:2124-2136. (from Pfam) NF014083.5 PF01981.21 PTH2 23 23 115 domain Y Y N peptidyl-tRNA hydrolase GO:0004045 12475929 131567 cellular organisms no rank 10922 EBI-EMBL Peptidyl-tRNA hydrolase PTH2 peptidyl-tRNA hydrolase Peptidyl-tRNA hydrolases are enzymes that release tRNAs from peptidyl-tRNA during translation. [1]. 12475929. Orthologs of a novel archaeal and of the bacterial peptidyl-tRNA hydrolase are nonessential in yeast. Rosas-Sandoval G, Ambrogelly A, Rinehart J, Wei D, Cruz-Vera LR, Graham DE, Stetter KO, Guarneros G, Soll D;. Proc Natl Acad Sci U S A 2002;99:16707-16712. (from Pfam) NF014084.5 PF01982.21 CTP-dep_RFKase 25 25 121 PfamAutoEq Y Y N DUF120 domain-containing protein GO:0016773 18073108 131567 cellular organisms no rank 1566 EBI-EMBL Domain of unknown function DUF120 Domain of unknown function DUF120 This domain is a CTP-dependent riboflavin kinase (RFK), found in archaea, that catalyses the phosphorylation of riboflavin to form flavin mononucleotide in riboflavin biosynthesis EC:2.7.1.26. Its structure resembles a RIFT barrel, structurally similar to but topologically distinct from bacterial and eukaryotic examples. The N-terminal is a winged helix-turn-helix DNA-binding domain, and the C-terminal half is most similar in sequence to a group of cradle-loop barrels. Swiss:O28174 has this domain attached to Pfam:PF00325. [1]. 18073108. A CTP-Dependent Archaeal Riboflavin Kinase Forms a Bridge in the Evolution of Cradle-Loop Barrels. Ammelburg M, Hartmann MD, Djuranovic S, Alva V, Koretke KK, Martin J, Sauer G, Truffault V, Zeth K, Lupas AN, Coles M;. Structure. 2007;15:1577-1590. (from Pfam) NF014085.5 PF01983.21 CofC 22 22 217 PfamEq Y N N Guanylyl transferase CofC like GO:0043814 18260642 131567 cellular organisms no rank 18559 EBI-EMBL Guanylyl transferase CofC like Guanylyl transferase CofC like Coenzyme F420 is a hydride carrier cofactor that functions during methanogenesis. This family of proteins represents CofC, a nucleotidyl transferase that is involved in coenzyme F420 biosynthesis. CofC has been shown to catalyse the formation of lactyl-2-diphospho-5'-guanosine from 2-phospho-L-lactate and GTP [1]. [1]. 18260642. Identification and characterization of the 2-phospho-L-lactate guanylyltransferase involved in coenzyme F420 biosynthesis. Grochowski LL, Xu H, White RH;. Biochemistry. 2008;47:3033-3037. (from Pfam) NF014086.5 PF01984.25 dsDNA_bind 26 26 106 domain Y Y N DNA-binding protein GO:0003677 11017201 131567 cellular organisms no rank 1205 EBI-EMBL Double-stranded DNA-binding domain Double-stranded DNA-binding domain This domain is believed to bind double-stranded DNA [1] of 20 bases length. [1]. 11017201. Structural proteomics of an archaeon. Christendat D, Yee A, Dharamsi A, Kluger Y, Savchenko A, Cort JR, Booth V, Mackereth CD, Saridakis V, Ekiel I, Kozlov G, Maxwell KL, Wu N, McIntosh LP, Gehring K, Kennedy MA, Davidson AR, Pai EF, Gerstein M, Edwards AM, Arrowsmith CH;. Nat Struct Biol 2000;7:903-909. (from Pfam) NF014087.5 PF01985.26 CRS1_YhbY 27 27 84 domain Y Y N YhbY family RNA-binding protein GO:0003723 11565746,12360533,12429100,17105995,18065687 131567 cellular organisms no rank 18462 EBI-EMBL CRS1 / YhbY (CRM) domain CRS1 / YhbY (CRM) domain Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants [4]. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing [5]. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes [4]. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [1][2]. [1]. 12429100. Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins. Ostheimer GJ, Barkan A, Matthews BW;. Structure (Camb) 2002;10:1593-1601. [2]. 12360533. Structure of HI1333 (YhbY), a putative RNA-binding protein from Haemophilus influenzae. Willis MA, Krajewski W, Chalamasetty VR, Reddy P, Howard A, Herzberg O;. Proteins 2002;49:423-426. [3]. 11565746. CRS1 is a novel group II intron splicing factor that was derived from a domain of ancient origin. Till B, Schmitz-Linneweber C, Williams-Carrier R, Barkan A;. RNA 2001;7:1227-1238. [4]. 17105995. The CRM domain: an RNA binding module derived from an ancient ribosome-associa. TRUNCATED at 1650 bytes (from Pfam) NF014088.5 PF01986.21 DUF123 25 25 95 PfamAutoEq Y Y N DUF123 domain-containing protein 131567 cellular organisms no rank 2787 EBI-EMBL Domain of unknown function DUF123 Domain of unknown function DUF123 This archaebacterial domain has no known function. It is attached to an endonuclease domain in Swiss:Q58030. The domain contains several conserved cysteines and histidines. This suggests that the domain may be a zinc binding nucleic acid interaction domain (Bateman A unpubl.). (from Pfam) NF014089.5 PF01987.22 AIM24 25.7 25.7 205 domain Y Y N AIM24 family protein 19300474 131567 cellular organisms no rank 60487 EBI-EMBL Mitochondrial biogenesis AIM24 AIM24 family protein In eukaryotes, this domain is involved in mitochondrial biogenesis [1]. Its function in prokaryotes in unknown. [1]. 19300474. Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. Hess DC, Myers CL, Huttenhower C, Hibbs MA, Hayes AP, Paw J, Clore JJ, Mendoza RM, Luis BS, Nislow C, Giaever G, Costanzo M, Troyanskaya OG, Caudy AA;. PLoS Genet. 2009;5:e1000407. (from Pfam) NF014090.5 PF01988.24 VIT1 28.1 28.1 214 domain Y Y N VIT1/CCC1 transporter family protein GO:0005384,GO:0030026 7941738 131567 cellular organisms no rank 44185 EBI-EMBL VIT family VIT1/CCC1 transporter family protein This family includes the vacuolar Fe2+/Mn2+ uptake transporter Swiss:P47818, Ccc1 [1] and the vacuolar iron transporter VIT1 Swiss:Q9ZUA5. [1]. 7941738. Sequence, mapping and disruption of CCC1, a gene that cross-complements the Ca(2+)-sensitive phenotype of csg1 mutants. Fu D, Beeler T, Dunn T;. Yeast 1994;10:515-521. (from Pfam) NF014091.5 PF01989.21 AcnX_swivel_put 27 27 80 domain Y Y N aconitase X swivel domain-containing protein 14568143,30224495 131567 cellular organisms no rank 7321 EBI-EMBL Aconitase X swivel domain Aconitase X swivel domain This is a putative aconitase X swivel domain, which has been predicted by comparative genomic analysis. The domain is mainly found in archaeal and proteobacterial proteins. As such, the prediction should be treated with caution [1]. One member of this entry from Aeropyrum pernix which has been annotated as a putative aconitase, has been characterised in vitro and catalyses the dehydration of mevalonate 5-phosphate to form trans-anhydromevalonate 5-phosphate, a previously unknown intermediate [2], being involved in a "modified" mevalonate pathway. [1]. 14568143. Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis. Makarova KS, Koonin EV;. FEMS Microbiol Lett. 2003;227:17-23. [2]. 30224495. Modified mevalonate pathway of the archaeon Aeropyrum pernix proceeds via trans-anhydromevalonate 5-phosphate. Hayakawa H, Motoyama K, Sobue F, Ito T, Kawaide H, Yoshimura T, Hemmi H;. Proc Natl Acad Sci U S A. 2018;115:10034-10039. (from Pfam) NF014092.5 PF01990.22 ATP-synt_F 23.5 23.5 91 domain Y Y N V-type ATP synthase subunit F GO:0034220,GO:0046961 8621738,8682310,8702544 131567 cellular organisms no rank 5051 EBI-EMBL ATP synthase (F/14-kDa) subunit V-type ATP synthase subunit F This family includes 14-kDa subunit from vATPases [1], which is in the peripheral catalytic part of the complex [2]. The family also includes archaebacterial ATP synthase subunit F [3]. [1]. 8682310. The Drosophila melanogaster gene vha14 encoding a 14-kDa F-subunit of the vacuolar ATPase. Guo Y, Kaiser K, Wieczorek H, Dow JA;. Gene 1996;172:239-243. [2]. 8621738. Identification of a 14-kDa subunit associated with the catalytic sector of clathrin-coated vesicle H+-ATPase. Peng SB, Crider BP, Tsai SJ, Xie XS, Stone DK;. J Biol Chem 1996;271:3324-3327. [3]. 8702544. Subunit structure and organization of the genes of the A1A0 ATPase from the Archaeon Methanosarcina mazei Go1. Wilms R, Freiberg C, Wegerle E, Meier I, Mayer F, Muller V;. J Biol Chem 1996;271:18843-18852. (from Pfam) NF014093.5 PF01991.23 vATP-synt_E 24.2 24.2 199 domain Y Y N V-type ATP synthase subunit E family protein GO:0033178,GO:0046961,GO:1902600 2145285,8702544 131567 cellular organisms no rank 5179 EBI-EMBL ATP synthase (E/31 kDa) subunit V-type ATP synthase subunit E family protein This family includes the vacuolar ATP synthase E subunit [1], as well as the archaebacterial ATP synthase E subunit [2]. [1]. 2145285. The 31-kDa polypeptide is an essential subunit of the vacuolar ATPase in Saccharomyces cerevisiae. Foury F;. J Biol Chem 1990;265:18554-18560. [2]. 8702544. Subunit structure and organization of the genes of the A1A0 ATPase from the Archaeon Methanosarcina mazei Go1. Wilms R, Freiberg C, Wegerle E, Meier I, Mayer F, Muller V;. J Biol Chem 1996;271:18843-18852. (from Pfam) NF014094.5 PF01992.21 vATP-synt_AC39 29 29 339 domain Y Y N V-type ATPase subunit GO:0046961 8157629,8509410,8702544 131567 cellular organisms no rank 7989 EBI-EMBL ATP synthase (C/AC39) subunit V-type ATPase subunit This family includes the AC39 subunit from vacuolar ATP synthase Swiss:P32366 [1], and the C subunit from archaebacterial ATP synthase [2]. The family also includes subunit C from the Sodium transporting ATP synthase from Enterococcus hirae Swiss:P43456 [3]. [1]. 8509410. The Saccharomyces cerevisiae VMA6 gene encodes the 36-kDa subunit of the vacuolar H(+)-ATPase membrane sector. Bauerle C, Ho MN, Lindorfer MA, Stevens TH;. J Biol Chem 1993;268:12749-12757. [2]. 8702544. Subunit structure and organization of the genes of the A1A0 ATPase from the Archaeon Methanosarcina mazei Go1. Wilms R, Freiberg C, Wegerle E, Meier I, Mayer F, Muller V;. J Biol Chem 1996;271:18843-18852. [3]. 8157629. Sequencing and characterization of the ntp gene cluster for vacuolar- type Na(+)-translocating ATPase of Enterococcus hirae. Takase K, Kakinuma S, Yamato I, Konishi K, Igarashi K, Kakinuma Y;. J Biol Chem 1994;269:11037-11044. (from Pfam) NF014095.5 PF01993.23 MTD 25 25 274 PfamEq Y Y N F420-dependent methylenetetrahydromethanopterin dehydrogenase GO:0008901,GO:0015948 7852356 131567 cellular organisms no rank 471 EBI-EMBL methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase F420-dependent methylenetetrahydromethanopterin dehydrogenase This enzyme family is involved in formation of methane from carbon dioxide EC:1.5.99.9. The enzyme requires coenzyme F420 [1]. [1]. 7852356. Cloning, sequencing, and transcriptional analysis of the coenzyme F420- dependent methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase gene from Methanobacterium thermoautotrophicum strain Marburg and functional expression in Escherichia coli. Mukhopadhyay B, Purwantini E, Pihl TD, Reeve JN, Daniels L;. J Biol Chem 1995;270:2827-2832. (from Pfam) NF014096.5 PF01994.21 Trm56 25 25 119 PfamEq Y N N tRNA ribose 2'-O-methyltransferase, aTrm56 GO:0002128,GO:0005737,GO:0008175 15987815,16164996,18068186 131567 cellular organisms no rank 1324 EBI-EMBL tRNA ribose 2'-O-methyltransferase, aTrm56 tRNA ribose 2'-O-methyltransferase, aTrm56 This family is an aTrm56 that catalyses the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Biochemical assays showed that aTrm56 forms a dimer and prefers the L-shaped tRNA to the lambda form as its substrate [1] [2]. aTrm56 consists of the SPOUT domain, which contains the characteristic deep trefoil knot for AdoMet binding, and a unique C-terminal beta-hairpin [3]. [1]. 15987815. The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP. Renalier MH, Joseph N, Gaspin C, Thebault P, Mougin A;. RNA. 2005;11:1051-1063. [2]. 16164996. Two different mechanisms for tRNA ribose methylation in Archaea: a short survey. Clouet-d'Orval B, Gaspin C, Mougin A;. Biochimie. 2005;87:889-895. [3]. 18068186. Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA. Kuratani M, Bessho Y, Nishimoto M, Grosjean H, Yokoyama S;. J Mol Biol. 2008;375:1064-1075. (from Pfam) NF014097.5 PF01995.21 NRD1_2 25 25 238 domain Y Y N NrpR regulatory domain-containing protein 21070950 131567 cellular organisms no rank 890 EBI-EMBL NrpR regulatory domains NRD1 and 2 NrpR regulatory domains NRD1 and 2 This entry comprises two domains found in the nitrogen regulatory protein NrpR that bind DNA and repress transcription of nitrogen assimilation genes. The two NrpR regulatory domains (NRD1 and NRD2) that sense and bind 2-oxoglutarate (2OG) are both structurally and functionally homologous and share a high degree of sequence conservation. Mutational analysis of NrpR from Methanococcus maripaludis (MmNrpR) indicated that the two most critical residues for 2OG binding are Cys389 and His435 (Cys395 and His441, respectively in thermophilic archaeon Methanocaldococcus jannaschii (MjNrpR)). Both the Cys395 and His441 are conserved among NrpR proteins from diverse species [1]. [1]. 21070950. Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR. Wisedchaisri G, Dranow DM, Lie TJ, Bonanno JB, Patskovsky Y, Ozyurt SA, Sauder JM, Almo SC, Wasserman SR, Burley SK, Leigh JA, Gonen T;. Structure. 2010;18:1512-1521. (from Pfam) NF014098.5 PF01996.21 F420_ligase 25 25 218 domain Y Y N coenzyme F420-0:L-glutamate ligase 6.3.2.31 12867481,15215601,2110564,8577249 131567 cellular organisms no rank 21405 EBI-EMBL F420-0:Gamma-glutamyl ligase coenzyme F420-0:L-glutamate ligase F420-0:Gamma-glutamyl ligase (EC:6.3.2.-) is an enzyme involved in F420 biosynthesis pathway. It catalyses the GTP-dependent successive addition of multiple gamma-linked L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0). This reaction produces polyglutamated F420 derivatives. GTP + F420-0 + n L-glutamate -> GDP + phosphate + F420-n [1]. 15215601. Identification and cloning of the gene involved in the final step of chlortetracycline biosynthesis in Streptomyces aureofaciens. Nakano T, Miyake K, Endo H, Dairi T, Mizukami T, Katsumata R;. Biosci Biotechnol Biochem. 2004;68:1345-1352. [2]. 8577249. Molecular characterization of the lincomycin-production gene cluster of Streptomyces lincolnensis 78-11. Peschke U, Schmidt H, Zhang HZ, Piepersberg W;. Mol Microbiol. 1995;16:1137-1156. [3]. 12867481. Methanococcus jannaschii coenzyme F420 analogs contain a terminal alpha-linked glutamate. Graupner M, White RH;. J Bacteriol. 2003;185:4662-4665. [4]. 2110564. DNA photoreactivating enzyme from the cyanobacterium Anacystis nidulans. Eker AP, Kooiman P, Hessels JK, Yasui A;. J Biol Chem. 1990;265:8009-8015. (from Pfam) NF014099.5 PF01997.21 Translin 25.9 25.9 205 PfamEq Y N N Translin family GO:0043565 9013868 131567 cellular organisms no rank 348 EBI-EMBL Translin family Translin family Members of this family include Translin Swiss:Q15631 that interacts with DNA and forms a ring around the DNA. This family also includes Swiss:Q99598, that was found to interact with translin with yeast two-hybrid screen [1]. [1]. 9013868. Isolation and characterization of a cDNA encoding a Translin-like protein, TRAX. Aoki K, Ishida R, Kasai M;. FEBS Lett 1997;401:109-112. (from Pfam) NF014100.5 PF01998.22 DUF131 22 22 62 domain Y Y N DUF131 domain-containing protein 131567 cellular organisms no rank 534 EBI-EMBL Protein of unknown function DUF131 Protein of unknown function DUF131 This archaebacterial protein family has no known function. The proteins are predicted to contain two transmembrane helices. (from Pfam) NF014101.5 PF02001.21 DUF134 27 27 98 domain Y Y N DUF134 domain-containing protein 32967357 131567 cellular organisms no rank 6356 EBI-EMBL Protein of unknown function DUF134 Protein of unknown function DUF134 This family of archaeal proteins has no known function. A study suggests that some members may be G-quadruplex binding proteins [1]. [1]. 32967357. G-Quadruplexes in the Archaea Domain. Brazda V, Luo Y, Bartas M, Kaura P, Porubiakova O, Stastny J, Pecinka P, Verga D, Da Cunha V, Takahashi TS, Forterre P, Myllykallio H, Fojta M, Mergny JL;. Biomolecules. 2020; [Epub ahead of print] (from Pfam) NF014102.5 PF02002.22 TFIIE_alpha 22.9 22.9 105 domain Y N N TFIIE alpha subunit 1454543,1956403,9389475 131567 cellular organisms no rank 3973 EBI-EMBL TFIIE alpha subunit TFIIE alpha subunit The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha Swiss:P29083 and TFIIE-beta Swiss:P29084 and joins the pre-initiation complex after RNA polymerase II and TFIIF [1]. This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha [2] and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits also Swiss:O29501 [3]. [1]. 1956403. Structural motifs and potential sigma homologies in the large subunit of human general transcription factor TFIIE. Ohkuma Y, Sumimoto H, Hoffmann A, Shimasaki S, Horikoshi M, Roeder RG;. Nature 1991;354:398-401. [2]. 1454543. Identification of two large subdomains in TFIIE-alpha on the basis of homology between Xenopus and human sequences. Ohkuma Y, Hashimoto S, Roeder RG, Horikoshi M;. Nucleic Acids Res 1992;20:5838-5838. [3]. 9389475. The complete genome sequence of the hyperthermophilic, sulphate- reducing archaeon Archaeoglobus fulgidus. Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, McKenney K. Nature 1997;390:364-370. (from Pfam) NF014103.5 PF02005.21 TRM 27 27 376 domain Y N N N2,N2-dimethylguanosine tRNA methyltransferase GO:0003723,GO:0008033 3299379,9685492 131567 cellular organisms no rank 3571 EBI-EMBL N2,N2-dimethylguanosine tRNA methyltransferase N2,N2-dimethylguanosine tRNA methyltransferase This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA. The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs [1]. The enzyme is found in both eukaryotes and archaebacteria [2] [1]. 3299379. Amino-terminal extension generated from an upstream AUG codon is not required for mitochondrial import of yeast N2,N2-dimethylguanosine- specific tRNA methyltransferase. Ellis SR, Hopper AK, Martin NC;. Proc Natl Acad Sci U S A 1987;84:5172-5176. [2]. 9685492. The tRNA(guanine-26,N2-N2) methyltransferase (Trm1) from the hyperthermophilic archaeon Pyrococcus furiosus: cloning, sequencing of the gene and its expression in Escherichia coli. Constantinesco F, Benachenhou N, Motorin Y, Grosjean H;. Nucleic Acids Res 1998;26:3753-3761. (from Pfam) NF014104.5 PF02006.21 PPS_PS 26.4 26.4 176 subfamily Y Y N phosphopantothenate/pantothenate synthetase family protein 18422645,19666462 131567 cellular organisms no rank 1403 EBI-EMBL Phosphopantothenate/pantothenate synthetase phosphopantothenate/pantothenate synthetase family protein This family of archaeal proteins includes pantothenate synthetase from Methanosarcina mazei and 4-phosphopantoate--beta-alanine ligase (phosphopantothenate synthetase) from Pyrococcus kodakaraensis. Pantothenate synthetase catalyses the condensation of pantoate with beta-alanine in an ATP-dependent and ADP-producing reaction [1]. 4-phosphopantoate--beta-alanine ligase catalyses the conversion of (R)-4-phosphopantoate and beta-alanine to 4'-phosphopantothenate in the CoA biosynthesis pathway. It cannot use (R)-pantoate as substrate and thus does not display pantothenate synthetase activity [2]. [1]. 18422645. A novel isoform of pantothenate synthetase in the Archaea. Ronconi S, Jonczyk R, Genschel U;. FEBS J. 2008;275:2754-2764. [2]. 19666462. Pantoate kinase and phosphopantothenate synthetase, two novel enzymes necessary for CoA biosynthesis in the Archaea. Yokooji Y, Tomita H, Atomi H, Imanaka T;. J Biol Chem. 2009;284:28137-28145. (from Pfam) NF014105.5 PF02007.23 MtrH 22.8 22.8 299 domain Y N N Tetrahydromethanopterin S-methyltransferase MtrH subunit GO:0006730,GO:0008168 7737157 131567 cellular organisms no rank 983 EBI-EMBL Tetrahydromethanopterin S-methyltransferase MtrH subunit Tetrahydromethanopterin S-methyltransferase MtrH subunit The enzyme tetrahydromethanopterin S-methyltransferase EC:2.1.1.86 is composed of eight subunits [1]. The enzyme is a membrane- associated enzyme complex which catalyses an energy-conserving, sodium-ion-translocating step in methanogenesis from hydrogen and carbon dioxide [1]. [1]. 7737157. The energy conserving N5-methyltetrahydromethanopterin:coenzyme M methyltransferase complex from Methanobacterium thermoautotrophicum is composed of eight different subunits. Harms U, Weiss DS, Gartner P, Linder D, Thauer RK;. Eur J Biochem 1995;228:640-648. (from Pfam) NF014108.5 PF02010.20 REJ 25 25 452 domain Y Y N REJ domain-containing protein 8666666,9949214 131567 cellular organisms no rank 1916 EBI-EMBL REJ domain REJ domain The REJ (Receptor for Egg Jelly) domain is found in PKD1 Swiss:P98161, and the sperm receptor for egg jelly Swiss:Q26627. The function of this domain is unknown. The domain is 600 amino acids long so is probably composed of multiple structural domains. There are six completely conserved cysteine residues that may form disulphide bridges. This region contains tandem PKD-like domains. [1]. 8666666. The sea urchin sperm receptor for egg jelly is a modular protein with extensive homology to the human polycystic kidney disease protein, PKD1. Moy GW, Mendoza LM, Schulz JR, Swanson WJ, Glabe CG, Vacquier VD;. J Cell Biol 1996;133:809-817. [2]. 9949214. Identification of a human homologue of the sea urchin receptor for egg jelly: a polycystic kidney disease-like protein. Hughes J, Ward CJ, Aspinwall R, Butler R, Harris PC;. Hum Mol Genet 1999;8:543-549. (from Pfam) NF014110.5 PF02012.25 BNR 27 12.4 12 repeat Y N N BNR/Asp-box repeat protein 11266614,2562507 131567 cellular organisms no rank 22332 EBI-EMBL BNR/Asp-box repeat BNR/Asp-box repeat Members of this family contain multiple BNR (bacterial neuraminidase repeat) repeats or Asp-boxes. The repeats are short, however the repeats are never found closer than 40 residues together suggesting that the repeat is structurally longer. These repeats are found in many glycosyl hydrolases as well as other extracellular proteins of unknown function. [1]. 2562507. Conserved sequences in bacterial and viral sialidases. Roggentin P, Rothe B, Kaper JB, Galen J, Lawrisuk L, Vimr ER, Schauer R;. Glycoconj J 1989;6:349-353. [2]. 11266614. Sialidase-like Asp-boxes: sequence-similar structures within different protein folds. Copley RR, Russell RB, Ponting CP;. Protein Sci 2001;10:285-292. (from Pfam) NF014112.5 PF02014.21 Reeler 21 21 131 domain Y Y N reeler domain-containing protein 131567 cellular organisms no rank 148 EBI-EMBL Reeler domain reeler domain NF014114.5 PF02016.20 Peptidase_S66 25 25 121 domain Y Y N LD-carboxypeptidase 10428950,16162494,7559516,8522520 131567 cellular organisms no rank 69995 EBI-EMBL LD-carboxypeptidase N-terminal domain LD-carboxypeptidase N-terminal domain Muramoyl-tetrapeptide carboxypeptidase hydrolyses a peptide bond between a di-basic amino acid and the C-terminal D-alanine in the tetrapeptide moiety in peptidoglycan. This cleaves the bond between an L- and a D-amino acid. The function of this activity is in murein recycling. This family also includes the microcin c7 self-immunity protein Swiss:Q47511. This family corresponds to Merops family S66. [1]. 8522520. Structure and organization of plasmid genes required to produce the translation inhibitor microcin C7. Gonzalez-Pastor JE, San Millan JL, Castilla MA, Moreno F;. J Bacteriol 1995;177:7131-7140. [2]. 7559516. Chemical structure and translation inhibition studies of the antibiotic microcin C7. Guijarro JI, Gonzalez-Pastor JE, Baleux F, San Millan JL, Castilla MA, Rico M, Moreno F, Delepierre M;. J Biol Chem 1995;270:23520-23532. [3]. 10428950. A defect in cell wall recycling triggers autolysis during the stationary growth phase of Escherichia coli. Templin MF, Ursinus A, Holtje JV;. EMBO J 1999;18:4108-4117. [4]. 16162494. P. aeruginosa LD-carboxypeptidase: A serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow. Korza HJ, Bochtler M;. J Biol Chem 2005; [Epub ahead of print] (from Pfam) NF014116.5 PF02018.22 CBM_4_9 25.9 25.9 136 domain Y Y N carbohydrate binding domain-containing protein GO:0016798 8916925 131567 cellular organisms no rank 56594 EBI-EMBL Carbohydrate binding domain Carbohydrate binding domain This family includes diverse carbohydrate binding domains. [1]. 8916925. Structure of the N-terminal cellulose-binding domain of Cellulomonas fimi CenC determined by nuclear magnetic resonance spectroscopy. Johnson PE, Joshi MD, Tomme P, Kilburn DG, McIntosh LP;. Biochemistry 1996;35:14381-14394. (from Pfam) NF014119.5 PF02021.22 UPF0102 23.6 23.6 80 PfamEq Y Y N YraN family protein 131567 cellular organisms no rank 53854 EBI-EMBL Uncharacterised protein family UPF0102 YraN family protein The function of this family is unknown. (from Pfam) NF014120.5 PF02022.24 Integrase_Zn 22.6 22.6 38 domain Y N N Integrase Zinc binding domain GO:0008270 9228950 131567 cellular organisms no rank 4 EBI-EMBL Integrase Zinc binding domain Integrase Zinc binding domain Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain Pfam:PF00665. The carboxyl terminal domain is a DNA binding domain Pfam:PF00552. [1]. 9228950. Solution structure of the N-terminal zinc binding domain of HIV-1 integrase. Cai M, Zheng R, Caffrey M, Craigie R, Clore GM, Gronenborn AM;. Nat Struct Biol 1997;4:567-577. (from Pfam) NF014124.5 PF02026.21 RyR 27.4 27.4 91 domain Y Y N RyR domain-containing protein 10664581 131567 cellular organisms no rank 2475 EBI-EMBL RyR domain RyR domain This domain is called RyR for Ryanodine receptor [1]. The domain is found in four copies in the ryanodine receptor. The function of this domain is unknown. [1]. 10664581. Novel repeats in ryanodine and IP3 receptors and protein O-mannosyltransferases. Ponting CP;. Trends Biochem Sci 2000;25:48-50. (from Pfam) NF014126.5 PF02028.22 BCCT 27 27 485 domain Y Y N BCCT family transporter GO:0016020,GO:0022857,GO:0071705 12163501 131567 cellular organisms no rank 93984 EBI-EMBL BCCT, betaine/carnitine/choline family transporter BCCT family transporter NF014132.5 PF02036.22 SCP2 21.3 21.3 101 domain Y Y N SCP2 sterol-binding domain-containing protein 8243660,8667025 131567 cellular organisms no rank 60601 EBI-EMBL SCP-2 sterol transfer family SCP-2 sterol transfer family This domain is involved in binding sterols. It is found in the SCP2 protein Swiss:P22307, as well as the C terminus of Swiss:P51659 the enzyme estradiol 17 beta-dehydrogenase EC:1.1.1.62. The UNC-24 protein Swiss:Q17372 contains an SPFH domain Pfam:PF01145 [2]. [1]. 8243660. NMR determination of the secondary structure and the three-dimensional polypeptide backbone fold of the human sterol carrier protein 2. Szyperski T, Scheek S, Johansson J, Assmann G, Seedorf U, Wuthrich K;. FEBS Lett 1993;335:18-26. [2]. 8667025. The Caenorhabditis elegans behavioral gene unc-24 encodes a novel bipartite protein similar to both erythrocyte band 7.2 (stomatin) and nonspecific lipid transfer protein. Barnes TM, Jin Y, Horvitz HR, Ruvkun G, Hekimi S;. J Neurochem 1996;67:46-57. (from Pfam) NF014133.5 PF02037.32 SAP 27.7 27.7 35 domain Y Y N SAP domain-containing protein 10694879,16797182 131567 cellular organisms no rank 1713 EBI-EMBL SAP domain SAP domain The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins. [1]. 10694879. SAP - a putative DNA-binding motif involved in chromosomal organization. Aravind L, Koonin EV;. Trends Biochem Sci 2000;25:112-114. [2]. 16797182. Conserved ribonuclease, Eri1, negatively regulates heterochromatin assembly in fission yeast. Iida T, Kawaguchi R, Nakayama J;. Curr Biol. 2006;16:1459-1464. (from Pfam) NF014135.5 PF02040.20 ArsB 22.2 22.2 423 subfamily Y Y N ArsB/NhaD family transporter GO:0015105,GO:0015700,GO:0016020 131567 cellular organisms no rank 53080 EBI-EMBL Arsenical pump membrane protein ArsB/NhaD family transporter NF014136.5 PF02041.21 Auxin_BP 21 21 167 PfamEq Y N N Auxin binding protein GO:0010011 131567 cellular organisms no rank 1789 EBI-EMBL Auxin binding protein Auxin binding protein NF014147.5 PF02055.21 Glyco_hydro_30 23 23 348 domain Y N N Glycosyl hydrolase family 30 TIM-barrel domain 131567 cellular organisms no rank 22970 EBI-EMBL Glycosyl hydrolase family 30 TIM-barrel domain Glycosyl hydrolase family 30 TIM-barrel domain NF014148.5 PF02056.21 Glyco_hydro_4 23.2 23.2 183 domain Y N N Family 4 glycosyl hydrolase GO:0004553,GO:0005975 131567 cellular organisms no rank 61541 EBI-EMBL Family 4 glycosyl hydrolase Family 4 glycosyl hydrolase NF014156.5 PF02065.23 Melibiase 27 27 347 domain Y Y N alpha-galactosidase 3.2.1.22 21639842 131567 cellular organisms no rank 67235 EBI-EMBL Melibiase alpha-galactosidase Glycoside hydrolase families GH27, GH31 and GH36 form the glycoside hydrolase clan GH-D. Glycoside hydrolase family 36 can be split into 11 families, GH36A to GH36K [1]. This family includes enzymes from GH36A-B and GH36D-K and from GH27. [1]. 21639842. Hierarchical classification of glycoside hydrolases. Naumoff DG;. Biochemistry (Mosc). 2011;76:622-635. (from Pfam) NF014164.5 PF02073.20 Peptidase_M29 27 27 406 subfamily Y Y N aminopeptidase 3.4.11.- GO:0004177,GO:0006508 16242715,23999297,9362117 131567 cellular organisms no rank 33414 EBI-EMBL Thermophilic metalloprotease (M29) aminopeptidase NF014165.5 PF02074.20 Peptidase_M32 25.1 25.1 489 PfamEq Y N N Carboxypeptidase Taq (M32) metallopeptidase GO:0004181,GO:0006508 131567 cellular organisms no rank 25986 EBI-EMBL Carboxypeptidase Taq (M32) metallopeptidase Carboxypeptidase Taq (M32) metallopeptidase NF014166.5 PF02075.22 RuvC 22.2 22.2 148 PfamEq Y Y N crossover junction endodeoxyribonuclease RuvC 3.1.21.10 GO:0004520,GO:0006281,GO:0006310 1661673,8057369 131567 cellular organisms no rank 45641 EBI-EMBL Crossover junction endodeoxyribonuclease RuvC crossover junction endodeoxyribonuclease RuvC This entry includes endodeoxyribonucleases found in bacteria, such as RuvC. RuvC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli RuvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices [2]. The Escherichia coli RuvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination [1]. RuvC protein (EC:3.1.22.4) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo [1]. [1]. 1661673. Escherichia coli RuvC protein is an endonuclease that resolves the Holliday structure. Iwasaki H, Takahagi M, Shiba T, Nakata A, Shinagawa H;. EMBO J. 1991;10:4381-4389. [2]. 8057369. Preliminary crystallographic study of Escherichia coli RuvC protein. An endonuclease specific for Holliday junctions. Ariy. TRUNCATED at 1650 bytes (from Pfam) NF014171.5 PF02080.26 TrkA_C 27 27 71 domain Y Y N TrkA C-terminal domain-containing protein GO:0006813,GO:0008324 11292341 131567 cellular organisms no rank 196745 EBI-EMBL TrkA-C domain TrkA-C domain This domain is often found next to the Pfam:PF02254 domain. The exact function of this domain is unknown. It has been suggested that it may bind an unidentified ligand [1]. The domain is predicted to adopt an all beta structure [1]. [1]. 11292341. Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. Anantharaman V, Koonin EV, Aravind L;. J Mol Biol 2001;307:1271-1292. (from Pfam) NF014173.5 PF02082.25 Rrf2 30 30 132 domain Y Y N Rrf2 family transcriptional regulator 23644595 131567 cellular organisms no rank 127955 EBI-EMBL Iron-dependent Transcriptional regulator Rrf2 family transcriptional regulator Several proteins in this family form iron-sulfur clusters enabling iron dependent DNA transcription regulation [1]. The iron binding is mediated by three conserved cysteine residues. Members of this family can also bind O-acetyl-L-serine, [Fe-S] and nitric oxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 23644595. Studies of IscR reveal a unique mechanism for metal-dependent regulation of DNA binding specificity. Rajagopalan S, Teter SJ, Zwart PH, Brennan RG, Phillips KJ, Kiley PJ;. Nat Struct Mol Biol. 2013;20:740-747. (from Pfam) NF014176.5 PF02085.21 Cytochrom_CIII 22.9 22.9 101 domain Y Y N cytochrome c3 family protein GO:0009055,GO:0020037 6249799,8819167 131567 cellular organisms no rank 5757 EBI-EMBL Class III cytochrome C family cytochrome c3 family protein NF014177.5 PF02086.20 MethyltransfD12 22 22 253 domain Y Y N DNA adenine methylase GO:0009007,GO:0009307 131567 cellular organisms no rank 66036 EBI-EMBL D12 class N6 adenine-specific DNA methyltransferase DNA adenine methylase NF014180.5 PF02089.20 Palm_thioest 26.8 26.8 254 domain Y N N Palmitoyl protein thioesterase 131567 cellular organisms no rank 29724 EBI-EMBL Palmitoyl protein thioesterase Palmitoyl protein thioesterase NF014182.5 PF02091.20 tRNA-synt_2e 27 27 278 PfamEq Y Y N glycine--tRNA ligase subunit alpha 6.1.1.14 GO:0000166,GO:0004820,GO:0005524,GO:0005737,GO:0006426 131567 cellular organisms no rank 30598 EBI-EMBL Glycyl-tRNA synthetase alpha subunit glycine--tRNA ligase subunit alpha NF014183.5 PF02092.22 tRNA_synt_2f 29.2 29.2 536 PfamEq Y Y N glycine--tRNA ligase subunit beta 6.1.1.14 GO:0000166,GO:0004820,GO:0005524,GO:0005737,GO:0006426 131567 cellular organisms no rank 59178 EBI-EMBL Glycyl-tRNA synthetase beta subunit glycine--tRNA ligase subunit beta NF014186.5 PF02096.25 60KD_IMP 35 35 163 domain Y Y N YidC/Oxa1 family membrane protein insertase GO:0016020,GO:0032977 131567 cellular organisms no rank 88800 EBI-EMBL 60Kd inner membrane protein YidC/Oxa1 family membrane protein insertase NF014193.5 PF02104.20 SURF1 23.4 23.4 205 subfamily Y Y N SURF1 family cytochrome oxidase biogenesis protein GO:0016020 21167962,21945856 131567 cellular organisms no rank 56420 EBI-EMBL SURF1 family SURF1 family cytochrome oxidase biogenesis protein NF014198.5 PF02110.20 HK 27 27 247 domain Y Y N hydroxyethylthiazole kinase 2.7.1.50 GO:0000287,GO:0004417,GO:0005524,GO:0009228 131567 cellular organisms no rank 40429 EBI-EMBL Hydroxyethylthiazole kinase family hydroxyethylthiazole kinase NF014200.5 PF02113.20 Peptidase_S13 22.8 22.8 444 domain Y Y N D-alanyl-D-alanine carboxypeptidase 3.4.16.4 GO:0004185,GO:0006508 16411754,1741619,7845208 131567 cellular organisms no rank 67545 EBI-EMBL D-Ala-D-Ala carboxypeptidase 3 (S13) family D-alanyl-D-alanine carboxypeptidase This family of serine peptidases belong to MEROPS peptidase family S13 (D-Ala-D-Ala carboxypeptidase C, clan SE). The active site residues occur in the motif SXXK. D-Ala-D-Ala carboxypeptidase C is involved in the metabolism of cell components [1,2]. There are three families of serine-type D-Ala-D-Ala peptidase (designated S11, S12 and S13), which are also known as low molecular weight penicillin-binding proteins. Family S13 comprises D-Ala-D-Ala peptidases that have sufficient sequence similarity around their active sites to assume a distant evolutionary relationship to other clan members; members of the S13 family also bind penicillin and have D-amino-peptidase activity [3,4]. [1]. 16411754. Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics. Kishida H, Unzai S, Roper DI, Lloyd A, Park SY, Tame JR;. Biochemistry. 2006;45:783-792. [2]. 1741619. Serine beta-lactamases and penicillin-binding proteins. Ghuysen JM;. Annu Rev Microbiol. 1991;45:37-67. [3]. 7845208. Families of Serine Peptidases. Rawlings ND, Barrett AJ;. Meth Enzymol 1994;244:19-61. (from Pfam) NF014201.5 PF02114.21 Phosducin 23 23 265 PfamEq Y N N Phosducin 131567 cellular organisms no rank 129 EBI-EMBL Phosducin Phosducin NF014212.5 PF02126.23 PTE 22.4 22.4 298 domain Y N N Phosphotriesterase family GO:0008270,GO:0009056 131567 cellular organisms no rank 22229 EBI-EMBL Phosphotriesterase family Phosphotriesterase family NF014213.5 PF02127.20 Peptidase_M18 24 24 432 domain Y N N Aminopeptidase I zinc metalloprotease (M18) GO:0004177,GO:0006508,GO:0008270 131567 cellular organisms no rank 30778 EBI-EMBL Aminopeptidase I zinc metalloprotease (M18) Aminopeptidase I zinc metalloprotease (M18) NF014214.5 PF02128.20 Peptidase_M36 23.3 23.3 368 domain Y Y N M36 family metallopeptidase GO:0004222,GO:0005615,GO:0008270 131567 cellular organisms no rank 8852 EBI-EMBL Fungalysin metallopeptidase (M36) M36 family metallopeptidase NF014215.5 PF02129.23 Peptidase_S15 23 23 262 domain Y Y N CocE/NonD family hydrolase GO:0016787 12369817,20436035 131567 cellular organisms no rank 310869 EBI-EMBL X-Pro dipeptidyl-peptidase (S15 family) CocE/NonD family hydrolase NF014217.5 PF02132.20 RecR_ZnF 22 22 21 PfamEq Y N N RecR, Cys4-zinc finger motif GO:0046872 23019218,25460918,29633970 131567 cellular organisms no rank 41642 EBI-EMBL RecR, Cys4-zinc finger motif RecR, Cys4-zinc finger motif The bacterial protein RecR is an important regulator in the RecFOR homologous recombination pathway during DNA repair. It acts with RecF and RecO forming a complex that facilitates the loading of RecA onto ssDNA. RecR is a zinc metalloprotein consisting of a N-terminal helix-hairpin-helix (HhH) motif, a middle region containing a zinc finger motif and a Toprim domain (Pfam:PF13662) and a C-terminal domain comprising a Walker B motif and a C-terminal helix [1,2]. This is the zinc finger motif, which consists of four strictly conserved cysteine residues which coordinate a zinc ion. This motif is the most conserved domain in RecR proteins and plays a structural role stabilizing the 3D structure of the protein [3]. [1]. 23019218. RecOR complex including RecR N-N dimer and RecO monomer displays a high affinity for ssDNA. Tang Q, Gao P, Liu YP, Gao A, An XM, Liu S, Yan XX, Liang DC;. Nucleic Acids Res. 2012;40:11115-11125. [2]. 29633970. Crystal structure of RecR, a member of the RecFOR DNA-repair pathway, from Pseudomonas aeruginosa PAO1. Che S, Chen Y, Liang Y, Zhang Q, Bartlam M;. Acta Crystallogr F Struct Biol Commun. 2018;74:222-230. [3]. 25460918. Structural and functional characterization of Cys4 zinc finger motif in the recombination mediator protein RecR. Tang Q, Liu YP, Yan XX, Liang DC;. DNA Repair (Amst). 2014;24:10-14. (from Pfam) NF014218.5 PF02133.20 Transp_cyt_pur 23.5 23.5 440 domain Y Y N cytosine permease GO:0016020,GO:0022857,GO:0055085 10827169,1640834 131567 cellular organisms no rank 115752 EBI-EMBL Permease for cytosine/purines, uracil, thiamine, allantoin cytosine permease NF014220.5 PF02136.25 NTF2 21 21 116 domain Y Y N ketosteroid isomerase family protein 9533885 131567 cellular organisms no rank 15130 EBI-EMBL Nuclear transport factor 2 (NTF2) domain Nuclear transport factor 2 (NTF2) domain This family includes the NTF2-like Delta-5-3-ketosteroid isomerase proteins. [1]. 9533885. Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran. Stewart M, Kent HM, McCoy AJ;. J Mol Biol 1998;277:635-646. (from Pfam) NF014225.5 PF02142.27 MGS 24.1 24.1 94 domain Y N N MGS-like domain 10526357 131567 cellular organisms no rank 174319 EBI-EMBL MGS-like domain MGS-like domain This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site [1]. [1]. 10526357. Structure classification-based assessment of CASP3 predictions for the fold recognition targets. Murzin AG;. Proteins 1999;37:88-103. (from Pfam) NF014228.5 PF02146.22 SIR2 24 24 180 domain Y Y N Sir2 family NAD-dependent protein deacetylase 2.3.1.286 GO:0070403 15128440 131567 cellular organisms no rank 82274 EBI-EMBL Sir2 family Sir2 family NAD-dependent protein deacetylase This region is characteristic of Silent information regulator 2 (Sir2) proteins, or sirtuins. These are protein deacetylases that depend on nicotine adenine dinucleotide (NAD). They are found in many subcellular locations, including the nucleus, cytoplasm and mitochondria. Eukaryotic forms play in important role in the regulation of transcriptional repression. Moreover, they are involved in microtubule organisation and DNA damage repair processes [1].i [1]. 15128440. Sirtuins: Sir2-related NAD-dependent protein deacetylases. North BJ, Verdin E;. Genome Biol 2004;5:224. (from Pfam) NF014229.5 PF02148.24 zf-UBP 22.7 22.7 63 domain Y Y N UBP-type zinc finger domain-containing protein GO:0008270 131567 cellular organisms no rank 19439 EBI-EMBL Zn-finger in ubiquitin-hydrolases and other protein Zn-finger in ubiquitin-hydrolases and other protein NF014231.5 PF02150.21 RNA_POL_M_15KD 25.2 25.2 36 domain Y N N RNA polymerases M/15 Kd subunit GO:0006351 131567 cellular organisms no rank 2125 EBI-EMBL RNA polymerases M/15 Kd subunit RNA polymerases M/15 Kd subunit NF014232.5 PF02151.24 UVR 21.5 21.5 36 domain Y Y N UvrB/UvrC motif-containing protein GO:0005515 131567 cellular organisms no rank 212428 EBI-EMBL UvrB/uvrC motif UvrB/uvrC motif NF014233.5 PF02152.23 FolB 31.8 31.8 113 domain Y Y N dihydroneopterin aldolase 4.1.2.25 GO:0004150,GO:0006760 9651328 131567 cellular organisms no rank 55778 EBI-EMBL Dihydroneopterin aldolase dihydroneopterin aldolase This enzyme EC:4.1.2.25 catalyses the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin in the biosynthetic pathway of tetrahydrofolate. [1]. 9651328. Biosynthesis of pteridines in Escherichia coli. Structural and mechanistic similarity of dihydroneopterin-triphosphate epimerase and dihydroneopterin aldolase. Haussmann C, Rohdich F, Schmidt E, Bacher A, Richter G;. J Biol Chem 1998;273:17418-17424. (from Pfam) NF014234.5 PF02153.22 PDH_N 26.5 26.5 154 subfamily Y Y N prephenate dehydrogenase/arogenate dehydrogenase family protein GO:0006571,GO:0008977,GO:0033730,GO:0070403 31750992 131567 cellular organisms no rank 77691 EBI-EMBL Prephenate dehydrogenase, nucleotide-binding domain Prephenate dehydrogenase, nucleotide-binding domain Members of this family are prephenate dehydrogenases (PDHs) EC:1.3.1.12 involved in tyrosine biosynthesis. This is the N-terminal nucleotide-binding domain of PDHs, which has a modified Rossmann nucleotide-binding fold with an extended beta-sheet sandwiched by three helices on each face [1]. [1]. 31750992. Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain. Shabalin IG, Gritsunov A, Hou J, Slawek J, Miks CD, Cooper DR, Minor W, Christendat D;. FEBS J. 2020;287:2235-2255. (from Pfam) NF014237.5 PF02156.20 Glyco_hydro_26 20.2 20.2 311 domain Y Y N glycosyl hydrolase GO:0004553 131567 cellular organisms no rank 30872 EBI-EMBL Glycosyl hydrolase family 26 glycosyl hydrolase family 26 NF014244.5 PF02163.27 Peptidase_M50 27.2 27.2 221 domain Y Y N site-2 protease family protein GO:0004222,GO:0006508 131567 cellular organisms no rank 138585 EBI-EMBL Peptidase family M50 site-2 protease family protein NF014250.5 PF02171.22 Piwi 28.9 28.9 302 domain Y Y N Piwi domain-containing protein GO:0003676 11050429,15284453 131567 cellular organisms no rank 1602 EBI-EMBL Piwi domain Piwi domain This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as Slicer, the enzyme that cleaves mRNA in the RNAi RISC complex [2]. In addition, Mg+2 dependence and production of 3'-OH and 5' phosphate products are shared characteristics of RNaseH and RISC. The PIWI domain core has a tertiary structure belonging to the RNase H family of enzymes. RNase H fold proteins all have a five-stranded mixed beta-sheet surrounded by helices. By analogy to RNase H enzymes which cleave single-stranded RNA guided by the DNA strand in an RNA/DNA hybrid, the PIWI domain can be inferred to cleave single-stranded RNA, for example mRNA, guided by double stranded siRNA. Redefinition of the Piwi domain. [1]. 11050429. Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain. Cerutti L, Mian N, Bateman A;. Trends Biochem Sci 2000;25:481-482. [2]. 15284453. Crystal structure of Argonaute and its implications for RISC slicer activity. Song JJ, Smith SK, Hannon GJ, Joshua-Tor L;. Science 2004;305:1434-1437. (from Pfam) NF014261.5 PF02182.22 SAD_SRA 30.7 30.7 148 domain Y Y N YDG/SRA domain-containing protein 11238985,11691919,17994007,18772891,19411852,21507349 131567 cellular organisms no rank 2110 EBI-EMBL SAD/SRA domain SAD/SRA domain The domain goes by several names including SAD [1], SRA [2] and YDG [3]. It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria [4]. Versions of this domain are known to bind hemi-methylated CpG dinucleotides and also other 5mC containing dinucleotides. The domain binds DNA by flipping out the methylated cytosine base from the DNA double helix [5].The conserved tyrosine and aspartate residues and a glycine rich patch are critical for recognition of the flipped out base [4][5]. Mammalian UHRF1 that contains this domain plays an important role in maintenance of methylation at CpG dinucleotides by recruiting DNMT1 to hemimethylated sites associated with replication forks [2]. The SAD/SRA domain has been combined with other domains involved in the ubiquitin pathway on multiple occasions and such proteins link recognition of DNA methylation to chromatin-protein ubiquitination [4]. The domain is also found in species that lack DNA methylation, such as certain apicomplexans, suggestive of other DNA-binding modes or functions [4]. A highly derived and distinct version of the domain is also found in fungi where it is fused to AlkB-type 2OGFeDO domains [6]. In bacteria, the domain is usually fused or associated with restriction endonucleases, many of which target methylated or hemi-methylated DNA [4]. [1]. 11238985. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin EV, Daly MJ;. Microbiol Mol Biol Rev. 2001;65:44-. TRUNCATED at 1650 bytes (from Pfam) NF014269.5 PF02190.21 LON_substr_bdg 28.7 28.7 200 domain Y Y N LON peptidase substrate-binding domain-containing protein 16199667,19191354,20834233 131567 cellular organisms no rank 96298 EBI-EMBL ATP-dependent protease La (LON) substrate-binding domain ATP-dependent protease La (LON) substrate-binding domain This domain has been shown to be part of the PUA superfamily [2]. This domain represents a general protein and polypeptide interaction domain for the ATP-dependent serine peptidase, LON, Peptidase_S16, Pfam:PF05362. ATP-dependent Lon proteases are conserved in all living organisms and catalyse rapid turnover of short-lived regulatory proteins and many damaged or denatured proteins. [1]. 16199667. Crystal structure of the N-terminal domain of E. coli Lon protease. Li M, Rasulova F, Melnikov EE, Rotanova TV, Gustchina A, Maurizi MR, Wlodawer A;. Protein Sci. 2005;14:2895-2900. [2]. 19191354. Structural genomics reveals EVE as a new ASCH/PUA-related domain. Bertonati C, Punta M, Fischer M, Yachdav G, Forouhar F, Zhou W, Kuzin AP, Seetharaman J, Abashidze M, Ramelot TA, Kennedy MA, Cort JR, Belachew A, Hunt JF, Tong L, Montelione GT, Rost B;. Proteins. 2009;75:760-773. [3]. 20834233. Crystal structure of Lon protease: molecular architecture of gated entry to a sequestered degradation chamber. Cha SS, An YJ, Lee CR, Lee HS, Kim YG, Kim SJ, Kwon KK, De Donatis GM, Lee JH, Maurizi MR, Kang SG;. EMBO J. 2010;29:3520-3530. (from Pfam) NF014273.5 PF02195.23 ParBc 21.9 21.9 90 domain Y Y N ParB N-terminal domain-containing protein 12603730,15448164 131567 cellular organisms no rank 196082 EBI-EMBL ParB/Sulfiredoxin domain ParB/Sulfiredoxin domain Proteins containing this domain include Escherichia coli plasmid protein ParB and mammalian Sulfiredoxin-1. ParB is involved in chromosome partition. It localises to both poles of the predivisional cell following completion of DNA replication [1]. Sulfiredoxin-1 contributes to oxidative stress resistance by reducing cysteine-sulfinic acid formed under exposure to oxidants in the peroxiredoxins PRDX1, PRDX2, PRDX3 and PRDX4 [2]. [1]. 12603730. Productive interaction between the chromosome partitioning proteins, ParA and ParB, is required for the progression of the cell cycle in Caulobacter crescentus. Figge RM, Easter J, Gober JW;. Mol Microbiol. 2003;47:1225-1237. [2]. 15448164. Characterization of mammalian sulfiredoxin and its reactivation of hyperoxidized peroxiredoxin through reduction of cysteine sulfinic acid in the active site to cysteine. Chang TS, Jeong W, Woo HA, Lee SM, Park S, Rhee SG;. J Biol Chem. 2004;279:50994-51001. (from Pfam) NF014281.5 PF02203.20 TarH 25.2 23 177 domain Y Y N Tar ligand binding domain-containing protein GO:0006935,GO:0007165 1660187,27292793 131567 cellular organisms no rank 100901 EBI-EMBL Tar ligand binding domain homologue Tar ligand binding domain homologue This entry represents the ligand-binding domain found in a number of methyl-accepting chemotaxis receptors, such as E.coli Tar (taxis to aspartate and repellents), which is a receptor for the attractant L-aspartate [1,2] and also recognises proteogenic amino acids, phthalic acid, Malic acid, 3,4-dihydroxymandelic acid, citrate, benzoate and derivatives, protocatechuate, vanillate, quinate, shikimate and dehydroshikimate (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 1660187. Three-dimensional structures of the ligand-binding domain of the bacterial aspartate receptor with and without a ligand. Milburn MV, Prive GG, Milligan DL, Scott WG, Yeh J, Jancarik J, Koshland DE Jr, Kim SH;. Science. 1991;254:1342-1347. [2]. 27292793. Structural Analysis of the Ligand-Binding Domain of the Aspartate Receptor Tar from Escherichia coli. Mise T;. Biochemistry. 2016;55:3708-3713. (from Pfam) NF014288.5 PF02210.30 Laminin_G_2 22.9 22.9 126 domain Y Y N LamG domain-containing protein 131567 cellular organisms no rank 17409 EBI-EMBL Laminin G domain laminin G-like domain This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily. (from Pfam) NF014289.5 PF02211.20 NHase_beta_C 27.7 27.7 98 domain Y Y N SH3-like domain-containing protein 4.2.1.84 GO:0018822 14717710,17222425,9195885 131567 cellular organisms no rank 8964 EBI-EMBL Nitrile hydratase beta subunit, C-terminal Nitrile hydratase beta subunit, C-terminal Nitrile hydratases (NHase) EC:4.2.1.84 are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit [1]. Beta subunit consists of an N-terminal helical domain and a C-terminal SH3-like domain (represented in this entry) [2,3]. Thiocyanate hydrolase (SCNase) is a member of the NHase family, comprises alpha, beta and gamma subunits which share amino acid sequence similarities with NHase beta subunit C-terminal, beta subunit N-terminal and NHase alpha subunit, respectively [3]. [1]. 9195885. Crystal structure of nitrile hydratase reveals a novel iron centre in a novel fold. Huang W, Jia J, Cummings J, Nelson M, Schneider G, Lindqvist Y;. Structure 1997;5:691-699. [2]. 14717710. Mutational and structural analysis of cobalt-containing nitrile hydratase on substrate and metal binding. Miyanaga A, Fushinobu S, Ito K, Shoun H, Wakagi T;. Eur J Biochem. 2004;271:429-438. [3]. 17222425. Structure of thiocyanate hydrolase: a new nitrile hydratase family protein with a novel five-coordinate cobalt(III) center. Arakawa T, Kawano Y, Kataoka S, Katayama Y, Kamiya N, Yohda M, Odaka M;. J Mol Biol. 2007;366:1497-1509. (from Pfam) NF014296.5 PF02219.22 MTHFR 24 24 287 domain Y Y N methylenetetrahydrofolate reductase 1.5.1.20 GO:0004489,GO:0006555 10201405 131567 cellular organisms no rank 70031 EBI-EMBL Methylenetetrahydrofolate reductase methylenetetrahydrofolate reductase This family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from bacteria and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The structure for this domain is known [1] to be a TIM barrel. [1]. 10201405. The structure and properties of methylenetetrahydrofolate reductase from Escherichia coli suggest how folate ameliorates human hyperhomocysteinemia [see comments]. Guenther BD, Sheppard CA, Tran P, Rozen R, Matthews RG, Ludwig ML;. Nat Struct Biol 1999;6:359-365. (from Pfam) NF014298.5 PF02222.27 ATP-grasp 27 27 171 domain Y Y N ATP-grasp domain-containing protein 9416615 131567 cellular organisms no rank 363667 EBI-EMBL ATP-grasp domain ATP-grasp domain This family does not contain all known ATP-grasp domain members. This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity. [1]. 9416615. A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity. Galperin MY, Koonin EV;. Protein Sci 1997;6:2639-2643. (from Pfam) NF014299.5 PF02223.22 Thymidylate_kin 27 27 185 domain Y N N Thymidylate kinase 131567 cellular organisms no rank 81895 EBI-EMBL Thymidylate kinase Thymidylate kinase NF014300.5 PF02224.23 Cytidylate_kin 26 26 211 domain Y Y N (d)CMP kinase GO:0004127,GO:0005524,GO:0006139 9862805 131567 cellular organisms no rank 62902 EBI-EMBL Cytidylate kinase (d)CMP kinase Cytidylate kinase EC:2.7.4.14 catalyses the phosphorylation of cytidine 5'-monophosphate (dCMP) to cytidine 5'-diphosphate (dCDP) in the presence of ATP or GTP. [1]. 9862805. Structures of escherichia coli CMP kinase alone and in complex with CDP: a new fold of the nucleoside monophosphate binding domain and insights into cytosine nucleotide specificity. Briozzo P, Golinelli-Pimpaneau B, Gilles AM, Gaucher JF, Burlacu-Miron S, Sakamoto H, Janin J, Barzu O;. Structure 1998;6:1517-1527. (from Pfam) NF014301.5 PF02225.27 PA 23.9 23.9 95 domain Y Y N PA domain-containing protein 11246007 131567 cellular organisms no rank 62393 EBI-EMBL PA domain PA domain The PA (Protease associated) domain is found as an insert domain in diverse proteases. The PA domain is also found in a plant vacuolar sorting receptor Swiss:O22925 and members of the RZF family Swiss:O43567. It has been suggested that this domain forms a lid-like structure that covers the active site in active proteases, and is involved in protein recognition in vacuolar sorting receptors [1]. [1]. 11246007. The protease-associated domain: a homology domain associated with multiple classes of proteases. Luo X, Hofmann K;. Trends Biochem Sci 2001;26:147-148. (from Pfam) NF014304.5 PF02229.21 PC4 25 25 52 subfamily Y Y N PC4/YdbC family ssDNA-binding protein GO:0003677,GO:0006355 23303792,34534740,8062392,9360603 131567 cellular organisms no rank 4101 EBI-EMBL Transcriptional Coactivator p15 (PC4) PC4/YdbC family ssDNA-binding protein This domain is found at the C-terminal end of Activated RNA polymerase II transcriptional coactivator p15 from humans, YdbC from Lactococcus lactis, and other PC4 family members. p15 has a bipartite structure composed of an N-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain [1-4]. Activity is controlled by protein kinases that target the regulatory domain. [1]. 8062392. A novel mediator of class II gene transcription with homology to viral immediate-early transcriptional regulators. Kretzschmar M, Kaiser K, Lottspeich F, Meisterernst M;. Cell 1994;78:525-534. [2]. 23303792. Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome. Rossi P, Barbieri CM, Aramini JM, Bini E, Lee HW, Janjua H, Xiao R, Acton TB, Montelione GT;. Nucleic Acids Res. 2013;41:2756-2768. [3]. 9360603. C-terminal domain of transcription cofactor PC4 reveals dimeric ssDNA binding site. Brandsen J, Werten S, van der Vliet PC, Meisterernst M, Kroon J, Gros P;. Nat Struct Biol. 1997;4:900-903. [4]. 34534740. Insights on the disruption of the complex between human positive coactivator 4 and p53 by small molecules. Pandey B, Dev A, Chakravorty D, Bhandare VV, Polley S, Roy S, Basu G;. Biochem Biophys Res Commun. 2021;578:15-20. (from Pfam) NF014305.5 PF02230.21 Abhydrolase_2 23 23 217 domain Y N N Phospholipase/Carboxylesterase GO:0016787 9438866,9644627 131567 cellular organisms no rank 81116 EBI-EMBL Phospholipase/Carboxylesterase Phospholipase/Carboxylesterase This family consists of both phospholipases [1] and carboxylesterases with broad substrate specificity, and is structurally related to alpha/beta hydrolases Pfam:PF00561 [2]. [1]. 9644627. cDNA cloning and expression of a novel family of enzymes with calcium-independent phospholipase A2 and lysophospholipase activities. Portilla D, Crew MD, Grant D, Serrero G, Bates LM, Dai G, Sasner M, Cheng J, Buonanno A;. J Am Soc Nephrol 1998;9:1178-1186. [2]. 9438866. Crystal structure of carboxylesterase from Pseudomonas fluorescens, an alpha/beta hydrolase with broad substrate specificity. Kim KK, Song HK, Shin DH, Hwang KY, Choe S, Yoo OJ, Suh SW;. Structure 1997;5:1571-1584. (from Pfam) NF014307.5 PF02233.21 PNTB 31.7 31.7 456 PfamEq Y Y N NAD(P)(+) transhydrogenase (Re/Si-specific) subunit beta 1633824 131567 cellular organisms no rank 39948 EBI-EMBL NAD(P) transhydrogenase beta subunit NAD(P)(+) transhydrogenase (Re/Si-specific) subunit beta This family corresponds to the beta subunit of NADP transhydrogenase in prokaryotes, and either the protein N- or C terminal in eukaryotes. The domain is often found in conjunction with Pfam:PF01262. Pyridine nucleotide transhydrogenase catalyses the reduction of NAD+ to NADPH. A complete loss of activity occurs upon mutation of Gly314 in E. coli [1]. [1]. 1633824. A mutation at Gly314 of the beta subunit of the Escherichia coli pyridine nucleotide transhydrogenase abolishes activity and affects the NADP(H)-induced conformational change. Ahmad S, Glavas NA, Bragg PD;. Eur J Biochem 1992;207:733-739. (from Pfam) NF014310.5 PF02237.22 BPL_C 21 21 48 PfamEq Y N N Biotin protein ligase C terminal domain GO:0036211 131567 cellular organisms no rank 58381 EBI-EMBL Biotin protein ligase C terminal domain Biotin protein ligase C terminal domain The function of this structural domain is unknown. It is found to the C terminus of the biotin protein ligase catalytic domain Pfam:PF01317. (from Pfam) NF014312.5 PF02239.21 Cytochrom_D1 25.5 25.5 368 domain Y Y N cytochrome D1 domain-containing protein 9311786 131567 cellular organisms no rank 19954 EBI-EMBL Cytochrome D1 heme domain Cytochrome D1 heme domain Cytochrome cd1 (nitrite reductase) catalyses the conversion of nitrite to nitric oxide in the nitrogen cycle. This family represents the d1 heme binding domain of cytochrome cd1, in which His/Tyr side chains ligate the d1 heme iron of the active site in the oxidised state [1]. [1]. 9311786. Haem-ligand switching during catalysis in crystals of a nitrogen-cycle enzyme. Williams PA, Fulop V, Garman EF, Saunders NF, Ferguson SJ, Hajdu J;. Nature 1997;389:406-412. (from Pfam) NF014313.5 PF02240.21 MCR_gamma 25 25 246 PfamEq Y Y N coenzyme-B sulfoethylthiotransferase subunit gamma mcrG 2.8.4.1 GO:0015948,GO:0050524 9367957 131567 cellular organisms no rank 518 EBI-EMBL Methyl-coenzyme M reductase gamma subunit coenzyme-B sulfoethylthiotransferase subunit gamma Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (Pfam:PF02249), 2 beta (Pfam:PF02241), and 2 gamma (this family) subunits with two identical nickel porphinoid active sites [1]. [1]. 9367957. Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation. Ermler U, Grabarse W, Shima S, Goubeaud M, Thauer RK;. Science 1997;278:1457-1462. (from Pfam) NF014316.5 PF02245.21 Pur_DNA_glyco 27 27 181 PfamEq Y Y N DNA-3-methyladenine glycosylase 3.2.2.- GO:0003677,GO:0003905,GO:0006284 9790531 131567 cellular organisms no rank 35867 EBI-EMBL Methylpurine-DNA glycosylase (MPG) DNA-3-methyladenine glycosylase Methylpurine-DNA glycosylase is a base excision-repair protein. It is responsible for the hydrolysis of the deoxyribose N-glycosidic bond, excising 3-methyladenine and 3-methylguanine from damaged DNA. [1]. 9790531. Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision. Lau AY, Scharer OD, Samson L, Verdine GL, Ellenberger T;. Cell 1998;95:249-258. (from Pfam) NF014320.5 PF02249.22 MCR_alpha 25 25 127 domain Y N N Methyl-coenzyme M reductase alpha subunit, C-terminal domain GO:0015948,GO:0050524 9367957 131567 cellular organisms no rank 555 EBI-EMBL Methyl-coenzyme M reductase alpha subunit, C-terminal domain Methyl-coenzyme M reductase alpha subunit, C-terminal domain Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (this family), 2 beta (Pfam:PF02241), and 2 gamma (Pfam:PF02240) subunits with two identical nickel porphinoid active sites [1]. The C-terminal domain is comprised of an all-alpha multi-helical bundle. [1]. 9367957. Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation. Ermler U, Grabarse W, Shima S, Goubeaud M, Thauer RK;. Science 1997;278:1457-1462. (from Pfam) NF014325.5 PF02254.23 TrkA_N 23.8 22.8 116 domain Y Y N NAD-binding protein GO:0006813 11292341,8412700,9478130 131567 cellular organisms no rank 252062 EBI-EMBL TrkA-N domain TrkA-N domain This domain is found in a wide variety of proteins. These protein include potassium channels Swiss:P31069, phosphoesterases Swiss:Q59027, and various other transporters. This domain binds to NAD. Domain called KTN in figure 2. [1]. 9478130. A novel family of predicted phosphoesterases includes Drosophila prune protein and bacterial RecJ exonuclease. Aravind L, Koonin EV;. Trends Biochem Sci 1998;23:17-19. [2]. 8412700. NAD+ binding to the Escherichia coli K(+)-uptake protein TrkA and sequence similarity between TrkA and domains of a family of dehydrogenases suggest a role for NAD+ in bacterial transport. Schlosser A, Hamann A, Bossemeyer D, Schneider E, Bakker EP;. Mol Microbiol 1993;9:533-543. Called TRKA-N domain. See alignment in figure 8a. [3]. 11292341. Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. Anantharaman V, Koonin EV, Aravind L;. J Mol Biol 2001;307:1271-1292. (from Pfam) NF014332.5 PF02261.21 Asp_decarbox 25 25 115 PfamEq Y Y N aspartate 1-decarboxylase 4.1.1.11 GO:0004068,GO:0006523 9546220 131567 cellular organisms no rank 30557 EBI-EMBL Aspartate decarboxylase aspartate 1-decarboxylase Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase EC:4.1.1.11 which requires a pyruvoyl group for its activity. It is synthesised initially as a proenzyme which is then proteolytically cleaved to an alpha (C-terminal) and beta (N-terminal) subunit and a pyruvoyl group. This family contains both chains of aspartate decarboxylase. [1]. 9546220. Crystal structure of aspartate decarboxylase at 2.2 A resolution provides evidence for an ester in protein self-processing. Albert A, Dhanaraj V, Genschel U, Khan G, Ramjee MK, Pulido R, Sibanda BL, von Delft F, Witty M, Blundell TL, Smith AG, Abell C;. Nat Struct Biol 1998;5:289-293. (from Pfam) NF014336.5 PF02265.21 S1-P1_nuclease 29.5 29.5 258 PfamEq Y Y N S1/P1 nuclease GO:0003676,GO:0004519,GO:0006308 9726413 131567 cellular organisms no rank 10987 EBI-EMBL S1/P1 Nuclease S1/P1 nuclease This family contains both S1 and P1 nucleases (EC:3.1.30.1) which cleave RNA and single stranded DNA with no base specificity. [1]. 9726413. Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs. Romier C, Dominguez R, Lahm A, Dahl O, Suck D;. Proteins 1998;32:414-424. (from Pfam) NF014342.5 PF02272.24 DHHA1 25.9 25.9 138 domain Y Y N DHHA1 domain-containing protein GO:0003676 9478130 131567 cellular organisms no rank 226421 EBI-EMBL DHHA1 domain DHHA1 domain DHHA1 ( DHH-associated domain) is often found with DHH, and is suggested to have an RNA-binding function. NF014343.5 PF02273.20 Acyl_transf_2 20.3 20.3 294 PfamEq Y N N Acyl transferase GO:0006631,GO:0016746 8472957 131567 cellular organisms no rank 2289 EBI-EMBL Acyl transferase Acyl transferase This bacterial family of Acyl transferases (or myristoyl-acp-specific thioesterases) catalyse the first step in the bioluminescent fatty acid reductase system. [1]. 8472957. Sequence of the luxD gene encoding acyltransferase of the lux operon from Photobacterium leiognathi. Chao YF, Weng SF, Lin JW;. Gene 1993;126:155-156. (from Pfam) NF014344.5 PF02274.22 ADI 22.8 22.8 377 subfamily Y Y N arginine deiminase family protein 11504612,14675764,9393705 131567 cellular organisms no rank 43950 EBI-EMBL Arginine deiminase arginine deiminase family protein This family contains arginine deiminases, EC:3.5.3.6., enzymes that catalyse the reaction: arginine + H2O citrulline + NH3. These enzymes belong to the amidinotranferase (AT) superfamily, which share the alpha/beta fold including structurally important residues, i.e buried hydrophobic residues, buried hydrophilic residues hydrogen-bonded with mainchain groups and a structural hallmark of three consecutive buried Gly residues near the C-terminus, conserved among these proteins [1-3]. [1]. 9393705. The arginine deiminase pathway in Rhizobium etli: DNA sequence analysis and functional study of the arcABC genes. D'Hooghe I, Vander Wauven C, Michiels J, Tricot C, de Wilde P, Vanderleyden J, Stalon V;. J Bacteriol 1997;179:7403-7409. [2]. 11504612. A novel superfamily of enzymes that catalyze the modification of guanidino groups. Shirai H, Blundell TL, Mizuguchi K;. Trends Biochem Sci 2001;26:465-468. [3]. 14675764. Prediction of the structure and function of AstA and AstB, the first two enzymes of the arginine succinyltransferase pathway of arginine catabolism. Shirai H, Mizuguchi K;. FEBS Lett 2003;555:505-510. (from Pfam) NF014345.5 PF02275.23 CBAH 20.4 20.4 316 domain Y Y N linear amide C-N hydrolase 7618863 131567 cellular organisms no rank 29594 EBI-EMBL Linear amide C-N hydrolases, choloylglycine hydrolase family linear amide C-N hydrolase This family includes several hydrolases which cleave carbon-nitrogen bonds, other than peptide bonds, in linear amides. These include choloylglycine hydrolase (conjugated bile acid hydrolase, CBAH) EC:3.5.1.24, penicillin acylase EC:3.5.1.11 and acid ceramidase EC:3.5.1.23. This domain forms the alpha-subunit for members from vertebral species, see family NAAA-beta, Pfam:PF15508. [1]. 7618863. Cloning and characterization of a conjugated bile acid hydrolase gene from Clostridium perfringens. Coleman JP, Hudson LL;. Appl Environ Microbiol 1995;61:2514-2520. (from Pfam) NF014347.5 PF02277.22 DBI_PRT 22.6 22.6 329 domain Y Y N nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase 2.4.2.21 GO:0008939,GO:0009236 12101181,8501034 131567 cellular organisms no rank 64727 EBI-EMBL Phosphoribosyltransferase nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase This family of proteins represent the nicotinate-nucleotide- dimethylbenzimidazole phosphoribosyltransferase (NN:DBI PRT) enzymes involved in dimethylbenzimidazole synthesis. This function is essential to de novo cobalamin (vitamin B12) production in bacteria. Nicotinate mononucleotide (NaMN):5,6-dimethylbenzimidazole (DMB) phosphoribosyltransferase (CobT) from Salmonella enterica plays a central role in the synthesis of alpha-ribazole-5'-phosphate, an intermediate for the lower ligand of cobalamin [2]. [1]. 8501034. Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM;. J Bacteriol 1993;175:3303-3316. [2]. 12101181. Capture of a labile substrate by expulsion of water molecules from the active site of nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) from Salmonella enterica. Cheong CG, Escalante-Semerena JC, Rayment I;. J Biol Chem 2002;277:41120-41127. (from Pfam) NF014348.5 PF02278.23 Lyase_8 27 27 254 domain Y Y N polysaccharide lyase family 8 super-sandwich domain-containing protein GO:0005576,GO:0016829 10329169,7557301 131567 cellular organisms no rank 26522 EBI-EMBL Polysaccharide lyase family 8, super-sandwich domain Polysaccharide lyase family 8, super-sandwich domain This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen. [1]. 7557301. Cloning, nucleotide sequence determination and expression of the Staphylococcus aureus hyaluronate lyase gene. Farrell AM, Taylor D, Holland KT;. FEMS Microbiol Lett 1995;130:81-85. [2]. 10329169. Crystal structure of chondroitin AC lyase, a representative of a family of glycosaminoglycan degrading enzymes. Fethiere J, Eggimann B, Cygler M;. J Mol Biol 1999;288:635-647. (from Pfam) NF014351.5 PF02283.21 CobU 27 27 168 PfamEq Y Y N bifunctional adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase GO:0000166,GO:0009236,GO:0043752 9601028 131567 cellular organisms no rank 48061 EBI-EMBL Cobinamide kinase / cobinamide phosphate guanyltransferase bifunctional adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase This family is composed of a group of bifunctional cobalamin biosynthesis enzymes which display cobinamide kinase and cobinamide phosphate guanyltransferase activity. The crystal structure of the enzyme reveals the molecule to be a trimer with a propeller-like shape [1]. [1]. 9601028. Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase from Salmonella typhimurium determined to 2.3 A resolution,. Thompson TB, Thomas MG, Escalante-Semerena JC, Rayment I;. Biochemistry 1998;37:7686-7695. (from Pfam) NF014357.5 PF02289.21 MCH 25 25 311 PfamEq Y Y N methenyltetrahydromethanopterin cyclohydrolase GO:0006730,GO:0018759 9651254 131567 cellular organisms no rank 2938 EBI-EMBL Cyclohydrolase (MCH) methenyltetrahydromethanopterin cyclohydrolase Methenyl tetrahydromethanopterin cyclohydrolase EC:3.5.4.27 is involved in methanogenesis in bacteria and archaea, producing methane from carbon monoxide or carbon dioxide. [1]. 9651254. C1 transfer enzymes and coenzymes linking methylotrophic bacteria and methanogenic Archaea. Chistoserdova L, Vorholt JA, Thauer RK, Lidstrom ME;. Science 1998;281:99-102. (from Pfam) NF014360.5 PF02293.20 AmiS_UreI 25 25 166 PfamEq Y Y N AmiS/UreI family transporter GO:0016020 10642549 131567 cellular organisms no rank 4180 EBI-EMBL AmiS/UreI family transporter AmiS/UreI family transporter This family includes UreI and proton gated urea channel as well as putative amide transporters [1]. [1]. 10642549. A H+-gated urea channel: the link between Helicobacter pylori urease and gastric colonization. Weeks DL, Eskandari S, Scott DR, Sachs G;. Science 2000;287:482-485. (from Pfam) NF014371.5 PF02305.22 Phage_F 25 25 501 PfamEq Y Y N major capsid protein GO:0005198 8642594 131567 cellular organisms no rank 494 EBI-EMBL Capsid protein (F protein) major capsid protein This is a family of proteins from single-stranded DNA bacteriophages. Protein F is the major capsid component, sixty copies of which are found in the virion. [1]. 8642594. Atomic structure of the degraded procapsid particle of the bacteriophage G4: induced structural changes in the presence of calcium ions and functional implications. McKenna R, Bowman BR, Ilag LL, Rossmann MG, Fane BA;. J Mol Biol 1996;256:736-750. (from Pfam) NF014373.5 PF02308.21 MgtC 31.4 31.4 121 domain Y Y N MgtC/SapB family protein GO:0016020 10550680 131567 cellular organisms no rank 54193 EBI-EMBL MgtC family MgtC/SapB family protein The MgtC protein is found in an operon with the Mg2+ transporter protein MgtB. The function of MgtC and its homologues is not known. [1]. 10550680. Magnesium transport in prokaryotes. Moncrief MB, Maguire ME;. J Biol Inorg Chem 1999;4:523-527. (from Pfam) NF014375.5 PF02310.24 B12-binding 32.1 32.1 121 domain Y Y N cobalamin-dependent protein GO:0031419,GO:0046872 11914353,18315685,9739092 131567 cellular organisms no rank 204370 EBI-EMBL B12 binding domain B12-binding domain This domain binds to B12 (adenosylcobamide)[1-3], it is found in several enzymes, such as glutamate mutase Swiss:Q05488, methionine synthase Swiss:Q99707 and methylmalonyl-CoA mutase Swiss:P22033. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding [2]. [1]. 9739092. How a protein prepares for B12 binding: structure and dynamics of the B12-binding subunit of glutamate mutase from Clostridium tetanomorphum. Tollinger M, Konrat R, Hilbert BH, Marsh EN, Krautler B;. Structure 1998;6:1021-1033. [2]. 11914353. Role for vitamin B(12) in light induction of gene expression in the bacterium Myxococcus xanthus. Cervantes M, Murillo FJ;. J Bacteriol. 2002;184:2215-2224. [3]. 18315685. Vitamin B12 partners the CarH repressor to downregulate a photoinducible promoter in Myxococcus xanthus. Perez-Marin MC, Padmanabhan S, Polanco MC, Murillo FJ, Elias-Arnanz M;. Mol Microbiol. 2008;67:804-819. (from Pfam). Presence of a B(12) (cobalamin)-binding domain implies dependence on cobalamin itself, in one of its several forms, or in some unusual lineages, dependence on a cobalamin-like analog. NF014376.5 PF02311.24 AraC_binding 21.1 21.1 135 domain Y Y N AraC family ligand binding domain-containing protein GO:0006355 9103202 131567 cellular organisms no rank 473968 EBI-EMBL AraC-like ligand binding domain AraC-like ligand binding domain This family represents the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif Pfam:PF00165. This domain is distantly related to the Cupin domain Pfam:PF00190. [1]. 9103202. Structural basis for ligand-regulated oligomerization of AraC. Soisson SM, MacDougall-Shackleton B, Schleif R, Wolberger C;. Science 1997;276:421-425. (from Pfam) NF014381.5 PF02317.22 Octopine_DH 30 30 150 PfamEq Y Y N NAD/NADP octopine/nopaline dehydrogenase family protein GO:0016491 8045881,9665174 131567 cellular organisms no rank 8804 EBI-EMBL NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain This group of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. The Pfam family consists mainly of octopine and nopaline dehydrogenases from Ti plasmids. [1]. 8045881. Octopine and nopaline oxidases from Ti plasmids of Agrobacterium tumefaciens: molecular analysis, relationship, and functional characterization. Zanker H, Lurz G, Langridge U, Langridge P, Kreusch D, Schroder J;. J Bacteriol 1994;176:4511-4517. [2]. 9665174. Crystal structure and active site location of N-(1-D-carboxylethyl)-L-norvaline dehydrogenase. Britton KL, Asano Y, Rice DW;. Nat Struct Biol 1998;5:593-601. (from Pfam) NF014386.5 PF02322.20 Cyt_bd_oxida_II 35.6 35.6 302 domain Y Y N cytochrome d ubiquinol oxidase subunit II 1.10.3.- GO:0016020 8626304,9274021 131567 cellular organisms no rank 82618 EBI-EMBL Cytochrome bd terminal oxidase subunit II cytochrome d ubiquinol oxidase subunit II This family consists of cytochrome bd type terminal oxidases that catalyse quinol-dependent, Na+-independent oxygen uptake [2]. Members of this family are integral membrane proteins and contain a protohaem IX centre B558. One member of the family Swiss:O05192 is implicated in having an important role in micro-aerobic nitrogen fixation in the enteric bacterium Klebsiella pneumoniae [1]. The family forms an integral functional unit with subunit I, family Bac_Ubq_Cox, Pfam:PF01654. [1]. 9274021. The Klebsiella pneumoniae cytochrome bd' terminal oxidase complex and its role in microaerobic nitrogen fixation. Juty NS, Moshiri F, Merrick M, Anthony C, Hill S;. Microbiology 1997;143:2673-2683. [2]. 8626304. Purification of a cytochrome bd terminal oxidase encoded by the Escherichia coli app locus from a delta cyo delta cyd strain complemented by genes from Bacillus firmus OF4. Sturr MG, Krulwich TA, Hicks DB;. J Bacteriol 1996;178:1742-1749. (from Pfam) NF014388.5 PF02324.21 Glyco_hydro_70 24 24 831 domain Y Y N glycoside hydrolase family 70 protein GO:0009250,GO:0046527 1747104,8982063 131567 cellular organisms no rank 6142 EBI-EMBL Glycosyl hydrolase family 70 glycoside hydrolase family 70 protein Members of this family belong to glycosyl hydrolase family 70 [1] Glucosyltransferases or sucrose 6-glycosyl transferases (GTF-S) catalyse the transfer of D-glucopyramnosyl units from sucrose onto acceptor molecules [2], EC:2.4.1.5. This family roughly corresponds to the N-terminal catalytic domain of the enzyme. Members of this family also contain the Putative cell wall binding domain Pfam:PF01473, which corresponds with the C-terminal glucan-binding domain. [1]. 1747104. A classification of glycosyl hydrolases based on amino acid sequence similarities. Henrissat B;. Biochem J 1991;280:309-316. [2]. 8982063. Cloning and sequencing of a gene coding for a novel dextransucrase from Leuconostoc mesenteroides NRRL B-1299 synthesizing only alpha (1-6) and alpha (1-3) linkages. Monchois V, Willemot RM, Remaud-Simeon M, Croux C, Monsan P;. Gene 1996;182:23-32. (from Pfam) NF014395.5 PF02332.23 Phenol_Hydrox 24.4 24.4 230 domain Y N N Methane/Phenol/Alkene Hydroxylase GO:0008152 11456616,17873074,7753034,9312093 131567 cellular organisms no rank 9054 EBI-EMBL Methane/Phenol/Alkene Hydroxylase Methane/Phenol/Alkene Hydroxylase This protein family includes several components of multicomponent enzyme systems predominantly found in Proteobacteria and Actinobacteria, including subunits alpha and beta of a methane monooxygenase and an alkene monooxygenase system, small and large subunits of propane 2-monooxygenase system and P1 protein of phenol hydroxylase [1-4]. [1]. 7753034. Localization and organization of phenol degradation genes of Pseudomonas putida strain H. Herrmann H, Muller C, Schmidt I, Mahnke J, Petruschka L, Hahnke K;. Mol Gen Genet 1995;247:240-246. [2]. 11456616. Crystal structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath) demonstrating geometrical variability at the dinuclear iron active site. Whittington DA, Lippard SJ;. J Am Chem Soc. 2001;123:827-838. [3]. 17873074. An inducible propane monooxygenase is responsible for N-nitrosodimethylamine degradation by Rhodococcus sp. strain RHA1. Sharp JO, Sales CM, LeBlanc JC, Liu J, Wood TK, Eltis LD, Mohn WW, Alvarez-Cohen L;. Appl Environ Microbiol. 2007;73:6930-6938. [4]. 9312093. Alkene monooxygenase from Xanthobacter strain Py2. Purification and characterization of a four-component system central to the bacterial metabolism of aliphatic alkenes. Small FJ, Ensign SA;. J Biol Chem. 1997;272:24913-24920. (from Pfam) NF014396.5 PF02333.20 Phytase 21 21 375 PfamEq Y Y N phytase GO:0016158 10655618,9603817 131567 cellular organisms no rank 13506 EBI-EMBL Phytase phytase Phytase is a secreted enzyme which hydrolyses phytate to release inorganic phosphate. This family appears to represent a novel enzyme that shows phytase activity [1] and has been shown to have a six- bladed propeller folding architecture [2]. [1]. 9603817. Isolation, characterization, molecular gene cloning, and sequencing of a novel phytase from Bacillus subtilis. Kerovuo J, Lauraeus M, Nurminen P, Kalkkinen N, Apajalahti J;. Appl Environ Microbiol 1998;64:2079-2085. [2]. 10655618. Crystal structures of a novel, thermostable phytase in partially and fully calcium-loaded states. Ha NC, Oh BC, Shin S, Kim HJ, Oh TK, Kim YO, Choi KY, Oh BH;. Nat Struct Biol 2000;7:147-153. (from Pfam) NF014397.5 PF02334.21 RTP 26.7 26.7 113 PfamEq Y N N Replication terminator protein GO:0003677,GO:0006274 8670817 131567 cellular organisms no rank 743 EBI-EMBL Replication terminator protein Replication terminator protein The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site. [1]. 8670817. The structure and function of the replication terminator protein of Bacillus subtilis: identification of the 'winged helix' DNA-binding domain. Pai KS, Bussiere DE, Wang F, Hutchison CA 3rd, White SW, Bastia D;. EMBO J 1996;15:3164-3173. (from Pfam) NF014408.5 PF02347.21 GDC-P 26 26 429 domain Y N N Glycine cleavage system P-protein GO:0004375,GO:0006546 7498764,8181752 131567 cellular organisms no rank 90296 EBI-EMBL Glycine cleavage system P-protein Glycine cleavage system P-protein This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1.2.10 (GDC) also annotated as glycine cleavage system or glycine synthase. GDC consists of four proteins P, H, L and T [2]. The reaction catalysed by this protein is:- Glycine + lipoylprotein S-aminomethyldihydrolipoylprotein + CO2 [1]. 7498764. Genetics of the synthesis of serine from glycine and the utilization of glycine as sole nitrogen source by Saccharomyces cerevisiae. Sinclair DA, Dawes IW;. Genetics 1995;140:1213-1222. [2]. 8181752. Characterization of the Escherichia coli gcv operon. Stauffer LT, Fogarty SJ, Stauffer GV;. Gene 1994;142:17-22. (from Pfam) NF014409.5 PF02348.24 CTP_transf_3 22.6 22.6 217 domain Y Y N cytidylyltransferase domain-containing protein 11577688,7543480,8663048,9689047 131567 cellular organisms no rank 114703 EBI-EMBL Cytidylyltransferase cytidylyltransferase domain This family consists of two main Cytidylyltransferase activities: 1) 3-deoxy-manno-octulosonate cytidylyltransferase, [3], EC:2.7.7.38 catalysing the reaction:- CTP + 3-deoxy-D-manno-octulosonate diphosphate + CMP-3-deoxy-D-manno-octulosonate, 2) acylneuraminate cytidylyltransferase EC:2.7.7.43, [1,2], catalysing the reaction:- CTP + N-acylneuraminate diphosphate + CMP-N-acylneuraminate. NeuAc cytydilyltransferase of Mannheimia haemolytica has been characterised describing kinetics and regulation by substrate charge, energetic charge and amino-sugar demand[4]. [1]. 9689047. Mammalian cytidine 5'-monophosphate N-acetylneuraminic acid synthetase: a nuclear protein with evolutionarily conserved structural motifs. Munster AK, Eckhardt M, Potvin B, Muhlenhoff M, Stanley P, Gerardy-Schahn R;. Proc Natl Acad Sci U S A 1998;95:9140-9145. [2]. 8663048. Purification, cloning, and expression of a cytidine 5'-monophosphate N-acetylneuraminic acid synthetase from Haemophilus ducreyi. Tullius MV, Munson RS Jr, Wang J, Gibson BW;. J Biol Chem 1996;271:15373-15380. [3]. 7543480. Expression of genes kdsA and kdsB involved in 3-deoxy-D-manno-octulosonic acid metabolism and biosynthesis of enterobacterial lipopolysaccharide is growth phase regulated primarily at the transcriptional level in Escherichia coli K-12. Strohmaier H, Remler P, Renner W, Hogenauer G;. J Bacteriol 1995;177:4488-4500. [4]. 11577688. Kinetic properties of the acylneuraminate cytidylyltransferase from Pasteurella haemolytica A2. Bravo IG, Barrallo S, Ferrero MA, Rodriguez-Aparicio LB, Martinez-Blanco H, Reglero A;. Biochem J 2001;358:585-598. (from Pfam) NF014411.5 PF02350.24 Epimerase_2 30.6 30.6 347 domain Y Y N UDP-N-acetylglucosamine 2-epimerase 9305888,9440531,9515923 131567 cellular organisms no rank 77348 EBI-EMBL UDP-N-acetylglucosamine 2-epimerase UDP-N-acetylglucosamine 2-epimerase This family consists of UDP-N-acetylglucosamine 2-epimerases EC:5.1.3.14 this enzyme catalyses the production of UDP-ManNAc from UDP-GlcNAc. Note that some of the enzymes is this family are bifunctional such as Swiss:O35826 and Swiss:Q9Z0P6 in this instance Pfam matches only the N-terminal half of the protein suggesting that the additional C-terminal part (when compared to mono-functional members of this family) is responsible for the UPD-N-acetylmannosamine kinase activity of these enzymes. This hypothesis is further supported by the assumption that the C-terminal part of Swiss:O35826 is the kinase domain [3]. [1]. 9515923. Characterization of the gene cassette required for biosynthesis of the (alpha1-->6)-linked N-acetyl-D-mannosamine-1-phosphate capsule of serogroup A Neisseria meningitidis. Swartley JS, Liu LJ, Miller YK, Martin LE, Edupuganti S, Stephens DS;. J Bacteriol. 1998;180:1533-1539. [2]. 9440531. Staphylococcus aureus cap5O and cap5P genes functionally complement mutations affecting enterobacterial common-antigen biosynthesis in Escherichia coli. Kiser KB, Lee JC;. J Bacteriol 1998;180:403-406. [3]. 9305888. A bifunctional enzyme catalyzes the first two steps in N-acetylneuraminic acid biosynthesis of rat liver. Molecular cloning and functional expression of UDP-N-acetyl-glucosamine 2-epimerase/N-acetylmannosamine kinase. Stasche R, Hinderlich S, Weise C, Effertz K, Lucka L, Moormann P, Reutter W;. J Biol Chem 1997;272:24319-24324. (from Pfam) NF014414.5 PF02353.25 CMAS 27 27 273 domain Y Y N class I SAM-dependent methyltransferase 2.1.1.- 10882107,7592990,8917504 131567 cellular organisms no rank 203368 EBI-EMBL Mycolic acid cyclopropane synthetase class I SAM-dependent methyltransferase This family consist of Cyclopropane-fatty-acyl-phospholipid synthase or CFA synthase EC:2.1.1.79 this enzyme catalyse the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid. [1]. 8917504. A common mechanism for the biosynthesis of methoxy and cyclopropyl mycolic acids in Mycobacterium tuberculosis. Yuan Y, Barry CE 3rd;. Proc Natl Acad Sci U S A 1996;93:12828-12833. [2]. 7592990. The biosynthesis of cyclopropanated mycolic acids in Mycobacterium tuberculosis. Identification and functional analysis of CMAS-2. George KM, Yuan Y, Sherman DR, Barry CE 3d;. J Biol Chem 1995;270:27292-27298. [3]. 10882107. A novel mycolic acid cyclopropane synthetase is required for cording, persistence, and virulence of Mycobacterium tuberculosis. Glickman MS, Cox JS, Jacobs WR Jr;. Mol Cell. 2000;5:717-727. (from Pfam) NF014416.5 PF02355.21 SecD_SecF 20.5 20.5 189 domain Y N N Protein export membrane protein 8112309,9694879 131567 cellular organisms no rank 274404 EBI-EMBL Protein export membrane protein Protein export membrane protein This family consists of various prokaryotic SecD and SecF protein export membrane proteins. This SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC [1]. SecD and SecF are required to maintain a proton motive force [2]. [1]. 9694879. SecDF of Bacillus subtilis, a molecular Siamese twin required for the efficient secretion of proteins. Bolhuis A, Broekhuizen CP, Sorokin A, van Roosmalen ML, Venema G, Bron S, Quax WJ, van Dijl JM;. J Biol Chem 1998;273:21217-21224. [2]. 8112309. SecD and SecF are required for the proton electrochemical gradient stimulation of preprotein translocation. Arkowitz RA, Wickner W;. EMBO J 1994;13:954-963. (from Pfam) NF014417.5 PF02357.24 NusG 22.2 22.2 93 domain Y Y N transcription termination/antitermination NusG family protein GO:0006354,GO:0006355,GO:0140673 131567 cellular organisms no rank 63693 EBI-EMBL Transcription termination factor nusG transcription termination/antitermination NusG family protein NF014418.5 PF02358.21 Trehalose_PPase 27 27 235 domain Y Y N trehalose-phosphatase GO:0003824,GO:0005992 8045430,9681009 131567 cellular organisms no rank 36713 EBI-EMBL Trehalose-phosphatase trehalose-phosphatase This family consist of trehalose-phosphatases EC:3.1.3.12 these enzyme catalyse the de-phosphorylation of trehalose-6-phosphate to trehalose and orthophosphate. The aligned region is present in trehalose-phosphatases and comprises the entire length of the protein it is also found in the C-terminus of trehalose-6-phosphate synthase EC:2.4.1.15 adjacent to the trehalose-6-phosphate synthase domain - Pfam:PF00982. It would appear that the two equivalent genes in the E. coli otsBA operon [2] otsA the trehalose-6-phosphate synthase and otsB trehalose-phosphatase (this family) have undergone gene fusion in most eukaryotes e.g. Swiss:P31688 and Swiss:P93653. Trehalose is a common disaccharide of bacteria, fungi and invertebrates that appears to play a major role in desiccation tolerance [1]. [1]. 9681009. Trehalose-6-phosphate phosphatases from Arabidopsis thaliana: identification by functional complementation of the yeast tps2 mutant. Vogel G, Aeschbacher RA, Muller J, Boller T, Wiemken A;. Plant J 1998;13:673-683. [2]. 8045430. Analysis of the otsBA operon for osmoregulatory trehalose synthesis in Escherichia coli and homology of the OtsA and OtsB proteins to the yeast trehalose-6-phosphate synthase/phosphatase complex. Kaasen I, McDougall J, Strom AR;. Gene 1994;145:9-15. (from Pfam) NF014419.5 PF02359.23 CDC48_N 35.1 35.1 85 domain Y N N Cell division protein 48 (CDC48), N-terminal domain 10531028 131567 cellular organisms no rank 8312 EBI-EMBL Cell division protein 48 (CDC48), N-terminal domain Cell division protein 48 (CDC48), N-terminal domain This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the N-terminus. The VAT-N domain found in AAA ATPases Pfam:PF00004 is a substrate 185-residue recognition domain [1]. [1]. 10531028. The solution structure of VAT-N reveals a 'missing link' in the evolution of complex enzymes from a simple betaalphabetabeta element. Coles M, Diercks T, Liermann J, Groger A, Rockel B, Baumeister W, Koretke KK, Lupas A, Peters J, Kessler H;. Curr Biol 1999;9:1158-1168. (from Pfam) NF014420.5 PF02361.21 CbiQ 25 25 216 domain Y Y N CbiQ family ECF transporter T component 8501034 131567 cellular organisms no rank 95555 EBI-EMBL Cobalt transport protein CbiQ family ECF transporter T component This family consists of various cobalt transport proteins Most of which are found in Cobalamin (Vitamin B12) biosynthesis operons. In Salmonella the cbiN cbiQ (product CbiQ in this family) and cbiO are likely to form an active cobalt transport system [1]. [1]. 8501034. Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM;. J Bacteriol 1993;175:3303-3316. (from Pfam) NF014425.5 PF02366.23 PMT 22.7 22.7 245 domain Y Y N phospholipid carrier-dependent glycosyltransferase GO:0000030,GO:0006493,GO:0016020 26515403,26912703,7852348,8650217,8918452 131567 cellular organisms no rank 86991 EBI-EMBL Dolichyl-phosphate-mannose-protein mannosyltransferase phospholipid carrier-dependent glycosyltransferase This is a family of Dolichyl-phosphate-mannose-protein mannosyltransferase proteins EC:2.4.1.109. These proteins are responsible for O-linked glycosylation of proteins, they catalyse the reaction:- Dolichyl phosphate D-mannose + protein dolichyl phosphate + O-D-mannosyl-protein. Also in this family is Swiss:Q94891 Drosophila rotated abdomen protein which is a putative mannosyltransferase [2]. This family appears to be distantly related to Pfam:PF02516 (A Bateman pers. obs.). This family also contains sequences from ArnTs (4-amino-4-deoxy-L-arabinose lipid A transferase). They catalyse the addition of 4-amino-4-deoxy-l-arabinose (l-Ara4N) to the lipid A moiety of the lipopolysaccharide [4]. This is a critical modification enabling bacteria (e.g. Escherichia coli and Salmonella typhimurium) to resist killing by antimicrobial peptides such as polymyxins [5]. Members such as Swiss:O52327 are predicted to have 12 trans-membrane regions. The N-terminal portion of these proteins is hypothesised to have a conserved glycosylation activity which is shared between distantly related oligosaccharyltransferases ArnT and PglB families [4]. [1]. 8918452. The PMT gene family: protein O-glycosylation in Saccharomyces cerevisiae is vital. Gentzsch M, Tanner W;. EMBO J 1996;15:5752-5759. [2]. 8650217. Mutations in the rotated abdomen locus affect muscle development and reveal an intrinsic asymmetry in Drosophila. Martin-Blanco E, Garcia-Bellido A;. Proc Natl Acad Sci U S A 1996;93:6048-6052. [3]. 7852348. Protein O-glycosylation in yeast. The PMT2 gene specifies a second protein O-mannosyltransferase that functions in addition to the PM. TRUNCATED at 1650 bytes (from Pfam) NF014426.5 PF02367.22 TsaE 26.6 26.6 128 PfamEq Y Y N tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex ATPase subunit type 1 TsaE 2.3.1.234 GO:0002949 22378793,23072323 131567 cellular organisms no rank 62483 EBI-EMBL Threonylcarbamoyl adenosine biosynthesis protein TsaE tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex ATPase subunit type 1 TsaE This family of proteins is involved in the synthesis of threonylcarbamoyl adenosine (t(6)A) [1-2]. [1]. 22378793. Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. Deutsch C, El Yacoubi B, de Crecy-Lagard V, Iwata-Reuyl D;. J Biol Chem. 2012;287:13666-13673. [2]. 23072323. Mechanism of N6-threonylcarbamoyladenonsine (t(6)A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP. Lauhon CT;. Biochemistry. 2012;51:8950-8963. (from Pfam) NF014427.5 PF02368.23 Big_2 22.8 22.8 79 domain Y Y N Ig-like domain-containing protein 10201396 131567 cellular organisms no rank 81265 EBI-EMBL Bacterial Ig-like domain (group 2) Bacterial Ig-like domain (group 2) This family consists of bacterial domains with an Ig-like fold. Members of this family are found in bacterial and phage surface proteins such as intimins. [1]. 10201396. Structure of the cell-adhesion fragment of intimin from enteropathogenic Escherichia coli. Kelly G, Prasannan S, Daniell S, Fleming K, Frankel G, Dougan G, Connerton I, Matthews S;. Nat Struct Biol 1999;6:313-318. (from Pfam) NF014428.5 PF02369.21 Big_1 33.9 33.9 93 domain Y Y N Ig-like domain-containing protein 131567 cellular organisms no rank 30565 EBI-EMBL Bacterial Ig-like domain (group 1) bacterial Ig-like domain (group 1) This family consists of bacterial domains with an Ig-like fold. Members of this family are found in bacterial surface proteins such as intimins and invasins involved in pathogenicity. (from Pfam) NF014430.5 PF02371.21 Transposase_20 21.3 21.3 87 domain Y Y N transposase GO:0003677,GO:0004803,GO:0006313 131567 cellular organisms no rank 152928 EBI-EMBL Transposase IS116/IS110/IS902 family transposase Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. This region is often found with Pfam:PF01548. The exact function of this region is uncertain. This family contains a HHH motif suggesting a DNA-binding function. (from Pfam) NF014433.5 PF02374.20 ArsA_ATPase 24.3 21.6 305 domain Y Y N ArsA-related P-loop ATPase 1704144 131567 cellular organisms no rank 232200 EBI-EMBL Anion-transporting ATPase ArsA-related P-loop ATPase This Pfam family represents a conserved domain, which is sometimes repeated, in an anion-transporting ATPase. The ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell. [1]. 1704144. The plasmid-encoded arsenical resistance pump: an anion-translocating ATPase. Rosen BP;. Res Microbiol 1990;141:336-341. (from Pfam) NF014439.5 PF02381.23 MraZ 23 23 72 PfamEq Y N N MraZ protein, putative antitoxin-like 15146477 131567 cellular organisms no rank 30166 EBI-EMBL MraZ protein, putative antitoxin-like MraZ protein, putative antitoxin-like This small 70 amino acid domain is found duplicated in a family of bacterial proteins. These proteins may be DNA-binding transcription factors (Pers. comm. A Andreeva & A Murzin). It is likely, due to the similarity of fold, that this family acts as a bacterial antitoxin like the MazE antitoxin family. [1]. 15146477. Crystal structure of a protein associated with cell division from Mycoplasma pneumoniae (GI: 13508053): a novel fold with a conserved sequence motif. Chen S, Jancrick J, Yokota H, Kim R, Kim SH;. Proteins. 2004;55:785-791. (from Pfam) NF014442.5 PF02384.21 N6_Mtase 20.4 20.4 311 domain Y Y N N-6 DNA methylase GO:0003677,GO:0008170 9108149,9440532,9593305 131567 cellular organisms no rank 256298 EBI-EMBL N-6 DNA Methylase N-6 DNA methylase Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The R-M system is a complex containing three polypeptides: M (this family), S (Pfam:PF01420), and R [1]. This family consists of N-6 adenine-specific DNA methylase EC:2.1.1.72 from Type I and Type IC restriction systems. These methylases have the same sequence specificity as their corresponding restriction enzymes. [1]. 9440532. A type IC restriction-modification system in Lactococcus lactis. Schouler C, Clier F, Lerayer AL, Ehrlich SD, Chopin MC;. J Bacteriol 1998;180:407-411. [2]. 9593305. Combinational variation of restriction modification specificities in Lactococcus lactis. Schouler C, Gautier M, Ehrlich SD, Chopin MC;. Mol Microbiol 1998;28:169-178. [3]. 9108149. The specificity of sty SKI, a type I restriction enzyme, implies a structure with rotational symmetry. Thorpe PH, Ternent D, Murray NE;. Nucleic Acids Res 1997;25:1694-1700. (from Pfam) NF014443.5 PF02386.21 TrkH 27 27 502 domain Y Y N potassium transporter TrkG GO:0006812,GO:0008324,GO:0055085 10629185,7896723,8948101 131567 cellular organisms no rank 83401 EBI-EMBL Cation transport protein potassium transporter TrkG This family consists of various cation transport proteins (Trk) and V-type sodium ATP synthase subunit J or translocating ATPase J EC:3.6.1.34. These proteins are involved in active sodium up-take utilising ATP in the process. TrkH a member of the family Swiss:P76769 from E. coli is a hydrophobic membrane protein and determines the specificity and kinetics of cation transport by the TrK system in E. coli [2]. [1]. 8948101. Sequencing analysis of a 40.2 kb fragment of yeast chromosome X reveals 19 open reading frames including URA2 (5' end), TRK1, PBS2, SPT10, GCD14, RPE1, PHO86, NCA3, ASF1, CCT7, GZF3, two tRNA genes, three remnant delta elements and a Ty4 transposon. Cziepluch C, Kordes E, Pujol A, Jauniaux JC;. Yeast 1996;12:1471-1474. [2]. 7896723. TrkH and its homolog, TrkG, determine the specificity and kinetics of cation transport by the Trk system of Escherichia coli. Schlosser A, Meldorf M, Stumpe S, Bakker EP, Epstein W;. J Bacteriol 1995;177:1908-1910. [3]. 10629185. Trk1 and Trk2 define the major K(+) transport system in fission yeast. Calero F, Gomez N, Arino J, Ramos J;. J Bacteriol 2000;182:394-399. (from Pfam) NF014445.5 PF02388.21 FemAB 24 24 406 subfamily Y Y N peptidoglycan bridge formation glycyltransferase FemA/FemB family protein GO:0016755,GO:0044038 10209768,2559314,8383661,8981974,9393725 131567 cellular organisms no rank 32374 EBI-EMBL FemAB family peptidoglycan bridge formation glycyltransferase FemA/FemB family protein The femAB operon codes for two nearly identical approximately 50-kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan [1]. These proteins are also considered as a factor influencing the level of methicillin resistance [2]. [1]. 9393725. Specificities of FemA and FemB for different glycine residues: FemB cannot substitute for FemA in staphylococcal peptidoglycan pentaglycine side chain formation. Ehlert K, Schroder W, Labischinski H;. J Bacteriol 1997;179:7573-7576. [2]. 10209768. Molecular characterization of femA from Staphylococcus hominis and Staphylococcus saprophyticus, and femA-based discrimination of staphylococcal species. Vannuffel P, Heusterspreute M, Bouyer M, Vandercam B, Philippe M, Gala JL;. Res Microbiol 1999;150:129-141. [3]. 2559314. FemA, a host-mediated factor essential for methicillin resistance in Staphylococcus aureus: molecular cloning and characterization. Berger-Bachi B, Barberis-Maino L, Strassle A, Kayser FH;. Mol Gen Genet 1989;219:263-269. [4]. 8981974. Cell wall monoglycine cross-bridges and methicillin hypersusceptibility in a femAB null mutant of methicillin-resistant Staphylococcus aureus. Stranden AM, Ehlert K, Labischinski H, Berger-Bachi B;. J Bacteriol 1997;179:9-16. [5]. 8383661. Influence of femB on methicillin resistance and peptidoglycan metabolism in Staphylococcus aureus. Henze U, Sidow T, Wecke J, Labischinski H, Berger-Bachi B;. J Bacteriol 1993;175:1612-1620. (from Pfam) NF014447.5 PF02390.22 Methyltransf_4 24 24 173 domain Y N N Putative methyltransferase GO:0006400,GO:0008176 131567 cellular organisms no rank 115949 EBI-EMBL Putative methyltransferase Putative methyltransferase This is a family of putative methyltransferases. The aligned region contains the GXGXG S-AdoMet binding site suggesting a putative methyltransferase activity. (from Pfam) NF014448.5 PF02391.22 MoaE 23.4 23.4 114 domain Y Y N molybdenum cofactor biosynthesis protein MoaE GO:0006777 8514782 131567 cellular organisms no rank 53131 EBI-EMBL MoaE protein molybdenum cofactor biosynthesis protein MoaE This family contains the MoaE protein that is involved in biosynthesis of molybdopterin [1]. Molybdopterin, the universal component of the pterin molybdenum cofactors, contains a dithiolene group serving to bind Mo. Addition of the dithiolene sulfurs to a molybdopterin precursor requires the activity of the converting factor. Converting factor contains the MoaE and MoaD proteins. [1]. 8514782. The biosynthesis of molybdopterin in Escherichia coli. Purification and characterization of the converting factor. Pitterle DM, Rajagopalan KV;. J Biol Chem 1993;268:13499-13505. (from Pfam) NF014453.5 PF02397.21 Bac_transf 27 27 179 domain Y Y N sugar transferase 9423846 131567 cellular organisms no rank 165462 EBI-EMBL Bacterial sugar transferase sugar transferase This Pfam family represents a conserved region from a number of different bacterial sugar transferases, involved in diverse biosynthesis pathways. [1]. 9423846. Identification of a genetic locus essential for serotype b-specific antigen synthesis in Actinobacillus actinomycetemcomitans. Yoshida Y, Nakano Y, Yamashita Y, Koga T;. Infect Immun 1998;66:107-114. (from Pfam) NF014458.5 PF02403.27 Seryl_tRNA_N 28.2 28.2 108 PfamEq Y N N Seryl-tRNA synthetase N-terminal domain 8654381 131567 cellular organisms no rank 73026 EBI-EMBL Seryl-tRNA synthetase N-terminal domain Seryl-tRNA synthetase N-terminal domain This domain is found associated with the Pfam tRNA synthetase class II domain (Pfam:PF00587) and represents the N-terminal domain of seryl-tRNA synthetase. [1]. 8654381. The crystal structure of the ternary complex of T.thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site. Cusack S, Yaremchuk A, Tukalo M;. EMBO J 1996;15:2834-2842. (from Pfam) NF014461.5 PF02406.22 MmoB_DmpM 25 25 85 domain Y Y N MmoB/DmpM family protein GO:0004497,GO:0008152 10231531,10393915,9012665 131567 cellular organisms no rank 3323 EBI-EMBL MmoB/DmpM family MmoB/DmpM family protein This family consists of monooxygenase components such as MmoB methane monooxygenase (EC:1.14.13.25) regulatory protein B. When MmoB is present at low concentration it converts methane monooxygenase from an oxidase to a hydroxylase and stabilises intermediates required for the activation of dioxygen [1]. Also found in this family is DmpM or Phenol hydroxylase (EC:1.14.13.7) protein component P2, this protein lacks redox co-factors and is required for optimal turnover of Phenol hydroxylase [3]. [1]. 10393915. Structure of the soluble methane monooxygenase regulatory protein B. Walters KJ, Gassner GT, Lippard SJ, Wagner G;. Proc Natl Acad Sci U S A 1999;96:7877-7882. [2]. 10231531. Solution structure of component B from methane monooxygenase derived through heteronuclear NMR and molecular modeling. Chang SL, Wallar BJ, Lipscomb JD, Mayo KH;. Biochemistry 1999;38:5799-5812. [3]. 9012665. Solution structure of phenol hydroxylase protein component P2 determined by NMR spectroscopy. Qian H, Edlund U, Powlowski J, Shingler V, Sethson I;. Biochemistry 1997;36:495-504. (from Pfam) NF014464.5 PF02410.20 RsfS 21.6 21.6 98 PfamEq Y Y N RsfS/YbeB/iojap family protein 22829778 131567 cellular organisms no rank 43948 EBI-EMBL Ribosomal silencing factor during starvation RsfS/YbeB/iojap family protein This family is expressed by almost all bacterial and eukaryotic genomes but not by archaea. Its function is to down-regulate protein synthesis under conditions of nutrient shortage, and it does this by binding to protein L14 of the large ribosomal subunit, thus acting as a ribosomal silencing factor (RsfS) by blocking the joining of the ribosomal subunits [1]. This family is structurally homologous to nucleotidyltransferases. [1]. 22829778. RsfA (YbeB) proteins are conserved ribosomal silencing factors. Hauser R, Pech M, Kijek J, Yamamoto H, Titz B, Naeve F, Tovchigrechko A, Yamamoto K, Szaflarski W, Takeuchi N, Stellberger T, Diefenbacher ME, Nierhaus KH, Uetz P;. PLoS Genet. 2012;8:e1002815. (from Pfam) NF014466.5 PF02412.23 TSP_3 25 13.6 36 domain Y Y N thrombospondin type 3 repeat-containing protein GO:0005509,GO:0007155 15014436,2430973 131567 cellular organisms no rank 13517 EBI-EMBL Thrombospondin type 3 repeat Thrombospondin type 3 repeat The thrombospondin repeat is a short aspartate rich repeat which binds to calcium ions. The repeat was initially identified in thrombospondin proteins that contained 7 of these repeats [1]. The repeat lacks defined secondary structure [2]. [1]. 2430973. The structure of human thrombospondin, an adhesive glycoprotein with multiple calcium-binding sites and homologies with several different proteins. Lawler J, Hynes RO;. J Cell Biol 1986;103:1635-1648. [2]. 15014436. Structure of a thrombospondin C-terminal fragment reveals a novel calcium core in the type 3 repeats. Kvansakul M, Adams JC, Hohenester E;. EMBO J. 2004;23:1223-1233. (from Pfam) NF014469.5 PF02415.22 Chlam_PMP 20.6 12.5 19 repeat Y N N POMP-like repeat-containing protein 11583841 131567 cellular organisms no rank 13102 EBI-EMBL Chlamydia polymorphic membrane protein (Chlamydia_PMP) repeat Chlamydia polymorphic outer membrane protein repeat This family contains several Chlamydia polymorphic membrane proteins. Chlamydia pneumoniae is an obligate intracellular bacterium and a common human pathogen causing infection of the upper and lower respiratory tract. Common for the Pmps are the tetrapeptide GGA(I/V/L) motif repeated several times in the N-terminal part. The C-terminal half is characterised by conserved tryptophans and a carboxy-terminal phenylalanine. A signal peptide leader sequence is predicted in 20 C. pneumoniae Pmps, which indicates an outer membrane localisation. Pmp10 and Pmp11 contain a signal peptidase II cleavage site suggesting lipid modification. The C. pneumoniae pmp genes represent 17.5% of the chlamydia-specific coding capacity and they are all transcribed during chlamydial growth but the function of Pmps remains unknown [1]. This family shows some similarity to Pfam:PF05594 and hence is likely to also form a beta-helical structure (personal obs:C Yeats). [1]. 11583841. Differential expression of Pmp10 in cell culture infected with Chlamydia pneumoniae CWL029. Pedersen AS, Christiansen G, Birkelund S;. FEMS Microbiol Lett 2001;203:153-159. (from Pfam) NF014470.5 PF02416.21 TatA_B_E 21 21 53 domain Y Y N twin-arginine translocase TatA/TatE family subunit GO:0015031 9367960,9546395 131567 cellular organisms no rank 88683 EBI-EMBL mttA/Hcf106 family twin-arginine translocase TatA/TatE family subunit Members of this protein family are involved in a sec independent translocation mechanism. This pathway has been called the DeltapH pathway in chloroplasts [2]. Members of this family in E.coli are involved in export of redox proteins with a "twin arginine" leader motif [1]. [1]. 9546395. A novel and ubiquitous system for membrane targeting and secretion of cofactor-containing proteins. Weiner JH, Bilous PT, Shaw GM, Lubitz SP, Frost L, Thomas GH, Cole JA, Turner RJ;. Cell 1998;93:93-101. [2]. 9367960. Sec-independent protein translocation by the maize Hcf106 protein. Settles AM, Yonetani A, Baron A, Bush DR, Cline K, Martienssen R;. Science 1997;278:1467-1470. (from Pfam) NF014471.5 PF02417.20 Chromate_transp 28.6 28.6 166 domain Y Y N chromate transporter GO:0015109,GO:0015703 2152903,2180932 131567 cellular organisms no rank 83263 EBI-EMBL Chromate transporter chromate transporter Members of this family probably act as chromate transporters [1,2]. Members of this family are found in both bacteria and archaebacteria. The proteins are composed of one or two copies of this region. The alignment contains two conserved motifs, FGG and PGP. [1]. 2152903. Cloning, nucleotide sequence, and expression of the chromate resistance determinant of Pseudomonas aeruginosa plasmid pUM505. Cervantes C, Ohtake H, Chu L, Misra TK, Silver S;. J Bacteriol 1990;172:287-291. [2]. 2180932. Nucleotide sequence and expression of a plasmid-encoded chromate resistance determinant from Alcaligenes eutrophus. Nies A, Nies DH, Silver S;. J Biol Chem. 1990;265:5648-5653. (from Pfam) NF014474.5 PF02421.23 FeoB_N 27 27 156 domain Y Y N FeoB small GTPase domain-containing protein GO:0005525 8407793 131567 cellular organisms no rank 444403 EBI-EMBL Ferrous iron transport protein B Ferrous iron transport protein B Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions [1]. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent [1]. [1]. 8407793. Characterization of the ferrous iron uptake system of Escherichia coli. Kammler M, Schon C, Hantke K;. J Bacteriol 1993;175:6212-6219. (from Pfam) NF014476.5 PF02423.20 OCD_Mu_crystall 24 24 314 domain Y N N Ornithine cyclodeaminase/mu-crystallin family 1384048,2644238 131567 cellular organisms no rank 82462 EBI-EMBL Ornithine cyclodeaminase/mu-crystallin family Ornithine cyclodeaminase/mu-crystallin family This family contains the bacterial Ornithine cyclodeaminase enzyme EC:4.3.1.12, which catalyses the deamination of ornithine to proline [1]. This family also contains mu-Crystallin the major component of the eye lens in several Australian marsupials, mRNA for this protein has also been found in human retina [2]. [1]. 2644238. Ornithine cyclodeaminase from octopine Ti plasmid Ach5: identification, DNA sequence, enzyme properties, and comparison with gene and enzyme from nopaline Ti plasmid C58. Schindler U, Sans N, Schroder J;. J Bacteriol 1989;171:847-854. [2]. 1384048. mu-crystallin is a mammalian homologue of Agrobacterium ornithine cyclodeaminase and is expressed in human retina. Kim RY, Gasser R, Wistow GJ;. Proc Natl Acad Sci U S A 1992;89:9292-9296. (from Pfam) NF014477.5 PF02424.20 ApbE 25.6 25.6 266 domain Y Y N FAD:protein FMN transferase GO:0017013 10572132,16779835,23558683,9473043 131567 cellular organisms no rank 83244 EBI-EMBL ApbE family FAD:protein FMN transferase This prokaryotic family of lipoproteins are related to ApbE from Salmonella typhimurium. ApbE is involved in thiamine synthesis [1]. It acts as an FAD:protein FMN-transferase, catalysing the attachment of an FMN residue to a threonine residue of a protein via a phosphoester bond in such bacterial flavoproteins [4]. [1]. 9473043. The apbE gene encodes a lipoprotein involved in thiamine synthesis in Salmonella typhimurium. Beck BJ, Downs DM;. J Bacteriol 1998;180:885-891. [2]. 10572132. A periplasmic location is essential for the role of the ApbE lipoprotein in thiamine synthesis in Salmonella typhimurium. Beck BJ, Downs DM;. J Bacteriol 1999;181:7285-7290. [3]. 16779835. Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 A resolution. Han GW, Sri Krishna S, Schwarzenbacher R, McMullan D, Ginalski K, Elsliger MA, Brittain SM, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod H, Canaves JM, Chiu HJ, DiDonato M, Grzechnik SK, Hale J, Hampton E, Haugen J, Jaroszewski L, Jin KK, Klock. Proteins. 2006;64:1083-1090. [4]. 23558683. Alternative Pyrimidine Biosynthesis Protein ApbE Is a Flavin Transferase Catalyzing Covalent Attachment of FMN to a Threonine Residue in Bacterial Flavoproteins. Bertsova YV, Fadeeva MS, Kostyrko VA, Serebryakova MV, Baykov AA, Bogachev AV;. J Biol Chem. 2013;288:14276-14286. (from Pfam) NF014479.5 PF02426.21 MIase 26.7 26.7 90 PfamEq Y Y N muconolactone Delta-isomerase family protein 2926818 131567 cellular organisms no rank 11223 EBI-EMBL Muconolactone delta-isomerase muconolactone Delta-isomerase family protein This small enzyme forms a homodecameric complex, that catalyses the third step in the catabolism of catechol to succinate- and acetyl-coa in the beta-ketoadipate pathway EC:5.3.3.4. The protein has a ferredoxin-like fold according to SCOP. [1]. 2926818. Crystal structure of muconolactone isomerase at 3.3 A resolution. Katti SK, Katz BA, Wyckoff HW;. J Mol Biol 1989;205:557-571. (from Pfam) NF014486.5 PF02433.20 FixO 29.6 29.6 219 domain Y Y N cbb3-type cytochrome c oxidase subunit II 9791120 131567 cellular organisms no rank 22906 EBI-EMBL Cytochrome C oxidase, mono-heme subunit/FixO cbb3-type cytochrome c oxidase subunit II The bacterial oxidase complex, fixNOPQ or cytochrome cbb3, is thought to be required for respiration in endosymbiosis. FixO is a membrane bound mono-heme constituent of the fixNOPQ complex. [1]. 9791120. A cytochrome cbb3 (cytochrome c) terminal oxidase in Azospirillum brasilense Sp7 supports microaerobic growth. Marchal K, Sun J, Keijers V, Haaker H, Vanderleyden J;. J Bacteriol 1998;180:5689-5696. (from Pfam) NF014487.5 PF02434.21 Fringe 21 21 250 PfamEq Y N N Fringe-like GO:0016020,GO:0016757 10899003 131567 cellular organisms no rank 60 EBI-EMBL Fringe-like Fringe-like The drosophila protein fringe (FNG) is a glucosaminyltransferase that controls the response of the Notch receptor to specific ligands [1]. FNG is localised to the Golgi apparatus [1] (not secreted as previously thought). Modification of Notch occurs through glycosylation by FNG. The xenopus homologue, lunatic fringe, has been implicated in a variety of functions. [1]. 10899003. The Notch signalling regulator Fringe acts in the Golgi apparatus and requires the glycosyltransferase signature motif DXD. Munro S, Freeman M;. Curr Biol 2000;10:813-820. (from Pfam) NF014488.5 PF02435.21 Glyco_hydro_68 27 27 424 domain Y Y N glycoside hydrolase family 68 protein GO:0009758,GO:0050053 9726857 131567 cellular organisms no rank 6886 EBI-EMBL Levansucrase/Invertase glycoside hydrolase family 68 protein This Pfam family consists of the glycosyl hydrolase 68 family, including several bacterial levansucrase enzymes, and invertase from zymomonas. [1]. 9726857. Cloning, nucleotide sequence, and expression in Escherichia coli of levansucrase genes from the plant pathogens Pseudomonas syringae pv. glycinea and P. syringae pv. phaseolicola. Hettwer U, Jaeckel FR, Boch J, Meyer M, Rudolph K, Ullrich MS;. Appl Environ Microbiol 1998;64:3180-3187. (from Pfam) NF014489.5 PF02436.23 PYC_OADA 27 27 201 domain Y N N Conserved carboxylase domain 9478969 131567 cellular organisms no rank 63986 EBI-EMBL Conserved carboxylase domain Conserved carboxylase domain This domain represents a conserved region in pyruvate carboxylase (PYC), oxaloacetate decarboxylase alpha chain (OADA), and transcarboxylase 5s subunit. The domain is found adjacent to the HMGL-like domain (Pfam:PF00682) and often close to the biotin_lipoyl domain (Pfam:PF00364) of biotin requiring enzymes. [1]. 9478969. Purification, regulation, and molecular and biochemical characterization of pyruvate carboxylase from Methanobacterium thermoautotrophicum strain deltaH. Mukhopadhyay B, Stoddard SF, Wolfe RS;. J Biol Chem 1998;273:5155-5166. (from Pfam) NF014494.5 PF02441.24 Flavoprotein 22.7 22.7 162 domain Y Y N flavoprotein GO:0003824 1644762,8181743,8345520 131567 cellular organisms no rank 138388 EBI-EMBL Flavoprotein flavoprotein This family contains diverse flavoprotein enzymes. This family includes epidermin biosynthesis protein, EpiD Swiss:P30197, which has been shown to be a flavoprotein that binds FMN [1]. This enzyme catalyses the removal of two reducing equivalents from the cysteine residue of the C-terminal meso-lanthionine of epidermin to form a --C==C-- double bond. This family also includes the B chain of dipicolinate synthase a small polar molecule that accumulates to high concentrations in bacterial endospores, and is thought to play a role in spore heat resistance, or the maintenance of heat resistance [2]. dipicolinate synthase catalyses the formation of dipicolinic acid from dihydroxydipicolinic acid. This family also includes phenyl-acrylic acid decarboxylase Swiss:P33751 (EC:4.1.1.-) [3]. [1]. 1644762. Purification and characterization of EpiD, a flavoprotein involved in the biosynthesis of the lantibiotic epidermin. Kupke T, Stevanovic S, Sahl HG, Gotz F;. J Bacteriol 1992;174:5354-5361. [2]. 8345520. Cloning, DNA sequence, functional analysis and transcriptional regulation of the genes encoding dipicolinic acid synthetase required for sporulation in Bacillus subtilis. Daniel RA, Errington J;. J Mol Biol 1993;232:468-483. [3]. 8181743. PAD1 encodes phenylacrylic acid decarboxylase which confers resistance to cinnamic acid in Saccharomyces cerevisiae. Clausen M, Lamb CJ, Megnet R, Doerner PW;. Gene 1994;142:107-112. (from Pfam) NF014498.5 PF02445.21 NadA 27 27 295 PfamEq Y Y N quinolinate synthase NadA nadA 2.5.1.72 GO:0008987,GO:0009435,GO:0051539 10648170,2841129 131567 cellular organisms no rank 56522 EBI-EMBL Quinolinate synthetase A protein quinolinate synthase NadA Quinolinate synthetase catalyses the second step of the de novo biosynthetic pathway of pyridine nucleotide formation. In particular, quinolinate synthetase is involved in the condensation of dihydroxyacetone phosphate and iminoaspartate to form quinolinic acid [2]. This synthesis requires two enzymes, a FAD-containing "B protein" and an "A protein". [1]. 2841129. Molecular biology of pyridine nucleotide biosynthesis in Escherichia coli. Cloning and characterization of quinolinate synthesis genes nadA and nadB. Flachmann R, Kunz N, Seifert J, Gutlich M, Wientjes FJ, Laufer A , Gassen HG;. Eur J Biochem 1988;175:221-228. [2]. 10648170. Cloning, overexpression, and purification of Escherichia coli quinolinate synthetase. Ceciliani F, Caramori T, Ronchi S, Tedeschi G, Mortarino M, Galizzi A;. Protein Expr Purif 2000;18:64-70. (from Pfam) NF014499.5 PF02446.22 Glyco_hydro_77 25 25 465 PfamEq Y Y N 4-alpha-glucanotransferase 2.4.1.25 GO:0004134,GO:0005975 7678257 131567 cellular organisms no rank 64409 EBI-EMBL 4-alpha-glucanotransferase 4-alpha-glucanotransferase These enzymes EC:2.4.1.25 transfer a segment of a (1,4)-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or (1,4)-alpha-D-glucan [1]. [1]. 7678257. Disproportionating enzyme (4-alpha-glucanotransferase; EC 2.4.1.25) of potato. Purification, molecular cloning, and potential role in starch metabolism. Takaha T, Yanase M, Okada S, Smith SM;. J Biol Chem 1993;268:1391-1396. (from Pfam) NF014500.5 PF02447.21 GntP_permease 22.5 22.5 440 subfamily Y N N GntP family permease GO:0015128,GO:0016020,GO:0035429 9045817,9135111 131567 cellular organisms no rank 81919 EBI-EMBL GntP family permease GntP family permease This is a family of integral membrane permeases that are involved in gluconate uptake. E. coli contains several members of this family including GntU Swiss:P46858 a low affinity transporter [1] and GntT Swiss:P39835 a high affinity transporter [2]. [1]. 9135111. Gene organization and transcriptional regulation of the gntRKU operon involved in gluconate uptake and catabolism of Escherichia coli. Izu H, Adachi O, Yamada M;. J Mol Biol 1997;267:778-793. [2]. 9045817. Molecular genetic characterization of the Escherichia coli gntT gene of GntI, the main system for gluconate metabolism. Porco A, Peekhaus N, Bausch C, Tong S, Isturiz T, Conway T;. J Bacteriol 1997;179:1584-1590. (from Pfam) NF014502.5 PF02449.20 Glyco_hydro_42 21 21 376 domain Y Y N beta-galactosidase 3.2.1.23 GO:0004565,GO:0005975,GO:0009341 8577281 131567 cellular organisms no rank 95171 EBI-EMBL Beta-galactosidase beta-galactosidase This group of beta-galactosidase enzymes belong to the glycosyl hydrolase 42 family. The enzyme catalyses the hydrolysis of terminal, non-reducing terminal beta-D-galactosidase residues. [1]. 8577281. Sequence analysis of flanking regions of the pfoA gene of Clostridium perfringens: beta-galactosidase gene (pbg) is located in the 3'-flanking region. Shimizu T, Kobayashi T, Ba-Thein W, Ohtani K, Hayashi H;. Microbiol Immunol 1995;39:677-686. (from Pfam) NF014503.5 PF02450.20 LCAT 21 21 392 domain Y Y N lipase/acyltransferase domain-containing protein GO:0006629,GO:0008374 9219904 131567 cellular organisms no rank 16292 EBI-EMBL Lecithin:cholesterol acyltransferase LCAT family lipase/acyltransferase-like domain Lecithin:cholesterol acyltransferase (LCAT) is involved in extracellular metabolism of plasma lipoproteins, including cholesterol. [1]. 9219904. Cloning and in vitro expression of rat lecithin:cholesterol acyltransferase. Wang J, Gebre AK, Anderson RA, Parks JS;. Biochim Biophys Acta 1997;1346:207-211. (from Pfam) NF014505.5 PF02452.22 PemK_toxin 23.1 23.1 109 domain Y Y N type II toxin-antitoxin system PemK/MazF family toxin GO:0003677 21927020,22060041,8226627 131567 cellular organisms no rank 62380 EBI-EMBL PemK-like, MazF-like toxin of type II toxin-antitoxin system type II toxin-antitoxin system PemK/MazF family toxin PemK is a growth inhibitor in E. coli known to bind to the promoter region of the Pem operon, auto-regulating synthesis. This family represents the toxin molecule of a typical bacterial toxin-antitoxin system pairing. The family includes a number of different toxins, such as MazF, Kid, PemK, ChpA, ChpB and ChpAK. [1]. 8226627. chpA and chpB, Escherichia coli chromosomal homologs of the pem locus responsible for stable maintenance of plasmid R100. Masuda Y, Miyakawa K, Nishimura Y, Ohtsubo E;. J Bacteriol 1993;175:6850-6856. [2]. 22060041. Toxin-antitoxin systems in bacteria and archaea. Yamaguchi Y, Park JH, Inouye M;. Annu Rev Genet. 2011;45:61-79. [3]. 21927020. Regulation of growth and death in Escherichia coli by toxin-antitoxin systems. Yamaguchi Y, Inouye M;. Nat Rev Microbiol. 2011;9:779-790. (from Pfam) NF014509.5 PF02456.20 Adeno_IVa2 21 21 370 PfamEq Y N N Adenovirus IVa2 protein GO:0019073 10684284,8207818 131567 cellular organisms no rank 613 EBI-EMBL Adenovirus IVa2 protein Adenovirus IVa2 protein IVa2 protein can interact with the adenoviral packaging signal and that this interaction involves DNA sequences that have previously been demonstrated to be required for packaging [1]. During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter [2]. [1]. 10684284. Interaction of the adenovirus IVa2 protein with viral packaging sequences. Zhang W, Imperiale MJ;. J Virol 2000;74:2687-2693. [2]. 8207818. The product of the adenovirus intermediate gene IVa2 is a transcriptional activator of the major late promoter. Tribouley C, Lutz P, Staub A, Kedinger C;. J Virol 1994;68:4450-4457. (from Pfam) NF014510.5 PF02457.21 DAC 27 27 119 domain Y Y N diadenylate cyclase 18439896,32095817 131567 cellular organisms no rank 30565 EBI-EMBL DisA bacterial checkpoint controller nucleotide-binding diadenylate cyclase The DisA protein is a bacterial checkpoint protein that dimerises into an octameric complex. The protein consists of three distinct domains. This domain is the first and is a globular, nucleotide-binding region; the next 146-289 residues constitute the DisA-linker family, Pfam:PF10635, that consists of an elongated bundle of three alpha helices (alpha-6, alpha-10, and alpha-11), one side of which carries an additional three helices (alpha7-9), which thus forms a spine like-linker between domains 1 and 3. The C-terminal residues, of domain 3, are represented by family HHH, Pfam:PF00633, the specific DNA-binding domain. The octameric complex thus has structurally linked nucleotide-binding and DNA-binding HhH domains and the nucleotide-binding domains are bound to a cyclic di-adenosine phosphate such that DisA is a specific di-adenylate cyclase. This N-terminal domain has been identified as a diadenylate cyclase (DAC) responsible for producing c-di-AMP from two molecules of ATP [1]. The di-adenylate cyclase activity is strongly suppressed by binding to branched DNA, but not to duplex or single-stranded DNA, suggesting a role for DisA as a monitor of the presence of stalled replication forks or recombination intermediates via DNA structure-modulated c-di-AMP synthesis [2]. [1]. 32095817. Cyclic di-AMP, a second messenger of primary importance: tertiary structures and binding mechanisms. He J, Yin W, Galperin MY, Chou SH;. Nucleic Acids Res. 2020 Feb 25. pii: 5755; [Epub ahead of print]. [2]. 18439896. Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination . TRUNCATED at 1650 bytes (from Pfam) NF014513.5 PF02460.23 Patched 23 23 792 domain Y N N Patched family GO:0016020 131567 cellular organisms no rank 18656 EBI-EMBL Patched family Patched family The transmembrane protein Patched Swiss:P18502 is a receptor for the morphogene Sonic Hedgehog. This protein associates with the smoothened protein to transduce hedgehog signals. (from Pfam) NF014516.5 PF02463.24 SMC_N 40 40 220 domain Y N N RecF/RecN/SMC N terminal domain 10429180,9640531 131567 cellular organisms no rank 276304 EBI-EMBL RecF/RecN/SMC N terminal domain RecF/RecN/SMC N terminal domain This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics [1]. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. [1]. 10429180. Structural maintenance of chromosomes (SMC) proteins: conserved molecular properties for multiple biological functions. Strunnikov AV, Jessberger R;. Eur J Biochem 1999;263:6-13. [2]. 9640531. SMC protein complexes and higher-order chromosome dynamics. Hirano T;. Curr Opin Cell Biol 1998;10:317-322. (from Pfam) NF014517.5 PF02464.22 CinA 22.3 22.3 155 domain Y Y N CinA family protein 21953451,7538190 131567 cellular organisms no rank 81021 EBI-EMBL Competence-damaged protein CinA family protein CinA is the first gene in the competence-inducible (cin) operon, and is thought to be specifically required at some stage in the process of transformation [1]. This Pfam family consists of putative competence-damaged proteins from the cin operon. Some members of this family have nicotinamide mononucleotide (NMN) deamidase activity [2]. [1]. 7538190. The recA gene of Streptococcus pneumoniae is part of a competence-induced operon and controls lysogenic induction. Martin B, Garcia P, Castanie MP, Claverys JP;. Mol Microbiol 1995;15:367-379. [2]. 21953451. Identification of nicotinamide mononucleotide deamidase of the bacterial pyridine nucleotide cycle reveals a novel broadly conserved amidohydrolase family. Galeazzi L, Bocci P, Amici A, Brunetti L, Ruggieri S, Romine M, Reed S, Osterman AL, Rodionov DA, Sorci L, Raffaelli N;. J Biol Chem. 2011;286:40365-40375. (from Pfam) NF014522.5 PF02469.27 Fasciclin 22 22 123 domain Y Y N fasciclin domain-containing protein 9512662 131567 cellular organisms no rank 48803 EBI-EMBL Fasciclin domain Fasciclin domain This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria [1]. [1]. 9512662. Structural and phylogenetic analyses of RGD-CAP/beta ig-h3, a fasciclin-like adhesion protein expressed in chick chondrocytes. Kawamoto T, Noshiro M, Shen M, Nakamasu K, Hashimoto K, Kawashima-Ohya Y, Gotoh O, Kato Y;. Biochim Biophys Acta 1998;1395:288-292. (from Pfam) NF014525.5 PF02472.21 ExbD 25.4 25.4 128 domain Y Y N biopolymer transporter ExbD GO:0022857,GO:0055085 3294803,9371459 131567 cellular organisms no rank 100015 EBI-EMBL Biopolymer transport protein ExbD/TolR biopolymer transporter ExbD This group of proteins are membrane bound transport proteins essential for ferric ion uptake in bacteria [1]. The Pfam family consists of ExbD, and TolR which are involved in TonB-dependent transport of various receptor bound substrates including colicins [2]. [1]. 9371459. Unusual structure of the tonB-exb DNA region of Xanthomonas campestris pv. campestris: tonB, exbB, and exbD1 are essential for ferric iron uptake, but exbD2 is not. Wiggerich HG, Klauke B, Koplin R, Priefer UB, Puhler A;. J Bacteriol 1997;179:7103-7110. [2]. 3294803. Nucleotide sequence of a gene cluster involved in entry of E colicins and single-stranded DNA of infecting filamentous bacteriophages into Escherichia coli. Sun TP, Webster RE;. J Bacteriol 1987;169:2667-2674. (from Pfam) NF014527.5 PF02475.21 Met_10 21 21 198 domain Y N N Met-10+ like-protein 7557397 131567 cellular organisms no rank 141362 EBI-EMBL Met-10+ like-protein Met-10+ like-protein The methionine-10 mutant allele of N. crassa codes for a protein of unknown function, Swiss:O27901. However, homologous proteins have been found in yeast (Swiss:P38793) suggesting this protein may be involved in methionine biosynthesis, transport and/or utilisation [1]. [1]. 7557397. Sequence of the met-10+ locus of Neurospora crassa: homology to a sequence of unknown function in Saccharomyces cerevisiae chromosome 8. Chow CM, Kang S, Metzenberg RL, RajBhandary UL;. Gene 1995;162:111-115. (from Pfam) NF014533.5 PF02481.20 DNA_processg_A 29.6 29.6 212 domain Y Y N DNA-processing protein DprA GO:0009294 10640603,17803906 131567 cellular organisms no rank 98156 EBI-EMBL DNA recombination-mediator protein A DNA-processing protein DprA The SMF family, of DNA processing chain A, dprA, are a group of bacterial proteins. In H. pylori, dprA is required for natural chromosomal and plasmid transformation [1]. It has now been shown that DprA is found to bind cooperatively to single-stranded DNA (ssDNA) and to interact with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyse the homology-dependent formation of joint molecules. While the E.coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier. It is proposed that DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation [2]. [1]. 10640603. The dprA gene is required for natural transformation of Helicobacter pylori. Smeets LC, Bijlsma JJ, Kuipers EJ, Vandenbroucke-Grauls CM, Kusters JG;. FEMS Immunol Med Microbiol 2000;27:99-102. [2]. 17803906. A key presynaptic role in transformation for a widespread bacterial protein: DprA conveys incoming ssDNA to RecA. Mortier-Barriere I, Velten M, Dupaigne P, Mirouze N, Pietrement O, McGovern S, Fichant G, Martin B, Noirot P, Le Cam E, Polard P, Claverys JP;. Cell. 2007;130:824-836. (from Pfam) NF014534.5 PF02482.24 Ribosomal_S30AE 23.7 23.7 88 domain Y Y N HPF/RaiA family ribosome-associated protein GO:0044238 8063707 131567 cellular organisms no rank 54932 EBI-EMBL Sigma 54 modulation protein / S30EA ribosomal protein HPF/RaiA family ribosome-associated protein This Pfam family contains the sigma-54 modulation protein family and the S30AE family of ribosomal proteins which includes the light- repressed protein (lrtA) (Swiss:P47908) [1]. [1]. 8063707. A light-repressed transcript found in Synechococcus PCC 7002 is similar to a chloroplast-specific small subunit ribosomal protein and to a transcription modulator protein associated with sigma 54. Tan X, Varughese M, Widger WRM;. J Biol Chem 1994;269:20905-20912. (from Pfam) NF014536.5 PF02485.26 Branch 23.4 23.4 250 domain Y Y N beta-1,6-N-acetylglucosaminyltransferase GO:0016020,GO:0016757 22629278,8449405,9915862 131567 cellular organisms no rank 11013 EBI-EMBL Core-2/I-Branching enzyme beta-1,6-N-acetylglucosaminyltransferase This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme (eg Swiss:Q06430) and core-2 branching enzyme (eg Swiss:Q02742). I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development [1]. Core-2 branching enzyme forms crucial side-chain branches in O-glycans [2]. This is a fmmily of glycosyl-transferases that are Type II membrane proteins that are found in the endoplasmic reticulum (ER) and Golgi apparatus [2]. [1]. 8449405. Expression of the developmental I antigen by a cloned human cDNA encoding a member of a beta-1,6-N-acetylglucosaminyltransferase gene family. Bierhuizen MF, Mattei MG, Fukuda M;. Genes Dev 1993;7:468-478. [2]. 9915862. Molecular cloning and expression of a novel beta-1, 6-N-acetylglucosaminyltransferase that forms core 2, core 4, and I branches. Yeh JC, Ong E, Fukuda M;. J Biol Chem 1999;274:3215-3221. [3]. 22629278. Plant Glycosyltransferases Beyond CAZy: A Perspective on DUF Families. Hansen SF, Harholt J, Oikawa A, Scheller HV;. Front Plant Sci. 2012;3:59. (from Pfam) NF014542.5 PF02492.24 cobW 20.7 20.7 180 domain Y Y N GTP-binding protein 1624427,1655697,8423137,9140970,9209019 131567 cellular organisms no rank 239345 EBI-EMBL CobW/HypB/UreG, nucleotide-binding domain CobW/HypB/UreG, nucleotide-binding domain This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif [2,3]. HypB has GTPase activity and is a guanine nucleotide binding protein [3]. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression [1]. UreG is required for functional incorporation of the urease nickel metallocenter.[4] GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins [1]. This family of domains also contains P47K (Swiss:P31521), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product (Swiss:P29937), which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans [5]. [1]. 9140970. The HypB protein from Bradyrhizobium japonicum can store nickel and is required for the nickel-dependent transcriptional regulation of hydrogenase. Olson JW, Fu C, Maier RJ;. Mol Microbiol 1997;24:119-128. [2]. 9209019. Characterization of UreG, identification of a UreD-UreF-UreG complex, and evidence suggesting that a nucleotide-binding site in UreG is required for in vivo metallocenter assembly of Klebsiella aerogenes urease. Moncrief MB, Hausinger RP;. J Bacteriol 1997;179:4081-4086. [3]. 8423137. The product of the hypB gene, which is required for nickel incorporation into hydrogenases, is a novel guanine nucleotide-binding protein. Maier T, Jacobi A, Sauter M, Bock A;. J Bacteriol 1993;175:630-635. [4]. 1624427. Klebsi. TRUNCATED at 1650 bytes (from Pfam) NF014543.5 PF02493.25 MORN 22.5 5 23 repeat Y N N MORN repeat protein 10949023 131567 cellular organisms no rank 16111 EBI-EMBL MORN repeat MORN repeat The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii [1]. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton [1]. [1]. 10949023. Junctophilins: a novel family of junctional membrane complex proteins. Takeshima H, Komazaki S, Nishi M, Iino M, Kangawa K;. Mol Cell. 2000;6:11-22. (from Pfam) NF014544.5 PF02494.21 HYR 21.7 21.7 81 domain Y Y N HYR domain-containing protein 10933504 131567 cellular organisms no rank 7075 EBI-EMBL HYR domain HYR domain This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion [1]. [1]. 10933504. HYR, an extracellular module involved in cellular adhesion and related to the immunoglobulin-like fold. Callebaut I, Gilges D, Vigon I, Mornon JP;. Protein Sci 2000;9:1382-1390. (from Pfam) NF014548.5 PF02498.22 Bro-N 25.6 25.6 96 domain Y Y N BRO family protein 10888617,9847359 131567 cellular organisms no rank 43674 EBI-EMBL BRO family, N-terminal domain BRO N-terminal domain This family includes the N-terminus of baculovirus BRO and ALI motif proteins. The function of BRO proteins is unknown. It has been suggested that BRO-A and BRO-C are DNA binding proteins that influence host DNA replication and/or transcription [1]. This Pfam domain does not include the characteristic invariant alanine, leucine, isoleucine motif of the ALI proteins [2]. [1]. 10888617. Evidence for nucleic acid binding ability and nucleosome association of bombyx mori nucleopolyhedrovirus BRO proteins. Zemskov EA, Kang W, Maeda S;. J Virol 2000;74:6784-6789. [2]. 9847359. The genome of Melanoplus sanguinipes entomopoxvirus. Afonso CL, Tulman ER, Lu Z, Oma E, Kutish GF, Rock DL;. J Virol 1999;73:533-552. (from Pfam) NF014552.5 PF02502.23 LacAB_rpiB 24.7 24.7 138 domain Y Y N RpiB/LacA/LacB family sugar-phosphate isomerase 5.3.1.- GO:0005975,GO:0016853 16682767,8576032 131567 cellular organisms no rank 55489 EBI-EMBL Ribose/Galactose Isomerase RpiB/LacA/LacB family sugar-phosphate isomerase This family of proteins contains the sugar isomerase enzymes ribose 5-phosphate isomerase B (rpiB), galactose isomerase subunit A (LacA) and galactose isomerase subunit B (LacB). [1]. 8576032. Ribose catabolism of Escherichia coli: characterization of the rpiB gene encoding ribose phosphate isomerase B and of the rpiR gene, which is involved in regulation of rpiB expression. Sorensen KI, Hove-Jensen B;. J Bacteriol 1996;178:1003-1011. [2]. 16682767. Structure of ribose 5-phosphate isomerase from Plasmodium falciparum. Holmes MA, Buckner FS, Van Voorhis WC, Verlinde CL, Mehlin C, Boni E, DeTitta G, Luft J, Lauricella A, Anderson L, Kalyuzhniy O, Zucker F, Schoenfeld LW, Earnest TN, Hol WG, Merritt EA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006;62:427-431. (from Pfam) NF014553.5 PF02503.22 PP_kinase 31 31 183 domain Y N N Polyphosphate kinase middle domain 9501429 131567 cellular organisms no rank 65223 EBI-EMBL Polyphosphate kinase middle domain Polyphosphate kinase middle domain Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. [1]. 9501429. Transcription of ppk from Acinetobacter sp. strain ADP1, encoding a putative polyphosphate kinase, is induced by phosphate starvation. Geissdorfer W, Ratajczak A, Hillen W;. Appl Environ Microbiol 1998;64:896-901. (from Pfam) NF014557.5 PF02508.19 Rnf-Nqr 23.8 23.8 174 domain Y Y N Rnf-Nqr domain containing protein GO:0016020 9492268 131567 cellular organisms no rank 41874 EBI-EMBL Rnf-Nqr subunit, membrane protein Rnf-Nqr subunit, membrane protein This is a family of integral membrane proteins including Rhodobacter-specific nitrogen fixation (rnf) proteins RnfA and RnfE [1] and Na+-translocating NADH:ubiquinone oxidoreductase (Na+-NQR) subunits NqrD and NqrE. [1]. 9492268. Overexpression in Escherichia coli of the rnf genes from Rhodobacter capsulatus--characterization of two membrane-bound iron-sulfur proteins. Jouanneau Y, Jeong HS, Hugo N, Meyer C, Willison JC;. Eur J Biochem 1998;251:54-64. (from Pfam) NF014560.5 PF02511.20 Thy1 24.8 24.8 191 PfamEq Y Y N FAD-dependent thymidylate synthase 2.1.1.148 GO:0006231,GO:0050660,GO:0050797 12029065,15046578,17890305,9665876 131567 cellular organisms no rank 20704 EBI-EMBL Thymidylate synthase complementing protein FAD-dependent thymidylate synthase Thymidylate synthase complementing protein (Thy1) complements the thymidine growth requirement of the organisms in which it is found, but shows no homology to thymidylate synthase. The bacterial members of this family at least are flavin-dependent thymidylate synthases [2,3,4]. [1]. 9665876. Complete genome sequence of Treponema pallidum, the syphilis spirochete [see comments]. Fraser CM, Norris SJ, Weinstock GM, White O, Sutton GG, Dodson R, Gwinn M, Hickey EK, Clayton R, Ketchum KA, Sodergren E, Hardham JM, McLeod MP, Salzberg S, Peterson J, Khalak H, Richardson D, Howell JK, Chidambaram M, Utterback T, McDonald L, Artiach P,. Science 1998;281:375-388. [2]. 12029065. An alternative flavin-dependent mechanism for thymidylate synthesis. Myllykallio H, Lipowski G, Leduc D, Filee J, Forterre P, Liebl U;. Science. 2002;297:105-107. [3]. 15046578. Two distinct pathways for thymidylate (dTMP) synthesis in (hyper)thermophilic Bacteria and Archaea. Leduc D, Graziani S, Meslet-Cladiere L, Sodolescu A, Liebl U, Myllykallio H;. Biochem Soc Trans. 2004;32:231-235. [4]. 17890305. Flavin-dependent thymidylate synthase ThyX activity: implications for the folate cycle in bacteria. Leduc D, Escartin F, Nijhout HF, Reed MC, Liebl U, Skouloubris S, Myllykallio H;. J Bacteriol. 2007;189:8537-8545. (from Pfam) NF014563.5 PF02514.21 CobN-Mg_chel 24.5 24.5 1090 domain Y Y N cobaltochelatase subunit CobN 6.6.1.2 GO:0009058 1655697,8404842 131567 cellular organisms no rank 47501 EBI-EMBL CobN/Magnesium Chelatase cobaltochelatase subunit CobN This family contains a domain common to the cobN protein and to magnesium protoporphyrin chelatase. CobN is implicated in the conversion of hydrogenobyrinic acid a,c-diamide to cobyrinic acid [1]. Magnesium protoporphyrin chelatase is involved in chlorophyll biosynthesis [2]. [1]. 1655697. Nucleotide sequence and genetic analysis of a 13.1-kilobase-pair Pseudomonas denitrificans DNA fragment containing five cob genes and identification of structural genes encoding Cob(I)alamin adenosyltransferase, cobyric acid synthase, and bifunctional cob. Crouzet J, Levy-Schil S, Cameron B, Cauchois L, Rigault S, Rouyez MC, Blanche F, Debussche L, Thibaut D;. J Bacteriol 1991;173:6074-6087. [2]. 8404842. Olive: a key gene required for chlorophyll biosynthesis in Antirrhinum majus. Hudson A, Carpenter R, Doyle S, Coen ES;. EMBO J 1993;12:3711-3719. (from Pfam) NF014564.5 PF02515.22 CoA_transf_3 23.3 23.3 366 domain Y Y N CoA transferase GO:0003824,GO:0008410 11749953 131567 cellular organisms no rank 265484 EBI-EMBL CoA-transferase family III CoA transferase CoA-transferases are found in organisms from all lines of descent. Most of these enzymes belong to two well-known enzyme families, but recent work on unusual biochemical pathways of anaerobic bacteria has revealed the existence of a third family of CoA-transferases. The members of this enzyme family differ in sequence and reaction mechanism from CoA-transferases of the other families. Currently known enzymes of the new family are a formyl-CoA: oxalate CoA-transferase, a succinyl-CoA: (R)-benzylsuccinate CoA-transferase, an (E)-cinnamoyl-CoA: (R)-phenyllactate CoA-transferase, and a butyrobetainyl-CoA: (R)-carnitine CoA-transferase. In addition, a large number of proteins of unknown or differently annotated function from Bacteria, Archaea and Eukarya apparently belong to this enzyme family. Properties and reaction mechanisms of the CoA-transferases of family III are described and compared to those of the previously known CoA-transferases. [1]. 11749953. A new family of CoA-transferases. Heider J;. FEBS Lett 2001;509:345-349. (from Pfam) NF014565.5 PF02516.19 STT3 24.5 24.5 405 domain Y Y N STT3 domain-containing protein GO:0004576,GO:0006486,GO:0016020 17996897,18046457,7588624,8838310 131567 cellular organisms no rank 4472 EBI-EMBL Oligosaccharyl transferase STT3, N-terminal Oligosaccharyl transferase STT3, N-terminal This entry consists of the oligosaccharyl transferase STT3 subunit and related proteins. The STT3 subunit is part of the oligosaccharyl transferase (OTase) complex of proteins and is required for its activity [2]. In eukaryotes, OTase transfers a lipid-linked core-oligosaccharide to selected asparagine residues in the ER [2]. In the archaea STT3 occurs alone, rather than in an OTase complex, and is required for N-glycosylation of asparagines [3-4]. This entry represents the N-terminal domain, consisting of transmembrane helices. [1]. 8838310. Molecular cloning of a highly conserved mouse and human integral membrane protein (Itm1) and genetic mapping to mouse chromosome 9. Hong G, Deleersnijder W, Kozak CA, Van Marck E, Tylzanowski P, Merregaert J;. Genomics 1996;31:295-300. [2]. 7588624. STT3, a highly conserved protein required for yeast oligosaccharyl transferase activity in vivo. Zufferey R, Knauer R, Burda P, Stagljar I, te Heesen S, Lehle L, Aebi M;. EMBO J 1995;14:4949-4960. [3]. 17996897. Haloferax volcanii AglB and AglD are involved in N-glycosylation of the S-layer glycoprotein and proper assembly of the surface layer. Abu-Qarn M, Yurist-Doutsch S, Giordano A, Trauner A, Morris HR, Hitchen P, Medalia O, Dell A, Eichler J;. J Mol Biol. 2007;374:1224-1236. [4]. 18046457. Structure-guided identification of a new catalytic motif of oligosaccharyltransferase. Igura M, Maita N, Kamishikiryo J, Yamada M, Obita T, Maenaka K, Kohda D;. EMBO J. 2008;27:234-243. (from Pfam) NF014566.5 PF02517.21 Rce1-like 22.4 22.4 93 domain Y Y N type II CAAX prenyl endopeptidase Rce1 family protein 3.4.26.- GO:0016020,GO:0070007 16361710,20154137,24291792,29424242 131567 cellular organisms no rank 220159 EBI-EMBL Type II CAAX prenyl endopeptidase Rce1-like CPBP family glutamic-type intramembrane protease This family (also known as the ABI (abortive infection) family) contains putative IMPs and has homologues in all three domains of life, including Rce1 from S. cerevisiae [1]. Rce1 is a type II CAAX prenyl protease that processes all farnesylated and geranylgeranylated CAAX proteins. It is an integral membrane endoprotease localized to the endoplasmic reticulum that mediates the cleavage of the carboxyl-terminal three amino acids from CaaX proteins. It is involved in processing the Ras family of small GTPases, the gamma-subunit of heterotrimeric GTPases, nuclear lamins, and protein kinases and phosphatases [2]. Three residues of S. cerevisiae Rce1 -E156, H194 and H248- are critical for catalysis [3]. The structure of Rce1 from the archaea Methanococcus (MmRce1) suggests that this group of proteins represents a novel IMP (intramembrane protease) family, the glutamate IMPs [4]. There is a conserved sequence motif EExxxR. [1]. 20154137. The abi proteins and their involvement in bacteriocin self-immunity. Kjos M, Snipen L, Salehian Z, Nes IF, Diep DB;. J Bacteriol. 2010;192:2068-2076. [2]. 29424242. Rce1: mechanism and inhibition. Hampton SE, Dore TM, Schmidt WK;. Crit Rev Biochem Mol Biol. 2018;53:157-174. [3]. 16361710. Mutational analysis of the ras converting enzyme reveals a requirement for glutamate and histidine residues. Plummer LJ, Hildebrandt ER, Porter SB, Rogers VA, McCracken J, Schmidt WK;. J Biol Chem. 2006;281:4596-4605. [4]. 24291792. Mechanism of farnesylated CAAX protein processing by the intramembrane protease Rce1. Manolaridis I, Kulkarni K, Dodd RB, Ogasawara S, Zhang Z, Bineva G, Reilly NO, Hanrahan SJ, Th. TRUNCATED at 1650 bytes (from Pfam) NF014567.5 PF02518.31 HATPase_c 26.4 26.4 111 domain Y Y N ATP-binding protein 18361456 131567 cellular organisms no rank 3728214 EBI-EMBL Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ATP-binding protein This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90. [1]. 18361456. Crystal structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source. Li Y, Bahti P, Shaw N, Song G, Chen S, Zhang X, Zhang M, Cheng C, Yin J, Zhu JY, Zhang H, Che D, Xu H, Abbas A, Wang BC, Liu ZJ;. Proteins 2008;71:2109-13. (from Pfam) NF014571.5 PF02522.19 Antibiotic_NAT 25 25 232 domain Y Y N AAC(3) family N-acetyltransferase GO:0046353,GO:0046677 1761222,2060791,21601576 131567 cellular organisms no rank 18652 EBI-EMBL Aminoglycoside 3-N-acetyltransferase AAC(3) family N-acetyltransferase This family consists of bacterial aminoglycoside 3-N-acetyltransferases EC:2.3.1.81, these catalyse the reaction: Acetyl-Co + a 2-deoxystreptamine antibiotic CoA + N3'-acetyl-2-deoxystreptamine antibiotic. The enzyme can use a range of antibiotics with 2-deoxystreptamine rings as acceptor for its acetyltransferase activity, this inactivates and confers resistance to gentamicin, kanamycin, tobramycin, neomycin and apramycin amongst others. [1]. 1761222. Nucleotide sequence and transcriptional start point of the kan gene encoding an aminoglycoside 3-N-acetyltransferase from Streptomyces griseus SS-1198PR. Ishikawa J, Hotta K;. Gene 1991;108:127-132. [2]. 2060791. Characterisation of aminoglycoside acetyltransferase-encoding genes of neomycin-producing Micromonospora chalcea and Streptomyces fradiae. Salauze D, Perez-Gonzalez JA, Piepersberg W, Davies J;. Gene 1991;101:143-148. [3]. 21601576. Structural analysis of a putative aminoglycoside N-acetyltransferase from Bacillus anthracis. Klimecka MM, Chruszcz M, Font J, Skarina T, Shumilin I, Onopryienko O, Porebski PJ, Cymborowski M, Zimmerman MD, Hasseman J, Glomski IJ, Lebioda L, Savchenko A, Edwards A, Minor W;. J Mol Biol. 2011;410:411-423. (from Pfam) NF014573.5 PF02525.22 Flavodoxin_2 27 27 198 domain Y Y N NAD(P)H-dependent oxidoreductase 2168383,7568029 131567 cellular organisms no rank 291913 EBI-EMBL Flavodoxin-like fold NAD(P)H-dependent oxidoreductase This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyse the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species [1]. This enzyme uses a FAD co-factor. The equation for this reaction is:- NAD(P)H + acceptor NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy [1]. The family also includes acyl carrier protein phosphodiesterase EC:3.1.4.14. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP [2]. This family is related to Pfam:PF03358 and Pfam:PF00258. [1]. 7568029. The three-dimensional structure of NAD(P)H:quinone reductase, a flavoprotein involved in cancer chemoprotection and chemotherapy: mechanism of the two-electron reduction. Li R, Bianchet MA, Talalay P, Amzel LM;. Proc Natl Acad Sci U S A 1995;92:8846-8850. [2]. 2168383. Isolation and properties of acyl carrier protein phosphodiesterase of Escherichia coli. Fischl AS, Kennedy EP;. J Bacteriol 1990;172:5445-5449. (from Pfam) NF014575.5 PF02527.20 GidB 27 27 184 domain Y Y N RsmG family class I SAM-dependent methyltransferase 2.1.1.- GO:0005737,GO:0006364,GO:0008649 12001236,17238915,17573471,9795152 131567 cellular organisms no rank 71367 EBI-EMBL rRNA small subunit methyltransferase G RsmG family class I SAM-dependent methyltransferase Most member of this methyltransferase family are the 16S RNA G527 methyltransferase RsmG, previously known as GidB (glucose inhibited division protein B). NF014581.5 PF02534.19 T4SS-DNA_transf 20.1 20.1 468 domain Y Y N type IV secretory system conjugative DNA transfer family protein GO:0016020 11976307,17259614,18717787,9767571 131567 cellular organisms no rank 101359 EBI-EMBL Type IV secretory system Conjugative DNA transfer type IV secretory system conjugative DNA transfer family protein These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems [2]. The C-terminus of this domain interacts with the relaxosome component TraM via the latter's tetramerisation domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore [3]. The family contains a number of different DNA transfer proteins [4]. [1]. 9767571. Sequence and analysis of the 60 kb conjugative, bacteriocin-producing plasmid pMRC01 from Lactococcus lactis DPC3147. Dougherty BA, Hill C, Weidman JF, Richardson DR, Venter JC, Ross RP;. Mol Microbiol 1998;29:1029-1038. [2]. 11976307. TraG-like proteins of DNA transfer systems and of the Helicobacter pylori type IV secretion system: inner membrane gate for exported substrates?. Schroder G, Krause S, Zechner EL, Traxler B, Yeo HJ, Lurz R, Waksman G, Lanka E;. J Bacteriol 2002;184:2767-2779. [3]. 18717787. Structural basis of specific TraD-TraM recognition during F plasmid-mediated bacterial conjugation. Lu J, Wong JJ, Edwards RA, Manchak J, Frost LS, Glover JN;. Mol Microbiol. 2008;70:89-99. [4]. 17259614. Interaction between the co-inherited TraG coupling protein and the TraJ membrane-associated protein of the H-plasmid conjugative DNA transfer system resembles chromosomal DNA translocases. Gunton JE, Gilmour MW, Baptista KP, Lawley TD, Taylor DE;. Microbiology. 2007;153:428-441. (from Pfam) NF014582.5 PF02535.27 Zip 35.1 35.1 323 domain Y Y N ZIP family metal transporter GO:0016020,GO:0055085 9618566 131567 cellular organisms no rank 40646 EBI-EMBL ZIP Zinc transporter ZIP family metal transporter The ZIP family consists of zinc transport proteins and many putative metal transporters. The main contribution to this family is from the Arabidopsis thaliana ZIP protein family these proteins are responsible for zinc uptake in the plant [1]. Also found within this family are C. elegans proteins of unknown function which are annotated as being similar to human growth arrest inducible gene product, although this protein in not found within this family. [1]. 9618566. Identification of a family of zinc transporter genes from Arabidopsis that respond to zinc deficiency. Grotz N, Fox T, Connolly E, Park W, Guerinot ML, Eide D;. Proc Natl Acad Sci U S A 1998;95:7220-7224. (from Pfam) NF014584.5 PF02537.20 CRCB 32.9 32.9 103 domain Y Y N CrcB family protein GO:0016020 12904550,8844142 131567 cellular organisms no rank 85869 EBI-EMBL CrcB-like protein, Camphor Resistance (CrcB) CrcB family protein CRCB is a family of bacterial integral membrane proteins with four TMs.. Over expression in E. coli also leads to camphor resistance [1,2]. [1]. 8844142. Overproduction of three genes leads to camphor resistance and chromosome condensation in Escherichia coli. Hu KH, Liu E, Dean K, Gingras M, DeGraff W, Trun NJ;. Genetics 1996;143:1521-1532. [2]. 12904550. Phenotypic characterization of overexpression or deletion of the Escherichia coli crcA, cspE and crcB genes. Sand O, Gingras M, Beck N, Hall C, Trun N;. Microbiology. 2003;149:2107-2117. (from Pfam) NF014585.5 PF02538.19 Hydantoinase_B 26.8 26.8 519 domain Y Y N hydantoinase B/oxoprolinase family protein GO:0003824 1732229 131567 cellular organisms no rank 50471 EBI-EMBL Hydantoinase B/oxoprolinase hydantoinase B/oxoprolinase family protein This family includes N-methylhydaintoinase B which converts hydantoin to N-carbamyl-amino acids, and 5-oxoprolinase (Swiss:P97608) EC:3.5.2.9 which catalyses the formation of L-glutamate from 5-oxo-L-proline. These enzymes are part of the oxoprolinase family and are related to Pfam:PF01968. [1]. 1732229. Cloning and sequencing of the genes involved in the conversion of 5-substituted hydantoins to the corresponding L-amino acids from the native plasmid of Pseudomonas sp. strain NS671. Watabe K, Ishikawa T, Mukohara Y, Nakamura H;. J Bacteriol 1992;174:962-969. (from Pfam) NF014586.5 PF02540.22 NAD_synthase 21 21 242 domain Y N N NAD synthase 8895556 131567 cellular organisms no rank 211015 EBI-EMBL NAD synthase NAD synthase NAD synthase (EC:6.3.5.1) is involved in the de novo synthesis of NAD and is induced by stress factors such as heat shock and glucose limitation. [1]. 8895556. Crystal structure of NH3-dependent NAD+ synthetase from Bacillus subtilis. Rizzi M, Nessi C, Mattevi A, Coda A, Bolognesi M, Galizzi A;. EMBO J 1996;15:5125-5134. (from Pfam) NF014587.5 PF02541.21 Ppx-GppA 27 27 285 domain Y N N Ppx/GppA phosphatase family 8212131 131567 cellular organisms no rank 101717 EBI-EMBL Ppx/GppA phosphatase family Ppx/GppA phosphatase family This family consists of the N-terminal region of exopolyphosphatase (Ppx) EC:3.6.1.11 and guanosine pentaphosphate phospho-hydrolase (GppA) EC:3.6.1.40. [1]. 8212131. Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp 70 superfamily. Reizer J, Reizer A, Saier MH Jr, Bork P, Sander C;. Trends Biochem Sci 1993;18:247-248. (from Pfam) NF014589.5 PF02543.20 Carbam_trans_N 24 24 346 domain Y Y N carbamoyltransferase N-terminal domain-containing protein GO:0003824,GO:0009058 22383337,7557411,7559434 131567 cellular organisms no rank 31390 EBI-EMBL Carbamoyltransferase N-terminus Carbamoyltransferase N-terminus This domain is found in NodU from Rhizobium, CmcH from Nocardia lactamdurans and the bifunctional carbamoyltransferase TobZ from Streptoalloteichus tenebrarius. NodU a Rhizobium nodulation protein involved in the synthesis of nodulation factors has 6-O-carbamoyltransferase-like activity [1]. CmcH is involved in cephamycin (antibiotic) biosynthesis and has 3-hydroxymethylcephem carbamoyltransferase activity [2], EC:2.1.3.7 catalysing the reaction: Carbamoyl phosphate + 3-hydroxymethylceph-3-EM-4-carboxylate phosphate + 3-carbamoyloxymethylcephem. TobZ functions as an ATP carbamoyltransferase and tobramycin carbamoyltransferase [3]. These proteins contain two domains, this is the larger, N-terminal, domain. [1]. 7559434. Involvement of nodS in N-methylation and nodU in 6-O-carbamoylation of Rhizobium sp. NGR234 nod factors. Jabbouri S, Fellay R, Talmont F, Kamalaprija P, Burger U, Relic B, Prome JC, Broughton WJ;. J Biol Chem 1995;270:22968-22973. [2]. 7557411. Characterization of the cmcH genes of Nocardia lactamdurans and Streptomyces clavuligerus encoding a functional 3'-hydroxymethylcephem O-carbamoyltransferase for cephamycin biosynthesis. Coque JJ, Perez-Llarena FJ, Enguita FJ, Fuente JL, Martin JF, Liras P;. Gene 1995;162:21-27. [3]. 22383337. The O-carbamoyltransferase TobZ catalyzes an ancient enzymatic reaction. Parthier C, Gorlich S, Jaenecke F, Breithaupt C, Brauer U, Fandrich U, Clausnitzer D, Wehmeier UF, Bottcher C, Scheel D, Stubbs MT;. Angew Chem Int Ed Engl. 2012;51:4046-4052. (from Pfam) NF014590.5 PF02544.21 Steroid_dh 22.6 22.6 150 domain Y N N 3-oxo-5-alpha-steroid 4-dehydrogenase GO:0006629,GO:0016627 1686016,1944596,8602526 131567 cellular organisms no rank 15720 EBI-EMBL 3-oxo-5-alpha-steroid 4-dehydrogenase 3-oxo-5-alpha-steroid 4-dehydrogenase This family consists of 3-oxo-5-alpha-steroid 4-dehydrogenases, EC:1.3.99.5 Also known as Steroid 5-alpha-reductase, the reaction catalysed by this enzyme is: 3-oxo-5-alpha-steroid + acceptor 3-oxo-delta(4)-steroid + reduced acceptor. The Steroid 5-alpha-reductase enzyme is responsible for the formation of dihydrotestosterone, this hormone promotes the differentiation of male external genitalia and the prostate during fetal development [2]. In humans mutations in this enzyme can cause a form of male pseudohermaphorditism in which the external genitalia and prostate fail to develop normally [2]. A related enzyme is also found in plants is Swiss:Q38944 (DET2) a steroid reductase from Arabidopsis. Mutations in this enzyme cause defects in light-regulated development [1]. [1]. 8602526. A role for brassinosteroids in light-dependent development of Arabidopsis. Li J, Nagpal P, Vitart V, McMorris TC, Chory J;. Science 1996;272:398-401. [2]. 1686016. Characterization and chromosomal mapping of a human steroid 5 alpha-reductase gene and pseudogene and mapping of the mouse homologue. Jenkins EP, Hsieh CL, Milatovich A, Normington K, Berman DM, Francke U, Russell DW;. Genomics 1991;11:1102-1112. [3]. 1944596. Deletion of steroid 5 alpha-reductase 2 gene in male pseudohermaphroditism. Andersson S, Berman DM, Jenkins EP, Russell DW;. Nature 1991;354:159-161. (from Pfam) NF014591.5 PF02545.19 Maf 27 27 187 domain Y Y N Maf family protein GO:0047429 1400224,8387996 131567 cellular organisms no rank 92629 EBI-EMBL Maf-like protein Maf family protein Maf is a putative inhibitor of septum formation [1] in eukaryotes, bacteria, and archaea. [1]. 8387996. Amplification of the Bacillus subtilis maf gene results in arrested septum formation. Butler YX, Abhayawardhane Y, Stewart GC;. J Bacteriol 1993;175:3139-3145. [2]. 1400224. Identification of Bacillus subtilis genes for septum placement and shape determination. Levin PA, Margolis PS, Setlow P, Losick R, Sun D;. J Bacteriol 1992;174:6717-6728. (from Pfam) NF014592.5 PF02547.20 Queuosine_synth 25 25 322 domain Y Y N S-adenosylmethionine:tRNA ribosyltransferase-isomerase GO:0016740,GO:0016853 12731872,18552185,8347586 131567 cellular organisms no rank 69094 EBI-EMBL Queuosine biosynthesis protein S-adenosylmethionine:tRNA ribosyltransferase-isomerase Queuosine (Q) biosynthesis protein, or S-adenosylmethionine:tRNA -ribosyltransferase-isomerase, is required for the synthesis of the queuosine precursor (oQ). It catalyses the transfer and isomerisation of the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to form epoxyqueuosine (oQ-tRNA). Q is a hypermodified nucleoside usually found at the first position of the anticodon of asparagine, aspartate, histidine, and tyrosine tRNAs [1,2]. In Streptococcus gordonii , QueA has been shown to play a role in the regulation of arginine deiminase genes [3]. [1]. 8347586. A new function of S-adenosylmethionine: the ribosyl moiety of AdoMet is the precursor of the cyclopentenediol moiety of the tRNA wobble base queuine. Slany RK, Bosl M, Crain PF, Kersten H;. Biochemistry 1993;32:7811-7817. [2]. 12731872. Kinetic mechanism of the tRNA-modifying enzyme S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA). Van Lanen SG, Iwata-Reuyl D;. Biochemistry. 2003;42:5312-5320. [3]. 18552185. Environmental and growth phase regulation of the Streptococcus gordonii arginine deiminase genes. Liu Y, Dong Y, Chen YY, Burne RA;. Appl Environ Microbiol. 2008;74:5023-5030. (from Pfam) NF014593.5 PF02548.20 Pantoate_transf 28.7 28.7 259 domain Y Y N 3-methyl-2-oxobutanoate hydroxymethyltransferase 2.1.2.11 GO:0003864,GO:0015940 8096212 131567 cellular organisms no rank 60849 EBI-EMBL Ketopantoate hydroxymethyltransferase 3-methyl-2-oxobutanoate hydroxymethyltransferase Ketopantoate hydroxymethyltransferase (EC:2.1.2.11) is the first enzyme in the pantothenate biosynthesis pathway. [1]. 8096212. Cloning and sequencing of the Escherichia coli panB gene, which encodes ketopantoate hydroxymethyltransferase, and overexpression of the enzyme. Jones CE, Brook JM, Buck D, Abell C, Smith AG;. J Bacteriol 1993;175:2125-2130. (from Pfam) NF014594.5 PF02550.20 AcetylCoA_hydro 24 24 198 domain Y N N Acetyl-CoA hydrolase/transferase N-terminal domain GO:0008775 1441754,8550525 131567 cellular organisms no rank 32341 EBI-EMBL Acetyl-CoA hydrolase/transferase N-terminal domain Acetyl-CoA hydrolase/transferase N-terminal domain This family contains several enzymes which take part in pathways involving acetyl-CoA. Acetyl-CoA hydrolase EC:3.1.2.1 (Swiss:P32316) catalyses the formation of acetate from acetyl-CoA, CoA transferase (CAT1) EC:2.8.3.- (Swiss:P38946) produces succinyl-CoA, and acetate-CoA transferase EC:2.8.3.8 (Swiss:Q59323) utilises acyl-CoA and acetate to form acetyl-CoA. [1]. 1441754. An 11.4 kb DNA segment on the left arm of yeast chromosome II carries the carboxypeptidase Y sorting gene PEP1, as well as ACH1, FUS3 and a putative ARS. Van Dyck L, Purnelle B, Skala J, Goffeau A;. Yeast 1992;8:769-776. [2]. 8550525. Molecular analysis of the anaerobic succinate degradation pathway in Clostridium kluyveri. Sohling B, Gottschalk G;. J Bacteriol 1996;178:871-880. (from Pfam) NF014596.5 PF02552.21 CO_dh 21 21 168 domain Y Y N carbon monoxide dehydrogenase beta subunit family protein GO:0019385 8550451,8662887 131567 cellular organisms no rank 2925 EBI-EMBL CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit carbon monoxide dehydrogenase beta subunit family protein This family consists of Carbon monoxide dehydrogenase I/II beta subunit EC:1.2.99.2 and acetyl-CoA synthase epsilon subunit. Carbon monoxide beta subunit catalyses the reaction: CO + H2O + acceptor CO2 + reduced acceptor. [1]. 8662887. Carbon monoxide dehydrogenase from Methanosarcina frisia Go1. Characterization of the enzyme and the regulated expression of two operon-like cdh gene clusters. Eggen RIL, van Kranenburg R, Vriesema AJ, Geerling AC, Verhagen MF, Hagen WR, de Vos WM;. J Biol Chem 1996;271:14256-14263. [2]. 8550451. Characterization of the cdhD and cdhE genes encoding subunits of the corrinoid/iron-sulfur enzyme of the CO dehydrogenase complex from Methanosarcina thermophila. Maupin-Furlow J, Ferry JG;. J Bacteriol 1996;178:340-346. (from Pfam) NF014597.5 PF02553.20 CbiN 25 25 67 PfamEq Y Y N energy-coupling factor ABC transporter substrate-binding protein GO:0006824,GO:0009236,GO:0015087,GO:0016020 8501034 131567 cellular organisms no rank 6079 EBI-EMBL Cobalt transport protein component CbiN energy-coupling factor ABC transporter substrate-binding protein CbiN is part of the active cobalt transport system involved in uptake of cobalt in to the cell involved with cobalamin biosynthesis (vitamin B12). It has been suggested that CbiN may function as the periplasmic binding protein component of the active cobalt transport system [1]. [1]. 8501034. Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM;. J Bacteriol 1993;175:3303-3316. (from Pfam) NF014598.5 PF02554.19 CstA 27 27 560 domain Y Y N carbon starvation CstA family protein GO:0009267,GO:0016020 12867454,1848300,29358499 131567 cellular organisms no rank 53335 EBI-EMBL Carbon starvation protein CstA carbon starvation CstA family protein This family consists of Carbon starvation protein CstA a predicted membrane protein. It has been suggested that CstA is involved in peptide utilisation [1]. [1]. 1848300. Molecular and functional characterization of a carbon starvation gene of Escherichia coli. Schultz JE, Matin A;. J Mol Biol 1991;218:129-140. [2]. 12867454. CsrA regulates translation of the Escherichia coli carbon starvation gene, cstA, by blocking ribosome access to the cstA transcript. Dubey AK, Baker CS, Suzuki K, Jones AD, Pandit P, Romeo T, Babitzke P;. J Bacteriol. 2003;185:4450-4460. [3]. 29358499. Peptide Transporter CstA Imports Pyruvate in Escherichia coli K-12. Hwang S, Choe D, Yoo M, Cho S, Kim SC, Cho S, Cho BK;. J Bacteriol. 2018;200:e00771-e00717. (from Pfam) NF014599.5 PF02556.19 SecB 26 26 141 PfamEq Y Y N protein-export chaperone SecB GO:0015031,GO:0051082,GO:0051262 2656409 131567 cellular organisms no rank 17578 EBI-EMBL Preprotein translocase subunit SecB protein-export chaperone SecB This family consists of preprotein translocase subunit SecB. SecB is required for the normal export of envelope proteins out of the cell cytoplasm [1]. [1]. 2656409. Characterization of the Escherichia coli protein-export gene secB. Kumamoto CA, Nault AK;. Gene 1989;75:167-175. (from Pfam) NF014601.5 PF02558.21 ApbA 22.2 22.2 150 domain Y Y N 2-dehydropantoate 2-reductase N-terminal domain-containing protein 9488683,9721324 131567 cellular organisms no rank 245395 EBI-EMBL Ketopantoate reductase PanE/ApbA Ketopantoate reductase PanE/ApbA This is a family of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, EC:1.1.1.169. The reaction catalysed by this enzyme is: (R)-pantoate + NADP(+) 2-dehydropantoate + NADPH. AbpA catalyses the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway [2]. ApbA and PanE are allelic [2]. ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway [1]. [1]. 9488683. ApbA, the ketopantoate reductase enzyme of Salmonella typhimurium is required for the synthesis of thiamine via the alternative pyrimidine biosynthetic pathway. Frodyma ME, Downs D;. J Biol Chem 1998;273:5572-5576. [2]. 9721324. The panE gene, encoding ketopantoate reductase, maps at 10 minutes and is allelic to apbA in Salmonella typhimurium. Frodyma ME, Downs D;. J Bacteriol 1998;180:4757-4759. (from Pfam) NF014603.5 PF02560.19 Cyanate_lyase 25 25 69 domain Y N N Cyanate lyase C-terminal domain GO:0009439 10801492,3049588 131567 cellular organisms no rank 10593 EBI-EMBL Cyanate lyase C-terminal domain Cyanate lyase C-terminal domain Cyanate lyase (also known as cyanase) EC:4.2.1.104 is responsible for the hydrolysis of cyanate, allowing organisms that possess the enzyme to overcome the toxicity of environmental cyanate. This enzyme is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain [2]. [1]. 3049588. Characterization of the cyn operon in Escherichia coli K12. Sung YC, Fuchs JA;. J Biol Chem 1988;263:14769-14775. [2]. 10801492. Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site. Walsh MA, Otwinowski Z, Perrakis A, Anderson PM, Joachimiak A;. Structure Fold Des 2000;8:505-514. (from Pfam) NF014605.5 PF02562.21 PhoH 27 27 205 domain Y Y N PhoH family protein GO:0005524 8444794 131567 cellular organisms no rank 90176 EBI-EMBL PhoH-like protein PhoH family protein PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation. [1]. 8444794. Molecular analysis of the phoH gene, belonging to the phosphate regulon in Escherichia coli. Kim SK, Makino K, Amemura M, Shinagawa H, Nakata A;. J Bacteriol 1993;175:1316-1324. (from Pfam) NF014608.5 PF02566.24 OsmC 27.5 27.5 100 domain Y Y N OsmC family protein 9573147 131567 cellular organisms no rank 167223 EBI-EMBL OsmC-like protein OsmC family protein Osmotically inducible protein C (OsmC) (Swiss:P23929) is a stress -induced protein found in E. Coli. This family also contains a organic hydroperoxide detoxification protein (Swiss:O68390) that has a novel pattern of oxidative stress regulation [1]. [1]. 9573147. Identification and characterization of a new organic hydroperoxide resistance (ohr) gene with a novel pattern of oxidative stress regulation from Xanthomonas campestris pv. phaseoli. Mongkolsuk S, Praituan W, Loprasert S, Fuangthong M, Chamnongpol S;. J Bacteriol 1998;180:2636-2643. (from Pfam) NF014609.5 PF02567.21 PhzC-PhzF 27 27 281 domain Y Y N PhzF family phenazine biosynthesis protein GO:0003824,GO:0009058 11562236 131567 cellular organisms no rank 109318 EBI-EMBL Phenazine biosynthesis-like protein PhzF family phenazine biosynthesis protein PhzC/PhzF is involved in dimerisation of two 2,3-dihydro-3-oxo-anthranilic acid molecules to create PCA by P. fluorescens [1]. This family also contains Swiss:P28176, though there is no significant sequence similarity to Pfam:PF00303 members. This family appears to be distantly related to Pfam:PF01678, including containing a weak internal duplication. However members of this family do not contain the conserved cysteines that are hypothesised to be active site residues (Bateman A pers obs). [1]. 11562236. Phenazine biosynthesis in Pseudomonas fluorescens: branchpoint from the primary shikimate biosynthetic pathway and role of phenazine-1,6-dicarboxylic acid. McDonald M, Mavrodi DV, Thomashow LS, Floss HG;. J Am Chem Soc 2001;123:9459-9460. (from Pfam) NF014610.5 PF02568.19 ThiI 20.5 20.5 197 domain Y N N Thiamine biosynthesis protein (ThiI) GO:0004810 9209060 131567 cellular organisms no rank 60887 EBI-EMBL Thiamine biosynthesis protein (ThiI) Thiamine biosynthesis protein (ThiI) ThiI is required for thiazole synthesis, required for thiamine biosynthesis [1]. [1]. 9209060. Characterization of thiI, a new gene involved in thiazole biosynthesis in Salmonella typhimurium. Webb E, Claas K, Downs DM;. J Bacteriol 1997;179:4399-4402. (from Pfam) NF014611.5 PF02569.20 Pantoate_ligase 20.7 20.7 268 PfamEq Y Y N pantoate--beta-alanine ligase GO:0004592,GO:0015940 374975 131567 cellular organisms no rank 66096 EBI-EMBL Pantoate-beta-alanine ligase pantoate--beta-alanine ligase Pantoate-beta-alanine ligase, also know as pantothenate synthase, (EC:6.3.2.1) catalyses the formation of pantothenate from pantoate and alanine [1]. [1]. 374975. Pantothenate synthetase from Escherichia coli [D-pantoate: beta-alanine ligase (AMP-forming), EC 6.3.2.1]. Miyatake K, Nakano Y, Kitaoka S;. Methods Enzymol 1979;62:215-219. (from Pfam) NF014612.5 PF02570.20 CbiC 22.5 22.5 196 PfamEq Y Y N precorrin-8X methylmutase 5.4.99.61 GO:0009236,GO:0016993 8501034,9742225 131567 cellular organisms no rank 31075 EBI-EMBL Precorrin-8X methylmutase precorrin-8X methylmutase This is a family Precorrin-8X methylmutases also known as Precorrin isomerase, CbiC/CobH, EC:5.4.1.2. This enzyme catalyses the reaction: Precorrin-8X hydrogenobyrinate. This enzyme is part of the Cobalamin (vitamin B12) biosynthetic pathway and catalyses a methyl rearrangement [1,2]. [1]. 9742225. Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon. Raux E, Lanois A, Warren MJ, Rambach A, Thermes C;. Biochem J 1998;335:159-166. [2]. 8501034. Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM;. J Bacteriol 1993;175:3303-3316. (from Pfam) NF014613.5 PF02571.19 CbiJ 28.6 28.6 234 PfamEq Y Y N precorrin-6A/cobalt-precorrin-6A reductase 1.3.1.106 GO:0009236,GO:0016994 8501034,9742225 131567 cellular organisms no rank 36468 EBI-EMBL Precorrin-6x reductase CbiJ/CobK precorrin-6A/cobalt-precorrin-6A reductase This family consists of Precorrin-6x reductase EC:1.3.1.54. This enzyme catalyses the reaction: precorrin-6Y + NADP(+) precorrin-6X + NADPH. CbiJ and CobK both catalyse the reduction of macocycle in the colbalmin biosynthesis pathway [1,2]. [1]. 9742225. Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon. Raux E, Lanois A, Warren MJ, Rambach A, Thermes C;. Biochem J 1998;335:159-166. [2]. 8501034. Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM;. J Bacteriol 1993;175:3303-3316. (from Pfam) NF014614.5 PF02572.20 CobA_CobO_BtuR 25.7 25.7 172 domain Y Y N cob(I)yrinic acid a,c-diamide adenosyltransferase 2.5.1.17 GO:0005524,GO:0008817,GO:0009236 9742225 131567 cellular organisms no rank 37027 EBI-EMBL ATP:corrinoid adenosyltransferase BtuR/CobO/CobP cob(I)yrinic acid a,c-diamide adenosyltransferase This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin adenosyltransferase, EC:2.5.1.17, involved in cobalamin (vitamin B12) biosynthesis. These enzymes catalyse the adenosylation reaction: ATP + cob(I)alamin + H2O phosphate + diphosphate + adenosylcobalamin. [1]. 9742225. Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon. Raux E, Lanois A, Warren MJ, Rambach A, Thermes C;. Biochem J 1998;335:159-166. (from Pfam) NF014615.5 PF02574.21 S-methyl_trans 22 22 283 domain Y Y N homocysteine S-methyltransferase family protein 8798461,9013615,9882684 131567 cellular organisms no rank 120712 EBI-EMBL Homocysteine S-methyltransferase homocysteine S-methyltransferase family protein This is a family of related homocysteine S-methyltransferases enzymes: 5-methyltetrahydrofolate--homocysteine S-methyltransferases also known EC:2.1.1.13, [2]; Betaine--homocysteine S-methyltransferase (vitamin B12 dependent), EC:2.1.1.5, [3]; and Homocysteine S-methyltransferase, EC:2.1.1.10, [1]. [1]. 9882684. S-methylmethionine metabolism in Escherichia coli. Thanbichler M, Neuhierl B, Bock A;. J Bacteriol 1999;181:662-665. [2]. 9013615. Human methionine synthase. cDNA cloning, gene localization, and expression. Chen LH, Liu ML, Hwang HY, Chen LS, Korenberg J, Shane B;. J Biol Chem 1997;272:3628-3634. [3]. 8798461. Purification, kinetic properties, and cDNA cloning of mammalian betaine-homocysteine methyltransferase. Garrow TA;. J Biol Chem 1996;271:22831-22838. (from Pfam) NF014618.5 PF02577.19 BFN_dom 27 27 112 PfamEq Y Y N bifunctional nuclease domain-containing protein GO:0004518 20018603,24255121 131567 cellular organisms no rank 14605 EBI-EMBL Bifunctional nuclease domain Bifunctional nuclease domain This entry represents the bifunctional nuclease (BFN) domain which is specific to bacteria and plant organisms. It has both RNase and DNase activities [1]. The dimer of the BFN domain forms a wedge, each monomer being a basic triangular shape. The BFN domain is composed of an eight-stranded, distorted beta-sheet consisting of a four-stranded antiparallel beta-sheet, and a four-stranded mixed beta-sheet. This domain can be found in M. tuberculosis Carbon monoxide resistance (Cor) proteins. Cor consists entirely of this domain with homologues in a variety of organisms, including most mycobacteria, Bacteroides sp., Chlamydia sp., Streptomyces sp., and Rhodococcussp. One of the homologs from Oryza minuta protein OmBBD was reported to exhibit DNase and RNAse activity in vitro [1]. OmBBD carries a C-terminal UvrB domain that is absent in the mycobacterial sequences. UvrB is one component of the UvrABC endonuclease system. Hence, it was proposed that OmBBD's observed nuclease activity may come not from this domain but from an interaction of the C-terminal UvrB with the catalytic UvrC nuclease [2]. [1]. 20018603. Novel bifunctional nucleases, OmBBD and AtBBD1, are involved in abscisic acid-mediated callose deposition in Arabidopsis. You MK, Shin HY, Kim YJ, Ok SH, Cho SK, Jeung JU, Yoo SD, Kim JK, Shin JS;. Plant Physiol. 2010;152:1015-1029. [2]. 24255121. cor, a novel carbon monoxide resistance gene, is essential for Mycobacterium tuberculosis pathogenesis. Zacharia VM, Manzanillo PS, Nair VR, Marciano DK, Kinch LN, Grishin NV, Cox JS, Shiloh MU;. MBio. 2013;4:e00721-e00713. (from Pfam) NF014620.5 PF02579.22 Nitro_FeMo-Co 26.3 26.3 94 domain Y Y N NifB/NifX family molybdenum-iron cluster-binding protein 11823455 131567 cellular organisms no rank 24718 EBI-EMBL Dinitrogenase iron-molybdenum cofactor NifB/NifX family molybdenum-iron cluster-binding protein This family contains several NIF (B, Y and X) proteins which are iron-molybdenum cofactors (FeMo-co) in the dinitrogenase enzyme which catalyses the reduction of dinitrogen to ammonium. Dinitrogenase is a hetero-tetrameric (alpha(2)beta(2)) enzyme which contains the iron-molybdenum cofactor (FeMo-co) at its active site [1]. [1]. 11823455. Cloning and mutational analysis of the gamma gene from Azotobacter vinelandii defines a new family of proteins capable of metallocluster binding and protein stabilization. Rubio LM, Rangaraj P, Homer MJ, Roberts GP, Ludden PW;. J Biol Chem 2002;277:14299-14305. (from Pfam) NF014621.5 PF02580.21 Tyr_Deacylase 25 25 144 PfamEq Y Y N D-aminoacyl-tRNA deacylase GO:0002161,GO:0005737,GO:0051499 11568181,29410408 131567 cellular organisms no rank 48095 EBI-EMBL D-Tyr-tRNA(Tyr) deacylase D-aminoacyl-tRNA deacylase This family comprises of several D-Tyr-tRNA(Tyr) deacylase proteins. Cell growth inhibition by several d-amino acids can be explained by an in vivo production of d-aminoacyl-tRNA molecules. Escherichia coli and yeast cells express an enzyme, d-Tyr-tRNA(Tyr) deacylase, capable of recycling such d-aminoacyl-tRNA molecules into free tRNA and d-amino acid. Accordingly, upon inactivation of the genes of the above deacylases, the toxicity of d-amino acids increases. Orthologues of the deacylase are found in many cells [1].The D-aminoacyl-tRNA deacylase (DTD) enzyme is homodimeric with two active sites located at the dimeric interface. Each active site carries an invariant Gly-cisPro dipeptide motif in each monomer. The interaction between the dipeptide motifs from each monomer ensures substrate stereospecificity. This family also includes a subclass of DTDs which is present in Chordata and harbors a Gly-transPro motif. The cis to trans switch is the key to Animal DTDs (ATD) gaining of L-chiral selectivity. This 'gain of function' through relaxation of substrate chiral specificity underlies ATD's capability of correcting the error in tRNA selection [2]. [1]. 11568181. Structure of crystalline D-Tyr-tRNA(Tyr) deacylase. A representative of a new class of tRNA-dependent hydrolases. Ferri-Fioni ML, Schmitt E, Soutourina J, Plateau P, Mechulam Y, Blanquet S;. J Biol Chem 2001;276:47285-47290. [2]. 29410408. A chiral selectivity relaxed paralog of DTD for proofreading tRNA mischarging in Animalia. Kuncha SK, Mazeed M, Singh R, Kattula B, Routh SB, Sankaranarayanan R;. Nat Commun. 2018;9:511. (from Pfam) NF014622.5 PF02581.22 TMP-TENI 27 27 180 domain Y Y N thiamine phosphate synthase 1898926,21534620,9139923 131567 cellular organisms no rank 113802 EBI-EMBL Thiamine monophosphate synthase thiamine phosphate synthase Thiamine monophosphate synthase (TMP) (EC:2.5.1.3) catalyses the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole phosphate to yield thiamine phosphate [1]. This Pfam family also includes the regulatory protein TENI (Swiss:P25053), a protein from Bacillus subtilis that regulates the production of several extracellular enzymes by reducing alkaline protease production [2]. While TenI shows high sequence similarity with thiamin phosphate synthase, the purified protein has no thiamin phosphate synthase activity. Instead, it is a thiazole tautomerase [3]. [1]. 9139923. Characterization of the Bacillus subtilis thiC operon involved in thiamine biosynthesis. Zhang Y, Taylor SV, Chiu HJ, Begley TP;. J Bacteriol 1997;179:3030-3035. [2]. 1898926. Cloning and characterization of a pair of novel genes that regulate production of extracellular enzymes in Bacillus subtilis. Pang AS, Nathoo S, Wong SL;. J Bacteriol 1991;173:46-54. [3]. 21534620. A missing enzyme in thiamin thiazole biosynthesis: identification of TenI as a thiazole tautomerase. Hazra AB, Han Y, Chatterjee A, Zhang Y, Lai RY, Ealick SE, Begley TP;. J Am Chem Soc. 2011;133:9311-9319. (from Pfam) NF014624.5 PF02583.22 Trns_repr_metal 22.8 22.8 78 subfamily Y Y N metal-sensing transcriptional repressor GO:0003677,GO:0006355,GO:0046872 16956381,17143269,17186148,17293508,20395270 131567 cellular organisms no rank 51651 EBI-EMBL Metal-sensitive transcriptional repressor metal-sensing transcriptional repressor This is a family of metal-sensitive repressors, involved in resistance to metal ions. Members of this family bind copper, nickel or cobalt ions via conserved cysteine and histidine residues. In the absence of metal ions, these proteins bind to promoter regions and repress transcription. When bound to metal ions they are unable to bind DNA, leading to transcriptional derepression [1-5]. [1]. 17143269. CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator. Liu T, Ramesh A, Ma Z, Ward SK, Zhang L, George GN, Talaat AM, Sacchettini JC, Giedroc DP;. Nat Chem Biol. 2007;3:60-68. [2]. 20395270. Structural and functional characterization of the transcriptional repressor CsoR from Thermus thermophilus HB8. Sakamoto K, Agari Y, Agari K, Kuramitsu S, Shinkai A;. Microbiology. 2010;156:1993-2005. [3]. 17186148. High-level resistance to cobalt and nickel but probably no transenvelope efflux: Metal resistance in the Cuban Serratia marcescens strain C-1. Marrero J, Auling G, Coto O, Nies DH;. Microb Ecol. 2007;53:123-133. [4]. 17293508. Nickel-resistant determinant from Leptospirillum ferriphilum. Tian J, Wu N, Li J, Liu Y, Guo J, Yao B, Fan Y;. Appl Environ Microbiol. 2007;73:2364-2368. [5]. 16956381. Nickel homeostasis in Escherichia coli - the rcnR-rcnA efflux pathway and its linkage to NikR function. Iwig JS, Rowe JL, Chivers PT;. Mol Microbiol. 2006;62:252-262. (from Pfam) NF014625.5 PF02585.22 PIG-L 28.2 28.2 129 domain Y Y N PIG-L family deacetylase 10085243,12876312 131567 cellular organisms no rank 137121 EBI-EMBL GlcNAc-PI de-N-acetylase PIG-L family deacetylase Members of this family are related to PIG-L an N-acetylglucosaminylphosphatidylinositol de-N-acetylase (EC:3.5.1.89) that catalyses the second step in GPI biosynthesis [1,2]. [1]. 10085243. Mammalian PIG-L and its yeast homologue Gpi12p are N-acetylglucosaminylphosphatidylinositol de-N-acetylases essential in glycosylphosphatidylinositol biosynthesis. Watanabe R, Ohishi K, Maeda Y, Nakamura N, Kinoshita T;. Biochem J 1999;339:185-192. [2]. 12876312. Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8. Handa N, Terada T, Kamewari Y, Hamana H, Tame JR, Park SY, Kinoshita K, Ota M, Nakamura H, Kuramitsu S, Shirouzu M, Yokoyama S;. Protein Sci. 2003;12:1621-1632. (from Pfam) NF014626.5 PF02586.19 SRAP 27.1 27.1 214 domain Y Y N SOS response-associated peptidase family protein GO:0003697,GO:0006974 23945014 131567 cellular organisms no rank 78227 EBI-EMBL SOS response associated peptidase (SRAP) SOS response-associated peptidase family protein The SRAP family functions as a DNA-associated autoproteolytic switch that recruits diverse repair enzymes onto DNA damage. We propose that the human protein Q96FZ2:UniProtKB, the eukaryotic member of the SRAP family, which has been recently shown to bind specifically to DNA with 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine, is a sensor for these oxidized bases generated by the TET (tetrahedral aminopeptidase of the M42 family) enzymes from methylcytosine. Hence, its autoproteolytic activity might help it act as a switch that recruits DNA repair enzymes to remove these oxidized methylcytosine species as part of the DNA demethylation pathway downstream of the TET enzymes. [1]. 23945014. Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems. Aravind L, Anand S, Iyer LM;. Biol Direct. 2013;8:20. (from Pfam) NF014628.5 PF02589.20 LUD_dom 22.6 22.6 189 domain Y Y N LUD domain-containing protein 19201793,24274019 131567 cellular organisms no rank 85803 EBI-EMBL LUD domain LUD domain This entry represents a domain found in lactate utilization proteins B (LutB) and C (LutC), as well as several uncharacterised proteins. LutB and LutC are encoded by th conserved LutABC operon in bacteria. They are involved in lactate utilization and is implicated in the oxidative conversion of L-lactate into pyruvate [1, 2] [1]. 19201793. A widely conserved gene cluster required for lactate utilization in Bacillus subtilis and its involvement in biofilm formation. Chai Y, Kolter R, Losick R;. J Bacteriol. 2009;191:2423-2430. [2]. 24274019. LUD, a new protein domain associated with lactate utilization. Hwang WC, Bakolitsa C, Punta M, Coggill PC, Bateman A, Axelrod HL, Rawlings ND, Sedova M, Peterson SN, Eberhardt RY, Aravind L, Pascual J, Godzik A;. BMC Bioinformatics. 2013;14:341. (from Pfam) NF014629.5 PF02590.22 SPOUT_MTase 27 27 154 PfamEq Y Y N 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH GO:0006364,GO:0008168 17338813 131567 cellular organisms no rank 40006 EBI-EMBL Predicted SPOUT methyltransferase 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH This family of proteins are predicted to be SPOUT methyltransferases [1]. [1]. 17338813. Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM;. BMC Bioinformatics. 2007;8:73. (from Pfam) NF014631.5 PF02592.20 Vut_1 27.2 27.2 152 domain Y Y N VUT family protein GO:1990397 131567 cellular organisms no rank 34258 EBI-EMBL Putative vitamin uptake transporter VUT family protein NF014632.5 PF02593.19 DUF166 24.4 24.4 221 subfamily Y Y N DUF166 family protein 10426953,11790254 131567 cellular organisms no rank 628 EBI-EMBL Domain of unknown function DUF166 family protein This family catalyses the synthesis of thymidine monophosphate (dTMP) from deoxyuridine monophosphate (dUMP). The physiological co-substrate has not yet been identified. Previous designation of this famliy as being thymidylate synthase from one paper, PMID:10436953, has been shown to be erroneous [1]. The proteins are uncharacterised. [1]. 10426953. Identifying two ancient enzymes in Archaea using predicted secondary structure alignment. Xu H, Aurora R, Rose GD, White RH;. Nat Struct Biol. 1999;6:750-754. [2]. 11790254. Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences. Iyer LM, Aravind L, Bork P, Hofmann K, Mushegian AR, Zhulin IB, Koonin EV;. Genome Biol. 2001;2:RESEARCH0051. (from Pfam) NF014633.5 PF02594.21 DUF167 30.9 30.9 76 subfamily Y Y N DUF167 family protein 12975589 131567 cellular organisms no rank 17037 EBI-EMBL Uncharacterised ACR, YggU family COG1872 DUF167 family protein NF014635.5 PF02596.20 DUF169 27 27 209 domain Y Y N DUF169 domain-containing protein 131567 cellular organisms no rank 5066 EBI-EMBL Uncharacterised ArCR, COG2043 Uncharacterised ArCR, COG2043 NF014636.5 PF02597.25 ThiS 22.5 22.5 76 domain Y Y N MoaD/ThiS family protein 10781607 131567 cellular organisms no rank 102045 EBI-EMBL ThiS family MoaD/ThiS family protein ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer Swiss:O32583. ThiS is coded in the thiCEFSGH operon in E. coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS [1]. MoaD, Swiss:P30748 a protein involved sulphur transfer in molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end. [1]. 10781607. The iscS gene in Escherichia coli is required for the biosynthesis of 4-thiouridine, thiamin, and NAD. Lauhon CT, Kambampati R;. J Biol Chem 2000;275:20096-20103. (from Pfam) NF014637.5 PF02598.22 Methyltrn_RNA_3 27 27 302 PfamEq Y Y N putative RNA uridine N3 methyltransferase 12486711,17338813,18844986 131567 cellular organisms no rank 1067 EBI-EMBL Putative RNA methyltransferase putative RNA uridine N3 methyltransferase Members of this family are SPOUT family RNA methyltransferases, found in archaea and in eukaryotes, and predicted to be responsible for N3 methylated uridine modifications to RNA. NF014639.5 PF02600.21 DsbB 22.1 22.1 148 domain Y Y N disulfide bond formation protein B GO:0006457,GO:0015035,GO:0016020 7957076,8430071 131567 cellular organisms no rank 40232 EBI-EMBL Disulfide bond formation protein DsbB disulfide bond formation protein B This family consists of disulfide bond formation protein DsbB from bacteria. The DsbB protein oxidises the periplasmic protein DsbA which in turn oxidises cysteines in other periplasmic proteins in order to make disulfide bonds [1]. DsbB acts as a redox potential transducer across the cytoplasmic membrane and is an integral membrane protein [2]. DsbB posses six cysteines four of which are necessary for it proper function in vivo [1]. [1]. 7957076. Two cysteines in each periplasmic domain of the membrane protein DsbB are required for its function in protein disulfide bond formation. Jander G, Martin NL, Beckwith J;. EMBO J 1994;13:5121-5127. [2]. 8430071. A pathway for disulfide bond formation in vivo. Bardwell JC, Lee JO, Jander G, Martin N, Belin D, Beckwith J;. Proc Natl Acad Sci U S A 1993;90:1038-1042. (from Pfam) NF014640.5 PF02601.20 Exonuc_VII_L 35.9 35.9 315 domain Y Y N exodeoxyribonuclease VII large subunit GO:0008855 6284744 131567 cellular organisms no rank 85179 EBI-EMBL Exonuclease VII, large subunit exodeoxyribonuclease VII large subunit This family consist of exonuclease VII, large subunit EC:3.1.11.6 This enzyme catalyses exonucleolytic cleavage in either 5'->3' or 3'->5' direction to yield 5'-phosphomononucleotides. This exonuclease VII enzyme is composed of one large subunit and 4 small ones [1]. [1]. 6284744. Subunit structure of Escherichia coli exonuclease VII. Vales LD, Rabin BA, Chase JW;. J Biol Chem 1982;257:8799-8805. (from Pfam) NF014641.5 PF02602.20 HEM4 27.5 27.5 231 domain Y Y N uroporphyrinogen-III synthase 4.2.1.75 GO:0004852,GO:0033014 7597845,8829650 131567 cellular organisms no rank 93772 EBI-EMBL Uroporphyrinogen-III synthase HemD uroporphyrinogen-III synthase This family consists of uroporphyrinogen-III synthase HemD EC:4.2.1.75 also known as Hydroxymethylbilane hydrolyase (cyclizing) from eukaryotes, bacteria and archaea. This enzyme catalyses the reaction: Hydroxymethylbilane uroporphyrinogen-III + H(2)O. Some members of this family are multi-functional proteins possessing other enzyme activities related to porphyrin biosynthesis, such as Swiss:Q59294 with Pfam:PF00590, however the aligned region corresponds with the uroporphyrinogen-III synthase EC:4.2.1.75 activity only. Uroporphyrinogen-III synthase is the fourth enzyme in the heme pathway [2]. Mutant forms of the Uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria in humans a recessive inborn error of metabolism also known as Gunther disease [1]. [1]. 8829650. Molecular basis of congenital erythropoietic porphyria: mutations in the human uroporphyrinogen III synthase gene. Xu W, Astrin KH, Desnick RJ;. Hum Mutat 1996;7:187-192. [2]. 7597845. Isolation of the gene HEM4 encoding uroporphyrinogen III synthase in Saccharomyces cerevisiae. Amillet JM, Labbe-Bois R;. Yeast 1995;11:419-424. (from Pfam) NF014643.5 PF02604.24 PhdYeFM_antitox 29.8 29.8 74 domain Y Y N type II toxin-antitoxin system Phd/YefM family antitoxin 14659018,20603017 131567 cellular organisms no rank 75767 EBI-EMBL Antitoxin Phd_YefM, type II toxin-antitoxin system type II toxin-antitoxin system Phd/YefM family antitoxin Members of this family act as antitoxins in type II toxin-antitoxin systems [1]. When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin [2]. This domain complexes with Txe toxins containing Pfam:PF06769, Fic/DOC toxins containing Pfam:PF02661 and YafO toxins containing Pfam:PF13957. [1]. 14659018. New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Anantharaman V, Aravind L;. Genome Biol 2003;4:R81. [2]. 20603017. Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity. Garcia-Pino A, Balasubramanian S, Wyns L, Gazit E, De Greve H, Magnuson RD, Charlier D, van Nuland NA, Loris R;. Cell. 2010;142:101-111. (from Pfam) NF014646.5 PF02607.22 B12-binding_2 23 23 74 domain Y Y N B12-binding domain-containing protein 7992050 131567 cellular organisms no rank 108425 EBI-EMBL B12 binding domain B12 binding domain This B12 binding domain is found in methionine synthase EC:2.1.1.13 Swiss:Q99707, and other shorter proteins that bind to B12. This domain is always found to the N-terminus of Pfam:PF02310. The structure of this domain is known [1], it is a 4 helix bundle. Many of the conserved residues in this domain are involved in B12 binding, such as those in the MXXVG motif. [1]. 7992050. How a protein binds B12: A 3.0 A X-ray structure of B12-binding domains of methionine synthase. Drennan CL, Huang S, Drummond JT, Matthews RG, Lidwig ML;. Science 1994;266:1669-1674. (from Pfam) NF014647.5 PF02608.19 Bmp 24.1 24.1 301 domain Y Y N BMP family ABC transporter substrate-binding protein GO:0005886 16418175,17501984,23404400,9335269,9350727 131567 cellular organisms no rank 70223 EBI-EMBL ABC transporter substrate-binding protein PnrA-like BMP family ABC transporter substrate-binding protein Proteins containing this domain were originally annotated as basic membrane lipoproteins [1]. However, several proteins containing this domain were later predicted as ABC transporter substrate-binding proteins, such as PnrA (also known as TmpC or TP0319) and RfuA (also known as Tpn38 or TP0298) from Treponema pallidum. PnrA transports purine nucleosides [3], while RfuA transports riboflavin [4]. Proteins containing this domain also include Med from Bacillus subtilis. Med was annotated as a transcriptional activator protein that regulates comK [2]. This domain can also found at the N terminus of glutamate receptor-like proteins from Dictyostelium (slime mold) [5]. [1]. 9350727. Heterogeneity of BmpA (P39) among European isolates of Borrelia burgdorferi sensu lato and influence of interspecies variability on serodiagnosis. Roessler D, Hauser U, Wilske B;. J Clin Microbiol 1997;35:2752-2758. [2]. 9335269. A new Bacillus subtilis gene, med, encodes a positive regulator of comK. Ogura M, Ohshiro Y, Hirao S, Tanaka T;. J Bacteriol 1997;179:6244-6253. [3]. 16418175. The PnrA (Tp0319; TmpC) lipoprotein represents a new family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC)-like operon in Treponema pallidum. Deka RK, Brautigam CA, Yang XF, Blevins JS, Machius M, Tomchick DR, Norgard MV;. J Biol Chem. 2006;281:8072-8081. [4]. 23404400. Evidence for an ABC-type riboflavin transporter system in pathogenic spirochetes. Deka RK, Brautigam CA, Biddy BA, Liu WZ, Norgard MV;. MBio. 2013;4:e00615-e00612. [5]. 17501984. GrlJ, a Dictyostelium GABAB-like receptor with roles in post-aggregation develo. TRUNCATED at 1650 bytes (from Pfam) NF014648.5 PF02609.21 Exonuc_VII_S 24 24 52 PfamEq Y Y N exodeoxyribonuclease VII small subunit 3.1.11.6 GO:0006308,GO:0008855,GO:0009318 6284744 131567 cellular organisms no rank 42495 EBI-EMBL Exonuclease VII small subunit exodeoxyribonuclease VII small subunit This family consist of exonuclease VII, small subunit EC:3.1.11.6 This enzyme catalyses exonucleolytic cleavage in either 5'->3' or 3'->5' direction to yield 5'-phosphomononucleotides. This exonuclease VII enzyme is composed of one large subunit and 4 small ones [1]. [1]. 6284744. Subunit structure of Escherichia coli exonuclease VII. Vales LD, Rabin BA, Chase JW;. J Biol Chem 1982;257:8799-8805. (from Pfam) NF014649.5 PF02610.20 Arabinose_Isome 29.4 29.4 356 PfamEq Y N N L-arabinose isomerase GO:0008733 9084180 131567 cellular organisms no rank 25198 EBI-EMBL L-arabinose isomerase L-arabinose isomerase This is a family of L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyse the reaction: L-arabinose L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme [1]. [1]. 9084180. The Bacillus subtilis L-arabinose (ara) operon: nucleotide sequence, genetic organization and expression. Sa-Nogueira I, Nogueira TV, Soares S, de Lencastre H;. Microbiology 1997;143:957-969. (from Pfam) NF014651.5 PF02613.20 Nitrate_red_del 22.2 22.2 136 domain Y Y N molecular chaperone TorD family protein 12766163,9738886 131567 cellular organisms no rank 53282 EBI-EMBL Nitrate reductase delta subunit molecular chaperone TorD family protein This family is the delta subunit of the nitrate reductase enzyme, The delta subunit is not part of the nitrate reductase enzyme but is most likely needed for assembly of the multi-subunit enzyme complex [1]. In the absence of the delta subunit the core alpha beta enzyme complex is unstable [1]. The delta subunit is essential for enzyme activity in vivo and in vitro [1]. The nitrate reductase enzyme, EC:1.7.99.4 catalyse the conversion of nitrite to nitrate via the reduction of an acceptor. The nitrate reductase enzyme is composed of three subunits [1]. Nitrate is the most widely used alternative electron acceptor after oxygen [1]. This family also now contains the family TorD, a family of cytoplasmic chaperone proteins; like many prokaryotic molybdoenzymes, the TMAO reductase (TorA) of Escherichia coli requires the insertion of a bis(molybdopterin guanine dinucleotide) molybdenum (bis(MGD)Mo) cofactor in its catalytic site to be active and translocated to the periplasm. The TorD chaperone increases apoTorA activation up to four-fold, allowing maturation of most of the apoprotein. Therefore TorD is involved in the first step of TorA maturation to make it competent to receive the cofactor [2]. [1]. 9738886. Identification and characterization of the Staphylococcus carnosus nitrate reductase operon. Pantel I, Lindgren PE, Neubauer H, Gotz F;. Mol Gen Genet 1998;259:105-114. [2]. 12766163. Involvement of a mate chaperone (TorD) in the maturation pathway of molybdoenzyme TorA. Ilbert M, Mejean V, Giudici-Orticoni MT, Samama JP, Iobbi-Nivol C;. J Biol Chem 2003;23:1-2. (from Pfam) NF014652.5 PF02614.19 UxaC 25 25 464 domain Y Y N glucuronate isomerase 5.3.1.12 GO:0006064,GO:0008880 131567 cellular organisms no rank 30679 EBI-EMBL Glucuronate isomerase glucuronate isomerase This is a family of Glucuronate isomerases also known as D-glucuronate isomerase, uronic isomerase, uronate isomerase, or uronic acid isomerase, EC:5.3.1.12. This enzyme catalyses the reactions: D-glucuronate D-fructuronate and D-galacturonate D-tagaturonate. It is not however clear where the experimental evidence for this functional assignment came from and thus this family has no literature reference. (from Pfam) NF014653.5 PF02615.19 Ldh_2 38.8 38.8 333 subfamily Y Y N Ldh family oxidoreductase GO:0016491 2110059,8405966 131567 cellular organisms no rank 49103 EBI-EMBL Malate/L-lactate dehydrogenase Ldh family oxidoreductase This family consists of bacterial and archaeal Malate/L-lactate dehydrogenase. L-lactate dehydrogenase, EC:1.1.1.27, catalyses the reaction (S)-lactate + NAD(+) pyruvate + NADH. Malate dehydrogenase, EC:1.1.1.37 and EC:1.1.1.82, catalyses the reactions: (S)-malate + NAD(+) oxaloacetate + NADH, and (S)-malate + NADP(+) oxaloacetate + NADPH respectively. [1]. 8405966. The Alcaligenes eutrophus ldh structural gene encodes a novel type of lactate dehydrogenase. Jendrossek D, Kratzin HD, Steinbuchel A;. FEMS Microbiol Lett 1993;112:229-235. [2]. 2110059. Properties and primary structure of the L-malate dehydrogenase from the extremely thermophilic archaebacterium Methanothermus fervidus. Honka E, Fabry S, Niermann T, Palm P, Hensel R;. Eur J Biochem 1990;188:623-632. (from Pfam) NF014654.5 PF02616.19 SMC_ScpA 24.6 24.6 232 PfamEq Y Y N segregation/condensation protein A 12667442,23353789,23541893 131567 cellular organisms no rank 54965 EBI-EMBL Segregation and condensation protein ScpA segregation/condensation protein A This is a family of proteins that from part of the condensin complex that regulates chromosome segregation. This is the A subunit, which binds to the ScpB subunit, Pfam:PF04079, and SMC, Pfam:PF02463, to participate in chromosomal partition during cell division [2,3]. The condensin complex pulls DNA away from the mid-cell into both cell halves [1]. These proteins are part of the Kleisin superfamily. [1]. 12667442. Kleisins: a superfamily of bacterial and eukaryotic SMC protein partners. Schleiffer A, Kaitna S, Maurer-Stroh S, Glotzer M, Nasmyth K, Eisenhaber F;. Mol Cell 2003;11:571-575. [2]. 23353789. An asymmetric SMC-kleisin bridge in prokaryotic condensin. Burmann F, Shin HC, Basquin J, Soh YM, Gimenez-Oya V, Kim YG, Oh BH, Gruber S;. Nat Struct Mol Biol. 2013;20:371-379. [3]. 23541893. Molecular basis of SMC ATPase activation: role of internal structural changes of the regulatory subcomplex ScpAB. Kamada K, Miyata M, Hirano T;. Structure. 2013;21:581-594. (from Pfam) NF014658.5 PF02621.19 VitK2_biosynth 26 26 252 subfamily Y Y N MqnA/MqnD/SBP family protein 18801996,19602440 131567 cellular organisms no rank 28726 EBI-EMBL Menaquinone biosynthesis MqnA/MqnD/SBP family protein High-scoring members of this family include two enzymes, MqnA and MqnD, of the futalosine pathway of menaquinone biosynthesis found in species lacking the MenA pathway. However, the family also includes low-scoring proteins, e.g. WP_006442938.1, are identified as ABC transporter substrate-binding proteins (SBP) by homology and context. NF014661.5 PF02624.21 YcaO 25.7 25.7 325 domain Y Y N YcaO-like family protein 25129028 131567 cellular organisms no rank 51885 EBI-EMBL YcaO cyclodehydratase, ATP-ad Mg2+-binding YcaO-like family protein YcaO is an ATP- an Mg2+-binding protein involved in the peptidic biosynthesis of azoline. There three motifs involved in the binding are, in UniProtKB:P75838, 71-79: Sx3ExxER, 184-203: Sx6Ex3Qx3ExxER, and 286-290: RxxxE. Three slightly different functional families are represented in this family, proteins involved in TOMM (thiazole/oxazole-modified microcin) biogenesis, non-TOMM proteins such as UniProtKB:P75838, and TfuA-associated non-TOMM proteins involved in trifolitoxin biosynthesis. UniProtKB:P75838 hydrolyses ATP to AMP and pyrophosphate [1]. [1]. 25129028. Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis. Dunbar KL, Chekan JR, Cox CL, Burkhart BJ, Nair SK, Mitchell DA;. Nat Chem Biol. 2014;10:823-829. (from Pfam) NF014662.5 PF02625.21 XdhC_CoxI 24.3 24.3 68 domain Y Y N XdhC family protein 10217763 131567 cellular organisms no rank 84378 EBI-EMBL XdhC and CoxI family XdhC family protein This domain is often found in association with an NAD-binding region, related to TrkA-N (Pfam:PF02254; personal obs:C. Yeats). XdhC is believed to be involved in the attachment of molybdenum to Xanthine Dehydrogenase ([1]). [1]. 10217763. Role of XDHC in Molybdenum cofactor insertion into xanthine dehydrogenase of Rhodobacter capsulatus. Leimkuhler S, Klipp W;. J Bacteriol 1999;181:2745-2751. (from Pfam) NF014663.5 PF02626.20 CT_A_B 25 25 261 domain Y N N Carboxyltransferase domain, subdomain A and B 20884691,9334321 131567 cellular organisms no rank 82481 EBI-EMBL Carboxyltransferase domain, subdomain A and B Carboxyltransferase domain, subdomain A and B Urea carboxylase (UC) catalyses a two-step, ATP- and biotin-dependent carboxylation reaction of urea. It is composed of biotin carboxylase (BC), carboxyltransferase (CT), and biotin carboxyl carrier protein (BCCP) domains. The CT domain of UC consists of four subdomains, named A, B, C and D. This domain covers the A and B subdomains of the CT domain. This domain covers the whole length of KipA (kinase A) from Bacillus subtilis [1]. It can also be found in S. cerevisiae urea amidolyase Dur1,2, which is a multifunctional biotin-dependent enzyme with domains for urea carboxylase and allophanate (urea carboxylate) hydrolase activity[2]. [1]. 9334321. A novel histidine kinase inhibitor regulating development in Bacillus subtilis. Wang L, Grau R, Perego M, Hoch JA;. Genes Dev. 1997;11:2569-2579. [2]. 20884691. Dur3 is the major urea transporter in Candida albicans and is co-regulated with the urea amidolyase Dur1,2. Navarathna DH, Das A, Morschhauser J, Nickerson KW, Roberts DD;. Microbiology. 2011;157:270-279. (from Pfam) NF014664.5 PF02627.25 CMD 23 23 84 domain Y Y N carboxymuconolactone decarboxylase family protein GO:0051920 16597838,9495744 131567 cellular organisms no rank 262870 EBI-EMBL Carboxymuconolactone decarboxylase family carboxymuconolactone decarboxylase family protein Carboxymuconolactone decarboxylase (CMD) EC:4.1.1.44 is involved in protocatechuate catabolism. In some bacteria a gene fusion event leads to expression of CMD with a hydrolase involved in the same pathway [1]. In these bifunctional proteins (e.g. Swiss:O67982) CMD represents the C-terminal domain, Pfam:PF00561 represents the N-terminal domain. [1]. 9495744. Characterization of a protocatechuate catabolic gene cluster from Rhodococcus opacus 1CP: evidence for a merged enzyme with 4-carboxymuconolactone-decarboxylating and 3-oxoadipate enol-lactone-hydrolyzing activity. Eulberg D, Lakner S, Golovleva LA, Schlomann M;. J Bacteriol 1998;180:1072-1081. [2]. 16597838. Crystal structure of the conserved protein TTHA0727 from Thermus thermophilus HB8 at 1.9 A resolution: A CMD family member distinct from carboxymuconolactone decarboxylase (CMD) and AhpD. Ito K, Arai R, Fusatomi E, Kamo-Uchikubo T, Kawaguchi S, Akasaka R, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S;. Protein Sci. 2006;15:1187-1192. (from Pfam) NF014665.5 PF02628.20 COX15-CtaA 29.9 29.9 322 PfamEq Y Y N COX15/CtaA family protein GO:0006784,GO:0016020,GO:0016491 2549006 131567 cellular organisms no rank 50628 EBI-EMBL Cytochrome oxidase assembly protein COX15/CtaA family protein This is a family of integral membrane proteins. CtaA is required for cytochrome aa3 oxidase assembly in Bacillus subtilis [1]. COX15 is required for cytochrome c oxidase assembly in yeast (Swiss:P40086). [1]. 2549006. Isolation and sequence of ctaA, a gene required for cytochrome aa3 biosynthesis and sporulation in Bacillus subtilis. Mueller JP, Taber HW;. J Bacteriol 1989;171:4967-4978. (from Pfam) NF014666.5 PF02629.24 CoA_binding 22.3 22.3 97 domain Y N N CoA binding domain 8144675 131567 cellular organisms no rank 148397 EBI-EMBL CoA binding domain CoA binding domain This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases. [1]. 8144675. The crystal structure of succinyl-CoA synthetase from Escherichia coli at 2.5-A resolution. Wolodko WT, Fraser ME, James MN, Bridger WA;. J Biol Chem 1994;269:10883-10890. (from Pfam) NF014667.5 PF02630.19 SCO1-SenC 22.8 22.8 134 domain Y Y N SCO family protein 1944230,7592491 131567 cellular organisms no rank 76385 EBI-EMBL SCO1/SenC SCO family protein This family is involved in biogenesis of respiratory and photosynthetic systems. SCO1 (Swiss:P23833) is required for a post-translational step in the accumulation of subunits COXI and COXII of cytochrome c oxidase [1]. SenC (Swiss:Q52720) is required for optimal cytochrome c oxidase activity and maximal induction of genes encoding the light-harvesting and reaction centre complexes of R. capsulatus [2]. [1]. 1944230. Immunological identification of yeast SCO1 protein as a component of the inner mitochondrial membrane. Buchwald P, Krummeck G, Rodel G;. Mol Gen Genet 1991;229:413-420. [2]. 7592491. Cloning and characterization of senC, a gene involved in both aerobic respiration and photosynthesis gene expression in Rhodobacter capsulatus. Buggy J, Bauer CE;. J Bacteriol 1995;177:6958-6965. (from Pfam) NF014669.5 PF02632.19 BioY 25 25 140 domain Y Y N biotin transporter BioY GO:0005886,GO:0015225,GO:0015878 12368242,17301237,2110099 131567 cellular organisms no rank 41867 EBI-EMBL BioY family biotin transporter BioY A number of bacterial genes are involved in bioconversion of pimelate into dethiobiotin [1]. BioY is a component of the BioMNY transport system involved in biotin uptake in prokaryotes [3]. [1]. 2110099. Cloning and characterization of the Bacillus sphaericus genes controlling the bioconversion of pimelate into dethiobiotin. Gloeckler R, Ohsawa I, Speck D, Ledoux C, Bernard S, Zinsius M, Villeval D, Kisou T, Kamogawa K, Lemoine Y;. Gene 1990;87:63-70. [2]. 12368242. Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. Rodionov DA, Mironov AA, Gelfand MS;. Genome Res. 2002;12:1507-1516. [3]. 17301237. Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module. Hebbeln P, Rodionov DA, Alfandega A, Eitinger T;. Proc Natl Acad Sci U S A. 2007;104:2909-2914. (from Pfam) NF014670.5 PF02633.19 Creatininase 31.3 31.3 238 domain Y Y N creatininase family protein 7670196 131567 cellular organisms no rank 41217 EBI-EMBL Creatinine amidohydrolase creatininase family protein Creatinine amidohydrolase (EC:3.5.2.10), or creatininase, catalyses the hydrolysis of creatinine to creatine [1]. [1]. 7670196. Cloning of the creatinine amidohydrolase gene from Pseudomonas sp. PS-7. Yamamoto K, Oka M, Kikuchi T, Emi S;. Biosci Biotechnol Biochem 1995;59:1331-1332. (from Pfam) NF014671.5 PF02634.20 FdhD-NarQ 27.2 27.2 237 domain Y Y N formate dehydrogenase accessory sulfurtransferase FdhD GO:0016783 21890906,7860592 131567 cellular organisms no rank 57934 EBI-EMBL FdhD/NarQ family formate dehydrogenase accessory sulfurtransferase FdhD A pan-bacterial lineage of proteins. Nitrate assimilation protein, NarQ, [1] and FdhD (Swiss:P32177) are required for formate dehydrogenase activity. Structurally, they possess a deaminase fold with a characteristic binding pocket, suggesting that they might bind a nucleotide or related molecule allosterically to regulate the formate dehydrogenase catalytic subunit [2]. [1]. 7860592. Identification and isolation of a gene required for nitrate assimilation and anaerobic growth of Bacillus subtilis. Glaser P, Danchin A, Kunst F, Zuber P, Nakano MM;. J Bacteriol 1995;177:1112-1115. [2]. 21890906. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Iyer LM, Zhang D, Rogozin IB, Aravind L;. Nucleic Acids Res. 2011; [Epub ahead of print] (from Pfam) NF014672.5 PF02635.20 DsrE 22.7 22.7 116 domain Y Y N DsrE family protein 16387657,9695921 131567 cellular organisms no rank 57808 EBI-EMBL DsrE/DsrF-like family DsrE family protein DsrE is a small soluble protein involved in intracellular sulfur reduction [1]. This family also includes DsrF and the homologues TusD/C. n E. coli, the DsrEFH homologue TusBCD interacts with the DsrC homologue TusE in a sulfur relay system during 2-thiouridine biosynthesis [2]. [1]. 9695921. Sirohaem sulfite reductase and other proteins encoded by genes at the dsr locus of Chromatium vinosum are involved in the oxidation of intracellular sulfur. Pott AS, Dahl C;. Microbiology 1998;144:1881-1894. [2]. 16387657. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T;. Mol Cell. 2006;21:97-108. (from Pfam) NF014673.5 PF02636.22 Methyltransf_28 23.3 23.3 249 PfamEq Y Y N SAM-dependent methyltransferase 2.1.1.- 17517780,20406883 131567 cellular organisms no rank 35017 EBI-EMBL Putative S-adenosyl-L-methionine-dependent methyltransferase SAM-dependent methyltransferase This family is a putative S-adenosyl-L-methionine (SAM)-dependent methyltransferase [1,2]. In eukaryotes it plays a role in mitochondrial complex I activity [2]. [1]. 17517780. COMPASS server for remote homology inference. Sadreyev RI, Tang M, Kim BH, Grishin NV;. Nucleic Acids Res. 2007;35:W653-W658. [2]. 20406883. MidA is a putative methyltransferase that is required for mitochondrial complex I function. Carilla-Latorre S, Gallardo ME, Annesley SJ, Calvo-Garrido J, Grana O, Accari SL, Smith PK, Valencia A, Garesse R, Fisher PR, Escalante R;. J Cell Sci. 2010;123:1674-1683. (from Pfam) NF014674.5 PF02637.23 GatB_Yqey 27 27 148 domain Y N N GatB domain GO:0016884 131567 cellular organisms no rank 61279 EBI-EMBL GatB domain GatB domain This domain is found in GatB. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB Swiss:O30509 which transamidates Glu-tRNA to Gln-tRNA. (from Pfam) NF014675.5 PF02638.20 GHL10 27.9 27.9 311 domain Y Y N family 10 glycosylhydrolase 20556855,22295578 131567 cellular organisms no rank 44572 EBI-EMBL Glycosyl hydrolase-like 10 family 10 glycosylhydrolase This is family of bacterial glycosyl-hydrolase-like proteins falling into the family GHL10 as described above, [1,2]. [1]. 20556855. Gh101 family of glycoside hydrolases: subfamily structure and evolutionary connections with other families. Naumoff DG;. J Bioinform Comput Biol. 2010;8:437-451. [2]. 22295578. [GHL1-GHL15: new families of hypothetical glycoside hydrolases]. Naumov DG;. Mol Biol (Mosk). 2011;45:1073-1083. (from Pfam) NF014676.5 PF02639.19 DUF188 24.3 24.3 130 PfamEq Y Y N DUF188 domain-containing protein 131567 cellular organisms no rank 27345 EBI-EMBL Uncharacterized BCR, YaiI/YqxD family COG1671 Uncharacterized BCR, YaiI/YqxD family COG1671 NF014677.5 PF02641.20 DUF190 23.4 23.4 97 PfamEq Y Y N DUF190 domain-containing protein 131567 cellular organisms no rank 11705 EBI-EMBL Uncharacterized ACR, COG1993 Uncharacterized ACR, COG1993 NF014678.5 PF02643.20 DUF192 27 27 96 domain Y Y N DUF192 domain-containing protein 131567 cellular organisms no rank 29103 EBI-EMBL Uncharacterized ACR, COG1430 Uncharacterized ACR, COG1430 Two structures have been solved for members of this large (>500 members) family of bacterial proteins present mostly in environmental bacteria and metagenomes (distant homologues are also present in several Plasmodium species). TOPSAN analysis for pdb:3pjy shows that there is much similarity with the other solved structure, pdb:3m7a, solved for UniProt:Q2GA55 (Saro_0823), a homologue of Thermotoga maritima TM1668, UniProt:Q9X1Z6., The homologue in Caulobacter crescentus (CC1388), UniProt:Q9A8G6, is associated with CspD, a cold shock protein (CC1387), UniProt:Q9A8G7. However, the genomic context of UniProt:Q2GA55 is most conserved with a putative xylose isomerase, suggesting a possible role in extracellular sugar processing. Saro_0821, UniProt:Q2GA57, is annotated as an AMP-dependent synthetase and ligase. PDB:3m7a structure corresponds to the C-terminal (27-165) fragment of the YP_496102 (Saro_0823) protein and it is structurally unique, as the best hits from Dali have a Z-score of 3.8 (1nt0, 2j1t, 3kq4) and it is thus a likely candidate for a new fold. Interestingly, many of the top Dali hits are involved in sugar metabolism. There are no obvious active site-like cavities on the protein surface of 3m7a (http://www.topsan.org/Proteins/JCSG/). (from Pfam) NF014680.5 PF02646.21 RmuC 26 26 291 PfamEq Y Y N DNA recombination protein RmuC rmuC 10886369 131567 cellular organisms no rank 52816 EBI-EMBL RmuC family DNA recombination protein RmuC This family contains several bacterial RmuC DNA recombination proteins. The function of the RMUC protein is unknown but it is suspected that it is either a structural protein that protects DNA against nuclease action, or is itself involved in DNA cleavage at the regions of DNA secondary structures [1] [1]. 10886369. Genes involved in the determination of the rate of inversions at short inverted repeats. Slupska MM, Chiang JH, Luther WM, Stewart JL, Amii L, Conrad A, Miller JH;. Genes Cells 2000;5:425-437. (from Pfam) NF014681.5 PF02649.19 GCHY-1 25 25 260 subfamily Y Y N GTP cyclohydrolase, FolE2/MptA family 3.5.4.- GO:0003933 17032654,19767425 131567 cellular organisms no rank 17581 EBI-EMBL Type I GTP cyclohydrolase folE2 GTP cyclohydrolase, FolE2/MptA family This is a family of prokaryotic proteins with type I GTP cyclohydrolase activity. GTP cyclohydrolase I is the first enzyme of the de novo tetrahydrofolate biosynthetic pathway present in bacteria, fungi, and plants, and encoded in Escherichia coli by the folE gene; it is also the first enzyme of the biopterin (BH4) pathway in Homo sapiens[1]. The invariate, highly conserved glutamate residue at position 216 in Swiss:Q5F9K6 is likely to be the substrate ligand and the metal ligand is likely to be the cysteine at position 147. The enzyme is Zinc 2+ dependent [2]. [1]. 17032654. Discovery of a new prokaryotic type I GTP cyclohydrolase family. El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crecy-Lagard V;. J Biol Chem. 2006;281:37586-37593. [2]. 19767425. Zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for GTP cyclohydrolase IB. Sankaran B, Bonnett SA, Shah K, Gabriel S, Reddy R, Schimmel P, Rodionov DA, de Crecy-Lagard V, Helmann JD, Iwata-Reuyl D, Swairjo MA;. J Bacteriol. 2009;191:6936-6949. (from Pfam) NF014683.5 PF02652.19 Lactate_perm 27 27 522 domain Y Y N L-lactate permease GO:0005886,GO:0015129,GO:0015727 8407843 131567 cellular organisms no rank 50533 EBI-EMBL L-lactate permease L-lactate permease L-lactate permease is an integral membrane protein probably involved in L-lactate transport [1]. [1]. 8407843. Three overlapping lct genes involved in L-lactate utilization by Escherichia coli. Dong JM, Taylor JS, Latour DJ, Iuchi S, Lin EC;. J Bacteriol 1993;175:6671-6678. (from Pfam) NF014684.5 PF02653.21 BPD_transp_2 26.8 26.8 269 domain Y Y N ABC transporter permease subunit GO:0016020,GO:0022857,GO:0055085 1719366,2195019,7921236 131567 cellular organisms no rank 789932 EBI-EMBL Branched-chain amino acid transport system / permease component ABC transporter permease subunit Members of this family are ABC transporter permease subunits. Known substrates for family members include branched chain amino acids, phenylalanine, alanine, D-allose, galactofuranose, etc. NF014685.5 PF02654.20 CobS 23.2 23.2 207 PfamEq Y Y N adenosylcobinamide-GDP ribazoletransferase 2.7.8.26 GO:0008818,GO:0009236,GO:0051073 10518530,8501034 131567 cellular organisms no rank 51162 EBI-EMBL Cobalamin-5-phosphate synthase adenosylcobinamide-GDP ribazoletransferase This is family of Colbalmin-5-phosphate synthases, CobS, from bacteria. The CobS enzyme catalyses the synthesis of AdoCbl-5'-p from AdoCbi-GDP and alpha-ribazole-5'-P [1]. This enzyme is involved in the cobalamin (vitamin B12) biosynthesis pathway in particular the nucleotide loop assembly stage in conjunction with CobC, CobU and CobT [1]. [1]. 10518530. In vitro synthesis of the nucleotide loop of cobalamin by Salmonella typhimurium enzymes. Maggio-Hall LA, Escalante-Semerena JC;. Proc Natl Acad Sci U S A 1999;96:11798-11803. [2]. 8501034. Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM;. J Bacteriol 1993;175:3303-3316. (from Pfam) NF014686.5 PF02655.19 ATP-grasp_3 23.2 23.2 160 domain Y Y N ATP-grasp domain-containing protein GO:0005524,GO:0046872 131567 cellular organisms no rank 250094 EBI-EMBL ATP-grasp domain ATP-grasp domain No functional information or experimental verification of function is known in this family. This family appears to be an ATP-grasp domain (Pers. obs. A Bateman). (from Pfam) NF014687.5 PF02656.20 DUF202 23.4 23.4 68 domain Y Y N DUF202 domain-containing protein 131567 cellular organisms no rank 33982 EBI-EMBL Domain of unknown function (DUF202) Domain of unknown function (DUF202) This family consists of hypothetical proteins some of which are putative membrane proteins. No functional information or experimental verification of function is known. This domain is around 100 amino acids long. (from Pfam) NF014688.5 PF02657.20 SufE 27 27 121 domain Y Y N SufE family protein 11251816 131567 cellular organisms no rank 33864 EBI-EMBL Fe-S metabolism associated domain Fe-S metabolism associated domain This family consists of the SufE-related proteins. These have been implicated in Fe-S metabolism and export [1]). [1]. 11251816. SoxR-dependent response to oxidative stress and virulence of Erwinia chrysanthemi: the key role of SufC, an orphan ABC ATPase. Nachin L, El Hassouni M, Loiseau L, Expert D, Barras F;. Mol Microbiol 2001;39:960-972. (from Pfam) NF014689.5 PF02659.20 Mntp 24.4 24.4 152 domain Y Y N manganese efflux pump 21908668 131567 cellular organisms no rank 26028 EBI-EMBL Putative manganese efflux pump manganese efflux pump MntP is a family of bacterial proteins with a signal peptide and four transmembrane domains. It is a putative manganese efflux pump, since deletion of the gene leads to profound manganese sensitivity and elevated intracellular manganese levels in bacteria. Manganese is a highly important trace nutrient for organisms from bacteria to humans, and acts as an important element in the defence against oxidative stress and as an enzyme cofactor [1]. [1]. 21908668. The Escherichia coli MntR miniregulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis. Waters LS, Sandoval M, Storz G;. J Bacteriol. 2011;193:5887-5897. (from Pfam) NF014691.5 PF02661.23 Fic 24 24 93 domain Y Y N Fic family protein 1656497,18757857,8411153 131567 cellular organisms no rank 139431 EBI-EMBL Fic/DOC family Fic family protein This family consists of the Fic (filamentation induced by cAMP) protein and doc (death on curing). The Fic protein is involved in cell division and is suggested to be involved in the synthesis of PAB or folate, indicating that the Fic protein and cAMP are involved in a regulatory mechanism of cell division via folate metabolism [1]. This family contains a central conserved motif HPFXXGNG in most members. The exact molecular function of these proteins is uncertain. P1 lysogens of Escherichia coli carry the prophage as a stable low copy number plasmid. The frequency with which viable cells cured of prophage are produced is about 10(-5) per cell per generation [1]. A significant part of this remarkable stability can be attributed to a plasmid-encoded mechanism that causes death of cells that have lost P1 [2]. In other words, the lysogenic cells appear to be addicted to the presence of the prophage. The plasmid withdrawal response depends on a gene named doc (death on curing) that is represented by this family [2]. Doc induces a reversible growth arrest of E. coli cells by targetting the protein synthesis machinery. Doc hosts the C-terminal domain of its antitoxin partner Phd (prevents host death) through fold complementation, a domain that is intrinsically disordered in solution but that folds into an alpha-helix on binding to Doc [3].This domain forms complexes with Phd antitoxins containing Pfam:PF02604. [1]. 1656497. Functional analysis of the fic gene involved in regulation of cell division. Komano T, Utsumi R, Kawamukai M;. Res Microbiol 1991;142:269-277. [2]. 8411153. Plasmid addiction genes of bacteriophage P1: do. TRUNCATED at 1650 bytes (from Pfam) NF014692.5 PF02662.21 FlpD 22.3 22.3 123 domain Y Y N hydrogenase iron-sulfur subunit 7730278 131567 cellular organisms no rank 4137 EBI-EMBL Methyl-viologen-reducing hydrogenase, delta subunit hydrogenase iron-sulfur subunit This family consist of methyl-viologen-reducing hydrogenase, delta subunit / heterodisulphide reductase. No specific functions have been assigned to this subunit. The aligned region corresponds to almost the entire delta chain sequence and contains 4 conserved cysteine residues. However, in two Archaeoglobus sequences this region corresponds to only the C-terminus of these proteins Swiss:O29030 and Swiss:029595. [1]. 7730278. Organization and growth phase-dependent transcription of methane genes in two regions of the Methanobacterium thermoautotrophicum genome. Nolling J, Pihl TD, Vriesema A, Reeve JN;. J Bacteriol 1995;177:2460-2468. (from Pfam) NF014693.5 PF02663.19 FmdE 22.9 22.9 133 domain Y Y N FmdE family protein 8954165 131567 cellular organisms no rank 4888 EBI-EMBL FmdE, Molybdenum formylmethanofuran dehydrogenase operon FmdE family protein This entry represents the FmdE protein that is encode by the molybdenum formylmethanofuran dehydrogenase operon. FmdE does not co-purify with the molybdenum isozyme that is formed by FmdC and FmdB [1]. The domain is typically found as a single copy, but is repeated in some sequence two to three times. It is also common place to find this domain co-occurs with a zinc-beta ribbon domain, suggesting that is may bind nucleic acid and be involved in transcription regulation. [1]. 8954165. The molybdenum formylmethanofuran dehydrogenase operon and the tungsten formylmethanofuran dehydrogenase operon from Methanobacterium thermoautotrophicum. Structures and transcriptional regulation. Hochheimer A, Linder D, Thauer RK, Hedderich R;. Eur J Biochem. 1996;242:156-162. (from Pfam) NF014695.5 PF02665.19 Nitrate_red_gam 22.9 22.9 217 domain Y Y N respiratory nitrate reductase subunit gamma 1.7.99.4 9738886 131567 cellular organisms no rank 22632 EBI-EMBL Nitrate reductase gamma subunit respiratory nitrate reductase subunit gamma This family is the gamma subunit of the nitrate reductase enzyme, the gamma subunit is a b-type cytochrome that receives electrons from the quinone pool [1]. It then transfers these via the iron-sulfur clusters of the beta subunit to the molybdenum cofactor found in the alpha subunit [1]. The nitrate reductase enzyme, EC:1.7.99.4 catalyses the conversion of nitrite to nitrate via the reduction of an acceptor. The nitrate reductase enzyme is composed of three subunits [1]. Nitrate is the most widely used alternative electron acceptor after oxygen [1]. [1]. 9738886. Identification and characterization of the Staphylococcus carnosus nitrate reductase operon. Pantel I, Lindgren PE, Neubauer H, Gotz F;. Mol Gen Genet 1998;259:105-114. (from Pfam) NF014696.5 PF02666.20 PS_Dcarbxylase 22 22 198 domain Y Y N phosphatidylserine decarboxylase GO:0004609,GO:0008654 7890740,9422599 131567 cellular organisms no rank 56232 EBI-EMBL Phosphatidylserine decarboxylase phosphatidylserine decarboxylase This is a family of phosphatidylserine decarboxylases, EC:4.1.1.65. These enzymes catalyse the reaction: Phosphatidyl-L-serine phosphatidylethanolamine + CO2. Phosphatidylserine decarboxylase plays a central role in the biosynthesis of aminophospholipids by converting phosphatidylserine to phosphatidylethanolamine [2]. [1]. 9422599. Cloning, sequencing, and disruption of the Bacillus subtilis psd gene coding for phosphatidylserine decarboxylase. Matsumoto K, Okada M, Horikoshi Y, Matsuzaki H, Kishi T, Itaya M, Shibuya I;. J Bacteriol 1998;180:100-106. [2]. 7890740. Phosphatidylserine decarboxylase 2 of Saccharomyces cerevisiae. Cloning and mapping of the gene, heterologous expression, and creation of the null allele. Trotter PJ, Pedretti J, Yates R, Voelker DR;. J Biol Chem 1995;270:6071-6080. (from Pfam) NF014697.5 PF02667.19 SCFA_trans 27 27 453 domain Y Y N TIGR00366 family protein 131567 cellular organisms no rank 21698 EBI-EMBL Short chain fatty acid transporter TIGR00366 family protein This family consists of two sequences annotated as short chain fatty acid transporters, however, there are no references giving details of experimental characterisation of this function. (from Pfam) NF014699.5 PF02669.20 KdpC 24.1 24.1 182 domain Y Y N potassium-transporting ATPase subunit C 7.2.2.6 GO:0006813,GO:0008556,GO:0016020 9858692 131567 cellular organisms no rank 43007 EBI-EMBL K+-transporting ATPase, c chain potassium-transporting ATPase subunit C This family consists of K+-transporting ATPase, c chain, KdpC. KdpC forms strong interactions with the KdpA subunit, serving to assemble and stabilise the Kdp complex [1]. It has been suggested that KdpC could be one of the connecting links between the energy providing subunit KdpB and the K+-transporting subunit KdpA [1]. The K+ transport system actively transports K+ ions via ATP hydrolysis. [1]. 9858692. Assembly of the Kdp complex, the multi-subunit K+-transport ATPase of Escherichia coli. Gassel M, Siebers A, Epstein W, Altendorf K;. Biochim Biophys Acta 1998;1415:77-84. (from Pfam) NF014700.5 PF02670.21 DXP_reductoisom 21.7 21.7 129 PfamEq Y N N 1-deoxy-D-xylulose 5-phosphate reductoisomerase GO:0070402 9707569 131567 cellular organisms no rank 67656 EBI-EMBL 1-deoxy-D-xylulose 5-phosphate reductoisomerase 1-deoxy-D-xylulose 5-phosphate reductoisomerase This is a family of 1-deoxy-D-xylulose 5-phosphate reductoisomerases. This enzyme catalyses the formation of 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose-5-phosphate in the presence of NADPH [1]. This reaction is part of the terpenoid biosynthesis pathway. [1]. 9707569. A 1-deoxy-D-xylulose 5-phosphate reductoisomerase catalyzing the formation of 2-C-methyl-D-erythritol 4-phosphate in an alternative nonmevalonate pathway for terpenoid biosynthesis. Takahashi S, Kuzuyama T, Watanabe H, Seto H;. Proc Natl Acad Sci U S A 1998;95:9879-9884. (from Pfam) NF014703.5 PF02673.23 BacA 33.4 33.4 257 domain Y Y N undecaprenyl-diphosphate phosphatase GO:0016020,GO:0016311,GO:0050380 15138271,15778224,8389741 131567 cellular organisms no rank 73550 EBI-EMBL Bacitracin resistance protein BacA undecaprenyl-diphosphate phosphatase Bacitracin resistance protein (BacA) is a putative undecaprenol kinase. BacA confers resistance to bacitracin, probably by phosphorylation of undecaprenol [1]. More recent studies show that BacA has undecaprenyl pyrophosphate phosphatase activity. Undecaprenyl phosphate is a key lipid intermediate involved in the synthesis of various bacterial cell wall polymers. Bacitracin, a mixture of related cyclic polypeptide antibiotics, is used to treat surface tissue infections. Its primary mode of action is the inhibition of bacterial cell wall synthesis through sequestration of the essential carrier lipid undecaprenyl pyrophosphate, C55-PP, resulting in the loss of cell integrity and lysis [2,3]. The characteristic phosphatase sequence-motif in this family is likely to be the PGxSRSGG, compared with the PSGH of the PAP family of phosphatases [3]. [1]. 8389741. Amplification of the bacA gene confers bacitracin resistance to Escherichia coli. Cain BD, Norton PJ, Eubanks W, Nick HS, Allen CM;. J Bacteriol 1993;175:3784-3789. [2]. 15138271. The bacA gene of Escherichia coli encodes an undecaprenyl pyrophosphate phosphatase activity. El Ghachi M, Bouhss A, Blanot D, Mengin-Lecreulx D;. J Biol Chem. 2004;279:30106-30113. [3]. 15778224. Identification of multiple genes encoding membrane proteins with undecaprenyl pyrophosphate phosphatase (UppP) activity in Escherichia coli. El Ghachi M, Derbise A, Bouhss A, Mengin-Lecreulx D;. J Biol Chem. 2005;280:18689-18695. (from Pfam) NF014705.5 PF02675.20 AdoMet_dc 25 25 107 domain Y Y N S-adenosylmethionine decarboxylase 4.1.1.50 GO:0004014,GO:0008295 10844697,11526206 131567 cellular organisms no rank 18620 EBI-EMBL S-adenosylmethionine decarboxylase S-adenosylmethionine decarboxylase This family contains several S-adenosylmethionine decarboxylase proteins from bacterial and archaebacterial species. S-adenosylmethionine decarboxylase (AdoMetDC), a key enzyme in the biosynthesis of spermidine and spermine, is first synthesised as a proenzyme, which is cleaved post translationally to form alpha and beta subunits. The alpha subunit contains a covalently bound pyruvoyl group derived from serine that is essential for activity [1,2]. [1]. 11526206. In vivo mechanism-based inactivation of S-adenosylmethionine decarboxylases from Escherichia coli, Salmonella typhimurium, and Saccharomyces cerevisiae. Li YF, Hess S, Pannell LK, White Tabor C, Tabor H;. Proc Natl Acad Sci U S A 2001;98:10578-10583. [2]. 10844697. S-adenosylmethionine decarboxylase of Bacillus subtilis is closely related to archaebacterial counterparts. Sekowska A, Coppee JY, Le Caer JP, Martin-Verstraete I, Danchin A;. Mol Microbiol 2000;36:1135-1147. (from Pfam) NF014708.5 PF02678.21 Pirin 26.1 26.1 108 domain Y Y N pirin family protein 10362352,11485202,14573596,9079676 131567 cellular organisms no rank 134612 EBI-EMBL Pirin pirin family protein This family consists of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localised within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures [1]. A tomato homologue of human Pirin has been found to be induced during programmed cell death [2]. Human Pirin interacts with Bcl-3 and NFI [3] and hence is probably involved in the regulation of DNA transcription and replication. It appears to be an Fe(II)-containing member of the Cupin superfamily. [1]. 9079676. Identification of pirin, a novel highly conserved nuclear protein. Wendler WM, Kremmer E, Forster R, Winnacker EL;. J Biol Chem 1997;272:8482-8489. [2]. 11485202. A tomato homologue of the human protein PIRIN is induced during programmed cell death. Orzaez D, de Jong AJ, Woltering EJ;. Plant Mol Biol 2001;46:459-468. [3]. 10362352. The Bcl-3 oncoprotein acts as a bridging factor between NF-kappaB/Rel and nuclear co-regulators. Dechend R, Hirano F, Lehmann K, Heissmeyer V, Ansieau S, Wulczyn FG, Scheidereit C, Leutz A;. Oncogene 1999;18:3316-3323. [4]. 14573596. Crystal structure of human pirin: an iron-binding nuclear protein and transcription cofactor. Pang H, Bartlam M, Zeng Q, Miyatake H, Hisano T, Miki K, Wong LL, Gao GF, Rao Z;. J Biol Chem 2004;279:1491-1498. (from Pfam) NF014709.5 PF02679.20 ComA 25.2 25.2 243 domain Y Y N phosphosulfolactate synthase 4.4.1.19 11830598 131567 cellular organisms no rank 4202 EBI-EMBL (2R)-phospho-3-sulfolactate synthase (ComA) phosphosulfolactate synthase In methanobacteria (2R)-phospho-3-sulfolactate synthase (ComA) catalyses the first step of the biosynthesis of coenzyme M from phosphoenolpyruvate (P-enolpyruvate). This novel enzyme catalyses the stereospecific Michael addition of sulfite to P-enolpyruvate, forming L-2-phospho-3-sulfolactate (PSL). It is suggested that the ComA-catalysed reaction is analogous to those reactions catalysed by beta-elimination enzymes that proceed through an enolate intermediate [1]. [1]. 11830598. Identification of coenzyme M biosynthetic phosphosulfolactate synthase: a new family of sulfonate-biosynthesizing enzymes. Graham DE, Xu H, White RH;. J Biol Chem 2002;277:13421-13429. (from Pfam) NF014710.5 PF02680.19 DUF211 22.1 22.1 89 domain Y Y N DUF211 domain-containing protein 131567 cellular organisms no rank 831 EBI-EMBL Uncharacterized ArCR, COG1888 Uncharacterized ArCR, COG1888 NF014711.5 PF02681.19 DUF212 26.5 26.5 126 domain Y Y N divergent PAP2 family protein 131567 cellular organisms no rank 7038 EBI-EMBL Divergent PAP2 family divergent PAP2 family protein This family is related to the Pfam:PF01569 family (personal obs: C Yeats). (from Pfam) NF014712.5 PF02682.21 CT_C_D 22.1 22.1 202 domain Y Y N carboxyltransferase domain-containing protein 20884691,9334321 131567 cellular organisms no rank 78887 EBI-EMBL Carboxyltransferase domain, subdomain C and D carboxyltransferase domain-containing protein Urea carboxylase (UC) catalyses a two-step, ATP- and biotin-dependent carboxylation reaction of urea. It is composed of biotin carboxylase (BC), carboxyltransferase (CT), and biotin carboxyl carrier protein (BCCP) domains. The CT domain of UC consists of four subdomains, named A, B, C and D. This domain covers the C and D subdomains of the CT domain. This domain covers the whole length of kipI (kinase A inhibitor) from Bacillus subtilis [1]. It can also be found in S. cerevisiae urea amidolyase Dur1,2, which is a multifunctional biotin-dependent enzyme with domains for urea carboxylase and allophanate (urea carboxylate) hydrolase activity[2]. [1]. 9334321. A novel histidine kinase inhibitor regulating development in Bacillus subtilis. Wang L, Grau R, Perego M, Hoch JA;. Genes Dev. 1997;11:2569-2579. [2]. 20884691. Dur3 is the major urea transporter in Candida albicans and is co-regulated with the urea amidolyase Dur1,2. Navarathna DH, Das A, Morschhauser J, Nickerson KW, Roberts DD;. Microbiology. 2011;157:270-279. (from Pfam) NF014713.5 PF02683.20 DsbD 27.5 27.5 213 domain Y Y N cytochrome c biogenesis protein CcdA GO:0016020,GO:0017004 7623667,7628442 131567 cellular organisms no rank 124925 EBI-EMBL Cytochrome C biogenesis protein transmembrane region cytochrome c biogenesis protein CcdA This family consists of the transmembrane (i.e. non-catalytic) region of Cytochrome C biogenesis proteins also known as disulphide interchange proteins. These proteins posses a protein disulphide isomerase like domain that is not found within the aligned region of this family. [1]. 7623667. The biogenesis of c-type cytochromes in Escherichia coli requires a membrane-bound protein, DipZ, with a protein disulphide isomerase-like domain. Crooke H, Cole J;. Mol Microbiol 1995;15:1139-1150. [2]. 7628442. Identification and characterization of a new disulfide isomerase-like protein (DsbD) in Escherichia coli. Missiakas D, Schwager F, Raina S;. EMBO J 1995;14:3415-3424. (from Pfam) NF014714.5 PF02684.20 LpxB 22.6 22.6 374 PfamEq Y N N Lipid-A-disaccharide synthetase GO:0008915,GO:0009245 2824445,8917090 131567 cellular organisms no rank 45053 EBI-EMBL Lipid-A-disaccharide synthetase Lipid-A-disaccharide synthetase This is a family of lipid-A-disaccharide synthetases, EC:2.4.2.128. These enzymes catalyse the reaction: UDP-2,3-bis(3-hydroxytetradecanoyl) glucosamine + 2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate UDP + 2,3-bis(3-hydroxytetradecanoyl)-D-glucosaminyl-1,6 -beta-D-2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate. These enzymes catalyse the fist disaccharide step in the synthesis of lipid-A-disaccharide. [1]. 8917090. Cloning and expression of genes encoding lipid A biosynthesis from Haemophilus influenzae type b. Servos S, Khan S, Maskell D;. Gene 1996;175:137-141. [2]. 2824445. Nucleotide sequence of the Escherichia coli gene for lipid A disaccharide synthase. Crowell DN, Reznikoff WS, Raetz CR;. J Bacteriol 1987;169:5727-5734. (from Pfam) NF014716.5 PF02686.20 GatC 23 23 66 PfamEq Y N N Glu-tRNAGln amidotransferase C subunit GO:0006450 25548166,9342321 131567 cellular organisms no rank 33250 EBI-EMBL Glu-tRNAGln amidotransferase C subunit Glu-tRNAGln amidotransferase C subunit This is a family of Glu-tRNAGln amidotransferase C subunits. The Glu-tRNA Gln amidotransferase enzyme itself is an important translational fidelity mechanism replacing incorrectly charged Glu-tRNAGln with the correct Gln-tRANGln via transmidation of the misacylated Glu-tRNAGln [1,2]. This activity supplements the lack of glutaminyl-tRNA synthetase activity in gram-positive eubacterteria, cyanobacteria, Archaea, and organelles [1]. This entry includes the C subunit of the bacterial/archaeal aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferases and eukaryotic Glu-tRNAGln amidotransferases (GatC). [1]. 9342321. Glu-tRNAGln amidotransferase: a novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Curnow AW, Hong Kw, Yuan R, Kim Si, Martins O, Winkler W, Henkin TM, Soll D;. Proc Natl Acad Sci U S A 1997;94:11819-11826. [2]. 25548166. Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis. Suzuki T, Nakamura A, Kato K, Soll D, Tanaka I, Sheppard K, Yao M;. Proc Natl Acad Sci U S A. 2015;112:382-387. (from Pfam) NF014717.5 PF02687.26 FtsX 25.5 25.5 120 domain Y Y N FtsX-like permease family protein GO:0016020 131567 cellular organisms no rank 703928 EBI-EMBL FtsX-like permease family FtsX-like permease family protein This is a family of predicted permeases and hypothetical transmembrane proteins. Swiss:P57382 has been shown to transport lipids targeted to the outer membrane across the inner membrane. Both Swiss:P57382 and Swiss:O54500 have been shown to require ATP. This region contains three transmembrane helices. (from Pfam) NF014719.5 PF02690.20 Na_Pi_cotrans 29.1 29.1 137 domain Y N N Na+/Pi-cotransporter GO:0005436,GO:0016020,GO:0044341 9826740 131567 cellular organisms no rank 42657 EBI-EMBL Na+/Pi-cotransporter Na+/Pi-cotransporter This is a family of mainly mammalian type II renal Na+/Pi-cotransporters with other related sequences from lower eukaryotes and bacteria some of which are also Na+/Pi-cotransporters. In the kidney the type II renal Na+/Pi-cotransporters protein allows re-absorption of filtered Pi in the proximal tubule [1]. [1]. 9826740. Characterization of a murine type II sodium-phosphate cotransporter expressed in mammalian small intestine. Hilfiker H, Hattenhauer O, Traebert M, Forster I, Murer H, Biber J;. Proc Natl Acad Sci U S A 1998;95:14564-14569. (from Pfam) NF014721.5 PF02694.20 UPF0060 24.9 24.9 107 PfamEq Y N N Uncharacterised BCR, YnfA/UPF0060 family GO:0016020 29769716 131567 cellular organisms no rank 24094 EBI-EMBL Uncharacterised BCR, YnfA/UPF0060 family Uncharacterised BCR, YnfA/UPF0060 family Some members of this family have been proposed to function as a thallium-specific efflux pump [1]. [1]. 29769716. Mutant phenotypes for thousands of bacterial genes of unknown function. Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM;. Nature. 2018;557:503-509. (from Pfam) NF014722.5 PF02696.19 SelO 22.8 22.8 466 PfamEq Y Y N protein adenylyltransferase SelO family protein 24751718,30270044 131567 cellular organisms no rank 51997 EBI-EMBL Protein adenylyltransferase SelO protein adenylyltransferase SelO family protein SelO and its homologues are widespread among most eukaryotic taxa, and are also common in many major bacterial taxa. SelO is a conserved pseudokinase that transfers AMP from ATP to Ser, Thr, and Tyr residues on protein substrates (AMPylation). It contains a protein kinase fold with ATP flipped in the active site [1]. In eukaryotes, it is a mitochondrial protein that may be involved in redox biology [2]. [1]. 30270044. Protein AMPylation by an Evolutionarily Conserved Pseudokinase. Sreelatha A, Yee SS, Lopez VA, Park BC, Kinch LN, Pilch S, Servage KA, Zhang J, Jiou J, Karasiewicz-Urbanska M, Lobocka M, Grishin NV, Orth K, Kucharczyk R, Pawlowski K, Tomchick DR, Tagliabracci VS;. Cell. 2018;175:809-821. [2]. 24751718. Characterization of mammalian selenoprotein o: a redox-active mitochondrial protein. Han SJ, Lee BC, Yim SH, Gladyshev VN, Lee SR;. PLoS One. 2014;9:e95518. (from Pfam) NF014723.5 PF02697.19 VAPB_antitox 27.9 27.9 69 domain Y Y N antitoxin VapB family protein 15718296 131567 cellular organisms no rank 1732 EBI-EMBL Putative antitoxin antitoxin VapB family protein Proteins in this family are possibly the antitoxin component of a VAPBC-like toxin-antitoxin (TA) module, which is widespread in the in both archaea and bacteria [1]. [1]. 15718296. Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Pandey DP, Gerdes K;. Nucleic Acids Res. 2005;33:966-976. (from Pfam) NF014724.5 PF02698.22 DUF218 24.8 24.8 133 domain Y Y N ElyC/SanA/YdcF family protein 8550448,9738879 131567 cellular organisms no rank 123175 EBI-EMBL DUF218 domain DUF218 domain-containing protein This large family of proteins contains several highly conserved charged amino acids, suggesting this may be an enzymatic domain (Bateman A pers. obs). The family includes SanA Swiss:P33017 that is involved in Vancomycin resistance [1]. This protein may be involved in murein synthesis [2]. [1]. 8550448. Amplification of a novel gene, sanA, abolishes a vancomycin-sensitive defect in Escherichia coli. Rida S, Caillet J, Alix JH;. J Bacteriol 1996;178:94-102. [2]. 9738879. The sfiX, rfe and metN genes of Salmonella typhimurium and their involvement in the His(c) pleiotropic response. Mouslim C, Cano DA, Casadesus J;. Mol Gen Genet 1998;259:46-53. (from Pfam) NF014726.5 PF02700.19 PurS 22.2 22.2 77 PfamEq Y Y N phosphoribosylformylglycinamidine synthase subunit PurS 6.3.5.3 10071207 131567 cellular organisms no rank 20457 EBI-EMBL Phosphoribosylformylglycinamidine (FGAM) synthase phosphoribosylformylglycinamidine synthase subunit PurS This family forms a component of the de novo purine biosynthesis pathway. [1]. 10071207. Isolation and characterization of a purC(orf)QLF operon from Lactococcus [correction of Lactobacillus] lactis MG1614. Peltonen T, Mantsala P;. Mol Gen Genet 1999;261:31-41. (from Pfam) NF014728.5 PF02702.22 KdpD 26.1 26.1 210 domain Y N N Osmosensitive K+ channel His kinase sensor domain GO:0000155,GO:0000160,GO:0004673,GO:0016020 1532388,34424339,9226259 131567 cellular organisms no rank 57238 EBI-EMBL Osmosensitive K+ channel His kinase sensor domain Osmosensitive K+ channel His kinase sensor domain This entry represents an N-terminal domain found in KdpD sensor kinase proteins that regulate the kdpFABC operon responsible for potassium transport [1]. The aligned region corresponds to a cytoplasmic part of the protein which functions as the sensor domain responsible for sensing turgor pressure [2]. It recognises C-di-AMP and K+ [3]. [1]. 9226259. The kdp system of Clostridium acetobutylicum: cloning, sequencing, and transcriptional regulation in response to potassium concentration. Treuner-Lange A, Kuhn A, Durre P;. J Bacteriol 1997;179:4501-4512. [2]. 1532388. KdpD and KdpE, proteins that control expression of the kdpABC operon, are members of the two-component sensor-effector class of regulators. Walderhaug MO, Polarek JW, Voelkner P, Daniel JM, Hesse JE, Altendorf K, Epstein W;. J Bacteriol 1992;174:2152-2159. [3]. 34424339. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. Matilla MA, Velando F, Martin-Mora D, Monteagudo-Cascales E, Krell T;. FEMS Microbiol Rev. 2022;46:fuab043. (from Pfam) NF014731.5 PF02705.21 K_trans 24.8 24.8 454 domain Y Y N KUP/HAK/KT family potassium transporter GO:0015079,GO:0016020 7621817,8226635,9350997 131567 cellular organisms no rank 40262 EBI-EMBL K+ potassium transporter integral membrane domain K+ potassium transporter integral membrane domain This is a family of K+ potassium transporters that are conserved across phyla, having both bacterial (KUP) Swiss:P30016 [3], yeast (HAK) Swiss:P50505 [2], and plant (AtKT) Swiss:O22397 [1] sequences as members. This entry represents the N-terminal integral membrane domain. [1]. 9350997. A new family of K+ transporters from Arabidopsis that are conserved across phyla. Quintero FJ, Blatt MR;. FEBS Lett 1997;415:206-211. [2]. 7621817. A potassium transporter of the yeast Schwanniomyces occidentalis homologous to the Kup system of Escherichia coli has a high concentrative capacity. Banuelos MA, Klein RD, Alexander-Bowman SJ, Rodriguez-Navarro A;. EMBO J 1995;14:3021-3027. [3]. 8226635. Nucleotide sequence and 3'-end deletion studies indicate that the K(+)-uptake protein kup from Escherichia coli is composed of a hydrophobic core linked to a large and partially essential hydrophilic C terminus. Schleyer M, Bakker EP;. J Bacteriol 1993;175:6925-6931. (from Pfam) NF014732.5 PF02706.20 Wzz 25.5 25.5 91 domain Y Y N Wzz/FepE/Etk N-terminal domain-containing protein GO:0009103,GO:0016020 9573151 131567 cellular organisms no rank 140685 EBI-EMBL Chain length determinant protein Wzz/FepE/Etk N-terminal domain This HMM describes an N-terminal region of homology share by two different classes of chain length determinant proteins (also known as polysaccharide co-polymerases) and by membrane-bound tyrosine kinases such Etk, involved in the polysaccharide export. NF014734.5 PF02709.19 Glyco_transf_7C 23 23 78 domain Y Y N galactosyltransferase-related protein 9435216,9792633 131567 cellular organisms no rank 25928 EBI-EMBL N-terminal domain of galactosyltransferase galactosyltransferase-related protein This is the N-terminal domain of a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases. EC:2.4.1.90, N-acetyllactosamine synthase; EC:2.4.1.38, Beta-N-acetylglucosaminyl-glycopeptide beta-1,4- galactosyltransferase; and EC:2.4.1.22 Lactose synthase. Note that N-acetyllactosamine synthase is a component of Lactose synthase along with alpha-lactalbumin, in the absence of alpha-lactalbumin EC:2.4.1.90 is the catalysed reaction. [1]. 9435216. Molecular cloning of a human cDNA encoding beta-1,4-galactosyltransferase with 37% identity to mammalian UDP-Gal:GlcNAc beta-1,4-galactosyltransferase. Sato T, Furukawa K, Bakker H, Van den Eijnden DH, Van Die I;. Proc Natl Acad Sci U S A 1998;95:472-477. [2]. 9792633. Cloning of a novel member of the UDP-galactose:beta-N-acetylglucosamine beta1,4-galactosyltransferase family, beta4Gal-T4, involved in glycosphingolipid biosynthesis. Schwientek T, Almeida R, Levery SB, Holmes EH, Bennett E, Clausen H;. J Biol Chem 1998;273:29331-29340. (from Pfam) NF014740.5 PF02719.20 Polysacc_synt_2 20.2 20.2 293 domain Y Y N polysaccharide biosynthesis protein 7961465,9079898 131567 cellular organisms no rank 613496 EBI-EMBL Polysaccharide biosynthesis protein polysaccharide biosynthesis protein This is a family of diverse bacterial polysaccharide biosynthesis proteins including the CapD protein (Swiss:P39853) [1], WalL protein (Swiss:O86159) mannosyl-transferase (Swiss:O05349) [2] and several putative epimerases (e.g. WbiI Swiss:O69130). [1]. 7961465. Sequence analysis and molecular characterization of genes required for the biosynthesis of type 1 capsular polysaccharide in Staphylococcus aureus. Lin WS, Cunneen T, Lee CY;. J Bacteriol 1994;176:7005-7016. [2]. 9079898. Identification of additional genes required for O-antigen biosynthesis in Vibrio cholerae O1. Fallarino A, Mavrangelos C, Stroeher UH, Manning PA;. J Bacteriol 1997;179:2147-2153. (from Pfam) NF014747.5 PF02727.21 Cu_amine_oxidN2 21 21 87 PfamEq Y N N Copper amine oxidase, N2 domain GO:0005507,GO:0008131,GO:0009308,GO:0048038 8591028 131567 cellular organisms no rank 11274 EBI-EMBL Copper amine oxidase, N2 domain Copper amine oxidase, N2 domain This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). [1]. 8591028. Crystal structure of a quinoenzyme: copper amine oxidase of Escherichia coli at 2 A resolution. Parsons MR, Convery MA, Wilmot CM, Yadav KD, Blakeley V, Corner AS, Phillips SE, McPherson MJ, Knowles PF;. Structure 1995;3:1171-1184. (from Pfam) NF014748.5 PF02728.21 Cu_amine_oxidN3 22.6 22.6 100 domain Y N N Copper amine oxidase, N3 domain GO:0005507,GO:0008131,GO:0009308,GO:0048038 8591028 131567 cellular organisms no rank 13316 EBI-EMBL Copper amine oxidase, N3 domain Copper amine oxidase, N3 domain This domain is the second or third structural domain in copper amine oxidases, it is known as the N3 domain. Its function is uncertain. The catalytic domain can be found in Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). [1]. 8591028. Crystal structure of a quinoenzyme: copper amine oxidase of Escherichia coli at 2 A resolution. Parsons MR, Convery MA, Wilmot CM, Yadav KD, Blakeley V, Corner AS, Phillips SE, McPherson MJ, Knowles PF;. Structure 1995;3:1171-1184. (from Pfam) NF014749.5 PF02729.26 OTCace_N 29.9 29.9 148 domain Y N N Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain GO:0006520,GO:0016743 10318893 131567 cellular organisms no rank 142215 EBI-EMBL Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain NF014750.5 PF02730.20 AFOR_N 29.8 29.8 199 domain Y Y N aldehyde ferredoxin oxidoreductase N-terminal domain-containing protein GO:0016491,GO:0016625,GO:0051536 7878465 131567 cellular organisms no rank 12378 EBI-EMBL Aldehyde ferredoxin oxidoreductase, N-terminal domain Aldehyde ferredoxin oxidoreductase, N-terminal domain Aldehyde ferredoxin oxidoreductase (AOR) catalyses the reversible oxidation of aldehydes to their corresponding carboxylic acids with their accompanying reduction of the redox protein ferredoxin. This domain interacts with the tungsten cofactor [1]. [1]. 7878465. Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase. Chan MK, Mukund S, Kletzin A, Adams MW, Rees DC;. Science 1995;267:1463-1469. (from Pfam) NF014752.5 PF02732.20 ERCC4 24 24 140 domain Y Y N ERCC4 domain-containing protein GO:0003677,GO:0004518 11719193,14527419,22638584 131567 cellular organisms no rank 4495 EBI-EMBL ERCC4 domain ERCC4 domain This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase [2-3]. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease. [2]. 14527419. The endogenous Mus81-Eme1 complex resolves Holliday junctions by a nick and counternick mechanism. Gaillard PH, Noguchi E, Shanahan P, Russell P;. Mol Cell. 2003;12:747-759. [3]. 11719193. Mus81-Eme1 are essential components of a Holliday junction resolvase. Boddy MN, Gaillard PH, McDonald WH, Shanahan P, Yates JR 3rd, Russell P;. Cell. 2001;107:537-548. [3]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF014753.5 PF02733.22 Dak1 31.4 31.4 313 domain Y Y N dihydroxyacetone kinase subunit DhaK 2.7.1.121 GO:0004371,GO:0006071 131567 cellular organisms no rank 54582 EBI-EMBL Dak1 domain Dak1 domain This is the kinase domain of the dihydroxyacetone kinase family EC:2.7.1.29. (from Pfam) NF014754.5 PF02734.22 Dak2 27 27 174 domain Y Y N DAK2 domain-containing protein GO:0004371,GO:0006071 131567 cellular organisms no rank 85191 EBI-EMBL DAK2 domain DAK2 domain This domain is the predicted phosphatase domain of the dihydroxyacetone kinase family. (from Pfam) NF014755.5 PF02735.21 Ku 25 25 190 domain Y Y N Ku protein GO:0003677,GO:0006303 11483577,11493912 131567 cellular organisms no rank 47229 EBI-EMBL Ku70/Ku80 beta-barrel domain Ku70/Ku80 beta-barrel domain The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 Swiss:P12956 and Ku80 Swiss:P13010 proteins that form a DNA binding heterodimer [1]. [1]. 11493912. Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Walker JR, Corpina RA, Goldberg J;. Nature 2001;412:607-614. [2]. 11483577. Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system. Aravind L, Koonin EV;. Genome Res 2001;11:1365-1374. (from Pfam) NF014757.5 PF02737.23 3HCDH_N 22 22 180 domain Y Y N 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein GO:0006631,GO:0070403 3479790 131567 cellular organisms no rank 345476 EBI-EMBL 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain The term 3-hydroxyacyl-CoA dehydrogenase, corresponding to EC 1.1.1.35, covers a range of specificities, as the acyl group is not specified. Beta-hydroxyacyl dehydrogenase is a synonym. There may be mulitple members of the family in a single genome, e.g. FadB, FabJ, and PaaH from Escherichia coli K-12. NF014758.5 PF02738.23 MoCoBD_1 27 27 244 domain Y Y N molybdopterin cofactor-binding domain-containing protein GO:0016491 10430865,7502041 131567 cellular organisms no rank 217637 EBI-EMBL Molybdopterin cofactor-binding domain Molybdopterin cofactor-binding domain NF014759.5 PF02739.21 5_3_exonuc_N 34.3 34.3 164 domain Y N N 5'-3' exonuclease, N-terminal resolvase-like domain GO:0003677 8657312,8717047 131567 cellular organisms no rank 130445 EBI-EMBL 5'-3' exonuclease, N-terminal resolvase-like domain 5'-3' exonuclease, N-terminal resolvase-like domain NF014761.5 PF02741.20 FTR_C 25 25 149 domain Y N N FTR, proximal lobe GO:0006730,GO:0016740 9195883 131567 cellular organisms no rank 2417 EBI-EMBL FTR, proximal lobe FTR, proximal lobe The FTR (Formylmethanofuran--tetrahydromethanopterin formyltransferase) enzyme EC:2.3.1.101 is involved in archaebacteria in the formation of methane from carbon dioxide. C-terminal proximal lobe of alpha+beta ferredoxin-like fold. SCOP reports fold duplication with N-terminal distal lobe. [1]. 9195883. Formylmethanofuran: tetrahydromethanopterin formyltransferase from Methanopyrus kandleri - new insights into salt-dependence and thermostability. Ermler U, Merckel M, Thauer R, Shima S;. Structure 1997;5:635-646. (from Pfam) NF014762.5 PF02742.20 Fe_dep_repr_C 27 27 70 domain Y Y N iron dependent repressor, metal binding and dimerization domain protein GO:0046914,GO:0046983 7568230,7743135 131567 cellular organisms no rank 43106 EBI-EMBL Iron dependent repressor, metal binding and dimerisation domain Iron dependent repressor, metal binding and dimerisation domain This family includes the Diphtheria toxin repressor [1]. It acts as an iron-binding repressor of diphtheria toxin gene expression and may serve as a global regulator of gene expression. DTXR comprises an N-terminal DNA-binding domain, an interface domain (which contains two metal-binding sites) and a third, very flexible C-terminal domain. The second domain is responsible for dimerization and metal binding. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation [2]. This domain can also bind Cd(II), Ca(II) and Cu(II) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 7568230. Structures of the apo- and the metal ion-activated forms of the diphtheria tox repressor from Corynebacterium diphtheriae. Schiering N, Tao X, Zeng H, Murphy JR, Petsko GA, Ringe D;. Proc Natl Acad Sci USA 1995;92:9843-9850. [2]. 7743135. Three-dimensional structure of the diphtheria toxin repressor in complex with divalent cation co-repressors. Qiu X, Verlinde CL, Zhang S, Schmitt MP, Holmes RK, Hol WG;. Structure 1995;3:87-100. (from Pfam) NF014763.5 PF02743.23 dCache_1 45 45 240 domain Y Y N cache domain-containing protein 11084361,27049771 131567 cellular organisms no rank 185063 EBI-EMBL Cache domain cache domain Double cache domain 1 covers the last three strands from the membrane distal PAS-like domain, the first two strands of the membrane proximal domain, and the connecting elements between the two domains [2]. This domain when present in chemoreceptors recognise several signals such as proteinogenic amino acids, GABA, Histamine and polyamines, decanoic acid, Autoinducer-2, purine derivatives, quaternary amines, citrate and taurine, among others. When associated with histidine kinases, it recognises C3/C4-dicarboxylic acids, Spermine, guanosine and Autoinducer-2 (Mantilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1 https://doi.org/10.1093/femsre/fuab043). [1]. 11084361. Cache - a signaling domain common to animal Ca(2+)-channel subunits and a class of prokaryotic chemotaxis receptors. Anantharaman V, Aravind L;. Trends Biochem Sci 2000;25:535-537. [2]. 27049771. Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes. Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB;. PLoS Comput Biol. 2016;12:e1004862. (from Pfam) NF014764.5 PF02744.22 GalP_UDP_tr_C 29.2 29.2 165 domain Y N N Galactose-1-phosphate uridyl transferase, C-terminal domain GO:0006012,GO:0008108 7669762 131567 cellular organisms no rank 44219 EBI-EMBL Galactose-1-phosphate uridyl transferase, C-terminal domain Galactose-1-phosphate uridyl transferase, C-terminal domain SCOP reports fold duplication with N-terminal domain. Both involved in Zn and Fe binding. [1]. 7669762. Three-dimensional structure of galactose-1-phosphate uridylyltransferase from Escherichia coli at 1.8 A resolution. Wedekind JE, Frey PA, Rayment I;. Biochemistry 1995;34:11049-11061. (from Pfam) NF014765.5 PF02745.20 MCR_alpha_N 27 27 269 domain Y N N Methyl-coenzyme M reductase alpha subunit, N-terminal domain GO:0015948,GO:0050524 9367957 131567 cellular organisms no rank 560 EBI-EMBL Methyl-coenzyme M reductase alpha subunit, N-terminal domain Methyl-coenzyme M reductase alpha subunit, N-terminal domain Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (this family), 2 beta (Pfam:PF02241), and 2 gamma (Pfam:PF02240) subunits with two identical nickel porphinoid active sites [1]. The N-terminal domain has a ferredoxin-like fold. [1]. 9367957. Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation. Ermler U, Grabarse W, Shima S, Goubeaud M, Thauer RK;. Science 1997;278:1457-1462. (from Pfam) NF014766.5 PF02746.21 MR_MLE_N 22 22 117 domain Y N N Mandelate racemase / muconate lactonizing enzyme, N-terminal domain 3612800 131567 cellular organisms no rank 207871 EBI-EMBL Mandelate racemase / muconate lactonizing enzyme, N-terminal domain Mandelate racemase / muconate lactonizing enzyme, N-terminal domain SCOP reports fold similarity with enolase N-terminal domain. [1]. 3612800. Crystal structure of muconate lactonizing enzyme at 3 A resolution. Goldman A, Ollis DL, Steitz TA;. J Mol Biol 1987;194:143-153. (from Pfam) NF014767.5 PF02747.20 PCNA_C 23 23 128 domain Y N N Proliferating cell nuclear antigen, C-terminal domain GO:0003677,GO:0006275 8001157 131567 cellular organisms no rank 1127 EBI-EMBL Proliferating cell nuclear antigen, C-terminal domain Proliferating cell nuclear antigen, C-terminal domain N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA. [1]. 8001157. Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Krishna TS, Kong XP, Gary S, Burgers PM, Kuriyan J;. Cell 1994;79:1233-1243. (from Pfam) NF014768.5 PF02748.20 PyrI_C 23.4 23.4 48 PfamEq Y N N Aspartate carbamoyltransferase regulatory chain, metal binding domain 10651286,364472 131567 cellular organisms no rank 7287 EBI-EMBL Aspartate carbamoyltransferase regulatory chain, metal binding domain Aspartate carbamoyltransferase regulatory chain, metal binding domain The regulatory chain is involved in allosteric regulation of aspartate carbamoyltransferase. The C-terminal metal binding domain has a rubredoxin-like fold and provides the interface with the catalytic chain. [1]. 364472. Three-dimensional structures of aspartate carbamoyltransferase from Escherichia coli and of its complex with cytidine triphosphate. Monaco HL, Crawford JL, Lipscomb WN;. Proc Natl Acad Sci U S A 1978;75:5276-5280. [2]. 10651286. Insights into the mechanisms of catalysis and heterotropic regulation of Escherichia coli aspartate transcarbamoylase based upon a structure of the enzyme complexed with the bisubstrate analogue N-phosphonacetyl-L-aspartate at 2.1 A. Jin L, Stec B, Lipscomb WN, Kantrowitz ER;. Proteins 1999;37:729-742. (from Pfam) NF014769.5 PF02749.21 QRPTase_N 27 27 82 domain Y N N Quinolinate phosphoribosyl transferase, N-terminal domain GO:0016763 26042198,8561507,9016724 131567 cellular organisms no rank 70430 EBI-EMBL Quinolinate phosphoribosyl transferase, N-terminal domain Quinolinate phosphoribosyl transferase, N-terminal domain Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase EC:2.4.2.19 is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [1,2]. The QA substrate is bound between the C-terminal domain of one subunit, and the N-terminal domain of the other. The N-terminal domain has an alpha/beta hammerhead fold. [1]. 9016724. A new function for a common fold: the crystal structure of quinolinic acid phosphoribosyltransferase. Eads JC, Ozturk D, Wexler TB, Grubmeyer C, Sacchettini JC;. Structure 1997;5:47-58. [2]. 8561507. The sequencing expression, purification, and steady-state kinetic analysis of quinolinate phosphoribosyl transferase from Escherichia coli. Bhatia R, Calvo KC;. Arch Biochem Biophys 1996;325:270-278. [3]. 26042198. Crystal structure of human nicotinic acid phosphoribosyltransferase. Marletta AS, Massarotti A, Orsomando G, Magni G, Rizzi M, Garavaglia S;. FEBS Open Bio. 2015;5:419-428. (from Pfam) NF014770.5 PF02750.19 Synapsin_C 22.5 22.5 203 domain Y N N Synapsin, ATP binding domain 9463376 131567 cellular organisms no rank 272 EBI-EMBL Synapsin, ATP binding domain Synapsin, ATP binding domain Ca dependent ATP binding in this ATP grasp fold. Function unknown. [1]. 9463376. Synapsin I is structurally similar to ATP-utilizing enzymes. Esser L, Wang CR, Hosaka M, Smagula CS, Sudhof TC, Deisenhofer J;. EMBO J 1998;17:977-984. (from Pfam) NF014774.5 PF02754.21 CCG 20.6 11.8 85 domain Y Y N heterodisulfide reductase-related iron-sulfur binding cluster 11952791,8606183 131567 cellular organisms no rank 161630 EBI-EMBL Cysteine-rich domain Cysteine-rich domain The key element of this family is the CX31-38CCX33-34CXXC sequence motif normally found at the C-terminus in archaeal and bacterial Hdr-like proteins [2]. There may be one or two copies, and the motif is probably an iron-sulfur binding cluster. In some instances one of the cysteines is replaced by an aspartate, and aspartate can in principle also function as a ligand of an iron-sulfur cluster [2]. The family includes a subunit from heterodisulphide reductase and a subunit from glycolate oxidase [1] Swiss:P52074 and glycerol-3-phosphate dehydrogenase. [1]. 8606183. glc locus of Escherichia coli: characterization of genes encoding the subunits of glycolate oxidase and the glc regulator protein. Pellicer MT, Badia J, Aguilar J, Baldoma L;. J Bacteriol 1996;178:2051-2059. [2]. 11952791. Purification and characterization of a membrane-bound enzyme complex from the sulfate-reducing archaeon Archaeoglobus fulgidus related to heterodisulfide reductase from methanogenic archaea. Mander GJ, Duin EC, Linder D, Stetter KO, Hedderich R;. Eur J Biochem. 2002;269:1895-1904. (from Pfam) NF014786.5 PF02767.21 DNA_pol3_beta_2 27 27 116 PfamEq Y N N DNA polymerase III beta subunit, central domain GO:0003887,GO:0006260,GO:0008408,GO:0009360 1349852 131567 cellular organisms no rank 68525 EBI-EMBL DNA polymerase III beta subunit, central domain DNA polymerase III beta subunit, central domain A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold. [1]. 1349852. Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. Kong XP, Onrust R, O'Donnell M, Kuriyan J;. Cell 1992;69:425-437. (from Pfam) NF014788.5 PF02769.27 AIRS_C 23.1 23.1 156 domain Y Y N AIR synthase-related protein 10508786 131567 cellular organisms no rank 278460 EBI-EMBL AIR synthase related protein, C-terminal domain AIR synthase C-terminal domain-related protein This family includes Hydrogen expression/formation protein HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The function of the C-terminal domain of AIR synthase is unclear, but the cleft formed between N and C domains is postulated as a sulphate binding site [1]. [1]. 10508786. X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 A resolution. Li C, Kappock TJ, Stubbe J, Weaver TM, Ealick SE;. Structure Fold Des 1999;7:1155-1166. (from Pfam) NF014789.5 PF02770.24 Acyl-CoA_dh_M 33.3 33.3 97 domain Y Y N acyl-CoA dehydrogenase family protein GO:0016627 7857927,8356049 131567 cellular organisms no rank 783557 EBI-EMBL Acyl-CoA dehydrogenase, middle domain Acyl-CoA dehydrogenase, middle domain Central domain of Acyl-CoA dehydrogenase has a beta-barrel fold. [1]. 7857927. Three-dimensional structure of butyryl-CoA dehydrogenase from Megasphaera elsdenii. Djordjevic S, Pace CP, Stankovich MT, Kim JJ;. Biochemistry. 1995;34:2163-2171. [2]. 8356049. Crystal structures of medium-chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate. Kim JJ, Wang M, Paschke R;. Proc Natl Acad Sci U S A 1993;90:7523-7527. (from Pfam) NF014790.5 PF02771.21 Acyl-CoA_dh_N 22.9 22.9 113 domain Y Y N acyl-CoA dehydrogenase family protein GO:0016627,GO:0050660 7857927,8356049 131567 cellular organisms no rank 861708 EBI-EMBL Acyl-CoA dehydrogenase, N-terminal domain Acyl-CoA dehydrogenase, N-terminal domain The N-terminal domain of Acyl-CoA dehydrogenase is an all-alpha domain. [1]. 7857927. Three-dimensional structure of butyryl-CoA dehydrogenase from Megasphaera elsdenii. Djordjevic S, Pace CP, Stankovich MT, Kim JJ;. Biochemistry. 1995;34:2163-2171. [2]. 8356049. Crystal structures of medium-chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate. Kim JJ, Wang M, Paschke R;. Proc Natl Acad Sci U S A 1993;90:7523-7527. (from Pfam) NF014791.5 PF02772.21 S-AdoMet_synt_M 29 29 120 PfamEq Y N N S-adenosylmethionine synthetase, central domain GO:0004478,GO:0006556 8611562 131567 cellular organisms no rank 65240 EBI-EMBL S-adenosylmethionine synthetase, central domain S-adenosylmethionine synthetase, central domain The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold. [1]. 8611562. Structure and function of S-adenosylmethionine synthetase: crystal structures of S-adenosylmethionine synthetase with ADP, BrADP, and PPi at 28 angstroms resolution. Takusagawa F, Kamitori S, Markham GD;. Biochemistry 1996;35:2586-2596. (from Pfam) NF014792.5 PF02773.21 S-AdoMet_synt_C 25 25 138 PfamEq Y Y N methionine adenosyltransferase domain-containing protein GO:0004478,GO:0006556 8611562 131567 cellular organisms no rank 66206 EBI-EMBL S-adenosylmethionine synthetase, C-terminal domain S-adenosylmethionine synthetase, C-terminal domain The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold. [1]. 8611562. Structure and function of S-adenosylmethionine synthetase: crystal structures of S-adenosylmethionine synthetase with ADP, BrADP, and PPi at 28 angstroms resolution. Takusagawa F, Kamitori S, Markham GD;. Biochemistry 1996;35:2586-2596. (from Pfam) NF014793.5 PF02774.23 Semialdhyde_dhC 26 26 184 domain Y Y N Asd/ArgC dimerization domain-containing protein GO:0008652,GO:0016620,GO:0046983 10369777 131567 cellular organisms no rank 143968 EBI-EMBL Semialdehyde dehydrogenase, dimerisation domain Asd/ArgC dimerization domain This Pfam domain model identifies C-terminal domains of N-acetyl-glutamine semialdehyde dehydrogenase (AgrC), aspartate-semialdehyde dehydrogenase (Asd) and a few other, less common enzymes. NF014794.5 PF02775.26 TPP_enzyme_C 21.9 21.9 151 domain Y Y N thiamine pyrophosphate-dependent enzyme GO:0003824,GO:0030976 8604141 131567 cellular organisms no rank 542787 EBI-EMBL Thiamine pyrophosphate enzyme, C-terminal TPP binding domain thiamine pyrophosphate-binding domain NF014795.5 PF02776.23 TPP_enzyme_N 26.8 26.8 119 domain Y Y N thiamine pyrophosphate-binding protein GO:0030976 8604141 131567 cellular organisms no rank 395656 EBI-EMBL Thiamine pyrophosphate enzyme, N-terminal TPP binding domain thiamine pyrophosphate-binding domain NF014796.5 PF02777.23 Sod_Fe_C 20.9 20.9 102 domain Y Y N Fe-Mn family superoxide dismutase GO:0004784,GO:0006801,GO:0046872 9878438 131567 cellular organisms no rank 68248 EBI-EMBL Iron/manganese superoxide dismutases, C-terminal domain Iron/manganese superoxide dismutases, C-terminal domain superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. C-terminal domain is a mixed alpha/beta fold. [1]. 9878438. Refined crystal structure of a superoxide dismutase from the hyperthermophilic archaeon Sulfolobus acidocaldarius at 2.2 A resolution. Knapp S, Kardinahl S, Hellgren N, Tibbelin G, Schafer G, Ladenstein R;. J Mol Biol 1999;285:689-702. (from Pfam) NF014798.5 PF02779.29 Transket_pyr 27 27 174 domain Y N N Transketolase, pyrimidine binding domain 1628611,8176731 131567 cellular organisms no rank 401642 EBI-EMBL Transketolase, pyrimidine binding domain Transketolase, pyrimidine binding domain This family includes transketolase enzymes, pyruvate dehydrogenases, and branched chain alpha-keto acid decarboxylases. [1]. 8176731. Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 A resolution. Nikkola M, Lindqvist Y, Schneider G;. J Mol Biol 1994;238:387-404. [2]. 1628611. Three-dimensional structure of transketolase, a thiamine diphosphate dependent enzyme, at 2.5 A resolution. Lindqvist Y, Schneider G, Ermler U, Sundstrom M;. EMBO J 1992;11:2373-2379. (from Pfam) NF014799.5 PF02780.25 Transketolase_C 25.9 25.9 124 domain Y Y N transketolase C-terminal domain-containing protein 1628611,8176731 131567 cellular organisms no rank 344453 EBI-EMBL Transketolase, C-terminal domain Transketolase, C-terminal domain The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site [2]. [1]. 8176731. Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 A resolution. Nikkola M, Lindqvist Y, Schneider G;. J Mol Biol 1994;238:387-404. [2]. 1628611. Three-dimensional structure of transketolase, a thiamine diphosphate dependent enzyme, at 2.5 A resolution. Lindqvist Y, Schneider G, Ermler U, Sundstrom M;. EMBO J 1992;11:2373-2379. (from Pfam) NF014801.5 PF02782.21 FGGY_C 27 27 198 domain Y Y N FGGY-family carbohydrate kinase GO:0005975,GO:0016301 8430315,9843423 131567 cellular organisms no rank 304917 EBI-EMBL FGGY family of carbohydrate kinases, C-terminal domain FGGY family of carbohydrate kinases, C-terminal domain This domain adopts a ribonuclease H-like fold and is structurally related to the N-terminal domain. [1]. 8430315. Structure of the regulatory complex of Escherichia coli IIIGlc with glycerol kinase. Hurley JH, Faber HR, Worthylake D, Meadow ND, Roseman S, Pettigrew DW, Remington SJ;. Science. 1993;259:673-677. [2]. 9843423. Crystal structure of a complex of Escherichia coli glycerol kinase and an allosteric effector fructose 1,6-bisphosphate. Ormo M, Bystrom CE, Remington SJ;. Biochemistry 1998;37:16565-16572. (from Pfam) NF014803.5 PF02784.21 Orn_Arg_deC_N 23.4 23.4 247 domain Y N N Pyridoxal-dependent decarboxylase, pyridoxal binding domain GO:0003824 10378276 131567 cellular organisms no rank 161613 EBI-EMBL Pyridoxal-dependent decarboxylase, pyridoxal binding domain Pyridoxal-dependent decarboxylase, pyridoxal binding domain These pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates This domain has a TIM barrel fold. [1]. 10378276. Structure of mammalian ornithine decarboxylase at 1.6 A resolution: stereochemical implications of PLP-dependent amino acid decarboxylases. Kern AD, Oliveira MA, Coffino P, Hackert ML;. Structure Fold Des 1999;7:567-581. (from Pfam) NF014804.5 PF02785.24 Biotin_carb_C 32.4 32.4 108 domain Y N N Biotin carboxylase C-terminal domain 7915138 131567 cellular organisms no rank 225837 EBI-EMBL Biotin carboxylase C-terminal domain Biotin carboxylase C-terminal domain Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference [1] are in this C-terminal domain. [1]. 7915138. Three-dimensional structure of the biotin carboxylase subunit. of acetyl-CoA carboxylase. Waldrop GL, Rayment I, Holden HM;. Biochemistry 1994;33:10249-10256. (from Pfam) NF014805.5 PF02786.22 CPSase_L_D2 19.8 19.8 211 domain Y N N Carbamoyl-phosphate synthase L chain, ATP binding domain GO:0005524 10089390,1972379,7915138 131567 cellular organisms no rank 548852 EBI-EMBL Carbamoyl-phosphate synthase L chain, ATP binding domain Carbamoyl-phosphate synthase L chain, ATP binding domain Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines [2]. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See Pfam:PF00988. The small chain has a GATase domain in the carboxyl terminus. See Pfam:PF00117. The ATP binding domain (this one) has an ATP-grasp fold. [1]. 7915138. Three-dimensional structure of the biotin carboxylase subunit. of acetyl-CoA carboxylase. Waldrop GL, Rayment I, Holden HM;. Biochemistry 1994;33:10249-10256. [2]. 1972379. Mammalian carbamyl phosphate synthetase (CPS). DNA sequence and evolution of the CPS domain of the Syrian hamster multifunctional protein CAD. Simmer JP, Kelly RE, Rinker AG Jr, Scully JL, Evans DR;. Biol Chem 1990;265:10395-10402. [3]. 10089390. The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution. Thoden JB, Raushel FM, Benning MM, Rayment I, Holden HM;. Acta Crystallogr D Biol Crystallogr 1999;55:8-24. (from Pfam) NF014806.5 PF02787.24 CPSase_L_D3 26.6 26.6 80 PfamEq Y N N Carbamoyl-phosphate synthetase large chain, oligomerisation domain 10089390 131567 cellular organisms no rank 92523 EBI-EMBL Carbamoyl-phosphate synthetase large chain, oligomerisation domain Carbamoyl-phosphate synthetase large chain, oligomerisation domain Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. [1]. 10089390. The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution. Thoden JB, Raushel FM, Benning MM, Rayment I, Holden HM;. Acta Crystallogr D Biol Crystallogr 1999;55:8-24. (from Pfam) NF014807.5 PF02788.21 RuBisCO_large_N 20.7 15 120 domain Y N N Ribulose bisphosphate carboxylase large chain, N-terminal domain GO:0015977,GO:0016984 9034362 131567 cellular organisms no rank 13493 EBI-EMBL Ribulose bisphosphate carboxylase large chain, N-terminal domain Ribulose bisphosphate carboxylase large chain, N-terminal domain The N-terminal domain of RuBisCO large chain adopts a ferredoxin-like fold. [1]. 9034362. The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate. Taylor TC, Andersson I;. J Mol Biol 1997;265:432-444. (from Pfam) NF014808.5 PF02789.22 Peptidase_M17_N 23.4 23.4 129 domain Y Y N M17 family peptidase N-terminal domain-containing protein GO:0006508,GO:0070006 2395881 131567 cellular organisms no rank 59809 EBI-EMBL Cytosol aminopeptidase family, N-terminal domain Cytosol aminopeptidase family, N-terminal domain NF014809.5 PF02790.20 COX2_TM 22.8 18 88 domain Y Y N cytochrome c oxidase subunit II transmembrane domain-containing protein GO:0016020,GO:0022900 8638158 131567 cellular organisms no rank 34945 EBI-EMBL Cytochrome C oxidase subunit II, transmembrane domain Cytochrome C oxidase subunit II, transmembrane domain The N-terminal domain of cytochrome C oxidase contains two transmembrane alpha-helices. [1]. 8638158. The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A. Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S;. Science 1996;272:1136-1144. (from Pfam) NF014814.5 PF02796.20 HTH_7 23.8 23.8 45 domain Y Y N helix-turn-helix domain-containing protein GO:0000150,GO:0003677,GO:0006310 7628011 131567 cellular organisms no rank 82401 EBI-EMBL Helix-turn-helix domain of resolvase helix-turn-helix domain-containing protein NF014816.5 PF02798.25 GST_N 20.9 20.9 76 domain Y N N Glutathione S-transferase, N-terminal domain GO:0005515,GO:0006749 9680481 131567 cellular organisms no rank 318447 EBI-EMBL Glutathione S-transferase, N-terminal domain Glutathione S-transferase, N-terminal domain Function: conjugation of reduced glutathione to a variety of targets. Also included in the alignment, but not GSTs: S-crystallins from squid (similarity to GST previously noted); eukaryotic elongation factors 1-gamma (not known to have GST activity and similarity not previously recognised); HSP26 family of stress-related proteins including auxin-regulated proteins in plants and stringent starvation proteins in E. coli (not known to have GST activity and similarity not previously recognised). The glutathione molecule binds in a cleft between the N- and C-terminal domains - the catalytically important residues are proposed to reside in the N-terminal domain [1]. [1]. 9680481. Three-dimensional structure of Escherichia coli glutathione S-transferase complexed with glutathione sulfonate: catalytic roles of Cys10 and His106. Nishida M, Harada S, Noguchi S, Satow Y, Inoue H, Takahashi K;. J Mol Biol 1998;281:135-147. (from Pfam) NF014818.5 PF02800.25 Gp_dh_C 24.4 24.4 158 domain Y N N Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain GO:0016620 7578111 131567 cellular organisms no rank 114126 EBI-EMBL Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. C-terminal domain is a mixed alpha/antiparallel beta fold. [1]. 7578111. Crystal structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Leishmania mexicana: implications for structure-based drug design and a new position for the inorganic phosphate binding site. Kim H, Feil IK, Verlinde CL, Petra PH, Hol WG;. Biochemistry 1995;34:14975-14986. (from Pfam) NF014820.5 PF02803.23 Thiolase_C 27 27 123 domain Y N N Thiolase, C-terminal domain GO:0016747 9402066 131567 cellular organisms no rank 359081 EBI-EMBL Thiolase, C-terminal domain Thiolase, C-terminal domain Thiolase is reported to be structurally related to beta-ketoacyl synthase (Pfam:PF00109), and also chalcone synthase. [1]. 9402066. The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: implications for substrate binding and reaction mechanism. Mathieu M, Modis Y, Zeelen JP, Engel CK, Abagyan RA, Ahlberg A, Rasmussen B, Lamzin VS, Kunau WH, Wierenga RK;. J Mol Biol 1997;273:714-728. (from Pfam) NF014821.5 PF02805.21 Ada_Zn_binding 23 23 65 domain Y Y N Ada metal-binding domain-containing protein GO:0003677,GO:0006281,GO:0006355,GO:0008168,GO:0008270 1581309,8500619 131567 cellular organisms no rank 67010 EBI-EMBL Metal binding domain of Ada Metal binding domain of Ada The Escherichia coli Ada protein repairs O6-methylguanine residues and methyl phosphotriesters in DNA by direct transfer of the methyl group to a cysteine residue. This domain contains four conserved cysteines that form a zinc binding site [1,2]. One of these cysteines is a methyl group acceptor. The methylated domain can then specifically bind to the ada box on a DNA duplex [2]. [1]. 1581309. Zinc binding by the methylation signaling domain of the Escherichia coli Ada protein. Myers LC, Terranova MP, Nash HM, Markus MA, Verdine GL;. Biochemistry 1992;31:4541-4547. [2]. 8500619. Folding topology and DNA binding of the N-terminal fragment of Ada protein. Sakashita H, Sakuma T, Ohkubo T, Kainosho M, Sakumi K, Sekiguchi M, Morikawa K;. FEBS Lett 1993;323:252-256. (from Pfam) NF014822.5 PF02806.23 Alpha-amylase_C 21.2 17 95 domain Y Y N alpha amylase C-terminal domain-containing protein GO:0003824,GO:0005975,GO:0043169 8107092,9600843 131567 cellular organisms no rank 102818 EBI-EMBL Alpha amylase, C-terminal all-beta domain Alpha amylase, C-terminal all-beta domain Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain. [1]. 8107092. Refined molecular structure of pig pancreatic alpha-amylase at 2.1 A resolution. Larson SB, Greenwood A, Cascio D, Day J, McPherson A;. J Mol Biol 1994;235:1560-1584. [2]. 9600843. Crystal structure of yellow meal worm alpha-amylase at 1.64 A resolution. Strobl S, Maskos K, Betz M, Wiegand G, Huber R, Gomis-Ruth FX, Glockshuber R;. J Mol Biol 1998;278:617-628. (from Pfam) NF014825.5 PF02810.20 SEC-C 20.4 20.4 19 domain Y Y N SEC-C metal-binding domain-containing protein GO:0046872 14517549,15488768 131567 cellular organisms no rank 123861 EBI-EMBL SEC-C motif SEC-C metal-binding domain Domains containing the SEC-C motif (SecA C-terminal motif) is found broadly in bacteria. In Escherichia coli K-12, for example, it occurs in YchJ (once at each end of the protein), YecA, and SecA. The motif typically is CXCX(8)CH or CXCX(8)CC, although the spacing may vary. NF014826.5 PF02811.24 PHP 26.4 26.4 164 domain Y Y N PHP domain-containing protein GO:0003824 9685491 131567 cellular organisms no rank 296612 EBI-EMBL PHP domain PHP domain The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. [1]. 9685491. Phosphoesterase domains associated with DNA polymerases of diverse origins. Aravind L, Koonin EV;. Nucleic Acids Res 1998;26:3746-3752. (from Pfam) NF014827.5 PF02812.23 ELFV_dehydrog_N 25.3 25.3 129 domain Y Y N Glu/Leu/Phe/Val dehydrogenase dimerization domain-containing protein GO:0006520,GO:0016491 8591046 131567 cellular organisms no rank 100481 EBI-EMBL Glu/Leu/Phe/Val dehydrogenase, dimerisation domain Glu/Leu/Phe/Val dehydrogenase, dimerisation domain NF014829.5 PF02814.20 UreE_N 26.9 26.9 62 PfamEq Y N N UreE urease accessory protein, N-terminal domain 11591723 131567 cellular organisms no rank 22753 EBI-EMBL UreE urease accessory protein, N-terminal domain UreE urease accessory protein, N-terminal domain UreE is a urease accessory protein. Urease Pfam:PF00449 hydrolyses urea into ammonia and carbamic acid. [1]. 11591723. Crystal structure of Klebsiella aerogenes UreE, a nickel-binding metallochaperone for urease activation. Song HK, Mulrooney SB, Huber R, Hausinger RP;. J Biol Chem 2001;276:49359-49364. (from Pfam) NF014832.5 PF02817.22 E3_binding 23.7 23.7 36 domain Y Y N E3 binding domain-containing protein GO:0016746 8805537 131567 cellular organisms no rank 200822 EBI-EMBL e3 binding domain e3 binding domain This family represents a small domain of the E2 subunit of 2-oxo-acid dehydrogenases responsible for the binding of the E3 subunit. [1]. 8805537. Protein-protein interactions in the pyruvate dehydrogenase multienzyme complex: dihydrolipoamide dehydrogenase complexed with the binding domain of dihydrolipoamide acetyltransferase. Mande SS, Sarfaty S, Allen MD, Perham RN, Hol WG;. Structure 1996;4:277-286. (from Pfam) NF014838.5 PF02823.21 ATP-synt_DE_N 27 27 80 PfamEq Y N N ATP synthase, Delta/Epsilon chain, beta-sandwich domain GO:0015986 9331422 131567 cellular organisms no rank 43071 EBI-EMBL ATP synthase, Delta/Epsilon chain, beta-sandwich domain ATP synthase, Delta/Epsilon chain, beta-sandwich domain Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. The subunit is called epsilon in bacteria and delta in mitochondria. In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP (Pfam:PF00213). [1]. 9331422. Crystal structure of the epsilon subunit of the proton-translocating ATP synthase from Escherichia coli. Uhlin U, Cox GB, Guss JM;. Structure 1997;5:1219-1230. (from Pfam) NF014839.5 PF02824.26 TGS 22.2 22.2 60 domain Y Y N TGS domain-containing protein 10319817,10447505 131567 cellular organisms no rank 151705 EBI-EMBL TGS domain TGS domain The TGS domain is named after ThrRS, GTPase, and SpoT [1]. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role [1]. [1]. 10447505. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Wolf YI, Aravind L, Grishin NV, Koonin EV;. Genome Res 1999;9:689-710. [2]. 10319817. The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site. Sankaranarayanan R, Dock-Bregeon AC, Romby P, Caillet J, Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D;. Cell 1999;97:371-381. (from Pfam) NF014841.5 PF02826.24 2-Hacid_dh_C 25.1 25.1 178 domain Y Y N NAD(P)-dependent oxidoreductase GO:0051287 9126843 131567 cellular organisms no rank 603475 EBI-EMBL D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family Pfam:PF00389. [1]. 9126843. Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution. Dengler U, Niefind K, Kiess M, Schomburg D;. J Mol Biol 1997;267:640-660. (from Pfam) NF014844.5 PF02829.19 3H 25 25 97 domain Y Y N 3H domain-containing protein GO:0036094 11292341 131567 cellular organisms no rank 8237 EBI-EMBL 3H domain 3H domain This domain is predicted to be a small molecule binding domain, based on its occurrence with other domains [1]. The domain is named after its three conserved histidine residues. [1]. 11292341. Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. Anantharaman V, Koonin EV, Aravind L;. J Mol Biol 2001;307:1271-1292. (from Pfam) NF014845.5 PF02830.23 V4R 31 31 62 domain Y Y N V4R domain-containing protein 11292341 131567 cellular organisms no rank 9299 EBI-EMBL V4R domain V4R domain The V4R (vinyl 4 reductase) domain is found in vinyl 4 reductase-like enzymes and in aromatic compound-binding transcription factors such as MopR and PoxR. NF014848.5 PF02833.19 DHHA2 27 27 126 domain Y Y N DHHA2 domain-containing protein GO:0005737,GO:0016462 9478130 131567 cellular organisms no rank 20562 EBI-EMBL DHHA2 domain DHHA2 domain This domain is often found adjacent to the DHH domain Pfam:PF01368 and is called DHHA2 for DHH associated domain. This domain is diagnostic of DHH subfamily 2 members [1]. The domain is about 120 residues long and contains a conserved DXK motif at its amino terminus. [1]. 9478130. A novel family of predicted phosphoesterases includes Drosophila prune protein and bacterial RecJ exonuclease. Aravind L, Koonin EV;. Trends Biochem Sci 1998;23:17-19. (from Pfam) NF014849.5 PF02834.21 LigT_PEase 23.3 23.3 87 domain Y Y N 2'-5' RNA ligase family protein 11080166,12466548 131567 cellular organisms no rank 54633 EBI-EMBL LigT like Phosphoesterase 2'-5' RNA ligase family protein Members of this family are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known [1]. They belong to the 2H phosphoesterase superfamily [2]. They share a common active site, characterised by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins. [1]. 11080166. Structure and mechanism of activity of the cyclic phosphodiesterase of Appr>p, a product of the tRNA splicing reaction. Hofmann A, Zdanov A, Genschik P, Ruvinov S, Filipowicz W, Wlodawer A;. EMBO J 2000;19:6207-6217. [2]. 12466548. Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily. Mazumder R, Iyer LM, Vasudevan S, Aravind L;. Nucleic Acids Res 2002;30:5229-5243. (from Pfam) NF014850.5 PF02836.22 Glyco_hydro_2_C 21 21 302 domain Y Y N glycoside hydrolase family 2 TIM barrel-domain containing protein GO:0004553,GO:0005975 8008071 131567 cellular organisms no rank 180598 EBI-EMBL Glycosyl hydrolases family 2, TIM barrel domain Glycosyl hydrolases family 2, TIM barrel domain This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities. [1]. 8008071. Three-dimensional structure of beta-galactosidase from E. coli. Jacobson RH, Zhang XJ, DuBose RF, Matthews BW;. Nature. 1994;369:761-766. (from Pfam) NF014851.5 PF02837.23 Glyco_hydro_2_N 28 28 169 domain Y Y N sugar-binding domain-containing protein GO:0004553,GO:0005975 8008071 131567 cellular organisms no rank 180615 EBI-EMBL Glycosyl hydrolases family 2, sugar binding domain glycosyl hydrolases family 2-like sugar-binding domain This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities and has a jelly-roll fold. The domain binds the sugar moiety during the sugar-hydrolysis reaction. [1]. 8008071. Three-dimensional structure of beta-galactosidase from E. coli. Jacobson RH, Zhang XJ, DuBose RF, Matthews BW;. Nature. 1994;369:761-766. (from Pfam) NF014852.5 PF02838.20 Glyco_hydro_20b 26.1 26.1 124 domain Y Y N glycoside hydrolase family 20 zincin-like fold domain-containing protein 8673609 131567 cellular organisms no rank 107793 EBI-EMBL Glycosyl hydrolase family 20, domain 2 Glycosyl hydrolase family 20, domain 2 This domain has a zincin-like fold. [1]. 8673609. Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay-Sachs disease. Tews I, Perrakis A, Oppenheim A, Dauter Z, Wilson KS, Vorgias CE;. Nat Struct Biol 1996;3:638-648. (from Pfam) NF014853.5 PF02839.19 CBM_5_12 26.2 26.2 44 domain Y Y N carbohydrate-binding protein GO:0004553,GO:0005576,GO:0005975,GO:0030246 10788483,16516924,16567413,24272751,25479092 131567 cellular organisms no rank 65654 EBI-EMBL Carbohydrate-binding module family 5/12 carbohydrate-binding domain This short domain is found in many different glycosyl hydrolase enzymes, representing the carbohydrate-binding module family 5/12, including proteins such as chitinase A1, chitinase B, and endoglucanase. The domain has a carbohydrate-binding function and contains six aromatic groups that may be important for binding. These modules have a core structure consisting of a 3-stranded meander beta-sheet [1-5]. [1]. 10788483. Solution structure of the chitin-binding domain of Bacillus circulans WL-12 chitinase A1. Ikegami T, Okada T, Hashimoto M, Seino S, Watanabe T, Shirakawa M;. J Biol Chem. 2000;275:13654-13661. Paper describing PDB structure 1wvu. [2]. 16516924. Structural studies of a two-domain chitinase from Streptomyces griseus HUT6037. Kezuka Y, Ohishi M, Itoh Y, Watanabe J, Mitsutomi M, Watanabe T, Nonaka T;. J Mol Biol. 2006;358:472-484. Paper describing PDB structure 2d49. [3]. 16567413. Identification of the substrate interaction region of the chitin-binding domain of Streptomyces griseus chitinase C. Akagi K, Watanabe J, Hara M, Kezuka Y, Chikaishi E, Yamaguchi T, Akutsu H, Nonaka T, Watanabe T, Ikegami T;. J Biochem. 2006;139:483-493.DR CAZY; CBM5;. Paper describing PDB structure 2rts. [4]. 24272751. Solution structure of the chitin-binding domain 1 (ChBD1) of a hyperthermophilic chitinase from Pyrococcus furiosus. Mine S, Nakamura T, Sato T, Ikegami T, Uegaki K;. J Biochem. 2014;155:115-122. [5]. 25479092. Structure-based analysis of domain function of chitin oligosaccharide deacetylase from Vibrio parahaemolyticus. Hirano T, Sugiyama K, Sakaki Y, Hakamata W, Park SY, Nishio T;. FEBS Lett. 2015;589:145-15. TRUNCATED at 1650 bytes (from Pfam) NF014856.5 PF02843.21 GARS_C 34.8 34.8 92 domain Y Y N phosphoribosylglycinamide synthetase C domain-containing protein GO:0004637,GO:0009113 2687276,9843369 131567 cellular organisms no rank 82997 EBI-EMBL Phosphoribosylglycinamide synthetase, C domain Phosphoribosylglycinamide synthetase, C domain Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the C-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (see Pfam:PF02787). [1]. 2687276. Nucleotide sequence analysis of genes purH and purD involved in the de novo purine nucleotide biosynthesis of Escherichia coli. Aiba A, Mizobuchi K;. J Biol Chem 1989;264:21239-21246. [2]. 9843369. X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli. Wang W, Kappock TJ, Stubbe J, Ealick SE;. Biochemistry 1998;37:15647-15662. (from Pfam) NF014857.5 PF02844.20 GARS_N 29.5 29.5 100 PfamEq Y N N Phosphoribosylglycinamide synthetase, N domain GO:0004637,GO:0009113 2687276,9843369 131567 cellular organisms no rank 82484 EBI-EMBL Phosphoribosylglycinamide synthetase, N domain Phosphoribosylglycinamide synthetase, N domain Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (see Pfam:PF00289). This domain is structurally related to the PreATP-grasp domain. [1]. 2687276. Nucleotide sequence analysis of genes purH and purD involved in the de novo purine nucleotide biosynthesis of Escherichia coli. Aiba A, Mizobuchi K;. J Biol Chem 1989;264:21239-21246. [2]. 9843369. X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli. Wang W, Kappock TJ, Stubbe J, Ealick SE;. Biochemistry 1998;37:15647-15662. (from Pfam) NF014860.5 PF02852.27 Pyr_redox_dim 25.3 25.3 110 domain Y N N Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain GO:0045454 8771196 131567 cellular organisms no rank 316058 EBI-EMBL Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. [1]. 8771196. The crystal structure of trypanothione reductase from the human pathogen Trypanosoma cruzi at 2.3 A resolution. Zhang Y, Bond CS, Bailey S, Cunningham ML, Fairlamb AH, Hunter WN;. Protein Sci 1996;5:52-61. (from Pfam) NF014862.5 PF02861.25 Clp_N 20.7 7.4 53 domain Y Y N Clp protease N-terminal domain-containing protein 10982797,22184413,24381728 131567 cellular organisms no rank 208561 EBI-EMBL Clp amino terminal domain, pathogenicity island component Clp amino terminal domain, pathogenicity island component This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site [1]. In many bacterial species, including E.coli, this region represents the N-terminus of one of the key components of the pathogenicity island complex that injects toxin from one bacterium into another [2,3]. [1]. 10982797. Structure and activity of ClpB from Escherichia coli. Role of the amino-and -carboxyl-terminal domains. Barnett ME, Zolkiewska A, Zolkiewski M;. J Biol Chem 2000;275:37565-37571. [2]. 22184413. Hcp family proteins secreted via the type VI secretion system coordinately regulate Escherichia coli K1 interaction with human brain microvascular endothelial cells. Zhou Y, Tao J, Yu H, Ni J, Zeng L, Teng Q, Kim KS, Zhao GP, Guo X, Yao Y;. Infect Immun. 2012;80:1243-1251. [3]. 24381728. The rise of the Type VI secretion system. Filloux A;. F1000Prime Rep. 2013;5:52. (from Pfam) NF014867.5 PF02866.23 Ldh_1_C 22.6 22.6 174 domain Y N N lactate/malate dehydrogenase, alpha/beta C-terminal domain GO:0016616 10075524 131567 cellular organisms no rank 72725 EBI-EMBL lactate/malate dehydrogenase, alpha/beta C-terminal domain lactate/malate dehydrogenase, alpha/beta C-terminal domain L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. [1]. 10075524. Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD. Chapman AD, Cortes A, Dafforn TR, Clarke AR, Brady RL;. J Mol Biol 1999;285:703-712. (from Pfam) NF014868.5 PF02867.20 Ribonuc_red_lgC 23.9 23.9 523 domain Y N N Ribonucleotide reductase, barrel domain GO:0006260 8052308 131567 cellular organisms no rank 115385 EBI-EMBL Ribonucleotide reductase, barrel domain Ribonucleotide reductase, barrel domain NF014869.5 PF02868.20 Peptidase_M4_C 24.4 24.4 165 domain Y Y N M4 family metallopeptidase GO:0004222 7674922,9753696 131567 cellular organisms no rank 72225 EBI-EMBL Thermolysin metallopeptidase, alpha-helical domain Thermolysin metallopeptidase, alpha-helical domain NF014870.5 PF02870.20 Methyltransf_1N 21 21 71 domain Y N N 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain GO:0003908,GO:0006281 8156986 131567 cellular organisms no rank 89523 EBI-EMBL 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain This entry represents the N-terminal ribonuclease-like domain associated with 6-O-methylguanine DNA methyltransferase activity. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (also known as O-6-methylguanine-DNA-alkyltransferase) [1]. 8156986. Crystal structure of a suicidal DNA repair protein: the Ada O6-methylguanine-DNA methyltransferase from E. coli. Moore MH, Gulbis JM, Dodson EJ, Demple B, Moody PC;. EMBO J 1994;13:1495-1501. (from Pfam) NF014871.5 PF02872.23 5_nucleotid_C 23.6 23.6 158 domain Y Y N 5'-nucleotidase C-terminal domain-containing protein GO:0009166,GO:0016787 10331872 131567 cellular organisms no rank 153595 EBI-EMBL 5'-nucleotidase, C-terminal domain 5'-nucleotidase, C-terminal domain NF014872.5 PF02873.21 MurB_C 27 27 99 PfamEq Y N N UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain GO:0008762 8805513 131567 cellular organisms no rank 82649 EBI-EMBL UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain Members of this family are UDP-N-acetylenolpyruvoylglucosamine reductase enzymes EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan. [1]. 8805513. The structure of the substrate-free form of MurB, an essential enzyme for the synthesis of bacterial cell walls. Benson TE, Walsh CT, Hogle JM;. Structure 1996;4:47-54. (from Pfam) NF014873.5 PF02874.28 ATP-synt_ab_N 20.9 19 69 domain Y N N ATP synthase alpha/beta family, beta-barrel domain GO:0046034,GO:1902600 8065448,9261073 131567 cellular organisms no rank 134306 EBI-EMBL ATP synthase alpha/beta family, beta-barrel domain ATP synthase alpha/beta family, beta-barrel domain This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella. [1]. 8065448. Structure at 2.8 A resolution of F1-ATPase from bovine heart mitochondria. Abrahams JP, Leslie AG, Lutter R, Walker JE;. Nature 1994;370:621-628. [2]. 9261073. The crystal structure of the nucleotide-free alpha 3 beta 3 subcomplex of F1-ATPase from the thermophilic Bacillus PS3 is a symmetric trimer. Shirakihara Y, Leslie AG, Abrahams JP, Walker JE, Ueda T, Sekimoto Y, Kambara M, Saika K, Kagawa Y, Yoshida M;. Structure 1997;5:825-836. (from Pfam) NF014874.5 PF02875.26 Mur_ligase_C 28.4 28.4 127 domain Y Y N glutamate ligase domain-containing protein GO:0009058,GO:0016881 25130693,27031227,9218784,9652408 131567 cellular organisms no rank 456267 EBI-EMBL Mur ligase, glutamate ligase domain Mur ligase, glutamate ligase domain This entry contains a number of related ligase enzymes which have EC numbers 6.3.2.* which includes: MurC (Swiss:P17952), MurD (Swiss:P14900), MurE (Swiss:P22188), MurF (Swiss:P11880), Mpl (Swiss:P37773) and FolC (Swiss:P08192). MurC, MurD, MurE and MurF catalyse consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesised by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine [1,3,4]. This entry also includes folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin) [2]. [1]. 9218784. Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli. Bertrand JA, Auger G, Fanchon E, Martin L, Blanot D, van Heijenoort J, Dideberg O;. EMBO J 1997;16:3416-3425. [2]. 9652408. Molecular characterization of cyanophycin synthetase, the enzyme catalyzing the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin). Ziegler K, Diener A, Herpin C, Richter R, Deutzmann R, Lockau W;. Eur J Biochem. 1998;254:154-159. [3]. 25130693. The biology of Mur ligases as an antibacterial target. Ko. TRUNCATED at 1650 bytes (from Pfam) NF014877.5 PF02878.21 PGM_PMM_I 22.5 22.5 138 domain Y N N Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I GO:0005975,GO:0016868 1532581 131567 cellular organisms no rank 236628 EBI-EMBL Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I NF014878.5 PF02879.21 PGM_PMM_II 29.3 29.3 103 domain Y N N Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II GO:0005975 1532581 131567 cellular organisms no rank 234356 EBI-EMBL Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II NF014879.5 PF02880.21 PGM_PMM_III 20.7 20.7 115 domain Y N N Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III GO:0005975,GO:0016868 1532581 131567 cellular organisms no rank 232936 EBI-EMBL Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III NF014880.5 PF02881.24 SRP54_N 22.4 22.4 75 domain Y Y N signal recognition particle receptor subunit alpha GO:0005525,GO:0006614 9002525 131567 cellular organisms no rank 144929 EBI-EMBL SRP54-type protein, helical bundle domain SRP54-type protein, helical bundle domain NF014881.5 PF02882.24 THF_DHG_CYH_C 27 27 160 domain Y N N Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain GO:0004488 9519408 131567 cellular organisms no rank 77956 EBI-EMBL Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain NF014883.5 PF02884.22 Lyase_8_C 22 22 69 domain Y Y N polysaccharide lyase beta-sandwich domain-containing protein GO:0005576,GO:0016829 10329169,7557301 131567 cellular organisms no rank 22787 EBI-EMBL Polysaccharide lyase family 8, C-terminal beta-sandwich domain Polysaccharide lyase family 8, C-terminal beta-sandwich domain This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen. [1]. 7557301. Cloning, nucleotide sequence determination and expression of the Staphylococcus aureus hyaluronate lyase gene. Farrell AM, Taylor D, Holland KT;. FEMS Microbiol Lett 1995;130:81-85. [2]. 10329169. Crystal structure of chondroitin AC lyase, a representative of a family of glycosaminoglycan degrading enzymes. Fethiere J, Eggimann B, Cygler M;. J Mol Biol 1999;288:635-647. (from Pfam) NF014884.5 PF02885.22 Glycos_trans_3N 26 26 63 domain Y N N Glycosyl transferase family, helical bundle domain 2199449 131567 cellular organisms no rank 134376 EBI-EMBL Glycosyl transferase family, helical bundle domain Glycosyl transferase family, helical bundle domain This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate. [1]. 2199449. Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 A resolution. Walter MR, Cook WJ, Cole LB, Short SA, Koszalka GW, Krenitsky TA, Ealick SE;. J Biol Chem 1990;265:14016-14022. (from Pfam) NF014886.5 PF02887.21 PK_C 28 28 114 domain Y Y N pyruvate kinase alpha/beta domain-containing protein 10751408,11960989,12798932,29748232,9308890 131567 cellular organisms no rank 76837 EBI-EMBL Pyruvate kinase, alpha/beta domain Pyruvate kinase, alpha/beta domain Pyruvate kinase catalyses the final step in glycolysis, the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP [1,2]. The structure of several pyruvate kinases from various organisms have been determined [2, 3,4]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain (represented in this entry). This domain is at the C-terminal of pyruvate kinases and contains the FBP (fructose 1,6-bisphosphate) binding site [2,4,5]. [1]. 9308890. Ligand-induced domain movement in pyruvate kinase: structure of the enzyme from rabbit muscle with Mg2+, K+, and L-phospholactate at 2.7 A resolution. Larsen TM, Benning MM, Wesenberg GE, Rayment I, Reed GH;. Arch Biochem Biophys 1997;345:199-206. [2]. 10751408. The allosteric regulation of pyruvate kinase. Valentini G, Chiarelli L, Fortin R, Speranza ML, Galizzi A, Mattevi A;. J Biol Chem. 2000;275:18145-18152. [3]. 12798932. Pyruvate kinase: current status of regulatory and functional properties. Munoz ME, Ponce E;. Comp Biochem Physiol B Biochem Mol Biol. 2003;135:197-218. [4]. 11960989. Structure and function of human erythrocyte pyruvate kinase. Molecular basis of nonspherocytic hemolytic anemia. Valentini G, Chiarelli LR, Fortin R, Dolzan M, Galizzi A, Abraham DJ, Wang C, Bianchi P, Zanella A, Mattevi A;. J Biol Chem. 2002;277:23807-23814. [5]. 29748232. An allostatic mechanism for M2 pyruvate kinase as an amino-acid sensor. Yuan M, McNae IW, Chen Y, Blackburn . TRUNCATED at 1650 bytes (from Pfam) NF014892.5 PF02893.25 GRAM 23.6 23.6 112 domain Y Y N GRAM domain-containing protein 11050430 131567 cellular organisms no rank 986 EBI-EMBL GRAM domain GRAM domain The GRAM domain is found in in glucosyltransferases, myotubularins and other putative membrane-associated proteins. Note the alignment is lacking the last two beta strands and alpha helix. [1]. 11050430. GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins. Doerks T, Strauss M, Brendel M, Bork P;. Trends Biochem Sci 2000;25:483-485. (from Pfam) NF014893.5 PF02894.22 GFO_IDH_MocA_C 22.9 22.9 218 domain Y Y N Gfo/Idh/MocA family oxidoreductase 8994968 131567 cellular organisms no rank 402002 EBI-EMBL Oxidoreductase family, C-terminal alpha/beta domain Gfo/Idh/MocA family oxidoreductase, C-terminal alpha/beta domain This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot. [1]. 8994968. The structure of glucose-fructose oxidoreductase from Zymomonas mobilis: an osmoprotective periplasmic enzyme containing non-dissociable NADP. Kingston RL, Scopes RK, Baker EN;. Structure 1996;4:1413-1428. (from Pfam) NF014894.5 PF02895.19 H-kinase_dim 23 23 68 domain Y N N Signal transducing histidine kinase, homodimeric domain GO:0000155,GO:0000160,GO:0004673,GO:0005737,GO:0006935 9989504 131567 cellular organisms no rank 67828 EBI-EMBL Signal transducing histidine kinase, homodimeric domain Signal transducing histidine kinase, homodimeric domain This helical bundle domain is the homodimer interface of the signal transducing histidine kinase family. [1]. 9989504. Structure of CheA, a signal-transducing histidine kinase. Bilwes AM, Alex LA, Crane BR, Simon MI;. Cell 1999;96:131-141. (from Pfam) NF014895.5 PF02896.23 PEP-utilizers_C 22.8 22.8 293 domain Y Y N putative PEP-binding protein GO:0016310,GO:0016772 18052212 131567 cellular organisms no rank 172906 EBI-EMBL PEP-utilising enzyme, PEP-binding domain phosphoenolpyruvate-binding TIM barrel domain This entry represents a TIM barrel domain found at the C terminus of a number of PEP (phosphoenolpyruvate)-utilising proteins. In PPDK (Pyruvate phosphate dikinase) this C-terminal domain has been shown to be a PEP-binding domain [1]. [1]. 18052212. Swiveling domain mechanism in pyruvate phosphate dikinase. Lim K, Read RJ, Chen CC, Tempczyk A, Wei M, Ye D, Wu C, Dunaway-Mariano D, Herzberg O;. Biochemistry. 2007;46:14845-14853. (from Pfam) NF014896.5 PF02897.20 Peptidase_S9_N 24 24 414 domain Y N N Prolyl oligopeptidase, N-terminal beta-propeller domain GO:0004252 9695945 131567 cellular organisms no rank 88217 EBI-EMBL Prolyl oligopeptidase, N-terminal beta-propeller domain Prolyl oligopeptidase, N-terminal beta-propeller domain This unusual 7-stranded beta-propeller domain protects the catalytic triad of prolyl oligopeptidase (see Pfam:PF00326), excluding larger peptides and proteins from proteolysis in the cytosol. [1]. 9695945. Prolyl oligopeptidase: an unusual beta-propeller domain regulates proteolysis. Fulop V, Bocskei Z, Polgar L;. Cell 1998;94:161-170. (from Pfam) NF014897.5 PF02898.20 NO_synthase 22.7 22.7 362 PfamEq Y Y N nitric oxide synthase oxygenase GO:0004517,GO:0006809 9516116 131567 cellular organisms no rank 10111 EBI-EMBL Nitric oxide synthase, oxygenase domain Nitric oxide synthase, oxygenase domain NF014898.5 PF02899.22 Phage_int_SAM_1 22.3 22.3 83 domain Y Y N site-specific integrase GO:0003677,GO:0015074 9311978 131567 cellular organisms no rank 190903 EBI-EMBL Phage integrase, N-terminal SAM-like domain Phage integrase, N-terminal SAM-like domain NF014899.5 PF02900.23 LigB 26.3 26.3 269 domain Y N N Catalytic LigB subunit of aromatic ring-opening dioxygenase GO:0008152,GO:0008198,GO:0016491 10467151 131567 cellular organisms no rank 69032 EBI-EMBL Catalytic LigB subunit of aromatic ring-opening dioxygenase Catalytic LigB subunit of aromatic ring-opening dioxygenase NF014902.5 PF02903.19 Alpha-amylase_N 23 23 120 PfamEq Y Y N alpha amylase N-terminal ig-like domain-containing protein GO:0004553,GO:0005975 10222200 131567 cellular organisms no rank 21658 EBI-EMBL Alpha amylase, N-terminal ig-like domain Alpha amylase, N-terminal ig-like domain NF014904.5 PF02906.19 Fe_hyd_lg_C 22.1 22.1 245 domain Y Y N [Fe-Fe] hydrogenase large subunit C-terminal domain-containing protein 9836629 131567 cellular organisms no rank 21418 EBI-EMBL Iron only hydrogenase large subunit, C-terminal domain Iron only hydrogenase large subunit, C-terminal domain NF014907.5 PF02910.25 Succ_DH_flav_C 20.8 20.8 130 domain Y N N Fumarate reductase flavoprotein C-term GO:0016491 10373108 131567 cellular organisms no rank 150405 EBI-EMBL Fumarate reductase flavoprotein C-term Fumarate reductase flavoprotein C-term This family contains fumarate reductases, succinate dehydrogenases and L-aspartate oxidases. [1]. 10373108. Structure of the Escherichia coli fumarate reductase respiratory complex. Iverson TM, Luna-Chavez C, Cecchini G, Rees DC;. Science 1999;284:1961-1966. (from Pfam) NF014908.5 PF02911.23 Formyl_trans_C 21.1 21.1 100 domain Y N N Formyl transferase, C-terminal domain GO:0009058,GO:0016742 8887566 131567 cellular organisms no rank 109558 EBI-EMBL Formyl transferase, C-terminal domain Formyl transferase, C-terminal domain NF014909.5 PF02912.23 Phe_tRNA-synt_N 22.3 22.3 69 domain Y N N Aminoacyl tRNA synthetase class II, N-terminal domain GO:0000166,GO:0004826,GO:0005524,GO:0005737,GO:0006432 7664121 131567 cellular organisms no rank 57250 EBI-EMBL Aminoacyl tRNA synthetase class II, N-terminal domain Aminoacyl tRNA synthetase class II, N-terminal domain NF014910.5 PF02913.24 FAD-oxidase_C 21.2 13.9 248 domain Y Y N FAD-linked oxidase C-terminal domain-containing protein GO:0003824,GO:0050660 9141139 131567 cellular organisms no rank 218429 EBI-EMBL FAD linked oxidases, C-terminal domain FAD linked oxidases, C-terminal domain This domain has a ferredoxin-like fold. [1]. 9141139. Crystallization and preliminary X-ray analysis of the flavoenzyme vanillyl-alcohol oxidase from Penicillium simplicissimum. Mattevi A, Fraaije MW, Coda A, van Berkel WJ;. Proteins 1997;27:601-603. (from Pfam) NF014912.5 PF02915.22 Rubrerythrin 22.8 22.8 137 domain Y Y N ferritin family protein GO:0016491,GO:0046872 8646540 131567 cellular organisms no rank 55912 EBI-EMBL Rubrerythrin ferritin family protein This domain has a ferritin-like fold. [1]. 8646540. The structure of Desulfovibrio vulgaris rubrerythrin reveals a unique combination of rubredoxin-like FeS4 and ferritin-like diiron domains. deMare F, Kurtz DM Jr, Nordlund P;. Nat Struct Biol 1996;3:539-546. (from Pfam) NF014919.5 PF02922.23 CBM_48 22.4 22.4 83 domain Y N N Carbohydrate-binding module 48 (Isoamylase N-terminal domain) GO:0004553,GO:0005975 12747836,12747837,14673168,9719642 131567 cellular organisms no rank 204754 EBI-EMBL Carbohydrate-binding module 48 (Isoamylase N-terminal domain) Carbohydrate-binding module 48 (Isoamylase N-terminal domain) This domain is found in a range of enzymes that act on branched substrates - isoamylase, pullulanase and branching enzyme. This family also contains the beta subunit of 5' AMP activated kinase. [1]. 9719642. Three-dimensional structure of Pseudomonas isoamylase at 2.2 A resolution. Katsuya Y, Mezaki Y, Kubota M, Matsuura Y;. J Mol Biol 1998;281:885-897. [2]. 14673168. Mutations in the gal83 glycogen-binding domain activate the snf1/gal83 kinase pathway by a glycogen-independent mechanism. Wiatrowski HA, Van Denderen BJ, Berkey CD, Kemp BE, Stapleton D, Carlson M;. Mol Cell Biol 2004;24:352-361. [3]. 12747837. AMPK beta subunit targets metabolic stress sensing to glycogen. Polekhina G, Gupta A, Michell BJ, van Denderen B, Murthy S, Feil SC, Jennings IG, Campbell DJ, Witters LA, Parker MW, Kemp BE, Stapleton D;. Curr Biol 2003;13:867-871. [4]. 12747836. A novel domain in AMP-activated protein kinase causes glycogen storage bodies similar to those seen in hereditary cardiac arrhythmias. Hudson ER, Pan DA, James J, Lucocq JM, Hawley SA, Green KA, Baba O, Terashima T, Hardie DG;. Curr Biol 2003;13:861-866. (from Pfam) NF014920.5 PF02923.20 BamHI 22.8 22.8 157 domain Y N N Restriction endonuclease BamHI 8145855 131567 cellular organisms no rank 375 EBI-EMBL Restriction endonuclease BamHI Restriction endonuclease BamHI NF014922.5 PF02925.21 gpD 25 25 141 PfamEq Y N N Bacteriophage scaffolding protein D GO:0046797 9305849 131567 cellular organisms no rank 19 EBI-EMBL Bacteriophage scaffolding protein D Bacteriophage scaffolding protein D NF014923.5 PF02926.22 THUMP 20.6 20.6 84 domain Y Y N THUMP domain-containing protein GO:0003723 11295541,16343540,36833309 131567 cellular organisms no rank 76682 EBI-EMBL THUMP domain THUMP domain The THUMP domain is named after after thiouridine synthases, methylases and PSUSs [1]. The THUMP domain consists of about 110 amino acid residues. This domain is found in many tRNA modification enzymes classified into five types, namely 4-thiouridine synthetase, deaminase, methyltransferase, a partner protein of acetyltransferase and pseudouridine synthase [3]. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains [2-3] and was first predicted to function by delivering a variety of RNA modification enzymes to their targets [1]. Studies performed in tRNA 4-thiouridine synthetase, tRNA methyltransferases and tRNA deaminase suggest that the THUMP domain captures the 3'-end of RNA but in some cases this is not applicable due to the modification patterns observed in tRNA [3]. Several THUMP-related proteins are also involved in other RNAs modifications, such as rRNA modification [3]. [1]. 11295541. THUMP - a predicted RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases. Aravind L, Koonin EV;. Trends Biochem Sci 2001;26:215-217. [2]. 16343540. Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain. Waterman DG, Ortiz-Lombardia M, Fogg MJ, Koonin EV, Antson AA;. J Mol Biol. 2006;356:97-110. [3]. 36833309. Transfer RNA Modification Enzymes with a Thiouridine Synthetase, Methyltransferase and Pseudouridine Synthase (THUMP) Domain and the Nucleosides They Produce in tRNA. Hori H;. Genes (Basel). 2023;14:382. (from Pfam) NF014924.5 PF02927.19 CelD_N 24.6 24.6 86 domain Y Y N cellulase N-terminal Ig-like domain-containing protein GO:0005975,GO:0008810 8632467 131567 cellular organisms no rank 21920 EBI-EMBL Cellulase N-terminal ig-like domain Cellulase N-terminal ig-like domain NF014926.5 PF02929.22 Bgal_small_N 25 25 248 domain Y N N Beta galactosidase small chain GO:0004565,GO:0005975,GO:0009341 131567 cellular organisms no rank 73193 EBI-EMBL Beta galactosidase small chain Beta galactosidase small chain This domain comprises the small chain of dimeric beta-galactosidases EC:3.2.1.23. This domain is also found in single chain beta-galactosidase. (from Pfam) NF014927.5 PF02931.28 Neur_chan_LBD 26 26 216 PfamEq Y N N Neurotransmitter-gated ion-channel ligand binding domain GO:0006811,GO:0016020 11357122,19917292 131567 cellular organisms no rank 805 EBI-EMBL Neurotransmitter-gated ion-channel ligand binding domain Neurotransmitter-gated ion-channel ligand binding domain This family is the extracellular ligand binding domain of these ion channels [1]. This domain forms a pentameric arrangement in the known structure. [1]. 11357122. Crystal structure of an ACh-binding protein reveals the ligand-binding domain of nicotinic receptors. Brejc K, van Dijk WJ, Klaassen RV, Schuurmans M, van Der Oost J, Smit AB, Sixma TK;. Nature 2001;411:269-276. [2]. 19917292. Crystal Structure of the Extracellular Domain of a Bacterial Ligand-Gated Ion Channel. Nury H, Bocquet N, Le Poupon C, Raynal B, Haouz A, Corringer PJ, Delarue M;. J Mol Biol. 2009; [Epub ahead of print] (from Pfam) NF014929.5 PF02933.22 CDC48_2 22.4 22.4 64 domain Y N N Cell division protein 48 (CDC48), domain 2 10531028 131567 cellular organisms no rank 5485 EBI-EMBL Cell division protein 48 (CDC48), domain 2 Cell division protein 48 (CDC48), domain 2 This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C-terminus. The VAT-N domain found in AAA ATPases Pfam:PF00004 is a substrate 185-residue recognition domain [1]. [1]. 10531028. The solution structure of VAT-N reveals a 'missing link' in the evolution of complex enzymes from a simple betaalphabetabeta element. Coles M, Diercks T, Liermann J, Groger A, Rockel B, Baumeister W, Koretke KK, Lupas A, Peters J, Kessler H;. Curr Biol 1999;9:1158-1168. (from Pfam) NF014930.5 PF02934.20 GatB_N 23.4 23.4 277 PfamEq Y N N GatB/GatE catalytic domain GO:0016874 16216574 131567 cellular organisms no rank 60599 EBI-EMBL GatB/GatE catalytic domain GatB/GatE catalytic domain This domain is found in the GatB and GatE proteins [1]. [1]. 16216574. Structural basis for tRNA-dependent amidotransferase function. Schmitt E, Panvert M, Blanquet S, Mechulam Y;. Structure. 2005;13:1421-1433. (from Pfam) NF014934.5 PF02938.19 GAD 23.4 23.4 95 domain Y Y N GAD domain-containing protein 131567 cellular organisms no rank 75802 EBI-EMBL GAD domain GAD domain This domain is found in some members of the GatB and aspartyl tRNA synthetases. (from Pfam) NF014939.5 PF02943.20 FeThRed_B 22 22 106 domain Y Y N ferredoxin-thioredoxin reductase catalytic domain-containing protein GO:0016730 10649999 131567 cellular organisms no rank 2172 EBI-EMBL Ferredoxin thioredoxin reductase catalytic beta chain Ferredoxin thioredoxin reductase catalytic beta chain NF014941.5 PF02945.20 Endonuclease_7 23.6 23.6 82 domain Y Y N endonuclease domain-containing protein 10075917 131567 cellular organisms no rank 9915 EBI-EMBL Recombination endonuclease VII recombination endonuclease VII domain Members of this family include recombination endonuclease VII of phage T4 and endonucleases of restriction enzymes such as Hpy99I. NF014948.5 PF02952.22 Fucose_iso_C 29.3 29.3 143 PfamEq Y N N L-fucose isomerase, C-terminal domain GO:0005737,GO:0006004,GO:0008736 9367760 131567 cellular organisms no rank 14770 EBI-EMBL L-fucose isomerase, C-terminal domain L-fucose isomerase, C-terminal domain NF014950.5 PF02954.24 HTH_8 22 22 42 domain Y Y N helix-turn-helix domain-containing protein GO:0043565 1946369 131567 cellular organisms no rank 382457 EBI-EMBL Bacterial regulatory protein, Fis family Bacterial regulatory protein, Fis family NF014951.5 PF02955.21 GSH-S_ATP 23 23 175 domain Y N N Prokaryotic glutathione synthetase, ATP-grasp domain GO:0004363,GO:0005524,GO:0006750 8445637 131567 cellular organisms no rank 61282 EBI-EMBL Prokaryotic glutathione synthetase, ATP-grasp domain Prokaryotic glutathione synthetase, ATP-grasp domain NF014954.5 PF02958.25 EcKL 22 22 294 domain Y N N Ecdysteroid kinase-like family 16899460,32540344 131567 cellular organisms no rank 35656 EBI-EMBL Ecdysteroid kinase-like family Ecdysteroid kinase-like family This family includes ecdysteroid 22-kinase, an enzyme responsible for the phosphorylation of ecdysteroids (insect growth and moulting hormones) at C-22, to form physiologically inactive ecdysteroid 22-phosphates [1]. Most insects contain 12 to 105 genes encoding this family and yet so far only one enzyme (ecdysteroid 22-kinase from Bombyx mori) has characterised substrates (2-deoxyecdysone, ecdysone, 20-hydroxyecdysone). There are good reasons to believe that this family includes kinases that act on other small molecule substrates and that they may function in detoxification processes [2]. [1]. 16899460. Purification, kinetic characterization, and molecular cloning of a novel enzyme, ecdysteroid 22-kinase. Sonobe H, Ohira T, Ieki K, Maeda S, Ito Y, Ajimura M, Mita K, Matsumoto H, Wilder MN;. J Biol Chem. 2006;281:29513-29524. [2]. 32540344. Genomic and transcriptomic analyses in Drosophila suggest that the ecdysteroid kinase-like (EcKL) gene family encodes the 'detoxification-by-phosphorylation' enzymes of insects. Scanlan JL, Gledhill-Smith RS, Battlay P, Robin C;. Insect Biochem Mol Biol. 2020; [Epub ahead of print] (from Pfam) NF014959.5 PF02963.21 EcoRI 22 22 257 PfamEq Y Y N EcoRI family type II restriction endonuclease GO:0000287,GO:0003677,GO:0009036,GO:0009307 22638584,2399465 131567 cellular organisms no rank 693 EBI-EMBL Restriction endonuclease EcoRI EcoRI family type II restriction endonuclease NF014961.5 PF02965.22 Met_synt_B12 25 25 273 domain Y Y N vitamin B12 dependent-methionine synthase activation domain-containing protein GO:0008705,GO:0009086 8939751 131567 cellular organisms no rank 70562 EBI-EMBL Vitamin B12 dependent methionine synthase, activation domain Vitamin B12 dependent methionine synthase, activation domain NF014963.5 PF02969.22 TAF 21 21 66 domain Y N N TATA box binding protein associated factor (TAF) GO:0006352 8598927 131567 cellular organisms no rank 576 EBI-EMBL TATA box binding protein associated factor (TAF) TATA box binding protein associated factor (TAF) TAF proteins adopt a histone-like fold. [1]. 8598927. Structural similarity between TAFs and the heterotetrameric core of the histone octamer. Xie X, Kokubo T, Cohen SL, Mirza UA, Hoffmann A, Chait BT, Roeder RG, Nakatani Y, Burley SK;. Nature 1996;380:316-322. (from Pfam) NF014965.5 PF02971.19 FTCD 24 24 145 domain Y N N Formiminotransferase domain GO:0005542,GO:0016740 10673422 131567 cellular organisms no rank 3873 EBI-EMBL Formiminotransferase domain Formiminotransferase domain NF014970.5 PF02976.20 MutH 23 23 103 domain Y Y N MutH/Sau3AI family endonuclease GO:0003677,GO:0004519 22638584,9482749 131567 cellular organisms no rank 10130 EBI-EMBL DNA mismatch repair enzyme MutH MutH/Sau3AI family endonuclease Members of this family included the DNA mismatch repair protein MutH and the Sau3AI family of type II restriction endonucleases NF014972.5 PF02978.24 SRP_SPB 27 27 91 domain Y N N Signal peptide binding domain GO:0006614,GO:0008312,GO:0048500 10497032 131567 cellular organisms no rank 62210 EBI-EMBL Signal peptide binding domain Signal peptide binding domain NF014973.5 PF02979.21 NHase_alpha 27.2 27.2 184 domain Y Y N nitrile hydratase subunit alpha 4.2.1.84 GO:0003824,GO:0008152,GO:0046914 9586994 131567 cellular organisms no rank 9760 EBI-EMBL Nitrile hydratase, alpha chain nitrile hydratase subunit alpha NF014979.5 PF02985.27 HEAT 23.5 17.6 31 repeat Y N N HEAT repeat protein GO:0005515 7550332,9989501 131567 cellular organisms no rank 26560 EBI-EMBL HEAT repeat HEAT repeat The HEAT repeat family is related to armadillo/beta-catenin-like repeats (see Pfam:PF00514). [1]. 7550332. HEAT repeats in the Huntington's disease protein. Andrade MA, Bork P;. Nat Genet 1995;11:115-116. [2]. 9989501. The structure of the protein phosphatase 2A PR65/A subunit reveals the conformation of its 15 tandemly repeated HEAT motifs. Groves MR, Hanlon N, Turowski P, Hemmings BA, Barford D;. Cell 1999;96:99-110. (from Pfam) NF014989.5 PF02995.22 DUF229 25 25 496 domain Y Y N DUF229 domain-containing protein 131567 cellular organisms no rank 5859 EBI-EMBL Protein of unknown function (DUF229) Protein of unknown function (DUF229) Members of this family are uncharacterised. They are 500-1200 amino acids in length and share a long region conservation that probably corresponds to several domains. The Go annotation for the protein indicates that it is involved in nematode larval development and has a positive regulation on growth rate. (from Pfam) NF014990.5 PF02996.22 Prefoldin 23.2 23.2 120 PfamEq Y N N Prefoldin subunit 12456645 131567 cellular organisms no rank 1367 EBI-EMBL Prefoldin subunit Prefoldin subunit This family comprises of several prefoldin subunits. The biogenesis of the cytoskeletal proteins actin and tubulin involves interaction of nascent chains of each of the two proteins with the oligomeric protein prefoldin (PFD) and their subsequent transfer to the cytosolic chaperonin CCT (chaperonin containing TCP-1). Electron microscopy shows that eukaryotic PFD, which has a similar structure to its archaeal counterpart, interacts with unfolded actin along the tips of its projecting arms. In its PFD-bound state, actin seems to acquire a conformation similar to that adopted when it is bound to CCT [1]. [1]. 12456645. Structure of eukaryotic prefoldin and of its complexes with unfolded actin and the cytosolic chaperonin CCT. Martin-Benito J, Boskovic J, Gomez-Puertas P, Carrascosa JL, Simons CT, Lewis SA, Bartolini F, Cowan NJ, Valpuesta JM;. EMBO J 2002;21:6377-6386. (from Pfam) NF014998.5 PF03007.21 WS_DGAT_cat 23.6 23.6 263 domain Y Y N wax ester/triacylglycerol synthase domain-containing protein GO:0004144,GO:0045017 12502715,31559109 131567 cellular organisms no rank 40506 EBI-EMBL Wax ester synthase/diacylglycerol acyltransferase catalytic domain Wax ester synthase/diacylglycerol acyltransferase catalytic domain This domain is found in wax ester synthases/diacylglycerol O-acyltransferases (WS/DAGs), largely found in bacteria, plants and animals. They catalyse the condensation of a fatty alcohol and a fatty acyl-Coenzyme A (acyl-CoA) and they can also catalyse the transesterification of acyl-CoAs with diacylglycerols. These are bifunctional enzymes (WS/DAGs) that share low overall sequence similarity but all WS/DGATs share a conserved HHXXXDG motif, which is also found in other acyltransferases [1,2]. This entry represents the N-terminal catalytic domain of WS/DAGs which contains the conserved HHXXXDG motif. It consists of a mixed beta-sheet flanked by four alpha-helices and a small antiparallel beta-sheet [2]. [1]. 12502715. A novel bifunctional wax ester synthase/acyl-CoA:diacylglycerol acyltransferase mediates wax ester and triacylglycerol biosynthesis in Acinetobacter calcoaceticus ADP1. Kalscheuer R, Steinbuchel A;. J Biol Chem. 2003;278:8075-8082. [2]. 31559109. Structural and Biochemical Studies of a Biocatalyst for the Enzymatic Production of Wax Esters. Petronikolou N, Nair SK;. ACS Catal. 2018;8:6334-6344. (from Pfam) NF014999.5 PF03008.19 DUF234 22.5 22.5 100 domain Y Y N DUF234 domain-containing protein 131567 cellular organisms no rank 13418 EBI-EMBL Archaea bacterial proteins of unknown function Archaea bacterial proteins of unknown function NF015000.5 PF03009.22 GDPD 23.6 23.6 244 domain Y Y N glycerophosphodiester phosphodiesterase family protein GO:0006629,GO:0008081 9393724 131567 cellular organisms no rank 200924 EBI-EMBL Glycerophosphoryl diester phosphodiesterase family glycerophosphodiester phosphodiesterase family E. coli has two sequence related isozymes of glycerophosphoryl diester phosphodiesterase (GDPD) - periplasmic and cytosolic. This family also includes agrocinopine synthase, the similarity to GDPD has been noted [1]. This family appears to have weak but not significant matches to mammalian phospholipase C Pfam:PF00388, which suggests that this family may adopt a TIM barrel fold. [1]. 9393724. Characterization of the acc operon from the nopaline-type Ti plasmid pTiC58, which encodes utilization of agrocinopines A and B and susceptibility to agrocin 84. Kim H, Farrand SK;. J Bacteriol 1997;179:7559-7572. (from Pfam) NF015004.5 PF03013.19 Pyr_excise 23 23 81 domain Y Y N pyrimidine dimer DNA glycosylase/endonuclease V 1575827 131567 cellular organisms no rank 11256 EBI-EMBL Pyrimidine dimer DNA glycosylase pyrimidine dimer DNA glycosylase/endonuclease V Pyrimidine dimer DNA glycosylases excise pyrimidine dimers by hydrolysis of the glycosylic bond of the 5' pyrimidine, followed by the intra-pyrimidine phosphodiester bond. Pyrimidine dimers are the major UV-lesions of DNA. [1]. 1575827. X-ray structure of T4 endonuclease V: an excision repair enzyme specific for a pyrimidine dimer. Morikawa K, Matsumoto O, Tsujimoto M, Katayanagi K, Ariyoshi M, Doi T, Ikehara M, Inaoka T, Ohtsuka E;. Science 1992;256:523-526. (from Pfam) NF015007.5 PF03016.20 Exostosin 33.4 33.4 293 domain Y Y N exostosin family protein 9756849 131567 cellular organisms no rank 836 EBI-EMBL Exostosin family exostosin family protein The EXT family is a family of tumour suppressor genes. Mutations of EXT1 Swiss:Q16394 on 8q24.1, EXT2 Swiss:Q93063 on 11p11-13, and EXT3 on 19p have been associated with the autosomal dominant disorder known as hereditary multiple exostoses (HME). This is the most common known skeletal dysplasia. The chromosomal locations of other EXT genes suggest association with other forms of neoplasia. EXT1 and EXT2 have both been shown to encode a heparan sulphate polymerase with both D-glucuronyl (GlcA) and N-acetyl-D-glucosaminoglycan (GlcNAC) transferase activities [1]. The nature of the defect in heparan sulphate biosynthesis in HME is unclear. [1]. 9756849. The putative tumor suppressors EXT1 and EXT2 are glycosyltransferases required for the biosynthesis of heparan sulfate. Lind T, Tufaro F, McCormick C, Lindahl U, Lidholt K;. J Biol Chem 1998;273:26265-26268. (from Pfam) NF015012.5 PF03022.21 MRJP 19.8 19.8 288 subfamily Y Y N L-dopachrome tautomerase-related protein 9791542 131567 cellular organisms no rank 11935 EBI-EMBL Major royal jelly protein major royal jelly protein/L-dopachrome tautomerase-related protein Royal jelly is the food of queen bee larvae, and is responsible for the high reproductive ability of the queen. Major royal jelly proteins make up around 90% of larval jelly proteins. This family also the sequence-related yellow protein of drosophila which controls pigmentation of the adult cuticle and larval mouth parts. [1]. 9791542. A family of major royal jelly proteins of the honeybee Apis mellifera L. Schmitzova J, Klaudiny J, Albert S, Schroder W, Schreckengost W, Hanes J, Judova J, Simuth J;. Cell Mol Life Sci 1998;54:1020-1030. (from Pfam) NF015013.5 PF03023.19 MurJ 27.4 27.4 451 domain Y Y N lipid II flippase MurJ 18832143,24688094,28024149 131567 cellular organisms no rank 137143 EBI-EMBL Lipid II flippase MurJ lipid II flippase MurJ Peptidoglycan synthesis (PG) biosynthesis involves the formation of peptidoglycan precursor lipid II (undecaprenyl-pyrophosphate-linked N-acetyl glucosamine-N-acetyl muramic acid-pentapeptide) on the cytosolic face of the cell membrane. Lipid II is then translocated across the membrane and its glycopeptide moiety becomes incorporated into the growing cell wall mesh. MviN, renamed as MurJ, is a lipid II flippase essential for cell wall peptidoglycan synthesis [1, 2]. MurJ belongs to the MVF (mouse virulence factor) family of MOP superfamily transporters, which also includes the MATE (multidrug and toxic compound extrusion) transporter and eukaryotic OLF (oligosaccharidyl-lipid flippase) families. In addition to the canonical MOP transporter core consisting of 12 transmembrane helices (TMs), MurJ has two additional C-terminal TMs (13 and 14) of unknown function. Structural analysis indicates that the N lobe (TMs 1-6) and C lobe (TMs 7-14) are arranged in an inward-facing N-shape conformation, rather than the outward-facing V-shape conformation observed in all existing MATE transporter structures. Furthermore, a hydrophobic groove is formed by two C-terminal transmembrane helices, which leads into a large central cavity that is mostly cationic. Mutagenesis studies, revealed a solvent-exposed cavity that is essential for function. Mutation of conserved residues (Ser17, Arg18, Arg24, Arg52, and Arg255) at the proximal site failed to complement MurJ function, consistent with the idea that these residues are important for recognizing the diphosphate and/or sugar moieties of lipid II. It has also been suggested that the chloride i. TRUNCATED at 1650 bytes (from Pfam) NF015018.5 PF03029.22 ATP_bind_1 27 27 240 domain Y Y N ATP/GTP-binding protein 131567 cellular organisms no rank 54797 EBI-EMBL Conserved hypothetical ATP binding protein ATP/GTP-binding protein Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity. (from Pfam) NF015019.5 PF03030.21 H_PPase 29.7 29.7 645 PfamEq Y Y N sodium/proton-translocating pyrophosphatase GO:0004427,GO:0009678,GO:0016020,GO:1902600 11335173 131567 cellular organisms no rank 30938 EBI-EMBL Inorganic H+ pyrophosphatase sodium/proton-translocating pyrophosphatase The H+ pyrophosphatase is an transmembrane proton pump involved in establishing the H+ electrochemical potential difference between the vacuole lumen and the cell cytosol. Vacuolar-type H(+)-translocating inorganic pyrophosphatases have long been considered to be restricted to plants and to a few species of photo-trophic bacteria. However, in recent investigations, these pyrophosphatases have been found in organisms as disparate as thermophilic Archaea and parasitic protists [1]. [1]. 11335173. Vacuolar H(+) pyrophosphatases: from the evolutionary backwaters into the mainstream. Drozdowicz YM, Rea PA;. Trends Plant Sci 2001;6:206-211. (from Pfam) NF015020.5 PF03031.23 NIF 21.8 21.8 160 subfamily Y Y N NIF family HAD-type phosphatase 12556522 131567 cellular organisms no rank 2552 EBI-EMBL NLI interacting factor-like phosphatase NIF family HAD-type phosphatase This family contains a number of NLI interacting factor isoforms (eg. Swiss:Q9PTJ8) and also an N-terminal regions of RNA polymerase II CTC phosphatase (Swiss:Q9Y5BO) and FCP1 serine phosphatase (Swiss:Q9PT70). This region has been identified as the minimal phosphatase domain [1]. [1]. 12556522. Defining the active site of Schizosaccharomyces pombe CTD phosphatase Fcp1. Hausmann S, Shuman S;. J Biol Chem 2003;0:0-0. (from Pfam) NF015022.5 PF03033.25 Glyco_transf_28 26.2 26.2 139 domain Y Y N glycosyltransferase 2.4.-.- GO:0005975,GO:0016758,GO:0030259 1649817 131567 cellular organisms no rank 103048 EBI-EMBL Glycosyltransferase family 28 N-terminal domain Glycosyltransferase family 28 N-terminal domain The glycosyltransferase family 28 includes monogalactosyldiacylglycerol synthase (Swiss:P93115, EC 2.4.1.46) and UDP-N-acetylglucosamine transferase (Swiss:P74657, EC 2.4.1.-). This N-terminal domain contains the acceptor binding site and likely membrane association site. This family also contains a large number of proteins that probably have quite distinct activities. [1]. 1649817. The murG gene of Escherichia coli codes for the UDP-N-acetylglucosamine: N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase involved in the membrane steps of peptidoglycan synthesis. Mengin-Lecreulx D, Texier L, Rousseau M, van Heijenoort J;. J Bacteriol 1991;173:4625-4636. (from Pfam) NF015038.5 PF03050.19 DDE_Tnp_IS66 23.1 23.1 284 domain Y Y N transposase 6095299,8167368 131567 cellular organisms no rank 103465 EBI-EMBL Transposase IS66 family transposase Transposase proteins are necessary for efficient DNA transposition. This family includes IS66 from Agrobacterium tumefaciens [2]. [1]. 8167368. An open reading frame downstream of Rhizobium meliloti nodQ1 shows nucleotide sequence similarity to an Agrobacterium tumefaciens insertion sequence. Schwedock J, Long SR;. Mol Plant Microbe Interact 1994;7:151-153. Naming of IS66. [2]. 6095299. Nucleotide sequence of the insertion sequence found in the T-DNA region of mutant Ti plasmid pTiA66 and distribution of its homologues in octopine Ti plasmid. Machida Y, Sakurai M, Kiyokawa S, Ubasawa A, Suzuki Y, Ikeda JE;. Proc Natl Acad Sci USA 1984;81:7495-7499. (from Pfam) NF015042.5 PF03054.21 tRNA_Me_trans 20.6 20.6 202 domain Y N N tRNA methyl transferase HUP domain 16871210,23444054,23816837,28655838,3298234,8548458 131567 cellular organisms no rank 134683 EBI-EMBL tRNA methyl transferase HUP domain tRNA methyl transferase HUP domain This family represents the N-terminal HUP domain in tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs [1]. [1]. 3298234. Transfer RNA(5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities. Hagervall TG, Edmonds CG, McCloskey JA, Bjork GR;. J Biol Chem 1987;262:8488-8495. Paper describing PDB structure 1gpm. [2]. 8548458. The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families. Tesmer JJ, Klem TJ, Deras ML, Davisson VJ, Smith JL;. Nat Struct Biol 1996;3:74-86. Paper describing PDB structure 2der. [3]. 16871210. Snapshots of tRNA sulphuration via an adenylated intermediate. Numata T, Ikeuchi Y, Fukai S, Suzuki T, Nureki O;. Nature. 2006;442:419-424. Paper describing PDB structure 2vxo. [4]. 23816837. Substrate specificity and oligomerization of human GMP synthetase. Welin M, Lehtio L, Johansson A, Flodin S, Nyman T, Tresaugues L, Hammarstrom M, Graslund S, Nordlund P;. J Mol Biol. 2013;425:4323-4333. Paper describing PDB structure 3vrh. [5]. 23444054. Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA. Nakagawa H, Kuratani M, Goto-Ito S, Ito T, Katsura K, Terada T, Shirouzu M, Sekine S, Shigi N, Yokoyama S;. Proteins. 2013;81:1232-1244. Paper describing PDB structure 5mko. [6]. 28655838. Nonredox thiolation in tRNA occurring via sulfur activation by a [4Fe-4S] cluster. Arragain S, Bimai O, Legrand P, Caillat S, Ravanat JL, T. TRUNCATED at 1650 bytes (from Pfam) NF015043.5 PF03055.20 RPE65 27 27 469 domain Y Y N carotenoid oxygenase family protein GO:0016702 7633413 131567 cellular organisms no rank 25782 EBI-EMBL Retinal pigment epithelial membrane protein carotenoid oxygenase family protein This family represents a retinal pigment epithelial membrane receptor which is abundantly expressed in retinal pigment epithelium, and binds plasma retinal binding protein. The family also includes the sequence related neoxanthin cleavage enzyme in plants and lignostilbene-alpha,beta-dioxygenase in bacteria. [1]. 7633413. Molecular characterization of the human gene encoding an abundant 61 kDa protein specific to the retinal pigment epithelium. Nicoletti A, Wong DJ, Kawase K, Gibson LH, Yang-Feng TL, Richards JE, Thompson DA;. Hum Mol Genet 1995;4:641-649. (from Pfam) NF015046.5 PF03059.21 NAS 27.1 27.1 276 subfamily Y Y N nicotianamine synthase family protein GO:0030410,GO:0030418 10359845,19805277,9952442 131567 cellular organisms no rank 1484 EBI-EMBL Nicotianamine synthase protein nicotianamine synthase family protein Nicotianamine synthase EC:2.5.1.43 catalyses the trimerisation of S-adenosylmethionine to yield one molecule of nicotianamine. Nicotianamine has an important role in plant iron uptake mechanisms. Plants adopt two strategies (termed I and II) of iron acquisition. Strategy I is adopted by all higher plants except graminaceous plants, which adopt strategy II [1,2]. In strategy I plants, the role of nicotianamine is not fully determined: possible roles include the formation of more stable complexes with ferrous than with ferric ion, which might serve as a sensor of the physiological status of iron within a plant, or which might be involved in the transport of iron [1]. In strategy II (graminaceous) plants, nicotianamine is the key intermediate (and nicotianamine synthase the key enzyme) in the synthesis of the mugineic family (the only known family in plants) of phytosiderophores. Phytosiderophores are iron chelators whose secretion by the roots is greatly increased in instances of iron deficiency [2]. The 3D structures of five example NAS from Methanothermobacter thermautotrophicus reveal the monomer to consist of a five-helical bundle N-terminal domain on top of a classic Rossmann fold C-terminal domain. The N-terminal domain is unique to the NAS family, whereas the C-terminal domain is homologous to the class I family of SAM-dependent methyltransferases. An active site is created at the interface of the two domains, at the rim of a large cavity that corresponds to the nucleotide binding site such as is found in other proteins adopting a Rossmann fold [3]. [1]. 10359845. Map-based cloning of chloronerva, a gene involved in. TRUNCATED at 1650 bytes (from Pfam) NF015047.5 PF03060.20 NMO 28 28 331 domain Y Y N nitronate monooxygenase GO:0018580 15582992,16682407,19577534,19683782,9501443 131567 cellular organisms no rank 195553 EBI-EMBL Nitronate monooxygenase nitronate monooxygenase Nitronate monooxygenase (NMO), formerly referred to as 2-nitropropane dioxygenase (NPD) (EC:1.13.11.32), is an FMN-dependent enzyme that uses molecular oxygen to oxidize (anionic) alkyl nitronates and, in the case of the enzyme from Neurospora crassa, (neutral) nitroalkanes to the corresponding carbonyl compounds and nitrite. Previously classified as 2-nitropropane dioxygenase [1,2,3], but it is now recognized that this was the result of the slow ionization of nitroalkanes to their nitronate (anionic) forms [4]. The enzymes from the fungus Neurospora crassa and the yeast Williopsis saturnus var. mrakii (formerly classified as Hansenula mrakii) contain non-covalently bound FMN as the cofactor. Active towards linear alkyl nitronates of lengths between 2 and 6 carbon atoms and, with lower activity, towards propyl-2-nitronate. The enzyme from N. crassa can also utilize neutral nitroalkanes, but with lower activity. One atom of oxygen is incorporated into the carbonyl group of the aldehyde product. The reaction appears to involve the formation of an enzyme-bound nitronate radical and an a-peroxynitroethane species, which then decomposes, either in the active site of the enzyme or after release, to acetaldehyde and nitrite. [1]. 9501443. Purification, characterization, and mechanism of a flavin mononucleotide-dependent 2-nitropropane dioxygenase from Neurospora crassa. Gorlatova N, Tchorzewski M, Kurihara T, Soda K, Esaki N;. Appl Environ Microbiol 1998;64:1029-1033. [2]. 15582992. Involvement of a flavosemiquinone in the enzymatic oxidation of nitroalkanes catalyzed by 2-nitropropane dioxygenase. Francis K, Russell B, Gadda G;.. TRUNCATED at 1650 bytes (from Pfam) NF015048.5 PF03061.27 4HBT 20.6 20.6 79 domain Y Y N hotdog domain-containing protein 8805534,9837940 131567 cellular organisms no rank 389616 EBI-EMBL Thioesterase superfamily Thioesterase superfamily This family contains a wide variety of enzymes, principally thioesterases. This family includes 4HBT (EC 3.1.2.23) which catalyses the final step in the biosynthesis of 4-hydroxybenzoate from 4-chlorobenzoate in the soil dwelling microbe Pseudomonas CBS-3. This family includes various cytosolic long-chain acyl-CoA thioester hydrolases. Long-chain acyl-CoA hydrolases hydrolyse palmitoyl-CoA to CoA and palmitate, they also catalyse the hydrolysis of other long chain fatty acyl-CoA thioesters. [1]. 9837940. The three-dimensional structure of 4-hydroxybenzoyl-CoA thioesterase from Pseudomonas sp. Strain CBS-3. Benning MM, Wesenberg G, Liu R, Taylor KL, Dunaway-Mariano D, Holden HM;. J Biol Chem 1998;273:33572-33579. [2]. 8805534. Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site. Leesong M, Henderson BS, Gillig JR, Schwab JM, Smith JL;. Structure 1996;4:253-264. (from Pfam) NF015049.5 PF03062.24 MBOAT 27 27 337 domain Y Y N MBOAT family O-acyltransferase 2.3.-.- GO:0016746 10694878 131567 cellular organisms no rank 52133 EBI-EMBL MBOAT, membrane-bound O-acyltransferase family MBOAT family O-acyltransferase The MBOAT (membrane bound O-acyl transferase) family of membrane proteins contains a variety of acyltransferase enzymes. A conserved histidine has been suggested to be the active site residue [1]. [1]. 10694878. A superfamily of membrane-bound O-acyltransferases with implications for wnt signaling. Hofmann K;. Trends Biochem Sci 2000;25:111-112. (from Pfam) NF015050.5 PF03063.25 Prismane 27 27 513 domain Y N N Prismane/CO dehydrogenase family GO:0016491 10651802,12374823 131567 cellular organisms no rank 25701 EBI-EMBL Prismane/CO dehydrogenase family Prismane/CO dehydrogenase family This family includes both hybrid-cluster proteins and the beta chain of carbon monoxide dehydrogenase. The hybrid-cluster proteins contain two Fe/S centres - a [4Fe-4S] cubane cluster, and a hybrid [4Fe-2S-2O] cluster. The physiological role of this protein is as yet unknown, although a role in nitrate/nitrite respiration has been suggested [1]. The prismane protein from Escherichia coli was shown to contain hydroxylamine reductase activity (NH2OH + 2e + 2 H+ -> NH3 + H2O). This activity is rather low. Hydroxylamine reductase activity was also found in CO-dehydrogenase in which the active site Ni was replaced by Fe [2]. The CO dehydrogenase contains a Ni-3Fe-2S-3O centre. [1]. 10651802. The hybrid-cluster protein ('prismane protein') from Escherichia coli. Characterization of the hybrid-cluster protein, redox properties of the [2Fe-2S] and [4Fe-2S-2O] clusters and identification of an associated NADH oxidoreductase containing FAD and [2F. van den Berg WA, Hagen WR, van Dongen WM;. Eur J Biochem 2000;267:666-676. [2]. 12374823. Hydroxylamine reductase activity of the hybrid cluster protein from Escherichia coli. Wolfe MT, Heo J, Garavelli JS, Ludden PW;. J Bacteriol 2002;184:5898-5902. (from Pfam) NF015052.5 PF03065.20 Glyco_hydro_57 21.2 21.2 291 domain Y N N Glycosyl hydrolase family 57 GO:0003824,GO:0005975 8226989 131567 cellular organisms no rank 32158 EBI-EMBL Glycosyl hydrolase family 57 Glycosyl hydrolase family 57 This family includes alpha-amylase (EC:3.2.1.1), 4--glucanotransferase (EC:2.4.1.-) and amylopullulanase enzymes. [1]. 8226989. The purification and characterization of an extremely thermostable alpha-amylase from the hyperthermophilic archaebacterium Pyrococcus furiosus. Laderman KA, Davis BR, Krutzsch HC, Lewis MS, Griko YV, Privalov PL, Anfinsen CB;. J Biol Chem 1993;268:24394-24401. (from Pfam) NF015054.5 PF03067.20 LPMO_10 23 23 183 domain Y Y N lytic polysaccharide monooxygenase 24912171,7815940 131567 cellular organisms no rank 48643 EBI-EMBL Lytic polysaccharide mono-oxygenase, cellulose-degrading lytic polysaccharide monooxygenase This domain is found associated with a wide variety of cellulose binding domains. This is a family of two very closely related proteins that together act as both a C1- and a C4-oxidising lytic polysaccharide mono-oxygenase [2], degrading cellulose. This domain is also found in baculoviral spheroidins and spindolins, protein of unknown function. [1]. 7815940. The novel lectin-like protein CHB1 is encoded by a chitin-inducible Streptomyces olivaceoviridis gene and binds specifically to crystalline alpha-chitin of fungi and other organisms. Schnellmann J, Zeltins A, Blaak H, Schrempf H;. Mol Microbiol 1994;13:807-819. [2]. 24912171. Structural and functional characterization of a conserved pair of bacterial cellulose-oxidizing lytic polysaccharide monooxygenases. Forsberg Z, Mackenzie AK, Sorlie M, Rohr AK, Helland R, Arvai AS, Vaaje-Kolstad G, Eijsink VG;. Proc Natl Acad Sci U S A. 2014;111:8446-8451. (from Pfam) NF015056.5 PF03069.20 FmdA_AmdA 27 27 373 domain Y Y N acetamidase/formamidase family protein GO:0016811 131567 cellular organisms no rank 33193 EBI-EMBL Acetamidase/Formamidase family acetamidase/formamidase family protein This family includes amidohydrolases of formamide EC:3.5.1.49 and acetamide. Swiss:Q50228 forms a homotrimer suggesting all the members of this family also do. (from Pfam) NF015057.5 PF03070.21 TENA_THI-4 22 22 210 domain Y N N TENA/THI-4/PQQC family 12437981,1898926,8662211 131567 cellular organisms no rank 53382 EBI-EMBL TENA/THI-4/PQQC family TENA/THI-4/PQQC family Members of this family are found in all the three major phyla of life: archaebacteria, eubacteria, and eukaryotes. In Bacillus subtilis, TENA is one of a number of proteins that enhance the expression of extracellular enzymes, such as alkaline protease, neutral protease and levansucrase [1]. The THI-4 protein, which is involved in thiamine biosynthesis, is also a member of this family. The C-terminal part of these proteins consistently show significant sequence similarity to TENA proteins. This similarity was first noted with the Neurospora crassa THI-4 [2]. This family includes bacterial coenzyme PQQ synthesis protein C or PQQC proteins. Pyrroloquinoline quinone (PQQ) is the prosthetic group of several bacterial enzymes,including methanol dehydrogenase of methylotrophs and the glucose dehydrogenase of a number of bacteria [3]. PQQC has been found to be required in the synthesis of PQQ but its function is unclear. The exact molecular function of members of this family is uncertain. [1]. 1898926. Cloning and characterization of a pair of novel genes that regulate production of extracellular enzymes in Bacillus subtilis. Pang AS, Nathoo S, Wong SL;. J Bacteriol 1991;173:46-54. [2]. 8662211. Molecular cloning of thi-4, a gene necessary for the biosynthesis of thiamine in Neurospora crassa. Akiyama M, Nakashima H;. Curr Genet 1996;30:62-67. [3]. 12437981. PqqC/D, which converts a biosynthetic intermediate to pyrroloquinoline quinone. Toyama H, Fukumoto H, Saeki M, Matsushita K, Adachi O, Lidstrom ME;. Biochem Biophys Res Commun 2002;299:268-272. (from Pfam) NF015058.5 PF03071.20 GNT-I 25.4 25.4 434 PfamEq Y N N GNT-I family GO:0006486,GO:0008375 10406843 131567 cellular organisms no rank 484 EBI-EMBL GNT-I family GNT-I family Alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase (GNT-I, GLCNAC-T I) EC:2.4.1.101 transfers N-acetyl-D-glucosamine from UDP to high-mannose glycoprotein N-oligosaccharide. This is an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides. The enzyme is an integral membrane protein localised to the Golgi apparatus, and is probably distributed in all tissues. The catalytic domain is located at the C-terminus [1]. [1]. 10406843. Molecular cloning and characterization of cDNA coding for beta1, 2N-acetylglucosaminyltransferase I (GlcNAc-TI) from Nicotiana tabacum. Strasser R, Mucha J, Schwihla H, Altmann F, Glossl J, Steinkellner H;. Glycobiology 1999;9:779-785. (from Pfam) NF015060.5 PF03073.20 TspO_MBR 24 24 145 domain Y Y N tryptophan-rich sensory protein GO:0016020 10681549,7673149,9144197 131567 cellular organisms no rank 28727 EBI-EMBL TspO/MBR family tryptophan-rich sensory protein Tryptophan-rich sensory protein (TspO) is an integral membrane protein that acts as a negative regulator of the expression of specific photosynthesis genes in response to oxygen/light [1]. It is involved in the efflux of porphyrin intermediates from the cell. This reduces the activity of coproporphyrinogen III oxidase, which is thought to lead to the accumulation of a putative repressor molecule that inhibits the expression of specific photosynthesis genes. Several conserved aromatic residues are necessary for TspO function: they are thought to be involved in binding porphyrin intermediates [3]. In [2], the rat mitochondrial peripheral benzodiazepine receptor (MBR) was shown to not only retain its structure within a bacterial outer membrane, but also to be able to functionally substitute for TspO in TspO- mutants, and to act in a similar manner to TspO in its in situ location: the outer mitochondrial membrane. The biological significance of MBR remains unclear, however. It is thought to be involved in a variety of cellular functions, including cholesterol transport in steroidogenic tissues. [1]. 7673149. A sensory transducer homologous to the mammalian peripheral-type benzodiazepine receptor regulates photosynthetic membrane complex formation in Rhodobacter sphaeroides 2.4.1. Yeliseev AA, Kaplan S;. J Biol Chem 1995;270:21167-21175. [2]. 9144197. A mammalian mitochondrial drug receptor functions as a bacterial oxygen sensor. Yeliseev AA, Krueger KE, Kaplan S;. Proc Natl Acad Sci U S A 1997;94:5101-5106. [3]. 10681549. TspO of rhodobacter sphaeroides. A structural and functional model for the mammalian peripheral benzodiaze. TRUNCATED at 1650 bytes (from Pfam) NF015065.5 PF03079.19 ARD 27 27 157 domain Y N N ARD/ARD' family GO:0010309 11371200,9880484 131567 cellular organisms no rank 14360 EBI-EMBL ARD/ARD' family ARD/ARD' family The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence Swiss:Q9ZFE7, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions [1,2]. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalysed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels [1,2]. This family also contains other members, whose functions are not well characterised. [1]. 11371200. Mechanistic Studies of Two Dioxygenases in the Methionine Salvage Pathway of Klebsiella pneumoniae(,). Dai Y, Pochapsky TC, Abeles RH;. Biochemistry 2001;40:6379-6387. [2]. 9880484. One protein, two enzymes. Dai Y, Wensink PC, Abeles RH;. J Biol Chem 1999;274:1193-1195. (from Pfam) NF015069.5 PF03083.21 MtN3_slv 23.7 23.7 87 subfamily Y Y N SemiSWEET family transporter GO:0016020 21107422,8630032,8634476,9739134 131567 cellular organisms no rank 8913 EBI-EMBL Sugar efflux transporter for intercellular exchange SemiSWEET family transporter This family includes proteins such as drosophila saliva [1], MtN3 involved in root nodule development [3] and a protein involved in activation and expression of recombination activation genes (RAGs) [2]. Although the molecular function of these proteins is unknown, they are almost certainly transmembrane proteins. This family contains a region of two transmembrane helices that is found in two copies in most members of the family. This family also contains specific sugar efflux transporters that are essential for the maintenance of animal blood glucose levels, plant nectar production, and plant seed and pollen development. In many organisims it meditaes gluose transport; in Arabidopsis it is necessary for pollen viability; and two of the rice homologues are specifically exploited by bacterial pathogens for virulence by means of direct binding of a bacterial effector to the SWEET promoter [4]. [1]. 9739134. saliva, a new Drosophila gene expressed in the embryonic salivary glands with homologues in plants and vertebrates. Artero RD, Terol-Alcayde J, Paricio N, Ring J, Bargues M, Torres A, Perez-Alonso M;. Mech Dev 1998;75:159-162. [2]. 8630032. Molecular cloning and characterization of a novel stromal cell-derived cDNA encoding a protein that facilitates gene activation of recombination activating gene (RAG)-1 in human lymphoid progenitors. Tagoh H, Kishi H, Muraguchi A;. Biochem Biophys Res Commun 1996;221:744-749. [3]. 8634476. Use of a subtractive hybridization approach to identify new Medicago truncatula genes induced during root nodule development. Gamas P, Niebel Fd, Lescure N, Cullimore J;. Mol Plant Microbe Interact 1. TRUNCATED at 1650 bytes (from Pfam) NF015074.5 PF03088.21 Str_synth 25 25 89 domain Y N N Strictosidine synthase GO:0009058,GO:0016844 1567228 131567 cellular organisms no rank 11782 EBI-EMBL Strictosidine synthase Strictosidine synthase Strictosidine synthase (E.C. 4.3.3.2) is a key enzyme in alkaloid biosynthesis. It catalyses the condensation of tryptamine with secologanin to form strictosidine. [1]. 1567228. Strictosidine synthase from Rauvolfia serpentina: analysis of a gene involved in indole alkaloid biosynthesis. Bracher D, Kutchan TM;. Arch Biochem Biophys 1992;294:717-723. (from Pfam) NF015077.5 PF03091.20 CutA1 22.4 22.4 99 PfamEq Y Y N divalent cation tolerance protein CutA cutA GO:0010038 7623666,9260936 131567 cellular organisms no rank 21822 EBI-EMBL CutA1 divalent ion tolerance protein divalent cation tolerance protein CutA Several gene loci with a possible involvement in cellular tolerance to copper have been identified [1]. One such locus in eubacteria and archaebacteria, cutA, is thought to be involved in cellular tolerance to a wide variety of divalent cations other than copper. The cutA locus consists of two operons, of one and two genes. The CutA1 protein is a cytoplasmic protein, encoded by the single-gene operon and has been linked to divalent cation tolerance. It has no recognised structural motifs [2]. This family also contains putative proteins from eukaryotes (human and Drosophila). [1]. 7623666. Molecular genetics of a chromosomal locus involved in copper tolerance in Escherichia coli K-12. Fong ST, Camakaris J, Lee BT;. Mol Microbiol 1995;15:1127-1137. [2]. 9260936. A Salmonella typhimurium genetic locus which confers copper tolerance on copper-sensitive mutants of Escherichia coli. Gupta SD, Wu HC, Rick PD;. J Bacteriol 1997;179:4977-4984. (from Pfam) NF015078.5 PF03092.21 BT1 22 22 432 domain Y N N BT1 family 10589984,7984172 131567 cellular organisms no rank 12532 EBI-EMBL BT1 family BT1 family Members of this family are transmembrane proteins. Several are Leishmania putative proteins that are thought to be pteridine transporters. One such protein Swiss:Q25272, previously termed (and is still annotated as) ORFG, was shown to encode a biopterin transport protein using null mutants [1], thus being subsequently renamed BT1. The significant similarity of ORFG/BT1 to Trypanosoma brucei ESAG10 (a putative transmembrane protein and another member of this family) was previously noted [2]. This family also contains five putative Arabidopsis thaliana proteins of unknown function. In addition, it also contains two predicted prokaryotic proteins (from the cyanobacteria Synechocystis and Synechococcus). [1]. 10589984. The Leishmania donovani LD1 locus gene ORFG encodes a biopterin transporter (BT1). Lemley C, Yan S, Dole VS, Madhubala R, Cunningham ML, Beverley SM, Myler PJ, Stuart KD;. Mol Biochem Parasitol 1999;104:93-105. [2]. 7984172. An amplified DNA element in Leishmania encodes potential integral membrane and nucleotide-binding proteins. Myler PJ, Lodes MJ, Merlin G, de Vos T, Stuart KD;. Mol Biochem Parasitol 1994;66:11-20. (from Pfam) NF015081.5 PF03096.19 Ndr 23.3 23.3 283 domain Y N N Ndr family 10581191 131567 cellular organisms no rank 80518 EBI-EMBL Ndr family Ndr family This family consists of proteins from different gene families: Ndr1/RTP/Drg1, Ndr2, and Ndr3. Their similarity was previously noted [1]. The precise molecular and cellular function of members of this family is still unknown. Yet, they are known to be involved in cellular differentiation events. The Ndr1 group was the first to be discovered. Their expression is repressed by the proto-oncogenes N-myc and c-myc, and in line with this observation, Ndr1 protein expression is down-regulated in neoplastic cells, and is reactivated when differentiation is induced by chemicals such as retinoic acid. Ndr2 and Ndr3 expression is not under the control of N-myc or c-myc. Ndr1 expression is also activated by several chemicals: tunicamycin and homocysteine induce Ndr1 in human umbilical endothelial cells; nickel induces Ndr1 in several cell types. Members of this family are found in wide variety of multicellular eukaryotes, including an Ndr1 type protein in Helianthus annuus (sunflower), known as Sf21 Swiss:O23969. Interestingly, the highest scoring matches in the noise are all alpha/beta hydrolases Pfam:PF00561, suggesting that this family may have an enzymatic function (Bateman A pers. obs.). [1]. 10581191. Identification of new genes ndr2 and ndr3 which are related to Ndr1/RTP/Drg1 but show distinct tissue specificity and response to N-myc. Okuda T, Kondoh H;. Biochem Biophys Res Commun 1999;266:208-215. (from Pfam) NF015083.5 PF03098.20 An_peroxidase 25 25 530 domain Y Y N peroxidase family protein 15979004 131567 cellular organisms no rank 11948 EBI-EMBL Animal haem peroxidase peroxidase family protein NF015084.5 PF03099.24 BPL_LplA_LipB 21 21 133 domain Y N N Biotin/lipoate A/B protein ligase family GO:0036211 10470036,11106165,1409631,16221579,8206909 131567 cellular organisms no rank 131654 EBI-EMBL Biotin/lipoate A/B protein ligase family Biotin/lipoate A/B protein ligase family This family includes biotin protein ligase, lipoate-protein ligase A and B. Biotin is covalently attached at the active site of certain enzymes that transfer carbon dioxide from bicarbonate to organic acids to form cellular metabolites. Biotin protein ligase (BPL) is the enzyme responsible for attaching biotin to a specific lysine at the active site of biotin enzymes. Each organism probably has only one BPL. Biotin attachment is a two step reaction that results in the formation of an amide linkage between the carboxyl group of biotin and the epsilon-amino group of the modified lysine [2]. Lipoate-protein ligase A (LPLA) catalyses the formation of an amide linkage between lipoic acid and a specific lysine residue in lipoate dependent enzymes [3]. The unusual biosynthesis pathway of lipoic acid is mechanistically intertwined with attachment of the cofactor [5]. [1]. 1409631. Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains. Wilson KP, Shewchuk LM, Brennan RG, Otsuka AJ, Matthews BW;. Proc Natl Acad Sci USA 1992;89:9257-9261. A comprehensive review of biotinylation. [2]. 10470036. The enzymatic biotinylation of proteins: a post-translational modification of exceptional specificity. Chapman-Smith A, Cronan JE Jr;. Trends Biochem Sci 1999;24:359-363. [3]. 8206909. Identification of the gene encoding lipoate-protein ligase A of Escherichia coli. Molecular cloning and characterization of the lplA gene and gene product. Morris TW, Reed KE, Cronan JE Jr;. J Biol Chem 1994;269:16091-16100. [4]. 11106165. Lipoylating and biotinylating enzymes contain a homo. TRUNCATED at 1650 bytes (from Pfam) NF015085.5 PF03100.20 CcmE 24.6 24.6 128 PfamEq Y Y N cytochrome c maturation protein CcmE GO:0017003,GO:0017004,GO:0020037 7635817,7715601 131567 cellular organisms no rank 21718 EBI-EMBL CcmE cytochrome c maturation protein CcmE CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor. [1]. 7635817. Escherichia coli genes required for cytochrome c maturation. Thony-Meyer L, Fischer F, Kunzler P, Ritz D, Hennecke H;. J Bacteriol 1995;177:4321-4326. [2]. 7715601. The cycHJKL gene cluser plays an essential role in the biogenesis of c-type cytochromes in Bradyrhizobium japonicum. Ritz D, Thony-Meyer L, Hennecke H;. Mol Gen Genet 1995;247:27-38. (from Pfam) NF015087.5 PF03102.19 NeuB 22.1 22.1 241 domain Y Y N N-acetylneuraminate synthase family protein GO:0016051 10873658 131567 cellular organisms no rank 54810 EBI-EMBL NeuB family N-acetylneuraminate synthase family protein NeuB is the prokaryotic N-acetylneuraminic acid (Neu5Ac) synthase. It catalyses the direct formation of Neu5Ac (the most common sialic acid) by condensation of phosphoenolpyruvate (PEP) and N-acetylmannosamine (ManNAc). This reaction has only been observed in prokaryotes; eukaryotes synthesise the 9-phosphate form, Neu5Ac-9-P, and utilise ManNAc-6-P instead of ManNAc. Such eukaryotic enzymes are not present in this family [1]. This family also contains SpsE spore coat polysaccharide biosynthesis proteins. [1]. 10873658. Molecular cloning and expression of the mouse N-acetylneuraminic acid 9-phosphate synthase which does not have deaminoneuraminic acid (KDN) 9-phosphate synthase activity. Nakata D, Close BE, Colley KJ, Matsuda T, Kitajima K;. Biochem Biophys Res Commun 2000;273:642-648. (from Pfam) NF015089.5 PF03104.24 DNA_pol_B_exo1 23 23 242 domain Y Y N 3'-5' exonuclease 8679562,9757117 131567 cellular organisms no rank 31796 EBI-EMBL DNA polymerase family B, exonuclease domain DNA polymerase family B, exonuclease domain This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold. [1]. 8679562. Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions. Wang J, Yu P, Lin TC, Konigsberg WH, Steitz TA;. Biochemistry 1996;35:8110-8119. [2]. 9757117. Crystallization and preliminary diffraction analysis of a hyperthermostable DNA polymerase from a Thermococcus archaeon. Zhou M, Mao C, Rodriguez AC, Kiefer JR, Kucera RB, Beese LS;. Acta Crystallogr D Biol Crystallogr 1998;54:994-995. (from Pfam) NF015094.5 PF03109.21 ABC1 22.9 22.9 244 domain Y Y N AarF/UbiB family protein 1648478,9422602 131567 cellular organisms no rank 268296 EBI-EMBL ABC1 atypical kinase-like domain ABC1 atypical kinase-like domain This HMM describes a region found in AarF/ABC1/UbiB family proteins. We do not use the term ABC1 (activator of bc1 complex) in protein product names assigned because of the risk of confusion with ABC (ATP-binding cassette) transporter proteins. NF015100.5 PF03116.20 NQR2_RnfD_RnfE 27.7 27.7 296 domain Y Y N RnfABCDGE type electron transport complex subunit D GO:0016020,GO:0055085 10077658,9154934 131567 cellular organisms no rank 36742 EBI-EMBL NQR2, RnfD, RnfE family RnfABCDGE type electron transport complex subunit D This family of bacterial proteins includes a sodium-translocating NADH-ubiquinone oxidoreductase (i.e. a respiration linked sodium pump). In Vibrio cholerae, it negatively regulates the expression of virulence factors through inhibiting (by an unknown mechanism) the transcription of the transcriptional activator ToxT [1]. The family also includes proteins involved in nitrogen fixation, RnfD and RnfE. The similarity of these proteins to NADH-ubiquinone oxidoreductases was previously noted [2]. [1]. 10077658. Effects of changes in membrane sodium flux on virulence gene expression in Vibrio cholerae. Hase CC, Mekalanos JJ;. Proc Natl Acad Sci U S A 1999;96:3183-3187. [2]. 9154934. Membrane localization, topology, and mutual stabilization of the rnfABC gene products in Rhodobacter capsulatus and implications for a new family of energy-coupling NADH oxidoreductases. Kumagai H, Fujiwara T, Matsubara H, Saeki K;. Biochemistry 1997;36:5509-5521. (from Pfam) NF015103.5 PF03119.21 DNA_ligase_ZBD 25.8 25.8 27 PfamEq Y N N NAD-dependent DNA ligase C4 zinc finger domain GO:0003911,GO:0006260,GO:0006281 10698952 131567 cellular organisms no rank 78472 EBI-EMBL NAD-dependent DNA ligase C4 zinc finger domain NAD-dependent DNA ligase C4 zinc finger domain DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor [1]. This family is a small zinc binding motif that is presumably DNA binding [1]. IT is found only in NAD dependent DNA ligases [1]. [1]. 10698952. Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications. Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW;. EMBO J 2000;19:1119-1129. (from Pfam) NF015104.5 PF03120.21 DNA_ligase_OB 32.9 32.9 79 domain Y N N NAD-dependent DNA ligase OB-fold domain GO:0003911,GO:0006260,GO:0006281 10698952 131567 cellular organisms no rank 114723 EBI-EMBL NAD-dependent DNA ligase OB-fold domain NAD-dependent DNA ligase OB-fold domain DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor [1]. This family is a small domain found after the adenylation domain Pfam:PF01653 in NAD dependent ligases [1]. OB-fold domains generally are involved in nucleic acid binding. [1]. 10698952. Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications. Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW;. EMBO J 2000;19:1119-1129. (from Pfam) NF015113.5 PF03129.25 HGTP_anticodon 21 21 94 domain Y Y N His/Gly/Thr/Pro-type tRNA ligase C-terminal domain-containing protein 10447505,9115984 131567 cellular organisms no rank 276640 EBI-EMBL Anticodon binding domain His/Gly/Thr/Pro-type tRNA ligase C-terminal domain This HMM hits a C-terminal region, thought to be the anticodin-binding domain, of tRNA ligases for amino acids His, Gly, Thr, and Pro. Proteins named by this HMM are mostly partials, scoring below cutoffs of more specific models because incomplete sequences generate insufficient scores. NF015114.5 PF03130.21 HEAT_PBS 20.9 13 27 domain Y N N PBS lyase HEAT-like repeat 10708746,8132596,9023176,9882677 131567 cellular organisms no rank 46348 EBI-EMBL PBS lyase HEAT-like repeat PBS lyase HEAT-like repeat This family contains a short bi-helical repeat that is related to Pfam:PF02985. Cyanobacteria and red algae harvest light energy using macromolecular complexes known as phycobilisomes (PBS), peripherally attached to the photosynthetic membrane. The major components of PBS are the phycobiliproteins. These heterodimeric proteins are covalently attached to phycobilins: open-chain tetrapyrrole chromophores, which function as the photosynthetic light-harvesting pigments. Phycobiliproteins differ in sequence and in the nature and number of attached phycobilins to each of their subunits. This family includes the lyase enzymes that specifically attach particular phycobilins to apophycobiliprotein subunits. The most comprehensively studied of these is the CpcE/F lyase Swiss:P31967 Swiss:P31968, which attaches phycocyanobilin (PCB) to the alpha subunit of apophycocyanin [1]. Similarly, MpeU/V attaches phycoerythrobilin to phycoerythrin II, while CpeY/Z is thought to be involved in phycoerythrobilin (PEB) attachment to phycoerythrin (PE) I (PEs I and II differ in sequence and in the number of attached molecules of PEB: PE I has five, PE II has six) [2]. All the reactions of the above lyases involve an apoprotein cysteine SH addition to a terminal delta 3,3'-double bond. Such a reaction is not possible in the case of phycoviolobilin (PVB), the phycobilin of alpha-phycoerythrocyanin (alpha-PEC). It is thought that in this case, PCB, not PVB, is first added to apo-alpha-PEC, and is then isomerised to PVB. The addition reaction has been shown to occur in the presence of either of the components of alpha-PEC-PVB lyase PecE or PecF (or bo. TRUNCATED at 1650 bytes (from Pfam) NF015116.5 PF03133.20 TTL 20.1 20.1 292 domain Y N N Tubulin-tyrosine ligase family GO:0036211 10339593,10685598,11431336,20023723,8093886,9538689 131567 cellular organisms no rank 4002 EBI-EMBL Tubulin-tyrosine ligase family Tubulin-tyrosine ligase family Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL) [2]. The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyses the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness [3]. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis [4]. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain [6]. [1]. 8093886. Characterization of the tubulin-tyrosine ligase. Ersfeld K, Wehland J, Plessmann U, Dodemont H, Gerke V, Weber K;. J Cell Biol 1993;120:725-732. [2]. 10685598. Tubulin-tyrosine ligase, a long-lasting enigma. Erck C, Frank R, Wehland J;. Neurochem Res 2000;25:5-10. [3]. 11431336. Tubulin detyrosination is a frequen. TRUNCATED at 1650 bytes (from Pfam) NF015118.5 PF03135.19 CagE_TrbE_VirB 21 21 204 domain Y N N CagE, TrbE, VirB family, component of type IV transporter system GO:0005524 10438776,11104802,11447179 131567 cellular organisms no rank 30110 EBI-EMBL CagE, TrbE, VirB family, component of type IV transporter system CagE, TrbE, VirB family, component of type IV transporter system This family includes the Helicobacter pylori protein CagE Swiss:Q48252, which together with other proteins from the cag pathogenicity island (PAI), encodes a type IV transporter secretion system. The precise role of CagE is not known, but studies in animal models have shown that it is essential for pathogenesis in Helicobacter pylori induced gastritis and peptic ulceration [1]. Indeed, the expression of the cag PAI has been shown to be essential for stimulating human gastric epithelial cell apoptosis in vitro [2]. Similar type IV transport systems are also found in other bacteria. This family includes the TrbE Swiss:P54910 and VirB Swiss:P05353 proteins from the respective trb and Vir conjugal transfer systems in Agrobacterium tumefaciens. Homologues of VirB proteins from other species are also members of this family, e.g. VirB from Brucella suis Swiss:Q9RPY1. [1]. 11104802. Virulence factors of Helicobacter pylori responsible for gastric diseases in Mongolian gerbil. Ogura K, Maeda S, Nakao M, Watanabe T, Tada M, Kyutoku T, Yoshida H, Shiratori Y, Omata M;. J Exp Med 2000;192:1601-1610. [2]. 11447179. Epithelial Intestinal Cell Apoptosis Induced by Helicobacter pylori Depends on Expression of the cag Pathogenicity Island Phenotype. Le'Negrate G, Ricci V, Hofman V, Mograbi B, Hofman P, Rossi B;. Infect Immun 2001;69:5001-5009. [3]. 10438776. Essential components of the Ti plasmid trb system, a type IV macromolecular transporter. Li PL, Hwang I, Miyagi H, True H, Farrand SK;. J Bacteriol 1999;181:5033-5041. (from Pfam) NF015120.5 PF03137.25 OATP 25.8 25.8 545 domain Y N N Organic Anion Transporter Polypeptide (OATP) family GO:0016020,GO:0055085 10873595 131567 cellular organisms no rank 10693 EBI-EMBL Organic Anion Transporter Polypeptide (OATP) family Organic Anion Transporter Polypeptide (OATP) family This family consists of several eukaryotic Organic-Anion-Transporting Polypeptides (OATPs). Several have been identified mostly in human and rat. Different OATPs vary in tissue distribution and substrate specificity. Since the numbering of different OATPs in particular species was based originally on the order of discovery, similarly numbered OATPs in humans and rats did not necessarily correspond in function, tissue distribution and substrate specificity (in spite of the name, some OATPs also transport organic cations and neutral molecules). Thus, Tamai et al. [1] initiated the current scheme of using digits for rat OATPs and letters for human ones. Prostaglandin transporter (PGT) proteins (e.g. Swiss:Q92959) are also considered to be OATP family members. In addition, the methotrexate transporter OATK (Swiss:P70502) is closely related to OATPs. This family also includes several predicted proteins from Caenorhabditis elegans and Drosophila melanogaster. This similarity was not previously noted. Note: Members of this family are described (in the Swiss-Prot database) as belonging to the SLC21 family of transporters. [1]. 10873595. Molecular identification and characterization of novel members of the human organic anion transporter (OATP) family. Tamai I, Nezu J, Uchino H, Sai Y, Oku A, Shimane M, Tsuji A;. Biochem Biophys Res Commun 2000;273:251-260. (from Pfam) NF015121.5 PF03139.20 AnfG_VnfG 27 27 111 domain Y Y N Fe-only/vanadium nitrogenase subunit delta GO:0009399,GO:0016163 10543806,11018539 131567 cellular organisms no rank 471 EBI-EMBL Vanadium/alternative nitrogenase delta subunit Fe-only/vanadium nitrogenase subunit delta The nitrogenase complex EC:1.18.6.1 catalyses the conversion of molecular nitrogen to ammonia (nitrogen fixation) as follows: 8 reduced ferredoxin + 8 H(+) + N(2) + 16 ATP 8 oxidised ferredoxin + 2 NH(3) + 16 ADP + 16 phosphate. The complex is hexameric, consisting of 2 alpha, 2 beta, and 2 delta subunits. This family represents the delta subunit of a group of nitrogenases that do not utilise molybdenum (Mo) as a cofactor, but instead use either vanadium (V nitrogenases), or iron (alternative nitrogenases). V nitrogenases are encoded by vnf operons, and alternative nitrogenases by anf operons. The delta subunits are VnfG and AnfG, respectively. [1]. 10543806. Culture-independent characterization of a gene responsible for nitrogen fixation in the symbiotic microbial community in the gut of the termite Neotermes koshunensis. Noda S, Ohkuma M, Usami R, Horikoshi K, Kudo T;. Appl Environ Microbiol 1999;65:4935-4942. [2]. 11018539. Activation of vanadium nitrogenase expression in Azotobacter vinelandii DJ54 revertant in the presence of molybdenum. Lei S, Pulakat L, Gavini N;. FEBS Lett 2000;482:149-153. (from Pfam) NF015123.5 PF03141.21 Methyltransf_29 23 23 506 domain Y N N Putative S-adenosyl-L-methionine-dependent methyltransferase GO:0008168 17461780,18167546 131567 cellular organisms no rank 34096 EBI-EMBL Putative S-adenosyl-L-methionine-dependent methyltransferase Putative S-adenosyl-L-methionine-dependent methyltransferase This family is a putative S-adenosyl-L-methionine (SAM)-dependent methyltransferase [1,2]. [1]. 17461780. The TUMOROUS SHOOT DEVELOPMENT2 gene of Arabidopsis encoding a putative methyltransferase is required for cell adhesion and co-ordinated plant development. Krupkova E, Immerzeel P, Pauly M, Schmulling T;. Plant J. 2007;50:735-750. [2]. 18167546. The OSU1/QUA2/TSD2-encoded putative methyltransferase is a critical modulator of carbon and nitrogen nutrient balance response in Arabidopsis. Gao P, Xin Z, Zheng ZL;. PLoS One. 2008;3:e1387. (from Pfam) NF015124.5 PF03142.20 Chitin_synth_2 27 27 527 PfamEq Y N N Chitin synthase 8810520 131567 cellular organisms no rank 15936 EBI-EMBL Chitin synthase Chitin synthase Members of this family are fungal chitin synthase EC:2.4.1.16 enzymes. They catalyse chitin synthesis as follows: UDP-N-acetyl-D-glucosamine + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N) UDP + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N+1). [1]. 8810520. The chsD and chsE genes of Aspergillus nidulans and their roles in chitin synthesis. Specht CA, Liu Y, Robbins PW, Bulawa CE, Iartchouk N, Winter KR, Riggle PJ, Rhodes JC, Dodge CL, Culp DW, Borgia PT;. Fungal Genet Biol 1996;20:153-167. (from Pfam) NF015125.5 PF03143.22 GTP_EFTU_D3 27 27 106 domain Y N N Elongation factor Tu C-terminal domain 7491491,9253415 131567 cellular organisms no rank 70105 EBI-EMBL Elongation factor Tu C-terminal domain Elongation factor Tu C-terminal domain Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA [1] and binding to EF-Ts Pfam:PF00889 [2]. [1]. 7491491. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark BF, Nyborg J;. Science 1995;270:1464-1472. [2]. 9253415. Crystal structure of the EF-Tu.EF-Ts complex from Thermus thermophilus. Wang Y, Jiang Y, Meyering-Voss M, Sprinzl M, Sigler PB;. Nat Struct Biol 1997;4:650-656. (from Pfam) NF015126.5 PF03144.30 GTP_EFTU_D2 30.3 30.3 73 domain Y Y N EF-Tu/IF-2/RF-3 family GTPase GO:0005525 7491491 131567 cellular organisms no rank 366170 EBI-EMBL Elongation factor Tu domain 2 elongation factor Tu domain 2-like domain Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain. [1]. 7491491. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark BF, Nyborg J;. Science 1995;270:1464-1472. (from Pfam) NF015129.5 PF03147.19 FDX-ACB 31.1 31.1 94 PfamEq Y N N Ferredoxin-fold anticodon binding domain 10447505,9016717 131567 cellular organisms no rank 99477 EBI-EMBL Ferredoxin-fold anticodon binding domain Ferredoxin-fold anticodon binding domain This is the anticodon binding domain found in some phenylalanyl tRNA synthetases. The domain has a ferredoxin fold [1,2]. [1]. 10447505. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Wolf YI, Aravind L, Grishin NV, Koonin EV;. Genome Res 1999;9:689-710. [2]. 9016717. The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe. Goldgur Y, Mosyak L, Reshetnikova L, Ankilova V, Lavrik O, Khodyreva S, Safro M;. Structure 1997;5:59-68. (from Pfam) NF015131.5 PF03150.19 CCP_MauG 25.6 25.6 149 domain Y Y N cytochrome c peroxidase 1.11.1.5 GO:0016491 8591033,9202457 131567 cellular organisms no rank 53485 EBI-EMBL Di-haem cytochrome c peroxidase cytochrome c peroxidase This is a family of distinct cytochrome c peroxidases (CCPs) that contain two haem groups. Similar to other cytochrome c peroxidases, they reduce hydrogen peroxide to water using c-type haem as an oxidisable substrate. However, since they possess two, instead of one, haem prosthetic groups, bacterial CCPs reduce hydrogen peroxide without the need to generate semi-stable free radicals. The two haem groups have significantly different redox potentials. The high potential (+320 mV) haem feeds electrons from electron shuttle proteins to the low potential (-330 mV) haem, where peroxide is reduced (indeed, the low potential site is known as the peroxidatic site) [1]. The CCP protein itself is structured into two domains, each containing one c-type haem group, with a calcium-binding site at the domain interface. This family also includes MauG proteins, whose similarity to di-haem CCP was previously recognised [2]. [1]. 8591033. Crystal structure of the di-haem cytochrome c peroxidase from Pseudomonas aeruginosa. Fulop V, Ridout CJ, Greenwood C, Hajdu J;. Structure 1995;3:1225-1233. [2]. 9202457. Organization of methylamine utilization genes (mau) in 'Methylobacillus flagellatum' KT and analysis of mau mutants. Gak ER, Tsygankov YD, Chistoserdov AY;. Microbiology 1997;143:1827-1835. (from Pfam) NF015132.5 PF03151.21 TPT 30 30 291 domain Y N N Triose-phosphate Transporter family 11432728 131567 cellular organisms no rank 8007 EBI-EMBL Triose-phosphate Transporter family Triose-phosphate Transporter family This family includes transporters with a specificity for triose phosphate [1]. [1]. 11432728. The drug/metabolite transporter superfamily. Jack DL, Yang NM, Saier MH Jr;. Eur J Biochem 2001;268:3620-3639. (from Pfam) NF015140.5 PF03160.19 Calx-beta 27 6.8 119 domain Y Y N Calx-beta domain-containing protein GO:0007154,GO:0016020 10390612,9294196 131567 cellular organisms no rank 30262 EBI-EMBL Calx-beta domain Calx-beta domain NF015141.5 PF03161.18 LAGLIDADG_2 25 25 168 domain Y N N LAGLIDADG DNA endonuclease family GO:0004519 9358175 131567 cellular organisms no rank 994 EBI-EMBL LAGLIDADG DNA endonuclease family LAGLIDADG family homing endonuclease domain This is a family of site-specific DNA endonucleases encoded by DNA mobile elements. Similar to Pfam:PF00961, the members of this family are also LAGLIDADG endonucleases. [1]. 9358175. Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family. Dalgaard JZ, Klar AJ, Moser MJ, Holley WR, Chatterjee A, Mian IS;. Nucleic Acids Res 1997;25:4626-4638. (from Pfam) NF015142.5 PF03162.18 Y_phosphatase2 27 27 165 PfamEq Y N N Tyrosine phosphatase family 131567 cellular organisms no rank 6846 EBI-EMBL Tyrosine phosphatase family Tyrosine phosphatase family This family is closely related to the Pfam:PF00102 and Pfam:PF00782 families. (from Pfam) NF015146.5 PF03167.24 UDG 24.3 24.3 142 domain Y Y N uracil-DNA glycosylase family protein 11178247,9489705 131567 cellular organisms no rank 184627 EBI-EMBL Uracil DNA glycosylase superfamily uracil-DNA glycosylase family protein NF015147.5 PF03168.18 LEA_2 25.4 25.4 98 domain Y Y N LEA type 2 family protein 16155204,9426604 131567 cellular organisms no rank 9743 EBI-EMBL Late embryogenesis abundant protein LEA type 2 family protein Different types of LEA proteins are expressed at different stages of late embryogenesis in higher plant seed embryos and under conditions of dehydration stress. The function of these proteins is unknown. This family represents a group of LEA proteins that appear to be distinct from those in Pfam:PF02987. The family DUF1511, Pfam:PF07427, has now been merged into this family. [1]. 9426604. ER5, a tomato cDNA encoding an ethylene-responsive LEA-like protein: characterization and expression in response to drought, ABA and wounding. Zegzouti H, Jones B, Marty C, Lelievre JM, Latche A, Pech JC, Bouzayen M;. Plant Mol Biol 1997;35:847-854. [2]. 16155204. Solution structure of a late embryogenesis abundant protein (LEA14) from Arabidopsis thaliana, a cellular stress-related protein. Singh S, Cornilescu CC, Tyler RC, Cornilescu G, Tonelli M, Lee MS, Markley JL;. Protein Sci. 2005;14:2601-2609. (from Pfam) NF015148.5 PF03169.20 OPT 25.8 25.8 623 PfamEq Y Y N OPT/YSL family transporter GO:0035673,GO:0055085 9643541 131567 cellular organisms no rank 20831 EBI-EMBL OPT oligopeptide transporter protein OPT/YSL family transporter The OPT family of oligopeptide transporters is distinct from the ABC Pfam:PF00005 and PTR Pfam:PF00854 transporter families. OPT transporters were first recognised in fungi (Candida albicans and Schizosaccharomyces pombe), but this alignment also includes orthologues from Arabidopsis thaliana. OPT transporters are thought to have 12-14 transmembrane domains and contain the following motif: SPYxEVRxxVxxxDDP [1]. [1]. 9643541. Schizosaccharomyces pombe isp4 encodes a transporter representing a novel family of oligopeptide transporters. Lubkowitz MA, Barnes D, Breslav M, Burchfield A, Naider F, Becker JM;. Mol Microbiol 1998;28:729-741. (from Pfam) NF015154.5 PF03175.18 DNA_pol_B_2 25.8 25.8 468 domain Y Y N DNA polymerase GO:0000166,GO:0003677,GO:0003887,GO:0006260 11282628,1934129 131567 cellular organisms no rank 1053 EBI-EMBL DNA polymerase type B, organellar and viral DNA polymerase Like Pfam:PF00136, members of this family are also DNA polymerase type B proteins. Those included here are found in plant and fungal mitochondria, and in viruses. (from Pfam) NF015155.5 PF03176.20 MMPL 20.5 20.5 333 domain Y Y N MMPL family transporter GO:0016020 10694977 131567 cellular organisms no rank 569132 EBI-EMBL MMPL family MMPL family transporter Members of this family are putative integral membrane proteins from bacteria. Several of the members are mycobacterial proteins. Many of the proteins contain two copies of this aligned region. The function of these proteins is not known, although it has been suggested that they may be involved in lipid transport [1]. [1]. 10694977. Analysis of the proteome of Mycobacterium tuberculosis in silico. Tekaia F, Gordon SV, Garnier T, Brosch R, Barrell BG, Cole ST;. Tuber Lung Dis 1999;79:329-342. (from Pfam) NF015159.5 PF03180.19 Lipoprotein_9 27 27 236 subfamily Y Y N MetQ/NlpA family ABC transporter substrate-binding protein 12169620,12819857,23852867,3003106,30352853 131567 cellular organisms no rank 92905 EBI-EMBL NlpA lipoprotein MetQ/NlpA family ABC transporter substrate-binding protein This entry represents bacterial lipoproteins that belong to the NlpA family [1,2]. It contains several antigenic members, that may be involved in bacterial virulence. This entry includes the D-methionine binding lipoprotein MetQ, which is the substrate-binding component of a D-methionine permease, a binding protein-dependent, ATP-driven transport system [2,3]. Other members of this family, such as NlpA, have been identified as putative substrate-binding components of ABC transporters. NlpA, is an inner-membrane-anchored lipoprotein that has been shown to have a minor role in methionine import [4,5]. [1]. 3003106. Lipoprotein-28, a cytoplasmic membrane lipoprotein from Escherichia coli. Cloning, DNA sequence, and expression of its gene. Yu F, Inouye S, Inouye M;. J Biol Chem 1986;261:2284-2288. [2]. 12169620. The metD D-methionine transporter locus of Escherichia coli is an ABC transporter gene cluster. Gal J, Szvetnik A, Schnell R, Kalman M;. J Bacteriol. 2002;184:4930-4932. [3]. 30352853. Noncanonical role for the binding protein in substrate uptake by the MetNI methionine ATP Binding Cassette (ABC) transporter. Nguyen PT, Lai JY, Lee AT, Kaiser JT, Rees DC;. Proc Natl Acad Sci U S A. 2018;115:E10596. [4]. 23852867. Synthetic effect between envelope stress and lack of outer membrane vesicle production in Escherichia coli. Schwechheimer C, Kuehn MJ;. J Bacteriol. 2013;195:4161-4173. [5]. 12819857. A transporter of Escherichia coli specific for L- and D-methionine is the prototype for a new family within the ABC superfamily. Zhang Z, Feige JN, Chang AB, Anderson IJ, Brodianski VM, Vitreschak AG, Gelfand MS, Saier MH J. TRUNCATED at 1650 bytes (from Pfam) NF015162.5 PF03184.24 DDE_1 22 22 177 domain Y N N DDE superfamily endonuclease GO:0003676 131567 cellular organisms no rank 907 EBI-EMBL DDE superfamily endonuclease DDE superfamily endonuclease This family of proteins are related to Pfam:PF00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere. (from Pfam) NF015164.5 PF03186.18 CobD_Cbib 34.4 34.4 282 domain Y Y N cobalamin biosynthesis protein GO:0009236,GO:0016020,GO:0048472 7635831,9446573 131567 cellular organisms no rank 52782 EBI-EMBL CobD/Cbib protein cobalamin biosynthesis protein This family includes CobD proteins from a number of bacteria, in Salmonella this protein is called Cbib. Salmonella CobD is a different protein [1]. This protein is involved in cobalamin biosynthesis and is probably an enzyme responsible for the conversion of adenosylcobyric acid to adenosylcobinamide or adenosylcobinamide phosphate [1]. [1]. 7635831. Identification and sequence analysis of genes involved in late steps in cobalamin (vitamin B12) synthesis in Rhodobacter capsulatus. Pollich M, Klug G;. J Bacteriol 1995;177:4481-4487. See figure 6 for proposed reaction of this enzyme. [2]. 9446573. CobD, a novel enzyme with L-threonine-O-3-phosphate decarboxylase activity, is responsible for the synthesis of (R)-1-amino-2-propanol O-2-phosphate, a proposed new intermediate in cobalamin biosynthesis in Salmonella typhimurium LT2. Brushaber KR, O'Toole GA, Escalante-Semerena JC;. J Biol Chem 1998;273:2684-2691. (from Pfam) NF015166.5 PF03188.21 Cytochrom_B561 23 23 137 PfamEq Y N N Eukaryotic cytochrome b561 9602148 131567 cellular organisms no rank 579 EBI-EMBL Eukaryotic cytochrome b561 Eukaryotic cytochrome b561 Cytochrome b561 is a secretory vesicle-specific electron transport protein. It is an integral membrane protein, that binds two heme groups non-covalently. This is a eukaryotic family. Members of the 'prokaryotic cytochrome b561' family can be found in Pfam: PF01292. [1]. 9602148. Structural basis for the electron transfer across the chromaffin vesicle membranes catalyzed by cytochrome b561: analyses of cDNA nucleotide sequences and visible absorption spectra. Okuyama E, Yamamoto R, Ichikawa Y, Tsubaki M;. Biochim Biophys Acta. 1998;1383:269-278. (from Pfam) NF015168.5 PF03190.20 Thioredox_DsbH 27 27 163 domain Y Y N DUF255 domain-containing protein 131567 cellular organisms no rank 50892 EBI-EMBL Protein of unknown function, DUF255 Protein of unknown function, DUF255 NF015170.5 PF03193.21 RsgA_GTPase 30 30 174 domain Y Y N GTPase RsgA rsgA GO:0003924,GO:0005525 12220175 131567 cellular organisms no rank 94054 EBI-EMBL RsgA GTPase GTPase RsgA RsgA (also known as EngC and YjeQ) represents a protein family whose members are broadly conserved in bacteria and are indispensable for growth. The GTPase domain of RsgA is very similar to several P-loop GTPases, but differs in having a circular permutation of the GTPase structure described by a G4-G1-G3 pattern [1]. [1]. 12220175. YjeQ, an essential, conserved, uncharacterized protein from Escherichia coli, is an unusual GTPase with circularly permuted G-motifs and marked burst kinetics. Daigle DM, Rossi L, Berghuis AM, Aravind L, Koonin EV, Brown ED;. Biochemistry. 2002;41:11109-11117. (from Pfam) NF015177.5 PF03200.21 Glyco_hydro_63 22.4 22.4 492 domain Y N N Glycosyl hydrolase family 63 C-terminal domain 23536181 131567 cellular organisms no rank 10046 EBI-EMBL Glycosyl hydrolase family 63 C-terminal domain Glycosyl hydrolase family 63 C-terminal domain This is a family of eukaryotic enzymes belonging to glycosyl hydrolase family 63. They catalyse the specific cleavage of the non-reducing terminal glucose residue from Glc(3)Man(9)GlcNAc(2). Mannosyl oligosaccharide glucosidase EC:3.2.1.106 is the first enzyme in the N-linked oligosaccharide processing pathway. This family represents the C-terminal catalytic domain [1]. [1]. 23536181. Specificity of Processing alpha-glucosidase I is guided by the substrate conformation: crystallographic and in silico studies. Barker MK, Rose DR;. J Biol Chem. 2013;288:13563-13574. (from Pfam) NF015178.5 PF03201.21 HMD 23.1 23.1 97 domain Y Y N 5,10-methenyltetrahydromethanopterin hydrogenase family protein 8599536 131567 cellular organisms no rank 265 EBI-EMBL H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase 5,10-methenyltetrahydromethanopterin hydrogenase family protein NF015181.5 PF03205.19 MobB 26.6 26.6 133 PfamEq Y Y N molybdopterin-guanine dinucleotide biosynthesis protein MobB GO:0005525,GO:0006777 131567 cellular organisms no rank 28326 EBI-EMBL Molybdopterin guanine dinucleotide synthesis protein B molybdopterin-guanine dinucleotide biosynthesis protein MobB This protein contains a P-loop. (from Pfam) NF015185.5 PF03209.20 PUCC 21 21 401 domain Y Y N PucC family protein 9130598 131567 cellular organisms no rank 22169 EBI-EMBL PUCC protein PucC family protein This protein is required for high-level transcription of the PUC operon. [1]. 9130598. Gene cloning and regulation of gene expression of the puc operon from Rhodovulum sulfidophilum. Hagemann GE, Katsiou E, Forkl H, Steindorf AC, Tadros MH;. Biochim Biophys Acta 1997;1351:341-358. (from Pfam) NF015190.5 PF03214.18 RGP 23.8 23.8 342 PfamEq Y N N Reversibly glycosylated polypeptide 9536051 131567 cellular organisms no rank 694 EBI-EMBL Reversibly glycosylated polypeptide Reversibly glycosylated polypeptide NF015191.5 PF03215.20 Rad17 23.8 23.8 186 domain Y N N Rad17 P-loop domain 10208430 131567 cellular organisms no rank 17674 EBI-EMBL Rad17 P-loop domain Rad17 P-loop domain NF015207.5 PF03232.18 COQ7 23.5 23.5 169 PfamEq Y Y N demethoxyubiquinone hydroxylase family protein GO:0004497,GO:0006744 131567 cellular organisms no rank 13165 EBI-EMBL Ubiquinone biosynthesis protein COQ7 demethoxyubiquinone hydroxylase family protein Members of this family contain two repeats of about 90 amino acids, that contains two conserved motifs. One of these DXEXXH may be part of an enzyme active site. (from Pfam) NF015210.5 PF03235.19 DUF262 33.2 33.2 199 domain Y Y N DUF262 domain-containing protein 131567 cellular organisms no rank 86507 EBI-EMBL Protein of unknown function DUF262 Protein of unknown function DUF262 NF015211.5 PF03237.20 Terminase_6N 22 22 215 domain Y Y N terminase large subunit domain-containing protein 11382219,12235385,12399927,12466275 131567 cellular organisms no rank 68201 EBI-EMBL Terminase large subunit, T4likevirus-type, N-terminal Terminase large subunit, T4likevirus-type, N-terminal This entry represents the N-terminal domain of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. It includes the terminase large subunit of Bacteriophage T4 (terminase gene 17, Gp17) [1,3]. Homologues are also found in Gene Transfer Agents (GTA) [2], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in 4]. [1]. 12235385. Sequence analysis of bacteriophage T4 DNA packaging/terminase genes 16 and 17 reveals a common ATPase center in the large subunit of viral terminases. Mitchell MS, Matsuzaki S, Imai S, Rao VB;. Nucleic Acids Res. 2002;30:4009-4021. [2]. 11382219. The gene transfer agent of Rhodobacter capsulatus and "constitutive transduction" in prokaryotes. Lang AS, Beatty JT;. Arch Microbiol. 2001;175:241-249. [3]. 12466275. Isolation and characterization of T4 bacteriophage gp17 terminase, a large subunit multimer with enhanced ATPase activity. Baumann RG, Black LW;. J Biol Chem. 2003;278:4618-4627. [4]. 12399927. Evolutionary implications of phylogenetic analyses of the gene transfer agent (GTA) of Rhodobacter capsulatus. Lang AS, Taylor TA, Beatty JT;. J Mol Evol. 2002;55:534-543. (from Pfam) NF015213.5 PF03239.19 FTR1 25.3 25.3 284 domain Y Y N FTR1 family protein GO:0005381,GO:0016020,GO:0033573,GO:0034755 8599111 131567 cellular organisms no rank 39712 EBI-EMBL Iron permease FTR1 family FTR1 family protein NF015214.5 PF03241.18 HpaB 25 25 202 domain Y Y N 4-hydroxyphenylacetate 3-hydroxylase C-terminal domain-containing protein 10383985,8077235 131567 cellular organisms no rank 20445 EBI-EMBL 4-hydroxyphenylacetate 3-hydroxylase C terminal 4-hydroxyphenylacetate 3-hydroxylase C terminal HpaB Swiss:Q57160 encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli [2]. HpaB is part of a heterodimeric enzyme that also requires HpaC. The enzyme is NADH-dependent and uses FAD as the redox chromophore. This family also includes PvcC Swiss:O30372 may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis [1]. [1]. 10383985. The pvc gene cluster of Pseudomonas aeruginosa: role in synthesis of the pyoverdine chromophore and regulation by PtxR and PvdS. Stintzi A, Johnson Z, Stonehouse M, Ochsner U, Meyer JM, Vasil ML, Poole K;. J Bacteriol 1999;181:4118-4124. [2]. 8077235. Molecular characterization of 4-hydroxyphenylacetate 3-hydroxylase of Escherichia coli. A two-protein component enzyme. Prieto MA, Garcia JL;. J Biol Chem 1994;269:22823-22829. (from Pfam) NF015216.5 PF03243.20 MerB 27 27 126 domain Y Y N organomercurial lyase merB 4.99.1.2 GO:0018836 131567 cellular organisms no rank 3737 EBI-EMBL Alkylmercury lyase organomercurial lyase Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. (from Pfam) NF015226.5 PF03253.19 UT 25 25 292 PfamEq Y Y N urea transporter GO:0015204,GO:0016020,GO:0071918 131567 cellular organisms no rank 12673 EBI-EMBL Urea transporter urea transporter Members of this family transport urea across membranes. The family includes a bacterial homologue Swiss:Q9S408. (from Pfam) NF015228.5 PF03255.19 ACCA 23 23 310 PfamEq Y N N Acetyl co-enzyme A carboxylase carboxyltransferase-like GO:0003989,GO:0006633,GO:0009317,GO:0016743 10470374 131567 cellular organisms no rank 181190 EBI-EMBL Acetyl co-enzyme A carboxylase carboxyltransferase-like Acetyl co-enzyme A carboxylase carboxyltransferase-like Acetyl co-enzyme A carboxylase carboxyltransferase is composed of an alpha and beta subunit. This protein family includes the alpha subunit and similar sequences. [1]. 10470374. The regulation of acetyl-CoA carboxylase--a potential target for the action of hypolipidemic agents. Munday MR, Hemingway CJ;. Adv Enzyme Regul 1999;39:205-234. (from Pfam) NF015232.5 PF03259.22 Robl_LC7 23 23 91 domain Y Y N roadblock/LC7 domain-containing protein 10402468,11084347,11416132,2464581 131567 cellular organisms no rank 56861 EBI-EMBL Roadblock/LC7 domain Roadblock/LC7 domain This family includes proteins that are about 100 amino acids long and have been shown to be related [3]. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions [2]. This family also includes Swiss:Q9Y2Q5 Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus Swiss:Q50883, a protein involved in gliding motility [4]. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role. [1]. 11416132. Site-specific recognition of a 70-base-pair element containing d(GA)(n) repeats mediates bithoraxoid polycomb group response element-dependent silencing. Hodgson JW, Argiropoulos B, Brock HW;. Mol Cell Biol 2001;21:4528-4543. [2]. 10402468. Drosophila roadblock and Chlamydomonas LC7: a conserved family of dynein-associated proteins involved in axonal transport, flagellar motility, and mitosis. Bowman AB, Patel-King RS, Benashski SE, McCaffery JM, Goldstein LS, King SM;. J Cell Biol 1999;146:165-180. This paper shows the relationship of this family to the MglB family. [3]. 11084347. Dynein light chains of the Roadblock/LC7 group belong to an ancient protein superfamily implicated in NTPase regulation. Koonin EV, Aravind L;. Curr Biol 2000;10:774-776. [4]. 2464581. Gliding motility in Myxococcus xanthus: mgl locus, RNA, and predicted protein products. Stephens K, Hartzell P, Kaiser D;. J Bacteriol 1989;171:819-830. (from Pfam) NF015239.5 PF03266.20 NTPase_1 23.9 23.9 168 domain Y Y N nucleoside-triphosphatase GO:0017111 14503925,15777481,17291528 131567 cellular organisms no rank 3637 EBI-EMBL NTPase nucleoside-triphosphatase This domain is found across all species from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase [1]. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme [2]. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [3]. [1]. 14503925. Thermophile-specific proteins: the gene product of aq_1292 from Aquifex aeolicus is an NTPase. Klinger C, Rossbach M, Howe R, Kaufmann M;. BMC Biochem. 2003;4:12. [2]. 15777481. Crystal structure of THEP1 from the hyperthermophile Aquifex aeolicus: a variation of the RecA fold. Rossbach M, Daumke O, Klinger C, Wittinghofer A, Kaufmann M;. BMC Struct Biol. 2005;5:7. [3]. 17291528. NMR structure and functional characterization of a human cancer-related nucleoside triphosphatase. Placzek WJ, Almeida MS, Wuthrich K;. J Mol Biol. 2007;367:788-801. (from Pfam) NF015241.5 PF03269.19 DUF268 25 25 176 domain Y Y N DUF268 domain-containing protein 131567 cellular organisms no rank 727 EBI-EMBL Caenorhabditis protein of unknown function, DUF268 Caenorhabditis protein of unknown function, DUF268 NF015247.5 PF03275.18 GLF 26.3 26.3 203 domain Y Y N UDP-galactopyranose mutase GO:0008767 8576037 131567 cellular organisms no rank 27379 EBI-EMBL UDP-galactopyranose mutase UDP-galactopyranose mutase NF015254.5 PF03283.18 PAE 26.6 26.6 355 subfamily Y Y N pectin acetylesterase-family hydrolase GO:0016787 131567 cellular organisms no rank 2470 EBI-EMBL Pectinacetylesterase pectin acetylesterase-family hydrolase NF015259.5 PF03288.21 Pox_D5 21.4 21.4 86 domain Y Y N primase-like DNA-binding domain-containing protein 7636979 131567 cellular organisms no rank 23778 EBI-EMBL Poxvirus D5 protein-like primase-like DNA-binding domain This family includes D5 from Poxviruses which is necessary for viral DNA replication, and is a nucleic acid independent nucleoside triphosphatase. Members of this family are also found outside of poxviruses. This domain is a DNA-binding winged HTH domain. [1]. 7636979. The vaccinia virus D5 protein, which is required for DNA replication, is a nucleic acid-independent nucleoside triphosphatase. Evans E, Klemperer N, Ghosh R, Traktman P;. J Virol 1995;69:5353-5361. (from Pfam) NF015262.5 PF03291.21 mRNA_G-N7_MeTrfase 26.6 26.6 315 PfamEq Y N N mRNA (guanine-N(7))-methyltransferase domain 10679253,24607143,27422871,9275164,9790902 131567 cellular organisms no rank 917 EBI-EMBL mRNA (guanine-N(7))-methyltransferase domain mRNA (guanine-N(7))-methyltransferase domain This entry represents mRNA (guanine-N(7))-methyltransferase, which can either be found as a single domain protein, or as a domain within the mRNA-capping enzyme catalytic subunit. mRNA (guanine-N(7))-methyltransferase methylates the N7 position of the added guanosine to the 5'-cap structure of mRNAs. It binds RNA containing 5'-terminal GpppC [1-5]. Viral mRNA capping enzymes, meanwhile, are multidomain proteins that catalyse the first two reactions in the mRNA cap formation pathway [5]. They are heterodimers consisting of a large (catalytic) and small subunit. [1]. 9275164. Phylogeny of mRNA capping enzymes. Wang SP, Deng L, Ho CK, Shuman S;. Proc Natl Acad Sci U S A 1997;94:9573-9578. [2]. 10679253. Cloning and characterization of mRNA capping enzyme and mRNA (Guanine-7-)-methyltransferase cDNAs from Xenopus laevis. Yokoska J, Tsukamoto T, Miura Ki, Shiokawa K, Mizumoto K;. Biochem Biophys Res Commun. 2000;268:617-624. [3]. 9790902. Cloning and characterization of three human cDNAs encoding mRNA (guanine-7-)-methyltransferase, an mRNA cap methylase. Tsukamoto T, Shibagaki Y, Niikura Y, Mizumoto K;. Biochem Biophys Res Commun. 1998;251:27-34. [4]. 27422871. Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM. Varshney D, Petit AP, Bueren-Calabuig JA, Jansen C, Fletcher DA, Peggie M, Weidlich S, Scullion P, Pisliakov AV, Cowling VH;. Nucleic Acids Res. 2016;44:10423-10436. [5]. 24607143. Crystal structure of vaccinia virus mRNA capping enzyme provides insights into the mechanism and evolution of the capping apparatus. Kyrieleis OJ, Chang J, de la Pena M, Shuman S, Cusack S;. Structure. 2014;22:452-46. TRUNCATED at 1650 bytes (from Pfam) NF015268.5 PF03297.20 Ribosomal_S25 28.8 28.8 101 PfamEq Y N N S25 ribosomal protein 10050887 131567 cellular organisms no rank 169 EBI-EMBL S25 ribosomal protein S25 ribosomal protein NF015272.5 PF03301.18 Trp_dioxygenase 34.9 34.9 346 subfamily Y Y N tryptophan 2,3-dioxygenase family protein GO:0004833,GO:0019441,GO:0020037 8666386 131567 cellular organisms no rank 28991 EBI-EMBL Tryptophan 2,3-dioxygenase tryptophan 2,3-dioxygenase family protein NF015277.5 PF03306.18 AAL_decarboxy 25 25 219 domain Y Y N acetolactate decarboxylase 4.1.1.5 GO:0045151,GO:0047605 10986242,11097941 131567 cellular organisms no rank 12355 EBI-EMBL Alpha-acetolactate decarboxylase acetolactate decarboxylase NF015279.5 PF03308.21 MeaB 23.1 23.1 273 domain Y N N Methylmalonyl Co-A mutase-associated GTPase MeaB 25832174 131567 cellular organisms no rank 64729 EBI-EMBL Methylmalonyl Co-A mutase-associated GTPase MeaB Methylmalonyl Co-A mutase-associated GTPase MeaB Family members were previously thought to be ArgK proteins acting as ATPase enzymes and kinases. They are now believed to be methylmalonyl Co-A mutase-associated GTPase MeaB. Structural studies of MeaB and the human ortholog (methylmalonyl associated protein A) MMAA, reveal alpha-helical domains at the N- and C-termini as well as a Ras-like GTPase domain. Mutational analysis of MeaB, show prohibited growth in Methylobacterium due to the inability to convert methylmalonyl-CoA to succinyl-CoA caused by an inactive form of methylmalonyl-CoA mutatase (mcm). In humans, mutations in (MMAA) are associated with the fatal disease methylmalonyl aciduria [1]. [1]. 25832174. Crystal structures of Mycobacterial MeaB and MMAA-like GTPases. Edwards TE, Baugh L, Bullen J, Baydo RO, Witte P, Thompkins K, Phan IQ, Abendroth J, Clifton MC, Sankaran B, Van Voorhis WC, Myler PJ, Staker BL, Grundner C, Lorimer DD;. J Struct Funct Genomics. 2015;16:91-99. (from Pfam) NF015280.5 PF03309.19 Pan_kinase 24.7 24.7 205 PfamEq Y Y N type III pantothenate kinase 2.7.1.33 GO:0004594 16855243 131567 cellular organisms no rank 45369 EBI-EMBL Type III pantothenate kinase type III pantothenate kinase Type III pantothenate kinase catalyses the phosphorylation of pantothenate (Pan), the first step in the universal pathway of CoA biosynthesis. [1]. 16855243. Crystal structure of a type III pantothenate kinase: insight into the mechanism of an essential coenzyme A biosynthetic enzyme universally distributed in bacteria. Yang K, Eyobo Y, Brand LA, Martynowski D, Tomchick D, Strauss E, Zhang H;. J Bacteriol. 2006;188:5532-5540. (from Pfam) NF015284.5 PF03313.20 SDH_alpha 26.4 26.4 260 domain Y Y N L-serine ammonia-lyase, iron-sulfur-dependent, subunit alpha 4.3.1.17 25380533 131567 cellular organisms no rank 90897 EBI-EMBL Serine dehydratase alpha chain L-serine ammonia-lyase, iron-sulfur-dependent, subunit alpha L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyses the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway. Members included in this entry adopt and all-helical structure [1]. [1]. 25380533. Structure of L-serine dehydratase from Legionella pneumophila: novel use of the C-terminal cysteine as an intrinsic competitive inhibitor. Thoden JB, Holden HM, Grant GA;. Biochemistry. 2014;53:7615-7624. (from Pfam) NF015286.5 PF03315.20 SDH_beta 26 26 155 domain Y Y N serine dehydratase beta chain GO:0003941,GO:0006094,GO:0051539 131567 cellular organisms no rank 72462 EBI-EMBL Serine dehydratase beta chain serine dehydratase beta chain L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyses the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway. (from Pfam) NF015290.5 PF03320.18 FBPase_glpX 27 27 307 domain Y Y N fructose-bisphosphatase class II 3.1.3.11 GO:0006071,GO:0006094,GO:0042132 10986273 131567 cellular organisms no rank 31182 EBI-EMBL Bacterial fructose-1,6-bisphosphatase, glpX-encoded fructose-bisphosphatase class II NF015291.5 PF03321.18 GH3 23.6 23.6 534 domain Y Y N GH3 auxin-responsive promoter family protein 10066623 131567 cellular organisms no rank 18545 EBI-EMBL GH3 auxin-responsive promoter GH3 auxin-responsive promoter family protein NF015297.5 PF03328.19 HpcH_HpaI 25 25 221 subfamily Y Y N aldolase/citrate lyase family protein GO:0003824 8529896,9073078 131567 cellular organisms no rank 141162 EBI-EMBL HpcH/HpaI aldolase/citrate lyase family aldolase/citrate lyase family protein This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase and 4-hydroxy-2-oxovalerate aldolase. [1]. 9073078. The bphDEF meta-cleavage pathway genes involved in biphenyl/polychlorinated biphenyl degradation are located on a linear plasmid and separated from the initial bphACB genes in Rhodococcus sp. strain RHA1. Masai E, Sugiyama K, Iwashita N, Shimizu S, Hauschild JE, Hatta T, Kimbara K, Yano K, Fukuda M;. Gene 1997;187:141-149. [2]. 8529896. Sequence of the Escherichia coli C homoprotocatechuic acid degradative operon completed with that of the 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase-encoding gene (hpcH). Stringfellow JM, Turpin B, Cooper RA;. Gene 1995;166:73-76. (from Pfam) NF015300.5 PF03332.18 PMM 22.4 22.4 221 domain Y N N Eukaryotic phosphomannomutase GO:0004615,GO:0009298 10571009,11530212,9878760 131567 cellular organisms no rank 3530 EBI-EMBL Eukaryotic phosphomannomutase Eukaryotic phosphomannomutase This enzyme EC:5.4.2.8 is involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions. [1]. 9878760. The dolichol pathway of N-linked glycosylation. Burda P, Aebi M;. Biochim Biophys Acta 1999;1426:239-257. [2]. 11530212. Balancing N-linked glycosylation to avoid disease. Freeze HH, Westphal V;. Biochimie 2001;83:791-799. [3]. 10571009. Carbohydrate-deficient glycoprotein syndrome type IA (phosphomannomutase-deficiency). Carchon H, Van Schaftingen E, Matthijs G, Jaeken J;. Biochim Biophys Acta 1999;1455:155-165. (from Pfam) NF015302.5 PF03334.19 PhaG_MnhG_YufB 23.4 23.4 80 domain Y Y N monovalent cation/H(+) antiporter subunit G GO:0015297,GO:0051139,GO:0098662,GO:1902600 9680201,9852009 131567 cellular organisms no rank 30309 EBI-EMBL Na+/H+ antiporter subunit monovalent cation/H(+) antiporter subunit G This family includes PhaG from Rhizobium meliloti Swiss:Q9ZNG0, MnhG from Staphylococcus aureus Swiss:Q9ZNG0, YufB from Bacillus subtilis Swiss:O05227. [1]. 9680201. The pha gene cluster of Rhizobium meliloti involved in pH adaptation and symbiosis encodes a novel type of K+ efflux system. Putnoky P, Kereszt A, Nakamura T, Endre G, Grosskopf E, Kiss P, Kondorosi A;. Mol Microbiol 1998;28:1091-1101. [2]. 9852009. A putative multisubunit Na+/H+ antiporter from Staphylococcus aureus. Hiramatsu T, Kodama K, Kuroda T, Mizushima T, Tsuchiya T;. J Bacteriol 1998;180:6642-6648. (from Pfam) NF015317.5 PF03350.21 UPF0114 23.1 23.1 117 PfamEq Y Y N YqhA family protein 131567 cellular organisms no rank 14771 EBI-EMBL Uncharacterized protein family, UPF0114 YqhA family protein NF015318.5 PF03351.22 DOMON 32.7 32.7 124 domain Y Y N DOMON domain-containing protein 17878204 131567 cellular organisms no rank 447 EBI-EMBL DOMON domain DOMON domain The DOMON (named after dopamine beta-monooxygenase N-terminal) domain is 110-125 residues long. It is predicted to form an all beta fold with up to 11 strands and is secreted to the extracellular compartment. The beta-strand folding produces a hydrophobic pocket which appears to bind soluble haem. This is consistent with the predominant architectures where the protein is associated with cytochromes or enzymatic domains whose activity involves redox or electron transfer reactions potentially as a direct participant in the electron transfer process. The DOMON domain superfamily, of which this is just one member, shows (1) multiple hydrophobic residues that contribute to the hydrophobic core of the strands of the beta-sandwich, and small residues found at the boundaries of strands and loops, (2) a strongly conserved charged residue (usually arginine/lysine) at the end of strand 9, which possibly stabilises the loop between 9 and 10, and (3) a polar residue (usually histidine, lysine or arginine), that interacts or coordinates with ligands [1]. The suggested superfamily includes both haem- and sugar-binding members: the haem-binding families being the ethyl-Benzoate dehydrogenase family EB_dh, Pfam:PF09459, the cellobiose dehydrogenase family CBDH and this family, and the sugar-binding families being the xylanases, CBM_4_9, Pfam:PF02018. The common feature of the superfamily is the 11-beta-strand structure, although the first and eleventh strands are not well conserved either within families or between families. [1]. 17878204. The DOMON domains are involved in heme and sugar recognition. Iyer LM, Anantharaman V, Aravind L;. Bi. TRUNCATED at 1650 bytes (from Pfam) NF015319.5 PF03352.18 Adenine_glyco 25 25 177 domain Y Y N DNA-3-methyladenine glycosylase I 3.2.2.20 GO:0006284,GO:0008725 8502545 131567 cellular organisms no rank 67964 EBI-EMBL Methyladenine glycosylase DNA-3-methyladenine glycosylase I The DNA-3-methyladenine glycosylase I is constitutively expressed and is specific for the alkylated 3-methyladenine DNA. [1]. 8502545. Excision of 3-methylguanine from alkylated DNA by 3-methyladenine DNA glycosylase I of Escherichia coli. Bjelland S, Bjoras M, Seeberg E;. Nucleic Acids Res 1993;21:2045-2049. (from Pfam) NF015321.5 PF03354.20 TerL_ATPase 23.7 23.7 178 PfamEq Y Y N terminase large subunit domain-containing protein 26150523,28100693,7812447 131567 cellular organisms no rank 48454 EBI-EMBL Terminase large subunit, ATPase domain terminase large subunit Terminase large subunit (TerL) from bacteriophages and evolutionarily related viruses, is an important component of the DNA packing machinery and comprises an ATPase domain, which powers DNA translocation and a nuclease domain that cuts concatemeric DNA [1,2]. TerL forms pentamers in which the ATPase domains form a ring distal to the capsid. This is the ATPase domain which contains a C-terminal subdomain that sits above the ATPase active site, called the "Lid subdomain" with reference to analogous lid subdomains found in other ATPases [3]. It contains a hydrophobic patch (Trp and Tyr residues) that mediates critical interactions in the interface between adjacent ATPase subunits and assists the positioning of the arginine finger residue that catalyses ATP hydrolysis [2,3]. This entry also includes bacterial proteins of unknown function. [1]. 7812447. Sequence and organization of the lactococcal prolate-headed bIL67 phage genome. Schouler C, Ehrlich SD, Chopin MC;. Microbiology 1994;140:3061-3069. [2]. 28100693. Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism. Xu RG, Jenkins HT, Chechik M, Blagova EV, Lopatina A, Klimuk E, Minakhin L, Severinov K, Greive SJ, Antson AA;. Nucleic Acids Res. 2017;45:3580-3590. [3]. 26150523. Structure and mechanism of the ATPase that powers viral genome packaging. Hilbert BJ, Hayes JA, Stone NP, Duffy CM, Sankaran B, Kelch BA;. Proc Natl Acad Sci U S A. 2015;112:E3792-E3799. (from Pfam) NF015324.5 PF03357.26 Snf7 27.3 27.3 171 subfamily Y Y N Snf7 family protein GO:0007034 12194857,14583093,15469844 131567 cellular organisms no rank 65 EBI-EMBL Snf7 Snf7 family protein This family of proteins are involved in protein sorting and transport from the endosome to the vacuole/lysosome in eukaryotic cells. Vacuoles/lysosomes play an important role in the degradation of both lipids and cellular proteins. In order to perform this degradative function, vacuoles/lysosomes contain numerous hydrolases which have been transported in the form of inactive precursors via the biosynthetic pathway and are proteolytically activated upon delivery to the vacuole/lysosome. The delivery of transmembrane proteins, such as activated cell surface receptors to the lumen of the vacuole/lysosome, either for degradation/downregulation, or in the case of hydrolases, for proper localisation, requires the formation of multivesicular bodies (MVBs). These late endosomal structures are formed by invaginating and budding of the limiting membrane into the lumen of the compartment. During this process, a subset of the endosomal membrane proteins is sorted into the forming vesicles. Mature MVBs fuse with the vacuole/lysosome, thereby releasing cargo containing vesicles into its hydrolytic lumen for degradation. Endosomal proteins that are not sorted into the intralumenal MVB vesicles are either recycled back to the plasma membrane or Golgi complex, or remain in the limiting membrane of the MVB and are thereby transported to the limiting membrane of the vacuole/lysosome as a consequence of fusion. Therefore, the MVB sorting pathway plays a critical role in the decision between recycling and degradation of membrane proteins [1]. A few archaeal sequences are also present within this family. [1]. 12194857. Escrt-III: an endosome-a. TRUNCATED at 1650 bytes (from Pfam) NF015325.5 PF03358.20 FMN_red 24 24 152 domain Y Y N NAD(P)H-dependent oxidoreductase GO:0016491 10049377,10506196 131567 cellular organisms no rank 384474 EBI-EMBL NADPH-dependent FMN reductase NAD(P)H-dependent oxidoreductase NF015331.5 PF03364.25 Polyketide_cyc 23.4 23.4 126 domain Y Y N SRPBCC family protein 16511226 131567 cellular organisms no rank 131184 EBI-EMBL Polyketide cyclase / dehydrase and lipid transport SRPBCC family protein This family contains polyketide cylcases/dehydrases which are enzymes involved in polyketide synthesis. The family also includes proteins which are involved in the binding/transport of lipids. (from Pfam) NF015332.5 PF03366.21 YEATS 22 22 80 PfamEq Y N N YEATS family GO:0006355 10913114,11439343,11522644 131567 cellular organisms no rank 176 EBI-EMBL YEATS family YEATS family We have named this family the YEATS family, after `YNK7', `ENL', `AF-9', and `TFIIF small subunit'. This family also contains the GAS41 protein. All these proteins are thought to have a transcription stimulatory activity [1]. 10913114. GAS41, a highly conserved protein in eukaryotic nuclei, binds to NuMA. Harborth J, Weber K, Osborn M;. J Biol Chem 2000;275:31979-31985. [2]. 11522644. MLL-ENL causes a reversible and myc-dependent block of myelomonocytic cell differentiation. Schreiner S, Birke M, Garcia-Cuellar MP, Zilles O, Greil J, Slany RK;. Cancer Res 2001;61:6480-6486. [3]. 11439343. The polycomb protein MPc3 interacts with AF9, an MLL fusion partner in t(9;11)(p22;q23) acute leukemias. Hemenway CS, de Erkenez AC, Gould GC;. Oncogene 2001;20:3798-3805. (from Pfam) NF015333.5 PF03367.18 zf-ZPR1 23 23 56 PfamEq Y N N ZPR1 zinc-finger domain GO:0008270 17704259,8650580,9763455,9852145 131567 cellular organisms no rank 475 EBI-EMBL ZPR1 zinc-finger domain ZPR1 zinc-finger domain This entry represents the zinc-ribbon domain found in ZPR1 family. The zinc-finger protein ZPR1 is ubiquitous among eukaryotes. It is indeed known to be an essential protein in yeast. In quiescent cells, ZPR1 is localised to the cytoplasm. But in proliferating cells treated with EGF or with other mitogens, ZPR1 accumulates in the nucleolus. ZPR1 interacts with the cytoplasmic domain of the inactive EGF receptor (EGFR) and is thought to inhibit the basal protein tyrosine kinase activity of EGFR. This interaction is disrupted when cells are treated with EGF, though by themselves, inactive EGFRs are not sufficient to sequester ZPR1 to the cytoplasm [1,2,3]. Upon stimulation by EGF, ZPR1 directly binds the eukaryotic translation elongation factor-1alpha (eEF-1alpha) to form ZPR1/eEF-1alpha complexes [1]. These move into the nucleus, localising particularly at the nucleolus. Indeed, the interaction between ZPR1 and eEF-1alpha has been shown to be essential for normal cellular proliferation [1], and ZPR1 is thought to be involved in pre-ribosomal RNA expression [2]. ZPR1 binds preferentially to GDP-bound eEF1A but does not directly influence the kinetics of nucleotide exchange or GTP hydrolysis [4]. The alignment for the ZPR1 family shows a duplicated set composed of a zinc-ribbon domain (this entry) followed by a jelly-roll domain. This family also includes several hypothetical archaeal proteins (from both Crenarchaeota and Euryarchaeota). This similarity between ZPR1 and archaeal proteins was not previously noted. [1]. 9852145. Interaction of ZPR1 with translation elongation factor-1alpha in proliferating cells. Gangwani L, Mi. TRUNCATED at 1650 bytes (from Pfam) NF015338.5 PF03372.28 Exo_endo_phos 24.5 24.5 225 domain Y Y N endonuclease/exonuclease/phosphatase family protein GO:0003824 10838565,1748997,7885481 131567 cellular organisms no rank 366975 EBI-EMBL Endonuclease/Exonuclease/phosphatase family endonuclease/exonuclease/phosphatase family protein This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3.1.21.1 e.g. Swiss:P24855, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56 Swiss:O43426, Sphingomyelinase EC:3.1.4.12 Swiss:P11889 and Nocturnin Swiss:O35710. [1]. 10838565. Functionally unrelated signalling proteins contain a fold similar to Mg2+-dependent endonucleases. Dlakic M;. Trends Biochem Sci 2000;25:272-273. [2]. 7885481. Structure and function of the multifunctional DNA-repair enzyme exonuclease III. Mol CD, Kuo CF, Thayer MM, Cunningham RP, Tainer JA;. Nature 1995;374:381-386. [3]. 1748997. DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex. Lahm A, Suck D;. J Mol Biol 1991;222:645-667. (from Pfam) NF015344.5 PF03379.18 CcmB 24.9 24.9 215 domain Y Y N heme exporter protein CcmB GO:0015232,GO:0015886,GO:0016020,GO:0017004 7635817 131567 cellular organisms no rank 23843 EBI-EMBL CcmB protein heme exporter protein CcmB CcmB is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor. CcmB is required for the export of haem to the periplasm. [1]. 7635817. Escherichia coli genes required for cytochrome c maturation. Thony-Meyer L, Fischer F, Kunzler P, Ritz D, Hennecke H;. J Bacteriol 1995;177:4321-4326. (from Pfam) NF015347.5 PF03382.19 DUF285 25 10 120 domain Y Y N BspA family leucine-rich repeat surface protein 131567 cellular organisms no rank 26665 EBI-EMBL Mycoplasma protein of unknown function, DUF285 BspA-type leucine-rich repeat region This region appears distantly related to leucine rich repeats. (from Pfam) NF015350.5 PF03385.22 STELLO 27.8 27.8 387 PfamAutoEq Y Y N STELLO glycosyltransferase family protein 27277162 131567 cellular organisms no rank 231 EBI-EMBL STELLO glycosyltransferases STELLO glycosyltransferase family protein This domain family is found in Metazoa and in Virdiplantae. Two of the family members are characterized in Arabidopsis thaliana. Swiss:O22943 and Swiss:Q9SCN0 and named STELLO1 (STL1) and STELLO2 (STL2) respectively. They are Golgi-localized proteins that can interact with CesAs (cellulose synthase A) and control cellulose quantity. In the absence of STELLO function, the spatial distribution within the Golgi, secretion and activity of the CSCs are impaired indicating a central role of the STELLO proteins in CSC assembly. Point mutations in the predicted catalytic domains of the STELLO proteins indicate that they are glycosyltransferases facing the Golgi lumen. STL homologues are present throughout the plant kingdom, but STL proteins are distinct from distantly related proteins in nematodes, fungi and molluscs [1]. [1]. 27277162. Golgi-localized STELLO proteins regulate the assembly and trafficking of cellulose synthase complexes in Arabidopsis. Zhang Y, Nikolovski N, Sorieul M, Vellosillo T, McFarlane HE, Dupree R, Kesten C, Schneider R, Driemeier C, Lathe R, Lampugnani E, Yu X, Ivakov A, Doblin MS, Mortimer JC, Brown SP, Persson S, Dupree P;. Nat Commun. 2016;7:11656. (from Pfam) NF015353.5 PF03388.19 Lectin_leg-like 24 24 230 domain Y N N Legume-like lectin family GO:0016020 10090935,8205612,8868475 131567 cellular organisms no rank 1097 EBI-EMBL Legume-like lectin family Legume-like lectin family Lectins are structurally diverse proteins that bind to specific carbohydrates. This family includes the VIP36 Swiss:P49256 and ERGIC-53 Swiss:P49257 lectins. These two proteins were the first recognised members of a family of animal lectins similar (19-24%) to the leguminous plant lectins [1]. The alignment for this family aligns residues lying towards the N-terminus, where the similarity of VIP36 and ERGIC-53 is greatest. However, while Fiedler and Simons [1] identified these proteins as a new family of animal lectins, our alignment also includes yeast sequences. ERGIC-53 is a 53kD protein, localised to the intermediate region between the endoplasmic reticulum and the Golgi apparatus (ER-Golgi-Intermediate Compartment, ERGIC). It was identified as a calcium-dependent, mannose-specific lectin [2]. Its dysfunction has been associated with combined factors V and VIII deficiency OMIM:227300 OMIM:601567, suggesting an important and substrate-specific role for ERGIC-53 in the glycoprotein- secreting pathway [2,3]. [1]. 8205612. A putative novel class of animal lectins in the secretory pathway homologous to leguminous lectins. Fiedler K, Simons K;. Cell 1994;77:625-626. [2]. 8868475. ERGIC-53 is a functional mannose-selective and calcium-dependent human homologue of leguminous lectins. Itin C, Roche AC, Monsigny M, Hauri HP;. Mol Biol Cell 1996;7:483-493. [3]. 10090935. ERGIC-53 gene structure and mutation analysis in 19 combined factors V and VIII deficiency families. Nichols WC, Terry VH, Wheatley MA, Yang A, Zivelin A, Ciavarella N, Stefanile C, Matsushita T, Saito H, de Bosch NB, Ruiz-Saez A, Torres A, Thompson AR, Feinstein. TRUNCATED at 1650 bytes (from Pfam) NF015354.5 PF03389.20 MobA_MobL 26.7 26.7 224 domain Y Y N MobA/MobL family protein 131567 cellular organisms no rank 41539 EBI-EMBL MobA/MobL family MobA/MobL family protein This family includes of the MobA protein from the E. coli plasmid RSF1010, and the MobL protein from the Thiobacillus ferrooxidans plasmid PTF1. These sequences are mobilisation proteins, which are essential for specific plasmid transfer. (from Pfam) NF015366.5 PF03401.19 TctC 27 27 274 subfamily Y Y N tripartite tricarboxylate transporter substrate-binding protein 12562821,14499931,6141166 131567 cellular organisms no rank 239557 EBI-EMBL Tripartite tricarboxylate transporter family receptor tripartite tricarboxylate transporter substrate-binding protein These probable extra-cytoplasmic solute receptors are strongly overrepresented in several beta-proteobacteria [1]. This family, formerly known as Bug - Bordetella uptake gene (bug) product - is a family of bacterial tripartite tricarboxylate receptors of the extracytoplasmic solute binding receptor-dependent transporter group of families, distinct from the ABC and TRAP-T families [3]. The TctABC system has been characterised in S. typhimurium [2], and TctC is the extracytoplasmic tricarboxylate-binding receptor which binds the transporters TctA and TctB, two integral membrane proteins. Complete three-component systems are found only in bacteria [2]. [1]. 12562821. Overrepresentation of a gene family encoding extracytoplasmic solute receptors in Bordetella. Antoine R, Jacob-Dubuisson F, Drobecq H, Willery E, Lesjean S, Locht C;. J Bacteriol 2003;185:1470-1474. [2]. 14499931. The tripartite tricarboxylate transporter (TTT) family. Winnen B, Hvorup RN, Saier MH Jr;. Res Microbiol. 2003;154:457-465. [3]. 6141166. Tricarboxylate-binding proteins of Salmonella typhimurium. Purification, crystallization, and physical properties. Sweet GD, Kay CM, Kay WW;. J Biol Chem. 1984;259:1586-1592. (from Pfam) NF015368.5 PF03403.18 PAF-AH_p_II 20 20 372 domain Y N N Platelet-activating factor acetylhydrolase, isoform II GO:0003847,GO:0016042 9218411,9645224 131567 cellular organisms no rank 41905 EBI-EMBL Platelet-activating factor acetylhydrolase, isoform II Platelet-activating factor acetylhydrolase, isoform II Platelet-activating factor acetylhydrolase (PAF-AH) is a subfamily of phospholipases A2, responsible for inactivation of platelet-activating factor through cleavage of an acetyl group. Three known PAF-AHs are the brain heterotrimeric PAF-AH Ib, whose catalytic beta and gamma subunits are aligned in Pfam:PF02266, the extracellular, plasma PAF-AH (pPAF-AH), and the intracellular PAF-AH isoform II (PAF-AH II). This family aligns pPAF-AH and PAF-AH II, whose similarity was previously noted. [1]. 9645224. The structure and function of platelet-activating factor acetylhydrolases. Derewenda ZS, Derewenda U;. Cell Mol Life Sci 1998;54:446-455. [2]. 9218411. Platelet-activating factor acetylhydrolases. Stafforini DM, McIntyre TM, Zimmerman GA, Prescott SM;. J Biol Chem 1997;272:17895-17898. (from Pfam) NF015369.5 PF03404.21 Mo-co_dimer 22.7 22.7 138 domain Y N N Mo-co oxidoreductase dimerisation domain GO:0016491,GO:0030151 9428520 131567 cellular organisms no rank 25947 EBI-EMBL Mo-co oxidoreductase dimerisation domain Mo-co oxidoreductase dimerisation domain This domain is found in molybdopterin cofactor (Mo-co) oxidoreductases. It is involved in dimer formation, and has an Ig-fold structure [1]. [1]. 9428520. Molecular basis of sulfite oxidase deficiency from the structure of sulfite oxidase. Kisker C, Schindelin H, Pacheco A, Wehbi WA, Garrett RM, Rajagopalan KV, Enemark JH, Rees DC;. Cell 1997;91:973-983. (from Pfam) NF015372.5 PF03407.21 Nucleotid_trans 22 22 208 domain Y Y N putative nucleotide-diphospho-sugar transferase 15215454 131567 cellular organisms no rank 1970 EBI-EMBL Nucleotide-diphospho-sugar transferase putative nucleotide-diphospho-sugar transferase Proteins in this family have been been predicted to be nucleotide-diphospho-sugar transferases. [1]. 15215454. Detecting distant homology with Meta-BASIC. Ginalski K, von Grotthuss M, Grishin NV, Rychlewski L;. Nucleic Acids Res. 2004;32:576-581. (from Pfam) NF015377.5 PF03412.20 Peptidase_C39 22 22 133 domain Y Y N cysteine peptidase family C39 domain-containing protein GO:0005524,GO:0006508,GO:0008233,GO:0016020 7565085,7674922 131567 cellular organisms no rank 78979 EBI-EMBL Peptidase C39 family cysteine peptidase family C39 domain This domain often occurs confers as the leader peptidase domain of transporter subunits involved in cleaving peptides or proteins, such as bacteriocins with a double-glycine type leader peptide, during export. NF015378.5 PF03413.24 PepSY 24 17.8 60 domain Y Y N PepSY domain-containing protein 15124630,15583150,7674922 131567 cellular organisms no rank 75331 EBI-EMBL Peptidase propeptide and YPEB domain Peptidase propeptide and YPEB domain This region is likely to have an protease inhibitory function (personal obs:C Yeats). This model is likely to miss some members of this family as the separation from signal to noise is not clear. The name is derived from Peptidase & Bacillus subtilis YPEB. [1]. 7674922. Evolutionary families of metallopeptidases. Rawlings ND, Barrett AJ;. Meth Enzymol 1995;248:183-228. [2]. 15124630. The PepSY domain: a regulator of peptidase activity in the microbial environment?. Yeats C, Rawlings ND, Bateman A;. Trends Biochem Sci 2004;29:169-172. [3]. 15583150. Identification of residues in the Pseudomonas aeruginosa elastase propeptide required for chaperone and secretion activities. McIver KS, Kessler E, Ohman DE;. Microbiology 2004;150:3969-3977. (from Pfam) NF015380.5 PF03415.19 Peptidase_C11 25.8 25.8 359 domain Y Y N clostripain-related cysteine peptidase 9891971 131567 cellular organisms no rank 6374 EBI-EMBL Clostripain family clostripain-related cysteine peptidase The C11 family of cysteine peptidases, defined by MEROPS, includes clostripain from several members of the genus Clostridium, including C. perfringens. NF015382.5 PF03417.21 AAT 23.2 23.2 225 domain Y Y N carcinine hydrolase/isopenicillin-N N-acyltransferase family protein 16299587,2120195,7557412 131567 cellular organisms no rank 31144 EBI-EMBL Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase carcinine hydrolase/isopenicillin-N N-acyltransferase family protein Members of this family include hydrolases and N-acyltransferases. Most members of this family have an N-terminal region with an peptidase active site Cys residue, used autocatalytically during enzyme activation in the case of the penicillin biosynthesis enzyme PenDE (AatA) and responsible for classification of many members of this family as C45-family peptidases. NF015385.5 PF03420.18 Peptidase_S77 27 27 198 PfamEq Y N N Prohead core protein serine protease 131567 cellular organisms no rank 127 EBI-EMBL Prohead core protein serine protease Prohead core protein serine protease NF015387.5 PF03422.20 CBM_6 28.9 21.5 125 domain Y Y N carbohydrate-binding protein GO:0030246 131567 cellular organisms no rank 78701 EBI-EMBL Carbohydrate binding module (family 6) carbohydrate-binding protein NF015390.5 PF03425.18 CBM_11 20.7 20.7 182 domain Y Y N carbohydrate binding domain-containing protein GO:0008810,GO:0030245 131567 cellular organisms no rank 6654 EBI-EMBL Carbohydrate binding domain (family 11) Carbohydrate binding domain (family 11) NF015397.5 PF03432.19 Relaxase 24.6 24.6 132 domain Y Y N relaxase/mobilization nuclease domain-containing protein 10482518,10940031,9350859 131567 cellular organisms no rank 81182 EBI-EMBL MobA/VirD2-like, nuclease domain MobA/VirD2-like, nuclease domain Relaxases/mobilisation proteins are required for the horizontal transfer of genetic information contained on plasmids that occurs during bacterial conjugation. The relaxase, in conjunction with several auxiliary proteins, forms the relaxation complex or relaxosome. Relaxases nick duplex DNA in a specific manner by catalysing trans-esterification [1-3]. This entry represents the nuclease domain of VirD2 and similar sequences. [1]. 9350859. Nicking by transesterification: the reaction catalysed by a relaxase. Byrd DR, Matson SW;. Mol Microbiol 1997;25:1011-1022. [2]. 10940031. Identification of the mob genes of plasmid pSC101 and characterization of a hybrid pSC101-R1162 system for conjugal mobilization. Meyer R;. J Bacteriol 2000;182:4875-4881. [3]. 10482518. Bacterial conjugation protein MobA mediates integration of complex DNA structures into plant cells. Bravo-Angel AM, Gloeckler V, Hohn B, Tinland B;. J Bacteriol 1999;181:5758-5765. (from Pfam) NF015400.5 PF03435.23 Sacchrp_dh_NADP 25.1 25.1 129 domain Y Y N saccharopine dehydrogenase NADP-binding domain-containing protein GO:0016491 11080625,11354603 131567 cellular organisms no rank 139539 EBI-EMBL Saccharopine dehydrogenase NADP binding domain Saccharopine dehydrogenase NADP binding domain This family contains the NADP binding domain of saccharopine dehydrogenase. In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase. The saccharopine dehydrogenase can also function as a saccharopine reductase. [1]. 11080625. Crystal structure of saccharopine reductase from Magnaporthe grisea, an enzyme of the alpha-aminoadipate pathway of lysine biosynthesis. Johansson E, Steffens JJ, Lindqvist Y, Schneider G;. Structure Fold Des 2000;8:1037-1047. [2]. 11354603. Lysine metabolism in higher plants. Azevedo RA, Lea PJ;. Amino Acids 2001;20:261-279. (from Pfam) NF015402.5 PF03437.20 BtpA 30 30 254 subfamily Y Y N BtpA/SgcQ family protein 10806238 131567 cellular organisms no rank 6971 EBI-EMBL BtpA family BtpA/SgcQ family protein Members of this family include BtpA from photosynthetic bacteria and SgcQ from Escherichia coli K-12. NF015404.5 PF03439.18 Spt5-NGN 22.4 22.4 84 PfamEq Y N N Early transcription elongation factor of RNA pol II, NGN section 12202748,19460865 131567 cellular organisms no rank 1039 EBI-EMBL Early transcription elongation factor of RNA pol II, NGN section Early transcription elongation factor of RNA pol II, NGN section Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4 [1]. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit [2]. [1]. 12202748. Novel domains and orthologues of eukaryotic transcription elongation factors. Ponting CP;. Nucleic Acids Res. 2002;30:3643-3652. [2]. 19460865. Characterization of the Schizosaccharomyces pombe Spt5-Spt4 complex. Schwer B, Schneider S, Pei Y, Aronova A, Shuman S;. RNA. 2009; [Epub ahead of print] (from Pfam) NF015406.5 PF03441.19 FAD_binding_7 27 27 203 domain Y Y N FAD-binding domain-containing protein 15576622,9360600 131567 cellular organisms no rank 84051 EBI-EMBL FAD binding domain of DNA photolyase FAD binding domain of DNA photolyase NF015407.5 PF03442.19 CBM_X2 28.9 28.9 83 domain Y Y N X2-like carbohydrate binding domain-containing protein 11080456,15375114 131567 cellular organisms no rank 6636 EBI-EMBL Carbohydrate binding domain X2 scaffolding protein CipC X2-like carbohydrate binding domain This domain binds to cellulose and to bacterial cell walls. It is found in glycosyl hydrolases and in scaffolding proteins of cellulosomes (multiprotein glycosyl hydrolase complexes). In the cellulosome it may aid cellulose degradation by anchoring the cellulosome to the bacterial cell wall and by binding it to its substrate [1]. This domain has an Ig-like fold [2]. [1]. 15375114. Hydrophilic domains of scaffolding protein CbpA promote glycosyl hydrolase activity and localization of cellulosomes to the cell surface of Clostridium cellulovorans. Kosugi A, Amano Y, Murashima K, Doi RH;. J Bacteriol. 2004;186:6351-6359. [2]. 11080456. Solution structure of the module X2 1 of unknown function of the cellulosomal scaffolding protein CipC of Clostridium cellulolyticum. Mosbah A, Belaich A, Bornet O, Belaich JP, Henrissat B, Darbon H;. J Mol Biol 2000;304:201-217. (from Pfam) NF015409.5 PF03444.20 HrcA_DNA-bdg 21 21 79 domain Y N N Winged helix-turn-helix transcription repressor, HrcA DNA-binding GO:0003677,GO:0006355 131567 cellular organisms no rank 25305 EBI-EMBL Winged helix-turn-helix transcription repressor, HrcA DNA-binding Winged helix-turn-helix transcription repressor, HrcA DNA-binding This domain is always found with a pair of CBS domains Pfam:PF00571. (from Pfam) NF015410.5 PF03445.18 DUF294 21 21 138 domain Y Y N DUF294 nucleotidyltransferase-like domain-containing protein GO:0008773 131567 cellular organisms no rank 40708 EBI-EMBL Putative nucleotidyltransferase DUF294 DUF294 nucleotidyltransferase-like domain This domain is found associated with Pfam:PF00571. This region is uncharacterised, however it seems to be similar to Pfam:PF01909, conserving the DXD motif. This strongly suggests that members of this family are also nucleotidyltransferases (Bateman A pers. obs.). (from Pfam) NF015411.5 PF03446.20 NAD_binding_2 21 21 161 domain Y Y N NAD(P)-binding domain-containing protein GO:0050661 131567 cellular organisms no rank 732854 EBI-EMBL NAD binding domain of 6-phosphogluconate dehydrogenase NAD(P)-binding domain, 6-phosphogluconate dehydrogenase family The NAD binding domain of 6-phosphogluconate dehydrogenase adopts a Rossmann fold. (from Pfam) NF015412.5 PF03447.21 NAD_binding_3 24 24 116 domain Y N N Homoserine dehydrogenase, NAD binding domain GO:0016491,GO:0050661 131567 cellular organisms no rank 187543 EBI-EMBL Homoserine dehydrogenase, NAD binding domain Homoserine dehydrogenase, NAD binding domain This domain adopts a Rossmann NAD binding fold. The C-terminal domain of homoserine dehydrogenase contributes a single helix to this structural domain, which is not included in the Pfam model. (from Pfam) NF015413.5 PF03448.22 MgtE_N 25.9 25.9 102 domain Y Y N magnesium transporter MgtE N-terminal domain-containing protein 17700703 131567 cellular organisms no rank 70324 EBI-EMBL MgtE intracellular N domain magnesium transporter MgtE N-terminal domain This domain is found at the N-terminus of eubacterial magnesium transporters of the MgtE family Pfam:PF01769. This domain is an intracellular domain that has an alpha-helical structure. The crystal structure of the MgtE transporter [1] shows two of 5 magnesium ions are in the interface between the N domain and the CBS domains. In the absence of magnesium there is a large shift between the N and CBS domains. [1]. 17700703. Crystal structure of the MgtE Mg2+ transporter. Hattori M, Tanaka Y, Fukai S, Ishitani R, Nureki O;. Nature. 2007;448:1072-1075. (from Pfam) NF015415.5 PF03450.22 CO_deh_flav_C 25.5 25.5 102 domain Y N N CO dehydrogenase flavoprotein C-terminal domain 131567 cellular organisms no rank 93339 EBI-EMBL CO dehydrogenase flavoprotein C-terminal domain CO dehydrogenase flavoprotein C-terminal domain NF015417.5 PF03452.19 Anp1 28.8 28.8 263 domain Y N N Anp1 9430634 131567 cellular organisms no rank 852 EBI-EMBL Anp1 Anp1 The members of this family (Anp1, Van1 and Mnn9) are membrane proteins required for proper Golgi function. These proteins co-localise within the cis Golgi, and that they are physically associated in two distinct complexes[1]. [1]. 9430634. Multi-protein complexes in the cis Golgi of Saccharomyces cerevisiae with alpha-1,6-mannosyltransferase activity. Jungmann J, Munro S;. EMBO J 1998;17:423-434. (from Pfam) NF015418.5 PF03453.22 MoeA_N 30.8 30.8 160 domain Y N N MoeA N-terminal region (domain I and II) GO:0032324 131567 cellular organisms no rank 119354 EBI-EMBL MoeA N-terminal region (domain I and II) MoeA N-terminal region (domain I and II) This family contains two structural domains. One of these contains the conserved DGXA motif. This region is found in proteins involved in biosynthesis of molybdopterin cofactor however the exact molecular function of this region is uncertain. (from Pfam) NF015419.5 PF03454.20 MoeA_C 22.1 22.1 72 domain Y N N MoeA C-terminal region (domain IV) GO:0032324 11525167 131567 cellular organisms no rank 107273 EBI-EMBL MoeA C-terminal region (domain IV) MoeA C-terminal region (domain IV) This domain is found in proteins involved in biosynthesis of molybdopterin cofactor however the exact molecular function of this domain is uncertain. The structure of this domain is known [1] and forms an incomplete beta barrel. [1]. 11525167. The crystal structure of Escherichia coli MoeA and its relationship to the multifunctional protein gephyrin. Xiang S, Nichols J, Rajagopalan KV, Schindelin H;. Structure 2001;9:299-310. (from Pfam) NF015423.5 PF03458.18 Gly_transporter 23.5 23.5 78 domain Y Y N TRIC cation channel family protein 28524849,29769716 131567 cellular organisms no rank 49273 EBI-EMBL Glycine transporter TRIC cation channel family protein This domain contains three transmembrane helices. Proteins containing this domain are important for glycine utilisation, being identified as glycine transporters. Some members of the family are also important for alanine utilisation. In these proteins this domain is found in pairs [1]. An archaeal member of this family which contains this domain is a TRIC-type potassium channel [2]. [1]. 29769716. Mutant phenotypes for thousands of bacterial genes of unknown function. Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM;. Nature. 2018;557:503-509. [2]. 28524849. Structural basis for conductance through TRIC cation channels. Su M, Gao F, Yuan Q, Mao Y, Li DL, Guo Y, Yang C, Wang XH, Bruni R, Kloss B, Zhao H, Zeng Y, Zhang FB, Marks AR, Hendrickson WA, Chen YH;. Nat Commun. 2017;8:15103. (from Pfam) NF015424.5 PF03459.22 TOBE 22.3 22.3 64 domain Y Y N TOBE domain-containing protein 10829230 131567 cellular organisms no rank 109454 EBI-EMBL TOBE domain TOBE domain The TOBE domain [1] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (eg Swiss:P46930) and sulfate (Swiss:P16676). Found in ABC transporters immediately after the ATPase domain. [1]. 10829230. Protein fold recognition using sequence profiles and its application in structural genomics. Koonin EV, Wolf YI, Aravind L;. Adv Protein Chem 2000;54:245-275. (from Pfam) NF015425.5 PF03460.22 NIR_SIR_ferr 24 24 69 domain Y N N Nitrite/Sulfite reductase ferredoxin-like half domain GO:0016491 7569952 131567 cellular organisms no rank 155481 EBI-EMBL Nitrite/Sulfite reductase ferredoxin-like half domain Nitrite/Sulfite reductase ferredoxin-like half domain Sulfite and Nitrite reductases are key to both biosynthetic assimilation of sulfur and nitrogen and dissimilation of oxidised anions for energy transduction [1]. Two copies of this repeat are found in Nitrite and Sulfite reductases and form a single structural domain. [1]. 7569952. Sulfite reductase structure at 1.6 A: evolution and catalysis for reduction of inorganic anions. Crane BR, Siegel LM, Getzoff ED;. Science 1995;270:59-67. (from Pfam) NF015426.5 PF03461.20 TRCF 25 25 95 domain Y Y N TRCF domain-containing protein GO:0006281 131567 cellular organisms no rank 103824 EBI-EMBL TRCF domain TRCF domain NF015428.5 PF03463.20 eRF1_1 23.8 23.8 123 domain Y N N eRF1 domain 1 10676813 131567 cellular organisms no rank 2809 EBI-EMBL eRF1 domain 1 eRF1 domain 1 The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known [1]. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site [1]. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification. [1]. 10676813. The crystal structure of human eukaryotic release factor eRF1--mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. Song H, Mugnier P, Das AK, Webb HM, Evans DR, Tuite MF, Hemmings BA, Barford D;. Cell 2000;100:311-321. (from Pfam) NF015429.5 PF03464.20 eRF1_2 27.1 27.1 133 domain Y N N eRF1 domain 2 10676813 131567 cellular organisms no rank 2644 EBI-EMBL eRF1 domain 2 eRF1 domain 2 The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known [1]. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site [1]. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification. [1]. 10676813. The crystal structure of human eukaryotic release factor eRF1--mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. Song H, Mugnier P, Das AK, Webb HM, Evans DR, Tuite MF, Hemmings BA, Barford D;. Cell 2000;100:311-321. (from Pfam) NF015430.5 PF03465.20 eRF1_3 25.8 25.8 106 domain Y N N eRF1 domain 3 10676813 131567 cellular organisms no rank 2998 EBI-EMBL eRF1 domain 3 eRF1 domain 3 The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known [1]. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site [1]. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification. [1]. 10676813. The crystal structure of human eukaryotic release factor eRF1--mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. Song H, Mugnier P, Das AK, Webb HM, Evans DR, Tuite MF, Hemmings BA, Barford D;. Cell 2000;100:311-321. (from Pfam) NF015436.5 PF03471.22 CorC_HlyC 27 27 81 domain Y Y N transporter associated domain-containing protein 131567 cellular organisms no rank 182810 EBI-EMBL Transporter associated domain Transporter associated domain This small domain is found in a family of proteins with the Pfam:PF01595 domain and two CBS domains with this domain found at the C-terminus of the proteins, the domain is also found at the C terminus of some Na+/H+ antiporters. This domain is also found in CorC that is involved in Magnesium and cobalt efflux. The function of this domain is uncertain but might be involved in modulating transport of ion substrates. (from Pfam) NF015438.5 PF03473.22 MOSC 22.7 22.7 120 domain Y Y N MOSC domain-containing protein GO:0003824,GO:0030151,GO:0030170 11886751 131567 cellular organisms no rank 111155 EBI-EMBL MOSC domain MOSC domain The MOSC (MOCO sulfurase C-terminal) domain is a superfamily of beta-strand-rich domains identified in the molybdenum cofactor sulfurase and several other proteins from both prokaryotes and eukaryotes. These MOSC domains contain an absolutely conserved cysteine and occur either as stand-alone forms such as Swiss:P32157, or fused to other domains such as NifS-like catalytic domain in Molybdenum cofactor sulfurase. The MOSC domain is predicted to be a sulfur-carrier domain that receives sulfur abstracted by the pyridoxal phosphate-dependent NifS-like enzymes, on its conserved cysteine, and delivers it for the formation of diverse sulfur-metal clusters. [1]. 11886751. MOSC domains: ancient, predicted sulfur-carrier domains, present in diverse metal--sulfur cluster biosynthesis proteins including Molybdenum cofactor sulfurases. Anantharaman V, Aravind L;. FEMS Microbiol Lett 2002;207:55-61. (from Pfam) NF015440.5 PF03475.19 YiiM_3-alpha 22.7 22.7 44 domain Y Y N 3-alpha domain-containing protein 11886751,29459651 131567 cellular organisms no rank 19992 EBI-EMBL YiiM-like, 3-alpha helix domain YiiM-like, 3-alpha helix domain This small triple helical domain has been predicted to assume a topology similar to helix-turn-helix domains. These domains are found at the C-terminus of proteins related to Swiss:P32157 [1,2]. See figure 2. [1]. 11886751. MOSC domains: ancient, predicted sulfur-carrier domains, present in diverse metal--sulfur cluster biosynthesis proteins including Molybdenum cofactor sulfurases. Anantharaman V, Aravind L;. FEMS Microbiol Lett 2002;207:55-61. [2]. 29459651. Crystal structure of the hydroxylaminopurine resistance protein, YiiM, and its putative molybdenum cofactor-binding catalytic site. Namgung B, Kim JH, Song WS, Yoon SI;. Sci Rep. 2018;8:3304. (from Pfam) NF015441.5 PF03476.21 MOSC_N 25 25 119 domain Y Y N MOSC N-terminal beta barrel domain-containing protein 11886751 131567 cellular organisms no rank 44431 EBI-EMBL MOSC N-terminal beta barrel domain MOSC N-terminal beta barrel domain This domain is found to the N-terminus of Pfam:PF03473. The function of this domain is unknown, however it is predicted to adopt a beta barrel fold. See figure 2. [1]. 11886751. MOSC domains: ancient, predicted sulfur-carrier domains, present in diverse metal--sulfur cluster biosynthesis proteins including Molybdenum cofactor sulfurases. Anantharaman V, Aravind L;. FEMS Microbiol Lett 2002;207:55-61. (from Pfam) NF015442.5 PF03477.21 ATP-cone 25.8 25.8 88 domain Y Y N ATP cone domain-containing protein 10939243 131567 cellular organisms no rank 96465 EBI-EMBL ATP cone domain ATP cone domain NF015444.5 PF03479.20 PCC 25 25 117 PfamAutoEq Y Y N PCC domain-containing protein 15604740,17295322 131567 cellular organisms no rank 14857 EBI-EMBL Plants and Prokaryotes Conserved (PCC) domain Plants and Prokaryotes Conserved (PCC) domain This is a Plants and Prokaryotes Conserved (PPC) domain found in proteins that contain AT-hook motifs Pfam:PF02178 which strongly suggests a DNA-binding function for the proteins as a whole. Proteins with PPC domains are found in Bacteria, Archaea and the plant kingdom [1, 2].The PPC domain has a single alpha-helix packed against an antiparallel beta-sheet, which is formed by five beta-strands. There are three highly conserved histidine residues, eg at 117, 119 and 133 in Swiss:Q46QL5 which appear to form a zinc-binding site, and the domain has been observed to form homotrimers. The domain co-occurs with a thioredoxin-like domain in uncharacterized cyanobacterial proteins [2]. [1]. 15604740. Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces. Fujimoto S, Matsunaga S, Yonemura M, Uchiyama S, Azuma T, Fukui K;. Plant Mol Biol. 2004;56:225-239. [2]. 17295322. Crystal structure of Pyrococcus horikoshii PPC protein at 1.60 A resolution. Lin L, Nakano H, Nakamura S, Uchiyama S, Fujimoto S, Matsunaga S, Kobayashi Y, Ohkubo T, Fukui K;. Proteins. 2007;67:505-507. (from Pfam) NF015445.5 PF03480.18 DctP 23.4 23.4 286 domain Y N N Bacterial extracellular solute-binding protein, family 7 GO:0055085 16262798,16702222,1809844,20656493 131567 cellular organisms no rank 162461 EBI-EMBL Bacterial extracellular solute-binding protein, family 7 Bacterial extracellular solute-binding protein, family 7 This family of proteins is involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes Swiss:P37735, a C4-dicarboxylate-binding protein [1] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins [2]. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [2]. [1]. 1809844. Purification, characterization and nucleotide sequence of the periplasmic C4-dicarboxylate-binding protein (DctP) from Rhodobacter capsulatus. Shaw JG, Hamblin MJ, Kelly DJ;. Mol Microbiol 1991;5:3055-3062. [2]. 16702222. Conservation of structure and mechanism in primary and secondary transporters exemplified by SiaP, a sialic acid binding virulence factor from Haemophilus influenzae. Muller A, Severi E, Mulligan C, Watts AG, Kelly DJ, Wilson KS, Wilkinson AJ, Thomas GH;. J Biol Chem. 2006;281:22212-22222. [3]. 16262798. Sialic acid transport in Haemophilus influenzae is essential for lipopolysaccharide sialylation and serum resistance and is dependent on a novel tripartite ATP-independent periplasmic transporter. Severi E, Randle G, Kivlin P, Whitfield K, Young R, Moxon R, Kelly D, Hood D, Thomas GH;. Mol Microbiol. 2005;58:1173-1185. [4]. 20656493. Caught in a TRAP: substrate-binding proteins in secondary transport. Fischer M, Zhang QY, Hubbard RE, Thomas GH;. Trends Microbiol. 2010;18:471-478. (from Pfam) NF015446.5 PF03481.18 Sua5_C 22.9 22.9 136 domain Y Y N Sua5 family C-terminal domain-containing protein 18004774,19287007,23072323 131567 cellular organisms no rank 34151 EBI-EMBL Threonylcarbamoyl-AMP synthase, C-terminal domain Threonylcarbamoyl-AMP synthase, C-terminal domain This domain can be found in the C terminus of threonylcarbamoyl-AMP synthases, including Sua5 from Saccharomyces cerevisiae and YwlC from Bacillus subtilis. Threonylcarbamoyl-AMP synthase is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t6A37) in tRNAs that read codons beginning with adenine [1,2]. This domain adopts the Rossmann fold and may be involved in GTP and/or tRNA binding based on structural similarity with both GTP and tRNA binding proteins [3]. [1]. 19287007. The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F, Williamson JR, Schimmel P, Swairjo MA, de Crecy-Lagard V;. Nucleic Acids Res. 2009;37:2894-2909. [2]. 23072323. Mechanism of N6-threonylcarbamoyladenonsine (t(6)A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP. Lauhon CT;. Biochemistry. 2012;51:8950-8963. [3]. 18004774. X-ray crystal structure of a hypothetical Sua5 protein from Sulfolobus tokodaii strain 7. Agari Y, Sato S, Wakamatsu T, Bessho Y, Ebihara A, Yokoyama S, Kuramitsu S, Shinkai A;. Proteins. 2008;70:1108-1111. (from Pfam) NF015448.5 PF03483.22 B3_4 29.3 29.3 174 domain Y Y N phenylalanine--tRNA ligase beta subunit-related protein GO:0003723,GO:0004826 10447505 131567 cellular organisms no rank 120748 EBI-EMBL B3/4 domain B3/4 domain This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins. [1]. 10447505. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Wolf YI, Aravind L, Grishin NV, Koonin EV;. Genome Res 1999;9:689-710. (from Pfam) NF015449.5 PF03484.20 B5 28.6 28.6 67 PfamEq Y N N tRNA synthetase B5 domain GO:0000287,GO:0003723,GO:0005524,GO:0006432 10447505 131567 cellular organisms no rank 102674 EBI-EMBL tRNA synthetase B5 domain tRNA synthetase B5 domain This domain is found in phenylalanine-tRNA synthetase beta subunits. [1]. 10447505. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Wolf YI, Aravind L, Grishin NV, Koonin EV;. Genome Res 1999;9:689-710. (from Pfam) NF015450.5 PF03485.21 Arg_tRNA_synt_N 21.5 21.5 85 domain Y N N Arginyl tRNA synthetase N terminal domain GO:0000166,GO:0004814,GO:0005524,GO:0005737,GO:0006420 9736621 131567 cellular organisms no rank 94702 EBI-EMBL Arginyl tRNA synthetase N terminal domain Arginyl tRNA synthetase N terminal domain This domain is found at the amino terminus of Arginyl tRNA synthetase, also called additional domain 1 (Add-1). It is about 140 residues long and it has been suggested that this domain will be involved in tRNA recognition [1]. [1]. 9736621. L-arginine recognition by yeast arginyl-tRNA synthetase. Cavarelli J, Delagoutte B, Eriani G, Gangloff J, Moras D;. EMBO J 1998;17:5438-5448. (from Pfam) NF015451.5 PF03486.19 HI0933_like 50 50 244 domain Y Y N NAD(P)/FAD-dependent oxidoreductase 131567 cellular organisms no rank 83789 EBI-EMBL HI0933-like protein Rossmann domain HI0933-like protein Rossmann domain This entry represents the Rossmann like domain in the HI0933 protein. (from Pfam) NF015454.5 PF03489.22 SapB_2 21 21 34 domain Y N N Saposin-like type B, region 2 12518053,26616259,7610480 131567 cellular organisms no rank 35 EBI-EMBL Saposin-like type B, region 2 Saposin-like type B, region 2 Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity [1,2]. It is one of the most studied members of the saposin protein family and it is involved in the hydrolysis of glycolipids and glycerolipids. SapB is unique in the saposin family in that it facilitates degradation by interacting with the substrate, not the enzymes [3]. [1]. 7610480. Swaposins: circular permutations within genes encoding saposin homologues. Ponting CP, Russell RB;. Trends Biochem Sci 1995;20:179-180. [2]. 12518053. Crystal structure of saposin B reveals a dimeric shell for lipid binding. Ahn VE, Faull KF, Whitelegge JP, Fluharty AL, Prive GG;. Proc Natl Acad Sci U S A. 2003;100:38-43. [3]. 26616259. The Lysosomal Protein Saposin B Binds Chloroquine. Huta BP, Mehlenbacher MR, Nie Y, Lai X, Zubieta C, Bou-Abdallah F, Doyle RP;. ChemMedChem. 2016;11:277-282. (from Pfam) NF015457.5 PF03492.20 Methyltransf_7 29.8 29.8 335 domain Y N N SAM dependent carboxyl methyltransferase GO:0008168 10852939,10984041,11108716,11287667 131567 cellular organisms no rank 1311 EBI-EMBL SAM dependent carboxyl methyltransferase SAM dependent carboxyl methyltransferase This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesised through sequential three-step methylation of xanthine derivatives at positions 7-N, 3-N, and 1-N. The protein 7-methylxanthine methyltransferase (designated as CaMXMT) catalyses the second step to produce theobromine [1]. [1]. 11108716. 7-Methylxanthine methyltransferase of coffee plants. Gene isolation and enzymatic properties. Ogawa M, Herai Y, Koizumi N, Kusano T, Sano H;. J Biol Chem 2001;276:8213-8218. [2]. 10984041. Caffeine synthase gene from tea leaves. Kato M, Mizuno K, Crozier A, Fujimura T, Ashihara H;. Nature 2000;406:956-957. [3]. 11287667. Jasmonic acid carboxyl methyltransferase: a key enzyme for jasmonate-regulated plant responses. Seo HS, Song JT, Cheong JJ, Lee YH, Lee YW, Hwang I, Lee JS, Choi YD;. Proc Natl Acad Sci U S A 2001;98:4788-4793. [4]. 10852939. Developmental regulation of methyl benzoate biosynthesis and emission in snapdragon flowers. Dudareva N, Murfitt LM, Mann CJ, Gorenstein N, Kolosova N, Kish CM, Bonham C, Wood K;. Plant Cell 2000;12:949-961. (from Pfam) NF015460.5 PF03495.19 Binary_toxB 25 10 78 domain Y Y N binary toxin-like calcium binding domain-containing protein 131567 cellular organisms no rank 1427 EBI-EMBL Clostridial binary toxin B/anthrax toxin PA Ca-binding domain binary toxin-like calcium binding domain This domain is a calcium binding domain in the anthrax toxin protective antigen. (from Pfam) NF015461.5 PF03496.19 ADPrib_exo_Tox 23.4 21.9 196 domain Y Y N ADP-ribosyltransferase GO:0005576 10024602,12498797 131567 cellular organisms no rank 8722 EBI-EMBL ADP-ribosyltransferase exoenzyme ADP-ribosyltransferase This is a family of bacterial and viral bi-glutamic acid ADP-ribosyltransferases, where, in Swiss:Q93Q17, E403 is the catalytic residue and E401 contributes to the transfer of ADP-ribose to the target protein. In clostridial species it is actin that is being ADP-ribosylated; this result is lethal and dermonecrotic in infected mammals. [1]. 10024602. Pseudomonas aeruginosa exoenzyme S is a biglutamic acid ADP-ribosyltransferase. Radke J, Pederson KJ, Barbieri JT;. Infect Immun. 1999;67:1508-1510. [2]. 12498797. Crystal structure and site-directed mutagenesis of enzymatic components from Clostridium perfringens iota-toxin. Tsuge H, Nagahama M, Nishimura H, Hisatsune J, Sakaguchi Y, Itogawa Y, Katunuma N, Sakurai J;. J Mol Biol. 2003;325:471-483. (from Pfam) NF015497.5 PF03534.18 SpvB 22 22 287 domain Y Y N SpvB/TcaC N-terminal domain-containing protein GO:0005737 11260464,11286884 131567 cellular organisms no rank 14196 EBI-EMBL Salmonella virulence plasmid 65kDa B protein SpvB/TcaC N-terminal domain NF015500.5 PF03537.18 Glyco_hydro_114 27 27 231 domain Y Y N endo alpha-1,4 polygalactosaminidase 21954604 131567 cellular organisms no rank 21305 EBI-EMBL Glycoside-hydrolase family GH114 endo alpha-1,4 polygalactosaminidase This family is recognised as a glycosyl-hydrolase family, number 114. It is endo-alpha-1,4-polygalactosaminidase, a rare enzyme. It is proposed to be TIM-barrel, the most common structure amongst the catalytic domains of glycosyl-hydrolases [1]. [1]. 21954604. [Endo-alpha-1-4-polygalactosaminidases and their homologues: structure and evolution]. Naumov DG, Stepushchenko OO;. Mol Biol (Mosk). 2011;45:703-714. (from Pfam) NF015501.5 PF03538.19 VRP1 22 22 328 domain Y Y N Tc toxin subunit A 131567 cellular organisms no rank 5344 EBI-EMBL Salmonella virulence plasmid 28.1kDa A protein Tc toxin subunit A Sequences belonging to this family include SpvA (Salmonella plasmid virulence protein A, which is also called VirA, MkfA, or VRP4), the A subunit of various Tc (toxin complex) toxins, and the VRP1 domain of longer toxins. NF015509.5 PF03547.23 Mem_trans 25.7 25.7 343 domain Y Y N AEC family transporter GO:0016020,GO:0055085 131567 cellular organisms no rank 102175 EBI-EMBL Membrane transport protein AEC family transporter This family includes auxin efflux carrier proteins and other transporter proteins from all domains of life. (from Pfam) NF015510.5 PF03548.20 LolA 23.6 23.6 165 domain Y Y N outer-membrane lipoprotein carrier protein LolA 131567 cellular organisms no rank 44863 EBI-EMBL Outer membrane lipoprotein carrier protein LolA outer-membrane lipoprotein carrier protein LolA NF015513.5 PF03551.19 PadR 27 27 75 domain Y Y N helix-turn-helix transcriptional regulator 131567 cellular organisms no rank 218831 EBI-EMBL Transcriptional regulator PadR-like family helix-turn-helix transcriptional regulator Members of this family are transcriptional regulators that appear to be related to the Pfam:PF01047 family. This family includes PadR Swiss:Q9EXE6 a protein that is involved in negative regulation of phenolic acid metabolism. (from Pfam) NF015514.5 PF03552.19 Cellulose_synt 24.7 24.7 722 domain Y N N Cellulose synthase GO:0016020,GO:0016760,GO:0030244 11178255,8901635 131567 cellular organisms no rank 28869 EBI-EMBL Cellulose synthase Cellulose synthase Cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues, is the major component of wood and thus paper, and is synthesised by plants, most algae, some bacteria and fungi, and even some animals. The genes that synthesise cellulose in higher plants differ greatly from the well-characterised genes found in Acetobacter and Agrobacterium sp. More correctly designated as 'cellulose synthase catalytic subunits', plant cellulose synthase (CesA) proteins are integral membrane proteins, approximately 1,000 amino acids in length. There are a number of highly conserved residues, including several motifs shown to be necessary for processive glycosyltransferase activity [1]. [1]. 8901635. Higher plants contain homologs of the bacterial celA genes encoding the catalytic subunit of cellulose synthase. Pear JR, Kawagoe Y, Schreckengost WE, Delmer DP, Stalker DM;. Proc Natl Acad Sci U S A 1996;93:12637-12642. [2]. 11178255. Higher plant cellulose synthases. Richmond T;. Genome Biol 2000;1:1-6. (from Pfam) NF015515.5 PF03553.19 Na_H_antiporter 23 23 303 domain Y Y N Na+/H+ antiporter NhaC family protein GO:0016020 9190799 131567 cellular organisms no rank 115122 EBI-EMBL Na+/H+ antiporter family Na+/H+ antiporter NhaC family protein This family includes integral membrane proteins, some of which are NA+/H+ antiporters [1]. [1]. 9190799. Role of the nhaC-encoded Na+/H+ antiporter of alkaliphilic Bacillus firmus OF4. Ito M, Guffanti AA, Zemsky J, Ivey DM, Krulwich TA;. J Bacteriol 1997;179:3851-3857. (from Pfam) NF015521.5 PF03559.19 Hexose_dehydrat 25 25 203 domain Y Y N NDP-hexose 2,3-dehydratase family protein GO:0016829 8655529,8955419,9831526 131567 cellular organisms no rank 6209 EBI-EMBL NDP-hexose 2,3-dehydratase NDP-hexose 2,3-dehydratase family protein This family includes a range of proteins from antibiotic production pathways. The family includes gra-ORF27 Swiss:Q9ZA32 product that probably functions at an early step, most likely as a dTDP-4-keto-6- deoxyglucose-2,3-dehydratase [1]. Its homologues include dnmT from the daunorubicin biosynthetic gene cluster in S. peucetius [2], a similar gene from the daunomycin biosynthetic cluster in Streptomyces sp. strain C5 Swiss:Q53880 [3] , eryBVI from the erythromycin cluster in S. erythraea and snoH from the nogalamycin cluster in S. nogalater. The proteins in this family are composed of two copies of a 200 amino acid long unit that may be a structural domain. [1]. 9831526. The granaticin biosynthetic gene cluster of Streptomyces violaceoruber Tu22: sequence analysis and expression in a heterologous host. Ichinose K, Bedford DJ, Tornus D, Bechthold A, Bibb MJ, Revill WP, Floss HG, Hopwood DA;. Chem Biol 1998;5:647-659. [2]. 8955419. Enhanced antibiotic production by manipulation of the Streptomyces peucetius dnrH and dnmT genes involved in doxorubicin (adriamycin) biosynthesis. Scotti C, Hutchinson CR;. J Bacteriol 1996;178:7316-7321. [3]. 8655529. Cloning, sequencing, and analysis of aklaviketone reductase from Streptomyces sp. strain C5. Dickens ML, Ye J, Strohl WR;. J Bacteriol 1996;178:3384-3388. (from Pfam) NF015527.5 PF03567.19 Sulfotransfer_2 22 22 252 domain Y Y N sulfotransferase family 2 domain-containing protein GO:0008146,GO:0016020 11956326,12492399 131567 cellular organisms no rank 14523 EBI-EMBL Sulfotransferase family Sulfotransferase family This family includes a variety of sulfotransferase enzymes. Chondroitin 6-sulfotransferase catalyses the transfer of sulfate to position 6 of the N-acetylgalactosamine residue of chondroitin. This family also includes Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan sulfate 6-sulfotransferase (HS6ST). Heparan sulfate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. Mice that lack HS2ST undergo developmental failure only after midgestation,the most dramatic effect being the complete failure of kidney development [1]. Heparan sulphate 6- O -sulfotransferase (HS6ST) catalyses the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate [2]. [1]. 11956326. Increased responsiveness of hypoxic endothelial cells to FGF2 is mediated by HIF-1alpha-dependent regulation of enzymes involved in synthesis of heparan sulfate FGF2-binding sites. Li J, Shworak NW, Simons M;. J Cell Sci 2002;115:1951-1959. [2]. 12492399. Biosynthesis of heparan sulphate with diverse structures and functions: two alternatively spliced forms of human heparan sulphate 6-O-sulphotransferase-2 having different expression patterns and properties. Habuchi H, Miyake G, Nogami K, Kuroiwa A, Matsuda Y, Kusche-Gullberg M, Habuchi O, Tanaka M, Kimata K;. Biochem J 2003;371:131-142. (from Pfam) NF015531.5 PF03572.23 Peptidase_S41 24 24 165 domain Y Y N S41 family peptidase GO:0006508,GO:0008236 131567 cellular organisms no rank 175996 EBI-EMBL Peptidase family S41 S41 family peptidase The serine endopeptidases in this family include C-terminal processing proteases such as the periplasmic protease Prc from Escherichia coli, involved in processing penicillin-binding protein (PBP) 3, and carboxyl-terminal processing protease CtpA from Pseudomonas aeruginosa. NF015534.5 PF03575.22 Peptidase_S51 23.9 23.9 206 domain Y Y N Type 1 glutamine amidotransferase-like domain-containing protein GO:0006508,GO:0008236 10762256,11106384 131567 cellular organisms no rank 57884 EBI-EMBL Peptidase family S51 Peptidase family S51 NF015535.5 PF03576.19 Peptidase_S58 23.9 23.9 307 domain Y Y N P1 family peptidase 131567 cellular organisms no rank 44574 EBI-EMBL Peptidase family S58 P1 family peptidase NF015536.5 PF03577.20 Peptidase_C69 23 23 402 domain Y Y N C69 family dipeptidase 3.4.13.- GO:0006508,GO:0016805,GO:0070004 12717035 131567 cellular organisms no rank 22865 EBI-EMBL Peptidase family C69 C69 family dipeptidase NF015545.5 PF03587.19 EMG1 28.2 28.2 197 PfamEq Y N N EMG1/NEP1 methyltransferase GO:0070037,GO:0070475 11935223,18063569 131567 cellular organisms no rank 341 EBI-EMBL EMG1/NEP1 methyltransferase EMG1/NEP1 methyltransferase Members of this family are essential for 40S ribosomal biogenesis. The structure of EMG1 has revealed that it is a novel member of the superfamily of alpha/beta knot fold methyltransferases [2]. [1]. 11935223. Nep1p (Emg1p), a novel protein conserved in eukaryotes and archaea, is involved in ribosome biogenesis. Eschrich D, Buchhaupt M, Kotter P, Entian KD;. Curr Genet 2002;40:326-338. [2]. 18063569. The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases. Leulliot N, Bohnsack MT, Graille M, Tollervey D, Van Tilbeurgh H;. Nucleic Acids Res. 2008;36:629-639. (from Pfam) NF015549.5 PF03591.19 AzlC 32.1 32.1 137 domain Y Y N AzlC family ABC transporter permease 131567 cellular organisms no rank 72549 EBI-EMBL AzlC protein AzlC family ABC transporter permease NF015551.5 PF03594.18 BenE 27 27 378 domain Y Y N benzoate/H(+) symporter BenE family transporter GO:0016020,GO:0042919,GO:0042925 131567 cellular organisms no rank 37801 EBI-EMBL Benzoate membrane transport protein benzoate/H(+) symporter BenE family transporter NF015552.5 PF03595.22 SLAC1 27.9 27.9 331 domain Y N N Voltage-dependent anion channel GO:0016020,GO:0055085 18305484,20981093 131567 cellular organisms no rank 42182 EBI-EMBL Voltage-dependent anion channel Voltage-dependent anion channel This family of transporters has ten alpha helical transmembrane segments [1]. The structure of a bacterial homologue of SLAC1 shows it to have a trimeric arrangement. The pore is composed of five helices with a conserved Phe residue involved in gating. One homologue, Mae1 from the yeast Schizosaccharomyces pombe, functions as a malate uptake transporter; another, Ssu1 from Saccharomyces cerevisiae and other fungi including Aspergillus fumigatus, is characterised as a sulfite efflux pump; and TehA from Escherichia coli is identified as a tellurite resistance protein by virtue of its association in the tehA/tehB operon. In plants, this family is found in the stomatal guard cells functioning as an anion-transporting pore [2]. Many homologues are incorrectly annotated as tellurite resistance or dicarboxylate transporter (TDT) proteins. [1]. 20981093. Homologue structure of the SLAC1 anion channel for closing stomata in leaves. Chen YH, Hu L, Punta M, Bruni R, Hillerich B, Kloss B, Rost B, Love J, Siegelbaum SA, Hendrickson WA;. Nature. 2010;467:1074-1080. [2]. 18305484. SLAC1 is required for plant guard cell S-type anion channel function in stomatal signalling. Vahisalu T, Kollist H, Wang YF, Nishimura N, Chan WY, Valerio G, Lamminmaki A, Brosche M, Moldau H, Desikan R, Schroeder JI, Kangasjarvi J;. Nature. 2008;452:487-491. (from Pfam) NF015553.5 PF03596.18 Cad 26.2 26.2 192 domain Y Y N cadmium resistance transporter 131567 cellular organisms no rank 10723 EBI-EMBL Cadmium resistance transporter cadmium resistance transporter NF015554.5 PF03597.20 FixS 23.1 23.1 44 PfamEq Y Y N cbb3-type cytochrome oxidase assembly protein CcoS ccoS 131567 cellular organisms no rank 16809 EBI-EMBL Cytochrome oxidase maturation protein cbb3-type cbb3-type cytochrome oxidase assembly protein CcoS NF015555.5 PF03598.20 CdhC 24 24 155 domain Y N N CO dehydrogenase/acetyl-CoA synthase complex beta subunit GO:0006084,GO:0043885 131567 cellular organisms no rank 1440 EBI-EMBL CO dehydrogenase/acetyl-CoA synthase complex beta subunit CO dehydrogenase/acetyl-CoA synthase complex beta subunit NF015556.5 PF03599.21 CdhD 24.8 24.8 387 domain Y N N CO dehydrogenase/acetyl-CoA synthase delta subunit 131567 cellular organisms no rank 7808 EBI-EMBL CO dehydrogenase/acetyl-CoA synthase delta subunit CO dehydrogenase/acetyl-CoA synthase delta subunit NF015557.5 PF03600.21 CitMHS 31.9 31.9 336 subfamily Y Y N SLC13 family permease GO:0016020,GO:0055085 131567 cellular organisms no rank 299751 EBI-EMBL Citrate transporter SLC13 family permease The SLC13 family permease is also known as DASS (Divalent Anion:Na+ Symporter). Characterized members are symporters of a substrate anion with sodium cations. NF015558.5 PF03601.19 Cons_hypoth698 24.5 24.5 304 subfamily Y Y N putative sulfate exporter family transporter GO:0016020 131567 cellular organisms no rank 56094 EBI-EMBL Conserved hypothetical protein 698 putative sulfate exporter family transporter NF015559.5 PF03602.20 Cons_hypoth95 24 24 182 domain Y Y N RsmD family RNA methyltransferase 131567 cellular organisms no rank 240511 EBI-EMBL Conserved hypothetical protein 95 RsmD family RNA methyltransferase NF015561.5 PF03604.18 DNA_RNApol_7kD 24 24 32 PfamEq Y N N DNA directed RNA polymerase, 7 kDa subunit GO:0003677,GO:0003899,GO:0006351 131567 cellular organisms no rank 472 EBI-EMBL DNA directed RNA polymerase, 7 kDa subunit DNA directed RNA polymerase, 7 kDa subunit NF015567.5 PF03610.21 EIIA-man 21.4 21.4 116 domain Y N N PTS system fructose IIA component GO:0009401,GO:0016020 131567 cellular organisms no rank 75763 EBI-EMBL PTS system fructose IIA component PTS system fructose IIA component NF015573.5 PF03616.19 Glt_symporter 26 26 368 domain Y Y N sodium/glutamate symporter GO:0015501,GO:0015813,GO:0016020 2017136 131567 cellular organisms no rank 22725 EBI-EMBL Sodium/glutamate symporter sodium/glutamate symporter NF015581.5 PF03625.19 DUF302 23 23 63 domain Y Y N DUF302 domain-containing protein 12625841,15481054 131567 cellular organisms no rank 24109 EBI-EMBL Domain of unknown function DUF302 Domain of unknown function DUF302 Domain is found in an undescribed set of proteins [1]. Normally occurs uniquely within a sequence, but is found as a tandem repeat (Swiss:Q9X8B8). Shows interesting phylogenetic distribution with majority of examples in bacteria and archaea, but it is also found in some fungal proteins. The hypothetical protein TT1751 from Thermus thermophilus has a beta-alpha-beta(4)-alpha structural fold [2]. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. [2]. 15481054. Crystal structure of a conserved hypothetical protein TT1751 from Thermus thermophilus HB8. Kishishita S, Tatsuguchi A, Ushikoshi-Nakayama R, Terada T, Kuramitsu S, Park SY, Tame JR, Shirouzu M, Yokoyama S;. Proteins. 2004;57:883-887. (from Pfam) NF015582.5 PF03626.19 COX4_pro 28.9 28.9 72 domain Y Y N cytochrome C oxidase subunit IV family protein GO:0016020 8638158 131567 cellular organisms no rank 29572 EBI-EMBL Prokaryotic Cytochrome C oxidase subunit IV cytochrome C oxidase subunit IV family protein Cytochrome c oxidase (COX) is a multi-subunit enzyme complex that catalyses the final step of electron transfer through the respiratory chain on the mitochondrial inner membrane. This family is composed of cytochrome c oxidase subunit 4 from prokaryotes. [1]. 8638158. The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A. Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S;. Science 1996;272:1136-1144. (from Pfam) NF015587.5 PF03631.20 Virul_fac_BrkB 33.7 33.7 259 subfamily Y Y N YhjD/YihY/BrkB family envelope integrity protein 15764599,7927748,8955422 131567 cellular organisms no rank 130467 EBI-EMBL Virulence factor BrkB YhjD/YihY/BrkB family envelope integrity protein YhjD and YihY are paralogs in Escherichia coli K-12. YhjD appears to have a transporter-like function in transporting lipid IV-A, a precursor of lipopolysaccharide (LPS). Mutation of BrkB in Bordetella pertussis increases serum resistance, which has led to it being called a virulence factor, but the finding would be consistent with a housekeeping role in cell envelope maintenance. NF015588.5 PF03632.20 Glyco_hydro_65m 27 27 371 domain Y N N Glycosyl hydrolase family 65 central catalytic domain GO:0003824,GO:0005975 11587643 131567 cellular organisms no rank 50262 EBI-EMBL Glycosyl hydrolase family 65 central catalytic domain Glycosyl hydrolase family 65 central catalytic domain This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyses the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The central domain is the catalytic domain, which binds a phosphate ion that is proximal the the highly conserved Glu. The arrangement of the phosphate and the glutamate is thought to cause nucleophilic attack on the anomeric carbon atom [1]. The catalytic domain also forms the majority of the dimerisation interface. [1]. 11587643. Crystal structure of maltose phosphorylase from Lactobacillus brevis: unexpected evolutionary relationship with glucoamylases. Egloff MP, Uppenberg J, Haalck L, van Tilbeurgh H;. Structure (Camb) 2001;9:689-697. (from Pfam) NF015589.5 PF03633.20 Glyco_hydro_65C 22 22 62 domain Y Y N glycosyl hydrolase family 65 protein 11587643 131567 cellular organisms no rank 51367 EBI-EMBL Glycosyl hydrolase family 65, C-terminal domain Glycosyl hydrolase family 65, C-terminal domain This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyses the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The C-terminal domain forms a two layered jelly roll motif. This domain is situated at the base of the catalytic domain, however its function remains unknown [1]. [1]. 11587643. Crystal structure of maltose phosphorylase from Lactobacillus brevis: unexpected evolutionary relationship with glucoamylases. Egloff MP, Uppenberg J, Haalck L, van Tilbeurgh H;. Structure (Camb) 2001;9:689-697. (from Pfam) NF015592.5 PF03636.20 Glyco_hydro_65N 26.6 26.6 233 domain Y N N Glycosyl hydrolase family 65, N-terminal domain GO:0003824,GO:0005975 11587643 131567 cellular organisms no rank 48914 EBI-EMBL Glycosyl hydrolase family 65, N-terminal domain Glycosyl hydrolase family 65, N-terminal domain This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyses the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. This domain is believed to be essential for catalytic activity [1] although its precise function remains unknown. [1]. 11587643. Crystal structure of maltose phosphorylase from Lactobacillus brevis: unexpected evolutionary relationship with glucoamylases. Egloff MP, Uppenberg J, Haalck L, van Tilbeurgh H;. Structure (Camb) 2001;9:689-697. (from Pfam) NF015595.5 PF03639.18 Glyco_hydro_81 25.6 25.6 323 domain Y N N Glycosyl hydrolase family 81 N-terminal domain 19542306 131567 cellular organisms no rank 179 EBI-EMBL Glycosyl hydrolase family 81 N-terminal domain Glycosyl hydrolase family 81 N-terminal domain Family of eukaryotic beta-1,3-glucanases. Within the Aspergillus fumigatus protein Swiss:Q9UVV0 two perfectly conserved Glu residues (E550 or E554) have been proposed as putative nucleophiles of the active site of the Engl1 endoglucanase, while the proton donor would be D475. The endo-beta-1,3-glucanase activity is essential for efficient spore release [1]. This entry represents the N-terminal beta sandwich domain. [1]. 19542306. {beta}-glucanase Eng2 is required for ascus wall endolysis after sporulation in the fission yeast Schizosaccharomyces pombe. Encinar del Dedo J, Duenas E, Arnaiz Y, del Rey F, Vazquez de Aldana CR;. Eukaryot Cell. 2009;8:1278-1286. (from Pfam) NF015596.5 PF03640.20 Lipoprotein_15 24.4 24.4 47 repeat Y N N SCO0930 family repeat-containing protein 12625841 131567 cellular organisms no rank 23901 EBI-EMBL Secreted repeat of unknown function SCO0930 family repeat This family occurs as tandem repeats in a set of lipoproteins. The alignment contains a Y-X4-D motif. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF015597.5 PF03641.19 Lysine_decarbox 27 27 131 domain Y Y N LOG family protein 131567 cellular organisms no rank 88809 EBI-EMBL Possible lysine decarboxylase LOG family protein The members of this family share a highly conserved motif PGGXGTXXE that is probably functionally important. This family includes proteins annotated as lysine decarboxylases, although the evidence for this is not clear. (from Pfam) NF015604.5 PF03648.19 Glyco_hydro_67N 24.3 24.3 120 domain Y Y N alpha-glucuronidase family glycosyl hydrolase GO:0045493,GO:0046559 11937059 131567 cellular organisms no rank 7316 EBI-EMBL Glycosyl hydrolase family 67 N-terminus alpha-glucuronidase family glycosyl hydrolase Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. This family represents the N-terminal region of alpha-glucuronidase. The N-terminal domain forms a two-layer sandwich, each layer being formed by a beta sheet of five strands. A further two helices form part of the interface with the central, catalytic, module (Pfam:PF07488) [1]. [1]. 11937059. The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A. Nurizzo D, Nagy T, Gilbert HJ, Davies GJ;. Structure (Camb) 2002;10:547-556. (from Pfam) NF015605.5 PF03649.18 UPF0014 22.6 22.6 242 PfamEq Y Y N ABC transporter permease 15659095,24038693 131567 cellular organisms no rank 23244 EBI-EMBL Uncharacterised protein family (UPF0014) ABC transporter permease Characterised proteins in this family include probable iron export permease protein FetB, which is part of the ABC transporter complex FetAB, probably involved in iron export [1], and aluminium sensitive 3 protein, also part of an ABC transporter required for aluminum (Al) resistance [2]. This family also includes integral membrane proteins currently uncharacterised. [1]. 24038693. Overexpression of fetA (ybbL) and fetB (ybbM), Encoding an Iron Exporter, Enhances Resistance to Oxidative Stress in Escherichia coli. Nicolaou SA, Fast AG, Nakamaru-Ogiso E, Papoutsakis ET;. Appl Environ Microbiol. 2013;79:7210-7219. [2]. 15659095. ALS3 encodes a phloem-localized ABC transporter-like protein that is required for aluminum tolerance in Arabidopsis. Larsen PB, Geisler MJ, Jones CA, Williams KM, Cancel JD;. Plant J. 2005;41:353-363. (from Pfam) NF015610.5 PF03657.18 UPF0113 23.8 23.8 73 domain Y N N UPF0113 PUA domain 15522784 131567 cellular organisms no rank 284 EBI-EMBL UPF0113 PUA domain UPF0113 PUA domain NF015612.5 PF03659.19 Glyco_hydro_71 34 34 375 subfamily Y Y N endo-1,3-alpha-glucanase family glycosylhydrolase GO:0051118 131567 cellular organisms no rank 2187 EBI-EMBL Glycosyl hydrolase family 71 endo-1,3-alpha-glucanase family Family of alpha-1,3-glucanases. (from Pfam) NF015616.5 PF03663.19 Glyco_hydro_76 25.9 25.9 366 domain Y Y N glycoside hydrolase family 76 protein 25772148 131567 cellular organisms no rank 16124 EBI-EMBL Glycosyl hydrolase family 76 glycoside hydrolase family 76 protein Family of alpha-1,6-mannanases. (from Pfam) NF015625.5 PF03673.18 UPF0128 21 21 221 subfamily Y Y N UPF0128 family protein 131567 cellular organisms no rank 95 EBI-EMBL Uncharacterised protein family (UPF0128) UPF0128 family protein The members of this family are about 240 amino acids in length. The proteins are as yet uncharacterised. (from Pfam) NF015629.5 PF03682.18 UPF0158 21.1 21.1 157 subfamily Y Y N UPF0158 family protein 131567 cellular organisms no rank 3673 EBI-EMBL Uncharacterised protein family (UPF0158) UPF0158 family protein NF015630.5 PF03683.18 UPF0175 27.9 27.9 75 domain Y Y N UPF0175 family protein 131567 cellular organisms no rank 6467 EBI-EMBL Uncharacterised protein family (UPF0175) UPF0175 family protein This family contains small proteins of unknown function. (from Pfam) NF015633.5 PF03686.18 UPF0146 26 26 129 subfamily Y Y N UPF0146 family protein 131567 cellular organisms no rank 1075 EBI-EMBL Uncharacterised protein family (UPF0146) UPF0146 family protein The function of this family of proteins is unknown. (from Pfam) NF015637.5 PF03690.18 UPF0160 22.1 22.1 318 PfamEq Y Y N MYG1 family protein 131567 cellular organisms no rank 3893 EBI-EMBL Uncharacterised protein family (UPF0160) MYG1 family protein This family of proteins contains a large number of metal binding residues. The patterns are suggestive of a phosphoesterase function. The conserved DHH motif may mean this family is related to Pfam:PF01368. (from Pfam) NF015639.5 PF03692.20 CxxCxxCC 23 23 85 domain Y Y N YkgJ family cysteine cluster protein 131567 cellular organisms no rank 68539 EBI-EMBL Putative zinc- or iron-chelating domain Putative zinc- or iron-chelating domain This family of proteins contains 8 conserved cysteines. It has in the past been annotated as being one of the complex of proteins of the flagellar Fli complex. However this was due to a mis-annotation of the original Salmonella LT2 Genbank entry of 'fliB'. With all its conserved cysteines it is possibly a domain that chelates iron or zinc ions. (from Pfam) NF015640.5 PF03693.19 ParD_antitoxin 21 21 81 domain Y Y N type II toxin-antitoxin system ParD family antitoxin 15718296,20143871,20487277 131567 cellular organisms no rank 22380 EBI-EMBL Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH type II toxin-antitoxin system ParD family antitoxin ParD is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is ParE in, Pfam:PF05016. The family contains several related antitoxins from Cyanobacteria, Proteobacteria and Actinobacteria. Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerises with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible alpha helices at the C-terminus. This C-terminus is the toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all type II antitoxins. [1]. 15718296. Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Pandey DP, Gerdes K;. Nucleic Acids Res. 2005;33:966-976. [2]. 20487277. Interaction specificity, toxicity and regulation of a paralogous set of ParE/RelE-family toxin-antitoxin systems. Fiebig A, Castro Rojas CM, Siegal-Gaskins D, Crosson S;. Mol Microbiol. 2010;77:236-251. [3]. 20143871. A conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex. Dalton KM, Crosson S;. Biochemistry. 2010;49:2205-2215. (from Pfam) NF015644.5 PF03699.18 UPF0182 27 27 770 domain Y Y N UPF0182 family protein GO:0016020 131567 cellular organisms no rank 22900 EBI-EMBL Uncharacterised protein family (UPF0182) COG1615 family transporter This family contains uncharacterised integral membrane proteins. (from Pfam) NF015647.5 PF03702.19 AnmK 24 24 367 PfamEq Y Y N anhydro-N-acetylmuramic acid kinase 2.7.1.170 GO:0005524,GO:0006040,GO:0009254,GO:0016773 15901686,16452451 131567 cellular organisms no rank 48399 EBI-EMBL Anhydro-N-acetylmuramic acid kinase anhydro-N-acetylmuramic acid kinase Anhydro-N-acetylmuramic acid kinase catalyses the specific phosphorylation of 1,6-anhydro-N-acetylmuramic acid (anhMurNAc) with the simultaneous cleavage of the 1,6-anhydro ring, generating MurNAc-6-P. It is also required for the utilization of anhMurNAc, either imported from the medium, or derived from its own cell wall murein, and in so doing plays a role in cell wall recycling [1,2]. [1]. 15901686. Recycling of the anhydro-N-acetylmuramic acid derived from cell wall murein involves a two-step conversion to N-acetylglucosamine-phosphate. Uehara T, Suefuji K, Valbuena N, Meehan B, Donegan M, Park JT;. J Bacteriol. 2005;187:3643-3649. [2]. 16452451. MurQ Etherase is required by Escherichia coli in order to metabolize anhydro-N-acetylmuramic acid obtained either from the environment or from its own cell wall. Uehara T, Suefuji K, Jaeger T, Mayer C, Park JT;. J Bacteriol. 2006;188:1660-1662. (from Pfam) NF015648.5 PF03703.19 bPH_2 22 22 78 domain Y Y N PH domain-containing protein 12625841,19913036 131567 cellular organisms no rank 86623 EBI-EMBL Bacterial PH domain Bacterial PH domain Domain found in uncharacterised family of membrane proteins. 1-3 copies found in each protein, with each copy flanked by transmembrane helices. Members of this family have a PH domain like structure [2]. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. [2]. 19913036. Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain. Xu Q, Bateman A, Finn RD, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. J Mol Biol. 2010 Feb 12;396(1):31-46. Epub 2009 Nov 10. (from Pfam) NF015649.5 PF03704.22 BTAD 22.1 22.1 146 domain Y Y N BTAD domain-containing putative transcriptional regulator 12625841 131567 cellular organisms no rank 208630 EBI-EMBL Bacterial transcriptional activator domain bacterial transcriptional activation domain BTAD The bacterial transcriptional activation domain BTAD, as found in Mycobacterium tuberculosis protein EmbR, typically occurs in proteins with adjacent recognizable DNA-binding domains and is suggested to act in recruitment of RNA polymerase. The BTAD contains TPR repeats. NF015650.5 PF03705.20 CheR_N 27 27 53 domain Y N N CheR methyltransferase, all-alpha domain 9115443 131567 cellular organisms no rank 62868 EBI-EMBL CheR methyltransferase, all-alpha domain CheR methyltransferase, all-alpha domain CheR proteins are part of the chemotaxis signaling mechanism in bacteria. CheR methylates the chemotaxis receptor at specific glutamate residues. CheR is an S-adenosylmethionine- dependent methyltransferase. [1]. 9115443. Crystal structure of the chemotaxis receptor methyltransferase CheR suggests a conserved structural motif for binding S-adenosylmethionine. Djordjevic S, Stock AM;. Structure 1997;5:545-558. (from Pfam) NF015651.5 PF03706.18 LPG_synthase_TM 33.4 33.4 302 domain Y Y N lysylphosphatidylglycerol synthase domain-containing protein 11342591,12496209,14769468 131567 cellular organisms no rank 100840 EBI-EMBL Lysylphosphatidylglycerol synthase TM region Lysylphosphatidylglycerol synthase TM region LPG_synthase_TM is the N-terminal region of this family of bacterial phosphatidylglycerol lysyltransferases. The function of the family is to add lysyl groups to membrane lipids, and this region is the transmembrane domain of 7xTMs. In order to counteract attack by membrane-damaging external cationic antimicrobial molecules - from host immune systems, bacteriocins, defensins, etc - bacteria modify their anionic membrane phosphatidylglycerol with positively-charged L-lysine; this results in repulsion of the foreign cationic peptides [1,2,3]. [1]. 11342591. Staphylococcus aureus resistance to human defensins and evasion of neutrophil killing via the novel virulence factor MprF is based on modification of membrane lipids with l-lysine. Peschel A, Jack RW, Otto M, Collins LV, Staubitz P, Nicholson G, Kalbacher H, Nieuwenhuizen WF, Jung G, Tarkowski A, van Kessel KP, van Strijp JA;. J Exp Med 2001;193:1067-1076. [2]. 12496209. MprF-mediated lysinylation of phospholipids in Staphylococcus aureus leads to protection against oxygen-independent neutrophil killing. Kristian SA, Durr M, Van Strijp JA, Neumeister B, Peschel A;. Infect Immun. 2003;71:546-549. [3]. 14769468. MprF-mediated biosynthesis of lysylphosphatidylglycerol, an important determinant in staphylococcal defensin resistance. Staubitz P, Neumann H, Schneider T, Wiedemann I, Peschel A;. FEMS Microbiol Lett. 2004;231:67-71. (from Pfam) NF015656.5 PF03711.20 OKR_DC_1_C 24.2 24.2 132 domain Y N N Orn/Lys/Arg decarboxylase, C-terminal domain GO:0003824 7563080 131567 cellular organisms no rank 67529 EBI-EMBL Orn/Lys/Arg decarboxylase, C-terminal domain Orn/Lys/Arg decarboxylase, C-terminal domain NF015658.5 PF03713.18 DUF305 27 27 151 domain Y Y N DUF305 domain-containing protein 12625841 131567 cellular organisms no rank 64703 EBI-EMBL Domain of unknown function (DUF305) Domain of unknown function (DUF305) Domain found in small family of bacterial secreted proteins with no known function. Also found in Paramecium bursaria chlorella virus 1. This domain is short and found in one or two copies. The domain has a conserved HH motif that may be functionally important. This domain belongs to the ferritin superfamily. It contains two sequence similar repeats each of which is composed of two alpha helices. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF015664.5 PF03719.20 Ribosomal_S5_C 21.5 21.5 71 PfamEq Y N N Ribosomal protein S5, C-terminal domain GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 29200 EBI-EMBL Ribosomal protein S5, C-terminal domain Ribosomal protein S5, C-terminal domain NF015665.5 PF03720.20 UDPG_MGDP_dh_C 30 30 103 domain Y Y N UDP binding domain-containing protein GO:0016616,GO:0051287 2470755,9013585 131567 cellular organisms no rank 168783 EBI-EMBL UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [2]. [1]. 2470755. Purification and characterization of guanosine diphospho-D-mannose dehydrogenase. A key enzyme in the biosynthesis of alginate by Pseudomonas aeruginosa. Roychoudhury S, May TB, Gill JF, Singh SK, Feingold DS, Chakrabarty AM;. J Biol Chem 1989;264:9380-9385. [2]. 9013585. Properties and kinetic analysis of UDP-glucose dehydrogenase from group A streptococci. Irreversible inhibition by UDP-chloroacetol. Campbell RE, Sala RF, van de Rijn I, Tanner ME;. J Biol Chem 1997;272:3416-3422. (from Pfam) NF015666.5 PF03721.19 UDPG_MGDP_dh_N 27 27 187 domain Y N N UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain GO:0016616,GO:0051287 2470755,9013585 131567 cellular organisms no rank 176222 EBI-EMBL UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [2]. [1]. 2470755. Purification and characterization of guanosine diphospho-D-mannose dehydrogenase. A key enzyme in the biosynthesis of alginate by Pseudomonas aeruginosa. Roychoudhury S, May TB, Gill JF, Singh SK, Feingold DS, Chakrabarty AM;. J Biol Chem 1989;264:9380-9385. [2]. 9013585. Properties and kinetic analysis of UDP-glucose dehydrogenase from group A streptococci. Irreversible inhibition by UDP-chloroacetol. Campbell RE, Sala RF, van de Rijn I, Tanner ME;. J Biol Chem 1997;272:3416-3422. (from Pfam) NF015669.5 PF03724.21 META 24 24 109 domain Y Y N META domain-containing protein 10403759,12625841 131567 cellular organisms no rank 47108 EBI-EMBL META domain META domain Small domain family found in proteins of of unknown function. Some are secreted (e.g. Swiss:O25998) and implicated in motility in bacteria. Also occurs in Leishmania spp. as an essential gene. Over-expression in L.amazonensis increases virulence (Swiss:O43987; [1]). A pair of cysteine residues show correlated conservation, suggesting that they form a disulphide bond. [1]. 10403759. Leishmania: overexpression and comparative structural analysis of the stage-regulated meta 1 gene. Uliana SR, Goyal N, Freymuller E, Smith DF;. Exp Parasitol 1999;92:183-191. [2]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF015670.5 PF03725.20 RNase_PH_C 20.8 20.8 67 domain Y N N 3' exoribonuclease family, domain 2 9390555 131567 cellular organisms no rank 97757 EBI-EMBL 3' exoribonuclease family, domain 2 3' exoribonuclease family, domain 2 This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components, Swiss:P46948 Swiss:Q12277 and Swiss:P25359 contain a copy of this domain [1]. Swiss:Q10205, a hypothetical protein from S. pombe appears to belong to an uncharacterised subfamily. This subfamily is found in both eukaryotes and archaebacteria. [1]. 9390555. The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases. Mitchell P, Petfalski E, Shevchenko A, Mann M, Tollervey D;. Cell 1997;91:457-466. (from Pfam) NF015671.5 PF03726.19 PNPase 24.6 24.6 81 PfamEq Y N N Polyribonucleotide nucleotidyltransferase, RNA binding domain GO:0003723,GO:0006396 131567 cellular organisms no rank 64977 EBI-EMBL Polyribonucleotide nucleotidyltransferase, RNA binding domain Polyribonucleotide nucleotidyltransferase, RNA binding domain This family contains the RNA binding domain of Polyribonucleotide nucleotidyltransferase (PNPase) PNPase is involved in mRNA degradation in a 3'-5' direction. (from Pfam) NF015674.5 PF03729.18 DUF308 25 15 73 domain Y Y N DUF308 domain-containing protein 12625841 131567 cellular organisms no rank 45960 EBI-EMBL Short repeat of unknown function (DUF308) Short repeat of unknown function (DUF308) Family of short repeats that occurs in a limited number of membrane proteins. It may divide further in short repeats of around 7-10 residues of the pattern G-#-X(2)-#(2)-X (#=hydrophobic). [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF015678.5 PF03733.18 YccF 27 27 51 domain Y Y N YccF domain-containing protein 12625841,15919996 131567 cellular organisms no rank 17779 EBI-EMBL Inner membrane component domain Inner membrane component domain Domain occurs as one or more copies in bacterial and eukaryotic proteins. These are membrane proteins of four TM regions, two appearing in each of the two copies when both are present. Many of the latter members also carry the sodium/calcium exchanger protein family Pfam:PF01699, which have multipass membrane regions. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. [2]. 15919996. Global topology analysis of the Escherichia coli inner membrane proteome. Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G;. Science. 2005;308:1321-1323. (from Pfam) NF015681.5 PF03736.22 EPTP 21 21 42 repeat Y N N EPTP repeat-containing protein 12095917,12217514 131567 cellular organisms no rank 404 EBI-EMBL EPTP domain EPTP repeat The EPTP repeat, found in proteins implicated in epileptic disorders, is rare in bacteria but occurs in the intracellular pathogen Legionella pneumophila. NF015682.5 PF03737.20 RraA-like 24.5 24.5 152 domain Y N N Aldolase/RraA 14499605,24359411 131567 cellular organisms no rank 78918 EBI-EMBL Aldolase/RraA Aldolase/RraA Members of this family include regulator of ribonuclease E activity A (RraA) and 4-hydroxy-4-methyl-2-oxoglutarate (HMG)/4-carboxy- 4-hydroxy-2-oxoadipate (CHA) aldolase, also known as RraA-like protein [1]. RraA acts as a trans-acting modulator of RNA turnover, binding essential endonuclease RNase E and inhibiting RNA processing [2]. RraA-like proteins seem to contain aldolase and/or decarboxylase activity either in place of or in addition to the RNase E inhibitor functions [1]. [1]. 24359411. Biochemical and structural analysis of RraA proteins to decipher their relationships with 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipa te aldolases. Mazurkewich S, Wang W, Seah SY;. Biochemistry. 2014;53:542-553. [2]. 14499605. The X-ray structure of Escherichia coli RraA (MenG), A protein inhibitor of RNA processing. Monzingo AF, Gao J, Qiu J, Georgiou G, Robertus JD;. J Mol Biol. 2003;332:1015-1024. (from Pfam) NF015686.5 PF03741.21 TerC 27.8 27.8 178 domain Y Y N TerC family protein GO:0016020 10069007,11016400 131567 cellular organisms no rank 125803 EBI-EMBL Integral membrane protein TerC family TerC family protein This family contains a number of integral membrane proteins that also contains the TerC protein. TerC has been implicated in resistance to tellurium. This protein may be involved in efflux of tellurium ions. The tellurite-resistant Escherichia coli strain KL53 was found during testing of the group of clinical isolates for antibiotics and heavy metal ion resistance [2]. Determinant of the tellurite resistance of the strain was located on a large conjugative plasmid. Analyses showed, the genes terB, terC, terD and terE are essential for conservation of the resistance. The members of the family contain a number of conserved aspartates that could be involved in binding to metal ions. [1]. 11016400. DNA sequence analysis of the tellurite-resistance determinant from clinical strain of Escherichia coli and identification of essential genes. Kormutakova R, Klucar L, Turna J;. Biometals 2000;13:135-139. [2]. 10069007. In vivo and in vitro cloning and phenotype characterization of tellurite resistance determinant conferred by plasmid pTE53 of a clinical isolate of Escherichia coli. Burian J, Tu N, Kl'ucar L, Guller L, Lloyd-Jones G, Stuchlik S, Fejdi P, Siekel P, Turna J;. Folia Microbiol (Praha) 1998;43:589-599. (from Pfam) NF015689.5 PF03744.18 BioW 25 25 239 PfamEq Y Y N 6-carboxyhexanoate--CoA ligase GO:0005524,GO:0009102,GO:0042410 1445232 131567 cellular organisms no rank 2897 EBI-EMBL 6-carboxyhexanoate--CoA ligase 6-carboxyhexanoate--CoA ligase This family contains the enzyme 6-carboxyhexanoate--CoA ligase EC:6.2.1.14. This enzyme is involved in the first step of biotin synthesis, where it converts pimelate into pimeloyl-CoA [1]. The enzyme requires magnesium as a cofactor and forms a homodimer [1]. [1]. 1445232. Investigation of the first step of biotin biosynthesis in Bacillus sphaericus. Purification and characterization of the pimeloyl-CoA synthase, and uptake of pimelate. Ploux O, Soularue P, Marquet A, Gloeckler R, Lemoine Y;. Biochem J 1992;287:685-690. (from Pfam) NF015690.5 PF03745.19 DUF309 27 27 59 PfamAutoEq Y Y N DUF309 domain-containing protein 131567 cellular organisms no rank 18182 EBI-EMBL Domain of unknown function (DUF309) Domain of unknown function (DUF309) This domain is found in eubacterial and archaebacterial proteins of unknown function. The proteins contain a motif HXXXEXX(W/Y) where X can be any amino acid. This motif is likely to be functionally important and may be involved in metal binding. (from Pfam) NF015691.5 PF03746.21 LamB_YcsF 22 22 239 domain Y Y N LamB/YcsF family protein 1729609 131567 cellular organisms no rank 53779 EBI-EMBL LamB/YcsF family LamB/YcsF family protein This family includes LamB. The lam locus of Aspergillus nidulans consists of two divergently transcribed genes, lamA and lamB, involved in the utilisation of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression [1]. The exact molecular function of the proteins in this family is unknown. [1]. 1729609. Molecular characterization of the lam locus and sequences involved in regulation by the AmdR protein of Aspergillus nidulans. Richardson IB, Katz ME, Hynes MJ;. Mol Cell Biol 1992;12:337-346. (from Pfam) NF015692.5 PF03747.19 ADP_ribosyl_GH 26.2 26.2 287 domain Y Y N ADP-ribosylglycohydrolase family protein 2506427,8349667,8505315 131567 cellular organisms no rank 111342 EBI-EMBL ADP-ribosylglycohydrolase ADP-ribosylglycohydrolase family protein This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine [1]. The family also includes dinitrogenase reductase activating glycohydrolase [2]. Most surprisingly the family also includes jellyfish crystallins [2], these proteins appear to have lost the presumed active site residues. [1]. 8349667. Cloning and site-directed mutagenesis of human ADP-ribosylarginine hydrolase. Takada T, Iida K, Moss J;. J Biol Chem 1993;268:17837-17843. [2]. 2506427. Genes coding for the reversible ADP-ribosylation system of dinitrogenase reductase from Rhodospirillum rubrum. Fitzmaurice WP, Saari LL, Lowery RG, Ludden PW, Roberts GP;. Mol Gen Genet 1989;218:340-347. [3]. 8505315. J1-crystallins of the cubomedusan jellyfish lens constitute a novel family encoded in at least three intronless genes. Piatigorsky J, Horwitz J, Norman BL;. J Biol Chem 1993;268:11894-11901. (from Pfam) NF015694.5 PF03749.18 SfsA 22.8 22.8 138 PfamEq Y Y N DNA/RNA nuclease SfsA 11272834,2013578 131567 cellular organisms no rank 23065 EBI-EMBL Sugar fermentation stimulation protein RE domain Sugar fermentation stimulation protein RE domain This family contains Sugar fermentation stimulation proteins. Which is probably a regulatory factor involved in maltose metabolism. SfsA has been shown to bind DNA [2] and it contains a helix-turn-helix motif that probably binds DNA at its C-terminus. [1]. 2013578. Nucleotide sequence and characterization of the sfs1 gene: sfs1 is involved in CRP*-dependent mal gene expression in Escherichia coli. Kawamukai M, Utsumi R, Takeda K, Higashi A, Matsuda H, Choi YL, Komano T;. J Bacteriol 1991;173:2644-2648. [2]. 11272834. Effects of the Escherichia coli sfsA gene on mal genes expression and a DNA binding activity of SfsA. Takeda K, Akimoto C, Kawamukai M;. Biosci Biotechnol Biochem 2001;65:213-217. (from Pfam) NF015695.5 PF03750.18 Csm2_III-A 24.8 24.8 115 PfamAutoEq Y Y N type III-A CRISPR-associated protein Csm2 csm2 17442114,21552286 131567 cellular organisms no rank 1941 EBI-EMBL Csm2 Type III-A type III-A CRISPR-associated protein Csm2 Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-associated) proteins [1]. This entry represents Csm2 Type III-A, a family of Cas proteins also known as TM1810/Csm2 [2]. [1]. 17442114. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Kunin V, Sorek R, Hugenholtz P;. Genome Biol. 2007;8:R61. [2]. 21552286. Evolution and classification of the CRISPR-Cas systems. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV;. Nat Rev Microbiol. 2011;9:467-477. (from Pfam) NF015706.5 PF03764.23 EFG_IV 24 24 121 domain Y N N Elongation factor G, domain IV GO:0003746,GO:0005525 131567 cellular organisms no rank 122505 EBI-EMBL Elongation factor G, domain IV Elongation factor G, domain IV This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold. (from Pfam) NF015709.5 PF03767.19 Acid_phosphat_B 27 27 230 domain Y Y N HAD family acid phosphatase 9193092,9747802 131567 cellular organisms no rank 25513 EBI-EMBL HAD superfamily, subfamily IIIB (Acid phosphatase) HAD family acid phosphatase This family proteins includes acid phosphatases and a number of vegetative storage proteins. (from Pfam) NF015714.5 PF03772.21 Competence 23 23 270 PfamEq Y Y N ComEC/Rec2 family competence protein 7934834,7968523,8063112,9573156 131567 cellular organisms no rank 113799 EBI-EMBL Competence protein ComEC/Rec2 family competence protein Members of this family are integral membrane proteins with 6 predicted transmembrane helices. Some members of this family have been shown to be essential for bacterial competence in uptake of extracellular DNA [1,4]. These proteins may transport DNA across the cell membrane. These proteins contain a highly conserved motif in the amino terminal transmembrane region that has two histidines that may form a metal binding site. [1]. 7934834. A novel determinant (comA) essential for natural transformation competence in Neisseria gonorrhoeae and the effect of a comA defect on pilin variation. Facius D, Meyer TF;. Mol Microbiol 1993;10:699-712. [2]. 7968523. Characterization of comE, a late competence operon of Bacillus subtilis required for the binding and uptake of transforming DNA. Hahn J, Inamine G, Kozlov Y, Dubnau D;. Mol Microbiol 1993;10:99-111. [3]. 8063112. Sequence of the rec-2 locus of Haemophilus influenzae: homologies to comE-ORF3 of Bacillus subtilis and msbA of Escherichia coli. Clifton SW, McCarthy D, Roe BA;. Gene 1994;146:95-100. [4]. 9573156. Isolation and characterization of three Streptococcus pneumoniae transformation-specific loci by use of a lacZ reporter insertion vector. Pestova EV, Morrison DA;. J Bacteriol 1998;180:2701-2710. (from Pfam) NF015715.5 PF03773.18 ArsP_1 32.3 32.3 294 domain Y Y N permease 131567 cellular organisms no rank 53918 EBI-EMBL Predicted permease permease This family of integral membrane proteins are predicted to be permeases of unknown specificity. (from Pfam) NF015720.5 PF03779.19 SPW 21 21 48 domain Y Y N SPW repeat protein 12625841 131567 cellular organisms no rank 12643 EBI-EMBL SPW repeat SPW repeat A short repeat found in a small family of membrane-bound proteins. This repeat contains a conserved SPW motif in the first of two transmembrane helices. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF015722.5 PF03781.21 FGE-sulfatase 23.3 23.3 255 domain Y Y N SUMF1/EgtB/PvdO family nonheme iron enzyme 14563551,15064399,15146462,15907468,18157819,20420449 131567 cellular organisms no rank 138582 EBI-EMBL Sulfatase-modifying factor enzyme 1 SUMF1/EgtB/PvdO family nonheme iron enzyme This domain is found in eukaryotic proteins [1] required for post-translational sulfatase modification (SUMF1). These proteins are associated with the rare disorder multiple sulfatase deficiency (MSD) [2]. The protein product of the SUMF1 gene is FGE, formylglycine (FGly),-generating enzyme, which is a sulfatase. Sulfatases are enzymes essential for degradation and remodelling of sulfate esters, and formylglycine (FGly), the key catalytic in the active site, is unique to sulfatases [3]. FGE is localised to the endoplasmic reticulum (ER) and interacts with and modifies the unfolded form of newly synthesised sulfatases. FGE is a single-domain monomer with a surprising paucity of secondary structure that adopts a unique fold which is stabilised by two Ca2+ ions. The effect of all mutations found in MSD patients is explained by the FGE structure, providing a molecular basis for MSD. A redox-active disulfide bond is present in the active site of FGE. An oxidised cysteine residue, possibly cysteine sulfenic acid, has been detected that may allow formulation of a structure-based mechanism for FGly formation from cysteine residues in all sulfatases [4]. In Mycobacteria and Treponema denticola this enzyme functions as an iron(II)-dependent oxidoreductase [5,6]. [1]. 14563551. The human SUMF1 gene, required for posttranslational sulfatase modification, defines a new gene family which is conserved from pro- to eukaryotes. Landgrebe J, Dierks T, Schmidt B, von Figura K;. Gene 2003;316:47-56. [2]. 15146462. Molecular and functional analysis of SUMF1 mutations in multiple sulfatase deficiency. Cosma MP, Pepe S, Parenti G, Settembre C,. TRUNCATED at 1650 bytes (from Pfam) NF015726.5 PF03785.19 Peptidase_C25_C 25 25 79 domain Y Y N C25 family peptidase C-terminal domain-containing protein GO:0006508,GO:0008233 22086950 131567 cellular organisms no rank 349 EBI-EMBL Peptidase family C25, C terminal ig-like domain Peptidase family C25, C terminal ig-like domain NF015727.5 PF03786.18 UxuA 23.7 23.7 352 domain Y Y N mannonate dehydratase 4.2.1.8 GO:0006064,GO:0008927 131567 cellular organisms no rank 29750 EBI-EMBL D-mannonate dehydratase (UxuA) mannonate dehydratase UxuA (this family) and UxuB are required for hexuronate degradation. (from Pfam) NF015728.5 PF03787.20 RAMPs 22.1 22.1 189 domain Y Y N RAMP superfamily CRISPR-associated protein 131567 cellular organisms no rank 20178 EBI-EMBL RAMP superfamily RAMP domain The molecular function of these proteins is not yet known. However, they have been identified and called the RAMP (Repair Associated Mysterious Proteins) superfamily. The members of this family have no known function they are around 300 amino acids in length and have several conserved motifs. (from Pfam) NF015729.5 PF03788.19 LrgA 28 28 94 domain Y Y N CidA/LrgA family protein GO:0016020 8824633 131567 cellular organisms no rank 30256 EBI-EMBL LrgA family CidA/LrgA family protein This family is uncharacterised. It contains the protein LrgA that has been hypothesised to export murein hydrolases [1]. [1]. 8824633. Identification of LytSR-regulated genes from Staphylococcus aureus. Brunskill EW, Bayles KW;. J Bacteriol 1996;178:5810-5812. (from Pfam) NF015734.5 PF03793.24 PASTA 23.2 23.2 64 domain Y Y N PASTA domain-containing protein 12217513,12625841 131567 cellular organisms no rank 128602 EBI-EMBL PASTA domain PASTA domain This domain is found at the C termini of several Penicillin-binding proteins and bacterial serine/threonine kinases [1]. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain. [1]. 12217513. The PASTA domain: a beta-lactam-binding domain. Yeats C, Finn R, Bateman A;. Trends Biochem Sci 2002;27:438-440. [2]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF015735.5 PF03795.19 YCII 24 24 95 domain Y Y N YciI family protein 12625841 131567 cellular organisms no rank 135233 EBI-EMBL YCII-related domain YciI family protein The majority of proteins in this family consist of a single copy of this domain, though it is also found as a repeat (Swiss:Q9AJZ7). A strongly conserved histidine and a aspartate suggest that the domain has an enzymatic function. This family also now includes the family formerly known as the DGPF domain (COG3795). Although its function is unknown it is found fused to a sigma-70 factor family domain in Swiss:Q9A8M4. Suggesting that this domain plays a role in transcription initiation (Bateman A per. obs.). This domain is named after the most conserved motif in the alignment. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF015736.5 PF03796.20 DnaB_C 27 27 255 domain Y Y N DnaB-like helicase C-terminal domain-containing protein GO:0003678,GO:0005524,GO:0006260 10645945 131567 cellular organisms no rank 117115 EBI-EMBL DnaB-like helicase C terminal domain DnaB-like helicase C terminal domain The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. (from Pfam) NF015737.5 PF03797.24 Autotransporter 26 26 255 domain Y Y N autotransporter domain-containing protein 11980709,15014442,3027577,9778731 131567 cellular organisms no rank 188076 EBI-EMBL Autotransporter beta-domain Autotransporter beta-domain Secretion of protein products occurs by a number of different pathways in bacteria. One of these pathways known as the type V pathway was first described for the IgA1 protease [2]. The protein component that mediates secretion through the outer membrane is contained within the secreted protein itself, hence the proteins secreted in this way are called autotransporters. This family corresponds to the presumed integral membrane beta-barrel domain that transports the protein. This domain is found at the C terminus of the proteins it occurs in. The N terminus contains the variable passenger domain that is translocated across the membrane. Once the passenger domain is exported it is cleaved auto-catalytically in some proteins, in others a different protease is used and in some cases no cleavage occurs [1]. [1]. 9778731. The great escape: structure and function of the autotransporter proteins. Henderson IR, Navarro-Garcia F, Nataro JP;. Trends Microbiol 1998;6:370-378. [2]. 3027577. Gene structure and extracellular secretion of Neisseria gonorrhoeae IgA protease. Pohlner J, Halter R, Beyreuther K, Meyer TF;. Nature 1987;325:458-462. [3]. 11980709. Export of autotransported proteins proceeds through an oligomeric ring shaped by C-terminal domains. Veiga E, Sugawara E, Nikaido H, de Lorenzo V, Fernandez LA;. EMBO J 2002;21:2122-2131. [4]. 15014442. Structure of the translocator domain of a bacterial autotransporter. Oomen CJ, Van Ulsen P, Van Gelder P, Feijen M, Tommassen J, Gros P;. EMBO J 2004;23:1257-1266. (from Pfam) NF015743.5 PF03803.20 Scramblase 25.4 25.4 221 subfamily Y Y N phospholipid scramblase-related protein GO:0017121,GO:0017128 11487015 131567 cellular organisms no rank 4686 EBI-EMBL Scramblase phospholipid scramblase-related protein Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury [1]. [1]. 11487015. Unraveling the mysteries of phospholipid scrambling. Sims PJ, Wiedmer T;. Thromb Haemost 2001;86:266-275. (from Pfam) NF015746.5 PF03806.18 ABG_transport 27 27 502 domain Y Y N AbgT family transporter GO:0015558,GO:1902604 131567 cellular organisms no rank 29420 EBI-EMBL AbgT putative transporter family AbgT family transporter NF015747.5 PF03807.22 F420_oxidored 21.6 21.6 94 domain Y Y N NAD(P)-binding domain-containing protein 131567 cellular organisms no rank 668498 EBI-EMBL NADP oxidoreductase coenzyme F420-dependent NADP oxidoreductase coenzyme F420-dependent NF015753.5 PF03814.20 KdpA 22.6 22.6 548 domain Y Y N potassium-transporting ATPase subunit KdpA 7.2.2.6 GO:0006813,GO:0008556 131567 cellular organisms no rank 52578 EBI-EMBL Potassium-transporting ATPase A subunit potassium-transporting ATPase subunit KdpA NF015755.5 PF03816.19 LytR_cpsA_psr 24.6 24.6 150 domain Y Y N LCP family protein 21964069 131567 cellular organisms no rank 177271 EBI-EMBL LytR_cpsA_psr family LCP family protein The entry represents a domain found in a number of LCP (LytR-Cps2A-Psr) family proteins. LCP family is also known as TagU family. LCP family proteins have been reported to be required for the synthesis of anionic cell wall polymers [1]. [1]. 21964069. A widespread family of bacterial cell wall assembly proteins. Kawai Y, Marles-Wright J, Cleverley RM, Emmins R, Ishikawa S, Kuwano M, Heinz N, Bui NK, Hoyland CN, Ogasawara N, Lewis RJ, Vollmer W, Daniel RA, Errington J;. EMBO J. 2011;30:4931-4941. (from Pfam) NF015758.5 PF03819.22 MazG 22 22 74 domain Y Y N MazG nucleotide pyrophosphohydrolase domain-containing protein 12218018 131567 cellular organisms no rank 100282 EBI-EMBL MazG nucleotide pyrophosphohydrolase domain MazG nucleotide pyrophosphohydrolase domain This domain is about 100 amino acid residues in length. It is found in the MazG protein from E. coli. It contains four conserved negatively charged residues that probably form an active site or metal binding site. This domain is found in isolation in some proteins as well as associated with Pfam:PF00590. This domain is clearly related to Pfam:PF01503 another pyrophosphohydrolase involved in histidine biosynthesis. This family may be structurally related to the NUDIX domain Pfam:PF00293 (Bateman A pers. obs.). [1]. 12218018. MazG, a nucleoside triphosphate pyrophosphohydrolase, interacts with Era, an essential GTPase in Escherichia coli. Zhang J, Inouye M;. J Bacteriol 2002;184:5323-5329. (from Pfam) NF015763.5 PF03824.21 NicO 27.7 27.7 287 domain Y N N High-affinity nickel-transport protein GO:0005886,GO:0015099,GO:0035444 7651142,7934894,8197192,8288539 131567 cellular organisms no rank 45659 EBI-EMBL High-affinity nickel-transport protein High-affinity nickel-transport protein High affinity nickel transporters involved in the incorporation of nickel into H2-uptake hydrogenase [2] and urease [3] enzymes. Essential for the expression of catalytically active hydrogenase and urease. Ion uptake is dependent on proton motive force. HoxN in Alcaligenes eutrophus is thought to be an integral membrane protein with seven transmembrane helices [4]. The family also includes a cobalt transporter. [1]. 8288539. Cloning, sequencing, and expression of thermophilic Bacillus sp. strain TB-90 urease gene complex in Escherichia coli. Maeda M, Hidaka M, Nakamura A, Masaki H, Uozumi T;. J Bacteriol 1994;176:432-442. [2]. 8197192. Bacterial genes involved in incorporation of nickel into a hydrogenase enzyme. Fu C, Javedan S, Moshiri F, Maier RJ;. Proc Natl Acad Sci U S A 1994;91:5099-5103. [3]. 7651142. Helicobacter pylori nickel-transport gene nixA: synthesis of catalytically active urease in Escherichia coli independent of growth conditions. Mobley HL, Garner RM, Bauerfeind P;. Mol Microbiol 1995;16:97-109. [4]. 7934894. A topological model for the high-affinity nickel transporter of Alcaligenes eutrophus. Eitinger T, Friedrich B;. Mol Microbiol 1994;12:1025-1032. (from Pfam) NF015772.5 PF03833.18 PolC_DP2 24.3 24.3 868 PfamEq Y N N DNA polymerase II large subunit DP2 131567 cellular organisms no rank 1526 EBI-EMBL DNA polymerase II large subunit DP2 DNA polymerase II large subunit DP2 NF015777.5 PF03838.19 RecU 25 25 162 PfamEq Y Y N Holliday junction resolvase RecU 3.1.21.10 GO:0006281 131567 cellular organisms no rank 10414 EBI-EMBL Recombination protein U Holliday junction resolvase RecU NF015780.5 PF03841.18 SelA 22.8 22.8 367 domain Y N N L-seryl-tRNA selenium transferase 131567 cellular organisms no rank 41597 EBI-EMBL L-seryl-tRNA selenium transferase L-seryl-tRNA selenium transferase NF015783.5 PF03845.18 Spore_permease 23.4 23.4 321 subfamily Y Y N GerAB/ArcD/ProY family transporter GO:0009847,GO:0016020 131567 cellular organisms no rank 99857 EBI-EMBL Spore germination protein GerAB/ArcD/ProY family transporter NF015786.5 PF03848.19 TehB 20.4 20.4 193 domain Y N N Tellurite resistance protein TehB 131567 cellular organisms no rank 157332 EBI-EMBL Tellurite resistance protein TehB Tellurite resistance protein TehB NF015789.5 PF03851.19 UvdE 24 24 275 domain Y N N UV-endonuclease UvdE GO:0004519,GO:0006289,GO:0009411 131567 cellular organisms no rank 10579 EBI-EMBL UV-endonuclease UvdE UV-endonuclease UvdE NF015790.5 PF03852.20 Vsr 27 27 74 domain Y N N DNA mismatch endonuclease Vsr GO:0004519,GO:0006298 131567 cellular organisms no rank 30579 EBI-EMBL DNA mismatch endonuclease Vsr DNA mismatch endonuclease Vsr NF015791.5 PF03853.20 YjeF_N 24.9 24.9 169 domain Y Y N NAD(P)H-hydrate epimerase 15257761 131567 cellular organisms no rank 80049 EBI-EMBL YjeF-related protein N-terminus NAD(P)H-hydrate epimerase YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases [1]. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and FLJ21128) [1], where they may be involved in decapping and catalyze hydrolytic RNA-processing reactions [1]. [1]. 15257761. Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability. Anantharaman V, Aravind L;. BMC Genomics. 2004;5:45. (from Pfam) NF015798.5 PF03860.21 DUF326 20.4 20.4 21 PfamAutoEq Y Y N four-helix bundle copper-binding protein 12625841 131567 cellular organisms no rank 10047 EBI-EMBL Domain of Unknown Function (DUF326) four-helix bundle copper-binding protein This family is a small cysteine-rich repeat. The cysteines mostly follow a C-X(2)-C-X(3)-C-X(2)-C-X(3) pattern, though they often appear at other positions in the repeat as well. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF015800.5 PF03862.18 SpoVAC_SpoVAEB 25 25 117 domain Y Y N SpoVA/SpoVAEb family sporulation membrane protein 11751839,24666282,27044622 131567 cellular organisms no rank 12081 EBI-EMBL SpoVAC/SpoVAEB sporulation membrane protein SpoVA/SpoVAEb family sporulation membrane protein Members of this family are all transcribed from the spoVA operon [1]. Bacillus and Clostridium are two well studied endospore forming bacteria. Spore formation provides a resistance mechanism in response to extreme or unfavourable environmental conditions such as heat, radiation, and chemical agents or nutrient deprivation. The reverse process termed germination takes place where spores develop into growing cells in response to nutrient availability or stress reduction. Nutrient germinant receptors (GRs) and the SpoVA proteins are important players in the germination process. In B.subtilis the SpoVAC and SpoVAEB, belonging to this domain family, are predicted to be membrane proteins, with two to five membrane spanning. Biophysical and biochemical studies suggest that SpoVAC acts as a mechano-sensitive channel with properties that would allow the release of Ca-DPA (dipicolinic acid) and amino acids during germination of the spore. The release of Ca-DPA is a crucial event during spore germination. When expressed in E.coli SpoVAC provides protection against osmotic downshift. Furthermore, SpoVAC acts as channel that facilitates the efflux down the concentration gradient of osmolytes up to a mass of at least 600 Da [2]. Another conserved SpoVA protein in all spore-forming bacteria is SpoVAEb, which appears to be an integral membrane protein with no known function [3]. [1]. 11751839. The products of the spoVA operon are involved in dipicolinic acid uptake into developing spores of Bacillus subtilis. Tovar-Rojo F, Chander M, Setlow B, Setlow P;. J Bacteriol 2002;184:584-587. [2]. 24666282. Bacillus subtilis spore protein SpoVAC. TRUNCATED at 1650 bytes (from Pfam) NF015812.5 PF03874.21 RNA_pol_Rpb4 25.6 25.6 116 PfamEq Y N N RNA polymerase Rpb4 GO:0006352,GO:0030880 11741548,12482973,16818233,8065349 131567 cellular organisms no rank 1167 EBI-EMBL RNA polymerase Rpb4 RNA polymerase Rpb4 This family includes the Rpb4 protein. This family also includes C17 (aka CGRP-RCP) is an essential subunit of RNA polymerase III. C17 forms a subcomplex with C25 [4] which is likely to be the counterpart of subcomplex Rpb4/7 in Pol II [3]. [1]. 11741548. Structure of an archaeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex. Todone F, Brick P, Werner F, Weinzierl RO, Onesti S;. Mol Cell 2001;8:1137-1143. [2]. 12482973. An Rpb4/Rpb7-like complex in yeast RNA polymerase III contains the orthologue of mammalian CGRP-RCP. Siaut M, Zaros C, Levivier E, Ferri ML, Court M, Werner M, Callebaut I, Thuriaux P, Sentenac A, Conesa C;. Mol Cell Biol. 2003;23:195-205. [3]. 8065349. C25, an essential RNA polymerase III subunit related to the RNA polymerase II subunit RPB7. Sadhale PP, Woychik NA;. Mol Cell Biol. 1994;14:6164-6170. [4]. 16818233. Structural biology of RNA polymerase III: subcomplex C17/25 X-ray structure and 11 subunit enzyme model. Jasiak AJ, Armache KJ, Martens B, Jansen RP, Cramer P;. Mol Cell. 2006;23:71-81. (from Pfam) NF015817.5 PF03880.20 DbpA 25.6 25.6 72 domain Y Y N DbpA RNA binding domain-containing protein 10481020,12460566 131567 cellular organisms no rank 69160 EBI-EMBL DbpA RNA binding domain DbpA RNA binding domain This RNA binding domain is found at the C-terminus of a number of DEAD helicase proteins [1]. It is sufficient to confer specificity for hairpin 92 of 23S rRNA, which is part of the ribosomal A-site. However, several members of this family lack specificity for 23S rRNA. These can proteins can generally be distinguished by a basic region that extends beyond this domain [Karl Kossen, unpublished data]. [1]. 10481020. Cloning and biochemical characterization of Bacillus subtilis YxiN, a DEAD protein specifically activated by 23S rRNA: delineation of a novel sub-family of bacterial DEAD proteins. Kossen K, Uhlenbeck OC;. Nucleic Acids Res 1999;27:3811-3820. [2]. 12460566. The carboxy-terminal domain of the DExDH protein YxiN is sufficient to confer specificity for 23S rRNA. Kossen K, Karginov FV, Uhlenbeck OC;. J Mol Biol 2002;324:625-636. (from Pfam) NF015818.5 PF03881.19 Fructosamin_kin 22.4 22.4 288 domain Y Y N fructosamine kinase family protein 11016445 131567 cellular organisms no rank 36668 EBI-EMBL Fructosamine kinase fructosamine kinase family protein This family includes eukaryotic fructosamine-3-kinase enzymes [1]. The family also includes bacterial members that have not been characterised but probably have a similar or identical function. [1]. 11016445. Identification, cloning, and heterologous expression of a mammalian fructosamine-3-kinase. Delpierre G, Rider MH, Collard F, Stroobant V, Vanstapel F, Santos H, Van Schaftingen E;. Diabetes 2000;49:1627-1634. (from Pfam) NF015820.5 PF03883.19 H2O2_YaaD 29.6 29.6 236 PfamEq Y Y N peroxide stress protein YaaA yaaA 21378183 131567 cellular organisms no rank 52475 EBI-EMBL Peroxide stress protein YaaA peroxide stress protein YaaA YaaA is a key element of the stress response to H2O2. It acts by reducing the level of intracellular iron levels after peroxide stress, thereby attenuating the Fenton reaction and the DNA damage that this would cause [1]. The molecular mechanism of action is not known. [1]. 21378183. The YaaA protein of the Escherichia coli OxyR regulon lessens hydrogen peroxide toxicity by diminishing the amount of intracellular unincorporated iron. Liu Y, Bauer SC, Imlay JA;. J Bacteriol. 2011;193:2186-2196. (from Pfam) NF015822.5 PF03885.18 DUF327 25.8 25.8 143 PfamAutoEq Y Y N DUF327 family protein 131567 cellular organisms no rank 4673 EBI-EMBL Protein of unknown function (DUF327) DUF327 family protein The proteins in this family are around 140-170 residues in length. The proteins contain many conserved residues. with the most conserved motifs found in the central and C-terminal region. The function of these proteins is unknown. (from Pfam) NF015825.5 PF03888.19 MucB_RseB 22.3 22.3 178 domain Y Y N sigma-E factor regulatory protein RseB domain-containing protein 17496148,8412698,8606151 131567 cellular organisms no rank 17114 EBI-EMBL MucB/RseB N-terminal domain MucB/RseB N-terminal domain Members of this family are regulators of the anti-sigma E protein RseD. [1]. 8412698. Differentiation of Pseudomonas aeruginosa into the alginate-producing form: inactivation of mucB causes conversion to mucoidy. Martin DW, Schurr MJ, Mudd MH, Deretic V;. Mol Microbiol 1993;9:497-506. [2]. 8606151. Characterization of the genes coding for the putative sigma factor AlgU and its regulators MucA, MucB, MucC, and MucD in Azotobacter vinelandii and evaluation of their roles in alginate biosynthesis. Martinez-Salazar JM, Moreno S, Najera R, Boucher JC, Espin G, Soberon-Chavez G, Deretic V;. J Bacteriol 1996;178:1800-1808. [3]. 17496148. Crystal structure of RseB and a model of its binding mode to RseA. Kim DY, Jin KS, Kwon E, Ree M, Kim KK;. Proc Natl Acad Sci U S A. 2007;104:8779-8784. (from Pfam) NF015835.5 PF03900.20 Porphobil_deamC 26 26 74 PfamEq Y N N Porphobilinogen deaminase, C-terminal domain GO:0004418,GO:0033014 131567 cellular organisms no rank 67630 EBI-EMBL Porphobilinogen deaminase, C-terminal domain Porphobilinogen deaminase, C-terminal domain NF015836.5 PF03901.22 Glyco_transf_22 23.8 23.8 414 domain Y N N Alg9-like mannosyltransferase family GO:0016757 10954751,12030331,12200473,9576863 131567 cellular organisms no rank 1830 EBI-EMBL Alg9-like mannosyltransferase family Alg9-like mannosyltransferase family Members of this family are mannosyltransferase enzymes [1-2]. At least some members are localised in endoplasmic reticulum and involved in GPI anchor biosynthesis [3-4]. [1]. 12030331. A mannosyltransferase gene at 11q23 is disrupted by a translocation breakpoint that co-segregates with bipolar affective disorder in a small family. Baysal BE, Willett-Brozick JE, Badner JA, Corona W, Ferrell RE, Nimgaonkar VL, Detera-Wadleigh SD;. Neurogenetics 2002;4:43-53. [2]. 12200473. Common origin and evolution of glycosyltransferases using Dol-P-monosaccharides as donor substrate. Oriol R, Martinez-Duncker I, Chantret I, Mollicone R, Codogno P;. Mol Biol Evol 2002;19:1451-1463. [3]. 10954751. Critical roles of glycosylphosphatidylinositol for Trypanosoma brucei. Nagamune K, Nozaki T, Maeda Y, Ohishi K, Fukuma T, Hara T, Schwarz RT, Sutterlin C, Brun R, Riezman H, Kinoshita T;. Proc Natl Acad Sci U S A 2000;97:10336-10341. [4]. 9576863. Saccharomyces cerevisiae GPI10, the functional homologue of human PIG-B, is required for glycosylphosphatidylinositol-anchor synthesis. Sutterlin C, Escribano MV, Gerold P, Maeda Y, Mazon MJ, Kinoshita T, Schwarz RT, Riezman H;. Biochem J 1998;332:153-159. (from Pfam) NF015846.5 PF03911.21 Sec61_beta 27 27 41 PfamEq Y Y N preprotein translocase subunit Sec61beta 11943537 131567 cellular organisms no rank 988 EBI-EMBL Sec61beta family preprotein translocase subunit Sec61beta This family consists of homologues of Sec61beta - a component of the Sec61/SecYEG protein secretory system. The domain is found in eukaryotes and archaea and is possibly homologous to the bacterial SecG. It consists of a single putative transmembrane helix, preceded by a short stretch containing various charged residues; this arrangement may help determine orientation in the cell membrane [1]. [1]. 11943537. Sec61beta - a component of the archaeal protein secretory system. Kinch LN, Saier MH Jr, Grishin NV;. Trends Biochem Sci 2002;27:170-171. (from Pfam) NF015851.5 PF03916.19 NrfD 25.8 25.8 313 domain Y Y N NrfD/PsrC family molybdoenzyme membrane anchor subunit nrfD 8057835 131567 cellular organisms no rank 33106 EBI-EMBL Polysulphide reductase, NrfD NrfD/PsrC family molybdoenzyme membrane anchor subunit Members of this family include the NF015853.5 PF03918.19 CcmH 25 25 143 domain Y Y N cytochrome c-type biogenesis protein CcmH 9914305 131567 cellular organisms no rank 31021 EBI-EMBL Cytochrome C biogenesis protein cytochrome c-type biogenesis protein CcmH Members of this family include NrfF, CcmH, CycL, Ccl2. [1]. 9914305. Characterization of the Escherichia coli CcmH protein reveals new insights into the redox pathway required for cytochrome c maturation. Fabianek RA, Hofer T, Thony-Meyer L;. Arch Microbiol 1999;171:92-100. (from Pfam) NF015859.5 PF03924.18 CHASE 25 25 189 domain Y Y N CHASE domain-containing protein 11590000,11590001 131567 cellular organisms no rank 37851 EBI-EMBL CHASE domain CHASE domain This domain is found in the extracellular portion of receptor-like proteins - such as serine/threonine kinases and adenylyl cyclases [1,2]. This is a ligand-binding domain that binds cytokinin (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 11590000. The CHASE domain: a predicted ligand-binding module in plant cytokinin receptors and other eukaryotic and bacterial receptors. Anantharaman V, Aravind L;. Trends Biochem Sci 2001;26:579-582. [2]. 11590001. CHASE: an extracellular sensing domain common to transmembrane receptors from prokaryotes, lower eukaryotes and plants. Mougel C, Zhulin IB;. Trends Biochem Sci 2001;26:582-584. (from Pfam) NF015862.5 PF03928.19 HbpS-like 25 25 128 domain Y Y N heme-binding protein 19244623,8606183 131567 cellular organisms no rank 64045 EBI-EMBL Haem degrading protein HbpS-like heme-binding protein This entry includes haem degrading protein HbpS from Streptomyces reticuli (swiss:Q9RIM2) and and GlcG from Escherichia coli [1]. HbpS is up-regulated in response to haemin- and peroxide-based oxidative stress. It interacts with the SenS/SenR two-component signal transduction system. Iron binds to surface-exposed lysine residues of an octomeric assembly of the protein [2]. The structure of GlcG is composed of an alpha-beta(2)-alpha(3)-beta(2)-alpha fold, similar to the Roadblock/LC7 domain. [1]. 8606183. glc locus of Escherichia coli: characterization of genes encoding the subunits of glycolate oxidase and the glc regulator protein. Pellicer MT, Badia J, Aguilar J, Baldoma L;. J Bacteriol 1996;178:2051-2059. [2]. 19244623. The oligomeric assembly of the novel haem-degrading protein HbpS is essential for interaction with its cognate two-component sensor kinase. Ortiz de Orue Lucana D, Bogel G, Zou P, Groves MR;. J Mol Biol. 2009;386:1108-1122. (from Pfam) NF015868.5 PF03935.21 SKN1_KRE6_Sbg1 30 30 501 domain Y N N Beta-glucan synthesis-associated protein SKN1/KRE6/Sbg1 GO:0006078 10601196,27749909,27898700 131567 cellular organisms no rank 5545 EBI-EMBL Beta-glucan synthesis-associated protein SKN1/KRE6/Sbg1 Beta-glucan synthesis-associated protein SKN1/KRE6/Sbg1 This family consists of the beta-glucan synthesis-associated proteins KRE6, SKN1 and Sbg1. Beta1,6-Glucan is a key component of the yeast cell wall, interconnecting cell wall proteins, beta1,3-glucan, and chitin. SKN1 and KRE6 show similarities to glycoside hydrolase family 16 glycoside hydrolases, suggesting that they are glycosyl hydrolases or transglycosylases. They are related with the synthesis and anchorage of cell wall proteins of glucan polymers of the yeast cell wall, although they play redundant roles [1,2]. SKN1, KRE6 and Sbg1 share the SKN1 domain which is conserved in SKN1 and KRE6 proteins of many fungal species. Sbg1 is an integral membrane protein essential for contractile-ring constriction and septum formation during cytokinesis, which interacts with the conserved beta-glucan synthase Bgs1 and regulates its protein levels ans localisation [2,3]. [1]. 10601196. Localization of synthesis of beta1,6-glucan in Saccharomyces cerevisiae. Montijn RC, Vink E, Muller WH, Verkleij AJ, Van Den Ende H, Henrissat B, Klis FM;. J Bacteriol 1999;181:7414-7420. [2]. 27749909. A New Membrane Protein Sbg1 Links the Contractile Ring Apparatus and Septum Synthesis Machinery in Fission Yeast. Sethi K, Palani S, Cortes JC, Sato M, Sevugan M, Ramos M, Vijaykumar S, Osumi M, Naqvi NI, Ribas JC, Balasubramanian M;. PLoS Genet. 2016;12:e1006383. [3]. 27898700. Sbg1 Is a Novel Regulator for the Localization of the beta-Glucan Synthase Bgs1 in Fission Yeast. Davidson R, Pontasch JA, Wu JQ;. PLoS One. 2016;11:e0167043. (from Pfam) NF015877.5 PF03944.19 Endotoxin_C 21 21 142 domain Y Y N delta endotoxin C-terminal domain-containing protein GO:0090729 1658659,9729609 131567 cellular organisms no rank 1556 EBI-EMBL delta endotoxin delta endotoxin This family contains insecticidal toxins produced by Bacillus species of bacteria. During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins they are activated by proteolytic cleavage. The N terminus is cleaved in all of the proteins and a C terminal extension is cleaved in some members. Once activated the endotoxin binds to the gut epithelium and causes cell lysis leading to death. This activated region of the delta endotoxin is composed of three structural domains. The N-terminal helical domain is involved in membrane insertion and pore formation. The second and third domains are involved in receptor binding. [1]. 1658659. Crystal structure of insecticidal delta-endotoxin from Bacillus thuringiensis at 2.5 angstroms resolution. Li J, Carroll J, Ellar DJ;. Nature 1991;353:815-821. [2]. 9729609. Bacillus thuringiensis and its pesticidal crystal proteins. Schnepf E, Crickmore N, Van Rie J, Lereclus D, Baum J, Feitelson J, Zeigler DR, Dean DH;. Microbiol Mol Biol Rev 1998;62:775-806. (from Pfam) NF015879.5 PF03946.19 Ribosomal_L11_N 32.9 32.9 58 PfamEq Y N N Ribosomal protein L11, N-terminal domain 131567 cellular organisms no rank 28886 EBI-EMBL Ribosomal protein L11, N-terminal domain Ribosomal protein L11, N-terminal domain The N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain. (from Pfam) NF015880.5 PF03947.23 Ribosomal_L2_C 33.7 33.7 126 PfamEq Y N N Ribosomal Proteins L2, C-terminal domain GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 35899 EBI-EMBL Ribosomal Proteins L2, C-terminal domain Ribosomal Proteins L2, C-terminal domain NF015882.5 PF03949.20 Malic_M 23.5 23.5 258 domain Y Y N malic enzyme-like NAD(P)-binding protein GO:0051287 131567 cellular organisms no rank 104975 EBI-EMBL Malic enzyme, NAD binding domain malic enzyme-like NAD(P)-binding domain Enzymes containing this domain include NAD and NADP-dependent forms of malic enzyme (EC 1.1.1.38 and EC 1.1.1.40), as well as malolactic enzyme (EC 4.1.1.101). NF015883.5 PF03950.23 tRNA-synt_1c_C 23.9 23.9 91 PfamEq Y N N tRNA synthetases class I (E and Q), anti-codon binding domain GO:0000166,GO:0004812,GO:0005524,GO:0005737,GO:0006418 9562563 131567 cellular organisms no rank 37443 EBI-EMBL tRNA synthetases class I (E and Q), anti-codon binding domain tRNA synthetases class I (E and Q), anti-codon binding domain This entry represents the first of the two ribosomal L25-like domains of the anticodon binding domain. Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln). [1]. 9562563. How glutaminyl-tRNA synthetase selects glutamine. Rath VL, Silvian LF, Beijer B, Sproat BS, Steitz TA;. Structure 1998;6:439-449. (from Pfam) NF015884.5 PF03951.24 Gln-synt_N 33.4 33.4 82 domain Y Y N glutamine synthetase beta-grasp domain-containing protein GO:0004356,GO:0006542,GO:0008152 131567 cellular organisms no rank 68238 EBI-EMBL Glutamine synthetase, beta-Grasp domain Glutamine synthetase, beta-Grasp domain NF015885.5 PF03952.21 Enolase_N 35 35 131 domain Y N N Enolase, N-terminal domain 131567 cellular organisms no rank 63830 EBI-EMBL Enolase, N-terminal domain Enolase, N-terminal domain NF015889.5 PF03956.18 Lys_export 23.8 23.8 190 domain Y Y N LysO family transporter GO:0015661,GO:1903401 25845847 131567 cellular organisms no rank 13340 EBI-EMBL Lysine exporter LysO LysO family transporter Members of this family contain a conserved core of four predicted transmembrane segments. Some members have an additional pair of N-terminal transmembrane helices. This family includes lysine exporter LysO (YbjE) from E. coli [1]. [1]. 25845847. Distinct Paths for Basic Amino Acid Export in Escherichia coli: YbjE (LysO) Mediates Export of L-Lysine. Pathania A, Sardesai AA;. J Bacteriol. 2015;197:2036-2047. (from Pfam) NF015892.5 PF03959.18 FSH1 21 21 211 domain Y N N Serine hydrolase (FSH1) 15802654 131567 cellular organisms no rank 38963 EBI-EMBL Serine hydrolase (FSH1) Serine hydrolase (FSH1) This is a family of serine hydrolases [1]. [1]. 15802654. Crystal structure of yeast YHR049W/FSH1, a member of the serine hydrolase family. Quevillon-Cheruel S, Leulliot N, Graille M, Hervouet N, Coste F, Benedetti H, Zelwer C, Janin J, Van Tilbeurgh H;. Protein Sci 2005;14:1350-1356. (from Pfam) NF015893.5 PF03960.20 ArsC 24 24 79 domain Y Y N ArsC/Spx/MgsR family protein 11709171,18643936,22904090 131567 cellular organisms no rank 93143 EBI-EMBL ArsC family ArsC/Spx/MgsR family protein Members of this family include both regulatory proteins such as Spx or MgsR and the arsenate reductase ArsC. Some ArsC proteins are selenoproteins. NF015898.5 PF03965.21 Penicillinase_R 22.6 22.6 115 domain Y Y N BlaI/MecI/CopY family transcriptional regulator GO:0003677,GO:0045892 8226686 131567 cellular organisms no rank 75946 EBI-EMBL Penicillinase repressor BlaI/MecI/CopY family transcriptional regulator The penicillinase repressor negatively regulates expression of the penicillinase gene. The N-terminal region of this protein is involved in operator recognition, while the C-terminal is responsible for dimerisation of the protein [1]. [1]. 8226686. Functional domains of the penicillinase repressor of Bacillus licheniformis. Wittman V, Lin HC, Wong HC;. J Bacteriol 1993;175:7383-7390. (from Pfam) NF015899.5 PF03966.21 Trm112p 22 22 40 domain Y Y N Trm112 family protein 15899842,17008308 131567 cellular organisms no rank 23474 EBI-EMBL Trm112p-like protein Trm112 family protein The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. Trm112p is required for tRNA methylation in S. cerevisiae and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W [1]. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast [2]. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices [2]. [1]. 15899842. Trm11p and Trm112p Are both Required for the Formation of 2-Methylguanosine at Position 10 in Yeast tRNA. Purushothaman SK, Bujnicki JM, Grosjean H, Lapeyre B;. Mol Cell Biol 2005;25:4359-4370. [2]. 17008308. The zinc finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast. Heurgue-Hamard V, Graille M, Scrima N, Ulryck N, Champ S, van Tilbeurgh H, Buckingham RH;. J Biol Chem. 2006;281:36140-36148. (from Pfam) NF015904.5 PF03971.19 IDH 25 25 734 PfamEq Y Y N NADP-dependent isocitrate dehydrogenase 1.1.1.42 GO:0004450,GO:0006099 7836312,8226630 131567 cellular organisms no rank 35025 EBI-EMBL Monomeric isocitrate dehydrogenase NADP-dependent isocitrate dehydrogenase NADP(+)-dependent isocitrate dehydrogenase (ICD) is an important enzyme of the intermediary metabolism, as it controls the carbon flux within the citric acid cycle and supplies the cell with 2-oxoglutarate EC:1.1.1.42 and NADPH for biosynthetic purposes [2]. [1]. 8226630. Genes encoding two isocitrate dehydrogenase isozymes of a psychrophilic bacterium, Vibrio sp. strain ABE-1. Ishii A, Suzuki M, Sahara T, Takada Y, Sasaki S, Fukunaga N;. J Bacteriol 1993;175:6873-6880. [2]. 7836312. Cloning, sequence analysis, expression, and inactivation of the Corynebacterium glutamicum icd gene encoding isocitrate dehydrogenase and biochemical characterization of the enzyme. Eikmanns BJ, Rittmann D, Sahm H;. J Bacteriol 1995;177:774-782. (from Pfam) NF015905.5 PF03972.19 MmgE_PrpD_N 32.1 32.1 244 domain Y Y N MmgE/PrpD family protein GO:0016829 11294638,16934291,18584171,28956599,31548418 131567 cellular organisms no rank 62162 EBI-EMBL MmgE/PrpD N-terminal domain MmgE/PrpD N-terminal domain This entry represents the N-terminal domain of 2-methylcitrate dehydratase EC:4.2.1.79 (PrpD) that is required for propionate catabolism. It catalyses the third step of the 2-methylcitric acid cycle [1]. This enzyme consists of two domains: a large domain with an all-helical fold and a smaller domain that folds into an alpha/beta domain [2]. Cis-aconitic acid decarboxylase (CAD) shares high identity with proteins of the MmgE/PrpD family [3,4]. Citrate/2-methylcitrate dehydratase from Bacillus subtilis is involved in the tricarboxylic acid (TCA) and methylcitric acid cycles as it has both 2-methylcitrate dehydratase and citrate dehydratase activities [5]. This entry represents the N-terminal domain of 2-methylcitrate dehydratase PrpD, which has an all-helical fold. [1]. 11294638. In vitro conversion of propionate to pyruvate by Salmonella enterica enzymes: 2-methylcitrate dehydratase (PrpD) and aconitase Enzymes catalyze the conversion of 2-methylcitrate to 2-methylisocitrate. Horswill AR, Escalante-Semerena JC;. Biochemistry 2001;40:4703-4713. [2]. 16934291. Three-dimensional structure of iminodisuccinate epimerase defines the fold of the MmgE/PrpD protein family. Lohkamp B, Bauerle B, Rieger PG, Schneider G;. J Mol Biol. 2006;362:555-566. [3]. 31548418. Crystal structure of cis-aconitate decarboxylase reveals the impact of naturally occurring human mutations on itaconate synthesis. Chen F, Lukat P, Iqbal AA, Saile K, Kaever V, van den Heuvel J, Blankenfeldt W, Bussow K, Pessler F;. Proc Natl Acad Sci U S A. 2019;116:20644-20654. [4]. 18584171. Cloning and functional characterization of the cis-aconitic acid decarboxylase. TRUNCATED at 1650 bytes (from Pfam) NF015908.5 PF03975.18 CheD 25 25 108 domain Y N N CheD chemotactic sensory transduction GO:0006935,GO:0050568 12011078,16469702,17908686,8866475 131567 cellular organisms no rank 17564 EBI-EMBL CheD chemotactic sensory transduction CheD chemotactic sensory transduction This chemotaxis protein stimulates methylation of MCP proteins [1]. The chemotaxis machinery of Bacillus subtilis is similar to that of the well characterised system of Escherichia coli. However, B. subtilis contains several chemotaxis genes not found in the E. coli genome, such as CheC and CheD, indicating that the B. subtilis chemotactic system is more complex. CheD plays an important role in chemotactic sensory transduction for many organisms. CheD deamidates other B. subtilis chemoreceptors including McpB and McpC. Deamidation by CheD is required for B. subtilis chemoreceptors to effectively transduce signals to the CheA kinase [2]. The structure of a complex between the signal-terminating phosphatase, CheC, and the receptor-modifying deamidase, CheD, reveals how CheC mimics receptor substrates to inhibit CheD and how CheD stimulates CheC phosphatase activity. CheD resembles other cysteine deamidases from bacterial pathogens that inactivate host Rho-GTPases. Phospho-CheY, the intracellular signal and CheC target, stabilises the CheC-CheD complex and reduces availability of CheD [3]. A model is proposed whereby CheC acts as a CheY-P-induced regulator of CheD; CheY-P would cause CheC to sequester CheD from the chemoreceptors, inducing adaptation of the chemotaxis system [4]. [1]. 8866475. CheC and CheD interact to regulate methylation of Bacillus subtilis methyl-accepting chemotaxis proteins. Rosario MM, Ordal GW;. Mol Microbiol 1996;21:511-518. [2]. 12011078. Bacillus subtilis CheD is a chemoreceptor modification enzyme required for chemotaxis. Kristich CJ, Ordal GW;. J Biol Chem. 2002;277:25356-25362. [3]. 16469702. A . TRUNCATED at 1650 bytes (from Pfam) NF015909.5 PF03976.19 PPK2 22.3 22.3 229 domain Y N N Polyphosphate kinase 2 (PPK2) 12482933,12486232,19001261 131567 cellular organisms no rank 74296 EBI-EMBL Polyphosphate kinase 2 (PPK2) Polyphosphate kinase 2 (PPK2) Inorganic polyphosphate (polyP) plays a role in metabolism and regulation and has been proposed to serve as a energy source in a pre-ATP world. In prokaryotes, the synthesis and utilisation of polyP are catalysed by PPK1, PPK2 and polyphosphatases. Proteins with a single PPK2 domain catalyse polyP-dependent phosphorylation of ADP to ATP, whereas proteins containing 2 fused PPK2 domains phosphorylate AMP to ADP. The structure of PPK2 from Pseudomonas aeruginosa has revealed a a 3-layer alpha/beta/alpha sandwich fold with an alpha-helical lid similar to the structures of microbial thymidylate kinases [3]. [1]. 12486232. A polyphosphate kinase (PPK2) widely conserved in bacteria. Zhang H, Ishige K, Kornberg A;. Proc Natl Acad Sci U S A 2002;99:16678-16683. [2]. 12482933. Polyphosphate kinase (PPK2), a potent, polyphosphate-driven generator of GTP. Ishige K, Zhang H, Kornberg A;. Proc Natl Acad Sci U S A 2002;99:16684-16688. [3]. 19001261. Polyphosphate-dependent synthesis of ATP and ADP by the family-2 polyphosphate kinases in bacteria. Nocek B, Kochinyan S, Proudfoot M, Brown G, Evdokimova E, Osipiuk J, Edwards AM, Savchenko A, Joachimiak A, Yakunin AF;. Proc Natl Acad Sci U S A. 2008;105:17730-17735. (from Pfam) NF015910.5 PF03977.18 OAD_beta 31.6 31.6 349 subfamily Y Y N sodium ion-translocating decarboxylase subunit beta 7.2.4.- GO:0006814,GO:0016829 2549031,9428714 131567 cellular organisms no rank 27227 EBI-EMBL Na+-transporting oxaloacetate decarboxylase beta subunit sodium ion-translocating decarboxylase subunit beta Members of this family are integral membrane proteins. The decarboxylation reactions they catalyse are coupled to the vectorial transport of Na+ across the cytoplasmic membrane, thereby creating a sodium ion motive force that is used for ATP synthesis [2]. [1]. 2549031. The sodium ion translocating oxaloacetate decarboxylase of Klebsiella pneumoniae. Sequence of the integral membrane-bound subunits beta and gamma. Laussermair E, Schwarz E, Oesterhelt D, Reinke H, Beyreuther K, Dimroth P;. J Biol Chem 1989;264:14710-14715. [2]. 9428714. Methylmalonyl-CoA decarboxylase from Propionigenium modestum--cloning and sequencing of the structural genes and purification of the enzyme complex. Bott M, Pfister K, Burda P, Kalbermatter O, Woehlke G, Dimroth P;. Eur J Biochem 1997;250:590-599. (from Pfam) NF015912.5 PF03979.19 Sigma70_r1_1 22.5 22.5 81 domain Y Y N RNA polymerase sigma factor region1.1 domain-containing protein GO:0003677,GO:0006355 10613885,9927430 131567 cellular organisms no rank 37692 EBI-EMBL Sigma-70 factor, region 1.1 Sigma-70 factor, region 1.1 Region 1.1 modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [1,2]. Region 1.1 is also involved in promoter binding [1] [1]. 9927430. A mutation in region 1.1 of sigma70 affects promoter DNA binding by Escherichia coli RNA polymerase holoenzyme. Bowers CW, Dombroski AJ;. EMBO J 1999;18:709-716. [2]. 10613885. Effects of amino acid substitutions at conserved and acidic residues within region 1.1 of Escherichia coli sigma(70). Bowers CW, McCracken A, Dombroski AJ;. J Bacteriol 2000;182:221-224. (from Pfam) NF015917.5 PF03984.18 DUF346 22 22 39 repeat Y N N DUF346 repeat protein 12625841,27758853,33765407 131567 cellular organisms no rank 1782 EBI-EMBL Repeat of unknown function (DUF346) DUF346 repeat protein This repeat is found as seven tandem copies in carbohydrate-binding proteins, including Fucose-binding Lectin from Photorhabdus laumondii (Swiss:Q7N8J0) and similar fungal and bacterial proteins. It is composed of beta-strands and forms a seven-bladed beta-propeller structure [2,3]. It is found in association with BNR repeats, which also form a beta-propeller. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. [2]. 27758853. A Novel Fucose-binding Lectin from Photorhabdus luminescens (PLL) with an Unusual Heptabladed beta-Propeller Tetrameric Structure. Kumar A, Sykorova P, Demo G, Dobes P, Hyrsl P, Wimmerova M;. J Biol Chem. 2016;291:25032-25049. [3]. 33765407. Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions. Gajdos L, Blakeley MP, Kumar A, Wimmerova M, Haertlein M, Forsyth VT, Imberty A, Devos JM;. Structure. 2021;29:1003-1013. (from Pfam) NF015921.5 PF03988.17 DUF347 28.2 28.2 52 repeat Y N N DUF347 repeat membrane protein 12625841 131567 cellular organisms no rank 17491 EBI-EMBL Repeat of Unknown Function (DUF347) DUF347 repeat This repeat is found as four tandem repeats in a family of bacterial membrane proteins. Each repeat contains two transmembrane regions and a conserved tryptophan. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF015922.5 PF03989.18 DNA_gyraseA_C 27 6.1 48 domain Y Y N DNA gyrase C-terminal beta-propeller domain-containing protein GO:0003677,GO:0003916,GO:0005524,GO:0006265 11948780,1657531 131567 cellular organisms no rank 142198 EBI-EMBL DNA gyrase C-terminal domain, beta-propeller DNA gyrase C-terminal domain, beta-propeller This repeat is found as 6 tandem copies at the C-termini of GyrA and ParC DNA gyrases. It is predicted to form 4 beta strands and to probably form a beta-propeller structure [1]. This region has been shown to bind DNA non-specifically and may stabilise the DNA-topoisomerase complex [2]. [1]. 11948780. C-terminal domain of gyrase A is predicted to have a beta-propeller structure. Qi Y, Pei J, Grishin NV;. Proteins 2002;47:258-264. [2]. 1657531. DNA gyrase: structure and function. Reece RJ, Maxwell A;. Crit Rev Biochem Mol Biol 1991;26:335-375. (from Pfam) NF015925.5 PF03992.21 ABM 23.1 20.9 78 domain Y Y N antibiotic biosynthesis monooxygenase 12625841 131567 cellular organisms no rank 195089 EBI-EMBL Antibiotic biosynthesis monooxygenase antibiotic biosynthesis monooxygenase This domain is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species. It's occurrence as a repeat in Streptomyces coelicolor SCO1909 (Swiss:Q9X9W3) is suggestive that the other proteins function as multimers. There is also a conserved histidine which is likely to be an active site residue. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF015927.5 PF03994.19 DUF350 22.2 22.2 55 domain Y Y N DUF350 domain-containing protein 12625841 131567 cellular organisms no rank 18844 EBI-EMBL Domain of Unknown Function (DUF350) Domain of Unknown Function (DUF350) This domain occurs in a small set of of bacterial proteins. It has two transmembrane regions, and often occurs as tandem repeats. The are no conserved catalytic residues. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF015928.5 PF03995.18 Inhibitor_I36 21.1 21.1 69 domain Y Y N peptidase inhibitor family I36 protein 12625841,9735297 131567 cellular organisms no rank 27414 EBI-EMBL Peptidase inhibitor family I36 peptidase inhibitor family I36 protein This domain is currently only found in a small set of S. coelicolor secreted proteins. There are four conserved cysteines that probably form two disulphide bonds. Proteins 2SCK31.15C (Swiss:Q9ADK5) and SCO3675 (Swiss:Q9X8V7) also have probable beta-propellers at their C-termini. This family includes Swiss:P01077 a known peptidase inhibitor of known structure. This protein has a crystallin like fold Pfam:PF00030 and is distantly related by sequence. It is not known whether other members of this family are peptidase inhibitors. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. [2]. 9735297. NMR structure of the Streptomyces metalloproteinase inhibitor, SMPI, isolated from Streptomyces nigrescens TK-23: another example of an ancestral beta gamma-crystallin precursor structure. Ohno A, Tate S, Seeram SS, Hiraga K, Swindells MB, Oda K, Kainosho M;. J Mol Biol 1998;282:421-433. (from Pfam) NF015935.5 PF04002.20 RadC 22.1 22.1 121 domain Y Y N JAB domain-containing protein 10224240,11053371,21890906 131567 cellular organisms no rank 80947 EBI-EMBL RadC-like JAB domain RadC-like JAB domain A family of proteins present widely across the bacteria. This family was named initially with reference to the E. coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions [1]. However the relevant mutation has subsequently been shown to be in recG, where radC is in fact an allele of recG [2]. In addition, a personal communication from Claverys, J-P, et al, indicates a total failure of all attempts to characterise a radiation-related function for RadC in Streptococcus pneumoniae, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair. Computational analysis, however, provides a possible function. The RadC-like family belong to the JAB superfamily of metalloproteins [3]. The domain shows fusions to an N-terminal Helix-hairpin-Helix (HhH) domain in most instances. Other domain combinations include fusions to the anti-restriction module ArdC, the DinG/RAD3-like superfamily II helicases and the DNAG-like primase. In some bacteria, closely related DinG/Rad3- like superfamily II helicases are fused to a 3'-5' exonuclease in the same position as the RadC-like JAB domain. These conserved domain associations lead to the hypothesis that the RadC-like JAB domains might function as a nuclease [3]. [1]. 10224240. Tandem repeat recombination induced by replication fork defects in Escherichia coli requires a novel factor, RadC. Saveson CJ, Lovett ST;. Genetics 1999;152:5-13. [2]. 11053371. radC102 of Escherichia coli is an allele of recG. Lombardo MJ, Rosenberg SM;. J Bacteriol. 2000;182:6287-6291. [3]. 21890906. Evolu. TRUNCATED at 1650 bytes (from Pfam) NF015940.5 PF04007.17 DUF354 22 22 349 domain Y Y N DUF354 domain-containing protein 131567 cellular organisms no rank 3138 EBI-EMBL Protein of unknown function (DUF354) Protein of unknown function (DUF354) Members of this family are around 350 amino acids in length. They are found in archaebacteria and have no known function. (from Pfam) NF015941.5 PF04008.19 Adenosine_kin 25 25 154 PfamEq Y Y N adenosine-specific kinase 16737961 131567 cellular organisms no rank 2138 EBI-EMBL Adenosine specific kinase adenosine-specific kinase The structure of a member of this family from the hyperthermophilic archaeon Pyrobaculum aerophilum contains a modified histidine residue which is interpreted as stable phosphorylation [1]. In vitro binding studies confirmed that adenosine and AMP but not ADP or ATP bind to the protein [1]. [1]. 16737961. The structure of an ancient conserved domain establishes a structural basis for stable histidine phosphorylation and identifies a new family of adenosine-specific kinases. Lott JS, Paget B, Johnston JM, Delbaere LT, Sigrell-Simon JA, Banfield MJ, Baker EN;. J Biol Chem. 2006;281:22131-22141. (from Pfam) NF015944.5 PF04011.17 LemA 26.2 26.2 149 domain Y Y N LemA family protein 8758895 131567 cellular organisms no rank 43380 EBI-EMBL LemA family LemA family protein The members of this family are related to the LemA protein Swiss:P71452 [1]. LemA contains an amino terminal predicted transmembrane helix. It has been predicted that the small amino terminus is extracellular [1]. The exact molecular function of this protein is uncertain. [1]. 8758895. Identification of an H2-M3-restricted Listeria epitope: implications for antigen presentation by M3. Lenz LL, Dere B, Bevan MJ;. Immunity 1996;5:63-72. (from Pfam) NF015945.5 PF04012.17 PspA_IM30 33.9 33.9 220 domain Y Y N PspA/IM30 family protein 10629175,12079332 131567 cellular organisms no rank 43234 EBI-EMBL PspA/IM30 family PspA/IM30 family protein This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma(54) containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [2]. [1]. 10629175. The PspA protein of Escherichia coli is a negative regulator of sigma(54)-dependent transcription. Dworkin J, Jovanovic G, Model P;. J Bacteriol 2000;182:311-319. [2]. 12079332. Mechanism of Action of the Escherichia coli Phage Shock Protein PspA in Repression of the AAA Family Transcription Factor PspF. Elderkin S, Jones S, Schumacher J, Studholme D, Buck M;. J Mol Biol 2002;320:23-37. (from Pfam) NF015946.5 PF04013.17 Methyltrn_RNA_2 25.5 25.5 198 PfamEq Y N N Putative SAM-dependent RNA methyltransferase GO:0008175 21098051,22274954 131567 cellular organisms no rank 1912 EBI-EMBL Putative SAM-dependent RNA methyltransferase Putative SAM-dependent RNA methyltransferase This family is likely to be an S-adenosyl-L-methionine (SAM)-dependent RNA methyltransferase [1]. It is responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs [2]. [1]. 21098051. Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class RNA methyltransferase. Chen HY, Yuan YA;. J Mol Cell Biol. 2010;2:366-374. [2]. 22274954. Identification of the enzyme responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs. Wurm JP, Griese M, Bahr U, Held M, Heckel A, Karas M, Soppa J, Wohnert J;. RNA. 2012;18:412-420. (from Pfam) NF015947.5 PF04014.23 MazE_antitoxin 24.7 24.7 48 domain Y Y N AbrB/MazE/SpoVT family DNA-binding domain-containing protein GO:0003677 12718874,15101989,22140099 131567 cellular organisms no rank 56875 EBI-EMBL Antidote-toxin recognition MazE, bacterial antitoxin AbrB/MazE/SpoVT family DNA-binding domain AbrB-like is a family of small proteins that operate in conjunction with a cognate toxin molecule. The commonly attributed role of toxin-antitoxin systems is to maintain low-copy number plasmids from one generation to the next. Such gene-pairs are also found on chromosomes and to be associated with a number of biological functions such as: reduction of protein synthesis, gene regulation and retardation of cell growth under nutritional stress [1]. This family includes proteins from a number of different pairings, eg MazE, AbrB, VapB [2], PhoU, PemI-like and SpoVT. MazE is the antidote to the toxin MazF of E. coli. MazE-MazF in E. coli is a regulated prokaryotic chromosomal addiction module. MazE antidote is degraded by the ClpPA protease of the bacterial proteasome. MazE-MazF is thought to play a role in programmed cell death when cells suffer nutrient deprivation [3], and MazE-MazF modules have also been implicated in the bacteriostatic effects of other addiction modules [3]. [1]. 15101989. Identification of AbrB-regulated genes involved in biofilm formation by Bacillus subtilis. Hamon MA, Stanley NR, Britton RA, Grossman AD, Lazazzera BA;. Mol Microbiol. 2004;52:847-860. [2]. 22140099. Crystal structure of the DNA-bound VapBC2 antitoxin/toxin pair from Rickettsia felis. Mate MJ, Vincentelli R, Foos N, Raoult D, Cambillau C, Ortiz-Lombardia M;. Nucleic Acids Res. 2012;40:3245-3258. [3]. 12718874. Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition. Kamada K, Hanaoka F, Burley SK;. Mol Cell. 2003;11:875-884. (from Pfam) NF015948.5 PF04015.17 DUF362 24 24 200 domain Y Y N DUF362 domain-containing protein 131567 cellular organisms no rank 16429 EBI-EMBL Domain of unknown function (DUF362) Domain of unknown function (DUF362) Domain that is sometimes present in iron-sulphur proteins. (from Pfam) NF015949.5 PF04016.17 DUF364 23 23 147 domain Y Y N Rossmann-like domain-containing protein 20944207 131567 cellular organisms no rank 6838 EBI-EMBL Putative heavy-metal chelation Putative heavy-metal chelation This domain of unknown function has a PLP-dependent transferase-like fold. Its genomic context suggests that it may have a role in anaerobic vitamin B12 biosynthesis. This domain is often found at the C-terminus of proteins containing DUF4213, Pfam:PF13938. The structure of UnioProtKB:B8FUJ5, PDB:3l5o, suggests that the protein has an enolase N-terminal-like fold and this Rossmann-like C-terminal domain. Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The protein may be playing a role in heavy-metal chelation [1]. [1]. 20944207. Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation. Miller MD, Aravind L, Bakolitsa C, Rife CL, Carlton D, Abdubek P, Astakhova T, Axelrod HL, Chiu HJ, Clayton T, Deller MC, Duan L, Feuerhelm J, Grant JC, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Reyes R, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:1167-1173. (from Pfam) NF015950.5 PF04017.17 DUF366 29.9 29.9 184 PfamAutoEq Y Y N DUF366 family protein 131567 cellular organisms no rank 540 EBI-EMBL Domain of unknown function (DUF366) DUF366 family protein Archaeal domain of unknown function. (from Pfam) NF015951.5 PF04018.18 VCA0040-like 26 26 246 PfamAutoEq Y Y N undecaprenyl phosphate translocase family protein 36450355 131567 cellular organisms no rank 18669 EBI-EMBL Undecaprenyl phosphate translocase-like undecaprenyl phosphate translocase family protein This family represents a group of prokaryotic proteins associated with transmembrane transport of undecaprenyl phosphate lipids, which is required for the biogenesis of microbial cell surface polymers, including VCA0040 (Swiss:Q9KNC5) from Vibrio cholerae [1]. Family members have between 6 and 9 predicted transmembrane segments. [1]. 36450355. Undecaprenyl phosphate translocases confer conditional microbial fitness. Sit B, Srisuknimit V, Bueno E, Zingl FG, Hullahalli K, Cava F, Waldor MK;. Nature. 2023;613:721-728. (from Pfam) NF015952.5 PF04019.17 DUF359 25 25 126 PfamAutoEq Y Y N DUF359 domain-containing protein GO:0015937,GO:0016301 131567 cellular organisms no rank 1372 EBI-EMBL Protein of unknown function (DUF359) Protein of unknown function (DUF359) This family of archaebacterial proteins are about 170 amino acids in length. They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its function. (from Pfam) NF015953.5 PF04020.18 Phage_holin_4_2 28.8 28.8 105 domain Y Y N phage holin family protein 23043507 131567 cellular organisms no rank 33728 EBI-EMBL Mycobacterial 4 TMS phage holin, superfamily IV phage holin family protein These proteins are predicted transmembrane proteins with probably four transmembrane spans. The 1.E.40 is represented by the mycobacterial 4 phage holin, but it also contains many cyanobacterial. proteobacterial and firmicute proteins. Holins are encoded within the genomes of Gram-positive and Gram-negative bacteria as well as in those of the bacteriophage of these organisms. The primary function of holins appears to be transport of murein hydrolases across the cytoplasmic membrane to the cell wall where these enzymes hydrolyse the cell wall polymer as a prelude to cell lysis. When chromosomally encoded the enzymes are therefore autolysins. Holins may also facilitate leakage of electrolytes and nutrients from the cell cytoplasm, thereby promoting cell death. Some may catalyse export of nucleases. [1]. 23043507. Diversity in bacterial lysis systems: bacteriophages show the way. Catalao MJ, Gil F, Moniz-Pereira J, Sao-Jose C, Pimentel M;. FEMS Microbiol Rev. 2012; [Epub ahead of print] (from Pfam) NF015954.5 PF04021.17 Class_IIIsignal 23.7 23.7 27 domain Y Y N class III signal peptide-containing protein 17114255 131567 cellular organisms no rank 1284 EBI-EMBL Class III signal peptide Class III signal peptide This family of archaeal proteins contains. an amino terminal motif QXSXEXXXL that has been suggested to be part of a class III signal sequence. With the Q being the +1 residue of the signal peptidase cleavage site [1]. Two members of this family are cleaved by a type IV pilin-like signal peptidase. [1]. 17114255. Identification of diverse archaeal proteins with class III signal peptides cleaved by distinct archaeal prepilin peptidases. Szabo Z, Stahl AO, Albers SV, Kissinger JC, Driessen AJ, Pohlschroder M;. J Bacteriol. 2007;189:772-778. (from Pfam) NF015956.5 PF04023.19 FeoA 23 23 74 domain Y Y N FeoA domain-containing protein GO:0046914 8407793 131567 cellular organisms no rank 59825 EBI-EMBL FeoA domain FeoA domain This family includes FeoA a small protein, probably involved in Fe2+ transport [1]. This presumed short domain is also found at the C-terminus of a variety of metal dependent transcriptional regulators. This suggests that this domain may be metal-binding. In most cases this is likely to be either iron or manganese. [1]. 8407793. Characterization of the ferrous iron uptake system of Escherichia coli. Kammler M, Schon C, Hantke K;. J Bacteriol 1993;175:6212-6219. (from Pfam) NF015957.5 PF04024.17 PspC 25 25 58 domain Y Y N PspC domain-containing protein 1712397 131567 cellular organisms no rank 68502 EBI-EMBL PspC domain PspC domain This family includes Phage shock protein C (PspC) that is thought to be a transcriptional regulator. The presumed domain is 60 amino acid residues in length. [1]. 1712397. Characterization and sequence of the Escherichia coli stress-induced psp operon. Brissette JL, Weiner L, Ripmaster TL, Model P;. J Mol Biol 1991;220:35-48. (from Pfam) NF015959.5 PF04026.17 SpoVG 29.6 29.6 82 domain Y Y N septation protein SpoVG family protein GO:0030435 1373326,8755892 131567 cellular organisms no rank 5895 EBI-EMBL SpoVG septation protein SpoVG family protein Stage V sporulation protein G. Essential for sporulation and specific to stage V sporulation in Bacillus megaterium and subtilis [2]. In B. subtilis, expression decreases after 30-60 minutes of cold shock [1]. [1]. 8755892. Cold shock stress-induced proteins in Bacillus subtilis. Graumann P, Schroder K, Schmid R, Marahiel MA;. J Bacteriol 1996;178:4611-4619. [2]. 1373326. spoVG sequence of Bacillus megaterium and Bacillus subtilis. Hudspeth DS, Vary PS;. Biochim Biophys Acta 1992;1130:229-231. (from Pfam) NF015960.5 PF04027.18 DUF371 25 25 133 PfamAutoEq Y Y N DUF371 domain-containing protein 131567 cellular organisms no rank 1388 EBI-EMBL Domain of unknown function (DUF371) Domain of unknown function (DUF371) Archaeal domain of unknown function. (from Pfam) NF015962.5 PF04029.19 2-ph_phosp 26.4 26.4 226 domain Y Y N 2-phosphosulfolactate phosphatase GO:0000287,GO:0050532 11589710 131567 cellular organisms no rank 17704 EBI-EMBL 2-phosphosulpholactate phosphatase 2-phosphosulfolactate phosphatase Thought to catalyse 2-phosphosulpholactate = sulpholactate + phosphate. Probable magnesium cofactor. Involved in the second step of coenzyme M biosynthesis. Inhibited by vanadate in Methanococcus jannaschii. Also known as the ComB family [1]. [1]. 11589710. Identification of coenzyme M biosynthetic 2-phosphosulfolactate phosphatase. A member of a new class of Mg(2+)-dependent acid phosphatases. Graham DE, Graupner M, Xu H, White RH;. Eur J Biochem 2001;268:5176-5188. (from Pfam) NF015963.5 PF04030.19 ALO 23.1 23.1 258 domain Y Y N D-arabinono-1,4-lactone oxidase GO:0003885,GO:0016020 10094636 131567 cellular organisms no rank 43599 EBI-EMBL D-arabinono-1,4-lactone oxidase D-arabinono-1,4-lactone oxidase This domain is specific to D-arabinono-1,4-lactone oxidase EC:1.1.3.- , which is involved in the final step of the D-erythroascorbic acid biosynthesis pathway [1]. [1]. 10094636. D-Erythroascorbic acid is an important antioxidant molecule in Saccharomyces cerevisiae. Huh WK, Lee BH, Kim ST, Kim YR, Rhie GE, Baek YW, Hwang CS, Lee JS, Kang SO;. Mol Microbiol 1998;30:895-903. (from Pfam) NF015965.5 PF04032.21 Rpr2 29.3 29.3 90 PfamEq Y N N RNAse P Rpr2/Rpp21/SNM1 subunit domain GO:0006396 10523674,11497433 131567 cellular organisms no rank 1263 EBI-EMBL RNAse P Rpr2/Rpp21/SNM1 subunit domain RNAse P Rpr2/Rpp21/SNM1 subunit domain This family contains a ribonuclease P subunit of humans and yeast. Other members of the family include the probable archaeal homologues. This family includes SNM1 [2]. It is a subunit of RNase MRP (mitochondrial RNA processing), a ribonucleoprotein endoribonuclease that has roles in both mitochondrial DNA replication and nuclear 5.8S rRNA processing. SNM1 is an RNA binding protein that binds the MRP RNA specifically [2]. This subunit possibly binds the precursor tRNA [1]. [1]. 11497433. Function and subnuclear distribution of Rpp21, a protein subunit of the human ribonucleoprotein ribonuclease P. Jarrous N, Reiner R, Wesolowski D, Mann H, Guerrier-Takada C, Altman S;. RNA 2001;7:1153-1164. [2]. 10523674. Mutagenesis of SNM1, which encodes a protein component of the yeast RNase MRP, reveals a role for this ribonucleoprotein endoribonuclease in plasmid segregation. Cai T, Reilly TR, Cerio M, Schmitt ME;. Mol Cell Biol 1999;19:7857-7869. (from Pfam) NF015966.5 PF04033.17 DUF365 25.9 25.9 96 domain Y Y N DUF365 domain-containing protein 131567 cellular organisms no rank 122 EBI-EMBL Domain of unknown function (DUF365) Domain of unknown function (DUF365) Archaeal domain of unknown function. (from Pfam) NF015967.5 PF04034.18 Ribo_biogen_C 29.9 29.9 127 PfamAutoEq Y Y N ribosome biogenesis domain-containing protein 25566315 131567 cellular organisms no rank 1186 EBI-EMBL Ribosome biogenesis protein, C-terminal Ribosome biogenesis protein, C-terminal This family represents the C-terminal domain of some putative ribosome biogenesis proteins in archaea. It has also been identified in the eukaryotic protein Tsr3, which is involved in ribosomal RNA biogenesis [1]. [1]. 25566315. Analysis of two domains with novel RNA-processing activities throws light on the complex evolution of ribosomal RNA biogenesis. Burroughs AM, Aravind L;. Front Genet. 2014;5:424. (from Pfam) NF015970.5 PF04039.18 MnhB 22.5 22.5 127 domain Y Y N MnhB domain-containing protein 11356194,9852009 131567 cellular organisms no rank 43003 EBI-EMBL Domain related to MnhB subunit of Na+/H+ antiporter Domain related to MnhB subunit of Na+/H+ antiporter Possible subunit of Na+/H+ antiporter [1], [2]. Predicted integral membrane protein, usually four transmembrane regions in this domain. Often found in bacterial NADH dehydrogenase subunit. [1]. 9852009. A putative multisubunit Na+/H+ antiporter from Staphylococcus aureus. Hiramatsu T, Kodama K, Kuroda T, Mizushima T, Tsuchiya T;. J Bacteriol 1998;180:6642-6648. [2]. 11356194. Mrp-dependent Na(+)/H(+) antiporters of Bacillus exhibit characteristics that are unanticipated for completely secondary active transporters. Ito M, Guffanti AA, Krulwich TA;. FEBS Lett 2001;496:117-120. (from Pfam) NF015971.5 PF04041.18 Glyco_hydro_130 26 26 320 domain Y N N beta-1,4-mannooligosaccharide phosphorylase 11093261,21539815,23093406,23943617 131567 cellular organisms no rank 21384 EBI-EMBL beta-1,4-mannooligosaccharide phosphorylase beta-1,4-mannooligosaccharide phosphorylase This is a family of glycosyl-hydrolases of the CAZy GH130 family. Several have been characterised as mannosylglucose phosphorylase [2,3,4]. This enzyme is part of the mannan catalytic pathway and feeds into the glycolysis cycle [2]. Specifically it catalyses the reversible phosphorolysis of beta-1,4-D-mannosyl-N-acetyl-D-glucosamine [4]. This family was noted to belong to the Beta fructosidase superfamily in [1]. [1]. 11093261. beta-fructosidase superfamily: homology with some alpha-L-arabinases and beta-D-xylosidases. Naumoff DG;. Proteins. 2001;42:66-76. [2]. 21539815. New microbial mannan catabolic pathway that involves a novel mannosylglucose phosphorylase. Senoura T, Ito S, Taguchi H, Higa M, Hamada S, Matsui H, Ozawa T, Jin S, Watanabe J, Wasaki J, Ito S;. Biochem Biophys Res Commun. 2011;408:701-706. [3]. 23093406. Metabolic mechanism of mannan in a ruminal bacterium, Ruminococcus albus, involving two mannoside phosphorylases and cellobiose 2-epimerase: discovery of a new carbohydrate phosphorylase, beta-1,4-mannooligosaccharide phosphorylase. Kawahara R, Saburi W, Odaka R, Taguchi H, Ito S, Mori H, Matsui H;. J Biol Chem. 2012;287:42389-42399. [4]. 23943617. Discovery of beta-1,4-D-mannosyl-N-acetyl-D-glucosamine phosphorylase involved in the metabolism of N-glycans. Nihira T, Suzuki E, Kitaoka M, Nishimoto M, Ohtsubo K, Nakai H;. J Biol Chem. 2013;288:27366-27374. (from Pfam) NF015972.5 PF04042.21 DNA_pol_E_B 29.1 29.1 210 PfamEq Y N N DNA polymerase alpha/epsilon subunit B GO:0003677,GO:0006260 11872158,8621497 131567 cellular organisms no rank 1381 EBI-EMBL DNA polymerase alpha/epsilon subunit B DNA polymerase alpha/epsilon subunit B This family contains a number of DNA polymerase subunits. The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast. The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18. Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure [1]. [1]. 11872158. The Second Largest Subunit of Mouse DNA Polymerase epsilon, DPE2, Interacts with SAP18 and Recruits the Sin3 Co-Repressor Protein to DNA. Wada M, Miyazawa H, Wang RS, Mizuno T, Sato A, Asashima M, Hanaoka F;. J Biochem (Tokyo) 2002;131:307-311. [2]. 8621497. Phosphorylation of the DNA polymerase alpha-primase B subunit is dependent on its association with the p180 polypeptide. Ferrari M, Lucchini G, Plevani P, Foiani M;. J Biol Chem 1996;271:8661-8666. (from Pfam) NF015983.5 PF04055.26 Radical_SAM 29.5 29.5 166 domain Y Y N radical SAM protein GO:0003824,GO:0051539 11222759,16766528,17335281 131567 cellular organisms no rank 1145486 EBI-EMBL Radical SAM superfamily radical SAM domain Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. [1]. 11222759. Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE;. Nucleic Acids Res 2001;29:1097-1106. [2]. 17335281. Anaerobic sulfatase-maturating enzymes: radical SAM enzymes able to catalyze in vitro sulfatase post-translational modification. Benjdia A, Leprince J, Guillot A, Vaudry H, Rabot S, Berteau O;. J Am Chem Soc. 2007;129:3462-3463. [3]. 16766528. A new type of bacterial sulfatase reveals a novel maturation pathway in prokaryotes. Berteau O, Guillot A, Benjdia A, Rabot S;. J Biol Chem. 2006;281:22464-22470. (from Pfam) NF015984.5 PF04056.19 Ssl1 27 27 193 PfamEq Y N N Ssl1-like 7891722 131567 cellular organisms no rank 46 EBI-EMBL Ssl1-like Ssl1-like Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex. [1]. 7891722. The yeast TFB1 and SSL1 genes, which encode subunits of transcription factor IIH, are required for nucleotide excision repair and RNA polymerase II transcription. Wang Z, Buratowski S, Svejstrup JQ, Feaver WJ, Wu X, Kornberg RD, Donahue TF, Friedberg EC;. Mol Cell Biol 1995;15:2288-2293. (from Pfam) NF015987.5 PF04060.18 FeS 23 23 33 domain Y Y N (Fe-S)-binding protein GO:0051536 131567 cellular organisms no rank 31321 EBI-EMBL Putative Fe-S cluster (Fe-S)-binding protein This family includes a domain with four conserved cysteines that probably form an Fe-S redox cluster. (from Pfam) NF015993.5 PF04066.18 MrpF_PhaF 23.3 23.3 53 subfamily Y Y N monovalent cation/H+ antiporter complex subunit F GO:0015075,GO:0016020,GO:0034220 10198001,11356194,9680201 131567 cellular organisms no rank 26040 EBI-EMBL Multiple resistance and pH regulation protein F (MrpF / PhaF) monovalent cation/H+ antiporter complex subunit F Members of the PhaF / MrpF family are predicted to be an integral membrane proteins with three transmembrane regions, involved in regulation of pH. PhaF is part of a potassium efflux system involved in pH regulation. It is also involved in symbiosis in Rhizobium meliloti [1]. MrpF is part of a Na+/H+ antiporter complex, also involved in pH homeostasis. MrpF is thought to be an efflux system for Na+ and cholate [2]. The Mrp system in Bacilli may also have primary energisation capacities [3]. [1]. 9680201. The pha gene cluster of Rhizobium meliloti involved in pH adaptation and symbiosis encodes a novel type of K+ efflux system. Putnoky P, Kereszt A, Nakamura T, Endre G, Grosskopf E, Kiss P, Kondorosi A;. Mol Microbiol 1998;28:1091-1101. [2]. 10198001. mrp, a multigene, multifunctional locus in Bacillus subtilis with roles in resistance to cholate and to Na+ and in pH homeostasis. Ito M, Guffanti AA, Oudega B, Krulwich TA;. J Bacteriol 1999;181:2394-2402. [3]. 11356194. Mrp-dependent Na(+)/H(+) antiporters of Bacillus exhibit characteristics that are unanticipated for completely secondary active transporters. Ito M, Guffanti AA, Krulwich TA;. FEBS Lett 2001;496:117-120. (from Pfam) NF015994.5 PF04068.20 RLI 23 23 35 domain Y N N Possible Fer4-like domain in RNase L inhibitor, RLI 7539425,9524254 131567 cellular organisms no rank 2398 EBI-EMBL Possible Fer4-like domain in RNase L inhibitor, RLI Possible Fer4-like domain in RNase L inhibitor, RLI Possible metal-binding domain in endoribonuclease RNase L inhibitor. Found at the N-terminal end of RNase L inhibitor proteins, adjacent to the 4Fe-4S binding domain, fer4, Pfam:PF00037. Also often found adjacent to the DUF367 domain Pfam:PF04034 in uncharacterised proteins. The RNase L system plays a major role in the anti-viral and anti-proliferative activities of interferons [1], and could possibly play a more general role in the regulation of RNA stability in mammalian cells. Inhibitory activity requires concentration-dependent association of RLI with RNase L [2]. [1]. 9524254. cDNA cloning and expression analysis of the murine ribonuclease L inhibitor. Benoit De Coignac A, Bisbal C, Lebleu B, Salehzada T;. Gene 1998;209:149-156. [2]. 7539425. Cloning and characterization of a RNAse L inhibitor. A new component of the interferon-regulated 2-5A pathway. Bisbal C, Martinand C, Silhol M, Lebleu B, Salehzada T;. J Biol Chem 1995;270:13308-13317. (from Pfam) NF015995.5 PF04069.17 OpuAC 21.2 21.2 257 domain Y Y N glycine betaine ABC transporter substrate-binding protein GO:0022857,GO:0043190,GO:0055085 10216873,11055912,7622480 131567 cellular organisms no rank 229939 EBI-EMBL Substrate binding domain of ABC-type glycine betaine transport system glycine betaine ABC transporter substrate-binding protein Part of a high affinity multicomponent binding-protein-dependent transport system involved in bacterial osmoregulation. This domain is often fused to the permease component of the transporter complex. Family members are often integral membrane proteins or predicted to be attached to the membrane by a lipid anchor. Glycine betaine is involved in protection from high osmolarity environments for example in Bacillus subtilis [1]. The family member OpuBC is closely related, and involved in choline transport. Choline is necessary for the biosynthesis of glycine betaine [2]. L-carnitine is important for osmoregulation in Listeria monocytogenes. Family also contains proteins binding l-proline (ProX), histidine (HisX) and taurine (TauA). [1]. 7622480. OpuA, an osmotically regulated binding protein-dependent transport system for the osmoprotectant glycine betaine in Bacillus subtilis. Kempf B, Bremer E;. J Biol Chem 1995;270:16701-16713. [2]. 10216873. Two evolutionarily closely related ABC transporters mediate the uptake of choline for synthesis of the osmoprotectant glycine betaine in Bacillus subtilis. Kappes RM, Kempf B, Kneip S, Boch J, Gade J, Meier-Wagner J, Bremer E;. Mol Microbiol 1999;32:203-216. [3]. 11055912. Identification and characterization of an ATP binding cassette L-carnitine transporter in Listeria monocytogenes. Fraser KR, Harvie D, Coote PJ, O'Byrne CP;. Appl Environ Microbiol 2000;66:4696-4704. (from Pfam) NF015996.5 PF04070.17 DUF378 25 25 60 domain Y Y N DUF378 domain-containing protein 131567 cellular organisms no rank 6032 EBI-EMBL Domain of unknown function (DUF378) Domain of unknown function (DUF378) Predicted transmembrane domain of unknown function. The majority of the family have two predicted transmembrane regions. (from Pfam) NF015997.5 PF04071.17 zf-like 27 27 82 domain Y Y N cysteine-rich small domain-containing protein 131567 cellular organisms no rank 2198 EBI-EMBL Cysteine-rich small domain Cysteine-rich small domain Probable metal-binding domain. (from Pfam) NF015998.5 PF04072.19 LCM 22.3 22.3 187 domain Y Y N class I SAM-dependent methyltransferase 2.1.1.- GO:0008168 131567 cellular organisms no rank 54469 EBI-EMBL Leucine carboxyl methyltransferase class I SAM-dependent methyltransferase Family of leucine carboxyl methyltransferases EC:2.1.1.- . This family may need divides a the full alignment contains a significantly shorter mouse sequence. (from Pfam) NF015999.5 PF04073.20 tRNA_edit 25.5 25.5 123 domain Y Y N YbaK/EbsC family protein GO:0002161 10813833,14663147,15886196,16087664,21768119 131567 cellular organisms no rank 171281 EBI-EMBL Aminoacyl-tRNA editing domain Aminoacyl-tRNA editing domain This domain is found either on its own or in association with the tRNA synthetase class II core domain (Pfam:PF00587). It is involved in the tRNA editing of mis-charged tRNAs including Cys-tRNA(Pro), Cys-tRNA(Cys), Ala-tRNA(Pro)[2-5]. The structure of this domain shows a novel fold [1]. [1]. 10813833. Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications. Zhang H, Huang K, Li Z, Banerjei L, Fisher KE, Grishin NV, Eisenstein E, Herzberg O;. Proteins 2000;40:86-97. [2]. 15886196. The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNA Cys deacylase. Ruan B, Soll D;. J Biol Chem. 2005;280:25887-25891. [3]. 14663147. Trans-editing of mischarged tRNAs. Ahel I, Korencic D, Ibba M, Soll D;. Proc Natl Acad Sci U S A. 2003;100:15422-15427. [4]. 16087664. Cys-tRNA(Pro) editing by Haemophilus influenzae YbaK via a novel synthetase.YbaK.tRNA ternary complex. An S, Musier-Forsyth K;. J Biol Chem. 2005;280:34465-34472. [5]. 21768119. Substrate-mediated fidelity mechanism ensures accurate decoding of proline codons. So BR, An S, Kumar S, Das M, Turner DA, Hadad CM, Musier-Forsyth K;. J Biol Chem. 2011;286:31810-31820. (from Pfam) NF016001.5 PF04075.19 F420H2_quin_red 22 22 130 subfamily Y Y N nitroreductase/quinone reductase family protein GO:0016491 16387854,19039139,23240649 131567 cellular organisms no rank 65580 EBI-EMBL F420H(2)-dependent quinone reductase nitroreductase family deazaflavin-dependent oxidoreductase This family of proteins is found in the genera Mycobacterium and Streptomyces. Member protein Rv3547 has been characterised as a deazaflavin-dependent nitroreductase [1, 2]. Rv1558 is an F420H(2)-dependent quinone reductase involved in oxidative stress protection [3]. [1]. 16387854. Identification of a nitroimidazo-oxazine-specific protein involved in PA-824 resistance in Mycobacterium tuberculosis. Manjunatha UH, Boshoff H, Dowd CS, Zhang L, Albert TJ, Norton JE, Daniels L, Dick T, Pang SS, Barry CE 3rd;. Proc Natl Acad Sci U S A. 2006;103:431-436. [2]. 19039139. PA-824 kills nonreplicating Mycobacterium tuberculosis by intracellular NO release. Singh R, Manjunatha U, Boshoff HI, Ha YH, Niyomrattanakit P, Ledwidge R, Dowd CS, Lee IY, Kim P, Zhang L, Kang S, Keller TH, Jiricek J, Barry CE 3rd;. Science. 2008;322:1392-1395. [3]. 23240649. A novel F(420) -dependent anti-oxidant mechanism protects Mycobacterium tuberculosis against oxidative stress and bactericidal agents. Gurumurthy M, Rao M, Mukherjee T, Rao SP, Boshoff HI, Dick T, Barry CE 3rd, Manjunatha UH;. Mol Microbiol. 2013;87:744-755. (from Pfam) NF016003.5 PF04077.17 DsrH 24.4 24.4 88 subfamily Y Y N DsrH/TusB family sulfur metabolism protein GO:0002143,GO:0005737 9695921 131567 cellular organisms no rank 9655 EBI-EMBL DsrH like protein DsrH/TusB family sulfur metabolism protein DsrH is involved in oxidation of intracellular sulphur in the phototrophic sulphur bacterium Chromatium vinosum D [1]. [1]. 9695921. Sirohaem sulfite reductase and other proteins encoded by genes at the dsr locus of Chromatium vinosum are involved in the oxidation of intracellular sulfur. Pott AS, Dahl C;. Microbiology 1998;144:1881-1894. (from Pfam) NF016005.5 PF04079.21 SMC_ScpB 27.4 27.4 160 PfamEq Y Y N SMC-Scp complex subunit ScpB GO:0051304 23353789,23541893 131567 cellular organisms no rank 54370 EBI-EMBL Segregation and condensation complex subunit ScpB SMC-Scp complex subunit ScpB This is a family of prokaryotic proteins that form one of the subunits, ScpB, of the segregation and condensation complex, condensin, that plays a key role in the maintenance of the chromosome. In prokaryotes the complex consists of three proteins, SMC, ScpA (kleisin) and ScpB. ScpB dimerises and binds to ScpA. As originally predicted, ScpB is structurally a winged-helix at both its N- and C-terminal halves. IN Bacillus subtilis,one Smc dimer is bridged by a single ScpAB to generate asymmetric tripartite rings analogous to eukaryotic SMC complex ring-shaped assemblies [1,2]. [1]. 23353789. An asymmetric SMC-kleisin bridge in prokaryotic condensin. Burmann F, Shin HC, Basquin J, Soh YM, Gimenez-Oya V, Kim YG, Oh BH, Gruber S;. Nat Struct Mol Biol. 2013;20:371-379. [2]. 23541893. Molecular basis of SMC ATPase activation: role of internal structural changes of the regulatory subcomplex ScpAB. Kamada K, Miyata M, Hirano T;. Structure. 2013;21:581-594. (from Pfam) NF016013.5 PF04087.19 DUF389 23.9 23.9 137 domain Y Y N DUF389 domain-containing protein 131567 cellular organisms no rank 26289 EBI-EMBL Domain of unknown function (DUF389) Domain of unknown function (DUF389) Family of hypothetical bacterial proteins with an undetermined function. (from Pfam) NF016021.5 PF04095.21 NAPRTase 20.8 20.8 239 domain Y N N Nicotinate phosphoribosyltransferase (NAPRTase) family 10825532 131567 cellular organisms no rank 59491 EBI-EMBL Nicotinate phosphoribosyltransferase (NAPRTase) family Nicotinate phosphoribosyltransferase (NAPRTase) family Nicotinate phosphoribosyltransferase (EC:2.4.2.11) is the rate limiting enzyme that catalyses the first reaction in the NAD salvage synthesis. This family also includes Pre-B cell enhancing factor that is a cytokine Swiss:P43490. This family is related to Quinolinate phosphoribosyltransferase Pfam:PF01729. [1]. 10825532. Salvage pathway for NAD biosynthesis in Brevibacterium ammoniagenes: regulatory properties of triphosphate-dependent nicotinate phosphoribosyltransferase. Dulyaninova NG, Podlepa EM, Toulokhonova1 LV, Bykhovsky VY;. Biochim Biophys Acta 2000;1478:211-220. (from Pfam) NF016027.5 PF04101.21 Glyco_tran_28_C 22 22 166 domain Y Y N glycosyltransferase GO:0016758 1649817 131567 cellular organisms no rank 168812 EBI-EMBL Glycosyltransferase family 28 C-terminal domain glycosyltransferase family 28 C-terminal domain The sequences scoring highest to this HMM are C-terminal regions of MurG enzymes (undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase), including the UDP-GlcNAc binding site. Those enzymes belong to glycosyltransferase family 28, but lower scoring members of this family include glycosyltransferases from other families that transfer different sugars. NF016028.5 PF04102.17 SlyX 30 30 67 PfamEq Y Y N SlyX family protein 131567 cellular organisms no rank 13372 EBI-EMBL SlyX SlyX family protein The SlyX protein has no known function. It is short less than 80 amino acids and is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C-terminus. The protein may be a coiled-coil structure. (from Pfam) NF016030.5 PF04104.19 DNA_primase_lrg 22.4 22.4 266 PfamEq Y N N Eukaryotic and archaeal DNA primase, large subunit GO:0006269 16027112,16273105,2023935,2528682,8026492 131567 cellular organisms no rank 1530 EBI-EMBL Eukaryotic and archaeal DNA primase, large subunit Eukaryotic and archaeal DNA primase, large subunit DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 (58 kDa in the yeast S. cerevisiae) [1]. The large subunit of DNA primase forms interactions with the small subunit and the structure implicates that it is not directly involved in catalysis, but plays roles in correctly positioning the primase/DNA complex, and in the transfer of RNA to DNA polymerase [4]. [1]. 2528682. A single essential gene, PRI2, encodes the large subunit of DNA primase in Saccharomyces cerevisiae. Foiani M, Santocanale C, Plevani P, Lucchini G;. Mol Cell Biol 1989;9:3081-3087. [2]. 2023935. Mutations in conserved yeast DNA primase domains impair DNA replication in vivo. Francesconi S, Longhese MP, Piseri A, Santocanale C, Lucchini G, Plevani P;. Proc Natl Acad Sci U S A 1991;88:3877-3881. [3]. 8026492. DNA replication in vitro by recombinant DNA-polymerase-alpha-primase. Stadlbauer F, Brueckner A, Rehfuess C, Eckerskorn C, Lottspeich F, Forster V, Tseng BY, Nasheuer HP;. Eur J Biochem 1994;222:781-793. [4]. 16273105. Structure of the heterodimeric core primase. Lao-Sirieix SH, Nookala RK, Roversi P, Bell SD, Pellegrini L;. Nat Struct Mol Biol. 2005;12:1137-1144. [5]. 16027112. Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Iyer LM, Koonin EV, Leipe DD, Aravind L;. Nucleic Acids Res. 2005;33:3875-3896. (from Pfam) NF016032.5 PF04107.18 GCS2 21 21 291 subfamily Y Y N glutamate-cysteine ligase family protein GO:0004357,GO:0042398 7937837 131567 cellular organisms no rank 74956 EBI-EMBL Glutamate-cysteine ligase family 2(GCS2) glutamate-cysteine ligase family protein Most members of this family are glutamate-cysteine ligases. but the family also includes members such as YbdK from Escherichia coli K-12, a carboxylate-amine ligase whose glutamate-cysteine ligase activity is weak and may not be its physiologically relevant activity. NF016041.5 PF04116.18 FA_hydroxylase 31 31 132 domain Y Y N sterol desaturase family protein GO:0005506,GO:0008610,GO:0016491 10344195,10431816,1864507,26515067,8552601,8718622,9353282 131567 cellular organisms no rank 84446 EBI-EMBL Fatty acid hydroxylase sterol desaturase family protein This entry includes fatty acid and carotene hydroxylases and sterol desaturases. Beta-carotene hydroxylase is involved in zeaxanthin synthesis by hydroxylating beta-carotene, but the enzyme may be involved in other pathways [1]. This family includes C-5 sterol desaturase and C-4 sterol methyl oxidase [2,3,6]. Members of this family are involved in cholesterol biosynthesis and biosynthesis a plant cuticular wax [4]. These enzymes contain two copies of a HXHH motif which coordinate two irons at the catalytic centre. Members of this family are ER integral membrane proteins that share a novel mushroom-shaped fold consisting of four transmembrane (TM1-TM4) helices that anchor them to the membrane capped by a cytosolic domain containing the unique histidine- coordinating di metal centre [5]. [1]. 9353282. Fah1p, a Saccharomyces cerevisiae cytochrome b5 fusion protein, and its Arabidopsis thaliana homolog that lacks the cytochrome b5 domain both function in the alpha-hydroxylation of sphingolipid-associated very long chain fatty acids. Mitchell AG, Martin CE;. J Biol Chem 1997;272:28281-28288. [1]. 10431816. The zeaxanthin biosynthesis enzyme beta-carotene hydroxylase is involved in myxoxanthophyll synthesis in Synechocystis sp. PCC 6803. Lagarde D, Vermaas W;. FEBS Lett 1999;454:247-251. [2]. 1864507. Cloning, disruption and sequence of the gene encoding yeast C-5 sterol desaturase. Arthington BA, Bennett LG, Skatrud PL, Guynn CJ, Barbuch RJ, Ulbright CE, Bard M;. Gene 1991;102:39-44. [3]. 8552601. Cloning and characterization of ERG25, the Saccharomyces cerevisiae gene encoding C-4 sterol methyl oxidase. Bard M, Bruner DA, Pier. TRUNCATED at 1650 bytes (from Pfam) NF016048.5 PF04123.18 DUF373 28.3 28.3 335 subfamily Y Y N DUF373 family protein 131567 cellular organisms no rank 1779 EBI-EMBL Domain of unknown function (DUF373) DUF373 family protein Archaeal domain of unknown function. Predicted to be an integral membrane protein with six transmembrane regions. (from Pfam) NF016050.5 PF04126.18 Cyclophil_like 27 27 120 domain Y Y N cyclophilin-like family protein 16544291,17610131 131567 cellular organisms no rank 3286 EBI-EMBL Cyclophilin-like cyclophilin-like family protein This domain has a cyclophilin-like fold, consisting of an eight-stranded beta-barrel with an alpha helix located between the beta-2 and beta-3 strands and a 310 helix located between the beta-7 and beta-8 strands. The catalytic site found in human cyclophilin is not conserved in this domain, suggesting a different function for this domain [1,2]. [1]. 16544291. Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold. Jin KK, Krishna SS, Schwarzenbacher R, McMullan D, Abdubek P, Agarwalla S, Ambing E, Axelrod H, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Feuerhelm J, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife C, Stevens RC, Spraggon G, van den Bedem H, Velasquez J, White A, Wolf G, Han GW, Xu Q, Hodgson KO, Wooley J, Wilson IA;. Proteins. 2006;63:1112-1118. [2]. 17610131. Hypothetical protein AF2241 from Archaeoglobus fulgidus adopts a cyclophilin-like fold. Ai X, Li L, Semesi A, Yee A, Arrowsmith CH, Li SS, Choy WY;. J Biomol NMR. 2007;38:353-358. (from Pfam) NF016051.5 PF04127.20 DFP 22 22 186 domain Y Y N phosphopantothenoylcysteine decarboxylase 3123465 131567 cellular organisms no rank 82473 EBI-EMBL DNA / pantothenate metabolism flavoprotein phosphopantothenoylcysteine decarboxylase The DNA/pantothenate metabolism flavoprotein (EC:4.1.1.36) affects synthesis of DNA, and pantothenate metabolism. [1]. 3123465. beta-Alanine auxotrophy associated with dfp, a locus affecting DNA synthesis in Escherichia coli. Spitzer ED, Jimenez-Billini HE, Weiss B;. J Bacteriol 1988;170:872-876. (from Pfam) NF016054.5 PF04131.19 NanE 27 27 192 domain Y N N Putative N-acetylmannosamine-6-phosphate epimerase GO:0006051,GO:0047465 9864311 131567 cellular organisms no rank 19524 EBI-EMBL Putative N-acetylmannosamine-6-phosphate epimerase Putative N-acetylmannosamine-6-phosphate epimerase This family represents a putative ManNAc-6-P-to-GlcNAc-6P epimerase in the N-acetylmannosamine (ManNAc) utilisation pathway found mainly in pathogenic bacteria. [1]. 9864311. Convergent pathways for utilization of the amino sugars N-acetylglucosamine, N-acetylmannosamine, and N-acetylneuraminic acid by Escherichia coli. Plumbridge J, Vimr E;. J Bacteriol 1999;181:47-54. (from Pfam) NF016056.5 PF04134.17 DCC1-like 27.8 27.8 113 domain Y Y N DCC1-like thiol-disulfide oxidoreductase family protein GO:0015035 28724620 131567 cellular organisms no rank 42950 EBI-EMBL DCC1-like thiol-disulfide oxidoreductase DCC1-like thiol-disulfide oxidoreductase family protein Members of this family have two highly conserved cysteine residues within the DxxCxxC motif at the N-terminal. This motif is conserved in the thiol-disulfide oxidoreductase family [1]. This family includes At5g50100 (also known as DCC1) from Arabidopsis thaliana, a thioredoxin that modulates ROS homeostasis resulting in de novo shoot initiation and may be involved in the improvement of the capacity of plant regeneration [1]. Uncharacterised proteins from bacteria are also included in this family. [1]. 28724620. Thioredoxin-Mediated ROS Homeostasis Explains Natural Variation in Plant Regeneration. Zhang H, Zhang TT, Liu H, Shi Y, Wang M, Bie XM, Li XG, Zhang XS;. Plant Physiol. 2018;176:2231-2250. (from Pfam) NF016060.5 PF04138.19 GtrA 26.1 26.1 117 domain Y Y N GtrA family protein GO:0000271,GO:0016020 10358040,10376843,11029438 131567 cellular organisms no rank 106516 EBI-EMBL GtrA-like protein GtrA family protein Members of this family are predicted to be integral membrane proteins with three or four transmembrane spans. They are involved in the synthesis of cell surface polysaccharides. The GtrA family are a subset of this family. GtrA is predicted to be an integral membrane protein with 4 transmembrane spans. It is involved is in O antigen modification by Shigella flexneri bacteriophage X (SfX), but does not determine the specificity of glucosylation. Its function remains unknown, but it may play a role in translocation of undecaprenyl phosphate linked glucose (UndP-Glc) across the cytoplasmic membrane [1]. Another member of this family is a DTDP-glucose-4-keto-6-deoxy-D-glucose reductase, which catalyses the conversion of dTDP-4-keto-6-deoxy-D-glucose to dTDP-D-fucose, which is involved in the biosynthesis of the serotype-specific polysaccharide antigen of Actinobacillus actinomycetemcomitans Y4 (serotype b)[2]. This family also includes the teichoic acid glycosylation protein, GtcA, which is a serotype-specific protein in some Listeria innocua and monocytogenes strains. Its exact function is not known, but it is essential for decoration of cell wall teichoic acids with glucose and galactose [3]. [1]. 10376843. Functional analysis of the O antigen glucosylation gene cluster of Shigella flexneri bacteriophage SfX. Guan S, Bastin DA, Verma NK;. Microbiology 1999;145:1263-1273. [2]. 10358040. A novel NDP-6-deoxyhexosyl-4-ulose reductase in the pathway for the synthesis of thymidine diphosphate-D-fucose. Yoshida Y, Nakano Y, Nezu T, Yamashita Y, Koga T;. J Biol Chem 1999;274:16933-16939. [3]. 11029438. A sheep in wolf's clothing. TRUNCATED at 1650 bytes (from Pfam) NF016062.5 PF04140.19 ICMT 24 24 95 domain Y Y N isoprenylcysteine carboxylmethyltransferase family protein GO:0004671,GO:0006481,GO:0016020 11451995 131567 cellular organisms no rank 46021 EBI-EMBL Isoprenylcysteine carboxyl methyltransferase (ICMT) family isoprenylcysteine carboxylmethyltransferase family protein The isoprenylcysteine o-methyltransferase (EC:2.1.1.100) family carry out carboxyl methylation of cleaved eukaryotic proteins that terminate in a CaaX motif. In Saccharomyces cerevisiae this methylation is carried out by Ste14p, an integral endoplasmic reticulum membrane protein. Ste14p is the founding member of the isoprenylcysteine carboxyl methyltransferase (ICMT) family, whose members share significant sequence homology [1]. [1]. 11451995. Topological and mutational analysis of Saccharomyces cerevisiae Ste14p, founding member of the isoprenylcysteine carboxyl methyltransferase family. Romano JD, Michaelis S;. Mol Biol Cell 2001;12:1957-1971. (from Pfam) NF016064.5 PF04143.19 Sulf_transp 27 27 310 domain Y Y N YeeE/YedE thiosulfate transporter family protein 21183667 131567 cellular organisms no rank 62687 EBI-EMBL Sulphur transport YeeE/YedE thiosulfate transporter family protein YeeE (TsuA) and YedE are paralogous transporters in E. coli that differ substantially. Both show evidence of an internal duplication, with the strongest similarity being between the N-terminal half of YeeE and the C-terminal half of YedE. YeeE, with partner sulfurtransferase YeeD (TsuB), are involved in thiosulfate utilization. Some members of the broader family are selenoproteins, which is observed only rarely for transporter families. NF016071.5 PF04151.20 PPC 25.9 25.9 70 domain Y Y N pre-peptidase C-terminal domain-containing protein 12625841 131567 cellular organisms no rank 47716 EBI-EMBL Bacterial pre-peptidase C-terminal domain Bacterial pre-peptidase C-terminal domain This domain is normally found at the C-terminus of secreted bacterial peptidases. They are not present in the active peptidase. It is possible that they fulfill a similar role to the PKD (Pfam:PF00801) domain, which also are found in this context. Visual analysis suggests that PKD and PPC are distantly related (personal obs:Bateman A, Yeats C). [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF016083.5 PF04165.17 DUF401 24 24 393 subfamily Y Y N DUF401 family protein 131567 cellular organisms no rank 1335 EBI-EMBL Protein of unknown function (DUF401) DUF401 family protein Members if this family are predicted to have 10 transmembrane regions. (from Pfam) NF016084.5 PF04166.17 PdxA 27 27 286 domain Y Y N 4-hydroxythreonine-4-phosphate dehydrogenase PdxA 1.1.1.262 GO:0051287 10225425 131567 cellular organisms no rank 61442 EBI-EMBL Pyridoxal phosphate biosynthetic protein PdxA 4-hydroxythreonine-4-phosphate dehydrogenase PdxA In Escherichia coli the coenzyme pyridoxal 5'-phosphate is synthesised de novo by a pathway that is thought to involve the condensation of 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose, catalysed by the enzymes PdxA and PdxJ, to form either pyridoxine (vitamin B6) or pyridoxine 5'-phosphate [1]. [1]. 10225425. Vitamin B6 biosynthesis: formation of pyridoxine 5'-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein. Laber B, Maurer W, Scharf S, Stepusin K, Schmidt FS;. FEBS Lett 1999;449:45-48. (from Pfam) NF016085.5 PF04167.18 DUF402 23.9 23.9 68 domain Y Y N DUF402 domain-containing protein 30010320,33955674,7500951 131567 cellular organisms no rank 30874 EBI-EMBL Protein of unknown function (DUF402) Protein of unknown function (DUF402) Family member FomD is a protein encoded in the fosfomycin biosynthesis gene cluster [1,2], which hydrolyses (S)-HPP-CMP to give (S)-HPP and CMP in the presence of Mn2 or Co2 [2]. FomD also hydrolyses cytidylyl 2-hydroxyethylphosphonate (HEP-CMP), which is a biosynthetic intermediate before C-methylation. FomD structure revealed that it has a beta-barrel fold consisting of a large twisted antiparallel beta-sheet, a key feature of DUF402-containing proteins. The function of this domain is unknown. It has a Tyr residue which activates a water molecule to promote nucleophilic attack on the phosphorus atom of the phosphonate moiety [2]. This domain has also been found in Ntdp (nucleoside tri- and diphosphatase, also known as Sa1684) from Staphylococcus aureus [3]. [1]. 7500951. Cloning and nucleotide sequence of fosfomycin biosynthetic genes of Streptomyces wedmorensis. Hidaka T, Goda M, Kuzuyama T, Takei N, Hidaka M, Seto H;. Mol Gen Genet 1995;249:274-280. [2]. 30010320. Biochemical and Structural Analysis of FomD That Catalyzes the Hydrolysis of Cytidylyl ( S)-2-Hydroxypropylphosphonate in Fosfomycin Biosynthesis. Sato S, Miyanaga A, Kim SY, Kuzuyama T, Kudo F, Eguchi T;. Biochemistry. 2018;57:4858-4866. [3]. 33955674. The structural mechanism for the nucleoside tri- and diphosphate hydrolysis activity of Ntdp from Staphylococcus aureus. Wang Z, Shen H, He B, Teng M, Guo Q, Li X;. FEBS J. 2021;288:6019-6034. (from Pfam) NF016086.5 PF04168.17 Alpha-E 20.8 20.8 294 domain Y Y N alpha-E domain-containing protein 20023723 131567 cellular organisms no rank 37427 EBI-EMBL A predicted alpha-helical domain with a conserved ER motif. A predicted alpha-helical domain with a conserved ER motif. An uncharacterized alpha helical domain containing a highly conserved ER motif and typically found as a tandem duplication. Contextual analysis suggests that it functions in a distinct peptide synthesis/modification system comprising of a transglutaminase, a peptidase of the NTN-hydrolase superfamily, an active and inactive circularly permuted ATP-grasp domains and a transglutaminase fused N-terminal to a circularly permuted COOH-NH2 ligase domain [1]. [1]. 20023723. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L;. Mol Biosyst. 2009;5:1636-1660. (from Pfam) NF016088.5 PF04172.21 LrgB 25 25 214 domain Y Y N LrgB family protein 10714982 131567 cellular organisms no rank 35043 EBI-EMBL LrgB-like family LrgB family protein The two products of the lrgAB operon are potential membrane proteins, and LrgA and LrgB are both thought to control of murein hydrolase activity and penicillin tolerance [1]. [1]. 10714982. The Staphylococcus aureus lrgAB operon modulates murein hydrolase activity and penicillin tolerance. Groicher KH, Firek BA, Fujimoto DF, Bayles KW;. J Bacteriol 2000;182:1794-1801. (from Pfam) NF016089.5 PF04173.18 DoxD 22.7 22.7 167 domain Y Y N TQO small subunit DoxD 15306018,9023221 131567 cellular organisms no rank 21676 EBI-EMBL TQO small subunit DoxD TQO small subunit DoxD Swiss:P97207 is a subunit of the terminal quinol oxidase present in the plasma membrane of Acidianus ambivalens, with calculated molecular mass of 20.4 kDa [1]. Thiosulphate:quinone oxidoreductase (TQO) is one of the early steps in elemental sulphur oxidation. A novel TQO enzyme was purified from the thermo-acidophilic archaeon Acidianus ambivalens and shown to consist of a large subunit (DoxD) and a smaller subunit (DoxA). The DoxD- and DoxA-like two subunits are fused together in a single polypeptide in Swiss:Q8AAF0. [1]. 9023221. The terminal quinol oxidase of the hyperthermophilic archaeon Acidianus ambivalens exhibits a novel subunit structure and gene organization. Purschke WG, Schmidt CL, Petersen A, Schafer G;. J Bacteriol 1997;179:1344-1353. [2]. 15306018. Coupling of the pathway of sulphur oxidation to dioxygen reduction: characterization of a novel membrane-bound thiosulphate:quinone oxidoreductase. Muller FH, Bandeiras TM, Urich T, Teixeira M, Gomes CM, Kletzin A;. Mol Microbiol. 2004;53:1147-1160. (from Pfam) NF016090.5 PF04174.18 CP_ATPgrasp_1 23.1 23.1 332 domain Y N N A circularly permuted ATPgrasp 20023723 131567 cellular organisms no rank 42255 EBI-EMBL A circularly permuted ATPgrasp A circularly permuted ATPgrasp An ATP-grasp family that is present both as catalytically active and inactive versions. Contextual analysis suggests that it functions in a distinct peptide synthesis/modification system that additionally contains a transglutaminase, an NTN-hydrolase, the Alpha-E domain, and a transglutaminase fused N-terminal to a circularly permuted COOH-NH2 ligase. The inactive forms are often fused N-terminal to the Alpha-E domain [1]. [1]. 20023723. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L;. Mol Biosyst. 2009;5:1636-1660. (from Pfam) NF016098.5 PF04182.17 B-block_TFIIIC 22 22 73 domain Y N N B-block binding subunit of TFIIIC 1279682 131567 cellular organisms no rank 5129 EBI-EMBL B-block binding subunit of TFIIIC B-block binding subunit of TFIIIC Yeast transcription factor IIIC (TFIIIC) is a multi-subunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding [1]. [1]. 1279682. TFC3: gene encoding the B-block binding subunit of the yeast transcription factor IIIC. Lefebvre O, Carles C, Conesa C, Swanson RN, Bouet F, Riva M, Sentenac A;. Proc Natl Acad Sci U S A 1992;89:10512-10516. (from Pfam) NF016099.5 PF04183.17 IucA_IucC 25 25 239 domain Y Y N IucA/IucC family protein GO:0019290 3087960 131567 cellular organisms no rank 75484 EBI-EMBL IucA / IucC family IucA/IucC family protein IucA and IucC catalyse discrete steps in biosynthesis of the siderophore aerobactin from N epsilon-acetyl-N epsilon-hydroxylysine and citrate [1]. This family represents the N-terminal region. The C-terminal region appears to be related to iron transporter proteins. [1]. 3087960. Characterization of iucA and iucC genes of the aerobactin system of plasmid ColV-K30 in Escherichia coli. de Lorenzo V, Neilands JB;. J Bacteriol 1986;167:350-355. (from Pfam) NF016100.5 PF04184.17 ST7 24.3 24.3 533 PfamEq Y N N ST7 protein 11279520 131567 cellular organisms no rank 368 EBI-EMBL ST7 protein ST7 protein The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene. The molecular function of this protein is uncertain. [1]. 11279520. Mutational and functional analyses reveal that ST7 is a highly conserved tumor-suppressor gene on human chromosome 7q31. Zenklusen JC, Conti CJ, Green ED;. Nat Genet 2001;27:392-398. (from Pfam) NF016101.5 PF04185.19 Phosphoesterase 23 23 356 domain Y Y N alkaline phosphatase family protein GO:0016788 11073936,20507939 131567 cellular organisms no rank 68625 EBI-EMBL Phosphoesterase family alkaline phosphatase family protein This family includes both bacterial phospholipase C enzymes EC:3.1.4.3, but also eukaryotic acid phosphatases EC:3.1.3.2. (from Pfam) NF016102.5 PF04186.18 FxsA 25.2 25.2 109 PfamEq Y Y N FxsA family protein GO:0016020 10497017 131567 cellular organisms no rank 31098 EBI-EMBL FxsA cytoplasmic membrane protein FxsA family protein This is a bacterial family of cytoplasmic membrane proteins. It includes two transmembrane regions. The molecular function of FxsA is unknown, but in Escherichia coli its over-expression has been shown to alleviate the exclusion of phage T7 in those cells with an F plasmid. [1]. 10497017. Increased synthesis of an Escherichia coli membrane protein suppresses F exclusion of bacteriophage T7. Wang WF, Margolin W, Molineux IJ;. J Mol Biol 1999;292:501-512. (from Pfam) NF016104.5 PF04188.18 Mannosyl_trans2 22.4 22.4 443 domain Y Y N mannosyltransferase family protein GO:0000009,GO:0004376,GO:0006506 15623507,15720390 131567 cellular organisms no rank 7542 EBI-EMBL Mannosyltransferase (PIG-V) mannosyltransferase family protein This is a family of eukaryotic ER membrane proteins that are involved in the synthesis of glycosylphosphatidylinositol (GPI), a glycolipid that anchors many proteins to the eukaryotic cell surface. Proteins in this family are involved in transferring the second mannose in the biosynthetic pathway of GPI [1] [2]. [1]. 15623507. PIG-V Involved in Transferring the Second Mannose in Glycosylphosphatidylinositol. Kang JY, Hong Y, Ashida H, Shishioh N, Murakami Y, Morita YS, Maeda Y, Kinoshita T;. J Biol Chem 2005;280:9489-9497. [2]. 15720390. Saccharomyces cerevisiae Ybr004c and its human homologue are required for addition of the second mannose during glycosylphosphatidylinositol precursor assembly. Fabre AL, Orlean P, Taron CH;. FEBS J 2005;272:1160-1168. (from Pfam) NF016107.5 PF04191.18 PEMT 25 25 105 domain Y Y N methyltransferase 2445736 131567 cellular organisms no rank 58036 EBI-EMBL Phospholipid methyltransferase methyltransferase Members of this family include both N- and O-methyltransferases. NF016109.5 PF04193.19 PQ-loop 22 22 61 domain Y Y N PQ-loop domain-containing transporter 11150305,11689434,11731489,22232659,22822152,23169667 131567 cellular organisms no rank 8683 EBI-EMBL PQ loop repeat PQ loop repeat This domain is named for the invariant PQ dipeptide in the most conserved central region of the defining seed alignment for the HMM. Eukaryotic family members, called SWEET family transporters, typically have two separated domains matching the model. Most bacterial proteins in the family have just one copy of the domain that represents most of the length of the protein, and are called SemiSWEET. NF016115.5 PF04199.18 Cyclase 23.1 23.1 142 domain Y Y N cyclase family protein GO:0004061,GO:0019441 9573189 131567 cellular organisms no rank 74525 EBI-EMBL Putative cyclase cyclase family protein Proteins in this family are thought to be cyclase enzymes. They are found in proteins involved in antibiotic synthesis. However they are also found in organisms that do not make antibiotics pointing to a wider role for these proteins. The proteins contain a conserved motif HXGTHXDXPXH that is likely to form part of the active site. [1]. 9573189. The Streptomyces peucetius dpsY and dnrX genes govern early and late steps of daunorubicin and doxorubicin biosynthesis. Lomovskaya N, Doi-Katayama Y, Filippini S, Nastro C, Fonstein L, Gallo M, Colombo AL, Hutchinson CR;. J Bacteriol. 1998;180:2379-2386. (from Pfam) NF016119.5 PF04203.18 Sortase 26.6 26.6 125 domain Y Y N sortase domain-bontaining protein 10427003,11239768 131567 cellular organisms no rank 142021 EBI-EMBL Sortase domain Sortase domain The founder member of this family is S. aureus sortase, a transpeptidase that attaches surface proteins by the threonine of an LPXTG motif to the cell wall [1]. [1]. 10427003. Staphylococcus aureus sortase, an enzyme that anchors surface proteins to the cell wall. Mazmanian SK, Liu G, Ton-That H, Schneewind O;. Science 1999;285:760-763. [2]. 11239768. An embarrassment of sortases - a richness of substrates?. Pallen MJ, Lam AC, Antonio M, Dunbar K;. Trends Microbiol 2001;9:97-102. (from Pfam) NF016120.5 PF04204.21 HTS 27 27 298 PfamEq Y Y N homoserine O-succinyltransferase 2.3.1.46 17442255,17546672,26790714 131567 cellular organisms no rank 22782 EBI-EMBL Homoserine O-succinyltransferase homoserine O-succinyltransferase The activation of homoserine through succinylation of homoserine in some bacteria, such as Escherichia coli and Bacillus cereus, is carried out by homoserine O-succinyltransferase (HTS, EC:2.3.1.46), while other bacteria, such as Haemophilus influenzae, Pseudomonas aeruginosa, and Mycobacterium tuberculosis, acetylate homoserine via homoserine O-acetyltransferase (HTA;EC:2.3.1.31) [1,2]. This family also includes serine acetyltransferase CysE (EC:2.3.1.30) from Lactobacillus casei, which catalyses the formation of O-acetyl serine from L-serine and acetyl-CoA, and is involved in cysteine biosynthesis [3]. [1]. 17442255. Assessing the roles of essential functional groups in the mechanism of homoserine succinyltransferase. Coe DM, Viola RE;. Arch Biochem Biophys. 2007;461:211-218. [2]. 17546672. Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolution. Zubieta C, Krishna SS, McMullan D, Miller MD, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, Deller M, DiDonato M, Duan L, Elsliger MA, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kumar A, Marciano D, Morse AT, Nigoghossian E, Oommachen S, Reyes R, Rife CL, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Proteins. 2007;68:999-1005. [3]. 26790714. Cysteine biosynthesis in Lactobacillus casei: identification and characterization of a serine acetyltransferase. Bogicevic B, Berthoud H, Portmann R, Bavan T, Meile L, Irmler S;. FEMS Microbiol Lett. 2016; [Epub ahead of print] (from Pfam) NF016121.5 PF04205.19 FMN_bind 22 22 77 domain Y Y N FMN-binding protein GO:0010181,GO:0016020 11248234,12625841,34032212 131567 cellular organisms no rank 75587 EBI-EMBL FMN-binding domain FMN-binding domain This conserved region includes the FMN-binding site of the NqrC protein [1] as well as the NosR and NirI regulatory proteins. This domain is post-translationally flavinylated that may facilitate electron transfer, and thus, resembles multiheme cytochromes [3]. [1]. 11248234. Expression and mutagenesis of the NqrC subunit of the NQR respiratory Na(+) pump from Vibrio cholerae with covalently attached FMN. Barquera B, Hase CC, Gennis RB;. FEBS Lett 2001;492:45-49. [2]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. [3]. 34032212. Post-translational flavinylation is associated with diverse extracytosolic redox functionalities throughout bacterial life. Meheust R, Huang S, Rivera-Lugo R, Banfield JF, Light SH;. Elife. 2021; [Epub ahead of print] (from Pfam) NF016122.5 PF04206.17 MtrE 26.6 26.6 271 PfamEq Y Y N tetrahydromethanopterin S-methyltransferase subunit E 7.2.1.4 GO:0005737,GO:0006814,GO:0012506,GO:0030269 9559648 131567 cellular organisms no rank 394 EBI-EMBL Tetrahydromethanopterin S-methyltransferase, subunit E tetrahydromethanopterin S-methyltransferase subunit E The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump [1]. [1]. 9559648. Cloning, sequencing and expression of the genes encoding the sodium translocating N5-methyltetrahydromethanopterin : coenzyme M methyltransferase of the methylotrophic archaeon Methanosarcina mazei Go1. Lienard T, Gottschalk G;. FEBS Lett 1998;425:204-208. (from Pfam) NF016124.5 PF04208.19 MtrA 25 25 173 domain Y N N Tetrahydromethanopterin S-methyltransferase, subunit A 9559648 131567 cellular organisms no rank 989 EBI-EMBL Tetrahydromethanopterin S-methyltransferase, subunit A Tetrahydromethanopterin S-methyltransferase, subunit A The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump [1]. [1]. 9559648. Cloning, sequencing and expression of the genes encoding the sodium translocating N5-methyltetrahydromethanopterin : coenzyme M methyltransferase of the methylotrophic archaeon Methanosarcina mazei Go1. Lienard T, Gottschalk G;. FEBS Lett 1998;425:204-208. (from Pfam) NF016125.5 PF04209.18 HgmA_C 21 21 153 domain Y Y N homogentisate 1,2-dioxygenase domain-containing protein 1.13.11.5 GO:0004411,GO:0006559,GO:0006570 10876237 131567 cellular organisms no rank 27372 EBI-EMBL Homogentisate 1,2-dioxygenase C-terminal Homogentisate 1,2-dioxygenase C-terminal Homogentisate dioxygenase cleaves the aromatic ring during the metabolic degradation of Phe and Tyr. Homogentisate dioxygenase deficiency causes alkaptonuria. The structure of homogentisate dioxygenase shows that the enzyme forms a hexamer arrangement comprised of a dimer of trimers. The active site iron ion is coordinated near the interface between the trimers [1]. This entry represents the C-terminal active site domain. [1]. 10876237. Crystal structure of human homogentisate dioxygenase. Titus GP, Mueller HA, Burgner J, Rodriguez De Cordoba S, Penalva MA, Timm DE;. Nat Struct Biol 2000;7:542-546. (from Pfam) NF016128.5 PF04212.23 MIT 30 30 66 domain Y N N MIT (microtubule interacting and transport) domain 11085978,16174732,16193069 131567 cellular organisms no rank 100 EBI-EMBL MIT (microtubule interacting and transport) domain MIT (microtubule interacting and transport) domain The MIT domain forms an asymmetric three-helix bundle [3] and binds ESCRT-III (endosomal sorting complexes required for transport) substrates [2]. Identification and naming as ESP domain. [1]. 11085978. Identification and characterization of SNX15, a novel sorting nexin involved in protein trafficking. Phillips SA, Barr VA, Haft DH, Taylor SI, Haft CR;. J Biol Chem 2001;276:5074-5084. [2]. 16193069. Structural and mechanistic studies of VPS4 proteins. Scott A, Chung HY, Gonciarz-Swiatek M, Hill GC, Whitby FG, Gaspar J, Holton JM, Viswanathan R, Ghaffarian S, Hill CP, Sundquist WI;. EMBO J. 2005;24:3658-3669. [3]. 16174732. Structure and ESCRT-III protein interactions of the MIT domain of human VPS4A. Scott A, Gaspar J, Stuchell-Brereton MD, Alam SL, Skalicky JJ, Sundquist WI;. Proc Natl Acad Sci U S A. 2005;102:13813-13818. (from Pfam) NF016130.5 PF04214.18 DUF411 27 27 48 domain Y Y N DUF411 domain-containing protein 131567 cellular organisms no rank 17278 EBI-EMBL Protein of unknown function, DUF Protein of unknown function, DUF The function of the members of this bacterial protein family is unknown. Some members may be involved in conferring cation resistance. (from Pfam) NF016131.5 PF04216.17 FdhE 27.6 27.6 289 PfamEq Y Y N formate dehydrogenase accessory protein FdhE fdhE GO:0005737 1648557,2170340 131567 cellular organisms no rank 12322 EBI-EMBL Protein involved in formate dehydrogenase formation formate dehydrogenase accessory protein FdhE The function of these proteins is unknown. They may possibly be involved in the formation of formate dehydrogenase. [1]. 2170340. Identification and expression of the Escherichia coli fdhD and fdhE genes, which are involved in the formation of respiratory formate dehydrogenase. Schlindwein C, Giordano G, Santini CL, Mandrand MA;. J Bacteriol 1990;172:6112-6121. [2]. 1648557. Genetic evidence that genes fdhD and fdhE do not control synthesis of formate dehydrogenase-N in Escherichia coli K-12. Stewart V, Lin JT, Berg BL;. J Bacteriol 1991;173:4417-4423. (from Pfam) NF016133.5 PF04218.18 CENP-B_N 21.2 21.2 53 domain Y N N CENP-B N-terminal DNA-binding domain GO:0003677 9451007 131567 cellular organisms no rank 7639 EBI-EMBL CENP-B N-terminal DNA-binding domain CENP-B N-terminal DNA-binding domain Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [1]. [1]. 9451007. A helix-turn-helix structure unit in human centromere protein B (CENP-B). Iwahara J, Kigawa T, Kitagawa K, Masumoto H, Okazaki T, Yokoyama S;. EMBO J 1998;17:827-837. (from Pfam) NF016136.5 PF04221.17 RelB 22.4 22.4 82 domain Y Y N type II toxin-antitoxin system RelB/DinJ family antitoxin 11274135,12123459 131567 cellular organisms no rank 20898 EBI-EMBL RelB antitoxin type II toxin-antitoxin system RelB/DinJ family antitoxin RelE and RelB form a toxin-antitoxin system. RelE represses translation, probably through binding ribosomes ([1], [2]). RelB stably binds RelE, presumably deactivating it. [1]. 11274135. Purification of the RelB and RelE proteins of Escherichia coli: RelE binds to RelB and to ribosomes. Galvani C, Terry J, Ishiguro EE;. J Bacteriol 2001;183:2700-2703. [2]. 12123459. Rapid induction and reversal of a bacteriostatic condition by controlled expression of toxins and antitoxins. Pedersen K, Christensen SK, Gerdes K;. Mol Microbiol 2002;45:501-510. (from Pfam) NF016143.5 PF04228.18 Zn_peptidase 23.2 23.2 290 domain Y Y N neutral zinc metallopeptidase 131567 cellular organisms no rank 44813 EBI-EMBL Putative neutral zinc metallopeptidase neutral zinc metallopeptidase Members of this family have a predicted zinc binding motif characteristic of neutral zinc metallopeptidases (Prosite:PDOC00129). (from Pfam) NF016144.5 PF04229.19 GrpB 25.5 25.5 159 domain Y Y N GrpB family protein 19833706,19876400 131567 cellular organisms no rank 35302 EBI-EMBL GrpB protein GrpB family protein This family has been suggested to belong to the nucleotidyltransferase superfamily [1]. It occurs at the C-terminus of dephospho-CoA kinase (CoaE) in a number of cases, where it plays a role in the proper folding of the enzyme [2]. [1]. 19833706. Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. Kuchta K, Knizewski L, Wyrwicz LS, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2009; [Epub ahead of print]. [2]. 19876400. The role of UPF0157 in the folding of M. tuberculosis dephosphocoenzyme A kinase and the regulation of the latter by CTP. Walia G, Kumar P, Surolia A;. PLoS One. 2009;4:e7645. (from Pfam) NF016145.5 PF04230.18 PS_pyruv_trans 25.3 25.3 280 domain Y Y N polysaccharide pyruvyl transferase family protein 10970841,8118055 131567 cellular organisms no rank 71499 EBI-EMBL Polysaccharide pyruvyl transferase polysaccharide pyruvyl transferase family protein Pyruvyl-transferases involved in peptidoglycan-associated polymer biosynthesis. CsaB in Bacillus anthracis is necessary for the non-covalent anchoring of proteins containing an SLH (S-layer homology) domain to peptidoglycan-associated pyruvylated polysaccharides. WcaK and AmsJ are involved in the biosynthesis of colanic acid in Escherichia coli and of amylovoran in Erwinia amylovora [1]. [1]. 10970841. Bacterial SLH domain proteins are non-covalently anchored to the cell surface via a conserved mechanism involving wall polysaccharide pyruvylation. Mesnage S, Fontaine T, Mignot T, Delepierre M, Mock M, Fouet A;. EMBO J 2000;19:4473-4484. [2]. 8118055. Analysis of the Rhizobium meliloti genes exoU, exoV, exoW, exoT, and exoI involved in exopolysaccharide biosynthesis and nodule invasion: exoU and exoW probably encode glucosyltransferases. Becker A, Kleickmann A, Kuster H, Keller M, Arnold W, Puhler A;. Mol Plant Microbe Interact. 1993;6:735-744. (from Pfam) NF016148.5 PF04233.19 Phage_Mu_F 29.6 29.6 112 domain Y Y N phage minor head protein 16899078 131567 cellular organisms no rank 48314 EBI-EMBL Phage Mu protein F like protein phage minor head protein domain Sequences in this family appear primarily as domain within minor head proteins of double-stranded DNA phage that are described as morphogenesis proteins, but occur also as a domain N-terminal to the NAD+--arginine ADP-ribosyltransferase domain of toxin EFV of Enterococcus faecalis. Phage minor head protein examples include Gp7 of SPP1 and protein F (Gp30) of phage Mu. NF016149.5 PF04234.17 CopC 23.3 23.3 92 domain Y Y N copper resistance protein CopC GO:0005507,GO:0042597,GO:0046688 1924351 131567 cellular organisms no rank 53518 EBI-EMBL CopC domain CopC domain CopC is a bacterial blue copper protein that binds 1 atom of copper per protein molecule. Along with CopA, CopC mediates copper resistance by sequestration of copper in the periplasm [1]. [1]. 1924351. Copper resistance in Pseudomonas syringae mediated by periplasmic and outer membrane proteins. Cha JS, Cooksey DA;. Proc Natl Acad Sci U S A 1991;88:8915-8919. (from Pfam) NF016150.5 PF04235.17 DUF418 23.6 23.6 163 domain Y Y N DUF418 domain-containing protein 131567 cellular organisms no rank 53817 EBI-EMBL Protein of unknown function (DUF418) Protein of unknown function (DUF418) Probable integral membrane protein. (from Pfam) NF016152.5 PF04237.18 YjbR 30.1 30.1 88 domain Y Y N MmcQ/YjbR family DNA-binding protein 23044854 131567 cellular organisms no rank 67246 EBI-EMBL YjbR MmcQ/YjbR family DNA-binding protein YjbR has a CyaY-like fold [1]. [1]. 23044854. Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing. Anantharaman V, Iyer LM, Aravind L;. Mol Biosyst. 2012;8:3142-3165. (from Pfam) NF016153.5 PF04238.17 DUF420 30.5 30.5 130 PfamAutoEq Y Y N DUF420 domain-containing protein 131567 cellular organisms no rank 9900 EBI-EMBL Protein of unknown function (DUF420) Protein of unknown function (DUF420) Predicted membrane protein with four transmembrane helices. (from Pfam) NF016154.5 PF04239.17 DUF421 23.6 23.6 129 domain Y Y N YetF domain-containing protein 131567 cellular organisms no rank 50718 EBI-EMBL YetF C-terminal domain YetF C-terminal domain This domain is found at the C-terminal end of the YetF protein, which contains three N-terminal transmembrane helices. (from Pfam) NF016155.5 PF04240.17 Caroten_synth 25 25 209 PfamEq Y Y N carotenoid biosynthesis protein 25712483 131567 cellular organisms no rank 8623 EBI-EMBL Carotenoid biosynthesis protein carotenoid biosynthesis protein The representative member of this family is CruF, a C50 carotenoid 2',3'-hydratase involved in the synthesis of the C50 carotenoid bacterioruberin in the halophilic archaeon Haloarcula japonica [1]. [1]. 25712483. Complete biosynthetic pathway of the C50 carotenoid bacterioruberin from lycopene in the extremely halophilic archaeon Haloarcula japonica. Yang Y, Yatsunami R, Ando A, Miyoko N, Fukui T, Takaichi S, Nakamura S;. J Bacteriol. 2015;197:1614-1623. (from Pfam) NF016158.5 PF04244.18 DPRP 22.1 22.1 224 PfamEq Y Y N cryptochrome/photolyase family protein 131567 cellular organisms no rank 25035 EBI-EMBL Deoxyribodipyrimidine photo-lyase-related protein cryptochrome/photolyase family protein This family appears to be related to Pfam:PF00875. (from Pfam) NF016162.5 PF04248.18 NTP_transf_9 22.1 22.1 93 domain Y Y N DUF427 domain-containing protein 25569776 131567 cellular organisms no rank 35747 EBI-EMBL Domain of unknown function (DUF427) Domain of unknown function (DUF427) This domain contains a beta-tent fold [1]. [1]. 25569776. The thalidomide-binding domain of cereblon defines the CULT domain family and is a new member of the beta-tent fold. Lupas AN, Zhu H, Korycinski M;. PLoS Comput Biol. 2015;11:e1004023. (from Pfam) NF016163.5 PF04250.18 DUF429 23 23 214 PfamAutoEq Y Y N DUF429 domain-containing protein 131567 cellular organisms no rank 13156 EBI-EMBL Protein of unknown function (DUF429) Protein of unknown function (DUF429) NF016164.5 PF04252.18 SFM1-like 27 27 201 domain Y N N Protein arginine N-methyltransferase SFM1-like GO:0008168 15215454,20525789 131567 cellular organisms no rank 197 EBI-EMBL Protein arginine N-methyltransferase SFM1-like Protein arginine N-methyltransferase SFM1-like This family of proteins includes Protein arginine N-methyltransferase SFM1 from Saccharomyces cerevisiae and similar proteins from fungi and archaea. Sfm1 is a S-adenosyl-L-methionine-dependent protein- arginine N-methyltransferase that monomethylates ribosomal protein S3 (RPS3) at 'Arg-146' [2]. [1]. 15215454. Detecting distant homology with Meta-BASIC. Ginalski K, von Grotthuss M, Grishin NV, Rychlewski L;. Nucleic Acids Res. 2004;32:576-581. [2]. 20525789. New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA. Kempenaers M, Roovers M, Oudjama Y, Tkaczuk KL, Bujnicki JM, Droogmans L;. Nucleic Acids Res. 2010;38:6533-6543. (from Pfam) NF016166.5 PF04254.18 DUF432 21 21 123 domain Y Y N DUF432 domain-containing protein 131567 cellular organisms no rank 525 EBI-EMBL Protein of unknown function (DUF432) Protein of unknown function (DUF432) Archaeal protein of unknown function. (from Pfam) NF016167.5 PF04255.19 DUF433 23.6 23.6 56 domain Y Y N DUF433 domain-containing protein 131567 cellular organisms no rank 20808 EBI-EMBL Protein of unknown function (DUF433) Protein of unknown function (DUF433) NF016168.5 PF04256.17 DUF434 27 27 56 PfamAutoEq Y Y N DUF434 domain-containing protein 131567 cellular organisms no rank 1673 EBI-EMBL Protein of unknown function (DUF434) Protein of unknown function (DUF434) NF016170.5 PF04258.18 Peptidase_A22B 23.3 23.3 286 PfamEq Y N N Signal peptide peptidase GO:0004190,GO:0016020,GO:0042500 11714810,12077416,12145199,12419218 131567 cellular organisms no rank 60 EBI-EMBL Signal peptide peptidase Signal peptide peptidase The members of this family are membrane proteins. In some proteins this region is found associated with Pfam:PF02225. This family corresponds with Merops subfamily A22B, the type example of which is signal peptide peptidase. There is a sequence-similarity relationship with Pfam:PF01080. [1]. 12419218. Requirements for signal peptide peptidase-catalyzed intramembrane proteolysis. Lemberg MK, Martoglio B;. Mol Cell 2002;10:735-744. [2]. 12145199. Intramembrane proteolysis promotes trafficking of hepatitis C virus core protein to lipid droplets. McLauchlan J, Lemberg MK, Hope G, Martoglio B;. EMBO J 2002;21:3980-3988. [3]. 12077416. Identification of signal peptide peptidase, a presenilin-type aspartic protease. Weihofen A, Binns K, Lemberg MK, Ashman K, Martoglio B;. Science 2002;296:2215-2218. [4]. 11714810. Intramembrane proteolysis of signal peptides: an essential step in the generation of HLA-E epitopes. Lemberg MK, Bland FA, Weihofen A, Braud VM, Martoglio B;. J Immunol 2001;167:6441-6446. (from Pfam) NF016174.5 PF04262.19 Glu_cys_ligase 27 27 372 PfamEq Y N N Glutamate-cysteine ligase GO:0004357,GO:0006750 131567 cellular organisms no rank 26514 EBI-EMBL Glutamate-cysteine ligase Glutamate-cysteine ligase Family of bacterial f glutamate-cysteine ligases (EC:6.3.2.2) that carry out the first step of the glutathione biosynthesis pathway. (from Pfam) NF016175.5 PF04263.21 TPK_catalytic 30.7 30.7 113 PfamEq Y N N Thiamin pyrophosphokinase, catalytic domain GO:0004788,GO:0005524,GO:0009229 11435118 131567 cellular organisms no rank 28478 EBI-EMBL Thiamin pyrophosphokinase, catalytic domain Thiamin pyrophosphokinase, catalytic domain Family of thiamin pyrophosphokinase (EC:2.7.6.2). Thiamin pyrophosphokinase (TPK) catalyses the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggest that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis [1]. [1]. 11435118. The crystal structure of yeast thiamin pyrophosphokinase. Baker LJ, Dorocke JA, Harris RA, Timm DE;. Structure 2001;9:539-546. (from Pfam) NF016176.5 PF04264.18 YceI 23.7 23.7 150 domain Y Y N YceI family protein 12107143,15741337 131567 cellular organisms no rank 112976 EBI-EMBL YceI-like domain YceI-like domain E. coli YceI is a base-induced periplasmic protein [1]. The recent structure of a member of this family shows that it binds to poly-isoprenoid [2]. The structure consists of an extended, eight-stranded, antiparallel beta-barrel that resembles the lipocalin fold. [1]. 12107143. pH-Dependent Expression of Periplasmic Proteins and Amino Acid Catabolism in Escherichia coli. Stancik LM, Stancik DM, Schmidt B, Barnhart DM, Yoncheva YN, Slonczewski JL;. J Bacteriol 2002;184:4246-4258. [2]. 15741337. Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8. Handa N, Terada T, Doi-Katayama Y, Hirota H, Tame JR, Park SY, Kuramitsu S, Shirouzu M, Yokoyama S;. Protein Sci. 2005;14:1004-1010. (from Pfam) NF016178.5 PF04266.19 ASCH 21.2 21.2 103 domain Y Y N ASCH domain-containing protein 16322048 131567 cellular organisms no rank 42010 EBI-EMBL ASCH domain ASCH domain The ASCH domain adopts a beta-barrel fold similar to the Pfam:PF01472 domain [1]. It is thought to function as an RNA-binding domain during coactivation, RNA-processing and possibly during prokaryotic translation regulation [1]. [1]. 16322048. The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism. Iyer LM, Burroughs AM, Aravind L;. Bioinformatics. 2005; [Epub ahead of print]DR SCOP; 88697; (from Pfam) NF016187.5 PF04277.18 OAD_gamma 27 27 76 subfamily Y Y N OadG family transporter subunit GO:0008948,GO:0015081,GO:0016020,GO:0036376 11802728 131567 cellular organisms no rank 12087 EBI-EMBL Oxaloacetate decarboxylase, gamma chain OadG family transporter subunit NF016189.5 PF04279.20 IspA 28.7 28.7 176 domain Y Y N septation protein IspZ GO:0016020 26391555,26454142,30368949,33431434,8830250,9746567 131567 cellular organisms no rank 20576 EBI-EMBL Intracellular septation protein A septation protein IspZ Inner membrane-spanning protein YciB (also known as intracellular septation protein A) is a family of proteins which are essential for both normal cell division and bacterial virulence and are believed to play a role in the septation process [1,2,3]. These proteins play a role in cell envelope biogenesis, maintenance of cell envelope integrity and membrane homeostasis [3,4,5,6]. [1]. 8830250. Identification and characterization of ispA, a Shigella flexneri chromosomal gene essential for normal in vivo cell division and intracellular spreading. Mac Siomoin RA, Nakata N, Murai T, Yoshikawa M, Tsuji H, Sasakawa C.;. Mol Microbiol 1996;19:599-609. [2]. 9746567. Identification of two Shigella flexneri chromosomal loci involved in intercellular spreading. Hong M, Gleason Y, Wyckoff EE, Payne SM;. Infect Immun. 1998;66:4700-4710. [3]. 26391555. Escherichia coli inner membrane protein YciB interacts with ZipA that is important for cell division. Badaluddin NA, Kitakawa M;. Genes Cells. 2015;20:956-965. [4]. 26454142. Characterization of inner membrane protein YciB in Escherichia coli: YciB interacts with cell elongation and division proteins. Li G, Badaluddin NA, Kitakawa M;. Microbiol Immunol. 2015;59:700-704. [5]. 30368949. A synergistic role for two predicted inner membrane proteins of Escherichia coli in cell envelope integrity. Mychack A, Amrutha RN, Chung C, Cardenas Arevalo K, Reddy M, Janakiraman A;. Mol Microbiol. 2019;111:317-337. [6]. 33431434. Defects in The First Step of Lipoprotein Maturation Underlie The Synthetic Lethality of Escherichia coli Lacking The Inner Membrane Proteins YciB And DcrB. Mychack A, Janakirama. TRUNCATED at 1650 bytes (from Pfam) NF016190.5 PF04280.20 Tim44 29.6 29.6 147 domain Y Y N TIM44-like domain-containing protein 10430866,16511294,16647716 131567 cellular organisms no rank 25066 EBI-EMBL Tim44-like domain Tim44-like domain Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane [1]. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region [1]. This family includes the C-terminal region of Tim44 that has been shown to form a stable proteolytic fragment in yeast. This region is also found in a set of smaller bacterial proteins. The molecular function of the bacterial members of this family is unknown but transport seems likely. The crystal structure of the C terminal of Tim44 has revealed a large hydrophobic pocket which might play an important role in interacting with the acyl chains of lipid molecules in the mitochondrial membrane [3]. [1]. 10430866. Domain structure and lipid interaction of recombinant yeast Tim44. Weiss C, Oppliger W, Vergeres G, Demel R, Jeno P, Horst M, de Kruijff B, Schatz G, Azem A;. Proc Natl Acad Sci U S A 1999;96:8890-8894. [2]. 16511294. Preliminary crystallographic studies of yeast mitochondrial peripheral membrane protein Tim44p. Josyula R, Jin Z, McCombs D, DeLucas L, Sha B;. Acta Crystallograph Sect F Struct Biol Cryst Commun. 2006;62:172-174. [3]. 16647716. Crystal structure of yeast mitochondrial peripheral membrane protein Tim44p C-terminal domain. Josyula R, Jin Z, Fu Z, Sha B;. J Mol Biol. 2006;359:798-804. (from Pfam) NF016192.5 PF04282.18 DUF438 25 25 67 PfamAutoEq Y Y N DUF438 domain-containing protein 131567 cellular organisms no rank 6474 EBI-EMBL Family of unknown function (DUF438) Family of unknown function (DUF438) NF016195.5 PF04285.17 DUF444 27 27 418 PfamAutoEq Y Y N DUF444 family protein 29769716 131567 cellular organisms no rank 18861 EBI-EMBL Protein of unknown function (DUF444) DUF444 family protein Bacterial protein of unknown function. One family member (Swiss:Q97LI1) is predicted to contain a von Willebrand factor (vWF) type A domain (Smart:VWA). Another family member YeaH is predicted to be part of a conserved signalling pathway with the kinase YeaG and the SpoVR protein YcgB. The pathway may be involved in nitrogen metabolism (see Supplementary note 5 in [1].) [1]. 29769716. Mutant phenotypes for thousands of bacterial genes of unknown function. Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM;. Nature. 2018;557:503-509. (from Pfam) NF016196.5 PF04286.17 DUF445 33.8 33.8 368 domain Y Y N DUF445 family protein 131567 cellular organisms no rank 42238 EBI-EMBL Protein of unknown function (DUF445) DUF445 family protein Predicted to be a membrane protein. (from Pfam) NF016199.5 PF04289.17 DUF447_N 24 24 114 PfamAutoEq Y Y N DUF447 domain-containing protein 22201035 131567 cellular organisms no rank 3250 EBI-EMBL Protein of unknown function (DUF447) N-terminal domain DUF447 family protein Archaeal protein of unknown function. A fungal member UniProtKB:M2LN89 is clearly a Flavine-reductase enzyme by homology, and UniProtKB:O28442 has been shown to bind riboflavin 5'-phosphate (unpublished structural Xray analysis). [1]. 22201035. 1H, 15N and 13C chemical shift assignments of the BA42 protein of the psychrophilic bacteria Bizionia argentinensis sp. nov. Smal C, Aran M, Lanzarotti E, Papouchado M, Foti M, Marti MA, Coria SH, Vazquez SC, Bercovich A, Mac Cormack WP, Turjanski AG, Gallo M, Cicero DO;. Biomol NMR Assign. 2012;6:181-183. (from Pfam) NF016200.5 PF04290.17 DctQ 28.3 28.3 132 domain Y Y N TRAP transporter small permease subunit 10627041,11524131 131567 cellular organisms no rank 130937 EBI-EMBL Tripartite ATP-independent periplasmic transporters, DctQ component TRAP transporter small permease subunit The function of the members of this family is unknown, but DctQ homologues are invariably found in the tripartite ATP-independent periplasmic transporters [1]. [1]. 10627041. TRAP transporters: an ancient family of extracytoplasmic solute-receptor-dependent secondary active transporters. Rabus R, Jack DL, Kelly DJ, Saier MH Jr;. Microbiology 1999;145:3431-3445. [2]. 11524131. The tripartite ATP-independent periplasmic (TRAP) transporters of bacteria and archaea. Kelly DJ, Thomas GH;. FEMS Microbiol Rev 2001;25:405-424. (from Pfam) NF016201.5 PF04293.18 SpoVR 27 27 419 PfamEq Y Y N SpoVR family protein 29769716,8144469,8982457 131567 cellular organisms no rank 20318 EBI-EMBL SpoVR like protein SpoVR family protein Family member Swiss:P37875 is Bacillus subtilis stage V sporulation protein R, which is involved in spore cortex formation [1]. Little is known about cortex biosynthesis, except that it depends on several sigma E controlled genes, including spoVR [2]. Another family member is an uncharacterised protein YcgB. YcgB has been suggested to be part of a conserved signalling pathway with YeaH and YeaG. This pathway may be involved in nitrogen metabolism (see Supplementary note 5 in [3].) [1]. 8144469. Cloning and characterization of spoVR, a gene from Bacillus subtilis involved in spore cortex formation. Beall B, Moran CP Jr;. J Bacteriol 1994;176:2003-2012. [2]. 8982457. Molecular genetics of sporulation in Bacillus subtilis. Stragier P, Losick R;. Annu Rev Genet 1996;30:297-341. [3]. 29769716. Mutant phenotypes for thousands of bacterial genes of unknown function. Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM;. Nature. 2018;557:503-509. (from Pfam) NF016202.5 PF04294.18 VanW 27 27 130 domain Y Y N VanW family protein 11036060,11376048 131567 cellular organisms no rank 28701 EBI-EMBL VanW like protein VanW family protein Family members include vancomycin resistance protein W (VanW). Genes encoding members of this family have been found in vancomycin resistance gene clusters vanB [1] and vanG [2]. The function of VanW is unknown. [1]. 11376048. High prevalence of VanB2 vancomycin-resistant Enterococcus faecium in Taiwan. Lu JJ, Perng CL, Ho MF, Chiueh TS, Lee WH;. J Clin Microbiol 2001;39:2140-2145. [2]. 11036060. Genetic characterization of vanG, a novel vancomycin resistance locus of Enterococcus faecalis. McKessar SJ, Berry AM, Bell JM, Turnidge JD, Paton JC;. Antimicrob Agents Chemother 2000;44:3224-3228. (from Pfam) NF016203.5 PF04295.18 GD_AH_second 27.3 27.3 136 domain Y Y N UxaA family hydrolase GO:0016829 15146494,3038546,31811683,9579062,9772162 131567 cellular organisms no rank 47033 EBI-EMBL D-galactarate dehydratase/Altronate hydrolase, second domain D-galactarate dehydratase/Altronate hydrolase, second domain This entry includes D-galactarate dehydratase (GarD, EC:4.2.1.42) which catalyses the reaction D-galactarate = 5-keto-4-deoxy-D glucarate + H2O, [1] and altronate hydrolase (altronic acid hydratase, EC:4.2.1.7), which catalyses D-altronate = 2-keto-2- deoxygluconate + H2O [2]. As purified, both enzymes are catalytically inactive in the absence of added Fe2+, Mn2+, and beta-mercaptoethanol. Synergistic activation of altronate hydrolase activity is seen in the presence of both iron and manganese ions, suggesting that the enzyme may have two ion binding sites. Mn2+ appears to be part of the enzyme active centre, but the function of the single bound Fe2+ ion is unknown. The hydratase has no Fe-S core [3]. GarD structure revealed that it is a dimer in solution; each monomer has three domains, an N-terminal SAF domain (Pfam:PF08666), a second domain represented in this entry and a C-terminal domain [5]. This domain consists of three parallel beta-strands, surrounded by three alpha-helices and it interacts with the C-terminal domain from the second chain to form a dimerisation surface [5]. [1]. 9772162. Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli. Hubbard BK, Koch M, Palmer DR, Babbitt PC, Gerlt JA;. Biochemistry 1998;37:14369-14375. [2]. 9579062. A 35.7 kb DNA fragment from the Bacillus subtilis chromosome containing a putative 12.3 kb operon involved in hexuronate catabolism and a perfectly symmetrical hypothetical catabolite-responsive element. Rivolta C, Soldo B, Lazarevic V, Joris B, Mauel C, Karamata D;. Microbiology 1. TRUNCATED at 1650 bytes (from Pfam) NF016205.5 PF04297.19 UPF0122 22.7 22.7 101 domain Y N N Putative helix-turn-helix protein, YlxM / p13 like 9070906 131567 cellular organisms no rank 16403 EBI-EMBL Putative helix-turn-helix protein, YlxM / p13 like Putative helix-turn-helix protein, YlxM / p13 like Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (Swiss:O05290). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [1]. [1]. 9070906. A 13-kDa protein with a helix-turn-helix motif is encoded by bacterial operons related to the SRP pathway. Samuelsson T, Macao B, Bolske G;. Biochem Biophys Res Commun 1997;231:839-843. (from Pfam) NF016207.5 PF04299.17 FMN_bind_2 22.4 22.4 168 domain Y Y N FMN-binding negative transcriptional regulator 2108124 131567 cellular organisms no rank 38777 EBI-EMBL Putative FMN-binding domain Putative FMN-binding domain In Bacillus subtilis, family member Swiss:P21341 (PAI 2/ORF-2) was found to be essential for growth [1]. The SUPERFAMILY database finds that this domain is related to FMN-binding domains, suggesting this protein is also FMN-binding. [1]. 2108124. A novel Bacillus subtilis gene involved in negative control of sporulation and degradative-enzyme production. Honjo M, Nakayama A, Fukazawa K, Kawamura K, Ando K, Hori M, Furutani Y;. J Bacteriol 1990;172:1783-1790. (from Pfam) NF016210.5 PF04303.18 PrpF 27 27 371 domain Y Y N PrpF domain-containing protein 17567742 131567 cellular organisms no rank 37506 EBI-EMBL PrpF protein PrpF protein PrpF is a protein found in the 2-methylcitrate pathway. It is structurally similar to DAP epimerase and proline racemase. This protein is likely to acts to isomerise trans-aconitate to cis-aconitate [1]. [1]. 17567742. The three-dimensional crystal structure of the PrpF protein of Shewanella oneidensis complexed with trans-aconitate: insights into its biological function. Garvey GS, Rocco CJ, Escalante-Semerena JC, Rayment I;. Protein Sci. 2007;16:1274-1284. (from Pfam) NF016211.5 PF04304.18 DUF454 35.1 35.1 115 domain Y Y N DUF454 family protein 131567 cellular organisms no rank 25907 EBI-EMBL Protein of unknown function (DUF454) DUF454 family protein Predicted membrane protein. (from Pfam) NF016213.5 PF04306.18 DUF456 29.4 29.4 139 PfamAutoEq Y Y N DUF456 family protein 16179394 131567 cellular organisms no rank 19329 EBI-EMBL Protein of unknown function (DUF456) DUF456 family protein This family is a putative membrane protein that contains glycine zipper motifs [1]. [1]. 16179394. Transmembrane glycine zippers: physiological and pathological roles in membrane proteins. Kim S, Jeon TJ, Oberai A, Yang D, Schmidt JJ, Bowie JU;. Proc Natl Acad Sci U S A. 2005;102:14278-14283. (from Pfam) NF016214.5 PF04307.19 YdjM 29 29 176 domain Y Y N metal-dependent hydrolase 22958895 131567 cellular organisms no rank 53433 EBI-EMBL LexA-binding, inner membrane-associated putative hydrolase metal-dependent hydrolase YdjM is a family of putative LexA-binding proteins. Members are predicted to be membrane-bound metal-dependent hydrolases that may be acting as phospholipases. It is a member of the SOS network, that rescues cells from UV and other DNA-damage. Expression of YdjM is regulated by LexA [1]. [1]. 22958895. A phylogenomic analysis of Escherichia coli / Shigella group: implications of genomic features associated with pathogenicity and ecological adaptation. Zhang Y, Lin K;. BMC Evol Biol. 2012;12:174. (from Pfam) NF016219.5 PF04312.18 DUF460 28 28 135 PfamAutoEq Y Y N DUF460 domain-containing protein 131567 cellular organisms no rank 1202 EBI-EMBL Protein of unknown function (DUF460) Protein of unknown function (DUF460) Archaeal protein of unknown function. (from Pfam) NF016220.5 PF04313.19 HSDR_N 25.1 25.1 198 domain Y Y N type I restriction endonuclease GO:0003677,GO:0004519,GO:0006304 10449767,11555298 131567 cellular organisms no rank 114764 EBI-EMBL Type I restriction enzyme R protein N terminus (HSDR_N) type I restriction enzyme endonuclease domain This HMM described the endonuclease domain of HsdR family type I restriction endonucleases. These enzymes also have RecA-like helicase domains. NF016221.5 PF04314.18 PCuAC 29.4 29.4 109 domain Y Y N copper chaperone PCu(A)C 22248670 131567 cellular organisms no rank 43916 EBI-EMBL Copper chaperone PCu(A)C copper chaperone PCu(A)C PCu(A)C is a periplasmic copper chaperone. Its role may be to capture and transfer copper to two other copper chaperones, PrrC and Cox11, which in turn deliver Cu(I) to cytochrome c oxidase [1]. [1]. 22248670. The roles of Rhodobacter sphaeroides copper chaperones PCu(A)C and Sco (PrrC) in the assembly of the copper centers of the aa(3)-type and the cbb(3)-type cytochrome c oxidases. Thompson AK, Gray J, Liu A, Hosler JP;. Biochim Biophys Acta. 2012;1817:955-964. (from Pfam) NF016228.5 PF04321.22 RmlD_sub_bind 27 27 287 domain Y Y N sugar nucleotide-binding protein 10802738,12057193 131567 cellular organisms no rank 718268 EBI-EMBL RmlD substrate binding domain sugar nucleotide-binding domain L-rhamnose is a saccharide required for the virulence of some bacteria. Its precursor, dTDP-L-rhamnose, is synthesised by four different enzymes the final one of which is RmlD. The RmlD substrate binding domain is responsible for binding a sugar nucleotide [1,2]. [1]. 12057193. Variation on a Theme of SDR. dTDP-6-Deoxy-L- lyxo-4-Hexulose Reductase (RmlD) Shows a New Mg(2+)-Dependent Dimerization Mode. Blankenfeldt W, Kerr ID, Giraud MF, McMiken HJ, Leonard G, Whitfield C, Messner P, Graninger M, Naismith JH;. Structure (Camb) 2002;10:773-786. [2]. 10802738. RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of epimerase. Giraud MF, Leonard GA, Field RA, Berlind C, Naismith JH;. Nat Struct Biol 2000;7:398-402. (from Pfam) NF016230.5 PF04324.20 Fer2_BFD 26 26 50 domain Y Y N (2Fe-2S)-binding protein 8639572,8954950,9889981 131567 cellular organisms no rank 162842 EBI-EMBL BFD-like [2Fe-2S] binding domain BFD-like [2Fe-2S] binding domain The two Fe ions are each coordinated by two conserved cysteine residues. This domain occurs alone in small proteins such as Bacterioferritin-associated ferredoxin (BFD, Swiss:P13655). The function of BFD is not known, but it may may be a general redox and/or regulatory component involved in the iron storage or mobilisation functions of bacterioferritin in bacteria [1]. This domain is also found in nitrate reductase proteins in association with Nitrite and sulphite reductase 4Fe-4S domain [2] (Pfam:PF01077), Nitrite/Sulfite reductase ferredoxin-like half domain (Pfam:PF03460) and Pyridine nucleotide-disulphide oxidoreductase (Pfam:PF00070). It is also found in NifU nitrogen fixation proteins, in association with NifU-like N terminal domain (Pfam:PF01592) and NifU-like domain [3] (Pfam:PF01106). [1]. 8639572. A [2Fe-2S] protein encoded by an open reading frame upstream of the Escherichia coli bacterioferritin gene. Garg RP, Vargo CJ, Cui X, Kurtz DM Jr;. Biochemistry 1996;35:6297-6301. [2]. 8954950. Spectroscopic and voltammetric characterisation of the bacterioferritin-associated ferredoxin of Escherichia coli. Quail MA, Jordan P, Grogan JM, Butt JN, Lutz M, Thomson AJ, Andrews SC, Guest JR;. Biochem Biophys Res Commun 1996;229:635-642. [3]. 9889981. Iron storage in bacteria. Andrews SC;. Adv Microb Physiol 1998;40:281-351. (from Pfam) NF016232.5 PF04326.19 SLFN_AlbA_2 25.3 25.3 118 domain Y Y N RNA-binding domain-containing protein 31026779,34571887 131567 cellular organisms no rank 55563 EBI-EMBL Schlafen, AlbA_2 Schlafen, AlbA_2 This is the AlbA_2 domain from the Schlafen (SLFN) family of proteins which are important in cell differentiation and defense against viruses [1,2]. This domain is present at the N-terminal of all SLFN proteins and includes the SLFN box, a sequence unique to these proteins that may form a dimer interface [1]. The AlbA_2 domain is RNA-binding and RNase region as it contains the highly conserved catalytic glutamic acid residues [1]. [1]. 31026779. Deciphering the three-domain architecture in schlafens and the structures and roles of human schlafen12 and serpinB12 in transcriptional regulation. Chen J, Kuhn LA;. J Mol Graph Model. 2019;90:59-76. [2]. 34571887. Schlafens: Emerging Proteins in Cancer Cell Biology. Al-Marsoummi S, Vomhof-DeKrey EE, Basson MD;. Cells. 2021; [Epub ahead of print] (from Pfam) NF016235.5 PF04332.20 DUF475 27 27 293 PfamAutoEq Y Y N DUF475 domain-containing protein 131567 cellular organisms no rank 15552 EBI-EMBL Protein of unknown function (DUF475) Protein of unknown function (DUF475) Predicted to be an integral membrane protein with multiple membrane spans. (from Pfam) NF016242.5 PF04339.17 FemAB_like 27 27 369 domain Y Y N peptidogalycan biosysnthesis protein 20537955 131567 cellular organisms no rank 32032 EBI-EMBL Peptidogalycan biosysnthesis/recognition peptidogalycan biosysnthesis protein FemAB_like is a family of both baterial and Viridiplantae proteins with responsibility for building interpeptide bridges in peptidoglycan. Such a function is feasible for bacteria but less likely for the plant members of this family. Perhaps the plant-members are using homologous proteins to recognise bacterial peptidoglcans as part of their innate immune system [1]. [1]. 20537955. The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. Goonesekere NC, Shipely K, O'Connor K;. Comput Biol Chem. 2010;34:210-214. (from Pfam) NF016244.5 PF04341.17 DUF485 28 28 88 domain Y Y N DUF485 domain-containing protein 29769716 131567 cellular organisms no rank 33709 EBI-EMBL Protein of unknown function, DUF485 Protein of unknown function, DUF485 This family represents a putative component of ActP-like carboxylate transporters. Several members are cofit with adjacent ActP-like permeases, and the family appears to represent a membrane protein. It has been suggested to be involved in pyruvate utilisation [1]. [1]. 29769716. Mutant phenotypes for thousands of bacterial genes of unknown function. Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM;. Nature. 2018;557:503-509. (from Pfam) NF016245.5 PF04342.17 DMT_6 25 25 104 subfamily Y Y N DMT family protein 131567 cellular organisms no rank 8671 EBI-EMBL Putative member of DMT superfamily (DUF486) DUF486 family DMT transporter This family contains several proteins of uncharacterised function. The family is represented in the Transport classification database as 2.A.7.34, though the exact nature of what is transported is not known. (from Pfam) NF016246.5 PF04343.18 DUF488 22.2 22.2 121 domain Y Y N DUF488 family protein 36968430 131567 cellular organisms no rank 46617 EBI-EMBL Domain of unknown function DUF488 DUF488 family protein This entry has been described to include subclades of DUF488 domains (namely DUF488-s, for DUF488-short subclade, DUF488-l for long subclade and DUF488-u for DUF488-standalone subclade) which all which contain the ancestral core of the domain. DUF488-s commonly pairs with the DUF488-l subclade on the genome. In the case of DUF488-l and DUF488-u, the core domain is followed by a single beta-strand that stacks at the C-terminus of the core beta-sheet and a multi-helical 'cap' [1]. Unlike the DUF488-s and DUF488-l subclades, DUF488-u is not found adjacent to other DUF488 subclades on the genome [1]. [1]. 36968430. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. Burroughs AM, Aravind L;. NAR Genom Bioinform. 2023;5:lqad029. (from Pfam) NF016248.5 PF04345.18 Chor_lyase 23.6 23.6 168 PfamEq Y Y N chorismate lyase 4.1.3.40 GO:0005737,GO:0006744,GO:0008813 11455603 131567 cellular organisms no rank 14871 EBI-EMBL Chorismate lyase chorismate lyase Chorismate lyase catalyses the first step in ubiquinone synthesis, i.e. the removal of pyruvate from chorismate, to yield 4-hydroxybenzoate. [1]. 11455603. The crystal structure of chorismate lyase shows a new fold and a tightly retained product. Gallagher DT, Mayhew M, Holden MJ, Howard A, Kim KJ, Vilker VL;. Proteins 2001;44:304-311. (from Pfam) NF016251.5 PF04348.18 LppC 28.8 28.8 563 PfamEq Y Y N penicillin-binding protein activator 131567 cellular organisms no rank 27192 EBI-EMBL LppC putative lipoprotein penicillin-binding protein activator This family includes several bacterial outer membrane antigens, whose molecular function is unknown. (from Pfam) NF016260.5 PF04357.18 TamB 22.4 22.4 381 PfamEq Y Y N translocation/assembly module TamB domain-containing protein GO:0005886,GO:0009306 22466966,25195908 131567 cellular organisms no rank 69849 EBI-EMBL TamB, inner membrane protein subunit of TAM complex TamB, inner membrane protein subunit of TAM complex TamB is an integral inner membrane protein that forms a complex - the translocation and assembly module or TAM [2] - with the outer membrane protein, TamA. TAM is responsible for the efficient secretion of the adhesin protein Ag43 in E.coli K-12 [1]. [1]. 22466966. Discovery of an archetypal protein transport system in bacterial outer membranes. Selkrig J, Mosbahi K, Webb CT, Belousoff MJ, Perry AJ, Wells TJ, Morris F, Leyton DL, Totsika M, Phan MD, Celik N, Kelly M, Oates C, Hartland EL, Robins-Browne RM, Ramarathinam SH, Purcell AW, Schembri MA, Strugnell RA, Henderson IR, Walker D, Lithgow T;. Nat Struct Mol Biol. 2012;19:506-510. [2]. 25195908. Recombinant expression, purification, crystallization and preliminary X-ray diffraction analysis of the C-terminal DUF490(963-1138) domain of TamB from Escherichia coli. Josts I, Grinter R, Kelly SM, Mosbahi K, Roszak A, Cogdell R, Smith BO, Byron O, Walker D;. Acta Crystallogr F Struct Biol Commun. 2014;70:1272-1275. (from Pfam) NF016261.5 PF04358.18 DsrC 24.9 24.9 107 PfamEq Y Y N TusE/DsrC/DsvC family sulfur relay protein 11722571,1555572,9493389,9695921 131567 cellular organisms no rank 11330 EBI-EMBL DsrC like protein TusE/DsrC/DsvC family sulfur relay protein Family member Swiss:P45573 has been observed to co-purify with Desulfovibrio vulgaris dissimilatory sulfite reductase [1], and many members of this family are annotated as the third (gamma) subunit of dissimilatory sulphite reductase. However, this protein appears to be only loosely associated to the sulfite reductase, which suggests that DsrC may not be an integral part of the dissimilatory sulphite reductase. Members of this family are found in organisms such as E. coli and H. influenzae which do not contain dissimilatory sulphite reductases but can synthesise assimilatory sirohaem sulphite and nitrite reductases. It is speculated that DsrC may be involved in the assembly, folding or stabilisation of sirohaem proteins [2]. The strictly conserved cysteine in the C terminus suggests that DsrC may have a catalytic function in the metabolism of sulphur compounds [3]. [1]. 1555572. The third subunit of desulfoviridin-type dissimilatory sulfite reductases. Pierik AJ, Duyvis MG, van Helvoort JM, Wolbert RB, Hagen WR;. Eur J Biochem 1992;205:111-115. [2]. 9493389. A dissimilatory sirohaem-sulfite-reductase-type protein from the hyperthermophilic archaeon Pyrobaculum islandicum. Molitor M, Dahl C, Molitor I, Schafer U, Speich N, Huber R, Deutzmann R, Truper HG;. Microbiology 1998;144:529-541. [3]. 9695921. Sirohaem sulfite reductase and other proteins encoded by genes at the dsr locus of Chromatium vinosum are involved in the oxidation of intracellular sulfur. Pott AS, Dahl C;. Microbiology 1998;144:1881-1894. [4]. 11722571. Solution structure of Pyrobaculum aerophilum DsrC, an archaeal homologue of the gamma subunit of d. TRUNCATED at 1650 bytes (from Pfam) NF016268.5 PF04365.18 BrnT_toxin 34.5 34.5 77 domain Y Y N BrnT family toxin 22334680 131567 cellular organisms no rank 16991 EBI-EMBL Ribonuclease toxin, BrnT, of type II toxin-antitoxin system BrnT family toxin BrnT is a ribonuclease toxin of a type II toxin-antitoxin system that exhibits a RelE-like fold. The antitoxin that neutralises this toxin is Pfam:PF14384. BrnT is found in bacteria, archaea, bacteriophage, and plasmids. BrnT-BrnA forms a 2:2 tetrameric complex and autoregulates its own expression, which is induced by a number of different environmental stresses. Expression of BrnT alone results in cessation of bacterial growth which can be rescued after subsequent expression of BrnA [1]. [1]. 22334680. Molecular structure and function of the novel BrnT/BrnA toxin-antitoxin system of Brucella abortus. Heaton BE, Herrou J, Blackwell AE, Wysocki VH, Crosson S;. J Biol Chem. 2012;287:12098-12110. (from Pfam) NF016270.5 PF04367.18 DUF502 23.8 23.8 107 domain Y Y N DUF502 domain-containing protein 131567 cellular organisms no rank 17914 EBI-EMBL Protein of unknown function (DUF502) Protein of unknown function (DUF502) Predicted to be an integral membrane protein. (from Pfam) NF016274.5 PF04371.20 PAD_porph 25 25 321 domain Y Y N agmatine deiminase family protein GO:0004668,GO:0009446 10377098,11504612 131567 cellular organisms no rank 54257 EBI-EMBL Porphyromonas-type peptidyl-arginine deiminase agmatine deiminase family protein Peptidyl-arginine deiminase (PAD) enzymes catalyse the deimination of the guanidino group from carboxy-terminal arginine residues of various peptides to produce ammonia. PAD from Porphyromonas gingivalis (PPAD) appears to be evolutionarily unrelated to mammalian PAD (Pfam:PF03068), which is a metalloenzyme. PPAD is thought to belong to the same superfamily as aminotransferase and arginine deiminase, and to form an alpha/beta propeller structure. This family has previously been named PPADH (Porphyromonas peptidyl-arginine deiminase homologues) [1]. The predicted catalytic residues in PPAD (Swiss:Q9RQJ2) are Asp130, Asp187, His236, Asp238 and Cys351 [1]. These are absolutely conserved with the exception of Asp187 which is absent in two family members. PPAD is also able to catalyse the deimination of free L-arginine, but has primarily peptidyl-arginine specificity. It may have a FMN cofactor [2]. [1]. 11504612. A novel superfamily of enzymes that catalyze the modification of guanidino groups. Shirai H, Blundell TL, Mizuguchi K;. Trends Biochem Sci 2001;26:465-468. [2]. 10377098. Purification, characterization, and sequence analysis of a potential virulence factor from Porphyromonas gingivalis, peptidylarginine deiminase. McGraw WT, Potempa J, Farley D, Travis J;. Infect Immun 1999;67:3248-3256. (from Pfam) NF016278.5 PF04378.18 RsmJ 27 27 245 PfamEq Y Y N 23S rRNA (adenine(2030)-N(6))-methyltransferase RlmJ rlmJ GO:0008649,GO:0070475 22847818,23945937 131567 cellular organisms no rank 24684 EBI-EMBL Ribosomal RNA large subunit methyltransferase D, RlmJ 23S rRNA (adenine(2030)-N(6))-methyltransferase RlmJ RlmJ is ribosomal RNA large subunit methyltransferase J is required for full methylation of 23S ribosomal RNA (rRNA) during ribosome biogenesis. The ribosomal RNA of E. coli carries 24 residues that require methylation, and this methyltransferase is the last to be described, that modifies A2030 [1]. RlmJ displays a variant of the Rossmann-like methyltransferase (MTase) fold with an inserted helical subdomain. On binding cofactor and substrate a large shift of the N-terminal motif X tail is induced in order to make it cover the cofactor-binding site and to trigger active-site changes in motifs IV and VIII [2]. [1]. 22847818. The last rRNA methyltransferase of E. coli revealed: the yhiR gene encodes adenine-N6 methyltransferase specific for modification of A2030 of 23S ribosomal RNA. Golovina AY, Dzama MM, Osterman IA, Sergiev PV, Serebryakova MV, Bogdanov AA, Dontsova OA;. RNA. 2012;18:1725-1734. [2]. 23945937. Structural and functional insights into the molecular mechanism of rRNA m6A methyltransferase RlmJ. Punekar AS, Liljeruhm J, Shepherd TR, Forster AC, Selmer M;. Nucleic Acids Res. 2013; [Epub ahead of print] (from Pfam) NF016283.5 PF04383.18 KilA-N 23.8 23.8 107 domain Y Y N KilA-N domain-containing protein 11897024,9299332 131567 cellular organisms no rank 16788 EBI-EMBL KilA-N domain KilA-N domain The amino-terminal module of the D6R/N1R proteins defines a novel, conserved DNA-binding domain (the KilA-N domain) that is found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. The KilA-N domain family also includes the previously defined APSES domain. The KilA-N and APSES domains may also share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease [1]. [1]. 11897024. Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors. Iyer LM, Koonin EV, Aravind L;. Genome Biol 2002;3:RESEARCH0012. [2]. 9299332. The X-ray structure of the DNA-binding domain from the Saccharomyces cerevisiae cell-cycle transcription factor Mbp1 at 2.1 A resolution. Taylor IA, Treiber MK, Olivi L, Smerdon SJ;. J Mol Biol 1997;272:1-8. (from Pfam) NF016289.5 PF04389.22 Peptidase_M28 21.3 21.3 193 domain Y Y N M28 family peptidase 131567 cellular organisms no rank 308804 EBI-EMBL Peptidase family M28 M28 family peptidase NF016292.5 PF04392.17 ABC_sub_bind 25.9 25.9 293 subfamily Y Y N ABC transporter substrate binding protein 131567 cellular organisms no rank 40931 EBI-EMBL ABC transporter substrate binding protein ABC transporter substrate binding protein This family contains many hypothetical proteins and some ABC transporter substrate binding proteins. (from Pfam) NF016296.5 PF04397.20 LytTR 22.6 22.6 98 domain Y Y N LytTR family transcriptional regulator DNA-binding domain-containing protein GO:0003677 12034833 131567 cellular organisms no rank 187623 EBI-EMBL LytTr DNA-binding domain LytTr DNA-binding domain This domain is found in a variety of bacterial transcriptional regulators. The domain binds to a specific DNA sequence pattern (see [1]). [1]. 12034833. A novel type of conserved DNA-binding domain in the transcriptional regulators of the AlgR/AgrA/LytR family. Nikolskaya AN, Galperin MY;. Nucleic Acids Res 2002;30:2453-2459. (from Pfam) NF016300.5 PF04402.19 SIMPL 25.2 25.2 205 subfamily Y Y N SIMPL domain-containing protein 11096118,11207567 131567 cellular organisms no rank 59974 EBI-EMBL Protein of unknown function (DUF541) SIMPL domain Members of this family have so far been found in bacteria and mouse SwissProt or TrEMBL entries. However possible family members have also been identified in translated rat (Genbank:AW144450) and human (Genbank:AI478629) ESTs. A mouse family member has been named SIMPL (signalling molecule that associates with mouse pelle-like kinase). SIMPL appears to facilitate and/or regulate complex formation between IRAK/mPLK (IL-1 receptor-associated kinase) and IKK (inhibitor of kappa-B kinase) containing complexes, and thus regulate NF-kappa-B activity [1]. Separate experiments demonstrate that a mouse family member (named LaXp180) binds the Listeria monocytogenes surface protein ActA, which is a virulence factor that induces actin polymerisation. It may also bind stathmin, a protein involved in signal transduction and in the regulation of microtubule dynamics [2]. In bacteria its function is unknown, but it is thought to be located in the periplasm or outer membrane. [1]. 11096118. SIMPL is a tumor necrosis factor-specific regulator of nuclear factor-kappaB activity. Vig E, Green M, Liu Y, Yu KY, Kwon HJ, Tian J, Goebl MG, Harrington MA;. J Biol Chem 2001;276:7859-7866. [2]. 11207567. LaXp180, a mammalian ActA-binding protein, identified with the yeast two-hybrid system, co-localizes with intracellular Listeria monocytogenes. Pfeuffer T, Goebel W, Laubinger J, Bachmann M, Kuhn M;. Cell Microbiol 2000;2:101-114. (from Pfam). The SIMPL domain is named for its presence in mouse protein SIMPL (signalling molecule that associates with mouse pelle-like kinase). Bacterial member BP26, from Brucella, was shown to assemble into a channel-like structure, while YggE from E. coli has been associated with resistance to oxidative stress. NF016302.5 PF04404.17 ERF 25 25 153 domain Y Y N ERF family protein 11914131 131567 cellular organisms no rank 13613 EBI-EMBL ERF superfamily ERF family protein The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to ERF [1]. [1]. 11914131. Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52. Iyer LM, Koonin EV, Aravind L;. BMC Genomics 2002;3:8-8. (from Pfam) NF016304.5 PF04406.19 TP6A_N 26 26 62 PfamEq Y N N Type IIB DNA topoisomerase GO:0003677,GO:0003824,GO:0005524,GO:0005694,GO:0006259 10545127 131567 cellular organisms no rank 1380 EBI-EMBL Type IIB DNA topoisomerase Type IIB DNA topoisomerase Type II DNA topoisomerases are ubiquitous enzymes that catalyse the ATP-dependent transport of one DNA duplex through a second DNA segment via a transient double-strand break. Type II DNA topoisomerases are now subdivided into two sub-families, type IIA and IIB DNA topoisomerases. TP6A_N is present in type IIB topoisomerase and is thought to be involved in DNA binding owing to its sequence similarity to E. coli catabolite activator protein (CAP) [1]. [1]. 10545127. Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11. Nichols MD, DeAngelis K, Keck JL, Berger JM;. EMBO J 1999;18:6177-6188. (from Pfam) NF016309.5 PF04411.17 PDDEXK_7 22.1 22.1 164 domain Y Y N nuclease domain-containing protein 17584917 131567 cellular organisms no rank 5652 EBI-EMBL PD-(D/E)XK nuclease superfamily PD-(D/E)XK superfamily nuclease domain 7 This domain has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches [1]. The domain has two additional beta-strands inserted to the core fold after the first core alpha-helix. It has been speculated that it could function as s methylation-dependent restriction [1]. The domain has two additional beta-strands inserted into the core fold after the first core alpha-helix. The PD-(D/E)XK signature is clearly conserved corresponding to an invariant PD (motif II) and DAK (motif III) motifs. There is also a conserved glutamic acid in motif I that is most likely to be involved in metal ion binding. The second core alpha-helix contains an invariant MHXYRD motif. It has been speculated that it could function as s methylation-dependent restriction enzyme [1]. [1]. 17584917. Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches. Knizewski L, Kinch LN, Grishin NV, Rychlewski L, Ginalski K;. BMC Struct Biol. 2007;7:40. (from Pfam) NF016310.5 PF04412.18 AcnX 31.5 31.5 400 domain Y Y N aconitase X 14568143,27929065 131567 cellular organisms no rank 8271 EBI-EMBL Aconitase X aconitase X Aconitase X (AcnX) is a subfamily of Acn superfamily. It is encoded in the genomes of many archaea, proteobacteria and fungi. Among archaea, the pattern of aconitase X occurrence complements that of aconitase A such that together the two enzymes account for aconitase activity in all archaea [1]. This protein catalyzes the dehydration of cis-3-hydroxy-L-proline to delta1-pyrroline-2-carboxylate [2]. [1]. 14568143. Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis. Makarova KS, Koonin EV;. FEMS Microbiol Lett. 2003;227:17-23. [2]. 27929065. Functional characterization of aconitase X as a cis-3-hydroxy-L-proline dehydratase. Watanabe S, Tajima K, Fujii S, Fukumori F, Hara R, Fukuda R, Miyazaki M, Kino K, Watanabe Y;. Sci Rep. 2016;6:38720. (from Pfam) NF016312.5 PF04414.17 tRNA_deacylase 33.6 33.6 205 domain Y Y N D-aminoacyl-tRNA deacylase GO:0016788,GO:0051499 17251192 131567 cellular organisms no rank 1534 EBI-EMBL D-aminoacyl-tRNA deacylase D-aminoacyl-tRNA deacylase Several aminoacyl-tRNA synthetases have the ability to transfer the D-isomer of their amino acid onto their cognate tRNA. D-aminoacyl-tRNA deacylases hydrolyse the ester bond between the polynucleotide and the D-amino acid, thereby preventing the accumulation of such mis-acylated and metabolically inactive tRNA molecules. [1]. 17251192. GEK1, a gene product of Arabidopsis thaliana involved in ethanol tolerance, is a D-aminoacyl-tRNA deacylase. Wydau S, Ferri-Fioni ML, Blanquet S, Plateau P;. Nucleic Acids Res. 2007;35:930-938. (from Pfam) NF016313.5 PF04415.17 DUF515 29 29 449 PfamAutoEq Y Y N DUF515 domain-containing protein 131567 cellular organisms no rank 313 EBI-EMBL Protein of unknown function (DUF515) Protein of unknown function (DUF515) Family of hypothetical Archaeal proteins. (from Pfam) NF016319.5 PF04422.18 FrhB_FdhB_N 22 22 78 domain Y Y N coenzyme F420 hydrogenase/dehydrogenase beta subunit N-terminal domain-containing protein 10751389,2207102,3531194 131567 cellular organisms no rank 11600 EBI-EMBL Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the N termini of F420 hydrogenase and dehydrogenase beta subunits [1], [2]. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (EC:1.2.1.2, Swiss:P06130) is also a member of this family [3]. This region is often found in association with the 4Fe-4S binding domain, fer4 (Pfam:PF00037). [1]. 2207102. Cloning, sequence determination, and expression of the genes encoding the subunits of the nickel-containing 8-hydroxy-5-deazaflavin reducing hydrogenase from Methanobacterium thermoautotrophicum delta H. Alex LA, Reeve JN, Orme-Johnson WH, Walsh CT;. Biochemistry 1990;29:7237-7244. [2]. 10751389. The F420H2 dehydrogenase from Methanosarcina mazei is a Redox-driven proton pump closely related to NADH dehydrogenases. Baumer S, Ide T, Jacobi C, Johann A, Gottschalk G, Deppenmeier U;. J Biol Chem 2000;275:17968-17973. [3]. 3531194. Cloning, expression, and nucleotide sequence of the formate dehydrogenase genes from Methanobacterium formicicum. Shuber AP, Orr EC, Recny MA, Schendel PF, May HD, Schauer NL, Ferry JG;. J Biol Chem 1986;261:12942-12947. (from Pfam) NF016320.5 PF04423.19 Rad50_zn_hook 24.3 24.3 52 PfamEq Y N N Rad50 zinc hook motif 12151226,12152085 131567 cellular organisms no rank 1225 EBI-EMBL Rad50 zinc hook motif Rad50 zinc hook motif The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side. [1]. 12152085. The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair. Hopfner KP, Craig L, Moncalian G, Zinkel RA, Usui T, Owen BA, Karcher A, Henderson B, Bodmer JL, McMurray CT, Carney JP, Petrini JH, Tainer JA;. Nature 2002;418:562-566. [2]. 12151226. Tethering on the brink: the evolutionarily conserved Mre11-Rad50 complex. Connelly JC, Leach DR;. Trends Biochem Sci 2002;27:410-418. (from Pfam) NF016326.5 PF04430.19 DUF498 33 33 109 PfamAutoEq Y Y N MTH938/NDUFAF3 family protein 11746696 131567 cellular organisms no rank 12537 EBI-EMBL Protein of unknown function (DUF498/DUF598) MTH938/NDUFAF3 family protein Members of this family, found in all domains of life, include MTH938 in Methanobacterium thermoautotrophicum, and NDUFAF3, called the NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 3. NF016328.5 PF04432.18 FrhB_FdhB_C 23.3 23.3 150 domain Y Y N Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C-terminal domain 10751389,2207102,3531194 131567 cellular organisms no rank 14339 EBI-EMBL Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C-terminal domain Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C termini of F420 hydrogenase and dehydrogenase beta subunits [1], [2]. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (EC:1.2.1.2, Swiss:P06130) is also a member of this family [3]. This region is often found in association with the 4Fe-4S binding domain, fer4 (Pfam:PF00037). [1]. 2207102. Cloning, sequence determination, and expression of the genes encoding the subunits of the nickel-containing 8-hydroxy-5-deazaflavin reducing hydrogenase from Methanobacterium thermoautotrophicum delta H. Alex LA, Reeve JN, Orme-Johnson WH, Walsh CT;. Biochemistry 1990;29:7237-7244. [2]. 10751389. The F420H2 dehydrogenase from Methanosarcina mazei is a Redox-driven proton pump closely related to NADH dehydrogenases. Baumer S, Ide T, Jacobi C, Johann A, Gottschalk G, Deppenmeier U;. J Biol Chem 2000;275:17968-17973. [3]. 3531194. Cloning, expression, and nucleotide sequence of the formate dehydrogenase genes from Methanobacterium formicicum. Shuber AP, Orr EC, Recny MA, Schendel PF, May HD, Schauer NL, Ferry JG;. J Biol Chem 1986;261:12942-12947. (from Pfam) NF016330.5 PF04434.22 SWIM 19.6 7.5 38 domain Y Y N SWIM zinc finger family protein GO:0008270 12151216 131567 cellular organisms no rank 65259 EBI-EMBL SWIM zinc finger SWIM zinc finger family protein This domain is found in bacterial, archaeal and eukaryotic proteins. It is predicted to be organised into two N-terminal beta-strands and a C-terminal alpha helix, thus possibly adopting a fold similar to that of the C2H2 zinc finger (Pfam:PF00096). SWIM is thought to be a versatile domain that can interact with DNA or proteins in different contexts [1]. [1]. 12151216. SWIM, a novel Zn-chelating domain present in bacteria, archaea and eukaryotes. Makarova KS, Aravind L, Koonin EV;. Trends Biochem Sci 2002;27:384-386. (from Pfam) NF016334.5 PF04439.17 Adenyl_transf 22 22 279 domain Y Y N aminoglycoside 6-adenylyltransferase 9211644 131567 cellular organisms no rank 9911 EBI-EMBL Streptomycin adenylyltransferase aminoglycoside 6-adenylyltransferase Also known as Aminoglycoside 6- adenylyltransferase (EC:2.7.7.-), this protein confers resistance to aminoglycoside antibiotics. [1]. 9211644. Bacterial resistance to aminoglycoside antibiotics. Davies J, Wright GD;. Trends Microbiol 1997;5:234-240. (from Pfam) NF016338.5 PF04443.17 LuxE 24.9 24.9 391 PfamEq Y N N Acyl-protein synthetase, LuxE GO:0008218,GO:0047474 2023262,8529890,8941351 131567 cellular organisms no rank 11695 EBI-EMBL Acyl-protein synthetase, LuxE Acyl-protein synthetase, LuxE LuxE is an acyl-protein synthetase found in bioluminescent bacteria. LuxE catalyses the formation of an acyl-protein thioester from a fatty acid and a protein. This is the second step in the bioluminescent fatty acid reduction system, which converts tetradecanoic acid to the aldehyde substrate of the luciferase-catalysed bioluminescence reaction [1] A conserved cysteine found at position 364 in Photobacterium phosphoreum LuxE (Swiss:Q52100) is thought to be acylated during the transfer of the acyl group from the synthetase subunit to the reductase. The carboxyl terminal of the synthetase is though to act as a flexible arm to transfer acyl groups between the sites of activation and reduction [2]. This family also includes Vibrio cholerae RBFN protein (Swiss:Q06961), which is involved in the biosynthesis of the O-antigen component 3-deoxy-L-glycero-tetronic acid. [1]. 8941351. Nucleotide sequence and functional analysis of the luxE gene encoding acyl-protein synthetase of the lux operon from Photobacterium leiognathi. Lin JW, Chao YF, Weng SF;. Biochem Biophys Res Commun 1996;228:764-773. [2]. 2023262. Identification of the acyl transfer site of fatty acyl-protein synthetase from bioluminescent bacteria. Soly RR, Meighen EA;. J Mol Biol 1991;219:69-77. [3]. 8529890. A putative pathway for biosynthesis of the O-antigen component, 3-deoxy-L-glycero-tetronic acid, based on the sequence of the Vibrio cholerae O1 rfb region. Morona R, Stroeher UH, Karageorgos LE, Brown MH, Manning PA;. Gene 1995;166:19-31. (from Pfam) NF016341.5 PF04446.17 Thg1 29.2 29.2 130 domain Y Y N tRNA(His) guanylyltransferase Thg1 family protein GO:0000287,GO:0006400,GO:0008193 14633974,20591188,21059936 131567 cellular organisms no rank 2316 EBI-EMBL tRNAHis guanylyltransferase tRNA(His) guanylyltransferase Thg1 family protein The Thg1 protein from Saccharomyces cerevisiae is responsible for adding a GMP residue to the 5' end of tRNA His [1]. The catalytic domain Thg1 contains a RRM (ferredoxin) fold palm domain, just like the viral RNA-dependent RNA polymerases, reverse transcriptases, family A and B DNA polymerases, adenylyl cyclases, diguanylate cyclases (GGDEF domain) and the predicted polymerase of the CRISPR system [2]. Thg1 possesses an active site with three acidic residues that chelate Mg++ cations [2]. Thg1 catalyzes polymerization similar to the 5'-3' polymerases [2][3]. [1]. 14633974. tRNAHis maturation: An essential yeast protein catalyzes addition of a guanine nucleotide to the 5' end of tRNAHis. Gu W, Jackman JE, Lohan AJ, Gray MW, Phizicky EM;. 17;0:0-0. [2]. 20591188. Presence of a classical RRM-fold palm domain in Thg1-type 3'- 5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains. Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2010;5:43. [3]. 21059936. tRNA(His) guanylyltransferase (THG1), a unique 3'-5' nucleotidyl transferase, shares unexpected structural homology with canonical 5'-3' DNA polymerases. Hyde SJ, Eckenroth BE, Smith BA, Eberley WA, Heintz NH, Jackman JE, Doublie S;. Proc Natl Acad Sci U S A. 2010;107:20305-20310. (from Pfam) NF016345.5 PF04450.17 BSP 23.8 23.8 207 domain Y Y N basic secretory protein-like protein 10202814 131567 cellular organisms no rank 3119 EBI-EMBL Peptidase of plants and bacteria basic secretory protein-like protein These basic secretory proteins (BSPs) are believed to be part of the plants defence mechanism against pathogens [1]. [1]. 10202814. Abscisic acid-induced secretory proteins in suspension-cultured cells of winter wheat. Kuwabara C, Arakawa K, Yoshida S;. Plant Cell Physiol 1999;40:184-191. (from Pfam) NF016349.5 PF04454.17 Linocin_M18 24.3 24.3 253 PfamEq Y Y N encapsulin GO:0008233,GO:0042742 19172747,7986050,8919789 131567 cellular organisms no rank 7152 EBI-EMBL Encapsulating protein for peroxidase encapsulin The Linocin_M18 is found in eubacteria and archaea [1,2]. These proteins, referred to as encapsulins, form nanocompartments within the bacterium which contain ferritin-like proteins or peroxidases, enzymes involved in oxidative-stress response. These enzymes are targeted to the interior of encapsulins via unique C-terminal extensions [3]. [1]. 8919789. Nucleotide sequence and taxonomical distribution of the bacteriocin gene lin cloned from Brevibacterium linens M18. Valdes-Stauber N, Scherer S;. Appl Environ Microbiol 1996;62:1283-1286. [2]. 7986050. Isolation and characterization of Linocin M18, a bacteriocin produced by Brevibacterium linens. Valdes-Stauber N, Scherer S;. Appl Environ Microbiol 1994;60:3809-3814. [3]. 19172747. Structural basis of enzyme encapsulation into a bacterial nanocompartment. Sutter M, Boehringer D, Gutmann S, Gunther S, Prangishvili D, Loessner MJ, Stetter KO, Weber-Ban E, Ban N;. Nat Struct Mol Biol. 2008;15:939-947. (from Pfam) NF016350.5 PF04455.17 Saccharop_dh_N 23.5 23.5 100 PfamEq Y N N LOR/SDH bifunctional enzyme conserved region 9426595,9654071 131567 cellular organisms no rank 2300 EBI-EMBL LOR/SDH bifunctional enzyme conserved region LOR/SDH bifunctional enzyme conserved region Lysine-oxoglutarate reductase/Saccharopine dehydrogenase (LOR/SDH) is a bifunctional enzyme. This conserved region is commonly found immediately N-terminal to Saccharop_dh (Pfam:PF03435) in eukaryotes [1,2]. [1]. 9426595. Lysine-ketoglutarate reductase and saccharopine dehydrogenase from Arabidopsis thaliana: nucleotide sequence and characterization. Epelbaum S, McDevitt R, Falco SC;. Plant Mol Biol 1997;35:735-748. [2]. 9654071. Structure and regulation of the bifunctional enzyme lysine-oxoglutarate reductase-saccharopine dehydrogenase in maize. Kemper EL, Cord-Neto G, Capella AN, Goncalves-Butruile M, Azevedo RA, Arruda P;. Eur J Biochem 1998;253:720-729. (from Pfam) NF016352.5 PF04457.17 MJ1316 26.3 26.3 75 PfamAutoEq Y Y N RNA repair domain-containing protein 27536007 131567 cellular organisms no rank 3411 EBI-EMBL MJ1316 RNA cyclic group end recognition domain MJ1316 RNA cyclic group end recognition domain RNA repair domain predicted to be involved specifically in the recognition of RNA 3' ends with 2'-3' cyclic phosphate groups [1]. [1]. 27536007. RNA damage in biological conflicts and the diversity of responding RNA repair systems. Burroughs AM, Aravind L;. Nucleic Acids Res. 2016;44:8525-8555. (from Pfam) NF016353.5 PF04458.17 DUF505 28.7 28.7 622 domain Y Y N DUF505 family protein 131567 cellular organisms no rank 169 EBI-EMBL Protein of unknown function (DUF505) DUF505 family protein Family of uncharacterised prokaryotic proteins. (from Pfam) NF016354.5 PF04459.17 DUF512 25 25 202 PfamAutoEq Y Y N DUF512 domain-containing protein 131567 cellular organisms no rank 5897 EBI-EMBL Protein of unknown function (DUF512) Protein of unknown function (DUF512) Family of uncharacterised prokaryotic proteins. (from Pfam) NF016356.5 PF04463.17 2-thiour_desulf 34.7 34.7 141 domain Y Y N 2-thiouracil desulfurase family protein 29194984 131567 cellular organisms no rank 33530 EBI-EMBL 2-thiouracil desulfurase 2-thiouracil desulfurase family protein This family of proteins, predominantly found in Bacteria, are involved in the desulfuration of 2-thiouracil into uracil in the 2-thiouridine degradation pathway. It has been demonstrated that these proteins contain a Fe-S cluster required for their activity [1]. [1]. 29194984. A gene encoding a DUF523 domain protein is involved in the conversion of 2-thiouracil into uracil. Aucynaite A, Rutkiene R, Gasparaviciute R, Meskys R, Urbonavicius J;. Environ Microbiol Rep. 2018;10:49-56. (from Pfam) NF016357.5 PF04464.19 Glyphos_transf 22.1 22.1 367 domain Y Y N CDP-glycerol glycerophosphotransferase family protein GO:0016020,GO:0047355 10648531 131567 cellular organisms no rank 90848 EBI-EMBL CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase CDP-glycerol glycerophosphotransferase family protein Wall-associated teichoic acids are a heterogeneous class of phosphate-rich polymers that are covalently linked to the cell wall peptidoglycan of gram-positive bacteria. They consist of a main chain of phosphodiester-linked polyols and/or sugar moieties attached to peptidoglycan via a linkage unit. CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase is responsible for the polymerisation of the main chain of the teichoic acid by sequential transfer of glycerol-phosphate units from CDP-glycerol to the linkage unit lipid [1]. [1]. 10648531. Molecular analysis of the tagF gene, encoding CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase of Staphylococcus epidermidis ATCC 14990. Fitzgerald SN, Foster TJ;. J Bacteriol 2000;182:1046-1052. (from Pfam) NF016358.5 PF04465.17 DUF499 23 23 1024 domain Y Y N DUF499 domain-containing protein 131567 cellular organisms no rank 5605 EBI-EMBL Protein of unknown function (DUF499) Protein of unknown function (DUF499) Family of uncharacterised hypothetical prokaryotic proteins. (from Pfam) NF016359.5 PF04466.18 Terminase_3 23.2 23.2 201 subfamily Y Y N phage terminase large subunit 10930407,1548711 131567 cellular organisms no rank 27533 EBI-EMBL Phage terminase large subunit phage terminase large subunit Initiation of packaging of double-stranded viral DNA involves the specific interaction of the prohead with viral DNA in a process mediated by a phage-encoded terminase protein. The terminase enzymes are usually hetero-oligomers composed of a small and a large subunit. This region is found on the large subunit and possess an endonuclease and ATPase activity that require Mg2+ and a neutral or slightly basic reaction. This region is also found in bacterial sequences [1,2]. [1]. 10930407. Functional analysis of the terminase large subunit, G2P, of Bacillus subtilis bacteriophage SPP1. Gual A, Camacho AG, Alonso JC;. J Biol Chem 2000;275:35311-35319. [2]. 1548711. Molecular analysis of the Bacillus subtilis bacteriophage SPP1 region encompassing genes 1 to 6. The products of gene 1 and gene 2 are required for pac cleavage. Chai S, Bravo A, Luder G, Nedlin A, Trautner TA, Alonso JC;. J Mol Biol 1992;224:87-102. (from Pfam) NF016360.5 PF04467.17 DUF483 25 25 122 PfamAutoEq Y Y N DUF483 domain-containing protein 131567 cellular organisms no rank 101 EBI-EMBL Protein of unknown function (DUF483) Protein of unknown function (DUF483) Family of uncharacterised prokaryotic proteins. (from Pfam) NF016362.5 PF04471.17 Mrr_cat 21 21 115 domain Y Y N restriction endonuclease 3.1.21.- GO:0003677,GO:0004519,GO:0009307 11313145,1650347 131567 cellular organisms no rank 89309 EBI-EMBL Restriction endonuclease restriction endonuclease Prokaryotic family found in type II restriction enzymes containing the hallmark (D/E)-(D/E)XK active site. Presence of catalytic residues implicates this region in the enzymatic cleavage of DNA [1,2]. [1]. 1650347. Characterization and expression of the Escherichia coli Mrr restriction system. Waite-Rees PA, Keating CJ, Moran LS, Slatko BE, Hornstra LJ, Benner JS;. J Bacteriol 1991;173:5207-5219. [2]. 11313145. Identification of a PD-(D/E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs. Bujnicki JM, Rychlewski L;. Gene 2001;267:183-191. (from Pfam) NF016363.5 PF04472.17 SepF 27 27 72 subfamily Y Y N cell division protein SepF sepF GO:0090529 16420366 131567 cellular organisms no rank 28504 EBI-EMBL Cell division protein SepF cell division protein SepF SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation [1]. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This family also includes archaeal related proteins of unknown function. [1]. 16420366. SepF, a novel FtsZ-interacting protein required for a late step in cell division. Hamoen LW, Meile JC, de Jong W, Noirot P, Errington J;. Mol Microbiol. 2006;59:989-999. (from Pfam) NF016364.5 PF04473.17 DUF553 20.5 20.5 140 domain Y Y N transglutaminase-like domain-containing protein 12366374 131567 cellular organisms no rank 24574 EBI-EMBL Transglutaminase-like domain Transglutaminase-like domain This family of uncharacterised archaeal proteins are related to Transglutaminase-like domains. This family has previously been called DUF553 and UPF0252. (from Pfam) NF016365.5 PF04474.17 DUF554 25.1 25.1 220 subfamily Y Y N DUF554 family protein 131567 cellular organisms no rank 15496 EBI-EMBL Protein of unknown function (DUF554) DUF554 family protein Family of uncharacterised prokaryotic proteins. Multiple predicted transmembrane regions suggest that the region is membrane associated. (from Pfam) NF016367.5 PF04476.18 4HFCP_synth 22.4 22.4 228 domain Y Y N (5-formylfuran-3-yl)methyl phosphate synthase 24977328,25372812,25905665 131567 cellular organisms no rank 4159 EBI-EMBL 4-HFC-P synthase (5-formylfuran-3-yl)methyl phosphate synthase (5-formylfuran-3-yl)methyl phosphate synthase, also known as 4-HFC-P synthase, is involved in the production of methanofuran [1,2]. This family has a classical TIM-barrel structure whose biological unit is a homohexamer [1]. [1]. 24977328. Biosynthesis of the 5-(Aminomethyl)-3-furanmethanol moiety of methanofuran. Miller D, Wang Y, Xu H, Harich K, White RH;. Biochemistry. 2014;53:4635-4647. [2]. 25905665. Mechanism of the Enzymatic Synthesis of 4-(Hydroxymethyl)-2- furancarboxaldehyde-phosphate (4-HFC-P) from Glyceraldehyde-3-phosphate Catalyzed by 4-HFC-P Synthase. Wang Y, Jones MK, Xu H, Ray WK, White RH;. Biochemistry. 2015;54:2997-3008. [3]. 25372812. Structure of the methanofuran/methanopterin-biosynthetic enzyme MJ1099 from Methanocaldococcus jannaschii. Bobik TA, Morales EJ, Shin A, Cascio D, Sawaya MR, Arbing M, Yeates TO, Rasche ME;. Acta Crystallogr F Struct Biol Commun. 2014;70:1472-1479. (from Pfam) NF016370.5 PF04480.17 DUF559 20.6 20.6 109 domain Y Y N DUF559 domain-containing protein 131567 cellular organisms no rank 63541 EBI-EMBL Protein of unknown function (DUF559) Protein of unknown function (DUF559) NF016371.5 PF04481.17 DUF561 21.6 21.6 243 PfamAutoEq Y Y N DUF561 domain-containing protein 131567 cellular organisms no rank 11387 EBI-EMBL Protein of unknown function (DUF561) Protein of unknown function (DUF561) Protein of unknown function found in a cyanobacterium, and the chloroplasts of algae. (from Pfam) NF016377.5 PF04488.20 Gly_transf_sug 23 23 93 domain Y Y N glycosyltransferase 9653120 131567 cellular organisms no rank 22840 EBI-EMBL Glycosyltransferase sugar-binding region containing DXD motif glycosyltransferase DXD motif-containing sugar-binding region The DXD motif is a short conserved motif found in many families of glycosyltransferases, which add a range of different sugars to other sugars, phosphates and proteins. DXD-containing glycosyltransferases all use nucleoside diphosphate sugars as donors and require divalent cations, usually manganese. The DXD motif is expected to play a carbohydrate binding role in sugar-nucleoside diphosphate and manganese dependent glycosyltransferases [1]. [1]. 9653120. Activity of the yeast MNN1 alpha-1,3-mannosyltransferase requires a motif conserved in many other families of glycosyltransferases. Wiggins CA, Munro S;. Proc Natl Acad Sci U S A 1998;95:7945-7950. (from Pfam) NF016382.5 PF04493.19 Endonuclease_5 23.4 23.4 198 PfamEq Y Y N endonuclease V GO:0004519,GO:0006281 6246346,8990280 131567 cellular organisms no rank 21248 EBI-EMBL Endonuclease V endonuclease V Endonuclease V is specific for single-stranded DNA or for duplex DNA that contains uracil or that is damaged by a variety of agents [1]. [1]. 8990280. nfi, the gene for endonuclease V in Escherichia coli K-12. Guo G, Ding Y, Weiss B;. J Bacteriol 1997;179:310-316. [2]. 6246346. Purification and properties of Escherichia coli endodeoxyribonuclease V. Demple B, Gates FT 3rd, Linn S;. Methods Enzymol 1980;65:224-231. (from Pfam) NF016395.5 PF04506.18 Rft-1 23.8 23.8 512 domain Y Y N oligosaccharide translocation protein RFT1 GO:0006488,GO:0016020 11807558,7673248 131567 cellular organisms no rank 53 EBI-EMBL Rft protein oligosaccharide translocation protein RFT1 NF016397.5 PF04508.17 Pox_A_type_inc 21.4 21.4 23 repeat Y N N Viral A-type inclusion protein repeat GO:0016032 2826668 131567 cellular organisms no rank 70 EBI-EMBL Viral A-type inclusion protein repeat Viral A-type inclusion protein repeat The repeat is found in the A-type inclusion protein of the Poxvirus family [1]. [1]. 2826668. Cloning and characterization of the gene encoding the major protein of the A-type inclusion body of cowpox virus. Funahashi S, Sato T, Shida H;. J Gen Virol 1988;69:35-47. (from Pfam) NF016398.5 PF04509.17 CheC 22 22 38 domain Y Y N chemotaxis protein CheC GO:0016787 14749334,15187186 131567 cellular organisms no rank 19506 EBI-EMBL CheC-like family chemotaxis protein CheC The restoration of pre-stimulus levels of the chemotactic response regulator, CheY-P, is important for allowing bacteria to respond to new environmental stimuli. The members of this family, CheC, CheX, CheA and FliY are CheY-P phosphatase [1,2]. CheC appears to be primarily involved in restoring normal CheY-P levels, whereas FliY seems to act on CheY-P constitutively. CheD enhances the activity of CheC 5-fold, which is normally relatively low [1,2]. In some cases, the region represented by this entry is present as multiple copies. [1]. 14749334. Bacillus subtilis CheC and FliY are members of a novel class of CheY-P-hydrolyzing proteins in the chemotactic signal transduction cascade. Szurmant H, Muff TJ, Ordal GW;. J Biol Chem 2004;279:21787-21792. [2]. 15187186. Diversity in chemotaxis mechanisms among the bacteria and archaea. Szurmant H, Ordal GW;. Microbiol Mol Biol Rev 2004;68:301-319. (from Pfam) NF016408.5 PF04519.18 Bactofilin 27.9 27.9 98 domain Y Y N polymer-forming cytoskeletal protein 19959992 131567 cellular organisms no rank 28489 EBI-EMBL Polymer-forming cytoskeletal polymer-forming cytoskeletal protein This is a family of bactofilins, a functionally diverse class of cytoskeletal, polymer-forming, proteins that is widely conserved among bacteria. In the example species C. crescentus, two bactofilins assemble into a membrane-associated laminar structure that shows cell-cycle-dependent polar localisation and acts as a platform for the recruitment of a cell wall biosynthetic enzyme involved in polar morphogenesis. Bactofilins display distinct subcellular distributions and dynamics in different bacterial species, suggesting that they are versatile structural elements that have adopted a range of different cellular functions. [1]. 19959992. Bactofilins, a ubiquitous class of cytoskeletal proteins mediating polar localization of a cell wall synthase in Caulobacter crescentus. Kuhn J, Briegel A, Morschel E, Kahnt J, Leser K, Wick S, Jensen GJ, Thanbichler M;. EMBO J. 2009; [Epub ahead of print] (from Pfam) NF016413.5 PF04525.17 LOR 24.5 24.5 187 PfamEq Y Y N LURP-one-related family protein 18346188,19010806 131567 cellular organisms no rank 9976 EBI-EMBL LURP-one-related LURP-one-related family protein The structure of this family has been solved. It comprises a 12-stranded beta barrel with a central C-terminal alpha helix. This helix is thought to be a transmembrane helix. It is structurally similar to the C-terminal domain of the Tubby protein [1]. In plants it plays a role in defense against pathogens [2]. [1]. 19010806. Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. Bateman A, Finn RD, Sims PJ, Wiedmer T, Biegert A, Soding J;. Bioinformatics. 2009;25:159-162. [2]. 18346188. The oomycete response gene LURP1 is required for defense against Hyaloperonospora parasitica in Arabidopsis thaliana. Knoth C, Eulgem T;. Plant J. 2008;55:53-64. (from Pfam) NF016424.5 PF04536.19 TPM_phosphatase 27 27 125 domain Y Y N TPM domain-containing protein 17576201,21653280,21908686 131567 cellular organisms no rank 77858 EBI-EMBL TPM domain TPM domain This family was first named TPM domain after its founding proteins: TLP18.3, Psb32 and MOLO-1. In Arabidopsis, this domain is called the thylakoid acid phosphatase -TAP - domain and has a Rossmann-like fold [1]. In plants, the family resides in the thylakoid lumen attached to the outer membrane of the chloroplast/plastid. It is active in the photosystem II [2,3]. [1]. 21908686. Structural and Functional Assays of AtTLP18.3 Identify Its Novel Acid Phosphatase Activity in Thylakoid Lumen. Wu HY, Liu MS, Lin TP, Cheng YS;. Plant physiol. 2011;9:0-0. [2]. 17576201. TLP18.3, a novel thylakoid lumen protein regulating photosystem II repair cycle. Sirpio S, Allahverdiyeva Y, Suorsa M, Paakkarinen V, Vainonen J, Battchikova N, Aro EM;. Biochem J. 2007;406:415-425. [3]. 21653280. The Psb32 protein aids in repairing photodamaged photosystem II in the cyanobacterium Synechocystis 6803. Wegener KM, Bennewitz S, Oelmuller R, Pakrasi HB;. Mol Plant. 2011;4:1052-1061. (from Pfam) NF016432.5 PF04545.21 Sigma70_r4 24.1 24.1 50 domain Y Y N sigma factor-like helix-turn-helix DNA-binding protein GO:0003700,GO:0006352,GO:0006355 11931761 131567 cellular organisms no rank 959007 EBI-EMBL Sigma-70, region 4 sigma factor-like helix-turn-helix DNA-binding domain Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives. [1]. 11931761. Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA;. Mol Cell 2002;9:527-539. (from Pfam) NF016435.5 PF04548.21 AIG1 27 27 212 domain Y N N AIG1 family GO:0005525 8742710 131567 cellular organisms no rank 57577 EBI-EMBL AIG1 family AIG1 family Arabidopsis protein AIG1 appears to be involved in plant resistance to bacteria. [1]. 8742710. Isolation of Arabidopsis genes that differentiate between resistance responses mediated by the RPS2 and RPM1 disease resistance genes. Reuber TL, Ausubel FM;. Plant Cell 1996;8:241-249. (from Pfam) NF016442.5 PF04555.18 XhoI 25 25 191 domain Y Y N PaeR7I family type II restriction endonuclease GO:0003677,GO:0009036,GO:0009307 22638584,3001639 131567 cellular organisms no rank 1508 EBI-EMBL Restriction endonuclease XhoI PaeR7I family type II restriction endonuclease This family consists of type II restriction enzymes (EC:3.1.21.4) that recognise the double-stranded sequence CTCGAG and cleave after C-1. [1]. 3001639. Nucleotide sequence of the PaeR7 restriction/modification system and partial characterization of its protein products. Theriault G, Roy PH, Howard KA, Benner JS, Brooks JE, Waters AF, Gingeras TR;. Nucleic Acids Res 1985;13:8441-8461. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF016443.5 PF04556.17 DpnII 23 23 278 PfamEq Y Y N DpnII family type II restriction endonuclease 3.1.21.4 GO:0003677,GO:0009036,GO:0009307 11133943 131567 cellular organisms no rank 3457 EBI-EMBL DpnII restriction endonuclease DpnII family type II restriction endonuclease Members of this family include various GATC-recognizing type II restriction enzymes such as DpnII from Streptococcus pneumoniae. NF016447.5 PF04560.25 RNA_pol_Rpb2_7 32.1 32.1 87 PfamEq Y N N RNA polymerase Rpb2, domain 7 GO:0003677,GO:0003899,GO:0006351 11313498 131567 cellular organisms no rank 65066 EBI-EMBL RNA polymerase Rpb2, domain 7 RNA polymerase Rpb2, domain 7 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1]. [1]. 11313498. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Cramer P, Bushnell DA, Kornberg RD;. Science 2001;292:1863-1876. (from Pfam) NF016448.5 PF04561.19 RNA_pol_Rpb2_2 21.7 21.7 190 PfamEq Y N N RNA polymerase Rpb2, domain 2 GO:0003677,GO:0003899,GO:0006351 11313498 131567 cellular organisms no rank 65531 EBI-EMBL RNA polymerase Rpb2, domain 2 RNA polymerase Rpb2, domain 2 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI). [1]. 11313498. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Cramer P, Bushnell DA, Kornberg RD;. Science 2001;292:1863-1876. (from Pfam) NF016450.5 PF04563.20 RNA_pol_Rpb2_1 28.2 28.2 203 PfamEq Y N N RNA polymerase beta subunit GO:0003677,GO:0003899,GO:0006351 11313498,3116266 131567 cellular organisms no rank 65135 EBI-EMBL RNA polymerase beta subunit RNA polymerase beta subunit RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain [1]. The other lobe (Pfam:PF04561) is nested within this domain. [1]. 3116266. RNA polymerase II of Drosophila. Relation of its 140,000 Mr subunit to the beta subunit of Escherichia coli RNA polymerase. Falkenburg D, Dworniczak B, Faust DM, Bautz EK;. J Mol Biol 1987;195:929-937. [2]. 11313498. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Cramer P, Bushnell DA, Kornberg RD;. Science 2001;292:1863-1876. (from Pfam) NF016452.5 PF04565.21 RNA_pol_Rpb2_3 21 10.3 68 PfamEq Y N N RNA polymerase Rpb2, domain 3 GO:0003677,GO:0003899,GO:0006351 11313498 131567 cellular organisms no rank 66364 EBI-EMBL RNA polymerase Rpb2, domain 3 RNA polymerase Rpb2, domain 3 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site [1]. [1]. 11313498. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Cramer P, Bushnell DA, Kornberg RD;. Science 2001;292:1863-1876. (from Pfam) NF016453.5 PF04566.18 RNA_pol_Rpb2_4 28.7 28.7 62 PfamEq Y N N RNA polymerase Rpb2, domain 4 GO:0003677,GO:0003899,GO:0006351 11313498 131567 cellular organisms no rank 1319 EBI-EMBL RNA polymerase Rpb2, domain 4 RNA polymerase Rpb2, domain 4 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain [1]. [1]. 11313498. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Cramer P, Bushnell DA, Kornberg RD;. Science 2001;292:1863-1876. (from Pfam) NF016454.5 PF04567.22 RNA_pol_Rpb2_5 21.1 21.1 66 PfamEq Y N N RNA polymerase Rpb2, domain 5 GO:0006351 11313498 131567 cellular organisms no rank 1318 EBI-EMBL RNA polymerase Rpb2, domain 5 RNA polymerase Rpb2, domain 5 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain [1]. [1]. 11313498. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Cramer P, Bushnell DA, Kornberg RD;. Science 2001;292:1863-1876. (from Pfam) NF016464.5 PF04577.19 Glyco_transf_61 27 27 137 domain Y Y N glycosyltransferase 61 family protein GO:0016757 22024534,23671640,23929950 131567 cellular organisms no rank 10268 EBI-EMBL Glycosyltransferase 61 glycosyltransferase 61 family protein This family represents the Glycosyltransferase Family 61. Members in this family are further processed into a mature form. It includes O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 (POMGnT2, also known as AGO61 or EOGLT) [1] and EGF domain-specific O-linked N-acetylglucosamine transferase (EOGT) [2]. This family also includes plant beta-1,2-xylosyltransferases [3]. [1]. 23929950. SGK196 is a glycosylation-specific O-mannose kinase required for dystroglycan function. Yoshida-Moriguchi T, Willer T, Anderson ME, Venzke D, Whyte T, Muntoni F, Lee H, Nelson SF, Yu L, Campbell KP;. Science. 2013;341:896-899. [2]. 23671640. The EGF repeat-specific O-GlcNAc-transferase Eogt interacts with notch signaling and pyrimidine metabolism pathways in Drosophila. Muller R, Jenny A, Stanley P;. PLoS One. 2013;8:e62835. [3]. 22024534. Arabidopsis beta1,2-xylosyltransferase: substrate specificity and participation in the plant-specific N-glycosylation pathway. Kajiura H, Okamoto T, Misaki R, Matsuura Y, Fujiyama K;. J Biosci Bioeng. 2012;113:48-54. (from Pfam) NF016471.5 PF04586.22 Peptidase_S78 21 21 165 domain Y Y N HK97 family phage prohead protease GO:0008233,GO:0019082 131567 cellular organisms no rank 36283 EBI-EMBL Caudovirus prohead serine protease HK97 family phage prohead protease Family of Caudovirus prohead serine proteases also found in a number of bacteria possibly as the result of horizontal transfer. (from Pfam) NF016472.5 PF04587.20 ADP_PFK_GK 27 27 430 domain Y Y N ADP-dependent glucokinase/phosphofructokinase GO:0005975,GO:0016773 10409652,11342216,11717273 131567 cellular organisms no rank 1574 EBI-EMBL ADP-specific Phosphofructokinase/Glucokinase conserved region ADP-dependent glucokinase/phosphofructokinase In archaea a novel type of glycolytic pathway exists that is deviant from the classical Embden-Meyerhof pathway. This pathway utilises two novel proteins: an ADP-dependent Glucokinase and an ADP-dependent Phosphofructokinase. This conserved region is present at the C-terminal of both these proteins. Interestingly this family contains sequences from higher eukaryotes. [1,2,3]. [1]. 10409652. Molecular and biochemical characterization of the ADP-dependent phosphofructokinase from the hyperthermophilic archaeon Pyrococcus furiosus. Tuininga JE, Verhees CH, van der Oost J, Kengen SW, Stams AJ, de Vos WM;. J Biol Chem 1999;274:21023-21028. [2]. 11717273. ADP-dependent phosphofructokinases in mesophilic and thermophilic methanogenic archaea. Verhees CH, Tuininga JE, Kengen SW, Stams AJ, van der Oost J, de Vos WM;. J Bacteriol 2001;183:7145-7153. [3]. 11342216. Sequencing, expression, characterisation and phylogeny of the ADP-dependent phosphofructokinase from the hyperthermophilic, euryarchaeal Thermococcus zilligii. Ronimus RS, de Heus E, Morgan HW;. Biochim Biophys Acta 2001;1517:384-391. (from Pfam) NF016488.5 PF04607.22 RelA_SpoT 27 27 113 domain Y N N Region found in RelA / SpoT proteins GO:0015969 2005134 131567 cellular organisms no rank 126069 EBI-EMBL Region found in RelA / SpoT proteins Region found in RelA / SpoT proteins This region of unknown function is found in RelA and SpoT of Escherichia coli, and their homologues in plants and in other eubacteria. RelA is a guanosine 3',5'-bis-pyrophosphate (ppGpp) synthetase (EC:2.7.6.5) while SpoT is thought to be a bifunctional enzyme catalysing both ppGpp synthesis and degradation (ppGpp 3'-pyrophosphohydrolase, (EC:3.1.7.2)) [1]. This region is often found in association with HD (Pfam:PF01966), a metal-dependent phosphohydrolase, TGS (Pfam:PF02824) which is a possible nucleotide-binding region, and the ACT regulatory domain (Pfam:PF01842). [1]. 2005134. Residual guanosine 3',5'-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations. Xiao H, Kalman M, Ikehara K, Zemel S, Glaser G, Cashel M;. J Biol Chem 1991;266:5980-5990. (from Pfam) NF016489.5 PF04608.18 PgpA 28 28 141 PfamEq Y Y N phosphatidylglycerophosphatase A 3.1.3.27 GO:0006629,GO:0008962 1309518 131567 cellular organisms no rank 28098 EBI-EMBL Phosphatidylglycerophosphatase A phosphatidylglycerophosphatase A This family represents a family of bacterial phosphatidylglycerophosphatases (EC:3.1.3.27), known as PgpA. It appears that bacteria possess several phosphatidylglycerophosphatases, and thus, PgpA is not essential in Escherichia coli [1]. [1]. 1309518. The pgpA and pgpB genes of Escherichia coli are not essential: evidence for a third phosphatidylglycerophosphate phosphatase. Funk CR, Zimniak L, Dowhan W;. J Bacteriol 1992;174:205-213. (from Pfam) NF016494.5 PF04613.19 LpxD 30.8 30.8 70 domain Y Y N LpxD N-terminal domain-containing protein GO:0009245,GO:0016747 8366125 131567 cellular organisms no rank 40540 EBI-EMBL UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (EC 2.3.1.-) catalyses an early step in lipid A biosynthesis: UDP-3-O-(3-hydroxytetradecanoyl)glucosamine + (R)-3-hydroxytetradecanoyl- [acyl carrier protein] -> UDP-2,3-bis(3-hydroxytetradecanoyl)glucosamine + [acyl carrier protein] [1]. Members of this family also contain a hexapeptide repeat (Pfam:PF00132). This family constitutes the non-repeating region of LPXD proteins. [1]. 8366125. The firA gene of Escherichia coli encodes UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase. The third step of endotoxin biosynthesis. Kelly TM, Stachula SA, Raetz CR, Anderson MS;. J Biol Chem 1993;268:19866-19874. (from Pfam) NF016497.5 PF04616.19 Glyco_hydro_43 32.2 32.2 288 domain Y Y N family 43 glycosylhydrolase GO:0004553,GO:0005975 12198486 131567 cellular organisms no rank 174583 EBI-EMBL Glycosyl hydrolases family 43 family 43 glycosylhydrolase The glycosyl hydrolase family 43 contains members that are arabinanases. Arabinanases hydrolyse the alpha-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans. The structure of arabinanase Arb43A from Cellvibrio japonicus reveals a five-bladed beta-propeller fold. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller [1]. [1]. 12198486. Cellvibrio japonicus alpha-L-arabinanase 43A has a novel five-blade beta-propeller fold. Nurizzo D, Turkenburg JP, Charnock SJ, Roberts SM, Dodson EJ, McKie VA, Taylor EJ, Gilbert HJ, Davies GJ;. Nat Struct Biol 2002;9:665-668. (from Pfam) NF016503.5 PF04622.17 ERG2_Sigma1R 21 21 210 PfamEq Y N N ERG2 and Sigma1 receptor like protein 8082205,8755605,9425306 131567 cellular organisms no rank 157 EBI-EMBL ERG2 and Sigma1 receptor like protein ERG2 and Sigma1 receptor like protein This family consists of the fungal C-8 sterol isomerase and mammalian sigma1 receptor. C-8 sterol isomerase (delta-8--delta-7 sterol isomerase), catalyses a reaction in ergosterol biosynthesis, which results in unsaturation at C-7 in the B ring of sterols [1]. Sigma 1 receptor is a low molecular mass mammalian protein located in the endoplasmic reticulum [2], which interacts with endogenous steroid hormones, such as progesterone and testosterone [3]. It also binds the sigma ligands, which are are a set of chemically unrelated drugs including haloperidol, pentazocine, and ditolylguanidine [2]. Sigma1 effectors are not well understood, but sigma1 agonists have been observed to affect NMDA receptor function, the alpha-adrenergic system and opioid analgesia. [1]. 8082205. Isolation of the ERG2 gene, encoding sterol delta 8-->delta 7 isomerase, from the rice blast fungus Magnaporthe grisea and its expression in the maize smut pathogen Ustilago maydis. Keon JP, James CS, Court S, Baden-Daintree C, Bailey AM, Burden RS, Bard M, Hargreaves JA;. Curr Genet 1994;25:531-537. [2]. 8755605. Purification, molecular cloning, and expression of the mammalian sigma1-binding site. Hanner M, Moebius FF, Flandorfer A, Knaus HG, Striessnig J, Kempner E, Glossmann H;. Proc Natl Acad Sci U S A 1996;93:8072-8077. [3]. 9425306. Cloning and structural analysis of the cDNA and the gene encoding the murine type 1 sigma receptor. Seth P, Leibach FH, Ganapathy V;. Biochem Biophys Res Commun 1997;241:535-540. (from Pfam) NF016513.5 PF04632.17 FUSC 30.9 30.9 660 domain Y Y N FUSC family protein GO:0005886,GO:0022857,GO:0055085 1370369 131567 cellular organisms no rank 108863 EBI-EMBL Fusaric acid resistance protein family FUSC family protein This family includes a conserved region found in two proteins associated with fusaric acid resistance, Swiss:P24128 from Burkholderia cepacia[1] and Swiss:Q48403 from Klebsiella oxytoca. These proteins are likely to be membrane transporter proteins. [1]. 1370369. Molecular cloning and characterization of the fusaric acid-resistance gene from Pseudomonas cepacia. Utsumi R, Yagi T, Katayama S, Katsuragi K, Tachibana K, Toyoda H, Ouchi S, Obata K, Shibano Y, Noda M;. Agric Biol Chem 1991;55:1913-1918. (from Pfam) NF016532.5 PF04654.17 DUF599 27 27 211 PfamAutoEq Y Y N DUF599 family protein 131567 cellular organisms no rank 8146 EBI-EMBL Protein of unknown function, DUF599 DUF599 family protein This family includes several uncharacterised proteins. (from Pfam) NF016535.5 PF04657.18 DMT_YdcZ 24 24 140 domain Y Y N DMT family transporter 131567 cellular organisms no rank 41615 EBI-EMBL Putative inner membrane exporter, YdcZ DMT family transporter DMT_YdcZ is a family of putative inner membrane exporters from both Gram-positive and Gram-negative bacteria. (from Pfam) NF016537.5 PF04659.18 Arch_fla_DE 21 21 96 domain Y Y N FlaD/FlaE family flagellar protein GO:0097588 11717274 131567 cellular organisms no rank 1351 EBI-EMBL Archaeal flagella protein FlaD/FlaE family flagellar protein Family of archaeal flaD and flaE proteins. Conserved region found at N-terminus of flaE but towards the C-terminus of flaD [1]. [1]. 11717274. Characterization of flagellum gene families of methanogenic archaea and localization of novel flagellum accessory proteins. Thomas NA, Jarrell KF;. J Bacteriol 2001;183:7154-7164. (from Pfam) NF016543.5 PF04665.17 Pox_A32 22.8 22.8 242 domain Y Y N ATPase/DNA packaging protein 9621036 131567 cellular organisms no rank 278 EBI-EMBL Poxvirus A32 protein ATPase/DNA packaging protein The A32 protein is thought to be involved in viral DNA packaging. [1]. 9621036. DNA packaging mutant: repression of the vaccinia virus A32 gene results in noninfectious, DNA-deficient, spherical, enveloped particles. Cassetti MC, Merchlinsky M, Wolffe EJ, Weisberg AS, Moss B;. J Virol 1998;72:5769-5780. (from Pfam) NF016548.5 PF04670.17 Gtr1_RagA 22 22 232 domain Y N N Gtr1/RagA G protein conserved region GO:0005525 10388807,11073942,1620108,7499430 131567 cellular organisms no rank 11473 EBI-EMBL Gtr1/RagA G protein conserved region Gtr1/RagA G protein conserved region GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B [1,2,3,4]. [1]. 1620108. Putative GTP-binding protein, Gtr1, associated with the function of the Pho84 inorganic phosphate transporter in Saccharomyces cerevisiae. Bun-Ya M, Harashima S, Oshima Y;. Mol Cell Biol 1992;12:2958-2966. [2]. 7499430. Cloning of a novel family of mammalian GTP-binding proteins (RagA, RagBs, RagB1) with remote similarity to the Ras-related GTPases. Schurmann A, Brauers A, Massmann S, Becker W, Joost HG;. J Biol Chem 1995;270:28982-28988. [3]. 10388807. Saccharomyces cerevisiae putative G protein, Gtr1p, which forms complexes with itself and a novel protein designated as Gtr2p, negatively regulates the Ran/Gsp1p G protein cycle through Gtr2p. Nakashima N, Noguchi E, Nishimoto T;. Genetics 1999;152:853-867. [4]. 11073942. Novel G proteins, Rag C and Rag D, interact with GTP-binding proteins, Rag A and Rag B. Sekiguchi T, Hirose E, Nakashima N, Ii M, Nishimoto T;. J Biol Chem 2001;276:7246-7257. (from Pfam) NF016553.5 PF04675.19 DNA_ligase_A_N 24.6 24.6 174 PfamEq Y N N DNA ligase N terminus GO:0003677,GO:0003910,GO:0006281,GO:0006310 9016621 131567 cellular organisms no rank 26628 EBI-EMBL DNA ligase N terminus DNA ligase N terminus This region is found in many but not all ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (Swiss:P18858), and in Saccharomyces cerevisiae (Swiss:P04819), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In vaccinia virus (Swiss:P16272) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation [1]. [1]. 9016621. Domain structure of vaccinia DNA ligase. Sekiguchi J, Shuman S;. Nucleic Acids Res 1997;25:727-734. (from Pfam) NF016555.5 PF04677.20 CwfJ_C_1 21 21 122 PfamEq Y N N Protein similar to CwfJ C-terminus 1 11884590 131567 cellular organisms no rank 16236 EBI-EMBL Protein similar to CwfJ C-terminus 1 Protein similar to CwfJ C-terminus 1 This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ (Swiss:Q09909). CwfJ is part of the Cdc5p complex involved in mRNA splicing [1]. [1]. 11884590. Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs. Ohi MD, Link AJ, Ren L, Jennings JL, McDonald WH, Gould KL;. Mol Cell Biol 2002;22:2011-2024. (from Pfam) NF016557.5 PF04679.20 DNA_ligase_A_C 27.5 27.5 94 domain Y N N ATP dependent DNA ligase C terminal region GO:0003910,GO:0006281,GO:0006310 9016621 131567 cellular organisms no rank 92936 EBI-EMBL ATP dependent DNA ligase C terminal region ATP dependent DNA ligase C terminal region This region is found in many but not all ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase [1]. [1]. 9016621. Domain structure of vaccinia DNA ligase. Sekiguchi J, Shuman S;. Nucleic Acids Res 1997;25:727-734. (from Pfam) NF016563.5 PF04685.18 DUF608 26.3 26.3 361 domain Y Y N GH116 family glycosyl hydrolase GO:0004553 17105727,20427274,23332917 131567 cellular organisms no rank 6066 EBI-EMBL Glycosyl-hydrolase family 116, catalytic region GH116 family glycosyl hydrolase This represents a family of archaeal, bacterial and eukaryotic glycosyl hydrolases, that belong to superfamily GH116. The primary catabolic pathway for glucosylceramide is catalysis by the lysosomal enzyme glucocerebrosidase. In higher eukaryotes, glucosylceramide is the precursor of glycosphingolipids, a complex group of ubiquitous membrane lipids [1]. Mutations in the human protein cause motor-neurone defects in hereditary spastic paraplegia [3]. The catalytic nucleophile, identified in UniProtKB:Q97YG8_SULSO, is a glutamine-335, with the likely acid/base at Asp-442 and the aspartates at Asp-406 and Asp-458 residues also playing a role in the catalysis of glucosides and xylosides that are beta-bound to hydrophobic groups. The family is defined as GH116, which presently includes enzymes with beta-glucosidase, EC:3.2.1.21, beta-xylosidase, EC:3.2.1.37, and glucocerebrosidase EC:3.2.1.45 activity [1,2]. [1]. 17105727. Identification of the non-lysosomal glucosylceramidase as beta-glucosidase 2. Boot RG, Verhoek M, Donker-Koopman W, Strijland A, van Marle J, Overkleeft HS, Wennekes T, Aerts JM;. J Biol Chem. 2007;282:1305-1312. [2]. 20427274. A new archaeal beta-glycosidase from Sulfolobus solfataricus: seeding a novel retaining beta-glycan-specific glycoside hydrolase family along with the human non-lysosomal glucosylceramidase GBA2. Cobucci-Ponzano B, Aurilia V, Riccio G, Henrissat B, Coutinho PM, Strazzulli A, Padula A, Corsaro MM, Pieretti G, Pocsfalvi G, Fiume I, Cannio R, Rossi M, Moracci M;. J Biol Chem. 2010;285:20691-20703. [3]. 23332917. Mutations in GBA2 cause autosomal-recessive cerebellar ataxia with spasticity.. TRUNCATED at 1650 bytes (from Pfam) NF016571.5 PF04693.17 DDE_Tnp_2 20.2 20.2 327 domain Y N N Archaeal putative transposase ISC1217 131567 cellular organisms no rank 4663 EBI-EMBL Archaeal putative transposase ISC1217 Archaeal putative transposase ISC1217 NF016581.5 PF04703.17 FaeA 20.7 20.7 62 domain Y Y N FaeA/PapI family transcriptional regulator GO:0006355 7476191,8846772 131567 cellular organisms no rank 9766 EBI-EMBL FaeA-like protein FaeA/PapI family transcriptional regulator This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase [1,2]. [1]. 7476191. Negative control of fae (K88) expression by the 'global' regulator Lrp is modulated by the 'local' regulator FaeA and affected by DNA methylation. Huisman TT, de Graaf FK;. Mol Microbiol 1995;16:943-953. [2]. 8846772. Differential binding of Lrp to two sets of pap DNA binding sites mediated by Pap I regulates Pap phase variation in Escherichia coli. Nou X, Braaten B, Kaltenbach L, Low DA;. EMBO J 1995;14:5785-5797. (from Pfam) NF016593.5 PF04715.18 Anth_synt_I_N 23 23 140 domain Y N N Anthranilate synthase component I, N terminal region GO:0009058 11371633,11450855 131567 cellular organisms no rank 114503 EBI-EMBL Anthranilate synthase component I, N terminal region Anthranilate synthase component I, N terminal region Anthranilate synthase (EC:4.1.3.27) catalyses the first step in the biosynthesis of tryptophan. Component I catalyses the formation of anthranilate using ammonia and chorismate. The catalytic site lies in the adjacent region, described in the chorismate binding enzyme family (Pfam:PF00425). This region is involved in feedback inhibition by tryptophan [1]. This family also contains a region of Para-aminobenzoate synthase component I (EC 4.1.3.-). [1]. 11371633. The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan. Spraggon G, Kim C, Nguyen-Huu X, Yee MC, Yanofsky C, Mills SE;. Proc Natl Acad Sci U S A 2001;98:6021-6026. [2]. 11450855. A metabolic node in action: chorismate-utilizing enzymes in microorganisms. Dosselaere F, Vanderleyden J;. Crit Rev Microbiol 2001;27:75-131. (from Pfam) NF016602.5 PF04724.18 Glyco_transf_17 26 26 348 PfamEq Y N N Glycosyltransferase family 17 GO:0003830,GO:0006487,GO:0016020 11784313,11986323 131567 cellular organisms no rank 1493 EBI-EMBL Glycosyltransferase family 17 Glycosyltransferase family 17 This family represents beta-1,4-mannosyl-glycoprotein beta-1,4-N-acetylglucosaminyltransferase (EC:2.4.1.144). This enzyme transfers the bisecting GlcNAc to the core mannose of complex N-glycans. The addition of this residue is regulated during development and has functional consequences for receptor signalling, cell adhesion, and tumour progression [1,2]. [1]. 11986323. Truncated, inactive N-acetylglucosaminyltransferase III (GlcNAc-TIII) induces neurological and other traits absent in mice that lack GlcNAc-TIII. Bhattacharyya R, Bhaumik M, Raju TS, Stanley P;. J Biol Chem 2002;277:26300-26309. [2]. 11784313. A catalytically inactive beta 1,4-N-acetylglucosaminyltransferase III (GnT-III) behaves as a dominant negative GnT-III inhibitor. Ihara H, Ikeda Y, Koyota S, Endo T, Honke K, Taniguchi N;. Eur J Biochem 2002;269:193-201. (from Pfam) NF016604.5 PF04726.18 Microvir_J 19 19 37 domain Y Y N phage DNA packaging protein J GO:0003677 911774 131567 cellular organisms no rank 124 EBI-EMBL Microvirus J protein phage DNA packaging protein J The founding member of this protein family occurs in phage phiX174. As of version PF04726.18 of this HMM, the cutoff was too low, but a rebuilt version with higher cutoffs is pending. One member of this family is encoded by phage DNA commonly used as a positive control for DNA sequencing instruments. NF016611.5 PF04733.19 Coatomer_E 21 21 290 PfamEq Y N N Coatomer epsilon subunit 10469566 131567 cellular organisms no rank 2959 EBI-EMBL Coatomer epsilon subunit Coatomer epsilon subunit This family represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex [1]. [1]. 10469566. Segregation of COPI-rich and anterograde-cargo-rich domains in endoplasmic-reticulum-to-Golgi transport complexes. Shima DT, Scales SJ, Kreis TE, Pepperkok R;. Curr Biol 1999;9:821-824. (from Pfam) NF016612.5 PF04734.18 Ceramidase_alk 32.1 32.1 509 PfamEq Y Y N neutral/alkaline non-lysosomal ceramidase N-terminal domain-containing protein 10593963,10753931,10781606,19088069 131567 cellular organisms no rank 9972 EBI-EMBL Neutral/alkaline non-lysosomal ceramidase, N-terminal Neutral/alkaline non-lysosomal ceramidase, N-terminal This family represents N-terminal domain of a group of neutral/alkaline ceramidases found in both bacteria and eukaryotes [1,2,3]. The EC classification is EC:3.5.1.23. The enzyme hydrolyses ceramide to generate sphingosine and fatty acid. The enzyme plays a regulatory role in a variety of physiological events in eukaryotes and also functions as an exotoxin in particular bacteria. This N-terminal domain carries two metal-binding sites, the first for Zn2+ residing within the domain, and the second, for Mg2+/Ca2+ lying at the interface between the two domains [4]. [1]. 10753931. Molecular cloning of the full-length cDNA encoding mouse neutral ceramidase. A novel but highly conserved gene family of neutral/alkaline ceramidases. Tani M, Okino N, Mori K, Tanigawa T, Izu H, Ito M;. J Biol Chem 2000;275:11229-11234. [2]. 10781606. Molecular cloning and characterization of a human mitochondrial ceramidase. El Bawab S, Roddy P, Qian T, Bielawska A, Lemasters JJ, Hannun YA;. J Biol Chem 2000;275:21508-21513. [3]. 10593963. Molecular cloning, sequencing, and expression of the gene encoding alkaline ceramidase from Pseudomonas aeruginosa. Cloning of a ceramidase homologue from Mycobacterium tuberculosis. Okino N, Ichinose S, Omori A, Imayama S, Nakamura T, Ito M;. J Biol Chem 1999;274:36616-36622. [4]. 19088069. Mechanistic insights into the hydrolysis and synthesis of ceramide by neutral ceramidase. Inoue T, Okino N, Kakuta Y, Hijikata A, Okano H, Goda HM, Tani M, Sueyoshi N, Kambayashi K, Matsumura H, Kai Y, Ito M;. J Biol Chem. 2009;284:9566-9577. (from Pfam) NF016619.5 PF04744.17 Monooxygenase_B 22.7 22.7 380 domain Y Y N methane monooxygenase/ammonia monooxygenase subunit B 10698759,11807563 131567 cellular organisms no rank 541 EBI-EMBL Monooxygenase subunit B protein methane monooxygenase/ammonia monooxygenase subunit B Family of membrane associated monooxygenases (EC 1.13.12.-) which utilise O(2) to oxidise their substrate. Family members include both ammonia and methane monooxygenases involved in the oxidation of their respective substrates. These enzymes are multi-subunit complexes. This family represents the B subunit of the enzyme; the A subunit is thought to contain the active site. [1,2]. [1]. 11807563. Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Norton JM, Alzerreca JJ, Suwa Y, Klotz MG;. Arch Microbiol 2002;177:139-149. [2]. 10698759. Molecular analysis of the pmo (particulate methane monooxygenase) operons from two type II methanotrophs. Gilbert B, McDonald IR, Finch R, Stafford GP, Nielsen AK, Murrell JC;. Appl Environ Microbiol 2000;66:966-975. (from Pfam) NF016631.5 PF04756.18 OST3_OST6 27 27 294 PfamEq Y N N OST3 / OST6 family, transporter family 10358084,15804357,7622558 131567 cellular organisms no rank 4331 EBI-EMBL OST3 / OST6 family, transporter family OST3 / OST6 family, transporter family The proteins in this family are part of a complex of eight ER proteins that transfers core oligosaccharide from dolichol carrier to Asn-X-Ser/Thr motifs [1]. This family includes both OST3 and OST6, each of which contains four predicted transmembrane helices. Disruption of OST3 and OST6 leads to a defect in the assembly of the complex. Hence, the function of these genes seems to be essential for recruiting a fully active complex necessary for efficient N-glycosylation [2]. These proteins are also thought to be novel Mg2+ transporters [3]. [1]. 7622558. Functional characterization of Ost3p. Loss of the 34-kD subunit of the Saccharomyces cerevisiae oligosaccharyltransferase results in biased underglycosylation of acceptor substrates. Karaoglu D, Kelleher DJ, Gilmore R;. J Cell Biol 1995;130:567-577. [2]. 10358084. The oligosaccharyltransferase complex from Saccharomyces cerevisiae. Isolation of the OST6 gene, its synthetic interaction with OST3, and analysis of the native complex. Knauer R, Lehle L;. J Biol Chem 1999;274:17249-17256. [3]. 15804357. Identification and characterization of a novel mammalian Mg2+ transporter with channel-like properties. Goytain A, Quamme GA;. BMC Genomics. 2005;6:48. (from Pfam) NF016633.5 PF04758.19 Ribosomal_S30 27 27 58 PfamEq Y Y N 30S ribosomal protein S30e GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 135 EBI-EMBL Ribosomal protein S30 30S ribosomal protein S30e NF016635.5 PF04760.20 IF2_N 25.3 25.3 53 PfamEq Y Y N translation initiation factor IF-2 N-terminal domain-containing protein 12600987,1764105 131567 cellular organisms no rank 89114 EBI-EMBL Translation initiation factor IF-2, N-terminal region Translation initiation factor IF-2, N-terminal region This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase. [1]. 1764105. Tandem translation of E. coli initiation factor IF2 beta: purification and characterization in vitro of two active forms. Nyengaard NR, Mortensen KK, Lassen SF, Hershey JW, Sperling-Petersen HU;. Biochem Biophys Res Commun 1991;181:1572-1579. [2]. 12600987. A conserved structural motif at the N-terminus of bacterial translation initiation factor IF2. Laursen BS, Mortensen KK, Sperling-Petersen HU, Hoffman DW;. 0;0:0-0. (from Pfam) NF016640.5 PF04765.18 TOD1_MUCI70 21.4 21.4 314 domain Y Y N glycosyltransferase domain-containing protein 25591940,30228108,31591153,33735469 131567 cellular organisms no rank 1583 EBI-EMBL TOD1/MUCI70, glycosyltransferase-like domain TOD1/MUCI70, glycosyltransferase-like domain This entry represents a glycosyltransferase-like domain found in alkaline ceramidase TOD1 and the probable hexosyltransferase MUCI70 from Arabidopsis. MUCI70 is a predicted glycosyltransferase essential for the accumulation of seed mucilage, a gelatinous wall rich in unbranched rhamnogalacturonan I (RG I), and for shaping the surface morphology of seeds [1,2]. TOD1 is an endoplasmic reticulum ceramidase that catalyses the hydrolysis of ceramides into sphingosine and free fatty acids at alkaline pH (e.g. pH 9.5) [3,4]. [1]. 30228108. Identification of Key Enzymes for Pectin Synthesis in Seed Mucilage. Voiniciuc C, Engle KA, Gunl M, Dieluweit S, Schmidt MH, Yang JY, Moremen KW, Mohnen D, Usadel B;. Plant Physiol. 2018;178:1045-1064. [2]. 31591153. Natural Variation Reveals a Key Role for Rhamnogalacturonan I in Seed Outer Mucilage and Underlying Genes. Fabrissin I, Cueff G, Berger A, Granier F, Salle C, Poulain D, Ralet MC, North HM;. Plant Physiol. 2019;181:1498-1518. [3]. 25591940. The Arabidopsis alkaline ceramidase TOD1 is a key turgor pressure regulator in plant cells. Chen LY, Shi DQ, Zhang WJ, Tang ZS, Liu J, Yang WC;. Nat Commun. 2015;6:6030. [4]. 33735469. Turgor regulation defect 1 proteins play a conserved role in pollen tube reproductive innovation of the angiosperms. Ke CJ, Lin XJ, Zhang BY, Chen LY;. Plant J. 2021;106:1356-1365. (from Pfam) NF016650.5 PF04775.19 Bile_Hydr_Trans 27 27 126 domain Y Y N acyl-CoA thioesterase/BAAT N-terminal domain-containing protein 10567408,11673457 131567 cellular organisms no rank 4001 EBI-EMBL Acyl-CoA thioester hydrolase/BAAT N-terminal region Acyl-CoA thioester hydrolase/BAAT N-terminal region This family consists of the amino termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT) [1]. This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism [2]. For example, in peroxisomes, the hydrolase acts on bile-CoA esters [1]. [1]. 11673457. Characterization of an acyl-coA thioesterase that functions as a major regulator of peroxisomal lipid metabolism. Hunt MC, Solaas K, Kase BF, Alexson SE;. J Biol Chem 2002;277:1128-1138. [2]. 10567408. Peroxisome proliferator-induced long chain acyl-CoA thioesterases comprise a highly conserved novel multi-gene family involved in lipid metabolism. Hunt MC, Nousiainen SE, Huttunen MK, Orii KE, Svensson LT, Alexson SE;. J Biol Chem 1999;274:34317-34326. (from Pfam) NF016654.5 PF04780.17 DUF629 23.1 23.1 465 domain Y Y N DUF629 domain-containing protein 131567 cellular organisms no rank 5 EBI-EMBL Protein of unknown function (DUF629) Protein of unknown function (DUF629) This family represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family. (from Pfam) NF016658.5 PF04784.19 DUF547 27 27 125 domain Y Y N DUF547 domain-containing protein 131567 cellular organisms no rank 9653 EBI-EMBL Protein of unknown function, DUF547 Protein of unknown function, DUF547 Family of uncharacterised proteins from C. elegans and A. thaliana. (from Pfam) NF016670.5 PF04796.17 RepA_C 26 26 181 subfamily Y Y N replication protein RepA 11914352 131567 cellular organisms no rank 3723 EBI-EMBL Plasmid encoded RepA protein replication protein RepA Family of plasmid encoded proteins involved in plasmid replication. The role of RepA in the replication process is not clearly understood [1]. [1]. 11914352. Origin binding activity of the Mycobacterial plasmid pAL5000 replication protein RepB is stimulated through interactions with host factors and coupled expression of repA. Basu A, Chawla-Sarkar M, Chakrabarti S, Das Gupta SK;. J Bacteriol 2002;184:2204-2214. (from Pfam) NF016674.5 PF04800.17 NDUS4 31.9 31.9 96 domain Y Y N NADH dehydrogenase ubiquinone Fe-S protein 4 GO:0016651,GO:0022900 19675153,7947902 131567 cellular organisms no rank 7293 EBI-EMBL NADH dehydrogenase ubiquinone Fe-S protein 4 NADH dehydrogenase ubiquinone Fe-S protein 4 This entry represents NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), initially identified in Neurospora crassa as a 21 kDa protein [1,2]. It is believed that members of this family are not to be involved in catalysis. [1]. 7947902. Complementary DNA sequences of the 24 kDa and 21 kDa subunits of complex I from Neurospora. Azevedo JE, Duarte M, Belo JA, Werner S, Videira A;. Biochim Biophys Acta 1994;1188:159-161. [2]. 19675153. Remodeled respiration in ndufs4 with low phosphorylation efficiency suppresses Arabidopsis germination and growth and alters control of metabolism at night. Meyer EH, Tomaz T, Carroll AJ, Estavillo G, Delannoy E, Tanz SK, Small ID, Pogson BJ, Millar AH;. Plant Physiol. 2009;151:603-619. (from Pfam) NF016689.5 PF04816.17 TrmK 27 27 205 PfamEq Y Y N tRNA (adenine(22)-N(1))-methyltransferase TrmK 18420655 131567 cellular organisms no rank 20677 EBI-EMBL tRNA (adenine(22)-N(1))-methyltransferase tRNA (adenine(22)-N(1))-methyltransferase TrmK tRNA_MT is a family of bacterial tRNA (adenine(22)-N(1))-methyltransferase enzymes with a Rossmann-like fold. This enzyme carries out the function of N1-adenosine methylation at position 22 of bacterial tRNA [1]. [1]. 18420655. The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK). Roovers M, Kaminska KH, Tkaczuk KL, Gigot D, Droogmans L, Bujnicki JM;. Nucleic Acids Res. 2008;36:3252-3262. (from Pfam) NF016693.5 PF04820.19 Trp_halogenase 21 21 458 domain Y Y N tryptophan 7-halogenase GO:0004497 10547442 131567 cellular organisms no rank 69945 EBI-EMBL Tryptophan halogenase tryptophan 7-halogenase Tryptophan halogenase catalyses the chlorination of tryptophan to form 7-chlorotryptophan. This is the first step in the biosynthesis of pyrrolnitrin, an antibiotic with broad-spectrum anti-fungal activity. Tryptophan halogenase is NADH-dependent [1]. [1]. 10547442. Conservation of the pyrrolnitrin biosynthetic gene cluster among six pyrrolnitrin-producing strains. Hammer PE, Burd W, Hill DS, Ligon JM, van Pee K;. FEMS Microbiol Lett 1999;180:39-44. (from Pfam) NF016697.5 PF04824.21 Rad21_Rec8 22.7 22.7 55 PfamEq Y N N Conserved region of Rad21 / Rec8 like protein 10207075,11687503 131567 cellular organisms no rank 259 EBI-EMBL Conserved region of Rad21 / Rec8 like protein Conserved region of Rad21 / Rec8 like protein This family represents a conserved region found in eukaryotic cohesins of the Rad21, Rec8 and Scc1 families. Members of this family mediate sister chromatid cohesion during mitosis and meiosis, as part of the cohesin complex [1]. Cohesion is necessary for homologous recombination (including double-strand break repair) and correct chromatid segregation. These proteins may also be involved in chromosome condensation. Dissociation at the metaphase to anaphase transition causes loss of cohesion and chromatid segregation [2]. [1]. 11687503. The molecular basis of sister-chromatid cohesion. Lee JY, Orr-Weaver TL;. Annu Rev Cell Dev Biol 2001;17:753-777. [2]. 10207075. Rec8p, a meiotic recombination and sister chromatid cohesion phosphoprotein of the Rad21p family conserved from fission yeast to humans. Parisi S, McKay MJ, Molnar M, Thompson MA, van der Spek PJ, van Drunen-Schoenmaker E, Kanaar R, Lehmann E, Hoeijmakers JH, Kohli J;. Mol Cell Biol 1999;19:3515-3528. (from Pfam) NF016705.5 PF04832.17 SOUL 27 27 173 PfamEq Y Y N heme-binding protein 10640688 131567 cellular organisms no rank 4858 EBI-EMBL SOUL heme-binding protein heme-binding protein This family represents a group of putative heme-binding proteins [1]. Our family includes archaeal and bacterial homologues. [1]. 10640688. Discovery of a putative heme-binding protein family (SOUL/HBP) by two-tissue suppression subtractive hybridization and database searches. Zylka MJ, Reppert SM;. Brain Res Mol Brain Res 1999;74:175-181. (from Pfam) NF016724.5 PF04851.20 ResIII 22.5 22.5 164 domain Y Y N DEAD/DEAH box helicase family protein GO:0003677,GO:0005524,GO:0016787 131567 cellular organisms no rank 1248131 EBI-EMBL Type III restriction enzyme, res subunit DEAD/DEAH box helicase family protein NF016732.5 PF04860.17 Phage_portal 39.1 39.1 321 subfamily Y Y N phage portal protein 11839289 131567 cellular organisms no rank 77764 EBI-EMBL Phage portal protein phage portal protein Bacteriophage portal proteins form a dodecamer and is located at a five-fold vertex of the viral capsid. The portal complex forms a channel through which the viral DNA is packaged into the capsid, and exits during infection. The portal protein is though to rotate during DNA packaging [1]. Portal proteins from different phage show little sequence homology, so this family does not represent all portal proteins. [1]. 11839289. DNA packaging: a new class of molecular motors. Moore SD, Prevelige PE Jr;. Curr Biol 2002;12:96-98. (from Pfam) NF016733.5 PF04862.17 DUF642 27 20 157 domain Y Y N DUF642 domain-containing protein 131567 cellular organisms no rank 3110 EBI-EMBL Protein of unknown function (DUF642) Protein of unknown function (DUF642) This family represents a duplicated conserved region found in a number of uncharacterised plant proteins, potentially in the stem. There is a conserved CGP sequence motif. (from Pfam) NF016735.5 PF04864.18 Alliinase_C 22 22 363 domain Y N N Allinase GO:0016846 12235163 131567 cellular organisms no rank 8401 EBI-EMBL Allinase Allinase Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesised from sulfoxide cysteine derivatives by alliinase (EC:4.4.1.4), whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system. [1]. 12235163. The active principle of garlic at atomic resolution. Kuettner EB, Hilgenfeld R, Weiss MS;. J Biol Chem 2002;0:0-0. (from Pfam) NF016736.5 PF04865.19 Baseplate_J 21.1 21.1 255 domain Y Y N baseplate J/gp47 family protein 7483254 131567 cellular organisms no rank 80123 EBI-EMBL Baseplate J-like protein baseplate J/gp47 family protein The P2 bacteriophage J protein lies at the edge of the baseplate. This family also includes a number of bacterial homologues, which are thought to have been horizontally transferred. [1]. 7483254. Bacteriophage P2: genes involved in baseplate assembly. Haggard-Ljungquist E, Jacobsen E, Rishovd S, Six EW, Nilssen O, Sunshine MG, Lindqvist BH, Kim KJ, Barreiro V, Koonin EV, et al.;. Virology 1995;213:109-121. (from Pfam) NF016750.5 PF04879.21 Molybdop_Fe4S4 22.7 22.7 55 domain Y N N Molybdopterin oxidoreductase Fe4S4 domain GO:0016491 9036855 131567 cellular organisms no rank 263424 EBI-EMBL Molybdopterin oxidoreductase Fe4S4 domain Molybdopterin oxidoreductase Fe4S4 domain This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of PDB:1aa6 is an Fe4S4 cluster just below the protein surface [1]. [1]. 9036855. Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster. Boyington JC, Gladyshev VN, Khangulov SV, Stadtman TC, Sun PD;. Science. 1997;275:1305-1308. (from Pfam) NF016754.5 PF04883.17 HK97-gp10_like 21.4 21.4 78 domain Y Y N HK97 gp10 family phage protein 131567 cellular organisms no rank 29193 EBI-EMBL Bacteriophage HK97-gp10, putative tail-component HK97 gp10 family phage protein This family of proteins is found in the caudovirales. It may be a tail component. (from Pfam) NF016763.5 PF04892.17 VanZ 30.1 30.1 126 domain Y Y N VanZ family protein 7867956 131567 cellular organisms no rank 86509 EBI-EMBL VanZ like family VanZ family protein This family contains several examples of the VanZ protein, but also contains examples of phosphotransbutyrylases [1]. [1]. 7867956. The vanZ gene of Tn1546 from Enterococcus faecium BM4147 confers resistance to teicoplanin. Arthur M, Depardieu F, Molinas C, Reynolds P, Courvalin P;. Gene 1995;154:87-92. (from Pfam) NF016764.5 PF04893.22 Yip1 28.6 28.6 173 domain Y Y N YIP1 family protein GO:0016020 9724632 131567 cellular organisms no rank 29882 EBI-EMBL Yip1 domain Yip1 domain The Yip1 integral membrane domain contains four transmembrane alpha helices. The domain is characterised by the motifs DLYGP and GY. The Yip1 protein is a golgi protein involved in vesicular transport that interacts with GTPases [1]. [1]. 9724632. Specific binding to a novel and essential Golgi membrane protein (Yip1p) functionally links the transport GTPases Ypt1p and Ypt31p. Yang X, Matern HT, Gallwitz D;. EMBO J 1998;17:4954-4963. (from Pfam) NF016765.5 PF04894.17 Nre_N 25 25 270 domain Y N N Archaeal Nre, N-terminal 26337406 131567 cellular organisms no rank 1600 EBI-EMBL Archaeal Nre, N-terminal Archaeal Nre, N-terminal This conserved region is found in the N-terminal region of archaeal Nre proteins. While most archaeal organisms encode only a single Nre protein, some encode two, NreA and NreB. [1]. 26337406. A novel archaeal DNA repair factor that acts with the UvrABC system to repair mitomycin C-induced DNA damage in a PCNA-dependent manner. Giroux X, MacNeill SA;. Mol Microbiol. 2016;99:1-14. (from Pfam) NF016766.5 PF04895.17 Nre_C 27 27 110 domain Y N N Archaeal Nre, C-terminal 26337406 131567 cellular organisms no rank 1589 EBI-EMBL Archaeal Nre, C-terminal Archaeal Nre, C-terminal This conserved region is found in the C-terminal region of archaeal Nre proteins. While most archaeal organisms encode only a single Nre protein, some encode two, NreA and NreB. [1]. 26337406. A novel archaeal DNA repair factor that acts with the UvrABC system to repair mitomycin C-induced DNA damage in a PCNA-dependent manner. Giroux X, MacNeill SA;. Mol Microbiol. 2016;99:1-14. (from Pfam) NF016767.5 PF04896.17 AmoC 26.7 26.7 245 subfamily Y Y N methane monooxygenase/ammonia monooxygenase subunit C 10376840,9785456 131567 cellular organisms no rank 802 EBI-EMBL Ammonia monooxygenase/methane monooxygenase, subunit C methane monooxygenase/ammonia monooxygenase subunit C Ammonia monooxygenase plays a key role in the nitrogen cycle and degrades a wide range of hydrocarbons and halogenated hydrocarbons. This family represents the AmoC subunit. It also includes the particulate methane monooxygenase subunit PmoC from methanotrophic bacteria [1,2]. [1]. 9785456. Transcription of the amoC, amoA and amoB genes in Nitrosomonas europaea and Nitrosospira sp. NpAV. Sayavedra-Soto LA, Hommes NG, Alzerreca JJ, Arp DJ, Norton JM, Klotz MG;. FEMS Microbiol Lett 1998;167:81-88. [2]. 10376840. Role of multiple gene copies in particulate methane monooxygenase activity in the methane-oxidizing bacterium Methylococcus capsulatus Bath. Stolyar S, Costello AM, Peeples TL, Lidstrom ME;. Microbiology 1999;145:1235-1244. (from Pfam) NF016768.5 PF04898.19 Glu_syn_central 22.8 22.8 277 domain Y Y N glutamate synthase central domain-containing protein GO:0008152,GO:0015930 11967268 131567 cellular organisms no rank 88248 EBI-EMBL Glutamate synthase central domain Glutamate synthase central domain The central domain of glutamate synthase connects the amino terminal amidotransferase domain with the FMN-binding domain and has an alpha / beta overall topology [1]. This domain appears to be a rudimentary form of the FMN-binding TIM barrel according to SCOP. [1]. 11967268. Structural studies on the synchronization of catalytic centers in glutamate synthase. van den Heuvel RH, Ferrari D, Bossi RT, Ravasio S, Curti B, Vanoni MA, Florencio FJ, Mattevi A;. J Biol Chem 2002;277:24579-24583. (from Pfam) NF016770.5 PF04900.17 Fcf1 21.4 21.4 99 PfamEq Y N N Fcf1 GO:0032040 16762320 131567 cellular organisms no rank 200 EBI-EMBL Fcf1 Fcf1 Fcf1 is a nucleolar protein involved in pre-rRNA processing [1]. Depletion of yeast Fcf1 and Fcf2 leads to a decrease in synthesis of the 18S rRNA and results in a deficit in 40S ribosomal subunits [1]. [1]. 16762320. Fcf1p and Fcf2p are novel nucleolar Saccharomyces cerevisiae proteins involved in pre-rRNA processing. Rempola B, Karkusiewicz I, Piekarska I, Rytka J;. Biochem Biophys Res Commun. 2006;346:546-554. (from Pfam) NF016776.5 PF04908.20 SH3BGR 21 21 99 PfamEq Y N N SH3-binding, glutamic acid-rich protein 9050928 131567 cellular organisms no rank 2126 EBI-EMBL SH3-binding, glutamic acid-rich protein SH3-binding, glutamic acid-rich protein NF016777.5 PF04909.19 Amidohydro_2 26.4 26.4 289 domain Y Y N amidohydrolase family protein GO:0016787 9144792 131567 cellular organisms no rank 225560 EBI-EMBL Amidohydrolase amidohydrolase family protein These proteins are amidohydrolases that are related to Pfam:PF01979 [1]. [1]. 9144792. An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Holm L, Sander C;. Proteins 1997;28:72-82. (from Pfam) NF016784.5 PF04916.18 Phospholip_B 27 27 487 PfamEq Y N N Phospholipase B GO:0004620 15193148,8892229 131567 cellular organisms no rank 872 EBI-EMBL Phospholipase B Phospholipase B Phospholipase B (PLB) catalyses the hydrolytic cleavage of both acylester bonds of glycerophospholipids. This family of PLB enzymes has been identified in mammals, flies and nematodes but not in yeast [1]. In Drosophila this protein was named LAMA for laminin ancestor since it is expressed in the neuronal and glial precursors that surround the lamina [2]. [1]. 15193148. Identification of phospholipase B from Dictyostelium discoideum reveals a new lipase family present in mammals, flies and nematodes, but not yeast. Morgan CP, Insall R, Haynes L, Cockcroft S;. Biochem J 2004;382:441-449. [2]. 8892229. Molecular and genetic analyses of lama, an evolutionarily conserved gene expressed in the precursors of the Drosophila first optic ganglion. Perez SE, Steller H;. Mech Dev 1996;59:11-27. (from Pfam) NF016787.5 PF04919.17 DUF655 22.2 22.2 181 PfamAutoEq Y Y N DUF655 domain-containing protein 131567 cellular organisms no rank 2844 EBI-EMBL Protein of unknown function (DUF655) Protein of unknown function (DUF655) This family includes several uncharacterised archaeal proteins. This protein appears to contain two HHH motifs. (from Pfam) NF016798.5 PF04930.20 FUN14 22.5 22.5 92 PfamEq Y Y N FUN14 domain-containing protein 22267086 131567 cellular organisms no rank 890 EBI-EMBL FUN14 family FUN14 family This family of short proteins are found in eukaryotes and some archaea. Although the function of these proteins is not known they may contain transmembrane helices. (from Pfam) NF016800.5 PF04932.20 Wzy_C 31.7 31.7 149 domain Y Y N O-antigen ligase family protein 1624462 131567 cellular organisms no rank 162083 EBI-EMBL O-Antigen ligase O-antigen ligase family protein This group of bacterial proteins is involved in the synthesis of O-antigen, a lipopolysaccharide found in the outer membrane in gram-negative bacteria. This family includes O-antigen ligases such as E. coli RfaL [1]. [1]. 1624462. Comparison of lipopolysaccharide biosynthesis genes rfaK, rfaL, rfaY, and rfaZ of Escherichia coli K-12 and Salmonella typhimurium. Klena JD, Pradel E, Schnaitman CA;. J Bacteriol. 1992;174:4746-4752. (from Pfam) NF016811.5 PF04945.18 YHS 30.3 30.3 47 domain Y Y N YHS domain-containing protein 131567 cellular organisms no rank 26339 EBI-EMBL YHS domain YHS domain This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Swiss:Q9CNI0. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases. (from Pfam) NF016816.5 PF04951.18 Peptidase_M55 25 25 264 domain Y Y N M55 family metallopeptidase 11473256 131567 cellular organisms no rank 16238 EBI-EMBL D-aminopeptidase M55 family metallopeptidase Bacillus subtilis DppA is a binuclear zinc-dependent, D-specific aminopeptidase. The structure reveals that DppA is a new example of a 'self-compartmentalising protease', a family of proteolytic complexes. Proteasomes are the most extensively studied representatives of this family. The DppA enzyme is composed of identical 30 kDa subunits organised in a decamer with 52 point-group symmetry. A 20 A wide channel runs through the complex, giving access to a central chamber holding the active sites. The structure shows DppA to be a prototype of a new family of metalloaminopeptidases characterised by the SXDXEG key sequence [1]. The only known substrates are D-ala-D-ala and D-ala-gly-gly. [1]. 11473256. Structure of the Bacillus subtilis D-aminopeptidase DppA reveals a novel self-compartmentalizing protease. Remaut H, Bompard-Gilles C, Goffin C, Frere JM, Van Beeumen J;. Nat Struct Biol 2001;8:674-678. (from Pfam) NF016817.5 PF04952.19 AstE_AspA 25 25 290 domain Y Y N succinylglutamate desuccinylase/aspartoacylase family protein GO:0016788 8252036 131567 cellular organisms no rank 77917 EBI-EMBL Succinylglutamate desuccinylase / Aspartoacylase family succinylglutamate desuccinylase/aspartoacylase family protein This family includes Succinylglutamate desuccinylase EC:3.1.-.- that catalyses the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway. The family also include aspartoacylase EC:3.5.1.15 which cleaves acylaspartate into a fatty acid and aspartate. Mutations in Swiss:P45381 lead to Canavan disease disease [1]. This family is probably structurally related to Pfam:PF00246 (Bateman A pers. obs.). [1]. 8252036. Cloning of the human aspartoacylase cDNA and a common missense mutation in Canavan disease. Kaul R, Gao GP, Balamurugan K, Matalon R;. Nat Genet 1993;5:118-123. (from Pfam) NF016820.5 PF04956.18 TrbC 27.9 27.9 98 domain Y Y N TrbC/VirB2 family protein 12160637,12421311 131567 cellular organisms no rank 19891 EBI-EMBL TrbC/VIRB2 pilin TrbC/VirB2 family protein TrbC is a pilin found in bacterial type IV secretion systems. The protein undergoes three processing steps before gaining its mature cyclic structure [1]. This family also contains VIRB2 type IV secretion proteins [2]. This alignment contains two predicted transmembrane helices. [1]. 12160637. Tying rings for sex. Kalkum M, Eisenbrandt R, Lurz R, Lanka E;. Trends Microbiol 2002;10:382-387. [2]. 12421311. The VirB/VirD4 type IV secretion system of Bartonella is essential for establishing intraerythrocytic infection. Schulein R, Dehio C;. Mol Microbiol 2002;46:1053-1067. (from Pfam) NF016825.5 PF04961.17 FTCD_C 24.5 24.5 182 domain Y Y N cyclodeaminase/cyclohydrolase family protein GO:0003824,GO:0008152 7654689 131567 cellular organisms no rank 11504 EBI-EMBL Formiminotransferase-cyclodeaminase cyclodeaminase/cyclohydrolase family protein Members of this family are thought to be Formiminotransferase- cyclodeaminase enzymes EC:4.3.1.4. This domain is found in the C-terminus of the bifunctional animal members of the family. [1]. 7654689. The two monofunctional domains of octameric formiminotransferase-cyclodeaminase exist as dimers. Murley LL, MacKenzie RE;. Biochemistry 1995;34:10358-10364. (from Pfam) NF016826.5 PF04962.17 KduI 23.9 23.9 262 domain Y Y N 5-deoxy-glucuronate isomerase GO:0016861 11566986,1766386 131567 cellular organisms no rank 44999 EBI-EMBL KduI/IolB family 5-deoxy-glucuronate isomerase This family includes the 5-keto 4-deoxyuronate isomerase enzyme EC:5.3.1.17 that is involved in pectin degradation. This family aldo includes bacterial Myo-inositol catabolism (IolB) proteins. The Bacillus subtilis inositol operon (iolABCDEFGHIJ) is involved in myo-inositol catabolism. Glucose repression of the iol operon induced by inositol is exerted through catabolite repression mediated by CcpA and the iol induction system mediated by IolR [2]. The exact function of IolB is unknown. Members of this family possess a Cupin like structure. [1]. 1766386. Analysis of an Erwinia chrysanthemi gene cluster involved in pectin degradation. Condemine G, Robert-Baudouy J;. Mol Microbiol 1991;5:2191-2202. [2]. 11566986. Involvement of two distinct catabolite-responsive elements in catabolite repression of the Bacillus subtilis myo-inositol (iol) operon. Miwa Y, Fujita Y;. J Bacteriol 2001;183:5877-5884. (from Pfam) NF016831.5 PF04967.17 HTH_10 23.1 23.1 53 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 21567 EBI-EMBL HTH DNA binding domain HTH DNA binding domain NF016833.5 PF04969.21 CS 21.3 10 78 domain Y Y N CS domain-containing protein 10571178,14761955,21849505 131567 cellular organisms no rank 1990 EBI-EMBL CS domain CS domain The CS and CHORD (Pfam:PF04968) are fused into a single polypeptide chain in metazoans but are found in separate proteins in plants; this is thought to be indicative of an interaction between CS and CHORD [1]. It has been suggested that the CS domain is a binding module for HSP90, implying that CS domain-containing proteins are involved in recruiting heat shock proteins to multiprotein assemblies [2]. Two CS domains are found at the N-terminus of Ubiquitin carboxyl-terminal hydrolase 19 (USP19) (Swiss:O94966), these domains may play a role in the interaction of USP19 with cellular inhibitor of apoptosis 2 [3]. [1]. 10571178. A novel class of eukaryotic zinc-binding proteins is required for disease resistance signaling in barley and development in C. elegans. Shirasu K, Lahaye T, Tan MW, Zhou F, Azevedo C, Schulze-Lefert P;. Cell 1999;99:355-366. [2]. 14761955. Human Sgt1 binds HSP90 through the CHORD-Sgt1 domain and not the tetratricopeptide repeat domain. Lee YT, Jacob J, Michowski W, Nowotny M, Kuznicki J, Chazin WJ;. J Biol Chem 2004;279:16511-16517. [3]. 21849505. The USP19 deubiquitinase regulates the stability of c-IAP1 and c-IAP2. Mei Y, Hahn AA, Hu S, Yang X;. J Biol Chem. 2011;286:35380-35387. (from Pfam) NF016836.5 PF04972.22 BON 27 16.5 69 domain Y Y N BON domain-containing protein 12878000 131567 cellular organisms no rank 99844 EBI-EMBL BON domain BON domain This domain is found in a family of osmotic shock protection proteins (e.g. Swiss:P27291). It is also found in some Secretins and a group of potential haemolysins. Its likely function is attachment to phospholipid membranes [1]. [1]. 12878000. The BON domain: a putative membrane-binding domain. Yeats C, Bateman A;. Trends Biochem Sci 2003;28:352-355. (from Pfam) NF016837.5 PF04973.17 NMN_transporter 27.3 27.3 175 domain Y Y N nicotinamide mononucleotide transporter GO:0016020,GO:0034257,GO:0034258 2198247,2546921 131567 cellular organisms no rank 44699 EBI-EMBL Nicotinamide mononucleotide transporter nicotinamide mononucleotide transporter Members of this family are integral membrane proteins that are involved in transport of nicotinamide mononucleotide [1,2]. [1]. 2198247. Regulation of NAD metabolism in Salmonella typhimurium: molecular sequence analysis of the bifunctional nadR regulator and the nadA-pnuC operon. Foster JW, Park YK, Penfound T, Fenger T, Spector MP;. J Bacteriol 1990;172:4187-4196. [2]. 2546921. Genetic characterization of the pnuC gene, which encodes a component of the nicotinamide mononucleotide transport system in Salmonella typhimurium. Zhu N, Olivera BM, Roth JR;. J Bacteriol 1989;171:4402-4409. (from Pfam) NF016842.5 PF04981.18 NMD3 24.9 24.9 243 domain Y Y N NMD3-related protein 10022925 131567 cellular organisms no rank 1512 EBI-EMBL NMD3 family NMD3 N-terminal domain The NMD3 protein is involved in nonsense mediated mRNA decay. This amino terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [1]. [1]. 10022925. NMD3 encodes an essential cytoplasmic protein required for stable 60S ribosomal subunits in Saccharomyces cerevisiae. Ho JH, Johnson AW;. Mol Cell Biol 1999;19:2389-2399. (from Pfam) NF016843.5 PF04982.18 HPP 27.2 27.2 122 domain Y Y N HPP family protein 131567 cellular organisms no rank 27485 EBI-EMBL HPP family HPP family protein These proteins are integral membrane proteins with four transmembrane spanning helices. The most conserved region of the alignment is a motif HPP. The function of these proteins is uncertain but they may be transporters. (from Pfam) NF016844.5 PF04983.23 RNA_pol_Rpb1_3 28.9 28.9 162 PfamEq Y N N RNA polymerase Rpb1, domain 3 GO:0003677,GO:0003899,GO:0006351 11313498,8910400 131567 cellular organisms no rank 67674 EBI-EMBL RNA polymerase Rpb1, domain 3 RNA polymerase Rpb1, domain 3 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2]. [1]. 8910400. Structural modules of the large subunits of RNA polymerase. Introducing archaebacterial and chloroplast split sites in the beta and beta' subunits of Escherichia coli RNA polymerase. Severinov K, Mustaev A, Kukarin A, Muzzin O, Bass I, Darst SA, Goldfarb A;. J Biol Chem 1996;271:27969-27974. [2]. 11313498. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Cramer P, Bushnell DA, Kornberg RD;. Science 2001;292:1863-1876. (from Pfam) NF016845.5 PF04984.19 Phage_sheath_1 31.4 31.4 168 domain Y Y N phage tail sheath subtilisin-like domain-containing protein 1825255,2963141,7676633 131567 cellular organisms no rank 54883 EBI-EMBL Phage tail sheath protein subtilisin-like domain Phage tail sheath protein subtilisin-like domain This entry represents the second domain in a variety of phage tail sheath proteins. According to ECOD this domain has a subtilisin-like structure. [1]. 7676633. Tail sheath and tail tube genes of the temperate coliphage 186. Xue Q, Egan JB;. Virology 1995;212:218-221. [2]. 1825255. Nucleotide sequence of the genes encoding the major tail sheath and tail tube proteins of bacteriophage P2. Temple LM, Forsburg SL, Calendar R, Christie GE;. Virology 1991;181:353-358. [3]. 2963141. Nucleotide sequence of the tail tube structural gene of bacteriophage T4. Arisaka F, Ishimoto L, Kassavetis G, Kumazaki T, Ishii S;. J Virol 1988;62:882-886. (from Pfam) NF016850.5 PF04989.17 RMNT_CmcI 23.2 23.2 206 subfamily Y Y N CmcI family methyltransferase GO:0008168,GO:0008610 15292265,16527306,9696752 131567 cellular organisms no rank 5013 EBI-EMBL Rhamnosyl O-methyltransferase/CmcI CmcI family methyltransferase The founding member of this family, CmcI of Streptomyces clavuligerus, forms a complex with CmcJ, and the pair performs a two-step methoxylation in the biosynthesis of a cephalosporin antibiotic. While CmcI was originally called a hydroxylase, but was shown in more recent studies to bind S-adenosyl-L-methionine in the manner of SAM-dependent methyltransferases, and so it seems much more likely to be a methyltransferase. NF016852.5 PF04991.18 LicD 22.6 22.6 227 domain Y Y N LicD family protein 10200966,19833706 131567 cellular organisms no rank 15915 EBI-EMBL LicD family LicD family protein The LICD family of proteins show high sequence similarity and are involved in phosphorylcholine metabolism. There is evidence to show that LicD2 mutants have a reduced ability to take up choline, have decreased ability to adhere to host cells and are less virulent [1]. These proteins are part of the nucleotidyltransferase superfamily [2]. [1]. 10200966. Pneumococcal licD2 gene is involved in phosphorylcholine metabolism. Zhang JR, Idanpaan-Heikkila I, Fischer W, Tuomanen EI;. Mol Microbiol 1999;31:1477-1488. [2]. 19833706. Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. Kuchta K, Knizewski L, Wyrwicz LS, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2009; [Epub ahead of print] (from Pfam) NF016854.5 PF04993.18 TfoX_N 30.1 30.1 91 domain Y Y N TfoX/Sxy family protein 7724607,7961436 131567 cellular organisms no rank 24581 EBI-EMBL TfoX N-terminal domain TfoX N-terminal domain TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes [1]. This family corresponds to the N-terminal presumed domain of TfoX. The domain is found as an isolated domain in some proteins suggesting this is an autonomous domain. [1]. 7724607. Identification of a DNA transformation gene required for com101A+ expression and supertransformer phenotype in Haemophilus influenzae. Zulty JJ, Barcak GJ;. Proc Natl Acad Sci U S A 1995;92:3616-3620. [2]. 7961436. The Haemophilus influenzae sxy-1 mutation is in a newly identified gene essential for competence. Williams PM, Bannister LA, Redfield RJ;. J Bacteriol 1994;176:6789-6794. (from Pfam) NF016855.5 PF04994.18 TfoX_C 23.1 23.1 81 domain Y Y N TfoX/Sxy family DNA transformation protein 7724607,7961436 131567 cellular organisms no rank 11733 EBI-EMBL TfoX C-terminal domain TfoX C-terminal domain TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes [1]. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found associated with Pfam:PF00383 in Swiss:Q9JZR1. It is also found as an isolated domain in some proteins suggesting this is an autonomous domain. [1]. 7724607. Identification of a DNA transformation gene required for com101A+ expression and supertransformer phenotype in Haemophilus influenzae. Zulty JJ, Barcak GJ;. Proc Natl Acad Sci U S A 1995;92:3616-3620. [2]. 7961436. The Haemophilus influenzae sxy-1 mutation is in a newly identified gene essential for competence. Williams PM, Bannister LA, Redfield RJ;. J Bacteriol 1994;176:6789-6794. (from Pfam) NF016858.5 PF04997.17 RNA_pol_Rpb1_1 39.7 39.7 312 PfamEq Y N N RNA polymerase Rpb1, domain 1 GO:0003677,GO:0003899,GO:0006351 11313498,8910400 131567 cellular organisms no rank 66341 EBI-EMBL RNA polymerase Rpb1, domain 1 RNA polymerase Rpb1, domain 1 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2]. [1]. 8910400. Structural modules of the large subunits of RNA polymerase. Introducing archaebacterial and chloroplast split sites in the beta and beta' subunits of Escherichia coli RNA polymerase. Severinov K, Mustaev A, Kukarin A, Muzzin O, Bass I, Darst SA, Goldfarb A;. J Biol Chem 1996;271:27969-27974. [2]. 11313498. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Cramer P, Bushnell DA, Kornberg RD;. Science 2001;292:1863-1876. (from Pfam) NF016859.5 PF04998.22 RNA_pol_Rpb1_5 28.5 28.5 267 PfamEq Y N N RNA polymerase Rpb1, domain 5 GO:0003677,GO:0003899,GO:0006351 11313498,8910400 131567 cellular organisms no rank 67963 EBI-EMBL RNA polymerase Rpb1, domain 5 RNA polymerase Rpb1, domain 5 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2]. [1]. 8910400. Structural modules of the large subunits of RNA polymerase. Introducing archaebacterial and chloroplast split sites in the beta and beta' subunits of Escherichia coli RNA polymerase. Severinov K, Mustaev A, Kukarin A, Muzzin O, Bass I, Darst SA, Goldfarb A;. J Biol Chem 1996;271:27969-27974. [2]. 11313498. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Cramer P, Bushnell DA, Kornberg RD;. Science 2001;292:1863-1876. (from Pfam) NF016861.5 PF05000.22 RNA_pol_Rpb1_4 24.8 24.8 107 PfamEq Y N N RNA polymerase Rpb1, domain 4 GO:0003677,GO:0003899,GO:0006351 11313498,8910400 131567 cellular organisms no rank 66356 EBI-EMBL RNA polymerase Rpb1, domain 4 RNA polymerase Rpb1, domain 4 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2]. [1]. 8910400. Structural modules of the large subunits of RNA polymerase. Introducing archaebacterial and chloroplast split sites in the beta and beta' subunits of Escherichia coli RNA polymerase. Severinov K, Mustaev A, Kukarin A, Muzzin O, Bass I, Darst SA, Goldfarb A;. J Biol Chem 1996;271:27969-27974. [2]. 11313498. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Cramer P, Bushnell DA, Kornberg RD;. Science 2001;292:1863-1876. (from Pfam) NF016868.5 PF05007.18 Mannosyl_trans 23.4 23.4 259 PfamEq Y N N Mannosyltransferase (PIG-M) GO:0004376,GO:0006506,GO:0016020,GO:0051751 11226175 131567 cellular organisms no rank 1509 EBI-EMBL Mannosyltransferase (PIG-M) Mannosyltransferase (PIG-M) PIG-M has a DXD motif. The DXD motif is found in many glycosyltransferases that utilise nucleotide sugars. It is thought that the motif is involved in the binding of a manganese ion that is required for association of the enzymes with nucleotide sugar substrates [1]. [1]. 11226175. PIG-M transfers the first mannose to glycosylphosphatidylinositol on the lumenal side of the ER. Maeda Y, Watanabe R, Harris CL, Hong Y, Ohishi K, Kinoshita K, Kinoshita T;. EMBO J 2001;20:250-261. (from Pfam) NF016873.5 PF05013.17 FGase 28.9 28.9 219 domain Y Y N N-formylglutamate amidohydrolase 3308850 131567 cellular organisms no rank 49296 EBI-EMBL N-formylglutamate amidohydrolase N-formylglutamate amidohydrolase Formylglutamate amidohydrolase (FGase) catalyses the terminal reaction in the five-step pathway for histidine utilisation in Pseudomonas putida. By this action, N-formyl-L-glutamate (FG) is hydrolysed to produce L-glutamate plus formate [1]. [1]. 3308850. Purification and properties of formylglutamate amidohydrolase from Pseudomonas putida. Hu L, Mulfinger LM, Phillips AT;. J Bacteriol 1987;169:4696-4702. (from Pfam) NF016874.5 PF05014.20 Nuc_deoxyrib_tr 28.8 28.8 117 domain Y Y N nucleoside 2-deoxyribosyltransferase 7797550 131567 cellular organisms no rank 14892 EBI-EMBL Nucleoside 2-deoxyribosyltransferase nucleoside 2-deoxyribosyltransferase Nucleoside 2-deoxyribosyltransferase EC:2.4.2.6 catalyses the cleavage of the glycosidic bonds of 2`-deoxyribonucleosides [1]. [1]. 7797550. Identification of the active site nucleophile in nucleoside 2-deoxyribosyltransferase as glutamic acid 98. Porter DJ, Merrill BM, Short SA;. J Biol Chem 1995;270:15551-15556. (from Pfam) NF016876.5 PF05016.20 ParE_toxin 23 23 89 domain Y Y N type II toxin-antitoxin system RelE/ParE family toxin 1459960,14659018,20487277 131567 cellular organisms no rank 120793 EBI-EMBL ParE toxin of type II toxin-antitoxin system, parDE type II toxin-antitoxin system RelE/ParE family toxin ParE is the toxin family of a type II toxin-antitoxin family. It is toxic towards DNA gyrase, but is neutralised by the antitoxin ParD. The family also encompasses RelE/ParE described in [2]. [1]. 1459960. Definition of a minimal plasmid stabilization system from the broad-host-range plasmid RK2. Roberts RC, Helinski DR;. J Bacteriol 1992;174:8119-8132. [2]. 14659018. New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Anantharaman V, Aravind L;. Genome Biol 2003;4:R81. [3]. 20487277. Interaction specificity, toxicity and regulation of a paralogous set of ParE/RelE-family toxin-antitoxin systems. Fiebig A, Castro Rojas CM, Siegal-Gaskins D, Crosson S;. Mol Microbiol. 2010;77:236-251. (from Pfam) NF016879.5 PF05019.18 Coq4 22.9 22.9 221 subfamily Y Y N Coq4 family protein GO:0006744 11469793 131567 cellular organisms no rank 4372 EBI-EMBL Coenzyme Q (ubiquinone) biosynthesis protein Coq4 Coq4 family protein Coq4p was shown to peripherally associate with the matrix face of the mitochondrial inner membrane. The putative mitochondrial- targeting sequence present at the amino-terminus of the polypeptide efficiently imported it to mitochondria. The function of Coq4p is unknown, although its presence is required to maintain a steady-state level of Coq7p, another component of the Q biosynthetic pathway [1]. The overall structure of Coq4 is alpha helical and shows resemblance to haemoglobin/myoglobin (information from TOPSAN). [1]. 11469793. Yeast COQ4 encodes a mitochondrial protein required for coenzyme Q synthesis. Belogrudov GI, Lee PT, Jonassen T, Hsu AY, Gin P, Clarke CF;. Arch Biochem Biophys 2001;392:48-58. (from Pfam) NF016883.5 PF05023.19 Phytochelatin 24.9 24.9 210 domain Y Y N phytochelatin synthase family protein GO:0010038,GO:0016756,GO:0046872,GO:0046938 10369673,11814595,16339904 131567 cellular organisms no rank 2514 EBI-EMBL Phytochelatin synthase phytochelatin synthase family protein Phytochelatin synthase is the enzyme responsible for the synthesis of heavy-metal-binding peptides (phytochelatins) from glutathione and related thiols [2]. The crystal structure of a member of this family shows it to possess a papain fold [3]. The enzyme catalyses the deglycination of a GSH donor molecule [3]. The enzyme contains a catalytic triad of cysteine, histidine and aspartate residues. [1]. 10369673. Tolerance to toxic metals by a gene family of phytochelatin synthases from plants and yeast. Clemens S, Kim EJ, Neumann D, Schroeder JI;. EMBO J 1999;18:3325-3333. [2]. 11814595. Worms take the 'phyto' out of 'phytochelatins'. Vatamaniuk OK, Bucher EA, Ward JT, Rea PA;. Trends Biotechnol 2002;20:61-64. [3]. 16339904. A papain-like enzyme at work: native and acyl-enzyme intermediate structures in phytochelatin synthesis. Vivares D, Arnoux P, Pignol D;. Proc Natl Acad Sci U S A. 2005;102:18848-18853. (from Pfam) NF016893.5 PF05034.18 MAAL_N 27 27 159 domain Y N N Methylaspartate ammonia-lyase N-terminus 11748244,11796115,1420191 131567 cellular organisms no rank 2181 EBI-EMBL Methylaspartate ammonia-lyase N-terminus Methylaspartate ammonia-lyase N-terminus Methylaspartate ammonia-lyase EC:4.3.1.2 catalyses the second step of fermentation of glutamate. It is a homodimer. This family represents the N-terminal region of Methylaspartate ammonia-lyase. This domain is structurally related to Pfam:PF03952 [2]. This domain is associated with the catalytic domain Pfam:PF07476. [1]. 1420191. Cloning, sequencing, and expression in Escherichia coli of the Clostridium tetanomorphum gene encoding beta-methylaspartase and characterization of the recombinant protein. Goda SK, Minton NP, Botting NP, Gani D;. Biochemistry 1992;31:10747-10756. [2]. 11796115. Insights into enzyme evolution revealed by the structure of methylaspartate ammonia lyase. Levy CW, Buckley PA, Sedelnikova S, Kato Y, Asano Y, Rice DW, Baker PJ;. Structure (Camb) 2002;10:105-113. [3]. 11748244. The structure of 3-methylaspartase from Clostridium tetanomorphum functions via the common enolase chemical step. Asuncion M, Blankenfeldt W, Barlow JN, Gani D, Naismith JH;. J Biol Chem 2002;277:8306-8311. (from Pfam) NF016903.5 PF05045.17 RgpF 25 25 503 domain Y Y N rhamnan synthesis F family protein 12010977 131567 cellular organisms no rank 11487 EBI-EMBL Rhamnan synthesis protein F rhamnan synthesis F family protein This family consists of a group of proteins which are related to the Streptococcus rhamnose-glucose polysaccharide assembly protein (RgpF). Rhamnan backbones are found in several O polysaccharides of phytopathogenic bacteria and are regarded as pathogenic factors [1]. [1]. 12010977. Expression and characterization of streptococcal rgp genes required for rhamnan synthesis in Escherichia coli. Shibata Y, Yamashita Y, Ozaki K, Nakano Y, Koga T;. Infect Immun 2002;70:2891-2898. (from Pfam) NF016906.5 PF05048.18 NosD 23.6 23.6 212 domain Y Y N NosD domain-containing protein 8626275 131567 cellular organisms no rank 80135 EBI-EMBL Periplasmic copper-binding protein (NosD) Periplasmic copper-binding protein (NosD) NosD is a periplasmic protein which is thought to insert copper into the exported reductase apoenzyme (NosZ) [1]. This region forms a parallel beta helix domain. [1]. 8626275. Identification and analysis of the dissimilatory nitrous oxide reduction genes, nosRZDFY, of Rhizobium meliloti. Holloway P, McCormick W, Watson RJ, Chan YK;. J Bacteriol 1996;178:1505-1514. (from Pfam) NF016908.5 PF05050.17 Methyltransf_21 22.7 22.7 173 domain Y Y N FkbM family methyltransferase 131567 cellular organisms no rank 64208 EBI-EMBL Methyltransferase FkbM domain Methyltransferase FkbM domain This family has members from bacteria to human, and appears to be a methyltransferase. (from Pfam) NF016915.5 PF05057.19 DUF676 20.3 20.3 217 domain Y N N Putative serine esterase (DUF676) 131567 cellular organisms no rank 40430 EBI-EMBL Putative serine esterase (DUF676) Putative serine esterase (DUF676) This family of proteins are probably serine esterase type enzymes with an alpha/beta hydrolase fold. (from Pfam) NF016921.5 PF05063.19 MT-A70 23.9 23.9 172 subfamily Y Y N MT-A70 family methyltransferase 12355263 131567 cellular organisms no rank 12175 EBI-EMBL MT-A70 MT-A70 family methyltransferase MT-A70 is the S-adenosylmethionine-binding subunit of human mRNA:m6A methyl-transferase (MTase), an enzyme that sequence-specifically methylates adenines in pre-mRNAs. [1]. 12355263. Structure Prediction and Phylogenetic Analysis of a Functionally Diverse Family of Proteins Homologous to the MT-A70 Subunit of the Human mRNA:m6A Methyltransferase. Bujnicki JM, Feder M, Radlinska M, Blumenthal RM;. J Mol Evol 2002;55:431-444. (from Pfam) NF016923.5 PF05065.18 Phage_capsid 24.2 24.2 280 domain Y Y N phage major capsid protein 131567 cellular organisms no rank 69309 EBI-EMBL Phage capsid family phage major capsid protein Family of bacteriophage hypothetical proteins and capsid proteins. (from Pfam) NF016924.5 PF05066.18 HARE-HTH 25.9 25.9 71 domain Y Y N HTH domain-containing protein GO:0006355 10336502,22186017,7545758 131567 cellular organisms no rank 9874 EBI-EMBL HB1, ASXL, restriction endonuclease HTH domain HB1, ASXL, restriction endonuclease HTH domain A winged helix-turn-helix domain present in the plant HB1, vertebrate ASXL, the H. pylori restriction endonuclease HpyAIII(HgrA), the RNA polymerase delta subunit(RpoE) of Gram positive bacteria and several restriction endonucleases [1]. The domain is distinguished by the presence of a conserved one-turn helix between helix-3 and the preceding conserved turn. Its diverse architectures in eukaryotic species with extensive gene body methylation is suggestive of a chromatin function. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as hmC [1]. Bacterial versions include fusions to diverse restriction endonucleases, and a DNA glycosylase where it may play a similar role in detecting modified DNA. Certain bacterial version of the HARE-HTH domain show fusions to the helix-hairpin-helix domain of the RNA polymerase alpha subunit and the HTH domains found in regions 3 and 4 of the sigma factors [1]. These versions are predicted to function as a novel inhibitor of the binding of RNA polymerase to transcription start sites, similar to the Bacillus delta protein [2,3]. [1]. 10336502. Expression, abundance, and RNA polymerase binding properties of the delta factor of Bacillus subtilis. Lopez de Saro FJ, Yoshikawa N, Helmann JD;. J Biol Chem 1999;274:15953-15958. [2]. 7545758. Structural analysis of the Bacillus subtilis delta factor: a protein polyanion which displaces RNA from RNA polymerase. Lopez de Saro FJ, Woody AY, Helmann JD;. J Mol Biol 1995;252:189-202. [3]. 22186017. TRUNCATED at 1650 bytes (from Pfam) NF016925.5 PF05067.17 Mn_catalase 27 27 284 domain Y Y N manganese catalase family protein 11587647,8939876 131567 cellular organisms no rank 21934 EBI-EMBL Manganese containing catalase manganese catalase family protein Catalases are important antioxidant metalloenzymes that catalyse disproportionation of hydrogen peroxide, forming dioxygen and water. Two families of catalases are known, one having a heme cofactor, and this family that is a structurally distinct family containing non-heme manganese [2]. [1]. 8939876. Molecular cloning of manganese catalase from Lactobacillus plantarum. Igarashi T, Kono Y, Tanaka K;. J Biol Chem 1996;271:29521-29524. [2]. 11587647. Crystal structure of manganese catalase from Lactobacillus plantarum. Barynin VV, Whittaker MM, Antonyuk SV, Lamzin VS, Harrison PM, Artymiuk PJ, Whittaker JW;. Structure (Camb) 2001;9:725-738. (from Pfam) NF016932.5 PF05076.18 SUFU 25 25 172 domain Y Y N suppressor of fused domain protein 12068298,12150819,21306995 131567 cellular organisms no rank 22731 EBI-EMBL Suppressor of fused protein (SUFU) suppressor of fused domain protein SUFU, encoding the human orthologue of Drosophila suppressor of fused, appears to have a conserved role in the repression of Hedgehog signaling. SUFU exerts its repressor role by physically interacting with GLI proteins in both the cytoplasm and the nucleus [1]. SUFU has been found to be a tumour-suppressor gene that predisposes individuals to medulloblastoma by modulating the SHH signaling pathway [2]. Genomic contextual analysis of bacterial SUFU versions revealed that they are immunity proteins against diverse nuclease toxins in polymorphic toxin systems [3]. [1]. 12150819. Medulloblastoma: A problem of developmental biology. Rubin JB, Rowitch DH;. Cancer Cell 2002;2:7-8. [2]. 12068298. Mutations in SUFU predispose to medulloblastoma. Taylor MD, Liu L, Raffel C, Hui CC, Mainprize TG, Zhang X, Agatep R, Chiappa S, Gao L, Lowrance A, Hao A, Goldstein AM, Stavrou T, Scherer SW, Dura WT, Wainwright B, Squire JA, Rutka JT, Hogg D;. Nat Genet 2002;31:306-310. [3]. 21306995. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Zhang D, Iyer LM, Aravind L;. Nucleic Acids Res. 2011;39:4532-4552. (from Pfam) NF016944.5 PF05088.17 Bac_GDH_CD 22.8 22.8 497 domain Y Y N NAD-glutamate dehydrogenase domain-containing protein GO:0004352 10924516,34083757 131567 cellular organisms no rank 40619 EBI-EMBL Bacterial NAD-glutamate dehydrogenase, catalytic domain Bacterial NAD-glutamate dehydrogenase, catalytic domain This entry represents the catalytic domain of several proteins which are closely related to NAD-glutamate dehydrogenase found in Streptomyces clavuligerus. Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia [1]. The structure of GDH from Mycobacterium smegmatis revealed that it has long N- and C-terminal segments flanking the catalytic core which provide dimer-like interactions between pairs of monomers [2]. The N-terminal segment is flexible and contains ACT-like and PAS-type domains that may play a role as metabolic sensors for allosteric regulation [2]. [1]. 10924516. A new class of glutamate dehydrogenases (GDH). Biochemical and genetic characterization of the first member, the AMP-requiring NAD-specific GDH of Streptomyces clavuligerus. Minambres B, Olivera ER, Jensen RA, Luengo JM;. J Biol Chem 2000;275:39529-39542. [2]. 34083757. 3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme. Lazaro M, Melero R, Huet C, Lopez-Alonso JP, Delgado S, Dodu A, Bruch EM, Abriata LA, Alzari PM, Valle M, Lisa MN;. Commun Biol. 2021;4:684. (from Pfam) NF016945.5 PF05089.17 NAGLU 25.5 25.5 336 domain Y Y N alpha-N-acetylglucosaminidase TIM-barrel domain-containing protein 10588735,12049639,18443291 131567 cellular organisms no rank 10760 EBI-EMBL Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate [1]. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations [2]. The structure shows that the enzyme is composed of three domains. This central domain has a tim barrel fold [3]. [1]. 10588735. Mouse model of Sanfilippo syndrome type B produced by targeted disruption of the gene encoding alpha-N-acetylglucosaminidase. Li HH, Yu WH, Rozengurt N, Zhao HZ, Lyons KM, Anagnostaras S, Fanselow MS, Suzuki K, Vanier MT, Neufeld EF;. Proc Natl Acad Sci U S A 1999;96:14505-14510. [2]. 12049639. Correction of mucopolysaccharidosis type IIIb fibroblasts by lentiviral vector-mediated gene transfer. Villani GR, Follenzi A, Vanacore B, Di Domenico C, Naldini L, Di Natale P;. Biochem J 2002;364:747-753. [3]. 18443291. Structural and mechanistic insight into the basis of mucopolysaccharidosis IIIB. Ficko-Blean E, Stubbs KA, Nemirovsky O, Vocadlo DJ, Boraston AB;. Proc Natl Acad Sci U S A. 2008;105:6560-6565. (from Pfam) NF016946.5 PF05090.19 HTTM 27.7 27.7 259 domain Y Y N HTTM domain-containing protein GO:0008488,GO:0017187 10748045,14729325 131567 cellular organisms no rank 8047 EBI-EMBL HTTM domain HTTM domain This entry represents the HTTM (for horizontally transferred transmembrane) domain found at the N-terminal in metazoan Vitamin K-dependent gamma-carboxylase and in diverse domain architectures in bacterial proteins. This domain shows four transmembrane regions [2]. [1]. 10748045. Identification of a Drosophila vitamin K-dependent gamma-glutamyl carboxylase. Li T, Yang CT, Jin D, Stafford DW;. J Biol Chem 2000;275:18291-18296. [2]. 14729325. HTTM, a horizontally transferred transmembrane domain. Schultz J;. Trends Biochem Sci. 2004;29:4-7. (from Pfam) NF016952.5 PF05096.17 Glu_cyclase_2 22.3 22.3 249 PfamEq Y Y N glutaminyl-peptide cyclotransferase GO:0016603,GO:0017186 11035947 131567 cellular organisms no rank 12817 EBI-EMBL Glutamine cyclotransferase glutaminyl-peptide cyclotransferase This family of enzymes EC:2.3.2.5 catalyse the cyclization of free L-glutamine and N-terminal glutaminyl residues in proteins to pyroglutamate (5-oxoproline) and pyroglutamyl residues respectively [1]. This family includes plant and bacterial enzymes and seems unrelated to the mammalian enzymes. [1]. 11035947. Carica papaya glutamine cyclotransferase belongs to a novel plant enzyme subfamily: cloning and characterization of the recombinant enzyme. Dahl SW, Slaughter C, Lauritzen C, Bateman RC Jr, Connerton I, Pedersen J;. Protein Expr Purif 2000;20:27-36. (from Pfam) NF016955.5 PF05099.18 TerB 24.4 24.4 118 domain Y Y N TerB family tellurite resistance protein 10069007,3049247 131567 cellular organisms no rank 54308 EBI-EMBL Tellurite resistance protein TerB TerB family tellurite resistance protein This family contains the TerB tellurite resistance proteins from a a number of bacteria. [1]. 3049247. The nucleotide sequence of a plasmid determinant for resistance to tellurium anions. Jobling MG, Ritchie DA;. Gene 1988;66:245-258. [2]. 10069007. In vivo and in vitro cloning and phenotype characterization of tellurite resistance determinant conferred by plasmid pTE53 of a clinical isolate of Escherichia coli. Burian J, Tu N, Kl'ucar L, Guller L, Lloyd-Jones G, Stuchlik S, Fejdi P, Siekel P, Turna J;. Folia Microbiol (Praha) 1998;43:589-599. (from Pfam) NF016961.5 PF05105.17 Phage_holin_4_1 22.2 22.2 116 domain Y Y N phage holin family protein 11444771,22436471,8432697,9440507 131567 cellular organisms no rank 16303 EBI-EMBL Bacteriophage holin family phage holin family protein Phage holins and lytic enzymes are both necessary for bacterial lysis and virus dissemination. This family also includes TcdE/UtxA involved in toxin secretion in Clostridium difficile [1]. The 1.E.10 family is represented by Bacillus subtilis phi29 holin [2,3]; 1.E.16 represents the Cph1 holin[4]; and the 1.E.19 family is represented by the Clostridium difficile TcdE holin. Toxigenic strains of C. difficile produce two large toxins (TcdA and TcdB) encoded within a pathogenicity locus. tcdE, encoded between tcdA and tcdB, encodes a 166 aa protein which causes death to E. coli when expressed, and the structure of TcdE resembles holins. TcdE acts on the bacterial membrane. Since TcdA and TcdB lack signal peptides, they may be released via TcdE either prior to or subsequent to cell lysis [1]. [1]. 11444771. Evidence for holin function of tcdE gene in the pathogenicity of Clostridium difficile. Tan KS, Wee BY, Song KP;. J Med Microbiol 2001;50:613-619. [2]. 8432697. The missing link in phage lysis of gram-positive bacteria: gene 14 of Bacillus subtilis phage phi 29 encodes the functional homolog of lambda S protein. Steiner M, Lubitz W, Blasi U;. J Bacteriol. 1993;175:1038-1042. [3]. 22436471. Characterization and determination of holin protein of Streptococcus suis bacteriophage SMP in heterologous host. Shi Y, Yan Y, Ji W, Du B, Meng X, Wang H, Sun J;. Virol J. 2012;9:70. [4]. 9440507. Functional analysis of the two-gene lysis system of the pneumococcal phage Cp-1 in homologous and heterologous host cells. Martin AC, Lopez R, Garcia P;. J Bacteriol. 1998;180:210-217. (from Pfam) NF016963.5 PF05107.17 Cas_Cas7 33.2 33.2 249 domain Y Y N type I CRISPR-associated protein Cas7 GO:0043571 24459147 131567 cellular organisms no rank 8601 EBI-EMBL CRISPR-associated protein Cas7 type I CRISPR-associated protein Cas7 CRISPR-associated protein Cas7 is one of the components of the type I-B cascade-like antiviral defence complex. In Haloferax volcanii, Cas5, Cas6 and Cas7 form a small complex that aids the stability of CRISPR-derived RNA [1]. [1]. 24459147. A complex of Cas proteins 5, 6, and 7 is required for the biogenesis and stability of clustered regularly interspaced short palindromic repeats (crispr)-derived rnas (crrnas) in Haloferax volcanii. Brendel J, Stoll B, Lange SJ, Sharma K, Lenz C, Stachler AE, Maier LK, Richter H, Nickel L, Schmitz RA, Randau L, Allers T, Urlaub H, Backofen R, Marchfelder A;. J Biol Chem. 2014;289:7164-7177. (from Pfam) NF016970.5 PF05114.18 DUF692 25 25 263 subfamily Y Y N DUF692 family multinuclear iron-containing protein GO:0005506 35320042,35362960,37252350 131567 cellular organisms no rank 37076 EBI-EMBL Protein of unknown function (DUF692) DUF692 family multinuclear iron-containing protein Members of this family of multinuclear iron-containing proteins include RiPP precursor modification enzymes MbnB, TglH, and ChrH. NF016972.5 PF05116.18 S6PP 20.3 20.3 247 domain Y Y N HAD family hydrolase 11050182 131567 cellular organisms no rank 198091 EBI-EMBL Sucrose-6F-phosphate phosphohydrolase HAD family hydrolase This family consists of Sucrose-6F-phosphate phosphohydrolase proteins found in plants and cyanobacteria. Sucrose-6(F)-phosphate phosphohydrolase catalyses the final step in the pathway of sucrose biosynthesis [1]. [1]. 11050182. Purification, molecular cloning, and sequence analysis of sucrose-6F-phosphate phosphohydrolase from plants. Lunn JE, Ashton AR, Hatch MD, Heldt HW;. Proc Natl Acad Sci U S A 2000;97:12914-12919. (from Pfam) NF016976.5 PF05120.17 GvpG 30.6 30.6 67 domain Y Y N gas vesicle protein GvpG 12625841,15126480,9573198 131567 cellular organisms no rank 7466 EBI-EMBL Gas vesicle protein G gas vesicle protein GvpG Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in water to access oxygen and/or light. Proteins containing this family are found in gas vesicles and play a role in the formation of gas vesicles [1-3]. [1]. 9573198. Gas vesicle genes identified in Bacillus megaterium and functional expression in Escherichia coli. Li N, Cannon MC;. J Bacteriol 1998;180:2450-2458. [2]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. [3]. 15126480. Complexity of gas vesicle biogenesis in Halobacterium sp. strain NRC-1: identification of five new proteins. Shukla HD, DasSarma S;. J Bacteriol. 2004;186:3182-3186. (from Pfam) NF016977.5 PF05121.17 GvpK 25 25 85 domain Y Y N gas vesicle protein GvpK gvpK GO:0031412 12625841,1404376 131567 cellular organisms no rank 7626 EBI-EMBL Gas vesicle protein K gas vesicle protein GvpK These proteins are involved in the formation of gas vesicles ([1]). [1]. 1404376. Three different but related gene clusters encoding gas vesicles in halophilic archaea. Englert C, Kruger K, Offner S, Pfeifer F;. J Mol Biol 1992;227:586-592. [2]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF016980.5 PF05124.17 S_layer_C 23.9 23.9 177 domain Y N N S-layer like family, outer domain 12382110,8132478 131567 cellular organisms no rank 487 EBI-EMBL S-layer like family, outer domain S-layer like family, outer domain This entry represents a domain composed of the N and C-terminal segments of the protein. [1]. 8132478. Identification of the Methanococcus voltae S-layer structural gene. Konisky J, Lynn D, Hoppert M, Mayer F, Haney P;. J Bacteriol 1994;176:1790-1792. [2]. 12382110. Genes and derived amino acid sequences of S-layer proteins from mesophilic, thermophilic, and extremely thermophilic methanococci. Akca E, Claus H, Schultz N, Karbach G, Schlott B, Debaerdemaeker T, Declercq JP, Konig H;. Extremophiles. 2002;6:351-358. (from Pfam) NF016982.5 PF05127.19 Helicase_RecD 22.7 22.7 176 domain Y N N Helicase 15538360,19322199 131567 cellular organisms no rank 60898 EBI-EMBL Helicase Helicase This domain contains a P-loop (Walker A) motif, suggesting that it has ATPase activity, and a Walker B motif. In tRNA(Met) cytidine acetyltransferase (TmcA) it may function as an RNA helicase motor (driven by ATP hydrolysis) which delivers the wobble base to the active centre of the GCN5-related N-acetyltransferase (GNAT) domain [1]. It is found in the bacterial exodeoxyribonuclease V alpha chain (RecD), which has 5'-3' helicase activity. It is structurally similar to the motor domain 1A in other SF1 helicases [2]. [1]. 19322199. RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon. Chimnaronk S, Suzuki T, Manita T, Ikeuchi Y, Yao M, Suzuki T, Tanaka I;. EMBO J. 2009;28:1362-1373. [2]. 15538360. Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks. Singleton MR, Dillingham MS, Gaudier M, Kowalczykowski SC, Wigley DB;. Nature. 2004;432:187-193. (from Pfam) NF016984.5 PF05129.18 Elf1 29.8 29.8 79 PfamEq Y N N Transcription elongation factor Elf1 like 16260625 131567 cellular organisms no rank 109 EBI-EMBL Transcription elongation factor Elf1 like Transcription elongation factor Elf1 like This family of short proteins contains a putative zinc binding domain with four conserved cysteines. Swiss:P36053 has been identified as a transcription elongation factor in Saccharomyces cerevisiae [1]. [1]. 16260625. Identification and characterization of Elf1, a conserved transcription elongation factor in Saccharomyces cerevisiae. Prather D, Krogan NJ, Emili A, Greenblatt JF, Winston F;. Mol Cell Biol 2005;25:10122-10135. (from Pfam) NF016988.5 PF05133.19 Phage_prot_Gp6 25.5 25.5 416 domain Y Y N phage portal protein 11501993,17363899,25991862 131567 cellular organisms no rank 29212 EBI-EMBL Phage portal protein, SPP1 Gp6-like phage portal protein This bacteriophage protein forms a gateway that enables DNA passage during packaging and ejection of the phage genome. It also forms the junction between the phage head (capsid) and the tail proteins. During SPP1 morphogenesis, the portal protein, Gp6, participates in the procapsid assembly reaction [1,2]. In the mature SPP1 virion, Gp6 exists as a dodecamer, while recombinant SPP1 Gp6 has been shown to form 13-subunit assemblies [1,3]. This protein is common to Siphoviridae (phages with long non-contractile tails) and Myoviridae (phages with contractile tails). It is also found in a number of bacterial species. This family also includes the old Pfam family Phage_min_cap (PF:PF05126). RC Paper describing PDB structure 2jes [1]. 11501993. Structural organisation of the head-to-tail interface of a bacterial virus. Lurz R, Orlova EV, Gunther D, Dube P, Droge A, Weise F, van Heel M, Tavares P;. J Mol Biol 2001;310:1027-1037. [2]. 25991862. Structural rearrangements in the phage head-to-tail interface during assembly and infection. Chaban Y, Lurz R, Brasiles S, Cornilleau C, Karreman M, Zinn-Justin S, Tavares P, Orlova EV;. Proc Natl Acad Sci U S A. 2015;112:7009-7014. [3]. 17363899. Structural framework for DNA translocation via the viral portal protein. Lebedev AA, Krause MH, Isidro AL, Vagin AA, Orlova EV, Turner J, Dodson EJ, Tavares P, Antson AA;. EMBO J. 2007;26:1984-1994. (from Pfam) NF016993.5 PF05138.17 PaaA_PaaC 28.5 28.5 263 domain Y Y N Phenylacetic acid catabolic protein GO:0010124 9748275 131567 cellular organisms no rank 52155 EBI-EMBL Phenylacetic acid catabolic protein Phenylacetic acid catabolic protein This family includes proteins such as PaaA and PaaC that are part of a catabolic pathway of phenylacetic acid [1]. These proteins may form part of a dioxygenase complex. [1]. 9748275. Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway. Ferrandez A, Minambres B, Garcia B, Olivera ER, Luengo JM, Garcia JL, Diaz E;. J Biol Chem 1998;273:25974-25986. (from Pfam) NF016994.5 PF05139.19 Erythro_esteras 26.4 26.4 358 domain Y Y N erythromycin esterase family protein GO:0046677 3523438,3899861 131567 cellular organisms no rank 32773 EBI-EMBL Erythromycin esterase erythromycin esterase family protein This family includes erythromycin esterase enzymes [1,2] that confer resistance to the erythromycin antibiotic. [1]. 3899861. Nucleotide sequence of the gene ereA encoding the erythromycin esterase in Escherichia coli. Ounissi H, Courvalin P;. Gene 1985;35:271-278. [2]. 3523438. Analysis of the nucleotide sequence of the ereB gene encoding the erythromycin esterase type II. Arthur M, Autissier D, Courvalin P;. Nucleic Acids Res 1986;14:4987-4999. (from Pfam) NF016995.5 PF05140.19 ResB 24.6 24.6 486 domain Y Y N cytochrome c biogenesis protein ResB 10844653,8631715 131567 cellular organisms no rank 44489 EBI-EMBL ResB-like family cytochrome c biogenesis protein ResB This family includes both ResB and cytochrome c biogenesis proteins [1,2]. Mutations in ResB indicate that they are essential for growth [1]. ResB is predicted to be a transmembrane protein [1]. [1]. 10844653. Genes required for cytochrome c synthesis in Bacillus subtilis. Le Brun NE, Bengtsson J, Hederstedt L;. Mol Microbiol 2000;36:638-650. [2]. 8631715. Regulators of aerobic and anaerobic respiration in Bacillus subtilis. Sun G, Sharkova E, Chesnut R, Birkey S, Duggan MF, Sorokin A, Pujic P, Ehrlich SD, Hulett FM;. J Bacteriol 1996;178:1374-1385. (from Pfam) NF017000.5 PF05147.18 LANC_like 23.2 23.2 350 domain Y Y N lanthionine synthetase LanC family protein GO:0031179 11376939,12127987 131567 cellular organisms no rank 38897 EBI-EMBL Lanthionine synthetase C-like protein lanthionine synthetase LanC family protein Lanthionines are thioether bridges that are putatively generated by dehydration of Ser and Thr residues followed by addition of cysteine residues within the peptide. This family contains the lanthionine synthetase C-like proteins 1 and 2 which are related to the bacterial lanthionine synthetase components C (LanC). LANCL1 (P40 seven-transmembrane-domain protein) and LANCL2 (testes-specific adriamycin sensitivity protein) are thought to be peptide-modifying enzyme components in eukaryotic cells. Both proteins are produced in large quantities in the brain and testes and may have role in the immune surveillance of these organs [1]. Lanthionines are found in lantibiotics, which are peptide-derived, post-translationally modified antimicrobials produced by several bacterial strains [2]. This region contains seven internal repeats. [1]. 11376939. Characterization of rat LANCL1, a novel member of the lanthionine synthetase C-like protein family, highly expressed in testis and brain. Mayer H, Bauer H, Breuss J, Ziegler S, Prohaska R;. Gene 2001;269:73-80. [2]. 12127987. Heterologous expression and purification of SpaB involved in subtilin biosynthesis. Xie L, Chatterjee C, Balsara R, Okeley NM, van der Donk WA;. Biochem Biophys Res Commun 2002;295:952-957. (from Pfam) NF017001.5 PF05148.20 Methyltransf_8 27 27 219 domain Y N N Hypothetical methyltransferase GO:0008168 131567 cellular organisms no rank 12813 EBI-EMBL Hypothetical methyltransferase Hypothetical methyltransferase This family consists of several uncharacterised eukaryotic proteins which are related to methyltransferases Pfam:PF01209. (from Pfam) NF017005.5 PF05152.17 DUF705 20.4 20.4 304 PfamAutoEq Y Y N DUF705 domain-containing protein 131567 cellular organisms no rank 193 EBI-EMBL Protein of unknown function (DUF705) Protein of unknown function (DUF705) This family contains several uncharacterised Baculovirus proteins. (from Pfam) NF017007.5 PF05154.21 TM2 27.9 27.9 51 domain Y Y N NINE protein 131567 cellular organisms no rank 29366 EBI-EMBL TM2 domain TM2 domain This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts. (from Pfam) NF017011.5 PF05159.19 Capsule_synth 20 20 310 domain Y N N Capsule polysaccharide biosynthesis protein GO:0000271,GO:0015774 8326861 131567 cellular organisms no rank 29775 EBI-EMBL Capsule polysaccharide biosynthesis protein Capsule polysaccharide biosynthesis protein This family includes export proteins involved in capsule polysaccharide biosynthesis, such as KpsS Swiss:P42218 and LipB Swiss:P57038. [1]. 8326861. Phospholipid substitution of capsular polysaccharides and mechanisms of capsule formation in Neisseria meningitidis. Frosch M, Muller A;. Mol Microbiol 1993;8:483-493. (from Pfam) NF017013.5 PF05161.18 MOFRL 28.3 28.3 106 domain Y Y N MOFRL family protein 131567 cellular organisms no rank 20372 EBI-EMBL MOFRL family MOFRL family protein MOFRL(multi-organism fragment with rich Leucine) family exists in bacteria and eukaryotes. The function of this domain is not clear, although it exists in some putative enzymes such as reductases and kinases. (from Pfam) NF017017.5 PF05165.17 GCH_III 21.3 21.3 246 PfamEq Y Y N GTP cyclohydrolase IIa 3.5.4.29 GO:0009058,GO:0043740 18052207 131567 cellular organisms no rank 1437 EBI-EMBL GTP cyclohydrolase III GTP cyclohydrolase IIa GTP cyclohydrolase (GCH) III from Methanocaldococcus jannaschi catalyses the conversion of GTP to 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (FAPy). The reaction requires two bound magnesium ions for the catalysis and is activated by monovalent cations such as potassium and ammonium. The enzyme is a tetramer of identical subunits; each monomer is composed of an N- and a C-terminal domain that adopt nearly superimposible structures, suggesting that the protein has arisen by gene duplication [1]. The family is found in archaea and bacteria. [1]. 18052207. A new use for a familiar fold: the X-ray crystal structure of GTP-bound GTP cyclohydrolase III from Methanocaldococcus jannaschii reveals a two metal ion catalytic mechanism. Morrison SD, Roberts SA, Zegeer AM, Montfort WR, Bandarian V;. Biochemistry. 2008;47:230-242. (from Pfam) NF017019.5 PF05167.17 DUF711 25 25 413 PfamAutoEq Y Y N DUF711 family protein 131567 cellular organisms no rank 12379 EBI-EMBL Uncharacterised ACR (DUF711) DUF711 family protein The proteins in this family are functionally uncharacterised. The proteins are around 450 amino acids long and includes Streptococcus pneumoniae Sp0239 which is structurally similar to ribonucleotide reductase (RNR) and pyruvate formate lyase (PFL). It is likely that this family represents a group of glycerol-3-phosphate dehydrogenases. (from Pfam) NF017020.5 PF05168.19 HEPN 22 22 117 domain Y Y N HEPN domain-containing protein 12765831 131567 cellular organisms no rank 18276 EBI-EMBL HEPN domain HEPN domain NF017022.5 PF05171.17 HemS 24 24 128 domain Y N N Haemin-degrading HemS.ChuX domain GO:0006826 7997183 131567 cellular organisms no rank 18275 EBI-EMBL Haemin-degrading HemS.ChuX domain Haemin-degrading HemS.ChuX domain The Yersinia enterocolitica O:8 periplasmic binding-protein- dependent transport system consisted of four proteins: the periplasmic haemin-binding protein HemT, the haemin permease protein HemU, the ATP-binding hydrophilic protein HemV and the haemin-degrading protein HemS (this family). The structure for HemS has been solved and consists of a tandem repeat of this domain. [1]. 7997183. Transport of haemin across the cytoplasmic membrane through a haemin-specific periplasmic binding-protein-dependent transport system in Yersinia enterocolitica. Stojiljkovic I, Hantke K;. Mol Microbiol 1994;13:719-732. (from Pfam) NF017024.5 PF05173.19 DapB_C 27 27 121 domain Y Y N dihydrodipicolinate reductase C-terminal domain-containing protein GO:0008839,GO:0009089 7893645,8873595,9398235 131567 cellular organisms no rank 73021 EBI-EMBL Dihydrodipicolinate reductase, C-terminus Dihydrodipicolinate reductase, C-terminus Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The C-terminal domain of DapB has been proposed to be the substrate- binding domain. [1]. 8873595. Interaction of pyridine nucleotide substrates with Escherichia coli dihydrodipicolinate reductase: thermodynamic and structural analysis of binary complexes. Reddy SG, Scapin G, Blanchard JS;. Biochemistry 1996;35:13294-13302. [2]. 9398235. Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase in complex with NADH and the inhibitor 2,6-pyridinedicarboxylate. Scapin G, Reddy SG, Zheng R, Blanchard JS;. Biochemistry 1997;36:15081-15088. [3]. 7893645. Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase. Scapin G, Blanchard JS, Sacchettini JC;. Biochemistry 1995;34:3502-3512. (from Pfam) NF017026.5 PF05175.19 MTS 23 23 170 domain Y Y N methyltransferase GO:0008168 131567 cellular organisms no rank 840811 EBI-EMBL Methyltransferase small domain Methyltransferase small domain This domain is found in ribosomal RNA small subunit methyltransferase C (eg Swiss:P44453) as well as other methyltransferases (eg Swiss:Q53742). (from Pfam) NF017027.5 PF05176.19 ATP-synt_10 22.3 22.3 256 PfamEq Y N N ATP10 protein 2141026 131567 cellular organisms no rank 222 EBI-EMBL ATP10 protein ATP10 protein ATP 10 is essential for the assembly of a functional mitochondrial ATPase complex [1]. [1]. 2141026. ATP 10, a yeast nuclear gene required for the assembly of the mitochondrial F1-F0 complex. Ackerman SH, Tzagoloff A;. J Biol Chem 1990;265:9952-9959. (from Pfam) NF017034.5 PF05183.17 RdRP 23.8 23.8 582 subfamily Y Y N RNA dependent RNA polymerase GO:0003968 10850496,11719187,12553882 131567 cellular organisms no rank 807 EBI-EMBL RNA dependent RNA polymerase RNA dependent RNA polymerase This family of proteins are eukaryotic RNA dependent RNA polymerases. These proteins are involved in post transcriptional gene silencing where they are thought to amplify dsRNA templates. [1]. 11719187. On the role of RNA amplification in dsRNA-triggered gene silencing. Sijen T, Fleenor J, Simmer F, Thijssen KL, Parrish S, Timmons L, Plasterk RH, Fire A;. Cell 2001;107:465-476. [2]. 10850496. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Dalmay T, Hamilton A, Rudd S, Angell S, Baulcombe DC;. Cell 2000;101:543-553. [3]. 12553882. Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases. Iyer LM, Koonin EV, Aravind L;. BMC Struct Biol. 2003;3:1. (from Pfam) NF017038.5 PF05187.18 ETF_QO 24 24 104 domain Y Y N 4Fe-4S dicluster domain-containing protein 8306995,9294455 131567 cellular organisms no rank 32835 EBI-EMBL Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S Electron-transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) in the inner mitochondrial membrane accepts electrons from electron-transfer flavoprotein which is located in the mitochondrial matrix and reduces ubiquinone in the mitochondrial membrane. The two redox centres in the protein, FAD and a [4Fe4S] cluster, are present in a 64-kDa monomer [1]. [1]. 8306995. Molecular cloning and expression of a cDNA encoding human electron transfer flavoprotein-ubiquinone oxidoreductase. Goodman SI, Axtell KM, Bindoff LA, Beard SE, Gill RE, Frerman FE;. Eur J Biochem 1994;219:277-286. [2]. 9294455. mucK, a gene in Acinetobacter calcoaceticus ADP1 (BD413), encodes the ability to grow on exogenous cis,cis-muconate as the sole carbon source. Williams PA, Shaw LE;. J Bacteriol 1997;179:5935-5942. (from Pfam) NF017039.5 PF05188.22 MutS_II 25 25 133 PfamEq Y N N MutS domain II GO:0005524,GO:0006298,GO:0030983 11048710,8036718,8510668,9722634 131567 cellular organisms no rank 71779 EBI-EMBL MutS domain II MutS domain II This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with Pfam:PF00488, Pfam:PF01624, Pfam:PF05192 and Pfam:PF05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [2]. This domain corresponds to domain II in Thermus aquaticus MutS as characterised in [4], and has similarity resembles RNAse-H-like domains (see Pfam:PF00075). [1]. 9722634. Domain organization and functional analysis of Thermus thermophilus MutS protein [published erratum appears in Nucleic Acids Res 1998 Oct 15;26(20):following 4789]. Tachiki H, Kato R, Masui R, Hasegawa K, Itakura H, Fukuyama K, Kuramitsu S;. Nucleic Acids Res 1998;26:4153-4159. [2]. 8036718. Colon cancer and DNA repair: have mismatches met their match?. Jiricny J;. Trends Genet 1994;10:164-168. [3]. 8510668. The yeast gene MSH3 defines a new class of eukaryotic MutS homologues. New L, Liu K, Crouse GF;. Mol Gen Genet 1993;239:97-108. [4]. 11048710. Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Obmolova G, Ban C, Hsieh P, Yang W;. Nature 2000;407:703-710. (from Pfam) NF017040.5 PF05189.18 RTC_insert 23 23 102 PfamEq Y N N RNA 3'-terminal phosphate cyclase (RTC), insert domain 10673421 131567 cellular organisms no rank 6635 EBI-EMBL RNA 3'-terminal phosphate cyclase (RTC), insert domain RNA 3'-terminal phosphate cyclase (RTC), insert domain RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate [1]. The structure of RTC demonstrates that RTCs are comprised two domain. The larger domain contains an insert domain of approximately 100 amino acids [1]. [1]. 10673421. Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology. Palm GJ, Billy E, Filipowicz W, Wlodawer A;. Structure Fold Des 2000;8:13-23. (from Pfam) NF017041.5 PF05190.23 MutS_IV 22 22 92 PfamEq Y N N MutS family domain IV GO:0005524,GO:0006298,GO:0030983 11048710,8036718,8510668,9722634 131567 cellular organisms no rank 73882 EBI-EMBL MutS family domain IV MutS family domain IV This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with Pfam:PF01624, Pfam:PF05188, Pfam:PF05192 and Pfam:PF00488. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [2]. The aligned region corresponds in part with globular domain IV, which is involved in DNA binding, in Thermus aquaticus MutS as characterised in [4]. [1]. 9722634. Domain organization and functional analysis of Thermus thermophilus MutS protein [published erratum appears in Nucleic Acids Res 1998 Oct 15;26(20):following 4789]. Tachiki H, Kato R, Masui R, Hasegawa K, Itakura H, Fukuyama K, Kuramitsu S;. Nucleic Acids Res 1998;26:4153-4159. [2]. 8036718. Colon cancer and DNA repair: have mismatches met their match?. Jiricny J;. Trends Genet 1994;10:164-168. [3]. 8510668. The yeast gene MSH3 defines a new class of eukaryotic MutS homologues. New L, Liu K, Crouse GF;. Mol Gen Genet 1993;239:97-108. [4]. 11048710. Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Obmolova G, Ban C, Hsieh P, Yang W;. Nature 2000;407:703-710. (from Pfam) NF017042.5 PF05191.19 ADK_lid 26.6 26.6 36 PfamEq Y N N Adenylate kinase, active site lid GO:0004017 9715904 131567 cellular organisms no rank 31646 EBI-EMBL Adenylate kinase, active site lid Adenylate kinase, active site lid Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain, is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [1]. [1]. 9715904. Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+. Berry MB, Phillips GN Jr;. Proteins 1998;32:276-288. (from Pfam) NF017043.5 PF05192.23 MutS_III 34.1 34.1 194 PfamEq Y N N MutS domain III GO:0005524,GO:0006298,GO:0030983 11048710,8036718,8510668,9722634 131567 cellular organisms no rank 77087 EBI-EMBL MutS domain III MutS domain III This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with Pfam:PF00488, Pfam:PF05188, Pfam:PF01624 and Pfam:PF05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [2]. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterised in [4]. [1]. 9722634. Domain organization and functional analysis of Thermus thermophilus MutS protein [published erratum appears in Nucleic Acids Res 1998 Oct 15;26(20):following 4789]. Tachiki H, Kato R, Masui R, Hasegawa K, Itakura H, Fukuyama K, Kuramitsu S;. Nucleic Acids Res 1998;26:4153-4159. [2]. 8036718. Colon cancer and DNA repair: have mismatches met their match?. Jiricny J;. Trends Genet 1994;10:164-168. [3]. 8510668. The yeast gene MSH3 defines a new class of eukaryotic MutS homologues. New L, Liu K, Crouse GF;. Mol Gen Genet 1993;239:97-108. [4]. 11048710. Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Obmolova G, Ban C, Hsieh P, Yang W;. Nature 2000;407:703-710. (from Pfam) NF017044.5 PF05193.26 Peptidase_M16_C 23 23 181 domain Y Y N insulinase family protein 11470436 131567 cellular organisms no rank 242479 EBI-EMBL Peptidase M16 inactive domain Peptidase M16 inactive domain Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp [1]. [1]. 11470436. Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences. Taylor AB, Smith BS, Kitada S, Kojima K, Miyaura H, Otwinowski Z, Ito A, Deisenhofer J;. Structure (Camb) 2001;9:615-625. (from Pfam) NF017045.5 PF05194.17 UreE_C 23 23 87 PfamEq Y N N UreE urease accessory protein, C-terminal domain GO:0016151,GO:0019627,GO:0065003 11591723 131567 cellular organisms no rank 21696 EBI-EMBL UreE urease accessory protein, C-terminal domain UreE urease accessory protein, C-terminal domain UreE is a urease accessory protein. Urease Pfam:PF00449 hydrolyses urea into ammonia and carbamic acid. The C-terminal region of members of this family contains a His rich Nickel binding site. [1]. 11591723. Crystal structure of Klebsiella aerogenes UreE, a nickel-binding metallochaperone for urease activation. Song HK, Mulrooney SB, Huber R, Hausinger RP;. J Biol Chem 2001;276:49359-49364. (from Pfam) NF017046.5 PF05195.21 AMP_N 24.6 24.6 121 PfamEq Y Y N aminopeptidase P N-terminal domain-containing protein GO:0030145,GO:0070006 9520390 131567 cellular organisms no rank 52913 EBI-EMBL Aminopeptidase P, N-terminal domain Aminopeptidase P, N-terminal domain This domain is structurally very similar [1] to the creatinase N-terminal domain (Pfam:PF01321). However, little or no sequence similarity exists between the two families. [1]. 9520390. Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli. Wilce MC, Bond CS, Dixon NE, Freeman HC, Guss JM, Lilley PE, Wilce JA;. Proc Natl Acad Sci U S A 1998;95:3472-3477. (from Pfam) NF017050.5 PF05199.18 GMC_oxred_C 24.6 24.6 139 domain Y Y N GMC oxidoreductase GO:0016614 131567 cellular organisms no rank 217905 EBI-EMBL GMC oxidoreductase GMC oxidoreductase C-terminal domain This domain found associated with Pfam:PF00732. (from Pfam) NF017051.5 PF05201.20 GlutR_N 27 27 151 PfamEq Y N N Glutamyl-tRNAGlu reductase, N-terminal domain GO:0008883,GO:0033014,GO:0050661 3075378 131567 cellular organisms no rank 53770 EBI-EMBL Glutamyl-tRNAGlu reductase, N-terminal domain Glutamyl-tRNAGlu reductase, N-terminal domain NF017053.5 PF05203.21 Hom_end_hint 32.1 32.1 228 domain Y Y N Hint domain-containing homing endonuclease GO:0030908 12219083 131567 cellular organisms no rank 1531 EBI-EMBL Hom_end-associated Hint Hom_end-associated Hint Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life. The crystal structure of the homing nuclease PI-Sce [1] revealed two domains: an endonucleolytic centre resembling the C-terminal domain of Drosophila melanogaster Hedgehog protein, and a second domain containing the protein-splicing active site. This Domain corresponds to the latter protein-splicing domain. [1]. 12219083. Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence. Moure CM, Gimble FS, Quiocho FA;. Nat Struct Biol 2002;9:764-770. (from Pfam) NF017054.5 PF05204.19 Hom_end 21.1 21.1 110 PfamEq Y N N Homing endonuclease GO:0003677,GO:0004519,GO:0030908 12219083 131567 cellular organisms no rank 1512 EBI-EMBL Homing endonuclease Homing endonuclease Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life. [1]. 12219083. Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence. Moure CM, Gimble FS, Quiocho FA;. Nat Struct Biol 2002;9:764-770. (from Pfam) NF017069.5 PF05219.17 DREV 26 26 265 domain Y N N DREV methyltransferase GO:0106370 11132146 131567 cellular organisms no rank 7573 EBI-EMBL DREV methyltransferase DREV methyltransferase This family contains DREV protein homologues from several eukaryotes. The function of this protein is unknown [1]. However, these proteins appear to be related to other methyltransferases (Bateman A pers obs). [1]. 11132146. The mouse and human IGSF6 (DORA) genes map to the inflammatory bowel disease 1 locus and are embedded in an intron of a gene of unknown function. Bates EE, Kissenpfennig A, Peronne C, Mattei MG, Fossiez F, Malissen B, Lebecque S;. Immunogenetics 2000;52:112-120. (from Pfam) NF017071.5 PF05221.22 AdoHcyase 25 25 299 PfamEq Y Y N adenosylhomocysteinase 3.13.2.1 131567 cellular organisms no rank 49805 EBI-EMBL S-adenosyl-L-homocysteine hydrolase adenosylhomocysteinase NF017072.5 PF05222.20 AlaDh_PNT_N 30.4 30.4 136 domain Y N N Alanine dehydrogenase/PNT, N-terminal domain 11354603 131567 cellular organisms no rank 102545 EBI-EMBL Alanine dehydrogenase/PNT, N-terminal domain Alanine dehydrogenase/PNT, N-terminal domain This family now also contains the lysine 2-oxoglutarate reductases. [1]. 11354603. Lysine metabolism in higher plants. Azevedo RA, Lea PJ;. Amino Acids 2001;20:261-279. (from Pfam) NF017073.5 PF05223.16 MecA_N 22 22 117 domain Y Y N NTF2-like N-terminal transpeptidase domain-containing protein GO:0046677 12389036 131567 cellular organisms no rank 30985 EBI-EMBL NTF2-like N-terminal transpeptidase domain NTF2-like N-terminal transpeptidase domain The structure of this domain from MecA is known [1] Swiss:Q53707 and is found to be similar to that found in NTF2 Pfam:PF02136. This domain seems unlikely to have an enzymatic function, and its role remains unknown. [1]. 12389036. Structural basis for the beta lactam resistance of PBP2a from methicillin-resistant Staphylococcus aureus. Lim D, Strynadka NC;. Nat Struct Biol 2002;9:870-876. (from Pfam) NF017075.5 PF05225.21 HTH_psq 20.4 20.4 45 domain Y Y N helix-turn-helix domain-containing protein GO:0003677 11731471,11976954,9774480 131567 cellular organisms no rank 4542 EBI-EMBL helix-turn-helix, Psq domain helix-turn-helix, Psq domain This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster [1]. In pipsqueak this domain binds to GAGA sequence [1]. [1]. 9774480. The pipsqueak protein of Drosophila melanogaster binds to GAGA sequences through a novel DNA-binding domain. Lehmann M, Siegmund T, Lintermann KG, Korge G;. J Biol Chem 1998;273:28504-28509. [2]. 11976954. The Drosophila Pipsqueak protein defines a new family of helix-turn-helix DNA-binding proteins. Siegmund T, Lehmann M;. Dev Genes Evol 2002;212:152-157. [3]. 11731471. The Drosophila ribbon gene encodes a nuclear BTB domain protein that promotes epithelial migration and morphogenesis. Shim K, Blake KJ, Jack J, Krasnow MA;. Development 2001;128:4923-4933. (from Pfam) NF017077.5 PF05227.18 CHASE3 28 28 138 domain Y Y N CHASE3 domain-containing protein 12486065 131567 cellular organisms no rank 52416 EBI-EMBL CHASE3 domain CHASE3 domain CHASE3 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in bacteria. Specifically, CHASE3 domains are found in histidine kinases, adenylate cyclases, methyl-accepting chemotaxis proteins and predicted diguanylate cyclases/phosphodiesterases [1]. This domain recognises pyrene (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 12486065. Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea. Zhulin IB, Nikolskaya AN, Galperin MY;. J Bacteriol 2003;185:285-294. (from Pfam) NF017078.5 PF05228.18 CHASE4 26.2 26.2 140 domain Y Y N CHASE4 domain-containing protein 12486065 131567 cellular organisms no rank 20390 EBI-EMBL CHASE4 domain CHASE4 domain CHASE4. This is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in prokaryotes. Specifically, CHASE4 domains are found in histidine kinases in Archaea and in predicted diguanylate cyclases/phosphodiesterases in Bacteria. Environmental factors that are recognised by CHASE4 domains are not known at this time [1]. [1]. 12486065. Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea. Zhulin IB, Nikolskaya AN, Galperin MY;. J Bacteriol 2003;185:285-294. (from Pfam) NF017085.5 PF05235.19 CHAD 25.6 25.6 228 domain Y Y N CHAD domain-containing protein 12456267 131567 cellular organisms no rank 58799 EBI-EMBL CHAD domain CHAD domain The CHAD domain is an alpha-helical domain functionally associated with the Pfam:PF01928 domains. It has conserved histidines that may chelate metals [1]. [1]. 12456267. The catalytic domains of thiamine triphosphatase and CyaB-like adenylyl cyclase define a novel superfamily of domains that bind organic phosphates. Iyer LM, Aravind L;. BMC Genomics 2002;3:33-33. (from Pfam) NF017088.5 PF05239.21 PRC 21.2 21.2 78 domain Y Y N PRC-barrel domain-containing protein 10024457,12429060 131567 cellular organisms no rank 122378 EBI-EMBL PRC-barrel domain PRC-barrel domain The PRC-barrel is an all beta barrel domain found in photosystem reaction centre subunit H of the purple bacteria and RNA metabolism proteins of the RimM group. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the carboxyl terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain [1]. [1]. 12429060. The PRC-barrel: a widespread, conserved domain shared by photosynthetic reaction center subunits and proteins of RNA metabolism. Anantharaman V, Aravind L;. Genome Biol 2002;3:RESEARCH0061. [2]. 10024457. Refined crystal structures of reaction centres from Rhodopseudomonas viridis in complexes with the herbicide atrazine and two chiral atrazine derivatives also lead to a new model of the bound carotenoid. Lancaster CR, Michel H;. J Mol Biol 1999;286:883-898. (from Pfam) NF017116.5 PF05272.16 VapE-like_dom 25 25 217 domain Y Y N VapE domain-containing protein 131567 cellular organisms no rank 26350 EBI-EMBL Virulence-associated protein E-like domain virulence-associated protein VapE C-terminal domain Members of this family are related to VapE (virulence-associated protein E) of Dichelobacter nodosus. NF017121.5 PF05277.17 DUF726 22.6 22.6 343 PfamAutoEq Y Y N DUF726 domain-containing protein 131567 cellular organisms no rank 2435 EBI-EMBL Protein of unknown function (DUF726) Protein of unknown function (DUF726) This family consists of several uncharacterised eukaryotic proteins. (from Pfam) NF017128.5 PF05284.17 DUF736 22.1 22.1 99 subfamily Y Y N DUF736 family protein 131567 cellular organisms no rank 12536 EBI-EMBL Protein of unknown function (DUF736) DUF736 family protein This family consists of several uncharacterised bacterial proteins of unknown function. (from Pfam) NF017142.5 PF05299.17 Peptidase_M61 22 22 118 domain Y N N M61 glycyl aminopeptidase 11359790 131567 cellular organisms no rank 25283 EBI-EMBL M61 glycyl aminopeptidase M61 glycyl aminopeptidase Glycyl aminopeptidase is an unusual peptidase in that it has a preference for substrates with an N-terminal glycine or alanine. These proteins are found in Bacteria and in Archaea. [1]. 11359790. Aminopeptidase from Sphingomonas capsulata. Byun T, Tang M, Sloma A, Brown KM, Marumoto C, Fujii M, Blinkovsky AM;. J Biol Chem 2001;276:17902-17907. (from Pfam) NF017157.5 PF05315.16 ICEA 24 24 218 PfamEq Y N N ICEA Protein 11843964 131567 cellular organisms no rank 638 EBI-EMBL ICEA Protein ICEA Protein This family consists of several ICEA proteins from Helicobacter pylori. Helicobacter pylori infection causes gastritis and peptic ulcer disease, and is classified as a definite carcinogen of gastric cancer. ICEA1 is speculated to be associated with peptic ulcer disease [1]. [1]. 11843964. Distribution of distinct vacA, cagA and iceA alleles in Helicobacter pylori in Hong Kong. Wong BC, Yin Y, Berg DE, Xia HH, Zhang JZ, Wang WH, Wong WM, Huang XR, Tang VS, Lam SK;. Helicobacter 2001;6:317-324. (from Pfam) NF017174.5 PF05336.18 rhaM 23.4 23.4 105 domain Y Y N L-rhamnose mutarotase 5.1.3.32 GO:0016857 15876375 131567 cellular organisms no rank 30092 EBI-EMBL L-rhamnose mutarotase L-rhamnose mutarotase This family contains L-rhamnose mutarotase which is a glycosyl hydrolase that converts the monosaccharide L-rhamnopyranose from the alpha to the beta stereoisomer. In Escherichia coli this enzyme is the product of the rhaM gene (also known as yiiL). The tertiary structure has been solved, in complex with L-rhamnose, and the catalytic mechanism determined. His22 is the proton donor. The enzyme naturally exists as a dimer. [1]. 15876375. Structural insights into the monosaccharide specificity of Escherichia coli rhamnose mutarotase. Ryu KS, Kim JI, Cho SJ, Park D, Park C, Cheong HK, Lee JO, Choi BS;. J Mol Biol. 2005;349:153-162. (from Pfam) NF017181.5 PF05343.19 Peptidase_M42 23.2 23.2 292 domain Y N N M42 glutamyl aminopeptidase 10218575,11798173,11980710,8535515 131567 cellular organisms no rank 72272 EBI-EMBL M42 glutamyl aminopeptidase M42 glutamyl aminopeptidase These peptidases are found in Archaea and Bacteria. The example in Lactococcus lactis, PepA, aids growth on milk [1]. Pyrococcus horikoshii contain a thermostable de-blocking aminopeptidase member of this family used commercially for N-terminal protein sequencing [2]. [1]. 8535515. A non-essential glutamyl aminopeptidase is required for optimal growth of Lactococcus lactis MG1363 in milk. l'Anson KJ, Movahedi S, Griffin HG, Gasson MJ, Mulholland F;. Microbiology 1995;141:2873-2881. [2]. 11798173. Active site of deblocking aminopeptidase from Pyrococcus horikoshii. Onoe S, Ando S, Ataka M, Ishikawa K;. Biochem Biophys Res Commun 2002;290:994-997. [3]. 10218575. Thermostable aminopeptidase from Pyrococcus horikoshii. Ando S, Ishikawa K, Ishida H, Kawarabayasi Y, Kikuchi H, Kosugi Y;. FEBS Lett 1999;447:25-28. [4]. 11980710. Tetrahedral aminopeptidase: a novel large protease complex from archaea. Franzetti B, Schoehn G, Hernandez JF, Jaquinod M, Ruigrok RW, Zaccai G;. EMBO J 2002;21:2132-2138. (from Pfam) NF017183.5 PF05345.17 He_PIG 24 22.1 96 domain Y Y N putative Ig domain-containing protein 12606174 131567 cellular organisms no rank 56580 EBI-EMBL Putative Ig domain Putative Ig domain This alignment represents the conserved core region of ~90 residue repeat found in several haemagglutinins and other cell surface proteins. Sequence similarities to (Pfam:PF02494) and (Pfam:PF00801) suggest an Ig-like fold (personal obs:C. Yeats). So this family may be similar in function to the (Pfam:PF02639) and (Pfam:PF02638) domains. This domain is also found in the WisP family of proteins of Tropheryma whipplei ([1]). [1]. 12606174. Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei. Bentley SD, Maiwald M, Murphy LD, Pallen MJ, Yeats CA, Dover LG, Norbertczak HT, Besra GS, Quail MA, Harris DE, von Herbay A, Goble A, Rutter S, Squares R, Squares S, Barrell BG, Parkhill J, Relman DA;. Lancet 2003;361:637-644. (from Pfam) NF017190.5 PF05352.17 Phage_connector 25.6 25.6 281 PfamEq Y N N Phage Connector (GP10) 11130079,11526317 131567 cellular organisms no rank 138 EBI-EMBL Phage Connector (GP10) Phage Connector (GP10) The head-tail connector of bacteriophage 29 is composed of 12 36 kDa subunits with 12 fold symmetry. It is the central component of a rotary motor that packages the genomic dsDNA into pre-formed proheads. This motor consists of the head-tail connector, surrounded by a 29-encoded, 174-base, RNA and a viral ATPase protein [1,2]. [1]. 11526317. Structure determination of the head-tail connector of bacteriophage phi29. Simpson AA, Leiman PG, Tao Y, He Y, Badasso MO, Jardine PJ, Anderson DL, Rossmann MG;. Acta Crystallogr D Biol Crystallogr 2001;57:1260-1269. [2]. 11130079. Structure of the bacteriophage phi29 DNA packaging motor. Simpson AA, Tao Y, Leiman PG, Badasso MO, He Y, Jardine PJ, Olson NH, Morais MC, Grimes S, Anderson DL, Baker TS, Rossmann MG;. Nature 2000;408:745-750. (from Pfam) NF017200.5 PF05362.18 Lon_C 21.1 21.1 205 domain Y Y N S16 family serine protease 3.4.21.- GO:0004176,GO:0004252,GO:0006508 12208506 131567 cellular organisms no rank 205294 EBI-EMBL Lon protease (S16) C-terminal proteolytic domain S16 family serine protease C-terminal domain The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops. [1]. 12208506. Domain structure and ATP-induced conformational changes in Escherichia coli protease Lon revealed by limited proteolysis and autolysis. Vasilyeva OV, Kolygo KB, Leonova YF, Potapenko NA, Ovchinnikova TV;. FEBS Lett 2002;526:66-70. (from Pfam) NF017206.5 PF05368.18 NmrA 21.4 21.4 236 domain Y Y N NmrA family NAD(P)-binding protein 11726498 131567 cellular organisms no rank 526870 EBI-EMBL NmrA-like family NmrA family NAD(P)-binding protein NmrA is a negative transcriptional regulator involved in the post-translational modification of the transcription factor AreA. NmrA is part of a system controlling nitrogen metabolite repression in fungi [1]. This family only contains a few sequences as iteration results in significant matches to other Rossmann fold families. [1]. 11726498. The structure of the negative transcriptional regulator NmrA reveals a structural superfamily which includes the short-chain dehydrogenase/reductases. Stammers DK, Ren J, Leslie K, Nichols CE, Lamb HK, Cocklin S, Dodds A, Hawkins AR;. EMBO J 2001;20:6619-6626. (from Pfam) NF017207.5 PF05369.17 MtmB 25 25 450 domain Y Y N monomethylamine:corrinoid methyltransferase GO:0008168 12029132,12121639 131567 cellular organisms no rank 272 EBI-EMBL Monomethylamine methyltransferase MtmB monomethylamine:corrinoid methyltransferase Monomethylamine methyltransferase of the archaebacterium Methanosarcina barkeri contains a novel amino acid, pyrrolysine, encoded by the termination codon UAG [1,2]. The structure reveals a homohexamer comprised of individual subunits with a TIM barrel fold [2]. [1]. 12121639. Genetic code: introducing pyrrolysine. Ibba M, Soll D;. Curr Biol 2002;12:464-466. [2]. 12029132. A new UAG-encoded residue in the structure of a methanogen methyltransferase. Hao B, Gong W, Ferguson TK, James CM, Krzycki JA, Chan MK;. Science 2002;296:1462-1466. (from Pfam) NF017214.5 PF05377.16 FlaC_arch 27.8 27.8 55 domain Y Y N flagella accessory protein C 11250034,11717274 131567 cellular organisms no rank 776 EBI-EMBL Flagella accessory protein C (FlaC) flagella accessory protein C Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct[1]. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [2]. [1]. 11250034. The archaeal flagellum: a different kind of prokaryotic motility structure. Thomas NA, Bardy SL, Jarrell KF;. FEMS Microbiol Rev 2001;25:147-174. [2]. 11717274. Characterization of flagellum gene families of methanogenic archaea and localization of novel flagellum accessory proteins. Thomas NA, Jarrell KF;. J Bacteriol 2001;183:7154-7164. (from Pfam) NF017215.5 PF05378.18 Hydant_A_N 25.2 25.2 176 domain Y Y N hydantoinase/oxoprolinase N-terminal domain-containing protein 8943290 131567 cellular organisms no rank 67080 EBI-EMBL Hydantoinase/oxoprolinase N-terminal region Hydantoinase/oxoprolinase N-terminal region This family is found at the N-terminus of the Pfam:PF01968 family. (from Pfam) NF017221.5 PF05384.16 DegS 27.6 27.6 159 PfamEq Y N N Sensor protein DegS GO:0007165,GO:0016301 12471443 131567 cellular organisms no rank 3658 EBI-EMBL Sensor protein DegS Sensor protein DegS This is small family of Bacillus DegS proteins. The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon [1]. The family also contains one sequence Swiss:Q8R9D3 from Thermoanaerobacter tengcongensis which are described as sensory transduction histidine kinases. [1]. 12471443. Bacillus subtilis functional genomics: genome-wide analysis of the DegS-DegU regulon by transcriptomics and proteomics. Mader U, Antelmann H, Buder T, Dahl MK, Hecker M, Homuth G;. Mol Genet Genomics 2002;268:455-467. (from Pfam) NF017238.5 PF05401.16 NodS 24 24 201 domain Y Y N SAM-dependent methyltransferase GO:0008757,GO:0009312 11344149 131567 cellular organisms no rank 74429 EBI-EMBL Nodulation protein S (NodS) NodS-related SAM-dependent methyltransferase This family consists of nodulation S (NodS) proteins. The products of the rhizobial nodulation genes are involved in the biosynthesis of lipochitin oligosaccharides (LCOs), which are host-specific signal molecules required for nodule formation. NodS is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase involved in N methylation of LCOs. NodS uses N-deacetylated chitooligosaccharides, the products of the NodBC proteins, as its methyl acceptors [1]. [1]. 11344149. Rhizobial NodL O-acetyl transferase and NodS N-methyl transferase functionally interfere in production of modified Nod factors. Lopez-Lara IM, Kafetzopoulos D, Spaink HP, Thomas-Oates JE;. J Bacteriol 2001;183:3408-3416. (from Pfam) NF017239.5 PF05402.17 PqqD 23.4 23.4 67 subfamily_domain Y Y N PqqD family peptide modification chaperone 12437981,8002620 131567 cellular organisms no rank 30813 EBI-EMBL Coenzyme PQQ synthesis protein D (PqqD) PqqD family peptide modification chaperone This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis [1,2]. [1]. 8002620. Transcriptional analysis of pqqD and study of the regulation of pyrroloquinoline quinone biosynthesis in Methylobacterium extorquens AM1. Ramamoorthi R, Lidstrom ME;. J Bacteriol 1995;177:206-211. [2]. 12437981. PqqC/D, which converts a biosynthetic intermediate to pyrroloquinoline quinone. Toyama H, Fukumoto H, Saeki M, Matsushita K, Adachi O, Lidstrom ME;. Biochem Biophys Res Commun 2002;299:268-272. (from Pfam) NF017262.5 PF05425.18 CopD 32.1 32.1 105 domain Y Y N CopD family protein GO:0016020 7917425 131567 cellular organisms no rank 72185 EBI-EMBL Copper resistance protein D CopD family protein Copper sequestering activity displayed by some bacteria is determined by copper-binding protein products of the copper resistance operon (cop). CopD, together with CopC, perform copper uptake into the cytoplasm [1]. [1]. 7917425. Molecular mechanisms of copper resistance and accumulation in bacteria. Cooksey DA;. FEMS Microbiol Rev 1994;14:381-386. (from Pfam) NF017263.5 PF05426.17 Alginate_lyase 22.2 22.2 275 domain Y Y N alginate lyase family protein GO:0016829,GO:0042597 10390348,9683471 131567 cellular organisms no rank 35301 EBI-EMBL Alginate lyase alginate lyase family protein This family contains several bacterial alginate lyase proteins. Alginate is a family of 1-4-linked copolymers of beta -D-mannuronic acid (M) and alpha -L-guluronic acid (G). It is produced by brown algae and by some bacteria belonging to the genera Azotobacter and Pseudomonas. Alginate lyases catalyse the depolymerisation of alginates by beta -elimination, generating a molecule containing 4-deoxy-L-erythro-hex-4-enepyranosyluronate at the nonreducing end [1]. This family adopts an all alpha fold [2]. [1]. 9683471. Biochemical properties and substrate specificities of a recombinantly produced Azotobacter vinelandii alginate lyase. Ertesvag H, Erlien F, Skjak-Braek G, Rehm BH, Valla S;. J Bacteriol 1998;180:3779-3784. [2]. 10390348. Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 A resolution. Yoon HJ, Mikami B, Hashimoto W, Murata K;. J Mol Biol 1999;290:505-514. (from Pfam) NF017266.5 PF05430.16 Methyltransf_30 22 22 124 domain Y Y N MnmC family methyltransferase GO:0016645 15247431,18186482 131567 cellular organisms no rank 45472 EBI-EMBL S-adenosyl-L-methionine-dependent methyltransferase MnmC family methyltransferase This family is a S-adenosyl-L-methionine (SAM)-dependent methyltransferase. It is often found in association with Pfam:PF01266, where it is responsible for catalysing the transfer of a methyl group from S-adenosyl-L-methionine to 5-aminomethyl-2-thiouridine to form 5-methylaminomethyl-2-thiouridine [1,2]. [1]. 15247431. Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA. Bujnicki JM, Oudjama Y, Roovers M, Owczarek S, Caillet J, Droogmans L;. RNA. 2004;10:1236-1242. [2]. 18186482. Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA. Roovers M, Oudjama Y, Kaminska KH, Purta E, Caillet J, Droogmans L, Bujnicki JM;. Proteins. 2008;71:2076-2085. (from Pfam) NF017269.5 PF05433.20 Rick_17kDa_Anti 24.2 24.2 43 domain Y Y N glycine zipper 2TM domain-containing protein GO:0019867 16179394,3139629 131567 cellular organisms no rank 45993 EBI-EMBL Glycine zipper 2TM domain Glycine zipper 2TM domain This family includes a putative two transmembrane alpha-helical region that contains glycine zipper motifs [2]. This family includes several Rickettsia genus specific 17 kDa surface antigen proteins [1]. [1]. 3139629. Expression of the gene encoding the 17-kilodalton antigen from Rickettsia rickettsii: transcription and posttranslational modification. Anderson BE, Baumstark BR, Bellini WJ;. J Bacteriol 1988;170:4493-4500. [2]. 16179394. Transmembrane glycine zippers: physiological and pathological roles in membrane proteins. Kim S, Jeon TJ, Oberai A, Yang D, Schmidt JJ, Bowie JU;. Proc Natl Acad Sci U S A. 2005;102:14278-14283. (from Pfam) NF017273.5 PF05437.17 AzlD 23.7 23.7 99 domain Y Y N AzlD domain-containing protein 9287000 131567 cellular organisms no rank 55195 EBI-EMBL Branched-chain amino acid transport protein (AzlD) Branched-chain amino acid transport protein (AzlD) This family consists of a number of bacterial and archaeal branched-chain amino acid transport proteins. AzlD is known to be involved in conferring resistance to 4-azaleucine although its exact role is uncertain [1]. [1]. 9287000. An lrp-like gene of Bacillus subtilis involved in branched-chain amino acid transport. Belitsky BR, Gustafsson MC, Sonenshein AL, Von Wachenfeldt C;. J Bacteriol 1997;179:5448-5457. (from Pfam) NF017277.5 PF05443.16 ROS_MUCR 25.4 25.4 123 domain Y Y N MucR family transcriptional regulator GO:0003677,GO:0006355,GO:0008270 10656595,2013576,7756693 131567 cellular organisms no rank 17110 EBI-EMBL ROS/MUCR transcriptional regulator protein MucR family transcriptional regulator This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti. This gene encodes a 15.5-kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [1] and is necessary for succinoglycan production [2]. Sinorhizobium meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of alfalfa nodules. MucR from Sinorhizobium meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [3]. [1]. 2013576. The virC and virD operons of the Agrobacterium Ti plasmid are regulated by the ros chromosomal gene: analysis of the cloned ros gene. Cooley MB, D'Souza MR, Kado CI;. J Bacteriol 1991;173:2608-2616. [2]. 7756693. Molecular analysis of the Rhizobium meliloti mucR gene regulating the biosynthesis of the exopolysaccharides succinoglycan and galactoglucan. Keller M, Roxlau A, Weng WM, Schmidt M, Quandt J, Niehaus K, Jording D, Arnold W, Puhler A;. Mol Plant Microbe Interact 1995;8:267-277. [3]. 10656595. MucR is necessary for galactoglucan production in Sinorhizobium meliloti EFB1. Martin M, Lloret J, Sanchez-Contreras M, Bonilla I, Rivilla R;. Mol Plant Microbe Interact 2000;13:129-135. (from Pfam) NF017280.5 PF05448.17 AXE1 21 21 321 domain Y Y N acetylxylan esterase 10878123 131567 cellular organisms no rank 68008 EBI-EMBL Acetyl xylan esterase (AXE1) acetylxylan esterase This family consists of several bacterial acetyl xylan esterase proteins. Acetyl xylan esterases are enzymes that hydrolyse the ester linkages of the acetyl groups in position 2 and/or 3 of the xylose moieties of natural acetylated xylan from hardwood. These enzymes are one of the accessory enzymes which are part of the xylanolytic system, together with xylanases, beta-xylosidases, alpha-arabinofuranosidases and methylglucuronidases; these are all required for the complete hydrolysis of xylan [1]. [1]. 10878123. The acetyl xylan esterase of Bacillus pumilus belongs to a family of esterases with broad substrate specificity. Degrassi G, Kojic M, Ljubijankic G, Venturi V;. Microbiology 2000;146:1585-1591. (from Pfam) NF017282.5 PF05450.20 Nicastrin 25 25 218 domain Y N N Nicastrin 10993067,11295540,12507492,12584255 131567 cellular organisms no rank 1101 EBI-EMBL Nicastrin Nicastrin Nicastrin and presenilin are two major components of the gamma-secretase complex, which executes the intramembrane proteolysis of type I integral membrane proteins such as the amyloid precursor protein (APP) and Notch. Nicastrin is synthesised in fibroblasts and neurons as an endoglycosidase-H-sensitive glycosylated precursor protein (immature nicastrin) and is then modified by complex glycosylation in the Golgi apparatus and by sialylation in the trans-Golgi network (mature nicastrin) [1]. A region featured in this family has a fold similar to human transferrin receptor (TfR, Swiss:P02786) and a bacterial aminopeptidase (Swiss:P80561). It is implicated in the pathogenesis of Alzheimer's disease [4]. [1]. 12584255. gamma-Secretase activity requires the presenilin-dependent trafficking of nicastrin through the Golgi apparatus but not its complex glycosylation. Herreman A, Van Gassen G, Bentahir M, Nyabi O, Craessaerts K, Mueller U, Annaert W, De Strooper B;. J Cell Sci 2003;116:1127-1136. [2]. 12507492. Nicastrin is a resident lysosomal membrane protein. Bagshaw RD, Pasternak SH, Mahuran DJ, Callahan JW;. Biochem Biophys Res Commun 2003;300:615-618. [3]. 10993067. Nicastrin modulates presenilin-mediated notch/glp-1 signal transduction and betaAPP processing. Yu G, Nishimura M, Arawaka S, Levitan D, Zhang L, Tandon A, Song YQ, Rogaeva E, Chen F, Kawarai T, Supala A, Levesque L, Yu H, Yang DS, Holmes E, Milman P, Liang Y, Zhang DM, Xu DH, Sato C, Rogaev E, Smith M, Janus C, Zhang Y, Aebersold R, Farrer LS, Sorb. Nature 2000;407:48-54. [4]. 11295540. Nicastrin, a presenilin-interacting protein, contains an aminopeptidase/tran. TRUNCATED at 1650 bytes (from Pfam) NF017287.5 PF05455.16 GvpH 22 22 177 PfamEq Y Y N gas vesicle protein GvpH gvpH 9211710 131567 cellular organisms no rank 534 EBI-EMBL GvpH gas vesicle protein GvpH This family consists of archaeal GvpH proteins which are thought to be involved in gas vesicle synthesis [1]. [1]. 9211710. The characterization of the nv-gvpACNOFGH gene cluster involved in gas vesicle formation in Natronobacterium vacuolatum. Mayr A, Pfeifer F;. Arch Microbiol 1997;168:24-32. (from Pfam) NF017317.5 PF05491.18 RuvB_C 24.7 24.7 72 domain Y Y N Holliday junction DNA helicase RuvB C-terminal domain-containing protein GO:0003677,GO:0006281,GO:0006310,GO:0009378 12423347 131567 cellular organisms no rank 56282 EBI-EMBL RuvB C-terminal winged helix domain RuvB C-terminal winged helix domain The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein [1]. This family consists of the C-terminal region of the RuvB protein which is thought to be helicase DNA-binding domain. [1]. 12423347. The RuvABC resolvasome. Dickman MJ, Ingleston SM, Sedelnikova SE, Rafferty JB, Lloyd RG, Grasby JA, Hornby DP;. Eur J Biochem 2002;269:5492-5501. (from Pfam) NF017320.5 PF05495.17 zf-CHY 31.3 31.3 68 domain Y Y N CHY zinc finger protein GO:0008270 15294910,19043414 131567 cellular organisms no rank 4614 EBI-EMBL CHY zinc finger CHY zinc finger domain This family is mostly eukaryotic, and no prokaryotic version is characterized yet. In prokaryotes, this domain tends represent nearly the full length of the protein. NF017321.5 PF05496.17 RuvB_N 27 27 159 domain Y N N Holliday junction DNA helicase RuvB P-loop domain GO:0006281,GO:0006310,GO:0009378 12423347 131567 cellular organisms no rank 163926 EBI-EMBL Holliday junction DNA helicase RuvB P-loop domain Holliday junction DNA helicase RuvB P-loop domain The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein [1]. This family contains the N-terminal region of the protein. [1]. 12423347. The RuvABC resolvasome. Dickman MJ, Ingleston SM, Sedelnikova SE, Rafferty JB, Lloyd RG, Grasby JA, Hornby DP;. Eur J Biochem 2002;269:5492-5501. (from Pfam) NF017338.5 PF05514.16 HR_lesion 22.6 22.6 138 PfamEq Y N N HR-like lesion-inducing 131567 cellular organisms no rank 1557 EBI-EMBL HR-like lesion-inducing HR-like lesion-inducing Family of plant proteins that are associated with the hypersensitive response (HR) pathway of defence against plant pathogens. (from Pfam) NF017343.5 PF05521.16 Phage_H_T_join 22 22 96 domain Y Y N head-tail adaptor protein 131567 cellular organisms no rank 30227 EBI-EMBL Phage head-tail joining protein head-tail adaptor protein NF017345.5 PF05523.16 FdtA 23 23 131 domain Y Y N WxcM-like domain-containing protein 11589581,12740380 131567 cellular organisms no rank 13212 EBI-EMBL WxcM-like, C-terminal WxcM-like, C-terminal This family includes FdtA (Swiss:Q6T1W8) from Aneurinibacillus thermoaerophilus, which has been characterised as a dtdp-6-deoxy-3,4-keto-hexulose isomerase [1]. It also includes WxcM (Swiss:Q93S92) from Xanthomonas campestris (pv. campestris) [2]. [1]. 12740380. Biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-galactose in Aneurinibacillus thermoaerophilus L420-91T. Pfoestl A, Hofinger A, Kosma P, Messner P;. J Biol Chem 2003;278:26410-26417. [2]. 11589581. Lipopolysaccharide biosynthesis in Xanthomonas campestris pv. campestris: a cluster of 15 genes is involved in the biosynthesis of the LPS O-antigen and the LPS core. Vorholter FJ, Niehaus K, Puhler A;. Mol Genet Genomics 2001;266:79-95. (from Pfam) NF017346.5 PF05524.18 PEP-utilisers_N 24.4 24.4 121 domain Y Y N phosphoenolpyruvate-utilizing N-terminal domain-containing protein GO:0009401 131567 cellular organisms no rank 101842 EBI-EMBL PEP-utilising enzyme, N-terminal PEP-utilising enzyme, N-terminal NF017352.5 PF05531.17 NPV_P10 29.8 29.8 75 domain Y N N Nucleopolyhedrovirus P10 protein GO:0019028,GO:0039679 9634101 131567 cellular organisms no rank 69 EBI-EMBL Nucleopolyhedrovirus P10 protein Nucleopolyhedrovirus P10 protein This family consists of several nucleopolyhedrovirus P10 proteins which are thought to be involved in the morphogenesis of the polyhedra [1]. [1]. 9634101. The single-nucleocapsid nucleopolyhedrovirus of Buzura suppressaria encodes a P10 protein. van Oers MM, Hu Z, Arif BM, van Strien EA, van Lent JW, Vlak JM;. J Gen Virol 1998;79:1553-1562. (from Pfam) NF017353.5 PF05532.17 CsbD 40 40 53 domain Y Y N CsbD family protein 11988534 131567 cellular organisms no rank 45377 EBI-EMBL CsbD-like CsbD family protein CsbD is a bacterial general stress response protein. It's expression is mediated by sigma-B, an alternative sigma factor [1]. The role of CsbD in stress response is unclear. [1]. 11988534. Regulatory interactions between the Pho and sigma(B)-dependent general stress regulons of Bacillus subtilis. Pragai Z, Harwood CR;. Microbiology 2002;148:1593-1602. (from Pfam) NF017355.5 PF05534.17 HicB 21 21 51 domain Y Y N toxin-antitoxin system HicB family antitoxin 9721313 131567 cellular organisms no rank 20574 EBI-EMBL HicB family toxin-antitoxin system HicB family antitoxin This family consists of several bacterial HicB related proteins. The function of HicB is unknown although it is thought to be involved in pilus formation. It has been speculated that HicB performs a function antagonistic to that of pili and yet is necessary for invasion of certain niches [1]. [1]. 9721313. Evolution of the major pilus gene cluster of Haemophilus influenzae. Mhlanga-Mutangadura T, Morlin G, Smith AL, Eisenstark A, Golomb M;. J Bacteriol 1998;180:4693-4703. (from Pfam) NF017365.5 PF05544.16 Pro_racemase 27 27 325 domain Y Y N proline racemase family protein 10932226,3755058 131567 cellular organisms no rank 43061 EBI-EMBL Proline racemase proline racemase family protein This family consists of proline racemase (EC 5.1.1.4) proteins which catalyse the interconversion of L- and D-proline in bacteria [1]. This family also contains several similar eukaryotic proteins including Swiss:Q9NCP4 a sequence with B-cell mitogenic properties which has been characterised as a co-factor-independent proline racemase [2]. [1]. 3755058. Energetics of proline racemase: racemization of unlabeled proline in the unsaturated, saturated, and oversaturated regimes. Fisher LM, Albery WJ, Knowles JR;. Biochemistry 1986;25:2529-2537. [2]. 10932226. A B-cell mitogen from a pathogenic trypanosome is a eukaryotic proline racemase. Reina-San-Martin B, Degrave W, Rougeot C, Cosson A, Chamond N, Cordeiro-Da-Silva A, Arala-Chaves M, Coutinho A, Minoprio P;. Nat Med 2000;6:890-897. (from Pfam) NF017368.5 PF05547.16 Peptidase_M6 22 22 294 domain Y Y N immune inhibitor A domain-containing protein GO:0006508,GO:0008233 10475957,11429458,12029046,2089225,26745529,9371455 131567 cellular organisms no rank 26455 EBI-EMBL Immune inhibitor A peptidase M6, catalytic domain Immune inhibitor A peptidase M6, catalytic domain The insect pathogenic Gram-positive Bacillus thuringiensis secretes immune inhibitor A, a metallopeptidase, which specifically cleaves host antibacterial proteins. A homologue of immune inhibitor A, PrtV, has been identified in the Gram-negative human pathogen Vibrio cholerae [4]. The structure revealed four domains: a pro-peptide, a catalytic domain (represented in this entry), a domain reminiscent of viral envelope glycoproteins (VEG) and a MAM domain grafted into the latter [6]. [1]. 11429458. Identification of genes involved in the activation of the Bacillus thuringiensis inhA metalloprotease gene at the onset of sporulation. Grandvalet C, Gominet M, Lereclus D;. Microbiology 2001;147:1805-1813. [2]. 10475957. Characterization of the exosporium of Bacillus cereus. Charlton S, Moir AJ, Baillie L, Moir A;. J Appl Microbiol 1999;87:241-245. [3]. 2089225. Molecular characterization of immune inhibitor A, a secreted virulence protease from Bacillus thuringiensis. Lovgren A, Zhang M, Engstrom A, Dalhammar G, Landen R;. Mol Microbiol 1990;4:2137-2146. [4]. 9371455. Characterization of the Vibrio cholerae El Tor lipase operon lipAB and a protease gene downstream of the hly region. Ogierman MA, Fallarino A, Riess T, Williams SG, Attridge SR, Manning PA;. J Bacteriol 1997;179:7072-7080. [5]. 12029046. The InhA2 metalloprotease of Bacillus thuringiensis strain 407 is required for pathogenicity in insects infected via the oral route. Fedhila S, Nel P, Lereclus D;. J Bacteriol 2002;184:3296-3304. [6]. 26745529. Structural Basis for Latency and Function of Immune Inhibitor A Metallopeptidase, a Modulator of the Bacillus anthracis Se. TRUNCATED at 1650 bytes (from Pfam) NF017369.5 PF05548.16 Peptidase_M11 21 21 303 domain Y N N Gametolysin peptidase M11 11489172,11680823,12034745,12073093 131567 cellular organisms no rank 2604 EBI-EMBL Gametolysin peptidase M11 Gametolysin peptidase M11 In the unicellular biflagellated alga, Chlamydomonas reinhardtii, gametolysin, a zinc-containing metallo-protease, is responsible for the degradation of the cell wall. Homologues of gametolysin have also been reported in the simple multicellular organism, Volvox. [1]. 12073093. Genealogical relationships among laboratory strains of Chlamydomonas reinhardtii as inferred from matrix metalloprotease genes. Kubo T, Abe J, Saito T, Matsuda Y;. Curr Genet 2002;41:115-122. [2]. 11680823. Two tandemly-located matrix metalloprotease genes with different expression patterns in the chlamydomonas sexual cell cycle. Kubo T, Saito T, Fukuzawa H, Matsuda Y;. Curr Genet 2001;40:136-143. [3]. 12034745. An extracellular matrix-localized metalloproteinase with an exceptional QEXXH metal binding site prefers copper for catalytic activity. Heitzer M, Hallmann A;. J Biol Chem 2002;277:28280-28286. [4]. 11489172. Transcriptional activation by the sexual pheromone and wounding: a new gene family from Volvox encoding modular proteins with (hydroxy)proline-rich and metalloproteinase homology domains. Hallmann A, Amon P, Godl K, Heitzer M, Sumper M;. Plant J 2001;26:583-593. (from Pfam) NF017373.5 PF05552.17 MS_channel_1st_1 22 22 50 domain Y Y N mechanosensitive ion channel family protein 23012406,23074248,23339071 131567 cellular organisms no rank 36978 EBI-EMBL Mechanosensitive ion channel, conserved TM helix mechanosensitive ion channel family protein This alignment represents a conserved transmembrane helix, often found in small conductance mechanosensitive channels (MscS) in association with Pfam:PF00924 [1-3], such as Swiss:Q57634 and Swiss:Q58543 MscS assembles to a homoheptameric complex; each monomer consists of a N-terminal transmembrane region and a large cytoplasmic segment composed of a five-stranded antiparallel beta-sheet (middle/second) domain (Pfam:PF00924) and a C-terminal alpha/beta-domain (Pfam:PF21082) [1-3]. The N-terminal region consists of three membrane spanning helices (TM1, TM2 and TM3), TM1 is represented in this entry. In the heptamer, the permeation pathway is formed by the packing of TM3s, flanked by TM1-TM2 helical hairpins [1-3]. [1]. 23339071. Open and shut: crystal structures of the dodecylmaltoside solubilized mechanosensitive channel of small conductance from Escherichia coli and Helicobacter pylori at 4.4 A and 4.1 A resolutions. Lai JY, Poon YS, Kaiser JT, Rees DC;. Protein Sci. 2013;22:502-509. [2]. 23012406. Conformational state of the MscS mechanosensitive channel in solution revealed by pulsed electron-electron double resonance (PELDOR) spectroscopy. Pliotas C, Ward R, Branigan E, Rasmussen A, Hagelueken G, Huang H, Black SS, Booth IR, Schiemann O, Naismith JH;. Proc Natl Acad Sci U S A. 2012;109:E2675-E2682. [3]. 23074248. Structure and molecular mechanism of an anion-selective mechanosensitive channel of small conductance. Zhang X, Wang J, Feng Y, Ge J, Li W, Sun W, Iscla I, Yu J, Blount P, Li Y, Yang M;. Proc Natl Acad Sci U S A. 2012;109:18180-18185. (from Pfam) NF017380.5 PF05559.16 DUF763 35.5 35.5 319 PfamAutoEq Y Y N DUF763 domain-containing protein 131567 cellular organisms no rank 4853 EBI-EMBL Protein of unknown function (DUF763) Protein of unknown function (DUF763) This family consists of several uncharacterised bacterial and archaeal proteins of unknown function. (from Pfam) NF017386.5 PF05565.16 Sipho_Gp157 28.6 28.6 162 domain Y Y N siphovirus Gp157 family protein 9792848 131567 cellular organisms no rank 8764 EBI-EMBL Siphovirus Gp157 siphovirus Gp157 family protein This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophages. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage[1]. [1]. 9792848. A short noncoding viral DNA element showing characteristics of a replication origin confers bacteriophage resistance to Streptococcus thermophilus. Foley S, Lucchini S, Zwahlen MC, Brussow H;. Virology 1998;250:377-387. (from Pfam) NF017390.5 PF05569.16 Peptidase_M56 31 31 296 domain Y Y N M56 family metallopeptidase 11239156,11245199,23733187,9164468 131567 cellular organisms no rank 53468 EBI-EMBL BlaR1 peptidase M56 M56 family metallopeptidase Production of beta-Lactamase and penicillin-binding protein 2a (which mediate staphylococcal resistance to beta-lactam antibiotics) is regulated by a signal-transducing integral membrane protein and a transcriptional repressor. The signal transducer is a fusion protein with penicillin-binding and zinc metalloprotease domains. The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription. Homologues to this peptidase domain, which corresponds to Merops family M56, are also found in a number of other bacterial genome sequences. [1]. 11245199. Microbiology. Signaling antibiotic resistance in staphylococci. Archer GL, Bosilevac JM;. Science 2001;291:1915-1916. [2]. 11239156. A proteolytic transmembrane signaling pathway and resistance to beta-lactams in staphylococci. Zhang HZ, Hackbarth CJ, Chansky KM, Chambers HF;. Science 2001;291:1962-1965. [3]. 9164468. Mechanisms of methicillin resistance in staphylococci. Brakstad OG, Maeland JA;. APMIS 1997;105:264-276. [4]. 23733187. A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral membrane metallopeptidases. Lopez-Pelegrin M, Cerda-Costa N, Martinez-Jimenez F, Cintas-Pedrola A, Canals A, Peinado JR, Marti-Renom MA, Lopez-Otin C, Arolas JL, Gomis-Ruth FX;. J Biol Chem. 2013;288:21279-21294. (from Pfam) NF017393.5 PF05572.18 Peptidase_M43 23 23 152 domain Y Y N M43 family zinc metalloprotease 10913121,11161967,11713222,11897673 131567 cellular organisms no rank 15942 EBI-EMBL Pregnancy-associated plasma protein-A M43 family zinc metalloprotease Members of Merops family M43 of zinc metalloproteases include pregnancy-associated plasma protein A (PAPP-A) in human, ulilysin in archaea, and mirolysin in the oral pathogen Tannerella forsythia, a bacterium. Many members of the family are lipoproteins. NF017394.5 PF05573.17 NosL 24 24 131 domain Y Y N nitrous oxide reductase accessory protein NosL 11293413 131567 cellular organisms no rank 11948 EBI-EMBL NosL nitrous oxide reductase accessory protein NosL NosL is one of the accessory proteins of the nos (nitrous oxide reductase) gene cluster. NosL is a monomeric protein of 18,540 MW that specifically and stoichiometrically binds Cu(I). The copper ion in NosL is ligated by a Cys residue, and one Met and one His are thought to serve as the other ligands. It is possible that NosL is a copper chaperone involved in metallo-centre assembly [1]. [1]. 11293413. Expression, purification, and characterization of NosL, a novel Cu(I) protein of the nitrous oxide reductase (nos) gene cluster. McGuirl MA, Bollinger JA, Cosper N, Scott RA, Dooley DM;. J Biol Inorg Chem 2001;6:189-195. (from Pfam) NF017395.5 PF05575.16 V_cholerae_RfbT 27.9 27.9 286 PfamEq Y N N Vibrio cholerae RfbT protein 11035750,7688846 131567 cellular organisms no rank 1931 EBI-EMBL Vibrio cholerae RfbT protein Vibrio cholerae RfbT protein This family consists of several RfbT proteins from Vibrio cholerae. It has been found that genetic alteration of the rfbT gene is responsible for serotype conversion of Vibrio cholerae O1 [1] and determines the difference between the Ogawa and Inaba serotypes, in that the presence of rfbT is sufficient for Inaba-to-Ogawa serotype conversion [2]. [1]. 7688846. Mutations in the rfbT gene are responsible for the Ogawa to inaba serotype conversion in Vibrio cholerae O1. Ito T, Hiramatsu K, Ohshita Y, Yokota T;. Microbiol Immunol 1993;37:281-288. [2]. 11035750. Construction of a Vibrio cholerae vaccine candidate using transposon delivery and FLP recombinase-mediated excision. Chiang SL, Mekalanos JJ;. Infect Immun 2000;68:6391-6397. (from Pfam) NF017397.5 PF05577.17 Peptidase_S28 25 25 434 domain Y Y N S28 family serine protease GO:0006508,GO:0070008 10527559,11003393,11139392,11173530,11830581,12270155,9553770 131567 cellular organisms no rank 9170 EBI-EMBL Serine carboxypeptidase S28 S28 family serine protease These serine proteases include several eukaryotic enzymes such as lysosomal Pro-X carboxypeptidase, dipeptidyl-peptidase II, and thymus-specific serine peptidase. [1]. 9553770. Cellular carboxypeptidases. Skidgel RA, Erdos EG;. Immunol Rev 1998;161:129-141. [2]. 11830581. Identification and characterization of prolylcarboxypeptidase as an endothelial cell prekallikrein activator. Shariat-Madar Z, Mahdi F, Schmaier AH;. J Biol Chem 2002;277:17962-17969. [3]. 12270155. Development of potent and selective dipeptidyl peptidase II inhibitors. Senten K, Van der Veken P, Bal G, De Meester I, Lambeir AM, Scharpe S, Bauvois B, Haemers A, Augustyns K;. Bioorg Med Chem Lett 2002;12:2825-2828. [4]. 11173530. Purification, molecular cloning, and immunohistochemical localization of dipeptidyl peptidase II from the rat kidney and its identity with quiescent cell proline dipeptidase. Araki H, Li Y, Yamamoto Y, Haneda M, Nishi K, Kikkawa R, Ohkubo I;. J Biochem (Tokyo) 2001;129:279-288. [5]. 11139392. Cloning and functional expression of rat kidney dipeptidyl peptidase II. Fukasawa KM, Fukasawa K, Higaki K, Shiina N, Ohno M, Ito S, Otogoto J, Ota N;. Biochem J 2001;353:283-290. [6]. 11003393. Chromosomal localization of two mouse genes encoding thymus-specific serine peptidase and thymus-expressed acidic protein. Carrier A, Wurbel MA, Mattei MG, Kissenpfennig A, Malissen M, Malissen B;. Immunogenetics 2000;51:984-986. [7]. 10527559. Cloning of a novel MHC-encoded serine peptidase highly expressed by cortical epithelial cells of the thymus. Bowlus CL, Ahn J, Chu T, Gruen JR;. Cell Immunol 1999;196:80-86. (from Pfam) NF017402.5 PF05584.16 Sulfolobus_pRN 20.8 20.8 72 domain Y N N Sulfolobus plasmid regulatory protein 10430561,11054282 131567 cellular organisms no rank 224 EBI-EMBL Sulfolobus plasmid regulatory protein Sulfolobus plasmid regulatory protein This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus. [1]. 11054282. Evolution of the family of pRN plasmids and their integrase-mediated insertion into the chromosome of the crenarchaeon Sulfolobus solfataricus. Peng X, Holz I, Zillig W, Garrett RA, She Q;. J Mol Biol 2000;303:449-454. [2]. 10430561. Molecular analysis of pDL10 from Acidianus ambivalens reveals a family of related plasmids from extremely thermophilic and acidophilic archaea. Kletzin A, Lieke A, Urich T, Charlebois RL, Sensen CW;. Genetics 1999;152:1307-1314. (from Pfam) NF017410.5 PF05592.17 Bac_rhamnosid 22.2 22.2 102 subfamily_domain Y Y N family 78 glycoside hydrolase catalytic domain 10632887 131567 cellular organisms no rank 37747 EBI-EMBL Bacterial alpha-L-rhamnosidase concanavalin-like domain family 78 glycoside hydrolase catalytic domain The family 78 glycoside hydrolases include bacterial alpha-L-rhamnosidases. This HMM describes an (alpha/alpha)-6 barrel domain reported to be the catalytic domain. NF017415.5 PF05597.16 Phasin 28.8 28.8 126 domain Y Y N phasin family protein 12099824 131567 cellular organisms no rank 10423 EBI-EMBL Poly(hydroxyalcanoate) granule associated protein (phasin) phasin family protein Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon [1]. [1]. 12099824. Isolation and characterization of polyhydroxyalkanoates inclusions and their associated proteins in Pseudomonas sp. 61-3. Matsumoto K, Matsusaki H, Taguchi K, Seki M, Doi Y;. Biomacromolecules 2002;3:787-792. (from Pfam) NF017416.5 PF05598.16 DUF772 23.1 23.1 74 domain Y Y N transposase 131567 cellular organisms no rank 101436 EBI-EMBL Transposase domain (DUF772) transposase This presumed domain is found at the N-terminus of many proteins found in transposons. (from Pfam) NF017426.5 PF05610.16 DUF779 25 25 94 PfamAutoEq Y Y N DUF779 domain-containing protein 131567 cellular organisms no rank 17463 EBI-EMBL Protein of unknown function (DUF779) Protein of unknown function (DUF779) This family consists of several bacterial proteins of unknown function. (from Pfam) NF017434.5 PF05618.16 Zn_protease 27 27 138 domain Y Y N RimK/LysX family protein 131567 cellular organisms no rank 21842 EBI-EMBL Putative ATP-dependant zinc protease RimK/LysX family protein Proteins in this family are annotated as being ATP-dependant zinc proteases. (from Pfam) NF017436.5 PF05620.16 TMEM208_SND2 22.9 22.9 167 domain Y Y N SND2/TMEM208 family protein 16303567,21912603,23691174,27905431 131567 cellular organisms no rank 7 EBI-EMBL SRP-independent targeting protein 2/TMEM208 SND2/TMEM208 family protein This family includes SRP-independent targeting protein 2 (SND2) from yeast and transmembrane protein 208 (TMEM208) from mammals. Both are localized to the endoplasmic reticulum (ER) [1, 2]. SND2 works together with SND1 and SND3 in an alternative targeting route to the ER [1]. TMEM208 regulates both ER stress and autophagy. It contains three predicted transmembrane regions [2]. SND2 also known as Env10 in Saccharomyces cerevisiae, and its homologue as Mug69 in Schizosaccharomyces pombe. They were identified as proteins involved in vacuolar processing and morphology [3] and meiosis [4], respectively. [1]. 27905431. The SND proteins constitute an alternative targeting route to the endoplasmic reticulum. Aviram N, Ast T, Costa EA, Arakel EC, Chuartzman SG, Jan CH, Hassdenteufel S, Dudek J, Jung M, Schorr S, Zimmermann R, Schwappach B, Weissman JS, Schuldiner M;. Nature. 2016;540:134-138. [2]. 23691174. Transmembrane protein 208: a novel ER-localized protein that regulates autophagy and ER stress. Zhao Y, Hu J, Miao G, Qu L, Wang Z, Li G, Lv P, Ma D, Chen Y;. PLoS One. 2013;8:e64228. [3]. 21912603. A genome-wide immunodetection screen in S. cerevisiae uncovers novel genes involved in lysosomal vacuole function and morphology. Ricarte F, Menjivar R, Chhun S, Soreta T, Oliveira L, Hsueh T, Serranilla M, Gharakhanian E;. PLoS One. 2011;6:e23696. [4]. 16303567. A large-scale screen in S. pombe identifies seven novel genes required for critical meiotic events. Martin-Castellanos C, Blanco M, Rozalen AE, Perez-Hidalgo L, Garcia AI, Conde F, Mata J, Ellermeier C, Davis L, San-Segundo P, Smith GR, Moreno S;. Curr Biol. 2005;15:2056-2. TRUNCATED at 1650 bytes (from Pfam) NF017437.5 PF05621.16 TniB 22.4 22.4 189 domain Y Y N TniB family NTP-binding protein 8195081,8594337 131567 cellular organisms no rank 63755 EBI-EMBL Bacterial TniB protein TniB family NTP-binding protein This family consists of several bacterial TniB NTP-binding proteins. TniB is a probable ATP-binding protein [1] which is involved in Tn5053 mercury resistance transposition [2]. This entry represents a P-loop domain. [1]. 8195081. Transposon Tn5090 of plasmid R751, which carries an integron, is related to Tn7, Mu, and the retroelements. Radstrom P, Skold O, Swedberg G, Flensburg J, Roy PH, Sundstrom L;. J Bacteriol 1994;176:3257-3268. [2]. 8594337. Four genes, two ends, and a res region are involved in transposition of Tn5053: a paradigm for a novel family of transposons carrying either a mer operon or an integron. Kholodii GY, Mindlin SZ, Bass IA, Yurieva OV, Minakhina SV, Nikiforov VG;. Mol Microbiol 1995;17:1189-1200. (from Pfam) NF017442.5 PF05626.16 DUF790 28.8 28.8 387 domain Y Y N DUF790 family protein 131567 cellular organisms no rank 2317 EBI-EMBL Protein of unknown function (DUF790) DUF790 family protein This family consists of several hypothetical archaeal proteins of unknown function. (from Pfam) NF017446.5 PF05630.16 NPP1 21 21 197 domain Y Y N NPP1 family protein 12410814,12410815 131567 cellular organisms no rank 7700 EBI-EMBL Necrosis inducing protein (NPP1) NPP1 family protein This family consists of several NPP1 like necrosis inducing proteins from oomycetes, fungi and bacteria. Infiltration of NPP1 into leaves of Arabidopsis thaliana plants result in transcript accumulation of pathogenesis-related (PR) genes, production of ROS and ethylene, callose apposition, and HR-like cell death [1]. [1]. 12410815. NPP1, a Phytophthora-associated trigger of plant defense in parsley and Arabidopsis. Fellbrich G, Romanski A, Varet A, Blume B, Brunner F, Engelhardt S, Felix G, Kemmerling B, Krzymowska M, Nurnberger T;. Plant J 2002;32:375-390. [2]. 12410814. Expression of a Phytophthora sojae necrosis-inducing protein occurs during transition from biotrophy to necrotrophy. Qutob D, Kamoun S, Gijzen M;. Plant J 2002;32:361-373. (from Pfam) NF017447.5 PF05631.19 MFS_5 25 25 356 domain Y N N Sugar-tranasporters, 12 TM GO:0015098,GO:0015689,GO:0016020 16923188,21464289 131567 cellular organisms no rank 3840 EBI-EMBL Sugar-tranasporters, 12 TM Sugar-tranasporters, 12 TM MFS_5 is a family of sugar-transporters from both prokaryotes and eukaryotes. [1]. 21464289. Algae and humans share a molybdate transporter. Tejada-Jimenez M, Galvan A, Fernandez E;. Proc Natl Acad Sci U S A. 2011;108:6420-6425. [2]. 16923188. The monosaccharide transporter gene family in land plants is ancient and shows differential subfamily expression and expansion across lineages. Johnson DA, Hill JP, Thomas MA;. BMC Evol Biol. 2006;6-64. (from Pfam) NF017452.5 PF05636.16 HIGH_NTase1 27 27 402 PfamEq Y Y N nucleotidyltransferase family protein 131567 cellular organisms no rank 20435 EBI-EMBL HIGH Nucleotidyl Transferase nucleotidyltransferase family protein This family consists of HIGH Nucleotidyl Transferases (from Pfam) NF017464.5 PF05649.18 Peptidase_M13_N 32 32 381 domain Y N N Peptidase family M13 GO:0006508 11223883,12001226,7674922 131567 cellular organisms no rank 48707 EBI-EMBL Peptidase family M13 Peptidase family M13 M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk. [1]. 7674922. Evolutionary families of metallopeptidases. Rawlings ND, Barrett AJ;. Meth Enzymol 1995;248:183-228. [2]. 11223883. The neprilysin (NEP) family of zinc metalloendopeptidases: genomics and function. Turner AJ, Isaac RE, Coates D;. Bioessays 2001;23:261-269. [3]. 12001226. M13 endopeptidases: New conserved motifs correlated with structure, and simultaneous phylogenetic occurrence of PHEX and the bony fish. Bianchetti L, Oudet C, Poch O;. Proteins 2002;47:481-488. (from Pfam) NF017468.5 PF05653.19 Mg_trans_NIPA 26.2 26.2 295 domain Y Y N DMT family transporter GO:0015095,GO:0015693,GO:0016020 17166836,18667602 131567 cellular organisms no rank 10448 EBI-EMBL Magnesium transporter NIPA DMT family transporter NIPA (nonimprinted in Prader-Willi/Angelman syndrome) is a family of integral membrane proteins which function as magnesium transporters [1,2]. [1]. 17166836. NIPA1(SPG6), the basis for autosomal dominant form of hereditary spastic paraplegia, encodes a functional Mg2+ transporter. Goytain A, Hines RM, El-Husseini A, Quamme GA;. J Biol Chem. 2007;282:8060-8068. [2]. 18667602. Functional characterization of NIPA2, a selective Mg2+ transporter. Goytain A, Hines RM, Quamme GA;. Am J Physiol Cell Physiol. 2008;295:C944-C953. (from Pfam) NF017470.5 PF05656.19 DUF805 28.6 28.6 108 domain Y Y N DUF805 domain-containing protein GO:0016020 131567 cellular organisms no rank 50507 EBI-EMBL Protein of unknown function (DUF805) Protein of unknown function (DUF805) This family consists of several bacterial proteins of unknown function. (from Pfam) NF017482.5 PF05670.18 NFACT-R_1 29.8 29.8 112 PfamAutoEq Y Y N NFACT RNA binding domain-containing protein 24646681,8063411 131567 cellular organisms no rank 26751 EBI-EMBL NFACT protein RNA binding domain NFACT protein RNA binding domain This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from Swiss:O34693 where the N-terminal region is involved in this activity [1]. It is an RNA binding domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins. This NFACT-R family is found in two eukaryotic gene contexts: fused to the NFACT-N and NFACT-C domains in the NFACT protein involved in the ribosomal quality control pathway which contributes to CAT-tailing and as a standalone domain [2]. Additionally this domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important. [1]. 8063411. Cloning, sequencing, and expression of a fibronectin/fibrinogen-binding protein from group A streptococci. Courtney HS, Li Y, Dale JB, Hasty DL;. Infect Immun 1994;62:3937-3946. [2]. 24646681. A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications. Burroughs AM, Aravind L;. RNA Biol. 2014;11:360-372. (from Pfam) NF017485.5 PF05673.18 DUF815 23.8 23.8 249 domain Y Y N DUF815 domain-containing protein 131567 cellular organisms no rank 25418 EBI-EMBL Protein of unknown function (DUF815) Protein of unknown function (DUF815) This family consists of several bacterial proteins of unknown function. (from Pfam) NF017491.5 PF05679.21 CHGN 23 23 512 PfamEq Y N N Chondroitin N-acetylgalactosaminyltransferase GO:0008376,GO:0032580 11514575,11788602 131567 cellular organisms no rank 676 EBI-EMBL Chondroitin N-acetylgalactosaminyltransferase Chondroitin N-acetylgalactosaminyltransferase NF017493.5 PF05681.19 Fumerase 25 25 270 domain Y Y N fumarate hydratase 4.2.1.2 GO:0016829 11133938 131567 cellular organisms no rank 51913 EBI-EMBL Fumarate hydratase (Fumerase) fumarate hydratase This family consists of several bacterial fumarate hydratase proteins FumA and FumB. Fumarase, or fumarate hydratase (EC 4.2.1.2), is a component of the citric acid cycle. In facultative anaerobes such as Escherichia coli, fumarase also engages in the reductive pathway from oxaloacetate to succinate during anaerobic growth. Three fumarases, FumA, FumB, and FumC, have been reported in E. coli. fumA and fumB genes are homologous and encode products of identical sizes which form thermolabile dimers of Mr 120,000. FumA and FumB are class I enzymes and are members of the iron-dependent hydrolases, which include aconitase and malate hydratase. The active FumA contains a 4Fe-4S centre, and it can be inactivated upon oxidation to give a 3Fe-4S centre [1]. [1]. 11133938. Oxygen- and growth rate-dependent regulation of Escherichia coli fumarase (FumA, FumB, and FumC) activity. Tseng CP, Yu CC, Lin HH, Chang CY, Kuo JT;. J Bacteriol 2001;183:461-467. (from Pfam) NF017494.5 PF05683.17 Fumerase_C 22.2 22.2 205 domain Y Y N fumarate hydratase C-terminal domain-containing protein GO:0016836 11133938 131567 cellular organisms no rank 50315 EBI-EMBL Fumarase C-terminus Fumarase C-terminus This family consists of the C terminal region of several bacterial fumarate hydratase proteins (FumA and FumB). Fumarase, or fumarate hydratase (EC 4.2.1.2), is a component of the citric acid cycle. In facultative anaerobes such as Escherichia coli, fumarase also engages in the reductive pathway from oxaloacetate to succinate during anaerobic growth [1]. [1]. 11133938. Oxygen- and growth rate-dependent regulation of Escherichia coli fumarase (FumA, FumB, and FumC) activity. Tseng CP, Yu CC, Lin HH, Chang CY, Kuo JT;. J Bacteriol 2001;183:461-467. (from Pfam) NF017495.5 PF05684.17 DUF819 27 27 379 subfamily Y Y N DUF819 family protein 131567 cellular organisms no rank 10960 EBI-EMBL Protein of unknown function (DUF819) DUF819 family protein This family contains proteins of unknown function from archaeal, bacterial and plant species. (from Pfam) NF017501.5 PF05690.19 ThiG 23 23 247 domain Y N N Thiazole biosynthesis protein ThiG 9371431 131567 cellular organisms no rank 86874 EBI-EMBL Thiazole biosynthesis protein ThiG Thiazole biosynthesis protein ThiG This family consists of several bacterial thiazole biosynthesis protein G sequences. ThiG , together with ThiF and ThiH, is proposed to be involved in the synthesis of 4-methyl-5-(b-hydroxyethyl)thiazole (THZ) which is an intermediate in the thiazole production pathway [1]. This family also includes triosephosphate isomerase and pyridoxal 5'-phosphate synthase subunit PdxS. [1]. 9371431. Expression of thiamin biosynthetic genes (thiCOGE) and production of symbiotic terminal oxidase cbb3 in Rhizobium etli. Miranda-Rios J, Morera C, Taboada H, Davalos A, Encarnacion S, Mora J, Soberon M;. J Bacteriol 1997;179:6887-6893. (from Pfam) NF017502.5 PF05691.17 Raffinose_syn 20 20 750 domain Y Y N Sip1-related alpha-galactosidase 12244450,18335235,21639842 131567 cellular organisms no rank 3063 EBI-EMBL Raffinose synthase or seed imbibition protein Sip1 Sip1-related alpha-galactosidase This family consists of several raffinose synthase proteins, also known as seed imbibition (Sip1) proteins. Raffinose (O-alpha- D-galactopyranosyl- (1-->6)- O-alpha- D-glucopyranosyl-(12)- O-beta- D-fructofuranoside) is a widespread oligosaccharide in plant seeds and other tissues. Raffinose synthase (EC:2.4.1.82) is the key enzyme that channels sucrose into the raffinose oligosaccharide pathway [1]. Raffinose family oligosaccharides (RFOs) are ubiquitous in plant seeds and are thought to play critical roles in the acquisition of tolerance to desiccation and seed longevity. Raffinose synthases are alkaline alpha-galactosidases and are solely responsible for RFO breakdown in germinating maize seeds, whereas acidic galactosidases appear to have other functions [2]. Glycoside hydrolase family 36 can be split into 11 families, GH36A to GH36K [3]. This family includes enzymes from GH36C. [1]. 12244450. Functional expression of a cDNA encoding pea (Pisum sativum L.) raffinose synthase, partial purification of the enzyme from maturing seeds, and steady-state kinetic analysis of raffinose synthesis. Peterbauer T, Mach L, Mucha J, Richter A;. Planta 2002;215:839-846. [2]. 18335235. Enzymatic breakdown of raffinose oligosaccharides in pea seeds. Blochl A, Peterbauer T, Hofmann J, Richter A;. Planta. 2008;228:99-110. [3]. 21639842. Hierarchical classification of glycoside hydrolases. Naumoff DG;. Biochemistry (Mosc). 2011;76:622-635. (from Pfam) NF017504.5 PF05693.18 Glycogen_syn 27 27 639 PfamEq Y N N Glycogen synthase GO:0004373,GO:0005978 11415431,1908457,9691087 131567 cellular organisms no rank 3680 EBI-EMBL Glycogen synthase Glycogen synthase This family consists of the eukaryotic glycogen synthase proteins GYS1, GYS2 and GYS3 [1,2]. Glycogen synthase (GS) is the enzyme responsible for the synthesis of -1,4-linked glucose chains in glycogen. It is the rate limiting enzyme in the synthesis of the polysaccharide, and its activity is highly regulated through phosphorylation at multiple sites and also by allosteric effectors, mainly glucose 6-phosphate (G6P) [3]. [1]. 1908457. Two glycogen synthase isoforms in Saccharomyces cerevisiae are coded by distinct genes that are differentially controlled. Farkas I, Hardy TA, Goebl MG, Roach PJ;. J Biol Chem 1991;266:15602-15607. [2]. 9691087. Mutations in the liver glycogen synthase gene in children with hypoglycemia due to glycogen storage disease type 0. Orho M, Bosshard NU, Buist NR, Gitzelmann R, Aynsley-Green A, Blumel P, Gannon MC, Nuttall FQ, Groop LC;. J Clin Invest 1998;102:507-515. [3]. 11415431. Intracellular distribution of glycogen synthase and glycogen in primary cultured rat hepatocytes. Garcia-Rocha M, Roca A, De La Iglesia N, Baba O, Fernandez-Novell JM, Ferrer JC, Guinovart JJ;. Biochem J 2001;357:17-24. (from Pfam) NF017505.5 PF05694.16 SBP56 34 34 453 subfamily Y Y N selenium-binding protein SBP56-related protein GO:0008430 10799528,12026169,29255262 131567 cellular organisms no rank 5499 EBI-EMBL 56kDa selenium binding protein (SBP56) selenium-binding protein SBP56-related protein This family consists of several selenium binding proteins from eukaryotes, bacteria and archaea. It is thought that SP56 participates in late stages of intra-Golgi protein transport [1]. The Lotus japonicus homologue of SBP56, LjSBP, is thought to have more than one physiological role and can be implicated in controlling the oxidation/reduction status of target proteins, in vesicular Golgi transport [2]. Human selenium-binding protein 1 (SELENBP1) is a methanethiol oxidase (MTO) that converts methanethiol to H2O2, formaldehyde, and H2S [3]. [1]. 10799528. A 56-kDa selenium-binding protein participates in intra-Golgi protein transport. Porat A, Sagiv Y, Elazar Z;. J Biol Chem 2000;275:14457-14465. [2]. 12026169. Lotus japonicus gene Ljsbp is highly conserved among plants and animals and encodes a homologue to the mammalian selenium-binding proteins. Flemetakis E, Agalou A, Kavroulakis N, Dimou M, Martsikovskaya A, Slater A, Spaink HP, Roussis A, Katinakis P;. Mol Plant Microbe Interact 2002;15:313-322. [3]. 29255262. Mutations in SELENBP1, encoding a novel human methanethiol oxidase, cause extraoral halitosis. Pol A, Renkema GH, Tangerman A, Winkel EG, Engelke UF, de Brouwer APM, Lloyd KC, Araiza RS, van den Heuvel L, Omran H, Olbrich H, Oude Elberink M, Gilissen C, Rodenburg RJ, Sass JO, Schwab KO, Schafer H, Venselaar H, Sequeira JS, Op den Camp HJM, Wevers RA;. Nat Genet. 2018;50:120-129. (from Pfam) NF017509.5 PF05698.19 Trigger_C 22.7 22.7 162 domain Y N N Bacterial trigger factor protein (TF) C-terminus GO:0006457,GO:0015031 12603737,29222465,32358557 131567 cellular organisms no rank 67584 EBI-EMBL Bacterial trigger factor protein (TF) C-terminus Bacterial trigger factor protein (TF) C-terminus In the E. coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of three domains, an N-terminal domain which mediates association with the large ribosomal subunit (ribosome-binding domain, RBD), a central PPIase domain with homology to FKBP proteins, and a C-terminal substrate-binding domain (SBD) which forms the central body of the protein and has two helical arms that create a cavity [1,2]. The association between its N-terminal domain with the ribosomal protein L23 located next to the peptide tunnel exit is essential for the interaction with nascent polypeptides and its in vivo function [1]. This entry represents the C-terminal region of TF which has a multi-helical structure consisting of an irregular array of long and short helices structurally similar to the peptide-binding domain of the bacterial porin chaperone SurA [3]. [1]. 12603737. Trigger Factor and DnaK possess overlapping substrate pools and binding specificities. Deuerling E, Patzelt H, Vorderwulbecke S, Rauch T, Kramer G, Schaffitzel E, Mogk A, Schulze-Specking A, Langen H, Bukau B;. Mol Microbiol 2003;47:1317-1328. [2]. 29222465. The dynamic dimer structure of the chaperone Trigger Factor. Morgado L, Burmann BM, Sharpe T, Mazur A, Hiller S;. Nat Co. TRUNCATED at 1650 bytes (from Pfam) NF017515.5 PF05704.17 Caps_synth 24.5 24.5 278 domain Y Y N capsular polysaccharide synthesis protein GO:0016757 10094675,10688204,11179285,7752885,9838125 131567 cellular organisms no rank 12622 EBI-EMBL Capsular polysaccharide synthesis protein capsular polysaccharide synthesis protein This family consists of several capsular polysaccharide proteins. Capsular polysaccharide (CPS) is a major virulence factor in Streptococcus pneumoniae [1]. [1]. 11179285. Molecular characterization of Streptococcus pneumoniae type 4, 6B, 8, and 18C capsular polysaccharide gene clusters. Jiang SM, Wang L, Reeves PR;. Infect Immun 2001;69:1244-1255. [2]. 9838125. Molecular structure of the gene cluster responsible for the synthesis of the polysaccharide capsule of Streptococcus pneumoniae type 33F. Llull D, Lopez R, Garcia E, Munoz R;. Biochim Biophys Acta 1998;1443:217-224. [3]. 10688204. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Parkhill J, Wren BW, Mungall K, Ketley JM, Churcher C, Basham D, Chillingworth T, Davies RM, Feltwell T, Holroyd S, Jagels K, Karlyshev AV, Moule S, Pallen MJ, Penn CW, Quail MA, Rajandream MA, Rutherford KM, van Vliet AH, Whitehead S, Barrell BG;. Nature 2000;403:665-668. [4]. 7752885. Region II of the Haemophilus influenzae type be capsulation locus is involved in serotype-specific polysaccharide synthesis. Van Eldere J, Brophy L, Loynds B, Celis P, Hancock I, Carman S, Kroll JS, Moxon ER;. Mol Microbiol 1995;15:107-118. [5]. 10094675. acs1 of Haemophilus influenzae type a capsulation locus region II encodes a bifunctional ribulose 5-phosphate reductase- CDP-ribitol pyrophosphorylase. Follens A, Veiga-da-Cunha M, Merckx R, van Schaftingen E, van Eldere J;. J Bacteriol 1999;181:2001-2007. (from Pfam) NF017516.5 PF05705.19 DUF829 25 25 242 PfamAutoEq Y Y N DUF829 domain-containing protein 131567 cellular organisms no rank 44 EBI-EMBL Eukaryotic protein of unknown function (DUF829) Eukaryotic protein of unknown function (DUF829) This family consists of several uncharacterised eukaryotic proteins. (from Pfam) NF017517.5 PF05706.17 CDKN3 20.7 20.7 168 PfamEq Y N N Cyclin-dependent kinase inhibitor 3 (CDKN3) GO:0004721,GO:0004725 10987270,8127873 131567 cellular organisms no rank 6504 EBI-EMBL Cyclin-dependent kinase inhibitor 3 (CDKN3) Cyclin-dependent kinase inhibitor 3 (CDKN3) This family consists of cyclin-dependent kinase inhibitor 3 or kinase associated phosphatase proteins from several mammalian species. The cyclin-dependent kinase (Cdk)-associated protein phosphatase (KAP) is a human dual specificity protein phosphatase that dephosphorylates Cdk2 on threonine 160 in a cyclin-dependent manner [1,2]. [1]. 8127873. KAP: a dual specificity phosphatase that interacts with cyclin-dependent kinases. Hannon GJ, Casso D, Beach D;. Proc Natl Acad Sci U S A 1994;91:1731-1735. [2]. 10987270. Aberrant transcripts of the cyclin-dependent kinase-associated protein phosphatase in hepatocellular carcinoma. Yeh CT, Lu SC, Chen TC, Peng CY, Liaw YF;. Cancer Res 2000;60:4697-4700. (from Pfam) NF017518.5 PF05707.17 Zot 20.3 20.3 197 domain Y Y N zonular occludens toxin domain-containing protein 11947928,12532391 131567 cellular organisms no rank 17162 EBI-EMBL Zonular occludens toxin (Zot) Zonular occludens toxin (Zot) This family consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot). Zot is elaborated by bacteriophages present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers [1,2] [1]. 11947928. Zonula occludens toxin (Zot) interferes with the induction of nasal tolerance to gliadin. Rossi M, Maurano F, Luongo D, Fasano A, Uzzau S, Auricchio S, Troncone R;. Immunol Lett 2002;81:217-221. [2]. 12532391. Zonula occludens toxin increases the permeability of molecular weight markers and chemotherapeutic agents across the bovine brain microvessel endothelial cells. Karyekar CS, Fasano A, Raje S, Lu R, Dowling TC, Eddington ND;. J Pharm Sci 2003;92:414-423. (from Pfam) NF017519.5 PF05708.17 Peptidase_C92 27 27 166 domain Y Y N YiiX/YebB-like N1pC/P60 family cysteine hydrolase 21799766 131567 cellular organisms no rank 17851 EBI-EMBL Permuted papain-like amidase enzyme, YaeF/YiiX, C92 family YiiX/YebB-like N1pC/P60 family cysteine hydrolase Members of this family are cysteine hydrolases with a permuted papain-like catalytic core. Two high-scoring members of this family, YiiX and YebB from Escherichia coli K-12, are thought to be amidases. NF017520.5 PF05709.16 Sipho_tail 24.2 24.2 118 domain Y Y N phage tail domain-containing protein 131567 cellular organisms no rank 21181 EBI-EMBL Phage tail protein RIFT-related domain Phage tail protein RIFT-related domain This family consists of several Siphovirus and other phage tail component proteins as well as some bacterial proteins of unknown function. This entry represents the N-terminal RIFT-related barrel domain. (from Pfam) NF017522.5 PF05711.16 TylF 23 23 264 domain Y Y N TylF/MycF/NovP-related O-methyltransferase 2.1.1.- 10220165,19857499 131567 cellular organisms no rank 11547 EBI-EMBL Macrocin-O-methyltransferase (TylF) TylF/MycF/NovP-related O-methyltransferase High-scoring members of this family are O-methyltransferases involved in the biosynthesis of natural products such as the macrolide-class antibiotic tylosin and mycinamicin, and the aminocoumarin-class antibiotic novobiocin. Lower-scoring members of the family are methyltransferases acting on other substrates. NF017524.5 PF05713.16 MobC 23.2 23.2 45 domain Y Y N plasmid mobilization relaxosome protein MobC mobC 11976306,9302013 131567 cellular organisms no rank 33042 EBI-EMBL Bacterial mobilisation protein (MobC) plasmid mobilization relaxosome protein MobC This family consists of several bacterial MobC-like, mobilisation proteins. MobC proteins belong to the group of relaxases. Together with MobA and MobB they bind to a single cis-active site of a mobilising plasmid, the origin of transfer (oriT) region [1]. The absence of MobC has several different effects on oriT DNA. Site- and strand-specific nicking by MobA protein is severely reduced, accounting for the lower frequency of mobilisation. The localised DNA strand separation required for this nicking is less affected, but becomes more sensitive to the level of active DNA gyrase in the cell. In addition, strand separation is not efficiently extended through the region containing the nick site. These effects suggest a model in which MobC acts as a molecular wedge for the relaxosome-induced melting of oriT DNA. The effect of MobC on strand separation may be partially complemented by the helical distortion induced by supercoiling. However, MobC extends the melted region through the nick site, thus providing the single-stranded substrate required for cleavage by MobA [2]. [1]. 11976306. Characterization of two cryptic Helicobacter pylori plasmids: a putative source for horizontal gene transfer and gene shuffling. Hofreuter D, Haas R;. J Bacteriol 2002;184:2755-2766. [2]. 9302013. The relaxosome protein MobC promotes conjugal plasmid mobilization by extending DNA strand separation to the nick site at the origin of transfer. Zhang S, Meyer R;. Mol Microbiol 1997;25:509-516. (from Pfam) NF017528.5 PF05717.18 TnpB_IS66 26.6 26.6 101 domain Y Y N IS66 family insertion sequence element accessory protein TnpB tnpB 10489437,11418571 131567 cellular organisms no rank 46329 EBI-EMBL IS66 Orf2 like protein IS66 family insertion sequence element accessory protein TnpB This protein is found in insertion sequences related to IS66. The function of these proteins is uncertain, but they are probably essential for transposition [2]. [1]. 10489437. The Sinorhizobium meliloti insertion sequence (IS) element ISRm14 is related to a previously unrecognized IS element located adjacent to the Escherichia coli locus of enterocyte effacement (LEE) pathogenicity island. Schneiker S, Kosier B, Puhler A, Selbitschka W;. Curr Microbiol 1999;39:274-281. [2]. 11418571. Structural and functional characterization of IS679 and IS66-family elements. Han CG, Shiga Y, Tobe T, Sasakawa C, Ohtsubo E;. J Bacteriol 2001;183:4296-4304. (from Pfam) NF017532.5 PF05721.18 PhyH 22 22 213 domain Y Y N phytanoyl-CoA dioxygenase family protein 10767344,15128576 131567 cellular organisms no rank 92410 EBI-EMBL Phytanoyl-CoA dioxygenase (PhyH) phytanoyl-CoA dioxygenase family protein This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterised by the accumulation of phytanic acid in plasma and tissues [1]. [1]. 10767344. Human phytanoyl-CoA hydroxylase: resolution of the gene structure and the molecular basis of Refsum's disease. Jansen GA, Hogenhout EM, Ferdinandusse S, Waterham HR, Ofman R, Jakobs C, Skjeldal OH, Wanders RJ;. Hum Mol Genet 2000;9:1195-1200. [2]. 15128576. Functional expression of the ectoine hydroxylase gene (thpD) from Streptomyces chrysomallus in Halomonas elongata. Prabhu J, Schauwecker F, Grammel N, Keller U, Bernhard M;. Appl Environ Microbiol. 2004;70:3130-3132. (from Pfam) NF017534.5 PF05724.16 TPMT 26 26 218 domain Y N N Thiopurine S-methyltransferase (TPMT) GO:0008757 9780226 131567 cellular organisms no rank 56473 EBI-EMBL Thiopurine S-methyltransferase (TPMT) Thiopurine S-methyltransferase (TPMT) This family consists of thiopurine S-methyltransferase proteins from both eukaryotes and prokaryotes. Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme that catalyses S-methylation of aromatic and heterocyclic sulfhydryl compounds, including anticancer and immunosuppressive thiopurines [1]. [1]. 9780226. Functional characterization of the human thiopurine S-methyltransferase (TPMT) gene promoter. Fessing MY, Krynetski EY, Zambetti GP, Evans WE;. Eur J Biochem 1998;256:510-517. (from Pfam) NF017536.5 PF05726.18 Pirin_C 27 27 103 domain Y Y N pirin-like C-terminal cupin domain-containing protein 14697267,23716661 131567 cellular organisms no rank 83973 EBI-EMBL Pirin C-terminal cupin domain Pirin C-terminal cupin domain This region is found the C-terminal half of the Pirin protein. (from Pfam) NF017538.5 PF05728.17 UPF0227 21 21 187 subfamily Y Y N YqiA/YcfP family alpha/beta fold hydrolase 131567 cellular organisms no rank 28650 EBI-EMBL Uncharacterised protein family (UPF0227) YqiA/YcfP family alpha/beta fold hydrolase Despite being classed as uncharacterised proteins, the members of this family are almost certainly enzymes that are distantly related to the Pfam:PF00561. (from Pfam) NF017539.5 PF05729.17 NACHT 26.7 26.7 167 domain Y Y N NACHT domain-containing protein 10782090 131567 cellular organisms no rank 48059 EBI-EMBL NACHT domain NACHT domain This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation [1]. This family is closely related to Pfam:PF00931. [1]. 10782090. The NACHT family - a new group of predicted NTPases implicated in apoptosis and MHC transcription activation. Koonin EV, Aravind L;. Trends Biochem Sci 2000;25:223-224. (from Pfam) NF017541.5 PF05731.16 TROVE 23 23 442 domain Y Y N TROVE domain-containing protein GO:0003723 131567 cellular organisms no rank 9449 EBI-EMBL TROVE domain TROVE domain This presumed domain is found in TEP1 and Ro60 proteins, that are RNA-binding components of Telomerase, Ro and Vault RNPs. This domain has been named TROVE, (after Telomerase, Ro and Vault). This domain is probably RNA-binding. (from Pfam) NF017542.5 PF05732.16 RepL 20.3 20.3 164 domain Y Y N replication/maintenance protein RepL GO:0006260,GO:0006276 3091582,9143105 131567 cellular organisms no rank 7930 EBI-EMBL Firmicute plasmid replication protein (RepL) replication/maintenance protein RepL This family consists of Firmicute RepL proteins which are involved in plasmid replication. [1]. 9143105. Sequence analysis and characterization of pOM1, a small cryptic plasmid from Butyrivibrio fibrisolvens, and its use in construction of a new family of cloning vectors for Butyrivibrios. Hefford MA, Kobayashi Y, Allard SE, Forster RJ, Teather RM;. Appl Environ Microbiol 1997;63:1701-1711. [2]. 3091582. Nucleotide sequence of the constitutive macrolide-lincosamide-streptogramin B resistance plasmid pNE131 from Staphylococcus epidermidis and homologies with Staphylococcus aureus plasmids pE194 and pSN2. Lampson BC, Parisi JT;. J Bacteriol 1986;167:888-892. (from Pfam) NF017548.5 PF05738.18 Cna_B 22.3 17.1 87 domain Y Y N Cna B-type domain-containing protein 10673425 131567 cellular organisms no rank 24021 EBI-EMBL Cna protein B-type domain Cna protein B-type domain This domain is found in Staphylococcus aureus collagen-binding surface protein. The structure of the repetitive B-region has been solved [1] and forms a beta sandwich structure. [1]. 10673425. Novel fold and assembly of the repetitive B region of the Staphylococcus aureus collagen-binding surface protein. Deivanayagam CC, Rich RL, Carson M, Owens RT, Danthuluri S, Bice T, Hook M, Narayana SV;. Structure Fold Des 2000;8:67-78. (from Pfam) NF017551.5 PF05742.17 TANGO2 22.6 22.6 257 PfamEq Y Y N NRDE family protein 16452979,17877702,8268909 131567 cellular organisms no rank 20817 EBI-EMBL Transport and Golgi organisation 2 NRDE family protein In eukaryotes this family is predicted to play a role in protein secretion and Golgi organisation [1]. In plants this family includes Swiss:A9X6Y0, which is involved in water permeability in the cuticles of fruit [2]. Swiss:P54797 has been found to be expressed during early embryogenesis in mice [3]. This protein contains a conserved NRDE motif. This gene has been characterised in Drosophila melanogaster and named as transport and Golgi organisation 2, hence the name Tango2. [1]. 16452979. Functional genomics reveals genes involved in protein secretion and Golgi organization. Bard F, Casano L, Mallabiabarrena A, Wallace E, Saito K, Kitayama H, Guizzunti G, Hu Y, Wendler F, Dasgupta R, Perrimon N, Malhotra V;. Nature. 2006;439:604-607. [2]. 17877702. The identification of a gene (Cwp1), silenced during Solanum evolution, which causes cuticle microfissuring and dehydration when expressed in tomato fruit. Hovav R, Chehanovsky N, Moy M, Jetter R, Schaffer AA;. Plant J. 2007;52:627-639. [3]. 8268909. Isolation of a gene expressed during early embryogenesis from the region of 22q11 commonly deleted in DiGeorge syndrome. Halford S, Wilson DI, Daw SC, Roberts C, Wadey R, Kamath S, Wickremasinghe A, Burn J, Goodship J, Mattei MG, et al.;. Hum Mol Genet 1993;2:1577-1582. (from Pfam) NF017555.5 PF05746.20 DALR_1 22.3 22.3 117 domain Y Y N DALR anticodon-binding domain-containing protein GO:0004814,GO:0005524,GO:0006420 10447505 131567 cellular organisms no rank 147579 EBI-EMBL DALR anticodon binding domain DALR anticodon-binding domain This all alpha helical domain is the anticodon binding domain in Arginyl and glycyl tRNA synthetase. This domain is known as the DALR domain after characteristic conserved amino acids [1]. [1]. 10447505. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Wolf YI, Aravind L, Grishin NV, Koonin EV;. Genome Res 1999;9:689-710. (from Pfam) NF017559.5 PF05751.16 FixH 23 23 150 PfamEq Y Y N FixH family protein 2536685 131567 cellular organisms no rank 20233 EBI-EMBL FixH FixH family protein This family consists of several Rhizobium FixH like proteins. It has been suggested that suggested that the four proteins FixG, FixH, FixI, and FixS may participate in a membrane-bound complex coupling the FixI cation pump with a redox process catalysed by FixG [1]. [1]. 2536685. Rhizobium meliloti fixGHI sequence predicts involvement of a specific cation pump in symbiotic nitrogen fixation. Kahn D, David M, Domergue O, Daveran ML, Ghai J, Hirsch PR, Batut J;. J Bacteriol 1989;171:929-939. (from Pfam) NF017561.5 PF05753.19 TRAP_beta 22.4 22.4 178 domain Y N N Translocon-associated protein beta (TRAPB) 11204460 131567 cellular organisms no rank 485 EBI-EMBL Translocon-associated protein beta (TRAPB) Translocon-associated protein beta (TRAPB) This family consists of several eukaryotic translocon-associated protein beta (TRAPB) or signal sequence receptor beta subunit (SSR-beta) proteins. The normal translocation of nascent polypeptides into the lumen of the endoplasmic reticulum (ER) is thought to be aided in part by a translocon-associated protein (TRAP) complex consisting of 4 protein subunits. The association of mature proteins with the ER and Golgi, or other intracellular locales, such as lysosomes, depends on the initial targeting of the nascent polypeptide to the ER membrane. A similar scenario must also exist for proteins destined for secretion [1]. [1]. 11204460. The Translocon-Associated Protein beta (TRAPbeta) in zebrafish embryogenesis. I. Enhanced expression of transcripts in notochord and hatching gland precursors. Mangos S, Krawetz R, Kelly GM;. Mol Cell Biochem 2000;215:93-101. (from Pfam) NF017569.5 PF05762.19 VWA_CoxE 26.4 26.4 222 domain Y Y N VWA domain-containing protein 10433972 131567 cellular organisms no rank 83584 EBI-EMBL VWA domain containing CoxE-like protein VWA domain containing CoxE-like protein This family is annotated by SMART as containing a VWA (von Willebrand factor type A) domain. The exact function of this family is unknown. It is found as part of a CO oxidising (Cox) system operon is several bacteria [1]. [1]. 10433972. Sequence analysis, characterization and CO-specific transcription of the cox gene cluster on the megaplasmid pHCG3 of Oligotropha carboxidovorans. Santiago B, Schubel U, Egelseer C, Meyer O;. Gene 1999;236:115-124. (from Pfam) NF017574.5 PF05768.19 Glrx-like 26 26 77 domain Y Y N glutaredoxin family protein 10982364,11752136 131567 cellular organisms no rank 27955 EBI-EMBL Glutaredoxin-like domain (DUF836) glutaredoxin family protein These proteins are related to the Pfam:PF00462 family. This entry includes several viral glutaredoxins and many related bacterial and eukaryotic proteins of unknown function. The best characterised member is G4L (Swiss:P68460) from Vaccinia virus (strain Western Reserve/WR) (VACV), which is necessary for virion morphogenesis and replication [1]. This is a cytoplasmic protein which functions as a shuttle in a redox pathway between membrane-associated E10R and L1R or F9L [2]. [1]. 10982364. A glutaredoxin, encoded by the G4L gene of vaccinia virus, is essential for virion morphogenesis. White CL, Weisberg AS, Moss B;. J Virol. 2000;74:9175-9183. [2]. 11752136. Vaccinia virus G4L glutaredoxin is an essential intermediate of a cytoplasmic disulfide bond pathway required for virion assembly. White CL, Senkevich TG, Moss B;. J Virol. 2002;76:467-472. (from Pfam) NF017587.5 PF05783.16 DLIC 19.7 11 471 domain Y N N Dynein light intermediate chain (DLIC) 10545494,10893222,11907264,20298435 131567 cellular organisms no rank 10892 EBI-EMBL Dynein light intermediate chain (DLIC) Dynein light intermediate chain (DLIC) This family consists of several eukaryotic dynein light intermediate chain proteins. The light intermediate chains (LICs) of cytoplasmic dynein consist of multiple isoforms, which undergo post-translational modification to produce a large number of species. DLIC1 is known to be involved in assembly, organisation, and function of centrosomes and mitotic spindles when bound to pericentrin [1,2]. DLIC2 is a subunit of cytoplasmic dynein 2 that may play a role in maintaining Golgi organisation by binding cytoplasmic dynein 2 to its Golgi-associated cargo [3]. [1]. 10545494. Direct interaction of pericentrin with cytoplasmic dynein light intermediate chain contributes to mitotic spindle organization. Purohit A, Tynan SH, Vallee R, Doxsey SJ;. J Cell Biol 1999;147:481-492. [2]. 10893222. Light intermediate chain 1 defines a functional subfraction of cytoplasmic dynein which binds to pericentrin. Tynan SH, Purohit A, Doxsey SJ, Vallee RB;. J Biol Chem 2000;275:32763-32768. [3]. 11907264. Identification of a novel light intermediate chain (D2LIC) for mammalian cytoplasmic dynein 2. Grissom PM, Vaisberg EA, McIntosh JR;. Mol Biol Cell 2002;13:817-829. [4]. 20298435. Contribution of dynein light intermediate and intermediate chains to subcellular localization of the dynein-dynactin motor complex in Schizosaccharomyces pombe. Fujita I, Yamashita A, Yamamoto M;. Genes Cells. 2010;15:359-372. (from Pfam) NF017591.5 PF05787.18 PhoX 24 24 515 domain Y Y N alkaline phosphatase PhoX 25190793 131567 cellular organisms no rank 64353 EBI-EMBL Alkaline phosphatase PhoX alkaline phosphatase PhoX This family consists of proteins predominantly found in bacteria, including Alkaline phosphatase PhoX from Pseudomonas fluorescens (Swiss:Q3K5N8), a phosphomonoesterase with no phosphodiesterase activity. This protein adopts a six-bladed beta-propeller fold, with the active site located at the bottom of the cavity at the centre of the propeller [1]. [1]. 25190793. A complex iron-calcium cofactor catalyzing phosphotransfer chemistry. Yong SC, Roversi P, Lillington J, Rodriguez F, Krehenbrink M, Zeldin OB, Garman EF, Lea SM, Berks BC;. Science. 2014;345:1170-1173. (from Pfam) NF017603.5 PF05800.16 GvpO 25 25 94 PfamEq Y Y N gas vesicle protein GvpO gvpO GO:0031412 8606186 131567 cellular organisms no rank 7870 EBI-EMBL Gas vesicle synthesis protein GvpO gas vesicle protein GvpO This family consists of archaeal GvpO proteins which are required for gas vesicle synthesis [1]. The family also contains two related sequences from Streptomyces coelicolor. [1]. 8606186. Functional studies of the gvpACNO operon of Halobacterium salinarium reveal that the GvpC protein shapes gas vesicles. Offner S, Wanner G, Pfeifer F;. J Bacteriol 1996;178:2071-2078. (from Pfam) NF017617.5 PF05816.16 TelA 30 30 332 domain Y Y N toxic anion resistance protein 7665479,9406390 131567 cellular organisms no rank 25533 EBI-EMBL Toxic anion resistance protein (TelA) toxic anion resistance protein This family consists of several prokaryotic TelA like proteins. TelA and KlA are associated with tellurite resistance [1] and plasmid fertility inhibition [2]. [1]. 9406390. Identification and molecular genetic analysis of multiple loci contributing to high-level tellurite resistance in Rhodobacter sphaeroides 2.4.1. O'Gara JP, Gomelsky M, Kaplan S;. Appl Environ Microbiol 1997;63:4713-4720. [2]. 7665479. Phage inhibition, colicin resistance, and tellurite resistance are encoded by a single cluster of genes on the IncHI2 plasmid R478. Whelan KF, Colleran E, Taylor DE;. J Bacteriol 1995;177:5016-5027. (from Pfam) NF017633.5 PF05833.16 NFACT_N 31 31 456 domain Y Y N NFACT family protein 25578875,31155236 131567 cellular organisms no rank 28445 EBI-EMBL NFACT N-terminal and middle domains NFACT family protein This HMM contains the N-terminal and central domains of NFACT (NEMF, FbpA, Caliban, and Tae2) proteins. Many members of this family from eukaryotes, archaea, and bacteria act in ribosome quality control (RQC), including RqcH, shown to help add a poly-Ala tail to abortively translated proteins to tag them for degradation. This process is analogous to and partial redundant with the ssrA/tmRNA system. However, some other NFACT family members, such as bacterial proteins FbpA in Listeria or PavA in Streptococcus, are exported (despite lack of a classical signal peptide) and behave as fibronectin-binding adhesins associated with virulence. NF017634.5 PF05834.17 Lycopene_cycl 23.4 23.4 380 domain Y Y N lycopene cyclase family protein 11226339,8837512 131567 cellular organisms no rank 71245 EBI-EMBL Lycopene cyclase protein lycopene cyclase family protein This family consists of lycopene beta and epsilon cyclase proteins. Carotenoids with cyclic end groups are essential components of the photosynthetic membranes in all plants, algae, and cyanobacteria. These lipid-soluble compounds protect against photo-oxidation, harvest light for photosynthesis, and dissipate excess light energy absorbed by the antenna pigments. The cyclisation of lycopene (psi, psi-carotene) is a key branch point in the pathway of carotenoid biosynthesis. Two types of cyclic end groups are found in higher plant carotenoids: the beta and epsilon rings. Carotenoids with two beta rings are ubiquitous, and those with one beta and one epsilon ring are common; however, carotenoids with two epsilon rings are rare [1,2]. [1]. 8837512. Functional analysis of the beta and epsilon lycopene cyclase enzymes of Arabidopsis reveals a mechanism for control of cyclic carotenoid formation. Cunningham FX Jr, Pogson B, Sun Z, McDonald KA, DellaPenna D, Gantt E;. Plant Cell 1996;8:1613-1626. [2]. 11226339. One ring or two? Determination of ring number in carotenoids by lycopene epsilon-cyclases. Cunningham FX Jr, Gantt E;. Proc Natl Acad Sci U S A 2001;98:2905-2910. (from Pfam) NF017645.5 PF05845.17 PhnH 25 25 188 PfamEq Y Y N phosphonate C-P lyase system protein PhnH GO:0019634 1840580,2155230 131567 cellular organisms no rank 12748 EBI-EMBL Bacterial phosphonate metabolism protein (PhnH) phosphonate C-P lyase system protein PhnH This family consists of several bacterial PhnH sequences which are known to be involved in phosphonate metabolism [1,2]. [1]. 2155230. Molecular biology of carbon-phosphorus bond cleavage. Cloning and sequencing of the phn (psiD) genes involved in alkylphosphonate uptake and C-P lyase activity in Escherichia coli B. Chen CM, Ye QZ, Zhu ZM, Wanner BL, Walsh CT;. J Biol Chem 1990;265:4461-4471. [2]. 1840580. Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12. Makino K, Kim SK, Shinagawa H, Amemura M, Nakata A;. J Bacteriol 1991;173:2612-2665. (from Pfam) NF017652.5 PF05853.17 BKACE 24.8 24.8 274 domain Y Y N 3-keto-5-aminohexanoate cleavage protein GO:0016740,GO:0019475,GO:0043720 21632536,24240508 131567 cellular organisms no rank 46041 EBI-EMBL beta-keto acid cleavage enzyme 3-keto-5-aminohexanoate cleavage protein BKACE, beta-keto acid cleavage enzyme plays, a role in lysine degradation. In certain instances it catalyses the conversion of 3-keto-5-aminohexanoate and acetyl-CoA into acetoacetate and 3-aminobutyryl-CoA [1]. The family is found to have at least 14 slightly different potential new enzymatic activities, all of which can therefore be designated as beta-keto acid cleavage enzymes [2]. [1]. 21632536. 3-Keto-5-aminohexanoate cleavage enzyme: a common fold for an uncommon Claisen-type condensation. Bellinzoni M, Bastard K, Perret A, Zaparucha A, Perchat N, Vergne C, Wagner T, de Melo-Minardi RC, Artiguenave F, Cohen GN, Weissenbach J, Salanoubat M, Alzari PM;. J Biol Chem. 2011;286:27399-27405. [2]. 24240508. Revealing the hidden functional diversity of an enzyme family. Bastard K, Smith AA, Vergne-Vaxelaire C, Perret A, Zaparucha A, De Melo-Minardi R, Mariage A, Boutard M, Debard A, Lechaplais C, Pelle C, Pellouin V, Perchat N, Petit JL, Kreimeyer A, Medigue C, Weissenbach J, Artiguenave F, De Berardinis V, Vallenet D, Salanoubat M;. Nat Chem Biol. 2014;10:42-49. (from Pfam) NF017653.5 PF05854.16 MC1 23 23 96 domain Y Y N non-histone chromosomal MC1 family protein GO:0042262 2503033 131567 cellular organisms no rank 666 EBI-EMBL Non-histone chromosomal protein MC1 non-histone chromosomal MC1 family protein This family consists of archaeal chromosomal protein MC1 sequences which protect DNA against thermal denaturation [1]. [1]. 2503033. Primary structure of the chromosomal protein MC1 from the archaebacterium Methanosarcina sp. CHTI 55. Chartier F, Laine B, Belaiche D, Touzel JP, Sautiere P;. Biochim Biophys Acta 1989;1008:309-314. (from Pfam) NF017655.5 PF05857.16 TraX 25 25 217 subfamily Y Y N TraX family protein 7768788,8444800 131567 cellular organisms no rank 22442 EBI-EMBL TraX protein TraX family protein This family consists of several bacterial TraX proteins. TraX is responsible for the amino-terminal acetylation of F-pilin subunits [1,2]. [1]. 8444800. The Escherichia coli K-12 F plasmid gene traX is required for acetylation of F pilin. Moore D, Hamilton CM, Maneewannakul K, Mintz Y, Frost LS, Ippen-Ihler K;. J Bacteriol 1993;175:1375-1383. [2]. 7768788. Characterization of traX, the F plasmid locus required for acetylation of F-pilin subunits. Maneewannakul K, Maneewannakul S, Ippen-Ihler K;. J Bacteriol 1995;177:2957-2964. (from Pfam) NF017659.5 PF05861.17 PhnI 34.5 34.5 348 PfamEq Y Y N carbon-phosphorus lyase complex subunit PhnI GO:0019634 1335942 131567 cellular organisms no rank 14591 EBI-EMBL Bacterial phosphonate metabolism protein (PhnI) carbon-phosphorus lyase complex subunit PhnI This family consists of several Proteobacterial phosphonate metabolism protein (PhnI) sequences. Bacteria that use phosphonates as a phosphorus source must be able to break the stable carbon-phosphorus bond. In Escherichia coli phosphonates are broken down by a C-P lyase that has a broad substrate specificity. The genes for phosphonate uptake and degradation in E. coli are organised in an operon of 14 genes, named phnC to phnP. Three gene products (PhnC, PhnD and PhnE) comprise a binding protein-dependent phosphonate transporter, which also transports phosphate, phosphite, and certain phosphate esters such as phosphoserine; two gene products (PhnF and PhnO) may have a role in gene regulation; and nine gene products (PhnG, PhnH, PhnI, PhnJ, PhnK, PhnL, PhnM, PhnN, and PhnP) probably comprise a membrane-associated C-P lyase enzyme complex [1]. [1]. 1335942. Molecular genetic studies of a 10.9-kb operon in Escherichia coli for phosphonate uptake and biodegradation. Wanner BL, Metcalf WW;. FEMS Microbiol Lett 1992;79:133-139. (from Pfam) NF017669.5 PF05872.17 HerA_C 22 22 502 PfamAutoEq Y Y N helicase HerA-like domain-containing protein 14990749,25420454,25880130 131567 cellular organisms no rank 44883 EBI-EMBL Helicase HerA-like C-terminal DUF853 family protein HerA is a DNA helicase able to utilise either 3' or 5' single-stranded DNA extensions for loading and subsequent DNA duplex unwinding [1]. It forms a complex with NurA nuclease, this complex has the 5'-3' DNA end resection activity and is essential for cell viability in the crenarchaeon Sulfolobus islandicus [2]. This entry represents the C-terminal domain of HerA which seems to be involved in the conversion of ATP hydrolysis into DNA translocation [3]. [1]. 14990749. A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea. Constantinesco F, Forterre P, Koonin EV, Aravind L, Elie C;. Nucleic Acids Res. 2004;32:1439-1447. [2]. 25880130. Efficient 5'-3' DNA end resection by HerA and NurA is essential for cell viability in the crenarchaeon Sulfolobus islandicus. Huang Q, Liu L, Liu J, Ni J, She Q, Shen Y;. BMC Mol Biol. 2015;16:2. [3]. 25420454. Structure of the hexameric HerA ATPase reveals a mechanism of translocation-coupled DNA-end processing in archaea. Rzechorzek NJ, Blackwood JK, Bray SM, Maman JD, Pellegrini L, Robinson NP;. Nat Commun. 2014;5:5506. (from Pfam) NF017682.5 PF05889.18 SepSecS 21.1 21.1 389 domain Y N N O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS GO:0016740 10801173,11481605,17194211,17512006,18093968,18158303,19608919 131567 cellular organisms no rank 23315 EBI-EMBL O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS Early annotation suggested this family, SepSecS, of several eukaryotic and archaeal proteins, was involved in antigen-antibodies responses in the liver and pancreas [1,2]. Structural studies show that the family is O-phosphoseryl-tRNA(Sec) selenium transferase, an enzyme involved in the synthesis of the amino acid selenocysteine (Sec). Sec is the only amino acid whose biosynthesis occurs on its cognate transfer RNA (tRNA). SepSecS catalyses the final step in the formation of the amino acid [3,4,5,6]. The early observation that autoantibodies isolated from patients with type I autoimmune hepatitis targeted a ribonucleoprotein complex containing tRNASec led to the identification and characterisation of the archaeal and the human SepSecS [2]. SepSecS forms its own branch in the family of fold-type I pyridoxal phosphate (PLP) enzymes that goes back to the last universal common ancestor which explains why the archaeal sequences Swiss:Q8TXK0 and Swiss:Q8TYR3 are annotated as being pyridoxal phosphate-dependent enzymes. [1]. 10801173. Identification of target antigen for SLA/LP autoantibodies in autoimmune hepatitis. Wies I, Brunner S, Henninger J, Herkel J, Kanzler S, Meyer zum Buschenfelde KH, Lohse AW;. Lancet 2000;355:1510-1515. [2]. 11481605. A bioinformatical approach suggests the function of the autoimmune hepatitis target antigen soluble liver antigen/liver pancreas. Kernebeck T, Lohse AW, Grotzinger J;. Hepatology 2001;34:230-233. [3]. 17194211. Biosynthesis of selenocysteine on its tRNA in eukaryotes. Xu XM, Carlson BA, Mix H, Zhang Y, Saira K, Glass RS, Berry MJ, Gladyshev VN, Hatfield DL;. PLoS Biol. 2007;5:e4. [4]. . TRUNCATED at 1650 bytes (from Pfam) NF017684.5 PF05891.17 Methyltransf_PK 27 27 218 domain Y N N AdoMet dependent proline di-methyltransferase GO:0006480,GO:0008168 20481588 131567 cellular organisms no rank 4239 EBI-EMBL AdoMet dependent proline di-methyltransferase AdoMet dependent proline di-methyltransferase This protein is expressed in the tail neuron PVT and in uterine cells in C. elegans [worm-base]. In Saccharomyces cerevisiae this is AdoMet dependent proline di-methyltransferase. This enzyme catalyses the di-methylation of ribosomal proteins Rpl12 and Rps25 at N-terminal proline residues. The methyltransferases described here specifically recognise the N-terminal X-Pro-Lys sequence motif, and they may account for nearly all previously described eukaryotic protein N-terminal methylation reactions. A number of other yeast and human proteins also share the recognition motif and may be similarly modified [1]. As with other methyltransferases, this family carries the characteristic GxGxG motif. [1]. 20481588. Identification of protein N-terminal methyltransferases in yeast and humans. Webb KJ, Lipson RS, Al-Hadid Q, Whitelegge JP, Clarke SG;. Biochemistry. 2010;49:5225-5235. (from Pfam) NF017686.5 PF05893.19 LuxC 21 21 401 domain Y Y N acyl-CoA reductase GO:0003995,GO:0008218 9128139 131567 cellular organisms no rank 80399 EBI-EMBL Acyl-CoA reductase (LuxC) acyl-CoA reductase This family consists of several bacterial Acyl-CoA reductase (LuxC) proteins. The channelling of fatty acids into the fatty aldehyde substrate for the bacterial bioluminescence reaction is catalysed by a fatty acid reductase multienzyme complex, which channels fatty acids through the thioesterase (LuxD), synthetase (LuxE) and reductase (LuxC) components [1]. [1]. 9128139. Cysteine-286 as the site of acylation of the Lux-specific fatty acyl-CoA reductase. Lee CY, Meighen EA;. Biochim Biophys Acta 1997;1338:215-222. (from Pfam) NF017687.5 PF05894.17 Podovirus_Gp16 25 25 331 subfamily Y Y N phage DNA encapsidation protein 3879485 131567 cellular organisms no rank 143 EBI-EMBL Podovirus DNA encapsidation protein (Gp16) Podovirus DNA encapsidation protein This family consists of several DNA encapsidation protein (Gp16) sequences from the phi-29-like viruses. Gene product 16 catalyses the in vivo and in vitro genome-encapsidation reaction [1]. [1]. 3879485. The complete sequence of Bacillus phage phi 29 gene 16: a protein required for the genome encapsidation reaction. Garvey KJ, Saedi MS, Ito J;. Gene 1985;40:311-316. (from Pfam) NF017689.5 PF05896.16 NQRA 27 27 257 domain Y N N Na(+)-translocating NADH-quinone reductase subunit A (NQRA) GO:0006814,GO:0016655 10587447 131567 cellular organisms no rank 19573 EBI-EMBL Na(+)-translocating NADH-quinone reductase subunit A (NQRA) Na(+)-translocating NADH-quinone reductase subunit A (NQRA) This family consists of several bacterial Na(+)-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration [1]. [1]. 10587447. Sequencing and preliminary characterization of the Na+-translocating NADH:ubiquinone oxidoreductase from Vibrio harveyi. Zhou W, Bertsova YV, Feng B, Tsatsos P, Verkhovskaya ML, Gennis RB, Bogachev AV, Barquera B;. Biochemistry 1999;38:16246-16252. (from Pfam) NF017690.5 PF05899.17 Cupin_3 23.5 23.5 74 domain Y Y N cupin domain-containing protein 19935661,20038185,23144756,26448059 131567 cellular organisms no rank 80612 EBI-EMBL EutQ-like cupin domain EutQ-like cupin domain This entry represents the cupin domain, with a conserved jelly roll-like beta-barrel fold capable of homodimerisation found in bacteria, plant and fungi. It is present in EutQ family from the eut operon, involved in ethanolamine degradation. EutQ is essential during anoxic growth and has acetate kinase activity [1]. The cupin domain from EutQ does not possess the His residues responsible for metal coordination in other classes of cupins [2]. This domain is also found in (S)-ureidoglycine aminohydrolase (UGlyAH) from E.coli, which is involved in the anaerobic nitrogen utilisation via the assimilation of allantoin. It catalyses the deamination of allantoin to produce S-ureidoglycolate and ammonia from S-ureidoglycine [3,4]. [1]. 26448059. The EutQ and EutP proteins are novel acetate kinases involved in ethanolamine catabolism: physiological implications for the function of the ethanolamine metabolosome in Salmonella enterica. Moore TC, Escalante-Semerena JC;. Mol Microbiol. 2016;99:497-511. [2]. 23144756. Structural insight into the Clostridium difficile ethanolamine utilisation microcompartment. Pitts AC, Tuck LR, Faulds-Pain A, Lewis RJ, Marles-Wright J;. PLoS One. 2012;7:e48360. [3]. 19935661. Ureide catabolism in Arabidopsis thaliana and Escherichia coli. Werner AK, Romeis T, Witte CP;. Nat Chem Biol. 2010;6:19-21. [4]. 20038185. Chemical basis of nitrogen recovery through the ureide pathway: formation and hydrolysis of S-ureidoglycine in plants and bacteria. Serventi F, Ramazzina I, Lamberto I, Puggioni V, Gatti R, Percudani R;. ACS Chem Biol. 2010;5:203-214. (from Pfam) NF017691.5 PF05901.16 Excalibur 22 22 36 domain Y Y N excalibur calcium-binding domain-containing protein 12694917 131567 cellular organisms no rank 33553 EBI-EMBL Excalibur calcium-binding domain Excalibur calcium-binding domain Extracellular Ca2+-dependent nuclease YokF from Bacillus subtilis and several other surface-exposed proteins from diverse bacteria are encoded in the genomes in two paralogous forms that differ by a ~45 amino acid fragment, which comprises a novel conserved domain. Sequence analysis of this domain revealed a conserved DxDxDGxxCE motif, which is strikingly similar to the Ca2+-binding loop of the calmodulin-like EF-hand domains, suggesting an evolutionary relationship between them. Functions of many of the other proteins in which the novel domain, named Excalibur (extracellular calcium-binding region), is found, as well as a structural model of its conserved motif are consistent with the notion that the Excalibur domain binds calcium. This domain is but one more example of the diversity of structural contexts surrounding the EF-hand-like calcium-binding loop in bacteria. This loop is thus more widespread than hitherto recognised and the evolution of EF-hand-like domains is probably more complex than previously appreciated [1]. [1]. 12694917. An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands. Rigden DJ, Jedrzejas MJ, Galperin MY;. FEMS Microbiol Lett 2003;221:103-110. (from Pfam) NF017697.5 PF05908.16 Gamma_PGA_hydro 22 22 191 domain Y Y N poly-gamma-glutamate hydrolase family protein 26158264 131567 cellular organisms no rank 8639 EBI-EMBL Poly-gamma-glutamate hydrolase poly-gamma-glutamate hydrolase family protein This family consists of a number of bacterial and phage proteins that function as gamma-PGA hydrolase enzymes [1]. Structurally the protein in this family adopted an open alpha/beta mixed core structure with a seven-stranded parallel/anti-parallel beta-sheet. This structure shows similarity to mammalian carboxypeptidase A and related enzymes. [1]. 26158264. gamma-PGA Hydrolases of Phage Origin in Bacillus subtilis and Other Microbial Genomes. Mamberti S, Prati P, Cremaschi P, Seppi C, Morelli CF, Galizzi A, Fabbi M, Calvio C;. PLoS One. 2015;10:e0130810. (from Pfam) NF017701.5 PF05913.16 MupG_C 24.4 24.4 116 subfamily Y Y N phospho-sugar glycosidase domain-containing protein 30524387 131567 cellular organisms no rank 14978 EBI-EMBL 6-phospho-N-acetylmuramidase, C-terminal DUF871 family protein This entry represents the C-terminal domain of 6-phospho-N-acetylmuramidase (MupG) found in bacteria. It characterises putative phospho sugar glycosidases found in Gram-negative and -positive species, but mainly in firmicutes. MupG from Staphylococcus aureus [1], specifically cleaves MurNAc 6P-GlcNAc, a product of cell wall turnover, into the sugars MurNAc 6P and GlcNAc, being involved in cell wall turnover and recycling. Since some species, for example Lactobacillus plantarum, possess several putative paralogs, the substrate specificity of these proteins may not be limited to cell wall sugars, but may include phosphorylated disaccharides in general. Most proteins containing this domain appear to consist of two structural subdomains, as it can be seen in the two available crystal structures of Enterococcus faecalis (PDB:2p0o) and Bacillus cereus (PDB:1X7F). The larger N-terminal domain constitutes a TIM-barrel like structure and the C-terminal domain (this entry) is similar to the cyclophilin family. It should be noted that some proteins lack this domain. [1]. 30524387. Recovery of the Peptidoglycan Turnover Product Released by the Autolysin Atl in Staphylococcus aureus Involves the Phosphotransferase System Transporter MurP and the Novel 6-phospho-N-acetylmuramidase MupG. Kluj RM, Ebner P, Adamek M, Ziemert N, Mayer C, Borisova M;. Front Microbiol. 2018;9:2725. (from Pfam) NF017704.5 PF05916.16 Sld5 22.3 22.3 107 PfamEq Y N N GINS complex protein helical bundle domain 12730133,12730134,12768207,17170760 131567 cellular organisms no rank 310 EBI-EMBL GINS complex protein helical bundle domain GINS complex protein helical bundle domain This entry represents the C-terminal alpha helical bundle domain. The eukaryotic GINS complex is essential for the initiation and elongation phases of DNA replication [1-3]. It consists of four paralogous protein subunits (Sld5, Psf1, Psf2 and Psf3), all of which are included in this family. The GINS complex is conserved from yeast to humans, and has been shown in human to bind directly to DNA primase [4]. [1]. 12730133. A novel ring-like complex of Xenopus proteins essential for the initiation of DNA replication. Kubota Y, Takase Y, Komori Y, Hashimoto Y, Arata T, Kamimura Y, Araki H, Takisawa H;. Genes Dev 2003;17:1141-1152. [2]. 12730134. GINS, a novel multiprotein complex required for chromosomal DNA replication in budding yeast. Takayama Y, Kamimura Y, Okawa M, Muramatsu S, Sugino A, Araki H;. Genes Dev. 2003;17:1153-1165. [3]. 12768207. Functional proteomic identification of DNA replication proteins by induced proteolysis in vivo. Kanemaki M, Sanchez-Diaz A, Gambus A, Labib K;. Nature. 2003;423:720-724. [4]. 17170760. The human GINS complex binds to and specifically stimulates human DNA polymerase alpha-primase. De Falco M, Ferrari E, De Felice M, Rossi M, Hubscher U, Pisani FM;. EMBO Rep. 2007;8:99-103. (from Pfam) NF017709.5 PF05922.21 Inhibitor_I9 21.2 21.2 82 domain Y Y N protease inhibitor I9 family protein 7559646,9247157 131567 cellular organisms no rank 49294 EBI-EMBL Peptidase inhibitor I9 protease inhibitor I9 family protein This family includes the proteinase B inhibitor from Saccharomyces cerevisiae and the activation peptides from peptidases of the subtilisin family. The subtilisin propeptides are known to function as molecular chaperones, assisting in the folding of the mature peptidase [1], but have also been shown to act as 'temporary inhibitors' [2]. [1]. 7559646. Functional analysis of the propeptide of subtilisin E as an intramolecular chaperone for protein folding. Refolding and inhibitory abilities of propeptide mutants. Li Y, Hu Z, Jordan F, Inouye M;. J Biol Chem. 1995;270:25127-25132. [2]. 9247157. The propeptide of subtilisin BPN' as a temporary inhibitor and effect of an amino acid replacement on its inhibitory activity. Kojima S, Minagawa T, Miura K;. FEBS Lett. 1997;411:128-132. (from Pfam) NF017722.5 PF05935.16 Arylsulfotrans 24.2 24.2 374 domain Y Y N aryl-sulfate sulfotransferase GO:0004062 8887346 131567 cellular organisms no rank 19949 EBI-EMBL Arylsulfotransferase (ASST) aryl-sulfate sulfotransferase This family consists of several bacterial Arylsulfotransferase proteins. Arylsulfotransferase (ASST) transfers a sulfate group from phenolic sulfate esters to a phenolic acceptor substrate [1]. [1]. 8887346. Cloning and sequencing of the Klebsiella K-36 astA gene, encoding an arylsulfate sulfotransferase. Baek MC, Kim SK, Kim DH, Kim BK, Choi EC;. Microbiol Immunol 1996;40:531-537. (from Pfam) NF017727.5 PF05940.17 NnrS 28 28 371 domain Y Y N NnrS family protein 11882718,12618453,22511349,23935055 131567 cellular organisms no rank 21669 EBI-EMBL NnrS protein NnrS family protein This family consists of several bacterial NnrS like proteins. NnrS is a putative heme-Cu protein (NnrS) and a member of the short-chain dehydrogenase family [1]. Expression of nnrS is dependent on the transcriptional regulator NnrR, which also regulates expression of genes required for the reduction of nitrite to nitrous oxide, including nirK and nor. NnrS is a haem- and copper-containing membrane protein. Genes encoding putative orthologues of NnrS are sometimes but not always found in bacteria encoding nitrite and/or nitric oxide reductase [2]. NnrS contributes to nitrosative-stress tolerance in V. cholerae and protects the cellular iron pool from the formation of dinitrosyl iron complexes (DNICs), thus protecting critical metabolic pathways from inhibition [3,4]. [1]. 12618453. Operon structure and regulation of the nos gene region of Pseudomonas stutzeri, encoding an ABC-Type ATPase for maturation of nitrous oxide reductase. Honisch U, Zumft WG;. J Bacteriol 2003;185:1895-1902. [2]. 11882718. Characterization of a member of the NnrR regulon in Rhodobacter sphaeroides 2.4.3 encoding a haem-copper protein. Bartnikas TB, Wang Y, Bobo T, Veselov A, Scholes CP, Shapleigh JP;. Microbiology 2002;148:825-833. [3]. 23935055. A novel protein protects bacterial iron-dependent metabolism from nitric oxide. Stern AM, Liu B, Bakken LR, Shapleigh JP, Zhu J;. J Bacteriol. 2013;195:4702-4708. [4]. 22511349. The NorR regulon is critical for Vibrio cholerae resistance to nitric oxide and sustained colonization of the intestines. Stern AM, Hay AJ, Liu Z, Desland FA, Zhang J, Zhong Z, Zhu J;. mBio. 2012;3:e00013-e00012. (from Pfam) NF017743.5 PF05958.16 tRNA_U5-meth_tr 23 23 357 domain Y N N tRNA (Uracil-5-)-methyltransferase GO:0006396,GO:0008173 12003492 131567 cellular organisms no rank 137940 EBI-EMBL tRNA (Uracil-5-)-methyltransferase tRNA (Uracil-5-)-methyltransferase This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalysed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity [1]. [1]. 12003492. Dual function of the tRNA(m(5)U54)methyltransferase in tRNA maturation. Johansson MJ, Bystrom AS;. RNA 2002;8:324-335. (from Pfam) NF017745.5 PF05960.16 DUF885 32.4 32.4 532 subfamily Y Y N DUF885 family protein 131567 cellular organisms no rank 61073 EBI-EMBL Bacterial protein of unknown function (DUF885) DUF885 family protein This family consists of several hypothetical bacterial proteins several of which are putative membrane proteins. (from Pfam) NF017754.5 PF05970.19 PIF1 25.9 25.9 223 domain Y N N PIF1-like helicase GO:0000723,GO:0003678,GO:0006281 16522649,17172855,29202194,30698796 131567 cellular organisms no rank 30627 EBI-EMBL PIF1-like helicase PIF1-like helicase This family includes homologues of the PIF1 helicase, which inhibits telomerase activity and is cell cycle regulated [1-4]. This family includes a large number of largely uncharacterised plant proteins. This entry includes a P-loop motif that is involved in nucleotide binding. [1]. 17172855. Human PIF helicase is cell cycle regulated and associates with telomerase. Mateyak MK, Zakian VA;. Cell Cycle. 2006;5:2796-2804. [2]. 16522649. The human Pif1 helicase, a potential Escherichia coli RecD homologue, inhibits telomerase activity. Zhang DH, Zhou B, Huang Y, Xu LX, Zhou JQ;. Nucleic Acids Res. 2006;34:1393-1404. [3]. 30698796. Structural and functional analysis of the nucleotide and DNA binding activities of the human PIF1 helicase. Dehghani-Tafti S, Levdikov V, Antson AA, Bax B, Sanders CM;. Nucleic Acids Res. 2019;47:3208-3222. [4]. 29202194. Insights into the structural and mechanistic basis of multifunctional S. cerevisiae Pif1p helicase. Lu KY, Chen WF, Rety S, Liu NN, Wu WQ, Dai YX, Li D, Ma HY, Dou SX, Xi XG;. Nucleic Acids Res. 2018;46:1486-1500. (from Pfam) NF017755.5 PF05971.17 Methyltransf_10 23 23 299 domain Y Y N RlmF-related methyltransferase GO:0008168 27872311,28525753 131567 cellular organisms no rank 31735 EBI-EMBL RNA methyltransferase RlmF-related methyltransferase domain This homology domain was previously annotated as DUF890. High-scoring members of this family are annotated by other annotation rules as the 23S rRNA (adenine(1618)-N(6))-methyltransferase RlmF. However, the low cutoffs for this Pfam HMM allow qualifying hits to other types of methyltransferase. NF017757.5 PF05973.19 Gp49 23.9 23.9 90 domain Y Y N type II toxin-antitoxin system RelE/ParE family toxin 131567 cellular organisms no rank 38486 EBI-EMBL Phage derived protein Gp49-like (DUF891) type II toxin-antitoxin system RelE/ParE family toxin This family consists of hypothetical bacterial proteins of unknown function as well as phage Gp49 proteins. (from Pfam) NF017758.5 PF05974.17 DUF892 23.7 23.7 159 subfamily Y Y N DUF892 family protein 17001035 131567 cellular organisms no rank 24757 EBI-EMBL Domain of unknown function (DUF892) DUF892 family protein This protein family is found in bacteria, including Protein YciF from Escherichia coli. This protein is produced by bacteria in response to stress conditions. It adopts a dimeric configuration in which each monomer shows five alpha-helices. Its function is still unknown [1]. [1]. 17001035. The crystal structure of the E. coli stress protein YciF. Hindupur A, Liu D, Zhao Y, Bellamy HD, White MA, Fox RO;. Protein Sci. 2006;15:2605-2611. (from Pfam) NF017760.5 PF05977.18 MFS_3 27 27 524 domain Y Y N MFS transporter 12068807,15336408 131567 cellular organisms no rank 407907 EBI-EMBL Transmembrane secretion effector MFS transporter This is a family of transport proteins. Members of this family include a protein responsible for the secretion of the ferric chelator, enterobactin [1], and a protein involved in antibiotic resistance [2]. [1]. 12068807. Export of the siderophore enterobactin in Escherichia coli: involvement of a 43 kDa membrane exporter. Furrer JL, Sanders DN, Hook-Barnard IG, McIntosh MA;. Mol Microbiol. 2002;44:1225-1234. [2]. 15336408. The cme gene of Clostridium difficile confers multidrug resistance in Enterococcus faecalis. Lebel S, Bouttier S, Lambert T;. FEMS Microbiol Lett. 2004;238:93-100. (from Pfam) NF017761.5 PF05978.21 UNC-93 22.9 22.9 379 domain Y N N Ion channel regulatory protein UNC-93 14534247,27272503,27458005 131567 cellular organisms no rank 664 EBI-EMBL Ion channel regulatory protein UNC-93 Ion channel regulatory protein UNC-93 The proteins in this family are represented by UNC-93 from Caenorhabditis elegans and also includes protein unc-93 homologue A (UNC93A), protein unc-93 homologue B1 (UNC93B1), and UNC93-like protein MFSD11 (also called major facilitator superfamily domain- containing protein 11 or protein ET). UNC-93 colocalizes with SUP-10 and SUP-9 within muscle cells. UNC-93 acts as a regulatory subunit of a multi-subunit potassium channel complex that may function in coordinating muscle contraction in C. elegans [1]. UNC93B1 controls intracellular trafficking and transport of a subset of Toll-like receptors (TLRs), including TLR3, TLR7 and TLR9, from the endoplasmic reticulum to endolysosomes where they can engage pathogen nucleotides and activate signaling cascades [2]. MFSD11 is ubiquitously expressed in the periphery and the central nervous system of mice, where it is expressed in excitatory and inhibitory mouse brain neurons [3]. [1]. 14534247. sup-9, sup-10, and unc-93 may encode components of a two-pore K+ channel that coordinates muscle contraction in Caenorhabditis elegans. de la Cruz IP, Levin JZ, Cummins C, Anderson P, Horvitz HR;. J Neurosci. 2003;23:9133-9145. [2]. 27458005. Inhibiting TLR9 and other UNC93B1-dependent TLRs paradoxically increases accumulation of MYD88L265P plasmablasts in vivo. Wang JQ, Beutler B, Goodnow CC, Horikawa K;. Blood. 2016;128:1604-1608. [3]. 27272503. The Putative SLC Transporters Mfsd5 and Mfsd11 Are Abundantly Expressed in the Mouse Brain and Have a Potential Role in Energy Homeostasis. Perland E, Lekholm E, Eriksson MM, Bagchi S, Arapi V, Fredriksson R;. PLoS One. 2016;11:e0156912. (from Pfam) NF017765.5 PF05982.17 Sbt_1 27 27 308 PfamEq Y Y N sodium-dependent bicarbonate transport family permease 21688970 131567 cellular organisms no rank 7975 EBI-EMBL Na+-dependent bicarbonate transporter superfamily sodium-dependent bicarbonate transport family permease Family of bacterial proteins that are likely to be part of the Na(+)-dependent bicarbonate transporter (sbt) family. Members carry 10TMS in a 5+5 duplicated structure. The loop between helices 5 and 6 in Synechocystis PCC6803 is likely to be the location for regulatory mechanisms governing the activation of the transporter [1]. [1]. 21688970. Membrane topology of the cyanobacterial bicarbonate transporter, SbtA, and identification of potential regulatory loops. Price GD, Shelden MC, Howitt SM;. Mol Membr Biol. 2011;28:265-275. (from Pfam) NF017771.5 PF05988.17 DUF899 27 27 224 domain Y Y N DUF899 family protein 131567 cellular organisms no rank 28573 EBI-EMBL Bacterial protein of unknown function (DUF899) DUF899 family protein This family consists of several uncharacterised bacterial proteins of unknown function. (from Pfam) NF017773.5 PF05990.17 DUF900 20.5 20.5 232 domain Y Y N alpha/beta hydrolase 131567 cellular organisms no rank 18912 EBI-EMBL Alpha/beta hydrolase of unknown function (DUF900) alpha/beta hydrolase This family consists of several hypothetical proteins of unknown function mostly found in Rhizobium species. Members of this family have an alpha/beta hydrolase fold. (from Pfam) NF017778.5 PF05995.17 CDO_I 23 23 170 domain Y N N Cysteine dioxygenase type I GO:0005506,GO:0016702 131567 cellular organisms no rank 27446 EBI-EMBL Cysteine dioxygenase type I Cysteine dioxygenase type I Cysteine dioxygenase type I (EC:1.13.11.20) converts cysteine to cysteinesulphinic acid and is the rate-limiting step in sulphate production. (from Pfam) NF017788.5 PF06007.16 PhnJ 25 25 275 PfamEq Y Y N alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase PhnJ GO:0016829,GO:0019700,GO:0051539 1840580 131567 cellular organisms no rank 11148 EBI-EMBL Phosphonate metabolism protein PhnJ alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase PhnJ This family consists of several bacterial phosphonate metabolism (PhnJ) sequences. The exact role that PhnJ plays in phosphonate utilisation is unknown. [1]. 1840580. Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12. Makino K, Kim SK, Shinagawa H, Amemura M, Nakata A;. J Bacteriol 1991;173:2612-2665. (from Pfam) NF017803.5 PF06023.17 Csa1 27 27 292 subfamily Y Y N CRISPR-associated protein Cas4 cas4 22408157 131567 cellular organisms no rank 215 EBI-EMBL CRISPR-associated exonuclease Csa1 CRISPR-associated protein Cas4 CRISPR (clustered regularly interspaced short palindromic repeats) elements and cas (CRISPR-associated) genes are widespread in Bacteria and Archaea. The CRISPR/Cas system operates as a defense mechanism against mobile genetic elements (i.e., viruses or plasmids). Csa1 is part of the archaeal subtype I-A system. Cas1 has not yet been enzymatically characterised [1]. [1]. 22408157. Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax. Plagens A, Tjaden B, Hagemann A, Randau L, Hensel R;. J Bacteriol. 2012;194:2491-2500. (from Pfam) NF017806.5 PF06026.19 Rib_5-P_isom_A 26 26 173 PfamEq Y Y N ribose-5-phosphate isomerase A GO:0004751,GO:0009052 12211039 131567 cellular organisms no rank 35234 EBI-EMBL Ribose 5-phosphate isomerase A (phosphoriboisomerase A) ribose-5-phosphate isomerase A This family consists of several ribose 5-phosphate isomerase A or phosphoriboisomerase A (EC:5.3.1.6) from bacteria, eukaryotes and archaea. [1]. 12211039. Crystal structure of D-ribose-5-phosphate isomerase (RpiA) from Escherichia coli. Rangarajan ES, Sivaraman J, Matte A, Cygler M;. Proteins 2002;48:737-740. (from Pfam) NF017807.5 PF06027.17 SLC35F 21 21 299 domain Y N N Solute carrier family 35 GO:0016020,GO:0022857,GO:0055085 131567 cellular organisms no rank 13187 EBI-EMBL Solute carrier family 35 Solute carrier family 35 This is a family of putative solute carrier proteins from eukaryotes. (from Pfam) NF017812.5 PF06032.17 DUF917 27 27 158 subfamily Y Y N DUF917 family protein 131567 cellular organisms no rank 12303 EBI-EMBL Protein of unknown function (DUF917), N-terminal DUF917 family protein This 3-layer(aba) sandwich domain is found at the N terminus of uncharacterised proteins belonging to the DUF917 family, which consists of hypothetical bacterial, archaeal and eukaryotic proteins of unknown function. (from Pfam) NF017815.5 PF06035.16 Peptidase_C93 27 27 162 domain Y Y N transglutaminase-like cysteine peptidase 15288868 131567 cellular organisms no rank 19993 EBI-EMBL Bacterial transglutaminase-like cysteine proteinase BTLCP transglutaminase-like cysteine peptidase Members of this family are predicted to be bacterial transglutaminase-like cysteine proteinases. They contain a conserved Cys-His-Asp catalytic triad. Their structure is predicted to be similar to that of Salmonella typhimurium N-hydroxyarylamine O-acetyltransferase Swiss:Q00267, in Pfam:PF00797, however they lack the sub-domain which is important for arylamine recognition [1]. [1]. 15288868. BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases. Ginalski K, Kinch L, Rychlewski L, Grishin NV;. Trends Biochem Sci. 2004;29:392-395. (from Pfam) NF017816.5 PF06037.16 DUF922 20.4 20.4 159 domain Y Y N DUF922 domain-containing protein 23671590 131567 cellular organisms no rank 6903 EBI-EMBL Bacterial protein of unknown function (DUF922) Bacterial protein of unknown function (DUF922) This family of proteins has a conserved HEXXH motif, suggesting they are putative peptidases of zincin fold [1]. [1]. 23671590. CLCAs - A Family of Metalloproteases of Intriguing Phylogenetic Distribution and with Cases of Substituted Catalytic Sites. Lenart A, Dudkiewicz M, Grynberg M, Pawlowski K;. PLoS One. 2013;8:e62272. (from Pfam) NF017817.5 PF06039.20 Mqo 27 27 489 domain Y Y N malate:quinone oxidoreductase 1.1.5.4 GO:0006099,GO:0008924 9660197 131567 cellular organisms no rank 36419 EBI-EMBL Malate:quinone oxidoreductase (Mqo) malate:quinone oxidoreductase This family consists of several bacterial Malate:quinone oxidoreductase (Mqo) proteins (EC:1.1.99.16). Mqo takes part in the citric acid cycle. It oxidises L-malate to oxaloacetate and donates electrons to ubiquinone-1 and other artificial acceptors or, via the electron transfer chain, to oxygen. NAD is not an acceptor and the natural direct acceptor for the enzyme is most likely a quinone. The enzyme is therefore called malate:quinone oxidoreductase, abbreviated to Mqo. Mqo is a peripheral membrane protein and can be released from the membrane by addition of chelators [1]. [1]. 9660197. Biochemical and genetic characterization of the membrane-associated malate dehydrogenase (acceptor) from Corynebacterium glutamicum. Molenaar D, van der Rest ME, Petrovic S;. Eur J Biochem 1998;254:395-403. (from Pfam) NF017822.5 PF06044.17 DpnI 26.7 26.7 183 domain Y Y N DpnI domain-containing protein 11334887,22638584 131567 cellular organisms no rank 1142 EBI-EMBL Dam-replacing family Dam-replacing family Dam-replacing protein (DRP) is an restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [1]. [1]. 11334887. Evolution and function of the neisserial dam-replacing gene. Cantalupo G, Bucci C, Salvatore P, Pagliarulo C, Roberti V, Lavitola A, Bruni CB, Alifano P;. FEBS Lett 2001;495:178-183. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF017826.5 PF06048.16 DUF927 22.6 22.6 284 domain Y Y N DUF927 domain-containing protein 27571176 131567 cellular organisms no rank 20688 EBI-EMBL Domain of unknown function (DUF927) Domain of unknown function (DUF927) This entry represents a domain found in bacterial proteins of unknown function. The crystal structure has been solved for a protein containing this domain SWISS:Q0WXP6 [1]. [1]. 27571176. Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative. Mir-Sanchis I, Roman CA, Misiura A, Pigli YZ, Boyle-Vavra S, Rice PA;. Nat Struct Mol Biol. 2016; [Epub ahead of print] (from Pfam) NF017828.5 PF06050.18 HGD-D 28.4 28.4 342 domain Y Y N 2-hydroxyacyl-CoA dehydratase 11980491 131567 cellular organisms no rank 16119 EBI-EMBL 2-hydroxyglutaryl-CoA dehydratase, D-component 2-hydroxyacyl-CoA dehydratase Degradation of glutamate via the hydroxyglutarate pathway involves the syn-elimination of water from 2-hydroxyglutaryl-CoA. This anaerobic process is catalysed by 2-hydroxyglutaryl-CoA dehydratase, an enzyme with two components (A and D) that reversibly associate during reaction cycles. This component contains one non-reducible [4Fe-4S]2+ cluster and a reduced riboflavin 5'-monophosphate [1]. [1]. 11980491. Adenosine triphosphate-induced electron transfer in 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. Hans M, Bill E, Cirpus I, Pierik AJ, Hetzel M, Alber D, Buckel W;. Biochemistry 2002;41:5873-5882. (from Pfam) NF017830.5 PF06052.17 3-HAO 25 25 151 domain Y N N 3-hydroxyanthranilic acid dioxygenase GO:0000334,GO:0005506 12620844,16522801,9539135 131567 cellular organisms no rank 8210 EBI-EMBL 3-hydroxyanthranilic acid dioxygenase 3-hydroxyanthranilic acid dioxygenase In eukaryotes 3-hydroxyanthranilic acid dioxygenase (EC:1.13.11.6) is part of the kynurenine pathway for the degradation of tryptophan and the biosynthesis of nicotinic acid [1].The prokaryotic homolog is involved in the 2-nitrobenzoate degradation pathway [2]. [1]. 9539135. The yeast gene YJR025c encodes a 3-hydroxyanthranilic acid dioxygenase and is involved in nicotinic acid biosynthesis. Kucharczyk R, Zagulski M, Rytka J, Herbert CJ;. FEBS Lett 1998;424:127-130. [2]. 12620844. Prokaryotic homologs of the eukaryotic 3-hydroxyanthranilate 3,4-dioxygenase and 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase in the 2-nitrobenzoate degradation pathway of Pseudomonas fluorescens strain KU-7. Muraki T, Taki M, Hasegawa Y, Iwaki H, Lau PC;. Appl Environ Microbiol 2003;69:1564-1572. [3]. 16522801. Crystal structure of 3-hydroxyanthranilic acid 3,4-dioxygenase from Saccharomyces cerevisiae: a special subgroup of the type III extradiol dioxygenases. Li X, Guo M, Fan J, Tang W, Wang D, Ge H, Rong H, Teng M, Niu L, Liu Q, Hao Q;. Protein Sci. 2006;15:761-773. (from Pfam) NF017831.5 PF06053.16 DUF929 24.6 24.6 205 domain Y Y N DUF929 family protein 131567 cellular organisms no rank 631 EBI-EMBL Domain of unknown function (DUF929) DUF929 family protein Family of proteins from the archaeon Sulfolobus, with undetermined function. According to structure prediction this protein has a thioredoxin fold. (from Pfam) NF017832.5 PF06054.16 CoiA 20.3 20.3 377 subfamily Y Y N competence protein CoiA family protein 15972856 131567 cellular organisms no rank 19421 EBI-EMBL Competence protein CoiA-like family competence protein CoiA family protein Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein. [1]. 15972856. Identification of novel restriction endonuclease-like fold families among hypothetical proteins. Kinch LN, Ginalski K, Rychlewski L, Grishin NV;. Nucleic Acids Res. 2005;33:3598-3605. (from Pfam) NF017833.5 PF06055.17 ExoD 23.8 23.8 180 domain Y Y N exopolysaccharide biosynthesis protein 1987158 131567 cellular organisms no rank 12043 EBI-EMBL Exopolysaccharide synthesis, ExoD exopolysaccharide biosynthesis protein Among the bacterial genes required for nodule invasion are the exo genes. These genes are involved in the production of an extracellular polysaccharide. Mutations in the exoD result in altered exopolysaccharide production and defects in nodule invasion [1]. [1]. 1987158. The exoD gene of Rhizobium meliloti encodes a novel function needed for alfalfa nodule invasion. Reed JW, Walker GC;. J Bacteriol 1991;173:664-677. (from Pfam) NF017834.5 PF06056.17 Terminase_5 20.3 20.3 58 domain Y Y N terminase gpP N-terminus-related DNA-binding protein GO:0005524,GO:0019069 10949585,12235385 131567 cellular organisms no rank 41560 EBI-EMBL Putative ATPase subunit of terminase (gpP-like) terminase gpP N-terminal domain Protein hit regions in this family include the N-terminal region of NP_046758.1, the phage P2 terminase large subunit (a DNA-packing ATPase), as well as regions of various transposases, sigma factors, and other DNA-binding proteins. NF017835.5 PF06057.16 VirJ 22 22 191 domain Y Y N AcvB/VirJ family lysyl-phosphatidylglycerol hydrolase 12207700 131567 cellular organisms no rank 10188 EBI-EMBL Bacterial virulence protein (VirJ) AcvB/VirJ family protein AcvB (Agrobacterium chromosomal virulence protein B) from Agrobacterium tumefaciens is a periplasmic lysyl-phosphatidylglycerol hydrolase whose knockout blocks the function of the type IV secretion system (T4SS) responsible for secretion of T-DNA, a virulence function. The enzymatically active C-terminal region of AcvB, which is chromosomal, is homologous to plasmid-borne VirJ, which likewise is associated with virulence. NF017844.5 PF06068.18 TIP49 23.8 23.8 347 domain Y Y N RuvB-like domain-containing protein GO:0005524 10902922,12464178 131567 cellular organisms no rank 31020 EBI-EMBL TIP49 P-loop domain TIP49 P-loop domain This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the Pfam:PF00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway [1]. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [2]. [1]. 12464178. Reptin and pontin antagonistically regulate heart growth in zebrafish embryos. Rottbauer W, Saurin AJ, Lickert H, Shen X, Burns CG, Wo ZG, Kemler R, Kingston R, Wu C, Fishman M;. Cell 2002;111:661-672. [2]. 10902922. Chromosome mapping and expression of human tip49 family genes. Makino Y, Kanemaki M, Koga A, Osano K, Matsu-Ura T, Kurokawa Y, Kishimoto T, Tamura T;. DNA Seq 2000;11:145-148. (from Pfam) NF017850.5 PF06074.17 DUF935 34 34 518 subfamily Y Y N DUF935 family protein 131567 cellular organisms no rank 14864 EBI-EMBL Protein of unknown function (DUF935) DUF935 family protein This family consists of several bacterial proteins of unknown function as well as the Bacteriophage Mu gp29 protein Swiss:Q9T1W5. (from Pfam) NF017853.5 PF06078.16 DUF937 25.4 10 135 domain Y Y N DUF937 domain-containing protein 131567 cellular organisms no rank 13868 EBI-EMBL Bacterial protein of unknown function (DUF937) Bacterial protein of unknown function (DUF937) This family consists of several hypothetical bacterial proteins of unknown function. (from Pfam) NF017855.5 PF06080.17 DUF938 27 27 202 domain Y Y N DUF938 domain-containing protein 131567 cellular organisms no rank 12645 EBI-EMBL Protein of unknown function (DUF938) Protein of unknown function (DUF938) This family consists of several hypothetical proteins from both prokaryotes and eukaryotes. The function of this family is unknown. (from Pfam) NF017856.5 PF06081.16 ArAE_1 22 22 141 domain Y Y N aromatic acid exporter family protein 131567 cellular organisms no rank 60131 EBI-EMBL Aromatic acid exporter family member 1 aromatic acid exporter family protein This family consists of bacterial proteins with three transmembrane regions that are purported to be aromatic acid exporters. (from Pfam) NF017864.5 PF06089.17 Asparaginase_II 25 25 322 domain Y Y N asparaginase 3.5.1.1 10930734 131567 cellular organisms no rank 25850 EBI-EMBL L-asparaginase II asparaginase This family consists of several bacterial L-asparaginase II proteins. L-asparaginase (EC:3.5.1.1) catalyses the hydrolysis of L-asparagine to L-aspartate and ammonium. Rhizobium etli possesses two asparaginases: asparaginase I, which is thermostable and constitutive, and asparaginase II, which is thermolabile, induced by asparagine and repressed by the carbon source [1]. [1]. 10930734. The L-asparagine operon of Rhizobium etli contains a gene encoding an atypical asparaginase. Ortuno-Olea L, Duran-Vargas S;. FEMS Microbiol Lett 2000;189:177-182. (from Pfam) NF017867.5 PF06093.18 Spt4 25 25 77 PfamEq Y N N Spt4/RpoE2 zinc finger 11182892,19000817,8127719 131567 cellular organisms no rank 1000 EBI-EMBL Spt4/RpoE2 zinc finger Spt4/RpoE2 zinc finger This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 [2]. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles [1]. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in [3]. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery. [1]. 11182892. Control of eukaryotic transcription elongation. Winston F;. Genome Biol 2001;2:1006-1007. [2]. 8127719. A subunit of an archaeal DNA-dependent RNA polymerase contains the S1 motif. Langer D, Lottspeich F, Zillig W;. Nucleic Acids Res. 1994;22:694-694. [3]. 19000817. Core structure of the yeast spt4-spt5 complex: a conserved module for regulation of transcription elongation. Guo M, Xu F, Yamada J, Egelhofer T, Ga. TRUNCATED at 1650 bytes (from Pfam) NF017868.5 PF06094.17 GGACT 22.8 22.8 120 domain Y Y N gamma-glutamylcyclotransferase 16754964,17462573,20110353,20851126,8742710 131567 cellular organisms no rank 49325 EBI-EMBL Gamma-glutamyl cyclotransferase, AIG2-like gamma-glutamylcyclotransferase GGACT, gamma-glutamylamine cyclotransferase, is a ubiquitous enzyme found in bacteria, plants, and metazoans from Dictyostelium through to humans. It converts gamma-glutamylamines to free amines and 5-oxoproline. [1]. 8742710. Isolation of Arabidopsis genes that differentiate between resistance responses mediated by the RPS2 and RPM1 disease resistance genes. Reuber TL, Ausubel FM;. Plant Cell 1996;8:241-249. [2]. 16754964. Solution structure of Arabidopsis thaliana protein At5g39720.1, a member of the AIG2-like protein family. Lytle BL, Peterson FC, Tyler EM, Newman CL, Vinarov DA, Markley JL, Volkman BF;. Acta Crystallograph Sect F Struct Biol Cryst Commun. 2006;62:490-493. [3]. 20851126. Structural and biochemical studies elucidate the mechanism of rhamnogalacturonan lyase from Aspergillus aculeatus. Jensen MH, Otten H, Christensen U, Borchert TV, Christensen LL, Larsen S, Leggio LL;. J Mol Biol. 2010;404:100-111. [4]. 20110353. Identification and characterization of gamma-glutamylamine cyclotransferase, an enzyme responsible for gamma-glutamyl-epsilon-lysine catabolism. Oakley AJ, Coggan M, Board PG;. J Biol Chem. 2010;285:9642-9648. [5]. 17462573. Biosynthesis of butirosin: transfer and deprotection of the unique amino acid side chain. Llewellyn NM, Li Y, Spencer JB;. Chem Biol. 2007;14:379-386. (from Pfam) NF017873.5 PF06100.16 MCRA 23 23 495 PfamEq Y Y N oleate hydratase 4.2.1.53 GO:0006631,GO:0050151,GO:0071949 20145247,21329502,22955678,8188369 131567 cellular organisms no rank 17702 EBI-EMBL MCRA family oleate hydratase The MCRA (myosin-cross-reactive antigen) family of proteins were thought to have structural features in common with the beta chain of the class II antigens, as well as myosin, and may play an important role in the pathogenesis[1]. More recent work shows that these proteins act as hydratase enzymes that convert linoleic acid and oleic acid to their respective 10-hydroxy derivatives. It has been suggested that MCRA proteins catalyse the first step in conjugated linoleic acid production [2]. Proteins in this family act in an FAD dependent manner [3]. The structure of a fatty acid double-bond hydratase from Lactobacillus acidophilus has been recently solved showing four structural domains. [1]. 8188369. Cloning and sequence analysis of a gene encoding a 67-kilodalton myosin-cross-reactive antigen of Streptococcus pyogenes reveals its similarity with class II major histocompatibility antigens. Kil KS, Cunningham MW, Barnett LA;. Infect Immun 1994;62:2440-2449. [2]. 22955678. Myosin-cross-reactive antigens from four different lactic acid bacteria are fatty acid hydratases. Yang B, Chen H, Song Y, Chen YQ, Zhang H, Chen W;. Biotechnol Lett. 2013;35:75-81. [3]. 21329502. Myosin-cross-reactive antigen (MCRA) protein from Bifidobacterium breve is a FAD-dependent fatty acid hydratase which has a function in stress protection. Rosberg-Cody E, Liavonchanka A, Gobel C, Ross RP, O'Sullivan O, Fitzgerald GF, Feussner I, Stanton C;. BMC Biochem. 2011;12:9. [4]. 20145247. Myosin cross-reactive antigen of Streptococcus pyogenes M49 encodes a fatty acid double bond hydratase that plays a role in oleic acid detoxification and bacterial virul. TRUNCATED at 1650 bytes (from Pfam) NF017880.5 PF06108.17 DUF952 23.7 23.7 90 PfamAutoEq Y Y N DUF952 domain-containing protein 131567 cellular organisms no rank 18623 EBI-EMBL Protein of unknown function (DUF952) Protein of unknown function (DUF952) This family consists of several hypothetical bacterial and plant proteins of unknown function. (from Pfam) NF017885.5 PF06114.18 Peptidase_M78 22 22 123 domain Y Y N ImmA/IrrE family metallo-endopeptidase 15090522,18761623,19150362,22916289 131567 cellular organisms no rank 107632 EBI-EMBL IrrE N-terminal-like domain IrrE N-terminal-like domain This entry includes the catalytic domain of the protein ImmA, which is a metallopeptidase containing an HEXXH zinc-binding motif from peptidase family M78. ImmA is encoded on a conjugative transposon. Conjugating bacteria are able to transfer conjugative transposons that can, for example, confer resistance to antibiotics. The transposon is integrated into the chromosome, but during conjugation excises itself and then moves to the recipient bacterium and re-integrate into its chromosome. Typically a conjugative tranposon encodes only the proteins required for this activity and the proteins that regulate it. During exponential growth, the ICEBs1 transposon of Bacillus subtilis is inactivated by the immunity repressor protein ImmR, which is encoded by the transposon and represses the genes for excision and transfer. Cleavage of ImmR relaxes repression and allows transfer of the transposon. ImmA has been shown to be essential for the cleavage of ImmR [2]. This domain is also found in in metalloprotease IrrE, a central regulator of DNA damage repair in Deinococcaceae [1], HTH-type transcriptional regulators RamB [3] and PrpC [4]. [1]. 19150362. Crystal structure of the IrrE protein, a central regulator of DNA damage repair in deinococcaceae. Vujicic-Zagar A, Dulermo R, Le Gorrec M, Vannier F, Servant P, Sommer S, de Groot A, Serre L;. J Mol Biol. 2009;386:704-716. [2]. 18761623. A conserved anti-repressor controls horizontal gene transfer by proteolysis. Bose B, Auchtung JM, Lee CA, Grossman AD;. Mol Microbiol. 2008;70:570-582. [3]. 15090522. RamB, a novel transcriptional regulator of genes involved in acetate me. TRUNCATED at 1650 bytes (from Pfam) NF017889.5 PF06119.19 NIDO 25 25 186 domain Y Y N nidogen-like domain-containing protein GO:0007160 11893501 131567 cellular organisms no rank 1144 EBI-EMBL Nidogen-like Nidogen-like This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function [1]. [1]. 11893501. AMOP, a protein module alternatively spliced in cancer cells. Ciccarelli FD, Doerks T, Bork P;. Trends Biochem Sci 2002;27:113-115. (from Pfam) NF017902.5 PF06133.16 Com_YlbF 23.9 23.9 105 domain Y Y N YlbF family regulator 19202088,23490197 131567 cellular organisms no rank 16359 EBI-EMBL Control of competence regulator ComK, YlbF/YmcA YlbF family regulator YlbF Is a family of short Gram-positive and archaeal proteins that includes both YlbF and YmcA which may interact synergistically. The family is necessary for correct biofilm formation, as null mutants of ymcA and ylbF fail to form pellicles at air-liquid interfaces and grow on solid media as smooth, undifferentiated colonies. During development, YmcA, YlbF and YaaT, family PSPI, Pfam:PF04468, interact directly with one another forming a stable ternary complex, in vitro. All three proteins are required for competence, sporulation and the formation of biofilms. The YmcA-YlbF-YaaT complex affects the phosphotransfer between Spo0F and Spo0B, thus accelerating the production of Spo0A~P. The three processes of biofilm formation, mature spore formation and competence all require the active, phosphorylated form of Spo0A, as Spo0A-P [1,2]. [1]. 23490197. A complex of YlbF, YmcA and YaaT regulates sporulation, competence and biofilm formation by accelerating the phosphorylation of Spo0A. Carabetta VJ, Tanner AW, Greco TM, Defrancesco M, Cristea IM, Dubnau D;. Mol Microbiol. 2013;88:283-300. [2]. 19202088. Identification of genes required for different stages of dendritic swarming in Bacillus subtilis, with a novel role for phrC. Hamze K, Julkowska D, Autret S, Hinc K, Nagorska K, Sekowska A, Holland IB, Seror SJ;. Microbiology. 2009;155:398-412. (from Pfam) NF017913.5 PF06146.17 PsiE 23.9 23.9 122 domain Y Y N phosphate-starvation-inducible PsiE family protein 10986267 131567 cellular organisms no rank 15467 EBI-EMBL Phosphate-starvation-inducible E family phosphate-starvation-inducible PsiE family protein This entry represents an integral membrane protein with 4 transmembrane helices. The second alpha helix contains a conserved glutamic acid residue and the third helix contains a conserved arginine residue. These two buried charged residues may interact. The type example for this family is the Phosphate-starvation-inducible E (PsiE) expression protein, which is under direct positive and negative control by PhoB and cAMP-CRP, respectively [1]. The function of PsiE remains to be determined. This entry is sometimes found in proteins that contain other domains such as Pfam:PF11563. [1]. 10986267. Dual transcriptional regulation of the Escherichia coli phosphate-starvation-inducible psiE gene of the phosphate regulon by PhoB and the cyclic AMP (cAMP)-cAMP receptor protein complex. Kim SK, Kimura S, Shinagawa H, Nakata A, Lee KS, Wanner BL, Makino K;. J Bacteriol 2000;182:5596-5599. (from Pfam) NF017917.5 PF06150.17 ChaB 27 27 60 PfamEq Y Y N ChaB family protein 12460671 131567 cellular organisms no rank 7828 EBI-EMBL ChaB ChaB family protein This family of proteins contain a conserved 60 residue region. This protein is known as ChaB in E. coli and is found next to ChaA which is a cation transporter protein. ChaB may be regulate ChaA function in some way. [1]. 12460671. Expression of chaA, a sodium ion extrusion system of Escherichia coli, is regulated by osmolarity and pH. Shijuku T, Yamashino T, Ohashi H, Saito H, Kakegawa T, Ohta M, Kobayashi H;. Biochim Biophys Acta 2002;1556:142-148. (from Pfam) NF017919.5 PF06152.16 Phage_min_cap2 26.3 26.3 366 subfamily Y Y N phage minor capsid protein GO:0005198 8497043 131567 cellular organisms no rank 8411 EBI-EMBL Phage minor capsid protein 2 phage minor capsid protein Family of related phage minor capsid proteins. [1]. 8497043. Molecular comparison of the structural proteins encoding gene clusters of two related Lactobacillus delbrueckii bacteriophages. Vasala A, Dupont L, Baumann M, Ritzenthaler P, Alatossava T;. J Virol 1993;67:3061-3068. (from Pfam) NF017922.5 PF06155.17 GBBH-like_N 22.8 22.8 85 domain Y Y N gamma-butyrobetaine hydroxylase-like domain-containing protein 20599753,29769716 131567 cellular organisms no rank 19876 EBI-EMBL Gamma-butyrobetaine hydroxylase-like, N-terminal Gamma-butyrobetaine hydroxylase-like, N-terminal This domain is found in several proteins including gamma-butyrobetaine dioxygenase, Fe-S cluster assembly factor HCF101 and trimethyllysine dioxygenase proteins. Gamma-butyrobetaine hydroxylase (GBBH) is a alpha-ketoglutarate-dependent dioxygenase that catalyzes the biosynthesis of L-carnitine by hydroxylation of gamma-butyrobetaine (GBB). GBBH is a dimeric enzyme. The monomer consists of a catalytic double-stranded beta-helix domain and a smaller N-terminal domain. The N-terminal domain has a bound Zn ion, which is coordinated by three cysteines and one histidine. The N-terminal domain could facilitate dimer formation, but its precise function is not known [1]. Other family members have been suggested to be involved in FeS cluster maintenance (see Supplementary note 5 in [2].) [1]. 20599753. Crystal structure of human gamma-butyrobetaine hydroxylase. Tars K, Rumnieks J, Zeltins A, Kazaks A, Kotelovica S, Leonciks A, Sharipo J, Viksna A, Kuka J, Liepinsh E, Dambrova M;. Biochem Biophys Res Commun. 2010;398:634-639. [2]. 29769716. Mutant phenotypes for thousands of bacterial genes of unknown function. Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM;. Nature. 2018;557:503-509. (from Pfam) NF017930.5 PF06165.16 Glyco_transf_36 23 23 251 domain Y N N Glycosyltransferase family 36 131567 cellular organisms no rank 23436 EBI-EMBL Glycosyltransferase family 36 Glycosyltransferase family 36 The glycosyltransferase family 36 includes cellobiose phosphorylase (EC:2.4.1.20), cellodextrin phosphorylase (EC:2.4.1.49), chitobiose phosphorylase (EC:2.4.1.-). Many members of this family contain two copies of this domain. (from Pfam) NF017933.5 PF06168.16 DUF981 29 29 186 subfamily Y Y N DUF981 family protein 131567 cellular organisms no rank 1334 EBI-EMBL Protein of unknown function (DUF981) DUF981 family protein Family of uncharacterised proteins found in bacteria and archaea. (from Pfam) NF017936.5 PF06172.16 Cupin_5 25 25 139 PfamAutoEq Y Y N cupin domain-containing protein 15608122 131567 cellular organisms no rank 21649 EBI-EMBL Cupin superfamily (DUF985) Cupin superfamily (DUF985) Family of uncharacterised proteins found in bacteria and eukaryotes that belongs to the Cupin superfamily. [1]. 15608122. Crystal structure of the YML079w protein from Saccharomyces cerevisiae reveals a new sequence family of the jelly-roll fold. Zhou CZ, Meyer P, Quevillon-Cheruel S, De La Sierra-Gallay IL, Collinet B, Graille M, Blondeau K, Francois JM, Leulliot N, Sorel I, Poupon A, Janin J, Van Tilbeurgh H;. Protein Sci 2005;14:209-215. (from Pfam) NF017940.5 PF06176.16 WaaY 20.3 20.3 229 PfamEq Y Y N lipopolysaccharide core heptose(II) kinase RfaY 9756860 131567 cellular organisms no rank 5140 EBI-EMBL Lipopolysaccharide core biosynthesis protein (WaaY) lipopolysaccharide core heptose(II) kinase RfaY This family consists of several bacterial lipopolysaccharide core biosynthesis proteins (WaaY or RfaY). The waaY, waaQ, and waaP genes are located in the central operon of the waa (formerly rfa) locus on the chromosome of Escherichia coli. This locus contains genes whose products are involved in the assembly of the core region of the lipopolysaccharide molecule. WaaY is the enzyme that phosphorylates HepII in this system [1]. [1]. 9756860. Involvement of waaY, waaQ, and waaP in the modification of Escherichia coli lipopolysaccharide and their role in the formation of a stable outer membrane. Yethon JA, Heinrichs DE, Monteiro MA, Perry MB, Whitfield C;. J Biol Chem 1998;273:26310-26316. (from Pfam) NF017941.5 PF06177.16 QueT 33.7 33.7 141 domain Y Y N QueT transporter family protein 17384645,18305186 131567 cellular organisms no rank 8068 EBI-EMBL QueT transporter QueT transporter family protein This family includes the queT gene encoding a hypothetical integral membrane protein with 5 predicted transmembrane regions. The queT genes in Firmicutes are often preceded by the PreQ1 (7-aminomethyl-7-deazaguanine) riboswitches of two distinct classes [1-2], suggesting involvement of the QueT transporters in uptake of a queuosine biosynthetic intermediate. [1]. 17384645. A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Roth A, Winkler WC, Regulski EE, Lee BW, Lim J, Jona I, Barrick JE, Ritwik A, Kim JN, Welz R, Iwata-Reuyl D, Breaker RR;. Nat Struct Mol Biol. 2007;14:308-317. [2]. 18305186. Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria. Meyer MM, Roth A, Chervin SM, Garcia GA, Breaker RR;. RNA. 2008;14:685-695. (from Pfam) NF017944.5 PF06180.16 CbiK 26.2 26.2 262 domain Y Y N sirohydrochlorin cobaltochelatase GO:0016852,GO:0019251 9150215 131567 cellular organisms no rank 11724 EBI-EMBL Cobalt chelatase (CbiK) sirohydrochlorin cobaltochelatase This family consists of several bacterial cobalt chelatase (CbiK) proteins (EC:4.99.1.-). [1]. 9150215. A role for Salmonella typhimurium cbiK in cobalamin (vitamin B12) and siroheme biosynthesis. Raux E, Thermes C, Heathcote P, Rambach A, Warren MJ;. J Bacteriol 1997;179:3202-3212. (from Pfam) NF017946.5 PF06182.16 ABC2_membrane_6 22 22 229 domain Y Y N ABC-2 family transporter protein 19594831,20030718 131567 cellular organisms no rank 44410 EBI-EMBL ABC-2 family transporter protein ABC-2 family transporter protein This family acts as the transmembrane domain (TMD) of ABC transporters [1,2]. The family includes proteins responsible for the transport of herbicides [1]. [1]. 19594831. A novel ATP-binding cassette transporter is responsible for resistance to viologen herbicides in the cyanobacterium Synechocystis sp. PCC 6803. Prosecka J, Orlov AV, Fantin YS, Zinchenko VV, Babykin MM, Tichy M;. FEBS J. 2009;276:4001-4011. [2]. 20030718. Identification of a novel ABC transporter required for desiccation tolerance, and biofilm formation in Rhizobium leguminosarum bv. viciae 3841. Vanderlinde EM, Harrison JJ, Muszynski A, Carlson RW, Turner RJ, Yost CK;. FEMS Microbiol Ecol. 2010;71:327-340. (from Pfam) NF017952.5 PF06188.17 HrpE 23.5 23.5 191 domain Y Y N HrpE/YscL family type III secretion apparatus protein 15292229,16522800,7579617 131567 cellular organisms no rank 3047 EBI-EMBL HrpE/YscL/FliH and V-type ATPase subunit E HrpE/YscL family type III secretion apparatus protein This is a prokaryotic family that contains proteins of the FliH and HrpE/YscL family. These proteins are involved in type III secretion, which is the process that drives flagellar biosynthesis and mediates bacterial-eukaryotic interactions [1-2]. This family also V-type ATPase subunit E. This subunit appears to form a tight interaction with subunit G in the F0 complex [3]. Subunits E and G may act together as stators to prevent certain subunits from rotating with the central rotary element [3]. Pfam:PF01991 also contains V-type ATPase subunit E proteins. [1]. 7579617. The complete hrp gene cluster of Pseudomonas syringae pv. syringae 61 includes two blocks of genes required for harpinPss secretion that are arranged colinearly with Yersinia ysc homologs. Huang HC, Lin RH, Chang CJ, Collmer A, Deng WL;. Mol Plant Microbe Interact 1995;8:733-746. [2]. 16522800. Evolutionary links between FliH/YscL-like proteins from bacterial type III secretion systems and second-stalk components of the FoF1 and vacuolar ATPases. Pallen MJ, Bailey CM, Beatson SA;. Protein Sci. 2006;15:935-941. [3]. 15292229. Building the stator of the yeast vacuolar-ATPase: specific interaction between subunits E and G. Fethiere J, Venzke D, Diepholz M, Seybert A, Geerlof A, Gentzel M, Wilm M, Bottcher B;. J Biol Chem. 2004;279:40670-40676. (from Pfam) NF017954.5 PF06191.17 DUF995 20 20 140 domain Y Y N DUF995 domain-containing protein 131567 cellular organisms no rank 2022 EBI-EMBL Protein of unknown function (DUF995) Protein of unknown function (DUF995) Family of uncharacterised Proteobacteria proteins. (from Pfam) NF017957.5 PF06195.18 DUF996 31.3 31.3 138 domain Y Y N DUF996 domain-containing protein 131567 cellular organisms no rank 447 EBI-EMBL Protein of unknown function (DUF996) Protein of unknown function (DUF996) Family of uncharacterised bacterial and archaeal proteins. (from Pfam) NF017959.5 PF06197.18 DUF998 30 30 184 domain Y Y N DUF998 domain-containing protein 131567 cellular organisms no rank 33401 EBI-EMBL Protein of unknown function (DUF998) Protein of unknown function (DUF998) Family of conserved archaeal proteins. (from Pfam) NF017961.5 PF06199.16 Phage_tail_2 23.8 23.8 132 subfamily Y Y N phage tail tube protein 8610457 131567 cellular organisms no rank 12206 EBI-EMBL Phage tail tube protein phage tail tube protein Characterised members are major tail tube proteins from various phages, including lactococcal temperate bacteriophage TP901-1. [1]. 8610457. A genomic region of lactococcal temperate bacteriophage TP901-1 encoding major virion proteins. Johnsen MG, Appel KF, Madsen PL, Vogensen FK, Hammer K, Arnau J;. Virology 1996;218:306-315. (from Pfam) NF017964.5 PF06202.19 GDE_C 21 21 367 domain Y Y N amylo-alpha-1,6-glucosidase 11375985 131567 cellular organisms no rank 29445 EBI-EMBL Amylo-alpha-1,6-glucosidase amylo-alpha-1,6-glucosidase This family includes human glycogen branching enzyme Swiss:P35573. This enzyme contains a number of distinct catalytic activities. It has been shown for the yeast homologue Swiss:O93808 that mutations in this region disrupt the enzymes Amylo-alpha-1,6-glucosidase (EC:3.2.1.33). [1]. 11375985. Identification of the catalytic residues of bifunctional glycogen debranching enzyme. Nakayama A, Yamamoto K, Tabata S;. J Biol Chem 2001;276:28824-28828. (from Pfam) NF017966.5 PF06206.16 CpeT 21 21 181 subfamily Y Y N CpcT/CpeT family chromophore lyase GO:0016829,GO:0017009 16644722 131567 cellular organisms no rank 3175 EBI-EMBL CpeT/CpcT family (DUF1001) CpcT/CpeT family chromophore lyase This family consists of proteins of proteins belonging to the CpeT/CpcT family. These proteins are around 200 amino acids in length. The proteins contain a conserved motif PYR in the amino terminal half of the protein that may be functionally important. The species distribution of the family is interesting. So far it is restricted to cyanobacteria, cryptomonads and plants. It has been shown that CpcT encodes a bilin lyase responsible for attachment of phycocyanobilin to the beta subunit of phycocyanin [1]. [1]. 16644722. Identification and characterization of a new class of bilin lyase: the cpcT gene encodes a bilin lyase responsible for attachment of phycocyanobilin to Cys-153 on the beta-subunit of phycocyanin in Synechococcus sp. PCC 7002. Shen G, Saunee NA, Williams SR, Gallo EF, Schluchter WM, Bryant DA;. J Biol Chem. 2006;281:17768-17778. (from Pfam) NF017967.5 PF06207.16 DUF1002 26 26 220 PfamAutoEq Y Y N DUF1002 domain-containing protein 131567 cellular organisms no rank 9104 EBI-EMBL Protein of unknown function (DUF1002) Protein of unknown function (DUF1002) This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria. (from Pfam) NF017970.5 PF06210.16 DUF1003 27.4 27.4 103 domain Y Y N DUF1003 domain-containing protein 131567 cellular organisms no rank 26156 EBI-EMBL Protein of unknown function (DUF1003) Protein of unknown function (DUF1003) This family consists of several hypothetical bacterial proteins of unknown function. (from Pfam) NF017984.5 PF06224.17 AlkZ-like 25.9 25.9 329 subfamily Y Y N DNA glycosylase AlkZ-like family protein GO:0019104,GO:0036297 28396405,32409837 131567 cellular organisms no rank 90592 EBI-EMBL DNA glycosylase AlkZ-like crosslink repair DNA glycosylase YcaQ family protein Members of this family have two copies of a winged helix domain, suggsting DNA-binding. YcaQ from Escherichia coli was shown to be a DNA glycosylase that removes crosslinks between strands of DNA. NF017987.5 PF06228.18 ChuX_HutX 25 25 134 domain Y Y N ChuX/HutX family heme-like substrate-binding protein 17322535,19319934 131567 cellular organisms no rank 19884 EBI-EMBL Haem utilisation ChuX/HutX ChuX/HutX family heme-like substrate-binding protein This family is found within haem utilisation operons. It has a similar structure to that of Pfam:PF05171. Pfam:PF05171 usually occurs as a duplicated domain, but this domain occurs as a single domain and forms a dimer. The organisation of the dimer is very similar to that of the duplicated Pfam:PF05171 domains [1,2]. It binds haem via conserved histidines [2]. [1]. 17322535. Crystal structure of AGR_C_4470p from Agrobacterium tumefaciens. Vorobiev SM, Neely H, Seetharaman J, Ma LC, Xiao R, Acton TB, Montelione GT, Tong L;. Protein Sci. 2007;16:535-538. [2]. 19319934. Structure and heme binding properties of Escherichia coli O157:H7 ChuX. Suits MD, Lang J, Pal GP, Couture M, Jia Z;. Protein Sci. 2009;18:825-838. (from Pfam) NF017993.5 PF06234.17 TmoB 25 25 78 domain Y Y N toluene-4-monooxygenase system B family protein 16859499,1885512 131567 cellular organisms no rank 599 EBI-EMBL Toluene-4-monooxygenase system protein B (TmoB) toluene-4-monooxygenase system B family protein This family consists of several Toluene-4-monooxygenase system protein B (TmoB) sequences. Pseudomonas mendocina KR1 metabolises toluene as a carbon source. The initial step of the pathway is hydroxylation of toluene to form p-cresol by a multicomponent toluene-4-monooxygenase (T4MO) system [1]. TmoB adopts a ubiquitin fold [2]. Although TmoB is a component of the T4MO system, its precise role remains unclear. [1]. 1885512. Cloning and characterization of a Pseudomonas mendocina KR1 gene cluster encoding toluene-4-monooxygenase. Yen KM, Karl MR, Blatt LM, Simon MJ, Winter RB, Fausset PR, Lu HS, Harcourt AA, Chen KK;. J Bacteriol 1991;173:5315-5327. [2]. 16859499. The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. Iyer LM, Burroughs AM, Aravind L;. Genome Biol. 2006;7:R60. (from Pfam) NF017999.5 PF06240.18 COXG 22.2 22.2 140 domain Y Y N SRPBCC domain-containing protein 10433972 131567 cellular organisms no rank 31178 EBI-EMBL Carbon monoxide dehydrogenase subunit G (CoxG) SRPBCC domain The SRPBCC (START/RHOalphaC/PITP/Bet v1/CoxG/CalC) family includes carbon monoxide dehydrogenase subunit G (CoxG), but other proteins as well. NF018000.5 PF06241.17 Castor_Poll_mid 26.7 26.7 104 domain Y Y N CASTOR/POLLUX-related putative ion channel 18978069,19106374 131567 cellular organisms no rank 5184 EBI-EMBL Castor and Pollux, part of voltage-gated ion channel CASTOR/POLLUX-related putative ion channel This family represents a short region in the middle of largely plant proteins that belong to the TCDB:1.A.1.23.2 family of the voltage-gated ion channel superfamily, eg UniProtKB:Q5H8A6, Q5H8A5 and Q4VY51. [1]. 18978069. Antiquity and function of CASTOR and POLLUX, the twin ion channel-encoding genes key to the evolution of root symbioses in plants. Chen C, Fan C, Gao M, Zhu H;. Plant Physiol. 2009;149:306-317. [2]. 19106374. Lotus japonicus CASTOR and POLLUX are ion channels essential for perinuclear calcium spiking in legume root endosymbiosis. Charpentier M, Bredemeier R, Wanner G, Takeda N, Schleiff E, Parniske M;. Plant Cell. 2008;20:3467-3479. (from Pfam) NF018002.5 PF06243.16 PaaB 27 27 89 PfamEq Y N N Phenylacetic acid degradation B 9748275 131567 cellular organisms no rank 13254 EBI-EMBL Phenylacetic acid degradation B Phenylacetic acid degradation B Phenylacetic acid degradation protein B (PaaB) is thought to be part of a multicomponent oxygenase involved in phenylacetyl-CoA hydroxylation [1]. [1]. 9748275. Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway. Ferrandez A, Minambres B, Garcia B, Olivera ER, Luengo JM, Garcia JL, Diaz E;. J Biol Chem 1998;273:25974-25986. (from Pfam) NF018004.5 PF06245.16 DUF1015 25.8 25.8 325 PfamAutoEq Y Y N DUF1015 family protein 131567 cellular organisms no rank 23352 EBI-EMBL Protein of unknown function (DUF1015) DUF1015 family protein Family of proteins with unknown function found in archaea and bacteria. (from Pfam) NF018008.5 PF06249.17 EutQ 21 21 152 domain Y N N Ethanolamine utilisation protein EutQ 10464203 131567 cellular organisms no rank 13687 EBI-EMBL Ethanolamine utilisation protein EutQ Ethanolamine utilisation protein EutQ The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear [1]. [1]. 10464203. The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. Kofoid E, Rappleye C, Stojiljkovic I, Roth J;. J Bacteriol 1999;181:5317-5329. (from Pfam) NF018009.5 PF06250.16 YhcG_C 32.5 32.5 157 subfamily Y Y N PDDEXK nuclease domain-containing protein 16011798,19402753 131567 cellular organisms no rank 25103 EBI-EMBL YhcG PDDEXK nuclease domain DUF1016 family protein This domain can be found in uncharacterised proteins in viruses, archaea and bacteria, most notably it is found in YhcG proteins found in E.coli. This entry represents the C-terminal PDDEXK domain belonging to the PD-(D/E)XK superfamily of nucleases involved in DNA recombination and repair [1]. Profile HMM analysis identified a relationship between this C-terminal domain of YhcG and Pfam:PF01939 , a family of NucS endonucleases [2]. YHcG was identified in association with DNA processing enzymes, including the restriction complexes HsdMRS and McrABC, the integrases IntF and IntS, and the recombinase PinE [1]. [1]. 19402753. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. Hu P, Janga SC, Babu M, Diaz-Mejia JJ, Butland G, Yang W, Pogoutse O, Guo X, Phanse S, Wong P, Chandran S, Christopoulos C, Nazarians-Armavil A, Nasseri NK, Musso G, Ali M, Nazemof N, Eroukova V, Golshani A, Paccanaro A, Greenblatt JF, Moreno-Hagelsieb G, Emili A;. PLoS Biol. 2009;7:e96. [2]. 16011798. The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function. Kosinski J, Feder M, Bujnicki JM;. BMC Bioinformatics. 2005;6:172. (from Pfam) NF018011.5 PF06252.17 GemA 27 27 119 domain Y Y N phage protein GemA/Gp16 family protein 11278077 131567 cellular organisms no rank 9065 EBI-EMBL Bacteriophage Mu, GemA protein phage protein GemA/Gp16 family protein This family consists of several bacterial and phage proteins, including GemA (also known as gp16) protein from Bacteriophage Mu. GemA is an early protein responsible for decreasing host DNA gyrase activity, that promotes DNA relaxation of bacterial host genome. Modulates the expression of various host genes probably controlled by supercoiling of their promoters. Host genes affected include DNA replication and cell division determinants [1]. This family also includes the Mu-like prophage FluMu protein gp16 from Haemophilus influenzae. [1]. 11278077. The GemA protein of phage Mu and the GyrB gyrase subunit of Escherichia coli: the search for targets and interactions leading to the reversion of Mu-induced mutations. Abbes C, Joseleau-Petit D, Liebart JC, D'Ari R, Sezonov G;. Biochimie. 2001;83:261-267. (from Pfam) NF018012.5 PF06253.16 MTTB 25 25 500 subfamily Y Y N trimethylamine methyltransferase family protein GO:0008168,GO:0015948 10762254,12125824 131567 cellular organisms no rank 15584 EBI-EMBL Trimethylamine methyltransferase (MTTB) trimethylamine methyltransferase family protein This family consists of several trimethylamine methyltransferase (MTTB) (EC:2.1.1.-) proteins from numerous Rhizobium and Methanosarcina species. [1]. 10762254. The trimethylamine methyltransferase gene and multiple dimethylamine methyltransferase genes of Methanosarcina barkeri contain in-frame and read-through amber codons. Paul L, Ferguson DJ Jr, Krzycki JA;. J Bacteriol 2000;182:2520-2529. [2]. 12125824. The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. Deppenmeier U, Johann A, Hartsch T, Merkl R, Schmitz RA, Martinez-Arias R, Henne A, Wiezer A, Baumer S, Jacobi C, Bruggemann H, Lienard T, Christmann A, Bomeke M, Steckel S, Bhattacharyya A, Lykidis A, Overbeek R, Klenk HP, Gunsalus RP, Fritz HJ, Gottscha. J Mol Microbiol Biotechnol 2002;4:453-461. (from Pfam) NF018018.5 PF06259.17 Abhydrolase_8 20.5 20.5 178 domain Y Y N alpha/beta hydrolase 15688435 131567 cellular organisms no rank 39957 EBI-EMBL Alpha/beta hydrolase alpha/beta hydrolase Members of this family are predicted to have an alpha/beta hydrolase fold. They contain a predicted Ser-His-Asp catalytic triad, in which the serine is likely to act as a nucleophile [1]. [1]. 15688435. Protein domain of unknown function DUF1023 is an alpha/beta hydrolase. Zheng M, Ginalski K, Rychlewski L, Grishin NV;. Proteins. 2005;59:1-6. (from Pfam) NF018024.5 PF06267.17 DUF1028 26.2 26.2 193 domain Y Y N DUF1028 domain-containing protein 131567 cellular organisms no rank 16192 EBI-EMBL Family of unknown function (DUF1028) Family of unknown function (DUF1028) Family of bacterial and archaeal proteins with unknown function. Some members are associated with a C-terminal peptidoglycan binding domain. So perhaps this could be an enzyme involved in peptidoglycan metabolism. (from Pfam) NF018028.5 PF06271.17 RDD 24.1 24.1 137 domain Y Y N RDD family protein 131567 cellular organisms no rank 130789 EBI-EMBL RDD family RDD family protein This family of proteins contain three highly conserved amino acids: one arginine and two aspartates, hence the name of RDD family. This region contains two predicted transmembrane regions. The arginine occurs at the N terminus of the first helix and the first aspartate occurs in the middle of this helix. The molecular function of this region is unknown. However this region may be involved in transport of an as yet unknown set of ligands (Bateman A pers. obs.). (from Pfam) NF018031.5 PF06276.17 FhuF 25.2 25.2 161 domain Y Y N IucA/IucC family C-terminal-domain containing protein 9990318 131567 cellular organisms no rank 89057 EBI-EMBL Ferric iron reductase FhuF-like transporter Ferric iron reductase FhuF-like transporter This family consists of several bacterial ferric iron reductase protein (FhuF) sequences. FhuF is involved in the reduction of ferric iron in cytoplasmic ferrioxamine B [1]. This family also includes the IucA and IucC proteins. [1]. 9990318. FhuF, an iron-regulated protein of Escherichia coli with a new type of [2Fe-2S] center. Muller K, Matzanke BF, Schunemann V, Trautwein AX, Hantke K;. Eur J Biochem 1998;258:1001-1008. (from Pfam) NF018032.5 PF06277.16 EutA 27 27 475 domain Y Y N ethanolamine ammonia-lyase reactivating factor EutA 10464203 131567 cellular organisms no rank 16178 EBI-EMBL Ethanolamine utilisation protein EutA ethanolamine ammonia-lyase reactivating factor EutA This family consists of several bacterial EutA ethanolamine utilisation proteins. The EutA protein is thought to protect the lyase (EutBC) from inhibition by CNB12 [1]. [1]. 10464203. The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. Kofoid E, Rappleye C, Stojiljkovic I, Roth J;. J Bacteriol 1999;181:5317-5329. (from Pfam) NF018037.5 PF06282.16 DUF1036 23 23 113 domain Y Y N DUF1036 domain-containing protein 131567 cellular organisms no rank 5385 EBI-EMBL Protein of unknown function (DUF1036) Protein of unknown function (DUF1036) This family consists of several hypothetical bacterial proteins of unknown function. (from Pfam) NF018038.5 PF06283.16 ThuA 33.4 33.4 209 domain Y Y N ThuA domain-containing protein 12003938,19086182,23772075 131567 cellular organisms no rank 64677 EBI-EMBL Trehalose utilisation Trehalose utilisation This family consists of several bacterial ThuA-like proteins. ThuA appears to be involved in utilisation of trehalose [1]. The thuA and thuB genes form part of the trehalose/sucrose transport operon thuEFGKAB, which is located on the pSymB megaplasmid. The thuA and thuB genes are induced in vitro by trehalose but not by sucrose and the extent of its induction depends on the concentration of trehalose available in the medium [2]. ThuA is involved in the conversion of of disaccharides to their respective 3-keto derivatives [3]. [1]. 12003938. Redundancy in periplasmic binding protein-dependent transport systems for trehalose, sucrose, and maltose in Sinorhizobium meliloti. Jensen JB, Peters NK, Bhuvaneswari TV;. J Bacteriol. 2002;184:2978-2986. [2]. 19086182. Lack of trehalose catabolism in Sinorhizobium species increases their nodulation competitiveness on certain host genotypes. Ampomah OY, Jensen JB, Bhuvaneswari TV;. New Phytol. 2008;179:495-504. [3]. 23772075. The thuEFGKAB operon of rhizobia and agrobacterium tumefaciens codes for transport of trehalose, maltitol, and isomers of sucrose and their assimilation through the formation of their 3-keto derivatives. Ampomah OY, Avetisyan A, Hansen E, Svenson J, Huser T, Jensen JB, Bhuvaneswari TV;. J Bacteriol. 2013;195:3797-3807. (from Pfam) NF018047.5 PF06293.19 Kdo 21.3 21.3 207 domain Y Y N lipopolysaccharide kinase InaA family protein 10531340,11069912,12021457 131567 cellular organisms no rank 88854 EBI-EMBL Lipopolysaccharide kinase (Kdo/WaaP) family lipopolysaccharide kinase InaA family protein These lipopolysaccharide kinases are related to protein kinases Pfam:PF00069. This family includes waaP (rfaP) gene product is required for the addition of phosphate to O-4 of the first heptose residue of the lipopolysaccharide (LPS) inner core region. It has previously been shown that WaaP is necessary for resistance to hydrophobic and polycationic antimicrobials in E. coli and that it is required for virulence in invasive strains of S. enterica [1]. [1]. 11069912. Purification and characterization of WaaP from Escherichia coli, a lipopolysaccharide kinase essential for outer membrane stability. Yethon JA, Whitfield C;. J Biol Chem 2001;276:5498-5504. [2]. 12021457. Lipopolysaccharide phosphorylating enzymes encoded in the genomes of Gram-negative bacteria are related to the eukaryotic protein kinases. Krupa A, Srinivasan N;. Protein Sci 2002;11:1580-1584. [3]. 10531340. A Haemophilus influenzae gene that encodes a membrane bound 3-deoxy-D-manno-octulosonic acid (Kdo) kinase. Possible involvement of kdo phosphorylation in bacterial virulence. White KA, Lin S, Cotter RJ, Raetz CR;. J Biol Chem 1999;274:31391-31400. (from Pfam) NF018053.5 PF06299.17 DUF1045 24.3 22.6 159 domain Y Y N DUF1045 domain-containing protein 131567 cellular organisms no rank 8513 EBI-EMBL Protein of unknown function (DUF1045) Protein of unknown function (DUF1045) This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown. (from Pfam) NF018054.5 PF06300.17 Tsp45I 25 25 260 PfamEq Y N N Tsp45I type II restriction enzyme 22638584,9427549 131567 cellular organisms no rank 483 EBI-EMBL Tsp45I type II restriction enzyme Tsp45I type II restriction enzyme This family consists of several type II restriction enzymes. [1]. 9427549. The Tsp45I restriction-modification system is plasmid-borne within its thermophilic host. Wayne J, Holden M, Xu SY;. Gene 1997;202:83-88. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF018062.5 PF06309.16 Torsin 27 27 127 PfamEq Y N N Torsin GO:0005524,GO:0016887 12554684 131567 cellular organisms no rank 365 EBI-EMBL Torsin Torsin This family consists of several eukaryotic torsin proteins. Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of (Pfam:PF00004) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [1]. [1]. 12554684. Suppression of polyglutamine-induced protein aggregation in Caenorhabditis elegans by torsin proteins. Caldwell GA, Cao S, Sexton EG, Gelwix CC, Bevel JP, Caldwell KA;. Hum Mol Genet 2003;12:307-319. (from Pfam) NF018066.5 PF06314.16 ADC 29.8 29.8 238 domain Y Y N acetoacetate decarboxylase family protein GO:0016829 2254264 131567 cellular organisms no rank 22622 EBI-EMBL Acetoacetate decarboxylase (ADC) acetoacetate decarboxylase family protein This family consists of several acetoacetate decarboxylase (ADC) proteins (EC:4.1.1.4). [1]. 2254264. Cloning, sequencing, and molecular analysis of the acetoacetate decarboxylase gene region from Clostridium acetobutylicum. Gerischer U, Durre P;. J Bacteriol 1990;172:6907-6918. (from Pfam) NF018076.5 PF06325.18 PrmA 22 22 296 domain Y Y N 50S ribosomal protein L11 methyltransferase 8226664 131567 cellular organisms no rank 380176 EBI-EMBL Ribosomal protein L11 methyltransferase (PrmA) 50S ribosomal protein L11 methyltransferase This family consists of several Ribosomal protein L11 methyltransferase (EC:2.1.1.-) sequences. [1]. 8226664. Cotranscription of two genes necessary for ribosomal protein L11 methylation (prmA) and pantothenate transport (panF) in Escherichia coli K-12. Vanet A, Plumbridge JA, Alix JH;. J Bacteriol 1993;175:7178-7188. (from Pfam) NF018088.5 PF06339.17 Ectoine_synth 27 27 127 domain Y Y N ectoine synthase GO:0019491,GO:0033990 11823218 131567 cellular organisms no rank 10618 EBI-EMBL Ectoine synthase ectoine synthase This family consists of several bacterial ectoine synthase proteins. The ectABC genes encode the diaminobutyric acid acetyltransferase (EctA), the diaminobutyric acid aminotransferase (EctB), and the ectoine synthase (EctC). Together these proteins constitute the ectoine biosynthetic pathway [1]. [1]. 11823218. Osmotically regulated synthesis of the compatible solute ectoine in Bacillus pasteurii and related Bacillus spp. Kuhlmann AU, Bremer E;. Appl Environ Microbiol 2002;68:772-783. (from Pfam) NF018091.5 PF06342.17 DUF1057 21 21 297 domain Y Y N alpha/beta hydrolase 131567 cellular organisms no rank 17398 EBI-EMBL Alpha/beta hydrolase of unknown function (DUF1057) alpha/beta hydrolase This family consists of several Caenorhabditis elegans specific proteins of unknown function. Members of this family have an alpha/beta hydrolase fold. (from Pfam) NF018095.5 PF06347.18 SH3_4 24.1 21.1 56 domain Y Y N SH3 domain-containing protein 11256992,14731533,15335710,1639195,16597942,7531822,7953536 131567 cellular organisms no rank 48044 EBI-EMBL Bacterial SH3 domain bacterial-type SH3 domain SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [1, 2]. They are found in a great variety of intracellular or membrane-associated proteins [3, 4, 5] for example, in a variety of proteins with enzymatic activity, in adaptor proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes [6]. This family consists of several hypothetical bacterial proteins of unknown function, but that contain an SH-3 region. Family members include probable invasion-associated protein p60 that are conceptually translated from iap genes. The iap gene, which is regarded as a virulence-associated gene in L. monocytogenes, codes for a gene product that has murein-lytic activity and is involved in cell division [7]. [1]. 15335710. SH2 and SH3. TRUNCATED at 1650 bytes (from Pfam) NF018096.5 PF06348.16 DUF1059 21.1 21.1 56 domain Y Y N DUF1059 domain-containing protein 131567 cellular organisms no rank 6008 EBI-EMBL Protein of unknown function (DUF1059) Protein of unknown function (DUF1059) This family consists of several short hypothetical archaeal proteins of unknown function. (from Pfam) NF018112.5 PF06368.16 Met_asp_mut_E 26.6 26.6 441 PfamEq Y N N Methylaspartate mutase E chain (MutE) GO:0019670,GO:0050097 8051138 131567 cellular organisms no rank 6388 EBI-EMBL Methylaspartate mutase E chain (MutE) Methylaspartate mutase E chain (MutE) This family consists of several methylaspartate mutase E chain proteins (EC:5.4.99.1). Glutamate mutase catalyses the first step in the fermentation of glutamate by Clostridium tetanomorphum. This is an unusual isomerisation in which L-glutamate is converted to threo-beta-methyl L-aspartate [1]. [1]. 8051138. Adenosylcobalamin-dependent glutamate mutase from Clostridium tetanomorphum. Overexpression in Escherichia coli, purification, and characterization of the recombinant enzyme. Holloway DE, Marsh EN;. J Biol Chem 1994;269:20425-20430. (from Pfam) NF018125.5 PF06381.16 Abc1-like 33.8 33.8 357 subfamily Y Y N anti-CBASS protein Acb1 family protein 35395152 131567 cellular organisms no rank 16539 EBI-EMBL Anti-CBASS protein Acb1-like phage portal protein This family includes Anti-CBASS protein Acb1 which which counteracts or regulates the endogenous CBASS (cyclic oligonucleotide-based antiphage signalling system) antiviral defense system. It is a phosphodiesterase that enables metal-independent hydrolysis of the cyclic di- and trinucleotide CBASS signals [1]. [1]. 35395152. Phage anti-CBASS and anti-Pycsar nucleases subvert bacterial immunity. Hobbs SJ, Wein T, Lu A, Morehouse BR, Schnabel J, Leavitt A, Yirmiya E, Sorek R, Kranzusch PJ;. Nature. 2022;605:522-526. (from Pfam) NF018129.5 PF06386.16 GvpL_GvpF 23.6 23.6 245 subfamily Y Y N GvpL/GvpF family gas vesicle protein GO:0031411,GO:0031412 15126480,9063646 131567 cellular organisms no rank 23849 EBI-EMBL Gas vesicle synthesis protein GvpL/GvpF GvpL/GvpF family gas vesicle protein This family consists of several bacterial and archaeal gas vesicle synthesis protein (GvpL/GvpF) sequences. The exact function of this family is unknown [1]. GvpL/GvpF qualify as possible candidates for nucleation proteins. Two hypothesized roles for these proteins are in initiation of gas vesicle synthesis and in determination of the curvature of the vesicle membrane [2]. [1]. 9063646. Genes encoding proteins homologous to halobacterial Gvps N, J, K, F & L are located downstream of gvpC in the cyanobacterium Anabaena flos-aquae. Kinsman R, Hayes PK;. DNA Seq 1997;7:97-106. [2]. 15126480. Complexity of gas vesicle biogenesis in Halobacterium sp. strain NRC-1: identification of five new proteins. Shukla HD, DasSarma S;. J Bacteriol. 2004;186:3182-3186. (from Pfam) NF018140.5 PF06397.17 Desulfoferrod_N 23 23 36 domain Y N N Desulfoferrodoxin, N-terminal domain GO:0005506 10422844 131567 cellular organisms no rank 3625 EBI-EMBL Desulfoferrodoxin, N-terminal domain Desulfoferrodoxin, N-terminal domain Most members of this family are small (approximately 36 amino acids) proteins that from homodimeric complexes. Each subunit contains a high-spin iron atom tetrahedrally bound to four cysteinyl sulphur atoms This family has a similar fold to the rubredoxin metal binding domain [1]. It is also found as the N-terminal domain of desulfoferrodoxin, see (Pfam:PF01880). [1]. 10422844. Structural studies by X-ray diffraction on metal substituted desulforedoxin, a rubredoxin-type protein. Archer M, Carvalho AL, Teixeira S, Moura I, Moura JJ, Rusnak F, Romao MJ;. Protein Sci 1999;8:1536-1545. (from Pfam) NF018154.5 PF06414.17 Zeta_toxin 22.3 22.3 199 domain Y Y N zeta toxin family protein GO:0005524,GO:0016301 12571357 131567 cellular organisms no rank 120898 EBI-EMBL Zeta toxin zeta toxin family protein This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid [1]. [1]. 12571357. Crystal structure of the plasmid maintenance system epsilon/zeta: functional mechanism of toxin zeta and inactivation by epsilon 2 zeta 2 complex formation. Meinhart A, Alonso JC, Strater N, Saenger W;. Proc Natl Acad Sci U S A 2003;100:1661-1666. (from Pfam) NF018155.5 PF06415.18 iPGM_N 27 27 217 PfamEq Y N N BPG-independent PGAM N-terminus (iPGM_N) GO:0004619,GO:0005737,GO:0006007,GO:0030145 10764795 131567 cellular organisms no rank 43826 EBI-EMBL BPG-independent PGAM N-terminus (iPGM_N) BPG-independent PGAM N-terminus (iPGM_N) This family represents the N-terminal region of the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (or phosphoglyceromutase or BPG-independent PGAM) protein (EC:5.4.2.1). The family is found in conjunction with Pfam:PF01676 (located in the C-terminal region of the protein). [1]. 10764795. Mechanism of catalysis of the cofactor-independent phosphoglycerate mutase from Bacillus stearothermophilus. Crystal structure of the complex with 2-phosphoglycerate. Jedrzejas MJ, Chander M, Setlow P, Krishnasamy G;. J Biol Chem 2000;275:23146-23153. (from Pfam) NF018158.5 PF06418.19 CTP_synth_N 26.1 26.1 265 PfamEq Y N N CTP synthase N-terminus GO:0003883,GO:0006221 12522217 131567 cellular organisms no rank 60398 EBI-EMBL CTP synthase N-terminus CTP synthase N-terminus This family consists of the N-terminal region of the CTP synthase protein (EC:6.3.4.2). This family is found in conjunction with Pfam:PF00117 located in the C-terminal region of the protein. CTP synthase catalyses the synthesis of CTP from UTP by amination of the pyrimidine ring at the 4-position [1]. [1]. 12522217. Thr-431 and Arg-433 are part of a conserved sequence motif of the glutamine amidotransferase domain of CTP synthases and are involved in GTP activation of the Lactococcus lactis enzyme. Willemoes M;. J Biol Chem 2003;278:9407-9411. (from Pfam) NF018165.5 PF06426.19 SATase_N 21 21 105 domain Y N N Serine acetyltransferase, N-terminal GO:0005737,GO:0006535,GO:0009001 3309158,7608200 131567 cellular organisms no rank 15870 EBI-EMBL Serine acetyltransferase, N-terminal Serine acetyltransferase, N-terminal The N-terminal domain of serine acetyltransferase has a sequence that is conserved in plants [2] and bacteria [1]. [1]. 3309158. L-cysteine biosynthesis in Escherichia coli: nucleotide sequence and expression of the serine acetyltransferase (cysE) gene from the wild-type and a cysteine-excreting mutant. Denk D, Bock A;. J Gen Microbiol 1987;133:515-525. [2]. 7608200. Molecular cloning and characterization of a plant serine acetyltransferase playing a regulatory role in cysteine biosynthesis from watermelon. Saito K, Yokoyama H, Noji M, Murakoshi I;. J Biol Chem 1995;270:16321-16326. (from Pfam) NF018173.5 PF06434.18 Aconitase_2_N 27 27 204 PfamEq Y N N Aconitate hydratase 2 N-terminus GO:0003994,GO:0006099 10585860 131567 cellular organisms no rank 27439 EBI-EMBL Aconitate hydratase 2 N-terminus Aconitate hydratase 2 N-terminus This family represents the N-terminal region of several bacterial Aconitate hydratase 2 proteins and is found in conjunction with Pfam:PF00330. [1]. 10585860. Biochemical and spectroscopic characterization of Escherichia coli aconitases (AcnA and AcnB). Jordan PA, Tang Y, Bradbury AJ, Thomson AJ, Guest JR;. Biochem J 1999;344:739-746. (from Pfam) NF018178.5 PF06439.17 3keto-disac_hyd 26.8 26.8 187 domain Y Y N family 16 glycoside hydrolase GO:0016787 33657378 131567 cellular organisms no rank 64891 EBI-EMBL 3-keto-disaccharide hydrolase family 16 glycoside hydrolase This family has structural similarity to an endo-1,3-1,4-beta glucanase belonging to glycoside hydrolase family 16. A member containing this domain, BT2157 from B. thetaiotaomicron [1], hydrolyses 3-ketotrehalose during trehalose degradation that proceeds through a 3-keto-glycoside intermediate. Other members containing this domain are involved in disaccharide catabolism with 3-ketoglycoside intermediates [1]. [1]. 33657378. Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments. Liu H, Shiver AL, Price MN, Carlson HK, Trotter VV, Chen Y, Escalante V, Ray J, Hern KE, Petzold CJ, Turnbaugh PJ, Huang KC, Arkin AP, Deutschbauer AM;. Cell Rep. 2021;34:108789. (from Pfam) NF018180.5 PF06441.17 EHN 22.8 22.8 107 domain Y Y N epoxide hydrolase N-terminal domain-containing protein 10548561 131567 cellular organisms no rank 43222 EBI-EMBL Epoxide hydrolase N terminus Epoxide hydrolase N terminus This family represents the N-terminal region of the eukaryotic epoxide hydrolase protein. Epoxide hydrolases (EC:3.3.2.3) comprise a group of functionally related enzymes that catalyse the addition of water to oxirane compounds (epoxides), thereby usually generating vicinal trans-diols. EHs have been found in all types of living organisms, including mammals, invertebrates, plants, fungi and bacteria. In animals, the major interest in EH is directed towards their detoxification capacity for epoxides since they are important safeguards against the cytotoxic and genotoxic potential of oxirane derivatives that are often reactive electrophiles because of the high tension of the three-membered ring system and the strong polarization of the C--O bonds. This is of significant relevance because epoxides are frequent intermediary metabolites which arise during the biotransformation of foreign compounds [1]. This family is often found in conjunction with Pfam:PF00561. [1]. 10548561. Cloning and molecular characterization of a soluble epoxide hydrolase from Aspergillus niger that is related to mammalian microsomal epoxide hydrolase. Arand M, Hemmer H, Durk H, Baratti J, Archelas A, Furstoss R, Oesch F;. Biochem J 1999;344:273-280. (from Pfam) NF018184.5 PF06445.20 GyrI-like 26 26 155 domain Y Y N GyrI-like domain-containing protein 10802742,11948793,15281131 131567 cellular organisms no rank 123115 EBI-EMBL GyrI-like small molecule binding domain GyrI-like small molecule binding domain This family contains the small molecule binding domain of a number of different bacterial transcription activators [1]. This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecule binding [3]. The GyrI superfamily includes a family of secreted forms that is found only in animals and the bacterial pathogen Leptospira [3]. [1]. 10802742. Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA. Kwon HJ, Bennik MH, Demple B, Ellenberger T;. Nat Struct Biol 2000;7:424-430. [2]. 11948793. Crystal structure of the Escherichia coli SbmC protein that protects cells from the DNA replication inhibitor microcin B17. Romanowski MJ, Gibney SA, Burley SK;. Proteins 2002;47:403-407. [3]. 15281131. The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies. Anantharaman V, Aravind L;. Proteins. 2004;56:795-807. (from Pfam) NF018188.5 PF06450.17 NhaB 27 27 515 domain Y N N Bacterial Na+/H+ antiporter B (NhaB) GO:0006814,GO:0015385,GO:0016020 12562793,9518558 131567 cellular organisms no rank 12405 EBI-EMBL Bacterial Na+/H+ antiporter B (NhaB) Bacterial Na+/H+ antiporter B (NhaB) This family consists of several bacterial Na+/H+ antiporter B (NhaB) proteins. The exact function of this family is unknown [1,2]. [1]. 9518558. Topological study of Vibrio alginolyticus NhaB Na+/H+ antiporter using gene fusions in Escherichia coli cells. Enomoto H, Unemoto T, Nishibuchi M, Padan E, Nakamura T;. Biochim Biophys Acta 1998;1370:77-86. [2]. 12562793. Roles of NhaA, NhaB, and NhaD Na+/H+ antiporters in survival of Vibrio cholerae in a saline environment. Herz K, Vimont S, Padan E, Berche P;. J Bacteriol 2003;185:1236-1244. (from Pfam) NF018190.5 PF06452.16 CBM9_1 23.4 23.4 185 domain Y Y N sugar-binding protein GO:0004553,GO:0016052,GO:0030246 11371186 131567 cellular organisms no rank 18813 EBI-EMBL Carbohydrate family 9 binding domain-like sugar-binding protein CBM9_1 is a C-terminal domain on bacterial xylanase proteins, and it is tandemly repeated in a number of family-members. The CBM9 module binds to amorphous and crystalline cellulose and a range of soluble di- and monosaccharides as well as to cello- and xylo- oligomers of different degrees of polymerisation. Comparison of the glucose and cellobiose complexes during crystallisation reveals surprising differences in binding of these two substrates by CBM9-2. Cellobiose was found to bind in a distinct orientation from glucose, while still maintaining optimal stacking and electrostatic interactions with the reducing end sugar [1]. [1]. 11371186. Crystal structures of the family 9 carbohydrate-binding module from Thermotoga maritima xylanase 10A in native and ligand-bound forms. Notenboom V, Boraston AB, Kilburn DG, Rose DR;. Biochemistry. 2001;40:6248-6256. (from Pfam) NF018193.5 PF06455.16 NADH5_C 28.2 28.2 181 PfamEq Y N N NADH dehydrogenase subunit 5 C-terminus GO:0008137,GO:0042773 131567 cellular organisms no rank 3222 EBI-EMBL NADH dehydrogenase subunit 5 C-terminus NADH dehydrogenase subunit 5 C-terminus This family represents the C-terminal region of several NADH dehydrogenase subunit 5 proteins and is found in conjunction with Pfam:PF00361 and Pfam:PF00662. (from Pfam) NF018201.5 PF06463.18 Mob_synth_C 37.4 37.4 128 domain Y N N Molybdenum Cofactor Synthesis C GO:0006777,GO:0051539,GO:1990140 131567 cellular organisms no rank 70716 EBI-EMBL Molybdenum Cofactor Synthesis C Molybdenum Cofactor Synthesis C This region contains two iron-sulphur (3Fe-4S) binding sites. Mutations in this region of Swiss:O14940 cause MOCOD (Molybdenum Co-Factor Deficiency) type A. (from Pfam) NF018205.5 PF06467.19 zf-FCS 22.4 22.4 40 domain Y N N MYM-type Zinc finger with FCS sequence motif GO:0008270 11689653,8817323,9576949,9694738,9716603 131567 cellular organisms no rank 818 EBI-EMBL MYM-type Zinc finger with FCS sequence motif MYM-type Zinc finger with FCS sequence motif MYM-type zinc fingers were identified in MYM family proteins [1]. Human protein Swiss:Q14202 is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 [2]. Swiss:Q9UBW7 is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 [3]; in atypical myeloproliferative disorders it is rearranged [4]. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons [5]. [1]. 9716603. Consistent fusion of ZNF198 to the fibroblast growth factor receptor-1 in the t(8;13)(p11;q12) myeloproliferative syndrome. Reiter A, Sohal J, Kulkarni S, Chase A, Macdonald DH, Aguiar RC, Goncalves C, Hernandez JM, Jennings BA, Goldman JM, Cross NC;. Blood 1998;92:1735-1742. [2]. 8817323. Cloning and characterization of DXS6673E, a candidate gene for X-linked mental retardation in Xq13.1. van der Maarel SM, Scholten IH, Huber I, Philippe C, Suijkerbuijk RF, Gilgenkrantz S, Kere J, Cremers FP, Ropers HH;. Hum Mol Genet 1996;5:887-897. [3]. 9576949. Fibroblast growth factor receptor 1 is fused to FIM in stem-cell myeloproliferative disorder with t(8;13). Popovici C, Adelaide J, Ollendorff V, Chaffanet M, Guasch G, Jacrot M, Leroux D, Birnbaum D, Pebusque MJ;. Proc Natl Acad Sci U S A 1998;95:5712-5717. [4]. 9694738. The t(8;13) atypical myeloproliferative disorder: further analysis of the ZNF198 gene and. TRUNCATED at 1650 bytes (from Pfam) NF018206.5 PF06468.18 Spond_N 24 24 194 domain Y N N Spondin_N 11287656 131567 cellular organisms no rank 3821 EBI-EMBL Spondin_N Spondin_N This conserved region is found at the in the N-terminal half of several Spondin proteins. Spondins are involved in patterning axonal growth trajectory through either inhibiting or promoting adhesion of embryonic nerve cells ([1]). [1]. 11287656. F-spondin is a contact-repellent molecule for embryonic motor neurons. Tzarfati-Majar V, Burstyn-Cohen T, Klar A;. Proc Natl Acad Sci U S A 2001;98:4722-4727. (from Pfam) NF018208.5 PF06470.18 SMC_hinge 22.5 22.5 116 domain Y N N SMC proteins Flexible Hinge Domain GO:0005515,GO:0005524,GO:0005694,GO:0051276 12411491 131567 cellular organisms no rank 65412 EBI-EMBL SMC proteins Flexible Hinge Domain SMC proteins Flexible Hinge Domain This family represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction ([1]). [1]. 12411491. Hinge-mediated dimerization of SMC protein is essential for its dynamic interaction with DNA. Hirano M, Hirano T;. EMBO J 2002;21:5733-5744. (from Pfam) NF018210.5 PF06472.20 ABC_membrane_2 24.4 24.4 269 domain Y N N ABC transporter transmembrane region 2 GO:0005524,GO:0016020,GO:0042626,GO:0055085,GO:0140359 1301993,8441467,8670886 131567 cellular organisms no rank 34402 EBI-EMBL ABC transporter transmembrane region 2 ABC transporter transmembrane region 2 This domain covers the transmembrane of a small family of ABC transporters and shares sequence similarity with Pfam:PF00664. Mutations in this domain in Swiss:P28288 are believed responsible for Zellweger Syndrome-2 [1]; mutations in Swiss:P33897 are responsible for recessive X-linked adrenoleukodystrophy [2]. A Saccharomyces cerevisiae homolog is involved in the import of long-chain fatty acids [3]. [1]. 1301993. Mutations in the 70K peroxisomal membrane protein gene in Zellweger syndrome. Gartner J, Moser H, Valle D;. Nat Genet 1992;1:16-23. [2]. 8441467. Putative X-linked adrenoleukodystrophy gene shares unexpected homology with ABC transporters. Mosser J, Douar AM, Sarde CO, Kioschis P, Feil R, Moser H, Poustka AM, Mandel JL, Aubourg P;. Nature 1993;361:726-730. [3]. 8670886. The ABC transporter proteins Pat1 and Pat2 are required for import of long-chain fatty acids into peroxisomes of Saccharomyces cerevisiae. Hettema EH, van Roermund CW, Distel B, van den Berg M, Vilela C, Rodrigues-Pousada C, Wanders RJ, Tabak HF;. EMBO J 1996;15:3813-3822. (from Pfam) NF018213.5 PF06475.16 Glycolipid_bind 25 25 180 PfamEq Y Y N putative glycolipid-binding domain-containing protein 20944213 131567 cellular organisms no rank 10319 EBI-EMBL Putative glycolipid-binding Putative glycolipid-binding This family has a novel fold known as a spiral beta-roll, consisting of a 15-stranded beta sheet wrapped around a single alpha helix. It forms dimers. It has some structural similarity to the E. coli lipoprotein localisation factors LolA, Swiss:P61316 and LolB, Swiss:P61320. Its structure suggests that it may have a role in glycolipid binding. Its genomic context supports a role in glycolipid metabolism [1]. [1]. 20944213. The structure of the first representative of Pfam family PF06475 reveals a new fold with possible involvement in glycolipid metabolism. Bakolitsa C, Kumar A, McMullan D, Krishna SS, Miller MD, Carlton D, Najmanovich R, Abdubek P, Astakhova T, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Feuerhelm J, Grant JC, Grzechnik SK, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:1211-1217. (from Pfam) NF018228.5 PF06490.16 FleQ 22 22 108 domain Y N N Flagellar regulatory protein FleQ 10629180,11673434,12218010,12618438 131567 cellular organisms no rank 17642 EBI-EMBL Flagellar regulatory protein FleQ Flagellar regulatory protein FleQ This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators that are involved in regulation of flagellar motility e.g. FleQ in Pseudomonas aeruginosa. It is clearly related to Pfam:PF00072, but lacks the conserved aspartate residue that undergoes phosphorylation in the classic two-component system response regulator (Pfam:PF00072). [1]. 12218010. FleQ, the major flagellar gene regulator in Pseudomonas aeruginosa, binds to enhancer sites located either upstream or atypically downstream of the RpoN binding site. Jyot J, Dasgupta N, Ramphal R;. J Bacteriol 2002;184:5251-5260. [2]. 11673434. Interaction of the antiactivator FleN with the transcriptional activator FleQ regulates flagellar number in Pseudomonas aeruginosa. Dasgupta N, Ramphal R;. J Bacteriol 2001;183:6636-6644. [3]. 10629180. fleN, a gene that regulates flagellar number in Pseudomonas aeruginosa. Dasgupta N, Arora SK, Ramphal R;. J Bacteriol 2000;182:357-364. [4]. 12618438. Domain Architectures of sigma(54)-Dependent Transcriptional Activators. Studholme DJ, Dixon R;. J Bacteriol 2003;185:1757-1767. (from Pfam) NF018234.5 PF06500.16 FrsA-like 22 22 414 domain Y Y N alpha/beta hydrolase 15310761,17275835,21623357,23452154,23932525,30951551 131567 cellular organisms no rank 25171 EBI-EMBL Esterase FrsA-like alpha/beta hydrolase The FrsA-like family includes FrsA, an esterase found to have the alpha/beta-hydrolase fold [1,2,3]. t also includes the hydrolytic polyketide shortening protein Ayg1 from fungi [4], 2,6-dihydropseudooxynicotine hydrolase from Paenarthrobacter nicotinovorans [5] and Fus2 from Gibberella species [6]. The enzyme 2,6-dihydroxy-pseudo-oxynicotine hydrolase is involved in the nicotine-degradation pathway of Arthrobacter nicotinovorans [5]. Fus2 is part of the gene cluster that mediates the biosynthesis of the mycotoxin fusarin C. Fus2 catalyses closure of the 2-pyrrolidone ring of the intermediate 20-hydroxy-prefusarin to form another intermediate, 20-hydroxy-fusarin, which is then oxidized by Fus8 [6]. [1]. 30951551. Purification and biochemical characterization of FrsA protein from Vibrio vulnificus as an esterase. Wang X, Li ZM, Li Q, Shi M, Bao L, Xu D, Li Z;. PLoS One. 2019;14:e0215084. [2]. 23452154. Computational, structural, and kinetic evidence that Vibrio vulnificus FrsA is not a cofactor-independent pyruvate decarboxylase. Kellett WF, Brunk E, Desai BJ, Fedorov AA, Almo SC, Gerlt JA, Rothlisberger U, Richards NG;. Biochemistry. 2013;52:1842-1844. [3]. 21623357. FrsA functions as a cofactor-independent decarboxylase to control metabolic flux. Lee KJ, Jeong CS, An YJ, Lee HJ, Park SJ, Seok YJ, Kim P, Lee JH, Lee KH, Cha SS;. Nat Chem Biol. 2011;7:434-436. [4]. 15310761. Hydrolytic polyketide shortening by ayg1p, a novel enzyme involved in fungal melanin biosynthesis. Fujii I, Yasuoka Y, Tsai HF, Chang YC, Kwon-Chung KJ, Ebizuka Y;. J Biol Chem. 2004;279:44613-44620. [5]. 17275835. Structure and action of a C-C bond cle. TRUNCATED at 1650 bytes (from Pfam) NF018239.5 PF06505.16 XylR_N 23 23 101 domain Y Y N XylR N-terminal domain-containing protein 131567 cellular organisms no rank 5826 EBI-EMBL Activator of aromatic catabolism Activator of aromatic catabolism This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators in several proteobacteria, including activators of phenol degradation such as XylR. It is found adjacent to Pfam:PF02830. (from Pfam) NF018242.5 PF06508.18 QueC 22 22 210 domain Y Y N 7-cyano-7-deazaguanine synthase 6.3.4.20 14660578,16199558,18491386,19354300 131567 cellular organisms no rank 75618 EBI-EMBL Queuosine biosynthesis protein QueC 7-cyano-7-deazaguanine synthase This family of proteins participate in the biosynthesis of 7-carboxy-7-deazaguanine. They catalyse the conversion of 7-deaza-7-carboxyguanine to preQ0 [1-3]. [1]. 14660578. Identification of four genes necessary for biosynthesis of the modified nucleoside queuosine. Reader JS, Metzgar D, Schimmel P, de Crecy-Lagard V;. J Biol Chem. 2004;279:6280-6285. [2]. 16199558. Genetic analysis identifies a function for the queC (ybaX) gene product at an initial step in the queuosine biosynthetic pathway in Escherichia coli. Gaur R, Varshney U;. J Bacteriol. 2005;187:6893-6901. [3]. 19354300. The deazapurine biosynthetic pathway revealed: in vitro enzymatic synthesis of PreQ(0) from guanosine 5'-triphosphate in four steps. McCarty RM, Somogyi A, Lin G, Jacobsen NE, Bandarian V;. Biochemistry. 2009;48:3847-3852. [4]. 18491386. Crystal structure of QueC from Bacillus subtilis: an enzyme involved in preQ1 biosynthesis. Cicmil N, Huang RH;. Proteins. 2008;72:1084-1088. (from Pfam) NF018243.5 PF06510.16 DUF1102 22.2 22.2 141 domain Y Y N DUF1102 domain-containing protein 131567 cellular organisms no rank 645 EBI-EMBL Protein of unknown function (DUF1102) Protein of unknown function (DUF1102) This family consists of several hypothetical archaeal proteins of unknown function. (from Pfam) NF018249.5 PF06516.16 NUP 27 27 313 domain Y N N Purine nucleoside permease (NUP) GO:0055085 9802205 131567 cellular organisms no rank 5088 EBI-EMBL Purine nucleoside permease (NUP) Purine nucleoside permease (NUP) This family consists of several purine nucleoside permease from both bacteria and fungi [1]. [1]. 9802205. Cloning of the Candida albicans nucleoside transporter by complementation of nucleoside transport-deficient Saccharomyces. Detke S;. Yeast 1998;14:1257-1265. (from Pfam) NF018257.5 PF06525.16 SoxE 21 21 149 domain Y Y N sulfocyanin-like copper-binding protein GO:0005507 11163357 131567 cellular organisms no rank 2331 EBI-EMBL Sulfocyanin (SoxE) domain sulfocyanin-like copper-binding domain This family consists of several archaeal sulfocyanin (or blue copper protein) sequences from a number of Sulfolobus species. [1]. 11163357. Sulfocyanin and subunit II, two copper proteins with novel features, provide new insight into the archaeal SoxM oxidase supercomplex. Komorowski L, Schafer G;. FEBS Lett 2001;487:351-355. (from Pfam) NF018279.5 PF06550.16 SPP 23.9 23.9 283 PfamEq Y Y N presenilin family intramembrane aspartyl protease 3.4.23.- GO:0004190 23254940 131567 cellular organisms no rank 979 EBI-EMBL Signal-peptide peptidase, presenilin aspartyl protease presenilin family intramembrane aspartyl protease Members of this family, found in the archaea but not in bacteria, show homology to presenilin and to signal-peptide peptidase (SPP). NF018281.5 PF06552.17 TOM20_plant 20.6 20.6 187 PfamEq Y N N Plant specific mitochondrial import receptor subunit TOM20 12691756 131567 cellular organisms no rank 638 EBI-EMBL Plant specific mitochondrial import receptor subunit TOM20 Plant specific mitochondrial import receptor subunit TOM20 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins. Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [1]. [1]. 12691756. Peptide library approach with a disulfide tether to refine the Tom20 recognition motif in mitochondrial presequences. Obita T, Muto T, Endo T, Kohda D;. J Mol Biol 2003;328:495-504. (from Pfam) NF018285.5 PF06557.16 DUF1122 25 25 176 PfamAutoEq Y Y N DUF1122 family protein 26243886 131567 cellular organisms no rank 107 EBI-EMBL Protein of unknown function (DUF1122) DUF1122 family protein This family consists of several hypothetical archaeal and bacterial proteins of unknown function, including Swiss:O67778 from Aquifex aeolicus. The structure of this protein has been solved [1] but its function remains unknown. Members of this family seem to have an acyl-CoA N-acyltransferase topology. [1]. 26243886. On the predictability of the orientation of protein domains joined by a spanning alpha-helical linker. Lai YT, Jiang L, Chen W, Yeates TO;. Protein Eng Des Sel. 2015;28:491-499. (from Pfam) NF018287.5 PF06559.16 DCD_N 21.4 21.4 164 PfamEq Y Y N 2'-deoxycytidine 5'-triphosphate deaminase domain-containing protein GO:0008829,GO:0009394 15539408 131567 cellular organisms no rank 19870 EBI-EMBL 2'-deoxycytidine 5'-triphosphate deaminase (DCD) N-terminal domain 2'-deoxycytidine 5'-triphosphate deaminase (DCD) N-terminal domain This entry includes several bacterial 2'-deoxycytidine 5'-triphosphate deaminase proteins (EC:3.5.4.13) (DCD) which consist of two dUTPase-like domains (PDBe:2r9q). This entry represents the N-terminal catalytic domain, which contains the active site residues Arg115 and Glu138, important for its activity [1]. [1]. 15539408. Structures of dCTP deaminase from Escherichia coli with bound substrate and product: reaction mechanism and determinants of mono- and bifunctionality for a family of enzymes. Johansson E, Fano M, Bynck JH, Neuhard J, Larsen S, Sigurskjold BW, Christensen U, Willemoes M;. J Biol Chem. 2005;280:3051-3059. (from Pfam) NF018288.5 PF06560.16 GPI 20.7 20.7 182 domain Y Y N glucose-6-phosphate isomerase family protein GO:0004347,GO:0005737,GO:0006094,GO:0006096 11533028 131567 cellular organisms no rank 4778 EBI-EMBL Glucose-6-phosphate isomerase (GPI) glucose-6-phosphate isomerase family protein This family consists of several bacterial and archaeal glucose-6-phosphate isomerase (GPI) proteins (EC:5.3.1.9). [1]. 11533028. The phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus is a unique glycolytic enzyme that belongs to the cupin superfamily. Verhees CH, Huynen MA, Ward DE, Schiltz E, de Vos WM, van der Oost J;. J Biol Chem 2001;276:40926-40932. (from Pfam) NF018290.5 PF06564.17 CBP_BcsQ 21.3 21.3 234 domain Y Y N cellulose synthase operon protein YhjQ/BcsQ 11260463 131567 cellular organisms no rank 156227 EBI-EMBL Cellulose biosynthesis protein BcsQ cellulose synthase operon protein YhjQ/BcsQ This is a family of bacterial proteins involved in cellulose biosynthesis. (Roemling U. and Galperin M.Y. "Bacterial cellulose biosynthesis. Diversity of operons and subunits" (manuscript in preparation)). A second component of the extracellular matrix of the multicellular morphotype (rdar) of Salmonella typhimurium and Escherichia coli is cellulose. The family does contain a P-loop sequence motif suggesting a nucleotide binding function, but this has not been confirmed. [1]. 11260463. The multicellular morphotypes of Salmonella typhimurium and Escherichia coli produce cellulose as the second component of the extracellular matrix. Zogaj X, Nimtz M, Rohde M, Bokranz W, Romling U;. Mol Microbiol 2001;39:1452-1463. (from Pfam) NF018299.5 PF06574.17 FAD_syn 27 27 158 PfamEq Y N N FAD synthetase GO:0003919 15468322,3023344 131567 cellular organisms no rank 73074 EBI-EMBL FAD synthetase FAD synthetase This family corresponds to the N terminal domain of the bifunctional enzyme riboflavin kinase / FAD synthetase. These enzymes have both ATP:riboflavin 5'-phospho transferase and ATP:FMN-adenylyltransferase activity [1]. They catalyse the 5'-phosphorylation of riboflavin to FMN and the adenylylation of FMN to FAD [1]. This domain is thought to have the flavin mononucleotide (FMN) adenylyltransferase activity [2]. [1]. 3023344. Purification and characterization of FAD synthetase from Brevibacterium ammoniagenes. Manstein DJ, Pai EF;. J Biol Chem 1986;261:16169-16173. [2]. 15468322. Crystal structure of flavin binding to FAD synthetase of Thermotoga maritima. Wang W, Kim R, Yokota H, Kim SH;. Proteins 2005;58:246-248. (from Pfam) NF018322.5 PF06597.16 Clostridium_P47 27 27 461 domain Y Y N TULIP family P47-like protein 9767710 131567 cellular organisms no rank 796 EBI-EMBL Clostridium P-47 protein TULIP family P47-like protein This family consists of several P-47 proteins from various Clostridium species as well as two related sequences from Pseudomonas putida. The function of this family is unknown. [1]. 9767710. Characterization of the genes encoding the botulinum neurotoxin complex in a strain of Clostridium botulinum producing type B and F neurotoxins. Santos-Buelga JA, Collins MD, East AK;. Curr Microbiol 1998;37:312-318. (from Pfam) NF018332.5 PF06609.18 TRI12 23.2 23.2 599 domain Y N N Fungal trichothecene efflux pump (TRI12) GO:0022857,GO:0055085 10485289 131567 cellular organisms no rank 197016 EBI-EMBL Fungal trichothecene efflux pump (TRI12) Fungal trichothecene efflux pump (TRI12) This family consists of several fungal specific trichothecene efflux pump proteins. Many of the genes involved in trichothecene toxin biosynthesis in Fusarium sporotrichioides are present within a gene cluster.It has been suggested that TRI12 may play a role in F. sporotrichioides self-protection against trichothecenes [1]. [1]. 10485289. TRI12, a trichothecene efflux pump from Fusarium sporotrichioides: gene isolation and expression in yeast. Alexander NJ, McCormick SP, Hohn TM;. Mol Gen Genet 1999;261:977-984. (from Pfam) NF018339.5 PF06616.16 BsuBI_PstI_RE 27 27 154 subfamily Y Y N BsuBI/PstI family type II restriction endonuclease GO:0000287,GO:0003677,GO:0009036,GO:0009307 1480472,22638584 131567 cellular organisms no rank 3217 EBI-EMBL BsuBI/PstI restriction endonuclease domain BsuBI/PstI family type II restriction endonuclease C-terminal domain This family represents the C-terminus of bacterial enzymes similar to type II restriction endonucleases BsuBI and PstI (EC:3.1.21.4). The enzymes of the BsuBI restriction/modification (R/M) system recognise the target sequence 5'CTGCAG and are functionally identical with those of the PstI R/M system [1]. [1]. 1480472. BsuBI--an isospecific restriction and modification system of PstI: characterization of the BsuBI genes and enzymes. Xu GL, Kapfer W, Walter J, Trautner TA;. Nucleic Acids Res 1992;20:6517-6523. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF018349.5 PF06626.17 DUF1152 27 27 295 domain Y Y N DUF1152 domain-containing protein 131567 cellular organisms no rank 5685 EBI-EMBL Protein of unknown function (DUF1152) Protein of unknown function (DUF1152) This family consists of several hypothetical archaeal proteins of unknown function. (from Pfam) NF018351.5 PF06628.17 Catalase-rel 30.1 30.1 65 domain Y Y N catalase-related domain-containing protein 11351128,15585332 131567 cellular organisms no rank 94760 EBI-EMBL Catalase-related immune-responsive Catalase-related immune-responsive This family represents a small conserved region within catalase enzymes (EC:1.11.1.6). All members also contain the Catalase family, Pfam:PF00199 domain. Catalase decomposes hydrogen peroxide into water and oxygen, serving to protect cells from its toxic effects [1]. This domain carries the immune-responsive amphipathic octa-peptide that is recognised by T cells [2]. [1]. 11351128. Mitochondrial catalase and oxidative injury. Bai J, Cederbaum AI;. Biol Signals Recept 2001;10:189-199. [2]. 15585332. Do Th1 or Th2 sequence motifs exist in proteins? Identification of amphipatic immunomodulatory domains in Helicobacter pylori catalase. Guy B, Krell T, Sanchez V, Kennel A, Manin C, Sodoyer R;. Immunol Lett. 2005;96:261-275. (from Pfam) NF018357.5 PF06634.17 DUF1156 24 24 73 domain Y Y N DUF1156 domain-containing protein 21348639 131567 cellular organisms no rank 5173 EBI-EMBL Protein of unknown function (DUF1156) Protein of unknown function (DUF1156) This family represents a conserved region within hypothetical prokaryotic and archaeal proteins of unknown function. Structural modelling suggests this domain may bind nucleic acids [1]. [1]. 21348639. Ab Initio Modeling Led Annotation Suggests Nucleic Acid Binding Function for Many DUFs. Rigden DJ;. OMICS 2011;0:0-0. (from Pfam) NF018378.5 PF06662.18 C5-epim_C 23.3 23.3 188 domain Y Y N D-glucuronyl C5-epimerase family protein 9346972 131567 cellular organisms no rank 2542 EBI-EMBL D-glucuronyl C5-epimerase C-terminus D-glucuronyl C5-epimerase family protein This family represents the C-terminus of D-glucuronyl C5-epimerase (EC:5.1.3.-). Glucuronyl C5-epimerases catalyse the conversion of D-glucuronic acid (GlcUA) to L-iduronic acid (IdceA) units during the biosynthesis of glycosaminoglycans [1]. [1]. 9346972. Biosynthesis of heparin/heparan sulfate. cDNA cloning and expression of D-glucuronyl C5-epimerase from bovine lung. Li J, Hagner-McWhirter A, Kjellen L, Palgi J, Jalkanen M, Lindahl U;. J Biol Chem 1997;272:28158-28163. (from Pfam) NF018390.5 PF06675.16 DUF1177 25 25 272 PfamAutoEq Y Y N DUF1177 family protein 131567 cellular organisms no rank 3535 EBI-EMBL Protein of unknown function (DUF1177) DUF1177 family protein This family consists of several hypothetical archaeal and and bacterial proteins of around 300 residues in length. The function of this family is unknown. (from Pfam) NF018392.5 PF06677.17 Auto_anti-p27 24.1 24.1 40 domain Y Y N Sjogren's syndrome/scleroderma autoantigen 1 family protein 9486406 131567 cellular organisms no rank 1291 EBI-EMBL Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) Sjogren's syndrome/scleroderma autoantigen 1 family protein This family consists of several Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) sequences. It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [1]. [1]. 9486406. cDNA cloning of a novel autoantigen targeted by a minor subset of anti-centromere antibodies. Muro Y, Yamada T, Himeno M, Sugimoto K;. Clin Exp Immunol 1998;111:372-376. (from Pfam) NF018394.5 PF06679.17 DUF1180 27.7 27.7 167 domain Y Y N membrane protein FAM174 family protein 29851555 131567 cellular organisms no rank 13 EBI-EMBL Membrane protein FAM174-like membrane protein FAM174 family protein This entry represents a group of animal membrane proteins, including human Membrane protein FAM174B, which is essential for Golgi structural integrity [1]. [1]. 29851555. Targeted protein unfolding uncovers a Golgi-specific transcriptional stress response. Serebrenik YV, Hellerschmied D, Toure M, Lopez-Giraldez F, Brookner D, Crews CM;. Mol Biol Cell. 2018;29:1284-1298. (from Pfam) NF018399.5 PF06684.16 AA_synth 27 27 175 domain Y Y N amino acid synthesis family protein 20944209 131567 cellular organisms no rank 10646 EBI-EMBL Amino acid synthesis amino acid synthesis family protein This family of proteins is structurally similar to proteins with the Bacillus chorismate mutase-like (BCM-like) fold. This structure, combined with its genomic context, suggest that it has a role in amino acid synthesis [1]. [1]. 20944209. Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism. Bakolitsa C, Kumar A, Jin KK, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Burra P, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Elias Y, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Johnson HA, Klock HE, Knuth MW, Kozbial P, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Nopakun A, Okach L, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:1182-1189. (from Pfam) NF018400.5 PF06685.16 DUF1186 22 22 247 PfamAutoEq Y Y N DUF1186 domain-containing protein 131567 cellular organisms no rank 1313 EBI-EMBL Protein of unknown function (DUF1186) Protein of unknown function (DUF1186) This family consists of several hypothetical bacterial proteins of around 250 residues in length and is found in several Chlamydia and Anabaena species. The function of this family is unknown. (from Pfam) NF018405.5 PF06690.16 HcgC 31.4 31.4 248 PfamAutoEq Y Y N SAM-dependent methyltransferase HcgC family protein 27391308,28682478 131567 cellular organisms no rank 207 EBI-EMBL FeGP cofactor biosynthesis protein, methyltransferase HcgC SAM-dependent methyltransferase HcgC family protein The iron guanylylpyridinol (FeGP) cofactor biosynthesis enzymes are encoded in a cluster of at least seven conserved genes (hcgA-G). This family represents the (SAM)-dependent methyltransferase HgcC [1,2], which covalently attaches the methyl group at the 3-position of the pyridinol ring. It is predominantly found as a monomer in solution, composed of a Rossmann-like coenzyme-binding-domain consisting of six parallel and one peripheral antiparallel strand flanked by six alpha-helices and a smaller alpha/beta domain [1]. Paper describing PDB structure 5d4t. [1]. 27391308. Identification of HcgC as a SAM-Dependent Pyridinol Methyltransferase in [Fe]-Hydrogenase Cofactor Biosynthesis. Fujishiro T, Bai L, Xu T, Xie X, Schick M, Kahnt J, Rother M, Hu X, Ermler U, Shima S;. Angew Chem Int Ed Engl. 2016;55:9648-9651. Paper describing PDB structure 5o4h. [2]. 28682478. A Water-Bridged H-Bonding Network Contributes to the Catalysis of the SAM-Dependent C-Methyltransferase HcgC. Bai L, Wagner T, Xu T, Hu X, Ermler U, Shima S;. Angew Chem Int Ed Engl. 2017;56:10806-10809. (from Pfam) NF018410.5 PF06695.16 Sm_multidrug_ex 30.7 30.7 121 domain Y Y N small multi-drug export protein 131567 cellular organisms no rank 5575 EBI-EMBL Putative small multi-drug export protein small multi-drug export protein This family contains a small number of putative small multi-drug export proteins. (from Pfam) NF018413.5 PF06698.16 DUF1192 25.5 25.5 58 PfamAutoEq Y Y N DUF1192 family protein 131567 cellular organisms no rank 4657 EBI-EMBL Protein of unknown function (DUF1192) DUF1192 family protein This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown. (from Pfam) NF018420.5 PF06707.16 DUF1194 27 27 206 domain Y Y N DUF1194 domain-containing protein 131567 cellular organisms no rank 11080 EBI-EMBL Protein of unknown function (DUF1194) Protein of unknown function (DUF1194) This family consists of several hypothetical Rhizobiales specific proteins of around 270 residues in length. The function of this family is unknown. (from Pfam) NF018425.5 PF06713.16 bPH_4 22.9 22.9 74 domain Y Y N PH domain-containing protein GO:0030153 19913036 131567 cellular organisms no rank 7115 EBI-EMBL Bacterial PH domain Bacterial PH domain This family consists of several hypothetical proteins specific to Oceanobacillus and Bacillus species. Members of this family are typically around 130 residues in length. The function of this family is unknown. Members of this family have a PH domain like structure [1]. [1]. 19913036. Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain. Xu Q, Bateman A, Finn RD, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. J Mol Biol. 2010 Feb 12;396(1):31-46. Epub 2009 Nov 10. (from Pfam) NF018434.5 PF06722.17 EryCIII-like_C 31.7 31.7 145 domain Y Y N nucleotide disphospho-sugar-binding domain-containing protein 22056329 131567 cellular organisms no rank 90767 EBI-EMBL Erythromycin biosynthesis protein CIII-like, C-terminal domain Erythromycin biosynthesis protein CIII-like, C-terminal domain This domain is found at the C-terminal of Erythromycin biosynthesis protein CIII (EryCIII) from Saccharopolyspora erythraea and similar proteins found in bacteria and eukaryotes. This protein is organised into two domains, both of them with a Rossmann-like alpha/beta fold. The C-terminal domain contains the nucleotide disphospho-sugar (NDP-sugar) binding site [1]. [1]. 22056329. Structure of the glycosyltransferase EryCIII in complex with its activating P450 homologue EryCII. Moncrieffe MC, Fernandez MJ, Spiteller D, Matsumura H, Gay NJ, Luisi BF, Leadlay PF;. J Mol Biol. 2012;415:92-101. (from Pfam) NF018435.5 PF06723.18 MreB_Mbl 27 27 327 domain Y Y N rod shape-determining protein 12758091 131567 cellular organisms no rank 203624 EBI-EMBL MreB/Mbl protein rod shape-determining protein This family consists of bacterial MreB and Mbl proteins as well as two related archaeal sequences. MreB is known to be a rod shape-determining protein in bacteria and goes to make up the bacterial cytoskeleton. Genes coding for MreB/Mbl are only found in elongated bacteria, not in coccoid forms. It has been speculated that constituents of the eukaryotic cytoskeleton (tubulin, actin) may have evolved from prokaryotic precursor proteins closely related to today's bacterial proteins FtsZ and MreB/Mbl [1]. [1]. 12758091. Cytoskeletons in prokaryotes. Mayer F;. Cell Biol Int 2003;27:429-438. (from Pfam) NF018437.5 PF06725.16 3D 23.8 23.8 72 domain Y Y N 3D domain-containing protein GO:0004553,GO:0009254,GO:0019867 16139297 131567 cellular organisms no rank 55569 EBI-EMBL 3D domain 3D (Asp-Asp-Asp) domain This short presumed domain contains three conserved aspartate residues, hence the name 3D. It has been shown to be part of the catalytic double psi beta barrel domain of MltA [1]. [1]. 16139297. Crystal structure of MltA from Escherichia coli reveals a unique lytic transglycosylase fold. van Straaten KE, Dijkstra BW, Vollmer W, Thunnissen AM;. J Mol Biol 2005;352:1068-1080. (from Pfam) NF018444.5 PF06733.20 DEAD_2 21 21 172 domain Y N N DEAD_2 GO:0003677,GO:0003678,GO:0005524 10915862 131567 cellular organisms no rank 41111 EBI-EMBL DEAD_2 DEAD_2 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [1]. [1]. 10915862. Nucleotide excision repair in yeast. Prakash S, Prakash L;. Mutat Res 2000;451:13-24. (from Pfam) NF018446.5 PF06736.16 TMEM175 25 25 88 domain Y Y N TMEM175 family protein GO:0005267,GO:0015252 26317472,28723891,32267231 131567 cellular organisms no rank 22949 EBI-EMBL Endosomal/lysosomal potassium channel TMEM175 TMEM175 family protein This family represents the conserved region of transmembrane protein 175 which is an organelle-specific potassium channel responsible for potassium conductance in endosomes and lysosomes. It forms a potassium-permeable leak-like channel, which regulates luminal pH stability and is required for autophagosome-lysosome fusion. TMEM175 is the major lysosomal potassium conductance [1,2]. It is present in eukaryotes, where TMEM175 has two repeats of 6-transmembrane-spanning segments, and also in prokaryotes in which it has one copy [1-3]. [1]. 26317472. TMEM175 Is an Organelle K(+) Channel Regulating Lysosomal Function. Cang C, Aranda K, Seo YJ, Gasnier B, Ren D;. Cell. 2015;162:1101-1112. [2]. 28723891. The lysosomal potassium channel TMEM175 adopts a novel tetrameric architecture. Lee C, Guo J, Zeng W, Kim S, She J, Cang C, Ren D, Jiang Y;. Nature. 2017;547:472-475. [3]. 32267231. Structural basis for ion selectivity in TMEM175 K(+) channels. Brunner JD, Jakob RP, Schulze T, Neldner Y, Moroni A, Thiel G, Maier T, Schenck S;. Elife. 2020; [Epub ahead of print] (from Pfam) NF018448.5 PF06738.17 ThrE 26.3 26.3 241 domain Y Y N threonine/serine exporter family protein GO:0022857,GO:0055085 12089010,12111147 131567 cellular organisms no rank 51813 EBI-EMBL Putative threonine/serine exporter threonine/serine exporter family protein ThrE is a family of bacterial and Archaeal proteins that catalyse the export of L-threonine from the cell [1]. UniProtKB:Q79VD1 has been characterised as being necessary for this export. The domain exhibits 10 putative TMs and catalyses the proton-motive-force-dependent efflux of threonine and serine [2]. [1]. 12089010. Identification of glyA (encoding serine hydroxymethyltransferase) and its use together with the exporter ThrE to increase L-threonine accumulation by Corynebacterium glutamicum. Simic P, Willuhn J, Sahm H, Eggeling L;. Appl Environ Microbiol. 2002;68:3321-3327. [2]. 12111147. Influence of threonine exporters on threonine production in Escherichia coli. Kruse D, Kramer R, Eggeling L, Rieping M, Pfefferle W, Tchieu JH, Chung YJ, Jr Saier MH, Burkovski A;. Appl Microbiol Biotechnol. 2002;59:205-210. (from Pfam) NF018449.5 PF06739.16 SBBP 20.5 20.5 38 domain Y Y N SBBP repeat-containing protein 131567 cellular organisms no rank 5747 EBI-EMBL Beta-propeller repeat Beta-propeller repeat This family is related to Pfam:PF00400 and is likely to also form a beta-propeller. SBBP stands for Seven Bladed Beta Propeller. (from Pfam) NF018452.5 PF06742.16 DUF1214 25 15 112 domain Y Y N DUF1214 domain-containing protein 131567 cellular organisms no rank 41447 EBI-EMBL Protein of unknown function (DUF1214) Protein of unknown function (DUF1214) This family represents the C-terminal region of several hypothetical proteins of unknown function. Family members are mostly bacterial, but a few are also found in eukaryotes and archaea. (from Pfam) NF018455.5 PF06745.18 ATPase 26.6 26.6 231 domain Y Y N ATPase domain-containing protein 10064581 131567 cellular organisms no rank 131137 EBI-EMBL KaiC KaiC This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and eukaryotes. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria [1]. [1]. 10064581. Physical interactions among circadian clock proteins KaiA, KaiB and KaiC in cyanobacteria. Iwasaki H, Taniguchi Y, Ishiura M, Kondo T;. EMBO J 1999;18:1137-1145. (from Pfam) NF018464.5 PF06754.17 PhnG 32.4 32.4 142 PfamEq Y Y N phosphonate C-P lyase system protein PhnG GO:0015716,GO:0019634 9882650 131567 cellular organisms no rank 11556 EBI-EMBL Phosphonate metabolism protein PhnG phosphonate C-P lyase system protein PhnG This family consists of several bacterial phosphonate metabolism protein PhnG sequences. In Escherichia coli, the phn operon encodes proteins responsible for the uptake and breakdown of phosphonates. The exact function of PhnG is unknown, however it is thought likely that along with six other proteins PhnG makes up the the C-P (carbon-phosphorus) lyase [1]. [1]. 9882650. Rhizobium (Sinorhizobium) meliloti phn genes: characterization and identification of their protein products. Parker GF, Higgins TP, Hawkes T, Robson RL;. J Bacteriol 1999;181:389-395. (from Pfam) NF018471.5 PF06762.19 LMF1 34.2 34.2 442 PfamEq Y Y N lipase maturation factor family protein GO:0051604 17994020,20543905,24909692 131567 cellular organisms no rank 10759 EBI-EMBL Lipase maturation factor lipase maturation factor family protein This family of transmembrane proteins includes the lipase maturation factor, LMF1. Lipoprotein lipase and hepatic lipase require LMF1 to fold into their active states [1]. It acts as a chaperone required for maturation and transport of active lipoprotein lipase (LPL), through the secretory pathway [2,3]. [1]. 17994020. Mutations in LMF1 cause combined lipase deficiency and severe hypertriglyceridemia. Peterfy M, Ben-Zeev O, Mao HZ, Weissglas-Volkov D, Aouizerat BE, Pullinger CR, Frost PH, Kane JP, Malloy MJ, Reue K, Pajukanta P, Doolittle MH;. Nat Genet. 2007;39:1483-1487. [2]. 20543905. Mechanisms of lipase maturation. Doolittle MH, Peterfy M;. Clin Lipidol. 2010;5:71-85. [3]. 24909692. Purification, cellular levels, and functional domains of lipase maturation factor 1. Babilonia-Rosa MA, Neher SB;. Biochem Biophys Res Commun. 2014;450:423-428. (from Pfam) NF018479.5 PF06772.16 LtrA 31.9 31.9 356 domain Y Y N low temperature requirement protein A 8534098 131567 cellular organisms no rank 40198 EBI-EMBL Bacterial low temperature requirement A protein (LtrA) low temperature requirement protein A This family consists of several bacteria specific low temperature requirement A (LtrA) protein sequences which have been found to be essential for growth at low temperatures in Listeria monocytogenes [1]. [1]. 8534098. Differentiation of epidemic-associated strains of Listeria monocytogenes by restriction fragment length polymorphism in a gene region essential for growth at low temperatures (4 degrees C). Zheng W, Kathariou S;. Appl Environ Microbiol 1995;61:4310-4314. (from Pfam) NF018483.5 PF06777.16 HBB 30 30 190 PfamEq Y N N Helical and beta-bridge domain 18578568 131567 cellular organisms no rank 1620 EBI-EMBL Helical and beta-bridge domain Helical and beta-bridge domain HBB is the domain on DEAD-box eukaryotic DNA repair helicases (EC:3.6.1.-) that appears to be a unique fold. It's conformation is of alpha-helices 12-16 plus a short beta-bridge to the FeS-cluster domain at the N-terminal. The full-length XPD protein verifies the presence of damage to DNA and allows DNA repair to proceed. XPD is an assembly of several domains to form a doughnut-shaped molecule that is able to separate two DNA strands and scan the DNA for damage. HBB helps to form the overall DNA-clamping architecture [1]. This family represents a conserved region within a number of eukaryotic DNA repair helicases (EC:3.6.1.-). [1]. 18578568. Crystal structure of the FeS cluster-containing nucleotide excision repair helicase XPD. Wolski SC, Kuper J, Hanzelmann P, Truglio JJ, Croteau DL, Van Houten B, Kisker C;. PLoS Biol. 2008;6:e149. (from Pfam) NF018484.5 PF06778.17 Chlor_dismutase 25 25 189 PfamEq Y Y N chlorite dismutase family protein GO:0016491,GO:0020037 8929278 131567 cellular organisms no rank 19032 EBI-EMBL Chlorite dismutase chlorite dismutase family protein This family contains chlorite dismutase enzymes of bacterial and archaeal origin. This enzyme catalyses the disproportionation of chlorite into chloride and oxygen [1]. Note that many family members are hypothetical proteins. [1]. 8929278. Purification and characterization of chlorite dismutase: a novel oxygen-generating enzyme. van Ginkel CG, Rikken GB, Kroon AG, Kengen SW;. Arch Microbiol 1996;166:321-326. (from Pfam) NF018485.5 PF06779.19 MFS_4 26.3 26.3 364 subfamily Y Y N YbfB/YjiJ family MFS transporter 131567 cellular organisms no rank 195340 EBI-EMBL Uncharacterised MFS-type transporter YbfB YbfB/YjiJ family MFS transporter This family represents putative bacterial membrane proteins which may be sugar transporters. Members carry twelve transmembrane regions which are characteristic of members of the major facilitator sugar-transporter superfamily. (from Pfam) NF018493.5 PF06787.16 HcgF 25 25 163 PfamEq Y Y N FeGP cofactor biosynthesis protein HcgF family protein 25882909 131567 cellular organisms no rank 205 EBI-EMBL FeGP cofactor biosynthesis protein HcgF FeGP cofactor biosynthesis protein HcgF family protein This archaeal family includes the iron guanylylpyridinol (FeGP) cofactor biosynthesis protein HcgF which catalyses the transesterification of AMP-GP to afford a Cys (HcgF)-S-GP thioester [1]. Paper describing PDB structure 3wva. [1]. 25882909. Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]-hydrogenase cofactor. Fujishiro T, Kahnt J, Ermler U, Shima S;. Nat Commun. 2015;6:6895. (from Pfam) NF018498.5 PF06792.16 UPF0261 27 27 402 domain Y Y N Tm-1-like ATP-binding domain-containing protein 131567 cellular organisms no rank 10626 EBI-EMBL Uncharacterised protein family (UPF0261) Uncharacterised protein family (UPF0261) NF018504.5 PF06798.17 PrkA 25 25 255 PfamEq Y N N PrkA serine protein kinase C-terminal domain 8626065 131567 cellular organisms no rank 15530 EBI-EMBL PrkA serine protein kinase C-terminal domain PrkA serine protein kinase C-terminal domain This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This family corresponds to the C-terminal domain [1]. [1]. 8626065. Cloning and characterization of the Bacillus subtilis prkA gene encoding a novel serine protein kinase. Fischer C, Geourjon C, Bourson C, Deutscher J;. Gene 1996;168:55-60. (from Pfam) NF018508.5 PF06803.17 DUF1232 23 23 37 domain Y Y N DUF1232 domain-containing protein 131567 cellular organisms no rank 35531 EBI-EMBL Protein of unknown function (DUF1232) Protein of unknown function (DUF1232) This family represents a conserved region of approximately 60 residues within a number of hypothetical bacterial and archaeal proteins of unknown function. (from Pfam) NF018513.5 PF06808.17 DctM 23.8 23.8 413 domain Y Y N TRAP transporter large permease subunit 11803016 131567 cellular organisms no rank 215443 EBI-EMBL Tripartite ATP-independent periplasmic transporter, DctM component TRAP transporter large permease subunit This family contains a diverse range of predicted transporter proteins. Including the DctM subunit of the bacterial and archaeal TRAP C4-dicarboxylate transport (Dct) system permease. In general, C4-dicarboxylate transport systems allow C4-dicarboxylates like succinate, fumarate, and malate to be taken up. TRAP C4-dicarboxylate carriers are secondary carriers that use an electrochemical H+ gradient as the driving force for transport. DctM is an integral membrane protein that is one of the constituents of TRAP carriers [1]. Note that many family members are hypothetical proteins. [1]. 11803016. C4-dicarboxylate carriers and sensors in bacteria. Janausch IG, Zientz E, Tran QH, Kroger A, Unden G;. Biochim Biophys Acta 2002;1553:39-56. (from Pfam) NF018515.5 PF06810.16 Phage_GP20 31 31 149 domain Y Y N phage scaffolding protein GO:0019069 131567 cellular organisms no rank 6403 EBI-EMBL Phage minor structural protein GP20 phage scaffolding protein This family consists of several phage minor structural protein GP20 sequences of around 180 residues in length. The function of this family is unknown. (from Pfam) NF018517.5 PF06813.18 Nodulin-like 24.7 24.7 250 PfamEq Y N N Nodulin-like 16698901 131567 cellular organisms no rank 686 EBI-EMBL Nodulin-like Nodulin-like This entry represents a conserved domain within plant nodulin-like proteins. Including this domain is the Arabidopsis thaliana protein NFD4 (Nuclear Fusion Defective 4). NFD4 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus [1]. [1]. 16698901. NUCLEAR FUSION DEFECTIVE1 encodes the Arabidopsis RPL21M protein and is required for karyogamy during female gametophyte development and fertilization. Portereiko MF, Sandaklie-Nikolova L, Lloyd A, Dever CA, Otsuga D, Drews GN;. Plant Physiol. 2006;141:957-965. (from Pfam) NF018523.5 PF06819.16 Arc_PepC 23.4 23.4 110 domain Y Y N A24 family peptidase C-terminal domain-containing protein 131567 cellular organisms no rank 216 EBI-EMBL Archaeal Peptidase A24 C-terminal Domain Archaeal Peptidase A24 C-terminal Domain This region is of unknown function but is found in some archaeal Pfam:PF01478. It is predicted to be of mixed alpha/beta secondary structure by JPred. (from Pfam) NF018525.5 PF06821.18 Ser_hydrolase 22 22 172 domain Y Y N alpha/beta hydrolase GO:0016787 15159570,19004028,20080647 131567 cellular organisms no rank 49362 EBI-EMBL Serine hydrolase alpha/beta hydrolase Members of this family have serine hydrolase activity. They contain a conserved serine hydrolase motif, GXSXG/A, where the serine is a putative nucleophile [1]. This family has an alpha-beta hydrolase fold [2,3]. Eukaryotic members of this family have a conserved LXCXE motif, which binds to retinoblastomas. This motif is absent from prokaryotic members of this family [3]. [1]. 20080647. RBBP9: a tumor-associated serine hydrolase activity required for pancreatic neoplasia. Shields DJ, Niessen S, Murphy EA, Mielgo A, Desgrosellier JS, Lau SK, Barnes LA, Lesperance J, Bouvet M, Tarin D, Cravatt BF, Cheresh DA;. Proc Natl Acad Sci U S A. 2010;107:2189-2194. [2]. 15159570. Harvesting the high-hanging fruit: the structure of the YdeN gene product from Bacillus subtilis at 1.8 angstroms resolution. Janda I, Devedjiev Y, Cooper D, Chruszcz M, Derewenda U, Gabrys A, Minor W, Joachimiak A, Derewenda ZS;. Acta Crystallogr D Biol Crystallogr 2004;60:1101-1107. [3]. 19004028. Crystal structure of human retinoblastoma binding protein 9. Vorobiev SM, Su M, Seetharaman J, Huang YJ, Chen CX, Maglaqui M, Janjua H, Proudfoot M, Yakunin A, Xiao R, Acton TB, Montelione GT, Tong L;. Proteins. 2009;74:526-529. (from Pfam) NF018530.5 PF06826.17 Asp-Al_Ex 27 27 167 domain Y N N Predicted Permease Membrane Region 12003930 131567 cellular organisms no rank 27586 EBI-EMBL Predicted Permease Membrane Region Predicted Permease Membrane Region This family represents five transmembrane helices that are normally found flanking (five either side) a pair of Pfam:PF02080 domains. This suggests that the paired regions form a ten helical structure, probably forming the pore, whereas the Pfam:PF02080) binds a ligand for export or regulation of the pore. Swiss:Q8L3K8 is described as a aspartate-alanine antiporter ([1]). In conjunction with Swiss:Q8L3K9 it forms a 'proton motive metabolic cycle catalysed by an aspartate-alanine exchange'. The general conservation of domain architecture in this family suggests that they are functional orthologues. [1]. 12003930. Plasmid-encoded asp operon confers a proton motive metabolic cycle catalyzed by an aspartate-alanine exchange reaction. Abe K, Ohnishi F, Yagi K, Nakajima T, Higuchi T, Sano M, Machida M, Sarker RI, Maloney PC;. J Bacteriol 2002;184:2906-2913. (from Pfam) NF018531.5 PF06827.19 zf-FPG_IleRS 21.3 21.3 30 domain Y Y N zinc finger domain-containing protein GO:0008270 131567 cellular organisms no rank 131587 EBI-EMBL Zinc finger found in FPG and IleRS Zinc finger found in FPG and IleRS This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:3.2.2.23. (from Pfam) NF018533.5 PF06831.19 H2TH 34.7 34.7 93 domain Y N N Formamidopyrimidine-DNA glycosylase H2TH domain GO:0003684,GO:0003906,GO:0006284,GO:0008270,GO:0016799 11912217 131567 cellular organisms no rank 114841 EBI-EMBL Formamidopyrimidine-DNA glycosylase H2TH domain Formamidopyrimidine-DNA glycosylase H2TH domain Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidised purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain [1]. [1]. 11912217. Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA. Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz E, Kycia JH, Grollman AP, Shoham G;. J Biol Chem 2002;277:19811-19816. (from Pfam) NF018540.5 PF06838.16 Met_gamma_lyase 24.2 24.2 405 domain Y Y N methionine gamma-lyase family protein 9190812,9488680 131567 cellular organisms no rank 29845 EBI-EMBL Methionine gamma-lyase methionine gamma-lyase family protein This is a putative pyridoxal 5'-phosphate-dependent methionine gamma-lyase enzyme involved in methionine catabolism. [1]. 9190812. Molecular characterization of the mde operon involved in L-methionine catabolism of Pseudomonas putida. Inoue H, Inagaki K, Eriguchi SI, Tamura T, Esaki N, Soda K, Tanaka H;. J Bacteriol. 1997;179:3956-3962. [2]. 9488680. The primitive protozoon Trichomonas vaginalis contains two methionine gamma-lyase genes that encode members of the gamma-family of pyridoxal 5'-phosphate-dependent enzymes. McKie AE, Edlind T, Walker J, Mottram JC, Coombs GH;. J Biol Chem. 1998;273:5549-5556. (from Pfam) NF018543.5 PF06841.17 Phage_T4_gp19 28.2 28.2 134 domain Y Y N phage tail protein GO:0005198 2403438,3363870 131567 cellular organisms no rank 17576 EBI-EMBL T4-like virus tail tube protein gp19 phage tail protein This family consists of several tail tube protein gp19 sequences from the T4-like viruses [1,2]. This family also contains bacterial members which suggest lateral transfer of genes. [1]. 3363870. The structure of three bacteriophage T4 genes required for tail-tube assembly. Ishimoto LK, Ishimoto KS, Cascino A, Cipollaro M, Eiserling FA;. Virology 1988;164:81-90. [2]. 2403438. Structure of the bacteriophage T4 baseplate as determined by chemical cross-linking. Watts NR, Coombs DH;. J Virol 1990;64:143-154. (from Pfam) NF018546.5 PF06847.16 Arc_PepC_II 29.9 29.9 93 domain Y Y N A24 family peptidase C-terminal domain-containing protein 131567 cellular organisms no rank 868 EBI-EMBL Archaeal Peptidase A24 C-terminus Type II Archaeal Peptidase A24 C-terminus Type II This region is of unknown function but is found in some archaeal Pfam:PF01478. It is predicted to be of mixed alpha/beta secondary structure by Prof. (from Pfam) NF018547.5 PF06848.16 Disaggr_repeat 33.9 33.9 179 domain Y Y N disaggregatase related repeat-containing protein 131567 cellular organisms no rank 544 EBI-EMBL Disaggregatase related repeat Disaggregatase related repeat This family consists of several repeats which seem to be specific to the Methanosarcina archaea species and are often found in multiple copies in disaggregatase proteins. Members of this family are also found in single copies in several hypothetical proteins. This repeat is also known as DNRLRE repeat and is predicted form a mainly beta-strand structure with two alpha-helices [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16]. It is found in some cell surface proteins. (from Pfam) NF018548.5 PF06849.17 DUF1246 25 25 122 domain Y Y N DUF1246 domain-containing protein GO:0000287,GO:0005524,GO:0006188,GO:0016879 131567 cellular organisms no rank 1055 EBI-EMBL Protein of unknown function (DUF1246) Protein of unknown function (DUF1246) This family represents the N-terminus of a number of hypothetical archaeal proteins of unknown function. This family is structurally related to the PreATP-grasp domain. (from Pfam) NF018549.5 PF06850.16 PHB_depo_C 27 27 203 domain Y N N PHB de-polymerase C-terminus 12813072 131567 cellular organisms no rank 18574 EBI-EMBL PHB de-polymerase C-terminus PHB de-polymerase C-terminus This family represents the C-terminus of bacterial poly(3-hydroxybutyrate) (PHB) de-polymerase. This degrades PHB granules to oligomers and monomers of 3-hydroxy-butyric acid. [1]. 12813072. Ralstonia eutropha H16 encodes two and possibly three intracellular Poly[D-(-)-3-hydroxybutyrate] depolymerase genes. York GM, Lupberger J, Tian J, Lawrence AG, Stubbe J, Sinskey AJ;. J Bacteriol 2003;185:3788-3794. (from Pfam) NF018561.5 PF06863.17 DUF1254 22.2 22.2 133 domain Y Y N DUF1254 domain-containing protein 131567 cellular organisms no rank 35792 EBI-EMBL Protein of unknown function (DUF1254) Protein of unknown function (DUF1254) This family represents a conserved region about 130 residues long within hypothetical proteins of unknown function. Family members include eukaryotic, bacterial and archaeal proteins. (from Pfam) NF018565.5 PF06868.16 DUF1257 22.2 22.2 103 domain Y Y N DUF1257 domain-containing protein 131567 cellular organisms no rank 2070 EBI-EMBL Protein of unknown function (DUF1257) Protein of unknown function (DUF1257) This family contains hypothetical proteins of unknown function that are approximately 120 residues long. Family members include eukaryotic and bacterial proteins. (from Pfam) NF018580.5 PF06884.16 DUF1264 25 25 171 PfamAutoEq Y Y N DUF1264 domain-containing protein 131567 cellular organisms no rank 3721 EBI-EMBL Protein of unknown function (DUF1264) Protein of unknown function (DUF1264) This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 200 residues long. Some family members are annotated as putative lipoproteins. (from Pfam) NF018583.5 PF06888.17 Put_Phosphatase 27 27 234 PfamEq Y N N Putative Phosphatase GO:0016791 11161030 131567 cellular organisms no rank 4869 EBI-EMBL Putative Phosphatase Putative Phosphatase This family contains a number of putative eukaryotic acid phosphatases. Some family members represent the products of the PSI14 phosphatase family in Lycopersicon esculentum (Tomato) [1]. [1]. 11161030. Leps2, a phosphorus starvation-induced novel acid phosphatase from tomato. Baldwin JC, Karthikeyan AS, Raghothama KG;. Plant Physiol 2001;125:728-737. (from Pfam) NF018584.5 PF06889.16 DUF1266 27 27 175 domain Y Y N DUF1266 domain-containing protein 131567 cellular organisms no rank 15830 EBI-EMBL Protein of unknown function (DUF1266) Protein of unknown function (DUF1266) This family consists of several hypothetical bacterial proteins of around 235 residues in length. Members of this family seem to be found exclusively in the Enterobacteria Salmonella typhimurium and Escherichia coli. The function of this family is unknown. (from Pfam) NF018590.5 PF06897.17 DUF1269 26.9 26.9 100 domain Y Y N DUF1269 domain-containing protein 131567 cellular organisms no rank 9143 EBI-EMBL Protein of unknown function (DUF1269) Protein of unknown function (DUF1269) This family consists of several bacterial and archaeal proteins of around 200 residues in length. The function of this family is unknown. The family carries a repeated glycine-zipper sequence- motif, GxxxGxxxG, where the x following the G is frequently found to be an alanine. As glycine-zippers occur in membrane proteins, this family is likely to be found spanning a membrane. (from Pfam) NF018595.5 PF06902.16 Fer4_19 24 24 64 domain Y Y N (4Fe-4S)-binding protein 131567 cellular organisms no rank 28090 EBI-EMBL Divergent 4Fe-4S mono-cluster (4Fe-4S)-binding protein Members of this family contain three highly conserved cysteine residues. This family includes proteins containing divergent domains which are most likely to bind to iron-sulfur clusters. (from Pfam) NF018599.5 PF06906.16 DUF1272 25.3 25.3 57 PfamAutoEq Y Y N DUF1272 domain-containing protein 131567 cellular organisms no rank 10150 EBI-EMBL Protein of unknown function (DUF1272) Protein of unknown function (DUF1272) This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown. (from Pfam) NF018604.5 PF06912.16 DUF1275 25.4 25.4 193 domain Y Y N DUF1275 family protein 131567 cellular organisms no rank 46506 EBI-EMBL Protein of unknown function (DUF1275) DUF1275 family protein This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown although most members have 6 TM regions, and may be putative permeases. (from Pfam) NF018621.5 PF06935.16 DUF1284 25 25 102 PfamAutoEq Y Y N DUF1284 domain-containing protein 131567 cellular organisms no rank 3948 EBI-EMBL Protein of unknown function (DUF1284) Protein of unknown function (DUF1284) This family consists of several hypothetical bacterial and archaeal proteins of around 130 residues in length. The function of this family is unknown, although it is thought that they may be iron-sulphur binding proteins. (from Pfam) NF018627.5 PF06941.17 NT5C 24.8 24.8 180 subfamily Y Y N 5' nucleotidase, NT5C type GO:0008253,GO:0009264 10681516,12234672 131567 cellular organisms no rank 9945 EBI-EMBL 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C) 5' nucleotidase, NT5C type This family consists of several 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C (NT5C) proteins. 5'(3')-Deoxyribonucleotidase is a ubiquitous enzyme in mammalian cells whose physiological function is not known [1]. [1]. 10681516. Mammalian 5'(3')-deoxyribonucleotidase, cDNA cloning, and overexpression of the enzyme in Escherichia coli and mammalian cells. Rampazzo C, Johansson M, Gallinaro L, Ferraro P, Hellman U, Karlsson A, Reichard P, Bianchi V;. J Biol Chem 2000;275:5409-5415. [2]. 12234672. Mouse cytosolic and mitochondrial deoxyribonucleotidases: cDNA cloning of the mitochondrial enzyme, gene structures, chromosomal mapping and comparison with the human orthologs. Rampazzo C, Kost-Alimova M, Ruzzenente B, Dumanski JP, Bianchi V;. Gene 2002;294:109-117. (from Pfam) NF018630.5 PF06945.18 DUF1289 27 27 47 domain Y Y N DUF1289 domain-containing protein 21348639 131567 cellular organisms no rank 31996 EBI-EMBL Protein of unknown function (DUF1289) Protein of unknown function (DUF1289) This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N-terminus. The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids [1]. [1]. 21348639. Ab Initio Modeling Led Annotation Suggests Nucleic Acid Binding Function for Many DUFs. Rigden DJ;. OMICS 2011;0:0-0. (from Pfam) NF018633.5 PF06949.16 DUF1292 24 24 75 domain Y Y N DUF1292 domain-containing protein 131567 cellular organisms no rank 12673 EBI-EMBL Protein of unknown function (DUF1292) Protein of unknown function (DUF1292) This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown. (from Pfam) NF018635.5 PF06951.16 PLA2G12 34 34 184 PfamEq Y N N Group XII secretory phospholipase A2 precursor (PLA2G12) GO:0004623,GO:0005509,GO:0005576,GO:0016042 11278438 131567 cellular organisms no rank 66 EBI-EMBL Group XII secretory phospholipase A2 precursor (PLA2G12) Group XII secretory phospholipase A2 precursor (PLA2G12) This family consists of several group XII secretory phospholipase A2 precursor (PLA2G12) (EC:3.1.1.4) proteins. Group XII and group V PLA(2)s are thought to participate in helper T cell immune response through release of immediate second signals and generation of downstream eicosanoids [1]. [1]. 11278438. A novel group of phospholipase A2s preferentially expressed in type 2 helper T cells. Ho IC, Arm JP, Bingham CO 3rd, Choi A, Austen KF, Glimcher LH;. J Biol Chem 2001;276:18321-18326. (from Pfam) NF018637.5 PF06953.16 ArsD 27 27 123 subfamily Y Y N arsenic metallochaperone ArsD family protein GO:0003677,GO:0045892,GO:0046685 11980902,17439954,21188475 131567 cellular organisms no rank 6373 EBI-EMBL Arsenical resistance operon protein ArsD arsenic metallochaperone ArsD family protein ArsD was initially reported to be a trans-acting repressor of the arsRDABC operon, which confers resistance to arsenicals and antimonials in Escherichia coli [1]. It has since been shown to be a metallochaperone that delivers As(III) to ArsA (the catalytic subunit of the ArsAB pump encoded by arsRDABC), increasing its affinity for As(III) allowing resistance to environmental concentrations of arsenic [2,3]. ArsD has three conserved cysteines Cys(12), Cys(13), and Cys(18), which form a three sulfur-coordinated As(III) binding site that is essential for delivery of As(III) to, and activation of the ArsAB pump [2,3]. This family also includes ArsD homologues which do not contain the conserved CCxxxxC required for function. [1]. 11980902. Evidence for cooperativity between the four binding sites of dimeric ArsD, an As(III)-responsive transcriptional regulator. Li S, Rosen BP, Borges-Walmsley MI, Walmsley AR;. J Biol Chem 2002;277:25992-26002. [2]. 17439954. ArsD residues Cys12, Cys13, and Cys18 form an As(III)-binding site required for arsenic metallochaperone activity. Lin YF, Yang J, Rosen BP;. J Biol Chem. 2007;282:16783-16791. [3]. 21188475. The ArsD As(III) metallochaperone. Ajees AA, Yang J, Rosen BP;. Biometals. 2011;24:391-399. (from Pfam) NF018644.5 PF06961.18 DUF1294 25 25 55 PfamAutoEq Y Y N DUF1294 domain-containing protein 131567 cellular organisms no rank 25522 EBI-EMBL Protein of unknown function (DUF1294) Protein of unknown function (DUF1294) This family includes a number of hypothetical bacterial and archaeal proteins of unknown function. (from Pfam) NF018647.5 PF06964.17 Alpha-L-AF_C 27 27 165 domain Y Y N alpha-L-arabinofuranosidase C-terminal domain-containing protein GO:0046373,GO:0046556 7887599 131567 cellular organisms no rank 41015 EBI-EMBL Alpha-L-arabinofuranosidase C-terminal domain Alpha-L-arabinofuranosidase C-terminal domain This family represents the C-terminus (approximately 200 residues) of bacterial and eukaryotic alpha-L-arabinofuranosidase (EC:3.2.1.55). This catalyses the hydrolysis of nonreducing terminal alpha-L-arabinofuranosidic linkages in L-arabinose-containing polysaccharides [1]. [1]. 7887599. Purification and characterization of alpha-L-arabinofuranosidase from Bacillus stearothermophilus T-6. Gilead S, Shoham Y;. Appl Environ Microbiol 1995;61:170-174. (from Pfam) NF018649.5 PF06966.17 DUF1295 20.4 20.4 235 domain Y Y N DUF1295 domain-containing protein 131567 cellular organisms no rank 29485 EBI-EMBL Protein of unknown function (DUF1295) Protein of unknown function (DUF1295) This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 300 residues long. (from Pfam) NF018651.5 PF06968.18 BATS 22.2 22.2 88 domain Y N N Biotin and Thiamin Synthesis associated domain 12482614,12650933 131567 cellular organisms no rank 74387 EBI-EMBL Biotin and Thiamin Synthesis associated domain Biotin and Thiamin Synthesis associated domain Biotin synthase (BioB), EC:2.8.1.6 , catalyses the last step of the biotin biosynthetic pathway. The reaction consists in the introduction of a sulphur atom into dethiobiotin. BioB functions as a homodimer [1]. Thiamin synthesis if a complex process involving at least six gene products (ThiFSGH, ThiI and ThiJ). Two of the proteins required for the biosynthesis of the thiazole moiety of thiamine (vitamin B(1)) are ThiG and ThiH (this family) and form a heterodimer[2]. Both of these reactions are thought of involve the binding of co-factors, and both function as dimers [1,2]. This domain therefore may be involved in co-factor binding or dimerisation (Finn, RD personal observation). [1]. 12482614. The PLP-dependent biotin synthase from Escherichia coli: mechanistic studies. Ollagnier-de-Choudens S, Mulliez E, Fontecave M;. FEBS Lett 2002;532:465-468. [2]. 12650933. Thiamine biosynthesis in Escherichia coli: isolation and initial characterisation of the ThiGH complex. Leonardi R, Fairhurst SA, Kriek M, Lowe DJ, Roach PL;. FEBS Lett 2003;539:95-99. (from Pfam) NF018652.5 PF06969.21 HemN_C 24 24 67 domain Y N N HemN C-terminal domain 12196143,14633981 131567 cellular organisms no rank 94632 EBI-EMBL HemN C-terminal domain HemN C-terminal domain Members of this family are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [1], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain (Pfam:PF04055) suggest it may be a substrate binding domain. [1]. 12196143. Terminal steps of haem biosynthesis. Dailey HA;. Biochem Soc Trans 2002;30:590-595. [2]. 14633981. Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes. Layer G, Moser J, Heinz DW, Jahn D, Schubert WD;. EMBO J. 2003;22:6214-6224. (from Pfam) NF018656.5 PF06973.17 DUF1297 23.8 23.8 188 domain Y Y N DUF1297 domain-containing protein GO:0000287,GO:0005524,GO:0006188,GO:0016879 131567 cellular organisms no rank 1077 EBI-EMBL Domain of unknown function (DUF1297) Domain of unknown function (DUF1297) This family represents the C-terminus (approximately 200 residues) of a number of archaeal proteins of unknown function. One member is annotated as being a possible carboligase enzyme. (from Pfam) NF018663.5 PF06983.18 3-dmu-9_3-mt 24 24 116 domain Y Y N VOC family protein 131567 cellular organisms no rank 69538 EBI-EMBL 3-demethylubiquinone-9 3-methyltransferase VOC family protein This family represents a conserved region approximately 100 residues long within a number of bacterial and archaeal 3-demethylubiquinone-9 3-methyltransferases (EC:2.1.1.64). Note that some family members contain more than one copy of this region, and that many members are hypothetical proteins. (from Pfam) NF018672.5 PF06993.17 DUF1304 26.9 26.9 110 PfamAutoEq Y Y N DUF1304 family protein 131567 cellular organisms no rank 21458 EBI-EMBL Protein of unknown function (DUF1304) DUF1304 family protein This family consists of several hypothetical bacterial proteins of around 120 residues in length. The function of this family is unknown. (from Pfam) NF018682.5 PF07005.16 SBD_N 25 22 230 domain Y Y N four-carbon acid sugar kinase family protein 27294475,27402745 131567 cellular organisms no rank 46051 EBI-EMBL Sugar-binding N-terminal domain Sugar-binding N-terminal domain This is the N-terminal domain found in proteins in a range of Proteobacteria as well as the Gram-positive Oceanobacillus iheyensis. Structural analysis of the whole protein indicates the N- and C-termini act together to produce a surface into which a threonate-ADP complex is bound, demonstrating that a sugar binding site is on the N-terminal domain, and a nucleotide binding site is in the C-terminal domain [1]. There is a critical motif, DDXTG, at approximately residues 22-25. Proteins containing this domain have been predicted as kinases. Some members are associated with PdxA2 by physical clustering and gene fusion with PdxA2. Some members that are fused with PdxA2 have been shown to be involved in L-4-hydroxythreonine (4HT) phosphorylation, part of the alternative pathway to make PLP (pyridoxal 5'-phosphate) out of a toxic metabolite, 4HT. However, 4HT phosphorylation might not be the main function of this group of proteins. Moreover, some members that are not associated with pdxA2, and even one that is associated with pdxA2, have lost 4HT kinase activity [2]. Functional analysis demonstrate that family members include D-Threonate kinases (DtnK), D-Erythronate kinases (DenK) and 3-Oxo-tetronate kinases (OtnK) [1]. [1]. 27402745. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Zhang X, Carter MS, Vetting MW, San Francisco B, Zhao S, Al-Obaidi NF, Solbiati JO, Thiaville JJ, de Crecy-Lagard V, Jacobson MP, Almo SC, Gerlt JA;. Proc Natl Acad Sci U S A. 2016;113:E4161-E4169. [2]. 27294475. Members of a Novel Kinase Family (DUF1537) Can Recycle Toxic. TRUNCATED at 1650 bytes (from Pfam) NF018691.5 PF07015.16 VirC1 24 24 231 domain Y N N VirC1 protein 2592351 131567 cellular organisms no rank 22859 EBI-EMBL VirC1 protein VirC1 protein This family consists of several bacterial VirC1 proteins. In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon which enhances T-DNA processing probably does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA [1]. [1]. 2592351. The Agrobacterium tumefaciens virC1 gene product binds to overdrive, a T-DNA transfer enhancer. Toro N, Datta A, Carmi OA, Young C, Prusti RK, Nester EW;. J Bacteriol 1989;171:6845-6849. (from Pfam) NF018696.5 PF07021.17 MetW 21 21 193 domain Y Y N methionine biosynthesis protein MetW 11479715 131567 cellular organisms no rank 139927 EBI-EMBL Methionine biosynthesis protein MetW methionine biosynthesis protein MetW This family consists of several bacterial and one archaeal methionine biosynthesis MetW proteins. Biosynthesis of methionine from homoserine in Pseudomonas putida takes place in three steps. The first step is the acylation of homoserine to yield an acyl-L-homoserine. This reaction is catalysed by the products of the metXW genes and is equivalent to the first step in enterobacteria, gram-positive bacteria and fungi, except that in these microorganisms the reaction is catalysed by a single polypeptide (the product of the metA gene in Escherichia coli and the met5 gene product in Neurospora crassa). In Pseudomonas putida, as in gram-positive bacteria and certain fungi, the second and third steps are a direct sulfhydrylation that converts the O-acyl-L-homoserine into homocysteine and further methylation to yield methionine. The latter reaction can be mediated by either of the two methionine synthetases present in the cells [1]. [1]. 11479715. The methionine biosynthetic pathway from homoserine in Pseudomonas putida involves the metW, metX, metZ, metH and metE gene products. Alaminos M, Ramos JL;. Arch Microbiol 2001;176:151-154. (from Pfam) NF018697.5 PF07022.18 Phage_CI_repr 22 22 65 domain Y Y N helix-turn-helix domain-containing protein GO:0003677,GO:0045892 2370665 131567 cellular organisms no rank 51545 EBI-EMBL Bacteriophage CI repressor helix-turn-helix domain Bacteriophage CI repressor helix-turn-helix domain This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [1]. [1]. 2370665. Control of gene expression in the temperate coliphage 186. VIII. Control of lysis and lysogeny by a transcriptional switch involving face-to-face promoters. Dodd IB, Kalionis B, Egan JB;. J Mol Biol 1990;214:27-37. (from Pfam) NF018704.5 PF07030.17 Phage_Mu_Gp36 24.7 24.7 124 domain Y Y N phage protein Gp36 family protein 131567 cellular organisms no rank 8335 EBI-EMBL Bacteriophage Mu, Gp36 phage protein Gp36 family protein This family is represented by the Bacteriophage Mu, Gp36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. (from Pfam) NF018712.5 PF07040.16 DUF1326 25 25 177 domain Y Y N DUF1326 domain-containing protein 131567 cellular organisms no rank 7117 EBI-EMBL Protein of unknown function (DUF1326) Protein of unknown function (DUF1326) This family consists of several hypothetical bacterial proteins which seem to be found exclusively in Rhizobium and Ralstonia species. Members of this family are typically around 210 residues in length and contain 5 highly conserved cysteine residues at their N-terminus. The function of this family is unknown. (from Pfam) NF018715.5 PF07043.18 DUF1328 27 27 39 subfamily Y Y N DUF1328 family protein GO:0005886 131567 cellular organisms no rank 12108 EBI-EMBL Protein of unknown function (DUF1328) DUF1328 family protein This family consists of several hypothetical bacterial proteins of around 50 residues in length. The function of this family is unknown. (from Pfam) NF018717.5 PF07045.16 DUF1330 23 23 94 domain Y Y N DUF1330 domain-containing protein 131567 cellular organisms no rank 37428 EBI-EMBL Domain of unknown function (DUF1330) Domain of unknown function (DUF1330) This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown. (from Pfam) NF018736.5 PF07068.16 Gp23 24.4 24.4 376 domain Y N N Major capsid protein Gp23 131567 cellular organisms no rank 170 EBI-EMBL Major capsid protein Gp23 Major capsid protein Gp23 This family contains a number of major capsid Gp23 proteins approximately 500 residues long, from T4-like bacteriophages. (from Pfam) NF018738.5 PF07070.16 Spo0M 23 23 213 domain Y Y N sporulation protein 9795118 131567 cellular organisms no rank 22460 EBI-EMBL SpoOM protein sporulation protein This family consists of several bacterial SpoOM proteins which are thought to control sporulation in Bacillus subtilis.Spo0M exerts certain negative effects on sporulation and its gene expression is controlled by sigmaH [1]. [1]. 9795118. A novel sporulation-control gene (spo0M) of Bacillus subtilis with a sigmaH-regulated promoter. Han WD, Kawamoto S, Hosoya Y, Fujita M, Sadaie Y, Suzuki K, Ohashi Y, Kawamura F, Ochi K;. Gene 1998;217:31-40. (from Pfam) NF018743.5 PF07075.16 NamZ_N 26.9 26.9 203 domain Y Y N exo-beta-N-acetylmuramidase NamZ domain-containing protein GO:0033922 33684445 131567 cellular organisms no rank 26325 EBI-EMBL Exo-beta-N-acetylmuramidase NamZ, N-terminal Exo-beta-N-acetylmuramidase NamZ, N-terminal NamZ is an exo-beta-N-acetylmuramidase which catalyzes an exo-lytic cleavage of beta-1,4-acetylmuramic acid from from the non-reducing ends of peptidoglycan chains [1] and it is a founding member of a new family of glycosidases (GH171). NamZ consists of a N-terminal catalytic domain with a Rossmann-like fold (represented in this entry) and a C-terminal auxiliary alpha/beta domain [1]. [1]. 33684445. The exo-beta-N-acetylmuramidase NamZ from Bacillus subtilis is the founding member of a family of exo-lytic peptidoglycan hexosaminidases. Muller M, Calvert M, Hottmann I, Kluj RM, Teufel T, Balbuchta K, Engelbrecht A, Selim KA, Xu Q, Borisova M, Titz A, Mayer C;. J Biol Chem. 2021;296:100519. (from Pfam) NF018745.5 PF07077.16 DUF1345 31.8 31.8 173 PfamAutoEq Y Y N DUF1345 domain-containing protein 131567 cellular organisms no rank 17553 EBI-EMBL Protein of unknown function (DUF1345) Protein of unknown function (DUF1345) This family consists of several hypothetical bacterial proteins of around 230 residues in length. The function of this family is unknown. (from Pfam) NF018748.5 PF07080.16 DUF1348 22.1 22.1 130 PfamAutoEq Y Y N DUF1348 family protein 131567 cellular organisms no rank 20474 EBI-EMBL Protein of unknown function (DUF1348) DUF1348 family protein This family consists of several highly conserved hypothetical proteins of around 150 residues in length. The function of this family is unknown. (from Pfam) NF018749.5 PF07081.17 DUF1349 32.4 32.4 179 domain Y Y N DUF1349 domain-containing protein 131567 cellular organisms no rank 23669 EBI-EMBL Protein of unknown function (DUF1349) Protein of unknown function (DUF1349) This family consists of several hypothetical bacterial proteins but contains one sequence (Swiss:P40893) from Saccharomyces cerevisiae. Members of this family are typically around 200 residues in length. The function of this family is unknown. (from Pfam) NF018753.5 PF07085.17 DRTGG 25.2 25.2 105 domain Y Y N DRTGG domain-containing protein 131567 cellular organisms no rank 41138 EBI-EMBL DRTGG domain DRTGG domain This presumed domain is about 120 amino acids in length. It is found associated with CBS domains Pfam:PF00571, as well as the CbiA domain Pfam:PF01656. The function of this domain is unknown. It is named the DRTGG domain after some of the most conserved residues. This domain may be very distantly related to a pair of CBS domains. There are no significant sequence similarities, but its length and association with CBS domains supports this idea (Bateman A, pers. obs.). (from Pfam) NF018756.5 PF07088.16 GvpD_P-loop 24 24 189 domain Y Y N gas vesicle protein GvpD P-loop domain-containing protein gvpD GO:0005524 11160801,12864859,17379705,25648404,31191505,8763925 131567 cellular organisms no rank 1064 EBI-EMBL GvpD gas vesicle protein, P-loop domain GvpD gas vesicle protein, P-loop domain This family consists of several archaeal GvpD gas vesicle regulatory proteins. GvpD is involved in the regulation of gas vesicle formation and functions as a repressor through the interaction and the breakdown induction of the transcriptional activator GvpE [1,2,3, 4,5]. This domain includes the P-loop and the basic region 1 (bR1, an arginine-rich region) which are essential for GvpD repressive function [3,4]. [1]. 8763925. Transcript analysis of the c-vac region and differential synthesis of the two regulatory gas vesicle proteins GvpD and GvpE in Halobacterium salinarium PHH4. Kruger K, Pfeifer F;. J Bacteriol 1996;178:4012-4019. [2]. 12864859. Regulation of the expression of gas vesicle genes in Haloferax mediterranei: interaction of the two regulatory proteins GvpD and GvpE. Zimmermann P, Pfeifer F;. Mol Microbiol 2003;49:783-794. [3]. 17379705. GvpD-induced breakdown of the transcriptional activator GvpE of halophilic archaea requires a functional p-loop and an arginine-rich region of GvpD. Scheuch S, Pfeifer F;. Microbiology (Reading). 2007;153:947-958. [4]. 11160801. A p-loop motif and two basic regions in the regulatory protein GvpD are important for the repression of gas vesicle formation in the archaeon Haloferax mediterranei. Pfeifer F, Zotzel J, Kurenbach B, Roder R, Zimmermann P;. Microbiology (Reading). 2001;147:63-73. [5]. 25648404. Haloarchaea and the formation of gas vesicles. Pfeifer F;. Life (Basel). 2015;5:385-402. [6]. 31191505. Improved GFP Variants to Study Gene Expression in Haloarchaea. Born J, Pfeifer F;. Front Microbiol. 2019;10:1200. (from Pfam) NF018757.5 PF07090.16 GATase1_like 27 27 247 domain Y Y N glutamine amidotransferase 17968677 131567 cellular organisms no rank 7571 EBI-EMBL Putative glutamine amidotransferase glutamine amidotransferase This family consists of several hypothetical bacterial proteins of around 250 residues in length. The function of this family is unknown. The structure of this cytoplasmic domain was solved by the Midwest Center for Structural Genomics (MCSG). The structure has been classified as part of the Class-I Glutamine amidotransferase superfamily owing to similarity with other known structures. The monomer combines with itself to form a hexamer, and this hexamer exposes a potential catalytic surface rich in Glu, Asp, Tyr, Ser.Trp and His residues [1]. [1]. 17968677. Novel hexamerization motif is discovered in a conserved cytoplasmic protein from Salmonella typhimurium. Petrova T, Cuff ME, Wu R, Kim Y, Holzle D, Joachimiak A;. J Struct Funct Genomics. 2007;8:19-25. (from Pfam) NF018767.5 PF07100.16 ASRT 25 25 119 subfamily Y Y N sensory rhodopsin transducer 12622809,19682383 131567 cellular organisms no rank 2337 EBI-EMBL Anabaena sensory rhodopsin transducer sensory rhodopsin transducer The family of bacterial Anabaena sensory rhodopsin transducers are likely to bind sugars or related metabolites. The entire protein is comprised of a single globular domain with an eight-stranded beta-sandwich fold. There are a few characteristics which define this beta-sandwich fold as being distinct from other so-named folds, and these are: 1) a well conserved tryptophan, usually following a polar residue, present at the start of the first strand; this tryptophan appears to be central to a hydrophobic interaction required to hold the two beta-sheets of the sandwich together, and 2) a nearly absolutely conserved asparagine located at the end of the second beta-strand, that hydrogen bonds with the backbone carbonyls of the residues 2 and 4 positions downstream from it, thereby stabilising the characteristic tight turn between strands 2 and 3 of the structure. [1]. 12622809. Demonstration of a sensory rhodopsin in eubacteria. Jung KH, Trivedi VD, Spudich JL;. Mol Microbiol. 2003;47:1513-1522. [2]. 19682383. The Anabaena sensory rhodopsin transducer defines a novel superfamily of prokaryotic small-molecule binding domains. De Souza RF, Iyer LM, Aravind L;. Biol Direct. 2009; [Epub ahead of print] (from Pfam) NF018773.5 PF07106.18 TBPIP 22.8 22.8 62 domain Y N N TBPIP/Hop2 winged helix domain 10806355,11447128,15192114,9345291,9708739 131567 cellular organisms no rank 503 EBI-EMBL TBPIP/Hop2 winged helix domain TBPIP/Hop2 winged helix domain This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [1]. TBPIP was found to be an activator that specifically stimulates the homologous pairing catalyzed by DMC1. Family members also include yeast homologous-pairing protein 2 (Hop2) and its homologues from animals and plants. They are required for proper homologous pairing and efficient cross-over and intragenic recombination during meiosis [2, 3, 4, 5]. [1]. 10806355. Molecular cloning and characterization of a human homologue of TBPIP, a BRCA1 locus-related gene. Ijichi H, Tanaka T, Nakamura T, Yagi H, Hakuba A, Sato M;. Gene 2000;248:99-107. [2]. 9708739. The meiosis-specific Hop2 protein of S. cerevisiae ensures synapsis between homologous chromosomes. Leu JY, Chua PR, Roeder GS;. Cell. 1998;94:375-386. [3]. 11447128. A novel meiosis-specific protein of fission yeast, Meu13p, promotes homologous pairing independently of homologous recombination. Nabeshima K, Kakihara Y, Hiraoka Y, Nojima H;. EMBO J. 2001;20:3871-3881. [4]. 15192114. Positive role of the mammalian TBPIP/HOP2 protein in DMC1-mediated homologous pairing. Enomoto R, Kinebuchi T, Sato M, Yagi H, Shibata T, Kurumizak. TRUNCATED at 1650 bytes (from Pfam) NF018777.5 PF07110.16 EthD 22 22 96 domain Y Y N EthD domain-containing protein GO:0016491 11673424 131567 cellular organisms no rank 16339 EBI-EMBL EthD domain EthD domain This family consists of several bacterial sequences which are related to the EthD protein of Rhodococcus ruber (Swiss:Q93EX2). In Rhodococcus ruber, EthD is thought to be involved in the degradation of ethyl tert-butyl ether (ETBE). EthD synthesis is induced by ETBE but it's exact function is unknown, it is however thought to be essential to the ETBE degradation system. [1]. 11673424. Cloning of a genetically unstable cytochrome P-450 gene cluster involved in degradation of the pollutant ethyl tert-butyl ether by Rhodococcus ruber. Chauvaux S, Chevalier F, Le Dantec C, Fayolle F, Miras I, Kunst F, Beguin P;. J Bacteriol 2001;183:6551-6557. (from Pfam) NF018783.5 PF07118.16 DUF1374 21 21 92 domain Y Y N DUF1374 domain-containing protein 131567 cellular organisms no rank 48 EBI-EMBL Protein of unknown function (DUF1374) Protein of unknown function (DUF1374) This family consists of several hypothetical Sulfolobus virus proteins of around 100 residues in length. The function of this family is unknown. (from Pfam) NF018805.5 PF07143.16 CrtC 22.5 22.5 168 domain Y Y N lipocalin-like domain-containing protein 20944205 131567 cellular organisms no rank 16621 EBI-EMBL CrtC N-terminal lipocalin domain CrtC N-terminal lipocalin domain This family contains the members of the old Pfam family DUF2006. Structural characterisation of family member Swiss:Q82US3 (from DUF2006 now merged into this family) has revealed a lipocalin-like fold with domain duplication. [1]. 20944205. Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism. Chiu HJ, Bakolitsa C, Skerra A, Lomize A, Carlton D, Miller MD, Krishna SS, Abdubek P, Astakhova T, Axelrod HL, Clayton T, Deller MC, Duan L, Feuerhelm J, Grant JC, Grzechnik SK, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Paulsen J, Reyes R, Rife CL, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:1153-1159. (from Pfam) NF018816.5 PF07155.17 ECF-ribofla_trS 26.7 26.7 172 domain Y Y N ECF transporter S component GO:0016020 17693491,20972419 131567 cellular organisms no rank 32573 EBI-EMBL ECF-type riboflavin transporter, S component ECF transporter S component This family is the substrate-binding component (S component) of the energy coupling-factor (ECF)-type riboflavin transporter. It is a transmembrane protein which binds riboflavin, and is responsible for riboflavin-uptake by cells [1,2]. [1]. 17693491. Characterization of riboflavin (vitamin B2) transport proteins from Bacillus subtilis and Corynebacterium glutamicum. Vogl C, Grill S, Schilling O, Stulke J, Mack M, Stolz J;. J Bacteriol. 2007;189:7367-7375. [2]. 20972419. Structure and mechanism of the S component of a bacterial ECF transporter. Zhang P, Wang J, Shi Y;. Nature. 2010;468:717-720. (from Pfam) NF018817.5 PF07156.19 Prenylcys_lyase 27 27 363 PfamEq Y N N Prenylcysteine lyase GO:0016670,GO:0030328 11716481,12186880 131567 cellular organisms no rank 34 EBI-EMBL Prenylcysteine lyase Prenylcysteine lyase This family contains prenylcysteine lyases (EC:1.8.3.5) that are approximately 500 residues long. Prenylcysteine lyase is a FAD-dependent thioether oxidase that degrades a variety of prenylcysteines, producing free cysteine, an isoprenoid aldehyde and hydrogen peroxide as products of the reaction [1]. It has been noted that this enzyme has considerable homology with ClP55, a 55 kDa protein that is associated with chloride ion pumps [2]. [1]. 12186880. Stereospecificity and kinetic mechanism of human prenylcysteine lyase, an unusual thioether oxidase. Digits JA, Pyun HJ, Coates RM, Casey PJ;. J Biol Chem 2002;277:41086-41093. [2]. 11716481. Molecular cloning and characterization of the Cl(-) pump-associated 55-kDa protein in rat brain. Kitagawa K, Yagyu K, Yamamoto A, Hattori N, Omori K, Zeng XT, Inagaki C;. Biochem Biophys Res Commun 2001;289:363-371. (from Pfam) NF018819.5 PF07158.16 MatC_N 23 23 149 domain Y N N Dicarboxylate carrier protein MatC N-terminus 9826185 131567 cellular organisms no rank 12792 EBI-EMBL Dicarboxylate carrier protein MatC N-terminus Dicarboxylate carrier protein MatC N-terminus This family represents the N-terminal region of the bacterial dicarboxylate carrier protein MatC. The MatC protein is an integral membrane protein that could function as a malonate carrier [1]. [1]. 9826185. A gene cluster encoding malonyl-CoA decarboxylase (MatA), malonyl-CoA synthetase (MatB) and a putative dicarboxylate carrier protein (MatC) in Rhizobium trifolii--cloning, sequencing, and expression of the enzymes in Escherichia coli. An JH, Kim YS;. Eur J Biochem 1998;257:395-402. (from Pfam) NF018822.5 PF07161.18 LppX_LprAFG 24 24 192 domain Y Y N LppX_LprAFG lipoprotein 12581360,14998516,15294983,16541102,16785538,9387238 131567 cellular organisms no rank 4904 EBI-EMBL LppX_LprAFG lipoprotein LppX_LprAFG lipoprotein This entry consists of several lipoproteins mainly from Mycobacterium species, collectively known as the LppX_ LprAFG family. Proteins in this entry include LprG, LppX, LprF and lprA [1, 2, 3, 4, 5, 6]. [1]. 9387238. A novel 27 kDa lipoprotein antigen from Mycobacterium bovis. Bigi F, Espitia C, Alito A, Zumarraga M, Romano MI, Cravero S, Cataldi A;. Microbiology. 1997;143:3599-3605. [2]. 14998516. The knockout of the lprG-Rv1410 operon produces strong attenuation of Mycobacterium tuberculosis. Bigi F, Gioffre A, Klepp L, Santangelo MP, Alito A, Caimi K, Meikle V, Zumarraga M, Taboga O, Romano MI, Cataldi A;. Microbes Infect. 2004;6:182-187. [3]. 15294983. Mycobacterium tuberculosis LprG (Rv1411c): a novel TLR-2 ligand that inhibits human macrophage class II MHC antigen processing. Gehring AJ, Dobos KM, Belisle JT, Harding CV, Boom WH;. J Immunol. 2004;173:2660-2668. [4]. 16541102. LppX is a lipoprotein required for the translocation of phthiocerol dimycocerosates to the surface of Mycobacterium tuberculosis. Sulzenbacher G, Canaan S, Bordat Y, Neyrolles O, Stadthagen G, Roig-Zamboni V, Rauzier J, Maurin D, Laval F, Daffe M, Cambillau C, Gicquel B, Bourne Y, Jackson M;. EMBO J. 2006;25:1436-1444. [5]. 12581360. Interaction of the sensor module of Mycobacterium tuberculosis H37Rv KdpD with members of the Lpr family. Steyn AJ, Joseph J, Bloom BR;. Mol Microbiol. 2003;47:1075-1089. [6]. 16785538. Mycobacterium tuberculosis LprA is a lipoprotein agonist of TLR2 that regulates innate immunity and APC function. Pecora ND, Gehring AJ, Canaday DH, Boom WH, Harding CV;. J Immunol. 2006;177:422-429. (from Pfam) NF018827.5 PF07167.18 PhaC_N 23.7 23.7 173 domain Y N N Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus GO:0042619 10427049 131567 cellular organisms no rank 34332 EBI-EMBL Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus This family represents the N-terminal region of the bacterial poly-beta-hydroxybutyrate polymerase (PhaC). Polyhydroxyalkanoic acids (PHAs) are carbon and energy reserve polymers produced in some bacteria when carbon sources are plentiful and another nutrient, such as nitrogen, phosphate, oxygen, or sulfur, becomes limiting. PHAs composed of monomeric units ranging from 3 to 14 carbons exist in nature. When the carbon source is exhausted, PHA is utilised by the bacterium. PhaC links D-(-)-3-hydroxybutyrl-CoA to an existing PHA molecule by the formation of an ester bond [1]. This family appears to be a partial segment of an alpha/beta hydrolase domain. [1]. 10427049. Cloning, molecular analysis, and expression of the polyhydroxyalkanoic acid synthase (phaC) gene from Chromobacterium violaceum. Kolibachuk D, Miller A, Dennis D;. Appl Environ Microbiol 1999;65:3561-3565. (from Pfam) NF018829.5 PF07171.17 MlrC_C 27.2 27.2 178 domain Y Y N MlrC C-terminal domain-containing protein 17640697,36136540 131567 cellular organisms no rank 22383 EBI-EMBL MlrC C-terminus MlrC C-terminus This family represents the C-terminus (approximately 200 residues) of the product of a bacterial gene cluster that is involved in the degradation of the cyanobacterial toxin microcystin LR. Many members of this family are hypothetical proteins. (from Pfam) NF018837.5 PF07179.17 SseB 21 21 124 domain Y Y N SseB family protein 12724372,7982894 131567 cellular organisms no rank 43815 EBI-EMBL SseB protein N-terminal domain SseB protein N-terminal domain This family consists of several SseB proteins which appear to be found exclusively in Enterobacteria. SseB is known to enhance serine-sensitivity in Escherichia coli [1] and is part of the Salmonella pathogenicity island 2 (SPI-2) translocon [2]. This entry contains the presumed N-terminal domain of SseB. [1]. 7982894. Enhancement of serine-sensitivity by a gene encoding rhodanese-like protein in Escherichia coli. Hama H, Kayahara T, Ogawa W, Tsuda M, Tsuchiya T;. J Biochem (Tokyo) 1994;115:1135-1140. [2]. 12724372. SseA is a chaperone for the SseB and SseD translocon components of the Salmonella pathogenicity-island-2-encoded type III secretion system. Ruiz-Albert J, Mundy R, Yu XJ, Beuzon CR, Holden DW;. Microbiology 2003;149:1103-1111. (from Pfam) NF018843.5 PF07185.16 DUF1404 29.4 29.4 169 domain Y Y N DUF1404 family protein 131567 cellular organisms no rank 217 EBI-EMBL Protein of unknown function (DUF1404) DUF1404 family protein This family consists of several archaeal proteins of around 180 residues in length. Members of this family seem to be found exclusively in Sulfolobus tokodaii and Sulfolobus solfataricus. The function of this family is unknown. (from Pfam) NF018844.5 PF07187.16 DUF1405 25 25 160 PfamAutoEq Y Y N DUF1405 domain-containing protein 131567 cellular organisms no rank 6433 EBI-EMBL Protein of unknown function (DUF1405) Protein of unknown function (DUF1405) This family consists of several bacterial and related archaeal protein of around 180 residues in length. The function of this family is unknown. (from Pfam) NF018851.5 PF07194.16 P2 23 23 81 domain Y N N P2 response regulator binding domain GO:0000155,GO:0000160,GO:0004673 10564504 131567 cellular organisms no rank 10799 EBI-EMBL P2 response regulator binding domain P2 response regulator binding domain The response regulators for CheA bind to the P2 domain, which is found between Pfam:PF01627 and Pfam:PF02895 as either one or two copies. Highly flexible linkers connect P2 to the rest of CheA and impart remarkable mobility to the P2 domain. This feature is thought to enhance the inter CheA dimer phosphotransfer reactions within the signalling complex, thereby amplifying the phosphorylation signal [1]. [1]. 10564504. Histidine kinases: diversity of domain organization. Dutta R, Qin L, Inouye M;. Mol Microbiol 1999;34:633-640. (from Pfam) NF018852.5 PF07195.17 FliD_C 25.4 25.4 236 equivalog_domain Y Y N flagellar filament capping protein FliD fliD GO:0007155,GO:0009288 11230454,8195064,9488388 131567 cellular organisms no rank 44845 EBI-EMBL Flagellar hook-associated protein 2 C-terminus flagellar filament capping protein FliD The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria [2]. This alignment covers the C-terminal region of this family of proteins. [1]. 8195064. The Bacillus subtilis sigma D-dependent operon encoding the flagellar proteins FliD, FliS, and FliT. Chen L, Helmann JD;. J Bacteriol 1994;176:3093-3101. [2]. 9488388. The Pseudomonas aeruginosa flagellar cap protein, FliD, is responsible for mucin adhesion. Arora SK, Ritchings BW, Almira EC, Lory S, Ramphal R;. Infect Immun 1998;66:1000-1007. [3]. 11230454. Molecular characterization of fliD gene encoding flagellar cap and its expression among Clostridium difficile isolates from different serogroups. Tasteyre A, Karjalainen T, Avesani V, Delmee M, Collignon A, Bourlioux P, Barc MC;. J Clin Microbiol 2001;39:1178-1183. (from Pfam) NF018856.5 PF07199.16 DUF1411 22.3 22.3 194 PfamAutoEq Y Y N DUF1411 domain-containing protein 131567 cellular organisms no rank 14 EBI-EMBL Protein of unknown function (DUF1411) Protein of unknown function (DUF1411) This entry represents a domain approximately 150 residues long that is sometimes repeated within some Babesia bovis proteins of unknown function. (from Pfam) NF018867.5 PF07210.17 DUF1416 23 22.1 97 domain Y Y N DUF1416 domain-containing protein 131567 cellular organisms no rank 11615 EBI-EMBL Protein of unknown function (DUF1416) Protein of unknown function (DUF1416) This family consists of several hypothetical bacterial proteins of around 100 residues in length. Members of this family appear to be Actinomycete specific. The function of this family is unknown. (from Pfam) NF018877.5 PF07221.16 GlcNAc_2-epim 23.4 23.4 347 domain Y Y N AGE family epimerase/isomerase GO:0016853 131567 cellular organisms no rank 37822 EBI-EMBL N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) AGE family epimerase/isomerase This family contains a number of eukaryotic and bacterial N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) enzymes (EC:5.1.3.8) approximately 500 residues long. This converts N-acyl-D-glucosamine to N-acyl-D-mannosamine. (from Pfam) NF018880.5 PF07224.16 Chlorophyllase 20.7 20.7 307 domain Y N N Chlorophyllase GO:0015996,GO:0047746 10611389,12552153 131567 cellular organisms no rank 24697 EBI-EMBL Chlorophyllase Chlorophyllase This family consists of several plant specific Chlorophyllase proteins (EC:3.1.1.14). Chlorophyllase (Chlase) is the first enzyme involved in chlorophyll (Chl) degradation and catalyses the hydrolysis of ester bond to yield chlorophyllide and phytol [1]. [1]. 10611389. Cloning of chlorophyllase, the key enzyme in chlorophyll degradation: finding of a lipase motif and the induction by methyl jasmonate. Tsuchiya T, Ohta H, Okawa K, Iwamatsu A, Shimada H, Masuda T, Takamiya K;. Proc Natl Acad Sci U S A 1999;96:15362-15367. [2]. 12552153. Chlorophyllase as a serine hydrolase: identification of a putative catalytic triad. Tsuchiya T, Suzuki T, Yamada T, Shimada H, Masuda T, Ohta H, Takamiya K;. Plant Cell Physiol 2003;44:96-101. (from Pfam) NF018884.5 PF07228.17 SpoIIE 25 25 192 domain Y Y N SpoIIE family protein phosphatase GO:0016791 8830262 131567 cellular organisms no rank 428993 EBI-EMBL Stage II sporulation protein E (SpoIIE) SpoIIE family protein phosphatase This family contains a number of bacterial stage II sporulation E proteins (EC:3.1.3.16). These are required for formation of a normal polar septum during sporulation. The N-terminal region is hydrophobic and is expected to contain up to 12 membrane-spanning segments [1]. [1]. 8830262. Structure and function of the Bacillus SpoIIE protein and its localization to sites of sporulation septum assembly. Barak I, Behari J, Olmedo G, Guzman P, Brown DP, Castro E, Walker D, Westpheling J, Youngman P;. Mol Microbiol 1996;19:1047-1060. (from Pfam) NF018886.5 PF07230.16 Portal_Gp20 22.9 22.9 433 subfamily Y Y N portal protein 8918937 131567 cellular organisms no rank 207 EBI-EMBL Bacteriophage T4-like portal protein (Gp20) T4-type portal protein Members of this family include the well-studied gp20 (AAD42425.1) of bacteriophage T4, which structural work shows to be a portal protein. Note that this functional assignment seems to contradict a MEROPS classification of family members as S80 family serine proteases involved in phage prohead assembly. NF018888.5 PF07232.16 DUF1424 23 23 329 domain Y N N Putative rep protein (DUF1424) 131567 cellular organisms no rank 213 EBI-EMBL Putative rep protein (DUF1424) Putative rep protein (DUF1424) This family consists of several archaeal proteins of around 320 residues in length. Members of this family seem to be found exclusively in Halobacterium and Haloferax species. The function of this family is unknown. This protein is probably a rep protein due to conservation of functional motifs. (from Pfam) NF018891.5 PF07235.16 DUF1427 27.1 27.1 84 subfamily Y Y N DUF1427 family protein 131567 cellular organisms no rank 6829 EBI-EMBL Protein of unknown function (DUF1427) DUF1427 family protein This family consists of several bacterial proteins of around 100 residues in length. The function of this family is unknown. (from Pfam) NF018893.5 PF07237.16 DUF1428 27 27 102 PfamAutoEq Y Y N DUF1428 family protein 131567 cellular organisms no rank 10222 EBI-EMBL Protein of unknown function (DUF1428) DUF1428 family protein This family consists of several hypothetical bacterial and one archaeal sequence of around 120 residues in length. The function of this family is unknown. The structure of this family shows it to be part of the Dimeric-alpha-beta-barrel superfamily. Many members are annotated as being RNA signal recognition particle 4.5S RNA, but this could not be verified. (from Pfam) NF018902.5 PF07247.17 AATase 22 22 500 domain Y N N Alcohol acetyltransferase 7764365 131567 cellular organisms no rank 914 EBI-EMBL Alcohol acetyltransferase Alcohol acetyltransferase This family contains a number of alcohol acetyltransferase (EC:2.3.1.84) enzymes approximately 500 residues long found in both bacteria and metazoa. These catalyse the esterification of isoamyl alcohol by acetyl coenzyme A [1]. [1]. 7764365. The purification, properties and internal peptide sequences of alcohol acetyltransferase isolated from Saccharomyces cerevisiae Kyokai No. 7. Minetoki T, Bogaki T, Iwamatsu A, Fujii T, Hamachi M;. Biosci Biotechnol Biochem 1993;57:2094-2098. (from Pfam) NF018905.5 PF07250.16 Glyoxal_oxid_N 37.5 37.5 243 domain Y N N Glyoxal oxidase N-terminus 10593910 131567 cellular organisms no rank 425 EBI-EMBL Glyoxal oxidase N-terminus Glyoxal oxidase N-terminus This family represents the N-terminus (approximately 300 residues) of a number of plant and fungal glyoxal oxidase enzymes. Glyoxal oxidase catalyses the oxidation of aldehydes to carboxylic acids, coupled with reduction of dioxygen to hydrogen peroxide. It is an essential component of the extracellular lignin degradation pathways of the wood-rot fungus Phanerochaete chrysosporium [1]. [1]. 10593910. Identification of catalytic residues in glyoxal oxidase by targeted mutagenesis. Whittaker MM, Kersten PJ, Cullen D, Whittaker JW;. J Biol Chem 1999;274:36226-36232. (from Pfam) NF018917.5 PF07264.16 EI24 32 32 199 domain Y Y N EI24 domain-containing protein 10594026,29792261,8649819 131567 cellular organisms no rank 35781 EBI-EMBL Sulfate transporter CysZ/Etoposide-induced protein 2.4 Sulfate transporter CysZ/Etoposide-induced protein 2.4 This family contains a number of eukaryotic etoposide-induced 2.4 (EI24) proteins approximately 350 residues long as well as bacterial CysZ proteins (formerly known as DUF540). In cells treated with the cytotoxic drug etoposide, EI24 is induced by p53 [1]. It has been suggested to play an important role in negative cell growth control [2]. [1]. 8649819. Identification and cloning of EI24, a gene induced by p53 in etoposide-treated cells. Lehar SM, Nacht M, Jacks T, Vater CA, Chittenden T, Guild BC;. Oncogene 1996;12:1181-1187. [2]. 10594026. ei24, a p53 response gene involved in growth suppression and apoptosis. Gu Z, Flemington C, Chittenden T, Zambetti GP;. Mol Cell Biol 2000;20:233-241. [3]. 29792261. Structure-based analysis of CysZ-mediated cellular uptake of sulfate. Assur Sanghai Z, Liu Q, Clarke OB, Belcher-Dufrisne M, Wiriyasermkul P, Giese MH, Leal-Pinto E, Kloss B, Tabuso S, Love J, Punta M, Banerjee S, Rajashankar KR, Rost B, Logothetis D, Quick M, Hendrickson WA, Mancia F;. Elife. 2018;7:e27829. (from Pfam) NF018933.5 PF07282.16 OrfB_Zn_ribbon 26.3 26.3 69 domain Y Y N zinc ribbon domain-containing protein 131567 cellular organisms no rank 163964 EBI-EMBL Putative transposase DNA-binding domain zinc ribbon domain Proteins containing this zinc ribbon domain at the C-terminus include the RNA-guided DNA endonuclease TnpB, found as an accessory protein (that is, not required for transposition) in many IS (insertion sequence) elements. NF018938.5 PF07287.16 AtuA 22.8 22.8 349 domain Y Y N acyclic terpene utilization AtuA family protein 17064376 131567 cellular organisms no rank 32012 EBI-EMBL Acyclic terpene utilisation family protein AtuA acyclic terpene utilization AtuA family protein This family consists of several bacterial and plant proteins of around 400 residues in length. One member of this family has been characterised in Pseudomonas citronellolis as AtuA, a member of a gene cluster that is essential for the acyclic terpene utilisation (Atu) pathway [1]. [1]. 17064376. Identification and characterization of the acyclic terpene utilization gene cluster of Pseudomonas citronellolis. Forster-Fromme K, Jendrossek D;. FEMS Microbiol Lett. 2006;264:220-225. (from Pfam) NF018942.5 PF07291.16 MauE 27 27 128 domain Y Y N MauE/DoxX family redox-associated membrane protein GO:0016020,GO:0030416 9403107 131567 cellular organisms no rank 55534 EBI-EMBL Methylamine utilisation protein MauE MauE/DoxX family redox-associated membrane protein This family consists of several bacterial methylamine utilisation MauE proteins. Synthesis of enzymes involved in methylamine oxidation via methylamine dehydrogenase (MADH) is encoded by genes present in the mau cluster. MauE and MauD are specifically involved in the processing, transport, and/or maturation of the beta-subunit and that the absence of each of these proteins leads to production of a non-functional beta-subunit which becomes rapidly degraded [1]. [1]. 9403107. MauE and MauD proteins are essential in methylamine metabolism of Paracoccus denitrificans. van der Palen CJ, Reijnders WN, de Vries S, Duine JA, van Spanning RJ;. Antonie Van Leeuwenhoek 1997;72:219-228. (from Pfam) NF018949.5 PF07298.16 NnrU 24.7 24.7 188 subfamily Y Y N NnrU family protein 9171397 131567 cellular organisms no rank 14558 EBI-EMBL NnrU protein NnrU family protein This domain is found in several plant and bacterial NnrU proteins. NnrU is thought to be involved in the reduction of nitric oxide. The exact function of NnrU is unclear. It is thought however that NnrU and perhaps NnrT are required for expression of both nirK and nor [1]. [1]. 9171397. Characterization of the nitric oxide reductase-encoding region in Rhodobacter sphaeroides 2.4.3. Bartnikas TB, Tosques IE, Laratta WP, Shi J, Shapleigh JP;. J Bacteriol 1997;179:3534-3540. (from Pfam) NF018951.5 PF07301.16 DUF1453 24.6 24.6 145 subfamily Y Y N CcdC protein domain-containing protein 131567 cellular organisms no rank 5728 EBI-EMBL CcdC protein DUF1453 family protein This family includes protein CcdC from Bacillus subtilis. The function of Ccdc is not known. (from Pfam) NF018960.5 PF07310.18 PAS_5 22 22 137 domain Y Y N PAS domain-containing protein 131567 cellular organisms no rank 9467 EBI-EMBL PAS domain PAS domain This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long. This region is is distantly similar to other PAS domains. (from Pfam) NF018961.5 PF07311.17 Dodecin 22.5 22.5 64 domain Y Y N dodecin domain-containing protein 12679016,15281131 131567 cellular organisms no rank 14083 EBI-EMBL Dodecin Dodecin Dodecin is a flavin-binding protein [1],found in several bacteria and few archaea and represents a stand-alone version of the SHS2 domain [2]. It most closely resembles the SHS2 domains of FtsA and Rpb7p, and represents a single domain small-molecule binding form[1]. [1]. 15281131. The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies. Anantharaman V, Aravind L;. Proteins. 2004;56:795-807. [2]. 12679016. Crystal structure of halophilic dodecin: a novel, dodecameric flavin binding protein from Halobacterium salinarum. Bieger B, Essen LO, Oesterhelt D;. Structure. 2003;11:375-385. (from Pfam) NF018968.5 PF07318.17 DUF1464 23.5 23.5 327 PfamAutoEq Y Y N DUF1464 family protein 131567 cellular organisms no rank 248 EBI-EMBL Protein of unknown function (DUF1464) DUF1464 family protein This family consists of several hypothetical archaeal proteins of around 350 residues in length. The function of this family is unknown. (from Pfam) NF018979.5 PF07331.16 TctB 29.1 29.1 137 domain Y Y N tripartite tricarboxylate transporter TctB family protein 131567 cellular organisms no rank 53916 EBI-EMBL Tripartite tricarboxylate transporter TctB family tripartite tricarboxylate transporter TctB family protein This family consists of several hypothetical bacterial proteins of around 150 residues in length. This family was formerly known as DUF1468. (from Pfam) NF018983.5 PF07335.16 Glyco_hydro_75 27 27 165 domain Y Y N glycoside hydrolase family 75 protein GO:0016977 11115392,11388486 131567 cellular organisms no rank 6220 EBI-EMBL Fungal chitosanase of glycosyl hydrolase group 75 glycoside hydrolase family 75 protein This family consists of several fungal chitosanase proteins. Chitin, xylan, 6-O-sulphated chitosan and O-carboxymethyl chitin are indigestible by chitosanase [1]. EC:3.2.1.132. The mechanism is likely to be inverting, and the probable catalytic neutrophile base is Asp, with the probable catalytic proton donor being Glu. (see the Chitosanase web-page from CAZY). [1]. 11115392. An Aspergillus chitosanase with potential for large-scale preparation of chitosan oligosaccharides. Cheng CY, Li YK;. Biotechnol Appl Biochem 2000;32:197-203. [2]. 11388486. Cloning and characterization of a chitosanase gene from the koji mold Aspergillus oryzae strain IAM 2660. Zhang XY, Dai AL, Kuroiwa K, Kodaira R, Nogawa M, Shimosaka M, Okazaki M;. Biosci Biotechnol Biochem 2001;65:977-981. (from Pfam) NF019009.5 PF07362.17 CcdA 22.4 22.4 71 domain Y Y N type II toxin-antitoxin system CcdA family antitoxin 10196173 131567 cellular organisms no rank 7965 EBI-EMBL Post-segregation antitoxin CcdA type II toxin-antitoxin system CcdA family antitoxin This family consists of several Enterobacterial post-segregation antitoxin CcdA proteins. The F plasmid-carried bacterial toxin, the CcdB protein, is known to act on DNA gyrase in two different ways. CcdB poisons the gyrase-DNA complex, blocking the passage of polymerases and leading to double-strand breakage of the DNA. Alternatively, in cells that overexpress CcdB, the A subunit of DNA gyrase (GyrA) has been found as an inactive complex with CcdB. Both poisoning and inactivation can be prevented and reversed in the presence of the F plasmid-encoded antidote, the CcdA protein [1]. [1]. 10196173. Interactions of CcdB with DNA gyrase. Inactivation of Gyra, poisoning of the gyrase-DNA complex, and the antidote action of CcdA. Bahassi EM, O'Dea MH, Allali N, Messens J, Gellert M, Couturier M;. J Biol Chem 1999;274:10936-10944. (from Pfam) NF019011.5 PF07364.17 DUF1485 22.8 22.8 290 domain Y Y N M81 family metallopeptidase 131567 cellular organisms no rank 22464 EBI-EMBL Metallopeptidase family M81 M81 family metallopeptidase This is a family of proteobacterial metallo-peptidases. (from Pfam) NF019013.5 PF07366.17 SnoaL 28.4 28.4 126 domain Y Y N ester cyclase GO:0030638 15071504 131567 cellular organisms no rank 100739 EBI-EMBL SnoaL-like polyketide cyclase ester cyclase This family includes SnoaL [1] a polyketide cyclase involved in nogalamycin biosynthesis. This family was formerly known as DUF1486. The proteins in this family adopt a distorted alpha-beta barrel fold [1]. Structural data together with site-directed mutagenesis experiments have shown that SnoaL has a different mechanism to that of the classical aldolase for catalysing intramolecular aldol condensation [1]. [1]. 15071504. Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation. Sultana A, Kallio P, Jansson A, Wang JS, Niemi J, Mantsala P, Schneider G;. EMBO J 2004;23:1911-1921. (from Pfam) NF019027.5 PF07381.16 DUF1495 22 22 90 subfamily Y Y N archaellum operon transcriptional activator EarA family protein 27314758 131567 cellular organisms no rank 222 EBI-EMBL Winged helix DNA-binding domain (DUF1495) archaellum operon transcriptional activator EarA family protein This family consists of several hypothetical archaeal proteins of around 110 residues in length. The structure of this domain possesses a winged helix DNA-binding domain suggesting these proteins are bacterial transcription factors. (from Pfam) NF019028.5 PF07382.16 HC2 40 40 194 domain Y Y N histone H1-like repetitive region-containing protein GO:0003677,GO:0030261,GO:0030527 8733229 131567 cellular organisms no rank 5817 EBI-EMBL Histone H1-like nucleoprotein HC2 histone H1-like repetitive region This family of basic, repetitive prokaryotic sequences includes Hc2 proteins from Chlamydia, and a distinct family from Burkholderia and related species that has a conserved non-repetitive C-terminal region. Additional uncharacterized predicted proteins include tandem repeats resembling KKAAA, suggesting, based on which proteins are called similar to histone H1 from eukaryotes. NF019031.5 PF07385.17 Lyx_isomer 20.8 20.8 222 subfamily Y Y N D-lyxose/D-mannose family sugar isomerase 17189362,20615418,21520290,34422783 131567 cellular organisms no rank 6548 EBI-EMBL D-lyxose isomerase D-lyxose/D-mannose family sugar isomerase Members of this family of sugar isomerases belong to the cupin superfamily and consist of group I and II of D-lyxose isomerases [3]. The enzyme from Cohnella laevoribosii has been shown to be specific for D-lyxose, L-ribose, and D-mannose [1]. E. coli sugar isomerase (EcSI) shows a preference for D-lyxose and D-mannose [2] and its active site is highly similar to YdaE from the sigma B regulon of Bacillus subtilis [3]. [1]. 17189362. Characterization of a novel D-lyxose isomerase from Cohnella laevoribosii RI-39 sp. nov. Cho EA, Lee DW, Cha YH, Lee SJ, Jung HC, Pan JG, Pyun YR;. J Bacteriol. 2007;189:1655-1663. [2]. 20615418. Structure-based annotation of a novel sugar isomerase from the pathogenic E. coli O157:H7. van Staalduinen LM, Park CS, Yeom SJ, Adams-Cioaba MA, Oh DK, Jia Z;. J Mol Biol. 2010;401:866-881. [3]. 34422783. Biochemical and Structural Characterisation of a Novel D-Lyxose Isomerase From the Hyperthermophilic Archaeon Thermofilum sp. De Rose SA, Kuprat T, Isupov MN, Reinhardt A, Schonheit P, Littlechild JA;. Front Bioeng Biotechnol. 2021;9:711487. [4]. 21520290. The structure of a D-lyxose isomerase from the sigmaB regulon of Bacillus subtilis. Marles-Wright J, Lewis RJ;. Proteins. 2011;79:2015-2019. (from Pfam) NF019032.5 PF07386.16 DUF1499 22.6 22.6 114 domain Y Y N DUF1499 domain-containing protein 131567 cellular organisms no rank 14374 EBI-EMBL Protein of unknown function (DUF1499) Protein of unknown function (DUF1499) This family consists of several hypothetical bacterial and plant proteins of around 125 residues in length. The function of this family is unknown. (from Pfam) NF019034.5 PF07388.16 A-2_8-polyST 23.3 23.3 316 domain Y Y N polysialyltransferase family glycosyltransferase 12578835 131567 cellular organisms no rank 13361 EBI-EMBL Alpha-2,8-polysialyltransferase (POLYST) polysialyltransferase family glycosyltransferase Members of this NF019040.5 PF07394.17 DUF1501 27 27 390 domain Y Y N DUF1501 domain-containing protein 131567 cellular organisms no rank 41699 EBI-EMBL Protein of unknown function (DUF1501) Protein of unknown function (DUF1501) This family contains a number of hypothetical bacterial proteins of unknown function approximately 400 residues long. (from Pfam) NF019057.5 PF07411.17 DUF1508 22 22 48 domain Y Y N DUF1508 domain-containing protein 131567 cellular organisms no rank 16511 EBI-EMBL Domain of unknown function (DUF1508) Domain of unknown function (DUF1508) This family represents a series of bacterial domains of unknown function of around 50 residues in length. Members of this family are often found as tandem repeats and in some cases represent the whole protein. All member proteins are described as being hypothetical. (from Pfam) NF019076.5 PF07432.18 Hc1 23.5 23.5 57 domain Y N N Histone H1-like protein Hc1 GO:0003677,GO:0030527 2023942 131567 cellular organisms no rank 2984 EBI-EMBL Histone H1-like protein Hc1 Histone H1-like protein Hc1 This family consists of several bacterial histone H1-like Hc1 proteins. In Chlamydia, Hc1 is expressed in the late stages of the life cycle, concomitant with the reorganisation of chlamydial reticulate bodies into elementary bodies. This suggests that Hc1 protein plays a role in the condensation of chromatin during intracellular differentiation [1]. [1]. 2023942. Chlamydia trachomatis developmentally regulated protein is homologous to eukaryotic histone H1. Hackstadt T, Baehr W, Ying Y;. Proc Natl Acad Sci U S A 1991;88:3937-3941. (from Pfam) NF019083.5 PF07439.16 DUF1515 22.2 22.2 113 domain Y Y N DUF1515 family protein 131567 cellular organisms no rank 734 EBI-EMBL Protein of unknown function (DUF1515) DUF1515 family protein This family consists of several hypothetical bacterial proteins of around 130 residues in length. Members of this family seem to be found exclusively in Rhizobium species. The function of this family is unknown. (from Pfam) NF019085.5 PF07441.16 BofA 26.1 26.1 75 PfamEq Y Y N pro-sigmaK processing inhibitor BofA family protein 10464210 131567 cellular organisms no rank 5112 EBI-EMBL SigmaK-factor processing regulatory protein BofA pro-sigmaK processing inhibitor BofA family protein This family contains the sigmaK-factor processing regulatory protein BofA (Bypass-of-forespore protein A) (approximately 80 residues long). During sporulation in Bacillus subtilis, transcription is controlled in the developing sporangium by a cascade of sporulation-specific transcription factors (sigma factors). Following engulfment, processing of sigmaK is inhibited by BofA. It has been suggested that this effect is exerted by alteration of the level of the SpoIVFA protein [1]. [1]. 10464210. Role of the sporulation protein BofA in regulating activation of the Bacillus subtilis developmental transcription factor sigmaK. Resnekov O;. J Bacteriol 1999;181:5384-5388. (from Pfam) NF019088.5 PF07444.16 Ycf66_N 22.3 22.3 76 domain Y Y N Ycf66 family protein 131567 cellular organisms no rank 2390 EBI-EMBL Ycf66 protein N-terminus Ycf66 family N-terminus This family represents the N-terminus (approximately 80 residues) of Ycf66, a protein that seems to be restricted to eukaryotes that contain chloroplasts and to cyanobacteria. (from Pfam) NF019092.5 PF07449.16 HyaE 22 22 108 subfamily Y N N Hydrogenase-1 expression protein HyaE 12914940 131567 cellular organisms no rank 8638 EBI-EMBL Hydrogenase-1 expression protein HyaE Hydrogenase-1 expression protein HyaE This family contains bacterial hydrogenase-1 expression proteins approximately 120 residues long. This includes the E. coli protein HyaE, and the homologous proteins HoxO of R. eutropha and HupG of R. leguminosarum. Deletion of the hoxO gene in R. eutropha led to complete loss of the uptake [NiFe] hydrogenase activity, suggesting that it has a critical role in hydrogenase assembly [1]. [1]. 12914940. Assembly of Tat-dependent [NiFe] hydrogenases: identification of precursor-binding accessory proteins. Dubini A, Sargent F;. FEBS Lett 2003;549:141-146. (from Pfam) NF019094.5 PF07451.16 SpoVAD 22.1 22.1 329 domain Y N N Stage V sporulation protein AD (SpoVAD) 11751839 131567 cellular organisms no rank 8890 EBI-EMBL Stage V sporulation protein AD (SpoVAD) Stage V sporulation protein AD (SpoVAD) This family contains the bacterial stage V sporulation protein AD (SpoVAD), which is approximately 340 residues long. This is one of six proteins encoded by the spoVA operon, which is transcribed exclusively in the forespore at about the time of dipicolinic acid (DPA) synthesis in the mother cell. The functions of the proteins encoded by the spoVA operon are unknown, but it has been suggested they are involved in DPA transport during sporulation [1]. [1]. 11751839. The products of the spoVA operon are involved in dipicolinic acid uptake into developing spores of Bacillus subtilis. Tovar-Rojo F, Chander M, Setlow B, Setlow P;. J Bacteriol 2002;184:584-587. (from Pfam) NF019095.5 PF07452.17 CHRD 24.1 24.1 117 domain Y Y N CHRD domain-containing protein 13678956 131567 cellular organisms no rank 11494 EBI-EMBL CHRD domain CHRD domain CHRD (after SWISS-PROT abbreviation for chordin) is a novel domain identified in chordin, an inhibitor of bone morphogenetic proteins. This family includes bacterial homologues. It is anticipated to have an immunoglobulin-like beta-barrel structure based on limited similarity to superoxide dismutases but, as yet, no clear functional prediction can be made. Its most conserved feature is a GE[I/L]RCG[V/I/L] motif towards its C-terminal end Most bacterial proteins in this family have only one CHRD domain, whereas it is found repeated in many eukaryotic proteins such as human chordin (Swiss:Q9H2X0) and Drosophila SOG (Swiss:Q24025). [1]. [1]. 13678956. CHRD, a novel domain in the BMP inhibitor chordin, is also found in microbial proteins. Hyvonen M;. Trends Biochem Sci 2003;28:470-473. (from Pfam) NF019096.5 PF07453.18 NUMOD1 22.8 13.5 37 domain Y Y N NUMOD1 domain-containing DNA-binding protein 13678957 131567 cellular organisms no rank 1488 EBI-EMBL NUMOD1 domain NUMOD1 domain This domain probably represents a DNA-binding helix-turn-helix based on its similarity to other families (Bateman A pers obs). [1]. 13678957. New types of conserved sequence domains in DNA-binding regions of homing endonucleases. Sitbon E, Pietrokovski S;. Trends Biochem Sci 2003;28:473-477. (from Pfam) NF019103.5 PF07460.16 NUMOD3 20.4 11.1 37 domain Y Y N NUMOD3 domain-containing DNA-binding protein GO:0003677 13678957 131567 cellular organisms no rank 1693 EBI-EMBL NUMOD3 motif NUMOD3 DNA-binding domain NUMOD3 is a DNA-binding motif found in homing endonucleases and related proteins. It occurs on its own or in tandem repeats in GIY-YIG (Pfam:PF01541) and HTH proteins. It constitutes a beta-turn-loop-helix subregion of the the DNA-binding domain of I-TevI homing endonuclease (Swiss:P13299) [1]. [1]. 13678957. New types of conserved sequence domains in DNA-binding regions of homing endonucleases. Sitbon E, Pietrokovski S;. Trends Biochem Sci 2003;28:473-477. (from Pfam) NF019106.5 PF07463.16 NUMOD4 23.4 23.4 49 domain Y Y N NUMOD4 domain-containing protein GO:0016788 13678957 131567 cellular organisms no rank 7190 EBI-EMBL NUMOD4 motif NUMOD4 motif NUMOD4 is a putative DNA-binding motif found in homing endonucleases and related proteins [1]. [1]. 13678957. New types of conserved sequence domains in DNA-binding regions of homing endonucleases. Sitbon E, Pietrokovski S;. Trends Biochem Sci 2003;28:473-477. (from Pfam) NF019113.5 PF07470.18 Glyco_hydro_88 26.6 26.6 352 domain Y Y N glycoside hydrolase family 88 protein 12777820 131567 cellular organisms no rank 52770 EBI-EMBL Glycosyl Hydrolase Family 88 glycoside hydrolase family 88 protein Unsaturated glucuronyl hydrolase catalyses the hydrolytic release of unsaturated glucuronic acids from oligosaccharides (EC:3.2.1.-) produced by the reactions of polysaccharide lyases [1]. [1]. 12777820. Crystallization and preliminary X-ray analysis of a novel unsaturated glucuronyl hydrolase from Bacillus sp. GL1. Mori S, Akao S, Miyake O, Nankai H, Hashimoto W, Mikami B, Murata K;. Acta Crystallogr D Biol Crystallogr 2003;59:946-949. (from Pfam) NF019118.5 PF07475.17 Hpr_kinase_C 33.3 33.3 171 PfamEq Y N N HPr Serine kinase C-terminal domain GO:0000155,GO:0000160,GO:0004672,GO:0005524,GO:0006109 11904409,9570401 131567 cellular organisms no rank 22636 EBI-EMBL HPr Serine kinase C-terminal domain HPr Serine kinase C-terminal domain This family represents the C terminal kinase domain of Hpr Serine/threonine kinase PtsK. This kinase is the sensor in a multicomponent phosphorelay system in control of carbon catabolic repression in bacteria [1]. This kinase in unusual in that it recognises the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes [1]. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller [2]. [1]. 9570401. A novel protein kinase that controls carbon catabolite repression in bacteria. Reizer J, Hoischen C, Titgemeyer F, Rivolta C, Rabus R, Stulke J, Karamata D, Saier MH Jr, Hillen W;. Mol Microbiol 1998;27:1157-1169. [2]. 11904409. Structure of the full-length HPr kinase/phosphatase from Staphylococcus xylosus at 1.95 A resolution: Mimicking the product/substrate of the phospho transfer reactions. Marquez JA, Hasenbein S, Koch B, Fieulaine S, Nessler S, Russell RB, Hengstenberg W, Scheffzek K;. Proc Natl Acad Sci U S A 2002;99:3458-3463. (from Pfam) NF019119.5 PF07476.16 MAAL_C 27 27 249 domain Y N N Methylaspartate ammonia-lyase C-terminus 11748244,1420191 131567 cellular organisms no rank 7624 EBI-EMBL Methylaspartate ammonia-lyase C-terminus Methylaspartate ammonia-lyase C-terminus Methylaspartate ammonia-lyase EC:4.3.1.2 catalyses the second step of fermentation of glutamate. It is a homodimer. This family represents the C-terminal region of Methylaspartate ammonia-lyase and contains a TIM barrel fold similar to the Pfam:PF01188. This family represents the catalytic domain and contains a metal binding site [2]. [1]. 1420191. Cloning, sequencing, and expression in Escherichia coli of the Clostridium tetanomorphum gene encoding beta-methylaspartase and characterization of the recombinant protein. Goda SK, Minton NP, Botting NP, Gani D;. Biochemistry 1992;31:10747-10756. [2]. 11748244. The structure of 3-methylaspartase from Clostridium tetanomorphum functions via the common enolase chemical step. Asuncion M, Blankenfeldt W, Barlow JN, Gani D, Naismith JH;. J Biol Chem 2002;277:8306-8311. (from Pfam) NF019120.5 PF07477.17 Glyco_hydro_67C 27 27 223 PfamEq Y N N Glycosyl hydrolase family 67 C-terminus GO:0005576,GO:0045493,GO:0046559 11937059 131567 cellular organisms no rank 10173 EBI-EMBL Glycosyl hydrolase family 67 C-terminus Glycosyl hydrolase family 67 C-terminus Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. This family represents the C terminal region of alpha-glucuronidase which is mainly alpha-helical. It wraps around the catalytic domain (Pfam:PF07488), making additional interactions both with the N-terminal domain (Pfam:PF03648) of its parent monomer and also forming the majority of the dimer-surface with the equivalent C-terminal domain of the other monomer of the dimer [1]. [1]. 11937059. The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A. Nurizzo D, Nagy T, Gilbert HJ, Davies GJ;. Structure (Camb) 2002;10:547-556. (from Pfam) NF019121.5 PF07478.18 Dala_Dala_lig_C 24 24 204 domain Y N N D-ala D-ala ligase C-terminus GO:0008716 10908650,12499203,9054558 131567 cellular organisms no rank 427639 EBI-EMBL D-ala D-ala ligase C-terminus D-ala D-ala ligase C-terminus This family represents the C-terminal, catalytic domain of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF) [3]. [1]. 9054558. D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant. Fan C, Park IS, Walsh CT, Knox JR;. Biochemistry 1997;36:2531-2538. [2]. 10908650. The molecular basis of vancomycin resistance in clinically relevant Enterococci: crystal structure of D-alanyl-D-lactate ligase (VanA). Roper DI, Huyton T, Vagin A, Dodson G;. Proc Natl Acad Sci U S A 2000;97:8921-8925. [3]. 12499203. Roles of Mycobacterium smegmatis D-alanine:D-alanine ligase and D-alanine racemase in the mechanisms of action of and resistance to the peptidoglycan inhibitor D-cycloserine. Feng Z, Barletta RG;. Antimicrob Agents Chemother 2003;47:283-291. (from Pfam) NF019122.5 PF07479.19 NAD_Gly3P_dh_C 25 25 142 domain Y N N NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus GO:0005975,GO:0047952 10801498,12032156 131567 cellular organisms no rank 70180 EBI-EMBL NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyses the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the C-terminal substrate-binding domain [2]. [1]. 12032156. Kinetic regulation of the mitochondrial glycerol-3-phosphate dehydrogenase by the external NADH dehydrogenase in Saccharomyces cerevisiae. Pahlman IL, Larsson C, Averet N, Bunoust O, Boubekeur S, Gustafsson L, Rigoulet M;. J Biol Chem 2002;277:27991-27995. [2]. 10801498. A potential target enzyme for trypanocidal drugs revealed by the crystal structure of NAD-dependent glycerol-3-phosphate dehydrogenase from Leishmania mexicana. Suresh S, Turley S, Opperdoes FR, Michels PA, Hol WG;. Structure Fold Des 2000;8:541-552. (from Pfam) NF019126.5 PF07484.17 Collar 24 24 57 domain Y Y N tail fiber protein 12888344,1597418 131567 cellular organisms no rank 66790 EBI-EMBL Phage Tail Collar Domain tail fiber protein This region is occasionally found in conjunction with Pfam:PF03335. Most of the family appear to be phage tail proteins; however some appear to be involved in other processes. For instance Swiss:Q03314 from Rhizobium leguminosarum may be involved in plant-microbe interactions ([1]). A related protein Swiss:Q9L3N1 is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate (Swiss:P10930) suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop ([2]) and three beta-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologues but the intervening sequence is not. Much of the function of Swiss:P10930 appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the 'collar'. The domain may bind SO4, however the residues accredited with this vary between the PDB file and the Swiss-Prot entry. The long unconserved region maybe due to domain swapping in and out of a loop or reflective of rapid evolution. [1]. 1597418. Molecular characterization and regulation of the rhizosphere-expressed genes rhiABCR that can influence nodulation by Rhizobium leguminosarum biovar viciae. Cubo MT, Economou A, Murphy G, Johnston AW, Downie JA;. J Bacteriol 1992;174:4026-4035. [2]. 12888344. The structure of the receptor-binding domain of the bacteriophage T4 short tail fibre reveals a knitted trimeric metal-binding fold. Thoma. TRUNCATED at 1650 bytes (from Pfam) NF019127.5 PF07485.16 DUF1529 25 25 121 domain Y Y N DUF1259 domain-containing protein 131567 cellular organisms no rank 6447 EBI-EMBL Domain of Unknown Function (DUF1259) Domain of Unknown Function (DUF1259) This family is the lppY/lpqO homologue family. (from Pfam) NF019130.5 PF07488.17 Glyco_hydro_67M 23.5 23.5 326 domain Y N N Glycosyl hydrolase family 67 middle domain GO:0005576,GO:0045493,GO:0046559 11937059 131567 cellular organisms no rank 9913 EBI-EMBL Glycosyl hydrolase family 67 middle domain Glycosyl hydrolase family 67 middle domain Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. This family represents the central catalytic domain of alpha-glucuronidase [1]. [1]. 11937059. The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A. Nurizzo D, Nagy T, Gilbert HJ, Davies GJ;. Structure (Camb) 2002;10:547-556. (from Pfam) NF019138.5 PF07497.17 Rho_RNA_bind 27 27 73 PfamEq Y N N Rho termination factor, RNA-binding domain GO:0003723,GO:0006353 10230401 131567 cellular organisms no rank 57329 EBI-EMBL Rho termination factor, RNA-binding domain Rho termination factor, RNA-binding domain The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [1]. [1]. 10230401. The structural basis for terminator recognition by the Rho transcription termination factor. Bogden CE, Fass D, Bergman N, Nichols MD, Berger JM;. Mol Cell 1999;3:487-493. (from Pfam) NF019139.5 PF07498.17 Rho_N 24.9 24.9 43 domain Y Y N Rho termination factor N-terminal domain-containing protein GO:0006353 10230401 131567 cellular organisms no rank 59147 EBI-EMBL Rho termination factor, N-terminal domain Rho termination factor, N-terminal domain The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [1]. This domain is found to the N-terminus of the RNA binding domain (Pfam:PF07497). [1]. 10230401. The structural basis for terminator recognition by the Rho transcription termination factor. Bogden CE, Fass D, Bergman N, Nichols MD, Berger JM;. Mol Cell 1999;3:487-493. (from Pfam) NF019140.5 PF07499.18 RuvA_C 24 24 47 PfamEq Y N N RuvA, C-terminal domain GO:0005524,GO:0006281,GO:0006310,GO:0009378,GO:0009379 10890893 131567 cellular organisms no rank 55252 EBI-EMBL RuvA, C-terminal domain RuvA, C-terminal domain Homologous recombination is a crucial process in all living organisms. In bacteria, this process the RuvA, RuvB, and RuvC proteins are involved. More specifically the proteins process the Holliday junction DNA. RuvA is comprised of three distinct domains. The domain represents the C-terminal domain and plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB [1]. Within the Holliday junction, the C-terminal domain makes no interaction with DNA [1]. [1]. 10890893. Crystal structure of the holliday junction DNA in complex with a single RuvA tetramer. Ariyoshi M, Nishino T, Iwasaki H, Shinagawa H, Morikawa K;. Proc Natl Acad Sci U S A 2000;97:8257-8262. (from Pfam) NF019144.5 PF07503.17 zf-HYPF 23 23 34 domain Y N N HypF finger GO:0008270 9492269 131567 cellular organisms no rank 34853 EBI-EMBL HypF finger HypF finger The HypF family of proteins are involved in the maturation and regulation of hydrogenase ([1]). In the N-terminus they appear to have two Zinc finger domains, as modelled by this family. [1]. 9492269. Rhodobacter capsulatus HypF is involved in regulation of hydrogenase synthesis through the HupUV proteins. Colbeau A, Elsen S, Tomiyama M, Zorin NA, Dimon B, Vignais PM;. Eur J Biochem 1998;251:65-71. (from Pfam) NF019145.5 PF07504.18 FTP 21 21 51 domain Y N N Fungalysin/Thermolysin Propeptide Motif 12589825,8636020 131567 cellular organisms no rank 54704 EBI-EMBL Fungalysin/Thermolysin Propeptide Motif Fungalysin/Thermolysin Propeptide Motif This motif is found in both the bacterial M4 peptidase propeptide and the fungal M36 propeptide. Its exact function is not clear, but it is likely to either inhibit the peptidase, so as to prevent its premature activation, or has a chaperone activity. Both of these roles have been ascribed to the M4 and M36 propeptides ([1], [2]). [1]. 12589825. General function of N-terminal propeptide on assisting protein folding and inhibiting catalytic activity based on observations with a chimeric thermolysin-like protease. Tang B, Nirasawa S, Kitaoka M, Marie-Claire C, Hayashi K;. Biochem Biophys Res Commun 2003;301:1093-1098. [2]. 8636020. Specific inhibition of mature fungal serine proteinases and metalloproteinases by their propeptides. Markaryan A, Lee JD, Sirakova TD, Kolattukudy PE;. J Bacteriol 1996;178:2211-2215. (from Pfam) NF019146.5 PF07505.16 DUF5131 28.9 28.9 243 subfamily Y Y N DUF5131 family protein 131567 cellular organisms no rank 13801 EBI-EMBL Protein of unknown function (DUF5131) DUF5131 family protein This is a family of bacterial and phage proteins of unknown function. There are three highly conserved cysteine residues in the disposition, Cx6Cxxc, amongst many highly conserved residues. (from Pfam) NF019149.5 PF07508.18 Recombinase 21.1 21.1 102 domain Y Y N recombinase family protein GO:0000150,GO:0003677 131567 cellular organisms no rank 132477 EBI-EMBL Recombinase recombinase family protein This domain is usually found associated with Pfam:PF00239 in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages. (from Pfam) NF019150.5 PF07509.16 DUF1523 23 23 176 PfamAutoEq Y Y N DUF1523 family protein 131567 cellular organisms no rank 4258 EBI-EMBL Protein of unknown function (DUF1523) DUF1523 family protein NF019151.5 PF07510.16 DUF1524 23 23 138 domain Y Y N DUF1524 domain-containing protein 131567 cellular organisms no rank 76089 EBI-EMBL Protein of unknown function (DUF1524) Protein of unknown function (DUF1524) This family of uncharacterised proteins contain a conserved HXXP motif. A similar motif is seen in protein families in the His-Me finger endonuclease superfamily which suggests this family of proteins may also act as endonucleases. (from Pfam) NF019156.5 PF07517.19 SecA_DEAD 24.6 24.6 290 domain Y N N SecA DEAD-like domain GO:0005524,GO:0016020,GO:0017038 12242434,2542029,9644254 131567 cellular organisms no rank 99269 EBI-EMBL SecA DEAD-like domain SecA DEAD-like domain SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP dependent manner [1,2]. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the Pfam:PF00270 [3]. [1]. 9644254. Amino-terminal region of SecA is involved in the function of SecG for protein translocation into Escherichia coli membrane vesicles. Mori H, Sugiyama H, Yamanaka M, Sato K, Tagaya M, Mizushima S;. J Biochem (Tokyo) 1998;124:122-129. [2]. 2542029. SecA protein hydrolyzes ATP and is an essential component of the protein translocation ATPase of Escherichia coli. Lill R, Cunningham K, Brundage LA, Ito K, Oliver D, Wickner W;. EMBO J 1989;8:961-966. [3]. 12242434. Nucleotide control of interdomain interactions in the conformational reaction cycle of SecA. Hunt JF, Weinkauf S, Henry L, Fak JJ, McNicholas P, Oliver DB, Deisenhofer J;. Science 2002;297:2018-2026. (from Pfam) NF019159.5 PF07521.17 RMMBL 21.6 21.6 63 domain Y Y N MBL fold metallo-hydrolase RNA specificity domain-containing protein 12177301,17128255,20544974,21764917 131567 cellular organisms no rank 88889 EBI-EMBL Zn-dependent metallo-hydrolase RNA specificity domain Zn-dependent metallo-hydrolase RNA specificity domain The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in Pfam:PF00753 and are common to all metallo-beta-lactamases. This, the fifth motif [1], appears to be specific to Zn-dependent metallohydrolases such as ribonuclease J 2 [4] which are involved in the processing of mRNA [2,3]. This domain adds essential structural elements to the CASP-domain and is unique to RNA/DNA-processing nucleases, showing that they are pre-mRNA 3'-end-processing endonucleases [2,3,4]. [1]. 12177301. Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP family. Callebaut I, Moshous D, Mornon JP, de Villartay JP;. Nucleic Acids Res 2002;30:3592-3601. [2]. 17128255. Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease. Mandel CR, Kaneko S, Zhang H, Gebauer D, Vethantham V, Manley JL, Tong L;. Nature. 2006;444:953-956. [3]. 20544974. Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii. Nishida Y, Ishikawa H, Baba S, Nakagawa N, Kuramitsu S, Masui R;. Proteins. 2010;78:2395-2398. [4]. 21764917. Characterization of components of the Staphylococcus aureus mRNA degradosome holoenzyme-like complex. Roux CM, DeMuth JP, Dunman PM;. J Bacteriol. 2011;193:5520-5526. (from Pfam) NF019162.5 PF07524.18 Bromo_TP 24.6 24.6 77 domain Y N N Bromodomain associated 11779830 131567 cellular organisms no rank 219 EBI-EMBL Bromodomain associated Bromodomain associated This domain is predicted to bind DNA [1] and is often found associated with Pfam:PF00439 and in transcription factors. It has a histone-like fold. [1]. 11779830. Systematic identification of novel protein domain families associated with nuclear functions. Doerks T, Copley RR, Schultz J, Ponting CP, Bork P;. Genome Res 2002;12:47-56. (from Pfam) NF019170.5 PF07532.16 Big_4 22.1 22.1 59 domain Y Y N Ig-like domain-containing protein 131567 cellular organisms no rank 21524 EBI-EMBL Bacterial Ig-like domain (group 4) Bacterial Ig-like domain (group 4) This family consists of bacterial domains with an Ig-like fold. Members of this family are found in a variety of bacterial surface proteins. (from Pfam) NF019172.5 PF07534.21 TLD 23 23 139 domain Y Y N TLD domain-containing protein 11779830,22434723 131567 cellular organisms no rank 172 EBI-EMBL TLD TLD domain This domain is predicted to be an enzyme [1] and is often found associated with Pfam:PF01476. It's structure consists of a beta-sandwich surrounded by two helices and two one-turn helices [2]. [1]. 11779830. Systematic identification of novel protein domain families associated with nuclear functions. Doerks T, Copley RR, Schultz J, Ponting CP, Bork P;. Genome Res 2002;12:47-56. [2]. 22434723. Crystal structure of the TLDc domain of oxidation resistance protein 2 from zebrafish. Blaise M, Alsarraf HM, Wong JE, Midtgaard SR, Laroche F, Schack L, Spaink H, Stougaard J, Thirup S;. Proteins. 2012;80:1694-1698. (from Pfam) NF019174.5 PF07536.19 HWE_HK 22.8 22.8 83 domain Y Y N HWE histidine kinase domain-containing protein GO:0004673 14702314,28193573 131567 cellular organisms no rank 84313 EBI-EMBL HWE histidine kinase HWE histidine kinase Two-component systems, consisting of a histidine kinase and a cognate response regulator protein, represent the best-known apparatus for transducing external cues into a physiological response in bacteria. The HWE domain is found in a subset of two-component system kinases, belonging to the same superfamily as Pfam:PF00512 [1] and Pfam:PF07568 [2]. The family was defined by [1] the presence of a highly conserved H residue in the kinase domain and a WxE motif in a C-terminal ATPase domain that is related to Pfam:PF02518. It has been demonstrated to show structural and functional correlation with Pfam:PF07568 [2]. These proteins are found in a variety of alpha- and gamma- proteobacteria, with significant enrichment in the rhizobia. [1]. 14702314. The HWE Histidine Kinases, a New Family of Bacterial Two-Component Sensor Kinases with Potentially Diverse Roles in Environmental Signaling. Karniol B, Vierstra RD;. J Bacteriol 2004;186:445-453. [2]. 28193573. Structure and function of HWE/HisKA2-family sensor histidine kinases. Herrou J, Crosson S, Fiebig A;. Curr Opin Microbiol. 2017;36:47-54. (from Pfam) NF019176.5 PF07538.16 ChW 22 22 35 repeat Y N N ChW repeat protein 11466286 131567 cellular organisms no rank 7050 EBI-EMBL Clostridial hydrophobic W ChW repeat ChW (clostridial hydrophobic domain with a conserved W) NF019179.5 PF07541.17 EIF_2_alpha 22.8 22.8 114 PfamEq Y N N Eukaryotic translation initiation factor 2 alpha subunit GO:0003723,GO:0003743 12762044,14532131,14607111,2649894 131567 cellular organisms no rank 1307 EBI-EMBL Eukaryotic translation initiation factor 2 alpha subunit Eukaryotic translation initiation factor 2 alpha subunit These proteins share a region of similarity that falls towards the C terminus from Pfam:PF00575. [1]. 2649894. Yeast translation initiation suppressor sui2 encodes the alpha subunit of eukaryotic initiation factor 2 and shares sequence identity with the human alpha subunit. Cigan AM, Pabich EK, Feng L, Donahue TF;. Proc Natl Acad Sci U S A 1989;86:2784-2788. [2]. 14607111. The crystal structure of the N-terminal region of the alpha subunit of translation initiation factor 2 (eIF2alpha) from Saccharomyces cerevisiae provides a view of the loop containing serine 51, the target of the eIF2alpha-specific kinases. Dhaliwal S, Hoffman DW;. J Mol Biol 2003;334:187-195. [3]. 14532131. The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis. Antoun A, Pavlov MY, Andersson K, Tenson T, Ehrenberg M;. EMBO J 2003;22:5593-5601. [4]. 12762044. Universal translation initiation factor IF2/eIF5B. Dever TE, Roll-Mecak A, Choi SK, Lee JH, Cao C, Shin BS, Burley SK;. Cold Spring Harb Symp Quant Biol 2001;66:417-424. (from Pfam) NF019187.5 PF07549.19 Sec_GG 20.3 12 28 domain Y N N SecD/SecF GG Motif 8112309,9694879 131567 cellular organisms no rank 98526 EBI-EMBL SecD/SecF GG Motif SecD/SecF GG Motif This family consists of various prokaryotic SecD and SecF protein export membrane proteins. This SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC [1]. SecD and SecF are required to maintain a proton motive force [2]. This alignment encompasses a -GG- motif typically found in N-terminal half of the SecD/SecF proteins . [1]. 9694879. SecDF of Bacillus subtilis, a molecular Siamese twin required for the efficient secretion of proteins. Bolhuis A, Broekhuizen CP, Sorokin A, van Roosmalen ML, Venema G, Bron S, Quax WJ, van Dijl JM;. J Biol Chem 1998;273:21217-21224. [2]. 8112309. SecD and SecF are required for the proton electrochemical gradient stimulation of preprotein translocation. Arkowitz RA, Wickner W;. EMBO J 1994;13:954-963. (from Pfam) NF019191.5 PF07553.16 Lipoprotein_Ltp 23.2 23.2 48 domain Y Y N Ltp family lipoprotein 23692331,9454717 131567 cellular organisms no rank 7721 EBI-EMBL Host cell surface-exposed lipoprotein Ltp family lipoprotein This domain is found as 1 to 5 copies in lipoproteins that are involved in superinfection exclusion. Proteins in this group have been shown to act at the stage of DNA release from the phage head into the cell [1]. This domain shows a three-helix bundle belonging to the HTH superfamily [2]. [1]. 9454717. Comparison of the lysogeny modules from the temperate Streptococcus thermophilus bacteriophages TP-J34 and Sfi21: implications for the modular theory of phage evolution. Neve H, Zenz KI, Desiere F, Koch A, Heller KJ, Brussow H;. Virology. 1998;241:61-72. [2]. 23692331. X-ray structure of a superinfection exclusion lipoprotein from phage TP-J34 and identification of the tape measure protein as its target. Bebeacua C, Lorenzo Fajardo JC, Blangy S, Spinelli S, Bollmann S, Neve H, Cambillau C, Heller KJ;. Mol Microbiol. 2013;89:152-165. (from Pfam) NF019193.5 PF07555.18 NAGidase 25 25 295 domain Y Y N beta-N-acetylglucosaminidase domain-containing protein 16822234,8177218,9811929 131567 cellular organisms no rank 18280 EBI-EMBL beta-N-acetylglucosaminidase beta-N-acetylglucosaminidase This family has previously been described as a hyaluronidase [1,2]. However, more recently it has been shown that this family has beta-N-acetylglucosaminidase activity [3]. [1]. 9811929. Novel immunogenic antigen homologous to hyaluronidase in meningioma. Heckel D, Comtesse N, Brass N, Blin N, Zang KD, Meese E;. Hum Mol Genet 1998;7:1859-1872. [2]. 8177218. Molecular genetic analysis of the nagH gene encoding a hyaluronidase of Clostridium perfringens. Canard B, Garnier T, Saint-Joanis B, Cole ST;. Mol Gen Genet 1994;243:215-224. [3]. 16822234. Functional analysis of a group A streptococcal glycoside hydrolase Spy1600 from family 84 reveals it is a beta-N-acetylglucosaminidase and not a hyaluronidase. Sheldon WL, Macauley MS, Taylor EJ, Robinson CE, Charnock SJ, Davies GJ, Vocadlo DJ, Black GW;. Biochem J. 2006;399:241-247. (from Pfam) NF019194.5 PF07556.16 DUF1538 22.6 22.6 211 domain Y Y N DUF1538 family protein 131567 cellular organisms no rank 7687 EBI-EMBL Protein of unknown function (DUF1538) DUF1538 family protein This family contains several conserved glycines and phenylalanines. (from Pfam) NF019199.5 PF07561.16 DUF1540 22.1 8.8 40 domain Y Y N DUF1540 domain-containing protein 131567 cellular organisms no rank 9523 EBI-EMBL Domain of Unknown Function (DUF1540) Domain of Unknown Function (DUF1540) This family has four conserved cysteines, which is suggestive of a metal binding function. (from Pfam) NF019205.5 PF07568.17 HisKA_2 22.3 22.3 76 domain Y Y N histidine kinase dimerization/phosphoacceptor domain -containing protein 10500846,28193573 131567 cellular organisms no rank 74893 EBI-EMBL Histidine kinase Histidine kinase This is the dimerisation and phosphoacceptor domain of a sub-family of histidine kinases [1]. It shares sequence similarity with Pfam:PF00512 and Pfam:PF07536 [2]. It is usually found adjacent to a C-terminal ATPase domain (Pfam:PF02518). This domain is found in a wide range of Bacteria and also several Archaea. [1]. 10500846. The histidine protein kinase superfamily. Grebe TW, Stock JB;. Adv Microb Physiol 1999;41:139-227. [2]. 28193573. Structure and function of HWE/HisKA2-family sensor histidine kinases. Herrou J, Crosson S, Fiebig A;. Curr Opin Microbiol. 2017;36:47-54. (from Pfam) NF019214.5 PF07578.16 LAB_N 26.7 26.7 71 PfamEq Y Y N lipid-A-disaccharide synthase N-terminal domain-containing protein GO:0008915,GO:0009245 131567 cellular organisms no rank 4922 EBI-EMBL Lipid A Biosynthesis N-terminal domain Lipid A Biosynthesis N-terminal domain This family is found at the N-terminus of a group of Chlamydial Lipid A biosynthesis proteins. It is also found by itself in a family of proteins of unknown function. (from Pfam) NF019217.5 PF07581.17 Glug 20.5 18 28 domain Y Y N GLUG motif-containing protein 12841855,8926055 131567 cellular organisms no rank 12613 EBI-EMBL The GLUG motif The GLUG motif This family is found in the IgA1 (M26) peptidases, which attached to the cell wall peptidoglycan by an amide bond ([1]). IgA1 protease selectively cleaves human IgA1 and is likely to be a pathogenicity factor in some pathogens ([2]). This family is also found in various other contexts, including with Pfam:PF05860. It is named GLUG after the mostly conserved G-L-any-G motif. [1]. 8926055. Characterization of the Streptococcus pneumoniae immunoglobulin A1 protease gene (iga) and its translation product. Poulsen K, Reinholdt J, Kilian M;. Infect Immun 1996;64:3957-3966. [2]. 12841855. The three extra-cellular zinc metalloproteinases of Streptococcus pneumoniae have a different impact on virulence in mice. Chiavolini D, Memmi G, Maggi T, Iannelli F, Pozzi G, Oggioni MR;. BMC Microbiol 2003;3:14. (from Pfam) NF019220.5 PF07584.16 BatA 25.9 25.9 77 domain Y Y N BatA domain-containing protein 10216867,18582330 131567 cellular organisms no rank 31584 EBI-EMBL Aerotolerance regulator N-terminal Aerotolerance regulator N-terminal These proteins share a highly-conserved sequence at their N-terminus. They include several proteins from Rhodopirellula baltica and also several from proteobacteria. The proteins are produced by the Batl operon which appears to be important in pathogenicity and aerotolerance. This family is the conserved N-terminus, but the full length proteins carry multiple membrane-spanning domains [1]. BatA ensures bacterial survival in the early stages of the infection process, when the infected sites are aerobic, and is produced under conditions of oxidative stress [2]. [1]. 10216867. Characterization of the Batl (Bacteroides aerotolerance) operon in Bacteroides fragilis: isolation of a B. fragilis mutant with reduced aerotolerance and impaired growth in in vivo model systems. Tang YP, Dallas MM, Malamy MH;. Mol Microbiol. 1999;32:139-149. [2]. 18582330. Expression patterns of genes induced by oxidative stress in Porphyromonas gingivalis. Meuric V, Gracieux P, Tamanai-Shacoori Z, Perez-Chaparro J, Bonnaure-Mallet M;. Oral Microbiol Immunol. 2008;23:308-314. (from Pfam) NF019227.5 PF07591.16 PT-HINT 27.7 27.7 137 domain Y Y N polymorphic toxin-type HINT domain-containing protein 21306995 131567 cellular organisms no rank 30630 EBI-EMBL Pretoxin HINT domain polymorphic toxin-type HINT autoproteolysis domain A member of the HINT superfamily of proteases that is usually found N-terminal to the toxin module in polymorphic toxin systems. The domain is predicted to function in releasing the toxin domain by autoproteolysis [1]. [1]. 21306995. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Zhang D, Iyer LM, Aravind L;. Nucleic Acids Res. 2011;39:4532-4552. (from Pfam) NF019228.5 PF07592.16 DDE_Tnp_ISAZ013 26.9 26.9 308 domain Y Y N ISAzo13-like element transposase-related protein 131567 cellular organisms no rank 4790 EBI-EMBL Rhodopirellula transposase DDE domain Rhodopirellula transposase DDE domain These transposases are found in the planctomycete Rhodopirellula baltica, the cyanobacterium Nostoc, and the Gram-positive bacterium Streptomyces. (from Pfam) NF019229.5 PF07593.17 UnbV_ASPIC 23.4 23.4 68 domain Y Y N ASPIC/UnbV domain-containing protein 12536216 131567 cellular organisms no rank 20495 EBI-EMBL ASPIC and UnbV ASPIC and UnbV This conserved sequence is found associated with Pfam:PF00515 in several paralogous proteins in Rhodopirellula baltica. It is also found associated with Pfam:PF01839 in several eukaryotic integrin-like proteins (e.g. human ASPIC Swiss:Q9NQ78) and in several other bacterial proteins (e.g. Swiss:Q84HN1 [1]). [1]. 12536216. A genomics-guided approach for discovering and expressing cryptic metabolic pathways. Zazopoulos E, Huang K, Staffa A, Liu W, Bachmann BO, Nonaka K, Ahlert J, Thorson JS, Shen B, Farnet CM;. Nat Biotechnol 2003;21:187-190. (from Pfam) NF019236.5 PF07602.16 DUF1565 20.3 20.3 257 domain Y Y N DUF1565 domain-containing protein 131567 cellular organisms no rank 14363 EBI-EMBL Protein of unknown function (DUF1565) Protein of unknown function (DUF1565) These proteins share a region of homology in their N termini, and are found in several phylogenetically diverse bacteria and in the archaeon Methanosarcina acetivorans. Some of these proteins also contain characterised domains such as Pfam:PF00395 (e.g. Swiss:Q8YWJ6) and Pfam:PF03422 (e.g. Swiss:Q9FBS2). (from Pfam) NF019237.5 PF07603.16 DUF1566 34.9 34.9 117 domain Y Y N DUF1566 domain-containing protein 131567 cellular organisms no rank 17484 EBI-EMBL Protein of unknown function (DUF1566) Protein of unknown function (DUF1566) These proteins of unknown function are found in Leptospira interrogans and in several gamma proteobacteria. (from Pfam) NF019240.5 PF07608.16 DUF1571 27 27 208 domain Y Y N DUF1571 domain-containing protein 131567 cellular organisms no rank 2315 EBI-EMBL Protein of unknown function (DUF1571) Protein of unknown function (DUF1571) A family of paralogous proteins in Rhodopirellula baltica. (from Pfam) NF019242.5 PF07610.16 DUF1573 26.1 26.1 98 domain Y Y N DUF1573 domain-containing protein 131567 cellular organisms no rank 20104 EBI-EMBL Protein of unknown function (DUF1573) Protein of unknown function (DUF1573) These hypothetical proteins, from bacteria such as Rhodopirellula baltica, Bacteroides thetaiotaomicron, and Porphyromonas gingivalis, share a region of conserved sequence towards their N-termini. (from Pfam) NF019244.5 PF07613.16 DUF1576 25 25 178 PfamAutoEq Y Y N DUF1576 domain-containing protein 131567 cellular organisms no rank 2524 EBI-EMBL Protein of unknown function (DUF1576) Protein of unknown function (DUF1576) This small family is found in several undescribed proteins. The alignment is distinguished by the frequent occurrence of conserved glycine and aromatic residues. (from Pfam) NF019247.5 PF07617.16 DUF1579 25.2 25.2 155 domain Y Y N DUF1579 family protein 131567 cellular organisms no rank 5723 EBI-EMBL Protein of unknown function (DUF1579) DUF1579 family protein A family of paralogous hypothetical proteins identified in Rhodopirellula baltica that also has members in Gloeobacter violaceus, Sinorhizobium meliloti and Agrobacterium tumefaciens. (from Pfam) NF019260.5 PF07632.16 Sde182_NH-like 26.8 26.8 268 domain Y Y N nucleoside hydrolase-like domain-containing protein 21905122 131567 cellular organisms no rank 5517 EBI-EMBL Cellulose-binding Sde182, nucleoside hydrolase-like domain Cellulose-binding Sde182, nucleoside hydrolase-like domain This Rossmann-related domain is found at the N-terminal end of the C-terminal domain region of the cellulose-binding protein Sde182 from Saccharophagus degradans (Swiss:Q21PD3), which seems to have capacity to bind plant carbohydrates. This domain shows an alpha/beta configuration with a central beta-sheet of eight beta-strands and 12 alpha-helices. It is structurally similar to pyrimidine-specific ribonucleoside hydrolases (NH) [1]. This domain is also found in other uncharacterised bacterial and fungal proteins. [1]. 21905122. Ab initio phasing of a nucleoside hydrolase-related hypothetical protein from Saccharophagus degradans that is associated with carbohydrate metabolism. Hehemann JH, Marsters C, Boraston AB;. Proteins. 2011;79:2992-2998. (from Pfam) NF019265.5 PF07638.16 Sigma70_ECF 21.1 21.1 185 domain Y Y N ECF-type sigma factor 12073657 131567 cellular organisms no rank 280458 EBI-EMBL ECF sigma factor ECF-type sigma factor These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily [1] and show sequence similarity to Pfam:PF04542 and Pfam:PF04545. [1]. 12073657. The extracytoplasmic function (ECF) sigma factors. Helmann JD;. Adv Microb Physiol 2002;46:47-110. (from Pfam) NF019272.5 PF07646.20 Kelch_2 21.3 21.3 48 repeat Y N N kelch repeat protein GO:0005515 15475350,2002850,8126718 131567 cellular organisms no rank 14178 EBI-EMBL Kelch motif kelch motif The kelch motif was initially discovered in Kelch (Swiss:Q04652). In this protein there are six copies of the motif. It has been shown that Swiss:Q04652 is related to Galactose Oxidase [1] for which a structure has been solved [2]. The kelch motif forms a beta sheet. Several of these sheets associate to form a beta propeller structure as found in Pfam:PF00064, Pfam:PF00400 and Pfam:PF00415. [1]. 8126718. Drosophila kelch motif is derived from a common enzyme fold. Bork P, Doolittle RF;. J Mol Biol 1994;236:1277-1282. [2]. 2002850. Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase. Ito N, Phillips SE, Stevens C, Ogel ZB, McPherson MJ, Keen JN, Yadav KD, Knowles PF;. Nature 1991;350:87-90. [3]. 15475350. Crystal structure of the Kelch domain of human Keap1. Li X, Zhang D, Hannink M, Beamer LJ;. J Biol Chem 2004;279:54750-54758. (from Pfam) NF019274.5 PF07648.20 Kazal_2 22.8 11 48 domain Y Y N Kazal-type serine protease inhibitor domain-containing protein GO:0005515 131567 cellular organisms no rank 1699 EBI-EMBL Kazal-type serine protease inhibitor domain Kazal-type serine protease inhibitor domain Usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors. Kazal domains often occur in tandem arrays. Small alpha+beta fold containing three disulphides. (from Pfam) NF019275.5 PF07650.22 KH_2 22 22 78 domain Y Y N KH domain-containing protein GO:0003723 8036511,8612276 131567 cellular organisms no rank 98402 EBI-EMBL KH domain KH domain NF019277.5 PF07652.19 Flavi_DEAD 21 21 148 PfamEq Y N N Flavivirus DEAD domain GO:0004386,GO:0005524 131567 cellular organisms no rank 1495 EBI-EMBL Flavivirus DEAD domain Flavivirus DEAD domain NF019278.5 PF07653.22 SH3_2 21.8 21.8 55 domain Y Y N SH3 domain-containing protein GO:0005515 12169629 131567 cellular organisms no rank 3688 EBI-EMBL Variant SH3 domain variant SH3 domain SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase Swiss:P12931. The structure is a partly opened beta barrel. [1]. 12169629. Diverse recognition of non-PxxP peptide ligands by the SH3 domains from p67(phox), Grb2 and Pex13p. Kami K, Takeya R, Sumimoto H, Kohda D;. EMBO J 2002;21:4268-4276. (from Pfam) NF019279.5 PF07654.20 C1-set 21 21 86 domain Y N N Immunoglobulin C1-set domain 131567 cellular organisms no rank 92 EBI-EMBL Immunoglobulin C1-set domain Immunoglobulin C1-set domain NF019282.5 PF07659.16 DUF1599 25 25 61 domain Y Y N nucleotide modification associated domain-containing protein 23814188 131567 cellular organisms no rank 5802 EBI-EMBL Nucleotide modification associated domain 1 Nucleotide modification associated domain 1 An alpha helical domain with conserved polar residues suggestive of enzymatic function. The domain is associated with the 5-hydroxymethyl uridine synthase and is predicted to play a role in modified base biosynthesis pathways [1]. [1]. 23814188. Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA. Iyer LM, Zhang D, Burroughs AM, Aravind L;. Nucleic Acids Res. 2013;41:7635-7655. (from Pfam) NF019287.5 PF07664.17 FeoB_C 26.6 26.6 54 domain Y N N Ferrous iron transport protein B C terminus GO:0006826,GO:0015093,GO:0016020 12446835,8407793 131567 cellular organisms no rank 62523 EBI-EMBL Ferrous iron transport protein B C terminus Ferrous iron transport protein B C terminus Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions [1]. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N-terminus has been previously erroneously described as being ATP-binding [1]. Recent work shows that it is similar to eukaryotic G-proteins and that it is a GTPase [2]. [1]. 8407793. Characterization of the ferrous iron uptake system of Escherichia coli. Kammler M, Schon C, Hantke K;. J Bacteriol 1993;175:6212-6219. [2]. 12446835. The membrane protein FeoB contains an intramolecular G protein essential for Fe(II) uptake in bacteria. Marlovits TC, Haase W, Herrmann C, Aller SG, Unger VM;. Proc Natl Acad Sci U S A 2002;99:16243-16248. (from Pfam) NF019291.5 PF07669.16 Eco57I 25.3 25.3 171 domain Y Y N Eco57I restriction-modification methylase domain-containing protein GO:0003677,GO:0003824,GO:0006304 1334261,8995524 131567 cellular organisms no rank 159576 EBI-EMBL Eco57I restriction-modification methylase Eco57I restriction-modification methylase Homologues of the Escherichia coli Eco57I restriction-modification methylase are found in several phylogenetically diverse bacteria. The structure of TaqI has been solved [1]. [1]. 1334261. Cloning and sequence analysis of the genes coding for Eco57I type IV restriction-modification enzymes. Janulaitis A, Vaisvila R, Timinskas A, Klimasauskas S, Butkus V;. Nucleic Acids Res 1992;20:6051-6056. [2]. 8995524. Differential binding of S-adenosylmethionine S-adenosylhomocysteine and Sinefungin to the adenine-specific DNA methyltransferase M.TaqI. Schluckebier G, Kozak M, Bleimling N, Weinhold E, Saenger W;. J Mol Biol. 1997;265:56-67. (from Pfam) NF019292.5 PF07670.19 Gate 29.6 29.6 104 domain Y Y N nucleoside recognition domain-containing protein 10455109,12781516 131567 cellular organisms no rank 148654 EBI-EMBL Nucleoside recognition Nucleoside recognition This region in the nucleoside transporter proteins are responsible for determining nucleoside specificity in the human CNT1 and CNT2 proteins (e.g Swiss:O00337) [1]. In the FeoB proteins (e.g. Swiss:O25396), which are believed to be Fe2+ transporters, it includes the membrane pore region, so the function of this region is likely to be more general than just nucleoside specificity [2]. This family may represent the pore and gate, with a wide potential range of specificity. Hence its name 'Gate'. [1]. 10455109. Identification of amino acid residues responsible for the pyrimidine and purine nucleoside specificities of human concentrative Na(+) nucleoside cotransporters hCNT1 and hCNT2. Loewen SK, Ng AM, Yao SY, Cass CE, Baldwin SA, Young JD;. J Biol Chem 1999;274:24475-24484. [2]. 12781516. Is the bacterial ferrous iron transporter FeoB a living fossil?. Hantke K;. Trends Microbiol 2003;11:192-195. (from Pfam) NF019294.5 PF07672.18 MFS_Mycoplasma 24 24 297 domain Y N N Mycoplasma MFS transporter 131567 cellular organisms no rank 1017 EBI-EMBL Mycoplasma MFS transporter Mycoplasma MFS transporter These proteins share some similarity with members of the Major Facilitator Superfamily (MFS). (from Pfam) NF019297.5 PF07677.19 A2M_recep 21.7 21.7 95 domain Y N N A-macroglobulin receptor binding domain GO:0005576 10625650,10825534,11106161,11387479,22290936 131567 cellular organisms no rank 253 EBI-EMBL A-macroglobulin receptor binding domain A-macroglobulin receptor binding domain This family includes the receptor binding domain region of the alpha-2-macroglobulin family. [1]. 10625650. NMR solution structure of the receptor binding domain of human alpha(2)-macroglobulin. Huang W, Dolmer K, Liao X, Gettins PG;. J Biol Chem 2000;275:1089-1094. [2]. 11106161. Structure of a rat alpha 1-macroglobulin receptor-binding domain dimer. Xiao T, DeCamp DL, Spran SR;. Protein Sci 2000;9:1889-1897. [3]. 11387479. Structure of complement receptor 2 in complex with its C3d ligand. Szakonyi G, Guthridge JM, Li D, Young K, Holers VM, Chen XS;. Science 2001;292:1725-1728. [4]. 10825534. Structure at 1.44 A resolution of an N-terminally truncated form of the rat serum complement C3d fragment. Zanotti G, Bassetto A, Battistutta R, Folli C, Arcidiaco P, Stoppini M, Berni R;. Biochim Biophys Acta 2000;1478:232-238. [5]. 22290936. The crystal structure of human alpha2-macroglobulin reveals a unique molecular cage. Marrero A, Duquerroy S, Trapani S, Goulas T, Guevara T, Andersen GR, Navaza J, Sottrup-Jensen L, Gomis-Ruth FX;. Angew Chem Int Ed Engl. 2012;51:3340-3344. (from Pfam) NF019298.5 PF07678.19 TED_complement 22 22 312 PfamEq Y N N A-macroglobulin TED domain GO:0005615 10625650,10825534,11106161,11387479 131567 cellular organisms no rank 27173 EBI-EMBL A-macroglobulin TED domain A-macroglobulin TED domain This entry corresponds to the TED domain of the complement components such as C3, C4 and C5. This domain contains a short highly conserved region of proteinase-binding alpha-macro-globulins contains the cysteine and a glutamine of a thiol-ester bond that is cleaved at the moment of proteinase binding, and mediates the covalent binding of the alpha-macro-globulin to the proteinase. The GCGEQ motif is highly conserved. [1]. 10625650. NMR solution structure of the receptor binding domain of human alpha(2)-macroglobulin. Huang W, Dolmer K, Liao X, Gettins PG;. J Biol Chem 2000;275:1089-1094. [2]. 11106161. Structure of a rat alpha 1-macroglobulin receptor-binding domain dimer. Xiao T, DeCamp DL, Spran SR;. Protein Sci 2000;9:1889-1897. [3]. 11387479. Structure of complement receptor 2 in complex with its C3d ligand. Szakonyi G, Guthridge JM, Li D, Young K, Holers VM, Chen XS;. Science 2001;292:1725-1728. [4]. 10825534. Structure at 1.44 A resolution of an N-terminally truncated form of the rat serum complement C3d fragment. Zanotti G, Bassetto A, Battistutta R, Folli C, Arcidiaco P, Stoppini M, Berni R;. Biochim Biophys Acta 2000;1478:232-238. (from Pfam) NF019300.5 PF07680.16 DoxA 27 27 131 domain Y Y N TQO small subunit DoxA domain-containing protein 15306018 131567 cellular organisms no rank 1453 EBI-EMBL TQO small subunit DoxA TQO small subunit DoxA Thiosulphate:quinone oxidoreductase (TQO) is one of the early steps in elemental sulphur oxidation. A novel TQO enzyme was purified from the thermo-acidophilic archaeon Acidianus ambivalens and shown to consist of a large subunit (DoxD) and a smaller subunit (DoxA). The DoxD- and DoxA-like two subunits are fused together in a single polypeptide in Swiss:Q8AAF0. [1]. 15306018. Coupling of the pathway of sulphur oxidation to dioxygen reduction: characterization of a novel membrane-bound thiosulphate:quinone oxidoreductase. Muller FH, Bandeiras TM, Urich T, Teixeira M, Gomes CM, Kletzin A;. Mol Microbiol. 2004;53:1147-1160. (from Pfam) NF019301.5 PF07681.17 DoxX 23.6 23.6 85 domain Y Y N DoxX family membrane protein 15306018 131567 cellular organisms no rank 168992 EBI-EMBL DoxX DoxX family membrane protein These proteins appear to have some sequence similarity with Pfam:PF04173 but their function is unknown [1]. [1]. 15306018. Coupling of the pathway of sulphur oxidation to dioxygen reduction: characterization of a novel membrane-bound thiosulphate:quinone oxidoreductase. Muller FH, Bandeiras TM, Urich T, Teixeira M, Gomes CM, Kletzin A;. Mol Microbiol. 2004;53:1147-1160. (from Pfam) NF019302.5 PF07682.16 SOR 25 25 300 subfamily Y Y N sulfur oxygenase reductase family protein 11111027,12664265,15030315,2493451 131567 cellular organisms no rank 142 EBI-EMBL Sulphur oxygenase reductase sulfur oxygenase reductase family protein The sulphur oxygenase/reductase (SOR) of the thermo-acidophilic archaeon Acidianus ambivalens is an unusual enzyme consisting of 24 identical subunits arranged in a perfectly symmetrical hollow sphere and containing a mononuclear non-heme iron centre (personal communication: A. Kletzin). At 85 degrees C in vitro, elemental sulphur is oxidised to sulphite, thiosulphate and hydrogen sulphide with no external cofactors needed. The proposed equation is: 4S + O2 + 4 H2O ---> 2 HSO3- + 2 H2S + 2 H+. [1]. 2493451. Coupled enzymatic production of sulfite, thiosulfate, and hydrogen sulfide from sulfur: purification and properties of a sulfur oxygenase reductase from the facultatively anaerobic archaebacterium Desulfurolobus ambivalens. Kletzin A;. J Bacteriol 1989;171:1638-1643. [2]. 11111027. Cloning and heterologous expression of a sulfur oxygenase/reductase gene from the thermoacidophilic archaeon Acidianus sp. S5 in Escherichia coli. He Z, Li Y, Zhou P, Liu S;. FEMS Microbiol Lett 2000;193:217-221. [3]. 12664265. Purification and properties of the sulfur oxygenase/reductase from the acidothermophilic archaeon, Acidianus strain S5. Sun CW, Chen ZW, He ZG, Zhou PJ, Liu SJ;. Extremophiles 2003;7:131-134. [4]. 15030315. The sulphur oxygenase reductase from Acidianus ambivalens is a multimeric protein containing a low-potential mononuclear non-haem iron centre. Urich T, Bandeiras TM, Leal SS, Rachel R, Albrecht T, Zimmermann P, Scholz C, Teixeira M, Gomes CM, Kletzin A;. Biochem J 2004; [Epub ahead of print] (from Pfam) NF019303.5 PF07683.19 CobW_C 22 22 94 domain Y Y N GTP-binding protein 1655697,19822009 131567 cellular organisms no rank 122335 EBI-EMBL Cobalamin synthesis protein cobW C-terminal domain Cobalamin synthesis protein cobW C-terminal domain This is a large and diverse family of putative metal chaperones that can be separated into up to 15 subgroups. In addition to known roles in cobalamin biosynthesis [1] and the activation of the Fe-type nitrile hydratase, this family is also known to be involved in the response to zinc limitation. The CobW subgroup involved in cobalamin synthesis represents only a small sub-fraction of the family [2]. [1]. 1655697. Nucleotide sequence and genetic analysis of a 13.1-kilobase-pair Pseudomonas denitrificans DNA fragment containing five cob genes and identification of structural genes encoding Cob(I)alamin adenosyltransferase, cobyric acid synthase, and bifunctional cob. Crouzet J, Levy-Schil S, Cameron B, Cauchois L, Rigault S, Rouyez MC, Blanche F, Debussche L, Thibaut D;. J Bacteriol 1991;173:6074-6087. [2]. 19822009. A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. Haas CE, Rodionov DA, Kropat J, Malasarn D, Merchant SS, de Crecy-Lagard V;. BMC Genomics. 2009;10:470. (from Pfam) NF019305.5 PF07685.19 GATase_3 27 27 196 domain Y N N CobB/CobQ-like glutamine amidotransferase domain GO:0003824 10966576 131567 cellular organisms no rank 184247 EBI-EMBL CobB/CobQ-like glutamine amidotransferase domain CobB/CobQ-like glutamine amidotransferase domain NF019307.5 PF07687.19 M20_dimer 21 21 107 domain Y Y N peptidase dimerization domain-containing protein 7674922,9083113 131567 cellular organisms no rank 609641 EBI-EMBL Peptidase dimerisation domain Peptidase dimerisation domain This domain consists of 4 beta strands and two alpha helices which make up the dimerisation surface of members of the M20 family of peptidases [1]. This family includes a range of zinc metallopeptidases belonging to several families in the peptidase classification [2]. Family M20 are Glutamate carboxypeptidases. Peptidase family M25 contains X-His dipeptidases. [1]. 9083113. Crystal structure of carboxypeptidase G2, a bacterial enzyme with applications in cancer therapy. Rowsell S, Pauptit RA, Tucker AD, Melton RG, Blow DM, Brick P;. Structure 1997;5:337-347. [2]. 7674922. Evolutionary families of metallopeptidases. Rawlings ND, Barrett AJ;. Meth Enzymol 1995;248:183-228. (from Pfam) NF019309.5 PF07689.17 KaiB 27 27 82 domain Y Y N circadian clock KaiB family protein GO:0048511 15071498 131567 cellular organisms no rank 5679 EBI-EMBL KaiB domain KaiB domain The cyanobacterial clock proteins KaiA and KaiB are proposed as regulators of the circadian rhythm in cyanobacteria. Mutations in both proteins have been reported to alter or abolish circadian rhythmicity. KaiB adopts an alpha-beta meander motif and is found to be a dimer [1]. [1]. 15071498. Anabaena circadian clock proteins KaiA and KaiB reveal a potential common binding site to their partner KaiC. Garces RG, Wu N, Gillon W, Pai EF;. EMBO J 2004;23:1688-1698. (from Pfam) NF019310.5 PF07690.21 MFS_1 33.4 33.4 347 subfamily Y Y N MFS transporter GO:0022857,GO:0055085 131567 cellular organisms no rank 4074928 EBI-EMBL Major Facilitator Superfamily MFS transporter NF019311.5 PF07691.17 PA14 24 24 147 domain Y Y N PA14 domain-containing protein 15236739 131567 cellular organisms no rank 52586 EBI-EMBL PA14 domain PA14 domain This domain forms an insert in bacterial beta-glucosidases and is found in other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins, including anthrax protective antigen (PA). The domain also occurs in a Dictyostelium prespore-cell-inducing factor Psi and in fibrocystin, the mammalian protein whose mutation leads to polycystic kidney and hepatic disease. The crystal structure of PA shows that this domain (named PA14 after its location in the PA20 pro-peptide) has a beta-barrel structure. The PA14 domain sequence suggests a binding function, rather than a catalytic role. The PA14 domain distribution is compatible with carbohydrate binding. [1]. 15236739. The PA14 domain, a conserved all-beta domain in bacterial toxins, enzymes, adhesins and signaling molecules. Rigden DJ, Mello LV, Galperin MY;. Trends Biochem Sci. 2004;29:335-339. (from Pfam) NF019313.5 PF07693.19 KAP_NTPase 20 18 293 domain Y Y N P-loop NTPase fold protein 15128444 131567 cellular organisms no rank 45570 EBI-EMBL KAP family P-loop domain KAP family P-loop NTPase fold protein The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [1]. [1]. 15128444. A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain. Aravind L, Iyer LM, Leipe DD, Koonin EV;. Genome Biol 2004;5:R30. (from Pfam) NF019314.5 PF07694.17 5TM-5TMR_LYT 24.6 24.6 169 domain Y Y N LytS/YhcK type 5TM receptor domain-containing protein GO:0000155,GO:0000160,GO:0004673,GO:0016020,GO:0071555 12914674 131567 cellular organisms no rank 37057 EBI-EMBL 5TMR of 5TMR-LYT 5TMR of 5TMR-LYT This entry represents the transmembrane region of the 5TM-LYT (5TM Receptors of the LytS-YhcK type) [1]. [1]. 12914674. Application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria. Anantharaman V, Aravind L;. BMC Genomics 2003;4:34. (from Pfam) NF019318.5 PF07698.16 7TM-7TMR_HD 29.4 29.4 190 PfamEq Y N N 7TM receptor with intracellular HD hydrolase 12914674 131567 cellular organisms no rank 14113 EBI-EMBL 7TM receptor with intracellular HD hydrolase 7TM receptor with intracellular HD hydrolase These bacterial 7TM receptor proteins have an intracellular Pfam:PF01966. This entry corresponds to the 7 helix transmembrane domain. These proteins also contain an N-terminal extracellular domain. [1]. 12914674. Application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria. Anantharaman V, Aravind L;. BMC Genomics 2003;4:34. (from Pfam) NF019320.5 PF07700.20 HNOB 25.5 24.5 163 domain Y Y N heme NO-binding domain-containing protein GO:0020037 12590654,15326296,15472039 131567 cellular organisms no rank 7076 EBI-EMBL Haem-NO-binding Haem-NO-binding The HNOB (Haem NO Binding) domain, is a predominantly alpha-helical domain and binds heme via a covalent linkage to histidine. It is a haem protein sensor (SONO) that displays femtomolar affinity for nitrous oxide, NO [3]. It is predicted to function as a haem-dependent sensor for gaseous ligands and to transduce diverse downstream signals in both bacteria and animals. [1]. 12590654. Ancient conserved domains shared by animal soluble guanylyl cyclases and bacterial signaling proteins. Iyer LM, Anantharaman V, Aravind L;. BMC Genomics 2003;4:5. [2]. 15326296. Crystal structure of an oxygen-binding heme domain related to soluble guanylate cyclases. Pellicena P, Karow DS, Boon EM, Marletta MA, Kuriyan J;. Proc Natl Acad Sci U S A 2004;101:12854-12859. [3]. 15472039. Femtomolar sensitivity of a NO sensor from Clostridium botulinum. Nioche P, Berka V, Vipond J, Minton N, Tsai AL, Raman CS;. Science. 2004;306:1550-1553. (from Pfam) NF019322.5 PF07702.18 UTRA 23.8 23.8 141 domain Y Y N UTRA domain-containing protein GO:0003677,GO:0006355 12757941 131567 cellular organisms no rank 242570 EBI-EMBL UTRA domain UTRA domain The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain that has a similar fold to Pfam:PF04345 [1]. It is believed to modulate activity of bacterial transcription factors in response to binding small molecules [1] sugar phosphates and urocanate, Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 12757941. HutC/FarR-like bacterial transcription factors of the GntR family contain a small molecule-binding domain of the chorismate lyase fold. Aravind L, Anantharaman V;. FEMS Microbiol Lett 2003;222:17-23. (from Pfam) NF019323.5 PF07703.19 A2M_BRD 22.7 22.7 140 domain Y N N Alpha-2-macroglobulin bait region domain 22290936,25221932 131567 cellular organisms no rank 51506 EBI-EMBL Alpha-2-macroglobulin bait region domain Alpha-2-macroglobulin bait region domain Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. However, A2M-like proteins were identified in pathogenically invasive bacteria and species that colonize higher eukaryotes. This domain is found in eukaryotic and bacterial proteins. In human A2Ms, this domain encompasses macroglobulin-like domain MG5 and 6 including bait region. In Salmonella enterica ser A2Ms, this domain encompasses MG7 and MG8 including the bait region [1] [2]. The Bait region is cleaved by proteases, followed by a large conformational change that blocks the target protease within a cage-like complex. This model of protease entrapment is recognised as the Venus flytrap mechanism [1]. [1]. 25221932. Structure of a bacterial alpha2-macroglobulin reveals mimicry of eukaryotic innate immunity. Wong SG, Dessen A;. Nat Commun. 2014;5:4917. [2]. 22290936. The crystal structure of human alpha2-macroglobulin reveals a unique molecular cage. Marrero A, Duquerroy S, Trapani S, Goulas T, Guevara T, Andersen GR, Navaza J, Sottrup-Jensen L, Gomis-Ruth FX;. Angew Chem Int Ed Engl. 2012;51:3340-3344. (from Pfam) NF019325.5 PF07705.16 CARDB 22.7 22.7 101 domain Y Y N CARDB domain-containing protein 131567 cellular organisms no rank 24980 EBI-EMBL CARDB CARDB Cell adhesion related domain found in bacteria. (from Pfam) NF019334.5 PF07714.22 PK_Tyr_Ser-Thr 23.1 23.1 258 domain Y Y N protein kinase GO:0004672,GO:0006468 1956325,3291115,7768349,9020587 131567 cellular organisms no rank 654984 EBI-EMBL Protein tyrosine and serine/threonine kinase protein kinase Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity [1]; Serine/threonine-protein kinases, tyrosine-protein kinases, and dual specificity protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins). This entry represents the catalytic domain found in a number of serine/threonine- and tyrosine-protein kinases. It does not include the catalytic domain of dual specificity kinases. [1]. 3291115. The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. Hanks SK, Quinn AM, Hunter T;. Science. 1988;241:42-52. [2]. 1956325. Protein kinase catalytic domain sequence database: identification of conserved features of primary structure and classification of family members. Hanks SK, Quinn AM;. Methods Enzymol 1991;200:38-62. [3]. 7768349. Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification. Hanks SK, Hunter T;. FASEB J 1995;9:576-596. [4]. 9020587. The protein kinases of budding yeast: six score and more. Hunter T, Plowman GD;. Trends Biochem Sci 1997;22:18-22. (from Pfam) NF019335.5 PF07715.20 Plug 23.9 23.9 107 domain Y Y N TonB-dependent receptor plug domain-containing protein 15111112 131567 cellular organisms no rank 1281876 EBI-EMBL TonB-dependent Receptor Plug Domain TonB-dependent Receptor Plug Domain The Plug domain has been shown to be an independently folding subunit of the TonB-dependent receptors ([1]). It acts as the channel gate, blocking the pore until the channel is bound by ligand. At this point it under goes conformational changes opens the channel. [1]. 15111112. The plug domain of a neisserial TonB-dependent transporter retains structural integrity in the absence of its transmembrane beta-barrel. Oke M, Sarra R, Ghirlando R, Farnaud S, Gorringe AR, Evans RW, Buchanan SK;. FEBS Lett 2004;564:294-300. (from Pfam) NF019339.5 PF07719.22 TPR_2 27 22.9 34 domain Y Y N tetratricopeptide repeat protein 7667876,9482716 131567 cellular organisms no rank 249421 EBI-EMBL Tetratricopeptide repeat Tetratricopeptide repeat This Pfam entry includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by Pfam:PF00515. [1]. 7667876. Tetratrico peptide repeat interactions: to TPR or not to TPR?. Lamb JR, Tugendreich S, Hieter P;. Trends Biochem Sci 1995;20:257-259. [2]. 9482716. The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions. Das AK, Cohen PW, Barford D;. EMBO J 1998;17:1192-1199. (from Pfam) NF019340.5 PF07720.17 TPR_3 20.7 11 34 domain Y Y N tetratricopeptide repeat protein 12799000 131567 cellular organisms no rank 8923 EBI-EMBL Tetratricopeptide repeat Tetratricopeptide repeat This Pfam entry includes tetratricopeptide-like repeats found in the LcrH/SycD-like chaperones [1]. [1]. 12799000. Tetratricopeptide-like repeats in type-III-secretion chaperones and regulators. Pallen MJ, Francis MS, Futterer K;. FEMS Microbiol Lett 2003;223:53-60. (from Pfam) NF019341.5 PF07721.19 TPR_4 27 10 26 repeat Y N N tetratricopeptide repeat protein GO:0042802 131567 cellular organisms no rank 45767 EBI-EMBL Tetratricopeptide repeat tetratricopeptide repeat This Pfam entry includes tetratricopeptide-like repeats not detected by the Pfam:PF00515, Pfam:PF07719 and Pfam:PF07720 models. (from Pfam) NF019342.5 PF07722.18 Peptidase_C26 20.5 20.5 219 domain Y Y N gamma-glutamyl-gamma-aminobutyrate hydrolase family protein GO:0016787 11953431 131567 cellular organisms no rank 336695 EBI-EMBL Peptidase C26 C26 family cysteine hydrolase domain These peptidases have gamma-glutamyl hydrolase activity; that is they catalyse the cleavage of the gamma-glutamyl bond in poly-gamma-glutamyl substrates. They are structurally related to Pfam:PF00117, but contain extensions in four loops and at the C terminus [1]. [1]. 11953431. Three-dimensional structure of human gamma -glutamyl hydrolase. A class I glatamine amidotransferase adapted for a complex substate. Li H, Ryan TJ, Chave KJ, Van Roey P;. J Biol Chem 2002;277:24522-24529. (from Pfam). Members of this family of hydrolases with an active site Cys residue belong to MEROPS family C26. NF019344.5 PF07724.19 AAA_2 27 27 166 domain Y Y N AAA family ATPase GO:0005524,GO:0016887 7646486,9927482 131567 cellular organisms no rank 394016 EBI-EMBL AAA domain (Cdc48 subfamily) AAA family ATPase This Pfam entry includes some of the AAA proteins not detected by the Pfam:PF00004 model. [1]. 7646486. A 200-amino acid ATPase module in search of a basic function. Confalonieri F, Duguet M;. Bioessays 1995;17:639-650. A large extension of the family. [2]. 9927482. AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Neuwald AF, Aravind L, Spouge JL, Koonin EV;. Genome Res 1999;9:27-43. (from Pfam) NF019346.5 PF07726.16 AAA_3 27 27 131 domain Y Y N AAA family ATPase GO:0005524,GO:0016887 7646486,9927482 131567 cellular organisms no rank 117613 EBI-EMBL ATPase family associated with various cellular activities (AAA) AAA family ATPase This Pfam entry includes some of the AAA proteins not detected by the Pfam:PF00004 model. [1]. 7646486. A 200-amino acid ATPase module in search of a basic function. Confalonieri F, Duguet M;. Bioessays 1995;17:639-650. A large extension of the family. [2]. 9927482. AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Neuwald AF, Aravind L, Spouge JL, Koonin EV;. Genome Res 1999;9:27-43. (from Pfam) NF019347.5 PF07727.19 RVT_2 31.6 31.6 243 domain Y Y N reverse transcriptase domain-containing protein 1698615 131567 cellular organisms no rank 315 EBI-EMBL Reverse transcriptase (RNA-dependent DNA polymerase) reverse transcriptase domain A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. This Pfam entry includes reverse transcriptases not recognised by the Pfam:PF00078 model. [1]. 1698615. Origin and evolution of retroelements based upon their reverse transcriptase sequences. Xiong Y, Eickbush TH;. EMBO J 1990;9:3353-3362. (from Pfam) NF019348.5 PF07728.19 AAA_5 22 22 139 domain Y Y N AAA family ATPase GO:0005524,GO:0016887 7646486,9927482 131567 cellular organisms no rank 1336869 EBI-EMBL AAA domain (dynein-related subfamily) AAA family ATPase This Pfam entry includes some of the AAA proteins not detected by the Pfam:PF00004 model. [1]. 7646486. A 200-amino acid ATPase module in search of a basic function. Confalonieri F, Duguet M;. Bioessays 1995;17:639-650. A large extension of the family. [2]. 9927482. AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Neuwald AF, Aravind L, Spouge JL, Koonin EV;. Genome Res 1999;9:27-43. (from Pfam) NF019349.5 PF07729.17 FCD 24.3 24.3 125 domain Y Y N FCD domain-containing protein 11013219 131567 cellular organisms no rank 554773 EBI-EMBL FCD domain FCD domain This domain is the C-terminal ligand binding domain of many members of the GntR family. This domain binds to a range of effector molecules, including Lactate, Zn(II), Ni(II), Ca(II), Mg(II), citrate, sugar acids, sialic acid and N-acetylglucosamine-6-P, that regulate the transcription of genes through the action of the N-terminal DNA-binding domain Pfam:PF00392 (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). This domain is found in Swiss:P45427 and Swiss:P31460 that are regulators of sugar biosynthesis operons. It is also in the known structure of FadR where it binds to acyl-coA, the domain is alpha helical [1]. This family has been named as FCD for (FadR C-terminal Domain). [1]. 11013219. Crystal structure of FadR, a fatty acid-responsive transcription factor with a novel acyl coenzyme A-binding fold. van Aalten DM, DiRusso CC, Knudsen J, Wierenga RK;. EMBO J 2000;19:5167-5177. (from Pfam) NF019351.5 PF07731.19 Cu-oxidase_2 20.4 20.4 137 domain Y Y N multicopper oxidase domain-containing protein GO:0005507,GO:0016491 10573417,1548698,2404764,7599131 131567 cellular organisms no rank 120210 EBI-EMBL Multicopper oxidase Multicopper oxidase This entry contains many divergent copper oxidase-like domains that are not recognised by the Pfam:PF00394 model. [1]. 2404764. The blue oxidases, ascorbate oxidase, laccase and ceruloplasmin. Modelling and structural relationships. Messerschmidt A, Huber R;. Eur J Biochem 1990;187:341-352. [2]. 1548698. Refined crystal structure of ascorbate oxidase at 1.9 A resolution. Messerschmidt A, Ladenstein R, Huber R, Bolognesi M, Avigliano L, Petruzzelli R, Rossi A, Finazzi-Agro A;. J Mol Biol 1992;224:179-205. [3]. 10573417. Natural engineering principles of electron tunnelling in biological oxidation-reduction. Page CC, Moser CC, Chen X, Dutton PL;. Nature 1999;402:47-52. [4]. 7599131. X-ray absorption studies and homology modeling define the structural features that specify the nature of the copper site in rusticyanin. Grossmann JG, Ingledew WJ, Harvey I, Strange RW, Hasnain SS;. Biochemistry 1995;34:8406-8414. (from Pfam) NF019352.5 PF07732.20 Cu-oxidase_3 21 21 119 domain Y Y N multicopper oxidase domain-containing protein GO:0005507 10573417,1548698,2404764,7599131 131567 cellular organisms no rank 118083 EBI-EMBL Multicopper oxidase Multicopper oxidase This entry contains many divergent copper oxidase-like domains that are not recognised by the Pfam:PF00394 model. [1]. 2404764. The blue oxidases, ascorbate oxidase, laccase and ceruloplasmin. Modelling and structural relationships. Messerschmidt A, Huber R;. Eur J Biochem 1990;187:341-352. [2]. 1548698. Refined crystal structure of ascorbate oxidase at 1.9 A resolution. Messerschmidt A, Ladenstein R, Huber R, Bolognesi M, Avigliano L, Petruzzelli R, Rossi A, Finazzi-Agro A;. J Mol Biol 1992;224:179-205. [3]. 10573417. Natural engineering principles of electron tunnelling in biological oxidation-reduction. Page CC, Moser CC, Chen X, Dutton PL;. Nature 1999;402:47-52. [4]. 7599131. X-ray absorption studies and homology modeling define the structural features that specify the nature of the copper site in rusticyanin. Grossmann JG, Ingledew WJ, Harvey I, Strange RW, Hasnain SS;. Biochemistry 1995;34:8406-8414. (from Pfam) NF019359.5 PF07739.18 TipAS 23.8 23.8 117 domain Y Y N TipAS antibiotic-recognition domain-containing protein 12682015 131567 cellular organisms no rank 40720 EBI-EMBL TipAS antibiotic-recognition domain TipAS antibiotic-recognition domain This domain is found at the C-terminus of some MerR family transcription factors. The domain has an alpha-helical globin-like fold [1]. The family includes Mta a central regulator of multidrug resistance in Bacillus subtilis. [1]. 12682015. Structural basis for antibiotic recognition by the TipA class of multidrug-resistance transcriptional regulators. Kahmann JD, Sass HJ, Allan MG, Seto H, Thompson CJ, Grzesiek S;. EMBO J 2003;22:1824-1834. (from Pfam) NF019365.5 PF07745.18 Glyco_hydro_53 24 24 340 domain Y Y N glycosyl hydrolase 53 family protein GO:0015926 12484750,12691742 131567 cellular organisms no rank 18400 EBI-EMBL Glycosyl hydrolase family 53 glycosyl hydrolase 53 family protein This domain belongs to family 53 of the glycosyl hydrolase classification [1]. These enzymes are enzymes are endo-1,4- beta-galactanases (EC:3.2.1.89). The structure of this domain is known [2] and has a TIM barrel fold. [1]. 12691742. An evolving hierarchical family classification for glycosyltransferases. Coutinho PM, Deleury E, Davies GJ, Henrissat B;. J Mol Biol 2003;328:307-317. [2]. 12484750. Aspergillus aculeatus beta-1,4-galactanase: substrate recognition and relations to other glycoside hydrolases in clan GH-A. Ryttersgaard C, Lo Leggio L, Coutinho PM, Henrissat B, Larsen S;. Biochemistry 2002;41:15135-15143. (from Pfam) NF019366.5 PF07746.16 LigA 25.3 25.3 87 domain Y N N Aromatic-ring-opening dioxygenase LigAB, LigA subunit 10467151 131567 cellular organisms no rank 7072 EBI-EMBL Aromatic-ring-opening dioxygenase LigAB, LigA subunit Aromatic-ring-opening dioxygenase LigAB, LigA subunit This is a family of aromatic ring opening dioxygenases which catalyse the ring-opening reaction of protocatechuate and related compounds [1]. [1]. 10467151. Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions. Sugimoto K, Senda T, Aoshima H, Masai E, Fukuda M, Mitsui Y;. Structure Fold Des 1999;7:953-965. (from Pfam) NF019367.5 PF07747.16 MTH865 25 25 70 domain Y Y N MTH865 family protein 11693569 131567 cellular organisms no rank 898 EBI-EMBL MTH865-like family MTH865 family protein This domain has an EF-hand like fold. (from Pfam) NF019368.5 PF07748.18 Glyco_hydro_38C 25 25 206 domain Y Y N glycoside hydrolase family 38 C-terminal domain-containing protein GO:0004559,GO:0006013 9649738 131567 cellular organisms no rank 49165 EBI-EMBL Glycosyl hydrolases family 38 C-terminal domain Glycosyl hydrolases family 38 C-terminal domain Glycosyl hydrolases are key enzymes of carbohydrate metabolism. [1]. 9649738. Glycosidase families. Henrissat B. Biochem Soc Trans 1998;26:153-156. (from Pfam) NF019370.5 PF07750.16 GcrA 26.9 26.9 155 domain Y Y N GcrA family cell cycle regulator 15087506 131567 cellular organisms no rank 11047 EBI-EMBL GcrA cell cycle regulator GcrA family cell cycle regulator GcrA is a master cell cycle regulator that, together with CtrA (see Pfam:PF00072 and Pfam:PF00486), is involved in controlling cell cycle progression and asymmetric polar morphogenesis [1]. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes [1]. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [1]. [1]. 15087506. Oscillating global regulators control the genetic circuit driving a bacterial cell cycle. Holtzendorff J, Hung D, Brende P, Reisenauer A, Viollier PH, McAdams HH, Shapiro L;. Science 2004;304:983-987. (from Pfam) NF019371.5 PF07751.16 Abi_2 25.6 25.6 184 domain Y Y N Abi family protein 7601848,7601849,8534099 131567 cellular organisms no rank 23092 EBI-EMBL Abi-like protein Abi family protein This family, found in various bacterial species, contains sequences that are similar to the Abi group of proteins, which are involved in bacteriophage resistance mediated by abortive infection in Lactococcus species [1,2]. The proteins are thought to have helix-turn-helix motifs, found in many DNA-binding proteins, allowing them to perform their function [3]. [1]. 8534099. Cloning and DNA sequence analysis of two abortive infection phage resistance determinants from the lactococcal plasmid pNP40. Garvey P, Fitzgerald GF, Hill C;. Appl Environ Microbiol 1995;61:4321-4328. [2]. 7601848. Characterization of the lactococcal abiD1 gene coding for phage abortive infection. Anba J, Bidnenko E, Hillier A, Ehrlich D, Chopin MC;. J Bacteriol 1995;177:3818-3823. [3]. 7601849. Phage operon involved in sensitivity to the Lactococcus lactis abortive infection mechanism AbiD1. Bidnenko E, Ehrlich D, Chopin MC;. J Bacteriol 1995;177:3824-3829. (from Pfam) NF019375.5 PF07755.16 DUF1611 25 25 201 domain Y Y N DUF1611 domain-containing protein 131567 cellular organisms no rank 11757 EBI-EMBL Domain of unknown function (DUF1611_C) P-loop domain Domain of unknown function (DUF1611_C) P-loop domain This region is found in a number of hypothetical bacterial and archaeal proteins. According to structure it has a P-loop structure. (from Pfam) NF019378.5 PF07758.16 DUF1614 23.9 23.9 171 domain Y Y N DUF1614 domain-containing protein 131567 cellular organisms no rank 1534 EBI-EMBL Protein of unknown function (DUF1614) Protein of unknown function (DUF1614) This is a family of sequences coming from hypothetical proteins found in both bacterial and archaeal species. (from Pfam) NF019380.5 PF07760.16 DUF1616 31.6 31.6 307 domain Y Y N DUF1616 domain-containing protein 131567 cellular organisms no rank 2523 EBI-EMBL Protein of unknown function (DUF1616) Protein of unknown function (DUF1616) This is a family of sequences from hypothetical archaeal proteins. The region in question is approximately 330 amino acid residues long. (from Pfam) NF019401.5 PF07784.16 DUF1622 24 24 78 domain Y Y N DUF1622 domain-containing protein 131567 cellular organisms no rank 8889 EBI-EMBL Protein of unknown function (DUF1622) Protein of unknown function (DUF1622) This is a family of 14 highly conserved sequences, from hypothetical proteins expressed by both bacterial and archaeal species. (from Pfam) NF019403.5 PF07786.17 HGSNAT_cat 22 22 222 domain Y Y N heparan-alpha-glucosaminide N-acetyltransferase domain-containing protein 20650889 131567 cellular organisms no rank 43635 EBI-EMBL Heparan-alpha-glucosaminide N-acetyltransferase, catalytic Heparan-alpha-glucosaminide N-acetyltransferase, catalytic This entry includes the catalytic domain of HGSNAT (Heparan-alpha-glucosaminide N-acetyltransferase). It contains the conserved histidine in the active site (His269), thought to hold the acetyl group during the transfer across the membrane and required for its enzymatic activity. HGSNAT transfers an acetyl group from cytoplasmically derived acetyl-CoA to terminal N-glucosamine residues of heparan sulfate within the lysosomes [1]. [1]. 20650889. Analysis of the biogenesis of heparan sulfate acetyl-CoA:alpha-glucosaminide N-acetyltransferase provides insights into the mechanism underlying its complete deficiency in mucopolysaccharidosis IIIC. Durand S, Feldhammer M, Bonneil E, Thibault P, Pshezhetsky AV;. J Biol Chem. 2010;285:31233-31242. (from Pfam) NF019405.5 PF07788.16 PDDEXK_10 21.2 21.2 74 domain Y N N PD-(D/E)XK nuclease superfamily 10382966,17584917 131567 cellular organisms no rank 703 EBI-EMBL PD-(D/E)XK nuclease superfamily PD-(D/E)XK nuclease superfamily This family is found to carry modified motifs characteristic of PD-(D/E)XK endonuclease superfamily. These are the conserved Glu of motif I, the Asp surreounded by hydrophobics of motif II, EIKS of motif III, and the lysine of mmotif IV has migrated to an alpha-helix following the third core beta-strand. The conserved patch of positively charged lysine and arginine residues in the motif IV apha-helix might be involved in substrate-binding or be contributing to active site formation [2]. Members with an additional N-terminal coi9led-coil domain, are annotated as tropomyosin, coiled-coil or microtubule binding proteins [1,2]. [1]. 10382966. Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. Kawarabayasi Y, Hino Y, Horikawa H, Yamazaki S, Haikawa Y, Jin-no K, Takahashi M, Sekine M, Baba S, Ankai A, Kosugi H, Hosoyama A, Fukui S, Nagai Y, Nishijima K, Nakazawa H, Takamiya M, Masuda S, Funahashi T, Tanaka T, Kudoh Y, Yamazaki J, Kushida N, Oguc. DNA Res 1999;6:83-101. [2]. 17584917. Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches. Knizewski L, Kinch LN, Grishin NV, Rychlewski L, Ginalski K;. BMC Struct Biol. 2007;7:40. (from Pfam) NF019407.5 PF07790.16 Pilin_N 25.2 25.2 78 domain Y Y N type IV pilin 23794623 131567 cellular organisms no rank 5707 EBI-EMBL Archaeal Type IV pilin, N-terminal type IV pilin This entry represents the N-terminal domain of archaeal pilins, which play important roles in surface adhesion. Sequences covered by this domain are not mixed up with sequences having such an extremely high sequence conservation as described in [1]. [1]. 23794623. Novel archaeal adhesion pilins with a conserved N terminus. Esquivel RN, Xu R, Pohlschroder M;. J Bacteriol. 2013;195:3808-3818. (from Pfam) NF019413.5 PF07796.16 DUF1638 27 27 161 domain Y Y N DUF1638 domain-containing protein 131567 cellular organisms no rank 5301 EBI-EMBL Protein of unknown function (DUF1638) Protein of unknown function (DUF1638) This family contains sequences covering an approximately 270 amino acid stretch of a group of hypothetical proteins. These proteins are expressed by archaeal species of the Methanosarcina genus. (from Pfam) NF019415.5 PF07798.16 CCDC90-like 33.5 33.5 175 domain Y Y N coiled-coil domain-containing protein 23178883,25565209,26445506,26976564,27184846 131567 cellular organisms no rank 474 EBI-EMBL Coiled-coil domain-containing protein 90-like Coiled-coil domain-containing protein 90-like This entry includes coiled-coil domain-containing proteins 90 (CCDC90) and related proteins. CCDC90A is a key regulator of the mitochondrial calcium uniporter (MCU) and hence was renamed MCUR1 [1,2,3]. A study in mammals and in yeast homologue fmp32 has reported that MCUR1 is a cytochrome c oxidase assembly factor and that it has an indirect role as a regulator of MCU [4], however, subsequent publications confirmed the function of MCUR1 as a regulator of MCU [1,5]. The role of CCDC90B proteins is still not known. [1]. 27184846. MCUR1 Is a Scaffold Factor for the MCU Complex Function and Promotes Mitochondrial Bioenergetics. Tomar D, Dong Z, Shanmughapriya S, Koch DA, Thomas T, Hoffman NE, Timbalia SA, Goldman SJ, Breves SL, Corbally DP, Nemani N, Fairweather JP, Cutri AR, Zhang X, Song J, Jana F, Huang J, Barrero C, Rabinowitz JE, Luongo TS, Schumacher SM, Rockman ME, Dietrich A, Merali S, Caplan J, Stathopulos P, Ahima RS, Cheung JY, Houser SR, Koch WJ, Patel V, Gohil VM, Elrod JW, Rajan S, Madesh M;. Cell Rep. 2016;15:1673-1685. [2]. 23178883. MCUR1 is an essential component of mitochondrial Ca2+ uptake that regulates cellular metabolism. Mallilankaraman K, Cardenas C, Doonan PJ, Chandramoorthy HC, Irrinki KM, Golenar T, Csordas G, Madireddi P, Yang J, Muller M, Miller R, Kolesar JE, Molgo J, Kaufman B, Hajnoczky G, Foskett JK, Madesh M;. Nat Cell Biol. 2012;14:1336-1343. [3]. 26976564. Mitochondrial calcium uniporter regulator 1 (MCUR1) regulates the calcium threshold for the mitochondrial permeability transition. Chaudhuri D, Artiga DJ, Abiria SA, Clapham DE;. Proc Natl Acad Sci U S A. 2016;113:E1872-E1880. [4]. 255652. TRUNCATED at 1650 bytes (from Pfam) NF019416.5 PF07799.17 DUF1643 22.5 22.5 134 domain Y Y N DUF1643 domain-containing protein 131567 cellular organisms no rank 10557 EBI-EMBL Protein of unknown function (DUF1643) Protein of unknown function (DUF1643) The members of this family are all sequences found within hypothetical proteins expressed by various bacterial species. The region concerned is approximately 150 residues long. (from Pfam) NF019421.5 PF07804.17 HipA_C 30.5 30.5 213 domain Y Y N HipA domain-containing protein 1715862,8021189 131567 cellular organisms no rank 63791 EBI-EMBL HipA-like C-terminal domain HipA-like C-terminal domain The members of this family are similar to a region close to the C-terminus of the HipA protein expressed by various bacterial species (for example Swiss:P23874). This protein is known to be involved in high-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis [1]. When expressed alone, it is toxic to bacterial cells [1], but it is usually tightly associated with HipB [2], and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with cell division genes or their products [2]. [1]. 1715862. Structure and organization of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. Black DS, Kelly AJ, Mardis MJ, Moyed HS;. J Bacteriol 1991;173:5732-5739. [2]. 8021189. Autoregulation of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. Black DS, Irwin B, Moyed HS;. J Bacteriol 1994;176:4081-4091. (from Pfam) NF019428.5 PF07811.17 TadE 22.9 22.9 43 domain Y Y N TadE/TadG family type IV pilus assembly protein 11553455 131567 cellular organisms no rank 82229 EBI-EMBL TadE-like protein TadE/TadG family type IV pilus assembly protein The members of this family are similar to a region of the protein product of the bacterial tadE locus (Swiss:Q9S4A6). In various bacterial species, the tad locus is closely linked to flp-like genes, which encode proteins required for the production of pili involved in adherence to surfaces [1]. It is thought that the tad loci encode proteins that act to assemble or export an Flp pilus in various bacteria [1]. All tad loci but TadA have putative transmembrane regions [1], and in fact the region in question is this family has a high proportion of hydrophobic amino acid residues. [1]. 11553455. Genes for tight adherence of Actinobacillus actinomycetemcomitans: from plaque to plague to pond scum. Kachlany SC, Planet PJ, DeSalle R, Fine DH, Figurski DH;. Trends Microbiol 2001;9:429-437. (from Pfam) NF019429.5 PF07812.17 TfuA 25 25 119 domain Y Y N TfuA-like protein 8763943 131567 cellular organisms no rank 5957 EBI-EMBL TfuA-like protein TfuA-like protein This family consists of a group of sequences that are similar to a region of TfuA protein (Swiss:Q52872). This protein is involved in the production of trifolitoxin (TFX), an gene-encoded, post-translationally modified peptide antibiotic [1]. The role of TfuA in TFX synthesis is unknown, and it may be involved in other cellular processes [1]. [1]. 8763943. A newly discovered gene, tfuA, involved in the production of the ribosomally synthesized peptide antibiotic trifolitoxin. Breil B, Borneman J, Triplett EW;. J Bacteriol 1996;178:4150-4156. (from Pfam) NF019436.5 PF07819.18 PGAP1 24.3 24.3 233 domain Y N N PGAP1-like protein GO:0016788 14734546,19959834 131567 cellular organisms no rank 50865 EBI-EMBL PGAP1-like protein PGAP1-like protein The sequences found in this family are similar to PGAP1 (Swiss:Q765A7). This is an endoplasmic reticulum membrane protein with a catalytic serine containing motif that is conserved in a number of lipases. PGAP1 functions as a GPI inositol-deacylase; this deacylation is important for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body [1]. This entry also includes Tgl2, a mitochondria protein that serves as a triacylglycerol lipase in budding yeasts [2]. [1]. 14734546. Inositol deacylation of glycosylphosphatidylinositol-anchored proteins is mediated by mammalian PGAP1 and yeast Bst1p. Tanaka S, Maeda Y, Tashima Y, Kinoshita T;. J Biol Chem. 2004;279:14256-14263. [2]. 19959834. The TGL2 gene of Saccharomyces cerevisiae encodes an active acylglycerol lipase located in the mitochondria. Ham HJ, Rho HJ, Shin SK, Yoon HJ;. J Biol Chem. 2010;285:3005-3013. (from Pfam) NF019440.5 PF07823.16 CPDase 21 21 199 PfamEq Y N N Cyclic phosphodiesterase-like protein GO:0004112 11080166 131567 cellular organisms no rank 345 EBI-EMBL Cyclic phosphodiesterase-like protein Cyclic phosphodiesterase-like protein Cyclic phosphodiesterase (CPDase, Swiss:O04147) is involved in the tRNA splicing pathway. This protein exhibits a bilobal arrangement of two alpha-beta modules. Two antiparallel helices are found on the outer side of each lobe and frame an antiparallel beta-sheet that is wrapped around an accessible cleft. Moreover, the beta-strands of each lobe interact with the other lobe. The central water-filled cavity houses the enzyme's active site [1]. [1]. 11080166. Structure and mechanism of activity of the cyclic phosphodiesterase of Appr>p, a product of the tRNA splicing reaction. Hofmann A, Zdanov A, Genschik P, Ruvinov S, Filipowicz W, Wlodawer A;. EMBO J 2000;19:6207-6217. (from Pfam) NF019443.5 PF07826.16 IMP_cyclohyd 28.1 28.1 192 PfamEq Y Y N IMP cyclohydrolase GO:0003937,GO:0006164,GO:0006188 12012346 131567 cellular organisms no rank 3646 EBI-EMBL IMP cyclohydrolase-like protein IMP cyclohydrolase This enzyme (Swiss:O27099) is may catalyse the cyclization of 5-formylamidoimidazole-4-carboxamide ribonucleotide to inosine monophosphate (IMP), a reaction which is important in de novo purine biosynthesis in archaeal species. This single domain protein is arranged to form an overall fold that consists of a four-layered alpha-beta-beta-alpha core structure. The two antiparallel beta-sheets pack against each other and are covered by alpha-helices on one face of the molecule. The protein is structurally similar to members of the N-terminal nucleophile (NTN) hydrolase superfamily. A deep pocket was in fact found on the surface of IMP cyclohydrolase in a position equivalent to that of active sites of NTN-hydrolases, but an N-terminal nucleophile could not be found. Therefore, it is thought that this enzyme is structurally but not functionally similar to members of the NTN-hydrolase family [1]. [1]. 12012346. Crystal structure of Methanobacterium thermoautotrophicum conserved protein MTH1020 reveals an NTN-hydrolase fold. Saridakis V, Christendat D, Thygesen A, Arrowsmith CH, Edwards AM, Pai EF;. Proteins 2002;48:141-143. (from Pfam) NF019448.5 PF07831.18 PYNP_C 27 27 75 PfamEq Y N N Pyrimidine nucleoside phosphorylase C-terminal domain GO:0006213,GO:0016763 2199449,9817849 131567 cellular organisms no rank 47160 EBI-EMBL Pyrimidine nucleoside phosphorylase C-terminal domain Pyrimidine nucleoside phosphorylase C-terminal domain This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases [1,2]. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP, Swiss:P77826) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as E. coli thymidine phosphorylase (TP, Swiss:P07650) [1]. The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer [1]. [1]. 9817849. The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation. Pugmire MJ, Ealick SE;. Structure 1998;6:1467-1479. [2]. 2199449. Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 A resolution. Walter MR, Cook WJ, Cole LB, Short SA, Koszalka GW, Krenitsky TA, Ealick SE;. J Biol Chem 1990;265:14016-14022. (from Pfam) NF019453.5 PF07836.16 DmpG_comm 27 27 63 domain Y N N DmpG-like communication domain GO:0009056,GO:0016833 12764229 131567 cellular organisms no rank 19465 EBI-EMBL DmpG-like communication domain DmpG-like communication domain This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C-terminus of the N-terminal TIM barrel domain [1]. The communication domain is thought to play an important role in the heterodimerisation of the enzyme [1]. [1]. 12764229. Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate. Manjasetty BA, Powlowski J, Vrielink A;. Proc Natl Acad Sci U S A 2003;100:6992-6997. (from Pfam) NF019454.5 PF07837.17 FTCD_N 27 27 176 domain Y N N Formiminotransferase domain, N-terminal subdomain GO:0005542,GO:0016740 10673422 131567 cellular organisms no rank 3914 EBI-EMBL Formiminotransferase domain, N-terminal subdomain Formiminotransferase domain, N-terminal subdomain The formiminotransferase (FT) domain of formiminotransferase- cyclodeaminase (FTCD) forms a homodimer, and each protomer comprises two subdomains. The N-terminal subdomain is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains [1]. [1]. 10673422. The crystal structure of the formiminotransferase domain of formiminotransferase-cyclodeaminase: implications for substrate channeling in a bifunctional enzyme. Kohls D, Sulea T, Purisima EO, MacKenzie RE, Vrielink A;. Structure Fold Des 2000;8:35-46. (from Pfam) NF019459.5 PF07843.16 DUF1634 27.5 27.5 102 PfamAutoEq Y Y N DUF1634 domain-containing protein 131567 cellular organisms no rank 3729 EBI-EMBL Protein of unknown function (DUF1634) Protein of unknown function (DUF1634) This family contains many hypothetical bacterial and archaeal proteins. A few members of this family are annotated as being putative transmembrane proteins, and the region in question in fact contains many hydrophobic residues. (from Pfam) NF019463.5 PF07848.17 PaaX 24.8 24.8 70 domain Y N N PaaX-like protein 10766858 131567 cellular organisms no rank 31050 EBI-EMBL PaaX-like protein PaaX-like protein This family contains proteins that are similar to the product of the paaX gene of Escherichia coli (Swiss:P76086). This protein is involved in the regulation of expression of a group of proteins known to participate in the metabolism of phenylacetic acid [1]. In fact, some members of this family are annotated by InterPro as containing a winged helix DNA-binding domain (Interpro:IPR009058). [1]. 10766858. Transcriptional regulation of the divergent paa catabolic operons for phenylacetic acid degradation in Escherichia coli. Ferrandez A, Garcia JL, Diaz E;. J Biol Chem 2000;275:12214-12222. (from Pfam) NF019464.5 PF07849.16 DUF1641 21 21 39 domain Y Y N DUF1641 domain-containing protein 131567 cellular organisms no rank 6427 EBI-EMBL Protein of unknown function (DUF1641) Protein of unknown function (DUF1641) Archaeal and bacterial hypothetical proteins are found in this family, with the region in question being approximately 40 residues long. (from Pfam) NF019468.5 PF07853.16 DUF1648 28.7 28.7 49 domain Y Y N DUF1648 domain-containing protein 16469701 131567 cellular organisms no rank 23397 EBI-EMBL Domain of unknown function (DUF1648) Domain of unknown function (DUF1648) This domain is found in proteins expressed by bacterial or archaeal species. Some of these are annotated as being transmembrane proteins, and in fact many of these sequences contain a high proportion of hydrophobic residues. One protein containing this domain is immunity protein SdpI (swiss:O32241) from Bacillus subtilis, which provides protection for the cell against the toxic effects of its own SdpC killing factor, and also functions as a receptor/signal transduction protein [1]. [1]. 16469701. A three-protein signaling pathway governing immunity to a bacterial cannibalism toxin. Ellermeier CD, Hobbs EC, Gonzalez-Pastor JE, Losick R;. Cell. 2006;124:549-559. (from Pfam) NF019469.5 PF07854.17 DUF1646 21.4 21.4 347 domain Y Y N DUF1646 family protein 131567 cellular organisms no rank 1444 EBI-EMBL Protein of unknown function (DUF1646) DUF1646 family protein Some of the members of this family are hypothetical bacterial and archaeal proteins, but others are annotated as being cation transporters expressed by the archaebacterium Methanosarcina mazei (Swiss:Q8PXG5, Swiss:Q8PXG7 and Swiss:Q8PXG8). (from Pfam) NF019473.5 PF07858.17 LEH 24 24 122 domain Y Y N limonene-1,2-epoxide hydrolase family protein 12773375 131567 cellular organisms no rank 7720 EBI-EMBL Limonene-1,2-epoxide hydrolase catalytic domain Limonene-1,2-epoxide hydrolase catalytic domain Epoxide hydrolases catalyse the hydrolysis of epoxides to corresponding diols, which is important in detoxification, synthesis of signal molecules, or metabolism. Limonene-1,2- epoxide hydrolase (LEH) differs from many other epoxide hydrolases in its structure and its novel one-step catalytic mechanism. Its main fold consists of a six-stranded mixed beta-sheet, with three N-terminal alpha helices packed to one side to create a pocket that extends into the protein core. A fourth helix lies in such a way that it acts as a rim to this pocket. Although mainly lined by hydrophobic residues, this pocket features a cluster of polar groups that lie at its deepest point and constitute the enzyme's active site [1]. [1]. 12773375. Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site. Arand M, Hallberg BM, Zou J, Bergfors T, Oesch F, van der Werf MJ, de Bont JA, Jones TA, Mowbray SL;. EMBO J 2003;22:2583-2592. (from Pfam) NF019474.5 PF07859.18 Abhydrolase_3 25 25 210 domain Y Y N alpha/beta hydrolase fold domain-containing protein GO:0016787 1409539 131567 cellular organisms no rank 363663 EBI-EMBL alpha/beta hydrolase fold alpha/beta hydrolase fold This catalytic domain is found in a very wide range of enzymes. [1]. 1409539. The alpha/beta hydrolase fold. Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J, Sussman JL, Verschueren KHG, Goldman A;. Protein Eng 1992;5:197-211. (from Pfam) NF019477.5 PF07862.16 Nif11 23.8 23.8 48 domain Y Y N Nif11 family protein 20500830,2644218 131567 cellular organisms no rank 5285 EBI-EMBL Nif11 domain Nif11 domain This domain is found mainly in the Cyanobacteria and in Proteobacteria such as the nitrogen-fixing bacterium Azotobacter vinelandii. It is found in Nif11, a protein described in Azotobacter as linked to nitrogen fixation [1]. It also constitutes a leader peptide in Nif11-derived peptides (N11P), which are thought to be post-translationally modified microcins derived from a putative nitrogen-fixing protein [2]. N11P sequences have a classic leader peptide cleavage motif, usually Gly-Gly, which marks the end of family-wide similarity area and the beginning of a low-complexity region rich in Cys, Gly and Ser [2]. [1]. 2644218. Physical and genetic map of the major nif gene cluster from Azotobacter vinelandii. Jacobson MR, Brigle KE, Bennett LT, Setterquist RA, Wilson MS, Cash VL, Beynon J, Newton WE, Dean DR;. J Bacteriol 1989;171:1017-1027. [2]. 20500830. Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family. Haft DH, Basu MK, Mitchell DA;. BMC Biol. 2010;8:70. (from Pfam) NF019481.5 PF07866.16 DUF1653 23.5 23.5 62 PfamAutoEq Y Y N DUF1653 domain-containing protein 131567 cellular organisms no rank 11846 EBI-EMBL Protein of unknown function (DUF1653) Protein of unknown function (DUF1653) This is a family of hypothetical bacterial proteins of unknown function. (from Pfam) NF019489.5 PF07874.16 DUF1660 21.4 21.4 63 subfamily Y Y N DUF1660 family phage protein 131567 cellular organisms no rank 746 EBI-EMBL Prophage protein (DUF1660) DUF1660 family phage protein This protein is found in Lactobacillae prophages. (from Pfam) NF019491.5 PF07876.17 Dabb 25 25 96 domain Y Y N Dabb family protein 10705449,14704136,14872131 131567 cellular organisms no rank 32195 EBI-EMBL Stress responsive A/B Barrel Domain Dabb family protein The function of this family is unknown, but it is upregulated in response to salt stress in Populus balsamifera ([1]). It is also found at the C-terminus of an fructose 1,6-bisphosphate aldolase from Hydrogenophilus thermoluteolus (Swiss:Q9ZA13; [2]). Swiss:Q93NG5 is found in the pA01 plasmid, which encodes genes for molybdopterin uptake and degradation of plant alkaloid nicotine. The structure of one has been solved (Swiss:Q9LUV2) and the domain forms an a/b barrel dimer ([3]). Although there is a clear duplication within the domain it is not obviously detectable in the sequence. [1]. 14704136. Transcript identification and profiling during salt stress and recovery of Populus euphratica. Gu R, Fonseca S, Puskas LG, Hackler L Jr, Zvara A, Dudits D, Pais MS;. Tree Physiol 2004;24:265-276. [2]. 10705449. Structure of ribulose 1,5-bisphosphate carboxylase/oxygenase gene cluster from a thermophilic hydrogen-oxidizing bacterium, Hydrogenophilus thermoluteolus, and phylogeny of the fructose 1,6-bisphosphate aldolase encoded by cbbA in the cluster. Hayashi NR, Terazono K, Kodama T, Igarashi Y;. Biosci Biotechnol Biochem 2000;64:61-71. [3]. 14872131. Structure of the hypothetical protein At3g17210 from Arabidopsis thaliana. Lytle BL, Peterson FC, Kjer KL, Frederick RO, Zhao Q, Thao S, Bingman C, Johnson KA, Phillips GN Jr, Volkman BF;. J Biomol NMR 2004;28:397-400. (from Pfam) NF019493.5 PF07878.16 RHH_5 26 26 43 domain Y Y N ribbon-helix-helix domain-containing protein 15864262 131567 cellular organisms no rank 3725 EBI-EMBL CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5 ribbon-helix-helix fold domain This family contains bacterial proteins that form a ribbon-helix-helix fold. This fold occurs in many examples of bacterial antitoxins [1]. [1]. 15864262. Prokaryotic toxin-antitoxin stress response loci. Gerdes K, Christensen SK, Lobner-Olesen A;. Nat Rev Microbiol. 2005;3:371-382. (from Pfam) NF019498.5 PF07883.16 Cupin_2 27.2 27.2 70 domain Y Y N cupin domain-containing protein 9573603 131567 cellular organisms no rank 597379 EBI-EMBL Cupin domain cupin domain This family represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). [1]. 9573603. Cupins: a new superfamily of functionally diverse proteins that include germins and plant storage proteins. Dunwell JM;. Biotechnol Genet Eng Rev 1998;15:1-32. (from Pfam) NF019499.5 PF07884.19 VKOR 27.5 27.5 134 domain Y Y N vitamin K epoxide reductase family protein 15276181 131567 cellular organisms no rank 24684 EBI-EMBL Vitamin K epoxide reductase family vitamin K epoxide reductase family protein Vitamin K epoxide reductase (VKOR) recycles reduced vitamin K, which is used subsequently as a co-factor in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. VKORC1 is a member of a large family of predicted enzymes that are present in vertebrates, Drosophila, plants, bacteria and archaea [1]. Four cysteine residues and one residue, which is either serine or threonine, are identified as likely active-site residues [1]. In some plant and bacterial homologues the VKORC1 homologous domain is fused with domains of the thioredoxin family of oxidoreductases [1]. [1]. 15276181. Vitamin K epoxide reductase: homology, active site and catalytic mechanism. Goodstadt L, Ponting CP;. Trends Biochem Sci 2004;29:289-292. (from Pfam) NF019500.5 PF07885.21 Ion_trans_2 22.5 22.5 79 domain Y Y N ion channel 11836519 131567 cellular organisms no rank 112417 EBI-EMBL Ion channel ion channel This family includes the two membrane helix type ion channels found in bacteria. [1]. 11836519. Potassium channel structures. Choe S;. Nat Rev Neurosci 2002;3:115-121. (from Pfam) NF019504.5 PF07889.17 DUF1664 34.6 34.6 124 PfamAutoEq Y Y N DUF1664 domain-containing protein 131567 cellular organisms no rank 13 EBI-EMBL Protein of unknown function (DUF1664) Protein of unknown function (DUF1664) The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long. (from Pfam) NF019507.5 PF07892.16 DUF1667 27 27 82 domain Y Y N DUF1667 domain-containing protein 131567 cellular organisms no rank 4446 EBI-EMBL Protein of unknown function (DUF1667) Protein of unknown function (DUF1667) Hypothetical archaeal and bacterial proteins make up this family. A few proteins are annotated as being potential metal-binding proteins, and in fact the members of this family have four highly conserved cysteine residues, but no further literature evidence was found in this regard. (from Pfam) NF019515.5 PF07900.16 DUF1670 25 25 220 domain Y Y N DUF1670 domain-containing protein 131567 cellular organisms no rank 388 EBI-EMBL Protein of unknown function (DUF1670) Protein of unknown function (DUF1670) The hypothetical eukaryotic proteins found in this family are of unknown function. (from Pfam) NF019522.5 PF07907.16 YibE_F 27.2 27.2 241 domain Y Y N YibE/F family protein 131567 cellular organisms no rank 27615 EBI-EMBL YibE/F-like protein YibE/F family protein The sequences featured in this family are similar to two proteins expressed by Lactococcus lactis, YibE (Swiss:Q9CHC5) and YibF (Swiss:Q9CHC4). Most of the members of this family are annotated as being putative membrane proteins, and in fact the sequences contain a high proportion of hydrophobic residues. (from Pfam) NF019533.5 PF07920.16 DUF1684 25 25 139 domain Y Y N DUF1684 domain-containing protein 131567 cellular organisms no rank 23890 EBI-EMBL Protein of unknown function (DUF1684) Protein of unknown function (DUF1684) The sequences featured in this family are found in hypothetical archaeal and bacterial proteins of unknown function. The region in question is approximately 200 amino acids long. (from Pfam) NF019535.5 PF07922.16 Glyco_transf_52 26.1 26.1 272 subfamily Y Y N glycosyltransferase family 52 11842084,12691742,8910446,9933604 131567 cellular organisms no rank 3226 EBI-EMBL Glycosyltransferase family 52 glycosyltransferase family 52 This family features glycosyltransferases belonging to glycosyltransferase family 52 [1], which have alpha-2,3- sialyltransferase (EC:4.2.99.4) and alpha-glucosyltransferase (EC 2.4.1.-) activity. For example, beta-galactoside alpha-2,3- sialyltransferase expressed by Neisseria meningitidis (Swiss:P72097) is a member of this family and is involved in a step of lipooligosaccharide biosynthesis requiring sialic acid transfer; these lipooligosaccharides are thought to be important in the process of pathogenesis [2]. This family includes several bacterial lipooligosaccharide sialyltransferases similar to the Haemophilus ducreyi LST protein. Haemophilus ducreyi is the cause of the sexually transmitted disease chancroid and produces a lipooligosaccharide (LOS) containing a terminal sialyl N-acetyllactosamine trisaccharide [3]. [1]. 12691742. An evolving hierarchical family classification for glycosyltransferases. Coutinho PM, Deleury E, Davies GJ, Henrissat B;. J Mol Biol 2003;328:307-317. [2]. 8910446. Cloning of the lipooligosaccharide alpha-2,3-sialyltransferase from the bacterial pathogens Neisseria meningitidis and Neisseria gonorrhoeae. Gilbert M, Watson DC, Cunningham AM, Jennings MP, Young NM, Wakarchuk WW;. J Biol Chem 1996;271:28271-28276. [3]. 9933604. Haemophilus ducreyi produces a novel sialyltransferase. Identification of the sialyltransferase gene and construction of mutants deficient in the production of the sialic acid-containing glycoform of the lipooligosaccharide. Bozue JA, Tullius MV, Wang J, Gibson BW, Munson RS Jr;. J Biol Chem 1999;274:4106-4114. [4]. 11842084. Haemophilus influenzae type b strain A2 ha. TRUNCATED at 1650 bytes (from Pfam) NF019540.5 PF07927.17 HicA_toxin 27 27 58 domain Y Y N type II toxin-antitoxin system HicA family toxin GO:0003729 16895922,19060138,21927020 131567 cellular organisms no rank 29815 EBI-EMBL HicA toxin of bacterial toxin-antitoxin, type II toxin-antitoxin system HicA family toxin HicA_toxin is a bacterial family of toxins that act as mRNA interferases. The antitoxin that neutralises this is family HicB, Pfam:PF15919 [1,2,3]. [1]. 16895922. The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria. Makarova KS, Grishin NV, Koonin EV;. Bioinformatics. 2006;22:2581-2584. [2]. 19060138. HicA of Escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea. Jorgensen MG, Pandey DP, Jaskolska M, Gerdes K;. J Bacteriol. 2009;191:1191-1199. [3]. 21927020. Regulation of growth and death in Escherichia coli by toxin-antitoxin systems. Yamaguchi Y, Inouye M;. Nat Rev Microbiol. 2011;9:779-790. (from Pfam) NF019542.5 PF07929.16 PRiA4_ORF3 26.6 26.6 173 domain Y Y N IS1096 element passenger TnpR family protein 2226811 131567 cellular organisms no rank 21558 EBI-EMBL Plasmid pRiA4b ORF-3-like protein IS1096 element passenger TnpR family protein Members of this family are seen plasmid pRiA4b ORF-3 and as putative passenger proteins in occasional members of different groups of (IS) element, including ISKra4-like, IS66-like, ISL3-like, and Tn3-like elements, and least sometimes given the name TnpR. NF019544.5 PF07931.17 CPT 22 22 172 domain Y Y N phosphotransferase-like protein 11468347 131567 cellular organisms no rank 20946 EBI-EMBL Chloramphenicol phosphotransferase-like protein chloramphenicol phosphotransferase-like protein The members of this family are all similar to chloramphenicol 3-O phosphotransferase (CPT, Swiss:Q56148) expressed by Streptomyces venezuelae. Chloramphenicol (Cm) is a metabolite produced by this bacterium that can inhibit ribosomal peptidyl transferase activity and therefore protein production. By transferring a phosphate group to the C-3 hydroxyl group of Cm, CPT inactivates this potentially lethal metabolite [1]. [1]. 11468347. Structural basis for chloramphenicol tolerance in Streptomyces venezuelae by chloramphenicol phosphotransferase activity. Izard T;. Protein Sci 2001;10:1508-1513. (from Pfam) NF019546.5 PF07934.17 OGG_N 23 23 115 domain Y Y N DNA glycosylase GO:0003684,GO:0006289,GO:0008534 10706276,11902834 131567 cellular organisms no rank 7808 EBI-EMBL 8-oxoguanine DNA glycosylase, N-terminal domain DNA glycosylase Members of this family are DNA glycosylases performing base excision for DNA repair. Substrates include 8-oxoguanine and 3-methyladenine. NF019547.5 PF07935.16 SSV1_ORF_D-335 22 22 68 domain Y Y N putative integrase 1926776 131567 cellular organisms no rank 117 EBI-EMBL ORF D-335-like protein putative integrase The sequences featured in this family are similar to a probable integrase (Swiss:P20214) expressed by the SSV1 virus of the archaebacterium Sulfolobus shibatae. This protein may be necessary for the integration of the virus into the host genome by a process of site-specific recombination [1]. [1]. 1926776. Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobus shibatae. Palm P, Schleper C, Grampp B, Yeats S, McWilliam P, Reiter WD, Zillig W;. Virology 1991;185:242-250. (from Pfam) NF019552.5 PF07940.18 Hepar_II_III 24 24 237 domain Y Y N heparinase II/III family protein GO:0016829 23011846,8702264 131567 cellular organisms no rank 46835 EBI-EMBL Heparinase II/III-like protein heparinase II/III family protein This family features sequences that are similar to a region of the Flavobacterium heparinum proteins heparinase II (Swiss:Q46080) and heparinase III (Swiss:Q59289). The former is known to degrade heparin and heparin sulphate, whereas the latter predominantly degrades heparin sulphate. Both are secreted into the periplasmic space upon induction with heparin [1]. [1]. 8702264. Isolation and expression in Escherichia coli of hepB and hepC, genes coding for the glycosaminoglycan-degrading enzymes heparinase II and heparinase III, respectively, from Flavobacterium heparinum. Su H, Blain F, Musil RA, Zimmermann JJ, Gu K, Bennett DC;. Appl Environ Microbiol 1996;62:2723-2734. [2]. 23011846. Structural basis of heparan sulfate-specific degradation by heparinase III. Dong W, Lu W, McKeehan WL, Luo Y, Ye S;. Protein Cell. 2012;3:950-961. (from Pfam) NF019556.5 PF07944.17 Beta-AFase-like_GH127_cat 24.9 24.9 376 domain Y Y N beta-L-arabinofuranosidase domain-containing protein 24385433,24680821 131567 cellular organisms no rank 47043 EBI-EMBL Beta-L-arabinofuranosidase, GH127 catalytic domain Beta-L-arabinofuranosidase, GH127 catalytic domain This entry represents the catalytic domain of Non-reducing end beta-L-arabinofuranosidase from Bifidobacterium longum (Beta -AFase) and similar proteins that belong to the glycoside hydrolase family 127 (GH127). This domain folds into an (alpha /alpha)6 barrel. Beta-AFase has been characterised as an unusual beta-L-arabinofuranosidase enzyme, EC:3.2.1.185. It releases l-arabinose from the l-arabinofuranose (Araf)-beta1,2-Araf disaccharide and also transglycosylates 1-alkanols with retention of the anomeric configuration [1,2]. [1]. 24385433. Characterization of a novel beta-L-arabinofuranosidase in Bifidobacterium longum: functional elucidation of a DUF1680 protein family member. Fujita K, Takashi Y, Obuchi E, Kitahara K, Suganuma T;. J Biol Chem. 2014;289:5240-5249. [2]. 24680821. Crystal structure of glycoside hydrolase family 127 beta-l-arabinofuranosidase from Bifidobacterium longum. Ito T, Saikawa K, Kim S, Fujita K, Ishiwata A, Kaeothip S, Arakawa T, Wakagi T, Beckham GT, Ito Y, Fushinobu S;. Biochem Biophys Res Commun. 2014;447:32-37. (from Pfam) NF019559.5 PF07947.19 YhhN 25.6 25.6 182 subfamily Y Y N lysoplasmalogenase family protein GO:0016020 21515882,26335199 131567 cellular organisms no rank 27613 EBI-EMBL YhhN family lysoplasmalogenase family protein The members of this family are similar to the hypothetical protein yhhN expressed by E. coli (Swiss:P37616). Many are annotated as possible transmembrane proteins, and in fact they all have a high proportion of hydrophobic residues. A human member of this family, formerly known as TMEM86B, is a lysoplasmalogenase that catalyzes the hydrolysis of the vinyl ether bond of lysoplasmalogen[1]. Putative conserved active site residues have been proposed for the YhhN family [2]. [1]. 21515882. Purification, identification, and cloning of lysoplasmalogenase, the enzyme that catalyzes hydrolysis of the vinyl ether bond of lysoplasmalogen. Wu LC, Pfeiffer DR, Calhoon EA, Madiai F, Marcucci G, Liu S, Jurkowitz MS;. J Biol Chem. 2011;286:24916-24930. [2]. 26335199. Large-scale determination of previously unsolved protein structures using evolutionary information. Ovchinnikov S, Kinch L, Park H, Liao Y, Pei J, Kim DE, Kamisetty H, Grishin NV, Baker D;. Elife. 2015; [Epub ahead of print] (from Pfam) NF019565.5 PF07953.18 Toxin_R_bind_N 22 22 195 domain Y Y N botulinum neurotoxin N-terminal receptor binding domain-containing protein GO:0005576 9783750 131567 cellular organisms no rank 914 EBI-EMBL Clostridium neurotoxin, N-terminal receptor binding Clostridium neurotoxin, N-terminal receptor binding The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (Pfam:PF01742), the central translocation domains and two receptor binding domains [1]. This domains is the N-terminal receptor binding domain,which is comprised of two seven-stranded beta-sheets sandwiched together to form a jelly role motif [1]. The role of this domain in receptor binding appears to be indirect. [1]. 9783750. Crystal structure of botulinum neurotoxin type A and implications for toxicity. Lacy DB, Tepp W, Cohen AC, DasGupta BR, Stevens RC;. Nat Struct Biol 1998;5:898-902. (from Pfam) NF019581.5 PF07969.16 Amidohydro_3 29.7 29.7 472 domain Y Y N amidohydrolase family protein 131567 cellular organisms no rank 598720 EBI-EMBL Amidohydrolase family amidohydrolase family protein NF019585.5 PF07973.19 tRNA_SAD 24 24 44 domain Y N N Threonyl and Alanyl tRNA synthetase second additional domain GO:0004812,GO:0005524,GO:0043039 10319817 131567 cellular organisms no rank 195555 EBI-EMBL Threonyl and Alanyl tRNA synthetase second additional domain Threonyl and Alanyl tRNA synthetase second additional domain The catalytically active from of threonyl/alanyl tRNA synthetase is a dimer. Within the tRNA synthetase class II dimer, the bound tRNA interacts with both monomers making specific interactions with the catalytic domain, the C-terminal domain, and this domain (the second additional domain). The second additional domain is comprised of a pair of perpendicularly orientated antiparallel beta sheets, of four and three strands, respectively, that surround a central alpha helix that forms the core of the domain [1]. [1]. 10319817. The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site. Sankaranarayanan R, Dock-Bregeon AC, Romby P, Caillet J, Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D;. Cell 1999;97:371-381. (from Pfam) NF019590.5 PF07978.18 NIPSNAP 22.3 22.3 102 domain Y Y N NIPSNAP family protein 9661659 131567 cellular organisms no rank 27604 EBI-EMBL NIPSNAP NIPSNAP family protein Members of this family include many hypothetical proteins. It also includes members of the NIPSNAP family which have putative roles in vesicular transport [1]. This domain is often found in duplicate. [1]. 9661659. Characterization of the human NIPSNAP1 gene from 22q12: a member of a novel gene family. Seroussi E, Pan HQ, Kedra D, Roe BA, Dumanski JP;. Gene 1998;212:13-20. (from Pfam) NF019601.5 PF07989.16 Cnn_1N 28.5 28.5 74 domain Y Y N centrosomin N-terminal motif 1-containing protein GO:0005815 11864908,15004232,15120067,17671162 131567 cellular organisms no rank 6 EBI-EMBL Centrosomin N-terminal motif 1 Centrosomin N-terminal motif 1 This domain has been identified in two microtubule associated proteins in Schizosaccharomyces pombe, Mto1 and Pcp1. Mto1 has been identified in association with spindle pole body and non-spindle pole body microtubules [1]. The pericentrin homologue Pcp1 is also associated with the fungal centrosome or spindle pole body (SPB) [2]. Members of this family have been named centrosomins, and are an essential mitotic centrosome component required for assembly of all other known pericentriolar matrix proteins in order to achieve microtubule-organising activity in fission yeast [3]. Cnn_1N is a short conserved motif towards the N-terminus. Motif 1 is found to be necessary for proper recruitment of gamma-tubulin, D-TACC (the homolog of vertebrate transforming acidic coiled-coil proteins [TACC]), and Minispindles (Msps) to embryonic centrosomes but is not required for assembly of other centrosome components including Aurora A kinase and CP60 in Drosophila [4]. [1]. 15004232. Identification and characterization of two novel proteins affecting fission yeast gamma-tubulin complex function. Venkatram S, Tasto JJ, Feoktistova A, Jennings JL, Link AJ, Gould KL;. Mol Biol Cell 2004;15:2287-2301. [2]. 11864908. Pcp1p, an Spc110p-related calmodulin target at the centrosome of the fission yeast Schizosaccharomyces pombe. Flory MR, Morphew M, Joseph JD, Means AR, Davis TN;. Cell Growth Differ. 2002;13:47-58. [3]. 15120067. Microtubule nucleation at non-spindle pole body microtubule-organizing centers requires fission yeast centrosomin-related protein mod20p. Sawin KE, Lourenco PC, Snaith HA;. Curr Biol. 2004;14:763-775. [4]. 17671162. Proper r. TRUNCATED at 1650 bytes (from Pfam) NF019603.5 PF07991.17 IlvN 20.6 20.6 165 domain Y N N Acetohydroxy acid isomeroreductase, NADPH-binding domain 16322583,19362563,9218783 131567 cellular organisms no rank 183593 EBI-EMBL Acetohydroxy acid isomeroreductase, NADPH-binding domain Acetohydroxy acid isomeroreductase, NADPH-binding domain Acetohydroxy acid isomeroreductase catalyses the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine. This N-terminal region of the enzyme carries the binding-site for NADPH. The active-site for enzymatic activity lies in the C-terminal part, IlvC, Pfam:PF01450. [1]. 9218783. The crystal structure of plant acetohydroxy acid isomeroreductase complexed with NADPH, two magnesium ions and a herbicidal transition state analog determined at 1.65 A resolution. Biou V, Dumas R, Cohen-Addad C, Douce R, Job D, Pebay-Peyroula E;. EMBO J 1997;16:3405-3415. [2]. 16322583. The crystal structure of a bacterial class II ketol-acid reductoisomerase: domain conservation and evolution. Tyagi R, Duquerroy S, Navaza J, Guddat LW, Duggleby RG;. Protein Sci. 2005;14:3089-3100. [3]. 19362563. Conformational changes in a plant ketol-acid reductoisomerase upon Mg(2+) and NADPH binding as revealed by two crystal structures. Leung EW, Guddat LW;. J Mol Biol. 2009;389:167-182. (from Pfam) NF019604.5 PF07992.19 Pyr_redox_2 26.1 26.1 291 domain Y Y N FAD-dependent oxidoreductase GO:0016491 8805537 131567 cellular organisms no rank 1627372 EBI-EMBL Pyridine nucleotide-disulphide oxidoreductase FAD-dependent oxidoreductase This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain. [1]. 8805537. Protein-protein interactions in the pyruvate dehydrogenase multienzyme complex: dihydrolipoamide dehydrogenase complexed with the binding domain of dihydrolipoamide acetyltransferase. Mande SS, Sarfaty S, Allen MD, Perham RN, Hol WG;. Structure 1996;4:277-286. (from Pfam) NF019605.5 PF07993.17 NAD_binding_4 20.1 20.1 258 domain Y Y N SDR family oxidoreductase 9351246 131567 cellular organisms no rank 546438 EBI-EMBL Male sterility protein SDR family oxidoreductase This family represents the C-terminal region of the male sterility protein in a number of arabidopsis and drosophila. A sequence-related jojoba acyl CoA reductase is also included. [1]. 9351246. The Arabidopsis MALE STERILITY 2 protein shares similarity with reductases in elongation/condensation complexes. Aarts MG, Hodge R, Kalantidis K, Florack D, Wilson ZA, Mulligan BJ, Stiekema WJ, Scott R, Pereira A;. Plant J 1997;12:615-623. (from Pfam) NF019606.5 PF07994.17 NAD_binding_5 25 25 321 domain Y Y N inositol-3-phosphate synthase GO:0004512,GO:0006021,GO:0008654 7975896 131567 cellular organisms no rank 10707 EBI-EMBL Myo-inositol-1-phosphate synthase inositol-3-phosphate synthase This is a family of myo-inositol-1-phosphate synthases. Inositol-1-phosphate catalyses the conversion of glucose-6- phosphate to inositol-1-phosphate, which is then dephosphorylated to inositol [1]. Inositol phosphates play an important role in signal transduction. [1]. 7975896. Comparison of INO1 gene sequences and products in Candida albicans and Saccharomyces cerevisiae. Klig LS, Zobel PA, Devry CG, Losberger C;. Yeast 1994;10:789-800. (from Pfam) NF019607.5 PF07995.16 GSDH 25 25 332 domain Y Y N PQQ-dependent sugar dehydrogenase 10364396 131567 cellular organisms no rank 143517 EBI-EMBL Glucose / Sorbosone dehydrogenase PQQ-dependent sugar dehydrogenase Members of this family are glucose/sorbosone dehydrogenases that possess a beta-propeller fold. [1]. 10364396. Ascorbic acid metabolism in pea seedlings. A comparison of D-glucosone, L-sorbosone, and L-galactono-1,4-lactone as ascorbate precursors . Pallanca JE, Smirnoff N;. Plant Physiol 1999;120:453-462. (from Pfam) NF019610.5 PF07998.16 Peptidase_M54 24.4 24.4 194 domain Y N N Peptidase family M54 GO:0006508,GO:0008233 15972818 131567 cellular organisms no rank 3010 EBI-EMBL Peptidase family M54 Peptidase family M54 This is a family of metallopeptidases. Two human proteins have been reported to degrade synthetic substrates and peptides [1]. [1]. 15972818. Identification and characterization of human archaemetzincin-1 and -2, two novel members of a family of metalloproteases widely distributed in Archaea. Diaz-Perales A, Quesada V, Peinado JR, Ugalde AP, Alvarez J, Suarez MF, Gomis-Ruth FX, Lopez-Otin C;. J Biol Chem. 2005;280:30367-30375. (from Pfam) NF019612.5 PF08000.16 bPH_1 27.7 27.7 122 domain Y Y N PH domain-containing protein 19913036 131567 cellular organisms no rank 12865 EBI-EMBL Bacterial PH domain Bacterial PH domain This family contains many bacterial hypothetical proteins. The structures of Swiss:A1SD03, PDB:3hsa, and Swiss:A3QB43, PDB:3dcx, show similarities to the PH or pleckstrin homology domain. First evidence of PH-like domains in bacteria suggests role in cell envelope stress response [1]. [1]. 19913036. Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain. Xu Q, Bateman A, Finn RD, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. J Mol Biol. 2010 Feb 12;396(1):31-46. Epub 2009 Nov 10. (from Pfam) NF019614.5 PF08002.16 DUF1697 24.4 24.4 137 domain Y Y N DUF1697 domain-containing protein 131567 cellular organisms no rank 28763 EBI-EMBL Protein of unknown function (DUF1697) Protein of unknown function (DUF1697) This family contains many hypothetical bacterial proteins. (from Pfam) NF019615.5 PF08003.16 Methyltransf_9 23.8 23.8 315 domain Y Y N DUF1698 domain-containing protein 131567 cellular organisms no rank 68551 EBI-EMBL Protein of unknown function (DUF1698) Protein of unknown function (DUF1698) This family contains many hypothetical proteins. It also includes two putative methyltransferase proteins, Swiss:Q8EEE6 and Swiss:Q88MX8. (from Pfam) NF019619.5 PF08007.17 JmjC_2 22 22 127 domain Y Y N JmjC domain-containing protein 19502796,20057358,23103944,24530688,24814345 131567 cellular organisms no rank 44754 EBI-EMBL JmjC domain cupin domain-containing protein This entry includes proteins with a JmjC domain that belong to the cupin superfamily, including Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 [1], Ribosomal oxygenase 1/2 [2,3], and 50S ribosomal protein L16 3-hydroxylase from Escherichia coli [4,5]. Proteins are bifunctional, acting as histone lysine demethylases and ribosomal histidine hydroxylases. [1]. 20057358. SLR-2 and JMJC-1 regulate an evolutionarily conserved stress-response network. Kirienko NV, Fay DS;. EMBO J. 2010;29:727-739. [2]. 23103944. Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans. Ge W, Wolf A, Feng T, Ho CH, Sekirnik R, Zayer A, Granatino N, Cockman ME, Loenarz C, Loik ND, Hardy AP, Claridge TDW, Hamed RB, Chowdhury R, Gong L, Robinson CV, Trudgian DC, Jiang M, Mackeen MM, Mccullagh JS, Gordiyenko Y, Thalhammer A, Yamamoto A, Yang M, Liu-Yi P, Zhang Z, Schmidt-Zachmann M, Kessler BM, Ratcliffe PJ, Preston GM, Coleman ML, Schofield CJ;. Nat Chem Biol. 2012;8:960-962. [3]. 19502796. Lung cancer-associated JmjC domain protein mdig suppresses formation of tri-methyl lysine 9 of histone H3. Lu Y, Chang Q, Zhang Y, Beezhold K, Rojanasakul Y, Zhao H, Castranova V, Shi X, Chen F;. Cell Cycle. 2009;8:2101-2109. [4]. 24530688. Structure and functional analysis of YcfD, a novel 2-oxoglutarate/Fe(2)(+)-dependent oxygenase involved in translational regulation in Escherichia coli. van Staalduinen LM, Novakowski SK, Jia Z;. J Mol Biol. 2014;426:1898-1910. [5]. 24814345. Ribosomal oxygenases are structurally conserved from prokaryotes to humans. Chowdhury R, Sekirnik R, Brissett NC, Krojer T, Ho CH, Ng SS, Clifto. TRUNCATED at 1650 bytes (from Pfam) NF019622.5 PF08010.16 Phage_30_3 36 36 138 PfamEq Y N N Bacteriophage protein GP30.3 8088550,9272856 131567 cellular organisms no rank 203 EBI-EMBL Bacteriophage protein GP30.3 Bacteriophage protein GP30.3 Proteins in this family are bacteriophage GP30.3 proteins. Their function is poorly characterised [1][2]. [1]. 8088550. Cloning and expression of genes from the genomic region between genes cd and 30 of bacteriophage T4. Zajanckauskaite A, Raudonikiene A, Nivinskas R;. Gene 1994;147:71-76. [2]. 9272856. A rare type of overlapping genes in bacteriophage T4: gene 30.3' is completely embedded within gene 30.3 by one position downstream. Zajanckauskaite A, Malys N, Nivinskas R;. Gene 1997;194:157-162. (from Pfam) NF019623.5 PF08011.16 PDDEXK_9 25.5 25.5 105 domain Y Y N PD-(D/E)XK nuclease domain-containing protein 17584917 131567 cellular organisms no rank 28586 EBI-EMBL PD-(D/E)XK nuclease superfamily PD-(D/E)XK nuclease superfamily This family contains many hypothetical bacterial proteins. It has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches [1]. DUF1703 has the predicted secondary structure pattern of the restriction endonuclease-like fold core and contains an additional beta-strand at the C-terminus [1]. [1]. 17584917. Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches. Knizewski L, Kinch LN, Grishin NV, Rychlewski L, Ginalski K;. BMC Struct Biol. 2007;7:40. (from Pfam) NF019626.5 PF08014.16 MATCAP 27 27 365 PfamAutoEq Y Y N tyrosine/phenylalanine carboxypeptidase domain-containing protein 35482892 131567 cellular organisms no rank 8547 EBI-EMBL Microtubule-associated tyrosine carboxypeptidase Microtubule-associated tyrosine carboxypeptidase This entry includes microtubule-associated tyrosine carboxypeptidases, proteins that remove the C-terminal tyrosine residue of alpha-tubulin, thereby regulating microtubule dynamics and function [1]. They are also able to remove the C-terminal phenylalanine residue of alpha-tubulin TUBA8 [1]. These proteins recognise adjacent tubulin dimers along the same protofilament [1]. [1]. 35482892. Posttranslational modification of microtubules by the MATCAP detyrosinase. Landskron L, Bak J, Adamopoulos A, Kaplani K, Moraiti M, van den Hengel LG, Song JY, Bleijerveld OB, Nieuwenhuis J, Heidebrecht T, Henneman L, Moutin MJ, Barisic M, Taraviras S, Perrakis A, Brummelkamp TR;. Science. 2022;376:eabn6020. (from Pfam) NF019628.5 PF08016.17 PKD_channel 22.4 22.4 225 PfamEq Y N N Polycystin cation channel 10517637,11264013,29567962 131567 cellular organisms no rank 9701 EBI-EMBL Polycystin cation channel Polycystin cation channel This family contains the cation channel region from group II of Transient receptor potential (TRP) channels, the TRPP subfamily, including PKD1, PKD2, PKD2L and mucolipin proteins [1,2,3]. [1]. 10517637. Polycystin-L is a calcium-regulated cation channel permeable to calcium ions. Chen XZ, Vassilev PM, Basora N, Peng JB, Nomura H, Segal Y, Brown EM, Reeders ST, Hediger MA, Zhou J;. Nature 1999;401:383-386. [2]. 11264013. Polycystin-2 is a novel cation channel implicated in defective intracellular Ca(2+) homeostasis in polycystic kidney disease. Vassilev PM, Guo L, Chen XZ, Segal Y, Peng JB, Basora N, Babakhanlou H, Cruger G, Kanazirska M, Ye Cp, Brown EM, Hediger MA, Zhou J;. Biochem Biophys Res Commun 2001;282:341-350. [3]. 29567962. Cryo-EM structure of the polycystic kidney disease-like channel PKD2L1. Su Q, Hu F, Liu Y, Ge X, Mei C, Yu S, Shen A, Zhou Q, Yan C, Lei J, Zhang Y, Liu X, Wang T;. Nat Commun. 2018;9:1192. (from Pfam) NF019634.5 PF08022.17 FAD_binding_8 22 22 109 domain Y N N FAD-binding domain GO:0016491 131567 cellular organisms no rank 14644 EBI-EMBL FAD-binding domain FAD-binding domain NF019640.5 PF08028.16 Acyl-CoA_dh_2 22.7 22.7 134 domain Y N N Acyl-CoA dehydrogenase, C-terminal domain 131567 cellular organisms no rank 689082 EBI-EMBL Acyl-CoA dehydrogenase, C-terminal domain Acyl-CoA dehydrogenase, C-terminal domain NF019641.5 PF08029.16 HisG_C 23.5 23.5 73 PfamEq Y N N HisG, C-terminal domain GO:0000105,GO:0000287,GO:0003879,GO:0005737 131567 cellular organisms no rank 25708 EBI-EMBL HisG, C-terminal domain HisG, C-terminal domain NF019642.5 PF08030.17 NAD_binding_6 22.2 22.2 156 domain Y N N Ferric reductase NAD binding domain GO:0016491 131567 cellular organisms no rank 11339 EBI-EMBL Ferric reductase NAD binding domain Ferric reductase NAD binding domain NF019643.5 PF08031.17 BBE 20.6 20.6 45 domain Y Y N BBE domain-containing protein GO:0016491,GO:0050660 7592663,8972604 131567 cellular organisms no rank 54360 EBI-EMBL Berberine and berberine like Berberine and berberine like This domain is found in the berberine bridge and berberine bridge- like enzymes which are involved in the biosynthesis of numerous isoquinoline alkaloids. They catalyse the transformation of the N-methyl group of (S)-reticuline into the C-8 berberine bridge carbon of (S)-scoulerine [1][2]. [1]. 8972604. Molecular characterization of berberine bridge enzyme genes from opium poppy. Facchini PJ, Penzes C, Johnson AG, Bull D;. Plant Physiol 1996;112:1669-1677. [2]. 7592663. Characterization and mechanism of the berberine bridge enzyme, a covalently flavinylated oxidase of benzophenanthridine alkaloid biosynthesis in plants. Kutchan TM, Dittrich H;. J Biol Chem 1995;270:24475-24481. (from Pfam) NF019644.5 PF08032.17 SpoU_sub_bind 22.8 22.8 76 domain Y Y N RNA methyltransferase substrate-binding domain-containing protein GO:0008168 131567 cellular organisms no rank 97036 EBI-EMBL RNA 2'-O ribose methyltransferase substrate binding RNA 2'-O ribose methyltransferase substrate binding This domain is a RNA 2'-O ribose methyltransferase substrate binding domain. (from Pfam) NF019656.5 PF08044.16 DUF1707 27.6 27.6 53 domain Y Y N DUF1707 domain-containing protein 131567 cellular organisms no rank 48515 EBI-EMBL DUF1707 SHOCT-like domain DUF1707 SHOCT-like domain This domain is found in a variety of Actinomycetales proteins. All of the proteins containing this domain are uncharacterised and probably membrane bound or associated. It is unclear to the function of this domain. (from Pfam) NF019679.5 PF08068.17 DKCLD 27 27 58 domain Y N N DKCLD (NUC011) domain 15112237 131567 cellular organisms no rank 1296 EBI-EMBL DKCLD (NUC011) domain DKCLD (NUC011) domain This is a TruB_N/PUA domain associated N-terminal domain of Dyskerin-like proteins [1]. [1]. 15112237. Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire. Staub E, Fiziev P, Rosenthal A, Hinzmann B;. Bioessays 2004;26:567-581. (from Pfam) NF019680.5 PF08069.17 Ribosomal_S13_N 25.4 25.4 60 PfamEq Y N N Ribosomal S13/S15 N-terminal domain GO:0003735,GO:0005840,GO:0006412 15112237 131567 cellular organisms no rank 1165 EBI-EMBL Ribosomal S13/S15 N-terminal domain Ribosomal S13/S15 N-terminal domain This domain is found at the N-terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [1]. [1]. 15112237. Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire. Staub E, Fiziev P, Rosenthal A, Hinzmann B;. Bioessays 2004;26:567-581. (from Pfam) NF019682.5 PF08071.17 RS4NT 27 27 37 domain Y N N RS4NT (NUC023) domain 15112237 131567 cellular organisms no rank 1214 EBI-EMBL RS4NT (NUC023) domain RS4NT (NUC023) domain This is the N-terminal domain of Ribosomal S4 / S4e proteins. This domain is associated with S4 and KOW domains [1]. [1]. 15112237. Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire. Staub E, Fiziev P, Rosenthal A, Hinzmann B;. Bioessays 2004;26:567-581. (from Pfam) NF019724.5 PF08113.16 CoxIIa 20.7 20.7 33 PfamEq Y Y N cytochrome c oxidase subunit 2A 11152118 131567 cellular organisms no rank 771 EBI-EMBL Cytochrome c oxidase subunit IIa family cytochrome c oxidase subunit 2A This family consists of the cytochrome c oxidase subunit IIa family. The bax-type cytochrome c oxidase from Thermus thermophilus is known as a two subunit enzyme. From its crystal structure, it was discovered that an additional transmembrane helix 'subunit IIa' spans the membrane. This subunit consists of 34 residues forming one helix across the membrane. The presence of this subunit seems to be important for the function of cytochrome c oxidases [1]. [1]. 11152118. Primary structure of a novel subunit in ba3-cytochrome oxidase from Thermus thermophilus. Soulimane T, Than ME, Dewor M, Huber R, Buse G;. Protein Sci 2000;9:2068-2073. (from Pfam) NF019735.5 PF08124.16 Lyase_8_N 24 24 323 domain Y N N Polysaccharide lyase family 8, N terminal alpha-helical domain 10329169 131567 cellular organisms no rank 21433 EBI-EMBL Polysaccharide lyase family 8, N terminal alpha-helical domain Polysaccharide lyase family 8, N terminal alpha-helical domain This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen. [1]. 10329169. Crystal structure of chondroitin AC lyase, a representative of a family of glycosaminoglycan degrading enzymes. Fethiere J, Eggimann B, Cygler M;. J Mol Biol 1999;288:635-647. (from Pfam) NF019737.5 PF08126.16 Propeptide_C25 22 22 205 domain Y Y N C25 family peptidase propeptide domain-containing protein GO:0004197 10523290 131567 cellular organisms no rank 715 EBI-EMBL Propeptide_C25 Propeptide_C25 This is found at the N terminal end of some of the members of the C25 peptidase family (PF01364). Little is known about the function of this motif. (from Pfam) NF019813.5 PF08206.16 OB_RNB 24 24 58 domain Y N N Ribonuclease B OB domain 131567 cellular organisms no rank 72310 EBI-EMBL Ribonuclease B OB domain Ribonuclease B OB domain This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies. (from Pfam) NF019814.5 PF08207.17 EFP_N 23 23 58 domain Y N N Elongation factor P (EF-P) KOW-like domain 131567 cellular organisms no rank 41447 EBI-EMBL Elongation factor P (EF-P) KOW-like domain Elongation factor P (EF-P) KOW-like domain NF019818.5 PF08211.17 dCMP_cyt_deam_2 25 25 130 domain Y N N Cytidine and deoxycytidylate deaminase zinc-binding region GO:0004126,GO:0008270,GO:0009972 8203015 131567 cellular organisms no rank 44227 EBI-EMBL Cytidine and deoxycytidylate deaminase zinc-binding region Cytidine and deoxycytidylate deaminase zinc-binding region NF019826.5 PF08220.17 HTH_DeoR 21 21 57 domain Y Y N DeoR family transcriptional regulator GO:0003700,GO:0006355 131567 cellular organisms no rank 340884 EBI-EMBL DeoR-like helix-turn-helix domain DeoR-like helix-turn-helix domain NF019829.5 PF08223.16 PaaX_C 22 22 91 domain Y Y N PaaX family transcriptional regulator C-terminal domain-containing protein 10766858 131567 cellular organisms no rank 31979 EBI-EMBL PaaX-like protein C-terminal domain PaaX-like protein C-terminal domain This family contains proteins that are similar to the product of the paaX gene of Escherichia coli (Swiss:P76086). This protein is involved in the regulation of expression of a group of proteins known to participate in the metabolism of phenylacetic acid [1]. [1]. 10766858. Transcriptional regulation of the divergent paa catabolic operons for phenylacetic acid degradation in Escherichia coli. Ferrandez A, Garcia JL, Diaz E;. J Biol Chem 2000;275:12214-12222. (from Pfam) NF019832.5 PF08226.16 DUF1720 21.4 21.4 75 domain Y Y N DUF1720 domain-containing protein 131567 cellular organisms no rank 65 EBI-EMBL Domain of unknown function (DUF1720) Domain of unknown function (DUF1720) This domain is found in different combinations with cortical patch components EF hand, SH3 and ENTH and is therefore likely to be involved in cytoskeletal processes. This family contains many hypothetical proteins. (from Pfam) NF019836.5 PF08230.16 CW_7 25 25 40 repeat Y N N CW_7 repeat protein 15539074,20720016,23056389,2311937 131567 cellular organisms no rank 3196 EBI-EMBL CW_7 repeat CW_7 repeat This domain was originally found in the C-terminal moiety of the Cpl-7 lysozyme encoded by the Streptococcus pneumoniae bacteriophage Cp-7 (Swiss:P19385). It is also found in the cell wall hydrolases of human and life-stock pathogens. CW_7 repeats make up a cell wall binding motif [3][4]. [1]. 2311937. Modular organization of the lytic enzymes of Streptococcus pneumoniae and its bacteriophages. Garcia P, Garcia JL, Garcia E, Sanchez-Puelles JM, Lopez R;. Gene 1990;86:81-88. [2]. 15539074. Recent trends on the molecular biology of pneumococcal capsules, lytic enzymes, and bacteriophage. Lopez R, Garcia E;. FEMS Microbiol Rev 2004;28:553-580. [3]. 23056389. Thermal stability of Cpl-7 endolysin from the streptococcus pneumoniae bacteriophage Cp-7; cell wall-targeting of its CW_7 motifs. Bustamante N, Rico-Lastres P, Garcia E, Garcia P, Menendez M;. PLoS One. 2012;7:e46654. [4]. 20720016. Cpl-7, a lysozyme encoded by a pneumococcal bacteriophage with a novel cell wall-binding motif. Bustamante N, Campillo NE, Garcia E, Gallego C, Pera B, Diakun GP, Saiz JL, Garcia P, Diaz JF, Menendez M;. J Biol Chem. 2010;285:33184-33196. (from Pfam) NF019843.5 PF08238.17 Sel1 30.7 2.4 36 repeat Y N N SEL1-like repeat protein 8722778 131567 cellular organisms no rank 149804 EBI-EMBL Sel1 repeat Sel1 repeat This short repeat is found in the Sel1 protein [1]. It is related to TPR repeats. [1]. 8722778. The Caenorhabditis elegans sel-1 gene, a negative regulator of lin-12 and glp-1, encodes a predicted extracellular protein. Grant B, Greenwald I;. Genetics 1996;143:237-247. (from Pfam) NF019844.5 PF08239.16 SH3_3 27 27 54 domain Y Y N SH3 domain-containing protein 131567 cellular organisms no rank 125610 EBI-EMBL Bacterial SH3 domain SH3 domain-containing protein NF019845.5 PF08240.17 ADH_N 23.5 23.5 104 domain Y Y N alcohol dehydrogenase catalytic domain-containing protein 10556240,8804825 131567 cellular organisms no rank 1034644 EBI-EMBL Alcohol dehydrogenase GroES-like domain Alcohol dehydrogenase GroES-like domain This is the catalytic domain of alcohol dehydrogenases. Many of them contain an inserted zinc binding domain. This domain has a GroES-like structure [1-2]. [1]. 8804825. Structural classification of proteins: new superfamilies. Murzin AG;. Curr Opin Struct Biol 1996;6:386-394. [2]. 10556240. Conserved structural features and sequence patterns in the GroES fold family. Taneja B, Mande SC;. Protein Eng 1999;12:815-818. (from Pfam) NF019846.5 PF08241.17 Methyltransf_11 21.2 21.2 95 domain Y Y N methyltransferase domain-containing protein GO:0008757 131567 cellular organisms no rank 1857867 EBI-EMBL Methyltransferase domain Methyltransferase domain Members of this family are SAM dependent methyltransferases. (from Pfam) NF019847.5 PF08242.17 Methyltransf_12 30 30 98 domain Y Y N methyltransferase 131567 cellular organisms no rank 1325568 EBI-EMBL Methyltransferase domain Methyltransferase domain Members of this family are SAM dependent methyltransferases. (from Pfam) NF019849.5 PF08244.18 Glyco_hydro_32C 21.9 21.9 158 domain Y Y N GH32 C-terminal domain-containing protein 14973124 131567 cellular organisms no rank 64811 EBI-EMBL Glycosyl hydrolases family 32 C terminal Glycosyl hydrolases family 32 C terminal This domain corresponds to the C terminal domain of glycosyl hydrolase family 32. It forms a beta sandwich module [1]. [1]. 14973124. The three-dimensional structure of invertase (beta-fructosidase) from Thermotoga maritima reveals a bimodular arrangement and an evolutionary relationship between retaining and inverting glycosidases. Alberto F, Bignon C, Sulzenbacher G, Henrissat B, Czjzek M;. J Biol Chem 2004;279:18903-18910. (from Pfam) NF019850.5 PF08245.17 Mur_ligase_M 24 24 200 domain Y Y N Mur ligase family protein GO:0005524,GO:0009058,GO:0016881 9218784 131567 cellular organisms no rank 507315 EBI-EMBL Mur ligase middle domain Mur ligase family middle domain This HMM hits multiple proteins of peptidoglycan (murein) biosynthesis, such as MurC, MurD, MurE, and MurF of Escherichia coli. NF019869.5 PF08264.18 Anticodon_1 25.1 25.1 148 domain Y Y N class I tRNA ligase family protein GO:0004812,GO:0006418 11114335 131567 cellular organisms no rank 329047 EBI-EMBL Anticodon-binding domain of tRNA ligase class I tRNA ligase family protein This domain is found mainly hydrophobic tRNA synthetases. The domain binds to the anticodon of the tRNA ligase. [1]. 11114335. Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase. Fukai S, Nureki O, Sekine S, Shimada A, Tao J, Vassylyev DG, Yokoyama S;. Cell 2000;103:793-803. (from Pfam) NF019872.5 PF08267.17 Meth_synt_1 27 27 313 PfamEq Y N N Cobalamin-independent synthase, N-terminal domain GO:0003871,GO:0008270,GO:0008652 15326182 131567 cellular organisms no rank 54193 EBI-EMBL Cobalamin-independent synthase, N-terminal domain Cobalamin-independent synthase, N-terminal domain The N-terminal domain and C-terminal domains of cobalamin-independent synthases together define a catalytic cleft in the enzyme. The N-terminal domain is thought to bind the substrate, in particular, the negatively charged polyglutamate chain. The N-terminal domain is also thought to stabilise a loop from the C-terminal domain [1]. [1]. 15326182. Crystal structures of cobalamin-independent methionine synthase complexed with zinc, homocysteine, and methyltetrahydrofolate. Ferrer JL, Ravanel S, Robert M, Dumas R;. J Biol Chem 2004;279:44235-44238. (from Pfam) NF019874.5 PF08269.16 dCache_2 26.5 26.5 298 domain Y Y N cache domain-containing protein 11084361,27049771 131567 cellular organisms no rank 64789 EBI-EMBL Cache domain Cache domain Double Cache domain 2 (dCache_2) may be a result of single Cache domain 2 (sCache_2) duplication [2]. [1]. 11084361. Cache - a signaling domain common to animal Ca(2+)-channel subunits and a class of prokaryotic chemotaxis receptors. Anantharaman V, Aravind L;. Trends Biochem Sci 2000;25:535-537. [2]. 27049771. Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes. Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB;. PLoS Comput Biol. 2016;12:e1004862. (from Pfam) NF019876.5 PF08271.17 TF_Zn_Ribbon 29 29 43 domain Y Y N TFIIB-type zinc ribbon-containing protein 11045620 131567 cellular organisms no rank 6242 EBI-EMBL TFIIB zinc-binding TFIIB zinc-binding The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure [1]. [1]. 11045620. Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription. Chen HT, Legault P, Glushka J, Omichinski JG, Scott RA;. Protein Sci 2000;9:1743-1752. (from Pfam) NF019880.5 PF08275.16 DNAG_N 26 26 128 PfamEq Y N N DNA primase catalytic core, N-terminal domain 12769857,8294018 131567 cellular organisms no rank 87765 EBI-EMBL DNA primase catalytic core, N-terminal domain DNA primase catalytic core, N-terminal domain DNA primase (DNAG) is a a nucleotidyltransferase which synthesises the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell division [1]. Primases comprise three domains: a zinc-binding domain at the N-terminal (Pfam:PF01807), a polymerase domain (catalytic core), and a domain that interacts with the replicative helicase (Pfam:PF01807). The catalytic core consists of an alpha+beta domain at the N-terminal (this entry) and a TOPRIM domain at the C-terminal (Pfam:PF13155) [1,2]. [1]. 8294018. The Haemophilus influenzae dnaG sequence and conserved bacterial primase motifs. Versalovic J, Lupski JR;. Gene 1993;136:281-286. [2]. 12769857. Modular architecture of the bacteriophage T7 primase couples RNA primer synthesis to DNA synthesis. Kato M, Ito T, Wagner G, Richardson CC, Ellenberger T;. Mol Cell 2003;11:1349-1360. (from Pfam) NF019884.5 PF08279.17 HTH_11 25 25 55 domain Y Y N HTH domain-containing protein 131567 cellular organisms no rank 428202 EBI-EMBL HTH domain HTH domain This family includes helix-turn-helix domains in a wide variety of proteins. (from Pfam) NF019885.5 PF08280.16 HTH_Mga 23 23 59 domain Y Y N helix-turn-helix domain-containing protein 11952907 131567 cellular organisms no rank 21324 EBI-EMBL M protein trans-acting positive regulator (MGA) HTH domain M protein trans-acting positive regulator (MGA) HTH domain Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [1]. [1]. 11952907. Two DNA-binding domains of Mga are required for virulence gene activation in the group A streptococcus. McIver KS, Myles RL;. Mol Microbiol 2002;43:1591-1601. (from Pfam) NF019886.5 PF08281.17 Sigma70_r4_2 25.7 25.7 54 domain Y Y N sigma factor-like helix-turn-helix DNA-binding protein GO:0003677,GO:0003700,GO:0006352,GO:0006355,GO:0016987 11931761 131567 cellular organisms no rank 1321504 EBI-EMBL Sigma-70, region 4 sigma factor-like helix-turn-helix DNA-binding domain Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. [1]. 11931761. Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA;. Mol Cell 2002;9:527-539. (from Pfam) NF019887.5 PF08282.17 Hydrolase_3 20.9 20.9 255 domain Y Y N HAD hydrolase family protein 131567 cellular organisms no rank 493193 EBI-EMBL haloacid dehalogenase-like hydrolase HAD hydrolase family protein This family contains haloacid dehalogenase-like hydrolase enzymes. (from Pfam) NF019893.5 PF08288.17 PIGA 27 27 90 PfamEq Y N N PIGA (GPI anchor biosynthesis) GO:0006506 12488505 131567 cellular organisms no rank 35 EBI-EMBL PIGA (GPI anchor biosynthesis) PIGA (GPI anchor biosynthesis) This domain is found on phosphatidylinositol n-acetylglucosaminyltransferase proteins. These proteins are involved in GPI anchor biosynthesis and are associated with disease the paroxysmal nocturnal haemoglobinuria [1]. [1]. 12488505. The effect of GPI-anchor deficiency on apoptosis in mice carrying a Piga gene mutation in hematopoietic cells. Kulkarni S, Bessler M;. J Leukoc Biol 2002;72:1228-1233. (from Pfam) NF019896.5 PF08291.16 Peptidase_M15_3 23.2 23.2 108 domain Y Y N D-Ala-D-Ala carboxypeptidase family metallohydrolase 131567 cellular organisms no rank 31035 EBI-EMBL Peptidase M15 D-Ala-D-Ala carboxypeptidase family metallohydrolase C-terminal domain NF019902.5 PF08298.16 AAA_PrkA 25 25 358 domain Y N N PrkA AAA domain 8626065 131567 cellular organisms no rank 23923 EBI-EMBL PrkA AAA domain PrkA AAA domain This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain [1]. [1]. 8626065. Cloning and characterization of the Bacillus subtilis prkA gene encoding a novel serine protein kinase. Fischer C, Geourjon C, Bourson C, Deutscher J;. Gene 1996;168:55-60. (from Pfam) NF019903.5 PF08299.16 Bac_DnaA_C 31.5 31.5 69 domain Y Y N helix-turn-helix domain-containing protein GO:0005524,GO:0006270,GO:0006275,GO:0043565 12682358 131567 cellular organisms no rank 66653 EBI-EMBL Bacterial dnaA protein helix-turn-helix Bacterial dnaA protein helix-turn-helix NF019908.5 PF08305.16 NPCBM 23.9 23.9 137 domain Y Y N NPCBM/NEW2 domain-containing protein 15285616,16212961,34061031 131567 cellular organisms no rank 32886 EBI-EMBL NPCBM/NEW2 domain NPCBM/NEW2 domain This novel putative carbohydrate binding module (NPCBM) domain is found at the N-terminus of glycosyl hydrolase family 98 proteins [1]. This domain has also been called the NEW2 domain [2]. NPCBM domains found in bacterial conflict systems are predicted to interact with invasive molecules and recruit downstream effectors [3]. [1]. 16212961. Analysis of glycoside hydrolase family 98: catalytic machinery, mechanism and a novel putative carbohydrate binding module. Rigden DJ;. FEBS Lett. 2005;579:5466-5472. [2]. 15285616. [Phylogenetic analysis of alpha-galactosidases of the GH27 family]. Naumov DG;. Mol Biol (Mosk). 2004;38:463-476. [3]. 34061031. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. Kaur G, Iyer LM, Burroughs AM, Aravind L;. Elife. 2021; [Epub ahead of print] (from Pfam) NF019911.5 PF08308.16 PEGA 20.8 20.8 71 domain Y Y N PEGA domain-containing protein 131567 cellular organisms no rank 23135 EBI-EMBL PEGA domain PEGA domain This domain is found in both archaea and bacteria and has similarity to S-layer (surface layer) proteins. It is named after the characteristic PEGA sequence motif found in this domain. The secondary structure of this domain is predicted to be beta-strands [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16]. (from Pfam) NF019912.5 PF08309.16 LVIVD 20.2 7.3 42 repeat Y N N LVIVD repeat protein 18629042 131567 cellular organisms no rank 22047 EBI-EMBL LVIVD repeat LVIVD repeat This repeat is found in bacterial and archaeal cell surface proteins, many of which are hypothetical. The secondary structure corresponding to this repeat is predicted to comprise from 1-7 of 4-beta-strands which may associate to form a beta-propeller [1]. The repeat copy number varies from 3-29. This repeat is sometimes found with the PKD domain Pfam:PF00801. [1]. 18629042. Identification and analysis of novel tandem repeats in the cell surface proteins of archaeal and bacterial genomes using computational tools. Adindla S, Inampudi KK, Guruprasad K, Guruprasad L;. Comp Funct Genomics. 2004;5:2-16. (from Pfam) NF019913.5 PF08310.16 LGFP 22 22 53 repeat Y N N LGFP repeat protein 12740729 131567 cellular organisms no rank 18953 EBI-EMBL LGFP repeat LGFP repeat This 54 amino acid repeat is found in many hypothetical proteins. Several hypothetical proteins from C.glutamicum and C.efficiens along with PS1 protein contain this repeat region. The N-terminus region of PS1 contains an esterase domain which transfers corynomycolic acid. The C-terminus region consists of 4 tandem LGFP repeats. It is hypothesised that the PS1 proteins in Corynebacterium, when associated with the cell wall, may be anchored via the LGFP tandem repeats that may be important for maintaining cell wall integrity [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16]. Deletion of Swiss:Q01377 protein results in a 10-fold increase in the cell volume of the organism and infers the corresponding proteins involvement in the cell shape formation [1]. The secondary structure of each repeat is predicted to comprise two beta-strands and one alpha-helix [Adindla et al. 2004]. [1]. 12740729. Identification and functional analysis of six mycolyltransferase genes of Corynebacterium glutamicum ATCC 13032: the genes cop1, cmt1, and cmt2 can replace each other in the synthesis of trehalose dicorynomycolate, a component of the mycolic acid layer of. Brand S, Niehaus K, Puhler A, Kalinowski J;. Arch Microbiol 2003;180:33-44. (from Pfam) NF019924.5 PF08323.16 Glyco_transf_5 22.7 22.7 239 domain Y Y N glycogen/starch synthase 131567 cellular organisms no rank 64991 EBI-EMBL Starch synthase catalytic domain Starch synthase catalytic domain NF019926.5 PF08325.15 WLM 26 26 190 domain Y Y N Wss1p-related putative metallopeptidase 15483401 131567 cellular organisms no rank 4387 EBI-EMBL WLM domain WLM domain This is a predicted metallopeptidase domain called WLM (Wss1p-like metalloproteases). These are linked to the Ub-system by virtue of fusions with the UB-binding PUG (PUB), Ub-like, and Little Finger domains. More specifically, genetic evidence implicates the WLM family in de-SUMOylation [1]. [1]. 15483401. Novel predicted peptidases with a potential role in the ubiquitin signaling pathway. Iyer LM, Koonin EV, Aravind L;. Cell Cycle 2004;3:1440-1450. (from Pfam) NF019928.5 PF08327.16 AHSA1 22.1 22.1 125 domain Y Y N SRPBCC domain-containing protein 11554768,12504007,12604615,20818668 131567 cellular organisms no rank 199976 EBI-EMBL Activator of Hsp90 ATPase homolog 1-like protein Activator of Hsp90 ATPase homolog 1-like protein This family includes eukaryotic, prokaryotic and archaeal proteins that bear similarity to a C-terminal region of human activator of 90 kDa heat shock protein ATPase homolog 1 (AHSA1/p38, Swiss:O95433). This protein is known to interact with the middle domain of Hsp90, and stimulate its ATPase activity [1]. It is probably a general upregulator of Hsp90 function, particularly contributing to its efficiency in conditions of increased stress [2]. p38 is also known to interact with the cytoplasmic domain of the VSV G protein, and may thus be involved in protein transport [3]. It has also been reported as being underexpressed in Down's syndrome. This region is found repeated in two members of this family (Swiss:Q8XY04 and Swiss:Q6MH87). The structure of YndB from Bacillus subtilis showed the helix-grip fold consisting of a beta-sheet with two small and one long alpha-helix which form a hydrophobic cavity that preferentially binds lipid-like molecules. This structure confirms its similarity with the eukaryote protein Aha1 and its classification as a member of the AHSA1 family) [4]. [1]. 12604615. Aha1 binds to the middle domain of Hsp90, contributes to client protein activation and stimulates the ATPase activity of the molecular chaperone. Lotz GP, Lin H, Harst A, Obermann WM;. J Biol Chem 2003;0:0-0. [2]. 12504007. Activation of the ATPase activity of hsp90 by the stress-regulated cochaperone aha1. Panaretou B, Siligardi G, Meyer P, Maloney A, Sullivan JK, Singh S, Millson SH, Clarke PA, Naaby-Hansen S, Stein R, Cramer R, Mollapour M, Workman P, Piper PW, Pearl LH, Prodromou C;. Mol Cell 2002;10:1307-1318. [3]. 11554768. p38: A. TRUNCATED at 1650 bytes (from Pfam) NF019929.5 PF08328.16 ASL_C 35 35 115 PfamEq Y N N Adenylosuccinate lyase C-terminal GO:0004018,GO:0006188 8530047 131567 cellular organisms no rank 30067 EBI-EMBL Adenylosuccinate lyase C-terminal Adenylosuccinate lyase C-terminal This domain is found at the C-terminus of adenylosuccinate lyase(ASL; PurB in E. coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain Pfam:PF00206. ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate [1]. [1]. 8530047. Characterization of the cDNA and the gene encoding murine adenylosuccinate lyase. Wong LJ, O'Brien WE;. Genomics 1995;28:341-343. (from Pfam) NF019930.5 PF08329.15 ChitinaseA_N 21.2 21.2 133 domain Y Y N chitinase N-terminal domain-containing protein GO:0004568,GO:0006032 7704527,9377712 131567 cellular organisms no rank 7361 EBI-EMBL Chitinase A, N-terminal domain Chitinase A, N-terminal domain This domain is found in a number of bacterial chitinases and similar viral proteins. It is organised into a fibronectin III module domain-like fold, comprising only beta strands. Its function is not known, but it may be involved in interaction with the enzyme substrate, chitin [1,2]. It is separated by a hinge region from the catalytic domain (Pfam:PF00704); this hinge region is probably mobile, allowing the N-terminal domain to have different relative positions in solution [1]. [1]. 7704527. Crystal structure of a bacterial chitinase at 2.3 A resolution. Perrakis A, Tews I, Dauter Z, Oppenheim AB, Chet I, Wilson KS, Vorgias CE;. Structure 1994;2:1169-1180. [2]. 9377712. Evolution of immunoglobulin-like modules in chitinases: their structural flexibility and functional implications. Perrakis A, Ouzounis C, Wilson KS;. Fold Des 1997;2:291-294. (from Pfam) NF019932.5 PF08332.15 CaMKII_AD 22.1 22.1 128 domain Y N N Calcium/calmodulin dependent protein kinase II association domain GO:0004683,GO:0005516,GO:0006468 12603201,14993460 131567 cellular organisms no rank 17522 EBI-EMBL Calcium/calmodulin dependent protein kinase II association domain Calcium/calmodulin dependent protein kinase II association domain This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (Pfam:PF00069) at their N-terminus [1]. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers [2]. [1]. 12603201. Differential functional properties of calmodulin-dependent protein kinase IIgamma variants isolated from smooth muscle. Gangopadhyay SS, Barber AL, Gallant C, Grabarek Z, Smith JL, Morgan KG;. Biochem J 2003;372:347-357. [2]. 14993460. CaMKII, an enzyme on the move: regulation of temporospatial localization. Griffith LC, Lu CS, Sun XX;. Mol Interv 2003;3:386-403. (from Pfam) NF019938.5 PF08338.16 DUF1731 27 27 47 PfamAutoEq Y Y N DUF1731 domain-containing protein 131567 cellular organisms no rank 59639 EBI-EMBL Domain of unknown function (DUF1731) Domain of unknown function (DUF1731) This domain of unknown function appears towards the C-terminus of proteins of the NAD dependent epimerase/dehydratase family (Pfam:PF01370) in bacteria, eukaryotes and archaea. Many of the proteins in which it is found are involved in cell-division inhibition. (from Pfam) NF019941.5 PF08341.16 TED 22 22 102 domain Y Y N Cys-Gln thioester bond-forming surface protein 20729215 131567 cellular organisms no rank 20437 EBI-EMBL Thioester domain Cys-Gln thioester bond-forming domain This HMM describes a domain commonly found in surface-anchored bacterial proteins such as adhesins, in which a thioester bond forms between a conserved Cys and a conserved Gln. NF019948.5 PF08349.16 DUF1722 22.5 22.5 117 PfamAutoEq Y Y N DUF1722 domain-containing protein 131567 cellular organisms no rank 18133 EBI-EMBL Protein of unknown function (DUF1722) Protein of unknown function (DUF1722) This domain of unknown function is found in bacteria and archaea and is homologous to the hypothetical protein ybgA from E. coli. (from Pfam) NF019950.5 PF08351.16 TmcA_N 22.7 22.7 178 PfamAutoEq Y Y N tRNA(Met) cytidine acetyltransferase TmcA domain-containing protein 18668122,19322199,25402480,25653167,31491951 131567 cellular organisms no rank 14290 EBI-EMBL tRNA(Met) cytidine acetyltransferase TmcA, N-terminal tRNA(Met) cytidine acetyltransferase TmcA, N-terminal This domain of unknown function is often found at the N-terminus of the bacterial tRNA(Met) cytidine acetyltransferase TmcA. TmcA catalyses the formation of N(4)-acetylcytidine (ac4C) at the wobble position of tRNA(Met) by using acetyl-CoA as an acetyl donor and either ATP or GTP [1,2,5]. This modification is thought to ensure precise recognition of the AUG codon by strengthening C-G base-pair interaction and also prevent misrecognition of the near cognate AUA codon [1]. This domain is also found in mammalian N-acetyltransferase 10 (NAT10) and fungal protein Kre33. Kre33 and NAT10 are RNA cytosine acetyltransferases with specificity toward both 18S rRNA and tRNAs and contain additional putative nuclear and nucleolar localization signals (NLS and NoLS respectively) [3,4,5]. [1]. 19322199. RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon. Chimnaronk S, Suzuki T, Manita T, Ikeuchi Y, Yao M, Suzuki T, Tanaka I;. EMBO J. 2009;28:1362-1373. [2]. 18668122. The RNA acetyltransferase driven by ATP hydrolysis synthesizes N4-acetylcytidine of tRNA anticodon. Ikeuchi Y, Kitahara K, Suzuki T;. EMBO J. 2008;27:2194-2203. [3]. 25653167. Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1. Sharma S, Langhendries JL, Watzinger P, Kotter P, Entian KD, Lafontaine DL;. Nucleic Acids Res. 2015;43:2242-2258. [4]. 25402480. RNA cytidine acetyltransferase of small-subunit ribosomal RNA: identification of acetylation sites and the responsible acetyltransferase in fission yeast, Schizosaccharomyces pombe. Taoka M, Ishik. TRUNCATED at 1650 bytes (from Pfam) NF019951.5 PF08352.17 oligo_HPY 27.1 14.5 65 domain Y N N Oligopeptide/dipeptide transporter, C-terminal region GO:0000166,GO:0005524,GO:0015833 131567 cellular organisms no rank 537940 EBI-EMBL Oligopeptide/dipeptide transporter, C-terminal region Oligopeptide/dipeptide transporter, C-terminal region This family features a region found towards the C-terminus of oligopeptide ABC transporter ATP binding proteins, immediately following the ATP-binding domain (Pfam:PF00005). All characterised members appear able to be involved in the transport of oligopeptides or dipeptides. Some are important for sporulation or antibiotic resistance. Some dipeptide transporters also act on the heme precursor delta-aminolevulinic acid. (from Pfam) NF019952.5 PF08353.15 MurT_C 25 25 110 PfamAutoEq Y Y N MurT ligase domain-containing protein 30154570 131567 cellular organisms no rank 20263 EBI-EMBL MurT ligase C-terminal MurT ligase C-terminal This entry represents the C-terminal domain of MurT ligase from Gram-positive bacteria. MurT is part of the bi-enzymatic complex MurT-GatD involved in the amidation of the alpha-carboxyl group of the D-isoglutamate residue in Lipid II in the peptidoglycan layer to produce D-isoglutamine. This domain contains an aspartate at position 349, the third residue in the catalytic triad GatD-C94, GatD-H189, MurT-D349. This C-terminal domain is built around a central six-stranded, predominantly parallel beta-sheet that is sandwiched between four alpha-helices on one side and two alpha-helices on the other. The MurT-GatD heterodimer adopts a boomerang-shaped conformation, with GatD packing against the C-terminal domain of MurT [1]. [1]. 30154570. Structural basis of cell wall peptidoglycan amidation by the GatD/MurT complex of Staphylococcus aureus. Noldeke ER, Muckenfuss LM, Niemann V, Muller A, Stork E, Zocher G, Schneider T, Stehle T;. Sci Rep. 2018;8:12953. (from Pfam) NF019956.5 PF08357.16 SEFIR 23 23 150 domain Y Y N SEFIR domain-containing protein 12765832,22037611 131567 cellular organisms no rank 4827 EBI-EMBL SEFIR domain SEFIR domain This family comprises IL17 receptors (IL17Rs, e.g. Swiss:Q60943) and SEF proteins (e.g. Swiss:Q8QHJ9). The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (Pfam:PF01582), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways [1]. [1]. 12765832. The STIR-domain superfamily in signal transduction, development and immunity. Novatchkova M, Leibbrandt A, Werzowa J, Neubuser A, Eisenhaber F;. Trends Biochem Sci 2003;28:226-229. [2]. 22037611. Evolution of prokaryotic homologues of the eukaryotic SEFIR protein domain. Wu B, Gong J, Liu L, Li T, Wei T, Bai Z;. Gene. 2011; [Epub ahead of print] (from Pfam) NF019958.5 PF08359.16 TetR_C_4 21 21 133 domain Y Y N TetR/AcrR family transcriptional regulator C-terminal domain-containing protein 131567 cellular organisms no rank 15013 EBI-EMBL YsiA-like protein, C-terminal region YsiA-like protein, C-terminal region The members of this family are thought to be TetR-type transcriptional regulators that bear particular similarity to YsiA (Swiss:P94548), a hypothetical protein expressed by B. subtilis. (from Pfam) NF019959.5 PF08360.16 TetR_C_5 21 21 131 domain Y Y N TetR family transcriptional regulator C-terminal domain-containing protein GO:0003700,GO:0045892 11739955,9660841 131567 cellular organisms no rank 3521 EBI-EMBL QacR-like protein, C-terminal region QacR-like protein, C-terminal region This family features the C-terminal region of a number of proteins that bear similarity to the QacR protein (Swiss:P23217), a transcriptional regulator of the TetR family. QacR is able to bind various environmental agents, which include a number of cationic lipophilic compounds, and thus regulate the transcription of QacA (Swiss:P23215), a multidrug efflux pump [1]. The C-terminal region contains the multifaceted, expansive drug-binding pocket, which is composed of several separate, but linked, binding sites [2]. [1]. 9660841. QacR is a repressor protein that regulates expression of the Staphylococcus aureus multidrug efflux pump QacA. Grkovic S, Brown MH, Roberts NJ, Paulsen IT, Skurray RA;. J Biol Chem 1998;273:18665-18673. [2]. 11739955. Structural mechanisms of QacR induction and multidrug recognition. Schumacher MA, Miller MC, Grkovic S, Brown MH, Skurray RA, Brennan RG;. Science 2001;294:2158-2163. (from Pfam) NF019968.5 PF08369.15 PCP_red 32.5 32.5 45 domain Y N N Proto-chlorophyllide reductase 57 kD subunit GO:0015979,GO:0015995,GO:0016491 131567 cellular organisms no rank 5088 EBI-EMBL Proto-chlorophyllide reductase 57 kD subunit Proto-chlorophyllide reductase 57 kD subunit This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of Nitrogenase component 1 type Oxidoreductases (Pfam:PF00148) and sometimes independently in bacterial proteins such as the Proto-chlorophyllide reductase 57 kD subunit of the Cyanobacterium Synechocystis. (from Pfam) NF019976.5 PF08378.16 NERD 22.1 22.1 111 domain Y Y N NERD domain-containing protein 15055202 131567 cellular organisms no rank 82404 EBI-EMBL Nuclease-related domain Nuclease-related domain The nuclease-related domain (NERD) is found in a range of bacterial as well as archaeal and plant proteins. It has distant similarity to endonucleases (hence its name) and its predicted secondary structure is helix - sheet - sheet - sheet - sheet - weak sheet/long loop - helix - sheet - sheet. The majority of NERD-containing proteins are single-domain, but in several cases proteins containing NERD have additional domains which in 75% of cases are involved in DNA processing [1]. [1]. 15055202. NERD: a DNA processing-related domain present in the anthrax virulence plasmid, pXO1. Grynberg M, Godzik A;. Trends Biochem Sci 2004;29:106-110. (from Pfam) NF019977.5 PF08379.15 Bact_transglu_N 27 27 80 domain Y Y N transglutaminase N-terminal domain-containing protein 131567 cellular organisms no rank 52382 EBI-EMBL Bacterial transglutaminase-like N-terminal region Bacterial transglutaminase-like N-terminal region This region is found towards the N-terminus of various archaeal and bacterial hypothetical proteins. Some of these are annotated as being transglutaminase-like proteins, and in fact contain a transglutaminase-like superfamily domain (Pfam:PF01841). (from Pfam) NF019982.5 PF08386.15 Abhydrolase_4 21 21 103 domain Y Y N alpha/beta hydrolase 15574930 131567 cellular organisms no rank 199630 EBI-EMBL TAP-like protein alpha/beta hydrolase This is a family of putative bacterial peptidases and hydrolases that bear similarity to a tripeptidyl aminopeptidase isolated from Streptomyces lividans (Swiss:Q54410). A member of this family (Swiss:Q6E3K7) is thought to be involved in the C-terminal processing of propionicin F, a bacteriocidin characterised from Propionibacterium freudenreichii [1]. [1]. 15574930. Molecular and genetic characterization of propionicin F, a bacteriocin from Propionibacterium freudenreichii. Brede DA, Faye T, Johnsborg O, Odegard I, Nes IF, Holo H;. Appl Environ Microbiol 2004;70:7303-7310. (from Pfam) NF019984.5 PF08388.16 GIIM 23 23 80 domain Y Y N group II intron maturase-specific domain-containing protein 11959575 131567 cellular organisms no rank 50566 EBI-EMBL Group II intron, maturase-specific domain Group II intron, maturase-specific domain This region is found mainly in various bacterial and archaeal species, but a few members of this family are expressed by fungal and chlamydomonal species. It has been implicated in the binding of intron RNA during reverse transcription and splicing [1]. [1]. 11959575. Presence of a group II intron in a multiresistant Serratia marcescens strain that harbors three integrons and a novel gene fusion. Centron D, Roy PH;. Antimicrob Agents Chemother 2002;46:1402-1409. (from Pfam) NF019990.5 PF08394.15 Arc_trans_TRASH 20.8 20.8 37 domain Y Y N TRASH domain-containing protein 12713899 131567 cellular organisms no rank 627 EBI-EMBL Archaeal TRASH domain Archaeal TRASH domain This region is found in the C-terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [1]. [1]. 12713899. TRASH: a novel metal-binding domain predicted to be involved in heavy-metal sensing, trafficking and resistance. Ettema TJ, Huynen MA, de Vos WM, van der Oost J;. Trends Biochem Sci 2003;28:170-173. (from Pfam) NF019997.5 PF08401.16 ArdcN 22.6 22.6 123 domain Y Y N ArdC-like ssDNA-binding domain-containing protein GO:0003697 10686096,28559295,30396152,32348296 131567 cellular organisms no rank 36883 EBI-EMBL N-terminal domain of anti-restriction factor ArdC anti-restriction factor ArdC-like ssDNA-binding domain This is the ssDNA binding domain of anti-restriction factor ArdC deployed by plasmids and phages in polyvalent proteins related to the BHD domains of XPC/Rad4 and the Tc-38 domain found in kinetoplastid minicircle binding proteins [1,2,3]. The structure of this domain is composed of three alpha-helices and a three-stranded beta-sheet that supports a long and protuberant beta-hairpin [3]. This domain is also found in the N-terminal region of the RP4 TraC1 primase [4], together with the Toprim domain (pfam:PF01751, pfam:PF13362 and pfam:PF13662). [1]. 30396152. Unexpected Evolution of Lesion-Recognition Modules in Eukaryotic NER and Kinetoplast DNA Dynamics Proteins from Bacterial Mobile Elements. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. iScience. 2018;9:192-208. [2]. 28559295. Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. Iyer LM, Burroughs AM, Anand S, de Souza RF, Aravind L;. J Bacteriol. 2017; [Epub ahead of print]. [3]. 32348296. ArdC, a ssDNA-binding protein with a metalloprotease domain, overpasses the recipient hsdRMS restriction system broadening conjugation host range. Gonzalez-Montes L, Del Campo I, Garcillan-Barcia MP, de la Cruz F, Moncalian G;. PLoS Genet. 2020;16:e1008750. [4]. 10686096. Antirestriction protein Ard (Type C) encoded by IncW plasmid pSa has a high similarity to the "protein transport" domain of TraC1 primase of promiscuous plasmid RP4. Belogurov AA, Delver EP, Agafonova OV, Belogurova NG, Lee LY, Kado CI;. J Mol Biol. 2000;296:969-977. (from Pfam) NF019998.5 PF08402.15 TOBE_2 21 21 76 domain Y Y N TOBE domain-containing protein GO:0005524,GO:0022857,GO:0043190,GO:0055085 10829230 131567 cellular organisms no rank 366289 EBI-EMBL TOBE domain TOBE domain The TOBE domain [1] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (eg Swiss:P46930) and sulphate (Swiss:P16676). Found in ABC transporters immediately after the ATPase domain. In this family a strong RPE motif is found at the presumed N-terminus of the domain. [1]. 10829230. Protein fold recognition using sequence profiles and its application in structural genomics. Koonin EV, Wolf YI, Aravind L;. Adv Protein Chem 2000;54:245-275. (from Pfam) NF020002.5 PF08406.15 CbbQ_C 20.6 20.6 85 domain Y Y N CbbQ/NirQ/NorQ C-terminal domain-containing protein 10548510,10698784 131567 cellular organisms no rank 11638 EBI-EMBL CbbQ/NirQ/NorQ C-terminal CbbQ/NirQ/NorQ C-terminal This domain is found at the C-terminus of proteins of the CbbQ/NirQ/NorQ family of proteins which play a role in the post-translational activation of Rubisco [1]. It is also found in the Thauera aromatica TutH protein which is similar to the CbbQ/NirQ/NorQ family [2], as well as in putative chaperones. The ATPase family associated with various cellular activities (AAA) Pfam:PF07728 is found in the same bacterial and archaeal proteins as the domain described here. [1]. 10548510. The cbbQ genes, located downstream of the form I and form II RubisCO genes, affect the activity of both RubisCOs. Hayashi NR, Arai H, Kodama T, Igarashi Y;. Biochem Biophys Res Commun 1999;265:177-183. [2]. 10698784. Transcriptional analysis of the tutE tutFDGH gene cluster from Thauera aromatica strain T1. Coschigano PW;. Appl Environ Microbiol 2000;66:1147-1151. (from Pfam) NF020013.5 PF08421.16 Methyltransf_13 31.3 31.3 62 domain Y N N Putative zinc binding domain 131567 cellular organisms no rank 14868 EBI-EMBL Putative zinc binding domain Putative zinc binding domain This domain is found at the N-terminus of bacterial methyltransferases and contains four conserved cysteines suggesting a potential zinc binding domain. (from Pfam) NF020014.5 PF08423.16 Rad51 22 22 244 domain Y N N Rad51 16169964 131567 cellular organisms no rank 53014 EBI-EMBL Rad51 Rad51 Rad51 is a DNA repair and recombination protein and is a homologue of the bacterial ATPase RecA protein. [1]. 16169964. Arabidopsis RAD51C gene is important for homologous recombination in meiosis and mitosis. Abe K, Osakabe K, Nakayama S, Endo M, Tagiri A, Todoriki S, Ichikawa H, Toki S;. Plant Physiol. 2005;139:896-908. (from Pfam) NF020022.5 PF08433.15 KTI12 22 22 271 domain Y N N Chromatin associated protein KTI12 15772087 131567 cellular organisms no rank 33039 EBI-EMBL Chromatin associated protein KTI12 Chromatin associated protein KTI12 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II [1]. The Elongator complex has histone acetyltransferase activity. [1]. 15772087. Physical and functional interaction between Elongator and the chromatin-associated Kti12 protein. Petrakis TG, Sogaard TM, Erdjument-Bromage H, Tempst P, Svejstrup JQ;. J Biol Chem 2005;280:19454-19460. (from Pfam) NF020027.5 PF08438.15 YGR210-like_G4 24.7 24.7 108 domain Y N N Obg-like GTPase YGR210-like, G4 motif-containing domain 17430889 131567 cellular organisms no rank 2093 EBI-EMBL Obg-like GTPase YGR210-like, G4 motif-containing domain Obg-like GTPase YGR210-like, G4 motif-containing domain This domain is part of the G domain found at the C-terminus of Pfam:PF01926 in archaeal and eukaryotic GTP-binding proteins. Members of this entry form a subfamily within the Obg family of GTPases and includes YGR210 from yeasts and its homologues from archaea [1]. This domain seems to be necessary for the complete activity of the protein for binding of both adenine and guanine nucleotides, with a preference for guanine nucleotides. This domain contains the NKxD motif, known as the G4 motif [1]. [1]. 17430889. Human OLA1 defines an ATPase subfamily in the Obg family of GTP-binding proteins. Koller-Eichhorn R, Marquardt T, Gail R, Wittinghofer A, Kostrewa D, Kutay U, Kambach C;. J Biol Chem. 2007;282:19928-19937. (from Pfam) NF020028.5 PF08439.15 Peptidase_M3_N 25 25 70 domain Y N N Oligopeptidase F 7798200 131567 cellular organisms no rank 50403 EBI-EMBL Oligopeptidase F Oligopeptidase F This domain is found to the N-terminus of the Pfam:PF01432 domain in bacterial and archaeal proteins including Oligoendopeptidase F. An example of this protein is Lactococcus lactis PepF [1]. [1]. 7798200. Biochemical and genetic characterization of PepF, an oligopeptidase from Lactococcus lactis. Monnet V, Nardi M, Chopin A, Chopin MC, Gripon JC;. J Biol Chem 1994;269:32070-32076. (from Pfam) NF020031.5 PF08442.15 ATP-grasp_2 29.5 29.5 202 domain Y Y N ATP-grasp domain-containing protein 9416615 131567 cellular organisms no rank 51618 EBI-EMBL ATP-grasp domain ATP-grasp domain NF020032.5 PF08443.16 RimK 21 21 188 domain Y N N RimK-like ATP-grasp domain 9416615 131567 cellular organisms no rank 137301 EBI-EMBL RimK-like ATP-grasp domain RimK-like ATP-grasp domain This ATP-grasp domain is found in the ribosomal S6 modification enzyme RimK [1]. [1]. 9416615. A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity. Galperin MY, Koonin EV;. Protein Sci 1997;6:2639-2643. (from Pfam) NF020034.5 PF08445.15 FR47 22.1 22.1 86 domain Y Y N GNAT family N-acetyltransferase GO:0016747 131567 cellular organisms no rank 582614 EBI-EMBL FR47-like protein GNAT family N-acetyltransferase The members of this family are similar to the C-terminal region of the D. melanogaster hypothetical protein FR47 (Swiss:Q9VR51). This protein has been found to consist of two N-acyltransferase-like domains swapped with the C-terminal strands. (from Pfam) NF020036.5 PF08447.17 PAS_3 25.6 25.6 89 domain Y Y N PAS domain-containing protein GO:0005515 15009198,7756254,9301332,9382818 131567 cellular organisms no rank 590607 EBI-EMBL PAS fold PAS fold The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. [1]. 9301332. PAS domain S-boxes in archaea, bacteria and sensors for oxygen and redox. Zhulin IB, Taylor BL, Dixon R;. Trends Biochem Sci 1997;22:331-333. [2]. 7756254. 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore. Borgstahl GE, Williams DR, Getzoff ED;. Biochemistry 1995;34:6278-6287. [3]. 9382818. PAS: a multifunctional domain family comes to light. Ponting CP, Aravind L;. Curr Biol 1997;7:674-677. [4]. 15009198. The PAS fold: a redefination of the PAS domain based upon structural prediction. Hefti MH, Francoijs KJ, de Vries SC, Dixon R, Vervoort J;. Eur J Biochem 2004;271:1198-1208. (from Pfam) NF020037.5 PF08448.15 PAS_4 23.1 23.1 110 domain Y Y N PAS domain-containing protein 15009198,7756254,9301332,9382818 131567 cellular organisms no rank 964548 EBI-EMBL PAS fold PAS fold The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain is associated to signalling systems and works as a signal sensor domain. It recognises differently substituted aromatic hydrocarbons, oxygen, different dodecanoic acids, autoinducers, 3,5-dimethyl-pyrazin-2-ol and N-alanyl-aminoacetone (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 9301332. PAS domain S-boxes in archaea, bacteria and sensors for oxygen and redox. Zhulin IB, Taylor BL, Dixon R;. Trends Biochem Sci 1997;22:331-333. [2]. 7756254. 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore. Borgstahl GE, Williams DR, Getzoff ED;. Biochemistry 1995;34:6278-6287. [3]. 9382818. PAS: a multifunctional domain family comes to light. Ponting CP, Aravind L;. Curr Biol 1997;7:674-677. [4]. 15009198. The PAS fold: a redefination of the PAS domain based upon structural prediction. Hefti MH, Francoijs KJ, de Vries SC, Dixon R, Vervoort J;. Eur J Biochem 2004;271:1198-1208. (from Pfam) NF020038.5 PF08449.16 UAA 26.2 26.2 311 PfamEq Y N N UAA transporter family GO:0055085 11432728 131567 cellular organisms no rank 173 EBI-EMBL UAA transporter family UAA transporter family This family includes transporters with a specificity for UDP-N-acetylglucosamine [1]. [1]. 11432728. The drug/metabolite transporter superfamily. Jack DL, Yang NM, Saier MH Jr;. Eur J Biochem 2001;268:3620-3639. (from Pfam) NF020039.5 PF08450.17 SGL 26.3 26.3 246 domain Y Y N SMP-30/gluconolactonase/LRE family protein 131567 cellular organisms no rank 121631 EBI-EMBL SMP-30/Gluconolactonase/LRE-like region SMP-30/gluconolactonase/LRE family protein This family describes a region that is found in proteins expressed by a variety of eukaryotic and prokaryotic species. These proteins include various enzymes, such as senescence marker protein 30 (SMP-30, Swiss:Q15493), gluconolactonase (Swiss:Q01578) and luciferin-regenerating enzyme (LRE, Swiss:Q86DU5). SMP-30 is known to hydrolyse diisopropyl phosphorofluoridate in the liver, and has been noted as having sequence similarity, in the region described in this family, with PON1 (Swiss:P52430) and LRE. (from Pfam) NF020048.5 PF08459.16 UvrC_RNaseH_dom 22.3 22.3 159 PfamEq Y N N UvrC RNAse H endonuclease domain GO:0009381 17245438 131567 cellular organisms no rank 86232 EBI-EMBL UvrC RNAse H endonuclease domain UvrC RNAse H endonuclease domain This domain is found in the C subunits of the bacterial and archaeal UvrABC system which catalyses nucleotide excision repair in a multi-step process. UvrC catalyses the first incision on the fourth or fifth phosphodiester bond 3' and on the eighth phosphodiester bond 5' from the damage that is to be excised [1]. The domain described here represents the RNAse H endonuclease domain, located at the C-terminal, between the UvrBC and the (HhH)2 domains, nearby the N-terminal of the HhH. Despite the lack of sequence homology, the endonuclease domain has an RNase H-like fold, which is characteristic of enzymes with nuclease or polynucleotide transferase activities. RNase H-related enzymes typically contain a highly conserved carboxylate triad, usually DDE, in their catalytic centre. However, instead of a third carboxylate, UvrC of Thermotoga maritima was found to contain a highly conserved histidine (H488) on helix-4 in close proximity to two aspartates [1]. [1]. 17245438. Structure of the C-terminal half of UvrC reveals an RNase H endonuclease domain with an Argonaute-like catalytic triad. Karakas E, Truglio JJ, Croteau D, Rhau B, Wang L, Van Houten B, Kisker C;. EMBO J. 2007;26:613-622. (from Pfam) NF020050.5 PF08461.15 HTH_12 21.4 21.4 66 domain Y Y N winged-helix domain-containing protein 131567 cellular organisms no rank 17967 EBI-EMBL Ribonuclease R winged-helix domain Ribonuclease R winged-helix domain This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaebacteria. (from Pfam) NF020052.5 PF08463.15 EcoEI_R_C 24 24 163 domain Y Y N type I restriction-modification enzyme R subunit C-terminal domain-containing protein GO:0003677,GO:0003824,GO:0006304 10449767,8412658 131567 cellular organisms no rank 30531 EBI-EMBL EcoEI R protein C-terminal EcoEI R protein C-terminal The restriction enzyme EcoEI recognises 5'-GAGN(7)ATGC-3' and is composed of the three proteins R, M, and S. The domain described here is found at the C-terminus of the R protein (HsdR) which is required for both nuclease and ATPase activity [1,2]. [1]. 8412658. Conservation of motifs within the unusually variable polypeptide sequences of type I restriction and modification enzymes. Murray NE, Daniel AS, Cowan GM, Sharp PM;. Mol Microbiol 1993;9:133-143. [2]. 10449767. Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymes. Makovets S, Doronina VA, Murray NE;. Proc Natl Acad Sci U S A 1999;96:9757-9762. (from Pfam) NF020060.5 PF08471.15 Ribonuc_red_2_N 27 27 103 PfamEq Y N N Class II vitamin B12-dependent ribonucleotide reductase GO:0004748,GO:0050897 11832503 131567 cellular organisms no rank 17411 EBI-EMBL Class II vitamin B12-dependent ribonucleotide reductase Class II vitamin B12-dependent ribonucleotide reductase This domain is found to the N-terminus of the ribonucleotide reductase barrel domain (Pfam:PF02867). It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine) [1]. [1]. 11832503. Streptomyces spp. contain class Ia and class II ribonucleotide reductases: expression analysis of the genes in vegetative growth. Borovok I, Kreisberg-Zakarin R, Yanko M, Schreiber R, Myslovati M, Aslund F, Holmgren A, Cohen G, Aharonowitz Y;. Microbiology 2002;148:391-404. (from Pfam) NF020061.5 PF08472.15 S6PP_C 34.4 34.4 133 PfamEq Y N N Sucrose-6-phosphate phosphohydrolase C-terminal GO:0005986,GO:0050307 11050182 131567 cellular organisms no rank 38 EBI-EMBL Sucrose-6-phosphate phosphohydrolase C-terminal Sucrose-6-phosphate phosphohydrolase C-terminal This is the Sucrose-6-phosphate phosphohydrolase (S6PP or SPP) C-terminal domain [1] as found in in plant sucrose phosphatases. These enzymes irreversibly catalyse the last step in sucrose synthesis following the formation of Sucrose-6-Phosphate via sucrose-phosphate synthase (SPS). [1]. 11050182. Purification, molecular cloning, and sequence analysis of sucrose-6F-phosphate phosphohydrolase from plants. Lunn JE, Ashton AR, Hatch MD, Heldt HW;. Proc Natl Acad Sci U S A 2000;97:12914-12919. (from Pfam) NF020066.5 PF08477.18 Roc 27 27 119 domain Y N N Ras of Complex, Roc, domain of DAPkinase 12482879,14654223,15479738,18650931 131567 cellular organisms no rank 6673 EBI-EMBL Ras of Complex, Roc, domain of DAPkinase Ras of Complex, Roc, domain of DAPkinase Roc, or Ras of Complex, proteins are mitochondrial Rho proteins (Miro-1, Swiss:Q8IXI2, and Miro-2, Swiss:Q8IXI1) and atypical Rho GTPases. Full-length proteins have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (Pfam:PF00036) that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis [1,2,3,4]. [1]. 14654223. Roc, a Ras/GTPase domain in complex proteins. Bosgraaf L, Van Haastert PJ;. Biochim Biophys Acta. 2003;1643:5-10. [2]. 12482879. Atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Fransson A, Ruusala A, Aspenstrom P;. J Biol Chem 2003;278:6495-6502. [3]. 15479738. Yeast Miro GTPase, Gem1p, regulates mitochondrial morphology via a novel pathway. Frederick RL, McCaffery JM, Cunningham KW, Okamoto K, Shaw JM;. J Cell Biol. 2004;167:87-98. [4]. 18650931. Structure of the Roc-COR domain tandem of C. tepidum, a prokaryotic homologue of the human LRRK2 Parkinson kinase. Gotthardt K, Weyand M, Kortholt A, Van Haastert PJ, Wittinghofer A;. EMBO J. 2008;27:2239-2249. (from Pfam) NF020069.5 PF08480.15 Disaggr_assoc 22.6 22.6 194 domain Y N N Disaggregatase related 2082820 131567 cellular organisms no rank 665 EBI-EMBL Disaggregatase related Disaggregatase related This domain is found in disaggregatases and several hypothetical proteins of the archaeal genus Methanosarcina. Disaggregatases cause aggregates to separate into single cells [1] and contain parallel beta-helix repeats. Also see Pfam:PF06848. [1]. 2082820. Isolation and characterization of disaggregatase from Methanosarcina mazei LYC. Xun LY, Mah RA, Boone DR;. Appl Environ Microbiol 1990;56:3693-3698. (from Pfam) NF020073.5 PF08484.16 Methyltransf_14 23.5 23.5 160 domain Y N N C-methyltransferase C-terminal domain 131567 cellular organisms no rank 18055 EBI-EMBL C-methyltransferase C-terminal domain C-methyltransferase C-terminal domain This domain is found in bacterial C-methyltransferase proteins. This domain is found C-terminal to methyltransferase domains such as Pfam:PF08241 or Pfam:PF08242. But this domain is not a methyltransferase. (from Pfam) NF020074.5 PF08485.15 Polysacc_syn_2C 25 25 48 PfamEq Y N N Polysaccharide biosynthesis protein C-terminal GO:0003978,GO:0009103 7961465 131567 cellular organisms no rank 9637 EBI-EMBL Polysaccharide biosynthesis protein C-terminal Polysaccharide biosynthesis protein C-terminal This domain is found to the C-terminus of the Pfam:PF02719 domain in bacterial polysaccharide biosynthesis enzymes including the capsule protein CapD [1] and several putative epimerases/dehydratases. [1]. 7961465. Sequence analysis and molecular characterization of genes required for the biosynthesis of type 1 capsular polysaccharide in Staphylococcus aureus. Lin WS, Cunneen T, Lee CY;. J Bacteriol 1994;176:7005-7016. (from Pfam) NF020075.5 PF08486.15 SpoIID 23 23 97 domain Y Y N SpoIID/LytB domain-containing protein 10961456,12502745 131567 cellular organisms no rank 31215 EBI-EMBL Stage II sporulation protein Stage II sporulation protein This domain is found in the stage II sporulation protein SpoIID. SpoIID is necessary for membrane migration as well as for some of the earlier steps in engulfment during bacterial endospore formation [2]. The domain is also found in amidase enhancer proteins. Amidases, like SpoIID, are cell wall hydrolases [1]. [1]. 10961456. Biological roles of two new murein hydrolases of Streptococcus pneumoniae representing examples of module shuffling. Lopez R, Gonzalez MP, Garcia E, Garcia JL, Garcia P;. Res Microbiol 2000;151:437-443. [2]. 12502745. A cytoskeleton-like role for the bacterial cell wall during engulfment of the Bacillus subtilis forespore. Abanes-De Mello A, Sun YL, Aung S, Pogliano K;. Genes Dev 2002;16:3253-3264. (from Pfam) NF020076.5 PF08487.15 VIT 26.5 26.5 111 domain Y Y N VIT domain-containing protein 10830112,14744536 131567 cellular organisms no rank 11539 EBI-EMBL Vault protein inter-alpha-trypsin domain vault protein inter-alpha-trypsin inhibitor (VIT) domain Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition [1]. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (Pfam:PF00092) in ITI heavy chains (ITIHs) and their precursors. [1]. 14744536. ITIH5, a novel member of the inter-alpha-trypsin inhibitor heavy chain family is downregulated in breast cancer. Himmelfarb M, Klopocki E, Grube S, Staub E, Klaman I, Hinzmann B, Kristiansen G, Rosenthal A, Durst M, Dahl E;. Cancer Lett 2004;204:69-77. [2]. 10830112. VIT-1: the second member of a new branch of the von Willebrand factor A domain superfamily. Mayne R, Ren ZX, Liu J, Cook T, Carson M, Narayana S;. Biochem Soc Trans. 1999;27:832-835. (from Pfam) NF020078.5 PF08489.16 DUF1743 21 21 116 domain Y Y N DUF1743 domain-containing protein 20139989 131567 cellular organisms no rank 1732 EBI-EMBL Domain of unknown function (DUF1743) Domain of unknown function (DUF1743) This domain of unknown function is found in tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS. TiaS is an archaeal ATP-dependent agmatine transferase that catalyses the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2) [1]. This modified base specifically recognises AUA codons. [1]. 20139989. Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. Ikeuchi Y, Kimura S, Numata T, Nakamura D, Yokogawa T, Ogata T, Wada T, Suzuki T, Suzuki T;. Nat Chem Biol. 2010;6:277-282. (from Pfam) NF020079.5 PF08490.17 DUF1744 27 27 399 domain Y Y N DUF1744 domain-containing protein GO:0003887,GO:0005634,GO:0006260,GO:0008270 131567 cellular organisms no rank 6 EBI-EMBL Domain of unknown function (DUF1744) Domain of unknown function (DUF1744) This domain is found at the C-terminal of the epsilon catalytic subunit of DNA polymerase. It is found C terminal to Pfam:PF03104 and Pfam:PF00136. (from Pfam) NF020080.5 PF08491.15 SE 20.1 20.1 276 domain Y N N Squalene epoxidase GO:0004506,GO:0016020,GO:0050660 9161422 131567 cellular organisms no rank 41855 EBI-EMBL Squalene epoxidase Squalene epoxidase This domain is found in squalene epoxidase (SE) and related proteins which are found in taxonomically diverse groups of eukaryotes and also in bacteria. SE was first cloned from Saccharomyces cerevisiae where it was named ERG1. It contains a putative FAD binding site and is a key enzyme in the sterol biosynthetic pathway [1]. Putative transmembrane regions are found to the protein's C-terminus. [1]. 9161422. Cloning and expression of squalene epoxidase from the pathogenic yeast Candida albicans. Favre B, Ryder NS;. Gene 1997;189:119-126. (from Pfam) NF020083.5 PF08494.16 DEAD_assoc 23.5 23.5 191 domain Y N N DEAD/H associated GO:0005524,GO:0016818 131567 cellular organisms no rank 56136 EBI-EMBL DEAD/H associated DEAD/H associated This domain is found in ATP-dependent helicases as well as a number of hypothetical proteins together with the helicase conserved C-terminal domain (Pfam:PF00270) and the Pfam:PF00271 domain. (from Pfam) NF020084.5 PF08495.15 FIST 23.2 23.2 189 domain Y Y N FIST N-terminal domain-containing protein 17855421 131567 cellular organisms no rank 25632 EBI-EMBL FIST N domain FIST N domain The FIST N domain is a novel sensory domain, which is present in signal transduction proteins from Bacteria, Archaea and Eukarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids [1]. [1]. 17855421. FIST: a sensory domain for diverse signal transduction pathways in prokaryotes and ubiquitin signaling in eukaryotes. Borziak K, Zhulin IB;. Bioinformatics. 2007;23:2518-2521. (from Pfam) NF020086.5 PF08497.15 Radical_SAM_N 25 25 301 PfamEq Y N N Radical SAM N-terminal 131567 cellular organisms no rank 26629 EBI-EMBL Radical SAM N-terminal Radical SAM N-terminal This domain tends to occur to the N-terminus of the Pfam:PF04055 domain in hypothetical bacterial proteins. (from Pfam) NF020090.5 PF08501.16 Shikimate_dh_N 27 27 83 domain Y N N Shikimate dehydrogenase substrate binding domain GO:0004764 15735308 131567 cellular organisms no rank 116338 EBI-EMBL Shikimate dehydrogenase substrate binding domain Shikimate dehydrogenase substrate binding domain This domain is the substrate binding domain of shikimate dehydrogenase [1]. [1]. 15735308. Crystal structure of a novel shikimate dehydrogenase from Haemophilus influenzae. Singh S, Korolev S, Koroleva O, Zarembinski T, Collart F, Joachimiak A, Christendat D;. J Biol Chem 2005;280:17101-17108. (from Pfam) NF020091.5 PF08502.15 LeuA_dimer 24.9 24.9 131 domain Y Y N alpha-isopropylmalate synthase regulatory domain-containing protein GO:0003852,GO:0009098 15159544 131567 cellular organisms no rank 97809 EBI-EMBL LeuA allosteric (dimerisation) domain LeuA allosteric (dimerisation) domain This is the C-terminal regulatory (R) domain of alpha-isopropylmalate synthase, which catalyses the first committed step in the leucine biosynthetic pathway [1]. This domain, is an internally duplicated structure with a novel fold [1]. It comprises two similar units that are arranged such that the two -helices pack together in the centre, crossing at an angle of 34 degrees, sandwiched between the two three-stranded, antiparallel beta-sheets. The overall domain is thus constructed as a beta-alpha-beta three-layer sandwich [1]. [1]. 15159544. Crystal structure of LeuA from Mycobacterium tuberculosis, a key enzyme in leucine biosynthesis. Koon N, Squire CJ, Baker EN;. Proc Natl Acad Sci U S A 2004;101:8295-8300. (from Pfam) NF020108.5 PF08519.17 RFC1 23 23 158 PfamEq Y N N Replication factor RFC1 C terminal domain GO:0003689,GO:0005524,GO:0005663,GO:0006260 16040599,9092549 131567 cellular organisms no rank 15 EBI-EMBL Replication factor RFC1 C terminal domain Replication factor RFC1 C terminal domain This is the C terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo [1][2]. [1]. 16040599. Contrasting effects of Elg1-RFC and Ctf18-RFC inactivation in the absence of fully functional RFC in fission yeast. Kim J, Robertson K, Mylonas KJ, Gray FC, Charapitsa I, MacNeill SA;. Nucleic Acids Res 2005;33:4078-4089. [2]. 9092549. Deletion analysis of the large subunit p140 in human replication factor C reveals regions required for complex formation and replication activities. Uhlmann F, Cai J, Gibbs E, O'Donnell M, Hurwitz J;. J Biol Chem 1997;272:10058-10064. (from Pfam) NF020119.5 PF08530.15 PepX_C 22.5 22.5 217 domain Y Y N CocE/NonD family hydrolase C-terminal non-catalytic domain-containing protein GO:0008239 131567 cellular organisms no rank 100512 EBI-EMBL X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain This domain contains a beta sandwich domain. (from Pfam) NF020120.5 PF08531.15 Bac_rhamnosid_N 25 25 172 domain Y Y N alpha-L-rhamnosidase N-terminal domain-containing protein 10632887 131567 cellular organisms no rank 38793 EBI-EMBL Alpha-L-rhamnosidase N-terminal domain Alpha-L-rhamnosidase N-terminal domain This family consists of bacterial rhamnosidase A and B enzymes. This domain is probably involved in substrate recognition. [1]. 10632887. The thermostable alpha-L-rhamnosidase RamA of Clostridium stercorarium: biochemical characterization and primary structure of a bacterial alpha-L-rhamnoside hydrolase, a new type of inverting glycoside hydrolase. Zverlov VV, Hertel C, Bronnenmeier K, Hroch A, Kellermann J, Schwarz WH;. Mol Microbiol 2000;35:173-179. (from Pfam) NF020121.5 PF08532.15 Glyco_hydro_42M 25.8 25.8 207 domain Y Y N beta-galactosidase trimerization domain-containing protein GO:0004565,GO:0005975 12215416,8577281 131567 cellular organisms no rank 55257 EBI-EMBL Beta-galactosidase trimerisation domain Beta-galactosidase trimerisation domain This is non catalytic domain B of beta-galactosidase enzymes belong to the glycosyl hydrolase 42 family. This domain is related to glutamine amidotransferase enzymes, but the catalytic residues are replaced by non functional amino acids. This domain is involved in trimerisation [1]. [1]. 8577281. Sequence analysis of flanking regions of the pfoA gene of Clostridium perfringens: beta-galactosidase gene (pbg) is located in the 3'-flanking region. Shimizu T, Kobayashi T, Ba-Thein W, Ohtani K, Hayashi H;. Microbiol Immunol 1995;39:677-686. [2]. 12215416. Trimeric crystal structure of the glycoside hydrolase family 42 beta-galactosidase from Thermus thermophilus A4 and the structure of its complex with galactose. Hidaka M, Fushinobu S, Ohtsu N, Motoshima H, Matsuzawa H, Shoun H, Wakagi T;. J Mol Biol 2002;322:79-91. (from Pfam) NF020122.5 PF08533.15 Glyco_hydro_42C 21 21 58 domain Y Y N Beta-galactosidase C-terminal domain GO:0004565,GO:0006012 12215416 131567 cellular organisms no rank 37439 EBI-EMBL Beta-galactosidase C-terminal domain Beta-galactosidase C-terminal domain This domain is found at the C-terminus of beta-galactosidase enzymes that belong to the glycosyl hydrolase 42 family [1]. [1]. 12215416. Trimeric crystal structure of the glycoside hydrolase family 42 beta-galactosidase from Thermus thermophilus A4 and the structure of its complex with galactose. Hidaka M, Fushinobu S, Ohtsu N, Motoshima H, Matsuzawa H, Shoun H, Wakagi T;. J Mol Biol 2002;322:79-91. (from Pfam) NF020123.5 PF08534.15 Redoxin 26.6 26.6 148 domain Y Y N redoxin family protein GO:0016491 131567 cellular organisms no rank 479337 EBI-EMBL Redoxin redoxin family protein This family of redoxins includes peroxiredoxin, thioredoxin and glutaredoxin proteins. (from Pfam) NF020129.5 PF08540.15 HMG_CoA_synt_C 25.1 25.1 280 PfamEq Y Y N hydroxymethylglutaryl-CoA synthase GO:0004421,GO:0006084,GO:0010142 2865259 131567 cellular organisms no rank 12417 EBI-EMBL Hydroxymethylglutaryl-coenzyme A synthase C terminal hydroxymethylglutaryl-CoA synthase C-terminal domain NF020130.5 PF08541.15 ACP_syn_III_C 26.6 26.6 90 domain Y Y N 3-oxoacyl-[acyl-carrier-protein] synthase III C-terminal domain-containing protein 10600651 131567 cellular organisms no rank 172745 EBI-EMBL 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III EC:2.3.1.41, the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria. [1]. 10600651. Reaction mechanism of recombinant 3-oxoacyl-(acyl-carrier-protein) synthase III from Cuphea wrightii embryo, a fatty acid synthase type II condensing enzyme. Abbadi A, Brummel M, Schutt BS, Slabaugh MB, Schuch R, Spener F;. Biochem J 2000;345:153-160. (from Pfam) NF020131.5 PF08542.16 Rep_fac_C 23.6 23.6 88 domain Y N N Replication factor C C-terminal domain 15201901 131567 cellular organisms no rank 2150 EBI-EMBL Replication factor C C-terminal domain Replication factor C C-terminal domain This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA). The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A [1]. [1]. 15201901. Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex. Bowman GD, O'Donnell M, Kuriyan J;. Nature. 2004;429:724-730. (from Pfam) NF020132.5 PF08543.17 Phos_pyr_kin 27 27 246 domain Y Y N bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase 2.7.1.49,2.7.4.7 9244280 131567 cellular organisms no rank 218763 EBI-EMBL Phosphomethylpyrimidine kinase bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase This enzyme EC:2.7.4.7 is part of the Thiamine pyrophosphate (TPP) synthesis pathway, TPP is an essential cofactor for many enzymes [1]. [1]. 9244280. Identification and characterization of an operon in Salmonella typhimurium involved in thiamine biosynthesis. Petersen LA, Downs DM;. J Bacteriol 1997;179:4894-4900. (from Pfam) NF020133.5 PF08544.18 GHMP_kinases_C 21 21 85 domain Y N N GHMP kinases C terminal 131567 cellular organisms no rank 184150 EBI-EMBL GHMP kinases C terminal GHMP kinases C terminal This family includes homoserine kinases, galactokinases and mevalonate kinases. (from Pfam) NF020134.5 PF08545.15 ACP_syn_III 24 24 80 domain Y N N 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III GO:0004315,GO:0006633 10600651 131567 cellular organisms no rank 155380 EBI-EMBL 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III EC:2.3.1.180, the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria. [1]. 10600651. Reaction mechanism of recombinant 3-oxoacyl-(acyl-carrier-protein) synthase III from Cuphea wrightii embryo, a fatty acid synthase type II condensing enzyme. Abbadi A, Brummel M, Schutt BS, Slabaugh MB, Schuch R, Spener F;. Biochem J 2000;345:153-160. (from Pfam) NF020135.5 PF08546.16 ApbA_C 22.7 22.7 125 domain Y Y N ketopantoate reductase C-terminal domain-containing protein 9488683,9721324 131567 cellular organisms no rank 96043 EBI-EMBL Ketopantoate reductase PanE/ApbA C terminal Ketopantoate reductase PanE/ApbA C terminal This is a family of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, EC:1.1.1.169. The reaction catalysed by this enzyme is: (R)-pantoate + NADP(+) 2-dehydropantoate + NADPH. AbpA catalyses the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway [2]. ApbA and PanE are allelic [2]. ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway [1]. [1]. 9488683. ApbA, the ketopantoate reductase enzyme of Salmonella typhimurium is required for the synthesis of thiamine via the alternative pyrimidine biosynthetic pathway. Frodyma ME, Downs D;. J Biol Chem 1998;273:5572-5576. [2]. 9721324. The panE gene, encoding ketopantoate reductase, maps at 10 minutes and is allelic to apbA in Salmonella typhimurium. Frodyma ME, Downs D;. J Bacteriol 1998;180:4757-4759. (from Pfam) NF020136.5 PF08547.17 CIA30 24 24 157 PfamEq Y Y N CIA30 family protein 11935339,1518044 131567 cellular organisms no rank 6198 EBI-EMBL Complex I intermediate-associated protein 30 (CIA30) CIA30 family protein This protein is associated with mitochondrial Complex I intermediate-associated protein 30 (CIA30) in human and mouse. The family is also present in Schizosaccharomyces pombe which does not contain the NADH dehydrogenase component of complex I, or many of the other essential subunits. This means it is possible that this family of protein may not be directly involved in oxidative phosphorylation [1][2]. [1]. 11935339. CIA30 complex I assembly factor: a candidate for human complex I deficiency?. Janssen R, Smeitink J, Smeets R, van Den Heuvel L;. Hum Genet 2002;110:264-270. [2]. 1518044. Sequences of 20 subunits of NADH:ubiquinone oxidoreductase from bovine heart mitochondria. Application of a novel strategy for sequencing proteins using the polymerase chain reaction. Walker JE, Arizmendi JM, Dupuis A, Fearnley IM, Finel M, Medd SM, Pilkington SJ, Runswick MJ, Skehel JM;. J Mol Biol 1992;226:1051-1072. (from Pfam) NF020140.5 PF08551.15 DUF1751 22 22 99 PfamAutoEq Y Y N DUF1751 domain-containing protein GO:0006890,GO:0016020 14562095 131567 cellular organisms no rank 13806 EBI-EMBL Eukaryotic integral membrane protein (DUF1751) Eukaryotic integral membrane protein (DUF1751) This domain is found in eukaryotic integral membrane proteins. Swiss:Q12239, a Saccharomyces cerervisiae protein, has been shown to localise COP II vesicles [1]. [1]. 14562095. Global analysis of protein localization in budding yeast. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK;. Nature 2003;425:686-691. (from Pfam) NF020157.5 PF08570.15 DUF1761 31 31 123 subfamily Y Y N DUF1761 family protein 131567 cellular organisms no rank 8371 EBI-EMBL Protein of unknown function (DUF1761) DUF1761 family protein Family of conserved fungal and bacterial membrane proteins with unknown function. (from Pfam) NF020177.5 PF08592.16 Anthrone_oxy 27.3 27.3 106 domain Y Y N anthrone oxygenase family protein 21351751,22492455,24009710 131567 cellular organisms no rank 26822 EBI-EMBL Anthrone oxygenase anthrone oxygenase family protein This family consists of anthrone oxygenases found in bacteria and fungi, and involved in the synthesis of different products. GedH from Aspergillus terreus is part of the gene cluster that mediates the biosynthesis of geodin [1], EncC from Neosartorya fumigata is involved in the biosynthesis of endocrocin [2], and MdpH from Aspergillus nidulans in the biosynthesis of monodictyphenone [3]. [1]. 24009710. Heterologous reconstitution of the intact geodin gene cluster in Aspergillus nidulans through a simple and versatile PCR based approach. Nielsen MT, Nielsen JB, Anyaogu DC, Holm DK, Nielsen KF, Larsen TO, Mortensen UH;. PLoS One. 2013;8:e72871. [2]. 22492455. Genome-based cluster deletion reveals an endocrocin biosynthetic pathway in Aspergillus fumigatus. Lim FY, Hou Y, Chen Y, Oh JH, Lee I, Bugni TS, Keller NP;. Appl Environ Microbiol. 2012;78:4117-4125. [3]. 21351751. Genome-based deletion analysis reveals the prenyl xanthone biosynthesis pathway in Aspergillus nidulans. Sanchez JF, Entwistle R, Hung JH, Yaegashi J, Jain S, Chiang YM, Wang CC, Oakley BR;. J Am Chem Soc. 2011;133:4010-4017. (from Pfam) NF020192.5 PF08608.17 Wyosine_form 22 22 63 domain Y N N Wyosine base formation 16162496 131567 cellular organisms no rank 13235 EBI-EMBL Wyosine base formation Wyosine base formation Some proteins in this family appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that they participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW [1]. [1]. 16162496. Discovery of a gene family critical to wyosine base formation in a subset of phenylalanine-specific transfer RNAs. Waas WF, de Crecy-Lagard V, Schimmel P;. J Biol Chem. 2005;280:37616-37622. (from Pfam) NF020201.5 PF08617.15 CGI-121 25 25 159 PfamEq Y N N Kinase binding protein CGI-121 12659830,16564010 131567 cellular organisms no rank 1196 EBI-EMBL Kinase binding protein CGI-121 Kinase binding protein CGI-121 CGI-121 has been shown to bind to the p53-related protein kinase (PRPK) [1]. PRPK is a novel protein kinase which binds to and induces phosphorylation of the tumour suppressor protein p53. CGI-121 is part of a conserved protein complex, KEOPS. The KEOPS complex is involved in telomere uncapping and telomere elongation [2]. Interestingly this family also include archaeal homologues, formerly in the DUF509 family. A structure for these proteins has been solved by structural genomics. [1]. 12659830. Identification of CGI-121, a novel PRPK (p53-related protein kinase)-binding protein. Miyoshi A, Kito K, Aramoto T, Abe Y, Kobayashi N, Ueda N;. Biochem Biophys Res Commun. 2003;303:399-405. [2]. 16564010. A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator. Downey M, Houlsworth R, Maringele L, Rollie A, Brehme M, Galicia S, Guillard S, Partington M, Zubko MK, Krogan NJ, Emili A, Greenblatt JF, Harrington L, Lydall D, Durocher D;. Cell. 2006;124:1155-1168. (from Pfam) NF020219.5 PF08635.15 ox_reductase_C 22.5 22.5 142 domain Y N N Putative oxidoreductase C terminal domain 131567 cellular organisms no rank 2507 EBI-EMBL Putative oxidoreductase C terminal domain Putative oxidoreductase C terminal domain This is the C-terminal domain of a family of putative oxidoreductases. (from Pfam) NF020227.5 PF08643.15 DUF1776 25 25 294 domain Y Y N DUF1776 domain-containing protein 14576278 131567 cellular organisms no rank 30113 EBI-EMBL Fungal family of unknown function (DUF1776) Fungal family of unknown function (DUF1776) This is a fungal family of unknown function. One of the proteins in this family Swiss:P32792 has been localised to the mitochondria [1]. [1]. 14576278. The proteome of Saccharomyces cerevisiae mitochondria. Sickmann A, Reinders J, Wagner Y, Joppich C, Zahedi R, Meyer HE, Schonfisch B, Perschil I, Chacinska A, Guiard B, Rehling P, Pfanner N, Meisinger C;. Proc Natl Acad Sci U S A. 2003;100:13207-13212. (from Pfam) NF020229.5 PF08645.16 PNK3P 22 22 161 domain Y N N Polynucleotide kinase 3 phosphatase 10446193,11278831,11729194,12056900 131567 cellular organisms no rank 36937 EBI-EMBL Polynucleotide kinase 3 phosphatase Polynucleotide kinase 3 phosphatase Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin [1]. [1]. 11729194. Pnk1, a DNA kinase/phosphatase required for normal response to DNA damage by gamma-radiation or camptothecin in Schizosaccharomyces pombe. Meijer M, Karimi-Busheri F, Huang TY, Weinfeld M, Young D;. J Biol Chem. 2002;277:4050-4055. [2]. 12056900. Purification and partial characterization of a DNA 3'-phosphatase from Schizosaccharomyces pombe. Jilani A, Ramotar D;. Biochemistry. 2002;41:7688-7694. [3]. 11278831. Uncoupling of 3'-phosphatase and 5'-kinase functions in budding yeast. Characterization of Saccharomyces cerevisiae DNA 3'-phosphatase (TPP1). Vance JR, Wilson TE;. J Biol Chem. 2001;276:15073-15081. [4]. 10446193. Molecular characterization of a human DNA kinase. Karimi-Busheri F, Daly G, Robins P, Canas B, Pappin DJ, Sgouros J, Miller GG, Fakhrai H, Davis EM, Le Beau MM, Weinfeld M;. J Biol Chem. 1999;274:24187-24194. (from Pfam) NF020230.5 PF08646.15 Rep_fac-A_C 28.5 28.5 146 PfamEq Y N N Replication factor-A C terminal domain 10713540 131567 cellular organisms no rank 357 EBI-EMBL Replication factor-A C terminal domain Replication factor-A C terminal domain This domain is found at the C terminal of replication factor A. Replication factor A (RPA) binds single-stranded DNA and is involved in replication, repair, and recombination of DNA [1]. [1]. 10713540. Study of interaction of human replication factor A with DNA using new photoreactive analogs of dTTP. Kolpashchikov DM, Pestryakov PE, Wlassoff WA, Khodyreva SN, Lavrik OI;. Biochemistry (Mosc). 2000;65:160-163. (from Pfam) NF020243.5 PF08659.15 KR 22.6 22.6 180 domain Y Y N KR domain-containing protein 23790488 131567 cellular organisms no rank 2418227 EBI-EMBL KR domain KR domain This enzymatic domain is part of bacterial polyketide synthases and catalyses the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group [1]. [1]. 23790488. Structural and stereochemical analysis of a modular polyketide synthase ketoreductase domain required for the generation of a cis-alkene. Bonnett SA, Whicher JR, Papireddy K, Florova G, Smith JL, Reynolds KA;. Chem Biol. 2013;20:772-783. (from Pfam) NF020244.5 PF08660.16 Alg14 27 27 171 PfamEq Y N N Oligosaccharide biosynthesis protein Alg14 like GO:0006488 16100110 131567 cellular organisms no rank 4375 EBI-EMBL Oligosaccharide biosynthesis protein Alg14 like Oligosaccharide biosynthesis protein Alg14 like Alg14 is involved dolichol-linked oligosaccharide biosynthesis and anchors the catalytic subunit Alg13 to the ER membrane [1]. [1]. 16100110. Alg14 recruits Alg13 to the cytoplasmic face of the endoplasmic reticulum to form a novel bipartite UDP-N-acetylglucosamine transferase required for the second step of N-linked glycosylation. Gao XD, Tachikawa H, Sato T, Jigami Y, Dean N;. J Biol Chem. 2005;280:36254-36262. (from Pfam) NF020246.5 PF08662.16 eIF2A 20.5 20.5 194 domain Y Y N eIF2A-related protein 12133843 131567 cellular organisms no rank 7090 EBI-EMBL Eukaryotic translation initiation factor eIF2A eIF2A-related protein This is a family of eukaryotic translation initiation factors. [1]. 12133843. Characterization of mammalian eIF2A and identification of the yeast homolog. Zoll WL, Horton LE, Komar AA, Hensold JO, Merrick WC;. J Biol Chem. 2002;277:37079-37087. (from Pfam) NF020247.5 PF08663.15 HalX 23.2 23.2 68 domain Y Y N HalX domain-containing protein 16740923 131567 cellular organisms no rank 2519 EBI-EMBL HalX domain HalX domain HalX is a domain of unknown function, previously (mis)annotated as HoxA-like transcriptional regulator. [1]. 16740923. Structural classification of bacterial response regulators: diversity of output domains and domain combinations. Galperin MY;. J Bacteriol. 2006;188:4169-4182. (from Pfam) NF020249.5 PF08665.17 PglZ 25 25 179 domain Y Y N PglZ domain-containing protein 131567 cellular organisms no rank 17100 EBI-EMBL PglZ domain PglZ domain-containing protein This family is a member of the Alkaline phosphatase clan. (from Pfam) NF020250.5 PF08666.17 SAF 21 21 63 domain Y Y N SAF domain-containing protein 15146494 131567 cellular organisms no rank 137532 EBI-EMBL SAF domain SAF domain This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins. [1]. 15146494. The emergence of catalytic and structural diversity within the beta-clip fold. Iyer LM, Aravind L;. Proteins. 2004;55:977-991. (from Pfam) NF020251.5 PF08667.15 BetR 21.6 21.6 148 domain Y Y N helix-turn-helix domain-containing protein GO:0003677,GO:0006355 131567 cellular organisms no rank 6409 EBI-EMBL BetR domain BetR domain This domain of about 148 amino acids includes an N-terminal helix-turn-helix structure. Many members of the family contain response regulator domains toward the C-terminus. NF020252.5 PF08668.17 HDOD 22.9 22.9 196 domain Y Y N HDOD domain-containing protein 131567 cellular organisms no rank 87556 EBI-EMBL HDOD domain HDOD domain NF020253.5 PF08669.16 GCV_T_C 25.9 25.9 80 domain Y Y N glycine cleavage T C-terminal barrel domain-containing protein 9047339 131567 cellular organisms no rank 136231 EBI-EMBL Glycine cleavage T-protein C-terminal barrel domain Glycine cleavage T-protein C-terminal barrel domain This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. [1]. 9047339. Cloning, and molecular characterization of the GCV1 gene encoding the glycine cleavage T-protein from Saccharomyces cerevisiae. McNeil JB, Zhang F, Taylor BV, Sinclair DA, Pearlman RE, Bognar AL;. Gene 1997;186:13-20. (from Pfam) NF020254.5 PF08670.16 MEKHLA 23.7 23.7 143 domain Y Y N MEKHLA domain-containing protein 131567 cellular organisms no rank 4610 EBI-EMBL MEKHLA domain MEKHLA domain The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins. (from Pfam) NF020257.5 PF08673.15 RsbU_N 25.5 25.5 75 domain Y Y N phosphatase RsbU N-terminal domain-containing protein 15263010 131567 cellular organisms no rank 4352 EBI-EMBL Phosphoserine phosphatase RsbU, N-terminal domain Phosphoserine phosphatase RsbU, N-terminal domain RsbU is a phosphoserine phosphatase which acts as a positive regulator of the general stress-response factor of gram positive organisms, sigma-B. The phosphatase activity of RsbU is stimulated by association with the RsbT kinase. Deletions in the N terminal domain are deleterious to the activity of RsbU [1]. [1]. 15263010. Functional and structural characterization of RsbU, a stress signaling protein phosphatase 2C. Delumeau O, Dutta S, Brigulla M, Kuhnke G, Hardwick SW, Volker U, Yudkin MD, Lewis RJ;. J Biol Chem. 2004;279:40927-40937. (from Pfam) NF020260.5 PF08676.16 MutL_C 25 25 142 PfamEq Y N N MutL C terminal dimerisation domain GO:0005524,GO:0006298 15470502,16024043,8811176 131567 cellular organisms no rank 71187 EBI-EMBL MutL C terminal dimerisation domain MutL C terminal dimerisation domain MutL and MutS are key components of the DNA repair machinery that corrects replication errors [1]. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation [3]. [1]. 8811176. Mismatch repair in replication fidelity, genetic recombination, and cancer biology. Modrich P, Lahue R;. Annu Rev Biochem. 1996;65:101-133. [2]. 16024043. Analysis of the quaternary structure of the MutL C-terminal domain. Kosinski J, Steindorf I, Bujnicki JM, Giron-Monzon L, Friedhoff P;. J Mol Biol. 2005;351:895-909. [3]. 15470502. Structure of the MutL C-terminal domain: a model of intact MutL and its roles in mismatch repair. Guarne A, Ramon-Maiques S, Wolff EM, Ghirlando R, Hu X, Miller JH, Yang W;. EMBO J. 2004;23:4134-4145. (from Pfam) NF020263.5 PF08679.16 DsrD 24.2 24.2 65 domain Y Y N dissimilatory sulfite reductase D family protein 12962631 131567 cellular organisms no rank 384 EBI-EMBL Dissimilatory sulfite reductase D (DsrD) dissimilatory sulfite reductase D family protein The structure of the DsrD protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins [1]. The structure suggests a possible role for DsrD in transcription of translation of genes which catalyse dissimilatory sulfite reduction. [1]. 12962631. Crystal structure of dissimilatory sulfite reductase D (DsrD) protein--possible interaction with B- and Z-DNA by its winged-helix motif. Mizuno N, Voordouw G, Miki K, Sarai A, Higuchi Y;. Structure. 2003;11:1133-1140. (from Pfam) NF020280.5 PF08696.16 Dna2 22.4 22.4 204 PfamEq Y N N DNA replication factor Dna2 10880469 131567 cellular organisms no rank 971 EBI-EMBL DNA replication factor Dna2 DNA replication factor Dna2 Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, ( 5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways [1]. [1]. 10880469. Genetic analyses of Schizosaccharomyces pombe dna2(+) reveal that dna2 plays an essential role in Okazaki fragment metabolism. Kang HY, Choi E, Bae SH, Lee KH, Gim BS, Kim HD, Park C, MacNeill SA, Seo YS;. Genetics. 2000;155:1055-1067. (from Pfam) NF020287.5 PF08704.15 GCD14 26 26 247 domain Y N N tRNA methyltransferase complex GCD14 subunit GO:0030488,GO:0031515 9851972 131567 cellular organisms no rank 17443 EBI-EMBL tRNA methyltransferase complex GCD14 subunit tRNA methyltransferase complex GCD14 subunit GCD14 is a subunit of the tRNA methyltransferase complex and is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA [1]. [1]. 9851972. The essential Gcd10p-Gcd14p nuclear complex is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA. Anderson J, Phan L, Cuesta R, Carlson BA, Pak M, Asano K, Bjork GR, Tamame M, Hinnebusch AG;. Genes Dev 1998;12:3650-3662. (from Pfam) NF020289.5 PF08706.16 D5_N 22.4 22.4 145 domain Y N N D5 N terminal like 11929537,7636979 131567 cellular organisms no rank 37151 EBI-EMBL D5 N terminal like D5 N terminal like This domain is found in D5 proteins of DNA viruses and bacteriophage P4 DNA primases phages. [1]. 11929537. Phage P4 origin-binding domain structure reveals a mechanism for regulation of DNA-binding activity by homo- and heterodimerization of winged helix proteins. Yeo HJ, Ziegelin G, Korolev S, Calendar R, Lanka E, Waksman G;. Mol Microbiol. 2002;43:855-867. [2]. 7636979. The vaccinia virus D5 protein, which is required for DNA replication, is a nucleic acid-independent nucleoside triphosphatase. Evans E, Klemperer N, Ghosh R, Traktman P;. J Virol 1995;69:5353-5361. (from Pfam) NF020290.5 PF08707.16 PriCT_2 22 22 77 domain Y Y N PriCT-2 domain-containing protein GO:0016817 16027112 131567 cellular organisms no rank 9340 EBI-EMBL Primase C terminal 2 (PriCT-2) Primase C terminal 2 (PriCT-2) This alpha helical domain is found at the C terminal of primases. [1]. 16027112. Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Iyer LM, Koonin EV, Leipe DD, Aravind L;. Nucleic Acids Res. 2005;33:3875-3896. (from Pfam) NF020296.5 PF08713.16 DNA_alkylation 21 21 213 domain Y Y N DNA alkylation repair protein 131567 cellular organisms no rank 58632 EBI-EMBL DNA alkylation repair enzyme DNA alkylation repair protein Proteins in this family are predicted to be DNA alkylation repair enzymes. The structure of a hypothetical protein in this family shows it to adopt a supercoiled alpha helical structure. (from Pfam) NF020297.5 PF08714.16 Fae 27 27 159 domain Y Y N formaldehyde-activating enzyme GO:0016051,GO:0016840 11073907,15632161 131567 cellular organisms no rank 4306 EBI-EMBL Formaldehyde-activating enzyme (Fae) formaldehyde-activating enzyme Formaldehyde-activating enzyme is an enzyme required for energy metabolism and formaldehyde detoxification. It catalyses the condensation of formaldehyde and tetrahydromethanopterin to methylene tetrahydromethanopterin [1]. [1]. 11073907. Novel formaldehyde-activating enzyme in Methylobacterium extorquens AM1 required for growth on methanol. Vorholt JA, Marx CJ, Lidstrom ME, Thauer RK;. J Bacteriol. 2000;182:6645-6650. [2]. 15632161. How an enzyme binds the C1 carrier tetrahydromethanopterin. Structure of the tetrahydromethanopterin-dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1. Acharya P, Goenrich M, Hagemeier CH, Demmer U, Vorholt JA, Thauer RK, Ermler U;. J Biol Chem. 2005;280:13712-13719. (from Pfam) NF020302.5 PF08719.16 NADAR 35.1 35.1 163 domain Y Y N NADAR domain-containing protein 22399070 131567 cellular organisms no rank 22203 EBI-EMBL NADAR domain NADAR domain This is a domain of unknown function, it has been named been named the NADAR (NAD and ADP-ribose) domain [1]. [1]. 22399070. Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions. de Souza RF, Aravind L;. Mol Biosyst. 2012;8:1661-1677. (from Pfam) NF020317.5 PF08734.16 GYD 31.4 31.4 91 domain Y Y N GYD domain-containing protein 131567 cellular organisms no rank 7293 EBI-EMBL GYD domain GYD domain This protein is found in a range of bacteria. It is usually less than 100 amino acids in length. The function of the protein is unknown. It may belong to the dimeric alpha/beta barrel superfamily. (from Pfam) NF020318.5 PF08735.15 DUF1786 25 25 252 subfamily Y Y N DUF1786 family protein 15581584 131567 cellular organisms no rank 842 EBI-EMBL Putative pyruvate format-lyase activating enzyme (DUF1786) DUF1786 family protein This family is annotated as pyruvate formate-lyase activating enzyme (EC:1.97.1.4) in UniProt. It is not clear where this annotation comes from. [1]. 15581584. Pyruvate formate-lyase activating enzyme: elucidation of a novel mechanism for glycyl radical formation. Buis JM, Broderick JB;. Arch Biochem Biophys. 2005;433:288-296. (from Pfam) NF020327.5 PF08745.16 PIN_5 27 27 205 PfamEq Y Y N PIN domain-containing protein 21036780,28575517 131567 cellular organisms no rank 722 EBI-EMBL PINc domain ribonuclease PINc domain ribonuclease This is a family of bacterial and archaeal PINc domains. PIN domains are characterised by the conservation of three acidic residues, possibly four, an Asp at residue 13, a Glu at 63, and then Asps at 172 and 194 in UniProtKB:Q58360. Family members include Homologs of Aquifex RNase P (HARP) proteins [2]. [1]. 21036780. The PIN-domain ribonucleases and the prokaryotic VapBC toxin-antitoxin array. Arcus VL, McKenzie JL, Robson J, Cook GM;. Protein Eng Des Sel. 2011;24:33-40. [2]. 28575517. Comprehensive classification of the PIN domain-like superfamily. Matelska D, Steczkiewicz K, Ginalski K;. Nucleic Acids Res. 2017;45:6995-7020. (from Pfam) NF020329.5 PF08747.16 BrxB 26.8 26.8 124 PfamAutoEq Y Y N BREX protein BrxB domain-containing protein 25452498 131567 cellular organisms no rank 5551 EBI-EMBL BREX protein BrxB BREX protein BrxB This family includes BREX protein BrxB from Bacillus cereus, which is part of a type 1 BREX (bacteriophage exclusion) system, a system that provides immunity against bacteriophage, which allows phage adsorption but prevents phage DNA replication, without degradation of the phage DNA [1]. The exact function of BrxB is not clear. [1]. 25452498. BREX is a novel phage resistance system widespread in microbial genomes. Goldfarb T, Sberro H, Weinstock E, Cohen O, Doron S, Charpak-Amikam Y, Afik S, Ofir G, Sorek R;. EMBO J. 2015;34:169-183. (from Pfam) NF020334.5 PF08753.16 NikR_C 22 22 77 PfamEq Y N N NikR C terminal nickel binding domain 12970756 131567 cellular organisms no rank 8943 EBI-EMBL NikR C terminal nickel binding domain NikR C terminal nickel binding domain NikR is a transcription factor that regulates nickel uptake. It consists of two dimeric DNA binding domains separated by a tetrameric regulatory domain that binds nickel. This domain corresponds to the C terminal regulatory domain which contains four nickel binding sites at the tetramer interface [1]. [1]. 12970756. Crystal structure of the nickel-responsive transcription factor NikR. Schreiter ER, Sintchak MD, Guo Y, Chivers PT, Sauer RT, Drennan CL;. Nat Struct Biol. 2003;10:794-799. (from Pfam) NF020337.5 PF08757.16 CotH 23.8 23.8 322 domain Y Y N CotH kinase family protein 10198031,27185916,8755863 131567 cellular organisms no rank 20585 EBI-EMBL CotH kinase protein CotH kinase family protein Members of this family include the spore coat protein H (cotH). This protein is an atypical protein kinase that phosphorylates CotB and CotG [3]. [1]. 8755863. Bacillus subtilis spore coat assembly requires cotH gene expression. Naclerio G, Baccigalupi L, Zilhao R, De Felice M, Ricca E;. J Bacteriol. 1996;178:4375-4380. [2]. 10198031. Assembly requirements and role of CotH during spore coat formation in Bacillus subtilis. Zilhao R, Naclerio G, Henriques AO, Baccigalupi L, Moran CP Jr, Ricca E;. J Bacteriol. 1999;181:2631-2633. [3]. 27185916. Phosphorylation of spore coat proteins by a family of atypical protein kinases. Nguyen KB, Sreelatha A, Durrant ES, Lopez-Garrido J, Muszewska A, Dudkiewicz M, Grynberg M, Yee S, Pogliano K, Tomchick DR, Pawlowski K, Dixon JE, Tagliabracci VS;. Proc Natl Acad Sci U S A. 2016;113:E3482-E3491. (from Pfam) NF020339.5 PF08759.16 GT-D 27 27 225 domain Y Y N GT-D fold domain-containing glycosyltransferase 25023666 131567 cellular organisms no rank 3298 EBI-EMBL Glycosyltransferase GT-D fold Glycosyltransferase GT-D fold This domain is found at the C terminus of proteins such as the probable glycosyltransferase Gly (Swiss:Q9AEU2) that also contain the glycosyl transferase domain at the N terminus. It is also found N-terminal in numerous putative glycosyltransferases such as GalT1. GalT1 has been shown to catalyse the third step of Fap1 glycosylation [1]. This domain is structurally distinct from all known GT folds of glycosyltransferases and contains a metal binding site. This new glycosyltransferase fold has been named GT-D [1]. [1]. 25023666. The highly conserved domain of unknown function 1792 has a distinct glycosyltransferase fold. Zhang H, Zhu F, Yang T, Ding L, Zhou M, Li J, Haslam SM, Dell A, Erlandsen H, Wu H;. Nat Commun. 2014;5:4339. (from Pfam) NF020341.5 PF08761.16 dUTPase_2 22.9 22.9 162 domain Y Y N dUTP diphosphatase 3.6.1.23 15364583 131567 cellular organisms no rank 11611 EBI-EMBL dUTPase dUTP diphosphatase 2-Deoxyuridine 5-triphosphate nucleotidohydrolase (dUTPase) catalyses the hydrolysis of dUTP to dUMP and pyrophosphate (EC:3.6.1.23). Members of this family have a novel all-alpha fold and are unrelated to the all-beta fold found in dUTPases of the majority of organisms [1]. This family contains both dUTPase homologues of dUTPase including dCTPase of phage T4. [1]. 15364583. The crystal structure of a complex of Campylobacter jejuni dUTPase with substrate analogue sheds light on the mechanism and suggests the "basic module" for dimeric d(C/U)TPases. Moroz OV, Harkiolaki M, Galperin MY, Vagin AA, Gonzalez-Pacanowska D, Wilson KS;. J Mol Biol. 2004;342:1583-1597. (from Pfam) NF020354.5 PF08774.16 VRR_NUC 23.8 23.8 116 domain Y Y N VRR-NUC domain-containing protein GO:0016788 15972856,24981866,29514982,36226828 131567 cellular organisms no rank 21872 EBI-EMBL VRR-NUC domain VRR-NUC domain This is the VRR-NUC domain, a member of the PD-(D/E)XK nuclease superfamily found in FAN1 and type III restriction modification enzymes [1]. FAN1 is a a structure-selective DNA repair nuclease with 5' flap endonuclease activity, involved in the repair of interstrand DNA crosslinks [2,3]. FAN1 is the only eukaryotic protein with a VRR-NUC domain. This domain is also found in TseVs antibacterial effectors secreted by the type VI secretion system (T6SS). TseVs are evolutionary related to Holliday junction resolvases and enzymes involved in DNA interstrand crosslink repair [4]. [1]. 15972856. Identification of novel restriction endonuclease-like fold families among hypothetical proteins. Kinch LN, Ginalski K, Rychlewski L, Grishin NV;. Nucleic Acids Res. 2005;33:3598-3605. [2]. 24981866. FAN1 activity on asymmetric repair intermediates is mediated by an atypical monomeric virus-type replication-repair nuclease domain. Pennell S, Declais AC, Li J, Haire LF, Berg W, Saldanha JW, Taylor IA, Rouse J, Lilley DM, Smerdon SJ;. Cell Rep. 2014;8:84-93. [3]. 29514982. Structural mechanism of DNA interstrand cross-link unhooking by the bacterial FAN1 nuclease. Jin H, Roy U, Lee G, Scharer OD, Cho Y;. J Biol Chem. 2018;293:6482-6496. [4]. 36226828. Antibacterial T6SS effectors with a VRR-Nuc domain are structure-specific nucleases. Hespanhol JT, Sanchez-Limache DE, Nicastro GG, Mead L, Llontop EE, Chagas-Santos G, Farah CS, de Souza RF, Galhardo RDS, Lovering AL, Bayer-Santos E;. Elife. 2022;11:e82437. (from Pfam) NF020360.5 PF08780.16 NTase_sub_bind 31.8 31.8 126 domain Y Y N nucleotidyltransferase substrate binding protein 12486719 131567 cellular organisms no rank 6599 EBI-EMBL Nucleotidyltransferase substrate binding protein like nucleotidyltransferase substrate binding protein Nucleotidyltransferases (EC 2.7.7) comprise a large enzyme family with diverse roles in polynucleotide synthesis and modification. This domain is structurally related to kanamycin nucleotidyltransferase (KNTase) and forms a complex with HI0073, a sequence homolog of the nucleotide-binding domain of this nucleotidyltransferase superfamily [1]. [1]. 12486719. The HI0073/HI0074 protein pair from Haemophilus influenzae is a member of a new nucleotidyltransferase family: structure, sequence analyses, and solution studies. Lehmann C, Lim K, Chalamasetty VR, Krajewski W, Melamud E, Galkin A, Howard A, Kelman Z, Reddy PT, Murzin AG, Herzberg O;. Proteins. 2003;50:249-260. (from Pfam) NF020364.5 PF08784.16 RPA_C 22.6 22.6 106 PfamEq Y N N Replication protein A C terminal 16523492 131567 cellular organisms no rank 809 EBI-EMBL Replication protein A C terminal Replication protein A C terminal This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. [1]. 16523492. Functions of human replication protein A (RPA): From DNA replication to DNA damage and stress responses. Zou Y, Liu Y, Wu X, Shell SM;. J Cell Physiol. 2006; [Epub ahead of print] (from Pfam) NF020371.5 PF08792.15 A2L_zn_ribbon 22.9 22.9 33 domain Y N N A2L zinc ribbon domain 16494962 131567 cellular organisms no rank 266 EBI-EMBL A2L zinc ribbon domain A2L zinc ribbon domain This zinc ribbon domain is found associated with some viral A2L transcription factors [1]. [1]. 16494962. Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Iyer LM, Balaji S, Koonin EV, Aravind L;. Virus Res. 2006;117:156-184. (from Pfam) NF020374.5 PF08795.15 DUF1796 23 23 166 subfamily Y Y N DUF1796 family putative cysteine peptidase 16494962 131567 cellular organisms no rank 4368 EBI-EMBL Putative papain-like cysteine peptidase (DUF1796) DUF1796 family putative cysteine peptidase NF020376.5 PF08797.16 HIRAN 24.7 24.7 96 domain Y Y N HIRAN domain-containing protein GO:0003676,GO:0008270,GO:0016818 16627993 131567 cellular organisms no rank 8779 EBI-EMBL HIRAN domain HIRAN domain The HIRAN domain (HIP116, Rad5p N-terminal) is found in the N-terminal regions of the SWI2/SNF2 proteins typified by HIP116 and Rad5p. The HIRAN domain is found as a standalone protein in several bacteria and prophages, or fused to other catalytic domains, such as a nuclease of the restriction endonuclease fold and TDP1-like DNA phosphoesterases, in the eukaryotes [1]. It has been predicted that this domain functions as a DNA-binding domain that probably recognises features associated with damaged DNA or stalled replication forks [1] [1]. 16627993. The HIRAN domain and recruitment of chromatin remodeling and repair activities to damaged DNA. Iyer LM, Babu MM, Aravind L;. Cell Cycle. 2006;5:775-782. (from Pfam) NF020377.5 PF08798.16 CRISPR_assoc 25 25 223 PfamEq Y Y N type I-E CRISPR-associated protein Cas6/Cse3/CasE 131567 cellular organisms no rank 12499 EBI-EMBL CRISPR associated protein type I-E CRISPR-associated protein Cas6/Cse3/CasE This domain forms an anti-parallel beta strand structure with flanking alpha helical regions. (from Pfam) NF020387.5 PF08808.16 RES 23.2 23.2 157 domain Y Y N RES domain-containing protein 131567 cellular organisms no rank 43489 EBI-EMBL RES domain RES domain This presumed domain contains 3 highly conserved polar groups that could form an active site. These are an arginine, glutamate and serine, hence the RES domain. The domain is found widely distributed in bacteria. The domain is about 150 residues in length. (from Pfam) NF020397.5 PF08818.16 DUF1801 27.2 27.2 85 domain Y Y N DUF1801 domain-containing protein 21744456 131567 cellular organisms no rank 61360 EBI-EMBL Domain of unknown function (DU1801) Domain of unknown function (DU1801) This domain is found in the Intracellular iron chaperone frataxin YdhG [1] and the uncharacterised protein YdeI from Bacillus subtilis. [1]. 21744456. The frataxin homologue Fra plays a key role in intracellular iron channeling in Bacillus subtilis. Albrecht AG, Landmann H, Nette D, Burghaus O, Peuckert F, Seubert A, Miethke M, Marahiel MA;. Chembiochem. 2011;12:2052-2061. (from Pfam) NF020398.5 PF08819.16 DUF1802 25 25 174 subfamily Y Y N DUF1802 family protein 131567 cellular organisms no rank 3624 EBI-EMBL Domain of unknown function (DUF1802) DUF1802 family protein The function of this family is unknown. This region is found associated with a Pfam:PF04471 suggesting they could be part of a restriction modification system.. (from Pfam) NF020400.5 PF08821.16 CGGC 27 27 106 domain Y Y N CGGC domain-containing protein 131567 cellular organisms no rank 2178 EBI-EMBL CGGC domain CGGC domain This putative domain contains a quite highly conserved sequence of CGGC in its central region. The domain has many conserved cysteines and histidines suggestive of a zinc binding function. (from Pfam) NF020402.5 PF08823.16 PG_binding_2 21.1 21.1 74 domain Y Y N putative peptidoglycan binding domain-containing protein 131567 cellular organisms no rank 7857 EBI-EMBL Putative peptidoglycan binding domain Putative peptidoglycan binding domain This family may be a peptidoglycan binding domain. (from Pfam) NF020406.5 PF08827.16 DUF1805 29.5 29.5 64 PfamAutoEq Y Y N DUF1805 domain-containing protein 131567 cellular organisms no rank 2786 EBI-EMBL Domain of unknown function (DUF1805) Domain of unknown function (DUF1805) This domain is found in bacteria and archaea and has an N terminal tetramerisation region that is composed of beta sheets. (from Pfam) NF020413.5 PF08837.16 DUF1810 25 25 136 PfamAutoEq Y Y N DUF1810 family protein 131567 cellular organisms no rank 10337 EBI-EMBL Protein of unknown function (DUF1810) DUF1810 family protein This is a family of uncharacterised proteins. The structure of one of the members in this family has been solved and it adopts a mainly alpha helical structure. (from Pfam) NF020416.5 PF08840.16 BAAT_C 20.9 20.9 210 domain Y Y N acyl-CoA thioester hydrolase/BAAT C-terminal domain-containing protein 11694534 131567 cellular organisms no rank 38033 EBI-EMBL BAAT / Acyl-CoA thioester hydrolase C terminal BAAT / Acyl-CoA thioester hydrolase C terminal This catalytic domain is found at the C terminal of acyl-CoA thioester hydrolases and bile acid-CoA:amino acid N-acetyltransferases (BAAT). [1]. 11694534. The peroxisome proliferator-induced cytosolic type I acyl-CoA thioesterase (CTE-I) is a serine-histidine-aspartic acid alpha /beta hydrolase. Huhtinen K, O'Byrne J, Lindquist PJ, Contreras JA, Alexson SE;. J Biol Chem. 2002;277:3424-3432. (from Pfam) NF020419.5 PF08843.16 AbiEii 22.5 22.5 238 subfamily Y Y N nucleotidyl transferase AbiEii/AbiGii toxin family protein 19833706,24465005 131567 cellular organisms no rank 49383 EBI-EMBL Nucleotidyl transferase AbiEii toxin, Type IV TA system nucleotidyl transferase AbiEii/AbiGii toxin family protein This family was recently identified as belonging to the nucleotidyltransferase superfamily [1]. AbiEii is the cognate toxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is Pfam:PF13338 [2]. [1]. 19833706. Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. Kuchta K, Knizewski L, Wyrwicz LS, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2009; [Epub ahead of print]. [2]. 24465005. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Dy RL, Przybilski R, Semeijn K, Salmond GP, Fineran PC;. Nucleic Acids Res. 2014;42:4590-4605. (from Pfam) NF020425.5 PF08849.16 BrxA 23 23 184 PfamAutoEq Y Y N BrxA family protein 25452498 131567 cellular organisms no rank 5733 EBI-EMBL BrxA DUF1819 family protein BrxA is part of the phage resistance system BREX (Bacteriophage Exclusion). It shares structural homology with the RNA-binding antitermination protein NusB [1]. [1]. 25452498. BREX is a novel phage resistance system widespread in microbial genomes. Goldfarb T, Sberro H, Weinstock E, Cohen O, Doron S, Charpak-Amikam Y, Afik S, Ofir G, Sorek R;. EMBO J. 2015;34:169-183. (from Pfam) NF020432.5 PF08857.16 ParBc_2 23.6 23.6 158 domain Y Y N ParB-like protein 131567 cellular organisms no rank 7382 EBI-EMBL Putative ParB-like nuclease ParB-like protein This domain is probably distantly related to Pfam:PF02195. Suggesting these uncharacterised proteins have a nuclease function. (from Pfam) NF020434.5 PF08859.16 DGC 27 27 106 domain Y Y N putative zinc-binding protein 131567 cellular organisms no rank 3614 EBI-EMBL DGC domain DGC domain This domain appears to be a zinc binding domain from the conservation of four potential chelating cysteines. The domain is named after a conserved central motif. The function of this domain is unknown. (from Pfam) NF020436.5 PF08861.15 DUF1828 22 22 91 domain Y Y N DUF1828 domain-containing protein 131567 cellular organisms no rank 3510 EBI-EMBL Domain of unknown function DUF1828 Domain of unknown function DUF1828 This presumed domain is functionally uncharacterised. (from Pfam) NF020442.5 PF08867.16 FRG 25 25 94 domain Y Y N FRG domain-containing protein 131567 cellular organisms no rank 14282 EBI-EMBL FRG domain FRG domain This presumed domain contains a conserved N-terminal (F/Y)RG motif. It is functionally uncharacterised. (from Pfam) NF020445.5 PF08870.16 DndE 25 25 111 domain Y Y N DndE family protein 16102010 131567 cellular organisms no rank 3943 EBI-EMBL DNA sulphur modification protein DndE DndE family protein DndE is a small protein of 126 residues. It is a putative carboxylase homologous to NCAIR synthetase. It is encoded by an operon that is associated with a sulphur-based modification to DNA [1]. [1]. 16102010. A novel DNA modification by sulphur. Zhou X, He X, Liang J, Li A, Xu T, Kieser T, Helmann JD, Deng Z;. Mol Microbiol. 2005;57:1428-1438. (from Pfam) NF020448.5 PF08874.15 DUF1835 21.1 21.1 122 domain Y Y N DUF1835 domain-containing protein 131567 cellular organisms no rank 12602 EBI-EMBL Domain of unknown function (DUF1835) Domain of unknown function (DUF1835) This family of proteins are functionally uncharacterised. (from Pfam) NF020452.5 PF08878.16 HamA 25 25 230 PfamAutoEq Y Y N Hachiman antiphage defense system protein HamA GO:0000166 29371424,32508782 131567 cellular organisms no rank 7119 EBI-EMBL HamA Hachiman antiphage defense system protein HamA Hachiman antiphage defense system has been described in Ralstonia solanacearum species complex (RSSC), and is composed of two genes, hamAB, which encode a protein of unknown function HamA, represented in this entry, and an helicase (HamB). Only one strain (KACC10722) from phylotype IV shows this system complete and both genes are organised in an operon [1,2]. [1]. 29371424. Systematic discovery of antiphage defense systems in the microbial pangenome. Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R;. Science. 2018; [Epub ahead of print]. [2]. 32508782. Diversity and Evolutionary Dynamics of Antiphage Defense Systems in Ralstonia solanacearum Species Complex. Castillo JA, Secaira-Morocho H, Maldonado S, Sarmiento KN;. Front Microbiol. 2020;11:961. (from Pfam) NF020456.5 PF08882.16 Acetone_carb_G 21 21 113 domain Y Y N acetone carboxylase subunit gamma 12003937 131567 cellular organisms no rank 2228 EBI-EMBL Acetone carboxylase gamma subunit acetone carboxylase subunit gamma Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO(2) to form acetoacetate. [1]. 12003937. Biochemical, molecular, and genetic analyses of the acetone carboxylases from Xanthobacter autotrophicus strain Py2 and Rhodobacter capsulatus strain B10. Sluis MK, Larsen RA, Krum JG, Anderson R, Metcalf WW, Ensign SA;. J Bacteriol. 2002;184:2969-2977. (from Pfam) NF020461.5 PF08887.16 GAD-like 25 25 107 domain Y Y N GAD-like domain-containing protein 131567 cellular organisms no rank 5959 EBI-EMBL GAD-like domain GAD-like domain This domain is functionally uncharacterised, but it appears to be distantly related to the GAD domain Pfam:PF02938. (from Pfam) NF020463.5 PF08889.16 WbqC 21.3 21.3 218 PfamEq Y Y N WbqC family protein 12843098,14687563 131567 cellular organisms no rank 16174 EBI-EMBL WbqC-like protein family WbqC family protein This family of proteins are functionally uncharacterised. However it is found in an O-antigen gene cluster in E. coli [1] and other bacteria [2] suggesting a role in O-antigen production. Feng et al. suggest that wbnG may code for a glycine transferase [2]. [1]. 12843098. Sequence of the Escherichia coli O121 O-antigen gene cluster and detection of enterohemorrhagic E. coli O121 by PCR amplification of the wzx and wzy genes. Fratamico PM, Briggs CE, Needle D, Chen CY, DebRoy C;. J Clin Microbiol. 2003;41:3379-3383. [2]. 14687563. Structure of the Shigella dysenteriae 7 O antigen gene cluster and identification of its antigen specific genes. Feng L, Tao J, Guo H, Xu J, Li Y, Rezwan F, Reeves P, Wang L;. Microb Pathog. 2004;36:109-115. (from Pfam) NF020464.5 PF08890.16 Phage_TAC_5 27 27 135 subfamily Y Y N phage tail assembly chaperone 19251647,23542343,23542344 131567 cellular organisms no rank 4094 EBI-EMBL Phage XkdN-like tail assembly chaperone protein, TAC phage tail assembly chaperone This is a family of phage tail assembly chaperone proteins, TACs, from Gram-positive bacteriophages, in particular PBSX from Firmicutes. [1]. 19251647. The phage lambda major tail protein structure reveals a common evolution for long-tailed phages and the type VI bacterial secretion system. Pell LG, Kanelis V, Donaldson LW, Howell PL, Davidson AR;. Proc Natl Acad Sci U S A. 2009;106:4160-4165. [2]. 23542343. Tail tip proteins related to bacteriophage lambda gpL coordinate an iron-sulfur cluster. Tam W, Pell LG, Bona D, Tsai A, Dai XX, Edwards AM, Hendrix RW, Maxwell KL, Davidson AR;. J Mol Biol. 2013;425:2450-2462. [3]. 23542344. A conserved spiral structure for highly diverged phage tail assembly chaperones. Pell LG, Cumby N, Clark TE, Tuite A, Battaile KP, Edwards AM, Chirgadze NY, Davidson AR, Maxwell KL;. J Mol Biol. 2013;425:2436-2449. (from Pfam) NF020466.5 PF08892.16 YqcI_YcgG 27 27 211 domain Y Y N YqcI/YcgG family protein 131567 cellular organisms no rank 8669 EBI-EMBL YqcI/YcgG family YqcI/YcgG family protein This family of proteins are functionally uncharacterised. The family include YqcI and YcgG from B. subtilis. The alignment contains a conserved FPC motif at the N-terminus and CPF at the C-terminus. (from Pfam) NF020468.5 PF08894.16 DUF1838 25 25 232 domain Y Y N DUF1838 family protein 131567 cellular organisms no rank 3235 EBI-EMBL Protein of unknown function (DUF1838) DUF1838 family protein This family of proteins are functionally uncharacterised. (from Pfam) NF020473.5 PF08899.16 DUF1844 27 27 76 PfamAutoEq Y Y N DUF1844 domain-containing protein 131567 cellular organisms no rank 7696 EBI-EMBL Domain of unknown function (DUF1844) Domain of unknown function (DUF1844) This family of proteins are functionally uncharacterised. (from Pfam) NF020475.5 PF08901.16 DUF1847 25 25 157 domain Y Y N DUF1847 domain-containing protein 131567 cellular organisms no rank 2012 EBI-EMBL Protein of unknown function (DUF1847) Protein of unknown function (DUF1847) This family of proteins are functionally uncharacterised. THey contain 4 N-terminal cysteines that may form a zinc binding domain. (from Pfam) NF020476.5 PF08902.16 DUF1848 30.5 30.5 262 domain Y Y N DUF1848 family protein 16352836 131567 cellular organisms no rank 5490 EBI-EMBL Domain of unknown function (DUF1848) DUF1848 family protein This family of proteins are functionally uncharacterised. The C-terminus contains a cluster of cysteines that are similar to the iron-sulfur cluster found at the N-terminus of Pfam:PF04055. [1]. 16352836. Reconstruction and regulation of the central catabolic pathway in the thermophilic propionate-oxidizing syntroph Pelotomaculum thermopropionicum. Kosaka T, Uchiyama T, Ishii S, Enoki M, Imachi H, Kamagata Y, Ohashi A, Harada H, Ikenaga H, Watanabe K;. J Bacteriol. 2006;188:202-210. (from Pfam) NF020477.5 PF08903.16 DUF1846 27 27 333 PfamAutoEq Y Y N DUF1846 domain-containing protein 131567 cellular organisms no rank 7277 EBI-EMBL Domain of unknown function DUF1846, N-terminal DUF1846 family protein This domain is found in a family of proteins that are functionally uncharacterised, known as UPF0371. Some members of the family are annotated as ATP-dependent peptidases. This is a P-loop-like domain (pdbe:3BH1). (from Pfam) NF020479.5 PF08905.16 DUF1850 27 27 87 PfamAutoEq Y Y N DUF1850 domain-containing protein 131567 cellular organisms no rank 8175 EBI-EMBL Domain of unknown function (DUF1850) Domain of unknown function (DUF1850) This family of proteins are functionally uncharacterised. Some members of this family appear to be misannotated as RocC an amino acid transporter from B. subtilis. (from Pfam) NF020480.5 PF08906.16 T6SS_Tdi1_C 27.4 27.4 75 domain Y Y N T6SS immunity protein Tdi1 domain-containing protein 30839288 131567 cellular organisms no rank 6959 EBI-EMBL T6SS immunity protein Tdi1, C-terminal T6SS immunity protein Tdi1, C-terminal This domain is found at the C-terminal region of the type VI secretion system (T6SS) immunity protein Tdi1 from Agrobacterium tumefaciens (Atu4351, Swiss:Q7CUQ2) and similar bacterial proteins Tdi1 is organised into a N-terminal GAD-related domain (Pfam:PF08887) and a C-terminal domain likely to exist as an insertion in the GAD-like domain. This domain shows a two-stranded antiparallel beta-sheet and four helices. A positive groove that extends to both domains may be associated with nucleotide binding [1]. [1]. 30839288. Crystal structure of the type VI immunity protein Tdi1 (Atu4351) from Agrobacterium tumefaciens. Shi L, Gao Z, Zhang T, Zhang H, Dong Y;. Acta Crystallogr F Struct Biol Commun. 2019;75:153-158. (from Pfam) NF020483.5 PF08909.16 DUF1854 26.8 26.8 130 PfamAutoEq Y Y N DUF1854 domain-containing protein 131567 cellular organisms no rank 2906 EBI-EMBL Domain of unknown function (DUF1854) Domain of unknown function (DUF1854) This potential domain is functionally uncharacterised. It is found at the C-terminus of a number of ATP transporter proteins suggesting this domain may be involved in ligand binding. (from Pfam) NF020489.5 PF08915.16 tRNA-Thr_ED 30.2 30.2 137 domain Y Y N threonyl-tRNA synthetase editing domain-containing protein GO:0004829,GO:0005524,GO:0005737,GO:0008270 15908961 131567 cellular organisms no rank 1165 EBI-EMBL Archaea-specific editing domain of threonyl-tRNA synthetase Archaea-specific editing domain of threonyl-tRNA synthetase Archaea-specific editing domain of threonyl-tRNA synthetase, with marked structural similarity to D-amino acids deacylases found in eubacteria and eukaryotes. This domain can bind D-amino acids, and ensures high fidelity during translation. It is especially responsible for removing incorrectly attached serine from tRNA-Thr. The domain forms a fold that can be be defined as two layers of beta-sheets (a three-stranded sheet and a five-stranded sheet), with two alpha-helices located adjacent to the five-stranded sheet [1]. [1]. 15908961. A D-amino acid editing module coupled to the translational apparatus in archaea. Dwivedi S, Kruparani SP, Sankaranarayanan R;. Nat Struct Mol Biol. 2005;12:556-557. (from Pfam) NF020495.5 PF08921.16 DUF1904 24.1 24.1 108 PfamAutoEq Y Y N DUF1904 family protein 131567 cellular organisms no rank 3159 EBI-EMBL Domain of unknown function (DUF1904) DUF1904 family protein This domain is found in a set of hypothetical bacterial proteins. (from Pfam) NF020496.5 PF08922.16 DUF1905 24 24 81 domain Y Y N DUF1905 domain-containing protein 131567 cellular organisms no rank 21438 EBI-EMBL Domain of unknown function (DUF1905) Domain of unknown function (DUF1905) This domain is found in a set of hypothetical bacterial proteins. (from Pfam) NF020497.5 PF08923.15 MAPKK1_Int 25 25 119 PfamEq Y N N Mitogen-activated protein kinase kinase 1 interacting GO:0032006 15263099 131567 cellular organisms no rank 44 EBI-EMBL Mitogen-activated protein kinase kinase 1 interacting Mitogen-activated protein kinase kinase 1 interacting Mitogen-activated protein kinase kinase 1 interacting protein is a small subcellular adaptor protein required for MAPK signaling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer [1]. [1]. 15263099. Crystal structure of the p14/MP1 scaffolding complex: how a twin couple attaches mitogen-activated protein kinase signaling to late endosomes. Kurzbauer R, Teis D, de Araujo ME, Maurer-Stroh S, Eisenhaber F, Bourenkov GP, Bartunik HD, Hekman M, Rapp UR, Huber LA, Clausen T;. Proc Natl Acad Sci U S A. 2004;101:10984-10989. (from Pfam) NF020509.5 PF08937.16 ThsB_TIR 21.2 21.2 100 domain Y Y N TIR domain-containing protein 29371424,32499527,34853457 131567 cellular organisms no rank 17949 EBI-EMBL Thoeris protein ThsB, TIR-like domain Thoeris protein ThsB, TIR-like domain Thoeris is a bacterial antiphage defense system, which consists of two genes, thsA and thsB, via NAD+ degradation [1-3]. ThsA has robust NAD+ cleavage activity and and a two-domain architecture containing a N-terminal NAD-binding domain (denoted as sirtuin-like or Macro) and C-terminal SLOG-like domain. In some instances, such as in B. amyloliquefaciens ThsA has an N-terminal transmembrane domain [1]. ThsB (also referred to as TIR1 and TIR2) is structurally similar to TIR domain proteins but without enzymatic activity. This is the TIR-like domain of ThsB proteins, which adopts a Rossmann-like fold. ThsB is responsible for recognizing phage infection [2]. [1]. 29371424. Systematic discovery of antiphage defense systems in the microbial pangenome. Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R;. Science. 2018; [Epub ahead of print]. [2]. 34853457. Antiviral activity of bacterial TIR domains via immune signalling molecules. Ofir G, Herbst E, Baroz M, Cohen D, Millman A, Doron S, Tal N, Malheiro DBA, Malitsky S, Amitai G, Sorek R;. Nature. 2021;600:116-120. [3]. 32499527. Structural and functional evidence of bacterial antiphage protection by Thoeris defense system via NAD(+) degradation. Ka D, Oh H, Park E, Kim JH, Bae E;. Nat Commun. 2020;11:2816. (from Pfam) NF020511.5 PF08939.15 Bles03 23.1 23.1 255 PfamAutoEq Y Y N putative phosphothreonine lyase domain-containg protein 16511166,25062915 131567 cellular organisms no rank 511 EBI-EMBL Basophilic leukemia-expressed protein Bles03 putative phosphothreonine lyase domain-containg protein This domain is found in Basophilic leukemia-expressed protein Bles03 from humans (also known as UPF0696 protein C11orf68, Swiss:Q9H3H3) and various proteins from eukaryotes, bacteria and archaea. Bles03 has been suggested to have phosphothreonine lyase activity and to play a role in the biosynthesis of dehydro amino acids [1]. It shows a two-layer sandwich architecture with a a nine-stranded beta-sheet and three alpha-helices on each side [2]. [1]. 16511166. The structure at 2.5 A resolution of human basophilic leukemia-expressed protein BLES03. Bitto E, Bingman CA, Robinson H, Allard ST, Wesenberg GE, Phillips GN Jr;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005;61:812-817. [2]. 25062915. Genome-wide search for eliminylating domains reveals novel function for BLES03-like proteins. Khater S, Mohanty D;. Genome Biol Evol. 2014;6:2017-2033. (from Pfam) NF020512.5 PF08940.16 DUF1918 24 24 58 domain Y Y N DUF1918 domain-containing protein 131567 cellular organisms no rank 10039 EBI-EMBL Domain of unknown function (DUF1918) Domain of unknown function (DUF1918) This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF020514.5 PF08942.15 DUF1919 25 25 196 domain Y Y N DUF1919 domain-containing protein 131567 cellular organisms no rank 1978 EBI-EMBL Domain of unknown function (DUF1919) Domain of unknown function (DUF1919) This domain has no known function. It is found in various hypothetical and putative bacterial proteins. The structure of this domain is known (PDB:2g6t). (from Pfam) NF020530.5 PF08960.15 STIV_B116-like 26 26 101 domain Y Y N STIV orfB116 family protein 17336360 131567 cellular organisms no rank 421 EBI-EMBL STIV B116-like STIV orfB116 family protein The sulfolobus turreted icosahedral virus (STIV) infects Sulfolobus species found in the hot springs of Yellowstone National Park. It has 37 ORFs including B116, whose function is unknown. The structure of B116 reveals a fold consisting of a five-stranded beta-sheet flanked on one side by three alpha helices. Two subunits come together to form a homodimer with a 10-stranded mixed beta-sheet, where the topology of the central strands resembles an unclosed beta-barrel [1]. [1]. 17336360. A new DNA binding protein highly conserved in diverse crenarchaeal viruses. Larson ET, Eilers BJ, Reiter D, Ortmann AC, Young MJ, Lawrence CM;. Virology. 2007;363:387-396. (from Pfam) NF020537.5 PF08967.15 ENCP4 31.4 31.4 81 domain Y Y N Putative encapsulin shell family protein 34362927 131567 cellular organisms no rank 170 EBI-EMBL Putative type 4B encapsulin shell protein Putative encapsulin shell family protein Proteins in this entry may be the encapsulin shell protein in a type 4 A-domain encapsulin nanocompartment system. It has been shown that bacterial/archaeal encapsulin-like systems and HK97-type viruses share a common ancestor and it is likely that encapsulins have evolved from HK97-type phages [1]. [1]. 34362927. Large-scale computational discovery and analysis of virus-derived microbial nanocompartments. Andreas MP, Giessen TW;. Nat Commun. 2021;12:4748. (from Pfam) NF020542.5 PF08972.16 DUF1902 22 22 74 domain Y Y N DUF1902 domain-containing protein 16250002 131567 cellular organisms no rank 1819 EBI-EMBL Domain of unknown function (DUF1902) Domain of unknown function (DUF1902) Members of this family of prokaryotic proteins adopt a fold consisting of one alpha-helix and four beta-strands. Their function has not, as yet, been elucidated [1]. [1]. 16250002. Crystal structure of the hypothetical protein TTHA1013 from Thermus thermophilus HB8. Hattori M, Mizohata E, Manzoku M, Bessho Y, Murayama K, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S;. Proteins. 2005;61:1117-1120. (from Pfam) NF020543.5 PF08973.15 TM1506 27 27 130 PfamAutoEq Y Y N DUF1893 domain-containing protein 18275082,21890906 131567 cellular organisms no rank 1483 EBI-EMBL Domain of unknown function (DUF1893) Domain of unknown function (DUF1893) A member of the deaminase fold that binds an unknown ligand in the crystal structure. The protein is ADP-ribosylated at a conserved aspartate [1]. Contextual analysis suggests that the domain is likely to bind NAD or ADP ribose either to sense redox states or to function as a regulatory ADP ribosyltransferase [2]. [1]. 18275082. Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolution. Xu Q, Kozbial P, McMullan D, Krishna SS, Brittain SM, Ficarro SB, DiDonato M, Miller MD, Abdubek P, Axelrod HL, Chiu HJ, Clayton T, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Klock HE, Morse AT, Nigoghossian E, Paulsen J, Reyes R, Rife CL, van den Bedem H, White A, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Proteins. 2008;71:1546-1552. [2]. 21890906. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Iyer LM, Zhang D, Rogozin IB, Aravind L;. Nucleic Acids Res. 2011; [Epub ahead of print] (from Pfam) NF020544.5 PF08974.15 DUF1877 22 22 163 PfamAutoEq Y Y N DUF1877 family protein 131567 cellular organisms no rank 9555 EBI-EMBL Domain of unknown function (DUF1877) DUF1877 family protein This domain is found in a set of hypothetical bacterial proteins. (from Pfam) NF020553.5 PF08984.16 DUF1858 32.2 32.2 59 domain Y Y N DUF1858 domain-containing protein 131567 cellular organisms no rank 9390 EBI-EMBL Domain of unknown function (DUF1858) Domain of unknown function (DUF1858) This domain has no known function. It is found in various hypothetical bacterial proteins. (from Pfam) NF020571.5 PF09002.16 Card1_endonuc 26.4 26.4 136 subfamily Y Y N Card1-like endonuclease domain-containing protein 33461211 131567 cellular organisms no rank 3098 EBI-EMBL Card1-like, endonuclease domain DUF1887 family CARF protein DUF1887, part of the CARF (CRISPR-associated Rossmann Fold) superfamily, includes CARF3 and CARF4 group proteins. Many but not all members belong to CRISPR-Cas systems. NF020581.5 PF09012.15 FeoC 21 21 69 domain Y Y N FeoC-like transcriptional regulator 16718600 131567 cellular organisms no rank 7026 EBI-EMBL FeoC like transcriptional regulator FeoC-like transcriptional regulator This family contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependant transcriptional repressor [1]. [1]. 16718600. Feo--transport of ferrous iron into bacteria. Cartron ML, Maddocks S, Gillingham P, Craven CJ, Andrews SC;. Biometals. 2006;19:143-157. (from Pfam) NF020588.5 PF09019.16 EcoRII-C 25 25 165 subfamily Y Y N type II restriction endonuclease GO:0003677,GO:0009036,GO:0009307 14659759 131567 cellular organisms no rank 3567 EBI-EMBL EcoRII C terminal EcoRII family type II restriction endonuclease C-terminal domain The C-terminal catalytic domain of the Restriction Endonuclease EcoRII has a restriction endonuclease-like fold with a central five-stranded mixed beta-sheet surrounded on both sides by alpha-helices. It cleaves DNA specifically at single 5' CCWGG sites [1]. [1]. 14659759. Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold. Zhou XE, Wang Y, Reuter M, Mucke M, Kruger DH, Meehan EJ, Chen L;. J Mol Biol. 2004;335:307-319. (from Pfam) NF020602.5 PF09035.15 Tn916-Xis 22.9 22.9 69 PfamEq Y Y N excisionase 15733914 131567 cellular organisms no rank 3157 EBI-EMBL Excisionase from transposon Tn916 excisionase, Tn916-type The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix. It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilising distorted DNA structures [1]. [1]. 15733914. The structure of the excisionase (Xis) protein from conjugative transposon Tn916 provides insights into the regulation of heterobivalent tyrosine recombinases. Abbani M, Iwahara M, Clubb RT;. J Mol Biol. 2005;347:11-25. (from Pfam) NF020610.5 PF09043.16 Lys-AminoMut_A 25 25 508 domain Y Y N lysine 5,6-aminomutase subunit alpha TIM-barrel domain-containing protein 20106986 131567 cellular organisms no rank 3907 EBI-EMBL D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit Members of his family are involved in the 1,2 rearrangement of the terminal amino group of DL-lysine and of L-beta-lysine, using adenosylcobalamin (AdoCbl) and pyridoxal-5'-phosphate as co-factors. The structure is predominantly a PLP-binding TIM barrel domain, with several additional alpha-helices and beta-strands at the N and C termini. These helices and strands form an intertwined accessory clamp structure that wraps around the sides of the TIM barrel and extends up toward the Ado ligand of the Cbl co-factor, providing most of the interactions observed between the protein and the Ado ligand of the Cbl, suggesting that its role is mainly in stabilising AdoCbl in the precatalytic resting state [1]. This is a TIM-barrel domain. [1]. 20106986. Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase. Wolthers KR, Levy C, Scrutton NS, Leys D;. J Biol Chem. 2010;285:13942-13950. (from Pfam) NF020621.5 PF09055.16 Sod_Ni 25 25 127 PfamEq Y Y N superoxide dismutase [Ni] GO:0004784,GO:0016151,GO:0016209 15209499 131567 cellular organisms no rank 4338 EBI-EMBL Nickel-containing superoxide dismutase superoxide dismutase [Ni] Nickel containing superoxide dismutase (NiSOD) is a metalloenzyme containing a hexameric assembly of right-handed 4-helix bundles of up-down-up-down topology with an N-terminal His-Cys-X-X-Pro-Cys-Gly-X-Tyr motif that chelates the active site Ni ions. NiSOD catalyses the disproportionation of superoxide to peroxide and molecular oxygen through alternate oxidation and reduction of Ni, protecting cells from the toxic products of aerobic metabolism [1]. [1]. 15209499. Nickel superoxide dismutase structure and mechanism. Barondeau DP, Kassmann CJ, Bruns CK, Tainer JA, Getzoff ED;. Biochemistry. 2004;43:8038-8047. (from Pfam) NF020628.5 PF09062.15 Endonuc_subdom 24.4 24.4 98 domain Y N N PI-PfuI Endonuclease subdomain 10891276 131567 cellular organisms no rank 22 EBI-EMBL PI-PfuI Endonuclease subdomain PI-PfuI Endonuclease subdomain The endonuclease subdomain, found in the prokaryotic protein ribonucleotide reductase, assumes an alpha-beta-beta-alpha-beta-beta-alpha-alpha topology. The four stranded beta-sheet forms a saddle-shaped surface and assembles together through an interface made of alpha-helices. The presence of 14 basic residues on the surface of the beta-sheets suggests that this large groove may be involved in DNA binding [1]. [1]. 10891276. Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI. Ichiyanagi K, Ishino Y, Ariyoshi M, Komori K, Morikawa K;. J Mol Biol. 2000;300:889-901. (from Pfam) NF020645.5 PF09079.16 Cdc6_C 25.1 25.1 96 domain Y N N CDC6, C terminal winged helix domain 11030343 131567 cellular organisms no rank 5170 EBI-EMBL CDC6, C terminal winged helix domain CDC6, C terminal winged helix domain The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity [1]. [1]. 11030343. Structure and function of Cdc6/Cdc18: implications for origin recognition and checkpoint control. Liu J, Smith CL, DeRyckere D, DeAngelis K, Martin GS, Berger JM;. Mol Cell. 2000;6:637-648. (from Pfam) NF020650.5 PF09084.16 NMT1 20.5 20.5 216 domain Y Y N ABC transporter substrate-binding protein 12271461,12777485,23048037,2358444 131567 cellular organisms no rank 397264 EBI-EMBL NMT1/THI5 like ABC transporter substrate-binding protein This family contains the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine [1][2][3]. They are regulated by thiamine [2]. The protein adopts a fold related to the periplasmic binding protein (PBP) family. Both pyridoxal-5'-phosphate (PLP) and an iron atom are bound to the protein suggesting numerous residues of the active site necessary for HMP-P biosynthesis. The yeast protein is a dimer and, although exceptionally using PLP as a substrate, has notable similarities with enzymes dependent on this molecule as a cofactor [4]. [1]. 12271461. Functional analysis of yeast gene families involved in metabolism of vitamins B1 and B6. Rodriguez-Navarro S, Llorente B, Rodriguez-Manzaneque MT, Ramne A, Uber G, Marchesan D, Dujon B, Herrero E, Sunnerhagen P, Perez-Ortin JE;. Yeast. 2002;19:1261-1276. [2]. 2358444. nmt1 of fission yeast. A highly transcribed gene completely repressed by thiamine. Maundrell K;. J Biol Chem. 1990;265:10857-10864. [3]. 12777485. The THI5 gene family of Saccharomyces cerevisiae: distribution of homologues among the hemiascomycetes and functional redundancy in the aerobic biosynthesis of thiamin from pyridoxine. Wightman R, Meacock PA;. Microbiology. 2003;149:1447-1460. [4]. 23048037. The last piece in the vitamin B1 biosynthesis puzzle: structural and functional insight into yeast 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase. Coquille S, Roux C, Fitzpatrick TB, Thore S;. J Biol Chem. 2012;287:42333-42343. (from Pfam) NF020659.5 PF09094.16 AmyA-A_glucT_m 27 27 80 PfamAutoEq Y Y N alpha-amylase/4-alpha-glucanotransferase domain-containing protein 12618437 131567 cellular organisms no rank 929 EBI-EMBL Alpha-amylase/4-alpha-glucanotransferase, middle domain Alpha-amylase/4-alpha-glucanotransferase, middle domain This entry represents a domain found in prokaryotic alpha-amylase and 4-alpha-glucanotransferase. It is adjacent to the C-terminal domain (Pfam:PF09095). This domain adopts an immunoglobulin/ albumin-binding domain-like fold, with a bundle of three alpha-helices. Their function is, as yet, unknown [1]. [1]. 12618437. Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor. Imamura H, Fushinobu S, Yamamoto M, Kumasaka T, Jeon BS, Wakagi T, Matsuzawa H;. J Biol Chem. 2003;278:19378-19386. (from Pfam) NF020660.5 PF09095.16 AmyA-gluTrfs_C 22 22 284 PfamAutoEq Y Y N alpha-amylase/4-alpha-glucanotransferase domain-containing protein GO:0003824,GO:0005975,GO:0030246 12618437 131567 cellular organisms no rank 1169 EBI-EMBL Alpha-amylase/4-alpha-glucanotransferase, C-terminal Alpha-amylase/4-alpha-glucanotransferase, C-terminal This entry represents a domain found in prokaryotic alpha-amylase and 4-alpha-glucanotransferase. It adopts a beta-sandwich fold, in which two layers of anti-parallel beta-sheets are arranged in a nearly parallel fashion. The exact function of this family is, as yet, unknown, however it has been proposed that they may play a role in transglycosylation reactions [1]. [1]. 12618437. Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor. Imamura H, Fushinobu S, Yamamoto M, Kumasaka T, Jeon BS, Wakagi T, Matsuzawa H;. J Biol Chem. 2003;278:19378-19386. (from Pfam) NF020664.5 PF09099.15 Qn_am_d_aIII 22 22 82 domain Y N N Quinohemoprotein amine dehydrogenase, alpha subunit domain III 11704672,12925784 131567 cellular organisms no rank 2071 EBI-EMBL Quinohemoprotein amine dehydrogenase, alpha subunit domain III Quinohemoprotein amine dehydrogenase, alpha subunit domain III Members of this family, which are predominantly found in the prokaryotic protein quinohemoprotein amine dehydrogenase, adopt an immunoglobulin-like beta-sandwich fold, with seven strands arranged into two beta sheets; the fold is possibly related to the immunoglobulin and/or fibronectin type III superfamilies. The precise function of this domain has not, as yet, been defined [1,2]. [1]. 12925784. Structure of the phenylhydrazine adduct of the quinohemoprotein amine dehydrogenase from Paracoccus denitrificans at 1.7 A resolution. Datta S, Ikeda T, Kano K, Mathews FS;. Acta Crystallogr D Biol Crystallogr. 2003;59:1551-1556. [2]. 11704672. Crystal structure of quinohemoprotein amine dehydrogenase from Pseudomonas putida. Identification of a novel quinone cofactor encaged by multiple thioether cross-bridges. Satoh A, Kim JK, Miyahara I, Devreese B, Vandenberghe I, Hacisalihoglu A, Okajima T, Kuroda S, Adachi O, Duine JA, Van Beeumen J, Tanizawa K, Hirotsu K;. J Biol Chem. 2002;277:2830-2834. (from Pfam) NF020678.5 PF09113.15 N-glycanase_C 25 25 140 domain Y Y N peptide-N-glycosidase F-related protein 7881905 131567 cellular organisms no rank 3496 EBI-EMBL Peptide-N-glycosidase F, C terminal peptide-N-glycosidase F C-terminal domain Most proteins with this domain (peptide-N-glycosidase F, C-terminal) also have a domain recognized by PF09112 (peptide-N-glycosidase F, N-terminal). NF020683.5 PF09118.16 GO-like_E_set 25 25 100 domain Y Y N galactose oxidase-like domain-containing protein 10825529,11698678,11923309,12530525,15239382,8182749 131567 cellular organisms no rank 15067 EBI-EMBL Galactose oxidase-like, Early set domain Galactose oxidase-like, Early set domain E or 'early' set domains are associated with the catalytic domain of galactose oxidase at the C-terminal end. Galactose oxidase is an extracellular monomeric enzyme which catalyzes the stereospecific oxidation of a broad range of primary alcohol substrates, and possesses a unique mononuclear copper site essential for catalysing a two-electron transfer reaction during the oxidation of primary alcohols to corresponding aldehydes. The second redox active centre necessary for the reaction was found to be situated at a tyrosine residue. The C-terminal domain of galactose oxidase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end, and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family adopt a secondary structure consisting of a bundle of seven, mostly antiparallel, beta-strands surrounding a hydrophobic core. The 7 strands are arranged in 2 sheets, in a Greek-key topology [1]. This domain is found in sugar-utilising enzymes, such as galactose oxidase or chitinase [2-6]. [1]. 11698678. Crystal structure of the precursor of galactose oxidase: an unusual self-processing enzyme. Firbank SJ, Rogers MS, Wilmot CM, Dooley DM, Halcrow MA, Knowles PF, McPherson MJ, Phillips SE;. Proc Natl Acad Sci U S A. 2001;98:12932-12937. [2]. 11923309. Cyclomaltodextrinase, neopullulanase, and maltogenic amylase are nearly indistinguishable from each other. Lee HS, Kim MS, Cho HS, Kim JI, Kim TJ, Choi JH, Park C, Lee HS, Oh BH, Park KH;. J Biol Chem. 2002;277:21891-2189. TRUNCATED at 1650 bytes (from Pfam) NF020687.5 PF09123.16 DUF1931 21.8 21.8 138 domain Y Y N DUF1931 family protein 16287087 131567 cellular organisms no rank 1731 EBI-EMBL Domain of unknown function (DUF1931) DUF1931 family protein Members of this family, which are found in a set of hypothetical bacterial proteins, contain a core of six alpha-helices, where one central helix is surrounded by the other five. The exact function of this family has not, as yet, been determined [1]. The known structure shows this domain contains two copies of the histone fold [1]. [1]. 16287087. The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold. Qiu Y, Tereshko V, Kim Y, Zhang R, Collart F, Yousef M, Kossiakoff A, Joachimiak A;. Proteins. 2006;62:8-16. (from Pfam) NF020689.5 PF09125.15 COX2-transmemb 25 25 38 PfamEq Y N N Cytochrome C oxidase subunit II, transmembrane 10775261 131567 cellular organisms no rank 79 EBI-EMBL Cytochrome C oxidase subunit II, transmembrane Cytochrome C oxidase subunit II, transmembrane Members of this family adopt a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold [1]. [1]. 10775261. Structure and mechanism of the aberrant ba(3)-cytochrome c oxidase from thermus thermophilus. Soulimane T, Buse G, Bourenkov GP, Bartunik HD, Huber R, Than ME;. EMBO J. 2000;19:1766-1776. (from Pfam) NF020694.5 PF09130.16 DUF1932 25 25 70 domain Y Y N DUF1932 domain-containing protein 131567 cellular organisms no rank 11577 EBI-EMBL Domain of unknown function (DUF1932) Domain of unknown function (DUF1932) This domain is found in a set of hypothetical prokaryotic proteins. Its exact function has not, as yet, been described. (from Pfam) NF020700.5 PF09136.15 Glucodextran_B 27 27 83 domain Y N N Glucodextranase, domain B 14660574 131567 cellular organisms no rank 11027 EBI-EMBL Glucodextranase, domain B Glucodextranase, domain B Members of this family adopt a structure consisting of seven/eight-strand antiparallel beta-sheets, in a Greek-key topology, similar to the immunoglobulin beta-sandwich fold. They act as cell wall anchors, where they interact with the S-layer present in the cell wall of Gram-positive bacteria by hydrophobic interactions. In glucodextranase, Domain B is buried in the S-layer, and a flexible linker located between domain B and the catalytic unit confers motion to the catalytic unit, which is capable of efficient hydrolysis of the substrates located close to the cell surface [1]. [1]. 14660574. Structural insights into substrate specificity and function of glucodextranase. Mizuno M, Tonozuka T, Suzuki S, Uotsu-Tomita R, Kamitori S, Nishikawa A, Sakano Y;. J Biol Chem. 2004;279:10575-10583. (from Pfam) NF020701.5 PF09137.16 Glucodextran_N 24.1 24.1 263 PfamEq Y N N Glucodextranase, domain N 14660574 131567 cellular organisms no rank 5264 EBI-EMBL Glucodextranase, domain N Glucodextranase, domain N Members of this family, which are uniquely found in bacterial and archaeal glucoamylases and glucodextranases, adopt a structure consisting of 17 antiparallel beta-strands. These beta-strands are divided into two beta-sheets, and one of the beta-sheets is wrapped by an extended polypeptide, which appears to stabilise the domain. Members of this family are mainly concerned with catalytic activity, hydrolysing alpha-1,6-glucosidic linkages of dextran to release beta-D-glucose from the non-reducing end via an inverting reaction mechanism [1]. [1]. 14660574. Structural insights into substrate specificity and function of glucodextranase. Mizuno M, Tonozuka T, Suzuki S, Uotsu-Tomita R, Kamitori S, Nishikawa A, Sakano Y;. J Biol Chem. 2004;279:10575-10583. (from Pfam) NF020702.5 PF09138.16 Urm1 21.8 21.8 96 domain Y N N Urm1 (Ubiquitin related modifier) GO:0005737,GO:0034227 14551258,16864801 131567 cellular organisms no rank 361 EBI-EMBL Urm1 (Ubiquitin related modifier) Urm1 (Ubiquitin related modifier) Urm1 is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like pathway urmylation [1]. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily [2]. [1]. 16864801. Solution structure of Urm1 and its implications for the origin of protein modifiers. Xu J, Zhang J, Wang L, Zhou J, Huang H, Wu J, Zhong Y, Shi Y;. Proc Natl Acad Sci U S A. 2006;103:11625-11630. [2]. 14551258. Urmylation: a ubiquitin-like pathway that functions during invasive growth and budding in yeast. Goehring AS, Rivers DM, Sprague GF Jr;. Mol Biol Cell. 2003;14:4329-4341. (from Pfam) NF020704.5 PF09140.16 MipZ 20.7 20.7 262 domain Y Y N division plane positioning ATPase MipZ 16839883 131567 cellular organisms no rank 277690 EBI-EMBL ATPase MipZ division plane positioning ATPase MipZ MipZ is an ATPase that forms a complex with the chromosome partitioning protein ParB near the chromosomal origin of replication [1]. It is responsible for the temporal and spatial regulation of FtsZ ring formation [1]. [1]. 16839883. MipZ, a spatial regulator coordinating chromosome segregation with cell division in Caulobacter. Thanbichler M, Shapiro L;. Cell. 2006;126:147-162. (from Pfam) NF020710.5 PF09147.15 CarA_N 21 21 199 PfamAutoEq Y Y N carbapenam-3-carboxylate synthase domain-containing protein 12820893,12890666,17658887,19371088 131567 cellular organisms no rank 205 EBI-EMBL Carbapenam-3-carboxylate synthase, N-terminal Carbapenam-3-carboxylate synthase, N-terminal This domain is found in the N-terminal of carbapenam-3-carboxylate synthase (carA), and is composed of two antiparallel six-stranded beta-sheets that form a sandwich, flanked on each side by two alpha-helices [1]. carA is involved in the biosynthesis of carbapenam-3-carboxylate, a beta-lactam antibiotic of the carbapenem class. It catalyses the ATP-dependent formation of (3S,5S)-carbapenam-3-carboxylate from (2S,5S)-5-carboxymethylproline [2,3,4]. [1]. 12890666. Crystal structure of carbapenam synthetase (CarA). Miller MT, Gerratana B, Stapon A, Townsend CA, Rosenzweig AC;. J Biol Chem. 2003;278:40996-41002. [2]. 12820893. Inhibition and alternate substrate studies on the mechanism of carbapenam synthetase from Erwinia carotovora. Gerratana B, Stapon A, Townsend CA;. Biochemistry. 2003;42:7836-7847. [3]. 17658887. Rate-limiting steps and role of active site Lys443 in the mechanism of carbapenam synthetase. Arnett SO, Gerratana B, Townsend CA;. Biochemistry. 2007;46:9337-9345. [4]. 19371088. A conserved tyrosyl-glutamyl catalytic dyad in evolutionarily linked enzymes: carbapenam synthetase and beta-lactam synthetase. Raber ML, Arnett SO, Townsend CA;. Biochemistry. 2009;48:4959-4971. (from Pfam) NF020714.5 PF09151.15 DUF1936 25 25 34 domain Y Y N DUF1936 domain-containing protein 18021800 131567 cellular organisms no rank 9 EBI-EMBL Domain of unknown function (DUF1936) Domain of unknown function (DUF1936) This domain is found in a set of hypothetical Archaeal proteins. Its exact function has not, as yet, been defined. It possesses a zinc ribbon fold. [1]. 18021800. Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain. Proudfoot M, Sanders SA, Singer A, Zhang R, Brown G, Binkowski A, Xu L, Lukin JA, Murzin AG, Joachimiak A, Arrowsmith CH, Edwards AM, Savchenko AV, Yakunin AF;. J Mol Biol. 2008;375:301-315. (from Pfam) NF020716.5 PF09153.15 MGMT_N 22.1 22.1 90 PfamAutoEq Y Y N protein O6-alkylguanine-DNA alkyltransferase domain-containing protein GO:0005737 10497033 131567 cellular organisms no rank 97 EBI-EMBL Methylated DNA-protein cysteine methyltransferase, N-terminal Methylated DNA-protein cysteine methyltransferase, N-terminal This domain is found in the archaeal protein O6-alkylguanine-DNA alkyltransferase (also known as Methylated DNA-protein cysteine methyltransferase MGMT), adopt a secondary structure consisting of a three stranded antiparallel beta-sheet and three alpha helices. This entry represents the N-terminal ribonuclease H-like domain, associated with 6-O-methylguanine DNA methyltransferase activity. The exact function has not, as yet, been defined, though it has been postulated that they confer thermostability to the archaeal protein [1]. [1]. 10497033. Hyperthermostable protein structure maintained by intra and inter-helix ion-pairs in archaeal O6-methylguanine-DNA methyltransferase. Hashimoto H, Inoue T, Nishioka M, Fujiwara S, Takagi M, Imanaka T, Kai Y;. J Mol Biol. 1999;292:707-716. (from Pfam) NF020717.5 PF09154.15 Alpha-amy_C_pro 21 21 57 PfamAutoEq Y Y N alpha-amylase domain-containing protein GO:0004553 12482867 131567 cellular organisms no rank 7954 EBI-EMBL Alpha-amylase C-terminal Alpha-amylase C-terminal This entry represents a C-terminal domain associated with prokaryotic alpha-amylases, which adopt a secondary structure consisting of an eight-stranded antiparallel beta-sheet containing a Greek key motif. Their exact function has not, as yet, been determined [1]. [1]. 12482867. Differential regulation of a hyperthermophilic alpha-amylase with a novel (Ca,Zn) two-metal center by zinc. Linden A, Mayans O, Meyer-Klaucke W, Antranikian G, Wilmanns M;. J Biol Chem. 2003;278:9875-9884. (from Pfam) NF020733.5 PF09171.15 AGOG 26.1 26.1 248 domain Y Y N N-glycosylase/DNA lyase GO:0003906,GO:0016799 15604455,15642264 131567 cellular organisms no rank 271 EBI-EMBL N-glycosylase/DNA lyase N-glycosylase/DNA lyase This domain is predominantly found in the Archaeal protein N-glycosylase/DNA lyase. [1]. 15604455. Pa-AGOG, the founding member of a new family of archaeal 8-oxoguanine DNA-glycosylases. Sartori AA, Lingaraju GM, Hunziker P, Winkler FK, Jiricny J;. Nucleic Acids Res. 2004;32:6531-6539. [2]. 15642264. A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure. Lingaraju GM, Sartori AA, Kostrewa D, Prota AE, Jiricny J, Winkler FK;. Structure. 2005;13:87-98. (from Pfam) NF020735.5 PF09173.16 eIF2_C 22 22 86 PfamEq Y N N Initiation factor eIF2 gamma, C terminal 11927566 131567 cellular organisms no rank 1310 EBI-EMBL Initiation factor eIF2 gamma, C terminal Initiation factor eIF2 gamma, C terminal Members of this family, which are found in the initiation factors eIF2 and EF-Tu, adopt a structure consisting of a beta barrel with Greek key topology. They are required for formation of the ternary complex with GTP and initiator tRNA [1]. [1]. 11927566. The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors. Schmitt E, Blanquet S, Mechulam Y;. EMBO J. 2002;21:1821-1832. (from Pfam) NF020738.5 PF09176.16 Mpt_N 27 27 81 domain Y Y N methylene-tetrahydromethanopterin dehydrogenase N-terminal domain-containing protein 12176390 131567 cellular organisms no rank 2239 EBI-EMBL Methylene-tetrahydromethanopterin dehydrogenase, N-terminal Methylene-tetrahydromethanopterin dehydrogenase, N-terminal Members of this family adopt a alpha-beta structure, with a core comprising three alpha/beta/alpha layers, in which each sheet contains four strands. They are predominantly found in prokaryotic methylene-tetrahydromethanopterin dehydrogenase, which catalyses the dehydrogenation of methylene-tetrahydromethanopterin and the reversible dehydrogenation of methylene-H(4)F [1]. [1]. 12176390. Structure of methylene-tetrahydromethanopterin dehydrogenase from methylobacterium extorquens AM1. Ermler U, Hagemeier CH, Roth A, Demmer U, Grabarse W, Warkentin E, Vorholt JA;. Structure. 2002;10:1127-1137. (from Pfam) NF020742.5 PF09180.16 ProRS-C_1 31.5 31.5 71 PfamEq Y N N Prolyl-tRNA synthetase, C-terminal GO:0000166,GO:0004827,GO:0005524,GO:0005737,GO:0006433 12578991 131567 cellular organisms no rank 15801 EBI-EMBL Prolyl-tRNA synthetase, C-terminal Prolyl-tRNA synthetase, C-terminal Members of this family are predominantly found in prokaryotic prolyl-tRNA synthetase. They contain a zinc binding site, and adopt a structure consisting of alpha helices and antiparallel beta sheets arranged in 2 layers, in a beta-alpha-beta-alpha-beta motif [1]. [1]. 12578991. The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases. Kamtekar S, Kennedy WD, Wang J, Stathopoulos C, Soll D, Steitz TA;. Proc Natl Acad Sci U S A. 2003;100:1673-1678. (from Pfam) NF020745.5 PF09183.15 DUF1947 22.5 22.5 65 PfamAutoEq Y Y N DUF1947 domain-containing protein 131567 cellular organisms no rank 509 EBI-EMBL Domain of unknown function (DUF1947) Domain of unknown function (DUF1947) Members of this family are found in a set of hypothetical Archaeal proteins. Their exact function has not, as yet, been defined. (from Pfam) NF020748.5 PF09186.16 DUF1949 23.7 23.7 56 PfamAutoEq Y Y N DUF1949 domain-containing protein 15103642 131567 cellular organisms no rank 40078 EBI-EMBL Domain of unknown function (DUF1949) Domain of unknown function (DUF1949) Members of this family pertain to a set of functionally uncharacterised hypothetical bacterial proteins. They adopt a ferredoxin-like fold, with a beta-alpha-beta-beta-alpha-beta arrangement [1]. [1]. 15103642. Crystal structure of YIGZ, a conserved hypothetical protein from Escherichia coli k12 with a novel fold. Park F, Gajiwala K, Eroshkina G, Furlong E, He D, Batiyenko Y, Romero R, Christopher J, Badger J, Hendle J, Lin J, Peat T, Buchanan S;. Proteins. 2004;55:775-777. (from Pfam) NF020751.5 PF09189.15 DUF1952 22 22 73 PfamAutoEq Y Y N DUF1952 domain-containing protein 131567 cellular organisms no rank 74 EBI-EMBL Domain of unknown function (DUF1952) Domain of unknown function (DUF1952) Members of this family are found in various Thermus thermophilus proteins. Their exact function has not, as yet, been determined. (from Pfam) NF020752.5 PF09190.16 DALR_2 22 22 63 domain Y Y N DALR domain-containing protein GO:0000166,GO:0004817,GO:0005524,GO:0005737,GO:0006423 10447505 131567 cellular organisms no rank 72661 EBI-EMBL DALR domain DALR domain This DALR domain is found in cysteinyl-tRNA-synthetases [1]. [1]. 10447505. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Wolf YI, Aravind L, Grishin NV, Koonin EV;. Genome Res 1999;9:689-710. (from Pfam) NF020756.5 PF09194.15 Endonuc-BsobI 25 25 313 PfamEq Y Y N AvaI/BsoBI family type II restriction endonuclease GO:0003677,GO:0009036,GO:0009307 11250198,22638584 131567 cellular organisms no rank 313 EBI-EMBL Restriction endonuclease BsobI AvaI/BsoBI family type II restriction endonuclease Members of this family of prokaryotic restriction endonucleases recognise the double-stranded sequence CYCGRG (where Y = T/C, and R = A/G) and cleave after C-1. They catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates [1]. [1]. 11250198. Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis. van der Woerd MJ, Pelletier JJ, Xu S, Friedman AM;. Structure. 2001;9:133-144. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF020757.5 PF09195.16 Endonuc-BglII 26 26 163 subfamily Y Y N BglII/BstYI family type II restriction endonuclease GO:0009036,GO:0009307 10655616 131567 cellular organisms no rank 2030 EBI-EMBL Restriction endonuclease BglII BglII/BstYI family type II restriction endonuclease Members of this family are predominantly found in prokaryotic restriction endonuclease BglII, and adopt a structure consisting of an alpha/beta core containing a six-stranded beta-sheet surrounded by five alpha-helices, two of which are involved in homodimerisation of the endonuclease. They recognise the double-stranded DNA sequence AGATCT and cleave after A-1, resulting in specific double-stranded fragments with terminal 5'-phosphates [1]. [1]. 10655616. Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution. Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK;. Nat Struct Biol. 2000;7:134-140. (from Pfam) NF020764.5 PF09202.16 Rio2_N 27 27 82 PfamEq Y N N Rio2, N-terminal GO:0004674,GO:0005524,GO:0006468 15341724 131567 cellular organisms no rank 1085 EBI-EMBL Rio2, N-terminal Rio2, N-terminal Members of this family are found in Rio2, and are structurally homologous to the winged helix (wHTH) domain. They adopt a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains [1]. [1]. 15341724. Crystal structure of A. fulgidus Rio2 defines a new family of serine protein kinases. LaRonde-LeBlanc N, Wlodawer A;. Structure. 2004;12:1585-1594. (from Pfam) NF020766.5 PF09204.15 Colicin_immun 22 22 88 domain Y Y N colicin immunity domain-containing protein GO:0015643,GO:0030153 11741540,15014439 131567 cellular organisms no rank 1747 EBI-EMBL Bacterial self-protective colicin-like immunity Bacterial self-protective colicin-like immunity Colicin D, which is synthesised by various prokaryotes, adopts an antiparallel four helical bundle fold: the helices are tightly packed, forming a compact cylindrical molecule. The protein specifically cleaves the anticodon loop of all four tRNA-Arg isoacceptors, thereby inactivating prokaryotic protein synthesis and leading to cell death [1]. This family also contains immunity proteins to klebicins and microcins. Many bacteria produce proteins that destroy their competitors. Colicin D is one such. The immunity proteins are expressed on the same operon as their cognate bacteriocins and protect the expressing bacterium from the effects of its own bacteriocin [2]. [1]. 15014439. Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein. Graille M, Mora L, Buckingham RH, van Tilbeurgh H, de Zamaroczy M;. EMBO J. 2004;23:1474-1482. [2]. 11741540. Crystal structure of colicin E3: implications for cell entry and ribosome inactivation. Soelaiman S, Jakes K, Wu N, Li C, Shoham M;. Mol Cell. 2001;8:1053-1062. (from Pfam) NF020767.5 PF09205.15 DUF1955 26.4 26.4 159 PfamAutoEq Y Y N DUF1955 domain-containing protein 131567 cellular organisms no rank 46 EBI-EMBL Domain of unknown function (DUF1955) Domain of unknown function (DUF1955) Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus. Their exact function has not, as yet, been determined. (from Pfam) NF020772.5 PF09210.16 BE_C 25 25 101 PfamAutoEq Y Y N 1,4-alpha-glucan branching protein domain-containing protein 21097495,21104698 131567 cellular organisms no rank 5946 EBI-EMBL 1,4-alpha-glucan branching enzyme, C-terminal 1,4-alpha-glucan branching enzyme, C-terminal This entry represents the C-terminal domain found in bacterial 1,4-alpha-glucan branching enzymes, such as TTHA1902 from Thermus thermophilus and TK1436 from Thermococcus kodakarensis, which belong to the glycoside hydrolase family 57 (GH57). These enzymes catalyse the formation of branch points in alpha-glucans by cleavage of an alpha-1,4 glycosidic bond and subsequent transfer of the cleaved-off oligosaccharide to a new alpha-1,6 position. This is an alpha-helical domain composed of a four alpha-helical bundle. It plays a role in the formation of the active-site cleft, being essential for substrate binding and catalysis [1,2]. [1]. 21097495. Thermus thermophilus glycoside hydrolase family 57 branching enzyme: crystal structure, mechanism of action, and products formed. Palomo M, Pijning T, Booiman T, Dobruchowska JM, van der Vlist J, Kralj S, Planas A, Loos K, Kamerling JP, Dijkstra BW, van der Maarel MJ, Dijkhuizen L, Leemhuis H;. J Biol Chem. 2011;286:3520-3530. [2]. 21104698. Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Santos CR, Tonoli CC, Trindade DM, Betzel C, Takata H, Kuriki T, Kanai T, Imanaka T, Arni RK, Murakami MT;. Proteins. 2011;79:547-557. (from Pfam) NF020780.5 PF09218.15 DUF1959 24.3 24.3 116 PfamAutoEq Y Y N DUF1959 family protein 131567 cellular organisms no rank 264 EBI-EMBL Domain of unknown function (DUF1959) DUF1959 family protein This domain is found in a set of uncharacterised Archaeal hypothetical proteins. Its function has not, as yet, been described. (from Pfam) NF020785.5 PF09224.17 DUF1961 25 25 214 PfamAutoEq Y Y N DUF1961 family protein 131567 cellular organisms no rank 1767 EBI-EMBL Domain of unknown function (DUF1961) DUF1961 family protein Members of this family are found in a set of hypothetical bacterial proteins. Their exact function has not, as yet, been determined. (from Pfam) NF020794.5 PF09233.16 Endonuc-EcoRV 25 25 244 PfamEq Y Y N type II restriction endonuclease 15170321,22638584 131567 cellular organisms no rank 839 EBI-EMBL Restriction endonuclease EcoRV type II restriction endonuclease Members of this family of prokaryotic restriction endonucleases recognise the double-stranded sequence 5'-GATATC-3' and cleave after T-3. They catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates [1]. [1]. 15170321. DNA cleavage by EcoRV endonuclease: two metal ions in three metal ion binding sites. Horton NC, Perona JJ;. Biochemistry. 2004;43:6841-6857. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF020800.5 PF09239.16 Topo-VIb_trans 24 24 159 PfamEq Y N N Topoisomerase VI B subunit, transducer GO:0003677,GO:0003918,GO:0006265 12505993 131567 cellular organisms no rank 1568 EBI-EMBL Topoisomerase VI B subunit, transducer Topoisomerase VI B subunit, transducer Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme [1]. [1]. 12505993. Structure of the topoisomerase VI-B subunit: implications for type II topoisomerase mechanism and evolution. Corbett KD, Berger JM;. EMBO J. 2003;22:151-163. (from Pfam) NF020804.5 PF09243.15 Rsm22 23 23 275 domain Y Y N small ribosomal subunit Rsm22 family protein GO:0006412,GO:0008168 16835444 131567 cellular organisms no rank 12041 EBI-EMBL Mitochondrial small ribosomal subunit Rsm22 small ribosomal subunit Rsm22 family protein Rsm22 has been identified as a mitochondrial small ribosomal subunit [1] and is a methyltransferase. In Schizosaccharomyces pombe, Rsm22 is tandemly fused to Cox11 (a factor required for copper insertion into cytochrome oxidase) and the two proteins are proteolytically cleaved after import into the mitochondria [1]. [1]. 16835444. Sequential processing of a mitochondrial tandem protein: insights into protein import in Schizosaccharomyces pombe. Khalimonchuk O, Ott M, Funes S, Ostermann K, Rodel G, Herrmann JM;. Eukaryot Cell. 2006;5:997-1006. (from Pfam) NF020810.5 PF09249.16 tRNA_NucTransf2 27 27 113 domain Y N N tRNA nucleotidyltransferase, second domain GO:0004810 14636575 131567 cellular organisms no rank 1594 EBI-EMBL tRNA nucleotidyltransferase, second domain tRNA nucleotidyltransferase, second domain Members of this family adopt a structure consisting of a five helical bundle core. They are predominantly found in Archaeal tRNA nucleotidyltransferase, following the catalytic nucleotidyltransferase domain [1]. [1]. 14636575. Crystal structures of an archaeal class I CCA-adding enzyme and its nucleotide complexes. Xiong Y, Li F, Wang J, Weiner AM, Steitz TA;. Mol Cell. 2003;12:1165-1172. (from Pfam) NF020811.5 PF09250.16 Prim-Pol 22.8 22.8 158 domain Y Y N bifunctional DNA primase/polymerase 14730355 131567 cellular organisms no rank 62733 EBI-EMBL Bifunctional DNA primase/polymerase, N-terminal bifunctional DNA primase/polymerase Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities [1]. [1]. 14730355. Structure of a bifunctional DNA primase-polymerase. Lipps G, Weinzierl AO, von Scheven G, Buchen C, Cramer P;. Nat Struct Mol Biol. 2004;11:157-162. (from Pfam) NF020815.5 PF09254.16 FokI_cleav_dom 25 25 188 domain Y Y N restriction endonuclease FokI C-terminal domain-containing protein GO:0003677,GO:0009036,GO:0009307 22638584,9724743 131567 cellular organisms no rank 615 EBI-EMBL FokI, cleavage domain FokI, cleavage domain Members of this family are predominantly found in prokaryotic restriction endonuclease FokI, and adopt a structure consisting of an alpha/beta/alpha core containing a five-stranded beta-sheet. They recognise the double-stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand [1]. This entry represents the C-terminal cleavage domain of FokI. [1]. 9724743. Structure of FokI has implications for DNA cleavage. Wah DA, Bitinaite J, Schildkraut I, Aggarwal AK;. Proc Natl Acad Sci U S A. 1998;95:10564-10569. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF020819.5 PF09258.15 Glyco_transf_64 21.3 21.3 245 PfamEq Y N N Glycosyl transferase family 64 domain GO:0016020,GO:0016757 12562774 131567 cellular organisms no rank 369 EBI-EMBL Glycosyl transferase family 64 domain Glycosyl transferase family 64 domain Members of this family catalyse the transfer reaction of N-acetylglucosamine and N-acetylgalactosamine from the respective UDP-sugars to the non-reducing end of [glucuronic acid]beta 1-3[galactose]beta 1-O-naphthalenemethanol, an acceptor substrate analog of the natural common linker of various glycosylaminoglycans. They are also required for the biosynthesis of heparan-sulphate [1]. [1]. 12562774. Crystal structure of an alpha 1,4-N-acetylhexosaminyltransferase (EXTL2), a member of the exostosin gene family involved in heparan sulfate biosynthesis. Pedersen LC, Dong J, Taniguchi F, Kitagawa H, Krahn JM, Pedersen LG, Sugahara K, Negishi M;. J Biol Chem. 2003;278:14420-14428. (from Pfam) NF020822.5 PF09261.16 Alpha-mann_mid 31.1 31.1 96 domain Y N N Alpha mannosidase middle domain GO:0004559,GO:0006013 12634058 131567 cellular organisms no rank 48425 EBI-EMBL Alpha mannosidase middle domain Alpha mannosidase middle domain Members of this family adopt a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. They are predominantly found in the enzyme alpha-mannosidase [1]. [1]. 12634058. The structure of bovine lysosomal alpha-mannosidase suggests a novel mechanism for low-pH activation. Heikinheimo P, Helland R, Leiros HK, Leiros I, Karlsen S, Evjen G, Ravelli R, Schoehn G, Ruigrok R, Tollersrud OK, McSweeney S, Hough E;. J Mol Biol. 2003;327:631-644. (from Pfam) NF020835.5 PF09274.15 ParG 21.4 21.4 76 subfamily Y Y N plasmid partition protein ParG 14622405 131567 cellular organisms no rank 1391 EBI-EMBL ParG plasmid partition protein ParG Members of this family of plasmid partition proteins adopt a ribbon-helix-helix fold, with a core of four alpha-helices. They are an essential component of the DNA partition complex of the multidrug resistance plasmid TP228 [1]. [1]. 14622405. ParG, a protein required for active partition of bacterial plasmids, has a dimeric ribbon-helix-helix structure. Golovanov AP, Barilla D, Golovanova M, Hayes F, Lian LY;. Mol Microbiol. 2003;50:1141-1153. (from Pfam) NF020845.5 PF09285.16 Elong-fact-P_C 25 25 56 domain Y N N Elongation factor P, C-terminal GO:0005737,GO:0043043 15210970 131567 cellular organisms no rank 41346 EBI-EMBL Elongation factor P, C-terminal Elongation factor P, C-terminal Members of this family of nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology [1]. [1]. 15210970. Crystal structure of elongation factor P from Thermus thermophilus HB8. Hanawa-Suetsugu K, Sekine S, Sakai H, Hori-Takemoto C, Terada T, Unzai S, Tame JR, Kuramitsu S, Shirouzu M, Yokoyama S;. Proc Natl Acad Sci U S A. 2004;101:9595-9600. (from Pfam) NF020846.5 PF09286.16 Pro-kuma_activ 23.5 23.5 143 domain Y Y N protease pro-enzyme activation domain-containing protein GO:0008236 15242607 131567 cellular organisms no rank 15392 EBI-EMBL Pro-kumamolisin, activation domain kumamolisin-like protease pro-enzyme activation domain Members of this family are found in various subtilase propeptides, and adopt a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptide [1]. [1]. 15242607. 1.2 A crystal structure of the serine carboxyl proteinase pro-kumamolisin; structure of an intact pro-subtilase. Comellas-Bigler M, Maskos K, Huber R, Oyama H, Oda K, Bode W;. Structure. 2004;12:1313-1323. (from Pfam) NF020850.5 PF09290.16 AcetDehyd-dimer 26.6 26.6 138 domain Y N N Prokaryotic acetaldehyde dehydrogenase, dimerisation GO:0008774,GO:0009056 12764229 131567 cellular organisms no rank 19686 EBI-EMBL Prokaryotic acetaldehyde dehydrogenase, dimerisation Prokaryotic acetaldehyde dehydrogenase, dimerisation Members of this family are found in prokaryotic acetaldehyde dehydrogenase (acylating), and adopt a structure consisting of an alpha-beta-alpha-beta(3) core. They mediate dimerisation of the protein [1]. [1]. 12764229. Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate. Manjasetty BA, Powlowski J, Vrielink A;. Proc Natl Acad Sci U S A 2003;100:6992-6997. (from Pfam) NF020855.5 PF09295.15 ChAPs 20 20 395 domain Y N N ChAPs (Chs5p-Arf1p-binding proteins) 16498409 131567 cellular organisms no rank 4712 EBI-EMBL ChAPs (Chs5p-Arf1p-binding proteins) ChAPs (Chs5p-Arf1p-binding proteins) ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi. They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they form also interactions with each other [1]. [1]. 16498409. Arf1p, Chs5p and the ChAPs are required for export of specialized cargo from the Golgi. Trautwein M, Schindler C, Gauss R, Dengjel J, Hartmann E, Spang A;. EMBO J. 2006;25:943-954. (from Pfam) NF020856.5 PF09296.16 NUDIX-like 22 22 96 domain Y Y N NUDIX-like domain-containing protein GO:0016787 131567 cellular organisms no rank 25568 EBI-EMBL NADH pyrophosphatase-like rudimentary NUDIX domain NADH pyrophosphatase-like rudimentary NUDIX domain The N-terminal domain in NADH pyrophosphatase, which has a rudiment Nudix fold according to SCOP. (from Pfam) NF020857.5 PF09297.16 zf-NADH-PPase 24.8 24.8 32 domain Y Y N NADH pyrophosphatase zinc ribbon domain-containing protein GO:0016787,GO:0046872 131567 cellular organisms no rank 37837 EBI-EMBL NADH pyrophosphatase zinc ribbon domain NADH pyrophosphatase zinc ribbon domain This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure. (from Pfam) NF020859.5 PF09299.16 Mu-transpos_C 21 21 61 domain Y Y N Mu transposase C-terminal domain-containing protein 7628012 131567 cellular organisms no rank 35323 EBI-EMBL Mu transposase, C-terminal Mu transposase, C-terminal Members of this family are found in various prokaryotic integrases and transposases. They adopt a beta-barrel structure with Greek-key topology [1]. [1]. 7628012. Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration. Rice P, Mizuuchi K;. Cell. 1995;82:209-220. (from Pfam) NF020874.5 PF09314.16 DUF1972 25 25 186 domain Y Y N DUF1972 domain-containing protein 131567 cellular organisms no rank 12755 EBI-EMBL Domain of unknown function (DUF1972) Domain of unknown function (DUF1972) Members of this family of functionally uncharacterised domains are found in bacterial glycosyltransferases and rhamnosyltransferases. (from Pfam) NF020892.5 PF09334.16 tRNA-synt_1g 20.1 20.1 391 domain Y Y N class I tRNA ligase family protein GO:0000166,GO:0004812,GO:0005524,GO:0006418 131567 cellular organisms no rank 467068 EBI-EMBL tRNA synthetases class I (M) class I tRNA ligase family protein This family includes methionyl tRNA synthetases. (from Pfam) NF020893.5 PF09335.16 VTT_dom 33.9 33.9 123 domain Y Y N VTT domain-containing protein 16107716,17178117,30093494 131567 cellular organisms no rank 246562 EBI-EMBL VTT domain VTT domain This is the VTT (VMP1, TMEM41, and TVP38) domain found in sequences from all cellular organisms, including Golgi apparatus membrane protein TVP38 from Saccharomyces cerevisiae, which is involved in vesicular trafficking and spindle migration [1,2]. This domain was previously called SNARE-associated domain but was renamed as there is no evidence that it associates with SNARE proteins [3]. [1]. 16107716. Immunoisolaton of the yeast Golgi subcompartments and characterization of a novel membrane protein, Svp26, discovered in the Sed5-containing compartments. Inadome H, Noda Y, Adachi H, Yoda K;. Mol Cell Biol. 2005;25:7696-7710. [2]. 17178117. Tvp38, Tvp23, Tvp18 and Tvp15: novel membrane proteins in the Tlg2-containing Golgi/endosome compartments of Saccharomyces cerevisiae. Inadome H, Noda Y, Kamimura Y, Adachi H, Yoda K;. Exp Cell Res. 2007;313:688-697. [3]. 30093494. Genome-wide CRISPR screen identifies TMEM41B as a gene required for autophagosome formation. Morita K, Hama Y, Izume T, Tamura N, Ueno T, Yamashita Y, Sakamaki Y, Mimura K, Morishita H, Shihoya W, Nureki O, Mano H, Mizushima N;. J Cell Biol. 2018;217:3817-3828. (from Pfam) NF020894.5 PF09336.15 Vps4_C 21.3 21.3 61 domain Y N N Vps4 C terminal oligomerisation domain 16704411 131567 cellular organisms no rank 528 EBI-EMBL Vps4 C terminal oligomerisation domain Vps4 C terminal oligomerisation domain This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation [1]. [1]. 16704411. The beta domain is required for Vps4p oligomerization into a functionally active ATPase. Vajjhala PR, Wong JS, To HY, Munn AL;. FEBS J. 2006;273:2357-2373. (from Pfam) NF020897.5 PF09339.15 HTH_IclR 22 22 52 domain Y Y N helix-turn-helix domain-containing protein GO:0003677,GO:0006355 131567 cellular organisms no rank 620118 EBI-EMBL IclR helix-turn-helix domain helix-turn-helix domain-containing protein NF020899.5 PF09341.15 Pcc1 20.9 20.9 75 PfamEq Y Y N KEOPS complex subunit Pcc1 16874308 131567 cellular organisms no rank 1574 EBI-EMBL Transcription factor Pcc1 KEOPS complex subunit Pcc1 Pcc1 is a transcription factor that functions in regulating genes involved in cell cycle progression and polarised growth [1]. [1]. 16874308. Yeast homolog of a cancer-testis antigen defines a new transcription complex. Kisseleva-Romanova E, Lopreiato R, Baudin-Baillieu A, Rousselle JC, Ilan L, Hofmann K, Namane A, Mann C, Libri D;. EMBO J. 2006;25:3576-3585. (from Pfam) NF020901.5 PF09343.15 DUF2460 30.4 30.4 205 domain Y Y N DUF2460 domain-containing protein 131567 cellular organisms no rank 7267 EBI-EMBL Conserved hypothetical protein 2217 (DUF2460) Conserved hypothetical protein 2217 (DUF2460) This model represents a family of conserved hypothetical proteins. It is usually (but not always) found in apparent phage-derived regions of bacterial chromosomes. (from Pfam) NF020902.5 PF09344.15 Cas_CT1975 26 26 361 PfamEq Y Y N type I-E CRISPR-associated protein Cas7/Cse4/CasC 131567 cellular organisms no rank 12233 EBI-EMBL CT1975-like protein type I-E CRISPR-associated protein Cas7/Cse4/CasC CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family is represented by CT1975 of Chlorobium tepidum. (from Pfam) NF020904.5 PF09346.15 SMI1_KNR4 25.4 25.4 125 domain Y Y N SMI1/KNR4 family protein 21306995,7937796,8289782 131567 cellular organisms no rank 98956 EBI-EMBL SMI1 / KNR4 family (SUKH-1) SMI1/KNR4 family protein Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation [1][2]. Genome contextual information showed that SMI1 are primary immunity proteins in bacterial toxin systems [3]. [1]. 7937796. Cloning and characterization of a Neurospora crassa gene required for (1,3) beta-glucan synthase activity and cell wall formation. Enderlin CS, Selitrennikoff CP;. Proc Natl Acad Sci U S A. 1994;91:9500-9504. [2]. 8289782. Cloning and characterization of KNR4, a yeast gene involved in (1,3)-beta-glucan synthesis. Hong Z, Mann P, Brown NH, Tran LE, Shaw KJ, Hare RS, DiDomenico B;. Mol Cell Biol. 1994;14:1017-1025. [3]. 21306995. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Zhang D, Iyer LM, Aravind L;. Nucleic Acids Res. 2011;39:4532-4552. (from Pfam) NF020905.5 PF09347.15 DUF1989 27 27 168 domain Y Y N DUF1989 domain-containing protein 131567 cellular organisms no rank 36165 EBI-EMBL Domain of unknown function (DUF1989) Domain of unknown function (DUF1989) This family of proteins are functionally uncharacterised. (from Pfam) NF020907.5 PF09349.15 OHCU_decarbox 24 24 155 domain Y Y N 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase 16462750 131567 cellular organisms no rank 38964 EBI-EMBL OHCU decarboxylase 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase The proteins in this family are OHCU decarboxylase - enzymes of the purine catabolism that catalyse the conversion of OHCU into S(+)-allantoin [1]. This is the third step of the conversion of uric acid (a purine derivative) to allantoin. Step one is catalysed by urate oxidase (Pfam:PF01014) and step two is catalysed by HIUases (Pfam:PF00576). [1]. 16462750. Completing the uric acid degradation pathway through phylogenetic comparison of whole genomes. Ramazzina I, Folli C, Secchi A, Berni R, Percudani R;. Nat Chem Biol. 2006;2:144-148. (from Pfam) NF020912.5 PF09355.15 Phage_Gp19 22 22 116 subfamily Y Y N Gp19/Gp15/Gp42 family protein 9636706 131567 cellular organisms no rank 1907 EBI-EMBL Phage protein Gp19/Gp15/Gp42 Gp19/Gp15/Gp42 family protein This family of proteins are functionally uncharacterised. They are found in a variety of bacteriophage. [1]. 9636706. Genome structure of mycobacteriophage D29: implications for phage evolution. Ford ME, Sarkis GJ, Belanger AE, Hendrix RW, Hatfull GF;. J Mol Biol. 1998;279:143-164. (from Pfam) NF020916.5 PF09359.15 VTC 23 23 235 domain Y Y N VTC domain-containing protein 11823419 131567 cellular organisms no rank 13985 EBI-EMBL VTC domain VTC domain This presumed domain is found in the yeast vacuolar transport chaperone proteins VTC2, VTC3 and VTC4. This domain is also found in a variety of bacterial proteins. [1]. 11823419. The Vtc proteins in vacuole fusion: coupling NSF activity to V(0) trans-complex formation. Muller O, Bayer MJ, Peters C, Andersen JS, Mann M, Mayer A;. EMBO J. 2002;21:259-269. (from Pfam) NF020917.5 PF09360.15 zf-CDGSH 29.5 29.5 48 domain Y Y N CDGSH iron-sulfur domain-containing protein GO:0043231,GO:0051537 17376863,17584744,17766440 131567 cellular organisms no rank 21961 EBI-EMBL Iron-binding zinc finger CDGSH type Iron-binding zinc finger CDGSH type The CDGSH-type zinc finger domain binds iron rather than zinc as a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family [1]. The domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, MitoNEET_N, Pfam:PF10660 [2]. The domain forms a uniquely folded homo-dimer and spans the outer mitochondrial membrane, orienting the iron-binding residues towards the cytoplasm [3]. [1]. 17376863. MitoNEET is an iron-containing outer mitochondrial membrane protein that regulates oxidative capacity. Wiley SE, Murphy AN, Ross SA, van der Geer P, Dixon JE;. Proc Natl Acad Sci U S A. 2007;104:5318-5323. [2]. 17584744. The outer mitochondrial membrane protein mitoNEET contains a novel redox-active 2Fe-2S cluster. Wiley SE, Paddock ML, Abresch EC, Gross L, van der Geer P, Nechushtai R, Murphy AN, Jennings PA, Dixon JE;. J Biol Chem. 2007;282:23745-23749. [3]. 17766440. MitoNEET is a uniquely folded 2Fe 2S outer mitochondrial membrane protein stabilized by pioglitazone. Paddock ML, Wiley SE, Axelrod HL, Cohen AE, Roy M, Abresch EC, Capraro D, Murphy AN, Nechushtai R, Dixon JE, Jennings PA;. Proc Natl Acad Sci U S A. 2007;104:14342-14347. (from Pfam) NF020919.5 PF09362.15 DUF1996 27 27 237 domain Y Y N DUF1996 domain-containing protein 131567 cellular organisms no rank 20637 EBI-EMBL Domain of unknown function (DUF1996) Domain of unknown function (DUF1996) This family of proteins are functionally uncharacterised. (from Pfam) NF020921.5 PF09364.15 XFP_N 23.7 23.7 364 domain Y N N XFP N-terminal domain 11292814 131567 cellular organisms no rank 35267 EBI-EMBL XFP N-terminal domain XFP N-terminal domain Bacterial enzyme splits fructose-6-P and/or xylulose-5-P with the aid of inorganic phosphate into either acetyl-P and erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P EC:4.1.2.9, EC:4.1.2.22 [1]. This family is distantly related to transketolases e.g. Pfam:PF02779. [1]. 11292814. Characterization of the D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase gene (xfp) from Bifidobacterium lactis. Meile L, Rohr LM, Geissmann TA, Herensperger M, Teuber M;. J Bacteriol 2001;183:2929-2936. (from Pfam) NF020926.5 PF09369.15 MZB 24.2 24.2 80 domain Y Y N Zn-binding domain-containing protein 33300032 131567 cellular organisms no rank 48448 EBI-EMBL MrfA Zn-binding domain MrfA Zn-binding domain This is the C-terminal MrfA Zn+2-binding domain (MZB, also referred to as DUF1998) which contains a conserved four-cysteine signature motif. These four Cys reside in a short coil between two alpha-helices and form a metal ion-binding site [1]. This domain is frequently found at the C-terminal of ndNTPases, however, it is also found encoded in a standalone gene, downstream of putative helicase domain-encoding genes associated with bacterial anti-phage defense system DISARM. MrfA (Mitomycin repair factor A, also known as YprA in Bacillus subtilis) is a DNA helicase that supports repair of mitomycin C-induced DNA damage. MrfA homologues are widely distributed in bacteria and are also present in archaea, fungi and plants. The MrfA-homologue in yeast, Hrq1, also reduces mitomycin C sensitivity. Hrq1 has high similarity to human RecQ4 and was therefore assigned to the RecQ-like helicase family. MrfA homologues appear to be missing in Enterobacteria, however, certain pathogenic Escherichia coli and Salmonella strains harbour Z5898-like helicases with this domain [1]. [1]. 33300032. A skipping rope translocation mechanism in a widespread family of DNA repair helicases. Roske JJ, Liu S, Loll B, Neu U, Wahl MC;. Nucleic Acids Res. 2021;49:504-518. (from Pfam) NF020927.5 PF09370.15 PEP_hydrolase 33.8 33.8 267 domain Y Y N phosphoenolpyruvate hydrolase family protein 131567 cellular organisms no rank 7501 EBI-EMBL Phosphoenolpyruvate hydrolase-like phosphoenolpyruvate hydrolase family protein This domain has a TIM barrel fold related to IGPS and to phosphoenolpyruvate mutase/aldolase/carboxylase. (from Pfam) NF020928.5 PF09371.15 Tex_N 32 32 75 domain Y Y N Tex-like N-terminal domain-containing protein 18321528,8755871 131567 cellular organisms no rank 77107 EBI-EMBL Tex-like protein N-terminal domain Tex-like protein N-terminal domain This domain is found at the N-terminus of Tex protein Swiss:Q45388 and other related proteins. Tex protein defines a family of prokaryotic transcriptional accessory factors [1]. This domain is likely to be distantly related to PWI domain, an RNA/DNA binding domain. It is thought to be involved in ssDNA binding [2]. [1]. 8755871. A new gene locus of Bordetella pertussis defines a novel family of prokaryotic transcriptional accessory proteins. Fuchs TM, Deppisch H, Scarlato V, Gross R;. J Bacteriol. 1996;178:4445-4452. [2]. 18321528. Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa. Johnson SJ, Close D, Robinson H, Vallet-Gely I, Dove SL, Hill CP;. J Mol Biol. 2008;377:1460-1473. (from Pfam) NF020930.5 PF09373.15 PMBR 24.9 24.9 33 domain Y Y N pseudomurein-binding repeat-containing protein 21113291 131567 cellular organisms no rank 1191 EBI-EMBL Pseudomurein-binding repeat Pseudomurein-binding repeat Methanothermobacter thermautotrophicus is a methanogenic Gram-positive microorganism with a cell wall consisting of pseudomurein. This repeat specifically binds to pseudomurein. This repeat is found at the N terminus of PeiW and PeiP which are pseudomurein binding phage proteins. (from Pfam) NF020933.5 PF09376.15 NurA 21 21 254 domain Y Y N DNA double-strand break repair nuclease NurA 12052775,15466593 131567 cellular organisms no rank 4177 EBI-EMBL NurA domain NurA domain This family includes NurA a nuclease exhibiting both single-stranded endonuclease activity and 5'-3' exonuclease activity on single-stranded and double-stranded DNA from the hyperthermophilic archaeon Sulfolobus acidocaldarius [2]. [1]. 15466593. Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Iyer LM, Makarova KS, Koonin EV, Aravind L;. Nucleic Acids Res. 2004;32:5260-5279. [2]. 12052775. NurA, a novel 5'-3' nuclease gene linked to rad50 and mre11 homologs of thermophilic Archaea. Constantinesco F, Forterre P, Elie C;. EMBO Rep. 2002;3:537-542. (from Pfam) NF020935.5 PF09378.15 HAS-barrel 25.2 25.2 90 domain Y Y N HAS-barrel domain-containing protein 15466593 131567 cellular organisms no rank 2828 EBI-EMBL HAS barrel domain HAS barrel domain The HAS barrel is named after HerA-ATP Synthase. In ATP synthases, this domain is implicated in the assembly of the catalytic toroid and docking of accessory subunits, such as the subunit of the ATP synthase complex. Similar roles in docking of the functional partner, the NurA nuclease, and assembly of the HerA toroid complex appear likely for the HAS-barrel of the HerA family [1]. [1]. 15466593. Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Iyer LM, Makarova KS, Koonin EV, Aravind L;. Nucleic Acids Res. 2004;32:5260-5279. (from Pfam) NF020939.5 PF09382.15 RQC 23 23 114 domain Y Y N RQC domain-containing protein GO:0006260,GO:0006281,GO:0043138 16530788 131567 cellular organisms no rank 68223 EBI-EMBL RQC domain RQC domain The vast majority of proteins with this DNA-binding domain, called RQC, are RecQ itself, a DNA helicase involved in recombination, replication, and repair. But a few, including WP_003865531 and WP_016764356 represent distinct proteins families with different lengths and currently unknown functions. NF020940.5 PF09383.15 NIL 24 24 73 domain Y Y N NIL domain-containing protein 131567 cellular organisms no rank 63077 EBI-EMBL NIL domain NIL domain This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. (from Pfam) NF020946.5 PF09390.15 DUF1999 25 25 159 PfamAutoEq Y Y N DUF1999 family protein 131567 cellular organisms no rank 200 EBI-EMBL Protein of unknown function (DUF1999) DUF1999 family protein This family contains a putative Fe-S binding reductase (Swiss:Q72J89) whose structure adopts an alpha and beta fold. (from Pfam) NF020949.5 PF09393.15 DUF2001 27 27 139 subfamily Y Y N phage tail tube protein 23542344 131567 cellular organisms no rank 3872 EBI-EMBL Phage tail tube protein phage tail tube protein This is a family of phage tail tube proteins including protein XkdM from phage-like element PBSX protein (Swiss:P54332) whose structure adopts a beta barrel flanked with alpha helical regions. [1]. 23542344. A conserved spiral structure for highly diverged phage tail assembly chaperones. Pell LG, Cumby N, Clark TE, Tuite A, Battaile KP, Edwards AM, Chirgadze NY, Davidson AR, Maxwell KL;. J Mol Biol. 2013;425:2436-2449. (from Pfam) NF020950.5 PF09394.15 Inhibitor_I42 27.2 27.2 91 domain Y Y N protease inhibitor I42 family protein 11719560,17011790 131567 cellular organisms no rank 8329 EBI-EMBL Chagasin family peptidase inhibitor I42 protease inhibitor I42 family protein Chagasin is a cysteine peptidase inhibitor [1] which forms a beta barrel structure [2]. [1]. 11719560. Identification, characterization and localization of chagasin, a tight-binding cysteine protease inhibitor in Trypanosoma cruzi. Monteiro AC, Abrahamson M, Lima AP, Vannier-Santos MA, Scharfstein J;. J Cell Sci. 2001;114:3933-3942. [2]. 17011790. Crystal structure of chagasin, the endogenous cysteine-protease inhibitor from Trypanosoma cruzi. Figueiredo da Silva AA, Carvalho Vieira LD, Krieger MA, Goldenberg S, Tonin Zanchin NI, Guimaraes BG;. J Struct Biol. 2006; [Epub ahead of print] (from Pfam) NF020961.5 PF09406.15 DUF2004 22.6 22.6 122 domain Y Y N DUF2004 domain-containing protein 16374782 131567 cellular organisms no rank 21 EBI-EMBL Protein of unknown function (DUF2004) Protein of unknown function (DUF2004) This is a family of proteins with unknown function. The structure of one of the proteins in this family has revealed a novel alpha-beta fold [1]. [1]. 16374782. NMR structure of the conserved novel-fold protein TA0743 from Thermoplasma acidophilum. Kim B, Jung J, Hong E, Yee A, Arrowsmith CH, Lee W;. Proteins. 2006;62:819-821. (from Pfam) NF020962.5 PF09407.15 AbiEi_1 22.2 22.2 142 domain Y Y N type IV toxin-antitoxin system AbiEi family antitoxin 24465005 131567 cellular organisms no rank 3777 EBI-EMBL AbiEi antitoxin C-terminal domain AbiEi antitoxin C-terminal domain AbiEi_1 is the cognate antitoxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is Pfam:PF13338 [1]. [1]. 24465005. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Dy RL, Przybilski R, Semeijn K, Salmond GP, Fineran PC;. Nucleic Acids Res. 2014;42:4590-4605. (from Pfam) NF020965.5 PF09411.15 PagL 23 23 136 subfamily Y Y N acyloxyacyl hydrolase 16632613 131567 cellular organisms no rank 16949 EBI-EMBL Lipid A 3-O-deacylase (PagL) acyloxyacyl hydrolase PagL is an outer membrane protein with lipid A 3-O-deacylase activity. It forms an 8 stranded beta barrel structure [1]. [1]. 16632613. Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa. Rutten L, Geurtsen J, Lambert W, Smolenaers JJ, Bonvin AM, de Haan A, van der Ley P, Egmond MR, Gros P, Tommassen J;. Proc Natl Acad Sci U S A. 2006;103:7071-7076. (from Pfam) NF020968.5 PF09414.15 RNA_ligase 27 27 171 domain Y Y N RNA ligase family protein 17018278 131567 cellular organisms no rank 23843 EBI-EMBL RNA ligase RNA ligase family protein This is a family of RNA ligases. The enzyme repairs RNA strand breaks in nicked DNA:RNA and RNA:RNA but not in DNA:DNA duplexes. [1]. 17018278. RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward. Nandakumar J, Shuman S, Lima CD;. Cell. 2006;127:71-84. (from Pfam) NF020972.5 PF09419.15 PGP_phosphatase 20.4 20.4 168 PfamEq Y N N Mitochondrial PGP phosphatase GO:0008962 20485265 131567 cellular organisms no rank 11650 EBI-EMBL Mitochondrial PGP phosphatase Mitochondrial PGP phosphatase This is a family of proteins that acts as a mitochondrial phosphatase in cardiolipin biosynthesis. Cardiolipin is a unique dimeric phosphoglycerolipid predominantly present in mitochondrial membranes. The inverted phosphatase motif includes the highly conserved DKD triad [1]. [1]. 20485265. A mitochondrial phosphatase required for cardiolipin biosynthesis: the PGP phosphatase Gep4. Osman C, Haag M, Wieland FT, Brugger B, Langer T;. EMBO J. 2010;29:1976-1987 (from Pfam) NF020976.5 PF09423.15 PhoD 27 27 343 domain Y Y N alkaline phosphatase D family protein 131567 cellular organisms no rank 77687 EBI-EMBL PhoD-like phosphatase alkaline phosphatase D family protein NF020977.5 PF09424.15 YqeY 27 27 143 PfamEq Y Y N GatB/YqeY domain-containing protein 131567 cellular organisms no rank 38680 EBI-EMBL Yqey-like protein Yqey-like protein The function of this domain found in the YqeY protein is uncertain. (from Pfam) NF020983.5 PF09430.15 EMC7_beta-sandw 26.6 26.6 122 PfamAutoEq Y Y N beta-sandwich domain-containing protein 15257293,29809151,30415835,32439656,32459176 131567 cellular organisms no rank 1407 EBI-EMBL ER membrane protein complex subunit 7, beta-sandwich domain ER membrane protein complex subunit 7, beta-sandwich domain This is the beta-sandwich domain found in ER membrane protein complex subunit 7 (EMC7) [1,2], which is an integral membrane component of the EMC. EMC is widely conserved and involved in membrane protein biogenesis. It mediates the insertion into endoplasmic reticulum membranes of newly synthesized membrane proteins in an energy-independent manner, both post-translational insertions of tail-anchored proteins and co-translational insertion of multipass membrane proteins [3,4]. This entry includes UPF0620 protein C83.10 from S. pombe, an orthologue of animal EMC7. This domain is also found in nodal modulators, which have been identified as part of a protein complex that participates in the nodal signalling pathway during vertebrate development [5]. [1]. 32439656. Structural basis for membrane insertion by the human ER membrane protein complex. Pleiner T, Tomaleri GP, Januszyk K, Inglis AJ, Hazu M, Voorhees RM;. Science. 2020;369:433-436. [2]. 32459176. The architecture of EMC reveals a path for membrane protein insertion. O'Donnell JP, Phillips BP, Yagita Y, Juszkiewicz S, Wagner A, Malinverni D, Keenan RJ, Miller EA, Hegde RS;. Elife. 2020; [Epub ahead of print]. [3]. 29809151. The ER membrane protein complex interacts cotranslationally to enable biogenesis of multipass membrane proteins. Shurtleff MJ, Itzhak DN, Hussmann JA, Schirle Oakdale NT, Costa EA, Jonikas M, Weibezahn J, Popova KD, Jan CH, Sinitcyn P, Vembar SS, Hernandez H, Cox J, Burlingame AL, Brodsky JL, Frost A, Borner GH, Weissman JS;. Elife. 2018; [Epub ahead of print]. [4]. 30415835. EMC Is Required to Initiate Accurate Membrane Protein Topogenesis. Chitwoo. TRUNCATED at 1650 bytes (from Pfam) NF020990.5 PF09439.15 SRPRB 25 25 178 domain Y N N Signal recognition particle receptor beta subunit 7844142 131567 cellular organisms no rank 7873 EBI-EMBL Signal recognition particle receptor beta subunit Signal recognition particle receptor beta subunit The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane [1]. [1]. 7844142. The beta subunit of the signal recognition particle receptor is a transmembrane GTPase that anchors the alpha subunit, a peripheral membrane GTPase, to the endoplasmic reticulum membrane. Miller JD, Tajima S, Lauffer L, Walter P;. J Cell Biol. 1995;128:273-282. (from Pfam) NF020996.5 PF09445.15 Methyltransf_15 22 22 165 domain Y N N RNA cap guanine-N2 methyltransferase GO:0001510,GO:0008168,GO:0036261 17284461 131567 cellular organisms no rank 111134 EBI-EMBL RNA cap guanine-N2 methyltransferase RNA cap guanine-N2 methyltransferase RNA cap guanine-N2 methyltransferases such as Schizosaccharomyces pombe Tgs1 and Giardia lamblia Tgs2 catalyse methylation of the exocyclic N2 amine of 7-methylguanosine [1]. [1]. 17284461. Biochemical and Genetic Analysis of RNA Cap Guanine-N2 Methyltransferases from Giardia lamblia and Schizosaccharomyces pombe. Hausmann S, Ramirez A, Schneider S, Schwer B, Shuman S;. Nucleic Acids Res. 2007; [Epub ahead of print] (from Pfam) NF021006.5 PF09455.15 Csx1_HEPN 23 23 71 domain Y Y N TM1812 family CRISPR-associated protein 16292354,26647461,26763118 131567 cellular organisms no rank 213 EBI-EMBL CRISPR system endoribonuclease Csx1, HEPN domain CRISPR system endoribonuclease Csx1, HEPN domain CRISPR system endoribonuclease Csx1 is a metal-independent, endoribonuclease that acts selectively on ssRNA and cleaves specifically after adenosines, as part of the type III-B CRISP-Cas system and it is homologous to Csm6 [1-3], sharing the same domain domain architecture consisting of a CARF domain at the N-terminal that is relatively well conserved, and a HEPN nuclease domain at the C-terminal. This entry represents the HEPN domain, which is has less conservation except for the typical R-X4-H motif [1-3]. [1]. 16292354. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. Haft DH, Selengut J, Mongodin EF, Nelson KE;. PLoS Comput Biol. 2005;1:e60. [2]. 26647461. The CRISPR-associated Csx1 protein of Pyrococcus furiosus is an adenosine-specific endoribonuclease. Sheppard NF, Glover CV 3rd, Terns RM, Terns MP;. RNA. 2016;22:216-224. [3]. 26763118. Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6. Niewoehner O, Jinek M;. RNA. 2016;22:318-329. (from Pfam) NF021009.5 PF09458.15 H_lectin 24 24 67 domain Y Y N H-type lectin domain-containing protein GO:0007155,GO:0030246 16704980 131567 cellular organisms no rank 1918 EBI-EMBL H-type lectin domain H-type lectin domain The H-type lectin domain is a unit of six beta chains, combined into a homo-hexamer. It is involved in self/non-self recognition of cells, through binding with carbohydrates [1]. It is sometimes found in association with the F5_F8_type_C domain Pfam:PF00754. [1]. 16704980. Biochemical and structural analysis of Helix pomatia agglutinin. A hexameric lectin with a novel fold. Sanchez JF, Lescar J, Chazalet V, Audfray A, Gagnon J, Alvarez R, Breton C, Imberty A, Mitchell EP;. J Biol Chem. 2006;281:20171-20180. (from Pfam) NF021010.5 PF09459.15 EB_dh 33.3 33.3 236 domain Y Y N ethylbenzene dehydrogenase-related protein GO:0020037 16962969 131567 cellular organisms no rank 2837 EBI-EMBL Ethylbenzene dehydrogenase ethylbenzene dehydrogenase-related protein Eythylbenzene dehydrogenase is a heterotrimer of three subunits that catalyses the anaerobic degradation of hydrocarbons. The alpha subunit contains the catalytic centre as a Molybdenum cofactor-complex. This removes an electron-pair from the hydrocarbon and passes it along an electron transport system involving iron-sulphur complexes held in the beta subunit and a Haem b molecule contained in the gamma subunit. The electron-pair is then subsequently passed to an as yet unknown receiver [1]. The enzyme is found in a variety of different bacteria. [1]. 16962969. Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum. Kloer DP, Hagel C, Heider J, Schulz GE;. Structure. 2006;14:1377-1388. (from Pfam) NF021016.5 PF09466.15 Yqai 20.2 19.6 66 domain Y Y N YqaI family protein 131567 cellular organisms no rank 1228 EBI-EMBL Hypothetical protein Yqai YqaI family protein This hypothetical protein is expressed in bacteria, particularly Bacillus subtilis. It forms a homo-dimer, with each monomer containing an alpha helix and four beta strands. (from Pfam) NF021021.5 PF09471.15 Peptidase_M64 26 26 302 domain Y Y N M64 family metallopeptidase 11815614 131567 cellular organisms no rank 10980 EBI-EMBL IgA Peptidase M64 M64 family metallo-endopeptidase domain The M64 family of metallo-endopeptidases includes an IgA proteinase from Clostridium ramosum that lacks detectable homology to any previously studied IgA protease. Members of this family also include the Legionella Dot/Icm T4SS effector Lpg1667. NF021022.5 PF09472.15 MtrF 22 22 62 domain Y Y N tetrahydromethanopterin S-methyltransferase subunit F GO:0015948,GO:0016020,GO:0030269 10338124 131567 cellular organisms no rank 348 EBI-EMBL Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF) tetrahydromethanopterin S-methyltransferase subunit F Many archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This domain is mostly found in MtrF, where it covers the entire length of the protein. This polypeptide is one of eight subunits of the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase complex found in methanogenic archaea. This is a membrane-associated enzyme complex that uses methyl-transfer reactions to drive a sodium-ion pump. MtrF itself is involved in the transfer of the methyl group from N5-methyltetrahydromethanopterin to coenzyme M. Subsequently, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase. In some organisms this domain is found at the C terminal region of what appears to be a fusion of the MtrA and MtrF proteins. The function of these proteins is unknown, though it is likely that they are involved in C1 metabolism. (from Pfam) NF021028.5 PF09479.15 Flg_new 27 13.6 65 domain Y Y N InlB B-repeat-containing protein 21345802,27789707 131567 cellular organisms no rank 35167 EBI-EMBL Listeria-Bacteroides repeat domain (List_Bact_rpt) Listeria-Bacteroides repeat domain (List_Bact_rpt) This model describes a conserved core region of about 43 residues [1] which occurs in more than 400 mostly secreted or cell surface-located proteins from over 300 eubacterial and few archaeal species. These proteins contain between one and 34 copies of the domain that often occur in tandem arrays with up to more than 20 copies [2]. [1]. 21345802. Fold and function of the InlB B-repeat. Ebbes M, Bleymuller WM, Cernescu M, Nolker R, Brutschy B, Niemann HH;. J Biol Chem. 2011;286:15496-15506. [2]. 27789707. MET-activating Residues in the B-repeat of the Listeria monocytogenes Invasion Protein InlB. Bleymuller WM, Lammermann N, Ebbes M, Maynard D, Geerds C, Niemann HH;. J Biol Chem. 2016;291:25567-25577. (from Pfam) NF021030.5 PF09481.15 CRISPR_Cse1 24.7 24.7 450 PfamEq Y Y N type I-E CRISPR-associated protein Cse1/CasA 131567 cellular organisms no rank 13706 EBI-EMBL CRISPR-associated protein Cse1 (CRISPR_cse1) type I-E CRISPR-associated protein Cse1/CasA Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry, represented by CT1972 from Chlorobaculum tepidum, is found in the CRISPR/Cas subtype Ecoli regions of many bacteria (most of which are mesophiles), and not in Archaea. It is designated Cse1. (from Pfam) NF021033.5 PF09484.15 Cas_TM1802 25.1 25.1 602 domain Y Y N TM1802 family CRISPR-associated protein 16292354 131567 cellular organisms no rank 1395 EBI-EMBL CRISPR-associated protein TM1802 (cas_TM1802) TM1802 family CRISPR-associated protein Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This minor cas protein is found in at least five prokaryotic genomes: Methanosarcina mazei, Sulfurihydrogenibium azorense, Thermotoga maritima, Carboxydothermus hydrogenoformans, and Dictyoglomus thermophilum, the first of which is archaeal while the rest are bacterial. (from Pfam) NF021034.5 PF09485.15 CRISPR_Cse2 24.6 24.6 137 PfamEq Y Y N type I-E CRISPR-associated protein Cse2/CasB 131567 cellular organisms no rank 10825 EBI-EMBL CRISPR-associated protein Cse2 (CRISPR_cse2) type I-E CRISPR-associated protein Cse2/CasB Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family of proteins, represented by CT1973 from Chlorobaculum tepidum, is encoded by genes found in the CRISPR/Cas subtype Ecoli regions of many bacteria (most of which are mesophiles), and not in Archaea. It is designated Cse2. (from Pfam) NF021037.5 PF09488.15 Osmo_MPGsynth 27 27 381 PfamEq Y Y N mannosyl-3-phosphoglycerate synthase GO:0005737,GO:0050504,GO:0051479 12788726,20356840 131567 cellular organisms no rank 295 EBI-EMBL Mannosyl-3-phosphoglycerate synthase (osmo_MPGsynth) mannosyl-3-phosphoglycerate synthase This family consists of examples of mannosyl-3-phosphoglycerate synthase (MPGS), which together with mannosyl-3-phosphoglycerate phosphatase (MPGP) EC:2.4.1.217, comprises a two-step pathway for mannosylglycerate biosynthesis. Mannosylglycerate is a compatible solute that tends to be restricted to extreme thermophiles of archaea and bacteria. Note that in Rhodothermus marinus, this pathway is one of two; the other is condensation of GDP-mannose with D-glycerate by mannosylglycerate synthase. (from Pfam) NF021038.5 PF09489.15 CbtB 27 27 51 PfamEq Y Y N CbtB-domain containing protein 12869542 131567 cellular organisms no rank 9673 EBI-EMBL Probable cobalt transporter subunit (CbtB) Probable cobalt transporter subunit (CbtB) This entry represents a family of proteins which have been proposed to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems. Evidence for this assignment includes 1) prediction of a single transmembrane segment and a C-terminal histidine-rich motif likely to be a metal-binding site, 2) positional gene linkage with known B12 biosynthesis genes, 3) upstream proximity of B12 transcriptional regulatory sites, 4) the absence of other known cobalt import systems and 5) the obligate co-localisation with a protein (CbtA) predicted to have five additional transmembrane segments. (from Pfam) NF021039.5 PF09490.15 CbtA 30.7 30.7 239 PfamEq Y Y N CbtA family protein 131567 cellular organisms no rank 17146 EBI-EMBL Probable cobalt transporter subunit (CbtA) CbtA family protein This entry represents a family of proteins which have been proposed to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems. Evidence for this assignment includes 1) prediction of five transmembrane segments, 2) positional gene linkage with known B12 biosynthesis genes, 3) upstream proximity of B12 transcriptional regulatory sites, 4) the absence of other known cobalt import systems and 5) the obligate co-localisation with a small protein (CbtB) having a single additional transmembrane segment and a C-terminal histidine-rich motif likely to be a metal-binding site. (from Pfam) NF021040.5 PF09491.15 RE_AlwI 23.1 23.1 441 PfamEq Y Y N AlwI family type II restriction endonuclease 3.1.21.- 22638584 131567 cellular organisms no rank 3052 EBI-EMBL AlwI restriction endonuclease AlwI family type II restriction endonuclease This family includes the AlwI (recognises GGATC), Bsp6I (recognises GC^NGC) , BstNBI (recognises GASTC), PleI(recognises GAGTC) and MlyI (recognises GAGTC) restriction endonucleases. [1]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021041.5 PF09492.15 Pec_lyase 22 22 292 domain Y Y N pectate lyase 12221284,15618218 131567 cellular organisms no rank 6020 EBI-EMBL Pectic acid lyase pectate lyase Members of this family are isozymes of pectate lyase (EC:4.2.2.2), also called polygalacturonic transeliminase and alpha-1,4-D-endopolygalacturonic acid lyase. (from Pfam) NF021052.5 PF09504.15 RE_Bsp6I 25 25 179 PfamEq Y Y N Bsp6I family type II restriction endonuclease 3.1.21.- 22638584 131567 cellular organisms no rank 154 EBI-EMBL Bsp6I restriction endonuclease Bsp6I family type II restriction endonuclease This family includes the Bsp6I (recognises and cleaves GC^NGC) restriction endonucleases. [1]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021057.5 PF09509.15 Hypoth_Ymh 25 25 119 domain Y Y N TIGR02391 family protein 131567 cellular organisms no rank 6773 EBI-EMBL Protein of unknown function (Hypoth_ymh) TIGR02391 family protein This entry consists of a relatively rare prokaryotic protein family (about 8 occurrences per 200 genomes). Genes for members of this family appear to be associated variously with phage and plasmid regions, restriction system loci, transposons, and housekeeping genes. Their function is unknown. (from Pfam) NF021059.5 PF09511.15 RNA_lig_T4_1 28.3 28.3 227 domain Y Y N RNA ligase 12933796 131567 cellular organisms no rank 4133 EBI-EMBL RNA ligase RNA ligase Members of this family include T4 phage proteins with ATP-dependent RNA ligase activity. Host defence to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage. The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL. This family also includes fungal tRNA ligases that have adenylyltransferase activity [1]. tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns.i [1]. 12933796. Genetic and biochemical analysis of the functional domains of yeast tRNA ligase. Sawaya R, Schwer B, Shuman S;. J Biol Chem 2003;278:43928-43938. (from Pfam) NF021060.5 PF09512.15 ThiW 30.3 30.3 150 PfamEq Y Y N energy coupling factor transporter S component ThiW 131567 cellular organisms no rank 5088 EBI-EMBL Thiamine-precursor transporter protein (ThiW) energy coupling factor transporter S component ThiW Levels of thiamine pyrophosphate (TPP) or thiamine regulate transcription or translation of a number of thiamine biosynthesis, salvage, or transport genes in a wide range of prokaryotes. The mechanism involves direct binding, with no protein involved, to a structural element called THI found in the untranslated upstream region of thiamine metabolism gene operons. This element is called a riboswitch and is seen also for other metabolites such as FMN and glycine. This protein family consists of proteins identified in operons controlled by the THI riboswitch and designated ThiW. The hydrophobic nature of this protein and reconstructed metabolic background suggests that this protein acts in transport of a thiazole precursor of thiamine. (from Pfam) NF021062.5 PF09515.15 Thia_YuaJ 25.8 25.8 177 domain Y Y N energy-coupled thiamine transporter ThiT GO:0005886,GO:0015234,GO:0015888 131567 cellular organisms no rank 8666 EBI-EMBL Thiamine transporter protein (Thia_YuaJ) energy-coupled thiamine transporter ThiT Members of this protein family have been assigned as thiamine transporters by a phylogenetic analysis of families of genes regulated by the THI element, a broadly conserved RNA secondary structure element through which thiamine pyrophosphate (TPP) levels can regulate transcription of many genes related to thiamine transport, salvage, and de novo biosynthesis. Species with this protein always lack the ThiBPQ ABC transporter. In some species (e.g. Streptococcus mutans and Streptococcus pyogenes), yuaJ is the only THI-regulated gene. Evidence from Bacillus cereus indicates thiamine uptake is coupled to proton translocation. (from Pfam) NF021064.5 PF09517.15 RE_Eco29kI 30.8 30.8 164 domain Y Y N Eco29kI family restriction endonuclease 3.1.21.- 131567 cellular organisms no rank 1800 EBI-EMBL Eco29kI restriction endonuclease Eco29kI family restriction endonuclease This family includes the Eco29kI (recognises and cleaves CCGC^GG ) restriction endonuclease. (from Pfam) NF021066.5 PF09519.15 RE_HindVP 25 25 332 PfamEq Y Y N HindVP family restriction endonuclease 3.1.21.- GO:0003677,GO:0009036,GO:0009307 22638584 131567 cellular organisms no rank 561 EBI-EMBL HindVP restriction endonuclease HindVP family restriction endonuclease This family includes the HindVP (recognises GRCGYC bu the cleavage site is unknown) restriction endonucleases. [1]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021067.5 PF09520.15 RE_TdeIII 27.2 27.2 242 PfamEq Y Y N TdeIII family type II restriction endonuclease 3.1.21.- GO:0003677,GO:0009036,GO:0009307 21602384,22638584 131567 cellular organisms no rank 935 EBI-EMBL Type II restriction endonuclease, TdeIII TdeIII family type II restriction endonuclease This family includes many TdeIII restriction endonucleases that recognise and cleave at GGNCC sites. TdeIII cleave unmethylated double-stranded DNA [1]. [1]. 21602384. Disruption of a type II endonuclease (TDE0911) enables Treponema denticola ATCC 35405 to accept an unmethylated shuttle vector. Bian J, Li C;. Appl Environ Microbiol. 2011;77:4573-4578. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021068.5 PF09521.15 RE_NgoPII 25 25 262 domain Y Y N NgoPII family restriction endonuclease 3.1.21.- GO:0003677,GO:0009036,GO:0009307 22638584 131567 cellular organisms no rank 511 EBI-EMBL NgoPII restriction endonuclease NgoPII family restriction endonuclease This family includes the NgoPII (recognises and cleaves GG^CC) restriction endonuclease. [1]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021073.5 PF09527.15 ATPase_gene1 26.6 26.6 54 PfamEq Y Y N AtpZ/AtpI family protein 12917488 131567 cellular organisms no rank 19104 EBI-EMBL Putative F0F1-ATPase subunit Ca2+/Mg2+ transporter AtpZ/AtpI family protein This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophobic stretches and is presumed to be a subunit of the enzyme. It carries two transmembrane helices and is a magnesium or calcium uniporter. The atp operon of alkaliphilic Bacillus pseudofirmus OF4, as in most prokaryotes, contains the eight structural genes for the F-ATPase (ATP synthase), which are preceded by an atpI gene that encodes a membrane protein with 2 TMSs. A tenth gene, atpZ, has been found in this operon, which is upstream of and overlapping with atpI [1]. [1]. 12917488. A tenth atp gene and the conserved atpI gene of a Bacillus atp operon have a role in Mg2+ uptake. Hicks DB, Wang Z, Wei Y, Kent R, Guffanti AA, Banciu H, Bechhofer DH, Krulwich TA;. Proc Natl Acad Sci U S A. 2003;100:10213-10218. (from Pfam) NF021082.5 PF09537.15 DUF2383 30.8 30.8 111 domain Y Y N DUF2383 domain-containing protein 23295481 131567 cellular organisms no rank 13798 EBI-EMBL Domain of unknown function (DUF2383) Domain of unknown function (DUF2383) This domain is found in found in uncharacterised proteins predominantly from bacteria. The uncharacterised Swiss:Q9I1U6 from Pseudomonas aeruginosa shows a ferritin-like topology with a four-helix-bundle fold that lacks metal-ion-binding site typical of the ferritin family (Pfam:PF00210) but has a potential metal-binding site [1]. The function is unknown. [1]. 23295481. The AEROPATH project targeting Pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery. Moynie L, Schnell R, McMahon SA, Sandalova T, Boulkerou WA, Schmidberger JW, Alphey M, Cukier C, Duthie F, Kopec J, Liu H, Jacewicz A, Hunter WN, Naismith JH, Schneider G;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013;69:25-34. (from Pfam) NF021087.5 PF09545.15 RE_AccI 22 22 366 PfamEq Y Y N AccI family restriction endonuclease 3.1.21.- 6278447 131567 cellular organisms no rank 145 EBI-EMBL AccI restriction endonuclease AccI family restriction endonuclease This family includes the AccI (recognises and cleaves GT^MKAC) restriction endonuclease. [1]. 6278447. Purification and characterization of two new modification methylases: MClaI from Caryophanon latum L and MTaqI from Thermus aquaticus YTI. McClelland M;. Nucleic Acids Res. 1981;9:6795-6804. (from Pfam) NF021091.5 PF09549.15 RE_Bpu10I 25 25 218 PfamEq Y Y N Bpu10I family restriction endonuclease 3.1.21.- 22638584,9461472 131567 cellular organisms no rank 528 EBI-EMBL Bpu10I restriction endonuclease Bpu10I family restriction endonuclease This family includes the Bpu10I (recognises and cleaves CCTNAGC (-5/-2)) restriction endonucleases. [1]. 9461472. Cloning and analysis of the four genes coding for Bpu10I restriction-modification enzymes. Stankevicius K, Lubys A, Timinskas A, Vaitkevicius D, Janulaitis A;. Nucleic Acids Res. 1998;26:1084-1091. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021094.5 PF09552.15 RE_BstXI 25 25 290 domain Y Y N BstXI family restriction endonuclease 3.1.21.- 10702254 131567 cellular organisms no rank 162 EBI-EMBL BstXI restriction endonuclease BstXI family restriction endonuclease This family includes the BstXI (recognises and cleaves CCANNNNN^NTGG) restriction endonuclease. [1]. 10702254. Reactions of BglI and other type II restriction endonucleases with discontinuous recognition sites. Gormley NA, Bath AJ, Halford SE;. J Biol Chem. 2000;275:6928-6936. (from Pfam) NF021095.5 PF09553.15 RE_Eco47II 25.9 25.9 202 PfamEq Y Y N Eco47II family restriction endonuclease 3.1.21.- GO:0003677,GO:0009036,GO:0009307 22638584,7607524 131567 cellular organisms no rank 1243 EBI-EMBL Eco47II restriction endonuclease Eco47II family restriction endonuclease This family includes the Eco47II (which recognises GGNCC, but the cleavage site unknown) restriction endonuclease. [1]. 7607524. Cloning and characterization of the unusual restriction-modification system comprising two restriction endonucleases and one methyltransferase. Stankevicius K, Povilionis P, Lubys A, Menkevicius S, Janulaitis A;. Gene. 1995;157:49-53. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021097.5 PF09556.15 RE_HaeIII 25 25 298 PfamEq Y Y N HaeIII family restriction endonuclease 3.1.21.- 7607519 131567 cellular organisms no rank 1107 EBI-EMBL HaeIII restriction endonuclease HaeIII family restriction endonuclease This family includes the HaeIII (recognises and cleaves GG^CC) restriction endonuclease. [1]. 7607519. New restriction endonucleases from thermophilic soil bacteria. Repin VE, Lebedev LR, Puchkova L, Serov GD, Tereschenko T, Chizikov VE, Andreeva I;. Gene. 1995;157:321-322. (from Pfam) NF021098.5 PF09557.15 DUF2382 23 23 111 domain Y Y N DUF2382 domain-containing protein 131567 cellular organisms no rank 18109 EBI-EMBL Domain of unknown function (DUF2382) Domain of unknown function (DUF2382) This entry describes an uncharacterized domain, sometimes found in association with a PRC-barrel domain Pfam:PF05239 which is also found in rRNA processing protein RimM and in a photosynthetic reaction centre complex protein). This domain is found in proteins from Bacillus subtilis, Deinococcus radiodurans, Nostoc sp. PCC 7120, Myxococcus xanthus, and several other species. The function is not known. (from Pfam) NF021101.5 PF09560.15 Spore_YunB 25 25 91 domain Y Y N sporulation protein YunB 12662922 131567 cellular organisms no rank 5751 EBI-EMBL Sporulation protein YunB (Spo_YunB) sporulation protein YunB Spo_YunB is the sporulation protein YunB. In Bacillus subtilis its expression is controlled by sigmaE.The gene YunB seems to code for a protein involved, at least indirectly, in the pathway leading to the activation of sigmaK. Inactivation of YunB delays sigmaK activation and results in reduced sporulation efficiency. (from Pfam) NF021102.5 PF09561.15 RE_HpaII 25 25 359 PfamEq Y Y N HpaII family restriction endonuclease 3.1.21.- 16723432,22638584 131567 cellular organisms no rank 1773 EBI-EMBL HpaII restriction endonuclease HpaII family restriction endonuclease This family includes the HpaII (recognises and cleaves C^CGG) restriction endonuclease. [1]. 16723432. DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force. Gemmen GJ, Millin R, Smith DE;. Nucleic Acids Res. 2006;34:2864-2877. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021103.5 PF09562.15 RE_LlaMI 25 25 266 PfamEq Y Y N LlaMI family restriction endonuclease 3.1.21.- 16144727,22638584 131567 cellular organisms no rank 120 EBI-EMBL LlaMI restriction endonuclease LlaMI family restriction endonuclease This family includes the LlaMI (recognises and cleaves CC^NGG) restriction endonuclease. [1]. 16144727. In vitro expression of the restriction endonucleases LlaMI and ScrFI isolated from Lactococcus lactis M19 and UC503. Szatmari G, Hua NM, Vzdornov D, Daigle F, Smoragiewicz W, Mamet-Bratley MD, Karska-Wysocki B;. J Biotechnol. 2006;121:144-153. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021104.5 PF09563.15 RE_LlaJI 23.6 23.6 365 PfamEq Y Y N LlaJI family restriction endonuclease 3.1.21.- 16646963 131567 cellular organisms no rank 2661 EBI-EMBL LlaJI restriction endonuclease LlaJI family restriction endonuclease This family includes the LlaJI (recognises GACGC) restriction endonucleases. [1]. 16646963. A genetic dissection of the LlaJI restriction cassette reveals insights on a novel bacteriophage resistance system. O'Driscoll J, Heiter DF, Wilson GG, Fitzgerald GF, Roberts R, van Sinderen D;. BMC Microbiol. 2006;6:40. (from Pfam) NF021105.5 PF09564.15 RE_NgoBV 25 25 238 domain Y Y N NgoBV family restriction endonuclease 3.1.21.- GO:0009036,GO:0090304 22638584,7607490 131567 cellular organisms no rank 405 EBI-EMBL NgoBV restriction endonuclease NgoBV family restriction endonuclease This family includes the NgoBV (recognises GGNNCC but cleavage site is unknown) restriction endonuclease. [1]. 7607490. Restriction and modification systems of Neisseria gonorrhoeae. Stein DC, Gunn JS, Radlinska M, Piekarowicz A;. Gene. 1995;157:19-22. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021106.5 PF09565.15 RE_NgoFVII 23.8 23.8 162 domain Y Y N restriction endonuclease PLD domain-containing protein 3.1.21.- 25429979,9988771 131567 cellular organisms no rank 8557 EBI-EMBL NgoFVII restriction endonuclease N-terminal PLD domain NgoFVII restriction endonuclease N-terminal PLD domain This family includes the NgoFVII (recognises GCSGC but cleavage site unknown) restriction endonuclease. [1]. 9988771. Regions of endonuclease EcoRII involved in DNA target recognition identified by membrane-bound peptide repertoires. Reuter M, Schneider-Mergener J, Kupper D, Meisel A, Mackeldanz P, Kruger DH, Schroeder C;. J Biol Chem. 1999;274:5213-5221. [2]. 25429979. Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII. Tamulaitiene G, Silanskas A, Grazulis S, Zaremba M, Siksnys V;. Nucleic Acids Res. 2014;42:14022-14030. (from Pfam) NF021107.5 PF09566.15 RE_SacI 19.3 19.3 276 PfamEq Y Y N restriction endonuclease, SacI family 3.1.21.- 10593932,22638584 131567 cellular organisms no rank 477 EBI-EMBL SacI restriction endonuclease restriction endonuclease, SacI family This family includes the SacI (recognises and cleaves GAGCT^C) restriction endonuclease. [1]. 10593932. Reactions of type II restriction endonucleases with 8-base pair recognition sites. Bilcock DT, Daniels LE, Bath AJ, Halford SE;. J Biol Chem. 1999;274:36379-36386. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021108.5 PF09567.15 RE_MamI 25 25 183 PfamEq Y Y N MamI family restriction endonuclease 3.1.21.- GO:0003677,GO:0009036,GO:0009307 8654988 131567 cellular organisms no rank 112 EBI-EMBL MamI restriction endonuclease MamI family restriction endonuclease This family includes the MamI (recognises and cleaves GATNN^NNATC) restriction endonuclease. [1]. 8654988. Cloning and characterization of the MamI restriction-modification system from Microbacterium ammoniaphilum in Escherichia coli. Striebel HM, Seeber S, Jarsch M, Kessler C;. Gene. 1996;172:41-46. (from Pfam) NF021109.5 PF09568.15 RE_MjaI 22.7 22.7 164 domain Y Y N MjaI family restriction endonuclease 3.1.21.- GO:0003677,GO:0009036,GO:0009307 22638584 131567 cellular organisms no rank 342 EBI-EMBL MjaI restriction endonuclease MjaI family restriction endonuclease This family includes the MjaI (recognises CTAG but cleavage site unknown) restriction endonuclease. [1]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021110.5 PF09569.15 RE_ScaI 25 25 192 PfamEq Y Y N ScaI family restriction endonuclease 3.1.21.- 22638584,9862476 131567 cellular organisms no rank 241 EBI-EMBL ScaI restriction endonuclease ScaI family restriction endonuclease This family includes the ScaI (recognises and cleaves AGT^ACT) restriction endonuclease. [1]. 9862476. Cloning and expression of the ApaLI, NspI, NspHI, SacI, ScaI, and SapI restriction-modification systems in Escherichia coli. Xu SY, Xiao JP, Ettwiller L, Holden M, Aliotta J, Poh CL, Dalton M, Robinson DP, Petronzio TR, Moran L, Ganatra M, Ware J, Slatko B, Benner J;. Mol Gen Genet. 1998;260:226-231. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021111.5 PF09570.15 RE_SinI 22 22 218 PfamEq Y Y N SinI family restriction endonuclease 3.1.21.- GO:0003677,GO:0009036,GO:0009307 22638584,8919860 131567 cellular organisms no rank 550 EBI-EMBL SinI restriction endonuclease SinI family restriction endonuclease This family includes the SinI (recognises and cleaves G^GWCC) restriction endonuclease. [1]. 8919860. Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems. Jeltsch A, Pingoud A;. J Mol Evol. 1996;42:91-96. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021112.5 PF09571.15 RE_XcyI 25 25 305 PfamEq Y Y N XcyI family restriction endonuclease 3.1.21.- GO:0000287,GO:0003677,GO:0009036,GO:0009307 22638584,7607515 131567 cellular organisms no rank 224 EBI-EMBL XcyI restriction endonuclease XcyI family restriction endonuclease This family includes the XcyI (recognises and cleaves C^CCGGG) restriction endonucleases. [1]. 7607515. Sequence similarity among type-II restriction endonucleases, related by their recognized 6-bp target and tetranucleotide-overhang cleavage. Siksnys V, Timinskas A, Klimasauskas S, Butkus V, Janulaitis A;. Gene. 1995;157:311-314. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021113.5 PF09572.15 RE_XamI 25 25 256 PfamEq Y Y N XamI family restriction endonuclease 3.1.21.- GO:0003677,GO:0009036,GO:0009307 22638584,415144 131567 cellular organisms no rank 635 EBI-EMBL XamI restriction endonuclease XamI family restriction endonuclease This family includes the XamI (recognises GTCGAC but cleavage site unknown) restriction endonuclease. [1]. 415144. A new restriction endonuclease from Streptomyces albus G. Arrand JR, Myers PA, Roberts RJ;. J Mol Biol. 1978;118:127-135. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021119.5 PF09579.15 Spore_YtfJ 25 25 81 subfamily Y Y N spore germination protein GerW family protein 23921501 131567 cellular organisms no rank 8092 EBI-EMBL Sporulation protein YtfJ (Spore_YtfJ) spore germination protein GerW family protein Most members of this family are GerW (previously YtfJ), a protein required for germination in endospore-forming Firmicutes in response to alanine, but additional members of the family are found in Actinobacteria, Cyanobacteria, Archaea, etc. NF021122.5 PF09582.15 AnfO_nitrog 30.3 30.3 190 subfamily Y Y N Fe-only nitrogenase accessory AnfO family protein 11781802,2644222 131567 cellular organisms no rank 680 EBI-EMBL Iron only nitrogenase protein AnfO (AnfO_nitrog) Fe-only nitrogenase accessory AnfO family protein Proteins in this entry include Anf1 from Rhodobacter capsulatus (Rhodopseudomonas capsulata) and AnfO from Azotobacter vinelandii. They are found exclusively in species which contain the iron-only nitrogenase, and are encoded immediately downstream of the structural genes for the nitrogenase enzyme in these species. (from Pfam) NF021125.5 PF09585.15 Lin0512_fam 23.4 23.4 114 domain Y Y N Lin0512 family protein 131567 cellular organisms no rank 3617 EBI-EMBL Conserved hypothetical protein (Lin0512_fam) Lin0512 family protein This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a well conserved motif GxGxDxHG near the N-terminus. (from Pfam) NF021126.5 PF09586.15 YfhO 28.5 28.5 835 domain Y Y N YfhO family protein 16306698 131567 cellular organisms no rank 40095 EBI-EMBL Bacterial membrane protein YfhO YfhO family protein This protein is a conserved membrane protein [1]. The yfhO gene is transcribed in Difco sporulation medium and the transcription is affected by the YvrGHb two-component system. Some members of this family have been annotated as glycosyl transferases of the PMT family. [1]. 16306698. Functional analysis of the YvrGHb two-component system of Bacillus subtilis: identification of the regulated genes by DNA microarray and northern blot analyses. Serizawa M, Kodama K, Yamamoto H, Kobayashi K, Ogasawara N, Sekiguchi J;. Biosci Biotechnol Biochem. 2005;69:2155-2169. (from Pfam) NF021127.5 PF09587.15 PGA_cap 27 27 255 domain Y Y N CapA family protein 16689787 131567 cellular organisms no rank 60710 EBI-EMBL Bacterial capsule synthesis protein PGA_cap CapA family protein This protein is a putative poly-gamma-glutamate capsule biosynthesis protein found in bacteria. Poly-gamma-glutamate is a natural polymer that may be involved in virulence and may help bacteria survive in high salt concentrations. It is a surface-associated protein [1]. [1]. 16689787. Poly-gamma-glutamate in bacteria. Candela T, Fouet A;. Mol Microbiol. 2006;60:1091-1098. (from Pfam) NF021128.5 PF09588.15 YqaJ 22 22 150 domain Y Y N YqaJ viral recombinase family protein 12670970 131567 cellular organisms no rank 31084 EBI-EMBL YqaJ-like viral recombinase domain YqaJ-like viral recombinase domain This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit [1]. [1]. 12670970. Bacteriophage SPP1 Chu is an alkaline exonuclease in the SynExo family of viral two-component recombinases. Vellani TS, Myers RS;. J Bacteriol. 2003;185:2465-2474. (from Pfam) NF021134.5 PF09594.15 GT87 25 25 237 domain Y Y N glycosyltransferase 87 family protein GO:0016758 16803893,18627460 131567 cellular organisms no rank 88098 EBI-EMBL Glycosyltransferase family 87 glycosyltransferase 87 family protein The enzymes in this family are glycosyltransferases. PimE is involved in phosphatidylinositol mannoside (PIM) synthesis, a major class of glycolipids in all mycobacteria. PimE is a polyprenol-phosphate-mannose-dependent mannosyltransferase that transfers the fifth mannose of PIM [1]. The family also includes alpha(1-->3) arabinofuranosyltransferase, invloved in the synthesis of of mycobacterial arabinogalactan [2]. [1]. 16803893. PimE is a polyprenol-phosphate-mannose-dependent mannosyltransferase that transfers the fifth mannose of phosphatidylinositol mannoside in mycobacteria. Morita YS, Sena CB, Waller RF, Kurokawa K, Sernee MF, Nakatani F, Haites RE, Billman-Jacobe H, McConville MJ, Maeda Y, Kinoshita T;. J Biol Chem. 2006;281:25143-25155. [2]. 18627460. Biosynthesis of mycobacterial arabinogalactan: identification of a novel alpha(1-->3) arabinofuranosyltransferase. Birch HL, Alderwick LJ, Bhatt A, Rittmann D, Krumbach K, Singh A, Bai Y, Lowary TL, Eggeling L, Besra GS;. Mol Microbiol. 2008;69:1191-1206. (from Pfam) NF021144.5 PF09604.15 Potass_KdpF 21.2 21.2 24 domain Y Y N potassium-transporting ATPase subunit F 7.2.2.6 GO:0005886,GO:0008556,GO:0043462 131567 cellular organisms no rank 12942 EBI-EMBL F subunit of K+-transporting ATPase (Potass_KdpF) potassium-transporting ATPase subunit F This entry describes a very small integral membrane peptide KdpF, a subunit of the K(+)-translocating Kdp complex. It is found upstream of the KdpA subunit (IPR004623). Because of its very small size and highly hydrophobic character, it is sometimes missed in genome annotation. (from Pfam) NF021145.5 PF09605.15 Trep_Strep 28.7 28.7 185 domain Y Y N MptD family putative ECF transporter S component 131567 cellular organisms no rank 7296 EBI-EMBL Hypothetical bacterial integral membrane protein (Trep_Strep) MptD family putative ECF transporter S component This family consists of strongly hydrophobic proteins about 190 amino acids in length with a strongly basic motif near the C-terminus. It is found in rather few species, but in paralogous families of 12 members in the oral pathogenic spirochaete Treponema denticola and 2 in Streptococcus pneumoniae R6. (from Pfam) NF021149.5 PF09609.15 Cas_GSU0054 21 21 552 PfamEq Y N N CRISPR-associated protein, GSU0054 family (Cas_GSU0054) 131567 cellular organisms no rank 558 EBI-EMBL CRISPR-associated protein, GSU0054 family (Cas_GSU0054) CRISPR-associated protein, GSU0054 family (Cas_GSU0054) This entry represents a rare CRISPR-associated protein. So far, members are found in Geobacter sulfurreducens and in two unpublished genomes: Gemmata obscuriglobus and Actinomyces naeslundii. CRISPR-associated proteins typically are found near CRISPR repeats and other CRISPR-associated proteins, have low levels of sequence identify, have sequence relationships that suggest lateral transfer, and show some sequence similarity to DNA-active proteins such as helicases and repair proteins. (from Pfam) NF021156.5 PF09617.15 Cas_GSU0053 25 25 168 domain Y Y N type I-U CRISPR-associated protein Cas7 16292354 131567 cellular organisms no rank 1390 EBI-EMBL CRISPR-associated protein GSU0053 (Cas_GSU0053) type I-U CRISPR-associated protein Cas7 This entry is found in CRISPR-associated (cas) proteins in the genomes of Geobacter sulfurreducens PCA and Desulfotalea psychrophila LSv54 (both Desulfobacterales from the Deltaproteobacteria), Gemmata obscuriglobus (a Planctomycete), and Actinomyces naeslundii MG1 (Actinobacteria). (from Pfam) NF021157.5 PF09618.15 Cas_Csy4 25 25 181 PfamEq Y Y N type I-F CRISPR-associated endoribonuclease Cas6/Csy4 GO:0004519,GO:0043571 131567 cellular organisms no rank 4763 EBI-EMBL CRISPR-associated protein (Cas_Csy4) type I-F CRISPR-associated endoribonuclease Cas6/Csy4 CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family, typified by YPO2462 of Yersinia pestis, is a CRISPR-associated (Cas) family strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy4, for CRISPR/Cas Subtype Ypest protein 4. (from Pfam) NF021159.5 PF09620.15 Cas_csx3 21 21 78 domain Y Y N CRISPR-associated protein Csx3 131567 cellular organisms no rank 546 EBI-EMBL CRISPR-associated protein (Cas_csx3) CRISPR-associated protein Csx3 This entry is encoded in CRISPR-associated (cas) gene clusters, near CRISPR repeats, in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). It is not yet assigned to a specific CRISPR/cas subtype (hence the x designation csx3). (from Pfam) NF021161.5 PF09622.15 DUF2391 22 22 275 PfamAutoEq Y Y N DUF2391 family protein 131567 cellular organisms no rank 3066 EBI-EMBL Putative integral membrane protein (DUF2391) DUF2391 family protein This entry is found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus in a conserved two-gene neighbourhood. Proteins containing this entry appear to span the membrane seven times. (from Pfam) NF021162.5 PF09623.15 Cas_NE0113 23 23 208 domain Y Y N CRISPR-associated ring nuclease 131567 cellular organisms no rank 1526 EBI-EMBL CRISPR-associated protein NE0113 (Cas_NE0113) CRISPR-associated ring nuclease Members of this minor CRISPR-associated (Cas) protein family are encoded in cas gene clusters in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, Mannheimia succiniciproducens MBEL55E, and Verrucomicrobium spinosum. (from Pfam) NF021169.5 PF09630.15 DUF2024 27 27 81 PfamAutoEq Y Y N DUF2024 family protein 131567 cellular organisms no rank 1265 EBI-EMBL Domain of unknown function (DUF2024) DUF2024 family protein This protein of 86 residues is expressed in bacteria. It consists of four alpha helices and two beta strands. Its function is unknown. One UniProt entry gives the gene name as Traf5. (from Pfam) NF021172.5 PF09633.15 DUF2023 27 27 101 PfamAutoEq Y Y N DUF2023 family protein 131567 cellular organisms no rank 922 EBI-EMBL Protein of unknown function (DUF2023) DUF2023 family protein This protein of approx.120 residues consists of three beta strands and five alpha helices, thought to fold into a homo-dimer. It is expressed in bacteria. (from Pfam) NF021189.5 PF09651.15 Cas_APE2256 24.8 24.8 136 domain Y N N CRISPR-associated protein (Cas_APE2256) 131567 cellular organisms no rank 951 EBI-EMBL CRISPR-associated protein (Cas_APE2256) CRISPR-associated protein (Cas_APE2256) This entry represents a conserved region of about 150 amino acids found in at least five archaeal and three bacterial species. These species all contain CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats). In six of eight species, the protein is encoded the vicinity of a CRISPR/Cas locus. (from Pfam) NF021190.5 PF09652.15 Cas_VVA1548 25 25 91 domain Y Y N CRISPR-associated protein Csx16 16292354,16545108 131567 cellular organisms no rank 609 EBI-EMBL Putative CRISPR-associated protein (Cas_VVA1548) CRISPR-associated protein Csx16 This entry represents a conserved region of about 95 amino acids found exclusively in species with CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats). In all bacterial species that contain this entry, the genes encoding the proteins are in the midst of a cluster of cas (CRISPR-associated) genes. (from Pfam) NF021201.5 PF09664.15 DUF2399 23.4 23.4 152 domain Y Y N DUF2399 domain-containing protein 131567 cellular organisms no rank 8466 EBI-EMBL Protein of unknown function C-terminus (DUF2399) Protein of unknown function C-terminus (DUF2399) Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Beta-proteobacteria). Just the C-terminal region is ioncluded here. (from Pfam) NF021205.5 PF09668.15 Asp_protease 21 21 124 domain Y N N Aspartyl protease GO:0004190,GO:0006508 17010377 131567 cellular organisms no rank 2225 EBI-EMBL Aspartyl protease Aspartyl protease This family of eukaryotic aspartyl proteases have a fold similar to retroviral proteases which implies they function proteolytically during regulated protein turnover [1]. [1]. 17010377. Ddi1, a eukaryotic protein with the retroviral protease fold. Sirkis R, Gerst JE, Fass D;. J Mol Biol. 2006;364:376-387. (from Pfam) NF021207.5 PF09670.15 Cas_Cas02710 27 27 153 domain Y N N Csm6 HEPN domain 26763118,31326273,33461211 131567 cellular organisms no rank 802 EBI-EMBL Csm6 HEPN domain Csm6 HEPN domain Members of this entry are found, exclusively in the vicinity of CRISPR repeats and other CRISPR-associated (cas) genes, in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum), Thermus thermophilus (Deinococcus-Thermus), Chloroflexus aurantiacus (Chloroflexi), and Thermomicrobium roseum (Thermomicrobia). Among its members is Csm6 from Thermus thermophilus, a ssRNA-specific endoribonuclease that provides an auxiliary RNA-targeting interference mechanism in type III-A CRISPR-Cas systems, working together with the RNA- and DNA-targeting endonuclease activities of the Csm effector complex. Csm6 consists of a CARF domain at the N-terminal, a six-helix (6H) central domain and the HEPN domain at the C-terminal, which is represented in this entry [1-3]. This domain forms a dimer that constitutes a composite ribonuclease active site. [1]. 26763118. Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6. Niewoehner O, Jinek M;. RNA. 2016;22:318-329. [2]. 33461211. The Card1 nuclease provides defence during type III CRISPR immunity. Rostol JT, Xie W, Kuryavyi V, Maguin P, Kao K, Froom R, Patel DJ, Marraffini LA;. Nature. 2021;590:624-629. [3]. 31326273. CRISPR-Cas III-A Csm6 CARF Domain Is a Ring Nuclease Triggering Stepwise cA(4) Cleavage with ApA>p Formation Terminating RNase Activity. Jia N, Jones R, Yang G, Ouerfelli O, Patel DJ;. Mol Cell. 2019;75:944-956. (from Pfam) NF021210.5 PF09674.15 DUF2400 25 25 225 PfamAutoEq Y Y N DUF2400 family protein 131567 cellular organisms no rank 8906 EBI-EMBL Protein of unknown function (DUF2400) DUF2400 family protein Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation. (from Pfam) NF021214.5 PF09678.15 Caa3_CtaG 27.7 27.7 237 domain Y Y N cytochrome c oxidase assembly protein 131567 cellular organisms no rank 42530 EBI-EMBL Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG) cytochrome c oxidase assembly protein Members of this family are the CtaG protein required for assembly of active cytochrome c oxidase of the caa3 type, as found in Bacillus subtilis. (from Pfam) NF021220.5 PF09684.15 Tail_P2_I 20.6 20.6 139 domain Y Y N phage tail protein 131567 cellular organisms no rank 36548 EBI-EMBL Phage tail protein (Tail_P2_I) phage tail protein These sequences represent the family of phage P2 protein I and related tail proteins from a number of temperate phage of Gram-negative bacteria. (from Pfam) NF021221.5 PF09685.15 DUF4870 25 25 107 domain Y Y N DUF4870 domain-containing protein 131567 cellular organisms no rank 25723 EBI-EMBL Domain of unknown function (DUF4870) Domain of unknown function (DUF4870) NF021235.5 PF09699.15 Paired_CXXCH_1 20.6 20.6 41 domain Y Y N cytochrome c3 family protein 12356749 131567 cellular organisms no rank 13441 EBI-EMBL Doubled CXXCH motif (Paired_CXXCH_1) Doubled CXXCH motif (Paired_CXXCH_1) This entry represents a domain of about 41 amino acids that contains, among other motifs, two copies of the motif CXXCH associated with haem binding. This domain is predicted to be a high molecular weight c-type cytochrome and is often found in multiple copies. Members are found mostly in species of Shewanella, Geobacter, and Vibrio. (from Pfam) NF021236.5 PF09700.15 Cas_Cmr3 21 21 367 domain Y Y N type III-B CRISPR module-associated Cmr3 family protein 23583914 131567 cellular organisms no rank 2586 EBI-EMBL CRISPR-associated protein (Cas_Cmr3) type III-B CRISPR module-associated Cmr3 family protein CRISPR is a term for Clustered Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This highly divergent family, found in at least ten different archaeal and bacterial species, is represented by TM1793 from Thermotoga maritima. (from Pfam) NF021237.5 PF09701.15 Cas_Cmr5 21 21 119 domain Y Y N type III-B CRISPR module-associated protein Cmr5 19173314,23370277 131567 cellular organisms no rank 1458 EBI-EMBL CRISPR-associated protein (Cas_Cmr5) type III-B CRISPR module-associated protein Cmr5 CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family, represented by TM1791.1 of Thermotoga maritima, is found in both archaeal and bacterial species. (from Pfam) NF021238.5 PF09702.15 Cas_Csa5 23 23 101 PfamEq Y N N CRISPR-associated protein (Cas_Csa5) 131567 cellular organisms no rank 80 EBI-EMBL CRISPR-associated protein (Cas_Csa5) CRISPR-associated protein (Cas_Csa5) CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry represents a minor family of Cas proteins found in various species of Sulfolobus and Pyrococcus (all archaeal). It is found with two different CRISPR loci in Sulfolobus solfataricus. (from Pfam) NF021240.5 PF09704.15 Cas_Cas5d 23 23 217 domain Y Y N type I-E CRISPR-associated protein Cas5/CasD GO:0043571 25123481,26863189 131567 cellular organisms no rank 21442 EBI-EMBL CRISPR-associated protein (Cas_Cas5) type I-E CRISPR-associated protein Cas5/CasD CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This small Cas family is represented by CT1134 of Chlorobium tepidum. (from Pfam) NF021241.5 PF09706.15 Cas_CXXC_CXXC 21 21 69 domain Y Y N Cas8a1 family CRISPR/Cas system-associated protein 16292354,16545108 131567 cellular organisms no rank 1363 EBI-EMBL CRISPR-associated protein (Cas_CXXC_CXXC) Cas8a1 family CRISPR/Cas system-associated protein CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry describes a conserved region of about 65 amino acids from an otherwise highly divergent protein found in a minority of CRISPR-associated protein regions. This region features two motifs of CXXC. (from Pfam) NF021242.5 PF09707.15 Cas_Cas2CT1978 24.7 24.7 86 PfamEq Y Y N type I-E CRISPR-associated endoribonuclease Cas2 131567 cellular organisms no rank 7772 EBI-EMBL CRISPR-associated protein (Cas_Cas2CT1978) type I-E CRISPR-associated endoribonuclease Cas2 This entry represents a minor branch of the Cas2 family of CRISPR-associated protein which are found in IPR003799. Cas proteins are found adjacent to a characteristic short, palindromic repeat cluster termed CRISPR, a probable mobile DNA element. (from Pfam) NF021243.5 PF09709.15 Cas_Csd1 27 27 559 domain Y Y N type I-C CRISPR-associated protein Cas8c/Csd1 131567 cellular organisms no rank 7625 EBI-EMBL CRISPR-associated protein (Cas_Csd1) type I-C CRISPR-associated protein Cas8c/Csd1 CRISPR loci appear to be mobile elements with a wide host range. This entry represents proteins that tend to be found near CRISPR repeats. The species range, so far, is exclusively bacterial and mesophilic, although CRISPR loci are particularly common among the archaea and thermophilic bacteria. Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. (from Pfam) NF021245.5 PF09711.15 Cas_Csn2 23.7 23.7 181 PfamEq Y N N CRISPR-associated protein (Cas_Csn2) 131567 cellular organisms no rank 2193 EBI-EMBL CRISPR-associated protein (Cas_Csn2) CRISPR-associated protein (Cas_Csn2) CRISPR loci appear to be mobile elements with a wide host range. This entry represents proteins found only in CRISPR-containing species, near other CRISPR-associated proteins (cas). The species range so far for these proteins is pathogenic bacteria only. Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). (from Pfam) NF021246.5 PF09712.15 PHA_synth_III_E 25.7 25.7 311 domain Y Y N poly(R)-hydroxyalkanoic acid synthase subunit PhaE 14715006,7763384 131567 cellular organisms no rank 3197 EBI-EMBL Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E) poly(R)-hydroxyalkanoic acid synthase subunit PhaE This entry represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species. (from Pfam) NF021252.5 PF09719.15 C_GCAxxG_C_C 27 27 118 subfamily Y Y N C-GCAxxG-C-C family (seleno)protein 17626042 131567 cellular organisms no rank 10002 EBI-EMBL Putative redox-active protein (C_GCAxxG_C_C) C-GCAxxG-C-C family (seleno)protein This entry represents a putative redox-active protein of about 140 residues, with four perfectly conserved Cys residues. It includes a CGAXXG motif. Most members are found within one or two loci of transporter or oxidoreductase genes. A member from Geobacter sulfurreducens, located in a molybdenum transporter operon, has a TAT (twin-arginine translocation) signal sequence for Sec-independent transport across the plasma membrane, a hallmark of bound prosthetic groups such as FeS clusters. (from Pfam) NF021253.5 PF09720.15 Unstab_antitox 23.3 23.3 54 domain Y Y N addiction module protein 131567 cellular organisms no rank 6214 EBI-EMBL Putative addiction module component addiction module protein This entry defines several short bacterial proteins, typically about 75 amino acids long, which are always found as part of a pair (at least) of small genes. The other protein in the pair always belongs to a family of plasmid stabilisation proteins (IPR007712). It is likely that this protein and its partner comprise some form of addiction module - a pair of genes consisting of a stable toxin and an unstable antitoxin which mediate programmed cell death - although these gene-pairs are usually found on the bacterial main chromosome. (from Pfam) NF021254.5 PF09721.15 Exosortase_EpsH 25.7 25.7 254 domain Y Y N archaeosortase/exosortase family protein 131567 cellular organisms no rank 11964 EBI-EMBL Transmembrane exosortase (Exosortase_EpsH) archaeosortase/exosortase family protein Members of this family are designated exosortase, analogous to sortase in cell wall sorting mediated by LPXTG domains in Gram-positive bacteria. The phylogenetic distribution of the proteins in this entry is nearly perfectly correlated with the distribution of the proteins having the PEP-CTERM anchor motif, IPR013424. Members of this entry are integral membrane proteins with eight predicted transmembrane helices in common. Some members of this family have long trailing sequences past the region described by this model. This model does not include the region of the first predicted transmembrane region. The best characterised member is EpsH of Methylobacillus sp. 12S, where it is part of a locus associated with biosynthesis of the exopolysaccharide methanol-an. (from Pfam) NF021256.5 PF09723.15 Zn-ribbon_8 34.4 34.4 41 domain Y Y N zinc ribbon domain-containing protein 131567 cellular organisms no rank 35234 EBI-EMBL Zinc ribbon domain Zinc ribbon domain This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence. (from Pfam) NF021282.5 PF09749.14 HVSL 26.8 26.8 242 PfamEq Y N N Uncharacterised conserved protein GO:0004518,GO:0034477 131567 cellular organisms no rank 201 EBI-EMBL Uncharacterised conserved protein Uncharacterised conserved protein This entry is of proteins of approximately 300 residues conserved from plants to humans. It contains two conserved motifs, HxSL and FHVSL. The function is unknown. (from Pfam) NF021285.5 PF09752.14 ABHD18 21 21 351 domain Y Y N alpha/beta hydrolase family protein 131567 cellular organisms no rank 3474 EBI-EMBL Alpha/beta hydrolase domain containing 18 abhydrolase domain-containing protein 18 This entry represents alpha/beta hydrolase domain-containing protein 18 (ABHD18). Its function is not clear. (from Pfam) NF021287.5 PF09754.14 PAC2 25.8 25.8 215 domain Y Y N PAC2 family protein 16251969,17431397,17707236,18786393 131567 cellular organisms no rank 28477 EBI-EMBL PAC2 family PAC2 family protein This PAC2 (Proteasome assembly chaperone) family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 247 and 307 amino acids in length. These proteins function as a chaperone for the 26S proteasome. The 26S proteasome mediates ubiquitin-dependent proteolysis in eukaryotic cells. A number of studies including very recent ones have revealed that assembly of its 20S catalytic core particle is an ordered process that involves several conserved proteasome assembly chaperones (PACs). Two heterodimeric chaperones, PAC1-PAC2 and PAC3-PAC4, promote the assembly of rings composed of seven alpha subunits [4]. [1]. 17431397. beta-Subunit appendages promote 20S proteasome assembly by overcoming an Ump1-dependent checkpoint. Li X, Kusmierczyk AR, Wong P, Emili A, Hochstrasser M;. EMBO J. 2007;26:2339-2349. [2]. 17707236. 20S proteasome assembly is orchestrated by two distinct pairs of chaperones in yeast and in mammals. Le Tallec B, Barrault MB, Courbeyrette R, Guerois R, Marsolier-Kergoat MC, Peyroche A;. Mol Cell. 2007;27:660-674. [3]. 16251969. A heterodimeric complex that promotes the assembly of mammalian 20S proteasomes. Hirano Y, Hendil KB, Yashiroda H, Iemura S, Nagane R, Hioki Y, Natsume T, Tanaka K, Murata S;. Nature. 2005;437:1381-1385. [4]. 18786393. PACemakers of proteasome core particle assembly. Ramos PC, Dohmen RJ;. Structure. 2008;16:1296-1304. (from Pfam) NF021288.5 PF09755.14 DUF2046 24.7 24.7 305 domain Y Y N DUF2046 domain-containing protein 131567 cellular organisms no rank 14 EBI-EMBL Uncharacterized conserved protein H4 (DUF2046) Uncharacterized conserved protein H4 (DUF2046) This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain. (from Pfam) NF021347.5 PF09818.14 ABC_ATPase 23.2 23.2 283 domain Y Y N P-loop domain-containing protein 26117548 131567 cellular organisms no rank 10619 EBI-EMBL P-loop domain P-loop domain This is the C-terminal ATPase domain from bacterial ABC class ATPases. This entry also includes MRB1590 (Swiss:Q57ZF2) from Trypanosoma brucei brucei has a central ATPase domain homologous to this domain [1]. [1]. 26117548. Structures of the T. brucei kRNA editing factor MRB1590 reveal unique RNA-binding pore motif contained within an ABC-ATPase fold. Shaw PL, McAdams NM, Hast MA, Ammerman ML, Read LK, Schumacher MA;. Nucleic Acids Res. 2015;43:7096-7109. (from Pfam) NF021348.5 PF09819.14 ABC_cobalt 25.2 25.2 121 PfamEq Y Y N ECF transporter S component 131567 cellular organisms no rank 12805 EBI-EMBL ABC-type cobalt transport system, permease component ECF transporter S component Members of this family of prokaryotic proteins include various hypothetical proteins as well as ABC-type cobalt transport systems. (from Pfam) NF021349.5 PF09820.14 AAA-ATPase_like 26.1 26.1 279 domain Y Y N AAA family ATPase 17584917 131567 cellular organisms no rank 33133 EBI-EMBL Predicted AAA-ATPase AAA family ATPase This family contains many hypothetical bacterial proteins. This family was previously the N-terminal part of the Pfam DUF1703 (Pfam:PF08011) family before it was split into two. This region is predicted to be an AAA-ATPase domain [1]. [1]. 17584917. Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches. Knizewski L, Kinch LN, Grishin NV, Rychlewski L, Ginalski K;. BMC Struct Biol. 2007;7:40. (from Pfam) NF021350.5 PF09821.14 AAA_assoc_C 27.6 27.6 119 domain Y Y N AAA-associated domain-containing protein 131567 cellular organisms no rank 7327 EBI-EMBL C-terminal AAA-associated domain C-terminal AAA-associated domain This had been thought to be an ATPase domain of ABC-transporter proteins. However, only one member has any trans-membrane regions. It is associated with an upstream ATP-binding cassette family, Pfam:PF00005. (from Pfam) NF021351.5 PF09822.14 ABC_transp_aux 34.7 34.7 266 domain Y Y N Gldg family protein 131567 cellular organisms no rank 18531 EBI-EMBL ABC-type uncharacterized transport system Gldg family protein This domain is found in various eukaryotic and prokaryotic intra-flagellar transport proteins involved in gliding motility, as well as in several hypothetical proteins. (from Pfam) NF021352.5 PF09823.14 DUF2357 23.3 23.3 251 PfamAutoEq Y Y N DUF2357 domain-containing protein 17584917 131567 cellular organisms no rank 6124 EBI-EMBL Domain of unknown function (DUF2357) Domain of unknown function (DUF2357) This entry was previously the N terminal portion of DUF524 (Pfam:PF04411) before it was split into two. This domain has no known function. It is predicted to adopt an all beta secondary structure pattern followed by mainly alpha-helical structures [1]. [1]. 17584917. Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches. Knizewski L, Kinch LN, Grishin NV, Rychlewski L, Ginalski K;. BMC Struct Biol. 2007;7:40. (from Pfam) NF021354.5 PF09825.14 BPL_N 24.2 24.2 283 domain Y Y N BPL-N domain-containing protein 18809372,7649444 131567 cellular organisms no rank 3781 EBI-EMBL Biotin-protein ligase, N terminal BPL-N domain Members of this family share a domain with the N-terminal region of certain eukaryotic type of biotin--protein ligases (BPL-N), such as BPL1_YEAST (P48445.1). The domain is not associated with BirA-type biotin--protein ligases. NF021355.5 PF09826.14 Beta_propel 22.4 22.4 495 domain Y Y N beta-propeller domain-containing protein 131567 cellular organisms no rank 5802 EBI-EMBL Beta propeller domain Beta propeller domain Members of this family comprise secreted bacterial proteins containing C-terminal beta-propeller domain distantly related to WD-40 repeats. Jpred secondary-structure prediction shows family to be a series of 4 short beta-strands, characteristic of beta-propeller families. (from Pfam) NF021356.5 PF09827.14 CRISPR_Cas2 23.8 23.8 74 domain Y N N CRISPR associated protein Cas2 17379808,18482976,22241770,24793649,30905284 131567 cellular organisms no rank 20734 EBI-EMBL CRISPR associated protein Cas2 CRISPR associated protein Cas2 This entry represents members of the family of Cas2, one of the first four protein families found to be associated with prokaryotic genomes containing multiple CRISPR elements. CRISPR systems protect against invasive nucleic acid sequences, including phage. Cas2 proteins have been characterised as either endoribonuclease (for ssRNA) or endodeoxyribonuclease (for dsDNA), depending on the system to which the Cas2 belongs [1,2]. The cas genes usually are found near the palindromic repeats. The structural subunit of Cas2, belongs to the VapD family of interferases. The interferase catalytic site is intact in the majority of the Cas2 proteins but is disrupted in some, and is not required for spacer acquisition [3,4]. This entry also includes the endoribonuclease VapD [5]. [1]. 17379808. CRISPR provides acquired resistance against viruses in prokaryotes. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P;. Science. 2007;315:1709-1712. [2]. 18482976. A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. Beloglazova N, Brown G, Zimmerman MD, Proudfoot M, Makarova KS, Kudritska M, Kochinyan S, Wang S, Chruszcz M, Minor W, Koonin EV, Edwards AM, Savchenko A, Yakunin AF;. J Biol Chem. 2008;283:20361-20371. [3]. 30905284. Origins and evolution of CRISPR-Cas systems. Koonin EV, Makarova KS;. Philos Trans R Soc Lond B Biol Sci. 2019;374:20180087. [4]. 24793649. Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nunez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA;. Na. TRUNCATED at 1650 bytes (from Pfam) NF021357.5 PF09828.14 ChrB_C 25 25 132 domain Y Y N chromate resistance protein ChrB domain-containing protein 12471500,2180932,24223748 131567 cellular organisms no rank 9710 EBI-EMBL ChrB, C-terminal domain ChrB, C-terminal domain This domain is found at the C-terminal end of Protein ChrB from the Proteobacteria Cupriavidus metallidurans, a protein involved in the reduction of chromate accumulation that is essential for chromate resistance [1,2]. This domain may carry the metal detection motives that are important for its function [3]. [1]. 12471500. New genes involved in chromate resistance in Ralstonia metallidurans strain CH34. Juhnke S, Peitzsch N, Hubener N, Grosse C, Nies DH;. Arch Microbiol. 2002;179:15-25. [2]. 2180932. Nucleotide sequence and expression of a plasmid-encoded chromate resistance determinant from Alcaligenes eutrophus. Nies A, Nies DH, Silver S;. J Biol Chem. 1990;265:5648-5653. [3]. 24223748. Identification and characterization of the transcriptional regulator ChrB in the chromate resistance determinant of Ochrobactrum tritici 5bvl1. Branco R, Morais PV;. PLoS One. 2013;8:e77987. (from Pfam) NF021362.5 PF09834.14 DUF2061 23.1 23.1 52 domain Y Y N DUF2061 domain-containing protein 131567 cellular organisms no rank 8738 EBI-EMBL Predicted membrane protein (DUF2061) Predicted membrane protein (DUF2061) This domain, found in various prokaryotic proteins, has no known function. (from Pfam) NF021363.5 PF09835.14 DUF2062 27.4 27.4 147 PfamAutoEq Y Y N DUF2062 domain-containing protein 131567 cellular organisms no rank 19064 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2062) Uncharacterized protein conserved in bacteria (DUF2062) This domain, found in various prokaryotic proteins, has no known function. (from Pfam) NF021365.5 PF09837.14 DUF2064 25.8 25.8 120 PfamAutoEq Y Y N DUF2064 domain-containing protein 131567 cellular organisms no rank 20875 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2064) Uncharacterized protein conserved in bacteria (DUF2064) This family has structural similarity to proteins in the nucleotide-diphospho-sugar transferases superfamily. The similarity suggests that it is an enzyme with a sugar substrate. (from Pfam) NF021368.5 PF09840.14 DUF2067 24.9 24.9 187 PfamAutoEq Y Y N DUF2067 family protein 131567 cellular organisms no rank 200 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2067) DUF2067 family protein This domain, found in various archaeal proteins, has no known function. (from Pfam) NF021370.5 PF09843.14 DUF2070 30 30 561 PfamAutoEq Y Y N DUF2070 family protein 131567 cellular organisms no rank 1091 EBI-EMBL Predicted membrane protein (DUF2070) DUF2070 family protein This is a family of Archaeal 7-TM proteins. There are 6 closely assembled TM-regions at the N-terminus followed by a long intracellular, from residues 220-590, highly conserved region, of unknown function, terminating with one more TM-region. The short 25 residue section between TMs 5 and 6 might lie on the outer surface of the membrane and be acting as a receptor (from TMHMM). (from Pfam) NF021371.5 PF09844.14 DUF2071 27 27 212 domain Y Y N DUF2071 domain-containing protein 131567 cellular organisms no rank 18663 EBI-EMBL Uncharacterized conserved protein (COG2071) Uncharacterized conserved protein (COG2071) This conserved protein (similar to YgjF), found in various prokaryotes, has no known function. (from Pfam) NF021372.5 PF09845.14 DUF2072 23 23 133 PfamEq Y Y N Zn-ribbon containing protein 131567 cellular organisms no rank 982 EBI-EMBL Zn-ribbon containing protein DUF2072 family Zn-ribbon containing protein Members of this archaeal protein family have an N-terminal predicted Zn-ribbon domain and a conserved C-terminal region. Hits to this HMM are frequently broken up because of a central region variable in both length and sequence. NF021373.5 PF09846.14 DUF2073 27 27 104 PfamAutoEq Y Y N DUF2073 domain-containing protein 131567 cellular organisms no rank 688 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2073) Uncharacterized protein conserved in archaea (DUF2073) This archaeal protein has no known function. (from Pfam) NF021374.5 PF09847.14 12TM_1 33.2 33.2 448 domain Y N N Membrane protein of 12 TMs 131567 cellular organisms no rank 215 EBI-EMBL Membrane protein of 12 TMs Membrane protein of 12 TMs This family carries twelve transmembrane regions. It does not have any characteristic nucleotide-binding-domains of the GxSGSGKST type. so it may not be an ATP-binding cassette transporter. However, it may well be a transporter of some description. ABC transporters always have two nucleotide binding domains; this has two unusual conserved sequence-motifs: 'KDhKxhhR' and 'LxxLP'. (from Pfam) NF021375.5 PF09848.14 SLFN-g3_helicase 24 24 354 domain Y Y N DNA/RNA helicase domain-containing protein 18355440,23570387,31504772 131567 cellular organisms no rank 39851 EBI-EMBL Schlafen group 3, DNA/RNA helicase domain Schlafen group 3, DNA/RNA helicase domain This domain is found in at the C terminus of group 3 Schlafen proteins from mammals, and represents the DNA/RNA helicase domain [2]. Schlafen proteins are involved in the control of cell proliferation, induction of immune responses, and in the regulation of viral replication [1,2,3]. These proteins inhibit DNA replication and promote cell death in response to DNA damage. They play a role in genome surveillance to kill cells with defective replication [3]. This domain is also found in various uncharacterised prokaryotic proteins fused to a DNA helicase, GIY-YIG or PD-(D/E)XK catalytic domain or HsdR-N(terminal) domain, which are similar to AAA DNA helicase, Type III restriction enzyme ATPase, RecD and RuvB helicase [3]. [1]. 23570387. The schlafen family of proteins and their regulation by interferons. Mavrommatis E, Fish EN, Platanias LC;. J Interferon Cytokine Res. 2013;33:206-210. [2]. 18355440. Subcellular localization of the Schlafen protein family. Neumann B, Zhao L, Murphy K, Gonda TJ;. Biochem Biophys Res Commun. 2008;370:62-66. [3]. 31504772. A protein architecture guided screen for modification dependent restriction endonucleases. Lutz T, Flodman K, Copelas A, Czapinska H, Mabuchi M, Fomenkov A, He X, Bochtler M, Xu SY;. Nucleic Acids Res. 2019;47:9761-9776. (from Pfam) NF021378.5 PF09851.14 SHOCT 27 15.3 28 domain Y Y N SHOCT domain-containing protein 131567 cellular organisms no rank 55431 EBI-EMBL Short C-terminal domain Short C-terminal domain NF021379.5 PF09852.14 DUF2079 28.2 28.2 459 domain Y Y N DUF2079 domain-containing protein 131567 cellular organisms no rank 11319 EBI-EMBL Predicted membrane protein (DUF2079) Predicted membrane protein (DUF2079) This domain, found in various hypothetical prokaryotic proteins, has no known function. (from Pfam) NF021380.5 PF09853.14 DUF2080 21.5 21.5 50 domain Y Y N DUF2080 family transposase-associated protein 131567 cellular organisms no rank 387 EBI-EMBL Putative transposon-encoded protein (DUF2080) DUF2080 family transposase-associated protein This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021381.5 PF09855.14 zinc_ribbon_13 23 23 63 subfamily Y Y N zinc ribbon domain-containing protein 131567 cellular organisms no rank 3022 EBI-EMBL Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082) zinc ribbon domain-containing protein This domain, found in various hypothetical prokaryotic proteins, as well as some Zn-ribbon nucleic-acid-binding proteins has no known function. (from Pfam) NF021384.5 PF09858.14 DUF2085 25 25 90 domain Y Y N DUF2085 domain-containing protein 131567 cellular organisms no rank 2654 EBI-EMBL Predicted membrane protein (DUF2085) Predicted membrane protein (DUF2085) This domain, found in various hypothetical prokaryotic proteins, has no known function. (from Pfam) NF021386.5 PF09860.14 DUF2087 22.4 22.4 69 domain Y Y N DUF2087 domain-containing protein 21348639 131567 cellular organisms no rank 16759 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2087) Uncharacterized protein conserved in bacteria (DUF2087) This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function. Structural modelling suggests this domain may bind nucleic acids [1]. [1]. 21348639. Ab Initio Modeling Led Annotation Suggests Nucleic Acid Binding Function for Many DUFs. Rigden DJ;. OMICS 2011;0:0-0. (from Pfam) NF021387.5 PF09861.14 Lar_N 23.3 23.3 204 domain Y Y N lactate racemase domain-containing protein GO:0050043 24710389 131567 cellular organisms no rank 13301 EBI-EMBL Lactate racemase N-terminal domain Lactate racemase N-terminal domain This is the N-terminal domain found in Lactate racemase enzymes EC:5.1.2.1. LarA is a nickel-dependent lactate racemase from the larA-E operon of Lactobacillus plantarum, whereas LarB, LarC and LarE are accessory proteins required for the incorporation of Ni in the lactate racemase apoprotein. LarA contains 18 beta-strands and 16 alpha-helices arranged in a novel fold composed of two domains of similar size. This entry represents the N-terminal domain of LarA and related proteins [1]. [1]. 24710389. Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. Desguin B, Goffin P, Viaene E, Kleerebezem M, Martin-Diaconescu V, Maroney MJ, Declercq JP, Soumillion P, Hols P;. Nat Commun. 2014;5:3615. (from Pfam) NF021388.5 PF09862.14 DUF2089 33.4 33.4 47 domain Y Y N DUF2089 family protein 131567 cellular organisms no rank 4933 EBI-EMBL Domain of unknown function (DUF2089)-HTH DUF2089 family protein This domain, found in various hypothetical prokaryotic proteins, has no known function. It occurs as a fusion of ZnR+HTH+SHOCT-like. (from Pfam) NF021391.5 PF09865.14 DUF2092 21.2 21.2 212 domain Y Y N DUF2092 domain-containing protein 131567 cellular organisms no rank 5401 EBI-EMBL Predicted periplasmic protein (DUF2092) Predicted periplasmic protein (DUF2092) This domain, found in various hypothetical prokaryotic proteins, has no known function. (from Pfam) NF021398.5 PF09872.14 DUF2099 25 25 257 subfamily Y Y N DUF2099 family protein 131567 cellular organisms no rank 693 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2099) DUF2099 family protein This domain, found in various hypothetical prokaryotic proteins, has no known function. (from Pfam) NF021399.5 PF09873.14 DUF2100 23 23 210 PfamAutoEq Y Y N DUF2100 domain-containing protein 131567 cellular organisms no rank 93 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2100) Uncharacterized protein conserved in archaea (DUF2100) This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021400.5 PF09874.14 DUF2101 22 22 206 PfamAutoEq Y Y N DUF2101 family protein 131567 cellular organisms no rank 193 EBI-EMBL Predicted membrane protein (DUF2101) DUF2101 family protein This domain, found in various archaeal and bacterial proteins, has no known function. (from Pfam) NF021402.5 PF09876.14 DUF2103 22.4 22.4 98 domain Y Y N DUF2103 domain-containing protein 131567 cellular organisms no rank 1630 EBI-EMBL Predicted metal-binding protein (DUF2103) DUF2103 domain This domain, found in various putative metal binding prokaryotic proteins, has no known function. (from Pfam) NF021408.5 PF09882.14 DUF2109 23.1 23.1 76 PfamAutoEq Y Y N DUF2109 family protein 131567 cellular organisms no rank 258 EBI-EMBL Predicted membrane protein (DUF2109) DUF2109 family protein This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021409.5 PF09883.14 DUF2110 23.2 23.2 223 PfamAutoEq Y Y N DUF2110 family protein 131567 cellular organisms no rank 776 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2110) DUF2110 family protein This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021413.5 PF09887.14 DUF2114 25 25 449 PfamAutoEq Y Y N DUF2114 family protein 131567 cellular organisms no rank 482 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2114) DUF2114 family protein This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021414.5 PF09888.14 DUF2115 25 25 162 domain Y Y N DUF2115 family protein 131567 cellular organisms no rank 997 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2115) DUF2115 family protein This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021415.5 PF09889.14 DUF2116 21.8 21.8 59 PfamAutoEq Y Y N DUF2116 family Zn-ribbon domain-containing protein 21348639 131567 cellular organisms no rank 1030 EBI-EMBL Uncharacterized protein containing a Zn-ribbon (DUF2116) Uncharacterized protein containing a Zn-ribbon (DUF2116) This domain, found in various hypothetical archaeal proteins, has no known function. Structural modelling suggests this domain may bind nucleic acids [1]. [1]. 21348639. Ab Initio Modeling Led Annotation Suggests Nucleic Acid Binding Function for Many DUFs. Rigden DJ;. OMICS 2011;0:0-0. (from Pfam) NF021416.5 PF09890.14 DUF2117 25 25 325 domain Y Y N DUF2117 domain-containing protein 131567 cellular organisms no rank 547 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2117) Uncharacterized protein conserved in archaea (DUF2117) This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021417.5 PF09891.14 DUF2118 20.5 20.5 149 PfamAutoEq Y Y N DUF2118 domain-containing protein 131567 cellular organisms no rank 698 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2118) Uncharacterized protein conserved in archaea (DUF2118) This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021418.5 PF09892.14 DUF2119 30.5 30.5 188 PfamAutoEq Y Y N DUF2119 family protein 131567 cellular organisms no rank 343 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2119) DUF2119 family protein This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021425.5 PF09900.14 DUF2127 24.3 24.3 140 PfamAutoEq Y Y N DUF2127 domain-containing protein 131567 cellular organisms no rank 6971 EBI-EMBL Predicted membrane protein (DUF2127) Predicted membrane protein (DUF2127) This domain, found in various hypothetical prokaryotic and archaeal proteins, has no known function. (from Pfam) NF021427.5 PF09903.14 DUF2130 26.7 26.7 255 PfamAutoEq Y Y N DUF2130 domain-containing protein 131567 cellular organisms no rank 10538 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2130) Uncharacterized protein conserved in bacteria (DUF2130) This domain, found in various hypothetical prokaryotic proteins, has no known function. (from Pfam) NF021436.5 PF09913.14 DUF2142 30.1 30.1 395 domain Y Y N DUF2142 domain-containing protein 131567 cellular organisms no rank 9345 EBI-EMBL Predicted membrane protein (DUF2142) Predicted membrane protein (DUF2142) This domain, found in various hypothetical prokaryotic proteins, has no known function. (from Pfam) NF021439.5 PF09918.14 DUF2148 25 25 68 subfamily_domain Y Y N DUF2148 domain-containing protein 131567 cellular organisms no rank 1236 EBI-EMBL Uncharacterized protein containing a ferredoxin domain (DUF2148) Uncharacterized protein containing a ferredoxin domain (DUF2148) This HMM describes the conserved C-terminal domain of a protein family in which most members share a ferredoxin-like central motif with four conserved Cys residues. One of those Cys residues is included in this HMM's seed alignment. NF021440.5 PF09919.14 DUF2149 27.1 27.1 92 domain Y Y N DUF2149 domain-containing protein 131567 cellular organisms no rank 2751 EBI-EMBL Uncharacterized conserved protein (DUF2149) Uncharacterized conserved protein (DUF2149) This domain, found in various hypothetical prokaryotic proteins, has no known function. (from Pfam) NF021442.5 PF09921.14 DUF2153 23 23 123 PfamAutoEq Y Y N DUF2153 family protein 131567 cellular organisms no rank 98 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2153) DUF2153 family protein This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021443.5 PF09922.14 LiaF-like_C 29 29 114 domain Y Y N LiaF domain-containing protein 16923071,19889788 131567 cellular organisms no rank 19700 EBI-EMBL Cell wall-active antibiotics response LiaF, C-terminal Cell wall-active antibiotics response LiaF, C-terminal This domain is found in various prokaryotic proteins, including cell wall-active antibiotic response proteins. This entry includes protein product of the yvqF gene, LiaF, located immediately upstream of vraS. It is associated with glycopeptide resistance in Staphylococcus aureus [2]. This domain has been described as toast rack from its structural resemblance. [1]. 16923071. The VraS/VraR two-component regulatory system required for oxacillin resistance in community-acquired methicillin-resistant Staphylococcus aureus. Boyle-Vavra S, Yin S, Daum RS;. FEMS Microbiol Lett. 2006;262:163-171. [2]. 19889788. Genetic changes associated with glycopeptide resistance in Staphylococcus aureus: predominance of amino acid substitutions in YvqF/VraSR. Kato Y, Suzuki T, Ida T, Maebashi K;. J Antimicrob Chemother. 2010;65:37-45. (from Pfam) NF021445.5 PF09924.14 LPG_synthase_C 27.5 27.5 298 domain Y Y N phosphatidylglycerol lysyltransferase domain-containing protein 14769468,19649276,30563904 131567 cellular organisms no rank 64193 EBI-EMBL Phosphatidylglycerol lysyltransferase, C-terminal Phosphatidylglycerol lysyltransferase, C-terminal This domain can be found in the C-terminal region of phosphatidylglycerol lysyltransferase mprF, which catalyses the transfer of a lysyl group from L-lysyl-tRNA(Lys) to to membrane-bound phosphatidylglycerol (PG), which produces lysylphosphatidylglycerol (LPG) [1,3]. This domain can also be found in lysylphosphatidylglycerol biosynthesis bifunctional protein LysX, which is the two-domain lysyl-transferase (mprF)-lysyl-tRNA synthetase (lysU) protein is responsible for LPG production [2]. [1]. 14769468. MprF-mediated biosynthesis of lysylphosphatidylglycerol, an important determinant in staphylococcal defensin resistance. Staubitz P, Neumann H, Schneider T, Wiedemann I, Peschel A;. FEMS Microbiol Lett. 2004;231:67-71. [2]. 19649276. The two-domain LysX protein of Mycobacterium tuberculosis is required for production of lysinylated phosphatidylglycerol and resistance to cationic antimicrobial peptides. Maloney E, Stankowska D, Zhang J, Fol M, Cheng QJ, Lun S, Bishai WR, Rajagopalan M, Chatterjee D, Madiraju MV;. PLoS Pathog. 2009;5:e1000534. [3]. 30563904. Gain-of-Function Mutations in the Phospholipid Flippase MprF Confer Specific Daptomycin Resistance. Ernst CM, Slavetinsky CJ, Kuhn S, Hauser JN, Nega M, Mishra NN, Gekeler C, Bayer AS, Peschel A;. mBio. 2018; [Epub ahead of print] (from Pfam) NF021446.5 PF09925.14 DUF2157 32.4 32.4 146 PfamAutoEq Y Y N DUF2157 domain-containing protein 131567 cellular organisms no rank 15207 EBI-EMBL Predicted membrane protein (DUF2157) Predicted membrane protein (DUF2157) This domain, found in various hypothetical prokaryotic proteins, has no known function. (from Pfam) NF021450.5 PF09930.14 DUF2162 34.4 34.4 223 subfamily Y Y N DUF2162 family putative transporter 131567 cellular organisms no rank 543 EBI-EMBL Predicted transporter (DUF2162) DUF2162 family putative transporter Members of this family of bacterial proteins are thought to be membrane transporters, but their exact function has not, as yet, been elucidated. (from Pfam) NF021452.5 PF09932.14 DUF2164 27 27 74 PfamAutoEq Y Y N DUF2164 family protein 131567 cellular organisms no rank 7560 EBI-EMBL Uncharacterized conserved protein (DUF2164) DUF2164 family protein This domain, found in various hypothetical prokaryotic proteins, has no known function. (from Pfam) NF021455.5 PF09936.14 Methyltrn_RNA_4 22.6 22.6 182 domain Y Y N RNA methyltransferase 18831037 131567 cellular organisms no rank 1774 EBI-EMBL SAM-dependent RNA methyltransferase RNA methyltransferase This family has a Rossmanoid fold, with a deep trefoil knot in its C-terminal region. It has structural similarity to RNA methyltransferases, and is likely to function as an S-adenosyl-L-methionine (SAM)-dependent RNA 2'-O methyltransferase [1]. [1]. 18831037. Crystal structure of Thermotoga maritima SPOUT superfamily RNA methyltransferase Tm1570 in complex with S-adenosyl-L-methionine. Kim do J, Kim HS, Lee SJ, Suh SW;. Proteins. 2009;74:245-249. (from Pfam) NF021458.5 PF09939.14 DUF2171 25 25 64 domain Y Y N DUF2171 domain-containing protein 131567 cellular organisms no rank 5199 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2171) Uncharacterized protein conserved in bacteria (DUF2171) This domain, found in various hypothetical prokaryotic proteins, has no known function. (from Pfam) NF021459.5 PF09940.14 DUF2172 27 25 92 PfamAutoEq Y Y N DUF2172 domain-containing protein 131567 cellular organisms no rank 6441 EBI-EMBL Domain of unknown function (DUF2172) Domain of unknown function (DUF2172) This domain, found in various hypothetical prokaryotic proteins, has no known function. An aminopeptidase domain is conserved within the family, but its relevance has not been established yet. Rebuilding from PDB:3kt9 shows this is an inserted (nested domain within the amino-peptidase). The function of this small domain is not known. (from Pfam) NF021460.5 PF09941.14 DUF2173 26.1 26.1 106 subfamily Y Y N DUF2173 family protein 131567 cellular organisms no rank 387 EBI-EMBL Uncharacterized conserved protein (DUF2173) DUF2173 family protein This domain, found in various hypothetical prokaryotic proteins, has no known function. (from Pfam) NF021461.5 PF09943.14 DUF2175 25.1 25.1 98 PfamAutoEq Y Y N DUF2175 family protein 131567 cellular organisms no rank 95 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2175) DUF2175 family protein This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021463.5 PF09946.14 DUF2178 22.8 22.8 104 domain Y Y N DUF2178 domain-containing protein 131567 cellular organisms no rank 882 EBI-EMBL Predicted membrane protein (DUF2178) Predicted membrane protein (DUF2178) This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021464.5 PF09947.14 DUF2180 22.2 22.2 68 subfamily Y Y N DUF2180 family protein 131567 cellular organisms no rank 1382 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2180) DUF2180 family protein This domain, found in various hypothetical archaeal proteins, has no known function. A few of the family members contain a zinc finger domain. (from Pfam) NF021465.5 PF09948.14 DUF2182 28.7 28.7 188 domain Y Y N DUF2182 domain-containing protein 131567 cellular organisms no rank 10939 EBI-EMBL Predicted metal-binding integral membrane protein (DUF2182) Predicted metal-binding integral membrane protein (DUF2182) This domain, found in various hypothetical bacterial membrane proteins having predicted metal-binding properties, has no known function. (from Pfam) NF021468.5 PF09951.14 DUF2185 25.4 25.4 85 PfamAutoEq Y Y N DUF2185 domain-containing protein 131567 cellular organisms no rank 4037 EBI-EMBL Protein of unknown function (DUF2185) Protein of unknown function (DUF2185) This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021469.5 PF09952.14 AbiEi_2 21 21 143 PfamEq Y Y N type IV toxin-antitoxin system AbiEi family antitoxin 24465005 131567 cellular organisms no rank 3915 EBI-EMBL Transcriptional regulator, AbiEi antitoxin, Type IV TA system type IV toxin-antitoxin system AbiEi family antitoxin AbiEi_2 is the cognate antitoxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is Pfam:PF13338 [1]. [1]. 24465005. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Dy RL, Przybilski R, Semeijn K, Salmond GP, Fineran PC;. Nucleic Acids Res. 2014;42:4590-4605. (from Pfam) NF021471.5 PF09954.14 DUF2188 22 22 62 domain Y Y N DUF2188 domain-containing protein 32868406 131567 cellular organisms no rank 13854 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2188) Uncharacterized protein conserved in bacteria (DUF2188) This domain represents a ribosome-associating protein predicted to mediate translation inhibition alongside repair of DNA damage or restriction in conflict contexts. A subset of this family contains a conserved histidine residue, raising the possibility that it directly acts as a RNase or in RNA end-processing [1]. [1]. 32868406. Identification of Uncharacterized Components of Prokaryotic Immune Systems and Their Diverse Eukaryotic Reformulations. Burroughs AM, Aravind L;. J Bacteriol. 2020; [Epub ahead of print] (from Pfam) NF021473.5 PF09956.14 DUF2190 23.1 23.1 103 subfamily Y Y N capsid cement protein 36656854 131567 cellular organisms no rank 7646 EBI-EMBL Uncharacterized conserved protein (DUF2190) capsid cement protein This domain, found in various hypothetical prokaryotic proteins has no known function. (from Pfam) NF021474.5 PF09957.14 VapB_antitoxin 23.4 23.4 47 domain Y Y N type II toxin-antitoxin system VapB family antitoxin 15718296,20011113 131567 cellular organisms no rank 12575 EBI-EMBL Bacterial antitoxin of type II TA system, VapB type II toxin-antitoxin system VapB family antitoxin VapB is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is VapC, Pfam:PF05016. The family contains several related antitoxins from Cyanobacteria and Actinobacterial families. Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerises with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible alpha helices at the C-terminus. This C-terminus is the Toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all antitoxins. [1]. 15718296. Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Pandey DP, Gerdes K;. Nucleic Acids Res. 2005;33:966-976. [2]. 20011113. Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution. Ramage HR, Connolly LE, Cox JS;. PLoS Genet. 2009;5:e1000767. (from Pfam) NF021475.5 PF09958.14 DUF2192 21 21 229 domain Y Y N DUF2192 domain-containing protein 131567 cellular organisms no rank 155 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2192) Uncharacterized protein conserved in archaea (DUF2192) This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021476.5 PF09959.14 DUF2193 25 25 498 PfamAutoEq Y Y N DUF2193 family protein 131567 cellular organisms no rank 399 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2193) DUF2193 family protein This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021477.5 PF09960.14 DUF2194 30.4 30.4 582 PfamAutoEq Y Y N DUF2194 domain-containing protein 131567 cellular organisms no rank 2661 EBI-EMBL Uncharacterised protein conserved in bacteria (DUF2194) Uncharacterised protein conserved in bacteria (DUF2194) This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021479.5 PF09962.14 DUF2196 25 25 61 domain Y Y N DUF2196 domain-containing protein 131567 cellular organisms no rank 5729 EBI-EMBL Uncharacterized conserved protein (DUF2196) Uncharacterized conserved protein (DUF2196) This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021483.5 PF09966.14 DUF2200 22.8 22.8 111 PfamAutoEq Y Y N DUF2200 family protein 131567 cellular organisms no rank 10330 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2200) DUF2200 family protein This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021484.5 PF09967.14 DUF2201 26.4 26.4 123 domain Y Y N VWA-like domain-containing protein 131567 cellular organisms no rank 15747 EBI-EMBL VWA-like domain (DUF2201) VWA-like domain This domain, found in various hypothetical bacterial proteins, has no known function. However, it is clearly related to the VWA domain. (from Pfam) NF021485.5 PF09968.14 DUF2202 22 22 162 domain Y Y N DUF2202 domain-containing protein 21604308 131567 cellular organisms no rank 2354 EBI-EMBL Uncharacterized protein domain (DUF2202) Uncharacterized protein domain (DUF2202) This domain is found in Uncharacterized protein MJ0754 from Methanocaldococcus jannaschii and similar proteins from bacteria and archaea. MJ0754 adopts a dimeric assembly, with each monomer consisting of six alpha-helices [1]. It is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins whose function is unknown. The conserved residues of a diiron centre are present within the putative active site. [1]. 21604308. Structural insights into the metal binding properties of hypothetical protein MJ0754 from Methanococcus jannaschii. Lee EH, Kim HS, Kim HY, Jeon YH, Hwang KY;. Proteins. 2011;79:2358-2363. (from Pfam) NF021486.5 PF09969.14 DUF2203 24 24 122 PfamAutoEq Y Y N DUF2203 family protein 131567 cellular organisms no rank 2531 EBI-EMBL Uncharacterized conserved protein (DUF2203) DUF2203 family protein This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021487.5 PF09970.14 DUF2204 20.3 20.3 181 PfamAutoEq Y Y N nucleotidyltransferase 19833706 131567 cellular organisms no rank 2382 EBI-EMBL Nucleotidyl transferase of unknown function (DUF2204) nucleotidyltransferase This domain, found in various hypothetical archaeal proteins, has no known function. However, this family was identified as belonging to the nucleotidyltransferase superfamily [1]. [1]. 19833706. Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. Kuchta K, Knizewski L, Wyrwicz LS, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2009; [Epub ahead of print] (from Pfam) NF021488.5 PF09971.14 DUF2206 35.6 35.6 368 domain Y Y N DUF2206 domain-containing protein 131567 cellular organisms no rank 489 EBI-EMBL Predicted membrane protein (DUF2206) Predicted membrane protein (DUF2206) This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021489.5 PF09972.14 DUF2207 24.4 24.4 172 domain Y Y N DUF2207 domain-containing protein 131567 cellular organisms no rank 22944 EBI-EMBL Predicted membrane protein (DUF2207) N-terminal domain Predicted membrane protein (DUF2207) N-terminal domain This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021490.5 PF09973.14 DUF2208 24.3 24.3 231 PfamAutoEq Y Y N DUF2208 family protein 131567 cellular organisms no rank 108 EBI-EMBL Predicted membrane protein (DUF2208) DUF2208 family protein This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021492.5 PF09976.14 TPR_21 25.5 25.5 193 domain Y Y N tetratricopeptide repeat protein 131567 cellular organisms no rank 31151 EBI-EMBL Tetratricopeptide repeat-like domain Tetratricopeptide repeat-like domain This family resembles a single unit of a TPR repeat. (from Pfam) NF021493.5 PF09977.14 Tad_C 22.1 22.1 93 domain Y Y N TadG family pilus assembly protein 131567 cellular organisms no rank 9049 EBI-EMBL Putative Tad-like Flp pilus-assembly TadG family pilus assembly protein N-terminal domain This HMM (PF09977) hits many of the same proteins in the N-terminal half, while PF13400 hits these same proteins even further upstream. Member proteins include TadG, involved in Flp pilus assembly. NF021494.5 PF09979.14 DUF2213 22 22 167 domain Y Y N DUF2213 domain-containing protein 131567 cellular organisms no rank 10191 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2213) Uncharacterized protein conserved in bacteria (DUF2213) Members of this family of bacterial proteins comprise various hypothetical and phage-related proteins. The exact function of these proteins has not, as yet, been determined. (from Pfam) NF021498.5 PF09983.14 JetD_C 22 22 179 domain Y Y N Wadjet anti-phage system protein JetD domain-containing protein 29371424 131567 cellular organisms no rank 12162 EBI-EMBL Wadjet protein JetD, C-terminal DUF2220 C-terminal domain This is a domain found at the C-terminal of Wadjet protein JetD from Bacillus cereus. JetD is a component of the antiplasmid transformation system Wadjet type I, composed of JetA, JetB, JetC and JetD. Expression of Wadjet type I in B.subtilis (strain BEST7003) reduces the transformation efficiency of plasmid pHCMC05 [1]. This domain is structurally similar to DNA topoisomerases, therefore, it may be a DNA-binding domain. [1]. 29371424. Systematic discovery of antiphage defense systems in the microbial pangenome. Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R;. Science. 2018; [Epub ahead of print] (from Pfam) NF021500.5 PF09985.14 Glucodextran_C 22 22 228 domain Y Y N glucodextranase DOMON-like domain-containing protein 14660574 131567 cellular organisms no rank 3088 EBI-EMBL C-terminal binding-module, SLH-like, of glucodextranase C-terminal binding-module, SLH-like, of glucodextranase Glucodextran_C is the C-terminal domain of glucodextranase-like proteins found in various prokaryotic membrane-anchored proteins. It shows homology to the carbohydrate-binding unit of some glycosidases [1]. [1]. 14660574. Structural insights into substrate specificity and function of glucodextranase. Mizuno M, Tonozuka T, Suzuki S, Uotsu-Tomita R, Kamitori S, Nishikawa A, Sakano Y;. J Biol Chem. 2004;279:10575-10583. (from Pfam) NF021501.5 PF09986.14 DUF2225 21 21 214 PfamAutoEq Y Y N DUF2225 domain-containing protein 131567 cellular organisms no rank 4465 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2225) Uncharacterized protein conserved in bacteria (DUF2225) This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021502.5 PF09987.14 DUF2226 22 22 252 domain Y Y N DUF2226 domain-containing protein 131567 cellular organisms no rank 202 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2226) Uncharacterized protein conserved in archaea (DUF2226) This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021503.5 PF09988.14 DUF2227 25 25 169 PfamAutoEq Y Y N DUF2227 family putative metal-binding protein 131567 cellular organisms no rank 1893 EBI-EMBL Uncharacterized metal-binding protein (DUF2227) DUF2227 family putative metal-binding protein Members of this family of hypothetical bacterial proteins possess metal binding properties; however, their exact function has not, as yet, been determined. (from Pfam) NF021504.5 PF09989.14 DUF2229 29.4 29.4 218 domain Y Y N acyl-CoA dehydratase activase-related protein 131567 cellular organisms no rank 16878 EBI-EMBL CoA enzyme activase uncharacterised domain (DUF2229) acyl-CoA dehydratase activase-related protein Members of this family include various bacterial hypothetical proteins, as well as CoA enzyme activases. The exact function of this domain has not, as yet, been defined. (from Pfam) NF021505.5 PF09990.14 DUF2231 26.4 26.4 139 domain Y Y N DUF2231 domain-containing protein 131567 cellular organisms no rank 30074 EBI-EMBL Predicted membrane protein (DUF2231) Predicted membrane protein (DUF2231) This domain, found in various hypothetical bacterial proteins, has no known function. It has similarity to Pfam:PF01292 suggesting it is a haem-binding cytochrome. (from Pfam) NF021507.5 PF09992.14 NAGPA 25 25 169 domain Y Y N phosphodiester glycosidase family protein 20147709,23572527 131567 cellular organisms no rank 47734 EBI-EMBL Phosphodiester glycosidase phosphodiester glycosidase family protein This is a family conserved from bacteria to humans. The structure of a member from Bacteroides has been crystallised and modelled onto the luminal region of the human member of the family, the transmembrane glycoprotein N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase. There is some conservation of potentially functional residues, implying that in the bacterial members this family acts in some way as a phosphodiester glycosidase [1]. The human protein is also present, so the eukaryotic members are likely to be catalysing the second step in the formation of the mannose 6-phosphate targeting signal on lysosomal enzyme oligosaccharides [2]. [1]. 23572527. Structure and function of the DUF2233 domain in bacteria and in the human mannose 6-phosphate uncovering enzyme. Das D, Lee WS, Grant JC, Chiu HJ, Farr CL, Vance J, Klock HE, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Kornfeld S, Wilson IA;. J Biol Chem. 2013;288:16789-16799. [2]. 20147709. Mutations in the lysosomal enzyme-targeting pathway and persistent stuttering. Kang C, Riazuddin S, Mundorff J, Krasnewich D, Friedman P, Mullikin JC, Drayna D;. N Engl J Med. 2010;362:677-685. (from Pfam) NF021510.5 PF09996.14 DUF2237 25 25 115 PfamAutoEq Y Y N DUF2237 family protein 131567 cellular organisms no rank 7822 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2237) DUF2237 family protein This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021511.5 PF09997.14 DUF2238 26.4 26.4 140 PfamAutoEq Y Y N DUF2238 domain-containing protein 131567 cellular organisms no rank 13617 EBI-EMBL Predicted membrane protein (DUF2238) Predicted membrane protein (DUF2238) This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021513.5 PF09999.14 DUF2240 22.3 22.3 144 PfamAutoEq Y Y N DUF2240 family protein 131567 cellular organisms no rank 954 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2240) DUF2240 family protein This domain, found in various hypothetical archaeal proteins, has no known function. (from Pfam) NF021514.5 PF10000.14 ACT_3 25 25 70 PfamEq Y Y N ACT domain-containing protein 131567 cellular organisms no rank 10305 EBI-EMBL ACT domain ACT domain This domain, found in various hypothetical bacterial proteins, has no known function. However, its structure is similar to the ACT domain which suggests that it binds to amino acids and regulates other protein activity. This family was formerly known as DUF2241. (from Pfam) NF021516.5 PF10002.14 DUF2243 25 25 140 PfamAutoEq Y Y N DUF2243 domain-containing protein 131567 cellular organisms no rank 8101 EBI-EMBL Predicted membrane protein (DUF2243) Predicted membrane protein (DUF2243) This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021519.5 PF10005.14 zinc-ribbon_6 23.4 23.4 93 domain Y Y N zinc-ribbon domain-containing protein 131567 cellular organisms no rank 11024 EBI-EMBL zinc-ribbon domain zinc-ribbon domain This family appears to be a true zinc-ribbon, with two sets of putative zinc-binding domains in tandem. (from Pfam) NF021520.5 PF10006.14 DUF2249 29.5 29.5 70 domain Y Y N DUF2249 domain-containing protein 131567 cellular organisms no rank 11503 EBI-EMBL Uncharacterized conserved protein (DUF2249) Uncharacterized conserved protein (DUF2249) Members of this family of hypothetical bacterial proteins have no known function. (from Pfam) NF021521.5 PF10007.14 DUF2250 24.4 24.4 93 PfamAutoEq Y Y N DUF2250 domain-containing protein 131567 cellular organisms no rank 408 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2250) Uncharacterized protein conserved in archaea (DUF2250) Members of this family of hypothetical archaeal proteins have no known function. (from Pfam) NF021523.5 PF10009.14 DUF2252 22.3 22.3 392 domain Y Y N DUF2252 family protein 131567 cellular organisms no rank 37299 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2252) DUF2252 family protein This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021524.5 PF10011.14 DUF2254 28.8 28.8 368 subfamily Y Y N DUF2254 family protein 131567 cellular organisms no rank 23328 EBI-EMBL Predicted membrane protein (DUF2254) DUF2254 family protein Members of this family of bacterial proteins comprises various hypothetical and putative membrane proteins. Their exact function, has not, as yet, been defined. (from Pfam) NF021525.5 PF10012.14 DUF2255 29.8 29.8 115 PfamAutoEq Y Y N DUF2255 family protein 131567 cellular organisms no rank 5314 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2255) DUF2255 family protein Members of this family of hypothetical bacterial proteins have no known function. (from Pfam) NF021530.5 PF10017.14 Methyltransf_33 23 23 304 PfamEq Y Y N L-histidine N(alpha)-methyltransferase 2.1.1.44 20420449 131567 cellular organisms no rank 28480 EBI-EMBL Histidine-specific methyltransferase, SAM-dependent L-histidine N(alpha)-methyltransferase The mycobacterial members of this family are expressed from part of the ergothioneine biosynthetic gene cluster. EGTD is the histidine methyltransferase that transfers three methyl groups to the alpha-amino moiety of histidine, in the first stage of the production of this histidine betaine derivative that carries a thiol group attached to the C2 atom of an imidazole ring [1]. [1]. 20420449. In vitro reconstitution of Mycobacterial ergothioneine biosynthesis. Seebeck FP;. J Am Chem Soc. 2010;132:6632-6633. (from Pfam) NF021532.5 PF10020.14 DUF2262 29.8 29.8 142 domain Y Y N DUF2262 domain-containing protein 131567 cellular organisms no rank 3671 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2262) Uncharacterized protein conserved in bacteria (DUF2262) This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021533.5 PF10021.14 PARG_cat_microb 23.5 23.5 146 domain Y Y N poly(ADP-ribose) glycohydrolase domain-containing protein 21892188,30940816 131567 cellular organisms no rank 10371 EBI-EMBL Microbial-type PARG, catalytic domain Microbial-type PARG, catalytic domain Poly(ADP-ribose) glycohydrolase (PARG) hydrolyses the ribose-ribose bonds present in poly(ADP-ribose) (PAR) chains. This entry represents the PARG homologue present in bacteria and fungi. Its structure shows a typical macrodomain folding consisting of a seven-stranded beta-sheet sandwiched between nine alpha-helices [1,2]. [1]. 21892188. The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase. Slade D, Dunstan MS, Barkauskaite E, Weston R, Lafite P, Dixon N, Ahel M, Leys D, Ahel I;. Nature. 2011;477:616-620. [2]. 30940816. Structural and biochemical evidence supporting poly ADP-ribosylation in the bacterium Deinococcus radiodurans. Cho CC, Chien CY, Chiu YC, Lin MH, Hsu CH;. Nat Commun. 2019;10:1491. (from Pfam) NF021534.5 PF10022.14 DUF2264 25 25 353 domain Y Y N DUF2264 domain-containing protein 131567 cellular organisms no rank 24259 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2264) Uncharacterized protein conserved in bacteria (DUF2264) Members of this family of hypothetical bacterial proteins have no known function. (from Pfam) NF021536.5 PF10025.14 DUF2267 29.8 29.8 122 domain Y Y N DUF2267 domain-containing protein 131567 cellular organisms no rank 21718 EBI-EMBL Uncharacterized conserved protein (DUF2267) Uncharacterized conserved protein (DUF2267) This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021537.5 PF10026.14 DUF2268 23.6 23.6 195 domain Y Y N DUF2268 domain-containing putative Zn-dependent protease 131567 cellular organisms no rank 13506 EBI-EMBL Predicted Zn-dependent protease (DUF2268) DUF2268 putative Zn-dependent protease domain This domain, found in various hypothetical bacterial proteins, as well as predicted zinc dependent proteases, has no known function. (from Pfam). predicted Zn-dependent protease with a strongly conserved HExxH motif NF021538.5 PF10027.14 DUF2269 28 28 150 subfamily Y Y N DUF2269 family protein 131567 cellular organisms no rank 14282 EBI-EMBL Predicted integral membrane protein (DUF2269) DUF2269 family protein Members of this family of bacterial hypothetical integral membrane proteins have no known function. (from Pfam) NF021539.5 PF10028.14 DUF2270 25 25 184 domain Y Y N DUF2270 domain-containing protein 131567 cellular organisms no rank 2881 EBI-EMBL Predicted integral membrane protein (DUF2270) Predicted integral membrane protein (DUF2270) This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021541.5 PF10030.14 DUF2272 27 27 191 PfamAutoEq Y Y N DUF2272 domain-containing protein 131567 cellular organisms no rank 3189 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2272) Uncharacterized protein conserved in bacteria (DUF2272) Members of this family of hypothetical bacterial proteins have no known function. However, given its similarity to the CHAP domain it seems likely that this is an enzyme involved in cleaving peptidoglycan. (from Pfam) NF021546.5 PF10035.14 DUF2179 22.8 22.8 55 domain Y Y N DUF2179 domain-containing protein 131567 cellular organisms no rank 54550 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2179) Uncharacterized protein conserved in bacteria (DUF2179) This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021551.5 PF10040.14 CRISPR_Cas6 25 25 89 domain Y Y N CRISPR system precrRNA processing endoribonuclease RAMP protein Cas6 cas6 16292354,16545108,19141480 131567 cellular organisms no rank 5632 EBI-EMBL CRISPR-associated endoribonuclease Cas6 CRISPR system precrRNA processing endoribonuclease RAMP protein Cas6 Cas6 is a member of the RAMP (repeat-associated mysterious protein) superfamily [1]. It is among the most widely distributed Cas proteins and is found in both bacteria and archaea [2]. Cas6 functions in the generation of CRISPR-derived guide RNAs for invader defense in prokaryotes [3]. [1]. 16545108. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV;. Biol Direct. 2006;1:7. [2]. 16292354. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. Haft DH, Selengut J, Mongodin EF, Nelson KE;. PLoS Comput Biol. 2005;1:e60. [3]. 19141480. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Carte J, Wang R, Li H, Terns RM, Terns MP;. Genes Dev. 2008;22:3489-3496. (from Pfam) NF021553.5 PF10042.14 DUF2278 25 25 206 PfamAutoEq Y Y N DUF2278 family protein 131567 cellular organisms no rank 4827 EBI-EMBL Uncharacterized conserved protein (DUF2278) DUF2278 family protein Members of this family of hypothetical bacterial proteins have no known function. (from Pfam) NF021558.5 PF10047.14 DUF2281 26.5 26.5 64 domain Y Y N DUF2281 domain-containing protein 131567 cellular organisms no rank 4020 EBI-EMBL Protein of unknown function (DUF2281) Protein of unknown function (DUF2281) Members of this family of hypothetical bacterial proteins have no known function. (from Pfam) NF021560.5 PF10049.14 DUF2283 23 23 49 domain Y Y N DUF2283 domain-containing protein 131567 cellular organisms no rank 6430 EBI-EMBL Protein of unknown function (DUF2283) Protein of unknown function (DUF2283) Members of this family of hypothetical bacterial proteins have no known function. (from Pfam) NF021561.5 PF10050.14 DUF2284 25 25 161 domain Y Y N DUF2284 domain-containing protein 131567 cellular organisms no rank 3294 EBI-EMBL Predicted metal-binding protein (DUF2284) DUF2284 domain Members of this family of metal-binding hypothetical bacterial proteins have no known function. (from Pfam) NF021564.5 PF10053.14 DUF2290 25 25 204 PfamAutoEq Y Y N DUF2290 domain-containing protein 131567 cellular organisms no rank 1216 EBI-EMBL Uncharacterized conserved protein (DUF2290) Uncharacterized conserved protein (DUF2290) Members of this family of hypothetical bacterial proteins have no known function. (from Pfam) NF021570.5 PF10060.14 DUF2298 27.8 27.8 488 domain Y Y N DUF2298 domain-containing protein 131567 cellular organisms no rank 1723 EBI-EMBL Uncharacterized membrane protein (DUF2298) DUF2298 domain This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021571.5 PF10061.14 DUF2299 22.8 22.8 138 domain Y Y N DUF2299 family protein 131567 cellular organisms no rank 373 EBI-EMBL Uncharacterized conserved protein (DUF2299) DUF2299 family protein Members of this family of hypothetical bacterial proteins have no known function. (from Pfam) NF021575.5 PF10066.14 DUF2304 25.5 25.5 106 PfamAutoEq Y Y N DUF2304 family protein 131567 cellular organisms no rank 8903 EBI-EMBL Uncharacterized conserved protein (DUF2304) DUF2304 family protein Members of this family of hypothetical archaeal proteins have no known function. (from Pfam) NF021576.5 PF10067.14 DUF2306 31.6 31.6 147 domain Y Y N DUF2306 domain-containing protein 131567 cellular organisms no rank 19352 EBI-EMBL Predicted membrane protein (DUF2306) Predicted membrane protein (DUF2306) Members of this family of hypothetical bacterial proteins have no known function. (from Pfam) NF021577.5 PF10069.14 DICT 23.8 23.8 129 domain Y Y N DICT sensory domain-containing protein 131567 cellular organisms no rank 5441 EBI-EMBL Sensory domain in DIguanylate Cyclases and Two-component system DICT sensory domain DICT is a sensory domain found associated with GGDEF, EAL, HD-GYP, STAS, and two component systems (histidine-kinase type). It assumes an alpha+beta fold with a 4-stranded beta-sheet and might have a role in light response (Natural history of sensor domains in bacterial signaling systems by Aravind L, LM Iyer, Anantharaman V, from 'Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition.' Caister Academic Press. 2010) - see (http://de.scribd.com/doc/28576661/Bacterial-Signaling-Chapter) (from Pfam) NF021578.5 PF10070.14 DabA 25 25 747 PfamAutoEq Y Y N putative inorganic carbon transporter subunit DabA 31406332 131567 cellular organisms no rank 11828 EBI-EMBL Probable inorganic carbon transporter subunit DabA putative inorganic carbon transporter subunit DabA This entry represents the probable inorganic carbon transporter subunit DabA, which is part of an energy-coupled inorganic carbon pump together with DabB subunit in DAB operons (DAB1 and DAB2), found in a wide range of bacteria and archaea. Members of this family were previously known as UPF0753. DAB operon is required for CO2 concentrating mechanisms [1]. The substrate of this subunit may be CO2 rather than carbonate ions based on kinetic calculations and in experimental assays in which E.coli was deleted of its carbonic anhydrase genes and expression of DAB2 operon restores its growth. Structural homology modelling suggests that DabA contains a domain that is distantly homologous to a type II beta-carbonic anhydrase (CA). [1]. 31406332. DABs are inorganic carbon pumps found throughout prokaryotic phyla. Desmarais JJ, Flamholz AI, Blikstad C, Dugan EJ, Laughlin TG, Oltrogge LM, Chen AW, Wetmore K, Diamond S, Wang JY, Savage DF;. Nat Microbiol. 2019;4:2204-2215. (from Pfam) NF021586.5 PF10079.14 BshC 27 27 539 PfamEq Y Y N bacillithiol biosynthesis BshC bshC 20308541 131567 cellular organisms no rank 13268 EBI-EMBL Bacillithiol biosynthesis BshC bacillithiol biosynthesis BshC Members of this protein family include BshC, which is an enzyme required for bacillithiol biosynthesis and described as a cysteine-adding enzyme [1]. [1]. 20308541. Biosynthesis and functions of bacillithiol, a major low-molecular-weight thiol in Bacilli. Gaballa A, Newton GL, Antelmann H, Parsonage D, Upton H, Rawat M, Claiborne A, Fahey RC, Helmann JD;. Proc Natl Acad Sci U S A. 2010;107:6482-6486. (from Pfam) NF021587.5 PF10080.14 FtrD-like 26.3 26.3 101 PfamAutoEq Y Y N Fe-S-containing protein 22924881 131567 cellular organisms no rank 4740 EBI-EMBL Membrane iron-sulfur containing protein FtrD-like Membrane iron-sulfur containing protein FtrD-like Members of this family are bacterial membrane proteins associated with the FTR1 protein, an homologous to FtrC in the FtrABCD complex. This complex is a ferric iron transporter in which the ferric iron is generated by ferrous oxidation that requires the electron transfer by iron-sulfur cluster-containing FrtD. Proteins in this family are part of the iron-sulfur-containing Rieske superfamily and are likely to have an analogous function to FtrD in iron transport [1]. [1]. 22924881. Iron and pH-responsive FtrABCD ferrous iron utilization system of Bordetella species. Brickman TJ, Armstrong SK;. Mol Microbiol. 2012;86:580-593. (from Pfam) NF021590.5 PF10083.14 DUF2321 24 24 157 PfamAutoEq Y Y N DUF2321 domain-containing protein 131567 cellular organisms no rank 580 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2321) Uncharacterized protein conserved in bacteria (DUF2321) Members of this family of hypothetical bacterial proteins have no known function. (from Pfam) NF021592.5 PF10086.14 YhfC 24.2 24.2 222 subfamily Y Y N YhfC family glutamic-type intramembrane protease 3.4.-.- GO:0070007 21570408 131567 cellular organisms no rank 5191 EBI-EMBL YhfC intramembrane metalloprotease YhfC family glutamic-type intramembrane protease This family includes proteins that are mainly from Firmicutes and Proteobacteria. Family members bear the consensus signature of 'EExxR' the second motif 'HxxxE' and the third motif 'H/Qxxxs'. The fourth motif, 'HxxxB', is shared by the PrsW proteases Pfam:PF13367 and the CPBP Pfam:PF02517, and APH-1 families. There are currently no experimental functional data for members of this group, however, they are predicted to be integral membrane proteins with several transmembrane segments and hypothesized metalloprotease function. YhfC intramembrane metalloprotease, CPBP family (type II CAAX Proteases and Bacteriocin Processing enzymes), PrsW proteases and APH-1 are distantly related. They share four predicted core transmembrane segments and possess similar, yet distinct sets of sequence motifs [1]. [1]. 21570408. Expansion of type II CAAX proteases reveals evolutionary origin of gamma-secretase subunit APH-1. Pei J, Mitchell DA, Dixon JE, Grishin NV;. J Mol Biol. 2011;410:18-26. (from Pfam) NF021594.5 PF10088.14 DUF2326 28.7 28.7 141 PfamAutoEq Y Y N DUF2326 domain-containing protein 131567 cellular organisms no rank 5793 EBI-EMBL Uncharacterised protein conserved in bacteria (DUF2326) Uncharacterised protein conserved in bacteria (DUF2326) This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021595.5 PF10090.14 HPTransfase 22.9 22.9 123 domain Y Y N histidine phosphotransferase family protein 22949187 131567 cellular organisms no rank 7482 EBI-EMBL Histidine phosphotransferase C-terminal domain Histidine phosphotransferase C-terminal domain HPTransfase is a family of essential histidine phosphotransferases. It controls the activity of the master bacterial cell-cycle regulator CtrA through phosphorylation. It behaves as a homodimer by adopting the domain architecture of the intracellular part of class I histidine kinases. Each subunit consists of two distinct domains: an N-terminal helical hairpin domain and a C-terminal [alpha]/[beta] domain. The two N-terminal domains are adjacent within the dimer, forming a four-helix bundle. The C-terminal domain adopts an atypical Bergerat ATP-binding fold [1]. [1]. 22949187. Structural insights into ChpT, an essential dimeric histidine phosphotransferase regulating the cell cycle in Caulobacter crescentus. Fioravanti A, Clantin B, Dewitte F, Lens Z, Verger A, Biondi EG, Villeret V;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012;68:1025-1029. (from Pfam) NF021596.5 PF10091.14 Glycoamylase 27 27 221 domain Y Y N glucoamylase family protein 131567 cellular organisms no rank 27273 EBI-EMBL Putative glucoamylase glucoamylase family protein The structure of UniProt:Q5LIB7 has an alpha/alpha toroid fold and is similar structurally to a number of glucoamylases. Most of these structural homologues are glucoamylases, involved in breaking down complex sugars (e.g. starch). The biologically relevant state is likely to be monomeric. The putative active site is located at the centre of the toroid with a well defined large cavity. (from Pfam) NF021597.5 PF10092.14 DUF2330 24.7 24.7 279 PfamAutoEq Y Y N DUF2330 domain-containing protein 131567 cellular organisms no rank 4615 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2330) Uncharacterized protein conserved in bacteria (DUF2330) Members of this family of hypothetical bacterial proteins have no known function. (from Pfam) NF021598.5 PF10093.14 EarP 25 25 372 PfamAutoEq Y Y N elongation factor P maturation arginine rhamnosyltransferase EarP earP GO:0106361 25686373,26060278,26840407,28451135,28451332,28951478 131567 cellular organisms no rank 12154 EBI-EMBL Elongation-Factor P (EF-P) rhamnosyltransferase EarP elongation factor P maturation arginine rhamnosyltransferase EarP This entry includes family members such as EarP enzymes which are essential for post-translational activation of elongation factor P(EF-P). It was identified as EF-P arginine R32 specific rhamnosyl transferase in Shewanella oneidensis using dTDP-beta-L-rhamnose as donor substrate [1]. This was further confirmed for Pseudomonas aeruginosa [2], Pseudomonas putida [3] and Neisseria meningitidis [4]. As for S. oneidensis [5] and P. aeruginosa [6], EarP enzyme acts as an inverting glycosyltransferase, thus mediating the formation of an alpha-L-rhamnosidic linkage. Structural analysis show that EarP is composed of two opposing domains with Rossmann folds, thus constituting a B pattern-type glycosyltransferase (GT-B) and provide basis for arginine glycosylation by EarP [3]. Mutational analysis of efp and earP genes, resulted in a substantial decrease in the production of rhamnolipids and pyocyanin (important factors for colonization and invasion during infection) of P. aeruginosa. Collectively this indicates that EarP and EF-P are essential for P. aeruginosa pathogenicity [1].The protein family is also annotated in the CaZy Database as GT104. [1]. 25686373. Arginine-rhamnosylation as new strategy to activate translation elongation factor P. Lassak J, Keilhauer EC, Furst M, Wuichet K, Godeke J, Starosta AL, Chen JM, Sogaard-Andersen L, Rohr J, Wilson DN, Haussler S, Mann M, Jung K;. Nat Chem Biol. 2015;11:266-270. [2]. 26060278. Cyclic Rhamnosylated Elongation Factor P Establishes Antibiotic Resistance in Pseudomonas aeruginosa. Rajkovic A, Erickson S, Witzky A, Branson OE, Seo J, Gafken PR, Frietas MA, Whitelegge JP, Faull KF, Na. TRUNCATED at 1650 bytes (from Pfam) NF021599.5 PF10094.14 DUF2332 25 25 334 PfamAutoEq Y Y N DUF2332 family protein 131567 cellular organisms no rank 13245 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2332) DUF2332 family protein Members of this family of hypothetical bacterial proteins have no known function. (from Pfam) NF021601.5 PF10096.14 DUF2334 26 26 203 domain Y Y N DUF2334 domain-containing protein 131567 cellular organisms no rank 18656 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2334) Uncharacterized protein conserved in bacteria (DUF2334) This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021604.5 PF10099.14 RskA_C 29.4 29.4 135 domain Y Y N anti-sigma factor domain-containing protein GO:0005886,GO:0016020 17064366,24699647 131567 cellular organisms no rank 43725 EBI-EMBL Anti-sigma-K factor rskA, C-terminal Anti-sigma-K factor rskA, C-terminal This domain, formerly known as DUF2337, is found at the C-terminal end of the anti-sigma-K factor from Mycobacterium tuberculosis (RskA), which positively regulates expression of the antigenic proteins MPB70 and MPB83 [1,2]. [1]. 17064366. Mutations in Mycobacterium tuberculosis Rv0444c, the gene encoding anti-SigK, explain high level expression of MPB70 and MPB83 in Mycobacterium bovis. Said-Salim B, Mostowy S, Kristof AS, Behr MA;. Mol Microbiol. 2006;62:1251-1263. [2]. 24699647. Structural basis for the redox sensitivity of the Mycobacterium tuberculosis SigK-RskA sigma-anti-sigma complex. Shukla J, Gupta R, Thakur KG, Gokhale R, Gopal B;. Acta Crystallogr D Biol Crystallogr. 2014;70:1026-1036. (from Pfam) NF021606.5 PF10101.14 DUF2339 33.6 33.6 659 PfamAutoEq Y Y N DUF2339 domain-containing protein 131567 cellular organisms no rank 30133 EBI-EMBL Predicted membrane protein (DUF2339) Predicted membrane protein (DUF2339) This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF021607.5 PF10102.14 DUF2341 23.4 23.4 84 PfamAutoEq Y Y N DUF2341 domain-containing protein 131567 cellular organisms no rank 4810 EBI-EMBL Domain of unknown function (DUF2341) Domain of unknown function (DUF2341) Members of this family are found in various bacterial proteins, including MotA/TolQ/ExbB proton channels and other transport proteins. The exact function of this set of domains has not, as yet, been determined. (from Pfam) NF021608.5 PF10103.14 Zincin_2 25 25 344 domain Y Y N zinc-dependent metalloprotease 23671590 131567 cellular organisms no rank 29544 EBI-EMBL Zincin-like metallopeptidase zinc-dependent metalloprotease This family of proteins has a conserved HEXXH motif, suggesting they are putative peptidases of zincin fold [1]. The structure of this family has similarity to Peptidase_M1 (Pfam:PF01433, PDB:3CMN). [1]. 23671590. CLCAs - A Family of Metalloproteases of Intriguing Phylogenetic Distribution and with Cases of Substituted Catalytic Sites. Lenart A, Dudkiewicz M, Grynberg M, Pawlowski K;. PLoS One. 2013;8:e62272. (from Pfam) NF021612.5 PF10107.14 Endonuc_Holl 23.8 23.8 159 PfamEq Y Y N Holliday junction resolvase-like protein 22638584 131567 cellular organisms no rank 906 EBI-EMBL Endonuclease related to archaeal Holliday junction resolvase Holliday junction resolvase-like protein This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases. [1]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF021613.5 PF10108.14 DNA_pol_B_exo2 24 24 213 PfamEq Y N N Predicted 3'-5' exonuclease related to the exonuclease domain of PolB 131567 cellular organisms no rank 13500 EBI-EMBL Predicted 3'-5' exonuclease related to the exonuclease domain of PolB Predicted 3'-5' exonuclease related to the exonuclease domain of PolB This domain is found in various prokaryotic 3'-5' exonucleases and hypothetical proteins. (from Pfam) NF021615.5 PF10110.14 GPDPase_memb 29.6 29.6 321 domain Y Y N glycerophosphoryl diester phosphodiesterase membrane domain-containing protein 131567 cellular organisms no rank 16889 EBI-EMBL Membrane domain of glycerophosphoryl diester phosphodiesterase Membrane domain of glycerophosphoryl diester phosphodiesterase Members of this family comprise the membrane domain of the prokaryotic enzyme glycerophosphoryl diester phosphodiesterase. (from Pfam) NF021616.5 PF10111.14 Glyco_tranf_2_2 27.3 27.3 276 domain Y N N Glycosyltransferase like family 2 11953367,9515923 131567 cellular organisms no rank 361702 EBI-EMBL Glycosyltransferase like family 2 Glycosyltransferase like family 2 Members of this family of prokaryotic proteins include putative glucosyltransferase, which are involved in bacterial capsule biosynthesis [1][2]. [1]. 9515923. Characterization of the gene cassette required for biosynthesis of the (alpha1-->6)-linked N-acetyl-D-mannosamine-1-phosphate capsule of serogroup A Neisseria meningitidis. Swartley JS, Liu LJ, Miller YK, Martin LE, Edupuganti S, Stephens DS;. J Bacteriol. 1998;180:1533-1539. [2]. 11953367. Novel Aeromonas hydrophila PPD134/91 genes involved in O-antigen and capsule biosynthesis. Zhang YL, Arakawa E, Leung KY;. Infect Immun. 2002;70:2326-2335. (from Pfam) NF021618.5 PF10113.14 Fibrillarin_2 25 25 501 subfamily Y Y N FeGP cofactor biosynthesis family protein hmdC 25882909 131567 cellular organisms no rank 237 EBI-EMBL FeGP cofactor biosynthesis protein, fibrillarin family 5,10-methenyltetrahydromethanopterin hydrogenase cofactor biosynthesis protein HmdC Members of this family of proteins include archaeal fibrillarin homologs also known as HcgG which is involved in biosynthesis of Iron-guanylylpyridinol (FeGP) cofactor [1]. [1]. 25882909. Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]-hydrogenase cofactor. Fujishiro T, Kahnt J, Ermler U, Shima S;. Nat Commun. 2015;6:6895. (from Pfam) NF021619.5 PF10114.14 PocR 23.9 23.9 162 domain Y Y N PocR ligand-binding domain-containing protein 15814558 131567 cellular organisms no rank 10037 EBI-EMBL Sensory domain found in PocR Sensory domain found in PocR PocR, a ligand binding domain, has a novel variant of the PAS-like Fold. Evidence suggests that it binds small hydrocarbon derivatives such as 1,3-propanediol [1]. In (Natural history of sensor domains in bacterial signaling systems by Aravind L, LM Iyer, Anantharaman V, from 'Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition.' Caister Academic Press. 2010) - see (http://de.scribd.com/doc/28576661/Bacterial-Signaling-Chapter) [1]. 15814558. MEDS and PocR are novel domains with a predicted role in sensing simple hydrocarbon derivatives in prokaryotic signal transduction systems. Anantharaman V, Aravind L;. Bioinformatics. 2005;21:2805-2811. (from Pfam) NF021622.5 PF10117.14 McrBC 23.9 23.9 318 PfamEq Y Y N 5-methylcytosine restriction system specificity protein McrC 2050643,2203735 131567 cellular organisms no rank 23710 EBI-EMBL McrBC 5-methylcytosine restriction system component 5-methylcytosine restriction system specificity protein McrC Members of this family of bacterial proteins modify the specificity of mcrB restriction by expanding the range of modified sequences restricted [1][2]. [1]. 2203735. Genetic and sequence organization of the mcrBC locus of Escherichia coli K-12. Dila D, Sutherland E, Moran L, Slatko B, Raleigh EA;. J Bacteriol. 1990;172:4888-4900. [2]. 2050643. Overproduction and purification of McrC protein from Escherichia coli K-12. Zheng L, Braymer HD;. J Bacteriol. 1991;173:3918-3920. (from Pfam) NF021625.5 PF10120.14 ThiP_synth 25 25 165 domain Y Y N thiamine-phosphate synthase family protein GO:0004789 12794638,22559199 131567 cellular organisms no rank 2398 EBI-EMBL Thiamine-phosphate synthase thiamine-phosphate synthase family protein This family is thiamine-phosphate synthase, and it belongs to the SCOP phosphomethylpyrimidine kinase C-terminal domain-like family. Vitamin B1 (thiamine pyrophosphate) is involved in several microbial metabolic functions. Thiamine biosynthesis is accomplished by joining two intermediate molecules that are synthesized separately, HMP-PP and HET-P. In the archaeon Natrialba magadii, ThiE and ThiN, are known to join HMP-PP ( hydroxymethylpyrimidine pyrophosphate) and HET-P (hydroxyethylthiazole phosphate) to generate thiamine phosphate. Whereas ThiE in Natrialba magadii is a mono-functional protein, ThiN exists as a C-terminal domain in a ThiDN fusion protein - examples of all three forms, from various prokaryotes, are found in this family [1,2]. [1]. 12794638. Systematic discovery of analogous enzymes in thiamin biosynthesis. Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B, Bork P;. Nat Biotechnol. 2003;21:790-795. [2]. 22559199. A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T. Siddaramappa S, Challacombe JF, Decastro RE, Pfeiffer F, Sastre DE, Gimenez MI, Paggi RA, Detter JC, Davenport KW, Goodwin LA, Kyrpides N, Tapia R, Pitluck S, Lucas S, Woyke T, Maupin-Furlow JA;. BMC Genomics. 2012;13:165. (from Pfam) NF021627.5 PF10123.14 Mu-like_Pro 25.2 25.2 330 domain Y Y N phage protease 131567 cellular organisms no rank 8579 EBI-EMBL Mu-like prophage I protein phage protease Members of this family of proteins comprise various viral Mu-like prophage I proteins. (from Pfam) NF021628.5 PF10124.14 Mu-like_gpT 20.1 20.1 289 domain Y Y N Mu-like prophage major head subunit gpT family protein 131567 cellular organisms no rank 10676 EBI-EMBL Mu-like prophage major head subunit gpT Mu-like prophage major head subunit gpT family protein Members of this family of proteins comprise various caudoviral prophage proteins, including the Mu-like prophage major head subunit gpT. (from Pfam) NF021629.5 PF10125.14 NADHdeh_related 27 27 218 domain Y N N NADH dehydrogenase I, subunit N related protein 131567 cellular organisms no rank 2894 EBI-EMBL NADH dehydrogenase I, subunit N related protein NADH dehydrogenase I, subunit N related protein This family comprises a set of NADH dehydrogenase I, subunit N related proteins found in archaea. Their exact function, has not, as yet, been determined. (from Pfam) NF021631.5 PF10127.14 RlaP 23 23 249 domain Y Y N DNA polymerase beta superfamily protein 27536007 131567 cellular organisms no rank 28515 EBI-EMBL RNA repair pathway DNA polymerase beta family DNA polymerase beta superfamily protein Family of the DNA polymerase beta superfamily, with closest affinities to the Minimal Nucleotide Transferase clade (MNT). Observed in diverse RNA repair genome contexts centered on both RtcB and Rnl-type (ATP-grasp fold) repair ligases [1]. Members of this family of bacterial proteins catalyze the transfer of nucleotide residues from nucleoside diphosphates or triphosphates into dimer or polymer forms. [1]. 27536007. RNA damage in biological conflicts and the diversity of responding RNA repair systems. Burroughs AM, Aravind L;. Nucleic Acids Res. 2016;44:8525-8555. (from Pfam) NF021633.5 PF10129.14 OpgC_C 21.4 21.4 358 domain Y Y N OpgC domain-containing protein opgC 12027885 131567 cellular organisms no rank 18026 EBI-EMBL OpgC protein succinyl transferase OpgC This domain, found in various hypothetical and OpgC prokaryotic proteins. It is likely to act as an acyltransferase enzyme. (from Pfam) NF021634.5 PF10130.14 PIN_2 22.4 22.4 133 domain Y Y N PIN domain-containing protein 131567 cellular organisms no rank 2253 EBI-EMBL PIN domain PIN domain Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases). (from Pfam) NF021635.5 PF10131.14 PTPS_related 26.4 26.4 621 domain Y Y N 6-pyruvoyl-tetrahydropterin synthase-related protein 131567 cellular organisms no rank 1748 EBI-EMBL 6-pyruvoyl-tetrahydropterin synthase related domain; membrane protein 6-pyruvoyl-tetrahydropterin synthase-related domain This domain is found in various bacterial hypothetical membrane proteins, as well as in tetratricopeptide TPR_2 repeat protein. The exact function of the domain has not, as yet, been established. (from Pfam) NF021636.5 PF10133.14 CooT 27 27 60 subfamily Y Y N CooT family nickel-binding protein 28447092 131567 cellular organisms no rank 911 EBI-EMBL CO dehydrogenase accessory protein CooT CooT family nickel-binding protein CooT is an accessory protein required for maturation of Carbon Monoxide Dehydrogenase (CODH). It is a member of a Ni(ii)-binding protein family, linked to anaerobic metabolism in bacteria and archaea, and in most cases to the presence of CODH. Structure analysis indicates that it is a homodimer featuring a fold that resembles an Sm-like domain [1]. [1]. 28447092. The CO dehydrogenase accessory protein CooT is a novel nickel-binding protein. Timm J, Brochier-Armanet C, Perard J, Zambelli B, Ollagnier-de-Choudens S, Ciurli S, Cavazza C;. Metallomics. 2017;9:575-583. (from Pfam) NF021640.5 PF10137.14 CAP12-PCTIR_TIR 24.7 24.7 119 domain Y Y N TIR domain-containing protein GO:0050135 32877915,34644530 131567 cellular organisms no rank 9105 EBI-EMBL CAP12/Pycsar effector protein, TIR domain CAP12/Pycsar effector protein, TIR domain This entry represents a TIR domain found in prokaryotic nucleotide-binding proteins, including CD-NTase-associated protein 12 (CAP12) and Pycsar effector proteins (E.C:3.2.2.5). Members of this entry are part of anti phage resistance systems that provide immunity against bacteriophage. CAP12 is part of the CBASS (cyclic oligonucleotide-based anti phage signaling system) and binds c-di-GMP and 3'-3'-cGAMP, cyclic nucleotides synthesized by the CD-NTase protein in response to infection that serve as specific second messenger signals to activate a diverse range of effectors, leading to bacterial cell death and thus abortive phage infection [1,2]. Pycsar effector proteins are part of the Pycsar (pyrimidine cyclase system for anti phage resistance) and are activated by cyclic nucleotides produced by the pyrimidine cyclase (PycC) in response to infection. The TIR effector domain oligomerises and functions as NADase that deplete the cell of NAD+. [1]. 34644530. Cyclic CMP and cyclic UMP mediate bacterial immunity against phages. Tal N, Morehouse BR, Millman A, Stokar-Avihail A, Avraham C, Fedorenko T, Yirmiya E, Herbst E, Brandis A, Mehlman T, Oppenheimer-Shaanan Y, Keszei AFA, Shao S, Amitai G, Kranzusch PJ, Sorek R;. Cell. 2021;184:5728-5739. [2]. 32877915. STING cyclic dinucleotide sensing originated in bacteria. Morehouse BR, Govande AA, Millman A, Keszei AFA, Lowey B, Ofir G, Shao S, Sorek R, Kranzusch PJ;. Nature. 2020;586:429-433. (from Pfam) NF021646.5 PF10143.14 PhosphMutase 21.5 21.5 170 domain Y N N 2,3-bisphosphoglycerate-independent phosphoglycerate mutase GO:0003824,GO:0046537 17576516 131567 cellular organisms no rank 6064 EBI-EMBL 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 2,3-bisphosphoglycerate-independent phosphoglycerate mutase This family represents 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGAM), a metalloenzyme found particularly in archaea and some eubacteria, which catalyses the interconversion of 2-phosphoglycerate and 3-phosphoglycerate in the reaction: [(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate] (EC 5.4.2.12) [1]. [1]. 17576516. Characterization of cofactor-dependent and cofactor-independent phosphoglycerate mutases from Archaea. Johnsen U, Schonheit P;. Extremophiles. 2007;11:647-657. (from Pfam) NF021648.5 PF10145.14 PhageMin_Tail 33.2 33.2 201 domain Y Y N phage tail tape measure protein 131567 cellular organisms no rank 94363 EBI-EMBL Phage-related minor tail protein phage tail tape measure protein Members of this family are found in putative phage tail tape measure proteins. (from Pfam) NF021653.5 PF10150.14 RNase_E_G 25.5 25.5 270 domain Y Y N ribonuclease E/G GO:0003723 16237448 131567 cellular organisms no rank 104539 EBI-EMBL Ribonuclease E/G family ribonuclease E/G Ribonuclease E and Ribonuclease G are related enzymes that cleave a wide variety of RNAs [1]. [1]. 16237448. Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Callaghan AJ, Marcaida MJ, Stead JA, McDowall KJ, Scott WG, Luisi BF;. Nature. 2005;437:1187-1191. (from Pfam) NF021665.5 PF10162.14 G8 22.9 22.9 124 domain Y Y N G8 domain-containing protein 16632497 131567 cellular organisms no rank 1136 EBI-EMBL G8 domain G8 domain This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix. [1]. 16632497. G8: a novel domain associated with polycystic kidney disease and non-syndromic hearing loss. He QY, Liu XH, Li Q, Studholme DJ, Li XW, Liang SP;. Bioinformatics. 2006;22:2189-2191. (from Pfam) NF021721.5 PF10224.14 DUF2205 26.7 26.7 75 domain Y Y N short coiled-coil protein 16725058,22354037 131567 cellular organisms no rank 3 EBI-EMBL Short coiled-coil protein short coiled-coil protein This entry represents a highly conserved 100 residue coiled-coil region which is found in short coiled-coil protein (SCOC) in human and UNC-69 in Caenorhabditis elegans. In human, SCOC is required for autophagosome formation during amino acid starvation. It forms a starvation-sensitive trimeric complex with UVRAG (UV radiation resistance associated gene) and FEZ1 and may regulate ULK1 and Beclin 1 complex activities [1]. In C. elegans, this small, evolutionarily conserved coiled-coil domain-containing protein, UNC-69, acts as a binding partner of UNC-76. Together they participate in a common genetic pathway necessary for axon extension and cooperate to regulate the size and position of synaptic vesicles in axons. Moreover, both proteins colocalize as puncta in neuronal processes and mutations in UNC-69 preferentially disrupt membrane traffic within axons [2]. [1]. 22354037. Genome-wide siRNA screen reveals amino acid starvation-induced autophagy requires SCOC and WAC. McKnight NC, Jefferies HB, Alemu EA, Saunders RE, Howell M, Johansen T, Tooze SA;. EMBO J. 2012;31:1931-1946. [2]. 16725058. The short coiled-coil domain-containing protein UNC-69 cooperates with UNC-76 to regulate axonal outgrowth and normal presynaptic organization in Caenorhabditis elegans. Su CW, Tharin S, Jin Y, Wightman B, Spector M, Meili D, Tsung N, Rhiner C, Bourikas D, Stoeckli E, Garriga G, Horvitz HR, Hengartner MO;. J Biol. 2006;5:9. (from Pfam) NF021726.5 PF10230.14 LIDHydrolase 27 27 262 PfamEq Y N N Lipid-droplet associated hydrolase GO:0005811,GO:0016298,GO:0019915 21478430,21478434,24357060 131567 cellular organisms no rank 2249 EBI-EMBL Lipid-droplet associated hydrolase Lipid-droplet associated hydrolase This family of proteins is conserved from plants to humans. The function is as a lipid-droplet hydrolase. Human LDAH plays a role in cholesterol homeostasis [3]. [1]. 21478430. The putative Saccharomyces cerevisiae hydrolase Ldh1p is localized to lipid droplets. Thoms S, Debelyy MO, Connerth M, Daum G, Erdmann R;. Eukaryot Cell. 2011;10:770-775. [2]. 21478434. Involvement of the Saccharomyces cerevisiae hydrolase Ldh1p in lipid homeostasis. Debelyy MO, Thoms S, Connerth M, Daum G, Erdmann R;. Eukaryot Cell. 2011;10:776-781. [3]. 24357060. Novel lipid droplet-associated serine hydrolase regulates macrophage cholesterol mobilization. Goo YH, Son SH, Kreienberg PB, Paul A;. Arterioscler Thromb Vasc Biol. 2014;34:386-396. (from Pfam) NF021758.5 PF10262.14 Rdx 22.6 22.6 74 domain Y Y N Rdx family protein 11278576,12405536,17034973,17503775 131567 cellular organisms no rank 11839 EBI-EMBL Rdx family Rdx family protein This entry is an approximately 100 residue region of selenoprotein-T, conserved from plants to humans. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [1]. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins, including selenoprotein T. However, despite its binding to UGTR and that its mRNA is up-regulated in extended asphyxia, the function of the protein and hence of this region of it is unknown [2]. Selenoprotein W contains selenium as selenocysteine in the primary protein structure and levels of this selenoprotein are affected by selenium [3]. [1]. 11278576. Association between the 15-kDa selenoprotein and UDP-glucose:glycoprotein glucosyltransferase in the endoplasmic reticulum of mammalian cells. Korotkov KV, Kumaraswamy E, Zhou Y, Hatfield DL, Gladyshev VN;. J Biol Chem. 2001;276:15330-15336. [2]. 17034973. Identification of novel genes expressed in hypoxic brain condition by fluorescence differential display. Ikematsu K, Tsuda R, Tsuruya S, Nakasono I;. Forensic Sci Int. 2007;169:168-172. [3]. 12405536. Selenoprotein W gene regulation by selenium in L8 cells. Gu QP, Ream W, Whanger PD;. Biometals 2002;15:411-420. [4]. 17503775. SelT, SelW, SelH, and Rdx12: genomics and molecular insights into the functions of selenoproteins of a novel thioredoxin-like family. Dikiy A, Novoselov SV, Fomenko DE, Sengupta A, Carlson BA, Cerny RL, Ginalski K, Grishin NV, Hatfield DL, Gladyshev VN;. Biochemistry. 2007;46:. TRUNCATED at 1650 bytes (from Pfam) NF021759.5 PF10263.14 SprT-like 25.6 25.6 108 PfamEq Y Y N SprT-like domain-containing protein 131567 cellular organisms no rank 40328 EBI-EMBL SprT-like family SprT-like family This family represents a domain found in eukaryotes and prokaryotes. The domain contains a characteristic motif of the zinc metallopeptidases. This family includes the bacterial SprT protein. (from Pfam) NF021778.5 PF10282.14 Lactonase 21.7 21.7 344 domain Y Y N beta-propeller fold lactonase family protein 11937053 131567 cellular organisms no rank 93940 EBI-EMBL Lactonase, 7-bladed beta-propeller beta-propeller fold lactonase family protein This entry contains bacterial 6-phosphogluconolactonases (6PGL)YbhE-type (EC:3.1.1.31) which hydrolyse 6-phosphogluconolactone to 6-phosphogluconate. The entry also contains the fungal muconate lactonising enzyme carboxy-cis,cis-muconate cyclase (EC:5.5.1.5) and muconate cycloisomerase (EC:5.5.1.1), which convert cis,cis-muconates to muconolactones and vice versa as part of the microbial beta-ketoadipate pathway. Structures of proteins in this family have revealed a 7-bladed beta-propeller fold [1]. [1]. 11937053. The structure of Neurospora crassa 3-carboxy-cis,cis-muconate lactonizing enzyme, a beta propeller cycloisomerase. Kajander T, Merckel MC, Thompson A, Deacon AM, Mazur P, Kozarich JW, Goldman A;. Structure. 2002;10:483-492. (from Pfam) NF021788.5 PF10294.14 Methyltransf_16 21 21 174 domain Y N N Lysine methyltransferase 12872006,20975703,22948820,23349634,23921388 131567 cellular organisms no rank 54531 EBI-EMBL Lysine methyltransferase Lysine methyltransferase Methyltrans_16 is a lysine methyltransferase. Characterised members of this family are protein methyltransferases targetting Lys residues in specific proteins, including calmodulin, VCP, Kin17 and Hsp70 proteins [2,3,4,5]. [1]. 12872006. Automated identification of putative methyltransferases from genomic open reading frames. Katz JE, Dlakic M, Clarke S;. Mol Cell Proteomics 2003;2:525-540. [2]. 20975703. Calmodulin methyltransferase is an evolutionarily conserved enzyme that trimethylates Lys-115 in calmodulin. Magnani R, Dirk LM, Trievel RC, Houtz RL;. Nat Commun. 2010;1:43. [3]. 22948820. Lysine methylation of VCP by a member of a novel human protein methyltransferase family. Kernstock S, Davydova E, Jakobsson M, Moen A, Pettersen S, Maelandsmo GM, Egge-Jacobsen W, Falnes PO;. Nat Commun. 2012;3:1038. [4]. 23349634. A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. Cloutier P, Lavallee-Adam M, Faubert D, Blanchette M, Coulombe B;. PLoS Genet. 2013;9:e1003210. [5]. 23921388. Identification and characterization of a novel human methyltransferase modulating Hsp70 protein function through lysine methylation. Jakobsson ME, Moen A, Bousset L, Egge-Jacobsen W, Kernstock S, Melki R, Falnes PO;. J Biol Chem. 2013;288:27752-27763. (from Pfam) NF021793.5 PF10300.14 Iml2-TPR_39 22.2 22.2 467 PfamAutoEq Y Y N tetratricopeptide repeat protein 14562095,21738485,22842922,26004510,9461476 131567 cellular organisms no rank 278 EBI-EMBL Iml2/Tetratricopeptide repeat protein 39 tetratricopeptide repeat protein This is a family of proteins conserved from fungi to humans, including fungal Inclusion body clearance protein Iml2 protein, animal tetratricopeptide repeat protein 39A/B/C (TT39A/B/C) and some uncharacterised proteins. Members of this family carry a tetratricopeptide repeat Pfam:PF07719 at their C terminus. This entry includes Iml2 and its paralogue-YKR018C from S. cerevisiae; Iml2 localises to the cytoplasm and nucleus [1], and its expression is increased in response to DNA replication stress [2]. It is found to be involved in lipid droplet-mediated inclusion body clearing after protein folding stress [3]. In humans, TTC39A (also known as DEME6) is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. It is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive [4]. TTC39B has been linked to lipid metabolism [5]. [1]. 14562095. Global analysis of protein localization in budding yeast. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK;. Nature 2003;425:686-691. [2]. 22842922. Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Tkach JM, Yimit A, Lee AY, Riffle M, Costanzo M, Jaschob D, Hendry JA, Ou J, Moffat J, Boone C, Davis TN, Nislow C, Brown GW;. Nat Cell Biol. 2012;14:966-976. [3]. 26004510. Lipid Droplets Are Essential for Efficient Clearance of Cytosolic Inclusion Bodies. Moldavski O, Amen T, Levin-Zaidman S, Eisenstein M, Rogachev I, Brandis A, Kaganovich D, . TRUNCATED at 1650 bytes (from Pfam) NF021795.5 PF10303.14 DUF2408 25 25 130 domain Y Y N DUF2408 domain-containing protein 131567 cellular organisms no rank 4 EBI-EMBL Protein of unknown function (DUF2408) Protein of unknown function (DUF2408) This is a family of proteins conserved in fungi. The function is unknown. (from Pfam) NF021824.5 PF10335.14 DUF294_C 22.5 22.5 145 domain Y Y N putative nucleotidyltransferase substrate binding domain-containing protein 131567 cellular organisms no rank 30634 EBI-EMBL Putative nucleotidyltransferase substrate binding domain Putative nucleotidyltransferase substrate binding domain This domain is found associated with presumed nucleotidyltransferase domains and seems to be distantly related to other helical substrate binding domains. (from Pfam) NF021829.5 PF10340.14 Say1_Mug180 21 21 374 domain Y Y N steryl acetyl hydrolase 16303567,18034159 131567 cellular organisms no rank 54079 EBI-EMBL Steryl acetyl hydrolase steryl acetyl hydrolase This entry includes budding yeast steryl acetyl hydrolase 1 (Say1) and fission yeast Mug180. Say1 is a a membrane-anchored deacetylase required for the deacetylation of acetylated sterols. It is involved in the resistance to eugenol and pregnenolone toxicity [1]. Mug180 has a role in meiosis [2]. [1]. 18034159. An acetylation/deacetylation cycle controls the export of sterols and steroids from S. cerevisiae. Tiwari R, Koffel R, Schneiter R;. EMBO J. 2007;26:5109-5119. [2]. 16303567. A large-scale screen in S. pombe identifies seven novel genes required for critical meiotic events. Martin-Castellanos C, Blanco M, Rozalen AE, Perez-Hidalgo L, Garcia AI, Conde F, Mata J, Ellermeier C, Davis L, San-Segundo P, Smith GR, Moreno S;. Curr Biol. 2005;15:2056-2062. (from Pfam) NF021831.5 PF10342.14 Kre9_KNH 24.6 24.6 94 domain Y Y N Ser-Thr-rich GPI-anchored membrane family protein 11545413,16204227,17383119 131567 cellular organisms no rank 714 EBI-EMBL Kre9/KNH-like N-terminal Ig-like domain Kre9/KNH-like N-terminal Ig-like domain This entry represents the N-terminal Ig-like domain found in a family of serine- threonine-rich membrane-anchored proteins, anchored by glycosyl-phosphatidylinositol. This family includes Kre9. In A. fumigatus these proteins play a role in fungal cell wall organisation [2]. In Lentinula edodes this family is involved in fruiting body formation, and may have a more general role in signalling in other organisms as it interacts with MAPK [3]. The family is also found in archaea and bacteria. [1]. 11545413. Proteome analysis of Aspergillus fumigatus identifies glycosylphosphatidylinositol-anchored proteins associated to the cell wall biosynthesis. Bruneau JM, Magnin T, Tagat E, Legrand R, Bernard M, Diaquin M, Fudali C, Latge JP;. Electrophoresis. 2001;22:2812-2823. [2]. 16204227. Glycosylphosphatidylinositol-anchored fungal polysaccharide in Aspergillus fumigatus. Costachel C, Coddeville B, Latge JP, Fontaine T;. J Biol Chem. 2005;280:39835-39842. [3]. 17383119. Le.MAPK and its interacting partner, Le.DRMIP, in fruiting body development in Lentinula edodes. Szeto CY, Leung GS, Kwan HS;. Gene. 2007;393:87-93. (from Pfam) NF021832.5 PF10343.14 Q_salvage 25 25 285 domain Y Y N queuosine salvage family protein 24911101,35940128 131567 cellular organisms no rank 230 EBI-EMBL Queuosine salvage protein queuosine salvage family protein Queuosine salvage proteins occur in most Eukarya as well as in a few bacteria possible via horizontal gene-transfer. Queuosine (Q) is a chemical modification found at the wobble position of tRNAs that have GUN anticodons, and it ensures faithful translation of the respective C- and U-ending codons. Most bacteria synthesize queuosine de novo, whereas eukaryotes rely solely on salvaging this essential component from the environment or the gut flora. This entry represents queuosine salvage proteins (Qng1, also known as DUF2419) which have been identified as a queuosine nucleoside glycosylases that play an essential role in allowing eukaryotic cells to salvage Q from bacterial sources and to recycle Q from endogenous tRNAs [1,2]. [1]. 24911101. The plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family. Zallot R, Brochier-Amanet C, Gaston KW, Forouhar F, Limbach PA, Hunt JF, De Crecy-Lagard V;. ACS Chem Biol. 2014; [Epub ahead of print]. [2]. 35940128. Queuosine salvage in fission yeast by Qng1-mediated hydrolysis to queuine. Patel BI, Heiss M, Samel-Pommerencke A, Carell T, Ehrenhofer-Murray AE;. Biochem Biophys Res Commun. 2022;624:146-150. (from Pfam) NF021841.5 PF10354.14 BMT5-like 24.7 24.7 168 PfamAutoEq Y Y N Rossmann-like fold-containing protein GO:0070042,GO:0070475 24335083 131567 cellular organisms no rank 718 EBI-EMBL rRNA (uridine-N3-)-methyltransferase BTM5-like rRNA (uridine-N3-)-methyltransferase BTM5-like This is the N-terminal domain found in proteins from plants, yeast and humans, including 25S rRNA (uridine-N(3))-methyltransferase BMT5 from S. cerevisiae and the poorly characterised Ferredoxin-fold anticodon-binding domain-containing protein 1 from human and Heavy metal-associated isoprenylated plant protein 41 from Arabidopsis. This domain has a characteristic Rossmann-like fold of S-adenosyl-L-methionine (SAM) binding domains [1]. BTM5 is a SAM-dependent methyltransferase that specifically methylates the N3 position of uridine in 25S rRNA. [1]. 24335083. Identification of novel methyltransferases, Bmt5 and Bmt6, responsible for the m3U methylations of 25S rRNA in Saccharomyces cerevisiae. Sharma S, Yang J, Duttmann S, Watzinger P, Kotter P, Entian KD;. Nucleic Acids Res. 2014;42:3246-3260. (from Pfam) NF021855.5 PF10369.14 ALS_ss_C 23.2 23.2 74 PfamEq Y N N Small subunit of acetolactate synthase 9197540 131567 cellular organisms no rank 32904 EBI-EMBL Small subunit of acetolactate synthase Small subunit of acetolactate synthase ALS_ss_C is the C-terminal half of a family of proteins which are the small subunits of acetolactate synthase. Acetolactate synthase is a tetrameric enzyme, containing probably two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides [1]. [1]. 9197540. Identification of an acetolactate synthase small subunit gene in two eukaryotes. Duggleby RG;. Gene. 1997;190:245-249. (from Pfam) NF021856.5 PF10370.14 Rv2993c-like_N 21.3 21.3 50 domain Y Y N Rv2993c-like domain-containing protein 8223600 131567 cellular organisms no rank 22871 EBI-EMBL Rv2993c-like, N-terminal Rv2993c-like, N-terminal This is the N-terminal 50 amino acids of a group of bacterial proteins annotated as fumarylacetoacetate hydrolase-containing enzymes, including Rv2993c from Mycobacterium tuberculosis. In most cases members are associated with FAA_hydrolase Pfam:PF01557 further towards the C-terminus. [1]. 8223600. Purification, nucleotide sequence and some properties of a bifunctional isomerase/decarboxylase from the homoprotocatechuate degradative pathway of Escherichia coli C. Roper DI, Cooper RA;. Eur J Biochem 1993;217:575-580. (from Pfam) NF021859.5 PF10373.14 EST1_DNA_bind 22 22 282 PfamEq Y N N Est1 DNA/RNA binding domain 10688642,12169735,12454059,12676088 131567 cellular organisms no rank 582 EBI-EMBL Est1 DNA/RNA binding domain Est1 DNA/RNA binding domain Est1 is a protein which recruits or activates telomerase at the site of polymerisation [1][2]. This is the DNA/RNA binding domain of EST1 [3][4]. [1]. 12169735. Est1p as a cell cycle-regulated activator of telomere-bound telomerase. Taggart AK, Teng SC, Zakian VA;. Science. 2002;297:1023-1026. [2]. 12454059. The Est1 subunit of Saccharomyces cerevisiae telomerase makes multiple contributions to telomere length maintenance. Evans SK, Lundblad V;. Genetics. 2002;162:1101-1115. [3]. 12676088. Telomere maintenance in fission yeast requires an Est1 ortholog. Beernink HT, Miller K, Deshpande A, Bucher P, Cooper JP;. Curr Biol. 2003;13:575-580. [4]. 10688642. The Est1 subunit of yeast telomerase binds the Tlc1 telomerase RNA. Zhou J, Hidaka K, Futcher B;. Mol Cell Biol. 2000;20:1947-1955. (from Pfam) NF021871.5 PF10385.14 RNA_pol_Rpb2_45 28.2 28.2 66 PfamEq Y N N RNA polymerase beta subunit external 1 domain GO:0003899,GO:0006351 11313498 131567 cellular organisms no rank 65115 EBI-EMBL RNA polymerase beta subunit external 1 domain RNA polymerase beta subunit external 1 domain RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region [1]. [1]. 11313498. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Cramer P, Bushnell DA, Kornberg RD;. Science 2001;292:1863-1876. (from Pfam) NF021872.5 PF10386.14 DUF2441 25 25 141 PfamAutoEq Y Y N DUF2441 domain-containing protein 131567 cellular organisms no rank 1685 EBI-EMBL Protein of unknown function (DUF2441) Protein of unknown function (DUF2441) This is a family of highly conserved, predicted, proteins from Bacillus species. The structure forms a homo-dimer. The function is unknown. (from Pfam) NF021883.5 PF10397.14 ADSL_C 32.7 32.7 79 domain Y N N Adenylosuccinate lyase C-terminus 17485188,9274883 131567 cellular organisms no rank 65733 EBI-EMBL Adenylosuccinate lyase C-terminus Adenylosuccinate lyase C-terminus This is the C-terminal seven alpha helices of the structure whose full length represents the enzyme adenylosuccinate lyase. This sequence lies C-terminal to the conserved motif necessary for beta-elimination reactions [1], Adenylosuccinate lyase catalyses two steps in the synthesis of purine nucleotides: the conversion of succinylaminoimidazole-carboxamide ribotide into aminoimidazole-carboxamide ribotide, the eighth step of the de novo pathway, and the formation of adenosine monophosphate (AMP) from adenylosuccinate, the second step in the conversion of inosine monophosphate into AMP [2]. [1]. 9274883. Characterisation of the gene encoding adenylosuccinate lyase of Plasmodium falciparum. Marshall VM, Coppel RL;. Mol Biochem Parasitol. 1997;88:237-241. [2]. 17485188. Adenylosuccinate lyase deficiency: The first identified polish patient. Jurkiewicz E, Mierzewska H, Kusmierska K;. Brain Dev. 2007;29:600-602. (from Pfam) NF021886.5 PF10400.14 Vir_act_alpha_C 22.4 22.4 78 domain Y N N Virulence activator alpha C-term 131567 cellular organisms no rank 42981 EBI-EMBL Virulence activator alpha C-term Virulence activator alpha C-term This structure is homo-dimeric, and the domain here is the C-terminal half of the structure, often associated with PadR upstream, (Pfam:PF03551), which is a transcriptional regulator. (from Pfam) NF021897.5 PF10412.14 TrwB_AAD_bind 20.5 20.5 387 domain Y Y N type IV secretion system DNA-binding domain-containing protein 11214325,11748238 131567 cellular organisms no rank 119030 EBI-EMBL Type IV secretion-system coupling protein DNA-binding domain Type IV secretion-system coupling protein DNA-binding domain The plasmid conjugative coupling protein TrwB forms hexamers from six structurally very similar protomers [1]. This hexamer contains a central channel running from the cytosolic pole (made up by the AADs) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB_AAD (all-alpha domain) domain appears to be the DNA-binding domain of the structure. TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein, is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export [2]. [1]. 11214325. The bacterial conjugation protein TrwB resembles ring helicases and F1-ATPase. Gomis-Ruth FX, Moncalian G, Perez-Luque R, Gonzalez A, Cabezon E, de la Cruz F, Coll M;. Nature. 2001;409:637-641. [2]. 11748238. Conjugative plasmid protein TrwB, an integral membrane type IV secretion system coupling protein. Detailed structural features and mapping of the active site cleft. Gomis-Ruth FX, Moncalian G, de la Cruz F, Coll M;. J Biol Chem. 2002;277:7556-7566. (from Pfam) NF021900.5 PF10415.14 FumaraseC_C 32.5 32.5 54 domain Y N N Fumarase C C-terminus GO:0006099,GO:0016829 8909293 131567 cellular organisms no rank 99941 EBI-EMBL Fumarase C C-terminus Fumarase C C-terminus Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Kreb's cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit [1]. FumaraseC_C does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. [1]. 8909293. Crystallographic studies of the catalytic and a second site in fumarase C from Escherichia coli. Weaver T, Banaszak L;. Biochemistry. 1996;35:13955-13965. (from Pfam) NF021902.5 PF10417.14 1-cysPrx_C 21.1 21.1 41 domain Y N N C-terminal domain of 1-Cys peroxiredoxin GO:0051920 15004285,9587003 131567 cellular organisms no rank 42837 EBI-EMBL C-terminal domain of 1-Cys peroxiredoxin C-terminal domain of 1-Cys peroxiredoxin This is the C-terminal domain of 1-Cys peroxiredoxin (1-cysPrx), a member of the peroxiredoxin superfamily which protect cells against membrane oxidation through glutathione (GSH)-dependent reduction of phospholipid hydroperoxides to corresponding alcohols [1]. The C-terminal domain is crucial for providing the extra cysteine necessary for dimerisation of the whole molecule. Loss of the enzyme's peroxidase activity is associated with oxidation of the catalytic cysteine, upstream of this domain; and glutathionylation, presumably through its disruption of protein structure, facilitates access for GSH, resulting in spontaneous reduction of the mixed disulfide to the sulfhydryl and consequent activation of the enzyme [2]. The domain is associated with family AhpC-TSA, Pfam:PF00578, which carries the catalytic cysteine. [1]. 9587003. Crystal structure of a novel human peroxidase enzyme at 2.0 A resolution. Choi HJ, Kang SW, Yang CH, Rhee SG, Ryu SE;. Nat Struct Biol. 1998;5:400-406. [2]. 15004285. Activation of the antioxidant enzyme 1-CYS peroxiredoxin requires glutathionylation mediated by heterodimerization with pi GST. Manevich Y, Feinstein SI, Fisher AB;. Proc Natl Acad Sci U S A. 2004;101:3780-3785. (from Pfam) NF021903.5 PF10418.14 DHODB_Fe-S_bind 23.9 23.9 41 domain Y N N Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B 11188687 131567 cellular organisms no rank 34418 EBI-EMBL Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B Lactococcus lactis is one of the few organisms with two dihydroorotate dehydrogenases, DHODs, A and B [1]. The B enzyme is a prototype for DHODs in Gram-positive bacteria that use NAD+ as the second substrate. DHODB is a hetero-tetramer composed of a central homodimer of PyrDB subunits resembling the DHODA structure and two PyrK subunits along with three different cofactors: FMN, FAD, and a [2Fe-2S] cluster. The [2Fe-2S] iron-sulfur cluster binds to this C-terminal domain of the PyrK subunit, which is at the interface between the flavin and NAD binding domains and contains three beta-strands. The four cysteine residues at the N-terminal part of this domain are the ones that bind, in pairs, to the iron-sulfur cluster. The conformation of the whole molecule means that the iron-sulfur cluster is localised in a well-ordered part of this domain close to the FAD binding site [1]. The FAD and and NAD binding domains are FAD_binding_6, Pfam:PF00970 and NAD_binding_1, Pfam:PF00175. [1]. 11188687. Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster. Rowland P, Norager S, Jensen KF, Larsen S;. Structure. 2000;8:1227-1238. (from Pfam) NF021915.5 PF10431.14 ClpB_D2-small 21.9 21.9 81 domain Y N N C-terminal, D2-small domain, of ClpB protein 14567920 131567 cellular organisms no rank 284935 EBI-EMBL C-terminal, D2-small domain, of ClpB protein C-terminal, D2-small domain, of ClpB protein This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, Pfam:PF00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilise the functional assembly [1]. The domain is associated with two Clp_N, Pfam:PF02861, at the N-terminus as well as AAA, Pfam:PF00004 and AAA_2, Pfam:PF07724. [1]. 14567920. The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state. Lee S, Sowa ME, Watanabe YH, Sigler PB, Chiu W, Yoshida M, Tsai FT;. Cell. 2003;115:229-240. (from Pfam) NF021916.5 PF10432.14 bact-PGI_C 24.5 24.5 151 domain Y Y N SIS domain-containing protein GO:0004347,GO:0004476,GO:0005975 15252053 131567 cellular organisms no rank 9385 EBI-EMBL Bacterial phospho-glucose isomerase C-terminal SIS domain Bacterial phospho-glucose isomerase C-terminal SIS domain This is the C-terminal SIS domain of a bacterial phospho-glucose isomerase EC:5.3.1.9 protein which is similar to eukaryote homologues to the extent that the sequence includes the cluster of threonines and serines that forms the sugar phosphate-binding site in conventional PGI. This domain contributes a good proportion of the active catalytic site residues. This PGI uses the same catalytic mechanisms for both glucose ring-opening and isomerisation for the interconversion of glucose 6-phosphate to fructose 6-phosphate [1]. It is associated with family SIS, Pfam:PF01380. [1]. 15252053. A novel phosphoglucose isomerase (PGI)/phosphomannose isomerase from the crenarchaeon Pyrobaculum aerophilum is a member of the PGI superfamily: structural evidence at 1.16-A resolution. Swan MK, Hansen T, Schonheit P, Davies C;. J Biol Chem. 2004;279:39838-39845. (from Pfam) NF021919.5 PF10435.14 BetaGal_dom2 25 25 180 domain Y N N Beta-galactosidase, domain 2 15491613 131567 cellular organisms no rank 4295 EBI-EMBL Beta-galactosidase, domain 2 Beta-galactosidase, domain 2 This is the second domain of the five-domain beta-galactosidase enzyme that altogether catalyses the hydrolysis of beta(1-3) and beta(1-4) galactosyl bonds in oligosaccharides as well as the inverse reaction of enzymatic condensation and trans-glycosylation. This domain is made up of 16 antiparallel beta-strands and an alpha-helix at its C terminus. The fold of this domain appears to be unique. In addition, the last seven strands of the domain form a subdomain with an immunoglobulin-like (I-type Ig) fold in which the first strand is divided between the two beta-sheets. In penicillin spp this strand is interrupted by a 12-residue insertion which forms an additional edge-strand to the second beta-sheet of the sub-domain. The remainder of the second domain forms a series of beta-hairpins at its N terminus, four strands of which are contiguous with part of the Ig-like sub-domain, forming in total a seven-stranded antiparallel beta-sheet. This domain is associated with family Glyco_hydro_35, Pfam:PF01301, which is N-terminal to it, but itself has no metazoan members. [1]. 15491613. Crystal structures of beta-galactosidase from Penicillium sp. and its complex with galactose. Rojas AL, Nagem RA, Neustroev KN, Arand M, Adamska M, Eneyskaya EV, Kulminskaya AA, Garratt RC, Golubev AM, Polikarpov I;. J Mol Biol. 2004;343:1281-1292. (from Pfam) NF021921.5 PF10437.14 Lip_prot_lig_C 24 24 85 domain Y Y N lipoate protein ligase C-terminal domain-containing protein 16384580,19520844,20089862 131567 cellular organisms no rank 23197 EBI-EMBL Bacterial lipoate protein ligase C-terminus Bacterial lipoate protein ligase C-terminus This is the C-terminal domain of a bacterial lipoate protein ligase. There is no conservation between this C-terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with the domain BPL_LipA_LipB Pfam:PF03099, further upstream. This domain is required for adenylation of lipoic acid by lipoate protein ligases. The domain is not required for transfer of lipoic acid from the adenylate to the lipoyl domain. Upon adenylation, this domain rotates 180 degrees away from the active site cleft. Therefore, the domain does not interact with the lipoyl domain during transfer. [1]. 16384580. Structure of a putative lipoate protein ligase from Thermoplasma acidophilum and the mechanism of target selection for post-translational modification. McManus E, Luisi BF, Perham RN;. J Mol Biol. 2006;356:625-637. [2]. 19520844. The Thermoplasma acidophilum LplA-LplB complex defines a new class of bipartite lipoate-protein ligases. Christensen QH, Cronan JE;. J Biol Chem. 2009;284:21317-21326. [3]. 20089862. Global conformational change associated with the two-step reaction catalyzed by Escherichia coli lipoate-protein ligase A. Fujiwara K, Maita N, Hosaka H, Okamura-Ikeda K, Nakagawa A, Taniguchi H;. J Biol Chem. 2010;285:9971-9980. (from Pfam) NF021922.5 PF10438.14 Cyc-maltodext_C 22.2 22.2 76 domain Y Y N cyclomaltodextrinase C-terminal domain-containing protein 10825529 131567 cellular organisms no rank 7777 EBI-EMBL Cyclo-malto-dextrinase C-terminal domain Cyclo-malto-dextrinase C-terminal domain This domain is at the very C-terminus of cyclo-malto-dextrinase proteins and consists of 8 beta strands, is largely globular and appears to help stabilise the acitve sites created by upstream domains, Cyc-maltodext_N Pfam:PF09087, and Alpha-amylase Pfam:PF00128. Cyclo-malto-dextrinases hydrolyse cyclodextrans to maltose and glucose and catalyse trans-glycosylation of oligosaccharides to the C3-, C4- or C6-hydroxyl groups of various acceptor sugar molecules. [1]. 10825529. Structure, specificity and function of cyclomaltodextrinase, a multispecific enzyme of the alpha-amylase family. Park KH, Kim TJ, Cheong TK, Kim JW, Oh BH, Svensson B;. Biochim Biophys Acta. 2000;1478:165-185. (from Pfam) NF021926.5 PF10442.14 FIST_C 28.5 28.5 131 domain Y Y N FIST C-terminal domain-containing protein 17855421 131567 cellular organisms no rank 25314 EBI-EMBL FIST C domain FIST C domain The FIST C domain is a novel sensory domain, which is present in signal transduction proteins from Bacteria, Archaea and Eukarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids [1]. [1]. 17855421. FIST: a sensory domain for diverse signal transduction pathways in prokaryotes and ubiquitin signaling in eukaryotes. Borziak K, Zhulin IB;. Bioinformatics. 2007;23:2518-2521. (from Pfam) NF021945.5 PF10462.14 Peptidase_M66 20.6 20.6 306 domain Y Y N M66 family metalloprotease 12123444 131567 cellular organisms no rank 6837 EBI-EMBL Peptidase M66 M66 family metalloprotease This family of metallopeptidases contains StcE, a virulence factor found in Shiga toxigenic Escherichia coli organisms. StcE peptidase cleaves C1 esterase inhibitor (a glycoprotein), but also large numbers of mucins at motifs in the form S*/T*-X-S/T, cleaving after the X, where the asterisk marks an O-glycosylated residue. NF021952.5 PF10469.14 AKAP7_NLS 24.4 24.4 208 PfamEq Y N N AKAP7 2'5' RNA ligase-like domain 12804576,16483255 131567 cellular organisms no rank 10078 EBI-EMBL AKAP7 2'5' RNA ligase-like domain AKAP7 2'5' RNA ligase-like domain AKAP7_NLS is the N-terminal domain of the cyclic AMP-dependent protein kinase A, PKA, anchor protein AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes [1]. AKAP7_NLS carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein [2]. Binding to the regulatory subunits RI and RII of PKA is mediated via the family AKAP7_RIRII_bdg. at the C-terminus. This family represents a region that contains two 2'5' RNA ligase like domains Pfam:PF02834. Presumably this domain carried out some as yet unknown enzymatic function. [1]. 12804576. AKAP7gamma is a nuclear RI-binding AKAP. Brown RL, August SL, Williams CJ, Moss SB;. Biochem Biophys Res Commun. 2003;306:394-401. [2]. 16483255. High-affinity AKAP7delta-protein kinase A interaction yields novel protein kinase A-anchoring disruptor peptides. Hundsrucker C, Krause G, Beyermann M, Prinz A, Zimmermann B, Diekmann O, Lorenz D, Stefan E, Nedvetsky P, Dathe M, Christian F, McSorley T, Krause E, McConnachie G, Herberg FW, Scott JD, Rosenthal W, Klussmann E;. Biochem J. 2006;396:297-306. (from Pfam) NF021981.5 PF10502.14 Peptidase_S26 22.9 22.9 168 domain Y Y N S26 family signal peptidase GO:0004252,GO:0006465 131567 cellular organisms no rank 155385 EBI-EMBL Signal peptidase, peptidase S26 S26 family signal peptidase This is a family of membrane signal serine endopeptidases which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal, signal peptides as proteins are translocated across membranes. The active site residues take the form of a catalytic dyad that is Ser, Lys in subfamily S26A; the Ser is the nucleophile in catalysis, and the Lys is the general base. (from Pfam) NF021982.5 PF10503.14 Esterase_PHB 23 23 219 domain Y Y N PHB depolymerase family esterase GO:0005576,GO:0016787 2644188 131567 cellular organisms no rank 36828 EBI-EMBL Esterase PHB depolymerase PHB depolymerase family esterase This family of proteins include acetyl xylan esterases (AXE), feruloyl esterases (FAE), and poly(3-hydroxybutyrate) (PHB) depolymerases. (from Pfam) NF021988.5 PF10509.14 GalKase_gal_bdg 23.1 23.1 49 domain Y Y N galactokinase family protein 10359639,12796487,15526155 131567 cellular organisms no rank 52288 EBI-EMBL Galactokinase galactose-binding signature galactokinase family protein This is the highly conserved galactokinase signature sequence which appears to be present in all galactokinases irrespective of how many other ATP binding sites, etc that they carry [1]. The function of this domain appears to be to bind galactose [2], and the domain is normally at the N-terminus of the enzymes, EC:2.7.1.6 [3]. This domain is associated with the families GHMP_kinases_C, Pfam:PF08544 and GHMP_kinases_N, Pfam:PF00288. [1]. 10359639. The trappin gene family: proteins defined by an N-terminal transglutaminase substrate domain and a C-terminal four-disulphide core. Schalkwijk J, Wiedow O, Hirose S;. Biochem J. 1999;340:569-577. [2]. 12796487. Molecular structure of galactokinase. Thoden JB, Holden HM;. J Biol Chem. 2003;278:33305-33311. [3]. 15526155. Galactokinase: structure, function and role in type II galactosemia. Holden HM, Thoden JB, Timson DJ, Reece RJ;. Cell Mol Life Sci. 2004;61:2471-2484. (from Pfam) NF021995.5 PF10516.14 SHNi-TPR 21 21 38 domain Y N N SHNi-TPR 18158900 131567 cellular organisms no rank 142 EBI-EMBL SHNi-TPR SHNi-TPR SHNi-TPR family members contain a reiterated sequence motif that is an interrupted form of TPR repeat [1]. [1]. 18158900. A NASP (N1/N2)-Related Protein, Sim3, Binds CENP-A and Is Required for Its Deposition at Fission Yeast Centromeres. Dunleavy EM, Pidoux AL, Monet M, Bonilla C, Richardson W, Hamilton GL, Ekwall K, McLaughlin PJ, Allshire RC;. Mol Cell. 2007;28:1029-1044. (from Pfam) NF021996.5 PF10517.14 DM13 25 25 105 PfamEq Y Y N DM13 domain-containing protein 17878204 131567 cellular organisms no rank 10901 EBI-EMBL Electron transfer DM13 Electron transfer DM13 The DM13 domain is a component of a novel electron-transfer system potentially involved in oxidative modification of animal cell-surface proteins [1]. It contains a nearly absolutely conserved cysteine, which could be involved in a redox reaction, either as a naked thiol group or through binding a prosthetic group like heme [1]. [1]. 17878204. The DOMON domains are involved in heme and sugar recognition. Iyer LM, Anantharaman V, Aravind L;. Bioinformatics. 2007;23:2660-2664. (from Pfam) NF021997.5 PF10518.14 TAT_signal 22.7 22.7 21 domain Y Y N twin-arginine translocation signal domain-containing protein 8939424 131567 cellular organisms no rank 27619 EBI-EMBL TAT (twin-arginine translocation) pathway signal sequence TAT (twin-arginine translocation) pathway signal sequence NF022004.5 PF10528.14 GLEYA 26.2 26.2 91 domain Y Y N GLEYA domain-containing protein 16079914,17870620,23770896,24591055,25452419 131567 cellular organisms no rank 1811 EBI-EMBL GLEYA domain GLEYA domain The GLEYA domain is related to lectin-like binding domains found in the S. cerevisiae Flo proteins and the C. glabrata Epa proteins [1]. It is a carbohydrate-binding domain that is found in fungal adhesins (also referred to as agglutinins or flocculins) [2]. Adhesins with a GLEYA domain possess a typical N-terminal signal peptide and a domain of conserved sequence repeats, but lack glycosylphosphatidylinositol (GPI) anchor attachment signals [3]. They contain a conserved motif G(M/L)(E/A/N/Q)YA, hence the name GLEYA. Based on sequence homology, it is suggested that the GLEYA domain would predominantly contain beta sheets [1]. The GLEYA domain is also found in S. pombe protein Swiss:Q92344, thought to be a kinetochore portein (Sim4 complex subunit), however no direct evidence for kinetochore association has been found [4]. Furthermore, a global protein localisation study in S. pombe identified it as a secreted protein localized to the Golgi complex [5]. [1]. 17870620. Molecular phylogenetics of ascomycotal adhesins-A novel family of putative cell-surface adhesive proteins in fission yeasts. Linder T, Gustafsson CM;. Fungal Genet Biol. 2007; [Epub ahead of print]. [2]. 23770896. Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum. Andersson KM, Meerupati T, Levander F, Friman E, Ahren D, Tunlid A;. Appl Environ Microbiol. 2013;79:4993-5004. [3]. 24591055. A novel lily anther-specific gene encodes adhesin-like proteins associated with exine formation during anther development. Liu MC, Yang CS, Yeh FL, Wei CH, Jane WN, Chung MC, Wang CS;. J Exp Bot. 2014;65:2023-2037. [4]. 16079914. Molecular analys. TRUNCATED at 1650 bytes (from Pfam) NF022007.5 PF10531.14 SLBB 27 15 55 domain Y Y N SLBB domain-containing protein 17250770 131567 cellular organisms no rank 179934 EBI-EMBL SLBB domain SLBB domain NF022018.5 PF10543.14 ORF6N 27.8 27.8 86 domain Y Y N ORF6N domain-containing protein 11897024 131567 cellular organisms no rank 14846 EBI-EMBL ORF6N domain ORF6N domain This domain was identified by Iyer and colleagues [1]. [1]. 11897024. Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors. Iyer LM, Koonin EV, Aravind L;. Genome Biol 2002;3:RESEARCH0012. (from Pfam) NF022019.5 PF10544.14 T5orf172 20 20 101 domain Y Y N GIY-YIG nuclease family protein 11897024 131567 cellular organisms no rank 29882 EBI-EMBL T5orf172 domain T5orf172 domain This domain was identified by Iyer and colleagues [1]. [1]. 11897024. Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors. Iyer LM, Koonin EV, Aravind L;. Genome Biol 2002;3:RESEARCH0012. (from Pfam) NF022026.5 PF10551.14 MULE 27.6 27.6 99 domain Y N N MULE transposase domain 17130173 131567 cellular organisms no rank 19177 EBI-EMBL MULE transposase domain MULE transposase domain This domain was identified by Babu and colleagues [1]. [1]. 17130173. The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons. Babu MM, Iyer LM, Balaji S, Aravind L;. Nucleic Acids Res. 2006; [Epub ahead of print] (from Pfam) NF022030.5 PF10555.14 MraY_sig1 20.1 11.3 13 PfamEq Y N N Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1 131567 cellular organisms no rank 42403 EBI-EMBL Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1 Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1 Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) (mraY) is a bacterial enzyme responsible for the formation of the first lipid intermediate of the cell wall peptidoglycan synthesis. It catalyses the formation of undecaprenyl-pyrophosphoryl-N-acetylmuramoyl-pentapeptide from UDP-MurNAc-pentapeptide and undecaprenyl-phosphate. It is an integral membrane protein with probably ten transmembrane domains. This domain is located at the end of the first cytoplasmic loop and the beginning of the second transmembrane domain. (from Pfam) NF022033.5 PF10559.14 Plug_translocon 22.1 22.1 35 PfamEq Y N N Plug domain of Sec61p 16822836 131567 cellular organisms no rank 1296 EBI-EMBL Plug domain of Sec61p Plug domain of Sec61p The Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side.The plug is unlikely to be important for sealing the translocation pore in yeast but it plays a role in stabilising Sec61p during translocon formation. The domain runs from residues 52-74 [1]. [1]. 16822836. The plug domain of yeast Sec61p is important for efficient protein translocation, but is not essential for cell viability. Junne T, Schwede T, Goder V, Spiess M;. Mol Biol Cell. 2006;17:4063-4068. (from Pfam) NF022039.5 PF10566.14 Glyco_hydro_97 32.5 32.5 275 domain Y Y N glycoside hydrolase family 97 catalytic domain-containing protein 16131397,18848471,18981178 131567 cellular organisms no rank 30839 EBI-EMBL Glycoside hydrolase 97 Glycoside hydrolase 97 This domain is the catalytic region of the bacterial glycosyl-hydrolase family 97. This central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, form two additional non-catalytic domains [1]. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands [2,3]. [1]. 16131397. GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily. Naumoff DG;. BMC Genomics. 2005;6:112. [2]. 18848471. Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora. Gloster TM, Turkenburg JP, Potts JR, Henrissat B, Davies GJ;. Chem Biol. 2008;15:1058-1067. [3]. 18981178. Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron. Kitamura M, Okuyama M, Tanzawa F, Mori H, Kitago Y, Watanabe N, Kimura A, Tanaka I, Yao M;. J Biol Chem. 2008;283:36328-36337. (from Pfam) NF022044.5 PF10571.14 UPF0547 29 29 26 domain Y Y N zinc ribbon domain-containing protein 23752268 131567 cellular organisms no rank 1733 EBI-EMBL Uncharacterised protein family UPF0547 Uncharacterised protein family UPF0547 This domain contains a zinc-ribbon motif. (from Pfam) NF022048.5 PF10576.14 EndIII_4Fe-2S 20.5 19.6 17 domain Y N N Iron-sulfur binding domain of endonuclease III GO:0051539 16096281,16967954,7664751,9045706 131567 cellular organisms no rank 69366 EBI-EMBL Iron-sulfur binding domain of endonuclease III Iron-sulfur binding domain of endonuclease III Escherichia coli endonuclease III (EC 4.2.99.18) [1] is a DNA repair enzyme that acts both as a DNA N-glycosylase, removing oxidised pyrimidines from DNA, and as an apurinic/apyrimidinic (AP) endonuclease, introducing a single-strand nick at the site from which the damaged base was removed. Endonuclease III is an iron-sulfur protein that binds a single 4Fe-4S cluster. The 4Fe-4S cluster does not seem to be important for catalytic activity, but is probably involved in the proper positioning of the enzyme along the DNA strand [2]. The 4Fe-4S cluster is bound by four cysteines which are all located in a 17 amino acid region at the C-terminal end of endonuclease III. A similar region is also present in the central section of mutY and in the C-terminus of ORF-10 and of the Micro-coccus UV endonuclease [4]. [1]. 7664751. Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure. Thayer MM, Ahern H, Xing D, Cunningham RP, Tainer JA;. EMBO J. 1995;14:4108-4120. [2]. 9045706. Cloning and expression of the cDNA encoding the human homologue of the DNA repair enzyme, Escherichia coli endonuclease III. Hilbert TP, Chaung W, Boorstein RJ, Cunningham RP, Teebor GW;. J Biol Chem. 1997;272:6733-6740. [3]. 16096281. Engineering functional changes in Escherichia coli endonuclease III based on phylogenetic and structural analyses. Watanabe T, Blaisdell JO, Wallace SS, Bond JP;. J Biol Chem. 2005;280:34378-34384. [4]. 16967954. Direct electrochemistry of endonuclease III in the presence and absence of DNA. Gorodetsky AA, Boal AK, Barton JK;. J Am Chem Soc. 2006;128:12082-12083. (from Pfam) NF022051.5 PF10579.14 Rapsyn_N 23 23 80 domain Y N N Rapsyn N-terminal myristoylation and linker region GO:0007268,GO:0033130,GO:0043495 15730871 131567 cellular organisms no rank 394 EBI-EMBL Rapsyn N-terminal myristoylation and linker region Rapsyn N-terminal myristoylation and linker region Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane. Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane [1]. [1]. 15730871. Deletion of N-terminal rapsyn domains disrupts clustering and has dominant negative effects on clustering of full-length rapsyn. Eckler SA, Kuehn R, Gautam M;. Neuroscience. 2005;131:661-670. (from Pfam) NF022055.5 PF10584.14 Proteasome_A_N 27.7 27.7 23 domain Y N N Proteasome subunit A N-terminal signature GO:0006511,GO:0019773 131567 cellular organisms no rank 1832 EBI-EMBL Proteasome subunit A N-terminal signature Proteasome subunit A N-terminal signature This domain is conserved in the A subunits of the proteasome complex proteins. (from Pfam) NF022058.5 PF10588.14 NADH-G_4Fe-4S_3 27 27 40 domain Y N N NADH-ubiquinone oxidoreductase-G iron-sulfur binding region GO:0016491 131567 cellular organisms no rank 85180 EBI-EMBL NADH-ubiquinone oxidoreductase-G iron-sulfur binding region NADH-ubiquinone oxidoreductase-G iron-sulfur binding region NF022059.5 PF10589.14 NADH_4Fe-4S 23.5 23.5 85 domain Y Y N NADH-ubiquinone oxidoreductase-F iron-sulfur binding region domain-containing protein GO:0051539 10587449,9299297 131567 cellular organisms no rank 75971 EBI-EMBL NADH-ubiquinone oxidoreductase-F iron-sulfur binding region NADH-ubiquinone oxidoreductase-F iron-sulfur binding region NF022061.5 PF10591.14 SPARC_Ca_bdg 22 22 113 PfamEq Y N N Secreted protein acidic and rich in cysteine Ca binding region GO:0005509 16121393 131567 cellular organisms no rank 542 EBI-EMBL Secreted protein acidic and rich in cysteine Ca binding region Secreted protein acidic and rich in cysteine Ca binding region The SPARC_Ca_bdg domain of Secreted Protein Acidic and Rich in Cysteine is responsible for the anti-spreading activity of human urothelial cells. It is rich in alpha-helices. This extracellular calcium-binding domain contains two EF-hands that each coordinates one Ca2+ ion, forming a helix-loop-helix structure that not only drives the conformation of the protein but is also necessary for biological activity. The anti-spreading activity was dependent on the coordination of Ca2+ by a Glu residue at the Z position of EF-hand 2 [1]. [1]. 16121393. The C-terminal Ca2+-binding domain of SPARC confers anti-spreading activity to human urothelial cells. Delostrinos CF, Hudson AE, Feng WC, Kosman J, Bassuk JA;. J Cell Physiol. 2006;206:211-220. (from Pfam) NF022062.5 PF10592.14 AIPR 25 25 308 PfamEq Y Y N AIPR family protein 18346280 131567 cellular organisms no rank 15551 EBI-EMBL AIPR protein AIPR family protein This family of proteins was identified in [1] as an abortive infection phage resistance protein often found in restriction modification system operons. [1]. 18346280. MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases. Iyer LM, Abhiman S, Aravind L;. Biol Direct. 2008;3:8. (from Pfam) NF022063.5 PF10593.14 Z1 25 25 228 domain Y Y N Z1 domain-containing protein 18346280 131567 cellular organisms no rank 11322 EBI-EMBL Z1 domain Z1 domain This uncharacterised domain was identified by Iyer and colleagues [1]. It is found associated with a helicase domain of superfamily type II. [1]. 18346280. MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases. Iyer LM, Abhiman S, Aravind L;. Biol Direct. 2008;3:8. (from Pfam) NF022070.5 PF10601.14 zf-LITAF-like 23.8 23.8 70 PfamEq Y Y N LITAF-like zinc ribbon domain-containing protein 11731489,12527760,17408970 131567 cellular organisms no rank 67 EBI-EMBL LITAF-like zinc ribbon domain LITAF-like zinc ribbon domain Members of this family display a conserved zinc ribbon structure [1] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS)[2]. The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [3]. [1]. 12527760. Structural classification of zinc fingers: survey and summary. Krishna SS, Majumdar I, Grishin NV;. Nucleic Acids Res. 2003;31:532-550. [2]. 17408970. Molecular cloning and characterization of a putative lipopolysaccharide-induced TNF-alpha factor (LITAF) gene homologue from Zhikong scallop Chlamys farreri. Yu Y, Qiu L, Song L, Zhao J, Ni D, Zhang Y, Xu W;. Fish Shellfish Immunol. 2007;23:419-429. [3]. 11731489. Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution. Ponting CP, Mott R, Bork P, Copley RR;. Genome Res 2001;11:1996-2008. (from Pfam) NF022072.5 PF10604.14 Polyketide_cyc2 27.4 27.4 142 domain Y Y N SRPBCC family protein 11276083 131567 cellular organisms no rank 274626 EBI-EMBL Polyketide cyclase / dehydrase and lipid transport SRPBCC family protein This family contains polyketide cylcases/dehydrases which are enzymes involved in polyketide synthesis. It also includes other proteins of the START superfamily [1]. [1]. 11276083. Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily. Iyer LM, Koonin EV, Aravind L;. Proteins. 2001;43:134-144. (from Pfam) NF022077.5 PF10609.14 ParA 27.1 27.1 246 domain Y Y N P-loop NTPase 15728363,2149583 131567 cellular organisms no rank 311642 EBI-EMBL NUBPL iron-transfer P-loop NTPase P-loop NTPase This family contains ATPases involved in plasmid partitioning [1]. It also contains the cytosolic Fe-S cluster assembling factor NBP35 which is required for biogenesis and export of both ribosomal subunits [2]. [1]. 2149583. A family of ATPases involved in active partitioning of diverse bacterial plasmids. Motallebi-Veshareh M, Rouch DA, Thomas CM;. Mol Microbiol 1990;4:1455-1463. [2]. 15728363. The eukaryotic P loop NTPase Nbp35: an essential component of the cytosolic and nuclear iron-sulfur protein assembly machinery. Hausmann A, Aguilar Netz DJ, Balk J, Pierik AJ, Muhlenhoff U, Lill R;. Proc Natl Acad Sci U S A. 2005;102:3266-3271. (from Pfam) NF022081.5 PF10613.14 Lig_chan-Glu_bd 30 30 115 domain Y N N Ligated ion channel L-glutamate- and glycine-binding site GO:0015276,GO:0016020 10465381,8428958 131567 cellular organisms no rank 67747 EBI-EMBL Ligated ion channel L-glutamate- and glycine-binding site Ligated ion channel L-glutamate- and glycine-binding site This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine [2]. It is found in association with Lig_chan, Pfam:PF00060. [1]. 8428958. Molecular characterization of the family of the N-methyl-D-aspartate receptor subunits. Ishii T, Moriyoshi K, Sugihara H, Sakurada K, Kadotani H, Yokoi M, Akazawa C, Shigemoto R, Mizuno N, Masu M, et al.;. J Biol Chem. 1993;268:2836-2843. [2]. 10465381. Subunit- and site-specific pharmacology of the NMDA receptor channel. Yamakura T, Shimoji K;. Prog Neurobiol. 1999;59:279-298. (from Pfam) NF022088.5 PF10621.14 FpoO 25.2 25.2 110 PfamEq Y Y N F420H2 dehydrogenase subunit FpoO fpoO 10940377,15168610 131567 cellular organisms no rank 126 EBI-EMBL F420H2 dehydrogenase subunit FpoO F420H2 dehydrogenase subunit FpoO This is the FpoO subunit of F420H2 dehydrogenase, an enzyme which oxidises reduced coenzyme F420. Reduced coenzyme F420 is a universal electron carrier in methanogens. [1]. 10940377. The respiratory complex I of bacteria, archaea and eukarya and its module common with membrane-bound multisubunit hydrogenases. Friedrich T, Scheide D;. FEBS Lett. 2000;479:1-5. [2]. 15168610. The membrane-bound electron transport system of Methanosarcina species. Deppenmeier U;. J Bioenerg Biomembr. 2004;36:55-64. (from Pfam) NF022100.5 PF10633.14 NPCBM_assoc 24.4 24.4 78 domain Y Y N NEW3 domain-containing protein 15285616,16131397 131567 cellular organisms no rank 30595 EBI-EMBL NPCBM-associated, NEW3 domain of alpha-galactosidase NEW3 domain The English-language version of the first reference can be found on pages 388-399 of the above. This domain has been named NEW3 but its actual function is not known. It is found on proteins which are bacterial galactosidases [1]. The domain is associated with the NPCBM family, Pfam:PF08305, a novel putative carbohydrate binding module found at the N-terminus of glycosyl hydrolases. [1]. 15285616. [Phylogenetic analysis of alpha-galactosidases of the GH27 family]. Naumov DG;. Mol Biol (Mosk). 2004;38:463-476. [2]. 16131397. GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily. Naumoff DG;. BMC Genomics. 2005;6:112. (from Pfam) NF022101.5 PF10634.14 Iron_transport 21 21 150 PfamEq Y Y N iron transporter 131567 cellular organisms no rank 4724 EBI-EMBL Fe2+ transport protein iron transporter This is a bacterial family of periplasmic proteins that are thought to function in high-affinity Fe2+ transport. (from Pfam) NF022106.5 PF10639.14 TMEM234 30.1 30.1 113 PfamEq Y N N Putative transmembrane family 234 131567 cellular organisms no rank 432 EBI-EMBL Putative transmembrane family 234 Putative transmembrane family 234 TMEM234 is a family of putative inner membrane proteins. Many bacterial members are annotated as putative L-Ara4N-phosphoundecaprenol flippase subunit ArnE, and as inner membrane proteins. They may be transporters of the multi-drug-resistant superfamily. (from Pfam) NF022113.5 PF10647.14 Gmad1 20.5 20.5 251 subfamily_domain Y Y N LpqB family beta-propeller domain-containing protein 16934981 131567 cellular organisms no rank 18798 EBI-EMBL Lipoprotein LpqB beta-propeller domain Lipoprotein LpqB beta-propeller domain The Gmad1 domain is found associated with the GerMN family, Pfam:PF10646, in bacterial spore formation. It is predicted to have a beta-propeller fold and to have a passive binding role rather than a catalytic function owing to the low number of conserved hydrophilic residues. [1]. 16934981. MtrAB-LpqB: a conserved three-component system in actinobacteria?. Hoskisson PA, Hutchings MI;. Trends Microbiol. 2006;14:444-449. (from Pfam) NF022115.5 PF10649.14 DUF2478 22.3 22.3 159 domain Y Y N DUF2478 domain-containing protein 131567 cellular organisms no rank 4440 EBI-EMBL Protein of unknown function (DUF2478) Protein of unknown function (DUF2478) This is a family of hypothetical bacterial proteins found in the vicinity of Molybdenum ABC transporter ATP-binding gene-products MobA MobB and MobC. However the function could not be confirmed. This family appears to belong to the P-loop superfamily by alignment to Pfam:PF03266. However, the characteristic P-loop sequence motif appears to have diverged beyond recognition in this family. (from Pfam) NF022118.5 PF10652.14 DUF2480 25 25 165 subfamily Y Y N DUF2480 family protein 131567 cellular organisms no rank 4630 EBI-EMBL Protein of unknown function (DUF2480) DUF2480 family protein All the members of this family are uncharacterised proteins, but the environment in which they are found on the bacterial genome suggests a function as a glucose-6-phosphate isomerase (EC 5.3.1.9). This could not, however, be confirmed. (from Pfam) NF022128.5 PF10662.14 PduV-EutP 21 21 143 domain Y Y N EutP/PduV family microcompartment system protein GO:0005524,GO:0006576 10464203,10498708,15516577,20417607 131567 cellular organisms no rank 41466 EBI-EMBL Ethanolamine utilisation - propanediol utilisation EutP/PduV family microcompartment system protein Members of this family function in ethanolamine and propanediol degradation pathways [1-3]. PduV may be involved in the association of the bacterial microcompartments (BMCs) to filaments [4]. [1]. 15516577. Evidence that a B12-adenosyl transferase is encoded within the ethanolamine operon of Salmonella enterica. Sheppard DE, Penrod JT, Bobik T, Kofoid E, Roth JR;. J Bacteriol. 2004;186:7635-7644. [2]. 10464203. The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. Kofoid E, Rappleye C, Stojiljkovic I, Roth J;. J Bacteriol 1999;181:5317-5329. [3]. 10498708. The propanediol utilization (pdu) operon of Salmonella enterica serovar Typhimurium LT2 includes genes necessary for formation of polyhedral organelles involved in coenzyme B(12)-dependent 1, 2-propanediol degradation. Bobik TA, Havemann GD, Busch RJ, Williams DS, Aldrich HC;. J Bacteriol. 1999;181:5967-5975. [4]. 20417607. Synthesis of empty bacterial microcompartments, directed organelle protein incorporation, and evidence of filament-associated organelle movement. Parsons JB, Frank S, Bhella D, Liang M, Prentice MB, Mulvihill DP, Warren MJ;. Mol Cell. 2010;38:305-315. (from Pfam) NF022133.5 PF10668.14 Phage_terminase 22 22 67 domain Y Y N phage terminase small subunit-related protein 3294420 131567 cellular organisms no rank 5775 EBI-EMBL Phage terminase small subunit phage terminase small subunit N-terminal domain Members of this family share a small domain, about 67 amino acids in length, with a region found N-terminal to PF03592 in phage terminal small subunit proteins, but most members of this family lack a PF03592-like domain. However, many of those missing a PF03592 domain are found adjacent to a terminase large subunit protein. NF022135.5 PF10670.14 DUF4198 34 34 209 domain Y Y N DUF4198 domain-containing protein 131567 cellular organisms no rank 20313 EBI-EMBL Domain of unknown function (DUF4198) Domain of unknown function (DUF4198) This family was previously missannotated in Pfam as NikM. (from Pfam) NF022137.5 PF10672.14 Methyltrans_SAM 27 27 286 domain Y Y N class I SAM-dependent methyltransferase 2.1.1.- GO:0008168 12504684 131567 cellular organisms no rank 79063 EBI-EMBL S-adenosylmethionine-dependent methyltransferase class I SAM-dependent methyltransferase Members of this family are S-adenosylmethionine-dependent methyltransferases from gamma-proteobacterial species. The diversity in the roles of methylation is matched by the almost bewildering number of methyltransferase enzymes that catalyse the methylation reaction. Although several classes of methyltransferase enzymes are known, the great majority of methylation reactions are catalysed by the S-adenosylmethionine-dependent methyltransferases. [1]. 12504684. SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold. Martin JL, McMillan FM;. Curr Opin Struct Biol. 2002;12:783-793. (from Pfam) NF022151.5 PF10686.14 YAcAr 28.2 28.2 66 domain Y Y N SLOG family protein 26590262 131567 cellular organisms no rank 9259 EBI-EMBL YspA, cpYpsA-related SLOG family SLOG family protein Family in the SLOG superfamily, related to YspA and cpYpsA families and shows associations with NAD utilization and ADP-ribosylation domains including NUDIX, NADAR and MACRO. Members of this family are predicted to function as sensors of nucleotide, nucleotide-derived ligands, or nucleic acids, which are potentially processed/modified by associating effectors. Also associates in a distinct system with a phosphoribosyltransferase (PRTase) domain [1]. [1]. 26590262. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;. Nucleic Acids Res. 2015;43:10633-10654. (from Pfam) NF022152.5 PF10688.14 Imp-YgjV 23.5 23.5 159 domain Y Y N YgjV family protein 11867724 131567 cellular organisms no rank 7753 EBI-EMBL Bacterial inner membrane protein YgjV family protein This is a family of inner membrane proteins. Many of the members are YgjV protein. [1]. 11867724. Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis. Drew D, Sjostrand D, Nilsson J, Urbig T, Chin CN, de Gier JW, von Heijne G;. Proc Natl Acad Sci U S A. 2002;99:2690-2695. (from Pfam) NF022163.5 PF10702.14 DUF2507 35 35 123 PfamAutoEq Y Y N DUF2507 domain-containing protein 131567 cellular organisms no rank 3590 EBI-EMBL Protein of unknown function (DUF2507) Protein of unknown function (DUF2507) This family is conserved in Firmicutes. The function is not known. (from Pfam) NF022165.5 PF10704.14 DUF2508 22.5 22.5 71 PfamAutoEq Y Y N DUF2508 family protein 131567 cellular organisms no rank 4329 EBI-EMBL Protein of unknown function (DUF2508) DUF2508 family protein This family is conserved in Firmicutes. Several members are annotated as being the protein YaaL. The function is not known. (from Pfam) NF022167.5 PF10706.14 Aminoglyc_resit 21 21 149 domain Y Y N nucleotidyltransferase domain-containing protein 17030911,25564464,28734024,3024112 131567 cellular organisms no rank 11764 EBI-EMBL Aminoglycoside-2''-adenylyltransferase Aminoglycoside-2''-adenylyltransferase This family is conserved in Bacteria. It confers resistance to kanamycin, gentamicin, and tobramycin [1-4]. The protein is also produced by plasmids in various bacterial species and confers resistance to essentially all clinically available aminoglycosides except streptomycin, and it eliminates the synergism between aminoglycosides and cell-wall active agents [2]. [1]. 3024112. Nucleotide sequence of the AAD(2'') aminoglycoside adenylyltransferase determinant aadB. Evolutionary relationship of this region with those surrounding aadA in R538-1 and dhfrII in R388. Cameron FH, Groot Obbink DJ, Ackerman VP, Hall RM;. Nucleic Acids Res. 1986;14:8625-8635. [2]. 17030911. Insertion sequence ISEcp1-like element connected with a novel aph(2'') allele [aph(2'')-Ie] conferring high-level gentamicin resistance and a novel streptomycin adenylyltransferase gene in Enterococcus. Chen YG, Qu TT, Yu YS, Zhou JY, Li LJ;. J Med Microbiol. 2006;55:1521-1525. [3]. 25564464. Structural and molecular basis for resistance to aminoglycoside antibiotics by the adenylyltransferase ANT(2'')-Ia. Cox G, Stogios PJ, Savchenko A, Wright GD;. mBio. 2015;6:e02180-e02114. [4]. 28734024. Effect of solvent and protein dynamics in ligand recognition and inhibition of aminoglycoside adenyltransferase 2''-Ia. Bacot-Davis VR, Bassenden AV, Sprules T, Berghuis AM;. Protein Sci. 2017;26:1852-1863. (from Pfam) NF022172.5 PF10711.14 DUF2513 29.6 29.6 100 domain Y Y N DUF2513 domain-containing protein 131567 cellular organisms no rank 4501 EBI-EMBL Hypothetical protein (DUF2513) Hypothetical protein (DUF2513) This family is found in bacteria. The function is not known. (from Pfam) NF022182.5 PF10722.14 YbjN 22 22 126 domain Y Y N YbjN domain-containing protein 16701556 131567 cellular organisms no rank 34260 EBI-EMBL Putative bacterial sensory transduction regulator Putative bacterial sensory transduction regulator YbjN is a putative sensory transduction regulator protein found in Proteobacteria. As it is a multi-copy suppressor of the coenzyme A-associated temperature sensitivity in temperature-sensitive mutant strains of Escherichia coli the suggestion is that it both helps CoA-A1 and possibly works as a general stabiliser for some other unstable proteins [1]. This family was expanded to subsume other related families: DUF1790, DUF1821 and DUF2596. [1]. 16701556. Analysis of the temperature-sensitive mutation of Escherichia coli pantothenate kinase reveals YbjN as a possible protein stabilizer. Chen X, Shen D, Zhou B;. Biochem Biophys Res Commun. 2006;345:834-842. (from Pfam) NF022187.5 PF10727.14 Rossmann-like 23 23 131 domain Y N N Rossmann-like domain 131567 cellular organisms no rank 35500 EBI-EMBL Rossmann-like domain Rossmann-like domain This family of proteins contain a Rossmann-like domain. (from Pfam) NF022197.5 PF10737.14 GerPC 22.4 22.4 174 PfamEq Y Y N spore germination protein GerPC gerPC 10715007,2252393 131567 cellular organisms no rank 2700 EBI-EMBL Spore germination protein GerPC spore germination protein GerPC GerPC is required for the formation of functionally normal spores. The gerP locus encodes a number of proteins which are thought to be involved in the establishment of normal spore coat structure and/or permeability, which allows the access of germinants to their receptor [2]. [1]. 2252393. The genetics of bacterial spore germination. Moir A, Smith DA;. Annu Rev Microbiol. 1990;44:531-553. [2]. 10715007. Mutations in the gerP locus of Bacillus subtilis and Bacillus cereus affect access of germinants to their targets in spores. Behravan J, Chirakkal H, Masson A, Moir A;. J Bacteriol. 2000;182:1987-1994. (from Pfam) NF022216.5 PF10756.14 bPH_6 22 22 73 domain Y Y N PH domain-containing protein 131567 cellular organisms no rank 30691 EBI-EMBL Bacterial PH domain Bacterial PH domain This HMM describes a primarily a bacterial (Actinomycetales) branch of the PH (Pleckstrin Homology) domain. NF022229.5 PF10771.14 DUF2582 24.2 24.2 65 domain Y Y N winged helix-turn-helix domain-containing protein 22223187 131567 cellular organisms no rank 1824 EBI-EMBL Winged helix-turn-helix domain (DUF2582) winged helix-turn-helix domain-containing protein This family is conserved in bacteria and archaea. The function is not known. The structure of two proteins in this family were solved using NMR and shown to adopt a winged helix-turn-helix fold [1]. Structural analysis shows that these proteins form an unusual dimeric conformation. This dimer was shown to be similar to that found in the FadR and TubR wHTH domains. It was suggested [1] that these proteins are not very likely to bind to DNA. [1]. 22223187. Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771. Eletsky A, Petrey D, Zhang QC, Lee HW, Acton TB, Xiao R, Everett JK, Prestegard JH, Honig B, Montelione GT, Szyperski T;. J Struct Funct Genomics. 2012;13:1-7. (from Pfam) NF022235.5 PF10778.14 DehI 28.9 28.9 148 domain Y Y N halocarboxylic acid dehydrogenase DehI family protein GO:0019120 18353360 131567 cellular organisms no rank 314 EBI-EMBL Halocarboxylic acid dehydrogenase DehI halocarboxylic acid dehydrogenase DehI family protein Haloacid dehalogenases catalyse the removal of halides from organic haloacids. DehI can process both L- and D-substrates. A crucial aspartate residue is predicted to activate a water molecule for nucleophilic attack of the substrate chiral centre resulting in an inversion of the configuration of either L- or D-substrates in contrast to D-only enzymes [1]. [1]. 18353360. The crystal structure of DehI reveals a new alpha-haloacid dehalogenase fold and active-site mechanism. Schmidberger JW, Wilce JA, Weightman AJ, Whisstock JC, Wilce MC;. J Mol Biol. 2008;378:284-294. (from Pfam) NF022247.5 PF10790.14 DUF2604 25 25 85 domain Y Y N DUF2604 domain-containing protein 131567 cellular organisms no rank 212 EBI-EMBL Protein of Unknown function (DUF2604) Protein of Unknown function (DUF2604) Family of bacterial proteins with undetermined function. (from Pfam) NF022279.5 PF10823.13 DUF2568 24.2 24.2 92 domain Y Y N DUF2568 domain-containing protein 131567 cellular organisms no rank 7449 EBI-EMBL Protein of unknown function (DUF2568) Protein of unknown function (DUF2568) One member in this family is annotated as yrdB which is part of a four gene operon however currently no function is known. (from Pfam) NF022282.5 PF10826.13 DUF2551 23.4 23.4 83 domain Y Y N DUF2551 domain-containing protein 131567 cellular organisms no rank 296 EBI-EMBL Protein of unknown function (DUF2551) Protein of unknown function (DUF2551) This Archaeal family of proteins has no known function. (from Pfam) NF022300.5 PF10844.13 DUF2577 22 22 96 domain Y Y N DUF2577 family protein 131567 cellular organisms no rank 4095 EBI-EMBL Protein of unknown function (DUF2577) DUF2577 family protein This family of proteins has no known function (from Pfam) NF022321.5 PF10865.13 DUF2703 23.6 23.6 120 domain Y Y N DUF2703 domain-containing protein 131567 cellular organisms no rank 823 EBI-EMBL Domain of unknown function (DUF2703) Domain of unknown function (DUF2703) This family of protein has no known function, but it may be distantly related to the thioredoxin fold. It contains the CXXC motif that is characteristic of thioredoxins. (from Pfam) NF022325.5 PF10869.13 DUF2666 23 23 135 PfamAutoEq Y Y N DUF2666 family protein 22616997 131567 cellular organisms no rank 127 EBI-EMBL Domain of unknown function (DUF2666) DUF2666 family protein This domain found in archaeal proteins, including PF2050 from Pyrococcus furiosus (Swiss:Q8TZE5). PF2050, with an overall globular structure, contain this domain twice, each showing an antiparallel beta-sheet and an alpha-helical bundle, and shows a positively charged basic cleft on one side. This protein interacts with circular and linear dsDNA [1]. [1]. 22616997. Crystal structure of Pyrococcus furiosus PF2050, a member of the DUF2666 protein family. Han BG, Jeong KC, Cho JW, Jeong BC, Song HK, Lee JY, Shin DH, Lee S, Lee BI;. FEBS Lett. 2012;586:1384-1388. (from Pfam) NF022338.5 PF10882.13 bPH_5 22.5 22.5 100 domain Y Y N PH domain-containing protein 19913036 131567 cellular organisms no rank 4692 EBI-EMBL Bacterial PH domain pleckstrin homology domain, bacterial family This family of proteins with unknown function appear to be related to bacterial PH domains. This family was formerly known as DUF2679. [1]. 19913036. Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain. Xu Q, Bateman A, Finn RD, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. J Mol Biol. 2010 Feb 12;396(1):31-46. Epub 2009 Nov 10. (from Pfam) NF022340.5 PF10884.13 DUF2683 27 27 66 domain Y Y N DUF2683 family protein 131567 cellular organisms no rank 1821 EBI-EMBL Protein of unknown function (DUF2683) DUF2683 family protein This family of proteins with unknown function appears to be restricted to Methanosarcinaceae. (from Pfam) NF022354.5 PF10899.13 AbiGi 22.4 22.4 185 subfamily Y Y N abortive infection system antitoxin AbiGi family protein 12023079,8795193,9872803 131567 cellular organisms no rank 1998 EBI-EMBL Putative abortive phage resistance protein AbiGi, antitoxin abortive infection system antitoxin AbiGi family protein This is a bacterial family of proteins with unknown function. AbiGi is a family of putative type IV toxin-antitoxin system antitoxins. The AbiG abortive phage resistance system affects lactococcal bacteriophages phiP335 and phiQ30 but not the other P335 phage species. AbiGii toxin appears to confer resistance to phages by a mechanism of abortive infection that acts by interfering with phage RNA synthesis [1]. The cognate toxin is found in Pfam:PF16873. [1]. 12023079. Effectiveness of the lactococcal abortive infection systems AbiA, AbiE, AbiF and AbiG against P335 type phages. Tangney M, Fitzgerald GF;. FEMS Microbiol Lett. 2002;210:67-72. [2]. 8795193. AbiG, a genotypically novel abortive infection mechanism encoded by plasmid pCI750 of Lactococcus lactis subsp. cremoris UC653. O'Connor L, Coffey A, Daly C, Fitzgerald GF;. Appl Environ Microbiol. 1996;62:3075-3082. [3]. 9872803. Expression, regulation, and mode of action of the AbiG abortive infection system of lactococcus lactis subsp. cremoris UC653. O'Connor L, Tangney M, Fitzgerald GF;. Appl Environ Microbiol. 1999;65:330-335. (from Pfam) NF022366.5 PF10912.13 DUF2700 22.3 22.3 146 domain Y Y N DUF2700 domain-containing protein 131567 cellular organisms no rank 18 EBI-EMBL Protein of unknown function (DUF2700) Protein of unknown function (DUF2700) This family of proteins with unknown function appears to be restricted to Caenorhabditis elegans. (from Pfam) NF022376.5 PF10923.13 BrxC_BrxD 22.2 22.2 414 subfamily Y Y N BREX system ATP-binding domain-containing protein 25452498 131567 cellular organisms no rank 10481 EBI-EMBL BREX system ATP-binding protein BrxC/D DUF2791 family P-loop domain-containing protein This is the ATP-binding domain found in proteins that are associated with Bacteriophage Exclusion (BREX) system, a defense system that allows bacteriophage adsorption but blocks phage DNA replication [1]. This domain is found in the ATP-binding proteins BrxC/pglY (due to its homology with pglY from Pgl system) and BrxD [1]. [1]. 25452498. BREX is a novel phage resistance system widespread in microbial genomes. Goldfarb T, Sberro H, Weinstock E, Cohen O, Doron S, Charpak-Amikam Y, Afik S, Ofir G, Sorek R;. EMBO J. 2015;34:169-183. (from Pfam) NF022379.5 PF10926.13 DUF2800 21 21 368 domain Y Y N DUF2800 domain-containing protein 131567 cellular organisms no rank 14341 EBI-EMBL Protein of unknown function (DUF2800) Protein of unknown function (DUF2800) This is a family of uncharacterised proteins found in bacteria and viruses. Some members of this family are annotated as being Phi APSE P51-like proteins. (from Pfam) NF022382.5 PF10929.13 DUF2811 26.6 26.6 57 domain Y Y N DUF2811 domain-containing protein 131567 cellular organisms no rank 1074 EBI-EMBL Protein of unknown function (DUF2811) Protein of unknown function (DUF2811) This is a bacterial family of uncharacterised proteins. (from Pfam) NF022387.5 PF10934.13 DUF2634 32.9 32.9 104 domain Y Y N DUF2634 domain-containing protein 131567 cellular organisms no rank 6475 EBI-EMBL Protein of unknown function (DUF2634) Protein of unknown function (DUF2634) Some members in this family of proteins are annotated as phage related, xkdS however currently there is no known function. (from Pfam) NF022388.5 PF10935.13 DUF2637 22.8 22.8 161 domain Y Y N DUF2637 domain-containing protein 131567 cellular organisms no rank 47940 EBI-EMBL Protein of unknown function (DUF2637) Protein of unknown function (DUF2637) This family of proteins has no known function. (from Pfam) NF022389.5 PF10936.13 DUF2617 22.3 22.3 160 PfamAutoEq Y Y N DUF2617 family protein 131567 cellular organisms no rank 6755 EBI-EMBL Protein of unknown function DUF2617 DUF2617 family protein This bacterial family of proteins has no known function. (from Pfam) NF022410.5 PF10957.13 Spore_Cse60 20.7 20.7 60 PfamEq Y Y N sporulation protein Cse60 8990290 131567 cellular organisms no rank 1360 EBI-EMBL Sporulation protein Cse60 sporulation protein Cse60 Cse60 is expressed during sporulation in Bacillus subtilis. Transcription commences around 2h after the start of sporulation and had an absolute requirement for the transcription factor sigmaE. Cse60 is an acidic product of only 60 residues, whose function is not known [1]. [1]. 8990290. cse15, cse60, and csk22 are new members of mother-cell-specific sporulation regulons in Bacillus subtilis. Henriques AO, Bryan EM, Beall BW, Moran CP Jr;. J Bacteriol. 1997;179:389-398. (from Pfam) NF022420.5 PF10967.13 DUF2769 22.8 22.8 57 domain Y Y N DUF2769 domain-containing protein 131567 cellular organisms no rank 529 EBI-EMBL Protein of unknown function (DUF2769) Protein of unknown function (DUF2769) This family of proteins have no known function. (from Pfam) NF022427.5 PF10974.13 DUF2804_N 26.9 26.9 197 subfamily Y Y N DUF2804 family protein 20944205,36419248 131567 cellular organisms no rank 10217 EBI-EMBL Domain of unknown function (DUF2804), N-terminal DUF2804 family protein This entry represents a domain with unknown function. This domain has been described as structurally similar to Pfam: PF07143 (PDB:2ich, residues:24 to 220) [1,2]. [1]. 36419248. DALI shines a light on remote homologs: One hundred discoveries. Holm L, Laiho A, Toronen P, Salgado M;. Protein Sci. 2023;32:e4519. [2]. 20944205. Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism. Chiu HJ, Bakolitsa C, Skerra A, Lomize A, Carlton D, Miller MD, Krishna SS, Abdubek P, Astakhova T, Axelrod HL, Clayton T, Deller MC, Duan L, Feuerhelm J, Grant JC, Grzechnik SK, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Paulsen J, Reyes R, Rife CL, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:1153-1159. (from Pfam) NF022430.5 PF10977.13 DUF2797 25 25 227 PfamAutoEq Y Y N DUF2797 domain-containing protein 131567 cellular organisms no rank 18879 EBI-EMBL Protein of unknown function (DUF2797) Protein of unknown function (DUF2797) This family of proteins has no known function. (from Pfam) NF022432.5 PF10979.13 DUF2786 23.9 23.9 40 domain Y Y N DUF2786 domain-containing protein 131567 cellular organisms no rank 22587 EBI-EMBL Protein of unknown function (DUF2786) Protein of unknown function (DUF2786) This family of proteins has no known function. (from Pfam) NF022436.5 PF10983.13 DUF2793 27 27 87 domain Y Y N DUF2793 domain-containing protein 131567 cellular organisms no rank 7550 EBI-EMBL Protein of unknown function (DUF2793) Protein of unknown function (DUF2793) This is a bacterial family of proteins with unknown function. (from Pfam) NF022441.5 PF10988.13 DUF2807 24.2 24.2 181 domain Y Y N GIN domain-containing protein 14765110,18688279 131567 cellular organisms no rank 33947 EBI-EMBL Putative auto-transporter adhesin, head GIN domain Putative auto-transporter adhesin, head GIN domain This bacterial family of proteins shows structural similarity to other pectin lyase families. Although structures from this family align with acetyl-transferases, there is no conservation of catalytic residues found. It is likely that the function is one of cell-adhesion. In PDB:3jx8, it is interesting to note that the sequence of contains several well defined sequence repeats, centred around GSG motifs defining the tight beta turn between the two sheets of the super-helix; there are 8 such repeats in the C-terminal half of the protein, which could be grouped into 4 repeats of two. It seems likely that this family belongs to the superfamily of trimeric auto-transporter adhesins (TAAs), which are important virulence factors in Gram-negative pathogens [1] [2]. In the case of Parabacteroides distasonis, which is a component of the normal distal human gut microbiota, TAA-like complexes probably modulate adherence to the host (information derived from TOPSAN). [1]. 14765110. The Yersinia adhesin YadA collagen-binding domain structure is a novel left-handed parallel beta-roll. Nummelin H, Merckel MC, Leo JC, Lankinen H, Skurnik M, Goldman A;. EMBO J. 2004;23:701-711. [2]. 18688279. Structure of the head of the Bartonella adhesin BadA. Szczesny P, Linke D, Ursinus A, Bar K, Schwarz H, Riess TM, Kempf VA, Lupas AN, Martin J, Zeth K;. PLoS Pathog. 2008;4:e1000119. (from Pfam) NF022442.5 PF10989.13 DUF2808 25.3 25.3 146 domain Y Y N DUF2808 domain-containing protein 131567 cellular organisms no rank 2555 EBI-EMBL Protein of unknown function (DUF2808) Protein of unknown function (DUF2808) This family of proteins with unknown function appears to be restricted to Cyanobacteria. (from Pfam) NF022449.5 PF10996.13 Beta-Casp 27.7 27.7 120 domain Y N N Beta-Casp domain 17128255 131567 cellular organisms no rank 30153 EBI-EMBL Beta-Casp domain Beta-Casp domain The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains [1]. [1]. 17128255. Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease. Mandel CR, Kaneko S, Zhang H, Gebauer D, Vethantham V, Manley JL, Tong L;. Nature. 2006;444:953-956. (from Pfam) NF022463.5 PF11010.13 DUF2848 23.4 23.4 194 domain Y Y N DUF2848 family protein 131567 cellular organisms no rank 6378 EBI-EMBL Protein of unknown function (DUF2848) DUF2848 family protein This bacterial family of proteins has no known function. (from Pfam) NF022476.5 PF11023.13 DUF2614 21 21 111 subfamily Y Y N DUF2614 family zinc ribbon-containing protein 131567 cellular organisms no rank 2686 EBI-EMBL Zinc-ribbon containing domain DUF2614 family zinc ribbon-containing protein Members of this family, including YgzB from Bacillus subtilis, average about 120 amino acids in length, with a hydrophobic central region and a C-terminal predicted zinc ribbon structure. NF022479.5 PF11026.13 DUF2721 28.3 28.3 129 domain Y Y N DUF2721 domain-containing protein 131567 cellular organisms no rank 8960 EBI-EMBL Protein of unknown function (DUF2721) Protein of unknown function (DUF2721) This family is conserved in bacteria. The function is not known. (from Pfam) NF022481.5 PF11028.13 TMEM260-like 24.2 24.2 179 domain Y Y N protein O-mannosyl-transferase family 37186866 131567 cellular organisms no rank 11173 EBI-EMBL Protein O-mannosyl-transferase TMEM260-like protein O-mannosyl-transferase family This family includes human Protein O-mannosyl-transferase TMEM260 and similar sequences from bacteria and eukaryota. TMEM260 transfers mannosyl residues to the hydroxyl group of serine or threonine residues of proteins [1]. [1]. 37186866. The SHDRA syndrome-associated gene TMEM260 encodes a protein-specific O-mannosyltransferase. Larsen ISB, Povolo L, Zhou L, Tian W, Mygind KJ, Hintze J, Jiang C, Hartill V, Prescott K, Johnson CA, Mullegama SV, McConkie-Rosell A, McDonald M, Hansen L, Vakhrushev SY, Schjoldager KT, Clausen H, Worzfeld T, Joshi HJ, Halim A;. Proc Natl Acad Sci U S A. 2023;120:e2302584120. (from Pfam) NF022503.5 PF11051.13 Mannosyl_trans3 22 22 273 domain Y N N Mannosyltransferase putative GO:0006486,GO:0016757 131567 cellular organisms no rank 561 EBI-EMBL Mannosyltransferase putative Mannosyltransferase putative This family is conserved in fungi. Several members are annotated as being alpha-1,3-mannosyltransferase but this could not be confirmed. (from Pfam) NF022525.5 PF11074.13 DUF2779 23.3 23.3 126 domain Y Y N DUF2779 domain-containing protein 131567 cellular organisms no rank 3772 EBI-EMBL Domain of unknown function(DUF2779) Domain of unknown function(DUF2779) This domain is conserved in bacteria. The function is not known. (from Pfam) NF022554.5 PF11104.13 PilM_2 27 27 340 domain Y Y N pilus assembly protein PilM pilM 16857013,21596754,8550460 131567 cellular organisms no rank 34020 EBI-EMBL Type IV pilus assembly protein PilM; pilus assembly protein PilM The type IV pilus assembly protein PilM is required for competency and pilus biogenesis [1-2]. It binds to PilN and ATP [3]. [1]. 8550460. Characterization of genes required for pilus expression in Pseudomonas syringae pathovar phaseolicola. Roine E, Nunn DN, Paulin L, Romantschuk M;. J Bacteriol. 1996;178:410-417. [2]. 16857013. Identification, subcellular localization and functional interactions of PilMNOWQ and PilA4 involved in transformation competency and pilus biogenesis in the thermophilic bacterium Thermus thermophilus HB27. Rumszauer J, Schwarzenlander C, Averhoff B;. FEBS J. 2006;273:3261-3272. [3]. 21596754. Structure of the PilM-PilN inner membrane type IV pilus biogenesis complex from Thermus thermophilus. Karuppiah V, Derrick JP;. J Biol Chem. 2011;286:24434-24442. (from Pfam) NF022564.5 PF11114.13 Minor_capsid_2 27.7 27.7 113 PfamEq Y Y N minor capsid protein 131567 cellular organisms no rank 3217 EBI-EMBL Minor capsid protein minor capsid protein Most of the members of this family are annotated as being minor capsid proteins. The genomes carrying the genes usually have three similar proteins adjacent to each other, hence this one being named as No.2. (from Pfam) NF022577.5 PF11127.13 YgaP-like_TM 25.1 25.1 66 domain Y Y N YgaP-like transmembrane domain 24958726 131567 cellular organisms no rank 35473 EBI-EMBL Inner membrane protein YgaP-like, transmembrane domain Inner membrane protein YgaP-like, transmembrane domain This domain is found in proteins from bacteria and archaea, including Inner membrane protein YgaP from Escherichia coli, a membrane protein with a rhodanese domain (Pfam: PF00581) that may have sulfurtransferase activity. YgaP adopts a dimeric assembly. This entry represents the transmembrane domain. It consist of two slightly tilted alpha-helices [1]. [1]. 24958726. Solution NMR structure and functional analysis of the integral membrane protein YgaP from Escherichia coli. Eichmann C, Tzitzilonis C, Bordignon E, Maslennikov I, Choe S, Riek R;. J Biol Chem. 2014;289:23482-23503. (from Pfam) NF022589.5 PF11139.13 SfLAP 35 35 213 subfamily Y Y N GAP family protein 22194604 131567 cellular organisms no rank 16409 EBI-EMBL Sap, sulfolipid-1-addressing protein GAP family protein SAP is a transmembrane transport protein with six predicted transmembrane helices, with a hydrophilic domain between helices 3 and 4. This hyrodphobic region is highly variable among identified Gap-like (GPL, peptidoglycolipid, addressing protein) proteins and may be involved in substrate recognition. SAP also belongs to the LysE protein superfamily (Pfam:PF01810), whose members have been implicated in small molecule transport in bacteria. Other Gap proteins export metabolites across the cell membrane so it is possible that Sap specifically may be involved in transport of sulfolipid-1 across the membrane [1]. [1]. 22194604. Elucidation and chemical modulation of sulfolipid-1 biosynthesis in Mycobacterium tuberculosis. Seeliger JC, Holsclaw CM, Schelle MW, Botyanszki Z, Gilmore SA, Tully SE, Niederweis M, Cravatt BF, Leary JA, Bertozzi CR;. J Biol Chem. 2012;287:7990-8000. (from Pfam) NF022599.5 PF11150.13 DUF2927 26.2 26.2 206 domain Y Y N DUF2927 domain-containing protein 131567 cellular organisms no rank 7107 EBI-EMBL Protein of unknown function (DUF2927) Protein of unknown function (DUF2927) This family is conserved in Proteobacteria. Several members are described as being putative lipoproteins, but otherwise the function is not known. (from Pfam) NF022606.5 PF11158.13 DUF2938 31.4 31.4 150 PfamAutoEq Y Y N DUF2938 family protein 131567 cellular organisms no rank 8064 EBI-EMBL Protein of unknown function (DUF2938) DUF2938 family protein This bacterial family of proteins has no known function. Some members are thought to be membrane proteins however this cannot be confirmed. (from Pfam) NF022608.5 PF11160.13 Hva1_TUDOR 24.1 24.1 59 subfamily Y Y N HVA1 family protein 27583447 131567 cellular organisms no rank 10862 EBI-EMBL Hypervirulence associated proteins TUDOR domain HVA1 family protein Family members include HVA1 (hypervirulence-associated protein 1) whose absence is associated with a hypervirulent phenotype in mice. Metabolomics analysis suggests that when HVA1 is absent there is a block in the citric acid cycle, while structural analysis of the Hva1 protein suggests a potential interaction with NADPH. The structural architecture of Hva1 bears similarity with Tudor domains [1]. [1]. 27583447. A Small Protein Associated with Fungal Energy Metabolism Affects the Virulence of Cryptococcus neoformans in Mammals. McClelland EE, Ramagopal UA, Rivera J, Cox J, Nakouzi A, Prabu MM, Almo SC, Casadevall A;. PLoS Pathog. 2016;12:e1005849. (from Pfam) NF022615.5 PF11167.13 DUF2953 22 22 53 domain Y Y N DUF2953 domain-containing protein 131567 cellular organisms no rank 7142 EBI-EMBL Protein of unknown function (DUF2953) Protein of unknown function (DUF2953) This family of proteins has no known function. (from Pfam) NF022619.5 PF11171.13 DUF2958 21 21 111 domain Y Y N DUF2958 domain-containing protein 131567 cellular organisms no rank 5718 EBI-EMBL Protein of unknown function (DUF2958) Protein of unknown function (DUF2958) Some members are annotated as lipoproteins however this cannot be confirmed. This family of proteins has no known function. (from Pfam) NF022623.5 PF11175.13 DUF2961 27 27 235 domain Y Y N DUF2961 domain-containing protein 131567 cellular organisms no rank 8914 EBI-EMBL Protein of unknown function (DUF2961) Protein of unknown function (DUF2961) This family of proteins has no known function. (from Pfam) NF022633.5 PF11185.13 DUF2971 22 22 89 domain Y Y N DUF2971 domain-containing protein 131567 cellular organisms no rank 19162 EBI-EMBL Protein of unknown function (DUF2971) Protein of unknown function (DUF2971) This bacterial family of proteins has no known function. (from Pfam) NF022636.5 PF11188.13 DUF2975 27 27 130 domain Y Y N DUF2975 domain-containing protein 131567 cellular organisms no rank 28579 EBI-EMBL Protein of unknown function (DUF2975) Protein of unknown function (DUF2975) This family of bacterial proteins have no known function. These proteins are likely to be integral membrane proteins. The proteins contain a highly conserved glutamic acid close to their C-terminus. (from Pfam) NF022637.5 PF11189.13 DUF2973 22.2 22.2 68 PfamAutoEq Y Y N DUF2973 domain-containing protein 131567 cellular organisms no rank 875 EBI-EMBL Protein of unknown function (DUF2973) Protein of unknown function (DUF2973) Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently they have no known function. (from Pfam) NF022641.5 PF11193.13 DUF2812 27.8 27.8 110 domain Y Y N DUF2812 domain-containing protein 131567 cellular organisms no rank 11113 EBI-EMBL Protein of unknown function (DUF2812) Protein of unknown function (DUF2812) This is a bacterial family of uncharacterised proteins, however some members of this family are annotated as membrane proteins. (from Pfam) NF022643.5 PF11196.13 DUF2834 22.9 22.9 96 domain Y Y N DUF2834 domain-containing protein 19737099 131567 cellular organisms no rank 5781 EBI-EMBL Protein of unknown function DUF2834 Protein of unknown function DUF2834 The function of DUF2834 is not clear. (from Pfam) NF022646.5 PF11199.13 DUF2891 25 25 325 PfamAutoEq Y Y N DUF2891 family protein 131567 cellular organisms no rank 9974 EBI-EMBL Protein of unknown function (DUF2891) DUF2891 family protein This is a bacterial family of uncharacterised proteins. (from Pfam) NF022657.5 PF11211.13 DUF2997 24.1 24.1 47 domain Y Y N DUF2997 domain-containing protein 131567 cellular organisms no rank 2427 EBI-EMBL Protein of unknown function (DUF2997) Protein of unknown function (DUF2997) This family of proteins has no known function. (from Pfam) NF022659.5 PF11213.13 DUF3006 32.3 32.3 67 domain Y Y N DUF3006 family protein 131567 cellular organisms no rank 4660 EBI-EMBL Protein of unknown function (DUF3006) DUF3006 family protein This family of proteins has no known function. (from Pfam) NF022684.5 PF11239.13 DUF3040 24.7 24.7 84 domain Y Y N DUF3040 domain-containing protein 131567 cellular organisms no rank 18253 EBI-EMBL Protein of unknown function (DUF3040) Protein of unknown function (DUF3040) Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed. (from Pfam) NF022691.5 PF11246.13 Phage_gp53 21 21 200 subfamily Y Y N baseplate wedge protein 53 12923574 131567 cellular organisms no rank 59 EBI-EMBL Base plate wedge protein 53 baseplate wedge protein 53 The baseplate of bacteriophage T4 controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. The structure of the baseplate suggests a mechanism of baseplate structural transition during the initial stages of T4 infection. The baseplate is assembled from six identical wedges that surround the central hub. Gp53, along with other T4 gene products, combine sequentially to assemble a wedge [1]. [1]. 12923574. Three-dimensional structure of bacteriophage T4 baseplate. Kostyuchenko VA, Leiman PG, Chipman PR, Kanamaru S, van Raaij MJ, Arisaka F, Mesyanzhinov VV, Rossmann MG;. Nat Struct Biol. 2003;10:688-693. (from Pfam) NF022696.5 PF11251.13 DUF3050 22.2 22.2 233 domain Y Y N DUF3050 domain-containing protein 131567 cellular organisms no rank 6748 EBI-EMBL Protein of unknown function (DUF3050) Protein of unknown function (DUF3050) This bacterial family of proteins has no known function. (from Pfam) NF022700.5 PF11255.13 DUF3054 25 25 110 PfamAutoEq Y Y N DUF3054 family protein 131567 cellular organisms no rank 6967 EBI-EMBL Protein of unknown function (DUF3054) DUF3054 family protein Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known. (from Pfam) NF022715.5 PF11271.13 PorA 29.5 29.5 297 subfamily Y Y N porin PorA family protein 23811360 131567 cellular organisms no rank 13548 EBI-EMBL Porin PorA porin PorA family protein Members of this family include PorA, a channel-forming protein found mostly in Gram-positive bacteria [1]. [1]. 23811360. Identification and characterization of the channel-forming protein in the cell wall of Corynebacterium amycolatum. Soltan Mohammadi N, Mafakheri S, Abdali N, Barcena-Uribarri I, Tauch A, Benz R;. Biochim Biophys Acta. 2013;1828:2574-2582. (from Pfam) NF022732.5 PF11288.13 DUF3089 23.4 23.4 207 domain Y Y N DUF3089 domain-containing protein 131567 cellular organisms no rank 5389 EBI-EMBL Protein of unknown function (DUF3089) Protein of unknown function (DUF3089) This family of proteins has no known function but appears to have an alpha/beta hydrolase domain and so is likely to be enzymatic. (from Pfam) NF022736.5 PF11292.13 DUF3093 23 23 140 PfamAutoEq Y Y N DUF3093 family protein 131567 cellular organisms no rank 12251 EBI-EMBL Protein of unknown function (DUF3093) DUF3093 family protein This family of proteins with unknown function appears to be restricted to Actinobacteria. Some members are annotated as alanine rich membrane proteins however this cannot be confirmed. (from Pfam) NF022739.5 PF11295.13 DUF3096 23.3 23.3 37 PfamAutoEq Y Y N DUF3096 domain-containing protein 131567 cellular organisms no rank 2079 EBI-EMBL Protein of unknown function (DUF3096) Protein of unknown function (DUF3096) This family of proteins with unknown function appears to be restricted to Proteobacteria. (from Pfam) NF022743.5 PF11299.13 DUF3100 27 27 235 domain Y Y N DUF3100 domain-containing protein 131567 cellular organisms no rank 5408 EBI-EMBL Protein of unknown function (DUF3100) Protein of unknown function (DUF3100) Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known. (from Pfam) NF022747.5 PF11303.13 DUF3105 25 25 130 domain Y Y N DUF3105 domain-containing protein 131567 cellular organisms no rank 13503 EBI-EMBL Protein of unknown function (DUF3105) Protein of unknown function (DUF3105) Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known. (from Pfam) NF022760.5 PF11316.13 Rhamno_transf 23 23 235 domain Y Y N glycosyltransferase 18210176 131567 cellular organisms no rank 4672 EBI-EMBL Putative rhamnosyl transferase glycosyltransferase Most members of this family are uncharacterised, but one is a putative side-chain-rhamnosyl transferase [1]. [1]. 18210176. Identification and organization of genes for diutan polysaccharide synthesis from Sphingomonas sp. ATCC 53159. Coleman RJ, Patel YN, Harding NE;. J Ind Microbiol Biotechnol. 2008;35:263-274. (from Pfam) NF022769.5 PF11325.13 DUF3127 27 27 85 domain Y Y N DUF3127 domain-containing protein 131567 cellular organisms no rank 5946 EBI-EMBL Domain of unknown function (DUF3127) Domain of unknown function (DUF3127) This bacterial family of proteins has no known function. However, it does show distant similarity to Pfam:PF00436, with proteins such as Swiss:D1W984 being similar to both families. This suggests that this family may have a DNA-binding function. (from Pfam) NF022773.5 PF11329.13 DUF3131 20.3 20.3 367 domain Y Y N DUF3131 domain-containing protein 131567 cellular organisms no rank 7698 EBI-EMBL Protein of unknown function (DUF3131) Protein of unknown function (DUF3131) This bacterial family of proteins has no known function. (from Pfam) NF022783.5 PF11339.13 DUF3141 29.7 29.7 582 domain Y Y N DUF3141 domain-containing protein 131567 cellular organisms no rank 7201 EBI-EMBL Protein of unknown function (DUF3141) Protein of unknown function (DUF3141) This family of proteins with unknown function appears to be restricted to Proteobacteria. (from Pfam) NF022789.5 PF11345.13 DUF3147 23.6 23.6 111 subfamily Y Y N DUF3147 family protein 131567 cellular organisms no rank 2319 EBI-EMBL Protein of unknown function (DUF3147) DUF3147 family protein Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known. (from Pfam) NF022810.5 PF11367.13 DUF3168 27.2 27.2 117 domain Y Y N DUF3168 domain-containing protein 131567 cellular organisms no rank 15835 EBI-EMBL Protein of unknown function (DUF3168) Protein of unknown function (DUF3168) This family of proteins has no known function but is likely to be a component of bacteriophage. (from Pfam) NF022812.5 PF11369.13 DUF3160 25 25 632 domain Y Y N DUF3160 domain-containing protein 131567 cellular organisms no rank 1232 EBI-EMBL Protein of unknown function (DUF3160) Protein of unknown function (DUF3160) This family of proteins has no known function. (from Pfam) NF022815.5 PF11373.13 DUF3175 27 27 86 domain Y Y N DUF3175 domain-containing protein 131567 cellular organisms no rank 2858 EBI-EMBL Protein of unknown function (DUF3175) Protein of unknown function (DUF3175) This family of proteins with unknown function appears to be restricted to Proteobacteria. (from Pfam) NF022818.5 PF11376.13 DUF3179 27 27 292 subfamily Y Y N DUF3179 domain-containing (seleno)protein 17626042 131567 cellular organisms no rank 4314 EBI-EMBL Protein of unknown function (DUF3179) DUF3179 domain-containing (seleno)protein Members of this family, also called OS_HP1, include selenoproteins. NF022823.5 PF11381.13 DUF3185 25.3 25.3 59 domain Y Y N DUF3185 family protein 131567 cellular organisms no rank 1454 EBI-EMBL Protein of unknown function (DUF3185) DUF3185 family protein Some members in this bacterial family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known. (from Pfam) NF022829.5 PF11387.13 DUF2795 25 25 44 domain Y Y N DUF2795 domain-containing protein 131567 cellular organisms no rank 11355 EBI-EMBL Protein of unknown function (DUF2795) Protein of unknown function (DUF2795) This family of proteins has no known function. (from Pfam) NF022833.5 PF11391.13 DUF2798 23.5 23.5 59 domain Y Y N DUF2798 domain-containing protein 131567 cellular organisms no rank 12882 EBI-EMBL Protein of unknown function (DUF2798) Protein of unknown function (DUF2798) This family of proteins has no known function. (from Pfam) NF022839.5 PF11397.13 GlcNAc 21 21 352 domain Y Y N GlcNAc-transferase family protein 12244115 131567 cellular organisms no rank 1439 EBI-EMBL Glycosyltransferase (GlcNAc) GlcNAc-transferase family protein GlcNAc is an enzyme that carries out the first glycosylation step of hydroxylated Skp1, a ubiquitous eukaryotic protein, in the cytoplasm [1]. [1]. 12244115. Molecular cloning and expression of a UDP-N-acetylglucosamine (GlcNAc):hydroxyproline polypeptide GlcNAc-transferase that modifies Skp1 in the cytoplasm of dictyostelium. Van Der Wel H, Morris HR, Panico M, Paxton T, Dell A, Kaplan L, West CM;. J Biol Chem. 2002;277:46328-46337. (from Pfam) NF022840.5 PF11398.13 DUF2813 21 21 372 domain Y Y N DUF2813 domain-containing protein 131567 cellular organisms no rank 34156 EBI-EMBL Protein of unknown function (DUF2813) Protein of unknown function (DUF2813) This entry contains YjbD from Escherichia coli (Swiss:P75828), which is annotated as a nucleotide triphosphate hydrolase. (from Pfam) NF022849.5 PF11408.13 Helicase_Sgs1 22.2 22.2 80 PfamEq Y N N Sgs1 RecQ helicase GO:0003676,GO:0043138 10647186 131567 cellular organisms no rank 1099 EBI-EMBL Sgs1 RecQ helicase Sgs1 RecQ helicase RecQ helicases unwind DNA in an ATP-dependent manner. Sgs1 has a HRDC (helicase and RNaseD C-terminal) domain which modulates the helicase function via auxiliary contacts to DNA [1]. [1]. 10647186. The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins. Liu Z, Macias MJ, Bottomley MJ, Stier G, Linge JP, Nilges M, Bork P, Sattler M;. Structure. 1999;7:1557-1566. (from Pfam) NF022860.5 PF11419.13 DUF3194 21.5 21.5 83 PfamAutoEq Y Y N DUF3194 domain-containing protein 15152082 131567 cellular organisms no rank 725 EBI-EMBL Protein of unknown function (DUF3194) Protein of unknown function (DUF3194) This family of proteins has no known function however the structure has been determined. The protein consists of two alpha-helices packed on the same side of a central beta-hairpin [1]. [1]. 15152082. Solution structure of the hypothetical protein Mth677 from Methanobacterium thermoautotrophicum: a novel alpha+beta fold. Blanco FJ, Yee A, Campos-Olivas R, Ortiz AR, Devos D, Valencia A, Arrowsmith CH, Rico M;. Protein Sci. 2004;13:1458-1465. (from Pfam) NF022867.5 PF11427.13 HTH_Tnp_Tc3_1 21.1 21.1 50 domain Y N N Tc3 transposase GO:0003677 9312061 131567 cellular organisms no rank 637 EBI-EMBL Tc3 transposase Tc3 transposase Tc3 is transposase with a specific DNA-binding domain which contains three alpha-helices, two of which form a helix-turn-helix motif which makes four base-specific contacts with the major groove. The N-terminus makes contacts with the minor groove. There is a base specific recognition between Tc3 and the transposon DNA. The DNA binding domain forms a dimer in which each monomer binds a separate transposon end. This implicates that the dimer has a role in synapsis and is necessary for the simultaneous cleavage of both transposon termini [1]. [1]. 9312061. Crystal structure of the specific DNA-binding domain of Tc3 transposase of C.elegans in complex with transposon DNA. van Pouderoyen G, Ketting RF, Perrakis A, Plasterk RH, Sixma TK;. EMBO J 1997;16:6044-6054. (from Pfam) NF022869.5 PF11429.13 Colicin_D 25 25 84 domain Y Y N colicin D domain-containing protein GO:0004540 15336558 131567 cellular organisms no rank 1717 EBI-EMBL Colicin D Colicin D Colicin D is a tRNase which kills sensitive E.coli cells via a specific tRNA cleavage. It targets the four isoaccepting tRNAs for Arg and cleaves the phosphodiester bond between positions 38 and 39 at the 3' junction of the anticodon stem and the loop [1]. [1]. 15336558. Relation between tRNase activity and the structure of colicin D according to X-ray crystallography. Yajima S, Nakanishi K, Takahashi K, Ogawa T, Hidaka M, Kezuka Y, Nonaka T, Ohsawa K, Masaki H;. Biochem Biophys Res Commun. 2004;322:966-973. (from Pfam) NF022883.5 PF11443.13 DUF2828 29 29 623 PfamAutoEq Y Y N DUF2828 family protein 131567 cellular organisms no rank 969 EBI-EMBL Domain of unknown function (DUF2828) DUF2828 family protein This is a uncharacterised domain found in eukaryotes and viruses. (from Pfam) NF022887.5 PF11447.13 DUF3201 25 25 153 PfamAutoEq Y Y N DUF3201 domain-containing protein 131567 cellular organisms no rank 114 EBI-EMBL Protein of unknown function (DUF3201) Protein of unknown function (DUF3201) This archaeal family of proteins has no known function. (from Pfam) NF022889.5 PF11449.13 ArsP_2 32.5 32.5 359 PfamEq Y Y N putative manganese transporter 131567 cellular organisms no rank 4773 EBI-EMBL Putative, 10TM heavy-metal exporter putative manganese transporter This is a family of putative manganese transporters with 9-11 TMs. Members carry two well-conserved characteristic sequence- motifs of 'PGCG'. (from Pfam) NF022896.5 PF11457.13 DUF3021 24.7 24.7 130 domain Y Y N DUF3021 family protein 131567 cellular organisms no rank 8283 EBI-EMBL Protein of unknown function (DUF3021) DUF3021 family protein This is a bacterial family of uncharacterised proteins. (from Pfam) NF022902.5 PF11463.13 R-HINP1I 25 25 208 PfamEq Y N N R.HinP1I restriction endonuclease 22638584 131567 cellular organisms no rank 327 EBI-EMBL R.HinP1I restriction endonuclease R.HinP1I restriction endonuclease Hinp1I is a type II restriction endonuclease, recognising and cleaving a palindromic tetranucleotide sequence (G/CGC) resulting in 2 nt 5' overhanging ends [1]. HINP1I has a conserved catalytic core domain containing an active site motif SDC18QXK and a DNA-binding domain [1]. [1]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF022921.5 PF11483.13 DUF3209 25 25 124 PfamAutoEq Y Y N DUF3209 family protein 131567 cellular organisms no rank 435 EBI-EMBL Protein of unknown function (DUF3209) DUF3209 family protein This family of proteins has no known function. (from Pfam) NF022924.5 PF11487.13 RestrictionSfiI 25 25 292 subfamily Y Y N SfiI family type II restriction endonuclease 3.1.21.- 22638584 131567 cellular organisms no rank 117 EBI-EMBL Type II restriction enzyme SfiI SfiI family type II restriction endonuclease SfiI is a restriction enzyme that can cleave two DNA sites simultaneously to leave 3-base 3' overhangs. It acts as a homo-tetramer and recognises a specific eight base-paid palindromic DNA sequence. After binding two copies of its recognition sequence, SfiI becomes activated leading to cleavage of all four DNA strands. The structure of SfiI consists of a central twisted beta-sheet surrounded by alpha-helices. [1]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF022931.5 PF11494.13 Ta0938 27 27 92 PfamEq Y Y N TA0938 family protein 17377985 131567 cellular organisms no rank 74 EBI-EMBL Ta0938 TA0938 family protein The founding member of this protein family is TA0938 from the archaeal species Thermoplasma acidophilum. NF022932.5 PF11495.13 Regulator_TrmB 22.2 22.2 233 domain Y Y N TrmB family transcriptional regulator sugar-binding domain-containing protein 16473881 131567 cellular organisms no rank 8932 EBI-EMBL Archaeal transcriptional regulator TrmB Archaeal transcriptional regulator TrmB TrmB is an alpha-glucoside sensing transcriptional regulator. The protein is the transcriptional repressor for gene cluster encoding trehalose/maltose ABC transporter in T.litoralis and P.furiosus [1]. TrmB has lost its DNA binding domain but retained its sugar recognition site. A nonreducing glucosyl residue is shared by all substrates bound to TrmB which suggests that its a common recognition motif [1]. [1]. 16473881. Crystal structure of the sugar binding domain of the archaeal transcriptional regulator TrmB. Krug M, Lee SJ, Diederichs K, Boos W, Welte W;. J Biol Chem. 2006;281:10976-10982. (from Pfam) NF022946.5 PF11511.13 RhodobacterPufX 25 25 67 PfamEq Y Y N RC-LH1 core complex protein PufX pufX 17161397 131567 cellular organisms no rank 200 EBI-EMBL Intrinsic membrane protein PufX RC-LH1 core complex protein PufX PufX is a small protein found in the photosynthetic reaction center–light harvesting complex 1 (RC–LH1) of species such as Rhodobacter sphaeroides. NF022953.5 PF11518.13 DUF3221 26.4 26.4 82 domain Y Y N DUF3221 domain-containing protein 131567 cellular organisms no rank 3920 EBI-EMBL Protein of unknown function (DUF3221) Protein of unknown function (DUF3221) This family of proteins with unknown function appears to be restricted to Bacillus. Some members in this family of proteins are annotated as YobA however this cannot be confirmed. YobA is a protein with unknown function. (from Pfam) NF022958.5 PF11523.13 DUF3223 21 21 75 PfamAutoEq Y Y N DUF3223 domain-containing protein 131567 cellular organisms no rank 1503 EBI-EMBL Protein of unknown function (DUF3223) Protein of unknown function (DUF3223) This family of proteins has no known function. (from Pfam) NF022959.5 PF11524.13 SeleniumBinding 27.9 27.9 82 subfamily Y Y N selenium-binding protein 18650445 131567 cellular organisms no rank 19 EBI-EMBL Selenium binding protein selenium-binding protein Selenium is an important nutrient that needs to be regulated since lack of the nutrient leads to cell abnormalities and high concentrations are toxic. SeBP regulates the level of free selenium in the cell by sequestering the nutrient during transport. SeBP acts as a pentamer and delivers the selenium to the selenophosphate synthetase enzyme [1]. Each subunit is composed of an alpha helix on top of a four stranded twisted ss sheet, stabilised by hydrogen bonds [1]. [1]. 18650445. Solution NMR structure of selenium-binding protein from methanococcus vannielii. Suzuki M, Lee DY, Inyamah N, Stadtman TC, Tjandra N;. J Biol Chem 2008; [Epub ahead of print] (from Pfam) NF022968.5 PF11533.13 AtzH-like 27 27 126 PfamAutoEq Y Y N AtzH-like domain-containing protein 30399173 131567 cellular organisms no rank 7437 EBI-EMBL AtzH-like AtzH-like This bacterial family of proteins includes AtzH from Pseudomonas sp. sp. AtzH is thought to be an amidase responsible for converting 1,3-dicarboxyurea to allophanate. This protein, which adopts a dimeric assembly, shows a seven-stranded anti-parallel beta- sheet and three helices [1]. [1]. 30399173. A novel decarboxylating amidohydrolase involved in avoiding metabolic dead ends during cyanuric acid catabolism in Pseudomonas sp. strain ADP. Esquirol L, Peat TS, Wilding M, Hartley CJ, Newman J, Scott C;. PLoS One. 2018;13:e0206949. (from Pfam) NF022969.5 PF11534.13 HTHP 25 25 72 domain Y Y N hexameric tyrosine-coordinated heme protein 17395199 131567 cellular organisms no rank 1746 EBI-EMBL Hexameric tyrosine-coordinated heme protein (HTHP) hexameric tyrosine-coordinated heme protein HTHP is from the marine bacterium Silicibacter pomeroyi and has peroxidase and catalase activity. HTHP consists of six monomers which each binds a solvent accessible heme group and is stabilised by the interaction of three neighbouring monomers [1]. The heme iron is penta-coordinated with a tyrosine residue as proximal ligand [1]. [1]. 17395199. HTHP: a novel class of hexameric, tyrosine-coordinated heme proteins. Jeoung JH, Pippig DA, Martins BM, Wagener N, Dobbek H;. J Mol Biol. 2007;368:1122-1131. (from Pfam) NF022970.5 PF11535.13 Calci_bind_CcbP 21.5 21.5 105 domain Y Y N calcium-binding protein 15469503,15811937 131567 cellular organisms no rank 1007 EBI-EMBL Calcium binding calcium-binding protein CcbP is a Ca(2+) binding protein which, in Anabaena, is thought to bind Ca(2+) by protein surface charge. When bound to Ca(2+), the protein becomes more compact and the level of free calcium decreases. The free Ca(2+) concentration which is regulated by CcbP is critical for the differentiation process [1]. Calcium signalling is widespread in bacterial species, and prokaryotic cells like eukaryotes are equipped with all the elements to maintain Ca2+ homeostasis [2]. [1]. 15811937. CcbP, a calcium-binding protein from Anabaena sp. PCC 7120, provides evidence that calcium ions regulate heterocyst differentiation. Zhao Y, Shi Y, Zhao W, Huang X, Wang D, Brown N, Brand J, Zhao J;. Proc Natl Acad Sci U S A. 2005;102:5744-5748. [2]. 15469503. Calcium signalling in bacteria. Dominguez DC;. Mol Microbiol. 2004;54:291-297. (from Pfam) NF022971.5 PF11536.13 DUF3226 27 27 208 domain Y Y N DUF3226 domain-containing protein 131567 cellular organisms no rank 3596 EBI-EMBL Protein of unknown function (DUF3226) Protein of unknown function (DUF3226) This archaeal family of proteins has no known function. (from Pfam) NF022995.5 PF11563.13 Protoglobin 25 25 158 domain Y Y N protoglobin domain-containing protein GO:0019825,GO:0020037 12962628,18188182 131567 cellular organisms no rank 25665 EBI-EMBL Protoglobin Protoglobin This family includes protoglobin from Methanosarcina acetivorans C2A. It is also found near the N-terminus of the Haem-based aerotactic transducer HemAT in Bacillus subtilis (Swiss:O07621). It is part of the haemoglobin superfamily. Protoglobin has specific loops and an amino-terminal extension which leads to the burying of the haem within the matrix of the protein. Protoglobin-specific apolar tunnels allow the access of O2, CO and NO to the haem distal site [1]. In HemAT it acts as an oxygen sensor domain [2]. It can also recognise cyanide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 18188182. Archaeal protoglobin structure indicates new ligand diffusion paths and modulation of haem-reactivity. Nardini M, Pesce A, Thijs L, Saito JA, Dewilde S, Alam M, Ascenzi P, Coletta M, Ciaccio C, Moens L, Bolognesi M;. EMBO Rep. 2008;9:157-163. [2]. 12962628. Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry. Zhang W, Phillips GN Jr;. Structure. 2003;11:1097-1110. (from Pfam) NF022996.5 PF11564.13 BpuJI_N 25 25 278 PfamEq Y N N Restriction endonuclease BpuJI - N terminal 18433771 131567 cellular organisms no rank 498 EBI-EMBL Restriction endonuclease BpuJI - N terminal Restriction endonuclease BpuJI - N terminal BpuJI is a restriction endonuclease which recognises the asymmetric sequence 5'-CCCGT and cuts at multiple sites in the surrounding area of the target sequence. This family of proteins is the N terminal domain of BpuJI which has DNA recognition functions. The recognition domain has two subdomains D1 and D2. The recognition of the target sequence occurs through major groove contacts of amino acids on the helix-turn-helix region and the N-terminal arm [1]. [1]. 18433771. The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3-A resolution. Sukackaite R, Grazulis S, Bochtler M, Siksnys V;. J Mol Biol. 2008;378:1084-1093. (from Pfam) NF023008.5 PF11576.13 HcgB 25 25 153 PfamAutoEq Y Y N FeGP cofactor biosynthesis guanylyltransferase HcgB family protein 25882909,28294213 131567 cellular organisms no rank 189 EBI-EMBL FeGP cofactor biosynthesis protein HcgB, guanylyltransferase FeGP cofactor biosynthesis guanylyltransferase HcgB family protein This entry represents the guanylyltransferase component of the Iron-guanylylpyridinol (FeGP) cofactor biosynthesis protein HcgB [1]. This family of proteins with unknown function appears to be restricted to Methanobacteria. [1]. 25882909. Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]-hydrogenase cofactor. Fujishiro T, Kahnt J, Ermler U, Shima S;. Nat Commun. 2015;6:6895. [2]. 28294213. Towards artificial methanogenesis: biosynthesis of the [Fe]-hydrogenase cofactor and characterization of the semi-synthetic hydrogenase. Bai L, Fujishiro T, Huang G, Koch J, Takabayashi A, Yokono M, Tanaka A, Xu T, Hu X, Ermler U, Shima S;. Faraday Discuss. 2017;198:37-58. (from Pfam) NF023010.5 PF11578.13 DUF3237 24 24 149 subfamily Y Y N DUF3237 family protein 131567 cellular organisms no rank 10626 EBI-EMBL Protein of unknown function (DUF3237) DUF3237 family protein This family of proteins has no known function (from Pfam) NF023011.5 PF11579.13 DUF3238 21.1 21.1 193 domain Y Y N DUF3238 domain-containing protein 131567 cellular organisms no rank 1999 EBI-EMBL Protein of unknown function (DUF3238) Protein of unknown function (DUF3238) This family of proteins with unknown function appears to be restricted to Bacillus cereus. (from Pfam) NF023014.5 PF11582.13 DUF3240 21 21 102 PfamAutoEq Y Y N DUF3240 family protein 131567 cellular organisms no rank 2359 EBI-EMBL Protein of unknown function (DUF3240) DUF3240 family protein This family of proteins with unknown function appears to be restricted to Proteobacteria. (from Pfam) NF023020.5 PF11588.13 DUF3243 27 27 79 subfamily Y Y N DUF3243 family protein 131567 cellular organisms no rank 3632 EBI-EMBL Protein of unknown function (DUF3243) DUF3243 family protein This family of proteins with unknown function appears to be restricted to Firmicutes. (from Pfam) NF023021.5 PF11589.13 DUF3244 25 25 96 domain Y Y N DUF3244 domain-containing protein 29847585 131567 cellular organisms no rank 2861 EBI-EMBL Domain of unknown function (DUF3244) Domain of unknown function (DUF3244) This domain adopts an immunoglobulin-like beta-sandwich fold and structurally is most similar to fibronectin. This domain is found at the C-terminus of the Listeria monocytogenes InlP protein. This domain shares some similarity with the secretion signal domain of type X secretion systems Pfam:PF18962. This domain is also found at the C-terminus of likely cell surface proteins suggesting this domain has a similar function. [1]. 29847585. Listeria monocytogenes InlP interacts with afadin and facilitates basement membrane crossing. Faralla C, Bastounis EE, Ortega FE, Light SH, Rizzuto G, Gao L, Marciano DK, Nocadello S, Anderson WF, Robbins JR, Theriot JA, Bakardjiev AI;. PLoS Pathog. 2018;14:e1007094. (from Pfam) NF023043.5 PF11611.13 DUF4352 25.9 25.9 122 domain Y Y N DUF4352 domain-containing protein 131567 cellular organisms no rank 22977 EBI-EMBL Domain of unknown function (DUF4352) Domain of unknown function (DUF4352) Members of these family are putative lipoproteins that fall into the Antigen MPT63/MPB63 (immunoprotective extracellular protein) superfamily. (from Pfam) NF023045.5 PF11614.13 FixG_C 25.6 25.6 119 domain Y Y N FixG Ig-like domain-containing protein 12620739,8661920 131567 cellular organisms no rank 32854 EBI-EMBL IG-like fold at C-terminal of FixG, putative oxidoreductase IG-like fold at C-terminal of FixG, putative oxidoreductase This domain is part of a transmembrane protein, FixG, itself part of the FixGHIS operon closely associated with the FixNOPQ operon that is the symbiotically essential cbb3-type haem-copper oxidase complex. FixG expression is induced by oxygen-deprivation. This C-terminal domain adopts an E-set Ig-like fold. [1]. 8661920. The Bradyrhizobium japonicum fixGHIS genes are required for the formation of the high-affinity cbb3-type cytochrome oxidase. Preisig O, Zufferey R, Hennecke H;. Arch Microbiol. 1996;165:297-305. [2]. 12620739. Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae. Makino K, Oshima K, Kurokawa K, Yokoyama K, Uda T, Tagomori K, Iijima Y, Najima M, Nakano M, Yamashita A, Kubota Y, Kimura S, Yasunaga T, Honda T, Shinagawa H, Hattori M, Iida T;. Lancet. 2003;361:743-749. (from Pfam) NF023048.5 PF11617.13 Cu-binding_MopE 27 3 30 domain Y Y N MopE-related protein 131567 cellular organisms no rank 3547 EBI-EMBL Putative metal-binding motif Putative metal-binding motif The seqeunce of structure 2vov is not matched in any other sequence either in UniProt or in NCBI (Sep2014). The model is of a short repeat not found on the G1UBC6 - 2vov - protein. The presence of conserved cysteine residues and the lack of hydrophobic residues suggests that this repeat might be a metal-binding site, perhaps for zinc or calcium ions. (from Pfam) NF023070.5 PF11639.13 HapK 25 25 104 domain Y N N REDY-like protein HapK 17729271 131567 cellular organisms no rank 976 EBI-EMBL REDY-like protein HapK REDY-like protein HapK This family of proteins represents HapK, a protein of unknown function, with two homologues PigK and RedY. The monomer structure of the protein contains a four-stranded anti parallel beta-sheet, three alpha-helices and a short C terminal tail which it uses for dimer formation [1]. The surface of HapK has a deep cavity with consists of a kinked helix and a beta-four strand. HapK could be involved in prodigiosin biosynthesis, specifically the binding of a bipyrrole intermediate such as HBM or MBM [1]. [1]. 17729271. Structural insight of the role of the Hahella chejuensis HapK protein in prodigiosin biosynthesis. Cho HJ, Kim KJ, Kim MH, Kang BS;. Proteins. 2008;70:257-262. (from Pfam) NF023075.5 PF11645.13 PDDEXK_5 26.1 26.1 138 PfamEq Y Y N group I intron-associated PD-(D/E)XK endonuclease 11251845,17410205,22638584 131567 cellular organisms no rank 1794 EBI-EMBL PD-(D/E)XK endonuclease group I intron-associated PD-(D/E)XK endonuclease This family of endonucleases includes a group I intron-encoded endonuclease [1]. This family belongs to the PD-(D/E)XK superfamily [2-3]. [1]. 11251845. A novel group I intron-encoded endonuclease specific for the anticodon region of tRNA(fMet) genes. Bonocora RP, Shub DA;. Mol Microbiol. 2001;39:1299-1306. [2]. 17410205. The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif. Zhao L, Bonocora RP, Shub DA, Stoddard BL;. EMBO J. 2007;26:2432-2442. [3]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF023076.5 PF11646.13 DUF3258 25 25 116 PfamAutoEq Y Y N DUF3258 domain-containing protein 131567 cellular organisms no rank 63 EBI-EMBL Protein of unknown function DUF3258 Protein of unknown function DUF3258 This viral family are possible phage integrase proteins however this cannot be confirmed. (from Pfam) NF023081.5 PF11651.13 P22_CoatProtein 24 24 423 PfamEq Y Y N P22 phage major capsid protein family protein 16709746 131567 cellular organisms no rank 6072 EBI-EMBL P22 coat protein - gene protein 5 P22 phage major capsid protein family protein This family of proteins represents gene product 5 from bacteriophage P22. This protein is involved in the formation of the pro-capsid shells in the bacteriophage. In total, there are 415 molecules of the coat protein which are arranged in an icosahedral shell [1]. [1]. 16709746. The structure of an infectious P22 virion shows the signal for headful DNA packaging. Lander GC, Tang L, Casjens SR, Gilcrease EB, Prevelige P, Poliakov A, Potter CS, Carragher B, Johnson JE;. Science. 2006;312:1791-1795. (from Pfam) NF023085.5 PF11655.13 DUF2589 23 23 154 domain Y Y N DUF2589 domain-containing protein 131567 cellular organisms no rank 5020 EBI-EMBL Protein of unknown function (DUF2589) Protein of unknown function (DUF2589) This family of proteins has no known function. (from Pfam) NF023091.5 PF11661.13 DUF2986 21.4 21.4 43 PfamAutoEq Y Y N DUF2986 domain-containing protein 131567 cellular organisms no rank 3260 EBI-EMBL Protein of unknown function (DUF2986) Protein of unknown function (DUF2986) This family of proteins has no known function. (from Pfam) NF023092.5 PF11662.13 DUF3263 22.3 22.3 74 domain Y Y N DUF3263 domain-containing protein 131567 cellular organisms no rank 12692 EBI-EMBL Protein of unknown function (DUF3263) Protein of unknown function (DUF3263) This family of proteins with unknown function appears to be restricted to Actinobacteria. (from Pfam) NF023095.5 PF11666.13 DUF2933 21 21 52 domain Y Y N DUF2933 domain-containing protein 131567 cellular organisms no rank 5134 EBI-EMBL Protein of unknown function (DUF2933) Protein of unknown function (DUF2933) This bacterial family of proteins has no known function. (from Pfam) NF023096.5 PF11667.13 DUF3267 27.1 27.1 108 domain Y Y N metalloprotease family protein 23671590 131567 cellular organisms no rank 9475 EBI-EMBL Putative zincin peptidase metalloprotease family protein This family of proteins has a conserved HEXXH motif, suggesting the members are putative peptidases of zincin fold [1]. [1]. 23671590. CLCAs - A Family of Metalloproteases of Intriguing Phylogenetic Distribution and with Cases of Substituted Catalytic Sites. Lenart A, Dudkiewicz M, Grynberg M, Pawlowski K;. PLoS One. 2013;8:e62272. (from Pfam) NF023104.5 PF11675.13 DUF3271 22.5 22.5 248 domain Y Y N DUF3271 domain-containing protein 131567 cellular organisms no rank 2 EBI-EMBL Protein of unknown function (DUF3271) Protein of unknown function (DUF3271) This family of proteins with unknown function appears to be restricted to Plasmodium. (from Pfam) NF023109.5 PF11680.13 DUF3276 23.1 23.1 131 domain Y Y N DUF3276 family protein 131567 cellular organisms no rank 4360 EBI-EMBL Protein of unknown function (DUF3276) DUF3276 family protein This bacterial family of proteins has no known function. (from Pfam) NF023127.5 PF11699.13 CENP-C_C 29 29 85 PfamEq Y N N Mif2/CENP-C like 18701705,19503796,21353555 131567 cellular organisms no rank 628 EBI-EMBL Mif2/CENP-C like Mif2/CENP-C like CENP-C_C is a C-terminal family of fungal and eukaryote proteins necessary for centromere formation. CENP-C is the inner-kinetochore centromere (CEN) binding protein. In the budding-yeast, Mif2, the yeast homologue, binds in the CDEIII region of the centromere, and has been shown to recruit a substantial subset of all inner and outer kinetochore proteins [1]. Mif2 adopts a cupin fold and is extremely similar both in polypeptide chain conformation and in dimer geometry to the dimerisation domain of a bacterial transcription factor [1]. The Mif2 dimer appears to be part of an enhanceosome-like structure that nucleates kinetochore assembly in budding yeast [1]. This C-terminal domain is the region via which CENP-C localises to centromeres throughout the cell cycle 2,3]. [1]. 18701705. Structural and Functional Dissection of Mif2p, a Conserved DNA-binding Kinetochore Protein. Cohen RL, Espelin CW, De Wulf P, Sorger PK, Harrison SC, Simons KT;. Mol Biol Cell. 2008; [Epub ahead of print]. [2]. 19503796. The C-terminal domain of CENP-C displays multiple and critical functions for mammalian centromere formation. Trazzi S, Perini G, Bernardoni R, Zoli M, Reese JC, Musacchio A, Della Valle G;. PLoS One. 2009;4:e5832. [3]. 21353555. CENP-C is a structural platform for kinetochore assembly. Przewloka MR, Venkei Z, Bolanos-Garcia VM, Debski J, Dadlez M, Glover DM;. Curr Biol. 2011;21:399-405. (from Pfam) NF023128.5 PF11700.13 ATG22 24.1 24.1 482 PfamEq Y Y N MFS transporter 17204852 131567 cellular organisms no rank 39747 EBI-EMBL Vacuole effluxer Atg22 like MFS transporter Autophagy is a major survival survival mechanism in which eukaryotes recycle cellular nutrients during stress conditions. Atg22, Avt3 and Avt4 are partially redundant vacuolar effluxes, which mediate the efflux of leucine and other amino acids resulting from autophagy [1]. This family also includes other transporter proteins. [1]. 17204852. Permeases recycle amino acids resulting from autophagy. Yang Z, Klionsky DJ;. Autophagy. 2007;3:149-150. (from Pfam) NF023149.5 PF11721.13 Malectin 23 23 163 domain Y Y N malectin domain-containing carbohydrate-binding protein GO:0030246 18524852 131567 cellular organisms no rank 8784 EBI-EMBL Malectin domain malectin domain Malectin is a membrane-anchored protein of the endoplasmic reticulum that recognises and binds Glc2-N-glycan. It carries a signal peptide from residues 1-26, a C-terminal transmembrane helix from residues 255-274, and a highly conserved central part of approximately 190 residues followed by an acidic, glutamate-rich region. Carbohydrate-binding is mediated by the four aromatic residues, Y67, Y89, Y116, and F117 and the aspartate at D186. NMR-based ligand-screening studies has shown binding of the protein to maltose and related oligosaccharides, on the basis of which the protein has been designated "malectin", and its endogenous ligand is found to be Glc2-high-mannose N-glycan [1]. [1]. 18524852. Malectin: a novel carbohydrate-binding protein of the endoplasmic reticulum and a candidate player in the early steps of protein N-glycosylation. Schallus T, Jaeckh C, Feher K, Palma AS, Liu Y, Simpson JC, Mackeen M, Stier G, Gibson TJ, Feizi T, Pieler T, Muhle-Goll C;. Mol Biol Cell. 2008;19:3404-3414. (from Pfam) NF023159.5 PF11731.13 Cdd1 25.5 25.5 86 domain Y Y N helix-hairpin-helix domain-containing protein 8973304 131567 cellular organisms no rank 3826 EBI-EMBL Pathogenicity locus Pathogenicity locus Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria [1]. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed. [1]. 8973304. Definition of the single integration site of the pathogenicity locus in Clostridium difficile. Braun V, Hundsberger T, Leukel P, Sauerborn M, von Eichel-Streiber C;. Gene. 1996;181:29-38. (from Pfam) NF023174.5 PF11746.13 DUF3303 21.2 21.2 92 domain Y Y N DUF3303 family protein 131567 cellular organisms no rank 4612 EBI-EMBL Domain of unknown function (DUF3303) DUF3303 family protein Several members are annotated as being LysM domain-like proteins, but these did not match any LysM domains reported in the literature. (from Pfam) NF023178.5 PF11750.13 DUF3307 23 23 127 PfamAutoEq Y Y N DUF3307 domain-containing protein 131567 cellular organisms no rank 10508 EBI-EMBL Protein of unknown function (DUF3307) Protein of unknown function (DUF3307) This family of bacterial proteins has no known function. (from Pfam) NF023181.5 PF11753.13 DUF3310 24 24 60 domain Y Y N DUF3310 domain-containing protein 131567 cellular organisms no rank 6969 EBI-EMBL Protein of unknwon function (DUF3310) Protein of unknwon function (DUF3310) This is a family of conserved bacteriophage proteins of unknown function. (from Pfam) NF023183.5 PF11755.13 DUF3311 30 30 61 domain Y Y N DUF3311 domain-containing protein 131567 cellular organisms no rank 12919 EBI-EMBL Protein of unknown function (DUF3311) Protein of unknown function (DUF3311) This is a family of short bacterial proteins of unknown function. (from Pfam) NF023188.5 PF11760.13 CbiG_N 25 25 82 PfamEq Y N N Cobalamin synthesis G N-terminal 16866557,9742225 131567 cellular organisms no rank 26043 EBI-EMBL Cobalamin synthesis G N-terminal Cobalamin synthesis G N-terminal Members of this family are involved in cobalamin synthesis. The gene encoded by Swiss:P72862 has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process [1]. Within the cobalamin synthesis pathway CbiG catalyses the both the opening of the lactone ring and the extrusion of the two-carbon fragment of cobalt-precorrin-5A from C-20 and its associated methyl group (deacylation) to give cobalt-precorrin-5B [2]. The N-terminal of the enzyme is conserved in this family, and the C-terminal and the mid-sections are conserved independently in other families, CbiG_C and CbiG_mid, although the distinct function of each region is unclear. [1]. 9742225. Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon. Raux E, Lanois A, Warren MJ, Rambach A, Thermes C;. Biochem J 1998;335:159-166. [2]. 16866557. Genetically engineered synthesis and structural characterization of cobalt-precorrin 5A and -5B, two new intermediates on the anaerobic pathway to vitamin B12: definition of the roles of the CbiF and CbiG enzymes. Kajiwara Y, Santander PJ, Roessner CA, Perez LM, Scott AI;. J Am Chem Soc. 2006;128:9971-9978. (from Pfam) NF023189.5 PF11761.13 CbiG_mid 22.7 22.7 88 domain Y Y N cobalamin biosynthesis central domain-containing protein 9742225 131567 cellular organisms no rank 10922 EBI-EMBL Cobalamin biosynthesis central region Cobalamin biosynthesis central region Members of this family are involved in cobalamin synthesis. The gene encoded by Swiss:P72862 has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process [1]. [1]. 9742225. Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon. Raux E, Lanois A, Warren MJ, Rambach A, Thermes C;. Biochem J 1998;335:159-166. (from Pfam) NF023190.5 PF11762.13 Arabinose_Iso_C 25 25 114 PfamEq Y N N L-arabinose isomerase C-terminal domain 9084180 131567 cellular organisms no rank 20533 EBI-EMBL L-arabinose isomerase C-terminal domain L-arabinose isomerase C-terminal domain This is a family of L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyse the reaction: L-arabinose L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme [1]. This is a C-terminal non catalytic domain. [1]. 9084180. The Bacillus subtilis L-arabinose (ara) operon: nucleotide sequence, genetic organization and expression. Sa-Nogueira I, Nogueira TV, Soares S, de Lencastre H;. Microbiology 1997;143:957-969. (from Pfam) NF023203.5 PF11775.13 CobT_C 21 21 220 domain Y Y N cobaltochelatase CobT-related protein 1917840 131567 cellular organisms no rank 16800 EBI-EMBL Cobalamin biosynthesis protein CobT VWA domain Cobalamin biosynthesis protein CobT VWA domain This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid [1]. [1]. 1917840. Genetic and sequence analyses of a Pseudomonas denitrificans DNA fragment containing two cob genes. Cameron B, Guilhot C, Blanche F, Cauchois L, Rouyez MC, Rigault S, Levy-Schil S, Crouzet J;. J Bacteriol 1991;173:6058-6065. (from Pfam) NF023209.5 PF11781.13 zf-RRN7 27.1 27.1 32 domain Y Y N TFIIB-type zinc finger domain-containing protein 28340337,7958901,8887672 131567 cellular organisms no rank 858 EBI-EMBL Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7 Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7 This is the zinc-finger at the start of transcription-binding factor that associates strongly with both Rrn6 and Rrn7 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [1,2,3]. [1]. 7958901. RRN6 and RRN7 encode subunits of a multiprotein complex essential for the initiation of rDNA transcription by RNA polymerase I in Saccharomyces cerevisiae. Keys DA, Vu L, Steffan JS, Dodd JA, Yamamoto RT, Nogi Y, Nomura M;. Genes Dev. 1994;8:2349-2362. [2]. 8887672. A novel 66-kilodalton protein complexes with Rrn6, Rrn7, and TATA-binding protein to promote polymerase I transcription initiation in Saccharomyces cerevisiae. Lin CW, Moorefield B, Payne J, Aprikian P, Mitomo K, Reeder RH;. Mol Cell Biol. 1996;16:6436-6443. [3]. 28340337. Structural Basis of RNA Polymerase I Transcription Initiation. Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky C, Cramer P;. Cell. 2017;169:120-131. (from Pfam) NF023211.5 PF11783.13 Cytochrome_cB 22.1 22.1 173 domain Y N N Cytochrome c bacterial 131567 cellular organisms no rank 1994 EBI-EMBL Cytochrome c bacterial Cytochrome c bacterial This is a family of long bacterial cytochrome c proteins, found in Proteobacteria and Chlorobi families. (from Pfam) NF023212.5 PF11784.13 DUF3320 25 25 50 PfamAutoEq Y Y N DUF3320 domain-containing protein 131567 cellular organisms no rank 8003 EBI-EMBL Protein of unknown function (DUF3320) Protein of unknown function (DUF3320) This family is conserved in Proteobacteria and Chlorobi families. Many members are annotated as being putative DNA helicase-related proteins. (from Pfam) NF023218.5 PF11790.13 Glyco_hydro_cc 21 21 237 domain Y Y N glycosyl hydrolase GO:0016798 21965406 131567 cellular organisms no rank 7783 EBI-EMBL Glycosyl hydrolase catalytic core glycosyl hydrolase This family is probably a glycosyl hydrolase, and is conserved in fungi and some Proteobacteria. The pombe member is annotated as being from IPR013781. (from Pfam) NF023219.5 PF11791.13 Aconitase_B_N 25.8 25.8 153 PfamEq Y N N Aconitate B N-terminal domain GO:0003994,GO:0006099 10585860 131567 cellular organisms no rank 27129 EBI-EMBL Aconitate B N-terminal domain Aconitate B N-terminal domain This family represents the N-terminal domain of Aconitase B. [1]. 10585860. Biochemical and spectroscopic characterization of Escherichia coli aconitases (AcnA and AcnB). Jordan PA, Tang Y, Bradbury AJ, Thomson AJ, Guest JR;. Biochem J 1999;344:739-746. (from Pfam) NF023222.5 PF11794.13 HpaB_N 35 35 270 domain Y Y N 4-hydroxyphenylacetate 3-hydroxylase N-terminal domain-containing protein 10383985,8077235 131567 cellular organisms no rank 20448 EBI-EMBL 4-hydroxyphenylacetate 3-hydroxylase N terminal 4-hydroxyphenylacetate 3-hydroxylase N terminal HpaB Swiss:Q57160 encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli [2]. HpaB is part of a heterodimeric enzyme that also requires HpaC. The enzyme is NADH-dependent and uses FAD as the redox chromophore. This family also includes PvcC Swiss:O30372 may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis [1]. [1]. 10383985. The pvc gene cluster of Pseudomonas aeruginosa: role in synthesis of the pyoverdine chromophore and regulation by PtxR and PvdS. Stintzi A, Johnson Z, Stonehouse M, Ochsner U, Meyer JM, Vasil ML, Poole K;. J Bacteriol 1999;181:4118-4124. [2]. 8077235. Molecular characterization of 4-hydroxyphenylacetate 3-hydroxylase of Escherichia coli. A two-protein component enzyme. Prieto MA, Garcia JL;. J Biol Chem 1994;269:22823-22829. (from Pfam) NF023223.5 PF11795.13 DUF3322 22 22 190 domain Y Y N DUF3322 domain-containing protein 131567 cellular organisms no rank 5324 EBI-EMBL Uncharacterized protein conserved in bacteria N-term (DUF3322) DUF3322 domain This domain, found in various hypothetical bacterial proteins, has no known function. The family represents just the N-terminus. (from Pfam) NF023226.5 PF11798.13 IMS_HHH 24.4 24.4 32 domain Y N N IMS family HHH motif 131567 cellular organisms no rank 75525 EBI-EMBL IMS family HHH motif IMS family HHH motif These proteins are involved in UV protection, eg (Swiss:P07375). (from Pfam) NF023227.5 PF11799.13 IMS_C 20.7 20.7 109 domain Y N N impB/mucB/samB family C-terminal domain GO:0003684,GO:0006281 131567 cellular organisms no rank 169513 EBI-EMBL impB/mucB/samB family C-terminal domain impB/mucB/samB family C-terminal domain These proteins are involved in UV protection (Swiss). (from Pfam) NF023242.5 PF11814.13 DUF3335 25 25 206 PfamEq Y Y N peptidase C39 family protein 131567 cellular organisms no rank 6327 EBI-EMBL Peptidase_C39 like family peptidase C39 family protein NF023249.5 PF11821.13 ActD 25.7 25.7 170 domain Y Y N quinol:electron acceptor oxidoreductase subunit ActD 29695868,32832681 131567 cellular organisms no rank 5962 EBI-EMBL Alternative complex III, ActD subunit quinol:electron acceptor oxidoreductase subunit ActD Alternative complex III (ACIII) is a multisubunit quinol:electron acceptor oxidoreductase that couples quinol oxidation with transmembrane proton translocation similar to bc1 complex (or complex III). It is a key component of the respiratory and photosynthetic electron transport chains in many bacteria. It has six subunits (ActA-F), ActD subunit represented in this entry. The transmembrane regions of this subunit form part of the TM arm of the complex [1,2]. Although the function of this subunit is not clear, it may play a role in stabilizing the TM region of ACIII which contributes to a stable menaquinol binding pocket and proton translocation passage [2]. [1]. 29695868. Structure of the alternative complex III in a supercomplex with cytochrome oxidase. Sun C, Benlekbir S, Venkatakrishnan P, Wang Y, Hong S, Hosler J, Tajkhorshid E, Rubinstein JL, Gennis RB;. Nature. 2018;557:123-126. [2]. 32832681. Cryo-EM structures of the air-oxidized and dithionite-reduced photosynthetic alternative complex III from Roseiflexus castenholzii. Shi Y, Xin Y, Wang C, Blankenship RE, Sun F, Xu X;. Sci Adv. 2020;6:eaba2739. (from Pfam) NF023251.5 PF11823.13 Se_S_carrier 25 25 69 domain Y Y N putative Se/S carrier-like protein 25638258 131567 cellular organisms no rank 7989 EBI-EMBL Putative Se/S carrier protein-like putative Se/S carrier-like protein This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length. It has been suggested that this family of proteins may be chaperones involved in Se or S trafficking in the cell [1]. [1]. 25638258. Comparative genomics reveals new candidate genes involved in selenium metabolism in prokaryotes. Lin J, Peng T, Jiang L, Ni JZ, Liu Q, Chen L, Zhang Y;. Genome Biol Evol. 2015;7:664-676. (from Pfam) NF023252.5 PF11824.13 DUF3344 27.2 27.2 275 domain Y Y N DUF3344 domain-containing protein 131567 cellular organisms no rank 1280 EBI-EMBL Protein of unknown function (DUF3344) Protein of unknown function (DUF3344) This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 367 to 1857 amino acids in length. (from Pfam) NF023266.5 PF11838.13 ERAP1_C 38.2 38.2 318 domain Y Y N ERAP1-like C-terminal domain-containing protein 21478864 131567 cellular organisms no rank 53738 EBI-EMBL ERAP1-like C-terminal domain ERAP1-like C-terminal domain This large domain is composed of 16 alpha helices organized as 8 HEAT-like repeats. This domain forms a concave face that faces towards the active site of the peptidase. [1]. 21478864. Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1. Nguyen TT, Chang SC, Evnouchidou I, York IA, Zikos C, Rock KL, Goldberg AL, Stratikos E, Stern LJ;. Nat Struct Mol Biol. 2011;18:604-613. (from Pfam) NF023267.5 PF11839.13 Alanine_zipper 23.1 23.1 69 domain Y Y N alanine-zipper protein 131567 cellular organisms no rank 2803 EBI-EMBL Alanine-zipper, major outer membrane lipoprotein alanine-zipper domain This is a family of a major outer membrane lipoprotein, OprL that is an alanine-zipper. Zipper motifs are a seven-repeat motif where the first and fourth positions are occupied by an aliphatic residue, usually a leucine. These residues are positioned on the outside of the coil such as to bind firmly to one or more monomers of the protein to create a triple or five-helical coiled-coil that probably forms a seam in a membrane. (from Pfam) NF023270.5 PF11842.13 DUF3362 27.6 27.6 151 PfamAutoEq Y Y N DUF3362 domain-containing protein 131567 cellular organisms no rank 25467 EBI-EMBL Domain of unknown function (DUF3362) Domain of unknown function (DUF3362) This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is typically between 117 to 158 amino acids in length. (from Pfam) NF023273.5 PF11845.13 DUF3365 24.1 24.1 144 domain Y Y N DUF3365 domain-containing protein 28428249 131567 cellular organisms no rank 12425 EBI-EMBL Protein of unknown function (DUF3365) Protein of unknown function (DUF3365) This family includes Tll0287 protein from Thermosynechococcus vestitus (Q8DM36) and similar bacterial proteins. Tll0287 is a c-type heme protein that shows a beta-sheet with four antiparallel beta-strands surrounded by five alpha-helices. This structure is similar to some kinases and sensor proteins, but its specific function is unknown [1]. [1]. 28428249. Crystal structure and redox properties of a novel cyanobacterial heme protein with a His/Cys heme axial ligation and a Per-Arnt-Sim (PAS)-like domain. Motomura T, Suga M, Hienerwadel R, Nakagawa A, Lai TL, Nitschke W, Kuma T, Sugiura M, Boussac A, Shen JR;. J Biol Chem. 2017;292:9599-9612. (from Pfam) NF023275.5 PF11847.13 DUF3367 26 26 661 PfamAutoEq Y Y N alpha-(1->3)-arabinofuranosyltransferase family protein GO:0016740 19654261 131567 cellular organisms no rank 9761 EBI-EMBL Alpha-(1->3)-arabinofuranosyltransferase alpha-(1->3)-arabinofuranosyltransferase family protein Family members include alpha-(1->3)-arabinofuranosyltransferase (AftD, EC:2.4.2.47) which is involved in the biosynthesis of the arabinogalactan (AG) region of the mycolylarabinogalactan-peptidoglycan (mAGP) complex, an essential component of the mycobacterial cell wall. It catalyzes the addition of an arabinofuranosyl (Araf) residue from the sugar donor decaprenyl-phospho-arabinose (DPA) on the C-3 of an alpha-(1->5)-linked Araf from the arabinan backbone of AG [1]. [1]. 19654261. AftD, a novel essential arabinofuranosyltransferase from mycobacteria. Skovierova H, Larrouy-Maumus G, Zhang J, Kaur D, Barilone N, Kordulakova J, Gilleron M, Guadagnini S, Belanova M, Prevost MC, Gicquel B, Puzo G, Chatterjee D, Brennan PJ, Nigou J, Jackson M;. Glycobiology. 2009;19:1235-1247. (from Pfam) NF023276.5 PF11848.13 DUF3368 27.3 27.3 46 domain Y Y N DUF3368 domain-containing protein 131567 cellular organisms no rank 4174 EBI-EMBL Domain of unknown function (DUF3368) Domain of unknown function (DUF3368) This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length. (from Pfam) NF023283.5 PF11855.13 DUF3375 28.6 28.6 474 PfamAutoEq Y Y N DUF3375 family protein 131567 cellular organisms no rank 8920 EBI-EMBL Protein of unknown function (DUF3375) DUF3375 family protein This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 amino acids in length. (from Pfam) NF023284.5 PF11856.13 DUF3376 25 25 514 PfamAutoEq Y Y N DUF3376 domain-containing protein 131567 cellular organisms no rank 3714 EBI-EMBL Protein of unknown function (DUF3376) Protein of unknown function (DUF3376) This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 770 to 1142 amino acids in length. (from Pfam) NF023295.5 PF11867.13 T1RH-like_C 26.8 26.8 329 domain Y Y N type I restriction enzyme endonuclease domain-containing protein 12654995 131567 cellular organisms no rank 24085 EBI-EMBL Type I restriction enzyme HindI endonuclease subunit-like, C-terminal Type I restriction enzyme HindI endonuclease subunit-like, C-terminal This domain is found at the C-terminal of Type I restriction enzyme HindI endonuclease subunit (also known as R protein) from Haemophilus influenzae related sequences from bacteria and archaea [1]. This domain is typically between 255 to 340 amino acids in length and its function is unknown. This domain is found associated with Pfam:PF04851, Pfam:PF04313. [1]. 12654995. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev SKh, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Kruger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY;. Nucleic Acids Res. 2003;31:1805-1812. (from Pfam) NF023302.5 PF11874.13 DUF3394 28.2 28.2 181 PfamAutoEq Y Y N DUF3394 domain-containing protein 131567 cellular organisms no rank 8643 EBI-EMBL Domain of unknown function (DUF3394) Domain of unknown function (DUF3394) This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 190 amino acids in length. This domain is found associated with Pfam:PF06808. (from Pfam) NF023324.5 PF11896.13 GlgE_dom_N_S 25 25 179 PfamAutoEq Y Y N maltotransferase domain-containing protein GO:0004553 11257505,21914799,9302327 131567 cellular organisms no rank 34260 EBI-EMBL Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S This entry represents domain N and S of GlgE. GlgE is a homodimer and a member of the GH13_3 CAZy subfamily. Each subunit of GlgE is composed of five domains, domain A is a (beta/alpha)8 barrel, typical of the catalytic domain of this family of enzymes, that forms part of the dimer interface. Domain B corresponds to an insertion after the third beta-strand of domain A [1]. In GlgE, domain B is fairly typical for a GH13 enzyme [2] in having a pair of anti-parallel strands and one short helix. The C-terminal domain C has a beta-sandwich fold. The N-terminal domain N, which also consists of a beta-sandwich fold, forms the core of the dimer interface. The final domain arises from an insertion within domain N and forms a four-helix bundle where the last helix is discontinuous and slightly kinked. This domain, which will henceforth be referred to as domain S, participates in the dimer interface and interacts directly with domain B of the neighbouring subunit [3]. [1]. 11257505. Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes. MacGregor EA, Janecek S, Svensson B;. Biochim Biophys Acta. 2001;1546:1-20. [2]. 9302327. Domain evolution in the alpha-amylase family. Janecek S, Svensson B, Henrissat B;. J Mol Evol. 1997;45:322-331. [3]. 21914799. Structure of Streptomyces maltosyltransferase GlgE, a homologue of a genetically validated anti-tuberculosis target. Syson K, Stevenson CEM, Rejzek M, Fairhurst SA, Nair A, Bruton CJ, Field RA, Chater KF, Lawson DM, Bornemann S;. J Biol Chem. 2011;286:38298-38310. (from Pfam) NF023325.5 PF11897.13 DUF3417 25 25 109 PfamAutoEq Y Y N DUF3417 domain-containing protein 131567 cellular organisms no rank 20177 EBI-EMBL Protein of unknown function (DUF3417) Protein of unknown function (DUF3417) This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 145 to 860 amino acids in length. This protein is found associated with Pfam:PF00343. This protein has a conserved AYF sequence motif. (from Pfam) NF023330.5 PF11902.13 DUF3422 25 25 418 PfamAutoEq Y Y N DUF3422 family protein 131567 cellular organisms no rank 9901 EBI-EMBL Protein of unknown function (DUF3422) DUF3422 family protein This family of proteins are functionally uncharacterised. This protein is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 426 to 444 amino acids in length. (from Pfam) NF023334.5 PF11906.13 DUF3426 27.7 27.7 147 PfamAutoEq Y Y N DUF3426 domain-containing protein 131567 cellular organisms no rank 15170 EBI-EMBL Protein of unknown function (DUF3426) Protein of unknown function (DUF3426) This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 262 to 463 amino acids in length. (from Pfam) NF023335.5 PF11907.13 DUF3427 27.7 27.7 280 PfamAutoEq Y Y N DUF3427 domain-containing protein 131567 cellular organisms no rank 20500 EBI-EMBL Domain of unknown function (DUF3427) Domain of unknown function (DUF3427) This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is typically between 243 to 275 amino acids in length. This domain is found associated with Pfam:PF04851, Pfam:PF00271. (from Pfam) NF023344.5 PF11917.13 DUF3435 25.8 25.8 418 PfamAutoEq Y Y N DUF3435 domain-containing protein 131567 cellular organisms no rank 115 EBI-EMBL Protein of unknown function (DUF3435) Protein of unknown function (DUF3435) This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 435 to 791 amino acids in length. This family is related to Pfam:PF00589 suggesting it may be an integrase enzyme. (from Pfam) NF023366.5 PF11940.13 DUF3458 28.6 28.6 95 PfamAutoEq Y Y N DUF3458 domain-containing protein 131567 cellular organisms no rank 38896 EBI-EMBL Domain of unknown function (DUF3458) Ig-like fold Domain of unknown function (DUF3458) Ig-like fold This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. The domain has an Ig-like fold. This domain is found associated with Pfam:PF01433. (from Pfam) NF023367.5 PF11941.13 DUF3459 22 22 90 domain Y Y N DUF3459 domain-containing protein 131567 cellular organisms no rank 106405 EBI-EMBL Domain of unknown function (DUF3459) Domain of unknown function (DUF3459) This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 110 amino acids in length. This domain is found associated with Pfam:PF00128, Pfam:PF02922. (from Pfam) NF023372.5 PF11946.13 DUF3463 31.3 31.3 134 PfamAutoEq Y Y N DUF3463 domain-containing protein 131567 cellular organisms no rank 7742 EBI-EMBL Domain of unknown function (DUF3463) Domain of unknown function (DUF3463) This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is about 140 amino acids in length. This domain is found associated with Pfam:PF04055. This domain has two conserved sequence motifs: CTPWG and PCYL, plus a highly conserved CxxCxxHC motif. (from Pfam) NF023375.5 PF11949.13 DUF3466 25.1 25.1 609 domain Y Y N DUF3466 family protein 131567 cellular organisms no rank 5157 EBI-EMBL Protein of unknown function (DUF3466) DUF3466 family protein This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 564 to 612 amino acids in length. (from Pfam) NF023376.5 PF11950.13 DUF3467 25 25 92 PfamAutoEq Y Y N DUF3467 domain-containing protein 131567 cellular organisms no rank 5970 EBI-EMBL Protein of unknown function (DUF3467) Protein of unknown function (DUF3467) This family of proteins are functionally uncharacterised. This protein is found in bacteria, archaea and viruses. Proteins in this family are typically between 101 to 118 amino acids in length. (from Pfam) NF023380.5 PF11954.13 DUF3471 29.3 29.3 103 domain Y Y N DUF3471 domain-containing protein 131567 cellular organisms no rank 18032 EBI-EMBL Domain of unknown function (DUF3471) Domain of unknown function (DUF3471) This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 98 to 114 amino acids in length. This domain is found associated with Pfam:PF00144. (from Pfam) NF023384.5 PF11958.14 DUF3472 24.8 24.8 269 domain Y Y N DUF3472 domain-containing protein 131567 cellular organisms no rank 5870 EBI-EMBL Domain of unknown function (DUF3472) Domain of unknown function (DUF3472) This presumed domain is functionally uncharacterised. This domain is found in bacteria, eukaryotes and viruses. This domain is typically between 174 to 190 amino acids in length. This domain has a single completely conserved residue G that may be functionally important. (from Pfam) NF023385.5 PF11959.13 DUF3473 29.6 29.6 130 domain Y Y N DUF3473 domain-containing protein 131567 cellular organisms no rank 4954 EBI-EMBL Domain of unknown function (DUF3473) Domain of unknown function (DUF3473) This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is about 130 amino acids in length. This domain is found associated with Pfam:PF01522. This domain has two completely conserved residues (P and H) that may be functionally important. (from Pfam) NF023388.5 PF11962.13 Peptidase_G2 25 25 228 domain Y Y N peptidase G2 autoproteolytic cleavage domain-containing protein 21330133 131567 cellular organisms no rank 4147 EBI-EMBL Peptidase_G2, IMC autoproteolytic cleavage domain Peptidase_G2, IMC autoproteolytic cleavage domain This domain is found at the very C-terminus of bacteriophage parallel beta-helical tailspike proteins. It carries the enzymic residues that induce autoproteolytic cleavage to bring about maturation of the folding process of the helix in a chaperone-like manner. The domain thus mediates the assembly of a large tailspike protein and then releases itself after maturation. These C-terminal regions that autoproteolytically release themselves after maturation are exchangeable between functionally unrelated N-terminal proteins and have been identified in a number of bacteriophage tailspike proteins [1]. [1]. 21330133. Knitting and snipping: chaperones in beta-helix folding. Schulz EC, Ficner R;. Curr Opin Struct Biol. 2011; [Epub ahead of print] (from Pfam) NF023390.5 PF11964.13 SpoIIAA-like 25 25 106 domain Y Y N STAS/SEC14 domain-containing protein 20944218 131567 cellular organisms no rank 12902 EBI-EMBL SpoIIAA-like SpoIIAA-like These proteins adopt an alpha/beta SpoIIAA-like fold, similar to that found in STAT (Pfam:PF01740). They adopt open and closed conformations arising from different arrangements of their alpha-2 and alpha-3 helices. They may be membrane associated and may function as carriers of non-polar compounds [1]. [1]. 20944218. Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding. Kumar A, Lomize A, Jin KK, Carlton D, Miller MD, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Klock HE, Knuth MW, Kozbial P, Krishna SS, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:1245-1253. (from Pfam) NF023391.5 PF11965.13 DUF3479 27.4 27.4 159 domain Y Y N DUF3479 domain-containing protein GO:0016851 131567 cellular organisms no rank 4149 EBI-EMBL Domain of unknown function (DUF3479) Domain of unknown function (DUF3479) This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is about 160 amino acids in length. This domain is found associated with Pfam:PF02514. (from Pfam) NF023395.5 PF11969.13 DcpS_C 24 24 114 domain Y N N Scavenger mRNA decapping enzyme C-term binding 12198172 131567 cellular organisms no rank 86755 EBI-EMBL Scavenger mRNA decapping enzyme C-term binding Scavenger mRNA decapping enzyme C-term binding This family consists of several scavenger mRNA decapping enzymes (DcpS) and is the C-terminal region. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' decay of an mRNA. The association of DcpS with 3' to 5' exonuclease exosome components suggests that these two activities are linked and there is a coupled exonucleolytic decay-dependent decapping pathway. The C-terminal domain contains a histidine triad (HIT) sequence with three histidines separated by hydrophobic residues. The central histidine within the DcpS HIT motif is critical for decapping activity and defines the HIT motif as a new mRNA decapping domain, making DcpS the first member of the HIT family of proteins with a defined biological function. [1]. 12198172. The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. Liu H, Rodgers ND, Jiao X, Kiledjian M;. EMBO J 2002;21:4699-4708. (from Pfam) NF023398.5 PF11972.13 HTH_13 26.1 26.1 54 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 4709 EBI-EMBL HTH DNA binding domain helix-turn-helix domain 13 This is a helix-turn-helix DNA binding domain. (from Pfam) NF023401.5 PF11975.13 Glyco_hydro_4C 24.1 24.1 211 domain Y N N Family 4 glycosyl hydrolase C-terminal domain GO:0004553 131567 cellular organisms no rank 61588 EBI-EMBL Family 4 glycosyl hydrolase C-terminal domain Family 4 glycosyl hydrolase C-terminal domain NF023402.5 PF11976.13 Rad60-SLD 23.8 23.8 72 domain Y N N Ubiquitin-2 like Rad60 SUMO-like 15660128,19363481 131567 cellular organisms no rank 1031 EBI-EMBL Ubiquitin-2 like Rad60 SUMO-like Ubiquitin-2 like Rad60 SUMO-like The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl family member, and although SUMO-1 shares structural similarity to Ub, SUMO's cellular functions remain distinct insomuch as SUMO modification alters protein function through changes in activity, cellular localisation, or by protecting substrates from ubiquitination [1]. Rad60 family members contain functionally enigmatic, integral SUMO-like domains (SLDs). Despite their divergence from SUMO, each Rad60 SLD interacts with a subset of SUMO pathway enzymes: SLD2 specifically binds the SUMO E2 conjugating enzyme (Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also called Uba2) activating and E3 (Pli1, also called Siz1 and Siz2) specificity enzymes. Structural analysis of PDB:2uyz reveals a mechanistic basis for the near-synonymous roles of Rad60 and SUMO in survival of genotoxic stress and suggest unprecedented DNA-damage-response functions for SLDs in regulating SUMOylation [2]. The Rad60 branch of this family is also known as RENi (Rad60-Esc2-Nip45), and biologically it should be two distinct families SUMO and RENi (Rad60-Esc2-Nip45). [1]. 15660128. Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1. Lois LM, Lima CD;. EMBO J. 2005;24:439-451. [2]. 19363481. Molecular mimicry of SUMO promotes DNA repair. Prudden J, Perry JJ, Arvai AS, Tainer JA, Boddy MN;. Nat Struct Mol Biol. 2009;16:509-516. (from Pfam) NF023403.5 PF11977.13 RNase_Zc3h12a 23 23 154 domain Y Y N NYN domain-containing protein 17114934,19322177 131567 cellular organisms no rank 1433 EBI-EMBL Zc3h12a-like Ribonuclease NYN domain Zc3h12a-like ribonuclease NYN domain This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes [1]. It has been suggested that this domain belongs to the PIN domain superfamily [1]. This domain has also been identified as part of the NYN domain family [2]. [1]. 19322177. Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay. Matsushita K, Takeuchi O, Standley DM, Kumagai Y, Kawagoe T, Miyake T, Satoh T, Kato H, Tsujimura T, Nakamura H, Akira S;. Nature;458:1185-1190. [2]. 17114934. The NYN Domains: Novel Predicted RNAses with a PIN Domain-Like Fold. Anantharaman V, Aravind L;. RNA Biol. 2006; [Epub ahead of print] (from Pfam) NF023410.5 PF11984.13 DUF3485 26.1 26.1 203 subfamily_domain Y Y N exosortase-associated EpsI family protein 131567 cellular organisms no rank 6100 EBI-EMBL Protein of unknown function (DUF3485) exosortase system EpsI domain This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 223 to 526 amino acids in length. This protein is found associated with Pfam:PF09721. (from Pfam) NF023413.5 PF11987.13 IF-2 27 27 117 PfamEq Y N N Translation-initiation factor 2 10878130,16169924,17086204 131567 cellular organisms no rank 81903 EBI-EMBL Translation-initiation factor 2 Translation-initiation factor 2 IF-2 is a translation initiator in each of the three main phylogenetic domains (Eukaryotes [1], Bacteria [2] and Archaea [3]). IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3 and both ribosomal subunits [2]. Through these interactions, IF2 promotes the binding of the initiator tRNA to the A site in the smaller ribosomal subunit and catalyses the hydrolysis of GTP following initiation-complex formation [2]. [1]. 17086204. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Aury JM, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Segurens B, Daubin V, Anthouard V, Aiach N, Arnaiz O, Billaut A, Beisson J, Blanc I, Bouhouche K, Camara F, Duharcourt S, Guigo R, Gogendeau D, Katinka M, Keller AM, Kissmehl R, Klotz C, Koll F, Le. Nature. 2006;444:171-178. [2]. 10878130. Investigation of the translation-initiation factor IF2 gene, infB, as a tool to study the population structure of Streptococcus agalactiae. Hedegaard J, Hauge M, Fage-Larsen J, Mortensen KK, Kilian M, Sperling-Petersen HU, Poulsen K;. Microbiology. 2000;146:1661-1670. [3]. 16169924. Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis. Falb M, Pfeiffer F, Palm P, Rodewald K, Hickmann V, Tittor J, Oesterhelt D;. Genome Res. 2005;15:1336-1343. (from Pfam) NF023418.5 PF11992.13 TgpA_N 30 30 333 PfamAutoEq Y Y N transglutaminaseTgpA domain-containing protein 23209712,30599211 131567 cellular organisms no rank 40689 EBI-EMBL TgpA N-terminal domain TgpA N-terminal domain This domain can be found at the N terminus of TgpA from Pseudomonas aeruginosa. TgpA is a transglutaminase that plays a critical role in the viability of Pseudomonas aeruginosa [1,2]. This domain is composed of 5 transmembrane helices [2]. [1]. 23209712. TgpA, a protein with a eukaryotic-like transglutaminase domain, plays a critical role in the viability of Pseudomonas aeruginosa. Milani A, Vecchietti D, Rusmini R, Bertoni G;. PLoS One. 2012;7:e50323. [2]. 30599211. Structural and functional characterization of TgpA, a critical protein for the viability of Pseudomonas aeruginosa. Uruburu M, Mastrangelo E, Bolognesi M, Ferrara S, Bertoni G, Milani M;. J Struct Biol. 2019;205:18-25. (from Pfam) NF023423.5 PF11997.13 DUF3492 23.3 23.3 268 domain Y Y N DUF3492 domain-containing protein 131567 cellular organisms no rank 18032 EBI-EMBL Domain of unknown function (DUF3492) Domain of unknown function (DUF3492) This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 259 to 282 amino acids in length. This domain is found associated with Pfam:PF00534. This domain has two conserved sequence motifs: GGVS and EHGIY. (from Pfam) NF023425.5 PF11999.13 Ice_binding 28.7 28.7 208 domain Y Y N ice-binding family protein 22303017,24699650,30680879 131567 cellular organisms no rank 7530 EBI-EMBL Ice-binding-like ice-binding family protein This family includes members found in bacteria, fungi and archaea, many of which are ice-binding proteins (IBPs) [1]. In Antarctic bacterium Flavobacterium frigoris PS1, FfIBP is an ice-binding protein that inhibits ice growth through direct interaction with ice crystals to permit the survival of polar organisms in extremely cold environments [2]. In arctic yeast Leucosporidium sp, LeIBP, an ice-binding protein, can lower the freezing point below the melting point once it binds to ice [3]. Family members also have a single completely conserved glycine residue that may be functionally important. [1]. 30680879. Ice-binding proteins and the 'domain of unknown function' 3494 family. Vance TDR, Bayer-Giraldi M, Davies PL, Mangiagalli M;. FEBS J. 2019;286:855-873. [2]. 24699650. Structure-based characterization and antifreeze properties of a hyperactive ice-binding protein from the Antarctic bacterium Flavobacterium frigoris PS1. Do H, Kim SJ, Kim HJ, Lee JH;. Acta Crystallogr D Biol Crystallogr. 2014;70:1061-1073. [3]. 22303017. Structural basis for antifreeze activity of ice-binding protein from arctic yeast. Lee JH, Park AK, Do H, Park KS, Moh SH, Chi YM, Kim HJ;. J Biol Chem. 2012;287:11460-11468. (from Pfam) NF023428.5 PF12002.13 MgsA_C 27 27 167 PfamEq Y N N MgsA AAA+ ATPase C terminal 15743409 131567 cellular organisms no rank 78895 EBI-EMBL MgsA AAA+ ATPase C terminal MgsA AAA+ ATPase C terminal The MgsA protein possesses DNA-dependent ATPase and ssDNA annealing activities [1]. MgsA contributes to the recovery of stalled replication forks and therefore prevents genomic instability caused by aberrant DNA replication [1]. Additionally, MgsA may play a role in chromosomal segregation [1]. This is consistent with a report that MgsA co-localises with the replisome and affects chromosome segregation [1]. This domain represents the C terminal region of MgsA. [1]. 15743409. Functional overlap between RecA and MgsA (RarA) in the rescue of stalled replication forks in Escherichia coli. Shibata T, Hishida T, Kubota Y, Han YW, Iwasaki H, Shinagawa H;. Genes Cells. 2005;10:181-191. (from Pfam) NF023432.5 PF12007.13 DUF3501 25 25 187 PfamAutoEq Y Y N DUF3501 family protein 131567 cellular organisms no rank 2315 EBI-EMBL Protein of unknown function (DUF3501) DUF3501 family protein This family of proteins is functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are about 200 amino acids in length. The structure of protein Swiss:Q63J81 from B. pseudomallei has been solved. This protein contains two domains, domain I (1:31, 46:81) is a helical domain, domain II (32:45,82-193) is a mainly beta protein with a beta barrel. According to crystal contacts the proteins probably functions as a dimer. The gene neighbourhood analysis suggests that this protein may be functionally related to rubrerythrin and ferredoxin. The wedge surface between the two domains might be functionally important. The fold of this protein could best be described as a circularly permuted C2-like fold (details derived from TOPSAN). (from Pfam) NF023433.5 PF12008.13 EcoR124_C 23.1 23.1 260 PfamEq Y Y N type I restriction endonuclease subunit R, EcoR124 family 2784505 131567 cellular organisms no rank 27033 EBI-EMBL Type I restriction and modification enzyme - subunit R C terminal type I restriction endonuclease subunit R, EcoR124 family, C-terminal domain This enzyme has been characterised and shown to belong to a new family of the type I class of restriction and modification enzymes. This family is involved in bacterial defence by making double strand breaks in specific double stranded DNA sequences, e.g. that of invading bacteriophages. EcoR124 is made up of three subunits, HsdR, HsdS and HsdM. The R subunit has ATPase and restriction endonuclease activity. This domain is the C terminal of the R subunit [1]. [1]. 2784505. Basis for changes in DNA recognition by the EcoR124 and EcoR124/3 type I DNA restriction and modification enzymes. Price C, Lingner J, Bickle TA, Firman K, Glover SW;. J Mol Biol. 1989;205:115-125. (from Pfam) NF023450.5 PF12025.13 Phage_C 25 25 68 PfamEq Y Y N phage DNA packaging protein C GO:0019073 131567 cellular organisms no rank 19 EBI-EMBL Phage protein C phage DNA packaging protein C This family of phage proteins is functionally uncharacterised. Proteins in this family are typically between 68 to 86 amino acids in length. (from Pfam). Protein C, as found in phage phi X174, is a small protein required for packaging DNA into the phage prohead. NF023474.5 PF12051.13 DUF3533 27.6 27.6 380 domain Y Y N DUF3533 domain-containing protein 131567 cellular organisms no rank 18820 EBI-EMBL Protein of unknown function (DUF3533) Protein of unknown function (DUF3533) This family of transmembrane proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 393 to 772 amino acids in length. (from Pfam) NF023478.5 PF12055.13 DUF3536 25 25 284 domain Y Y N DUF3536 domain-containing protein 131567 cellular organisms no rank 1936 EBI-EMBL Domain of unknown function (DUF3536) Domain of unknown function (DUF3536) This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is typically between 274 to 285 amino acids in length. This domain is found associated with Pfam:PF03065. (from Pfam) NF023495.5 PF12072.13 RNase_Y_N 32 32 201 PfamAutoEq Y Y N Rnase Y domain-containing protein 131567 cellular organisms no rank 21661 EBI-EMBL RNase Y N-terminal region RNase Y N-terminal region NF023504.5 PF12081.13 GldM_1st 25 25 194 PfamEq Y N N GldM N-terminal domain 16199564 131567 cellular organisms no rank 5963 EBI-EMBL GldM N-terminal domain GldM N-terminal domain This domain is found in bacteria at the N-terminus of the GldM protein. This domain is typically between 169 to 182 amino acids in length. This domain has two completely conserved residues (Y and N) that may be functionally important. GldM, is named for the member from Cytophaga johnsonae (Flavobacterium johnsoniae), which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes [1]. [1]. 16199564. Flavobacterium johnsoniae gliding motility genes identified by mariner mutagenesis. Braun TF, Khubbar MK, Saffarini DA, McBride MJ;. J Bacteriol. 2005;187:6943-6952. (from Pfam) NF023511.5 PF12089.13 DUF3566 22.2 22.2 118 PfamAutoEq Y Y N DUF3566 domain-containing protein 131567 cellular organisms no rank 14549 EBI-EMBL Transmembrane domain of unknown function (DUF3566) Transmembrane domain of unknown function (DUF3566) This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 136 to 304 amino acids in length. This region represents a transmembrane region found at the C-terminus of the proteins. (from Pfam) NF023520.5 PF12098.13 DUF3574 25 25 103 PfamAutoEq Y Y N DUF3574 domain-containing protein 131567 cellular organisms no rank 7878 EBI-EMBL Protein of unknown function (DUF3574) Protein of unknown function (DUF3574) This family of proteins is functionally uncharacterised. This protein is found in bacteria and viruses. Proteins in this family are typically between 144 to 163 amino acids in length. This protein has a conserved TPRF sequence motif. (from Pfam) NF023521.5 PF12099.13 DUF3575 21.1 21.1 177 domain Y Y N DUF3575 domain-containing protein 131567 cellular organisms no rank 13802 EBI-EMBL Protein of unknown function (DUF3575) Protein of unknown function (DUF3575) This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family are typically between 187 to 236 amino acids in length. (from Pfam) NF023524.5 PF12102.13 MrcB_N 25 25 183 PfamAutoEq Y Y N MrcB family domain-containing protein 22570415,7781618 131567 cellular organisms no rank 5408 EBI-EMBL MrcB-like, N-terminal domain MrcB-like, N-terminal domain This model describes the N-terminal domain of a group of mostly uncharacterised proteins, including 5-methylcytosine-specific restriction enzyme B (also known as MrcB) from E. coli. MrcB recognises N4- and C5-methylcytosine (and 5-hydroxy-methylcytosines) produced by a broad range of DNA methylases and appears to act against 5-methylcytosine preceded by a purine residue [1]. The N-terminal domain of MrcB has been shown to be a DNA-binding domain, and the crystal structure has been solved [2]. [1]. 7781618. McrB: a prokaryotic protein specifically recognizing DNA containing modified cytosine residues. Kruger T, Wild C, Noyer-Weidner M;. EMBO J. 1995;14:2661-2669. [2]. 22570415. The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine. Sukackaite R, Grazulis S, Tamulaitis G, Siksnys V;. Nucleic Acids Res. 2012;40:7552-7562. (from Pfam) NF023550.5 PF12128.13 DUF3584 31 31 1191 PfamAutoEq Y Y N ATP-binding protein 131567 cellular organisms no rank 3907 EBI-EMBL Protein of unknown function (DUF3584) ATP-binding protein This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication. (from Pfam) NF023559.5 PF12137.13 RapA_C 26.8 26.8 360 PfamEq Y N N RNA polymerase recycling family C-terminal GO:0016817 18786404 131567 cellular organisms no rank 18508 EBI-EMBL RNA polymerase recycling family C-terminal RNA polymerase recycling family C-terminal This domain is found in bacteria. This domain is about 360 amino acids in length. This domain is found associated with Pfam:PF00271, Pfam:PF00176. The function of this domain is not known, but structurally it forms an alpha-beta fold in nature with a central beta-sheet flanked by helices and loops, the beta-sheet being mainly antiparallel and flanked by four alpha helices, among which the two longer helices exhibit a coiled-coil arrangement. [1]. 18786404. Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription. Shaw G, Gan J, Zhou YN, Zhi H, Subburaman P, Zhang R, Joachimiak A, Jin DJ, Ji X;. Structure. 2008;16:1417-1427. (from Pfam) NF023560.5 PF12138.13 Spherulin4 30.2 30.2 239 domain Y Y N spherulation-specific family 4 protein 7998920 131567 cellular organisms no rank 11143 EBI-EMBL Spherulation-specific family 4 spherulation-specific family 4 protein This protein is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 250 and 398 amino acids in length. There is a conserved NPG sequence motif and there are two completely conserved G residues that may be functionally important. Starvation will often induce spherulation - the production of spores - and this process may involve DNA-methylation. Changes in the methylation of spherulin4 are associated with the formation of spherules, but these changes are probably transient. Methylation of the gene accompanies its transcriptional activation, and spherulin4 mRNA is only detectable in late spherulating cultures and mature spherules. It is a spherulation-specific protein. [1]. 7998920. DNA methylation during differentiation of a lower eukaryote, Physarum polycephalum. Fronk J, Magiera R;. Biochem J. 1994;304:101-104. (from Pfam) NF023561.5 PF12139.13 APS-reductase_C 25 25 82 PfamEq Y N N Adenosine-5'-phosphosulfate reductase beta subunit 17600048 131567 cellular organisms no rank 689 EBI-EMBL Adenosine-5'-phosphosulfate reductase beta subunit Adenosine-5'-phosphosulfate reductase beta subunit This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 112 to 142 amino acids in length. This family is found in association with Pfam:PF00037, and has a conserved FPIRTT sequence motif. The whole beta subunit has the enzymic properties of EC:1.8.99.2. [1]. 17600048. Phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5'-phosphosulfate (APS) reductase from sulfate-reducing prokaryotes--origin and evolution of the dissimilatory sulfate-reduction pathway. Meyer B, Kuever J;. Microbiology. 2007;153:2026-2044. (from Pfam) NF023568.5 PF12146.13 Hydrolase_4 27 27 239 domain Y Y N serine aminopeptidase domain-containing protein 131567 cellular organisms no rank 1370853 EBI-EMBL Serine aminopeptidase, S33 Serine aminopeptidase, S33 This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with Pfam:PF00561. The majority of the members in this family carry the exopeptidase active-site residues of Ser-122, Asp-239 and His-269 as in UniProtKB:Q7ZWC2. (from Pfam) NF023569.5 PF12147.13 Methyltransf_20 21 21 309 domain Y Y N class I SAM-dependent methyltransferase family protein 2.1.1.- 131567 cellular organisms no rank 12191 EBI-EMBL Putative methyltransferase class I SAM-dependent methyltransferase family protein This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with Pfam:PF00561. The family shows homology to methyltransferases. (from Pfam) NF023578.5 PF12156.13 ATPase-cat_bd 27 27 86 PfamEq Y Y N heavy metal translocating P-type ATPase metal-binding domain-containing protein 131567 cellular organisms no rank 23784 EBI-EMBL Putative metal-binding domain of cation transport ATPase Putative metal-binding domain of cation transport ATPase This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with Pfam:PF00403, Pfam:PF00122, Pfam:PF00702. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases. (from Pfam) NF023580.5 PF12158.13 DUF3592 25.3 25.3 139 domain Y Y N DUF3592 domain-containing protein 131567 cellular organisms no rank 33589 EBI-EMBL Protein of unknown function (DUF3592) Protein of unknown function (DUF3592) This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 150 and 242 amino acids in length. (from Pfam) NF023583.5 PF12161.13 HsdM_N 24.5 24.5 135 domain Y Y N type I restriction-modification system subunit M N-terminal domain-containing protein 1833555 131567 cellular organisms no rank 106536 EBI-EMBL HsdM N-terminal domain HsdM N-terminal domain This domain is found at the N-terminus of the methylase subunit of Type I DNA methyltransferases. This domain family is found in bacteria and archaea, and is typically between 123 and 138 amino acids in length. The family is found in association with Pfam:PF02384. Mutations in this region of EcoKI methyltransferase Swiss:P08957 abolish the normally strong preference of this system for methylating hemimethylated substrate [1]. The structure of this domain has been shown to be all alpha-helical. [1]. 1833555. Mutations that confer de novo activity upon a maintenance methyltransferase. Kelleher JE, Daniel AS, Murray NE;. J Mol Biol. 1991;221:431-440. (from Pfam) NF023594.5 PF12172.13 DUF35_N 23.2 23.2 37 domain Y Y N zinc ribbon domain-containing protein 131567 cellular organisms no rank 53839 EBI-EMBL Rubredoxin-like zinc ribbon domain (DUF35_N) rubredoxin-like zinc ribbon domain This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in Swiss:O53566. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. (from Pfam) NF023598.5 PF12176.13 MtaB 25 25 460 subfamily Y Y N methyltransferase MtaB domain-containing protein 17142327 131567 cellular organisms no rank 533 EBI-EMBL Methanol-cobalamin methyltransferase B subunit Methanol-cobalamin methyltransferase B subunit This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 460 amino acids in length. MtaB folds as a TIM barrel and contains a novel zinc-binding motif. Zinc(II) lies at the bottom of a funnel formed at the C-terminal beta-barrel end and ligates to two cysteinyl sulfurs (Cys-220 and Cys-269) and one carboxylate oxygen (Glu-164). The function of this protein is to catalyse the cleavage of the C O bond in methanol by an SN2 mechanism. It complexes with MtaA and MtaC to perform this function. [1]. 17142327. Insight into the mechanism of biological methanol activation based on the crystal structure of the methanol-cobalamin methyltransferase complex. Hagemeier CH, Krer M, Thauer RK, Warkentin E, Ermler U;. Proc Natl Acad Sci U S A. 2006;103:18917-18922. (from Pfam) NF023605.5 PF12183.13 NotI 22 22 238 PfamEq Y Y N NotI family restriction endonuclease 18400177,22638584 131567 cellular organisms no rank 651 EBI-EMBL Restriction endonuclease NotI NotI family restriction endonuclease This family of proteins is found in bacteria. Proteins in this family are typically between 270 and 341 amino acids in length. There is a conserved CPF sequence motif. The type IIP restriction enzyme, NotI, is a homodimer that recognises the 8 bp DNA sequence 5'-GC/GGCCGC-3' and cleaves both strands of DNA to create 5', 4 base cohesive overhangs. [1]. 18400177. Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding. Lambert AR, Sussman D, Shen B, Maunus R, Nix J, Samuelson J, Xu SY, Stoddard BL;. Structure. 2008;16:558-569. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF023608.5 PF12187.13 VirArc_Nuclease 20.1 20.1 190 subfamily Y Y N nuclease 22638584 131567 cellular organisms no rank 34 EBI-EMBL Viral/Archaeal nuclease nuclease This family of proteins is found in archaea and viruses. Proteins in this family are typically between 211 and 244 amino acids in length. These proteins are nucleases from fusseloviruses and sulfolobus archaea. [1]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF023621.5 PF12200.13 DUF3597 29.8 29.8 127 domain Y Y N DUF3597 family protein 131567 cellular organisms no rank 5236 EBI-EMBL Domain of unknown function (DUF3597) DUF3597 family protein This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. (from Pfam) NF023636.5 PF12215.13 Glyco_hydr_116N 30.2 30.2 312 domain Y Y N GH116 family glycosyl-hydrolase 3.2.1.- GO:0004553 17105727,20427274,23332916,23332917 131567 cellular organisms no rank 4699 EBI-EMBL beta-glucosidase 2, glycosyl-hydrolase family 116 N-term GH116 family glycosyl-hydrolase N-terminal domain This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 320 to 354 amino acids in length. This domain is found associated with Pfam:PF04685. It is found just after the extreme N terminus. The N-terminal is thought to be the luminal domain while the C terminal is the cytosolic domain. The catalytic domain of GBA-2 is unknown. The primary catabolic pathway for glucosylceramide is catalysis by the lysosomal enzyme glucocerebrosidase. In higher eukaryotes, glucosylceramide is the precursor of glycosphingolipids, a complex group of ubiquitous membrane lipids [1]. Mutations in the human protein cause motor-neurone defects in hereditary spastic paraplegia [2,3]. The catalytic nucleophile, identified in UniProtKB:Q97YG8_SULSO, is a glutamine-335 in the downstream family Pfam:PF04685 [4]. [1]. 17105727. Identification of the non-lysosomal glucosylceramidase as beta-glucosidase 2. Boot RG, Verhoek M, Donker-Koopman W, Strijland A, van Marle J, Overkleeft HS, Wennekes T, Aerts JM;. J Biol Chem. 2007;282:1305-1312. [2]. 23332916. Loss of function of glucocerebrosidase GBA2 is responsible for motor neuron defects in hereditary spastic paraplegia. Martin E, Schule R, Smets K, Rastetter A, Boukhris A, Loureiro JL, Gonzalez MA, Mundwiller E, Deconinck T, Wessner M, Jornea L, Oteyza AC, Durr A, Martin JJ, Schols L, Mhiri C, Lamari F, Zuchner S, De Jonghe P, Kabashi E, Brice A, Stevanin G;. Am J Hum Genet. 2013;92:238-244. [3]. 23332917. Mutations in GBA2 cause autosomal-recessive cerebellar ataxia with spasticity. Hammer MB, Eleuch-Fayache G, Schottlaender LV, Nehdi H, Gibbs JR, Arepalli SK, Chong SB, Her. TRUNCATED at 1650 bytes (from Pfam) NF023643.5 PF12222.13 PNGaseA 22.6 22.6 434 PfamEq Y Y N peptide-N4-asparagine amidase 8940027 131567 cellular organisms no rank 4402 EBI-EMBL Peptide N-acetyl-beta-D-glucosaminyl asparaginase amidase A peptide-N4-asparagine amidase This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 558 and 775 amino acids in length. There is a conserved TGG sequence motif. PNGase A is a protein which cleaves glycopeptides. [1]. 8940027. Haemonchus contortus glycoproteins contain N-linked oligosaccharides with novel highly fucosylated core structures. Haslam SM, Coles GC, Munn EA, Smith TS, Smith HF, Morris HR, Dell A;. J Biol Chem. 1996;271:30561-30570. (from Pfam) NF023645.5 PF12224.13 Amidoligase_2 22 22 245 domain Y Y N amidoligase family protein 18980670 131567 cellular organisms no rank 6725 EBI-EMBL Putative amidoligase enzyme amidoligase family protein This family of proteins are likely to act as amidoligase enzymes [1] Protein in this family are found in conserved gene neighborhoods encoding a glutamine amidotransferase-like thiol peptidase (in proteobacteria) or an Aig2 family cyclotransferase protein (in firmicutes) [1]. [1]. 18980670. Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination. Iyer LM, Burroughs AM, Aravind L;. Biol Direct. 2008;3:45. (from Pfam) NF023646.5 PF12225.13 DUF5981 23 23 95 PfamEq Y Y N methylenetetrahydrofolate reductase C-terminal domain-containing protein 19610625 131567 cellular organisms no rank 5023 EBI-EMBL Methylene-tetrahydrofolate reductase C terminal Methylene-tetrahydrofolate reductase C terminal This family is found in bacteria and archaea, and is approximately 100 amino acids in length. There is a conserved NGPCGG sequence motif. This family is the C terminal of methylene-tetrahydrofolate reductase. This protein reduces FAD using the reducing equivalents from reduced FAD, subsequently reduces tetrahydrofolate. The C terminal of MTHFR contains the FAD binding site and is the catalytic portion of the enzyme. [1]. 19610625. Functional Role for the Conformationally Mobile Phenylalanine 223 in the Reaction of Methylenetetrahydrofolate Reductase from Escherichia coli. Lee MN, Takawira D, Nikolova AP, Ballou DP, Furtado VC, Phung NL, Still BR, Thorstad MK, Tanner JJ, Trimmer EE;. Biochemistry. 2009; [Epub ahead of print] (from Pfam) NF023649.5 PF12228.13 DUF3604 20.4 20.4 591 domain Y Y N DUF3604 domain-containing protein 131567 cellular organisms no rank 5079 EBI-EMBL Protein of unknown function (DUF3604) Protein of unknown function (DUF3604) This family of proteins is found in bacteria. Proteins in this family are typically between 621 and 693 amino acids in length. (from Pfam) NF023676.5 PF12255.13 TcdB_toxin_midC 25 25 147 domain Y Y N toxin TcdB middle/C-terminal domain-containing protein 17573906 131567 cellular organisms no rank 5039 EBI-EMBL Insecticide toxin TcdB middle/C-terminal region Insecticide toxin TcdB middle/C-terminal region This domain family is found in bacteria, and is approximately 150 amino acids in length. The family is found in association with Pfam:PF03534. This family is the C-terminal-sided middle region of the bacterial insecticide toxin TcdB. [1]. 17573906. Expression and insecticidal activity of Yersinia pseudotuberculosis and Photorhabdus luminescens toxin complex proteins. Pinheiro VB, Ellar DJ;. Cell Microbiol. 2007;9:2372-2380. (from Pfam) NF023677.5 PF12256.13 TcdB_toxin_midN 24.8 24.8 181 domain Y Y N toxin TcdB middle/N-terminal domain-containing protein 17573906 131567 cellular organisms no rank 9481 EBI-EMBL Insecticide toxin TcdB middle/N-terminal region Insecticide toxin TcdB middle/N-terminal region This domain family is found in bacteria and archaea, and is typically between 164 and 180 amino acids in length. The family is found in association with Pfam:PF05593. This family is the N-terminal-sided middle region of the bacterial insecticide toxin TcdB. This region appears related to the FG-GAP repeat Pfam:PF01839. [1]. 17573906. Expression and insecticidal activity of Yersinia pseudotuberculosis and Photorhabdus luminescens toxin complex proteins. Pinheiro VB, Ellar DJ;. Cell Microbiol. 2007;9:2372-2380. (from Pfam) NF023680.5 PF12259.13 Baculo_F 24.1 24.1 609 domain Y Y N envelope fusion protein 10846096 131567 cellular organisms no rank 5 EBI-EMBL Baculovirus F protein envelope fusion protein This protein is found in a variety of baculoviruses. It is known as the F protein. Matches to this family are additionally found in some presumed transposons. [1]. 10846096. Identification of the lymantria dispar nucleopolyhedrovirus envelope fusion protein provides evidence for a phylogenetic division of the Baculoviridae. Pearson MN, Groten C, Rohrmann GF;. J Virol. 2000;74:6126-6131. (from Pfam) NF023739.5 PF12320.13 SbcD_C 24.4 24.4 94 PfamEq Y Y N exonuclease SbcCD subunit D C-terminal domain-containing protein 17704228 131567 cellular organisms no rank 48501 EBI-EMBL Type 5 capsule protein repressor C-terminal domain Type 5 capsule protein repressor C-terminal domain This domain is found in bacteria and archaea. This domain is about 90 amino acids in length. This domain is found associated with Pfam:PF00149. SbcD works in complex with SbdC (SbcDC) which is a transcription regulator. It down-regulates transcription of arl and mgr to inhibit type 5 capsule protein production. It acts as part of the SOS pathway of bacteria. [1]. 17704228. The sbcDC locus mediates repression of type 5 capsule production as part of the SOS response in Staphylococcus aureus. Chen Z, Luong TT, Lee CY;. J Bacteriol. 2007;189:7343-7350. (from Pfam) NF023741.5 PF12322.13 T4_baseplate 24.5 24.5 205 PfamEq Y N N T4 bacteriophage base plate protein 2763463 131567 cellular organisms no rank 194 EBI-EMBL T4 bacteriophage base plate protein T4 bacteriophage base plate protein This protein is found in viruses. Proteins in this family are typically between 208 to 249 amino acids in length. This protein has a single completely conserved residue S that may be functionally important. This family includes the two base plate proteins in T4 bacteriophages. These are gp51 and gp26, encoded by late genes. [1]. 2763463. Bacteriophage T4 late gene expression: overlapping promoters direct divergent transcription of the base plate gene cluster. Scarlato V, Storlazzi A, Gargano S, Cascino A;. Virology. 1989;171:475-483. (from Pfam) NF023742.5 PF12323.13 HTH_OrfB_IS605 21 21 47 domain Y Y N helix-turn-helix domain-containing protein 2553665,7557457,8386127 131567 cellular organisms no rank 104476 EBI-EMBL Helix-turn-helix domain Helix-turn-helix domain This is the N terminal helix-turn-helix domain of Transposase_2 Pfam:PF01385. [1]. 2553665. Characterization of an insertion sequence (IS891) of novel structure from the cyanobacterium Anabaena sp. strain M-131. Bancroft I, Wolk CP;. J Bacteriol 1989;171:5949-5954. [2]. 8386127. IS1136, an insertion element in the erythromycin gene cluster of Saccharopolyspora erythraea. Donadio S, Staver MJ;. Gene 1993;126:147-151. Sequence of IS1341. [3]. 7557457. A novel insertion sequence (IS)-like element of the thermophilic bacterium PS3 promotes expression of the alanine carrier protein-encoding gene. Murai N, Kamata H, Nagashima Y, Yagisawa H, Hirata H;. gene 1995;163:103-107. (from Pfam) NF023746.5 PF12327.13 FtsZ_C 27 27 95 PfamEq Y N N FtsZ family, C-terminal domain 9428770,9628483 131567 cellular organisms no rank 57673 EBI-EMBL FtsZ family, C-terminal domain FtsZ family, C-terminal domain This family includes the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. [1]. 9628483. Tubulin and FtsZ form a distinct family of GTPases. Nogales E, Downing KH, Amos LA, Lowe J;. Nat Struct Biol 1998;5:451-458. [3]. 9428770. Crystal structure of the bacterial cell-division protein FtsZ [see comments]. Lowe J, Amos LA;. Nature 1998;391:203-206. (from Pfam) NF023762.5 PF12344.13 UvrB 27 27 43 PfamEq Y N N Ultra-violet resistance protein B 7721686 131567 cellular organisms no rank 76939 EBI-EMBL Ultra-violet resistance protein B Ultra-violet resistance protein B This domain family is found in bacteria, archaea and eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00271, Pfam:PF02151, Pfam:PF04851. There are two conserved sequence motifs: YAD and RRR. This family is the C terminal region of the UvrB protein which conveys mutational resistance against UV light to various different species. [1]. 7721686. A promoter associated with the neisserial repeat can be used to transcribe the uvrB gene from Neisseria gonorrhoeae. Black CG, Fyfe JA, Davies JK;. J Bacteriol. 1995;177:1952-1958. (from Pfam) NF023767.5 PF12349.13 Sterol-sensing 22.3 22.3 153 domain Y N N Sterol-sensing domain of SREBP cleavage-activation 12482938,17604677,9242699,9488713 131567 cellular organisms no rank 25346 EBI-EMBL Sterol-sensing domain of SREBP cleavage-activation Sterol-sensing domain of SREBP cleavage-activation Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER [1]. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini [2]. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein [4]. WD40 domains are found towards the C-terminus. [1]. 9488713. Cleavage of sterol regulatory element-binding proteins (SREBPs) at site-1 requires interaction with SREBP cleavage-activating protein. Evidence from in vivo competition studies. Sakai J, Nohturfft A, Goldstein JL, Brown MS;. J Biol Chem. 1998;273:5785-5793. [2]. 17604677. Endoplasmic reticulum stress causes the activation of sterol regulatory element binding protein-2. Colgan SM, Tang D, Werstuck GH, Austin RC;. Int J Biochem Cell Biol. 2007;39:1843-1851. [3]. 9242699. Identification of complexes between the COOH-terminal domains of sterol regulatory element-binding proteins (SREBPs) and SREBP cleavage-activating protein. Sakai J, Nohturfft A, Cheng D, Ho YK, Brown MS, Goldstein JL;. J Biol Chem. 1997;272:20213-20221. [4]. 12482938. Three mutations in sterol-sensing doma. TRUNCATED at 1650 bytes (from Pfam) NF023776.5 PF12358.13 DUF3644 27.6 27.6 183 PfamAutoEq Y Y N DUF3644 domain-containing protein 131567 cellular organisms no rank 3735 EBI-EMBL Domain of unknown function (DUF3644) Domain of unknown function (DUF3644) This entry represents a HEPN-like domain found in bacterial proteins. The AlphaFold structures show this entry is a part of the Nucleotidyltransferase substrate binding domain superfamily. (from Pfam) NF023785.5 PF12367.13 PFO_beta_C 24 24 66 PfamEq Y N N Pyruvate ferredoxin oxidoreductase beta subunit C terminal 11401501 131567 cellular organisms no rank 5250 EBI-EMBL Pyruvate ferredoxin oxidoreductase beta subunit C terminal Pyruvate ferredoxin oxidoreductase beta subunit C terminal This domain family is found in bacteria and archaea, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF02775. There are two completely conserved residues (A and G) that may be functionally important. PFO is involved in carbon dioxide fixation via a reductive TCA cycle. It forms a heterodimer (alpha/beta). The beta subunit has binding motifs for Fe-S clusters and thiamine pyrophosphate. [1]. 11401501. The genes for anabolic 2-oxoglutarate: ferredoxin oxidoreductase from Hydrogenobacter thermophilus TK-6. Yun NR, Arai H, Ishii M, Igarashi Y;. Biochem Biophys Res Commun. 2001;282:589-594. (from Pfam) NF023788.5 PF12371.13 TMEM131_like_N 28.8 28.8 84 PfamEq Y N N Transmembrane protein 131-like N-terminal 23690469 131567 cellular organisms no rank 199 EBI-EMBL Transmembrane protein 131-like N-terminal Transmembrane protein 131-like N-terminal TMEM131_like is a family of bacterial, plant and other metazoa transmembrane proteins. Many of the members are multi-pass transmembrane proteins. This domain represents the N-terminal region which contains a conserved homology domain (CHD1) [1]. [1]. 23690469. Identification of TMEM131L as a novel regulator of thymocyte proliferation in humans. Maharzi N, Parietti V, Nelson E, Denti S, Robledo-Sarmiento M, Setterblad N, Parcelier A, Pla M, Sigaux F, Gluckman JC, Canque B;. J Immunol. 2013;190:6187-6197. (from Pfam) NF023802.5 PF12385.13 Peptidase_C70 19 19 141 domain Y Y N papain-like cysteine protease family protein 10361296,18705889 131567 cellular organisms no rank 13550 EBI-EMBL Papain-like cysteine protease AvrRpt2 papain-like cysteine protease family protein This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis [2]. AvrRpt2 from Pseudomonas syringae pv. tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2 [1]. [1]. 10361296. Characterization of the Pseudomonas syringae pv. tomato AvrRpt2 protein: demonstration of secretion and processing during bacterial pathogenesis. Mudgett MB, Staskawicz BJ;. Mol Microbiol. 1999;32:927-941. [2]. 18705889. Papain-like cysteine proteases: key players at molecular battlefields employed by both plants and their invaders. Shindo T, Van der Hoorn RA;. Mol Plant Pathol. 2008;9:119-125. (from Pfam) NF023803.5 PF12386.13 Peptidase_C71 22 22 149 domain Y N N Pseudomurein endo-isopeptidase Pei 11934493 131567 cellular organisms no rank 278 EBI-EMBL Pseudomurein endo-isopeptidase Pei Pseudomurein endo-isopeptidase Pei This peptidase has the catalytic triad C-H-D at the C-terminal end, a triad similar to that in thiol proteases and animal transglutaminases. It catalyses the in vitro lysis of M. marburgensis cells under reducing conditions and exhibits characteristics of metal-activated peptidases. [1]. 11934493. Pseudomurein endoisopeptidases PeiW and PeiP, two moderately related members of a novel family of proteases produced in Methanothermobacter strains. Luo Y, Pfister P, Leisinger T, Wasserfallen A;. FEMS Microbiol Lett. 2002;208:47-51. (from Pfam) NF023805.5 PF12388.13 Peptidase_M57 21 21 212 subfamily Y Y N M57 family metalloprotease 9370274 131567 cellular organisms no rank 5866 EBI-EMBL Dual-action HEIGH metallo-peptidase M57 family metalloprotease Proteins scoring well to this HMM (> 100 bits) belong to MEROPs family M57. Members of other MEROPs families are detected, including M10 and M27, are detected with lower scores. NF023806.5 PF12389.13 Peptidase_M73 22.5 22.5 196 subfamily Y Y N TasA family protein 29531041 131567 cellular organisms no rank 7020 EBI-EMBL Camelysin metallo-endopeptidase TasA family protein Members of this family include M73 family metalloproteases but also TasA, which is apparently enzymatically inactive and instead is the major secreted protein of Bacillus subtilis biofilm matrix. NF023809.5 PF12392.13 DUF3656 22.1 22.1 109 PfamEq Y Y N DUF3656 domain-containing protein 131567 cellular organisms no rank 27465 EBI-EMBL Collagenase Collagenase This domain family is found in bacteria, archaea and eukaryotes, and is approximately 120 amino acids in length. The family is found in association with Pfam:PF01136. (from Pfam) NF023812.5 PF12395.13 DUF3658 23.3 23.3 107 domain Y Y N DUF3658 domain-containing protein 131567 cellular organisms no rank 7541 EBI-EMBL Protein of unknown function DUF3658 domain-containing protein Most members of this family have an N-terminal DUF1835 (PF08874) domain and this domain (DUF3658) as the C-terminal domain. NF023816.5 PF12399.13 BCA_ABC_TP_C 25.5 25.5 27 domain Y N N Branched-chain amino acid ATP-binding cassette transporter 2195019,31431556 131567 cellular organisms no rank 172836 EBI-EMBL Branched-chain amino acid ATP-binding cassette transporter Branched-chain amino acid ATP-binding cassette transporter This domain family is found in bacteria, archaea and eukaryotes, and is approximately 30 amino acids in length. The family is found in association with Pfam:PF00005. There is a conserved AYLG sequence motif. This family is the C terminal of an ATP dependent branched-chain amino acid transporter [1]. This domain is essential for LPS transport, through critical interactions with Walker A and switch helix domains [2]. [1]. 2195019. Nucleotide sequence and genetic characterization reveal six essential genes for the LIV-I and LS transport systems of Escherichia coli. Adams MD, Wagner LM, Graddis TJ, Landick R, Antonucci TK, Gibson AL, Oxender DL;. J Biol Chem 1990;265:11436-11443. [2]. 31431556. Combining Mutations That Inhibit Two Distinct Steps of the ATP Hydrolysis Cycle Restores Wild-Type Function in the Lipopolysaccharide Transporter and Shows that ATP Binding Triggers Transport. Simpson BW, Pahil KS, Owens TW, Lundstedt EA, Davis RM, Kahne D, Ruiz N;. mBio. 2019; [Epub ahead of print] (from Pfam) NF023835.5 PF12419.13 DUF3670 27.6 27.6 136 domain Y Y N SNF2 helicase-associated domain-containing protein 131567 cellular organisms no rank 33168 EBI-EMBL SNF2 Helicase protein SNF2 Helicase protein This domain family is found in bacteria, archaea and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with Pfam:PF00271, Pfam:PF00176. Most of the proteins in this family are annotated as SNF2 helicases but there is little accompanying literature to confirm this. (from Pfam) NF023853.5 PF12437.13 GSIII_N 25 25 160 domain Y Y N glutamine synthetase III GO:0004356 16237031 131567 cellular organisms no rank 15328 EBI-EMBL Glutamine synthetase type III N terminal glutamine synthetase III This domain family is found in bacteria and eukaryotes, and is approximately 160 amino acids in length. The family is found in association with Pfam:PF00120. This family is the N terminal region of glutamine synthetase type III which is one of the enzymes responsible for generation of glutamine through conversion glutamate to glutamine by the incorporation of ammonia (NH3). [1]. 16237031. Biochemical and mutational analysis of glutamine synthetase type III from the rumen anaerobe Ruminococcus albus 8. Amaya KR, Kocherginskaya SA, Mackie RI, Cann IK;. J Bacteriol. 2005;187:7481-7491. (from Pfam) NF023855.5 PF12439.13 GDE_N 27 27 219 domain Y Y N glycogen debranching enzyme N-terminal domain-containing protein 18051301 131567 cellular organisms no rank 7815 EBI-EMBL Glycogen debranching enzyme N terminal Glycogen debranching enzyme N terminal This domain family is found in bacteria and archaea, and is typically between 218 and 229 amino acids in length. The family is found in association with Pfam:PF06202. Glycogen debranching enzyme catalyses the debranching of amylopectin in glycogen. This is done by transferring three glucose subunits of glycogen from one parallel chain to another. This has the effect of enabling the glucose residues to become more accessible for glycolysis. [1]. 18051301. Cloning and characterization of glycogen-debranching enzyme from hyperthermophilic archaeon Sulfolobus shibatae. Van TT, Ryu SI, Lee KJ, Kim EJ, Lee SB;. J Microbiol Biotechnol. 2007;17:792-799. (from Pfam) NF023857.5 PF12441.13 CopG_antitoxin 28 28 79 domain Y Y N CopG family antitoxin 15864262 131567 cellular organisms no rank 3132 EBI-EMBL CopG antitoxin of type II toxin-antitoxin system CopG family antitoxin CopG antitoxin is a member of a type II toxin-antitoxin system family found in bacteria and archaea. Most antitoxins encoded by the relBE and parDE loci belong to the MetJ/Arc/CopG family of dimeric proteins which bind DNA through N-terminal ribbon-helix-helix (RHH) motifs [1]. The toxin for CopG proteins falls into the family BrnT_toxin, Pfam:PF04365. [1]. 15864262. Prokaryotic toxin-antitoxin stress response loci. Gerdes K, Christensen SK, Lobner-Olesen A;. Nat Rev Microbiol. 2005;3:371-382. (from Pfam) NF023880.5 PF12464.13 Mac 22.1 22.1 53 domain Y Y N maltose acetyltransferase domain-containing protein GO:0016407 1856235 131567 cellular organisms no rank 45962 EBI-EMBL Maltose acetyltransferase hexapeptide capping motif Maltose acetyltransferase hexapeptide capping motif This family is found in bacteria, archaea and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with Pfam:PF00132. Mac uses acetyl-CoA as acetyl donor to acetylated cytoplasmic maltose. This region is a short capping motif. [1]. 1856235. Maltose transacetylase of Escherichia coli. Mapping and cloning of its structural, gene, mac, and characterization of the enzyme as a dimer of identical polypeptides with a molecular weight of 20,000. Brand B, Boos W;. J Biol Chem. 1991;266:14113-14118. (from Pfam) NF023885.5 PF12469.13 Cmr2_N 25 25 111 domain Y Y N type III-B CRISPR-associated protein Cas10/Cmr2 25280103 131567 cellular organisms no rank 2661 EBI-EMBL CRISPR-associated protein Cmr2, N-terminal type III-B CRISPR-associated protein Cas10/Cmr2 This domain family is typically between 101 and 138 amino acids in length and it is found in subunit Crm2 of the CRISPR RNA-Cas protein complex (Cmr complex) [1]. [1]. 25280103. Structural model of a CRISPR RNA-silencing complex reveals the RNA-target cleavage activity in Cmr4. Benda C, Ebert J, Scheltema RA, Schiller HB, Baumgartner M, Bonneau F, Mann M, Conti E;. Mol Cell. 2014;56:43-54. (from Pfam) NF023892.5 PF12476.13 DUF3696 22 22 52 PfamAutoEq Y Y N DUF3696 domain-containing protein 131567 cellular organisms no rank 5394 EBI-EMBL Protein of unknown function (DUF3696) Protein of unknown function (DUF3696) This domain family is found in bacteria and archaea, and is approximately 50 amino acids in length. (from Pfam) NF023897.5 PF12481.13 DUF3700 27 27 228 domain Y N N Aluminium induced protein 131567 cellular organisms no rank 16258 EBI-EMBL Aluminium induced protein Aluminium induced protein This domain family is found in eukaryotes, and is approximately 120 amino acids in length. There are two conserved sequence motifs: YGL and LRDR. This family is related to GATase enzyme domains. (from Pfam) NF023899.5 PF12483.13 GIDE 23.6 23.6 160 domain Y Y N GIDE domain-containing protein GO:0004842,GO:0006996,GO:0016567 18591963 131567 cellular organisms no rank 2270 EBI-EMBL E3 Ubiquitin ligase GIDE domain GIDE (Growth Inhibition and Death E3 Ligase) is a mitochondrial protein with a C-terminal RING finger and with E3 ubiquitin ligase activity, that is, recruit an E2 ubiquitin-conjugating enzyme to specific targets; the human genome has an estimated 600 E3 ligases from four different families. This HMM describes a region of GIDE found N-terminally to the RING finger domain. NF023946.5 PF12532.13 DUF3732 25 25 186 PfamAutoEq Y Y N DUF3732 domain-containing protein 131567 cellular organisms no rank 5618 EBI-EMBL Protein of unknown function (DUF3732) Protein of unknown function (DUF3732) This domain family is found in bacteria and eukaryotes, and is typically between 180 and 198 amino acids in length. There is a conserved DQP sequence motif. (from Pfam) NF023949.5 PF12535.13 Nudix_N 27 27 56 PfamEq Y Y N NUDIX hydrolase N-terminal domain-containing protein 8810257 131567 cellular organisms no rank 10087 EBI-EMBL Hydrolase of X-linked nucleoside diphosphate N terminal Hydrolase of X-linked nucleoside diphosphate N terminal This family of proteins is found in eukaryotes. Proteins in this family are typically between 847 and 5344 amino acids in length. These enzymes hydrolyse the molecular motif of a nucleoside diphosphate linked to some other moiety, X. [1]. 8810257. The MutT proteins or "Nudix" hydrolases, a family of versatile, widely distributed, "housecleaning" enzymes. Bessman MJ, Frick DN, O'Handley SF;. J Biol Chem. 1996;271:25059-25062. (from Pfam) NF023950.5 PF12536.13 DUF3734 22 22 106 domain Y Y N DUF3734 domain-containing protein 131567 cellular organisms no rank 9468 EBI-EMBL Patatin phospholipase Patatin phospholipase This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF01734. There are two completely conserved residues (F and G) that may be functionally important. The proteins in this family are frequently annotated as patatin family phospholipases however there is little accompanying literature to confirm this. (from Pfam) NF023955.5 PF12541.13 DUF3737 23.9 23.9 275 PfamAutoEq Y Y N DUF3737 family protein 131567 cellular organisms no rank 4026 EBI-EMBL Protein of unknown function (DUF3737) DUF3737 family protein This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 281 and 297 amino acids in length. (from Pfam) NF023958.5 PF12544.13 LAM_C 26.7 26.7 127 domain Y N N Lysine-2,3-aminomutase 16166264 131567 cellular organisms no rank 8378 EBI-EMBL Lysine-2,3-aminomutase Lysine-2,3-aminomutase This domain family is found in bacteria, archaea and eukaryotes, and is typically between 111 and 127 amino acids in length. The family is found in association with Pfam:PF04055. LAM catalyses the interconversion of L-alpha-lysine and L-beta-lysine, which proceeds by migration of the amino group from C2 to C3 concomitant with cross-migration of the 3-pro-R hydrogen of L-alpha-lysine to the 2-pro-R position of L-beta-lysine. [1]. 16166264. The x-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale. Lepore BW, Ruzicka FJ, Frey PA, Ringe D;. Proc Natl Acad Sci U S A. 2005;102:13819-13824. (from Pfam) NF023978.5 PF12564.13 TypeIII_RM_meth 25 25 56 domain Y Y N site-specific DNA-methyltransferase 9925601 131567 cellular organisms no rank 5666 EBI-EMBL Type III restriction/modification enzyme methylation subunit site-specific DNA-methyltransferase This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF01555. There are two completely conserved residues (F and S) that may be functionally important. This family is a bacterial phage resistance protein. It functions in a type III restriction/modification enzyme complex. It is part of the methylation subunit of the complex. It binds DNA and methylates it. [1]. 9925601. LlaFI, a type III restriction and modification system in Lactococcus lactis. Su P, Im H, Hsieh H, Kang'A S, Dunn NW;. Appl Environ Microbiol. 1999;65:686-693. (from Pfam) NF024002.5 PF12588.13 PSDC 23.4 23.4 138 PfamEq Y Y N phophatidylserine decarboxylase associated domain-containing protein 9370338 131567 cellular organisms no rank 2763 EBI-EMBL Phophatidylserine decarboxylase Phophatidylserine decarboxylase This domain family is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with Pfam:PF02666. Phosphatidylserine decarboxylase (PSD) is an important enzyme in the synthesis of phosphatidylethanolamine in both prokaryotes and eukaryotes. [1]. 9370338. Phosphatidylserine decarboxylase. Voelker DR;. Biochim Biophys Acta. 1997;1348:236-244. (from Pfam) NF024025.5 PF12611.13 Flagellar_put 21.1 21.1 24 PfamEq Y N N Putative flagellar 131567 cellular organisms no rank 3786 EBI-EMBL Putative flagellar putative flagellar protein Proteins in this entry are encoded in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. (from Pfam) NF024031.5 PF12617.13 LdpA_C 22.2 22.2 184 domain Y Y N LdpA C-terminal domain-containing domain 12562813 131567 cellular organisms no rank 1177 EBI-EMBL Iron-Sulfur binding protein C terminal Iron-Sulfur binding protein C terminal This domain family is found in bacteria and eukaryotes, and is typically between 179 and 201 amino acids in length. The family is found in association with Pfam:PF00037. LdpA (light-dependent period) plays a role in controlling the redox state in cyanobacteria to modulate its. circadian clock. LdpA is a protein with Iron-Sulfur cluster-binding motifs. [1]. 12562813. ldpA encodes an iron-sulfur protein involved in light-dependent modulation of the circadian period in the cyanobacterium Synechococcus elongatus PCC 7942. Katayama M, Kondo T, Xiong J, Golden SS;. J Bacteriol. 2003;185:1415-1422. (from Pfam) NF024041.5 PF12627.12 PolyA_pol_RNAbd 22 22 64 domain Y N N Probable RNA and SrmB- binding site of polymerase A 10361280 131567 cellular organisms no rank 105393 EBI-EMBL Probable RNA and SrmB- binding site of polymerase A Probable RNA and SrmB- binding site of polymerase A This region encompasses much of the RNA and SrmB binding motifs on polymerase A. [1]. 10361280. Poly(A) polymerase I of Escherichia coli: characterization of the catalytic domain, an RNA binding site and regions for the interaction with proteins involved in mRNA degradation. Raynal LC, Carpousis AJ;. Mol Microbiol. 1999;32:765-775. (from Pfam) NF024049.5 PF12635.12 DUF3780 27 27 184 PfamAutoEq Y Y N DUF3780 domain-containing protein 131567 cellular organisms no rank 749 EBI-EMBL Protein of unknown function (DUF3780) Protein of unknown function (DUF3780) This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria. Proteins in this family are typically between 189 and 206 amino acids in length. There are two conserved sequence motifs: PEERWWL and GWR. This family is found in a very sporadic set of bacterial species, suggesting that it may have been horizontally transferred. One protein is annotated as plasmid borne. (from Pfam) NF024050.5 PF12636.12 DUF3781 27 27 72 domain Y Y N DUF3781 domain-containing protein 131567 cellular organisms no rank 1418 EBI-EMBL Protein of unknown function (DUF3781) Protein of unknown function (DUF3781) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 82 and 98 amino acids in length. There are two conserved sequence motifs: GKNWY and ITA. (from Pfam) NF024051.5 PF12637.12 TSCPD 22.1 22.1 74 domain Y Y N TSCPD domain-containing protein 131567 cellular organisms no rank 4443 EBI-EMBL TSCPD domain TSCPD domain This family of proteins is found in bacteria, archaea and viruses. The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD after which the domain is named. Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulfur cluster. This domain is found at the C-terminus of some ribonucleoside-diphosphate reductase enzymes. (from Pfam) NF024053.5 PF12639.12 Colicin-DNase 25 25 96 domain Y Y N HNH endonuclease 10368275,11741540 131567 cellular organisms no rank 11955 EBI-EMBL DNase/tRNase domain of colicin-like bacteriocin HNH endonuclease Colicin-like bacteriocins are complex structures with an N-terminal beta-barrel translocation domain (Pfam:PF09000), a long double-alpha-helical receptor-binding domain (Pfam:PF11570) and this C-terminal RNAse/DNase domain with endonuclease activity. Their competitor bacteriocidal action is by a process that involves binding to a surface receptor, entering the cell, and, finally, killing it. The lethal action of colicin E3 is a specific cleavage in the ribosomal decoding A site. The crystal structure of colicin E3 reveals a Y-shaped molecule with the receptor binding domain forming a 100 Angstrom long stalk and the two globular heads of the translocation domain and this catalytic domain comprising the two arms [2]. [1]. 10368275. The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein. Ko TP, Liao CC, Ku WY, Chak KF, Yuan HS;. Structure. 1999;7:91-102. [2]. 11741540. Crystal structure of colicin E3: implications for cell entry and ribosome inactivation. Soelaiman S, Jakes K, Wu N, Li C, Shoham M;. Mol Cell. 2001;8:1053-1062. (from Pfam) NF024054.5 PF12640.12 UPF0489 27 27 167 PfamEq Y Y N UPF0489 family protein 131567 cellular organisms no rank 933 EBI-EMBL UPF0489 domain UPF0489 domain This family is probably an enzyme which is related to the Arginase family. (from Pfam) NF024055.5 PF12641.12 Flavodoxin_3 27.5 27.5 160 domain Y Y N flavodoxin family protein GO:0010181 131567 cellular organisms no rank 13653 EBI-EMBL Flavodoxin domain Flavodoxin domain This family represents a flavodoxin domain. (from Pfam) NF024057.5 PF12643.12 MazG-like 27 27 85 domain Y Y N MazG-like family protein GO:0009143,GO:0047429 20529853 131567 cellular organisms no rank 22285 EBI-EMBL MazG-like family MazG-like family protein This family of short proteins are distantly related to the MazG enzyme. This suggests that these proteins are enzymes that catalyse a related reaction. (from Pfam) NF024058.5 PF12644.12 DUF3782 24.4 24.4 78 domain Y Y N DUF3782 domain-containing protein 131567 cellular organisms no rank 1474 EBI-EMBL Protein of unknown function (DUF3782) Protein of unknown function (DUF3782) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 91 and 186 amino acids in length. (from Pfam) NF024060.5 PF12646.12 DUF3783 27 27 56 PfamAutoEq Y Y N DUF3783 domain-containing protein 131567 cellular organisms no rank 3220 EBI-EMBL Domain of unknown function (DUF3783) Domain of unknown function (DUF3783) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 60 amino acids in length. (from Pfam) NF024063.5 PF12650.12 DUF3784 28.1 28.1 94 domain Y Y N DUF3784 domain-containing protein 131567 cellular organisms no rank 5874 EBI-EMBL Domain of unknown function (DUF3784) Domain of unknown function (DUF3784) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 96 and 110 amino acids in length. (from Pfam) NF024064.5 PF12651.12 RHH_3 21.6 21.6 44 domain Y Y N ribbon-helix-helix domain-containing protein 131567 cellular organisms no rank 3794 EBI-EMBL Ribbon-helix-helix domain Ribbon-helix-helix domain This short bacterial protein contains a ribbon-helix-helix domain that is likely to be DNA-binding. (from Pfam) NF024067.5 PF12654.12 DUF3786 27 27 176 domain Y Y N DUF3786 domain-containing protein 131567 cellular organisms no rank 2132 EBI-EMBL Domain of unknown function (DUF3786) Domain of unknown function (DUF3786) This presumed domain is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 201 and 257 amino acids in length. Some proteins also contains an iron-sulfur cluster. (from Pfam) NF024080.5 PF12668.12 DUF3791 25 25 60 domain Y Y N DUF3791 domain-containing protein 131567 cellular organisms no rank 3343 EBI-EMBL Protein of unknown function (DUF3791) Protein of unknown function (DUF3791) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 71 and 125 amino acids in length. (from Pfam) NF024081.5 PF12669.12 FeoB_associated 27 27 44 PfamEq Y Y N FeoB-associated Cys-rich membrane protein 131567 cellular organisms no rank 7458 EBI-EMBL FeoB-associated Cys-rich membrane protein FeoB-associated Cys-rich membrane protein Members of this family typically are small proteins encoded next to FeoB, part of a ferrous iron uptake system. They consist of a highly hydrophobic predicted membrane segment, followed by a short, Cys-rich region, for an average length of less than sixty amino acids. In some cases, member proteins are fusion proteins, with the region described by this family occurring as a C-terminal extension to FeoB. (from Pfam) NF024082.5 PF12670.12 DUF3792 31.3 31.3 115 PfamAutoEq Y Y N DUF3792 family protein 131567 cellular organisms no rank 4857 EBI-EMBL Protein of unknown function (DUF3792) DUF3792 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. These proteins are integral membrane proteins. (from Pfam) NF024083.5 PF12671.12 Amidase_6 23.2 23.2 163 domain Y Y N amidase domain-containing protein 131567 cellular organisms no rank 14402 EBI-EMBL Putative amidase domain Putative amidase domain NF024084.5 PF12672.12 DUF3793 25.1 25.1 167 PfamAutoEq Y Y N DUF3793 family protein 131567 cellular organisms no rank 4693 EBI-EMBL Protein of unknown function (DUF3793) DUF3793 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 187 and 211 amino acids in length. There are two conserved sequence motifs: PHE and LGYP. (from Pfam) NF024086.5 PF12674.12 Zn_ribbon_2 22.5 22.5 81 domain Y Y N zinc ribbon domain-containing protein 131567 cellular organisms no rank 6497 EBI-EMBL Putative zinc ribbon domain Putative zinc ribbon domain This domain appears to be a zinc binding DNA-binding domain. (from Pfam) NF024087.5 PF12675.12 DUF3795 22.6 22.6 83 domain Y Y N DUF3795 domain-containing protein 131567 cellular organisms no rank 3960 EBI-EMBL Protein of unknown function (DUF3795) Protein of unknown function (DUF3795) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 99 and 171 amino acids in length. This protein is likely to be zinc binding given the conserved cysteines. (from Pfam) NF024091.5 PF12679.12 ABC2_membrane_2 27.2 27.2 283 domain Y Y N ABC transporter permease subunit GO:0055085,GO:0140359 1303751 131567 cellular organisms no rank 234232 EBI-EMBL ABC-2 family transporter protein ABC transporter permease subunit This family is related to the ABC-2 membrane transporter family [1]. [1]. 1303751. A new subfamily of bacterial ABC-type transport systems catalyzing export of drugs and carbohydrates. Reizer J, Reizer A, Saier MH Jr;. Protein Sci 1992;1:1326-1332. (from Pfam) NF024092.5 PF12680.12 SnoaL_2 27 27 102 domain Y Y N nuclear transport factor 2 family protein 131567 cellular organisms no rank 372356 EBI-EMBL SnoaL-like domain SnoaL-like domain This family contains a large number of proteins that share the SnoaL fold. (from Pfam) NF024093.5 PF12681.12 Glyoxalase_2 30.1 29.6 118 domain Y N N Glyoxalase-like domain 131567 cellular organisms no rank 27875 EBI-EMBL Glyoxalase-like domain Glyoxalase-like domain This domain is related to the Glyoxalase domain Pfam:PF00903. (from Pfam) NF024094.5 PF12682.12 Flavodoxin_4 24 24 155 subfamily Y Y N flavodoxin GO:0010181 131567 cellular organisms no rank 21466 EBI-EMBL Flavodoxin flavodoxin This is a family of flavodoxins. Flavodoxins are electron transfer proteins that carry a molecule of non-covalently bound FMN. (from Pfam) NF024098.5 PF12686.12 DUF3800 21 21 149 domain Y Y N DUF3800 domain-containing protein 131567 cellular organisms no rank 20999 EBI-EMBL Protein of unknown function (DUF3800) Protein of unknown function (DUF3800) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 215 and 302 amino acids in length. There is a DE motif at the N-terminus and a QXXD motif at the C-terminus that may be functionally important. (from Pfam) NF024100.5 PF12688.12 TPR_5 24.2 10 119 PfamEq Y Y N tetratricopeptide repeat protein 131567 cellular organisms no rank 16604 EBI-EMBL Tetratrico peptide repeat Tetratrico peptide repeat BH0479 of Bacillus halodurans is a hypothetical protein which contains a tetratrico peptide repeat (TPR) structural motif. The TPR motif is often involved in mediating protein-protein interactions. This protein is likely to function as a dimer. The first 48 amino acids are not present in the clone construct. This Pfam entry includes tetratricopeptide-like repeats not detected by the Pfam:PF00515, Pfam:PF07719, Pfam:PF07720 and Pfam:PF07221 models. (from Pfam) NF024101.5 PF12689.12 Acid_PPase 27 27 169 PfamEq Y N N Acid Phosphatase GO:0016791 10889041,11601995 131567 cellular organisms no rank 391 EBI-EMBL Acid Phosphatase Acid Phosphatase This family contains phosphatase enzymes and other proteins of the HAD superfamily. It includes MDP-1 which is a eukaryotic magnesium-dependent acid phosphatase [1-2]. [1]. 10889041. MDP-1: A novel eukaryotic magnesium-dependent phosphatase. Selengut JD, Levine RL;. Biochemistry. 2000;39:8315-8324. [2]. 11601995. MDP-1 is a new and distinct member of the haloacid dehalogenase family of aspartate-dependent phosphohydrolases. Selengut JD;. Biochemistry. 2001;40:12704-12711. (from Pfam) NF024102.5 PF12690.12 BsuPI 22.9 22.9 101 domain Y Y N BsuPI-related putative proteinase inhibitor 24555072,8226659 131567 cellular organisms no rank 3167 EBI-EMBL Intracellular proteinase inhibitor BsuPI-related putative proteinase inhibitor This is a bacterial domain which has been named BsuPI in Bacillus subtilis. This domain is found in Swiss:P39804, where it has been suggested to regulate the major intracellular proteinase (ISP-1) activity in vivo [1]. The structure of proteins in this family adopt an Ig-like fold [2]. [1]. 8226659. Characterization of the gene encoding an intracellular proteinase inhibitor of Bacillus subtilis and its role in regulation of the major intracellular proteinase. Shiga Y, Yamagata H, Udaka S;. J Bacteriol. 1993;175:7130-7137. [2]. 24555072. The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold. Rigden DJ, Xu Q, Chang Y, Eberhardt RY, Finn RD, Rawlings ND;. F1000Res. 2013;2:154. (from Pfam) NF024103.5 PF12691.12 Minor_capsid_3 23.8 23.8 118 PfamEq Y Y N minor capsid protein 131567 cellular organisms no rank 4681 EBI-EMBL Bacteriophage minor capsid protein minor capsid protein This family is from one of three adjacent genes, all of which are involved in formation of the minor phage capsid. (from Pfam) NF024107.5 PF12695.12 Abhydrolase_5 27 27 164 domain Y Y N alpha/beta hydrolase GO:0016787 12369917 131567 cellular organisms no rank 33233 EBI-EMBL Alpha/beta hydrolase family alpha/beta hydrolase This family contains a diverse range of alpha/beta hydrolase enzymes. (from Pfam) NF024108.5 PF12696.12 TraG-D_C 22 22 126 domain Y Y N TraM recognition domain-containing protein 11976307,18717787 131567 cellular organisms no rank 113985 EBI-EMBL TraM recognition site of TraD and TraG TraM recognition site of TraD and TraG This family includes both TraG and TraD as well as VirD4 proteins. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems [1]. This domain interacts with the relaxosome component TraM via the latter's tetramerisation domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore [2]. [1]. 11976307. TraG-like proteins of DNA transfer systems and of the Helicobacter pylori type IV secretion system: inner membrane gate for exported substrates?. Schroder G, Krause S, Zechner EL, Traxler B, Yeo HJ, Lurz R, Waksman G, Lanka E;. J Bacteriol 2002;184:2767-2779. [2]. 18717787. Structural basis of specific TraD-TraM recognition during F plasmid-mediated bacterial conjugation. Lu J, Wong JJ, Edwards RA, Manchak J, Frost LS, Glover JN;. Mol Microbiol. 2008;70:89-99. (from Pfam) NF024109.5 PF12697.12 Abhydrolase_6 26.3 26.3 217 subfamily Y Y N alpha/beta fold hydrolase 131567 cellular organisms no rank 1716855 EBI-EMBL Alpha/beta hydrolase family alpha/beta fold hydrolase This family contains alpha/beta hydrolase enzymes of diverse specificity. (from Pfam) NF024110.5 PF12698.12 ABC2_membrane_3 31.6 31.6 347 domain Y Y N ABC transporter permease GO:0016020,GO:0140359 1303751 131567 cellular organisms no rank 475428 EBI-EMBL ABC-2 family transporter protein ABC transporter permease This family is related to the ABC-2 membrane transporter family Pfam:PF01061 [1]. [1]. 1303751. A new subfamily of bacterial ABC-type transport systems catalyzing export of drugs and carbohydrates. Reizer J, Reizer A, Saier MH Jr;. Protein Sci 1992;1:1326-1332. (from Pfam) NF024116.5 PF12704.12 MacB_PCD 27 27 207 domain Y Y N ABC transporter permease 19432486 131567 cellular organisms no rank 379201 EBI-EMBL MacB-like periplasmic core domain MacB-like periplasmic core domain This family represents the periplasmic core domain found in a variety of ABC transporters. The structure of this family has been solved for the MacB protein [1]. Some structural similarity was found to the periplasmic domain of the AcrB multidrug efflux transporter. [1]. 19432486. Crystal structure of the periplasmic region of MacB, a noncanonic ABC transporter. Xu Y, Sim SH, Nam KH, Jin XL, Kim HM, Hwang KY, Lee K, Ha NC;. Biochemistry. 2009;48:5218-5225. (from Pfam) NF024117.5 PF12705.12 PDDEXK_1 22 22 247 domain Y Y N PD-(D/E)XK nuclease family protein 15972856 131567 cellular organisms no rank 236322 EBI-EMBL PD-(D/E)XK nuclease superfamily PD-(D/E)XK nuclease family protein Members of this family belong to the PD-(D/E)XK nuclease superfamily [1]. 15972856. Identification of novel restriction endonuclease-like fold families among hypothetical proteins. Kinch LN, Ginalski K, Rychlewski L, Grishin NV;. Nucleic Acids Res. 2005;33:3598-3605. (from Pfam) NF024118.5 PF12706.12 Lactamase_B_2 27 27 200 domain Y Y N MBL fold metallo-hydrolase 131567 cellular organisms no rank 480934 EBI-EMBL Beta-lactamase superfamily domain MBL fold metallo-hydrolase domain The MBL fold superfamily includes the metallo-beta-lactamases (class B beta-lactamases), but includes also a much larger family of hydrolases that are not beta-lactamases at all. See also the related family PF00753. NF024120.5 PF12708.12 Pectate_lyase_3 27 27 213 domain Y Y N glycosyl hydrolase family 28-related protein 131567 cellular organisms no rank 56464 EBI-EMBL Pectate lyase superfamily protein pectate lyase-like beta-helical domain This family of proteins possesses a beta helical structure like Pectate lyase. This family is most closely related to glycosyl hydrolase family 28. (from Pfam) NF024122.5 PF12710.12 HAD 27 27 189 domain Y Y N haloacid dehalogenase-like hydrolase 131567 cellular organisms no rank 423724 EBI-EMBL haloacid dehalogenase-like hydrolase haloacid dehalogenase-like hydrolase NF024126.5 PF12715.12 Abhydrolase_7 21 21 388 domain Y Y N alpha/beta hydrolase family protein 131567 cellular organisms no rank 5711 EBI-EMBL Abhydrolase family alpha/beta hydrolase family protein This is a family of probable bacterial abhydrolases. (from Pfam) NF024128.5 PF12717.12 Cnd1 26.4 26.4 162 domain Y N N non-SMC mitotic condensation complex subunit 1 10485849,11378401 131567 cellular organisms no rank 829 EBI-EMBL non-SMC mitotic condensation complex subunit 1 non-SMC mitotic condensation complex subunit 1 The three non-SMC (structural maintenance of chromosomes) subunits of the mitotic condensation complex are Cnd1-3. The whole complex is essential for viability and the condensing of chromosomes in mitosis. [1]. 11378401. Chromosome condensation: packaging the genome. Uhlmann F;. Curr Biol. 2001;11:R384-R387. [2]. 10485849. Fission yeast condensin complex: essential roles of non-SMC subunits for condensation and Cdc2 phosphorylation of Cut3/SMC4. Sutani T, Yuasa T, Tomonaga T, Dohmae N, Takio K, Yanagida M;. Genes Dev 1999;13:2271-2283. (from Pfam) NF024135.5 PF12724.12 Flavodoxin_5 27 27 145 domain Y Y N flavodoxin domain-containing protein 28380286 131567 cellular organisms no rank 49950 EBI-EMBL Flavodoxin domain Flavodoxin domain This is a family of flavodoxins. Flavodoxins are electron transfer proteins that carry a molecule of non-covalently bound FMN. (from Pfam) NF024138.5 PF12727.12 PBP_like 27 27 193 domain Y Y N substrate-binding domain-containing protein 131567 cellular organisms no rank 55049 EBI-EMBL PBP superfamily domain PBP superfamily domain This family belongs to the periplasmic binding domain superfamily. It is often associated with a helix-turn-helix domain. (from Pfam) NF024139.5 PF12728.12 HTH_17 27 27 51 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 232663 EBI-EMBL Helix-turn-helix domain Helix-turn-helix domain This domain is a DNA-binding helix-turn-helix domain. (from Pfam) NF024140.5 PF12729.12 4HB_MCP_1 27 27 181 domain Y Y N MCP four helix bundle domain-containing protein 16306392 131567 cellular organisms no rank 146985 EBI-EMBL Four helix bundle sensory module for signal transduction Four helix bundle sensory module for signal transduction This family is a four helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors. This domain recognises citrate and TCA cycle intermediates, cis-aconitate, boric acid, Phenanthrene, pyrene and benzopyrene (Matilla et el., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 16306392. Four-helix bundle: a ubiquitous sensory module in prokaryotic signal transduction. Ulrich LE, Zhulin IB;. Bioinformatics. 2005;21:iii45-iii48. (from Pfam) NF024141.5 PF12730.12 ABC2_membrane_4 27 27 179 domain Y Y N ABC transporter permease 1303751 131567 cellular organisms no rank 120340 EBI-EMBL ABC-2 family transporter protein ABC transporter permease This family is related to the ABC-2 membrane transporter family Pfam:PF01061 [1]. [1]. 1303751. A new subfamily of bacterial ABC-type transport systems catalyzing export of drugs and carbohydrates. Reizer J, Reizer A, Saier MH Jr;. Protein Sci 1992;1:1326-1332. (from Pfam) NF024144.5 PF12733.12 Cadherin-like 24.2 24.2 89 domain Y Y N cadherin-like beta sandwich domain-containing protein 20056006 131567 cellular organisms no rank 12668 EBI-EMBL Cadherin-like beta sandwich domain Cadherin-like beta sandwich domain This domain is found in several bacterial, metazoan and chlorophyte algal proteins. A profile-profile comparison recovered the cadherin domain and a comparison of the predicted structure of this domain with the crystal structure of the cadherin showed a congruent seven stranded secondary structure. The domain is widespread in bacteria and seen in the firmicutes, actinobacteria, certain proteobacteria, bacteroides and chlamydiae with an expansion in Clostridium. In contrast, it is limited in its distribution in eukaryotes suggesting that it was derived through lateral transfer from bacteria. In prokaryotes, this domain is widely fused to other domains such as FNIII (Fibronectin Type III), TIG, SLH (S-layer homology), discoidin, cell-wall-binding repeat domain and alpha-amylase-like glycohydrolases. These associations are suggestive of a carbohydrate-binding function for this cadherin-like domain. In animal proteins it is associated with an ATP-grasp domain. [1]. 20056006. Novel eukaryotic enzymes modifying cell-surface biopolymers. Anantharaman V, Aravind L;. Biol Direct. 2010;5:1. (from Pfam) NF024151.5 PF12740.12 Chlorophyllase2 27 27 256 domain Y Y N chlorophyllase/cutinase-like alpha/beta fold protein GO:0050525,GO:0052689 20393707,22183084,24728714,25910960,28671263,30761732,33387709 131567 cellular organisms no rank 12878 EBI-EMBL Cutinase chlorophyllase/cutinase-like alpha/beta fold protein This family consists of bacterial cutinases (EC:3.1.1.74), which catalyse the hydrolysis of cutin, a polyester that forms the structure of plant cuticle [1,2]. These enzymes also show esterase activity towards p-nitrophenol-linked aliphatic esters [3,4]. Cutinase est2 can also depolymerize the synthetic polyesters poly(epsilon-caprolactone) (PCL), poly(butylene succinate-co-adipate) (PBSA), poly(butylene succinate) (PBS), and poly(lactic acid) (PLA) [5,6,7]. Members of this family are able to degrade the plastic poly(ethylene terephthalate) (PET). [1]. 24728714. Structural and functional studies on a thermostable polyethylene terephthalate degrading hydrolase from Thermobifida fusca. Roth C, Wei R, Oeser T, Then J, Follner C, Zimmermann W, Strater N;. Appl Microbiol Biotechnol. 2014;98:7815-7823. [2]. 28671263. Small cause, large effect: Structural characterization of cutinases from Thermobifida cellulosilytica. Ribitsch D, Hromic A, Zitzenbacher S, Zartl B, Gamerith C, Pellis A, Jungbauer A, Lyskowski A, Steinkellner G, Gruber K, Tscheliessnig R, Herrero Acero E, Guebitz GM;. Biotechnol Bioeng. 2017;114:2481-2488. [3]. 25910960. Comparison of genetic structures and biochemical properties of tandem cutinase-type polyesterases from Thermobifida alba AHK119. Thumarat U, Kawabata T, Nakajima M, Nakajima H, Sugiyama A, Yazaki K, Tada T, Waku T, Tanaka N, Kawai F;. J Biosci Bioeng. 2015;120:491-497. [4]. 33387709. Decolorization of molasses alcohol wastewater by thermophilic hydrolase with practical application value. Zhang Z, Wang W, Li D, Xiao J, Wu L, Geng X, Wu G, Zeng Z, Hu J;. Bioresour Technol. 2021;323:124609. [5]. 2039. TRUNCATED at 1650 bytes (from Pfam) NF024156.5 PF12745.12 HGTP_anticodon2 24.4 24.4 261 domain Y N N Anticodon binding domain of tRNAs 131567 cellular organisms no rank 169 EBI-EMBL Anticodon binding domain of tRNAs Anticodon binding domain of tRNAs This is an HGTP_anticodon binding domain, found largely on Gcn2 proteins which bind tRNA to down regulate translation in certain stress situations. (from Pfam) NF024157.5 PF12746.12 GNAT_acetyltran 26 26 243 domain Y Y N GNAT family N-acetyltransferase 2.3.1.- 131567 cellular organisms no rank 25592 EBI-EMBL GNAT acetyltransferase GNAT family N-acetyltransferase Many of the members are annotated s being Zwittermicin A resistance proteins, whereas others are listed as being GNAT acetyltransferases. The family has similarities to the GNAT acetyltransferase family. (from Pfam) NF024170.5 PF12760.12 Zn_Tnp_IS1595 25.4 25.4 46 domain Y Y N transposase 131567 cellular organisms no rank 13521 EBI-EMBL Transposase zinc-ribbon domain Transposase zinc-ribbon domain This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It is likely a zinc-binding beta ribbon domain that could bind the DNA. (from Pfam) NF024172.5 PF12762.12 DDE_Tnp_IS1595 27 27 153 domain Y Y N transposase 131567 cellular organisms no rank 27023 EBI-EMBL ISXO2-like transposase domain ISXO2-like transposase domain This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2. (from Pfam) NF024175.5 PF12765.12 Cohesin_HEAT 21 8.9 42 domain Y N N HEAT repeat associated with sister chromatid cohesion 11042144 131567 cellular organisms no rank 833 EBI-EMBL HEAT repeat associated with sister chromatid cohesion HEAT repeat associated with sister chromatid cohesion This HEAT repeat is found most frequently in sister chromatid cohesion proteins such as Nipped-B. HEAT repeats are found tandemly repeated in many proteins, and they appear to serve as flexible scaffolding on which other components can assemble. [1]. 11042144. HEAT repeats associated with condensins, cohesins, and other complexes involved in chromosome-related functions. Neuwald AF, Hirano T;. Genome Res. 2000;10:1445-1452. (from Pfam) NF024176.5 PF12766.12 Pyridox_oxase_2 26 26 100 domain Y N N Pyridoxamine 5'-phosphate oxidase GO:0010181 12686112,12824491 131567 cellular organisms no rank 32367 EBI-EMBL Pyridoxamine 5'-phosphate oxidase Pyridoxamine 5'-phosphate oxidase Pyridoxamine 5'-phosphate oxidase catalyses the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP), the terminal step in the de novo biosynthesis of PLP in Escherichia coli and part of the salvage pathway of this coenzyme in both E. coli and mammalian cells. This region is the flavoprotein FMN-binding domain. [1]. 12686112. Structure and mechanism of Escherichia coli pyridoxine 5'-phosphate oxidase. di Salvo ML, Safo MK, Musayev FN, Bossa F, Schirch V;. Biochim Biophys Acta. 2003;1647:76-82. [2]. 12824491. Structure and properties of recombinant human pyridoxine 5'-phosphate oxidase. Musayev FN, Di Salvo ML, Ko TP, Schirch V, Safo MK;. Protein Sci. 2003;12:1455-1463. (from Pfam) NF024179.5 PF12769.12 PNTB_4TM 26.2 26.2 85 PfamEq Y Y N proton-translocating transhydrogenase family protein 131567 cellular organisms no rank 31676 EBI-EMBL 4TM region of pyridine nucleotide transhydrogenase, mitoch proton-translocating transhydrogenase family protein PNTB_4TM is the region upstream of family PNTB, Pfam:PF02233, that carries four of this transporters transmembrane regions. PNTB is the beta-subunit of pyridine nucleotide transhydrogenase. This family forms part of the Proton-translocating Transhydrogenase (PTH) Family. (from Pfam) NF024180.5 PF12770.12 CHAT 24 24 289 domain Y Y N CHAT domain-containing protein 11835511 131567 cellular organisms no rank 73872 EBI-EMBL CHAT domain CHAT domain These proteins appear to be related to peptidases in peptidase clan CD that includes the caspases. This domain has been termed the CHAT domain for Caspase HetF Associated with Tprs. This family has been identified as a sister group to the separins [1]. [1]. 11835511. Classification of the caspase-hemoglobinase fold: detection of new families and implications for the origin of the eukaryotic separins. Aravind L, Koonin EV;. Proteins. 2002;46:355-367. (from Pfam) NF024183.5 PF12773.12 DZR 27.3 27.3 45 domain Y Y N double zinc ribbon domain-containing protein 131567 cellular organisms no rank 24582 EBI-EMBL Double zinc ribbon double zinc ribbon domain Members of this family contain at least one tandem pair of zinc ribbon domains. NF024189.5 PF12779.12 WXXGXW 18 7.5 26 repeat Y N N YXWGXW repeat-containing protein 22912595 131567 cellular organisms no rank 7999 EBI-EMBL WXXGXW repeat (2 copies) WXXGXW repeat (2 copies) This short repeat contains the motif WXXGXW where X can be any amino acid. It is generally found in 2-5 copies in short secreted bacterial proteins. Its precise function is as yet unknown, but evidence suggests that members of this family are important for the function of specific sub-types of two-partner secretion systems [1]. [1]. 22912595. The Burkholderia bcpAIOB genes define unique classes of two-partner secretion and contact dependent growth inhibition systems. Anderson MS, Garcia EC, Cotter PA;. PLoS Genet. 2012;8:e1002877. (from Pfam) NF024194.5 PF12784.12 PDDEXK_2 27.4 27.4 229 domain Y Y N PD-(D/E)XK nuclease family transposase 15972856 131567 cellular organisms no rank 37488 EBI-EMBL PD-(D/E)XK nuclease family transposase PD-(D/E)XK nuclease family transposase Members of this family belong to the PD-(D/E)XK nuclease superfamily [1]. These proteins are transposase proteins. [1]. 15972856. Identification of novel restriction endonuclease-like fold families among hypothetical proteins. Kinch LN, Ginalski K, Rychlewski L, Grishin NV;. Nucleic Acids Res. 2005;33:3598-3605. (from Pfam) NF024199.5 PF12789.12 PTR 27 7 60 repeat Y N N HTH motif repeat-containing protein 131567 cellular organisms no rank 1925 EBI-EMBL Phage tail repeat like Phage tail repeat like This family largely contains proteins from the eukaryote Trichomonas vaginalis. These proteins contain multiple HXH repeats. Some proteins in this family are annotated as having phage tail repeats. The function of this family is unknown. (from Pfam) NF024201.5 PF12791.12 RsgI_N 21.4 21.4 53 domain Y Y N anti-sigma factor domain-containing protein 11157964,17185538 131567 cellular organisms no rank 5162 EBI-EMBL Anti-sigma factor N-terminus anti-sigma factor domain-containing protein The heat shock genes in B. subtilis can be classified into several groups according to their regulation [1], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes [1]. Regulation of sigma factor I is carried out by RsgI from the same operon, and this N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) has been shown to interact directly with Sigma-I [2]. [1]. 11157964. Putative sigma factor SigI (YkoZ) of Bacillus subtilis is induced by heat shock. Zuber U, Drzewiecki K, Hecker M;. J Bacteriol. 2001;183:1472-1475. [2]. 17185538. Regulatory role of RsgI in sigI expression in Bacillus subtilis. Asai K, Ootsuji T, Obata K, Matsumoto T, Fujita Y, Sadaie Y;. Microbiology. 2007;153:92-101. (from Pfam) NF024206.5 PF12796.12 Ank_2 27.3 27.3 90 domain Y Y N ankyrin repeat domain-containing protein GO:0005515 131567 cellular organisms no rank 137972 EBI-EMBL Ankyrin repeats (3 copies) Ankyrin repeats (3 copies) NF024207.5 PF12797.12 Fer4_2 24.5 24.5 22 domain Y N N 4Fe-4S binding domain 131567 cellular organisms no rank 97760 EBI-EMBL 4Fe-4S binding domain 4Fe-4S binding domain This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. (from Pfam) NF024208.5 PF12798.12 Fer4_3 27 12.6 15 domain Y N N 4Fe-4S binding domain 131567 cellular organisms no rank 33249 EBI-EMBL 4Fe-4S binding domain 4Fe-4S binding domain This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. (from Pfam) NF024209.5 PF12799.12 LRR_4 27 27 44 domain Y Y N leucine-rich repeat domain-containing protein 7817399 131567 cellular organisms no rank 40167 EBI-EMBL Leucine Rich repeats (2 copies) Leucine Rich repeats (2 copies) Leucine rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. These repeats are usually involved in protein-protein interactions. Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains. Review of LRR proteins. [1]. 7817399. The leucine-rich repeat: a versatile binding motif. Kobe B, Deisenhofer J;. Trends Biochem Sci 1994;19:415-421. (from Pfam) NF024210.5 PF12800.12 Fer4_4 24 10 17 domain Y N N 4Fe-4S binding domain 131567 cellular organisms no rank 145719 EBI-EMBL 4Fe-4S binding domain 4Fe-4S binding domain This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. (from Pfam) NF024211.5 PF12801.12 Fer4_5 22 7 48 domain Y Y N 4Fe-4S binding protein 131567 cellular organisms no rank 69545 EBI-EMBL 4Fe-4S binding domain 4Fe-4S binding domain Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. (from Pfam) NF024212.5 PF12802.12 MarR_2 27 27 61 domain Y Y N MarR family transcriptional regulator GO:0003700,GO:0006355 11473263,9068629 131567 cellular organisms no rank 1046736 EBI-EMBL MarR family MarR family transcriptional regulator The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds [1]. The structure of MarR is known [2] and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif. [1]. 9068629. The Salmonella typhimurium mar locus: molecular and genetic analyses and assessment of its role in virulence. Sulavik MC, Dazer M, Miller PF;. J Bacteriol 1997;179:1857-1866. [2]. 11473263. The crystal structure of MarR, a regulator of multiple antibiotic resistance, at 2.3 A resolution. Alekshun MN, Levy SB, Mealy TR, Seaton BA, Head JF;. Nat Struct Biol 2001;8:710-714. (from Pfam) NF024214.5 PF12804.12 NTP_transf_3 27 27 160 domain Y Y N NTP transferase domain-containing protein 131567 cellular organisms no rank 569922 EBI-EMBL MobA-like NTP transferase domain MobA-like NTP transferase domain This family includes the MobA protein (Molybdopterin-guanine dinucleotide biosynthesis protein A). The family also includes a wide range of other NTP transferase domain. (from Pfam) NF024220.5 PF12810.12 Gly_rich 24.5 24.5 252 domain Y Y N glycine-rich protein 131567 cellular organisms no rank 3012 EBI-EMBL Glycine rich protein glycine-rich protein This family of proteins is greatly expanded in Trichomonas vaginalis. The proteins are composed of several glycine rich motifs interspersed through the sequence. Although many proteins have been annotated by similarity in the family these annotations given the biased composition of the sequences these are unlikely to be functionally relevant. (from Pfam) NF024221.5 PF12811.12 BaxI_1 26.2 22.3 233 PfamEq Y Y N Bax inhibitor-1/YccA family protein 12875974,18440869 131567 cellular organisms no rank 19520 EBI-EMBL Bax inhibitor 1 like Bax inhibitor-1/YccA family protein The Bax-inhibitor-1 region of the receptor molecules is conserved from bacteria to humans. [1]. 12875974. Bax inhibitor-1 is overexpressed in prostate cancer and its specific down-regulation by RNA interference leads to cell death in human prostate carcinoma cells. Grzmil M, Thelen P, Hemmerlein B, Schweyer S, Voigt S, Mury D, Burfeind P;. Am J Pathol. 2003;163:543-552. [2]. 18440869. Comparative genomics and function analysis on BI1 family. Zhou J, Zhu T, Hu C, Li H, Chen G, Xu G, Wang S, Zhou J, Ma D;. Comput Biol Chem. 2008;32:159-162. (from Pfam) NF024228.5 PF12819.12 Malectin_like 24.5 24.5 331 domain Y N N Malectin-like domain 18524852 131567 cellular organisms no rank 509 EBI-EMBL Malectin-like domain Malectin-like domain Malectin is a membrane-anchored protein of the endoplasmic reticulum that recognises and binds Glc2-N-glycan. The domain is found on a number of plant receptor kinases and is distantly related to malectin domains. [1]. 18524852. Malectin: a novel carbohydrate-binding protein of the endoplasmic reticulum and a candidate player in the early steps of protein N-glycosylation. Schallus T, Jaeckh C, Feher K, Palma AS, Liu Y, Simpson JC, Mackeen M, Stier G, Gibson TJ, Feizi T, Pieler T, Muhle-Goll C;. Mol Biol Cell. 2008;19:3404-3414. (from Pfam) NF024231.5 PF12822.12 ECF_trnsprt 30.7 30.7 169 subfamily Y Y N ECF transporter S component GO:0022857 18931129,21890906 131567 cellular organisms no rank 50698 EBI-EMBL ECF transporter, substrate-specific component ECF transporter S component Energy-coupling factor (ECF) transporters consist of a substrate-specific component (known as the S component), and an energy-coupling module [2]. The substrate-binding component is a small integral membrane protein which captures specific substrates and forms an active transporter in the presence of the energy-coupling AT module. [1]. 21890906. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Iyer LM, Zhang D, Rogozin IB, Aravind L;. Nucleic Acids Res. 2011; [Epub ahead of print]. [2]. 18931129. A novel class of modular transporters for vitamins in prokaryotes. Rodionov DA, Hebbeln P, Eudes A, ter Beek J, Rodionova IA, Erkens GB, Slotboom DJ, Gelfand MS, Osterman AL, Hanson AD, Eitinger T;. J Bacteriol. 2009;191:42-51. (from Pfam) NF024235.5 PF12826.12 HHH_2 27 27 64 domain Y Y N helix-hairpin-helix domain-containing protein 18439896,8692686 131567 cellular organisms no rank 136421 EBI-EMBL Helix-hairpin-helix motif Helix-hairpin-helix motif The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [2]. [1]. 8692686. The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. Doherty AJ, Serpell LC, Ponting CP;. Nucleic Acids Res 1996;24:2488-2497. [2]. 18439896. Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates. Witte G, Hartung S, Buttner K, Hopfner KP;. Mol Cell. 2008;30:167-178. (from Pfam) NF024240.5 PF12831.12 FAD_oxidored 27 27 416 domain Y Y N FAD-dependent oxidoreductase 131567 cellular organisms no rank 696820 EBI-EMBL FAD dependent oxidoreductase FAD-dependent oxidoreductase This family of proteins contains FAD dependent oxidoreductases and related proteins. (from Pfam) NF024241.5 PF12832.12 MFS_1_like 25.2 25.2 373 domain Y Y N MFS transporter 131567 cellular organisms no rank 257934 EBI-EMBL MFS_1 like family MFS transporter This family contains proteins related to the MFS superfamily. (from Pfam) NF024242.5 PF12833.12 HTH_18 33.6 33.6 80 domain Y Y N helix-turn-helix domain-containing protein GO:0003700,GO:0006355,GO:0043565 131567 cellular organisms no rank 1674966 EBI-EMBL Helix-turn-helix domain Helix-turn-helix domain NF024244.5 PF12835.12 Integrase_1 23 23 149 domain Y Y N integrase domain-containing protein 131567 cellular organisms no rank 9566 EBI-EMBL Integrase Integrase This is a family of DNA-binding prophage integrases found in Proteobacteria. (from Pfam) NF024245.5 PF12836.12 HHH_3 27 27 65 domain Y Y N helix-hairpin-helix domain-containing protein 18439896,8692686 131567 cellular organisms no rank 158361 EBI-EMBL Helix-hairpin-helix motif Helix-hairpin-helix motif The HhH domain is a short DNA-binding domain [2]. [1]. 8692686. The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. Doherty AJ, Serpell LC, Ponting CP;. Nucleic Acids Res 1996;24:2488-2497. [2]. 18439896. Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates. Witte G, Hartung S, Buttner K, Hopfner KP;. Mol Cell. 2008;30:167-178. (from Pfam) NF024246.5 PF12837.12 Fer4_6 25 24 24 domain Y N N 4Fe-4S binding domain 131567 cellular organisms no rank 210124 EBI-EMBL 4Fe-4S binding domain 4Fe-4S binding domain This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. (from Pfam) NF024247.5 PF12838.12 Fer4_7 27 27 52 domain Y Y N 4Fe-4S dicluster domain-containing protein 131567 cellular organisms no rank 515694 EBI-EMBL 4Fe-4S dicluster domain 4Fe-4S dicluster domain Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters. (from Pfam) NF024248.5 PF12840.12 HTH_20 27 27 51 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 462597 EBI-EMBL Helix-turn-helix domain helix-turn-helix domain-containing protein This domain represents a DNA-binding Helix-turn-helix domain found in transcriptional regulatory proteins. (from Pfam) NF024252.5 PF12844.12 HTH_19 30.2 30.2 64 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 339636 EBI-EMBL Helix-turn-helix domain helix-turn-helix domain-containing protein Members of this family contains a DNA-binding helix-turn-helix domain. This family contains many example antitoxins from bacterial toxin-antitoxin systems. These antitoxins are likely to be DNA-binding domains. (from Pfam) NF024254.5 PF12846.12 AAA_10 27.5 27.5 362 domain Y Y N ATP-binding protein 12533481,26884154 131567 cellular organisms no rank 28706 EBI-EMBL AAA-like domain AAA-like domain This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins, including VirB4 components of the Type IV secretory pathway and conjugal transfer protein TrbE. This entry includes the arcaheal Vir4/HerA homologue CedB [2], a membrane-bound protein that is highly induced upon UV treatment and essential for DNA transfer between Sulfolobus cells [2]. [1]. 12533481. The VirB4 family of proposed traffic nucleoside triphosphatases: common motifs in plasmid RP4 TrbE are essential for conjugation and phage adsorption. Rabel C, Grahn AM, Lurz R, Lanka E;. J Bacteriol. 2003;185:1045-1058. [2]. 26884154. The archaeal Ced system imports DNA. van Wolferen M, Wagner A, van der Does C, Albers SV;. Proc Natl Acad Sci U S A. 2016;113:2496-2501. (from Pfam) NF024255.5 PF12847.12 Methyltransf_18 27 27 151 domain Y Y N SAM-dependent methyltransferase 2.1.1.- 131567 cellular organisms no rank 34657 EBI-EMBL Methyltransferase domain Methyltransferase domain Protein in this family function as methyltransferases. (from Pfam) NF024256.5 PF12848.12 ABC_tran_Xtn 25.9 25.9 85 domain Y N N ABC transporter 131567 cellular organisms no rank 251573 EBI-EMBL ABC transporter ABC transporter This domain is an extension of some members of Pfam:PF00005 and other ABC-transporter families. (from Pfam) NF024257.5 PF12849.12 PBP_like_2 27 27 267 domain Y Y N substrate-binding domain-containing protein 131567 cellular organisms no rank 132298 EBI-EMBL PBP superfamily domain PBP superfamily domain This domain belongs to the periplasmic binding protein superfamily. (from Pfam) NF024258.5 PF12850.12 Metallophos_2 27 27 154 domain Y Y N metallophosphoesterase family protein 9685491 131567 cellular organisms no rank 188414 EBI-EMBL Calcineurin-like phosphoesterase superfamily domain Calcineurin-like phosphoesterase superfamily domain Members of this family are part of the Calcineurin-like phosphoesterase superfamily. [1]. 9685491. Phosphoesterase domains associated with DNA polymerases of diverse origins. Aravind L, Koonin EV;. Nucleic Acids Res 1998;26:3746-3752. (from Pfam) NF024260.5 PF12852.12 Cupin_6 26.7 26.7 183 domain Y Y N cupin domain-containing protein 131567 cellular organisms no rank 71847 EBI-EMBL Cupin Cupin This is a family of bacterial and eukaryotic proteins that belong to the Cupin superfamily. Some of the proteins in this family are annotated as being members of the AraC family of transcription factors, in which case this domain corresponds to the ligand binding domain. (from Pfam) NF024265.5 PF12857.12 TOBE_3 27 27 59 PfamEq Y Y N TOBE-like domain-containing protein 10829230 131567 cellular organisms no rank 15739 EBI-EMBL TOBE-like domain TOBE-like domain The TOBE domain [1] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (eg Swiss:P46930) and sulfate (Swiss:P16676). Found in ABC transporters immediately after the ATPase domain. [1]. 10829230. Protein fold recognition using sequence profiles and its application in structural genomics. Koonin EV, Wolf YI, Aravind L;. Adv Protein Chem 2000;54:245-275. (from Pfam) NF024267.5 PF12860.12 PAS_7 27 27 115 domain Y Y N PAS-domain containing protein 15009198,7756254,9301332,9382818 131567 cellular organisms no rank 76694 EBI-EMBL PAS fold PAS fold The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. [1]. 9301332. PAS domain S-boxes in archaea, bacteria and sensors for oxygen and redox. Zhulin IB, Taylor BL, Dixon R;. Trends Biochem Sci 1997;22:331-333. [2]. 7756254. 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore. Borgstahl GE, Williams DR, Getzoff ED;. Biochemistry 1995;34:6278-6287. [3]. 9382818. PAS: a multifunctional domain family comes to light. Ponting CP, Aravind L;. Curr Biol 1997;7:674-677. [4]. 15009198. The PAS fold: a redefination of the PAS domain based upon structural prediction. Hefti MH, Francoijs KJ, de Vries SC, Dixon R, Vervoort J;. Eur J Biochem 2004;271:1198-1208. (from Pfam) NF024269.5 PF12862.12 ANAPC5 23 3.9 91 domain Y N N Anaphase-promoting complex subunit 5 15082755,16896351,19584054 131567 cellular organisms no rank 9001 EBI-EMBL Anaphase-promoting complex subunit 5 Anaphase-promoting complex subunit 5 Apc5 is a subunit of the anaphase-promoting complex/cyclosome (APC/C) which is a multi-subunit ubiquitin ligase that mediates the proteolysis of cell cycle proteins in mitosis and G1. Apc5, although it does not harbour a classical RNA binding domain, Apc5 binds the poly(A) binding protein (PABP), which directly binds the internal ribosome entry site (IRES) of growth factor 2 mRNA. PABP was found to enhance IRES-mediated translation, whereas Apc5 over-expression counteracted this effect. In addition to its association with the APC/C complex, Apc5 binds much heavier complexes and co-sediments with the ribosomal fraction [1,2]. The N-terminus of Afi1 serves to stabilise the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC [3]. This region of the Apc5 member proteins carries a TPR-like motif. [1]. 15082755. The Apc5 subunit of the anaphase-promoting complex/cyclosome interacts with poly(A) binding protein and represses internal ribosome entry site-mediated translation. Koloteva-Levine N, Pinchasi D, Pereman I, Zur A, Brandeis M, Elroy-Stein O;. Mol Cell Biol. 2004;24:3577-3587. [2]. 16896351. The anaphase promoting complex/cyclosome: a machine designed to destroy. Peters JM;. Nat Rev Mol Cell Biol. 2006;7:644-656. [3]. 19584054. The transcription factor Atf1 binds and activates the APC/C ubiquitin ligase in fission yeast. Ors A, Grimaldi M, Kimata Y, Wilkinson CR, Jones N, Yamano H;. J Biol Chem. 2009;284:23989-23994. (from Pfam) NF024270.5 PF12863.12 DUF3821 23 23 204 domain Y Y N DUF3821 domain-containing protein 131567 cellular organisms no rank 352 EBI-EMBL Domain of unknown function (DUF3821) Domain of unknown function (DUF3821) This is a domain largely confined to sequences from Methanomicrobiales found on putative lipases. The function is not known. (from Pfam) NF024271.5 PF12864.12 DUF3822 24.9 24.9 241 PfamAutoEq Y Y N DUF3822 family protein 131567 cellular organisms no rank 6290 EBI-EMBL Protein of unknown function (DUF3822) DUF3822 family protein This is a family of uncharacterised bacterial proteins. However, structural-similarity searches indicate the family takes on an actin-like ATPase fold. (from Pfam) NF024273.5 PF12867.12 DinB_2 24.8 24.8 128 domain Y Y N DinB family protein 20208147 131567 cellular organisms no rank 275091 EBI-EMBL DinB superfamily DinB family protein The DinB family are an uncharacterised family of potential enzymes. The structure of these proteins is composed of a four helix bundle [1]. [1]. 20208147. The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily. Cooper DR, Grelewska K, Kim CY, Joachimiak A, Derewenda ZS;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:219-224. (from Pfam) NF024275.5 PF12869.12 tRNA_anti-like 23.5 23.5 146 domain Y Y N OB-fold protein 20944219 131567 cellular organisms no rank 4602 EBI-EMBL tRNA_anti-like OB-fold protein This is a family of bacterial, archeael and viral proteins that is related to the tRNA_anti family Pfam:PF01336. The major characteristic of families like tRNA_anti is their OB-fold, and many of them bind DNA. (from Pfam) NF024278.5 PF12872.12 OST-HTH 23.8 11 71 domain Y Y N OST-HTH/LOTUS domain-containing protein 20302647,20305267 131567 cellular organisms no rank 19181 EBI-EMBL OST-HTH/LOTUS domain OST-HTH/LOTUS domain A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood [1][2]. The domain adopts the winged helix-turn- helix fold and bind RNA with a potential specificity for dsRNA [1].In eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized RNase domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains [1]. [1]. 20302647. OST-HTH: a novel predicted RNA-binding domain. Anantharaman V, Zhang D, Aravind L;. Biol Direct. 2010;5:13. [2]. 20305267. LOTUS, a new domain associated with small RNA pathways in the germline. Callebaut I, Mornon JP;. Bioinformatics. 2010;26:1140-1144. (from Pfam) NF024282.5 PF12876.12 Cellulase-like 25 25 355 domain Y Y N cellulase-like family protein 131567 cellular organisms no rank 1512 EBI-EMBL Sugar-binding cellulase-like cellulase-like family protein This is a putative cellulase family. The structure is a TIM-barrel. (from Pfam) NF024294.5 PF12890.12 DHOase 21.2 21.2 142 PfamEq Y N N Dihydro-orotase-like 131567 cellular organisms no rank 35798 EBI-EMBL Dihydro-orotase-like Dihydro-orotase-like This is a small family of dihydro-orotase-like proteins from various bacteria. (from Pfam) NF024297.5 PF12893.12 Lumazine_bd_2 22.1 22.1 116 domain Y Y N nuclear transport factor 2 family protein 131567 cellular organisms no rank 15947 EBI-EMBL Putative lumazine-binding nuclear transport factor 2 family protein This is a family of uncharacterised proteins. However, the family belongs to the NTF2-like superfamily of various enzymes, and some of the members of the family are putative dehydrogenases. (from Pfam) NF024298.5 PF12894.12 ANAPC4_WD40 22.9 21.1 91 domain Y N N Anaphase-promoting complex subunit 4 WD40 domain 12049731,16896351,19584054 131567 cellular organisms no rank 26763 EBI-EMBL Anaphase-promoting complex subunit 4 WD40 domain Anaphase-promoting complex subunit 4 WD40 domain Apc4 contains an N-terminal propeller-shaped WD40 domain.The N-terminus of Afi1 serves to stabilise the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC, [1]. 12049731. The anaphase-promoting complex: proteolysis in mitosis and beyond. Peters JM;. Mol Cell. 2002;9:931-943. [2]. 16896351. The anaphase promoting complex/cyclosome: a machine designed to destroy. Peters JM;. Nat Rev Mol Cell Biol. 2006;7:644-656. [3]. 19584054. The transcription factor Atf1 binds and activates the APC/C ubiquitin ligase in fission yeast. Ors A, Grimaldi M, Kimata Y, Wilkinson CR, Jones N, Yamano H;. J Biol Chem. 2009;284:23989-23994. (from Pfam) NF024299.5 PF12895.12 ANAPC3 27.2 27.2 82 domain Y Y N CDC27 family protein 12049731,12956947,16896351 131567 cellular organisms no rank 32924 EBI-EMBL Anaphase-promoting complex, cyclosome, subunit 3 CDC27 family protein Apc3, otherwise known as Cdc27, is one of the subunits of the anaphase-promoting complex or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes [1, 2]. The protein members of this family contain TPR repeats just as those of Apc7 do, and it appears that these TPR units bind the C-termini of the APC co-activators CDH1 and CDC20 [3]. [1]. 12049731. The anaphase-promoting complex: proteolysis in mitosis and beyond. Peters JM;. Mol Cell. 2002;9:931-943. [2]. 16896351. The anaphase promoting complex/cyclosome: a machine designed to destroy. Peters JM;. Nat Rev Mol Cell Biol. 2006;7:644-656. [3]. 12956947. TPR subunits of the anaphase-promoting complex mediate binding to the activator protein CDH1. Vodermaier HC, Gieffers C, Maurer-Stroh S, Eisenhaber F, Peters JM;. Curr Biol. 2003;13:1459-1468. (from Pfam) NF024301.5 PF12897.12 Asp_aminotransf 27 27 421 domain Y N N Aspartate amino-transferase GO:0004069 27355211 131567 cellular organisms no rank 82388 EBI-EMBL Aspartate amino-transferase Aspartate amino-transferase These proteins catalyse the reversible transfer of an amino group from the amino acid substrate to an acceptor alpha-keto acid. They require pyridoxal 5'-phosphate (PLP) as a cofactor to catalyse this reaction. Trans-amination reactions are of central importance in amino acid metabolism and in links to carbohydrate and fat metabolism. This class of amino-transferases acts as dimers in a head-to-tail configuration. It has been demonstrated that these proteins are aspartate amino-transferases from Bacteria (Jansen, R.S. et al. Nat Commun 11, 1960 (2020)) [1]. [1]. 27355211. Structural Insights into a Novel Class of Aspartate Aminotransferase from Corynebacterium glutamicum. Son HF, Kim KJ;. PLoS One. 2016;11:e0158402. (from Pfam) NF024304.5 PF12900.12 Pyridox_ox_2 27 27 140 domain Y Y N pyridoxamine 5'-phosphate oxidase family protein 131567 cellular organisms no rank 94067 EBI-EMBL Pyridoxamine 5'-phosphate oxidase pyridoxamine 5'-phosphate oxidase family protein Pyridoxamine 5'-phosphate oxidase is a FMN flavoprotein that catalyses the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This entry contains several pyridoxamine 5'-phosphate oxidases, and related proteins. (from Pfam) NF024306.5 PF12902.12 Ferritin-like 22.3 22.3 221 domain Y Y N ferritin-like domain-containing protein 11075927,15100990 131567 cellular organisms no rank 8513 EBI-EMBL Ferritin-like ferritin-like domain This is a family of bacterial ferritin-like substances that also includes a C-terminal domain of VioB, polyketide synthase enzymes, that make up one of the key components of the violacein biosynthesis pathway. Violacein is a purple-coloured, broad-spectrum antibacterial pigment. [1]. 11075927. Sequence analysis and functional characterization of the violacein biosynthetic pathway from Chromobacterium violaceum. August PR, Grossman TH, Minor C, Draper MP, MacNeil IA, Pemberton JM, Call KM, Holt D, Osburne MS;. J Mol Microbiol Biotechnol. 2000;2:513-519. [2]. 15100990. Genetic analysis of violacein biosynthesis by Chromobacterium violaceum. Antonio RV, Creczynski-Pasa TB;. Genet Mol Res. 2004;3:85-91. (from Pfam) NF024307.5 PF12903.12 DUF3830 26 26 143 PfamAutoEq Y Y N DUF3830 family protein 131567 cellular organisms no rank 5896 EBI-EMBL Protein of unknown function (DUF3830) DUF3830 family protein This is a family of bacterial and archaeal proteins, the structure for one of whose members has been characterised. PDB:3kop from Swiss:A0JVT3 probably adopts a new hexameric form compared to previous structures. The putative active is near the domain interface. 3kop is most closely related, structurally to PDB:1zx8, where the potential active site is located near residues E51 and Y53 (conserved in 1zx8). Beyond the two residues above, the other residues are not conserved. Also the shape of the active site differs from that of 1zx8. PDB:1zx8 belongs to family DUF369. Pfam:PF04126, which is part of the cyclophilin-like clan. (from Pfam) NF024308.5 PF12904.12 Collagen_bind_2 22 22 92 domain Y Y N putative collagen-binding domain-containing protein 131567 cellular organisms no rank 4807 EBI-EMBL Putative collagen-binding domain of a collagenase Putative collagen-binding domain of a collagenase This domain is likely to be the collagen-binding domain of a family of bacterial collagenase enzymes. It is the C-terminal part of the PDB:3kzs structure determined from Swiss:Q8A905 (information derived from TOPSAN). (from Pfam) NF024309.5 PF12905.12 Glyco_hydro_101 25 25 272 domain Y Y N endo-alpha-N-acetylgalactosaminidase family protein GO:0033926 19788271,20556855 131567 cellular organisms no rank 10362 EBI-EMBL Endo-alpha-N-acetylgalactosaminidase endo-alpha-N-acetylgalactosaminidase family protein Virulence of pathogenic organisms such as the Gram-positive Streptococcus pneumoniae is largely determined by the ability to degrade host glycoproteins and to metabolise the resultant carbohydrates. This family is the enzymatic region, EC:3.2.1.97, of the cell surface proteins that specifically cleave Gal-beta-1,3-GalNAc-alpha-Ser/Thr (T-antigen, galacto-N-biose), the core 1 type O-linked glycan common to mucin glycoproteins. This reaction is exemplified by the S. pneumoniae protein Swiss:B2DRU5, where Asp764 is the catalytic nucleophile-base and Glu796 the catalytic proton donor. [1]. 19788271. Mechanistic investigation of the endo-alpha-N-acetylgalactosaminidase from Streptococcus pneumoniae R6. Willis LM, Zhang R, Reid A, Withers SG, Wakarchuk WW;. Biochemistry. 2009;48:10334-10341. [2]. 20556855. Gh101 family of glycoside hydrolases: subfamily structure and evolutionary connections with other families. Naumoff DG;. J Bioinform Comput Biol. 2010;8:437-451. (from Pfam) NF024313.5 PF12911.12 OppC_N 23.9 23.9 53 domain Y N N N-terminal TM domain of oligopeptide transport permease C 1738314 131567 cellular organisms no rank 225226 EBI-EMBL N-terminal TM domain of oligopeptide transport permease C N-terminal TM domain of oligopeptide transport permease C Oligopeptide permeases (Opp) have been identified in numerous gram-negative and -positive bacteria. These transport systems belong to the superfamily of highly conserved ATP-binding cassette transporters. Typically, Opp importers comprise a complex of five proteins. The oligopeptide-binding protein OppA is responsible for the capture of peptides from the external medium. Two integral highly hydrophobic membrane spanning proteins, OppB and OppC, form a channel through the membrane used for peptide translocation. This N-terminal domain appears to be the first TM domain of the molecule [1]. [1]. 1738314. Membrane topology of the integral membrane components, OppB and OppC, of the oligopeptide permease of Salmonella typhimurium. Pearce SR, Mimmack ML, Gallagher MP, Gileadi U, Hyde SC, Higgins CF;. Mol Microbiol. 1992;6:47-57. (from Pfam) NF024318.5 PF12916.12 DUF3834 22 22 202 domain Y Y N DUF3834 domain-containing protein 131567 cellular organisms no rank 236 EBI-EMBL Protein of unknown function (DUF3834) Protein of unknown function (DUF3834) This family is likely to be related to solute-binding lipo-proteins. (from Pfam) NF024319.5 PF12917.12 YfbR-like 25.9 25.9 182 domain Y Y N YfbR-like 5'-deoxynucleotidase 15489502,15808744,17827303,18353368,33926954 131567 cellular organisms no rank 33590 EBI-EMBL 5'-deoxynucleotidase YfbR-like YfbR-like 5'-deoxynucleotidase This entry contains Escherichia coli (strain K12) YfbR. It a 5'-deoxynucleotidase that functions as a dCMP phosphohydrolase in a salvage pathway for the synthesis of dUMP in a dcd/deoA mutant [1]. YfbR contains a conserved HD domain [2]. YfbR has phosphatase activity with deoxyribonucleoside 5'-monophosphates and does not hydrolyze ribonucleotides or deoxyribonucloside 3'-monophosphates [2,3]. Crystal structures of YfbR have been solved, it was suggested that the biological unit is a dimer [4]. This family also includes phage HD domain-containing hydrolase-like enzymes, such as A0A2H5BHG9 and A0A2L0V156 from Acinetobacter phage SH-Ab15497 [5], which are associated with PurZ, an enzyme that catalyses the synthesis of diaminopurine (Z), a DNA modification that gives phages an advantage for evading host restriction enzymes activity. They have 2'-deoxyadenine 5'-triphosphate triphosphohydrolase (dATPase) activity and catalyse the hydrolysis of 2'-deoxyadenine 5'-triphosphate dATP to 2'-deoxyadenine (dA) and triphosphate. These enzymes are highly specific for dATP and also catalyse the hydrolysis of dADP and dAMP into dA, releasing pyrophosphate and phosphate, respectively. Thus, these dATPases facilitate the synthesis of Z-genome synthesis removing dATP and dADP from the nucleotide pool of the host [5]. [1]. 17827303. The deoxycytidine pathway for thymidylate synthesis in Escherichia coli. Weiss B;. J Bacteriol. 2007;189:7922-7926. [2]. 15489502. General enzymatic screens identify three new nucleotidases in Escherichia coli. Biochemical characterization of SurE, YfbR, and YjjG. Proudfoot M, Kuznetsova E, Brown G, Rao NN, Kita. TRUNCATED at 1650 bytes (from Pfam) NF024329.5 PF12927.12 DUF3835 21 7.9 78 domain Y Y N DUF3835 domain-containing protein 131567 cellular organisms no rank 4 EBI-EMBL Domain of unknown function (DUF3835) Domain of unknown function (DUF3835) This is a C-terminal domain conserved in fungi. (from Pfam) NF024352.5 PF12950.12 TaqI_C 27.6 27.6 118 domain Y Y N TaqI-like C-terminal specificity domain-containing protein 11175899 131567 cellular organisms no rank 14512 EBI-EMBL TaqI-like C-terminal specificity domain TaqI-like C-terminal specificity domain This domain is found at the C-terminus of the TaqI protein and is involved in DNA-binding and substrate recognition. (from Pfam) NF024355.5 PF12953.12 DUF3842 28.5 28.5 130 domain Y Y N DUF3842 family protein 131567 cellular organisms no rank 1578 EBI-EMBL Domain of unknown function (DUF3842) DUF3842 family protein This short protein is found mainly in firmicute bacteria. It is functionally uncharacterised. (from Pfam) NF024359.5 PF12957.12 DUF3846 27.5 27.5 91 domain Y Y N DUF3846 domain-containing protein 20532204 131567 cellular organisms no rank 4691 EBI-EMBL Domain of unknown function (DUF3846) Domain of unknown function (DUF3846) A family of uncharacterized proteins found by clustering human gut metagenomic sequences [1]. This domain is found associated with an Pfam:PF07275 like domain. This suggests that this family may also be involved in evading host restriction. [1]. 20532204. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. Ellrott K, Jaroszewski L, Weizhong L, Wooley J, Godzik, A. PLoS Computational Biology, 2010 (from Pfam) NF024362.5 PF12960.12 DUF3849 25 25 123 domain Y Y N DUF3849 domain-containing protein 20532204 131567 cellular organisms no rank 1700 EBI-EMBL Protein of unknown function (DUF3849) Protein of unknown function (DUF3849) A family of uncharacterized proteins found by clustering human gut metagenomic sequences [1]. This domain frequently seen with DUF3848. [1]. 20532204. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. Ellrott K, Jaroszewski L, Weizhong L, Wooley J, Godzik, A. PLoS Computational Biology, 2010 (from Pfam) NF024363.5 PF12961.12 DUF3850 22.9 22.9 77 domain Y Y N DUF3850 domain-containing protein 16322048 131567 cellular organisms no rank 4924 EBI-EMBL Domain of unknown function (DUF3850) Domain of unknown function (DUF3850) The search results from NCBI sequence alignment indicates a conserved domain belonging to ASCH superfamily [1]. Dali searching results show that the protein is a structurally similar to the PUA domain, suggesting it may be involved in RNA recognition. It has been reported that the deletion of PUA genes results in impaired growth (RluD) and competitive disadvantage (TruB) in Escherichia coli. Suggestions have been put forward that, apart from their usual catalytic role, certain PUS enzymes (e.g. TruB) may also act as chaperones for RNA folding. The interface interaction indicates that the biomolecule of protein NP_809782.1 should be a dimer. [1]. 16322048. The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism. Iyer LM, Burroughs AM, Aravind L;. Bioinformatics. 2005; [Epub ahead of print]DR SCOP; 88697; (from Pfam) NF024367.5 PF12965.12 DUF3854 23 23 130 domain Y Y N DUF3854 domain-containing protein 20532204 131567 cellular organisms no rank 4205 EBI-EMBL Domain of unknown function (DUF3854) Domain of unknown function (DUF3854) A family of uncharacterised proteins found by clustering human gut metagenomic sequences [1]. This domain is likely to be related to the Toprim domain. [1]. 20532204. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. Ellrott K, Jaroszewski L, Weizhong L, Wooley J, Godzik, A. PLoS Computational Biology, 2010 (from Pfam) NF024368.5 PF12966.12 AtpR 26 26 86 domain Y Y N ATP synthase subunit I 20472544 131567 cellular organisms no rank 1993 EBI-EMBL N-ATPase, AtpR subunit ATP synthase subunit I Membrane protein with three predicted transmembrane segments, two of which contain conserved Arg residues. AtpR genes are found in the N-ATPase (archaeal-type F1-Fo-ATPase) operons and are predicted to interact with the conserved Glu/Asp residues in the c subunits, regulating the assembly and/or function of the membrane-embedded ring of 'c' (proteolipid) subunits (PFAM:PF00137). [1]. 20472544. Characterization of the N-ATPase, a distinct, laterally transferred Na+-translocating form of the bacterial F-type membrane ATPase. Dibrova DV, Galperin MY, Mulkidjanian AY;. Bioinformatics. 2010; [Epub ahead of print] (from Pfam) NF024370.5 PF12968.12 DUF3856 27 27 143 PfamAutoEq Y Y N DUF3856 domain-containing protein 131567 cellular organisms no rank 88 EBI-EMBL Domain of Unknown Function (DUF3856) Domain of Unknown Function (DUF3856) TPR-like protein. The 2hr2 structure belongs to the SCOP all alpha class, TPR-like superfamily, CT2138-like family. A DALI search gives hits with the putative peptidyl-prolyl isomerase 2fbn (Z=16), the SGTA protein (Z=16), the PLCR protein 2qfc (Z=16), a putative FK506-binding protein (PDB:1qz2-A; DALI Z-score 15.3; RMSD 2.9; 16% sequence identity within 132 superimposed residues), and with the tetratricopeptide repeats of the protein phosphatase 5 (PDB:2bug; DALI Z-score 15.1; RMSD 2.5; 19% sequence identity within 117 superimposed residues). (from Pfam) NF024373.5 PF12971.12 NAGLU_N 28.3 28.3 82 domain Y Y N alpha-N-acetylglucosaminidase N-terminal domain-containing protein 10588735,12049639,18443291 131567 cellular organisms no rank 10317 EBI-EMBL Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate [1]. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations [2]. The structure shows that the enzyme is composed of three domains. This N-terminal domain has an alpha-beta fold [3]. [1]. 10588735. Mouse model of Sanfilippo syndrome type B produced by targeted disruption of the gene encoding alpha-N-acetylglucosaminidase. Li HH, Yu WH, Rozengurt N, Zhao HZ, Lyons KM, Anagnostaras S, Fanselow MS, Suzuki K, Vanier MT, Neufeld EF;. Proc Natl Acad Sci U S A 1999;96:14505-14510. [2]. 12049639. Correction of mucopolysaccharidosis type IIIb fibroblasts by lentiviral vector-mediated gene transfer. Villani GR, Follenzi A, Vanacore B, Di Domenico C, Naldini L, Di Natale P;. Biochem J 2002;364:747-753. [3]. 18443291. Structural and mechanistic insight into the basis of mucopolysaccharidosis IIIB. Ficko-Blean E, Stubbs KA, Nemirovsky O, Vocadlo DJ, Boraston AB;. Proc Natl Acad Sci U S A. 2008;105:6560-6565. (from Pfam) NF024374.5 PF12972.12 NAGLU_C 25 25 268 domain Y Y N alpha-N-acetylglucosaminidase C-terminal domain-containing protein 10588735,12049639,18443291 131567 cellular organisms no rank 10736 EBI-EMBL Alpha-N-acetylglucosaminidase (NAGLU) C-terminal domain Alpha-N-acetylglucosaminidase (NAGLU) C-terminal domain Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate [1]. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations [2]. The structure shows that the enzyme is composed of three domains. This C-terminal domain has an all alpha helical fold [3]. [1]. 10588735. Mouse model of Sanfilippo syndrome type B produced by targeted disruption of the gene encoding alpha-N-acetylglucosaminidase. Li HH, Yu WH, Rozengurt N, Zhao HZ, Lyons KM, Anagnostaras S, Fanselow MS, Suzuki K, Vanier MT, Neufeld EF;. Proc Natl Acad Sci U S A 1999;96:14505-14510. [2]. 12049639. Correction of mucopolysaccharidosis type IIIb fibroblasts by lentiviral vector-mediated gene transfer. Villani GR, Follenzi A, Vanacore B, Di Domenico C, Naldini L, Di Natale P;. Biochem J 2002;364:747-753. [3]. 18443291. Structural and mechanistic insight into the basis of mucopolysaccharidosis IIIB. Ficko-Blean E, Stubbs KA, Nemirovsky O, Vocadlo DJ, Boraston AB;. Proc Natl Acad Sci U S A. 2008;105:6560-6565. (from Pfam) NF024375.5 PF12973.12 Cupin_7 27 27 105 domain Y Y N cupin domain-containing protein 131567 cellular organisms no rank 43939 EBI-EMBL ChrR Cupin-like domain ChrR Cupin-like domain Members of this family are part of the cupin superfamily. This family includes the transcriptional activator ChrR Swiss:P40685. (from Pfam) NF024376.5 PF12974.12 Phosphonate-bd 27 27 242 domain Y Y N PhnD/SsuA/transferrin family substrate-binding protein 131567 cellular organisms no rank 242438 EBI-EMBL ABC transporter, phosphonate, periplasmic substrate-binding protein PhnD/SsuA/transferrin family substrate-binding protein This is a family of periplasmic proteins which are part of the transport system for alkylphosphonate uptake. (from Pfam) NF024387.5 PF12985.12 DUF3869 24.5 24.5 85 domain Y Y N DUF3869 domain-containing protein 131567 cellular organisms no rank 560 EBI-EMBL Domain of unknown function (DUF3869) Domain of unknown function (DUF3869) A family based on the N-terminal domain of 3KOG, which shows weak but consistent remote homology with adhesive families such as immunoglobulins and cadherins, suggesting it might form an attachment module. (from Pfam) NF024398.5 PF12996.12 DUF3880 25.2 25.2 78 domain Y Y N DUF3880 domain-containing protein 19321416 131567 cellular organisms no rank 7550 EBI-EMBL DUF based on E. rectale Gene description (DUF3880) DUF based on E. rectale Gene description (DUF3880) Based on Eubacterium rectale gene EUBREC_3218. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14737), It appears to be upregulated in the presence of Bacteroides thetaiotaomicron vs when isolated in culture [1]. [1]. 19321416. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ et al. Proc Natl Acad Sci U S A 2009 Apr 7;106(14):5859-64. (from Pfam) NF024399.5 PF12997.12 DUF3881 27 27 283 PfamAutoEq Y Y N DUF3881 family protein 19321416 131567 cellular organisms no rank 1012 EBI-EMBL Domain of unknown function, E. rectale Gene description (DUF3881) DUF3881 family protein Based on Eubacterium rectale gene EUBREC_3695. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14737), it appears to be upregulated in the presence of Bacteroides thetaiotaomicron vs when isolated in culture [1]. [1]. 19321416. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ et al. Proc Natl Acad Sci U S A 2009 Apr 7;106(14):5859-64. (from Pfam) NF024405.5 PF13004.12 BACON 25 18 61 domain Y Y N BACON domain-containing protein 20416301,24463512 131567 cellular organisms no rank 18860 EBI-EMBL Putative binding domain, N-terminal BACON domain The BACON (Bacteroidetes-Associated Carbohydrate-binding Often N-terminal) domain is an all-beta domain found in diverse architectures, principally in combination with carbohydrate-active enzymes and proteases. These architectures suggest a carbohydrate-binding function which is also supported by the nature of BACON's few conserved amino-acids. The phyletic distribution of BACON and other data tentatively suggest that it may frequently function to bind mucin [1]. Further work with the characterised structure of a member of glycoside hydrolase family 5 enzyme, PDB:3ZMR, has found no evidence for carbohydrate-binding for this domain [2]. [1]. 20416301. Mining metagenomic data for novel domains: BACON, a new carbohydrate-binding module. Mello LV, Chen X, Rigden DJ;. FEBS Lett. 2010;584:2421-2426. [2]. 24463512. A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes. Larsbrink J, Rogers TE, Hemsworth GR, McKee LS, Tauzin AS, Spadiut O, Klinter S, Pudlo NA, Urs K, Koropatkin NM, Creagh AL, Haynes CA, Kelly AG, Cederholm SN, Davies GJ, Martens EC, Brumer H;. Nature. 2014;506:498-502. (from Pfam) NF024406.5 PF13005.12 zf-IS66 27.3 27.3 46 domain Y Y N IS66 family transposase zinc-finger binding domain-containing protein 11418571 131567 cellular organisms no rank 48367 EBI-EMBL zinc-finger binding domain of transposase IS66 zinc-finger binding domain of transposase IS66 This is a zinc-finger region of the N-terminus of the insertion element IS66 transposase. [1]. 11418571. Structural and functional characterization of IS679 and IS66-family elements. Han CG, Shiga Y, Tobe T, Sasakawa C, Ohtsubo E;. J Bacteriol 2001;183:4296-4304. (from Pfam) NF024412.5 PF13011.11 LZ_Tnp_IS481 22.2 22.2 85 domain Y Y N leucine zipper domain-containing protein 17065269 131567 cellular organisms no rank 21769 EBI-EMBL leucine-zipper of insertion element IS481 leucine zipper domain, IS481 transposase-type This is the upstream region of the conjoined ORF AB of insertion element 481. The significance of IS481 in the detection of Bordetella pertussis is discussed in [1]. The B portion of the ORF AB carries the transposase activity in family rve, PFAM:PF00665. [1]. 17065269. Prevalence and sequence variants of IS481 in Bordetella bronchiseptica: implications for IS481-based detection of Bordetella pertussis. Register KB, Sanden GN;. J Clin Microbiol. 2006;44:4577-4583. (from Pfam) NF024420.5 PF13020.11 NOV_C 22.1 22.1 91 domain Y Y N protein NO VEIN domain-containing protein 15266054,20729639,22638584 131567 cellular organisms no rank 16223 EBI-EMBL Protein NO VEIN, C-terminal Protein NO VEIN, C-terminal This domain of unknown function is found at the C-terminal of Protein NO VEIN from Arabidopsis, a protein essential for cell fate determination during embryogenesis [2]. It mediates this process through an auxin-dependent pathway [3]. This domain is also found in some restriction endonucleases. [1]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. [2]. 15266054. Identification of genes required for embryo development in Arabidopsis. Tzafrir I, Pena-Muralla R, Dickerman A, Berg M, Rogers R, Hutchens S, Sweeney TC, McElver J, Aux G, Patton D, Meinke D;. Plant Physiol. 2004;135:1206-1220. [3]. 20729639. NO VEIN facilitates auxin-mediated development in Arabidopsis. Tsugeki R, Ditengou FA, Palme K, Okada K;. Plant Signal Behav. 2010;5:1249-1251. (from Pfam) NF024422.5 PF13022.11 HTH_Tnp_1_2 27.9 27.9 122 domain Y Y N phBC6A51 family helix-turn-helix protein 131567 cellular organisms no rank 2930 EBI-EMBL Helix-turn-helix of insertion element transposase phBC6A51 family helix-turn-helix protein This is a family of largely phage proteins which are likely to be a helix-turn-helix insertion elements. (from Pfam) NF024423.5 PF13023.11 HD_3 22.5 22.5 165 domain Y Y N HD domain-containing protein 9868367 131567 cellular organisms no rank 32220 EBI-EMBL HD domain HD domain HD domains are metal dependent phosphohydrolases. [1]. 9868367. The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Aravind L, Koonin EV;. Trends Biochem Sci 1998;23:469-472. (from Pfam) NF024426.5 PF13026.11 DUF3887 31.8 31.8 91 domain Y Y N DUF3887 domain-containing protein 131567 cellular organisms no rank 5876 EBI-EMBL Protein of unknown function (DUF3887) Protein of unknown function (DUF3887) This domain family is found in bacteria and archaea, and is approximately 90 amino acids in length. (from Pfam) NF024427.5 PF13027.11 DUF3888 22.2 21.8 87 domain Y Y N DUF3888 domain-containing protein 131567 cellular organisms no rank 3499 EBI-EMBL Protein of unknown function (DUF3888) Protein of unknown function (DUF3888) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 111 and 149 amino acids in length. (from Pfam) NF024430.5 PF13030.11 DUF3891 24 24 219 PfamAutoEq Y Y N DUF3891 family protein 131567 cellular organisms no rank 3540 EBI-EMBL Protein of unknown function (DUF3891) DUF3891 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 250 amino acids in length. (from Pfam) NF024431.5 PF13031.11 DUF3892 22.3 22.3 71 domain Y Y N DUF3892 domain-containing protein 32868406 131567 cellular organisms no rank 6635 EBI-EMBL Protein of unknown function (DUF3892) Protein of unknown function (DUF3892) DUF3892 is related to the truncated RNaseH fold-containing ribosome hibernation factors. Predicted to function as a possible conflict effector domain at the ribosome, based on comparable genome contextual associations with DUF2188, including repeated association with nucleotide-activated effector conflict systems [1]. [1]. 32868406. Identification of Uncharacterized Components of Prokaryotic Immune Systems and Their Diverse Eukaryotic Reformulations. Burroughs AM, Aravind L;. J Bacteriol. 2020; [Epub ahead of print] (from Pfam) NF024441.5 PF13041.11 PPR_2 30 30 50 domain Y N N PPR repeat family 10664580 131567 cellular organisms no rank 63 EBI-EMBL PPR repeat family PPR repeat family This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR [1]. [1]. 10664580. The PPR motif - a TPR-related motif prevalent in plant organellar proteins. Small ID, Peeters I;. Trends Biochem Sci 2000;25:45-47. (from Pfam) NF024472.5 PF13072.11 MciZ 22.2 22.2 37 PfamAutoEq Y Y N Z-ring formation inhibitor MciZ mciZ 25848052 131567 cellular organisms no rank 1272 EBI-EMBL Mother cell inhibitor of FtsZ Z-ring formation inhibitor MciZ This family of proteins is found in bacteria. Family members are approximately 40 amino acids in length. There is a conserved GKAW sequence motif. There is a single completely conserved residue G that may be functionally important. Family members include the Bacillus subtilis cell-division inhibitor, MciZ (mother cell inhibitor of FtsZ) which blocks the assembly of FtsZ. FtsZ (filamentation temperature-sensitive Z) is the bacterial homolog of tubulin. Crystal structure reveals that MciZ binds to the C-terminal polymerization interface of FtsZ, the equivalent of the minus end of tubulin, causing shortening of protofilaments and blocking the assembly of higher-order FtsZ structures. Hence, MciZ provides a capping-based regulatory mechanism for FtsZ [1]. [1]. 25848052. FtsZ filament capping by MciZ, a developmental regulator of bacterial division. Bisson-Filho AW, Discola KF, Castellen P, Blasios V, Martins A, Sforca ML, Garcia W, Zeri AC, Erickson HP, Dessen A, Gueiros-Filho FJ;. Proc Natl Acad Sci U S A. 2015;112:E2130-E2138. (from Pfam) NF024485.5 PF13085.11 Fer2_3 27 27 107 domain Y Y N 2Fe-2S iron-sulfur cluster-binding protein GO:0009055,GO:0051536 131567 cellular organisms no rank 82756 EBI-EMBL 2Fe-2S iron-sulfur cluster binding domain 2Fe-2S iron-sulfur cluster-binding domain The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which abeta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. (from Pfam) NF024486.5 PF13086.11 AAA_11 27 27 257 domain Y Y N AAA domain-containing protein GO:0004386 131567 cellular organisms no rank 87049 EBI-EMBL AAA domain AAA domain family 11 This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. (from Pfam) NF024487.5 PF13087.11 AAA_12 27 27 195 domain Y Y N AAA domain-containing protein 131567 cellular organisms no rank 84261 EBI-EMBL AAA domain AAA domain This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. (from Pfam) NF024488.5 PF13088.11 BNR_2 31.4 31.4 277 domain Y Y N exo-alpha-sialidase 3.2.1.18 131567 cellular organisms no rank 49125 EBI-EMBL BNR repeat-like domain BNR repeat-like domain This family of proteins contains BNR-like repeats suggesting these proteins may act as sialidases. (from Pfam) NF024489.5 PF13089.11 PP_kinase_N 23.8 23.8 107 domain Y N N Polyphosphate kinase N-terminal domain 131567 cellular organisms no rank 64713 EBI-EMBL Polyphosphate kinase N-terminal domain Polyphosphate kinase N-terminal domain Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. (from Pfam) NF024490.5 PF13090.11 PP_kinase_C 25.8 25.8 172 domain Y N N Polyphosphate kinase C-terminal domain 2 15947782 131567 cellular organisms no rank 65499 EBI-EMBL Polyphosphate kinase C-terminal domain 2 Polyphosphate kinase C-terminal domain 2 Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C2-terminal domain has a structure similar to phospholipase D. It is one of two closely related carboxy-terminal domains (C1 and C2 domains). Both the C1 and C2 domains (residues 322-502 and 503-687, respectively) consist of a sevenstranded mixed beta-sheet flanked by five alpha-helices. However, the structural topology and relative orientations of the helices to the beta-sheet in these two domains are different. The C1 and C2 domains are highly conserved in the PPK family. Some of the residues previously shown to be crucial for the enzyme catalytic activity are located in these two domains [1]. [1]. 15947782. Crystal structure of a polyphosphate kinase and its implications for polyphosphate synthesis. Zhu Y, Huang W, Lee SS, Xu W;. EMBO Rep. 2005;6:681-687. (from Pfam) NF024491.5 PF13091.11 PLDc_2 27 27 132 domain Y Y N phospholipase D-like domain-containing protein 131567 cellular organisms no rank 251400 EBI-EMBL PLD-like domain phospholipase D-like domain NF024498.5 PF13098.11 Thioredoxin_2 27 27 104 domain Y Y N thioredoxin fold domain-containing protein 131567 cellular organisms no rank 267470 EBI-EMBL Thioredoxin-like domain Thioredoxin-like domain NF024501.5 PF13101.11 DUF3945 21.9 11.1 50 domain Y Y N DUF3945 domain-containing protein 20532204 131567 cellular organisms no rank 6697 EBI-EMBL Protein of unknown function (DUF3945) Protein of unknown function (DUF3945) A family of uncharacterized proteins found by clustering human gut metagenomic sequences [1]. This is a C-terminal repeated region. [1]. 20532204. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. Ellrott K, Jaroszewski L, Weizhong L, Wooley J, Godzik, A. PLoS Computational Biology, 2010 (from Pfam) NF024502.5 PF13102.11 Phage_int_SAM_5 22.3 22.3 98 domain Y Y N phage integrase SAM-like domain-containing protein 20532204 131567 cellular organisms no rank 111241 EBI-EMBL Phage integrase SAM-like domain Phage integrase SAM-like domain A family of uncharacterised proteins found by clustering human gut metagenomic sequences [1]. This family appears related to the N-terminal domain of phage integrases. [1]. 20532204. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. Ellrott K, Jaroszewski L, Weizhong L, Wooley J, Godzik, A. PLoS Computational Biology, 2010 (from Pfam) NF024515.5 PF13115.11 YtkA 25.9 25.9 85 domain Y Y N FixH family protein 16607952 131567 cellular organisms no rank 14321 EBI-EMBL YtkA-like FixH family protein NF024545.5 PF13145.11 Rotamase_2 27 27 121 domain Y Y N peptidyl-prolyl cis-trans isomerase GO:0003755 131567 cellular organisms no rank 131771 EBI-EMBL PPIC-type PPIASE domain PPIC-type PPIASE domain NF024547.5 PF13148.11 DUF3987 27 27 364 domain Y Y N DUF3987 domain-containing protein 20532204 131567 cellular organisms no rank 25979 EBI-EMBL Protein of unknown function (DUF3987) Protein of unknown function (DUF3987) A family of uncharacterised proteins found by clustering human gut metagenomic sequences [1]. [1]. 20532204. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. Ellrott K, Jaroszewski L, Weizhong L, Wooley J, Godzik, A. PLoS Computational Biology, 2010 (from Pfam) NF024550.5 PF13151.11 DUF3990 32.2 32.2 152 domain Y Y N DUF3990 domain-containing protein 20532204 131567 cellular organisms no rank 6831 EBI-EMBL Protein of unknown function (DUF3990) Protein of unknown function (DUF3990) A family of uncharacterised proteins found by clustering human gut metagenomic sequences [1]. [1]. 20532204. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. Ellrott K, Jaroszewski L, Weizhong L, Wooley J, Godzik, A. PLoS Computational Biology, 2010 (from Pfam) NF024554.5 PF13155.11 Toprim_2 22.1 22.1 88 domain Y Y N toprim domain-containing protein 131567 cellular organisms no rank 132250 EBI-EMBL Toprim-like toprim domain This is a family or Toprim-like proteins. (from Pfam) NF024555.5 PF13156.11 Mrr_cat_2 22 22 127 domain Y N N Restriction endonuclease 11313145,1650347 131567 cellular organisms no rank 28027 EBI-EMBL Restriction endonuclease Restriction endonuclease Prokaryotic family found in type II restriction enzymes containing the hallmark (D/E)-(D/E)XK active site. Presence of catalytic residues implicates this region in the enzymatic cleavage of DNA [1,2] [1]. 1650347. Characterization and expression of the Escherichia coli Mrr restriction system. Waite-Rees PA, Keating CJ, Moran LS, Slatko BE, Hornstra LJ, Benner JS;. J Bacteriol 1991;173:5207-5219. [2]. 11313145. Identification of a PD-(D/E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs. Bujnicki JM, Rychlewski L;. Gene 2001;267:183-191. (from Pfam) NF024559.5 PF13160.11 DUF3995 34.3 34.3 124 domain Y Y N DUF3995 domain-containing protein 131567 cellular organisms no rank 8607 EBI-EMBL Protein of unknown function (DUF3995) Protein of unknown function (DUF3995) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 138 and 149 amino acids in length. There are two completely conserved residues (W and P) that may be functionally important. (from Pfam) NF024565.5 PF13166.11 AAA_13 36 36 713 domain Y Y N AAA family ATPase 1691706 131567 cellular organisms no rank 18794 EBI-EMBL AAA domain AAA domain This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease [1]. [1]. 1691706. The optional E. coli prr locus encodes a latent form of phage T4-induced anticodon nuclease. Levitz R, Chapman D, Amitsur M, Green R, Snyder L, Kaufmann G;. EMBO J. 1990;9:1383-1389. (from Pfam) NF024566.5 PF13167.11 GTP-bdg_N 25.4 25.4 89 PfamEq Y N N GTP-binding GTPase N-terminal 19109926,19181811,19824612 131567 cellular organisms no rank 70367 EBI-EMBL GTP-binding GTPase N-terminal GTP-binding GTPase N-terminal This is the N-terminal region of GTP-binding HflX-like proteins. The full-length members bind and interact with the 50S ribosome and are GTPases, hydrolysing GTP/GDP/ATP/ADP. This N-terminal region is necessary for stability of the whole protein. [1]. 19109926. E. coli HflX interacts with 50S ribosomal subunits in presence of nucleotides. Jain N, Dhimole N, Khan AR, De D, Tomar SK, Sajish M, Dutta D, Parrack P, Prakash B;. Biochem Biophys Res Commun. 2009;379:201-205. [2]. 19181811. Properties of HflX, an enigmatic protein from Escherichia coli. Dutta D, Bandyopadhyay K, Datta AB, Sardesai AA, Parrack P;. J Bacteriol. 2009;191:2307-2314. [3]. 19824612. Toward understanding the function of the universally conserved GTPase HflX from Escherichia coli: a kinetic approach. Shields MJ, Fischer JJ, Wieden HJ;. Biochemistry. 2009;48:10793-10802. (from Pfam) NF024570.5 PF13171.11 DUF4004 27 27 197 PfamAutoEq Y Y N DUF4004 family protein 131567 cellular organisms no rank 2413 EBI-EMBL Protein of unknown function (DUF4004) DUF4004 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 210 amino acids in length. (from Pfam) NF024571.5 PF13173.11 AAA_14 27 27 129 domain Y Y N AAA family ATPase 131567 cellular organisms no rank 82222 EBI-EMBL AAA domain AAA domain This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. (from Pfam) NF024572.5 PF13174.11 TPR_6 26.3 12.2 33 domain Y Y N tetratricopeptide repeat protein GO:0005515 131567 cellular organisms no rank 248737 EBI-EMBL Tetratricopeptide repeat Tetratricopeptide repeat NF024573.5 PF13175.11 AAA_15 32.1 32.1 374 domain Y Y N AAA family ATPase 131567 cellular organisms no rank 241000 EBI-EMBL AAA ATPase domain AAA ATPase domain This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. (from Pfam) NF024574.5 PF13176.11 TPR_7 27.9 14 36 repeat Y N N tetratricopeptide repeat protein GO:0005515 131567 cellular organisms no rank 173857 EBI-EMBL Tetratricopeptide repeat Tetratricopeptide repeat NF024575.5 PF13177.11 DNA_pol3_delta2 27 27 161 domain Y N N DNA polymerase III, delta subunit 11432857 131567 cellular organisms no rank 184243 EBI-EMBL DNA polymerase III, delta subunit DNA polymerase III, delta subunit DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction [1]. The delta subunit is also known as HolA. [1]. 11432857. The delta and delta ' subunits of the DNA polymerase III holoenzyme are essential for initiation complex formation and processive elongation. Song MS, Pham PT, Olson M, Carter JR, Franden MA, Schaaper RM, McHenry CS;. J Biol Chem 2001;276:35165-35175. (from Pfam) NF024578.5 PF13180.11 PDZ_2 27 27 80 domain Y Y N PDZ domain-containing protein GO:0005515 131567 cellular organisms no rank 345110 EBI-EMBL PDZ domain PDZ domain NF024579.5 PF13181.11 TPR_8 25.7 11.8 34 repeat Y N N tetratricopeptide repeat protein GO:0005515 131567 cellular organisms no rank 566659 EBI-EMBL Tetratricopeptide repeat tetratricopeptide repeat NF024580.5 PF13182.11 DUF4007 27 27 288 PfamAutoEq Y Y N DUF4007 family protein 131567 cellular organisms no rank 4211 EBI-EMBL Protein of unknown function (DUF4007) DUF4007 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 284 and 326 amino acids in length. This domain is found associated with Pfam:PF01507 in some proteins, suggesting a functional link. (from Pfam) NF024581.5 PF13183.11 Fer4_8 27 27 68 domain Y Y N 4Fe-4S dicluster domain-containing protein 131567 cellular organisms no rank 326553 EBI-EMBL 4Fe-4S dicluster domain 4Fe-4S dicluster domain Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters. (from Pfam) NF024582.5 PF13184.11 KH_5 27 27 69 domain Y N N NusA-like KH domain GO:0003723 131567 cellular organisms no rank 54718 EBI-EMBL NusA-like KH domain NusA-like KH domain NF024583.5 PF13185.11 GAF_2 28.6 28.6 136 domain Y Y N GAF domain-containing protein GO:0005515 11032796,20004158,9433123 131567 cellular organisms no rank 525077 EBI-EMBL GAF domain GAF domain The GAF domain is named after some of the proteins it is found in, including cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA. It is also found in guanylyl cyclases and phytochromes [1,2]. The structure of a GAF domain shows that the domain shares a similar fold with the PAS domain [3]. This domain can bind O2, CO and NO (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 9433123. The GAF domain: an evolutionary link between diverse phototransducing proteins. Aravind L, Ponting CP;. Trends Biochem Sci 1997;22:458-459. [2]. 20004158. Cyclic nucleotide binding GAF domains from phosphodiesterases: structural and mechanistic insights. Heikaus CC, Pandit J, Klevit RE;. Structure. 2009;17:1551-1557. [3]. 11032796. Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor. Ho YS, Burden LM, Hurley JH;. EMBO J. 2000;19:5288-5299. (from Pfam) NF024584.5 PF13186.11 SPASM 21.5 21.5 67 domain Y Y N SPASM domain-containing protein 21478363 131567 cellular organisms no rank 78807 EBI-EMBL Iron-sulfur cluster-binding domain Iron-sulfur cluster-binding domain This domain occurs as an additional C-terminal iron-sulfur cluster binding domain in many radical SAM domain, Pfam:PF04055 proteins. The domain occurs in a number of proteins that modify a protein to become an active enzyme, or a peptide to become a ribosomal natural product. The domain is named SPASM because it occurs in the maturases of Subilitosin, PQQ, Anaerobic Sulfatases, and Mycofactocin. [1]. 21478363. Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification. Haft DH, Basu MK;. J Bacteriol. 2011;193:2745-2755. (from Pfam) NF024585.5 PF13187.11 Fer4_9 27 27 52 domain Y Y N 4Fe-4S dicluster domain-containing protein 3351918 131567 cellular organisms no rank 271279 EBI-EMBL 4Fe-4S dicluster domain 4Fe-4S dicluster domain NF024586.5 PF13188.12 PAS_8 21.8 14.5 65 domain Y Y N PAS domain-containing protein 10357859 131567 cellular organisms no rank 737685 EBI-EMBL PAS domain PAS domain PAS domains are involved in many signalling proteins where they are used as a signal sensor domain [1]. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Heme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. This domain recognises oxygen and CO (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 10357859. PAS domains: internal sensors of oxygen, redox potential, and light. Taylor BL, Zhulin IB;. Microbiol Mol Biol Rev. 1999;63:479-506. (from Pfam) NF024587.5 PF13189.11 Cytidylate_kin2 28 28 176 domain Y Y N cytidylate kinase family protein 131567 cellular organisms no rank 48386 EBI-EMBL Cytidylate kinase-like family cytidylate kinase family protein This family includes enzymes related to cytidylate kinase. (from Pfam) NF024588.5 PF13190.11 PDGLE 27 27 102 domain Y Y N PDGLE domain-containing protein 131567 cellular organisms no rank 12605 EBI-EMBL PDGLE domain PDGLE domain This short presumed domain is usually found on its own. However, it is also found associated with Pfam:PF01891 suggesting it may have a role in cobalt uptake. The domain is named after a short motif found within many members of the family. (from Pfam) NF024589.5 PF13191.11 AAA_16 32.6 32.6 167 domain Y Y N AAA family ATPase 131567 cellular organisms no rank 315002 EBI-EMBL AAA ATPase domain AAA ATPase domain This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. (from Pfam) NF024590.5 PF13192.11 Thioredoxin_3 24.8 24.8 76 domain Y Y N thioredoxin family protein 131567 cellular organisms no rank 53624 EBI-EMBL Thioredoxin domain Thioredoxin domain NF024591.5 PF13193.11 AMP-binding_C 24.5 24.5 76 domain Y Y N AMP-binding enzyme 131567 cellular organisms no rank 1238658 EBI-EMBL AMP-binding enzyme C-terminal domain AMP-binding enzyme C-terminal domain This is a small domain that is found C terminal to Pfam:PF00501. It has a central beta sheet core that is flanked by alpha helices. (from Pfam) NF024592.5 PF13194.11 DUF4010 30 30 210 domain Y Y N DUF4010 domain-containing protein 131567 cellular organisms no rank 12069 EBI-EMBL Domain of unknown function (DUF4010) Domain of unknown function (DUF4010) This is a family of putative membrane proteins found in archaea and bacteria. It is sometimes found C terminal to Pfam:PF02308. (from Pfam) NF024593.5 PF13195.11 DUF4011 22.2 22.2 158 domain Y Y N DUF4011 domain-containing protein 131567 cellular organisms no rank 18635 EBI-EMBL Protein of unknown function (DUF4011) Protein of unknown function (DUF4011) This family of proteins is found in archaea and bacteria. Many members are annotated as being putative DNA helicase-related proteins. (from Pfam) NF024594.5 PF13196.11 DUF4012 28 28 144 domain Y Y N DUF4012 domain-containing protein 131567 cellular organisms no rank 8687 EBI-EMBL Protein of unknown function (DUF4012) Protein of unknown function (DUF4012) This is a family of uncharacterised proteins found in archaea and bacteria. (from Pfam) NF024595.5 PF13197.11 DUF4013 26.9 26.9 168 domain Y Y N DUF4013 domain-containing protein 131567 cellular organisms no rank 4118 EBI-EMBL Protein of unknown function (DUF4013) Protein of unknown function (DUF4013) This is a family of uncharacterised proteins that is found in archaea and bacteria. (from Pfam) NF024597.5 PF13199.11 Glyco_hydro_66 23.7 23.7 546 domain Y Y N glycoside hydrolase family 66 protein 131567 cellular organisms no rank 3363 EBI-EMBL Glycosyl hydrolase family 66 glycoside hydrolase family 66 protein This family is a set of glycosyl hydrolase enzymes including cycloisomaltooligosaccharide glucanotransferase (EC:2.4.1.-) and dextranase (EC:3.2.1.11) activities. (from Pfam) NF024598.5 PF13200.11 DUF4015 27 27 313 domain Y Y N putative glycoside hydrolase 131567 cellular organisms no rank 11278 EBI-EMBL Putative glycosyl hydrolase domain Putative glycosyl hydrolase domain This domain is related to other known glycosyl hydrolases suggesting this domain is also involved in carbohydrate break down. (from Pfam) NF024600.5 PF13202.11 EF-hand_5 25.9 11.5 25 repeat Y N N EF-hand domain-containing protein GO:0005509 131567 cellular organisms no rank 60603 EBI-EMBL EF hand EF-hand domain NF024601.5 PF13203.11 DUF2201_N 23.2 23.2 271 domain Y Y N DUF2201 family putative metallopeptidase 131567 cellular organisms no rank 18504 EBI-EMBL Putative metallopeptidase domain DUF2201 family N-terminal putative metallopeptidase domain Many proteins with this uncharacterized domain share a conserved HExxH domain that typically suggests zinc metallopeptidase activity. NF024602.5 PF13204.11 DUF4038 26.5 26.5 320 domain Y Y N DUF4038 domain-containing protein 131567 cellular organisms no rank 9071 EBI-EMBL Protein of unknown function (DUF4038) Protein of unknown function (DUF4038) A family of putative cellulases. (from Pfam) NF024603.5 PF13205.11 Big_5 23.6 23.6 105 domain Y Y N Ig-like domain-containing protein 131567 cellular organisms no rank 50040 EBI-EMBL Bacterial Ig-like domain Bacterial Ig-like domain NF024605.5 PF13207.11 AAA_17 27 27 136 domain Y Y N AAA family ATPase 131567 cellular organisms no rank 73899 EBI-EMBL AAA domain AAA domain NF024606.5 PF13208.11 TerB_N 25 25 207 PfamEq Y Y N TerB N-terminal domain-containing protein 23044854 131567 cellular organisms no rank 6059 EBI-EMBL TerB N-terminal domain TerB N-terminal domain The TerB_N domain is found N-terminal to TerB, and TerB_C containing proteins [1]. It has a predominantly alpha-helical structure and contains an absolutely conserved glutamate [1]. The presence of a conserved acidic residue suggests that it might chelate metal like TerB [1]. These proteins occur in a two-gene operon containing an AAA+ ATPase and SF-II DNA helicase suggesting a role in stress-response or phage defence [1]. [1]. 23044854. Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing. Anantharaman V, Iyer LM, Aravind L;. Mol Biosyst. 2012;8:3142-3165. (from Pfam) NF024620.5 PF13222.11 DUF4030 25.2 25.2 142 domain Y Y N DUF4030 domain-containing protein 131567 cellular organisms no rank 1285 EBI-EMBL Protein of unknown function (DUF4030) Protein of unknown function (DUF4030) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 164 and 197 amino acids in length. (from Pfam) NF024626.5 PF13228.11 DUF4037 22.1 22.1 101 domain Y Y N DUF4037 domain-containing protein 131567 cellular organisms no rank 9278 EBI-EMBL Domain of unknown function (DUF4037) Domain of unknown function (DUF4037) This presumed domain is functionally uncharacterised. This domain family is found in bacteria and eukaryotes, and is approximately 100 amino acids in length. There is a single completely conserved residue P that may be functionally important. (from Pfam) NF024627.5 PF13229.11 Beta_helix 25.9 25.9 158 domain Y Y N right-handed parallel beta-helix repeat-containing protein 131567 cellular organisms no rank 154043 EBI-EMBL Right handed beta helix region Right handed beta helix region This region contains a parallel beta helix region that shares some similarity with Pectate lyases. (from Pfam) NF024628.5 PF13230.11 GATase_4 23 23 272 domain Y Y N class II glutamine amidotransferase 131567 cellular organisms no rank 64772 EBI-EMBL Glutamine amidotransferases class-II class II glutamine amidotransferase This family captures members that are not found in Pfam:PF00310. (from Pfam) NF024629.5 PF13231.11 PMT_2 26.1 26.1 160 domain Y Y N glycosyltransferase family 39 protein 2.4.-.- 131567 cellular organisms no rank 170152 EBI-EMBL Dolichyl-phosphate-mannose-protein mannosyltransferase glycosyltransferase family 39 protein This family contains members that are not captured by Pfam:PF02366. (from Pfam) NF024634.5 PF13237.11 Fer4_10 25.5 24.6 53 domain Y Y N 4Fe-4S dicluster domain-containing protein 131567 cellular organisms no rank 429030 EBI-EMBL 4Fe-4S dicluster domain 4Fe-4S dicluster domain This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich. (from Pfam) NF024635.5 PF13238.11 AAA_18 29.4 29.4 128 domain Y Y N AAA family ATPase 131567 cellular organisms no rank 108411 EBI-EMBL AAA domain AAA domain NF024636.5 PF13239.11 2TM 24.8 22.9 79 domain Y Y N 2TM domain-containing protein 131567 cellular organisms no rank 18341 EBI-EMBL 2TM domain Pr2TM family membrane protein Proteins of this family are defined as prokaryotic 2 TMS domain proteins (Pr2TMs) by TCDB (http://www.tcdb.org/search/result.php?tc=9.B.304). It may be involved in cell lysis or peptidoglycan turnover. NF024637.5 PF13240.11 zinc_ribbon_2 25 25 23 domain Y Y N zinc-ribbon domain-containing protein 131567 cellular organisms no rank 57706 EBI-EMBL zinc-ribbon domain zinc-ribbon domain This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR. Pfam:PF12773. (from Pfam) NF024638.5 PF13241.11 NAD_binding_7 22.1 22.1 104 domain Y Y N NAD(P)-dependent oxidoreductase 12408752,18588505 131567 cellular organisms no rank 112745 EBI-EMBL Putative NAD(P)-binding NAD(P)-dependent oxidoreductase This domain is found in fungi, plants, archaea and bacteria. (from Pfam) NF024639.5 PF13242.11 Hydrolase_like 22 22 75 domain Y Y N HAD hydrolase-like protein 131567 cellular organisms no rank 516287 EBI-EMBL HAD-hyrolase-like HAD hydrolase-like protein NF024640.5 PF13243.11 SQHop_cyclase_C 26.1 26.1 319 domain Y N N Squalene-hopene cyclase C-terminal domain 12617471,12747780,9931258 131567 cellular organisms no rank 26014 EBI-EMBL Squalene-hopene cyclase C-terminal domain Squalene-hopene cyclase C-terminal domain Squalene-hopene cyclase, EC:5.4.99.17, catalyses the cyclisation of squalene into hopene in bacteria. This reaction is part of a cationic cyclisation cascade, which is homologous to a key step in cholesterol biosynthesis. This family is the C-terminal half of the molecule. [1]. 9931258. The structure of the membrane protein squalene-hopene cyclase at 2.0 A resolution. Wendt KU, Lenhart A, Schulz GE;. J Mol Biol. 1999;286:175-187. [2]. 12747780. Binding structures and potencies of oxidosqualene cyclase inhibitors with the homologous squalene-hopene cyclase. Lenhart A, Reinert DJ, Aebi JD, Dehmlow H, Morand OH, Schulz GE;. J Med Chem. 2003;46:2083-2092. [3]. 12617471. Subcellular localization of oxidosqualene cyclases from Arabidopsis thaliana, Trypanosoma cruzi, and Pneumocystis carinii expressed in yeast. Milla P, Viola F, Oliaro Bosso S, Rocco F, Cattel L, Joubert BM, LeClair RJ, Matsuda SP, Balliano G;. Lipids. 2002;37:1171-1176. (from Pfam) NF024641.5 PF13244.11 MbhD 27.2 27.2 67 domain Y Y N hydrogenase subunit MbhD domain-containing protein 29754813,32735215,33229520 131567 cellular organisms no rank 48524 EBI-EMBL MBH, subunit D MBH, subunit D Hydrogen gas-evolving membrane-bound hydrogenase (MBH) is a respiratory complex homologous to the quinone-reducing Complex I. Like Complex I, MBH has peripheral and membrane arms. MBH is made of 14 subunits (MbhA-N). MbhJ, K, L, N and M form the Membrane-anchored hydrogenase module. MbhJ, K, L, N are predicted to be exposed to the cytoplasm and form the peripheral arm. The remaining 10 subunits are predicted to be integral membrane proteins forming the membrane arm, made of 44 transmembrane helices (TMH) [2, 3]. MbhA, B, C and F form the Sodium translocation module. MbhD, E, G and H form the Proton translocation module. MbhI is the linker between the hydrogenase module and the proton-translocating membrane module. It anchors the discontinuous TMH7 of MbhH via its middle lateral helix and the C-terminal of TMH2, found in MbhE. MbhD and MbhE together are equivalent to Nqo10 of Complex I [1]. MbhD has three TM helices. Paper describing PDB structure 6cfw. [1]. 29754813. Structure of an Ancient Respiratory System. Yu H, Wu CH, Schut GJ, Haja DK, Zhao G, Peters JW, Adams MWW, Li H;. Cell. 2018;173:1636-1649. [2]. 33229520. Structure of the Dietzia Mrp complex reveals molecular mechanism of this giant bacterial sodium proton pump. Li B, Zhang K, Nie Y, Wang X, Zhao Y, Zhang XC, Wu XL;. Proc Natl Acad Sci U S A. 2020;117:31166-31176. [3]. 32735215. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. Steiner J, Sazanov L;. Elife. 2020; [Epub ahead of print] (from Pfam) NF024642.5 PF13245.11 AAA_19 25.1 25.1 134 domain Y Y N AAA family ATPase 131567 cellular organisms no rank 645677 EBI-EMBL AAA domain AAA domain NF024643.5 PF13246.11 Cation_ATPase 21.7 21.7 91 domain Y N N Cation transport ATPase (P-type) 1384045,21653810 131567 cellular organisms no rank 108148 EBI-EMBL Cation transport ATPase (P-type) Cation transport ATPase (P-type) This domain is found in cation transport ATPases, including phospholipid-transporting ATPases, calcium-transporting ATPases, and sodium-potassium ATPases [1-2]. [1]. 21653810. Physiological adaptation of an Antarctic Na+/K+-ATPase to the cold. Galarza-Munoz G, Soto-Morales SI, Holmgren M, Rosenthal JJ;. J Exp Biol. 2011;214:2164-2174. [2]. 1384045. Higher plant Ca(2+)-ATPase: primary structure and regulation of mRNA abundance by salt. Wimmers LE, Ewing NN, Bennett AB;. Proc Natl Acad Sci U S A. 1992;89:9205-9209. (from Pfam) NF024644.5 PF13247.11 Fer4_11 26.2 26.2 100 domain Y Y N 4Fe-4S dicluster domain-containing protein 131567 cellular organisms no rank 118851 EBI-EMBL 4Fe-4S dicluster domain 4Fe-4S dicluster domain Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters. (from Pfam) NF024645.5 PF13248.11 zf-ribbon_3 27 27 26 domain Y Y N zinc ribbon domain-containing protein 131567 cellular organisms no rank 13892 EBI-EMBL zinc-ribbon domain zinc-ribbon domain This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR. Pfam:PF12773. (from Pfam) NF024646.5 PF13249.11 SQHop_cyclase_N 26.2 26.2 291 domain Y N N Squalene-hopene cyclase N-terminal domain 12747780,9931258 131567 cellular organisms no rank 19518 EBI-EMBL Squalene-hopene cyclase N-terminal domain Squalene-hopene cyclase N-terminal domain Squalene-hopene cyclase, EC:5.4.99.17, catalyses the cyclisation of squalene into hopene in bacteria. This reaction is part of a cationic cyclisation cascade, which is homologous to a key step in cholesterol biosynthesis. This family is the N-terminal domain. [1]. 9931258. The structure of the membrane protein squalene-hopene cyclase at 2.0 A resolution. Wendt KU, Lenhart A, Schulz GE;. J Mol Biol. 1999;286:175-187. [2]. 12747780. Binding structures and potencies of oxidosqualene cyclase inhibitors with the homologous squalene-hopene cyclase. Lenhart A, Reinert DJ, Aebi JD, Dehmlow H, Morand OH, Schulz GE;. J Med Chem. 2003;46:2083-2092. (from Pfam) NF024647.5 PF13250.11 DUF4041 27 27 56 PfamAutoEq Y Y N DUF4041 domain-containing protein 131567 cellular organisms no rank 6743 EBI-EMBL Domain of unknown function (DUF4041) Domain of unknown function (DUF4041) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and viruses, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF10544. (from Pfam) NF024660.5 PF13263.11 PHP_C 21.3 21.3 56 domain Y Y N PHP-associated domain-containing protein 131567 cellular organisms no rank 10396 EBI-EMBL PHP-associated PHP-associated This is a subunit, probably the alpha, of bacterial and eukaryotic DNA polymerase III, associated with the PHP domain, Pfam:PF02811. (from Pfam) NF024668.5 PF13271.11 DUF4062 24.7 24.7 82 domain Y Y N DUF4062 domain-containing protein 131567 cellular organisms no rank 11261 EBI-EMBL Domain of unknown function (DUF4062) Domain of unknown function (DUF4062) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 80 amino acids in length. There is a conserved SST sequence motif. (from Pfam) NF024671.5 PF13274.11 SocA_Panacea 25.7 25.7 113 domain Y Y N type II toxin-antitoxin system antitoxin SocA domain-containing protein 24239291,35121656 131567 cellular organisms no rank 17199 EBI-EMBL Antitoxin SocA-like, Panacea domain Antitoxin SocA-like, Panacea domain This domain is found in Antitoxin SocA from Caulobacter vibrioides and in similar proteins widespread across bacteria, archaea and tailed bacteriophages. SocA is the antitoxin component of an atypical type II toxin-antitoxin (TA) system which neutralises the toxic activity of toxin SocB by acting as an adapter to promote its degradation by the protease ClpXP [1,2]. [1]. 35121656. A hyperpromiscuous antitoxin protein domain for the neutralization of diverse toxin domains. Kurata T, Saha CK, Buttress JA, Mets T, Brodiazhenko T, Turnbull KJ, Awoyomi OF, Oliveira SRA, Jimmy S, Ernits K, Delannoy M, Persson K, Tenson T, Strahl H, Hauryliuk V, Atkinson GC;. Proc Natl Acad Sci U S A. 2022; [Epub ahead of print]. [2]. 24239291. A bacterial toxin inhibits DNA replication elongation through a direct interaction with the beta sliding clamp. Aakre CD, Phung TN, Huang D, Laub MT;. Mol Cell. 2013;52:617-628. (from Pfam) NF024673.5 PF13276.11 HTH_21 28.1 28.1 60 domain Y Y N IS3 family transposase 131567 cellular organisms no rank 188348 EBI-EMBL HTH-like domain IS3 family transposase This domain contains a predicted helix-turn-helix suggesting a DNA-binding function. (from Pfam) NF024675.5 PF13279.11 4HBT_2 25.5 25.5 122 domain Y Y N thioesterase family protein 15307895 131567 cellular organisms no rank 170079 EBI-EMBL Thioesterase-like superfamily thioesterase family protein This family contains a wide variety of enzymes, principally thioesterases. These enzymes are part of the Hotdog fold superfamily [1]. [1]. 15307895. The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases. Dillon SC, Bateman A;. BMC Bioinformatics 2004;5:109-109. (from Pfam) NF024676.5 PF13280.11 WYL 25.8 25.8 172 domain Y Y N WYL domain-containing protein 23535141,24817877 131567 cellular organisms no rank 228205 EBI-EMBL WYL domain WYL domain The WYL domain occurs regularly in CRISPR-associated (Cas) proteins. NF024677.5 PF13281.11 MAP3K_TRAF_bd 24.1 23.4 371 PfamAutoEq Y Y N TRAFs-binding domain-containing protein 28242696 131567 cellular organisms no rank 1006 EBI-EMBL MAP3K TRAFs-binding domain MAP3K TRAFs-binding domain This entry corresponds to the TNF receptor-associated factors (TRAFs)-binding domain found at the N-terminus of some MAP3Ks, like Apoptosis signal-regulating kinases (ASK). This domain is flanked by a thioredoxin-binding domain and a PH-like domain. It includes seven tetratricopeptide repeats (TPRs) and, together with the PH-like domain, constitutes the central regulatory domain of ASK1 [1]. [1]. 28242696. Structural basis of autoregulatory scaffolding by apoptosis signal-regulating kinase 1. Weijman JF, Kumar A, Jamieson SA, King CM, Caradoc-Davies TT, Ledgerwood EC, Murphy JM, Mace PD;. Proc Natl Acad Sci U S A. 2017;114:E2096. (from Pfam) NF024682.5 PF13286.11 HD_assoc 22.2 22.2 91 domain Y N N Phosphohydrolase-associated domain 131567 cellular organisms no rank 52231 EBI-EMBL Phosphohydrolase-associated domain Phosphohydrolase-associated domain This domain is found on bacterial and archaeal metal-dependent phosphohydrolases. (from Pfam) NF024683.5 PF13287.11 Fn3_assoc 23 23 59 domain Y Y N FN3 associated domain-containing protein 131567 cellular organisms no rank 38570 EBI-EMBL Fn3 associated Fn3 associated NF024685.5 PF13289.11 SIR2_2 24.5 24.5 141 domain Y Y N SIR2 family protein 131567 cellular organisms no rank 41155 EBI-EMBL SIR2-like domain SIR2-like domain This family of proteins are related to the sirtuins. (from Pfam) NF024686.5 PF13290.11 CHB_HEX_C_1 22 22 67 domain Y Y N chitobiase/beta-hexosaminidase C-terminal domain-containing protein 131567 cellular organisms no rank 41518 EBI-EMBL Chitobiase/beta-hexosaminidase C-terminal domain Chitobiase/beta-hexosaminidase C-terminal domain NF024687.5 PF13291.11 ACT_4 27 27 80 domain Y Y N ACT domain-containing protein 131567 cellular organisms no rank 104106 EBI-EMBL ACT domain ACT domain ACT domains bind to amino acids and regulate associated enzyme domains. These ACT domains are found at the C-terminus of the RelA protein. (from Pfam) NF024688.5 PF13292.11 DXP_synthase_N 21.2 21.2 274 domain Y Y N 1-deoxy-D-xylulose-5-phosphate synthase N-terminal domain-containing protein GO:0008661,GO:0016114 9371765 131567 cellular organisms no rank 168727 EBI-EMBL 1-deoxy-D-xylulose-5-phosphate synthase 1-deoxy-D-xylulose-5-phosphate synthase This family contains 1-deoxyxylulose-5-phosphate synthase (DXP synthase), an enzyme which catalyses the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate, to yield 1-deoxy-D- xylulose-5-phosphate, a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). [1]. 9371765. Identification of a thiamin-dependent synthase in Escherichia coli required for the formation of the 1-deoxy-D-xylulose 5-phosphate precursor to isoprenoids, thiamin, and pyridoxol. Sprenger GA, Schorken U, Wiegert T, Grolle S, de Graaf AA, Taylor SV, Begley TP, Bringer-Meyer S, Sahm H;. Proc Natl Acad Sci U S A. 1997;94:12857-12862. (from Pfam) NF024694.5 PF13298.11 LigD_N 31.1 31.1 107 domain Y Y N DNA polymerase ligase N-terminal domain-containing protein 21208981 131567 cellular organisms no rank 33399 EBI-EMBL DNA polymerase Ligase (LigD) DNA polymerase Ligase (LigD) This is the N terminal region of ATP dependant DNA ligase. (from Pfam) NF024698.5 PF13302.12 Acetyltransf_3 25.4 25.4 138 subfamily Y Y N GNAT family N-acetyltransferase 2.3.1.- GO:0016747 131567 cellular organisms no rank 909062 EBI-EMBL Acetyltransferase (GNAT) domain Acetyltransferase (GNAT) domain This domain catalyses N-acetyltransferase reactions. (from Pfam) NF024700.5 PF13304.11 AAA_21 27 27 304 domain Y Y N AAA family ATPase GO:0005524,GO:0016887 131567 cellular organisms no rank 1242126 EBI-EMBL AAA domain, putative AbiEii toxin, Type IV TA system AAA family ATPase Several members are annotated as being of the abortive phage resistance system, in which case the family would be acting as the toxin for a type IV toxin-antitoxin resistance system. (from Pfam) NF024702.5 PF13306.11 LRR_5 27.7 10 127 domain Y Y N leucine-rich repeat protein 131567 cellular organisms no rank 56373 EBI-EMBL BspA type Leucine rich repeat region (6 copies) leucine-rich repeat protein This family includes a number of leucine rich repeats. This family contains a large number of BSPA-like surface antigens from Trichomonas vaginalis. (from Pfam) NF024703.5 PF13307.11 Helicase_C_2 25.3 25.3 170 domain Y Y N helicase C-terminal domain-containing protein GO:0003676,GO:0004386,GO:0005524,GO:0006139,GO:0016818 131567 cellular organisms no rank 103486 EBI-EMBL Helicase C-terminal domain Helicase C-terminal domain This domain is found at the C-terminus of DEAD-box helicases. (from Pfam) NF024706.5 PF13310.11 Virulence_RhuM 33.7 33.7 252 subfamily Y Y N RhuM family protein rhuM 12775700,9922266 131567 cellular organisms no rank 20534 EBI-EMBL Virulence protein RhuM family RhuM family protein There are currently no experimental data for members of this group or their homologues. However, these proteins are implicated in virulence/pathogenicity because RhuM is encoded in the SPI-3 pathogenicity island in Salmonella typhimurium [1-2]. [1]. 9922266. The SPI-3 pathogenicity island of Salmonella enterica. Blanc-Potard AB, Solomon F, Kayser J, Groisman EA;. J Bacteriol. 1999;181:998-1004. [2]. 12775700. Variation between pathogenic serovars within Salmonella pathogenicity islands. Amavisit P, Lightfoot D, Browning GF, Markham PF;. J Bacteriol. 2003;185:3624-3635. (from Pfam) NF024711.5 PF13315.11 DUF4085 24.1 24.1 205 domain Y Y N DUF4085 family protein 131567 cellular organisms no rank 1345 EBI-EMBL Protein of unknown function (DUF4085) DUF4085 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 101 and 269 amino acids in length. (from Pfam) NF024716.5 PF13320.11 GH123_cat 23.1 23.1 324 domain Y Y N glycoside hydrolase domain-containing protein 27038508,27546776 131567 cellular organisms no rank 8193 EBI-EMBL Glycoside hydrolase 123, catalytic domain Glycoside hydrolase 123, catalytic domain This domain is found at the C terminus of protein members of the glycoside hydrolase family 123, including N-acetylgalactosaminidase from Clostridium perfringens. This enzyme removes specific terminal N-D-acetylgalactosamine from glycosphingolipids. This catalytic domain adopts an alpha/beta barrel configuration with a two-stranded beta sheet and a pair of alpha-helices at the C-terminal end [1,2]. [1]. 27038508. The Details of Glycolipid Glycan Hydrolysis by the Structural Analysis of a Family 123 Glycoside Hydrolase from Clostridium perfringens. Noach I, Pluvinage B, Laurie C, Abe KT, Alteen MG, Vocadlo DJ, Boraston AB;. J Mol Biol. 2016;428:3253-3265. [2]. 27546776. Structural and mechanistic insights into a Bacteroides vulgatus retaining N-acetyl-beta-galactosaminidase that uses neighbouring group participation. Roth C, Petricevic M, John A, Goddard-Borger ED, Davies GJ, Williams SJ;. Chem Commun (Camb). 2016;52:11096-11099. (from Pfam) NF024724.5 PF13328.11 HD_4 27.2 27.2 156 domain Y Y N HD domain-containing protein 9868367 131567 cellular organisms no rank 116324 EBI-EMBL HD domain HD domain HD domains are metal dependent phosphohydrolases. [1]. 9868367. The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Aravind L, Koonin EV;. Trends Biochem Sci 1998;23:469-472. (from Pfam) NF024729.5 PF13333.11 rve_2 22 22 56 domain Y Y N IS3 family transposase GO:0015074 131567 cellular organisms no rank 226239 EBI-EMBL Integrase core domain IS3 family transposase NF024731.5 PF13335.11 Mg_chelatase_C 26 26 94 PfamEq Y N N Magnesium chelatase, subunit ChlI C-terminal 131567 cellular organisms no rank 72447 EBI-EMBL Magnesium chelatase, subunit ChlI C-terminal Magnesium chelatase, subunit ChlI C-terminal This is a family of the C-terminal of putative bacterial magnesium chelatase subunit ChlI proteins. Most members have the associated Pfam:PF01078. (from Pfam) NF024732.5 PF13336.11 AcetylCoA_hyd_C 23.7 23.7 154 domain Y Y N acetyl-CoA hydrolase/transferase C-terminal domain-containing protein 1441754,8550525 131567 cellular organisms no rank 55382 EBI-EMBL Acetyl-CoA hydrolase/transferase C-terminal domain Acetyl-CoA hydrolase/transferase C-terminal domain This family contains several enzymes which take part in pathways involving acetyl-CoA. Acetyl-CoA hydrolase EC:3.1.2.1 (Swiss:P32316) catalyses the formation of acetate from acetyl-CoA, CoA transferase (CAT1) EC:2.8.3.- (Swiss:P38946) produces succinyl-CoA, and acetate-CoA transferase EC:2.8.3.8 (Swiss:Q59323) utilises acyl-CoA and acetate to form acetyl-CoA. [1]. 1441754. An 11.4 kb DNA segment on the left arm of yeast chromosome II carries the carboxypeptidase Y sorting gene PEP1, as well as ACH1, FUS3 and a putative ARS. Van Dyck L, Purnelle B, Skala J, Goffeau A;. Yeast 1992;8:769-776. [2]. 8550525. Molecular analysis of the anaerobic succinate degradation pathway in Clostridium kluyveri. Sohling B, Gottschalk G;. J Bacteriol 1996;178:871-880. (from Pfam) NF024733.5 PF13337.11 BrxL_ATPase 25 25 313 domain Y Y N BREX system Lon protease-like protein BrxL 25452498 131567 cellular organisms no rank 7362 EBI-EMBL Lon-like protease BrxL-like, ATPase domain Lon-like protease BrxL-like, ATPase domain This entry represents the ATPase domain found in BREX system Lon protease-like protein BrxL from Bacillus cereus and similar proteins. BrxL is part of a type 1 BREX system which contains a C-terminal Lon-like protease domain (Pfam:PF05362. BREX systems (bacteriophage exclusion) provide immunity against bacteriophage, a system that allows phage adsorption but prevents phage DNA replication, without degradation of the phage DNA [1]. Methylation of bacterial DNA by PglX probably guides self/non-self discrimination. This entry also includes a few uncharacterised viral sequences. [1]. 25452498. BREX is a novel phage resistance system widespread in microbial genomes. Goldfarb T, Sberro H, Weinstock E, Cohen O, Doron S, Charpak-Amikam Y, Afik S, Ofir G, Sorek R;. EMBO J. 2015;34:169-183. (from Pfam) NF024734.5 PF13338.11 AbiEi_4 25 25 49 domain Y Y N type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein 24465005 131567 cellular organisms no rank 20057 EBI-EMBL Transcriptional regulator, AbiEi antitoxin Transcriptional regulator, AbiEi antitoxin AbiEi_4 is the cognate antitoxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is Pfam:PF13338 [1]. [1]. 24465005. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Dy RL, Przybilski R, Semeijn K, Salmond GP, Fineran PC;. Nucleic Acids Res. 2014;42:4590-4605. (from Pfam) NF024736.5 PF13340.11 DUF4096 34.3 34.3 76 domain Y Y N transposase 131567 cellular organisms no rank 100089 EBI-EMBL Putative transposase of IS4/5 family (DUF4096) transposase NF024738.5 PF13342.11 Toprim_Crpt 32 32 60 domain Y Y N topoisomerase C-terminal repeat-containing protein 131567 cellular organisms no rank 27374 EBI-EMBL C-terminal repeat of topoisomerase C-terminal repeat of topoisomerase This short domain is found in multiple copies at the C-terminus of some topoisomerase enzymes. (from Pfam) NF024739.5 PF13343.11 SBP_bac_6 24.6 24.6 245 domain Y Y N ABC transporter substrate-binding protein 131567 cellular organisms no rank 290260 EBI-EMBL Bacterial extracellular solute-binding protein ABC transporter substrate-binding protein This family includes bacterial extracellular solute-binding proteins. (from Pfam) NF024740.5 PF13344.11 Hydrolase_6 27 27 101 domain Y N N Haloacid dehalogenase-like hydrolase 131567 cellular organisms no rank 66087 EBI-EMBL Haloacid dehalogenase-like hydrolase Haloacid dehalogenase-like hydrolase This family is part of the HAD superfamily. (from Pfam) NF024741.5 PF13346.11 ABC2_membrane_5 25 25 205 domain Y Y N ABC-2 transporter permease 1303751 131567 cellular organisms no rank 33050 EBI-EMBL ABC-2 family transporter protein ABC-2 transporter permease This family is related to the ABC-2 membrane transporter family Pfam:PF01061 [1]. [1]. 1303751. A new subfamily of bacterial ABC-type transport systems catalyzing export of drugs and carbohydrates. Reizer J, Reizer A, Saier MH Jr;. Protein Sci 1992;1:1326-1332. (from Pfam) NF024742.5 PF13347.11 MFS_2 27 27 427 domain Y Y N MFS transporter 131567 cellular organisms no rank 243524 EBI-EMBL MFS/sugar transport protein MFS transporter This family is part of the major facilitator superfamily of membrane transport proteins. (from Pfam) NF024743.5 PF13349.11 DUF4097 22.9 22.9 247 domain Y Y N DUF4097 family beta strand repeat-containing protein 131567 cellular organisms no rank 76142 EBI-EMBL Toastrack DUF4097 Toastrack DUF4097 This an all-beta structure with a twenty-residue repeat with a highly conserved repeating GD, gly-asp, motif that has been described as Toastrack DUF4097, whose function is unknown. It has been suggested to form part of a bacterial adhesin. Toastrack has been transferred from bacteria to certain eukaryotes, such as FAM185A from human and its orthologues in animals and other eukaryotes. (from Pfam) NF024744.5 PF13350.11 Y_phosphatase3 22.2 22.2 240 domain Y Y N tyrosine-protein phosphatase GO:0004721 131567 cellular organisms no rank 61625 EBI-EMBL Tyrosine phosphatase family tyrosine-protein phosphatase This family is closely related to the Pfam:PF00102 and Pfam:PF00782 families. (from Pfam) NF024747.5 PF13353.11 Fer4_12 22 22 137 domain Y Y N 4Fe-4S cluster-binding domain-containing protein 131567 cellular organisms no rank 240249 EBI-EMBL 4Fe-4S single cluster domain 4Fe-4S single cluster domain This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich. (from Pfam) NF024748.5 PF13354.11 Beta-lactamase2 22 22 214 domain Y Y N serine hydrolase GO:0008800,GO:0030655 19100272 131567 cellular organisms no rank 241385 EBI-EMBL Beta-lactamase enzyme family serine hydrolase This is the catalytic domain of class A beta-lactamases [1]. It is closely related to Beta-lactamase, Pfam:PF00144, the serine beta-lactamase-like superfamily, which contains the distantly related Pfam:PF00905 and PF00768 D-alanyl-D-alanine carboxypeptidase. [1]. 19100272. Structure of PBP-A from Thermosynechococcus elongatus, a penicillin-binding protein closely related to class A beta-lactamases. Urbach C, Evrard C, Pudzaitis V, Fastrez J, Soumillion P, Declercq JP;. J Mol Biol. 2009;386:109-120. (from Pfam) NF024751.5 PF13358.11 DDE_3 28.6 28.6 146 domain Y Y N transposase 131567 cellular organisms no rank 81350 EBI-EMBL DDE superfamily endonuclease transposase This family of proteins are related to Pfam:PF00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. (from Pfam) NF024752.5 PF13359.11 DDE_Tnp_4 24.8 24.8 158 domain Y Y N transposase family protein 15169610 131567 cellular organisms no rank 53331 EBI-EMBL DDE superfamily endonuclease transposase family protein This family of proteins are related to Pfam:PF00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. (from Pfam) NF024753.5 PF13360.11 PQQ_2 27.6 19.7 233 domain Y Y N PQQ-binding-like beta-propeller repeat protein 131567 cellular organisms no rank 206206 EBI-EMBL PQQ-like domain PQQ-like domain This domain contains several repeats of the PQQ repeat. (from Pfam) NF024754.5 PF13361.11 UvrD_C 25.6 25.6 350 domain Y Y N 3'-5' exonuclease GO:0005524,GO:0016787 10514496,23580545 131567 cellular organisms no rank 388152 EBI-EMBL UvrD-like helicase C-terminal domain UvrD-like helicase C-terminal domain This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold. (from Pfam) NF024757.5 PF13364.11 BetaGal_ABD2 23 21 112 domain Y Y N beta galactosidase jelly roll domain-containing protein 15491613 131567 cellular organisms no rank 21512 EBI-EMBL Beta-galactosidase second all-beta domain Beta-galactosidase second all-beta domain This domain is the second all-beta domain from beta galactosidase enzymes which has a jelly roll fold [1]. These enzymes consist of a TIM-barrel catalytic domain and two all-beta domains (ABD), ABD1 is represented in Pfam:PF21317 and this entry represents ABD2. [1]. 15491613. Crystal structures of beta-galactosidase from Penicillium sp. and its complex with galactose. Rojas AL, Nagem RA, Neustroev KN, Arand M, Adamska M, Eneyskaya EV, Kulminskaya AA, Garratt RC, Golubev AM, Polikarpov I;. J Mol Biol. 2004;343:1281-1292. (from Pfam) NF024758.5 PF13365.11 Trypsin_2 27.6 27.6 144 domain Y Y N trypsin-like peptidase domain-containing protein 131567 cellular organisms no rank 354366 EBI-EMBL Trypsin-like peptidase domain Trypsin-like peptidase domain This family includes trypsin-like peptidase domains. (from Pfam) NF024759.5 PF13366.11 PDDEXK_3 22 22 117 domain Y Y N GxxExxY protein 15972856 131567 cellular organisms no rank 14126 EBI-EMBL PD-(D/E)XK nuclease superfamily GxxExxY protein Members of this family belong to the PD-(D/E)XK nuclease superfamily [1]. 15972856. Identification of novel restriction endonuclease-like fold families among hypothetical proteins. Kinch LN, Ginalski K, Rychlewski L, Grishin NV;. Nucleic Acids Res. 2005;33:3598-3605. (from Pfam) NF024760.5 PF13367.11 PrsW-protease 23.5 23.5 196 domain Y Y N PrsW family glutamic-type intramembrane protease 3.4.-.- GO:0008233,GO:0070007 16816000,21570408 131567 cellular organisms no rank 33415 EBI-EMBL PrsW family intramembrane metalloprotease PrsW family glutamic-type intramembrane protease Members of this family previously were thought to be metalloproteases but are now recognized to be glutamic-type intramembrane proteases. NF024762.5 PF13369.11 Transglut_core2 23.5 23.5 155 domain Y Y N transglutaminase family protein 131567 cellular organisms no rank 20858 EBI-EMBL Transglutaminase-like superfamily transglutaminase family protein NF024763.5 PF13370.11 Fer4_13 24.5 24.5 58 domain Y Y N 4Fe-4S domain-containing protein 7803404 131567 cellular organisms no rank 63167 EBI-EMBL 4Fe-4S single cluster domain of Ferredoxin I 4Fe-4S single cluster domain of Ferredoxin I Fer4_13 is a ferredoxin I from sulfate-reducing bacteria. Chemical sequence analysis suggests that this characteristic [4Fe-4S] cluster sulfur environment is widely distributed among ferredoxins [1]. [1]. 7803404. Crystal structure of the ferredoxin I from Desulfovibrio africanus at 2.3 A resolution. Sery A, Housset D, Serre L, Bonicel J, Hatchikian C, Frey M, Roth M;. Biochemistry. 1994;33:15408-15417. (from Pfam) NF024764.5 PF13371.11 TPR_9 35 35 73 PfamEq Y Y N tetratricopeptide repeat protein 131567 cellular organisms no rank 20872 EBI-EMBL Tetratricopeptide repeat Tetratricopeptide repeat NF024767.5 PF13374.11 TPR_10 27.5 14.7 42 domain Y Y N tetratricopeptide repeat protein 131567 cellular organisms no rank 220644 EBI-EMBL Tetratricopeptide repeat Tetratricopeptide repeat NF024769.5 PF13376.11 OmdA 25.6 25.6 60 domain Y Y N YdeI/OmpD-associated family protein 17010160,19767429 131567 cellular organisms no rank 46854 EBI-EMBL Bacteriocin-protection, YdeI or OmpD-Associated YdeI/OmpD-associated family protein This is a family of archaeal and bacterial proteins predicted to be periplasmic. YdeI is important for resistance to polymyxin B in broth and for bacterial survival in mice upon oral, but not intraperitoneal inoculation, suggesting a role for YdeI in the gastrointestinal tract of mice [1]. Production of the ydeI gene is regulated by the Rcs (regulator of capsule synthesis) phospho-relay system pathway independently of RcsA, and additionally transcription of the protein is regulated by the stationary-phase sigma factor, RpoS (sigma-S) [1]. YdeI confers protection against cationic AMPs (Antimicrobial peptides) or bacteriocins in conjunction with the general porin Omp, thus justifying its name of OmdA, for OmpD-Associated protein [2]. [1]. 17010160. The Rcs phosphorelay system is specific to enteric pathogens/commensals and activates ydeI, a gene important for persistent Salmonella infection of mice. Erickson KD, Detweiler CS;. Mol Microbiol. 2006;62:883-894. [2]. 19767429. A protein important for antimicrobial peptide resistance, YdeI/OmdA, is in the periplasm and interacts with OmpD/NmpC. Pilonieta MC, Erickson KD, Ernst RK, Detweiler CS;. J Bacteriol. 2009;191:7243-7252. (from Pfam) NF024771.5 PF13378.11 MR_MLE_C 29.4 29.4 219 domain Y Y N enolase C-terminal domain-like protein 15134446 131567 cellular organisms no rank 286750 EBI-EMBL Enolase C-terminal domain-like enolase C-terminal domain-like protein This domain appears at the C-terminus of many of the proteins that carry the MR_MLE_N Pfam:PF02746 domain. EC:4.2.1.40. (from Pfam) NF024772.5 PF13379.11 NMT1_2 24.7 24.7 252 domain Y Y N ABC transporter substrate-binding protein 10779519,16777960 131567 cellular organisms no rank 241696 EBI-EMBL NMT1-like family ABC transporter substrate-binding protein This family is closely related to the Pfam:PF09084 family. (from Pfam) NF024773.5 PF13380.11 CoA_binding_2 22.8 22.8 116 domain Y Y N CoA-binding protein 131567 cellular organisms no rank 131421 EBI-EMBL CoA binding domain CoA binding domain This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases. (from Pfam) NF024774.5 PF13382.11 Adenine_deam_C 27 27 169 domain Y Y N adenine deaminase C-terminal domain-containing protein 131567 cellular organisms no rank 36542 EBI-EMBL Adenine deaminase C-terminal domain Adenine deaminase C-terminal domain This family represents a C-terminal region of the adenine deaminase enzyme. (from Pfam) NF024775.5 PF13383.11 Methyltransf_22 22.4 22.4 252 domain Y N N Methyltransferase domain 131567 cellular organisms no rank 291 EBI-EMBL Methyltransferase domain Methyltransferase domain This family appears to be a methyltransferase domain. (from Pfam) NF024776.5 PF13384.11 HTH_23 24.6 24.6 50 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 243862 EBI-EMBL Homeodomain-like domain Homeodomain-like domain NF024777.5 PF13385.12 Laminin_G_3 27.6 27.6 151 domain Y Y N LamG-like jellyroll fold domain-containing protein 10368284,9480764 131567 cellular organisms no rank 129838 EBI-EMBL Concanavalin A-like lectin/glucanases superfamily LamG-like jellyroll fold domain This domain belongs to the Concanavalin A-like lectin/glucanases superfamily. (from Pfam) NF024778.5 PF13386.11 DsbD_2 24.9 24.9 199 domain Y Y N sulfite exporter TauE/SafE family protein 131567 cellular organisms no rank 87158 EBI-EMBL Cytochrome C biogenesis protein transmembrane region sulfite exporter TauE/SafE family protein NF024779.5 PF13387.11 DUF4105 22.2 22.2 169 domain Y Y N DUF4105 domain-containing protein 131567 cellular organisms no rank 27933 EBI-EMBL Domain of unknown function (DUF4105) Domain of unknown function (DUF4105) This is a family of uncharacterised bacterial proteins. There is a highly conserved histidine residue and a well-conserved NCT motif. (from Pfam) NF024783.5 PF13391.11 HNH_2 21 20 66 domain Y Y N HNH endonuclease 131567 cellular organisms no rank 47873 EBI-EMBL HNH endonuclease HNH endonuclease NF024784.5 PF13392.11 HNH_3 24.8 24.8 46 domain Y Y N HNH endonuclease 12527760 131567 cellular organisms no rank 30151 EBI-EMBL HNH endonuclease HNH endonuclease This is a zinc-binding loop of Fold group 7 [1] as found in endo-deoxy-ribonucleases and HNH nucleases. [1]. 12527760. Structural classification of zinc fingers: survey and summary. Krishna SS, Majumdar I, Grishin NV;. Nucleic Acids Res. 2003;31:532-550. (from Pfam) NF024785.5 PF13393.11 tRNA-synt_His 25 25 308 domain Y Y N ATP phosphoribosyltransferase regulatory subunit 131567 cellular organisms no rank 113618 EBI-EMBL Histidyl-tRNA synthetase ATP phosphoribosyltransferase regulatory subunit This is a family of class II aminoacyl-tRNA synthetase-like and ATP phosphoribosyltransferase regulatory subunits. (from Pfam) NF024787.5 PF13395.11 HNH_4 22 22 54 domain Y Y N HNH endonuclease domain-containing protein 28844692 131567 cellular organisms no rank 40057 EBI-EMBL HNH endonuclease HNH endonuclease This HNH nuclease domain is found in CRISPR-related proteins. (from Pfam) NF024788.5 PF13396.11 PLDc_N 23.3 23.3 42 domain Y Y N PLDc N-terminal domain-containing protein 131567 cellular organisms no rank 85285 EBI-EMBL Phospholipase_D-nuclease N-terminal Phospholipase_D-nuclease N-terminal This family is often found at the very N-terminus of proteins from the phospholipase_D-nuclease family, PLDc, Pfam:PF00614. However, a large number of members are full-length within this family. (from Pfam) NF024790.5 PF13398.11 Peptidase_M50B 26 26 201 PfamEq Y Y N M50 family metallopeptidase 131567 cellular organisms no rank 18563 EBI-EMBL Peptidase M50B-like M50 family metallopeptidase This is a family of bacterial and plant peptidases in the same family as MEROPS:M50B. (from Pfam) NF024793.5 PF13401.11 AAA_22 27 27 130 domain Y Y N AAA family ATPase GO:0016887 131567 cellular organisms no rank 370980 EBI-EMBL AAA domain AAA domain NF024795.5 PF13403.11 Hint_2 28.4 28.4 147 domain Y Y N Hint domain-containing protein 131567 cellular organisms no rank 26510 EBI-EMBL Hint domain Hint domain This domain is found in inteins. (from Pfam) NF024796.5 PF13404.11 HTH_AsnC-type 27 27 42 domain Y Y N AsnC family transcriptional regulator GO:0043565 131567 cellular organisms no rank 273111 EBI-EMBL AsnC-type helix-turn-helix domain AsnC-type helix-turn-helix domain NF024797.5 PF13405.11 EF-hand_6 25 22.9 30 domain Y N N EF-hand domain GO:0005509 131567 cellular organisms no rank 12312 EBI-EMBL EF-hand domain EF-hand domain NF024798.5 PF13406.11 SLT_2 24.3 23.9 292 domain Y Y N lytic murein transglycosylase 2.4.-.- 131567 cellular organisms no rank 91910 EBI-EMBL Transglycosylase SLT domain Transglycosylase SLT domain This family is related to the SLT domain Pfam:PF01464. (from Pfam) NF024799.5 PF13407.11 Peripla_BP_4 35.1 35.1 258 domain Y Y N substrate-binding domain-containing protein 131567 cellular organisms no rank 768051 EBI-EMBL Periplasmic binding protein domain transporter/transcription factor substrate-binding domain This domain is found in a variety of bacterial periplasmic binding proteins. This domain recognises fructose (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). (from Pfam) NF024800.5 PF13408.11 Zn_ribbon_recom 25.3 25.3 58 domain Y Y N recombinase zinc beta ribbon domain-containing protein 131567 cellular organisms no rank 88903 EBI-EMBL Recombinase zinc beta ribbon domain Recombinase zinc beta ribbon domain This short bacterial protein contains a zinc ribbon domain that is likely to be DNA-binding. This domain is found in site specific recombinase proteins. This family appears most closely related to Pfam:PF04606. (from Pfam) NF024801.5 PF13409.11 GST_N_2 25 25 70 domain Y N N Glutathione S-transferase, N-terminal domain GO:0005515,GO:0006749 131567 cellular organisms no rank 378611 EBI-EMBL Glutathione S-transferase, N-terminal domain Glutathione S-transferase, N-terminal domain This family is closely related to Pfam:PF02798. (from Pfam) NF024802.5 PF13410.11 GST_C_2 24.9 24.9 69 domain Y Y N glutathione S-transferase C-terminal domain-containing protein 131567 cellular organisms no rank 241001 EBI-EMBL Glutathione S-transferase, C-terminal domain Glutathione S-transferase, C-terminal domain This domain is closely related to Pfam:PF00043. (from Pfam) NF024803.5 PF13411.11 MerR_1 21.6 21.6 69 domain Y Y N MerR family transcriptional regulator GO:0003677,GO:0006355 131567 cellular organisms no rank 583569 EBI-EMBL MerR HTH family regulatory protein MerR family transcriptional regulator NF024804.5 PF13412.11 HTH_24 21.9 21.9 48 domain Y Y N winged helix-turn-helix transcriptional regulator 131567 cellular organisms no rank 788814 EBI-EMBL Winged helix-turn-helix DNA-binding winged helix-turn-helix transcriptional regulator NF024805.5 PF13413.11 HTH_25 24.6 24.6 62 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 78994 EBI-EMBL Helix-turn-helix domain Helix-turn-helix domain This domain is a helix-turn-helix domain that probably binds to DNA. (from Pfam) NF024806.5 PF13414.11 TPR_11 26.8 26.8 42 domain Y Y N tetratricopeptide repeat protein 131567 cellular organisms no rank 124992 EBI-EMBL TPR repeat TPR repeat NF024807.5 PF13415.11 Kelch_3 22 22 48 domain Y Y N kelch repeat-containing protein 10603472 131567 cellular organisms no rank 13742 EBI-EMBL Galactose oxidase, central domain Galactose oxidase, central domain NF024808.5 PF13416.11 SBP_bac_8 27 27 279 subfamily Y Y N extracellular solute-binding protein 131567 cellular organisms no rank 840671 EBI-EMBL Bacterial extracellular solute-binding protein extracellular solute-binding protein This family includes bacterial extracellular solute-binding proteins. (from Pfam) NF024809.5 PF13417.11 GST_N_3 22 22 75 domain Y Y N glutathione S-transferase N-terminal domain-containing protein GO:0005515,GO:0006749 131567 cellular organisms no rank 354790 EBI-EMBL Glutathione S-transferase, N-terminal domain Glutathione S-transferase, N-terminal domain NF024810.5 PF13418.11 Kelch_4 21.6 19.9 49 domain Y Y N kelch repeat-containing protein 10603472,27293192 131567 cellular organisms no rank 18651 EBI-EMBL Galactose oxidase, central domain Galactose oxidase, central domain NF024811.5 PF13419.11 HAD_2 23.8 23.8 178 domain Y Y N HAD hydrolase-like protein 131567 cellular organisms no rank 708385 EBI-EMBL Haloacid dehalogenase-like hydrolase HAD hydrolase-like protein NF024812.5 PF13420.12 Acetyltransf_4 24.3 24.3 155 subfamily Y Y N GNAT family N-acetyltransferase 2.3.1.- 131567 cellular organisms no rank 324289 EBI-EMBL Acetyltransferase (GNAT) domain Acetyltransferase (GNAT) domain NF024813.5 PF13421.11 Band_7_1 24 24 211 domain Y Y N SPFH domain-containing protein 131567 cellular organisms no rank 21177 EBI-EMBL SPFH domain-Band 7 family SPFH domain-Band 7 family NF024816.5 PF13424.11 TPR_12 30.1 30.1 77 domain Y Y N tetratricopeptide repeat protein 131567 cellular organisms no rank 300904 EBI-EMBL Tetratricopeptide repeat Tetratricopeptide repeat NF024818.5 PF13426.12 PAS_9 27 9.5 103 domain Y Y N PAS domain-containing protein 131567 cellular organisms no rank 886639 EBI-EMBL PAS domain PAS domain This domain is found in many signalling proteins in which it functions as a sensor domain. It recognises FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). (from Pfam) NF024819.5 PF13427.11 AadA_C 22.2 22.2 103 domain Y Y N aminoglycoside adenylyltransferase domain-containing protein 26527143,29871922 131567 cellular organisms no rank 11977 EBI-EMBL Aminoglycoside adenylyltransferase, C-terminal domain Aminoglycoside adenylyltransferase, C-terminal domain This domain is found at the C-terminal end of Aminoglycoside adenylyltransferase from Salmonella typhimurium (AadA) and other proteins associated with methicillin-resistant bacteria. AadA adenylates the 3''-hydroxyl group of the streptomycin glucosamine ring and the 9-hydroxyl group of the spectinomycin actinamine ring, mediating bacterial resistance to these antibiotics. This enzyme is organised into two domains: a N-terminal domain with a nucleotidyltransferase fold (Pfam:PF01909) and a C-terminal domain (this entry) which consists of five alpha-helices forming an up-and-down alpha-helical bundle. This domain undergoes small conformational changes upon binding of ATP and magnesium that play a key role in the binding of the antibiotic compounds [1,2]. [1]. 26527143. Structure of AadA from Salmonella enterica: a monomeric aminoglycoside (3'')(9) adenyltransferase. Chen Y, Nasvall J, Wu S, Andersson DI, Selmer M;. Acta Crystallogr D Biol Crystallogr. 2015;71:2267-2277. [2]. 29871922. Structural mechanism of AadA, a dual-specificity aminoglycoside adenylyltransferase from Salmonella enterica. Stern AL, Van der Verren SE, Kanchugal P S, Nasvall J, Gutierrez-de-Teran H, Selmer M;. J Biol Chem. 2018;293:11481-11490. (from Pfam) NF024820.5 PF13428.11 TPR_14 23.5 23.5 44 domain Y Y N tetratricopeptide repeat protein 131567 cellular organisms no rank 67226 EBI-EMBL Tetratricopeptide repeat Tetratricopeptide repeat NF024821.5 PF13429.11 TPR_15 26.2 26.2 280 domain Y Y N tetratricopeptide repeat protein 131567 cellular organisms no rank 18159 EBI-EMBL Tetratricopeptide repeat Tetratricopeptide repeat NF024822.5 PF13430.11 DUF4112 23.3 23.3 105 PfamAutoEq Y Y N DUF4112 domain-containing protein 131567 cellular organisms no rank 9502 EBI-EMBL Domain of unknown function (DUF4112) Domain of unknown function (DUF4112) This family has several highly conserved GD sequence-motifs of unknown function. The family is found in bacteria, archaea and fungi. (from Pfam) NF024823.5 PF13431.11 TPR_17 24.4 21.9 34 domain Y Y N tetratricopeptide repeat protein 131567 cellular organisms no rank 93573 EBI-EMBL Tetratricopeptide repeat Tetratricopeptide repeat NF024824.5 PF13432.11 TPR_16 32.7 15.5 65 domain Y Y N tetratricopeptide repeat protein 131567 cellular organisms no rank 515032 EBI-EMBL Tetratricopeptide repeat Tetratricopeptide repeat This family is found predominantly at the C-terminus of transglutaminase enzyme core regions. (from Pfam) NF024825.5 PF13433.11 Peripla_BP_5 27 27 363 domain Y Y N transporter substrate-binding protein 131567 cellular organisms no rank 211567 EBI-EMBL Periplasmic binding protein domain Periplasmic binding protein domain This domain is found in a variety of bacterial periplasmic binding proteins. (from Pfam) NF024826.5 PF13434.11 Lys_Orn_oxgnase 21.3 21.3 339 domain Y Y N SidA/IucD/PvdA family monooxygenase 16233371,16461464,8106324 131567 cellular organisms no rank 224431 EBI-EMBL L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase SidA/IucD/PvdA family monooxygenase This is a family of Rossmann fold oxidoreductases that catalyse NADPH-dependent hydroxylation and are involved in siderophore biosynthesis. This family includes L-ornithine 5-monooxygenase, which catalyses the hydroxylation of L-ornithine at the N5 position [1,2], and L-lysine 6-monooxygenase, which catalyses the hydroxylation of lysine at the N6 position (EC:1.14.13.59) [3]. [1]. 8106324. Cloning and nucleotide sequence of the pvdA gene encoding the pyoverdin biosynthetic enzyme L-ornithine N5-oxygenase in Pseudomonas aeruginosa. Visca P, Ciervo A, Orsi N;. J Bacteriol. 1994;176:1128-1140. [2]. 16233371. dffA gene from Aspergillus oryzae encodes L-ornithine N5-oxygenase and is indispensable for deferriferrichrysin biosynthesis. Yamada O, Na Nan S, Akao T, Tominaga M, Watanabe H, Satoh T, Enei H, Akita O;. J Biosci Bioeng. 2003;95:82-88. [3]. 16461464. A genetic locus required for iron acquisition in Mycobacterium tuberculosis. Krithika R, Marathe U, Saxena P, Ansari MZ, Mohanty D, Gokhale RS;. Proc Natl Acad Sci U S A. 2006;103:2069-2074. (from Pfam) NF024827.5 PF13435.11 Cytochrome_C554 20.8 14.9 84 domain Y Y N multiheme c-type cytochrome 11372197,2829828,9808046 131567 cellular organisms no rank 21808 EBI-EMBL Cytochrome c554 and c-prime cytochrome c554-like tetraheme domain The HMM describes a tetraheme c-type cytochrome domain as found in cytochrome c-554, a protein involved in nitrification of ammonia in Nitrosomonas europaea. Proteins with this domain are multi-heme proteins. NF024831.5 PF13439.11 Glyco_transf_4 28.5 28.5 170 domain Y Y N glycosyltransferase 2.4.-.- 131567 cellular organisms no rank 710699 EBI-EMBL Glycosyltransferase Family 4 glycosyltransferase NF024832.5 PF13440.11 Polysacc_synt_3 23 23 293 domain Y Y N oligosaccharide flippase family protein 131567 cellular organisms no rank 148753 EBI-EMBL Polysaccharide biosynthesis protein oligosaccharide flippase family protein NF024833.5 PF13441.11 Gly-zipper_YMGG 28.9 28.9 45 domain Y Y N YMGG-like glycine zipper-containing protein 131567 cellular organisms no rank 24474 EBI-EMBL YMGG-like Gly-zipper YMGG-like glycine zipper domain NF024835.5 PF13443.11 HTH_26 22 22 63 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 479428 EBI-EMBL Cro/C1-type HTH DNA-binding domain Cro/C1-type HTH DNA-binding domain This is a helix-turn-helix domain that probably binds to DNA. (from Pfam) NF024836.5 PF13444.11 Acetyltransf_5 22.4 22.4 102 domain Y Y N GNAT family N-acyltransferase 2.3.1.- 131567 cellular organisms no rank 56287 EBI-EMBL Acetyltransferase (GNAT) domain Acetyltransferase (GNAT) domain Characterized proteins containing this GNAT domain (typically annotated as N-acetyltranferases) include N-acyltranferases with EC numbers 2.3.1.184, 2.3.2.30, 2.3.1.228, and 2.3.1.229. NF024839.5 PF13447.11 Multi-haem_cyto 21.9 16.2 269 domain Y Y N multiheme c-type cytochrome 131567 cellular organisms no rank 1570 EBI-EMBL Seven times multi-haem cytochrome CxxCH multiheme c-type cytochrome domain This domain carries up to seven CxxCH repeated sequence motifs, characteristic of multi-haem cytochromes. (from Pfam) NF024840.5 PF13448.11 DUF4114 27 27 85 domain Y Y N DUF4114 domain-containing protein 131567 cellular organisms no rank 6926 EBI-EMBL Domain of unknown function (DUF4114) Domain of unknown function (DUF4114) This is a repeated domain that is found towards the C-terminal of many different types of bacterial proteins. There are highly conserved glutamate and aspartate residues suggesting that this domain might carry enzymic activity. (from Pfam) NF024841.5 PF13449.11 Phytase-like 27.6 27.6 284 domain Y Y N esterase-like activity of phytase family protein 131567 cellular organisms no rank 52147 EBI-EMBL Esterase-like activity of phytase esterase-like activity of phytase family protein This is a repeated domain that carries several highly conserved Glu and Asp residues indicating the likelihood that the domain incorporates the enzymic activity of the PLC-like phospho-diesterase part of the proteins. (from Pfam) NF024842.5 PF13450.11 NAD_binding_8 21.9 21.9 68 domain Y Y N NAD(P)-binding protein 131567 cellular organisms no rank 1779126 EBI-EMBL NAD(P)-binding Rossmann-like domain NAD(P)-binding Rossmann-like domain NF024843.5 PF13451.11 zf-trcl 24 24 48 domain Y Y N zinc-ribbon domain containing protein 131567 cellular organisms no rank 3625 EBI-EMBL Probable zinc-ribbon domain Probable zinc-ribbon domain This is a probable zinc-binding domain with two CxxC sequence motifs, found in various families of bacteria. (from Pfam) NF024844.5 PF13452.11 MaoC_dehydrat_N 22 22 132 domain Y Y N MaoC family dehydratase N-terminal domain-containing protein 131567 cellular organisms no rank 127952 EBI-EMBL N-terminal half of MaoC dehydratase N-terminal half of MaoC dehydratase It is clear from the structures of bacterial members of MaoC dehydratase, Pfam:PF01575, that the full-length functional dehydratase enzyme is made up of two structures that dimerise to form a whole. Divergence of the N- and C- monomers in higher eukaryotes has led to two distinct domains, this one and MaoC_dehydratas. However, in order to function as an enzyme both are required together. (from Pfam) NF024845.5 PF13453.11 zf-TFIIB 22 22 41 domain Y Y N zf-TFIIB domain-containing protein 131567 cellular organisms no rank 15651 EBI-EMBL Transcription factor zinc-finger Transcription factor zinc-finger NF024846.5 PF13454.11 NAD_binding_9 21.8 21.8 155 domain Y Y N FAD/NAD(P)-binding protein 131567 cellular organisms no rank 99749 EBI-EMBL FAD-NAD(P)-binding FAD/NAD(P)-binding protein NF024847.5 PF13455.11 MUG113 22.3 22 73 domain Y Y N GIY-YIG nuclease family protein 16303567 131567 cellular organisms no rank 23412 EBI-EMBL Meiotically up-regulated gene 113 GIY-YIG nuclease family protein This is a family of fungal proteins found to be up-regulated in meiosis. [1]. 16303567. A large-scale screen in S. pombe identifies seven novel genes required for critical meiotic events. Martin-Castellanos C, Blanco M, Rozalen AE, Perez-Hidalgo L, Garcia AI, Conde F, Mata J, Ellermeier C, Davis L, San-Segundo P, Smith GR, Moreno S;. Curr Biol. 2005;15:2056-2062. (from Pfam) NF024848.5 PF13456.11 RVT_3 21.6 21.6 123 domain Y Y N reverse transcriptase-like protein GO:0003676,GO:0004523 131567 cellular organisms no rank 28780 EBI-EMBL Reverse transcriptase-like reverse transcriptase-like protein This domain is found in plants and appears to be part of a retrotransposon. (from Pfam) NF024850.5 PF13458.11 Peripla_BP_6 31.7 31.7 343 domain Y Y N ABC transporter substrate-binding protein 131567 cellular organisms no rank 340597 EBI-EMBL Periplasmic binding protein ABC transporter substrate-binding protein This family includes a diverse range of periplasmic binding proteins. (from Pfam) NF024851.5 PF13459.11 Fer4_15 22.4 22.4 66 domain Y Y N ferredoxin 131567 cellular organisms no rank 69800 EBI-EMBL 4Fe-4S single cluster domain 4Fe-4S single cluster domain NF024852.5 PF13460.11 NAD_binding_10 27.2 27.2 184 domain Y Y N NAD(P)H-binding protein 131567 cellular organisms no rank 879735 EBI-EMBL NAD(P)H-binding NAD(P)H-binding protein NF024853.5 PF13462.11 Thioredoxin_4 23.2 23.2 165 domain Y Y N thioredoxin domain-containing protein 131567 cellular organisms no rank 143615 EBI-EMBL Thioredoxin Thioredoxin NF024854.5 PF13463.11 HTH_27 22.2 22.2 68 domain Y Y N winged helix DNA-binding protein GO:0003700,GO:0006355 131567 cellular organisms no rank 472259 EBI-EMBL Winged helix DNA-binding domain winged helix DNA-binding domain NF024857.5 PF13466.11 STAS_2 29.2 29.2 80 domain Y Y N STAS domain-containing protein 10662676 131567 cellular organisms no rank 170714 EBI-EMBL STAS domain STAS domain The STAS (after Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C-terminal region of Sulphate transporters and bacterial antisigma factor antagonists. It has been suggested that this domain may have a general NTP binding function [1]. [1]. 10662676. The STAS domain - a link between anion transporters and antisigma-factor antagonists. Aravind L, Koonin EV;. CurrBiol 2000;10:53-55. (from Pfam) NF024858.5 PF13467.11 RHH_4 25 25 67 domain Y Y N ribbon-helix-helix domain-containing protein 131567 cellular organisms no rank 14843 EBI-EMBL Ribbon-helix-helix domain Ribbon-helix-helix domain This short bacterial protein contains a ribbon-helix-helix domain that is likely to be DNA-binding. (from Pfam) NF024859.5 PF13468.11 Glyoxalase_3 25.1 25.1 176 domain Y Y N VOC family protein 131567 cellular organisms no rank 59663 EBI-EMBL Glyoxalase-like domain Glyoxalase-like domain This domain is related to the Glyoxalase domain Pfam:PF00903. (from Pfam) NF024860.5 PF13469.11 Sulfotransfer_3 27 27 216 domain Y Y N sulfotransferase 131567 cellular organisms no rank 65908 EBI-EMBL Sulfotransferase family sulfotransferase NF024861.5 PF13470.11 PIN_3 27 27 115 domain Y Y N PIN domain-containing protein 131567 cellular organisms no rank 28801 EBI-EMBL PIN domain PIN domain Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases). (from Pfam) NF024862.5 PF13471.11 Transglut_core3 26 26 117 domain Y Y N lasso peptide biosynthesis protein 131567 cellular organisms no rank 13515 EBI-EMBL Transglutaminase-like superfamily lasso peptide biosynthesis protein This family includes uncharacterised proteins that are related to the transglutaminase like domain Pfam:PF01841. (from Pfam) NF024863.5 PF13472.11 Lipase_GDSL_2 32.9 32.9 178 domain Y Y N GDSL-type esterase/lipase family protein 10801485,7610479 131567 cellular organisms no rank 374039 EBI-EMBL GDSL-like Lipase/Acylhydrolase family GDSL-type esterase/lipase family protein This family of presumed lipases and related enzymes are similar to Pfam:PF00657. [1]. 7610479. A new family of lipolytic enzymes?. Upton C, Buckley JT;. Trends Biochem Sci 1995;20:178-179. [2]. 10801485. Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases. Molgaard A, Kauppinen S, Larsen S;. Structure Fold Des 2000;8:373-383. (from Pfam) NF024864.5 PF13473.11 Cupredoxin_1 27 27 104 domain Y Y N cupredoxin domain-containing protein 131567 cellular organisms no rank 56395 EBI-EMBL Cupredoxin-like domain Cupredoxin-like domain The cupredoxin-like fold consists of a beta-sandwich with 7 strands in 2 beta-sheets, which is arranged in a Greek-key beta-barrel. (from Pfam) NF024865.5 PF13474.11 SnoaL_3 22 22 121 domain Y Y N nuclear transport factor 2 family protein 131567 cellular organisms no rank 98739 EBI-EMBL SnoaL-like domain SnoaL-like domain This family contains a large number of proteins that share the SnoaL fold. (from Pfam) NF024867.5 PF13476.11 AAA_23 27 27 201 domain Y Y N AAA family ATPase GO:0006302,GO:0016887 131567 cellular organisms no rank 458246 EBI-EMBL AAA domain AAA domain NF024868.5 PF13477.11 Glyco_trans_4_2 23.4 23.4 139 domain Y Y N glycosyltransferase 131567 cellular organisms no rank 112027 EBI-EMBL Glycosyl transferase 4-like glycosyltransferase NF024869.5 PF13478.11 XdhC_C 29.7 29.7 125 domain Y Y N XdhC family protein 131567 cellular organisms no rank 88823 EBI-EMBL XdhC Rossmann domain XdhC Rossmann domain This entry is the rossmann domain found in the Xanthine dehydrogenase accessory protein. (from Pfam) NF024870.5 PF13479.11 AAA_24 27 27 195 domain Y Y N AAA family ATPase 131567 cellular organisms no rank 19300 EBI-EMBL AAA domain AAA domain This AAA domain is found in a wide variety of presumed phage proteins. (from Pfam) NF024871.5 PF13480.12 Acetyltransf_6 22 22 143 subfamily Y Y N GNAT family N-acetyltransferase 2.3.1.- 131567 cellular organisms no rank 169261 EBI-EMBL Acetyltransferase (GNAT) domain Acetyltransferase (GNAT) domain This family contains proteins with N-acetyltransferase functions. (from Pfam) NF024872.5 PF13481.11 AAA_25 27 27 195 domain Y Y N AAA family ATPase 131567 cellular organisms no rank 198264 EBI-EMBL AAA domain AAA domain This AAA domain is found in a wide variety of presumed DNA repair proteins. (from Pfam) NF024873.5 PF13482.11 RNase_H_2 22 22 165 domain Y Y N ribonuclease H-like domain-containing protein 131567 cellular organisms no rank 51854 EBI-EMBL RNase_H superfamily RNase_H superfamily NF024874.5 PF13483.11 Lactamase_B_3 24 24 160 domain Y Y N MBL fold metallo-hydrolase 131567 cellular organisms no rank 158692 EBI-EMBL Beta-lactamase superfamily domain Beta-lactamase superfamily domain This family is part of the beta-lactamase superfamily and is related to Pfam:PF00753. (from Pfam) NF024875.5 PF13484.11 Fer4_16 30 30 66 domain Y Y N 4Fe-4S double cluster binding domain-containing protein 131567 cellular organisms no rank 92753 EBI-EMBL 4Fe-4S double cluster binding domain 4Fe-4S double cluster binding domain NF024876.5 PF13485.11 Peptidase_MA_2 32.4 32.4 201 domain Y Y N peptidase MA family metallohydrolase 131567 cellular organisms no rank 2616 EBI-EMBL Peptidase MA superfamily peptidase MA family metallohydrolase NF024879.5 PF13488.11 Gly-zipper_Omp 25 25 46 domain Y Y N glycine zipper domain-containing protein 131567 cellular organisms no rank 37756 EBI-EMBL Glycine zipper glycine zipper NF024880.5 PF13489.11 Methyltransf_23 27 27 164 domain Y Y N methyltransferase domain-containing protein 131567 cellular organisms no rank 1303350 EBI-EMBL Methyltransferase domain Methyltransferase domain This family appears to be a methyltransferase domain. (from Pfam) NF024883.5 PF13492.11 GAF_3 27 27 129 domain Y Y N GAF domain-containing protein GO:0005515 131567 cellular organisms no rank 166208 EBI-EMBL GAF domain GAF domain NF024884.5 PF13493.11 DUF4118 28.4 28.4 107 domain Y Y N DUF4118 domain-containing protein 131567 cellular organisms no rank 72719 EBI-EMBL Domain of unknown function (DUF4118) Domain of unknown function (DUF4118) This domain is found in a wide variety of bacterial signalling proteins. It is likely to be a transmembrane domain involved in ligand sensing. (from Pfam) NF024886.5 PF13495.11 Phage_int_SAM_4 27 27 85 domain Y Y N phage integrase N-terminal SAM-like domain-containing protein GO:0003677,GO:0015074 9311978 131567 cellular organisms no rank 66535 EBI-EMBL Phage integrase, N-terminal SAM-like domain Phage integrase, N-terminal SAM-like domain NF024890.5 PF13499.11 EF-hand_7 30 30 67 domain Y Y N EF-hand domain-containing protein GO:0005509 131567 cellular organisms no rank 25120 EBI-EMBL EF-hand domain pair EF-hand domain pair NF024891.5 PF13500.11 AAA_26 27 27 198 domain Y Y N AAA family ATPase 131567 cellular organisms no rank 165716 EBI-EMBL AAA domain AAA domain This domain is found in a number of proteins involved in cofactor biosynthesis such as dethiobiotin synthase and cobyric acid synthase. This domain contains a P-loop motif. (from Pfam) NF024892.5 PF13501.11 SoxY 28.4 28.4 112 domain Y Y N thiosulfate oxidation carrier protein SoxY 17327392 131567 cellular organisms no rank 11743 EBI-EMBL Sulfur oxidation protein SoxY thiosulfate oxidation carrier protein SoxY This domain is found in the sulfur oxidation protein SoxY. It is closely related to the Desulfoferrodoxin family Pfam:PF01880. Dissimilatory oxidation of thiosulfate is carried out by the ubiquitous sulfur-oxidizing (Sox) multi-enzyme system. In this system, SoxY plays a key role, functioning as the sulfur substrate-binding protein that offers its sulfur substrate, which is covalently bound to a conserved C-terminal cysteine, to another oxidizing Sox enzyme [1]. The structure of this domain shows an Ig-like fold [1]. [1]. 17327392. X-ray crystallographic analysis of the sulfur carrier protein SoxY from Chlorobium limicola f. thiosulfatophilum reveals a tetrameric structure. Stout J, Van Driessche G, Savvides SN, Van Beeumen J;. Protein Sci. 2007;16:589-601. (from Pfam) NF024896.5 PF13506.11 Glyco_transf_21 21.7 21.7 174 domain Y Y N glycosyltransferase GO:0016757 131567 cellular organisms no rank 177608 EBI-EMBL Glycosyl transferase family 21 glycosyltransferase This is a family of ceramide beta-glucosyltransferases - EC:2.4.1.80. (from Pfam) NF024897.5 PF13507.11 GATase_5 27 27 260 PfamEq Y Y N phosphoribosylformylglycinamidine synthase subunit PurQ 6.3.5.3 10966576 131567 cellular organisms no rank 88251 EBI-EMBL CobB/CobQ-like glutamine amidotransferase domain CobB/CobQ-like glutamine amidotransferase domain This family captures members that are not found in Pfam:PF00310, Pfam:PF07685 and Pfam:PF13230. [1]. 10966576. The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase. Galperin MY, Grishin NV;. Proteins 2000;41:238-247. (from Pfam) NF024898.5 PF13508.12 Acetyltransf_7 27 27 84 subfamily Y Y N GNAT family N-acetyltransferase 2.3.1.- GO:0016747 131567 cellular organisms no rank 1552109 EBI-EMBL Acetyltransferase (GNAT) domain Acetyltransferase (GNAT) domain This domain catalyses N-acetyltransferase reactions. (from Pfam) NF024900.5 PF13510.11 Fer2_4 22.8 22.8 82 domain Y Y N 2Fe-2S iron-sulfur cluster-binding protein 131567 cellular organisms no rank 153221 EBI-EMBL 2Fe-2S iron-sulfur cluster binding domain 2Fe-2S iron-sulfur cluster-binding domain The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This cluster appears within sarcosine oxidase proteins. (from Pfam) NF024903.5 PF13513.11 HEAT_EZ 27 24.5 55 domain Y N N HEAT-like repeat 131567 cellular organisms no rank 2024 EBI-EMBL HEAT-like repeat HEAT-like repeat The HEAT repeat family is related to armadillo/beta-catenin-like repeats (see Pfam:PF00514). These EZ repeats are found in subunits of cyanobacterial phycocyanin lyase and other proteins and probably carry out a scaffolding role. (from Pfam) NF024904.5 PF13514.11 AAA_27 22 22 206 domain Y Y N AAA family ATPase 131567 cellular organisms no rank 86333 EBI-EMBL AAA domain AAA domain This domain is found in a number of double-strand DNA break proteins. This domain contains a P-loop motif. (from Pfam) NF024905.5 PF13515.11 FUSC_2 25.6 25.6 126 domain Y Y N FUSC family protein 131567 cellular organisms no rank 203198 EBI-EMBL Fusaric acid resistance protein-like FUSC family protein NF024906.5 PF13516.11 LRR_6 23.4 8.7 24 repeat Y N N leucine-rich repeat protein GO:0005515 131567 cellular organisms no rank 16937 EBI-EMBL Leucine Rich repeat leucine-rich repeat NF024907.5 PF13517.11 FG-GAP_3 26.9 26.9 61 domain Y Y N FG-GAP-like repeat-containing protein 131567 cellular organisms no rank 125992 EBI-EMBL FG-GAP-like repeat FG-GAP-like repeat This entry represents a repeat found in alpha integrins and related proteins in which form a 7-fold repeat that adopts a beta-propeller fold. This repeat contains a putative calcium-binding site. These repeats are found in multiple proteins from eukaryotes and bacteria and mediate diverse biological processes at both molecular and cellular levels, such as cell-cell interactions, host-pathogen recognition or innate immune responses. (from Pfam) NF024908.5 PF13518.11 HTH_28 25 25 52 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 167273 EBI-EMBL Helix-turn-helix domain helix-turn-helix domain-containing protein This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding. (from Pfam) NF024909.5 PF13519.11 VWA_2 27 27 107 domain Y Y N VWA domain-containing protein 131567 cellular organisms no rank 270744 EBI-EMBL von Willebrand factor type A domain von Willebrand factor type A domain NF024910.5 PF13520.11 AA_permease_2 27 27 427 subfamily Y Y N amino acid permease GO:0016020,GO:0022857,GO:0055085 131567 cellular organisms no rank 591870 EBI-EMBL Amino acid permease amino acid permease NF024911.5 PF13521.11 AAA_28 27 27 164 domain Y Y N AAA family ATPase 131567 cellular organisms no rank 57027 EBI-EMBL AAA domain AAA domain NF024912.5 PF13522.11 GATase_6 27 27 130 domain Y N N Glutamine amidotransferase domain 131567 cellular organisms no rank 264835 EBI-EMBL Glutamine amidotransferase domain Glutamine amidotransferase domain This domain is a class-II glutamine amidotransferase domain found in a variety of enzymes, such as asparagine synthetase and glutamine--fructose-6-phosphate transaminase. (from Pfam) NF024913.5 PF13523.11 Acetyltransf_8 27 27 145 subfamily Y Y N GNAT family N-acetyltransferase 2.3.1.- 131567 cellular organisms no rank 74392 EBI-EMBL Acetyltransferase (GNAT) domain Acetyltransferase (GNAT) domain This domain catalyses N-acetyltransferase reactions. (from Pfam) NF024914.5 PF13524.11 Glyco_trans_1_2 25 25 92 domain Y Y N glycosyltransferase 2.4.-.- 131567 cellular organisms no rank 439101 EBI-EMBL Glycosyl transferases group 1 glycosyltransferase NF024916.5 PF13526.11 DUF4125 25 25 197 PfamAutoEq Y Y N DUF4125 family protein 131567 cellular organisms no rank 1731 EBI-EMBL Protein of unknown function (DUF4125) DUF4125 family protein NF024917.5 PF13527.12 Acetyltransf_9 25 25 127 subfamily Y Y N GNAT family N-acetyltransferase 2.3.1.- 131567 cellular organisms no rank 196699 EBI-EMBL Acetyltransferase (GNAT) domain Acetyltransferase (GNAT) domain This domain catalyses N-acetyltransferase reactions. (from Pfam) NF024918.5 PF13528.11 Glyco_trans_1_3 25 25 322 domain Y Y N glycosyltransferase family protein 131567 cellular organisms no rank 10840 EBI-EMBL Glycosyl transferase family 1 glycosyltransferase family protein NF024919.5 PF13529.11 Peptidase_C39_2 24 24 143 domain Y Y N C39 family peptidase 131567 cellular organisms no rank 57132 EBI-EMBL Peptidase_C39 like family C39 family peptidase NF024920.5 PF13530.11 SCP2_2 23.2 23.2 105 domain Y Y N sterol carrier protein domain-containing protein 131567 cellular organisms no rank 39410 EBI-EMBL Sterol carrier protein domain Sterol carrier protein domain NF024921.5 PF13531.11 SBP_bac_11 25 25 227 domain Y Y N substrate-binding domain-containing protein 131567 cellular organisms no rank 385185 EBI-EMBL Bacterial extracellular solute-binding protein Bacterial extracellular solute-binding protein This family includes bacterial extracellular solute-binding proteins. (from Pfam) NF024922.5 PF13532.11 2OG-FeII_Oxy_2 31.2 31.2 194 domain Y Y N alpha-ketoglutarate-dependent dioxygenase AlkB 131567 cellular organisms no rank 54011 EBI-EMBL 2OG-Fe(II) oxygenase superfamily alpha-ketoglutarate-dependent dioxygenase AlkB NF024923.5 PF13533.11 Biotin_lipoyl_2 23.3 23.3 50 domain Y Y N biotin/lipoyl-binding protein 131567 cellular organisms no rank 671165 EBI-EMBL Biotin-lipoyl like biotin/lipoyl-binding protein NF024924.5 PF13534.11 Fer4_17 22.2 22.2 61 domain Y Y N 4Fe-4S dicluster domain-containing protein 131567 cellular organisms no rank 253424 EBI-EMBL 4Fe-4S dicluster domain 4Fe-4S dicluster domain This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich. (from Pfam) NF024925.5 PF13535.11 ATP-grasp_4 27 27 160 domain Y Y N ATP-grasp domain-containing protein 131567 cellular organisms no rank 77008 EBI-EMBL ATP-grasp domain ATP-grasp domain This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity. (from Pfam) NF024926.5 PF13536.11 EmrE 25 25 263 domain Y Y N multidrug resistance efflux transporter family protein 131567 cellular organisms no rank 6470 EBI-EMBL Putative multidrug resistance efflux transporter multidrug resistance efflux transporter family protein This is a membrane protein family whose members are purported to be related to the DMT or Drug/Metabolite Transporter (DMT) Superfamily. Members are all uncharacterised. (from Pfam) NF024927.5 PF13537.11 GATase_7 25 25 123 domain Y N N Glutamine amidotransferase domain 131567 cellular organisms no rank 253490 EBI-EMBL Glutamine amidotransferase domain Glutamine amidotransferase domain This domain is a class-II glutamine amidotransferase domain found in a variety of enzymes such as asparagine synthetase and glutamine-fructose-6-phosphate transaminase. (from Pfam) NF024928.5 PF13538.11 UvrD_C_2 27.4 27.4 52 domain Y Y N ATP-binding domain-containing protein 21725019 131567 cellular organisms no rank 292589 EBI-EMBL UvrD-like helicase C-terminal domain UvrD-like helicase C-terminal domain This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold. (from Pfam) NF024929.5 PF13539.11 Peptidase_M15_4 25 25 70 domain Y Y N M15 family metallopeptidase GO:0008233 131567 cellular organisms no rank 27431 EBI-EMBL D-alanyl-D-alanine carboxypeptidase M15 family metallopeptidase This family resembles VanY, Pfam:PF02557, which is part of the peptidase M15 family. (from Pfam) NF024930.5 PF13540.11 RCC1_2 22 22 30 repeat Y N N RCC1 protein 9510255 131567 cellular organisms no rank 21706 EBI-EMBL Regulator of chromosome condensation (RCC1) repeat RCC1 repeat NF024931.5 PF13541.11 ChlI 27 27 121 domain Y Y N magnesium chelatase domain-containing protein 9359397,9457877 131567 cellular organisms no rank 174944 EBI-EMBL Subunit ChlI of Mg-chelatase Subunit ChlI of Mg-chelatase NF024932.5 PF13542.11 HTH_Tnp_ISL3 27.4 27.4 51 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 28644 EBI-EMBL Helix-turn-helix domain of transposase family ISL3 Helix-turn-helix domain of transposase family ISL3 NF024934.5 PF13545.11 HTH_Crp_2 27 27 70 domain Y Y N helix-turn-helix domain-containing protein GO:0003677,GO:0006355 131567 cellular organisms no rank 225924 EBI-EMBL Crp-like helix-turn-helix domain Crp-like helix-turn-helix domain This family represents a crp-like helix-turn-helix domain that is likely to bind DNA. (from Pfam) NF024935.5 PF13546.11 DDE_5 27 27 272 domain Y Y N transposase 131567 cellular organisms no rank 47395 EBI-EMBL DDE superfamily endonuclease transposase This family of proteins are related to Pfam:PF00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. (from Pfam) NF024937.5 PF13548.11 DUF4126 27.5 27.5 175 domain Y Y N DUF4126 family protein 131567 cellular organisms no rank 17340 EBI-EMBL Domain of unknown function (DUF4126) DUF4126 family protein NF024938.5 PF13549.11 ATP-grasp_5 27.6 27.6 221 domain Y Y N acetate--CoA ligase family protein 131567 cellular organisms no rank 117584 EBI-EMBL ATP-grasp domain ATP-grasp domain This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity. (from Pfam) NF024940.5 PF13551.11 HTH_29 28.1 28.1 64 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 84470 EBI-EMBL Winged helix-turn helix Winged helix-turn helix This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding. (from Pfam) NF024944.5 PF13555.11 AAA_29 27 27 61 domain Y Y N ATP-binding protein 131567 cellular organisms no rank 116208 EBI-EMBL P-loop containing region of AAA domain P-loop containing region of AAA domain NF024947.5 PF13558.11 SbcC_Walker_B 27 27 90 domain Y Y N SbcC/MukB-like Walker B domain-containing protein 21892167,26896444,28134932,31492634 131567 cellular organisms no rank 112654 EBI-EMBL SbcC/RAD50-like, Walker B motif SbcC/MukB-like Walker B domain This entry represents the Walker B domain of RAD50 from eukaryotes and the prokaryotic homologue SbcCD complex subunit C. RAD50-ATPase forms a complex with Mre11-nuclease that detects and processes diverse and obstructed DNA ends. This domain is separated of the Walker A domain by a long coiled-coil domain and forms the nucleotide-binding domain (NBD) when the coiled coils fold back on themselves and bring together Walker A and B domains [1,2,3,4]. Two RAD50-NBDs forms heterotetramers with a Mre11 nuclease dimer that assemble as catalytic head module that binds and cleaves DNA in an ATP-dependent reaction. Through secondary structural analysis, it has been suggested that there is a wide structural conservation in the Rad50/SMC protein family as seen in structural similarities between RAD50's hook and ABC-ATPase MukB's elbow region [4]. [1]. 26896444. Structural mechanism of ATP-dependent DNA binding and DNA end bridging by eukaryotic Rad50. Seifert FU, Lammens K, Stoehr G, Kessler B, Hopfner KP;. EMBO J. 2016;35:759-772. [2]. 21892167. The Rad50 coiled-coil domain is indispensable for Mre11 complex functions. Hohl M, Kwon Y, Galvan SM, Xue X, Tous C, Aguilera A, Sung P, Petrini JH;. Nat Struct Mol Biol. 2011;18:1124-1131. [3]. 28134932. Eukaryotic Rad50 functions as a rod-shaped dimer. Park YB, Hohl M, Padjasek M, Jeong E, Jin KS, Krezel A, Petrini JH, Cho Y;. Nat Struct Mol Biol. 2017;24:248-257. [4]. 31492634. Mechanism of DNA End Sensing and Processing by the Mre11-Rad50 Complex. Kashammer L, Saathoff JH, Lammens K, Gut F, Bartho J, Alt A, Kessler B, Hopfner KP;. Mol Cell. 2019;76:382-394. (from Pfam) NF024948.5 PF13559.11 DUF4129 24.8 24.8 69 domain Y Y N DUF4129 domain-containing protein 131567 cellular organisms no rank 52772 EBI-EMBL Domain of unknown function (DUF4129) Domain of unknown function (DUF4129) This presumed domain is found at the C-terminus of proteins that contain a transglutaminase core domain. The function of this domain is unknown. The domain has a conserved TXXE motif. (from Pfam) NF024949.5 PF13560.11 HTH_31 27 27 64 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 1174063 EBI-EMBL Helix-turn-helix domain helix-turn-helix domain-containing protein This domain is a helix-turn-helix domain that probably binds to DNA. (from Pfam) NF024950.5 PF13561.11 adh_short_C2 27 27 236 subfamily Y Y N SDR family oxidoreductase 131567 cellular organisms no rank 2635186 EBI-EMBL Enoyl-(Acyl carrier protein) reductase SDR family oxidoreductase This domain is found in Enoyl-(Acyl carrier protein) reductases. (from Pfam) NF024951.5 PF13562.11 NTP_transf_4 27 27 153 subfamily Y Y N putative sugar nucleotidyl transferase 131567 cellular organisms no rank 5215 EBI-EMBL Sugar nucleotidyl transferase putative sugar nucleotidyl transferase This is a probable sugar nucleotidyl transferase family. (from Pfam) NF024952.5 PF13563.11 2_5_RNA_ligase2 27 27 152 domain Y Y N 2'-5' RNA ligase family protein 131567 cellular organisms no rank 89000 EBI-EMBL 2'-5' RNA ligase superfamily 2'-5' RNA ligase family protein This family contains proteins related to Pfam:PF02834. These proteins are likely to be enzymes, but they may not share the RNA ligase activity. (from Pfam) NF024953.5 PF13564.11 DoxX_2 26.3 26.3 103 domain Y Y N DoxX family protein 131567 cellular organisms no rank 56070 EBI-EMBL DoxX-like family DoxX family protein This family of uncharacterised proteins are related to DoxX Pfam:PF07681. (from Pfam) NF024954.5 PF13565.11 HTH_32 33.7 33.7 73 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 73186 EBI-EMBL Homeodomain-like domain Homeodomain-like domain NF024955.5 PF13566.11 DUF4130 27 27 146 PfamAutoEq Y Y N DUF4130 domain-containing protein 131567 cellular organisms no rank 19949 EBI-EMBL Domain of unknown function (DUF4130 Domain of unknown function (DUF4130 NF024959.5 PF13570.11 PQQ_3 22 18 40 domain Y Y N PQQ-binding-like beta-propeller repeat protein 131567 cellular organisms no rank 101303 EBI-EMBL PQQ-like domain PQQ-like domain NF024963.5 PF13574.11 Reprolysin_2 27 27 195 domain Y N N Metallo-peptidase family M12B Reprolysin-like 131567 cellular organisms no rank 11216 EBI-EMBL Metallo-peptidase family M12B Reprolysin-like Metallo-peptidase family M12B Reprolysin-like This zinc-binding metallo-peptidase has the characteristic binding motif HExxGHxxGxxH of Reprolysin-like peptidases of family M12B. (from Pfam) NF024964.5 PF13575.11 DUF4135 29 29 378 domain Y Y N DUF4135 domain-containing protein 131567 cellular organisms no rank 13407 EBI-EMBL Domain of unknown function (DUF4135) Domain of unknown function (DUF4135) This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 380 amino acids in length. The family is found in association with Pfam:PF05147. This domain may be involved in synthesis of a lantibiotic compound. (from Pfam) NF024965.5 PF13576.11 Pentapeptide_3 27 27 48 domain Y Y N pentapeptide repeat-containing protein 9655353 131567 cellular organisms no rank 31140 EBI-EMBL Pentapeptide repeats (9 copies) Pentapeptide repeats (9 copies) NF024966.5 PF13577.11 SnoaL_4 24 24 126 domain Y Y N nuclear transport factor 2 family protein 131567 cellular organisms no rank 121639 EBI-EMBL SnoaL-like domain SnoaL-like domain This family contains a large number of proteins that share the SnoaL fold. (from Pfam) NF024967.5 PF13578.11 Methyltransf_24 26.3 26.3 105 domain Y Y N class I SAM-dependent methyltransferase 2.1.1.- 131567 cellular organisms no rank 130767 EBI-EMBL Methyltransferase domain Methyltransferase domain This family appears to be a methyltransferase domain. (from Pfam) NF024968.5 PF13579.11 Glyco_trans_4_4 29.7 29.7 158 domain Y Y N glycosyltransferase 131567 cellular organisms no rank 487912 EBI-EMBL Glycosyl transferase 4-like domain Glycosyl transferase 4-like domain NF024969.5 PF13580.11 SIS_2 27 27 138 domain Y Y N SIS domain-containing protein GO:0097367,GO:1901135 10203754 131567 cellular organisms no rank 90382 EBI-EMBL SIS domain SIS domain SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars. [1]. 10203754. The SIS domain: a phosphosugar-binding domain. Bateman A;. Trends Biochem Sci 1999;24:94-95. (from Pfam) NF024970.5 PF13581.11 HATPase_c_2 27.4 27.4 127 domain Y Y N ATP-binding protein 131567 cellular organisms no rank 559231 EBI-EMBL Histidine kinase-like ATPase domain Histidine kinase-like ATPase domain NF024971.5 PF13582.11 Reprolysin_3 22.4 22.4 123 domain Y Y N zinc-dependent metalloprotease family protein 131567 cellular organisms no rank 23322 EBI-EMBL Metallo-peptidase family M12B Reprolysin-like zinc-dependent metalloprotease family protein This zinc-binding metallo-peptidase has the characteristic binding motif HExxGHxxGxxH of Reprolysin-like peptidases of family M12B. (from Pfam) NF024972.5 PF13583.11 Reprolysin_4 22 22 203 domain Y Y N reprolysin-like metallopeptidase GO:0008237,GO:0008270 131567 cellular organisms no rank 26119 EBI-EMBL Metallo-peptidase family M12B Reprolysin-like reprolysin-like metallopeptidase catalytic domain This zinc-binding metallo-peptidase has the characteristic binding motif HExxGHxxGxxH of Reprolysin-like peptidases of family M12B. (from Pfam) NF024973.5 PF13584.11 BatD 24.1 24.1 92 domain Y Y N BatD family protein 10216867 131567 cellular organisms no rank 24201 EBI-EMBL BatD DUF11 like domain BatD DUF11 like domain This domain that probably has an Ig-like fold is found in three copies in BatD proteins that are involved in tolerance to oxygen in in Bacteroides spp. [1]. 10216867. Characterization of the Batl (Bacteroides aerotolerance) operon in Bacteroides fragilis: isolation of a B. fragilis mutant with reduced aerotolerance and impaired growth in in vivo model systems. Tang YP, Dallas MM, Malamy MH;. Mol Microbiol. 1999;32:139-149. (from Pfam) NF024975.5 PF13586.11 DDE_Tnp_1_2 29.2 29.2 86 domain Y Y N transposase 131567 cellular organisms no rank 62172 EBI-EMBL Transposase DDE domain transposase Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. (from Pfam) NF024976.5 PF13588.11 HSDR_N_2 25 25 110 domain Y Y N type I restriction enzyme HsdR N-terminal domain-containing protein 10449767,11555298 131567 cellular organisms no rank 27088 EBI-EMBL Type I restriction enzyme R protein N terminus (HSDR_N) Type I restriction enzyme R protein N terminus (HSDR_N) This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA [1]. Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA [2]. [1]. 11555298. Analysis of type I restriction modification systems in the Neisseriaceae: genetic organization and properties of the gene products. Piekarowicz A, Klyz A, Kwiatek A, Stein DC;. Mol Microbiol 2001;41:1199-1210. [2]. 10449767. Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymes. Makovets S, Doronina VA, Murray NE;. Proc Natl Acad Sci U S A 1999;96:9757-9762. (from Pfam) NF024977.5 PF13589.11 HATPase_c_3 25 25 137 domain Y Y N ATP-binding protein 18361456 131567 cellular organisms no rank 213092 EBI-EMBL Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ATP-binding protein This family represents, additionally, the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90. [1]. 18361456. Crystal structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source. Li Y, Bahti P, Shaw N, Song G, Chen S, Zhang X, Zhang M, Cheng C, Yin J, Zhu JY, Zhang H, Che D, Xu H, Abbas A, Wang BC, Liu ZJ;. Proteins 2008;71:2109-13. (from Pfam) NF024980.5 PF13592.11 HTH_33 25 25 60 domain Y Y N winged helix-turn-helix domain-containing protein 131567 cellular organisms no rank 30520 EBI-EMBL Winged helix-turn helix Winged helix-turn helix This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding. (from Pfam) NF024981.5 PF13593.11 SBF_like 25 25 313 domain Y Y N bile acid:sodium symporter 131567 cellular organisms no rank 80444 EBI-EMBL SBF-like CPA transporter family (DUF4137) bile acid:sodium symporter These family members are 7TM putative membrane transporter proteins. The family is similar to the SBF family of bile-acid symporters, Pfam:PF01758. (from Pfam) NF024983.5 PF13596.11 PAS_10 22.1 22.1 106 domain Y Y N PAS domain-containing protein 131567 cellular organisms no rank 46663 EBI-EMBL PAS domain PAS domain This is a sensor domain that recognises O2, CO and NO (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). (from Pfam) NF024984.5 PF13597.11 NRDD 26.2 26.2 562 subfamily Y Y N anaerobic ribonucleoside-triphosphate reductase nrdD 1.1.98.6 GO:0006260,GO:0008998,GO:0016491 26147435 131567 cellular organisms no rank 41177 EBI-EMBL Anaerobic ribonucleoside-triphosphate reductase anaerobic ribonucleoside-triphosphate reductase NF024985.5 PF13598.11 DUF4139 31.8 31.8 205 domain Y Y N DUF4139 domain-containing protein 131567 cellular organisms no rank 18402 EBI-EMBL Domain of unknown function (DUF4139) Domain of unknown function (DUF4139) This family is usually found at the C-terminus of proteins. (from Pfam) NF024986.5 PF13599.11 Pentapeptide_4 27 27 78 domain Y Y N pentapeptide repeat-containing protein 9655353 131567 cellular organisms no rank 108054 EBI-EMBL Pentapeptide repeats (9 copies) Pentapeptide repeats (9 copies) NF024987.5 PF13600.11 DUF4140 27 27 98 domain Y Y N DUF4140 domain-containing protein 131567 cellular organisms no rank 14471 EBI-EMBL N-terminal domain of unknown function (DUF4140) N-terminal domain of unknown function (DUF4140) This family is often found at the N-terminus of its member proteins, with DUF4139, Pfam:PF13598, at the C-terminus. (from Pfam) NF024988.5 PF13601.11 HTH_34 27 27 80 domain Y Y N transcriptional regulator 131567 cellular organisms no rank 48341 EBI-EMBL Winged helix DNA-binding domain Winged helix DNA-binding domain NF024989.5 PF13602.11 ADH_zinc_N_2 27 27 134 domain Y Y N zinc-binding dehydrogenase 131567 cellular organisms no rank 714601 EBI-EMBL Zinc-binding dehydrogenase zinc-binding dehydrogenase NF024990.5 PF13603.11 tRNA-synt_1_2 25 25 185 domain Y N N Leucyl-tRNA synthetase, editing domain GO:0002161,GO:0006418 10811626,12718881,15663927,15970591,16277600 131567 cellular organisms no rank 186391 EBI-EMBL Leucyl-tRNA synthetase, editing domain Leucyl-tRNA synthetase, editing domain This entry represents the editing domain in Leucine-tRNA ligase or Leucyl-tRNA synthetase, EC:6.1.1.4. Paper describing PDB structure 1h3n. [1]. 10811626. The 2 A crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue. Cusack S, Yaremchuk A, Tukalo M;. EMBO J. 2000;19:2351-2361. Paper describing PDB structure 1obc. [2]. 12718881. Structural and mechanistic basis of pre- and posttransfer editing by leucyl-tRNA synthetase. Lincecum TL Jr, Tukalo M, Yaremchuk A, Mursinna RS, Williams AM, Sproat BS, Van Den Eynde W, Link A, Van Calenbergh S, Grotli M, Martinis SA, Cusack S;. Mol Cell. 2003;11:951-963. Paper describing PDB structure 1wk9. [3]. 15970591. Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain. Fukunaga R, Yokoyama S;. J Biol Chem. 2005;280:29937-29945. Paper describing PDB structure 1wkb. [4]. 15663927. Crystal structure of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii reveals a novel editing domain orientation. Fukunaga R, Yokoyama S;. J Mol Biol. 2005;346:57-71. Paper describing PDB structure 2ajg. [5]. 16277600. Crystal structures of the editing domain of Escherichia coli leucyl-tRNA synthetase and its complexes with Met and Ile reveal a lock-and-key mechanism for amino acid discrimination. Liu Y, Liao J, Zhu B, Wang ED, Ding J;. Biochem J. 2006;394:399-407. (from Pfam) NF024991.5 PF13604.11 AAA_30 27 27 191 domain Y Y N AAA family ATPase 131567 cellular organisms no rank 289601 EBI-EMBL AAA domain AAA domain This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B. (from Pfam) NF024993.5 PF13606.11 Ank_3 22.3 17.2 30 repeat Y N N ankyrin repeat protein GO:0005515 131567 cellular organisms no rank 78940 EBI-EMBL Ankyrin repeat ankyrin repeat Ankyrins are multifunctional adaptors that link specific proteins to the membrane-associated, spectrin- actin cytoskeleton. This repeat-domain is a 'membrane-binding' domain of up to 24 repeated units, and it mediates most of the protein's binding activities. (from Pfam) NF024994.5 PF13607.11 Succ_CoA_lig 27.4 27.4 138 domain Y N N Succinyl-CoA ligase like flavodoxin domain 11781092 131567 cellular organisms no rank 121664 EBI-EMBL Succinyl-CoA ligase like flavodoxin domain Succinyl-CoA ligase like flavodoxin domain This domain contains the catalytic domain from Succinyl-CoA ligase alpha subunit and other related enzymes. A conserved histidine is involved in phosphoryl transfer. [1]. 11781092. Two glutamate residues, Glu 208 alpha and Glu 197 beta, are crucial for phosphorylation and dephosphorylation of the active-site histidine residue in succinyl-CoA synthetase. Fraser ME, Joyce MA, Ryan DG, Wolodko WT;. Biochemistry. 2002;41:537-546. (from Pfam) NF024997.5 PF13610.11 DDE_Tnp_IS240 27 27 139 domain Y Y N DDE-type integrase/transposase/recombinase 131567 cellular organisms no rank 55684 EBI-EMBL DDE domain DDE-type integrase/transposase/recombinase This DDE domain is found in a wide variety of transposases including those found in IS240, IS26, IS6100 and IS26. (from Pfam) NF024999.5 PF13612.11 DDE_Tnp_1_3 27 27 155 domain Y Y N transposase 2542093,6268937,8335077 131567 cellular organisms no rank 42249 EBI-EMBL Transposase DDE domain Transposase DDE domain Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contains three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction [3]. [1]. 6268937. The sequence of IS4. Klaer R, Kuhn S, Tillmann E, Fritz HJ, Starlinger P;. Mol Gen Genet 1981;181:169-175. [2]. 2542093. IS421, a new insertion sequence in Escherichia coli. Sato S, Nakada Y, Shiratsuchi A;. FEBS Lett 1989;249:21-26. [3]. 8335077. Identification and analysis of the gas vesicle gene cluster on an unstable plasmid of Halobacterium halobium. DasSarma S;. Plasmid 1993;29:1-9. (from Pfam) NF025000.5 PF13613.11 HTH_Tnp_4 27 27 53 domain Y Y N transposase family protein 131567 cellular organisms no rank 28317 EBI-EMBL Helix-turn-helix of DDE superfamily endonuclease transposase family protein This domain is the probable DNA-binding region of transposase enzymes, necessary for efficient DNA transposition. Most of the members derive from the IS superfamily IS5 and rather fewer from IS4. (from Pfam) NF025001.5 PF13614.11 AAA_31 27 27 177 domain Y Y N AAA family ATPase 131567 cellular organisms no rank 493233 EBI-EMBL AAA domain AAA domain This family includes a wide variety of AAA domains including some that have lost essential nucleotide binding residues in the P-loop. (from Pfam) NF025002.5 PF13616.11 Rotamase_3 22.5 22.5 116 domain Y Y N peptidylprolyl isomerase 5.2.1.8 131567 cellular organisms no rank 128281 EBI-EMBL PPIC-type PPIASE domain PPIC-type PPIASE domain Rotamases increase the rate of protein folding by catalysing the interconversion of cis-proline and trans-proline. (from Pfam) NF025004.5 PF13618.11 Gluconate_2-dh3 23.4 23.4 135 domain Y Y N gluconate 2-dehydrogenase subunit 3 family protein 9352901 131567 cellular organisms no rank 25345 EBI-EMBL Gluconate 2-dehydrogenase subunit 3 gluconate 2-dehydrogenase subunit 3 family protein This family corresponds to subunit 3 of the Gluconate 2-dehydrogenase enzyme that catalyses the conversion of gluconate to 2-dehydro-D-gluconate [1] EC:1.1.99.3. [1]. 9352901. Cloning and expression of a gene cluster encoding three subunits of membrane-bound gluconate dehydrogenase from Erwinia cypripedii ATCC 29267 in Escherichia coli. Yum DY, Lee YP, Pan JG;. J Bacteriol. 1997;179:6566-6572. (from Pfam) NF025005.5 PF13619.11 KTSC 25 25 58 domain Y Y N KTSC domain-containing protein 131567 cellular organisms no rank 12827 EBI-EMBL KTSC domain KTSC domain This short domain is named after Lysine tRNA synthetase C-terminal domain. It is found at the C-terminus of some Lysyl tRNA synthetases as well as a single domain in bacterial proteins. The domain is about 60 amino acids in length and contains a reasonably conserved YXY motif in the centre of the sequence. The function of this domain is unknown but it could be an RNA binding domain. (from Pfam) NF025006.5 PF13620.11 CarboxypepD_reg 32.3 32.3 82 domain Y Y N carboxypeptidase regulatory-like domain-containing protein 131567 cellular organisms no rank 492222 EBI-EMBL Carboxypeptidase regulatory-like domain Carboxypeptidase regulatory-like domain NF025008.5 PF13622.11 4HBT_3 24.3 24.3 83 domain Y Y N acyl-CoA thioesterase domain-containing protein 15307895 131567 cellular organisms no rank 134865 EBI-EMBL Acyl-CoA thioesterase N-terminal domain Acyl-CoA thioesterase N-terminal domain This family contains a wide variety of enzymes, principally acyl-CoA thioesterases. These enzymes are part of the Hotdog fold superfamily [1]. This entry is usually found as the N-terminal part of a pair of HotDog domains. [1]. 15307895. The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases. Dillon SC, Bateman A;. BMC Bioinformatics 2004;5:109-109. (from Pfam) NF025009.5 PF13623.11 SurA_N_2 28.5 28.5 145 domain Y Y N SurA N-terminal domain-containing protein 12429090,20970503,32358557 131567 cellular organisms no rank 74959 EBI-EMBL SurA-like N-terminal domain SurA-like N-terminal domain This domain is found at the N-terminal of the chaperone SurA and related proteins such as PpiD and foldase PrsA [1,2,3]. This is a helical domain that together with the C-terminal forms a domain containing substrate-binding sites [2,3]. The C-terminal of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. [1]. 12429090. Crystallographic structure of SurA, a molecular chaperone that facilitates folding of outer membrane porins. Bitto E, McKay DB;. Structure. 2002;10:1489-1498. [2]. 32358557. Inter-domain dynamics in the chaperone SurA and multi-site binding to its outer membrane protein clients. Calabrese AN, Schiffrin B, Watson M, Karamanos TK, Walko M, Humes JR, Horne JE, White P, Wilson AJ, Kalli AC, Tuma R, Ashcroft AE, Brockwell DJ, Radford SE;. Nat Commun. 2020;11:2155. [3]. 20970503. The crystal structure of the leptospiral hypothetical protein LIC12922 reveals homology with the periplasmic chaperone SurA. Giuseppe PO, Von Atzingen M, Nascimento AL, Zanchin NI, Guimaraes BG;. J Struct Biol. 2011;173:312-322. (from Pfam) NF025010.5 PF13624.11 SurA_N_3 27.2 27.2 162 domain Y Y N SurA N-terminal domain-containing protein 12429090,20970503,32358557 131567 cellular organisms no rank 91653 EBI-EMBL SurA-like N-terminal domain SurA-like N-terminal domain This domain is found at the N-terminus of the chaperone SurA and related proteins such as PpiD and foldase PrsA [1,2]. It is a helical domain that together with the C-terminal, forms a domain containing substrate-binding sites [2,3]. The C-terminal of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. [1]. 12429090. Crystallographic structure of SurA, a molecular chaperone that facilitates folding of outer membrane porins. Bitto E, McKay DB;. Structure. 2002;10:1489-1498. [2]. 20970503. The crystal structure of the leptospiral hypothetical protein LIC12922 reveals homology with the periplasmic chaperone SurA. Giuseppe PO, Von Atzingen M, Nascimento AL, Zanchin NI, Guimaraes BG;. J Struct Biol. 2011;173:312-322. [3]. 32358557. Inter-domain dynamics in the chaperone SurA and multi-site binding to its outer membrane protein clients. Calabrese AN, Schiffrin B, Watson M, Karamanos TK, Walko M, Humes JR, Horne JE, White P, Wilson AJ, Kalli AC, Tuma R, Ashcroft AE, Brockwell DJ, Radford SE;. Nat Commun. 2020;11:2155. (from Pfam) NF025011.5 PF13625.11 Helicase_C_3 34.2 34.2 125 domain Y Y N helicase-associated domain-containing protein 131567 cellular organisms no rank 37598 EBI-EMBL Helicase conserved C-terminal domain Helicase conserved C-terminal domain This domain family is found in a wide variety of helicases and helicase-related proteins. (from Pfam) NF025013.5 PF13628.11 DUF4142 27 27 138 domain Y Y N DUF4142 domain-containing protein 131567 cellular organisms no rank 58383 EBI-EMBL Domain of unknown function (DUF4142) Domain of unknown function (DUF4142) This is a bacterial family of unknown function. (from Pfam) NF025014.5 PF13629.11 T2SS-T3SS_pil_N 23 23 72 domain Y Y N pilus assembly protein N-terminal domain-containing protein 131567 cellular organisms no rank 29830 EBI-EMBL Pilus formation protein N terminal region Pilus formation protein N terminal region NF025015.5 PF13630.11 SdpI 28.2 28.2 71 domain Y Y N SdpI family protein 16469701 131567 cellular organisms no rank 18400 EBI-EMBL SdpI/YfhL protein family SdpI family protein This family of proteins includes the SdpI and YfhL proteins from B. subtilis. The SdpI protein is a multipass integral membrane protein that protects toxin-producing cells from being killed. Killing is mediated by the exported toxic protein SdpC an extracellular protein that induces the synthesis of an immunity protein [1]. [1]. 16469701. A three-protein signaling pathway governing immunity to a bacterial cannibalism toxin. Ellermeier CD, Hobbs EC, Gonzalez-Pastor JE, Losick R;. Cell. 2006;124:549-559. (from Pfam) NF025016.5 PF13631.11 Cytochrom_B_N_2 27 27 169 domain Y Y N cytochrome b N-terminal domain-containing protein GO:0009055,GO:0016020,GO:0016491 131567 cellular organisms no rank 47091 EBI-EMBL Cytochrome b(N-terminal)/b6/petB Cytochrome b(N-terminal)/b6/petB NF025017.5 PF13632.11 Glyco_trans_2_3 27 27 198 domain Y Y N glycosyltransferase family 2 protein 11953367,9515923 131567 cellular organisms no rank 248961 EBI-EMBL Glycosyl transferase family group 2 glycosyltransferase family 2 protein Members of this family of prokaryotic proteins include putative glucosyltransferases, which are involved in bacterial capsule biosynthesis [1][2]. [1]. 9515923. Characterization of the gene cassette required for biosynthesis of the (alpha1-->6)-linked N-acetyl-D-mannosamine-1-phosphate capsule of serogroup A Neisseria meningitidis. Swartley JS, Liu LJ, Miller YK, Martin LE, Edupuganti S, Stephens DS;. J Bacteriol. 1998;180:1533-1539. [2]. 11953367. Novel Aeromonas hydrophila PPD134/91 genes involved in O-antigen and capsule biosynthesis. Zhang YL, Arakawa E, Leung KY;. Infect Immun. 2002;70:2326-2335. (from Pfam) NF025019.5 PF13635.11 DUF4143 28.1 28.1 160 domain Y Y N DUF4143 domain-containing protein 131567 cellular organisms no rank 53593 EBI-EMBL Domain of unknown function (DUF4143) Domain of unknown function (DUF4143) This domain is almost always found C-terminal to an ATPase core family. (from Pfam) NF025020.5 PF13636.11 Methyltranf_PUA 27.6 27.6 49 domain Y Y N methyltransferase RsmF C-terminal domain-like protein 20558545 131567 cellular organisms no rank 25572 EBI-EMBL RNA-binding PUA-like domain of methyltransferase RsmF methyltransferase RsmF C-terminus-like domain Methyltranf_PUA is the second of two C-terminal domains found on bacterial methyltransferase RsmF that modifies the 16S ribosomal RNA. It has some structural similarity to the RNA-binding PUA domains suggesting that it is involved in RNA recognition. It lies downstream of the catalytic centre of this methyltransferase, family Pfam:PF01189 [1]. [1]. 20558545. Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus. Demirci H, Larsen LH, Hansen T, Rasmussen A, Cadambi A, Gregory ST, Kirpekar F, Jogl G;. RNA. 2010;16:1584-1596. (from Pfam) NF025021.5 PF13637.11 Ank_4 22.7 22.7 50 domain Y Y N ankyrin repeat domain-containing protein GO:0005515 131567 cellular organisms no rank 104809 EBI-EMBL Ankyrin repeats (many copies) Ankyrin repeats (many copies) NF025022.5 PF13638.11 PIN_4 21.9 21.9 132 domain Y Y N PIN domain-containing protein 131567 cellular organisms no rank 34326 EBI-EMBL PIN domain PIN domain Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases). (from Pfam) NF025024.5 PF13640.11 2OG-FeII_Oxy_3 27 27 98 domain Y Y N 2OG-Fe(II) oxygenase GO:0016491 11276424 131567 cellular organisms no rank 58693 EBI-EMBL 2OG-Fe(II) oxygenase superfamily 2OG-Fe(II) oxygenase This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1]. [1]. 11276424. The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. Aravind L, Koonin EV;. Genome Biol 2001;2:RESEARCH0007. (from Pfam) NF025025.5 PF13641.11 Glyco_tranf_2_3 27 27 230 domain Y Y N glycosyltransferase 2.4.-.- 11953367,9515923 131567 cellular organisms no rank 797178 EBI-EMBL Glycosyltransferase like family 2 glycosyltransferase Members of this family of prokaryotic proteins include putative glucosyltransferase, which are involved in bacterial capsule biosynthesis [1][2]. [1]. 9515923. Characterization of the gene cassette required for biosynthesis of the (alpha1-->6)-linked N-acetyl-D-mannosamine-1-phosphate capsule of serogroup A Neisseria meningitidis. Swartley JS, Liu LJ, Miller YK, Martin LE, Edupuganti S, Stephens DS;. J Bacteriol. 1998;180:1533-1539. [2]. 11953367. Novel Aeromonas hydrophila PPD134/91 genes involved in O-antigen and capsule biosynthesis. Zhang YL, Arakawa E, Leung KY;. Infect Immun. 2002;70:2326-2335. (from Pfam) NF025027.5 PF13643.11 DUF4145 23.1 23.1 88 domain Y Y N DUF4145 domain-containing protein 131567 cellular organisms no rank 23326 EBI-EMBL Domain of unknown function (DUF4145) Domain of unknown function (DUF4145) This domain is found in a variety of restriction endonuclease enzymes. The exact function of this domain is uncertain. (from Pfam) NF025030.5 PF13646.11 HEAT_2 27.7 27.7 88 domain Y Y N HEAT repeat domain-containing protein 131567 cellular organisms no rank 111245 EBI-EMBL HEAT repeats HEAT repeats This family includes multiple HEAT repeats. (from Pfam) NF025033.5 PF13649.11 Methyltransf_25 27 27 97 domain Y Y N methyltransferase domain-containing protein 131567 cellular organisms no rank 1929136 EBI-EMBL Methyltransferase domain Methyltransferase domain This family appears to be a methyltransferase domain. (from Pfam) NF025034.5 PF13650.11 Asp_protease_2 24.3 24.3 90 domain Y Y N aspartyl protease family protein 131567 cellular organisms no rank 45736 EBI-EMBL Aspartyl protease aspartyl protease family protein This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix. (from Pfam) NF025035.5 PF13651.11 EcoRI_methylase 26.4 26.4 345 domain Y Y N adenine-specific methyltransferase EcoRI family protein 6257703 131567 cellular organisms no rank 3741 EBI-EMBL Adenine-specific methyltransferase EcoRI adenine-specific methyltransferase EcoRI family protein This methylase recognizes the double-stranded sequence GAATTC, causes specific methylation on A-3 on both strands, and protects the DNA from cleavage by the EcoRI endonuclease. [1]. 6257703. Sequence analysis of the DNA encoding the Eco RI endonuclease and methylase. Greene PJ, Gupta M, Boyer HW, Brown WE, Rosenberg JM;. J Biol Chem. 1981;256:2143-2153. (from Pfam) NF025037.5 PF13653.11 GDPD_2 27 27 30 domain Y N N Glycerophosphoryl diester phosphodiesterase family 9393724 131567 cellular organisms no rank 27523 EBI-EMBL Glycerophosphoryl diester phosphodiesterase family Glycerophosphoryl diester phosphodiesterase family This family also includes glycerophosphoryl diester phosphodiesterases as well as agrocinopine synthase, the similarity to GDPD has been noted [1]. This family appears to have weak but not significant matches to mammalian phospholipase C Pfam:PF00388, which suggests that this family may adopt a TIM barrel fold. [1]. 9393724. Characterization of the acc operon from the nopaline-type Ti plasmid pTiC58, which encodes utilization of agrocinopines A and B and susceptibility to agrocin 84. Kim H, Farrand SK;. J Bacteriol 1997;179:7559-7572. (from Pfam) NF025038.5 PF13654.11 AAA_32 21 21 133 domain Y Y N AAA family ATPase 23897463 131567 cellular organisms no rank 23715 EBI-EMBL LonB-like, AAA domain LonB-like, AAA domain This entry includes a wide variety of AAA domains, including some that have lost essential nucleotide binding residues in the P-loop. This domain is found in Lon proteases from archaea and bacteria [1]. [1]. 23897463. Structures of an ATP-independent Lon-like protease and its complexes with covalent inhibitors. Liao JH, Ihara K, Kuo CI, Huang KF, Wakatsuki S, Wu SH, Chang CI;. Acta Crystallogr D Biol Crystallogr. 2013;69:1395-1402. (from Pfam) NF025039.5 PF13655.11 RVT_N 28.1 28.1 83 domain Y Y N reverse transcriptase N-terminal domain-containing protein 131567 cellular organisms no rank 13219 EBI-EMBL N-terminal domain of reverse transcriptase N-terminal domain of reverse transcriptase This domain is found at the N-terminus of bacterial reverse transcriptases. (from Pfam) NF025040.5 PF13656.11 RNA_pol_L_2 27 27 75 domain Y Y N RpoL/Rpb11 RNA polymerase subunit family protein GO:0006351,GO:0046983 9657722 131567 cellular organisms no rank 1165 EBI-EMBL RNA polymerase Rpb3/Rpb11 dimerisation domain RNA polymerase Rpb3/Rpb11 dimerisation domain The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11. [1]. 9657722. Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain. Zhang G, Darst SA;. Science 1998;281:262-266. (from Pfam) NF025041.5 PF13657.11 Couple_hipA 22.5 22.5 99 domain Y Y N HipA N-terminal domain-containing protein 131567 cellular organisms no rank 46191 EBI-EMBL HipA N-terminal domain HipA N-terminal domain This domain is found to the N-terminus of HipA-like proteins. It is also found in isolation in some proteins. (from Pfam) NF025042.5 PF13660.11 DUF4147 23 23 234 domain Y Y N DUF4147 domain-containing protein 131567 cellular organisms no rank 20549 EBI-EMBL Domain of unknown function (DUF4147) Domain of unknown function (DUF4147) This domain is frequently found at the N-terminus of proteins carrying the glycerate kinase-like domain MOFRL, Pfam:PF05161. (from Pfam) NF025044.5 PF13662.11 Toprim_4 25 25 85 domain Y Y N toprim domain-containing protein 9722641 131567 cellular organisms no rank 145718 EBI-EMBL Toprim domain toprim domain The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation [1]. [1]. 9722641. Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Aravind L, Leipe DD, Koonin EV;. Nucleic Acids Res 1998;26:4205-4213. (from Pfam) NF025046.5 PF13664.11 DUF4149 24.6 24.6 102 PfamAutoEq Y Y N DUF4149 domain-containing protein 131567 cellular organisms no rank 7170 EBI-EMBL Domain of unknown function (DUF4149) Domain of unknown function (DUF4149) NF025049.5 PF13668.11 Ferritin_2 24.7 24.7 138 domain Y Y N ferritin-like domain-containing protein 131567 cellular organisms no rank 12214 EBI-EMBL Ferritin-like domain Ferritin-like domain This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins. (from Pfam) NF025050.5 PF13669.11 Glyoxalase_4 27 27 109 domain Y Y N VOC family protein 7481800,8504803 131567 cellular organisms no rank 183122 EBI-EMBL Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily VOC family protein NF025052.5 PF13671.11 AAA_33 27 27 143 domain Y Y N AAA family ATPase 131567 cellular organisms no rank 233258 EBI-EMBL AAA domain AAA domain This family of domains contain only a P-loop motif, that is characteristic of the AAA superfamily. Many of the proteins in this family are just short fragments so there is no Walker B motif. (from Pfam) NF025053.5 PF13672.11 PP2C_2 24 24 209 domain Y Y N protein phosphatase 2C domain-containing protein 9003755 131567 cellular organisms no rank 127416 EBI-EMBL Protein phosphatase 2C Protein phosphatase 2C Protein phosphatase 2C is a Mn++ or Mg++ dependent protein serine/threonine phosphatase. [1]. 9003755. Crystal structure of the protein serine/threonine phosphatase 2C at 2.0 A resolution. Das AK, Helps NR, Cohen PT, Barford D;. EMBO J 1996;15:6798-6809. (from Pfam) NF025054.5 PF13673.12 Acetyltransf_10 23.6 23.6 128 subfamily Y Y N GNAT family N-acetyltransferase 2.3.1.- GO:0016747 11893502,9175471 131567 cellular organisms no rank 1272656 EBI-EMBL Acetyltransferase (GNAT) domain Acetyltransferase (GNAT) domain This family contains proteins with N-acetyltransferase functions such as Elp3-related proteins. [1]. 9175471. GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein. Neuwald AF, Landsman D;. Trends Biochem Sci 1997;22:154-155. [2]. 11893502. A second catalytic domain in the Elp3 histone acetyltransferases: a candidate for histone demethylase activity?. Chinenov Y;. Trends Biochem Sci 2002;27:115-117. (from Pfam) NF025056.5 PF13676.11 TIR_2 28 28 122 domain Y Y N TIR domain-containing protein GO:0005515,GO:0007165 131567 cellular organisms no rank 67981 EBI-EMBL TIR domain TIR domain This is a family of Toll-like receptors. (from Pfam) NF025059.5 PF13679.11 Methyltransf_32 27 27 143 domain Y Y N methyltransferase 131567 cellular organisms no rank 32871 EBI-EMBL Methyltransferase domain Methyltransferase domain This family appears to be a methyltransferase domain. (from Pfam) NF025063.5 PF13683.11 rve_3 26.5 26.5 67 domain Y Y N integrase core domain-containing protein GO:0015074 131567 cellular organisms no rank 318407 EBI-EMBL Integrase core domain integrase core domain-containing protein NF025064.5 PF13684.11 FakA-like_C 23 23 216 domain Y N N Fatty acid kinase subunit A-like, C-terminal 36054360 131567 cellular organisms no rank 39444 EBI-EMBL Fatty acid kinase subunit A-like, C-terminal Fatty acid kinase subunit A-like, C-terminal This domain is found at the C-terminal of FakA (fatty acid subunit A) proteins, which is part of the fatty acid kinase machinery [1]. In the human pathogens Staphylococcus and Streptococcus, this system is used to scavenge host fatty acids. FakA is an ATP-binding subunit which interacts with varied FakB (fatty acid-binding protein) isoforms and synthesises acyl-phosphate from extracellular fatty acids [1]. FakA comprises three domains (FakA_N, FakA_M and FakA_C) and resembles an evolutionary mimic of the DhaK-DhaL kinase system. This entry represents FakA_C, which acts as a recipient of fatty acids transferred from FakB in the context of Fak activity [1]. [1]. 36054360. Structure and mechanism for streptococcal fatty acid kinase (Fak) system dedicated to host fatty acid scavenging. Shi Y, Zang N, Lou N, Xu Y, Sun J, Huang M, Zhang H, Lu H, Zhou C, Feng Y;. Sci Adv. 2022;8:eabq3944. (from Pfam) NF025065.5 PF13685.11 Fe-ADH_2 28 28 249 subfamily Y Y N iron-containing alcohol dehydrogenase 131567 cellular organisms no rank 261144 EBI-EMBL Iron-containing alcohol dehydrogenase iron-containing alcohol dehydrogenase NF025066.5 PF13686.11 DrsE_2 25 25 156 domain Y Y N DsrE/DsrF/DrsH-like family protein 9695921 131567 cellular organisms no rank 14001 EBI-EMBL DsrE/DsrF/DrsH-like family DsrE/DsrF/DrsH-like family protein DsrE is a small soluble protein involved in intracellular sulfur reduction [1]. The family also includes YrkE proteins. [1]. 9695921. Sirohaem sulfite reductase and other proteins encoded by genes at the dsr locus of Chromatium vinosum are involved in the oxidation of intracellular sulfur. Pott AS, Dahl C;. Microbiology 1998;144:1881-1894. (from Pfam) NF025068.5 PF13688.11 Reprolysin_5 27 27 196 domain Y Y N M12 family metallo-peptidase 131567 cellular organisms no rank 21040 EBI-EMBL Metallo-peptidase family M12 M12 family metallo-peptidase domain NF025070.5 PF13690.11 CheX 27 27 94 domain Y Y N chemotaxis protein CheX 15546616 131567 cellular organisms no rank 14621 EBI-EMBL Chemotaxis phosphatase CheX chemotaxis protein CheX CheX is very closely related to the CheC chemotaxis phosphatase, but it dimerises in a different way, via a continuous beta sheet between the subunits. CheC and CheX both dephosphorylate CheY, although CheC requires binding of CheD to achieve the activity of CheX. The ability of bacteria to modulate their swimming behaviour in the presence of external chemicals (nutrients and repellents) is one of the most rudimentary behavioural responses known, but the the individual components are very sensitively tuned [1]. [1]. 15546616. Structure and function of an unusual family of protein phosphatases: the bacterial chemotaxis proteins CheC and CheX. Park SY, Chao X, Gonzalez-Bonet G, Beel BD, Bilwes AM, Crane BR;. Mol Cell. 2004;16:563-574. (from Pfam) NF025071.5 PF13691.11 Lactamase_B_4 27 27 63 PfamEq Y N N tRNase Z endonuclease GO:0008033 21208191 131567 cellular organisms no rank 6573 EBI-EMBL tRNase Z endonuclease tRNase Z endonuclease This is family of tRNase Z enzymes, that are closely related structurally to the Lactamase_B family members. tRNase Z is the endonuclease that is involved in tRNA 3'-end maturation through removal of the 3'-trailer sequences from tRNA precursors. The fission yeast Schizosaccharomyces pombe contains two candidate tRNase Zs encoded by two essential genes. The first, Swiss:Q10155, is targeted to the nucleus and has an SV40 nuclear localisation signal at its N-terminus, consisting of four consecutive arginine and lysine residues between residues 208 and 211 (KKRK) that is critical for the NLS function. The second, Swiss:P87168, is targeted to the mitochondria, with an N-terminal mitochondrial targeting signal within the first 38 residues [1]. [1]. 21208191. The fission yeast Schizosaccharomyces pombe has two distinct tRNase ZLs encoded by two different genes and differentially targeted to the nucleus and mitochondria. Gan X, Yang J, Li J, Yu H, Dai H, Liu J, Huang Y;. Biochem J. 2011; [Epub ahead of print] (from Pfam) NF025072.5 PF13692.11 Glyco_trans_1_4 27 27 142 domain Y Y N glycosyltransferase 2.4.-.- 131567 cellular organisms no rank 1106696 EBI-EMBL Glycosyl transferases group 1 glycosyltransferase NF025078.5 PF13699.11 DUF4157 22 22 79 domain Y Y N DUF4157 domain-containing protein 131567 cellular organisms no rank 25959 EBI-EMBL Domain of unknown function (DUF4157) Domain of unknown function (DUF4157) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 80 amino acids in length. This domain contains an HEXXH motif that is characteristic of many families of metallopeptidases. However, no peptidase activity has been shown for this domain. (from Pfam) NF025080.5 PF13701.11 DDE_Tnp_1_4 34.7 34.7 435 domain Y Y N transposase 131567 cellular organisms no rank 24471 EBI-EMBL Transposase DDE domain group 1 transposase Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. (from Pfam) NF025082.5 PF13704.11 Glyco_tranf_2_4 27.5 27.5 98 domain Y Y N glycosyltransferase family 2 protein 131567 cellular organisms no rank 41388 EBI-EMBL Glycosyl transferase family 2 glycosyltransferase family 2 protein Members of this family of prokaryotic proteins include putative glucosyltransferases, (from Pfam) NF025084.5 PF13707.11 RloB 31.5 31.5 195 domain Y Y N RloB domain-containing protein 9990732 131567 cellular organisms no rank 10417 EBI-EMBL RloB-like protein RloB-like protein This family includes the RloB protein that is found within a bacterial restriction modification operon. This family includes the AbiLii protein that is found as part of a plasmid encoded phage abortive infection mechanism [1]. Deletion within abiLii abolished the phage resistance. The family includes some proteins annotated as CRISPR Csm2 proteins. [1]. 9990732. Genetic organization and functional analysis of a novel phage abortive infection system, AbiL, from Lactococcus lactis. Deng YM, Liu CQ, Dunn NW;. J Biotechnol. 1999;67:135-149. (from Pfam) NF025087.5 PF13710.11 ACT_5 27 27 62 domain Y Y N ACT domain-containing protein 11751050 131567 cellular organisms no rank 35893 EBI-EMBL ACT domain ACT domain ACT domains bind to amino acids and regulate associated enzyme domains. These ACT domains are found at the C-terminus of the RelA protein. (from Pfam) NF025088.5 PF13711.11 DUF4160 23 23 65 domain Y Y N DUF4160 domain-containing protein 131567 cellular organisms no rank 10389 EBI-EMBL Domain of unknown function (DUF4160) Domain of unknown function (DUF4160) NF025089.5 PF13712.11 Glyco_tranf_2_5 27 27 210 domain Y Y N glycosyltransferase 131567 cellular organisms no rank 7600 EBI-EMBL Glycosyltransferase like family glycosyltransferase Members of this family of prokaryotic proteins include putative glucosyltransferases, which are involved in bacterial capsule biosynthesis. (from Pfam) NF025091.5 PF13714.11 PEP_mutase 31.5 31.5 240 domain Y Y N isocitrate lyase/phosphoenolpyruvate mutase family protein 9673017 131567 cellular organisms no rank 116314 EBI-EMBL Phosphoenolpyruvate phosphomutase isocitrate lyase/phosphoenolpyruvate mutase family protein This domain includes the enzyme Phosphoenolpyruvate phosphomutase (EC:5.4.2.9). This protein Swiss:O86937 has been characterised as catalysing the formation of a carbon-phosphorus bond by converting phosphoenolpyruvate (PEP) to phosphonopyruvate (P-Pyr) [1]. This enzyme has a TIM barrel fold. [1]. 9673017. Isolation and characterization of the PEP-phosphomutase and the phosphonopyruvate decarboxylase genes from the phosphinothricin tripeptide producer Streptomyces viridochromogenes Tu494. Schwartz D, Recktenwald J, Pelzer S, Wohlleben W;. FEMS Microbiol Lett. 1998;163:149-157. (from Pfam) NF025092.5 PF13715.11 CarbopepD_reg_2 32.2 32.2 88 domain Y Y N carboxypeptidase-like regulatory domain-containing protein 10986238,11717282 131567 cellular organisms no rank 468293 EBI-EMBL CarboxypepD_reg-like domain CarboxypepD_reg-like domain This domain family is found in bacteria, archaea and eukaryotes, and is approximately 90 amino acids in length. The family is found in association with Pfam:PF07715 and Pfam:PF00593. [1]. 10986238. Characterization of four outer membrane proteins involved in binding starch to the cell surface of Bacteroides thetaiotaomicron. Shipman JA, Berleman JE, Salyers AA;. J Bacteriol. 2000;182:5365-5372. [2]. 11717282. Biochemical analysis of interactions between outer membrane proteins that contribute to starch utilization by Bacteroides thetaiotaomicron. Cho KH, Salyers AA;. J Bacteriol 2001;183:7224-7230. (from Pfam) NF025094.5 PF13717.11 zinc_ribbon_4 30.3 30.3 36 domain Y Y N zinc-ribbon domain-containing protein 131567 cellular organisms no rank 18471 EBI-EMBL zinc-ribbon domain zinc-ribbon domain This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR, Pfam:PF12773. (from Pfam) NF025095.5 PF13718.11 GNAT_acetyltr_2 24.6 24.6 229 PfamEq Y Y N GNAT family N-acetyltransferase 2.3.1.- GO:0016747 14592445,19322199 131567 cellular organisms no rank 19377 EBI-EMBL GNAT acetyltransferase 2 GNAT family N-acetyltransferase This domain has N-acetyltransferase activity [1,2]. It has a GCN5-related N-acetyltransferase (GNAT) fold [2]. [1]. 14592445. Molecular cloning of a novel human gene encoding histone acetyltransferase-like protein involved in transcriptional activation of hTERT. Lv J, Liu H, Wang Q, Tang Z, Hou L, Zhang B;. Biochem Biophys Res Commun. 2003;311:506-513. [2]. 19322199. RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon. Chimnaronk S, Suzuki T, Manita T, Ikeuchi Y, Yao M, Suzuki T, Tanaka I;. EMBO J. 2009;28:1362-1373. (from Pfam) NF025100.5 PF13723.11 Ketoacyl-synt_2 25 25 223 domain Y Y N beta-ketoacyl synthase chain length factor 131567 cellular organisms no rank 17489 EBI-EMBL Beta-ketoacyl synthase, N-terminal domain Beta-ketoacyl synthase, N-terminal domain NF025104.5 PF13727.11 CoA_binding_3 25 25 175 domain Y N N CoA-binding domain 131567 cellular organisms no rank 91365 EBI-EMBL CoA-binding domain CoA-binding domain NF025105.5 PF13728.11 TraF 23 23 224 domain Y Y N conjugal transfer protein TraF traF 20081027,3042757 131567 cellular organisms no rank 38487 EBI-EMBL F plasmid transfer operon protein conjugal transfer protein TraF TraF protein undergoes proteolytic processing associated with export. The 19 amino acids at the amino terminus of the polypeptides appear to constitute a typical membrane leader peptide - not included in this family, while the remainder of the molecule is predicted to be primarily hydrophilic in character [1]. F plasmid TraF and TraH are required for F pilus assembly and F plasmid transfer, and they are both localised to the outer membrane in the presence of the complete F transfer region, especially TraV, the putative anchor [2]. [1]. 3042757. The product of the F plasmid transfer operon gene, traF, is a periplasmic protein. Wu JH, Kathir P, Ippen-Ihler K;. J Bacteriol. 1988;170:3633-3639. [2]. 20081027. F plasmid TraF and TraH are components of an outer membrane complex involved in conjugation. Arutyunov D, Arenson B, Manchak J, Frost LS;. J Bacteriol. 2010;192:1730-1734. (from Pfam) NF025107.5 PF13730.11 HTH_36 25 25 55 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 61420 EBI-EMBL Helix-turn-helix domain Helix-turn-helix domain NF025109.5 PF13732.11 DUF4162 27.4 27.4 81 domain Y Y N DUF4162 domain-containing protein 131567 cellular organisms no rank 77923 EBI-EMBL Domain of unknown function (DUF4162) Domain of unknown function (DUF4162) This domain is found at the C-terminus of bacterial ABC transporter proteins. The function is not known. (from Pfam) NF025112.5 PF13735.11 tRNA_NucTran2_2 27 27 149 PfamEq Y N N tRNA nucleotidyltransferase domain 2 putative 131567 cellular organisms no rank 19942 EBI-EMBL tRNA nucleotidyltransferase domain 2 putative tRNA nucleotidyltransferase domain 2 putative NF025113.5 PF13737.11 DDE_Tnp_1_5 28.1 28.1 112 domain Y Y N transposase 6268937 131567 cellular organisms no rank 33933 EBI-EMBL Transposase DDE domain Transposase DDE domain Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. [1]. 6268937. The sequence of IS4. Klaer R, Kuhn S, Tillmann E, Fritz HJ, Starlinger P;. Mol Gen Genet 1981;181:169-175. (from Pfam) NF025114.5 PF13738.11 Pyr_redox_3 30 30 305 domain Y Y N NAD(P)-binding domain-containing protein 131567 cellular organisms no rank 648581 EBI-EMBL Pyridine nucleotide-disulphide oxidoreductase Pyridine nucleotide-disulphide oxidoreductase NF025116.5 PF13740.11 ACT_6 23 23 76 domain Y Y N ACT domain-containing protein 131567 cellular organisms no rank 38223 EBI-EMBL ACT domain ACT domain ACT domains bind to amino acids and regulate associated enzyme domains. (from Pfam) NF025118.5 PF13742.11 tRNA_anti_2 27 27 95 PfamEq Y Y N exodeoxyribonuclease VII large subunit 3.1.11.6 GO:0003676 2047877 131567 cellular organisms no rank 82328 EBI-EMBL OB-fold nucleic acid binding domain OB-fold nucleic acid binding domain This family contains OB-fold domains that bind to nucleic acids. [1]. 2047877. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D;. Science 1991;252:1682-1689. (from Pfam) NF025119.5 PF13743.11 Thioredoxin_5 27 27 186 domain Y Y N DsbA family protein 131567 cellular organisms no rank 21118 EBI-EMBL Thioredoxin DsbA family protein NF025121.5 PF13746.11 Fer4_18 27 27 114 domain Y Y N 4Fe-4S dicluster domain-containing protein 131567 cellular organisms no rank 34376 EBI-EMBL 4Fe-4S dicluster domain 4Fe-4S dicluster domain This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich. (from Pfam) NF025124.5 PF13749.11 HATPase_c_4 26 26 89 domain Y Y N ATP-binding protein 131567 cellular organisms no rank 38515 EBI-EMBL Putative ATP-dependent DNA helicase recG C-terminal ATP-binding protein This domain may well interact selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. (from Pfam) NF025125.5 PF13750.11 Big_3_3 27 15.4 157 domain Y Y N Ig-like domain-containing protein 131567 cellular organisms no rank 17137 EBI-EMBL Bacterial Ig-like domain (group 3) bacterial Ig-like domain (group 3) This family consists of bacterial domains with an Ig-like fold. Members of this family are found in a variety of bacterial surface proteins. (from Pfam) NF025126.5 PF13751.11 DDE_Tnp_1_6 25.1 25.1 125 domain Y Y N transposase 131567 cellular organisms no rank 78016 EBI-EMBL Transposase DDE domain Transposase DDE domain Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. (from Pfam) NF025129.5 PF13754.11 Big_3_4 27.3 27.3 106 domain Y Y N PF13754 domain-containing protein 131567 cellular organisms no rank 204 EBI-EMBL Domain of unknown function Ig-like domain This is a family of uncharacterised Clostridiales proteins. (from Pfam) NF025134.5 PF13759.11 2OG-FeII_Oxy_5 27 27 101 domain Y Y N putative 2OG-Fe(II) oxygenase 131567 cellular organisms no rank 8335 EBI-EMBL Putative 2OG-Fe(II) oxygenase putative 2OG-Fe(II) oxygenase This family has structural similarity to the 2OG-Fe(II) oxygenase superfamily. (from Pfam) NF025135.5 PF13761.11 DUF4166 23 23 184 domain Y Y N DUF4166 domain-containing protein 131567 cellular organisms no rank 11802 EBI-EMBL Domain of unknown function (DUF4166) Domain of unknown function (DUF4166) This domain is often found at the C-terminus of proteins containing Pfam:PF03435. (from Pfam) NF025141.5 PF13768.11 VWA_3 27 5.2 155 domain Y N N von Willebrand factor type A domain 131567 cellular organisms no rank 55720 EBI-EMBL von Willebrand factor type A domain von Willebrand factor type A domain NF025145.5 PF13772.11 AIG2_2 27 27 83 domain Y Y N gamma-glutamylcyclotransferase 131567 cellular organisms no rank 12396 EBI-EMBL AIG2-like family gamma-glutamylcyclotransferase This family is found in bacteria and metazoa. (from Pfam) NF025149.5 PF13776.11 DUF4172 25 25 82 PfamAutoEq Y Y N DUF4172 domain-containing protein 131567 cellular organisms no rank 11460 EBI-EMBL Domain of unknown function (DUF4172) Domain of unknown function (DUF4172) The family is often found in association with Pfam:PF02661. (from Pfam) NF025154.5 PF13781.11 DoxX_3 25 25 102 domain Y Y N DoxX-like family protein 131567 cellular organisms no rank 10601 EBI-EMBL DoxX-like family DoxX-like family protein This family of uncharacterised proteins are related to DoxX Pfam:PF07681. (from Pfam) NF025156.5 PF13783.11 DUF4177 25 25 65 domain Y Y N DUF4177 domain-containing protein 131567 cellular organisms no rank 8255 EBI-EMBL Domain of unknown function (DUF4177) Domain of unknown function (DUF4177) NF025157.5 PF13784.11 Fic_N 26.7 26.7 82 domain Y Y N Fic/DOC family N-terminal domain-containing protein 1656497,23738009 131567 cellular organisms no rank 14455 EBI-EMBL Fic/DOC family N-terminal Fic/DOC family N-terminal This domain is found at the N-terminus of the Fic/DOC family, Pfam:PF02661. (from Pfam) NF025160.5 PF13787.11 HXXEE 25 25 114 domain Y Y N HXXEE domain-containing protein 131567 cellular organisms no rank 8965 EBI-EMBL Protein of unknown function with HXXEE motif Protein of unknown function with HXXEE motif This domain contains an HXXEE motif, another conserved histidine and a YXPG motif. Its function is unknown. (from Pfam) NF025165.5 PF13793.11 Pribosyltran_N 25 25 117 domain Y Y N ribose-phosphate pyrophosphokinase-like domain-containing protein 10742175 131567 cellular organisms no rank 58998 EBI-EMBL N-terminal domain of ribose phosphate pyrophosphokinase N-terminal domain of ribose phosphate pyrophosphokinase This family is frequently found N-terminal to the Pribosyltran, Pfam:PF00156. (from Pfam) NF025166.5 PF13794.11 MiaE_2 25.2 25.2 185 PfamEq Y Y N ferritin-like fold-containing protein 131567 cellular organisms no rank 9968 EBI-EMBL tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)-like tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)-like This family, called tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)-like, corresponds to crystal structure 3ez0 of a protein of unknown protein, YP_832262.1, shown to have a ferritin-like fold. NF025168.5 PF13796.11 Sensor 28.2 28.2 162 domain Y Y N sensor domain-containing protein 131567 cellular organisms no rank 51732 EBI-EMBL Putative sensor Putative sensor This family is often found at the N-terminus of proteins containing Pfam:PF07730 and Pfam:PF02518. The N-termini of proteins containing these two domains often function in stimulus sensing. (from Pfam) NF025170.5 PF13798.11 PCYCGC 25 25 153 subfamily Y Y N PCYCGC motif-containing (lipo)protein 131567 cellular organisms no rank 3094 EBI-EMBL Protein of unknown function with PCYCGC motif PCYCGC motif-containing (lipo)protein Members of this family have a nearly invariant PCYCGC motif, plus four other well-conserved cysteines, one of which belongs to a predicted lipoprotein-type signal peptide that most family members share. Many members of this family are selenoproteins. NF025174.5 PF13802.11 Gal_mutarotas_2 27 27 184 domain Y N N Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain 131567 cellular organisms no rank 77063 EBI-EMBL Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain This entry represents the first of three common domains found in Glycosyl hydrolase 31 family proteins. It has a galactose mutarotase superfamily fold. (from Pfam) NF025175.5 PF13803.11 DUF4184 25 25 229 PfamAutoEq Y Y N DUF4184 family protein 131567 cellular organisms no rank 13905 EBI-EMBL Domain of unknown function (DUF4184) DUF4184 family protein This domain of unknown function contains several highly conserved histidines. (from Pfam) NF025178.5 PF13806.11 Rieske_2 27 27 104 domain Y Y N nitrite reductase (NAD(P)H) small subunit GO:0008942 131567 cellular organisms no rank 83092 EBI-EMBL Rieske-like [2Fe-2S] domain Rieske-like [2Fe-2S] domain NF025179.5 PF13807.11 GNVR 27.7 27.7 82 domain Y Y N GNVR domain-containing protein 131567 cellular organisms no rank 84631 EBI-EMBL G-rich domain on putative tyrosine kinase G-rich domain on putative tyrosine kinase This domain is found between two families, Wzz, Pfam:PF02706 and CbiA Pfam:PF01656. There is a highly conserved GNVR sequence motif which characterises this domain. The function is not known. (from Pfam) NF025181.5 PF13809.11 Tubulin_2 27 27 356 domain Y Y N tubulin-like doman-containing protein 131567 cellular organisms no rank 6536 EBI-EMBL Tubulin like Tubulin like Many of the residues conserved in Tubulin, Pfam:PF00091, are also highly conserved in this family. (from Pfam) NF025185.5 PF13813.11 MBOAT_2 25 25 85 domain Y Y N MBOAT family protein 131567 cellular organisms no rank 11015 EBI-EMBL Membrane bound O-acyl transferase family membrane bound O-acyl transferase (MBOAT) family protein NF025186.5 PF13814.11 Replic_Relax 25.3 25.3 191 domain Y Y N replication-relaxation family protein 11251827,11591133 131567 cellular organisms no rank 17387 EBI-EMBL Replication-relaxation replication-relaxation family protein This family includes proteins which are essential for plasmid replication [1] and plasmid DNA relaxation [2]. [1]. 11591133. Complete nucleotide sequence and characterization of pUA140, a cryptic plasmid from Streptococcus mutans. Zou X, Caufield PW, Li Y, Qi F;. Plasmid. 2001;46:77-85. [2]. 11251827. Two atypical mobilization proteins are involved in plasmid CloDF13 relaxation. Nunez B, De La Cruz F;. Mol Microbiol. 2001;39:1088-1099. (from Pfam) NF025188.5 PF13816.11 Dehydratase_hem 25 25 310 PfamEq Y Y N phenylacetaldoxime dehydratase family protein 10651646,16233624,19740758 131567 cellular organisms no rank 2653 EBI-EMBL Haem-containing dehydratase phenylacetaldoxime dehydratase family protein This family includes aldoxime dehydratase, EC:4.99.1.5. This is a haem-containing enzyme, which catalyses the dehydration of aldoximes to their corresponding nitrile [1]. It also includes phenylacetaldoxime dehydratase, EC:4.99.1.7. This haem-containing enzyme catalyses the dehydration of Z-phenylacetaldoxime to phenylacetonitrile [2]. The enzyme forms an elliptic beta barrel, composed of eight beta-strands, flanked by alpha-helices [3]. [1]. 16233624. Aldoxime dehydratase co-existing with nitrile hydratase and amidase in the iron-type nitrile hydratase-producer Rhodococcus sp. N-771. Kato Y, Yoshida S, Xie SX, Asano Y;. J Biosci Bioeng. 2004;97:250-259. [2]. 10651646. Novel heme-containing lyase, phenylacetaldoxime dehydratase from Bacillus sp. strain OxB-1: purification, characterization, and molecular cloning of the gene. Kato Y, Nakamura K, Sakiyama H, Mayhew SG, Asano Y;. Biochemistry. 2000;39:800-809. [3]. 19740758. X-ray crystal structure of michaelis complex of aldoxime dehydratase. Sawai H, Sugimoto H, Kato Y, Asano Y, Shiro Y, Aono S;. J Biol Chem. 2009;284:32089-32096. (from Pfam) NF025189.5 PF13817.11 DDE_Tnp_IS66_C 30 30 39 domain Y Y N transposase domain-containing protein 131567 cellular organisms no rank 56819 EBI-EMBL IS66 C-terminal element IS66 C-terminal element NF025196.5 PF13826.11 Monooxy_af470-like 25 25 118 PfamAutoEq Y Y N monooxygenase family protein 23488861,24568283 131567 cellular organisms no rank 10140 EBI-EMBL Monooxygenase af470-like monooxygenase family protein This entry includes Monooxygenase af470-like from Aspergillus fumigatus, which is part of the fma gene cluster that mediates the biosynthesis of fumagillin, a meroterpenoid with numerous biological activities [1]. It has been suggested that af470 mediates the oxidative cleavage of the terminal alkene of the dodecapentaenoate side chain into the carboxylic acid present in fumagillin [2]. [1]. 23488861. The fumagillin biosynthetic gene cluster in Aspergillus fumigatus encodes a cryptic terpene cyclase involved in the formation of beta-trans-bergamotene. Lin HC, Chooi YH, Dhingra S, Xu W, Calvo AM, Tang Y;. J Am Chem Soc. 2013;135:4616-4619. [2]. 24568283. Generation of complexity in fungal terpene biosynthesis: discovery of a multifunctional cytochrome P450 in the fumagillin pathway. Lin HC, Tsunematsu Y, Dhingra S, Xu W, Fukutomi M, Chooi YH, Cane DE, Calvo AM, Watanabe K, Tang Y;. J Am Chem Soc. 2014;136:4426-4436. (from Pfam) NF025198.5 PF13828.11 DUF4190 35 35 62 domain Y Y N DUF4190 domain-containing protein 131567 cellular organisms no rank 34467 EBI-EMBL Domain of unknown function (DUF4190) Domain of unknown function (DUF4190) This integral membrane domain is functionally uncharacterised. One of the membrane helices contains two GXXG motifs that are usually associated with dimerisation. (from Pfam) NF025203.5 PF13833.11 EF-hand_8 28 13.8 54 domain Y Y N EF-hand domain-containing protein GO:0005509 131567 cellular organisms no rank 18386 EBI-EMBL EF-hand domain pair EF-hand domain pair NF025205.5 PF13835.11 DUF4194 32.7 32.7 165 domain Y Y N DUF4194 domain-containing protein 131567 cellular organisms no rank 10461 EBI-EMBL Domain of unknown function (DUF4194) Domain of unknown function (DUF4194) NF025210.5 PF13840.11 ACT_7 27 27 65 domain Y Y N ACT domain-containing protein 16987805,18368466 131567 cellular organisms no rank 85966 EBI-EMBL ACT domain ACT domain The ACT domain is a structural motif of 70-90 amino acids that functions in the control of metabolism, solute transport and signal transduction. They are thus found in a variety of different proteins in a variety of different arrangements [1]. In mammalian phenylalanine hydroxylase the domain forms no contacts but promotes an allosteric effect despite the apparent lack of ligand binding [2]. [1]. 16987805. The ACT domain: a small molecule binding domain and its role as a common regulatory element. Grant GA;. J Biol Chem. 2006;281:33825-33829. [2]. 18368466. Searching distant homologs of the regulatory ACT domain in phenylalanine hydroxylase. Siltberg-Liberles J, Martinez A;. Amino Acids. 2009;36:235-249. (from Pfam) NF025213.5 PF13843.11 DDE_Tnp_1_7 22.4 22.4 349 domain Y N N Transposase IS4 131567 cellular organisms no rank 225 EBI-EMBL Transposase IS4 Transposase IS4 NF025217.5 PF13847.11 Methyltransf_31 27 27 145 domain Y Y N methyltransferase domain-containing protein 131567 cellular organisms no rank 1587372 EBI-EMBL Methyltransferase domain Methyltransferase domain This family appears to have methyltransferase activity. (from Pfam) NF025221.5 PF13852.11 DUF4197 24.9 24.9 199 PfamAutoEq Y Y N DUF4197 family protein 131567 cellular organisms no rank 10763 EBI-EMBL Protein of unknown function (DUF4197) DUF4197 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 228 and 249 amino acids in length. (from Pfam) NF025223.5 PF13854.11 Kelch_5 27 21.4 42 repeat Y N N kelch repeat protein 15475350,2002850,8126718 131567 cellular organisms no rank 4067 EBI-EMBL Kelch motif kelch motif The kelch motif was initially discovered in Kelch (Swiss:Q04652). In this protein there are six copies of the motif. It has been shown that Swiss:Q04652 is related to Galactose Oxidase [1] for which a structure has been solved [2]. The kelch motif forms a beta sheet. Several of these sheets associate to form a beta propeller structure [3] as found in Pfam:PF00064, Pfam:PF00400 and Pfam:PF00415. [1]. 8126718. Drosophila kelch motif is derived from a common enzyme fold. Bork P, Doolittle RF;. J Mol Biol 1994;236:1277-1282. [2]. 2002850. Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase. Ito N, Phillips SE, Stevens C, Ogel ZB, McPherson MJ, Keen JN, Yadav KD, Knowles PF;. Nature 1991;350:87-90. [3]. 15475350. Crystal structure of the Kelch domain of human Keap1. Li X, Zhang D, Hannink M, Beamer LJ;. J Biol Chem 2004;279:54750-54758. (from Pfam) NF025224.5 PF13855.11 LRR_8 27 27 61 repeat Y N N leucine-rich repeat protein GO:0005515 131567 cellular organisms no rank 43006 EBI-EMBL Leucine rich repeat leucine-rich repeat NF025226.5 PF13857.11 Ank_5 27 27 56 domain Y Y N ankyrin repeat domain-containing protein GO:0005515 29157912 131567 cellular organisms no rank 63582 EBI-EMBL Ankyrin repeats (many copies) Ankyrin repeats (many copies) NF025228.5 PF13859.11 BNR_3 27 27 308 domain Y N N BNR repeat-like domain 131567 cellular organisms no rank 20135 EBI-EMBL BNR repeat-like domain BNR repeat-like domain This family of proteins contains BNR-like repeats suggesting these proteins may act as sialidases. (from Pfam) NF025229.5 PF13860.11 FlgD_ig 27 27 79 domain Y Y N FlgD immunoglobulin-like domain containing protein 18599076 131567 cellular organisms no rank 33571 EBI-EMBL FlgD Ig-like domain FlgD Ig-like domain This domains has an immunoglobulin like beta sandwich fold. It is found in the FlgD protein the flagellar hook capping protein. THe structure for this domain shows that it is inserted within a TUDOR like beta barrel domain [1]. [1]. 18599076. Crystal structure of the C-terminal domain of a flagellar hook-capping protein from Xanthomonas campestris. Kuo WT, Chin KH, Lo WT, Wang AH, Chou SH;. J Mol Biol. 2008;381:189-199. (from Pfam) NF025239.5 PF13870.11 DUF4201 31.6 31.6 177 domain Y Y N DUF4201 domain-containing protein 131567 cellular organisms no rank 4 EBI-EMBL Domain of unknown function (DUF4201) Domain of unknown function (DUF4201) This is a family of coiled-coil proteins from eukaryotes. The function is not known. (from Pfam) NF025241.5 PF13872.11 AAA_34 27 27 306 domain Y Y N strawberry notch-like NTP hydrolase domain-containing protein 131567 cellular organisms no rank 6791 EBI-EMBL P-loop containing NTP hydrolase pore-1 P-loop containing NTP hydrolase pore-1 NF025249.5 PF13880.11 Acetyltransf_13 22.8 22.8 69 PfamEq Y N N ESCO1/2 acetyl-transferase 131567 cellular organisms no rank 1273 EBI-EMBL ESCO1/2 acetyl-transferase ESCO1/2 acetyl-transferase NF025252.5 PF13883.11 Pyrid_oxidase_2 27 27 167 PfamEq Y N N Pyridoxamine 5'-phosphate oxidase 131567 cellular organisms no rank 10763 EBI-EMBL Pyridoxamine 5'-phosphate oxidase Pyridoxamine 5'-phosphate oxidase NF025253.5 PF13884.11 Peptidase_S74 22 22 58 domain Y Y N tail fiber domain-containing protein 17158460 131567 cellular organisms no rank 33131 EBI-EMBL Chaperone of endosialidase Chaperone of endosialidase This is the very C-terminal, chaperone, domain of the bacteriophage protein endosialidase. It releases itself, via the serine-lysine dyad at the N-terminus, from the remainder of the end-tail-spike. Cleavage occurs after the threonine which is the final residue of the End-tail-spike family, Pfam:PF12219. The endosialidase protein forms homotrimeric molecules in bacteriophages [1]. The catalytic dyad allows this portion of the molecule to be cleaved from the more N-terminal region such that the latter can fold and bind to polysialic acid in the bacterial outer envelope [1]. [1]. 17158460. Characterization of a novel intramolecular chaperone domain conserved in endosialidases and other bacteriophage tail spike and fiber proteins. Schwarzer D, Stummeyer K, Gerardy-Schahn R, Muhlenhoff M;. J Biol Chem. 2007;282:2821-2831. (from Pfam) NF025255.5 PF13886.11 DUF4203 29.2 29.2 201 PfamAutoEq Y Y N DUF4203 domain-containing protein 131567 cellular organisms no rank 441 EBI-EMBL Domain of unknown function (DUF4203) Domain of unknown function (DUF4203) This is the N-terminal region of 7tm proteins. The function is not known. (from Pfam) NF025262.5 PF13893.11 RRM_5 27 10 125 domain Y N N RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 8290338 131567 cellular organisms no rank 638 EBI-EMBL RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. [1]. 8290338. Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Birney E., Kumar S., Krainer A.R. Nucleic Acid Res 1993;21:5803-5816. (from Pfam) NF025263.5 PF13894.11 zf-C2H2_4 27 19.8 24 domain Y N N C2H2-type zinc finger 131567 cellular organisms no rank 340 EBI-EMBL C2H2-type zinc finger C2H2-type zinc finger This family contains a number of divergent C2H2 type zinc fingers. (from Pfam) NF025268.5 PF13899.11 Thioredoxin_7 27 27 83 domain Y Y N thioredoxin family protein 131567 cellular organisms no rank 128458 EBI-EMBL Thioredoxin-like thioredoxin family protein Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. (from Pfam) NF025273.5 PF13905.11 Thioredoxin_8 27 27 94 domain Y Y N thioredoxin-like domain-containing protein 131567 cellular organisms no rank 205121 EBI-EMBL Thioredoxin-like thioredoxin-like domain Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. (from Pfam) NF025274.5 PF13906.11 AA_permease_C 27 27 51 domain Y Y N amino acid permease C-terminal domain-containing protein 131567 cellular organisms no rank 55979 EBI-EMBL C-terminus of AA_permease C-terminus of AA_permease This is the C-terminus of AA-permease enzymes that is not captured by the models Pfam:PF00324 and Pfam:PF13520. (from Pfam) NF025278.5 PF13910.11 DUF4209 22.3 22.3 89 PfamAutoEq Y Y N DUF4209 domain-containing protein 131567 cellular organisms no rank 2882 EBI-EMBL Domain of unknown function (DUF4209) Domain of unknown function (DUF4209) This short domain is found in bacteria and eukaryotes, though not in yeasts or Archaea. It carries a highly conserved RNxxxHG sequence motif. (from Pfam) NF025279.5 PF13911.11 AhpC-TSA_2 27 27 114 domain Y Y N AhpC/TSA family protein 8041738 131567 cellular organisms no rank 6940 EBI-EMBL AhpC/TSA antioxidant enzyme AhpC/TSA family protein This family contains proteins related to alkyl hydro-peroxide reductase (AhpC) and thiol specific antioxidant (TSA). [1]. 8041738. Cloning and sequencing of thiol-specific antioxidant from mammalian brain: alkyl hydroperoxide reductase and thiol-specific antioxidant define a large family of antioxidant enzymes. Chae HZ, Robison K, Poole LB, Church G, Storz G, Rhee SG;. Proc Natl Acad Sci U S A 1994;91:7017-7021. (from Pfam) NF025280.5 PF13912.11 zf-C2H2_6 25 12.4 27 domain Y Y N C2H2-type zinc finger protein 131567 cellular organisms no rank 543 EBI-EMBL C2H2-type zinc finger C2H2-type zinc finger protein NF025295.5 PF13927.11 Ig_3 30 30 78 domain Y Y N immunoglobulin domain-containing protein 131567 cellular organisms no rank 4646 EBI-EMBL Immunoglobulin domain Immunoglobulin domain This family contains immunoglobulin-like domains. (from Pfam) NF025298.5 PF13930.11 Endonuclea_NS_2 27 27 132 domain Y Y N DNA/RNA non-specific endonuclease 131567 cellular organisms no rank 26830 EBI-EMBL DNA/RNA non-specific endonuclease DNA/RNA non-specific endonuclease NF025300.5 PF13932.12 GIDA_C 27.1 27.1 57 PfamEq Y N N tRNA modifying enzyme MnmG/GidA C-terminal helical bundle 18565343,19446527,19801413 131567 cellular organisms no rank 63632 EBI-EMBL tRNA modifying enzyme MnmG/GidA C-terminal helical bundle tRNA modifying enzyme MnmG/GidA C-terminal helical bundle The GidA associated domain is a domain that has been identified at the C-terminus of protein GidA. It consists of several helices, last three being rather short and forming small bundle and are represented in this entry. GidA is a tRNA modification enzyme found in bacteria and mitochondrial. Based on mutational analysis the C-terminal helices have been suggested to be implicated in binding of the D-stem of tRNA [2] and, specifically this domain, to be responsible for the interaction with protein MnmE [1]. Structures of GidA in complex with either tRNA or MnmE are missing. Reported to bind to Pfam family MnmE, Pfam:PF12631. [1]. 18565343. Crystal structures of the conserved tRNA-modifying enzyme GidA: implications for its interaction with MnmE and substrate. Meyer S, Scrima A, Versees W, Wittinghofer A;. J Mol Biol. 2008;380:532-547. [2]. 19446527. Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon. Osawa T, Ito K, Inanaga H, Nureki O, Tomita K, Numata T;. Structure. 2009;17:713-724. [3]. 19801413. Structure-function analysis of Escherichia coli MnmG (GidA), a highly conserved tRNA-modifying enzyme. Shi R, Villarroya M, Ruiz-Partida R, Li Y, Proteau A, Prado S, Moukadiri I, Benitez-Paez A, Lomas R, Wagner J, Matte A, Velazquez-Campoy A, Armengod ME, Cygler M;. J Bacteriol. 2009;191:7614-7619. (from Pfam) NF025304.5 PF13936.11 HTH_38 27 27 44 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 83539 EBI-EMBL Helix-turn-helix domain helix-turn-helix domain-containing protein This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding. (from Pfam) NF025305.5 PF13937.11 DUF4212 30 30 79 PfamAutoEq Y Y N DUF4212 domain-containing protein 29769716 131567 cellular organisms no rank 10188 EBI-EMBL Domain of unknown function (DUF4212) Domain of unknown function (DUF4212) This family includes several putative integral membrane proteins which have been predicted as the putative subunit of transporters for D-alanine or lactate (See Supplementary note 5 in [1]). [1]. 29769716. Mutant phenotypes for thousands of bacterial genes of unknown function. Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM;. Nature. 2018;557:503-509. (from Pfam) NF025306.5 PF13938.11 DUF4213 23.5 23.5 75 domain Y Y N enolase N-terminal-like fold-containing protein 20944207 131567 cellular organisms no rank 2499 EBI-EMBL Putative heavy-metal chelation Putative heavy-metal chelation This domain of unknown function has an enolase N-terminal domain-like fold. Its genomic context suggests that it may have a role in anaerobic vitamin B12 biosynthesis. This domain is often found at the N-terminus of proteins containing DUF364, Pfam:PF04016. The structure of UnioProtKB:B8FUJ5, PDB:3l5o, suggests that the whole protein has this enolase N-terminal-like fold and an Rossmann-like C-terminal domain. Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The protein may be playing a role in heavy-metal chelation [1]. [1]. 20944207. Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation. Miller MD, Aravind L, Bakolitsa C, Rife CL, Carlton D, Abdubek P, Astakhova T, Axelrod HL, Chiu HJ, Clayton T, Deller MC, Duan L, Feuerhelm J, Grant JC, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Reyes R, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:1167-1173. (from Pfam) NF025314.5 PF13946.11 DUF4214 23.2 23.2 72 domain Y Y N DUF4214 domain-containing protein 131567 cellular organisms no rank 12576 EBI-EMBL Domain of unknown function (DUF4214) Domain of unknown function (DUF4214) This domain is found on a variety of different proteins including transferases, and allergen V5/Tpx-1 related proteins. (from Pfam) NF025324.5 PF13958.11 ToxN_toxin 25 25 159 domain Y Y N type III toxin-antitoxin system ToxN/AbiQ family toxin GO:0003723,GO:0004521 19124776,21240270 131567 cellular organisms no rank 2022 EBI-EMBL Toxin ToxN, type III toxin-antitoxin system type III toxin-antitoxin system ToxN/AbiQ family toxin ToxN acts as a toxin, it is part of a type III toxin-antitoxin system. It acts as a ribosome independent endoribonuclease. It interacts with, and is inhibited by, the RNA antitoxin, ToxI [1,2]. Three ToxN monomers bind to three ToxI monomers to create a trimeric ToxN-ToxI complex [2]. [1]. 19124776. The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. Fineran PC, Blower TR, Foulds IJ, Humphreys DP, Lilley KS, Salmond GP;. Proc Natl Acad Sci U S A. 2009;106:894-899. [2]. 21240270. A processed noncoding RNA regulates an altruistic bacterial antiviral system. Blower TR, Pei XY, Short FL, Fineran PC, Humphreys DP, Luisi BF, Salmond GP;. Nat Struct Mol Biol. 2011;18:185-190. (from Pfam) NF025330.5 PF13964.11 Kelch_6 25.3 25.3 50 repeat Y N N kelch repeat protein 131567 cellular organisms no rank 16215 EBI-EMBL Kelch motif kelch motif NF025335.5 PF13969.11 Pab87_oct 27 27 96 domain Y N N Pab87 octamerisation domain 19266066 131567 cellular organisms no rank 172 EBI-EMBL Pab87 octamerisation domain Pab87 octamerisation domain This domain was first characterised as the C-terminal domain of Pab87 serine protease from Pyrococcus abyssi [1]. The domain is reported to play a crucial role in Pab87 octamerisation and active site compartmentalisation. Its up-and-down 8-stranded beta-barrel 3D structure is reminiscent of the one found in lipocalins. [1]. 19266066. Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family. Delfosse V, Girard E, Birck C, Delmarcelle M, Delarue M, Poch O, Schultz P, Mayer C;. PLoS One. 2009;4:e4712. (from Pfam) NF025341.5 PF13975.11 gag-asp_proteas 28.2 28.2 92 domain Y Y N retroviral-like aspartic protease family protein 131567 cellular organisms no rank 35649 EBI-EMBL gag-polyprotein putative aspartyl protease retroviral-like aspartic protease family protein This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins. (from Pfam) NF025343.5 PF13977.11 TetR_C_6 27 27 115 domain Y Y N TetR family transcriptional regulator C-terminal domain-containing protein 1431248,15944459 131567 cellular organisms no rank 126279 EBI-EMBL BetI-type transcriptional repressor, C-terminal BetI-type transcriptional repressor, C-terminal This family comprises the C-terminal portion of proteins that belong to the TetR family of transcriptional regulators. The C terminus represents the regulatory region, and does not include the DNA binding helix-turn-helix domain. The target proteins that are repressed are involved in the transcriptional control of multi-drug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity [1]. One of the target proteins is BetI, an osmoprotectant which controls the choline-glycine betaine pathway in E.coli [2]. [1]. 15944459. The TetR family of transcriptional repressors. Ramos JL, Martinez-Bueno M, Molina-Henares AJ, Teran W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R;. Microbiol Mol Biol Rev. 2005;69:326-356. [2]. 1431248. Growth of Escherichia coli in human urine: role of salt tolerance and accumulation of glycine betaine. Kunin CM, Hua TH, Van Arsdale White L, Villarejo M;. J Infect Dis. 1992;166:1311-1315. (from Pfam) NF025374.5 PF14008.11 Metallophos_C 23 23 63 domain Y N N Iron/zinc purple acid phosphatase-like protein C 12021284 131567 cellular organisms no rank 269 EBI-EMBL Iron/zinc purple acid phosphatase-like protein C Iron/zinc purple acid phosphatase-like protein C This domain is found at the C-terminus of Purple acid phosphatase proteins. [1]. 12021284. Purple acid phosphatases of Arabidopsis thaliana. Comparative analysis and differential regulation by phosphate deprivation. Li D, Zhu H, Liu K, Liu X, Leggewie G, Udvardi M, Wang D;. J Biol Chem. 2002;277:27772-27781. (from Pfam) NF025376.5 PF14010.11 PEPcase_2 25 25 493 PfamEq Y Y N phosphoenolpyruvate carboxylase 4.1.1.31 GO:0006099,GO:0008964,GO:0015977 15262949 131567 cellular organisms no rank 8910 EBI-EMBL Phosphoenolpyruvate carboxylase phosphoenolpyruvate carboxylase This family of phosphoenolpyruvate carboxylases is based on seqeunces not picked up by the model for PEPcase, PF00311. Most of the family members are from Archaea. [1]. 15262949. The phosphoenolpyruvate carboxylase from Methanothermobacter thermautotrophicus has a novel structure. Patel HM, Kraszewski JL, Mukhopadhyay B;. J Bacteriol. 2004;186:5129-5137. (from Pfam) NF025381.5 PF14015.11 DUF4231 24.7 24.7 103 PfamAutoEq Y Y N DUF4231 domain-containing protein 131567 cellular organisms no rank 9697 EBI-EMBL Protein of unknown function (DUF4231) Protein of unknown function (DUF4231) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 148 and 288 amino acids in length. (from Pfam) NF025384.5 PF14018.11 DUF4234 25.3 25.3 70 domain Y Y N DUF4234 domain-containing protein 131567 cellular organisms no rank 3804 EBI-EMBL Domain of unknown function (DUF4234) Domain of unknown function (DUF4234) This presumed integral membrane protein domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 70 amino acids in length. (from Pfam) NF025387.5 PF14021.11 TNT 27 27 88 domain Y Y N glycohydrolase toxin TNT-related protein GO:0050135 24753609,26237511 131567 cellular organisms no rank 10529 EBI-EMBL Tuberculosis necrotizing toxin glycohydrolase toxin TNT-related domain This is the C-terminal domain secreted by Mycobacterium tuberculosis (Mtb). It induces necrosis of infected cells to evade immune responses. Mtb utilizes the protein CpnT to kill human macrophages by secreting its C-terminal domain (CTD), named tuberculosis necrotizing toxin (TNT) that induces necrosis. It acts as a NAD+ glycohydrolase which hydrolyzes the essential cellular coenzyme NAD+ in the cytosol of infected macrophages resulting in necrotic cell death [1]. CpnT transports its toxic CTD from the cell surface of M. tuberculosis by proteolytic cleavage, where the toxin is cleaved to induce host cell death [2]. Structural analysis determined that the TNT core contains only six beta-strands as opposed to seven found in all known NAD+-utilizing toxins, and is significantly smaller, with only two short alpha-helices and two 3/10 helices. Furthermore, the putative NAD+ binding pocket identified Q822, Y765 and R757 as residues possibly involved in NAD+-binding and hydrolysis based on similar positions of catalytic amino acids of ADP-ribosylating toxins. While glutamine 822 residue was detected to be highly conserved among TNT homologs [1]. [1]. 26237511. The tuberculosis necrotizing toxin kills macrophages by hydrolyzing NAD. Sun J, Siroy A, Lokareddy RK, Speer A, Doornbos KS, Cingolani G, Niederweis M;. Nat Struct Mol Biol. 2015;22:672-678. [2]. 24753609. An outer membrane channel protein of Mycobacterium tuberculosis with exotoxin activity. Danilchanka O, Sun J, Pavlenok M, Maueroder C, Speer A, Siroy A, Marrero J, Trujillo C, Mayhew DL, Doornbos KS, Munoz LE, Herrmann M, Ehrt S, Berens C, Niederweis M;. Proc Natl Acad Sc. TRUNCATED at 1650 bytes (from Pfam). This protein contains a domain related to Tuberculosis Necrotizing Toxin, which is the C-terminal effector domain of outer membrane channel protein CpnT, and which has a lethal NAD+-glycohydrolase activity. NF025388.5 PF14022.11 DUF4238 27 27 281 domain Y Y N DUF4238 domain-containing protein 131567 cellular organisms no rank 11713 EBI-EMBL Protein of unknown function (DUF4238) Protein of unknown function (DUF4238) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 274 and 374 amino acids in length. (from Pfam) NF025389.5 PF14023.11 DUF4239 22.5 22.5 217 domain Y Y N DUF4239 domain-containing protein 131567 cellular organisms no rank 3942 EBI-EMBL Protein of unknown function (DUF4239) Protein of unknown function (DUF4239) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 254 and 270 amino acids in length. (from Pfam) NF025390.5 PF14024.11 DUF4240 27 27 129 domain Y Y N DUF4240 domain-containing protein 131567 cellular organisms no rank 15716 EBI-EMBL Protein of unknown function (DUF4240) Protein of unknown function (DUF4240) This presumed domain is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 169 and 263 amino acids in length. This domain is often associated with the WGR domain Pfam:PF05406. (from Pfam) NF025391.5 PF14025.11 DUF4241 27 27 189 domain Y Y N DUF4241 domain-containing protein 131567 cellular organisms no rank 8087 EBI-EMBL Protein of unknown function (DUF4241) Protein of unknown function (DUF4241) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 205 and 315 amino acids in length. There is a conserved GDG sequence motif at the C-terminus. (from Pfam) NF025392.5 PF14026.11 SCO4226-like 28.5 28.5 76 PfamAutoEq Y Y N nickel-binding protein 25285530 131567 cellular organisms no rank 9394 EBI-EMBL Nickel responsive protein SCO4226-like nickel-binding protein This family of proteins is found in prokaryotes, including the nickel responsive protein SCO4226 from Streptomyces coelicolor (Swiss:Q9FCE4). SCO4226 adopts a dimeric configuration able to bind four nickel ions, with each monomer showing a typical ferredoxin-like fold with five beta-strands packing against two alpha-helices. It seems to play a role in cellular nickel homeostasis, detoxification, and/or nickel utilization in specialised cytoplasmic compartment [1]. [1]. 25285530. Streptomyces coelicolor SCO4226 is a nickel binding protein. Lu M, Jiang YL, Wang S, Jin H, Zhang RG, Virolle MJ, Chen Y, Zhou CZ;. PLoS One. 2014;9:e109660. (from Pfam) NF025394.5 PF14028.11 Lant_dehydr_C 24.4 24.4 255 domain Y Y N lantibiotic dehydratase C-terminal domain-containing protein 25363770,26877024,29158402,31409709 131567 cellular organisms no rank 24550 EBI-EMBL Lantibiotic biosynthesis dehydratase C-term Lantibiotic biosynthesis dehydratase C-term Lant_dehydr_C is the C-terminal domain of a family of dehydratases that are involved in the biosynthesis of lantibiotics. While the extensive N-terminal domain, Pfam:PF04738, is involved in the serine-threonine glutamylation step of the synthetic process, this C-terminal domain, once thought to be a separate domain from the dehydratase enzymic activity, is necessary for the final glutamate-elimination step in the generation of the lantibiotic [1]. Lantibiotics are a class of peptide antibiotic that contains one or more thioether bonds. [1]. 25363770. Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB. Ortega MA, Hao Y, Zhang Q, Walker MC, van der Donk WA, Nair SK;. Nature. 2014; [Epub ahead of print]. [2]. 26877024. Structure and tRNA Specificity of MibB, a Lantibiotic Dehydratase from Actinobacteria Involved in NAI-107 Biosynthesis. Ortega MA, Hao Y, Walker MC, Donadio S, Sosio M, Nair SK, van der Donk WA;. Cell Chem Biol. 2016;23:370-380. [3]. 29158402. Structural insights into enzymatic [4+2] aza-cycloaddition in thiopeptide antibiotic biosynthesis. Cogan DP, Hudson GA, Zhang Z, Pogorelov TV, van der Donk WA, Mitchell DA, Nair SK;. Proc Natl Acad Sci U S A. 2017;114:12928-12933. [4]. 31409709. Characterization of glutamyl-tRNA-dependent dehydratases using nonreactive substrate mimics. Bothwell IR, Cogan DP, Kim T, Reinhardt CJ, van der Donk WA, Nair SK;. Proc Natl Acad Sci U S A. 2019;116:17245-17250. (from Pfam) NF025397.5 PF14031.11 D-ser_dehydrat 22 22 97 domain Y N N Putative serine dehydratase domain 17937657 131567 cellular organisms no rank 43369 EBI-EMBL Putative serine dehydratase domain Putative serine dehydratase domain This domain is found at the C-terminus of yeast D-serine dehydratase [1]. Structures have been solved for two bacterial members of this family. The yeast protein has been shown to be a zinc dependant enzyme. [1]. 17937657. A novel zinc-dependent D-serine dehydratase from Saccharomyces cerevisiae. Ito T, Hemmi H, Kataoka K, Mukai Y, Yoshimura T;. Biochem J. 2008;409:399-406. (from Pfam) NF025423.5 PF14057.11 GGGtGRT 27 27 327 PfamEq Y Y N GGGtGRT protein 131567 cellular organisms no rank 3901 EBI-EMBL GGGtGRT protein GGGtGRT protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 330 amino acids in length and contain many highly conserved residues including a GGGtGRT motif. (from Pfam) NF025428.5 PF14062.11 DUF4253 27 27 109 domain Y Y N DUF4253 domain-containing protein 131567 cellular organisms no rank 10403 EBI-EMBL Domain of unknown function (DUF4253) Domain of unknown function (DUF4253) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 110 amino acids in length. (from Pfam) NF025431.5 PF14065.11 Pvc16_N 27 27 180 domain Y Y N Pvc16 family protein 30905475 131567 cellular organisms no rank 13902 EBI-EMBL Pvc16 N-terminal domain Pvc16 N-terminal domain This protein forms part of a contractile injection system [1]. Photorhabdus virulence cassette (PVC) represents one group of extracellular CISs that are present in both bacteria and archaea [1]. This entry include Pvc16. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 190 and 320 amino acids in length. This domain alone in Pvc16 is able to produce PVC particles with normal length but without the outer sheath, indicating the main function of this N-terminal domain in terminating the tube growth [1]. [1]. 30905475. Cryo-EM Structure and Assembly of an Extracellular Contractile Injection System. Jiang F, Li N, Wang X, Cheng J, Huang Y, Yang Y, Yang J, Cai B, Wang YP, Jin Q, Gao N;. Cell. 2019;177:370-383. (from Pfam) NF025432.5 PF14066.11 DUF4256 27 27 173 PfamAutoEq Y Y N DUF4256 domain-containing protein 131567 cellular organisms no rank 7019 EBI-EMBL Protein of unknown function (DUF4256) DUF4256 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 190 amino acids in length. (from Pfam) NF025438.5 PF14072.11 DndB 29.1 29.1 338 domain Y Y N DNA sulfur modification protein DndB 17439960 131567 cellular organisms no rank 14937 EBI-EMBL DNA-sulfur modification-associated DNA sulfur modification protein DndB This is family of bacterial proteins likely to be necessary for binding to DNA and recognising the modification sites. Members are found in bacteria, archaea and on viral plasmids, and are typically between 354 and 474 amino acids in length. There is a conserved DGQHR sequence motif. [1]. 17439960. DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites. Liang J, Wang Z, He X, Li J, Zhou X, Deng Z;. Nucleic Acids Res. 2007;35:2944-2954. (from Pfam) NF025442.5 PF14076.11 DUF4258 25 25 71 domain Y Y N DUF4258 domain-containing protein 131567 cellular organisms no rank 5098 EBI-EMBL Domain of unknown function (DUF4258) Domain of unknown function (DUF4258) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 95 and 124 amino acids in length. Structural models show this family adopts a structure found in bacterial toxins, suggesting this family are the toxins in a toxin-antitoxin system. (from Pfam) NF025445.5 PF14079.11 DUF4260 27 27 113 PfamAutoEq Y Y N DUF4260 family protein 131567 cellular organisms no rank 6943 EBI-EMBL Domain of unknown function (DUF4260) DUF4260 family protein This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 114 and 126 amino acids in length. There is a conserved GLK sequence motif. (from Pfam) NF025446.5 PF14080.11 DUF4261 27 27 77 domain Y Y N DUF4261 domain-containing protein 131567 cellular organisms no rank 5702 EBI-EMBL Domain of unknown function (DUF4261) Domain of unknown function (DUF4261) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 80 amino acids in length. (from Pfam) NF025448.5 PF14082.11 SduA_C 27 27 159 PfamAutoEq Y Y N Shedu anti-phage system protein SduA domain-containing protein 22638584,29371424 131567 cellular organisms no rank 7610 EBI-EMBL Shedu protein SduA, C-terminal Shedu protein SduA, C-terminal This domain is found mostly in bacteria. It is found at the C-terminal of Shedu protein SduA, the only component of antiviral defense system Shedu. Expression of Shedu in B.subtilis (strain BEST7003) confers resistance to phages phi105, phi29, rho14 and to a lesser extent to SPP1 [2]. This domain may have endonuclease activity [1]. [1]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. [2]. 29371424. Systematic discovery of antiphage defense systems in the microbial pangenome. Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R;. Science. 2018; [Epub ahead of print] (from Pfam) NF025449.5 PF14083.11 PGDYG 27 27 102 domain Y Y N PGDYG domain-containing protein 131567 cellular organisms no rank 1082 EBI-EMBL PGDYG protein PGDYG protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length. There is a conserved PGDYG motif. (from Pfam) NF025451.5 PF14085.11 DUF4265 27 27 115 domain Y Y N DUF4265 domain-containing protein 131567 cellular organisms no rank 7071 EBI-EMBL Domain of unknown function (DUF4265) Domain of unknown function (DUF4265) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 139 and 168 amino acids in length. (from Pfam) NF025454.5 PF14088.11 DUF4268 27 27 140 PfamAutoEq Y Y N DUF4268 domain-containing protein 131567 cellular organisms no rank 7608 EBI-EMBL Domain of unknown function (DUF4268) Domain of unknown function (DUF4268) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 151 and 387 amino acids in length. (from Pfam) NF025460.5 PF14094.11 DUF4272 27 27 208 PfamAutoEq Y Y N DUF4272 domain-containing protein 131567 cellular organisms no rank 4852 EBI-EMBL Domain of unknown function (DUF4272) Domain of unknown function (DUF4272) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 221 and 399 amino acids in length. (from Pfam) NF025464.5 PF14099.12 Polysacc_lyase 29.9 29.9 210 domain Y Y N heparin lyase I family protein 18978091,19306878,19801541,8615834 131567 cellular organisms no rank 7205 EBI-EMBL Polysaccharide lyase heparin lyase I family protein This family includes heparin lyase I, EC:4.2.2.7. Heparin lyase I depolymerises heparin by cleaving the glycosidic linkage next to an iduronic acid moiety [1,2]. The structure of heparin lyase I consists of a beta-jelly roll domain with a long, deep substrate-binding groove and an unusual thumb domain containing many basic residues extending from the main body of the enzyme [2]. This family also includes glucuronan lyase, EC:4.2.2.14 [3]. The structure glucuronan lyase is a beta-jelly roll [4]. [1]. 8615834. Expression in Escherichia coli, purification and characterization of heparinase I from Flavobacterium heparinum. Ernst S, Venkataraman G, Winkler S, Godavarti R, Langer R, Cooney CL, Sasisekharan R;. Biochem J. 1996;315:589-597. [2]. 19801541. Structural snapshots of heparin depolymerization by heparin lyase I. Han YH, Garron ML, Kim HY, Kim WS, Zhang Z, Ryu KS, Shaya D, Xiao Z, Cheong C, Kim YS, Linhardt RJ, Jeon YH, Cygler M;. J Biol Chem. 2009;284:34019-34027. [3]. 18978091. Cloning of the Trichoderma reesei cDNA encoding a glucuronan lyase belonging to a novel polysaccharide lyase family. Konno N, Igarashi K, Habu N, Samejima M, Isogai A;. Appl Environ Microbiol. 2009;75:101-107. [4]. 19306878. Crystal structure of polysaccharide lyase family 20 endo-beta-1,4-glucuronan lyase from the filamentous fungus Trichoderma reesei. Konno N, Ishida T, Igarashi K, Fushinobu S, Habu N, Samejima M, Isogai A;. FEBS Lett. 2009;583:1323-1326. (from Pfam) NF025465.5 PF14100.11 DUF6807 27 27 270 domain Y Y N DUF6807 family protein 17696992 131567 cellular organisms no rank 15415 EBI-EMBL Family of unknown function (DUF6807) DUF6807 family protein This family includes bacterial proteins of unknown function. (from Pfam) NF025466.5 PF14101.11 DUF4275 27 27 139 PfamAutoEq Y Y N DUF4275 family protein 131567 cellular organisms no rank 1753 EBI-EMBL Domain of unknown function (DUF4275) DUF4275 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. (from Pfam) NF025467.5 PF14102.11 Caps_synth_CapC 27 27 119 domain Y Y N poly-gamma-glutamate biosynthesis protein PgsC/CapC GO:0016020,GO:0045227 11751809 131567 cellular organisms no rank 2770 EBI-EMBL Capsule biosynthesis CapC poly-gamma-glutamate biosynthesis protein PgsC/CapC This family of proteins play a role in capsule biosynthesis. They are essential for gamma-polyglutamic acid (PGA) production [1]. [1]. 11751809. Characterization of the Bacillus subtilis ywsC gene, involved in gamma-polyglutamic acid production. Urushibata Y, Tokuyama S, Tahara Y;. J Bacteriol. 2002;184:337-343. (from Pfam) NF025468.5 PF14103.11 DUF4276 30.2 30.2 192 subfamily Y Y N DUF4276 family protein 131567 cellular organisms no rank 6071 EBI-EMBL Domain of unknown function (DUF4276) DUF4276 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 190 and 224 amino acids in length. There is a single completely conserved residue E that may be functionally important. (from Pfam) NF025469.5 PF14104.11 DUF4277 25.4 25.4 109 domain Y Y N DUF4277 domain-containing protein 131567 cellular organisms no rank 4103 EBI-EMBL Domain of unknown function (DUF4277) Domain of unknown function (DUF4277) This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 110 amino acids in length. There is a conserved NGLGF sequence motif. (from Pfam) NF025473.5 PF14108.11 ABA4-like 27 27 127 PfamAutoEq Y Y N abscisic acid-deficient protein Aba4 family protein 17470058 131567 cellular organisms no rank 5142 EBI-EMBL ABA DEFICIENT 4-like abscisic acid-deficient protein Aba4 family protein This family of proteins is found in bacteria and plants. It includes abscisic acid (ABA)-deficient 4 protein (ABA4) from Arabidopsis thaliana, which has a role in neoxanthin synthesis [1] and may be important for the de novo ABA synthesis specifically during dehydration [1]. [1]. 17470058. The Arabidopsis ABA-deficient mutant aba4 demonstrates that the major route for stress-induced ABA accumulation is via neoxanthin isomers. North HM, De Almeida A, Boutin JP, Frey A, To A, Botran L, Sotta B, Marion-Poll A;. Plant J. 2007;50:810-824. (from Pfam) NF025475.5 PF14110.11 DUF4282 27 27 86 domain Y Y N DUF4282 domain-containing protein 131567 cellular organisms no rank 4625 EBI-EMBL Domain of unknown function (DUF4282) Domain of unknown function (DUF4282) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 93 and 155 amino acids in length. There is a single completely conserved residue E that may be functionally important. (from Pfam) NF025479.5 PF14114.11 DUF4286 25.8 25.8 100 PfamAutoEq Y Y N DUF4286 family protein 131567 cellular organisms no rank 5150 EBI-EMBL Domain of unknown function (DUF4286) DUF4286 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 100 and 112 amino acids in length. (from Pfam) NF025486.5 PF14121.11 Porin_10 27 27 597 subfamily Y Y N putative porin 131567 cellular organisms no rank 8135 EBI-EMBL Putative porin putative porin This family of membrane bet-barrel proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 655 and 722 amino acids in length. Swiss:Q2S343 is identified by Gene3D as a membrane bound beta-barrel. These sequences are putative porins. (from Pfam) NF025490.5 PF14125.11 DUF4292 23 23 209 PfamAutoEq Y Y N DUF4292 domain-containing protein 131567 cellular organisms no rank 6766 EBI-EMBL Domain of unknown function (DUF4292) Domain of unknown function (DUF4292) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 243 and 287 amino acids in length. (from Pfam) NF025495.5 PF14130.11 Cap4_nuclease 26.2 26.2 200 PfamAutoEq Y Y N dsDNA nuclease domain-containing protein GO:0004518 32544385 131567 cellular organisms no rank 4959 EBI-EMBL Cap4, dsDNA endonuclease domain Cap4, dsDNA endonuclease domain This domain family corresponds to the N-terminal of CD-NTase associated protein 4 (Cap4) from bacteria and archaea. CD-NTase-associated protein 4 (Cap4) is a nucleotide second messenger sensor that functions is CBASS immunity. This is the effector domain which has dsDNA nuclease activity, sharing structural homology with type II restriction endonucleases and it has the putative active-site conserved residues required for divalent metal coordination. This domain is inactive as a monomer; after Cap4 signal recognition through its C-terminal SAVED domain (Pfam:PF18145), it oligomerises to closely locate two nuclease effector domains. This domain does not participates in ligand specificity and it has a promiscuous DNA cleavage response [1]. [1]. 32544385. CBASS Immunity Uses CARF-Related Effectors to Sense 3'-5'- and 2'-5'-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection. Lowey B, Whiteley AT, Keszei AFA, Morehouse BR, Mathews IT, Antine SP, Cabrera VJ, Kashin D, Niemann P, Jain M, Schwede F, Mekalanos JJ, Shao S, Lee ASY, Kranzusch PJ;. Cell. 2020; [Epub ahead of print] (from Pfam) NF025499.5 PF14134.11 DUF4301 27 27 507 PfamAutoEq Y Y N DUF4301 family protein 131567 cellular organisms no rank 5298 EBI-EMBL Domain of unknown function (DUF4301) DUF4301 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 505 and 516 amino acids in length. (from Pfam) NF025502.5 PF14137.11 DUF4304 23.2 23.2 115 domain Y Y N DUF4304 domain-containing protein 131567 cellular organisms no rank 4751 EBI-EMBL Domain of unknown function (DUF4304) Domain of unknown function (DUF4304) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 154 and 223 amino acids in length. (from Pfam) NF025510.5 PF14145.11 YrhK 26.1 26.1 58 PfamEq Y Y N YrhK family protein 20709900 131567 cellular organisms no rank 4190 EBI-EMBL YrhK-like protein YrhK family protein The YrhK-like protein family includes the B. subtilis YrhK protein Swiss:O05401 which is functionally uncharacterised. Its expression is under the control of the motility sigma factor sigma-D [1]. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 60 amino acids in length. [1]. 20709900. Small genes under sporulation control in the Bacillus subtilis genome. Schmalisch M, Maiques E, Nikolov L, Camp AH, Chevreux B, Muffler A, Rodriguez S, Perkins J, Losick R;. J Bacteriol. 2010;192:5402-5412. (from Pfam) NF025523.5 PF14158.11 YndJ 27 27 258 PfamEq Y Y N YndJ family transporter 18943917 131567 cellular organisms no rank 6059 EBI-EMBL YndJ-like protein YndJ family transporter The YndJ-like protein family includes the B. subtilis YndJ protein Swiss:O31813, which is functionally uncharacterised. This family is found in bacteria and archaea, and is typically between 222 and 269 amino acids in length. There are two completely conserved G residues that may be functionally important. (from Pfam) NF025533.5 PF14168.11 YjzC 25 25 55 PfamEq Y Y N YjzC family protein 131567 cellular organisms no rank 2204 EBI-EMBL YjzC-like protein YjzC family protein The YjzC-like protein family includes the B. subtilis YjzC protein Swiss:O34585, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. (from Pfam) NF025539.5 PF14175.11 YaaC 27 27 307 PfamEq Y Y N YaaC family protein 131567 cellular organisms no rank 5323 EBI-EMBL YaaC-like Protein YaaC family protein The YaaC-like protein family includes the B. subtilis YaaC protein Swiss:P37526, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 320 and 333 amino acids in length. AlphaFold shows that typical proteins in this family contain a largely alpha helical domain with a beta sheet domain nested within a loop. However, there also exist shorter homologues such as Swiss:L5N9K9 which lack the inserted domain. (from Pfam) NF025553.5 PF14190.11 DUF4313 27 27 104 domain Y Y N DUF4313 domain-containing protein 131567 cellular organisms no rank 1159 EBI-EMBL Domain of unknown function (DUF4313) Domain of unknown function (DUF4313) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 136 and 171 amino acids in length. (from Pfam) NF025554.5 PF14191.11 YodL 24 24 98 domain Y Y N YodL domain-containing protein 27215790 131567 cellular organisms no rank 4844 EBI-EMBL YodL-like YodL domain The YodL-like protein family includes the B. subtilis YodL protein Swiss:O30472, which is functionally uncharacterised. This domain family is found in bacteria, and is approximately 100 amino acids in length. There are two completely conserved residues (Y and D) that may be functionally important. (from Pfam) NF025555.5 PF14192.11 DUF4314 27 27 69 domain Y Y N DUF4314 domain-containing protein 131567 cellular organisms no rank 3276 EBI-EMBL Domain of unknown function (DUF4314) Domain of unknown function (DUF4314) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically between 56 and 93 amino acids in length. (from Pfam) NF025559.5 PF14196.11 ATC_hydrolase 28.1 28.1 145 domain Y Y N L-2-amino-thiazoline-4-carboxylic acid hydrolase 12092821,16550379 131567 cellular organisms no rank 7882 EBI-EMBL L-2-amino-thiazoline-4-carboxylic acid hydrolase L-2-amino-thiazoline-4-carboxylic acid hydrolase This family of enzymes catalyses the conversion of L-2-amino-delta2-thiazoline-4-carboxylic acid (L-ATC) to N-carbamoyl-L-cysteine [1]. It cleaves the carbon-sulphur bond in the ring structure of L-ATC to produce N-carbamoyl-L-cysteine [2]. [1]. 12092821. Identification, cloning, and sequencing of the genes involved in the conversion of D,L-2-amino-delta2-thiazoline-4-carboxylic acid to L-cysteine in Pseudomonas sp. strain ON-4a. Ohmachi T, Nishino M, Kawata M, Edo N, Funaki H, Narita M, Mori K, Tamura Y, Asada Y;. Biosci Biotechnol Biochem. 2002;66:1097-1104. [2]. 16550379. Purification and characterization of a novel L-2-amino-Delta2-thiazoline-4-carboxylic acid hydrolase from Pseudomonas sp. strain ON-4a expressed in E. coli. Tashima I, Yoshida T, Asada Y, Ohmachi T;. Appl Microbiol Biotechnol. 2006;72:499-507. (from Pfam) NF025563.5 PF14200.11 RicinB_lectin_2 25.6 25.6 89 domain Y Y N RICIN domain-containing protein 131567 cellular organisms no rank 175298 EBI-EMBL Ricin-type beta-trefoil lectin domain-like Ricin-type beta-trefoil lectin domain-like NF025568.5 PF14205.11 Cys_rich_KTR 25.5 25.5 54 domain Y Y N cysteine-rich KTR domain-containing protein 131567 cellular organisms no rank 2334 EBI-EMBL Cysteine-rich KTR Cysteine-rich KTR This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 60 amino acids in length. There are 4 conserved cysteines and a conserved KTR sequence motif. (from Pfam) NF025569.5 PF14206.11 Cys_rich_CPCC 24.5 24.5 75 domain Y Y N CPCC family cysteine-rich protein 131567 cellular organisms no rank 7887 EBI-EMBL Cysteine-rich CPCC CPCC family cysteine-rich protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 68 and 104 amino acids in length. There are six conserved cysteines and a conserved CPCC sequence motif. (from Pfam) NF025574.5 PF14213.11 DUF4325 23 23 64 domain Y Y N STAS-like domain-containing protein 131567 cellular organisms no rank 5167 EBI-EMBL STAS-like domain of unknown function (DUF4325) STAS-like domain of unknown function (DUF4325) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 99 and 341 amino acids in length. This domain is distantly related to the STAS domain. (from Pfam) NF025577.5 PF14216.11 DUF4326 25 25 82 domain Y Y N DUF4326 domain-containing protein 131567 cellular organisms no rank 5472 EBI-EMBL Domain of unknown function (DUF4326) Domain of unknown function (DUF4326) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 100 and 162 amino acids in length. There are two completely conserved residues (P and C) that may be functionally important. (from Pfam) NF025582.5 PF14221.11 DUF4330 27.6 27.6 167 subfamily Y Y N DUF4330 family protein 131567 cellular organisms no rank 1856 EBI-EMBL Domain of unknown function (DUF4330) DUF4330 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 165 and 177 amino acids in length. There is a single completely conserved residue G that may be functionally important. (from Pfam) NF025589.5 PF14229.11 DUF4332 23.2 23.2 122 PfamAutoEq Y Y N DUF4332 domain-containing protein 131567 cellular organisms no rank 4451 EBI-EMBL Domain of unknown function (DUF4332) Domain of unknown function (DUF4332) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 134 and 356 amino acids in length. This domain contains helix-hairpin-helix motifs. (from Pfam) NF025594.5 PF14234.11 DUF4336 28.5 28.5 321 domain Y Y N DUF4336 domain-containing protein 131567 cellular organisms no rank 5860 EBI-EMBL Domain of unknown function (DUF4336) Domain of unknown function (DUF4336) NF025595.5 PF14235.11 DUF4337 27 27 161 domain Y Y N DUF4337 family protein 131567 cellular organisms no rank 4304 EBI-EMBL Domain of unknown function (DUF4337) DUF4337 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 187 and 201 amino acids in length. There is a single completely conserved residue Q that may be functionally important. (from Pfam) NF025596.5 PF14236.11 DruA 27 27 297 domain Y Y N Druantia anti-phage system protein DruA 29371424 131567 cellular organisms no rank 2032 EBI-EMBL Druantia protein DruA Druantia anti-phage system protein DruA Druantia type I is an antiviral defense system composed of DruA, DruB, DruC, DruD and DruE. Expression of Druantia in E.coli (strain MG1655) confers resistance to phage lambda, SECphi18, SECphi27 and T4. This entry represents DruA [1]. [1]. 29371424. Systematic discovery of antiphage defense systems in the microbial pangenome. Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R;. Science. 2018; [Epub ahead of print] (from Pfam) NF025597.5 PF14237.11 GYF_2 25.8 25.8 50 domain Y Y N GYF domain-containing protein 20937886,24643499,27733515,28125316 131567 cellular organisms no rank 17899 EBI-EMBL GYF domain 2 GYF domain 2 This domain is found in bacteria, archaea and eukaryotes, and is approximately 50 amino acids in length. It contains an evolutionary conserved signature W-X-Y-X6-11-GPF-X4-M-X2-W-X3-GYF, the site of interaction with proline-rich peptides. Family members include RME-8 (Required for receptor-mediated endocytosis 8), a DNAJC13 protein. RME-8 was first identified as a protein that is required for endocytosis in Caenorhabditis elegans. It coordinates the activity of the WASH complex with the function of the retromer SNX dimer to control endosomal tubulation [1]. Family members found in Arabidopsis include Arabidopsis trithorax-related3 (Atxr3), also known as set domain group 2 (Sdg2). It is the major enzyme responsible for H3K4me3 in Arabidopsis and SDG2-dependent H3K4m3 is critical for regulating gene expression and plant development [2]. Another family member found in Arabidopsis is Tic56. It is an essential subunit of a 1-MDa protein complex at the inner chloroplast envelope membrane [3]. Furthermore, Tic56 is important for rRNA processing and chloroplast ribosome assembly [4]. [1]. 24643499. RME-8 coordinates the activity of the WASH complex with the function of the retromer SNX dimer to control endosomal tubulation. Freeman CL, Hesketh G, Seaman MN;. J Cell Sci. 2014;127:2053-2070. [2]. 20937886. SET DOMAIN GROUP2 is the major histone H3 lysine [corrected] 4 trimethyltransferase in Arabidopsis. Guo L, Yu Y, Law JA, Zhang X;. Proc Natl Acad Sci U S A. 2010;107:18557-18562. [3]. 28125316. Protein import-independent functions of Tic56, a component of the 1-MDa translocase at the inner chloroplast envelope membrane. Agne B, Ko. TRUNCATED at 1650 bytes (from Pfam) NF025598.5 PF14238.11 DUF4340 25 25 183 domain Y Y N DUF4340 domain-containing protein 131567 cellular organisms no rank 8865 EBI-EMBL Domain of unknown function (DUF4340) Domain of unknown function (DUF4340) This domain is found in bacteria, and is typically between 183 and 196 amino acids in length. (from Pfam) NF025599.5 PF14239.11 RRXRR 25 25 174 domain Y Y N RRXRR domain-containing protein 131567 cellular organisms no rank 6936 EBI-EMBL RRXRR protein RRXRR protein This domain is found in bacteria, eukaryotes and viruses, and is approximately 180 amino acids in length. It contains a conserved RRXRR motif. It is often found in association with Pfam:PF01844. (from Pfam) NF025600.5 PF14240.11 YHYH 25 25 193 domain Y Y N YHYH protein 131567 cellular organisms no rank 6076 EBI-EMBL YHYH protein YHYH protein This domain family is found in bacteria, eukaryotes and viruses, and is typically between 141 and 198 amino acids in length. There is a conserved YHYH sequence motif. (from Pfam) NF025601.5 PF14242.11 DUF4342 25 25 81 domain Y Y N DUF4342 domain-containing protein 131567 cellular organisms no rank 2889 EBI-EMBL Domain of unknown function (DUF4342) Domain of unknown function (DUF4342) This family of proteins is found in bacteria. Proteins in this family are typically between 97 and 206 amino acids in length. There is a single completely conserved residue P that may be functionally important. (from Pfam) NF025602.5 PF14243.11 R2K_3 26.3 26.3 169 domain Y Y N ATP-grasp domain-containing protein 25976611 131567 cellular organisms no rank 11470 EBI-EMBL ATP-grasp domain, R2K clade family 3 ATP-grasp domain, R2K clade family 3 Family of ATP-grasp enzymes belonging to the R2K clade, wherein one of the absolutely-conserved lysine residues has migrated to the RAGYNA domain which is a part of the core ATP-grasp module. This family is predicted to catalyze peptide ligation reactions on protein substrates in biological conflict contexts, probably between bacteriophages and their hosts [1]. [1]. 25976611. The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications. Burroughs AM, Zhang D, Aravind L;. Biol Direct. 2015;10:21. (from Pfam) NF025605.5 PF14246.11 TetR_C_7 22 22 119 domain Y Y N TetR/AcrR family transcriptional regulator C-terminal domain-containing protein 15141956 131567 cellular organisms no rank 74474 EBI-EMBL AefR-like transcriptional repressor, C-terminal domain AefR-like transcriptional repressor, C-terminal domain This family comprises the C-terminal domain of transcriptional regulators of the TetR family. It includes the AefR transcriptional regulator from P. syringae [1]. It is found in association with Pfam:PF00440. [1]. 15141956. Regulation of AHL production and its contribution to epiphytic fitness in Pseudomonas syringae. Quinones B, Pujol CJ, Lindow SE;. Mol Plant Microbe Interact. 2004;17:521-531. (from Pfam) NF025606.5 PF14247.11 DUF4344 29.6 29.6 220 domain Y Y N DUF4344 domain-containing metallopeptidase 131567 cellular organisms no rank 5519 EBI-EMBL Putative metallopeptidase Putative metallopeptidase This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 247 and 291 amino acids in length. There is a conserved EED sequence motif. This is a putative metallopeptidase. (from Pfam) NF025607.5 PF14248.11 DUF4345 26.5 26.5 119 domain Y Y N DUF4345 family protein 131567 cellular organisms no rank 9672 EBI-EMBL Domain of unknown function (DUF4345) DUF4345 family protein This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 125 and 141 amino acids in length. There is a single completely conserved residue E that may be functionally important. (from Pfam) NF025608.5 PF14249.11 Tocopherol_cycl 26.6 26.6 335 subfamily Y Y N tocopherol cyclase family protein GO:0009976 12213958 131567 cellular organisms no rank 3019 EBI-EMBL Tocopherol cyclase tocopherol cyclase family protein This family contains tocopherol cyclases. These enzymes are involved in the synthesis of tocopherols and tocotrienols (vitamin E) [1]. [1]. 12213958. Isolation of an Arabidopsis mutant lacking vitamin E and identification of a cyclase essential for all tocopherol biosynthesis. Porfirova S, Bergmuller E, Tropf S, Lemke R, Dormann P;. Proc Natl Acad Sci U S A. 2002;99:12495-12500. (from Pfam) NF025610.5 PF14251.11 DUF4346 29.6 29.6 118 domain Y Y N DUF4346 domain-containing protein 10426953 131567 cellular organisms no rank 1526 EBI-EMBL Domain of unknown function (DUF4346) Domain of unknown function (DUF4346) This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 127 and 502 amino acids in length. There are two conserved sequence motifs: LDP and DHA. Many members of this family have been annotated as dihydropteroate synthases, however no experimental evidence can be found for this and Swiss:Q57571 has been shown not to possess dihydropteroate synthase activity [1]. [1]. 10426953. Identifying two ancient enzymes in Archaea using predicted secondary structure alignment. Xu H, Aurora R, Rose GD, White RH;. Nat Struct Biol. 1999;6:750-754. (from Pfam) NF025611.5 PF14252.11 DUF4347 24.6 24.6 164 domain Y Y N DUF4347 domain-containing protein 131567 cellular organisms no rank 12537 EBI-EMBL Domain of unknown function (DUF4347) Domain of unknown function (DUF4347) This domain family is found in bacteria and eukaryotes, and is approximately 160 amino acids in length. There are two completely conserved residues (C and G) that may be functionally important. (from Pfam) NF025612.5 PF14253.11 AbiH 30.9 30.9 260 domain Y Y N AbiH family protein 8810513 131567 cellular organisms no rank 7978 EBI-EMBL Bacteriophage abortive infection AbiH AbiH family protein This family of proteins confers resistance to bacteriophage [1]. [1]. 8810513. Cloning and sequencing of the novel abortive infection gene abiH of Lactococcus lactis ssp. lactis biovar. diacetylactis S94. Prevots F, Daloyau M, Bonin O, Dumont X, Tolou S;. FEMS Microbiol Lett. 1996;142:295-299. (from Pfam) NF025615.5 PF14256.11 YwiC 25 25 126 PfamEq Y Y N YwiC-like family protein 131567 cellular organisms no rank 6058 EBI-EMBL YwiC-like protein YwiC-like family protein The YwiC-like protein family includes the B. subtilis YwiC protein Swiss:P46909, which is functionally uncharacterised. This domain family is found in bacteria, and is approximately 130 amino acids in length. There is a single completely conserved residue G that may be functionally important. (from Pfam) NF025616.5 PF14257.11 DUF4349 27.7 27.7 213 domain Y Y N DUF4349 domain-containing protein 131567 cellular organisms no rank 24930 EBI-EMBL Domain of unknown function (DUF4349) Domain of unknown function (DUF4349) This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 282 and 353 amino acids in length. There is a single completely conserved residue D that may be functionally important. The N-terminus contains a lipoprotein signal peptide sequence. (from Pfam) NF025617.5 PF14258.11 DUF4350 30.4 30.4 181 PfamAutoEq Y Y N DUF4350 domain-containing protein 131567 cellular organisms no rank 27070 EBI-EMBL Domain of unknown function (DUF4350) Domain of unknown function (DUF4350) This domain family is found in bacteria, archaea, and is approximately 170 to 200 amino acids in length. This domain is part of the glutaminase superfamily, suggesting it may have an enzymatic function. The domain is founded between two transmembrane helix domains giving it a membrane localisation. (from Pfam) NF025619.5 PF14261.11 DUF4351 25 25 59 domain Y Y N DUF4351 domain-containing protein 131567 cellular organisms no rank 11887 EBI-EMBL Domain of unknown function (DUF4351) Domain of unknown function (DUF4351) This domain is found in bacteria, and is approximately 60 amino acids in length. (from Pfam) NF025620.5 PF14262.11 Cthe_2159 25.8 25.8 262 domain Y Y N carbohydrate-binding domain-containing protein 25286843 131567 cellular organisms no rank 9551 EBI-EMBL Carbohydrate-binding domain-containing protein Cthe_2159 carbohydrate-binding domain-containing protein Cthe_2159 from Clostridium thermocellum is the first representative of a novel family of cellulose and/or acid-sugar binding beta-helix proteins that share structural similarities with polysaccharide lyases [1]. [1]. 25286843. A new family of beta-helix proteins with similarities to the polysaccharide lyases. Close DW, D'Angelo S, Bradbury AR;. Acta Crystallogr D Biol Crystallogr. 2014;70:2583-2592. (from Pfam) NF025625.5 PF14267.11 DUF4357 38.4 38.4 54 PfamAutoEq Y Y N DUF4357 domain-containing protein 131567 cellular organisms no rank 8142 EBI-EMBL Domain of unknown function (DUF4357) Domain of unknown function (DUF4357) This domain family is found in bacteria and archaea, and is approximately 60 amino acids in length. There are two completely conserved residues (G and W) that may be functionally important. (from Pfam) NF025626.5 PF14268.11 YoaP 25 25 44 domain Y Y N YoaP domain-containing protein 131567 cellular organisms no rank 3927 EBI-EMBL YoaP-like YoaP-like The YoaP-like domain is found at the C-terminus of the B. subtilis YoaP protein Swiss:O34983. It is found in bacteria and archaea, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00583. There is a single completely conserved residue A that may be functionally important. (from Pfam) NF025627.5 PF14269.11 Arylsulfotran_2 27 27 301 domain Y Y N arylsulfotransferase family protein 20043306,20157116 131567 cellular organisms no rank 13343 EBI-EMBL Arylsulfotransferase (ASST) arylsulfotransferase family protein NF025635.5 PF14277.11 DUF4364 26.9 26.9 162 PfamAutoEq Y Y N DUF4364 family protein 131567 cellular organisms no rank 2287 EBI-EMBL Domain of unknown function (DUF4364) DUF4364 family protein This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 180 amino acids in length. (from Pfam) NF025636.5 PF14278.11 TetR_C_8 26.1 26.1 103 domain Y Y N TetR/AcrR family transcriptional regulator C-terminal domain-containing protein 15944459 131567 cellular organisms no rank 42127 EBI-EMBL Transcriptional regulator C-terminal region Transcriptional regulator C-terminal region This domain is a tetracycline repressor, domain 2, or C-terminus. [1]. 15944459. The TetR family of transcriptional repressors. Ramos JL, Martinez-Bueno M, Molina-Henares AJ, Teran W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R;. Microbiol Mol Biol Rev. 2005;69:326-356. (from Pfam) NF025637.5 PF14279.11 HNH_5 27.5 27.5 56 domain Y Y N HNH endonuclease 24039739 131567 cellular organisms no rank 59188 EBI-EMBL HNH endonuclease HNH endonuclease This domain is related to other HNH domain families such as Pfam:PF01844. Suggesting that these proteins have a nucleic acid cleaving function. (from Pfam) NF025638.5 PF14280.11 DUF4365 24.3 24.3 139 domain Y Y N DUF4365 domain-containing protein 131567 cellular organisms no rank 13571 EBI-EMBL Domain of unknown function (DUF4365) Domain of unknown function (DUF4365) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 182 and 530 amino acids in length. There is a single completely conserved residue D that may be functionally important. (from Pfam) NF025639.5 PF14281.11 PDDEXK_4 22.3 22.3 183 domain Y Y N PD-(D/E)XK nuclease family protein 131567 cellular organisms no rank 9973 EBI-EMBL PD-(D/E)XK nuclease superfamily PD-(D/E)XK nuclease family protein Members of this family belong to the PD-(D/E)XK nuclease superfamily. (from Pfam) NF025641.5 PF14283.11 DUF4366 26 26 158 domain Y Y N CD1107 family mobile element protein 131567 cellular organisms no rank 4914 EBI-EMBL Domain of unknown function (DUF4366) CD1107 family mobile element protein C-terminal domain This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. (from Pfam) NF025643.5 PF14285.11 DUF4367 22.1 22.1 110 domain Y Y N DUF4367 domain-containing protein 131567 cellular organisms no rank 7552 EBI-EMBL Domain of unknown function (DUF4367) Domain of unknown function (DUF4367) This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 229 and 435 amino acids in length. (from Pfam) NF025653.5 PF14295.11 PAN_4 27 7.1 51 domain Y Y N PAN domain-containing protein 131567 cellular organisms no rank 2820 EBI-EMBL PAN domain PAN domain NF025654.5 PF14296.11 O-ag_pol_Wzy 26.6 26.6 468 PfamEq Y Y N O-antigen polysaccharide polymerase Wzy wzy 14670712,20453897 131567 cellular organisms no rank 3830 EBI-EMBL O-antigen polysaccharide polymerase Wzy O-antigen polysaccharide polymerase Wzy This family includes O-antigen polysaccharide polymerases [1]. These enzymes link O-units via a glycosidic linkage to form a long O-antigen [2]. These enzymes vary in specificity and sequence [2]. [1]. 20453897. Escherichia coli serogroup O2 and O28ac O-antigen gene cluster sequences and detection of pathogenic E. coli O2 and O28ac by PCR. Fratamico PM, Yan X, Liu Y, DebRoy C, Byrne B, Monaghan A, Fanning S, Bolton D;. Can J Microbiol. 2010;56:308-316. [2]. 14670712. Biosynthesis of O-antigens: genes and pathways involved in nucleotide sugar precursor synthesis and O-antigen assembly. Samuel G, Reeves P;. Carbohydr Res. 2003;338:2503-2519. (from Pfam) NF025660.5 PF14302.11 DUF4377 25 25 75 domain Y Y N DUF4377 domain-containing protein 131567 cellular organisms no rank 9289 EBI-EMBL Domain of unknown function (DUF4377) Domain of unknown function (DUF4377) This domain family is found in bacteria and archaea, and is approximately 80 amino acids in length. (from Pfam) NF025663.5 PF14305.11 ATPgrasp_TupA 25 25 241 domain Y Y N ATP-grasp fold amidoligase family protein 20023723 131567 cellular organisms no rank 11919 EBI-EMBL TupA-like ATPgrasp ATP-grasp fold amidoligase family protein This family includes the relatively rare teichuronopeptide (TUP) biosynthesis enzyme TupA of alkaliphiles Bacillus halodurans (NP_244523.1) and Bacillus lentus. NF025664.5 PF14306.11 PUA_2 27 27 159 domain Y N N PUA-like domain 11389593 131567 cellular organisms no rank 13181 EBI-EMBL PUA-like domain PUA-like domain This PUA like domain is found at the N-terminus of ATP-sulfurylase enzymes. [1]. 11389593. Crystal structure of ATP sulfurylase from Penicillium chrysogenum: insights into the allosteric regulation of sulfate assimilation. MacRae IJ, Segel IH, Fisher AJ;. Biochemistry. 2001;40:6795-6804. (from Pfam) NF025665.5 PF14307.11 Glyco_tran_WbsX 25.1 25.1 350 domain Y Y N glycoside hydrolase family 99-like domain-containing protein 15109730,16055280 131567 cellular organisms no rank 9391 EBI-EMBL Glycosyltransferase WbsX Glycosyltransferase WbsX Members of this family are found in within O-antigen biosynthesis clusters in Gram negative bacteria, where they are predicted to function as glycosyltransferases [1,2]. [1]. 15109730. The O-antigen gene cluster of Shigella boydii O11 and functional identification of its wzy gene. Tao J, Feng L, Guo H, Li Y, Wang L;. FEMS Microbiol Lett. 2004;234:125-132. [2]. 16055280. Structural and genetic characterization of the Shigella boydii type 18 O antigen. Feng L, Senchenkova SN, Wang W, Shashkov AS, Liu B, Shevelev SD, Liu D, Knirel YA, Wang L;. Gene. 2005;355:79-86. (from Pfam) NF025668.5 PF14310.11 Fn3-like 25 25 71 domain Y Y N fibronectin type III-like domain-contianing protein 20138890 131567 cellular organisms no rank 145164 EBI-EMBL Fibronectin type III-like domain Fibronectin type III-like domain This domain has a fibronectin type III-like structure [1]. It is often found in association with Pfam:PF00933 and Pfam:PF01915. Its function is unknown. [1]. 20138890. Structural and functional analyses of beta-glucosidase 3B from Thermotoga neapolitana: a thermostable three-domain representative of glycoside hydrolase 3. Pozzo T, Pasten JL, Karlsson EN, Logan DT;. J Mol Biol. 2010;397:724-739. (from Pfam) NF025669.5 PF14311.11 DUF4379 24.5 24.5 56 domain Y Y N zinc-ribbon domain-containing protein 131567 cellular organisms no rank 5164 EBI-EMBL Probable Zinc-ribbon domain DUF4379 family putative zinc-ribbon domain This domain is found in bacteria, eukaryotes and viruses, and is approximately 60 amino acids in length. It contains a CXXCXH motif and a CPXC motif. (from Pfam) NF025670.5 PF14312.11 FG-GAP_2 23 23 49 repeat Y N N FG-GAP repeat protein 131567 cellular organisms no rank 5059 EBI-EMBL FG-GAP repeat FG-GAP repeat This extracellular repeat typically is found seven (or fourteen) times, forming a beta-propeller structure. NF025675.5 PF14317.11 YcxB 23.3 23.3 61 domain Y Y N YcxB family protein 131567 cellular organisms no rank 14886 EBI-EMBL YcxB-like protein YcxB family protein The YcxB-like protein family includes the B. subtilis YcxB protein Swiss:Q08793, which is a functionally uncharacterised transmembrane protein. This family of proteins is found in bacteria, and is approximately 60 amino acids in length. (from Pfam) NF025679.5 PF14321.11 DUF4382 25 25 136 domain Y Y N DUF4382 domain-containing protein 131567 cellular organisms no rank 8885 EBI-EMBL Domain of unknown function (DUF4382) Domain of unknown function (DUF4382) This family is found in bacteria and archaea, and is typically between 142 and 161 amino acids in length. (from Pfam) NF025681.5 PF14323.11 GxGYxYP_C 27 27 242 domain Y N N GxGYxYP putative glycoside hydrolase C-terminal domain 131567 cellular organisms no rank 2900 EBI-EMBL GxGYxYP putative glycoside hydrolase C-terminal domain GxGYxYP putative glycoside hydrolase C-terminal domain This family carries a characteristic sequence motif, GxGYxYP, and is a putative glycoside hydrolase. This domain is found in association with Pfam:PF16216. Associated families are sugar-processing domains. (from Pfam) NF025683.5 PF14325.11 DUF4383 27 27 125 domain Y Y N DUF4383 domain-containing protein 131567 cellular organisms no rank 14962 EBI-EMBL Domain of unknown function (DUF4383) Domain of unknown function (DUF4383) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 137 and 164 amino acids in length. (from Pfam) NF025686.5 PF14328.11 DUF4385 27 27 148 PfamAutoEq Y Y N DUF4385 family protein 131567 cellular organisms no rank 3620 EBI-EMBL Domain of unknown function (DUF4385) DUF4385 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 149 and 163 amino acids in length. (from Pfam) NF025687.5 PF14329.11 DUF4386 27.6 27.6 210 subfamily Y Y N DUF4386 family protein 131567 cellular organisms no rank 10634 EBI-EMBL Domain of unknown function (DUF4386) DUF4386 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 214 and 245 amino acids in length. (from Pfam) NF025688.5 PF14330.11 DUF4387 27 27 98 PfamAutoEq Y Y N DUF4387 family protein 131567 cellular organisms no rank 3281 EBI-EMBL Domain of unknown function (DUF4387) DUF4387 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are approximately 110 amino acids in length. There is a conserved RSKN sequence motif. (from Pfam) NF025691.5 PF14333.11 DUF4389 25 25 76 PfamAutoEq Y Y N DUF4389 domain-containing protein 131567 cellular organisms no rank 9496 EBI-EMBL Domain of unknown function (DUF4389) Domain of unknown function (DUF4389) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 104 and 223 amino acids in length. There is a single completely conserved residue R that may be functionally important. (from Pfam) NF025693.5 PF14335.11 DUF4391 29.9 29.9 232 PfamAutoEq Y Y N DUF4391 domain-containing protein 131567 cellular organisms no rank 4976 EBI-EMBL Domain of unknown function (DUF4391) DUF4391 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 220 and 257 amino acids in length. (from Pfam) NF025694.5 PF14336.11 GLUCM-like_C 27.9 27.9 291 domain Y Y N glutamate cyclase domain-containing protein 27907125,28266638 131567 cellular organisms no rank 2431 EBI-EMBL D-glutamate cyclase-like, C-terminal D-glutamate cyclase-like, C-terminal This entry represents the C-terminal domain of mitochondrial D-glutamate cyclase, which converts D-glutamate to 5-oxo-D-proline [1]. This is a conserved domain also found in uncharacterised proteins from bacteria and archaea. Structural studies of the hypothetical protein TON_0340 from Thermococcus onnurineus revealed an active-site cavity harbouring a metal-binding site containing six invariant aspartate and glutamate residues that adopts an alpha/beta-structure [2]. Biochemical and mutational analysis show that TON_0340 is a Mn+2-dependent phosphatase [2]. [1]. 28266638. D-Glutamate is metabolized in the heart mitochondria. Ariyoshi M, Katane M, Hamase K, Miyoshi Y, Nakane M, Hoshino A, Okawa Y, Mita Y, Kaimoto S, Uchihashi M, Fukai K, Ono K, Tateishi S, Hato D, Yamanaka R, Honda S, Fushimura Y, Iwai-Kanai E, Ishihara N, Mita M, Homma H, Matoba S;. Sci Rep. 2017;7:43911. [2]. 27907125. Identification of a Highly Conserved Hypothetical Protein TON_0340 as a Probable Manganese-Dependent Phosphatase. Sohn YS, Lee SG, Lee KH, Ku B, Shin HC, Cha SS, Kim YG, Lee HS, Kang SG, Oh BH;. PLoS One. 2016;11:e0167549. (from Pfam) NF025695.5 PF14337.11 Abi_alpha 27.1 27.1 193 domain Y Y N Abi-alpha family protein 30634666 131567 cellular organisms no rank 4979 EBI-EMBL Abortive infection alpha Abi-alpha family protein Enterococci such as Enterococcus faecalis and Enterococcus faecium are part of the normal human gut microbiota. However they can also be a source of nosocomial infections specially in immunocompromised patients. Virulent bacteriophages, i.e., viruses that infect and obligatorily lyse bacteria might provide alternative options for combating them. Yet, bacterial resistance to phage is taking place in similar fashion to antibiotic resistance. This might be, in part due to temperate phages that are stably associated with their host. They compete for their bacterial host, in addition to repressor-dependent immunity against similar phages, some phage express genes conferring resistance to infection by more or less unrelated phages. They can encode abortive infection (Abi) mechanisms that cause an interruption of invasive phage development and a premature death of the infected bacteria. For instance, E. faecalis V583 prophage 6 confers resistance to the virulent phage Idefix infection mainly due to Abia-alpha protein. This Pfam family corresponds to Abi-alpha protein sequences which is mostly found in prophages, arguing that it is essentially a temperate phage weapon to fight against other phages [1]. [1]. 30634666. Enterococcus faecalis Countermeasures Defeat a Virulent Picovirinae Bacteriophage. Lossouarn J, Briet A, Moncaut E, Furlan S, Bouteau A, Son O, Leroy M, DuBow MS, Lecointe F, Serror P, Petit MA;. Viruses. 2019; [Epub ahead of print] (from Pfam) NF025696.5 PF14338.11 Mrr_N 29.5 29.5 87 domain Y Y N winged helix-turn-helix domain-containing protein 11313145,18951880 131567 cellular organisms no rank 11084 EBI-EMBL Mrr N-terminal domain Mrr N-terminal domain This domain is found at the N-terminus of the Mrr restriction endonuclease catalytic domain, Pfam:PF04471 [1,2]. Fold recognition analysis predicts that it is a diverged member of the winged helix variant of helix turn helix proteins. It may play a role in DNA sequence recognition [2]. [1]. 11313145. Identification of a PD-(D/E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs. Bujnicki JM, Rychlewski L;. Gene 2001;267:183-191. [2]. 18951880. Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr. Orlowski J, Mebrhatu MT, Michiels CW, Bujnicki JM, Aertsen A;. Biochem Biophys Res Commun. 2008;377:862-866. (from Pfam) NF025697.5 PF14339.11 DUF4394 29.6 29.6 230 domain Y Y N DUF4394 domain-containing protein 131567 cellular organisms no rank 6612 EBI-EMBL Domain of unknown function (DUF4394) Domain of unknown function (DUF4394) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 262 and 476 amino acids in length. (from Pfam) NF025698.5 PF14340.11 DUF4395 24.5 24.5 130 PfamAutoEq Y Y N DUF4395 family protein 131567 cellular organisms no rank 12071 EBI-EMBL Domain of unknown function (DUF4395) DUF4395 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 142 and 168 amino acids in length. There are two completely conserved C residues that may be functionally important. (from Pfam) NF025700.5 PF14342.11 DUF4396 27 27 141 domain Y Y N DUF4396 domain-containing protein 131567 cellular organisms no rank 11110 EBI-EMBL Domain of unknown function (DUF4396) Domain of unknown function (DUF4396) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 167 and 310 amino acids in length. (from Pfam) NF025701.5 PF14343.11 PrcB_C 24 24 56 domain Y Y N protease complex subunit PrcB family protein 20435733 131567 cellular organisms no rank 4471 EBI-EMBL PrcB C-terminal protease complex subunit PrcB family protein This domain is found at the C-terminus of Treponema denticola PrcB, Swiss:B8YNY4. PrcB interacts with the PrtP protease (dentilisin) and is required for the stability of the protease complex [1]. [1]. 20435733. Treponema denticola PrcB is required for expression and activity of the PrcA-PrtP (dentilisin) complex. Godovikova V, Wang HT, Goetting-Minesky MP, Ning Y, Capone RF, Slater CK, Fenno JC;. J Bacteriol. 2010;192:3337-3344. (from Pfam) NF025702.5 PF14344.11 DUF4397 30.6 30.6 119 domain Y Y N DUF4397 domain-containing protein 131567 cellular organisms no rank 16463 EBI-EMBL Domain of unknown function (DUF4397) Domain of unknown function (DUF4397) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 120 amino acids in length. (from Pfam) NF025703.5 PF14345.11 GDYXXLXY 27 27 153 PfamEq Y Y N GDYXXLXY domain-containing protein 131567 cellular organisms no rank 10912 EBI-EMBL GDYXXLXY protein GDYXXLXY protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 171 and 199 amino acids in length. It contains a conserved GDYXXLXY motif. (from Pfam) NF025705.5 PF14347.11 DUF4399 28 28 91 domain Y Y N DUF4399 domain-containing protein 131567 cellular organisms no rank 6236 EBI-EMBL Domain of unknown function (DUF4399) Domain of unknown function (DUF4399) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 135 and 1079 amino acids in length. (from Pfam) NF025711.5 PF14353.11 CpXC 25.4 25.4 121 domain Y Y N CpXC domain-containing protein 131567 cellular organisms no rank 2229 EBI-EMBL CpXC protein CpXC domain This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea, and is typically between 122 and 134 amino acids in length. It contains four conserved cysteines forming two CpXC motifs. (from Pfam) NF025712.5 PF14354.11 Lar_restr_allev 28.6 28.6 58 domain Y Y N Lar family restriction alleviation protein 7476171 131567 cellular organisms no rank 4742 EBI-EMBL Restriction alleviation protein Lar Lar family restriction alleviation protein This family includes the restriction alleviation protein Lar encoded by the Rac prophage of Escherichia coli, Swiss:P33229. This protein modulates the activity of the Escherichia coli restriction and modification system [1]. [1]. 7476171. Restriction alleviation and modification enhancement by the Rac prophage of Escherichia coli K-12. King G, Murray NE;. Mol Microbiol. 1995;16:769-777. (from Pfam) NF025713.5 PF14355.11 Abi_C 24 24 83 PfamEq Y Y N abortive infection family protein 8997719 131567 cellular organisms no rank 7823 EBI-EMBL Abortive infection C-terminus abortive infection family protein This domain is found at the C-terminus of the Lactococcus lactis abortive infection protein Abi-859, Swiss:Q48620. This protein confers bacteriophage resistance [1]. [1]. 8997719. A novel plasmid-encoded phage abortive infection system from Lactococcus lactis biovar. diacetylactis. Deng YM, Harvey ML, Liu CQ, Dunn NW.;. FEMS Microbiol. Lett. 1997;146:149-154. (from Pfam) NF025716.5 PF14358.11 DUF4405 26.7 26.7 66 domain Y Y N DUF4405 domain-containing protein 131567 cellular organisms no rank 8144 EBI-EMBL Domain of unknown function (DUF4405) Domain of unknown function (DUF4405) This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 50 amino acids in length. There are two conserved histidines that may be functionally important. This family is N-terminally truncated compared to other members of the clan. (from Pfam) NF025717.5 PF14359.11 DUF4406 22 22 91 domain Y Y N DUF4406 domain-containing protein 131567 cellular organisms no rank 6838 EBI-EMBL Domain of unknown function (DUF4406) Domain of unknown function (DUF4406) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 98 and 145 amino acids in length. (from Pfam) NF025718.5 PF14360.11 PAP2_C 27 27 74 domain Y Y N phosphatase PAP2-related protein 131567 cellular organisms no rank 2245 EBI-EMBL PAP2 superfamily C-terminal PAP2 superfamily C-terminal domain This family is closely related to the C-terminal a region of PAP2. (from Pfam) NF025719.5 PF14361.11 RsbRD_N 24.3 24.3 104 domain Y Y N RsbRD N-terminal domain-containing protein 15312768 131567 cellular organisms no rank 12618 EBI-EMBL RsbT co-antagonist protein rsbRD N-terminal domain RsbT co-antagonist protein rsbRD N-terminal domain This domain is found at the N-terminus of a number of anti-sigma-factor antagonist proteins including B. subtilis RsbRD, Swiss:P54504. These proteins are negative regulators of the general stress transcription factor sigma(B) [1]. It is found in association with Pfam:PF01740. [1]. 15312768. A multicomponent protein complex mediates environmental stress signaling in Bacillus subtilis. Kim TJ, Gaidenko TA, Price CW;. J Mol Biol. 2004;341:135-150. (from Pfam) NF025725.5 PF14367.11 DUF4411 23.5 23.5 159 PfamAutoEq Y Y N DUF4411 family protein 131567 cellular organisms no rank 4204 EBI-EMBL Domain of unknown function (DUF4411) DUF4411 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 153 and 170 amino acids in length. There is a single completely conserved residue D that may be functionally important. (from Pfam) NF025727.5 PF14369.11 zinc_ribbon_9 30.8 30.8 35 domain Y Y N zinc-ribbon domain-containing protein GO:0061630 27193484 131567 cellular organisms no rank 8 EBI-EMBL zinc-ribbon zinc-ribbon NF025728.5 PF14370.11 Topo_C_assoc 25.1 25.1 70 domain Y N N C-terminal topoisomerase domain 131567 cellular organisms no rank 68 EBI-EMBL C-terminal topoisomerase domain C-terminal topoisomerase domain This domain is found at the C-terminal of topoisomerase and other similar enzymes. (from Pfam) NF025729.5 PF14371.11 DUF4412 21.6 21.6 191 domain Y Y N DUF4412 domain-containing protein 131567 cellular organisms no rank 1854 EBI-EMBL Domain of unknown function (DUF4412) Domain of unknown function (DUF4412) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and eukaryotes, and is typically between 75 and 104 amino acids in length. (from Pfam) NF025733.5 PF14375.11 Cys_rich_CWC 24 24 50 PfamEq Y Y N cysteine-rich CWC family protein 131567 cellular organisms no rank 9412 EBI-EMBL Cysteine-rich CWC cysteine-rich CWC family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 74 and 102 amino acids in length. It contains eight conserved cysteines, including a conserved CWC sequence motif. (from Pfam) NF025736.5 PF14378.11 PAP2_3 27 27 190 domain Y Y N phosphatase PAP2 family protein 131567 cellular organisms no rank 114282 EBI-EMBL PAP2 superfamily phosphatase PAP2 family protein NF025744.5 PF14386.11 DUF4417 28.9 28.9 183 domain Y Y N DUF4417 domain-containing protein 131567 cellular organisms no rank 1876 EBI-EMBL Domain of unknown function (DUF4417) Domain of unknown function (DUF4417) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 220 and 340 amino acids in length. There is a single completely conserved residue G that may be functionally important. (from Pfam) NF025745.5 PF14387.11 DUF4418 27 27 117 PfamAutoEq Y Y N DUF4418 family protein 131567 cellular organisms no rank 1313 EBI-EMBL Domain of unknown function (DUF4418) DUF4418 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 132 and 150 amino acids in length. (from Pfam) NF025748.5 PF14390.11 DUF4420 27 27 306 PfamAutoEq Y Y N PD-(D/E)XK motif protein 22638584 131567 cellular organisms no rank 7268 EBI-EMBL Putative PD-(D/E)XK family member, (DUF4420) PD-(D/E)XK motif protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 310 and 334 amino acids in length. Advanced homology-detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses have established this family to be a member of the PD-(D/E)XK superfamily. [1]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF025751.5 PF14393.11 DUF4422 25 25 220 domain Y Y N DUF4422 domain-containing protein 131567 cellular organisms no rank 8044 EBI-EMBL Domain of unknown function (DUF4422) Domain of unknown function (DUF4422) This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 255 and 371 amino acids in length. (from Pfam) NF025755.5 PF14397.11 ATPgrasp_ST 31.4 31.4 278 domain Y Y N sugar-transfer associated ATP-grasp domain-containing protein 20023723 131567 cellular organisms no rank 11428 EBI-EMBL Sugar-transfer associated ATP-grasp Sugar-transfer associated ATP-grasp A member of the ATP-grasp fold predicted to be involved in the biosynthesis of cell surface polysaccharides [1]. [1]. 20023723. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L;. Mol Biosyst. 2009;5:1636-1660. (from Pfam) NF025756.5 PF14398.11 ATPgrasp_YheCD 26.8 26.8 255 domain Y Y N YheC/YheD family protein 20023723 131567 cellular organisms no rank 28778 EBI-EMBL YheC/D like ATP-grasp YheC/YheD family protein A member of the ATP-grasp fold predicted to be involved in the modification/biosynthesis of spore-wall and capsular proteins [1]. [1]. 20023723. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L;. Mol Biosyst. 2009;5:1636-1660. (from Pfam) NF025757.5 PF14399.11 BtrH_N 29.7 29.7 134 domain Y Y N BtrH N-terminal domain-containing protein 16156513,20851126 131567 cellular organisms no rank 9432 EBI-EMBL Butirosin biosynthesis protein H, N-terminal Butirosin biosynthesis protein H, N-terminal BtrH_N is the N-terminus of the acyl carrier protein:aminoglycoside acyltransferase BtrH. Alternatively it can be referred to as butirosin biosynthesis protein H. BtrH transfers the unique (S)-4-amino-2-hydroxybutyrate (AHBA) side chain, which protects the antibiotic butirosin from several common resistance mechanisms. Butirosin, an aminoglycoside antibiotic produced by Bacillus circulans, exhibits improved antibiotic properties over its parent molecule and retains bactericidal activity toward many aminoglycoside-resistant strains. Butirosin is unique in carrying the AHBA side-chain. BtrH transfers the AHBA from the acyl carrier protein BtrI to the parent aminoglycoside ribostamycin as a gamma-glutamylated dipeptide [1,2]. [1]. 16156513. Extended sequence and functional analysis of the butirosin biosynthetic gene cluster in Bacillus circulans SANK 72073. Kudo F, Numakura M, Tamegai H, Yamamoto H, Eguchi T, Kakinuma K;. J Antibiot (Tokyo). 2005;58:373-379. [2]. 20851126. Structural and biochemical studies elucidate the mechanism of rhamnogalacturonan lyase from Aspergillus aculeatus. Jensen MH, Otten H, Christensen U, Borchert TV, Christensen LL, Larsen S, Leggio LL;. J Mol Biol. 2010;404:100-111. (from Pfam) NF025759.5 PF14401.11 RLAN 25 25 150 domain Y Y N RimK-like ATPgrasp N-terminal domain-containing protein 20023723 131567 cellular organisms no rank 7466 EBI-EMBL RimK-like ATPgrasp N-terminal domain RimK-like ATPgrasp N-terminal domain An uncharacterized alpha+beta fold domain that is mostly fused to a RimK-like ATP-grasp and is found in bacteria and euryarchaea. Members of this family are almost always associated in gene neighborhoods with a GNAT-like acetyltransferase fused to a papain-like petidase. Additionally M20-like peptidases, GCS2, 4Fe-4S Ferredoxins, a distinct metal-sulfur cluster protein and ribosomal proteins are found in the gene neighborhoods. Contextual analysis suggests a role for these in peptide biosynthesis [1]. [1]. 20023723. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L;. Mol Biosyst. 2009;5:1636-1660. (from Pfam) NF025760.5 PF14402.11 7TM_transglut 25 25 248 domain Y Y N 7TM domain-containing protein 20023723 131567 cellular organisms no rank 5354 EBI-EMBL 7 transmembrane helices usually fused to an inactive transglutaminase 7 transmembrane helices usually fused to an inactive transglutaminase A family of seven transmembrane helices fused to an inactive transglutaminase domain. The transglutaminase domain is predicted to be extracellularly located. Members of this family are associated in gene neighborhoods with a pepsin-like peptidase and an ATP-grasp of the RimK-family. The ATP-grasp is predicted to modify the 7TM protein or a cofactor that interacts with it [1]. [1]. 20023723. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L;. Mol Biosyst. 2009;5:1636-1660. (from Pfam) NF025761.5 PF14403.11 CP_ATPgrasp_2 32 32 374 domain Y Y N circularly permuted type 2 ATP-grasp protein 20023723 131567 cellular organisms no rank 42445 EBI-EMBL Circularly permuted ATP-grasp type 2 circularly permuted type 2 ATP-grasp protein Circularly permuted ATP-grasp prototyped by Roseiflexus RoseRS_2616 that is associated in gene neighborhoods with a GCS2-like COOH-NH2 ligase, alpha/beta hydrolase fold peptidase, GAT-II -like amidohydrolase, and M20 peptidase. Members of this family are predicted to be involved in the biosynthesis of small peptides [1]. [1]. 20023723. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L;. Mol Biosyst. 2009;5:1636-1660. (from Pfam) NF025764.5 PF14407.11 Frankia_peptide 48 48 63 subfamily Y Y N Franean1_4349 family RiPP 20023723 131567 cellular organisms no rank 63 EBI-EMBL Ribosomally synthesized peptide prototyped by Frankia Franean1_4349. Franean1_4349 family RiPP Ribosomally synthesized peptide linked to cyclases in chloroflexi. It may have a link to cyclic nucleotide signaling [1]. [1]. 20023723. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L;. Mol Biosyst. 2009;5:1636-1660. (from Pfam) NF025767.5 PF14410.11 GH-E 25 25 68 domain Y Y N GH-E family nuclease 21306995 131567 cellular organisms no rank 2381 EBI-EMBL HNH/ENDO VII superfamily nuclease with conserved GHE residues GH-E family nuclease domain A predicted nuclease of the HNH/EndoVII superfamily of the treble clef fold which is closely related to the NucA-like family. The name is derived from the conserved G, H and E residues. It is found in several bacterial polymorphic toxin systems [1]. Some GH-E members preserve the conserved cysteines of the treble-clef suggesting that they might represent potential evolutionary intermediates from a classical HNH domain to the derived NucA-like form [1]. [1]. 21306995. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Zhang D, Iyer LM, Aravind L;. Nucleic Acids Res. 2011;39:4532-4552. (from Pfam) NF025769.5 PF14412.11 AHH 22.3 22.3 111 domain Y Y N AHH domain-containing protein 21306995 131567 cellular organisms no rank 12685 EBI-EMBL A nuclease family of the HNH/ENDO VII superfamily with conserved AHH A nuclease family of the HNH/ENDO VII superfamily with conserved AHH AHH is a predicted nuclease of the HNH/ENDO VII superfamily of the treble clef fold. The name is derived from the conserved motif, AHH. It is found in bacterial polymorphic toxin systems [1] and functions as a toxin module. Like WHH and LHH, the AHH nuclease contains 4 conserved histidines of which, the first one is predicted to bind a metal-ion and the other three ones are involved in activation of a water molecule for hydrolysis. [1]. 21306995. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Zhang D, Iyer LM, Aravind L;. Nucleic Acids Res. 2011;39:4532-4552. (from Pfam) NF025770.5 PF14413.11 Thg1C 26.3 26.3 116 PfamEq Y N N Thg1 C terminal domain 20591188 131567 cellular organisms no rank 1448 EBI-EMBL Thg1 C terminal domain Thg1 C terminal domain Thg1 polymerases contain an additional region of conservation C-terminal to the core palm domain that comprise of 5 helices and two strands [1]. This region has several well-conserved charged residues including a basic residue found towards the end of the first helix of this unit might contribute to the Thg1-specific active site [1]. This C-terminal module of Thg1 is predicted to form a helical bundle that functions equivalently to the fingers of the other nucleic acid polymerases, probably in interacting with the template HtRNA [1]. [1]. 20591188. Presence of a classical RRM-fold palm domain in Thg1-type 3'- 5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains. Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2010;5:43. (from Pfam) NF025771.5 PF14414.11 WHH 25.1 25.1 43 domain Y Y N HNH endonuclease 21306995 131567 cellular organisms no rank 14694 EBI-EMBL A nuclease of the HNH/ENDO VII superfamily with conserved WHH HNH endonuclease WHH is a predicted nuclease of the HNH/ENDO VII superfamily of the treble clef fold. The name is derived from the conserved motif WHH. It is found in bacterial polymorphic toxin systems [1] and functions as a toxin module. WHH is the shortest version of HNH nuclease families. Like AHH and LHH, the WHH nuclease contains 4 conserved histidines of which the first one is predicted to bind a metal-ion and other three ones are involved in activation of water molecule for hydrolysis [1]. [1]. 21306995. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Zhang D, Iyer LM, Aravind L;. Nucleic Acids Res. 2011;39:4532-4552. (from Pfam) NF025774.5 PF14417.11 MEDS 29.8 29.8 161 domain Y Y N MEDS domain-containing protein 15814558,1938878 131567 cellular organisms no rank 19736 EBI-EMBL MEDS: MEthanogen/methylotroph, DcmR Sensory domain MEDS: MEthanogen/methylotroph, DcmR Sensory domain MEDS is prototyped by DcmR and is likely to function with the PocR domain in certain organisms in sensing hydrocarbon derivatives [1][2] The MEDS domain occurs fused to Histidine Kinase and as stand-alone version [2]. Sequence analysis shows that it is a catalytically inactive version of the P-loop NTPase domain of the RecA superfamily. [1]. 1938878. Identification of dcmR, the regulatory gene governing expression of dichloromethane dehalogenase in Methylobacterium sp. strain DM4. La Roche SD, Leisinger T;. J Bacteriol. 1991;173:6714-6721. [2]. 15814558. MEDS and PocR are novel domains with a predicted role in sensing simple hydrocarbon derivatives in prokaryotic signal transduction systems. Anantharaman V, Aravind L;. Bioinformatics. 2005;21:2805-2811. (from Pfam) NF025776.5 PF14419.11 SPOUT_MTase_2 28.4 28.4 173 subfamily Y Y N SPOUT family RNA methylase 11763972 131567 cellular organisms no rank 173 EBI-EMBL AF2226-like SPOUT RNA Methylase fused to THUMP SPOUT family RNA methylase Most members of this SPOUT RNA methylase family have an additional N-terminal THUMP domain. NF025779.5 PF14423.11 Imm5 25 25 186 domain Y Y N Imm5 family immunity protein 21890906 131567 cellular organisms no rank 813 EBI-EMBL Immunity protein Imm5 Imm5 family immunity protein A predicted Immunity protein, with an all-alpha fold, present in bacterial polymorphic toxin systems as an immediate neighbor of the toxin [1] . [1]. 21890906. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Iyer LM, Zhang D, Rogozin IB, Aravind L;. Nucleic Acids Res. 2011; [Epub ahead of print] (from Pfam) NF025780.5 PF14424.11 Toxin-deaminase 29.6 29.6 146 domain Y Y N deaminase domain-containing protein 21890906 131567 cellular organisms no rank 4346 EBI-EMBL The BURPS668_1122 family of deaminases The BURPS668_1122 family of deaminases A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Burkholderia BURPS668_1122 [1]. Members of this family are found as toxins in polymorphic toxin systems in a wide range of bacteria and in the eukaryote Perkinsus. Members of this family typically possess a DxE catalytic motif in Helix-2 of the core fold instead of the more common C[H]xE motif. The Perkinsus versions are predicted to be inactive [1]. [1]. 21890906. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Iyer LM, Zhang D, Rogozin IB, Aravind L;. Nucleic Acids Res. 2011; [Epub ahead of print] (from Pfam) NF025783.5 PF14427.11 Pput2613-deam 25 25 118 PfamEq Y N N Pput_2613-like deaminase 21890906 131567 cellular organisms no rank 644 EBI-EMBL Pput_2613-like deaminase Pput_2613-like deaminase A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Pseudomonas Pput_2613 [1]. Members of this family are predicted to function as toxins in bacterial polymorphic toxin systems [1]. [1]. 21890906. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Iyer LM, Zhang D, Rogozin IB, Aravind L;. Nucleic Acids Res. 2011; [Epub ahead of print] (from Pfam) NF025786.5 PF14430.11 Imm1 22.4 22.4 125 subfamily Y Y N Imm1 family immunity protein 21890906 131567 cellular organisms no rank 3999 EBI-EMBL Immunity protein Imm1 Imm1 family immunity protein A predicted immunity protein, with an alpha+beta fold and a conserved C-terminal tryptophan residue. The protein is present in a wide range of bacteria in polymorphic toxin systems as an immediate gene neighbour of the toxin gene [1]. [1]. 21890906. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Iyer LM, Zhang D, Rogozin IB, Aravind L;. Nucleic Acids Res. 2011; [Epub ahead of print] (from Pfam) NF025789.5 PF14433.11 SUKH-3 23 23 146 domain Y Y N SUKH-3 domain-containing protein 21306995 131567 cellular organisms no rank 11730 EBI-EMBL SUKH-3 immunity protein SUKH-3 immunity protein This family belongs to the SUKH superfamily and functions as immunity proteins in bacterial toxin systems [1]. [1]. 21306995. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Zhang D, Iyer LM, Aravind L;. Nucleic Acids Res. 2011;39:4532-4552. (from Pfam) NF025792.5 PF14436.11 EndoU_bacteria 25.3 25.3 129 domain Y Y N EndoU domain-containing protein GO:0004519 21306995 131567 cellular organisms no rank 10005 EBI-EMBL Bacterial EndoU nuclease Bacterial EndoU nuclease This is a bacterial virion of EndoU nuclease. It is found at C-terminal region of polymorphic toxin proteins. [1]. 21306995. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Zhang D, Iyer LM, Aravind L;. Nucleic Acids Res. 2011;39:4532-4552. (from Pfam) NF025793.5 PF14437.11 MafB19-deam 27 27 142 domain Y Y N deaminase GO:0002100,GO:0008251 21890906 131567 cellular organisms no rank 199683 EBI-EMBL MafB19-like deaminase deaminase A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Neisseria MafB19 [1]. Members of this family are present in a wide phyletic range of bacteria and are predicted to function as toxins in bacterial polymorphic toxin systems [1]. [1]. 21890906. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Iyer LM, Zhang D, Rogozin IB, Aravind L;. Nucleic Acids Res. 2011; [Epub ahead of print] (from Pfam) NF025794.5 PF14438.11 SM-ATX 29.8 29.8 81 PfamEq Y N N Ataxin 2 SM domain 11917006,9462862 131567 cellular organisms no rank 112 EBI-EMBL Ataxin 2 SM domain Ataxin 2 SM domain This SM domain is found in Ataxin-2 [1]. [1]. 9462862. Ataxin-2, global regulators of bacterial gene expression, and spliceosomal snRNP proteins share a conserved domain. Neuwald AF, Koonin EV;. J Mol Med 1998;76:3-5. [2]. 11917006. Comparative genomics and evolution of proteins involved in RNA metabolism. Anantharaman V, Koonin EV, Aravind L;. Nucleic Acids Res. 2002;30:1427-1464. (from Pfam) NF025796.5 PF14440.11 XOO_2897-deam 27 27 101 domain Y Y N nucleic acid/nucleotide deaminase domain-containing protein 21890906 131567 cellular organisms no rank 13385 EBI-EMBL Xanthomonas XOO_2897-like deaminase Xanthomonas XOO_2897-like deaminase A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Xanthomonas XOO_2897 [1]. Members of this family are present in a wide phyletic range of bacteria and are predicted to function as toxins in bacterial polymorphic toxin systems [1]. The Xanthomonas XOO_2897 lack an immunity protein and is predicted to be deployed against its eukaryotic host [1]. [1]. 21890906. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Iyer LM, Zhang D, Rogozin IB, Aravind L;. Nucleic Acids Res. 2011; [Epub ahead of print] (from Pfam) NF025801.5 PF14445.11 Prok-RING_2 22.4 22.4 56 domain Y N N Prokaryotic RING finger family 2 21547297 131567 cellular organisms no rank 76 EBI-EMBL Prokaryotic RING finger family 2 Prokaryotic RING finger family 2 RING finger family found sporadically in bacteria and archaea, and associated with other components of the ubiquitin-based signaling and degradation system, including ubiquitin and the E1 and E2 proteins. The bacterial versions contain transmembrane helices [1]. [1]. 21547297. Functional diversification of the RING finger and other binuclear treble clef domains in prokaryotes and the early evolution of the ubiquitin system. Burroughs AM, Iyer LM, Aravind L;. Mol Biosyst. 2011;7:2261-2277. (from Pfam) NF025802.5 PF14446.11 Prok-RING_1 29.1 29.1 54 domain Y Y N RING finger protein 21547297 131567 cellular organisms no rank 736 EBI-EMBL Prokaryotic RING finger family 1 RING finger protein RING finger family found sporadically in bacteria and archaea, and associated in gene neighborhoods with other components of the ubiquitin-based signaling and degradation system, including ubiquitin, the E1 and E2 proteins and the JAB-like metallopeptidase. The bacterial versions contain transmembrane helices [1]. [1]. 21547297. Functional diversification of the RING finger and other binuclear treble clef domains in prokaryotes and the early evolution of the ubiquitin system. Burroughs AM, Iyer LM, Aravind L;. Mol Biosyst. 2011;7:2261-2277. (from Pfam) NF025806.5 PF14450.11 FtsA 31.8 31.8 127 domain Y Y N cell division FtsA domain-containing protein 15281131,9352931 131567 cellular organisms no rank 87176 EBI-EMBL Cell division protein FtsA Cell division protein FtsA FtsA is essential for bacterial cell division, and co-localises to the septal ring with FtsZ. It has been suggested that the interaction of FtsA-FtsZ has arisen through coevolution in different bacterial strains [1]. The FtsA protein contains two structurally related actin-like ATPase domains which are also structurally related to the ATPase domains of HSP70 (see PF00012). FtsA has a SHS2 domain PF02491 inserted in to the RnaseH fold PF02491 [2]. [1]. 9352931. Interactions between heterologous FtsA and FtsZ proteins at the FtsZ ring. Ma X, Sun Q, Wang R, Singh G, Jonietz EL, Margolin W;. J Bacteriol 1997;179:6788-6797. [2]. 15281131. The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies. Anantharaman V, Aravind L;. Proteins. 2004;56:795-807. (from Pfam) NF025807.5 PF14451.11 Ub-Mut7C 23 23 81 PfamEq Y N N Mut7-C ubiquitin 16859499 131567 cellular organisms no rank 11621 EBI-EMBL Mut7-C ubiquitin Mut7-C ubiquitin This member of the ubiquitin superfamily is found at the N-terminus of Mut7-C like RNAses, suggestive of an RNA-binding role [1]. [1]. 16859499. The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. Iyer LM, Burroughs AM, Aravind L;. Genome Biol. 2006;7:R60. (from Pfam) NF025808.5 PF14452.11 Multi_ubiq 24.5 24.5 69 PfamEq Y Y N multiubiquitin domain-containing protein 16859499 131567 cellular organisms no rank 3662 EBI-EMBL Multiubiquitin Multiubiquitin A ubiquitin superfamily domain that is often present in multiple tandem copies in the same polypeptide. Members of this family are associated in gene neighborhoods, or on occasions fused to, bacterial homologs of components of ubiquitin-dependent modification system such as the E1, E2 and JAB metallopeptidase enzymes and a distinct metal-binding domain [1]. The E2/UBC fold domain appears to be inactive. The JAB domain in these operons is usually fused to the E1 domain [1]. [1]. 16859499. The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. Iyer LM, Burroughs AM, Aravind L;. Genome Biol. 2006;7:R60. (from Pfam) NF025813.5 PF14457.11 Prok-E2_A 25 25 163 PfamEq Y N N Prokaryotic E2 family A 16859499,18276160 131567 cellular organisms no rank 2063 EBI-EMBL Prokaryotic E2 family A Prokaryotic E2 family A A member of the E2/UBC superfamily of proteins found in several bacteria. The active site residues are very similar to the eukaryotic E2 proteins [1,2]. Members of this family are usually fused to E1 and JAB domains C-terminal to the E2 domain. The protein is usually in the gene neighborhood of a gene encoding a distinct metallobetalactamase family protein [1]. [1]. 16859499. The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. Iyer LM, Burroughs AM, Aravind L;. Genome Biol. 2006;7:R60. [2]. 18276160. Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation. Burroughs AM, Jaffee M, Iyer LM, Aravind L;. J Struct Biol. 2008;162:205-218. (from Pfam) NF025817.5 PF14462.11 Prok-E2_E 25 25 123 domain Y Y N E2/UBC family protein 16859499,18276160 131567 cellular organisms no rank 1677 EBI-EMBL Prokaryotic E2 family E E2/UBC family protein A member of the E2/UBC superfamily of proteins found in diverse bacteria. Analysis of the active site residues suggest that members of this family are inactive as they lack the characteristic catalytic residues of the E2 enzymes [1,2]. They are usually fused to or in the neighborhood of a multi/poly ubiquitin domain protein. Other proteins of the ubiquitin modification pathway such as the E1 and JAB proteins are also found in its gene neighborhood along with a distinct predicted metal-binding protein. [1]. 16859499. The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. Iyer LM, Burroughs AM, Aravind L;. Genome Biol. 2006;7:R60. [2]. 18276160. Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation. Burroughs AM, Jaffee M, Iyer LM, Aravind L;. J Struct Biol. 2008;162:205-218. (from Pfam) NF025819.5 PF14464.11 Prok-JAB 25 25 114 domain Y Y N Mov34/MPN/PAD-1 family protein 12183636,16104727,16859499,21890906 131567 cellular organisms no rank 59967 EBI-EMBL Prokaryotic homologs of the JAB domain Prokaryotic homologs of the JAB domain These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signaling and protein turnover pathways in eukaryotes [1]. Prokaryotic JAB domains are predicted to have a similar role in their cognates of the ubiquitin modification pathway [2]. The domain is widely found in bacteria, archaea and phages where they are present in several gene contexts in addition to those that correspond to the prokaryotic cognates of the eukaryotic Ub pathway. Other contexts in which JAB domains are present include gene neighbor associations with ubiquitin fold domains in cysteine and siderophore biosynthesis, and phage tail morphogenesis, where they are shown or predicted to process the associated ubiquitin [2,3]. A distinct family, the RadC-like JAB domains are widespread in bacteria and are predicted to function as nucleases [4]. In halophilic archaea the JAB domain shows strong gene-neighborhood associations with a nucleotidyltransferase suggesting a role in nucleotide metabolism [4]. [1]. 12183636. Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Verma R, Aravind L, Oania R, McDonald WH, Yates JR 3rd, Koonin EV, Deshaies RJ;. Science. 2002;298:611-615. [2]. 16859499. The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. Iyer LM, Burroughs AM, Aravind L;. Genome Biol. 2006;7:R60. [3]. 16104727. Reconstitution of a new cysteine biosynthetic pathway in Mycobacterium tuberculosis. Burns KE, Baumgart S, Dorrestein PC, Zhai H, McLafferty FW, Begley TP;. J Am Chem Soc. 2005;127:11602. TRUNCATED at 1650 bytes (from Pfam) NF025825.5 PF14470.11 bPH_3 23 16 95 domain Y Y N PH domain-containing protein 131567 cellular organisms no rank 17246 EBI-EMBL Bacterial PH domain Bacterial PH domain Proteins in this family are distantly related to PH domains. (from Pfam) NF025826.5 PF14471.11 DUF4428 27.8 27.8 51 domain Y Y N DUF4428 domain-containing protein 131567 cellular organisms no rank 1435 EBI-EMBL Domain of unknown function (DUF4428) Domain of unknown function (DUF4428) This putative zinc finger domain is found in uncharacterised bacterial proteins. (from Pfam) NF025827.5 PF14472.11 DUF4429 25 15 95 domain Y Y N DUF4429 domain-containing protein 131567 cellular organisms no rank 13537 EBI-EMBL Domain of unknown function (DUF4429) Domain of unknown function (DUF4429) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and viruses, and is approximately 90 amino acids in length. This domain is often found in two tandem copies. (from Pfam) NF025833.5 PF14478.11 DUF4430 23.8 23.8 72 domain Y Y N DUF4430 domain-containing protein 131567 cellular organisms no rank 13217 EBI-EMBL Domain of unknown function (DUF4430) Domain of unknown function (DUF4430) Although this family has overlaps with SLBB, the majority of its sequences are unique. Several family members, eg UniProtKB:A0RGA8, that do not overlap have an LPXTG-cell wall anchor at their C-terminus, a SSF_Family 10_polysaccharide_lyase or Glycosyltransferase structure associated with them in the middle region, as shown by InterPro, as well as this domain at the N-terminus. (from Pfam) NF025839.5 PF14486.11 DUF4432 32.5 32.5 304 PfamAutoEq Y Y N DUF4432 family protein 131567 cellular organisms no rank 14073 EBI-EMBL Domain of unknown function (DUF4432) DUF4432 family protein NF025840.5 PF14487.11 DarT 22.5 22.5 201 PfamAutoEq Y Y N DarT ssDNA thymidine ADP-ribosyltransferase family protein 27939941 131567 cellular organisms no rank 7757 EBI-EMBL ssDNA thymidine ADP-ribosyltransferase, DarT DarT ssDNA thymidine ADP-ribosyltransferase family protein This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 201 and 230 amino acids in length. There is a single completely conserved residue E that may be functionally important. This family is distantly similar to Pfam:PF01885. Studies in search for novel ADP-ribosylation systems in bacterial genomes have identified an operon that encodes a conserved protein containing a distinct type of macrodomain associated with this family. This led to the identification of a toxin-antitoxin (TA) system, with DarT acting as the toxin. It is an enzyme that specifically modifies thymidines on single-stranded DNA in a sequence-specific manner by a nucleotide-type modification called ADP-ribosylation. This modification in turn can be removed by DarG, the antitoxin macrodomain protein. In addition, it was illustrated that substitution of the single completely conserved glutamate residue resulted in attenuation of function where DarT was non-toxic [1]. [1]. 27939941. The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA. Jankevicius G, Ariza A, Ahel M, Ahel I;. Mol Cell. 2016;64:1109-1116. (from Pfam) NF025841.5 PF14488.11 DUF4434 30 30 283 PfamAutoEq Y Y N DUF4434 domain-containing protein 131567 cellular organisms no rank 5981 EBI-EMBL Domain of unknown function (DUF4434) Domain of unknown function (DUF4434) This family has a TIM-barrel structure and appears to be related to a variety of glycosyl hydrolase enzymes. (from Pfam) NF025842.5 PF14489.11 QueF 27.3 27.3 81 PfamEq Y N N QueF-like protein GO:0008616,GO:0033739 15767583 131567 cellular organisms no rank 36263 EBI-EMBL QueF-like protein QueF-like protein This protein is involved in the biosynthesis of queuosine. In some proteins this domain appears to be fused to Pfam:PF06508. [1]. 15767583. From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold. Van Lanen SG, Reader JS, Swairjo MA, de Crecy-Lagard V, Lee B, Iwata-Reuyl D;. Proc Natl Acad Sci U S A. 2005;102:4264-4269. (from Pfam) NF025844.5 PF14491.11 DUF4435 27 27 238 domain Y Y N DUF4435 domain-containing protein 131567 cellular organisms no rank 6577 EBI-EMBL Protein of unknown function (DUF4435) Protein of unknown function (DUF4435) This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 285 and 362 amino acids in length. This domain is sometimes associated with AAA domains. (from Pfam) NF025845.5 PF14492.11 EFG_III 27 27 75 domain Y N N Elongation Factor G, domain III 23636399 131567 cellular organisms no rank 128867 EBI-EMBL Elongation Factor G, domain III Elongation Factor G, domain III This domain is found in Elongation Factor G. It shares a similar structure with domain V (Pfam:PF00679). Structural studies in drosophila indicate this is domain 3 [1]. [1]. 23636399. Structures of the human and Drosophila 80S ribosome. Anger AM, Armache JP, Berninghausen O, Habeck M, Subklewe M, Wilson DN, Beckmann R;. Nature. 2013;497:80-85. (from Pfam) NF025846.5 PF14493.11 HTH_40 27 27 89 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 23133 EBI-EMBL Helix-turn-helix domain Helix-turn-helix domain This presumed domain is found at the C-terminus of a large number of helicase proteins. (from Pfam) NF025850.5 PF14497.11 GST_C_3 21.6 21.6 104 domain Y Y N glutathione S-transferase family protein 131567 cellular organisms no rank 152402 EBI-EMBL Glutathione S-transferase, C-terminal domain Glutathione S-transferase, C-terminal domain This domain is closely related to Pfam:PF00043. (from Pfam) NF025851.5 PF14498.11 Glyco_hyd_65N_2 27.7 27.7 234 domain Y Y N glycoside hydrolase N-terminal domain-containing protein 131567 cellular organisms no rank 38501 EBI-EMBL Glycosyl hydrolase family 65, N-terminal domain Glycosyl hydrolase family 65, N-terminal domain This domain represents a domain found to the N-terminus of the glycosyl hydrolase 65 family catalytic domain. (from Pfam) NF025852.5 PF14499.11 DUF4437 24 24 250 domain Y Y N DUF4437 domain-containing protein 131567 cellular organisms no rank 4226 EBI-EMBL Domain of unknown function (DUF4437) Domain of unknown function (DUF4437) This family of proteins is found in bacteria. Proteins in this family are typically between 152 and 283 amino acids in length. (from Pfam) NF025854.5 PF14501.11 HATPase_c_5 22 22 102 domain Y Y N GHKL domain-containing protein 131567 cellular organisms no rank 243621 EBI-EMBL GHKL domain GHKL domain This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90. (from Pfam) NF025855.5 PF14502.11 HTH_41 25 25 48 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 23665 EBI-EMBL Helix-turn-helix domain Helix-turn-helix domain NF025858.5 PF14505.11 DUF4438 24.9 24.9 135 PfamAutoEq Y Y N DUF4438 domain-containing protein 131567 cellular organisms no rank 1042 EBI-EMBL Domain of unknown function (DUF4438), N-terminal Domain of unknown function (DUF4438), N-terminal This is the N-terminal domain of TM_1086 and related proteins. (from Pfam) NF025861.5 PF14508.11 GH97_N 25.3 25.3 229 domain Y Y N glycoside hydrolase family 97 N-terminal domain-containing protein 16131397,18848471,18981178 131567 cellular organisms no rank 30827 EBI-EMBL Glycosyl-hydrolase 97 N-terminal Glycosyl-hydrolase 97 N-terminal This N-terminal domain of glycosyl-hydrolase-97 [1]contributes part of the active site pocket. It is also important for contact with the catalytic and C-terminal domains of the whole [2,3]. [1]. 16131397. GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily. Naumoff DG;. BMC Genomics. 2005;6:112. [2]. 18848471. Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora. Gloster TM, Turkenburg JP, Potts JR, Henrissat B, Davies GJ;. Chem Biol. 2008;15:1058-1067. [3]. 18981178. Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron. Kitamura M, Okuyama M, Tanzawa F, Mori H, Kitago Y, Watanabe N, Kimura A, Tanaka I, Yao M;. J Biol Chem. 2008;283:36328-36337. (from Pfam) NF025862.5 PF14509.11 GH97_C 25 25 97 domain Y Y N glycoside hydrolase family 97 C-terminal domain-containing protein 16131397,18848471,18981178 131567 cellular organisms no rank 30747 EBI-EMBL Glycosyl-hydrolase 97 C-terminal, oligomerisation Glycosyl-hydrolase 97 C-terminal, oligomerisation Glycosyl-hydrolase-97 is made up of three tightly linked and highly conserved globular domains. The C-terminal domain is found to be necessary for oligomerisation of the whole molecule in order to create the active-site pocket and the Ca++-binding site. [1]. 16131397. GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily. Naumoff DG;. BMC Genomics. 2005;6:112. [2]. 18848471. Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora. Gloster TM, Turkenburg JP, Potts JR, Henrissat B, Davies GJ;. Chem Biol. 2008;15:1058-1067. [3]. 18981178. Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron. Kitamura M, Okuyama M, Tanzawa F, Mori H, Kitago Y, Watanabe N, Kimura A, Tanaka I, Yao M;. J Biol Chem. 2008;283:36328-36337. (from Pfam) NF025864.5 PF14511.11 RE_EcoO109I 22.5 22.5 198 subfamily Y Y N PmeII family type II restriction endonuclease 22638584 131567 cellular organisms no rank 1261 EBI-EMBL Type II restriction endonuclease EcoO109I PmeII family type II restriction endonuclease PmeII (AVO54257.1) is identified by REBASE as a type II restriction enzyme that cuts at GGWCC sites. The model is named by Pfam for EcoO109I (AAF06964.1), which is related, with a similar cut site, but which scores barely above model cutoffs. NF025865.5 PF14512.11 TM1586_NiRdase 27 27 215 domain Y Y N nitroreductase family protein 131567 cellular organisms no rank 16953 EBI-EMBL Putative TM nitroreductase nitroreductase family protein Compared with the more traditional NADH oxidase/flavin reductase family, this family is a duplication, consisting of two similar domains arranged as the subunits of the dimeric NADH oxidase/flavin reductase with one conserved active site. (from Pfam) NF025869.5 PF14516.11 AAA_35 27 27 331 domain Y Y N AAA-like domain-containing protein 131567 cellular organisms no rank 11010 EBI-EMBL AAA-like domain AAA-like domain This family of proteins are part of the AAA superfamily. (from Pfam) NF025871.5 PF14518.11 Haem_oxygenas_2 28.9 28.9 177 domain Y Y N iron-containing redox enzyme family protein 15087448 131567 cellular organisms no rank 44524 EBI-EMBL Iron-containing redox enzyme Iron-containing redox enzyme The CADD, Chlamydia protein associating with death domains, crystal structure reveals a dimer of seven-helical bundles. Each bundle contains a di-iron centre adjacent to an internal cavity that forms an active site similar to that of methane mono-oxygenase hydrolase [1]. [1]. 15087448. Structure of the Chlamydia protein CADD reveals a redox enzyme that modulates host cell apoptosis. Schwarzenbacher R, Stenner-Liewen F, Liewen H, Robinson H, Yuan H, Bossy-Wetzel E, Reed JC, Liddington RC;. J Biol Chem. 2004;279:29320-29324. (from Pfam) NF025873.5 PF14520.11 HHH_5 27 17 57 domain Y Y N helix-hairpin-helix domain-containing protein 131567 cellular organisms no rank 307515 EBI-EMBL Helix-hairpin-helix domain helix-hairpin-helix domain NF025874.5 PF14521.11 Aspzincin_M35 30 30 142 domain Y Y N M35 family metallo-endopeptidase 3.4.24.- GO:0004222 10448068,11223512,11679721,9644258 131567 cellular organisms no rank 3890 EBI-EMBL Lysine-specific metallo-endopeptidase M35 family metallo-endopeptidase catalytic region This is the catalytic region of aspzincins, a group of lysine-specific metallo-endopeptidases in the MEROPS:M35 family. They exhibit the following active-site architecture. The active site is composed of two helices and a loop region and includes the HExxH and GTxDxxYG motifs. In UniProt:P81054, His117, His121 and Asp130 coordinate to the catalytic zinc ligands. An electrostatically negative region composed of Asp154 and Glu157 attracts a positively charged Lys side chain of a substrate in a specific manner [4]. [1]. 9644258. Kinetic characterization of lysine-specific metalloendopeptidases from Grifola frondosa and Pleurotus ostreatus fruiting bodies. Nonaka T, Hashimoto Y, Takio K;. J Biochem. 1998;124:157-162. [2]. 10448068. The lysine-specific proteinase from Armillaria mellea is a member of a novel class of metalloendopeptidases located in Basidiomycetes. Healy V, O'Connell J, McCarthy TV, Doonan S;. Biochem Biophys Res Commun. 1999;262:60-63. [3]. 11223512. Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms. Hori T, Kumasaka T, Yamamoto M, Nonaka N, Tanaka N, Hashimoto Y, Ueki U, Takio K;. Acta Crystallogr D Biol Crystallogr. 2001;57:361-368. [4]. 11679721. A quick solution: ab initio structure determination of a 19 kDa metalloproteinase using ACORN. McAuley KE, Jia-Xing Y, Dodson EJ, Lehmbeck J, Ostergaard PR, Wilson KS;. Acta Crystallogr D Biol Crystallogr. 2001;57:1571-1578. (from Pfam) NF025875.5 PF14522.11 Cytochrome_C7 24.8 24.8 67 domain Y Y N cytochrome c3 family protein 10386369,15133162,17139260,18534185,19857457,21130881 131567 cellular organisms no rank 7712 EBI-EMBL Cytochrome c7 and related cytochrome c cytochrome c3 family protein This family includes cytochromes c7 and c7-type. In cytochromes c7 all three haems are bis-His co-ordinated, while in c7-type the last haem is His-Met co-ordinated [1-4]. Desulfuromonas acetoxidans and Geobacter metallireducens cytochrome c7 participate in the anaerobic iron respiration, but Geobacter metallireducens cytochrome c7 hasn't a Fe(III) reductase activity [5]. This entry also includes cytochrome c nitrite reductase subunit NrfH from Desulfovibrio vulgaris which forms a complex with cytochrome c nitrite reductase NrfA [6]. [1]. 21130881. Structure of a novel dodecaheme cytochrome c from Geobacter sulfurreducens reveals an extended 12 nm protein with interacting hemes. Pokkuluri PR, Londer YY, Duke NE, Pessanha M, Yang X, Orshonsky V, Orshonsky L, Erickson J, Zagyanskiy Y, Salgueiro CA, Schiffer M;. J Struct Biol. 2011;174:223-233. [2]. 18534185. Structural insights into the modulation of the redox properties of two Geobacter sulfurreducens homologous triheme cytochromes. Morgado L, Bruix M, Orshonsky V, Londer YY, Duke NE, Yang X, Pokkuluri PR, Schiffer M, Salgueiro CA;. Biochim Biophys Acta. 2008;1777:1157-1165. [3]. 15133162. Structure of a novel c7-type three-heme cytochrome domain from a multidomain cytochrome c polymer. Pokkuluri PR, Londer YY, Duke NE, Erickson J, Pessanha M, Salgueiro CA, Schiffer M;. Protein Sci. 2004;13:1684-1692. [4]. 19857457. Structural characterization of a family of cytochromes c(7) involved in Fe(III) respiration by Geobacter sulfurreducens. Pokkuluri PR, Londer YY, Yang X, Duke NE, Erickson J, Orshonsky V, Johnson G, Schiffer M;. Biochim Biophys Acta. 2010;1797:222-232. [5]. 10386. TRUNCATED at 1650 bytes (from Pfam) NF025877.5 PF14524.11 Wzt_C 30.4 30.4 143 domain Y Y N Wzt carbohydrate-binding domain-containing protein 18032609 131567 cellular organisms no rank 17266 EBI-EMBL Wzt C-terminal domain Wzt C-terminal domain This domain is found at the C-terminus of the Wzt protein [1]. The crystal structure of C-Wzt(O9a) reveals a beta sandwich with an immunoglobulin-like topology that contains the O-antigenic polysaccharide binding pocket. This domain is often associated with the ABC-transporter domain. [1]. 18032609. Substrate binding by a bacterial ABC transporter involved in polysaccharide export. Cuthbertson L, Kimber MS, Whitfield C;. Proc Natl Acad Sci U S A. 2007;104:19529-19534. (from Pfam) NF025878.5 PF14525.11 AraC_binding_2 27 27 173 domain Y N N AraC-binding-like domain 131567 cellular organisms no rank 72514 EBI-EMBL AraC-binding-like domain AraC-binding-like domain This domain is related to the AraC ligand binding domain Pfam:PF02311. (from Pfam) NF025879.5 PF14526.11 Cass2 27 27 150 domain Y Y N effector binding domain-containing protein 21390267 131567 cellular organisms no rank 83740 EBI-EMBL Integron-associated effector binding protein Integron-associated effector binding protein This family contains Cass2 from Vibrio cholerae, an integron-associated protein that has been shown [1] to bind cationic drug compounds with submicromolar affinity. Cass2 has been proposed to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and other closely-related species. [1]. 21390267. Crystal structure of an integron gene cassette-associated protein from Vibrio cholerae identifies a cationic drug-binding module. Deshpande CN, Harrop SJ, Boucher Y, Hassan KA, Di Leo R, Xu X, Cui H, Savchenko A, Chang C, Labbate M, Paulsen IT, Stokes HW, Curmi PM, Mabbutt BC;. PLoS One. 2011;6:e16934. (from Pfam) NF025880.5 PF14527.11 LAGLIDADG_WhiA 23.2 5.7 93 PfamEq Y N N WhiA LAGLIDADG-like domain 17603302,19836336 131567 cellular organisms no rank 20533 EBI-EMBL WhiA LAGLIDADG-like domain WhiA LAGLIDADG-like domain This domain is found within the sporulation regulator WhiA. It is a LAGLIDADG superfamily like domain [1-2]. [1]. 17603302. Bacterial DUF199/COG1481 Proteins Including Sporulation Regulator WhiA are Distant Homologs of LAGLIDADG Homing Endonucleases That Retained Only DNA Binding. Knizewski L, Ginalski K;. Cell Cycle. 2007;6:1666-1670. [2]. 19836336. The structure of a bacterial DUF199/WhiA protein: domestication of an invasive endonuclease. Kaiser BK, Clifton MC, Shen BW, Stoddard BL;. Structure. 2009;17:1368-1376. (from Pfam) NF025881.5 PF14528.11 LAGLIDADG_3 22.5 20 82 domain Y Y N LAGLIDADG family homing endonuclease GO:0004519 18974222 131567 cellular organisms no rank 19803 EBI-EMBL LAGLIDADG-like domain LAGLIDADG-like domain This domain is part of the LAGLIDADG superfamily [1]. [1]. 18974222. Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering. Marcaida MJ, Prieto J, Redondo P, Nadra AD, Alibes A, Serrano L, Grizot S, Duchateau P, Paques F, Blanco FJ, Montoya G;. Proc Natl Acad Sci U S A. 2008;105:16888-16893. (from Pfam) NF025882.5 PF14529.11 Exo_endo_phos_2 27.4 27.4 117 PfamEq Y N N Endonuclease-reverse transcriptase GO:0003824 1701254,18431403 131567 cellular organisms no rank 963 EBI-EMBL Endonuclease-reverse transcriptase Endonuclease-reverse transcriptase This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49. [1]. 1701254. Evidence for horizontal transmission of the mobile element jockey between distant Drosophila species. Mizrokhi LJ, Mazo AM;. Proc Natl Acad Sci U S A. 1990;87:9216-9220. [2]. 18431403. Revisiting horizontal transfer of transposable elements in Drosophila. Loreto EL, Carareto CM, Capy P;. Heredity. 2008;100:545-554. (from Pfam) NF025884.5 PF14531.11 Kinase-like 25 25 289 domain Y N N Kinase-like 19197235 131567 cellular organisms no rank 8938 EBI-EMBL Kinase-like Kinase-like This family includes the pseudokinases ROP2 and ROP8 from Toxoplasma gondii (Swiss:Q06AK3 and Swiss:O15693). These proteins have a typical bilobed protein kinase fold, but lack catalytic actvity [1]. [1]. 19197235. Novel structural and regulatory features of rhoptry secretory kinases in Toxoplasma gondii. Qiu W, Wernimont A, Tang K, Taylor S, Lunin V, Schapira M, Fentress S, Hui R, Sibley LD;. EMBO J. 2009;28:969-979. (from Pfam) NF025887.5 PF14534.11 DUF4440 25.2 25.2 107 domain Y Y N DUF4440 domain-containing protein 27406907 131567 cellular organisms no rank 150897 EBI-EMBL Domain of unknown function (DUF4440) Domain of unknown function (DUF4440) This domain is found in uncharacterised proteins from bacteria, archaea and eukaryotes, including NTF2-Like SgcJ protein from Streptomyces carzinostaticus, which plays a role in the biosynthesis of the 9-membered enediyne antitumor antibiotic C-1027. It shows a cone-like alpha+beta barrel structure with a long N-terminal alpha- helix, a curved six-stranded antiparallel beta-sheet and two additional shorter alpha-helices. Its specific function is still unkown [1]. [1]. 27406907. Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027. Huang T, Chang CY, Lohman JR, Rudolf JD, Kim Y, Chang C, Yang D, Ma M, Yan X, Crnovcic I, Bigelow L, Clancy S, Bingman CA, Yennamalli RM, Babnigg G, Joachimiak A, Phillips GN, Shen B;. J Antibiot (Tokyo). 2016;69:731-740. (from Pfam) NF025888.5 PF14535.11 AMP-binding_C_2 25 25 96 domain Y N N AMP-binding enzyme C-terminal domain 131567 cellular organisms no rank 37236 EBI-EMBL AMP-binding enzyme C-terminal domain AMP-binding enzyme C-terminal domain This is a small domain that is found C terminal to Pfam:PF00501. It has a central beta sheet core that is flanked by alpha helices. (from Pfam) NF025890.5 PF14537.11 Cytochrom_c3_2 25 25 79 domain Y Y N cytochrome c3 family protein 10861223,12080059 131567 cellular organisms no rank 8077 EBI-EMBL Cytochrome c3 cytochrome c3 family protein NF025892.5 PF14539.11 DUF4442 25 25 132 domain Y Y N DUF4442 domain-containing protein 131567 cellular organisms no rank 52858 EBI-EMBL Domain of unknown function (DUF4442) Domain of unknown function (DUF4442) This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 139 and 165 amino acids in length. There is a conserved PYF sequence motif. There is a single completely conserved residue N that may be functionally important. (from Pfam) NF025895.5 PF14542.11 Acetyltransf_CG 30 30 80 domain Y Y N N-acetyltransferase 18709443 131567 cellular organisms no rank 51836 EBI-EMBL GCN5-related N-acetyl-transferase N-acetyltransferase This family of GCN5-related N-acetyl-transferases bind both CoA and acetyl-CoA. They are characterised by highly conserved glycine, a cysteine residue in the acetyl-CoA binding site near the acetyl group, their small size compared with other GNATs and a lack of of an obvious substrate-binding site. It is proposed that they transfer an acetyl group from acetyl-CoA to one or more unidentified aliphatic amines via an acetyl (cysteine) enzyme intermediate. The substrate might be another macromolecule. [1]. 18709443. Structure of an acetyl-CoA binding protein from Staphylococcus aureus representing a novel subfamily of GCN5-related N-acetyltransferase-like proteins. Cort JR, Ramelot TA, Murray D, Acton TB, Ma LC, Xiao R, Montelione GT, Kennedy MA;. J Struct Funct Genomics. 2008;9:7-20. (from Pfam) NF025901.5 PF14550.11 Peptidase_S78_2 24 24 126 domain Y Y N XkdF-like putative serine protease domain-containing protein 33754443 131567 cellular organisms no rank 2809 EBI-EMBL Putative phage serine protease XkdF XkdF-like putative serine protease domain This phage-associated domain is named for its presence in XkdF from the Bacillus subtilis PBSX element, a defective prophage. NF025902.5 PF14551.11 MCM_N 24.9 24.9 95 domain Y N N MCM N-terminal domain 12548282,24378617 131567 cellular organisms no rank 1346 EBI-EMBL MCM N-terminal domain MCM N-terminal domain This family contains the N-terminal domain of MCM proteins. [1]. 12548282. The structure and function of MCM from archaeal M. Thermoautotrophicum. Fletcher RJ, Bishop BE, Leon RP, Sclafani RA, Ogata CM, Chen XS;. Nat Struct Biol. 2003;10:160-167. [2]. 24378617. The 1.8-A crystal structure of the N-terminal domain of an archaeal MCM as a right-handed filament. Fu Y, Slaymaker IM, Wang J, Wang G, Chen XS;. J Mol Biol. 2014;426:1512-1523. (from Pfam) NF025903.5 PF14552.11 Tautomerase_2 28 28 82 domain Y Y N tautomerase family protein 131567 cellular organisms no rank 27686 EBI-EMBL Tautomerase enzyme tautomerase family protein NF025908.5 PF14557.11 AphA_like 27 27 174 PfamEq Y N N Putative AphA-like transcriptional regulator 131567 cellular organisms no rank 676 EBI-EMBL Putative AphA-like transcriptional regulator Putative AphA-like transcriptional regulator Members of this family are putative transcriptional regulators that appear to be related to the Pfam:PF03551 family. This family includes AphA-like members. (from Pfam) NF025910.5 PF14559.11 TPR_19 25 25 68 domain Y Y N tetratricopeptide repeat protein 131567 cellular organisms no rank 419915 EBI-EMBL Tetratricopeptide repeat Tetratricopeptide repeat NF025911.5 PF14560.11 Ubiquitin_2 23.1 13 86 domain Y N N Ubiquitin-like domain GO:0005515 14536023,15364906 131567 cellular organisms no rank 359 EBI-EMBL Ubiquitin-like domain Ubiquitin-like domain This entry contains ubiquitin-like domains [1-2]. [1]. 15364906. Solution structure of a ubiquitin-like domain from tubulin-binding cofactor B. Lytle BL, Peterson FC, Qiu SH, Luo M, Zhao Q, Markley JL, Volkman BF;. J Biol Chem. 2004;279:46787-46793. [2]. 14536023. Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization. Grynberg M, Jaroszewski L, Godzik A;. BMC Bioinformatics. 2003;4:46. (from Pfam) NF025912.5 PF14561.11 TPR_20 25 25 90 PfamEq Y Y N tetratricopeptide repeat protein 131567 cellular organisms no rank 42566 EBI-EMBL Tetratricopeptide repeat Tetratricopeptide repeat NF025917.5 PF14566.11 PTPlike_phytase 27 27 158 PfamEq Y N N Inositol hexakisphosphate 15530366,18573100,9923613 131567 cellular organisms no rank 3178 EBI-EMBL Inositol hexakisphosphate Inositol hexakisphosphate Inositol hexakisphosphate, often called phytate, is found in abundance in seeds and acting as an inorganic phosphate reservoir. Phytases are phosphatases that hydrolyze phytate to less-phosphorylated myo-inositol derivatives and inorganic phosphate. The active-site sequence (HCXXGXGR) of the phytase identified from the gut micro-organism Selenomonas ruminantium forms a loop (P loop) at the base of a substrate binding pocket that is characteristic of protein tyrosine phosphatases (PTPs). The depth of this pocket is an important determinant of the substrate specificity of PTPs. In humans this enzyme is thought to aid bone mineralization and salvage the inositol moiety prior to apoptosis [3]. [1]. 15530366. Structures of the Selenomonas ruminantium phytase in complex with persulfated phytate: DSP phytase fold and mechanism for sequential substrate hydrolysis. Chu HM, Guo RT, Lin TW, Chou CC, Shr HL, Lai HL, Tang TY, Cheng KJ, Selinger BL, Wang AH;. Structure. 2004;12:2015-2024. [2]. 18573100. Effect of ionic strength and oxidation on the P-loop conformation of the protein tyrosine phosphatase-like phytase, PhyAsr. Gruninger RJ, Selinger LB, Mosimann SC;. FEBS J. 2008;275:3783-3792. [3]. 9923613. The human and rat forms of multiple inositol polyphosphate phosphatase: functional homology with a histidine acid phosphatase up-regulated during endochondral ossification. Caffrey JJ, Hidaka K, Matsuda M, Hirata M, Shears SB;. FEBS Lett. 1999;442:99-104. (from Pfam) NF025918.5 PF14567.11 SUKH_5 27 27 142 domain Y Y N SMI1/KNR4 family protein 131567 cellular organisms no rank 19592 EBI-EMBL SMI1-KNR4 cell-wall SMI1/KNR4 family protein Members of this family are related to the SMI1/KNR4-like or SUKH superfamily of proteins. (from Pfam) NF025919.5 PF14568.11 SUKH_6 27 26 119 domain Y Y N SMI1/KNR4 family protein 131567 cellular organisms no rank 49081 EBI-EMBL SMI1-KNR4 cell-wall SMI1/KNR4 family protein Members of this family are related to the SMI1/KNR4-like or SUKH superfamily of proteins. (from Pfam) NF025923.5 PF14572.11 Pribosyl_synth 27 27 184 domain Y N N Phosphoribosyl synthetase-associated domain GO:0000287,GO:0004749,GO:0009165 18409517,9545573 131567 cellular organisms no rank 56276 EBI-EMBL Phosphoribosyl synthetase-associated domain Phosphoribosyl synthetase-associated domain This family includes several examples of enzymes from class EC:2.7.6.1, phosphoribosyl-pyrophosphate transferase. [1]. 9545573. Molecular cloning of a human cDNA for the 41-kDa phosphoribosylpyrophosphate synthetase-associated protein. Katashima R, Iwahana H, Fujimura M, Yamaoka T, Ishizuka T, Tatibana M, Itakura M;. Biochim Biophys Acta. 1998;1396:245-250. [2]. 18409517. [Increased activity of PRPP synthetase]. Iizasa T;. Nihon Rinsho. 2008;66:694-698. (from Pfam) NF025925.5 PF14574.11 RACo_C_ter 27 27 261 domain Y Y N ASKHA domain-containing protein 22431597 131567 cellular organisms no rank 9646 EBI-EMBL C-terminal domain of RACo the ASKHA domain C-terminal domain of RACo the ASKHA domain This family includes reductive activator of CoFeSP (RACo) proteins, Swiss:Q3ACS2. Structure analysis of RACo indicate that it contains 4 regions: N-terminal region Pfam:PF00111 (residues 3-94) binding the [2Fe-2S] cluster, a linker region (residues 95-125), the middle region (residues 126-206), and the large C-terminal domain (residues 207-630). This entry is specific for the C-terminal domain which harbors the ATP-binding site. Structural studies show that the C-terminal domain contains the conserved beta-beta-beta-alpha-beta-alpha-beta-alpha topology characteristic of the ASKHA (acetate and sugar kinases/heat shock protein 70/actin). Despite the low-sequence identity shared between members of the ASKHA super family, they show a common central fold. Members of the ASKHA include proteins that catalyze phosphoryl transfers or hydrolysis of ATP in a variety of biological contexts. Asp, Asn, Glu, and Gln residues are well conserved in the core of the ASKHA proteins, where they interact with the phosphates of ATP and the bound Mg2+ ions. [1]. 22431597. Redox-dependent complex formation by an ATP-dependent activator of the corrinoid/iron-sulfur protein. Hennig SE, Jeoung JH, Goetzl S, Dobbek H;. Proc Natl Acad Sci U S A. 2012;109:5235-5240. (from Pfam) NF025929.5 PF14578.11 GTP_EFTU_D4 23.8 23.8 86 PfamEq Y N N Elongation factor Tu domain 4 131567 cellular organisms no rank 1724 EBI-EMBL Elongation factor Tu domain 4 Elongation factor Tu domain 4 Elongation factor Tu consists of several structural domains, and this is usually the fourth. (from Pfam) NF025930.5 PF14579.11 HHH_6 25.6 25.6 90 domain Y N N Helix-hairpin-helix motif 8692686 131567 cellular organisms no rank 178852 EBI-EMBL Helix-hairpin-helix motif Helix-hairpin-helix motif The HHH domain is a short DNA-binding domain [1]. [1]. 8692686. The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. Doherty AJ, Serpell LC, Ponting CP;. Nucleic Acids Res 1996;24:2488-2497. (from Pfam) NF025931.5 PF14580.11 LRR_9 30.5 30.5 175 PfamEq Y Y N leucine-rich repeat protein 131567 cellular organisms no rank 438 EBI-EMBL Leucine-rich repeat Leucine-rich repeat NF025933.5 PF14582.11 Metallophos_3 28.2 28.2 259 PfamEq Y N N Metallophosphoesterase, calcineurin superfamily 131567 cellular organisms no rank 1363 EBI-EMBL Metallophosphoesterase, calcineurin superfamily Metallophosphoesterase, calcineurin superfamily Members of this family are part of the Calcineurin-like phosphoesterase superfamily. (from Pfam) NF025934.5 PF14583.11 Pectate_lyase22 30 30 386 subfamily Y Y N oligogalacturonate lyase family protein GO:0045490,GO:0047487 20805221,20851883 131567 cellular organisms no rank 4596 EBI-EMBL Oligogalacturonate lyase oligogalacturonate lyase family protein This is a family of oligogalacturonate lyases, referred to more generally as pectate lyase family 22. These proteins fold into 7-bladed beta-propellers. [1]. 20805221. Structural and mechanistic classification of uronic acid-containing polysaccharide lyases. Garron ML, Cygler M;. Glycobiology. 2010;20:1547-1573. [2]. 20851883. The active site of oligogalacturonate lyase provides unique insights into cytoplasmic oligogalacturonate beta-elimination. Abbott DW, Gilbert HJ, Boraston AB;. J Biol Chem. 2010;285:39029-39038. (from Pfam) NF025935.5 PF14584.11 DUF4446 27.4 27.4 150 PfamAutoEq Y Y N DUF4446 family protein 131567 cellular organisms no rank 4307 EBI-EMBL Protein of unknown function (DUF4446) DUF4446 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 165 and 176 amino acids in length. (from Pfam) NF025938.5 PF14587.11 Glyco_hydr_30_2 27 27 364 domain Y Y N glycoside hydrolase GO:0004553 131567 cellular organisms no rank 11750 EBI-EMBL O-Glycosyl hydrolase family 30 glycoside hydrolase NF025939.5 PF14588.11 YjgF_endoribonc 35 35 148 subfamily Y Y N Atu1372/SO_1960 family protein 10595546 131567 cellular organisms no rank 38177 EBI-EMBL YjgF/chorismate_mutase-like, putative endoribonuclease Atu1372/SO_1960 family protein Members of this family are Rid superfamily proteins, related to YjgF from Salmonella, now called RidA (reactive intermediate imine deaminase A). NF025940.5 PF14589.11 NrfD_2 27 27 281 domain Y N N Polysulfide reductase 18536726 131567 cellular organisms no rank 3846 EBI-EMBL Polysulfide reductase Polysulfide reductase Bacterial polysulfide reductase is an integral membrane protein complex responsible for quinone-coupled reduction of polysulfide, a process important in extreme environments such as deep-sea vents and hot springs. Polysulfides are a class of compounds composed of chains of sulfur atoms, which in their simplest form are present as an anion with general formula Sn(2-). In nature, polysulfides are found in particularly high concentrations in extreme volcanic or geothermically active environments. Here, the reduction and oxidation of polysulfides are vital processes for many bacteria and are essential steps in the global sulfur cycle. In particular, the reduction of polysulfide to hydrogen sulfide in these environments is usually linked to energy-generating respiratory processes, supporting growth of many microorganisms, particularly hyperthermophiles. [1]. 18536726. Molecular mechanism of energy conservation in polysulfide respiration. Jormakka M, Yokoyama K, Yano T, Tamakoshi M, Akimoto S, Shimamura T, Curmi P, Iwata S;. Nat Struct Mol Biol. 2008;15:730-737. (from Pfam) NF025942.5 PF14591.11 AF0941-like 22.6 22.6 113 PfamEq Y N N AF0941-like 131567 cellular organisms no rank 149 EBI-EMBL AF0941-like AF0941-like Members of this family are of unknown function. (from Pfam) NF025943.5 PF14592.11 Chondroitinas_B 24 24 426 domain Y Y N chondroitinase-B domain-containing protein 12063249 131567 cellular organisms no rank 8424 EBI-EMBL Chondroitinase B Chondroitinase B This family includes chondroitinases. These enzymes cleave the glycosaminoglycan dermatan sulfate [1]. [1]. 12063249. Biochemical characterization of the chondroitinase B active site. Pojasek K, Raman R, Kiley P, Venkataraman G, Sasisekharan R;. J Biol Chem. 2002;277:31179-31186. (from Pfam) NF025945.5 PF14594.11 Sipho_Gp37 26.2 26.2 345 subfamily_domain Y Y N Gp37-like protein 21097585 131567 cellular organisms no rank 4011 EBI-EMBL Siphovirus ReqiPepy6 Gp37-like protein Gp37-like protein This family includes numerous phage proteins from Siphoviruses. The function of this protein is uncertain, but it is related to Pfam:PF06605. In Rhodococcus phage ReqiPepy6 this protein is called Gp37 [1]. [1]. 21097585. Genomic and functional analyses of Rhodococcus equi phages ReqiPepy6, ReqiPoco6, ReqiPine5, and ReqiDocB7. Summer EJ, Liu M, Gill JJ, Grant M, Chan-Cortes TN, Ferguson L, Janes C, Lange K, Bertoli M, Moore C, Orchard RC, Cohen ND, Young R;. Appl Environ Microbiol. 2011;77:669-683. (from Pfam) NF025946.5 PF14595.11 Thioredoxin_9 25 25 129 domain Y Y N thioredoxin family protein 131567 cellular organisms no rank 46436 EBI-EMBL Thioredoxin thioredoxin family protein NF025948.5 PF14597.11 Lactamase_B_5 28.4 28.4 199 domain Y N N Metallo-beta-lactamase superfamily 131567 cellular organisms no rank 993 EBI-EMBL Metallo-beta-lactamase superfamily Metallo-beta-lactamase superfamily This is a small family of putative metal-dependent hydrolases. (from Pfam) NF025949.5 PF14598.11 PAS_11 25 25 109 domain Y Y N PAS domain-containing protein 14757047 131567 cellular organisms no rank 6478 EBI-EMBL PAS domain PAS domain This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6) [1]. [1]. 14757047. Structure of the NCoA-1/SRC-1 PAS-B domain bound to the LXXLL motif of the STAT6 transactivation domain. Razeto A, Ramakrishnan V, Litterst CM, Giller K, Griesinger C, Carlomagno T, Lakomek N, Heimburg T, Lodrini M, Pfitzner E, Becker S;. J Mol Biol. 2004;336:319-329. (from Pfam) NF025953.5 PF14602.11 Hexapep_2 27 11 34 domain Y Y N DapH/DapD/GlmU-related protein 131567 cellular organisms no rank 310240 EBI-EMBL Hexapeptide repeat of succinyl-transferase DapH/DapD/GlmU-related hexapeptide repeat domain Members of this family share a hexapeptide repeat-containing domain with acetyltransferases and succinyltransferases such as DapH, DapD, and GlmU. NF025957.5 PF14606.11 Lipase_GDSL_3 27 27 178 domain Y Y N SGNH/GDSL hydrolase family protein 24363150 131567 cellular organisms no rank 16913 EBI-EMBL GDSL-like Lipase/Acylhydrolase family SGNH/GDSL hydrolase family protein NF025958.5 PF14607.11 GxDLY 27 27 146 domain Y Y N SGNH/GDSL hydrolase N-terminal domain-containing protein 131567 cellular organisms no rank 3598 EBI-EMBL N-terminus of Esterase_SGNH_hydro-type N-terminus of Esterase_SGNH_hydro-type This domain lies upstream of SGNH hydrolase, but its function is not known. There is a highly conserved GxDLY sequence-motif. (from Pfam) NF025973.5 PF14622.11 Ribonucleas_3_3 35 35 128 PfamEq Y N N Ribonuclease-III-like GO:0004525,GO:0006396 131567 cellular organisms no rank 55584 EBI-EMBL Ribonuclease-III-like Ribonuclease-III-like Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3. (from Pfam) NF025986.5 PF14635.11 HHH_7 27 27 104 PfamEq Y N N Helix-hairpin-helix motif 21094070,21844224,8692686 131567 cellular organisms no rank 62262 EBI-EMBL Helix-hairpin-helix motif Helix-hairpin-helix motif NF025990.5 PF14639.11 YqgF 35 35 150 PfamEq Y N N Holliday-junction resolvase-like of SPT6 21094070,21844224 131567 cellular organisms no rank 4874 EBI-EMBL Holliday-junction resolvase-like of SPT6 Holliday-junction resolvase-like of SPT6 The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC [1] but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage [2] [1]. 21094070. Structure and biological importance of the Spn1-Spt6 interaction, and its regulatory role in nucleosome binding. McDonald SM, Close D, Xin H, Formosa T, Hill CP;. Mol Cell. 2010;40:725-735. [2]. 21844224. Spt6 is required for heterochromatic silencing in the fission yeast Schizosaccharomyces pombe. Kiely CM, Marguerat S, Garcia JF, Madhani HD, Bahler J, Winston F;. Mol Cell Biol. 2011;31:4193-4204. (from Pfam) NF026010.5 PF14659.11 Phage_int_SAM_3 22.6 22.6 58 domain Y N N Phage integrase, N-terminal SAM-like domain GO:0003677,GO:0015074 131567 cellular organisms no rank 123617 EBI-EMBL Phage integrase, N-terminal SAM-like domain Phage integrase, N-terminal SAM-like domain This domain is found in a variety of phage integrase proteins. (from Pfam) NF026018.5 PF14667.11 Polysacc_synt_C 28.7 28.7 142 domain Y Y N polysaccharide biosynthesis C-terminal domain-containing protein 131567 cellular organisms no rank 340473 EBI-EMBL Polysaccharide biosynthesis C-terminal domain Polysaccharide biosynthesis C-terminal domain This family represents the C-terminal integral membrane region of polysaccharide biosynthesis proteins. (from Pfam) NF026032.5 PF14681.11 UPRTase 27 27 206 domain Y Y N uracil phosphoribosyltransferase 2189783,26271729 131567 cellular organisms no rank 46918 EBI-EMBL Uracil phosphoribosyltransferase uracil phosphoribosyltransferase This family includes the enzyme uracil phosphoribosyltransferase (EC:2.4.2.9). This enzyme catalyzes the first step of UMP biosynthesis. (from Pfam) NF026035.5 PF14684.11 Tricorn_C1 24 24 59 domain Y N N Tricorn protease C1 domain 11719810 131567 cellular organisms no rank 34951 EBI-EMBL Tricorn protease C1 domain Tricorn protease C1 domain This domain is the C1 core domain of tricorn protease. This is a mixed alpha-beta domain [1]. [1]. 11719810. Crystal structure of the tricorn protease reveals a protein disassembly line. Brandstetter H, Kim JS, Groll M, Huber R;. Nature. 2001;414:466-470. (from Pfam) NF026036.5 PF14685.11 Tricorn_PDZ 25 25 88 domain Y Y N PDZ domain-containing protein 11719810 131567 cellular organisms no rank 22979 EBI-EMBL Tricorn protease PDZ domain Tricorn protease PDZ domain This domain is the PDZ domain of tricorn protease [1]. [1]. 11719810. Crystal structure of the tricorn protease reveals a protein disassembly line. Brandstetter H, Kim JS, Groll M, Huber R;. Nature. 2001;414:466-470. (from Pfam) NF026037.5 PF14686.11 fn3_3 24.4 24.4 75 domain Y N N Polysaccharide lyase family 4, domain II 15135077 131567 cellular organisms no rank 5954 EBI-EMBL Polysaccharide lyase family 4, domain II Polysaccharide lyase family 4, domain II FnIII-like is domain II of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognises and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain displays an immunoglobulin-like or more specifically Fibronectin-III type fold and shows highest structural similarity to the C-terminal beta-sandwich subdomain of the pro-hormone/propeptide processing enzyme carboxypeptidase gp180 from duck. It serves to assist in producing the deep pocket, with domain III, into which the substrate fits [1]. [1]. 15135077. Rhamnogalacturonan lyase reveals a unique three-domain modular structure for polysaccharide lyase family 4. McDonough MA, Kadirvelraj R, Harris P, Poulsen JC, Larsen S;. FEBS Lett. 2004;565:188-194. (from Pfam) NF026040.5 PF14689.11 SPOB_a 28.1 28.1 62 domain Y Y N Spo0B domain-containing protein 9809070 131567 cellular organisms no rank 44005 EBI-EMBL Sensor_kinase_SpoOB-type, alpha-helical domain Sensor_kinase_SpoOB-type, alpha-helical domain Sporulation initiation phospho-transferase B or SpoOB is part of a phospho-relay that initiates sporulation in Bacillus subtilis. Spo0B is a two-domain protein consisting of an N-terminal alpha-helical hairpin domain and a C-terminal alpha/beta domain. Two subunits of Spo0B dimerise by a parallel association of helical hairpins to form a novel four-helix bundle from which the active histidine - involved in the auto-phosphorylation - protrudes. In the phospho-relay, the signal-receptor histidine kinases are dephosphorylated by a common response regulator, Spo0F. Spo0B then takes phosphorylated Spo0F as substrate thereby mediating the transfer of a phosphoryl group to Spo0A, the ultimate transcription factor. The exact function of this alpha-helical domain is not known; it does not always occur just as the N-terminal domain of SPOB_ab, Pfam:PF14682. SCOP describes this domain as a histidine kinase-like fold lacking the kinase ATP-binding site. [1]. 9809070. Formation of a novel four-helix bundle and molecular recognition sites by dimerization of a response regulator phosphotransferase. Varughese KI, Madhusudan, Zhou XZ, Whiteley JM, Hoch JA;. Mol Cell. 1998;2:485-493. (from Pfam) NF026041.5 PF14690.11 zf-ISL3 25.5 25.5 47 domain Y Y N transposase family protein 131567 cellular organisms no rank 46979 EBI-EMBL zinc-finger of transposase IS204/IS1001/IS1096/IS1165 transposase family protein NF026042.5 PF14691.11 Fer4_20 25.8 25.8 113 domain Y N N Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster 11796730 131567 cellular organisms no rank 120357 EBI-EMBL Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster Domain II of the enzyme dihydroprymidine dehydrogenase binds FAD. Dihydroprymidine dehydrogenase catalyses the first and rate-limiting step of pyrimidine degradation by converting pyrimidines to the corresponding 5,6- dihydro compounds [1]. This domain carries two Fe4-S4 clusters. [1]. 11796730. Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer. Dobritzsch D, Ricagno S, Schneider G, Schnackerz KD, Lindqvist Y;. J Biol Chem. 2002;277:13155-13166. (from Pfam) NF026048.5 PF14697.11 Fer4_21 35 35 59 domain Y Y N 4Fe-4S dicluster-binding protein GO:0051536 131567 cellular organisms no rank 54474 EBI-EMBL 4Fe-4S dicluster domain 4Fe-4S dicluster-binding domain Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters. (from Pfam) NF026049.5 PF14698.11 ASL_C2 27.3 27.3 69 domain Y N N Argininosuccinate lyase C-terminal 11698398,9256435 131567 cellular organisms no rank 73372 EBI-EMBL Argininosuccinate lyase C-terminal Argininosuccinate lyase C-terminal This domain is found at the C-terminus of argininosuccinate lyase [1-2]. [1]. 11698398. Mutational analysis of duck delta 2 crystallin and the structure of an inactive mutant with bound substrate provide insight into the enzymatic mechanism of argininosuccinate lyase. Sampaleanu LM, Yu B, Howell PL;. J Biol Chem. 2002;277:4166-4175. [2]. 9256435. Human argininosuccinate lyase: a structural basis for intragenic complementation. Turner MA, Simpson A, McInnes RR, Howell PL;. Proc Natl Acad Sci U S A. 1997;94:9063-9068. (from Pfam) NF026052.5 PF14701.11 hDGE_amylase 27 27 439 domain Y N N Glycogen debranching enzyme, glucanotransferase domain 131567 cellular organisms no rank 5640 EBI-EMBL Glycogen debranching enzyme, glucanotransferase domain Glycogen debranching enzyme, glucanotransferase domain This is a glucanotransferase catalytic domain of the eukaryotic variant of the glycogen debranching enzyme (GDE). The eukaryotic GDEs performs two functions: 4-alpha-D-glucanotransferase, EC:2.4.1.25, and Amylo-alpha-1,6-glucosidase, EC:3.2.1.33, performed by the, respectively N- and C- terminal halves of eukaryotic GDE enzymes. The domain is a catalytic domain responsible for the glucanotransferase function. It belongs to the alpha-amylase clan and is predicted to have a structure of a 8-stranded alpha/beta barrel (TIM barrel) where strands are interrupted by long loops and additional mini-domains. In most other amylases, the catalytic domain is followed by a beta- barrel substrate binding domain, but presence of such a domain cannot be verified in the human (and other eukaryotic) GDE enzymes. (from Pfam) NF026057.5 PF14706.11 Tnp_DNA_bind 24 24 58 domain Y Y N transposase DNA-binding-containing protein GO:0003677 10207011,15102449 131567 cellular organisms no rank 6224 EBI-EMBL Transposase DNA-binding Transposase DNA-binding This domain occurs at the C-terminus of transposases including E. coli tnpA (Swiss:Q46731). TnpA encodes a transposase and an inhibitor protein, the inhibitor only differs from the transposase by the absence of the N-terminal 55 amino acids, which includes most of this domain [1]. This domain consists of alpha helices and turns, and functions as a DNA-binding domain [2]. [1]. 10207011. The three-dimensional structure of a Tn5 transposase-related protein determined to 2.9-A resolution. Davies DR, Braam LM, Reznikoff WS, Rayment I;. J Biol Chem 1999;274:11904-11913. [2]. 15102449. Structure/function insights into Tn5 transposition. Steiniger-White M, Rayment I, Reznikoff WS;. Curr Opin Struct Biol. 2004;14:50-57. (from Pfam) NF026058.5 PF14707.11 Sulfatase_C 30.9 30.9 127 domain Y N N C-terminal region of aryl-sulfatase 9521684 131567 cellular organisms no rank 7224 EBI-EMBL C-terminal region of aryl-sulfatase C-terminal region of aryl-sulfatase NF026059.5 PF14709.12 DND1_DSRM 25.7 25.7 80 domain Y N N double strand RNA binding domain from DEAD END PROTEIN 1 131567 cellular organisms no rank 1029 EBI-EMBL double strand RNA binding domain from DEAD END PROTEIN 1 double strand RNA binding domain from DEAD END PROTEIN 1 A C-terminal domain in human dead end protein 1 (DND1_HUMAN) homologous to double strand RNA binding domains (PF00035, PF00333) (from Pfam) NF026061.5 PF14711.11 Nitr_red_bet_C 27 27 81 domain Y N N Respiratory nitrate reductase beta C-terminal 12910261 131567 cellular organisms no rank 24118 EBI-EMBL Respiratory nitrate reductase beta C-terminal Respiratory nitrate reductase beta C-terminal This domain occurs near the C-terminus of the respiratory nitrate reductase beta chain. The nitrate reductase complex is a dimer of heterotrimers each consisting of an alpha, beta and gamma chain. This domain plays a role in the interactions between subunits and shielding of the Fe-S clusters [1] [1]. 12910261. Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A. Bertero MG, Rothery RA, Palak M, Hou C, Lim D, Blasco F, Weiner JH, Strynadka NC;. Nat Struct Biol. 2003;10:681-687. (from Pfam) NF026066.5 PF14716.11 HHH_8 30 30 68 domain Y N N Helix-hairpin-helix domain 7516581 131567 cellular organisms no rank 29344 EBI-EMBL Helix-hairpin-helix domain Helix-hairpin-helix domain NF026070.5 PF14720.11 NiFe_hyd_SSU_C 27 27 80 domain Y N N NiFe/NiFeSe hydrogenase small subunit C-terminal 10378275,20673834,7854413 131567 cellular organisms no rank 18483 EBI-EMBL NiFe/NiFeSe hydrogenase small subunit C-terminal NiFe/NiFeSe hydrogenase small subunit C-terminal This domain is found at the C-terminus of hydrogenase small subunits including periplasmic [NiFeSe] hydrogenase small subunit, uptake hydrogenase small subunit and periplasmic [NiFe] hydrogenase small subunit. This C-terminal domain binds two of the three iron-sulfur clusters in this enzyme [1-3]. [1]. 20673834. The crystal structure of the [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum: characterization of the oxidized enzyme (Ni-A state). Ogata H, Kellers P, Lubitz W;. J Mol Biol. 2010;402:428-444. [2]. 7854413. Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas. Volbeda A, Charon MH, Piras C, Hatchikian EC, Frey M, Fontecilla-Camps JC;. Nature 1995;373:580-587. [3]. 10378275. The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center. Garcin E, Vernede X, Hatchikian EC, Volbeda A, Frey M, Fontecilla-Camps JC;. Structure. 1999;7:557-566. (from Pfam) NF026092.5 PF14742.11 GDE_N_bis 22.1 22.1 194 domain Y Y N glycogen debranching N-terminal domain-containing protein 131567 cellular organisms no rank 24629 EBI-EMBL N-terminal domain of (some) glycogen debranching enzymes N-terminal domain of (some) glycogen debranching enzymes This domain is found on the N-terminal of some glycogen debranching enzymes and is usually followed by the GDE_C (PF06202) and in this sense it is analogous (but probably not homologous) to the GDE_N (PF12439). Its exact function is unknown (from Pfam) NF026093.5 PF14743.11 DNA_ligase_OB_2 28 28 66 PfamEq Y N N DNA ligase OB-like domain 11106756,12930960,17618295 131567 cellular organisms no rank 8504 EBI-EMBL DNA ligase OB-like domain DNA ligase OB-like domain This domain has an OB-like fold, but does not appear to be related to Pfam:PF03120. It is found at the C-terminus of the ATP dependent DNA ligase domain Pfam:PF01068 [1-3]. [1]. 12930960. Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase-adenylate intermediate. Odell M, Malinina L, Sriskanda V, Teplova M, Shuman S;. Nucleic Acids Res. 2003;31:5090-5100. [2]. 11106756. Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining. Odell M, Sriskanda V, Shuman S, Nikolov DB;. Mol Cell. 2000;6:1183-1193. [3]. 17618295. Structural basis for nick recognition by a minimal pluripotent DNA ligase. Nair PA, Nandakumar J, Smith P, Odell M, Lima CD, Shuman S;. Nat Struct Mol Biol. 2007;14:770-778. (from Pfam) NF026098.5 PF14748.11 P5CR_dimer 25 25 105 domain Y Y N pyrroline-5-carboxylate reductase dimerization domain-containing protein 16233902 131567 cellular organisms no rank 85706 EBI-EMBL Pyrroline-5-carboxylate reductase dimerisation Pyrroline-5-carboxylate reductase dimerisation Pyrroline-5-carboxylate reductase consists of two domains, an N-terminal catalytic domain (Pfam:PF03807) and a C-terminal dimerisation domain. This is the dimerisation domain [1]. [1]. 16233902. Crystal structures of delta1-pyrroline-5-carboxylate reductase from human pathogens Neisseria meningitides and Streptococcus pyogenes. Nocek B, Chang C, Li H, Lezondra L, Holzle D, Collart F, Joachimiak A;. J Mol Biol. 2005;354:91-106. (from Pfam) NF026101.5 PF14751.11 DUF4474 23 23 240 domain Y Y N DUF4474 domain-containing protein 131567 cellular organisms no rank 773 EBI-EMBL Domain of unknown function (DUF4474) Domain of unknown function (DUF4474) Domain found on N-termina of few families of uncharacterized Clostridia proteins. Typically followed by a proline-rich domain or other kinds of repeats (from Pfam) NF026109.5 PF14759.11 Reductase_C 25 25 85 domain Y Y N oxidoreductase C-terminal domain-containing protein 15095867,17850818 131567 cellular organisms no rank 79399 EBI-EMBL Reductase C-terminal Reductase C-terminal This domain occurs at the C-terminus of various reductase enzymes, including putidaredoxin reductase, ferredoxin reductase, 3-phenylpropionate/cinnamic acid dioxygenase ferredoxin--NAD(+) reductase component, benzene 1,2-dioxygenase system ferredoxin--NAD(+) reductase subunit, rhodocoxin reductase, biphenyl dioxygenase system ferredoxin--NAD(+) reductase component, rubredoxin-NAD(+) reductase and toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component. In putidaredoxin reductase this domain is involved in dimerisation [1]. In the FAD-containing NADH-ferredoxin reductase (BphA4) it is responsible for interaction with the Rieske-type [2Fe-2S] ferredoxin (BphA3) [2]. [1]. 15095867. Crystal structure of putidaredoxin reductase from Pseudomonas putida, the final structural component of the cytochrome P450cam monooxygenase. Sevrioukova IF, Li H, Poulos TL;. J Mol Biol. 2004;336:889-902. [2]. 17850818. Molecular mechanism of the redox-dependent interaction between NADH-dependent ferredoxin reductase and Rieske-type [2Fe-2S] ferredoxin. Senda M, Kishigami S, Kimura S, Fukuda M, Ishida T, Senda T;. J Mol Biol. 2007;373:382-400. (from Pfam) NF026141.5 PF14791.11 DNA_pol_B_thumb 25 25 63 PfamEq Y N N DNA polymerase beta thumb 7516581 131567 cellular organisms no rank 14044 EBI-EMBL DNA polymerase beta thumb DNA polymerase beta thumb The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the thumb domain [1]. [1]. 7516581. Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. Sawaya MR, Pelletier H, Kumar A, Wilson SH, Kraut J;. Science. 1994;264:1930-1935. (from Pfam) NF026142.5 PF14792.11 DNA_pol_B_palm 25 25 113 PfamEq Y N N DNA polymerase beta palm 7516581 131567 cellular organisms no rank 1095 EBI-EMBL DNA polymerase beta palm DNA polymerase beta palm The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain [1]. [1]. 7516581. Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. Sawaya MR, Pelletier H, Kumar A, Wilson SH, Kraut J;. Science. 1994;264:1930-1935. (from Pfam) NF026151.5 PF14801.11 TrmI-like_N 24 24 50 PfamEq Y N N TrmI-like N-terminal 11554794,12682365,26189113 131567 cellular organisms no rank 12481 EBI-EMBL TrmI-like N-terminal TrmI-like N-terminal This is the N-terminal domain of tRNA (adenine(58)-N(1))- methyltransferase TrmI, a subunit of the tRNA methyltransferase complex that is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA [1]. The exact function of the N-terminus is not known but it is necessary for maintaining the overall folding and for full enzymatic activity. [1]. 11554794. Crystal structure of Rv2118c: an AdoMet-dependent methyltransferase from Mycobacterium tuberculosis H37Rv. Gupta A, Kumar PH, Dineshkumar TK, Varshney U, Subramanya HS;. J Mol Biol. 2001;312:381-391. [2]. 26189113. The m1A(58) modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI. Degut C, Ponchon L, Folly-Klan M, Barraud P, Tisne C;. Biophys Chem. 2016;210:27-34. [3]. 12682365. Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures. Droogmans L, Roovers M, Bujnicki JM, Tricot C, Hartsch T, Stalon V, Grosjean H;. Nucleic Acids Res. 2003;31:2148-2156. (from Pfam) NF026153.5 PF14803.11 Nudix_N_2 25.6 25.6 34 domain Y Y N zinc ribbon domain-containing protein 131567 cellular organisms no rank 10331 EBI-EMBL Nudix N-terminal Nudix N-terminal Ths domain occurs at the N-terminus of several Nudix (Nucleoside Diphosphate linked to X) hydrolases. (from Pfam) NF026155.5 PF14805.11 THDPS_N_2 25 25 67 PfamEq Y N N Tetrahydrodipicolinate N-succinyltransferase N-terminal 9671504 131567 cellular organisms no rank 23599 EBI-EMBL Tetrahydrodipicolinate N-succinyltransferase N-terminal Tetrahydrodipicolinate N-succinyltransferase N-terminal This is the N-terminal domain of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase [1]. [1]. 9671504. The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase. Beaman TW, Blanchard JS, Roderick SL;. Biochemistry. 1998;37:10363-10369. (from Pfam) NF026159.5 PF14809.11 TGT_C1 25.3 25.3 70 PfamEq Y N N C1 domain of tRNA-guanine transglycosylase dimerisation 12054814 131567 cellular organisms no rank 105 EBI-EMBL C1 domain of tRNA-guanine transglycosylase dimerisation C1 domain of tRNA-guanine transglycosylase dimerisation This short region of the tRNA-guanine transglycosylase enzyme acts as the dimerisation domain of the whole protein [1]. [1]. 12054814. Crystal structure of archaeosine tRNA-guanine transglycosylase. Ishitani R, Nureki O, Fukai S, Kijimoto T, Nameki N, Watanabe M, Kondo H, Sekine M, Okada N, Nishimura S, Yokoyama S;. J Mol Biol 2002;318:665-677. (from Pfam) NF026165.5 PF14815.11 NUDIX_4 35 35 113 domain Y Y N NUDIX domain-containing protein 131567 cellular organisms no rank 111649 EBI-EMBL NUDIX domain NUDIX domain NF026171.5 PF14821.11 Thr_synth_N 25 25 79 PfamEq Y N N Threonine synthase N terminus 11756443 131567 cellular organisms no rank 50504 EBI-EMBL Threonine synthase N terminus Threonine synthase N terminus This domain is found at the N-terminus of many threonine synthase enzymes [1]. [1]. 11756443. Structure and function of threonine synthase from yeast. Garrido-Franco M, Ehlert S, Messerschmidt A, Marinkovic' S, Huber R, Laber B, Bourenkov GP, Clausen T;. J Biol Chem. 2002;277:12396-12405. (from Pfam) NF026174.5 PF14824.11 Sirohm_synth_M 25 25 28 domain Y N N Sirohaem biosynthesis protein central 11980703 131567 cellular organisms no rank 30056 EBI-EMBL Sirohaem biosynthesis protein central Sirohaem biosynthesis protein central This is the central domain of a multifunctional enzyme which catalyses the biosynthesis of sirohaem. Both of the catalytic activities of this enzyme (precorrin-2 dehydrogenase EC:1.3.1.76) and sirohydrochlorin ferrochelatase (EC:4.99.1.4) are located in the N-terminal domain of this enzyme, Pfam:PF13241 [1]. [1]. 11980703. The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase. Schubert HL, Raux E, Brindley AA, Leech HK, Wilson KS, Hill CP, Warren MJ;. EMBO J. 2002;21:2068-2075. (from Pfam) NF026177.5 PF14827.11 dCache_3 25.7 25.7 239 domain Y Y N cache domain-containing protein 18701447,27049771 131567 cellular organisms no rank 13908 EBI-EMBL Double sensory domain of two-component sensor kinase Double sensory domain of two-component sensor kinase Cache_3 is the periplasmic sensor domains of sensor histidine kinase of E. coli DcuS. This domain forms one of the components of the two-component signalling system that allows bacteria to adapt to changing environments. The ability of bacteria to monitor and adapt to their environment is crucial to their survival, and two-component signal transduction systems mediate most of these adaptive responses. One component is a histidine kinase sensor - this domain - most commonly part of a homodimeric transmembrane sensor protein, and the second component is a cytoplasmic response regulator. The two components interact in tandem through a phospho-transfer cascade [1]. [1]. 18701447. Crystal structures of C4-dicarboxylate ligand complexes with sensor domains of histidine kinases DcuS and DctB. Cheung J, Hendrickson WA;. J Biol Chem. 2008;283:30256-30265. [2]. 27049771. Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes. Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB;. PLoS Comput Biol. 2016;12:e1004862. (from Pfam) NF026182.5 PF14832.11 Tautomerase_3 25.7 25.7 138 domain Y Y N tautomerase family protein 25565350 131567 cellular organisms no rank 2751 EBI-EMBL Putative oxalocrotonate tautomerase enzyme tautomerase family protein 4-oxalocrotonate tautomerase enzyme is involved in the anthranilate synthase pathway.1 (from Pfam) NF026183.5 PF14833.11 NAD_binding_11 30 30 122 domain Y Y N NAD-binding protein GO:0051287 16126223 131567 cellular organisms no rank 167848 EBI-EMBL NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase NAD-binding protein 3-Hydroxyisobutyrate is a central metabolite in the valine catabolic pathway, and is reversibly oxidised to methylmalonate semi-aldehyde by a specific dehydrogenase belonging to the 3-hydroxyacid dehydrogenase family. The reaction is NADP-dependent and this region of the enzyme binds NAD. The NAD-binding domain of 6-phosphogluconate dehydrogenase adopts an alpha helical structure [1]. [1]. 16126223. Crystal structure of novel NADP-dependent 3-hydroxyisobutyrate dehydrogenase from Thermus thermophilus HB8. Lokanath NK, Ohshima N, Takio K, Shiromizu I, Kuroishi C, Okazaki N, Kuramitsu S, Yokoyama S, Miyano M, Kunishima N;. J Mol Biol. 2005;352:905-917. (from Pfam) NF026195.5 PF14845.11 Glycohydro_20b2 27 27 130 domain Y Y N beta-N-acetylhexosaminidase N-terminal domain-containing protein 16698036,29239122 131567 cellular organisms no rank 6477 EBI-EMBL beta-acetyl hexosaminidase like beta-acetyl hexosaminidase like NF026203.5 PF14853.11 Fis1_TPR_C 25.3 25.3 53 PfamEq Y N N Fis1 C-terminal tetratricopeptide repeat 14623186,14705031 131567 cellular organisms no rank 512 EBI-EMBL Fis1 C-terminal tetratricopeptide repeat Fis1 C-terminal tetratricopeptide repeat The mitochondrial fission protein Fis1 consists of two tetratricopeptide repeats. This domain is the C-terminal tetratricopeptide repeat [1-2] [1]. 14623186. The solution structure of human mitochondria fission protein Fis1 reveals a novel TPR-like helix bundle. Suzuki M, Jeong SY, Karbowski M, Youle RJ, Tjandra N;. J Mol Biol. 2003;334:445-458. [2]. 14705031. Cytosolic domain of the human mitochondrial fission protein fis1 adopts a TPR fold. Dohm JA, Lee SJ, Hardwick JM, Hill RB, Gittis AG;. Proteins. 2004;54:153-156. (from Pfam) NF026213.5 PF14863.11 Alkyl_sulf_dimr 26 26 139 domain Y Y N alkyl sulfatase dimerization domain-containing protein GO:0046983 16684886 131567 cellular organisms no rank 28835 EBI-EMBL Alkyl sulfatase dimerisation Alkyl sulfatase dimerisation This domain is found in alkyl sulfatases such as the Pseudomonas aeruginosa SDS hydrolase (Swiss:Q9I5I9), where it acts as a dimerisation domain [1] [1]. 16684886. The crystal structure of SdsA1, an alkylsulfatase from Pseudomonas aeruginosa, defines a third class of sulfatases. Hagelueken G, Adams TM, Wiehlmann L, Widow U, Kolmar H, Tummler B, Heinz DW, Schubert WD;. Proc Natl Acad Sci U S A. 2006;103:7631-7636. (from Pfam) NF026214.5 PF14864.11 Alkyl_sulf_C 27 27 125 domain Y Y N alkyl sulfatase C-terminal domain-containing protein 16684886 131567 cellular organisms no rank 31323 EBI-EMBL Alkyl sulfatase C-terminal Alkyl sulfatase C-terminal This domain is found at the C-terminus of alkyl sulfatases. Together with the N-terminal catalytic domain, this domain forms a hydrophobic chute and may recruit hydrophobic substrates [1]. [1]. 16684886. The crystal structure of SdsA1, an alkylsulfatase from Pseudomonas aeruginosa, defines a third class of sulfatases. Hagelueken G, Adams TM, Wiehlmann L, Widow U, Kolmar H, Tummler B, Heinz DW, Schubert WD;. Proc Natl Acad Sci U S A. 2006;103:7631-7636. (from Pfam) NF026220.5 PF14870.11 PSII_BNR 27 26 303 domain Y Y N YCF48-related protein 18550538,21531723 131567 cellular organisms no rank 18378 EBI-EMBL Photosynthesis system II assembly factor YCF48 YCF48-related protein Members of this family include both YCF48 itself, which is a photosystem II assembly factor, and related proteins from outside of the cyanobacteria that have from one to more than ten domains related to the N-terminal portion of YCF48. NF026221.5 PF14871.11 GHL6 35 35 132 domain Y N N Hypothetical glycosyl hydrolase 6 20556855,21954604,22295578 131567 cellular organisms no rank 5902 EBI-EMBL Hypothetical glycosyl hydrolase 6 Hypothetical glycosyl hydrolase 6 GHL6 is a family of hypothetical glycoside hydrolases. [1]. 20556855. Gh101 family of glycoside hydrolases: subfamily structure and evolutionary connections with other families. Naumoff DG;. J Bioinform Comput Biol. 2010;8:437-451. [2]. 21954604. [Endo-alpha-1-4-polygalactosaminidases and their homologues: structure and evolution]. Naumov DG, Stepushchenko OO;. Mol Biol (Mosk). 2011;45:703-714. [3]. 22295578. [GHL1-GHL15: new families of hypothetical glycoside hydrolases]. Naumov DG;. Mol Biol (Mosk). 2011;45:1073-1083. (from Pfam) NF026222.5 PF14872.11 GHL5 23.7 23.7 809 PfamEq Y Y N glucosylglycerol hydrolase gghA 20556855,21954604,22295578 131567 cellular organisms no rank 466 EBI-EMBL Hypothetical glycoside hydrolase 5 glucosylglycerol hydrolase GHL5 is a family of hypothetical glycoside hydrolases. [1]. 20556855. Gh101 family of glycoside hydrolases: subfamily structure and evolutionary connections with other families. Naumoff DG;. J Bioinform Comput Biol. 2010;8:437-451. [2]. 21954604. [Endo-alpha-1-4-polygalactosaminidases and their homologues: structure and evolution]. Naumov DG, Stepushchenko OO;. Mol Biol (Mosk). 2011;45:703-714. [3]. 22295578. [GHL1-GHL15: new families of hypothetical glycoside hydrolases]. Naumov DG;. Mol Biol (Mosk). 2011;45:1073-1083. (from Pfam) NF026235.5 PF14885.11 GHL15 27 27 271 domain Y Y N putative glycoside hydrolase 20556855,21954604,22295578 131567 cellular organisms no rank 2504 EBI-EMBL Hypothetical glycosyl hydrolase family 15 putative glycoside hydrolase GHL15 is a family of hypothetical glycoside hydrolases. [1]. 20556855. Gh101 family of glycoside hydrolases: subfamily structure and evolutionary connections with other families. Naumoff DG;. J Bioinform Comput Biol. 2010;8:437-451. [2]. 21954604. [Endo-alpha-1-4-polygalactosaminidases and their homologues: structure and evolution]. Naumov DG, Stepushchenko OO;. Mol Biol (Mosk). 2011;45:703-714. [3]. 22295578. [GHL1-GHL15: new families of hypothetical glycoside hydrolases]. Naumov DG;. Mol Biol (Mosk). 2011;45:1073-1083. (from Pfam) NF026240.5 PF14890.11 Intein_splicing 35.8 35.8 155 domain Y N N Intein splicing domain 12878593 131567 cellular organisms no rank 8324 EBI-EMBL Intein splicing domain Intein splicing domain Inteins are segments of protein which excise themselves from a precursor protein and mediate the rejoining of the remainder of the precursor (the extein). Most inteins consist of a splicing domain which is split into two segments by a homing endonuclease domain. This domain represents the splicing domain [1]. [1]. 12878593. Crystal structure of a mini-intein reveals a conserved catalytic module involved in side chain cyclization of asparagine during protein splicing. Ding Y, Xu MQ, Ghosh I, Chen X, Ferrandon S, Lesage G, Rao Z;. J Biol Chem. 2003;278:39133-39142. (from Pfam) NF026248.5 PF14898.11 DUF4491 27 27 92 subfamily Y Y N DUF4491 family protein 131567 cellular organisms no rank 1423 EBI-EMBL Domain of unknown function (DUF4491) DUF4491 family protein This family of proteins is found in bacteria. Proteins in this family are typically between 94 and 107 amino acids in length. There is a conserved EYY sequence motif. (from Pfam) NF026257.5 PF14907.11 NTP_transf_5 31.2 31.2 249 domain Y Y N nucleotidyltransferase family protein 131567 cellular organisms no rank 22055 EBI-EMBL Uncharacterised nucleotidyltransferase nucleotidyltransferase family protein This family is likely to be an uncharacterised group of nucleotidyltransferases. (from Pfam) NF026271.5 PF14921.11 APCDDC 27 27 232 PfamEq Y N N Adenomatosis polyposis coli down-regulated 1 12384519,20393562 131567 cellular organisms no rank 82 EBI-EMBL Adenomatosis polyposis coli down-regulated 1 Adenomatosis polyposis coli down-regulated 1 The domain is duplicated in most members of this family. APCDD is directly regulated by the beta-catenin/Tcf complex, and its elevated expression promotes proliferation of colonic epithelial cells in vitro and in vivo [1]. APCDD1 has an N-terminal signal-peptide and a C-terminal transmembrane region. The domain is rich in cysteines, there being up to 12 such residues, a structural motif important for interaction between Wnt ligands and their receptors. APCDD1 is expressed in a broad repertoire of cell types, indicating that it may regulate a diverse range of biological processes controlled by Wnt signalling [2]. [1]. 12384519. Isolation of a novel human gene, APCDD1, as a direct target of the beta-Catenin/T-cell factor 4 complex with probable involvement in colorectal carcinogenesis. Takahashi M, Fujita M, Furukawa Y, Hamamoto R, Shimokawa T, Miwa N, Ogawa M, Nakamura Y;. Cancer Res. 2002;62:5651-5656. [2]. 20393562. APCDD1 is a novel Wnt inhibitor mutated in hereditary hypotrichosis simplex. Shimomura Y, Agalliu D, Vonica A, Luria V, Wajid M, Baumer A, Belli S, Petukhova L, Schinzel A, Brivanlou AH, Barres BA, Christiano AM;. Nature. 2010;464:1043-1047. (from Pfam) NF026288.5 PF14938.11 SNAP 25 25 282 domain Y N N Soluble NSF attachment protein, SNAP 10445030,8455721 131567 cellular organisms no rank 9220 EBI-EMBL Soluble NSF attachment protein, SNAP Soluble NSF attachment protein, SNAP The soluble NSF attachment protein (SNAP) proteins are involved in vesicular transport between the endoplasmic reticulum and Golgi apparatus [1]. They act as adaptors between SNARE (integral membrane SNAP receptor) proteins and NSF (N-ethylmaleimide-sensitive factor) [2]. They are structurally similar to TPR repeats [2]. [1]. 8455721. SNAP family of NSF attachment proteins includes a brain-specific isoform. Whiteheart SW, Griff IC, Brunner M, Clary DO, Mayer T, Buhrow SA, Rothman JE;. Nature. 1993;362:353-355. [2]. 10445030. Crystal structure of the vesicular transport protein Sec17: implications for SNAP function in SNARE complex disassembly. Rice LM, Brunger AT;. Mol Cell. 1999;4:85-95. (from Pfam) NF026297.5 PF14947.11 HTH_45 25.5 25.5 77 domain Y Y N winged helix-turn-helix domain-containing protein 15312764 131567 cellular organisms no rank 2628 EBI-EMBL Winged helix-turn-helix Winged helix-turn-helix This winged helix-turn-helix domain contains an extended C-terminal alpha helix which is responsible for dimerisation of this domain [1]. [1]. 15312764. The hyperthermophile protein Sso10a is a dimer of winged helix DNA-binding domains linked by an antiparallel coiled coil rod. Chen L, Chen LR, Zhou XE, Wang Y, Kahsai MA, Clark AT, Edmondson SP, Liu ZJ, Rose JP, Wang BC, Meehan EJ, Shriver JW;. J Mol Biol. 2004;341:73-91. (from Pfam) NF026766.5 PF15428.11 Imm26 23.3 23.3 107 domain Y Y N Imm26 family immunity protein 22731697 131567 cellular organisms no rank 5283 EBI-EMBL Immunity protein 26 Imm26 family immunity protein A predicted immunity protein with mostly all-beta fold and several conserved hydrophobic residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-URI1 or Tox-HNH family [1]. The protein is also found heterogeneous poly-immunity loci. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF026799.5 PF15461.11 BCD 28 28 267 domain Y Y N Brp/Blh family beta-carotene 15,15'-dioxygenase GO:0016702 11092896,19366683,20229064 131567 cellular organisms no rank 2957 EBI-EMBL Beta-carotene 15,15'-dioxygenase Brp/Blh family beta-carotene 15,15'-dioxygenase This is a family of bacterial and archaeal proteins that catalyses or regulates the conversion of beta-carotene to retinal [1]. Characterisation of BCD proteins shows them to cleave beta-carotene at its central double bond (15,15') to yield two molecules of all-trans-retinal. However, the oxygen atom of retinal originated not from water but from molecular oxygen, suggesting that the enzyme was a beta-carotene 15,15'-dioxygenase, rather than a mono-oxygenase that catalyses the same biochemical reaction [2,3]. [1]. 11092896. brp and blh are required for synthesis of the retinal cofactor of bacteriorhodopsin in Halobacterium salinarum. Peck RF, Echavarri-Erasun C, Johnson EA, Ng WV, Kennedy SP, Hood L, DasSarma S, Krebs MP;. J Biol Chem. 2001;276:5739-5744. [2]. 19366683. In vitro characterization of a recombinant Blh protein from an uncultured marine bacterium as a beta-carotene 15,15'-dioxygenase. Kim YS, Kim NH, Yeom SJ, Kim SW, Oh DK;. J Biol Chem. 2009;284:15781-15793. [3]. 20229064. Retinal production from beta-carotene by beta-carotene 15,15'-dioxygenase from an unculturable marine bacterium. Kim YS, Park CS, Oh DK;. Biotechnol Lett. 2010;32:957-961. (from Pfam) NF026849.5 PF15511.11 CENP-T_C 28.1 28.1 108 domain Y N N Centromere kinetochore component CENP-T histone fold 21464230,22304917,22391098 131567 cellular organisms no rank 368 EBI-EMBL Centromere kinetochore component CENP-T histone fold Centromere kinetochore component CENP-T histone fold CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3]. [1]. 22391098. Molecular architecture of vertebrate kinetochores. Takeuchi K, Fukagawa T;. Exp Cell Res. 2012;318:1367-1374. [2]. 21464230. Spindle microtubules generate tension-dependent changes in the distribution of inner kinetochore proteins. Suzuki A, Hori T, Nishino T, Usukura J, Miyagi A, Morikawa K, Fukagawa T;. J Cell Biol. 2011;193:125-140. [3]. 22304917. CENP-T-W-S-X forms a unique centromeric chromatin structure with a histone-like fold. Nishino T, Takeuchi K, Gascoigne KE, Suzuki A, Hori T, Oyama T, Morikawa K, Cheeseman IM, Fukagawa T;. Cell. 2012;148:487-501. (from Pfam) NF026852.5 PF15514.11 ThaI 25 25 203 subfamily Y Y N ThaI family type II restriction endonuclease 3.1.21.- 20861000,22638584 131567 cellular organisms no rank 181 EBI-EMBL Restriction endonuclease ThaI ThaI family type II restriction endonuclease This family of restriction endonucleases belongs to the PD-(D/E)XK superfamily. It cuts the recognition site CG^CG leaving blunt ends [1]. [1]. 20861000. DNA intercalation without flipping in the specific ThaI-DNA complex. Firczuk M, Wojciechowski M, Czapinska H, Bochtler M;. Nucleic Acids Res. 2011;39:744-754. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF026853.5 PF15515.11 MvaI_BcnI 25 25 227 PfamEq Y Y N MvaI/BcnI family restriction endonuclease 17344322,17445830,22638584 131567 cellular organisms no rank 2170 EBI-EMBL MvaI/BcnI restriction endonuclease family MvaI/BcnI family restriction endonuclease This family of proteins includes the restriction endonucleases MvaI and BcnI. These enzymes both function as monomers. MvaI cleaves the sequence CC/WGG, where W is an A or a T nucleotide, leaving sticky ends. BcnI cleaves the sequence CC/SGG, where S is G or C, leaving sticky ends [1-2]. [1]. 17344322. Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically. Kaus-Drobek M, Czapinska H, Sokolowska M, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M;. Nucleic Acids Res. 2007;35:2035-2046. [2]. 17445830. Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA. Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M;. J Mol Biol. 2007;369:722-734. [3]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF026878.5 PF15540.11 Ntox47 25 25 120 domain Y Y N polymorphic toxin type 47 domain-containing protein 22731697 131567 cellular organisms no rank 767 EBI-EMBL Bacterial toxin 47 polymorphic toxin type 47 domain (predicted RNase) A predicted RNase toxin found in bacterial polymorphic toxin systems that is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, and contains two conserved aspartates, a glutamate, a histidine and an arginine residue and an RT motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6 or type 7 secretion system [1]. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF026907.5 PF15569.11 Imm40 25 25 90 PfamEq Y Y N Imm40 family immunity protein imm40 22731697 131567 cellular organisms no rank 537 EBI-EMBL Immunity protein 40 Imm40 family immunity protein A predicted immunity protein with an alpha+beta fold and conserved phenylalanine and tryptophan residues and a GGD motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Ntox19 family [1]. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF026913.5 PF15575.11 Imm49 30.1 30.1 217 subfamily Y Y N Imm49 family immunity protein 22731697 131567 cellular organisms no rank 13628 EBI-EMBL Immunity protein 49 Imm49 family immunity protein A predicted immunity protein with an all alpha-helical fold and a conserved proline residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-REAse-1 or Tox-REase-6 families [1]. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF026933.5 PF15595.11 Imm51 29.8 29.8 104 subfamily Y Y N Imm51 family immunity protein 22731697 131567 cellular organisms no rank 2603 EBI-EMBL Immunity protein 51 Imm51 family immunity protein A predicted immunity protein with an alpha+beta fold and a conserved tryptophan and Dx[DE] motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-RES or Tox-URI1 families. Proteins containing this domain are present in heterogeneous poly immunity loci in polymorphic toxin systems [1]. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF026938.5 PF15600.11 Imm64 25 25 207 subfamily Y Y N Imm64 family immunity protein 22731697 131567 cellular organisms no rank 444 EBI-EMBL Immunity protein 64 Imm64 family immunity protein A predicted immunity protein with an alpha+beta fold and a conserved DxEA motif and arginine residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Tox-ColD family [1]. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF026939.5 PF15601.11 Imm70 26.7 26.7 131 PfamEq Y Y N Imm70 family immunity protein 22731697 131567 cellular organisms no rank 995 EBI-EMBL Immunity protein 70 Imm70 family immunity protein A predicted immunity protein with an alpha+beta fold and conserved tyrosine and tryptophan residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Tox-REase-10 family [1]. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF026946.5 PF15608.11 PELOTA_1 25 25 81 domain Y Y N RNA-binding protein 11917006,23044854 131567 cellular organisms no rank 15760 EBI-EMBL PELOTA RNA binding domain PELOTA RNA binding domain This RNA binding Pelota domain [1] is at the C-terminus of a PRTase family [2]. These PRTase+Pelota genes are found in the biosynthetic operon associated with the Ter stress-response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress response [2]. [1]. 11917006. Comparative genomics and evolution of proteins involved in RNA metabolism. Anantharaman V, Koonin EV, Aravind L;. Nucleic Acids Res. 2002;30:1427-1464. [2]. 23044854. Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing. Anantharaman V, Iyer LM, Aravind L;. Mol Biosyst. 2012;8:3142-3165. (from Pfam) NF026952.5 PF15615.11 TerB_C 26.3 26.3 148 domain Y Y N tellurite resistance TerB C-terminal domain-containing protein 23044854 131567 cellular organisms no rank 6619 EBI-EMBL TerB-C domain TerB-C domain TerB-C occurs C-terminal of TerB in TerB-N containing proteins. This domain displays multiple conserved acidic residues (TerBC) [1]. The presence of conserved acidic residues in both TerB-N and TerB-C suggests that they, like the TerB domain, might also chelate metals. These two domains may also occur together in the same protein independently of TerB [1]. [1]. 23044854. Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing. Anantharaman V, Iyer LM, Aravind L;. Mol Biosyst. 2012;8:3142-3165. (from Pfam) NF026954.5 PF15617.11 C-C_Bond_Lyase 28.4 28.4 320 domain Y Y N HpcH/HpaI aldolase/citrate lyase family protein 23044854 131567 cellular organisms no rank 42583 EBI-EMBL C-C_Bond_Lyase of the TIM-Barrel fold HpcH/HpaI aldolase/citrate lyase family protein This family of TIM-Barrel fold C-C bond lyase is related to citrate-lyase. These genes are found in the biosynthetic operon, with other enzymatic domains, associated with the Ter stress response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress response [1]. [1]. 23044854. Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing. Anantharaman V, Iyer LM, Aravind L;. Mol Biosyst. 2012;8:3142-3165. (from Pfam) NF026968.5 PF15632.11 ATPgrasp_Ter 29.1 29.1 131 domain Y Y N ATP-grasp domain-containing protein 23044854 131567 cellular organisms no rank 45941 EBI-EMBL ATP-grasp in the biosynthetic pathway with Ter operon ATP-grasp in the biosynthetic pathway with Ter operon This ATP-grasp family is related to carbamoyl phosphate synthetase. These genes are found in the biosynthetic operon associated with the Ter stress response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress response [1]. [1]. 23044854. Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing. Anantharaman V, Iyer LM, Aravind L;. Mol Biosyst. 2012;8:3142-3165. (from Pfam) NF026974.5 PF15638.11 Tox-MPTase2 25 25 196 domain Y N N Metallopeptidase toxin 2 22731697 131567 cellular organisms no rank 289 EBI-EMBL Metallopeptidase toxin 2 Metallopeptidase toxin 2 A zincin-like metallopeptidase domain found in bacterial polymorphic toxin systems [1]. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF026988.5 PF15652.11 Tox-SHH 22.7 22.7 96 domain Y N N HNH/Endo VII superfamily toxin with a SHH signature 22731697 131567 cellular organisms no rank 1508 EBI-EMBL HNH/Endo VII superfamily toxin with a SHH signature HNH/Endo VII superfamily toxin with a SHH signature A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with two conserved histidine residues. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6 or type 7 secretion system [1]. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF027050.5 PF15714.10 SpoVT_C 27.5 27.5 128 domain Y Y N stage V sporulation T C-terminal domain-containing protein 18996130 131567 cellular organisms no rank 5282 EBI-EMBL Stage V sporulation protein T C-terminal, transcription factor Stage V sporulation protein T C-terminal, transcription factor SpoVT_C is the C-terminal part of the stage V sporulation protein T, a transcription factor involved in endospore formation in Gram-positive bacteria such as Bacillus subtilis. Sporulation is induced by conditions of environmental stress to protect the genome. SpoVT behaves as a tetramer that shows an overall significant distortion mediated by electrostatic interactions. Two monomers dimerise via the highly charged N-terminal AbrB-like domains, family Pfam:PF04014, to form swapped-hairpin beta-barrels. These asymmetric dimers then form tetramers through the formation of mixed helix bundles between their C-terminal domains. The C-termini themselves fold as GAF (cGMP-specific and cGMP-stimulated phosphodiesterases, Anabaena adenylate cyclases, and Escherichia coli FhlA) domains [1]. [1]. 18996130. Crystal structure of SpoVT, the final modulator of gene expression during spore development in Bacillus subtilis. Asen I, Djuranovic S, Lupas AN, Zeth K;. J Mol Biol. 2009;386:962-975. (from Pfam) NF027067.5 PF15731.10 MqsA_antitoxin 30 30 131 domain Y Y N type II toxin-antitoxin system MqsA family antitoxin 14727089,16352847,16768798,20041169 131567 cellular organisms no rank 6684 EBI-EMBL Antitoxin component of bacterial toxin-antitoxin system, MqsA type II toxin-antitoxin system MqsA family antitoxin MqsA_antitoxin is a family of prokaryotic proteins that act as antidotes to the mRNA interferase MqsR. It has a zinc-binding at the very N-terminus indicating its DNA-binding capacity. MqsR is the gene most highly upregulated in E. Colo MqsR_toxin is a family of bacterial toxins that act as an mRNA interferase. MqsR is the gene most highly upregulated in E. coli persister cells [2] and it plays an essential role in biofilm regulation [3] and cell signalling [4]. It forms part of a bacterial toxin-antitoxin TA system, and as expected for a TA system, the expression of the MqsR toxin leads to growth arrest, while co-expression with its antitoxin, MqsA, rescues the growth arrest phenotype. In addition, MqsR associates with MqsA to form a tight, non-toxic complex and both MqsA alone and the MqsR:MqsA2:MqsR complex bind and regulate the mqsR promoter. The structure of MqsR shows that is is a member of the RelE/YoeB family of bacterial RNases that are structurally and functionally characterised bacterial toxins [1]. [1]. 20041169. Three dimensional structure of the MqsR:MqsA complex: a novel TA pair comprised of a toxin homologous to RelE and an antitoxin with unique properties. Brown BL, Grigoriu S, Kim Y, Arruda JM, Davenport A, Wood TK, Peti W, Page R;. PLoS Pathog. 2009;5:e1000706. [2]. 16768798. Persisters: a distinct physiological state of E. coli. Shah D, Zhang Z, Khodursky A, Kaldalu N, Kurg K, Lewis K;. BMC Microbiol. 2006;6:53. [3]. 16352847. Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022). Gonzalez Barrios AF, Zuo R, Hashimoto Y, Yang L, Ben. TRUNCATED at 1650 bytes (from Pfam) NF027074.5 PF15738.10 YafQ_toxin 30 30 88 domain Y Y N type II toxin-antitoxin system YafQ family toxin 17263853,19210620,19707553 131567 cellular organisms no rank 13089 EBI-EMBL Bacterial toxin of type II toxin-antitoxin system, YafQ type II toxin-antitoxin system YafQ family toxin YafQ is a family of bacterial toxin ribonucleases of type II toxin-antitoxin systems. The E.coli gene is expressed from the dinB operon [1,2]. The cognate antitoxin for the E. coli protein is DinJ, in family RelB_antitoxin, Pfam:PF02604. [1]. 17263853. Escherichia coli dinJ-yafQ genes act as a toxin-antitoxin module. Motiejunaite R, Armalyte J, Markuckas A, Suziedeliene E;. FEMS Microbiol Lett. 2007;268:112-119. [2]. 19210620. Bacterial toxin YafQ is an endoribonuclease that associates with the ribosome and blocks translation elongation through sequence-specific and frame-dependent mRNA cleavage. Prysak MH, Mozdzierz CJ, Cook AM, Zhu L, Zhang Y, Inouye M, Woychik NA;. Mol Microbiol. 2009;71:1071-1087. [3]. 19707553. A differential effect of E. coli toxin-antitoxin systems on cell death in liquid media and biofilm formation. Kolodkin-Gal I, Verdiger R, Shlosberg-Fedida A, Engelberg-Kulka H;. PLoS One. 2009;4:e6785. (from Pfam) NF027116.5 PF15780.10 ASH 27 27 98 domain Y N N Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin 16443634 131567 cellular organisms no rank 4667 EBI-EMBL Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin The ASH domain or N-terminal domain of abnormal spindle-like microcephaly-associated protein are found in proteins associated with cilia, flagella, the centrosome and the Golgi complex. The domain is also found in Hydin and OCRL whose deficiencies are associated with hydrocephalus and Lowe oculocerebrorenal syndrome (OCRL), respectively. The fact that Human ASPM protein carries an ASH domain indicates possible roles for ASPM in sperm flagellar or in ependymal cells' cilia. The presence of ASH in centrosomal and ciliary proteins indicates that ASPM may possess roles not only in mitotic spindle regulation, but also in ciliary and flagellar function [1]. [1]. 16443634. A novel domain suggests a ciliary function for ASPM, a brain size determining gene. Ponting CP;. Bioinformatics. 2006;22:1031-1035. (from Pfam) NF027117.5 PF15781.10 ParE-like_toxin 28 28 87 domain Y Y N type II toxin-antitoxin system RelE/ParE family toxin 131567 cellular organisms no rank 4195 EBI-EMBL ParE-like toxin of type II bacterial toxin-antitoxin system type II toxin-antitoxin system RelE/ParE family toxin NF027223.5 PF15891.10 Nuc_deoxyri_tr2 30 30 105 domain Y Y N nucleoside 2-deoxyribosyltransferase domain-containing protein 131567 cellular organisms no rank 4630 EBI-EMBL Nucleoside 2-deoxyribosyltransferase like Nucleoside 2-deoxyribosyltransferase like NF027224.5 PF15892.10 BNR_4 27.3 27.3 272 domain Y Y N BNR-4 repeat-containing protein 2562507 131567 cellular organisms no rank 9033 EBI-EMBL BNR repeat-containing family member BNR repeat-containing family member BNR_4 is a family which carries the unique sequence motif SxDxGxTW which is so characteristic of the repeats of the BNR family, Pfam:PF02012. It is unclear whether or not this unit is repeated throughout the sequences of this family, but if it is then the family is likely to be bacterial neuraminidase. [1]. 2562507. Conserved sequences in bacterial and viral sialidases. Roggentin P, Rothe B, Kaper JB, Galen J, Lawrisuk L, Vimr ER, Schauer R;. Glycoconj J 1989;6:349-353. (from Pfam) NF027230.5 PF15899.10 BNR_6 27 13 14 repeat Y N N BNR/Asp-box repeat protein 131567 cellular organisms no rank 2217 EBI-EMBL BNR-Asp box repeat BNR-Asp box repeat This BNR repeat is found in proteins such as human sortilin. The model complements family BNR_5. (from Pfam) NF027232.5 PF15902.10 Sortilin-Vps10 33 33 446 domain Y Y N VPS10 domain-containing protein 10085125,19122660,9013611,9756851 131567 cellular organisms no rank 12301 EBI-EMBL Sortilin, neurotensin receptor 3, VPS10 domain Sortilin, also known in mammals as neurotensin receptor-3, is the archetypical member of a Vps10-domain (Vps10-D) that binds neurotrophic factors and neuropeptides. This domain constitutes the entire luminal part of Sortilin and is activated in the trans-Golgi network by enzymatic propeptide cleavage [1,2]. The structure of the domain has been determined as a ten-bladed propeller, with up to 9 BNR or beta-hairpin turns in it. The mature receptor binds various ligands, including its own propeptide (Sort-pro), neurotensin, the pro-forms of nerve growth factor-beta (NGF)6 and brain-derived neurotrophic factor (BDNF)7, lipoprotein lipase (LpL), apo lipoprotein AV14 and the receptor-associated protein (RAP)1 [4,5]. [1]. 9013611. Molecular identification of a novel candidate sorting receptor purified from human brain by receptor-associated protein affinity chromatography. Petersen CM, Nielsen MS, Nykjaer A, Jacobsen L, Tommerup N, Rasmussen HH, Roigaard H, Gliemann J, Madsen P, Moestrup SK;. J Biol Chem. 1997;272:3599-3605. [2]. 9756851. The 100-kDa neurotensin receptor is gp95/sortilin, a non-G-protein-coupled receptor. Mazella J, Zsurger N, Navarro V, Chabry J, Kaghad M, Caput D, Ferrara P, Vita N, Gully D, Maffrand JP, Vincent JP;. J Biol Chem. 1998;273:26273-26276. [3]. 10085125. Sortilin/neurotensin receptor-3 binds and mediates degradation of lipoprotein lipase. Nielsen MS, Jacobsen C, Olivecrona G, Gliemann J, Petersen CM;. J Biol Chem. 1999;274:8832-8836. [4]. 19122660. Ligands bind to Sortilin in the tunnel of a ten-bladed beta-propeller domain. Quistgaard EM, Madsen P, Groftehauge MK, Nissen P, Petersen CM, Thirup SS;.. TRUNCATED at 1650 bytes (from Pfam) NF027249.5 PF15919.10 HicB_lk_antitox 27 27 123 domain Y Y N type II toxin-antitoxin system HicB family antitoxin 131567 cellular organisms no rank 27030 EBI-EMBL HicB_like antitoxin of bacterial toxin-antitoxin system type II toxin-antitoxin system HicB family antitoxin This is a family of HicB-like antitoxins. (from Pfam) NF027261.5 PF15931.10 DUF4747 27 27 257 PfamAutoEq Y Y N DUF4747 family protein 131567 cellular organisms no rank 1134 EBI-EMBL Domain of unknown function (DUF4747) DUF4747 family protein This family of proteins is found in bacteria. Proteins in this family are typically between 263 and 305 amino acids in length. (from Pfam) NF027286.5 PF15956.10 DUF4760 27 27 143 domain Y Y N DUF4760 domain-containing protein 131567 cellular organisms no rank 1986 EBI-EMBL Domain of unknown function (DUF4760) Domain of unknown function (DUF4760) This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 147 and 190 amino acids in length. There is a single completely conserved residue R that may be functionally important. (from Pfam) NF027301.5 PF15971.10 Mannosyl_trans4 33 33 163 domain Y Y N DolP-mannose mannosyltransferase GO:0004169,GO:0035269 23086206 131567 cellular organisms no rank 149 EBI-EMBL DolP-mannose mannosyltransferase DolP-mannose mannosyltransferase This family catalyses the transfer of mannose from DolP-mannose to the N-linked tetrasaccharide bound to the S-layer glycoprotein to form a pentasaccharide [1]. [1]. 23086206. AglS, a Novel Component of the Haloferax volcanii N-Glycosylation Pathway, Is a Dolichol Phosphate-Mannose Mannosyltransferase. Cohen-Rosenzweig C, Yurist-Doutsch S, Eichler J;. J Bacteriol. 2012;194:6909-6916. (from Pfam) NF027305.5 PF15975.10 Flot 27 27 124 domain Y Y N flotillin domain-containing protein 20018678,22194304,22215737,22882210 131567 cellular organisms no rank 21996 EBI-EMBL Flotillin Flotillin Flotillin is a family of lipid-membrane-associated proteins found in bacteria, archaea and eukaryotes. The family is found in association with Pfam:PF01145, another integral membrane-associated domain. Flotillins in vertebrates are associated with sphingolipids and cholesterol-enriched membrane microdomains known as lipid-rafts. These rafts along with other membrane components are important in cell-signalling. Flotillins in other organisms have roles in viral pathogenesis, endocytosis, and membrane shaping. [1]. 20018678. Plant flotillins are required for infection by nitrogen-fixing bacteria. Haney CH, Long SR;. Proc Natl Acad Sci U S A. 2010;107:478-483. [2]. 22194304. The roles of flotillin microdomains--endocytosis and beyond. Otto GP, Nichols BJ;. J Cell Sci. 2011;124:3933-3940. [3]. 22215737. Flotillin-1 (Reggie-2) contributes to Chlamydia pneumoniae growth and is associated with bacterial inclusion. Korhonen JT, Puolakkainen M, Haivala R, Penttila T, Haveri A, Markkula E, Lahesmaa R;. Infect Immun. 2012;80:1072-1078. [4]. 22882210. The biofilm formation defect of a Bacillus subtilis flotillin-defective mutant involves the protease FtsH. Yepes A, Schneider J, Mielich B, Koch G, Garcia-Betancur JC, Ramamurthi KS, Vlamakis H, Lopez D;. Mol Microbiol. 2012;86:457-471. (from Pfam) NF027309.5 PF15979.10 Glyco_hydro_115 27 27 335 domain Y Y N glycosyl hydrolase 115 family protein 131567 cellular organisms no rank 11173 EBI-EMBL Glycosyl hydrolase family 115 glycosyl hydrolase 115 family protein Glyco_hydro_115 is a family of glycoside hydrolases likely to have the activity of xylan a-1,2-glucuronidase, EC:3.2.1.131, or a-(4-O-methyl)-glucuronidase EC:3.2.1.-. (from Pfam) NF027338.5 PF16011.10 CBM9_2 25 25 199 subfamily Y Y N carbohydrate-binding family 9-like protein GO:0004553,GO:0016052,GO:0030246 131567 cellular organisms no rank 3750 EBI-EMBL Carbohydrate-binding family 9 carbohydrate-binding family 9-like protein CBM9_2 is a family of putative endoxylanase-like proteins that belong to the Carbohydrate-binding family 9. (from Pfam) NF027401.5 PF16075.10 DUF4815 30 30 570 domain Y Y N DUF4815 domain-containing protein 131567 cellular organisms no rank 1833 EBI-EMBL Domain of unknown function (DUF4815) Domain of unknown function (DUF4815) NF027421.5 PF16095.10 COR 34.9 34.9 195 domain Y Y N COR domain-containing protein 18650931 131567 cellular organisms no rank 2406 EBI-EMBL C-terminal of Roc, COR, domain C-terminal of Roc, COR, domain The C-terminal of Roc domain, COR, along with Roc functions as the putative regulator of kinase activity. It functions as a proper GTP-binding protein with a low GTPase activity somehow stimulating the kinase activity [1]. [1]. 18650931. Structure of the Roc-COR domain tandem of C. tepidum, a prokaryotic homologue of the human LRRK2 Parkinson kinase. Gotthardt K, Weyand M, Kortholt A, Van Haastert PJ, Wittinghofer A;. EMBO J. 2008;27:2239-2249. (from Pfam) NF027439.5 PF16113.10 ECH_2 27.2 27.2 335 domain Y Y N enoyl-CoA hydratase/isomerase family protein GO:0003860 131567 cellular organisms no rank 676683 EBI-EMBL Enoyl-CoA hydratase/isomerase enoyl-CoA hydratase/isomerase family protein This family contains a diverse set of enzymes including: enoyl-CoA hydratase, napthoate synthase, carnitate racemase, 3-hydroxybutyryl-CoA dehydratase and dodecanoyl-CoA delta-isomerase. This family differs from Pfam:PF00378 in the structure of it's C-terminus. (from Pfam) NF027440.5 PF16114.10 Citrate_bind 26.8 26.8 177 domain Y Y N ATP citrate lyase citrate-binding domain-containing protein 20558738 131567 cellular organisms no rank 759 EBI-EMBL ATP citrate lyase citrate-binding ATP citrate lyase citrate-binding This is the citrate-binding domain of ATP citrate lyase. This domain has a Rossmann fold [1]. [1]. 20558738. Identification of the citrate-binding site of human ATP-citrate lyase using X-ray crystallography. Sun T, Hayakawa K, Bateman KS, Fraser ME;. J Biol Chem. 2010;285:27418-27428. (from Pfam) NF027450.5 PF16124.10 RecQ_Zn_bind 25 25 66 domain Y Y N RecQ family zinc-binding domain-containing protein 14517231,19151156 131567 cellular organisms no rank 103071 EBI-EMBL RecQ zinc-binding RecQ zinc-binding This domain is the zinc-binding domain of ATP-dependent DNA helicase RecQ [1-2]. [1]. 14517231. High-resolution structure of the E.coli RecQ helicase catalytic core. Bernstein DA, Zittel MC, Keck JL;. EMBO J. 2003;22:4910-4921. [2]. 19151156. Structure of the human RECQ1 helicase reveals a putative strand-separation pin. Pike AC, Shrestha B, Popuri V, Burgess-Brown N, Muzzolini L, Costantini S, Vindigni A, Gileadi O;. Proc Natl Acad Sci U S A. 2009;106:1039-1044. (from Pfam) NF027452.5 PF16126.10 DUF4838 26.6 26.6 325 PfamAutoEq Y Y N DUF4838 domain-containing protein 131567 cellular organisms no rank 4203 EBI-EMBL Domain of unknown function (DUF4838) Domain of unknown function (DUF4838) This family consists of several uncharacterized proteins found in various Bacteroides and Chloroflexus species. The function of this family is unknown. (from Pfam) NF027463.5 PF16137.10 DUF4845 27 27 85 PfamAutoEq Y Y N DUF4845 domain-containing protein 131567 cellular organisms no rank 5522 EBI-EMBL Domain of unknown function (DUF4845) Domain of unknown function (DUF4845) This family consists of uncharacterized proteins around 120 residues in length and is mainly found in various Pseudomonas species. Distant homology analysis suggests that proteins from this family are related to pilin type IV proteins from the Bundlin (PF05307) family, this prediction is however not confirmed by any experimental evidence (from Pfam) NF027473.5 PF16147.10 DUF4855 27 27 313 domain Y Y N DUF4855 domain-containing protein 131567 cellular organisms no rank 2031 EBI-EMBL Domain of unknown function (DUF4855) Domain of unknown function (DUF4855) This family consists of uncharacterized proteins around 400 residues in length and is mainly found in various Bacteroides species. Several proteins are annotated as glycerophosphodiester phosphodiesterases, but the origin of this annotation is not clear. (from Pfam) NF027482.5 PF16156.10 DUF4864 27.1 27.1 100 PfamAutoEq Y Y N DUF4864 domain-containing protein 131567 cellular organisms no rank 4152 EBI-EMBL Domain of unknown function (DUF4864) Domain of unknown function (DUF4864) This family consists of uncharacterized proteins around 120 residues in length and is mainly found in various Anabaena and Nostoc species. Distant homology analysis suggests this family is related to NTF2-like proteins and specifically to proteins that bind small molecules. HMM partly overlaps with Tol_Tol_Ttg2 (PF05494) involved in Toluene tolerance and lumazine binding family (PF12870) and these families should form a clan. (from Pfam) NF027484.5 PF16158.10 N_BRCA1_IG 28 28 108 domain Y Y N NBR1-Ig-like domain-containing protein 131567 cellular organisms no rank 2237 EBI-EMBL Ig-like domain from next to BRCA1 gene NBR1-Ig-like domain This domain is found in the human protein NBR1 (Neighbor of BRCA1) and described as an Ig-like domain. Members of this family that occur in bacterial then to have an N-terminal helix-turn-helix domain of the type described by PF13560. NF027487.5 PF16161.10 DUF4867 28.7 28.7 201 domain Y Y N DUF4867 family protein 131567 cellular organisms no rank 2467 EBI-EMBL Domain of unknown function (DUF4867) DUF4867 family protein This family consists of uncharacterised proteins around 220 residues in length and is mainly found in various human gut Firmicutes and a few eubacteria species. It is also amply represented in human gut metagenomic datasets. Distant homology analysis and marginal HMM overlaps suggest this family is a distant homologue of Ureidoglycolate hydrolase Pfam:PF04115, but this prediction is not verified by experiment, therefore the function of this family is still unknown. (from Pfam) NF027488.5 PF16162.10 KwaB 26.3 26.3 186 PfamAutoEq Y Y N Kiwa anti-phage protein KwaB-like domain-containing protein 10754241,29371424 131567 cellular organisms no rank 3599 EBI-EMBL Kiwa protein KwaB-like Kiwa protein KwaB-like This family includes Kiwa protein KwaB from E.coli, a component of antiviral defense system Kiwa composed of KwaA and KwaB. The expression of Kiwa in E.coli (strain MG1655) confers resistance to phages lambda and SECphi18 [2]. This family also includes a phylogenetically broad range of bacteria associated with the human gut microbiome. A member of this family from Lactobacillus casei CRL 705 is part of the gene cluster involved in synthesis of bacteriocin toxin [1]. [1]. 10754241. Identification and nucleotide sequence of genes involved in the synthesis of lactocin 705, a two-peptide bacteriocin from Lactobacillus casei CRL 705. Cuozzo SA, Sesma F, Palacios JM, de Ruiz Holgado AP, Raya RR;. FEMS Microbiol Lett 2000;185:157-161. [2]. 29371424. Systematic discovery of antiphage defense systems in the microbial pangenome. Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R;. Science. 2018; [Epub ahead of print] (from Pfam) NF027492.5 PF16166.10 TIC20 28.6 28.6 181 domain Y Y N Tic20 family protein 19403728,20100520,9817756 131567 cellular organisms no rank 923 EBI-EMBL Chloroplast import apparatus Tic20-like Tic20 family protein Chloroplast function requires the import of nuclear encoded proteins from the cytoplasm across the chloroplast double membrane. This is accomplished by two protein complexes, the Toc complex located at the outer membrane and the Tic complex located at the inner membrane. The Toc complex recognises specific proteins by a cleavable N-terminal sequence and is primarily responsible for translocation through the outer membrane, while the Tic complex translocates the protein through the inner membrane. This entry represents Tic20, a core member of the Tic complex. This protein is deeply embedded in the inner envelope membrane and is thought to function as a protein- conducting component of the Tic complex. [1]. 9817756. Tic20 and Tic22 are new components of the protein import apparatus at the chloroplast inner envelope membrane. Kouranov A, Chen X, Fuks B, Schnell DJ;. J Cell Biol. 1998;143:991-1002. [2]. 19403728. Role of temperature stress on chloroplast biogenesis and protein import in pea. Dutta S, Mohanty S, Tripathy BC;. Plant Physiol. 2009;150:1050-1061. [3]. 20100520. Protein import into chloroplasts: the Tic complex and its regulation. Kovacs-Bogdan E, Soll J, Bolter B;. Biochim Biophys Acta. 2010;1803:740-747. (from Pfam) NF027495.5 PF16169.10 DUF4872 28 28 173 domain Y Y N DUF4872 domain-containing protein 20023723 131567 cellular organisms no rank 7923 EBI-EMBL Domain of unknown function (DUF4872) Domain of unknown function (DUF4872) Members of this family are often found in the gene neighbourhood, or fused to, non-ribosomal peptide synthetases. [1]. 20023723. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L;. Mol Biosyst. 2009;5:1636-1660. (from Pfam) NF027503.5 PF16177.10 ACAS_N 27 27 55 domain Y Y N acetyl-coenzyme A synthetase N-terminal domain-containing protein 131567 cellular organisms no rank 126655 EBI-EMBL Acetyl-coenzyme A synthetase N-terminus Acetyl-coenzyme A synthetase N-terminus This domain is found at the N-terminus of many acetyl-coenzyme A synthetase enzymes. (from Pfam) NF027510.5 PF16184.10 Cadherin_3 25.5 25.5 106 domain Y Y N cadherin-like domain-containing protein 19833921,23238717 131567 cellular organisms no rank 3774 EBI-EMBL Cadherin-like Cadherin-like NF027518.5 PF16192.10 PMT_4TMC 32.4 32.4 202 PfamEq Y N N C-terminal four TMM region of protein-O-mannosyltransferase 131567 cellular organisms no rank 23167 EBI-EMBL C-terminal four TMM region of protein-O-mannosyltransferase C-terminal four TMM region of protein-O-mannosyltransferase PMT_4TMC is the C-terminal four membrane-pass region of protein-O-mannosyltransferases and similar enzymes. (from Pfam) NF027519.5 PF16193.10 AAA_assoc_2 34.3 34.3 81 domain Y N N AAA C-terminal domain 131567 cellular organisms no rank 78391 EBI-EMBL AAA C-terminal domain AAA C-terminal domain AAA_assoc_2 is found at the C-terminus of a relatively small set of AAA domains in proteins ranging from archaeal to fungi, plants and mammals. (from Pfam) NF027523.5 PF16198.10 TruB_C_2 29.3 29.3 66 PfamEq Y N N tRNA pseudouridylate synthase B C-terminal domain 131567 cellular organisms no rank 68264 EBI-EMBL tRNA pseudouridylate synthase B C-terminal domain tRNA pseudouridylate synthase B C-terminal domain This C-terminal region is found on a subset of TruB_B protein family members Pfam:PF01509. It is found from bacteria and archaea to fungi, plants and human. (from Pfam) NF027524.5 PF16199.10 Radical_SAM_C 31.9 31.9 85 domain Y N N Radical_SAM C-terminal domain 131567 cellular organisms no rank 28775 EBI-EMBL Radical_SAM C-terminal domain Radical_SAM C-terminal domain This domain is found as a C-terminal extension to a subset of Radical_SAM domains. It is found in archaeal, bacterial, fungal, plant and human proteins. (from Pfam) NF027528.5 PF16203.10 ERCC3_RAD25_C 27 27 248 domain Y N N ERCC3/RAD25/XPB C-terminal helicase 23385459 131567 cellular organisms no rank 19713 EBI-EMBL ERCC3/RAD25/XPB C-terminal helicase ERCC3/RAD25/XPB C-terminal helicase This is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases [1]. [1]. 23385459. Structure of the C-terminal half of human XPB helicase and the impact of the disease-causing mutation XP11BE. Hilario E, Li Y, Nobumori Y, Liu X, Fan L;. Acta Crystallogr D Biol Crystallogr. 2013;69:237-246. (from Pfam) NF027541.5 PF16216.10 GxGYxYP_N 23.9 23.9 72 domain Y Y N GxGYxYP domain-containing protein 24938123 131567 cellular organisms no rank 2045 EBI-EMBL GxGYxYP_N 1st domain GxGYxYP family putative glycoside hydrolase N-terminal domain This entry represents a domain that is found repeated in three copies per protein and is likely to be involved in binding the bacterial cell wall. This domain is found in association with Pfam:PF14323. (from Pfam) NF027546.5 PF16221.10 HTH_47 27.1 27.1 78 domain Y Y N winged helix-turn-helix domain-containing protein 131567 cellular organisms no rank 6236 EBI-EMBL winged helix-turn-helix winged helix-turn-helix HTH_47 is an example of a circularly permuted winged helix-turn-helix domain. HTH_47 is found at the very C-terminus of DUF2172, which is structurally similar to M28-peptidases but lacking one of the key zinc-binding residues. (from Pfam) NF027563.5 PF16238.10 DUF4897 25 25 157 PfamAutoEq Y Y N DUF4897 domain-containing protein 131567 cellular organisms no rank 128 EBI-EMBL Domain of unknown function (DUF4897) Domain of unknown function (DUF4897) A small family of uncharacterized proteins around 200 residues in length and found in various Thermotoga species. The function of this family is unknown. (from Pfam) NF027564.5 PF16239.10 DUF4898 25 25 82 domain Y Y N DUF4898 domain-containing protein 131567 cellular organisms no rank 119 EBI-EMBL Domain of unknown function (DUF4898) Domain of unknown function (DUF4898) A small family of uncharacterized proteins around 100 residues in length and found in various Sulfolobus species. The function of this family is unknown. (from Pfam) NF027567.5 PF16242.10 Pyrid_ox_like 28.8 28.8 149 domain Y Y N pyridoxamine 5'-phosphate oxidase family protein 22751670 131567 cellular organisms no rank 25121 EBI-EMBL Pyridoxamine 5'-phosphate oxidase like pyridoxamine 5'-phosphate oxidase family protein This domain, approximately 140 residues in length, is mainly found in general stress proteins in various Xanthomonas species. It is composed of a six-stranded antiparallel beta-barrel flanked by five alpha-helices and can bind to FMN and FAD, suggesting that it may help the bacteria to react against the oxidative stress induced by the defense mechanisms of the plant [1]. [1]. 22751670. The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property. Hilario E, Li Y, Niks D and Fan L;. Acta Crystallogr. D Biol. Crystallogr. 2012;68(7):846-853. (from Pfam) NF027569.5 PF16244.10 DUF4901 27 27 148 domain Y Y N YcdB/YcdC domain-containing protein 131567 cellular organisms no rank 7090 EBI-EMBL YcdB, YcdC repeated domain YcdB, YcdC repeated domain This entry represents a domain that is generally found in two copies in YcdB and YcdC from B. subtilis. These proteins are uncharacterised. The C-terminal half of this domain appears to show similarity at the sequence level to the PEPSY domain. (from Pfam) NF027579.5 PF16254.10 DUF4910 26.6 26.6 247 PfamAutoEq Y Y N DUF4910 domain-containing protein 131567 cellular organisms no rank 7360 EBI-EMBL Domain of unknown function (DUF4910) Domain of unknown function (DUF4910) NF027582.5 PF16257.10 UxaE 27.1 27.1 475 subfamily Y Y N tagaturonate epimerase family protein GO:0016853 22925190 131567 cellular organisms no rank 1394 EBI-EMBL tagaturonate epimerase tagaturonate epimerase family protein This family consists of uncharacterized proteins around 500 residues in length and is mainly found in various Bacteria species, such as Thermotoga, Paenibacillus and Rhodothermus. A newly recognized enzyme from the galacturonate utilization pathway in T. maritima with tagaturonate epimerase activity [1]. [1]. 22925190. Tagaturonate- fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima. Rodionova, I. A., D. A. Scott, N. V. Grishin, A. L. Osterman and D. A. Rodionov. Environmental microbiology 14:2920-34 (2012) (from Pfam) NF027589.5 PF16264.10 SatD 29 29 211 PfamEq Y Y N SatD family protein 10075418,11274114 131567 cellular organisms no rank 5316 EBI-EMBL SatD family (SatD) SatD family protein This family consists of uncharacterized proteins around 220 residues in length and is mainly found in various Streptococcus species. The function of this family is involved in acid resistance [1,2]. [1]. 10075418. Streptococcus mutans ffh, a gene encoding a homologue of the 54 kDa subunit of the signal recognition particle, is involved in resistance to acid stress. Gutierrez,J.A., Crowley,P.J., Cvitkovitch,D.G., Brady,L.J., Hamilton,I.R., Hillman,J.D. and Bleiweis,A.S.;. Microbiology 145 (Pt 2), 357-366 (1999). [2]. 11274114. Characterization of the sat operon in Streptococcus mutans: evidence for a role of Ffh in acid tolerance. Kremer,B.H., van der Kraan,M., Crowley,P.J., Hamilton,I.R., Brady,L.J. and Bleiweis,A.S.;. J. Bacteriol. 183 (8), 2543-2552 (2001) (from Pfam) NF027593.5 PF16268.10 DUF4921 28.5 28.5 425 domain Y Y N DUF4921 family protein 131567 cellular organisms no rank 3015 EBI-EMBL Domain of unknown function (DUF4921) DUF4921 family protein This family consists of uncharacterized proteins around 450 residues in length and is mainly found in various Corynebacterium species. Several proteins are predicted as galactose-1-phosphate uridylytransferases. The function of this family is unknown. (from Pfam) NF027602.5 PF16277.10 DUF4926 29.1 29.1 57 domain Y Y N DUF4926 domain-containing protein 131567 cellular organisms no rank 3994 EBI-EMBL Domain of unknown function (DUF4926) Domain of unknown function (DUF4926) This family consists of uncharacterized proteins around 70 residues in length and is mainly found in various Caulobacter, Microcystis and Cyanothece species. The function of this family is unknown. (from Pfam) NF027609.5 PF16285.10 DUF4931_N 24.1 24.1 124 PfamAutoEq Y Y N DUF4931 domain-containing protein 131567 cellular organisms no rank 6416 EBI-EMBL Domain of unknown function (DUF4931) N-terminal domain Domain of unknown function (DUF4931) N-terminal domain This family consists of uncharacterized proteins around 270 residues in length and is mainly found in various Bacillus cereus species. Some members of this family are annotated as Galactose-1-phosphate uridylyltransferases, but the specific function of this family is unknown. (from Pfam) NF027610.5 PF16286.10 DUF4932 28.7 28.7 332 domain Y Y N DUF4932 domain-containing protein 131567 cellular organisms no rank 1896 EBI-EMBL Domain of unknown function (DUF4932) Domain of unknown function (DUF4932) This family consists of uncharacterized proteins around 460 residues in length and is mainly found in various Bacteroides species, such as Bacteroides fragilis, Bacteroides sp. and so on. Several members are annotated as putative metalloproteases, but the specific function of this family is unknown. (from Pfam) NF027613.5 PF16289.10 PIN_12 32 32 172 PfamAutoEq Y Y N PIN domain-containing protein 28575517 131567 cellular organisms no rank 8320 EBI-EMBL PIN domain PIN domain This domain is found on the N-terminal region of uncharacterized proteins. It shows homology to other PIN-like families and contains several acidic residues critical for chelating metal ions that are conserved in other PIN-like domains [1]. [1]. 28575517. Comprehensive classification of the PIN domain-like superfamily. Matelska D, Steczkiewicz K, Ginalski K;. Nucleic Acids Res. 2017;45:6995-7020. (from Pfam) NF027619.5 PF16295.10 TetR_C_10 28 28 132 PfamEq Y N N Tetracyclin repressor-like, C-terminal domain 28160603 131567 cellular organisms no rank 4292 EBI-EMBL Tetracyclin repressor-like, C-terminal domain Tetracyclin repressor-like, C-terminal domain This domain belongs to the TetR family of transcription factors. It is found in FadR, a fatty acyl-CoA dependent transcription factor that regulates genes encoding proteins involved in fatty-acid degradation and synthesis pathways. Structural and functional analysis indicate that B. subtilis FadR belongs to the TetR family of transcription factors, where it represses five fad operons involved in the fatty acid beta-oxidation cycle. FadR directly binds to upstream regions of the fadR, fadH, fadN, lcfB and fadF genes, and is deactivated by binding with long-chain acyl-CoAs in a similar manner as E. coli FadR [1]. [1]. 28160603. Structural basis of operator sites recognition and effector binding in the TetR family transcription regulator FadR. Yeo HK, Park YW, Lee JY;. Nucleic Acids Res. 2017;45:4244-4254. (from Pfam) NF027637.5 PF16313.10 DUF4953 24.2 23.5 316 domain Y Y N zinc-dependent metalloprotease 24095060 131567 cellular organisms no rank 19842 EBI-EMBL Met-zincin zinc-dependent metalloprotease This is a family of uncharacterised proteins that carry the highly characteristic met-zincin motif HExxHxxGxxH, the extended zinc-binding domain of metallopeptidases. [1]. 24095060. EcxAB is a founding member of a new family of metalloprotease AB5 toxins with a hybrid cholera-like B subunit. Ng NM, Littler DR, Paton AW, Le Nours J, Rossjohn J, Paton JC, Beddoe T;. Structure. 2013;21:2003-2013. (from Pfam) NF027638.5 PF16314.10 DUF4954 26.2 26.2 433 PfamAutoEq Y Y N DUF4954 family protein 131567 cellular organisms no rank 3233 EBI-EMBL Domain of unknown function (DUF4954) DUF4954 family protein This entry consists of an uncharacterised domain found in proteins of around 660 residues in length and is mainly found in various Bacteroides species. The function of these proteins is unknown. This domain consists of repeated strands. (from Pfam) NF027640.5 PF16316.10 DUF4956 30.6 30.6 169 domain Y Y N DUF4956 domain-containing protein 131567 cellular organisms no rank 12060 EBI-EMBL Domain of unknown function (DUF4956) Domain of unknown function (DUF4956) This family consists of uncharacterized proteins around 220 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. (from Pfam) NF027641.5 PF16317.10 Glyco_hydro_99 33 33 341 PfamEq Y N N Glycosyl hydrolase family 99 GO:0016798 22219371 131567 cellular organisms no rank 2591 EBI-EMBL Glycosyl hydrolase family 99 Glycosyl hydrolase family 99 This domain, around 350 residues, is mainly found in some uncharacterized proteins from bacteroides to human. Some proteins in this family, annotated as endo-alpha-mannosidases cleave mannoside linkages internally within an N-linked glycan chain, short circuiting the classical N-glycan biosynthetic pathway. This domain reveals a (beta-alpha)(8) barrel fold in which the catalytic centre is present in a long substrate-binding groove, consistent with cleavage within the N-glycan chain, providing a foundation upon which to develop new enzyme inhibitors targeting the hijacking of N-glycan synthesis in viral disease and cancer [1]. [1]. 22219371. Structural and mechanistic insight into N-glycan processing by endo-a-mannosidase. Thompson AJ, Williams RJ, Hakki Z, Alonzi DS, Wennekes T, Gloster TM, Songsrirote K, Thomas-Oates JE, Wrodnigg TM, Spreitz J, Stutz AE, Butters TD, Williams SJ, Davies GJ;. Proc. Natl. Acad. Sci. U.S.A. 109 (3), 781-786 (2012). (from Pfam) NF027642.5 PF16318.10 DUF4957 30.8 30.8 142 domain Y Y N DUF4957 domain-containing protein 131567 cellular organisms no rank 2010 EBI-EMBL Domain of unknown function (DUF4957) Domain of unknown function (DUF4957) This family consists of uncharacterised proteins around 150 residues in length and is mainly found in various Bacteroides and Prevotella species. The function of this protein is unknown. (from Pfam) NF027645.5 PF16321.10 Ribosom_S30AE_C 25 25 57 domain Y Y N sigma 54 modulation/S30EA ribosomal C-terminal domain-containing protein 131567 cellular organisms no rank 31143 EBI-EMBL Sigma 54 modulation/S30EA ribosomal protein C terminus Sigma 54 modulation/S30EA ribosomal protein C terminus This domain often occurs at the C-terminus of proteins containing Pfam:PF02482. (from Pfam) NF027648.5 PF16324.10 DUF4960 29.2 29.2 250 domain Y Y N DUF4960 domain-containing protein 131567 cellular organisms no rank 1240 EBI-EMBL Domain of unknown function (DUF4960) Domain of unknown function (DUF4960) This family consists of uncharacterised proteins around 460 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. (from Pfam) NF027651.5 PF16327.10 CcmF_C 28.7 28.7 323 domain Y Y N cytochrome c-type biogenesis CcmF C-terminal domain-containing protein 20382024,21958041,22723177 131567 cellular organisms no rank 42854 EBI-EMBL Cytochrome c-type biogenesis protein CcmF C-terminal Cytochrome c-type biogenesis protein CcmF C-terminal This C-terminal region of CcmF, one of the cytochrome c-type biogenesis proteins, is associated at the C-terminal with Cytochrome_C_asm family Pfam:PF01578. It is possible that it is this domain which delivers reductant to haem on CcmE. [1]. 20382024. Cytochrome c biogenesis: the Ccm system. Sanders C, Turkarslan S, Lee DW, Daldal F;. Trends Microbiol. 2010;18:266-274. [2]. 21958041. Cytochrome c biogenesis System I. Stevens JM, Mavridou DA, Hamer R, Kritsiligkou P, Goddard AD, Ferguson SJ;. FEBS J. 2011;278:4170-4178. [3]. 22723177. Continued surprises in the cytochrome c biogenesis story. Sawyer EB, Barker PD;. Protein Cell. 2012;3:405-409. (from Pfam) NF027657.5 PF16334.10 DUF4964 30.7 30.7 88 domain Y Y N DUF4964 domain-containing protein 131567 cellular organisms no rank 4269 EBI-EMBL Domain of unknown function (DUF4964) Domain of unknown function (DUF4964) This family consists of uncharacterized proteins around 840 residues in length and is mainly found in various Bacteroides species. Several proteins in this family are annotated as Glutaminases, but the function of this protein is unknown. (from Pfam) NF027658.5 PF16335.10 GtaA_6_Hairpin 24.9 24.9 343 domain Y Y N glutaminase domain-containing protein 10952006 131567 cellular organisms no rank 4980 EBI-EMBL Glutaminase A six helical-hairpin domain Glutaminase A six helical-hairpin domain This entry represents the six helical-hairpin domain found in homologues of Glutaminase A from Aspergillus oryzae. Glutaminase catalyzes the hydrolysis of glutamine to glutamic acid and plays a key role in nitrogen metabolism. It catalyzes the hydrolysis not only of L-glutamine but also of D-glutamine [1]. This domain share similarity with six-hairpin glycosidases. [1]. 10952006. Molecular cloning and characterization of a gene encoding glutaminase from Aspergillus oryzae. Koibuchi K, Nagasaki H, Yuasa A, Kataoka J, Kitamoto K;. Appl Microbiol Biotechnol. 2000;54:59-68. (from Pfam) NF027666.5 PF16347.10 SGSH_C 29.3 29.3 154 domain Y Y N sulfatase/phosphatase domain-containing protein 24816101,31285597 131567 cellular organisms no rank 134367 EBI-EMBL N-sulphoglucosamine sulphohydrolase, C-terminal N-sulphoglucosamine sulphohydrolase, C-terminal This domain is found at the C-terminal end of sulfatases and alkaline phosphatases from bacteria, eukaryotes and archaea, including N-sulphoglucosamine sulphohydrolase from humans (SGSH) and Bifunctional sulfatase/alpha-L-rhamnosidase from Formosa agariphila (P36_S1_25). It shows a four-stranded antiparallel beta-sheet, with four surrounding alpha-helices, followed by a C-terminal extension consisting of a small two-stranded antiparallel beta-sheet [1, 2]. [1]. 31285597. A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan. Reisky L, Prechoux A, Zuhlke MK, Baumgen M, Robb CS, Gerlach N, Roret T, Stanetty C, Larocque R, Michel G, Song T, Markert S, Unfried F, Mihovilovic MD, Trautwein-Schult A, Becher D, Schweder T, Bornscheuer UT, Hehemann JH;. Nat Chem Biol. 2019;15:803-812. [2]. 24816101. Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA. Sidhu NS, Schreiber K, Propper K, Becker S, Uson I, Sheldrick GM, Gartner J, Kratzner R, Steinfeld R;. Acta Crystallogr D Biol Crystallogr. 2014;70:1321-1335. (from Pfam) NF027669.5 PF16350.10 FAO_M 27 27 56 domain Y N N FAD dependent oxidoreductase central domain 131567 cellular organisms no rank 30750 EBI-EMBL FAD dependent oxidoreductase central domain FAD dependent oxidoreductase central domain This domain occurs in several FAD dependent oxidoreductases: Sarcosine dehydrogenase, Dimethylglycine dehydrogenase and Dimethylglycine dehydrogenase. It is situated between the DAO domain (Pfam:PF01266) and the GCV_T domain (Pfam:PF01571). (from Pfam) NF027672.5 PF16353.10 LacZ_4 27.3 27.3 87 domain Y Y N beta-galactosidase domain 4-containing protein 8008071 131567 cellular organisms no rank 68000 EBI-EMBL Beta-galactosidase, domain 4 Beta-galactosidase, domain 4 This entry represents domain 4 found in beta-galactosidase [1] and it is organised in a jelly-roll type barrel (Rutkiewicz-Krotewicz M. et al. Crystals 2018, 8(1), 13, https://doi.org/10.3390/cryst8010013). [1]. 8008071. Three-dimensional structure of beta-galactosidase from E. coli. Jacobson RH, Zhang XJ, DuBose RF, Matthews BW;. Nature. 1994;369:761-766. (from Pfam) NF027673.5 PF16355.10 DUF4982 23.9 23.9 61 domain Y Y N DUF4982 domain-containing protein 31285597 131567 cellular organisms no rank 35316 EBI-EMBL Domain of unknown function (DUF4982) Domain of unknown function (DUF4982) This domain is found towards the C terminus of Beta-glucuronidase from Formosa agariphila (P17_GH2) and similar proteins mainly from bacteria and fungi. P17_GH2 is involved in the degradation of the polysaccharide ulvan. The function of this domain, which shows an all-beta structure, is unknown [1]. [1]. 31285597. A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan. Reisky L, Prechoux A, Zuhlke MK, Baumgen M, Robb CS, Gerlach N, Roret T, Stanetty C, Larocque R, Michel G, Song T, Markert S, Unfried F, Mihovilovic MD, Trautwein-Schult A, Becher D, Schweder T, Bornscheuer UT, Hehemann JH;. Nat Chem Biol. 2019;15:803-812. (from Pfam) NF027678.5 PF16360.10 GTP-bdg_M 29.5 29.5 79 domain Y N N GTP-binding GTPase Middle Region 131567 cellular organisms no rank 69799 EBI-EMBL GTP-binding GTPase Middle Region GTP-binding GTPase Middle Region This family locates between the N-terminal domain and MMR_HSR1 50S ribosome-binding GTPase of GTP-binding HflX-like proteins. The full-length members bind and interact with the 50S ribosome and are GTPases, hydrolysing GTP/GDP/ATP/ADP. This region is unknown for its function. (from Pfam) NF027681.5 PF16363.10 GDP_Man_Dehyd 27 27 332 domain Y Y N GDP-mannose 4,6-dehydratase 4.2.1.47 131567 cellular organisms no rank 858574 EBI-EMBL GDP-mannose 4,6 dehydratase GDP-mannose 4,6-dehydratase NF027688.5 PF16370.10 MetallophosC 29.7 29.7 168 domain Y Y N calcineurin-like phosphoesterase C-terminal domain-containing protein 131567 cellular organisms no rank 7673 EBI-EMBL C terminal of Calcineurin-like phosphoesterase C terminal of Calcineurin-like phosphoesterase This is the C-terminal of Calcineurin-like phosphoesterases. It is around 150 residues in length from various Bacteroides species. The function of this family is unknown. (from Pfam) NF027710.5 PF16395.10 DUF5004 21.6 21.6 153 PfamAutoEq Y Y N DUF5004 domain-containing protein 131567 cellular organisms no rank 1287 EBI-EMBL Domain of unknown function (DUF5004) Domain of unknown function (DUF5004) This small family of proteins is functionally uncharacterized. This family is found in bacteroides. Proteins in this family are typically around 150 amino acids in length. (from Pfam) NF027716.5 PF16401.10 DUF5009 25 25 260 domain Y Y N DUF5009 domain-containing protein 131567 cellular organisms no rank 5434 EBI-EMBL Domain of unknown function (DUF5009) Domain of unknown function (DUF5009) This small family of proteins is functionally uncharacterised. This family is mainly found in various Bacteroides species. The members in this family are around 470 residues in length. (from Pfam) NF027718.5 PF16403.10 Bact_surface_Ig-like 27 27 71 domain Y Y N immunoglobulin-like domain-containing protein 23633591,24598737,28077872,28096352 131567 cellular organisms no rank 25457 EBI-EMBL Bacterial surface protein, Ig-like domain Bacterial surface protein, Ig-like domain This entry represents a bacterial immunoglobulin-like domain found in bacterial proteins, including Pesticidal crystal protein Cry22Aa from Bacillus thuringiensis, a protein with a toxic effect on several insect larvae and Chitinase 60 from Moritella marina (Swiss:B1VBB0), responsible for degradation of krill chitin. Paper describing PDB structure 4hmc. [1]. 23633591. Structure of a complete four-domain chitinase from Moritella marina, a marine psychrophilic bacterium. Malecki PH, Raczynska JE, Vorgias CE, Rypniewski W;. Acta Crystallogr D Biol Crystallogr. 2013;69:821-829. Paper describing PDB structure 4mb3. [2]. 24598737. Crystal structures of substrate-bound chitinase from the psychrophilic bacterium Moritella marina and its structure in solution. Malecki PH, Vorgias CE, Petoukhov MV, Svergun DI, Rypniewski W;. Acta Crystallogr D Biol Crystallogr. 2014;70:676-684. Paper describing PDB structure 5fq3. [3]. 28077872. Structural basis for nutrient acquisition by dominant members of the human gut microbiota. Glenwright AJ, Pothula KR, Bhamidimarri SP, Chorev DS, Basle A, Firbank SJ, Zheng H, Robinson CV, Winterhalter M, Kleinekathofer U, Bolam DN, van den Berg B;. Nature. 2017;541:407-411. Paper describing PDB structure 5kdj. [4]. 28096352. Recognition of protein-linked glycans as a determinant of peptidase activity. Noach I, Ficko-Blean E, Pluvinage B, Stuart C, Jenkins ML, Brochu D, Buenbrazo N, Wakarchuk W, Burke JE, Gilbert M, Boraston AB;. Proc Natl Acad Sci U S A. 2017;114:E679. (from Pfam) NF027725.5 PF16410.10 DUF5018 38.2 38.2 352 domain Y Y N DUF5018 domain-containing protein 131567 cellular organisms no rank 1956 EBI-EMBL Domain of unknown function (DUF5018) Domain of unknown function (DUF5018) This family of proteins is functionally uncharacterised. This family is found in various Bacteroides and Alistipes species. Proteins in this family are around 600 amino acids in length. (from Pfam) NF027763.5 PF16448.10 LapD_MoxY_N 25 25 124 domain Y Y N LapD/MoxY N-terminal periplasmic domain-containing protein 21304926,8392137 131567 cellular organisms no rank 12395 EBI-EMBL LapD/MoxY periplasmic domain LapD/MoxY periplasmic domain This domain is the N-terminal periplasmic domain of the LapD and MoxY receptor proteins [1-2]. [1]. 8392137. Identification of a two-component regulatory system controlling methanol dehydrogenase synthesis in Paracoccus denitrificans. Harms N, Reijnders WN, Anazawa H, van der Palen CJ, van Spanning RJ, Oltmann LF, Stouthamer AH;. Mol Microbiol. 1993;8:457-470. [2]. 21304926. Structural basis for c-di-GMP-mediated inside-out signaling controlling periplasmic proteolysis. Navarro MV, Newell PD, Krasteva PV, Chatterjee D, Madden DR, O'Toole GA, Sondermann H;. PLoS Biol. 2011;9:e1000588. (from Pfam) NF027765.5 PF16450.10 Prot_ATP_ID_OB_C 23 23 56 PfamEq Y N N Proteasomal ATPase OB C-terminal domain 19836337,20953180 131567 cellular organisms no rank 12403 EBI-EMBL Proteasomal ATPase OB C-terminal domain Proteasomal ATPase OB C-terminal domain This is the C-terminal interdomain (ID) or oligonucleotide binding (OB) domain of proteasomal ATPase [1-2] [1]. 19836337. Structural insights on the Mycobacterium tuberculosis proteasomal ATPase Mpa. Wang T, Li H, Lin G, Tang C, Li D, Nathan C, Darwin KH, Li H;. Structure. 2009;17:1377-1385. [2]. 20953180. Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation. Wang T, Darwin KH, Li H;. Nat Struct Mol Biol. 2010;17:1352-1357. (from Pfam) NF027787.5 PF16472.10 DUF5050 27 27 283 domain Y Y N DUF5050 domain-containing protein 131567 cellular organisms no rank 5643 EBI-EMBL Domain of unknown function (DUF5050) Domain of unknown function (DUF5050) NF027793.5 PF16478.10 DUF5055 25 25 105 domain Y Y N DUF5055 domain-containing protein 131567 cellular organisms no rank 78 EBI-EMBL Domain of unknown function (DUF5055) Domain of unknown function (DUF5055) This family consists of several uncharacterized proteins around 100 residues in length and is mainly found in butyrate-producing bacteriums. The function of this family is unknown. (from Pfam) NF027796.5 PF16481.10 DUF5058 28.2 28.2 222 subfamily Y Y N DUF5058 family protein 131567 cellular organisms no rank 1977 EBI-EMBL Domain of unknown function (DUF5058) DUF5058 family protein This family consists of uncharacterized proteins around 250 residues in length and is mainly found in various Firmicutes species. The function of this family is unknown. (from Pfam) NF027806.5 PF16491.10 Peptidase_M48_N 27 27 179 PfamEq Y N N CAAX prenyl protease N-terminal, five membrane helices 23539602,23539603 131567 cellular organisms no rank 18293 EBI-EMBL CAAX prenyl protease N-terminal, five membrane helices CAAX prenyl protease N-terminal, five membrane helices The five N-terminal five transmembrane alpha-helices of peptidase_M48 family proteins including the CAAX prenyl proteases reside completely within the membrane of the endoplasmic reticulum. [1]. 23539602. Structure of the integral membrane protein CAAX protease Ste24p. Pryor EE Jr, Horanyi PS, Clark KM, Fedoriw N, Connelly SM, Koszelak-Rosenblum M, Zhu G, Malkowski MG, Wiener MC, Dumont ME;. Science. 2013;339:1600-1604. [2]. 23539603. The structural basis of ZMPSTE24-dependent laminopathies. Quigley A, Dong YY, Pike AC, Dong L, Shrestha L, Berridge G, Stansfeld PJ, Sansom MS, Edwards AM, Bountra C, von Delft F, Bullock AN, Burgess-Brown NA, Carpenter EP;. Science. 2013;339:1604-1607. (from Pfam) NF027814.5 PF16499.10 Melibiase_2 23 23 284 domain Y N N Alpha galactosidase A GO:0004553,GO:0005975 131567 cellular organisms no rank 33357 EBI-EMBL Alpha galactosidase A Alpha galactosidase A NF027868.5 PF16554.10 OAM_dimer 25 25 78 domain Y Y N OAM dimerization domain-containing protein GO:0046983 20106986 131567 cellular organisms no rank 3435 EBI-EMBL Dimerisation domain of d-ornithine 4,5-aminomutase Dimerisation domain of d-ornithine 4,5-aminomutase This family is the short dimerisation domain of the enzyme D-ornithine 4,5-aminomutase. It sits between the TIM-barrel Pfam:PF09043 and Pfam:PF02310. The enzyme is an alpha2-beta2-heterodimer that converts D-ornithine to 2,4-diaminopentanoic acid by way of radical propagation from an adenosylcobalamin to a pyridoxal 5'-phosphate cofactor [1]. [1]. 20106986. Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase. Wolthers KR, Levy C, Scrutton NS, Leys D;. J Biol Chem. 2010;285:13942-13950. (from Pfam) NF027875.5 PF16561.10 AMPK1_CBM 26.8 26.8 85 domain Y N N Glycogen recognition site of AMP-activated protein kinase 16216577 131567 cellular organisms no rank 5991 EBI-EMBL Glycogen recognition site of AMP-activated protein kinase Glycogen recognition site of AMP-activated protein kinase AMPK1_CBM is a family found in close association with AMPKBI Pfam:PF04739. The surface of AMPK1_CBM reveals a carbohydrate-binding pocket [1]. [1]. 16216577. Structural basis for glycogen recognition by AMP-activated protein kinase. Polekhina G, Gupta A, van Denderen BJ, Feil SC, Kemp BE, Stapleton D, Parker MW;. Structure. 2005;13:1453-1462. (from Pfam) NF027889.5 PF16575.10 CLP1_P 26.6 26.6 188 domain Y Y N Clp1/GlmU family protein 17151076 131567 cellular organisms no rank 791 EBI-EMBL mRNA cleavage and polyadenylation factor CLP1 P-loop Clp1/GlmU family protein CLP1_P is the P-loop carrying domain of Clp1 mRNA cleavage and polyadenylation factor, Clp1, proteins in eukaryotes. Clp1 is essential for 3'-end processing of mRNAs. This region carries the P-loop suggesting it is the region that binds adenine or guanine nucleotide [1]. [1]. 17151076. Structure of a nucleotide-bound Clp1-Pcf11 polyadenylation factor. Noble CG, Beuth B, Taylor IA;. Nucleic Acids Res. 2007;35:87-99. (from Pfam) NF027895.5 PF16581.10 HIGH_NTase1_ass 26.7 26.7 205 domain Y N N Cytidyltransferase-related C-terminal region 131567 cellular organisms no rank 693 EBI-EMBL Cytidyltransferase-related C-terminal region Cytidyltransferase-related C-terminal region This domain is found as the C-terminal portion of some HIGH_NTase1 proteins. The exact function is not known. (from Pfam) NF027896.5 PF16582.10 TPP_enzyme_M_2 30.1 30.1 208 PfamEq Y N N Middle domain of thiamine pyrophosphate 18983854 131567 cellular organisms no rank 24743 EBI-EMBL Middle domain of thiamine pyrophosphate Middle domain of thiamine pyrophosphate TPP_enzyme_M_2 is the middle domain of thiamine pyrophosphate in sequences not captured by Pfam:PF00205. This enzyme is necessary for the first step of the biosynthesis of menaquinone, or vitamin K2, an important cofactor in electron transport in bacteria [1]. [1]. 18983854. Specificity and reactivity in menaquinone biosynthesis: the structure of Escherichia coli MenD (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxyla te synthase). Dawson A, Fyfe PK, Hunter WN;. J Mol Biol. 2008;384:1353-1368. (from Pfam) NF027900.5 PF16586.10 DUF5060 27.2 27.2 70 domain Y Y N DUF5060 domain-containing protein 131567 cellular organisms no rank 6157 EBI-EMBL Domain of unknown function (DUF5060) Domain of unknown function (DUF5060) This is the N-terminal domain of a putative glycoside hydrolase, DUF4038. It is found in a number of different bacterial orders. (from Pfam) NF027905.5 PF16591.10 HBM 29.8 29.8 254 domain Y Y N methyl-accepting chemotaxis protein 20498372,21360620,23112148,24347303 131567 cellular organisms no rank 11562 EBI-EMBL Helical bimodular sensor domain Helical bimodular sensor domain The HBM sensor domain has been identified primarily in bacterial chemoreceptors but is also present on histidine kinases. Characteristic features of this domain are its size of approximately 250 amino acids and its location in the bacterial periplasm [1]. The McpS chemoreceptor of Pseudomonas putida KT2440 was found to possess an HBM sensor domain and its 3D structure in complex with physiologically relevant ligands has been reported [2]. This domain is composed of 2 long and 4 short helices that form two modules each composed of a 4-helix bundle. The McpS chemoreceptor mediates chemotaxis towards a number of organic acids [1,3]. Both modules of the McpS HBM domain contain a ligand binding site. Chemo-attractants binds to each of these sites and their binding was shown to trigger a chemotactic response [4]. This domain is primarily found in different proteobacteria but also in archaea. Interestingly, amino acids in both ligand binding sites showed a high degree of conservation suggesting that members of this family sense similar ligands. This domain recognises Multiple TCA cycle intermediates, citrate and alpha-ketoglutarate (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 20498372. Identification of a chemoreceptor for tricarboxylic acid cycle intermediates: differential chemotactic response towards receptor ligands. Lacal J, Alfonso C, Liu X, Parales RE, Morel B, Conejero-Lara F, Rivas G, Duque E, Ramos JL, Krell T;. J Biol Chem. 2010;285:23126-23136. [2]. 21360620. Physiologically relevant divalent cations modulate citrate recognition by the McpS chemorecept. TRUNCATED at 1650 bytes (from Pfam) NF027906.5 PF16592.10 Cas9_REC 25 25 541 domain Y Y N CRISPR-associated endonuclease Cas9 REC1/REC2 domain-containing protein 24529477 131567 cellular organisms no rank 4681 EBI-EMBL REC lobe of CRISPR-associated endonuclease Cas9 REC lobe of CRISPR-associated endonuclease Cas9 The REC lobe of Cas9 - the CRISPR-associated endonuclease Cas9 - includes the REC1 and REC2 domains. REC1 forms an elongated, alpha-helical structure consisting of 25 alpha helices and two beta-sheets, whereas REC2 inserted within REC1 adopts a six-helix bundle structure. The REC lobe and the NUC lobe of Cas9 fold to present a positively charged groove at their interface which accommodates the negatively charged sgRNA:target DNA heteroduplex [1]. CRISPR (clustered regularly interspaced short palindromic repeat)-Cas system occurs naturally in bacteria as a defence against invasion by phages or other mobile genetic elements. Cas9 is targeted to specific genomic locations by sgRNAs or single guide RNAs, in order to complex with invading DNA in order to cleave it and render it inactive. [1]. 24529477. Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O;. Cell. 2014; [Epub ahead of print] (from Pfam) NF027907.5 PF16593.10 Cas9-BH 26.3 26.3 33 domain Y N N Bridge helix of CRISPR-associated endonuclease Cas9 24529477 131567 cellular organisms no rank 4546 EBI-EMBL Bridge helix of CRISPR-associated endonuclease Cas9 Bridge helix of CRISPR-associated endonuclease Cas9 Cas9-BH is the bridge helix between the NUC and the REC lobes of Cas9 - the CRISPR-associated endonuclease Cas9. The REC lobe and the NUC lobe of Cas9 fold to present a positively charged groove at their interface which accommodates the negatively charged sgRNA:target DNA heteroduplex [1]. CRISPR (clustered regularly interspaced short palindromic repeat)-Cas system occurs naturally in bacteria as a defence against invasion by phages or other mobile genetic elements. Cas9 is targeted to specific genomic locations by sgRNAs or single guide RNAs, in order to complex with invading DNA in order to cleave it and render it inactive. [1]. 24529477. Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O;. Cell. 2014; [Epub ahead of print] (from Pfam) NF027909.5 PF16595.10 Cas9_PI 25 25 265 domain Y Y N Cas9 endonuclease PAM-interacting domain-containing protein 24634220 131567 cellular organisms no rank 3956 EBI-EMBL PAM-interacting domain of CRISPR-associated endonuclease Cas9 PAM-interacting domain of CRISPR-associated endonuclease Cas9 Cas9_PI is a family found at the C-terminal of bacterial type II CRISPR system Cas9 endonuclease. This domain adopts a novel protein fold that is unique to the Cas9 family. It is positioned in the structure-DNA-complex to recognise the PAM sequence on the non-complementary DNA strand of the crRNA. PAM sequence is protospacer-adjacent motifs on DNA. See family CRISPR-DR2, Rfam:RF01315. Cas9 carries two nuclease domains, HNH and RuvC, which cleave the DNA strands that are complementary and non-complementary to the 20 nucleotide guide sequence in crRNAs, respectively [1]. [1]. 24634220. Cut site selection by the two nuclease domains of the Cas9 RNA-guided endonuclease. Chen H, Choi J, Bailey S;. J Biol Chem. 2014;289:13284-13294. (from Pfam) NF027952.5 PF16640.10 Big_3_5 35.5 35.5 88 domain Y Y N Ig-like domain repeat protein 131567 cellular organisms no rank 21456 EBI-EMBL Bacterial Ig-like domain (group 3) Ig-like domain repeat protein This family consists of bacterial domains with an Ig-like fold. (from Pfam) NF027964.5 PF16653.10 Sacchrp_dh_C 31 31 265 domain Y Y N saccharopine dehydrogenase C-terminal domain-containing protein 11080625,8885833 131567 cellular organisms no rank 41676 EBI-EMBL Saccharopine dehydrogenase C-terminal domain Saccharopine dehydrogenase C-terminal domain This family comprises the C-terminal domain of saccharopine dehydrogenase. In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase. The saccharopine dehydrogenase can also function as a saccharopine reductase. [1]. 8885833. Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum. Scapin G, Reddy SG, Blanchard JS;. Biochemistry. 1996;35:13540-13551. [2]. 11080625. Crystal structure of saccharopine reductase from Magnaporthe grisea, an enzyme of the alpha-aminoadipate pathway of lysine biosynthesis. Johansson E, Steffens JJ, Lindqvist Y, Schneider G;. Structure Fold Des 2000;8:1037-1047. (from Pfam) NF027965.5 PF16654.10 DAPDH_C 30 30 154 PfamEq Y N N Diaminopimelic acid dehydrogenase C-terminal domain 8885833 131567 cellular organisms no rank 7093 EBI-EMBL Diaminopimelic acid dehydrogenase C-terminal domain Diaminopimelic acid dehydrogenase C-terminal domain This family comprises the C-terminal domain of diaminopimelic acid dehydrogenase. Diaminopimelate dehydrogenase is a NADPH-dependent enzyme that catalyzes the oxidative deamination of meso-2,6-diaminopimelate, which is the direct precursor of L-lysine in bacterial lysine biosynthesis. [1]. 8885833. Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum. Scapin G, Reddy SG, Blanchard JS;. Biochemistry. 1996;35:13540-13551. (from Pfam) NF027966.5 PF16655.10 PhoD_N 30 30 90 domain Y Y N PhoD-like phosphatase N-terminal domain-containing protein 131567 cellular organisms no rank 57322 EBI-EMBL PhoD-like phosphatase, N-terminal domain PhoD-like phosphatase, N-terminal domain This domain is found at the N-terminus of proteins in the PhoD family Pfam:PF09423. (from Pfam) NF027967.5 PF16656.10 Pur_ac_phosph_N 30 30 93 domain Y Y N fibronectin type III domain-containing protein GO:0003993,GO:0046872 8683579 131567 cellular organisms no rank 29310 EBI-EMBL Purple acid Phosphatase, N-terminal domain Purple acid Phosphatase, N-terminal domain This domain is found at the N-terminus of Purple acid phosphatase proteins. [1]. 8683579. Mechanism of Fe(III)-Zn(II) purple acid phosphatase based on crystal structures. Klabunde T, Strater N, Frohlich R, Witzel H, Krebs B;. J Mol Biol. 1996;259:737-748. (from Pfam) NF027968.5 PF16657.10 Malt_amylase_C 27 27 75 domain Y Y N alpha-glucosidase C-terminal domain-containing protein 10473583 131567 cellular organisms no rank 78327 EBI-EMBL Maltogenic Amylase, C-terminal domain Maltogenic Amylase, C-terminal domain This is the C-terminal domain of Maltogenic amylase, an enzyme that hydrolyses starch material. Maltogenic amylases are central to carbohydrate metabolism. [1]. 10473583. Crystal structure of a maltogenic amylase provides insights into a catalytic versatility. Kim JS, Cha SS, Kim HJ, Kim TJ, Ha NC, Oh ST, Cho HS, Cho MJ, Kim MJ, Lee HS, Kim JW, Choi KY, Park KH, Oh BH;. J Biol Chem. 1999;274:26279-26286. (from Pfam) NF027971.5 PF16661.10 Lactamase_B_6 27 27 193 domain Y N N Metallo-beta-lactamase superfamily domain 17128255 131567 cellular organisms no rank 16439 EBI-EMBL Metallo-beta-lactamase superfamily domain Metallo-beta-lactamase superfamily domain This family is part of the metallo-beta-lactamase superfamily. [1]. 17128255. Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease. Mandel CR, Kaneko S, Zhang H, Gebauer D, Vethantham V, Manley JL, Tong L;. Nature. 2006;444:953-956. (from Pfam) NF027980.5 PF16670.10 PI-PLC-C1 29.9 29.9 329 subfamily Y Y N Ca2+-dependent phosphoinositide-specific phospholipase C 3.1.4.11 21906583,8602259 131567 cellular organisms no rank 6882 EBI-EMBL Phosphoinositide phospholipase C, Ca2+-dependent Ca2+-dependent phosphoinositide-specific phospholipase C PI-PLC-C1 is a family of calcium 2+-dependent phosphatidylinositol-specific phospholipase C1 enzymes from bacteria and fungi. The enzyme classification number is EC:3.1.4.11. This enzyme is involved in part of the myo-inositol phosphate metabolic pathway. [1]. 8602259. Crystal structure of a mammalian phosphoinositide-specific phospholipase C delta. Essen LO, Perisic O, Cheung R, Katan M, Williams RL;. Nature. 1996;380:595-602. [2]. 21906583. The correlation between multidomain enzymes and multiple activation mechanisms--the case of phospholipase Cbeta and its membrane interactions. Weinstein H, Scarlata S;. Biochim Biophys Acta. 2011;1808:2940-2947. (from Pfam) NF027987.5 PF16677.10 GP3_package 29.4 29.4 105 PfamEq Y Y N terminase small subunit 22771211 131567 cellular organisms no rank 2058 EBI-EMBL DNA-packaging protein gp3 terminase small subunit DNA-packaging protein gp3 (terminase small subunit) is involved in DNA packing in bacteriophage. it contains a channel where DNA is bound and passed to DNA-packaging protein gp2 (terminase large subunit) [1]. [1]. 22771211. Small terminase couples viral DNA binding to genome-packaging ATPase activity. Roy A, Bhardwaj A, Datta P, Lander GC, Cingolani G;. Structure. 2012;20:1403-1413. (from Pfam) NF027993.5 PF16683.10 TGase_elicitor 25 25 361 domain Y N N Transglutaminase elicitor GO:0016755 21994936 131567 cellular organisms no rank 394 EBI-EMBL Transglutaminase elicitor Transglutaminase elicitor TGase_elicitor is a family of largely oomycete sequences from plant pathogens that elicit transglutaminase/acyltransferase activity. The enzyme classification is E.C:2.3.2.13. From the presence of sequences from Vibrio spp one can propose a lateral gene transfer event having occurred between bacteria and oomycetes to the probable selective advantage of the pathogen [1]. [1]. 21994936. Structural and phylogenetic analyses of the GP42 transglutaminase from Phytophthora sojae reveal an evolutionary relationship between oomycetes and marine Vibrio bacteria. Reiss K, Kirchner E, Gijzen M, Zocher G, Loffelhardt B, Nurnberger T, Stehle T, Brunner F;. J Biol Chem. 2011;286:42585-42593. (from Pfam) NF028004.5 PF16694.10 Cytochrome_P460 27 27 125 domain Y Y N cytochrome P460 family protein 17583915 131567 cellular organisms no rank 7515 EBI-EMBL Cytochrome P460 cytochrome P460 family protein NF028007.5 PF16697.10 Yop-YscD_cpl 33.2 33.2 94 domain Y Y N FHA domain-containing protein 1860816,22349221 131567 cellular organisms no rank 111720 EBI-EMBL Inner membrane component of T3SS, cytoplasmic domain Inner membrane component of T3SS, cytoplasmic domain Yop-YscD-cpl is the cytoplasmic domain of Yop proteins like YscD from Proteobacteria. YscD forms part of the inner membrane component of the bacterial type III secretion injectosome apparatus [1,2]. [1]. 1860816. Analysis of virC, an operon involved in the secretion of Yop proteins by Yersinia enterocolitica. Michiels T, Vanooteghem JC, Lambert de Rouvroit C, China B, Gustin A, Boudry P, Cornelis GR;. J Bacteriol 1991;173:4994-5009. [2]. 22349221. Structure of the cytoplasmic domain of Yersinia pestis YscD, an essential component of the type III secretion system. Lountos GT, Tropea JE, Waugh DS;. Acta Crystallogr D Biol Crystallogr. 2012;68:201-209. (from Pfam) NF028019.5 PF16709.10 SCAB-Ig 23.1 23.1 98 PfamEq Y N N Ig domain of plant-specific actin-binding protein 22356912 131567 cellular organisms no rank 246 EBI-EMBL Ig domain of plant-specific actin-binding protein Ig domain of plant-specific actin-binding protein This family is an Ig-like domain found on plant-specific actin-binding proteins or SCABs. SCAB proteins bind, bundle and stabilise actin filaments and regulate stomatal movement. The Ig-PH fusion domain is at the C-terminus. This domain is an Ig beta-sandwich fold consisting of two antiparallel beta-sheets built from strands beta1 and beta2 and strands beta3-beta6, respectively. [1]. 22356912. Plant actin-binding protein SCAB1 is dimeric actin cross-linker with atypical pleckstrin homology domain. Zhang W, Zhao Y, Guo Y, Ye K;. J Biol Chem. 2012;287:11981-11990. (from Pfam) NF028048.5 PF16738.10 CBM26 28.1 28.1 70 domain Y Y N starch-binding protein 16230347 131567 cellular organisms no rank 5426 EBI-EMBL Starch-binding module 26 starch-binding protein CBM26 is a carbohydrate-binding module that binds starch [1]. [1]. 16230347. A structural and functional analysis of alpha-glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition. Boraston AB, Healey M, Klassen J, Ficko-Blean E, Lammerts van Bueren A, Law V;. J Biol Chem. 2006;281:587-598. (from Pfam) NF028055.5 PF16745.10 RsgA_N 27 27 54 PfamEq Y N N RsgA N-terminal domain 15223319 131567 cellular organisms no rank 20513 EBI-EMBL RsgA N-terminal domain RsgA N-terminal domain This domain is found at the N-terminus of RsgA domains. It has an OB fold [1]. [1]. 15223319. The crystal structure of YloQ, a circularly permuted GTPase essential for Bacillus subtilis viability. Levdikov VM, Blagova EV, Brannigan JA, Cladiere L, Antson AA, Isupov MN, Seror SJ, Wilkinson AJ;. J Mol Biol. 2004;340:767-782. (from Pfam) NF028067.5 PF16757.10 Fucosidase_C 25.6 25.6 88 domain Y Y N alpha-L-fucosidase C-terminal domain-containing protein 14715651 131567 cellular organisms no rank 9971 EBI-EMBL Alpha-L-fucosidase C-terminal domain Alpha-L-fucosidase C-terminal domain The C-terminal domain of PDB:1hl8 is constructed of eight anti-parallel-strands packed into two-sheets of five and three strands, respectively, forming a two-layer-sandwich containing a Greek key motif [1]. [1]. 14715651. Crystal structure of Thermotoga maritima alpha-L-fucosidase. Insights into the catalytic mechanism and the molecular basis for fucosidosis. Sulzenbacher G, Bignon C, Nishimura T, Tarling CA, Withers SG, Henrissat B, Bourne Y;. J Biol Chem. 2004;279:13119-13128. (from Pfam) NF028070.5 PF16760.10 CBM53 27.6 27.6 57 domain Y Y N carbohydrate-binding protein GO:2001070 131567 cellular organisms no rank 581 EBI-EMBL Starch/carbohydrate-binding module (family 53) starch/carbohydrate-binding module (family 53) NF028072.5 PF16762.10 RHH_6 27 27 77 domain Y Y N ribbon-helix-helix domain-containing protein 20060909 131567 cellular organisms no rank 539 EBI-EMBL Ribbon-helix-helix domain Ribbon-helix-helix domain This ribbon-helix-helix domain binds to DNA and may be a part of a toxin-antitoxin system [1]. [1]. 20060909. A new member of the ribbon-helix-helix transcription factor superfamily from the plant pathogen Xanthomonas axonopodis pv.citri. Gallo M, Ferrari E, Eliseo T, Amata I, Pertinhez TA, Katsuyama AM, Paci M, Farah CS, Spisni A, Cicero DO;. J Struct Biol. 2010;170:21-31. (from Pfam) NF028088.5 PF16778.10 Phage_tail_APC 26.6 26.6 60 domain Y Y N phage tail assembly chaperone 131567 cellular organisms no rank 5820 EBI-EMBL Phage tail assembly chaperone protein phage tail assembly chaperone domain Phage_tail_APC is a family of general phage tail assembly chaperone proteins from double-stranded DNA viruses with no RNA stage, many of which are unclassified. (from Pfam) NF028103.5 PF16793.10 RepB_primase 24.3 24.3 186 domain Y Y N DNA-primase RepB domain-containing protein 19416864 131567 cellular organisms no rank 2078 EBI-EMBL RepB DNA-primase N-terminal domain RepB DNA-primase N-terminal domain RepB_primase is a DNA-primase produced by P4-like phages. It is a zinc-independent primase unlike Pri-type primases. It takes up a dumbbell shaped consisting of an N-terminal catalytic domain separated by a long alpha-helix plus tether and a C-terminal helical-bundle domain. Primases are necessary for phage replication. RepBprime primases such as in this family recognise both ssiA and ssiB, ie only 1 single-stranded primase initiation site on each strand, independently of each other and then synthesise primers that are elongated by DNA polymerase III. The phage is thus replicated exclusively in leading strand mode [1]. [1]. 19416864. Structure and function of primase RepB' encoded by broad-host-range plasmid RSF1010 that replicates exclusively in leading-strand mode. Geibel S, Banchenko S, Engel M, Lanka E, Saenger W;. Proc Natl Acad Sci U S A. 2009;106:7810-7815. (from Pfam) NF028105.5 PF16795.10 Phage_integr_3 27 27 161 domain Y Y N integrase 22593158,22683788 131567 cellular organisms no rank 539 EBI-EMBL Archaeal phage integrase integrase Catalyses cleavage and ligation of DNA [1-2]. [1]. 22593158. The structure of an archaeal viral integrase reveals an evolutionarily conserved catalytic core yet supports a mechanism of DNA cleavage in trans. Eilers BJ, Young MJ, Lawrence CM;. J Virol. 2012;86:8309-8313. [2]. 22683788. Structural and functional characterization of the C-terminal catalytic domain of SSV1 integrase. Zhan Z, Ouyang S, Liang W, Zhang Z, Liu ZJ, Huang L;. Acta Crystallogr D Biol Crystallogr. 2012;68:659-670. (from Pfam) NF028129.5 PF16819.10 DUF5074 27.2 27.2 353 domain Y Y N DUF5074 domain-containing protein 22120742,22532667 131567 cellular organisms no rank 11215 EBI-EMBL Domain of unknown function (DUF5074) Domain of unknown function (DUF5074) This family of proteins from Bacteroidetes, is found with a PKD domain at the N-terminus. Several members are annotated as putative quinonprotein alcohol dehydrogenase-like proteins but this could not be confirmed. This entry represents a beta propeller like domain. [1]. 22120742. Structural basis for the DNA-binding activity of the bacterial beta-propeller protein YncE. Kagawa W, Sagawa T, Niki H, Kurumizaka H;. Acta Crystallogr D Biol Crystallogr. 2011;67:1045-1053. [2]. 22532667. A scissor blade-like closing mechanism implicated in transmembrane signaling in a Bacteroides hybrid two-component system. Lowe EC, Basle A, Czjzek M, Firbank SJ, Bolam DN;. Proc Natl Acad Sci U S A. 2012;109:7298-7303. (from Pfam) NF028148.5 PF16838.10 Caud_tail_N 27 27 120 PfamEq Y N N Caudoviral major tail protein N-terminus 22891295 131567 cellular organisms no rank 94 EBI-EMBL Caudoviral major tail protein N-terminus Caudoviral major tail protein N-terminus This is the N-terminal domain of the major tail protein, or knob protein, from Caudovirales [1]. [1]. 22891295. Structural investigations of a Podoviridae streptococcus phage C1, implications for the mechanism of viral entry. Aksyuk AA, Bowman VD, Kaufmann B, Fields C, Klose T, Holdaway HA, Fischetti VA, Rossmann MG;. Proc Natl Acad Sci U S A. 2012;109:14001-14006. (from Pfam) NF028169.5 PF16859.10 TetR_C_11 32 32 113 domain Y Y N TetR/AcrR family transcriptional regulator C-terminal ligand-binding domain-containing protein 15944459 131567 cellular organisms no rank 108939 EBI-EMBL Tetracyclin repressor-like, C-terminal domain Tetracyclin repressor-like, C-terminal domain This family of bacterial transcriptional repressors is characterised by the short approximately 50 amino acid stretch of residues constituting the helix-turn-helix DNA binding motif, around the YRFhY motif. The target proteins that are repressed are involved in the transcriptional control of multi-drug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity [1]. [1]. 15944459. The TetR family of transcriptional repressors. Ramos JL, Martinez-Bueno M, Molina-Henares AJ, Teran W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R;. Microbiol Mol Biol Rev. 2005;69:326-356. (from Pfam) NF028171.5 PF16861.10 Carbam_trans_C 27 27 170 domain Y Y N carbamoyltransferase C-terminal domain-containing protein 22383337,7557411,7559434 131567 cellular organisms no rank 25962 EBI-EMBL Carbamoyltransferase C-terminus Carbamoyltransferase C-terminus This domain is found in NodU from Rhizobium, CmcH from Nocardia lactamdurans and the bifunctional carbamoyltransferase TobZ from Streptoalloteichus tenebrarius. NodU a Rhizobium nodulation protein involved in the synthesis of nodulation factors has 6-O-carbamoyltransferase-like activity [1]. CmcH is involved in cephamycin (antibiotic) biosynthesis and has 3-hydroxymethylcephem carbamoyltransferase activity [2], EC:2.1.3.7 catalysing the reaction: Carbamoyl phosphate + 3-hydroxymethylceph-3-EM-4-carboxylate phosphate + 3-carbamoyloxymethylcephem. TobZ functions as an ATP carbamoyltransferase and tobramycin carbamoyltransferase [3]. These proteins contain two domains, this is the smaller, C-terminal, domain. [1]. 7559434. Involvement of nodS in N-methylation and nodU in 6-O-carbamoylation of Rhizobium sp. NGR234 nod factors. Jabbouri S, Fellay R, Talmont F, Kamalaprija P, Burger U, Relic B, Prome JC, Broughton WJ;. J Biol Chem 1995;270:22968-22973. [2]. 7557411. Characterization of the cmcH genes of Nocardia lactamdurans and Streptomyces clavuligerus encoding a functional 3'-hydroxymethylcephem O-carbamoyltransferase for cephamycin biosynthesis. Coque JJ, Perez-Llarena FJ, Enguita FJ, Fuente JL, Martin JF, Liras P;. Gene 1995;162:21-27. [3]. 22383337. The O-carbamoyltransferase TobZ catalyzes an ancient enzymatic reaction. Parthier C, Gorlich S, Jaenecke F, Breithaupt C, Brauer U, Fandrich U, Clausnitzer D, Wehmeier UF, Bottcher C, Scheel D, Stubbs MT;. Angew Chem Int Ed Engl. 2012;51:4046-4052. (from Pfam) NF028174.5 PF16864.10 Dimerisation2 27 27 90 domain Y Y N methyltransferase dimerization domain-containing protein 22775292 131567 cellular organisms no rank 23677 EBI-EMBL Dimerisation domain Dimerisation domain This domain, found in methyltransferases, functions as a dimerisation domain [1]. [1]. 22775292. Crystal structure and functional mapping of human ASMT, the last enzyme of the melatonin synthesis pathway. Botros HG, Legrand P, Pagan C, Bondet V, Weber P, Ben-Abdallah M, Lemiere N, Huguet G, Bellalou J, Maronde E, Beguin P, Haouz A, Shepard W, Bourgeron T;. J Pineal Res. 2013;54:46-57. (from Pfam) NF028177.5 PF16867.10 DMSP_lyase 27 27 162 subfamily Y Y N dimethylsulfonioproprionate lyase family protein GO:0047869 21249136 131567 cellular organisms no rank 4911 EBI-EMBL Dimethlysulfonioproprionate lyase dimethylsulfonioproprionate lyase family protein Breaks down into dimethylsulfoniopropionate (DMSP) into acrylate and dimethyl sulfide [1]. [1]. 21249136. Unusual regulation of a leaderless operon involved in the catabolism of dimethylsulfoniopropionate in Rhodobacter sphaeroides. Sullivan MJ, Curson AR, Shearer N, Todd JD, Green RT, Johnston AW;. PLoS One. 2011;6:e15972. (from Pfam) NF028178.5 PF16868.10 NMT1_3 27 27 289 domain Y Y N TAXI family TRAP transporter solute-binding subunit 20584082 131567 cellular organisms no rank 80817 EBI-EMBL NMT1-like family TAXI family TRAP transporter solute-binding subunit NF028182.5 PF16872.10 putAbiC 22 22 80 domain Y Y N putative phage abortive infection protein 1429469 131567 cellular organisms no rank 4379 EBI-EMBL Putative phage abortive infection protein putative phage abortive infection protein Several members are annotated as putative phage abortive infection proteins [1]. [1]. 1429469. Molecular characterization of a second abortive phage resistance gene present in Lactococcus lactis subsp. lactis ME2. Durmaz E, Higgins DL, Klaenhammer TR;. J Bacteriol. 1992;174:7463-7469. (from Pfam) NF028191.5 PF16881.10 LIAS_N 27 27 96 PfamEq Y N N N-terminal domain of lipoyl synthase of Radical_SAM family 131567 cellular organisms no rank 33249 EBI-EMBL N-terminal domain of lipoyl synthase of Radical_SAM family N-terminal domain of lipoyl synthase of Radical_SAM family LIAS_N is found as the N-terminal domain of the Radical_SAM family in the members that are lipoyl synthase enzymes, particularly the mitochondrial ones in metazoa but also those in bacteria. (from Pfam) NF028194.5 PF16884.10 ADH_N_2 31 31 108 domain Y N N N-terminal domain of oxidoreductase 131567 cellular organisms no rank 60715 EBI-EMBL N-terminal domain of oxidoreductase N-terminal domain of oxidoreductase N-terminal region of oxidoreductase and prostaglandin reductase and alcohol dehydrogenase. (from Pfam) NF028196.5 PF16886.10 ATP-synt_ab_Xtn 26.9 26.9 121 domain Y N N ATPsynthase alpha/beta subunit N-term extension 131567 cellular organisms no rank 10925 EBI-EMBL ATPsynthase alpha/beta subunit N-term extension ATPsynthase alpha/beta subunit N-term extension ATP-synt_ab_Xtn is an extension of the alpha-beta catalytic subunit of VATA or V-type proton ATPase catalytic subunit at the N-terminal end. It is found from bacteria to humans, and was not modelled in family ATP-synt_ab, Pfam:PF00006. (from Pfam) NF028199.5 PF16889.10 Hepar_II_III_N 22 22 340 domain Y Y N heparinase II/III family protein 23011846 131567 cellular organisms no rank 16389 EBI-EMBL Heparinase II/III N-terminus heparinase II/III family protein This is the N-terminal domain of heparinase II/III proteins. It is a toroid-like domain [1]. [1]. 23011846. Structural basis of heparan sulfate-specific degradation by heparinase III. Dong W, Lu W, McKeehan WL, Luo Y, Ye S;. Protein Cell. 2012;3:950-961. (from Pfam) NF028206.5 PF16896.10 PGDH_C 25 25 155 domain Y Y N phosphogluconate dehydrogenase C-terminal domain-containing protein 131567 cellular organisms no rank 3439 EBI-EMBL Phosphogluconate dehydrogenase (decarboxylating) C-term Phosphogluconate dehydrogenase (decarboxylating) C-term PGDH_C is the C-terminal domain of putative bacterial phosphogluconate dehydrogenase proteins. (from Pfam) NF028207.5 PF16897.10 MMR_HSR1_Xtn 35.2 35.2 106 PfamEq Y N N C-terminal region of MMR_HSR1 domain 131567 cellular organisms no rank 1305 EBI-EMBL C-terminal region of MMR_HSR1 domain C-terminal region of MMR_HSR1 domain MMR_HSR1_Xtn is the C-terminal region of some members of the MMR_HSR1 family. (from Pfam) NF028211.5 PF16901.10 DAO_C 31.4 31.4 126 domain Y Y N glycerol-3-phosphate dehydrogenase C-terminal domain-containing protein 131567 cellular organisms no rank 83813 EBI-EMBL C-terminal domain of alpha-glycerophosphate oxidase C-terminal domain of alpha-glycerophosphate oxidase DAO_C is the C-terminal region of alpha-glycerophosphate oxidase. (from Pfam) NF028216.5 PF16906.10 Ribosomal_L26 28.8 28.8 82 PfamEq Y Y N 60S ribosomal protein L26 GO:0003735,GO:0006412,GO:0015934 22431104 131567 cellular organisms no rank 1173 EBI-EMBL Ribosomal proteins L26 eukaryotic, L24P archaeal 60S ribosomal protein L26 Ribosomal_L26 is a family of the 50S and the 60S ribosomal proteins from eukaryotes - L26 - and archaea - L25. [1]. 22431104. Frameshift mutation in p53 regulator RPL26 is associated with multiple physical abnormalities and a specific pre-ribosomal RNA processing defect in diamond-blackfan anemia. Gazda HT, Preti M, Sheen MR, O'Donohue MF, Vlachos A, Davies SM, Kattamis A, Doherty L, Landowski M, Buros C, Ghazvinian R, Sieff CA, Newburger PE, Niewiadomska E, Matysiak M, Glader B, Atsidaftos E, Lipton JM, Gleizes PE, Beggs AH;. Hum Mutat. 2012;33:1037-1044. (from Pfam) NF028221.5 PF16911.10 PapA_C 30 30 203 domain Y Y N phthiocerol/phthiodiolone dimycocerosyl transferase family protein 15070765,15123643,15749014 131567 cellular organisms no rank 6617 EBI-EMBL Phthiocerol/phthiodiolone dimycocerosyl transferase C-terminus phthiocerol/phthiodiolone dimycocerosyl transferase C-terminal domain This entry represents the C-terminal domain of phthiocerol/phthiodiolone dimycocerosyl transferase. Proteins containing this domain include papA5 from Mycobacterium tuberculosis. PapA5 catalyses diesterification of phthiocerol and phthiodiolone with mycocerosic acids, the final step in the phthiocerol and phthiodiolone dimycocerosate esters (PDIM) synthesis [1,2,3]. [1]. 15123643. Crystal structure of PapA5, a phthiocerol dimycocerosyl transferase from Mycobacterium tuberculosis. Buglino J, Onwueme KC, Ferreras JA, Quadri LE, Lima CD;. J Biol Chem. 2004;279:30634-30642. [2]. 15749014. Dissecting the mechanism and assembly of a complex virulence mycobacterial lipid. Trivedi OA, Arora P, Vats A, Ansari MZ, Tickoo R, Sridharan V, Mohanty D, Gokhale RS;. Mol Cell. 2005;17:631-643. [3]. 15070765. Mycobacterial polyketide-associated proteins are acyltransferases: proof of principle with Mycobacterium tuberculosis PapA5. Onwueme KC, Ferreras JA, Buglino J, Lima CD, Quadri LE;. Proc Natl Acad Sci U S A. 2004;101:4608-4613. (from Pfam) NF028222.5 PF16912.10 Glu_dehyd_C 34.9 34.9 211 domain Y N N Glucose dehydrogenase C-terminus 16551747 131567 cellular organisms no rank 97539 EBI-EMBL Glucose dehydrogenase C-terminus Glucose dehydrogenase C-terminus NF028226.5 PF16916.10 ZT_dimer 26.7 26.7 79 domain Y Y N cation transporter dimerization domain-containing protein 17717154 131567 cellular organisms no rank 71441 EBI-EMBL Dimerisation domain of Zinc Transporter Dimerisation domain of Zinc Transporter ZT_dimer is the dimerisation region of the whole molecule of zinc transporters since the full-length members form a homodimer during activity. The domain lies within the cytoplasm and exhibits an overall structural similarity with the copper metallochaperone Hah1 UniProtKB:O00244, exhibiting an open alpha-beta domain with two alpha helices (H1 and H2) aligned on one side and a three-stranded mixed beta-sheet (S1 to S3) on the other side. The N-terminal part of the members is the Cation_efflux family, Pfam:PF01545 [1]. [1]. 17717154. Structure of the zinc transporter YiiP. Lu M, Fu D;. Science. 2007;317:1746-1748. (from Pfam) NF028227.5 PF16917.10 BPL_LplA_LipB_2 27 27 183 domain Y Y N biotin/lipoate--protein ligase family protein GO:0036211 131567 cellular organisms no rank 13589 EBI-EMBL Biotin/lipoate A/B protein ligase family biotin/lipoate--protein ligase family protein NF028231.5 PF16921.10 Tex_YqgF 27 27 126 PfamEq Y N N Tex protein YqgF-like domain 18321528 131567 cellular organisms no rank 77463 EBI-EMBL Tex protein YqgF-like domain Tex protein YqgF-like domain This is the YqgF-like domain of the bacterial Tex protein, which is involved in transcriptional processes [1]. [1]. 18321528. Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa. Johnson SJ, Close D, Robinson H, Vallet-Gely I, Dove SL, Hill CP;. J Mol Biol. 2008;377:1460-1473. (from Pfam) NF028234.5 PF16924.10 DpaA_N 29.2 29.2 116 PfamEq Y Y N dipicolinate synthase subunit DpsA 131567 cellular organisms no rank 4522 EBI-EMBL Dipicolinate synthase subunit A N-terminal domain dipicolinate synthase subunit DpsA N-terminal domain NF028235.5 PF16925.10 TetR_C_13 27 27 109 domain Y Y N TetR family transcriptional regulator C-terminal domain-containing protein 21249136 131567 cellular organisms no rank 153343 EBI-EMBL Tetracyclin repressor-like, C-terminal domain Tetracyclin repressor-like, C-terminal domain This domain is found in TetR-type regulators such as AcuR, acrylate-responsive repressor of acuR-acuI-dddL operons involved in acrylate catabolism [1]. [1]. 21249136. Unusual regulation of a leaderless operon involved in the catabolism of dimethylsulfoniopropionate in Rhodobacter sphaeroides. Sullivan MJ, Curson AR, Shearer N, Todd JD, Green RT, Johnston AW;. PLoS One. 2011;6:e15972. (from Pfam) NF028236.5 PF16926.10 HisKA_4TM 22.6 22.6 130 domain Y N N Archaeal 4TM region of histidine kinase 131567 cellular organisms no rank 945 EBI-EMBL Archaeal 4TM region of histidine kinase Archaeal 4TM region of histidine kinase This N-terminal region of histidine-kinases consists of 4xTMs and is found in Archaea. (from Pfam) NF028237.5 PF16927.10 HisKA_7TM 28.6 28.6 224 domain Y Y N histidine kinase N-terminal 7TM domain-containing protein 30008469 131567 cellular organisms no rank 15103 EBI-EMBL N-terminal 7TM region of histidine kinase N-terminal 7TM region of histidine kinase HisKA_7TM is an N-terminal region consisting of seven transmembrane domains found in Archaea and some bacteria. It is always found associated with histidine kinase. (from Pfam) NF028255.5 PF16945.10 Phage_r1t_holin 26.9 26.9 72 equivalog Y Y N holin 8730875 131567 cellular organisms no rank 2783 EBI-EMBL Putative lactococcus lactis phage r1t holin phage r1t family holin Phage_r1t_holin is a family of putative phage r1t holins from lactococcus. these holins carry two hydrophobic putative TMs separated by a short beta-turn region [1]. [1]. 8730875. Sequence analysis and molecular characterization of the temperate lactococcal bacteriophage r1t. van Sinderen D, Karsens H, Kok J, Terpstra P, Ruiters MH, Venema G, Nauta A;. Mol Microbiol. 1996;19:1343-1355. (from Pfam) NF028257.5 PF16947.10 Ferredoxin_N 25 25 65 domain Y Y N 4Fe-4S ferredoxin N-terminal domain-containing protein 131567 cellular organisms no rank 598 EBI-EMBL N-terminal region of 4Fe-4S ferredoxin iron-sulfur binding N-terminal region of 4Fe-4S ferredoxin iron-sulfur binding Ferredoxin_N is a short domain that is often found at the N-terminus of 4Fe-4S ferredoxin iron-sulfur binding domain proteins from Archaea and a few bacteria. (from Pfam) NF028262.5 PF16952.10 Gln-synt_N_2 35.7 35 112 PfamEq Y N N Glutamine synthetase N-terminal domain GO:0004356,GO:0006542,GO:0008152 23234431 131567 cellular organisms no rank 4442 EBI-EMBL Glutamine synthetase N-terminal domain Glutamine synthetase N-terminal domain NF028265.5 PF16955.10 OFeT_1 26.9 26.9 207 PfamEq Y N N Ferrous iron uptake permease, iron-lead transporter 131567 cellular organisms no rank 532 EBI-EMBL Ferrous iron uptake permease, iron-lead transporter Ferrous iron uptake permease, iron-lead transporter OFeT_1 is a family of conserved archaeal membrane proteins that are putative oxidase-dependent Fe2+ transporters. (from Pfam) NF028267.5 PF16957.10 Mal_decarbox_Al 25.4 25.4 546 PfamEq Y Y N malonate decarboxylase subunit alpha GO:0016740 18251085 131567 cellular organisms no rank 13355 EBI-EMBL Malonate decarboxylase, alpha subunit, transporter malonate decarboxylase subunit alpha Mal_decarbox_Al is a family of Na+-transporting carboxylic acid decarboxylases. [1]. 18251085. Purification and characterization of a cytoplasmic enzyme component of the Na+-activated malonate decarboxylase system of Malonomonas rubra: acetyl-S-acyl carrier protein: malonate acyl carrier protein-SH transferase. Hilbi H, Dimroth P;. Arch Microbiol. 1994;162:48-56. (from Pfam) NF028286.5 PF16976.10 RcpC 28.8 28.8 114 subfamily Y Y N RcpC/CpaB family pilus assembly protein 15146494,17435791 131567 cellular organisms no rank 34901 EBI-EMBL Flp pilus assembly protein RcpC/CpaB RcpC/CpaB family pilus assembly protein Members of this family are assembly proteins for Flp-type (fimbrial low-molecular weight protein) pili, a subclass within the type IVb pili in which the prepilin subunits are small in size, 50–80 amino acids long. NF028290.5 PF16980.10 CitMHS_2 25.7 25.7 448 PfamEq Y Y N sodium:proton antiporter 131567 cellular organisms no rank 8814 EBI-EMBL Putative citrate transport sodium:proton antiporter CitMHS is a family of putative citrate transporters, belonging to the Na+/H+ antiporter NhaD-like permease superfamily. (from Pfam) NF028293.5 PF16983.10 MFS_MOT1 30 30 111 domain Y Y N molybdate transporter family protein GO:0015098,GO:0015689 18077439 131567 cellular organisms no rank 11491 EBI-EMBL Molybdate transporter of MFS superfamily molybdate transporter family protein MFS_MOT1 is a family of molybdenate transporters. Molybdenum is an essential element that is taken up into the cell in the oxyanion molybdate. Molybdenum is used in the form of molybdopterin-cofactor, which participates in the active site of enzymes involved in key reactions of carbon, nitrogen, and sulfur metabolism. [1]. 18077439. A high-affinity molybdate transporter in eukaryotes. Tejada-Jimenez M, Llamas A, Sanz-Luque E, Galvan A, Fernandez E;. Proc Natl Acad Sci U S A. 2007;104:20126-20130. (from Pfam) NF028300.5 PF16990.10 CBM_35 28 28 121 domain Y Y N CBM35 domain-containing protein GO:0030246 15004012,15740741 131567 cellular organisms no rank 25209 EBI-EMBL Carbohydrate binding module (family 35) Carbohydrate binding module (family 35) This is a mannan-specific carbohydrate binding domain, previously known as the X4 module [1]. Unlike other carbohydrate binding modules, binding to substrate causes a conformational change [2]. [1]. 15004012. X4 modules represent a new family of carbohydrate-binding modules that display novel properties. Bolam DN, Xie H, Pell G, Hogg D, Galbraith G, Henrissat B, Gilbert HJ;. J Biol Chem. 2004;279:22953-22963. [2]. 15740741. Structure of a mannan-specific family 35 carbohydrate-binding module: evidence for significant conformational changes upon ligand binding. Tunnicliffe RB, Bolam DN, Pell G, Gilbert HJ, Williamson MP;. J Mol Biol. 2005;347:287-296. (from Pfam) NF028304.5 PF16994.10 Glyco_trans_4_5 26.6 26.6 172 PfamEq Y N N Glycosyl-transferase family 4 7883697 131567 cellular organisms no rank 665 EBI-EMBL Glycosyl-transferase family 4 Glycosyl-transferase family 4 NF028309.5 PF16999.10 V-ATPase_G_2 28 28 104 PfamEq Y Y N V-type ATPase subunit subunit G family protein 20173764,22178924,22353718 131567 cellular organisms no rank 278 EBI-EMBL Vacuolar (H+)-ATPase G subunit V-type ATPase subunit subunit G family protein This family represents vacuolar (H+)-ATPase G subunit from several bacterial and archaeal species. Subunit G is a component of the peripheral stalk of the ATPase complex [1-3] [1]. 22178924. Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase. Lau WC, Rubinstein JL;. Nature. 2011;481:214-218. [2]. 20173764. The structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase. Lee LK, Stewart AG, Donohoe M, Bernal RA, Stock D;. Nat Struct Mol Biol. 2010;17:373-378. [3]. 22353718. The dynamic stator stalk of rotary ATPases. Stewart AG, Lee LK, Donohoe M, Chaston JJ, Stock D;. Nat Commun. 2012;3:687. (from Pfam) NF028342.5 PF17032.10 zinc_ribbon_15 28.9 28.9 73 domain Y Y N zinc-ribbon domain-containing protein 24259309 131567 cellular organisms no rank 5440 EBI-EMBL zinc-ribbon family zinc-ribbon family This zinc-ribbon region is found on a set of largely microsporidia-specific proteins. [1]. 24259309. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T;. Genome Biol Evol. 2013;5:2285-2303. (from Pfam) NF028343.5 PF17033.10 Peptidase_M99 27 27 267 domain Y Y N M99 family carboxypeptidase catalytic domain-containing protein 25372672 131567 cellular organisms no rank 3961 EBI-EMBL Carboxypeptidase controlling helical cell shape catalytic Carboxypeptidase controlling helical cell shape catalytic This is the peptidase domain of a D,L-carboxypeptidase. The active site residues are Arg86, Glu222 and the metal ligands, in the peptidase domain, are Gln46, Glu49 and His128 in UniProtKB:O25708. The protein binds many zinc ions and a calcium ion and there are other metal binding sites. The catalytic activity is the release of m-Dpm from the peptide muramyl-Ala-gamma-D-Glu-m-Dpm; this is probably the precursor of the cell wall cross-linking peptide [1]. [1]. 25372672. Structural basis for the recognition of muramyltripeptide by Helicobacter pylori Csd4, a D,L-carboxypeptidase controlling the helical cell shape. Kim HS, Kim J, Im HN, An DR, Lee M, Hesek D, Mobashery S, Kim JY, Cho K, Yoon HJ, Han BW, Lee BI, Suh SW;. Acta Crystallogr D Biol Crystallogr. 2014;70:2800-2812. (from Pfam) NF028352.5 PF17042.10 NBD_C 28.3 28.3 168 domain Y Y N nucleotide-binding domain containing protein 27294475,27402745 131567 cellular organisms no rank 45756 EBI-EMBL Nucleotide-binding C-terminal domain Nucleotide-binding C-terminal domain This is the C-terminal domain found in proteins in a range of Proteobacteria as well as the Gram-positive Oceanobacillus iheyensis. Structural analysis of the whole protein indicates the N- and C-termini act together to produce a surface into which a threonate-ADP complex is bound, demonstrating that a sugar binding site is on the N-terminal domain, and a nucleotide binding site is in the C-terminal domain [1]. There is a critical motif, DDXTG, at approximately residues 22-25. Proteins containing this domain have been predicted as kinases. Some members are associated with PdxA2 by physical clustering and gene fusion with PdxA2. Some members that are fused with PdxA2 have been shown to be involved in L-4-hydroxythreonine (4HT) phosphorylation, part of the alternative pathway to make PLP (pyridoxal 5'-phosphate) out of a toxic metabolite, 4HT. However, 4HT phosphorylation might not be the main function of this group of proteins. Moreover, some members that are not associated with pdxA2, and even one that is associated with pdxA2, have lost 4HT kinase activity [2]. Functional analysis demonstrate that family members include D-Threonate kinases (DtnK), D-Erythronate kinases (DenK) and 3-Oxo-tetronate kinases (OtnK) [1]. [1]. 27402745. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Zhang X, Carter MS, Vetting MW, San Francisco B, Zhao S, Al-Obaidi NF, Solbiati JO, Thiaville JJ, de Crecy-Lagard V, Jacobson MP, Almo SC, Gerlt JA;. Proc Natl Acad Sci U S A. 2016;113:E4161-E4169. [2]. 27294475. Members of a Novel Kinase Family (DUF1537) Can Recycle Toxic. TRUNCATED at 1650 bytes (from Pfam) NF028409.5 PF17099.10 TrpP 27.2 27.2 169 PfamEq Y Y N tryptophan transporter 10735881 131567 cellular organisms no rank 3725 EBI-EMBL Tryptophan transporter TrpP tryptophan transporter TrpP is a bacterial transmembrane protein that is probably involved in tryptophan uptake. Its expression is regulated by tryptophan-activated RNA-binding regulatory protein (TRAP) [1]. [1]. 10735881. A Bacillus subtilis gene of previously unknown function, yhaG, is translationally regulated by tryptophan-activated TRAP and appears to be involved in tryptophan transport. Sarsero JP, Merino E, Yanofsky C;. J Bacteriol. 2000;182:2329-2331. (from Pfam) NF028425.5 PF17115.10 Toast_rack_N 22 22 92 domain Y Y N toast rack family protein 131567 cellular organisms no rank 580 EBI-EMBL N-terminal domain of toast_rack, DUF2154 toast rack N-terminal domain This short domain lies at the N-terminus of DUF2154, Pfam:PF09922, hereafter named Toast_rack from its structural resemblance. The function of both domains is unknown though DUF2154 is proposed to be a cell-adhesion protein. (from Pfam) NF028434.5 PF17124.10 ThiJ_like 30 30 186 domain Y Y N type 1 glutamine amidotransferase domain-containing protein 131567 cellular organisms no rank 18843 EBI-EMBL ThiJ/PfpI family-like ThiJ/PfpI family-like This is a family of fungal and bacterial ThiJ/PfpI-like proteins. (from Pfam) NF028435.5 PF17125.10 Methyltr_RsmF_N 34 34 86 PfamEq Y N N N-terminal domain of 16S rRNA methyltransferase RsmF 16793063,20558545 131567 cellular organisms no rank 26258 EBI-EMBL N-terminal domain of 16S rRNA methyltransferase RsmF N-terminal domain of 16S rRNA methyltransferase RsmF This is the N-terminal domain of the RsmF methyl transferase. RsmF is a multi-site-specific methyltransferase that is responsible for the synthesis of three modifications on cytidines in 16S ribosomal RNA. The N-terminus is critical for stabilising the catalytic core of the enzyme [1]. It has a ferredoxin-like fold. [1]. 16793063. The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain. Hallberg BM, Ericsson UB, Johnson KA, Andersen NM, Douthwaite S, Nordlund P, Beuscher AE 4th, Erlandsen H;. J Mol Biol. 2006;360:774-787. [2]. 20558545. Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus. Demirci H, Larsen LH, Hansen T, Rasmussen A, Cadambi A, Gregory ST, Kirpekar F, Jogl G;. RNA. 2010;16:1584-1596. (from Pfam) NF028441.5 PF17131.9 LolA_like 30 30 184 domain Y Y N outer membrane lipoprotein-sorting protein 131567 cellular organisms no rank 15788 EBI-EMBL Outer membrane lipoprotein-sorting protein outer membrane lipoprotein-sorting protein This is likely to be a family of outer-membrane lipoprotein-sorting proteins. (from Pfam) NF028442.5 PF17132.9 Glyco_hydro_106 29 29 743 domain Y Y N glycosyl hydrolase 15991055 131567 cellular organisms no rank 16232 EBI-EMBL alpha-L-rhamnosidase glycosyl hydrolase NF028445.5 PF17135.9 Ribosomal_L18 28 28 188 PfamEq Y N N Ribosomal protein 60S L18 and 50S L18e 18400176,19112492,21109664,22052974,22096102,25064512,8950179 131567 cellular organisms no rank 884 EBI-EMBL Ribosomal protein 60S L18 and 50S L18e Ribosomal protein 60S L18 and 50S L18e This is a family of ribosomal proteins, 60S L18 from eukaryotes and 50S L18e from Archaea. [1]. 8950179. The cloning and sequencing of a ribosomal L18 protein from an evolutionary divergent eukaryote, Trypanosoma brucei. Coulter LJ, Hide G;. Biochim Biophys Acta. 1996;1309:69-72. [2]. 18400176. Structure of the mammalian 80S ribosome at 8.7 A resolution. Chandramouli P, Topf M, Menetret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, Akey CW;. Structure. 2008;16:535-548. [3]. 19112492. Regulated nuclear trafficking of rpL10A mediated by NIK1 represents a defense strategy of plant cells against virus. Carvalho CM, Santos AA, Pires SR, Rocha CS, Saraiva DI, Machado JP, Mattos EC, Fietto LG, Fontes EP;. PLoS Pathog. 2008;4:e1000247. [4]. 21109664. Crystal structure of the eukaryotic ribosome. Ben-Shem A, Jenner L, Yusupova G, Yusupov M;. Science. 2010;330:1203-1209. [5]. 22052974. Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6. Klinge S, Voigts-Hoffmann F, Leibundgut M, Arpagaus S, Ban N;. Science. 2011;334:941-948. [6]. 22096102. The structure of the eukaryotic ribosome at 3.0 A resolution. Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M;. Science. 2011;334:1524-1529. [7]. 25064512. Structure of the mammalian 80S initiation complex with initiation factor 5B on HCV-IRES RNA. Yamamoto H, Unbehaun A, Loerke J, Behrmann E, Collier M, Burger J, Mielke T, Spahn CM;. Nat Struct Mol Biol. 2014;21:721-727. (from Pfam) NF028447.5 PF17137.9 DUF5110 27 27 71 domain Y Y N DUF5110 domain-containing protein 131567 cellular organisms no rank 39113 EBI-EMBL Domain of unknown function (DUF5110) Domain of unknown function (DUF5110) This domain is likely to be a carbohydrate-binding domain of some description as it is found immediately C-terminal to the glycosyl-hydrolase family Glyco_hydro_31, Pfam:PF01055. (from Pfam) NF028453.5 PF17144.9 Ribosomal_L5e 27 27 163 PfamEq Y N N Ribosomal large subunit proteins 60S L5, and 50S L18 GO:0003735,GO:0005840,GO:0006412,GO:0008097 11119702,11598216,23118189,23636399,8626719 131567 cellular organisms no rank 1184 EBI-EMBL Ribosomal large subunit proteins 60S L5, and 50S L18 Ribosomal large subunit proteins 60S L5, and 50S L18 This family contains the large 60S ribosomal L5 proteins from Eukaryota and the 50S L18 proteins from Archaea. It has been shown that the amino terminal 93 amino acids of Swiss:P09895 are necessary and sufficient to bind 5S rRNA in vitro [1], suggesting that the entire family has a function in rRNA binding [2,3,4,5]. [1]. 8626719. Distinct domains in ribosomal protein L5 mediate 5 S rRNA binding and nucleolar localization. Michael WM, Dreyfuss G;. J Biol Chem 1996;271:11571-11574. [2]. 11119702. 5S rRNA binding proteins from the hyperthermophilic archaeon, Pyrococcus furiosus. Furumoto H, Taguchi A, Itoh T, Morinaga T, Itoh T;. FEBS Lett. 2000;486:195-199. [3]. 11598216. The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome. Barakat A, Szick-Miranda K, Chang IF, Guyot R, Blanc G, Cooke R, Delseny M, Bailey-Serres J;. Plant Physiol. 2001;127:398-415. [4]. 23118189. Synchronizing nuclear import of ribosomal proteins with ribosome assembly. Kressler D, Bange G, Ogawa Y, Stjepanovic G, Bradatsch B, Pratte D, Amlacher S, Strauss D, Yoneda Y, Katahira J, Sinning I, Hurt E;. Science. 2012;338:666-671. [5]. 23636399. Structures of the human and Drosophila 80S ribosome. Anger AM, Armache JP, Berninghausen O, Habeck M, Subklewe M, Wilson DN, Beckmann R;. Nature. 2013;497:80-85. (from Pfam) NF028456.5 PF17147.9 PFOR_II 27 27 102 domain Y N N Pyruvate:ferredoxin oxidoreductase core domain II 10048931,20956531 131567 cellular organisms no rank 72589 EBI-EMBL Pyruvate:ferredoxin oxidoreductase core domain II Pyruvate:ferredoxin oxidoreductase core domain II PFOR_II is a core domain of the anaerobic enzyme pyruvate:ferredoxin oxidoreductase and is necessary for inter subunit contacts in conjunction with domains I and IV [1,2]. [1]. 10048931. Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate. Chabriere E, Charon MH, Volbeda A, Pieulle L, Hatchikian EC, Fontecilla-Camps JC;. Nat Struct Biol 1999;6:182-190. [2]. 20956531. Identification and characterization of oxalate oxidoreductase, a novel thiamine pyrophosphate-dependent 2-oxoacid oxidoreductase that enables anaerobic growth on oxalate. Pierce E, Becker DF, Ragsdale SW;. J Biol Chem. 2010;285:40515-40524. (from Pfam) NF028468.5 PF17159.9 MASE3 31 31 226 domain Y Y N MASE3 domain-containing protein 17628134 131567 cellular organisms no rank 5816 EBI-EMBL Membrane-associated sensor domain Membrane-associated sensor domain MASE3 (Membrane-Associated SEnsor) is an integral membrane sensor domain of unknown specificity found in histidine kinases, diguanylate cyclases and protein phosphatases in various bacteria and archaea [1]. [1]. 17628134. Identification of sensory and signal-transducing domains in two-component signaling systems. Galperin MY, Nikolskaya AN;. Methods Enzymol. 2007;422:47-74. (from Pfam) NF028473.5 PF17164.9 DUF5122 27 13.9 36 repeat Y N N delta-60 repeat domain-containing protein 131567 cellular organisms no rank 14447 EBI-EMBL Domain of unknown function (DUF5122) beta-propeller DUF5122 family beta-propeller repeat NF028476.5 PF17167.9 Glyco_hydro_36 27 27 420 domain Y Y N GH36-type glycosyl hydrolase domain-containing protein 15274915 131567 cellular organisms no rank 27387 EBI-EMBL Glycosyl hydrolase 36 superfamily, catalytic domain GH36-type glycosyl hydrolase domain This is the catalytic region of the superfamily of enzymes referred to as GH36. UniProtKB:Q76IQ9 is a chitobiose phosphorylase that catalyses the reversible phosphorolysis of chitobiose into alpha-GlcNAc-1-phosphate and GlcNAc with inversion of the anomeric configuration. The full-length enzyme comprises a beta sandwich domain and an (alpha/alpha)(6) barrel domain. The alpha-helical barrel component of the domain, this family, is the catalytic region [1]. [1]. 15274915. Chitobiose phosphorylase from Vibrio proteolyticus, a member of glycosyl transferase family 36, has a clan GH-L-like (alpha/alpha)(6) barrel fold. Hidaka M, Honda Y, Kitaoka M, Nirasawa S, Hayashi K, Wakagi T, Shoun H, Fushinobu S;. Structure. 2004;12:937-947. (from Pfam) NF028477.5 PF17168.9 DUF5127 28 28 229 domain Y Y N DUF5127 domain-containing protein 131567 cellular organisms no rank 4316 EBI-EMBL Domain of unknown function (DUF5127) Domain of unknown function (DUF5127) NF028479.5 PF17170.9 DUF5128 22.9 22.9 321 domain Y Y N 6-bladed beta-propeller 131567 cellular organisms no rank 18906 EBI-EMBL 6-bladed beta-propeller 6-bladed beta-propeller This family is a 6-bladed beta-propeller structure of unknown function. There is a highly conserved FDxxG motif which might be important. (from Pfam) NF028480.5 PF17171.9 GST_C_6 28 28 64 domain Y Y N glutathione S-transferase C-terminal domain-containing protein 21455499 131567 cellular organisms no rank 3522 EBI-EMBL Glutathione S-transferase, C-terminal domain Glutathione S-transferase, C-terminal domain This domain is closely related to PF00043. (from Pfam) NF028488.5 PF17179.9 Fer4_22 27 27 95 domain Y Y N 4Fe-4S dicluster domain-containing protein 131567 cellular organisms no rank 8532 EBI-EMBL 4Fe-4S dicluster domain 4Fe-4S dicluster domain NF028491.5 PF17182.9 OSK 27 27 202 domain Y N N OSK domain 26190108 131567 cellular organisms no rank 1780 EBI-EMBL OSK domain OSK domain This entry represents the OSK domain defined by Jeske and colleagues [1]. The domain is related to SGNH hydrolases but lacks the active site residues. The domain binds to RNA [1]. [1]. 26190108. The Crystal Structure of the Drosophila Germline Inducer Oskar Identifies Two Domains with Distinct Vasa Helicase- and RNA-Binding Activities. Jeske M, Bordi M, Glatt S, Muller S, Rybin V, Muller CW, Ephrussi A;. Cell Rep. 2015;12:587-598. (from Pfam) NF028495.5 PF17186.9 Lipocalin_9 26.2 26.2 131 domain Y Y N lipocalin family protein 20944205 131567 cellular organisms no rank 15756 EBI-EMBL Lipocalin-like domain Lipocalin-like domain This family contains the members of the old Pfam family DUF2006. Structural characterisation of family member Swiss:Q82US3 (from DUF2006 now merged into this family) has revealed a lipocalin-like fold with domain duplication. This entry represents the C-terminal domain of the pair. [1]. 20944205. Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism. Chiu HJ, Bakolitsa C, Skerra A, Lomize A, Carlton D, Miller MD, Krishna SS, Abdubek P, Astakhova T, Axelrod HL, Clayton T, Deller MC, Duan L, Feuerhelm J, Grant JC, Grzechnik SK, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Paulsen J, Reyes R, Rife CL, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:1153-1159. (from Pfam) NF028498.5 PF17189.9 Glyco_hydro_30C 22 22 65 domain Y Y N glycoside hydrolase family 30 beta sandwich domain-containing protein 12792654 131567 cellular organisms no rank 22197 EBI-EMBL Glycosyl hydrolase family 30 beta sandwich domain Glycosyl hydrolase family 30 beta sandwich domain NF028500.5 PF17191.9 RecG_wedge 23 23 162 domain Y N N RecG wedge domain 11595187 131567 cellular organisms no rank 81218 EBI-EMBL RecG wedge domain RecG wedge domain This DNA-binding domain has an OB-fold with large elaborations [1]. [1]. 11595187. Structural analysis of DNA replication fork reversal by RecG. Singleton MR, Scaife S, Wigley DB;. Cell. 2001;107:79-89. (from Pfam) NF028506.5 PF17197.9 DUF5134 29 29 152 PfamAutoEq Y Y N DUF5134 domain-containing protein 16122422 131567 cellular organisms no rank 10743 EBI-EMBL Domain of unknown function (DUF5134) Domain of unknown function (DUF5134) Proteins in this family are uncharacterised, but have been identified as members of a gene cluster for the synthesis of the tetramic-acid antibiotic streptolydigin, which inhibits bacterial RNA polymerase (RNAP) [1]. [1]. 16122422. Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Tuske S, Sarafianos SG, Wang X, Hudson B, Sineva E, Mukhopadhyay J, Birktoft JJ, Leroy O, Ismail S, Clark AD Jr, Dharia C, Napoli A, Laptenko O, Lee J, Borukhov S, Ebright RH, Arnold E;. Cell. 2005;122:541-552. (from Pfam) NF028509.5 PF17200.9 sCache_2 25 25 155 domain Y Y N cache domain-containing protein 27049771 131567 cellular organisms no rank 64923 EBI-EMBL Single Cache domain 2 Single Cache domain 2 This entry represents the single Cache domain 2 (sCache_2), which contains the long N-terminal helix domain [1]. This domain recognises pyruvate, acetate, propionate, glycolate, L-lactate, acetoacetate, urea and hydroxyurea, acetamide, formamide, L-malate and citromalate, malonate, methyl and bromosuccinate and citraconic acid (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 27049771. Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes. Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB;. PLoS Comput Biol. 2016;12:e1004862. (from Pfam) NF028510.5 PF17201.9 Cache_3-Cache_2 27.7 27.7 299 domain Y Y N Cache 3/Cache 2 fusion domain-containing protein 27049771 131567 cellular organisms no rank 65848 EBI-EMBL Cache 3/Cache 2 fusion domain Cache 3/Cache 2 fusion domain The Cache_3-Cache_2 domain likely originated as a fusion of sCache_3 and sCache_2 domains. [1]. 27049771. Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes. Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB;. PLoS Comput Biol. 2016;12:e1004862. (from Pfam) NF028511.5 PF17202.9 sCache_3_3 28.8 25 107 domain Y Y N cache domain-containing protein 27049771 131567 cellular organisms no rank 24995 EBI-EMBL Single cache domain 3 Single cache domain 3 NF028512.5 PF17203.9 sCache_3_2 28.4 28.4 140 domain Y N N Single cache domain 3 27049771 131567 cellular organisms no rank 86541 EBI-EMBL Single cache domain 3 Single cache domain 3 This domain is associated to sensor histidine kinases and recognises citrate and TCA cycle intermediates, Ag(II), Zn(II), Mg(II) (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 27049771. Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes. Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB;. PLoS Comput Biol. 2016;12:e1004862. (from Pfam) NF028516.5 PF17207.8 MCM_OB 24.8 24.8 126 domain Y N N MCM OB domain 12548282,24378617 131567 cellular organisms no rank 1908 EBI-EMBL MCM OB domain MCM OB domain This family contains an OB-fold found within MCM proteins. This domain contains an insertion at the zinc binding motif [2]. [1]. 12548282. The structure and function of MCM from archaeal M. Thermoautotrophicum. Fletcher RJ, Bishop BE, Leon RP, Sclafani RA, Ogata CM, Chen XS;. Nat Struct Biol. 2003;10:160-167. [2]. 24378617. The 1.8-A crystal structure of the N-terminal domain of an archaeal MCM as a right-handed filament. Fu Y, Slaymaker IM, Wang J, Wang G, Chen XS;. J Mol Biol. 2014;426:1512-1523. (from Pfam) NF028518.5 PF17209.8 Hfq 27 27 64 domain Y Y N RNA chaperone Hfq GO:0003723,GO:0006355 131567 cellular organisms no rank 17997 EBI-EMBL Hfq protein RNA chaperone Hfq NF028519.5 PF17210.8 SdrD_B 29.7 29.7 112 domain Y Y N SdrD B-like domain-containing protein 131567 cellular organisms no rank 50515 EBI-EMBL SdrD B-like domain SdrD B-like domain This family corresponds to the B-like domain from the SdrD protein. This domain has three calcium binding sites within a greek key beta sandwich fold. (from Pfam) NF028523.5 PF17214.8 KH_7 22.6 22.6 68 domain Y N N KH domain 21565697 131567 cellular organisms no rank 1478 EBI-EMBL KH domain KH domain NF028534.5 PF17225.8 DUF5301 23.1 23.1 97 PfamAutoEq Y Y N DUF5301 domain-containing protein 131567 cellular organisms no rank 1054 EBI-EMBL Domain of unknown function (DUF5300) DUF5301 domain-containing protein This small family of proteins is functionally uncharacterized. It is found mainly in Firmicutes. Proteins in this family are around 130 amino acids in length. Based on NMR structure 2MCT, it forms an alpha/beta structure with a 6 stranded antiparallel b-sheet planked by a single alpha helix. The only protein with similar structures is a putative lipoprotein (PDB code 4R7R). (from Pfam) NF033200.1 F430_CfbC 402 402 260 exception Y Y N Ni-sirohydrochlorin a,c-diamide reductive cyclase ATP-dependent reductase subunit cfbC 131567 cellular organisms no rank 434 NCBIFAM Ni-sirohydrochlorin a,c-diamide reductive cyclase ATP-dependent reductase subunit Ni-sirohydrochlorin a,c-diamide reductive cyclase ATP-dependent reductase subunit This family, very closely related to the nitrogenase iron protein, was identified as a subunit involved in biosynthesis of coenzyme F430 in archaeal methanogens and archaeal anaerobic methanotrophs. NF033208.1 choice_anch_E 23.8 23.8 172 domain Y Y N choice-of-anchor E domain-containing protein 131567 cellular organisms no rank 952 NCBIFAM choice-of-anchor E domain choice-of-anchor E domain-containing protein This HMM describes a domain just over 100 amino acids long and usually found in tandem copies. Members appear to be extracellular proteins that have some C-terminal anchoring domain, usually PEP-CTERM but occasionally a type IX secrection (T9SS) recognition domain. NF033223.2 YHYH_alt 30 30 25 domain Y Y N YHYH domain-containing protein 131567 cellular organisms no rank 4195 NCBIFAM YHYH domain-containing protein YHYH domain Proteins with this form of YHYH motif-containing domain have it located near the N-terminus of a protein just after a signal peptide region. The domain has two characteristic motifs, GxC and YH[YC]H, separated by a short spacer region of variable length. A different family of YHYH domain-domaining proteins, in which the YHYH domain is more C-terminal and is repeated, is described by Pfam model PF14240. NF033379.1 FrucBisAld_I 250 250 324 equivalog Y Y N class I fructose-bisphosphate aldolase 4.1.2.13 GO:0004332,GO:0006096 131567 cellular organisms no rank 6002 NCBIFAM fructose-bisphosphate aldolase class I class I fructose-bisphosphate aldolase This family consists of fructose-bisphosphate aldolase class I. All members of the seed alignment are from prokaryotes, although class I is the common form in plants and animals. The common form in prokaryotes is class II. NF033432.0 ThioGly_TfuA_rel 235.2 235.2 211 equivalog Y Y N TfuA-related McrA-glycine thioamidation protein 28880150 131567 cellular organisms no rank 467 NCBIFAM TfuA-related McrA-glycine thioamidation protein TfuA-related McrA-glycine thioamidation protein NF033438.1 BREX_BrxD 350 350 423 equivalog Y Y N BREX system ATP-binding protein BrxD brxD 25452498 131567 cellular organisms no rank 3007 NCBIFAM BREX system ATP-binding protein BrxD BREX system ATP-binding protein BrxD BrxD is an ATP-binding protein found in types 2 and 6 of BREX (bacteriophage exclusion) phage resistance systems. NF033441.0 BREX_BrxC 400 400 1173 hypoth_equivalog Y Y N BREX system P-loop protein BrxC brxC 25452498 131567 cellular organisms no rank 7941 NCBIFAM BREX system P-loop protein BrxC BREX system P-loop protein BrxC BrxC is a P-loop-containing protein, and probable ATPase, from BREX (bacteriophage exclusion) systems of type 1. NF033444.1 BREX_PglZ_5 250 250 704 exception Y Y N BREX-5 system phosphatase PglZ pglZ 25452498 131567 cellular organisms no rank 151 NCBIFAM BREX-5 system phosphatase PglZ BREX-5 system phosphatase PglZ NF033445.1 BREX_PglZ_4 140 140 741 exception Y Y N BREX-4 system phosphatase PglZ pglZ 25452498 131567 cellular organisms no rank 364 NCBIFAM BREX-4 system phosphatase PglZ BREX-4 system phosphatase PglZ NF033447.1 BrxE_fam 40 40 169 subfamily Y Y N BrxE family protein 131567 cellular organisms no rank 612 NCBIFAM BrxE family protein BrxE family protein This family is uncharacterized, but a subgroup within this family is BrxE, a protein of unknown function found in type 6 BREX phage resistance systems. NF033449.0 BREX_PglZ_3 250 250 642 exception Y Y N BREX-3 system phosphatase PglZ pglZ 25452498 131567 cellular organisms no rank 1007 NCBIFAM BREX-3 system phosphatase PglZ BREX-3 system phosphatase PglZ BREX is a phage defense system (BacteRiophage EXclusion), with a number of described subtypes. The first described, PGL (phage growth limitation), is not called BREX-2. This model describes one of the two core proteins universal across the first six defined BREX subtypes, the phosphatase-like PglZ domain protein, as found in BREX-3 systems. NF033450.1 BREX_PglZ_1_B 400 400 675 equivalog Y Y N BREX-1 system phosphatase PglZ type B pglZ 25452498 131567 cellular organisms no rank 901 NCBIFAM BREX-1 system phosphatase PglZ type B BREX-1 system phosphatase PglZ type B BREX (bacteriophage exclusion) is a phage resistance resistance, in which two protein families are core but other proteins are variable. BREX subtypes are based on PglZ domain protein, a putative phosphatase. This family is one of two major subtypes of PglZ as seen in type 1 BREX systems. Most members of this family contain an additional C-terminal domain that is not included in the seed alignment. Family TIGR02687 describes the alternative type A for PglZ of BREX-1. NF033452.1 BREX_1_MTaseX 500 500 1210 exception Y Y N BREX-1 system adenine-specific DNA-methyltransferase PglX pglX 2.1.1.72 GO:0003677,GO:0008170 25452498 131567 cellular organisms no rank 8356 NCBIFAM BREX-1 system adenine-specific DNA-methyltransferase PglX BREX-1 system adenine-specific DNA-methyltransferase PglX This protein, PglX, is a site-specific DNA methyltransferase associated BREX (bacteriophage exclusion) type 1 systems. The phage resistance appears not to be through restriction-modification, as phage DNA appears not to get degraded, but it does manage to inhibit phage replication. NF033453.1 BREX_3_BrxF 50 50 149 hypoth_equivalog Y Y N BREX-3 system P-loop-containing protein BrxF brxF 131567 cellular organisms no rank 1156 NCBIFAM BREX-3 system P-loop-containing protein BrxF BREX-3 system P-loop-containing protein BrxF This family of proteins that are about 150 amino acids in length includes BrxF from type 3 BREX (bacteriophage exclusion) systems. Most members have the P-loop motif GxxGxGKT, but the region is surprisingly poorly conserved in a sizable fraction of otherwise strongly similar proteins. NF033454.1 BREX_5_MTaseX 900 900 1404 exception Y Y N BREX-5 system adenine-specific DNA-methyltransferase PglX pglX 2.1.1.72 131567 cellular organisms no rank 179 NCBIFAM BREX-5 system adenine-specific DNA-methyltransferase PglX BREX-5 system adenine-specific DNA-methyltransferase PglX NF033474.1 DivGenRetAVD 80 80 104 equivalog Y Y N diversity-generating retroelement protein Avd avd 131567 cellular organisms no rank 948 NCBIFAM diversity-generating retroelement protein Avd diversity-generating retroelement protein Avd Avd (accessory variability determinant) is part of diversity-generating retroelement (GDR) system through which a portion of a protein-coding gene can be rewritten, creating diversity that can affect host range. The founding member of this family, bAvd, from a Bordetella bacteriophage, belongs to a retrohoming element called BPP-1. Members of this family are four-helix bundle proteins, related to those of family TIGR02436, some of whose members are found in long intervening sequence (IVS) regions in 23S rRNA. NF033480.1 bifunc_MprF 600 600 841 equivalog Y Y N bifunctional lysylphosphatidylglycerol flippase/synthetase MprF mprF 131567 cellular organisms no rank 18118 NCBIFAM bifunctional lysylphosphatidylglycerol flippase/synthetase MprF bifunctional lysylphosphatidylglycerol flippase/synthetase MprF The C-terminal region of MprF tranfers lysine from a charged tRNA onto phosphatidylglycerol to make lysylphosphatidylglycerol (EC 2.3.2.3). The N-terminal region of MprF acts as a flippase. MprF helps confer resistance to antimicrobial cationic peptides. NF033484.1 Stp1_PP2C_phos 230 230 232 equivalog Y Y N Stp1/IreP family PP2C-type Ser/Thr phosphatase GO:0004722,GO:0006470 22045988 131567 cellular organisms no rank 19062 NCBIFAM Stp1/IreP family PP2C-type Ser/Thr phosphatase Stp1/IreP family PP2C-type Ser/Thr phosphatase Many Gram-positive bacteria have a protein kinase/protein phosphatase gene pair that responds to peptidoglycan metabolites and can be instrumental in resistance to beta-lactam antibiotics. Characterized examples of the phosphatase component are Stp1 of Staphylococcus aureus and IreP of Enterococcus faecalis. NF033488.1 lmo0937_fam_TM 30 30 43 equivalog Y Y N lmo0937 family membrane protein 22128349 131567 cellular organisms no rank 6209 NCBIFAM lmo0937 family membrane protein lmo0937 family membrane protein Members of this family are very small (about 45 amino acids) and highly hydrophobic, suggesting a presence in the membrane, and have a broad phylogenetic distribution. The member protein lmo0937, from the pathogen Listeria monocytogenes, is described as up-regulated when the bacterium is in the mouse spleen, suggesting a role in stress response. NF033493.0 MetS_like_NSS 25 25 30 subfamily Y Y N MetS family NSS transporter small subunit 18991398 131567 cellular organisms no rank 4687 NCBIFAM MetS family NSS transporter small subunit MetS family NSS transporter small subunit MetS, as described in the Gram-positive bacterium Corynebacterium glutamicum, is the small subunit of MetPS, an NSS (Neurotransmitter:Sodium Symporter) transporter involved in methionine and alanine import. While MetS itself is small, only 60 amino acids, homologs in gamma proteobacteria such as Vibrio sp., similarly found next to an NSS transporter large subunit, may be barely half that length and consist almost entirely of a predicted hydrophobic region that would localize to within the plasma membrane. NF033496.0 DUF2080_fam_acc 22 22 34 subfamily Y Y N DUF2080 family transposase-associated protein 131567 cellular organisms no rank 622 NCBIFAM DUF2080 family transposase-associated protein DUF2080 family transposase-associated protein Members of this family appear restricted to the archaea. They tend to be encoded upstream of predicted transposase genes within insertion sequences such as ISNagr11, ISHca1, ISH36, etc. The widespread distribution suggests this protein may be more than a mere passenger gene and may participate in some transposase-associated function. See PF09853, COG3466, and arCOG03884 for alternative (currently narrow) treatments of this family. NF033497.1 rubre_like_arch 32 32 34 subfamily_domain Y Y N rubrerythrin-like domain-containing protein 131567 cellular organisms no rank 1217 NCBIFAM rubrerythrin-like domain-containing protein rubrerythrin-like domain This rubrerythrin-like domain is found primarily in the archaea, occasionally as part of a larger redox-active protein. It features two CxxC motifs with a spacer of 12 to 13 amino acids. NF033503.1 LarB 175 175 209 equivalog Y Y N nickel pincer cofactor biosynthesis protein LarB larB GO:0016787 10348865,16166538,24710389,27114550 131567 cellular organisms no rank 11041 NCBIFAM nickel pincer cofactor biosynthesis protein LarB nickel pincer cofactor biosynthesis protein LarB This protein, related to AIR carboxylase, is part of a three protein system involved in producing a specialized nicotinic acid-derived, nickel-containing cofactor, as used in the nickel-dependent lactate racemase of lactic acid bacteria. NF033504.1 Ni_dep_LarA 270 270 418 equivalog Y Y N nickel-dependent lactate racemase larA GO:0050043 131567 cellular organisms no rank 6869 NCBIFAM nickel-dependent lactate racemase nickel-dependent lactate racemase LarA from Lactobacillus plantarum is a nickel-dependent lactate racemase and the founding member of a family of isomerases that depend on a nicotinic acid-derived nickel pincer cofactor. While it is not yet clear which homologs of LarA act preferentially on lactate, this model identifies one clade of architecurally similar proteins from among a broader set of LarA homologs. Note that the crystal structure 4NAR, on deposit at PDB but not associated with any publication, represents a protein from Thermotoga maritima that falls outside the scope of this family and that is annotated in PDB as a putative uronate isomerase. NF033507.2 Loki-CTERM 23 23 27 subfamily_domain Y Y N Loki-CTERM sorting domain-containing protein 22037399 131567 cellular organisms no rank 17 NCBIFAM Loki-CTERM sorting domain-containing protein Loki-CTERM protein-sorting domain This C-terminal protein-sorting signal appears restricted to the Asgard archaea, including the Lokiarchaeota, but resembles the PGF-CTERM sorting signal found on the S-layer-forming major cell surface glycoprotein of halophilic archaea. The most likely sorting enzyme is archaeosortase H (ArtH, model NF041736), which is most closely related to ArtA, the processing enzyme for PGF-CTERM. Note that most Asgard archaeal sequence available to date comes from metagenome-assembled genomes rather than from cultured isolates. The closed genome of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 encodes more than 30 Loki-CTERM sorting domain-containing proteins. NF033516.0 transpos_IS3 160 140 369 equivalog Y Y N IS3 family transposase GO:0004803 131567 cellular organisms no rank 205203 NCBIFAM IS3 family transposase IS3 family transposase NF033517.1 transpos_IS66 180 180 387 equivalog Y Y N IS66 family transposase tnpC GO:0004803 16381877,20079432 131567 cellular organisms no rank 56881 NCBIFAM IS66 family transposase IS66 family transposase Members of this protein family are DDE transposases from the IS66 family insertion sequences, which typically consist of two accessary genes (TnpA and TnpB) and the third gene encoding the transposase. NF033518.0 transpos_IS607 110 110 187 equivalog Y Y N IS607 family transposase GO:0004803 131567 cellular organisms no rank 9564 NCBIFAM IS607 family transposase IS607 family transposase NF033519.0 transpos_ISAzo13 200 200 387 equivalog Y Y N ISAzo13 family transposase GO:0004803 131567 cellular organisms no rank 3173 NCBIFAM ISAzo13 family transposase ISAzo13 family transposase NF033520.1 transpos_IS982 130 130 243 equivalog Y Y N IS982 family transposase GO:0004803 131567 cellular organisms no rank 15285 NCBIFAM IS982 family transposase IS982 family transposase Currently, there are 46 seed sequences in this family. NF033521.1 lasso_leader_L3 19 19 20 domain Y Y N lasso RiPP family leader peptide-containing protein 25601074,26079760,28244986 131567 cellular organisms no rank 3297 NCBIFAM lasso RiPP family leader peptide-containing protein lasso RiPP family leader peptide NF033535.1 lass_lactam_cya 525 525 668 exception Y Y N lasso peptide isopeptide bond-forming cyclase 131567 cellular organisms no rank 569 NCBIFAM lasso peptide isopeptide bond-forming cyclase lasso peptide isopeptide bond-forming cyclase Members of this family are the isopeptide bond-forming cyclase of lasso peptide biosynthesis systems, from a subgroup that contains primarily cyanobacterial examples. These proteins resemble the glutamine-hydrolyzing asparagine synthase AsnB (EC 6.3.5.4). NF033536.1 lasso_PqqD_Bac 80 80 88 exception Y Y N lasso peptide biosynthesis PqqD family chaperone 131567 cellular organisms no rank 1525 NCBIFAM lasso peptide biosynthesis PqqD family chaperone lasso peptide biosynthesis PqqD family chaperone Members of this family are homologs of PqqD, a chaperone that binds RiPP peptide precursors for their modification into bioactive natural products. By context, this set is involved in the biosynthesis of threaded-lasso peptides. This model focuses on lasso peptide systems from Firmicutes. Similar systems, with different subfamilies of PqqD-related peptides, occur in lasso peptide systems in other lineages. NF033537.1 lasso_biosyn_B2 33 33 132 equivalog_domain Y Y N lasso peptide biosynthesis B2 protein 26079760,27800552 131567 cellular organisms no rank 12971 NCBIFAM lasso peptide biosynthesis B2 protein lasso peptide biosynthesis B2 protein NF033539.1 transpos_IS1380 180 180 419 equivalog Y Y N IS1380 family transposase GO:0004803 16381877 131567 cellular organisms no rank 15146 NCBIFAM IS1380 family transposase IS1380 family transposase Proteins of this family are DDE type transposases, which are encoded by IS1380 family elements. It was first identified and characterized in an Acetobacter pasteurianus mutant with ethanol oxidation deficiency caused by disruption of the cytochrome c gene by the IS1380 element. NF033540.1 transpos_IS701 180 180 345 equivalog Y Y N IS701 family transposase GO:0004803 131567 cellular organisms no rank 17654 NCBIFAM IS701 family transposase IS701 family transposase Members of this family are transposases in the family of that of insertion element IS701, narrowly defined. Note that a molecular phylogenetic tree of the broader sets of transposases from IS elements classified as IS701 family or IS4 family by ISFINDER shows the two groups interleaved. This model represents an unambiguous clade that includes IS701 itself and the majority of proteins called IS701 family. The poorly conserved C-terminal region of members of this family is not included in the seed alignment. NF033541.0 transpos_ISH3 225 225 298 equivalog Y Y N ISH3 family transposase GO:0004803 131567 cellular organisms no rank 874 NCBIFAM ISH3 family transposase ISH3 family transposase This family contains transposases from the insertion element ISH3, and related transposases from other mobile elements with similar transposases. This model reproduces the classification from ISFinder except for ISC1439B-like transposases, since those are extremely different. NF033542.1 transpos_IS110 140 140 343 equivalog Y Y N IS110 family transposase GO:0004803 16381877 131567 cellular organisms no rank 110443 NCBIFAM IS110 family transposase IS110 family transposase Proteins of this family are DEDD (Asp, Glu, Asp, Asp) type transposases, which are encoded by the IS110 family elements. NF033543.1 transpos_IS256 225 225 410 equivalog Y Y N IS256 family transposase GO:0004803 131567 cellular organisms no rank 48520 NCBIFAM IS256 family transposase IS256 family transposase Members of this family belong to the branch of the IS256-like family of transposases that includes the founding member. It excludes the IS1249 group. NF033545.0 transpos_IS630 100 100 299 equivalog Y Y N IS630 family transposase GO:0004803 131567 cellular organisms no rank 49843 NCBIFAM IS630 family transposase IS630 family transposase NF033546.1 transpos_IS21 160 160 294 equivalog Y Y N IS21 family transposase istA GO:0004803 131567 cellular organisms no rank 45250 NCBIFAM IS21 family transposase IS21 family transposase NF033547.1 transpos_IS1595 75 75 215 equivalog_domain Y Y N IS1595 family transposase GO:0004803 131567 cellular organisms no rank 23039 NCBIFAM IS1595 family transposase IS1595 family transposase Most transposases of this family of transposases, IS1595, have an additional short N-terminal domain with a pair of CxxC motifs. NF033550.5 transpos_ISL3 180 180 370 equivalog Y Y N ISL3 family transposase GO:0004803 131567 cellular organisms no rank 46146 NCBIFAM ISL3 family transposase ISL3 family transposase NF033551.1 transpos_IS1182 270 270 488 equivalog Y Y N IS1182 family transposase GO:0004803 131567 cellular organisms no rank 31156 NCBIFAM IS1182 family transposase IS1182 family transposase Members of this family are transposases of the IS1182 family. About two-thirds of the members of this family have an extra domain between the middle and the C-terminal domain, about 50 amino acids in size and containing four invariant Cys residues. NF033559.1 transpos_IS1634 100 100 463 equivalog Y Y N IS1634 family transposase GO:0004803 16381877 131567 cellular organisms no rank 14150 NCBIFAM IS1634 family transposase IS1634 family transposase Members of this protein family are DDE type transposases encoded by the IS1634 family elements, which were firstly identified and characterized in Mycoplasma mycoides. NF033563.0 transpos_IS30 80 80 267 equivalog Y Y N IS30 family transposase GO:0004803 131567 cellular organisms no rank 77166 NCBIFAM IS30 family transposase IS30 family transposase NF033564.0 transpos_ISAs1 70 70 314 equivalog Y Y N ISAs1 family transposase GO:0004803 131567 cellular organisms no rank 43088 NCBIFAM ISAs1 family transposase ISAs1 family transposase NF033573.1 transpos_IS200 55 55 126 equivalog Y Y N IS200/IS605 family transposase tnpA GO:0004803 22367867,23548000 131567 cellular organisms no rank 45934 NCBIFAM IS200/IS605 family transposase IS200/IS605 family transposase Most IS200/IS605 family insertion sequences encode both this transposase, TnpA, about 130 amino acids long, and larger accessory protein, TnpB, that may act as a methyltransferase. NF033576.1 mCpol 40 40 118 domain Y Y N mCpol domain-containing protein 26590262 131567 cellular organisms no rank 419 NCBIFAM mCpol domain-containing protein mCpol domain The mCpol domain (minimal CRISPR polymerase) is named for its homology relationship to catalytic domain of the CRISPR polymerases (often called Cmr2 or Cas10). It is predicted to generate cyclic nucleotides, potentially sensed by CARF domains which in turn activate various effector domain including HEPN RNases, CARF sensor and effectors are found in conserved genome contexts. It is part of a broader class of conflict systems reliant on the production of second messenger nucleotide or nucleotide derivatives. The putative function of the mCpol domain implies that CRISPR polymerases of the type III CRISPR/Cas systems have a nucleotide synthetase functional role. NF033577.2 transpos_IS481 224 224 284 equivalog Y Y N IS481 family transposase GO:0004803 131567 cellular organisms no rank 24762 NCBIFAM IS481 family transposase IS481 family transposase null NF033579.1 transpos_IS5_2 140 140 289 equivalog Y Y N IS5 family transposase GO:0004803 131567 cellular organisms no rank 29124 NCBIFAM IS5 family transposase IS5 family transposase NF033580.1 transpos_IS5_3 110 110 258 equivalog Y Y N IS5 family transposase GO:0004803 131567 cellular organisms no rank 77903 NCBIFAM IS5 family transposase IS5 family transposase NF033581.1 transpos_IS5_4 140 140 285 equivalog Y Y N IS5 family transposase GO:0004803 131567 cellular organisms no rank 29769 NCBIFAM IS5 family transposase IS5 family transposase NF033587.1 transpos_IS6 125 125 202 equivalog Y Y N IS6 family transposase GO:0004803 131567 cellular organisms no rank 36925 NCBIFAM IS6 family transposase IS6 family transposase NF033590.1 transpos_IS4_3 160 160 405 equivalog Y Y N IS4 family transposase GO:0004803 131567 cellular organisms no rank 5765 NCBIFAM IS4 family transposase IS4 family transposase NF033592.1 transpos_IS4_1 115 115 332 equivalog Y Y N IS4 family transposase GO:0004803 131567 cellular organisms no rank 36442 NCBIFAM IS4 family transposase IS4 family transposase NF033610.1 SLATT_3 45 45 170 domain Y Y N SLATT domain-containing protein 26590262 131567 cellular organisms no rank 3757 NCBIFAM SLATT domain-containing protein SLATT domain The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is always N-terminally fused to the SLATT_1 family, and is typically operonically linked to either inactive TIR domains or SLOG domains which could act as regulators of the SLATT channels. The SLATT domain defined here (170 residues long) is similar to the DUF4231 domain (105 residues long) described in Pfam model PF14015. NF033611.0 SAVED 33 33 261 domain Y Y N SAVED domain-containing protein 26590262 131567 cellular organisms no rank 5889 NCBIFAM SAVED domain-containing protein SAVED domain The SAVED (SMODS-Associated and fused to Various Effector Domains) domain is predicted to function as a sensor domain, sensing nucleotides or nucleotide derivatives generated by SMODS and other nucleotide synthetase domains. The sensing of ligands by SAVED is predicted to activate effectors deployed by a class of conflict systems which are reliant on the on the production and sensing of the nucleotide second messengers. NF033632.1 SLATT_4 55 55 154 domain Y Y N SLATT domain-containing protein 26590262 131567 cellular organisms no rank 3432 NCBIFAM SLATT domain-containing protein SLATT domain The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is often coupled to the SMODS nucleotide synthetase and is sometimes further embedded in other conflict systems like CRISPR/Cas or R-M systems. NF033634.1 SLATT_1 41 41 132 domain Y Y N SLATT domain-containing protein 26590262 131567 cellular organisms no rank 11012 NCBIFAM SLATT domain-containing protein SLATT domain The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is often C-terminally fused to the SLATT_3 family, and is typically operonically linked to either inactive TIR domains or SLOG domains which could act as regulators of the SLATT channels. In relatively rare instances, it is genomically linked as a standalone domain to the RelA/SpoT nucleotide synthetase and the predicted NA37/YejK sensor domain. NF033656.1 DMQ_monoox_COQ7 180 180 205 equivalog Y Y N 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone monooxygenase coq7 GO:0004497,GO:0006744 11749961,28927698 131567 cellular organisms no rank 8429 NCBIFAM 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone monooxygenase 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone monooxygenase NF033678.1 C69_fam_dipept 250 250 464 equivalog Y Y N C69 family dipeptidase 3.4.13.- GO:0006508,GO:0016805 17601807,8766699 131567 cellular organisms no rank 16505 NCBIFAM C69 family dipeptidase C69 family dipeptidase Members of the MEROPS C69 family (subfamily 001) are dipeptidases (EC 3.4.13.-). NF033679.1 DNRLRE_dom 34 34 164 domain Y Y N DNRLRE domain-containing protein 18629042,19054745 131567 cellular organisms no rank 34234 NCBIFAM DNRLRE domain-containing protein DNRLRE domain The DNRLRE domain, with a length of about 160 amino acids, appears typically in large, repetitive surface proteins of bacteria and archaea, sometimes repeated several times. It occurs, notably, three times in the C-terminal region of the enzyme disaggregatase from the archaeal species Methanosarcina mazei, each time with the motif DNRLRE, for which the domain is named. Archaeal proteins within this family are described particularly well by the currently more narrowly defined Pfam model, PF06848. Note that the catalytic region of disaggregatase, in the N-terminal portion of the protein, is modeled by a different HMM, PF08480. NF033681.1 ExeM_NucH_DNase 300 300 546 subfamily_domain Y Y N ExeM/NucH family extracellular endonuclease 30123203,8682799 131567 cellular organisms no rank 21284 NCBIFAM ExeM/NucH family extracellular endonuclease ExeM/NucH family extracellular endonuclease NF033684.1 suffix_2_RND 40 40 69 domain Y Y N transporter suffix domain-containing protein 131567 cellular organisms no rank 1555 NCBIFAM transporter suffix domain-containing protein transporter suffix domain Members of this protein family contain a highly hydrophobic region about 70 amino acids long that usually occurs as essentially the full length of a small membrane protein, but in some cases occurs as a C-terminal suffix domain for RND efflux transporter permease subunit proteins. NF033727.1 chaperon_ArsD 95 95 96 equivalog Y Y Y arsenite efflux transporter metallochaperone ArsD arsD GO:0003677,GO:0046685 17030823,17439954,21188475 131567 cellular organisms no rank 4972 NCBIFAM arsenite efflux transporter metallochaperone ArsD arsenite efflux transporter metallochaperone ArsD ArsD, previously widely viewed as a transcriptional regulator involved in arsenic (and antimony) resistance, is now recognized as a metallochaperone that helps pass arsenite, which is As(III), to ArsA, a component of the arsenite/antimonite efflux pump. A motif CCxxxxC near the amino terminus mediates binding to arsenic atoms, but most ArsD have one or two additional pairs of adjacent Cys residues near the C-terminal end of the protein. NF033749.1 bact_hemeryth 84 84 129 subfamily_domain Y Y N bacteriohemerythrin GO:0046872 22484247,25890483 131567 cellular organisms no rank 11485 NCBIFAM bacteriohemerythrin bacteriohemerythrin Bacteriohemerythrin, an O2-carrying protein that lacks a heme moiety, is named based on its homology to eukaryotic proteins such as myohemerythrin. NF033768.1 myxo_SS_tail 40 40 92 domain Y Y N AgmX/PglI C-terminal domain-containing protein 20487265,26132848 131567 cellular organisms no rank 3989 NCBIFAM AgmX/PglI C-terminal domain-containing protein AgmX/PglI C-terminal domain The AgmX/PglI C-terminal domain described by this HMM (myxo_SS_tail) occurs as the C-terminal domain in multiple proteins per genome for a number of species capable of surface gliding motility, e.g. 12 in Myxococcus xanthus. Member proteins include the adventurous gliding motility proteins AgmX (GltJ) and PglI in M. xanthus. The domain is about 92 amino acids long, and features a pair of Cys residues about 45 amino acids apart in almost all cases. NF033788.1 HTH_metalloreg 55 55 77 subfamily Y Y N metalloregulator ArsR/SmtB family transcription factor GO:0003700,GO:0006355 12829264,30191942 131567 cellular organisms no rank 314452 NCBIFAM metalloregulator ArsR/SmtB family transcription factor metalloregulator ArsR/SmtB family transcription factor Transcriptional repressors that sense toxic heavy metals such as arsenic or cadmium, and are released from DNA so that resistance factors will be expressed, include ArsR, SmtB, ZiaR, CadC, CadX, KmtR, etc. However, some members of this family, including the sporulation delaying system autorepressor SdpR and its family (see NF033789), may lack metal-binding cites and instead regulate other cellular processes. NF033789.1 repress_SdpR 100 100 79 subfamily Y Y N autorepressor SdpR family transcription factor GO:0003700,GO:0006355 16469701 131567 cellular organisms no rank 4267 NCBIFAM autorepressor SdpR family transcription factor autorepressor SdpR family transcription factor Transcription factors in the family of the sporulation delaying system autorepressor SdpR (of Bacillus subtilis) resemble metalloregulatory transcriptional repressors such as ArsR, SmtB, CadX, ZiaR, etc., but may lack the key metal-binding residues. NF033819.0 IS66_TnpB 50 50 90 equivalog Y Y N IS66 family insertion sequence element accessory protein TnpB tnpB 11418571 131567 cellular organisms no rank 40312 NCBIFAM IS66 family insertion sequence element accessory protein TnpB IS66 family insertion sequence element accessory protein TnpB The IS66 family insertion sequence element encodes a DDE transposase TnpC, and two accessory proteins, TnpA and TnpB. It has been assumed that the TnpA, TnpB, and TnpC proteins are produced independently in appropriate amounts and form a complex, which acts as a transposase to promote the transposition of an IS66 family element. TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase. NF033823.0 archmetzin 145 145 170 subfamily Y Y N archaemetzincin family Zn-dependent metalloprotease GO:0006508,GO:0008233,GO:0008237,GO:0008270 20597090 131567 cellular organisms no rank 992 NCBIFAM archaemetzincin family Zn-dependent metalloprotease archaemetzincin family Zn-dependent metalloprotease NF033832.1 sce7726_fam 70 70 184 subfamily Y Y N sce7726 family protein 131567 cellular organisms no rank 6004 NCBIFAM sce7726 family protein sce7726 family protein This family of uncharacterized proteins is named for founding member sce7726 from Sorangium cellulosum, from the Deltaproteobacteria. It belongs a gene pair found sporadically in genera as diverse as Enterococcus, Lactobacillus, Staphylococcus, Streptococcus, Acinetobacter, and Klebsiella, or in phage from those lineages. The partner in each gene pair is a member of the sce7725 family. NF033846.1 Rumino_NPXTG 23.5 23.5 30 domain Y Y N NPXTG-anchored protein 131567 cellular organisms no rank 1133 NCBIFAM NPXTG-anchored protein NPXTG family C-terminal sorting domain Rumino_NPXTG represents a flavor of C-terminal protein sorting signal in species related to Ruminococcus albus. In that lineage, multiple sortases per genome may be found, including multiple B-type sortases. Proteins found by this HMM (more than 12 encoded in a representative complete genome) may represent substrates of a panel of related sortases, while additional proteins found in Ruminococcus genomes with below-cutoff hits to this model may be processed by other sortases. NF033859.1 SMEK_N 30 30 97 domain Y Y N SMEK domain-containing protein 131567 cellular organisms no rank 3341 NCBIFAM SMEK domain-containing protein SMEK domain The SMEK domain is named for four genera in which multiple, diverse members of this uncommon family of bacterial proteins are found: Staphylococcus, Mycoplasma, Escherichia, and Klebsiella. Members of the family are highly variable in length. This domain occurs as the N-terminal region. The four scattered invariant residues in the seed alignment, which may provide a clue to function, are Glu, Asp, Gln, and Lys. NF033912.1 msc 100 100 365 subfamily Y Y N mechanosensitive ion channel GO:0008381,GO:0055085 131567 cellular organisms no rank 5580 NCBIFAM mechanosensitive ion channel mechanosensitive ion channel Proteins of this subfamily are mechanosensitive channels, involved in numerous biological functions. Representative proteins of this subfamily are WP_092311603 and WP_068170239 (TCDB accession: 1.A.23.8.3 and 1.A.23.8.5, respectively). NF033936.1 CuZnOut_SO0444 300 300 351 equivalog Y Y N SO_0444 family Cu/Zn efflux transporter 22125499 131567 cellular organisms no rank 2188 NCBIFAM SO_0444 family Cu/Zn efflux transporter SO_0444 family Cu/Zn efflux transporter Members of this family are apparent metal cation efflux transporters. Architectural features include an average length of about 400 residues, with well conserved and highly hydrophobic N-terminal and C-terminal domains. The central region is highly variable in length and sequence, and rich in both Cys and His residues, as often seen in proteins produced in response to toxic concentrations of certain metals. The founding member, SO_0444, was shown to confer resistance to high levels of Cu and Zn ions. The best conserved region of the protein is a CSCG motif in the N-terminal region, found at least twice as in a selenocysteine-containing form, USCG. NF033952.2 AcrID1_fam 30 30 93 equivalog Y Y N AcrID1 family anti-CRISPR protein 29507349 131567 cellular organisms no rank 15 NCBIFAM AcrID1 family anti-CRISPR protein The AcrID1 family of anti-CRISPR proteins occurs in virus infecting the Archaea, primarily Sulfolobus. It targets and inactivates type I-D CRISPR-Cas systems. NF036294.5 PF17253.7 DUF5320 27 27 99 domain Y Y N DUF5320 family protein 131567 cellular organisms no rank 1245 EBI-EMBL Family of unknown function (DUF5320) DUF5320 family protein A number of this family members have a coiled coil domain at the C terminal. (from Pfam) NF036305.5 PF17297.7 PEPCK_N 23.8 23.8 218 domain Y N N Phosphoenolpyruvate carboxykinase N-terminal domain GO:0004611,GO:0006094 131567 cellular organisms no rank 24271 EBI-EMBL Phosphoenolpyruvate carboxykinase N-terminal domain Phosphoenolpyruvate carboxykinase N-terminal domain Catalyses the formation of phosphoenolpyruvate by decarboxylation of oxaloacetate. (from Pfam) NF036309.5 PF17310.7 DUF5357 25 25 322 domain Y Y N DUF5357 family protein 131567 cellular organisms no rank 588 EBI-EMBL Family of unknown function (DUF5357) DUF5357 family protein This is a family of unknown function found in Cyanobacteria. Most of the family members are predicted to have several trans-membrane regions. (from Pfam) NF036314.5 PF17338.7 GP88 26 26 231 domain Y Y N GP88 family protein 131567 cellular organisms no rank 1002 EBI-EMBL Gene product 88 GP88 family protein This family of unknown function is found in Bacteria. (from Pfam) NF036315.5 PF17341.7 DUF5371 25 25 65 subfamily Y Y N DUF5371 family protein 131567 cellular organisms no rank 73 EBI-EMBL Family of unknown function (DUF5371) DUF5371 family protein This is a family of unknown function found in Euryarchaeota. (from Pfam) NF036323.5 PF17367.7 NiFe_hyd_3_EhaA 25.5 25.5 97 PfamEq Y Y N energy-converting NiFe hydrogenase A subunit EhaA ehaA 10491142,19455212,21559116 131567 cellular organisms no rank 205 EBI-EMBL NiFe-hydrogenase-type-3 Eha complex subunit A energy-converting NiFe hydrogenase A subunit EhaA Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. Energy-converting [NiFe] hydrogenases function as ion pumps, catalyzing the reduction of ferredoxin with H2 driven by the proton-motive force or the sodium-ion-motive force [1]. Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA, EhaB, EhaC, EhaD, EhaE, EhaF, EhaG, EhaI, EhaK, EhaL) and four hydrophobic subunits (EhaM, EhaR, EhS, EhT) [2]. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases [3]. Based on sequence similarity and genome context analysis, other organisms such as Methanopyrus kandleri, Methanocaldococcus jannaschii, and Methanothermobacter marburgensis also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar eha operon structure [3]. This domain family can be found on the small membrane proteins that are predicted to be the EhaA trans-membrane subunits of multisubunit membrane-bound [NiFe]-hydrogenase Eha complexes. [1]. 21559116. More than 200 genes required for methane formation from. TRUNCATED at 1650 bytes (from Pfam) NF036324.5 PF17379.7 DUF5400 25 25 100 PfamEq Y Y N DUF5400 family protein 131567 cellular organisms no rank 76 EBI-EMBL Family of unknown function (DUF5400) DUF5400 family protein This is a family of unknown function found in Methanobacteria and Methanococci. Members of this family are predicted to contain 4 trans-membrane regions. (from Pfam) NF036343.5 PF17450.7 Melibiase_2_C 22.5 22.5 87 domain Y N N Alpha galactosidase A C-terminal beta sandwich domain 131567 cellular organisms no rank 3740 EBI-EMBL Alpha galactosidase A C-terminal beta sandwich domain Alpha galactosidase A C-terminal beta sandwich domain NF036395.5 PF17648.6 Luciferase 23.7 23.7 96 domain Y Y N luciferase family protein 30478037 131567 cellular organisms no rank 4666 EBI-EMBL Luciferase luciferase family protein This family includes fungal luciferase which is part of the gene cluster that mediates the fungal bioluminescence cycle [1]. It may use the fungal luciferin 3-hydroxyhispidin as a substrate to produce an endoperoxide as a high-energy intermediate with decomposition that yields oxyluciferin (also known as caffeoylpyruvate) and light emission. The fungal bioluminescence cycle begins with the hispidin synthetase that catalyses the formation of hispidin which is further hydroxylated by the hispidin-3-hydroxylase, yielding the fungal luciferin 3-hydroxyhispidin. The luciferase then produces an endoperoxide as a high-energy intermediate with decomposition that yields oxyluciferin and light emission. Oxyluciferin can be recycled to caffeic acid by caffeoylpyruvate hydrolase [1]. This entry also includes uncharacterised bacterial sequences. [1]. 30478037. Genetically encodable bioluminescent system from fungi. Kotlobay AA, Sarkisyan KS, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova LI, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldon T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov FA, Yampolsky IV;. Proc Natl Acad Sci U S A. 2018;115:12728-12732. (from Pfam) NF036398.5 PF17660.6 BTRD1 23 10 50 repeat Y N N BTRD1 repeat protein 36762862 131567 cellular organisms no rank 1706 EBI-EMBL Polyglycine hydrolase-like, structural repeat bacterial tandem repeat domain 1 Polyglycine hydrolase from Fusarium vanettenii is a serine-type endopeptidase that cleaves Gly-Gly bonds in the polyglycine linker of host plant class IV chitinases to disrupt their chitin-binding, and thereby plays a role in lowering the defence responses of the host to fungi. It is formed by two distinct domains that are connected by a linker. The N-terminal domain is comprised of five nearly identical structural repeats consisting of three antiparallel beta-strands and an alpha-helix (this entry represents these structural repeats). This domain is often found associated to Pfam:PF00144 [1]. [1]. 36762862. Crystal structure of a polyglycine hydrolase determined using a RoseTTAFold model. Dowling NV, Naumann TA, Price NPJ, Rose DR;. Acta Crystallogr D Struct Biol. 2023;79:168-176. (from Pfam) NF036419.5 PF17284.7 Spermine_synt_N 22.1 22.1 53 domain Y N N Spermidine synthase tetramerisation domain 131567 cellular organisms no rank 17825 EBI-EMBL Spermidine synthase tetramerisation domain Spermidine synthase tetramerisation domain This domain represents the N-terminal tetramerization domain from spermidine synthase. (from Pfam) NF036421.5 PF17289.7 Terminase_6C 22.6 22.6 155 domain Y N N Terminase RNaseH-like domain 131567 cellular organisms no rank 49452 EBI-EMBL Terminase RNaseH-like domain Terminase RNaseH-like domain NF036437.5 PF17329.7 DUF5367 25 25 98 domain Y Y N DUF5367 family protein 131567 cellular organisms no rank 1323 EBI-EMBL Family of unknown function (DUF5367) DUF5367 family protein This bacterial family of proteins of unknown function is predicted to contain 3 or 4 trans-membrane regions. (from Pfam) NF036452.5 PF17231.7 DUF5305 29 29 217 subfamily Y Y N DUF5305 family protein 131567 cellular organisms no rank 1147 EBI-EMBL Family of unknown function (DUF5305) DUF5305 family protein This family consists of several hypothetical proteins of unknown function. (from Pfam) NF036468.5 PF17288.7 Terminase_3C 26.7 26.7 155 subfamily_domain Y Y N terminase large subunit 131567 cellular organisms no rank 14700 EBI-EMBL Terminase RNAseH like domain terminase large subunit C-terminal domain NF036481.5 PF17746.6 SfsA_N 25 25 63 domain Y N N SfsA N-terminal OB domain 11272834,2013578 131567 cellular organisms no rank 22778 EBI-EMBL SfsA N-terminal OB domain SfsA N-terminal OB domain This family contains Sugar fermentation stimulation proteins. Which is probably a regulatory factor involved in maltose metabolism. This domain corresponds to the N-terminal OB fold. [1]. 2013578. Nucleotide sequence and characterization of the sfs1 gene: sfs1 is involved in CRP*-dependent mal gene expression in Escherichia coli. Kawamukai M, Utsumi R, Takeda K, Higashi A, Matsuda H, Choi YL, Komano T;. J Bacteriol 1991;173:2644-2648. [2]. 11272834. Effects of the Escherichia coli sfsA gene on mal genes expression and a DNA binding activity of SfsA. Takeda K, Akimoto C, Kawamukai M;. Biosci Biotechnol Biochem 2001;65:213-217. (from Pfam) NF036482.5 PF17753.6 Ig_mannosidase 22.6 22.6 81 domain Y Y N glycoside hydrolase family 2 protein 24975648 131567 cellular organisms no rank 16089 EBI-EMBL Ig-fold domain mannosidase Ig-fold domain This Ig-like fold domain is found in mannosidase enzymes [1]. [1]. 24975648. Insights into the structure and function of fungal beta-mannosidases from glycoside hydrolase family 2 based on multiple crystal structures of the Trichoderma harzianum enzyme. Nascimento AS, Muniz JR, Aparicio R, Golubev AM, Polikarpov I;. FEBS J. 2014;281:4165-4178. (from Pfam) NF036483.5 PF17755.6 UvrA_DNA-bind 23.2 23.2 110 domain Y N N UvrA DNA-binding domain 19368888 131567 cellular organisms no rank 134175 EBI-EMBL UvrA DNA-binding domain UvrA DNA-binding domain NF036484.5 PF17760.6 UvrA_inter 23.3 23.3 109 domain Y N N UvrA interaction domain 131567 cellular organisms no rank 100632 EBI-EMBL UvrA interaction domain UvrA interaction domain This domain found in UvrA proteins interacts with the UvrB protein. (from Pfam) NF036491.5 PF17810.6 Arg_decarb_HB 23.3 23.3 84 domain Y N N Arginine decarboxylase helical bundle domain 20534592 131567 cellular organisms no rank 15673 EBI-EMBL Arginine decarboxylase helical bundle domain Arginine decarboxylase helical bundle domain This entry represents a helical bundle domain that is found between the two enzymatic domains of the arginine decarboxylases [1]. [1]. 20534592. Evolution of substrate specificity within a diverse family of beta/alpha-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine and carboxynorspermidine. Deng X, Lee J, Michael AJ, Tomchick DR, Goldsmith EJ, Phillips MA;. J Biol Chem. 2010;285:25708-25719. (from Pfam) NF036497.5 PF17820.6 PDZ_6 27 27 54 domain Y Y N PDZ domain-containing protein 131567 cellular organisms no rank 318321 EBI-EMBL PDZ domain PDZ domain This entry represents the PDZ domain from a wide variety of proteins. (from Pfam) NF036499.5 PF17829.6 GH115_C 24.1 24.1 172 domain Y N N Gylcosyl hydrolase family 115 C-terminal domain 24214982 131567 cellular organisms no rank 10201 EBI-EMBL Gylcosyl hydrolase family 115 C-terminal domain Gylcosyl hydrolase family 115 C-terminal domain This domain is found at the C-terminus of glycosyl hydrolase family 115 proteins [1]. This domain has a beta-sandwich fold [1]. [1]. 24214982. Evidence that GH115 alpha-glucuronidase activity, which is required to degrade plant biomass, is dependent on conformational flexibility. Rogowski A, Basle A, Farinas CS, Solovyova A, Mortimer JC, Dupree P, Gilbert HJ, Bolam DN;. J Biol Chem. 2014;289:53-64. (from Pfam) NF036501.5 PF17831.6 PDH_E1_M 23.2 23.2 229 domain Y N N Pyruvate dehydrogenase E1 component middle domain 11955070,14992577,16531404,17057342,17635929 131567 cellular organisms no rank 53990 EBI-EMBL Pyruvate dehydrogenase E1 component middle domain Pyruvate dehydrogenase E1 component middle domain This entry represents one of the thiamin diphosphate-binding domains found in pyruvate dehydrogenase E1 component [1]. [1]. 11955070. Structure of the pyruvate dehydrogenase multienzyme complex E1 component from Escherichia coli at 1.85 A resolution. Arjunan P, Nemeria N, Brunskill A, Chandrasekhar K, Sax M, Yan Y, Jordan F, Guest JR, Furey W;. Biochemistry. 2002;41:5213-5221. [2]. 14992577. Structural determinants of enzyme binding affinity: the E1 component of pyruvate dehydrogenase from Escherichia coli in complex with the inhibitor thiamin thiazolone diphosphate. Arjunan P, Chandrasekhar K, Sax M, Brunskill A, Nemeria N, Jordan F, Furey W;. Biochemistry. 2004;43:2405-2411. [3]. 16531404. A thiamin-bound, pre-decarboxylation reaction intermediate analogue in the pyruvate dehydrogenase E1 subunit induces large scale disorder-to-order transformations in the enzyme and reveals novel structural features in the covalently bound adduct. Arjunan P, Sax M, Brunskill A, Chandrasekhar K, Nemeria N, Zhang S, Jordan F, Furey W;. J Biol Chem. 2006;281:15296-15303. [4]. 17057342. Active-site changes in the pyruvate dehydrogenase multienzyme complex E1 apoenzyme component from Escherichia coli observed at 2.32 A resolution. Chandrasekhar K, Arjunan P, Sax M, Nemeria N, Jordan F, Furey W;. Acta Crystallogr D Biol Crystallogr. 2006;62:1382-1386. [5]. 17635929. A dynamic loop at the active center of the Escherichia coli pyruvate dehydrogenase complex E1 component modulates substrate utilization and chemical communication with the E2 component. Kale S, Arjunan P, Furey W, Jordan F;. J Biol Chem. 2007;282:28106-28116. (from Pfam) NF036512.5 PF17882.6 SBD 20 16 76 domain Y N N OAA-family lectin sugar binding domain 20961847,23480609 131567 cellular organisms no rank 1575 EBI-EMBL OAA-family lectin sugar binding domain OAA-family lectin sugar binding domain This domain is found in agglutinin family of lectins. Oscillatoria agardhii agglutinin (OAA)- family lectins comprise either one or two homologous domains, with a single domain possessing two glycan binding sites. OAA is one of the lectins with anti-HIV activity. This sugar binding domain is also found in Pseudomonas fluorescens agglutinin (PFA) and myxobacterial hemagglutinin (MBHA), where MBHA contains two sugar-binding domains (i.e. 4 sugar binding sites), whereas OAA and PFA are single-domain proteins (i.e. 2 sugar binding sites) [1]. [1]. 23480609. Burkholderia oklahomensis agglutinin is a canonical two-domain OAA-family lectin: structures, carbohydrate binding and anti-HIV activity. Whitley MJ, Furey W, Kollipara S, Gronenborn AM;. FEBS J. 2013;280:2056-2067. [2]. 20961847. Novel fold and carbohydrate specificity of the potent anti-HIV cyanobacterial lectin from Oscillatoria agardhii. Koharudin LM, Furey W, Gronenborn AM;. J Biol Chem. 2011;286:1588-1597. (from Pfam) NF036516.5 PF17899.6 Peptidase_M61_N 23 23 168 domain Y N N Peptidase M61 N-terminal domain 131567 cellular organisms no rank 24048 EBI-EMBL Peptidase M61 N-terminal domain Peptidase M61 N-terminal domain This domain is found at the N-terminus of Pfam:PF05299 and has a beta sandwich-like fold with similarity to the baculovirus p35 protein. (from Pfam) NF036518.5 PF17912.6 OB_MalK 27 27 53 domain Y N N MalK OB fold domain 131567 cellular organisms no rank 139597 EBI-EMBL MalK OB fold domain MalK OB fold domain This entry corresponds to one of two OB-fold domains found in the MalK transport protein. (from Pfam) NF036521.5 PF17922.6 TetR_C_17 26.1 26.1 100 domain Y N N Tetracyclin repressor-like, C-terminal domain 15944459,16862575,7707374 131567 cellular organisms no rank 3475 EBI-EMBL Tetracyclin repressor-like, C-terminal domain Tetracyclin repressor-like, C-terminal domain TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity [1]. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response [1]. This entry represents the C-terminal domain present in Yfir transcription regulator proteins found in Bacillus subtilus [2]. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis [3]. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain [3]. [1]. 15944459. The TetR family of transcriptional repressors. Ramos JL, Martinez-Bueno M, Molina-Henares AJ, Teran W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R;. Microbiol Mol Biol Rev. 2005;69:326-356. [2]. 16862575. Crystal structure of YfiR, an unusual TetR/CamR-type . TRUNCATED at 1650 bytes (from Pfam) NF036525.5 PF17932.6 TetR_C_24 26.4 26.4 114 domain Y N N Tetracyclin repressor-like, C-terminal domain 15944459,17189250,20167624,7707374 131567 cellular organisms no rank 100813 EBI-EMBL Tetracyclin repressor-like, C-terminal domain Tetracyclin repressor-like, C-terminal domain TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity [1]. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response [1]. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis [2]. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain [2]. This entry represents the C-terminal domain present in family members such as HTH-type transcriptional repressor KstR2 as well as fatty acid metabolism regulator proteins. In Mycobacterium smegmatis, KstR2 is involved in involved in cholesterol catabolism [3], while YsiA in Bacillus subtilis is involved in fatty acid degradation [4]. [1]. 15944459. The TetR family of transcriptional repressors. Ramos JL,. TRUNCATED at 1650 bytes (from Pfam) NF036527.5 PF17941.6 PP_kinase_C_1 25.7 25.7 167 domain Y N N Polyphosphate kinase C-terminal domain 1 15947782 131567 cellular organisms no rank 65919 EBI-EMBL Polyphosphate kinase C-terminal domain 1 Polyphosphate kinase C-terminal domain 1 Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C1-terminal domain has a structure similar to phospholipase D. It is one of two closely related carboxy-terminal domains (C1 and C2 domains). Both the C1 and C2 domains (residues 322-502 and 503-687, respectively) consist of a sevenstranded mixed beta-sheet flanked by five alpha-helices. However, the structural topology and relative orientations of the helices to the beta-sheet in these two domains are different. The C1 and C2 domains are highly conserved in the PPK family. Some of the residues previously shown to be crucial for the enzyme catalytic activity are located in these two domains [1]. [1]. 15947782. Crystal structure of a polyphosphate kinase and its implications for polyphosphate synthesis. Zhu Y, Huang W, Lee SS, Xu W;. EMBO Rep. 2005;6:681-687. (from Pfam) NF036537.5 PF17990.6 LodA_N 26.3 26.3 213 subfamily_domain Y Y N LodA/GoxA family CTQ-dependent oxidase 20025674,20599635,23908359 131567 cellular organisms no rank 4113 EBI-EMBL L-Lysine epsilon oxidase N-terminal LodA/GoxA family CTQ-dependent oxidase N-terminal domain This is the N-terminal domain found in antimicrobial protein (LodA) with lysine-epsilon oxidase activity (EC 1.4.3.20) which is produced by gram-negative marine bacteria such as Marinomonas mediterranea [1]. The enzyme, previously named marinocine, catalyzes the oxidative deamination of l-lysine into 6-semialdehyde 2-aminoadipic acid, ammonia, and hydrogen peroxide (H2O2). Orthologous proteins have been detected in other bacterial genera, where they participate in biofilm development and dispersal [2]. It has been shown that M. mediterranea LodA and its homologues induce cell death in the microcolonies formed in the process of biofilm development due to the hydrogen peroxide generated by their enzymatic activity. Moreover, cells dispersed from the biofilm by means of this mechanism show a phenotypic variation in growth and biofilm formation. The active form of LodA containing the quinonic cofactor is generated intracellularly only in the presence of LodB, suggesting that the latter protein is involved in this process [3]. [1]. 23908359. X-ray crystallographic evidence for the presence of the cysteine tryptophylquinone cofactor in L-lysine epsilon-oxidase from Marinomonas mediterranea. Okazaki S, Nakano S, Matsui D, Akaji S, Inagaki K, Asano Y;. J Biochem. 2013;154:233-236. [2]. 20599635. Determination of plasma and serum L-lysine using L-lysine epsilon-oxidase from Marinomonas mediterranea NBRC 103028(T). Matsuda M, Asano Y;. Anal Biochem. 2010;406:19-23. [3]. 20025674. Both genes in the Marinomonas mediterranea lodAB operon are required for the expression of the antimicrobial protein lysine oxidase. Gomez D, Lucas-Elio P,. TRUNCATED at 1650 bytes (from Pfam) NF036541.5 PF18009.6 Fer4_23 27 27 82 domain Y N N 4Fe-4S iron-sulfur cluster binding domain 17448684 131567 cellular organisms no rank 850 EBI-EMBL 4Fe-4S iron-sulfur cluster binding domain 4Fe-4S iron-sulfur cluster binding domain This is the C-terminal domain found in Deinococcus radiodurans protein DR2241 (a Ribosomal protein S2-related protein). This domain has been shown to harbour the sequence motifs CxxC and CxxxC which bind a [4Fe-4S] iron-sulphur cluster. Together with the preceding domain, it is heavily involved in the tetramer formation [1]. [1]. 17448684. The crystal structure of DR2241 from Deinococcus radiodurans at 1.9 A resolution reveals a multi-domain protein with structural similarity to chelatases but also with two additional novel domains. Leiros HK, McSweeney SM;. J Struct Biol. 2007;159:92-102. (from Pfam) NF036542.5 PF18011.6 Catalase_C 24.6 24.6 150 domain Y N N C-terminal domain found in long catalases 10488114,11455600,12777389,15342250,19109972,21332158,22172685,22820098,23832201,24223139,7663946 131567 cellular organisms no rank 38604 EBI-EMBL C-terminal domain found in long catalases C-terminal domain found in long catalases This domain is found at the C-terminus of a variety of large catalase enzymes from bacteria. Structurally it is related to class I glutamine amidotransferase domains. The precise molecular function of this domain is uncertain. [1]. 10488114. Mutants that alter the covalent structure of catalase hydroperoxidase II from Escherichia coli. Mate MJ, Sevinc MS, Hu B, Bujons J, Bravo J, Switala J, Ens W, Loewen PC, Fita I;. J Biol Chem. 1999;274:27717-27725. [2]. 11455600. Substrate flow in catalases deduced from the crystal structures of active site variants of HPII from Escherichia coli. Melik-Adamyan W, Bravo J, Carpena X, Switala J, Mate MJ, Fita I, Loewen PC;. Proteins. 2001;44:270-281. [3]. 7663946. Crystal structure of catalase HPII from Escherichia coli. Bravo J, Verdaguer N, Tormo J, Betzel C, Switala J, Loewen PC, Fita I;. Structure. 1995;3:491-502. [4]. 12777389. An electrical potential in the access channel of catalases enhances catalysis. Chelikani P, Carpena X, Fita I, Loewen PC;. J Biol Chem. 2003;278:31290-31296. [5]. 21332158. Modulation of heme orientation and binding by a single residue in catalase HPII of Escherichia coli. Jha V, Louis S, Chelikani P, Carpena X, Donald LJ, Fita I, Loewen PC;. Biochemistry. 2011;50:2101-2110. [6]. 22172685. Mutation of Phe413 to Tyr in catalase KatE from Escherichia coli leads to side chain damage and main chain cleavage. Jha V, Donald LJ, Loewen PC;. Arch Biochem Biophys. 2012;525:207-214. [7]. 24223139. Post-transcriptional regulator Hfq binds catalase HPII: crystal structure of the complex. Yonekura K, Watanabe M, Kageyama Y, Hirata K, Yamamoto M, Maki-Yonekura S;. PLoS One. TRUNCATED at 1650 bytes (from Pfam) NF036549.5 PF18032.6 FRP 26.6 26.6 99 domain Y N N Photoprotection regulator fluorescence recovery protein GO:0042651 23716688 131567 cellular organisms no rank 670 EBI-EMBL Photoprotection regulator fluorescence recovery protein Photoprotection regulator fluorescence recovery protein This family includes fluorescence recovery protein (FRP) domain, which is found in Synechocystis sp. PCC 6803 substr. Kazusa. FRP causes the dissociation of the orange carotenoid protein (OCP) from the phycobilisomes by interacting with the C-terminal domain of OCP, accelerating the conversion of the active red OCP to the inactive orange form. A patch of residues (W50, D54, H53, and R60), contributed by both chains of the FRP dimer cause the acceleration of the OCPr to OCPo conversion. Mutation of the absolutely conserved amino acids (R60) affect the activity of FRP [1]. [1]. 23716688. Crystal structure of the FRP and identification of the active site for modulation of OCP-mediated photoprotection in cyanobacteria. Sutter M, Wilson A, Leverenz RL, Lopez-Igual R, Thurotte A, Salmeen AE, Kirilovsky D, Kerfeld CA;. Proc Natl Acad Sci U S A. 2013;110:10022-10027. (from Pfam) NF036552.5 PF17236.7 DUF5309 25.8 25.8 283 domain Y Y N DUF5309 family protein 131567 cellular organisms no rank 3624 EBI-EMBL Family of unknown function (DUF5309) DUF5309 family protein This is a family of uncharacterised proteins found in viruses and bacteria. (from Pfam) NF036557.5 PF17247.7 DUF5316 28.7 28.7 74 subfamily Y Y N DUF5316 family protein 131567 cellular organisms no rank 1885 EBI-EMBL Family of unknown function (DUF5316) DUF5316 family protein This is a family of unknown function mainly found in Firmicutes. Might contain multiple trans-membrane sequences. (from Pfam) NF036560.5 PF17262.7 Cas6b_C 39.4 39.4 114 domain Y Y N CRISPR-associated endonuclease Cas6 25451598,26996962,28238733 131567 cellular organisms no rank 800 EBI-EMBL Cas6b C-terminal domain Cas6b C-terminal domain Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation [1]. Four Cas proteins (Cas5, Cas6b, Cas7 and Cas8b) are proposed to form a Type I-B Cascade complex that mediates the antiviral defense [2]. This is the C-terminal domain found in Cas6b proteins. Cas6b is a member of Cas6 RNA processing endoribonucleases found in bacteria and archaea whose RNA substrates have a wide range of structural features. Cocrystal structures of Cas6 from Methanococcus maripaludis (MmCas6b) bound with its repeat RNA revealed a dual-site binding structure and a cleavage site conformation poised for phosphodiester bond breakage [3]. [1]. 25451598. Crystal structure of the Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex. Numata T, Inanaga H, Sato C, Osawa T;. J Mol Biol. 2015;427:259-273. [2]. 28238733. Fragmentation of the CRISPR-Cas Type I-B signature protein Cas8b. Richter H, Rompf J, Wiegel J, Rau K, Randau L;. Biochim Biophys Acta. 2017; [Epub ahead of print]. [3]. 26996962. A Non-Stem-Loop CRISPR RNA Is Processed by Dual Binding Cas6. Shao Y, Richter H, Sun S, Sharma K, Urlaub H, Randau L, Li H;. Structure. 2016;24:547-554. (from Pfam) NF036563.5 PF17278.7 DUF5343 27 27 140 domain Y Y N DUF5343 domain-containing protein 131567 cellular organisms no rank 1196 EBI-EMBL Family of unknown function (DUF5343) Family of unknown function (DUF5343) This is a family of unknown function which is found in Bacteria and Archaea. (from Pfam) NF036574.5 PF17373.7 DUF5395 25 25 81 subfamily Y Y N DUF5395 family protein 131567 cellular organisms no rank 70 EBI-EMBL Family of unknown function (DUF5395) DUF5395 family protein This is a family of unknown function found in Archaea and Bacteria. (from Pfam) NF036578.5 PF17389.7 Bac_rhamnosid6H 24.5 24.5 339 domain Y N N Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain 10632887 131567 cellular organisms no rank 62012 EBI-EMBL Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are important bioactive compounds. For example, terpenyl glycosides, the glycosidic precursor of aromatic terpenoids, act as important flavouring substances in grapes. Other rhamnosides act as cytotoxic rhamnosylated terpenoids, as signal substances in plants or play a role in the antigenicity of pathogenic bacteria [1]. [1]. 10632887. The thermostable alpha-L-rhamnosidase RamA of Clostridium stercorarium: biochemical characterization and primary structure of a bacterial alpha-L-rhamnoside hydrolase, a new type of inverting glycoside hydrolase. Zverlov VV, Hertel C, Bronnenmeier K, Hroch A, Kellermann J, Schwarz WH;. Mol Microbiol 2000;35:173-179. (from Pfam) NF036579.5 PF17390.7 Bac_rhamnosid_C 22.1 22.1 78 domain Y Y N alpha-L-rhamnosidase C-terminal domain-containing protein 10632887 131567 cellular organisms no rank 44936 EBI-EMBL Bacterial alpha-L-rhamnosidase C-terminal domain Bacterial alpha-L-rhamnosidase C-terminal domain This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are important bioactive compounds. For example, terpenyl glycosides, the glycosidic precursor of aromatic terpenoids, act as important flavouring substances in grapes. Other rhamnosides act as cytotoxic rhamnosylated terpenoids, as signal substances in plants or play a role in the antigenicity of pathogenic bacteria [1]. [1]. 10632887. The thermostable alpha-L-rhamnosidase RamA of Clostridium stercorarium: biochemical characterization and primary structure of a bacterial alpha-L-rhamnoside hydrolase, a new type of inverting glycoside hydrolase. Zverlov VV, Hertel C, Bronnenmeier K, Hroch A, Kellermann J, Schwarz WH;. Mol Microbiol 2000;35:173-179. (from Pfam) NF036581.5 PF17396.7 DUF1611_N 22.6 22.6 95 domain Y Y N DUF1611 domain-containing protein 131567 cellular organisms no rank 10545 EBI-EMBL Domain of unknown function (DUF1611_N) Rossmann-like domain Domain of unknown function (DUF1611_N) Rossmann-like domain NF036590.5 PF17432.7 DUF3458_C 24 24 320 domain Y Y N aminopeptidase N C-terminal domain-containing protein 131567 cellular organisms no rank 39612 EBI-EMBL Domain of unknown function (DUF3458_C) ARM repeats aminopeptidase N C-terminal domain This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. (from Pfam) NF036614.5 PF17319.7 DUF5362 25 25 94 subfamily Y Y N DUF5362 family protein 131567 cellular organisms no rank 1551 EBI-EMBL Family of unknown function (DUF5362) DUF5362 family protein This is a family of unknown function found in Bacteria. Most of the family members are predicted to have 2 trans-membrane regions. (from Pfam) NF036632.5 PF17385.7 LBP_M 25.2 25.2 221 domain Y Y N lacto-N-biose phosphorylase central domain-containing protein 15933016 131567 cellular organisms no rank 4500 EBI-EMBL Lacto-N-biose phosphorylase central domain Lacto-N-biose phosphorylase central domain The gene which codes for this protein in gut-bacteria is located in a novel putative operon for galactose metabolism. The protein appears to be a carbohydrate-processing phosphorolytic enzyme (EC:2.4.1.211), unlike either glycoside hydrolases or glycoside lyase. Intestinal colonisation by bifidobacteria is important for human health, especially in pediatrics, because colonisation seems to prevent infection by some pathogenic bacteria that cause diarrhoea or other illnesses. The operon seems to be involved in intestinal colonisation by bifidobacteria mediated by metabolism of mucin sugars. In addition, it may also resolve the question of the nature of the bifidus factor in human milk as the lacto-N-biose structure found in milk oligosaccharides. [1]. 15933016. Novel putative galactose operon involving lacto-N-biose phosphorylase in Bifidobacterium longum. Kitaoka M, Tian J, Nishimoto M;. Appl Environ Microbiol. 2005;71:3158-3162. (from Pfam) NF036634.5 PF17391.7 Urocanase_N 23.2 23.2 127 domain Y N N Urocanase N-terminal domain 131567 cellular organisms no rank 49494 EBI-EMBL Urocanase N-terminal domain Urocanase N-terminal domain NF036635.5 PF17392.7 Urocanase_C 23.6 23.6 196 domain Y N N Urocanase C-terminal domain 131567 cellular organisms no rank 50017 EBI-EMBL Urocanase C-terminal domain Urocanase C-terminal domain NF036686.5 PF17645.6 Amdase 25.9 25.9 228 domain Y N N Arylmalonate decarboxylase 27610105 131567 cellular organisms no rank 29585 EBI-EMBL Arylmalonate decarboxylase Arylmalonate decarboxylase This entry contains members such as the arylmalonate decarboxylases (AMDase; EC 4.1.1.76), which belong to the family of carboxy-lyases (EC 4.1). Amdases are capable of decarboxylating a range of alpha-disubstituted malonic acid derivates to enantiopure products without the need for any cofactor. AMDases are members of the widespread Asp/Glu racemase family Pfam:PF01177 together with aspartate (EC 5.1.1.13) and glutamate racemases (EC 5.1.1.3), hydantoin racemases (EC 5.1.99.5) and maleate isomerases (EC 5.2.1.1) [1]. [1]. 27610105. Sequence-Based Screening for Rare Enzymes: New Insights into the World of AMDases Reveal a Conserved Motif and 58 Novel Enzymes Clustering in Eight Distinct Families. Maimanakos J, Chow J, Gassmeyer SK, Gullert S, Busch F, Kourist R, Streit WR;. Front Microbiol. 2016;7:1332. (from Pfam) NF036688.5 PF17647.6 DUF5518 27 27 116 domain Y Y N DUF5518 domain-containing protein 131567 cellular organisms no rank 2687 EBI-EMBL Family of unknown function (DUF5518) DUF5518 domain-containing protein This is a family of unknown function found in Archaea. Family members have multiple predicted trans-membrane regions. (from Pfam) NF036698.5 PF18062.6 RE_AspBHI_N 27 27 185 domain Y N N Restriction endonuclease AspBHI N-terminal 24604015 131567 cellular organisms no rank 2073 EBI-EMBL Restriction endonuclease AspBHI N-terminal Restriction endonuclease AspBHI N-terminal This is the N-terminal domain found in modification-dependent restriction endonuclease proteins such as AspBHI, which can be found in Azoarcus sp. AspBHI is a homo-tetrameric protein that recognizes 5-methylcytosine in the double-strand DNA sequence context of (C/T) (C/G) (5mC) nucleotide (C/G) and cleaves the two strands at a fixed distance (N12/N16) 3 to the modified cytosine. The N-terminal domain is responsible for DNA-recognition and resembles an SRA-like 5-methylcytosine binding domain in structure and function [1]. [1]. 24604015. Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI. Horton JR, Nugent RL, Li A, Mabuchi MY, Fomenkov A, Cohen-Karni D, Griggs RM, Zhang X, Wilson GG, Zheng Y, Xu SY, Cheng X;. Sci Rep. 2014;4:4246. (from Pfam) NF036704.5 PF18079.6 AglB_L1 23.6 23.6 87 domain Y N N Archaeal glycosylation protein B long peripheral domain 23815857,24127570 131567 cellular organisms no rank 1567 EBI-EMBL Archaeal glycosylation protein B long peripheral domain Archaeal glycosylation protein B long peripheral domain This domain is found in Archaeal Glycosylation B protein (AglB-Long) in A. fulgidus. When the domain, known as peripheral l (Pl), is combined with the central core (CC) and insertion (IS) sub-units, they form the C-terminal domain. It is thought that the C-terminal domain may contribute toward the increased thermal stability of the AglB proteins in the hyper-thermophilic [1]. [1]. 23815857. Crystal structure of the C-terminal globular domain of the third paralog of the Archaeoglobus fulgidus oligosaccharyltransferases. Matsumoto S, Shimada A, Kohda D;. BMC Struct Biol. 2013;13:11. [2]. 24127570. Crystal structures of an archaeal oligosaccharyltransferase provide insights into the catalytic cycle of N-linked protein glycosylation. Matsumoto S, Shimada A, Nyirenda J, Igura M, Kawano Y, Kohda D;. Proc Natl Acad Sci U S A. 2013;110:17868-17873. (from Pfam) NF036707.5 PF18089.6 DAPG_hydrolase 22.7 22.7 223 subfamily Y Y N DAPG hydrolase family protein GO:0016787 20018877 131567 cellular organisms no rank 3429 EBI-EMBL DAPG hydrolase PhiG domain 2,4-diacetylphloroglucinol hydrolase/phloretin hydrolase catalytic domain Members of this family share homology with the catalytic domain of the 2,4-diacetylphloroglucinol hydrolase PhiG from Pseudomonas fluorescens, phloretin hydrolase from Eubacterium ramulus, and the incompletely described C-C hydrolase Rv1775 from Mycobacterium tuberculosis. NF036708.5 PF18093.6 Trm5_N 22.7 22.7 47 domain Y N N tRNA methyltransferase 5 N-terminal domain 21602303 131567 cellular organisms no rank 1548 EBI-EMBL tRNA methyltransferase 5 N-terminal domain tRNA methyltransferase 5 N-terminal domain This is the N-terminal domain of tRNA methyltransferase 5 (Trm5) present in Methanocaldococcus jannaschii. Trm5 catalyzes the methyl transfer from S-adenosyl methionine (AdoMet) to N1 of G37. This domain, also known as the D1 domain, contacts the tertiary core (elbow) region of the tRNA L shape in a ternary complex of the enzyme with tRNA and AdoMet [1]. [1]. 21602303. Differentiating analogous tRNA methyltransferases by fragments of the methyl donor. Lahoud G, Goto-Ito S, Yoshida K, Ito T, Yokoyama S, Hou YM;. RNA. 2011;17:1236-1246. (from Pfam) NF036710.5 PF18099.6 CBM_35_2 23 23 112 domain Y Y N carbohydrate-binding domain-containing protein 19218457 131567 cellular organisms no rank 25056 EBI-EMBL Carbohydrate binding module (family 35) DUF5010 C-terminal domain The DUF5010 C-terminal domain is a putative carbohydrate-binding domain. NF036719.5 PF18134.6 AGS_C 26.7 26.7 129 domain Y Y N nucleotide-binding domain-containing protein 26590262 131567 cellular organisms no rank 4062 EBI-EMBL Adenylyl/Guanylyl and SMODS C-terminal sensor domain nucleotide-binding domain Predicted to function as a sensor domain, sensing nucleotides or nucleotide derivatives generated by bacterial adenylyl/guanylyl cyclase domains. The sensing of ligands by AGS-C is predicted to activate effectors deployed by a class of conflict systems which are reliant on the on the production and sensing of the nucleotide second messengers [1]. [1]. 26590262. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;. Nucleic Acids Res. 2015;43:10633-10654. (from Pfam) NF036720.5 PF18145.6 SAVED 26.2 26.2 190 domain Y N N SMODS-associated and fused to various effectors sensor domain 26590262,32544385,32839535 131567 cellular organisms no rank 5829 EBI-EMBL SMODS-associated and fused to various effectors sensor domain SMODS-associated and fused to various effectors sensor domain Predicted to function as a sensor domain, sensing nucleotides or nucleotide derivatives generated by SMODS and other nucleotide synthetase domains [1]. This domain has been characterised in CD-NTase-associated protein 4 (Cap4), the founding member of a major family of downstream receptors that specifically respond to nucleotide second messenger signals in CBASS immunity, a bacterial system that provides immunity against bacteriophage [2,3]. SAVED exhibits divergence in its nucleotide binding pocket which enables the recognition of a wide range of CD-NTase products such as bacterial second messengers with alternative ring size, nucleobase, and 3'-5' or 2'-5' phosphodiester linkages [2]. The sensing of ligands by SAVED activates effectors that are essential for CBASS-mediated protection of bacteria from phage infection. [1]. 26590262. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;. Nucleic Acids Res. 2015;43:10633-10654. [2]. 32544385. CBASS Immunity Uses CARF-Related Effectors to Sense 3'-5'- and 2'-5'-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection. Lowey B, Whiteley AT, Keszei AFA, Morehouse BR, Mathews IT, Antine SP, Cabrera VJ, Kashin D, Niemann P, Jain M, Schwede F, Mekalanos JJ, Shao S, Lee ASY, Kranzusch PJ;. Cell. 2020; [Epub ahead of print]. [3]. 32839535. Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems. Millman A, Melamed S, Amitai G, Sorek R;. Nat Microbiol. 2020;5:1608-1615. (from Pfam) NF036723.5 PF18158.6 AidB_N 22.9 22.9 156 domain Y N N Adaptive response protein AidB N-terminal domain 22004173 131567 cellular organisms no rank 46668 EBI-EMBL Adaptive response protein AidB N-terminal domain Adaptive response protein AidB N-terminal domain This is the N-terminal domain of Adaptive response protein AidB present in E. coli. AidB is upregulated in response to small doses of DNA-methylating agents initiates a response that mitigates the mutagenic and cytotoxic effects of DNA methylation. Tetramer formation is thought to be carried out by the N-terminal domain [1]. [1]. 22004173. Flavin-induced oligomerization in Escherichia coli adaptive response protein AidB. Hamill MJ, Jost M, Wong C, Elliott SJ, Drennan CL;. Biochemistry. 2011;50:10159-10169. (from Pfam) NF036726.5 PF18164.6 GNAT_C 22.8 22.8 142 domain Y N N GNAT-like C-terminal domain 25095906 131567 cellular organisms no rank 5719 EBI-EMBL GNAT-like C-terminal domain GNAT-like C-terminal domain This is the C-terminal domain found in N-acyltransferase (NAT) proteins present in Actinoplanes teichomyceticus. In this organism, NAT proteins are responsible for N-acylation in the synthesis of the antibiotic teicoplanin. The C-terminal domain undergoes a substantial conformational change upon binding to Acyl-CoA. The C-terminal domain is considered Gcn5-related N-acetyltransferase like (GNAT-like) but differs from the canonical GNAT fold in that it lacks the first beta strand and has an additional four alpha helices [1]. [1]. 25095906. Multiple complexes of long aliphatic N-acyltransferases lead to synthesis of 2,6-diacylated/2-acyl-substituted glycopeptide antibiotics, effectively killing vancomycin-resistant enterococcus. Lyu SY, Liu YC, Chang CY, Huang CJ, Chiu YH, Huang CM, Hsu NS, Lin KH, Wu CJ, Tsai MD, Li TL;. J Am Chem Soc. 2014;136:10989-10995. (from Pfam) NF036729.5 PF18178.6 Cap17-like_N 26.6 26.6 232 domain Y N N ATP nucleosidase Cap17-like, N-terminal 26590262,35536256 131567 cellular organisms no rank 405 EBI-EMBL ATP nucleosidase Cap17-like, N-terminal ATP nucleosidase Cap17-like, N-terminal This entry represents the N-terminal domain of ATP nucleosidase Cap17 from E.coli and related sequences. Cap17 is likely an effector protein with (d)ATP degrading activity of a CBASS (cyclic oligonucleotide-based antiphage signaling system) antivirus system which provides immunity against bacteriophages [2]. Members of this entry often co-occur genomically with the bacterial HORMA and Pch2/TRIP13 domains [1]. [1]. 26590262. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;. Nucleic Acids Res. 2015;43:10633-10654. [2]. 35536256. Control of bacterial immune signaling by a WYL domain transcription factor. Blankenchip CL, Nguyen JV, Lau RK, Ye Q, Gu Y, Corbett KD;. Nucleic Acids Res. 2022;50:5239-5250. (from Pfam) NF036745.5 PF18231.6 DUF5603 25 25 105 domain Y Y N DUF5603 domain-containing protein 28358477 131567 cellular organisms no rank 101 EBI-EMBL Domain of unknown function (DUF5603) DUF5603 domain This domain is found in the C-terminal region of free serine kinase (SerK) in the hyperthermophilic archaeon Thermococcus kodakarensis. SerK converts ADP and l-serine (Ser) into AMP and O-phospho-l-serine (Sep), which is a precursor of l-cysteine. The domain is not conserved in the ParB/Srx family. The differences between SerK and the other members of the ParB/Srx family is concentrated in the C-terminal region, which may include residues involved in the Sep binding [1]. [1]. 28358477. Structural Study on the Reaction Mechanism of a Free Serine Kinase Involved in Cysteine Biosynthesis. Nagata R, Fujihashi M, Kawamura H, Sato T, Fujita T, Atomi H, Miki K;. ACS Chem Biol. 2017;12:1514-1523. (from Pfam) NF036750.5 PF18262.6 PhetRS_B1 26.8 26.8 83 domain Y N N Phe-tRNA synthetase beta subunit B1 domain 20223217 131567 cellular organisms no rank 215 EBI-EMBL Phe-tRNA synthetase beta subunit B1 domain Phe-tRNA synthetase beta subunit B1 domain This is the N-terminal domain found in human cytosolic phenylalanyl tRNA synthetase beta subunit [1]. [1]. 20223217. Structure of human cytosolic phenylalanyl-tRNA synthetase: evidence for kingdom-specific design of the active sites and tRNA binding patterns. Finarov I, Moor N, Kessler N, Klipcan L, Safro MG;. Structure. 2010;18:343-353. (from Pfam) NF036757.5 PF18276.6 TcA_TcB_BD 25 25 287 domain Y N N Tc toxin complex TcA C-terminal TcB-binding domain 24572368 131567 cellular organisms no rank 6713 EBI-EMBL Tc toxin complex TcA C-terminal TcB-binding domain Tc toxin complex TcA C-terminal TcB-binding domain This domain is found in the C-terminal region of the Tc toxin TcA, present in Photorhabdus luminescens. Tc Toxin complexes bind to the cell surface, are endocytosed and perforate the host endosomal membrane by forming channels that translocate toxic enzymes into the host. This domain is responsible for binding to toxin TcB. Binding of TcA to TcB/TcC opens the beta-propeller gate [1]. [1]. 24572368. Mechanism of Tc toxin action revealed in molecular detail. Meusch D, Gatsogiannis C, Efremov RG, Lang AE, Hofnagel O, Vetter IR, Aktories K, Raunser S;. Nature. 2014;508:61-65. (from Pfam) NF036760.5 PF18299.6 R2K_2 26.2 26.2 147 domain Y N N ATP-grasp domain, R2K clade family 2 25976611 131567 cellular organisms no rank 8689 EBI-EMBL ATP-grasp domain, R2K clade family 2 ATP-grasp domain, R2K clade family 2 Family of ATP-grasp enzymes belonging to the R2K clade, wherein one of the absolutely-conserved lysine residues has migrated to the RAGYNA domain which is a part of the core ATP-grasp module. This family is predicted to catalyze peptide ligation reactions on protein substrates in biological conflict contexts, probably between bacteriophages and their hosts [1]. [1]. 25976611. The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications. Burroughs AM, Zhang D, Aravind L;. Biol Direct. 2015;10:21. (from Pfam) NF036761.5 PF18301.6 preATP-grasp_3 26.3 26.3 76 domain Y N N pre ATP-grasp 3 domain 131567 cellular organisms no rank 1315 EBI-EMBL pre ATP-grasp 3 domain pre ATP-grasp 3 domain This domain is found just before the N-terminal of the ATP grasp 3 domain (Pfam:PF02655). The domain is carried by species such as Azospirillum brasilense and Methylobacter tundripaludum. (from Pfam) NF036763.5 PF18310.6 DUF5605 25 25 73 domain Y Y N DUF5605 domain-containing protein 131567 cellular organisms no rank 3316 EBI-EMBL Domain of unknown function (DUF5605) Domain of unknown function (DUF5605) This domain is found in the C-terminal region of proteins carrying Pfam:PF16586 and Pfam:PF13204. The C-terminal domain is carried by species such as Bacteroides vulgatus. (from Pfam) NF036766.5 PF17650.6 RACo_linker 26.2 26.2 86 domain Y N N RACo linker region 22431597 131567 cellular organisms no rank 5567 EBI-EMBL RACo linker region RACo linker region This family includes reductive activator of CoFeSP (RACo) proteins, Swiss:Q3ACS2. Structure analysis of RACo indicate that it contains 4 regions: N-terminal region Pfam:PF00111 (residues 3-94) binding the [2Fe-2S] cluster, a linker region (residues 95-125), the middle region (residues 126-206), and the large C-terminal domain Pfam:PF14574 (residues 207-630). This entry pertains to the linker region. The linker region is only present in RACE (reductive activases for corrinoid enzymes) protein sequences with the N-terminal [2Fe-2S] cluster family Pfam:PF00111 and is absent in the RamA-like RACE proteins, suggesting that the linker domain and the N-terminal domain form one functional unit [1]. [1]. 22431597. Redox-dependent complex formation by an ATP-dependent activator of the corrinoid/iron-sulfur protein. Hennig SE, Jeoung JH, Goetzl S, Dobbek H;. Proc Natl Acad Sci U S A. 2012;109:5235-5240. (from Pfam) NF036772.5 PF17676.6 Peptidase_S66C 23.7 23.7 120 domain Y N N LD-carboxypeptidase C-terminal domain 10428950,16162494,7559516,8522520 131567 cellular organisms no rank 69586 EBI-EMBL LD-carboxypeptidase C-terminal domain LD-carboxypeptidase C-terminal domain Muramoyl-tetrapeptide carboxypeptidase hydrolyses a peptide bond between a di-basic amino acid and the C-terminal D-alanine in the tetrapeptide moiety in peptidoglycan. This cleaves the bond between an L- and a D-amino acid. The function of this activity is in murein recycling. This family also includes the microcin c7 self-immunity protein Swiss:Q47511. This family corresponds to Merops family S66. [1]. 8522520. Structure and organization of plasmid genes required to produce the translation inhibitor microcin C7. Gonzalez-Pastor JE, San Millan JL, Castilla MA, Moreno F;. J Bacteriol 1995;177:7131-7140. [2]. 7559516. Chemical structure and translation inhibition studies of the antibiotic microcin C7. Guijarro JI, Gonzalez-Pastor JE, Baleux F, San Millan JL, Castilla MA, Rico M, Moreno F, Delepierre M;. J Biol Chem 1995;270:23520-23532. [3]. 10428950. A defect in cell wall recycling triggers autolysis during the stationary growth phase of Escherichia coli. Templin MF, Ursinus A, Holtje JV;. EMBO J 1999;18:4108-4117. [4]. 16162494. P. aeruginosa LD-carboxypeptidase: A serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow. Korza HJ, Bochtler M;. J Biol Chem 2005; [Epub ahead of print] (from Pfam) NF036773.5 PF17677.6 Glyco_hydro38C2 22 22 72 domain Y Y N glycosyl hydrolase-related protein 9649738 131567 cellular organisms no rank 40394 EBI-EMBL Glycosyl hydrolases family 38 C-terminal beta sandwich domain glycosyl hydrolase family 38 C-terminal beta sandwich domain This domain is found at the C-terminal end of various glycosyl hydrolases belonging to family 38. The domain has a beta sandwich fold. [1]. 9649738. Glycosidase families. Henrissat B. Biochem Soc Trans 1998;26:153-156. (from Pfam) NF036789.5 PF17726.6 DpnI_C 23 23 70 domain Y N N Dam-replacing HTH domain 11334887,22638584 131567 cellular organisms no rank 1424 EBI-EMBL Dam-replacing HTH domain Dam-replacing HTH domain Dam-replacing protein (DRP) is an restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [1]. This domain represents the C-terminal HTH domain. [1]. 11334887. Evolution and function of the neisserial dam-replacing gene. Cantalupo G, Bucci C, Salvatore P, Pagliarulo C, Roberti V, Lavitola A, Bruni CB, Alifano P;. FEBS Lett 2001;495:178-183. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF036798.5 PF17758.6 Prot_ATP_ID_OB_N 23.4 23.4 62 domain Y N N Proteasomal ATPase OB N-terminal domain 19836337,20953180 131567 cellular organisms no rank 11343 EBI-EMBL Proteasomal ATPase OB N-terminal domain Proteasomal ATPase OB N-terminal domain This is N-terminal interdomain (ID), oligonucleotide binding (OB) domain of proteasomal ATPase [1-2]. [1]. 19836337. Structural insights on the Mycobacterium tuberculosis proteasomal ATPase Mpa. Wang T, Li H, Lin G, Tang C, Li D, Nathan C, Darwin KH, Li H;. Structure. 2009;17:1377-1385. [2]. 20953180. Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation. Wang T, Darwin KH, Li H;. Nat Struct Mol Biol. 2010;17:1352-1357. (from Pfam) NF036799.5 PF17759.6 tRNA_synthFbeta 22.4 22.4 214 domain Y N N Phenylalanyl tRNA synthetase beta chain CLM domain 21082706 131567 cellular organisms no rank 103953 EBI-EMBL Phenylalanyl tRNA synthetase beta chain CLM domain Phenylalanyl tRNA synthetase beta chain CLM domain This domain corresponds to the catalytic like domain (CLM) in the beta chain of phe tRNA synthetase [1]. [1]. 21082706. Idiosyncrasy and identity in the prokaryotic Phe-system: crystal structure of E. coli phenylalanyl-tRNA synthetase complexed with phenylalanine and AMP. Mermershtain I, Finarov I, Klipcan L, Kessler N, Rozenberg H, Safro MG;. Protein Sci. 2011;20:160-167. (from Pfam) NF036800.5 PF17762.6 HTH_ParB 22.6 22.6 52 domain Y N N HTH domain found in ParB protein 15228524 131567 cellular organisms no rank 70396 EBI-EMBL HTH domain found in ParB protein HTH domain found in ParB protein NF036804.5 PF17775.6 YchJ_M-like 22.7 22.7 99 subfamily Y Y N YchJ family metal-binding protein 32241912 131567 cellular organisms no rank 36842 EBI-EMBL YchJ, middle NTF2-like domain YchJ family metal-binding protein Members of this include YchJ from Escherichia coli K-12. Member proteins nearly always have an N-terminal SEC-C metal-binding motif, about 20 amino acids long (see PF02810), and some, including YchJ itself, have a C-terminal one as well. YchJ binds zinc primarily, but also binds small amounts of copper and iron. The function is not yet well understood. NF036805.5 PF17778.6 BLACT_WH 22.8 22.8 46 domain Y N N Beta-lactamase associated winged helix domain 26826708 131567 cellular organisms no rank 20856 EBI-EMBL Beta-lactamase associated winged helix domain Beta-lactamase associated winged helix domain This winged helix domain is found at the C-terminus of some beta lactamase enzymes [1]. [1]. 26826708. Identification of LACTB2, a metallo-beta-lactamase protein, as a human mitochondrial endoribonuclease. Levy S, Allerston CK, Liveanu V, Habib MR, Gileadi O, Schuster G;. Nucleic Acids Res. 2016;44:1813-1832. (from Pfam) NF036806.5 PF17782.6 DprA_WH 22.9 22.9 61 domain Y N N DprA winged helix domain 25138221 131567 cellular organisms no rank 58580 EBI-EMBL DprA winged helix domain DprA winged helix domain This winged helix domain is found in the DprA protein [1]. [1]. 25138221. Roles of Bacillus subtilis DprA and SsbA in RecA-mediated genetic recombination. Yadav T, Carrasco B, Serrano E, Alonso JC;. J Biol Chem. 2014;289:27640-27652. (from Pfam) NF036807.5 PF17784.6 Sulfotransfer_4 22.8 22.8 215 domain Y Y N sulfotransferase 24263136 131567 cellular organisms no rank 6966 EBI-EMBL Sulfotransferase domain Sulfotransferase domain This family of proteins are distantly related to sulfotransferase enzymes. This protein in S. mansonii [1] has been shown to be involved in resistance to oxamniquine and to have sulfotransferase activity. [1]. 24263136. Genetic and molecular basis of drug resistance and species-specific drug action in schistosome parasites. Valentim CL, Cioli D, Chevalier FD, Cao X, Taylor AB, Holloway SP, Pica-Mattoccia L, Guidi A, Basso A, Tsai IJ, Berriman M, Carvalho-Queiroz C, Almeida M, Aguilar H, Frantz DE, Hart PJ, LoVerde PT, Anderson TJ;. Science. 2013;342:1385-1389. (from Pfam) NF036808.5 PF17785.6 PUA_3 22.6 22.6 64 domain Y N N PUA-like domain GO:0003723 16260766 131567 cellular organisms no rank 39486 EBI-EMBL PUA-like domain PUA-like domain This PUA-like domain is found at the N-terminus of SAM-dependent methyltransferases [1]. [1]. 16260766. The crystal structure of a novel SAM-dependent methyltransferase PH1915 from Pyrococcus horikoshii. Sun W, Xu X, Pavlova M, Edwards AM, Joachimiak A, Savchenko A, Christendat D;. Protein Sci. 2005;14:3121-3128. (from Pfam) NF036809.5 PF17786.6 Mannosidase_ig 23.4 23.4 91 domain Y N N Mannosidase Ig/CBM-like domain 17287210 131567 cellular organisms no rank 14727 EBI-EMBL Mannosidase Ig/CBM-like domain Mannosidase Ig/CBM-like domain This domain corresponds to domain 4 in the structure of Bacteroides thetaiotaomicron beta-mannosidase, BtMan2A [1]. This domain has an Ig-like fold. [1]. 17287210. Mannose foraging by Bacteroides thetaiotaomicron: structure and specificity of the beta-mannosidase, BtMan2A. Tailford LE, Money VA, Smith NL, Dumon C, Davies GJ, Gilbert HJ;. J Biol Chem. 2007;282:11291-11299. (from Pfam) NF036810.5 PF17788.6 HypF_C 23 23 99 domain Y N N HypF Kae1-like domain 22740694 131567 cellular organisms no rank 35007 EBI-EMBL HypF Kae1-like domain HypF Kae1-like domain This domain is found in the HypF protein. In the structure it is one of the two subdomains of the Kae1 domain [1]. [1]. 22740694. Structural basis for the reaction mechanism of S-carbamoylation of HypE by HypF in the maturation of [NiFe]-hydrogenases. Shomura Y, Higuchi Y;. J Biol Chem. 2012;287:28409-28419. (from Pfam) NF036814.5 PF17803.6 Cadherin_4 25.1 25.1 71 domain Y N N Bacterial cadherin-like domain 131567 cellular organisms no rank 88412 EBI-EMBL Bacterial cadherin-like domain Bacterial cadherin-like domain This entry contains numerous bacterial cadherin-like domains found in extracelullar proteins. (from Pfam) NF036822.5 PF17836.6 PglD_N 23.4 23.4 78 domain Y N N PglD N-terminal domain 18198901,18667421,24064219 131567 cellular organisms no rank 28076 EBI-EMBL PglD N-terminal domain PglD N-terminal domain This alpha/beta domain is found at the N-terminus of proteins such as PglD [2]. This domain binds a UDP-sugar substrate [3]. [1]. 24064219. Biochemical analysis and structure determination of bacterial acetyltransferases responsible for the biosynthesis of UDP-N,N'-diacetylbacillosamine. Morrison MJ, Imperiali B;. J Biol Chem. 2013;288:32248-32260. [2]. 18198901. Structure and active site residues of PglD, an N-acetyltransferase from the bacillosamine synthetic pathway required for N-glycan synthesis in Campylobacter jejuni. Rangarajan ES, Ruane KM, Sulea T, Watson DC, Proteau A, Leclerc S, Cygler M, Matte A, Young NM;. Biochemistry. 2008;47:1827-1836. [3]. 18667421. Crystal structure and catalytic mechanism of PglD from Campylobacter jejuni. Olivier NB, Imperiali B;. J Biol Chem. 2008;283:27937-27946. (from Pfam) NF036823.5 PF17837.6 4PPT_N 27 27 68 domain Y N N 4'-phosphopantetheinyl transferase N-terminal domain 10997907,22993090,24963544 131567 cellular organisms no rank 34338 EBI-EMBL 4'-phosphopantetheinyl transferase N-terminal domain 4'-phosphopantetheinyl transferase N-terminal domain This entry represents the N-terminal domain from 4'- phosphopantetheinyl transferase enzymes. This domain is structurally related to the Pfam:PF01648 domain with which it forms a pseudodimeric arrangement [2]. [1]. 10997907. Crystal structures of substrate binding to Bacillus subtilis holo-(acyl carrier protein) synthase reveal a novel trimeric arrangement of molecules resulting in three active sites. Parris KD, Lin L, Tam A, Mathew R, Hixon J, Stahl M, Fritz CC, Seehra J, Somers WS;. Structure. 2000;8:883-895. [2]. 24963544. Structure, biochemistry, and inhibition of essential 4'-phosphopantetheinyl transferases from two species of Mycobacteria. Vickery CR, Kosa NM, Casavant EP, Duan S, Noel JP, Burkart MD;. ACS Chem Biol. 2014;9:1939-1944. [3]. 22993090. Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria. Halavaty AS, Kim Y, Minasov G, Shuvalova L, Dubrovska I, Winsor J, Zhou M, Onopriyenko O, Skarina T, Papazisi L, Kwon K, Peterson SN, Joachimiak A, Savchenko A, Anderson WF;. Acta Crystallogr D Biol Crystallogr. 2012;68:1359-1370. (from Pfam) NF036825.5 PF17849.6 OB_Dis3 22.8 22.8 77 domain Y N N Dis3-like cold-shock domain 2 (CSD2) 18374646,19879841,23376952,25119025 131567 cellular organisms no rank 9725 EBI-EMBL Dis3-like cold-shock domain 2 (CSD2) Dis3-like cold-shock domain 2 (CSD2) This domain has an OB fold and is found in the Dis3l2 protein [1]. This domain along with CSD1 binds to RNA. [1]. 25119025. Mechanism of Dis3l2 substrate recognition in the Lin28-let-7 pathway. Faehnle CR, Walleshauser J, Joshua-Tor L;. Nature. 2014;514:252-256. [2]. 18374646. Structure of the active subunit of the yeast exosome core, Rrp44: diverse modes of substrate recruitment in the RNase II nuclease family. Lorentzen E, Basquin J, Tomecki R, Dziembowski A, Conti E;. Mol Cell. 2008;29:717-728. [3]. 19879841. The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation. Bonneau F, Basquin J, Ebert J, Lorentzen E, Conti E;. Cell. 2009;139:547-559. [4]. 23376952. Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex. Makino DL, Baumgartner M, Conti E;. Nature. 2013;495:70-75. (from Pfam) NF036826.5 PF17851.7 GH43_C2 22.7 22.7 203 domain Y N N Beta xylosidase C-terminal Concanavalin A-like domain 131567 cellular organisms no rank 65738 EBI-EMBL Beta xylosidase C-terminal Concanavalin A-like domain Beta xylosidase C-terminal Concanavalin A-like domain This domain is found to the C-terminus of the Pfam:PF04616 domain. This domain adopts a concanavalin A-like fold. (from Pfam) NF036827.5 PF17854.6 FtsK_alpha 22.9 22.9 101 subfamily Y Y N DNA translocase FtsK 16916635 131567 cellular organisms no rank 123248 EBI-EMBL FtsK alpha domain DNA translocase FtsK alpha domain FtsK is a DNA translocase that coordinates chromosome segregation and cell division in bacteria [1]. In addition to its role as activator of XerCD site-specific recombination, FtsK can translocate double-stranded DNA (dsDNA) rapidly and directionally and reverse direction [1]. FtsK can be split into three domains called alpha (this entry), beta and gamma. The alpha and beta domains contain the core ATPase machinery of the DNA translocase [1]. [1]. 16916635. Double-stranded DNA translocation: structure and mechanism of hexameric FtsK. Massey TH, Mercogliano CP, Yates J, Sherratt DJ, Lowe J;. Mol Cell. 2006;23:457-469. (from Pfam) NF036828.5 PF17855.6 MCM_lid 27.4 27.4 87 domain Y N N MCM AAA-lid domain 8332451 131567 cellular organisms no rank 1852 EBI-EMBL MCM AAA-lid domain MCM AAA-lid domain This entry represents the AAA-lid domain found in MCM proteins. [1]. 8332451. A common set of conserved motifs in a vast variety of putative nucleic acid-dependent ATPases including MCM proteins involved in the initiation of eukaryotic DNA replication. Koonin EV;. Nucleic Acids Res 1993;21:2541-2547. (from Pfam) NF036831.5 PF17863.6 AAA_lid_2 22.7 22.7 74 domain Y N N AAA lid domain 11469861,20223218 131567 cellular organisms no rank 139740 EBI-EMBL AAA lid domain AAA lid domain This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. [1]. 11469861. Interplay between an AAA module and an integrin I domain may regulate the function of magnesium chelatase. Fodje MN, Hansson A, Hansson M, Olsen JG, Gough S, Willows RD, Al-Karadaghi S;. J Mol Biol. 2001;311:111-122. [2]. 20223218. ATP-induced conformational dynamics in the AAA+ motor unit of magnesium chelatase. Lundqvist J, Elmlund H, Wulff RP, Berglund L, Elmlund D, Emanuelsson C, Hebert H, Willows RD, Hansson M, Lindahl M, Al-Karadaghi S;. Structure. 2010;18:354-365. (from Pfam) NF036834.5 PF17871.6 AAA_lid_9 22.8 22.8 104 domain Y N N AAA lid domain 131567 cellular organisms no rank 223583 EBI-EMBL AAA lid domain AAA lid domain This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. (from Pfam) NF036844.5 PF17908.6 APAF1_C 22.8 22.8 135 domain Y N N APAF-1 helical domain 15829969,21827944,23521171 131567 cellular organisms no rank 1003 EBI-EMBL APAF-1 helical domain APAF-1 helical domain This domain represents the C-terminal alpha helical domain of the apoptotic Apaf-1 protein. [1]. 15829969. Structure of the apoptotic protease-activating factor 1 bound to ADP. Riedl SJ, Li W, Chao Y, Schwarzenbacher R, Shi Y;. Nature. 2005;434:926-933. [2]. 23521171. Changes in Apaf-1 conformation that drive apoptosome assembly. Yuan S, Topf M, Reubold TF, Eschenburg S, Akey CW;. Biochemistry. 2013;52:2319-2327. [3]. 21827944. Crystal structure of full-length Apaf-1: how the death signal is relayed in the mitochondrial pathway of apoptosis. Reubold TF, Wohlgemuth S, Eschenburg S;. Structure. 2011;19:1074-1083. (from Pfam) NF036846.5 PF17915.6 zf_Rg 25.5 25.5 49 domain Y N N Reverse gyrase zinc finger 23209025 131567 cellular organisms no rank 487 EBI-EMBL Reverse gyrase zinc finger Reverse gyrase zinc finger This is the N-terminal zinc finger domain present in reverse gyrase proteins. Most reverse gyrases conserve the N-terminal zinc finger of the zinc ribbon type, pointing to a crucial function of this domain. Structure of Thermotoga maritima reverse gyrase elucidates that the N-terminal zinc finger firmly attaches the H1 (helicase 1) domain to the topoisomerase domain contributing to double-strand DNA (dsDNA) binding [1]. [1]. 23209025. Crystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling. Rudolph MG, del Toro Duany Y, Jungblut SP, Ganguly A, Klostermeier D;. Nucleic Acids Res. 2013;41:1058-1070. (from Pfam) NF036848.5 PF18313.6 TLP1_add_C 26.1 26.1 83 domain Y N N Thiolase-like protein type 1 additional C-terminal domain 22844533 131567 cellular organisms no rank 5771 EBI-EMBL Thiolase-like protein type 1 additional C-terminal domain Thiolase-like protein type 1 additional C-terminal domain This domain is found in thiolase-like protein type 1 (TLP1) present in Mycobacterium smegmatis. Thiolase enzymes are acetyl-coenzyme A acetyltransferases which convert two units of acetyl-CoA to acetoacetyl CoA in the mevalonate pathway. This domain is deemed an additional C-terminal region, much like the SPC2-thiolase present in mammals which has an additional C-terminal domain termed the sterol carrier protein-2 (SPC2). However, the additional C-terminal domain in TLP1 folds differently to the traditional SCP2-fold observed in mammalian SPC2-thiolase. The topology of the C-terminal domain of TLP1 is reminiscent of single strand nucleic acid binding proteins [1]. [1]. 22844533. Crystal structure of a monomeric thiolase-like protein type 1 (TLP1) from Mycobacterium smegmatis. Janardan N, Harijan RK, Wierenga RK, Murthy MR;. PLoS One. 2012;7:e41894. (from Pfam) NF036850.5 PF18317.6 SDH_C 25.8 25.8 31 domain Y N N Shikimate 5'-dehydrogenase C-terminal domain 19215302 131567 cellular organisms no rank 69995 EBI-EMBL Shikimate 5'-dehydrogenase C-terminal domain Shikimate 5'-dehydrogenase C-terminal domain This domain is found in the C-terminal region of Shikimate 5'-dehydrogenase (SDH) present in Methanocaldococcus jannaschii. SDH catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway. The domain is found just after the C-terminal domain (Pfam:PF01488) which is responsible for NADP binding [1]. [1]. 19215302. X-ray crystallographic and enzymatic analyses of shikimate dehydrogenase from Staphylococcus epidermidis. Han C, Hu T, Wu D, Qu S, Zhou J, Ding J, Shen X, Qu D, Jiang H;. FEBS J. 2009;276:1125-1139. (from Pfam) NF036854.5 PF18348.6 SH3_16 25.8 25.8 49 domain Y N N Bacterial dipeptidyl-peptidase Sh3 domain 20944232 131567 cellular organisms no rank 18700 EBI-EMBL Bacterial dipeptidyl-peptidase Sh3 domain Bacterial dipeptidyl-peptidase Sh3 domain This is the first of two N-terminal bacterial SH3 (SH3b) domains found in bacterial dipeptidyl-peptidases VI such as gamma-D-glutamyl-L-diamino acid endopeptidases. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed [1]. [1]. 20944232. Structure of the gamma-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-gamma-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases. Xu Q, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Yeh A, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:1354-1364. (from Pfam) NF036870.5 PF18417.6 LodA_C 25 25 149 subfamily_domain Y Y N LodA/GoxA family CTQ-dependent oxidase 23908359 131567 cellular organisms no rank 4114 EBI-EMBL L-lysine epsilon oxidase C-terminal domain LodA/GoxA family CTQ-dependent oxidase C-terminal domain This is the C-terminal domain of L-Lysine epsilon-oxidase (LodA, EC 1.4.3.20), an enzyme which catalyses the oxidative deamination of free L-lysine into L-2-aminoadipate 6-semialdehyde, ammonia and hydrogen peroxide [1]. [1]. 23908359. X-ray crystallographic evidence for the presence of the cysteine tryptophylquinone cofactor in L-lysine epsilon-oxidase from Marinomonas mediterranea. Okazaki S, Nakano S, Matsui D, Akaji S, Inagaki K, Asano Y;. J Biochem. 2013;154:233-236. (from Pfam) NF036873.5 PF18435.6 EstA_Ig_like 26.7 26.7 120 domain Y N N Esterase Ig-like N-terminal domain 19013466 131567 cellular organisms no rank 4775 EBI-EMBL Esterase Ig-like N-terminal domain Esterase Ig-like N-terminal domain This is an N-terminal immunoglobulin (Ig)-like domain found in esterases such as EstA. Analysis of the EstA structure confirms that it is a member of the alpha/beta hydrolase family, with a conserved Ser-Asp-His catalytic triad. The Ig-like domain presumably plays a role in the multimerization of EstA into an unusual hexameric structure. Additionally, it may also participate in the catalysis of EstA by guiding the substrate to the active site [1]. [1]. 19013466. Crystal structure and biochemical properties of a novel thermostable esterase containing an immunoglobulin-like domain. Levisson M, Sun L, Hendriks S, Swinkels P, Akveld T, Bultema JB, Barendregt A, van den Heuvel RH, Dijkstra BW, van der Oost J, Kengen SW;. J Mol Biol. 2009;385:949-962. (from Pfam) NF036876.5 PF18462.6 DUF5612 25 25 143 domain Y Y N DUF5612 domain-containing protein 131567 cellular organisms no rank 386 EBI-EMBL Domain of unknown function (DUF5612) Domain of unknown function (DUF5612) This is a domain of unknown function which is mostly found at the C-terminal of ACT domains such as Pfam:PF01842. (from Pfam) NF036887.5 PF18505.6 DUF5619 25 25 85 subfamily Y Y N AF1514 family protein 18361456 131567 cellular organisms no rank 168 EBI-EMBL Domain of unknown function (DUF5619) AF1514 family protein This is a domain of unknown function found in bacteria and archaea. [1]. 18361456. Crystal structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source. Li Y, Bahti P, Shaw N, Song G, Chen S, Zhang X, Zhang M, Cheng C, Yin J, Zhu JY, Zhang H, Che D, Xu H, Abbas A, Wang BC, Liu ZJ;. Proteins 2008;71:2109-13. (from Pfam) NF036895.5 PF18537.6 CODH_A_N 32.2 32.2 83 domain Y N N Carbon monoxide dehydrogenase subunit alpha N-terminal domain 12627225 131567 cellular organisms no rank 903 EBI-EMBL Carbon monoxide dehydrogenase subunit alpha N-terminal domain Carbon monoxide dehydrogenase subunit alpha N-terminal domain Acetyl-coenzyme A (CoA) synthase/carbon monoxide dehydrogenase (ACS/CODH) is a bifunctional enzyme that catalyzes the reversible reduction of CO2 to CO (CODH activity). This entry is for the N-terminal domain found in ACS/CODH subunit alpha [1]. [1]. 12627225. Ni-Zn-[Fe4-S4] and Ni-Ni-[Fe4-S4] clusters in closed and open subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase. Darnault C, Volbeda A, Kim EJ, Legrand P, Vernede X, Lindahl PA, Fontecilla-Camps JC;. Nat Struct Biol. 2003;10:271-279. (from Pfam) NF036901.5 PF18564.6 Glyco_hydro_5_C 22 22 87 domain Y N N Glycoside hydrolase family 5 C-terminal domain 17329247 131567 cellular organisms no rank 4500 EBI-EMBL Glycoside hydrolase family 5 C-terminal domain Glycoside hydrolase family 5 C-terminal domain This is the C-terminal domain of endo-glycoceramidase II (EGC), a membrane-associated family 5 glycosidase Pfam:PF00150. The C-terminal domain assumes a beta-sandwich fold, which resembles that of many carbohydrate-binding modules [1]. [1]. 17329247. Structural and mechanistic analyses of endo-glycoceramidase II, a membrane-associated family 5 glycosidase in the Apo and GM3 ganglioside-bound forms. Caines ME, Vaughan MD, Tarling CA, Hancock SM, Warren RA, Withers SG, Strynadka NC;. J Biol Chem. 2007;282:14300-14308. (from Pfam) NF036906.5 PF18593.6 CdiI_2 26.7 26.7 91 subfamily Y Y N contact-dependent growth inhibition system immunity protein 28398546 131567 cellular organisms no rank 6819 EBI-EMBL CdiI immunity protein contact-dependent growth inhibition system immunity protein Contact-dependent growth inhibition (CDI) is an important mechanism of inter-bacterial competition found in many Gram-negative pathogens. CDI+ cells express cell-surface CdiA proteins that bind neighboring bacteria and deliver C-terminal toxin domains (CdiA-CT) to inhibit target-cell growth. CDI+ bacteria also produce CdiI immunity proteins, which specifically neutralize cognate CdiA-CT toxins to prevent self-inhibition. Structure analysis of CdiI immunity protein from Yersinia kristensenii shows that it is composed of eight alpha-helices packed together to form a nearly spherical structure with weak structural homology to a putative TetR family transcriptional repressor. The CdiI protein fits into the curved cavity of the CdiA-CTYkris toxin domain where it most likely neutralizes toxin activity by blocking access to RNA substrates [1]. This domain is mostly found in gammaproteobacteria. [1]. 28398546. The CDI toxin of Yersinia kristensenii is a novel bacterial member of the RNase A superfamily. Batot G, Michalska K, Ekberg G, Irimpan EM, Joachimiak G, Jedrzejczak R, Babnigg G, Hayes CS, Joachimiak A, Goulding CW;. Nucleic Acids Res. 2017;45:5013-5025. (from Pfam) NF036911.5 PF18626.6 Gln_deamidase_2 25 25 106 domain Y Y N protein-glutamine glutaminase family protein 21926168 131567 cellular organisms no rank 965 EBI-EMBL Glutaminase protein-glutamine glutaminase catalytic domain Protein glutaminase (PG, EC 3.5.1.44) can deamidate glutamine residues in proteins to glutamate residues. This entry represents the mature PG enzyme which bears partial homology to factor XIII-like Transglutaminase (TG), especially its Cys-His-Asp catalytic triad. A similar triad (Cys-His-Asn) is also shared by some cysteine proteases such as papain and actinidin. The mature PG is a monomer enzyme consisting of 185 amino acid residues [1]. [1]. 21926168. Crystal structures of protein glutaminase and its pro forms converted into enzyme-substrate complex. Hashizume R, Maki Y, Mizutani K, Takahashi N, Matsubara H, Sugita A, Sato K, Yamaguchi S, Mikami B;. J Biol Chem. 2011;286:38691-38702. (from Pfam) NF036920.5 PF18643.6 RE_BsaWI 26.2 26.2 105 subfamily Y Y N BsaWI family type II restriction enzyme 26240380 131567 cellular organisms no rank 1122 EBI-EMBL BsaWI restriction endonuclease type 2 BsaWI family type II restriction enzyme Type II restriction endonucleases recognize short 4-8 bp nucleotide sequences and cleave phosphodiester bonds within or close to their target site. BsaWI restriction endonuclease from the thermophilic bacterium Bacillus stearothermophilus W1718 belongs to a group of restriction endonucleases that share CCGG motif within their target sites, termed 'CCGG-family'. However, the R-(D/E)R motif residues, which are supposed to recognize CCGG from the major groove side, are poorly ordered and located far away from the DNA bases. BsaWI contacts with the CCGG tetranucleotide from the minor groove side. It is folded into two domains an N-terminal helical domain and a C-terminal catalytic domain. Furthermore, it carries a PDXKXE motif at the putative active site [1]. [1]. 26240380. Functional significance of protein assemblies predicted by the crystal structure of the restriction endonuclease BsaWI. Tamulaitis G, Rutkauskas M, Zaremba M, Grazulis S, Tamulaitiene G, Siksnys V;. Nucleic Acids Res. 2015;43:8100-8110. (from Pfam) NF036933.5 PF17517.7 IgGFc_binding 25.6 25.6 297 domain Y N N IgGFc binding protein 9182547 131567 cellular organisms no rank 5244 EBI-EMBL IgGFc binding protein IgGFc binding protein This domain is found at the N terminal of Swiss:Q9Y6R7 and has been shown to confer IgG Fc binding activity [1]. It may play a role in immune protection and inflammation in the intestines of primates [1]. [1]. 9182547. Human IgGFc binding protein (FcgammaBP) in colonic epithelial cells exhibits mucin-like structure. Harada N, Iijima S, Kobayashi K, Yoshida T, Brown WR, Hibi T, Oshima A, Morikawa M;. J Biol Chem. 1997;272:15232-15241. (from Pfam) NF036965.5 PF17651.6 Raco_middle 26.8 26.8 163 domain Y N N RACo middle region 22431597 131567 cellular organisms no rank 9460 EBI-EMBL RACo middle region RACo middle region This family includes reductive activator of CoFeSP (RACo) proteins, Swiss:Q3ACS2. Structure analysis of RACo indicate that it contains 4 regions: N-terminal region Pfam:PF00111 (residues 3-94) binding the [2Fe-2S] cluster, a linker region (residues 95-125), the middle region (residues 126-206), and the large C-terminal domain Pfam:PF14574 (residues 207-630). This entry pertains to the middle region. This region contains residues in their alpha-helices (H6 and H7) that mediate dimerization with subdomain I of the C-terminal domain. [1]. 22431597. Redox-dependent complex formation by an ATP-dependent activator of the corrinoid/iron-sulfur protein. Hennig SE, Jeoung JH, Goetzl S, Dobbek H;. Proc Natl Acad Sci U S A. 2012;109:5235-5240. (from Pfam) NF036966.5 PF17652.6 Glyco_hydro81C 25.6 25.6 349 domain Y Y N glycosyl hydrolase 19542306 131567 cellular organisms no rank 6217 EBI-EMBL Glycosyl hydrolase family 81 C-terminal domain glycosyl hydrolase family 81 C-terminal domain Family of eukaryotic beta-1,3-glucanases. Within the Aspergillus fumigatus protein Swiss:Q9UVV0 two perfectly conserved Glu residues (E550 or E554) have been proposed as putative nucleophiles of the active site of the Engl1 endoglucanase, while the proton donor would be D475. The endo-beta-1,3-glucanase activity is essential for efficient spore release [1]. This entry represents the helical C-terminal domain. [1]. 19542306. {beta}-glucanase Eng2 is required for ascus wall endolysis after sporulation in the fission yeast Schizosaccharomyces pombe. Encinar del Dedo J, Duenas E, Arnaiz Y, del Rey F, Vazquez de Aldana CR;. Eukaryot Cell. 2009;8:1278-1286. (from Pfam) NF036971.5 PF17667.6 Pkinase_fungal 24.1 24.1 387 domain Y N N Fungal protein kinase 131567 cellular organisms no rank 9355 EBI-EMBL Fungal protein kinase Fungal protein kinase This domain appears to be a variant of the protein kinase domain that is found in a variety of fungal species. (from Pfam) NF036972.5 PF17674.6 HHH_9 23.1 23.1 70 domain Y N N HHH domain 131567 cellular organisms no rank 77214 EBI-EMBL HHH domain HHH domain NF036989.5 PF17723.6 RHH_8 25.4 25.4 119 domain Y N N Ribbon-Helix-Helix transcriptional regulator family 131567 cellular organisms no rank 2893 EBI-EMBL Ribbon-Helix-Helix transcriptional regulator family Ribbon-Helix-Helix transcriptional regulator family This family of proteins are likely to be transcriptional regulators that have an N-terminal ribbon-helix-helix domain. Although some members of the family are annotated as CopG, this family does not include that protein. (from Pfam) NF036995.5 PF17761.6 DUF1016_N 32.8 32.8 137 domain Y Y N DUF1016 N-terminal domain-containing protein 131567 cellular organisms no rank 27052 EBI-EMBL DUF1016 N-terminal domain DUF1016 N-terminal domain This family may include an HTH domain. (from Pfam) NF036996.5 PF17763.6 Asparaginase_C 34.6 34.6 114 domain Y N N Glutaminase/Asparaginase C-terminal domain 16216574 131567 cellular organisms no rank 65448 EBI-EMBL Glutaminase/Asparaginase C-terminal domain Glutaminase/Asparaginase C-terminal domain This domain is found at the C-terminus of asparaginase enzymes. [1]. 16216574. Structural basis for tRNA-dependent amidotransferase function. Schmitt E, Panvert M, Blanquet S, Mechulam Y;. Structure. 2005;13:1421-1433. (from Pfam) NF036998.5 PF17767.6 NAPRTase_N 32.6 32.6 125 domain Y N N Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain 16154095 131567 cellular organisms no rank 62132 EBI-EMBL Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain Nicotinate phosphoribosyltransferase (EC:2.4.2.11) is the rate limiting enzyme that catalyses the first reaction in the NAD salvage synthesis. This is the N-terminal domain of the enzyme. [1]. 16154095. The structure of a eukaryotic nicotinic acid phosphoribosyltransferase reveals structural heterogeneity among type II PRTases. Chappie JS, Canaves JM, Han GW, Rife CL, Xu Q, Stevens RC;. Structure. 2005;13:1385-1396. (from Pfam) NF036999.5 PF17777.6 RL10P_insert 29.1 29.1 71 domain Y N N Insertion domain in 60S ribosomal protein L10P 20399793 131567 cellular organisms no rank 1387 EBI-EMBL Insertion domain in 60S ribosomal protein L10P Insertion domain in 60S ribosomal protein L10P This domain is found in prokaryotic and archaeal ribosomal L10 protein [1]. [1]. 20399793. Structure of a two-domain N-terminal fragment of ribosomal protein L10 from Methanococcus jannaschii reveals a specific piece of the archaeal ribosomal stalk. Kravchenko O, Mitroshin I, Nikonov S, Piendl W, Garber M;. J Mol Biol. 2010;399:214-220. (from Pfam) NF037000.5 PF17791.6 MG3 23.1 23.1 84 domain Y N N Macroglobulin domain MG3 131567 cellular organisms no rank 259 EBI-EMBL Macroglobulin domain MG3 Macroglobulin domain MG3 This entry corresponds to the MG3 domain found in complement components C3, C4 and C5. (from Pfam) NF037003.5 PF17801.6 Melibiase_C 22.9 22.9 71 domain Y N N Alpha galactosidase C-terminal beta sandwich domain 26330557 131567 cellular organisms no rank 30690 EBI-EMBL Alpha galactosidase C-terminal beta sandwich domain Alpha galactosidase C-terminal beta sandwich domain This domain is found at the C-terminus of alpha galactosidase enzymes. [1]. 26330557. Crystal Structure and Mutational Analysis of Isomalto-dextranase, a Member of Glycoside Hydrolase Family 27. Okazawa Y, Miyazaki T, Yokoi G, Ishizaki Y, Nishikawa A, Tonozuka T;. J Biol Chem. 2015;290:26339-26349. (from Pfam) NF037007.5 PF17938.6 TetR_C_29 26.2 26.2 119 domain Y N N Tetracyclin repressor-like, C-terminal domain 131567 cellular organisms no rank 26452 EBI-EMBL Tetracyclin repressor-like, C-terminal domain Tetracyclin repressor-like, C-terminal domain This domain is found in the C-terminal region of putative TetR-family regulatory proteins. (from Pfam) NF037009.5 PF17940.6 TetR_C_31 27.4 27.4 107 domain Y N N Tetracyclin repressor-like, C-terminal domain 131567 cellular organisms no rank 50288 EBI-EMBL Tetracyclin repressor-like, C-terminal domain Tetracyclin repressor-like, C-terminal domain This is the C-terminal domain found in putative transcriptional regulator, TetR family proteins. (from Pfam) NF037012.5 PF17954.6 Pirin_C_2 22.9 22.9 86 domain Y N N Quercetinase C-terminal cupin domain 15951572,18561187 131567 cellular organisms no rank 47191 EBI-EMBL Quercetinase C-terminal cupin domain Quercetinase C-terminal cupin domain Experiments on the YhhW protein show that is has quercetinase activity. This entry represents the C-terminal cupin domain from the two cupin domains that make up the protein [1]. This domain is usually associated with Pfam:PF02678. [1]. 15951572. Structural and biochemical analysis reveal pirins to possess quercetinase activity. Adams M, Jia Z;. J Biol Chem. 2005;280:28675-28682. [2]. 18561187. The crystal structure of the protein YhaK from Escherichia coli reveals a new subclass of redox sensitive enterobacterial bicupins. Gurmu D, Lu J, Johnson KA, Nordlund P, Holmgren A, Erlandsen H;. Proteins. 2009;74:18-31. (from Pfam) NF037013.5 PF17955.6 Cas6b_N 25 25 105 domain Y N N Cas6b N-terminal domain 25451598,26996962,28238733 131567 cellular organisms no rank 796 EBI-EMBL Cas6b N-terminal domain Cas6b N-terminal domain Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation [1]. Four Cas proteins (Cas5, Cas6b, Cas7 and Cas8b) are proposed to form a Type I-B Cascade complex that mediates the antiviral defense [2]. This is the N-terminal domain found in Cas6b proteins. Cas6b is a member of Cas6 RNA processing endoribonucleases found in bacteria and archaea whose RNA substrates have a wide range of structural features. Cocrystal structures of Cas6 from Methanococcus maripaludis (MmCas6b) bound with its repeat RNA revealed a dual-site binding structure and a cleavage site conformation poised for phosphodiester bond breakage [3]. [1]. 25451598. Crystal structure of the Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex. Numata T, Inanaga H, Sato C, Osawa T;. J Mol Biol. 2015;427:259-273. [2]. 28238733. Fragmentation of the CRISPR-Cas Type I-B signature protein Cas8b. Richter H, Rompf J, Wiegel J, Rau K, Randau L;. Biochim Biophys Acta. 2017; [Epub ahead of print]. [3]. 26996962. A Non-Stem-Loop CRISPR RNA Is Processed by Dual Binding Cas6. Shao Y, Richter H, Sun S, Sharma K, Urlaub H, Randau L, Li H;. Structure. 2016;24:547-554. (from Pfam) NF037014.5 PF17956.6 NAPRTase_C 23.3 23.3 111 domain Y N N Nicotinate phosphoribosyltransferase C-terminal domain 131567 cellular organisms no rank 20186 EBI-EMBL Nicotinate phosphoribosyltransferase C-terminal domain Nicotinate phosphoribosyltransferase C-terminal domain This domain is found at the C-terminus of some Nicotinate phosphoribosyltransferase enzymes. The function of this domain is uncertain. (from Pfam) NF037015.5 PF17957.6 Big_7 24.1 24.1 70 domain Y Y N Ig-like domain-containing protein 16171384,22349231 131567 cellular organisms no rank 39181 EBI-EMBL Bacterial Ig domain Ig-like domain This entry represents a bacterial ig-like domain that is found in glycosyl hydrolase enzymes. [1]. 22349231. Structure and function of the Clostridium thermocellum cellobiohydrolase A X1-module repeat: enhancement through stabilization of the CbhA complex. Brunecky R, Alahuhta M, Bomble YJ, Xu Q, Baker JO, Ding SY, Himmel ME, Lunin VV;. Acta Crystallogr D Biol Crystallogr. 2012;68:292-299. [2]. 16171384. The structure and characterization of a modular endo-beta-1,4-mannanase from Cellulomonas fimi. Le Nours J, Anderson L, Stoll D, Stalbrand H, Lo Leggio L;. Biochemistry. 2005;44:12700-12708. (from Pfam) NF037016.5 PF17963.6 Big_9 23.6 23.6 89 domain Y Y N Ig-like domain-containing protein 21606337 131567 cellular organisms no rank 151838 EBI-EMBL Bacterial Ig domain Ig-like domain This entry represents a wide variety of bacterial Ig domains. [1]. 21606337. Structure of a bacterial cell surface decaheme electron conduit. Clarke TA, Edwards MJ, Gates AJ, Hall A, White GF, Bradley J, Reardon CL, Shi L, Beliaev AS, Marshall MJ, Wang Z, Watmough NJ, Fredrickson JK, Zachara JM, Butt JN, Richardson DJ;. Proc Natl Acad Sci U S A. 2011;108:9384-9389. (from Pfam) NF037019.5 PF17974.6 GalBD_like 26 26 190 domain Y N N Galactose-binding domain-like 10467102,10586886,11780069,18784084,2002850 131567 cellular organisms no rank 9152 EBI-EMBL Galactose-binding domain-like Galactose-binding domain-like Proteins containing a galactose-binding domain-like fold can be found in several different protein families, in both eukaryotes and prokaryotes. The common function of these domains is to bind to specific ligands, such as cell-surface-attached carbohydrate substrates for galactose oxidase and sialidase [1], phospholipids on the outer side of the mammalian cell membrane for coagulation factor Va [2], membrane-anchored ephrin for the Eph family of receptor tyrosine kinases [3], and a complex of broken single-stranded DNA and DNA polymerase beta for XRCC1 [4]. The structure of the galactose-binding domain-like members consists of a beta-sandwich, in which the strands making up the sheets exhibit a jellyroll fold [5]. [1]. 2002850. Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase. Ito N, Phillips SE, Stevens C, Ogel ZB, McPherson MJ, Keen JN, Yadav KD, Knowles PF;. Nature 1991;350:87-90. [2]. 10586886. Crystal structures of the membrane-binding C2 domain of human coagulation factor V. Macedo-Ribeiro S, Bode W, Huber R, Quinn-Allen MA, Kim SW, Ortel TL, Bourenkov GP, Bartunik HD, Stubbs MT, Kane WH, Fuentes-Prior P;. Nature. 1999;402:434-439. [3]. 11780069. Crystal structure of an Eph receptor-ephrin complex. Himanen JP, Rajashankar KR, Lackmann M, Cowan CA, Henkemeyer M, Nikolov DB;. Nature. 2001;414:933-938. [4]. 10467102. Solution structure of the single-strand break repair protein XRCC1 N- terminal domain. Marintchev A, Mullen MA, Maciejewski MW, Pan B, Gryk MR, Mullen GP;. Nat Struct Biol 1999;6:884-893. [5]. 18784084. The structural basis for T-antigen hydrolysis by Streptococcus pneumoniae. TRUNCATED at 1650 bytes (from Pfam) NF037020.5 PF17991.6 Thioredoxin_10 27.1 27.1 142 domain Y N N Thioredoxin like C-terminal domain 16511006,26894533 131567 cellular organisms no rank 9467 EBI-EMBL Thioredoxin like C-terminal domain Thioredoxin like C-terminal domain This is the C-terminal thioredoxin like domain found in Rv2874 in the pathogenic bacterium Mycobacterium tuberculosis [1]. Structure analysis of Rv2874-C shows the presence of a C-terminal domain formed by the 128 residues Thr568-Gly695. These residues form a jelly-roll structure in which two antiparallel beta-sheets sandwich a hydrophobic core. This domain is combined with a second domain with a carbohydrate-binding module (CBM) fold [2]. [1]. 16511006. Crystallization and preliminary diffraction studies of the C-terminal domain of the DipZ homologue from Mycobacterium tuberculosis. Goldstone D, Baker EN, Metcalf P;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005;61:243-245. [2]. 26894533. Structure of the ectodomain of the electron transporter Rv2874 from Mycobacterium tuberculosis reveals a thioredoxin-like domain combined with a carbohydrate-binding module. Goldstone DC, Metcalf P, Baker EN;. Acta Crystallogr D Struct Biol. 2016;72:40-48. (from Pfam) NF037026.5 PF18014.6 Acetyltransf_18 22.7 22.7 124 domain Y N N Acetyltransferase (GNAT) domain 131567 cellular organisms no rank 28143 EBI-EMBL Acetyltransferase (GNAT) domain Acetyltransferase (GNAT) domain This entry represents a likely acetyltransferase enzyme that is related to Pfam:PF06852. (from Pfam) NF037028.5 PF18022.6 Lectin_C_term 27.1 27.1 102 domain Y N N Ricin-type beta-trefoil lectin C-terminal domain 21436237 131567 cellular organisms no rank 140 EBI-EMBL Ricin-type beta-trefoil lectin C-terminal domain Ricin-type beta-trefoil lectin C-terminal domain This is the C-terminal domain of the beta chain found in Polyporus squamosus lectin protein (PSL). PSL binds specifically to glycans terminating with the sequence: Neu5Ac.alpha2-6Gal.beta. The C-terminal domain is not involved in the binding to the Neu5Ac.alpha2-6Gal.beta. The C-terminal domain is characterized by a central five-stranded beta-sheet that is flanked by three alpha-helices and topped by a short strand. It shows high fold similarity to its closest relative, the Gal.alpha1-3Gal-binding agglutinin from the mushroom Marasmius oreades agglutinin (MOA) [1]. [1]. 21436237. Structure and binding analysis of Polyporus squamosus lectin in complex with the Neu5Ac{alpha}2-6Gal{beta}1-4GlcNAc human-type influenza receptor. Kadirvelraj R, Grant OC, Goldstein IJ, Winter HC, Tateno H, Fadda E, Woods RJ;. Glycobiology. 2011;21:973-984. (from Pfam) NF037030.5 PF18025.6 FucT_N 27.2 27.2 91 domain Y N N Alpha-(1,3)-fucosyltransferase FucT N-terminal domain 17251184 131567 cellular organisms no rank 3580 EBI-EMBL Alpha-(1,3)-fucosyltransferase FucT N-terminal domain Alpha-(1,3)-fucosyltransferase FucT N-terminal domain This is the N-terminal domain of the alpha chain found in Helicobacter pylori Fucosyltransferase protein which is involved in the production of Lewis x trisaccharide, a major component of lipopolysaccharide. The N-terminal domain contains the catalyst base, Glu-95 which is equivalent to the Asp-100 of other members of the glycosyltransferases-B family. The domain contains the pocket where LacNAc binds. The domain is composed of 2-10 heptad repeats and a conserved N-terminal alpha-beta-alpha motif which has little sequence similarity to the conserved N-terminal motif in other glycosyltransferases [1]. [1]. 17251184. Structure and mechanism of Helicobacter pylori fucosyltransferase. A basis for lipopolysaccharide variation and inhibitor design. Sun HY, Lin SW, Ko TP, Pan JF, Liu CL, Lin CN, Wang AH, Lin CH;. J Biol Chem. 2007;282:9973-9982. (from Pfam) NF037031.5 PF18027.6 Pepdidase_M14_N 23.2 23.2 107 subfamily_domain Y Y N M14-type cytosolic carboxypeptidase 24531462 131567 cellular organisms no rank 10899 EBI-EMBL Cytosolic carboxypeptidase N-terminal domain M14-type cytosolic carboxypeptidase N-terminal domain This entry corresponds to the N-terminal domain of cytosolic carboxypeptidases. The N-terminal domain folds into a nine-stranded antiparallel beta sandwich [1]. This domain is specific to CCP proteins and is absent in other carboxypeptidases. It has been hypothesised that the N-terminal domain might contribute to folding, might have a regulatory function and/or might be involved in binding other proteins. [1]. 24531462. High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB_REDO strategies. Rimsa V, Eadsforth TC, Joosten RP, Hunter WN;. Acta Crystallogr D Biol Crystallogr. 2014;70:279-289. (from Pfam) NF037032.5 PF18030.6 Rimk_N 26.4 26.4 94 domain Y N N RimK PreATP-grasp domain 23609986 131567 cellular organisms no rank 15383 EBI-EMBL RimK PreATP-grasp domain RimK PreATP-grasp domain This is the N-terminal domain found in Escherichia coli RimK proteins (Ribosomal protein S6-L-glutamate ligase). This domain precedes the ATP-grasp domain Pfam:PF08443 [1]. [1]. 23609986. Structure and function of Escherichia coli RimK, an ATP-grasp fold, L-glutamyl ligase enzyme. Zhao G, Jin Z, Wang Y, Allewell NM, Tuchman M, Shi D;. Proteins. 2013;81:1847-1854. (from Pfam) NF037034.5 PF18065.6 PatG_C 25.9 25.9 115 domain Y N N PatG C-terminal 25484206 131567 cellular organisms no rank 1890 EBI-EMBL PatG C-terminal PatG C-terminal This is the C-terminal domain of Prochloron sp. PatG, which process the precursor peptide to yield the cyclic Patellamide. The C-terminal domain of PatG is 56% structurally homologous to the C-terminal domain of PatA [1]. [1]. 25484206. The structure of the cyanobactin domain of unknown function from PatG in the patellamide gene cluster. Mann G, Koehnke J, Bent AF, Graham R, Houssen W, Jaspars M, Schwarz-Linek U, Naismith JH;. Acta Crystallogr F Struct Biol Commun. 2014;70:1597-1603. (from Pfam) NF037036.5 PF18067.6 Lipase_C 27 27 96 domain Y N N Lipase C-terminal domain 19447113 131567 cellular organisms no rank 1699 EBI-EMBL Lipase C-terminal domain Lipase C-terminal domain This domain is found in Archaeoglobus fulgidus lipase (AFL). The domain consists of a layer of seven beta-sheet. When the domain is combined with the proximal domain, which is also a layer of seven beta-sheet, they form a beta sandwich. The combination of these two domains is known as the C-terminal domain. It is likely that the C-terminal domain plays an important role in substrate specificity, catalytic efficiency but also attributes partly to AFLs stability [1]. [1]. 19447113. Structure of the alkalohyperthermophilic Archaeoglobus fulgidus lipase contains a unique C-terminal domain essential for long-chain substrate binding. Chen CK, Lee GC, Ko TP, Guo RT, Huang LM, Liu HJ, Ho YF, Shaw JF, Wang AH;. J Mol Biol. 2009;390:672-685. (from Pfam) NF037043.5 PF18096.6 Thump_like 26 26 78 domain Y Y N THUMP-like domain-containing protein 131567 cellular organisms no rank 26024 EBI-EMBL THUMP domain-like THUMP-like domain Most proteins with this domain at the C-terminus are annotated as methyltransferases. NF037045.5 PF18127.6 NAMPT_N 25 25 98 domain Y Y N nicotinamide phosphoribosyltransferase domain-containing protein 19819904 131567 cellular organisms no rank 7831 EBI-EMBL Nicotinamide phosphoribosyltransferase, N-terminal domain Nicotinamide phosphoribosyltransferase, N-terminal domain This is the N-terminal domain found in Nicotinamide phosphoribosyltransferase (NAMPT) present in Homo sapiens. NAMPT captures nicotinamide (NAM) and replenish the nicotinamide adenine dinucleotide (NAD+) pool during ADP-ribosylation and transferase reactions [1]. [1]. 19819904. Structure and reaction mechanism of human nicotinamide phosphoribosyltransferase. Takahashi R, Nakamura S, Nakazawa T, Minoura K, Yoshida T, Nishi Y, Kobayashi Y, Ohkubo T;. J Biochem. 2010;147:95-107. (from Pfam) NF037047.5 PF18130.6 ATPgrasp_N 27 27 81 domain Y N N ATP-grasp N-terminal domain 23090402 131567 cellular organisms no rank 13743 EBI-EMBL ATP-grasp N-terminal domain ATP-grasp N-terminal domain This is the N-terminal domain found in BL00235 present in Bacillus licheniformis. BL00235 is a ATP-grasp superfamily protein that catalyzes the formation of an alpha-peptide bond between two L-amino acids in an ATP-dependent manner. BL00235 has a highly restricted substrate specificity: the N-terminal substrate is confined to L-methionine an L-leucine, while the C-terminal substrates include small residues such as L-alanine, L-serine, L-threonine and L-cysteine [1]. [1]. 23090402. The structure of L-amino-acid ligase from Bacillus licheniformis. Suzuki M, Takahashi Y, Noguchi A, Arai T, Yagasaki M, Kino K, Saito J;. Acta Crystallogr D Biol Crystallogr. 2012;68:1535-1540. (from Pfam) NF037060.5 PF18182.6 mCpol 26.4 26.4 114 domain Y N N minimal CRISPR polymerase domain 26590262 131567 cellular organisms no rank 1000 EBI-EMBL minimal CRISPR polymerase domain minimal CRISPR polymerase domain Minimal version of the CRISPR polymerase domain. Predicted to generate cyclic nucleotides, potentially sensed by CARF domains which in turn activate various effector domain including HEPN RNases, CARF sensor and effectors are found in conserved genome contexts. Part of a broader class of conflict systems reliant on the production of second messenger nucleotide or nucleotide derivatives. Implicates CRISPR polymerase of the Type III CRISPR/Cas systems in a nucleotide synthetase functional role [1]. [1]. 26590262. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;. Nucleic Acids Res. 2015;43:10633-10654. (from Pfam) NF037061.5 PF18184.6 SLATT_3 26.3 26.3 155 domain Y N N SMODS and SLOG-associating 2TM effector domain 3 26590262 131567 cellular organisms no rank 4368 EBI-EMBL SMODS and SLOG-associating 2TM effector domain 3 SMODS and SLOG-associating 2TM effector domain 3 The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is always N-terminally fused to the SLATT_1 family, and is typically operonically linked to either inactive TIR domains or SLOG domains which could act as regulators of the SLATT channels [1]. [1]. 26590262. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;. Nucleic Acids Res. 2015;43:10633-10654. (from Pfam) NF037063.5 PF18201.6 PIH1_CS 23.3 23.3 100 domain Y N N PIH1 CS-like domain 24794838 131567 cellular organisms no rank 81 EBI-EMBL PIH1 CS-like domain PIH1 CS-like domain This domain is found in yeast PIH1 and its homologues. This domain consists of a seven-stranded beta sandwich with the topology of a CS domain, a structural motif also found in Hsp90 co-chaperones such as p23/Sba1 and Sgt1 [1]. [1]. 24794838. Structural basis for phosphorylation-dependent recruitment of Tel2 to Hsp90 by Pih1. Pal M, Morgan M, Phelps SE, Roe SM, Parry-Morris S, Downs JA, Polier S, Pearl LH, Prodromou C;. Structure. 2014;22:805-818. (from Pfam) NF037066.5 PF18211.6 Csm1_B 26.4 26.4 94 domain Y N N Csm1 subunit domain B 25773141 131567 cellular organisms no rank 2704 EBI-EMBL Csm1 subunit domain B Csm1 subunit domain B This domain is found in the Csm1 subunit of the Csm complex found in Thermococcus onnurineus. Csm is a type III-A CRISPR-Cas system, which is an RNA-guided immune defense mechanism that detects and destroys foreign DNA or RNA. This domain is known as domain A and is positioned side by side with domain C. Both domain A and domain C adopt the BABBA topology. Domain A interacts primarily with domain B [1]. [1]. 25773141. Crystal structure of the Csm1 subunit of the Csm complex and its single-stranded DNA-specific nuclease activity. Jung TY, An Y, Park KH, Lee MH, Oh BH, Woo E;. Structure. 2015;23:782-790. (from Pfam) NF037074.5 PF18243.6 BfiI_DBD 25 25 165 domain Y N N Metal-independent restriction enzyme BfiI DNA binding domain 16247004 131567 cellular organisms no rank 73 EBI-EMBL Metal-independent restriction enzyme BfiI DNA binding domain Metal-independent restriction enzyme BfiI DNA binding domain This domain is found in the metal-independent restriction enzyme BfiI present in Bacillus firmus. This domain is found in the C-terminal of the protein and is responsible for DNA binding. The domain exhibits a beta-barrel-like structure similar to the effector DNA-binding domain of the Mg2+ dependent restriction enzyme EcoRII and to the B3-like DNA-binding domain of plant transcription factors [1]. [1]. 16247004. Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease. Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V;. Proc Natl Acad Sci U S A. 2005;102:15797-15802. (from Pfam) NF037084.5 PF18318.6 Gln-synt_C-ter 22.7 22.7 118 domain Y N N Glutamine synthetase C-terminal domain 21481771 131567 cellular organisms no rank 14883 EBI-EMBL Glutamine synthetase C-terminal domain Glutamine synthetase C-terminal domain This domain is found in type III glutamine synthetase present in Bacteroides fragilis. Glutamine synthetase (GS) are large oligomeric enzymes that catalyze the condensation of ammonium and glutamate to form glutamine, the principal source of nitrogen for protein and nucleic acid synthesis. This domain is located in the C-terminal end of the protein [1]. [1]. 21481771. Crystal structure of Type III glutamine synthetase: surprising reversal of the inter-ring interface. van Rooyen JM, Abratt VR, Belrhali H, Sewell T;. Structure. 2011;19:471-483. (from Pfam) NF037094.5 PF18732.6 HEPN_AbiA_CTD 27 27 132 domain Y Y N Abia family HEPN domain-containing protein 23768067 131567 cellular organisms no rank 199 EBI-EMBL HEPN like, Abia C-terminal domain Abia C-terminal family HEPN domain AbiA-CTD-like HEPN nuclease. Fused to Reverse Transcriptase ; in operon with R-M system [1]. [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF037095.5 PF18733.6 HEPN_LA2681 27 27 204 domain Y Y N LA2681 family HEPN domain-containing protein 23768067 131567 cellular organisms no rank 2180 EBI-EMBL LA2681-like HEPN LA2681 family HEPN domain LA2681-like HEPN nuclease [1]. [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF037096.5 PF18739.6 HEPN_Apea 24.4 24.4 136 domain Y Y N HEPN domain-containing protein 23768067 131567 cellular organisms no rank 4529 EBI-EMBL Apea-like HEPN BMEI1217-like HEPN domain Apea-like HEPN nuclease. In epsilonproteobacteria embedded in R-M operons [1]. [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF037099.5 PF18761.6 Heliorhodopsin 26.7 26.7 242 domain Y N N Heliorhodopsin 29925949,31554965,32034096 131567 cellular organisms no rank 969 EBI-EMBL Heliorhodopsin Heliorhodopsin Heliorhodopsins, distantly related to type-1 rhodopsins, are embedded in the membrane with their N termini facing the cell cytoplasm, an orientation that is opposite to that of type-1 or type-2 rhodopsins. Heliorhodopsins show photocycles that are longer than one second, which is suggestive of light-sensory activity. Heliorhodopsin photocycles accompany retinal isomerization and proton transfer, as in type-1 and type-2 rhodopsins, but protons are never released from the protein [1].The structures of several heliorhodopsins have been solved displaying seven transmembrane helices (TM), six loops and short N and C termini [2,3]. Heliorhodopsins share a common fold with the type-1 rhodopsins, however there are clear structural differences, particularly within the loop regions and the large cavity in the cytoplasmic part of heliorhodpsin [2,3]. Heliorhodpsins are present in Archaea, Bacteria, Eukarya, and viruses [3]. [1]. 29925949. A distinct abundant group of microbial rhodopsins discovered using functional metagenomics. Pushkarev A, Inoue K, Larom S, Flores-Uribe J, Singh M, Konno M, Tomida S, Ito S, Nakamura R, Tsunoda SP, Philosof A, Sharon I, Yutin N, Koonin EV, Kandori H, Beja O;. Nature. 2018;558:595-599. [2]. 31554965. Crystal structure of heliorhodopsin. Shihoya W, Inoue K, Singh M, Konno M, Hososhima S, Yamashita K, Ikeda K, Higuchi A, Izume T, Okazaki S, Hashimoto M, Mizutori R, Tomida S, Yamauchi Y, Abe-Yoshizumi R, Katayama K, Tsunoda SP, Shibata M, Furutani Y, Pushkarev A, Beja O, Uchihashi T, Kandori H, Nureki O;. Nature. 2019;574:132-136. [3]. 32034096. High-resolution structural insights into the heliorhodopsi. TRUNCATED at 1650 bytes (from Pfam) NF037100.5 PF18765.6 Polbeta 26.9 26.9 93 domain Y N N Polymerase beta, Nucleotidyltransferase 22731697,28559295 131567 cellular organisms no rank 55923 EBI-EMBL Polymerase beta, Nucleotidyltransferase Polymerase beta, Nucleotidyltransferase A member of the nucleotidyltransferase fold found in polymorphic toxins (NTox45) and polyvalent proteins [1]. [1]. 28559295. Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. Iyer LM, Burroughs AM, Anand S, de Souza RF, Aravind L;. J Bacteriol. 2017; [Epub ahead of print]. [2]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF037126.5 PF18863.6 AbiJ_NTD4 34 34 152 domain Y Y N AbiJ-NTD4 domain-containing protein 23768067 131567 cellular organisms no rank 4205 EBI-EMBL AbiJ N-terminal domain 4 AbiJ-NTD4 domain Alpha + beta. Found fused to AbiJ-like HEPN and heat repeats [1]. [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF037127.5 PF18865.6 AbiJ_NTD5 26.7 26.7 93 domain Y N N AbiJ N-terminal domain 5 23768067 131567 cellular organisms no rank 490 EBI-EMBL AbiJ N-terminal domain 5 AbiJ N-terminal domain 5 Mostly alpha helical. Found fused to AbiJ-lke HEPN, and to other domains presumably involved in defense [1]. [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF037131.5 PF17805.6 AsnC_trans_reg2 27 27 86 domain Y N N AsnC-like ligand binding domain 24865947 131567 cellular organisms no rank 11465 EBI-EMBL AsnC-like ligand binding domain AsnC-like ligand binding domain This entry contains an AsnC-like ligand binding domain. [1]. 24865947. The structure, function and properties of sirohaem decarboxylase--an enzyme with structural homology to a transcription factor family that is part of the alternative haem biosynthesis pathway. Palmer DJ, Schroeder S, Lawrence AD, Deery E, Lobo SA, Saraiva LM, McLean KJ, Munro AW, Ferguson SJ, Pickersgill RW, Brown DG, Warren MJ;. Mol Microbiol. 2014;93:247-261. (from Pfam) NF037134.5 PF17835.6 NOG1_N 22.9 22.9 160 domain Y N N NOG1 N-terminal helical domain 131567 cellular organisms no rank 1601 EBI-EMBL NOG1 N-terminal helical domain NOG1 N-terminal helical domain This domain is found at the N-terminus of NOG1 GTPase proteins. (from Pfam) NF037139.5 PF17862.6 AAA_lid_3 27.2 27.2 45 domain Y N N AAA+ lid domain 131567 cellular organisms no rank 112363 EBI-EMBL AAA+ lid domain AAA+ lid domain This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. (from Pfam) NF037140.5 PF17864.6 AAA_lid_4 27 27 74 domain Y N N RuvB AAA lid domain 12423347 131567 cellular organisms no rank 56059 EBI-EMBL RuvB AAA lid domain RuvB AAA lid domain The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein [1]. This entry contains the AAA lid domain that is found to the C-terminus of the AAA domain. [1]. 12423347. The RuvABC resolvasome. Dickman MJ, Ingleston SM, Sedelnikova SE, Rafferty JB, Lloyd RG, Grasby JA, Hornby DP;. Eur J Biochem 2002;269:5492-5501. (from Pfam) NF037142.5 PF17884.6 DUF5591 26 26 150 domain Y Y N DUF5591 domain-containing protein 131567 cellular organisms no rank 1952 EBI-EMBL Domain of unknown function (DUF5591) Domain of unknown function (DUF5591) This is a domain of unknown function found in archaeal tRNA-guanine transglycosylase (EC:2.4.2.48) and in archaeosine synthase (EC:2.6.1.97) proteins. (from Pfam) NF037143.5 PF17886.6 ArsA_HSP20 22.5 22.5 63 domain Y N N HSP20-like domain found in ArsA 131567 cellular organisms no rank 48092 EBI-EMBL HSP20-like domain found in ArsA HSP20-like domain found in ArsA This domain is found at the C-terminus of ArsA like proteins. This domain is related to HSP20. (from Pfam) NF037144.5 PF17892.6 Cadherin_5 26.5 26.5 98 domain Y Y N cadherin-like domain-containing protein 131567 cellular organisms no rank 72379 EBI-EMBL Cadherin-like domain cadherin-like domain NF037152.5 PF17935.6 TetR_C_27 26.1 26.1 106 domain Y N N Tetracyclin repressor-like, C-terminal domain 131567 cellular organisms no rank 16890 EBI-EMBL Tetracyclin repressor-like, C-terminal domain Tetracyclin repressor-like, C-terminal domain This is the C-terminal domain present in putative TetR transcriptional regulators. (from Pfam) NF037153.5 PF17953.6 Csm4_C 25.9 25.9 91 domain Y N N CRISPR Csm4 C-terminal domain 25451598 131567 cellular organisms no rank 1501 EBI-EMBL CRISPR Csm4 C-terminal domain CRISPR Csm4 C-terminal domain Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. The interference complex of the type III-A CRISPR-Cas system is composed of five Cas proteins (Csm1-Csm5) and a crRNA, and targets invading DNA. This entry represents the C-terminal domain found in Csm4. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR-Cas interference complex. Studies indicate that Csm3-Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Structural analysis show , Csm3 and Csm4 have one and two ferredoxin-like folds (also known as an RRM-like fold), respectively. The long beta-hairpin inserted into the C-terminal ferredoxin-like fold of Csm4, is well-conserved in the Cmr3 structure. The corresponding beta-hairpin of Cmr3 binds the D1 domain of Cmr2, as observed in the Cmr2-Cmr3 complex structure. Furthermore, it is suggested that the hairpin of Csm4 is responsible for the interaction with Csm1 (ortholog of Cmr2) [1]. [1]. 25451598. Crystal structure of the Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex. Numata T, Inanaga H, Sato C, Osawa T;. J Mol Biol. 2015;427:259-273. (from Pfam) NF037161.5 PF17989.6 ALP_N 26.3 26.3 148 domain Y N N Actin like proteins N terminal domain 16500678,27310470 131567 cellular organisms no rank 11313 EBI-EMBL Actin like proteins N terminal domain Actin like proteins N terminal domain This is the N-terminal domain found in archaeal actin homolog Ta0583 found in thermophilic archaeon Thermoplasma acidophilum. Structural analysis indicate that the fold of Ta0583 contains the core structure of actin indicating that it belongs to the actin/Hsp70 superfamily of ATPases. Furthermore,Ta0583 co-crystallised with ADP shows that the nucleotide binds at the interface between the subdomains of Ta0583 in a manner similar to that of actin. It has been suggested that Ta0583 might function in the cellular organisation of T. acidophilum [1]. Other family members include ParM another actin-like protein found in Staphylococcus aureus. Crystal structure co-ordinates revealed that this protein is most structurally related to the chromosomally encoded Actin-like proteins (Alp) Ta0583 from the archaea Thermoplasma acidophilum. Furthermore, biophysical analyses have suggested that ParM filaments undergo a treadmilling-like mechanism of motion in vitro similar to that of F-actin. The recruitment of ParM to the segrosome complex, was shown to be required for the conversion of static ParM filaments to a dynamic form proficient for active segregation and facilitated by the C-terminus of ParR [2] [1]. 16500678. Crystal structure of an archaeal actin homolog. Roeben A, Kofler C, Nagy I, Nickell S, Hartl FU, Bracher A;. J Mol Biol. 2006;358:145-156. [2]. 27310470. Dynamic Filament Formation by a Divergent Bacterial Actin-Like ParM Protein. Brzoska AJ, Jensen SO, Barton DA, Davies DS, Overall RL, Skurray RA, Firth N;. PLoS One. 2016;11:e0156944. (from Pfam) NF037167.5 PF18015.6 Acetyltransf_19 23.8 23.8 113 domain Y N N Acetyltransferase (GNAT) domain 131567 cellular organisms no rank 845 EBI-EMBL Acetyltransferase (GNAT) domain Acetyltransferase (GNAT) domain This entry represents a likely acetyltransferase enzyme that is related to Pfam:PF13302. (from Pfam) NF037170.5 PF18029.6 Glyoxalase_6 23.6 23.6 106 domain Y Y N VOC family protein 131567 cellular organisms no rank 348746 EBI-EMBL Glyoxalase-like domain VOC family protein Members of this family belong to the VOC (vicinal oxygen chelate) superfamily, which includes enzymes such as glyoxalase I (lactoylglutathione lyase, EC 4.4.1.5). NF037180.5 PF18072.6 FGAR-AT_linker 26.6 26.6 50 domain Y N N Formylglycinamide ribonucleotide amidotransferase linker domain 15301531,16544324,17154526,18597481,22232163,22683785,24223728 131567 cellular organisms no rank 98300 EBI-EMBL Formylglycinamide ribonucleotide amidotransferase linker domain Formylglycinamide ribonucleotide amidotransferase linker domain This is the linker domain found in Formylglycinamide ribonucleotide amidotransferase (FGAR-AT), also known as Phosphoribosylformylglycinamidine synthase (EC:6.3.5.3), PurL and formylglycinamidine ribonucleotide (FGAM) synthase. This enzyme catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP, Pi, and glutamate in the fourth step of the purine biosynthetic pathway. The structure analysis of Salmonella typhimurium FGAR-AT reveals that this linker domain is made up of a long hydrophilic belt with an extended conformation [4]. [1]. 16544324. Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution. Mathews II, Krishna SS, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA;. Proteins. 2006;63:1106-1111. [2]. 17154526. Complexed structures of formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima describe a novel ATP binding protein superfamily. Morar M, Anand R, Hoskins AA, Stubbe J, Ealick SE;. Biochemistry. 2006;45:14880-14895. [3]. 18597481. Formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima: structural insights into complex formation. Morar M, Hoskins. TRUNCATED at 1650 bytes (from Pfam) NF037181.5 PF18073.6 Rubredoxin_2 25.7 25.7 28 domain Y N N Rubredoxin metal binding domain 26190574,28581365 131567 cellular organisms no rank 73141 EBI-EMBL Rubredoxin metal binding domain Rubredoxin metal binding domain This is the C-terminal rubredoxin metal binding domain found in Interest in lipopolysaccharide (LPS) assembly protein B (LapB) . Rubredoxin proteins form small non-heme iron binding sites that use four cysteine residues to coordinate a single metal ion in a tetrahedral environment. Rubredoxins are most commonly found in bacterial systems, but have also been found in eukaryotes. The key features of these rubredoxin-like domains are the extended loops or 'knuckles' and the tetracysteine mode of iron binding. Structural analysis of LapB from Escherichia coli show that the rubredoxin metal binding domain is intimately bound to the TPR motifs and that this association to the TPR motifs is essential to LPS regulation and growth in vivo [1]. Other family members include RadA proteins which play a role in DNA damage repair. In E. coli, a protein known as RadA (or Sms) participates in the recombinational repair of radiation-damaged DNA in a process that uses an undamaged DNA strand in one DNA duplex to fill a DNA strand gap in a homologous sister DNA duplex. RadA carries a zinc finger at the N-terminal domain [2]. [1]. 26190574. An Unexpected Duo: Rubredoxin Binds Nine TPR Motifs to Form LapB, an Essential Regulator of Lipopolysaccharide Synthesis. Prince C, Jia Z;. Structure. 2015;23:1500-1506. [2]. 28581365. Fine Epitope Mapping of Monoclonal Antibodies to the DNA Repair Protein, RadA. Stuart MK, Hudman DA, Nachtrab SN, Hiatt JL, Seo J, Pullen SJ, Sargentini NJ;. Monoclon Antib Immunodiagn Immunother. 2017;36:83-94. (from Pfam) NF037183.5 PF18075.6 FtsX_ECD 23.5 23.5 96 subfamily_domain Y Y N permease-like cell division protein FtsX 24843173 131567 cellular organisms no rank 41753 EBI-EMBL FtsX extracellular domain FtsX extracellular domain This is the extracellular domain (ECD) found in FtsX enzyme, a homolog of the transmembrane PG-hydrolase regulator. The FtsX extracellular domain binds the PG peptidase Rv2190c/RipC N-terminal segment, causing a conformational change that activates the enzyme ileading to PG hydrolysis in Mycobacterium tuberculosis. Structural analysis of FtsX ECD reveals fold containing two lobes connected by a flexible hinge. Mutations in the hydrophobic cleft between the lobes showed reduction in RipC binding in vitro and inhibition of FtsX function in Mycobacterium smegmatis [1]. [1]. 24843173. Mycobacterium tuberculosis FtsX extracellular domain activates the peptidoglycan hydrolase, RipC. Mavrici D, Marakalala MJ, Holton JM, Prigozhin DM, Gee CL, Zhang YJ, Rubin EJ, Alber T;. Proc Natl Acad Sci U S A. 2014;111:8037-8042. (from Pfam) NF037185.5 PF18080.6 Gal_mutarotas_3 27 27 241 domain Y N N Galactose mutarotase-like fold domain 18784084 131567 cellular organisms no rank 9473 EBI-EMBL Galactose mutarotase-like fold domain Galactose mutarotase-like fold domain This domain is found in endo-alpha-N-acetylgalactosaminidase present in Streptococcus pneumoniae. Endo-alpha-N-acetylgalactosaminidase is a cell surface-anchored glycoside hydrolase involved in the breakdown of mucin type O-linked glycans. The domain, known as domain 2, exhibits strong structural similarlity to the galactose mutarotase-like fold but lacks the active site residues. Domains, found in a number of glycoside hydrolases, structurally similar to domain 2 confer stability to the multidomain architectures [1]. [1]. 18784084. The structural basis for T-antigen hydrolysis by Streptococcus pneumoniae: a target for structure-based vaccine design. Caines ME, Zhu H, Vuckovic M, Willis LM, Withers SG, Wakarchuk WW, Strynadka NC;. J Biol Chem. 2008;283:31279-31283. (from Pfam) NF037202.5 PF18135.6 Type_ISP_C 25.9 25.9 342 domain Y Y N type ISP restriction/modification enzyme 26389736 131567 cellular organisms no rank 24586 EBI-EMBL Type ISP C-terminal specificity domain type ISP restriction/modification enzyme target recognition domain This is the C-terminal domain of Type ISP restriction-modification enzyme LLaBIII present in Lactococcus lactis subsp. cremoris. Type ISP restriction-modification (RM) enzymes provide a potent defence against infection by foreign and bacteriophage DNA. This domain interacts extensively with DNA and is known as the target recognition domain (TRD). TRD works by recognising 6/7 base pairs of asymmetric sequence [1]. [1]. 26389736. Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymes. Chand MK, Nirwan N, Diffin FM, van Aelst K, Kulkarni M, Pernstich C, Szczelkun MD, Saikrishnan K;. Nat Chem Biol. 2015;11:870-877. (from Pfam) NF037206.5 PF18159.6 S_4TM 26.9 26.9 291 subfamily Y Y N S-4TM family putative pore-forming effector 26590262 131567 cellular organisms no rank 2386 EBI-EMBL SMODS-associating 4TM effector domain SMODS-associating 4TM effector domain Members of this putative pore-forming family are found associated with DncV-like enzymes renamed SMODS (Second Messenger Oligonucleotide or Dinucleotide Synthetase) in putative conflict systems, and interpreted to be effectors of defense via cell suicide. NF037211.5 PF18330.6 Lig_C 25 25 125 domain Y N N Ligase Pab1020 C-terminal region 18511537 131567 cellular organisms no rank 676 EBI-EMBL Ligase Pab1020 C-terminal region Ligase Pab1020 C-terminal region This is the C-terminal region of RNA ligase Pab1020 present in Pyrococcus abyssi. Pab1020 catalyzes the nucleotidylation of oligo-ribonucleotides in an ATP-dependent reaction. This region contains both a dimerization domain and a C-terminal domain [1]. [1]. 18511537. The structure of an archaeal homodimeric ligase which has RNA circularization activity. Brooks MA, Meslet-Cladiere L, Graille M, Kuhn J, Blondeau K, Myllykallio H, van Tilbeurgh H;. Protein Sci. 2008;17:1336-1345. (from Pfam) NF037213.5 PF18335.6 SH3_13 41 41 65 domain Y N N ATP-dependent RecD-like DNA helicase SH3 domain 18668125,19490894,27644322 131567 cellular organisms no rank 36151 EBI-EMBL ATP-dependent RecD-like DNA helicase SH3 domain ATP-dependent RecD-like DNA helicase SH3 domain This is an SH3 (SRC homology domain 3) domain found in RecD helicases (EC 3.6.4.12) that belong to the bacterial Superfamily 1B (SF1B). This superfamily of helicases translocate in a 5'-3' direction and are required for a range of cellular activities across all domains of life [2]. Structural analysis indicate that the extension of the 5'-tail of the unwound DNA duplex induces a large conformational change in the RecD subunit, that is transferred through the RecC subunit to activate the nuclease domain of the RecB subunit. The process involves this SH3 domain that binds to a region of the RecB subunit. Studies of RecD in E. coli also revealed that the SH3 domain interacts with the ssDNA tail in a location different to that normally occupied by a peptide in canonical eukaryotic SH3 domains, thus retaining the potential to bind peptide at the same time as the ssDNA tail [3]. [1]. 18668125. DNA binding to RecD: role of the 1B domain in SF1B helicase activity. Saikrishnan K, Griffiths SP, Cook N, Court R, Wigley DB;. EMBO J. 2008;27:2222-2229. [2]. 19490894. Mechanistic basis of 5'-3' translocation in SF1B helicases. Saikrishnan K, Powell B, Cook NJ, Webb MR, Wigley DB;. Cell. 2009;137:849-859. [3]. 27644322. Mechanism for nuclease regulation in RecBCD. Wilkinson M, Chaban Y, Wigley DB;. Elife. 2016; [Epub ahead of print] (from Pfam) NF037238.5 PF18413.6 Neuraminidase 25 25 171 domain Y Y N neuraminidase-like domain-containing protein 24572368 131567 cellular organisms no rank 6087 EBI-EMBL Neuraminidase-like domain neuraminidase-like domain This is a neuraminidase-like domain, which is structurally homologous to neuraminidases. It can be found in TcA subunit in tripartite Tc toxin complexes of bacterial pathogens. Functional analysis suggest that the neuraminidase-like domain acts as an electrostatic lock that opens at high or low pH values [1]. [1]. 24572368. Mechanism of Tc toxin action revealed in molecular detail. Meusch D, Gatsogiannis C, Efremov RG, Lang AE, Hofnagel O, Vetter IR, Aktories K, Raunser S;. Nature. 2014;508:61-65. (from Pfam) NF037241.5 PF18423.6 zf_CopZ 28.4 28.4 62 domain Y N N Zinc binding domain 17609202 131567 cellular organisms no rank 1224 EBI-EMBL Zinc binding domain Zinc binding domain This is N-terminal domain containing a mononuclear metal center for zinc binding found in copper chaperone CopZ proteins [1]. [1]. 17609202. Characterization and structure of a Zn2+ and [2Fe-2S]-containing copper chaperone from Archaeoglobus fulgidus. Sazinsky MH, LeMoine B, Orofino M, Davydov R, Bencze KZ, Stemmler TL, Hoffman BM, Arguello JM, Rosenzweig AC;. J Biol Chem. 2007;282:25950-25959. (from Pfam) NF037250.5 PF18454.6 Mtd_N 26.3 26.3 37 domain Y N N Major tropism determinant N-terminal domain 16170324,16314578,18532877,19438710 131567 cellular organisms no rank 1914 EBI-EMBL Major tropism determinant N-terminal domain Major tropism determinant N-terminal domain This is the N-terminal domain of major tropism determinant (Mtd), a retroelement-encoded receptor-binding protein. Mtd-N forms a three-fold symmetric beta-prism. This resembles the pseudo three-fold-symmetric beta-prisms of monocot lectins, but lacks residues in these lectins identified as binding carbohydrates. The beta-prism and beta-sandwich domains reinforce overall trimeric assembly and therefore may have indirect roles in stabilizing the backbone of the variable region [1]. [1]. 16170324. The C-type lectin fold as an evolutionary solution for massive sequence variation. McMahon SA, Miller JL, Lawton JA, Kerkow DE, Hodes A, Marti-Renom MA, Doulatov S, Narayanan E, Sali A, Miller JF, Ghosh P;. Nat Struct Mol Biol. 2005;12:886-892. [2]. 18532877. Selective ligand recognition by a diversity-generating retroelement variable protein. Miller JL, Le Coq J, Hodes A, Barbalat R, Miller JF, Ghosh P;. PLoS Biol. 2008;6:e131. [3]. 16314578. Structure of a group A streptococcal phage-encoded virulence factor reveals a catalytically active triple-stranded beta-helix. Smith NL, Taylor EJ, Lindsay AM, Charnock SJ, Turkenburg JP, Dodson EJ, Davies GJ, Black GW;. Proc Natl Acad Sci U S A. 2005;102:17652-17657. [4]. 19438710. Polysaccharide binding sites in hyaluronate lyase--crystal structures of native phage-encoded hyaluronate lyase and its complexes with ascorbic acid and lactose. Mishra P, Prem Kumar R, Ethayathulla AS, Singh N, Sharma S, Perbandt M, Betzel C, Kaur P, Srinivasan A, Bhakuni V, Singh TP;. FEBS J. 2009;276:3392-3402. (from Pfam) NF037255.5 PF18476.6 PIN_8 26.1 26.1 227 domain Y Y N PIN-like domain-containing protein 28575517 131567 cellular organisms no rank 6109 EBI-EMBL PIN like domain PIN-like domain This is a domain of unknown function, suggested to be a member of PIN like domains clan [1]. [1]. 28575517. Comprehensive classification of the PIN domain-like superfamily. Matelska D, Steczkiewicz K, Ginalski K;. Nucleic Acids Res. 2017;45:6995-7020. (from Pfam) NF037260.5 PF18516.6 RuvC_1 26.2 26.2 244 domain Y N N RuvC nuclease domain 28431230 131567 cellular organisms no rank 333 EBI-EMBL RuvC nuclease domain RuvC nuclease domain This is a RuvC nuclease domain found in type V CRISPR-associated protein Cas12a (Cpf1), used for genome editing applications. These proteins carry out endoribonuclease activity for processing its own guide RNAs and RNA-guided DNase activity for target DNA cleavage. The C-terminal region of Cas12a carries the RUVC domain, NUC domain Pfam:PF18510 and the arginine-rich bridge helix (BH). Both the NUC and BH domains are nested in the RuvC domain. Mutations in the RuvC domain impair cleavage of both strands in a target DNA duplex, while a mutation in the Nuc domain impaired target strand cleavage only. This indicates that the DNA nuclease active sites are located at the interface of the RuvC and Nuc domains and that cleavage of the non-target DNA strand by the RuvC domain is a prerequisite for target strand cleavage by the Nuc domain [1]. [1]. 28431230. Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a. Swarts DC, van der Oost J, Jinek M;. Mol Cell. 2017;66:221-233. (from Pfam) NF037269.5 PF18546.6 MetOD1 23.8 23.8 142 domain Y Y N methanogen output domain 1-containing protein 131567 cellular organisms no rank 2400 EBI-EMBL Methanogen output domain 1 methanogen output domain 1 MetOD1 (Methanogen output domain 1) is a protein domain that is found in euryarchaeal classes Methanobacteria and Methanomicrobia, either in stand-alone form or in combination with the Response_reg Pfam:PF00072 domain (Galperin et al., 2018, Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems). This domain is distantly related to the HNOB and V4R domains. (from Pfam) NF037270.5 PF18551.6 TackOD1 32 32 188 domain Y N N Thaumarchaeal output domain 1 131567 cellular organisms no rank 2113 EBI-EMBL Thaumarchaeal output domain 1 Thaumarchaeal output domain 1 TackOD1 (Thaumarchaeal output domain 1) is a predicted metal-binding domain found in archaea and in some bacteria. It contains 11 highly conserved Cys residues, which form 5 CxxC motifs and an HxxC motif. In several instances, it is found in combination with the Response_reg Pfam:PF00072 domain (Galperin et al., 2018, Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems). (from Pfam) NF037272.5 PF18560.6 Lectin_like 27 27 156 domain Y Y N lectin like domain-containing protein 25004975 131567 cellular organisms no rank 4420 EBI-EMBL Lectin like domain lectin like domain This is a lectin like domain found in Cwp84, a surface-located cysteine protease (a member of the C1A cysteine protease family, also known as papain proteases) responsible for the maturation of the SlpA precursor protein which has been implicated in the degradation of extracellular matrix proteins such as fibronectin, laminin and vitronectin. Structural comparison indicates that this domain is similar to carbohydrate-binding domains [1]. [1]. 25004975. The structure of the cysteine protease and lectin-like domains of Cwp84, a surface layer-associated protein from Clostridium difficile. Bradshaw WJ, Kirby JM, Thiyagarajan N, Chambers CJ, Davies AH, Roberts AK, Shone CC, Acharya KR;. Acta Crystallogr D Biol Crystallogr. 2014;70:1983-1993. (from Pfam) NF037284.5 PF18171.6 LSDAT_prok 25.4 25.4 195 domain Y N N SLOG in TRPM, prokaryote 26590262 131567 cellular organisms no rank 652 EBI-EMBL SLOG in TRPM, prokaryote SLOG in TRPM, prokaryote Family in the SLOG superfamily, fused to or operonically associating with SLATT domain in diverse prokaryotes. Predicted to function as ligand sensor in conjunction with the SLATT transmembrane domain [1]. [1]. 26590262. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;. Nucleic Acids Res. 2015;43:10633-10654. (from Pfam) NF037285.5 PF18173.6 bacHORMA_2 27.3 27.3 166 domain Y N N Bacterial HORMA domain 2 26590262,31932165,32839535 131567 cellular organisms no rank 444 EBI-EMBL Bacterial HORMA domain 2 Bacterial HORMA domain 2 Family of bacterial HORMA domains found in conserved genome contexts with Pch2/TRIP13 P-loop NTPases. Acts as a 'third component' in broad class of conflict systems reliant on the production of second messenger nucleotide or nucleotide derivatives. Together with Pch2/TRIP13, could act as co-effectors or in regulation of other effectors of the systems [1]. This domain found in bacterial proteins from the cyclic-oligonucleotide-based anti-phage signalling system (CBASS), such us CD-NTase-associated protein 7 from P. aeruginosa (Cap7), which is part of the type III-CBASS. CBSSs are a family of defence systems against bacteriophages [2,3]. [1]. 26590262. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;. Nucleic Acids Res. 2015;43:10633-10654. [2]. 32839535. Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems. Millman A, Melamed S, Amitai G, Sorek R;. Nat Microbiol. 2020;5:1608-1615. [3]. 31932165. HORMA Domain Proteins and a Trip13-like ATPase Regulate Bacterial cGAS-like Enzymes to Mediate Bacteriophage Immunity. Ye Q, Lau RK, Mathews IT, Birkholz EA, Watrous JD, Azimi CS, Pogliano J, Jain M, Corbett KD;. Mol Cell. 2020;77:709-722. (from Pfam) NF037286.5 PF18185.6 STALD 25.7 25.7 209 domain Y N N Sir2- and TIR-associating SLOG family 26590262 131567 cellular organisms no rank 2297 EBI-EMBL Sir2- and TIR-associating SLOG family Sir2- and TIR-associating SLOG family Family in the SLOG superfamily, associating with predicted Sir2- and TIR-like effector domains. Members of this family are predicted to functions as sensors of nucleotide or nucleotide-derived ligands, which are likely processed or modified by the associating effectors [1]. [1]. 26590262. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;. Nucleic Acids Res. 2015;43:10633-10654. (from Pfam) NF037287.5 PF18186.6 SLATT_4 27 27 165 domain Y N N SMODS and SLOG-associating 2TM effector domain family 4 26590262 131567 cellular organisms no rank 2222 EBI-EMBL SMODS and SLOG-associating 2TM effector domain family 4 SMODS and SLOG-associating 2TM effector domain family 4 The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is often coupled to the SMODS nucleotide synthetase and is sometimes further embedded in other conflict systems like CRISPR/Cas or R-M systems [1]. [1]. 26590262. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;. Nucleic Acids Res. 2015;43:10633-10654. (from Pfam) NF037289.5 PF18195.6 GatD_N 25.7 25.7 54 domain Y N N GatD N-terminal domain 16216574,16809540 131567 cellular organisms no rank 1465 EBI-EMBL GatD N-terminal domain GatD N-terminal domain This is the N-terminal domain of GatD protein present in Pyrococcus abyssi. Two GatD and two GatE associate to form a tetramer complex. The tetramer complex is able to mature Glutamic acid-tRNA Glutamine into Glutamine-tRNA Glutamine, a necessary step in the translation of proteins. The N-terminal domain is involved in anchoring GatD to GatE in order to form the tetramer [1]. [1]. 16809540. Structural basis of RNA-dependent recruitment of glutamine to the genetic code. Oshikane H, Sheppard K, Fukai S, Nakamura Y, Ishitani R, Numata T, Sherrer RL, Feng L, Schmitt E, Panvert M, Blanquet S, Mechulam Y, Soll D, Nureki O;. Science. 2006;312:1950-1954. [2]. 16216574. Structural basis for tRNA-dependent amidotransferase function. Schmitt E, Panvert M, Blanquet S, Mechulam Y;. Structure. 2005;13:1421-1433. (from Pfam) NF037322.5 PF18320.6 Csc2 25.5 25.5 298 domain Y N N Csc2 Crispr 16545108,25483036 131567 cellular organisms no rank 956 EBI-EMBL Csc2 Crispr Csc2 Crispr The Csc2 Crispr family of proteins forms a core RNA recognition motif-like domain, flanked by three peripheral insertion domains: a lid domain, a Zinc-binding domain and a helical domain [1]. The CRISPR-Cas system is possibly a mechanism of defence against invading pathogens and plasmids that functions analogously to the RNA interference (RNAi) systems in eukaryotes [2]. [1]. 25483036. Structural analyses of the CRISPR protein Csc2 reveal the RNA-binding interface of the type I-D Cas7 family. Hrle A, Maier LK, Sharma K, Ebert J, Basquin C, Urlaub H, Marchfelder A, Conti E;. RNA Biol. 2014;11:1072-1082. [2]. 16545108. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV;. Biol Direct. 2006;1:7. (from Pfam) NF037334.5 PF18370.6 RGI_lyase 27.8 27.8 86 domain Y N N Rhamnogalacturonan I lyases beta-sheet domain 17947240,19193638,20233299,24419797 131567 cellular organisms no rank 15194 EBI-EMBL Rhamnogalacturonan I lyases beta-sheet domain Rhamnogalacturonan I lyases beta-sheet domain This is the beta-sheet domain found in rhamnogalacturonan (RG) lyases [1], which are responsible for an initial cleavage of the RG type I (RG-I) region of plant cell wall pectin. Polysaccharide lyase family 11 carrying this domain, such as YesW (EC:4.2.2.23) and YesX (EC:4.2.2.24), cleave glycoside bonds between rhamnose and galacturonic acid residues in RG-I through a beta-elimination reaction [2]. Other family members carrying this domain are hemagglutinin A, lysine gingipain (Kgp) [3] and Chitinase C (EC:3.2.1.14). [1]. 17947240. A novel structural fold in polysaccharide lyases: Bacillus subtilis family 11 rhamnogalacturonan lyase YesW with an eight-bladed beta-propeller. Ochiai A, Itoh T, Maruyama Y, Kawamata A, Mikami B, Hashimoto W, Murata K;. J Biol Chem. 2007;282:37134-37145. [2]. 19193638. Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases. Ochiai A, Itoh T, Mikami B, Hashimoto W, Murata K;. J Biol Chem. 2009;284:10181-10189. [3]. 20233299. STRUCTURE DETERMINATION AND ANALYSIS OF A HEMOLYTIC GINGIPAIN ADHESIN DOMAIN FROM PORPHYROMONAS GINGIVALIS. Li N, Yun P, Nadkarni MA, Ghadikolaee NB, Nguyen KA, Lee M, Hunter N, Collyer CA;. Mol Microbiol. 2010; [Epub ahead of print]. [4]. 24419797. Design of thermostable rhamnogalacturonan lyase mutants from Bacillus licheniformis by combination of targeted single point mutations. Silva IR, Jers C, Otten H, Nyffenegger C, Larsen DM, Derkx PM, Meyer AS, Mikkelsen JD, Larsen S;. Appl Microbiol Biotechnol. 2014;98:4521-4531. (from Pfam) NF037336.5 PF18376.6 MDD_C 23.2 23.2 186 domain Y N N Mevalonate 5-diphosphate decarboxylase C-terminal domain 11698677,17583736,18823933 131567 cellular organisms no rank 12527 EBI-EMBL Mevalonate 5-diphosphate decarboxylase C-terminal domain Mevalonate 5-diphosphate decarboxylase C-terminal domain Mevalonate diphosphate decarboxylase (EC:4.1.1.33) catalyzes the ATP dependent decarboxylation of mevalonate 5-diphosphate (MVAPP) to form isopentenyl 5-diphosphate. The reaction is required for production of polyisoprenoids and sterols from acetyl-CoA. This entry represents the C-terminal domain of the mevalonate 5-diphosphate decarboxylase enzyme which is a member of the GHMP kinase superfamily. [1]. 11698677. Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. Bonanno JB, Edo C, Eswar N, Pieper U, Romanowski MJ, Ilyin V, Gerchman SE, Kycia H, Studier FW, Sali A, Burley SK;. Proc Natl Acad Sci U S A. 2001;98:12896-12901. [2]. 17583736. Crystal structures of Trypanosoma brucei and Staphylococcus aureus mevalonate diphosphate decarboxylase inform on the determinants of specificity and reactivity. Byres E, Alphey MS, Smith TK, Hunter WN;. J Mol Biol. 2007;371:540-553. [3]. 18823933. Human mevalonate diphosphate decarboxylase: characterization, investigation of the mevalonate diphosphate binding site, and crystal structure. Voynova NE, Fu Z, Battaile KP, Herdendorf TJ, Kim JJ, Miziorko HM;. Arch Biochem Biophys. 2008;480:58-67. (from Pfam) NF037339.5 PF18395.6 Cas3_C 27 27 107 domain Y N N Cas3 C-terminal domain 25132177,25368186 131567 cellular organisms no rank 6838 EBI-EMBL Cas3 C-terminal domain Cas3 C-terminal domain This is the C-temrinal domain of Cas3 proteins. The C-terminal domain (CTD) is shown to completely wrap ssDNA inside the helicase. Deletion of the CTD (aa 819-924) reduced CRISPR interference. It is suggested that the CTD regulates the N-terminal HD nuclease activity by functioning as a substrate filter [1]. [1]. 25132177. Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation. Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione MD Jr, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ke A;. Nat Struct Mol Biol. 2014;21:771-777. [2]. 25368186. Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3. Gong B, Shin M, Sun J, Jung CH, Bolt EL, van der Oost J, Kim JS;. Proc Natl Acad Sci U S A. 2014;111:16359-16364. (from Pfam) NF037341.5 PF18404.6 Glyco_transf_24 25.7 25.7 268 domain Y N N Glucosyltransferase 24 28739903 131567 cellular organisms no rank 10782 EBI-EMBL Glucosyltransferase 24 Glucosyltransferase 24 This is the catalytic domain found in UDP-glucose:glycoprotein glucosyltransferase (UGGT). This domain belongs to glucosyltransferase 24 family (GT24) A-type domain. The GT domain displays the expected glycosyltransferase type A (GT-A) fold [1]. [1]. 28739903. Interdomain conformational flexibility underpins the activity of UGGT, the eukaryotic glycoprotein secretion checkpoint. Roversi P, Marti L, Caputo AT, Alonzi DS, Hill JC, Dent KC, Kumar A, Levasseur MD, Lia A, Waksman T, Basu S, Soto Albrecht Y, Qian K, McIvor JP, Lipp CB, Siliqi D, Vasiljevic S, Mohammed S, Lukacik P, Walsh MA, Santino A, Zitzmann N;. Proc Natl Acad Sci U S A. 2017;114:8544-8549. (from Pfam) NF037344.5 PF18419.6 ATP-grasp_6 25 25 54 domain Y N N ATP-grasp-like domain 16339152,22226834 131567 cellular organisms no rank 5817 EBI-EMBL ATP-grasp-like domain ATP-grasp-like domain Glutathione biosynthesis is achieved in most organisms via a conserved two-step approach relying on the capacity of two independent and unrelated ligases to perform peptide synthesis coupled to ATP hydrolysis. In a first and rate-limiting step, gamma-glutamylcysteine ligase (gamma-ECL) (or GshA; EC:6.3.2.2) uses l-glutamate and l-cysteine to form gamma-glutamylcysteine (gamma-EC), which, in a second step, is condensed with glycine to glutathione by glutathione synthetase (GS) (or GshB; EC:6.3.2.3). However, several pathogenic and free-living bacteria carry out glutathione biosynthesis based on a single enzyme that catalyzes both the gamma-ECL and the GS reactions. Such bifunctional glutathione-synthesizing enzymes have been termed gamma-GCS-GS or GshF [1]. Hybrid GshF contains a typical gamma-proteobacterial gamma-ECL fused to an ATP-grasp-like domain [2]. The ATP-grasp-like module is responsible for the ensuing formation of glutathione from gamma-glutamylcysteine and glycine. The ATP-grasp-like domain has an antiparallel beta-sheet in the GshF structures in contrast to all structurally characterized members of the ATP-grasp superfamily [1]. [1]. 22226834. Glutathione biosynthesis in bacteria by bifunctional GshF is driven by a modular structure featuring a novel hybrid ATP-grasp fold. Stout J, De Vos D, Vergauwen B, Savvides SN;. J Mol Biol. 2012;416:486-494. [2]. 16339152. Characterization of the bifunctional gamma-glutamate-cysteine ligase/glutathione synthetase (GshF) of Pasteurella multocida. Vergauwen B, De Vos D, Van Beeumen JJ;. J Biol Chem. 2006;281:4380-4394. (from Pfam) NF037353.5 PF18458.6 XPB_DRD 26 26 57 domain Y N N Xeroderma pigmentosum group B helicase damage recognition domain 16600867 131567 cellular organisms no rank 2199 EBI-EMBL Xeroderma pigmentosum group B helicase damage recognition domain Xeroderma pigmentosum group B helicase damage recognition domain This domain is found in the N-terminal region of xeroderma pigmentosum group B (XPB) helicase present in Archaeoglobus fulgidus. XPB is essential for transcription, nucleotide excision repair, and TFIIH functional assembly. The domain is a damage recognition domain (DRD) which allows XPB to unwind damaged DNA as needed for nucleotide excision repair [1]. [1]. 16600867. Conserved XPB core structure and motifs for DNA unwinding: implications for pathway selection of transcription or excision repair. Fan L, Arvai AS, Cooper PK, Iwai S, Hanaoka F, Tainer JA;. Mol Cell. 2006;22:27-37. (from Pfam) NF037356.5 PF18465.6 Rieske_3 25 25 96 domain Y N N Rieske 3Fe-4S GO:0051536 11250197,24023621 131567 cellular organisms no rank 1180 EBI-EMBL Rieske 3Fe-4S Rieske 3Fe-4S This domain is comprised of the iron-sulphur cluster and Rieske subunit found in the large subunit of arsenite oxidase. Arsenite oxidase is a 100 kDa molybdenum- and iron-sulfur-containing protein located on the outer surface of the inner membrane of Gram-negative organisms. The large subunit of arsenite oxidase is similar to other members of the dimethylsulfoxide (DMSO) reductase family of molybdenum enzymes. The large subunit of arsenite oxidase is divided into four domains, with domain I binding the [3Fe-4S] cluster . Domain I, consists of three antiparallel beta sheets and six helices. The [3Fe-4S] cluster is coordinated by the motif Cys21-X2-Cys24-X3-Cys28 near the interface with domains III and IV. A large, flattened funnel-like cavity bounded by domains I, II, and III leads to the molybdenum center Pfam:PF00384 located near the center of the molecule [1]. [1]. 11250197. Crystal structure of the 100 kDa arsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64 A and 2.03 A. Ellis PJ, Conrads T, Hille R, Kuhn P;. Structure. 2001;9:125-132. [2]. 24023621. The respiratory arsenite oxidase: structure and the role of residues surrounding the rieske cluster. Warelow TP, Oke M, Schoepp-Cothenet B, Dahl JU, Bruselat N, Sivalingam GN, Leimkuhler S, Thalassinos K, Kappler U, Naismith JH, Santini JM;. PLoS One. 2013;8:e72535. (from Pfam) NF037378.5 PF18666.6 CBM64 25 25 74 domain Y N N Carbohydrate-binding module 64 26868291 131567 cellular organisms no rank 112 EBI-EMBL Carbohydrate-binding module 64 Carbohydrate-binding module 64 Spirochaeta thermophila secretes seven glycoside hydrolases for plant biomass degradation that carry a carbohydrate-binding module 64 (CBM64) appended at the C-terminus. CBM64 adsorbs to various beta1-4-linked pyranose substrates and shows high affinity for cellulose. Structure analysis indicates a jelly-roll-like fold corresponding to a surface-binding type A CBM [1]. [1]. 26868291. Structural basis for cellulose binding by the type A carbohydrate-binding module 64 of Spirochaeta thermophila. Schiefner A, Angelov A, Liebl W, Skerra A;. Proteins. 2016;84:855-858. (from Pfam) NF037401.5 PF18724.6 ADDT 26.2 26.2 232 domain Y N N Amino acid:DNA transferase 23814188,29555775,34522950 131567 cellular organisms no rank 747 EBI-EMBL Amino acid:DNA transferase Amino acid:DNA transferase This entry represents the alpha-helical domain of the glycinyl, putrescine and serinyltransferases (grouped as amino acid:DNA transferases, formerly known as alpha-putrescinyl/glutamylthymidine pyrophosphorylases (aGPT-Pplases) [1]) which catalyse thymidine hypermodifications in the viral genome [1-3], transferring glycine, putrescine or serine to 5-phosphomethyl-2'-deoxyuridine (5-PmdU) to produce Nalpha-GlyT, Nalpha-PutT and O-SerT, respectively. These modifications probably prevent degradation of the viral genome by the host restriction-modification antiviral defense system [2]. [1]. 23814188. Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA. Iyer LM, Zhang D, Burroughs AM, Aravind L;. Nucleic Acids Res. 2013;41:7635-7655. [2]. 34522950. Pathways of thymidine hypermodification. Lee YJ, Dai N, Muller SI, Guan C, Parker MJ, Fraser ME, Walsh SE, Sridar J, Mulholland A, Nayak K, Sun Z, Lin YC, Comb DG, Marks K, Gonzalez R, Dowling DP, Bandarian V, Saleh L, Correa IR, Weigele PR;. Nucleic Acids Res. 2022;50:3001-3017. [3]. 29555775. Identification and biosynthesis of thymidine hypermodifications in the genomic DNA of widespread bacterial viruses. Lee YJ, Dai N, Walsh SE, Muller S, Fraser ME, Kauffman KM, Guan C, Correa IR Jr, Weigele PR;. Proc Natl Acad Sci U S A. 2018;115:E3116. (from Pfam) NF037404.5 PF18728.6 HEPN_AbiV 27.1 27.1 155 domain Y N N AbiV 23768067 131567 cellular organisms no rank 2064 EBI-EMBL AbiV AbiV AbiV-like HEPN [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF037405.5 PF18741.6 MTES_1575 38.2 38.2 96 domain Y N N REase_MTES_1575 23768067 131567 cellular organisms no rank 30210 EBI-EMBL REase_MTES_1575 REase_MTES_1575 Vsr REase Fold. Fused to HEPN (SWT1/Abi2 family), along with Transglutaminase and wHTH [1]. [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF037406.5 PF18742.6 DpnII-MboI 27 27 150 domain Y N N REase_DpnII-MboI 23768067 131567 cellular organisms no rank 2155 EBI-EMBL REase_DpnII-MboI REase_DpnII-MboI REase Fold fused to DpnII/MboI-NTD [1]. [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF037410.5 PF18753.6 Nmad2 26.1 26.1 200 domain Y N N Nucleotide modification associated domain 2 23814188 131567 cellular organisms no rank 1618 EBI-EMBL Nucleotide modification associated domain 2 Nucleotide modification associated domain 2 A beta-strand rich domain containing a conserved cysteine and charged residues predicted to play a role in modified DNA base biosynthesis [1]. [1]. 23814188. Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA. Iyer LM, Zhang D, Burroughs AM, Aravind L;. Nucleic Acids Res. 2013;41:7635-7655. (from Pfam) NF037411.5 PF18754.6 Nmad3 27 27 247 domain Y N N Nucleotide modification associated domain 3 23814188 131567 cellular organisms no rank 1919 EBI-EMBL Nucleotide modification associated domain 3 Nucleotide modification associated domain 3 An alpha+beta fold domain with a high conserved HxD and D motifs suggestive of enzymatic function and predicted to be involved in modifed nucleotide biosynthesis [1]. [1]. 23814188. Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA. Iyer LM, Zhang D, Burroughs AM, Aravind L;. Nucleic Acids Res. 2013;41:7635-7655. (from Pfam) NF037413.5 PF18764.6 nos_propeller 30 30 71 domain Y N N Nitrous oxide reductase propeller repeat 21841804,26885878 131567 cellular organisms no rank 7087 EBI-EMBL Nitrous oxide reductase propeller repeat Nitrous oxide reductase propeller repeat Nitrous oxide reductases usually contain a seven-bladed beta-propeller domain with external short alpha-helices [1,2]. This entry represents a single blade of the propeller, with imperfect alpha-helix, usually at the C-terminus of the repeat region. [1]. 21841804. N2O binding at a [4Cu:2S] copper-sulphur cluster in nitrous oxide reductase. Pomowski A, Zumft WG, Kroneck PM, Einsle O;. Nature. 2011;477:234-237. [2]. 26885878. Role of Calcium in Secondary Structure Stabilization during Maturation of Nitrous Oxide Reductase. Schneider LK, Einsle O;. Biochemistry. 2016;55:1433-1440. (from Pfam) NF037417.5 PF18780.6 HNH_repeat 26 26 54 domain Y Y N homing endonuclease associated repeat-containing protein 19211047 131567 cellular organisms no rank 2773 EBI-EMBL Homing endonuclease associated repeat homing endonuclease associated repeat This 60-residue domain occurs sometimes in a single copy but more often in tandem duplications. A substantial fraction of proteins with this domain are HNH-type homing endonucleases. NF037429.5 PF18854.6 baeRF_family10 27.1 27.1 143 domain Y N N Bacterial archaeo-eukaryotic release factor family 10 29632312 131567 cellular organisms no rank 15806 EBI-EMBL Bacterial archaeo-eukaryotic release factor family 10 Bacterial archaeo-eukaryotic release factor family 10 Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome [1]. [1]. 29632312. Vms1 and ANKZF1 peptidyl-tRNA hydrolases release nascent chains from stalled ribosomes. Verma R, Reichermeier KM, Burroughs AM, Oania RS, Reitsma JM, Aravind L, Deshaies RJ;. Nature. 2018;557:446-451. (from Pfam) NF037430.5 PF18859.6 acVLRF1 27.1 27.1 130 domain Y Y N Vms1/Ankzf1 family peptidyl-tRNA hydrolase 29632312 131567 cellular organisms no rank 10465 EBI-EMBL Actinobacteria/chloroflexi VLRF1 release factor Vms1/Ankzf1 family peptidyl-tRNA hydrolase Archaeo-eukaryotic release factor domain family belonging to the VLRF1 clade, observed primarily in the actinbacteria and chloroflexi bacterial lineages. Contains a conserved glutamine residue in the release factor catalytic loop, suggesting it functions as an active peptidyl-tRNA hydrolase at the ribosome [1]. [1]. 29632312. Vms1 and ANKZF1 peptidyl-tRNA hydrolases release nascent chains from stalled ribosomes. Verma R, Reichermeier KM, Burroughs AM, Oania RS, Reitsma JM, Aravind L, Deshaies RJ;. Nature. 2018;557:446-451. (from Pfam) NF037434.5 PF18477.6 PIN_9 26.3 26.3 116 domain Y N N PIN like domain 28575517 131567 cellular organisms no rank 1322 EBI-EMBL PIN like domain PIN like domain This is a domain of unknown function that resembles the PIN like domains. Family members include Ribonuclease VapC9 [1]. [1]. 28575517. Comprehensive classification of the PIN domain-like superfamily. Matelska D, Steczkiewicz K, Ginalski K;. Nucleic Acids Res. 2017;45:6995-7020. (from Pfam) NF037435.5 PF18481.6 DUF5616 27.6 27.6 140 domain Y Y N DUF5616 domain-containing protein 28575517 131567 cellular organisms no rank 1743 EBI-EMBL Domain of unknown function (DUF5616) Domain of unknown function (DUF5616) This domain is found in a number of prokaryotic proteins. It is mostly found fused with the N-terminal domain Pfam:PF04256. This C-terminal domain is suggested to be a PIN like domain [1]. [1]. 28575517. Comprehensive classification of the PIN domain-like superfamily. Matelska D, Steczkiewicz K, Ginalski K;. Nucleic Acids Res. 2017;45:6995-7020. (from Pfam) NF037437.5 PF18495.6 VbhA 25.9 25.9 47 domain Y N N Antitoxin VbhA 22266942 131567 cellular organisms no rank 4291 EBI-EMBL Antitoxin VbhA Antitoxin VbhA VbhT is a bacterial Fic protein of the mammalian pathogen B. schoenbuchensis7,8. It is composed of an N-terminal FIC domain and a C-terminal BID domain. FIC domains are known to catalyse adenylylation (also called AMPylation). This entry represents VbhA, an antitoxin that binds FIC domain (filamentation induced by cyclic AMP) of VbhT and inhibits its activity. It inhibits the adenylylation activity of VbhT by positioning close to the putative ATP-binding site, hence competing with ATP binding [1]. [1]. 22266942. Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins. Engel P, Goepfert A, Stanger FV, Harms A, Schmidt A, Schirmer T, Dehio C;. Nature. 2012;482:107-110. (from Pfam) NF037440.5 PF18501.6 REC1 37.4 37.4 250 domain Y N N Alpha helical recognition lobe domain 28431230 131567 cellular organisms no rank 326 EBI-EMBL Alpha helical recognition lobe domain Alpha helical recognition lobe domain Cpf1 is an RNA-guided endonuclease of a type V CRISPR-Cas system. Cpf1 adopts a bilobed architecture consisting of an alpha-helical recognition (REC) lobe and a nuclease (NUC) lobe, with the small CRISPR RNAs (crRNAs)-target DNA heteroduplex bound to the positively charged, central channel between the two lobes. The REC lobe consists of the REC1 and REC2 domains where REC1 comprises 13 alpha helices, and REC2 comprises ten alpha helices and two beta strands that form a small antiparallel sheet [1]. This entry represents REC1 domain. [1]. 28431230. Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a. Swarts DC, van der Oost J, Jinek M;. Mol Cell. 2017;66:221-233. (from Pfam) NF037442.5 PF18506.6 RelB-like 31 31 47 domain Y N N RelB Antitoxin 19712680 131567 cellular organisms no rank 603 EBI-EMBL RelB Antitoxin RelB Antitoxin RelE-RelB (RelBE) is a toxin-antitoxin (TA) protein complex. It is suggested that the toxic action of RelE is counteracted by antitoxin RelB, which wraps around RelE, blocks its active site and prevents sterically the binding to the ribosomal A-site. The long alpha-helix of the tightly bound RelB covers the presumed active site of the toxin RelE that is formed by a central beta-sheet [1]. This entry represents RelB antitoxin from Methanocaldococcus jannaschii and similar prokaryotic proteins. [1]. 19712680. Crystal structure of the antitoxin-toxin protein complex RelB-RelE from Methanococcus jannaschii. Francuski D, Saenger W;. J Mol Biol. 2009;393:898-908. (from Pfam) NF037443.5 PF18510.6 NUC 25 25 162 domain Y N N Nuclease domain 27114038 131567 cellular organisms no rank 325 EBI-EMBL Nuclease domain Nuclease domain This is a nuclease (NUC) domain found in Cpf1, an RNA-guided endonuclease of a type V CRISPR-Cas system. Structural and functional analysis indicate that this domain is involved in DNA cleavage [1]. [1]. 27114038. Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA. Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O;. Cell. 2016;165:949-962. (from Pfam) NF037476.5 PF18612.6 Bac_A_amyl_C 25.9 25.9 69 domain Y N N Bacterial Alpha amylase C-terminal domain 131567 cellular organisms no rank 865 EBI-EMBL Bacterial Alpha amylase C-terminal domain Bacterial Alpha amylase C-terminal domain This is a bacterial alpha amaylase C-terminal domain found mostly in bacilli. (from Pfam) NF037477.5 PF18616.6 CdiI_3 28 28 95 subfamily Y Y N contact-dependent growth inhibition system immunity protein 27531961 131567 cellular organisms no rank 3554 EBI-EMBL CDI immunity proteins contact-dependent growth inhibition system immunity protein Contact-dependent growth inhibition (CDI) is a widespread mechanism of bacterial competition. CDI+ bacteria deliver the toxic C-terminal region of contact-dependent inhibition A proteins (CdiA-CT) into neighboring target bacteria and produce CDI immunity proteins (CdiI) which bind CdiA-CT domains and neutralize their toxic activity to protect against self-inhibition. CdiI immunity proteins are also variable and only neutralize their cognate CdiA-CT toxins. Structure analysis of CdiI from Escherichia coli 536 (EC536) shows that is composed of a single domain and that it blocks the interaction with substrate, strongly suggesting that the immunity protein occludes the nuclease active site [1]. [1]. 27531961. Unraveling the essential role of CysK in CDI toxin activation. Johnson PM, Beck CM, Morse RP, Garza-Sanchez F, Low DA, Hayes CS, Goulding CW;. Proc Natl Acad Sci U S A. 2016;113:9792-9797. (from Pfam) NF037498.5 PF18723.6 HMUDK_hel 25 25 281 subfamily Y Y N nucleotide kinase domain-containing protein 23814188,29555775,34522950 131567 cellular organisms no rank 1629 EBI-EMBL 5-hmdU DNA kinase, helical domain putative DNA base hypermodification protein This entry represents an alpha-helical domain found in 5-hmdU DNA kinase (HMUDK), a P-loop nucleotide kinase that phosphorylates 5-hydroxymethyluracil (5hmdU) into 5-phosphomethyl-2'-deoxyuridine (5-PmdU) on DNA as a step in the pathway leading to thymidine hypermodifications in the viral genome [2]. HMUDK also transfers glutamate to 5-pyrophosphoryloxymethyldeoxyuridine (5-PPmdU) to produce 5-Nalpha-glyutamylthymidine (Nalpha-GluT) [2,3]. These modifications probably prevent degradation of viral genome by the host restriction-modification antiviral defense system [1,2]. Members of this entry (formerly known as aGPT-Pplase1) are found in phages with hypermodified bases and eukaryotes such as fungi and stramenopiles [1,2]. [1]. 23814188. Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA. Iyer LM, Zhang D, Burroughs AM, Aravind L;. Nucleic Acids Res. 2013;41:7635-7655. [2]. 34522950. Pathways of thymidine hypermodification. Lee YJ, Dai N, Muller SI, Guan C, Parker MJ, Fraser ME, Walsh SE, Sridar J, Mulholland A, Nayak K, Sun Z, Lin YC, Comb DG, Marks K, Gonzalez R, Dowling DP, Bandarian V, Saleh L, Correa IR, Weigele PR;. Nucleic Acids Res. 2022;50:3001-3017. [3]. 29555775. Identification and biosynthesis of thymidine hypermodifications in the genomic DNA of widespread bacterial viruses. Lee YJ, Dai N, Walsh SE, Muller S, Fraser ME, Kauffman KM, Guan C, Correa IR Jr, Weigele PR;. Proc Natl Acad Sci U S A. 2018;115:E3116. (from Pfam) NF037501.5 PF18731.6 HEPN_Swt1 27.5 27.5 115 domain Y Y N Swt1 family HEPN domain-containing protein 23768067 131567 cellular organisms no rank 4094 EBI-EMBL Swt1-like HEPN Swt1 family HEPN domain Swt1-like HEPN. This HEPN domain might have a role in binding and sensing unspliced pre-mRNAs that are specifically targeted by the Swt1 nuclease at the nuclear envelope [1]. [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF037510.5 PF18766.6 SWI2_SNF2 26.7 26.7 221 domain Y N N SWI2/SNF2 ATPase 28559295 131567 cellular organisms no rank 158943 EBI-EMBL SWI2/SNF2 ATPase SWI2/SNF2 ATPase A SWi2/SNF2 ATPase found in polyvalent proteins [1]. [1]. 28559295. Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. Iyer LM, Burroughs AM, Anand S, de Souza RF, Aravind L;. J Bacteriol. 2017; [Epub ahead of print] (from Pfam) NF037514.5 PF18785.6 Inv-AAD 26.5 26.5 129 domain Y N N Invertebrate-AID/APOBEC-deaminase 29555751 131567 cellular organisms no rank 10280 EBI-EMBL Invertebrate-AID/APOBEC-deaminase Invertebrate-AID/APOBEC-deaminase A classical AID/APOBEC-like deaminases found in lophotrochozoans, echinoderms and cnidarians [1]. [1]. 29555751. Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity. Krishnan A, Iyer LM, Holland SJ, Boehm T, Aravind L;. Proc Natl Acad Sci U S A. 2018;115:E3201. (from Pfam) NF037521.5 PF18818.6 MPTase-PolyVal 27.5 27.5 126 domain Y Y N zincin-like metallopeptidase domain-containing protein 28559295 131567 cellular organisms no rank 23639 EBI-EMBL Zincin-like metallopeptidase antirestriction factor ArdC metallopeptidase-like domain Zincin-like Metallopeptidase frequently found in polyvalent proteins of phages and conjugative elements. The active site is comprised of a HEXXH motif and a C-terminal glutamate [1]. [1]. 28559295. Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. Iyer LM, Burroughs AM, Anand S, de Souza RF, Aravind L;. J Bacteriol. 2017; [Epub ahead of print] (from Pfam) NF037526.5 PF18844.6 baeRF_family2 26.9 26.9 149 domain Y N N Bacterial archaeo-eukaryotic release factor family 2 29632312 131567 cellular organisms no rank 8865 EBI-EMBL Bacterial archaeo-eukaryotic release factor family 2 Bacterial archaeo-eukaryotic release factor family 2 Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome. This family contains a well-conserved 'FP' motif in the catalytic loop [1]. [1]. 29632312. Vms1 and ANKZF1 peptidyl-tRNA hydrolases release nascent chains from stalled ribosomes. Verma R, Reichermeier KM, Burroughs AM, Oania RS, Reitsma JM, Aravind L, Deshaies RJ;. Nature. 2018;557:446-451. (from Pfam) NF037527.5 PF18845.6 baeRF_family3 31.5 31.5 168 domain Y N N Bacterial archaeo-eukaryotic release factor family 3 29632312 131567 cellular organisms no rank 11485 EBI-EMBL Bacterial archaeo-eukaryotic release factor family 3 Bacterial archaeo-eukaryotic release factor family 3 Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome [1]. [1]. 29632312. Vms1 and ANKZF1 peptidyl-tRNA hydrolases release nascent chains from stalled ribosomes. Verma R, Reichermeier KM, Burroughs AM, Oania RS, Reitsma JM, Aravind L, Deshaies RJ;. Nature. 2018;557:446-451. (from Pfam) NF037529.5 PF18857.6 LPD38 27 27 189 domain Y Y N LPD38 domain-containing protein 28559295 131567 cellular organisms no rank 3438 EBI-EMBL Large polyvalent protein associated domain 38 LPD38 domain This is an alpha and beta fold domain found in polyvalent proteins of phages and prophages [1]. [1]. 28559295. Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. Iyer LM, Burroughs AM, Anand S, de Souza RF, Aravind L;. J Bacteriol. 2017; [Epub ahead of print] (from Pfam) NF037531.5 PF18862.6 ApeA_NTD1 25.5 25.5 271 domain Y N N ApeA N-terminal domain 1 23768067 131567 cellular organisms no rank 4870 EBI-EMBL ApeA N-terminal domain 1 ApeA N-terminal domain 1 Mostly beta strands. Fused to HEPN (Apea). Several conserved aromatic residues, abundant but poorly conserved [1]. [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF037546.5 PF17419.7 MauJ 28 28 116 PfamEq Y Y N methylamine utilization protein MauJ mauJ 131567 cellular organisms no rank 671 EBI-EMBL Methylamine utilization protein MauJ methylamine utilization protein MauJ This domain family is found in MauJ proteins. The exact function of the MauJ proteins is unknown but thought to be involved in methylamine utilization. MauJ is predicted to be a cytoplasmic protein. MauJ itself is inactive HEPN, other members are active HEPN. (from Pfam) NF037556.5 PF17451.7 Glyco_hyd_101C 25 25 119 domain Y Y N glycoside hydrolase family 101 beta sandwich domain-containing protein 19788271,20556855 131567 cellular organisms no rank 9291 EBI-EMBL Glycosyl hydrolase 101 beta sandwich domain Glycosyl hydrolase 101 beta sandwich domain Virulence of pathogenic organisms such as the Gram-positive Streptococcus pneumoniae is largely determined by the ability to degrade host glycoproteins and to metabolise the resultant carbohydrates. This family is the enzymatic region, EC:3.2.1.97, of the cell surface proteins that specifically cleave Gal-beta-1,3-GalNAc-alpha-Ser/Thr (T-antigen, galacto-N-biose), the core 1 type O-linked glycan common to mucin glycoproteins. This reaction is exemplified by the S. pneumoniae protein Swiss:B2DRU5, where Asp764 is the catalytic nucleophile-base and Glu796 the catalytic proton donor. This domain represents C-terminal the beta sandwich domain. [1]. 19788271. Mechanistic investigation of the endo-alpha-N-acetylgalactosaminidase from Streptococcus pneumoniae R6. Willis LM, Zhang R, Reid A, Withers SG, Wakarchuk WW;. Biochemistry. 2009;48:10334-10341. [2]. 20556855. Gh101 family of glycoside hydrolases: subfamily structure and evolutionary connections with other families. Naumoff DG;. J Bioinform Comput Biol. 2010;8:437-451. (from Pfam) NF037565.5 PF17482.7 Phage_sheath_1C 26.9 26.9 104 domain Y Y N phage tail sheath C-terminal domain-containing protein 1825255,22153511,2963141,7676633 131567 cellular organisms no rank 57704 EBI-EMBL Phage tail sheath C-terminal domain Phage tail sheath C-terminal domain This entry represents the C-terminal domain in a variety of phage tail sheath proteins [4]. [1]. 7676633. Tail sheath and tail tube genes of the temperate coliphage 186. Xue Q, Egan JB;. Virology 1995;212:218-221. [2]. 1825255. Nucleotide sequence of the genes encoding the major tail sheath and tail tube proteins of bacteriophage P2. Temple LM, Forsburg SL, Calendar R, Christie GE;. Virology 1991;181:353-358. [3]. 2963141. Nucleotide sequence of the tail tube structural gene of bacteriophage T4. Arisaka F, Ishimoto L, Kassavetis G, Kumazaki T, Ishii S;. J Virol 1988;62:882-886. [4]. 22153511. Structural conservation of the myoviridae phage tail sheath protein fold. Aksyuk AA, Kurochkina LP, Fokine A, Forouhar F, Mesyanzhinov VV, Tong L, Rossmann MG;. Structure. 2011;19:1885-1894. (from Pfam) NF037610.5 PF17668.6 Acetyltransf_17 25 25 114 domain Y N N Acetyltransferase (GNAT) domain 131567 cellular organisms no rank 38757 EBI-EMBL Acetyltransferase (GNAT) domain Acetyltransferase (GNAT) domain NF037611.5 PF17678.6 Glyco_hydro_92N 34.5 34.5 236 domain Y N N Glycosyl hydrolase family 92 N-terminal domain 131567 cellular organisms no rank 77816 EBI-EMBL Glycosyl hydrolase family 92 N-terminal domain Glycosyl hydrolase family 92 N-terminal domain This domain is found at the N-terminus of family 92 glycosyl hydrolase proteins. (from Pfam) NF037617.5 PF17728.6 BsuBI_PstI_RE_N 27 27 140 domain Y N N BsuBI/PstI restriction endonuclease HTH domain 1480472,22638584 131567 cellular organisms no rank 2845 EBI-EMBL BsuBI/PstI restriction endonuclease HTH domain BsuBI/PstI restriction endonuclease HTH domain This family represents the C-terminus of bacterial enzymes similar to type II restriction endonucleases BsuBI and PstI (EC:3.1.21.4). The enzymes of the BsuBI restriction/modification (R/M) system recognise the target sequence 5'CTGCAG and are functionally identical with those of the PstI R/M system [1]. [1]. 1480472. BsuBI--an isospecific restriction and modification system of PstI: characterization of the BsuBI genes and enzymes. Xu GL, Kapfer W, Walter J, Trautner TA;. Nucleic Acids Res 1992;20:6517-6523. [2]. 22638584. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;. Nucleic Acids Res. 2012;40:7016-7045. (from Pfam) NF037626.5 PF17757.6 UvrB_inter 22.9 22.9 91 domain Y N N UvrB interaction domain 18158267,19287003 131567 cellular organisms no rank 183287 EBI-EMBL UvrB interaction domain UvrB interaction domain This domain is found in the UvrB protein where it interacts with the UvrA protein [2]. [1]. 18158267. Crystal structure of Bacillus stearothermophilus UvrA provides insight into ATP-modulated dimerization, UvrB interaction, and DNA binding. Pakotiprapha D, Inuzuka Y, Bowman BR, Moolenaar GF, Goosen N, Jeruzalmi D, Verdine GL;. Mol Cell. 2008;29:122-133. [2]. 19287003. A structural model for the damage-sensing complex in bacterial nucleotide excision repair. Pakotiprapha D, Liu Y, Verdine GL, Jeruzalmi D;. J Biol Chem. 2009;284:12837-12844. (from Pfam) NF037629.5 PF17769.6 PurK_C 22.6 22.6 56 domain Y N N Phosphoribosylaminoimidazole carboxylase C-terminal domain 131567 cellular organisms no rank 68235 EBI-EMBL Phosphoribosylaminoimidazole carboxylase C-terminal domain Phosphoribosylaminoimidazole carboxylase C-terminal domain This entry represents the C-terminal domain of the PurK enzyme. (from Pfam) NF037630.5 PF17773.6 UPF0176_N 26.2 26.2 92 domain Y N N UPF0176 acylphosphatase like domain 131567 cellular organisms no rank 39091 EBI-EMBL UPF0176 acylphosphatase like domain UPF0176 acylphosphatase like domain This domain is found at the N-terminus of UPF0176 family proteins. It adopts a fold similar to the Pfam:PF00708 family. (from Pfam) NF037633.5 PF17780.6 OCRE 24.7 24.7 52 domain Y Y N OCRE domain-containing protein 26712279,27894420 131567 cellular organisms no rank 196 EBI-EMBL OCRE domain OCRE domain The OCRE (OCtamer REpeat) domain contains within it an octameric repeat structure with a motif approximating GYYY. It is mostly eukaryotic but appears in a few bacterial proteins, e.g. WP_118320522.1 and its homologs, where it appears as a C-terminal domain immediately after a low-complexity acidic spacer region. NF037639.5 PF17802.6 SpaA 23.1 23.1 91 domain Y Y N SpaA isopeptide-forming pilin-related protein 19805181 131567 cellular organisms no rank 137266 EBI-EMBL Prealbumin-like fold domain SpaA pilin isopeptide-forming domain This HMM described a domain that is often repeated in pilins such as SpaA, and that often forms isopeptide bonds cross-linking amino acid side chains, giving the pilins added strength. NF037640.5 PF17806.6 SO_alpha_A3 23.1 23.1 87 domain Y N N Sarcosine oxidase A3 domain 16820168 131567 cellular organisms no rank 38756 EBI-EMBL Sarcosine oxidase A3 domain Sarcosine oxidase A3 domain This short domain is found in Heterotetrameric Sarcosine Oxidase's alpha A3 domain [1]. This domain binds to FMN in sarcosine oxidase. This domain is related to Pfam:PF04324 but lacks its iron binding cysteine residues. [1]. 16820168. Heterotetrameric sarcosine oxidase: structure of a diflavin metalloenzyme at 1.85 A resolution. Chen ZW, Hassan-Abdulah A, Zhao G, Jorns MS, Mathews FS;. J Mol Biol. 2006;360:1000-1018. (from Pfam) NF037646.5 PF17832.6 Pre-PUA 23.5 23.5 86 domain Y Y N Tma20 N-terminal domain-containing protein 131567 cellular organisms no rank 134 EBI-EMBL Pre-PUA-like domain Pre-PUA-like domain This Pre-PUA-like domain is found in a wide variety of proteins including Swiss:Q61211. the eukaryotic translation initiation factor 2D, where it is found at the N-terminus. (from Pfam). This domain, regularly found N-terminal to the PseudoUridine synthase and Archaeosine transglycosylase (PUA)-domain and therefore called Pre-PUA, occurs in yeast translation protein Tma20, and in homologous archaeal proteins. NF037652.5 PF17850.6 CysA_C_terminal 29.7 29.7 43 domain Y N N CysA C-terminal regulatory domain 15893314 131567 cellular organisms no rank 13492 EBI-EMBL CysA C-terminal regulatory domain CysA C-terminal regulatory domain ABC (ATP-binding cassette) transporters share a common architecture comprising two variable hydrophobic transmembrane domains (TMDs) that form the translocation pathway and two conserved hydrophilic ABC-ATPases that hydrolyze ATP. This is the C-terminal regulatory domain found at the ATPase subunit of CysA, a putative sulfate ABC transporter from Alicyclobacillus acidocaldarius. The regulatory domain of CysA is built up of an elongated beta-barrel composed of two beta-sandwiches that form a common hydrophobic core [1]. [1]. 15893314. Structure of the ATPase subunit CysA of the putative sulfate ATP-binding cassette (ABC) transporter from Alicyclobacillus acidocaldarius. Scheffel F, Demmer U, Warkentin E, Hulsmann A, Schneider E, Ermler U;. FEBS Lett. 2005;579:2953-2958. (from Pfam) NF037653.5 PF17853.6 GGDEF_2 24.5 24.5 116 domain Y N N GGDEF-like domain 131567 cellular organisms no rank 155281 EBI-EMBL GGDEF-like domain GGDEF-like domain This domain is distantly related to the GGDEF domain, suggesting these may by diguanylate cyclase enzymes. (from Pfam) NF037656.5 PF17866.6 AAA_lid_6 24.3 24.3 60 domain Y N N AAA lid domain 131567 cellular organisms no rank 38670 EBI-EMBL AAA lid domain AAA lid domain This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. (from Pfam) NF037658.5 PF17868.6 AAA_lid_8 22.8 22.8 72 domain Y N N AAA lid domain 21148420,25097238 131567 cellular organisms no rank 13322 EBI-EMBL AAA lid domain AAA lid domain This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. [1]. 21148420. Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity. El Bakkouri M, Gutsche I, Kanjee U, Zhao B, Yu M, Goret G, Schoehn G, Burmeister WP, Houry WA;. Proc Natl Acad Sci U S A. 2010;107:22499-22504. [2]. 25097238. Assembly principles of a unique cage formed by hexameric and decameric E. coli proteins. Malet H, Liu K, El Bakkouri M, Chan SW, Effantin G, Bacia M, Houry WA, Gutsche I;. Elife. 2014;3:e03653. (from Pfam) NF037660.5 PF17874.6 TPR_MalT 27 27 336 domain Y N N MalT-like TPR region 11709169,22171003,22215984,23519214,23526880,23526881 131567 cellular organisms no rank 113772 EBI-EMBL MalT-like TPR region MalT-like TPR region This entry contains a series of TPR repeats. [1]. 11709169. Crystal structure of transcription factor MalT domain III: a novel helix repeat fold implicated in regulated oligomerization. Steegborn C, Danot O, Huber R, Clausen T;. Structure. 2001;9:1051-1060. [2]. 22171003. Inscuteable and NuMA proteins bind competitively to Leu-Gly-Asn repeat-enriched protein (LGN) during asymmetric cell divisions. Culurgioni S, Alfieri A, Pendolino V, Laddomada F, Mapelli M;. Proc Natl Acad Sci U S A. 2011;108:20998-21003. [3]. 22215984. Structural basis of response regulator inhibition by a bacterial anti-activator protein. Baker MD, Neiditch MB;. PLoS Biol. 2011;9:e1001226. [4]. 23526880. Structural basis of Rap phosphatase inhibition by Phr peptides. Gallego del Sol F, Marina A;. PLoS Biol. 2013;11:e1001511. [5]. 23519214. Structural basis for kinesin-1:cargo recognition. Pernigo S, Lamprecht A, Steiner RA, Dodding MP;. Science. 2013;340:356-359. [6]. 23526881. Conformational change-induced repeat domain expansion regulates Rap phosphatase quorum-sensing signal receptors. Parashar V, Jeffrey PD, Neiditch MB;. PLoS Biol. 2013;11:e1001512. (from Pfam) NF037667.5 PF17900.6 Peptidase_M1_N 25.8 25.8 186 domain Y N N Peptidase M1 N-terminal domain 131567 cellular organisms no rank 153215 EBI-EMBL Peptidase M1 N-terminal domain Peptidase M1 N-terminal domain This domain is found at the N-terminus of aminopeptidases from the M1 family. (from Pfam) NF037668.5 PF17903.6 KH_8 23.4 23.4 81 domain Y N N Krr1 KH1 domain 24990943 131567 cellular organisms no rank 146 EBI-EMBL Krr1 KH1 domain Krr1 KH1 domain This entry represents the first KH domain in the KRR1 protein [1]. Krr1 is a ribosomal assembly factor. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1 [1]. [1]. 24990943. Interaction between ribosome assembly factors Krr1 and Faf1 is essential for formation of small ribosomal subunit in yeast. Zheng S, Lan P, Liu X, Ye K;. J Biol Chem. 2014;289:22692-22703. (from Pfam) NF037670.5 PF17910.6 FeoB_Cyto 23.4 23.4 90 domain Y N N FeoB cytosolic helical domain 19629046,19733088,20123128,20220129,21858085,22101824,22139154,24649829 131567 cellular organisms no rank 37776 EBI-EMBL FeoB cytosolic helical domain FeoB cytosolic helical domain FeoB is a G-protein coupled membrane protein essential for Fe(II) uptake in prokaryotes. In the structures, a canonical G-protein domain (G domain) is followed by a helical bundle domain (S-domain) which is represented by this entry. [1]. 20123128. Structural fold, conservation and Fe(II) binding of the intracellular domain of prokaryote FeoB. Hung KW, Chang YW, Eng ET, Chen JH, Chen YC, Sun YJ, Hsiao CD, Dong G, Spasov KA, Unger VM, Huang TH;. J Struct Biol. 2010;170:501-512. [2]. 19629046. Structural basis of GDP release and gating in G protein coupled Fe2+ transport. Guilfoyle A, Maher MJ, Rapp M, Clarke R, Harrop S, Jormakka M;. EMBO J. 2009;28:2677-2685. [3]. 19733088. Structural basis of novel interactions between the small-GTPase and GDI-like domains in prokaryotic FeoB iron transporter. Hattori M, Jin Y, Nishimasu H, Tanaka Y, Mochizuki M, Uchiumi T, Ishitani R, Ito K, Nureki O;. Structure. 2009;17:1345-1355. [4]. 22101824. A suite of Switch I and Switch II mutant structures from the G-protein domain of FeoB. Ash MR, Maher MJ, Guss JM, Jormakka M;. Acta Crystallogr D Biol Crystallogr. 2011;67:973-980. [5]. 20220129. Potassium-activated GTPase reaction in the G Protein-coupled ferrous iron transporter B. Ash MR, Guilfoyle A, Clarke RJ, Guss JM, Maher MJ, Jormakka M;. J Biol Chem. 2010;285:14594-14602. [6]. 21858085. The initiation of GTP hydrolysis by the G-domain of FeoB: insights from a transition-state complex structure. Ash MR, Maher MJ, Guss JM, Jormakka M;. PLoS One. 2011;6:e23355. [7]. 22139154. The structure of an N11A mutant of the G-protein domain of FeoB. Ash MR, Maher MJ, Guss JM, Jormakka M;. Acta Crys. TRUNCATED at 1650 bytes (from Pfam) NF037672.5 PF17914.6 HopA1 22.7 22.7 170 domain Y Y N T3SS effector HopA1 family protein 25681297 131567 cellular organisms no rank 3894 EBI-EMBL HopA1 effector protein family T3SS effector HopA1 domain This family includes the HopA1 effector protein from Pseudomonas syringae. Structurally this protein has an alpha + beta fold [1]. The effector protein HopA1 was shown to affect the EDS1 complex by binding EDS1 directly and activating the immune response signaling pathway. [1]. 25681297. Crystal structure of the effector protein HopA1 from Pseudomonas syringae. Park Y, Shin I, Rhee S;. J Struct Biol. 2015;189:276-280. (from Pfam) NF037677.5 PF17929.6 TetR_C_34 26.3 26.3 120 domain Y N N Tetracyclin repressor-like, C-terminal domain 15944459,7707374 131567 cellular organisms no rank 8506 EBI-EMBL Tetracyclin repressor-like, C-terminal domain Tetracyclin repressor-like, C-terminal domain TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity [1]. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response [1]. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis [2]. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain [2]. This entry represents the C-terminal domain present in putative TetR family transcriptional regulators found in bacteria. [1]. 15944459. The TetR family of transcriptional repressors. Ramos JL, Martinez-Bueno M, Molina-Henares AJ, Teran W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R;. Microbiol Mol Biol Rev. 2005;69:326-356. [2]. 7707374. The complex formed between Tet repressor and tetracycline. TRUNCATED at 1650 bytes (from Pfam) NF037695.5 PF17975.6 RNR_Alpha 26.4 26.4 101 domain Y N N Ribonucleotide reductase alpha domain 11875520,25734234,3286319,8511586 131567 cellular organisms no rank 1706 EBI-EMBL Ribonucleotide reductase alpha domain Ribonucleotide reductase alpha domain This is the alpha helical domain of ribonucleotide reductases. Family members include Ribonucleotide reductase (RNR, EC:1.17.4.1) [1, 2] which catalyse the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs divide into three classes on the basis of their metallocofactor usage. This domain is found in Class II. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Many organisms have more than one class of RNR present in their genomes. Ribonucleotide reductase is an oligomeric enzyme composed of a large sub-unit (700 to 1000 residues) and a small sub-unit (300 to 400 residues) - class II RNRs are less complex, using the small molecule B12 in place of the small chain [3]. Some family members carry ATP cone domain which acts as a functional regulator. Competitive binding of ATP and dATP to an N-terminal ATP-cone domain determines enzyme activity. As the ratio of dATP to ATP increases above a certain threshold, the enzyme activity is turned off. Substrate nucleotides are recognised by relatively simple H-bonding interactions at the N-terminus of one or more alpha helices. In the monomeric class II RNR, the effector binds in a pocket formed by helices in a 130 amino acid insertion which constitutes this domain [4]. [1]. 3286319. Structure-function studies of the large subunit of ribonucleotide reductase from Escherichia coli. Nilsson O, Lundqvist T, Hahne S, Sjoberg BM;. Biochem Soc Trans. 1988;16:91-94. [2]. 8511586. From RNA to DNA, why so many ribonucleotide reductases?. TRUNCATED at 1650 bytes (from Pfam) NF037703.5 PF18000.6 Top6b_C 28.6 28.6 111 domain Y N N Type 2 DNA topoisomerase 6 subunit B C-terminal domain 17603498 131567 cellular organisms no rank 863 EBI-EMBL Type 2 DNA topoisomerase 6 subunit B C-terminal domain Type 2 DNA topoisomerase 6 subunit B C-terminal domain This is the C-terminal domain found in archaeal type 2 DNA topoisomerase 6 subunit B (EC:5.99.1.3). This region is a small helix-two turns-helix (H2TH) domain inserted between the GHKL and transducer domains which adopts an immunoglobulin-like fold. Mutation analysis of this C-terminal domain showed that the overall activity of the mutant mesophilic methanogen M. mazei Top6B (MmT6) is modestly reduced but its relative activity on different substrates is not affected. Due to the similarity of the B subunit's CTD to known protein- and carbohydrate-binding modules, it has been suggested that it could regulate topo VI spatially, perhaps by localizing the enzyme to a specific subcellular region or functional partner [1]. [1]. 17603498. Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI. Corbett KD, Benedetti P, Berger JM;. Nat Struct Mol Biol. 2007;14:611-619. (from Pfam) NF037707.5 PF18019.6 Cas3_HD 23.1 23.1 207 domain Y Y N HD domain-containing protein 21775431,25132177,25368186 131567 cellular organisms no rank 25324 EBI-EMBL Cas3, HD domain HD domain PF18019 represents a branch of HD domain family that is found primarily as an N-terminal nuclease domain of Cas3 enzymes of CRISPR systems. NF037713.5 PF18047.6 PatG_D 27 27 111 domain Y N N PatG Domain 25484206 131567 cellular organisms no rank 1824 EBI-EMBL PatG Domain PatG Domain This is a domain found in PatG proteins, these proteins are involved in prfocessing the precursor peptide to yield the cyclic Patellamide. PatG can be found in Prochloron sp [1]. [1]. 25484206. The structure of the cyanobactin domain of unknown function from PatG in the patellamide gene cluster. Mann G, Koehnke J, Bent AF, Graham R, Houssen W, Jaspars M, Schwarz-Linek U, Naismith JH;. Acta Crystallogr F Struct Biol Commun. 2014;70:1597-1603. (from Pfam) NF037716.5 PF18050.6 Cyclophil_like2 22.7 22.7 115 subfamily Y Y N cyclophilin-like fold protein 131567 cellular organisms no rank 15299 EBI-EMBL Cyclophilin-like family cyclophilin-like fold protein This entry represents a family of cyclophilin-like proteins found in a range of bacterial species. (from Pfam) NF037718.5 PF18069.6 DR2241 26.4 26.4 111 domain Y Y N DR2241 family protein 17448684 131567 cellular organisms no rank 848 EBI-EMBL DR2241 stabilising domain DR2241 tetramer-stabilizing domain This is the middle domain found in DR2241, a multi-domain protein with an N-terminal cobalamin (vitamin B12) chelatase domain. DR2241 is found in D. radiodurans. The middle domain has four alpha-helices (alpha7-alpha10) in contact with the N-terminal domains and C-terminal domain and five anti-parallel beta-strands with strand order 12354 at the outer side of one monomer. The middle domain, as well as the C-terminal domain, are heavily involved in the tetramer stabilisation [1]. [1]. 17448684. The crystal structure of DR2241 from Deinococcus radiodurans at 1.9 A resolution reveals a multi-domain protein with structural similarity to chelatases but also with two additional novel domains. Leiros HK, McSweeney SM;. J Struct Biol. 2007;159:92-102. (from Pfam) NF037719.5 PF18082.6 NAT_N 27.8 27.8 129 domain Y Y N acyltransferase domain-containing protein 25095906 131567 cellular organisms no rank 5401 EBI-EMBL N-acyltransferase N-terminal domain N-acyltransferase N-terminal domain This is the N-terminal all helix domain found in N-acyltransferases (NATs), the gene products orf11 and dbv8. The all-helix domain is composed of eight helices with two helix-turn-helix motifs in tandem. It is structurally akin to the AAA+ protein family (ATPases associated with diverse cellular activities) [1]. [1]. 25095906. Multiple complexes of long aliphatic N-acyltransferases lead to synthesis of 2,6-diacylated/2-acyl-substituted glycopeptide antibiotics, effectively killing vancomycin-resistant enterococcus. Lyu SY, Liu YC, Chang CY, Huang CJ, Chiu YH, Huang CM, Hsu NS, Lin KH, Wu CJ, Tsai MD, Li TL;. J Am Chem Soc. 2014;136:10989-10995. (from Pfam) NF037722.5 PF18095.6 PAS_12 22.6 22.6 153 domain Y N N UPF0242 C-terminal PAS-like domain 131567 cellular organisms no rank 202 EBI-EMBL UPF0242 C-terminal PAS-like domain UPF0242 C-terminal PAS-like domain This domain is found at the C-terminus of proteins of the UPF0242 family. This domain is related to the PAS domain Pfam:PF13426. (from Pfam) NF037735.5 PF18143.6 HAD_SAK_2 27.5 27.5 139 domain Y Y N HAD domain-containing protein 27536007 131567 cellular organisms no rank 13676 EBI-EMBL HAD domain in Swiss Army Knife RNA repair proteins Swiss Army Knife RNA repair protein family HAD domain Family of HAD domain phophoesterases observed in large eukaryotic proteins with predicted role in RNA repair, the so-called 'Swiss Army Knife' repair proteins. May be involved in phosphate group removal during RNA re-ligation [1]. [1]. 27536007. RNA damage in biological conflicts and the diversity of responding RNA repair systems. Burroughs AM, Aravind L;. Nucleic Acids Res. 2016;44:8525-8555. (from Pfam) NF037736.5 PF18144.6 SMODS 26.5 30 164 domain Y Y N SMODS domain-containing nucleotidyltransferase 22500802,26590262 131567 cellular organisms no rank 11700 EBI-EMBL Second Messenger Oligonucleotide or Dinucleotide Synthetase domain SMODS domain Nucleotide synthetase enzyme of the DNA polymerase beta superfamily. Experimental studies have demonstrated cGAMP synthetase activity in the Vibrio cholerae DncV protein, a member of the SMODS family. The diversity inherent to the SMODS family suggests members of the family could generate a range of nucleotides, cyclic and/or linear. The nucleotide second messengers generated by the SMODS domains are predicted to activate effectors in a class of conflict systems reliant on the production and sensing of the nucleotide second messengers [1] [2]. [1]. 26590262. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;. Nucleic Acids Res. 2015;43:10633-10654. [2]. 22500802. Coordinated regulation of accessory genetic elements produces cyclic di-nucleotides for V. cholerae virulence. Davies BW, Bogard RW, Young TS, Mekalanos JJ;. Cell. 2012;149:358-370. (from Pfam) NF037740.5 PF18153.6 S_2TMBeta 31.2 31.2 181 domain Y N N SMODS-associating 2TM, beta-strand rich effector domain 26590262 131567 cellular organisms no rank 3022 EBI-EMBL SMODS-associating 2TM, beta-strand rich effector domain SMODS-associating 2TM, beta-strand rich effector domain Predicted sensor/effector coupled domain which occurs in conserved genome contexts with the SMODS nucleotide synthetase. In addition to the predicted pore-forming 2TM region, the domain contains seven predicted beta-strands, suggestive of a lipocalin-like beta-barrel structure which could act as the sensor which activates the pore-forming effector response [1]. [1]. 26590262. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;. Nucleic Acids Res. 2015;43:10633-10654. (from Pfam) NF037746.5 PF18181.6 SLATT_1 26.3 26.3 122 domain Y N N SMODS and SLOG-associating 2TM effector domain 1 26590262 131567 cellular organisms no rank 6144 EBI-EMBL SMODS and SLOG-associating 2TM effector domain 1 SMODS and SLOG-associating 2TM effector domain 1 The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is often C-terminally fused to the SLATT_3 family, and is typically operonically linked to either inactive TIR domains or SLOG domains which could act as regulators of the SLATT channels. In relatively rare instances, it is genomically linked as a standalone domain to the RelA/SpoT nucleotide synthetase and the predicted NA37/YejK sensor domain [1]. [1]. 26590262. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;. Nucleic Acids Res. 2015;43:10633-10654. (from Pfam) NF037749.5 PF18197.6 TTHB210-like 26.6 26.6 50 domain Y Y N DUF5602 domain-containing protein 22231934 131567 cellular organisms no rank 1022 EBI-EMBL Hypothetical protein TTHB210 Hypothetical protein TTHB210 This domain is found in TTHB210 protein present in Thermus thermophilus. TTHB210 is a Sigma-E factor regulated gene product that forms a homodecamer. This domain is chain G and can be classified with chains A, C, E and I based on its folds [1]. [1]. 22231934. Crystal structure of hypothetical protein TTHB210, controlled by the sigma(E) /anti-sigma(E) regulatory system in Thermus thermophilus HB8, reveals a novel homodecamer. Agari Y, Kuramitsu S, Shinkai A;. Proteins. 2012;80:958-962. (from Pfam) NF037753.5 PF18204.6 PGF-CTERM 18.8 18.8 23 domain Y Y N PGF-CTERM sorting domain-containing protein 22037399,26712937 131567 cellular organisms no rank 3824 EBI-EMBL PGF-CTERM motif PGF-CTERM sorting domain NF037763.5 PF18237.6 Tk-SP_N-pro 26.5 26.5 67 domain Y N N Tk-SP N-propeptide domain 20595040 131567 cellular organisms no rank 155 EBI-EMBL Tk-SP N-propeptide domain Tk-SP N-propeptide domain This is the N-propeptide domain found in Tk-SP, a subtilisin-like serine protease from Thermococcus kodakaraensis. The beta sheet of this domain packs tightly to the two nearly parallel alpha helices 2 and 3 located at the surface of the subtilisin domain. Gln105 and Asp107 of the N-propeptide domain also bind to the N-termini of these two alpha-helices to form helix caps [1]. [1]. 20595040. Crystal structure of a subtilisin homologue, Tk-SP, from Thermococcus kodakaraensis: requirement of a C-terminal beta-jelly roll domain for hyperstability. Foophow T, Tanaka S, Angkawidjaja C, Koga Y, Takano K, Kanaya S;. J Mol Biol. 2010;400:865-877. (from Pfam) NF037773.5 PF18267.6 Rubredoxin_C 25.9 25.9 70 domain Y N N Rubredoxin NAD+ reductase C-terminal domain 20017214 131567 cellular organisms no rank 80072 EBI-EMBL Rubredoxin NAD+ reductase C-terminal domain Rubredoxin NAD+ reductase C-terminal domain This is the C-terminal domain of NADH rubredoxin oxidoreductase present in Clostridium acetobutylicum. The majority of obligatory anaerobes detoxify micro-aerobic environments by consuming O2 via H2O-forming NADH oxidase. This enzyme offers an alternate reaction pathway for scavenging of O2 and reactive oxygen species, wherein the reducing equivalent is obtained from NADH [1]. [1]. 20017214. Crystal structure of NADH:rubredoxin oxidoreductase from Clostridium acetobutylicum: a key component of the dioxygen scavenging system in obligatory anaerobes. Nishikawa K, Shomura Y, Kawasaki S, Niimura Y, Higuchi Y;. Proteins. 2010;78:1066-1070. (from Pfam) NF037782.5 PF18297.6 NFACT-R_2 26.9 26.9 104 domain Y N N NFACT protein RNA binding domain 24646681 131567 cellular organisms no rank 25618 EBI-EMBL NFACT protein RNA binding domain NFACT protein RNA binding domain NFACT-R RNA binding family found found in bacteria fused to the ThiI domain as a variant of the canonical tRNA 4-thiouridylation pathway [1]. [1]. 24646681. A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications. Burroughs AM, Aravind L;. RNA Biol. 2014;11:360-372. (from Pfam) NF037785.5 PF18306.6 LDcluster4 26.3 26.3 151 domain Y N N SLOG cluster4 family 26590262 131567 cellular organisms no rank 95772 EBI-EMBL SLOG cluster4 family SLOG cluster4 family Family in the SLOG superfamily, observed as a standalone domain with little informative genome context, although related families in the SLOG superfamily are predicted to function in diverse conflict contexts [1]. [1]. 26590262. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;. Nucleic Acids Res. 2015;43:10633-10654. (from Pfam) NF037804.5 PF18389.6 TrmO_C 27.1 27.1 65 domain Y N N TrmO C-terminal domain 131567 cellular organisms no rank 16723 EBI-EMBL TrmO C-terminal domain TrmO C-terminal domain This domain is found at the C-terminus of TrmO tRNA methyltransferase proteins. This domain has a RelE fold. (from Pfam) NF037830.5 PF18478.6 PIN_10 26.2 26.2 84 domain Y N N PIN like domain 28575517 131567 cellular organisms no rank 5045 EBI-EMBL PIN like domain PIN like domain This is a bacterial domain of unknown function suggested to resemble PIN like domains [1]. [1]. 28575517. Comprehensive classification of the PIN domain-like superfamily. Matelska D, Steczkiewicz K, Ginalski K;. Nucleic Acids Res. 2017;45:6995-7020. (from Pfam) NF037832.5 PF18480.6 DUF5615 23.8 23.8 110 subfamily Y Y N DUF5615 family PIN-like protein 28575517 131567 cellular organisms no rank 12668 EBI-EMBL Domain of unknown function (DUF5615) DUF5615 family PIN-like protein This is a domain of unknown function found in potential toxin-antitoxin system component [1]. [1]. 28575517. Comprehensive classification of the PIN domain-like superfamily. Matelska D, Steczkiewicz K, Ginalski K;. Nucleic Acids Res. 2017;45:6995-7020. (from Pfam) NF037833.5 PF18483.7 Bact_lectin 23 23 191 domain Y Y N lectin-like domain-containing protein 131567 cellular organisms no rank 19901 EBI-EMBL Bacterial lectin bacterial lectin-like domain This entry primarily matches to legume-like lectin domains found in prokaryotes. (from Pfam) NF037850.5 PF18565.6 Glyco_hydro2_C5 32 32 103 domain Y N N Glycoside hydrolase family 2 C-terminal domain 5 27599737 131567 cellular organisms no rank 33771 EBI-EMBL Glycoside hydrolase family 2 C-terminal domain 5 Glycoside hydrolase family 2 C-terminal domain 5 Domain 5 is found in dimeric beta-D-galactosidase from Paracoccus sp. 32d, which contributes to stabilization of the functional dimer. It is suggested that the location of this domain 5, may be one of the factors responsible for the creation of a functional dimer and cold-adaptation of this enzyme [1]. [1]. 27599737. Structural studies of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d. Rutkiewicz-Krotewicz M, Pietrzyk-Brzezinska AJ, Sekula B, Cieslinski H, Wierzbicka-Wos A, Kur J, Bujacz A;. Acta Crystallogr D Struct Biol. 2016;72:1049-1061. (from Pfam) NF037860.5 PF18603.6 LAL_C2 29.4 29.4 78 domain Y N N L-amino acid ligase C-terminal domain 2 23090402 131567 cellular organisms no rank 27276 EBI-EMBL L-amino acid ligase C-terminal domain 2 L-amino acid ligase C-terminal domain 2 l-amino-acid ligases (LALs; EC 6.3.2.28) were discovered to be ATP-grasp superfamily enzymes that catalyze the formation of an alpha-peptide bond between two l-amino acids in an ATP-dependent manner. The members of this family share a common structural architecture that consists of three domains referred to as the A-domain, B-domain and C-domain. The C domain can be further divided into the C1-subdomain and the C2-subdomain [1]. This entry represents the C2 subdomain. [1]. 23090402. The structure of L-amino-acid ligase from Bacillus licheniformis. Suzuki M, Takahashi Y, Noguchi A, Arai T, Yagasaki M, Kino K, Saito J;. Acta Crystallogr D Biol Crystallogr. 2012;68:1535-1540. (from Pfam) NF037864.5 PF18614.6 RNase_II_C_S1 26.6 26.6 59 domain Y N N RNase II-type exonuclease C-terminal S1 domain 22133431 131567 cellular organisms no rank 13217 EBI-EMBL RNase II-type exonuclease C-terminal S1 domain RNase II-type exonuclease C-terminal S1 domain This entry describes the C-terminal S1 domain found in type 2 RNase exonucleases. DrR63 proteins from Deinococcus radiodurans are an RNase II-type enzymes (DrII). Structure analysis of DrII indicates that it has an N-terminal HTH domain which interacts with a flexible loop that connects two beta-strands from the conserved C-terminal S1 domain, forming a beta-wing fold common in wHTH domains [1]. [1]. 22133431. The structure and enzymatic properties of a novel RNase II family enzyme from Deinococcus radiodurans. Schmier BJ, Seetharaman J, Deutscher MP, Hunt JF, Malhotra A;. J Mol Biol. 2012;415:547-559. (from Pfam) NF037884.5 PF18714.6 PI-TkoII_IV 25 25 150 domain Y N N DNA polymerase II intein Domain IV 16493661,21914805 131567 cellular organisms no rank 48 EBI-EMBL DNA polymerase II intein Domain IV DNA polymerase II intein Domain IV This domain can be found in the hyperthermophilic archaeon Thermococcus kodakaraensis Pol-2 intein. It is suggested to be a potential DNA binding domain [1, 2]. [1]. 16493661. Crystal structure of intein homing endonuclease II encoded in DNA polymerase gene from hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1. Matsumura H, Takahashi H, Inoue T, Yamamoto T, Hashimoto H, Nishioka M, Fujiwara S, Takagi M, Imanaka T, Kai Y;. Proteins. 2006;63:711-715. [2]. 21914805. Structural and mutational studies of a hyperthermophilic intein from DNA polymerase II of Pyrococcus abyssi. Du Z, Liu J, Albracht CD, Hsu A, Chen W, Marieni MD, Colelli KM, Williams JE, Reitter JN, Mills KV, Wang C;. J Biol Chem. 2011;286:38638-38648. (from Pfam) NF037887.5 PF18730.6 HEPN_Cthe2314 27.1 27.1 174 domain Y Y N Cthe_2314 family HEPN domain-containing protein 23768067 131567 cellular organisms no rank 1889 EBI-EMBL Cthe_2314-like HEPN Cthe_2314 family HEPN domain Cthe_2314-like HEPN [1]. [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF037888.5 PF18734.6 HEPN_AbiU2 26.8 26.8 193 domain Y N N AbiU2 23768067 131567 cellular organisms no rank 2412 EBI-EMBL AbiU2 AbiU2 AbiU2-like HEPN [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF037889.5 PF18735.6 HEPN_RiboL-PSP 28.4 28.4 191 domain Y Y N HEPN domain-containing protein 23768067 131567 cellular organisms no rank 9155 EBI-EMBL RiboL-PSP-HEPN RiboL-PSP-HEPN RiboL-PSP-HEPN. Fused to endoRNase L-PSP ; in operon with ParB [1]. [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF037890.5 PF18737.6 HEPN_MAE_28990 26.8 26.8 211 subfamily Y Y N MAE_28990/MAE_18760 family HEPN-like nuclease 23768067 131567 cellular organisms no rank 4459 EBI-EMBL MAE_28990/MAE_18760-like HEPN MAE_28990/MAE_18760 family HEPN-like nuclease HEPN-like nuclease. MAE_28990 In operon with a ParB nuclease and DNA methylase genes. MAE_18760-like HEPN found fused to HEPN/RES-NTD1, HEPN/Toprim-NTD1, Schlafen and a novel beta rich domain. In operon with ParA/Soj ATPase of SIMIBI-type GTPase fold [1]. [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF037895.5 PF18755.6 RAMA 35.2 35.2 107 domain Y N N Restriction Enzyme Adenine Methylase Associated 26660621 131567 cellular organisms no rank 11602 EBI-EMBL Restriction Enzyme Adenine Methylase Associated Restriction Enzyme Adenine Methylase Associated An alpha+beta fold domain associated with restriction enzymes across prokaryotes and fused to JAB deubiquitinases, and chromatin proteins in a wide range of eukaryotes. The domain is predicted to function as a modified-DNA reader domain [1]. [1]. 26660621. Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification. Iyer LM, Zhang D, Aravind L;. Bioessays. 2016;38:27-40. (from Pfam) NF037897.5 PF18760.6 ART-PolyVal 31.2 31.2 140 domain Y N N ADP-Ribosyltransferase in polyvalent proteins 28559295 131567 cellular organisms no rank 1503 EBI-EMBL ADP-Ribosyltransferase in polyvalent proteins ADP-Ribosyltransferase in polyvalent proteins A family of ADP-Ribosyltransferases found in polyvalent proteins of phages and conjugative elements. These are in turn related to the Tox-ART-HYD2 group of ADP-Ribosyltransferases that are seen in polymorphic toxin systems and in toxin-antitoxin systems. These are predicted to modify host proteins [1]. [1]. 28559295. Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. Iyer LM, Burroughs AM, Anand S, de Souza RF, Aravind L;. J Bacteriol. 2017; [Epub ahead of print] (from Pfam) NF037908.5 PF18793.6 nos_propeller_2 29 24 70 domain Y N N Nitrous oxide reductase propeller repeat 2 21841804,26885878 131567 cellular organisms no rank 4386 EBI-EMBL Nitrous oxide reductase propeller repeat 2 Nitrous oxide reductase propeller repeat 2 Nitrous oxide reductases usually contain a seven-bladed beta-propeller domain with external short alpha-helices [1,2]. This entry represents a single blade of the propeller, without alpha- helical insertion. [1]. 21841804. N2O binding at a [4Cu:2S] copper-sulphur cluster in nitrous oxide reductase. Pomowski A, Zumft WG, Kroneck PM, Einsle O;. Nature. 2011;477:234-237. [2]. 26885878. Role of Calcium in Secondary Structure Stabilization during Maturation of Nitrous Oxide Reductase. Schneider LK, Einsle O;. Biochemistry. 2016;55:1433-1440. (from Pfam) NF037928.5 PF18856.6 baeRF_family12 27.7 27.7 138 domain Y N N Bacterial archaeo-eukaryotic release factor family 12 29632312 131567 cellular organisms no rank 10237 EBI-EMBL Bacterial archaeo-eukaryotic release factor family 12 Bacterial archaeo-eukaryotic release factor family 12 Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome [1]. [1]. 29632312. Vms1 and ANKZF1 peptidyl-tRNA hydrolases release nascent chains from stalled ribosomes. Verma R, Reichermeier KM, Burroughs AM, Oania RS, Reitsma JM, Aravind L, Deshaies RJ;. Nature. 2018;557:446-451. (from Pfam) NF037930.5 PF18864.6 AbiTii 27.6 27.6 189 domain Y N N AbiTii 23768067 131567 cellular organisms no rank 4529 EBI-EMBL AbiTii AbiTii Alpha + beta domain. Found fused to the N-terminus of the c2405 family of HEPN domains and in few cases to Ymh [1]. [1]. 23768067. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L;. Biol Direct. 2013;8:15. (from Pfam) NF037947.1 holin_4 70 70 75 subfamily Y Y N bacteriophage holin 131567 cellular organisms no rank 192 NCBIFAM bacteriophage holin Bacteriophage holin can cause host cell lysis to release progeny phage particles. Proteins of this family usually have two transmembrane domains. NF037959.1 MFS_SpdSyn 40 40 480 subfamily Y Y N fused MFS/spermidine synthase 31467246 131567 cellular organisms no rank 57479 NCBIFAM fused MFS/spermidine synthase Proteins of this family are fusion of a N-terminal MFS (Major Facilitator Superfamily) transporter domain and a C-terminal spermidine synthase (SpdSyn)-like domain. The encoding genes usually near the genes encoding S-adenosylmethionine decarboxylase (AdoMetDC) on many bacterial genomes. It has been shown in Shewanella oneidensis that the fused protein aminopropylates a substrate other than putrescine, and has a role outside of polyamine biosynthesis. NF037962.1 arsenic_eff 100 100 287 subfamily Y Y N arsenic efflux protein 131567 cellular organisms no rank 4700 NCBIFAM arsenic efflux protein Most proteins of this family have 8 transmembrane domains with two 4 transmembrane halves separated by a hydrophilic loop of variable sizes. It has been reported that some proteins of this family are involved in arsenate/arsenite resistance. NF037968.1 SemiSWEET_2 80 80 76 subfamily Y Y N SemiSWEET transporter GO:0051119 29872447 131567 cellular organisms no rank 6013 NCBIFAM SemiSWEET transporter The SWEET (Sugars Will Eventually be Exported Transporter) is a superfamily of sugar transporters found in both eukaryotes and prokaryotes. Eukaryotic SWEETs usually have seven transmembrane helices (TMHs), but most prokaryotic SWEETs (SemiSWEETs) have only three TMHs. Proteins of this family have 3 TMHs. NF037970.1 vanZ_1 20 20 109 subfamily Y Y N VanZ family protein 131567 cellular organisms no rank 26658 NCBIFAM VanZ family protein VanZ was originally identified in Enterococcus faecium. VanZ increases teicoplanin resistance in Enterococcus faecium, but has no impact on vancomycin resistance. Proteins of this family are homologs of the VanZ protein. They may be involved in teicoplanin resistance. NF037979.1 Na_transp 50 50 419 subfamily Y Y N sodium-dependent transporter GO:0016020 131567 cellular organisms no rank 57560 NCBIFAM sodium-dependent transporter NF037981.1 NCS2_1 40 40 419 subfamily Y Y N purine/pyrimidine permease GO:0022857,GO:0055085 131567 cellular organisms no rank 76953 NCBIFAM purine/pyrimidine permease Proteins of this family usually have 14 transmembrane domains. They belong to the NSC2 superfamily transporters. They are specific purine and/or pyrimidine permeases. NF037982.1 Nramp_1 50 50 404 equivalog Y Y N Nramp family divalent metal transporter GO:0016020,GO:0022857,GO:0055085 27839948 131567 cellular organisms no rank 58065 NCBIFAM Nramp family divalent metal transporter Nramp (natural resistance-associated macrophage protein) family divalent metal transporters are widely conserved divalent metal transporters, which enables manganese import in bacteria and dietary iron uptake in mammals. NF037995.1 TRAP_S1 50 50 271 subfamily Y Y N TRAP transporter substrate-binding protein DctP dctP GO:0055085 22306465 131567 cellular organisms no rank 152931 NCBIFAM TRAP transporter substrate-binding protein DctP Proteins of this family are members of the superfamily of Tripartite ATP-independent Periplasmic Transporter (TRAP-T). They transport hydrophobic substrates, usually lipoprotein. NF037997.1 Na_Pi_symport 50 50 294 subfamily Y Y N Na/Pi symporter GO:0005436,GO:0016020,GO:0035435,GO:0044341 131567 cellular organisms no rank 41828 NCBIFAM Na/Pi symporter Proteins of this family belong to the Phosphate:Na+ Symporter (PNaS) superfamily. NF038011.1 PelF 100 100 489 equivalog Y Y N GT4 family glycosyltransferase PelF pelF GO:0016757 23435893 131567 cellular organisms no rank 10220 NCBIFAM GT4 family glycosyltransferase PelF Proteins of this family are components of the exopolysaccharide Pel transporter. It has been reported that PelF is a soluble glycosyltransferase that uses UDP-glucose as the substrate for the synthesis of exopolysaccharide Pel, whereas PelG is a Wzx-like and PST family exopolysaccharide transporter. NF038013.1 AceTr_1 50 50 176 equivalog Y Y N acetate uptake transporter 131567 cellular organisms no rank 9452 NCBIFAM acetate uptake transporter Proteins of this family are acetate transporters, which usually have 6 transmembrane regions. The homologue in E. coli is YaaH. NF038017.1 ABC_perm1 100 100 184 subfamily Y Y N ABC transporter permease GO:0016020,GO:0055085 30672551 131567 cellular organisms no rank 9656 NCBIFAM ABC transporter permease Proteins of this family are the permease subunit of an ABC transporter complex, which may be involved in tungstate uptake. NF038018.1 qmoC 300 300 360 equivalog Y Y N quinone-interacting membrane-bound oxidoreductase complex subunit QmoC qmoC 131567 cellular organisms no rank 364 NCBIFAM quinone-interacting membrane-bound oxidoreductase complex subunit QmoC Proteins of this family are the transmembrane subunit of the quinone-interacting membrane-bound oxidoreductase complex, which consists of the QmoA, QmoB, and QmoC proteins. It has been reported that the QmoABC complex is essential for efficiently delivering electron to adenosine 5'-phosphosulfate reductase AprAB, which is important in sulfate reduction in sulfate reducing prokaryotes (SRPs). NF038020.1 HeR 100 100 244 equivalog Y Y N heliorhodopsin HeR heR 29925949,31150215,31554965 131567 cellular organisms no rank 880 NCBIFAM heliorhodopsin HeR This HMM represents heliorhodopsins, a group of phylogenetically distinct microbial rhodopsins, which play an important role in absorbing and transferring light energy for numerous biological processes in bacteria. Heliorhodopsin was initially identified and characterized in a Gram-positive actinobacterium based on functional metagenomics and photochemical approaches. Heliorhodopsin have seven transmembrane domains, and exhibit similar biological function as microbial rhodopsins. However, heliorhodopsin form a distinct cluster based on phylogenetic analyses. Most microbial rhodopsins are hit by the Pfam HMM PF01036, which does not hit heliorhodopsins. NF038032.1 CehA_McbA_metalo 80 80 315 domain Y Y N CehA/McbA family metallohydrolase GO:0003824 11872471,29079626 131567 cellular organisms no rank 19816 NCBIFAM CehA/McbA family metallohydrolase domain This domain, a branch of the PHP superfamily, is found in several partially characterized metallohydrolases, including McbA and CehA. Both were studied as hydrolases of carbaryl, a xenobiotic compound that does not contain a phosphate group, suggesting that presuming members of this family to be phosphoesterases (like many PHP domain-containing proteins) may be incorrect. NF038037.1 cytob_DsrM 300 300 320 equivalog Y Y N sulfate reduction electron transfer complex DsrMKJOP subunit DsrM dsrM 16388601 131567 cellular organisms no rank 478 NCBIFAM sulfate reduction electron transfer complex DsrMKJOP subunit DsrM Proteins of this family are the DsrM subunit of the DsrMKJOP complex, which is a membrane-bound redox complex involved in sulfate reduction in Sulfate-reducing organisms (SROs). The dsrM gene encodes a cytochrome b reductase, which usually has six transmembrane helices and five conserved histidines. NF038038.1 cytoc_DsrJ 100 100 121 equivalog Y Y N sulfate reduction electron transfer complex DsrMKJOP subunit DsrJ dsrJ 16388601 131567 cellular organisms no rank 479 NCBIFAM sulfate reduction electron transfer complex DsrMKJOP subunit DsrJ Proteins of this family are the DsrJ subunit of the DsrMKJOP complex, which is a membrane-bound redox complex involved in sulfate reduction in Sulfate-reducing organisms (SROs). The dsrJ gene encodes a triheme periplasmic cytochrome c subunit, which contains three conserved heme c-binding sites (CXXCH) at the C terminal. NF038050.1 NrtS 25 25 56 subfamily Y Y N nitrate/nitrite transporter NrtS nrtS 31198965 131567 cellular organisms no rank 1305 NCBIFAM nitrate/nitrite transporter NrtS NrtS family proteins were first identified and characterized in Synechococcus sp. PCC 7002. The homologous proteins NrtS1 and NrtS2 are encoded by two neighboring genes on Synechococcus sp. PCC 7002 genome. The heteromeric transporter was shown to transport nitrite as well as nitrate. This HMM hits both NrtS1 and NrtS2 proteins, which have extremely high sequence identity and conserved motifs. NF038065.1 Pr6Pr 30 30 162 domain Y Y N Pr6Pr family membrane protein GO:0016020 131567 cellular organisms no rank 20356 NCBIFAM Pr6Pr family membrane protein This family is defined by TCDB as prokaryotic 6 TMS (Pr6Pr) family membrane protein(http://www.tcdb.org/search/result.php?tc=9.b.302). The function of this family proteins is not understood. NF038084.1 DHCW_cupin 70 70 106 hypoth_equivalog Y Y N DHCW motif cupin fold protein 131567 cellular organisms no rank 4472 NCBIFAM DHCW motif cupin fold protein Members of this uncharacterized protein family resemble other cupin superfamily small barrel proteins. This family has a signature motif, DHCW, for which the family is named. NF038085.1 MSMEG_6728_fam 100 100 149 subfamily Y Y N MSMEG_6728 family protein 131567 cellular organisms no rank 5106 NCBIFAM MSMEG_6728 family protein NF038101.1 Trm112_arch 77 77 59 equivalog Y Y N methytransferase partner Trm112 28134793,30010922 131567 cellular organisms no rank 681 NCBIFAM methytransferase partner Trm112 This HMM describes an archaeal branch of a small protein, Trm112, that is conserved in the three domains of life and that serves as general activator of methyltransferases for RNA or protein. NF038108.1 RiPP_NF038108 30 30 65 subfamily Y Y N Cys-every-fifth RiPP peptide CefA 131567 cellular organisms no rank 115 NCBIFAM Cys-every-fifth RiPP peptide CefA Members typically are shorter than 100 residues, with from nine to eleven Cys residues spaced strictly as every fifth residue and usually with at least one adjacent Gly. Most family members occur in the vicinity of a peptide-modifying radical SAM/SPASM domain protein, marking those family members as putative RiPP (ribosomally translated, post-translationally modified peptide) precursors. Because of the small size, richness in Cys and Gly residues, and strictly repetitive nature, it may be expected that some predicted proteins, scoring above the thresholds for the model, are related by convergent evolution rather than by homology, and are not themselves RiPP precursors. NF038114.1 rightmost 35 35 113 domain Y Y N PxKF domain-containing protein 131567 cellular organisms no rank 1382 NCBIFAM PxKF domain The PxKF domain is found in a number of extracellular proteins, always as the most C-terminal domain (710 of 710 at the time of HMM construction). Upstream regions of proteins with the PxKF domain often mark them as members of largely surface-associated proteins, processed and anchored by the type IX secretion system, exosortases, rhombosortases, etc. The species distribution of PxKF domain-containing proteins is broad - mostly Actinobacteria, but also some Firmicutes, Deinococcus, etc. That broad taxonomic distribution, plus its large size (over 100 amino acids long) compared to most known N-terminal or C-terminal sorting signals that are recognized but then removed, suggests that the domain is retained in the mature protein, and has some function involved in surface-binding. NF038117.1 choice_anch_I 300 300 458 subfamily_domain Y Y N choice-of-anchor I family protein 14707128 131567 cellular organisms no rank 10493 NCBIFAM choice-of-anchor I domain This domain is found in the N-terminal third of the alkaline phosphatase PhoA of Synechocystis sp. PCC 6803 (see AGF50645.1), upstream of the region presumed to have phosphatase activity. It is found in a number of other cyanobacterial proteins called PhoA, although those annotations may be incorrect. Proteins with this domain include a number with the PEP-CTERM protein-sorting domain, but also a number with the LPXTG protein-sorting domain, making this a choice-of-anchor domain, that is, a new homology domain of what was previously "dark matter" (that is, lacking any HMM), whose members include proteins targeted for covalent attachment at the cell surface by at least two different protein-sorting systems. NF038123.1 NF038123_dom 40 40 206 domain Y Y N spondin domain-containing protein 21569239 131567 cellular organisms no rank 5969 NCBIFAM spondin domain NF038125.1 PEP_CTERM_THxN 85 85 246 subfamily Y Y N THxN family PEP-CTERM protein 131567 cellular organisms no rank 843 NCBIFAM THxN family PEP-CTERM protein This family of PEP-CTERM proteins is named for one of several well-conserved motifs. The function is unknown, but DVUA0032 is mentioned as a member protein whose expression depends on a 54-dependent promoter. PEP-CTERMs are expected to be expressed covalently attached to outer membrane. NF038128.1 choice_anch_J 30 30 162 domain Y Y N choice-of-anchor J domain-containing protein 131567 cellular organisms no rank 20723 NCBIFAM choice-of-anchor J domain The choice-of-anchor J domain, about 160 amino acids long, occurs as many as times in a protein, although most often only once. Proteins with the domain include proteins with serine hydrolase, metallohydrolase, or adhesin-associated domains. Notably, many members are also found with either the PEP-CTERM term domain, or the type IX secretion system type A domain, both associated with protein-sorting system expected to leave target proteins covalently attached to the bacterial outer membrane. NF038131.1 choice_anch_K 30 30 169 domain Y Y N choice-of-anchor K domain-containing protein 131567 cellular organisms no rank 2263 NCBIFAM choice-of-anchor K domain The choice-of-anchor K is a rather uncommon extracellular domain about 170 amino acids long. A substantial fraction of member proteins have C-terminal regions that target them for sorting to the cell surface, including PEP-CTERM, its variant VPLPA-CTERM, and LPXTG. The domain is found occasionally in RTX toxin-like proteins. NF038133.1 choice_anch_L 27 27 219 domain Y Y N choice-of-anchor L domain-containing protein 131567 cellular organisms no rank 8460 NCBIFAM choice-of-anchor L domain The choice-of-anchor L domain, about 220 amino acids long, is an extracellular domain found often with a C-terminal cell surface, such as PEP-CTERM or the type IX secretion system (T9SS) type B sorting signal. It tends to be found only once per protein, but the family contains some members proteins over 4000 residues long. NF038162.1 RctB_rel_intein 1150 1150 961 exception Y Y N intein-containing RctB family protein 16485279 131567 cellular organisms no rank 58 NCBIFAM intein-containing RctB family protein NF038196.1 ferrodoxin_EFR1 75 75 242 subfamily Y Y N EFR1 family ferrodoxin 17089149 131567 cellular organisms no rank 9447 NCBIFAM EFR1 family ferrodoxin Members of the family have a C-terminal ferrodoxin domain, with eight conserved Cys residues in two CxxCxxCxxxCP motifs, each of which binds a 4Fe-4S cluster. The N-terminal region resembles flavodoxin domains, with some members of the family recognized by Pfam models PF12724 (Flavodoxin_5) or PF00258 (Flavodoxin_1). N-terminal region resembles flavodoxins. C-terminal ferrodoxin region binds two 4Fe-4S clusters. NF038214.1 IS21_help_AAA 200 200 232 equivalog Y Y N IS21-like element helper ATPase IstB istB GO:0005524 26276634 131567 cellular organisms no rank 39029 NCBIFAM IS21-like element helper ATPase IstB This protein family model resembles PF01695, but was built to hit full-length AAA+ ATPases of IS21 family IS (insertion sequence) elements. NF038233.2 retron_St85_RT 235 235 289 exception Y Y N retron St85 family RNA-directed DNA polymerase GO:0001171,GO:0051607 24019407,26367458,33157039 131567 cellular organisms no rank 2915 NCBIFAM retron St85 family RNA-directed DNA polymerase All members of the seed alignment are reverse transcriptases of St85-like systems. However, members of this family may include reverse transcriptases from other types of retron system. NF038245.1 bile_salt_hydro 350 350 314 equivalog Y Y N choloylglycine hydrolase bsh 3.5.1.24 12180927,15633685,15664931,30098054 131567 cellular organisms no rank 4892 NCBIFAM choloylglycine hydrolase Bile salt hydrolase, also known as choloylglycine hydrolase, enables commensal or pathogenic bacteria in the digestive tract to escape the antimicrobial activity of bile acids, which are cholesterol derivatives conjugated to glycine or taurine. NF038281.1 IS200_TnpB 425 425 360 exception Y Y N IS200/IS605 family element RNA-guided endonuclease TnpB tnpB 22367867,23461641,32365520,34619744 131567 cellular organisms no rank 11270 NCBIFAM IS200/IS605 family element RNA-guided endonuclease TnpB NF038283.1 viperin_w_prok 180 180 281 equivalog Y Y N viperin family antiviral radical SAM protein 32937646 131567 cellular organisms no rank 1009 NCBIFAM viperin family antiviral radical SAM protein Homologs of a viral defense radical SAM enzyme found in Homo sapiens, viperin (RSAD2), occur in prokaryotes with a strong bias toward placement in phage defense islands, encoded next to CRISPR system and restriction enzyme genes. Further investigation shows members indeed perform the anti-viral function of synthesizing modified ribonucleotides such as ddhCTP, ddh-guanosine triphosphate (ddhGTP) and ddh-uridine triphosphate (ddhUTP). Those non-standard ribonucleotides can interfere with viral replication machinery. NF038316.1 DrmE_fam 80 80 838 subfamily Y Y N DrmE family protein 29085076 131567 cellular organisms no rank 535 NCBIFAM DrmE family protein Members of this extremely diverse family include DrmE, a protein of unknown function sometimes found as part of a DISARM antiphage defense systems. NF038317.1 DISARM_DrmD 610 610 1021 equivalog Y Y N DISARM system SNF2-like helicase DrmD drmD GO:0005524,GO:0140658 29085076 131567 cellular organisms no rank 3056 NCBIFAM DISARM system SNF2-like helicase DrmD, long form DrmD, a SNF2-like helicase, is a component of class 1 DISARM (Defence Island System Associated with Restriction Modification), which contains a DNA adenine N6 methyltransferase. NF038324.1 DrmB_fam 240 240 604 subfamily Y Y N DrmB family protein drmB 29085076 131567 cellular organisms no rank 8169 NCBIFAM DrmB family protein Members of the seed alignment for this HMM are the DISARM anti-phage system protein DrmB from both class I and class II. NF038326.1 DISARM_DrmAL 999 999 1329 exception Y Y N DISARM system helicase DrmA drmA 29085076 131567 cellular organisms no rank 127 NCBIFAM DISARM system helicase DrmA, long form This HMM identifies some DrmA helicases from class II DISARM anti-phage systems, and none from class I systems. Members distinguished from the shorter, more common form (see NF038325) both by sequence divergence in regions that align and by an insert that makes members of this set longer. NF038353.1 FxLYD_dom 23 23 71 domain Y Y N FxLYD domain-containing protein 131567 cellular organisms no rank 7781 NCBIFAM FxLYD domain The uncharacterized FxLYD domain, named for the strongest (but not invariant) motif, spans about 75 amino acids usually in the C-terminal region of a protein. NF038356.1 actino_DLW39 24 24 38 hypoth_equivalog Y Y N DLW-39 family protein 131567 cellular organisms no rank 2745 NCBIFAM DLW-39 family protein DLW-39 is a small protein, restricted to the Actinobacteria. Its sequence features a highly hydrophobic stretch of about 15 amino acids, flanked by pairs of basic residues, and C-terminal region in which most members share the motif DLW. Members typically are about 39 amino acids in length when a start site supported by sequence conservation is chosen. The family is uncharacterized. NF038364.1 AglZ_HisF2_fam 310 310 248 equivalog Y Y N AglZ/HisF2 family acetamidino modification protein 22408155,25733616,31862725 131567 cellular organisms no rank 1738 NCBIFAM AglZ/HisF2 family acetamidino modification protein NF038399.1 NH_RiPP_Os17 40 40 63 domain Y Y N Os1348 family NHLP clan protein 33324389 131567 cellular organisms no rank 367 NCBIFAM Os1348 family NHLP clan protein This HMM describes a region about 63 amino acids in length, including RiPP precursors Os1348 and Franean1_4349, showing some sequence similarity to both NHLP family RiPP precursors and to the nitrile hydratase alpha subunit itself. Some members of the family are long proteins, with this domain at or near the N-terminus. NF038402.1 TroA_like 30 30 219 subfamily Y Y N helical backbone metal receptor 131567 cellular organisms no rank 48946 NCBIFAM helical backbone metal receptor NF038403.1 perm_prefix_1 30 30 59 domain Y Y N permease prefix domain 1-containing protein 131567 cellular organisms no rank 19733 NCBIFAM permease prefix domain 1 The permease prefix domain 1 is found as the N-terminal domain of putative permeases resembling ABC transporter permeases, and also of hypothetical proteins of unknown function. In at least some permease families, this prefix domain is only variably present, and may be replaced by a different, seemingly unrelated prefix domain. NF039178.4 PF18887.5 MBG_3 25 15 72 domain Y Y N MBG domain-containing protein 131567 cellular organisms no rank 1542 EBI-EMBL MBG domain MBG domain This entry corresponds to an MBG (mirror beta grasp) domain. It is found in a variety of bacterial cell surface proteins. (from Pfam) NF039179.4 PF18889.5 Beta_helix_3 27 11 20 repeat Y N N beta-helix repeat protein 131567 cellular organisms no rank 1063 EBI-EMBL Beta helix repeat Beta helix repeat This entry contains a 30 residue repeat found in a variety of bacterial cell surface proteins. This repeat is related to Pfam:PF14262, meaning that it has a beta-helix structure. The sequence repeat is quite glycine rich. (from Pfam) NF039180.4 PF18893.5 DUF5652 23.4 23.4 71 subfamily Y Y N DUF5652 family protein 131567 cellular organisms no rank 264 EBI-EMBL Family of unknown function (DUF5652) DUF5652 family protein This entry represents a protein containing two transmembrane helices. Many of these proteins are found in organisms in the Candidate Phyla Radiation. (from Pfam) NF039181.4 PF18894.5 PhageMetallopep 23.7 23.7 134 domain Y Y N putative metallopeptidase 3.4.24.- GO:0004222 131567 cellular organisms no rank 8613 EBI-EMBL Putative phage metallopeptidase putative phage metallopeptidase Members of this family occur frequently in phage genomes or bacterial prophage regions, and typically have an HELYH motif, an example of the HExxH motif expected in many metallopeptidases NF039182.4 PF18898.5 DUF5654 23.8 23.8 71 subfamily Y Y N DUF5654 family protein 131567 cellular organisms no rank 349 EBI-EMBL Family of unknown function (DUF5654) DUF5654 family protein This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 79 and 98 amino acids in length. The region contains two predicted transmembrane helices. The Eukaryotic examples are found in the Foraminiferan Reticulomyxa filosa that contains several proteins with this family.s (from Pfam) NF039183.4 PF18902.5 DUF5658 25.2 25.2 82 subfamily Y Y N DUF5658 family protein 131567 cellular organisms no rank 2801 EBI-EMBL Domain of unknown function (DUF5658) DUF5658 family protein This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 101 and 135 amino acids in length. There is a completely conserved aspartate and a conserved EXNP motif that may be functionally important. (from Pfam) NF039184.4 PF18909.5 dGTP_diPhyd_N 27 27 99 domain Y Y N dATP/dGTP diphosphohydrolase domain-containing protein 33926954 131567 cellular organisms no rank 1336 EBI-EMBL dATP/dGTP diphosphohydrolase, N-terminal DUF5664 domain This entry represent the N-terminal region of SHab15497_00040, an Acinetobacter phage protein that catalyses the hydrolysis of dGTP into dGMP, which is needed among others for the first step of biosynthesis of dZTP (2-amino-2'-deoxyadenosine-5'- triphosphate) [1]. [1]. 33926954. A widespread pathway for substitution of adenine by diaminopurine in phage genomes. Zhou Y, Xu X, Wei Y, Cheng Y, Guo Y, Khudyakov I, Liu F, He P, Song Z, Li Z, Gao Y, Ang EL, Zhao H, Zhang Y, Zhao S;. Science. 2021;372:512-516. (from Pfam) NF039185.4 PF18912.5 DZR_2 27 27 56 domain Y Y N double zinc ribbon domain-containing protein 131567 cellular organisms no rank 22338 EBI-EMBL Double zinc ribbon domain double zinc ribbon domain This domain family is found in bacteria, archaea and eukaryotes, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF00156. This entry corresponds to two zinc ribbon motifs. This domain is found at the N-terminus of the ComF operon protein 3. (from Pfam) NF039186.4 PF18916.5 Lycopene_cyc 27 10 92 domain Y Y N lycopene cyclase domain-containing protein GO:0016872 131567 cellular organisms no rank 8418 EBI-EMBL Lycopene cyclase lycopene cyclase domain NF039187.4 PF18917.5 LiaI-LiaF-like_TM1 27 27 42 domain Y Y N LiaI-LiaF-like domain-containing protein 131567 cellular organisms no rank 7651 EBI-EMBL LiaI-LiaF-like transmembrane region DUF5668 domain This entry represents a transmembrane region found in sequences related to LiaI-LiaF proteins. It is composed of two transmembrane helices that are often found in 2 or three copies in a protein. The members of this family are functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 40 amino acids in length. This entry is often associated with Pfam:PF09922 a putative adhesive domain that adopts a beta helix fold. (from Pfam) NF039189.4 PF18920.5 DUF5671 28.4 28.4 132 domain Y Y N DUF5671 domain-containing protein 131567 cellular organisms no rank 1402 EBI-EMBL Domain of unknown function (DUF5671) Domain of unknown function (DUF5671) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 168 and 339 amino acids in length. These proteins are likely to be integral membrane proteins. (from Pfam) NF039192.4 PF18929.5 DUF5678 23.2 23.2 49 domain Y Y N DUF5678 domain-containing protein 131567 cellular organisms no rank 472 EBI-EMBL Family of unknown function (DUF5678) Family of unknown function (DUF5678) This presumed domain family is found in bacteria and archaea. Proteins in this family are typically between 64 and 76 amino acids in length. (from Pfam) NF039193.4 PF18930.5 DUF5679 27 27 40 domain Y Y N DUF5679 domain-containing protein 131567 cellular organisms no rank 968 EBI-EMBL Domain of unknown function (DUF5679) Domain of unknown function (DUF5679) This family of domains is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 48 and 68 amino acids in length. These domains contain four conserved cysteines suggesting that this domain is zinc binding (from Pfam) NF039195.4 PF18933.5 PsbP_2 27 27 184 domain Y Y N PsbP-related protein 131567 cellular organisms no rank 1556 EBI-EMBL PsbP-like protein PsbP-related domain Members of this family somewhat resemble PsbP of photosystem II, but are found often in non-photosynthetic species, including archaea and Gram-positive bacteria. NF039196.4 PF18947.5 HAMP_2 24.3 24.3 67 domain Y N N HAMP domain GO:0007165,GO:0016020 131567 cellular organisms no rank 55335 EBI-EMBL HAMP domain HAMP domain NF039197.4 PF18950.5 DUF5694 27.5 27.5 185 domain Y Y N DUF5694 domain-containing protein 131567 cellular organisms no rank 5966 EBI-EMBL Family of unknown function (DUF5694) DUF5694 domain This is a family of unknown function, mostly found in bacteria. (from Pfam) NF039198.4 PF18955.5 DUF5698 27.5 27.5 58 domain Y Y N DUF5698 domain-containing protein 131567 cellular organisms no rank 5175 EBI-EMBL Domain of unknown function (DUF5698) Domain of unknown function (DUF5698) This family is functionally uncharacterised. This family family is found in bacteria and archaea, and is approximately 60 amino acids in length and contains two probable transmembrane helices. This entry is found in association with Pfam:PF10035. The C-terminal transmembrane helix contains a GXXXGXXXG motif that is characteristic of transmembrane helices that dimerise. (from Pfam) NF039204.4 PF18979.5 DUF5715 26.8 26.8 171 subfamily Y Y N DUF5715 family protein 131567 cellular organisms no rank 2645 EBI-EMBL Family of unknown function (DUF5715) DUF5715 family protein This is a family of unknown function, mainly found in bacteria. (from Pfam) NF039205.4 PF18980.5 DUF5716_C 34.7 34.7 296 subfamily_domain Y Y N DUF5716 family protein 131567 cellular organisms no rank 1247 EBI-EMBL Family of unknown function (DUF5716) C-terminal DUF5716 family protein This is a C-terminal domain found in bacterial sequences of unknown function. (from Pfam) NF039222.4 PF19045.5 Ligase_CoA_2 23.7 23.7 162 domain Y N N Ligase-CoA domain GO:0043758 26787904 131567 cellular organisms no rank 23222 EBI-EMBL Ligase-CoA domain Ligase-CoA domain This domain is related to Pfam:PF00549 and adopts a flavodoxin fold [1]. [1]. 26787904. Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer. Weisse RH, Faust A, Schmidt M, Schonheit P, Scheidig AJ;. Proc Natl Acad Sci U S A. 2016;113:E519-E528. (from Pfam) NF039234.4 PF19103.5 DUF5790 26.8 26.8 126 subfamily Y Y N DUF5790 family protein 131567 cellular organisms no rank 592 EBI-EMBL Family of unknown function (DUF5790) DUF5790 family protein This is a family of proteins of unknown function found predominantly in Halobacteria. (from Pfam) NF039236.4 PF19112.5 VanA_C 23.5 23.5 193 domain Y N N Vanillate O-demethylase oxygenase C-terminal domain GO:0016491 131567 cellular organisms no rank 40471 EBI-EMBL Vanillate O-demethylase oxygenase C-terminal domain Vanillate O-demethylase oxygenase C-terminal domain This domain is found in a wide variety of oxygenases such as Vanillate O-demethylase oxygenase and Toluene-4-sulfonate monooxygenase. (from Pfam) NF039260.4 PF19200.5 MupG_N 24 24 237 subfamily Y Y N MupG family TIM beta-alpha barrel fold protein 30524387 131567 cellular organisms no rank 15120 EBI-EMBL 6-phospho-N-acetylmuramidase, N-terminal DUF871 N-terminal domain This domain represents the N-terminal domain of 6-phospho-N-acetylmuramidase (MupG) from Staphylococcus aureus [1], also found in putative phospho sugar glycosidases from Gram-negative and -positive species, but mainly firmicutes. MupG [1], specifically cleaves MurNAc 6P-GlcNAc, a product of cell wall turnover, into the sugars MurNAc 6P and GlcNAc, involved in cell wall turnover and recycling. Since some species, for example Lactobacillus plantarum, possess several putative paralogs, the substrate specificity of the proteins containing this domain may not be limited to cell wall sugars, but may include phosphorylated disaccharides in general. Most of these proteins appear to consist of two structural subdomains, as it can be seen in the two available crystal structures of Enterococcus faecalis (PDB:2p0o) and Bacillus cereus (PDB:1X7F). This entry is the larger N-terminal domain that constitutes a TIM-barrel like structure and the C-terminal domain is similar to the cyclophilin family. It should be noted that some proteins lack the C-terminal domain. [1]. 30524387. Recovery of the Peptidoglycan Turnover Product Released by the Autolysin Atl in Staphylococcus aureus Involves the Phosphotransferase System Transporter MurP and the Novel 6-phospho-N-acetylmuramidase MupG. Kluj RM, Ebner P, Adamek M, Ziemert N, Mayer C, Borisova M;. Front Microbiol. 2018;9:2725. (from Pfam) NF039279.4 PF19266.4 CIS_tube 27 27 158 domain Y N N Contractile injection system tube protein 30905475 131567 cellular organisms no rank 9827 EBI-EMBL Contractile injection system tube protein Contractile injection system tube protein This protein is part of a contractile injection system. This family includes the Pvc7 protein from the Photorhabdus asymbiotica virulence cassette (PVC) [1]. Pvc7 is made of a tube protein (this entry) and an additional LysM domain. The equivalents of these two parts in T4 phage are gp48 and gp53, respectively [1]. [1]. 30905475. Cryo-EM Structure and Assembly of an Extracellular Contractile Injection System. Jiang F, Li N, Wang X, Cheng J, Huang Y, Yang Y, Yang J, Cai B, Wang YP, Jin Q, Gao N;. Cell. 2019;177:370-383. (from Pfam) NF039283.4 PF19291.4 TREH_N 23.1 23.1 211 domain Y Y N trehalase-like domain-containing protein 131567 cellular organisms no rank 60594 EBI-EMBL Trehalase-like, N-terminal Trehalase-like, N-terminal This presumed domain is found at the N-terminal region of bacterial and archaeal trehalases which catalyse the hydrolysis of alpha,alpha-trehalose into two molecules of D-glucose, followed by the glycoside hydrolase domain (Pfam:PF00723). This domain is also found in the uncharacterised protein C4H3.03c from S. pombe. The function of this domain is not clear. (from Pfam) NF039286.4 PF19298.4 KshA_C 23.3 23.3 207 domain Y N N 3-Ketosteroid 9alpha-hydroxylase C-terminal domain GO:0008203,GO:0016491 19234303,25049233 131567 cellular organisms no rank 15181 EBI-EMBL 3-Ketosteroid 9alpha-hydroxylase C-terminal domain 3-Ketosteroid 9alpha-hydroxylase C-terminal domain KshAB is a complex of KshA and KshB that catalyses the 3-Ketosteroid 9alpha-hydroxylase reaction. This entry represents the C-terminal domain catalytic domain of KshA [1,2]. This domain The catalytic domain shares the TBP-like fold found in other Rieske oxygenases. Paper describing PDB structure 2zyl. [1]. 19234303. Characterization of 3-ketosteroid 9{alpha}-hydroxylase, a Rieske oxygenase in the cholesterol degradation pathway of Mycobacterium tuberculosis. Capyk JK, D'Angelo I, Strynadka NC, Eltis LD;. J Biol Chem. 2009;284:9937-9946. Paper describing PDB structure 4qck. [2]. 25049233. Substrate specificities and conformational flexibility of 3-ketosteroid 9alpha-hydroxylases. Penfield JS, Worrall LJ, Strynadka NC, Eltis LD;. J Biol Chem. 2014;289:25523-25536. (from Pfam) NF039287.4 PF19303.4 Anticodon_3 23.5 23.5 152 domain Y N N Anticodon binding domain of methionyl tRNA ligase 131567 cellular organisms no rank 83399 EBI-EMBL Anticodon binding domain of methionyl tRNA ligase Anticodon binding domain of methionyl tRNA ligase This domain is found in methionyl tRNA ligase. The domain binds to the anticodon of the tRNA ligase. (from Pfam) NF039288.4 PF19304.4 PGDH_inter 27 27 119 domain Y N N D-3-phosphoglycerate dehydrogenase intervening domain 15668249,18627175,22023909 131567 cellular organisms no rank 30566 EBI-EMBL D-3-phosphoglycerate dehydrogenase intervening domain D-3-phosphoglycerate dehydrogenase intervening domain This domain is found in the D-3-phosphoglycerate dehydrogenase enzyme. In the structure of the Mycobacterium tuberculosis enzyme this domain was described as the intervening domain, also known as the allosteric substrate binding domain (ASB) [1,2,3]. The intervening domain between the substrate-binding and regulatory domains is not present in E. coli PGDH. This domain is closely related to Pfam:PF03315. It serves as an anion-binding site and may function as an allosteric site for the control of enzyme activity [3]. Paper describing PDB structure 1ygy. [1]. 15668249. Crystal structure of Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase: extreme asymmetry in a tetramer of identical subunits. Dey S, Grant GA, Sacchettini JC;. J Biol Chem. 2005;280:14892-14899. Paper describing PDB structure 3ddn. [2]. 18627175. Structural analysis of substrate and effector binding in Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase. Dey S, Burton RL, Grant GA, Sacchettini JC;. Biochemistry. 2008;47:8271-8282. [3]. 22023909. Contrasting catalytic and allosteric mechanisms for phosphoglycerate dehydrogenases. Grant GA;. Arch Biochem Biophys. 2012;519:175-185. (from Pfam) NF039293.4 PF19327.4 Ap4A_phos_N 23.1 23.1 177 domain Y N N Ap4A phosphorylase N-terminal domain 23628156 131567 cellular organisms no rank 2634 EBI-EMBL Ap4A phosphorylase N-terminal domain Ap4A phosphorylase N-terminal domain This entry represents the N-terminal HIT-like domain from the Ap4A phosphorylase enzyme [1]. Paper describing PDB structure 4i5t. [1]. 23628156. Structures of yeast Apa2 reveal catalytic insights into a canonical AP(4)A phosphorylase of the histidine triad superfamily. Hou WT, Li WZ, Chen Y, Jiang YL, Zhou CZ;. J Mol Biol. 2013;425:2687-2698. (from Pfam) NF039315.4 PF19459.4 DUF5996 25 25 296 subfamily Y Y N DUF5996 family protein 19514719 131567 cellular organisms no rank 8056 EBI-EMBL Family of unknown function (DUF5996) DUF5996 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000434) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This family includes a protein from the SW-163C biosynthetic gene cluster from Streptomyces sp. SNA15896 [1]. [1]. 19514719. Escherichia coli allows efficient modular incorporation of newly isolated quinomycin biosynthetic enzyme into echinomycin biosynthetic pathway for rational design and synthesis of potent antibiotic unnatural natural product. Watanabe K, Hotta K, Nakaya M, Praseuth AP, Wang CC, Inada D, Takahashi K, Fukushi E, Oguri H, Oikawa H;. J Am Chem Soc. 2009;131:9347-9353. (from Pfam) NF039324.4 PF19484.4 DUF6020 28.3 28.3 604 subfamily Y Y N DUF6020 family protein 131567 cellular organisms no rank 4736 EBI-EMBL Family of unknown function (DUF6020) DUF6020 family protein This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in Firmicutes and Actinobacteria. Proteins in this family are typically between 587 and 710 amino acids in length. (from Pfam) NF039329.4 PF19501.4 PcRGLX_1st 22.1 22.1 83 domain Y N N PcRGLX-like N-terminal RIFT barrel domain 29574769 131567 cellular organisms no rank 7736 EBI-EMBL PcRGLX-like N-terminal RIFT barrel domain PcRGLX-like N-terminal RIFT barrel domain This family of proteins includes Exo-rhamnogalacturonan lyase from Penicillium chrysogenum 31B (PcRGLX). The family also includes YetA from B. subtilis is functionally uncharacterised. This family of proteins is found in Actinobacteria, Firmicutes, Proteobacteria and fungi. Proteins in this family are typically between 863 and 928 amino acids in length. This entry represents the N-terminal RIFT barrel like domain. Members of this family share a 3 domain architecture [1]. [1]. 29574769. Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26. Kunishige Y, Iwai M, Nakazawa M, Ueda M, Tada T, Nishimura S, Sakamoto T;. FEBS Lett. 2018;592:1378-1388. (from Pfam) NF039330.4 PF19502.4 DUF6036 23.6 23.6 164 domain Y Y N DUF6036 family nucleotidyltransferase 131567 cellular organisms no rank 4557 EBI-EMBL Nucleotidyltransferase of unknown function (DUF6036) DUF6036 family nucleotidyltransferase domain This family of proteins is functionally uncharacterised. It belongs to the nucleotidyltransferase superfamily. This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 172 and 232 amino acids in length. (from Pfam) NF039336.4 PF19531.4 DUF6058 25 25 126 subfamily Y Y N DUF6058 family natural product biosynthesis protein 28507698 131567 cellular organisms no rank 2143 EBI-EMBL Family of unknown function (DUF6058) DUF6058 family natural product biosynthesis protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001590) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the formicamycins A-M biosynthetic gene cluster from Streptomyces sp. KY5 [1]. [1]. 28507698. Formicamycins, antibacterial polyketides produced by Streptomyces formicae isolated from African Tetraponera plant-ants. Qin Z, Munnoch JT, Devine R, Holmes NA, Seipke RF, Wilkinson KA, Wilkinson B, Hutchings MI;. Chem Sci. 2017;8:3218-3227. (from Pfam) NF039337.4 PF19538.4 DUF6062 27 27 243 subfamily Y Y N DUF6062 family protein 131567 cellular organisms no rank 1040 EBI-EMBL Family of unknown function (DUF6062) DUF6062 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 234 and 254 amino acids in length. This family contains two repeated domains that each contain a conserved CXXC and GXCXXH sequence motif. This suggests that these proteins are likely to be metal binding. (from Pfam) NF039346.4 PF19583.4 ODP 27.2 27.2 194 domain Y N N ODP family beta lactamase 31270241 131567 cellular organisms no rank 48656 EBI-EMBL ODP family beta lactamase ODP family beta lactamase The ODP (Oxygen-binding Di-iron Protein) domain is a distinct member of the metallo-beta-lactamase superfamily recruited to various bacterial and archaeal signal transduction pathways, including chemotaxis, to function as oxygen and iron sensors (1). ODP was shown to act as a sensor for chemotactic responses to both iron and oxygen in the human pathogen Treponema denticola (Td). The ODP di-iron site binds oxygen at high affinity to reversibly form an unusually stable peroxo adduct. [1]. 31270241. A di-iron protein recruited as an Fe[II] and oxygen sensor for bacterial chemotaxis functions by stabilizing an iron-peroxy species. Muok AR, Deng Y, Gumerov VM, Chong JE, DeRosa JR, Kurniyati K, Coleman RE, Lancaster KM, Li C, Zhulin IB, Crane BR;. Proc Natl Acad Sci U S A. 2019;116:14955-14960. (from Pfam) NF039348.4 PF19590.4 TrbL_3 23 23 379 domain Y N N TrbL/VirB6 plasmid conjugal transfer like protein 131567 cellular organisms no rank 574 EBI-EMBL TrbL/VirB6 plasmid conjugal transfer like protein TrbL/VirB6 plasmid conjugal transfer like protein This family of proteins are related to the Type IV secretion system protein TrbL. This family of proteins is found in archaea. Proteins in this family are typically between 353 and 403 amino acids in length. (from Pfam) NF039352.4 PF19609.4 DUF6114 27.9 27.9 106 domain Y Y N DUF6114 domain-containing protein 15376556,19362651 131567 cellular organisms no rank 13900 EBI-EMBL Family of unknown function (DUF6114) Family of unknown function (DUF6114) This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000696) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the gentamicin biosynthetic gene cluster from Micromonospora echinospora and appears to be predominantly found in actinobacteria and firmicutes [1,2]. [1]. 15376556. Gene cluster in Micromonospora echinospora ATCC15835 for the biosynthesis of the gentamicin C complex. Unwin J, Standage S, Alexander D, Hosted T Jr, Horan AC, Wellington EM;. J Antibiot (Tokyo). 2004;57:436-445. [2]. 19362651. Enzymology of aminoglycoside biosynthesis-deduction from gene clusters. Wehmeier UF, Piepersberg W;. Methods Enzymol. 2009;459:459-491. (from Pfam) NF039354.4 PF19620.4 DUF6125 27 27 164 subfamily Y Y N DUF6125 family protein 131567 cellular organisms no rank 773 EBI-EMBL Family of unknown function (DUF6125) DUF6125 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 170 and 247 amino acids in length. (from Pfam) NF039358.4 PF19638.4 DUF6141 27 27 164 subfamily Y Y N DUF6141 family protein 131567 cellular organisms no rank 649 EBI-EMBL Family of unknown function (DUF6141) DUF6141 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 159 and 175 amino acids in length. (from Pfam) NF039360.4 PF19649.4 DUF6152 27 27 98 subfamily Y Y N DUF6152 family protein 131567 cellular organisms no rank 4176 EBI-EMBL Family of unknown function (DUF6152) DUF6152 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 122 and 152 amino acids in length. There are two conserved sequence motifs: AHH and NPH. (from Pfam) NF039362.4 PF19656.4 DUF6159 27 27 204 subfamily Y Y N DUF6159 family protein 131567 cellular organisms no rank 1391 EBI-EMBL Family of unknown function (DUF6159) DUF6159 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 277 and 315 amino acids in length. (from Pfam) NF039366.4 PF19668.4 DUF6171 27 27 80 subfamily Y Y N DUF6171 family protein 131567 cellular organisms no rank 1492 EBI-EMBL Family of unknown function (DUF6171) DUF6171 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 90 amino acids in length. (from Pfam) NF039368.4 PF19673.4 DUF6176 27 27 109 subfamily Y Y N DUF6176 family protein 19927167,24191063 131567 cellular organisms no rank 2714 EBI-EMBL Family of unknown function (DUF6176) DUF6176 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000198) is described by MIBiG as an example of the following biosynthetic classes, polyketide and saccharide. It includes a member from the arenimycin A biosynthetic gene cluster from Salinispora arenicola CNB527 [1,2]. [1]. 24191063. Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules. Kersten RD, Ziemert N, Gonzalez DJ, Duggan BM, Nizet V, Dorrestein PC, Moore BS;. Proc Natl Acad Sci U S A. 2013;110:E4407-E4416. [2]. 19927167. Arenimycin, an antibiotic effective against rifampin- and methicillin-resistant Staphylococcus aureus from the marine actinomycete Salinispora arenicola. Asolkar RN, Kirkland TN, Jensen PR, Fenical W;. J Antibiot (Tokyo). 2010;63:37-39. (from Pfam) NF039385.4 PF19744.4 DUF6232 27.4 27.4 117 subfamily Y Y N DUF6232 family protein 20690632 131567 cellular organisms no rank 6080 EBI-EMBL Family of unknown function (DUF6232) DUF6232 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000223) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the rabelomycin biosynthetic gene cluster from uncultured bacterium BAC AB649/1850 [1]. This family appears to be predominantly found in bacteria. [1]. 20690632. Fluostatins produced by the heterologous expression of a TAR reassembled environmental DNA derived type II PKS gene cluster. Feng Z, Kim JH, Brady SF;. J Am Chem Soc. 2010;132:11902-11903. (from Pfam) NF039390.4 PF19778.4 RE_endonuc 23.4 23.4 108 domain Y N N Endonuclease domain GO:0015668 26067164 131567 cellular organisms no rank 15438 EBI-EMBL Endonuclease domain Endonuclease domain This represents the C-terminal endonuclease domain found in a variety of class III restriction endonuclease proteins [1]. Paper describing PDB structure 4zcf. This domain is the non-resolved endonuclease domain. [1]. 26067164. Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I. Gupta YK, Chan SH, Xu SY, Aggarwal AK;. Nat Commun. 2015;6:7363. (from Pfam) NF039396.4 PF19791.4 DUF6275 22.6 22.6 81 subfamily Y Y N DUF6275 family protein 131567 cellular organisms no rank 1460 EBI-EMBL Family of unknown function (DUF6275) DUF6275 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in Firmicute bacteria and their phage. Proteins in this family are approximately 90 amino acids in length. (from Pfam) NF039397.4 PF19792.4 DUF6276 27 27 128 subfamily Y Y N DUF6276 family protein 131567 cellular organisms no rank 594 EBI-EMBL Family of unknown function (DUF6276) DUF6276 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in archaea. Proteins in this family are approximately 130 amino acids in length. They contain an N-terminal zinc binding domain. (from Pfam) NF039401.4 PF19805.4 DUF6288 26.3 26.3 402 domain Y Y N DUF6288 domain-containing protein 131567 cellular organisms no rank 617 EBI-EMBL Family of unknown function (DUF6288) Family of unknown function (DUF6288) This family of bacterial proteins is functionally uncharacterised. Proteins in this family are approximately 800 amino acids in length and they presumably contain PDZ domains. (from Pfam) NF039402.4 PF19807.4 DUF6290 27 27 72 subfamily Y Y N DUF6290 family protein 131567 cellular organisms no rank 4737 EBI-EMBL Family of unknown function (DUF6290) DUF6290 family protein This family of proteins is functionally uncharacterised, they are predominantly found in bacteria but also in viruses. Proteins in this family are approximately 80 amino acids in length and presumably contain a ribbon-helix-helix DNA-binding motif. (from Pfam) NF039403.4 PF19808.4 DUF6291 27.2 27.2 79 domain Y Y N DUF6291 domain-containing protein 131567 cellular organisms no rank 1688 EBI-EMBL Family of unknown function (DUF6291) Family of unknown function (DUF6291) This family of proteins, found in bacteria and viruses, is functionally uncharacterised. Proteins in this family are typically between 179 and 275 amino acids in length. There are two conserved residues, a leucine and a tyrosine. (from Pfam) NF039405.4 PF19827.4 DUF6308 27.3 27.3 193 subfamily Y Y N DUF6308 family protein 19362651 131567 cellular organisms no rank 3355 EBI-EMBL Family of unknown function (DUF6308) DUF6308 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000699) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the hygromycin A biosynthetic gene cluster from Streptomyces hygroscopicus subsp. hygroscopicus [1]. This family appears to be predominantly found in Actinobacteria. [1]. 19362651. Enzymology of aminoglycoside biosynthesis-deduction from gene clusters. Wehmeier UF, Piepersberg W;. Methods Enzymol. 2009;459:459-491. (from Pfam) NF039407.4 PF19845.4 DUF6320 29.9 29.9 186 domain Y Y N DUF6320 domain-containing protein 131567 cellular organisms no rank 2710 EBI-EMBL Family of unknown function (DUF6320) DUF6320 domain This family of proteins is functionally uncharacterised. This family of proteins is mainly found in Firmicute bacteria. Proteins in this family are typically between 220 and 604 amino acids in length. (from Pfam) NF039408.4 PF19851.4 DUF6326 24 24 135 subfamily Y Y N DUF6326 family protein 131567 cellular organisms no rank 2686 EBI-EMBL Family of unknown function (DUF6326) DUF6326 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 137 and 159 amino acids in length. (from Pfam) NF039409.4 PF19853.4 DUF6328 26.3 26.3 142 subfamily Y Y N DUF6328 family protein 18310024 131567 cellular organisms no rank 14109 EBI-EMBL Family of unknown function (DUF6328) DUF6328 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000219) is described by MIBiG as an example of the following biosynthetic classes, polyketide and saccharide, in particular the elloramycin biosynthetic gene cluster from Streptomyces olivaceus [1]. This family appears to be predominantly found in Actinobacteria. [1]. 18310024. Biosynthesis of elloramycin in Streptomyces olivaceus requires glycosylation by enzymes encoded outside the aglycon cluster. Ramos A, Lombo F, Brana AF, Rohr J, Mendez C, Salas JA;. Microbiology (Reading). 2008;154:781-788. (from Pfam) NF039412.4 PF19866.4 DUF6339 23.2 23.2 175 subfamily Y Y N DUF6339 family protein 131567 cellular organisms no rank 4065 EBI-EMBL Family of unknown function (DUF6339) DUF6339 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 247 and 267 amino acids in length. (from Pfam) NF039417.4 PF19891.4 DUF6364 27.3 27.3 70 subfamily Y Y N DUF6364 family protein 131567 cellular organisms no rank 3660 EBI-EMBL Family of unknown function (DUF6364) DUF6364 family protein This family of uncharacterised proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length and they seem to belong to the toxin-antitoxin system. They are likely to contain a ribbon-helix-helix DNA-binding motif. (from Pfam) NF039436.4 PF19975.4 DO-GTPase1 27 27 271 domain Y N N Double-GTPase 1 32101166 131567 cellular organisms no rank 1950 EBI-EMBL Double-GTPase 1 Double-GTPase 1 GTPase of a GTPase-centric, NTP-dependent ternary systems. The domain belongs to a previously unrecognised family of the TRAFAC clade with a conserved glutamate in its Walker B motif. [1]. 32101166. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. Kaur G, Burroughs AM, Iyer LM, Aravind L;. Elife. 2020; [Epub ahead of print] (from Pfam) NF039447.4 PF20016.4 ThsA_Macro 25 25 183 domain Y Y N macro domain-containing protein 29371424,32499527,34853457 131567 cellular organisms no rank 3350 EBI-EMBL Thoeris protein ThsA, Macro domain DUF6430 domain Thoeris is a bacterial antiphage defense system, which consists of two genes, thsA and thsB, via NAD+ degradation [1-4]. ThsA has robust NAD+ cleavage activity and and a two-domain architecture containing a N-terminal NAD-binding domain (denoted as sirtuin-like or Macro) and C-terminal SLOG-like domain. In some instances, such as in B. amyloliquefaciens ThsA has an N-terminal transmembrane domain [1]. ThsB (also referred to as TIR1 and TIR2) is structurally similar to TIR domain proteins but without enzymatic activity. This domain is found at the C-terminal of ThsA proteins which adopts a Rossmann-like fold that binds NAD+/NAD+derivatives. It has been characterised as the SLOG-like domain which binds NAD+ derivatives such as ADPR molecules produced by ThsB, which drives an oligomeric state change in ThsA and activates the NADase activity (represented in Pfam:PF18185) [1,3]. This entry represents the NAD+-binding Macro domain from B. amyloliquefaciens [1,2]. [1]. 29371424. Systematic discovery of antiphage defense systems in the microbial pangenome. Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R;. Science. 2018; [Epub ahead of print]. [2]. 32499527. Structural and functional evidence of bacterial antiphage protection by Thoeris defense system via NAD(+) degradation. Ka D, Oh H, Park E, Kim JH, Bae E;. Nat Commun. 2020;11:2816. [3]. 34853457. Antiviral activity of bacterial TIR domains via immune signalling molecules. Ofir G, Herbst E, Baroz M, Cohen D, Millman A, Doron S, Tal N, Malheiro DBA, Malitsky S, Amitai G, Sorek R;. Nature. 2021;600:116-120. (from Pfam) NF039453.4 PF20040.4 DUF6442 25 25 102 subfamily Y Y N DUF6442 family protein 131567 cellular organisms no rank 1669 EBI-EMBL Family of unknown function (DUF6442) DUF6442 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. (from Pfam) NF039455.4 PF20043.4 DUF6445 24 24 224 subfamily Y Y N DUF6445 family protein 131567 cellular organisms no rank 5624 EBI-EMBL Family of unknown function (DUF6445) DUF6445 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 229 and 242 amino acids in length. (from Pfam) NF039463.4 PF20064.4 DUF6463 26 26 119 subfamily Y Y N DUF6463 family protein 131567 cellular organisms no rank 2699 EBI-EMBL Family of unknown function (DUF6463) DUF6463 family protein This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. This family appears to be related to Pfam:PF03729. (from Pfam) NF039471.4 PF20102.4 DUF6492 22.9 22.9 291 subfamily Y Y N DUF6492 family protein 131567 cellular organisms no rank 3972 EBI-EMBL Family of unknown function (DUF6492) DUF6492 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 305 and 329 amino acids in length. (from Pfam) NF039475.4 PF20118.4 DUF6508 23.6 23.6 129 domain Y Y N DUF6508 domain-containing protein 131567 cellular organisms no rank 3063 EBI-EMBL Family of unknown function (DUF6508) Family of unknown function (DUF6508) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 131 and 449 amino acids in length. (from Pfam) NF039476.4 PF20122.4 DUF6512 26 26 181 subfamily Y Y N DUF6512 family protein 131567 cellular organisms no rank 1372 EBI-EMBL Family of unknown function (DUF6512) DUF6512 family protein This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically between 35 and 59 amino acids in length. (from Pfam) NF039478.4 PF20129.4 DUF6519 22.4 22.4 593 domain Y Y N DUF6519 domain-containing protein 131567 cellular organisms no rank 3339 EBI-EMBL Family of unknown function (DUF6519) DUF6519 domain This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 523 and 1105 amino acids in length. (from Pfam) NF039482.4 PF20143.4 NAD_kinase_C 23.7 23.7 126 domain Y N N ATP-NAD kinase C-terminal domain 131567 cellular organisms no rank 68248 EBI-EMBL ATP-NAD kinase C-terminal domain ATP-NAD kinase C-terminal domain Members of this family include ATP-NAD kinases EC:2.7.1.23, which catalyses the phosphorylation of NAD to NADP utilising ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus. Also includes NADH kinases EC:2.7.1.86. This entry represents the C-terminal beta sandwich domain. (from Pfam) NF039486.4 PF20161.4 VpsR 23.7 23.7 121 domain Y Y N VpsR-related response regulator 11160103 131567 cellular organisms no rank 9206 EBI-EMBL VpsR domain VpsR-related response regulator domain VpsR appears superficially to be a response regulator, based on extension of its alignment to response regulators AlgB and NrtC all the way to the N-terminus. Instead of being a response regulator with a histidine kinase partner, the sigma-54-dependent transcription factor VpsR directly binds to cyclic-di-GMP. Its regulon includes genes for the biosynthesis of the biofilm matrix component called Vibrio polysaccharide (VPS). [1]. 11160103. VpsR, a Member of the Response Regulators of the Two-Component Regulatory Systems, Is Required for Expression of vps Biosynthesis Genes and EPS(ETr)-Associated Phenotypes in Vibrio cholerae O1 El Tor. Yildiz FH, Dolganov NA, Schoolnik GK;. J Bacteriol. 2001;183:1716-1726. (from Pfam) NF039493.4 PF18895.5 T4SS_pilin 26.6 26.6 71 domain Y N N Type IV secretion system pilin 131567 cellular organisms no rank 3872 EBI-EMBL Type IV secretion system pilin Type IV secretion system pilin This entry represents likely Type IV secretion system pilins. (from Pfam) NF039494.4 PF18896.5 SLT_3 27 27 89 domain Y N N Lysozyme like domain 131567 cellular organisms no rank 3392 EBI-EMBL Lysozyme like domain Lysozyme like domain This entry represents a lysozyme like domain found in candidate phyla radiation bacteria. The domain contains several conserved cysteine and histidine residues suggesting that it may bind to zinc. (from Pfam) NF039495.4 PF18897.5 Gp3-like 23.6 23.6 191 domain Y N N Recombination directionality factor-like 21564337 131567 cellular organisms no rank 7228 EBI-EMBL Recombination directionality factor-like Recombination directionality factor-like This entry includes Gp3 from Streptomyces phage phiC31. Gp3 is a recombination directionality factor that interacts directly with the integrase tetramer to activate excision and inhibit integration [1]. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. [1]. 21564337. A phage protein that binds phiC31 integrase to switch its directionality. Khaleel T, Younger E, McEwan AR, Varghese AS, Smith MC;. Mol Microbiol. 2011;80:1450-1463. (from Pfam) NF039496.4 PF18899.5 DUF5655 24 24 109 domain Y Y N DUF5655 domain-containing protein 131567 cellular organisms no rank 17146 EBI-EMBL Domain of unknown function (DUF5655) Domain of unknown function (DUF5655) This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 122 and 304 amino acids in length. (from Pfam) NF039497.4 PF18923.5 DUF5673 26.7 26.7 66 domain Y Y N DUF5673 domain-containing protein 131567 cellular organisms no rank 390 EBI-EMBL Domain of unknown function (DUF5673) Domain of unknown function (DUF5673) This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 90 amino acids in length. The domain is usually found C-terminal to a pair of transmembrane helices. (from Pfam) NF039498.4 PF18926.5 DUF5676 27.6 27.6 82 subfamily Y Y N DUF5676 family membrane protein 131567 cellular organisms no rank 1113 EBI-EMBL 2TM family of unknown function (DUF5676) DUF5676 family 2TM protein This family of presumed integral membrane proteins is found in bacteria and archaea. Proteins in this family are approximately 90 amino acids in length and contain two predicted transmembrane helices. (from Pfam) NF039499.4 PF18928.5 DUF5677 27.1 27.1 166 domain Y Y N DUF5677 domain-containing protein 131567 cellular organisms no rank 7846 EBI-EMBL Family of unknown function (DUF5677) Family of unknown function (DUF5677) This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 250 and 347 amino acids in length. These proteins contain a conserved RXXXE motif an invariant Histidine that may be functionally important. (from Pfam) NF039500.4 PF18931.5 DUF5680 25 25 104 domain Y Y N DUF5680 domain-containing protein 131567 cellular organisms no rank 1756 EBI-EMBL Domain of unknown function (DUF5680) Domain of unknown function (DUF5680) This family of presumed domains is found in bacteria and archaea. Proteins in this family are typically between 152 and 220 amino acids in length. In some of the proteins this domain is associated with an N-terminal HTH domain, suggesting that they are transcriptional regulators. This suggests that this may be a previously unidentified ligand binding domain. (from Pfam) NF039504.4 PF18952.5 DUF5696 25.6 25.6 612 domain Y Y N DUF5696 domain-containing protein 131567 cellular organisms no rank 3918 EBI-EMBL Family of unknown function (DUF5696) DUF5696 domain This is a family of unknown function with some overlap with clan family members of CL0058. (from Pfam) NF039515.4 PF18991.5 DUF5724 25 25 342 domain Y Y N DUF5724 domain-containing protein 131567 cellular organisms no rank 3397 EBI-EMBL Family of unknown function (DUF5724) Family of unknown function (DUF5724) This is a family of unknown function mainly found in bacteria. (from Pfam) NF039543.4 PF19123.5 DUF5807 26.5 26.5 106 subfamily Y Y N DUF5807 family protein 131567 cellular organisms no rank 588 EBI-EMBL Family of unknown function (DUF5807) DUF5807 family protein This is a family of proteins of unknown function found in Halobacteria. (from Pfam) NF039544.4 PF19124.5 DUF5808 26.3 26.3 26 domain Y Y N DUF5808 domain-containing protein 131567 cellular organisms no rank 6897 EBI-EMBL Family of unknown function (DUF5808) Family of unknown function (DUF5808) This is a family of proteins of unknown function predominantly found in Firmicutes but also in Actinobacteria and Halobacteria. Members of this family are thought to be DUF1648 domain-containing proteins as they are membrane-components. (from Pfam) NF039545.4 PF19130.5 DUF5813 25 25 144 subfamily Y Y N DUF5813 family protein 131567 cellular organisms no rank 601 EBI-EMBL Family of unknown function (DUF5813) DUF5813 family protein This is a family of unknown function found predominantly in Halobacteria. (from Pfam) NF039546.4 PF19138.5 DUF5821 27.1 27.1 217 subfamily Y Y N DUF5821 family protein 131567 cellular organisms no rank 1117 EBI-EMBL Family of unknown function (DUF5821) DUF5821 family protein This is a family of proteins of unknown function predominantly found in Halobacteria. (from Pfam) NF039579.4 PF19275.4 HflX_C 26.4 26.4 102 domain Y N N HflX C-terminal domain 26458047 131567 cellular organisms no rank 15963 EBI-EMBL HflX C-terminal domain HflX C-terminal domain This entry represents the C-terminal domain of the HflX protein [1]. HflX binds to the intersubunit face of the 50S subunit. Its C-terminal domain (CTD) predominantly interacts with the NTD of uL11 at the bL12 stalk base. Truncation of the CTD rendered HflX inactive in 70S splitting [1]. Paper describing PDB structure 5ady. [1]. 26458047. HflX is a ribosome-splitting factor rescuing stalled ribosomes under stress conditions. Zhang Y, Mandava CS, Cao W, Li X, Zhang D, Li N, Zhang Y, Zhang X, Qin Y, Mi K, Lei J, Sanyal S, Gao N;. Nat Struct Mol Biol. 2015;22:906-913. (from Pfam) NF039581.4 PF19278.4 Hydant_A_C 21 21 193 domain Y N N Hydantoinase/oxoprolinase C-terminal domain 28054554,28775283 131567 cellular organisms no rank 44272 EBI-EMBL Hydantoinase/oxoprolinase C-terminal domain Hydantoinase/oxoprolinase C-terminal domain This domain is found at the C-terminus of acetophenone carboxylase alpha subunit [1]. According to ECOD this domain adopts a reverse ferredoxin fold. This domain is found at the C-terminus of a wide range of related enzymes subunits. Paper describing PDB structure 5l9w. [1]. 28054554. Structure of the acetophenone carboxylase core complex: prototype of a new class of ATP-dependent carboxylases/hydrolases. Weidenweber S, Schuhle K, Demmer U, Warkentin E, Ermler U, Heider J;. Sci Rep. 2017;7:39674. Paper describing PDB structure 5m45. [2]. 28775283. Structural Basis for the Mechanism of ATP-Dependent Acetone Carboxylation. Mus F, Eilers BJ, Alleman AB, Kabasakal BV, Wells JN, Murray JW, Nocek BP, DuBois JL, Peters JW;. Sci Rep. 2017;7:7234. (from Pfam) NF039584.4 PF19288.4 CofH_C 27 27 125 domain Y N N CofH/MqnC C-terminal region 131567 cellular organisms no rank 39612 EBI-EMBL CofH/MqnC C-terminal region CofH/MqnC C-terminal region This entry represents the C-terminal half of the CofH and MqnC enzymes. This entry is found to the C-terminus of Pfam:PF04055. (from Pfam) NF039585.4 PF19302.4 DUF5915 27 27 195 domain Y Y N DUF5915 domain-containing protein 131567 cellular organisms no rank 41075 EBI-EMBL Domain of unknown function (DUF5915) Domain of unknown function (DUF5915) This presumed domain is found at the C-terminus of isoleucyl tRNA ligase enzymes. (from Pfam) NF039588.4 PF19315.4 MC_hydratase 26.5 26.5 353 domain Y N N Mesaconyl-CoA hydratase GO:0016829 28932214 131567 cellular organisms no rank 24682 EBI-EMBL Mesaconyl-CoA hydratase Mesaconyl-CoA hydratase UniProt:G0HQ35 (HAH_1340) has been characterized as a mesaconyl-CoA hydratase [1]. This enzyme belongs to the HotDog superfamily and contains two HotDog domains. This enzyme is most closely related to Pfam:PF01575. [1]. 28932214. Succinyl-CoA:Mesaconate CoA-Transferase and Mesaconyl-CoA Hydratase, Enzymes of the Methylaspartate Cycle in Haloarcula hispanica. Borjian F, Johnsen U, Schonheit P, Berg IA;. Front Microbiol. 2017;8:1683. (from Pfam) NF039608.4 PF19403.4 SpaA_2 25 15 96 domain Y N N Prealbumin-like fold domain 131567 cellular organisms no rank 5142 EBI-EMBL Prealbumin-like fold domain Prealbumin-like fold domain Domain related to SpaA found as tandem repeats in bacterial surface proteins, associated with VWA and PA14 adhesins (from Pfam) NF039614.4 PF19420.4 DDAH_eukar 23 23 291 domain Y Y N arginine deiminase-related protein 11504612,14675764 131567 cellular organisms no rank 36693 EBI-EMBL N,N dimethylarginine dimethylhydrolase, eukaryotic arginine deiminase-related protein This family contains N(G),N(G)-dimethylarginine dimethylaminohydrolases (DDAH) from eukaryotes. It also includes arginine deiminases and DDAH from prokaryotes. These enzymes are involved in arginine metabolism and belong to the amidinotransferase (AT) superfamily as they share the alpha/beta propeller fold, which includes structurally important residues (buried hydrophobic residues, buried hydrophilic residues hydrogen-bonded with mainchain groups and the hallmark of three consecutive buried Gly residues near the C-terminus, conserved among its members [1,2]. [1]. 11504612. A novel superfamily of enzymes that catalyze the modification of guanidino groups. Shirai H, Blundell TL, Mizuguchi K;. Trends Biochem Sci 2001;26:465-468. [2]. 14675764. Prediction of the structure and function of AstA and AstB, the first two enzymes of the arginine succinyltransferase pathway of arginine catabolism. Shirai H, Mizuguchi K;. FEBS Lett 2003;555:505-510. (from Pfam) NF039623.4 PF19458.4 DUF5995 27 27 225 subfamily Y Y N DUF5995 family protein 15942003 131567 cellular organisms no rank 10448 EBI-EMBL Family of unknown function (DUF5995) DUF5995 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000354) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This includes a protein from the friulimicin A biosynthetic gene cluster from Actinoplanes friuliensis [1]. [1]. 15942003. An acyl-CoA dehydrogenase is involved in the formation of the Delta cis3 double bond in the acyl residue of the lipopeptide antibiotic friulimicin in Actinoplanes friuliensis. Heinzelmann E, Berger S, Muller C, Hartner T, Poralla K, Wohlleben W, Schwartz D;. Microbiology. 2005;151:1963-1974. (from Pfam) NF039626.4 PF19472.4 DUF6009 28.6 28.6 127 subfamily Y Y N DUF6009 family protein 10639366,12183628 131567 cellular organisms no rank 2957 EBI-EMBL Family of unknown function (DUF6009) DUF6009 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000965) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the C-1027 biosynthetic gene cluster from Streptomyces globisporus [1,2]. [1]. 10639366. Genes for production of the enediyne antitumor antibiotic C-1027 in Streptomyces globisporus are clustered with the cagA gene that encodes the C-1027 apoprotein. Liu W, Shen B;. Antimicrob Agents Chemother. 2000;44:382-392. [2]. 12183628. Biosynthesis of the enediyne antitumor antibiotic C-1027. Liu W, Christenson SD, Standage S, Shen B;. Science. 2002;297:1170-1173. (from Pfam) NF039634.4 PF19512.4 DUF6046 27.4 27.4 122 domain Y Y N DUF6046 domain-containing protein 131567 cellular organisms no rank 1356 EBI-EMBL Domain of unknown function (DUF6046) Domain of unknown function (DUF6046) This family of presumed domains is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 196 and 222 amino acids in length. (from Pfam) NF039639.4 PF19528.4 DUF6056 27 27 442 subfamily Y Y N DUF6056 family protein 131567 cellular organisms no rank 10415 EBI-EMBL Family of unknown function (DUF6056) DUF6056 family protein This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 448 and 528 amino acids in length. There is a conserved NYL sequence motif. (from Pfam) NF039641.4 PF19540.4 DUF6064 27 27 210 subfamily Y Y N DUF6064 family protein 131567 cellular organisms no rank 2001 EBI-EMBL Family of unknown function (DUF6064) DUF6064 family protein This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in Proteobacteria and Bacteroidetes. Proteins in this family are typically between 215 and 242 amino acids in length. (from Pfam) NF039643.4 PF19543.4 GH123_N 22 22 969 subfamily Y Y N glycoside hydrolase domain-containing protein 27038508,27546776 131567 cellular organisms no rank 4052 EBI-EMBL Glycoside hydrolase 123, N-terminal domain DUF6067 family protein This domain is found at the N-terminal end of protein members of the glycoside hydrolase family 123, including N-acetylgalactosaminidase from Clostridium perfringens. This enzyme removes specific terminal N-D-acetylgalactosamine from glycosphingolipids. This domain folds into a twisted beta-sandwich that consists of two 5-stranded beta-sheets, two small beta-strands and four small alpha-helices [1]. [1]. 27038508. The Details of Glycolipid Glycan Hydrolysis by the Structural Analysis of a Family 123 Glycoside Hydrolase from Clostridium perfringens. Noach I, Pluvinage B, Laurie C, Abe KT, Alteen MG, Vocadlo DJ, Boraston AB;. J Mol Biol. 2016;428:3253-3265. [2]. 27546776. Structural and mechanistic insights into a Bacteroides vulgatus retaining N-acetyl-beta-galactosaminidase that uses neighbouring group participation. Roth C, Petricevic M, John A, Goddard-Borger ED, Davies GJ, Williams SJ;. Chem Commun (Camb). 2016;52:11096-11099. (from Pfam) NF039648.4 PF19575.4 HTH_58 23.8 23.8 62 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 5657 EBI-EMBL Helix-turn-helix domain helix-turn-helix domain Most members of this family are putative transcriptional regulators found in the Actinobacteria. A longer member of the family, Cbp1 (SSO0454) from Saccharolobus solfataricus, is a CRISPR DNA repeat-binding protein. NF039657.4 PF19597.4 TrbL_4 27 27 276 subfamily Y Y N conjugal transfer protein TrbL family protein 131567 cellular organisms no rank 2592 EBI-EMBL Conjugal transfer protein TrbL DUF6102 family protein This family includes conjugal transfer proteins predominantly found in Firmicutes. Proteins in this family are typically between 198 and 292 amino acids in length. (from Pfam) NF039662.4 PF19614.4 DUF6119 27 27 524 subfamily Y Y N DUF6119 family protein 131567 cellular organisms no rank 6603 EBI-EMBL Family of unknown function (DUF6119) DUF6119 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 523 and 552 amino acids in length. (from Pfam) NF039671.4 PF19652.4 DUF6155 27 27 170 subfamily Y Y N DUF6155 family protein 131567 cellular organisms no rank 1877 EBI-EMBL Family of unknown function (DUF6155) DUF6155 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 169 and 185 amino acids in length. (from Pfam) NF039682.4 PF19694.4 DUF6194 27.1 27.1 146 subfamily Y Y N DUF6194 family protein 26818633 131567 cellular organisms no rank 4403 EBI-EMBL Family of unknown function (DUF6194) DUF6194 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001597) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the fluvirucin B2 biosynthetic gene cluster from Actinomadura fulva subsp. indica [1]. This family appears to be predominantly found in bacteria. [1]. 26818633. Identification of the Fluvirucin B2 (Sch 38518) Biosynthetic Gene Cluster from Actinomadura fulva subsp. indica ATCC 53714: substrate Specificity of the beta-Amino Acid Selective Adenylating Enzyme FlvN. Miyanaga A, Hayakawa Y, Numakura M, Hashimoto J, Teruya K, Hirano T, Shin-Ya K, Kudo F, Eguchi T;. Biosci Biotechnol Biochem. 2016;80:935-941. (from Pfam) NF039685.4 PF19709.4 DUF6206 30.4 30.4 271 subfamily Y Y N DUF6206 family protein 12000953,8843436 131567 cellular organisms no rank 441 EBI-EMBL Family of unknown function (DUF6206) DUF6206 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001063) is described by MIBiG as an example of the following biosynthetic classes, polyketide and NRP (non-ribosomal peptide). It includes a member from the undecylprodigiosin biosynthetic gene cluster from Streptomyces coelicolor A3(2) [1,2]. This family appears to be predominantly present in bacteria. [1]. 8843436. A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome. Redenbach M, Kieser HM, Denapaite D, Eichner A, Cullum J, Kinashi H, Hopwood DA;. Mol Microbiol. 1996;21:77-96. [2]. 12000953. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA;. Nature. 2002;417:141-147. (from Pfam) NF039694.4 PF19741.4 DUF6230 27.5 27.5 145 subfamily Y Y N DUF6230 family protein 29974638 131567 cellular organisms no rank 11635 EBI-EMBL Family of unknown function (DUF6230) DUF6230 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001774) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the MS-271 biosynthetic gene cluster from Streptomyces sp [1]. This family appears to be predominantly found in Actinobacteria. Some members of this family have been identified as putative cholesterol esterases. [1]. 29974638. Biosynthetic Gene Cluster of a d-Tryptophan-Containing Lasso Peptide, MS-271. Feng Z, Ogasawara Y, Nomura S, Dairi T;. Chembiochem. 2018;19:2045-2048. (from Pfam) NF039696.4 PF19749.4 DUF6236 26.2 26.2 324 subfamily Y Y N DUF6236 family protein 28128551 131567 cellular organisms no rank 2339 EBI-EMBL Family of unknown function (DUF6236) DUF6236 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001432) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the myxochromide D biosynthetic gene cluster from Stigmatella erecta [1]. [1]. 28128551. Genomics-Guided Exploitation of Lipopeptide Diversity in Myxobacteria. Burgard C, Zaburannyi N, Nadmid S, Maier J, Jenke-Kodama H, Luxenburger E, Bernauer HS, Wenzel SC;. ACS Chem Biol. 2017;12:779-786. (from Pfam) NF039701.4 PF19762.4 DUF6249 33 33 104 domain Y Y N DUF6249 domain-containing protein 131567 cellular organisms no rank 4541 EBI-EMBL Domain of unknown function (DUF6249) Domain of unknown function (DUF6249) This domain family is found in bacterial proteins, functionally uncharacterised. Proteins in this family are typically between 174 and 239 amino acids in length. This domain is thought to contain transmembrane regions. This family is distantly related to Pfam:PF11239. (from Pfam) NF039702.4 PF19763.5 DUF6250 26.9 26.9 165 domain Y Y N DUF6250 domain-containing protein 131567 cellular organisms no rank 3178 EBI-EMBL Domain of unknown function (DUF6250) Domain of unknown function (DUF6250) This domain is found in bacterial proteins which are functionally uncharacterised. Proteins in this family are typically between 225 and 1025 amino acids in length. There is a conserved Tryptophan residue at the N-terminal and a highly conserved SDLN sequence. (from Pfam) NF039707.4 PF19773.4 DUF6259 28.7 28.7 300 domain Y Y N DUF6259 domain-containing protein 131567 cellular organisms no rank 1296 EBI-EMBL Domain of unknown function (DUF6259) Domain of unknown function (DUF6259) This domain is found in bacterial proteins and it is functionally uncharacterised. However, some proteins are putative glycoside hydrolases and this domain has some overlaps with clan family members of CL0058. Proteins containing this domain are typically between 678 and 749 amino acids in length. (from Pfam) NF039709.4 PF19777.4 DUF6263 26.7 26.7 196 subfamily Y Y N DUF6263 family protein 131567 cellular organisms no rank 2463 EBI-EMBL Family of unknown function (DUF6263) DUF6263 family protein This family of proteins found in bacteria is functionally uncharacterised. Proteins in this family are typically between 298 and 349 amino acids in length. There is a conserved sequence pattern PxxxI/VxxGxxW. (from Pfam) NF039710.4 PF19786.4 DUF6270 27.5 27.5 222 domain Y Y N DUF6270 domain-containing protein 131567 cellular organisms no rank 3754 EBI-EMBL Family of unknown function (DUF6270) Family of unknown function (DUF6270) This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 258 and 528 amino acids in length. There is a conserved GSC sequence motif. (from Pfam) NF039711.4 PF19788.4 DUF6272 26.6 26.6 134 subfamily Y Y N DUF6272 family protein 131567 cellular organisms no rank 3183 EBI-EMBL Family of unknown function (DUF6272) DUF6272 family protein This family of proteins found in bacteria is functionally uncharacterised. Proteins in this family are approximately 180 amino acids in length. There are two conserved sequence motifs, ExxQN and GAGLG. (from Pfam) NF039722.4 PF19830.4 DUF6311 27 27 303 domain Y Y N DUF6311 domain-containing protein 131567 cellular organisms no rank 2305 EBI-EMBL Family of unknown function (DUF6311) Family of unknown function (DUF6311) This presumed integral membrane domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 300 amino acids in length. (from Pfam) NF039728.4 PF19850.4 DUF6325 23.4 23.4 141 subfamily Y Y N DUF6325 family protein 131567 cellular organisms no rank 5809 EBI-EMBL Family of unknown function (DUF6325) DUF6325 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 142 and 156 amino acids in length. (from Pfam) NF039733.4 PF19865.4 DUF6338 26.5 26.5 205 subfamily Y Y N DUF6338 family protein 28894917 131567 cellular organisms no rank 3573 EBI-EMBL Family of unknown function (DUF6338) DUF6338 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001593) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the ficellomycin biosynthetic gene cluster from Streptomyces ficellus [1]. [1]. 28894917. Identification and characterization of the ficellomycin biosynthesis gene cluster from Streptomyces ficellus. Liu Y, Li M, Mu H, Song S, Zhang Y, Chen K, He X, Wang H, Dai Y, Lu F, Yan Z, Zhang H;. Appl Microbiol Biotechnol. 2017;101:7589-7602. (from Pfam) NF039734.4 PF19872.4 DUF6345 26.9 26.9 221 domain Y Y N DUF6345 domain-containing protein 16766657 131567 cellular organisms no rank 951 EBI-EMBL Family of unknown function (DUF6345) DUF6345 domain This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [1]. This family appears to be predominantly found in bacteria and archaea. [1]. 16766657. Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Yanai K, Murakami T, Bibb M;. Proc Natl Acad Sci U S A. 2006;103:9661-9666. (from Pfam) NF039735.4 PF19875.4 DUF6348 27.7 27.7 195 subfamily Y Y N DUF6348 family protein 131567 cellular organisms no rank 2783 EBI-EMBL Family of unknown function (DUF6348) DUF6348 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0002011) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the ansacarbamitocin A biosynthetic gene cluster from Amycolatopsis alba DSM 44262. This family appears to be predominantly found in bacteria. (from Pfam) NF039739.4 PF19888.4 DUF6361 25 25 388 subfamily Y Y N DUF6361 family protein 131567 cellular organisms no rank 1827 EBI-EMBL Family of unknown function (DUF6361) DUF6361 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 388 and 411 amino acids in length. (from Pfam) NF039776.4 PF20009.4 GEVED 24.4 24.4 78 domain Y Y N GEVED domain-containing protein 27920201 131567 cellular organisms no rank 24314 EBI-EMBL GEVED domain GEVED domain Ths presumed domain is found in the CshA protein from Streptococcus gordonii. The domain is named after the sequence found in CshA in the conserved C-terminal region. The conserved negatively charged residues suggests that this domain may bind to calcium ions. This domain is part of the non-repetitive region NR3 [1]. [1]. 27920201. The Streptococcus gordonii Adhesin CshA Protein Binds Host Fibronectin via a Catch-Clamp Mechanism. Back CR, Sztukowska MN, Till M, Lamont RJ, Jenkinson HF, Nobbs AH, Race PR;. J Biol Chem. 2017;292:1538-1549. (from Pfam) NF039782.4 PF20026.4 DUF6434 26.8 26.8 64 domain Y Y N DUF6434 domain-containing protein 131567 cellular organisms no rank 4196 EBI-EMBL Domain of unknown function (DUF6434) Domain of unknown function (DUF6434) This domain of unknown function is found in uncharacterised proteins mainly from bacteria, but it is also found in eukaryotes. Some proteins containing this domain also contain zinc finger C2H2-type domains. There are three conserved motifs: TxI/V, RxFF and FxF, and a conserved W/Y residue at the C-terminal. (from Pfam) NF039785.4 PF20037.4 DUF6440 26.5 26.5 53 subfamily Y Y N DUF6440 family protein 131567 cellular organisms no rank 2381 EBI-EMBL Family of unknown function (DUF6440) DUF6440 family protein This family of proteins is functionally uncharacterised. This family of proteins is mainly found in Firmicutes but also in viruses. Proteins in this family are approximately 60 amino acids in length and they contain three conserved motifs: RF, TGxxY and TPLLD. Some members of this family are probably Xylan 1,4-beta-xylosidases. (from Pfam) NF039786.4 PF20046.4 DUF6448 27 27 147 subfamily Y Y N DUF6448 family protein 131567 cellular organisms no rank 845 EBI-EMBL Family of unknown function (DUF6448) DUF6448 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 187 and 219 amino acids in length and may contain a LysM domain. (from Pfam) NF039793.4 PF20085.4 TGL 23.7 23.7 245 domain Y N N Protein-glutamine gamma-glutamyltransferase GO:0003810 26322858 131567 cellular organisms no rank 3550 EBI-EMBL Protein-glutamine gamma-glutamyltransferase Protein-glutamine gamma-glutamyltransferase NF039796.4 PF20095.4 DUF6485 24 24 70 subfamily Y Y N DUF6485 family protein 131567 cellular organisms no rank 636 EBI-EMBL Domain of unknown function (DUF6485) DUF6485 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. (from Pfam) NF039801.4 PF20116.4 DUF6506 27 27 96 subfamily Y Y N DUF6506 family protein 131567 cellular organisms no rank 2091 EBI-EMBL Family of unknown function (DUF6506) DUF6506 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 100 amino acids in length. (from Pfam) NF039803.4 PF20126.4 DUF6516 23.4 23.4 81 subfamily Y Y N DUF6516 family protein 131567 cellular organisms no rank 4468 EBI-EMBL Family of unknown function (DUF6516) DUF6516 family protein This presumed domain is functionally uncharacterised. This domain family is found in archaea, and is approximately 60 amino acids in length. (from Pfam) NF039804.4 PF20130.4 DUF6520 25.4 25.4 83 subfamily Y Y N DUF6520 family protein 131567 cellular organisms no rank 1652 EBI-EMBL Family of unknown function (DUF6520) DUF6520 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 89 and 103 amino acids in length. (from Pfam) NF039805.4 PF20131.4 MC3 23.2 23.2 159 subfamily Y Y N three component ABC system middle component 32894288 131567 cellular organisms no rank 4219 EBI-EMBL ABC-three component (ABC-3C) system Middle Component 3 DUF6521 family protein Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses [1]. [1]. 32894288. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. Nucleic Acids Res. 2020;48:10045-10075. (from Pfam) NF039808.4 PF20137.4 DUF6527 23.6 23.6 63 subfamily Y Y N DUF6527 family protein 131567 cellular organisms no rank 4814 EBI-EMBL Family of unknown function (DUF6527) DUF6527 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 118 and 131 amino acids in length. (from Pfam) NF039815.4 PF18884.5 TSP3_bac 25 10 22 repeat Y N N TSP3 repeat-containing protein 131567 cellular organisms no rank 11963 EBI-EMBL Bacterial TSP3 repeat bacterial thrombospondin type 3 repeat This entry contains a novel bacterial thrombospondin type 3 repeat which differs from the typical consensus by containing a glutamate in place of one of the calcium binding aspartate residues. (from Pfam) NF039818.4 PF18905.5 DUF5661 27 27 65 subfamily Y Y N DUF5661 family protein 131567 cellular organisms no rank 665 EBI-EMBL Protein of unknown function (DUF5661) DUF5661 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 89 and 148 amino acids in length. (from Pfam) NF039819.4 PF18906.5 Phage_tube_2 27 27 266 PfamEq Y Y N phage tail tube protein 16876823 131567 cellular organisms no rank 10324 EBI-EMBL Phage tail tube protein phage tail tube protein This family of proteins are tube proteins which polymerise to form the phage tails. [1]. 16876823. Bacteriophage T5 structure reveals similarities with HK97 and T4 suggesting evolutionary relationships. Effantin G, Boulanger P, Neumann E, Letellier L, Conway JF;. J Mol Biol. 2006;361:993-1002. (from Pfam) NF039820.4 PF18907.5 DUF5662 27 27 156 subfamily Y Y N DUF5662 family protein 131567 cellular organisms no rank 2476 EBI-EMBL Family of unknown function (DUF5662) DUF5662 family protein This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 175 and 193 amino acids in length. Many proteins in this family are annotated as catalase, but this could not be verified. (from Pfam) NF039822.4 PF18914.5 DUF5666 27 15 60 domain Y Y N DUF5666 domain-containing protein 131567 cellular organisms no rank 8760 EBI-EMBL Domain of unknown function (DUF5666) Domain of unknown function (DUF5666) This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 60 amino acids in length. This domain is likely to adopt an OB-fold based on similarity to other families. (from Pfam) NF039823.4 PF18915.5 DUF5667 27 27 99 domain Y Y N DUF5667 domain-containing protein 131567 cellular organisms no rank 9864 EBI-EMBL Domain of unknown function (DUF5667) Domain of unknown function (DUF5667) This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is typically between 95 and 113 amino acids in length. (from Pfam) NF039824.4 PF18919.5 DUF5670 23.5 23.5 43 subfamily Y Y N DUF5670 family protein 131567 cellular organisms no rank 6807 EBI-EMBL Family of unknown function (DUF5670) DUF5670 family protein This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 50 amino acids in length. There is a single completely conserved residue W that may be functionally important. These proteins contain two transmembrane helices. (from Pfam) NF039825.4 PF18936.5 DUF5684 27.4 27.4 81 domain Y Y N DUF5684 domain-containing protein 131567 cellular organisms no rank 7827 EBI-EMBL Family of unknown function (DUF5684) Family of unknown function (DUF5684) This is a family of unknown function mostly found in bacteria. Some family members can be found at the N-terminal region of Pfam:PF00717. (from Pfam) NF039826.4 PF18937.5 DUF5685 26.7 26.7 272 subfamily Y Y N DUF5685 family protein 131567 cellular organisms no rank 12405 EBI-EMBL Family of unknown function (DUF5685) DUF5685 family protein This is a family of unknown function mostly found in bacteria. (from Pfam) NF039831.4 PF18949.5 DUF5693 29 29 609 subfamily Y Y N DUF5693 family protein 131567 cellular organisms no rank 3350 EBI-EMBL Family of unknown function (DUF5693) DUF5693 family protein This is a family of unknown function found in bacteria. (from Pfam) NF039832.4 PF18953.5 SAP_new25 26.3 26.3 51 domain Y N N SAP domain-containing new25 18831036,21270388 131567 cellular organisms no rank 4158 EBI-EMBL SAP domain-containing new25 SAP domain-containing new25 This family includes Schizosaccharomyces specific SAP domain containing proteins such as gene product new25 [1] . SAP ( SAF-A/B, Acinus and PIAS) motif is a DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins. For instance, the SAP domain of SUMO E3 ligase PIAS1 from human is shown to bind an A/T-rich DNA [2]. [1]. 21270388. Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability. Bitton DA, Wood V, Scutt PJ, Grallert A, Yates T, Smith DL, Hagan IM, Miller CJ;. Genetics. 2011;187:1207-1217. [2]. 18831036. Solution structures and DNA binding properties of the N-terminal SAP domains of SUMO E3 ligases from Saccharomyces cerevisiae and Oryza sativa. Suzuki R, Shindo H, Tase A, Kikuchi Y, Shimizu M, Yamazaki T;. Proteins. 2009;75:336-347. (from Pfam) NF039834.4 PF18975.5 DUF5711 26.3 26.3 344 subfamily Y Y N DUF5711 family protein 131567 cellular organisms no rank 2773 EBI-EMBL Family of unknown function (DUF5711) DUF5711 family protein This is a family of unknown function mostly found in bacteria and archea. Some members contain WD repeats. (from Pfam) NF039835.4 PF18998.5 Flg_new_2 23.6 10.3 73 domain Y Y N InlB B-repeat-containing protein 131567 cellular organisms no rank 29579 EBI-EMBL Divergent InlB B-repeat domain Divergent InlB B-repeat domain This family of domains are found in bacterial cell surface proteins. They are often found in tandem array. This domain is closely related to Pfam:PF09479. (from Pfam) NF039841.4 PF19026.5 HYPK_UBA 27 27 41 domain Y N N HYPK UBA domain 29754825 131567 cellular organisms no rank 905 EBI-EMBL HYPK UBA domain HYPK UBA domain This entry represents the UBA domain [1] found at the C-terminus of the HYPK protein and its homologues. This domain in HYPK mediates a protein interaction with the Naa15 C-terminus [1]. [1]. 29754825. Structure of Human NatA and Its Regulation by the Huntingtin Interacting Protein HYPK. Gottlieb L, Marmorstein R;. Structure. 2018;26:925-935. (from Pfam) NF039842.4 PF19027.5 DUF5752 23 23 208 subfamily Y Y N DUF5752 family protein 24318984 131567 cellular organisms no rank 295 EBI-EMBL Family of unknown function (DUF5752) DUF5752 family protein This family includes the OrfY protein from the hyperthermophilic archaeum Thermoproteus tenax. This protein co-occurs with the treS/P protein in an operon regulating the synthesis of trehalose. The structure of this protein shows it contains an internal duplication [1]. [1]. 24318984. Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T;. Proteins. 2014;82:26-42. (from Pfam) NF039850.4 PF19067.5 DUF5763 26.3 26.3 39 domain Y Y N DUF5763 domain-containing protein 131567 cellular organisms no rank 382 EBI-EMBL Family of unknown function (DUF5763) Family of unknown function (DUF5763) This is a family of uncharacterised proteins of unknown function found predominantly in viruses. However, some matches with predicted proteins from Archaea and Eukaryotes were also found. (from Pfam) NF039857.4 PF19094.5 EMC6_arch 26.7 26.7 87 domain Y N N EMC6-arch 131567 cellular organisms no rank 917 EBI-EMBL EMC6-arch EMC6-arch This family represents the ER membrane protein complex subunit 6 (EMC6) homologue from archaea. They contain three transmembrane regions. (from Pfam) NF039859.4 PF19098.5 DUF5785 28.9 28.9 98 subfamily Y Y N DUF5785 family protein 131567 cellular organisms no rank 543 EBI-EMBL Family of unknown function (DUF5785) DUF5785 family protein Family of unknown function predominantly found in Halobacteria. (from Pfam) NF039863.4 PF19110.5 DUF5797 25 25 163 subfamily Y Y N DUF5797 family protein 131567 cellular organisms no rank 642 EBI-EMBL Family of unknown function (DUF5797) DUF5797 family protein This is a family of proteins of unknown function predominantly found in Halobacteria. (from Pfam) NF039864.4 PF19111.5 DUF5798 27 27 89 subfamily Y Y N DUF5798 family protein 131567 cellular organisms no rank 590 EBI-EMBL Family of unknown function (DUF5798) DUF5798 family protein Family of unknown function predominantly found in Halobacteria. (from Pfam) NF039894.4 PF19238.4 Radical_SAM_2 26.7 26.7 151 domain Y N N Radical SAM-like domain 131567 cellular organisms no rank 6160 EBI-EMBL Radical SAM-like domain Radical SAM-like domain This family represents a set of radical SAM like domains that are often found associated with Pfam:PF04459. (from Pfam) NF039902.4 PF19269.4 Anticodon_2 23.6 23.6 141 domain Y N N Anticodon binding domain 11224561,12554668,20606262,20882017,28303005,7701318 131567 cellular organisms no rank 90192 EBI-EMBL Anticodon binding domain Anticodon binding domain This entry represents the anticodon binding domain found at the C-terminus of the class-I glutamyl tRNA synthetase enzyme. [1]. 11224561. Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase. Sekine S, Nureki O, Shimada A, Vassylyev DG, Yokoyama S;. Nat Struct Biol. 2001;8:203-206. [2]. 7701318. Architectures of class-defining and specific domains of glutamyl-tRNA synthetase. Nureki O, Vassylyev DG, Katayanagi K, Shimizu T, Sekine S, Kigawa T, Miyazawa T, Yokoyama S, Morikawa K;. Science. 1995;267:1958-1965. [3]. 12554668. ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. Sekine S, Nureki O, Dubois DY, Bernier S, Chenevert R, Lapointe J, Vassylyev DG, Yokoyama S;. EMBO J. 2003;22:676-688. [4]. 20606262. Structure of nondiscriminating glutamyl-tRNA synthetase from Thermotoga maritima. Ito T, Kiyasu N, Matsunaga R, Takahashi S, Yokoyama S;. Acta Crystallogr D Biol Crystallogr. 2010;66:813-820. [5]. 20882017. Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions. Ito T, Yokoyama S;. Nature. 2010;467:612-616. [6]. 28303005. Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms. Moen SO, Edwards TE, Dranow DM, Clifton MC, Sankaran B, Van Voorhis WC, Sharma A, Manoil C, Staker BL, Myler PJ, Lorimer DD;. Sci Rep. 2017;7:223. (from Pfam) NF039904.4 PF19276.4 HD_assoc_2 23.1 23.1 222 domain Y N N HD associated region 17565173,21757692,9868367 131567 cellular organisms no rank 18353 EBI-EMBL HD associated region HD associated region This entry represents a region that forms part of a larger HD domain [1,2].According to the original paper describing the HD domain this family represents cluster 1 [3]. Paper describing PDB structure 2hek. [1]. 17565173. Structure of O67745_AQUAE, a hypothetical protein from Aquifex aeolicus. Oganesyan V, Adams PD, Jancarik J, Kim R, Kim SH;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007;63:369-374. Paper describing PDB structure 2o6i. [2]. 21757692. Characterization of the deoxynucleotide triphosphate triphosphohydrolase (dNTPase) activity of the EF1143 protein from Enterococcus faecalis and crystal structure of the activator-substrate complex. Vorontsov II, Minasov G, Kiryukhina O, Brunzelle JS, Shuvalova L, Anderson WF;. J Biol Chem. 2011;286:33158-33166. [3]. 9868367. The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Aravind L, Koonin EV;. Trends Biochem Sci 1998;23:469-472. (from Pfam) NF039905.4 PF19279.4 YegS_C 27 27 158 domain Y N N YegS C-terminal NAD kinase beta sandwich-like domain 17351295,17393457,18611377 131567 cellular organisms no rank 88521 EBI-EMBL YegS C-terminal NAD kinase beta sandwich-like domain YegS C-terminal NAD kinase beta sandwich-like domain This entry represents the C-terminal domain found in the YegS protein [1,2]. It is related to the beta sandwich domain of NAD kinases. The structure of YegS reveals a two-domain protein with the active site crevice found between the two domains. The C-terminal domain contains 13 beta-strands and two alpha-helices. The likely substrate for YegS is phosphatidylglycerol [1]. Paper describing PDB structure 2bon. [1]. 17351295. Crystal structure of YegS, a homologue to the mammalian diacylglycerol kinases, reveals a novel regulatory metal binding site. Bakali HM, Herman MD, Johnson KA, Kelly AA, Wieslander A, Hallberg BM, Nordlund P;. J Biol Chem. 2007;282:19644-19652. Paper describing PDB structure 2p1r. [2]. 17393457. Characterization of Salmonella typhimurium YegS, a putative lipid kinase homologous to eukaryotic sphingosine and diacylglycerol kinases. Nichols CE, Lamb HK, Lockyer M, Charles IG, Pyne S, Hawkins AR, Stammers DK;. Proteins. 2007;68:13-25. Paper describing PDB structure 2qv7. [3]. 18611377. Analysis of the Staphylococcus aureus DgkB structure reveals a common catalytic mechanism for the soluble diacylglycerol kinases. Miller DJ, Jerga A, Rock CO, White SW;. Structure. 2008;16:1036-1046. (from Pfam) NF039907.4 PF19289.4 PmbA_TldD_3rd 22 22 220 subfamily_domain Y Y N metallopeptidase TldD-related protein 12029038,22950735,28943336 131567 cellular organisms no rank 111703 EBI-EMBL PmbA/TldA metallopeptidase C-terminal domain PmbA/TldA metallopeptidase C-terminal domain This family includes metalloproteases such as TdlD from E. coli K-12, with a characteristic HEXXXH motif, and also homologs such as PmbA (also called TldE) in which the metal-binding and active site motif HEXXXH is replaced. This HMM, which describes the C-terminal half of proteins such as TldD and PmbA, covers the HEXXXH region in its most N-terminal 25 positions of the model. NF039911.4 PF19306.4 Lhr_WH 27 27 147 domain Y N N Helicase Lhr winged helix domain 29165676 131567 cellular organisms no rank 22108 EBI-EMBL Helicase Lhr winged helix domain Helicase Lhr winged helix domain Mycobacterial Lhr is a DNA damage-inducible superfamily 2 helicase that uses adenosine triphosphate (ATP) hydrolysis to drive unidirectional 3' to 5' translocation along single-stranded DNA (ssDNA) [1]. This entry represents the third domain which has a winged helix domain fold [1]. Paper describing PDB structure 5v9x. [1]. 29165676. Structure of mycobacterial 3'-to-5' RNA:DNA helicase Lhr bound to a ssDNA tracking strand highlights distinctive features of a novel family of bacterial helicases. Ejaz A, Ordonez H, Jacewicz A, Ferrao R, Shuman S;. Nucleic Acids Res. 2018;46:442-455. (from Pfam) NF039912.4 PF19308.4 CRISPR_Cas6_N 23.9 23.9 147 domain Y N N CRISPR Cas6 N-terminal domain 24150936 131567 cellular organisms no rank 1170 EBI-EMBL CRISPR Cas6 N-terminal domain CRISPR Cas6 N-terminal domain In Type I and III CRISPR/Cas systems, the Cas6 family of endoribonucleases generates functional CRISPR-derived RNAs by site-specific cleavage of repeat sequences in precursor transcripts. The structure of Cas6 [1] showed it adopts a tandem ferredoxin/RRM fold. This entry represents the N-terminal domain. Paper describing PDB structure 4c98. [1]. 24150936. Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Niewoehner O, Jinek M, Doudna JA;. Nucleic Acids Res. 2014;42:1341-1353. (from Pfam) NF039927.4 PF19371.4 DUF5946 28 28 141 subfamily Y Y N DUF5946 family protein 131567 cellular organisms no rank 1483 EBI-EMBL Family of unknown function (DUF5946) DUF5946 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001707) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide). (from Pfam) NF039936.4 PF19408.4 PKD_6 25 20 82 domain Y N N PKD-like domain 131567 cellular organisms no rank 3628 EBI-EMBL PKD-like domain PKD-like domain Presumed PKD-like domain found as tandem repeats in bacterial cell surface proteins, commonly associated with PA14 and DUF11 domains. (from Pfam) NF039953.4 PF19451.4 DUF5989 27 27 49 subfamily Y Y N DUF5989 family protein 131567 cellular organisms no rank 1499 EBI-EMBL Family of unknown function (DUF5989) DUF5989 family protein This family of proteins is primarily found in bacteria. Proteins in this family are integral membrane proteins that are approximately 50 amino acids in length. There is a C-terminal conserved APFIY sequence motif. This family may have distant partial similarity to Pfam:PF02694 suggesting this may be a transporter protein. (from Pfam) NF039957.4 PF19473.4 DUF6010 27.3 27.3 120 subfamily Y Y N DUF6010 family protein 16806745 131567 cellular organisms no rank 2007 EBI-EMBL Family of unknown function (DUF6010) DUF6010 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001011) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the meridamycin biosynthetic gene cluster from Streptomyces sp. NRRL 30748 [1]. [1]. 16806745. Isolation and characterization of meridamycin biosynthetic gene cluster from Streptomyces sp. NRRL 30748. He M, Haltli B, Summers M, Feng X, Hucul J;. Gene. 2006;377:109-118. (from Pfam) NF039974.4 PF19537.4 DUF6061 23.7 23.7 81 subfamily Y Y N DUF6061 family protein 131567 cellular organisms no rank 2037 EBI-EMBL Family of unknown function (DUF6061) DUF6061 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. Several proteins in this family are annotated as toxin-antitoxin system proteins. (from Pfam) NF039975.4 PF19539.4 DUF6063 27 27 244 subfamily Y Y N DUF6063 family protein 131567 cellular organisms no rank 1371 EBI-EMBL Family of unknown function (DUF6063) DUF6063 family protein This family of proteins is functionally uncharacterised. This family of proteins is found primarily in bacteria. Proteins in this family are typically between 237 and 249 amino acids in length. They contain a central predicted transmembrane helix. (from Pfam) NF039976.4 PF19541.4 DUF6065 26.6 26.6 236 subfamily Y Y N DUF6065 family protein 28128551 131567 cellular organisms no rank 2579 EBI-EMBL Family of unknown function (DUF6065) DUF6065 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001418) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the myxochromide D biosynthetic gene cluster from Hyalangium minutum [1]. [1]. 28128551. Genomics-Guided Exploitation of Lipopeptide Diversity in Myxobacteria. Burgard C, Zaburannyi N, Nadmid S, Maier J, Jenke-Kodama H, Luxenburger E, Bernauer HS, Wenzel SC;. ACS Chem Biol. 2017;12:779-786. (from Pfam) NF039977.4 PF19545.4 DUF6069 27.2 27.2 129 subfamily Y Y N DUF6069 family protein 28892347 131567 cellular organisms no rank 8882 EBI-EMBL Family of unknown function (DUF6069) DUF6069 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001769) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the family saquayamycin A biosynthetic gene cluster from Streptomyces sp. and appears to be predominantly found in Actinobacteria [1]. [1]. 28892347. Two Cooperative Glycosyltransferases Are Responsible for the Sugar Diversity of Saquayamycins Isolated from Streptomyces sp. KY 40-1. Salem SM, Weidenbach S, Rohr J;. ACS Chem Biol. 2017;12:2529-2534. (from Pfam) NF039980.4 PF19553.4 DUF6076 23.5 23.5 168 domain Y Y N DUF6076 domain-containing protein 131567 cellular organisms no rank 1846 EBI-EMBL Family of unknown function (DUF6076) Family of unknown function (DUF6076) This family of proteins is functionally uncharacterised. This family of proteins is primarily found in Firmicute bacteria. Proteins in this family are typically between 251 and 390 amino acids in length. These proteins contain 4 conserved cysteines suggestive of a zinc-binding motif. (from Pfam) NF039982.4 PF19556.4 PRTRC_E 26 26 175 domain Y N N PRTRC system protein E 131567 cellular organisms no rank 2011 EBI-EMBL PRTRC system protein E PRTRC system protein E A novel genetic system characterized by six or seven major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family averages about 150 amino acids in length, but the last third contains low-complexity sequence that complicates sequence comparisons. (from Pfam) NF039983.4 PF19557.4 DUF6079 23 23 1238 subfamily Y Y N DUF6079 family protein 131567 cellular organisms no rank 2485 EBI-EMBL Family of unknown function (DUF6079) DUF6079 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically around 1200 amino acids in length. This family includes a P-loop domain at the N-terminus. (from Pfam) NF039984.4 PF19559.5 DUF6081 25.9 25.9 272 subfamily Y Y N DUF6081 family protein 30506464 131567 cellular organisms no rank 1402 EBI-EMBL Family of unknown function (DUF6081) DUF6081 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001964) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the alkylpyrone-407 biosynthetic gene cluster from Cystobacterineae bacterium [1]. [1]. 30506464. Genome mining reveals uncommon alkylpyrones as type III PKS products from myxobacteria. Hug JJ, Panter F, Krug D, Muller R;. J Ind Microbiol Biotechnol. 2019;46:319-334. (from Pfam) NF039986.4 PF19562.4 DUF6084 25 25 213 subfamily Y Y N DUF6084 family protein 22247174 131567 cellular organisms no rank 4177 EBI-EMBL Family of unknown function (DUF6084) DUF6084 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001065) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the herboxidiene biosynthetic gene cluster from Streptomyces chromofuscus and appears to be predominantly found in Actinobacteria [1]. [1]. 22247174. Identification of the herboxidiene biosynthetic gene cluster in Streptomyces chromofuscus ATCC 49982. Shao L, Zi J, Zeng J, Zhan J;. Appl Environ Microbiol. 2012;78:2034-2038. (from Pfam) NF039991.4 PF19585.4 DUF6092 28.7 28.7 86 subfamily Y Y N DUF6092 family protein 131567 cellular organisms no rank 442 EBI-EMBL Family of unknown function (DUF6092) DUF6092 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001986) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). This family includes a member from the purincyclamide biosynthetic gene cluster from Streptomyces chrestomyceticus and appears to be predominantly found in bacteria. (from Pfam) NF039993.4 PF19589.4 DUF6095 23.8 23.8 73 subfamily Y Y N DUF6095 family protein 131567 cellular organisms no rank 1807 EBI-EMBL Family of unknown function (DUF6095) DUF6095 family protein This family of predicted integral membrane proteins is functionally uncharacterised. This family of proteins is found in Bacteroidetes. Proteins in this family are approximately 70 amino acids in length. (from Pfam) NF039999.4 PF19617.4 DUF6122 27 27 102 subfamily Y Y N DUF6122 family protein 131567 cellular organisms no rank 3082 EBI-EMBL Family of unknown function (DUF6122) DUF6122 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 104 and 120 amino acids in length. There are two conserved sequence motifs: HYG and RCSI. (from Pfam) NF040008.4 PF19637.4 DUF6140 27 27 69 subfamily Y Y N DUF6140 family protein 131567 cellular organisms no rank 498 EBI-EMBL Family of unknown function (DUF6140) DUF6140 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. (from Pfam) NF040013.4 PF19663.4 DUF6166 27 27 93 domain Y Y N DUF6166 domain-containing protein 131567 cellular organisms no rank 1096 EBI-EMBL Family of unknown function (DUF6166) DUF6166 domain This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 104 and 215 amino acids in length. There are two conserved sequence motifs: GDRTIDG and VVANF. (from Pfam) NF040019.4 PF19700.4 DUF6198 27 27 217 subfamily Y Y N DUF6198 family protein 131567 cellular organisms no rank 7203 EBI-EMBL Family of unknown function (DUF6198) DUF6198 family protein This family represents a putative integral membrane protein that is likely to be the membrane component of an ABC transport system. (from Pfam) NF040028.4 PF19728.4 DUF6220 29.8 29.8 66 domain Y Y N DUF6220 domain-containing protein 26629885 131567 cellular organisms no rank 2190 EBI-EMBL Family of unknown function (DUF6220) Family of unknown function (DUF6220) This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001612) is described by MIBiG as an example of the following biosynthetic class, alkaloid. It includes a member from the ambiguine H isonitrile biosynthetic gene cluster from Fischerella ambigua UTEX 1903 [1]. This family appears to be predominantly found in bacteria. [1]. 26629885. Hapalindole/Ambiguine Biogenesis Is Mediated by a Cope Rearrangement, C-C Bond-Forming Cascade. Li S, Lowell AN, Yu F, Raveh A, Newmister SA, Bair N, Schaub JM, Williams RM, Sherman DH;. J Am Chem Soc. 2015;137:15366-15369. (from Pfam) NF040041.4 PF19776.4 DUF6262 29 29 110 subfamily Y Y N DUF6262 family protein 2846290 131567 cellular organisms no rank 7385 EBI-EMBL Family of unknown function (DUF6262) DUF6262 family protein This family of proteins, functionally uncharacterised, is found in bacteria. Proteins in this family are typically between 124 and 143 amino acids in length. Some members included in this family are hypothetical transposases, associated with transposon Tn554 [1]. There is a conserved sequence GV/LSR/K and a highly conserved tyrosine residue. [1]. 2846290. Transposon Tn554 encodes three products required for transposition. Bastos MC, Murphy E;. EMBO J. 1988;7:2935-2941. (from Pfam) NF040043.4 PF19799.4 DUF6282 26.8 26.8 196 subfamily Y Y N DUF6282 family protein 131567 cellular organisms no rank 4359 EBI-EMBL Family of unknown function (DUF6282) DUF6282 family protein This family of proteins is functionally uncharacterised and it is found in bacteria and archaea. Proteins in this family are typically between 280 and 313 amino acids in length. This family has some overlaps with families from the clan CL0034. (from Pfam) NF040048.4 PF19815.4 DUF6298 28.1 28.1 487 domain Y Y N DUF6298 domain-containing protein 131567 cellular organisms no rank 1810 EBI-EMBL Family of unknown function (DUF6298) Family of unknown function (DUF6298) This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 664 and 1043 amino acids in length. Some members of this family are thought to be pectin/pectate lyases. (from Pfam) NF040055.4 PF19833.4 RecG_dom3_C 26.8 26.8 87 domain Y N N ATP-dependent DNA helicase RecG, domain 3, C-terminal 11595187 131567 cellular organisms no rank 85791 EBI-EMBL ATP-dependent DNA helicase RecG, domain 3, C-terminal ATP-dependent DNA helicase RecG, domain 3, C-terminal This domain is found in ATP-dependent DNA helicase RecG from bacteria the homologue from Arabidopsis, which has a critical role in recombination and DNA repair. This protein comprises three structural domains, the largest N-terminal Domain 1 which interacts with DNA junctions, and Domains 2 and 3 at the C-terminal which contain the characteristic motifs that identify RecG as an SF2 helicase. This domain represents the C-terminal of Domain 3. Around 50 residues that extend from its end cross back to Domain 1 forming a hook that wraps around the extended alpha-helix. This interaction provides a link between Domain 1 and 3 and it is likely that these residues are involved in conformational changes associated with domain movements arising from ATP binding and hydrolysis [1]. [1]. 11595187. Structural analysis of DNA replication fork reversal by RecG. Singleton MR, Scaife S, Wigley DB;. Cell. 2001;107:79-89. (from Pfam) NF040057.4 PF19838.4 LptD_2 22.5 22.5 464 domain Y Y N putative LPS assembly protein LptD 131567 cellular organisms no rank 19403 EBI-EMBL LptD protein putative LPS assembly protein LptD This entry likely represents the LptD homologue of Bacteriodetes bacteria. LptD is an essential outer membrane protein that mediates the final transport of lipopolysaccharide (LPS) to outer leaflet. (from Pfam) NF040059.4 PF19842.4 YqeC 27.6 27.6 145 domain Y N N YqeC protein 131567 cellular organisms no rank 6568 EBI-EMBL YqeC protein YqeC protein This entry includes the E. coli YqeC protein. This protein belongs to the P-loop superfamily. (from Pfam) NF040068.4 PF19864.4 Radical_SAM_N2 29 29 151 domain Y N N Radical SAM proteins, N-terminal 11222759 131567 cellular organisms no rank 19467 EBI-EMBL Radical SAM proteins, N-terminal Radical SAM proteins, N-terminal This domain is found at the N-terminal of radical SAM proteins from bacteria and archaea. Proteins containing this domain are thought to catalyse diverse reactions, including methylations, isomerization, ring formation, anaerobic oxidation and protein radical formation [1, 2]. The function of this domain is unknown. [1]. 11222759. Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE;. Nucleic Acids Res 2001;29:1097-1106. (from Pfam) NF040080.4 PF19935.4 DUF6398 27.2 27.2 106 domain Y Y N DUF6398 domain-containing protein 131567 cellular organisms no rank 1035 EBI-EMBL Domain of unknown function (DUF6398) Domain of unknown function (DUF6398) This domain is functionally uncharacterised, it is present in proteins from bacteria and archaea. This domain is approximately typically 100 amino acids in length and contains a conserved WA sequence motif. (from Pfam) NF040095.4 PF19974.4 TCAD9 40 40 429 domain Y N N Ternary complex associated domain 9 32101166 131567 cellular organisms no rank 789 EBI-EMBL Ternary complex associated domain 9 Ternary complex associated domain 9 Novel uncharacterised protein domain found associated with the vWA-MoxR-VMAP ternary systems. This domain is likely a phosphotransferase enzyme. [1]. 32101166. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. Kaur G, Burroughs AM, Iyer LM, Aravind L;. Elife. 2020; [Epub ahead of print] (from Pfam) NF040097.4 PF19993.4 DO-GTPase2 27 27 226 domain Y Y N TRAFAC clade GTPase domain-containing protein 32101166 131567 cellular organisms no rank 6166 EBI-EMBL Double-GTPase 2 conflict system TRAFAC clade GTPase domain GTPase of a GTPase-centric, NTP-dependent ternary systems. The domain belongs to a previously unrecognised family of the TRAFAC clade with a conserved glutamate in its Walker B motif. [1]. 32101166. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. Kaur G, Burroughs AM, Iyer LM, Aravind L;. Elife. 2020; [Epub ahead of print] (from Pfam) NF040103.4 PF20020.4 DUF6431 26.6 26.6 82 domain Y Y N DUF6431 domain-containing protein 131567 cellular organisms no rank 2240 EBI-EMBL Domain of unknown function (DUF6431) Domain of unknown function (DUF6431) This domain of unknown function is found in uncharacterised proteins from bacteria. This domain is about 90 amino acids in length. It contains the conserved sequences CxxC, RxxCxxxxC and a conserved LP motif. (from Pfam) NF040105.4 PF20030.4 bpMoxR 27 27 205 domain Y N N MoxR domain in the MoxR-vWA-beta-propeller ternary systems 32101166 131567 cellular organisms no rank 108588 EBI-EMBL MoxR domain in the MoxR-vWA-beta-propeller ternary systems MoxR domain in the MoxR-vWA-beta-propeller ternary systems Core MoxR component domain of the MoxR-vWA-beta-propeller ternary systems, a class of NTP-dependent biological conflict systems. [1]. 32101166. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. Kaur G, Burroughs AM, Iyer LM, Aravind L;. Elife. 2020; [Epub ahead of print] (from Pfam) NF040111.4 PF20068.4 Amphi-Trp 27 27 93 domain Y Y N amphi-Trp domain-containing protein 131567 cellular organisms no rank 5459 EBI-EMBL Amphi-Trp domain amphi-Trp domain Derived by Pfam from TIGR04354 - see that model for more information NF040120.4 PF20108.4 DUF6498 23.7 23.7 207 domain Y Y N DUF6498-containing protein 131567 cellular organisms no rank 1920 EBI-EMBL Family of unknown function (DUF6498) DUF6498 domain This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 229 and 247 amino acids in length. (from Pfam) NF040121.4 PF20123.4 DUF6513 23.9 23.9 86 domain Y Y N DUF6513 domain-containing protein 131567 cellular organisms no rank 2082 EBI-EMBL Family of unknown function (DUF6513) Family of unknown function (DUF6513) This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is typically between 75 and 86 amino acids in length. (from Pfam) NF040136.4 PF18903.5 DUF5659 23.6 23.6 75 domain Y Y N DUF5659 domain-containing protein 131567 cellular organisms no rank 569 EBI-EMBL Domain of unknown function (DUF5659) DUF5659 domain This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 78 and 90 amino acids in length. (from Pfam) NF040138.4 PF18911.5 PKD_4 27 27 85 domain Y Y N PKD domain-containing protein 131567 cellular organisms no rank 95418 EBI-EMBL PKD domain PKD domain This entry is composed of PKD domains found in bacterial surface proteins. (from Pfam) NF040139.4 PF18913.5 FBPase_C 27 27 127 domain Y N N Fructose-1-6-bisphosphatase, C-terminal domain 131567 cellular organisms no rank 26554 EBI-EMBL Fructose-1-6-bisphosphatase, C-terminal domain Fructose-1-6-bisphosphatase, C-terminal domain This entry represents the C-terminal domain of Fructose-1-6-bisphosphatase enzymes. According to ECOD this domain has a Rossmann-like fold. (from Pfam) NF040141.4 PF18925.5 DUF5675 26.7 26.7 114 subfamily Y Y N DUF5675 family protein 131567 cellular organisms no rank 5497 EBI-EMBL Family of unknown function (DUF5675) DUF5675 family protein This presumed domain is found in bacteria, archaea, alveolata and caudoviruses. Proteins in this family are typically between 133 and 179 amino acids in length. (from Pfam) NF040144.4 PF18935.5 DUF5683 26.7 26.7 151 domain Y Y N DUF5683 domain-containing protein 131567 cellular organisms no rank 7240 EBI-EMBL Family of unknown function (DUF5683) DUF5683 domain This is a domain of unknown function found mostly in bacteria. (from Pfam) NF040146.4 PF18942.5 DUF5689 28.6 28.6 217 domain Y Y N DUF5689 domain-containing protein 131567 cellular organisms no rank 10440 EBI-EMBL Family of unknown function (DUF5689) Family of unknown function (DUF5689) This is a domain of unknown function. It is mostly found in bacteria and can be present in multiple copies. (from Pfam) NF040149.4 PF18958.5 DUF5700 25 25 283 domain Y Y N DUF5700 domain-containing putative Zn-dependent protease 131567 cellular organisms no rank 1410 EBI-EMBL Putative zinc dependent peptidase (DUF5700) DUF5700 putative Zn-dependent protease domain This entry represents a group of putative zinc dependent peptidases that have the characteristic HEXXH motif. This family is most related to Pfam:PF10026. (from Pfam) NF040152.4 PF18967.5 PycTM 27.2 27.2 107 domain Y Y N Pycsar system effector family protein 34644530 131567 cellular organisms no rank 15955 EBI-EMBL Pycsar effector protein Pycsar system effector family protein Pycsar (pyrimidine cyclase system for antiphage resistance) provides immunity against bacteriophage and consists of a pyrimidine cyclase (PycC), which synthesizes cyclic nucleotides in response to infection, and an effector protein. Cyclic nucleotides serve as specific second messenger signals, which activate the adjacent effector, leading to bacterial cell death and abortive phage infection [1]. This family represents the effector protein from Pycsar system. [1]. 34644530. Cyclic CMP and cyclic UMP mediate bacterial immunity against phages. Tal N, Morehouse BR, Millman A, Stokar-Avihail A, Avraham C, Fedorenko T, Yirmiya E, Herbst E, Brandis A, Mehlman T, Oppenheimer-Shaanan Y, Keszei AFA, Shao S, Amitai G, Kranzusch PJ, Sorek R;. Cell. 2021;184:5728-5739. (from Pfam) NF040157.4 PF18978.5 DUF5714 26.2 26.2 173 domain Y Y N DUF5714 domain-containing protein 131567 cellular organisms no rank 1388 EBI-EMBL Family of unknown function (DUF5714) DUF5714 domain This is a family of unknown function, mainly found in bacteria. It is distantly related to Pfam family Pfam:PF09719, which is a heme binding cytochrome. This domain is found associated with other domains such as the Radical SAM domain and a methyltransferase. (from Pfam) NF040179.4 PF19044.5 P-loop_TraG 25.8 25.8 413 domain Y N N TraG P-loop domain 131567 cellular organisms no rank 54316 EBI-EMBL TraG P-loop domain TraG P-loop domain This entry represents the P-loop domain found in the TraG conjugation protein. (from Pfam) NF040195.4 PF19086.5 Terpene_syn_C_2 23.7 23.7 199 domain Y Y N terpene synthase family protein 131567 cellular organisms no rank 39749 EBI-EMBL Terpene synthase family 2, C-terminal metal binding terpene synthase family protein NF040202.4 PF19113.5 DUF5799 26.2 26.2 148 subfamily Y Y N DUF5799 family protein 131567 cellular organisms no rank 592 EBI-EMBL Family of unknown function (DUF5799) DUF5799 family protein This is a family of proteins of unknown function predominantly found in Halobacteria. (from Pfam) NF040208.4 PF19146.5 DUF5828 27 27 175 subfamily Y Y N DUF5828 family protein 131567 cellular organisms no rank 635 EBI-EMBL Family of unknown function (DUF5828) DUF5828 family protein This is a family of proteins of unknown function predominantly found in Halobacteria. (from Pfam) NF040210.4 PF19148.5 DUF5830 26.8 26.8 114 subfamily Y Y N DUF5830 family protein 131567 cellular organisms no rank 605 EBI-EMBL Family of unknown function (DUF5830) DUF5830 family protein This is a family of proteins predominantly found in Halobacteria. Some members includes the MarR family transcriptional regulator. (from Pfam) NF040218.4 PF19190.5 BACON_2 25 15 94 domain Y Y N BACON domain-containing protein 31766550 131567 cellular organisms no rank 18825 EBI-EMBL Viral BACON domain BACON domain This family represents a distinct class of BACON domains found in crAss-like phages, the most common viral family in the human gut, in which they are found in tail fiber genes. This suggests they may play a role in phage-host interactions. [1]. 31766550. Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages. Jonge PA, Meijenfeldt FABV, Rooijen LEV, Brouns SJJ, Dutilh BE;. Viruses. 2019; [Epub ahead of print] (from Pfam) NF040238.4 PF19263.4 DUF5906 27.6 27.6 114 domain Y Y N DUF5906 domain-containing protein 131567 cellular organisms no rank 57399 EBI-EMBL Family of unknown function (DUF5906) Family of unknown function (DUF5906) This is a family of proteins of unknown function found in viruses. This family is a P-loop member whose proteins are thought to be SF3 helicases, which are involved in replication initiation. (from Pfam) NF040244.4 PF19290.4 PmbA_TldD_2nd 20.9 20.9 109 domain Y N N PmbA/TldA metallopeptidase central domain 12029038,22950735,28943336 131567 cellular organisms no rank 78241 EBI-EMBL PmbA/TldA metallopeptidase central domain PmbA/TldA metallopeptidase central domain This entry represents a group of metalloproteases. The tertiary structure of the Escherichia coli TdlD/TdlE complex has been solved, and shows that the TdlD subunit is the active peptidase, binding a single zinc ion at an HEXXXH motif in which the glutamic acid is a substrate-binding residue and the two histidines are zinc ligands. The third zinc ligand is a cysteine, C-terminal to the HEXXXH motif. The TldE (also known as PmbA) by itself has no catalytic activity, does not bind zinc, and does not carry the HEXXXH motif [1]. TldD and TldE were originally identified as regulators of DNA gyrase. Later, they are shown to be metalloproteases involved in CcdA degradation [2-3]. [1]. 28943336. The Origins of Specificity in the Microcin-Processing Protease TldD/E. Ghilarov D, Serebryakova M, Stevenson CEM, Hearnshaw SJ, Volkov DS, Maxwell A, Lawson DM, Severinov K;. Structure. 2017;25:1549-1561. [2]. 22950735. An archaeal protein evolutionarily conserved in prokaryotes is a zinc-dependent metalloprotease. Hu Y, Peng N, Han W, Mei Y, Chen Z, Feng X, Liang YX, She Q;. Biosci Rep. 2012;32:609-618. [3]. 12029038. The highly conserved TldD and TldE proteins of Escherichia coli are involved in microcin B17 processing and in CcdA degradation. Allali N, Afif H, Couturier M, Van Melderen L;. J Bacteriol. 2002;184:3224-3231. (from Pfam) NF040245.4 PF19295.4 SufBD_N 23.5 23.5 172 domain Y N N SufBD protein N-terminal region 26472926 131567 cellular organisms no rank 67253 EBI-EMBL SufBD protein N-terminal region SufBD protein N-terminal region This entry represents the N-terminal part of the SufB and SufD proteins. It has a right handed beta helix structure [1]. This family is associated with the C-terminal region Pfam:PF01458 Paper describing PDB structure 5awf. [1]. 26472926. Functional Dynamics Revealed by the Structure of the SufBCD Complex, a Novel ATP-binding Cassette (ABC) Protein That Serves as a Scaffold for Iron-Sulfur Cluster Biogenesis. Hirabayashi K, Yuda E, Tanaka N, Katayama S, Iwasaki K, Matsumoto T, Kurisu G, Outten FW, Fukuyama K, Takahashi Y, Wada K;. J Biol Chem. 2015;290:29717-29731. (from Pfam) NF040248.4 PF19300.4 BPD_transp_1_N 23.8 23.8 114 domain Y N N Binding-prot-dependent transport system membrane comp, N-term 131567 cellular organisms no rank 273248 EBI-EMBL Binding-prot-dependent transport system membrane comp, N-term Binding-prot-dependent transport system membrane comp, N-term This is the N-terminal transmembrane domain of the Binding-protein-dependent transport system inner membrane component. (from Pfam) NF040249.4 PF19305.4 MmgE_PrpD_C 32.1 32.1 173 domain Y N N MmgE/PrpD C-terminal domain 11294638 131567 cellular organisms no rank 60370 EBI-EMBL MmgE/PrpD C-terminal domain MmgE/PrpD C-terminal domain This entry represents the C-terminal domain of 2-methylcitrate dehydratase EC:4.2.1.79 (PrpD) that is required for propionate catabolism. It catalyses the third step of the 2-methylcitric acid cycle. This domain is related to the serine dehydratase beta chain. [1]. 11294638. In vitro conversion of propionate to pyruvate by Salmonella enterica enzymes: 2-methylcitrate dehydratase (PrpD) and aconitase Enzymes catalyze the conversion of 2-methylcitrate to 2-methylisocitrate. Horswill AR, Escalante-Semerena JC;. Biochemistry 2001;40:4703-4713. (from Pfam) NF040256.4 PF19326.4 AMP_deaminase 27 27 630 domain Y N N AMP deaminase GO:0003876,GO:0032264 16543243 131567 cellular organisms no rank 17617 EBI-EMBL AMP deaminase AMP deaminase NF040257.4 PF19328.4 DAP_DH_C 23.3 23.3 206 domain Y N N 2,4-diaminopentanoate dehydrogenase C-terminal domain 4684685 131567 cellular organisms no rank 18038 EBI-EMBL 2,4-diaminopentanoate dehydrogenase C-terminal domain 2,4-diaminopentanoate dehydrogenase C-terminal domain This entry represents the C-terminal presumed domain from the 2,4-diaminopentanoic acid C 4 dehydrogenase enzyme [1]. This enzyme is involved in the ornithine fermentation pathway. It catalyzes the oxidative deamination of (2R,4S)-2,4-diaminopentanoate (DAP) to yield 2-amino-4-ketopentanoate (AKP). The N-terminal domain has a Rossmann fold. [1]. 4684685. 2,4-diaminopentanoic acid C 4 dehydrogenase. Purification and properties of the protein. Somack R, Costilow RN;. J Biol Chem. 1973;248:385-388. (from Pfam) NF040269.4 PF19368.4 AraR_C 23.8 23.8 82 domain Y N N AraR C-terminal winged HTH domain GO:0003677 26438537 131567 cellular organisms no rank 32525 EBI-EMBL AraR C-terminal winged HTH domain AraR C-terminal winged HTH domain This entry represents the C-terminal DNA-binding domain of AraR proteins which are involved in regulating Arabinose utilisation [1]. This domain has a winged helix-turn-helix structure [1]. Paper describing PDB structure 5bs6. [1]. 26438537. A novel transcriptional regulator of L-arabinose utilization in human gut bacteria. Chang C, Tesar C, Li X, Kim Y, Rodionov DA, Joachimiak A;. Nucleic Acids Res. 2015;43:10546-10559. (from Pfam) NF040290.4 PF19436.4 ACS_CODH_B_C 25 25 245 domain Y N N ACS/CODH beta subunit C-terminal 11509720,11593006,12386327,12627225,14699043,19583207,19650626 131567 cellular organisms no rank 1301 EBI-EMBL ACS/CODH beta subunit C-terminal ACS/CODH beta subunit C-terminal Acetyl-CoA synthase/CO dehydrogenase (ACS/CODH) is a bifunctional enzyme that catalyses the reversible reduction of CO2 to CO (CODH activity, the beta subunit) and the synthesis or degradation of acetyl-CoA (catalysed by ACS, the alpha subunit). CODH contains the B-, C-, and D-clusters. This domain represents the middle and C-terminal regions of CODH which have an alpha/beta Rossmann-like fold and are the contribute ligands to the active site C-cluster. The C-cluster generates CO from CO2 and contains one Ni atom, four Fe atoms, and five labile sulfur atoms, arranged as an asymmetrical heteronuclear [Ni-4Fe-5S] cluster [1,2,6,7]. Paper describing PDB structure 1mjg. [1]. 12386327. A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase. Doukov TI, Iverson TM, Seravalli J, Ragsdale SW, Drennan CL;. Science. 2002;298:567-572. Paper describing PDB structure 1oao. [2]. 12627225. Ni-Zn-[Fe4-S4] and Ni-Ni-[Fe4-S4] clusters in closed and open subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase. Darnault C, Volbeda A, Kim EJ, Legrand P, Vernede X, Lindahl PA, Fontecilla-Camps JC;. Nat Struct Biol. 2003;10:271-279. Paper describing PDB structure 1ru3. [3]. 14699043. A functional Ni-Ni-[4Fe-4S] cluster in the monomeric acetyl-CoA synthase from Carboxydothermus hydrogenoformans. Svetlitchnyi V, Dobbek H, Meyer-Klaucke W, Meins T, Thiele B, Romer P, Huber R, Meyer O;. Proc Natl Acad Sci U S A. 2004;101:446-451. Paper describing PDB structure 3git. [4]. 19650626. Novel domain arrangement in the crystal structure of a truncated acetyl-CoA synthase from Moorella thermoacetica. Volbeda A, Darnault C. TRUNCATED at 1650 bytes (from Pfam) NF040293.4 PF19454.4 DUF5992 23.8 23.8 106 subfamily Y Y N DUF5992 family protein 131567 cellular organisms no rank 141 EBI-EMBL Family of unknown function (DUF5992) DUF5992 family protein This family of proteins is found in bacteria. Proteins in this family are typically between 105 and 116 amino acids in length. (from Pfam) NF040299.4 PF19474.4 DUF6011 26.6 26.6 37 domain Y Y N DUF6011 domain-containing protein 10383985,8704959 131567 cellular organisms no rank 3843 EBI-EMBL Family of unknown function (DUF6011) Family of unknown function (DUF6011) This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000413) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This family includes a protein encoded by the pyoverdin biosynthetic gene cluster from Pseudomonas protegens Pf-5 [1,2]. [1]. 8704959. Novel pyoverdine biosynthesis gene(s) of Pseudomonas aeruginosa PAO. Stintzi A, Cornelis P, Hohnadel D, Meyer JM, Dean C, Poole K, Kourambas S, Krishnapillai V;. Microbiology 1996;142:1181-1190. [2]. 10383985. The pvc gene cluster of Pseudomonas aeruginosa: role in synthesis of the pyoverdine chromophore and regulation by PtxR and PvdS. Stintzi A, Johnson Z, Stonehouse M, Ochsner U, Meyer JM, Vasil ML, Poole K;. J Bacteriol 1999;181:4118-4124. (from Pfam) NF040307.4 PF19510.4 DUF6044 27 27 564 subfamily Y Y N DUF6044 family protein 131567 cellular organisms no rank 3137 EBI-EMBL Protein of unknown function (DUF6044) DUF6044 family protein This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 557 and 582 amino acids in length. There is a conserved YNG sequence motif. (from Pfam) NF040319.4 PF19570.4 DUF6088 25 25 172 subfamily Y Y N DUF6088 family protein 131567 cellular organisms no rank 9267 EBI-EMBL Family of unknown function (DUF6088) DUF6088 family protein This family of proteins is functionally uncharacterised. This family of proteins is found primarily in bacteria. Proteins in this family are typically between 197 and 228 amino acids in length. This family appears to be distantly related to Pfam:PF13338 suggesting proteins in this family may be an antitoxin component of a toxin/antitoxin system. (from Pfam) NF040320.4 PF19571.4 ACT_8 23.5 23.5 141 domain Y N N ACT domain pair 131567 cellular organisms no rank 4101 EBI-EMBL ACT domain pair ACT domain pair This entry represents a pair of ACT domains. These domains bind to amino acids and often form regulatory subunits of enzymes. Proteins in this family are found in bacteria and archaea. Proteins in this family are approximately 140 amino acids in length. (from Pfam) NF040322.4 PF19580.4 Exo_endo_phos_3 27 27 311 domain Y N N Endonuclease/Exonuclease/phosphatase family GO:0003824 131567 cellular organisms no rank 28284 EBI-EMBL Endonuclease/Exonuclease/phosphatase family Endonuclease/Exonuclease/phosphatase family This domain appears to be related to Pfam:PF03372. (from Pfam) NF040323.4 PF19581.4 Glyoxalase_7 23.6 23.6 133 subfamily Y Y N glyoxalase superfamily protein GO:0046677 131567 cellular organisms no rank 12441 EBI-EMBL Glyoxalase superfamily protein glyoxalase superfamily protein NF040326.4 PF19605.4 DUF6110 26 26 85 subfamily Y Y N DUF6110 family protein 131567 cellular organisms no rank 1619 EBI-EMBL Family of unknown function (DUF6110) DUF6110 family protein This family of proteins is functionally uncharacterised. This family of proteins is found primarily in Firmicute bacteria. Proteins in this family are typically between 88 and 109 amino acids in length. (from Pfam) NF040329.4 PF19611.4 DUF6116 27 27 50 subfamily Y Y N DUF6116 family protein 131567 cellular organisms no rank 805 EBI-EMBL Family of unknown function (DUF6116) DUF6116 family protein This family of putative integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. (from Pfam) NF040332.4 PF19631.4 Trypco2 24.2 24.2 78 domain Y Y N trypco2 family protein 19478828,32101166 131567 cellular organisms no rank 6988 EBI-EMBL Trypsin-co-occurring domain 2 trypsin-co-occurring domain 2 domain Members of this primarily bacterial family can occur in the context of trypsin-like proteases in bioinformatically identified conflict system loci (e.g. WP_010356081.1 encoded next to WP_010356080.1 in Streptomyces acidiscabies), or in biosynthetic gene clusters (BGC). The molecular function is unknown. NF040334.4 PF19641.4 DUF6144 28.8 28.8 181 subfamily Y Y N DUF6144 family protein 131567 cellular organisms no rank 353 EBI-EMBL Family of unknown function (DUF6144) DUF6144 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 190 amino acids in length. (from Pfam) NF040350.4 PF19701.4 DUF6199 27.7 27.7 64 subfamily Y Y N DUF6199 family natural product biosynthesis protein 19025863 131567 cellular organisms no rank 1787 EBI-EMBL Family of unknown function (DUF6199) DUF6199 family natural product biosynthesis protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000087) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the lasalocid biosynthetic gene cluster from Streptomyces lasaliensis [1]. [1]. 19025863. Analysis of specific mutants in the lasalocid gene cluster: evidence for enzymatic catalysis of a disfavoured polyether ring closure. Smith L, Hong H, Spencer JB, Leadlay PF;. Chembiochem. 2008;9:2967-2975. (from Pfam) NF040368.4 PF19789.4 DUF6273 23.5 23.5 172 domain Y Y N DUF6273 domain-containing protein 131567 cellular organisms no rank 4840 EBI-EMBL Family of unknown function (DUF6273) Family of unknown function (DUF6273) This family of proteins is functionally uncharacterised. This family of proteins is found in Firmicute bacteria. Proteins in this family are typically between 204 and 573 amino acids in length. This region is found in proteins that are likely to be surface exposed. (from Pfam) NF040370.4 PF19798.4 Sulfotransfer_5 23.2 23.2 226 domain Y N N Sulfotransferase domain 22991895 131567 cellular organisms no rank 4459 EBI-EMBL Sulfotransferase domain Sulfotransferase domain This entry represents a family of sulfotransferase enzymes [1]. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 238 and 379 amino acids in length. Paper describing PDB structure 4gbm. [1]. 22991895. Structural basis of functional group activation by sulfotransferases in complex metabolic pathways. McCarthy JG, Eisman EB, Kulkarni S, Gerwick L, Gerwick WH, Wipf P, Sherman DH, Smith JL;. ACS Chem Biol. 2012;7:1994-2003. (from Pfam) NF040371.4 PF19810.4 DUF6293_N 30 30 120 subfamily Y Y N DUF6293 family protein 131567 cellular organisms no rank 1513 EBI-EMBL Domain of unknown function (DUF6293) DUF6293 family protein This domain is found in functionally uncharacterised archaeal proteins. It contains a conserved sequence motif HxxPxxG and a conserved asparagine residue. It is usually followed by winged helix domain and this domain organisation as well as the predicted structure are reminiscent of CRISPR-associated protein, Csa3. (from Pfam) NF040372.4 PF19811.4 DUF6294 34.9 34.9 88 subfamily Y Y N DUF6294 family protein 23360970 131567 cellular organisms no rank 424 EBI-EMBL Family of unknown function (DUF6294) DUF6294 family protein This BGC (BGC0000081) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650CC [1]. This family appears to be predominantly found in bacteria. [1]. 23360970. Cloning and sequencing of the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650 revealing new insights into biosynthesis of the enediyne family of antitumor antibiotics. Lohman JR, Huang SX, Horsman GP, Dilfer PE, Huang T, Chen Y, Wendt-Pienkowski E, Shen B;. Mol Biosyst. 2013;9:478-491. (from Pfam) NF040385.4 PF19880.4 DUF6353 25 25 253 subfamily Y Y N DUF6353 family protein 131567 cellular organisms no rank 551 EBI-EMBL Family of unknown function (DUF6353) DUF6353 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 255 and 305 amino acids in length. (from Pfam) NF040386.4 PF19883.4 DUF6356 24.4 24.4 64 subfamily Y Y N DUF6356 family protein 131567 cellular organisms no rank 2458 EBI-EMBL Family of unknown function (DUF6356) DUF6356 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 71 and 88 amino acids in length. There are two conserved sequence motifs: KTGS and RMV. (from Pfam) NF040388.4 PF19887.4 DUF6360 23.8 23.8 91 subfamily Y Y N DUF6360 family protein 131567 cellular organisms no rank 566 EBI-EMBL Family of unknown function (DUF6360) DUF6360 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in archaea. Proteins in this family are approximately 100 amino acids in length. (from Pfam) NF040395.4 PF19905.4 DUF6378 27.1 27.1 81 domain Y Y N DUF6378 domain-containing protein 131567 cellular organisms no rank 1083 EBI-EMBL Domain of unknown function (DUF6378) DUF6378 domain This domain of unknown function is found in proteins from bacteria and phages which are functionally uncharacterised. This domain is about 100 amino acids in length. It contains two conserved sequence motifs, KxxR and DxxxDxxGY. (from Pfam) NF040396.4 PF19906.4 DUF6379 27.6 27.6 112 domain Y Y N DUF6379 domain-containing protein 131567 cellular organisms no rank 2937 EBI-EMBL Domain of unknown function (DUF6379) DUF6379 domain This domain of unknown function is found in uncharacterised proteins from bacteria and eukaryotes. It is about 100 amino acids in length and contains a DG conserved motif. (from Pfam) NF040403.4 PF19952.4 DUF6414 25 25 249 subfamily Y Y N DUF6414 family protein 131567 cellular organisms no rank 871 EBI-EMBL Family of unknown function (DUF6414) DUF6414 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, mainly Firmicutes. Proteins in this family are typically between 231 and 275 amino acids in length. It has two conserved sequences motifs, GYY and RFN. (from Pfam) NF040416.4 PF20013.4 GAP1-N2 24 24 139 domain Y N N GTPase-associated protein 1, N-terminal domain type 2 32101166 131567 cellular organisms no rank 5699 EBI-EMBL GTPase-associated protein 1, N-terminal domain type 2 GTPase-associated protein 1, N-terminal domain type 2 One of two types of domain found at the N-terminus of the GTPase-associated protein 1 (GAP1) of the GTPase-centric ternary systems, a class of NTP-dependent biological conflict systems. This domain is predicted to mediate effector-GAP1 interactions. [1]. 32101166. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. Kaur G, Burroughs AM, Iyer LM, Aravind L;. Elife. 2020; [Epub ahead of print] (from Pfam) NF040417.4 PF20014.4 GAP1-M 24 24 101 domain Y N N GTPase-associated protein 1, middle domain 32101166 131567 cellular organisms no rank 5718 EBI-EMBL GTPase-associated protein 1, middle domain GTPase-associated protein 1, middle domain Middle domain found in the multidomain GTPase-associated protein 1 (GAP1) of the GTPase-centric systems, a class of NTP-dependent biological conflict systems. [1]. 32101166. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. Kaur G, Burroughs AM, Iyer LM, Aravind L;. Elife. 2020; [Epub ahead of print] (from Pfam) NF040422.4 PF20033.4 DUF6438 27.2 27.2 76 domain Y Y N DUF6438 domain-containing protein 131567 cellular organisms no rank 3120 EBI-EMBL Domain of unknown function (DUF6438) Domain of unknown function (DUF6438) This domain of unknown function is found in uncharacterised proteins from bacteria and archaea. This domain is about 75 amino acids in length and it contains the conserved motif CxxxGxCP. Towards the C-terminal there are two conserved residues, a Glycine and an Aspartate. Some of the proteins containing this domain also have an ankyrin repeat-containing region. (from Pfam) NF040425.4 PF20042.4 DUF6444 27 27 85 domain Y Y N DUF6444 domain-containing protein 131567 cellular organisms no rank 4913 EBI-EMBL Family of unknown function (DUF6444) Family of unknown function (DUF6444) This entry represents a region that is sometimes found a the N-terminus of transposon proteins. It is also sometimes found as part of a shorter protein, presumably involved in transposition. (from Pfam) NF040426.4 PF20055.4 DUF6454 22.3 22.3 292 subfamily Y Y N DUF6454 family protein 131567 cellular organisms no rank 946 EBI-EMBL Family of unknown function (DUF6454) DUF6454 family protein This family of proteins is functionally uncharacterised. This family of proteins is found primarily in bacteria. Proteins in this family are typically between 294 and 372 amino acids in length. (from Pfam) NF040432.4 PF20067.4 SSL_N 18.9 16.8 46 domain Y N N Strictosidine synthase-like, N-terminal 18280746,18513186,20033437,21948213 131567 cellular organisms no rank 12444 EBI-EMBL Strictosidine synthase-like, N-terminal Strictosidine synthase-like, N-terminal This domain is found at the N-terminal of strictosidine synthase-like (SSL) proteins including Adipocyte plasma membrane- associated proteins (APMAPs) from animals, Protein STRICTOSIDINE SYNTHASE-LIKE (SSLs) from Arabidopsis and SGL proteins, being also present in bacterial sequences. It is about 50 amino acids in length. It contains residues involved in metal coordination in the active site. This domain is also found in Gluconolactonase and Sugar lactone lactonase. These proteins share a six-bladed beta-propeller fold structure and have similar structural and mechanistic features to SS (strictosidine synthase) that involve nucleophilic attack on an electrophilic substrate, although they do not catalyse the SS reaction as they lack the catalytic glutamate required for SS activity; they catalyse hydrolytic reactions instead [1,2,3,4]. APMAPs shows similarity with paraoxonases (PON) and has a strong arylesterase activity with beta-naphthyl acetate and phenyl acetate. They are involved in adipocyte differentiation [1,3]. [1]. 18513186. Localization and characterization of the novel protein encoded by C20orf3. Ilhan A, Gartner W, Nabokikh A, Daneva T, Majdic O, Cohen G, Bohmig GA, Base W, Horl WH, Wagner L;. Biochem J. 2008;414:485-495. [2]. 18280746. 3D-Structure and function of strictosidine synthase--the key enzyme of monoterpenoid indole alkaloid biosynthesis. Stockigt J, Barleben L, Panjikar S, Loris EA;. Plant Physiol Biochem. 2008;46:340-355. [3]. 21948213. The evolution of function in strictosidine synthase-like proteins. Hicks MA, Barber AE 2nd, Giddings LA, Caldwell J, O'Connor SE, Babbitt PC;. Proteins. 2011;79:3082. TRUNCATED at 1650 bytes (from Pfam) NF040438.4 PF20091.4 Abhydrolase_10 23 23 429 domain Y Y N alpha/beta hydrolase domain-containing protein 131567 cellular organisms no rank 5727 EBI-EMBL Alpha/beta hydrolase domain alpha/beta hydrolase domain This entry represents a protein that belongs to the alpha/beta hydrolase superfamily. Although proteins in this family are uncharacterised they are likely to have an enzymatic activity. (from Pfam) NF040441.4 PF20097.4 DUF6487 24 24 67 subfamily Y Y N PF20097 family protein 131567 cellular organisms no rank 1496 EBI-EMBL Domain of unknown function (DUF6487) PF20097 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. This domain is likely to be a zinc-binding domain. (from Pfam) NF040451.4 PF20120.4 DUF6510 26.4 26.4 86 subfamily Y Y N DUF6510 family protein 131567 cellular organisms no rank 3352 EBI-EMBL Family of unknown function (DUF6510) DUF6510 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved RCP sequence motif. (from Pfam) NF040494.1 nitrored_ArsF 60 60 106 subfamily Y Y N nitrophenyl compound nitroreductase subunit ArsF family protein 31059239 131567 cellular organisms no rank 1081 NCBIFAM nitrophenyl compound nitroreductase subunit ArsF family protein The founding member of this family, ArsF, acts together with ArsE as a nitroreductase for trivalent forms (having As(III) instead of As(V)) of two synthetic aromatic organoarsenical biocides, nitarsone and roxarsone, reducing the nitro group to an amine, after which efflux confers resistance to the arsenical. Because the nitro group is rather far from the As(III) moiety of the known substrates, it is likely that conversed properties of members of this family include nitroreductase activity but not arsenical resistance activity. NF040495.1 tranport_ArsG 200 200 225 equivalog Y Y N aromatic aminobenezylarsenical efflux permease ArsG family transporter 31059239 131567 cellular organisms no rank 1027 NCBIFAM aromatic aminobenezylarsenical efflux permease ArsG family transporter ArsG belongs to a broadly conserved ArsEFG cassette that was found in Shewanella putrefaciens as part of an organoarsenical resistance locus. ArsG performs efflux after the nitroreductase pair, ArsEF, converts a nitro group into an amine on the aromatic ring that elsewhere carries the arsenical group. TCDB names the system the Aminobenzyl Carbon-arsenic Defining Exporter (ABCDE) Family, 2.A.131. NF040501.1 resist_ArsN2 125 125 133 equivalog Y Y Y arsenic resistance N-acetyltransferase ArsN2 arsN2 19016868,30993215 131567 cellular organisms no rank 2881 NCBIFAM arsenic resistance N-acetyltransferase ArsN2 ArsN2 is a GNAT family N-acetyltransferase regularly found in arsenic resistance operons. The ArsN2 sequence may appear as a fusion protein with arsenate reductase. Comparing ArsN2 to ArsN1, the ArsN2 sequences are more closely related to glutamate N-acetyltransferases (N-acetylglutamate synthases), while ArsN1 sequences are more closely related to phosphinothricin N-acetyltransferases. ArsN2 by itself reduces sensitivity to sodium arsenate. All members of the ArsN2 seed alignment were found encoded adjacent to other arsenic resistance genes. NF040504.1 resist_ArsN1b 210 210 159 equivalog Y Y Y arsinothricin resistance N-acetyltransferase ArsN1 family B GO:0008080 30993215 131567 cellular organisms no rank 1828 NCBIFAM arsinothricin resistance N-acetyltransferase ArsN1 family B Arsinothricin is an arsenic analog of phosphinothricin. Both are non-proteinogenic amino acid analogs of glutamate, and are natural product antibiotics. Selected members of the ArsN1, a GNAT family N-acetyltransferase, were shown to be selective for arsinothricin, and members of the family are often found encoded in arsenical resistance operons. Note that ArsN1 proteins are more closely related to phosphinothricin N-acetyltransferases, while ArsN2 proteins are more closely related to glutamate N-acetyltransferases (N-acetylglutamate synthases). This HMM represents what we call branch ArsN1b of the ArsN1 family. NF040521.1 C45_proenzyme 85 85 313 subfamily Y Y N C45 family autoproteolytic acyltransferase/hydolase 16299587,2120195,7557412 131567 cellular organisms no rank 23415 NCBIFAM C45 family autoproteolytic acyltransferase/hydolase Members of this family include hydrolases and N-acyltransferases, and belong to the Ntn (N-terminal nucleophile) hydrolase family. Members have an invariant Cys residue (Cys-103 in XP_002569112.1) required both for autoproteolytic processing into alpha and beta chains and for activity. The family is described by MEROPs as a cysteine protease, family C45, because of its autoproteolytic activity. Characterized members include TAN from Drosophila, which removes beta-alanine from both carcinine and N-beta-alanyl dopamine, and isopenicillin-N N-acyltransferase from various fungi. The latter has been heavily studied because of its role in penicillin biosynthesis. NF040559.1 CAS_Csx20 70 70 124 equivalog Y Y N CRISPR-associated protein Csx20 csx20 131567 cellular organisms no rank 439 NCBIFAM CRISPR-associated protein Csx20 NF040560.1 CAS_Csx15 35 35 125 equivalog Y Y N CRISPR-associated protein Csx15 csx15 24817877 131567 cellular organisms no rank 169 NCBIFAM CRISPR-associated protein Csx15 NF040563.1 guided_IscB 175 175 314 equivalog Y Y N RNA-guided endonuclease IscB iscB 34591643 131567 cellular organisms no rank 5104 NCBIFAM RNA-guided endonuclease IscB NF040570.1 guided_TnpB 100 100 389 subfamily Y Y N RNA-guided endonuclease TnpB family protein 131567 cellular organisms no rank 163435 NCBIFAM RNA-guided endonuclease TnpB family protein This family includes RNA-guided endonuclease TnpB from IS200/IS605 family elements (NF038281) and IS607 family elements (NF038280), but also many additional proteins. It exhibits homolog to or actually includes some CRISPR-associated (Cas) proteins such as the type V CRISPR-associated protein C2c8. For a long time, TnpB proteins were described as accessory proteins in IS (insertion sequence) elements, present as one of just one or two proteins encoded in the element but not necessary for transposition. The programmable RNA-guided endonuclease TnpB proteins may provide a CRISPR-like, widespread form of phage defense by RNA-guided DNA degradation. NF040586.1 FxSxx_TPR 300 300 830 equivalog Y Y N FxSxx-COOH system tetratricopeptide repeat protein fxsT 32101166,34164914 131567 cellular organisms no rank 18841 NCBIFAM FxSxx-COOH system tetratricopeptide repeat protein Members of this family are typically about 850 amino acids long, or 1300 long because of an additional N-terminal domain. Proteins have a P-loop motif, GxGGxGKT, near the N-terminus of the region covered by this HMM, and a region over 400 residues long of tetratricopeptide repeat sequence. The family is found regularly next to other components of FxSxx-COOH systems, which feature an FxsB family radical SAM protein and a protein modified by it, FxsA. Members of this FxsA family typically have an FxSxx motif as the final five amino acids. NF040603.2 choice_anch_P 27 27 185 subfamily Y Y N choice-of-anchor P family protein 131567 cellular organisms no rank 6012 NCBIFAM choice-of-anchor P family protein NF040647.1 IPPK_Arch 120 120 259 equivalog Y Y N isopentenyl phosphate kinase 2.7.4.26 GO:0008299,GO:0016301 16621811,19928876 131567 cellular organisms no rank 1603 NCBIFAM isopentenyl phosphate kinase NF040651.2 MtaB_Meth 720 720 460 equivalog Y Y N methanol--corrinoid protein co-methyltransferase MtaB mtaB 2.1.1.90 9057830,9363780,9654068 131567 cellular organisms no rank 312 NCBIFAM methanol--corrinoid protein co-methyltransferase MtaB MtaABC catalyze the formation of methyl-coenzyme M from methanol and coenzyme M. MtaB methylates the corrinoid protein MtaC. NF040667.1 hom_kin_desulfo 197 197 163 exception Y Y N homoserine kinase thrB 2.7.1.39 29324779 131567 cellular organisms no rank 233 NCBIFAM homoserine kinase, Desulfovibrio type NF040682.1 PorA_Arch 550 550 387 equivalog Y Y N pyruvate synthase subunit PorA porA 1.2.7.1 GO:0019164 12743680,8620891,9108258 131567 cellular organisms no rank 484 NCBIFAM pyruvate synthase subunit PorA NF040683.1 PorC_Meth_Thtga 270 270 177 equivalog Y Y N pyruvate synthase subunit PorC porC 1.2.7.1 GO:0019164 8550425,8620891,9108258 131567 cellular organisms no rank 189 NCBIFAM pyruvate synthase subunit PorC NF040684.1 PorD_Arch 120 120 85 equivalog Y Y N pyruvate synthase subunit PorD porD 1.2.7.1 8550425,8620891,9108258 131567 cellular organisms no rank 360 NCBIFAM pyruvate synthase subunit PorD NF040696.1 isopcys_mtase 160 160 190 equivalog Y Y N protein-S-isoprenylcysteine O-methyltransferase 2.1.1.100 GO:0004671 22195972 131567 cellular organisms no rank 1053 NCBIFAM protein-S-isoprenylcysteine O-methyltransferase NF040700.1 VPA1262_N_dom 80 80 478 domain Y Y N VPA1262 family N-terminal domain-containing protein 16672049 131567 cellular organisms no rank 1413 NCBIFAM VPA1262 family N-terminal domain The founding member VPA1262, of this domain family is a large protein of 1104 amino acids, found in a pathogenicity island of Vibrio parahaemolyticus RIMD 2210633. Many homologs of half that length share homology only to the N-terminal half. Members of the family share well-conserved DP[FY] and HDR motifs. The related model NF040699 describes full-length homologs of VPA1262. The function is unknown. NF040707.2 Siroheme_Dcarb_AhbB 200 200 153 equivalog Y Y N siroheme decarboxylase subunit beta ahbB 4.1.1.111 GO:0006783 21197080,24669201,24865947 131567 cellular organisms no rank 175 NCBIFAM siroheme decarboxylase subunit beta NF040708.2 Siroheme_Dcarb_AhbA 200 200 144 equivalog Y Y N siroheme decarboxylase subunit alpha ahbA 4.1.1.111 GO:0006783 21197080,24669201,24865947 131567 cellular organisms no rank 135 NCBIFAM siroheme decarboxylase subunit alpha NF040721.1 Trm14_Arch 280 280 370 equivalog Y Y N tRNA (guanine(6)-N2)-methyltransferase trm14 2.1.1.256 GO:0016423,GO:0030488 21693558 131567 cellular organisms no rank 30 NCBIFAM tRNA (guanine(6)-N2)-methyltransferase NF040764.1 CODH_ACS_al_bet 800 800 705 equivalog Y Y N acetyl-CoA decarbonylase/synthase complex subunit alpha/beta acsB 2.3.1.169 32967909,33101253 131567 cellular organisms no rank 933 NCBIFAM acetyl-CoA decarbonylase/synthase complex subunit alpha/beta Members of this family have both alpha and beta regions. Proteins scoring between 400 and 800 have only the C-terminal (beta) region. NF040770.1 hetero_SS_HdrA2 1100 1100 777 exception Y Y N CoB-CoM heterodisulfide reductase HdrA2 hdrA2 28174314 131567 cellular organisms no rank 175 NCBIFAM CoB-CoM heterodisulfide reductase HdrA2 HdrA2 represents a distinct subclass of the HdrA family, which is the A subunit of the CoB-CoM heterodisulfide reductase. HdrA2 from Methanosarcina acetivorans. A distinctive feature is a MvhD-like C-terminal domain, where MvhD is the signature delta subunit of the F420-non-reducing type of hydrogenase, Mvh. NF040772.1 double_cubane 350 350 372 equivalog Y Y N double-cubane-cluster-containing anaerobic reductase 29507223,32187824,36598231 131567 cellular organisms no rank 6374 NCBIFAM double-cubane-cluster-containing anaerobic reductase This subfamily of double-cubane proteins occurs strictly in anaerobes (facultative or obligate), such as Escherichia coli and Clostridium difficile. The enzyme always co-occurs with an accessory protein, an ATP-dependent activase. The cofactor contains a pair of 4Fe-4S cubane clusters, bridged by a sulfur atom, for an overall 8Fe-9S cofactor structure. However, we observe that that this family essentially always co-occurs in bacteria with SelD, the selenium donor protein required for biosynthesis of selenoproteins, selenouridine-modified tRNAs, selenium-dependent molybdenum hydroxylases, and selenoneine. NF040786.1 LysR_Sec_metab 250 250 298 equivalog Y Y N selenium metabolism-associated LysR family transcriptional regulator 25638258 131567 cellular organisms no rank 3892 NCBIFAM selenium metabolism-associated LysR family transcriptional regulator LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations. NF040815.2 recomb_XerA_Arch 220 220 263 equivalog Y Y N site-specific tyrosine recombinase/integron integrase xerA GO:0006313,GO:0008907,GO:0009037 20975945,23667562,36383678 131567 cellular organisms no rank 27371 NCBIFAM site-specific tyrosine recombinase/integron integrase Proteins of this family are site-specific tyrosine recombinases in Archaea. The recent study (PMID: 36383678) reported that they were the key components of archaeal integrons and were involved in cross-domain gene transfer. NF040817.1 GdhA_Arch 750 750 419 equivalog Y Y N glutamate dehydrogenase gdhA 1.4.1.3 GO:0004352,GO:0004354,GO:0006520 8060497,8406037 131567 cellular organisms no rank 102 NCBIFAM glutamate dehydrogenase NF040840.2 tungstate_WtpC 440 440 347 equivalog Y Y N tungstate ABC transporter ATP-binding protein WtpC wtpC 7.3.2.6 GO:1901238 16952940 131567 cellular organisms no rank 137 NCBIFAM tungstate ABC transporter ATP-binding protein WtpC NF040863.1 HgcA_corrinoid 275 275 325 equivalog Y Y N mercury methylation corrinoid protein HgcA hgcA GO:0042192 23393089,36598231 131567 cellular organisms no rank 357 NCBIFAM mercury methylation corrinoid protein HgcA HgcA and HgcB occur in a number of anaerobic bacteria and archaea, and are responsible for conversion of inorganic mercury to methylmercury, a highly toxic organomercurial compound. Most bacterial forms of HgcA are selenoproteins, with an N-terminal extension that has often been missed in structural annotation, featuring a CU (cysteine-selenocysteine) dipeptide motif. A minority of HgcB also are selenoproteins. NF040864.1 HgcB_ferredoxin 99 99 93 equivalog Y Y N mercury methylation ferredoxin HgcB hgcB GO:0042192 23393089,36598231 131567 cellular organisms no rank 345 NCBIFAM mercury methylation ferredoxin HgcB HgcA and HgcB occur in a number of anaerobic bacteria and archaea, and are responsible for conversion of inorganic mercury to methylmercury, a highly toxic organomercurial compound. A minority of HgcB are selenoproteins. So are the majority of bacterial forms of its partner HgcA are selenoproteins, with an N-terminal extension that has often been missed in structural annotation, featuring a CU (cysteine-selenocysteine) dipeptide motif. NF040865.1 a_tRNA_ed_AlaXM 300 300 234 equivalog Y Y N alanyl-tRNA editing protein AlaXM alaXM GO:0002161,GO:0006419 14663147,17327676,18723508 131567 cellular organisms no rank 222 NCBIFAM alanyl-tRNA editing protein AlaXM NF040867.1 prot_deacyl_CobB 320 320 242 equivalog Y Y N NAD-dependent protein deacetylase cobB 2.3.1.286 GO:0017136 11935028 131567 cellular organisms no rank 219 NCBIFAM NAD-dependent protein deacetylase NF040893.1 SAVMC3_10250 50 50 234 subfamily Y Y N SAVMC3_10250 family protein 131567 cellular organisms no rank 1600 NCBIFAM SAVMC3_10250 family protein NF040901.1 SeO3_TeO2_ExtH 200 200 430 equivalog Y Y N selenite/tellurite reduction operon rhodanese-like protein ExtH extH 29534491 131567 cellular organisms no rank 75 NCBIFAM selenite/tellurite reduction operon rhodanese-like protein ExtH NF040910.1 CD1375_fam 22.5 22.5 34 subfamily Y Y N CD1375 family protein 131567 cellular organisms no rank 2427 NCBIFAM CD1375 family phage-related protein Members of this family of usually small proteins are found typically in prophage regions of Gram-positive bacteria. NF040913.1 DsrE_rel_ELSE 152 152 125 equivalog Y Y N SaoD/DsrE family protein 131567 cellular organisms no rank 197 NCBIFAM SaoD/DsrE family protein Members of this family are closely related to SaoD (see NF040732), and both families are distantly related to DsrE. NF040955.1 Arch_DPS 250 250 177 equivalog Y Y N DNA protection during starvation protein dps 1.16.-.- GO:0004322,GO:0006880,GO:0008199,GO:0020037 16024730,16412514 131567 cellular organisms no rank 312 NCBIFAM DNA protection during starvation protein NF040962.1 near_HgcAB 70 70 70 equivalog Y Y N HgcAB-associated protein HgcC hgcC 36598231 131567 cellular organisms no rank 109 NCBIFAM HgcAB-associated protein HgcC Nearly have the members of this mostly archaeal protein family occur in species with methylmercury formation proteins HgcA and HgcB, encoded next to HgcA. While most HgcA proteins are selenoproteins (with many requiring corrections to structural annotation at the N-terminus to include the selenocysteine residue), examples of HgcA in the vicinity of this protein are not observed to be selenoproteins, and lack that N-terminal extension. This protein is here named HgcC. NF040973.1 restrict_Sau3AI 300 300 475 equivalog Y Y N Sau3AI family type II restriction endonuclease 131567 cellular organisms no rank 2590 NCBIFAM Sau3AI family type II restriction endonuclease Members of this family include type II restriction enzymes such as Sau3AI, while excluding proteins more closely related to the DNA repair protein MutH. Both Sau3AI and MutH endonucleases act on GATC sequences. NF041004.1 Beta_gal_BgaS 475 475 479 equivalog Y Y N beta-galactosidase BgaS bgaS 3.2.1.23 GO:0004565,GO:0005975 2508066 131567 cellular organisms no rank 193 NCBIFAM beta-galactosidase BgaS NF041018.1 glyceraldDH_alpha 790 790 741 equivalog Y Y N glyceraldehyde dehydrogenase subunit alpha cutA 1.2.99.8 GO:0005506,GO:0016903,GO:0043795 10095793 131567 cellular organisms no rank 170 NCBIFAM glyceraldehyde dehydrogenase subunit alpha NF041025.1 antiphage_deaminase 400 400 437 equivalog Y Y N anti-phage dCTP deaminase GO:0019239 35817891 131567 cellular organisms no rank 2426 NCBIFAM anti-phage dCTP deaminase It has been shown that proteins of this family prevented bacteria from phage infections by depleting deoxycytidine triphosphate (dCTP), which are important for the replication of viruses. The anti-phage dCTP deaminases have an N-terminal kinase and a C-terminal dCTP deaminase domains, however, the housekeeping dCTP deaminases usually do not have the N-terminal kinase. NF041046.1 UGSC_fam 125 125 147 equivalog Y Y N UGSC family (seleno)protein 131567 cellular organisms no rank 902 NCBIFAM UGSC family (seleno)protein This family includes selenoprotein members with a UGSC motif, and non-selenoprotein members with a CGSC motif. Selenoprotein members were discussed in Zhang, et al., "Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective" (2022). NF041052.1 OsmC_like_Se 95 95 144 domain Y Y N OsmC-related (seleno)protein 35883471 131567 cellular organisms no rank 354 NCBIFAM OsmC-related (seleno)protein Members of this family are distantly related to the hydroperoxide resistance protein OsmC (osmotically inducible protein) of Escherichia. Proteins found by the HMM include large numbers of selenoproteins, most of which currently are known only from Metagenome-Assembled Genomes (MAGs) of uncultured organisms, a large fraction of which are assigned to the Chloroflexi. NF041059.1 DpdA 200 200 406 equivalog Y Y N tRNA-guanine transglycosylase DpdA dpdA GO:0006400,GO:0016757 26929322,30159947 131567 cellular organisms no rank 1463 NCBIFAM tRNA-guanine transglycosylase DpdA NF041082.2 thermosome_alpha 450 450 519 equivalog Y Y N thermosome subunit alpha thsA GO:0016887,GO:0140662 10508614,7867646,9023959 131567 cellular organisms no rank 3543 NCBIFAM thermosome subunit alpha NF041083.2 thermosome_beta 400 400 520 equivalog Y Y N thermosome subunit beta thsB GO:0016887,GO:0140662 10508614,7867646,9023959 131567 cellular organisms no rank 3586 NCBIFAM thermosome subunit beta NF041095.1 dival_cat_tol_CutA 120 120 100 equivalog Y Y N divalent-cation tolerance protein CutA cutA GO:0005507,GO:0010038 14705033 131567 cellular organisms no rank 168 NCBIFAM divalent-cation tolerance protein CutA NF041097.1 keto_inos_dh_IolM 450 450 389 equivalog Y Y N scyllo-inosose 3-dehydrogenase iolM 1.1.1.- GO:0006020,GO:0016491 23441918 131567 cellular organisms no rank 218 NCBIFAM scyllo-inosose 3-dehydrogenase NF041098.2 diketo_inos_hlase_IolN 245 245 307 equivalog Y Y N 3-dehydro-scyllo-inosose hydrolase iolN 3.7.1.- GO:0006020,GO:0016491 23441918 131567 cellular organisms no rank 176 NCBIFAM 3-dehydro-scyllo-inosose hydrolase NF041109.1 VF_TspB_C_term 24 24 51 domain Y Y N virulence factor TspB C-terminal domain-related protein 131567 cellular organisms no rank 4544 NCBIFAM virulence factor TspB C-terminus-like domain Members of this family share a C-terminal domain, perhaps a surface-anchoring domain, with T and B Cell Stimulating Protein B (TspB) of Neisseria meningitidis, an IgG-binding protein that helps confer serum resistance. This short domain (51 residues long) contains two invariant Cys residues and an apparent C-terminal transmembrane segment, suggesting a role in anchoring to the surface of the outer membrane. Member proteins often are found in prophage regions. NF041117.1 CBASS_cyclase_b 200 200 275 equivalog Y Y N CBASS oligonucleotide cyclase GO:0016779 30787435,31533127,32839535 131567 cellular organisms no rank 744 NCBIFAM CBASS oligonucleotide cyclase NF041123.1 phpantohe_syn_Arch 300 300 213 equivalog Y Y N 4-phosphopantoate--beta-alanine ligase 6.3.2.36 GO:0015937,GO:0016881 18422645,19666462,22940806,23200110 131567 cellular organisms no rank 1214 NCBIFAM 4-phosphopantoate--beta-alanine ligase NF041126.1 FBP_aldo_phos 520 520 356 equivalog Y Y N fructose-1,6-bisphosphate aldolase/phosphatase fbp 3.1.3.11,4.1.2.13 GO:0004332,GO:0006094,GO:0042132 15317785,20348906 131567 cellular organisms no rank 884 NCBIFAM fructose-1,6-bisphosphate aldolase/phosphatase NF041129.1 maldex_phorlase_Thcocales 1500 1500 816 equivalog Y Y N maltodextrin phosphorylase malP 2.4.1.1 GO:0000023,GO:0004645,GO:0008184 10348846 131567 cellular organisms no rank 106 NCBIFAM maltodextrin phosphorylase NF041135.1 IPPtranDIPPsyn_Thcocales 580 580 419 equivalog Y Y N bifunctional L-myo-inositol-1-phosphate cytidylyltransferase/CDP-L-myo-inositol myo-inositolphosphotransferase 2.7.7.74,2.7.8.34 GO:0008654,GO:0016779,GO:0016780 17526717 131567 cellular organisms no rank 115 NCBIFAM bifunctional L-myo-inositol-1-phosphate cytidylyltransferase/CDP-L-myo-inositol myo-inositolphosphotransferase NF041155.2 encap_f1 100 100 261 equivalog Y Y N family 1 encapsulin nanocompartment shell protein GO:0140737 25024436,34362927,35146412 131567 cellular organisms no rank 6372 NCBIFAM family 1 encapsulin nanocompartment shell protein Capsid-like encapsulin nanocompartments are commonly found in bacteria and archaea. Encapsulin nanocompartments, which are assembled from shell proteins, encapsulate various cargo proteins, typically peroxidases or ferritin-like proteins, to protect cells from oxidative stress caused by peroxide. NF041170.1 Oxoac_fdxalpha_Archa 800 800 636 equivalog Y Y N 2-oxoacid:ferredoxin oxidoreductase subunit alpha 1.2.7.11 GO:0018491,GO:0019164,GO:0047553 15848165,16466637,27619895,8902625 131567 cellular organisms no rank 206 NCBIFAM 2-oxoacid:ferredoxin oxidoreductase subunit alpha NF041171.1 Oxoac_fdxbeta_Archa 423 423 296 equivalog Y Y N 2-oxoacid:ferredoxin oxidoreductase subunit beta 1.2.7.11 GO:0018491,GO:0019164,GO:0047553 15848165,16466637,27619895,8902625 131567 cellular organisms no rank 199 NCBIFAM 2-oxoacid:ferredoxin oxidoreductase subunit beta NF041175.1 RNAseHI_Thmprot 140 140 143 equivalog Y Y N ribonuclease HI rnhA 3.1.26.4 GO:0003677,GO:0003723,GO:0004523 15520465,21283826 131567 cellular organisms no rank 87 NCBIFAM ribonuclease HI NF041212.1 Uxx_star 66 66 70 subfamily Y Y N Uxx-star family glutaredoxin-like (seleno)protein 131567 cellular organisms no rank 248 NCBIFAM Uxx-star family glutaredoxin-like (seleno)protein A number of proteins with glutaredoxin-like folds, a length of about 75 amino acids, and a CxxC, C/UxxT, or CxxS motif near the N-terminus end with a UXX-COOH motif. That final motif typically is missed during coding region feature prediction by genome annotation pipelines. This HMM covers proteins from several distinctive families with this feature. The seed alignment illustrates the final selenocysteine or aligned Cys or Ser residues, but the HMM also hits proteins that lack an equivalent motif at the C-terminus. This C-terminal selenocysteine-containing motif has not yet been described in the literature. NF041216.1 CU044_2847_fam 23 23 91 subfamily Y Y N CU044_2847 family protein 131567 cellular organisms no rank 13595 NCBIFAM CU044_2847 family protein NF041257.1 GntH_guanitoxin 333 333 374 equivalog Y Y N guanitoxin biosynthesis MBL fold metallo-hydrolase GntH gntH 35583956 131567 cellular organisms no rank 643 NCBIFAM guanitoxin biosynthesis MBL fold metallo-hydrolase GntH Guanitoxin, an organophosphate, is a highly toxin cholinesterase inhibitor produced by some cyanobacteria. It was renamed from anatoxin-a(S) to avoid confusion with a structurally unrelated toxin. GntH, a member MBL (metallo-beta-lactamase) fold family of metallo-hydrolases, shares over 30 percent amino acid sequence identity with PNGM-1, cloned from an uncultured bacterium and reported to have both beta-lactamase and tRNAse activities. NF041302.1 HMG_CoAsyn_Halo 800 800 443 equivalog Y Y N hydroxymethylglutaryl-CoA synthase hmgB 2.3.3.10 GO:0004421,GO:0010142 23794621 131567 cellular organisms no rank 590 NCBIFAM hydroxymethylglutaryl-CoA synthase NF041359.1 GntG_guanitoxin 230 230 343 subfamily Y Y N GntG family PLP-dependent aldolase 35583956 131567 cellular organisms no rank 28541 NCBIFAM GntG family PLP-dependent aldolase NF041364.1 GntC_guanitoxin 415 415 356 equivalog Y Y N guanitoxin biosynthesis PLP-dependent (S)-gamma-hydroxy-L-arginine cyclodehydratase GntC gntC 35583956 131567 cellular organisms no rank 36 NCBIFAM guanitoxin biosynthesis PLP-dependent (S)-gamma-hydroxy-L-arginine cyclodehydratase GntC NF041373.1 HGG_STG 29 29 38 domain Y Y N HGGxSTG domain-containing protein 131567 cellular organisms no rank 3142 NCBIFAM HGGxSTG domain NF041374.1 GDCCVxC 40 40 58 domain Y Y N GDCCVxC domain-containing (seleno)protein 35883471 131567 cellular organisms no rank 5046 NCBIFAM GDCCVxC domain NF041388.1 DNAstvprot_Halo 170 170 171 equivalog Y Y N DNA starvation/stationary phase protection protein DpsA dpsA 1.16.-.- 12147354,15365182 131567 cellular organisms no rank 815 NCBIFAM DNA starvation/stationary phase protection protein DpsA NF041393.1 Frdxn_Halo 150 150 128 equivalog Y Y N ferredoxin Fer fer GO:0051537 7378468,8510664,8612076 131567 cellular organisms no rank 1107 NCBIFAM ferredoxin Fer NF041496.1 MobQ 200 200 197 equivalog Y Y N MobQ family relaxase mobQ 31584171 131567 cellular organisms no rank 20436 NCBIFAM MobQ family relaxase NF041518.1 choice_anch_Q 25 23 58 domain Y Y N choice-of-anchor Q domain-containing protein 131567 cellular organisms no rank 14745 NCBIFAM choice-of-anchor Q domain NF041523.1 post_COAP_1 40 40 115 domain Y Y N post-COAP-1 domain-containing protein 131567 cellular organisms no rank 118 NCBIFAM post-COAP-1 domain Post-COAP-1 was identified as a C-terminal domain, about 115 amino acids in length, found in a subset of proteins with the choice-of-anchor P (COAP) domain (see NF040603). This domain is seen primarily in non-cultured prokaryotes with a broad taxonomic bacteria and archaea. NF041539.1 choice_anch_R 30 30 155 domain Y Y N choice-of-anchor R domain-containing protein 131567 cellular organisms no rank 605 NCBIFAM choice-of-anchor R domain The most frequent C-terminal anchoring domain for members of this family is PEP-CTERM (see TIGR02595) or a PEP-CTERM-related variant sorting signal domain processed by one of the specialty exosortases. Some member proteins are found instead with dockerin-like C-terminal repeats and a GC motif at the extreme C-terminus. The GC-type dockerin domain occurs, so far, primarily in metagenome-assembled genomes from the taxonomic class Phycisphaerae, within the Planctomycetota, where it seems to anchor a number of otherwise unrelated proteins. NF041540.1 dockerin_GC 29 29 67 domain Y Y N GC-type dockerin domain-anchored protein 131567 cellular organisms no rank 43 NCBIFAM GC-type dockerin-like domain This domain begins and ends with a near invariant C, and GC, respectively. It occurs strictly at the C-terminus of proteins, and those protein are found almost exclusively in metagenome-assembled genomes of the taxonomic class Phycisphaerae, within the Planctomycetota. It shows apparent sequence homology to the type I dockerin domain (see PF00404), which likewise contains an internal repeat and which appears in strictly C-terminal positions of otherwise unrelated proteins. Type I dockerin domains occur in proteins that are organized by interaction with the cohesin domain (PF00963) in order to form the cellulosome. However, the GC-type dockerin domain described here is uncharacterized, and cohesin domains identifiable by PF00963 are not found in the same proteomes. NF041548.1 PssE 120 120 146 equivalog Y Y N PssE/Cps14G family polysaccharide biosynthesis glycosyltransferase pssE GO:0016740 9235953,9383197,9383201 131567 cellular organisms no rank 1260 NCBIFAM PssE/Cps14G family polysaccharide biosynthesis glycosyltransferase NF041549.1 PssD 110 110 151 equivalog Y Y N PssD/Cps14F family polysaccharide biosynthesis glycosyltransferase pssD GO:0016740 9235953,9383197,9383201 131567 cellular organisms no rank 2467 NCBIFAM PssD/Cps14F family polysaccharide biosynthesis glycosyltransferase NF041555.1 tannase_A 550 550 619 equivalog Y Y N subtype A tannase GO:0050318 30460533 131567 cellular organisms no rank 579 NCBIFAM subtype A tannase NF041591.1 CxxC_VVA0879 37 37 101 subfamily Y Y N VVA0879 family protein 131567 cellular organisms no rank 509 NCBIFAM VVA0879 family protein Members of this rare but broadly distributed family average about 120 amino acids in length, including an apparent redox-active disulfide motif CxxC and two other invariant Cys residues. The family is named for VVA0879 from Vibrio vulnificus but occurs also in Gram-positive species such as Clostridium botulinum. NF041612.1 fdxn_Clost 150 150 102 equivalog Y Y N 2Fe-2S ferredoxin GO:0046872,GO:0051537 7916603,8334159 131567 cellular organisms no rank 232 NCBIFAM 2Fe-2S ferredoxin NF041622.1 KwaA 100 100 182 equivalog Y Y N anti-phage protein KwaA kwaA 29371424,35538097 131567 cellular organisms no rank 795 NCBIFAM anti-phage protein KwaA NF041623.1 KwaB 200 200 306 equivalog Y Y N anti-phage protein KwaB kwaB 29371424,35538097 131567 cellular organisms no rank 558 NCBIFAM anti-phage protein KwaB NF041635.1 STM3941_fam 40 40 157 subfamily Y Y N STM3941 family protein 131567 cellular organisms no rank 4759 NCBIFAM STM3941 family protein NF041646.1 VC0807_fam 65 65 189 subfamily Y Y N VC0807 family protein 131567 cellular organisms no rank 13920 NCBIFAM VC0807 family protein Members of this broadly distributed bacterial protein family are hydrophobic in nature, and apparently homologous to members of the DUF3159 (PF11361) family. NF041656.1 CPBP_MmRce1 425 425 271 equivalog Y Y N MmRce1 family CPBP family CAAX prenyl protease mmrce1 3.4.26.- GO:0006605,GO:0070007 24291792 131567 cellular organisms no rank 72 NCBIFAM MmRce1 family CPBP family CAAX prenyl protease MmRce1, an archaeal member of the same family CPBP integral membrane glutamic-type protease as the eukaryotic type II CAAX prenyl endopeptidase Rce1 (Ras and a-factor converting enzyme 1), was crystalized and studied to gain insights into Rce1 function. It was shown to act as an endopeptidase on the eukaryotic protein-derived synthetic substrate ARSGAKASGCLVS, only if Cys residue is farnesylated. This model substrate ends with a CAAX motif (Cys-Aliphatic-Aliphatic-Anything). NF041664.1 RNAP_arch_Epp 50 50 57 equivalog Y Y N transcription elongation factor subunit Spt4 spt4 2.7.7.6 GO:0003711,GO:0006355 21386817,28248297 131567 cellular organisms no rank 1000 NCBIFAM archaeal transcription elongation factor subunit Spt4 Spt4, an archaeal zinc-binding protein, averaging about 64 amino acids in length, forms a heterodimer with Spt5. The Spt4/5 heterodimer is now considered a transcription elongation factor, responsible for making the archaeal DNA-directed RNA polymerase (RNAP) processive. Previously, Spt4 was treated as a part of the RNAP itself and was designated subnit E''. NF041731.1 transpos_ISH6 700 700 444 equivalog Y Y N ISH6 family transposase GO:0004803 16381877 131567 cellular organisms no rank 72 NCBIFAM ISH6 family transposase NF041755.1 RuMP_HxlAB 500 500 391 equivalog Y Y N bifunctional 3-hexulose-6-phosphate synthase/6-phospho-3-hexuloisomerase hxlAB 4.1.2.43,5.3.1.27 GO:0016853,GO:0043801,GO:1901135 16788179,17520247 131567 cellular organisms no rank 125 NCBIFAM bifunctional 3-hexulose-6-phosphate synthase/6-phospho-3-hexuloisomerase NF041766.1 choice_anch_U 32 32 92 domain Y Y N choice-of-anchor U domain-containing protein 131567 cellular organisms no rank 4773 NCBIFAM choice-of-anchor U domain NF041770.1 CFI_box_CTERM 40 40 69 domain Y Y N CFI-box-CTERM domain-containing protein 131567 cellular organisms no rank 2896 NCBIFAM CFI-box-CTERM domain The prokaryotic CFI-box motif was shown in model NF041763 to be a probable protein modification site, first modified on the Cys sidechain and then, most likely cleaved in a manner resembling the CAAX box in eukaryotes. At least 12 otherwise unrelated proteins in Desulfatibacillum aliphaticivorans strain AK-01 (CP001322.1) share the motif at or close to the C-terminal. ACL06505.1 has the CFI motif as the start of a longer tail region. This HMM models that CFI-box-containing tail region. This long form, of the CFI putative sorting signal, in which the CFI motif occurs at the start of a longer homology domain, is here designated the CFI-box-CTERM domain. NF041799.1 Hsp14 100 100 118 equivalog Y Y N archaeal heat shock protein Hsp14 hsp14 GO:0042026 34637594,35647036 131567 cellular organisms no rank 242 NCBIFAM archaeal heat shock protein Hsp14 NF041800.1 Hsp20 140 140 162 equivalog Y Y N archaeal heat shock protein Hsp20 hsp20 GO:0042026 30293966,35647036 131567 cellular organisms no rank 358 NCBIFAM archaeal heat shock protein Hsp20 NF041813.1 Avs2 1000 1000 1317 equivalog Y Y N AVAST type 2 anti-phage system protein Avs2 avs2 32855333 131567 cellular organisms no rank 476 NCBIFAM AVAST type 2 anti-phage system protein Avs2 NF041815.1 Avs4 1500 1500 1579 equivalog Y Y N AVAST type 4 anti-phage nuclease Avs4 avs4 32855333 131567 cellular organisms no rank 509 NCBIFAM AVAST type 4 anti-phage nuclease Avs4 NF041818.1 Dsr1 1400 1400 1263 equivalog Y Y N anti-phage defense-associated sirtuin Dsr1 dsr1 32855333 131567 cellular organisms no rank 741 NCBIFAM anti-phage defense-associated sirtuin Dsr1 NF041833.1 Fe_ADH_ErcA 550 550 382 equivalog Y Y N alcohol dehydrogenase-like regulatory protein ErcA ercA 23813731 131567 cellular organisms no rank 1786 NCBIFAM alcohol dehydrogenase-like regulatory protein ErcA Homology suggests this protein, designated ErcA, is an iron-containing alcohol dehydrogenase. It is encoded next to a histidine kinase, and its disruption leads to a defect in ethanol oxidation, suggesting a regulatory rather than a catabolic role. NF041874.1 EPS_EpsC 150 150 168 equivalog Y Y N serine O-acetyltransferase EpsC epsC GO:0006535,GO:0009001 32778557 131567 cellular organisms no rank 50010 NCBIFAM serine O-acetyltransferase EpsC NF041895.1 choice_anch_V 42 42 150 domain Y Y N choice-of-anchor V domain-containing protein 131567 cellular organisms no rank 603 NCBIFAM choice-of-anchor V domain This bacterial domain of about 150 amino acids in length is found typically immediately after the signal peptide in proteins with C-terminal sorting signals, mostly the MYXO-CTERM (as in MXAN_6652 and its equivalogs) or T9SS type A sorting domains. NF041908.1 HVO_2922 90 90 54 equivalog Y Y N HVO_2922 family protein 31161645 131567 cellular organisms no rank 600 NCBIFAM HVO_2922 family protein Short proteins of this family are differentially expressed in response to environmental stresses, such as changes in iron and salt concentrations. These proteins contain the DUF1508 domain of unknown function and are conserved among Haloarchaea and related archaeal species. NF041918.1 SAMP1 60 60 91 equivalog Y Y N ubiquitin-like small modifier protein 1 GO:0008641 20054389,21216237 131567 cellular organisms no rank 3569 NCBIFAM ubiquitin-like small modifier protein 1 NF041920.1 DmpI 70 70 59 equivalog Y Y N 4-oxalocrotonate tautomerase DmpI dmpI GO:0008152,GO:0016853 20709352 131567 cellular organisms no rank 1541 NCBIFAM 4-oxalocrotonate tautomerase DmpI Proteins of this family are 4-oxalocrotonate tautomerases of the tautomerase subfamily 3 and subfamily 4. The crystal structure of DmpI from Helicobacter pylori (HpDmpI) and Archaeoglobus fulgidus (AfDmpI) have been characterized. NF041928.1 choice_anch_W 45 45 196 domain Y Y N choice-of-anchor W domain-containing protein 131567 cellular organisms no rank 312 NCBIFAM choice-of-anchor W domain The great majority of proteins in the seed alignment are PEP-CTERM proteins, that is, proteins thought to be sorted to the cell surface in an exosortase-dependent process. Some members of the seed alignment instead have a possible alternative anchoring sequence with a TWGxxK motif near the C-terminus. A few members of the broader family have additional domains and a C-terminal LPXTG (sortase-dependent) sorting signal, or other unusual C-terminal regions whose significance is not yet clear. NF041940.1 choice_anch_X 25 25 37 domain Y Y N choice-of-anchor X domain-containing protein 131567 cellular organisms no rank 4161 NCBIFAM choice-of-anchor X domain Members of this domain family are highly variable in architecture, and found in both prokaryotes and eukaryotes. Prokaryotic members include proteins with C-terminal sorting signals for processing by rhombosortases and myxosortases and eventual surface attachment. Eukaryotic member proteins include human calcium-activated chloride channel regulator 4. NF042448.3 PF20168.3 PDS5 27 27 1053 hypoth_equivalog Y Y N sister chromatid cohesion protein PDS5 26923598 131567 cellular organisms no rank 248 EBI-EMBL Sister chromatid cohesion protein PDS5 protein sister chromatid cohesion protein PDS5 This entry represents the Sister chromatid cohesion protein PDS5. The large PDS5 molecule is exclusively alpha helical, composed of a large number of HEAT-like repeats and helical extensions/additions that deviate from the HEAT repeat pattern [1]. Paper describing PDB structure 5f0n. [1]. 26923598. Crystal Structure of the Cohesin Gatekeeper Pds5 and in Complex with Kleisin Scc1. Lee BG, Roig MB, Jansma M, Petela N, Metson J, Nasmyth K, Lowe J;. Cell Rep. 2016;14:2108-2115. (from Pfam) NF042458.3 PF20212.3 DUF6572 27 27 106 domain Y Y N DUF6572 domain-containing protein 21173271 131567 cellular organisms no rank 2486 EBI-EMBL Family of unknown function (DUF6572) DUF6572 domain This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 107 and 214 amino acids in length. These proteins may have a threefold symmetric beta-trefoil fold, a symmetric protein structure thought to be conserved in protein evolution [1]. Paper describing PDB structure 3o4c. [1]. 21173271. Experimental support for the evolution of symmetric protein architecture from a simple peptide motif. Lee J, Blaber M;. Proc Natl Acad Sci U S A. 2011;108:126-130. (from Pfam) NF042459.3 PF20213.3 DUF6573 27 27 138 subfamily Y Y N DUF6573 family protein 131567 cellular organisms no rank 1353 EBI-EMBL Family of unknown function (DUF6573) DUF6573 family protein This family of proteins is functionally uncharacterised. This family of proteins is mainly found in Proteobacteria. Proteins in this family are approximately 130 amino acids in length. (from Pfam) NF042460.3 PF20220.3 ABC_toxin_N 27 27 122 domain Y Y N neuraminidase-like domain-containing protein 31028251 131567 cellular organisms no rank 6364 EBI-EMBL ABC toxin N-terminal region ABC toxin N-terminal This entry represents the region found N-terminal to the neuraminidase domain in the pore forming ABC toxins [1]. Paper describing PDB structure 6ogd. [1]. 31028251. Cryo-EM structures of the pore-forming A subunit from the Yersinia entomophaga ABC toxin. Piper SJ, Brillault L, Rothnagel R, Croll TI, Box JK, Chassagnon I, Scherer S, Goldie KN, Jones SA, Schepers F, Hartley-Tassell L, Ve T, Busby JN, Dalziel JE, Lott JS, Hankamer B, Stahlberg H, Hurst MRH, Landsberg MJ;. Nat Commun. 2019;10:1952. (from Pfam) NF042461.3 PF20221.3 DUF6580 27 27 162 domain Y Y N DUF6580 family putative transport protein 131567 cellular organisms no rank 2921 EBI-EMBL Family of unknown function (DUF6580) DUF6580 family putative transport protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 200 amino acids in length. Some members are hypothetical ECF transporters related to the Gx transporter superfamily (CL0315). (from Pfam) NF042466.3 PF20258.3 tRNA_Me_trans_C 20.6 20.6 77 domain Y Y N aminomethyltransferase beta-barrel domain-containing protein 3298234 131567 cellular organisms no rank 74676 EBI-EMBL Aminomethyltransferase beta-barrel domain aminomethyltransferase beta-barrel domain-containing protein This domain is found at the C-terminus of tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs [1]. [1]. 3298234. Transfer RNA(5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities. Hagervall TG, Edmonds CG, McCloskey JA, Bjork GR;. J Biol Chem 1987;262:8488-8495. (from Pfam) NF042467.3 PF20259.3 tRNA_Me_trans_M 27 27 66 domain Y Y N tRNA methyl transferase PRC-barrel domain-containing protein 3298234 131567 cellular organisms no rank 74876 EBI-EMBL tRNA methyl transferase PRC-barrel domain tRNA methyl transferase PRC-barrel domain-containing protein This family represents a central PRC-barrel domain in tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs [1]. [1]. 3298234. Transfer RNA(5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities. Hagervall TG, Edmonds CG, McCloskey JA, Bjork GR;. J Biol Chem 1987;262:8488-8495. (from Pfam) NF042471.3 PF20277.3 CTD11 27.7 27.7 138 equivalog_domain Y Y N ABC-three component system protein 32894288 131567 cellular organisms no rank 1308 EBI-EMBL C-terminal domain 11 of the ABC-three component (ABC-3C) systems ABC-three component system protein C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector [1]. [1]. 32894288. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. Nucleic Acids Res. 2020;48:10045-10075. (from Pfam) NF042474.3 PF20288.3 MC2 26.9 26.9 145 equivalog_domain Y Y N ABC-three component system middle component 2 32894288 131567 cellular organisms no rank 2965 EBI-EMBL ABC-three component (ABC-3C) system Middle Component 2 ABC-three component (ABC-3C) system middle component 2 Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses [1]. [1]. 32894288. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. Nucleic Acids Res. 2020;48:10045-10075. (from Pfam) NF042476.3 PF20292.3 MC7 27 27 69 equivalog_domain Y Y N ABC-three component system middle component 7 32894288 131567 cellular organisms no rank 940 EBI-EMBL ABC-three component (ABC-3C) system Middle Component 7 ABC-three component system middle component 7 Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses. MC7 is a MC unifiable with the HTH fold [1]. [1]. 32894288. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. Nucleic Acids Res. 2020;48:10045-10075. (from Pfam) NF042477.3 PF20293.3 MC6 27.2 27.2 76 equivalog_domain Y Y N ABC-three component system middle component 6 32894288 131567 cellular organisms no rank 2854 EBI-EMBL ABC-three component (ABC-3C) system Middle Component 6 ABC-three component system middle component 6 Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses. MC6 is a MC unifiable with the HTH fold [1]. [1]. 32894288. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. Nucleic Acids Res. 2020;48:10045-10075. (from Pfam) NF042478.3 PF20314.3 DUF6610 27 27 198 subfamily Y Y N DUF6610 family protein 131567 cellular organisms no rank 450 EBI-EMBL Family of unknown function (DUF6610) DUF6610 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 304 and 335 amino acids in length. (from Pfam) NF042481.3 PF20328.3 DUF6623 27 27 149 subfamily Y Y N DUF6623 family protein 131567 cellular organisms no rank 163 EBI-EMBL Family of unknown function (DUF6623) DUF6623 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 147 and 199 amino acids in length. (from Pfam) NF042490.3 PF20355.3 DUF6650 27 27 150 subfamily Y Y N DUF6650 family protein 131567 cellular organisms no rank 517 EBI-EMBL Family of unknown function (DUF6650) DUF6650 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 150 and 175 amino acids in length. (from Pfam) NF042492.3 PF20358.3 DUF6653 27 27 170 subfamily Y Y N DUF6653 family protein 131567 cellular organisms no rank 2172 EBI-EMBL Family of unknown function (DUF6653) DUF6653 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 149 and 172 amino acids in length. (from Pfam) NF042511.3 PF20181.3 DUF6544 25 25 221 subfamily Y Y N DUF6544 family protein 131567 cellular organisms no rank 3791 EBI-EMBL Family of unknown function (DUF6544) DUF6544 family protein This entry represents a set of uncharacterised proteins found in bacteria. They share remote similarity to LolA, LolB outer-membrane lipoproteins. (from Pfam) NF042516.3 PF20202.3 DUF6564 25 25 230 domain Y Y N DUF6564 domain-containing protein 131567 cellular organisms no rank 877 EBI-EMBL Domain of unknown function (DUF6564) DUF6564 domain This domain is functionally uncharacterised and is found in proteins from bacteria and archaea. This domain is found in Protein LicC (swiss:P14183), a CTP:phosphocholine cytidylyltransferase involved in LPS biosynthesis. Members containing this domain are annotated as nucleotidyltransferases. It is probable that this domain has a Rossmann like fold. (from Pfam) NF042524.3 PF20229.3 ChrB_N 23 23 159 domain Y Y N Chromate resistance protein ChrB 12471500,2180932,24223748 131567 cellular organisms no rank 6878 EBI-EMBL Protein ChrB, N-terminal Chromate resistance protein ChrB N-terminal This is the N-terminal domain found in Chromate resistance protein ChrB, a protein involved in the reduction of chromate accumulation and are essential for chromate resistance [1,2]. This domain may be involved in DNA binding and contains two highly conserved arginine residues important for its function [3]. [1]. 12471500. New genes involved in chromate resistance in Ralstonia metallidurans strain CH34. Juhnke S, Peitzsch N, Hubener N, Grosse C, Nies DH;. Arch Microbiol. 2002;179:15-25. [2]. 2180932. Nucleotide sequence and expression of a plasmid-encoded chromate resistance determinant from Alcaligenes eutrophus. Nies A, Nies DH, Silver S;. J Biol Chem. 1990;265:5648-5653. [3]. 24223748. Identification and characterization of the transcriptional regulator ChrB in the chromate resistance determinant of Ochrobactrum tritici 5bvl1. Branco R, Morais PV;. PLoS One. 2013;8:e77987. (from Pfam) NF042530.3 PF20239.3 DUF6596 27 27 102 domain Y Y N DUF6596 domain-containing protein 131567 cellular organisms no rank 72774 EBI-EMBL Family of unknown function (DUF6596) DUF6596 domain-containing protein This presumed domain is found at the C-terminus of bacterial RNA polymerase ECF sigma factor proteins. (from Pfam) NF042532.3 PF20242.3 Emfourin 27 27 91 equivalog Y Y N protealysin inhibitor emfourin 33385454 131567 cellular organisms no rank 10995 EBI-EMBL Emfourin protealysin inhibitor emfourin This family represents a protealysin inhibitor called Emfourin, after M4 family inhibitor (M4in), as protealysin is a metallo- endopeptidase from MEROPS peptidase family M4 [1]. Emfourin is a potent inhibitor that forms a 1:1 stoichiometry complex with protealysin. [1]. 33385454. The protealysin operon encodes emfourin, a prototype of a novel family of protein metalloprotease inhibitors. Chukhontseva KN, Berdyshev IM, Safina DR, Karaseva MA, Bozin TN, Salnikov VV, Konarev PV, Volkov VV, Grishin AV, Kozlovskiy VI, Kostrov SV, Demidyuk IV;. Int J Biol Macromol. 2021;169:583-596. (from Pfam) NF042533.3 PF20251.3 Big_14 27 27 104 domain Y Y N immunoglobulin-like domain-containing protein 131567 cellular organisms no rank 3563 EBI-EMBL Bacterial Ig-like domain Ig-like domain This bacterial Ig-like domain shows some similarity to Pfam:PF12690 suggesting it may act as a protease inhibitor similar to B. subtilis BsuPI. (from Pfam) NF042538.3 PF20282.3 CTD6 26.4 26.4 130 equivalog_domain Y Y N ABC-three component system protein 32894288 131567 cellular organisms no rank 3011 EBI-EMBL C-terminal domain 6 of the ABC-three component (ABC-3C) systems ABC-three component (ABC-3C) system C-terminal domain 6 C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector [1]. [1]. 32894288. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. Nucleic Acids Res. 2020;48:10045-10075. (from Pfam) NF042539.3 PF20296.3 MTaX1 25 25 111 domain Y N N Methylase-associated X1 32894288 131567 cellular organisms no rank 916 EBI-EMBL Methylase-associated X1 Methylase-associated X1 This is a globular domain found across several restriction- modification systems [1]. [1]. 32894288. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. Nucleic Acids Res. 2020;48:10045-10075. (from Pfam) NF042542.3 PF20304.3 Sp-CxC 27.5 27.5 63 hypoth_equivalog Y Y N CxC ATPase DNA modification system associated small protein 32894288 131567 cellular organisms no rank 138 EBI-EMBL Small protein from certain CxC ATPase-based DNA modification systems CxC ATPase DNA modification system associated small protein Analogous to an antitoxin, this small protein potentially acts as a negative regulatory component that might sense the presence of invaders by acting as a binding factor or substrate for invader-encoded enzymes like viral peptidases in certain CxC ABC ATPase-based DNA modification systems [1]. [1]. 32894288. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. Nucleic Acids Res. 2020;48:10045-10075. (from Pfam) NF042543.3 PF20306.3 Sp-DndD 27.2 27.2 51 equivalog Y Y N DNA modification system-associated small protein 32894288 131567 cellular organisms no rank 611 EBI-EMBL Small protein found in certain Dnd DNA modification systems DNA modification system-associated small protein Analogous to an antitoxin, this small protein potentially acts as a negative regulatory component that might sense the presence of invaders by acting as a binding factor or substrate for invader-encoded enzymes like viral peptidases in certain Dnd systems [1]. [1]. 32894288. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. Nucleic Acids Res. 2020;48:10045-10075. (from Pfam) NF042547.3 PF20320.3 DUF6615 23.8 23.8 289 subfamily Y Y N DUF6615 family protein 131567 cellular organisms no rank 1150 EBI-EMBL Family of unknown function (DUF6615) DUF6615 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 301 and 317 amino acids in length. These proteins contain a conserved sequence motif FREE that may be functionally important. (from Pfam) NF042557.3 PF20369.3 DUF6664 27 27 105 subfamily Y Y N DUF6664 family protein 131567 cellular organisms no rank 359 EBI-EMBL Family of unknown function (DUF6664) DUF6664 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. (from Pfam) NF042572.3 PF20446.3 ABC_N 26.5 26.5 162 domain Y Y N ABC-ATPase domain-containing protein 26117548 131567 cellular organisms no rank 7685 EBI-EMBL ATPase of the ABC class N-terminal ABC-ATPase N-terminal This is the N-terminal domain of various bacterial predicted ABC class ATPases which shows sequence and structural similarities to the N-terminal domain of MRB1590 (swiss:Q57ZF2) from kinetoplastids, a core protein of the multiprotein mitochondrial RNA binding complex 1 (MRB1) involved in kinetoplastid RNA (kRNA) editing [1]. MRB1590 is a dimer and contains a central ABC ATPase fold (Pfam:PF09818) between novel N- and C-terminal regions. The N-terminal domains combine and form a RNA-binding basic pore which involves an arginine patch that has been suggested to act as a chaperone to bind and stabilize ssRNA during kRNA editing processes. N-terminal MRB1590 shows structural similarity to chaperones [1]. [1]. 26117548. Structures of the T. brucei kRNA editing factor MRB1590 reveal unique RNA-binding pore motif contained within an ABC-ATPase fold. Shaw PL, McAdams NM, Hast MA, Ammerman ML, Read LK, Schumacher MA;. Nucleic Acids Res. 2015;43:7096-7109. (from Pfam) NF042587.3 PF20511.3 PMI_typeI_cat 22 22 143 hypoth_equivalog Y Y N type I phosphomannose isomerase catalytic subunit GO:0004476,GO:0008270 8612079 131567 cellular organisms no rank 54116 EBI-EMBL Phosphomannose isomerase type I, catalytic domain type I phosphomannose isomerase catalytic subunit This entry represents the catalytic domain of Phosphomannose isomerase type I enzymes (EC 5.3.1.8) which contains a zinc-binding site. It is composed of beta-strands connected by long loops in a jelly roll conformation [1]. [1]. 8612079. The x-ray crystal structure of phosphomannose isomerase from Candida albicans at 1.7 angstrom resolution. Cleasby A, Wonacott A, Skarzynski T, Hubbard RE, Davies GJ, Proudfoot AE, Bernard AR, Payton MA, Wells TN;. Nat Struct Biol 1996;3:470-479. (from Pfam) NF042598.3 PF20551.3 DUF6765 26.6 26.6 325 subfamily Y Y N DUF6765 family protein 131567 cellular organisms no rank 1841 EBI-EMBL Family of unknown function (DUF6765) DUF6765 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 352 and 375 amino acids in length. It contains the conserved motifs FHFxxxP, GH and PD, and a conserved Phe residue at the C-terminal. (from Pfam) NF042608.3 PF20580.3 DUF6784 26.4 26.4 101 domain Y Y N DUF6784 domain-containing protein 131567 cellular organisms no rank 286 EBI-EMBL Domain of unknown function (DUF6784) DUF6784 domain This presumed domain is found at the C-terminal of uncharacterised proteins from bacteria. It contains the conserved sequence motifs WW/FPLHPLGY and RxGG. (from Pfam) NF042609.3 PF20582.3 UPF0758_N 27.1 27.1 77 domain Y Y N UPF0758 domain-containing protein 11053371,14737182,18556794,21890906 131567 cellular organisms no rank 39826 EBI-EMBL UPF0758 N-terminal UPF0758 domain-containing protein This domain is functionally uncharacterised, found at the N-terminal of the uncharacterised UPF0758 proteins from bacteria and archaea, and is approximately 90 amino acids in length. UPF0758 was previously known as the radC family, a name that was assigned according to the radC102 mutant of E. coli which was later demonstrated to be an allele of the transcription-repair-coupling factor recG [1, 2]. UPF0758 has been described as a putative JAMM-family deubiquitinating enzyme, but its function remains to be determined [3]. Structure prediction using Colab notebook from AlphaFold DB suggests that it has an alpha bundle fold. It may contain two helix-hairpin-helix (HhH) motifs. This domain is found in association with Pfam:PF04002 [4]. [1]. 11053371. radC102 of Escherichia coli is an allele of recG. Lombardo MJ, Rosenberg SM;. J Bacteriol. 2000;182:6287-6291. [2]. 18556794. RadC, a misleading name?. Attaiech L, Granadel C, Claverys JP, Martin B;. J Bacteriol. 2008;190:5729-5732. [3]. 14737182. JAMM: a metalloprotease-like zinc site in the proteasome and signalosome. Ambroggio XI, Rees DC, Deshaies RJ;. PLoS Biol. 2004;2:E2. [4]. 21890906. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Iyer LM, Zhang D, Rogozin IB, Aravind L;. Nucleic Acids Res. 2011; [Epub ahead of print] (from Pfam) NF042610.3 PF20587.3 DUF6789 27.1 27.1 144 subfamily Y Y N DUF6789 family protein 131567 cellular organisms no rank 2475 EBI-EMBL Family of unknown function (DUF6789) DUF6789 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. These are likely membrane proteins. (from Pfam) NF042613.3 PF20599.3 DUF6796 26.9 26.9 225 subfamily Y Y N DUF6796 family protein 131567 cellular organisms no rank 1488 EBI-EMBL Family of unknown function (DUF6796) DUF6796 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and fungi. Proteins in this family are typically between 220 and 250 amino acids in length. (from Pfam) NF042614.3 PF20604.3 DUF6798 26.9 26.9 61 domain Y Y N DUF6798 domain-containing protein 131567 cellular organisms no rank 597 EBI-EMBL Domain of unknown function (DUF6798) DUF6798 domain This presumed domain is functionally uncharacterised. This domain family is mainly found in bacteria and archaea, and is approximately 60 amino acids in length. There is a conserved WxxR sequence motif and a conserved Lys residue. Members of this entry may be transmembrane proteins. (from Pfam) NF042617.3 PF20612.3 SHOCT_2 24 24 53 domain Y Y N SHOCT domain-containing protein 131567 cellular organisms no rank 2033 EBI-EMBL SHOCT domain SHOCT domain This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 53 and 72 amino acids in length. This family of proteins is related to the SHOCT domain. (from Pfam) NF042619.3 PF20618.3 GPD_NAD_C_bact 27.6 27.6 66 domain Y Y N NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 131567 cellular organisms no rank 67954 EBI-EMBL Bacterial GPD, NAD-dependent C-terminal NAD(P)H-dependent glycerol-3-phosphate dehydrogenase This is the C-terminal domain of NAD-dependent glycerol-3-phosphate dehydrogenase (GPD) from bacteria and archaea. GPD catalyses the reversible reduction of dihydroxyacetone phosphate to glycerol-3-phosphate. (from Pfam) NF042625.3 PF20176.3 DUF6541 29 29 646 subfamily Y Y N DUF6541 family protein 131567 cellular organisms no rank 8155 EBI-EMBL Family of unknown function (DUF6541) DUF6541 family protein This family is composed of a group of large bacterial integral membrane proteins that likely have a transporter function. (from Pfam) NF042629.3 PF20187.3 DUF6550 27 27 190 subfamily Y Y N DUF6550 family protein 131567 cellular organisms no rank 761 EBI-EMBL Family of unknown function (DUF6550) DUF6550 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in Firmicutes. Proteins in this family are approximately 180 amino acids in length. There are two conserved sequence motifs at the C-terminal: FGW/I and I/VGxM. (from Pfam) NF042637.3 PF20208.3 ARPP-1 27 27 297 subfamily Y Y N ARPP-1 family domain-containing protein 36146784,36968430 131567 cellular organisms no rank 1003 EBI-EMBL ARG and Rhodanese-Phosphatase-superfamily-associated Protein domain DUF6569 family protein ARPP-1 shows a distinguishing group of absolutely conserved residues, including a cysteine and a glutamine, suggestive of enzymatic activity. Structural predictions reveal a core beta-sheet comprised of a duplicated four-stranded beta-meander with a beta-barrel domain bearing the absolutely conserved residues inserted into the first repeat. The unifying biochemical theme across its conserved contextual genome linkages is the presence of molecules with sugar moieties (ADPr, nucleotides, and polysaccharides). In genome contexts linking ARPP-1 with ARG and other counter viral ribosylation domains, ARPP is predicted to act on ribose moieties coming from ADPr. The presence of the conserved cysteine suggests that it could function analogous to the recently characterized SRAP domain by forming covalent cross-links with sugars [1,2]. [1]. 36146784. Apprehending the NAD(+)-ADPr-Dependent Systems in the Virus World. Iyer LM, Burroughs AM, Anantharaman V, Aravind L;. Viruses. 2022;14:1977. [2]. 36968430. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. Burroughs AM, Aravind L;. NAR Genom Bioinform. 2023;5:lqad029. (from Pfam) NF042646.3 PF20248.3 DUF6603 27 27 502 domain Y Y N DUF6603 domain-containing protein 131567 cellular organisms no rank 3779 EBI-EMBL Family of unknown function (DUF6603) Family of unknown function (DUF6603) This entry represents a large potential domain found in a wide range of uncharacterised fungal proteins. (from Pfam) NF042648.3 PF20254.3 DMFA2_C 27 27 374 domain Y Y N N,N-dimethylformamidase beta subunit family domain-containing protein 32452120 131567 cellular organisms no rank 21230 EBI-EMBL N,N-dimethylformamidase beta subunit-like, C-terminal N,N-dimethylformamidase beta subunit-like, C-terminal This entry represents a domain found at the C-terminal of bacterial proteins, including N,N-dimethylformamidase beta (DMFA2) subunit from Paracoccus [1], the large subunit of dimethylformamidase (DMFase), an enzyme containing a Fe+3 ion in the active site that catalyses the hydrolytic cleavage of the amide bond in N,N-dimethyl formamide. This domain is described as domain III, which adopts an alpha/beta/alpha fold, with five beta-strands that are parallel and sandwiched between alpha-helices. This domain is also found in some uncharacterised fungal sequences. [1]. 32452120. A 2-Tyr-1-carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase. Arya CK, Yadav S, Fine J, Casanal A, Chopra G, Ramanathan G, Vinothkumar KR, Subramanian R;. Angew Chem Int Ed Engl. 2020;59:16961-16966. (from Pfam) NF042649.3 PF20256.3 MoCoBD_2 27 27 283 domain Y Y N molybdopterin cofactor-binding domain-containing protein 10430865,7502041 131567 cellular organisms no rank 219366 EBI-EMBL Molybdopterin cofactor-binding domain molybdopterin cofactor-binding domain-containing protein NF042652.3 PF20268.3 SBDS_C 27 27 71 domain Y Y N SBDS family ribosome assembly factor 12496757,15701631,15701634,17353896,21536732 131567 cellular organisms no rank 1248 EBI-EMBL SBDS protein, C-terminal domain SBDS protein, C-terminal domain Members containing this domain are highly conserved in species ranging from archaea to vertebrates and plants [1], including several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. These proteins play a role in RNA metabolism [2,3]. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes [4]. The SBDS protein is composed of three domains. The N-terminal (Pfam:PF01172) (FYSH) domain (domain I) is the most frequent target for disease mutations and contains a novel mixed alpha/beta-fold, the central domain (domain II, Pfam:PF09377) consists of a three-helical bundle and this C-terminal domain which has a ferredoxin-like fold [3,5]. [1]. 12496757. Mutations in SBDS are associated with Shwachman-Diamond syndrome. Boocock GR, Morrison JA, Popovic M, Richards N, Ellis L, Durie PR, Rommens JM;. Nat Genet 2003;33:97-101. [2]. 15701634. The SHWACHMAN-Bodian-diamond syndromeprotein family is involved in RNA metabolism. Savchenko A, Krogan N, Cort JR, Evdokimova E, Lew JM, Yee AA, Sanchez-Pulido L, Andrade MA, Bochkarev A, Watson JD, Kennedy MA, Greenblatt J, Hughes T, Arrowsmith CH, Rommens JM, Edwards AM;. J Biol Chem 2005; [Epub ahead of print]. [3]. 15701631. Structural and mutational analysis of the SBDS protein family: insight into the leukemia-associated shwachman-diamond syndrome. Shammas C, Menne TF, Hilcenko C, Michell SR, Goyenechea B, Boocock GR, Duri. TRUNCATED at 1650 bytes (from Pfam) NF042656.3 PF20279.3 CTD12 25 25 144 equivalog_domain Y Y N ABC-three component system protein 32894288 131567 cellular organisms no rank 685 EBI-EMBL C-terminal domain 12 of the ABC-three component (ABC-3C) systems ABC-three component system protein C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector [1]. [1]. 32894288. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. Nucleic Acids Res. 2020;48:10045-10075. (from Pfam) NF042658.3 PF20283.3 CTD7 27.6 27.6 126 equivalog_domain Y Y N ABC-three component system protein 32894288 131567 cellular organisms no rank 3458 EBI-EMBL C-terminal domain 7 of the ABC-three component (ABC-3C) systems ABC-three component system protein C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector [1]. [1]. 32894288. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. Nucleic Acids Res. 2020;48:10045-10075. (from Pfam) NF042664.3 PF20308.3 TPR-S 27.6 27.6 102 domain Y Y N tetratricopeptide repeat-containing protein 32868406 131567 cellular organisms no rank 3172 EBI-EMBL Tetratricopeptide Repeats-Sensor tetratricopeptide repeat-containing protein This entry represents a sensor domain consisting of 7 TPR repeats forming a tightly-wound solenoid structure harbouring a deep central pocket. The TPR-S binding pocket is lined with several conserved aromatic and polar residues predicted to bind a NAD+-derived nucleotide in prokaryotic NAD+-derived nucleotide-activated effector conflict systems. It has been acquired at the base of the choanoflagellate-animal lineage as a core component of the ASK signalosome [1]. [1]. 32868406. Identification of Uncharacterized Components of Prokaryotic Immune Systems and Their Diverse Eukaryotic Reformulations. Burroughs AM, Aravind L;. J Bacteriol. 2020; [Epub ahead of print] (from Pfam) NF042666.3 PF20316.3 DUF6612 23.7 23.7 237 subfamily Y Y N DUF6612 family protein 131567 cellular organisms no rank 5463 EBI-EMBL Family of unknown function (DUF6612) DUF6612 family protein This family of proteins is functionally uncharacterised. However, based on similarity to other families it is likely to be involved in lipoprotein biosynthesis. This family of proteins is found in bacteria. Proteins in this family are typically between 263 and 293 amino acids in length. (from Pfam) NF042682.3 PF20169.3 DUF6537 27 27 203 domain Y Y N DUF6537 domain-containing protein 131567 cellular organisms no rank 29991 EBI-EMBL Family of unknown function (DUF6537) DUF6537 domain-containing protein This entry represents a presumed domain that is found associated with a variety of enzyme domains. The function of this domain is unknown. (from Pfam) NF042685.3 PF20188.3 DUF6551 26.8 26.8 242 subfamily Y Y N DUF6551 family protein 131567 cellular organisms no rank 1846 EBI-EMBL Family of unknown function (DUF6551) DUF6551 family protein This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 200 amino acids in length. Many sequences are related to ParB proteins, annotated as ParB-like or ParB domain-containing proteins. It contains the conserved motifs YQR, DGQH and EAxxF. (from Pfam) NF042686.3 PF20189.3 DUF6552 27 27 78 subfamily Y Y N DUF6552 family protein 131567 cellular organisms no rank 481 EBI-EMBL Family of unknown function (DUF6552) DUF6552 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, mainly Proteobacteria. Proteins in this family are approximately 90 amino acids in length and some members are associated with Ubiquinone biosynthesis methyltransferases. (from Pfam) NF042688.3 PF20194.3 DUF6557 27.8 27.8 144 subfamily Y Y N DUF6557 family protein 131567 cellular organisms no rank 501 EBI-EMBL Family of unknown function (DUF6557) DUF6557 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 140 and 200 amino acids in length. There is a quite conserved EMTFxxG motif. (from Pfam) NF042699.3 PF20247.3 DUF6602 27 27 104 domain Y Y N DUF6602 domain-containing protein 131567 cellular organisms no rank 6490 EBI-EMBL Domain of unknown function (DUF6602) Domain of unknown function (DUF6602) This entry represents a bacterial domain of unknown function. This domain is sometimes associated with a Pfam:PF14464 domain. This could suggest this domain has a role in a bacterial cognate of a Ubiquitin-like pathway. (from Pfam) NF042701.3 PF20257.3 SAM_HAT_C 25.5 25.5 84 domain Y Y N SAM hydroxide adenosyltransferase 17910070,18675376 131567 cellular organisms no rank 16338 EBI-EMBL SAM hydroxide adenosyltransferase C-terminal domain SAM hydroxide adenosyltransferase This is a family of proteins, previously known as DUF62, found in archaebacteria and bacteria. The structure of proteins in this family is similar to that of a bacterial fluorinating enzyme [1]. S-adenosyl-l-methionine hydroxide adenosyltransferases utilises a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion [2]. This family used to be known as DUF62. This entry represents the C-terminal domain of these enzymes. [1]. 17910070. Crystal structure of a conserved protein of unknown function (MJ1651) from Methanococcus jannaschii. Rao KN, Burley SK, Swaminathan S;. Proteins. 2008;70:572-577. [2]. 18675376. The fluorinase, the chlorinase and the duf-62 enzymes. Deng H, O'Hagan D;. Curr Opin Chem Biol. 2008;12:582-592. (from Pfam) NF042704.3 PF20274.3 cREC_REC 27 27 88 domain Y Y N cyclic-phosphate processing receiver domain-containing protein 33466489 131567 cellular organisms no rank 5183 EBI-EMBL Cyclic-phosphate processing Receiver domain cyclic-phosphate processing receiver domain This is a divergent version of the Receiver (Rec) domain linked to different NAD+/ADPr-processing enzymes. Unlike conventional Rec domains, cREC is never found in two-component Histidine Kinase signalling systems. Instead, it is found in association with NAD+-processing systems that generate or recognise cyclic nucleotides. Known Rec domains process phosphoester linkages by means of catalytic aspartate residues that are also conserved in cREC. Accordingly, it is predicted that these are cADPr or 2_-3_ cyclic nucleotide-processing enzymes. [1]. 33466489. Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts. M Iyer L, Anantharaman V, Krishnan A, Burroughs AM, Aravind L;. Viruses. 2021; [Epub ahead of print] (from Pfam) NF042705.3 PF20275.3 CTD10 28.1 28.1 134 equivalog_domain Y Y N ABC-three component system protein 32894288 131567 cellular organisms no rank 2962 EBI-EMBL C-terminal domain 10 of the ABC-three component (ABC-3C) systems ABC-three component system protein C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector. [1]. 32894288. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. Nucleic Acids Res. 2020;48:10045-10075. (from Pfam) NF042706.3 PF20286.3 divDNApol 25.7 25.7 705 subfamily Y Y N family B DNA polymerase 33466489 131567 cellular organisms no rank 86 EBI-EMBL Divergent Family B DNA polymerase family B DNA polymerase This family represents a Divergent Family B DNA polymerase found in PhiKZ/ group 1 phages [1]. [1]. 33466489. Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts. M Iyer L, Anantharaman V, Krishnan A, Burroughs AM, Aravind L;. Viruses. 2021; [Epub ahead of print] (from Pfam) NF042709.3 PF20295.3 MC8 25 25 48 equivalog_domain Y Y N ABC-three component system middle component 8 32894288 131567 cellular organisms no rank 486 EBI-EMBL ABC-three component (ABC-3C) system Middle Component 8 ABC-three component system middle component 8 Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses. MC8 is a MC unifiable with the HTH fold [1]. [1]. 32894288. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. Nucleic Acids Res. 2020;48:10045-10075. (from Pfam) NF042711.3 PF20300.3 prok_STING 27.1 27.1 137 domain Y Y N STING domain-containing protein 32868406 131567 cellular organisms no rank 428 EBI-EMBL Prokaryotic STING domain Prokaryotic STING domain This is a STING sensor domain found in certain prokaryotic nucleotide-activated effector conflict systems. Binding to a nucleotide activates fused effector proteins in conflict response against invasive elements. Certain versions in prokaryotes may additionally regulate bacterial ion channels. Transferred to eukaryotes on multiple occasions, representatives observed are in animal-choanoflagellate, haptophyte/stramenopile, and fungal lineages [1]. [1]. 32868406. Identification of Uncharacterized Components of Prokaryotic Immune Systems and Their Diverse Eukaryotic Reformulations. Burroughs AM, Aravind L;. J Bacteriol. 2020; [Epub ahead of print] (from Pfam) NF042714.3 PF20305.3 pYEATS 26.9 26.9 73 domain Y Y N pYEATS domain-containing protein 32868406 131567 cellular organisms no rank 626 EBI-EMBL prokaryotic YEATS domain prokaryotic YEATS domain This entry represents a prokaryotic YEATS domain. pYEATS is fused to diverse effector domains, suggesting that the binding to a ligand activates an effector-based response against an invasive threat. It has been predicted to specifically recognise invader-induced modifications of macromolecules by acyl moieties (e.g. phage-encoded acylations of surface polysaccharides) to unleash the fused effectors through a conformational change [1]. [1]. 32868406. Identification of Uncharacterized Components of Prokaryotic Immune Systems and Their Diverse Eukaryotic Reformulations. Burroughs AM, Aravind L;. J Bacteriol. 2020; [Epub ahead of print] (from Pfam) NF042715.3 PF20313.3 DUF6609 24 24 176 subfamily Y Y N DUF6609 family protein 131567 cellular organisms no rank 793 EBI-EMBL Family of unknown function (DUF6609) DUF6609 family protein This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 180 amino acids in length. (from Pfam) NF042734.3 PF20408.3 Abhydrolase_11 27 27 193 superfamily Y Y N alpha/beta family hydrolase 131567 cellular organisms no rank 38251 EBI-EMBL Alpha/beta hydrolase domain alpha/beta family hydrolase This entry represents a protein that belongs to the alpha/beta hydrolase superfamily. Although proteins in this family are uncharacterised they are likely to have an enzymatic activity. (from Pfam) NF042742.3 PF20436.3 LonB_AAA-LID 22.4 22.4 65 domain Y Y N Lon-insertion domain-containing protein 23897463 131567 cellular organisms no rank 14535 EBI-EMBL Archaeal LonB, AAA+ ATPase LID domain Lon-insertion domain-containing protein The species-specific Lon-insertion domain (LID) is characteristic of Lon proteases (also known as endopeptidase La) and is fused to the AAA+ module [1]. Bacterial and eukaryotic Lons (LonA) have a LID at the N-terminal of AAA+ module; in archaeal Lons (LonB) the LID, represented in this entry, is inserted within the AAA+ module in a series of transmembrane segments known as the membrane-anchoring region (MA). In the Lon-like protease LonC, which does not have ATPase activity, the LID is also within the AAA-like module similar to LonBs; in this case, it is predicted to contain coiled-coil regions rather than transmembrane segments [1]. [1]. 23897463. Structures of an ATP-independent Lon-like protease and its complexes with covalent inhibitors. Liao JH, Ihara K, Kuo CI, Huang KF, Wakatsuki S, Wu SH, Chang CI;. Acta Crystallogr D Biol Crystallogr. 2013;69:1395-1402. (from Pfam) NF042755.3 PF20382.3 DUF6677 24.3 24.3 116 subfamily Y Y N DUF6677 family protein 131567 cellular organisms no rank 707 EBI-EMBL Family of unknown function (DUF6677) DUF6677 family protein This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 135 and 210 amino acids in length. (from Pfam) NF042757.3 PF20389.3 DUF6684 24 24 79 subfamily Y Y N DUF6684 family protein 131567 cellular organisms no rank 507 EBI-EMBL Family of unknown function (DUF6684) DUF6684 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 77 and 127 amino acids in length. (from Pfam) NF042760.3 PF20393.3 Pro_CA_2 30 30 125 subfamily Y Y N carbonic anhydrase 131567 cellular organisms no rank 804 EBI-EMBL Putative carbonic anhydrase carbonic anhydrase This family of proteins are likely to be prokaryotic carbonic anhydrase enzymes related to Pfam:PF00484.. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 130 amino acids in length. (from Pfam) NF042761.3 PF20398.3 DUF6691 27 27 142 subfamily Y Y N DUF6691 family protein 131567 cellular organisms no rank 21573 EBI-EMBL Family of unknown function (DUF6691) DUF6691 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 137 and 165 amino acids in length. Proteins in this family are related to the thiosulfate transporter, but appear to be about half the length. Suggesting this family may operate as a dimer to make a functional transporter. (from Pfam) NF042769.3 PF20434.3 BD-FAE 26.8 26.8 215 domain Y N N BD-FAE 34059129 131567 cellular organisms no rank 427755 EBI-EMBL BD-FAE BD-FAE This family represents a novel bifunctional feruloyl and acetyl xylan esterase (BD-FAE, previously known as bifunctional carbohydrate esterase (CE)), which is active on complex natural xylans and was identified as the basis of a monophyletic clade gathering all homologs identified in PULs (polysaccharide utilisation loci) predicted to act on xylan. It adopts an alpha-beta-hydrolase fold with the catalytic triad Ser-Asp-His [1]. This new family of proteins is a new candidate for biomass processing due to its capacity to remove ferulic acid and acetic acid from natural corn and birchwood xylan substrates [1]. [1]. 34059129. Polysaccharide utilization loci-driven enzyme discovery reveals BD-FAE: a bifunctional feruloyl and acetyl xylan esterase active on complex natural xylans. Hameleers L, Penttinen L, Ikonen M, Jaillot L, Faure R, Terrapon N, Deuss PJ, Hakulinen N, Master ER, Jurak E;. Biotechnol Biofuels. 2021;14:127. (from Pfam) NF042777.3 PF20465.3 MmeI_hel 27 27 75 domain Y Y N type IIL restriction-modification enzyme MmeI 18931376,27082731,3016643,9858752 131567 cellular organisms no rank 12012 EBI-EMBL MmeI, helicase spacer domain MmeI helicase spacer domain Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide [2, 3, 4]. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919) [1]. The endonuclease cuts the two DNA strands at one site simultaneously with enzyme bound at two sites interacting to accomplish the cleavage [2]. This domain corresponds to the multi-helical spacer. It is thought to play a key role in positioning the endonuclease cleavage domain correctly. Paper describing PDB structure 5hr4. [1]. 27082731. Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities. Callahan SJ, Luyten YA, Gupta YK, Wilson GG, Roberts RJ, Morgan RD, Aggarwal AK;. PLoS Biol. 2016;14:e1002442. [2]. 18931376. MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection. Morgan RD, Bhatia TK, Lovasco L, Davis TB;. Nucleic Acids Res. 2008;36:6558-6570. [3]. 3016643. Isolation and computer-aided characterization of MmeI, a type II restriction endonuclease from Methylophilus methylotrophus. Boyd AC, Charles IG, Keyte JW, Brammar WJ;. Nucleic Acids Res. 1986;14:5255-5274. [4]. 9858752. Two intertwined methylation activities of the MmeI restriction-modification class-IIS system fro. TRUNCATED at 1650 bytes (from Pfam) NF042779.3 PF20469.3 OLD-like_TOPRIM 23.2 23.2 67 domain Y Y N TOPRIM nucleotidyl transferase/hydrolase domain-containing protein 32009148,7836278,9722641 131567 cellular organisms no rank 47675 EBI-EMBL Overcoming lysogenization defect protein-like, TOPRIM domain TOPRIM nucleotidyl transferase/hydrolase domain-containing protein This entry represents the topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity [1,2] consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain. The nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. The TOPRIM domain has two conserved motifs, one of which centres at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function [3]. [1]. 32009148. The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases. Schiltz CJ, Adams MC, Chappie JS;. Nucleic Acids Res. 2020;48:2762-2776. [2]. 7836278. The old exonuclease of bacteriophage P2. Myung H, Calendar R;. J Bacteriol. 1995;177:497-501. [3]. 9722641. Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Aravind L, Leipe DD, Koonin EV;. Nucleic Acids Res 1998;26:4205-4213. (from Pfam) NF042780.3 PF20471.3 DUF6716 27 27 342 domain Y Y N DUF6716 putative glycosyltransferase 131567 cellular organisms no rank 9616 EBI-EMBL Putative glycosyltransferase (DUF6716) DUF6716 putative glycosyltransferase domain This entry represents a group of uncharacterised proteins that belong to the GT- superfamily of glycosyltransferases. (from Pfam) NF042782.3 PF20479.3 TMEM128 23.9 23.9 124 subfamily Y Y N TMEM128 family protein 131567 cellular organisms no rank 35 EBI-EMBL TMEM128 protein TMEM128 family protein This entry represents the uncharacterised TMEM128 protein which contains four transmembrane helices. This protein is resident in the endoplasmic reticulum. (from Pfam) NF042789.3 PF20510.3 HgmA_N 20.2 20.2 273 domain Y Y N homogentisate 1,2-dioxygenase 10876237 131567 cellular organisms no rank 33767 EBI-EMBL Homogentisate 1,2-dioxygenase N-terminal homogentisate 1,2-dioxygenase Homogentisate dioxygenase cleaves the aromatic ring during the metabolic degradation of Phe and Tyr. Homogentisate dioxygenase deficiency causes alkaptonuria. The structure of homogentisate dioxygenase shows that the enzyme forms a hexamer arrangement comprised of a dimer of trimers. The active site iron ion is coordinated near the interface between the trimers [1]. This entry represents the N-terminal domain which forms a jelly roll of beta-strands [1]. [1]. 10876237. Crystal structure of human homogentisate dioxygenase. Titus GP, Mueller HA, Burgner J, Rodriguez De Cordoba S, Penalva MA, Timm DE;. Nat Struct Biol 2000;7:542-546. (from Pfam) NF042798.3 PF20546.3 DUF6760 27 27 89 subfamily Y Y N DUF6760 family protein 131567 cellular organisms no rank 2937 EBI-EMBL Family of unknown function (DUF6760) DUF6760 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically 89 amino acids in length. (from Pfam) NF042800.3 PF20557.3 DnaT_2 27 27 168 equivalog Y Y N DnaT-like ssDNA-binding protein 131567 cellular organisms no rank 3971 EBI-EMBL Putative DnaT-like ssDNA binding protein DnaT-like ssDNA-binding protein This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 110 amino acids in length. This domain is predicted to contain a complex four helical bundle structure. The structure shows similarity to the single stranded binding protein DnaT. (from Pfam) NF042802.3 PF20563.3 DUF6773 27 27 163 subfamily Y Y N DUF6773 family protein 131567 cellular organisms no rank 3542 EBI-EMBL Family of unknown function (DUF6773) DUF6773 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 151 and 172 amino acids in length. This family has a conserved sequence motif DER and two conserved residues, a Tyr and a Gly. (from Pfam) NF042804.3 PF20565.3 DUF6775 27 27 259 subfamily Y Y N DUF6775 family putative metallopeptidase 131567 cellular organisms no rank 355 EBI-EMBL Probable metallopeptidase family (DUF6775) DUF6775 family putative metallopeptidase This family is functionally uncharacterised. This domain family is found in archaea. An AlphaFold prediction shows close similarity to zinc dependent peptidases. (from Pfam) NF042809.3 PF20603.3 Bact_hydrolase 27 27 160 subfamily Y Y N hydrolase 131567 cellular organisms no rank 399 EBI-EMBL Bacterial hydrolase hydrolase This family of proteins, found in bacteria, is thought to have a hydrolase activity. (from Pfam) NF042810.3 PF20617.3 DUF6803 27 27 162 subfamily Y Y N DUF6803 family protein 131567 cellular organisms no rank 1125 EBI-EMBL Family of unknown function (DUF6803) DUF6803 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 162 and 222 amino acids in length. Structurally, proteins in this family are made of a Four Helix Bundle. (from Pfam) NF042811.3 PF20460.3 DUF6713 27 27 117 subfamily Y Y N DUF6713 family protein 131567 cellular organisms no rank 1022 EBI-EMBL Family of unknown function (DUF6713) DUF6713 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 117 and 141 amino acids in length. (from Pfam) NF042813.3 PF20467.3 MmeI_C 27 27 83 domain Y Y N type IIL restriction-modification enzyme MmeI 18931376,27082731,3016643,9858752 131567 cellular organisms no rank 9207 EBI-EMBL MmeI, C-terminal domain type IIL restriction-modification enzyme MmeI C-terminal Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide [2, 3, 4]. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919) [1]. The DNA is embedded between the TRD and the MTase domain. The TRD makes contacts to the DNA bases primarily in the major groove, while the MTase domain makes several contacts to the DNA in the minor groove [1]. This domain corresponds to the C-terminal region. Paper describing PDB structure 5hr4. [1]. 27082731. Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities. Callahan SJ, Luyten YA, Gupta YK, Wilson GG, Roberts RJ, Morgan RD, Aggarwal AK;. PLoS Biol. 2016;14:e1002442. [2]. 18931376. MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection. Morgan RD, Bhatia TK, Lovasco L, Davis TB;. Nucleic Acids Res. 2008;36:6558-6570. [3]. 3016643. Isolation and computer-aided characterization of MmeI, a type II restriction endonuclease from Methylophilus methylotrophus. Boyd AC, Charles IG, Keyte JW, Brammar WJ;. Nucleic Acids Res. 1986;14:5255-5274. [4]. 9858752. Two intertwined methylation activities of the MmeI restriction-modification class-IIS system from Methylophilus methylotroph. TRUNCATED at 1650 bytes (from Pfam) NF042814.3 PF20473.3 MmeI_Mtase 27 27 259 domain Y Y N DNA methyltransferase 18931376,23090406,27082731,28973912,3016643,9858752 131567 cellular organisms no rank 42838 EBI-EMBL MmeI, DNA-methyltransferase domain DNA methyltransferase Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide [2, 3, 4]. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919) [1]. The DNA is embedded between the TRD and the MTase domain. The TRD makes contacts to the DNA bases primarily in the major groove, while the MTase domain makes several contacts to the DNA in the minor groove [1]. This domain corresponds to the DNA-methyltransferase. Structurally, it consists of a twisted beta-sheet flanked by alpha-helices on both sides. Paper describing PDB structure 5hr4. [1]. 27082731. Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities. Callahan SJ, Luyten YA, Gupta YK, Wilson GG, Roberts RJ, Morgan RD, Aggarwal AK;. PLoS Biol. 2016;14:e1002442. [2]. 18931376. MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection. Morgan RD, Bhatia TK, Lovasco L, Davis TB;. Nucleic Acids Res. 2008;36:6558-6570. [3]. 3016643. Isolation and computer-aided characterization of MmeI, a type II restriction endonuclease from Methylophilus methylotrophus. Boyd AC, Charles IG, Keyte JW, Brammar WJ;. Nucleic Acids Res. 1986;14:5255-5274. [4]. 9858752. Two intertwined methylati. TRUNCATED at 1650 bytes (from Pfam) NF042818.3 PF20501.3 MbhE 27 27 98 PfamEq Y Y N hydrogen gas-evolving membrane-bound hydrogenase subunit E mbhE 22713092,26808919,29754813 131567 cellular organisms no rank 44475 EBI-EMBL MBH, subunit E hydrogen gas-evolving membrane-bound hydrogenase subunit E Hydrogen gas-evolving membrane-bound hydrogenase (MBH) is a respiratory complex homologous to the quinone-reducing Complex I. Like Complex I, MBH has peripheral and membrane arms. MBH is made of 14 subunits (MbhA-N). MbhJ, K, L, N and M form the Membrane-anchored hydrogenase module. MbhJ, K, L, N are predicted to be exposed to the cytoplasm and form the peripheral arm. The remaining 10 subunits are predicted to be integral membrane proteins forming the membrane arm, made of 44 transmembrane helices (TMH) [2, 3]. MbhA, B, C and F form the Sodium translocation module. MbhD, E, G and H form the Proton translocation module. MbhI is the linker between the hydrogenase module and the proton-translocating membrane module. It anchors the discontinuous TMH7 of MbhH via its middle lateral helix and the C-terminal of TMH2, found in MbhE. MbhD and MbhE together are equivalent to Nqo10 of Complex I [1]. MbhE has two transmembrane helices: TMH1 and TMH2. Paper describing PDB structure 6cfw. [1]. 29754813. Structure of an Ancient Respiratory System. Yu H, Wu CH, Schut GJ, Haja DK, Zhao G, Peters JW, Adams MWW, Li H;. Cell. 2018;173:1636-1649. [2]. 22713092. The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications. Schut GJ, Boyd ES, Peters JW, Adams MW;. FEMS Microbiol Rev. 2013;37:182-203. [3]. 26808919. The role of geochemistry and energetics in the evolution of modern respiratory complexes from a proton-reducing ancestor. Schut GJ, Zadvornyy O, Wu CH, Peters JW, Boyd ES, Adams MW;. Biochim Biophys Acta. 2016;1857:958-970. (from Pfam) NF042819.3 PF20505.3 DUF6731 27 27 295 subfamily Y Y N DUF6731 family protein 131567 cellular organisms no rank 1343 EBI-EMBL Family of unknown function (DUF6731) DUF6731 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 297 and 311 amino acids in length. (from Pfam) NF042824.3 PF20530.3 DUF6745 27 27 206 domain Y Y N DUF6745 domain-containing protein 131567 cellular organisms no rank 6900 EBI-EMBL Domain of unknown function (DUF6745) DUF6745 domain This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically 200 amino acids in length. (from Pfam) NF042826.3 PF20539.3 DUF6754 27 27 257 domain Y Y N DUF6754 domain-containing protein 131567 cellular organisms no rank 170 EBI-EMBL Domain of unknown function (DUF6754) DUF6754 domain This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 250 amino acids in length. (from Pfam) NF042830.3 PF20553.3 Methyltransf_35 27 27 309 hypoth_equivalog Y Y N O-methyltransferase 131567 cellular organisms no rank 944 EBI-EMBL Putative O-methyltransferase O-methyltransferase This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 312 and 330 amino acids in length. An AlphaFold model shows this family are similar to known O-methyltransferases. (from Pfam) NF042831.3 PF20554.3 DUF6766 27 27 221 subfamily Y Y N DUF6766 family protein 131567 cellular organisms no rank 6628 EBI-EMBL Domain of unknown function (DUF6766) DUF6766 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 215 and 226 amino acids in length. Structure prediction shows this family contains 4 alpha helices. (from Pfam) NF042834.3 PF20573.3 DUF6782 27 27 241 domain Y Y N DUF6782 family putative metallopeptidase 131567 cellular organisms no rank 1807 EBI-EMBL Putative metallopeptidase family (DUF6782) DUF6782 putative metallopeptidase domain This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 256 and 362 amino acids in length. There is a conserved HEXRH sequence motif which is characteristic of metallopeptidase enzymes. (from Pfam) NF042835.3 PF20575.3 HTH_63 23.9 23.9 148 domain Y Y N HTH domain-containing protein 131567 cellular organisms no rank 1193 EBI-EMBL Helix-turn-helix domain Helix-turn-helix domain This family of proteins is functionally uncharacterised. This family of proteins is found in archaea. Proteins in this family are typically between 161 and 201 amino acids in length. This family shares similarity with Pfam:PF01638 suggesting it is a transcriptional regulatory protein. (from Pfam) NF042838.3 PF20581.3 DUF6785 25 25 498 subfamily Y Y N DUF6785 family protein 131567 cellular organisms no rank 305 EBI-EMBL Family of unknown function (DUF6785) DUF6785 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. There are highly conserved sequence motifs: FSxWFF and ExxxFP. There are eleven conserved tryptophan residues, which may suggest to play an important role. (from Pfam) NF042840.3 PF20586.3 DUF6788 27.2 27.2 103 subfamily Y Y N DUF6788 family protein 131567 cellular organisms no rank 875 EBI-EMBL Family of unknown function (DUF6788) DUF6788 family protein This family of proteins is functionally uncharacterised. This family of proteins is mainly found in bacteria and archaea. Proteins in this family are around 100 amino acids in length. There are two conserved sequence motifs, CGxxxCxC containing three conserved Cys residues and HGP. (from Pfam) NF042842.3 PF20589.3 DUF6790 27.1 27.1 158 subfamily Y Y N DUF6790 family protein 131567 cellular organisms no rank 2081 EBI-EMBL Family of unknown function (DUF6790) DUF6790 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 159 and 176 amino acids in length. (from Pfam) NF042843.3 PF20590.3 DUF6791 25 25 149 domain Y Y N DUF6791 domain-containing protein 131567 cellular organisms no rank 2004 EBI-EMBL Domain of unknown function (DUF6791) Domain of unknown function (DUF6791) This presumed domain is functionally uncharacterised. This domain family is found, and is approximately 160 amino acids in length. The domain is found in sequences that belong to the Thif family and is in association with Pfam:PF00899, located at its N-terminal. (from Pfam) NF042844.3 PF20594.3 DUF6794 27.1 27.1 83 domain Y Y N DUF6794 domain-containing protein 131567 cellular organisms no rank 780 EBI-EMBL Domain of unknown function (DUF6794) DUF6794 domain This domain is functionally uncharacterised, found in bacteria. It is around 120 amino acids in length. There is a conserved sequence motif GxxxRN. (from Pfam) NF042846.3 PF20597.3 pAdhesive_15 23.8 23.8 254 domain Y Y N collagen-binding domain-containing protein 15456768 131567 cellular organisms no rank 15702 EBI-EMBL Putative Ice-binding-like adhesive domain collagen-binding domain This domain is found N-terminal to repeating stalk domains in bacterial surface proteins. The structure model of this domain is highly similar to the Ice_binding adhesive domain (Pfam:PF11999). However, the bacterial species in which this domain can be found, are less likely to be water-based and thus the function seems unlikely to be ice-binding. This domain is found in a Bacillus anthracis protein with the gene name BA_0871 or BASH2_04951, which was described to be collagen binding and to be involved in the bacterial pathogenicity [1]. [1]. 15456768. Identification and biochemical characterization of two novel collagen binding MSCRAMMs of Bacillus anthracis. Xu Y, Liang X, Chen Y, Koehler TM, Hook M;. J Biol Chem. 2004;279:51760-51768. (from Pfam) NF042851.3 PF20613.3 HipA_2 27 27 240 subfamily Y Y N HipA family kinase 131567 cellular organisms no rank 20091 EBI-EMBL HipA-like kinase HipA family kinase This family of proteins is distantly related to the HipA protein Swiss:P23874. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 254 and 265 amino acids in length. (from Pfam) NF042861.3 PF20432.3 Xre-like-HTH 25.8 25.8 63 domain Y Y N antitoxin Xre-like helix-turn-helix domain-containing protein GO:0003677 30315706,30792174 131567 cellular organisms no rank 17365 EBI-EMBL Antitoxin Xre-like helix-turn-helix domain antitoxin Xre-like helix-turn-helix domain-containing protein This entry represents the N-terminal domain of the antitoxin component Xre of a type II toxin-antitoxin (TA) system, which is the helix-turn-helix (HTH) DNA binding domain, structurally similar to the Cro repressor, therefore, also referred to as HTH/Cro-like DNA-binding domain [2]. This domain is also found in other antitoxin components, associated with a C-terminal toxin-binding domain Pfam:PF09722 [1,2]. [1]. 30792174. An NAD(+) Phosphorylase Toxin Triggers Mycobacterium tuberculosis Cell Death. Freire DM, Gutierrez C, Garza-Garcia A, Grabowska AD, Sala AJ, Ariyachaokun K, Panikova T, Beckham KSH, Colom A, Pogenberg V, Cianci M, Tuukkanen A, Boudehen YM, Peixoto A, Botella L, Svergun DI, Schnappinger D, Schneider TR, Genevaux P, de Carvalho LPS, Wilmanns M, Parret AHA, Neyrolles O;. Mol Cell. 2019;73:1282-1291. [2]. 30315706. The RES domain toxins of RES-Xre toxin-antitoxin modules induce cell stasis by degrading NAD+. Skjerning RB, Senissar M, Winther KS, Gerdes K, Brodersen DE;. Mol Microbiol. 2019;111:221-236. (from Pfam) NF042862.3 PF20437.3 LonC_helical 24 24 34 domain Y Y N Lon-like protease helical domain-containing protein 23897463 131567 cellular organisms no rank 11688 EBI-EMBL Lon-like LonC helical domain Lon-like protease helical domain-containing protein This domain represents the helical domain found in the Lon-like LonC protease from Meiothermus taiwanensis [1], a Lon-like protease with no ATPase activity. [1]. 23897463. Structures of an ATP-independent Lon-like protease and its complexes with covalent inhibitors. Liao JH, Ihara K, Kuo CI, Huang KF, Wakatsuki S, Wu SH, Chang CI;. Acta Crystallogr D Biol Crystallogr. 2013;69:1395-1402. (from Pfam) NF042863.3 PF20441.3 TerL_nuclease 24 24 286 PfamEq Y Y N terminase TerL endonuclease subunit GO:0004519 26150523,28100693 131567 cellular organisms no rank 49009 EBI-EMBL Terminase large subunit, endonuclease domain terminase TerL endonuclease subunit This is the endonuclease domain of Terminase large subunit TerL [1,2], a key component of the DNA packing machinery in tailed bacteriophages and related viruses. TerL comprises a N-terminal ATPase domain (Pfam:PF03354) which powers the DNA translocation and this C-terminal endonuclease domain that cuts concatemeric DNA first in the initiation phase in a sequence specific site and later in the completion stage of the DNA packaging process when the capsid is full [1,2]. Cryo-EM studies indicate that TerL forms a pentamer that binds to a dodecameric assembly called portal and attaches to the capsid. It has been proposed that nuclease domains form a radially arranged ring that is proximal to portal, playing a key role in pentamer assembly [2]. This nuclease domain has a RNAse H-like fold and it has been proposed to utilise a two-metal catalysis mechanism like in other RNAse H-like endonucleases such as RNase H, transposases, retroviral integrases and RuvC Holliday junction resolvases [1]. [1]. 28100693. Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism. Xu RG, Jenkins HT, Chechik M, Blagova EV, Lopatina A, Klimuk E, Minakhin L, Severinov K, Greive SJ, Antson AA;. Nucleic Acids Res. 2017;45:3580-3590. [2]. 26150523. Structure and mechanism of the ATPase that powers viral genome packaging. Hilbert BJ, Hayes JA, Stone NP, Duffy CM, Sankaran B, Kelch BA;. Proc Natl Acad Sci U S A. 2015;112:E3792-E3799. (from Pfam) NF042864.3 PF20442.3 BrxL_N 28.2 28.2 132 domain Y Y N anti-phage BREX system Lon protease BrxL GO:0051607 25452498 131567 cellular organisms no rank 6922 EBI-EMBL BREX system Lon protease-like protein BrxL N-terminal anti-phage BREX system Lon protease BrxL N-terminal This entry represents the N-terminal domain of BREX system Lon protease-like protein BrxL from Bacillus cereus and similar proteins. BrxL is part of a type 1 BREX system, which contains a C-terminal Lon-like protease domain (Pfam:PF05362). BREX systems (bacteriophage exclusion) provide immunity against bacteriophage, a system that allows phage adsorption but prevents phage DNA replication, without degradation of the phage DNA [1]. [1]. 25452498. BREX is a novel phage resistance system widespread in microbial genomes. Goldfarb T, Sberro H, Weinstock E, Cohen O, Doron S, Charpak-Amikam Y, Afik S, Ofir G, Sorek R;. EMBO J. 2015;34:169-183. (from Pfam) NF042868.3 PF20459.3 DUF6712 27 27 276 subfamily Y Y N DUF6712 family protein 131567 cellular organisms no rank 1305 EBI-EMBL Family of unknown function (DUF6712) DUF6712 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 270 and 340 amino acids in length. (from Pfam) NF042869.3 PF20463.3 PDH_C 22 22 102 domain Y Y N prephenate dehydrogenase dimerization domain-containing protein 31750992 131567 cellular organisms no rank 72801 EBI-EMBL Prephenate dehydrogenase, dimerization domain prephenate dehydrogenase dimerization domain-containing protein Members of this family are prephenate dehydrogenases EC:1.3.1.12 (PDHs) involved in tyrosine biosynthesis [1]. This is the C-terminal, helical dimerization domain of PDHs [1]. [1]. 31750992. Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain. Shabalin IG, Gritsunov A, Hou J, Slawek J, Miks CD, Cooper DR, Minor W, Christendat D;. FEBS J. 2020;287:2235-2255. (from Pfam) NF042870.3 PF20464.3 MmeI_N 27 27 181 domain Y Y N type IIL restriction-modification enzyme MmeI 18931376,27082731,3016643,9858752 131567 cellular organisms no rank 12030 EBI-EMBL MmeI, N-terminal domain type IIL restriction-modification enzyme MmeI N-terminal Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide [2, 3, 4]. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919) [1]. This domain corresponds to the N-terminal endonuclease, it cuts the two DNA strands at one site simultaneously with enzyme bound at two sites interacting to accomplish the cleavage [2]. Paper describing PDB structure 5hr4. [1]. 27082731. Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities. Callahan SJ, Luyten YA, Gupta YK, Wilson GG, Roberts RJ, Morgan RD, Aggarwal AK;. PLoS Biol. 2016;14:e1002442. [2]. 18931376. MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection. Morgan RD, Bhatia TK, Lovasco L, Davis TB;. Nucleic Acids Res. 2008;36:6558-6570. [3]. 3016643. Isolation and computer-aided characterization of MmeI, a type II restriction endonuclease from Methylophilus methylotrophus. Boyd AC, Charles IG, Keyte JW, Brammar WJ;. Nucleic Acids Res. 1986;14:5255-5274. [4]. 9858752. Two intertwined methylation activities of the MmeI restriction-modification class-IIS system from Methylophilus methylotrophus. Tucholski J, Zmijewski JW, Podhajska AJ;. Gene. 1998;223:293-302. (from Pfam) NF042871.3 PF20466.3 MmeI_TRD 27 27 207 domain Y Y N type IIL restriction-modification enzyme MmeI 18931376,27082731,3016643,9858752 131567 cellular organisms no rank 14533 EBI-EMBL MmeI, target recognition domain MmeI target recognition domain Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide [2, 3, 4]. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919) [1]. The DNA is embedded between the TRD and the MTase domain. The TRD makes contacts to the DNA bases primarily in the major groove, while the MTase domain makes several contacts to the DNA in the minor groove [1]. This domain corresponds to the TRD. It consists of two alpha/beta subdomains. Paper describing PDB structure 5hr4. [1]. 27082731. Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities. Callahan SJ, Luyten YA, Gupta YK, Wilson GG, Roberts RJ, Morgan RD, Aggarwal AK;. PLoS Biol. 2016;14:e1002442. [2]. 18931376. MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection. Morgan RD, Bhatia TK, Lovasco L, Davis TB;. Nucleic Acids Res. 2008;36:6558-6570. [3]. 3016643. Isolation and computer-aided characterization of MmeI, a type II restriction endonuclease from Methylophilus methylotrophus. Boyd AC, Charles IG, Keyte JW, Brammar WJ;. Nucleic Acids Res. 1986;14:5255-5274. [4]. 9858752. Two intertwined methylation activities of the MmeI restriction-modification class-IIS system . TRUNCATED at 1650 bytes (from Pfam) NF042872.3 PF20470.3 HTH_61 24.3 24.3 92 domain Y Y N HTH domain-containing protein 37409572 131567 cellular organisms no rank 770 EBI-EMBL Helix-turn-helix domain Helix-turn-helix domain This entry represents a presumed helix-turn-helix domain found in DNA polymerase theta. (from Pfam) NF042873.3 PF20472.3 PDDEXK_11 23.7 23.7 145 superfamily Y Y N PD-(D/E)XK nuclease superfamily protein 131567 cellular organisms no rank 1001 EBI-EMBL PD-(D/E)XK nuclease superfamily domain PD-(D/E)XK nuclease superfamily domain This family contains many hypothetical bacterial proteins. It has been identified as a member of the PD-(D/E)XK nuclease superfamily. (from Pfam) NF042889.3 PF20529.3 DUF6744 27 27 314 subfamily Y Y N DUF6744 family protein 131567 cellular organisms no rank 401 EBI-EMBL Family of unknown function (DUF6744) DUF6744 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 290 and 350 amino acids in length. (from Pfam) NF042892.3 PF20537.3 DUF6752 27 27 55 domain Y Y N DUF6752 domain-containing protein 131567 cellular organisms no rank 525 EBI-EMBL Domain of unknown function (DUF6752) DUF6752 domain This presumed domain family is functionally uncharacterised. It is found in bacterial proteins and is typically 54 amino acids in length. (from Pfam) NF042900.3 PF20585.3 Pectate_lyase_5 24.3 24.3 126 domain Y Y N pectate lyase-like adhesive domain-containing protein 29507249 131567 cellular organisms no rank 7215 EBI-EMBL Putative pectate lyase-like adhesive domain pectate lyase-like adhesive domain This putative domain is found at the N-terminus of a large number of bacterial proteins. Its adhesive function was described in Lactobacillus reuteri serine-rich repeat proteins [1]. Structure predictions show it is composed of a beta solenoid repeat related to Pectate lyase. [1]. 29507249. Structural basis for the role of serine-rich repeat proteins from Lactobacillus reuteri in gut microbe-host interactions. Sequeira S, Kavanaugh D, MacKenzie DA, Suligoj T, Walpole S, Leclaire C, Gunning AP, Latousakis D, Willats WGT, Angulo J, Dong C, Juge N;. Proc Natl Acad Sci U S A. 2018;115:E2706. (from Pfam) NF042903.3 PF20605.3 Antitox_RHH 27.2 27.2 50 domain Y Y N ribbon-helix-helix domain-containing protein 15864262,9857196 131567 cellular organisms no rank 1436 EBI-EMBL Antitoxin-like ribbon-helix-helix Antitoxin-like ribbon-helix-helix This presumed domain is found in bacteria, and is approximately 60 amino acids in length. Structure prediction suggests that it has a ribbon-helix-helix motif, a DNA-binding motif commonly found in antitoxin families [1,2]. Members containing this domain may be related to CopG antitoxin family. [1]. 9857196. The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator. Gomis-R th FX, Sol M, Acebo P, Parraga A, Guasch A, Eritja R, Gonzalez A, Espinosa M, del Solar G, Coll M. EMBO J 1998;17:7404-7415. [2]. 15864262. Prokaryotic toxin-antitoxin stress response loci. Gerdes K, Christensen SK, Lobner-Olesen A;. Nat Rev Microbiol. 2005;3:371-382. (from Pfam) NF042945.1 DUF4297_antiphage 300 300 400 equivalog Y Y N DUF4297 family anti-phage-associated protein 32855333 131567 cellular organisms no rank 560 NCBIFAM DUF4297 family anti-phage-associated protein Proteins of this family contain a DUF4297 domain and are associated with anti-phage activities. NF042961.1 DUF3780_antiphage 200 200 184 equivalog Y Y N anti-phage-associated DUF3780 domain-containing protein GO:0051607 32855333 131567 cellular organisms no rank 418 NCBIFAM anti-phage-associated DUF3780 domain-containing protein Proteins of this family are associated with the restriction-like anti-phage system. The role of the proteins in the anti-phage system has not been fully understood. NF042962.1 DUF499_antiphage 1200 1200 1025 equivalog Y Y N anti-phage-associated DUF499 domain-containing protein GO:0051607 32855333 131567 cellular organisms no rank 454 NCBIFAM anti-phage-associated DUF499 domain-containing protein Proteins of this family are associated with the restriction-like anti-phage system. The role of the proteins in the anti-phage system has not been fully understood. NF042963.1 DUF1156_antiphage 1000 1000 960 equivalog Y Y N anti-phage-associated DUF1156 domain-containing protein GO:0051607 32855333 131567 cellular organisms no rank 710 NCBIFAM anti-phage-associated DUF1156 domain-containing protein Proteins of this family are associated with the restriction-like anti-phage system. The role of the proteins in the anti-phage system has not been fully understood. NF042964.1 phospholipD_antiphage 1100 1100 895 equivalog Y Y N phospholipase D-like domain-containing anti-phage protein GO:0005524,GO:0051607 32855333 131567 cellular organisms no rank 682 NCBIFAM phospholipase D-like domain-containing anti-phage protein Proteins of this family are components of the restriction-like anti-phage system. These proteins contain a phospholipase D-like domain in the N-terminal and a helicase domain in the C-terminal. NF042973.1 ADPpolyPPhtase 450 450 285 equivalog Y Y N ADP-polyphosphate phosphotransferase 2.7.4.- GO:0006797,GO:0008976,GO:0016310 19001261 131567 cellular organisms no rank 538 NCBIFAM ADP-polyphosphate phosphotransferase NF043002.1 HProlDhtase 500 500 366 equivalog Y Y N cis-3-hydroxy-L-proline dehydratase 4.2.1.171 GO:0016836,GO:0016853,GO:1901605 25608448 131567 cellular organisms no rank 432 NCBIFAM cis-3-hydroxy-L-proline dehydratase NF043039.1 HgcAB_like 285 285 350 equivalog Y Y N HgcAB-like fusion protein 26601305 131567 cellular organisms no rank 21 NCBIFAM HgcAB-like fusion protein Members of this family have a long N-terminal region that resembles HgcA, and a shorter C-terminal region that resembles HgcB, where HgcA and HcgB are a protein pair both required for the methylation that converts inorganic mercury into the more toxic organic compound methylmercury, a neurotoxin in humans. The HgcAB-like fusion protein is not currently known to have this activity. Some members have an additional N-terminal methyltransferase domain, while others are encoded adjacent to an uncharacterized methyltransferase. NF043040.1 corrin_prot_MT 180 180 216 hypoth_equivalog Y Y N corrinoid protein-associated methyltransferase CpaM cpaM 2.1.1.- GO:0008757 131567 cellular organisms no rank 23 NCBIFAM corrinoid protein-associated methyltransferase CpaM NF043068.1 glycl_HYPD 1100 1100 784 equivalog Y Y N trans-4-hydroxy-L-proline dehydratase hypD 4.2.1.172 GO:0019471 28183913 131567 cellular organisms no rank 1544 NCBIFAM trans-4-hydroxy-L-proline dehydratase The trans-4-hydroxy-L-proline dehydratase HypD is a glycyl-radical enzyme that depends on an activator that is a radical SAM enzyme. It is involved in metabolism of trans-4-hydroxy-L-proline, the most abundant modified residue in human proteins. NF044283.2 PF20696.2 UbiD_C 24.2 24.2 127 domain Y N N 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain 23671667,25862228,26083754,28057757,28857436,782527 131567 cellular organisms no rank 51320 EBI-EMBL 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain This family has been characterised as 3-octaprenyl-4- hydroxybenzoate carboxy-lyase enzymes [1]. This enzyme catalyses the third reaction in ubiquinone biosynthesis. For optimal activity the carboxy-lase was shown to require Mn2+ [1]. This entry represents the C-terminal domain. [1]. 782527. Membrane-associated reactions in ubiquinone biosynthesis in Escherichia coli. 3-Octaprenyl-4-hydroxybenzoate carboxy-lyase. Leppik RA, Young IG, Gibson F;. Biochim Biophys Acta 1976;436:800-810. [2]. 23671667. Structural insights into the UbiD protein family from the crystal structure of PA0254 from Pseudomonas aeruginosa. Jacewicz A, Izumi A, Brunner K, Schnell R, Schneider G;. PLoS One. 2013;8:e63161. [3]. 25862228. Structure and Mechanism of Ferulic Acid Decarboxylase (FDC1) from Saccharomyces cerevisiae. Bhuiya MW, Lee SG, Jez JM, Yu O;. Appl Environ Microbiol. 2015;81:4216-4223. [4]. 26083754. New cofactor supports alpha,beta-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition. Payne KA, White MD, Fisher K, Khara B, Bailey SS, Parker D, Rattray NJ, Trivedi DK, Goodacre R, Beveridge R, Barran P, Rigby SE, Scrutton NS, Hay S, Leys D;. Nature. 2015;522:497-501. [5]. 28057757. Oxidative Maturation and Structural Characterization of Prenylated FMN Binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis. Marshall SA, Fisher K, Ni Cheallaigh A, White MD, Payne KA, Parker DA, Rigby SE, Leys D;. J Biol Chem. 2017;292:4623-4637. [6]. 28857436. Regioselective para-Carboxylation of Catechols with a Prenylated Flavin Dependent Decarboxylase. Payer SE, Marshall SA, Barland N, Sheng X, Reiter T, Dordic A, Steink. TRUNCATED at 1650 bytes (from Pfam) NF044284.2 PF20698.2 PIN-TPR-GreABC 27.8 27.8 138 domain Y Y N PIN domain-containing protein 34061031 131567 cellular organisms no rank 1888 EBI-EMBL PIN domain associated with the TPR-GreAB-C-PIN system PIN domain associated with the TPR-GreAB-C-PIN system This is a divergent PIN domain present in the TPR-GreAB-C-PIN type conflict system. These proteins have a constant module comprising of TPR-repeats, the GreA/B-C-terminal domain and the PIN domain. The N-terminal domain is variable and usually contains effector domains or EADs. The PIN domain is predicted to cleave emerging nascent transcripts [1]. [1]. 34061031. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. Kaur G, Iyer LM, Burroughs AM, Aravind L;. Elife. 2021; [Epub ahead of print] (from Pfam) NF044287.2 PF20703.2 nSTAND1 27.1 27.1 379 domain Y N N Novel STAND NTPase 1 34061031 131567 cellular organisms no rank 55673 EBI-EMBL Novel STAND NTPase 1 Novel STAND NTPase 1 This is a novel domain of the STAND-superfamily of AAA+ ATPases found in bacterial conflict systems [1]. [1]. 34061031. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. Kaur G, Iyer LM, Burroughs AM, Aravind L;. Elife. 2021; [Epub ahead of print] (from Pfam) NF044290.2 PF20712.2 CyanoTRADDas_TM 24.3 24.3 68 domain Y Y N TRADD-N-associated membrane domain-containing protein 34061031 131567 cellular organisms no rank 2772 EBI-EMBL Cyanobacterial TRADD-N associated 2-Transmembrane domain Cyanobacterial TRADD-N associated 2-Transmembrane domain This is a domain with two transmembrane helices predicted to function as a pore-forming effector and found mainly in bacterial conflict systems [1]. [1]. 34061031. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. Kaur G, Iyer LM, Burroughs AM, Aravind L;. Elife. 2021; [Epub ahead of print] (from Pfam) NF044293.2 PF20721.2 C19orf12 30 30 163 domain Y N N C19orf12-like protein 131567 cellular organisms no rank 124 EBI-EMBL C19orf12-like protein C19orf12-like protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are approximately 140 amino acids in length. This family includes the human protein C19orf12. These proteins contain a glycine zipper motif. (from Pfam) NF044296.2 PF20731.2 RE_NgoFVII_C 23.8 23.8 131 domain Y N N NgoFVII C-terminal B3-like DNA-binding domain 25429979,9988771 131567 cellular organisms no rank 1776 EBI-EMBL NgoFVII C-terminal B3-like DNA-binding domain NgoFVII C-terminal B3-like DNA-binding domain This family includes the NgoFVII (recognises GCSGC but cleavage site unknown) restriction endonuclease. This entry represents the RIFT related domain [1,2]. [1]. 9988771. Regions of endonuclease EcoRII involved in DNA target recognition identified by membrane-bound peptide repertoires. Reuter M, Schneider-Mergener J, Kupper D, Meisel A, Mackeldanz P, Kruger DH, Schroeder C;. J Biol Chem. 1999;274:5213-5221. [2]. 25429979. Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII. Tamulaitiene G, Silanskas A, Grazulis S, Zaremba M, Siksnys V;. Nucleic Acids Res. 2014;42:14022-14030. (from Pfam) NF044297.2 PF20736.2 Glyco_hydro127M 24.2 24.2 95 domain Y N N Beta-L-arabinofuranosidase, GH127 middle domain 24385433 131567 cellular organisms no rank 44632 EBI-EMBL Beta-L-arabinofuranosidase, GH127 middle domain Beta-L-arabinofuranosidase, GH127 middle domain This entry represents the first of two beta sandwich domains found in the beta-L-arabinofuranosidase enzyme, EC:3.2.1.185 [1]. This domain shows a similarity to C-terminal domains of GH44, GH27, and GH39 enzymes [1]. [1]. 24385433. Characterization of a novel beta-L-arabinofuranosidase in Bifidobacterium longum: functional elucidation of a DUF1680 protein family member. Fujita K, Takashi Y, Obuchi E, Kitahara K, Suganuma T;. J Biol Chem. 2014;289:5240-5249. (from Pfam) NF044298.2 PF20737.2 Glyco_hydro127C 23.7 23.7 71 domain Y N N Glycoside hydrolase family 127 C-terminal domain 24680821,28329766 131567 cellular organisms no rank 21938 EBI-EMBL Glycoside hydrolase family 127 C-terminal domain Glycoside hydrolase family 127 C-terminal domain This entry represents the second beta sandwich domain found in enzymes belonging to the glycosyl hydrolase 127 family [1]. The beta-sandwich domain is somewhat similar to the N-terminal domain of ErbB4 kinase and is involved in formation of a dimer, which is created by a crystallographic 2-fold axis [1]. Paper describing PDB structure 3wkw. [1]. 24680821. Crystal structure of glycoside hydrolase family 127 beta-l-arabinofuranosidase from Bifidobacterium longum. Ito T, Saikawa K, Kim S, Fujita K, Ishiwata A, Kaeothip S, Arakawa T, Wakagi T, Beckham GT, Ito Y, Fushinobu S;. Biochem Biophys Res Commun. 2014;447:32-37. Paper describing PDB structure 5mqo. [2]. 28329766. Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Ndeh D, Rogowski A, Cartmell A, Luis AS, Basle A, Gray J, Venditto I, Briggs J, Zhang X, Labourel A, Terrapon N, Buffetto F, Nepogodiev S, Xiao Y, Field RA, Zhu Y, O'Neil MA, Urbanowicz BR, York WS, Davies GJ, Abbott DW, Ralet MC, Martens EC, Henrissat B, Gilbert HJ;. Nature. 2017;544:65-70. (from Pfam) NF044310.2 PF20782.2 TssR_VWA 25.7 25.7 304 domain Y N N TssR protein VWA domain 26768901 131567 cellular organisms no rank 1535 EBI-EMBL TssR protein VWA domain TssR protein VWA domain This entry represents the VWA-like domain from the TssR protein. T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex [1]. [1]. 26768901. Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements. Coyne MJ, Roelofs KG, Comstock LE;. BMC Genomics. 2016;17:58. (from Pfam) NF044313.2 PF20791.2 Acyl-ACP_TE_C 21 21 101 domain Y N N Acyl-ACP thioesterase C-terminal domain 15531590,1621095,7479856 131567 cellular organisms no rank 53615 EBI-EMBL Acyl-ACP thioesterase C-terminal domain Acyl-ACP thioesterase C-terminal domain This family consists of various acyl-acyl carrier protein (ACP) thioesterases (TE) these terminate fatty acyl group extension via hydrolysing an acyl group on a fatty acid [1]. These proteins are usually composed of a pair of tandem HotDog domains. This entry represents the C-terminal one of the pair. [1]. 7479856. Modification of the substrate specificity of an acyl-acyl carrier protein thioesterase by protein engineering. Yuan L, Voelker TA, Hawkins DJ;. Proc Natl Acad Sci U S A 1995;92:10639-10643. [2]. 1621095. Fatty acid biosynthesis redirected to medium chains in transgenic oilseed plants. Voelker TA, Worrell AC, Anderson L, Bleibaum J, Fan C, Hawkins DJ, Radke SE, Davies HM;. Science 1992;257:72-74. [3]. 15531590. A structural model of the plant acyl-acyl carrier protein thioesterase FatB comprised of two helix/4-stranded sheet domains: The N-terminal domain containing residues that affect specificity, the C-terminal domain containing catalytic residues. Mayer KM, Shanklin J;. J Biol Chem 2004; [Epub ahead of print] (from Pfam) NF044352.2 PF20934.2 phi29_gp9_C 27 27 449 domain Y N N Bacillus phage phi29, Tail knob protein gp9, C-terminal domain 22891295,27309813 131567 cellular organisms no rank 66 EBI-EMBL Bacillus phage phi29, Tail knob protein gp9, C-terminal domain Bacillus phage phi29, Tail knob protein gp9, C-terminal domain This domain is found at the C-terminal end of Tail knob protein gp9 from Bacillus phage phi29 and similar proteins from tailed bacteriophages. This protein blocks the end of the tube before DNA ejection while forming a channel perforating the host membrane in the process by adopting a hexameric tube structure with six flexible hydrophobic loops. This entry represents the region of the protein that forms the central part of the tube. It is organised into an alpha/beta subdomain, a long loop that protrudes from the inner wall covering about two-thirds of the tube, and a beta-domain in which the beta-strands are almost parallel with the tube axis [1]. Paper describing PDB structure 5fb4. [1]. 27309813. The bacteriophage varphi29 tail possesses a pore-forming loop for cell membrane penetration. Xu J, Gui M, Wang D, Xiang Y;. Nature. 2016;534:544-547. Paper describing PDB structure 4eo2. [2]. 22891295. Structural investigations of a Podoviridae streptococcus phage C1, implications for the mechanism of viral entry. Aksyuk AA, Bowman VD, Kaufmann B, Fields C, Klose T, Holdaway HA, Fischetti VA, Rossmann MG;. Proc Natl Acad Sci U S A. 2012;109:14001-14006. (from Pfam) NF044358.2 PF20957.2 GxGYxYP_N_2nd 24.5 24.5 68 domain Y N N GxGYxYP_N second domain 131567 cellular organisms no rank 2399 EBI-EMBL GxGYxYP_N second domain GxGYxYP_N second domain This entry represents a domain that is found repeated in three copies per protein and is likely to be involved in binding the bacterial cell wall. This domain is found in association with Pfam:PF14323. (from Pfam) NF044374.2 PF20999.2 DUF4438_C 27 27 124 domain Y N N Domain of unknown function (DUF4438), C-terminal 131567 cellular organisms no rank 1042 EBI-EMBL Domain of unknown function (DUF4438), C-terminal Domain of unknown function (DUF4438), C-terminal This is the C-terminal domain of TM_1086 which consists of a 3-layer sandwich. (from Pfam) NF044377.2 PF21011.2 CetZ_C 21.6 21.6 180 domain Y N N Tubulin-like CetZ, C-terminal domain 25533961 131567 cellular organisms no rank 2175 EBI-EMBL Tubulin-like CetZ, C-terminal domain Tubulin-like CetZ, C-terminal domain This is the C-terminal domain of CetZ proteins, which are tubulin-like proteins involved in control cell shape in Archaea and some bacteria [1]. CetZ proteins are related with Tubulin/FtsZ, and has the Tubulin GTPase domain (Pfam:PF00091) at the N-terminal. This domain has a two-layer alpha-beta structure with an alpha-helical extension. [1]. 25533961. CetZ tubulin-like proteins control archaeal cell shape. Duggin IG, Aylett CH, Walsh JC, Michie KA, Wang Q, Turnbull L, Dawson EM, Harry EJ, Whitchurch CB, Amos LA, Lowe J;. Nature. 2015;519:362-365. (from Pfam) NF044379.2 PF21018.2 BipA_C 23.8 23.8 110 domain Y N N TypA/BipA C-terminal domain 26163516,26283392 131567 cellular organisms no rank 52872 EBI-EMBL TypA/BipA C-terminal domain TypA/BipA C-terminal domain This entry represents the C-terminal domain of the TypA/BipA protein. The C-terminal domain of BipA, consisting of residues, forms a unique motif with two crossed beta sheets (comprising of two and four beta-strands, respectively) wrapped by three short alpha helices forming a nearly equilateral triangle [1]. Paper describing PDB structure 4zci. [1]. 26163516. Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli. Fan H, Hahm J, Diggs S, Perry JJP, Blaha G;. J Biol Chem. 2015;290:20856-20864. Paper describing PDB structure 5a9v. [2]. 26283392. Structure of BipA in GTP form bound to the ratcheted ribosome. Kumar V, Chen Y, Ero R, Ahmed T, Tan J, Li Z, Wong AS, Bhushan S, Gao YG;. Proc Natl Acad Sci U S A. 2015;112:10944-10949. (from Pfam) NF044381.2 PF21027.2 Sde0182_C 27 27 83 domain Y N N Cellulose-binding protein Sde0182, C-terminal domain 21905122 131567 cellular organisms no rank 5817 EBI-EMBL Cellulose-binding protein Sde0182, C-terminal domain Cellulose-binding protein Sde0182, C-terminal domain This domain is found at the C-terminal end of Cellulose-binding protein Sde0182 from Saccharophagus degradans (Swiss:Q21PD3), which seems to have capacity to bind plant carbohydrates. This region shows a beta-sandwich fold that consists of two beta-sheets with seven beta-strands in total. It has structural similarity to a polycystic kidney domain (PKD, Pfam:PF00801) and lacks the solvent exposed aromatic residues typically associated with an ability to bind carbohydrates [1]. This domain is also found in other uncharacterised bacterial and fungal proteins. [1]. 21905122. Ab initio phasing of a nucleoside hydrolase-related hypothetical protein from Saccharophagus degradans that is associated with carbohydrate metabolism. Hehemann JH, Marsters C, Boraston AB;. Proteins. 2011;79:2992-2998. (from Pfam) NF044405.2 PF21120.2 MCM_WH_arc 26.1 26.1 63 domain Y N N Archaeal MCM, winged-helix 25712103 131567 cellular organisms no rank 985 EBI-EMBL Archaeal MCM, winged-helix Archaeal MCM, winged-helix This entry represents the conserved truncated winged helix domain of minichromosome maintenance complex (MCM, a replicative DNA helicase) from archaea, which lacks the two typical 'wings' of canonical WH domains [1]. Paper describing PDB structure 2ma3. [1]. 25712103. Structure and regulatory role of the C-terminal winged helix domain of the archaeal minichromosome maintenance complex. Wiedemann C, Szambowska A, Hafner S, Ohlenschlager O, Guhrs KH, Gorlach M;. Nucleic Acids Res. 2015;43:2958-2967. (from Pfam) NF044411.2 PF21148.2 NSUN5_fdxn-like 24.5 24.5 78 domain Y N N NOL1/NOP2/Sun domain family member 5, ferredoxin-like domain 14997580,23913415,31722427 131567 cellular organisms no rank 11 EBI-EMBL NOL1/NOP2/Sun domain family member 5, ferredoxin-like domain NOL1/NOP2/Sun domain family member 5, ferredoxin-like domain This is a ferredoxin-like domain of NOL1/NOP2/Sun domain family member 5, found at the N-terminal of the methyltransferase domain [1,4]. NSUN5 is a SAM-dependent methyltransferase that specifically methylates the C(5) position of cytosine 3782 in 28S rRNA [2,3]. Paper describing PDB structure 1ixk. [1]. 14997580. Crystal structure of human p120 homologue protein PH1374 from Pyrococcus horikoshii. Ishikawa I, Sakai N, Tamura T, Yao M, Watanabe N, Tanaka I;. Proteins. 2004;54:814-816. [2]. 23913415. Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA, respectively. Sharma S, Yang J, Watzinger P, Kotter P, Entian KD;. Nucleic Acids Res. 2013;41:9062-9076. [3]. 31722427. Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth. Heissenberger C, Liendl L, Nagelreiter F, Gonskikh Y, Yang G, Stelzer EM, Krammer TL, Micutkova L, Vogt S, Kreil DP, Sekot G, Siena E, Poser I, Harreither E, Linder A, Ehret V, Helbich TH, Grillari-Voglauer R, Jansen-Durr P, Kos M, Polacek N, Grillari J, Schosserer M;. Nucleic Acids Res. 2019;47:11807-11825. (from Pfam) NF044418.2 PF21172.2 CueP 27 27 138 domain Y N N Periplasmic copper-binding protein CueP 19538445,20534583,24100307 131567 cellular organisms no rank 3609 EBI-EMBL Periplasmic copper-binding protein CueP Periplasmic copper-binding protein CueP This protein family includes the periplasmic copper-binding protein CueP from Salmonella enterica and similar bacterial sequences. CueP is related to copper-resistance, copper-storage and is as an essential factor in the transfer of copper ions, playing a role in the suppression of oxidative stress. CueP, which adopts a dimeric assembly, consists of two domains: an N-terminal domain with two alpha-helices and three beta-strands organized into a beta-sheet and a larger C-terminal domain that comprises a four-stranded beta-sheet and a two-stranded beta-sheet that face each other [1-3]. Paper describing PDB structure 4gqz. [1]. 24100307. Structure of the periplasmic copper-binding protein CueP from Salmonella enterica serovar Typhimurium. Yoon BY, Kim YH, Kim N, Yun BY, Kim JS, Lee JH, Cho HS, Lee K, Ha NC;. Acta Crystallogr D Biol Crystallogr. 2013;69:1867-1875. [2]. 19538445. Alternative periplasmic copper-resistance mechanisms in Gram negative bacteria. Pontel LB, Soncini FC;. Mol Microbiol. 2009;73:212-225. [3]. 20534583. Copper homeostasis in Salmonella is atypical and copper-CueP is a major periplasmic metal complex. Osman D, Waldron KJ, Denton H, Taylor CM, Grant AJ, Mastroeni P, Robinson NJ, Cavet JS;. J Biol Chem. 2010;285:25259-25268. (from Pfam) NF044424.2 PF21196.2 PcrA_UvrD_tudor 23.9 23.9 48 domain Y N N PcrA/UvrD tudor domain 10388562,24143224,28160601,33097771,8934527 131567 cellular organisms no rank 65035 EBI-EMBL PcrA/UvrD tudor domain PcrA/UvrD tudor domain The PcrA/UvrD helicase binds directly to RNA polymerase (RNAP). This entry represents the C-terminal tudor domain that mediates interaction with RNA polymerase [1-5]. Paper describing PDB structure 1pjr. [1]. 8934527. Crystal structure of a DExx box DNA helicase. Subramanya HS, Bird LE, Brannigan JA, Wigley DB;. Nature. 1996;384:379-383. Paper describing PDB structure 1qhh. [2]. 10388562. DNA binding mediates conformational changes and metal ion coordination in the active site of PcrA helicase. Soultanas P, Dillingham MS, Velankar SS, Wigley DB;. J Mol Biol. 1999;290:137-148. Paper describing PDB structure 4c2t. [3]. 24143224. Structural and mechanistic insight into DNA unwinding by Deinococcus radiodurans UvrD. Stelter M, Acajjaoui S, McSweeney S, Timmins J;. PLoS One. 2013;8:e77364. Paper describing PDB structure 5dma. [4]. 28160601. The structure and function of an RNA polymerase interaction domain in the PcrA/UvrD helicase. Sanders K, Lin CL, Smith AJ, Cronin N, Fisher G, Eftychidis V, McGlynn P, Savery NJ, Wigley DB, Dillingham MS;. Nucleic Acids Res. 2017;45:3875-3887. Paper describing PDB structure 6yi2. [5]. 33097771. UvrD helicase-RNA polymerase interactions are governed by UvrD's carboxy-terminal Tudor domain. Kawale AA, Burmann BM;. Commun Biol. 2020;3:607. (from Pfam) NF044428.2 PF21211.2 FkbH_N 27 27 192 domain Y N N FkbH, N-terminal domain 131567 cellular organisms no rank 1659 EBI-EMBL FkbH, N-terminal domain FkbH, N-terminal domain This domain is found at the N-terminal end of a group of bacterial predicted enzymes, including BF1531 from Bacteroides fragilis. It shows an alpha-beta structure. (from Pfam) NF044433.2 PF21248.2 SoFic-like_C 27 27 76 domain Y N N Protein adenylyltransferase SoFic-like, C-terminal domain 19127588,22266942,23738009 131567 cellular organisms no rank 6407 EBI-EMBL Protein adenylyltransferase SoFic-like, C-terminal domain Protein adenylyltransferase SoFic-like, C-terminal domain This domain is found at the C-terminal end of Protein adenylyltransferase SoFic from Shewanella oneidensis and similar bacterial sequences. SoFic mediates the addition of adenosine 5'-monophosphate (AMP) to specific residues of target proteins. This is a winged-helix DNA-binding domain often found associated with Pfam:PF02661 [1-3]. Paper describing PDB structure 3eqx. [1]. 19127588. Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 A resolution. Das D, Krishna SS, McMullan D, Miller MD, Xu Q, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Burra P, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Elsliger MA, Ernst D, Feuerhelm J, Grzechnik A, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Sefcovic N, Tien H, Trame CB, Trout CV, van den Bedem H, Weekes D, White A, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Proteins. 2009;75:264-271. Paper describing PDB structure 3zcn. [2]. 23738009. Conserved inhibitory mechanism and competent ATP binding mode for adenylyltransferases with Fic fold. Goepfert A, Stanger FV, Dehio C, Schirmer T;. PLoS One. 2013;8:e64901. [3]. 22266942. Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins. Engel P, Goepfert A, Stanger FV, Harms A, Schmidt A, Schirmer T, Dehio C;. Nature. 2012;482:107-110. (from Pfam) NF044439.2 PF21280.2 Helicase_dom4_arc 27 27 125 domain Y N N Archaeal helicase, domain 4 17558417,18056710,19159486 131567 cellular organisms no rank 1669 EBI-EMBL Archaeal helicase, domain 4 Archaeal helicase, domain 4 This entry includes archaeal helicases from the helicase superfamily 2, and represents domain 4 described in [1,3]. This domain folds into a seven alpha-helix bundle structure and seems to be unique within this helicase family. The central helix acts as a ratchet and mediates stacking interactions on base moieties of the DNA [3]. Paper describing PDB structure 2p6r. [1]. 17558417. Structural basis for DNA duplex separation by a superfamily-2 helicase. Buttner K, Nehring S, Hopfner KP;. Nat Struct Mol Biol. 2007;14:647-652. Paper describing PDB structure 2va8. [2]. 18056710. Structure of the DNA repair helicase hel308 reveals DNA binding and autoinhibitory domains. Richards JD, Johnson KA, Liu H, McRobbie AM, McMahon S, Oke M, Carter L, Naismith JH, White MF;. J Biol Chem. 2008;283:5118-5126. Paper describing PDB structure 2zj2. [3]. 19159486. Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm. Oyama T, Oka H, Mayanagi K, Shirai T, Matoba K, Fujikane R, Ishino Y, Morikawa K;. BMC Struct Biol. 2009;9:2. (from Pfam) NF044440.2 PF21291.2 CYNS_N 27.1 27.1 69 domain Y N N Cyanate hydratase, N-terminal 10801492,25849512,28613863,32880586 131567 cellular organisms no rank 10157 EBI-EMBL Cyanate hydratase, N-terminal Cyanate hydratase, N-terminal Cyanate hydratase (also known as cyanate lyase) catalyses the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide, allowing the host organisms to overcome the toxicity of environmental cyanate [1-4]. It consists of an N-terminal five-helix bundle domain that shows structural similarity to DNA-binding HTH domains and a C-terminal catalytic domain, which has a unique fold [4]. Paper describing PDB structure 1dw9. [1]. 10801492. Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site. Walsh MA, Otwinowski Z, Perrakis A, Anderson PM, Joachimiak A;. Structure Fold Des 2000;8:505-514. Paper describing PDB structure 4y42. [2]. 25849512. Serendipitous crystallization and structure determination of cyanase (CynS) from Serratia proteamaculans. Butryn A, Stoehr G, Linke-Winnebeck C, Hopfner KP;. Acta Crystallogr F Struct Biol Commun. 2015;71:471-476. Paper describing PDB structure 5uk3. [3]. 28613863. Structural Characterization of a Eukaryotic Cyanase from Tetranychus urticae. Schlachter CR, Klapper V, Wybouw N, Radford T, Van Leeuwen T, Grbic M, Chruszcz M;. J Agric Food Chem. 2017;65:5453-5462. Paper describing PDB structure 6tv0. [4]. 32880586. Detecting the nature and solving the crystal structure of a contaminant protein from an opportunistic pathogen. Pederzoli R, Tarantino D, Gourlay LJ, Chaves-Sanjuan A, Bolognesi M;. Acta Crystallogr F Struct Biol Commun. 2020;76:392-397. (from Pfam) NF044447.2 PF21331.2 Isoamylase_C 27 27 107 domain Y N N Isoamylase, C-terminal 9719642 131567 cellular organisms no rank 2922 EBI-EMBL Isoamylase, C-terminal Isoamylase, C-terminal Isoamylase from Pseudomonas amyloderamosa hydrolyses alpha-1,6-glucosidic linkages of amylopectin and glycogen. It consists of three domains: the N-terminal (Pfam:PF02922), the catalytic domain (Pfam:PF00128) and the C-terminal all-beta domain, presented in this entry [1]. Paper describing PDB structure 1bf2. [1]. 9719642. Three-dimensional structure of Pseudomonas isoamylase at 2.2 A resolution. Katsuya Y, Mezaki Y, Kubota M, Matsuura Y;. J Mol Biol 1998;281:885-897. (from Pfam) NF044450.2 PF21345.2 PcRGLX_2nd 23.5 23.5 360 domain Y N N PcRGLX-like protein central beta sandwich domain 29574769 131567 cellular organisms no rank 7410 EBI-EMBL PcRGLX-like protein central beta sandwich domain PcRGLX-like protein central beta sandwich domain This family of proteins includes Exo-rhamnogalacturonan lyase from Penicillium chrysogenum 31B (PcRGLX). The family also includes YetA from B. subtilis is functionally uncharacterised. This family of proteins is found in Actinobacteria, Firmicutes, Proteobacteria and fungi. Proteins in this family are typically between 863 and 928 amino acids in length. This entry represents the central beta-sandwich domain. Members of this family share a 3 domain architecture [1]. [1]. 29574769. Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26. Kunishige Y, Iwai M, Nakazawa M, Ueda M, Tada T, Nishimura S, Sakamoto T;. FEBS Lett. 2018;592:1378-1388. (from Pfam) NF044456.2 PF21365.2 Glyco_hydro_31_3rd 24.4 24.4 87 domain Y N N Glycosyl hydrolase family 31 C-terminal domain 1747104,9649738 131567 cellular organisms no rank 95556 EBI-EMBL Glycosyl hydrolase family 31 C-terminal domain Glycosyl hydrolase family 31 C-terminal domain Glycosyl hydrolases are key enzymes of carbohydrate metabolism. Family 31 comprises of enzymes that are, or similar to, alpha- galactosidases. This entry represents the 3rd beta sandwich domain. [1]. 1747104. A classification of glycosyl hydrolases based on amino acid sequence similarities. Henrissat B;. Biochem J 1991;280:309-316. [2]. 9649738. Glycosidase families. Henrissat B. Biochem Soc Trans 1998;26:153-156. (from Pfam) NF044472.2 PF21423.2 AhtL-like_1st 27 27 55 domain Y N N Pyrogallol hydroxytransferase large subunit-like, domain 1 15284442 131567 cellular organisms no rank 880 EBI-EMBL Pyrogallol hydroxytransferase large subunit-like, domain 1 Pyrogallol hydroxytransferase large subunit-like, domain 1 This domain is found at the N-terminal end of Pyrogallol hydroxytransferase large subunit from Pelobacter acidigallici (AthL), which is involved in the isomerisation of pyrogallol to phloroglucin. This protein contains four domains, all of them similar to the domains of the DMSO reductase family [1]. [1]. 15284442. Crystal structure of pyrogallol-phloroglucinol transhydroxylase, an Mo enzyme capable of intermolecular hydroxyl transfer between phenols. Messerschmidt A, Niessen H, Abt D, Einsle O, Schink B, Kroneck PM;. Proc Natl Acad Sci U S A. 2004;101:11571-11576. (from Pfam) NF044474.2 PF21432.2 56B_RHH 27.2 27.2 32 domain Y N N 56B-like, Ribbon-helix-helix 19535331 131567 cellular organisms no rank 174 EBI-EMBL 56B-like, Ribbon-helix-helix 56B-like, Ribbon-helix-helix This entry includes Sulfolobus virus proteins, including 56B from Sulfolobus virus SIRV1, which have a ribbon-helix-helix fold [1], very similar to that of bacterial RHH proteins. 56B binds DNA. Paper describing PDB structure 2kel. [1]. 19535331. Structure, function, and targets of the transcriptional regulator SvtR from the hyperthermophilic archaeal virus SIRV1. Guilliere F, Peixeiro N, Kessler A, Raynal B, Desnoues N, Keller J, Delepierre M, Prangishvili D, Sezonov G, Guijarro JI;. J Biol Chem. 2009;284:22222-22237. (from Pfam) NF044475.2 PF21433.2 M3K_C 27 27 105 domain Y N N Mevalonate-3-kinase, C-terminal domain 25422158 131567 cellular organisms no rank 32 EBI-EMBL Mevalonate-3-kinase, C-terminal domain Mevalonate-3-kinase, C-terminal domain Mevalonate-3-kinase (M3K) is a mevalonate diphosphate decarboxylase (MDD) homologue from Thermoplasma acidophilum, which catalyses phosphorylation of (R)-mevalonate without concomitant decarboxylation [1]. This entry represents the C-terminal domain of M3K. Paper describing PDB structure 4rkp. [1]. 25422158. Structural analysis of mevalonate-3-kinase provides insight into the mechanisms of isoprenoid pathway decarboxylases. Vinokur JM, Korman TP, Sawaya MR, Collazo M, Cascio D, Bowie JU;. Protein Sci. 2015;24:212-220. (from Pfam) NF044477.2 PF21447.2 Ppx-GppA_III 27.3 27.3 177 domain Y N N Ppx/GppA phosphatase, domain III 16678853,16905100,31679177 131567 cellular organisms no rank 38006 EBI-EMBL Ppx/GppA phosphatase, domain III Ppx/GppA phosphatase, domain III Ppx/GppA phosphatases belong to ASKHA (acetate and sugar kinases, Hsp70, actin) which has an N-terminal (Pfam:PF02541) nucleotide-binding domain (domains I/II), domain III which corresponds to the catalytic phosphohydrolase domain with the common helical fold and domain IV [1-3]. This entry represents domain III. Paper describing PDB structure 1u6z. [1]. 16905100. Origin of exopolyphosphatase processivity: Fusion of an ASKHA phosphotransferase and a cyclic nucleotide phosphodiesterase homolog. Alvarado J, Ghosh A, Janovitz T, Jauregui A, Hasson MS, Sanders DA;. Structure. 2006;14:1263-1272. Paper describing PDB structure 2flo. [2]. 16678853. The structure of the exopolyphosphatase (PPX) from Escherichia coli O157:H7 suggests a binding mode for long polyphosphate chains. Rangarajan ES, Nadeau G, Li Y, Wagner J, Hung MN, Schrag JD, Cygler M, Matte A;. J Mol Biol. 2006;359:1249-1260. Paper describing PDB structure 6pbz. [3]. 31679177. Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori. Song H, Dharmasena MN, Wang C, Shaw GX, Cherry S, Tropea JE, Jin DJ, Ji X;. FEBS J. 2020;287:1865-1885. (from Pfam) NF044478.2 PF21448.2 DNMK 27.1 27.1 232 domain Y N N Deoxynucleotide monophosphate kinase 8670851 131567 cellular organisms no rank 2539 EBI-EMBL Deoxynucleotide monophosphate kinase Deoxynucleotide monophosphate kinase This entry includes Deoxynucleotide monophosphate kinases from phages which act on dGMP, dTMP and 5-hydroxymethyl-dCMP while excluding dCMP and dAMP [1]. Paper describing PDB structure 1dek. [1]. 8670851. Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP. Teplyakov A, Sebastiao P, Obmolova G, Perrakis A, Brush GS, Bessman MJ, Wilson KS;. EMBO J. 1996;15:3487-3497. (from Pfam) NF044504.2 PF21554.2 CCC_C_2nd_pro 27 27 132 domain Y N N Prokaryotic cation-chloride cotransporter, C-terminal domain, 2nd 19368887 131567 cellular organisms no rank 337 EBI-EMBL Prokaryotic cation-chloride cotransporter, C-terminal domain, 2nd Prokaryotic cation-chloride cotransporter, C-terminal domain, 2nd This domain is found at the C-terminal end of a group of prokaryotic cation-chloride cotransporters (CCCs), including Na-K-Cl cotransporter from Methanosarcina acetivorans (Swiss:Q8THK8). These proteins consist of an N-terminal transmembrane transport region (Pfam:PF00324 and Pfam:PF13520) followed by a cytoplasmic regulatory domain. The C-terminal domain adopts a compact trapezoid-shaped elongated structure with a mixed alpha-beta fold and can be divided in two structurally related subdomains. This entry represents second subdomain, which shows a central five-stranded parallel beta-sheet and three alpha-helices that pack on either face of the sheet [1]. Paper describing PDB structure 3g40. [1]. 19368887. X-ray structure of the C-terminal domain of a prokaryotic cation-chloride cotransporter. Warmuth S, Zimmermann I, Dutzler R;. Structure. 2009;17:538-546. (from Pfam) NF044507.2 PF21570.2 ArgZ-like_C_2nd 27 27 213 domain Y N N Arginine dihydrolase ArgZ-like, C-terminal, Rossmann fold 31914412,32198136 131567 cellular organisms no rank 3667 EBI-EMBL Arginine dihydrolase ArgZ-like, C-terminal, Rossmann fold Arginine dihydrolase ArgZ-like, C-terminal, Rossmann fold This domain is found at the C-terminal end of Arginine dihydrolase ArgZ from Synechocystis sp (also known as Sll1336 protein) and similar prokaryotic sequences. ArgZ is involved in an ornithine- ammonia cycle (OAC) in cyanobacteria, which confers substantial adaptability under environmental nitrogen fluctuations. This protein is organised into three domains: a N-terminal domain belonging to the guanidino group-modifying enzyme (GME) family, a middle oxoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme (Pfam:PF04455) and a C-terminal uncharacterized region that can be divided in two subdomains. This entry represents the most C-terminal region, which forms a large Rossmann fold domain. Its specific function is unknown [1]. Paper describing PDB structure 6juy. [1]. 31914412. Crystal structures and biochemical analyses of the bacterial arginine dihydrolase ArgZ suggests a "bond rotation" catalytic mechanism. Zhuang N, Zhang H, Li L, Wu X, Yang C, Zhang Y;. J Biol Chem. 2020;295:2113-2124. Paper describing PDB structure 6lrf. [2]. 32198136. Structural and mutational analyses of the bifunctional arginine dihydrolase and ornithine cyclodeaminase AgrE from the cyanobacterium Anabaena. Lee H, Rhee S;. J Biol Chem. 2020;295:5751-5760. (from Pfam) NF044525.2 PF21631.2 A9CJY8-like_N 27 27 45 domain Y N N A9CJY8-like, N-terminal domain 131567 cellular organisms no rank 2630 EBI-EMBL A9CJY8-like, N-terminal domain A9CJY8-like, N-terminal domain This domain is found at the N-terminal end of a group of prokaryotic uncharacterised proteins that contain an ACT domain (Pfam:PF13840) in the C-terminal region, including Swiss:A9CJY8 from Agrobacterium fabrum. This domain folds into several beta-strands. (from Pfam) NF044533.2 PF21648.2 M1E1E6-like 27 27 104 domain Y N N Integron cassette protein 23349695 131567 cellular organisms no rank 186 EBI-EMBL Integron cassette protein Integron cassette protein This domain family is found in a group of bacterial uncharacterised sequences from mobile gene cassettes, including Integron cassette protein from Vibrio cholerae (M1E1E6). This protein forms a dimer in which each protomer adopts a two-layered alpha+beta fold with an anti-parallel beta-sheet of five strands which curves around a pair of antiparallel helices [1]. Its specific function is unknown. Paper describing PDB structure 3fy6. [1]. 23349695. Integron gene cassettes: a repository of novel protein folds with distinct interaction sites. Sureshan V, Deshpande CN, Boucher Y, Koenig JE, Stokes HW, Harrop SJ, Curmi PM, Mabbutt BC;. PLoS One. 2013;8:e52934. (from Pfam) NF044548.2 PF21706.2 FCSD_central 27 27 116 domain Y N N Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain, central 22827326,29968673,7939681 131567 cellular organisms no rank 6743 EBI-EMBL Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain, central Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain, central This domain is located centrally in Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain from the proteobacteria Allochromatium vinosum, a component of the enzyme that catalyses the reversible conversion of sulphide to elemental sulfur in vitro. This domain is C-terminal to Pfam:PF07992 and N-terminal to Pfam:PF09242. This domain shows a five-stranded parallel beta-sheet flanked on one side by three alpha-helices and on the other side by a three-stranded anti parallel beta-sheet [1]. Paper describing PDB structure 1fcd. [1]. 7939681. The structure of flavocytochrome c sulfide dehydrogenase from a purple phototrophic bacterium. Chen ZW, Koh M, Van Driessche G, Van Beeumen JJ, Bartsch RG, Meyer TE, Cusanovich MA, Mathews FS;. Science. 1994;266:430-432. Paper describing PDB structure 3vrd. [2]. 22827326. Structure analysis and comparative characterization of the cytochrome c' and flavocytochrome c from thermophilic purple photosynthetic bacterium Thermochromatium tepidum. Hirano Y, Kimura Y, Suzuki H, Miki K, Wang ZY;. Biochemistry. 2012;51:6556-6567. Paper describing PDB structure 5n1t. [3]. 29968673. Structure of the flavocytochrome c sulfide dehydrogenase associated with the copper-binding protein CopC from the haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio paradoxusARh 1. Osipov EM, Lilina AV, Tsallagov SI, Safonova TN, Sorokin DY, Tikhonova TV, Popov VO;. Acta Crystallogr D Struct Biol. 2018;74:632-642. (from Pfam) NF044549.2 PF21715.2 CggR_N 30 30 71 domain Y N N CggR N-terminal DNA binding domain 17293407 131567 cellular organisms no rank 6978 EBI-EMBL CggR N-terminal DNA binding domain CggR N-terminal DNA binding domain The central glycolytic genes repressor (CggR) controls the transcription of the gapA operon encoding five key glycolytic enzymes in Bacillus subtilis. CggR recognizes a unique DNA target sequence comprising two direct repeats and fructose-1,6-bisphosphate (FBP) is the inducer that negatively controls this interaction. This entry represents the N-terminal DNA-binding domain [1]. [1]. 17293407. Inducer-modulated cooperative binding of the tetrameric CggR repressor to operator DNA. Zorrilla S, Doan T, Alfonso C, Margeat E, Ortega A, Rivas G, Aymerich S, Royer CA, Declerck N;. Biophys J. 2007;92:3215-3227. (from Pfam) NF044553.2 PF21722.2 Gly_rich_2 24.3 24.3 232 domain Y Y N glycine-rich domain-containing protein 131567 cellular organisms no rank 3935 EBI-EMBL Glycine-rich domain glycine-rich domain This glycine rich region forms a compact hexagonal lattice of polyglycine helices in a variety of likely bacterial and phage surface proteins. (from Pfam) NF044561.2 PF21748.2 UPF0150 27.3 27.3 64 domain Y N N UPF0150-like 17329807 131567 cellular organisms no rank 4962 EBI-EMBL UPF0150-like UPF0150-like This is a family of uncharacterized proteins that fold into an alpha-beta-beta-beta-alpha fold and are structurally similar to HicB-like antitoxin. They are probably involved in RNA metabolism, RNA cleavage and binding [1]. [1]. 17329807. Structure of a UPF0150-family protein from Thermus thermophilus HB8. Okazaki N, Kumei M, Manzoku M, Kuramitsu S, Shirouzu M, Shinkai A, Yokoyama S;. Acta Crystallograph Sect F Struct Biol Cryst Commun. 2007;63:173-177. (from Pfam) NF044568.2 PF21776.2 TetR_C_44 24.4 24.4 131 domain Y N N TetR/AcrR family transcriptional repressors, C-terminal domain 21349973 131567 cellular organisms no rank 578 EBI-EMBL TetR/AcrR family transcriptional repressors, C-terminal domain TetR/AcrR family transcriptional repressors, C-terminal domain TetR/AcrR family transcriptional repressors regulate a wide range of cellular activities, including multidrug resistance, virulence and pathogenicity of bacteria. Members of this family are two domain proteins consisting of N-terminal HTH DNA-binding domain and C-terminal ligand recognition domain. This entry represents the C-terminal domain that besides the ligand recognition, is involved in dimerisation. In contrast to the N-terminal domain, this domain is more diverse allowing different regulators in the TetR/AcrR family to accommodate specific sets of inducing ligands. Paper describing PDB structure 3ang. [1]. 21349973. TetR-family transcriptional repressor Thermus thermophilus FadR controls fatty acid degradation. Agari Y, Agari K, Sakamoto K, Kuramitsu S, Shinkai A;. Microbiology (Reading). 2011;157:1589-1601. (from Pfam) NF044570.2 PF21781.2 DUF6876 27 27 117 subfamily Y Y N DUF6876 family protein 131567 cellular organisms no rank 1269 EBI-EMBL Family of unknown function (DUF6876) DUF6876 family protein This entry represents a family of uncharacterised proteins that show structural similarity to Pfam:PF06124. (from Pfam) NF044575.2 PF21805.2 Imm5_like 24.2 24.2 129 domain Y Y N putative immunity protein 131567 cellular organisms no rank 7932 EBI-EMBL Imm-5 like putative immunity protein putative immunity protein, Imm5 family-like This family is suggested to be an immunity protein based on sequence similarity to the Imm5 family described by Pfam model PF14423. NF044580.2 PF20648.2 DUF6809 27 27 85 subfamily Y Y N DUF6809 family protein 131567 cellular organisms no rank 3463 EBI-EMBL Family of unknown function (DUF6809) DUF6809 family protein This family of proteins is functionally uncharacterised. Proteins in this family are found in bacteria, are typically around 85 amino acids in length and have a conserved motif FxxGF. (from Pfam) NF044592.2 PF20674.2 SpaA_3 24 10 121 domain Y N N Prealbumin-like fold domain 131567 cellular organisms no rank 3026 EBI-EMBL Prealbumin-like fold domain Prealbumin-like fold domain This entry represents a stalk domain found in bacterial cell surface proteins. It is likely to contain an isopeptide bond. (from Pfam) NF044593.2 PF20678.2 HV_Gp350_C-term 26.4 26.4 442 domain Y N N Herpesvirus Envelope glycoprotein GP350 C-terminal 17072314,32650039 131567 cellular organisms no rank 239 EBI-EMBL Herpesvirus Envelope glycoprotein GP350 C-terminal Herpesvirus Envelope glycoprotein GP350 C-terminal This entry consists of the envelope glycoprotein gp350 from Epstein-Barr virus (also known as BLLF1 viral late glycoprotein). It is the most abundantly expressed glycoprotein in the viral envelope of Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo [1]. It is a 907 residues long gp350 polypeptide containing an 18-residue peptide at the C-terminal that is located inside the viral membrane, a membrane-spanning domain and a large N-terminal segment (860 residues) predicted to extend outside the viral membrane. The extreme N-terminal region (1-470) is sufficient to bind receptor CR2 (also known as CD21) and fold into three distinct domains (denoted as A, B and C) which organise into an "L-shape" structure. This entry represents the C-terminal region of the Herpesvirus envelope glycoprotein GP350, which contains a IgK signal sequence (IgK SS), the TM domain and the short intracellular domain (IC) [2]. [1]. 17072314. Structure of the Epstein-Barr virus major envelope glycoprotein. Szakonyi G, Klein MG, Hannan JP, Young KA, Ma RZ, Asokan R, Holers VM, Chen XS;. Nat Struct Mol Biol. 2006;13:996-1001. [2]. 32650039. Recombinant Epstein-Barr virus glycoprotein 350 as a serological antigen. Persson Berg L, Thomsson E, Hasi G, Backstrom M, Bergstrom T;. J Virol Methods. 2020;284:113927. (from Pfam) NF044598.2 PF20697.2 NTase-conflict 24 24 259 domain Y N N Pol beta superfamily nucleotidyltransferase in conflict systems 34061031 131567 cellular organisms no rank 181 EBI-EMBL Pol beta superfamily nucleotidyltransferase in conflict systems Pol beta superfamily nucleotidyltransferase in conflict systems This is a Pol beta superfamily nucleotidyltransferase domain found in bacterial conflict systems and predicted to function as an effector [1]. [1]. 34061031. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. Kaur G, Iyer LM, Burroughs AM, Aravind L;. Elife. 2021; [Epub ahead of print] (from Pfam) NF044599.2 PF20702.2 nSTAND2 24 24 279 domain Y N N Novel STAND NTPase 2 34061031 131567 cellular organisms no rank 185 EBI-EMBL Novel STAND NTPase 2 Novel STAND NTPase 2 This is an inactive STAND-NTPase superfamily domain found in a mobile two-gene bacterial conflict systems. nSTAND2 is fused to various effector molecules. The neighbouring gene is an active STAND domain. These STAND NTPases define a novel family close to CR-ATPases, the mitochondrial apoptotic ribosomal protein S29/Dap3 and the mitochondria-associated STAND NTPase RNA12 [1]. [1]. 34061031. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. Kaur G, Iyer LM, Burroughs AM, Aravind L;. Elife. 2021; [Epub ahead of print] (from Pfam) NF044606.2 PF20730.2 YetF_N 26.5 26.5 76 domain Y N N YetF N-terminal transmembrane domain 131567 cellular organisms no rank 19269 EBI-EMBL YetF N-terminal transmembrane domain YetF N-terminal transmembrane domain This entry represents the N-terminal region of the YetF protein which is composed of three transmembrane helices. (from Pfam) NF044615.2 PF20767.2 DUF6839 24.4 24.4 67 domain Y N N Domain of unknown function (DUF6839) 131567 cellular organisms no rank 16 EBI-EMBL Domain of unknown function (DUF6839) Domain of unknown function (DUF6839) This entry represents a domain of unknown function found in a range of bacteria and phage. (from Pfam) NF044616.2 PF20768.2 Topo_VI_alpha 23.6 23.6 50 domain Y N N All-beta domain in DNA topoisomerase VI alpha subunit 10545127,17603498,18334211 131567 cellular organisms no rank 1225 EBI-EMBL All-beta domain in DNA topoisomerase VI alpha subunit All-beta domain in DNA topoisomerase VI alpha subunit In all organisms, type II DNA topoisomerases are essential for untangling chromosomal DNA. The archaeal type II protein is termed DNA topoisomerase VI. This entry represents an all beta domain found in these proteins. Paper describing PDB structure 1d3y. [1]. 10545127. Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11. Nichols MD, DeAngelis K, Keck JL, Berger JM;. EMBO J 1999;18:6177-6188. Paper describing PDB structure 2q2e. [2]. 17603498. Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI. Corbett KD, Benedetti P, Berger JM;. Nat Struct Mol Biol. 2007;14:611-619. Paper describing PDB structure 2zbk. [3]. 18334211. Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms. Graille M, Cladiere L, Durand D, Lecointe F, Gadelle D, Quevillon-Cheruel S, Vachette P, Forterre P, van Tilbeurgh H;. Structure. 2008;16:360-370. (from Pfam) NF044618.2 PF20773.3 InhA-like_MAM 26.9 26.9 191 domain Y N N Immune inhibitor A-like, MAM domain 26745529 131567 cellular organisms no rank 35272 EBI-EMBL Immune inhibitor A-like, MAM domain Immune inhibitor A-like, MAM domain Immune inhibitor A (InhA)-type metallopeptidases are potential virulence factors secreted by members of the Bacillus cereus group (BGC) and belong to the thuringilysin family within the metzincin clan of metallopeptidases, M6 in the MEROPS database. The structure revealed four domains: a pro-peptide, a catalytic domain, a domain reminiscent of viral envelope glycoproteins (VEG) and a MAM domain grafted into the latter [1]. This entry represents the MAM domain found in InhA and PrtV peptidases from Vibrio (a slightly more distant thuringilysin family members), which is required for proper protein expression and has certain flexibility. It is a beta-sandwich consisting of two five-stranded antiparallel beta-sheets, grafted between the second and third strands of the upper sheet of VEG [1]. This domain displays closest structural similarity with MAM domains such as the one from the human MP, meprin beta. [1]. 26745529. Structural Basis for Latency and Function of Immune Inhibitor A Metallopeptidase, a Modulator of the Bacillus anthracis Secretome. Arolas JL, Goulas T, Pomerantsev AP, Leppla SH, Gomis-Ruth FX;. Structure. 2016;24:25-36. (from Pfam) NF044634.2 PF20819.2 T4_Rnl1_C 27 27 122 domain Y N N T4 RNA ligase 1, C-terminal domain 16263720,28223499 131567 cellular organisms no rank 29 EBI-EMBL T4 RNA ligase 1, C-terminal domain T4 RNA ligase 1, C-terminal domain This domain is found at the C-terminal end of T4 RNA ligase 1 (Rnl1) from Bacteriophage T4 and similar proteins from tailed bacteriophages. Rnl1 is involved in countering a host defense mechanism by repairing tRNA. The C-terminal domain shows an all alpha-helical fold and has a charge distribution and architecture for helix-nucleic acid groove interaction compatible with tRNA binding. It confers specificity for the repair of tRNAs with breaks in the anticodon loop [1,2]. Paper describing PDB structure 2c5u. [1]. 16263720. Molecular architecture and ligand recognition determinants for T4 RNA ligase. El Omari K, Ren J, Bird LE, Bona MK, Klarmann G, LeGrice SF, Stammers DK;. J Biol Chem. 2006;281:1573-1579. Paper describing PDB structure 5tt6. [2]. 28223499. Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NAD(+)-dependent polynucleotide ligases. Unciuleac MC, Goldgur Y, Shuman S;. Proc Natl Acad Sci U S A. 2017;114:2592-2597. (from Pfam) NF044655.2 PF20922.2 Anamorsin_N 27.1 27.1 163 domain Y N N Anamorsin, N-terminal 14970183,18299278,18625724,21700214,22487307,23596212 131567 cellular organisms no rank 1981 EBI-EMBL Anamorsin, N-terminal Anamorsin, N-terminal Anamorsin (also named CIAPIN1 for cytokine-induced anti-apoptosis inhibitor 1), is the human homologue of yeast Dre2, a conserved soluble eukaryotic Fe-S cluster protein, that functions in cytosolic Fe-S protein biogenesis [1-3]. It is found in both the cytoplasm and in the mitochondrial intermembrane space (IMS) [4]. Anamorsin is found to be up-regulated in hepatocellular cancer, is considered to be a downstream effector of the receptor tyrosine kinase-Ras signalling pathway, and is essential in mouse definitive haematopoiesis [5]. In addition, it mediates the anti-apoptotic effects of various cytokines [6]. This entry represents the N-terminal domain, which has a S-adenosylmethionine methyltransferase-like fold. [1]. 21700214. Anamorsin is a [2Fe-2S] cluster-containing substrate of the Mia40-dependent mitochondrial protein trapping machinery. Banci L, Bertini I, Ciofi-Baffoni S, Boscaro F, Chatzi A, Mikolajczyk M, Tokatlidis K, Winkelmann J;. Chem Biol. 2011;18:794-804. [2]. 23596212. Molecular view of an electron transfer process essential for iron-sulfur protein biogenesis. Banci L, Bertini I, Calderone V, Ciofi-Baffoni S, Giachetti A, Jaiswal D, Mikolajczyk M, Piccioli M, Winkelmann J;. Proc Natl Acad Sci U S A. 2013;110:7136-7141. [3]. 22487307. A S-adenosylmethionine methyltransferase-like domain within the essential, Fe-S-containing yeast protein Dre2. Soler N, Craescu CT, Gallay J, Frapart YM, Mansuy D, Raynal B, Baldacci G, Pastore A, Huang ME, Vernis L;. FEBS J. 2012;279:2108-2119. [4]. 18625724. Dre2, a conserved eukaryotic Fe/S cluster protein, functions in cytosolic Fe/S protein biogenesis. Zhang Y, Lyver E. TRUNCATED at 1650 bytes (from Pfam) NF044666.2 PF20958.2 GxGYxYP_N_3rd 24.4 24.4 91 domain Y N N GxGYxYP third domain 131567 cellular organisms no rank 2495 EBI-EMBL GxGYxYP third domain GxGYxYP third domain This entry represents a domain that is found repeated in three copies per protein and is likely to be involved in binding the bacterial cell wall. This domain is found in association with Pfam:PF14323. (from Pfam) NF044671.2 PF20974.2 tRNA-synt_1c_C2 23.9 23.9 69 domain Y N N tRNA synthetases class I (E and Q), anti-codon binding domain 9562563 131567 cellular organisms no rank 37098 EBI-EMBL tRNA synthetases class I (E and Q), anti-codon binding domain tRNA synthetases class I (E and Q), anti-codon binding domain This entry represents the second ribosomal L25 like domain which is part of the anticodon binding domain. Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln). [1]. 9562563. How glutaminyl-tRNA synthetase selects glutamine. Rath VL, Silvian LF, Beijer B, Sproat BS, Steitz TA;. Structure 1998;6:439-449. (from Pfam) NF044673.2 PF20984.2 PT26-6P_helical 27 27 141 domain Y N N PT26-6P, helical domain 19319959 131567 cellular organisms no rank 76 EBI-EMBL PT26-6P, helical domain PT26-6P, helical domain This domain is found at the C-terminal end of PT26-6P, a large protein encoded by a plasmid from the hyperthermophilic archaea Thermococcus. This protein, present in all members of a family of mobile elements, has homologues in archaeal genomes. This entry represents the third and final domain, which folds as a five-helical bundle that contains five antiparallel helices [1]. Its function is unknown. [1]. 19319959. A protein encoded by a new family of mobile elements from Euryarchaea exhibits three domains with novel folds. Keller J, Leulliot N, Soler N, Collinet B, Vincentelli R, Forterre P, van Tilbeurgh H;. Protein Sci. 2009;18:850-855. (from Pfam) NF044675.2 PF21003.2 NucS_N 23.9 23.9 100 domain Y N N Endonuclease NucS N-terminal PH-like domain 19609302,22431731 131567 cellular organisms no rank 12583 EBI-EMBL Endonuclease NucS N-terminal PH-like domain Endonuclease NucS N-terminal PH-like domain Endonuclease NucS cleaves both 3' and 5' ssDNA extremities of branched DNA structures and it binds to ssDNA [1,2]. This entry represents the N-terminal PH-like domain of NucS. [1]. 22431731. Modulation of the Pyrococcus abyssi NucS endonuclease activity by replication clamp at functional and structural levels. Creze C, Ligabue A, Laurent S, Lestini R, Laptenok SP, Khun J, Vos MH, Czjzek M, Myllykallio H, Flament D;. J Biol Chem. 2012;287:15648-15660. [2]. 19609302. Structure and function of a novel endonuclease acting on branched DNA substrates. Ren B, Kuhn J, Meslet-Cladiere L, Briffotaux J, Norais C, Lavigne R, Flament D, Ladenstein R, Myllykallio H;. EMBO J. 2009;28:2479-2489. (from Pfam) NF044697.2 PF21068.2 ATPgraspMvdD 27 27 121 domain Y Y N MvdC/MvdD family ATP grasp protein 27669417,34028251,34664307 131567 cellular organisms no rank 10653 EBI-EMBL MvdD pre-ATP grasp domain MvdC/MvdD family N-terminal domain The pair of ATP-grasp proteins MvdD and MvdC (microviridin D and C), as well as an acetyltransferase, produce microviridin K, an example of a RiPP (ribosomally synthesized and posttranslationally modified peptide). Microviridins are peptidase inhibitors. This domain represents the pre-ATP grap domain. Paper describing PDB structure 5ig8. [1]. 27669417. Structural basis for precursor protein-directed ribosomal peptide macrocyclization. Li K, Condurso HL, Li G, Ding Y, Bruner SD;. Nat Chem Biol. 2016;12:973-979. Paper describing PDB structure 7m4s. [2]. 34664307. Structural and biochemical studies of an iterative ribosomal peptide macrocyclase. Li G, Patel K, Zhang Y, Pugmire JK, Ding Y, Bruner SD;. Proteins. 2022;90:670-679. Paper describing PDB structure 7mgv. [3]. 34028251. Structural Basis for a Dual Function ATP Grasp Ligase That Installs Single and Bicyclic omega-Ester Macrocycles in a New Multicore RiPP Natural Product. Zhao G, Kosek D, Liu HB, Ohlemacher SI, Blackburne B, Nikolskaya A, Makarova KS, Sun J, Barry Iii CE, Koonin EV, Dyda F, Bewley CA;. J Am Chem Soc. 2021;143:8056-8068. (from Pfam) NF044708.2 PF21113.2 LarA_C 25 25 152 domain Y N N Lactate racemase C-terminal domain 24710389,26138974,29489337,33093595 131567 cellular organisms no rank 7046 EBI-EMBL Lactate racemase C-terminal domain Lactate racemase C-terminal domain This entry represents the C-terminal domain of the nickel-dependent lactate racemase enzyme (LarA) [1]. LarA is part of a superfamily containing many different enzymes [4]. These include malate racemases, phenyllactate racemase, one alpha-hydroxyglutarate racemase, D-gluconate 2-epimerase, a short-chain aliphatic alpha-hydroxyacid racemase [4]. Paper describing PDB structure 2yjg. [1]. 24710389. Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. Desguin B, Goffin P, Viaene E, Kleerebezem M, Martin-Diaconescu V, Maroney MJ, Declercq JP, Soumillion P, Hols P;. Nat Commun. 2014;5:3615. Paper describing PDB structure 5huq. [2]. 26138974. METALLOPROTEINS. A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase. Desguin B, Zhang T, Soumillion P, Hols P, Hu J, Hausinger RP;. Science. 2015;349:66-69. Paper describing PDB structure 6c1w. [3]. 29489337. Lactate Racemase Nickel-Pincer Cofactor Operates by a Proton-Coupled Hydride Transfer Mechanism. Rankin JA, Mauban RC, Fellner M, Desguin B, McCracken J, Hu J, Varganov SA, Hausinger RP;. Biochemistry. 2018;57:3244-3251. Paper describing PDB structure 6d6z. [4]. 33093595. Uncovering a superfamily of nickel-dependent hydroxyacid racemases and epimerases. Desguin B, Urdiain-Arraiza J, Da Costa M, Fellner M, Hu J, Hausinger RP, Desmet T, Hols P, Soumillion P;. Sci Rep. 2020;10:18123. (from Pfam) NF044710.2 PF21117.2 MRB1590_C 27 15 102 domain Y N N MRB1590 C-terminal domain 26117548 131567 cellular organisms no rank 7605 EBI-EMBL MRB1590 C-terminal domain MRB1590 C-terminal domain This entry represents the C-terminal helix-turn-helix like domain from the T. brucei kRNA editing factor MRB1590 [1]. Paper describing PDB structure 4yix. [1]. 26117548. Structures of the T. brucei kRNA editing factor MRB1590 reveal unique RNA-binding pore motif contained within an ABC-ATPase fold. Shaw PL, McAdams NM, Hast MA, Ammerman ML, Read LK, Schumacher MA;. Nucleic Acids Res. 2015;43:7096-7109. (from Pfam) NF044715.2 PF21135.2 DRL_cat 27 27 164 domain Y N N Oxidoreductase DRL, catalytic domain 20660776,22442144 131567 cellular organisms no rank 11056 EBI-EMBL Oxidoreductase DRL, catalytic domain Oxidoreductase DRL, catalytic domain This domain is found in DRL from Brucella abortus (Swiss:Q2YIM3) and other bacterial putative oxidoreductases and homoserine dehydrogenases. DRL is involved in isoprenoid biosynthesis. This protein is organised into three structural domains: N-terminal, central, (catalytic, this entry), and C-terminal. The catalytic domain shows an alpha/beta fold with a central four-stranded mixed beta-sheet. The active site lid is formed by a protusion made of two antiparallel helices connected by a short loop [1-2]. Paper describing PDB structure 3upl. [1]. 22442144. Crystal structure of Brucella abortus deoxyxylulose-5-phosphate reductoisomerase-like (DRL) enzyme involved in isoprenoid biosynthesis. Perez-Gil J, Calisto BM, Behrendt C, Kurz T, Fita I, Rodriguez-Concepcion M;. J Biol Chem. 2012;287:15803-15809. [2]. 20660776. A new family of enzymes catalyzing the first committed step of the methylerythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis in bacteria. Sangari FJ, Perez-Gil J, Carretero-Paulet L, Garcia-Lobo JM, Rodriguez-Concepcion M;. Proc Natl Acad Sci U S A. 2010;107:14081-14086. (from Pfam) NF044716.2 PF21138.2 SMUBP-2_HCS1_1B 27 27 129 domain Y N N Helicase SMUBP-2/HCS1, 1B domain 22965130 131567 cellular organisms no rank 495 EBI-EMBL Helicase SMUBP-2/HCS1, 1B domain Helicase SMUBP-2/HCS1, 1B domain Proteins in this entry belong to the DNA2/NAM7 helicase family and includes SMUBP-2 (also known as IGHMBP2) from mammals and HCS1 (also known as DNA polymerase alpha-associated DNA helicase A) from yeasts. This entry represents the 1B domain consisting of a short alpha-helix and a beta-barrel. This domain forms the RNA-binding channel together with 1A, 2A and 1C domains [1]. Domains 1B and 1C directly interact with the 3'-end of RNA. Paper describing PDB structure 4b3f. [1]. 22965130. The Ighmbp2 helicase structure reveals the molecular basis for disease-causing mutations in DMSA1. Lim SC, Bowler MW, Lai TF, Song H;. Nucleic Acids Res. 2012;40:11009-11022. (from Pfam) NF044721.2 PF21156.2 ISOA1-3_C 27.3 27.3 106 domain Y N N Isoamylase 1-3, C-terminal 19074683,24993830 131567 cellular organisms no rank 3774 EBI-EMBL Isoamylase 1-3, C-terminal Isoamylase 1-3, C-terminal Isoamylases (ISOAs) are starch debranching enzymes, including ISOA1, ISOA2 and ISOA3. ISOA1-2 are known to form a large complex and being involved in the biosynthesis and crystallization of starch. ISOA3 is involved in starch catabolism and removes different branches than ISA1-ISA2, namely short chains that prevent amylopectin crystallization [2]. This is the C-terminal beta-sandwich domain from ISOA1-3. In ISOA1, this domain is involved in dimerisation of homodimers and suggests a similar interaction to form ISOA1-ISOA2 heterodimers [1]. Paper describing PDB structure 4j7r. [1]. 24993830. Crystal structure of the Chlamydomonas starch debranching enzyme isoamylase ISA1 reveals insights into the mechanism of branch trimming and complex assembly. Sim L, Beeren SR, Findinier J, Dauvillee D, Ball SG, Henriksen A, Palcic MM;. J Biol Chem. 2014;289:22991-23003. [2]. 19074683. Starch granule biosynthesis in Arabidopsis is abolished by removal of all debranching enzymes but restored by the subsequent removal of an endoamylase. Streb S, Delatte T, Umhang M, Eicke S, Schorderet M, Reinhardt D, Zeeman SC;. Plant Cell. 2008;20:3448-3466. (from Pfam) NF044723.2 PF21180.2 TOP6A-Spo11_Toprim 24.1 24.1 170 domain Y N N Topoisomerase 6 subunit A/Spo11, Toprim domain 10545127,17603498,18334211 131567 cellular organisms no rank 1881 EBI-EMBL Topoisomerase 6 subunit A/Spo11, Toprim domain Topoisomerase 6 subunit A/Spo11, Toprim domain This topoisomerase-primase (Toprim) nucleotidyl transferase/hydrolase domain is found in the type II topoisomerase VIA and Spo11, which structurally related. Spo11 is a meiosis-specific protein that is responsible for the initiation of recombination through the formation of DNA double-strand breaks by a type II DNA topoisomerase-like activity. Topoisomerase VI is a type IIB enzyme that breaks double-stranded DNA and assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis [1-3]. Paper describing PDB structure 1d3y. [1]. 10545127. Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11. Nichols MD, DeAngelis K, Keck JL, Berger JM;. EMBO J 1999;18:6177-6188. Paper describing PDB structure 2q2e. [2]. 17603498. Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI. Corbett KD, Benedetti P, Berger JM;. Nat Struct Mol Biol. 2007;14:611-619. Paper describing PDB structure 2zbk. [3]. 18334211. Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms. Graille M, Cladiere L, Durand D, Lecointe F, Gadelle D, Quevillon-Cheruel S, Vachette P, Forterre P, van Tilbeurgh H;. Structure. 2008;16:360-370. (from Pfam) NF044732.2 PF21221.2 B_lactamase-like_C 27 27 46 domain Y N N Metallo-beta-lactamase-like, C-terminal domain 18767153 131567 cellular organisms no rank 10477 EBI-EMBL Metallo-beta-lactamase-like, C-terminal domain Metallo-beta-lactamase-like, C-terminal domain This domain is found in Metallo-beta-lactamase family protein from Thermus thermophilus (TTHA1429) and similar bacterial enzymes. This domain is often found C-terminal to Pfam:PF00753. Paper describing PDB structure 2zo4. [1]. 18767153. Crystal structure of TTHA1429, a novel metallo-beta-lactamase superfamily protein from Thermus thermophilus HB8. Yamamura A, Ohtsuka J, Kubota K, Agari Y, Ebihara A, Nakagawa N, Nagata K, Tanokura M;. Proteins. 2008;73:1053-1057. (from Pfam) NF044734.2 PF21231.2 GH141_M 27 27 156 domain Y N N GH141 insertion domain 131567 cellular organisms no rank 5265 EBI-EMBL GH141 insertion domain GH141 insertion domain This domain is found in proteins that belong to Glycoside hydrolase family 141 (GH141). This domain consists of two subdomains: a beta-sandwich and a partly open beta-barrel that are inserted into the catalytic domain comprising a right-handed parallel beta-helix domain. (from Pfam) NF044739.2 PF21238.2 Pus10_C 27 27 232 domain Y N N Pus10, C-terminal 16286935,16427014,16456033,16943774,18059286,31819270,33023933 131567 cellular organisms no rank 1916 EBI-EMBL Pus10, C-terminal Pus10, C-terminal This is the C-terminal catalytic domain of tRNA pseudouridine synthase Pus10, conserved in archaea and eukaryotes [1-5]. In archaea it catalyses the formation of the pseudouridine at positions 54 and 55 in tRNA, while human Pus10 has different functions depending on its subcellular location: it is involved in miRNA processing in the nucleus and acts as a tRNA pseudouridylate synthase in the cytoplasm [6,7]. Paper describing PDB structure 2apo. [1]. 16286935. The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs. Hamma T, Reichow SL, Varani G, Ferre-D'Amare AR;. Nat Struct Mol Biol. 2005;12:1101-1107. Paper describing PDB structure 2aus. [2]. 16456033. Crystal structure determination and site-directed mutagenesis of the Pyrococcus abyssi aCBF5-aNOP10 complex reveal crucial roles of the C-terminal domains of both proteins in H/ACA sRNP activity. Manival X, Charron C, Fourmann JB, Godard F, Charpentier B, Branlant C;. Nucleic Acids Res. 2006;34:826-839. Paper describing PDB structure 2ey4. [3]. 16427014. Crystal structure of a Cbf5-Nop10-Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita. Rashid R, Liang B, Baker DL, Youssef OA, He Y, Phipps K, Terns RM, Terns MP, Li H;. Mol Cell. 2006;21:249-260. Paper describing PDB structure 2hvy. [4]. 16943774. Crystal structure of an H/ACA box ribonucleoprotein particle. Li L, Ye K;. Nature. 2006;443:302-307. Paper describing PDB structure 2rfk. [5]. 18059286. Substrate RNA positioning in the archaeal H/ACA ribonucleoprotein complex. Liang B, Xue S, Terns RM, Terns MP, Li H;. Nat Struct Mol Biol. 2007;14:1189-1195. [6]. 33023933. TRUNCATED at 1650 bytes (from Pfam) NF044742.2 PF21244.2 PurT_C 26.7 26.7 68 domain Y N N PurT, C-terminal 10913290,11953435 131567 cellular organisms no rank 28793 EBI-EMBL PurT, C-terminal PurT, C-terminal Formate-dependent phosphoribosylglycinamide formyltransferase (PurT) is involved in de novo purine biosynthesis. PurT belongs to the ATP-grasp superfamily of enzymes and catalyses the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR) [1,2]. This entry represents the C-terminal domain which has a rudiment single hybrid motif consisting of a sandwich of half-barrel shaped beta-sheets [2]. Paper describing PDB structure 1eyz. [1]. 10913290. Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase. Thoden JB, Firestine S, Nixon A, Benkovic SJ, Holden HM;. Biochemistry. 2000;39:8791-8802. Paper describing PDB structure 1kj8. [2]. 11953435. PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site. Thoden JB, Firestine SM, Benkovic SJ, Holden HM;. J Biol Chem. 2002;277:23898-23908. (from Pfam) NF044744.2 PF21249.2 GyrB_hook 23.7 23.7 29 domain Y N N GyrB, hook 20675723,24990966,31666516 131567 cellular organisms no rank 25433 EBI-EMBL GyrB, hook GyrB, hook This entry represents the N-terminal section of the 'Toprim hook' as described in [1], which is localised between the Toprim (Pfam:PF01751) and the insert (Pfam:PF18053) domains [1-3]. The C-terminal section of the hook is included in (Pfam:PF00986). The hook is flexible towards the Toprim domain. Paper describing PDB structure 3nuh. [1]. 20675723. A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function. Schoeffler AJ, May AP, Berger JM;. Nucleic Acids Res. 2010;38:7830-7844. Paper describing PDB structure 4tma. [2]. 24990966. Direct control of type IIA topoisomerase activity by a chromosomally encoded regulatory protein. Vos SM, Lyubimov AY, Hershey DM, Schoeffler AJ, Sengupta S, Nagaraja V, Berger JM;. Genes Dev. 2014;28:1485-1497. Paper describing PDB structure 6rks. [3]. 31666516. Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex. Vanden Broeck A, Lotz C, Ortiz J, Lamour V;. Nat Commun. 2019;10:4935. (from Pfam) NF044745.2 PF21252.2 Glyco_hydro_109_C 27 27 187 domain Y N N Glycosyl hydrolase 109, C-terminal domain 17401360 131567 cellular organisms no rank 12459 EBI-EMBL Glycosyl hydrolase 109, C-terminal domain Glycosyl hydrolase 109, C-terminal domain This domain is found at the C-terminal end of the group of bacterial glycosyl hydrolases 109, including Alpha-N-acetylgalactosaminidase from Elizabethkingia meningoseptica. This domain shows a large open-faced, seven-stranded, anti-parallel beta-sheet, adjacent to nine alpha-helices and an alpha-helical bundle covering the dinucleotide-binding tunnel [1]. Paper describing PDB structure 2ixa. [1]. 17401360. Bacterial glycosidases for the production of universal red blood cells. Liu QP, Sulzenbacher G, Yuan H, Bennett EP, Pietz G, Saunders K, Spence J, Nudelman E, Levery SB, White T, Neveu JM, Lane WS, Bourne Y, Olsson ML, Henrissat B, Clausen H;. Nat Biotechnol. 2007;25:454-464. (from Pfam) NF044746.2 PF21254.2 AGA-YXIM_GBD 27 27 138 domain Y N N Beta-agarase/YXIM esterase-like, galactose-binding domain-like 131567 cellular organisms no rank 3365 EBI-EMBL Beta-agarase/YXIM esterase-like, galactose-binding domain-like Beta-agarase/YXIM esterase-like, galactose-binding domain-like This entry represents the galactose-binding domain found at the C-terminal of beta-agarase A from Zobellia galactanivorans and the N-terminal of the uncharacterised esterase YXIM from Bacillus subtilis and similar sequences. (from Pfam) NF044749.2 PF21266.2 RRP4_S1 27.3 27.3 73 domain Y N N RRP4, S1 domain 17174896,17545563 131567 cellular organisms no rank 345 EBI-EMBL RRP4, S1 domain RRP4, S1 domain Exosome complex component RRP4 is a non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. It consists of a N-terminal beta-sandwich hybrid domain (Pfam:PF14382), a central S1 domain and a C-terminal KH domain (Pfam:PF15985). This entry represents the S1 RNA binding domain, which has an OB fold [1,2]. [1]. 17174896. Reconstitution, activities, and structure of the eukaryotic RNA exosome. Liu Q, Greimann JC, Lima CD;. Cell. 2006;127:1223-1237. [2]. 17545563. Human cell growth requires a functional cytoplasmic exosome, which is involved in various mRNA decay pathways. van Dijk EL, Schilders G, Pruijn GJ;. RNA. 2007;13:1027-1035. (from Pfam) NF044751.2 PF21274.2 Rng_hyd_C 27.5 27.5 107 domain Y N N Aromatic-ring hydroxylase, C-terminal 17669423,17873060,19364090,19744497,25737306,27557658 131567 cellular organisms no rank 83522 EBI-EMBL Aromatic-ring hydroxylase, C-terminal Aromatic-ring hydroxylase, C-terminal This is a thioredoxin-like domain found at the C-terminal of aromatic-ring hydroxylases [1-5], such as PgaE from Bacillus subtilis and Rifampicin monooxygenase from Streptomyces venezuelae. The function of this domain is not clear. It may be involved in folding and stability [6] as it lacks the catalytic cysteine residues of thioredoxin, therefore, is not likely to have a redox function [1]. Paper describing PDB structure 2qa1. [1]. 17669423. Crystal structures of two aromatic hydroxylases involved in the early tailoring steps of angucycline biosynthesis. Koskiniemi H, Metsa-Ketela M, Dobritzsch D, Kallio P, Korhonen H, Mantsala P, Schneider G, Niemi J;. J Mol Biol. 2007;372:633-648. Paper describing PDB structure 2r0c. [2]. 17873060. Crystallographic trapping in the rebeccamycin biosynthetic enzyme RebC. Ryan KS, Howard-Jones AR, Hamill MJ, Elliott SJ, Walsh CT, Drennan CL;. Proc Natl Acad Sci U S A. 2007;104:15311-15316. Paper describing PDB structure 3fmw. [3]. 19364090. Crystal structure of Baeyer-Villiger monooxygenase MtmOIV, the key enzyme of the mithramycin biosynthetic pathway . Beam MP, Bosserman MA, Noinaj N, Wehenkel M, Rohr J;. Biochemistry. 2009;48:4476-4487. Paper describing PDB structure 3ihg. [4]. 19744497. Structural basis for substrate recognition and specificity in aklavinone-11-hydroxylase from rhodomycin biosynthesis. Lindqvist Y, Koskiniemi H, Jansson A, Sandalova T, Schnell R, Liu Z, Mantsala P, Niemi J, Schneider G;. J Mol Biol. 2009;393:966-977. Paper describing PDB structure 4cy6. [5]. 25737306. Structures of the Apo and FAD-bound forms of 2-hydroxybiphenyl 3-monooxygenase (HbpA) locate activity. TRUNCATED at 1650 bytes (from Pfam) NF044759.2 PF21296.2 APAF-1-like_WHD 27 27 68 domain Y N N Apoptotic protease-activating factor 1-like, winged-helix domain 15829969,21827944,23521171,26543158,27697150 131567 cellular organisms no rank 79 EBI-EMBL Apoptotic protease-activating factor 1-like, winged-helix domain Apoptotic protease-activating factor 1-like, winged-helix domain This domain is found in Apoptotic protease-activating factor 1 from Mus musculus (APAF-1), responsible to ignite the downstream cascade of caspases in the mitochondrial pathway of apoptosis. This entry represents the winged-helix domain (WHD) [1-5]. Paper describing PDB structure 1z6t. [1]. 15829969. Structure of the apoptotic protease-activating factor 1 bound to ADP. Riedl SJ, Li W, Chao Y, Schwarzenbacher R, Shi Y;. Nature. 2005;434:926-933. Paper describing PDB structure 3j2t. [2]. 23521171. Changes in Apaf-1 conformation that drive apoptosome assembly. Yuan S, Topf M, Reubold TF, Eschenburg S, Akey CW;. Biochemistry. 2013;52:2319-2327. Paper describing PDB structure 3jbt. [3]. 26543158. Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1. Zhou M, Li Y, Hu Q, Bai XC, Huang W, Yan C, Scheres SH, Shi Y;. Genes Dev. 2015;29:2349-2361. Paper describing PDB structure 3sfz. [4]. 21827944. Crystal structure of full-length Apaf-1: how the death signal is relayed in the mitochondrial pathway of apoptosis. Reubold TF, Wohlgemuth S, Eschenburg S;. Structure. 2011;19:1074-1083. Paper describing PDB structure 5juy. [5]. 27697150. A near atomic structure of the active human apoptosome. Cheng TC, Hong C, Akey IV, Yuan S, Akey CW;. Elife. 2016; [Epub ahead of print] (from Pfam) NF044761.2 PF21303.2 TetR_C_39 27 27 92 domain Y N N Tetracyclin repressor-like, C-terminal domain 131567 cellular organisms no rank 2952 EBI-EMBL Tetracyclin repressor-like, C-terminal domain Tetracyclin repressor-like, C-terminal domain This domain is found at the C-terminal end of bacterial transcriptional regulators. It is normally found associated with Pfam:PF00440. (from Pfam) NF044766.2 PF21320.2 HTH_65 24.1 24.1 75 domain Y N N Rv2258c-like winged HTH domain 26772148 131567 cellular organisms no rank 10940 EBI-EMBL Rv2258c-like winged HTH domain Rv2258c-like winged HTH domain The Mycobacterium tuberculosis Rv2258c protein is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase (MTase) [1]. The monomer structure of Rv2258c consists of two domains which are linked by a long alpha-helix. The N-terminal domain, found in this entry, is essential for dimerization and the C-terminal domain has the Class I MTase fold. This domain has a winged Helix-Turn-Helix fold. Paper describing PDB structure 5f8c. [1]. 26772148. Crystal structure of Rv2258c from Mycobacterium tuberculosis H37Rv, an S-adenosyl-l-methionine-dependent methyltransferase. Im HN, Kim HS, An DR, Jang JY, Kim J, Yoon HJ, Yang JK, Suh SW;. J Struct Biol. 2016;193:172-180. (from Pfam) NF044770.2 PF21338.2 Top1B_N_bact 27 27 49 domain Y N N Bacterial DNA topoisomerase IB, N-terminal domain 16368685 131567 cellular organisms no rank 21983 EBI-EMBL Bacterial DNA topoisomerase IB, N-terminal domain Bacterial DNA topoisomerase IB, N-terminal domain This domain is found at the N-terminal end of Type I topoisomerase from Deinococcus radiodurans and similar bacterial sequences. This small-sized protein modify DNA topology by cleaving and resealing one strand of duplex DNA. This domain comprises three alpha-helices plus a five strand antiparallel beta-sheet [1]. It is found associated with Pfam:PF01028. Paper describing PDB structure 2f4q. [1]. 16368685. Crystal structure of a bacterial type IB DNA topoisomerase reveals a preassembled active site in the absence of DNA. Patel A, Shuman S, Mondragon A;. J Biol Chem. 2006;281:6030-6037. (from Pfam) NF044772.2 PF21342.2 SoxA-TsdA_cyt-c 27 27 88 domain Y N N SoxA/TsdA, cytochrome c domain 12411478,16297640,25673691,25673696,27694441 131567 cellular organisms no rank 16710 EBI-EMBL SoxA/TsdA, cytochrome c domain SoxA/TsdA, cytochrome c domain This entry represents the first cytochrome c domain of SoxA and TsdA proteins, heme proteins involved in sulfur oxidation [1-5]. Paper describing PDB structure 1h31. [1]. 12411478. Structural basis for the oxidation of thiosulfate by a sulfur cycle enzyme. Bamford VA, Bruno S, Rasmussen T, Appia-Ayme C, Cheesman MR, Berks BC, Hemmings AM;. EMBO J. 2002;21:5599-5610. Paper describing PDB structure 2c1d. [2]. 16297640. Structure of the cytochrome complex SoxXA of Paracoccus pantotrophus, a heme enzyme initiating chemotrophic sulfur oxidation. Dambe T, Quentmeier A, Rother D, Friedrich C, Scheidig AJ;. J Struct Biol. 2005;152:229-234. Paper describing PDB structure 4v2k. [3]. 25673696. Mechanism of thiosulfate oxidation in the SoxA family of cysteine-ligated cytochromes. Grabarczyk DB, Chappell PE, Eisel B, Johnson S, Lea SM, Berks BC;. J Biol Chem. 2015;290:9209-9221. Paper describing PDB structure 4wq7. [4]. 25673691. Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum: structural and functional insights into thiosulfate oxidation. Brito JA, Denkmann K, Pereira IA, Archer M, Dahl C;. J Biol Chem. 2015;290:9222-9238. Paper describing PDB structure 5lo9. [5]. 27694441. Electron Accepting Units of the Diheme Cytochrome c TsdA, a Bifunctional Thiosulfate Dehydrogenase/Tetrathionate Reductase. Kurth JM, Brito JA, Reuter J, Flegler A, Koch T, Franke T, Klein EM, Rowe SF, Butt JN, Denkmann K, Pereira IA, Archer M, Dahl C;. J Biol Chem. 2016;291:24804-24818. (from Pfam) NF044773.2 PF21344.2 LysW-like_globular 27 27 46 domain Y N N Alpha-aminoadipate carrier protein LysW-like, globular domain 16963084,23434852,25392000,26966182,27566549 131567 cellular organisms no rank 1804 EBI-EMBL Alpha-aminoadipate carrier protein LysW-like, globular domain Alpha-aminoadipate carrier protein LysW-like, globular domain This domain is found in a group of prokaryotic proteins, including Alpha-aminoadipate carrier protein LysW from Thermus thermophilus. LysW is an amino group-carrier protein that plays an important role in lysine biosynthesis. This globular domain is composed of five beta-strands and adopts a similar structure to members of the zinc ribbon superfamily. It is responsible for the binding of a zinc atom [1-5]. Paper describing PDB structure 2i13. [1]. 16963084. Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA. Segal DJ, Crotty JW, Bhakta MS, Barbas CF 3rd, Horton NC;. J Mol Biol. 2006;363:405-421. Paper describing PDB structure 3vpb. [2]. 23434852. Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Ouchi T, Tomita T, Horie A, Yoshida A, Takahashi K, Nishida H, Lassak K, Taka H, Mineki R, Fujimura T, Kosono S, Nishiyama C, Masui R, Kuramitsu S, Albers SV, Kuzuyama T, Nishiyama M;. Nat Chem Biol. 2013;9:277-283. Paper describing PDB structure 3wwl. [3]. 25392000. Structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the LysZ.LysW complex from Thermus thermophilus. Yoshida A, Tomita T, Fujimura T, Nishiyama C, Kuzuyama T, Nishiyama M;. J Biol Chem. 2015;290:435-447. Paper describing PDB structure 5ein. [4]. 26966182. Crystal Structure of the LysY.LysW Complex from Thermus thermophilus. Shimizu T, Tomita T, Kuzuyama T, Nishiyama M;. J Biol Chem. 2016;291:9948-9959. Paper describing PDB structure 5k2m. [5]. 27566549. Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic S. TRUNCATED at 1650 bytes (from Pfam) NF044774.2 PF21350.2 Cas6_I-A 27 27 101 domain Y N N CRISPR-associated protein Cas6, N-terminal 19141480,21300293,22447673 131567 cellular organisms no rank 1608 EBI-EMBL CRISPR-associated protein Cas6, N-terminal CRISPR-associated protein Cas6, N-terminal Cas6 is an endoribonuclease that generates crRNAs for invader defense in prokaryotes [1-3]. Cas6 consists of two two ferredoxin-like folds that are also found in other RNA-binding proteins. This entry represents the N-terminal ferredoxin-like domain from Cas6. Paper describing PDB structure 3i4h. [1]. 19141480. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Carte J, Wang R, Li H, Terns RM, Terns MP;. Genes Dev. 2008;22:3489-3496. Paper describing PDB structure 3pkm. [2]. 21300293. Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage. Wang R, Preamplume G, Terns MP, Terns RM, Li H;. Structure. 2011;19:257-264. Paper describing PDB structure 3ufc. [3]. 22447673. Crystal structure of a Cas6 paralogous protein from Pyrococcus furiosus. Park HM, Shin M, Sun J, Kim GS, Lee YC, Park JH, Kim BY, Kim JS;. Proteins. 2012;80:1895-1900. (from Pfam) NF044799.2 PF21436.2 STT3-PglB_core 23 23 131 domain Y N N STT3/PglB/AglB core domain 18046457,20007322,21677752,22865878,23177926 131567 cellular organisms no rank 2574 EBI-EMBL STT3/PglB/AglB core domain STT3/PglB/AglB core domain This entry represents the C-terminal core domain found in the oligosaccharyl transferase STT3 subunit and related proteins, such as bacterial PglB and archaeal AlgB. STT3 is part of the oligosccharyl transferase (OTase) complex and required for its activity, which transfers a lipid-linked core-oligosaccharide to selected asparagine residues in the ER. In the archaea STT3 occurs alone, rather than in an OTase complex, and is required for N-glycosylation of asparagines [1-5]. This is a globular domain which adopts a mixed alpha/beta fold and contains the highly conserved WWDYG motif, in which the aspartate residue is thought to function as a catalytic residue [1-5]. Paper describing PDB structure 2lgz. [1]. 22865878. Eukaryotic N-glycosylation occurs via the membrane-anchored C-terminal domain of the Stt3p subunit of oligosaccharyltransferase. Huang C, Bhaskaran R, Mohanty S;. J Biol Chem. 2012;287:32450-32458. Paper describing PDB structure 2zag. [2]. 18046457. Structure-guided identification of a new catalytic motif of oligosaccharyltransferase. Igura M, Maita N, Kamishikiryo J, Yamada M, Obita T, Maenaka K, Kohda D;. EMBO J. 2008;27:234-243. Paper describing PDB structure 3aag. [3]. 20007322. Comparative structural biology of eubacterial and archaeal oligosaccharyltransferases. Maita N, Nyirenda J, Igura M, Kamishikiryo J, Kohda D;. J Biol Chem. 2010;285:4941-4950. Paper describing PDB structure 3rce. [4]. 21677752. X-ray structure of a bacterial oligosaccharyltransferase. Lizak C, Gerber S, Numao S, Aebi M, Locher KP;. Nature. 2011;474:350-355. Paper describing PDB structure 3vu0. [5]. 23177926. Crystallographic and NM. TRUNCATED at 1650 bytes (from Pfam) NF044806.2 PF21478.2 GcvP2_C 27 27 122 domain Y N N Glycine dehydrogenase, C-terminal domain 15791207,24121504 131567 cellular organisms no rank 76378 EBI-EMBL Glycine dehydrogenase, C-terminal domain Glycine dehydrogenase, C-terminal domain This entry includes Glycine dehydrogenases, also known as glycine cleavage system P protein, which bind the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO2 is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. The monomer consists of two domains, a large domain and a small domain. This entry represents the small domain, which has a complex alpha/beta structure [1,2]. Paper describing PDB structure 1wyt. [1]. 15791207. Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia. Nakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N;. EMBO J. 2005;24:1523-1536. Paper describing PDB structure 4lgl. [2]. 24121504. Structure of the homodimeric glycine decarboxylase P-protein from Synechocystis sp. PCC 6803 suggests a mechanism for redox regulation. Hasse D, Andersson E, Carlsson G, Masloboy A, Hagemann M, Bauwe H, Andersson I;. J Biol Chem. 2013;288:35333-35345. (from Pfam) NF044815.2 PF21522.2 MreB-like_C 27.8 27.8 123 domain Y N N Archaeal actin homologue MreB-like, C-terminal 16500678,20106979 131567 cellular organisms no rank 8609 EBI-EMBL Archaeal actin homologue MreB-like, C-terminal Archaeal actin homologue MreB-like, C-terminal Archaeal actin homologue Ta0583 is an active ATPase at physiological temperatures, which has a propensity to form filaments [1]. It has the core actin structure and is highly homologous to MreB and ParM from bacteria [1,2]. This entry represents the C-terminal actin-like domain [1,2]. Paper describing PDB structure 2fsj. [1]. 16500678. Crystal structure of an archaeal actin homolog. Roeben A, Kofler C, Nagy I, Nickell S, Hartl FU, Bracher A;. J Mol Biol. 2006;358:145-156. [2]. 20106979. Structure and filament dynamics of the pSK41 actin-like ParM protein: implications for plasmid DNA segregation. Popp D, Xu W, Narita A, Brzoska AJ, Skurray RA, Firth N, Goshdastider U, Maeda Y, Robinson RC, Schumacher MA;. J Biol Chem. 2010;285:10130-10140. (from Pfam) NF044816.2 PF21531.2 Rv2175c_wHTH 27.1 27.1 57 domain Y N N DNA-binding protein Rv2175c, wHTH domain 19457863 131567 cellular organisms no rank 11270 EBI-EMBL DNA-binding protein Rv2175c, wHTH domain DNA-binding protein Rv2175c, wHTH domain This entry represents the N-terminal wHTH domain of Rv2175c from Mycobacterium tuberculosis, which has been shown to bind DNA [1]. The C-terminal domain (Pfam:PF18367) may play a regulatory role. [1]. 19457863. The Mycobacterium tuberculosis Ser/Thr kinase substrate Rv2175c is a DNA-binding protein regulated by phosphorylation. Cohen-Gonsaud M, Barthe P, Canova MJ, Stagier-Simon C, Kremer L, Roumestand C, Molle V;. J Biol Chem. 2009;284:19290-19300. (from Pfam) NF044825.2 PF21553.2 Formyl_trans_C_2 27 27 58 domain Y N N Methionyl-tRNA formyltransferase, C-terminal domain 131567 cellular organisms no rank 503 EBI-EMBL Methionyl-tRNA formyltransferase, C-terminal domain Methionyl-tRNA formyltransferase, C-terminal domain This domain is found at the C-terminal end of Methionyl-tRNA formyltransferase from Acetivibrio thermocellus and similar bacterial sequences. This domain is usually found associated with Pfam:PF00551. (from Pfam) NF044849.2 PF21688.2 FAD-depend_C 27 27 197 domain Y Y N FAD-dependent protein 131567 cellular organisms no rank 30762 EBI-EMBL FAD-dependent protein, C-terminal domain-like FAD-dependent protein C-terminal domain This domain is found towards the C-terminal of a group of bacterial and archaeal FAD-linked dehydrogenases, whose exact function is not yet clear. (from Pfam) NF044853.2 PF21702.2 GLGE_C 27 27 87 domain Y N N GLGE, C-terminal 21914799,24689960,26245983,26616850,27531751 131567 cellular organisms no rank 30697 EBI-EMBL GLGE, C-terminal GLGE, C-terminal This entry represents the C-terminal domain of alpha-1,4-glucan:maltose-1-phosphate maltosyltransferases (GLGE) which has an all-beta fold [1-5]. This domain, referred to domain C, together with the catalytic one, is involved in the binding of alpha-glucan chains [4]. Paper describing PDB structure 3zss. [1]. 21914799. Structure of Streptomyces maltosyltransferase GlgE, a homologue of a genetically validated anti-tuberculosis target. Syson K, Stevenson CEM, Rejzek M, Fairhurst SA, Nair A, Bruton CJ, Field RA, Chater KF, Lawson DM, Bornemann S;. J Biol Chem. 2011;286:38298-38310. Paper describing PDB structure 4cn1. [2]. 24689960. Structural insight into how Streptomyces coelicolor maltosyl transferase GlgE binds alpha-maltose 1-phosphate and forms a maltosyl-enzyme intermediate. Syson K, Stevenson CE, Rashid AM, Saalbach G, Tang M, Tuukkanen A, Svergun DI, Withers SG, Lawson DM, Bornemann S;. Biochemistry. 2014;53:2494-2504. Paper describing PDB structure 4u2y. [3]. 26245983. Crystal structures of Mycobacterium tuberculosis GlgE and complexes with non-covalent inhibitors. Lindenberger JJ, Veleti SK, Wilson BN, Sucheck SJ, Ronning DR;. Sci Rep. 2015;5:12830. Paper describing PDB structure 5cgm. [4]. 26616850. Structure of Mycobacterium thermoresistibile GlgE defines novel conformational states that contribute to the catalytic mechanism. Mendes V, Blaszczyk M, Maranha A, Empadinhas N, Blundell TL;. Sci Rep. 2015;5:17144. Paper describing PDB structure 5cvs. [5]. 27531751. Ligand-bound Structures and Site-directed Mutagenesis Identify the Acceptor and Secondary Binding Sites of Streptomyces coelicolor Maltosyltransferase Glg. TRUNCATED at 1650 bytes (from Pfam) NF044854.2 PF21704.2 POLH-Rev1_HhH 27 27 56 domain Y N N DNApol eta/Rev1, HhH motif 19464298,20577208,24759104,25947374,26503230 131567 cellular organisms no rank 1543 EBI-EMBL DNApol eta/Rev1, HhH motif DNApol eta/Rev1, HhH motif This entry represents the HhH motif from DNA polymerase eta and DNA repair protein REV1, members of the type-Y family of DNA polymerases [1-5]. Paper describing PDB structure 3gqc. [1]. 19464298. Structure of the human Rev1-DNA-dNTP ternary complex. Swan MK, Johnson RE, Prakash L, Prakash S, Aggarwal AK;. J Mol Biol. 2009;390:699-709. Paper describing PDB structure 3jaa. [2]. 26503230. Molecular architecture of the Ub-PCNA/Pol eta complex bound to DNA. Lau WC, Li Y, Zhang Q, Huen MS;. Sci Rep. 2015;5:15759. Paper describing PDB structure 3mr6. [3]. 20577208. Structure and mechanism of human DNA polymerase eta. Biertumpfel C, Zhao Y, Kondo Y, Ramon-Maiques S, Gregory M, Lee JY, Masutani C, Lehmann AR, Hanaoka F, Yang W;. Nature. 2010;465:1044-1048. Paper describing PDB structure 4o3s. [4]. 24759104. Kinetics, structure, and mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine bypass by human DNA polymerase eta. Patra A, Nagy LD, Zhang Q, Su Y, Muller L, Guengerich FP, Egli M;. J Biol Chem. 2014;289:16867-16882. Paper describing PDB structure 4yp3. [5]. 25947374. Roles of Residues Arg-61 and Gln-38 of Human DNA Polymerase eta in Bypass of Deoxyguanosine and 7,8-Dihydro-8-oxo-2'-deoxyguanosine. Su Y, Patra A, Harp JM, Egli M, Guengerich FP;. J Biol Chem. 2015;290:15921-15933. (from Pfam) NF044864.2 PF21758.2 PAC_bac 27 27 115 domain Y N N Bacterial proteasome assembling chaperone-like protein 131567 cellular organisms no rank 2331 EBI-EMBL Bacterial proteasome assembling chaperone-like protein Bacterial proteasome assembling chaperone-like protein This protein family includes LpdD Swiss:F9UT68 a protein found in the gallate decarboxylase operon. Structurally this protein is closely related to eukaryotic proteasome assembling chaperone. This suggests that the proteins in this family may play a similar role. Protein in this family have three highly conserved histidine residue that may be important for function. (from Pfam) NF044865.2 PF21761.2 RedAm-like_C 27 27 127 domain Y N N NADPH-dependent reductive aminase-like, C-terminal domain 23813853,25809902,28937665,29024400,29733377 131567 cellular organisms no rank 28155 EBI-EMBL NADPH-dependent reductive aminase-like, C-terminal domain NADPH-dependent reductive aminase-like, C-terminal domain This domain is found at the C-terminal end of NADPH-dependent reductive aminase from Aspergillus oryzae (RedAm) and similar proteins predominantly found in fungi and bacteria. RedAm catalyses the reductive coupling of a broad set of carbonyl compounds with a variety of primary and secondary amines. This protein folds into an N-terminal Rossman domain (Pfam:PF03446) and a C-terminal helical bundle (this entry) connected by a long inter-domain alpha-helix [3]. Paper describing PDB structure 3zgy. [1]. 23813853. Structure and activity of NADPH-dependent reductase Q1EQE0 from Streptomyces kanamyceticus, which catalyses the R-selective reduction of an imine substrate. Rodriguez-Mata M, Frank A, Wells E, Leipold F, Turner NJ, Hart S, Turkenburg JP, Grogan G;. Chembiochem. 2013;14:1372-1379. Paper describing PDB structure 4d3d. [2]. 25809902. Structure, Activity and Stereoselectivity of NADPH-Dependent Oxidoreductases Catalysing the S-Selective Reduction of the Imine Substrate 2-Methylpyrroline. Man H, Wells E, Hussain S, Leipold F, Hart S, Turkenburg JP, Turner NJ, Grogan G;. Chembiochem. 2015;16:1052-1059. Paper describing PDB structure 5g6r. [3]. 28937665. A reductive aminase from Aspergillus oryzae. Aleku GA, France SP, Man H, Mangas-Sanchez J, Montgomery SL, Sharma M, Leipold F, Hussain S, Grogan G, Turner NJ;. Nat Chem. 2017;9:961-969. Paper describing PDB structure 5ocm. [4]. 29733377. New imine-reducing enzymes from beta-hydroxyacid dehydrogenases by single amino acid substitutions. Lenz M, Fademrecht S, Sharma M, Pleiss J, Grogan G, Nestl BM;. Protein Eng Des Sel. 2018;31:109-120. Paper describing PDB structure 5ojl. [5. TRUNCATED at 1650 bytes (from Pfam) NF044870.2 PF21783.2 YNCE 27.1 27.1 339 domain Y N N YNCE-like beta-propeller 18931447,22120742 131567 cellular organisms no rank 30900 EBI-EMBL YNCE-like beta-propeller YNCE-like beta-propeller This entry includes bacterial YNCE proteins which consist of a beta-propeller structure (the so-called YVTN beta-propeller) [1,2] which binds DNA [2]. [1]. 22120742. Structural basis for the DNA-binding activity of the bacterial beta-propeller protein YncE. Kagawa W, Sagawa T, Niki H, Kurumizaka H;. Acta Crystallogr D Biol Crystallogr. 2011;67:1045-1053. [2]. 18931447. Overproduction, purification and preliminary X-ray diffraction analysis of YncE, an iron-regulated Sec-dependent periplasmic protein from Escherichia coli. Baba-Dikwa A, Thompson D, Spencer NJ, Andrews SC, Watson KA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008;64:966-969. (from Pfam) NF044873.2 PF21790.2 OGG 27 27 201 domain Y N N Putative 8-oxoguanine DNA glycosylase OGG-like protein 131567 cellular organisms no rank 3783 EBI-EMBL Putative 8-oxoguanine DNA glycosylase OGG-like protein Putative 8-oxoguanine DNA glycosylase OGG-like protein This family of proteins are structurally similar to 8-oxoguanine DNA glycosylase enzymes. These proteins are involved in DNA repair of the base excision repair pathway. (from Pfam) NF044878.2 PF21813.2 DUF6882 23.9 23.9 142 domain Y Y N DUF6882 domain-containing protein 131567 cellular organisms no rank 7145 EBI-EMBL Family of unknown function (DUF6882) DUF6882 domain This family of bacterial proteins is uncharacterised. (from Pfam) NF044879.2 PF21819.2 DUF6885 27 27 251 subfamily Y Y N DUF6885 family protein 131567 cellular organisms no rank 395 EBI-EMBL Family of unknown function (DUF6885) DUF6885 family protein This is a small family of proteins that are likely to adopt a papain-like fold. Most members of this family have conserved residues in equivalent positions as the residues that constitute the active site of cysteine proteases. (from Pfam) NF044896.2 PF20693.2 YobI-ATPase 27 27 363 domain Y N N YobI-like P-loop NTPase 15128444 131567 cellular organisms no rank 5437 EBI-EMBL YobI-like P-loop NTPase YobI-like P-loop NTPase This is a P-loop NTPase involved in antiviral immunity in bacteria. Members of this entry have a pair of transmembrane helices inserted into the P-loop NTPase domain [1]. [1]. 15128444. A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain. Aravind L, Iyer LM, Leipe DD, Koonin EV;. Genome Biol 2004;5:R30. (from Pfam) NF044908.2 PF20789.2 4HBT_3C 24.1 24.1 140 domain Y N N Acyl-CoA thioesterase C-terminal domain 15307895 131567 cellular organisms no rank 85167 EBI-EMBL Acyl-CoA thioesterase C-terminal domain Acyl-CoA thioesterase C-terminal domain This family contains a wide variety of enzymes, principally thioesterases. These enzymes are part of the Hotdog fold superfamily [1]. This domain represents the C-terminal domain in a pair of HotDog domains, usually found with Pfam:PF13622. [1]. 15307895. The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases. Dillon SC, Bateman A;. BMC Bioinformatics 2004;5:109-109. (from Pfam) NF044909.2 PF20795.2 DUF6841 27 27 129 domain Y N N NTF2-like protein (DUF6841) 131567 cellular organisms no rank 738 EBI-EMBL NTF2-like protein (DUF6841) NTF2-like protein (DUF6841) This entry represents a family of NTF2-like proteins of unknown function. (from Pfam) NF044910.2 PF20803.2 PaaX_M 24 24 83 domain Y N N PaaX protein central Cas2-like domain 131567 cellular organisms no rank 30179 EBI-EMBL PaaX protein central Cas2-like domain PaaX protein central Cas2-like domain This entry represents the central domain of the PaaX protein which are transcriptional regulators of protein involved in metabolism of phenylacetic acid. This domain is structurally related to the Cas2 ribonuclease domain, suggesting that these proteins may degrade mRNAs to carry out regulation. (from Pfam) NF044913.2 PF20815.2 GIY_YIG_2 22.4 22.4 153 domain Y Y N GIY-YIG nuclease family protein 131567 cellular organisms no rank 3926 EBI-EMBL GIY-YIG catalytic domain GIY-YIG catalytic domain This family represents a group of proteins that have a GIY-YIG-like domain related to homing endonucleases. (from Pfam) NF044937.2 PF20906.2 DUF917_C 27 27 190 domain Y N N Protein of unknown function DUF917, C-terminal 131567 cellular organisms no rank 12347 EBI-EMBL Protein of unknown function DUF917, C-terminal Protein of unknown function DUF917, C-terminal This beta barrel domain is found at the C-terminal of the uncharacterised proteins belonging to the DUF917 family. (from Pfam) NF044942.2 PF20921.2 DUF1846_C 27 27 153 domain Y N N Domain of unknown function DUF1846, C-terminal 131567 cellular organisms no rank 7083 EBI-EMBL Domain of unknown function DUF1846, C-terminal Domain of unknown function DUF1846, C-terminal This is the C-terminal domain found in the uncharacterised protein family UPF0371. It has a cytidine deaminase-like fold (pdbe:3bh1). (from Pfam) NF044945.2 PF20940.2 SSV1_D-63 27 27 60 domain Y N N Sulfolobus spindle-shape virus 1, protein D-63 15220417 131567 cellular organisms no rank 25 EBI-EMBL Sulfolobus spindle-shape virus 1, protein D-63 Sulfolobus spindle-shape virus 1, protein D-63 Protein D-63 from Sulfolobus spindle-shape virus 1 (SSV1) folds into a helix-turn-helix motif with the two helices running antiparallel to each other. It adopts a dimeric assembly and forms an antiparallel four-helix bundle. It might be involved in macromolecular assembly as an adaptor protein [1]. Paper describing PDB structure 1skv. [1]. 15220417. Structure of D-63 from sulfolobus spindle-shaped virus 1: surface properties of the dimeric four-helix bundle suggest an adaptor protein function. Kraft P, Kummel D, Oeckinghaus A, Gauss GH, Wiedenheft B, Young M, Lawrence CM;. J Virol. 2004;78:7438-7442. (from Pfam) NF044949.2 PF20973.2 VUPS 27 27 206 domain Y N N Vitamin uptake-like sensor 35311563 131567 cellular organisms no rank 1826 EBI-EMBL Vitamin uptake-like sensor Vitamin uptake-like sensor This is an integral membrane sensory domain related to the Putative vitamin uptake transporter Vut_1 (Pfam:PF02592, found in YhhQ protein from E. coli). This domain, named Vitamin uptake-like sensor (VUPS), is found in a variety of bacteria in combination with PAS (PF13188), GGDEF (Pfam:PF00990), and EAL (Pfam:PF00563) domains, and with histidine sensor kinases [1]. [1]. 35311563. Comparative Genomics of Cyclic di-GMP Metabolism and Chemosensory Pathways in Shewanella algae Strains: Novel Bacterial Sensory Domains and Functional Insights into Lifestyle Regulation. Martin-Rodriguez AJ, Higdon SM, Thorell K, Tellgren-Roth C, Sjoling A, Galperin MY, Krell T, Romling U;. mSystems. 2022; [Epub ahead of print] (from Pfam) NF044952.2 PF20979.2 Arginosuc_syn_C 27 27 219 domain Y N N Arginosuccinate synthase C-terminal domain 131567 cellular organisms no rank 59384 EBI-EMBL Arginosuccinate synthase C-terminal domain Arginosuccinate synthase C-terminal domain This entry represents the C-terminal domain of the Arginosuccinate synthase enzyme. (from Pfam) NF044955.2 PF20990.2 DUF2207_C 33 33 247 domain Y Y N DUF2207 family protein 131567 cellular organisms no rank 22988 EBI-EMBL Predicted membrane protein (DUF2207) C-terminal domain DUF2207 C-terminal domain This domain, found in various hypothetical bacterial proteins, has no known function. (from Pfam) NF044960.2 PF21016.2 RlmN_N 24 24 60 domain Y N N Ribosomal RNA large subunit methyltransferase N-terminal domain 21527678 131567 cellular organisms no rank 54190 EBI-EMBL Ribosomal RNA large subunit methyltransferase N-terminal domain Ribosomal RNA large subunit methyltransferase N-terminal domain This entry represents the N-terminal domain from the dual-specificity RNA methyltransferase RlmN. [1]. 21527678. Structural basis for methyl transfer by a radical SAM enzyme. Boal AK, Grove TL, McLaughlin MI, Yennawar NH, Booker SJ, Rosenzweig AC;. Science. 2011;332:1089-1092. (from Pfam) NF044969.2 PF21074.2 GDH_C 26 26 339 domain Y N N Glutamate dehydrogenase, C-terminal 10924516,34083757 131567 cellular organisms no rank 39539 EBI-EMBL Glutamate dehydrogenase, C-terminal Glutamate dehydrogenase, C-terminal Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia [1]. The structure of GDH from Mycobacterium smegmatis revealed that it has a long N- and C-terminal segments flanking the catalytic core, comprising several domains. The flexible N-terminal domain comprises ACT-like and PAS-type domains which could act as metabolic sensors for allosteric regulation [2]. This entry represents the helical C-terminal domain. [1]. 10924516. A new class of glutamate dehydrogenases (GDH). Biochemical and genetic characterization of the first member, the AMP-requiring NAD-specific GDH of Streptomyces clavuligerus. Minambres B, Olivera ER, Jensen RA, Luengo JM;. J Biol Chem 2000;275:39529-39542. [2]. 34083757. 3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme. Lazaro M, Melero R, Huet C, Lopez-Alonso JP, Delgado S, Dodu A, Bruch EM, Abriata LA, Alzari PM, Valle M, Lisa MN;. Commun Biol. 2021;4:684. (from Pfam) NF044972.2 PF21082.2 MS_channel_3rd 21 21 88 domain Y N N Mechanosensitive ion channel MscS, C-terminal 11159397,11275684,11296222,23074248,23339071,34376558 131567 cellular organisms no rank 168679 EBI-EMBL Mechanosensitive ion channel MscS, C-terminal Mechanosensitive ion channel MscS, C-terminal This entry includes small conductance mechanosensitive channels (MscS), which assembles to a homoheptameric complex [1-6]. Each monomer consists of a N-terminal transmembrane region and a large cytoplasmic segment composed of a five-stranded antiparallel beta-sheet domain (beta-domain, Pfam:PF00924) and a C-terminal alpha/beta-domain [1,2,3]. This is the C-terminal domain of McsS which, together with the middle beta-domain, creates a framework that connects to the cytoplasm through distinct openings [4-6]. [1]. 11296222. Structural and functional differences between two homologous mechanosensitive channels of Methanococcus jannaschii. Kloda A, Martinac B;. EMBO J 2001;20:1888-1896. [2]. 11159397. Molecular identification of a mechanosensitive channel in archaea. Kloda A, Martinac B;. Biophys J 2001;80:229-240. [3]. 11275684. Mechanosensitive channels in prokaryotes. Martinac B;. Cell Physiol Biochem 2001;11:61-76. [4]. 34376558. Mechanosensitive channel gating by delipidation. Flegler VJ, Rasmussen A, Borbil K, Boten L, Chen HA, Deinlein H, Halang J, Hellmanzik K, Loffler J, Schmidt V, Makbul C, Kraft C, Hedrich R, Rasmussen T, Bottcher B;. Proc Natl Acad Sci U S A. 2021; [Epub ahead of print]. [5]. 23339071. Open and shut: crystal structures of the dodecylmaltoside solubilized mechanosensitive channel of small conductance from Escherichia coli and Helicobacter pylori at 4.4 A and 4.1 A resolutions. Lai JY, Poon YS, Kaiser JT, Rees DC;. Protein Sci. 2013;22:502-509. [6]. 23074248. Structure and molecular mechanism of an anion-selective mechanosensitive channel of small conductance. Zhang X, Wang J, Feng Y, Ge J, Li W, Sun. TRUNCATED at 1650 bytes (from Pfam) NF044974.2 PF21086.2 ACT_PSP_2 24 24 77 domain Y N N ACT domain 21359836 131567 cellular organisms no rank 12873 EBI-EMBL ACT domain ACT domain This entry includes the second of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Paper describing PDB structure 3p96. [1]. 21359836. SAD phasing using iodide ions in a high-throughput structural genomics environment. Abendroth J, Gardberg AS, Robinson JI, Christensen JS, Staker BL, Myler PJ, Stewart LJ, Edwards TE;. J Struct Funct Genomics. 2011;12:83-95. (from Pfam) NF044984.2 PF21128.2 MCM4_WHD 22 22 48 domain Y N N MCM4, winged helix domain 26222030,26854665,28096349 131567 cellular organisms no rank 12 EBI-EMBL MCM4, winged helix domain MCM4, winged helix domain DNA replication licensing factor MCM4 is a component of the MCM2-MCM7 complex which consists of six sequence-related AAA+ type ATPases/helicases that form a heterohexameric ring essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells [1-3]. This is the winged helix domain (WHD) found at the C-terminal of MCM4 [1-3]. Upon ssDNA binding the MCM5-WHD moves out of the central channel and becomes disordered, the MCM6-WHD moves backward and away from the channel, and the MCM4-WHD now partially occludes the channel opening. These changes enable CMG (Cdc45, Mcm2-7, GINS, the eukaryotic replicative helicase) to encircle dsDNA, and is consistent with reports that showed the MCM2-7 matures into two fully assembled CMGs on dsDNA before origin DNA unwinding occurs [3]. Paper describing PDB structure 3ja8. [1]. 26222030. Structure of the eukaryotic MCM complex at 3.8 A. Li N, Zhai Y, Zhang Y, Li W, Yang M, Lei J, Tye BK, Gao N;. Nature. 2015;524:186-191. Paper describing PDB structure 3jc5. [2]. 26854665. Structure of the eukaryotic replicative CMG helicase suggests a pumpjack motion for translocation. Yuan Z, Bai L, Sun J, Georgescu R, Liu J, O'Donnell ME, Li H;. Nat Struct Mol Biol. 2016;23:217-224. Paper describing PDB structure 5u8s. [3]. 28096349. Structure of eukaryotic CMG helicase at a replication fork and implications to replisome architecture and origin initiation. Georgescu R, Yuan Z, Bai L, de Luna Almeida Santos R, Sun J, Zhang D, Yurieva O, Li H, O'Donnell ME;. Proc Natl Acad Sci U S A. 2017;114:E697. (from Pfam) NF045002.2 PF21189.2 PHA02142 27 27 92 domain Y N N PHA02142 OB-fold domain 26512110,32315072 131567 cellular organisms no rank 3596 EBI-EMBL PHA02142 OB-fold domain PHA02142 OB-fold domain This entry represents an N-terminal OB-fold domain found in the putative RNA-ligase PHA02142. DNA ligases and RNA capping enzymes have a shared core domain structure in which a conserved OB-fold domain is linked to the C-terminus of the NTase domain [1]. Paper describing PDB structure 5cot. [1]. 26512110. Structure and two-metal mechanism of a eukaryal nick-sealing RNA ligase. Unciuleac MC, Goldgur Y, Shuman S;. Proc Natl Acad Sci U S A. 2015;112:13868-13873. Paper describing PDB structure 6vt0. [2]. 32315072. Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation. Unciuleac MC, Goldgur Y, Shuman S;. Nucleic Acids Res. 2020;48:5603-5615. (from Pfam) NF045006.2 PF21210.2 RNA_helicase_helical 27 27 108 domain Y N N Putative ATP-dependent RNA helicase, helical bundle 15642269 131567 cellular organisms no rank 1387 EBI-EMBL Putative ATP-dependent RNA helicase, helical bundle Putative ATP-dependent RNA helicase, helical bundle This domain is found in the putative ATP-dependent RNA helicase from Pyrococcus furiosus (PF2015) and similar archaeal proteins. PF2015 is a Hef helicase that processes flap- or fork-DNA structures. This protein shows an SF2 helicase domain in the N-terminal two-thirds and an XPF/Mus81-type nuclease domain in the C-terminal one-third. The SF2 helicase domain is organised into three structural subdomains. This entry represents the second of them, which is composed of six alpha-helices that are tightly assembled into a hydrophobic core. Its surface is positively charged, suggesting that it is a potential DNA binding region [1]. Paper describing PDB structure 1wp9. [1]. 15642269. Crystal structure and functional implications of Pyrococcus furiosus hef helicase domain involved in branched DNA processing. Nishino T, Komori K, Tsuchiya D, Ishino Y, Morikawa K;. Structure. 2005;13:143-153. (from Pfam) NF045016.2 PF21247.2 Fic-like_C 27 27 64 domain Y Y N Fic family protein 131567 cellular organisms no rank 8279 EBI-EMBL Filamentation induced by cAMP protein Fic-like, C-terminal domain Filamentation induced by cAMP protein Fic-like, C-terminal domain This domain is found at the C-terminal end of Filamentation induced by cAMP protein Fic from Oleidesulfovibrio alaskensis and similar bacterial sequences. This domain shows a winged helix structure. It is often found associated with Pfam:PF02661. (from Pfam) NF045027.2 PF21294.3 Polysacc_lyase_14 27 27 215 domain Y Y N polysaccharide lyase 19846561,28011642,31682837 131567 cellular organisms no rank 2260 EBI-EMBL Polysaccharide lyase 14 polysaccharide lyase, family 14 This family of polysaccharide lyases, family 14, includes alginate lyases. NF045029.2 PF21300.2 LbR_Ice_bind 30 30 97 domain Y N N Grass antifreeze beta roll 22306740 131567 cellular organisms no rank 536 EBI-EMBL Grass antifreeze beta roll Grass antifreeze beta roll The grass Lolium perenne produces an ice-binding protein (LpIBP) that helps this perennial tolerate freezing by inhibiting the recrystallization of ice [1]. Ice-binding proteins (IBPs) are also produced by freeze-avoiding organisms to halt the growth of ice and are better known as antifreeze proteins (AFPs) [1]. The ice-binding site (IBS) is formed by a flat beta-sheet on one surface of the beta-roll [1]. This region folds as a left-handed beta-helix. Each of the eight beta-helical coils is composed of two seven-residue tandem repeats with a consensus sequence XXNXVXG where X is a solvent-exposed residue, typically with a polar side chain [1]. Paper describing PDB structure 3ult. [1]. 22306740. Antifreeze protein from freeze-tolerant grass has a beta-roll fold with an irregularly structured ice-binding site. Middleton AJ, Marshall CB, Faucher F, Bar-Dolev M, Braslavsky I, Campbell RL, Walker VK, Davies PL;. J Mol Biol. 2012;416:713-724. (from Pfam) NF045041.2 PF21347.2 DUF3108_like 27 27 199 domain Y N N DUF3108-like 131567 cellular organisms no rank 2099 EBI-EMBL DUF3108-like DUF3108-like This is a domain found in bacteria which adopts a beta-barrel fold of the YmcC-like type. (from Pfam) NF045042.2 PF21348.2 RGL11_C 27 27 490 domain Y N N Rhamnogalacturonan lyase family 11, C-terminal domain 17947240,19193638,24419797 131567 cellular organisms no rank 15254 EBI-EMBL Rhamnogalacturonan lyase family 11, C-terminal domain Rhamnogalacturonan lyase family 11, C-terminal domain This domain is found at the C-terminal end of Rhamnogalacturonan endolyase YesW and Rhamnogalacturonan exolyase YesX from Bacillus subtilis and other bacterial polysaccharide lyases from family 11 (RGL11). These proteins are responsible for an initial cleavage of the RG type I (RG-I) region of plant cell wall pectin. They consist of an N-terminal domain Pfam:PF18370 and a C-terminal eight-bladed beta-propeller domain (this entry) [1-3]. Paper describing PDB structure 2z8r. [1]. 17947240. A novel structural fold in polysaccharide lyases: Bacillus subtilis family 11 rhamnogalacturonan lyase YesW with an eight-bladed beta-propeller. Ochiai A, Itoh T, Maruyama Y, Kawamata A, Mikami B, Hashimoto W, Murata K;. J Biol Chem. 2007;282:37134-37145. Paper describing PDB structure 2zuy. [2]. 19193638. Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases. Ochiai A, Itoh T, Mikami B, Hashimoto W, Murata K;. J Biol Chem. 2009;284:10181-10189. Paper describing PDB structure 4cag. [3]. 24419797. Design of thermostable rhamnogalacturonan lyase mutants from Bacillus licheniformis by combination of targeted single point mutations. Silva IR, Jers C, Otten H, Nyffenegger C, Larsen DM, Derkx PM, Meyer AS, Mikkelsen JD, Larsen S;. Appl Microbiol Biotechnol. 2014;98:4521-4531. (from Pfam) NF045043.2 PF21349.2 RUBY_RBDX 26.5 26.5 30 domain Y Y N rubredoxin-like domain-containing protein GO:0005506 10201393,10216292,10555962,12459910,15468318,19118342 131567 cellular organisms no rank 20187 EBI-EMBL Rubrerythrin, rubredoxin-like domain rubredoxin-like domain Rubrerythrin (RUBY) is a fusion protein containing an N-terminal diiron-binding domain (Pfam:PF02915) and a C-terminal rubredoxin-like domain. RUBY may play a role in oxidative stress. This entry represents the rubredoxin-like domain of RUBY and reverse rubrerythrin 1/2 from Clostridium acetobutylicum (RRBR1/2) [1-5]. RRBRs function as the terminal component of an NADH peroxidase when using NADH:rubredoxin oxidoreductase (NROR) as the electron transport intermediary from NADH to RRBRs and play an important role in the oxidative stress defense system of C. acetobutylicum [6]. Paper describing PDB structure 1b2j. [1]. 10216292. Rubredoxin from Clostridium pasteurianum. Structures of G10A, G43A and G10VG43A mutant proteins. Mutation of conserved glycine 10 to valine causes the 9-10 peptide link to invert. Maher MJ, Xiao Z, Wilce MC, Guss JM, Wedd AG;. Acta Crystallogr D Biol Crystallogr. 1999;55:962-968. Paper describing PDB structure 1b71. [2]. 10201393. Alternative metal-binding sites in rubrerythrin. Sieker LC, Holmes M, Le Trong I, Turley S, Santarsiero BD, Liu MY, LeGall J, Stenkamp RE;. Nat Struct Biol. 1999;6:308-309. Paper describing PDB structure 1c09. [3]. 10555962. Modulation of the redox potential of the [Fe(SCys)(4)] site in rubredoxin by the orientation of a peptide dipole. Eidsness MK, Burden AE, Richie KA, Kurtz DM Jr, Scott RA, Smith ET, Ichiye T, Beard B, Min T, Kang C;. Biochemistry. 1999;38:14803-14809. Paper describing PDB structure 1jyb. [4]. 12459910. Crystal structure studies on rubrerythrin: enzymatic activity in relation to the zinc movement. Li M, Liu MY, LeGall J, Gui LL, Liao J, Jiang T, . TRUNCATED at 1650 bytes (from Pfam) NF045046.2 PF21360.2 PylC-like_N 27 27 96 domain Y N N PylC-like, N-terminal domain 22985965 131567 cellular organisms no rank 6905 EBI-EMBL PylC-like, N-terminal domain PylC-like, N-terminal domain This domain is found in 3-methyl-D-ornithine--L-lysine ligase from Methanosarcina barkeri (PylC) and similar sequences from prokaryotes. PylC is required for the biosynthesis of pyrrolysine. This ATP-grasp enzyme is composed of three domains. This entry represents the N-terminal domain, which is composed of a central four-stranded beta-sheet that is faced on both sides by two helices. It shows an adenine binding pocket that has not been observed in any homologous structure determined before [1]. Paper describing PDB structure 4ffl. [1]. 22985965. Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution. Quitterer F, List A, Beck P, Bacher A, Groll M;. J Mol Biol. 2012;424:270-282. (from Pfam) NF045049.2 PF21368.2 AI2M-like_HNH 23 23 49 domain Y N N AI2M/AI1M-like, HNH endonuclease 27136327 131567 cellular organisms no rank 5966 EBI-EMBL AI2M/AI1M-like, HNH endonuclease AI2M/AI1M-like, HNH endonuclease This is the HNH endonuclease domain found in a set of group II intron proteins, including AIM1/2 from yeast and its orthologue from S. pombe. This domain is also found in related bacterial sequences [1]. Paper describing PDB structure 5g2x. [1]. 27136327. Structure of a group II intron in complex with its reverse transcriptase. Qu G, Kaushal PS, Wang J, Shigematsu H, Piazza CL, Agrawal RK, Belfort M, Wang HW;. Nat Struct Mol Biol. 2016;23:549-557. (from Pfam) NF045058.2 PF21407.2 SduA_N 27 27 102 domain Y N N Shedu protein SduA, N-terminal 29371424 131567 cellular organisms no rank 126 EBI-EMBL Shedu protein SduA, N-terminal Shedu protein SduA, N-terminal This domain is found mostly in bacteria. It is found at the N-terminal of Shedu protein SduA, the only component of antiviral defense system Shedu. Expression of Shedu in B.subtilis (strain BEST7003) confers resistance to phages phi105, phi29, rho14 and to a lesser extent to SPP1 [1]. [1]. 29371424. Systematic discovery of antiphage defense systems in the microbial pangenome. Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R;. Science. 2018; [Epub ahead of print] (from Pfam) NF045064.2 PF21445.2 ADDB_N 26.6 26.6 290 domain Y N N ADDB, N-terminal 22307084,24670664 131567 cellular organisms no rank 25294 EBI-EMBL ADDB, N-terminal ADDB, N-terminal ATP-dependent helicase/deoxyribonuclease subunit B (ADDB) forms a heterodimer with ADDA which acts as both an ATP-dependent DNA helicase and an ATP-dependent single-stranded exonuclease, acting in both directions. This entry represents the N-terminal domain of ADDB, which contains the Walker A motif involved in ATP binding [1,2]. Paper describing PDB structure 3u44. [1]. 22307084. Insights into Chi recognition from the structure of an AddAB-type helicase-nuclease complex. Saikrishnan K, Yeeles JT, Gilhooly NS, Krajewski WW, Dillingham MS, Wigley DB;. EMBO J. 2012;31:1568-1578. Paper describing PDB structure 4ceh. [2]. 24670664. Structural basis for translocation by AddAB helicase-nuclease and its arrest at chi sites. Krajewski WW, Fu X, Wilkinson M, Cronin NB, Dillingham MS, Wigley DB;. Nature. 2014;508:416-419. (from Pfam) NF045072.2 PF21466.2 GH101_dom-5 27 27 145 domain Y N N Endo-alpha-N-acetylgalactosaminidase, domain 5 10075919,18784084,19502354,26304114,31645583 131567 cellular organisms no rank 8880 EBI-EMBL Endo-alpha-N-acetylgalactosaminidase, domain 5 Endo-alpha-N-acetylgalactosaminidase, domain 5 Endo-alpha-N-acetylgalactosaminidase is a member of glycoside hydrolase (GH) family 101 and hydrolases the O-glycosidic bonds in mucin-type O-glycan between alpha-GalNAc and Ser/Thr. It is a multidomain protein [1-5]. It contains a distorted (alpha/beta)8 barrel catalytic domain (referred to as domain 3) flanked by four additional domains, which are mainly made of beta-sheets (domains 2, 4, 5 and 6). This entry represents domain 5 which is part of the carbohydrate binding module. Paper describing PDB structure 1fnh. [1]. 10075919. Crystal structure of a heparin- and integrin-binding segment of human fibronectin. Sharma A, Askari JA, Humphries MJ, Jones EY, Stuart DI;. EMBO J. 1999;18:1468-1479. Paper describing PDB structure 2zxq. [2]. 19502354. Crystallographic and mutational analyses of substrate recognition of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum. Suzuki R, Katayama T, Kitaoka M, Kumagai H, Wakagi T, Shoun H, Ashida H, Yamamoto K, Fushinobu S;. J Biochem. 2009;146:389-398. Paper describing PDB structure 3ecq. [3]. 18784084. The structural basis for T-antigen hydrolysis by Streptococcus pneumoniae: a target for structure-based vaccine design. Caines ME, Zhu H, Vuckovic M, Willis LM, Withers SG, Wakarchuk WW, Strynadka NC;. J Biol Chem. 2008;283:31279-31283. Paper describing PDB structure 5a55. [4]. 26304114. Structural Analysis of a Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights into Its Mechanism. Gregg KJ, Suits MD, Deng L, Vocadlo DJ, Boraston AB;. J Biol Chem. 2015;290:25657-25669. Paper describing PDB structure 6qep. [5]. 31645583. Structural analysis of bio. TRUNCATED at 1650 bytes (from Pfam) NF045073.2 PF21467.2 BetaGal_gal-bd 27.3 27.3 62 domain Y N N Beta-galactosidase, galactose-binding domain 15491613,21130883,22128166,22593580,25210925 131567 cellular organisms no rank 25000 EBI-EMBL Beta-galactosidase, galactose-binding domain Beta-galactosidase, galactose-binding domain Beta-galactosidase belongs to Glycoside hydrolase family 35 [1-5]. This entry represents the galactose-binding domain. Paper describing PDB structure 1tg7. [1]. 15491613. Crystal structures of beta-galactosidase from Penicillium sp. and its complex with galactose. Rojas AL, Nagem RA, Neustroev KN, Arand M, Adamska M, Eneyskaya EV, Kulminskaya AA, Garratt RC, Golubev AM, Polikarpov I;. J Mol Biol. 2004;343:1281-1292. Paper describing PDB structure 3og2. [2]. 21130883. Crystal structures of Trichoderma reesei beta-galactosidase reveal conformational changes in the active site. Maksimainen M, Hakulinen N, Kallio JM, Timoharju T, Turunen O, Rouvinen J;. J Struct Biol. 2011;174:156-163. Paper describing PDB structure 3thc. [3]. 22128166. Crystal structure of human beta-galactosidase: structural basis of Gm1 gangliosidosis and morquio B diseases. Ohto U, Usui K, Ochi T, Yuki K, Satow Y, Shimizu T;. J Biol Chem. 2012;287:1801-1812. Paper describing PDB structure 4cu6. [4]. 25210925. Unravelling the multiple functions of the architecturally intricate Streptococcus pneumoniae beta-galactosidase, BgaA. Singh AK, Pluvinage B, Higgins MA, Dalia AB, Woodiga SA, Flynn M, Lloyd AR, Weiser JN, Stubbs KA, Boraston AB, King SJ;. PLoS Pathog. 2014;10:e1004364. Paper describing PDB structure 4e8c. [5]. 22593580. Structural insights into the substrate specificity of Streptococcus pneumoniae beta(1,3)-galactosidase BgaC. Cheng W, Wang L, Jiang YL, Bai XH, Chu J, Li Q, Yu G, Liang QL, Zhou CZ, Chen Y;. J Biol Chem. 2012;287:22910-22918. (from Pfam) NF045075.2 PF21485.2 IF5A-like_N 27.1 27.1 63 domain Y N N Translation initiation factor 5A-like, N-terminal 12640443,12761201,19280598,9724718,9753699 131567 cellular organisms no rank 1144 EBI-EMBL Translation initiation factor 5A-like, N-terminal Translation initiation factor 5A-like, N-terminal This is the N-terminal domain of Translation initiation factor 5A from eukaryotes and archaea, which has a SH2-like fold. These proteins are involved in translation elongation and eIF5A is specifically required to promote peptide-bond formation between consecutive proline residues [1-5]. This entry also includes Woronin body major protein Hex1, which is similar to eIF5A. Paper describing PDB structure 1bkb. [1]. 9753699. Structure of translation initiation factor 5A from Pyrobaculum aerophilum at 1.75 A resolution. Peat TS, Newman J, Waldo GS, Berendzen J, Terwilliger TC;. Structure 1998;6:1207-1214. Paper describing PDB structure 1eif. [2]. 9724718. Crystal structures of eukaryotic translation initiation factor 5A from Methanococcus jannaschii at 1.8 A resolution. Kim KK, Hung LW, Yokota H, Kim R, Kim SH;. Proc Natl Acad Sci U S A. 1998;95:10419-10424. Paper describing PDB structure 1iz6. [3]. 12761201. Crystal structure of hyperthermophilic archaeal initiation factor 5A: a homologue of eukaryotic initiation factor 5A (eIF-5A). Yao M, Ohsawa A, Kikukawa S, Tanaka I, Kimura M;. J Biochem. 2003;133:75-81. Paper describing PDB structure 1khi. [4]. 12640443. A HEX-1 crystal lattice required for Woronin body function in Neurospora crassa. Yuan P, Jedd G, Kumaran D, Swaminathan S, Shio H, Hewitt D, Chua NH, Swaminathan K;. Nat Struct Biol. 2003;10:264-270. Paper describing PDB structure 3cpf. [5]. 19280598. Crystal structure of human eIF5A1: insight into functional similarity of human eIF5A1 and eIF5A2. Tong Y, Park I, Hong BS, Nedyalkova L, Tempel W, Park HW;. Proteins. 2009;75:1040-1045. (from Pfam) NF045090.2 PF21545.2 T7SS_EccA1_N 27 27 272 domain Y N N T7SS, ESX-1 secretion system protein EccA1, N-terminal domain 21784982,23818233 131567 cellular organisms no rank 10755 EBI-EMBL T7SS, ESX-1 secretion system protein EccA1, N-terminal domain T7SS, ESX-1 secretion system protein EccA1, N-terminal domain This domain is found at the N-terminal end of ESX-1 secretion system protein EccA1 from Mycobacterium tuberculosis and similar proteins predominantly from Actinobacteria. EccA1 is part of the ESX-1 specialised secretion system (a cluster of the type VII secretion system, T7SS). EccA1 contains a C-terminal ATPase domain (Pfam:PF00004 and Pfam:PF17866) and a tetratricopeptide repeat (TPR) containing N-terminal domain (this entry). The six tandem TPR motifs of this domain packed in parallel create a series of repeating antiparallel alpha-helices that give rise to an overall superhelix structure [1,2]. Paper describing PDB structure 3as4. [1]. 21784982. Self-recognition mechanism of MamA, a magnetosome-associated TPR-containing protein, promotes complex assembly. Zeytuni N, Ozyamak E, Ben-Harush K, Davidov G, Levin M, Gat Y, Moyal T, Brik A, Komeili A, Zarivach R;. Proc Natl Acad Sci U S A. 2011;108:E480-E487. Paper describing PDB structure 4f3v. [2]. 23818233. Crystal structure of the N-terminal domain of EccA(1) ATPase from the ESX-1 secretion system of Mycobacterium tuberculosis. Wagner JM, Evans TJ, Korotkov KV;. Proteins. 2014;82:159-163. (from Pfam) NF045092.2 PF21555.2 CCC_C_1st_pro 27 27 128 domain Y N N Prokaryotic cation-chloride cotransporter, C-terminal domain, 1st 19368887 131567 cellular organisms no rank 330 EBI-EMBL Prokaryotic cation-chloride cotransporter, C-terminal domain, 1st Prokaryotic cation-chloride cotransporter, C-terminal domain, 1st This domain is found in the C-terminal region of a group of prokaryotic cation-chloride cotransporters (CCCs), including Na-K-Cl cotransporter from Methanosarcina acetivorans (Swiss:Q8THK8). These proteins consist of an N-terminal transmembrane transport region (Pfam:PF00324 and Pfam:PF13520) followed by a cytoplasmic regulatory domain. The C-terminal domain adopts a compact trapezoid-shaped elongated structure with a mixed alpha-beta fold and can be divided in two structurally related subdomains. This entry represents the first subdomain, which shows a central five-stranded parallel beta- sheet and three alpha-helices that pack on either face of the sheet [1]. Paper describing PDB structure 3g40. [1]. 19368887. X-ray structure of the C-terminal domain of a prokaryotic cation-chloride cotransporter. Warmuth S, Zimmermann I, Dutzler R;. Structure. 2009;17:538-546. (from Pfam) NF045098.2 PF21571.2 ArgZ-like_C_1st 27 27 84 domain Y N N Arginine dihydrolase ArgZ-like, C-terminal, first region 31914412,32198136 131567 cellular organisms no rank 2735 EBI-EMBL Arginine dihydrolase ArgZ-like, C-terminal, first region Arginine dihydrolase ArgZ-like, C-terminal, first region This domain is found at the C-terminal end of Arginine dihydrolase ArgZ from Synechocystis sp (also known as Sll1336 protein) and similar prokaryotic sequences. ArgZ is involved in an ornithine- ammonia cycle (OAC) in cyanobacteria, which confers substantial adaptability under environmental nitrogen fluctuations. This protein is organised into three domains: a N-terminal domain belonging to the guanidino group-modifying enzyme (GME) family, a middle oxoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme (Pfam:PF04455) and a C-terminal uncharacterized region that can be divided in two subdomains. This entry represents the small first region of the C-terminal domain, which folds into beta-strands. Its specific function is unknown [1]. Paper describing PDB structure 6juy. [1]. 31914412. Crystal structures and biochemical analyses of the bacterial arginine dihydrolase ArgZ suggests a "bond rotation" catalytic mechanism. Zhuang N, Zhang H, Li L, Wu X, Yang C, Zhang Y;. J Biol Chem. 2020;295:2113-2124. Paper describing PDB structure 6lrf. [2]. 32198136. Structural and mutational analyses of the bifunctional arginine dihydrolase and ornithine cyclodeaminase AgrE from the cyanobacterium Anabaena. Lee H, Rhee S;. J Biol Chem. 2020;295:5751-5760. (from Pfam) NF045119.2 PF21654.2 DncV-like_NTFase 24.9 24.9 90 domain Y Y N cyclic GMP-AMP synthase DncV-like nucleotidyltransferase 25131990,25201413,25865248,34077735 131567 cellular organisms no rank 7168 EBI-EMBL Cyclic GMP-AMP synthase DncV-like, nucleotidyltransferase domain cyclic GMP-AMP synthase DncV-like nucleotidyltransferase domain This is the nucleotidyltransferase domain of DncV from Vibrio cholerae (also known as Cyclic GMP-AMP synthase) and related proteins [1-4]. DncV catalyses the synthesis of 3'3'-cyclic GMP-AMP (3'3'-cGAMP) from GTP and ATP. It is part of the CBASS (cyclic oligonucleotide-based antiphage signaling system) which provides immunity against bacteriophage [1-4]. This protein is required for efficient V.cholerae intestinal colonization and and down-regulates the colonization-influencing process of chemotaxis. Paper describing PDB structure 4txy. [1]. 25131990. Structure-guided reprogramming of human cGAS dinucleotide linkage specificity. Kranzusch PJ, Lee ASY, Wilson SC, Solovykh MS, Vance RE, Berger JM, Doudna JA;. Cell. 2014;158:1011-1021. Paper describing PDB structure 4u03. [2]. 25201413. Structural biochemistry of a Vibrio cholerae dinucleotide cyclase reveals cyclase activity regulation by folates. Zhu D, Wang L, Shang G, Liu X, Zhu J, Lu D, Wang L, Kan B, Zhang JR, Xiang Y;. Mol Cell. 2014;55:931-937. Paper describing PDB structure 4xj1. [3]. 25865248. Structural Basis for the Catalytic Mechanism of DncV, Bacterial Homolog of Cyclic GMP-AMP Synthase. Kato K, Ishii R, Hirano S, Ishitani R, Nureki O;. Structure. 2015;23:843-850. Paper describing PDB structure 7ljo. [4]. 34077735. Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense. Govande AA, Duncan-Lowey B, Eaglesham JB, Whiteley AT, Kranzusch PJ;. Cell Rep. 2021;35:109206. (from Pfam) NF045129.2 PF21680.2 GIDA_C_1st 24.7 24.7 96 domain Y N N tRNA modifying enzyme MnmG/GidA C-terminal helical domain 18565343,19446527,19801413 131567 cellular organisms no rank 62438 EBI-EMBL tRNA modifying enzyme MnmG/GidA C-terminal helical domain tRNA modifying enzyme MnmG/GidA C-terminal helical domain The GidA associated domain is a domain that has been identified at the C-terminus of protein GidA. It consists of several helices, the last three being rather short and forming small bundle. GidA is an tRNA modification enzyme found in bacteria and mitochondrial. Based on mutational analysis this domain has been suggested to be implicated in binding of the D-stem of tRNA [2] and, in particular the small bundle, to be responsible for the interaction with protein MnmE [1]. Structures of GidA in complex with either tRNA or MnmE are missing. Reported to bind to Pfam family MnmE, Pfam:PF12631. This entry represents the first helices of the GidA associated domain. The last three helices are covered in Pfam:PF13932. [1]. 18565343. Crystal structures of the conserved tRNA-modifying enzyme GidA: implications for its interaction with MnmE and substrate. Meyer S, Scrima A, Versees W, Wittinghofer A;. J Mol Biol. 2008;380:532-547. [2]. 19446527. Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon. Osawa T, Ito K, Inanaga H, Nureki O, Tomita K, Numata T;. Structure. 2009;17:713-724. [3]. 19801413. Structure-function analysis of Escherichia coli MnmG (GidA), a highly conserved tRNA-modifying enzyme. Shi R, Villarroya M, Ruiz-Partida R, Li Y, Proteau A, Prado S, Moukadiri I, Benitez-Paez A, Lomas R, Wagner J, Matte A, Velazquez-Campoy A, Armengod ME, Cygler M;. J Bacteriol. 2009;191:7614-7619. (from Pfam) NF045135.2 PF21708.3 Glyco_hydro_59_C 27 27 175 domain Y N N Galactocerebrosidase, C-terminal lectin domain 21876145,24297913 131567 cellular organisms no rank 3882 EBI-EMBL Galactocerebrosidase, C-terminal lectin domain Galactocerebrosidase, C-terminal lectin domain This domain is found at the C-terminal end of Galactocerebrosidase from Mus musculus (GALCERase) and similar proteins predominantly found in animals and bacteria. GALCERase hydrolyses the galactose ester bonds of glycolipids such as galactosylceramide and galactosylsphingosine. It is responsible for the lysosomal catabolism of galactosylceramide, a major lipid in myelin, kidney and epithelial cells of small intestine and colon. This protein is organised into three domains, all of them contributing residues to the substrate- binding pocket. This entry represents the lectin domain, which is not present in other lysosomal enzymes, is likely to be be involved in processes that are not found in related enzymes. Mutations in this domain lead to Krabbe disease [1]. Paper describing PDB structure 3zr5. [1]. 21876145. Insights into Krabbe disease from structures of galactocerebrosidase. Deane JE, Graham SC, Kim NN, Stein PE, McNair R, Cachon-Gonzalez MB, Cox TM, Read RJ;. Proc Natl Acad Sci U S A. 2011;108:15169-15173. Paper describing PDB structure 4ccc. [2]. 24297913. Structural snapshots illustrate the catalytic cycle of beta-galactocerebrosidase, the defective enzyme in Krabbe disease. Hill CH, Graham SC, Read RJ, Deane JE;. Proc Natl Acad Sci U S A. 2013;110:20479-20484. (from Pfam) NF045152.2 PF21769.2 vRNAP_dom 27 27 145 domain Y N N Virion DNA-directed RNA polymerase domain 18362338,19061645,21321236 131567 cellular organisms no rank 29 EBI-EMBL Virion DNA-directed RNA polymerase domain Virion DNA-directed RNA polymerase domain This domain is found in Virion DNA-directed RNA polymerase from Bacteriophage N4 (vRNAP), responsible for the transcription of the early region of the double-stranded linear DNA genome of the lytic coliphage. This domain adopts a mostly alpha-helical configuration [1-3]. Paper describing PDB structure 2po4. [1]. 18362338. X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase. Murakami KS, Davydova EK, Rothman-Denes LB;. Proc Natl Acad Sci U S A. 2008;105:5046-5051. Paper describing PDB structure 3c2p. [2]. 19061645. Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase. Gleghorn ML, Davydova EK, Rothman-Denes LB, Murakami KS;. Mol Cell. 2008;32:707-717. Paper describing PDB structure 3q0a. [3]. 21321236. X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides. Gleghorn ML, Davydova EK, Basu R, Rothman-Denes LB, Murakami KS;. Proc Natl Acad Sci U S A. 2011;108:3566-3571. (from Pfam) NF045158.2 PF21806.2 DUF6879 23.9 23.9 167 subfamily Y Y N DUF6879 family protein 131567 cellular organisms no rank 23122 EBI-EMBL Family of unknown function (DUF6879) DUF6879 family protein This family of proteins are uncharacterised. However, they fold into a compact domain that is structurally related to the Phospholipase D protein family (Pfam:PF13091). This suggests they may have an enzymatic activity. (from Pfam) NF045161.2 PF21811.2 RdfA 27 27 195 PfamEq Y Y N rod-determining factor RdfA rdfA 131567 cellular organisms no rank 1362 EBI-EMBL Rod-determining factor RdfA rod-determining factor RdfA Rod-determining factor RdfA was identified in haloarchaea species and is required for cell-shape determination and motility. Proteins members of this family possess four highly conserved cysteine residues at the C-terminus that could potentially be involved in zinc binding. (from Pfam) NF045163.2 PF21818.2 DUF6884 30 30 135 domain Y Y N DUF6884 domain-containing protein 131567 cellular organisms no rank 11236 EBI-EMBL Family of unknown function (DUF6884) DUF6884 domain-containing protein This is a domain of unknown function that is found either as a standalone protein or in combination with other domains. Members of this family possess a highly conserved LSAXXG motif that may constitute an active site. This domain may be distantly related to oxidative stress response YaaA proteins. (from Pfam) NF045168.2 PF20628.2 Dyp_perox_C 20 20 166 domain Y N N Dyp-type peroxidase, C-terminal 10742277,17654545,21324904,22308037 131567 cellular organisms no rank 73705 EBI-EMBL Dyp-type peroxidase, C-terminal Dyp-type peroxidase, C-terminal Dyp-type (dye-decolorizing) peroxidases are a family of heme proteins found in a wide range of bacteria and fungi [1,2]. They have a wide substrate specificity and lack homology to most other peroxidases, with the ability to function well under much lower pH conditions compared with the other plant peroxidases [2,3,4]. They consist of two domains that adopt a ferredoxin-like fold [2,4], connected by a loop. This entry represents the C-terminal domain, which possess a large hydrophobic cavity for heme binding [2,3,4]. [1]. 10742277. Efficient heterologous expression in Aspergillus oryzae of a unique dye-decolorizing peroxidase, DyP, of Geotrichum candidum Dec 1. Sugano Y, Nakano R, Sasaki K, Shoda M;. Appl Environ Microbiol 2000;66:1754-1758. [2]. 21324904. Crystal structure and biochemical features of EfeB/YcdB from Escherichia coli O157: ASP235 plays divergent roles in different enzyme-catalyzed processes. Liu X, Du Q, Wang Z, Zhu D, Huang Y, Li N, Wei T, Xu S, Gu L;. J Biol Chem. 2011;286:14922-14931. [3]. 17654545. Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif. Zubieta C, Krishna SS, Kapoor M, Kozbial P, McMullan D, Axelrod HL, Miller MD, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Schimmel P, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Proteins. 20. TRUNCATED at 1650 bytes (from Pfam) NF045169.2 PF20629.2 GD_AH_C 26.8 26.8 242 domain Y N N D-galactarate/Altronate dehydratase, C-terminal 31811683 131567 cellular organisms no rank 46899 EBI-EMBL D-galactarate/Altronate dehydratase, C-terminal D-galactarate/Altronate dehydratase, C-terminal This entry represents the C-terminal domain of Galactarate dehydratase (GarD). GarD catalyses the dehydration of galactarate to 5-dehydro-4-deoxy-D-galactarate. In the crystal structure, GarD forms dimers and each monomer consists of three domains: the N-terminal SAF domain (Pfam:PF08666) connected to the second domain (Pfam:PF04295) through a long linker and the C-terminal domain which represents the core of the protein. This domain adopts a variant of a Rossmann fold with an unusual crossover, consisting of seven-stranded parallel beta-sheets surrounded by nine alpha-helices [1]. This domain may contain a catalytic metal binding site [1]. [1]. 31811683. Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment. Rosas-Lemus M, Minasov G, Shuvalova L, Wawrzak Z, Kiryukhina O, Mih N, Jaroszewski L, Palsson B, Godzik A, Satchell KJF;. Protein Sci. 2020;29:711-722. (from Pfam) NF045191.2 PF20695.2 UbiD_N 24.3 24.3 78 domain Y N N 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain 23671667,25862228,26083754,28057757,28857436,782527 131567 cellular organisms no rank 50137 EBI-EMBL 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain This family has been characterised as 3-octaprenyl-4- hydroxybenzoate carboxy-lyase enzymes [1]. This enzyme catalyses the third reaction in ubiquinone biosynthesis. For optimal activity the carboxy-lase was shown to require Mn2+ [1]. This entry represents the N-terminal domain. [1]. 782527. Membrane-associated reactions in ubiquinone biosynthesis in Escherichia coli. 3-Octaprenyl-4-hydroxybenzoate carboxy-lyase. Leppik RA, Young IG, Gibson F;. Biochim Biophys Acta 1976;436:800-810. [2]. 23671667. Structural insights into the UbiD protein family from the crystal structure of PA0254 from Pseudomonas aeruginosa. Jacewicz A, Izumi A, Brunner K, Schnell R, Schneider G;. PLoS One. 2013;8:e63161. [3]. 25862228. Structure and Mechanism of Ferulic Acid Decarboxylase (FDC1) from Saccharomyces cerevisiae. Bhuiya MW, Lee SG, Jez JM, Yu O;. Appl Environ Microbiol. 2015;81:4216-4223. [4]. 26083754. New cofactor supports alpha,beta-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition. Payne KA, White MD, Fisher K, Khara B, Bailey SS, Parker D, Rattray NJ, Trivedi DK, Goodacre R, Beveridge R, Barran P, Rigby SE, Scrutton NS, Hay S, Leys D;. Nature. 2015;522:497-501. [5]. 28057757. Oxidative Maturation and Structural Characterization of Prenylated FMN Binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis. Marshall SA, Fisher K, Ni Cheallaigh A, White MD, Payne KA, Parker DA, Rigby SE, Leys D;. J Biol Chem. 2017;292:4623-4637. [6]. 28857436. Regioselective para-Carboxylation of Catechols with a Prenylated Flavin Dependent Decarboxylase. Payer SE, Marshall SA, Barland N, Sheng X, Reiter T, Dordic A, Steink. TRUNCATED at 1650 bytes (from Pfam) NF045194.2 PF20706.2 GT4-conflict 26 26 385 domain Y N N Family 4 Glycosyltransferase in conflict systems 34061031 131567 cellular organisms no rank 438784 EBI-EMBL Family 4 Glycosyltransferase in conflict systems Family 4 Glycosyltransferase in conflict systems This entry corresponds to Family 4 Glycosyltransferase domain comprised of two Rossmann fold subdomains. The domain is found in architecturally-rich proteins of metazoan counter-invader systems and in bacterial conflict systems [1]. [1]. 34061031. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. Kaur G, Iyer LM, Burroughs AM, Aravind L;. Elife. 2021; [Epub ahead of print] (from Pfam) NF045198.2 PF20720.2 nSTAND3 27.2 27.2 155 domain Y N N Novel STAND NTPase 3 34061031 131567 cellular organisms no rank 20930 EBI-EMBL Novel STAND NTPase 3 Novel STAND NTPase 3 This entry represents a novel domain of the STAND-superfamily of AAA+ ATPases found in bacterial conflict systems and in metazoan TRADD-N associated counter-invader proteins [1]. [1]. 34061031. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. Kaur G, Iyer LM, Burroughs AM, Aravind L;. Elife. 2021; [Epub ahead of print] (from Pfam) NF045201.2 PF20732.2 NamZ_C 25 25 152 domain Y N N Exo-beta-N-acetylmuramidase NamZ, C-terminal 33684445 131567 cellular organisms no rank 26238 EBI-EMBL Exo-beta-N-acetylmuramidase NamZ, C-terminal Exo-beta-N-acetylmuramidase NamZ, C-terminal NamZ is an exo-beta-N-acetylmuramidase which catalyzes an exo-lytic cleavage of beta-1,4-acetylmuramic acid from from the non-reducing ends of peptidoglycan chains [1] and it is a founding member of a new family of glycosidases (GH171). NamZ consists of a N-terminal catalytic domain with a Rossmann-like fold and a C-terminal auxiliary alpha/beta domain (represented in this entry). [1]. 33684445. The exo-beta-N-acetylmuramidase NamZ from Bacillus subtilis is the founding member of a family of exo-lytic peptidoglycan hexosaminidases. Muller M, Calvert M, Hottmann I, Kluj RM, Teufel T, Balbuchta K, Engelbrecht A, Selim KA, Xu Q, Borisova M, Titz A, Mayer C;. J Biol Chem. 2021;296:100519. (from Pfam) NF045212.2 PF20766.2 DUF447_C 24.8 24.8 53 domain Y N N Protein of unknown function (DUF447) 22201035 131567 cellular organisms no rank 3130 EBI-EMBL Protein of unknown function (DUF447) Protein of unknown function (DUF447) This entry represents a spectrin-like domain found in the DUF447 family of proteins. [1]. 22201035. 1H, 15N and 13C chemical shift assignments of the BA42 protein of the psychrophilic bacteria Bizionia argentinensis sp. nov. Smal C, Aran M, Lanzarotti E, Papouchado M, Foti M, Marti MA, Coria SH, Vazquez SC, Bercovich A, Mac Cormack WP, Turjanski AG, Gallo M, Cicero DO;. Biomol NMR Assign. 2012;6:181-183. (from Pfam) NF045214.2 PF20774.2 InhA-like_VEG 27.6 27.6 158 domain Y N N Immune inhibitor A-like metallopeptidase, VEG domain 26745529 131567 cellular organisms no rank 17628 EBI-EMBL Immune inhibitor A-like metallopeptidase, VEG domain Immune inhibitor A-like metallopeptidase, VEG domain Immune inhibitor A(InhA)-type metallopeptidases are potential virulence factors secreted by members of the Bacillus cereus group (BCG) and belong to the thuringilysin family within the metzincin clan of metallopeptidases, M6 in the MEROPS database. The structure of these proteins consists of four domains: a pro-peptide, a catalytic domain, a domain reminiscent of viral envelope glycoproteins (VEG), and a MAM domain grafted into the latter [1]. This entry represents the VEG domain found at the C-terminal of InhA and PrtV peptidases (a slightly more distant thuringilysin family members). It consists of a central parallel beta-sandwich comprised by an upper five-stranded mixed sheet and a lower four-stranded antiparallel sheet [1]. [1]. 26745529. Structural Basis for Latency and Function of Immune Inhibitor A Metallopeptidase, a Modulator of the Bacillus anthracis Secretome. Arolas JL, Goulas T, Pomerantsev AP, Leppla SH, Gomis-Ruth FX;. Structure. 2016;24:25-36. (from Pfam) NF045246.2 PF20901.2 Sf6_terminase 27 27 106 domain Y N N Bacteriophage Sf6, terminase small subunit-like 20133842,22858866 131567 cellular organisms no rank 3587 EBI-EMBL Bacteriophage Sf6, terminase small subunit-like Bacteriophage Sf6, terminase small subunit-like In many tailed double-stranded DNA (dsDNA) virus such as Bacteriophage Sf6, the DNA newly synthesized is packaged into a preformed procapsid. The small subunit of the terminase is the component responsible for concatemeric viral DNA-recognition in the molecular machine that carries out this process. The small subunit of the terminase from phage Sf6, also known as gp1, consists of an N-terminal domain, a central alpha-helical domain and a C- terminal domain forming a beta-barrel, and adopts a ring-like octameric configuration composed of monomers [1,2]. [1]. 22858866. Structural and functional studies of the phage Sf6 terminase small subunit reveal a DNA-spooling device facilitated by structural plasticity. Zhao H, Kamau YN, Christensen TE, Tang L;. J Mol Biol. 2012;423:413-426. [2]. 20133842. Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine. Zhao H, Finch CJ, Sequeira RD, Johnson BA, Johnson JE, Casjens SR, Tang L;. Proc Natl Acad Sci U S A. 2010;107:1971-1976. (from Pfam) NF045247.2 PF20903.2 SPL 27 27 338 subfamily Y Y N spore photoproduct lyase family protein 22761404,23607538,25285338 131567 cellular organisms no rank 12769 EBI-EMBL Spore photoproduct lyase spore photoproduct lyase family protein Members of this family include the radical SAM enzyme spore photoproduct lyase SplB from endospore-forming Gram-positive bacteria, but also include somewhat distantly related homologs from other lineages in which SPL activity has not been shown. A tyrosine residue essential for photoproduct lyase activity is conserved. NF045254.2 PF20938.2 DUF2264_C 27 27 266 domain Y N N DUF2264 C-terminal domain 131567 cellular organisms no rank 7324 EBI-EMBL DUF2264 C-terminal domain DUF2264 C-terminal domain This domain is found at the C-terminus of DUF2264 family proteins. This domain adopts a beta sandwich domain that is structurally related to Pfam:PF07940, suggesting that DUF2264 proteins are oligosaccharide degrading enzymes. (from Pfam) NF045255.2 PF20939.2 MsrA_helical 23.7 23.7 51 domain Y N N Selenoprotein methionine sulfoxide reductase A, helical domain 24412203,26107511 131567 cellular organisms no rank 37 EBI-EMBL Selenoprotein methionine sulfoxide reductase A, helical domain Selenoprotein methionine sulfoxide reductase A, helical domain This domain is found in 1-Cys type selenoprotein methionine sulfoxide reductase A (MsrA) from the bacteria Clostridium oremlandii, a repair enzyme for proteins that have been inactivated by oxidation that is found both in prokaryotes and eukaryotes. MsrA catalyses the reduction of methionine sulfoxide in proteins to methionine. This enzyme is organised into a catalytic domain (Pfam:PF01625) and a helical domain (this entry) absent in most of the known MsrA structures. It consists of five helices, interacts with the catalytic domain and is essential for the active site formation [1,2]. Paper describing PDB structure 4lwj. [1]. 24412203. Structural analysis of 1-Cys type selenoprotein methionine sulfoxide reductase A. Lee EH, Kwak GH, Kim MJ, Kim HY, Hwang KY;. Arch Biochem Biophys. 2014;545:1-8. Paper describing PDB structure 4u66. [2]. 26107511. Evidence for the dimerization-mediated catalysis of methionine sulfoxide reductase A from Clostridium oremlandii. Lee EH, Lee K, Kwak GH, Park YS, Lee KJ, Hwang KY, Kim HY;. PLoS One. 2015;10:e0131523. (from Pfam) NF045261.2 PF20966.2 MASE6 27.4 27.4 170 domain Y N N MASE6 35311563 131567 cellular organisms no rank 3362 EBI-EMBL MASE6 MASE6 This entry represents a predicted integral membrane sensory domain (MASE6) [1], which has been observed in association with GGDEF domain (Pfam:PF00990) and histidine sensor kinases. [1]. 35311563. Comparative Genomics of Cyclic di-GMP Metabolism and Chemosensory Pathways in Shewanella algae Strains: Novel Bacterial Sensory Domains and Functional Insights into Lifestyle Regulation. Martin-Rodriguez AJ, Higdon SM, Thorell K, Tellgren-Roth C, Sjoling A, Galperin MY, Krell T, Romling U;. mSystems. 2022; [Epub ahead of print] (from Pfam) NF045268.2 PF21006.2 NHase_beta_N 21.5 21.5 115 domain Y N N Nitrile hydratase beta subunit, N-terminal 14717710,17222425,9195885 131567 cellular organisms no rank 14829 EBI-EMBL Nitrile hydratase beta subunit, N-terminal Nitrile hydratase beta subunit, N-terminal Nitrile hydratases (NHases) EC:4.2.1.84 are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit [1]. Beta subunit consists of an N-terminal helical domain, represented in this entry, and a C-terminal SH3-like domain (Pfam:PF02211) [2,3]. Thiocyanate hydrolase (SCNase) is a member of the NHase family and comprises alpha, beta and gamma subunits, which share amino acid sequence similarities with NHase beta subunit C-terminal, beta subunit N-terminal and NHase alpha subunit, respectively [3]. [1]. 9195885. Crystal structure of nitrile hydratase reveals a novel iron centre in a novel fold. Huang W, Jia J, Cummings J, Nelson M, Schneider G, Lindqvist Y;. Structure 1997;5:691-699. [2]. 14717710. Mutational and structural analysis of cobalt-containing nitrile hydratase on substrate and metal binding. Miyanaga A, Fushinobu S, Ito K, Shoun H, Wakagi T;. Eur J Biochem. 2004;271:429-438. [3]. 17222425. Structure of thiocyanate hydrolase: a new nitrile hydratase family protein with a novel five-coordinate cobalt(III) center. Arakawa T, Kawano Y, Kataoka S, Katayama Y, Kamiya N, Yohda M, Odaka M;. J Mol Biol. 2007;366:1497-1509. (from Pfam) NF045285.2 PF21079.2 GDH_HM2 21 21 45 domain Y N N Glutamate dehydrogenase, helical motif 2 10924516,34083757 131567 cellular organisms no rank 33278 EBI-EMBL Glutamate dehydrogenase, helical motif 2 Glutamate dehydrogenase, helical motif 2 Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia [1]. The structure of GDH from Mycobacterium smegmatis revealed that it has a long N- and C-terminal segments flanking the catalytic core, comprising several domains. The flexible N-terminal domain comprises ACT-like and PAS-type domains which could act as metabolic sensors for allosteric regulation [2]. It also has three helical motifs (HM1-3); this entry represents HM2. [1]. 10924516. A new class of glutamate dehydrogenases (GDH). Biochemical and genetic characterization of the first member, the AMP-requiring NAD-specific GDH of Streptomyces clavuligerus. Minambres B, Olivera ER, Jensen RA, Luengo JM;. J Biol Chem 2000;275:39529-39542. [2]. 34083757. 3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme. Lazaro M, Melero R, Huet C, Lopez-Alonso JP, Delgado S, Dodu A, Bruch EM, Abriata LA, Alzari PM, Valle M, Lisa MN;. Commun Biol. 2021;4:684. (from Pfam) NF045289.2 PF21088.2 MS_channel_1st 23.1 23.1 42 domain Y N N Mechanosensitive ion channel, transmembrane helices 2/3 11159397,11275684,11296222,23012406,23074248,23339071 131567 cellular organisms no rank 123985 EBI-EMBL Mechanosensitive ion channel, transmembrane helices 2/3 Mechanosensitive ion channel, transmembrane helices 2/3 This entry includes small conductance mechanosensitive channels (MscS), which assembles to a homoheptameric complex [1-6]. Each monomer consists of a N-terminal transmembrane region and a large cytoplasmic segment composed of a five-stranded antiparallel beta-sheet (middle/second) domain and a C-terminal alpha/beta-domain [4-7]. The N-terminal region consists of three membrane spanning helices (TM1, TM2 and TM3), TM2 and TM3 are represented in this entry. In the heptamer, the permeation pathway is formed by the packing of TM3s, flanked by TM1-TM2 helical hairpins [4]. [1]. 11296222. Structural and functional differences between two homologous mechanosensitive channels of Methanococcus jannaschii. Kloda A, Martinac B;. EMBO J 2001;20:1888-1896. [2]. 11159397. Molecular identification of a mechanosensitive channel in archaea. Kloda A, Martinac B;. Biophys J 2001;80:229-240. [3]. 11275684. Mechanosensitive channels in prokaryotes. Martinac B;. Cell Physiol Biochem 2001;11:61-76. [4]. 23339071. Open and shut: crystal structures of the dodecylmaltoside solubilized mechanosensitive channel of small conductance from Escherichia coli and Helicobacter pylori at 4.4 A and 4.1 A resolutions. Lai JY, Poon YS, Kaiser JT, Rees DC;. Protein Sci. 2013;22:502-509. [5]. 23074248. Structure and molecular mechanism of an anion-selective mechanosensitive channel of small conductance. Zhang X, Wang J, Feng Y, Ge J, Li W, Sun W, Iscla I, Yu J, Blount P, Li Y, Yang M;. Proc Natl Acad Sci U S A. 2012;109:18180-18185. [6]. 23012406. Conformational state of the MscS mechanosensitive channel in solution revealed by pulsed electron-electron double re. TRUNCATED at 1650 bytes (from Pfam) NF045293.2 PF21100.2 MCM_C 27 27 64 domain Y N N MCM protein C-terminal winged helix-turn-helix domain 19089981,23361460,25712103 131567 cellular organisms no rank 691 EBI-EMBL MCM protein C-terminal winged helix-turn-helix domain MCM protein C-terminal winged helix-turn-helix domain The minichromosome maintenance complex (MCM) represents the replicative DNA helicase both in eukaryotes and archaea. This entry represents a C-terminal winged helix-turn-helix domain found at the C-terminus of MCM proteins [1-3]. Paper describing PDB structure 2fna. [1]. 19089981. Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus. Xu Q, Rife CL, Carlton D, Miller MD, Krishna SS, Elsliger MA, Abdubek P, Astakhova T, Chiu HJ, Clayton T, Duan L, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, McMullan D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, van den Bedem H, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Proteins. 2009;74:1041-1049. Paper describing PDB structure 2m45. [2]. 25712103. Structure and regulatory role of the C-terminal winged helix domain of the archaeal minichromosome maintenance complex. Wiedemann C, Szambowska A, Hafner S, Ohlenschlager O, Guhrs KH, Gorlach M;. Nucleic Acids Res. 2015;43:2958-2967. Paper describing PDB structure 4fdg. [3]. 23361460. Mini-chromosome maintenance complexes form a filament to remodel DNA structure and topology. Slaymaker IM, Fu Y, Toso DB, Ranatunga N, Brewster A, Forsburg SL, Zhou ZH, Chen XS;. Nucleic Acids Res. 2013;41:3446-3456. (from Pfam) NF045300.2 PF21133.2 CAA_C 22.2 22.2 144 domain Y N N CCA-adding enzyme, C-terminal domain 14636575,18583961,21071662,25640237 131567 cellular organisms no rank 1573 EBI-EMBL CCA-adding enzyme, C-terminal domain CCA-adding enzyme, C-terminal domain Archaeal CCA-adding enzyme builds and repairs the 3'-end of tRNA [1-4]. This is the C-terminal domain (tail) of CCA-adding enzyme, which serves as a ruler to ensure that only tRNAs and tRNA-like transcripts are substrates for the enzyme and also contributes to the discrimination between stable and unstable RNA substrates [4]. Paper describing PDB structure 1r89. [1]. 14636575. Crystal structures of an archaeal class I CCA-adding enzyme and its nucleotide complexes. Xiong Y, Li F, Wang J, Weiner AM, Steitz TA;. Mol Cell. 2003;12:1165-1172. Paper describing PDB structure 2zh7. [2]. 18583961. Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme. Toh Y, Numata T, Watanabe K, Takeshita D, Nureki O, Tomita K;. EMBO J. 2008;27:1944-1952. Paper describing PDB structure 3ouy. [3]. 21071662. How the CCA-adding enzyme selects adenine over cytosine at position 76 of tRNA. Pan B, Xiong Y, Steitz TA;. Science. 2010;330:937-940. Paper describing PDB structure 4x4n. [4]. 25640237. On-enzyme refolding permits small RNA and tRNA surveillance by the CCA-adding enzyme. Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L;. Cell. 2015;160:644-658. (from Pfam) NF045305.2 PF21162.2 ETFQO_UQ-bd 27.7 27.7 96 domain Y N N ETF-QO, ubiquinone-binding 15386115,17050691 131567 cellular organisms no rank 37106 EBI-EMBL ETF-QO, ubiquinone-binding ETF-QO, ubiquinone-binding Electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) is a a 4Fe4S flavoprotein located in the inner mitochondrial membrane and catalyses ubiquinone (UQ) reduction. It forms a single structural domain with three functional regions (that bind FAD, the 4Fe4S cluster, and UQ) which are closely packed and share structural elements [1]. This domain includes the residues involved in UQ binding [1]. This domain is also found in FixC proteins from bacteria, which share similarities with ETF-QO [2]. Paper describing PDB structure 2gmh. [1]. 17050691. Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool. Zhang J, Frerman FE, Kim JJ;. Proc Natl Acad Sci U S A. 2006;103:16212-16217. [2]. 15386115. The electron transfer flavoprotein fixABCX gene products from Azospirillum brasilense show a NifA-dependent promoter regulation. Sperotto RA, Gross J, Vedoy C, Passaglia LM, Schrank IS;. Curr Microbiol. 2004;49:267-273. (from Pfam) NF045333.2 PF21269.2 TreT_GT1 27 27 144 domain Y N N Trehalose synthase, N-terminal domain 20888836 131567 cellular organisms no rank 1827 EBI-EMBL Trehalose synthase, N-terminal domain Trehalose synthase, N-terminal domain This domain is found at the N-terminal end of Trehalose synthase from Pyrococcus horikoshii (TreT) and similar proteins from prokaryotic organisms. TreT synthesises an alpha,alpha-trehalose from nucleoside diphosphate glucose and glucose. This protein has a typical GT-B glycosyltransferase structure with dual beta/alpha/ beta Rossmann-folds. The N-terminal domain shows a core of six beta-strands and seven associated helices [1]. Paper describing PDB structure 2x6q. [1]. 20888836. Structural insights on the new mechanism of trehalose synthesis by trehalose synthase TreT from Pyrococcus horikoshii. Woo EJ, Ryu SI, Song HN, Jung TY, Yeon SM, Lee HA, Park BC, Park KH, Lee SB;. J Mol Biol. 2010;404:247-259. (from Pfam) NF045341.2 PF21307.2 Glyco_hydro_95_C 27.6 27.6 94 domain Y Y N glycoside hydrolase family 95-like protein 17459873,26112186 131567 cellular organisms no rank 39872 EBI-EMBL Glycoside hydrolase family 95, C-terminal domain glycoside hydrolase family 95 C-terminal domain This domain is found in Alpha-fucosidase from Bifidobacterium bifidum (AfcA) and in other members of the glycoside hydrolase family 95 from bacteria and plants. AfcA hydrolyses the glycosidic linkage of Fuc1-2Gal via an inverting mechanism. This entry represents the C-terminal beta domain present within the catalytic region of this protein. The domain forms a two- layered jelly roll fold. Its specific function remains unknown [1,2]. Paper describing PDB structure 2eab. [1]. 17459873. Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum. Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, Kato R;. J Biol Chem. 2007;282:18497-18509. Paper describing PDB structure 4ufc. [2]. 26112186. Glycan complexity dictates microbial resource allocation in the large intestine. Rogowski A, Briggs JA, Mortimer JC, Tryfona T, Terrapon N, Lowe EC, Basle A, Morland C, Day AM, Zheng H, Rogers TE, Thompson P, Hawkins AR, Yadav MP, Henrissat B, Martens EC, Dupree P, Gilbert HJ, Bolam DN;. Nat Commun. 2015;6:7481. (from Pfam) NF045349.2 PF21328.2 Gp44_lid 27 27 63 domain Y N N Sliding-clamp-loader large subunit, AAA+ ATPase lid domain 16628222,22194570 131567 cellular organisms no rank 25 EBI-EMBL Sliding-clamp-loader large subunit, AAA+ ATPase lid domain Sliding-clamp-loader large subunit, AAA+ ATPase lid domain Sliding-clamp-loader large subunit (also known as Gp44) from Bacteriophage T4 forms the sliding-clamp-loader together with the small subunit. These are members of the AAA+ superfamily of ATPases which form pentameric complexes that load sliding DNA clamps onto the DNA, key for processive chromosomal replication [1,2]. This entry represents the AAA+ ATPase lid domain. Paper describing PDB structure 2chg. [1]. 16628222. Communication between subunits within an archaeal clamp-loader complex. Seybert A, Singleton MR, Cook N, Hall DR, Wigley DB;. EMBO J. 2006;25:2209-2218. Paper describing PDB structure 3u5z. [2]. 22194570. How a DNA polymerase clamp loader opens a sliding clamp. Kelch BA, Makino DL, O'Donnell M, Kuriyan J;. Science. 2011;334:1675-1680. (from Pfam) NF045351.2 PF21346.2 PcRGLX_3rd 23.8 23.8 411 domain Y N N PcRGLX-like protein C-terminal alpha/alpha toroid domain 29574769 131567 cellular organisms no rank 7382 EBI-EMBL PcRGLX-like protein C-terminal alpha/alpha toroid domain PcRGLX-like protein C-terminal alpha/alpha toroid domain This family of proteins includes Exo-rhamnogalacturonan lyase from Penicillium chrysogenum 31B (PcRGLX). The family also includes YetA from B. subtilis is functionally uncharacterised. This family of proteins is found in Actinobacteria, Firmicutes, Proteobacteria and fungi. Proteins in this family are typically between 863 and 928 amino acids in length. This entry represents the C-terminal alpha/alpha-toroid domain. Members of this family share a 3 domain architecture [1]. [1]. 29574769. Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26. Kunishige Y, Iwai M, Nakazawa M, Ueda M, Tada T, Nishimura S, Sakamoto T;. FEBS Lett. 2018;592:1378-1388. (from Pfam) NF045356.2 PF21374.2 WsaF_N 27 27 156 domain Y N N WsaF, N-terminal domain 20097205,25664731,27088764 131567 cellular organisms no rank 2125 EBI-EMBL WsaF, N-terminal domain WsaF, N-terminal domain WsaF from Geobacillus stearothermophilus catalyses the formation of beta-1-2-linkage of rhamnose sugars in the carbohydrate polymer. It consists of two domains the N-terminal domain (represented in this entry), which binds the acceptor (the growing rhamnan chain), and a C-terminal domain which binds the substrate (dTDP-beta-l-rhamnose) [1]. Paper describing PDB structure 2x0d. [1]. 20097205. Structural basis of substrate binding in WsaF, a rhamnosyltransferase from Geobacillus stearothermophilus. Steiner K, Hagelueken G, Messner P, Schaffer C, Naismith JH;. J Mol Biol. 2010;397:436-447. Paper describing PDB structure 4ozs. [2]. 25664731. The design and structural characterization of a synthetic pentatricopeptide repeat protein. Gully BS, Shah KR, Lee M, Shearston K, Smith NM, Sadowska A, Blythe AJ, Bernath-Levin K, Stanley WA, Small ID, Bond CS;. Acta Crystallogr D Biol Crystallogr. 2015;71:196-208. Paper describing PDB structure 5i9d. [3]. 27088764. Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins. Shen C, Zhang D, Guan Z, Liu Y, Yang Z, Yang Y, Wang X, Wang Q, Zhang Q, Fan S, Zou T, Yin P;. Nat Commun. 2016;7:11285. (from Pfam) NF045365.2 PF21410.2 MAP6 28.5 28.5 813 domain Y N N Microtubule-associated protein 6 12231625,16806091,24357581,25673876,28521134 131567 cellular organisms no rank 155 EBI-EMBL Microtubule-associated protein 6 Microtubule-associated protein 6 Microtubule-associated protein 6 (MAP6, previously named STOP proteins) is a calmodulin binding protein that is involved in microtubule stabilisation [1-4]. MAP6 is a major factor responsible for the intriguing stability properties of neuronal microtubules and is important for synaptic plasticity [2]. It regulates axonal growth during neuron polarization, which is controlled by a palmitoylation cycle [3]. MAP6 interacts with TMEM106B, and this interaction is crucial for controlling dendritic trafficking of lysosomes, presumably by acting as a molecular brake for retrograde transport [5]. This protein stabilize cold-resistant microtubules, which is essential for neuronal development, maintenance, and function. [1]. 16806091. Microtubule stabilizer ameliorates synaptic function and behavior in a mouse model for schizophrenia. Andrieux A, Salin P, Schweitzer A, Begou M, Pachoud B, Brun P, Gory-Faure S, Kujala P, Suaud-Chagny MF, Hofle G, Job D;. Biol Psychiatry. 2006;60:1224-1230. [2]. 12231625. The suppression of brain cold-stable microtubules in mice induces synaptic defects associated with neuroleptic-sensitive behavioral disorders. Andrieux A, Salin PA, Vernet M, Kujala P, Baratier J, Gory-Faure S, Bosc C, Pointu H, Proietto D, Schweitzer A, Denarier E, Klumperman J, Job D;. Genes Dev 2002;16:2350-2364. [3]. 28521134. Dynamic Palmitoylation Targets MAP6 to the Axon to Promote Microtubule Stabilization during Neuronal Polarization. Tortosa E, Adolfs Y, Fukata M, Pasterkamp RJ, Kapitein LC, Hoogenraad CC;. Neuron. 2017;94:809-825. [4]. 25673876. Human FAM154A (SAXO1) is a microtubule-stabilizing protein specific to cilia an. TRUNCATED at 1650 bytes (from Pfam) NF045370.2 PF21440.2 aSelB_III 19 19 108 domain Y N N Archaeal selenocysteine-specific elongation factor, domain III 15616587 131567 cellular organisms no rank 78 EBI-EMBL Archaeal selenocysteine-specific elongation factor, domain III Archaeal selenocysteine-specific elongation factor, domain III Selenocysteine-specific elongation factor (SelB) is a transcription factor necessary for the incorporation of selenocysteine into proteins. This entry represents domain III of archaeal SelB, which adopts a beta-barrel fold and is homologous to domain III of EF-Tu [1]. Paper describing PDB structure 4ac9. [1]. 15616587. Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors. Leibundgut M, Frick C, Thanbichler M, Bock A, Ban N;. EMBO J. 2005;24:11-22. (from Pfam) NF045375.2 PF21455.2 PylD_N 27 27 112 domain Y N N Pyrrolysine biosynthesis protein PylD, N-terminal domain 23720358,24916332 131567 cellular organisms no rank 263 EBI-EMBL Pyrrolysine biosynthesis protein PylD, N-terminal domain Pyrrolysine biosynthesis protein PylD, N-terminal domain This domain is found at the N-terminal end of Pyrrolysine biosynthesis protein PylD from Methanosarcina acetivorans, a dehydrogenase that catalyses the final step in the biosynthesis of the amino acid pyrrolysine [1,2]. Paper describing PDB structure 4j43. [1]. 23720358. Structure and reaction mechanism of pyrrolysine synthase (PylD). Quitterer F, Beck P, Bacher A, Groll M;. Angew Chem Int Ed Engl. 2013;52:7033-7037. Paper describing PDB structure 4q39. [2]. 24916332. The formation of pyrroline and tetrahydropyridine rings in amino acids catalyzed by pyrrolysine synthase (PylD). Quitterer F, Beck P, Bacher A, Groll M;. Angew Chem Int Ed Engl. 2014;53:8150-8153. (from Pfam) NF045408.2 PF21578.2 117-like_vir 27 27 101 domain Y N N Virus, 117-like 20419351 131567 cellular organisms no rank 2 EBI-EMBL Virus, 117-like Virus, 117-like This protein family represents a group of viral proteins, including Swiss:Q8QL45 from Sulfolobus islandicus rod-shaped virus 1 (117). Paper describing PDB structure 2x3g. [1]. 20419351. The Scottish Structural Proteomics Facility: targets, methods and outputs. Oke M, Carter LG, Johnson KA, Liu H, McMahon SA, Yan X, Kerou M, Weikart ND, Kadi N, Sheikh MA, Schmelz S, Dorward M, Zawadzki M, Cozens C, Falconer H, Powers H, Overton IM, van Niekerk CA, Peng X, Patel P, Garrett RA, Prangishvili D, Botting CH, Coote PJ, Dryden DT, Barton GJ, Schwarz-Linek U, Challis GL, Taylor GL, White MF, Naismith JH;. J Struct Funct Genomics. 2010;11:167-180. (from Pfam) NF045426.2 PF21645.2 FakA-like_M 24.9 24.9 80 domain Y N N Fatty acid kinase subunit A-like, middle domain 36054360 131567 cellular organisms no rank 34187 EBI-EMBL Fatty acid kinase subunit A-like, middle domain Fatty acid kinase subunit A-like, middle domain This domain is found in fatty acid kinase subunit A (FakA) from a bacterial fatty acid kinase (Fak) system and it is localised between Pfam:PF02734 and Pfam:PF13684. Two major human pathogens, Staphylococcus and Streptococcus, use this machinery to scavenge host fatty acids [1]. The Fak complex consists of an ATP-binding subunit FakA, which interacts with varied FakB (fatty acid-binding protein) isoforms, and synthesises acyl-phosphate from extracellular fatty acids [1]. FakA comprises three domains, denoted as FakA_N, FakA_M and FakA_C in [1] of which the middle domain is represented in this entry. It consists of four alpha-helices, four beta-strands and several long loops, containing a zinc finger motif. It shows similarities to the yeast copper chaperone ATX1, a metallochaperone/metal-binding protein. [1]. 36054360. Structure and mechanism for streptococcal fatty acid kinase (Fak) system dedicated to host fatty acid scavenging. Shi Y, Zang N, Lou N, Xu Y, Sun J, Huang M, Zhang H, Lu H, Zhou C, Feng Y;. Sci Adv. 2022;8:eabq3944. (from Pfam) NF045432.2 PF21686.2 LigD_Prim-Pol 27.4 27.4 254 domain Y N N LigD, primase-polymerase domain 11135672,14750947,16273105,16446439,17174332 131567 cellular organisms no rank 70035 EBI-EMBL LigD, primase-polymerase domain LigD, primase-polymerase domain This entry represents the primase-polymerase domain (Prim-Pol) of bacterial LigD proteins, such as LigD from Pseudomonas aeruginosa and Mycobacterium tuberculosis. LigD, together with Ku protein, is required for nonhomologous end-joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). This domain belongs to the archaeal/eukaryal primase (AEP) superfamily and mediates several nucleotidyl transferase activities, including DNA-dependent RNA primase, terminal transferase and DNA-dependent DNA/RNA gap-filling polymerase activities [1-5]. Paper describing PDB structure 1g71. [1]. 11135672. Crystal structure of a DNA-dependent RNA polymerase (DNA primase). Augustin MA, Huber R, Kaiser JT;. Nat Struct Biol. 2001;8:57-61. Paper describing PDB structure 1v33. [2]. 14750947. Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis. Ito N, Nureki O, Shirouzu M, Yokoyama S, Hanaoka F;. Genes Cells. 2003;8:913-923. Paper describing PDB structure 1zt2. [3]. 16273105. Structure of the heterodimeric core primase. Lao-Sirieix SH, Nookala RK, Roversi P, Bell SD, Pellegrini L;. Nat Struct Mol Biol. 2005;12:1137-1144. Paper describing PDB structure 2fao. [4]. 16446439. Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D. Zhu H, Nandakumar J, Aniukwu J, Wang LK, Glickman MS, Lima CD, Shuman S;. Proc Natl Acad Sci U S A. 2006;103:1711-1716. Paper describing PDB structure 2iru. [5]. 17174332. Structure and function of a mycobacterial NHEJ DNA repair polymerase. Pitcher RS, Brissett NC, Picher AJ, Andrade P, Juarez . TRUNCATED at 1650 bytes (from Pfam) NF045434.2 PF21699.2 TM1266-like 27 27 74 domain Y N N Iron-only hydrogenase system regulator, putative 131567 cellular organisms no rank 2543 EBI-EMBL Iron-only hydrogenase system regulator, putative Iron-only hydrogenase system regulator, putative This protein family includes Iron-only hydrogenase system regulator, putative from Thermotoga maritima (TM1266) and similar bacterial proteins. Members of this family are thought to play a role as a transcription factor. (from Pfam) NF045442.2 PF21732.2 DUF6864 27 27 114 domain Y Y N DUF6864 domain-containing function 131567 cellular organisms no rank 473 EBI-EMBL Domain of unknown function (DUF6864) DUF6864 domain This entry represents a family of bacterial proteins that adopt a beta-sandwich domain. The function of these proteins is currently unknown. (from Pfam) NF045446.2 PF21750.2 DACNH 27 27 107 domain Y N N Probable sensor domain DACNH 131567 cellular organisms no rank 1311 EBI-EMBL Probable sensor domain DACNH Probable sensor domain DACNH This entry represents a potential sensor domain found at the N-terminal of bacterial diadenylate cyclases which is typically followed by the DAC (Pfam:PF02457) domain. This domain may consist of two alpha-helices and seven beta-strands. In deltaproteobacteria members this domain is preceded by the DACND domain (Pfam:PF21749). (from Pfam) NF045447.2 PF21752.2 DACNG 27 27 208 domain Y N N Probable sensor domain DACNG 131567 cellular organisms no rank 872 EBI-EMBL Probable sensor domain DACNG Probable sensor domain DACNG This entry represents a potential sensor domain found at the N-terminal of bacterial diadenylate cyclases, which is typically followed by the DAC (Pfam:PF02457) domain. This domain may have five alpha-helices and four beta-strands according to structure predictions. (from Pfam) NF045449.2 PF21755.2 DacZ_P 27.4 27.4 125 domain Y N N Probable sensor domain DacZ_P 131567 cellular organisms no rank 256 EBI-EMBL Probable sensor domain DacZ_P Probable sensor domain DacZ_P This is a probable sensor domain found at the N-terminal of bacterial diadenylate cyclases, which are typically followed by the DAC (Pfam:PF02457) domain. It is distantly related to PK_C (Pfam:PF02887) and it consists of four alpha-helices and five beta-strands according to structure predictions. (from Pfam) NF045451.2 PF21760.2 SecD_1st 27 27 60 domain Y N N Protein translocase subunit SecDF, P1 domain, N-terminal 21562494,27924919,28467902,29398525 131567 cellular organisms no rank 74616 EBI-EMBL Protein translocase subunit SecDF, P1 domain, N-terminal Protein translocase subunit SecDF, P1 domain, N-terminal This domain is found in Protein translocase subunit SecDF from Thermus thermophilus, which belongs to the RND superfamily. SecDF shows 12 transmembrane (TM) regions and 6 periplasmic regions (P1-P6). This entry represents the N-terminal region of the base subdomain of the P1 domain that is located in the N- terminal half of the polypeptide, also known as SecD region. This domain folds into a a pseudo-symmetrical anti-parallel beta-sheet that rearranges to a beta-barrel architecture during ion transport. This domain, which covers the TM region [1-4], is related to Pfam:PF03176 and usually appears associated with Pfam:PF07549 and Pfam:PF02355. Paper describing PDB structure 3aqo. [1]. 21562494. Structure and function of a membrane component SecDF that enhances protein export. Tsukazaki T, Mori H, Echizen Y, Ishitani R, Fukai S, Tanaka T, Perederina A, Vassylyev DG, Kohno T, Maturana AD, Ito K, Nureki O;. Nature. 2011;474:235-238. Paper describing PDB structure 5mg3. [2]. 27924919. A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion. Botte M, Zaccai NR, Nijeholt JL, Martin R, Knoops K, Papai G, Zou J, Deniaud A, Karuppasamy M, Jiang Q, Roy AS, Schulten K, Schultz P, Rappsilber J, Zaccai G, Berger I, Collinson I, Schaffitzel C;. Sci Rep. 2016;6:38399. Paper describing PDB structure 5xam. [3]. 28467902. Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF. Furukawa A, Yoshikaie K, Mori T, Mori H, Morimoto YV, Sugano Y, Iwaki S, Minamino T, Sugita Y, Tanaka Y, Tsukazaki T;. Cell Rep. 2017;19:895-901. [4]. 29398525. Remote Coupled Drast. TRUNCATED at 1650 bytes (from Pfam) NF045452.2 PF21768.2 AF_1763-like_C 27 27 120 domain Y N N AF_1763-like, C-terminal domain 19447113 131567 cellular organisms no rank 587 EBI-EMBL AF_1763-like, C-terminal domain AF_1763-like, C-terminal domain This domain is found at the C-terminal end of a group of prokaryotic proteins, including the putative lipase AF_1763 from Archaeoglobus fulgidus. This protein contains a C-terminal lipid binding domain, which is formed by two layers of seven beta-strands [1]. This entry represents the second half of this domain. Paper describing PDB structure 2zyh. [1]. 19447113. Structure of the alkalohyperthermophilic Archaeoglobus fulgidus lipase contains a unique C-terminal domain essential for long-chain substrate binding. Chen CK, Lee GC, Ko TP, Guo RT, Huang LM, Liu HJ, Ho YF, Shaw JF, Wang AH;. J Mol Biol. 2009;390:672-685. (from Pfam) NF045455.2 PF21784.2 Bflower 25 25 116 domain Y Y N 4-fold beta flower protein 131567 cellular organisms no rank 1408 EBI-EMBL 4-fold beta flower protein 4-fold beta flower protein This family of proteins have a repetitive structure composed of pairs of beta strands. In this family the proteins usually have four copies of the beta hairpin repeat. (from Pfam) NF045456.2 PF21791.2 MDHAR3-like_C 27 27 88 domain Y N N Monodehydroascorbate reductase 3-like, C-terminal domain 27652777 131567 cellular organisms no rank 9 EBI-EMBL Monodehydroascorbate reductase 3-like, C-terminal domain Monodehydroascorbate reductase 3-like, C-terminal domain This domain is found at the C-terminal end of Monodehydroascorbate reductase 3 (MDHAR3) from Oryza sativa and similar plant sequences. MDHAR3 transfers an electron directly to its substrate, monodehydroascorbate (MDHA), which binds to its active site pocket. It consists of three domains: an NAD(P)-binding domain, an FAD-binding domain, and a C-terminal domain (this entry) [1]. This domain shows an alpha-beta structure. Paper describing PDB structure 5jci. [1]. 27652777. Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica. Park AK, Kim IS, Do H, Jeon BW, Lee CW, Roh SJ, Shin SC, Park H, Kim YS, Kim YH, Yoon HS, Lee JH, Kim HW;. Sci Rep. 2016;6:33903. (from Pfam) NF045460.2 PF21799.2 MurD-like_N 27 27 88 domain Y N N Mur ligase MurD-like, N-terminal domain 10966819,17507028,20804196,21524830,24900523,9218784 131567 cellular organisms no rank 60157 EBI-EMBL Mur ligase MurD-like, N-terminal domain Mur ligase MurD-like, N-terminal domain This domain is found at the N-terminal end of Mur ligases predominantly from proteobacteria, including UDP-N -acetylmuramoylalanine--D-glutamate ligase from Escherichia coli (MurD). Proteins in this family play a crucial role in the intracellular steps leading to the synthesis of bacterial peptidoglycan. MurD shows a three-domain topology, with the N-terminal (this entry) responsible for binding the UDP-precursor. This domain shows a Rossmann fold [1-6]. Paper describing PDB structure 1e0d. [1]. 10966819. "Open" structures of MurD: domain movements and structural similarities with folylpolyglutamate synthetase. Bertrand JA, Fanchon E, Martin L, Chantalat L, Auger G, Blanot D, van Heijenoort J, Dideberg O;. J Mol Biol. 2000;301:1257-1266. Paper describing PDB structure 2jff. [2]. 17507028. Structural and functional characterization of enantiomeric glutamic acid derivatives as potential transition state analogue inhibitors of MurD ligase. Kotnik M, Humljan J, Contreras-Martel C, Oblak M, Kristan K, Herve M, Blanot D, Urleb U, Gobec S, Dessen A, Solmajer T;. J Mol Biol. 2007;370:107-115. Paper describing PDB structure 2wjp. [3]. 20804196. Discovery of novel 5-benzylidenerhodanine and 5-benzylidenethiazolidine-2,4-dione inhibitors of MurD ligase. Zidar N, Tomasic T, Sink R, Rupnik V, Kovac A, Turk S, Patin D, Blanot D, Contreras Martel C, Dessen A, Muller Premru M, Zega A, Gobec S, Peterlin Masic L, Kikelj D;. J Med Chem. 2010;53:6584-6594. Paper describing PDB structure 2xpc. [4]. 21524830. Second-generation sulfonamide inhibitors of D-glutamic acid-adding enzyme: activity optimisation with conformationally rigid analogues of. TRUNCATED at 1650 bytes (from Pfam) NF045461.2 PF21800.2 KRR1-like_KH2 27 27 91 domain Y N N KRR1 small subunit processome component, second KH domain 17654551,20363226,24990943,27419870 131567 cellular organisms no rank 1107 EBI-EMBL KRR1 small subunit processome component, second KH domain KRR1 small subunit processome component, second KH domain This is the second K homology domain (KH2) found in KRR1 small subunit processome component from the fungus Chaetomium thermophilum and similar eukaryotic sequences. Paper describing PDB structure 2e3u. [1]. 17654551. Crystal structure of Dim2p: a preribosomal RNA processing factor, from Pyrococcus horikoshii OT3 at 2.30 A. Jia MZ, Ohtsuka J, Lee WC, Nagata K, Tanokura M;. Proteins. 2007;69:428-432. Paper describing PDB structure 3aev. [2]. 20363226. An archaeal Dim2-like protein, aDim2p, forms a ternary complex with a/eIF2 alpha and the 3' end fragment of 16S rRNA. Jia MZ, Horita S, Nagata K, Tanokura M;. J Mol Biol. 2010;398:774-785. Paper describing PDB structure 4qmf. [3]. 24990943. Interaction between ribosome assembly factors Krr1 and Faf1 is essential for formation of small ribosomal subunit in yeast. Zheng S, Lan P, Liu X, Ye K;. J Biol Chem. 2014;289:22692-22703. Paper describing PDB structure 5jpq. [4]. 27419870. Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome. Kornprobst M, Turk M, Kellner N, Cheng J, Flemming D, Kos-Braun I, Kos M, Thoms M, Berninghausen O, Beckmann R, Hurt E;. Cell. 2016;166:380-393. (from Pfam) NF045464.2 PF21814.2 DUF6883 27 27 110 domain Y Y N DUF6883 domain-containing protein 131567 cellular organisms no rank 3571 EBI-EMBL Domain of unknown function (DUF6883) DUF6883 domain This entry represents a protein domain that is often found in single domain proteins. It is also sometimes found in larger multi-domain proteins. The function of this domain is unknown. (from Pfam) NF045465.2 PF21815.2 PdeA_PAS 21 21 106 domain Y N N PdeA-like PAS domain 22682744 131567 cellular organisms no rank 700 EBI-EMBL PdeA-like PAS domain PdeA-like PAS domain This family is based on PAS domain from phosphodiesterase PdeA and similar proteins. PAS domains are found in all kingdoms of life and are involved in diverse functions but have an especially strong presence in signaling networks. They often serve as protein-protein interaction modules. In PdeA, the PAS domain serves as an adaptor recognition site needed for regulated proteolysis by the ClpXP protease [1]. Paper describing PDB structure 3u2a. [1]. 22682744. Adaptor-dependent degradation of a cell-cycle regulator uses a unique substrate architecture. Rood KL, Clark NE, Stoddard PR, Garman SC, Chien P;. Structure. 2012;20:1223-1232. (from Pfam) NF045470.1 Opp2B 350 350 300 equivalog Y Y N nickel ABC transporter permease nikB GO:0043190,GO:0140359 17496096,20662775 131567 cellular organisms no rank 8953 NCBIFAM nickel ABC transporter permease NF045474.1 Opp2C 300 300 236 equivalog Y Y N nickel transporter permease nikC GO:0043190,GO:0140359 17496096,20662775 131567 cellular organisms no rank 9730 NCBIFAM nickel transporter permease NF045477.1 LPO_1073_dom 45 45 257 subfamily Y Y N LPO_1073/Vpar_1526 family protein 27915212,28713344 131567 cellular organisms no rank 1819 NCBIFAM LPO_1073/Vpar_1526 family protein LPO_1073 was described as a lineage-specific marker for clade of Legionella pneumophila strains. Family member Vpar_1526 from Veillonella parvula, a member of the Negativicutes, was proposed to be an inner membrane protein. An AlphaFold structural prediction for family member A0A3N5W976 shows mostly alpha-helical structure. NF045478.1 XF1762_fam 50 50 143 equivalog Y Y N XF1762 family protein 28831124 131567 cellular organisms no rank 2737 NCBIFAM XF1762 family phage protein Members of this family include phi1026bp67 from Burkholderia virus phi1026b. NF045496.1 FormamaseFmdA 500 500 407 equivalog Y Y N formamidase fmdA 3.5.1.49 GO:0004328 8841393 131567 cellular organisms no rank 6143 NCBIFAM formamidase NF045502.1 variant_rSAM 125 125 357 domain Y Y N radical SAM protein 131567 cellular organisms no rank 8625 NCBIFAM radical SAM protein This HMM identifies members of an atypical set of radical SAM proteins, many of which score the cutoffs of Pfam model PF04055. This subgroup includes the MSMEG_0568 family, the 7-methyl bacteriochlorophyllide c oxygenase BciD, and a number of uncharacterized subfamilies. NF045503.1 repair_heli_XPB 610 610 548 equivalog Y Y N DNA repair helicase XPB 19199647,22615856,34936652 131567 cellular organisms no rank 14600 NCBIFAM DNA repair helicase XPB, bacterial type Rv0861c and the other members of this family are homologs to the eukarotic DNA repair helicase XPB (ERCC3), and therefore speculated to likewise play a role in some form of DNA repair. A C394F substitution in the family member TP_0380 ortholog from was observed in a Treponema pallidum strain with a somewhat elevated rate of SNP accumulation. NF045510.1 4Cys_prefix_kin 24 24 26 domain Y Y N 4-Cys prefix domain-containing protein 22530622 131567 cellular organisms no rank 8360 NCBIFAM kinase or phosphatase 4-Cys prefix domain Most proteins with this N-terminal domain are protein serine/threonine protein kinases that resemble eukaryotic ribosomal protein S6 kinase and the Mycobacterium tuberculosis serine/threonine protein kinases PknA and PknB, although those proteins lack this domain. Some, however, are protein serine/threonine phosphatases. Members of this domain family have an almost perfectly invariant CxxPxC and CxxCG motifs at the two ends of an N-terminal 22 to 25-amino region that begins the seed alignment for the HMM. AlphaFold predicted structure A0A3E0L7C2 shows this region to form a discrete N-terminal domain with very high pLDDT scores. NF045515.1 Glp_gephyrin 270 270 403 equivalog Y Y N gephyrin-like molybdotransferase Glp glp GO:0006777,GO:0061599,GO:1990586 37679597 131567 cellular organisms no rank 83422 NCBIFAM gephyrin-like molybdotransferase Glp Eukaryotic gephyrin-like molybdotransferase Glp and its membrane receptor GlpR bind to FtsZ and Wag31 to form a tight protein complex, which plays an important role in divisome-elongasome transition during cytokinesis in Corynebacteriales. NF045517.1 halo_surf_dom 40 40 88 domain Y Y N BGTF surface domain-containing protein 131567 cellular organisms no rank 1558 NCBIFAM BGTF surface domain Proteins with one or more copies of this domain are found in halophilic archaea surface proteins such as the S-layer glycoprotein of Haloferax gibbonsii. The domain is named for its best conserved motif, BGTF, where B represents either N or D. Over 70 percent of family members contain a C-terminal PGF-CTERM tripartite sorting signal, recognized and cleaved by the archaeosortase ArtA. NF045529.2 Heimdall-CTERM 24 24 26 domain Y Y N Heimdall-CTERM domain-containing surface protein 22037399 131567 cellular organisms no rank 6 NCBIFAM Heimdall-CTERM protein-sorting domain This HMM describes an archaeal, C-terminally-located protein sorting signal. Although this signal is quite similar to PGF-CTERM (TIGR04126), acted on by the archaeosortase ArtA, and hits overlap somewhat, true members of this family are found so far exclusively in metagenome-assembled genomes (MAGs) of the Heimdallarchaeota, the archaeal lineage considered the closest relative of the primoridial eukarotic cell. NF045539.1 MATE_efflux1 350 350 411 equivalog Y Y N MATE family Na+-driven efflux transporter GO:0015297,GO:0055085 23209200,33402425 131567 cellular organisms no rank 566 NCBIFAM MATE family Na+-driven efflux transporter NF045579.1 rhamnoside_JR 50 50 123 domain Y Y N glycosylhydrolase-like jelly roll fold domain-containing protein 15991055,31726038 131567 cellular organisms no rank 10576 NCBIFAM alpha-L rhamnosidase C-terminal-like jelly roll fold domain A crystalized member of this family, the alpha-L rhamnosidase PDB:6q2f from Novosphingobium sp. PP1Y, is a GH106 family hydrolase that cleaves alpha 1,6 and alpha 1,2 glycosidic bonds of L-rhamnose from a variety of flavonoid compounds. This domain usually is found near the protein C-terminus, but in a few proteins, such as WP_277638425.1 and WP_203558404.1, it is located N-terminally. The coverage of this domain HMM overlaps with that of PF02837, but the seed alignment sequences of the two models are quite different. NF045580.1 symport_access 35 35 33 equivalog Y Y N symporter small accessory protein 131567 cellular organisms no rank 784 NCBIFAM symporter small accessory protein Members of this family share a conserved N-terminal region of about 33 amino acids, with variable length C-terminal regions. As the conserved region is highly hydrophobic, and member proteins are nearly always encoded adjacent to sodium:solute symporter family proteins, typically with coding regions that overlap by at least one nucleotide, it seems likely that members of this family act as a transporter small subunit or assembly factor. Note that because members of this family may be shorter than 40 amino acids, members of this family may have been missed systematically by many annotation pipeline versions. Members of this family are found in both archaea and bacteria. NF045596.1 ECF_S_CD3073 180 180 174 equivalog Y Y N CD3073 family putative ECF transporter S component 131567 cellular organisms no rank 552 NCBIFAM CD3073 family putative ECF transporter S component Members of this family are called a putative ECF transporter S component by homology. Most, including founding protein CD3073 from Clostridioides difficile, are encoded in tandem with a CD3072 family TudS-related protein described by HMM NF045597. This gene pair shows a strong though imperfect correlation with both the selenide,water dikinase SelD and with the [Fe8-S9] double-cubane cluster family described by HMM NF040772. These observations suggest both a role in the import and utilization of some organic compound for anaerobic fermentation and a connection to anaerobic sulfur and/or selenium metabolism. NF045597.1 TudS_rel_CD3072 130 130 148 equivalog Y Y N CD3072 family TudS-related putative desulfidase 38082046 131567 cellular organisms no rank 1219 NCBIFAM CD3072 family TudS-related putative desulfidase Members of this family typically show weak sequence similary to the protein family described by PF04463.15, previously called DUF523 but now called the 2-thiouracil desulfurase (TudS) family. Intriguing aspects of this family include frequent co-occurrence with the selenide, water dikinase SelD and with the [Fe8-S9] double-cubane cluster family described by HMM NF040772, plus frequent occurrence in a tandem gene pair with the putative ECF transporter S component proteins of family NF045596. See articles PMID:29194984, PMID:32929873, and PMID:38082046 for more information about the related DUF523/TudS and an apparent [4Fe-5S] cluster formed transiently as a catalytic intermediate. These observations suggest both a role in the import and utilization of some organic compound for anaerobic fermentation and a connection to anaerobic sulfur and/or selenium metabolism. NF045646.2 rSAM_Se_TrsS 490 460 441 equivalog Y Y N radical SAM (seleno)protein TrsS trsS 131567 cellular organisms no rank 794 NCBIFAM radical SAM (seleno)protein TrsS TrsS (Third Radical SAM Selenoprotein) joins two others as radical SAM enzyme families with sufficiently abundant and therefore highly trusted examples of selenocysteine-containing family members. The other two are the arsenosugar biosynthesis radical SAM protein ArsS (TIGR04167) and the CUAEP/CCAEP-tail radical SAM protein (NF040546). In all three cases, the Sec residue occurs where the Cys normally present is part of a novel motif, not the signature [4Fe-4S]-binding signature motif near the N-terminus of the radical SAM domain described by Pfam model PF04055. TrsS shows its greatest sequence similarity, among characterized radical SAM proteins, to the molybdopterin cofactor biosynthesis protein MoaA, as found either in bacteria (TIGR02666) or archaea (TIGR02668), but is actually quite different, with novel additional domains both N-terminal and C-terminal to the shared radical SAM domain (PF04055). Even so, TrsS may play a related role in the maturation of a molybdopterin (MPT) required by the molybdopterin-dependent aldehyde oxidoreductase that is nearly always found encoded nearby. NF045650.1 CD1247_Nterm 30 30 70 equivalog_domain Y Y N CD1247 N-terminal domain-containing protein 131567 cellular organisms no rank 1799 NCBIFAM CD1247 N-terminal domain This HMM describes the N-terminal domain of a family of proteins names after CD1247 from Clostridioides difficile and found primarily in Gram-positive anaerobes. Most members share a C-terminal region with two CxxC motifs likely to have zinc-binding activity. NF045662.1 DVU0298_fam 75 75 213 equivalog_domain Y Y N DVU0298 family protein 20628586 131567 cellular organisms no rank 613 NCBIFAM DVU0298 family protein Members of this family occur primarily in sulfate-reducing bacteria. A HEAT repeat-region (see PF13513) scores above model cutoffs in many members of the family. DVU0298 was identified as candidate protein for involvement in carbon monoxide utilization as an electron donor during sulfate reduction. NF045702.1 rSAM_GDGT_ether 450 450 486 equivalog Y Y N tetraether lipid synthase Tes tes 1.21.98.5 GO:0046467,GO:0051539 25002541,35882349 131567 cellular organisms no rank 771 NCBIFAM tetraether lipid synthase Tes Members of this exclusively archaeal radical SAM enzyme perform the pair of C-C ligations that convert two archaeol molecules into the membrane-spanning, macrocyclic tetraether lipid, glycerol dibiphytanyl glycerol tetraether (GDGT). NF045718.1 two_CW_domain 35 35 80 domain Y Y N two-CW domain-containing protein 131567 cellular organisms no rank 285 NCBIFAM two-CW domain The two-CW domain is a 81-residue bacterial domain in its long form, with strong motifs with six invariant Cys residues. A shorter form exists, with gaps both sides of the motif that includes the third invariant Cys. The domain is named for CW dipeptides in the two strongest motifs, the N-terminal NCWEWxxCGREP and the central GRxCW. The domain may comprise the full length of a protein, or it may appear in much longer proteins. The function is unknown. NF045728.1 glycosyl_F510_1955 175 175 246 equivalog Y Y N F510_1955 family glycosylhydrolase 24603481 131567 cellular organisms no rank 4850 NCBIFAM F510_1955 family glycosylhydrolase Members of this family of glycosylhydrolases are named for F510_1955 (WP_239639246.1), a lipoprotein from the Gram-positive bacterium Anoxybacillus gonensis. NF045767.1 RuberyRbr 200 200 194 equivalog Y Y N rubrerythrin rbr 1.11.1.1 GO:0009055,GO:0016692 11972784,19118342,2835096,8646540,8955396 131567 cellular organisms no rank 7738 NCBIFAM rubrerythrin NF045768.1 RubredRD 90 90 54 equivalog Y Y N rubredoxin rd GO:0005506,GO:0009055,GO:0072592 11444870,19124587 131567 cellular organisms no rank 4108 NCBIFAM rubredoxin NF045778.1 gas_vesic_GvpL 200 200 260 equivalog Y Y N gas vesicle protein GvpL gvpL GO:0031411,GO:0031412 10894744 131567 cellular organisms no rank 263 NCBIFAM halophile-type gas vesicle protein GvpL NF045780.1 TrlF_fam_ATP 350 350 944 equivalog Y Y N TrlF family AAA-like ATPase 22529932,33101227 131567 cellular organisms no rank 6846 NCBIFAM TrlF family AAA-like ATPase TrlF (WP_011144772.1) from Photorhabdus laumondii was described as an 875-amino acid protein encoded in a small genomic island operon next to TrlG, whose mutation and loss of function restores an ability to grow at 36 degrees C. A related protein, Spaf_1101, although outside the scope of the model, has similar N-terminal and C-terminal domains and nucleotide-binding GxxGxGLS (P-loop) motif. Spaf_1101 is described as occurring at one end of a transposon, and the high frequency of pseudogenes among its close homologs suggests a role in mobile element function. NF045781.1 Spaf1101_AAA_ATP 475 475 836 equivalog Y Y N Spaf_1101 family AAA-like ATPase 22529932 131567 cellular organisms no rank 461 NCBIFAM Spaf_1101 family AAA-like ATPase The founding member of this family of AAA-like ATPases, Spaf_1101 from Streptococcus parasanguinis, was found at one end of a reported transposon. The high frequency of pseudogenes related to the intact members of this family, typical for genes with higher than average potential costs to the host species such as transposases, suggests a role in mobile element function. NF045796.1 DsrK 400 400 453 equivalog Y Y N sulfate reduction electron transfer complex DsrMKJOP subunit DsrK dsrK GO:0019420,GO:0051536 11952791,16388601,21747791,38285932 131567 cellular organisms no rank 906 NCBIFAM sulfate reduction electron transfer complex DsrMKJOP subunit DsrK Proteins of this family are members of the DsrMKJOP dissimilatory sulfate reduction complex. DsrK is involved in the reduction of sulfate to sulfide. NF045797.1 DsrO 200 200 235 equivalog Y Y N sulfate reduction electron transfer complex DsrMKJOP subunit DsrO dsrO GO:0019420 11952791,16388601,21747791,38285932 131567 cellular organisms no rank 4474 NCBIFAM sulfate reduction electron transfer complex DsrMKJOP subunit DsrO Proteins of this family are members of the DsrMKJOP dissimilatory sulfate reduction complex. NF045798.1 DsrP 350 350 346 equivalog Y Y N sulfate reduction electron transfer complex DsrMKJOP subunit DsrP dsrP GO:0019420 11952791,16388601,21747791,38285932 131567 cellular organisms no rank 975 NCBIFAM sulfate reduction electron transfer complex DsrMKJOP subunit DsrP Proteins of this family are members of the DsrMKJOP dissimilatory sulfate reduction complex. NF045806.1 GvpO_arch_Nterm 52 52 35 equivalog_domain Y Y N gas vesicle protein GvpO, halophile-type gvpO 131567 cellular organisms no rank 184 NCBIFAM gas vesicle protein GvpO, halophile-type, N-terminal domain This HMM describes a 35-amino acid sequence region, with three invariant Cys residues, found as the N-terminal domain of a majority of halophilic archaeal forms of the gas vesicle protein GvpO, but not found elsewhere. NF045877.1 CopZ_Nterm_CU 190 190 161 equivalog_domain Y Y N Csac_0668 family 2Fe-2S cluster-binding (seleno)protein 17609202,18417453,26196387 131567 cellular organisms no rank 307 NCBIFAM Csac_0668 family 2Fe-2S cluster-binding (seleno)protein Members of this family, including Csac_0668 from Caldicellulosiruptor saccharolyticus, are homologous to the N-terminal half of the copper chaperone CopZ from Archaeoglobus fulgidus. While the C-terminal half of CopZ resembles other previously known copper-binding domain, and binds a copper atom, the N-terminus was found to bind an additional copper and a 2Fe-2S iron-sulfur cluster. Members of the family described here contain an additional 20 amino acids N-terminal to region that aligns to CopZ, containing multiple Cys residues (sometimes four in a row) or selenocysteine in a suggested metal-binding CU motif. The proposed function for members of this family is as a metallochaperone. Note that some homologs outside the scope of this family, such as WP_240162626.1, similarly are selenoproteins but have the selenocysteine at different site. NF045974.1 conju_CD1108 100 100 190 subfamily Y Y N CD1108 family mobile element protein 21876735 131567 cellular organisms no rank 5336 NCBIFAM CD1108 family mobile element protein, central domain NF046006.1 MAG6450_fam 40 40 103 subfamily_domain Y Y N MAG6450 family protein 131567 cellular organisms no rank 264 NCBIFAM MAG6450 family protein Members of this uncommon protein family are found both within the Mycoplasmatota (e.g. MAG6450 from Mycoplasmopsis agalactiae) and outside of lineage. The function is unknown. NF046029.1 ProtAdlyltaseNmFic 230 230 177 equivalog Y Y N protein adenylyltransferase Fic fic 2.7.7.108 GO:0018117,GO:0042803,GO:0070733 22266942,23738009 131567 cellular organisms no rank 4241 NCBIFAM protein adenylyltransferase Fic NF046040.1 RelB_antitoxin 50 50 69 equivalog Y Y N type II toxin-antitoxin system RelB family antitoxin relB GO:0110001 30428568 131567 cellular organisms no rank 2514 NCBIFAM type II toxin-antitoxin system RelB family antitoxin NF046051.1 restrict_EcoAI 550 550 768 equivalog Y Y N EcoAI/FtnUII family type I restriction enzme subunit R hsdR GO:0003678,GO:0009307,GO:0015666 22848684,31085693,6325176 131567 cellular organisms no rank 10099 NCBIFAM EcoAI/FtnUII family type I restriction enzme subunit R Members of this family of helicase and endonuclease domain-containing type I restriction enzyme R subunits include EcoAI from Escherichia coli 15T-, FtnUII from Francisella tularensis subsp. novicida U112, and SpnD39IIIA from Streptococcus pneumoniae D39. Examples of described recognition sites for members of this family include CYYANNNNNNNCTC, CACNNNNNNNCTG, and GAGNNNNNNNGTCA. NF046055.1 restr_BPTD_3080 800 800 970 equivalog Y Y N BPTD_3080 family restriction endonuclease 3.1.21.5 GO:0003678,GO:0009307,GO:0015666 131567 cellular organisms no rank 1919 NCBIFAM BPTD_3080 family restriction endonuclease Members of this family are putative type III restriction enzyme endonucleases. NF046123.1 PF21832.1 DUF6892 24.6 24.6 136 domain Y Y N DUF6892 domain-containing protein 131567 cellular organisms no rank 2779 EBI-EMBL Family of unknown function (DUF6892) DUF6892 domain This entry represents a family of uncharacterised bacterial proteins. (from Pfam) NF046129.1 PF21849.1 DUF6908 27 27 123 domain Y Y N DUF6908 domain-containing protein 131567 cellular organisms no rank 1071 EBI-EMBL Domain of unknown function (DUF6908) DUF6908 domain This family of proteins are uncharacterised. This family is distantly related to Pfam:PF06853 currently known as DUF1249. (from Pfam) NF046146.1 PF21922.1 PBP_dimer_2 27 27 83 domain Y N N Penicillin binding protein A dimerisation domain 20206184,22365933,34356681 131567 cellular organisms no rank 35060 EBI-EMBL Penicillin binding protein A dimerisation domain Penicillin binding protein A dimerisation domain This domain is found in peptidoglycan D,D-transpeptidase also known as penicillin-binding protein A (PBPA). This domain consists of a four-stranded mixed beta-sheet with three short helices packed on one side [2]. Compared to the N-terminal domains of other class B High Molecular Mass (HMM) PBPs, the NTD of PBPA is relatively small because it contains only the so-called inter-domain linker region [1]. Paper describing PDB structure 3lo7. [1]. 20206184. Unusual conformation of the SxN motif in the crystal structure of penicillin-binding protein A from Mycobacterium tuberculosis. Fedarovich A, Nicholas RA, Davies C;. J Mol Biol. 2010;398:54-65. Paper describing PDB structure 3un7. [2]. 22365933. The role of the beta5-alpha11 loop in the active-site dynamics of acylated penicillin-binding protein A from Mycobacterium tuberculosis. Fedarovich A, Nicholas RA, Davies C;. J Mol Biol. 2012;418:316-330. Paper describing PDB structure 7onn. [3]. 34356681. Interaction Mode of the Novel Monobactam AIC499 Targeting Penicillin Binding Protein 3 of Gram-Negative Bacteria. Freischem S, Grimm I, Lopez-Perez A, Willbold D, Klenke B, Vuong C, Dingley AJ, Weiergraber OH;. Biomolecules. 2021; [Epub ahead of print] (from Pfam) NF046147.1 PF21926.1 FeeM 27 27 158 domain Y Y N N-acyl amino acid synthase FeeM domain-containing protein 16962973 131567 cellular organisms no rank 10852 EBI-EMBL N-acyl amino acid synthase FeeM N-acyl amino acid synthase FeeM This entry represents the catalytic core of the N-acyl amino acid synthase FeeM [1]. This domain folds into a central antiparallel beta-sheet packed on both sides with alpha-helices and closely resembles the conserved core of GNAT superfamily. Paper describing PDB structure 2g0b. [1]. 16962973. FeeM, an N-acyl amino acid synthase from an uncultured soil microbe: structure, mechanism, and acyl carrier protein binding. Van Wagoner RM, Clardy J;. Structure. 2006;14:1425-1435. (from Pfam) NF046155.1 PF21953.1 NadN_nucleosid_C 27 27 199 domain Y N N NAD nucleotidase, C-terminal domain 21933152 131567 cellular organisms no rank 856 EBI-EMBL NAD nucleotidase, C-terminal domain NAD nucleotidase, C-terminal domain This is the C-terminal domain of a family of Zn2+-dependent 5'-nucleotidases. This domain has a four-layered structure with a five-stranded beta-sheet forming the core [1]. Paper describing PDB structure 3ztv. [1]. 21933152. The high-resolution crystal structure of periplasmic Haemophilus influenzae NAD nucleotidase reveals a novel enzymatic function of human CD73 related to NAD metabolism. Garavaglia S, Bruzzone S, Cassani C, Canella L, Allegrone G, Sturla L, Mannino E, Millo E, De Flora A, Rizzi M;. Biochem J. 2012;441:131-141. (from Pfam) NF046158.1 PF21960.1 RCF1-5-like_lid 27 27 43 domain Y N N RCF1/5-like, AAA+ ATPase lid domain 15201901 131567 cellular organisms no rank 2621 EBI-EMBL RCF1/5-like, AAA+ ATPase lid domain RCF1/5-like, AAA+ ATPase lid domain Sliding clamps are DNA-tracking platforms that are essential for processive DNA replication and it is carried out by a five-protein clamp loader complex, the replication factor-C (RFC) complex. RFC forms a stable ATP-dependent complex with the eukaryotic sliding clamp, PCNA, which binds specifically to primed DNA. These proteins share the same domain architecture consisting of a AAA+ ATPase, a lid domain and a C-terminal helical domain. This entry represents the AAA+ ATPase lid from RFC proteins, such as RFC5 from yeast [1]. Paper describing PDB structure 1sxj. [1]. 15201901. Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex. Bowman GD, O'Donnell M, Kuriyan J;. Nature. 2004;429:724-730. (from Pfam) NF046159.1 PF21965.1 SAMP2 27 27 63 domain Y N N Small archaeal modifier protein 2 23821306 131567 cellular organisms no rank 1023 EBI-EMBL Small archaeal modifier protein 2 Small archaeal modifier protein 2 The ubiquitin-like small archaeal modifer protein 2 (SAMP2) is involved in sulfur transfer during molybdenum cofactor biosynthesis. SAMP2 has been demonstrated to form covalent conjugates with substrate proteins through an isopeptide linkage via C-terminal di-glycine motif in a streamlined archaeal E1-dependent pathway. SAMP2 also forms homo-conjugates through the intermolecular isopeptide bond between the C-terminal glycine and the Lys58 side chain, a feature that likely resembles polyubiquitination. This protein adopt a typical ubiquitin-like fold. Paper describing PDB structure 4hrs. [1]. 23821306. Crystal structure of the ubiquitin-like small archaeal modifier protein 2 from Haloferax volcanii. Li Y, Maciejewski MW, Martin J, Jin K, Zhang Y, Maupin-Furlow JA, Hao B;. Protein Sci. 2013;22:1206-1217. (from Pfam) NF046164.1 PF21983.1 NikA-like 27 27 72 domain Y Y N plasmid mobilization protein GO:0003677 31134011 131567 cellular organisms no rank 47166 EBI-EMBL Mobilization protein NikA plasmid mobilization protein Members of this family include plasmid mobilization proteins named MobB, MobC, NikA, PcfF, etc. NF046167.1 PF21999.1 IMS_HHH_1 27 27 53 domain Y Y N DNA polymerase thumb domain-containing protein 15254543,16195463,16216587,16819516,19464298 131567 cellular organisms no rank 57459 EBI-EMBL DNA polymerase-iota, thumb domain DNA polymerase-iota, thumb domain This is the thumb domain found in DNA polymerase iota and related proteins. This domain makes contacts with the minor groove of DNA. Paper describing PDB structure 1t3n. [1]. 15254543. Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing. Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK;. Nature. 2004;430:377-380. Paper describing PDB structure 2alz. [2]. 16216587. Human DNA polymerase iota incorporates dCTP opposite template G via a G.C + Hoogsteen base pair. Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK;. Structure. 2005;13:1569-1577. Paper describing PDB structure 2aq4. [3]. 16195463. Rev1 employs a novel mechanism of DNA synthesis using a protein template. Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK;. Science. 2005;309:2219-2222. Paper describing PDB structure 2dpi. [4]. 16819516. Hoogsteen base pair formation promotes synthesis opposite the 1,N6-ethenodeoxyadenosine lesion by human DNA polymerase iota. Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK;. Nat Struct Mol Biol. 2006;13:619-625. Paper describing PDB structure 3gqc. [5]. 19464298. Structure of the human Rev1-DNA-dNTP ternary complex. Swan MK, Johnson RE, Prakash L, Prakash S, Aggarwal AK;. J Mol Biol. 2009;390:699-709. (from Pfam) NF046172.1 PF22014.1 DUF6932 27 27 142 subfamily Y Y N DUF6932 family protein 131567 cellular organisms no rank 3775 EBI-EMBL Family of unknown function (DUF6932) DUF6932 family protein This is a family of uncharacterised bacterial proteins. They are remotely related to nucleotidyltransferases and share similar active site architecture. (from Pfam) NF046177.1 PF22036.1 MoaF_like 27 27 94 domain Y Y N MoaF-related domain-containing protein 131567 cellular organisms no rank 4951 EBI-EMBL MoaF-like MoaF-like This family consists mainly of uncharacterized proteins that are related to MoaF and adopt very similar beta-barrel structure. (from Pfam) NF046178.1 PF22042.1 EF-G_D2 27 27 84 domain Y N N Elongation factor G domain 2 11054294,11114334,8069622,8070396,8736554 131567 cellular organisms no rank 287858 EBI-EMBL Elongation factor G domain 2 Elongation factor G domain 2 Elongation factor G (EF-G) catalyzes the translocation step of translation. It consists of five structural domains, this entry represents the second domain [1]. This domain adopts a beta barrel structure. This family also includes domains found in other translation factors such as translation initiation factor IF-2, peptide chain release factor, etc. Paper describing PDB structure 1dar. [1]. 8736554. The structure of elongation factor G in complex with GDP: conformational flexibility and nucleotide exchange. al-Karadaghi S, Aevarsson A, Garber M, Zheltonosova J, Liljas A;. Structure. 1996;4:555-565. Paper describing PDB structure 1efg. [2]. 8070396. The crystal structure of elongation factor G complexed with GDP, at 2.7 A resolution. Czworkowski J, Wang J, Steitz TA, Moore PB;. EMBO J. 1994;13:3661-3668. Paper describing PDB structure 1eft. [3]. 8069622. The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation. Kjeldgaard M, Nissen P, Thirup S, Nyborg J;. Structure. 1993;1:35-50. Paper describing PDB structure 1fnm. [4]. 11054294. Structure of a mutant EF-G reveals domain III and possibly the fusidic acid binding site. Laurberg M, Kristensen O, Martemyanov K, Gudkov AT, Nagaev I, Hughes D, Liljas A;. J Mol Biol. 2000;303:593-603. Paper describing PDB structure 1g7r. [5]. 11114334. X-Ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding. Roll-Mecak A, Cao C, Dever TE, Burley SK;. Cell. 2000;103:781-792. (from Pfam) NF046196.1 PF22124.1 Glyco_hydro_95_cat 27 27 408 domain Y Y N glycosyl hydrolase family 95 catalytic domain-containing protein 11587643,17459873,24255995,26112186,34728215,36997505 131567 cellular organisms no rank 49035 EBI-EMBL Glycosyl hydrolase family 95 catalytic domain Glycosyl hydrolase family 95 catalytic domain The founding member of the GH95 family of glycosyl hydrolases is alpha-1,2-fucosidase that catalyses the hydrolysis of an alpha-1,2-linked fucose. A member of this family, FucOB from A. muciniphila was shown to hydrolyse all three types of H antigen structures to obtain the afucosylated Bombay phenotype [6]. Members of this family are multidomain proteins and contain a central catalytic domain with an (alpha/alpha)6 helical barrel topology, represented by this entry. Paper describing PDB structure 1h54. [1]. 11587643. Crystal structure of maltose phosphorylase from Lactobacillus brevis: unexpected evolutionary relationship with glucoamylases. Egloff MP, Uppenberg J, Haalck L, van Tilbeurgh H;. Structure (Camb) 2001;9:689-697. Paper describing PDB structure 2eab. [2]. 17459873. Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum. Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, Kato R;. J Biol Chem. 2007;282:18497-18509. Paper describing PDB structure 3wiq. [3]. 24255995. Structural and mutational analysis of substrate recognition in kojibiose phosphorylase. Okada S, Yamamoto T, Watanabe H, Nishimoto T, Chaen H, Fukuda S, Wakagi T, Fushinobu S;. FEBS J. 2014;281:778-786. Paper describing PDB structure 4ufc. [4]. 26112186. Glycan complexity dictates microbial resource allocation in the large intestine. Rogowski A, Briggs JA, Mortimer JC, Tryfona T, Terrapon N, Lowe EC, Basle A, Morland C, Day AM, Zheng H, Rogers TE, Thompson P, Hawkins AR, Yadav MP, Henrissat B, Martens EC, Dupree P, Gilbert HJ, Bolam DN;. Nat Commun. 2015;6:7481. Paper describing PDB str. TRUNCATED at 1650 bytes (from Pfam) NF046212.1 PF22217.1 ACDH-11_C 27 27 122 domain Y N N Acyl-CoA dehydrogenase 11 C-terminal domain-like 25981666 131567 cellular organisms no rank 492 EBI-EMBL Acyl-CoA dehydrogenase 11 C-terminal domain-like Acyl-CoA dehydrogenase 11 C-terminal domain-like Acyl-CoA dehydrogenase 11 (ACDH-11) sequesters C11/C12-chain fatty acids and prevents these fatty acids from activating nuclear hormone receptors and driving fat-7 expression. This enzyme consists of four domains, of which the C-terminal, represented by this entry, folds into a four-helical up-and-down bundle [1]. Paper describing PDB structure 4y9j. [1]. 25981666. Acyl-CoA Dehydrogenase Drives Heat Adaptation by Sequestering Fatty Acids. Ma DK, Li Z, Lu AY, Sun F, Chen S, Rothe M, Menzel R, Sun F, Horvitz HR;. Cell. 2015;161:1152-1163. (from Pfam) NF046219.1 PF22244.1 GCE_fung 27 27 231 domain Y N N Glucuronyl esterase, fungi 17275835,21661060,23275164,29222424,30083226 131567 cellular organisms no rank 5380 EBI-EMBL Glucuronyl esterase, fungi Glucuronyl esterase, fungi This entry includes fungal glucuronyl esterases, which seems to play a significant role in biomass degradation, as they can disconnect hemicellulose from lignin through the hydrolysis of the ester bond between 4-O-methyl-D-glucuronic acid residues of glucuronoxylans and aromatic alcohols of lignin. They belong to the carbohydrate esterase family 15 (CE15). Paper describing PDB structure 2jbw. [1]. 17275835. Structure and action of a C-C bond cleaving alpha/beta-hydrolase involved in nicotine degradation. Schleberger C, Sachelaru P, Brandsch R, Schulz GE;. J Mol Biol. 2007;367:409-418. Paper describing PDB structure 3pic. [2]. 21661060. Structure of the catalytic domain of glucuronoyl esterase Cip2 from Hypocrea jecorina. Pokkuluri PR, Duke NE, Wood SJ, Cotta MA, Li XL, Biely P, Schiffer M;. Proteins. 2011;79:2588-2592. Paper describing PDB structure 4g4g. [3]. 23275164. The structure of a novel glucuronoyl esterase from Myceliophthora thermophila gives new insights into its role as a potential biocatalyst. Charavgi MD, Dimarogona M, Topakas E, Christakopoulos P, Chrysina ED;. Acta Crystallogr D Biol Crystallogr. 2013;69:63-73. Paper describing PDB structure 6ehn. [4]. 29222424. Structural insight into a CE15 esterase from the marine bacterial metagenome. De Santi C, Gani OA, Helland R, Williamson A;. Sci Rep. 2017;7:17278. Paper describing PDB structure 6grw. [5]. 30083226. Biochemical and structural features of diverse bacterial glucuronoyl esterases facilitating recalcitrant biomass conversion. Arnling Baath J, Mazurkewich S, Knudsen RM, Poulsen JN, Olsson L, Lo Leggio L, Larsbrink J;. Biotechnol Biofuels. 2018;11:213. (from Pfam) NF046220.1 PF22247.1 Diox-like_N 27 27 60 domain Y N N Catechol 2,3-dioxygenase-like N-terminal domain 10368270,15028678,18826259,19828456,23066739 131567 cellular organisms no rank 3906 EBI-EMBL Catechol 2,3-dioxygenase-like N-terminal domain Catechol 2,3-dioxygenase-like N-terminal domain This entry includes a group of bacterial proteins that function as 2,3-dioxigenases [1-5]. Thsi entry represents the N-terminal domain. Paper describing PDB structure 1f1r. [1]. 15028678. Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases. Vetting MW, Wackett LP, Que L Jr, Lipscomb JD, Ohlendorf DH;. J Bacteriol. 2004;186:1945-1958. Paper describing PDB structure 1mpy. [2]. 10368270. An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Ppseudomonas putida mt-2. Kita A, Kita S, Fujisawa I, Inaka K, Ishida T, Horiike K, Nozaki M, Miki K;. Structure. 1999;7:25-34. Paper describing PDB structure 3ecj. [3]. 18826259. Intermediate in the O-O bond cleavage reaction of an extradiol dioxygenase. Kovaleva EG, Lipscomb JD;. Biochemistry. 2008;47:11168-11170. Paper describing PDB structure 3hpv. [4]. 19828456. Crystal structure and functional analysis of the extradiol dioxygenase LapB from a long-chain alkylphenol degradation pathway in Pseudomonas. Cho JH, Jung DK, Lee K, Rhee S;. J Biol Chem. 2009;284:34321-34330. Paper describing PDB structure 4ghc. [5]. 23066739. Structural basis for the role of tyrosine 257 of homoprotocatechuate 2,3-dioxygenase in substrate and oxygen activation. Kovaleva EG, Lipscomb JD;. Biochemistry. 2012;51:8755-8763. (from Pfam) NF046224.1 PF22278.1 DUF6958 27 27 90 subfamily Y Y N DUF6958 family protein 131567 cellular organisms no rank 1115 EBI-EMBL Family of unknown function (DUF6958) DUF6958 family protein This family is found in uncharacterised bacterial proteins. They share sequence similarity with several HTH winged helix domains, one of which Zinc uptake regulation protein FurB. (from Pfam) NF046237.1 PF22309.1 HK-GC-Chemotax_sensor 27 27 122 domain Y N N HK/GC/Chemotaxis protein-like, sensor domain 131567 cellular organisms no rank 3093 EBI-EMBL HK/GC/Chemotaxis protein-like, sensor domain HK/GC/Chemotaxis protein-like, sensor domain This entry represents a sensor domain found in methyl-accepting chemotaxis proteins, diguanylate-cyclase and histidine kinase receptors. Signals detected by the sensor domain are transmitted to the effector domain, implying a combinatorial molecular evolution. (from Pfam) NF046238.1 PF22317.1 PolB_N 27 27 54 domain Y N N DNA polymerase II small subunit, N-terminal domain 20598295,32221299,33115459,34568951 131567 cellular organisms no rank 115 EBI-EMBL DNA polymerase II small subunit, N-terminal domain DNA polymerase II small subunit, N-terminal domain This domain is found at the N-terminal end of DNA polymerase II small subunit from Pyrococcus horikoshii (PolB) and similar archaeal sequences. PolB possesses two activities: a DNA synthesis (polymerase) and an exonucleolytic activity that degrades single -stranded DNA in the 3' to 5' direction. This domain folds into a four alpha-helix bundle that includes a short parallel beta -sheet [1]. Paper describing PDB structure 2kxe. [1]. 20598295. Solution structure of the N-terminal domain of the archaeal D-family DNA polymerase small subunit reveals evolutionary relationship to eukaryotic B-family polymerases. Yamasaki K, Urushibata Y, Yamasaki T, Arisaka F, Matsui I;. FEBS Lett. 2010;584:3370-3375. Paper describing PDB structure 6knb. [2]. 33115459. Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy. Mayanagi K, Oki K, Miyazaki N, Ishino S, Yamagami T, Morikawa K, Iwasaki K, Kohda D, Shirai T, Ishino Y;. BMC Biol. 2020;18:152. Paper describing PDB structure 6t8h. [3]. 32221299. Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA. Madru C, Henneke G, Raia P, Hugonneau-Beaufet I, Pehau-Arnaudet G, England P, Lindahl E, Delarue M, Carroni M, Sauguet L;. Nat Commun. 2020;11:1591. Paper describing PDB structure 7e15. [4]. 34568951. Family D DNA polymerase interacts with GINS to promote CMG-helicase in the archaeal replisome. Oki K, Nagata M, Yamagami T, Numata T, Ishino S, Oyama T, Ishino Y;. Nucleic Acids Res. 2022;50:3601-3615. (from Pfam) NF046243.1 PF22327.1 Nudt16-like 27 27 161 domain Y N N U8 snoRNA-decapping enzyme-like 19278661,26100207,26121039,29844495,30976021 131567 cellular organisms no rank 3290 EBI-EMBL U8 snoRNA-decapping enzyme-like U8 snoRNA-decapping enzyme-like This entry represents the NUDIX hydrolase domain of U8 snoRNA -decapping enzyme from Xenopus laevis (Nudt16) and similar proteins from animals and bacteria. Nudt16 was initially described as an RNA-binding and decapping enzyme but it was later reported to be specialised in the removal of hazardous (deoxy)inosine diphosphate from the nucleotide pool. It adopts a canonical NUDIX fold, an alpha-beta-alpha sandwich constituted by two beta-sheets whose strands interact in a way that could also be described as a single extended beta-sheet [1]. Paper describing PDB structure 2xsq. [1]. 26121039. Structural Basis for the Specificity of Human NUDT16 and Its Regulation by Inosine Monophosphate. Tresaugues L, Lundback T, Welin M, Flodin S, Nyman T, Silvander C, Graslund S, Nordlund P;. PLoS One. 2015;10:e0131507. Paper describing PDB structure 3ees. [2]. 19278661. Structure and biological function of the RNA pyrophosphohydrolase BdRppH from Bdellovibrio bacteriovorus. Messing SA, Gabelli SB, Liu Q, Celesnik H, Belasco JG, Pineiro SA, Amzel LM;. Structure. 2009;17:472-481. Paper describing PDB structure 4zg0. [3]. 26100207. Crystal structure of syndesmos and its interaction with Syndecan-4 proteoglycan. Kim H, Yoo J, Lee I, Kang YJ, Cho HS, Lee W;. Biochem Biophys Res Commun. 2015;463:762-767. Paper describing PDB structure 5vy2. [4]. 30976021. Structural analyses of NudT16-ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins. Thirawatananond P, McPherson RL, Malhi J, Nathan S, Lambrecht MJ, Brichacek M, Hergenrother PJ, Leung AKL, Gabelli SB;. Sci Rep. 2019;9:5940. Paper de. TRUNCATED at 1650 bytes (from Pfam) NF046245.1 PF22335.1 Cas10-Cmr2_palm2 27 27 133 domain Y Y N Cas10/Cmr2 second palm domain-containing protein 22405013,22449983,23395183,23583914,25773141,33352158 131567 cellular organisms no rank 13308 EBI-EMBL Cas10/Cmr2, second palm domain Cas10/Cmr2, second palm domain This entry represents the second palm domain of Cas10 subunit (named Csm1 in Type III-A and Cmr2 in III-B systems) from type III CRISPR-Cas systems [6]. This domain contains a conserved GGDD motif that is important for DNA polymerase activity [1-5]. Paper describing PDB structure 3ung. [1]. 22405013. Structure of the Cmr2 subunit of the CRISPR-Cas RNA silencing complex. Cocozaki AI, Ramia NF, Shao Y, Hale CR, Terns RM, Terns MP, Li H;. Structure. 2012;20:545-553. Paper describing PDB structure 3w2v. [2]. 23583914. Crystal structure of the Cmr2-Cmr3 subcomplex in the CRISPR-Cas RNA silencing effector complex. Osawa T, Inanaga H, Numata T;. J Mol Biol. 2013;425:3811-3823. Paper describing PDB structure 4doz. [3]. 22449983. Crystal structure of Cmr2 suggests a nucleotide cyclase-related enzyme in type III CRISPR-Cas systems. Zhu X, Ye K;. FEBS Lett. 2012;586:939-945. Paper describing PDB structure 4h4k. [4]. 23395183. Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA silencing complex. Shao Y, Cocozaki AI, Ramia NF, Terns RM, Terns MP, Li H;. Structure. 2013;21:376-384. Paper describing PDB structure 4uw2. [5]. 25773141. Crystal structure of the Csm1 subunit of the Csm complex and its single-stranded DNA-specific nuclease activity. Jung TY, An Y, Park KH, Lee MH, Oh BH, Woo E;. Structure. 2015;23:782-790. [6]. 33352158. Mycobacterium tuberculosis CRISPR/Cas system Csm1 holds clues to the evolutionary relationship between DNA polymerase and cyclase activity. Zhang S, Li T, Huo Y, Yang J, Fleming J, Shi M, Wang Y, Wei W, Gu S, Bi L, Jiang T, Zhang H;. Int J Biol Macromol. 2021;170:140-149. (from Pfam) NF046269.1 PF22422.1 MGH1-like_GH 27 27 356 domain Y Y N MGH1-like glycoside hydrolase domain-containing protein 15274915,17455176,17936784,18586271,22102229,28329766 131567 cellular organisms no rank 85544 EBI-EMBL Mannosylglycerate hydrolase MGH1-like glycoside hydrolase domain Mannosylglycerate hydrolase MGH1-like glycoside hydrolase domain This entry represents the glycoside hydrolase domain found at the C-terminal of Mannosylglycerate hydrolase MGH1 and similar sequences. Paper describing PDB structure 1v7v. [1]. 15274915. Chitobiose phosphorylase from Vibrio proteolyticus, a member of glycosyl transferase family 36, has a clan GH-L-like (alpha/alpha)(6) barrel fold. Hidaka M, Honda Y, Kitaoka M, Nirasawa S, Hayashi K, Wakagi T, Shoun H, Fushinobu S;. Structure. 2004;12:937-947. Paper describing PDB structure 2jf4. [2]. 17455176. Molecular basis for trehalase inhibition revealed by the structure of trehalase in complex with potent inhibitors. Gibson RP, Gloster TM, Roberts S, Warren RA, Storch de Gracia I, Garcia A, Chiara JL, Davies GJ;. Angew Chem Int Ed Engl. 2007;46:4115-4119. Paper describing PDB structure 2okx. [3]. 17936784. Crystal structure of glycoside hydrolase family 78 alpha-L-Rhamnosidase from Bacillus sp. GL1. Cui Z, Maruyama Y, Mikami B, Hashimoto W, Murata K;. J Mol Biol. 2007;374:384-398. Paper describing PDB structure 3d3i. [4]. 18586271. Structural insights into the substrate specificity and function of Escherichia coli K12 YgjK, a glucosidase belonging to the glycoside hydrolase family 63. Kurakata Y, Uechi A, Yoshida H, Kamitori S, Sakano Y, Nishikawa A, Tonozuka T;. J Mol Biol. 2008;381:116-128. Paper describing PDB structure 3qde. [5]. 22102229. Structure of cellobiose phosphorylase from Clostridium thermocellum in complex with phosphate. Bianchetti CM, Elsen NL, Fox BG, Phillips GN Jr;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011;67:1345-1349. [6]. 28329766. Complex pectin metabolism by gut bacteria reveals novel catalyti. TRUNCATED at 1650 bytes (from Pfam) NF046293.1 PF22482.1 AsnC_trans_reg_3 24.4 24.4 95 domain Y N N PF0864 C-terminal dimeric alpha+beta barrel domain 131567 cellular organisms no rank 21299 EBI-EMBL PF0864 C-terminal dimeric alpha+beta barrel domain PF0864 C-terminal dimeric alpha+beta barrel domain This entry describes the C-terminal domain of the uncharacterized HTH-type transcriptional regulator PF0864, identified in the Pyrococcus furiosus archaea. The protein is 162 amino acids long and contains an HTH asnC-type domain (amino acids 6-78) responsible for DNA binding. The crystal structure of PF0864 (PDB: 2IA0) reveals a helix-turn-helix motif within the DNA-binding domain. The function and specific role of PF0864 in transcriptional regulation remain unknown. (from Pfam) NF046294.1 PF22483.1 Mu-transpos_C_2 27 27 73 domain Y Y N Mu transposase domain-containing protein 7628012 131567 cellular organisms no rank 41465 EBI-EMBL Mu transposase, C-terminal domain Mu transposase, C-terminal domain Members of this family are found in various prokaryotic integrases and transposases. They adopt a beta-barrel structure with Greek-key topology according to [1] or an OB fold according to ECOD. [1]. 7628012. Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration. Rice P, Mizuuchi K;. Cell. 1995;82:209-220. (from Pfam) NF046302.1 PF22505.1 RNase_J_b_CASP 27 27 126 domain Y N N Ribonuclease J, beta-CASP domain 18204464,21893285,21893286,25940620,26253740 131567 cellular organisms no rank 57397 EBI-EMBL Ribonuclease J, beta-CASP domain Ribonuclease J, beta-CASP domain This domain is found in Ribonuclease J from Thermus thermophilus (RNaseJ) and similar bacterial proteins. RNaseJ is an RNase that has endonuclease and possibly 5'-3' exonuclease activity. It is probably involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay. This protein shows three globular domains: the beta lactamase core (formed by two separate regions, Pfam:PF12706 and Pfam:PF07521), the beta-CASP (this entry) and the C-terminal domain (Pfam: PF17770). This domain consists of a central five-stranded parallel beta-sheet that is surrounded by five alpha-helices [1,2]. Paper describing PDB structure 3bk1. [1]. 18204464. Structural insights into the dual activity of RNase J. Li de la Sierra-Gallay I, Zig L, Jamalli A, Putzer H;. Nat Struct Mol Biol. 2008;15:206-212. Paper describing PDB structure 3t3n. [2]. 21893286. Molecular basis for the recognition and cleavage of RNA by the bifunctional 5'-3' exo/endoribonuclease RNase J. Dorleans A, Li de la Sierra-Gallay I, Piton J, Zig L, Gilet L, Putzer H, Condon C;. Structure. 2011;19:1252-1261. Paper describing PDB structure 3zq4. [3]. 21893285. Unusual, dual endo- and exonuclease activity in the degradosome explained by crystal structure analysis of RNase J1. Newman JA, Hewitt L, Rodrigues C, Solovyova A, Harwood CR, Lewis RJ;. Structure. 2011;19:1241-1251. Paper describing PDB structure 4xwt. [4]. 25940620. Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase J. Zhao Y, Lu M, Zhang H, Hu J, Zhou C, Xu Q, Ul Hussain Shah AM, Xu H, Wang L, Hua Y;. Nucleic Acids Res. 2015;43:5550-5559. Paper describing PDB stru. TRUNCATED at 1650 bytes (from Pfam) NF046303.1 PF22507.1 DUF6994 27 27 226 subfamily Y Y N DUF6994 family protein 131567 cellular organisms no rank 1082 EBI-EMBL Family of unknown function (DUF6994) DUF6994 family protein This is a family of uncharacterised bacterial proteins. They are probably remotely related to His-Me finger endonucleases. (from Pfam) NF046304.1 PF22515.1 DUF6996 27 27 71 subfamily Y Y N type II restriction enzyme GO:0009307,GO:0015666 131567 cellular organisms no rank 1537 EBI-EMBL Domain of unknown function (DUF6996) type II restriction enzyme recognizing GATC This domain is found N-terminal in a group of uncharacterised proteins. It is remotely related to AbiEi winged helix domain and it is predicted to adopt the same structure. (from Pfam) NF046308.1 PF22527.1 DEXQc_Suv3 27 27 154 domain Y N N DEXQ-box helicase domain of Suv3 22101826 131567 cellular organisms no rank 39837 EBI-EMBL DEXQ-box helicase domain of Suv3 DEXQ-box helicase domain of Suv3 This entry represents the DEXQ-box helicase domain of Suv3 [1]. Paper describing PDB structure 3rc3. [1]. 22101826. Human Suv3 protein reveals unique features among SF2 helicases. Jedrzejczak R, Wang J, Dauter M, Szczesny RJ, Stepien PP, Dauter Z;. Acta Crystallogr D Biol Crystallogr. 2011;67:988-996. (from Pfam) NF046309.1 PF22528.1 PRMT_C 27 27 164 domain Y N N Arginine methyltransferase oligomerization subdomain 10899106,11101900,12737817,17882261,21410432 131567 cellular organisms no rank 850 EBI-EMBL Arginine methyltransferase oligomerization subdomain Arginine methyltransferase oligomerization subdomain This entry represents a domain found C-terminal in protein arginine methyltransferases. This domain is involved in oligomerisation. Paper describing PDB structure 1f3l. [1]. 10899106. Crystal structure of the conserved core of protein arginine methyltransferase PRMT3. Zhang X, Zhou L, Cheng X;. EMBO J. 2000;19:3509-3519. Paper describing PDB structure 1g6q. [2]. 11101900. The structure and oligomerization of the yeast arginine methyltransferase, Hmt1. Weiss VH, McBride AE, Soriano MA, Filman DJ, Silver PA, Hogle JM;. Nat Struct Biol. 2000;7:1165-1171. Paper describing PDB structure 1or8. [3]. 12737817. Structure of the predominant protein arginine methyltransferase PRMT1 and analysis of its binding to substrate peptides. Zhang X, Cheng X;. Structure. 2003;11:509-520. Paper describing PDB structure 2v74. [4]. 17882261. Insights into histone code syntax from structural and biochemical studies of CARM1 methyltransferase. Yue WW, Hassler M, Roe SM, Thompson-Vale V, Pearl LH;. EMBO J. 2007;26:4402-4412. Paper describing PDB structure 2y1w. [5]. 21410432. Structural basis for CARM1 inhibition by indole and pyrazole inhibitors. Sack JS, Thieffine S, Bandiera T, Fasolini M, Duke GJ, Jayaraman L, Kish KF, Klei HE, Purandare AV, Rosettani P, Troiani S, Xie D, Bertrand JA;. Biochem J. 2011;436:331-339. (from Pfam) NF046312.1 PF22537.1 WbmS-like 27 27 186 domain Y N N Polysaccharide deacetylase 131567 cellular organisms no rank 564 EBI-EMBL Polysaccharide deacetylase Polysaccharide deacetylase This family represents a group of bacterial proteins, including the putative polysaccharide deacetylase WbmS from Bordetella bronchiseptica, which is involved in O-antigen biosynthesis. It adopts an alpha-beta barrel configuration. (from Pfam) NF046316.1 PF22558.1 REase-ARP 27 27 270 domain Y Y N PGN_0703 family putative restriction endonuclease 36146784 131567 cellular organisms no rank 1729 EBI-EMBL Restriction Endonuclease associating with ARP PGN_0703 family putative restriction endonuclease Members of this family include MCC5954244.1, predicted to be a restriction endonuclease in a study of putative bacteria vs phage conflict systems, PGN_0703 is cited here the as locus tag of an uncharacterized protein found by searching the PaperBLAST database with this HMM. NF046326.1 PF22613.1 Transketolase_C_1 27 27 113 domain Y Y N transketolase-like TK C-terminal-containing protein 11773632,11955070,12913150,15149284,9398292 131567 cellular organisms no rank 169424 EBI-EMBL Transketolase-like TK C-terminal domain Transketolase-like TK C-terminal domain This entry represents the C-terminal domain found in transketolase and transketolase-like enzymes [1-5], such as pyruvate dehydrogenase E1 component (OPD1) [4]. Paper describing PDB structure 1ay0. [1]. 9398292. Identification of catalytically important residues in yeast transketolase. Wikner C, Nilsson U, Meshalkina L, Udekwu C, Lindqvist Y, Schneider G;. Biochemistry. 1997;36:15643-15649. Paper describing PDB structure 1gpu. [2]. 11773632. Snapshot of a key intermediate in enzymatic thiamin catalysis: crystal structure of the alpha-carbanion of (alpha,beta-dihydroxyethyl)-thiamin diphosphate in the active site of transketolase from Saccharomyces cerevisiae. Fiedler E, Thorell S, Sandalova T, Golbik R, Konig S, Schneider G;. Proc Natl Acad Sci U S A. 2002;99:591-595. Paper describing PDB structure 1itz. [3]. 12913150. Structure and properties of an engineered transketolase from maize. Gerhardt S, Echt S, Busch M, Freigang J, Auerbach G, Bader G, Martin WF, Bacher A, Huber R, Fischer M;. Plant Physiol. 2003;132:1941-1949. Paper describing PDB structure 1l8a. [4]. 11955070. Structure of the pyruvate dehydrogenase multienzyme complex E1 component from Escherichia coli at 1.85 A resolution. Arjunan P, Nemeria N, Brunskill A, Chandrasekhar K, Sax M, Yan Y, Jordan F, Guest JR, Furey W;. Biochemistry. 2002;41:5213-5221. Paper describing PDB structure 1r9j. [5]. 15149284. Transketolase from Leishmania mexicana has a dual subcellular localization. Veitch NJ, Maugeri DA, Cazzulo JJ, Lindqvist Y, Barrett MP;. Biochem J. 2004;382:759-767. (from Pfam) NF046327.1 PF22614.1 Slo-like_RCK 24 24 119 domain Y Y N TrkA-related ion transporter 11301020,12037559,16227203,16990139,17287352 131567 cellular organisms no rank 5095 EBI-EMBL Calcium-activated potassium channel slowpoke-like RCK domain Calcium-activated potassium channel slowpoke-like RCK domain This entry includes calcium-activated potassium channels, known as BK channels or Slowpoke homologues (Slo1-3) which includes calcium-activated potassium channel slowpoke from Drosophila (Slo) and its homologues from vertebrates KCMA1, KCNT1/2 and KCNU1. This entry represents the C-terminal regulator of K+ conductance (RCK) domains which appear as tandem domains in these proteins [1-5]. The RCK domain has a Rossmann-fold topology with unique positions that compose a well-conserved salt bridge and a hydrophobic dimer interface. This domain is also presents in prokaryotic K+ channels. Paper describing PDB structure 1id1. [1]. 11301020. Structure of the RCK domain from the E. coli K+ channel and demonstration of its presence in the human BK channel. Jiang Y, Pico A, Cadene M, Chait BT, MacKinnon R;. Neuron. 2001;29:593-601. Paper describing PDB structure 1lnq. [2]. 12037559. Crystal structure and mechanism of a calcium-gated potassium channel. Jiang Y, Lee A, Chen J, Cadene M, Chait BT, MacKinnon R;. Nature. 2002;417:515-522. Paper describing PDB structure 2aef. [3]. 16227203. Structures of the MthK RCK domain and the effect of Ca2+ on gating ring stability. Dong J, Shi N, Berke I, Chen L, Jiang Y;. J Biol Chem. 2005;280:41716-41724. Paper describing PDB structure 2fy8. [4]. 16990139. Crystal structures of a ligand-free MthK gating ring: insights into the ligand gating mechanism of K+ channels. Ye S, Li Y, Chen L, Jiang Y;. Cell. 2006;126:1161-1173. Paper describing PDB structure 2ogu. [5]. 17287352. Dynamic oligomeric conversions of the cytoplasmic RCK domains mediate MthK potassium channel activity. Kuo MM, Baker KA, Wong . TRUNCATED at 1650 bytes (from Pfam) NF046328.1 PF22616.1 HMD_N 27 27 239 domain Y N N HMD N-terminal domain 16540118,18653896,19162018,23873755,26094576 131567 cellular organisms no rank 476 EBI-EMBL HMD N-terminal domain HMD N-terminal domain This entry represents the N-terminal domain of 5,10-methenyltetrahydromethanopterin hydrogenase (HMD) and related proteins, an enzyme of the methanogenic energy metabolism [1-5]. HMD is an iron-sulphur-cluster-free enzyme that contains an intrinsic CO ligand bound to iron. This domain has a Rossmann fold-like structure that contains a mononucleotide-binding site, which could harbour the GMP moiety of the cofactor [1-5]. Paper describing PDB structure 2b0j. [1]. 16540118. The crystal structure of the apoenzyme of the iron-sulphur cluster-free hydrogenase. Pilak O, Mamat B, Vogt S, Hagemeier CH, Thauer RK, Shima S, Vonrhein C, Warkentin E, Ermler U;. J Mol Biol. 2006;358:798-809. Paper describing PDB structure 3daf. [2]. 18653896. The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site. Shima S, Pilak O, Vogt S, Schick M, Stagni MS, Meyer-Klaucke W, Warkentin E, Thauer RK, Ermler U;. Science. 2008;321:572-575. Paper describing PDB structure 3f46. [3]. 19162018. The crystal structure of C176A mutated [Fe]-hydrogenase suggests an acyl-iron ligation in the active site iron complex. Hiromoto T, Ataka K, Pilak O, Vogt S, Stagni MS, Meyer-Klaucke W, Warkentin E, Thauer RK, Shima S, Ermler U;. FEBS Lett. 2009;583:585-590. Paper describing PDB structure 4jjf. [4]. 23873755. Crystal structures of [Fe]-hydrogenase in complex with inhibitory isocyanides: implications for the H2-activation site. Tamura H, Salomone-Stagni M, Fujishiro T, Warkentin E, Meyer-Klaucke W, Ermler U, Shima S;. Angew Chem Int Ed Engl. 2013;52:9656-9659. Paper describing PDB structure 4yt2. [5]. 26094576. Towards a functional identificat. TRUNCATED at 1650 bytes (from Pfam) NF046331.1 PF22624.1 AASDHPPT_N 27 27 100 domain Y N N 4'-phosphopantetheinyl transferase, N-terminal 10581256,18022563,24704508 131567 cellular organisms no rank 17137 EBI-EMBL 4'-phosphopantetheinyl transferase, N-terminal 4'-phosphopantetheinyl transferase, N-terminal This domain is found at the N-terminal end of human 4'-phosphopantetheinyl transferase (also known as L-aminoadipate -semialdehyde dehydrogenase-phosphopantetheinyl transferase, AASDHPPT), which catalyses the post-translational modification of target proteins by phosphopantetheine. This protein consists of two nearly identical domains (this entry and Pfam:PF01648) connected by a short linker region. Both domains show a pair of beta-sheets connected by a loop region [2]. Paper describing PDB structure 1qr0. [1]. 10581256. Crystal structure of the surfactin synthetase-activating enzyme sfp: a prototype of the 4'-phosphopantetheinyl transferase superfamily [In Process Citation]. Reuter K, Mofid MR, Marahiel MA, Ficner R;. EMBO J 1999;18:6823-6831. Paper describing PDB structure 2byd. [2]. 18022563. Mechanism and substrate recognition of human holo ACP synthase. Bunkoczi G, Pasta S, Joshi A, Wu X, Kavanagh KL, Smith S, Oppermann U;. Chem Biol. 2007;14:1243-1253. Paper describing PDB structure 4mrt. [3]. 24704508. Crystal structure of a PCP/Sfp complex reveals the structural basis for carrier protein posttranslational modification. Tufar P, Rahighi S, Kraas FI, Kirchner DK, Lohr F, Henrich E, Kopke J, Dikic I, Guntert P, Marahiel MA, Dotsch V;. Chem Biol. 2014;21:552-562. (from Pfam) NF046332.1 PF22626.1 LysX_preATP_grasp 27 27 84 domain Y N N LysX preATP-grasp domain 12963379,23434852 131567 cellular organisms no rank 2781 EBI-EMBL LysX preATP-grasp domain LysX preATP-grasp domain This entry represents the preATP-grasp domain found at the N-terminal of archaeal LysX and simialr proteins. LysX catalyses the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxyl group of the C-terminal glutamate residue in LysW. Paper describing PDB structure 1uc8. [1]. 12963379. Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8. Sakai H, Vassylyeva MN, Matsuura T, Sekine Si, Gotoh K, Nishiyama M, Terada T, Shirouzu M, Kuramitsu S, Vassylyev DG, Yokoyama S;. J Mol Biol. 2003;332:729-740. Paper describing PDB structure 3vpb. [2]. 23434852. Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Ouchi T, Tomita T, Horie A, Yoshida A, Takahashi K, Nishida H, Lassak K, Taka H, Mineki R, Fujimura T, Kosono S, Nishiyama C, Masui R, Kuramitsu S, Albers SV, Kuzuyama T, Nishiyama M;. Nat Chem Biol. 2013;9:277-283. (from Pfam) NF046333.1 PF22627.1 AglB_core-like 27 27 111 domain Y N N AglB core domain 18046457,22559858,22865878,23177926,23815857 131567 cellular organisms no rank 1261 EBI-EMBL AglB core domain AglB core domain This entry represents the C-terminal core domain of archaeal oligosaccharyltransferase AglB that transfers oligosaccharide chain from a lipid-linked oligosaccharide (LLO) donor to the asparagine residues in the N-glycosylation sequon, Asn-X-Ser/Thr (X=Pro) [1-5]. In the archaea AlgB, it occurs alone, rather than in complex as the eukaryotic homologue STT3. This domain adopts a mixed alpha/beta fold and contains a highly conserved WWDYG motif that may be of functional relevance. Paper describing PDB structure 2lgz. [1]. 22865878. Eukaryotic N-glycosylation occurs via the membrane-anchored C-terminal domain of the Stt3p subunit of oligosaccharyltransferase. Huang C, Bhaskaran R, Mohanty S;. J Biol Chem. 2012;287:32450-32458. Paper describing PDB structure 2zag. [2]. 18046457. Structure-guided identification of a new catalytic motif of oligosaccharyltransferase. Igura M, Maita N, Kamishikiryo J, Yamada M, Obita T, Maenaka K, Kohda D;. EMBO J. 2008;27:234-243. Paper describing PDB structure 3vgp. [3]. 22559858. Crystal structure of the C-terminal globular domain of oligosaccharyltransferase from Archaeoglobus fulgidus at 1.75 A resolution. Matsumoto S, Igura M, Nyirenda J, Matsumoto M, Yuzawa S, Noda N, Inagaki F, Kohda D;. Biochemistry. 2012;51:4157-4166. Paper describing PDB structure 3vu0. [4]. 23177926. Crystallographic and NMR evidence for flexibility in oligosaccharyltransferases and its catalytic significance. Nyirenda J, Matsumoto S, Saitoh T, Maita N, Noda NN, Inagaki F, Kohda D;. Structure. 2013;21:32-41. Paper describing PDB structure 3wai. [5]. 23815857. Crystal structure of the C-terminal globular domain o. TRUNCATED at 1650 bytes (from Pfam) NF046334.1 PF22633.1 F5_F8_type_C_2 27.8 27.8 91 domain Y N N NedA-like, galactose-binding domain 10586886,10586887,11418455,2002850,8591030 131567 cellular organisms no rank 146010 EBI-EMBL NedA-like, galactose-binding domain NedA-like, galactose-binding domain This galactose-binding domain is found in Sialidase from Micromonospora viridifaciens (NedA), which releases sialic acids for use as carbon and energy sources. This domain shows a jelly-roll topology [3]. Paper describing PDB structure 1czs. [1]. 10586886. Crystal structures of the membrane-binding C2 domain of human coagulation factor V. Macedo-Ribeiro S, Bode W, Huber R, Quinn-Allen MA, Kim SW, Ortel TL, Bourenkov GP, Bartunik HD, Stubbs MT, Kane WH, Fuentes-Prior P;. Nature. 1999;402:434-439. Paper describing PDB structure 1d7p. [2]. 10586887. Structure of the C2 domain of human factor VIII at 1.5 A resolution. Pratt KP, Shen BW, Takeshima K, Davie EW, Fujikawa K, Stoddard BL;. Nature. 1999;402:439-442. Paper describing PDB structure 1eut. [3]. 8591030. The three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll. Gaskell A, Crennell S, Taylor G;. Structure. 1995;3:1197-1205. Paper describing PDB structure 1gof. [4]. 2002850. Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase. Ito N, Phillips SE, Stevens C, Ogel ZB, McPherson MJ, Keen JN, Yadav KD, Knowles PF;. Nature 1991;350:87-90. Paper describing PDB structure 1iqd. [5]. 11418455. Structure of a factor VIII C2 domain-immunoglobulin G4kappa Fab complex: identification of an inhibitory antibody epitope on the surface of factor VIII. Spiegel PC Jr, Jacquemin M, Saint-Remy JM, Stoddard BL, Pratt KP;. Blood. 2001;98:13-19. (from Pfam) NF046335.1 PF22636.1 FlK 27 27 103 subfamily Y Y N thioesterase, FlK family 14997554,20430898,20836570 131567 cellular organisms no rank 10706 EBI-EMBL Fluoroacetyl-CoA-specific thioesterase thioesterase, FlK family Members of this family include FlK, a thioesterase active on fluoroacetyl-CoA but not acetyl-CoA. FlK provides host protection to Streptomyces cattleya, a rare producer of fluoroacetate and fluorothreonine. Other members of this family are likely to vary in their specific function. NF046336.1 PF22640.1 ManC_GMP_beta-helix 27 27 55 domain Y N N MannoseP isomerase/GMP-like beta-helix domain 20573954 131567 cellular organisms no rank 53778 EBI-EMBL MannoseP isomerase/GMP-like beta-helix domain MannoseP isomerase/GMP-like beta-helix domain This entry represents a left-handed beta-helix domain found at the C-terminal of Guanosine-diphospho-d-mannose Pyrophosphorylase (GMP) from Thermotoga maritima [1] and as a linker domain in mannose-1-phosphate guanylyltransferases, alginate biosynthesis protein AlgA and xanthan biosynthesis protein XanB, among others, located between the Nucleotidyl transferase domain at the N-terminal (Pfam:PF00483) and the C-terminal isomerase cupin domain (Pfam:PF01050). This domain is composed of an alpha-helix followed by a short left-handed beta-helix. GMP forms a dimer in which two molecules associate through a tail-to-tail arrangement of this domain [1].. Paper describing PDB structure 2x5s. [1]. 20573954. Structural insights into the catalytic mechanism of bacterial guanosine-diphospho-D-mannose pyrophosphorylase and its regulation by divalent ions. Pelissier MC, Lesley SA, Kuhn P, Bourne Y;. J Biol Chem. 2010;285:27468-27476. (from Pfam) NF046339.1 PF22656.1 At5g48480-like_N 27 27 59 domain Y N N Glyoxalase At5g48480-like, N-terminal domain 131567 cellular organisms no rank 980 EBI-EMBL Glyoxalase At5g48480-like, N-terminal domain Glyoxalase At5g48480-like, N-terminal domain This entry includes, mainly, plant sequences that belong to the Lactoylglutathione lyase/glyoxalase I family. They are poorly characterised and contain two characteristic VOC domains. Members of this entry contain conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. This entry represents the N-terminal domain. (from Pfam) NF046340.1 PF22658.1 YycE-like_N 27 27 52 domain Y N N YycE-like N-terminal domain 131567 cellular organisms no rank 8655 EBI-EMBL YycE-like N-terminal domain YycE-like N-terminal domain This entry represents a VOC-like domain found at the N-terminal of a group of uncharacterised bacterial sequences, such YycE from Bacillus subtilis. (from Pfam) NF046341.1 PF22662.1 Csa3_N 27 27 120 domain Y N N Csa3 CRISPR-associated Rossmann-like domain 21093452,34944496,35038453 131567 cellular organisms no rank 408 EBI-EMBL Csa3 CRISPR-associated Rossmann-like domain Csa3 CRISPR-associated Rossmann-like domain This domain is found N-terminal in CRISPR-associated protein Csa3 and related proteins. Csa3 consists of two domains [1-3]. The N-terminal domain is a unique variation on the dinucleotide binding domain and it is responsible for dimer formation. In addition, it utilizes two conserved sequence motifs T(h)GF(N/D)E(x)4R and L(x)2G(h)R to form a 2-fold symmetric pocket on the dimer axis. This pocket is likely to represent a regulatory ligand-binding site. Paper describing PDB structure 2wte. [1]. 21093452. The structure of the CRISPR-associated protein Csa3 provides insight into the regulation of the CRISPR/Cas system. Lintner NG, Frankel KA, Tsutakawa SE, Alsbury DL, Copie V, Young MJ, Tainer JA, Lawrence CM;. J Mol Biol. 2011;405:939-955. Paper describing PDB structure 6w11. [2]. 34944496. Cyclic Tetra-Adenylate (cA4) Recognition by Csa3; Implications for an Integrated Class 1 CRISPR-Cas Immune Response in Saccharolobus solfataricus. Charbonneau AA, Eckert DM, Gauvin CC, Lintner NG, Lawrence CM;. Biomolecules. 2021; [Epub ahead of print]. Paper describing PDB structure 6wxq. [3]. 35038453. Structural basis of cyclic oligoadenylate binding to the transcription factor Csa3 outlines cross talk between type III and type I CRISPR systems. Xia P, Dutta A, Gupta K, Batish M, Parashar V;. J Biol Chem. 2022;298:101591. (from Pfam) NF046343.1 PF22673.1 MCP-like_PDC_1 27 27 113 domain Y N N Methyl-accepting chemotaxis protein-like, first PDC sensor domain 20435045,23436677,26457436,26878914,26923153 131567 cellular organisms no rank 103256 EBI-EMBL Methyl-accepting chemotaxis protein-like, first PDC sensor domain Methyl-accepting chemotaxis protein-like, first PDC sensor domain This entry represents the first PDC (PhoQ/DcuS/CitA) sensor domain found in methyl-accepting chemotaxis proteins (MCPs) such as TLQP and MCPA/B. Paper describing PDB structure 3li8. [1]. 20435045. Structural characterization of the predominant family of histidine kinase sensor domains. Zhang Z, Hendrickson WA;. J Mol Biol. 2010;400:335-353. Paper describing PDB structure 4jgo. [2]. 23436677. Insight into the sporulation phosphorelay: crystal structure of the sensor domain of Bacillus subtilis histidine kinase, KinD. Wu R, Gu M, Wilton R, Babnigg G, Kim Y, Pokkuluri PR, Szurmant H, Joachimiak A, Schiffer M;. Protein Sci. 2013;22:564-576. Paper describing PDB structure 4wy9. [3]. 26923153. The crystal structure of the tandem-PAS sensing domain of Campylobacter jejuni chemoreceptor Tlp1 suggests indirect mechanism of ligand recognition. Machuca MA, Liu YC, Beckham SA, Gunzburg MJ, Roujeinikova A;. J Struct Biol. 2016;194:205-213. Paper describing PDB structure 4xmq. [4]. 26457436. Structural basis for amino-acid recognition and transmembrane signalling by tandem Per-Arnt-Sim (tandem PAS) chemoreceptor sensory domains. Liu YC, Machuca MA, Beckham SA, Gunzburg MJ, Roujeinikova A;. Acta Crystallogr D Biol Crystallogr. 2015;71:2127-2136. Paper describing PDB structure 5ave. [5]. 26878914. Identification of a Vibrio cholerae chemoreceptor that senses taurine and amino acids as attractants. Nishiyama S, Takahashi Y, Yamamoto K, Suzuki D, Itoh Y, Sumita K, Uchida Y, Homma M, Imada K, Kawagishi I;. Sci Rep. 2016;6:20866. (from Pfam) NF046346.1 PF22677.1 Ble-like_N 24.5 24.5 41 domain Y N N Bleomycin resistance protein-like N-terminal 11134052,15028678,18826259,23066739,7481800 131567 cellular organisms no rank 76741 EBI-EMBL Bleomycin resistance protein-like N-terminal Bleomycin resistance protein-like N-terminal This entry represents the N-terminal glyoxalase-like domain found in a group of bacterial proteins, such as bleomycin resistance protein (Ble) from Klebsiella pneumoniae, lactoglutathion lyase from Haemophilus influenzae, among others. Paper describing PDB structure 1f1r. [1]. 15028678. Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases. Vetting MW, Wackett LP, Que L Jr, Lipscomb JD, Ohlendorf DH;. J Bacteriol. 2004;186:1945-1958. Paper describing PDB structure 1han. [2]. 7481800. Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad. Han S, Eltis LD, Timmis KN, Muchmore SW, Bolin JT;. Science 1995;270:976-980. Paper describing PDB structure 2c21. [3]. 18826259. Intermediate in the O-O bond cleavage reaction of an extradiol dioxygenase. Kovaleva EG, Lipscomb JD;. Biochemistry. 2008;47:11168-11170. Paper describing PDB structure 4ghc. [4]. 23066739. Structural basis for the role of tyrosine 257 of homoprotocatechuate 2,3-dioxygenase in substrate and oxygen activation. Kovaleva EG, Lipscomb JD;. Biochemistry. 2012;51:8755-8763. [5]. 11134052. Crystal structures of the transposon Tn5-carried bleomycin resistance determinant uncomplexed and complexed with bleomycin. Maruyama M, Kumagai T, Matoba Y, Hayashida M, Fujii T, Hata Y, Sugiyama M;. J Biol Chem. 2001;276:9992-9999. (from Pfam) NF046348.1 PF22684.1 LFE_1968-like 27 27 123 domain Y N N LFE_1968-like 131567 cellular organisms no rank 13 EBI-EMBL LFE_1968-like LFE_1968-like This protein family includes a group of uncharacterised prokaryotic proteins that show an alpha-beta configuration with similarity to haem iron utilisation proteins, such as LFE_1968 from Leptospirillum ferrooxidans. (from Pfam) NF046352.1 PF22696.1 Putative_PNPOx_2 27 27 129 domain Y N N Pyridoxamine 5'-phosphate oxidase-like 131567 cellular organisms no rank 1019 EBI-EMBL Pyridoxamine 5'-phosphate oxidase-like Pyridoxamine 5'-phosphate oxidase-like This domain is found in bacterial Pyridoxamine 5'-phosphate oxidase-like proteins. It folds into a beta-barrel capped at the top and bottom with alpha-helices. (from Pfam) NF046354.1 PF22703.1 Cdc6_lid 27 27 68 domain Y N N Cdc6 AAA+ ATPase-type lid domain 11030343,15465044,17060327,17761879,17761880 131567 cellular organisms no rank 7862 EBI-EMBL Cdc6 AAA+ ATPase-type lid domain Cdc6 AAA+ ATPase-type lid domain This domain is found in Cdc6 and related proteins. Cdc6 is a key protein involved in the pre-replication complex assembly. It contains AAA+ ATPase domain that is capped by a lid domain, represented by this entry [1-2]. Paper describing PDB structure 1fnn. [1]. 11030343. Structure and function of Cdc6/Cdc18: implications for origin recognition and checkpoint control. Liu J, Smith CL, DeRyckere D, DeAngelis K, Martin GS, Berger JM;. Mol Cell. 2000;6:637-648. Paper describing PDB structure 1w5s. [2]. 15465044. Conformational changes induced by nucleotide binding in Cdc6/ORC from Aeropyrum pernix. Singleton MR, Morales R, Grainge I, Cook N, Isupov MN, Wigley DB;. J Mol Biol. 2004;343:547-557. Paper describing PDB structure 2c9o. [3]. 17060327. Crystal structure of the human AAA+ protein RuvBL1. Matias PM, Gorynia S, Donner P, Carrondo MA;. J Biol Chem. 2006;281:38918-38929. Paper describing PDB structure 2qby. [4]. 17761879. Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. Dueber EL, Corn JE, Bell SD, Berger JM;. Science. 2007;317:1210-1213. Paper describing PDB structure 2v1u. [5]. 17761880. Structural basis of DNA replication origin recognition by an ORC protein. Gaudier M, Schuwirth BS, Westcott SL, Wigley DB;. Science. 2007;317:1213-1216. (from Pfam) NF046356.1 PF22706.1 Tex_central_region 27 27 178 domain Y N N Tex central region-like 18321528,21419780,30135578,32541898,34526721 131567 cellular organisms no rank 77165 EBI-EMBL Tex central region-like Tex central region-like This domain is found in Tex protein and other related proteins. Tex belongs to a family of prokaryotic transcriptional accessory factors that likely function in a variety of transcriptional processes [1-5].This domain is mainly helical, consisting of a number of small helices that wrap around a long central helix. Paper describing PDB structure 3bzc. [1]. 18321528. Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa. Johnson SJ, Close D, Robinson H, Vallet-Gely I, Dove SL, Hill CP;. J Mol Biol. 2008;377:1460-1473. Paper describing PDB structure 3psf. [2]. 21419780. Crystal structures of the S. cerevisiae Spt6 core and C-terminal tandem SH2 domain. Close D, Johnson SJ, Sdano MA, McDonald SM, Robinson H, Formosa T, Hill CP;. J Mol Biol. 2011;408:697-713. Paper describing PDB structure 6gmh. [3]. 30135578. Structure of activated transcription complex Pol II-DSIF-PAF-SPT6. Vos SM, Farnung L, Boehning M, Wigge C, Linden A, Urlaub H, Cramer P;. Nature. 2018;560:607-612. Paper describing PDB structure 6ted. [4]. 32541898. Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation. Vos SM, Farnung L, Linden A, Urlaub H, Cramer P;. Nat Struct Mol Biol. 2020;27:668-677. Paper describing PDB structure 7oop. [5]. 34526721. Structural basis of human transcription-DNA repair coupling. Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P;. Nature. 2021;598:368-372. (from Pfam) NF046363.1 PF22738.1 NNH7 27 27 225 domain Y N N NACHT N-terminal Helical domain 7 37160116 131567 cellular organisms no rank 2377 EBI-EMBL NACHT N-terminal Helical domain 7 NACHT N-terminal Helical domain 7 This entry represents the helical domain found at the N-terminus of bacterial NACHT conflict systems. This position is frequently occupied by an effector domain [1]. [1]. 37160116. Bacterial NLR-related proteins protect against phage. Kibby EM, Conte AN, Burroughs AM, Nagy TA, Vargas JA, Whalen LA, Aravind L, Whiteley AT;. Cell. 2023;186:2410-2424. (from Pfam) NF046366.1 PF22751.1 DUF488-N3a 27 27 118 subfamily Y N N Active DUF488-N3 subclade 36968430 131567 cellular organisms no rank 34557 EBI-EMBL Active DUF488-N3 subclade Active DUF488-N3 subclade This entry represents a subclade of DUF488 domains with degenerate C-terminal core strand. Sometimes it is observed adjacent to the DUF488-s subclade, suggesting it preserves a catalytic activity comparable to other active DUF488 subclades [1]. [1]. 36968430. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. Burroughs AM, Aravind L;. NAR Genom Bioinform. 2023;5:lqad029. (from Pfam) NF046369.1 PF22765.1 DUF7010 27 27 172 subfamily Y Y N DUF7010 family protein 131567 cellular organisms no rank 3892 EBI-EMBL Family of unknown function (DUF7010) DUF7010 family protein This entry represents a family of uncharacterised bacterial proteins. They are predicted to adopt alpha-helical structure composed of six up-and-down helices. It is likely that these proteins are associated with the membrane. (from Pfam) NF046370.1 PF22768.1 Siphovirus-type_tail_C 25 25 97 domain Y Y N phage distal tail protein 20843802 131567 cellular organisms no rank 12574 EBI-EMBL Siphovirus-type tail component, C-terminal domain Siphovirus-type tail component, C-terminal domain This entry consists of several phage tail component proteins, including bacteriophage SPP1 distal tail protein Dit (also known as Gp19.1 or Gp19) [1], as well as some bacterial proteins of unknown function. This entry represents the C-terminal domain. [1]. 20843802. Crystal structure of bacteriophage SPP1 distal tail protein (gp19.1): a baseplate hub paradigm in gram-positive infecting phages. Veesler D, Robin G, Lichiere J, Auzat I, Tavares P, Bron P, Campanacci V, Cambillau C;. J Biol Chem. 2010;285:36666-36673. (from Pfam) NF046371.1 PF22769.1 DCD 27 27 153 domain Y Y N dCTP deaminase domain-containing protein 12756253,15539408,17651436,17996716,18164314 131567 cellular organisms no rank 79568 EBI-EMBL dCTP deaminase-like dCTP deaminase-like This entry represents a dCTP deaminase (DCD) domain found in archaea and bacteria [1-5]. Methanococcus jannaschii, has a bifunctional enzyme DCD-DUT, that harbors both dCTP deaminase and dUTP pyrophosphatase activities [1]. Paper describing PDB structure 1ogh. [1]. 12756253. Structure of the bifunctional dCTP deaminase-dUTPase from Methanocaldococcus jannaschii and its relation to other homotrimeric dUTPases. Johansson E, Bjornberg O, Nyman PO, Larsen S;. J Biol Chem. 2003;278:27916-27922. Paper describing PDB structure 1xs1. [2]. 15539408. Structures of dCTP deaminase from Escherichia coli with bound substrate and product: reaction mechanism and determinants of mono- and bifunctionality for a family of enzymes. Johansson E, Fano M, Bynck JH, Neuhard J, Larsen S, Sigurskjold BW, Christensen U, Willemoes M;. J Biol Chem. 2005;280:3051-3059. Paper describing PDB structure 2j4h. [3]. 17651436. Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP binding to an inactive form of the enzyme. Johansson E, Thymark M, Bynck JH, Fano M, Larsen S, Willemoes M;. FEBS J. 2007;274:4188-4198. Paper describing PDB structure 2qlp. [4]. 18164314. Mechanism of dTTP inhibition of the bifunctional dCTP deaminase:dUTPase encoded by Mycobacterium tuberculosis. Helt SS, Thymark M, Harris P, Aagaard C, Dietrich J, Larsen S, Willemoes M;. J Mol Biol. 2008;376:554-569. Paper describing PDB structure 2v9x. [5]. 17996716. Mutational analysis of the nucleotide binding site of Escherichia coli dCTP deaminase. Thymark M, Johansson E, Larsen S, Willemoes M;. Arch Biochem Biophys. 2008;470:20-26. (from Pfam) NF046381.1 PF22811.1 NrdR-like_N 27.2 27.2 32 domain Y N N Transcriptional repressor NrdR-like, N-terminal domain 35577776 131567 cellular organisms no rank 32393 EBI-EMBL Transcriptional repressor NrdR-like, N-terminal domain Transcriptional repressor NrdR-like, N-terminal domain This entry represents the N-terminal domain of the Transcriptional repressor NrdR and similar sequences, which is a zinc beta-ribbon domain, followed by an ATP-cone domain (Pfam:PF03477) [1]. These proteins negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes. This domain harbors two conserved CxxC motifs that coordinate a zinc ion, and binds to the highly conserved NrdR boxes [1]. [1]. 35577776. A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases. Rozman Grinberg I, Martinez-Carranza M, Bimai O, Nouairia G, Shahid S, Lundin D, Logan DT, Sjoberg BM, Stenmark P;. Nat Commun. 2022;13:2700. (from Pfam) NF046388.1 PF22848.1 ASD1_dom 22.2 22.2 239 domain Y N N Alpha-L-arabinofuranosidase 1 domain 18563919,21796714,22313787,23221536,33524585 131567 cellular organisms no rank 15201 EBI-EMBL Alpha-L-arabinofuranosidase 1 domain Alpha-L-arabinofuranosidase 1 domain This domain is found in Alpha-L-arabinofuranosidase 1 from Arabidopsis thaliana (ASD1), which may be involved in the coordinated dissolution of the cell wall matrix during abscission and in the secondary cell wall formation in xylem vessels. This domain is often found associated to Pfam:PF06964. Paper describing PDB structure 2vrk. [1]. 18563919. The structure of the complex between a branched pentasaccharide and Thermobacillus xylanilyticus GH-51 arabinofuranosidase reveals xylan-binding determinants and induced fit. Paes G, Skov LK, O'Donohue MJ, Remond C, Kastrup JS, Gajhede M, Mirza O;. Biochemistry. 2008;47:7441-7451. Paper describing PDB structure 3s2c. [2]. 21796714. Structure of a novel thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1. Souza TA, Santos CR, Souza AR, Oldiges DP, Ruller R, Prade RA, Squina FM, Murakami MT;. Protein Sci. 2011;20:1632-1637. Paper describing PDB structure 3ug3. [3]. 22313787. Crystal structures of glycoside hydrolase family 51 alpha-L-arabinofuranosidase from Thermotoga maritima. Im DH, Kimura K, Hayasaka F, Tanaka T, Noguchi M, Kobayashi A, Shoda S, Miyazaki K, Wakagi T, Fushinobu S;. Biosci Biotechnol Biochem. 2012;76:423-428. Paper describing PDB structure 4atw. [4]. 23221536. Structural analysis of alpha-L-arabinofuranosidase from Thermotoga maritima reveals characteristics for thermostability and substrate specificity. Dumbrepatil A, Park JM, Jung TY, Song HN, Jang MU, Han NS, Kim TJ, Woo EJ;. J Microbiol Biotechnol. 2012;22:1724-1730. Paper describing PDB structure 6zt6. [5]. 33524585. Probing the determinants of the transglycosylation/hydrolysis. TRUNCATED at 1650 bytes (from Pfam) NF046396.1 PF22888.1 FIMAH 24.8 24.8 81 domain Y Y N FIMAH domain-containing protein 37071393 131567 cellular organisms no rank 6203 EBI-EMBL FIMAH domain FIMAH domain This entry represents a small alpha helical bundle domain found in a large range of different domain architectures. The proteins containing these domains are extracellular enzymes often involved in cell wall processes. The domain is named for (Found In Many Architectures Helical). The precise function of this domain is unknown. This domain is usually found at the C-terminus of the protein. [1]. 37071393. Structural and functional characterization of a multi-domain GH92 alpha-1,2-mannosidase from Neobacillus novalis. Kolaczkowski BM, Moroz OV, Blagova E, Davies GJ, Moller MS, Meyer AS, Westh P, Jensen K, Wilson KS, Krogh KBRM;. Acta Crystallogr D Struct Biol. 2023;79:387-400. (from Pfam) NF046405.1 PF22920.1 UvrC_RNaseH 24.3 24.3 116 domain Y N N UvrC Ribonuclease H-like domain 131567 cellular organisms no rank 85608 EBI-EMBL UvrC Ribonuclease H-like domain UvrC Ribonuclease H-like domain This entry represents an RNaseH-like domain found in the UvrC protein. Nucleotide excision repair (NER) is a conserved DNA repair pathway that enables the repair of chemically and structurally distinct DNA lesions. In prokaryotes, the UvrA, UvrB and UvrC proteins mediate NER in a multistep, ATP-dependent reaction. UvrC catalyses the first incision on the fourth or fifth phosphodiester bond 3' and on the eighth phosphodiester bond 5' from the damage that is to be excised. (from Pfam) NF046439.1 PF21831.1 DUF6891 27 27 189 domain Y Y N DUF6891 domain-containing protein 131567 cellular organisms no rank 5860 EBI-EMBL Domain of unknown function (DUF6891) DUF6891 domain This entry represents a bacterial protein of unknown function. (from Pfam) NF046440.1 PF21836.1 DUF6895 23.8 23.8 289 subfamily Y Y N DUF6895 family protein 131567 cellular organisms no rank 7802 EBI-EMBL Domain of unknown function (DUF6895) DUF6895 family protein This entry contains a set of proteins that have a predicted 6-helical hairpin fold found in a wide range of glycosyl hydrolase enzymes, suggesting a potential function for these proteins. These proteins are largely found in actinobacteria and Alphaproteobacteria. (from Pfam) NF046442.1 PF21838.1 DUF6897 23.9 23.9 58 domain Y Y N DUF6897 domain-containing protein 131567 cellular organisms no rank 404 EBI-EMBL Domain of unknown function (DUF6897) DUF6897 domain This entry represents a family of small bacterial and archaeal proteins that have an SH3 like barrel structure that shows most similarity to the C-terminal domain of the ribosomal chaperone RimP Pfam:PF17384. (from Pfam) NF046445.1 PF21827.1 New_glue 31 31 94 domain Y N N New glue protein family 36005360 131567 cellular organisms no rank 81 EBI-EMBL New glue protein family New glue protein family This entry represents new glue proteins which are mucin-like proteins found in drosophila. [1]. 36005360. Drosophila Glue: A Promising Model for Bioadhesion. Monier M, Courtier-Orgogozo V;. Insects. 2022;13:734. (from Pfam) NF046451.1 PF21863.1 HTH_67 27 27 268 domain Y Y N helix-turn-helix domain-containing protein 131567 cellular organisms no rank 23424 EBI-EMBL Helix-turn-helix family Helix-turn-helix family This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 270 and 293 amino acids in length. These proteins are composed of a large alpha-helical domain which appears to be related to MarR transcription factors. (from Pfam) NF046467.1 PF21939.1 Gp10_C 27 27 139 domain Y Y N phage baseplate protein 16554069,26929357 131567 cellular organisms no rank 3117 EBI-EMBL Baseplate structural protein Gp10, C-terminal domain Baseplate structural protein Gp10, C-terminal domain This entry represents the C-terminal domain (CTD) of baseplate structural protein Gp10 that assembles into trimeric structures. The core structure and assembly of Gp10 has structural similarity to that of the head domain of Gp11 and the receptor binding domain of Gp12 [1]. The monomeric CTD of Gp10 consists of an alpha-helix followed by a three-stranded, antiparallel beta-sheet, which is almost perpendicular to the helix. The three symmetry related beta-sheets interact with their first beta-strands in the trimer, thus creating a flower-like arrangement with the alpha-helices being the flower stem and the three beta-sheets being the petals. Paper describing PDB structure 2fkk. [1]. 16554069. Evolution of bacteriophage tails: Structure of T4 gene product 10. Leiman PG, Shneider MM, Mesyanzhinov VV, Rossmann MG;. J Mol Biol. 2006;358:912-921. Paper describing PDB structure 5hx2. [2]. 26929357. Role of bacteriophage T4 baseplate in regulating assembly and infection. Yap ML, Klose T, Arisaka F, Speir JA, Veesler D, Fokine A, Rossmann MG;. Proc Natl Acad Sci U S A. 2016;113:2654-2659. (from Pfam) NF046470.1 PF21948.1 LplA-B_cat 27 27 200 domain Y Y N lipoyl protein ligase domain-containing protein 16043486,16141198,16384580,16735476,17570395 131567 cellular organisms no rank 109896 EBI-EMBL Lipoyl protein ligase A/B catalytic domain Lipoyl protein ligase A/B catalytic domain This entry represents the catalytic domain of a group of lipoyl ligases/lipoyltransferases, such as Lipoate-protein ligase A/B (LipA/B) from E.coli and mammalian lipoyltransferases [1-5]. These proteins catalyse the transfer of the lipoyl group from lipoyl-AMP to the specific lysine residue of lipoyl domains of lipoate-dependent enzymes. Lipoic acid is an essential cofactor of the alpha-ketoacid dehydrogenase complexes and the glycine cleavage system. Paper describing PDB structure 1w66. [1]. 16735476. The Mycobacterium tuberculosis LipB enzyme functions as a cysteine/lysine dyad acyltransferase. Ma Q, Zhao X, Nasser Eddine A, Geerlof A, Li X, Cronan JE, Kaufmann SH, Wilmanns M;. Proc Natl Acad Sci U S A. 2006;103:8662-8667. Paper describing PDB structure 1x2g. [2]. 16043486. Crystal structure of lipoate-protein ligase A from Escherichia coli. Determination of the lipoic acid-binding site. Fujiwara K, Toma S, Okamura-Ikeda K, Motokawa Y, Nakagawa A, Taniguchi H;. J Biol Chem. 2005;280:33645-33651. Paper describing PDB structure 2ars. [3]. 16141198. Crystal structure of lipoate-protein ligase A bound with the activated intermediate: insights into interaction with lipoyl domains. Kim DJ, Kim KH, Lee HH, Lee SJ, Ha JY, Yoon HJ, Suh SW;. J Biol Chem. 2005;280:38081-38089. Paper describing PDB structure 2c7i. [4]. 16384580. Structure of a putative lipoate protein ligase from Thermoplasma acidophilum and the mechanism of target selection for post-translational modification. McManus E, Luisi BF, Perham RN;. J Mol Biol. 2006;356:625-637. Paper describing PDB structure 2e5a. [5]. 17570395. Crystal structure of bovine lipoyltransfer. TRUNCATED at 1650 bytes (from Pfam) NF046473.1 PF21959.1 DUF6923 27 27 234 domain Y Y N DUF6923 family protein 131567 cellular organisms no rank 6677 EBI-EMBL Repeat of unknown function (DUF6923) DUF6923 multicopy domain This entry represents a beta propeller domain composed of five blades. It is often found in large extracellular proteins in one or more copies. It is uncertain whether this domain might have an enzymatic function or a ligand binding function. Structurally this domain appears to have a sixfold symmetry, but one of the blades takes up the space of normal repeats. This unusual blade is composed of three strands of the first repeat and a final C-terminal strand from the last repeat. (from Pfam) NF046476.1 PF21984.1 DnaD_N 27 27 101 domain Y N N DnaD N-terminal domain 18206906,18703019,22085181 131567 cellular organisms no rank 8929 EBI-EMBL DnaD N-terminal domain DnaD N-terminal domain DnaD is a primosomal protein that remodels supercoiled plasmids. It binds to supercoiled forms and converts them to open forms without nicking. The DnaD N-terminal domain has a scaffold-forming activity. This domain adopts classical winged helix fold decorated with extensions at both termini [1-2]. Paper describing PDB structure 2v79. [1]. 18206906. Structure of the N-terminal oligomerization domain of DnaD reveals a unique tetramerization motif and provides insights into scaffold formation. Schneider S, Zhang W, Soultanas P, Paoli M;. J Mol Biol. 2008;376:1237-1250. Paper describing PDB structure 2vn2. [2]. 18703019. Crystal structure of the N-terminal domain of Geobacillus kaustophilus HTA426 DnaD protein. Huang CY, Chang YW, Chen WT;. Biochem Biophys Res Commun. 2008;375:220-224. Paper describing PDB structure 3tgn. [3]. 22085181. Crystal structure of the zinc-dependent MarR family transcriptional regulator AdcR in the Zn(II)-bound state. Guerra AJ, Dann CE 3rd, Giedroc DP;. J Am Chem Soc. 2011;133:19614-19617. (from Pfam) NF046477.1 PF21986.1 AH_C 27 27 123 domain Y N N Allophanate hydrolase C-terminal domain 23282241,23754281,26249697,29263142 131567 cellular organisms no rank 23609 EBI-EMBL Allophanate hydrolase C-terminal domain Allophanate hydrolase C-terminal domain Allophanate hydrolase (AH) converts allophanate to ammonium and carbon dioxide. The AH structure is composed of N- and C-terminal domains. These domains catalyze sequential reactions: the N-terminal domain converts allophanate to N-carboxycarbamate, whereas the C-terminal domain converts it to carbon dioxide and ammonium [2]. The C-terminal domain folds into alpha/beta structure in which some of the beta-strands form a barrel-like shape. Paper describing PDB structure 4gyr. [1]. 23282241. The structure of allophanate hydrolase from Granulibacter bethesdensis provides insights into substrate specificity in the amidase signature family. Lin Y, St Maurice M;. Biochemistry. 2013;52:690-700. Paper describing PDB structure 4iss. [2]. 23754281. Structure and function of allophanate hydrolase. Fan C, Li Z, Yin H, Xiang S;. J Biol Chem. 2013;288:21422-21432. Paper describing PDB structure 5c5z. [3]. 26249697. Crystal structure analysis of c4763, a uropathogenic Escherichia coli-specific protein. Kim H, Choi J, Kim D, Kim KK;. Acta Crystallogr F Struct Biol Commun. 2015;71:1042-1047. Paper describing PDB structure 5i8i. [4]. 29263142. Structure and function of urea amidolyase. Zhao J, Zhu L, Fan C, Wu Y, Xiang S;. Biosci Rep. 2018; [Epub ahead of print] (from Pfam) NF046480.1 PF21995.1 RNR-II_ins_dom 27 27 107 domain Y N N B12-dependent ribonucleotide reductase, insertion domain 11875520 131567 cellular organisms no rank 2663 EBI-EMBL B12-dependent ribonucleotide reductase, insertion domain B12-dependent ribonucleotide reductase, insertion domain This entry represents the insertion domain of adenosylcobalamin-dependent ribonucleoside-triphosphate reductases (class II RNRs) from Lactococcus leichmannii and related sequences. RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA, a rate-limiting step of DNA biosynthesis. RNRs are classified in class I, II and III [1]. Class II RNRs are less complex and function as a monomer in contrast to class I and III RNRs, which controls substrate specificity as efficiently as a multimeric enzymes. This insertion domain provides the interface responsible for effector binding that, in oligomeric RNRs, is formed in the dimer interface [1]. Paper describing PDB structure 1l1l. [1]. 11875520. The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer. Sintchak MD, Arjara G, Kellogg BA, Stubbe J, Drennan CL;. Nat Struct Biol. 2002;9:293-300. (from Pfam) NF046482.1 PF22007.1 DUF6930 27 27 123 domain Y Y N DUF6930 domain-containing protein 131567 cellular organisms no rank 2187 EBI-EMBL Domain of unknown function (DUF6930) DUF6930 domain This domain is found C-terminal in uncharacterised bacterial proteins. It is remotely related to the integrase core domain with a partly conserved active site architecture. (from Pfam) NF046483.1 PF22008.1 BpuSI_TRD 27 27 241 domain Y N N Restriction endonuclease BpuSI, specificity domain 21724614 131567 cellular organisms no rank 81 EBI-EMBL Restriction endonuclease BpuSI, specificity domain Restriction endonuclease BpuSI, specificity domain This domain is found at the C-terminal end of the restriction endonuclease BpuSI from Bacillus pumilus (Swiss:G1K3S1) and similar bacterial sequences. BpuSI is a Type IIG restriction endonuclease that consists of three functional domains: an N-terminal domain Pfam:PF15516, a N-6 DNA Methylase domain Pfam:PF02384 and a C-terminal specificity domain (TRD, this entry), which includes a final domain with a mixed alpha/beta structure and unknown function [1]. Paper describing PDB structure 3s1s. [1]. 21724614. Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI. Shen BW, Xu D, Chan SH, Zheng Y, Zhu Z, Xu SY, Stoddard BL;. Nucleic Acids Res. 2011;39:8223-8236. (from Pfam) NF046486.1 PF22025.1 ThiI_fer 25 25 72 domain Y N N ThiI ferredoxin-like domain 16343540,17183176,24705700,36833309 131567 cellular organisms no rank 26929 EBI-EMBL ThiI ferredoxin-like domain ThiI ferredoxin-like domain This entry represents the ferredoxin-like domain found at the N-terminal of ThiI proteins (NFLD) [1-3]. ThiI is responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNA. This domain connects the C-terminal catalytic PP-loop pyrophosphatase domain with the THUMP (Pfam:PF02926). NFLD and the THUMP domains jointly form the tRNA-binding surface shaped like a channe which may be of particular importance in ThiI for the correct orientation and distance between residues involved in RNA binding and the active site of the enzyme [2,4]. Paper describing PDB structure 1vbk. [1]. 17183176. Purification, crystallization and preliminary crystallographic analysis of the putative thiamine-biosynthesis protein PH1313 from Pyrococcus horikoshii OT3. Sugahara M, Murai S, Sugahara M, Kunishima N;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007;63:56-58. Paper describing PDB structure 2c5s. [2]. 16343540. Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain. Waterman DG, Ortiz-Lombardia M, Fogg MJ, Koonin EV, Antson AA;. J Mol Biol. 2006;356:97-110. Paper describing PDB structure 4kr6. [3]. 24705700. Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification. Neumann P, Lakomek K, Naumann PT, Erwin WM, Lauhon CT, Ficner R;. Nucleic Acids Res. 2014;42:6673-6685. [4]. 36833309. Transfer RNA Modification Enzymes with a Thiouridine Synthetase, Methyltransferase and Pseudouridine Synthase (THUMP) Domain and the Nucleosides They Produce in tRNA. Hori H;. Genes (Basel). . TRUNCATED at 1650 bytes (from Pfam) NF046503.1 PF22083.1 I-HmuI_NUMOD-like 27 27 46 domain Y N N DNA endonuclease I-HmuI-like, NUMOD-like domain 15313606 131567 cellular organisms no rank 760 EBI-EMBL DNA endonuclease I-HmuI-like, NUMOD-like domain DNA endonuclease I-HmuI-like, NUMOD-like domain This entry represents a C-terminal NUMOD1-like DNA-binding (HTH superfamily) domain present in a set of intron-encoded endonucleases (homing endonucleases) such as I-HmuI from Bacteriophage SP01 and similar proteins [1]. Paper describing PDB structure 1u3e. [1]. 15313606. DNA binding and cleavage by the HNH homing endonuclease I-HmuI. Shen BW, Landthaler M, Shub DA, Stoddard BL;. J Mol Biol. 2004;342:43-56. (from Pfam) NF046505.1 PF22090.1 Gins51_C 27 27 48 domain Y N N Gins51, C-terminal domain 21527023,27599844 131567 cellular organisms no rank 794 EBI-EMBL Gins51, C-terminal domain Gins51, C-terminal domain This domain is found at the C-terminal end of the DNA replication complex GINS family protein TK0536 from Thermococcus kodakarensis (Gins51, Swiss:Q5JF31). This mobile domain acts as a hook to bind the archaeal GINS-associated nuclease to form the 'CGM' unwindosome complex. It shows an alpha-beta configuration [1,2]. Paper describing PDB structure 3anw. [1]. 21527023. Architectures of archaeal GINS complexes, essential DNA replication initiation factors. Oyama T, Ishino S, Fujino S, Ogino H, Shirai T, Mayanagi K, Saito M, Nagasawa N, Ishino Y, Morikawa K;. BMC Biol. 2011;9:28. Paper describing PDB structure 5ghr. [2]. 27599844. Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication. Oyama T, Ishino S, Shirai T, Yamagami T, Nagata M, Ogino H, Kusunoki M, Ishino Y;. Nucleic Acids Res. 2016;44:9505-9517. (from Pfam) NF046516.1 PF22128.1 Alp7A_like_C 22 22 156 domain Y N N Alp7A C-terminal domain 131567 cellular organisms no rank 3010 EBI-EMBL Alp7A C-terminal domain Alp7A C-terminal domain Bacterial Actin-Like Proteins (ALPs) participate in many biologically, clinically and commercially important processes, including segregation of low-copy plasmids. Alp7A is a bacterial actin that functions in plasmid segregation. It is composed of two domains both structurally similar to domains of actin-like ATPases. This entry represents the C-terminal domain. (from Pfam) NF046531.1 PF21891.1 DUF6917 27 27 127 domain Y Y N DUF6917 domain-containing protein 131567 cellular organisms no rank 1061 EBI-EMBL Family of unknown function (DUF6917) DUF6917 domain This family of proteins is found in bacteria. Proteins in this family are typically between 135 and 154 amino acids in length. These proteins share significant sequence similarity to the central part of mammalian cell entry (MCE) protein MlaD. (from Pfam) NF046537.1 PF21906.1 NrtR_WHD 27 27 61 domain Y Y N NrtR DNA-binding winged helix domain-containing protein 19604474,26438537 131567 cellular organisms no rank 43900 EBI-EMBL NrtR DNA-binding winged helix domain NrtR DNA-binding winged helix domain This entry represents the C-terminal DNA-binding domain of bacterial transcriptional regulator NrtR which is involved in regulating the transcription of NAD biosynthetic genes. This domain has a winged helix-turn-helix structure [1]. Paper describing PDB structure 3gz5. [1]. 19604474. Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism. Huang N, De Ingeniis J, Galeazzi L, Mancini C, Korostelev YD, Rakhmaninova AB, Gelfand MS, Rodionov DA, Raffaelli N, Zhang H;. Structure. 2009;17:939-951. Paper describing PDB structure 5bs6. [2]. 26438537. A novel transcriptional regulator of L-arabinose utilization in human gut bacteria. Chang C, Tesar C, Li X, Kim Y, Rodionov DA, Joachimiak A;. Nucleic Acids Res. 2015;43:10546-10559. (from Pfam) NF046541.1 PF21916.1 mtd_2nd 24.6 24.6 115 domain Y N N Mtd second domain 16170324,18532877 131567 cellular organisms no rank 726 EBI-EMBL Mtd second domain Mtd second domain This entry represents the second domain of Mtd. The major tropism determinant (Mtd, 40 kDa), the receptor-binding protein of Bordetella bacteriophage, varies greatly in sequence. Variation in Mtd depends on a phage-encoded retroelement that belongs to a family of retroelements implicated in generating sequence diversity in various phage and bacterial genomes. The second domain forms a beta sandwich structure. Paper describing PDB structure 1yu0. [1]. 16170324. The C-type lectin fold as an evolutionary solution for massive sequence variation. McMahon SA, Miller JL, Lawton JA, Kerkow DE, Hodes A, Marti-Renom MA, Doulatov S, Narayanan E, Sali A, Miller JF, Ghosh P;. Nat Struct Mol Biol. 2005;12:886-892. Paper describing PDB structure 2iou. [2]. 18532877. Selective ligand recognition by a diversity-generating retroelement variable protein. Miller JL, Le Coq J, Hodes A, Barbalat R, Miller JF, Ghosh P;. PLoS Biol. 2008;6:e131. (from Pfam) NF046543.1 PF21918.1 cas_Cpf1_2nd 27 27 225 domain Y N N CRISPR-associated endonuclease Cpf1 REC2 domain 27096363,27114038,27444870,28431230,28562584 131567 cellular organisms no rank 319 EBI-EMBL CRISPR-associated endonuclease Cpf1 REC2 domain CRISPR-associated endonuclease Cpf1 REC2 domain This Pfam entry represents the REC2 domain from the Cpf1 protein, an RNA-guided endonuclease of a type V CRISPR-Cas system that has been harnessed for genome editing. The REC2 domain is a part of the REC lobe of the bilobed architecture of Cpf1, which consists of both REC1 and REC2 domains. The REC2 domain comprises 10 alpha helices and 2 beta strands that form a small antiparallel sheet. The crRNA-target DNA heteroduplex is accommodated within the positively charged, central channel formed by the REC1, REC2, and RuvC domains, and is recognized by the protein in a sequence-independent manner. Paper describing PDB structure 5b43. [1]. 27114038. Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA. Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O;. Cell. 2016;165:949-962. Paper describing PDB structure 5id6. [2]. 27096363. The crystal structure of Cpf1 in complex with CRISPR RNA. Dong D, Ren K, Qiu X, Zheng J, Guo M, Guan X, Liu H, Li N, Zhang B, Yang D, Ma C, Wang S, Wu D, Ma Y, Fan S, Wang J, Gao N, Huang Z;. Nature. 2016;532:522-526. Paper describing PDB structure 5kk5. [3]. 27444870. Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition. Gao P, Yang H, Rajashankar KR, Huang Z, Patel DJ;. Cell Res. 2016;26:901-913. Paper describing PDB structure 5mga. [4]. 28562584. Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage. Stella S, Alcon P, Montoya G;. Nature. 2017;546:559-563. Paper describing PDB structure 5nfv. [5]. 28431230. Structural Basis for. TRUNCATED at 1650 bytes (from Pfam) NF046551.1 PF21941.1 SMEK_N 27 27 140 domain Y N N SMEK domain 131567 cellular organisms no rank 3361 EBI-EMBL SMEK domain SMEK domain This entry represents the SMEK domain, which is found at the N-terminal end of a group of bacterial proteins. It is named after four genera in which multiple, diverse members of this group of bacterial proteins are found: Staphylococcus, Mycoplasma, Escherichia, and Klebsiella. The SMEK domain is predicted to adopt an alpha/beta fold that resembles the core of restriction endonuclease enzymes. It contains four scattered invariant residues (Glu, Asp, Gln, and Lys) that may be functionally relevant. (from Pfam) NF046556.1 PF21969.1 MGS_GT 27 27 239 domain Y N N Mannosylglycerate synthase, GT domain 15951819,21288903 131567 cellular organisms no rank 104 EBI-EMBL Mannosylglycerate synthase, GT domain Mannosylglycerate synthase, GT domain Mannosylglycerate synthase catalyses the formation of the stress protectant 2-O-alpha-D-mannosyl glycerate [1]. It consists of a GT-like domain at the N-terminal and a C-terminal helical domain [1]. This entry represents the N-terminal glycosyltransferase domain (GT) which, at the sequence level, is most similar to family-GT2 inverting GTs, however, MGS is a retaining GT [1,2]. Paper describing PDB structure 2bo4. [1]. 15951819. Structural dissection and high-throughput screening of mannosylglycerate synthase. Flint J, Taylor E, Yang M, Bolam DN, Tailford LE, Martinez-Fleites C, Dodson EJ, Davis BG, Gilbert HJ, Davies GJ;. Nat Struct Mol Biol. 2005;12:608-614. Paper describing PDB structure 2y4j. [2]. 21288903. Substrate and metal ion promiscuity in mannosylglycerate synthase. Nielsen MM, Suits MD, Yang M, Barry CS, Martinez-Fleites C, Tailford LE, Flint JE, Dumon C, Davis BG, Gilbert HJ, Davies GJ;. J Biol Chem. 2011;286:15155-15164. (from Pfam) NF046558.1 PF21973.1 DUF6925 27 27 300 subfamily Y Y N DUF6925 family protein 131567 cellular organisms no rank 1094 EBI-EMBL Family of unknown function (DUF6925) DUF6925 family protein This is a family of uncharacterised bacterial proteins. They are probably distantly related to heme-binding proteins PhuS, ChuS, HmuS. (from Pfam) NF046562.1 PF21979.1 Hfq_1 27 27 61 domain Y Y N Hfq-like protein GO:0003723 19777643,31076551 131567 cellular organisms no rank 2401 EBI-EMBL Hfq related Hfq-like protein Hfq proteins participate in RNA folding and translational regulation through pairing of small RNAs and messenger RNAs. Hfq proteins share the distinctive Sm fold, and form ring-shaped structures similar to those of the Sm/Lsm proteins regulating mRNA turnover in eukaryotes [1-2]. Paper describing PDB structure 3hfn. [1]. 19777643. Cyanobacteria contain a structural homologue of the Hfq protein with altered RNA-binding properties. Boggild A, Overgaard M, Valentin-Hansen P, Brodersen DE;. FEBS J. 2009;276:3904-3915. Paper describing PDB structure 6gwk. [2]. 31076551. Caulobacter crescentus Hfq structure reveals a conserved mechanism of RNA annealing regulation. Santiago-Frangos A, Frohlich KS, Jeliazkov JR, Malecka EM, Marino G, Gray JJ, Luisi BF, Woodson SA, Hardwick SW;. Proc Natl Acad Sci U S A. 2019;116:10978-10987. (from Pfam) NF046564.1 PF21992.1 DUF6927 27 27 74 domain Y Y N DUF6927 domain-containing protein 131567 cellular organisms no rank 1109 EBI-EMBL Domain of unknown function (DUF6927) DUF6927 domain This domain is found C-terminal in uncharacterised bacterial proteins. It is probably remotely related to PemK-like, MazF-like toxins and is predicted to adopt SH3-like fold. (from Pfam) NF046565.1 PF21994.1 AGAO-like_N2 27.4 27.4 76 domain Y N N AGAO-like N2 domain 12134140,14979714,15533431,18607080,9405045 131567 cellular organisms no rank 8946 EBI-EMBL AGAO-like N2 domain AGAO-like N2 domain This entry represents the first N-terminal domain (N2) of a group of copper amine oxidases, including PAOX from Arthrobacter globiformis (Swiss:P46881, also known as AGAO) [1-5]. Paper describing PDB structure 1av4. [1]. 9405045. Crystal structures of the copper-containing amine oxidase from Arthrobacter globiformis in the holo and apo forms: implications for the biogenesis of topaquinone. Wilce MC, Dooley DM, Freeman HC, Guss JM, Matsunami H, McIntire WS, Ruggiero CE, Tanizawa K, Yamaguchi H;. Biochemistry. 1997;36:16116-16133. Paper describing PDB structure 1ivv. [2]. 12134140. X-ray snapshots of quinone cofactor biogenesis in bacterial copper amine oxidase. Kim M, Okajima T, Kishishita S, Yoshimura M, Kawamori A, Tanizawa K, Yamaguchi H;. Nat Struct Biol. 2002;9:591-596. Paper describing PDB structure 1rjo. [3]. 15533431. Using xenon as a probe for dioxygen-binding sites in copper amine oxidases. Duff AP, Trambaiolo DM, Cohen AE, Ellis PJ, Juda GA, Shepard EM, Langley DB, Dooley DM, Freeman HC, Guss JM;. J Mol Biol. 2004;344:599-607. Paper describing PDB structure 1ui7. [4]. 14979714. Chemical rescue of a site-specific mutant of bacterial copper amine oxidase for generation of the topa quinone cofactor. Matsunami H, Okajima T, Hirota S, Yamaguchi H, Hori H, Kuroda S, Tanizawa K;. Biochemistry. 2004;43:2178-2187. Paper describing PDB structure 1w5z. [5]. 18607080. Complexes of the copper-containing amine oxidase from Arthrobacter globiformis with the inhibitors benzylhydrazine and tranylcypromine. Langley DB, Trambaiolo DM, Duff AP, Dooley DM, Freeman HC, Guss JM;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008;6. TRUNCATED at 1650 bytes (from Pfam) NF046567.1 PF22019.1 GlgB_N 27 27 94 domain Y Y N GlgB N-terminal domain-containing protein 12196524,20444687,26280198,27139627,28193843 131567 cellular organisms no rank 56041 EBI-EMBL alpha-1,4-glucan branching enzyme GlgB, N-terminal domain alpha-1,4-glucan branching enzyme GlgB, N-terminal domain This is the N-terminal beta-sandwich domain of alpha-1,4-glucan branching enzyme GlgB and related proteins. This domain has a differential preference in substrate recognition and binding during amylase activity, when amylose is used as a substrate [2]. Paper describing PDB structure 1m7x. [1]. 12196524. The X-ray crystallographic structure of Escherichia coli branching enzyme. Abad MC, Binderup K, Rios-Steiner J, Arni RK, Preiss J, Geiger JH;. J Biol Chem. 2002;277:42164-42170. Paper describing PDB structure 3k1d. [2]. 20444687. Crystal structure of full-length Mycobacterium tuberculosis H37Rv glycogen branching enzyme: insights of N-terminal beta-sandwich in substrate specificity and enzymatic activity. Pal K, Kumar S, Sharma S, Garg SK, Alam MS, Xu HE, Agrawal P, Swaminathan K;. J Biol Chem. 2010;285:20897-20903. Paper describing PDB structure 4lpc. [3]. 26280198. Crystal Structures of Escherichia coli Branching Enzyme in Complex with Linear Oligosaccharides. Feng L, Fawaz R, Hovde S, Gilbert L, Chiou J, Geiger JH;. Biochemistry. 2015;54:6207-6218. Paper describing PDB structure 5e6y. [4]. 27139627. Crystal structures of Escherichia coli branching enzyme in complex with cyclodextrins. Feng L, Fawaz R, Hovde S, Sheng F, Nosrati M, Geiger JH;. Acta Crystallogr D Struct Biol. 2016;72:641-647. Paper describing PDB structure 5gqu. [5]. 28193843. Bound Substrate in the Structure of Cyanobacterial Branching Enzyme Supports a New Mechanistic Model. Hayashi M, Suzuki R, Colleoni C, Ball SG, Fujita N, Suzuki E;. J Biol Chem. 2017;292:5465-5475. (from Pfam) NF046568.1 PF22020.1 RlmL_1st 27 27 55 domain Y N N RlmL ferredoxin-like domain 22362734 131567 cellular organisms no rank 48674 EBI-EMBL RlmL ferredoxin-like domain RlmL ferredoxin-like domain This entry represents the ferredoxin-like domain found at the N-terminal of RmlL, referred to as NFLD domain usually fused to the THUMP domain [1]. Ribosomal RNA large subunit methyltransferase K/L from E.coli (also known as YcbY) specifically methylates the guanine in positions 2445 and 2069 of 23S rRNA before its assembly into 50S subunits [1]. Paper describing PDB structure 3v8v. [1]. 22362734. Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA. Wang KT, Desmolaize B, Nan J, Zhang XW, Li LF, Douthwaite S, Su XD;. Nucleic Acids Res. 2012;40:5138-5148. (from Pfam) NF046570.1 PF22023.1 Pus10_THUMP_arc 28 28 78 domain Y N N Pus10 THUMP domain, archaeal 18952823,29349599,36833309 131567 cellular organisms no rank 1533 EBI-EMBL Pus10 THUMP domain, archaeal Pus10 THUMP domain, archaeal This entry represents the THUMP domain found in Pus10 proteins from archaea. Pus10 is a tRNA pseudouridine synthase responsible for the synthesis of pseudouridine from uracil-54 and uracil-55 in the psi GC loop of transfer RNAs [1,2]. [1]. 18952823. Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA. Gurha P, Gupta R;. RNA. 2008;14:2521-2527. [2]. 36833309. Transfer RNA Modification Enzymes with a Thiouridine Synthetase, Methyltransferase and Pseudouridine Synthase (THUMP) Domain and the Nucleosides They Produce in tRNA. Hori H;. Genes (Basel). 2023;14:382. [3]. 29349599. Evolution of Eukaryal and Archaeal Pseudouridine Synthase Pus10. Fitzek E, Joardar A, Gupta R, Geisler M;. J Mol Evol. 2018;86:77-89. (from Pfam) NF046571.1 PF22026.1 Alpha-amylase_C_2 27 27 78 domain Y N N Alpha-amylase C-terminal domain 10222200,11226882,11330677,11527532,15138257 131567 cellular organisms no rank 5232 EBI-EMBL Alpha-amylase C-terminal domain Alpha-amylase C-terminal domain This is the C-terminal domain of alpha-amylase and related enzymes. This domain follows the catalytic beta/alpha domain. It folds into a beta-sandwich with a greek key topology. Paper describing PDB structure 1bvz. [1]. 10222200. Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution. Kamitori S, Kondo S, Okuyama K, Yokota T, Shimura Y, Tonozuka T, Sakano Y;. J Mol Biol 1999;287:907-921. Paper describing PDB structure 1g1y. [2]. 11226882. Studies on the hydrolyzing mechanism for cyclodextrins of Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structure of the mutant E354A complexed with beta-cyclodextrin, and kinetic analyses on cyclodextrins. Kondo S, Ohtaki A, Tonozuka T, Sakano Y, Kamitori S;. J Biochem. 2001;129:423-428. Paper describing PDB structure 1jf5. [3]. 11527532. Role of Phe286 in the recognition mechanism of cyclomaltooligosaccharides (cyclodextrins) by Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structures of the mutant TVAIIs, F286A and F286Y, and kinetic analyses of the Phe286-replaced mutant TVAIIs. Ohtaki A, Kondo S, Shimura Y, Tonozuka T, Sakano Y, Kamitori S;. Carbohydr Res. 2001;334:309-313. Paper describing PDB structure 1jib. [4]. 11330677. Structures of Thermoactinomyces vulgaris R-47 alpha-amylase II complexed with substrate analogues. Yokota T, Tonozuka T, Shimura Y, Ichikawa K, Kamitori S, Sakano Y;. Biosci Biotechnol Biochem. 2001;65:619-626. Paper describing PDB structure 1vfm. [5]. 15138257. Complex structures of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with acarbose and . TRUNCATED at 1650 bytes (from Pfam) NF046578.1 PF22053.1 DUF6938 27 27 236 domain Y Y N DUF6938 domain-containing protein 131567 cellular organisms no rank 504 EBI-EMBL Domain of unknown function (DUF6938) DUF6938 domain This domain is found C-terminal in a family of uncharacterised bacterial proteins. This domain has a significant sequence similarity to the C-terminal domains of a number of proteins members of UDP-Glycosyltransferase/glycogen phosphorylase superfamily. It is predicted to adopt the same alpha/beta structure. (from Pfam) NF046580.1 PF22059.1 GumK_N 27 27 171 domain Y N N Glucuronosyltransferase GumK, N-terminal domain 18596046 131567 cellular organisms no rank 1079 EBI-EMBL Glucuronosyltransferase GumK, N-terminal domain Glucuronosyltransferase GumK, N-terminal domain Beta-1,2-glucuronosyltransferase GumK is a membrane- associated protein that is involved in the biosynthesis of xanthan. The GumK enzyme is the founding member of the glycosyltransferase family 70 of carbohydrate-active enzymes, which is composed of bacterial glycosyltransferases involved in exopolysaccharide synthesis. This protein consists of two domains, N-terminal of which is represented by this entry [1]. Paper describing PDB structure 2hy7. [1]. 18596046. Structure and mechanism of GumK, a membrane-associated glucuronosyltransferase. Barreras M, Salinas SR, Abdian PL, Kampel MA, Ielpi L;. J Biol Chem. 2008;283:25027-25035. (from Pfam) NF046588.1 PF22082.1 TtuA_LIM_N 27 27 26 domain Y N N 2-thiouridine synthetase TtuA, N-terminal LIM domain 28439027 131567 cellular organisms no rank 2064 EBI-EMBL 2-thiouridine synthetase TtuA, N-terminal LIM domain 2-thiouridine synthetase TtuA, N-terminal LIM domain TtuA is an oxygen-labile iron-sulfur protein that is involved in a post-transcriptional thiolation of RNA. The iron-sulfur cluster of TtuA is required for sulfurtransferase activity. The enzyme structure consists of three domains: a central catalytic domain and two Zn-fingers [1]. This entry represents the N-terminal Zn-finger domain that share a significant similarity to LIM domains. Paper describing PDB structure 5b4e. [1]. 28439027. Biochemical and structural characterization of oxygen-sensitive 2-thiouridine synthesis catalyzed by an iron-sulfur protein TtuA. Chen M, Asai SI, Narai S, Nambu S, Omura N, Sakaguchi Y, Suzuki T, Ikeda-Saito M, Watanabe K, Yao M, Shigi N, Tanaka Y;. Proc Natl Acad Sci U S A. 2017;114:4954-4959. (from Pfam) NF046604.1 PF22157.1 SupH-like_C 27 27 58 domain Y N N Sucrose hydrolase-like, C-terminal domain 19966417 131567 cellular organisms no rank 5950 EBI-EMBL Sucrose hydrolase-like, C-terminal domain Sucrose hydrolase-like, C-terminal domain This domain is found at the C-terminal end of Sucrose hydrolase from Xanthomonas campestris (SupH, Swiss:Q6UVM5) and similar bacterial sequences. SupH shows a central domain that consists of an eight-stranded alpha/beta barrel (Pfam:PF00128). This beta-stranded domain is located on a side of the barrel fold [1]. Paper describing PDB structure 2wpg. [1]. 19966417. The apo structure of sucrose hydrolase from Xanthomonas campestris pv. campestris shows an open active-site groove. Champion E, Remaud-Simeon M, Skov LK, Kastrup JS, Gajhede M, Mirza O;. Acta Crystallogr D Biol Crystallogr. 2009;65:1309-1314. (from Pfam) NF046609.1 PF22173.1 APH-like_N 27 27 273 domain Y N N Acylamino-acid-releasing enzyme-like, N-terminal domain 15296741,17350041,18325786,21084296,25760596 131567 cellular organisms no rank 36 EBI-EMBL Acylamino-acid-releasing enzyme-like, N-terminal domain Acylamino-acid-releasing enzyme-like, N-terminal domain This domain is found at the N-terminal end of Acylamino-acid -releasing enzyme from Aeropyrum pernix (APH) and similar archaeal sequences. APH catalyses the removal of an N-acylated amino acid from peptides. This domain folds as a regular seven-bladed beta-propeller [1,2]. Paper describing PDB structure 1ve6. [1]. 15296741. Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1. Bartlam M, Wang G, Yang H, Gao R, Zhao X, Xie G, Cao S, Feng Y, Rao Z;. Structure. 2004;12:1481-1488. Paper describing PDB structure 2hu8. [2]. 17350041. The acylaminoacyl peptidase from Aeropyrum pernix K1 thought to be an exopeptidase displays endopeptidase activity. Kiss AL, Hornung B, Radi K, Gengeliczki Z, Sztaray B, Juhasz T, Szeltner Z, Harmat V, Polgar L;. J Mol Biol. 2007;368:509-520. Paper describing PDB structure 2qr5. [3]. 18325786. Structural and kinetic contributions of the oxyanion binding site to the catalytic activity of acylaminoacyl peptidase. Kiss AL, Pallo A, Naray-Szabo G, Harmat V, Polgar L;. J Struct Biol. 2008;162:312-323. Paper describing PDB structure 3o4h. [4]. 21084296. Structure and catalysis of acylaminoacyl peptidase: closed and open subunits of a dimer oligopeptidase. Harmat V, Domokos K, Menyhard DK, Pallo A, Szeltner Z, Szamosi I, Beke-Somfai T, Naray-Szabo G, Polgar L;. J Biol Chem. 2011;286:1987-1998. Paper describing PDB structure 4re5. [5]. 25760596. Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality. Menyhard DK, Orgovan Z, Szeltner Z, Szamosi I, Harmat V;. Acta Crys. TRUNCATED at 1650 bytes (from Pfam) NF046610.1 PF22175.1 Ogg-HhH 27 27 173 domain Y N N 8-oxoguanine DNA glycosylase 14517230,19446526,20083120 131567 cellular organisms no rank 2771 EBI-EMBL 8-oxoguanine DNA glycosylase 8-oxoguanine DNA glycosylase This entry represents 8-oxoguanine DNA glycosylases (Ogg) that are responsible for the recognition and excision of one of the most common DNA oxidative product, 7,8-dihydro-8-oxoguanine (8-oxoG). These enzymes share a common all-alpha architecture build around a central HhH motif [2]. Paper describing PDB structure 1pu6. [1]. 14517230. Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases. Eichman BF, O'Rourke EJ, Radicella JP, Ellenberger T;. EMBO J. 2003;22:4898-4909. Paper describing PDB structure 3fhf. [2]. 19446526. Crystal structures of two archaeal 8-oxoguanine DNA glycosylases provide structural insight into guanine/8-oxoguanine distinction. Faucher F, Duclos S, Bandaru V, Wallace SS, Doublie S;. Structure. 2009;17:703-712. Paper describing PDB structure 3knt. [3]. 20083120. The C-terminal lysine of Ogg2 DNA glycosylases is a major molecular determinant for guanine/8-oxoguanine distinction. Faucher F, Wallace SS, Doublie S;. J Mol Biol. 2010;397:46-56. (from Pfam) NF046616.1 PF22194.1 F-93_WHD 28 28 62 domain Y N N F-93, winged-helix domain 15479795 131567 cellular organisms no rank 226 EBI-EMBL F-93, winged-helix domain F-93, winged-helix domain This entry represents a WH-like domain (PDB: 1tbx) found in a putative transcription factor called F-93 from Sulfolobus spindle-shaped viruses (SSVs) (Swiss:P20222) [1]. Members of this family appear to be related to MarR (Pfam:PF01047) and PadR (Pfam:PF03551) families of prokaryotic transcription factors. Paper describing PDB structure 1tbx. [1]. 15479795. Crystal structure of F-93 from Sulfolobus spindle-shaped virus 1, a winged-helix DNA binding protein. Kraft P, Oeckinghaus A, Kummel D, Gauss GH, Gilmore J, Wiedenheft B, Young M, Lawrence CM;. J Virol. 2004;78:11544-11550. (from Pfam) NF046640.1 PF22337.1 Phage_fiber_rpt 27 15 34 domain Y N N Phage tail fiber repeats 131567 cellular organisms no rank 1269 EBI-EMBL Phage tail fiber repeats Phage tail fiber repeats This entry represents a beta solenoid repeat found in phage tail proteins from tailed bacteriophages and prophages mainly found in flavobacteria. (from Pfam) NF046642.1 PF22353.1 PF1197-like_C 27 27 50 domain Y N N NAD(P)H:rubredoxin oxidoreductase, C-terminal domain 131567 cellular organisms no rank 79 EBI-EMBL NAD(P)H:rubredoxin oxidoreductase, C-terminal domain NAD(P)H:rubredoxin oxidoreductase, C-terminal domain This domain is found at the C-terminal end of NAD(P)H:rubredoxin oxidoreductase from Pyrococcus furiosus (PF1197) and similar sequences mainly found in archaea. PF1197 catalyses the NADH -dependent reduction of rubredoxin (Rd), a small iron -containing redox protein. This domain, likely to be involved in dimerisation, is often found associated with Pfam:PF07992. (from Pfam) NF046646.1 PF22366.1 NDH2_C 27.7 27.7 62 domain Y N N NDH2 C-terminal domain 15590775,24709059,28195463 131567 cellular organisms no rank 15573 EBI-EMBL NDH2 C-terminal domain NDH2 C-terminal domain This entry represent the C-terminal domain of alternative NADH:quinone oxidoreductases known as NDH2 that deliver electrons to the respiratory chain by oxidation of NADH and reduction of quinones but does not pump protons. NDH-2 have particular relevance in yeasts like Saccharomyces cerevisiae and in several prokaryotes, whose respiratory chains are devoid of complex I, in which NDH-2 keep the balance and are the main entry point of electrons into the respiratory chains [2]. NDH2 proteins are found in bacteria, certain plant, fungal and protozoan mitochondria, but not in mammals, they have been used as a drug target for Mycoplasma tuberculosis, Plasmodium falciparum and Toxoplasma gondii [1,3]. [1]. 28195463. Target Elucidation by Cocrystal Structures of NADH-Ubiquinone Oxidoreductase of Plasmodium falciparum (PfNDH2) with Small Molecule To Eliminate Drug-Resistant Malaria. Yang Y, Yu Y, Li X, Li J, Wu Y, Yu J, Ge J, Huang Z, Jiang L, Rao Y, Yang M;. J Med Chem. 2017;60:1994-2005. [2]. 15590775. New insights into type II NAD(P)H:quinone oxidoreductases. Melo AM, Bandeiras TM, Teixeira M;. Microbiol Mol Biol Rev. 2004;68:603-616. [3]. 24709059. Characterization of the type 2 NADH:menaquinone oxidoreductases from Staphylococcus aureus and the bactericidal action of phenothiazines. Schurig-Briccio LA, Yano T, Rubin H, Gennis RB;. Biochim Biophys Acta. 2014;1837:954-963. (from Pfam) NF046668.1 PF22451.1 NirdL-like_HTH 27 27 47 domain Y N N Siroheme decarboxylase NirDL-like HTH domain 11230123,14976242,19004003,21338611,25083922 131567 cellular organisms no rank 17907 EBI-EMBL Siroheme decarboxylase NirDL-like HTH domain Siroheme decarboxylase NirDL-like HTH domain This entry represents the HTH domains found in siroheme decarboxylase NirdL from Hydrogenobacter thermophilus and related sequences [5]. NirdL is involved in heme d1 biosynthesis. It catalyses the decarboxylation of siroheme into didecarboxysiroheme. Paper describing PDB structure 1i1g. [1]. 11230123. Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus. Leonard PM, Smits SH, Sedelnikova SE, Brinkman AB, de Vos WM, van der Oost J, Rice DW, Rafferty JB;. EMBO J. 2001;20:990-997. Paper describing PDB structure 1ri7. [2]. 14976242. The archaeal feast/famine regulatory protein: potential roles of its assembly forms for regulating transcription. Koike H, Ishijima SA, Clowney L, Suzuki M;. Proc Natl Acad Sci U S A. 2004;101:2840-2845. Paper describing PDB structure 2l4a. [3]. 21338611. The design involved in PapI and Lrp regulation of the pap operon. Kawamura T, Vartanian AS, Zhou H, Dahlquist FW;. J Mol Biol. 2011;409:311-332. Paper describing PDB structure 2zny. [4]. 19004003. Interactions between the archaeal transcription repressor FL11 and its coregulators lysine and arginine. Yamada M, Ishijima SA, Suzuki M;. Proteins. 2009;74:520-525. Paper describing PDB structure 4ch7. [5]. 25083922. The crystal structure of siroheme decarboxylase in complex with iron-uroporphyrin III reveals two essential histidine residues. Haufschildt K, Schmelz S, Kriegler TM, Neumann A, Streif J, Arai H, Heinz DW, Layer G;. J Mol Biol. 2014;426:3272-3286. (from Pfam) NF046672.1 PF22461.1 SLBB_2 27 27 79 domain Y N N SLBB domain 16469879,17086202,17250770,19294709,27509854,27595392 131567 cellular organisms no rank 87189 EBI-EMBL SLBB domain SLBB domain This entry represents a set of SLBB domains [5]. Paper describing PDB structure 2fug. [1]. 16469879. Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. Sazanov LA, Hinchliffe P;. Science. 2006;311:1430-1436. Paper describing PDB structure 2j58. [2]. 17086202. Wza the translocon for E. coli capsular polysaccharides defines a new class of membrane protein. Dong C, Beis K, Nesper J, Brunkan-Lamontagne AL, Clarke BR, Whitfield C, Naismith JH;. Nature. 2006;444:226-229. Paper describing PDB structure 2w8h. [3]. 19294709. PELDOR spectroscopy distance fingerprinting of the octameric outer-membrane protein Wza from Escherichia coli. Hagelueken G, Ingledew WJ, Huang H, Petrovic-Stojanovska B, Whitfield C, ElMkami H, Schiemann O, Naismith JH;. Angew Chem Int Ed Engl. 2009;48:2904-2906. Paper describing PDB structure 5lc5. [4]. 27509854. Structure of mammalian respiratory complex I. Zhu J, Vinothkumar KR, Hirst J;. Nature. 2016;536:354-358. Paper describing PDB structure 5lnk. [5]. 27595392. Atomic structure of the entire mammalian mitochondrial complex I. Fiedorczuk K, Letts JA, Degliesposti G, Kaszuba K, Skehel M, Sazanov LA;. Nature. 2016;538:406-410. [5]. 17250770. A novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands. Burroughs AM, Balaji S, Iyer LM, Aravind L;. Biol Direct. 2007;2:4-4. (from Pfam) NF046682.1 PF22166.1 ArnR1-like_WHD 26 26 90 domain Y N N ArnR1-like, winged-helix domain 23461567,30828487 131567 cellular organisms no rank 14 EBI-EMBL ArnR1-like, winged-helix domain ArnR1-like, winged-helix domain This entry represents a WH-like domain present in ArnR1-like proteins (PDB:2pg4). ArnR1-like transcription factors have been implicated in regulating the expression of components found in both the archaeal adhesive pilus and UV-inducible pili systems [1,2]. [1]. 30828487. Two membrane-bound transcription factors regulate expression of various type-IV-pili surface structures in Sulfolobus acidocaldarius. Bischof LF, Haurat MF, Albers SV;. PeerJ. 2019;7:e6459. [2]. 23461567. The one-component system ArnR: a membrane-bound activator of the crenarchaeal archaellum. Lassak K, Peeters E, Wrobel S, Albers SV;. Mol Microbiol. 2013;88:125-139. (from Pfam) NF046683.1 PF22168.1 DIP2311-like_C 27 27 63 domain Y N N Transcriptional regulator DIP2311-like, C-terminal domain 131567 cellular organisms no rank 746 EBI-EMBL Transcriptional regulator DIP2311-like, C-terminal domain Transcriptional regulator DIP2311-like, C-terminal domain This domain is found at the C-terminal end of Transcriptional regulator DIP2311 from Corynebacterium diphtheriae (Swiss:Q6NEG3) and similar bacterial sequences. This domain, which shows a winged helix fold, is normally found associated to Pfam:PF04326. (from Pfam) NF046686.1 PF22180.1 RH3_dom 27 27 66 domain Y N N RH3 domain 22409376 131567 cellular organisms no rank 10 EBI-EMBL RH3 domain RH3 domain This domain family includes ORF E73 from Sulfolobus virus. This domain, called RH3 domain, show great similarity to domains found in proteins involved in transcriptional regulation, but with an additional third helix [1]. Paper describing PDB structure 4aai. [1]. 22409376. Structural studies of E73 from a hyperthermophilic archaeal virus identify the "RH3" domain, an elaborated ribbon-helix-helix motif involved in DNA recognition. Schlenker C, Goel A, Tripet BP, Menon S, Willi T, Dlakic M, Young MJ, Lawrence CM, Copie V;. Biochemistry. 2012;51:2899-2910. (from Pfam) NF046688.1 PF22184.1 CBM_56 27 27 75 domain Y N N Carbohydrate binding module family 56 28787048,28827308 131567 cellular organisms no rank 2685 EBI-EMBL Carbohydrate binding module family 56 Carbohydrate binding module family 56 CBM56 is a carbohydrate-binding module found in beta-1,3-glucanase, that binds to soluble beta-1,3-glucan laminarin and it is proposed to bind to quaternary polysaccharide structures, most likely to triple helix formed by polymerised beta-1,3-glucans. This domain adopts a typical Ig-like beta-sandwich [1-2]. Paper describing PDB structure 5h9x. [1]. 28787048. The recognition mechanism of triple-helical beta-1,3-glucan by a beta-1,3-glucanase. Qin Z, Yang D, You X, Liu Y, Hu S, Yan Q, Yang S, Jiang Z;. Chem Commun (Camb). 2017;53:9368-9371. Paper describing PDB structure 5t7a. [2]. 28827308. Properties of a family 56 carbohydrate-binding module and its role in the recognition and hydrolysis of beta-1,3-glucan. Hettle A, Fillo A, Abe K, Massel P, Pluvinage B, Langelaan DN, Smith SP, Boraston AB;. J Biol Chem. 2017;292:16955-16968. (from Pfam) NF046693.1 PF22201.1 FlaF_Ig-like 28.4 28.4 112 domain Y N N Conserved flagellar protein F, immunoglobulin-like domain 25865246,31844299 131567 cellular organisms no rank 37 EBI-EMBL Conserved flagellar protein F, immunoglobulin-like domain Conserved flagellar protein F, immunoglobulin-like domain This domain is found in Conserved flagellar protein F from Sulfolobus acidocaldarius (FlaF, Swiss:Q4J9K8) and similar archaeal proteins. FlaF is essential for archaellum assembly with an extended N-terminal alpha-helix connected to a globular domain (this entry). This domain adopts a beta-sandwich fold with eight anti-parallel beta-strands in two sheets [1,2]. Paper describing PDB structure 4p94. [1]. 25865246. FlaF Is a beta-Sandwich Protein that Anchors the Archaellum in the Archaeal Cell Envelope by Binding the S-Layer Protein. Banerjee A, Tsai CL, Chaudhury P, Tripp P, Arvai AS, Ishida JP, Tainer JA, Albers SV;. Structure. 2015;23:863-872. Paper describing PDB structure 5tug. [2]. 31844299. The structure of the periplasmic FlaG-FlaF complex and its essential role for archaellar swimming motility. Tsai CL, Tripp P, Sivabalasarma S, Zhang C, Rodriguez-Franco M, Wipfler RL, Chaudhury P, Banerjee A, Beeby M, Whitaker RJ, Tainer JA, Albers SV;. Nat Microbiol. 2020;5:216-225. (from Pfam) NF046705.1 PF22230.1 Csx1_CARF 24.7 24.7 163 domain Y N N CRISPR system endoribonuclease Csx1, CARF domain 16292354,26647461,26763118 131567 cellular organisms no rank 336 EBI-EMBL CRISPR system endoribonuclease Csx1, CARF domain CRISPR system endoribonuclease Csx1, CARF domain CRISPR system endoribonuclease Csx1 is a metal-independent, endoribonuclease that acts selectively on ssRNA and cleaves specifically after adenosines, as part of the type III-B CRISP-Cas system and it is homologous to Csm6 [1-3], sharing the same domain domain architecture consisting of a CARF domain at the N-terminal that is relatively well conserved, and a HEPN nuclease domain at the C-terminal. This entry represents the CARF (CRISPR-associated Rossmann fold) domain, which binds and cleaves the cyclic oligoadenylate molecule (cA) that then activates the HEPN domain. [1]. 16292354. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. Haft DH, Selengut J, Mongodin EF, Nelson KE;. PLoS Comput Biol. 2005;1:e60. [2]. 26647461. The CRISPR-associated Csx1 protein of Pyrococcus furiosus is an adenosine-specific endoribonuclease. Sheppard NF, Glover CV 3rd, Terns RM, Terns MP;. RNA. 2016;22:216-224. [3]. 26763118. Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6. Niewoehner O, Jinek M;. RNA. 2016;22:318-329. (from Pfam) NF046709.1 PF22237.2 SO2946-like_C 27 27 163 domain Y N N SO2946-like, C-terminal domain 18566914 131567 cellular organisms no rank 48 EBI-EMBL SO2946-like, C-terminal domain SO2946-like, C-terminal domain This entry represents the C-terminal domain of SO2946 from Shewanella oneidensis MR-1. The SO2946 protein consists of a short helical N-terminal domain and a large C-terminal domain with the jelly-roll topology, identified as a putative carbohydrate-binding module [1]. Paper describing PDB structure 2a5z. [1]. 18566914. Structure of SO2946 orphan from Shewanella oneidensis shows jelly-roll fold with carbohydrate-binding module. Nocek B, Bigelow L, Abdullah J, Joachimiak A;. J Struct Funct Genomics. 2008;9:1-6. (from Pfam) NF046718.1 PF22263.1 DUF6951 27 27 101 subfamily Y Y N DUF6951 family protein 131567 cellular organisms no rank 541 EBI-EMBL Family of unknown function (DUF6951) DUF6951 family protein This is a family of uncharacterised proteins found in archaea and bacteria. These proteins are predicted to adopt similar structure to the members of SufE/NifU superfamily. They contain three invariant cysteine residues and a fourth semi-conserved residue either cysteine or histidine. These residues are likely to define a potential Zn-binding site similar to the binding site observed in SufU. (from Pfam) NF046721.1 PF22271.1 DUF6955 27 27 91 subfamily Y Y N DUF6955 family protein 131567 cellular organisms no rank 207 EBI-EMBL Family of unknown function (DUF6955) DUF6955 family protein This is a family of small uncharacterised proteins found in bacteria and archaea. They are predicted to adopt an alpha/beta globular structure consisting of a cradle-like beta-sheet and alpha-helices packed on the convex side of the sheet. (from Pfam) NF046723.1 PF22277.1 EncFtn-like 27 27 85 domain Y N N EncFtn-like 27529188,30837306,32878987 131567 cellular organisms no rank 2571 EBI-EMBL EncFtn-like EncFtn-like This protein family includes Encapsulated ferritin-like protein from Rhodospirillum rubrum (EncFtn) and similar prokaryotic sequences. This encapsulated ferritin that acts as a ferroxidase adopts an open decameric structure. Each monomer has an N-terminal 3-10-helix, two long antiparallel alpha-helices and a shorter helix at the end [1]. Paper describing PDB structure 5da5. [1]. 27529188. Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments. He D, Hughes S, Vanden-Hehir S, Georgiev A, Altenbach K, Tarrant E, Mackay CL, Waldron KJ, Clarke DJ, Marles-Wright J;. Elife. 2016; [Epub ahead of print]. Paper describing PDB structure 5n5e. [2]. 30837306. Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea. He D, Piergentili C, Ross J, Tarrant E, Tuck LR, Mackay CL, McIver Z, Waldron KJ, Clarke DJ, Marles-Wright J;. Biochem J. 2019;476:975-989. Paper describing PDB structure 6suw. [3]. 32878987. Dissecting the structural and functional roles of a putative metal entry site in encapsulated ferritins. Piergentili C, Ross J, He D, Gallagher KJ, Stanley WA, Adam L, Mackay CL, Basle A, Waldron KJ, Clarke DJ, Marles-Wright J;. J Biol Chem. 2020;295:15511-15526. (from Pfam) NF046734.1 PF22322.1 DUF6973 27 27 124 domain Y Y N DUF6973 domain-containing protein 131567 cellular organisms no rank 7634 EBI-EMBL Domain of unknown function (DUF6973) DUF6973 domain This domain is found in uncharacterised proteins. It is predicted to adopt a globular structure consisting of five alpha-helices. It is probably distantly related to Wnt domains. (from Pfam) NF046740.1 PF22357.1 AF1548-like_C 23.9 23.9 56 domain Y N N AF1548-like, C-terminal 131567 cellular organisms no rank 510 EBI-EMBL AF1548-like, C-terminal AF1548-like, C-terminal This domain is found at the C-terminal end of the uncharacterised protein AF_1548 from Archaeoglobus fulgidus and similar prokaryotic proteins. This domain is often found associated with Pfam:PF04471. (from Pfam) NF046745.1 PF22397.1 DUF6977 27 27 212 subfamily Y Y N DUF6977 family protein 131567 cellular organisms no rank 1740 EBI-EMBL Family of unknown function (DUF6977) DUF6977 family protein This is a family of uncharacterised bacterial proteins. They share sequence similarity with proteins members of Pfam:PF22075. They are also predicted to adopt an alpha/beta globular structure that is globally similar to the structure of E.coli protein YbiA, a member of the NADAR domain family. (from Pfam) NF046746.1 PF22399.1 DUF6979 27 27 127 subfamily Y Y N DUF6979 family protein 131567 cellular organisms no rank 875 EBI-EMBL Family of unknown function (DUF6979) DUF6979 family protein This is a family of uncharacterised proteins. They are predicted to fold into a globular structure consisting mainly of alpha-helices. (from Pfam) NF046750.1 PF22468.1 ACT_9 27 27 61 domain Y Y N ACT domain-containing protein 16731588,16905770,17012784,17350037,18334478,19490113 131567 cellular organisms no rank 92864 EBI-EMBL ACT domain ACT domain This entry represents the ACT domain, which is found twice in Aspartate kinase from Methanocaldococcus jannaschii, the enzyme that catalyses the phosphorylation of aspartic acid [6]. This domain folds as a four-stranded antiparallel sheet with two alpha-helices parallel to the sheet and located on one side of the sheet [1]. Paper describing PDB structure 2cdq. [1]. 16731588. A novel organization of ACT domains in allosteric enzymes revealed by the crystal structure of Arabidopsis aspartate kinase. Mas-Droux C, Curien G, Robert-Genthon M, Laurencin M, Ferrer JL, Dumas R;. Plant Cell. 2006;18:1681-1692. Paper describing PDB structure 2dt9. [2]. 19490113. Crystal structures of the regulatory subunit of Thr-sensitive aspartate kinase from Thermus thermophilus. Yoshida A, Tomita T, Kono H, Fushinobu S, Kuzuyama T, Nishiyama M;. FEBS J. 2009;276:3124-3136. Paper describing PDB structure 2dtj. [3]. 17350037. Structural Insight into concerted inhibition of alpha 2 beta 2-type aspartate kinase from Corynebacterium glutamicum. Yoshida A, Tomita T, Kurihara T, Fushinobu S, Kuzuyama T, Nishiyama M;. J Mol Biol. 2007;368:521-536. Paper describing PDB structure 2hmf. [4]. 17012784. The initial step in the archaeal aspartate biosynthetic pathway catalyzed by a monofunctional aspartokinase. Faehnle CR, Liu X, Pavlovsky A, Viola RE;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006;62:962-966. Paper describing PDB structure 2j0w. [5]. 16905770. Structures of R- and T-state Escherichia coli aspartokinase III. Mechanisms of the allosteric transition and inhibition by lysine. Kotaka M, Ren J, Lockyer M, Hawkins AR, Stammers DK;. J Biol . TRUNCATED at 1650 bytes (from Pfam) NF046751.1 PF22484.1 DUF6986 27 27 408 subfamily Y Y N DUF6986 family protein 131567 cellular organisms no rank 21310 EBI-EMBL Domain of unknown function (DUF6986) DUF6986 family protein This entry represents a family of TIM barrel proteins that are most closely related to Pfam:PF03328. This strongly suggests that these proteins are enzyme with a possibly related function. (from Pfam) NF046753.1 PF22497.1 DUF6989 27 27 146 domain Y Y N DUF6989 domain-containing protein 131567 cellular organisms no rank 313 EBI-EMBL Domain of unknown function (DUF6989) DUF6989 domain This domain is found in a number of uncharacterised bacterial proteins that are likely associated with the membrane. (from Pfam) NF046760.1 PF22517.1 Mcm-like_N 26 26 82 domain Y N N Mcm-like, N-terminal domain, archaea 19217392 131567 cellular organisms no rank 2 EBI-EMBL Mcm-like, N-terminal domain, archaea Mcm-like, N-terminal domain, archaea This entry represents the N-terminal domain of a monomeric MCM homologue (known as Mcm2) from Methanopyrus kandleri [1]. The MCM (minichromosome maintenance) proteins, which belong to the AAA superfamily, serve as the replicative helicase in eukaryotic and archaeal organisms. Paper describing PDB structure 3f8t. [1]. 19217392. Insights into the architecture of the replicative helicase from the structure of an archaeal MCM homolog. Bae B, Chen YH, Costa A, Onesti S, Brunzelle JS, Lin Y, Cann IK, Nair SK;. Structure. 2009;17:211-222. (from Pfam) NF046761.1 PF22521.1 HypF_C_2 27 27 241 domain Y N N Carbamoyltransferase, Kae1-like Domain, second subdomain 17766251,18951093,19172740,22153500,22740694 131567 cellular organisms no rank 84934 EBI-EMBL Carbamoyltransferase, Kae1-like Domain, second subdomain Carbamoyltransferase, Kae1-like Domain, second subdomain This domain is found at the C-terminal end of Carbamoyltransferase from Caldanaerobacter subterraneus (HypF, Swiss:Q8RDB0) and similar prokaryotic sequences. HypF is involved in the biosynthesis of the nitrile group as a precursor of the cyano groups of hydrogenases. HypF consists of four domains: the acylphosphatase domain (Pfam:PF00708), the Zn finger-like domain (Pfam:PF07503), the YrdC-like domain (Pfam:PF01300) and the Kae1 (kinase-associated endopeptidase 1)-like domain, which is composed of two alpha-beta subdomains (Pfam:PF17788 and this entry) [5]. Paper describing PDB structure 2ivn. [1]. 17766251. An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro. Hecker A, Leulliot N, Gadelle D, Graille M, Justome A, Dorlet P, Brochier C, Quevillon-Cheruel S, Le Cam E, van Tilbeurgh H, Forterre P;. Nucleic Acids Res. 2007;35:6042-6051. Paper describing PDB structure 2vwb. [2]. 19172740. Structure of the archaeal Kae1/Bud32 fusion protein MJ1130: a model for the eukaryotic EKC/KEOPS subcomplex. Hecker A, Lopreiato R, Graille M, Collinet B, Forterre P, Libri D, van Tilbeurgh H;. EMBO J. 2008;27:2340-2351. Paper describing PDB structure 3en9. [3]. 18951093. Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine. Mao DY, Neculai D, Downey M, Orlicky S, Haffani YZ, Ceccarelli DF, Ho JS, Szilard RK, Zhang W, Ho CS, Wan L, Fares C, Rumpel S, Kurinov I, Arrowsmith CH, Durocher D, Sicheri F;. Mol Cell. 2008;32:259-275. Paper describing PDB structure 3tsp. [4]. 22153500. Structure . TRUNCATED at 1650 bytes (from Pfam) NF046762.1 PF22529.1 DUF7001 27 27 247 subfamily Y Y N DUF7001 family protein 131567 cellular organisms no rank 354 EBI-EMBL Family of unknown function (DUF7001) DUF7001 family protein This is a family of uncharacterised proteins found in Archaea. They have sequence similarity to Zincin-like metalloproteases and are predicted to adopt the same structure. Only one of the two zinc binding sites are conserved suggesting that these proteins may possess different function. (from Pfam) NF046768.1 PF22566.1 UBA_8 26 26 46 domain Y N N UBA-like domain 15029246,16563434,18206966,23104058,26268556 131567 cellular organisms no rank 149 EBI-EMBL UBA-like domain UBA-like domain This entry represents a UBA-like domain. Paper describing PDB structure 1v92. [1]. 15029246. Structure, dynamics and interactions of p47, a major adaptor of the AAA ATPase, p97. Yuan X, Simpson P, McKeown C, Kondo H, Uchiyama K, Wallis R, Dreveny I, Keetch C, Zhang X, Robinson C, Freemont P, Matthews S;. EMBO J. 2004;23:1463-1473. Paper describing PDB structure 2g3q. [2]. 16563434. Structural basis for monoubiquitin recognition by the Ede1 UBA domain. Swanson KA, Hicke L, Radhakrishnan I;. J Mol Biol. 2006;358:713-724. Paper describing PDB structure 2muu. [3]. 26268556. The N-terminal ubiquitin-binding region of ubiquitin-specific protease 28 modulates its deubiquitination function: NMR structural and mechanistic insights. Wen Y, Shi L, Ding Y, Cui R, He WT, Hu HY, Zhang N;. Biochem J. 2015;471:155-165. Paper describing PDB structure 3bq3. [4]. 18206966. Dcn1 functions as a scaffold-type E3 ligase for cullin neddylation. Kurz T, Chou YC, Willems AR, Meyer-Schaller N, Hecht ML, Tyers M, Peter M, Sicheri F;. Mol Cell. 2008;29:23-35. Paper describing PDB structure 4f1i. [5]. 23104058. Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2. Shi K, Kurahashi K, Gao R, Tsutakawa SE, Tainer JA, Pommier Y, Aihara H;. Nat Struct Mol Biol. 2012;19:1372-1377. (from Pfam) NF046770.1 PF22570.1 LiaF-TM 27 27 98 domain Y Y N LiaF transmembrane domain-containing protein 131567 cellular organisms no rank 12783 EBI-EMBL LiaF transmembrane domain LiaF transmembrane domain This entry represents the transmembrane region found at the N-terminal of LiaF (Swiss:O32199), which is thought to be a sensory domain (Preprint https://doi.org/10.1101/2020.09.24.301986). LiaF-TM may tie into a two-component system to regulate the membrane integrity and permeability in response to the stress signal. (from Pfam) NF046772.1 PF22583.1 UPF0425_C 27 27 70 domain Y N N UPF0425 C-terminal domain 16201757 131567 cellular organisms no rank 258 EBI-EMBL UPF0425 C-terminal domain UPF0425 C-terminal domain This entry represents de C-terminal domain of UPF0425 pyridoxal phosphate-dependent protein MJ0158 from Methanocaldococcus jannaschii and similar archaeal sequences [1]. Paper describing PDB structure 2aeu. [1]. 16201757. Structural and functional investigation of a putative archaeal selenocysteine synthase. Kaiser JT, Gromadski K, Rother M, Engelhardt H, Rodnina MV, Wahl MC;. Biochemistry. 2005;44:13315-13327. (from Pfam) NF046773.1 PF22590.1 Cas3-like_C_2 27 27 106 domain Y N N CRISPR-associated nuclease/helicase Cas3, C-terminal 11595187,15296731,15642269,16051820,16051821,27455460,27585537 131567 cellular organisms no rank 52918 EBI-EMBL CRISPR-associated nuclease/helicase Cas3, C-terminal CRISPR-associated nuclease/helicase Cas3, C-terminal This entry represents the C-terminal domain of CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST from Pseudomonas aeruginosa (Cas3), a DNA-degradation enzyme that forms part of the CRISPR-Cas bacterial immune system. Cas3 contains a Cas2 domain, an HD nuclease domain (Pfam:PF18019), RecA1, RecA2, a long linker region, and a C-terminal domain (this entry). This domain contains two alpha-helices and two six-stranded beta-blades [6]. Paper describing PDB structure 1gm5. [1]. 11595187. Structural analysis of DNA replication fork reversal by RecG. Singleton MR, Scaife S, Wigley DB;. Cell. 2001;107:79-89. Paper describing PDB structure 1t5i. [2]. 15296731. Crystal structure of UAP56, a DExD/H-box protein involved in pre-mRNA splicing and mRNA export. Zhao R, Shen J, Green MR, MacMorris M, Blumenthal T;. Structure. 2004;12:1373-1381. Paper describing PDB structure 1wp9. [3]. 15642269. Crystal structure and functional implications of Pyrococcus furiosus hef helicase domain involved in branched DNA processing. Nishino T, Komori K, Tsuchiya D, Ishino Y, Morikawa K;. Structure. 2005;13:143-153. Paper describing PDB structure 1yks. [4]. 16051820. Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing. Wu J, Bera AK, Kuhn RJ, Smith JL;. J Virol. 2005;79:10268-10277. Paper describing PDB structure 2bhr. [5]. 16051821. Structure of the Dengue virus helicase/nucleoside triphosphatase catalytic domain at a resolution of 2.4 A. Xu T, Sampath A, Chao A, Wen D, Nanao M, Chene P, Vasudevan SG, Lescar J;. J Virol. 2005;79:10278-10288. [6]. 27455460. Structural basis o. TRUNCATED at 1650 bytes (from Pfam) NF046776.1 PF22594.1 GTP-eEF1A_C 27 27 101 domain Y Y N elongation factor 1-alpha C-terminal domain-related protein 11106763,11574461,15099522,16387658,19417105 131567 cellular organisms no rank 57190 EBI-EMBL GTP-eEF1A C-terminal domain-like elongation factor 1-alpha C-terminal domain-related protein This entry represents a beta-barrel domain that is found C-terminal in homologues of elongation factor eEF1A. Paper describing PDB structure 1f60. [1]. 11106763. Structural basis for nucleotide exchange and competition with tRNA in the yeast elongation factor complex eEF1A:eEF1Balpha. Andersen GR, Pedersen L, Valente L, Chatterjee I, Kinzy TG, Kjeldgaard M, Nyborg J;. Mol Cell. 2000;6:1261-1266. Paper describing PDB structure 1jny. [2]. 11574461. The crystal structure of Sulfolobus solfataricus elongation factor 1alpha in complex with GDP reveals novel features in nucleotide binding and exchange. Vitagliano L, Masullo M, Sica F, Zagari A, Bocchini V;. EMBO J. 2001;20:5305-5311. Paper describing PDB structure 1r5b. [3]. 15099522. Crystal structure and functional analysis of the eukaryotic class II release factor eRF3 from S. pombe. Kong C, Ito K, Walsh MA, Wada M, Liu Y, Kumar S, Barford D, Nakamura Y, Song H;. Mol Cell. 2004;14:233-245. Paper describing PDB structure 1zun. [4]. 16387658. Molecular basis for G protein control of the prokaryotic ATP sulfurylase. Mougous JD, Lee DH, Hubbard SC, Schelle MW, Vocadlo DJ, Berger JM, Bertozzi CR;. Mol Cell. 2006;21:109-122. Paper describing PDB structure 3e1y. [5]. 19417105. Structural insights into eRF3 and stop codon recognition by eRF1. Cheng Z, Saito K, Pisarev AV, Wada M, Pisareva VP, Pestova TV, Gajda M, Round A, Kong C, Lim M, Nakamura Y, Svergun DI, Ito K, Song H;. Genes Dev. 2009;23:1106-1118. (from Pfam) NF046777.1 PF22604.1 TetR_HI_0893_C 27 27 112 domain Y N N Tetracyclin repressor-like HI_0893, C-terminal domain 131567 cellular organisms no rank 5363 EBI-EMBL Tetracyclin repressor-like HI_0893, C-terminal domain Tetracyclin repressor-like HI_0893, C-terminal domain This entry represents the C-terminal domain of some HTH-type transcriptional repressors, such as HI_0893 from Haemophilus influenzae. (from Pfam) NF046778.1 PF22607.1 FAD_binding-like 27 27 130 domain Y N N FAD binding domain-like 18440023 131567 cellular organisms no rank 5250 EBI-EMBL FAD binding domain-like FAD binding domain-like This domain is found in a number of FAD-binding enzymes. Paper describing PDB structure 2vou. [1]. 18440023. Structure of 2,6-dihydroxypyridine 3-hydroxylase from a nicotine-degrading pathway. Treiber N, Schulz GE;. J Mol Biol. 2008;379:94-104. (from Pfam) NF046780.1 PF22612.1 GH113 27 27 289 domain Y Y N glycoside hydrolase family 113 GO:0016798 18755688,24339341,29871927,32541663,33664385 131567 cellular organisms no rank 7356 EBI-EMBL Glycoside Hydrolase Family 113 glycoside hydrolase family 113 This family includes glycoside hydrolases of family 113, which includes a characterized beta-1,4-mannanase from Amphibacillus xylanus. NF046782.1 PF22622.1 MFE-2_hydrat-2_N 27 27 130 domain Y N N MFE-2 hydratase 2 N-terminal domain 15051722,15644212,16513976,16963641,17431182 131567 cellular organisms no rank 24610 EBI-EMBL MFE-2 hydratase 2 N-terminal domain MFE-2 hydratase 2 N-terminal domain This entry represents a domain found in N-terminal in MFE-2 hydratase 2 and related enzymes. This domain is housing the cavity for the aliphatic acyl part of the substrate molecule. The flexibility of region within this domain plays a role in substrate binding in mammalian hydratase 2 [2]. Paper describing PDB structure 1pn2. [1]. 15051722. A two-domain structure of one subunit explains unique features of eukaryotic hydratase 2. Koski MK, Haapalainen AM, Hiltunen JK, Glumoff T;. J Biol Chem. 2004;279:24666-24672. Paper describing PDB structure 1s9c. [2]. 15644212. Crystal structure of 2-enoyl-CoA hydratase 2 from human peroxisomal multifunctional enzyme type 2. Koski KM, Haapalainen AM, Hiltunen JK, Glumoff T;. J Mol Biol. 2005;345:1157-1169. Paper describing PDB structure 2c2i. [3]. 16963641. Structure and function of Rv0130, a conserved hypothetical protein from Mycobacterium tuberculosis. Johansson P, Castell A, Jones TA, Backbro K;. Protein Sci. 2006;15:2300-2309. Paper describing PDB structure 2cdh. [4]. 16513976. Architecture of a fungal fatty acid synthase at 5 A resolution. Jenni S, Leibundgut M, Maier T, Ban N;. Science. 2006;311:1263-1267. Paper describing PDB structure 2uv8. [5]. 17431182. Structural basis for substrate delivery by acyl carrier protein in the yeast fatty acid synthase. Leibundgut M, Jenni S, Frick C, Ban N;. Science. 2007;316:288-290. (from Pfam) NF046792.1 PF22667.1 Lon_lid 27 27 57 domain Y N N Lon protease AAA+ ATPase lid domain 15037242,20600124,24531457,27041592,27041593 131567 cellular organisms no rank 67194 EBI-EMBL Lon protease AAA+ ATPase lid domain Lon protease AAA+ ATPase lid domain This entry represents the AAA+ ATPase lid domain of Lon proteases [1-5]. Paper describing PDB structure 1qzm. [1]. 15037242. Crystal structure of the AAA+ alpha domain of E. coli Lon protease at 1.9A resolution. Botos I, Melnikov EE, Cherry S, Khalatova AG, Rasulova FS, Tropea JE, Maurizi MR, Rotanova TV, Gustchina A, Wlodawer A;. J Struct Biol. 2004;146:113-122. Paper describing PDB structure 3m6a. [2]. 20600124. Crystal structures of Bacillus subtilis Lon protease. Duman RE, Lowe J;. J Mol Biol. 2010;401:653-670. Paper describing PDB structure 4git. [3]. 24531457. Structural basis for DNA-mediated allosteric regulation facilitated by the AAA+ module of Lon protease. Lee AY, Chen YD, Chang YY, Lin YC, Chang CF, Huang SJ, Wu SH, Hsu CH;. Acta Crystallogr D Biol Crystallogr. 2014;70:218-230. Paper describing PDB structure 4ypl. [4]. 27041592. Structural Insights into the Allosteric Operation of the Lon AAA+ Protease. Lin CC, Su SC, Su MY, Liang PH, Feng CC, Wu SH, Chang CI;. Structure. 2016;24:667-675. Paper describing PDB structure 4ypm. [5]. 27041593. Structural Basis for the Magnesium-Dependent Activation and Hexamerization of the Lon AAA+ Protease. Su SC, Lin CC, Tai HC, Chang MY, Ho MR, Babu CS, Liao JH, Wu SH, Chang YC, Lim C, Chang CI;. Structure. 2016;24:676-686. (from Pfam) NF046801.1 PF22700.1 MVD-like_N 27 27 157 domain Y N N Diphosphomevalonate decarboxylase-like N-terminal domain 11698677,17583736,18823933,21561869,22734632 131567 cellular organisms no rank 14780 EBI-EMBL Diphosphomevalonate decarboxylase-like N-terminal domain Diphosphomevalonate decarboxylase-like N-terminal domain This entry represents the N-terminal domain of Diphosphomevalonate decarboxylases [1-5] whoch catalyse the ATP dependent decarboxylation of (R)-5-diphosphomevalonate to form isopentenyl diphosphate (IPP). Members of this entry function in the mevalonate pathway leading to isopentenyl diphosphate (IPP), a key precursor for the biosynthesis of isoprenoids and sterol synthesis. Paper describing PDB structure 1fi4. [1]. 11698677. Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. Bonanno JB, Edo C, Eswar N, Pieper U, Romanowski MJ, Ilyin V, Gerchman SE, Kycia H, Studier FW, Sali A, Burley SK;. Proc Natl Acad Sci U S A. 2001;98:12896-12901. Paper describing PDB structure 2hk2. [2]. 17583736. Crystal structures of Trypanosoma brucei and Staphylococcus aureus mevalonate diphosphate decarboxylase inform on the determinants of specificity and reactivity. Byres E, Alphey MS, Smith TK, Hunter WN;. J Mol Biol. 2007;371:540-553. Paper describing PDB structure 3d4j. [3]. 18823933. Human mevalonate diphosphate decarboxylase: characterization, investigation of the mevalonate diphosphate binding site, and crystal structure. Voynova NE, Fu Z, Battaile KP, Herdendorf TJ, Kim JJ, Miziorko HM;. Arch Biochem Biophys. 2008;480:58-67. Paper describing PDB structure 3qt5. [4]. 21561869. Crystal structures of Staphylococcus epidermidis mevalonate diphosphate decarboxylase bound to inhibitory analogs reveal new insight into substrate binding and catalysis. Barta ML, Skaff DA, McWhorter WJ, Herdendorf TJ, Miziorko HM, Geisbrecht BV;. J Biol Chem. 2011;286:23900-23910. Paper describing PDB structure 4dpw. [5]. 22734632. Structu. TRUNCATED at 1650 bytes (from Pfam) NF046806.1 PF22725.1 GFO_IDH_MocA_C3 27 27 124 domain Y N N GFO/IDH/MocA C-terminal domain 11099381,11705375,16906761,17121853,8994968 131567 cellular organisms no rank 473444 EBI-EMBL GFO/IDH/MocA C-terminal domain GFO/IDH/MocA C-terminal domain This entry includes the C-terminal domain found in a set of oxidorecuctases from GFO/IDH/MocA family, not included in Pfam:PF02894 [1-5]. Paper describing PDB structure 1evj. [1]. 11099381. Crystal structure of a truncated mutant of glucose-fructose oxidoreductase shows that an N-terminal arm controls tetramer formation. Lott JS, Halbig D, Baker HM, Hardman MJ, Sprenger GA, Baker EN;. J Mol Biol. 2000;304:575-584. Paper describing PDB structure 1h6a. [2]. 11705375. Crystal structures of the precursor form of glucose-fructose oxidoreductase from Zymomonas mobilis and its complexes with bound ligands. Nurizzo D, Halbig D, Sprenger GA, Baker EN;. Biochemistry. 2001;40:13857-13867. Paper describing PDB structure 1ofg. [3]. 8994968. The structure of glucose-fructose oxidoreductase from Zymomonas mobilis: an osmoprotective periplasmic enzyme containing non-dissociable NADP. Kingston RL, Scopes RK, Baker EN;. Structure 1996;4:1413-1428. Paper describing PDB structure 2glx. [4]. 16906761. Crystal structure of NADP(H)-dependent 1,5-anhydro-D-fructose reductase from Sinorhizobium morelense at 2.2 A resolution: construction of a NADH-accepting mutant and its application in rare sugar synthesis. Dambe TR, Kuhn AM, Brossette T, Giffhorn F, Scheidig AJ;. Biochemistry. 2006;45:10030-10042. Paper describing PDB structure 2nvw. [5]. 17121853. Understanding a transcriptional paradigm at the molecular level. The structure of yeast Gal80p. Thoden JB, Sellick CA, Reece RJ, Holden HM;. J Biol Chem. 2007;282:1534-1538. (from Pfam) NF046812.1 PF22742.1 PspAB 27 27 189 PfamEq Y Y N PspA-associated protein PspAB pspAB 38809013 131567 cellular organisms no rank 6393 EBI-EMBL PspA associated protein B PspA-associated protein PspAB PspA associated protein B is a component of the Psp system. It occurs in an operon with a membrane-associated metallopeptidase. In addition, these two genes occur in operon with the PspA-PspAA dyad. (from Pfam) NF046813.1 PF22743.1 PspAA 27 27 92 PfamEq Y Y N PspA-associated protein PspAA pspAA 38809013 131567 cellular organisms no rank 5395 EBI-EMBL PspA-Associated protein PspA-associated protein PspAA This entry represents a trihelical domain (alpha+beta) with absolutely conserved R and D, which occurs as a two-gene cluster with PspA. This domain, mostly occurs as a solo, but is occasionally found fused to an N-terminal PspA in actinobacteria and chloroflexi. (from Pfam) NF046814.1 PF22747.1 DUF2089_Zn_ribbon 27.6 27.6 32 domain Y Y N DUF2089-like zinc ribbon domain-containing protein 131567 cellular organisms no rank 2679 EBI-EMBL DUF2089 zinc ribbon DUF2089-like zinc ribbon domain This entry represents the zinc ribbon found at the N-terminal of DUF2089, which usually occurs as a fusion of ZnR+HTH+SHOCT-like. (from Pfam) NF046815.1 PF22752.1 DUF488-N3i 27 27 131 subfamily Y N N Inactive DUF488-N3 subclade 36968430 131567 cellular organisms no rank 28041 EBI-EMBL Inactive DUF488-N3 subclade Inactive DUF488-N3 subclade This entry represents a subclade of DUF488 domains lacking the catalytic residues common to the rhodanese-phosphatase superfamily. The C-terminal core strand is degenerate in this subclade [1]. [1]. 36968430. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. Burroughs AM, Aravind L;. NAR Genom Bioinform. 2023;5:lqad029. (from Pfam) NF046818.1 PF22763.1 NrS1-1_pol-like_HBD 27.9 27.9 64 domain Y N N NrS-1 polymerase HBD domain 32016421 131567 cellular organisms no rank 5043 EBI-EMBL NrS-1 polymerase HBD domain NrS-1 polymerase HBD domain This entry represents the helix bundle domain (HBD) domain of NrS-1 polymerase [1] which together with the N-terminal Prim/Pol domain, is responsible for DNA polymerization and de novo primer synthesis activities. This domain is critical for the primer synthesis activity of NrS-1 polymerase [1]. [1]. 32016421. Structural studies reveal a ring-shaped architecture of deep-sea vent phage NrS-1 polymerase. Chen X, Su S, Chen Y, Gao Y, Li Y, Shao Z, Zhang Y, Shao Q, Liu H, Li J, Ma J, Gan J;. Nucleic Acids Res. 2020;48:3343-3355. (from Pfam) NF046820.1 PF22778.1 VCPO_2nd 27 27 177 domain Y N N VCPO second helical-bundle domain 131567 cellular organisms no rank 1899 EBI-EMBL VCPO second helical-bundle domain VCPO second helical-bundle domain This domain is found in homologues of Vanadium-dependent haloperoxidases, NapH1 and NapH3, that catalyze stereospecific chlorofunctionalization reactions on naphthoquinone-based meroterpeneoids. These enzymes contain two similar helical domains composed of five alpha-helices. This domain harbours the catalytic residues. (from Pfam) NF046824.1 PF22798.1 DUF5817_CT 29 29 54 domain Y Y N DUF5817 family protein 131567 cellular organisms no rank 629 EBI-EMBL DUF5817, C-terminal domain DUF5817 family protein C-terminal domain This entry represents a helix-turn-helix (HTH) domain found in a group of functionally uncharacterized prokaryotic proteins, typically associated with the Domain of Unknown Function (DUF5817) (Pfam: PF19134). (from Pfam) NF046835.1 PF22458.1 RsmF-B_ferredox 27 27 74 domain Y N N Methyltr_RsmF/B-like, ferredoxin-like domain 14656444,14997580,16793063,21123870,30541086 131567 cellular organisms no rank 64825 EBI-EMBL Methyltr_RsmF/B-like, ferredoxin-like domain Methyltr_RsmF/B-like, ferredoxin-like domain This entry represents a ferredoxin-like domain found in methyltransferases RsmB, RsmF and related sequences [1-5]. Paper describing PDB structure 1ixk. [1]. 14997580. Crystal structure of human p120 homologue protein PH1374 from Pyrococcus horikoshii. Ishikawa I, Sakai N, Tamura T, Yao M, Watanabe N, Tanaka I;. Proteins. 2004;54:814-816. Paper describing PDB structure 1sqf. [2]. 14656444. The first structure of an RNA m5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate. Foster PG, Nunes CR, Greene P, Moustakas D, Stroud RM;. Structure. 2003;11:1609-1620. Paper describing PDB structure 2frx. [3]. 16793063. The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain. Hallberg BM, Ericsson UB, Johnson KA, Andersen NM, Douthwaite S, Nordlund P, Beuscher AE 4th, Erlandsen H;. J Mol Biol. 2006;360:774-787. Paper describing PDB structure 2yxl. [4]. 21123870. Structure of an archaeal homologue of the bacterial Fmu/RsmB/RrmB rRNA cytosine 5-methyltransferase. Hikida Y, Kuratani M, Bessho Y, Sekine SI, Yokoyama S;. Acta Crystallogr D Biol Crystallogr. 2010;66:1301-1307. Paper describing PDB structure 5zvd. [5]. 30541086. Archaeal NSUN6 catalyzes m5C72 modification on a wide-range of specific tRNAs. Li J, Li H, Long T, Dong H, Wang ED, Liu RJ;. Nucleic Acids Res. 2019;47:2041-2055. (from Pfam) NF046848.1 PF22518.1 DUF6997 27 27 175 domain Y Y N DUF6997 domain-containing protein 131567 cellular organisms no rank 1672 EBI-EMBL Domain of unknown function (DUF6997) DUF6997 domain This domain is found C-terminal in a group of uncharacterised proteins. It usually follows winged helix domain Pfam:PF22515. This domain is related to PD-(D/E)XK nucleases and it is predicted to adopt the same structure with similar active site architecture. (from Pfam) NF046852.1 PF22543.1 Sol_Rieske_ferrdox 27 27 40 domain Y N N Soluble Rieske-type ferredoxin 18703841 131567 cellular organisms no rank 58 EBI-EMBL Soluble Rieske-type ferredoxin Soluble Rieske-type ferredoxin This entry represents soluble Rieske-type ferredoxins from animals , referred to as MRF and HRF for the mouse and human proteins, respectively, whose function is not yet known [1]. Paper describing PDB structure 3d89. [1]. 18703841. X-ray structure of a soluble Rieske-type ferredoxin from Mus musculus. Levin EJ, Elsen NL, Seder KD, McCoy JG, Fox BG, Phillips GN Jr;. Acta Crystallogr D Biol Crystallogr. 2008;64:933-940. (from Pfam) NF046853.1 PF22544.1 HYDIN_VesB_CFA65-like_Ig 25.5 25.5 100 domain Y N N HYDIN/CFA65/VesB-like, Ig-like domain 24459146 131567 cellular organisms no rank 24594 EBI-EMBL HYDIN/CFA65/VesB-like, Ig-like domain HYDIN/CFA65/VesB-like, Ig-like domain VesB is a serine protease that is secreted by the type II secretion system (T2S) in Vibrio cholerae (Swiss:Q9KSQ6). It efficiently cleaves a trypsin substrate, but not chymotrypsin and elastase substrates [1]. It has been suggested to contribute to intestinal growth or pathogenesis, although is not the only factor required for intestinal survival. VesB can cleave the A subunit of cholera toxin, a process important for cholera toxin activation [1]. It consists of a protease domain (Pfam:PF00089) followed by a Ig-like domain, represented in this entry, which may be involved in one or more different functions such as stabilizing the protease domain, co-defining substrate specificity, binding to the bacterial surface and being part of a yet undefined secretion motif of the T2S system [1]. This protein belongs to the chymotrypsin subfamily A (which includes mostly eukaryotic proteases), having a structure and specificity profile resembling that of eukaryotic trypsin-like proteases. This domain is also found in some eukaryotic protein, such as HYDIN and CFA65 from human (which contain repeated Ig-like domains). Paper describing PDB structure 4lk4. [1]. 24459146. Functional and structural characterization of Vibrio cholerae extracellular serine protease B, VesB. Gadwal S, Korotkov KV, Delarosa JR, Hol WG, Sandkvist M;. J Biol Chem. 2014;289:8288-8298. (from Pfam) NF046855.1 PF22551.1 TY-Chap1 27 27 132 domain Y Y N T3SS (YopN, CesT) and YbjN peptide-binding chaperone 1 36146784,36968431 131567 cellular organisms no rank 3669 EBI-EMBL T3SS (YopN, CesT) and YbjN peptide-binding chaperone 1 T3SS (YopN, CesT) and YbjN peptide-binding chaperone 1 This domain is observed in host systems predicted to counter viral ribosylating toxins. They are predicted to function as peptide-binding chaperone domains that target proteins modified by ADPr and potentially misfolded as a consequence [1,2]. [1]. 36146784. Apprehending the NAD(+)-ADPr-Dependent Systems in the Virus World. Iyer LM, Burroughs AM, Anantharaman V, Aravind L;. Viruses. 2022;14:1977. [2]. 36968431. DiSiR: fast and robust method to identify ligand-receptor interactions at subunit level from single-cell RNA-sequencing data. Vahid MR, Kurlovs AH, Andreani T, Auge F, Olfati-Saber R, de Rinaldis E, Rapaport F, Savova V;. NAR Genom Bioinform. 2023;5:lqad030. (from Pfam) NF046861.1 PF22564.1 HAAS 27 27 55 domain Y Y N HAAS signaling domain-containing protein 38809013 131567 cellular organisms no rank 27869 EBI-EMBL HAAS HAAS signaling domain This entry represents the HAAS (HTH-associated alpha-helical signaling) domain, found N-terminal to DUF1700 (Pfam:PF08006) which represents the transmembrane segment (Preprint https://doi.org/10.1101/2020.09.24.301986). (from Pfam) NF046864.1 PF22578.1 GGR_cat 27 27 88 domain Y N N Geranylgeranyl reductase catalytic domain 20869368,21515284,24954619 131567 cellular organisms no rank 3908 EBI-EMBL Geranylgeranyl reductase catalytic domain Geranylgeranyl reductase catalytic domain This entry represents the catalytic domain of archaeal geranylgeranyl reductases (GGR) [1-3]. This domain contains the PxxYxWxFP sequence motif, which defines a specificity pocket in the structure, providing a structural basis for the substrate specificity of GGRs [2]. Paper describing PDB structure 3atq. [1]. 21515284. Structure and mutation analysis of archaeal geranylgeranyl reductase. Sasaki D, Fujihashi M, Iwata Y, Murakami M, Yoshimura T, Hemmi H, Miki K;. J Mol Biol. 2011;409:543-557. Paper describing PDB structure 3oz2. [2]. 20869368. Insights into substrate specificity of geranylgeranyl reductases revealed by the structure of digeranylgeranylglycerophospholipid reductase, an essential enzyme in the biosynthesis of archaeal membrane lipids. Xu Q, Eguchi T, Mathews II, Rife CL, Chiu HJ, Farr CL, Feuerhelm J, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Weekes D, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA;. J Mol Biol. 2010;404:403-417. Paper describing PDB structure 4opc. [3]. 24954619. Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase. Kung Y, McAndrew RP, Xie X, Liu CC, Pereira JH, Adams PD, Keasling JD;. Structure. 2014;22:1028-1036. (from Pfam) NF046867.1 PF22586.1 ANCHR-like_BBOX 27 27 39 domain Y N N ANCHR-like B-box zinc-binding domain 16529770,18220417,25355412,31078555,31204252 131567 cellular organisms no rank 15 EBI-EMBL ANCHR-like B-box zinc-binding domain ANCHR-like B-box zinc-binding domain This entry represents a B-box domain found in ANCHR, ZFYV1 and TRIM proteins, which is characterised by C6H2 zinc-binding consensus motif [1-5]. Paper describing PDB structure 2ffw. [1]. 16529770. Solution structure of the RBCC/TRIM B-box1 domain of human MID1: B-box with a RING. Massiah MA, Simmons BN, Short KM, Cox TC;. J Mol Biol. 2006;358:532-545. Paper describing PDB structure 2jun. [2]. 18220417. Structure of the MID1 tandem B-boxes reveals an interaction reminiscent of intermolecular ring heterodimers. Tao H, Simmons BN, Singireddy S, Jakkidi M, Short KM, Cox TC, Massiah MA;. Biochemistry. 2008;47:2450-2457. Paper describing PDB structure 2mvw. [3]. 25355412. The B-box 1 dimer of human promyelocytic leukemia protein. Huang SY, Naik MT, Chang CF, Fang PJ, Wang YH, Shih HM, Huang TH;. J Biomol NMR. 2014;60:275-281. Paper describing PDB structure 6h3a. [4]. 31204252. A Ubiquitin-Binding Domain that Binds a Structural Fold Distinct from that of Ubiquitin. Lim M, Newman JA, Williams HL, Masino L, Aitkenhead H, Gravard AE, Gileadi O, Svejstrup JQ;. Structure. 2019;27:1316-1325. Paper describing PDB structure 6o5k. [5]. 31078555. A Dissection of Oligomerization by the TRIM28 Tripartite Motif and the Interaction with Members of the Krab-ZFP Family. Sun Y, Keown JR, Black MM, Raclot C, Demarais N, Trono D, Turelli P, Goldstone DC;. J Mol Biol. 2019;431:2511-2527. (from Pfam) NF046871.1 PF22599.1 SecDF_P1_head 27 27 114 domain Y Y N SecDF P1 head subdomain-containing protein 21562494,27924919,28467902 131567 cellular organisms no rank 83632 EBI-EMBL SecDF, P1 head subdomain SecDF, P1 head subdomain This entry represents the head subdomain from P1 domain from SecDF proteins, which constitutes a critical element for proton transport [1-3]. P1 domain P1 binds an unfolded protein, and undergoes functionally important conformational changes. SecDF functions as a membrane-integrated chaperone that mediates ATP-independent protein translocation. Paper describing PDB structure 3aqo. [1]. 21562494. Structure and function of a membrane component SecDF that enhances protein export. Tsukazaki T, Mori H, Echizen Y, Ishitani R, Fukai S, Tanaka T, Perederina A, Vassylyev DG, Kohno T, Maturana AD, Ito K, Nureki O;. Nature. 2011;474:235-238. Paper describing PDB structure 5mg3. [2]. 27924919. A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion. Botte M, Zaccai NR, Nijeholt JL, Martin R, Knoops K, Papai G, Zou J, Deniaud A, Karuppasamy M, Jiang Q, Roy AS, Schulten K, Schultz P, Rappsilber J, Zaccai G, Berger I, Collinson I, Schaffitzel C;. Sci Rep. 2016;6:38399. Paper describing PDB structure 5xam. [3]. 28467902. Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF. Furukawa A, Yoshikaie K, Mori T, Mori H, Morimoto YV, Sugano Y, Iwaki S, Minamino T, Sugita Y, Tanaka Y, Tsukazaki T;. Cell Rep. 2017;19:895-901. (from Pfam) NF046872.1 PF22600.1 MTPAP-like_central 27 27 139 domain Y N N Poly(A) RNA polymerase, mitochondrial-like, central palm domain 10944102,10958780,15328606,16028221,16281058,21292163 131567 cellular organisms no rank 1265 EBI-EMBL Poly(A) RNA polymerase, mitochondrial-like, central palm domain Poly(A) RNA polymerase, mitochondrial-like, central palm domain This domain is found in human Poly(A) RNA polymerase, mitochondrial (MTPAP) and similar proteins from eukaryotes. MTPAP is a noncanonical polymerase that creates the 3' poly(A) tail of mitochondrial transcripts. It contains three domains: a N-terminal domain RL (Pfam:PF17797) and the canonical palm (this entry) and fingers domains. This domain shows a five -stranded beta-sheet with the three catalytic aspartic acid residues located on its surface [6], together with several alpha- helices, forming an alpha-beta configuration. Paper describing PDB structure 1f5a. [1]. 10944102. Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP. Martin G, Keller W, Doublie S;. EMBO J 2000;19:4193-4203. Paper describing PDB structure 1fa0. [2]. 10958780. Structure of yeast poly(A) polymerase alone and in complex with 3'-dATP. Bard J, Zhelkovsky AM, Helmling S, Earnest TN, Moore CL, Bohm A;. Science. 2000;289:1346-1349. Paper describing PDB structure 1no5. [3]. 16028221. Structure of HI0073 from Haemophilus influenzae, the nucleotide-binding domain of a two-protein nucleotidyl transferase. Lehmann C, Pullalarevu S, Krajewski W, Willis MA, Galkin A, Howard A, Herzberg O;. Proteins. 2005;60:807-811. Paper describing PDB structure 1q78. [4]. 15328606. Biochemical and structural insights into substrate binding and catalytic mechanism of mammalian poly(A) polymerase. Martin G, Moglich A, Keller W, Doublie S;. J Mol Biol. 2004;341:911-925. Paper describing PDB structure 2b4v. [5]. 16281058. Structural basis for UTP specificity of RNA editing TUTases from Trypanosoma brucei. Deng J, Ernst NL, Turley S, Stuart KD, Hol W. TRUNCATED at 1650 bytes (from Pfam) NF046874.1 PF22606.1 Cdc6-ORC-like_ATPase_lid 27 27 60 domain Y N N Cdc6/ORC-like, ATPase lid domain 11030343,15465044,17761879,17761880,25762138 131567 cellular organisms no rank 2041 EBI-EMBL Cdc6/ORC-like, ATPase lid domain Cdc6/ORC-like, ATPase lid domain This entry represents the AAA+ ATPase lid domain of eukaryotic Cdc6/ORC proteins and its homologues from archaea [1-5]. Paper describing PDB structure 1fnn. [1]. 11030343. Structure and function of Cdc6/Cdc18: implications for origin recognition and checkpoint control. Liu J, Smith CL, DeRyckere D, DeAngelis K, Martin GS, Berger JM;. Mol Cell. 2000;6:637-648. Paper describing PDB structure 1w5s. [2]. 15465044. Conformational changes induced by nucleotide binding in Cdc6/ORC from Aeropyrum pernix. Singleton MR, Morales R, Grainge I, Cook N, Isupov MN, Wigley DB;. J Mol Biol. 2004;343:547-557. Paper describing PDB structure 2qby. [3]. 17761879. Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. Dueber EL, Corn JE, Bell SD, Berger JM;. Science. 2007;317:1210-1213. Paper describing PDB structure 2v1u. [4]. 17761880. Structural basis of DNA replication origin recognition by an ORC protein. Gaudier M, Schuwirth BS, Westcott SL, Wigley DB;. Science. 2007;317:1213-1216. Paper describing PDB structure 4xgc. [5]. 25762138. Crystal structure of the eukaryotic origin recognition complex. Bleichert F, Botchan MR, Berger JM;. Nature. 2015;519:321-326. (from Pfam) NF046876.1 PF22617.1 HCS_D2 27 27 82 domain Y N N Homocitrate synthase post-HMGL domain-like 19776021,19996101,22352945,25128527,31023839 131567 cellular organisms no rank 68633 EBI-EMBL Homocitrate synthase post-HMGL domain-like Homocitrate synthase post-HMGL domain-like This entry represents domain found in diverse homologues of Homocitrate synthase (HCS) [2]. This domain follows the catalytic domain and is required for the enzymatic activity. Paper describing PDB structure 2ztj. [1]. 19996101. Mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from Thermus thermophilus. Okada T, Tomita T, Wulandari AP, Kuzuyama T, Nishiyama M;. J Biol Chem. 2010;285:4195-4205. Paper describing PDB structure 3ivs. [2]. 19776021. Crystal structure and functional analysis of homocitrate synthase, an essential enzyme in lysine biosynthesis. Bulfer SL, Scott EM, Couture JF, Pillus L, Trievel RC;. J Biol Chem. 2009;284:35769-35780. Paper describing PDB structure 3rmj. [3]. 22352945. Removal of the C-terminal regulatory domain of alpha-isopropylmalate synthase disrupts functional substrate binding. Huisman FH, Koon N, Bulloch EM, Baker HM, Baker EN, Squire CJ, Parker EJ;. Biochemistry. 2012;51:2289-2297. Paper describing PDB structure 4ov4. [4]. 25128527. Subdomain II of alpha-isopropylmalate synthase is essential for activity: inferring a mechanism of feedback inhibition. Zhang Z, Wu J, Lin W, Wang J, Yan H, Zhao W, Ma J, Ding J, Zhang P, Zhao GP;. J Biol Chem. 2014;289:27966-27978. Paper describing PDB structure 6e1j. [5]. 31023839. Molecular Basis of the Evolution of Methylthioalkylmalate Synthase and the Diversity of Methionine-Derived Glucosinolates. Kumar R, Lee SG, Augustine R, Reichelt M, Vassao DG, Palavalli MH, Allen A, Gershenzon J, Jez JM, Bisht NC;. Plant Cell. 2019;31:1633-1647. (from Pfam) NF046878.1 PF22629.1 AHAS-like_ACT 27 27 67 domain Y N N AHAS-like ACT domain 15035616,15823035,16458324,17586771,7719856 131567 cellular organisms no rank 77900 EBI-EMBL AHAS-like ACT domain AHAS-like ACT domain This entry represents the ACT domain found at the N-terminal of acetohydroxyacid synthase isozyme III from Escherichia coli and similar sequences. Paper describing PDB structure 1psd. [1]. 7719856. The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase. Schuller DJ, Grant GA, Banaszak LJ;. Nat Struct Biol 1995;2:69-76. Paper describing PDB structure 1sc6. [2]. 15035616. Multiconformational states in phosphoglycerate dehydrogenase. Bell JK, Grant GA, Banaszak LJ;. Biochemistry. 2004;43:3450-3458. Paper describing PDB structure 1yba. [3]. 15823035. Vmax regulation through domain and subunit changes. The active form of phosphoglycerate dehydrogenase. Thompson JR, Bell JK, Bratt J, Grant GA, Banaszak LJ;. Biochemistry. 2005;44:5763-5773. Paper describing PDB structure 2f1f. [4]. 16458324. Structure of the regulatory subunit of acetohydroxyacid synthase isozyme III from Escherichia coli. Kaplun A, Vyazmensky M, Zherdev Y, Belenky I, Slutzker A, Mendel S, Barak Z, Chipman DM, Shaanan B;. J Mol Biol. 2006;357:951-963. Paper describing PDB structure 2fgc. [5]. 17586771. Crystal structures of TM0549 and NE1324--two orthologs of E. coli AHAS isozyme III small regulatory subunit. Petkowski JJ, Chruszcz M, Zimmerman MD, Zheng H, Skarina T, Onopriyenko O, Cymborowski MT, Koclega KD, Savchenko A, Edwards A, Minor W;. Protein Sci. 2007;16:1360-1367. (from Pfam) NF046880.1 PF22638.1 FlgK_D1 28.6 28.6 233 domain Y Y N FlgK family flagellar hook-associated protein 25645451,29147015 131567 cellular organisms no rank 47561 EBI-EMBL Flagellar hook-associated protein FlgK helical domain Flagellar hook-associated protein FlgK helical domain This entry represents a mainly helical domain found in flagellar hook-associated protein FlgK and related proteins. FlgK is one of three hook associated proteins that form the hook-filament junction. This domain adopts a broken antiparallel helical bundle comprising six helical segments [1-2]. Paper describing PDB structure 4ut1. [1]. 25645451. From crystal structure to in silico epitope discovery in the Burkholderia pseudomallei flagellar hook-associated protein FlgK. Gourlay LJ, Thomas RJ, Peri C, Conchillo-Sole O, Ferrer-Navarro M, Nithichanon A, Vila J, Daura X, Lertmemongkolchai G, Titball R, Colombo G, Bolognesi M;. FEBS J. 2015;282:1319-1333. Paper describing PDB structure 5xbj. [2]. 29147015. Structure of FlgK reveals the divergence of the bacterial Hook-Filament Junction of Campylobacter. Bulieris PV, Shaikh NH, Freddolino PL, Samatey FA;. Sci Rep. 2017;7:15743. (from Pfam) NF046881.1 PF22649.1 Cgl0159 27 27 251 domain Y N N Cgl0159-like 12941964,15766250,17713928,19714241,20427286 131567 cellular organisms no rank 10454 EBI-EMBL Cgl0159-like Cgl0159-like This domain is found in the homologues of uncharacterised protein Cgl0159. It adopts classical (beta/alpha)8 barrel. Members of this family share significant similarity with Deoxyribose-phosphate aldolase. Paper describing PDB structure 1ojx. [1]. 12941964. Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins. Lorentzen E, Pohl E, Zwart P, Stark A, Russell RB, Knura T, Hensel R, Siebers B;. J Biol Chem. 2003;278:47253-47260. Paper describing PDB structure 1w8s. [2]. 15766250. Mechanism of the Schiff base forming fructose-1,6-bisphosphate aldolase: structural analysis of reaction intermediates. Lorentzen E, Siebers B, Hensel R, Pohl E;. Biochemistry. 2005;44:4222-4229. Paper describing PDB structure 2qjg. [3]. 17713928. Structure of 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid synthase, a catalyst in the archaeal pathway for the biosynthesis of aromatic amino acids. Morar M, White RH, Ealick SE;. Biochemistry. 2007;46:10562-10571. Paper describing PDB structure 3gkf. [4]. 19714241. The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF. Diaz Z, Xavier KB, Miller ST;. PLoS One. 2009;4:e6820. Paper describing PDB structure 3mhf. [5]. 20427286. Structure of a class I tagatose-1,6-bisphosphate aldolase: investigation into an apparent loss of stereospecificity. LowKam C, Liotard B, Sygusch J;. J Biol Chem. 2010;285:21143-21152. (from Pfam) NF046885.1 PF22660.1 RS_preATP-grasp-like 27 27 98 domain Y N N Ribonucleotide synthetase preATP-grasp domain 10569930,10913290,11953435,19053251,20050602 131567 cellular organisms no rank 93567 EBI-EMBL Ribonucleotide synthetase preATP-grasp domain Ribonucleotide synthetase preATP-grasp domain This domain precedes the ATP-grasp domain in a number of ribonucleotide synthetases [1-5]. Paper describing PDB structure 1b6r. [1]. 10569930. Three-dimensional structure of N5-carboxyaminoimidazole ribonucleotide synthetase: a member of the ATP grasp protein superfamily. Thoden JB, Kappock TJ, Stubbe J, Holden HM;. Biochemistry. 1999;38:15480-15492. Paper describing PDB structure 1eyz. [2]. 10913290. Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase. Thoden JB, Firestine S, Nixon A, Benkovic SJ, Holden HM;. Biochemistry. 2000;39:8791-8802. Paper describing PDB structure 1kj8. [3]. 11953435. PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site. Thoden JB, Firestine SM, Benkovic SJ, Holden HM;. J Biol Chem. 2002;277:23898-23908. Paper describing PDB structure 3eth. [4]. 19053251. Structural analysis of the active site geometry of N5-carboxyaminoimidazole ribonucleotide synthetase from Escherichia coli. Thoden JB, Holden HM, Firestine SM;. Biochemistry. 2008;47:13346-13353. Paper describing PDB structure 3k5h. [5]. 20050602. Structural and functional studies of Aspergillus clavatus N(5)-carboxyaminoimidazole ribonucleotide synthetase . Thoden JB, Holden HM, Paritala H, Firestine SM;. Biochemistry. 2010;49:752-760. (from Pfam) NF046887.1 PF22666.1 Glyco_hydro_2_N2 27 27 167 domain Y Y N glycosyl hydrolase 2 galactose-binding domain-containing protein 11045615,11732897,14621996,16171818,8599764 131567 cellular organisms no rank 147917 EBI-EMBL Glycosyl hydrolase 2 galactose-binding domain-like Glycosyl hydrolase 2 galactose-binding domain-like This domain is found in a number of proteins belonging to glycosyl hydrolase 2 family [1-5]. Paper describing PDB structure 1bhg. [1]. 8599764. Structure of human beta-glucuronidase reveals candidate lysosomal targeting and active-site motifs. Jain S, Drendel WB, Chen ZW, Mathews FS, Sly WS, Grubb JH;. Nat Struct Biol. 1996;3:375-381. Paper describing PDB structure 1dp0. [2]. 11045615. High resolution refinement of beta-galactosidase in a new crystal form reveals multiple metal-binding sites and provides a structural basis for alpha-complementation. Juers DH, Jacobson RH, Wigley D, Zhang XJ, Huber RE, Tronrud DE, Matthews BW;. Protein Sci. 2000;9:1685-1699. Paper describing PDB structure 1jyn. [3]. 11732897. A structural view of the action of Escherichia coli (lacZ) beta-galactosidase. Juers DH, Heightman TD, Vasella A, McCarter JD, Mackenzie L, Withers SG, Matthews BW;. Biochemistry. 2001;40:14781-14794. Paper describing PDB structure 1px3. [4]. 14621996. Structural basis for the altered activity of Gly794 variants of Escherichia coli beta-galactosidase. Juers DH, Hakda S, Matthews BW, Huber RE;. Biochemistry. 2003;42:13505-13511. Paper describing PDB structure 1yq2. [5]. 16171818. Cold-active beta-galactosidase from Arthrobacter sp. C2-2 forms compact 660 kDa hexamers: crystal structure at 1.9A resolution. Skalova T, Dohnalek J, Spiwok V, Lipovova P, Vondrackova E, Petrokova H, Duskova J, Strnad H, Kralova B, Hasek J;. J Mol Biol. 2005;353:282-294. (from Pfam) NF046890.1 PF22679.1 UvrB_D3-like 27 27 158 domain Y Y N UvrB domain 3-containing protein 10518516,10578047,10601012,15192705,16426634 131567 cellular organisms no rank 84908 EBI-EMBL UvrB domain 3 UvrB domain 3 This domain is found in homologs of UvrB and a number of type I restriction enzymes. This domain folds into an alpha/beta structure consisting of a central beta-sheet and alpha-helices packed on both sides of it. Paper describing PDB structure 1c4o. [1]. 10518516. Crystal structure of the DNA nucleotide excision repair enzyme UvrB from Thermus thermophilus. Machius M, Henry L, Palnitkar M, Deisenhofer J;. Proc Natl Acad Sci U S A. 1999;96:11717-11722. Paper describing PDB structure 1d2m. [2]. 10578047. Crystal structure of Thermus thermophilus HB8 UvrB protein, a key enzyme of nucleotide excision repair. Nakagawa N, Sugahara M, Masui R, Kato R, Fukuyama K, Kuramitsu S;. J Biochem. 1999;126:986-990. Paper describing PDB structure 1d9x. [3]. 10601012. Crystal structure of UvrB, a DNA helicase adapted for nucleotide excision repair. Theis K, Chen PJ, Skorvaga M, Van Houten B, Kisker C;. EMBO J. 1999;18:6899-6907. Paper describing PDB structure 1t5l. [4]. 15192705. Interactions between UvrA and UvrB: the role of UvrB's domain 2 in nucleotide excision repair. Truglio JJ, Croteau DL, Skorvaga M, DellaVecchia MJ, Theis K, Mandavilli BS, Van Houten B, Kisker C;. EMBO J. 2004;23:2498-2509. Paper describing PDB structure 2d7d. [5]. 16426634. Structural insights into the cryptic DNA-dependent ATPase activity of UvrB. Eryilmaz J, Ceschini S, Ryan J, Geddes S, Waters TR, Barrett TE;. J Mol Biol. 2006;357:62-72. (from Pfam) NF046891.1 PF22680.1 Glyco_hydro_123_N_2 27 27 142 domain Y N N Glycoside hydrolase 123 N-terminal domain 27038508,27546776 131567 cellular organisms no rank 5022 EBI-EMBL Glycoside hydrolase 123 N-terminal domain Glycoside hydrolase 123 N-terminal domain This entry represents the N-terminal domain of a group of glycoside hydrolases 123, from bacteria [1,2]. Paper describing PDB structure 5fqe. [1]. 27038508. The Details of Glycolipid Glycan Hydrolysis by the Structural Analysis of a Family 123 Glycoside Hydrolase from Clostridium perfringens. Noach I, Pluvinage B, Laurie C, Abe KT, Alteen MG, Vocadlo DJ, Boraston AB;. J Mol Biol. 2016;428:3253-3265. Paper describing PDB structure 5l7r. [2]. 27546776. Structural and mechanistic insights into a Bacteroides vulgatus retaining N-acetyl-beta-galactosaminidase that uses neighbouring group participation. Roth C, Petricevic M, John A, Goddard-Borger ED, Davies GJ, Williams SJ;. Chem Commun (Camb). 2016;52:11096-11099. (from Pfam) NF046892.1 PF22685.1 Gal80p_C-like 29 29 152 domain Y N N Gal80p, C-terminal domain 17121853,18292341,18701455,22302941,30224354 131567 cellular organisms no rank 7341 EBI-EMBL Gal80p, C-terminal domain Gal80p, C-terminal domain This domain is found in the homologues of Gal80p, an yeast regulatory protein closely related to glucose-fructose oxidoreductase. In Gal80p, this domain is likely involved in the binding of Gal4p [1]. Paper describing PDB structure 2nvw. [1]. 17121853. Understanding a transcriptional paradigm at the molecular level. The structure of yeast Gal80p. Thoden JB, Sellick CA, Reece RJ, Holden HM;. J Biol Chem. 2007;282:1534-1538. Paper describing PDB structure 3bts. [2]. 18292341. NADP regulates the yeast GAL induction system. Kumar PR, Yu Y, Sternglanz R, Johnston SA, Joshua-Tor L;. Science. 2008;319:1090-1092. Paper describing PDB structure 3e1k. [3]. 18701455. The interaction between an acidic transcriptional activator and its inhibitor. The molecular basis of Gal4p recognition by Gal80p. Thoden JB, Ryan LA, Reece RJ, Holden HM;. J Biol Chem. 2008;283:30266-30272. Paper describing PDB structure 3v2u. [4]. 22302941. The Gal3p transducer of the GAL regulon interacts with the Gal80p repressor in its ligand-induced closed conformation. Lavy T, Kumar PR, He H, Joshua-Tor L;. Genes Dev. 2012;26:294-303. Paper describing PDB structure 6a3f. [5]. 30224354. Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase. Sugiura M, Nakahara M, Yamada C, Arakawa T, Kitaoka M, Fushinobu S;. J Biol Chem. 2018;293:17375-17386. (from Pfam) NF046896.1 PF22698.1 Semialdhyde_dhC_1 27 27 165 domain Y N N Semialdehyde dehydrogenase, dimerisation domain 16240442,17316682,26966182 131567 cellular organisms no rank 74959 EBI-EMBL Semialdehyde dehydrogenase, dimerisation domain Semialdehyde dehydrogenase, dimerisation domain This entry represents the dimerisation domain found in N-acetyl-glutamine semialdehyde dehydrogenase (AgrC) and related sequences not included in Pfam:PF02774 [1-3]. Paper describing PDB structure 2cvo. [1]. 16240442. Crystal structure of putative N-acetyl-gamma-glutamyl-phosphate reductase (AK071544) from rice (Oryza sativa). Nonaka T, Kita A, Miura-Ohnuma J, Katoh E, Inagaki N, Yamazaki T, Miki K;. Proteins. 2005;61:1137-1140. Paper describing PDB structure 2i3a. [2]. 17316682. Crystal structure of N-acetyl-gamma-glutamyl-phosphate reductase from Mycobacterium tuberculosis in complex with NADP(+). Cherney LT, Cherney MM, Garen CR, Niu C, Moradian F, James MN;. J Mol Biol. 2007;367:1357-1369. Paper describing PDB structure 5ein. [3]. 26966182. Crystal Structure of the LysY.LysW Complex from Thermus thermophilus. Shimizu T, Tomita T, Kuzuyama T, Nishiyama M;. J Biol Chem. 2016;291:9948-9959. (from Pfam) NF046897.1 PF22701.1 Mala_s_1-like 27.5 27.5 195 domain Y N N Mal s 1 allergenic protein-like 11373616,11435114,12459547,12931195,14561773,17481656 131567 cellular organisms no rank 1214 EBI-EMBL Mal s 1 allergenic protein-like Mal s 1 allergenic protein-like This protein family includes Mal s 1 allergenic protein from the yeast Malassezia sympodialis (Mala s 1), which forms a relatively compact cup-like beta-propeller consisting of six blades each with four antiparallel beta-strands [6]. Paper describing PDB structure 1e1a. [1]. 11435114. Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris. Scharff EI, Koepke J, Fritzsch G, Lucke C, Ruterjans H;. Structure. 2001;9:493-502. Paper describing PDB structure 1ijq. [2]. 11373616. Implications for familial hypercholesterolemia from the structure of the LDL receptor YWTD-EGF domain pair. Jeon H, Meng W, Takagi J, Eck MJ, Springer TA, Blacklow SC;. Nat Struct Biol. 2001;8:499-504. Paper describing PDB structure 1n7d. [3]. 12459547. Structure of the LDL receptor extracellular domain at endosomal pH. Rudenko G, Henry L, Henderson K, Ichtchenko K, Brown MS, Goldstein JL, Deisenhofer J;. Science. 2002;298:2353-2358. Paper describing PDB structure 1npe. [4]. 12931195. Complex between nidogen and laminin fragments reveals a paradigmatic beta-propeller interface. Takagi J, Yang Y, Liu JH, Wang JH, Springer TA;. Nature. 2003;424:969-974. Paper describing PDB structure 1q7f. [5]. 14561773. Model of the brain tumor-Pumilio translation repressor complex. Edwards TA, Wilkinson BD, Wharton RP, Aggarwal AK;. Genes Dev. 2003;17:2508-2513. [6]. 17481656. Crystal structure of the major Malassezia sympodialis allergen Mala s 1 reveals a beta-propeller fold: a novel fold among allergens. Vilhelmsson M, Zargari A, Crameri R, Rasool O, Achour A, Scheynius A, Hallberg BM;. J Mol Biol. 2007;369:1079-1086. (from Pfam) NF046903.1 PF22722.1 NA-iREase1 27 27 106 domain Y N N NACHT-associated inactive Restriction Endonuclease 1 37160116 131567 cellular organisms no rank 31945 EBI-EMBL NACHT-associated inactive Restriction Endonuclease 1 NACHT-associated inactive Restriction Endonuclease 1 This entry represents a predicted sensor domain in bacterial NACHT conflict systems. It is likely to bind a ligand which could contribute to activation of enzymatic domains additionally fused to the N-terminus of the NACHT module [1]. [1]. 37160116. Bacterial NLR-related proteins protect against phage. Kibby EM, Conte AN, Burroughs AM, Nagy TA, Vargas JA, Whalen LA, Aravind L, Whiteley AT;. Cell. 2023;186:2410-2424. (from Pfam) NF046906.1 PF22735.1 NNH3 27 27 213 domain Y N N NACHT N-terminal Helical domain 3 37160116 131567 cellular organisms no rank 948 EBI-EMBL NACHT N-terminal Helical domain 3 NACHT N-terminal Helical domain 3 This is an helical domain found at the N-terminus of bacterial NACHT conflict systems [1]. This position is frequently occupied by an effector domain. [1]. 37160116. Bacterial NLR-related proteins protect against phage. Kibby EM, Conte AN, Burroughs AM, Nagy TA, Vargas JA, Whalen LA, Aravind L, Whiteley AT;. Cell. 2023;186:2410-2424. (from Pfam) NF046909.1 PF22746.1 SHOCT-like_DUF2089-C 27 27 32 domain Y Y N SHOCT-like domain-containing protein 131567 cellular organisms no rank 7440 EBI-EMBL SHOCT-like domain SHOCT-like domain This is a SHOCT-like domain that occurs as a fusion of ZnR+DUF2089-HTH+SHOCT-like. It is found at the C-terminal of DUF2089 (Pfam:PF09862). (from Pfam) NF046913.1 PF22772.1 WsaF_C 27 27 133 domain Y N N WsaF, C-terminal domain 20097205 131567 cellular organisms no rank 3191 EBI-EMBL WsaF, C-terminal domain WsaF, C-terminal domain This entry represents a domain found C-terminal in WsaF from Geobacillus stearothermophilus and related bacterial proteins. WsaF catalyses the formation of beta-1-2-linkage of rhamnose sugars in the carbohydrate polymer. It consists of two domains, the N-terminal of which binds the acceptor (the growing rhamnan chain), and a C-terminal which binds the substrate (dTDP-beta-l-rhamnose) [1]. [1]. 20097205. Structural basis of substrate binding in WsaF, a rhamnosyltransferase from Geobacillus stearothermophilus. Steiner K, Hagelueken G, Messner P, Schaffer C, Naismith JH;. J Mol Biol. 2010;397:436-447. (from Pfam) NF046915.1 PF22776.1 K_trans_C 24.8 24.8 151 domain Y Y N KUP/HAK/KT family potassium transporter 7621817,8226635,9350997 131567 cellular organisms no rank 37857 EBI-EMBL K+ potassium transporter C-terminal domain K+ potassium transporter C-terminal domain This is a family of K+ potassium transporters that are conserved across phyla, having both bacterial (KUP) Swiss:P30016 [3], yeast (HAK) Swiss:P50505 [2], and plant (AtKT) Swiss:O22397 [1] sequences as members. This entry represents the C-terminal non-membrane domain. [1]. 9350997. A new family of K+ transporters from Arabidopsis that are conserved across phyla. Quintero FJ, Blatt MR;. FEBS Lett 1997;415:206-211. [2]. 7621817. A potassium transporter of the yeast Schwanniomyces occidentalis homologous to the Kup system of Escherichia coli has a high concentrative capacity. Banuelos MA, Klein RD, Alexander-Bowman SJ, Rodriguez-Navarro A;. EMBO J 1995;14:3021-3027. [3]. 8226635. Nucleotide sequence and 3'-end deletion studies indicate that the K(+)-uptake protein kup from Escherichia coli is composed of a hydrophobic core linked to a large and partially essential hydrophilic C terminus. Schleyer M, Bakker EP;. J Bacteriol 1993;175:6925-6931. (from Pfam) NF046916.1 PF22780.1 HI0933_like_1st 27 27 165 domain Y N N HI0933-like protein barrel and H2TH domain 131567 cellular organisms no rank 79233 EBI-EMBL HI0933-like protein barrel and H2TH domain HI0933-like protein barrel and H2TH domain This entry represents two structural domains that are found inserted within a Rossmann domain. (from Pfam) NF046918.1 PF22785.1 Tc-R-P 27 27 106 domain Y N N Polymorphic toxin system, DSP-PTPase phosphatase 22731697,36968430 131567 cellular organisms no rank 23526 EBI-EMBL Polymorphic toxin system, DSP-PTPase phosphatase Polymorphic toxin system, DSP-PTPase phosphatase This domain occupies the toxin tip position in a subset of polymorphic toxin domains [1,2]. This domain is found at the extreme C-terminal of certain polymorphic toxin-related Tc-like toxins deployed by bacteria against eukaryotic host cells. This position is where the toxin module delivered into the target cells host resides [1]. [1]. 36968430. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. Burroughs AM, Aravind L;. NAR Genom Bioinform. 2023;5:lqad029. [2]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF046928.1 PF22809.1 DUF7014 27 27 137 domain Y Y N DUF7014 domain-containing protein 131567 cellular organisms no rank 1362 EBI-EMBL Domain of unknown function (DUF7014) Domain of unknown function (DUF7014) This domain is found in a group of bacterial proteins. It is often found C-terminal to Pfam:PF18863. It is predicted to adopt an all-alpha helical fold. (from Pfam) NF046935.1 PF22842.1 Pel9A-like_beta_helix 25.2 25.2 370 domain Y Y N right-handed parallel beta-helix repeat-containing protein 14670977 131567 cellular organisms no rank 11001 EBI-EMBL Pel9A-like, right handed beta helix region Pel9A-like, right handed beta helix region This region is found in Pectate lyase L from Erwinia chrysanthemi (Pel9A) and similar bacterial and fungal proteins. Pel9A shows endo-cleaving activity on polygalacturonate or partially methylated pectin and has an important role in soft -rot disease. This region forms a parallel beta helix domain [1]. [1]. 14670977. The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi. Jenkins J, Shevchik VE, Hugouvieux-Cotte-Pattat N, Pickersgill RW;. J Biol Chem. 2004;279:9139-9145. (from Pfam) NF046942.1 PF22866.1 DUF2804_C 27 27 121 domain Y Y N DUF2804 domain-containing protein 131567 cellular organisms no rank 10464 EBI-EMBL Domain of unknown function (DUF2804), C-terminal Domain of unknown function (DUF2804), C-terminal This entry represents a domain with unknown function. (from Pfam) NF046946.1 PF22880.1 DUF7019 22 22 212 subfamily Y Y N DUF7019 family protein 131567 cellular organisms no rank 1473 EBI-EMBL Family of unknown function (DUF7019) DUF7019 family protein This is a family of uncharacterised proteins found mainly in actinomycetes. Their function is unknown. They are predicted to adopt OB fold with significant similarity to Rpa. (from Pfam) NF046948.1 PF22887.1 DUF7022 27 27 166 subfamily Y Y N DUF7022 family protein 131567 cellular organisms no rank 5 EBI-EMBL Family of unknown function (DUF7022) DUF7022 family protein This uncharacterised protein is found in the T5 bacteriophage. The function of this protein is unknown. (from Pfam) NF046954.1 PF22912.1 zf-DPOE 24.5 24.5 65 domain Y N N Zinc finger domain of DNA polymerase-epsilon 30498216 131567 cellular organisms no rank 74 EBI-EMBL Zinc finger domain of DNA polymerase-epsilon Zinc finger domain of DNA polymerase-epsilon This zinc finger domain is found in the epsilon subunit of DNA polymerase. Paper describing PDB structure 6hv8. [1]. 30498216. Structure of DNA-CMG-Pol epsilon elucidates the roles of the non-catalytic polymerase modules in the eukaryotic replisome. Goswami P, Abid Ali F, Douglas ME, Locke J, Purkiss A, Janska A, Eickhoff P, Early A, Nans A, Cheung AMC, Diffley JFX, Costa A;. Nat Commun. 2018;9:5061. (from Pfam) NF046956.1 PF22924.1 ACOX_C_alpha1 27 27 169 domain Y N N Acyl-CoA oxidase, C-alpha1 domain 11872165,15581893,16699197,27551084,29198706 131567 cellular organisms no rank 119995 EBI-EMBL Acyl-CoA oxidase, C-alpha1 domain Acyl-CoA oxidase, C-alpha1 domain This entry represents the C-alpha1 domain from acyl-CoA oxidases which has an all-alpha helical structure that a forms a four-helix bundle [1-5]. This domain includes the FAD-binding and substrate-binding sites. Paper describing PDB structure 1is2. [1]. 11872165. Three-dimensional structure of the flavoenzyme acyl-CoA oxidase-II from rat liver, the peroxisomal counterpart of mitochondrial acyl-CoA dehydrogenase. Nakajima Y, Miyahara I, Hirotsu K, Nishina Y, Shiga K, Setoyama C, Tamaoki H, Miura R;. J Biochem. 2002;131:365-374. Paper describing PDB structure 1w07. [2]. 15581893. Acyl-CoA oxidase 1 from Arabidopsis thaliana. Structure of a key enzyme in plant lipid metabolism. Pedersen L, Henriksen A;. J Mol Biol. 2005;345:487-500. Paper describing PDB structure 2fon. [3]. 16699197. Structure determination and analysis of acyl-CoA oxidase (ACX1) from tomato. Powers RA, Rife CL, Schilmiller AL, Howe GA, Garavito RM;. Acta Crystallogr D Biol Crystallogr. 2006;62:683-686. Paper describing PDB structure 5k3g. [4]. 27551084. Structural characterization of acyl-CoA oxidases reveals a direct link between pheromone biosynthesis and metabolic state in Caenorhabditis elegans. Zhang X, Li K, Jones RA, Bruner SD, Butcher RA;. Proc Natl Acad Sci U S A. 2016;113:10055-10060. Paper describing PDB structure 5y9d. [5]. 29198706. Structural insight into the substrate specificity of acyl-CoA oxidase1 from Yarrowia lipolytica for short-chain dicarboxylyl-CoAs. Kim S, Kim KJ;. Biochem Biophys Res Commun. 2018;495:1628-1634. (from Pfam) NF046962.1 PF22936.1 Pol_BBD 27 27 81 domain Y N N Pol polyprotein, beta-barrel domain 131567 cellular organisms no rank 149 EBI-EMBL Pol polyprotein, beta-barrel domain Pol polyprotein, beta-barrel domain This domain is found in Retrovirus-related Pol polyproteins from transposon TNT 1-94. It is predicted to adopt a beta-barrel fold with significant similarity to retroviral acid proteases. (from Pfam) NF046973.1 PF22979.1 HTH_69 27 27 69 domain Y N N Winged helix-turn-helix domain 131567 cellular organisms no rank 21 EBI-EMBL Winged helix-turn-helix domain Winged helix-turn-helix domain This entry represents a winged helix-turn-helix domain that may bind to DNA. (from Pfam) NF046981.1 PF22825.1 HpiC1-like 27 27 174 domain Y N N HpiC1 cyclase 29531360 131567 cellular organisms no rank 624 EBI-EMBL HpiC1 cyclase HpiC1 cyclase This entry represents the homologues of HpiC1, a Stig cyclase that catalyzes the formation of 12-epi-hapalindole U. This enzyme folds into a beta-sandwich with jelly-roll topology that is distantly related to galactose-binding domains. HpiC1 has two integral Ca2+ ions, each with octahedral coordination geometry. Ca2+ ions are required for catalytic activity. [1]. 29531360. Structural basis of the Cope rearrangement and cyclization in hapalindole biogenesis. Newmister SA, Li S, Garcia-Borras M, Sanders JN, Yang S, Lowell AN, Yu F, Smith JL, Williams RM, Houk KN, Sherman DH;. Nat Chem Biol. 2018;14:345-351. (from Pfam) NF046985.1 PF22837.1 M_Eco57I_C 27 27 283 domain Y N N Type II methyltransferase M.Eco57I, C-terminal domain 131567 cellular organisms no rank 2847 EBI-EMBL Type II methyltransferase M.Eco57I, C-terminal domain Type II methyltransferase M.Eco57I, C-terminal domain This domain is found at the C-terminal of the gamma subtype methylase Type II methyltransferase M.Eco57I from Escherichia coli. This domain is predicted to adopt an alpha-beta configuration and is often found associated with Pfam:PF07669. (from Pfam) NF046989.1 PF22860.1 DUF7017 27.5 27.5 141 domain Y Y N DUF7017 domain-containing protein 131567 cellular organisms no rank 1658 EBI-EMBL Domain of unknown function (DUF7017) DUF7017 domain This entry represents a domain consisting of TPR repeats found at the N-terminal of of group of uncharacterised sequences predominantly from bacteria, which seem to be related to TOTE conflict systems as they are associated with Pfam:PF22708. (from Pfam) NF046994.1 PF22890.1 TPR_EMC2 27 27 145 domain Y N N EMC2 TPR-like repeat domain 32439656,32459176 131567 cellular organisms no rank 48 EBI-EMBL EMC2 TPR-like repeat domain EMC2 TPR-like repeat domain ER membrane protein complex subunit 2 (EMC2, also known as tetratricopeptide repeat protein 35) is a tetratricopeptide repeat-containing protein, and a component of the ER membrane protein complex (EMC), which is required for efficient folding of proteins in the endoplasmic reticulum (ER). EMC2 is a cytosolic component of the complex [2]. Purified recombinant EMC2 formed a stable complex with either EMC8 or EMC9 [2]. [1]. 32439656. Structural basis for membrane insertion by the human ER membrane protein complex. Pleiner T, Tomaleri GP, Januszyk K, Inglis AJ, Hazu M, Voorhees RM;. Science. 2020;369:433-436. Paper describing PDB structure 6y4l. [2]. 32459176. The architecture of EMC reveals a path for membrane protein insertion. O'Donnell JP, Phillips BP, Yagita Y, Juszkiewicz S, Wagner A, Malinverni D, Keenan RJ, Miller EA, Hegde RS;. Elife. 2020; [Epub ahead of print] (from Pfam) NF046998.1 PF22902.1 NOMO1-like_7th 27 27 75 domain Y N N BOS complex subunit NOMO1-like, beta sandwich domain 36261522 131567 cellular organisms no rank 47 EBI-EMBL BOS complex subunit NOMO1-like, beta sandwich domain BOS complex subunit NOMO1-like, beta sandwich domain This domain is found at the N-terminal end of human BOS complex subunit NOMO1 and similar sequences mainly from animals and plants. NOMO1 is a component of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes [1]. This domain is predicted to adopt a seven stranded beta sandwich fold. [1]. 36261522. Substrate-driven assembly of a translocon for multipass membrane proteins. Sundaram A, Yamsek M, Zhong F, Hooda Y, Hegde RS, Keenan RJ;. Nature. 2022;611:167-172. (from Pfam) NF047001.1 PF22922.1 GAF_NLP 24.1 24.1 175 domain Y N N NLP protein GAF domain 35871642 131567 cellular organisms no rank 338 EBI-EMBL NLP protein GAF domain NLP protein GAF domain This entry represents a GAF-like domain found in plant NLP proteins. Several NLP proteins contain two copies of this domain family. Members of the NLP family all contain an amino-terminal GAF domain, an intermediate RWP-RK domain, and a carboxy-terminal Phox and Bem1 (PB1) domain. Additionally, a nuclear export signal domain is predicted in the N-terminus [1]. [1]. 35871642. GAF domain is essential for nitrate-dependent AtNLP7 function. Wu J, Song Y, Zhang ZS, Wang JX, Zhang X, Zang JY, Bai MY, Yu LH, Xiang CB;. BMC Plant Biol. 2022;22:366. (from Pfam) NF047037.1 PF21848.1 DUF6907 26 26 116 domain Y Y N DUF6907 domain-containing protein 131567 cellular organisms no rank 4384 EBI-EMBL Domain of unknown function (DUF6907) DUF6907 domain This entry represents a family of Actinobacterial proteins of unknown function. AlphaFold predicts a confident dimeric arrangement. This family appears to be distantly realted to Pfam:PF19887. (from Pfam) NF047038.1 PF21850.1 DUF6909 27 27 535 subfamily Y Y N DUF6909 family protein 131567 cellular organisms no rank 3146 EBI-EMBL Family of unknown function (DUF6909) DUF6909 family protein This is a family of uncharacterised proteins. They are predicted to adopt a globular structure consisting of two domains. The predicted C-terminal domain share similarity with the catalytic domains of purine and uridine phosphorylases. (from Pfam) NF047043.1 PF21880.1 DUF6916 27 27 91 subfamily Y Y N DUF6916 family protein 131567 cellular organisms no rank 3468 EBI-EMBL Domain of unknown function (DUF6916) DUF6916 family protein This is a domain of unknown function found in bacterial proteins. It is predicted to adopt a RIFT-type beta(6)-barrel topology with a greater similarity to FAD-binding domains. (from Pfam) NF047050.1 PF21900.1 DUF6920 27 27 222 subfamily Y Y N DUF6920 family protein 131567 cellular organisms no rank 3764 EBI-EMBL Family of unknown function (DUF6920) DUF6920 family protein This entry represents a set of uncharacterised proteins found in prokaryotes. They share remote similarity to LolA and LolB outer-membrane lipoproteins. Similar to LolA and LolB these proteins are predicted to have a hydrophobic cavity consisting of an unclosed beta-barrel and an alpha-helical lid. (from Pfam) NF047061.1 PF21946.1 LppM 27 27 153 domain Y Y N LppM family (lipo)protein 27220037,27568926 131567 cellular organisms no rank 4143 EBI-EMBL LppM domain LppM family (lipo)protein LppM is a putative lipoprotein of Mycobacterium tuberculosis that has been shown to affect both phagocytosis by macrophages and progression of the phagosome into a more acidified compartment. Homologs of LppM, most of them appearing to be lipoproteins, are found broadly in the Actinomycetes. NF047071.1 PF21993.1 TetR_C_13_2 27 27 103 domain Y N N Transcriptional regulator LmrA/YxaF-like, C-terminal domain 16475182,17483215 131567 cellular organisms no rank 64923 EBI-EMBL Transcriptional regulator LmrA/YxaF-like, C-terminal domain Transcriptional regulator LmrA/YxaF-like, C-terminal domain This entry represents the C-terminal domain found in a group of TetR transcription regulators, including YxaF (also known as T1414) [1] and LmrA from Bacillus subtilis, which are paralogous to each other [2]. LmrA and YxaF are repressors that bind specifically to almost the same cis sequences, LmrA/YxaF boxes, located in the promoter regions of the lmrAB operon, the yxaF gene, and the yxaGH operon [2]. Paper describing PDB structure 1sgm. [1]. 16475182. Crystal structure of a putative HTH-type transcriptional regulator yxaF from Bacillus subtilis. Seetharaman J, Kumaran D, Bonanno JB, Burley SK, Swaminathan S;. Proteins. 2006;63:1087-1091. [2]. 17483215. Dual regulation of the Bacillus subtilis regulon comprising the lmrAB and yxaGH operons and yxaF gene by two transcriptional repressors, LmrA and YxaF, in response to flavonoids. Hirooka K, Kunikane S, Matsuoka H, Yoshida K, Kumamoto K, Tojo S, Fujita Y;. J Bacteriol. 2007;189:5170-5182. (from Pfam) NF047080.1 PF22022.1 Phage_int_M 27 27 96 domain Y Y N phage integrase central domain-containing protein 12887904,15973401,18540053,27223329 131567 cellular organisms no rank 129574 EBI-EMBL Phage integrase central domain Phage integrase central domain This is the central domain of phage integrases. This domain is known to mediate DNA binding and binds to the major groove adjacent to the site of DNA cleavage [1]. It consists of two pairs of antiparallel helices that pack together at nearly a right angle and form a four-helix bundle. Paper describing PDB structure 1p7d. [1]. 12887904. A conformational switch controls the DNA cleavage activity of lambda integrase. Aihara H, Kwon HJ, Nunes-Duby SE, Landy A, Ellenberger T;. Mol Cell. 2003;12:187-198. Paper describing PDB structure 1z19. [2]. 15973401. A structural basis for allosteric control of DNA recombination by lambda integrase. Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy A, Ellenberger T;. Nature. 2005;435:1059-1066. Paper describing PDB structure 2oxo. [3]. 18540053. Crystallization and structure determination of the core-binding domain of bacteriophage lambda integrase. Kamadurai HB, Jain R, Foster MP;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008;64:470-473. Paper describing PDB structure 5j0n. [4]. 27223329. Structure of a Holliday junction complex reveals mechanisms governing a highly regulated DNA transaction. Laxmikanthan G, Xu C, Brilot AF, Warren D, Steele L, Seah N, Tong W, Grigorieff N, Landy A, Van Duyne GD;. Elife. 2016; [Epub ahead of print] (from Pfam) NF047084.1 PF22039.1 HUTI_composite_bact 25.5 25.5 26 domain Y Y N imidazolonepropionase-like domain-containing protein 131567 cellular organisms no rank 16102 EBI-EMBL Imidazolonepropionase-like composite domain, bacteria Imidazolonepropionase-like composite domain, bacteria This entry represents the composite domain usually found in metal-dependent hydrolases which is interrupted by the catalytic alpha/beta barrel domain (Pfam:PF01979). This domain has a pseudo-barrel fold. This model covers the N-terminal segment of the composite domain of bacterial proteins, such as imidazolonepropionases. (from Pfam) NF047091.1 PF22073.1 Cep192_D4 27 27 112 domain Y N N Cep192 domain 4 35383272 131567 cellular organisms no rank 3778 EBI-EMBL Cep192 domain 4 Cep192 domain 4 Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation. Most of the metazoan Cep192 homologs consist of eight ASH/PapD-like domains. These are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion. This entry represents the fourth domain of the metazoan Cep192 homologs. This domain along with domain 5 constitutes the so-called Spd2 domain that is ubiquitously present in all SPD2/CEP192 homologues beyond Metazoa and represents the most conserved region amongst them [1]. [1]. 35383272. Structural validation and assessment of AlphaFold2 predictions for centrosomal and centriolar proteins and their complexes. van Breugel M, Rosa E Silva I, Andreeva A;. Commun Biol. 2022;5:312. (from Pfam) NF047093.1 PF22085.1 NorB_cytochrome_c-like 29 29 181 domain Y N N Nitric oxide reductase subunit B, cytochrome c-like domain 21109633,22266822,27185533,29483528,31489376 131567 cellular organisms no rank 8795 EBI-EMBL Nitric oxide reductase subunit B, cytochrome c-like domain Nitric oxide reductase subunit B, cytochrome c-like domain This domain is found in Nitric oxide reductase subunit B from Pseudomonas aeruginosa (NorB) and similar bacterial sequences. NorB is the large component of the anaerobic respiratory chain that transforms nitrate to dinitrogen (denitrification). This entry represents the cytochrome C-like domain of NorB, which has 12 alpha-helices in the transmembrane region with two heme irons and and one non-heme iron [2]. Paper describing PDB structure 3ayf. [1]. 22266822. Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus. Matsumoto Y, Tosha T, Pisliakov AV, Hino T, Sugimoto H, Nagano S, Sugita Y, Shiro Y;. Nat Struct Mol Biol. 2012;19:238-245. Paper describing PDB structure 3o0r. [2]. 21109633. Structural basis of biological N2O generation by bacterial nitric oxide reductase. Hino T, Matsumoto Y, Nagano S, Sugimoto H, Fukumori Y, Murata T, Iwata S, Shiro Y;. Science. 2010;330:1666-1670. Paper describing PDB structure 4xyd. [3]. 27185533. Structure of the Membrane-intrinsic Nitric Oxide Reductase from Roseobacter denitrificans. Crow A, Matsuda Y, Arata H, Oubrie A;. Biochemistry. 2016;55:3198-3203. Paper describing PDB structure 6fwf. [4]. 29483528. Characterization of the quinol-dependent nitric oxide reductase from the pathogen Neisseria meningitidis, an electrogenic enzyme. Gonska N, Young D, Yuki R, Okamoto T, Hisano T, Antonyuk S, Hasnain SS, Muramoto K, Shiro Y, Tosha T, Adelroth P;. Sci Rep. 2018;8:3637. Paper describing PDB structure 6qq5. [5]. 31489376. Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo-electron microscopy. Gopalasingam CC, Johns. TRUNCATED at 1650 bytes (from Pfam) NF047104.1 PF22117.1 Nqo3_Fer4 27 27 67 domain Y N N NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain 16469879,27509854,27595392,28844695,29395787 131567 cellular organisms no rank 67097 EBI-EMBL NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain NADH-quinone oxidoreductase subunit 3 (Nqo3) is a component of respiratory complex I. This protein is located at the peripheral arm of the complex and consists of multiple domains. This entry represents the second ferredoxin-like domain which contains Fe4-S4 cluster, one of the redox centers of the complex [1-5]. Paper describing PDB structure 2fug. [1]. 16469879. Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. Sazanov LA, Hinchliffe P;. Science. 2006;311:1430-1436. Paper describing PDB structure 5lc5. [2]. 27509854. Structure of mammalian respiratory complex I. Zhu J, Vinothkumar KR, Hirst J;. Nature. 2016;536:354-358. Paper describing PDB structure 5lnk. [3]. 27595392. Atomic structure of the entire mammalian mitochondrial complex I. Fiedorczuk K, Letts JA, Degliesposti G, Kaszuba K, Skehel M, Sazanov LA;. Nature. 2016;538:406-410. Paper describing PDB structure 5o31. [4]. 29395787. Structure of the Deactive State of Mammalian Respiratory Complex I. Blaza JN, Vinothkumar KR, Hirst J;. Structure. 2018;26:312-319. Paper describing PDB structure 5xtb. [5]. 28844695. Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2. Guo R, Zong S, Wu M, Gu J, Yang M;. Cell. 2017;170:1247-1257. (from Pfam) NF047111.1 PF22148.1 Fervidolysin_NPro-like 21 21 81 domain Y Y N S8 family serine peptidase 14687574 131567 cellular organisms no rank 8953 EBI-EMBL Fervidolysin N-terminal prodomain S8 family serine peptidase prodomain The founding member of this family is the N-terminal prodomain of fervidolysin, an extracellular subtilisin-like serine protease. This domain folds into a globular alpha/beta structure consisting of four-stranded antiparallel beta-sheet and two alpha-helices packed on one side of it [1]. The prodomain is proteolytically cleaved and removed from the proenzyme. Paper describing PDB structure 1r6v. [1]. 14687574. Crystal structure of fervidolysin from Fervidobacterium pennivorans, a keratinolytic enzyme related to subtilisin. Kim JS, Kluskens LD, de Vos WM, Huber R, van der Oost J;. J Mol Biol. 2004;335:787-797. (from Pfam) NF047115.1 PF22159.1 PSMA-like_N 26 26 329 domain Y N N Maltose-forming alpha-amylase-like, N-terminal domain 23884203,24914977 131567 cellular organisms no rank 103 EBI-EMBL Maltose-forming alpha-amylase-like, N-terminal domain Maltose-forming alpha-amylase-like, N-terminal domain This domain is found in the maltose-forming alpha-amylase from the hyperthermophilic archaeon Pyrococcus sp. ST04 (PSMA). This enzyme is able to hydrolyse both alpha-1,4-glucosidic and alpha-1,6-glucosidic bonds. PSMA protein consists of two domains: an N-terminal domain with a typical glycoside hydrolase 57 family (beta]/alpha)7-barrel fold and a C-terminal domain composed of alpha-helical bundles. This entry represents the N-terminal domain [1,2]. Paper describing PDB structure 4cmr. [1]. 24914977. Structural features underlying the selective cleavage of a novel exo-type maltose-forming amylase from Pyrococcus sp. ST04. Park KH, Jung JH, Park SG, Lee ME, Holden JF, Park CS, Woo EJ;. Acta Crystallogr D Biol Crystallogr. 2014;70:1659-1668. [2]. 23884203. Maltose-forming alpha-amylase from the hyperthermophilic archaeon Pyrococcus sp. ST04. Jung JH, Seo DH, Holden JF, Park CS;. Appl Microbiol Biotechnol. 2014;98:2121-2131. (from Pfam) NF047118.1 PF22167.1 PH0730-like_N 30.2 30.2 60 domain Y N N PH0730-like, N-terminal domain 131567 cellular organisms no rank 190 EBI-EMBL PH0730-like, N-terminal domain PH0730-like, N-terminal domain This domain is found at the N-terminal end of PH0730 from Pyrococcus horikoshii and similar archaeal proteins that contain the domain Pfam:PF14544 at the C-terminal. This domain adopts a winged helix fold. (from Pfam) NF047125.1 PF22199.1 FKBP26_IF 27 27 46 domain Y N N FKBP26, IF domain 12729748,21262232 131567 cellular organisms no rank 1417 EBI-EMBL FKBP26, IF domain FKBP26, IF domain This domain is centrally located in Long-type peptidyl-prolyl cis-trans isomerase from Methanocaldococcus jannaschii (FKBP26) and similar archaeal sequences. FKBP26 catalyses the cis-trans isomerisation of peptidyl prolyl bonds and exhibits chaperone -like activity. The latter activity requires a 50-residue insertion (IF domain, for 'Insert-in-Flap', this entry) in the catalytic FKBP domain (Pfam:PF00254). It resembles a fractured four-stranded beta-barrel with the first and second strands connected by a helix that partially covers the fracture. It shows a highly hydrophobic surface [1,2]. Paper describing PDB structure 1ix5. [1]. 12729748. Three-dimensional solution structure of an archaeal FKBP with a dual function of peptidyl prolyl cis-trans isomerase and chaperone-like activities. Suzuki R, Nagata K, Yumoto F, Kawakami M, Nemoto N, Furutani M, Adachi K, Maruyama T, Tanokura M;. J Mol Biol. 2003;328:1149-1160. Paper describing PDB structure 3pr9. [2]. 21262232. Structural analysis of protein folding by the long-chain archaeal chaperone FKBP26. Martinez-Hackert E, Hendrickson WA;. J Mol Biol. 2011;407:450-464. (from Pfam) NF047126.1 PF22205.1 Csm6_6H 27.6 27.6 93 domain Y N N Csm6 6H domain 26763118,31326273,33461211 131567 cellular organisms no rank 398 EBI-EMBL Csm6 6H domain Csm6 6H domain This entry represents the six-helix domain (6H) of Csm6 from Thermus termophilus and relates sequences [1]. Csm6 is a ssRNA-specific endoribonuclease that provides an auxiliary RNA-targeting interference mechanism in type III-A CRISPR-Cas systems, working together with the RNA- and DNA-targeting endonuclease activities of the Csm effector complex. Csm6 consists of a CARF domain at the N-terminal, a 6H central domain and the HEPN domain (Pfam:PF09670) at the C-terminal [1-3]. [1]. 26763118. Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6. Niewoehner O, Jinek M;. RNA. 2016;22:318-329. [2]. 33461211. The Card1 nuclease provides defence during type III CRISPR immunity. Rostol JT, Xie W, Kuryavyi V, Maguin P, Kao K, Froom R, Patel DJ, Marraffini LA;. Nature. 2021;590:624-629. [3]. 31326273. CRISPR-Cas III-A Csm6 CARF Domain Is a Ring Nuclease Triggering Stepwise cA(4) Cleavage with ApA>p Formation Terminating RNase Activity. Jia N, Jones R, Yang G, Ouerfelli O, Patel DJ;. Mol Cell. 2019;75:944-956. (from Pfam) NF047128.1 PF22222.1 Cpf1_PI-like 27 27 91 domain Y N N CRISPR-associated endonuclease Cpf1 PI domain 27096363,28431230,28562584,28781234,30503205 131567 cellular organisms no rank 278 EBI-EMBL CRISPR-associated endonuclease Cpf1 PI domain CRISPR-associated endonuclease Cpf1 PI domain The CRISPR-Cpf1 system is a class 2 CRISPR-Cas system that mediates robust DNA interference. Cpf1 differ from Cas9 in many aspects including the guide RNAs and substrate specificity. The Cpf1-crRNA complex cleaves a target double-stranded DNA containing a short T-rich PAM motif on the 5' end of the non-target strand. This PAM motif is recognized by the Cpf1 PI (PAM-interacting) domain. This domain folds into array of four helices and along with the helix-loop-helix motif in the REC1 domain, channel the PAM strand into a cavity leading to the nuclease site [1-2]. Paper describing PDB structure 5id6. [1]. 27096363. The crystal structure of Cpf1 in complex with CRISPR RNA. Dong D, Ren K, Qiu X, Zheng J, Guo M, Guan X, Liu H, Li N, Zhang B, Yang D, Ma C, Wang S, Wu D, Ma Y, Fan S, Wang J, Gao N, Huang Z;. Nature. 2016;532:522-526. Paper describing PDB structure 5mga. [2]. 28562584. Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage. Stella S, Alcon P, Montoya G;. Nature. 2017;546:559-563. Paper describing PDB structure 5nfv. [3]. 28431230. Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a. Swarts DC, van der Oost J, Jinek M;. Mol Cell. 2017;66:221-233. Paper describing PDB structure 5xus. [4]. 28781234. Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1. Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu H, Nureki O;. Mol Cell. 2017;67:633-645. Paper describing PDB structure 6gtc. [5]. 30503205. Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity. Stella S, Mesa P, Thomsen J, Pa. TRUNCATED at 1650 bytes (from Pfam) NF047132.1 PF22240.1 ISP_coupler 27 27 126 domain Y N N Type ISP restriction-modification enzyme, coupler domain 26389736,26975655,33826880 131567 cellular organisms no rank 7453 EBI-EMBL Type ISP restriction-modification enzyme, coupler domain Type ISP restriction-modification enzyme, coupler domain Type ISP restriction-modification (RM) enzymes cleave random DNA between distant target sites when two enzymes collide following convergent ATP-driven translocation. This entry represents the all-helical coupler domain of type ISP RM enzymes, which links the ATPase to the MTase and the C-terminal TRD (target recognition domain) domains and seems to play a key role in transferring conformational strain during initiation [1-3]. Paper describing PDB structure 4xqk. [1]. 26389736. Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymes. Chand MK, Nirwan N, Diffin FM, van Aelst K, Kulkarni M, Pernstich C, Szczelkun MD, Saikrishnan K;. Nat Chem Biol. 2015;11:870-877. Paper describing PDB structure 5ffj. [2]. 26975655. Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes. Kulkarni M, Nirwan N, van Aelst K, Szczelkun MD, Saikrishnan K;. Nucleic Acids Res. 2016;44:4396-4408. Paper describing PDB structure 7lo5. [3]. 33826880. Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM. Shen BW, Quispe JD, Luyten Y, McGough BE, Morgan RD, Stoddard BL;. Structure. 2021;29:521-530. (from Pfam) NF047147.1 PF22290.1 DmmA-like_N 33 33 124 domain Y N N Dimethylamine monooxygenase subunit DmmA-like, N-terminal domain 25088783,28304370 131567 cellular organisms no rank 16435 EBI-EMBL Dimethylamine monooxygenase subunit DmmA-like, N-terminal domain Dimethylamine monooxygenase subunit DmmA-like, N-terminal domain This entry represents the N-terminal domain of the dimethylamine monooxygenase subunit DmmA from Methylocella silvestris (Msil_3607, Swiss:B8EJ00) and similar sequences, mainly found in proteobacteria and actinomycetes. Dimethylamine (DMA) monooxygenase is required for metabolism of trimethylamine N-oxide (TMAO) [1,2]. This domain may adopt a Rossmann-like fold similar to Ferredoxin/Ferric reductase-like NAD binding domain. [1]. 25088783. Identification and characterization of trimethylamine N-oxide (TMAO) demethylase and TMAO permease in Methylocella silvestris BL2. Zhu Y, Jameson E, Parslow RA, Lidbury I, Fu T, Dafforn TR, Schafer H, Chen Y;. Environ Microbiol. 2014;16:3318-3330. [2]. 28304370. Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the methylated amine degradation pathway. Lidbury I, Mausz MA, Scanlan DJ, Chen Y;. ISME J. 2017;11:1592-1601. (from Pfam) NF047160.1 PF22352.1 K319L-like_PKD 27 27 84 domain Y Y N PKD domain-containing protein 16314409,17962295,21905122,21947205,23703618 131567 cellular organisms no rank 36728 EBI-EMBL K319L-like, PKD domain K319L-like, PKD domain This entry represents the PKD domain of Dyslexia-associated protein KIAA0319-like protein, in which it is found in four copies. This entry also includes Kunitz-type protease inhibitor 1 and LRP11 from human. Paper describing PDB structure 2c26. [1]. 16314409. Xyloglucan is recognized by carbohydrate-binding modules that interact with beta-glucan chains. Najmudin S, Guerreiro CI, Carvalho AL, Prates JA, Correia MA, Alves VD, Ferreira LM, Romao MJ, Gilbert HJ, Bolam DN, Fontes CM;. J Biol Chem. 2006;281:8815-8828. Paper describing PDB structure 2y3u. [2]. 21947205. Structure of collagenase G reveals a chew-and-digest mechanism of bacterial collagenolysis. Eckhard U, Schonauer E, Nuss D, Brandstetter H;. Nat Struct Mol Biol. 2011;18:1109-1114. Paper describing PDB structure 2yhg. [3]. 21905122. Ab initio phasing of a nucleoside hydrolase-related hypothetical protein from Saccharophagus degradans that is associated with carbohydrate metabolism. Hehemann JH, Marsters C, Boraston AB;. Proteins. 2011;79:2992-2998. Paper describing PDB structure 2z4t. [4]. 17962295. Crystal structure of Vibrionaceae Photobacterium sp. JT-ISH-224 alpha2,6-sialyltransferase in a ternary complex with donor product CMP and acceptor substrate lactose: catalytic mechanism and substrate recognition. Kakuta Y, Okino N, Kajiwara H, Ichikawa M, Takakura Y, Ito M, Yamamoto T;. Glycobiology. 2008;18:66-73. Paper describing PDB structure 4aqo. [5]. 23703618. Structural basis for activity regulation and substrate preference of clostridial collagenases G, H, and T. Eckhard U, Schonauer E, Brandstetter H;. J Biol Chem. 2013;288:20184-20194. (from Pfam) NF047162.1 PF22359.1 Big-like 27 27 48 domain Y N N Bacterial Ig-like domain 23794438 131567 cellular organisms no rank 5504 EBI-EMBL Bacterial Ig-like domain Bacterial Ig-like domain This entry represents bacterial domains that are structurally similar to an immunoglobulin-like domain of intimins. Members of this family include Beta-xylanase from the uncultured bacterium 35A30 [1]. [1]. 23794438. Biochemical characterization and crystal structure of a GH10 xylanase from termite gut bacteria reveal a novel structural feature and significance of its bacterial Ig-like domain. Han Q, Liu N, Robinson H, Cao L, Qian C, Wang Q, Xie L, Ding H, Wang Q, Huang Y, Li J, Zhou Z;. Biotechnol Bioeng. 2013;110:3093-3103. (from Pfam) NF047172.1 PF22381.1 Staph_reg_Sar_Rot 27 27 85 domain Y Y N transcriptional regulator, SarA/Rot family 11381122,12837797,16455801,25195759,25331435 131567 cellular organisms no rank 184791 EBI-EMBL Transcriptional regulator SarA/Rot transcriptional regulator, SarA/Rot family This entry represents transcriptional regulatory proteins in Staphylococcal species including SarA and Rot [1-5]. Sar is a global regulator with both positive and negative effects that controls expression of several virulence factors and biofilm formation process in a cell density-dependent manner. Rot plays a key role in regulating S. aureus virulence through activation or repression of promoters that control expression of a large number of critical virulence factors [5]. Paper describing PDB structure 1hsj. [1]. 11381122. Crystal structure of the SarR protein from Staphylococcus aureus. Liu Y, Manna A, Li R, Martin WE, Murphy RC, Cheung AL, Zhang G;. Proc Natl Acad Sci U S A. 2001;98:6877-6882. Paper describing PDB structure 1p4x. [2]. 12837797. Crystal structure of the SarS protein from Staphylococcus aureus. Li R, Manna AC, Dai S, Cheung AL, Zhang G;. J Bacteriol. 2003;185:4219-4225. Paper describing PDB structure 2fnp. [3]. 16455801. Structural and function analyses of the global regulatory protein SarA from Staphylococcus aureus. Liu Y, Manna AC, Pan CH, Kriksunov IA, Thiel DJ, Cheung AL, Zhang G;. Proc Natl Acad Sci U S A. 2006;103:2392-2397. Paper describing PDB structure 4q77. [4]. 25195759. Structure of Rot, a global regulator of virulence genes in Staphylococcus aureus. Zhu Y, Fan X, Zhang X, Jiang X, Niu L, Teng M, Li X;. Acta Crystallogr D Biol Crystallogr. 2014;70:2467-2476. Paper describing PDB structure 4rbr. [5]. 25331435. Structure-based functional characterization of repressor of toxin (Rot), a central regulator of Staphylococcus aureus virulence. Killikelly A, Benson MA, Ohneck EA, Sampson JM, Jakoncic . TRUNCATED at 1650 bytes (from Pfam) NF047178.1 PF22393.1 MLPTv-like_HTH 20 20 83 domain Y Y N winged helix-turn-helix domain-containing protein 20162616 131567 cellular organisms no rank 13 EBI-EMBL MLPTv-like, helix-turn-helix domain winged helix-turn-helix domain-containing protein This entry represents a winged helix-turn-helix (wHTH) domain present in MLPTv (MarR-like protein from Thermoplasma volcanium) [1]. Paper describing PDB structure 3lfk. [1]. 20162616. A reported archaeal mechanosensitive channel is a structural homolog of MarR-like transcriptional regulators. Liu Z, Walton TA, Rees DC;. Protein Sci. 2010;19:808-814. (from Pfam) NF047180.1 PF22421.1 SYY_C-terminal 27 27 83 domain Y N N Tyrosine--tRNA ligase SYY-like C-terminal domain 11007480,11014183,11296217,11567092,12005430 131567 cellular organisms no rank 57388 EBI-EMBL Tyrosine--tRNA ligase SYY-like C-terminal domain Tyrosine--tRNA ligase SYY-like C-terminal domain This entry represents the C-terminal domain of Tyrosine--tRNA ligases which contains the S4 motif that binds RNA [1-5]. Paper describing PDB structure 1fjg. [1]. 11014183. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V;. Nature. 2000;407:340-348. Paper describing PDB structure 1fka. [2]. 11007480. Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A;. Cell. 2000;102:615-623. Paper describing PDB structure 1i94. [3]. 11296217. Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3. Pioletti M, Schlunzen F, Harms J, Zarivach R, Gluhmann M, Avila H, Bashan A, Bartels H, Auerbach T, Jacobi C, Hartsch T, Yonath A, Franceschi F;. EMBO J. 2001;20:1829-1839. Paper describing PDB structure 1jh3. [4]. 12005430. Structure and dynamics of the anticodon arm binding domain of Bacillus stearothermophilus Tyrosyl-tRNA synthetase. Guijarro JI, Pintar A, Prochnicka-Chalufour A, Guez V, Gilquin B, Bedouelle H, Delepierre M;. Structure. 2002;10:311-317. Paper describing PDB structure 1jii. [5]. 11567092. Crystal structure of Staphylococcus aureus tyrosyl-tRNA synthetase in complex with a class of potent and specific inhibitors. Qiu X, Janson CA, Smith WW, Green SM, McDevitt P, Johanson K, Carter P, Hibbs M, Lewis C, Chalker A, Fosberry A, Lalonde J, Berge J, Brown P, Houge-Frydrych CS, Jarvest RL;. Protein. TRUNCATED at 1650 bytes (from Pfam) NF047182.1 PF22448.1 RepB_primase_C 26.1 26.1 54 domain Y N N RepB DNA-primase C-terminal helical domain 19416864 131567 cellular organisms no rank 721 EBI-EMBL RepB DNA-primase C-terminal helical domain RepB DNA-primase C-terminal helical domain RepB_primase is a DNA-primase produced by P4-like phages. It is a zinc-independent primase unlike Pri-type primases. It takes up a dumbbell shaped consisting of an N-terminal catalytic domain separated by a long alpha-helix plus tether and a C-terminal helical-bundle domain. Primases are necessary for phage replication. RepBprime primases such as in this family recognise both ssiA and ssiB, ie only 1 single-stranded primase initiation site on each strand, independently of each other and then synthesise primers that are elongated by DNA polymerase III. The phage is thus replicated exclusively in leading strand mode [1]. Paper describing PDB structure 3h20. [1]. 19416864. Structure and function of primase RepB' encoded by broad-host-range plasmid RSF1010 that replicates exclusively in leading-strand mode. Geibel S, Banchenko S, Engel M, Lanka E, Saenger W;. Proc Natl Acad Sci U S A. 2009;106:7810-7815. (from Pfam) NF047189.1 PF22494.1 choice_anch_I 32 32 489 domain Y Y N choice-of-anchor I domain-containing protein 131567 cellular organisms no rank 12201 EBI-EMBL Choice-of-anchor I domain choice-of-anchor I domain This entry represents the choice-of-anchor I domain. (from Pfam) NF047191.1 PF22503.1 DUF6992 27 27 122 subfamily Y Y N DUF6992 family protein 131567 cellular organisms no rank 1110 EBI-EMBL Family of unknown function (DUF6992) DUF6992 family protein This is a family of uncharacterised bacterial proteins. They are enriched with hydrophobic residues and are likely associated with the membrane. These proteins contain two conserved motifs GLDxxYxxxG and FLxxFD. (from Pfam) NF047194.1 PF22511.1 DUF6995 27 27 63 domain Y Y N DUF6995 domain-containing protein 131567 cellular organisms no rank 73 EBI-EMBL Family of unknown function (DUF6995) DUF6995 domain This is a family of uncharacterised proteins found mainly in Archaea. They are closely related to PBP2, a subunit of PolB1 enzyme that is a member of the archaeal B-family of DNA polymerases. These proteins are predicted to similarly adopt a winged helix (HTH) fold. (from Pfam) NF047196.1 PF22522.1 DUF6998 27 27 136 domain Y Y N DUF6998 domain-containing protein 131567 cellular organisms no rank 3000 EBI-EMBL Family of unknown function (DUF6998) DUF6998 domain This is a family of uncharacterised bacterial proteins. They share significant sequence similarity with PvuII endonucleases and are predicted to adopt similar structure. The predicted structures, however, do not suggest similarity in the active site architecture. (from Pfam) NF047197.1 PF22523.1 DUF6999 27 27 275 subfamily Y Y N DUF6999 family protein 131567 cellular organisms no rank 1426 EBI-EMBL Family of unknown function (DUF6999) DUF6999 family protein This is a family of uncharacterised bacterial proteins. They are predicted to adopt alpha-helical structure. These proteins contain several invariant histidines and aspartates that may have a functional role. (from Pfam) NF047198.1 PF22526.1 DUF7000 27 27 156 subfamily Y Y N DUF7000 family protein 131567 cellular organisms no rank 661 EBI-EMBL Family of unknown function (DUF7000) DUF7000 family protein This is a family of uncharacterised bacterial proteins. They are predicted to adopt an alpha/beta structure consisting of a cradle-like beta-sheet with alpha-helices pocked on the convex side of it. These proteins contain a highly conserved GYMDFTYF sequence motif that may be of functional importance. (from Pfam) NF047200.1 PF22539.1 DUF7004 27 27 155 subfamily Y Y N DUF7004 family protein 131567 cellular organisms no rank 192 EBI-EMBL Family of unknown function (DUF7004) DUF7004 family protein This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 160 amino acids in length. They are predicted to adopt globular alpha/beta structure. These proteins contain two highly conserved sequence motifs GxFDxWC and KRxKRLG that may be of functional importance. (from Pfam) NF047202.1 PF22548.1 AEP-TOTE 27 27 230 domain Y Y N TOTE conflict system archaeo-eukaryotic primase domain-containing protein 35609893 131567 cellular organisms no rank 7557 EBI-EMBL TOTE conflict system, Archaeo-Eukaryotic Primase domain TOTE conflict system, Archaeo-Eukaryotic Primase domain This entry represents the Archaeo-Eukaryotic Primase domain predicted to function as RNA polymerases in the TOTE (TPR, OB, TBP, Effector) conflict systems, potentially generating transcripts for hybrid duplex formation [1]. [1]. 35609893. Discovering Biological Conflict Systems Through Genome Analysis: Evolutionary Principles and Biochemical Novelty. Aravind L, Iyer LM, Burroughs AM;. Annu Rev Biomed Data Sci. 2022;5:367-391. (from Pfam) NF047206.1 PF22557.1 DuOB 27 27 210 domain Y Y N dual OB domain-containing protein 36968430 131567 cellular organisms no rank 1425 EBI-EMBL Dual OB-containing domain Dual OB-containing domain This entry contains two domain copies of the OB fold. There is nearly absolutely conserved cysteine, serine/threonine, arginine, and aspartate residues which are predicted to line a deep cleft formed at the interface of the two OB domains. The predicted spatial arrangement of the tandem OB domains closely parallels OB-dyads from single-stranded nucleic acid-end binding proteins, such as the telomere-binding domain alpha-subunit, with the nucleic acid being lodged in a cleft formed by the two OB domains. Drawing an analogy to the SRAP domain, it has been suggested that the DuOB domain could potentially form crosslinks to DNA at the abasic sites via its conserved cysteine. It is found on the genome adjacent to DUF488 and DUF4326 proteins, which could potentially also catalyse thiotransfer reactions required for forming or resolving the cysteine-DNA crosslinks, paralleling recent findings where HD phosphatases mediate the transfer of a phosphorylated substrate to a hydroxyl-group-containing residue [1]. [1]. 36968430. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. Burroughs AM, Aravind L;. NAR Genom Bioinform. 2023;5:lqad029. (from Pfam) NF047207.1 PF22560.1 GMT-wHTH 27 27 82 domain Y N N GMT-like wHTH domain 36968430 131567 cellular organisms no rank 1210 EBI-EMBL GMT-like wHTH domain GMT-like wHTH domain This entry represents a rapidly-evolving wHTH domain C-terminally fused to Rossmann fold methylase specifically related to the guanine methylase. Often co-occurs on the genome across a broad range of bacterial phylogenies with a further gene encoding a RADICAL SAM enzyme (DUF5131 Pfam:PF07505). This two-gene island is predicted to catalyse a DNA/RNA guanine modification comparable to the precursors of Wybutosine. This wHTH domain could be a sensor that recognises a rapidly-evolving nucleic acid sequence, implicating the gene pair in a conflict response to an invasive genic element [1]. [1]. 36968430. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. Burroughs AM, Aravind L;. NAR Genom Bioinform. 2023;5:lqad029. (from Pfam) NF047210.1 PF22569.1 DCD_C 22 22 192 domain Y N N 2'-deoxycytidine 5'-triphosphate deaminase (DCD), C-terminal domain 131567 cellular organisms no rank 16796 EBI-EMBL 2'-deoxycytidine 5'-triphosphate deaminase (DCD), C-terminal domain 2'-deoxycytidine 5'-triphosphate deaminase (DCD), C-terminal domain This entry includes several bacterial 2'-deoxycytidine 5'-triphosphate deaminase proteins (EC:3.5.4.13) (DCD) which consist of two dUTPase-like domains (PDBe:2r9q). This entry represents the C-terminal domain. (from Pfam) NF047213.1 PF22580.1 KYNU_C 27 27 90 domain Y N N Kynureninase C-terminal domain 14756555,17300176,19143568,25517350,27139833 131567 cellular organisms no rank 38634 EBI-EMBL Kynureninase C-terminal domain Kynureninase C-terminal domain This entry represents de C-terminal domain of kynureninase [1-5], a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyse the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases [1-5].. Paper describing PDB structure 1qz9. [1]. 14756555. Three-dimensional structure of kynureninase from Pseudomonas fluorescens. Momany C, Levdikov V, Blagova L, Lima S, Phillips RS;. Biochemistry. 2004;43:1193-1203. Paper describing PDB structure 2hzp. [2]. 17300176. Crystal structure of Homo sapiens kynureninase. Lima S, Khristoforov R, Momany C, Phillips RS;. Biochemistry. 2007;46:2735-2744. Paper describing PDB structure 3e9k. [3]. 19143568. Crystal structure of the Homo sapiens kynureninase-3-hydroxyhippuric acid inhibitor complex: insights into the molecular basis of kynureninase substrate specificity. Lima S, Kumar S, Gawandi V, Momany C, Phillips RS;. J Med Chem. 2009;52:389-396. Paper describing PDB structure 4pjq. [4]. 25517350. An artificial PPR scaffold for programmable RNA recognition. Coquille S, Filipovska A, Chia T, Rajappa L, Lingford JP, Razif MF, Thore S, Rackham O;. Nat Commun. 2014;5:5729. Paper describing PDB structure 5i90. [5]. 27139833. 1.2 A resolution crystal structure of the periplasmic aminotransferase PvdN from Pseudomonas aeruginosa. Drake EJ, Gulick AM;. Acta Crystallogr F Struct Biol Commun. 2016;72:403-408. (from Pfam) NF047219.1 PF22608.1 DNAX_ATPase_lid 27 27 49 domain Y N N DNA polymerase III clamp loader subunit, ATPase lid domain 11525729,12623013,15556993,19450514 131567 cellular organisms no rank 100474 EBI-EMBL DNA polymerase III clamp loader subunit, ATPase lid domain DNA polymerase III clamp loader subunit, ATPase lid domain This entry represents the AAA+ ATPase lid domain of DNA polymerase III clamp loader subunit [1-4]. Paper describing PDB structure 1jr3. [1]. 11525729. Crystal structure of the processivity clamp loader gamma (gamma) complex of E. coli DNA polymerase III. Jeruzalmi D, O'Donnell M, Kuriyan J;. Cell. 2001;106:429-441. Paper describing PDB structure 1njf. [2]. 12623013. Nucleotide-induced conformational changes in an isolated Escherichia coli DNA polymerase III clamp loader subunit. Podobnik M, Weitze TF, O'Donnell M, Kuriyan J;. Structure. 2003;11:253-263. Paper describing PDB structure 1xxi. [3]. 15556993. Structural analysis of the inactive state of the Escherichia coli DNA polymerase clamp-loader complex. Kazmirski SL, Podobnik M, Weitze TF, O'Donnell M, Kuriyan J;. Proc Natl Acad Sci U S A. 2004;101:16750-16755. Paper describing PDB structure 3glf. [4]. 19450514. The mechanism of ATP-dependent primer-template recognition by a clamp loader complex. Simonetta KR, Kazmirski SL, Goedken ER, Cantor AJ, Kelch BA, McNally R, Seyedin SN, Makino DL, O'Donnell M, Kuriyan J;. Cell. 2009;137:659-671. (from Pfam) NF047228.1 PF22637.1 CBM_4_9_1 27 27 148 domain Y N N BppA domain 1 11980475,12079353,18025086,22434778,26814179,8916925 131567 cellular organisms no rank 1838 EBI-EMBL BppA domain 1 BppA domain 1 This entry represents domain found in accessory protein BppA and related proteins. Given the structural similarity to carbohydrate binding domains, it is likely that this domain is a carbohydrate binding module. BppA is a virion's baseplate component. The precise role of this protein in absorption is elusive but the presence of a carbohydrate binding domain with an extended saccharidic binding site suggests that this protein probably participates in receptor binding together with the bona fide receptor binding proteins [6]. Paper describing PDB structure 1gu3. [1]. 12079353. Differential oligosaccharide recognition by evolutionarily-related beta-1,4 and beta-1,3 glucan-binding modules. Boraston AB, Nurizzo D, Notenboom V, Ducros V, Rose DR, Kilburn DG, Davies GJ;. J Mol Biol. 2002;319:1143-1156. Paper describing PDB structure 1k42. [2]. 11980475. The solution structure of the CBM4-2 carbohydrate binding module from a thermostable Rhodothermus marinus xylanase. Simpson PJ, Jamieson SJ, Abou-Hachem M, Karlsson EN, Gilbert HJ, Holst O, Williamson MP;. Biochemistry. 2002;41:5712-5719. Paper describing PDB structure 1ulo. [3]. 8916925. Structure of the N-terminal cellulose-binding domain of Cellulomonas fimi CenC determined by nuclear magnetic resonance spectroscopy. Johnson PE, Joshi MD, Tomme P, Kilburn DG, McIntosh LP;. Biochemistry 1996;35:14381-14394. Paper describing PDB structure 2y64. [4]. 22434778. Structural basis for carbohydrate-binding specificity--a comparative assessment of two engineered carbohydrate-binding modules. von Schantz L, Hakansson M, Logan DT, Walse B, Osterlin J, Nordberg-Karlsson E, Ohlin M;. Glycob. TRUNCATED at 1650 bytes (from Pfam) NF047232.1 PF22645.1 GKRP_SIS_N 27 27 113 domain Y N N Glucokinase regulatory protein N-terminal SIS domain 23621087,23733961,23957911,24226772,24251551 131567 cellular organisms no rank 41312 EBI-EMBL Glucokinase regulatory protein N-terminal SIS domain Glucokinase regulatory protein N-terminal SIS domain This domain is found N-terminal in glucokinase regulatory protein (GKRP) and related proteins. GKRP regulates glucokinase and it is activated by fructose 6-phosphate and inactivated by fructose 1-phosphate. It consists of two topologically identical SIS domains and and alpha-helical lid domain [1-4]. Paper describing PDB structure 3w0l. [1]. 23733961. Molecular basis for the role of glucokinase regulatory protein as the allosteric switch for glucokinase. Choi JM, Seo MH, Kyeong HH, Kim E, Kim HS;. Proc Natl Acad Sci U S A. 2013;110:10171-10176. Paper describing PDB structure 4bb9. [2]. 23621087. Crystal structure of glucokinase regulatory protein. Pautsch A, Stadler N, Lohle A, Rist W, Berg A, Glocker L, Nar H, Reinert D, Lenter M, Heckel A, Schnapp G, Kauschke SG;. Biochemistry. 2013;52:3523-3531. Paper describing PDB structure 4lc9. [3]. 23957911. Structural basis for regulation of human glucokinase by glucokinase regulatory protein. Beck T, Miller BG;. Biochemistry. 2013;52:6232-6239. Paper describing PDB structure 4ly9. [4]. 24226772. Antidiabetic effects of glucokinase regulatory protein small-molecule disruptors. Lloyd DJ, St Jean DJ Jr, Kurzeja RJ, Wahl RC, Michelsen K, Cupples R, Chen M, Wu J, Sivits G, Helmering J, Komorowski R, Ashton KS, Pennington LD, Fotsch C, Vazir M, Chen K, Chmait S, Zhang J, Liu L, Norman MH, Andrews KL, Bartberger MD, Van G, Galbreath EJ, Vonderfecht SL, Wang M, Jordan SR, Veniant MM, Hale C;. Nature. 2013;504:437-440. Paper describing PDB structure 4lzj. [5]. 24251551. Structure of MurNAc 6-phosphate hydrolase (MurQ) from Haemophilus influenzae with a bound inhibitor. Hadi T, Hazra S, T. TRUNCATED at 1650 bytes (from Pfam) NF047235.1 PF22665.1 DUF6293_C 27 27 101 domain Y Y N DUF6293 family protein 131567 cellular organisms no rank 820 EBI-EMBL DUF6293 C-terminal winged helix domain DUF6293 family protein C-terminal winged helix domain This domain is found C-terminal in functionally uncharacterised archaeal proteins. This domain is predicted to adopt winged helix domain structure. It is usually located upstream Pfam:PF19810 and this domain organisation as well as the predicted structure are reminiscent of CRISPR-associated protein, Csa3. (from Pfam) NF047238.1 PF22691.1 Thiolase_C_1 28 28 144 domain Y Y N thiolase C-terminal domain-containing protein 10764581,11278743,12501183,16040614,9402066 131567 cellular organisms no rank 87165 EBI-EMBL Thiolase C-terminal domain-like Thiolase C-terminal domain-like This domain is found C-terminal in a number of thiolases and their homologues. Thiolases are essential CoA-dependent enzymes in lipid metabolism. This domain folds into a four-stranded antiparallel beta-sheet with helices packed on one side. Paper describing PDB structure 1afw. [1]. 9402066. The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: implications for substrate binding and reaction mechanism. Mathieu M, Modis Y, Zeelen JP, Engel CK, Abagyan RA, Ahlberg A, Rasmussen B, Lamzin VS, Kunau WH, Wierenga RK;. J Mol Biol 1997;273:714-728. Paper describing PDB structure 1dlu. [2]. 10764581. Crystallographic analysis of the reaction pathway of Zoogloea ramigera biosynthetic thiolase. Modis Y, Wierenga RK;. J Mol Biol. 2000;297:1171-1182. Paper describing PDB structure 1hzp. [3]. 11278743. Crystal structure of the Mycobacterium tuberculosis beta-ketoacyl-acyl carrier protein synthase III. Scarsdale JN, Kazanina G, He X, Reynolds KA, Wright HT;. J Biol Chem. 2001;276:20516-20522. Paper describing PDB structure 1m1m. [4]. 16040614. Probing the mechanism of the Mycobacterium tuberculosis beta-ketoacyl-acyl carrier protein synthase III mtFabH: factors influencing catalysis and substrate specificity. Brown AK, Sridharan S, Kremer L, Lindenberg S, Dover LG, Sacchettini JC, Besra GS;. J Biol Chem. 2005;280:32539-32547. Paper describing PDB structure 1m1o. [5]. 12501183. The catalytic cycle of biosynthetic thiolase: a conformational journey of an acetyl group through four binding modes and two oxyanion holes. Kursula P, Ojala J, Lambeir AM, Wierenga RK;. Biochemistry. 2002;41:1. TRUNCATED at 1650 bytes (from Pfam) NF047239.1 PF22702.1 Cas9_RuvC 27 27 151 domain Y N N Cas9 RuvC domain 24505130,24529477,25079318,26113724,26990991 131567 cellular organisms no rank 6756 EBI-EMBL Cas9 RuvC domain Cas9 RuvC domain This entry represent a RuvC endonuclease domain (RNAseH-like) domain found in CRISPR-Cas9 from Streptococcus pyogenes and related sequences [1-5]. This domain, and the HNH (Pfam:PF13395) domain of Cas9, are used to cleave the DNA strands complementary (target) and non-complementary (non-target) to the crRNA, respectively [5]. This domain is related to Pfam:PF18541. Paper describing PDB structure 4cmp. [1]. 24505130. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S, Kaplan M, Iavarone AT, Charpentier E, Nogales E, Doudna JA;. Science. 2014;343:1247997. Paper describing PDB structure 4oo8. [2]. 24529477. Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O;. Cell. 2014; [Epub ahead of print]. Paper describing PDB structure 4un3. [3]. 25079318. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Anders C, Niewoehner O, Duerst A, Jinek M;. Nature. 2014;513:569-573. Paper describing PDB structure 4zt0. [4]. 26113724. STRUCTURAL BIOLOGY. A Cas9-guide RNA complex preorganized for target DNA recognition. Jiang F, Zhou K, Ma L, Gressel S, Doudna JA;. Science. 2015;348:1477-1481. Paper describing PDB structure 5b2r. [5]. 26990991. Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9. Hirano S, Nishimasu H, Ishitani R, Nureki O;. Mol Cell. 2016;61:886-894. (from Pfam) NF047247.1 PF22741.1 PTP-NADK 27 27 163 domain Y Y N fused DSP-PTPase phosphatase/NAD kinase-like protein 24968225,36968430 131567 cellular organisms no rank 11042 EBI-EMBL DSP-PTPase phosphatase fused to NAD+ Kinase fused DSP-PTPase phosphatase/NAD kinase-like protein While the land plant version of this DSP-PTPase domain is likely inactive as the catalytic cysteine is replaced by serine or threonine, the rest are predicted to be active. Keeping with the proposed sugar phosphatase activity in related members, these domains could potentially function as phosphatases converting NADP to NAD+. [1]. 36968430. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. Burroughs AM, Aravind L;. NAR Genom Bioinform. 2023;5:lqad029. [2]. 24968225. Genome-wide analysis of the NADK gene family in plants. Li WY, Wang X, Li R, Li WQ, Chen KM;. PLoS One. 2014;9:e101051. (from Pfam) NF047249.1 PF22745.1 Nlig-Ia 27 27 92 domain Y Y N DNA ligase LigA-related protein 11781321,22230472,36146784 131567 cellular organisms no rank 49178 EBI-EMBL DNA ligase-like, N-terminal NAD+-binding domain DNA ligase-like, N-terminal NAD+-binding domain The alpha-helical Nlig-Ia domain is found at the N-terminal of DNA ligases and it has been proposed to either swivel the NAD+ close to the ligase active site lysine on the RAGNYA domain or function as an allosteric NAD+ binding site. The Nlig-Ia domain is also observed as a solo protein in phages that do not encode a separate NAD+-dependent ligase catalytic module, suggesting the domain can function independently of a DNA ligase. It has been proposed that these domains likely function as NAD+ sensors which might help indicate to the phage the development of NADase host effectors or shield NAD+ from the action of such effectors [1-3]. [1]. 36146784. Apprehending the NAD(+)-ADPr-Dependent Systems in the Virus World. Iyer LM, Burroughs AM, Anantharaman V, Aravind L;. Viruses. 2022;14:1977. [2]. 22230472. Structure guided understanding of NAD+ recognition in bacterial DNA ligases. Lahiri SD, Gu RF, Gao N, Karantzeni I, Walkup GK, Mills SD;. ACS Chem Biol. 2012;7:571-580. [3]. 11781321. Conserved residues in domain Ia are required for the reaction of Escherichia coli DNA ligase with NAD+. Sriskanda V, Shuman S;. J Biol Chem. 2002;277:9695-9700. (from Pfam) NF047258.1 PF22777.1 VKGC_lumenal_dom 27.7 27.7 152 domain Y N N Vitamin K-dependent gamma-carboxylase, lumenal domain 10748045,14729325 131567 cellular organisms no rank 3885 EBI-EMBL Vitamin K-dependent gamma-carboxylase, lumenal domain Vitamin K-dependent gamma-carboxylase, lumenal domain Using reduced vitamin K, oxygen, and carbon dioxide, gamma-glutamyl carboxylase (VKGC) post-translationally modifies certain glutamates by adding carbon dioxide to the gamma position of those amino acids. In vertebrates, the modification of glutamate residues of target proteins is facilitated by an interaction between a propeptide present on target proteins and the gamma-glutamyl carboxylase [1]. This entry represents the lumenal domain found in animals and bacteria. This domain is associated with Pfam:PF05090 [1,2]. [1]. 10748045. Identification of a Drosophila vitamin K-dependent gamma-glutamyl carboxylase. Li T, Yang CT, Jin D, Stafford DW;. J Biol Chem 2000;275:18291-18296. [2]. 14729325. HTTM, a horizontally transferred transmembrane domain. Schultz J;. Trends Biochem Sci. 2004;29:4-7. (from Pfam) NF047262.1 PF22784.1 PTP-SAK 27 27 153 domain Y N N Swiss Army Knife protein, DSP-PTPase phosphatase domain 27536007,36968430 131567 cellular organisms no rank 32365 EBI-EMBL Swiss Army Knife protein, DSP-PTPase phosphatase domain Swiss Army Knife protein, DSP-PTPase phosphatase domain The Swiss Army Knife class of proteins features a diverse domain repertoire acting to repair RNA damaged in the wake of RNase attacks. PTP-SAK is one such domain, a phosphatase of the rhodanese-phosphatase superfamily. It is predicted to 'clean' RNA ends by removing phosphate groups, preparing them for ligation by their associating RNA ligases [1,2]. [1]. 36968430. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. Burroughs AM, Aravind L;. NAR Genom Bioinform. 2023;5:lqad029. [2]. 27536007. RNA damage in biological conflicts and the diversity of responding RNA repair systems. Burroughs AM, Aravind L;. Nucleic Acids Res. 2016;44:8525-8555. (from Pfam) NF047266.1 PF22814.1 WelO5 27 27 277 domain Y N N Carrier-protein-independent halogenase WelO5 27348090 131567 cellular organisms no rank 2338 EBI-EMBL Carrier-protein-independent halogenase WelO5 Carrier-protein-independent halogenase WelO5 This entry represents the homologues of the carrier-protein-independent halogenase WelO5. This enzyme chlorinates C13 of 12-epi-fischerindole U to yield 12-epi-fischerindole G. This enzymatic transformation constitutes the first step in the oxidative maturation to welwitindolinones. WelO5 adopts a cupin-like fold that is also characteristic of Fe/2OG enzymes [1]. [1]. 27348090. Structural basis for halogenation by iron- and 2-oxo-glutarate-dependent enzyme WelO5. Mitchell AJ, Zhu Q, Maggiolo AO, Ananth NR, Hillwig ML, Liu X, Boal AK;. Nat Chem Biol. 2016;12:636-640. (from Pfam) NF047268.1 PF22818.1 ApeI-like 28.5 28.5 119 domain Y N N ApeI dehydratase 30908039 131567 cellular organisms no rank 10827 EBI-EMBL ApeI dehydratase ApeI dehydratase This entry represents the homologues of ApeI dehydratase. This enzyme forms a heterodimer with ApeP that carries out dehydratation in APE biosynthesis. Both subunits in this complex adopt a typical hotdog fold comprising six antiparallel beta-strands and a central alpha-helix [1]. [1]. 30908039. An Uncommon Type II PKS Catalyzes Biosynthesis of Aryl Polyene Pigments. Grammbitter GLC, Schmalhofer M, Karimi K, Shi YM, Schoner TA, Tobias NJ, Morgner N, Groll M, Bode HB;. J Am Chem Soc. 2019;141:16615-16623. (from Pfam) NF047288.1 PF22879.1 AIPR_N 28 28 151 domain Y N N Abortive infection phage resistance protein N-terminal domain 18346280 131567 cellular organisms no rank 4339 EBI-EMBL Abortive infection phage resistance protein N-terminal domain Abortive infection phage resistance protein N-terminal domain This entry represents a N-terminal domain found in an abortive infection phage resistance protein often found in restriction modification system operons [1]. [1]. 18346280. MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases. Iyer LM, Abhiman S, Aravind L;. Biol Direct. 2008;3:8. (from Pfam) NF047292.1 PF22891.1 KH_PNO1_2nd 27 27 90 domain Y N N Eukaryotic type KH-domain (KH-domain type I) (327.11.2) 17654551,20363226,29155690,29875412 131567 cellular organisms no rank 935 EBI-EMBL Eukaryotic type KH-domain (KH-domain type I) (327.11.2) Eukaryotic type KH-domain (KH-domain type I) (327.11.2) This entry represents the second KH domain found in the PNO1 protein. PNO1 is part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. Paper describing PDB structure 2e3u. [1]. 17654551. Crystal structure of Dim2p: a preribosomal RNA processing factor, from Pyrococcus horikoshii OT3 at 2.30 A. Jia MZ, Ohtsuka J, Lee WC, Nagata K, Tanokura M;. Proteins. 2007;69:428-432. Paper describing PDB structure 3aev. [2]. 20363226. An archaeal Dim2-like protein, aDim2p, forms a ternary complex with a/eIF2 alpha and the 3' end fragment of 16S rRNA. Jia MZ, Horita S, Nagata K, Tanokura M;. J Mol Biol. 2010;398:774-785. Paper describing PDB structure 6eml. [3]. 29155690. Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae. Heuer A, Thomson E, Schmidt C, Berninghausen O, Becker T, Hurt E, Beckmann R;. Elife. 2017; [Epub ahead of print]. Paper describing PDB structure 6g18. [4]. 29875412. Visualizing late states of human 40S ribosomal subunit maturation. Ameismeier M, Cheng J, Berninghausen O, Beckmann R;. Nature. 2018;558:249-253. (from Pfam) NF047294.1 PF22898.1 NOMO1-like_1st 27 27 85 domain Y N N BOS complex subunit NOMO1-like, first beta sandwich domain 36261522 131567 cellular organisms no rank 29 EBI-EMBL BOS complex subunit NOMO1-like, first beta sandwich domain BOS complex subunit NOMO1-like, first beta sandwich domain This domain is found at the N-terminal end of human BOS complex subunit NOMO1 and similar sequences mainly from animals and plants. NOMO1 is a component of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes [1]. This domain is predicted to adopt a seven stranded beta sandwich fold. [1]. 36261522. Substrate-driven assembly of a translocon for multipass membrane proteins. Sundaram A, Yamsek M, Zhong F, Hooda Y, Hegde RS, Keenan RJ;. Nature. 2022;611:167-172. (from Pfam) NF047300.1 PF22919.1 ATP-synt_VA_C 24.7 24.7 101 domain Y N N C-terminal domain of V and A type ATP synthase 11032839,9687365,9736690 131567 cellular organisms no rank 66864 EBI-EMBL C-terminal domain of V and A type ATP synthase C-terminal domain of V and A type ATP synthase This entry represents a small alpha helical domain found at the C-terminus of a variety of ATP synthases. Paper describing PDB structure 1fx0. [1]. 11032839. The structure of the chloroplast F1-ATPase at 3.2 A resolution. Groth G, Pohl E;. J Biol Chem. 2001;276:1345-1352. Paper describing PDB structure 1mab. [2]. 9736690. The 2.8-A structure of rat liver F1-ATPase: configuration of a critical intermediate in ATP synthesis/hydrolysis. Bianchet MA, Hullihen J, Pedersen PL, Amzel LM;. Proc Natl Acad Sci U S A. 1998;95:11065-11070. Paper describing PDB structure 1nbm. [3]. 9687365. Bovine F1-ATPase covalently inhibited with 4-chloro-7-nitrobenzofurazan: the structure provides further support for a rotary catalytic mechanism. Orriss GL, Leslie AG, Braig K, Walker JE;. Structure. 1998;6:831-837. (from Pfam) NF047309.1 PF22977.1 WHD 27 27 221 domain Y N N Winged helix domain, variant 131567 cellular organisms no rank 12602 EBI-EMBL Winged helix domain, variant Winged helix domain, variant This domain is found in uncharacterised bacterial proteins. It is predicted to adopt a globular structure with similarity to MarR family of transcription factors (Pfam:PF12802). This domain is found usually in combination with AAA ATPase domains (Pfam:PF00004). (from Pfam) NF047311.1 PF22982.1 HRQ1_WHD 27 27 70 domain Y N N ATP-dependent helicase HRQ1, winged helix domain 23456718 131567 cellular organisms no rank 23622 EBI-EMBL ATP-dependent helicase HRQ1, winged helix domain ATP-dependent helicase HRQ1, winged helix domain This domain is found in the homologues of ATP-dependent helicase HRQ1. HRQ1 is a helicase with 3'-5' helicase activity involved in genome stability [1]. Hrq1 is able to unwind relatively long duplex DNA up to 120-bp and is significantly stimulated by a preexisting fork structure. This domain is predicted to form a globular structure with significant similarity to Winged helix HTH domains. [1]. 23456718. Hrq1 functions independently of Sgs1 to preserve genome integrity in Saccharomyces cerevisiae. Choi DH, Lee R, Kwon SH, Bae SH;. J Microbiol. 2013;51:105-112. (from Pfam) NF047352.1 P_loop_sacsin 50 50 80 domain Y Y N sacsin N-terminal ATP-binding-like domain-containing protein 131567 cellular organisms no rank 18587 NCBIFAM sacsin N-terminal ATP-binding-like domain This roughly 80-amino acid domain belongs to the clan of ATP-binding domains with the Walker A motif (P-loop). It starts and ends with well-conserved alpha-helical regions, interrupted by a region of beta-strands that are prone to insertions of additional sequence. In a large fraction of members, the critical lysine (K) of the P-loop motif GxxGxGK[ST] is replaced by phenylalanine (F), making the function of the motif in those family members unclear. This domain tends to occur as a N-terminal domain of proteins that average over 1000 amino acids in length, such as the human protein sacsin. NF047358.1 TenpIN 90 90 141 equivalog Y Y N type III toxin-antitoxin system TenpIN family toxin tenpIN GO:0003723,GO:0090729,GO:0110001 22434880 131567 cellular organisms no rank 595 NCBIFAM type III toxin-antitoxin system TenpIN family toxin A type III toxin-antitoxin system consists of a toxin protein and an antitoxin RNA. TenpIN family toxin is widely found in numerous bacteria and archaea. NF047359.1 CptIN 90 90 150 equivalog Y Y N type III toxin-antitoxin system CptIN family toxin cptIN GO:0003723,GO:0090729,GO:0110001 22434880,26350213 131567 cellular organisms no rank 507 NCBIFAM type III toxin-antitoxin system CptIN family toxin A type III toxin-antitoxin system consists of a toxin protein and an antitoxin RNA. CptIN family toxin is widely found in numerous bacteria and archaea. NF047376.1 TAA_AbiEi 150 150 172 equivalog Y Y N type IV toxin-antitoxin system AbiEi family antitoxin abiEi GO:0110001 23478446,24465005,29518409 131567 cellular organisms no rank 1614 NCBIFAM type IV toxin-antitoxin system AbiEi family antitoxin NF047389.1 ATPase_Sll1717 75 75 454 subfamily Y Y N P-loop ATPase, Sll1717 family 16452410 131567 cellular organisms no rank 7298 NCBIFAM P-loop ATPase, Sll1717 family Members of this P-loop-containing ATPase (or possibly GTPase) protein family have been annotated as DNA repair protein, FunZ, but the function is unknown. Members often appear next to or fused to a second P-loop-containing ATPase domain more similar to that of ParA family proteins. NF047398.1 AAA_KGGVGR 90 90 190 domain Y Y N KGGVGR-motif variant AAA ATPase 29036481 131567 cellular organisms no rank 8244 NCBIFAM KGGVGR-motif variant AAA ATPase domain Members of this P-loop-containing domain, related to various AAA-type ATPases, have a well-conserved xKGGVGR[ST] that differs from the more typical GxxGxGK[ST] of P-loop motifs. This domain often is found in long, multidomain proteins that have an additional ATP-binding domain of a different type (see NF047389.1). Member protein Sll1563 was found to be downregulated during nitrogen starvation as part of the NtcA regulon, but its function was not determined. NF047412.1 sig_GCG_CRPN_rpt 24 24 23 domain Y Y N GCG_CRPN prefix-to-repeats domain-containing protein 131567 cellular organisms no rank 2622 NCBIFAM GCG_CRPN prefix-to-repeats domain Members of this family have an architecture consisting of a signal peptide, then this conserved domain with a core region featuring two invariant Cys residues in the consensus sequence GCGPGFHRGPWGGCRPN, and then usually repetitive, low-complexity (reduced alphabet) sequence to the C-terminus. NF047446.1 barrel_OmpL47 40 40 68 domain Y Y N OmpL47-type beta-barrel domain-containing protein 19562037 131567 cellular organisms no rank 14654 NCBIFAM OmpL47-type beta-barrel domain The Leptospira surface-exposed protein OmpL47 (see NF047441) contains three tandem copies of this predicted beta-barrel domain. The AlphaFold prediction for Q04PQ5 illustrates the fold prediction. Proteins may have as many as 12 copies of the domain. Members of this family are often annotated as Ig-like domain-containing proteins or as carbohydrate-active enzymes, largely based on other domains present. While repeats of the domain often have a periodicity of 80 amino acids or more, this HMM built with a length of 68, in part because the final repeat is often shorter. NF047509.1 Rv3131_FMN_oxido 199 199 319 subfamily Y Y N Acg family FMN-binding oxidoreductase GO:0010181,GO:0016491 23148223,34798816 131567 cellular organisms no rank 21742 NCBIFAM Acg family FMN-binding oxidoreductase Paralogs Rv2032, Rv3131, and Rv3127 in Mycobacterium tuberculosis are recognizably homologous to classical nitroreductases (see Pfam model PF00881). Rv2032 is known as Acg (Acr-coregulated gene) because Rv2032 and Acr (Rv2031c) are both highly upregulated by DosR (dormancy survival regulator), a response regulator transcription factor involved in the response to hypoxia and to the macrophage intracellular environment. Rv3131 and Rv3127 likewise belong to the DosR regulon. MSMEG_3955 from Mycobacterium smegmatis, most closely related to Rv3131, was reported to be a trimeric NADPH-dependent FMN oxidoreductase, and to lack detectable nitroreductase activity. NF047510.1 LIC_10190_fam 100 100 424 subfamily Y Y N LIC_10190 family membrane protein 131567 cellular organisms no rank 1628 NCBIFAM LIC_10190 family membrane protein Members of this broadly distributed proteins family average about 600 amino acids in length and are highly hydrophobic. Two of the very few invariant amino acids occur in a DxxxY motif. Some members of this family show sequence similarity to dolichyl-phosphate-mannose-protein mannosyltransferases (see PF13231), suggesting they may be glycosyltranferases. NF047516.1 LA_3659_fam 36 36 221 equivalog Y Y N LA_3659 family protein 131567 cellular organisms no rank 915 NCBIFAM LA_3659 family protein This family is named for founding protein LA_3659, even though that protein appears not to be complete at the N-terminus. For members in the genus Leptospira, a large number of fragmentary sequences occur in non-redundant protein sequence databases, suggesting negative selection in certain growth conditions. Members of this family are also found broadly outside of Leptospira. The function is unknown. NF047558.1 TPR_END_plus 32 32 56 domain Y Y N TPR end-of-group domain-containing protein 131567 cellular organisms no rank 13476 NCBIFAM TPR end-of-group domain This HMM describes a 56 amino acid region found near or at the C-terminus of many bacterial tetratricopeptide repeat (TPR) proteins, containing a variant form of the TPR repeat (about 34 amino acids) followed by a stretch of sequence unique to this sequence region. NF047561.1 orf58_phage_fam 170 170 257 subfamily Y Y N phage protein 15292156 131567 cellular organisms no rank 3051 NCBIFAM phage protein Proteins of this family are homologs of the phage protein (orf58) annotated from the genome of Actinobacillus actinomycetemcomitans bacteriophage (PMID: 15292156). Their function is not clear yet. NF047593.1 IS66_ISAeme5_TnpA 28 28 79 equivalog Y Y N IS66 family insertion sequence element accessory protein TnpA tnpA 131567 cellular organisms no rank 11089 NCBIFAM IS66 family insertion sequence element accessory protein TnpA This family is based on IS66 family insertion sequence (IS element) accessory proteins for transposition, such as TnpA from ISAeme5. NF047619.1 NADase_discoid 38 38 130 domain Y Y N NADase-type glycan-binding domain-containing protein 34694903,9684896 131567 cellular organisms no rank 10443 NCBIFAM NADase-type glycan-binding domain This family includes the glycan-binding N-terminal domain (called the translocation domain) of the nicotine adenine dinucleotide glycohydrolase toxin (NADase) of Steptococcus pyogenes. Related domains are often referred to as the discoidin domain. NF047625.1 AcylSulfactDhSauS 600 600 464 equivalog Y Y N acylating sulfoacetaldehyde dehydrogenase sauS 1.2.1.81 GO:0016620 20693281 131567 cellular organisms no rank 1108 NCBIFAM acylating sulfoacetaldehyde dehydrogenase NF047630.1 SulOxRed 400 400 308 equivalog Y Y N sulfur oxygenase/reductase sor 1.13.11.55 GO:0033755,GO:0046872 15030315,1522063 131567 cellular organisms no rank 38 NCBIFAM sulfur oxygenase/reductase NF047643.1 seleno_TsoY 250 250 366 equivalog Y Y N selenoprotein TsoY tsoY 131567 cellular organisms no rank 43 NCBIFAM selenoprotein TsoY Members of this rare protein family are selenoproteins. The name TsoY derives from its discovery next to TsoR, a transcription factor more commonly associated with a Three Selenoprotein Operon, TsoABC. That operon occasionally contains a fourth selenoprotein, TsoX. NF047644.1 TsoY_fam 150 150 378 subfamily Y Y N TsoY family (seleno)protein 131567 cellular organisms no rank 1117 NCBIFAM TsoY family (seleno)protein This family of proteins is named for its most distinctive branch, TsoY, in which all proteins are selenoproteins. Members known so far that fall outside the TsoY branch always have Cys at a position equivalent to the Sec (U) in TsoY selenoproteins. The function is unknown. NF047645.1 CopZ_Nterm_CC 100 100 138 equivalog Y Y N putative iron-sulfur cluster-binding metallochaperone 17609202 131567 cellular organisms no rank 634 NCBIFAM putative iron-sulfur cluster-binding metallochaperone Members of this family are homologous to family NF045877 and to the N-terminal half of the copper chaperone CopZ from Archaeoglobus fulgidus. In contrast to NF045877, which contains a number selenoproteins with a CU motif near the N-terminus, it appears that all members of this family have cysteine only, usually including the motif CC. NF047751.1 HepT_toxin 60 60 120 equivalog Y Y N type VII toxin-antitoxin system HepT family RNase toxin hepT GO:0004540,GO:0110001 29555683,33045733,33290744 131567 cellular organisms no rank 5173 NCBIFAM type VII toxin-antitoxin system HepT family RNase toxin NF047752.1 MntA_antitoxin 60 60 106 equivalog Y Y N type VII toxin-antitoxin system MntA family adenylyltransferase antitoxin mntA GO:0016779,GO:0110001 29555683,33045733,33290744 131567 cellular organisms no rank 5104 NCBIFAM type VII toxin-antitoxin system MntA family adenylyltransferase antitoxin NF047767.1 LBF_2804_fam 80 80 352 subfamily Y Y N LBF_2804 family protein 131567 cellular organisms no rank 460 NCBIFAM LBF_2804 family protein NF047768.1 Clp_like_SDH 250 250 260 equivalog Y Y N SDH family Clp fold serine proteinase 3.4.21.- GO:0004252 15752073 131567 cellular organisms no rank 1370 NCBIFAM SDH family Clp fold serine proteinase Members of this family show a distant relation to Clp family serine proteinases, and are expected to have a related fold, but differ in the order of catalytic triad residues, SDH (Ser, Asp, His) instead of SHD. Members are found in both archaea and bacteria. NF047773.1 phas_rel_Lepto 35 35 68 domain Y Y N phasin-related domain-containing protein 131567 cellular organisms no rank 2123 NCBIFAM phasin-related domain Members of this family are homologous to the phasin family proteins of Pfam model PF05597, but are found regularly in bacteria that lack the poly-hydroxyalkanoate inclusions where phasins are found. Three members of this family are found in the model strain Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130, with locus tags LIC_10348, LIC_11972, and LIC_13183. NF047832.1 caspase_w_EACC1 140 140 211 subfamily_domain Y Y N caspase, EACC1-associated type 3.4.22.- 32101166 131567 cellular organisms no rank 12917 NCBIFAM caspase, EACC1-associated type The caspase domain described in this model occurs in bacterial conflict systems, generally as the N-terminal region of longer effector proteins that are encoded next to EACC1 (effector-associated constant component 1) proteins. NF047864.1 CBU_0592_membra 25 25 72 domain Y Y N CBU_0592 family membrane protein 131567 cellular organisms no rank 5516 NCBIFAM CBU_0592 family membrane protein Most members of this family are about 90 amino acids in length and rich in hydrophobic residues, suggesting location largely in the membrane. A minority have an additional C-terminal domain related to cyclic nucleotide-binding domains. Some members of this family have two copies of the domain. The family is named for CBU_0592 from Coxiella burnetii RSA 493. The function is unknown. TIGR00003.1 TIGR00003 TIGR00003 62 31 66 subfamily_domain Y Y N copper ion binding protein GO:0005507 131567 cellular organisms no rank 43110 JCVI copper ion binding protein copper ion binding protein This HMM describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family PF00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases. TIGR00004.1 TIGR00004 TIGR00004 106.25 106.25 125 subfamily Y Y N Rid family detoxifying hydrolase GO:0008152,GO:0019239 17506874,22094463,23749972,25975565 131567 cellular organisms no rank 39069 JCVI reactive intermediate/imine deaminase Rid family detoxifying hydrolase Members of this family, conserved in all domains of life and often with several members per bacterial genome, appear to catalyze a reaction that minimizes toxic by-products from reactions catalyzed by pyridoxal phosphate-dependent enzymes. Some members of this family are designated RidA and are designated 2-iminobutanoate/2-iminopropanoate deaminase (EC 3.5.99.10). For other paralogs, specific activities are less clear. Historically, this protein has been called an inhibitor of protein synthesis initiation, then endoribonuclease L-PSP active on single-stranded mRNA, but citations to those reports are now removed from this HMM. TIGR00005.1 TIGR00005 rluA_subfam 192.7 192.7 298 subfamily Y Y N RluA family pseudouridine synthase GO:0001522,GO:0003723,GO:0009451,GO:0009982 131567 cellular organisms no rank 127482 JCVI pseudouridine synthase, RluA family RluA family pseudouridine synthase In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. TIGR00006.1 TIGR00006 TIGR00006 154.3 154.3 310 equivalog Y Y N 16S rRNA (cytosine(1402)-N(4))-methyltransferase RsmH rsmH 2.1.1.199 GO:0016434 10572301,22561317,4563986 131567 cellular organisms no rank 69631 JCVI 16S rRNA (cytosine(1402)-N(4))-methyltransferase 16S rRNA (cytosine(1402)-N(4))-methyltransferase RsmH This HMM describes RsmH, a 16S rRNA methyltransferase. Previously, this gene was designated MraW, known to be essential in E. coli and widely conserved in bacteria. TIGR00007.1 TIGR00007 TIGR00007 228.95 228.95 231 equivalog Y Y N 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase hisA 5.3.1.16 GO:0000105,GO:0003949 12634849 131567 cellular organisms no rank 42473 JCVI 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase This protein family consists of HisA, phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase, the enzyme catalyzing the fourth step in histidine biosynthesis. It is closely related to the enzyme HisF for the sixth step. Examples of this enzyme in Actinobacteria have been found to be bifunctional, also possessing phosphoribosylanthranilate isomerase activity [1]; the trusted cutoff here has now been raised to 275.0 to exclude the bifunctional group, now represented by model TIGR01919. HisA from Lactococcus lactis was reported to be inactive (MEDLINE:93322317). TIGR00010.1 TIGR00010 TIGR00010 206 206 253 subfamily Y Y N YchF/TatD family DNA exonuclease GO:0004536 10747959,25114049 131567 cellular organisms no rank 69547 JCVI hydrolase, TatD family YchF/TatD family DNA exonuclease PSI-BLAST, starting with a urease alpha subunit, finds a large superfamily of proteins, including a number of different enzymes that act as hydrolases at C-N bonds other than peptide bonds (EC 3.5.-.-), many uncharacterized proteins, and the members of this family. Several genomes have multiple paralogs related to this family. However, a set of 17 proteins can be found, one each from 17 of the first 20 genomes, such that each member forms a bidirectional best hit across genomes with all other members of the set. This core set (and one other near-perfect member), but not the other paralogs, form the seed for this model. Additionally, members of the seed alignment and all trusted hits, but not all paralogs, have a conserved motif DxHxH near the amino end. The member from E. coli was recently shown to have DNase activity. TIGR00011.1 TIGR00011 YbaK_EbsC 153.25 153.25 152 equivalog Y Y N Cys-tRNA(Pro) deacylase ybaK GO:0002161,GO:0043039 10813833,14530268,16087664,23185990 131567 cellular organisms no rank 37579 JCVI Cys-tRNA(Pro) deacylase Cys-tRNA(Pro) deacylase This HMM represents the YbaK family, bacterial proteins whose full length sequence is homologous to an insertion domain in proline--tRNA ligases. The domain deacylates mischarged tRNAs. The YbaK protein of Haemophilus influenzae (HI1434) likewise deacylates Ala-tRNA(Pro), but not the correctly charged Pro-tRNA(Pro). A crystallographic study of HI1434 suggests a nucleotide binding function. Previously, a member of this family was described as EbsC and was thought to be involved in cell wall metabolism. TIGR00012.1 TIGR00012 L29 22.6 22.6 56 equivalog Y Y N 50S ribosomal protein L29 rpmC GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 24509 JCVI ribosomal protein uL29 50S ribosomal protein L29 This HMM describes a ribosomal large subunit protein, called L29 in prokaryotic (50S) large subunits and L35 in eukaryotic (60S) large subunits. TIGR00013.1 TIGR00013 taut 56.9 56.9 64 subfamily Y Y N 2-hydroxymuconate tautomerase family protein GO:0016853 11329265,12051677 131567 cellular organisms no rank 11700 JCVI 4-oxalocrotonate tautomerase family enzyme 2-hydroxymuconate tautomerase family protein 2-hydroxymuconate tautomerase (also called 4-oxalocrotonate tautomerase) is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because some species contain fairly divergent paralogs, the family is regarded as not necessarily uniform in function. TIGR00016.1 TIGR00016 ackA 293.4 293.4 405 subfamily Y Y N acetate/propionate family kinase 2.7.2.1 GO:0006082,GO:0016301,GO:0016774 9484901 131567 cellular organisms no rank 67348 JCVI acetate kinase acetate/propionate family kinase This model has been updated to recognize that members of this family include both acetate and propionate kinases, some of which have both functions. In previous releases, this model was treated as an equivalog model for acetate kinase. TIGR00021.1 TIGR00021 rpiA 126.4 126.4 218 equivalog Y Y N ribose 5-phosphate isomerase A rpiA 5.3.1.6 GO:0004751,GO:0006098 131567 cellular organisms no rank 34300 JCVI ribose 5-phosphate isomerase A ribose 5-phosphate isomerase A This HMM describes ribose 5-phosphate isomerase, an enzyme of the non-oxidative branch of the pentose phosphate pathway. TIGR00027.1 TIGR00027 mthyl_TIGR00027 93.55 93.55 259 subfamily Y Y N SAM-dependent methyltransferase 2.1.1.- GO:0008168 131567 cellular organisms no rank 34577 JCVI methyltransferase, TIGR00027 family SAM-dependent methyltransferase This model represents a set of probable methyltransferases, about 300 amino acids long, with essentially full length homology. Members share an N-terminal region described by Pfam model PF02409. Included are a paralogous family of 12 proteins in Mycobacterium tuberculosis, plus close homologs in related species, a family of 8 in the archaeon Methanosarcina acetivorans, and small numbers of members in other species, including plants. TIGR00031.1 TIGR00031 UDP-GALP_mutase 303.75 303.75 378 equivalog Y Y N UDP-galactopyranose mutase glf 5.4.99.9 GO:0008767,GO:0009273 8576037,9784509 131567 cellular organisms no rank 24868 JCVI UDP-galactopyranose mutase UDP-galactopyranose mutase This enzyme is involved in the conversion of UDP-GALP into UDP-GALF through a 2-keto intermediate. It contains FAD as a cofactor. The gene is known as glf, ceoA, and rfbD. It is known experimentally in E. coli, Mycobacterium tuberculosis, and Klebsiella pneumoniae. TIGR00032.1 TIGR00032 argG 268.2 268.2 394 equivalog Y Y N argininosuccinate synthase argG 6.3.4.5 GO:0004055,GO:0005524,GO:0042450 11809762 131567 cellular organisms no rank 54511 JCVI argininosuccinate synthase argininosuccinate synthase TIGR00033.1 TIGR00033 aroC 212.2 212.2 351 equivalog Y Y N chorismate synthase aroC 4.2.3.5 GO:0004107,GO:0009073 131567 cellular organisms no rank 70947 JCVI chorismate synthase chorismate synthase Homotetramer (noted in E.coli) suggests reason for good conservation. TIGR00035.1 TIGR00035 asp_race 93.1 93.1 236 subfamily Y Y N amino acid racemase 5.1.1.- GO:0006520,GO:0047661 28894939 131567 cellular organisms no rank 42995 JCVI aspartate racemase amino acid racemase Asparate racemases and some close homologs of unknown function are related to the more common glutamate racemases, but form a distinct evolutionary branch. This HMM identifies members of the aspartate racemase-related subset of amino acid racemases. Suggest hmmls for identification of probable aspartate racemases, hmmsw for general homologs. TIGR00036.1 TIGR00036 dapB 122 122 270 equivalog Y Y N 4-hydroxy-tetrahydrodipicolinate reductase dapB 1.17.1.8 GO:0008839,GO:0009089 9098082,9398235 131567 cellular organisms no rank 69896 JCVI 4-hydroxy-tetrahydrodipicolinate reductase 4-hydroxy-tetrahydrodipicolinate reductase TIGR00037.1 TIGR00037 eIF_5A 75.45 75.45 130 equivalog Y Y N translation initiation factor IF-5A eif5A GO:0003723,GO:0003746,GO:0043022,GO:0045901 19424157 131567 cellular organisms no rank 1131 JCVI translation elongation factor IF5A translation initiation factor IF-5A Recent work (2009) changed the view of eIF5A in eukaryotes and aIF5A in archaea, hypusine-containing proteins, from translation initiation factor to translation elongation factor. TIGR00038.1 TIGR00038 efp 185.8 185.8 184 equivalog Y Y N elongation factor P efp GO:0003746,GO:0005737,GO:0006414 23239623,29100052 131567 cellular organisms no rank 36619 JCVI translation elongation factor P elongation factor P Elongation factor P (EF-P) alleviates stalling of protein translation at polyproline sites. EF-P (and its archaeal and eukaryotic homologs) are post-translationally modified, on a critical lysine or arginine residue, in different ways in different lineages. Residues are modified with beta-lysine, rhamnose, 5-aminopentanol, or hypusine. The trusted cutoff of this model is set high enough to exclude members of TIGR02178, the EFP-like protein YeiP found in certain Gammaproteobacteria. TIGR00040.1 TIGR00040 yfcE 56.25 56.25 158 subfamily Y Y N YfcE family phosphodiesterase GO:0016788 15128743 131567 cellular organisms no rank 46772 JCVI phosphodiesterase, MJ0936 family YfcE family phosphodiesterase Members of this largely uncharacterized family share a motif approximating DXH(X25)GDXXD(X25)GNHD as found in several phosphoesterases, including the nucleases SbcD and Mre11, and a family of uncharacterized archaeal putative phosphoesterases described by TIGR00024. In this family, the His residue in GNHD portion of the motif is not conserved. The member MJ0936, one of two from Methanococcus jannaschii, was shown (PMID:15128743) to act on model phosphodiesterase substrates; a divalent cation was required. TIGR00041.1 TIGR00041 DTMP_kinase 83.25 83.25 196 equivalog Y Y N dTMP kinase tmk 2.7.4.9 GO:0004798,GO:0005524,GO:0006233 8631667 131567 cellular organisms no rank 62787 JCVI dTMP kinase dTMP kinase Catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP). TIGR00042.1 TIGR00042 TIGR00042 145.35 145.35 184 equivalog Y Y N RdgB/HAM1 family non-canonical purine NTP pyrophosphatase rdgB 3.6.1.66 GO:0006281,GO:0035870,GO:0036222 12730170,3533720,8789257 131567 cellular organisms no rank 64854 JCVI non-canonical purine NTP pyrophosphatase, RdgB/HAM1 family RdgB/HAM1 family non-canonical purine NTP pyrophosphatase Saccharomyces cerevisiae HAM1 protects against the mutagenic effects of the base analog 6-N-hydroxylaminopurine, which can be a natural product of monooxygenase activity on adenine. Methanococcus jannaschii MJ0226 and E. coli RdgB are also characterized as pyrophosphatases active against non-standard purines NTPs. E. coli RdgB appears to act by intercepting non-canonical deoxyribonucleotide triphosphates from replication precursor pools.[3] TIGR00044.1 TIGR00044 TIGR00044 106.25 106.25 229 hypoth_equivalog Y Y N YggS family pyridoxal phosphate-dependent enzyme GO:0030170 27426274 131567 cellular organisms no rank 74601 JCVI pyridoxal phosphate enzyme, YggS family YggS family pyridoxal phosphate-dependent enzyme Members of this protein family include YggS from Escherichia coli and YBL036C, an uncharacterized pyridoxal protein of Saccharomyces cerevisiae. TIGR00048.1 TIGR00048 rRNA_mod_RlmN 290 290 355 equivalog Y Y N 23S rRNA (adenine(2503)-C(2))-methyltransferase RlmN rlmN 2.1.1.192 GO:0008757,GO:0016433,GO:0030488,GO:0070475 10952608,11222759,18025251 131567 cellular organisms no rank 59297 JCVI 23S rRNA (adenine(2503)-C(2))-methyltransferase 23S rRNA (adenine(2503)-C(2))-methyltransferase RlmN Members of this family are RlmN, a 23S rRNA m2A2503 methyltransferase in the radical SAM enzyme family. Closely related is Cfr, a Staphylococcus sciuri plasmid-borne homolog to this family the confers transferrable resistance to chloramphenicol and florfenicol. Cfr methylates adenine(2503) of 23S RNA at position C(8), while RlmN methylates the same residue at a different site, position C(2). TIGR00049.1 TIGR00049 TIGR00049 58.8 58.8 106 subfamily Y Y N iron-sulfur cluster assembly accessory protein GO:0016226,GO:0051536 10322040,12207230,9582371 131567 cellular organisms no rank 50688 JCVI iron-sulfur cluster assembly accessory protein iron-sulfur cluster assembly accessory protein Proteins in this subfamily appear to be associated with the process of FeS-cluster assembly. The HesB proteins are associated with the nif gene cluster and the Rhizobium gene IscN has been shown to be required for nitrogen fixation [1]. Nitrogenase includes multiple FeS clusters and many genes for their assembly. The E. coli SufA protein is associated with SufS, a NifS homolog and SufD which are involved in the FeS cluster assembly of the FhnF protein [2]. The Azotobacter protein IscA (homologs of which are also found in E.coli) is associated which IscS, another NifS homolog and IscU, a nifU homolog as well as other factors consistent with a role in FeS cluster chemistry [3]. A homolog from Geobacter contains a selenocysteine in place of an otherwise invariant cysteine, further suggesting a role in redox chemistry. TIGR00050.1 TIGR00050 rRNA_methyl_1 167.15 167.15 233 subfamily Y Y N TrmJ/YjtD family RNA methyltransferase 2.1.1.- GO:0006396,GO:0008173 16848900,8265370 131567 cellular organisms no rank 28326 JCVI RNA methyltransferase, TrmH family, group 1 TrmJ/YjtD family RNA methyltransferase This is part of the trmH (spoU) family of S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases, and is now characterized, in E. coli, as a tRNA:Cm32/Um32 methyltransferase. It may be named TrMet(Xm32), or TrmJ, according to the nomenclature style chosen TIGR00051.1 TIGR00051 TIGR00051 68.7 68.7 117 subfamily Y Y N YbgC/FadM family acyl-CoA thioesterase 3.1.2.- GO:0047617 18338382,19684132 131567 cellular organisms no rank 41643 JCVI acyl-CoA thioester hydrolase, YbgC/YbaW family YbgC/FadM family acyl-CoA thioesterase This model describes a subset of related acyl-CoA thioesterases that include several at least partially characterized proteins. YbgC is an acyl-CoA thioesterase associated with the Tol-Pal system. YbaW is part of the FadM regulon. TIGR00055.1 TIGR00055 uppS 109.55 109.55 228 equivalog Y Y N polyprenyl diphosphate synthase uppS 2.5.1.- GO:0005737,GO:0009252 9677368,9882662 131567 cellular organisms no rank 76760 JCVI di-trans,poly-cis-decaprenylcistransferase polyprenyl diphosphate synthase This enzyme builds undecaprenyl diphosphate, or a closely related polyprenyl diphosphate. In bacteria, the product becomes a carrier used for synthesizing cell wall components, while in the Archaea, the product is most likely a precursor of glycosyl carrier lipids. While the fine specificity varies by species, reflected in a variety of EC numbers that may be assigned (2.5.1.31, 2.5.1.86, 2.5.1.87, 2.5.1.88, 2.5.1.89, etc.), the designation UppS is widely used. TIGR00057.1 TIGR00057 TIGR00057 123.2 123.2 202 equivalog Y Y N L-threonylcarbamoyladenylate synthase 2.7.7.87 GO:0003725,GO:0006400,GO:0061710 1325384,21775474,22378793 131567 cellular organisms no rank 82026 JCVI tRNA threonylcarbamoyl adenosine modification protein, Sua5/YciO/YrdC/YwlC family L-threonylcarbamoyladenylate synthase Has paralogs, but YrdC called a tRNA modification protein. Ref 2 authors say probably heteromultimeric complex. Paralogs may mean its does the final binding to the tRNA. TIGR00059.1 TIGR00059 L17 70.05 70.05 112 equivalog Y Y N 50S ribosomal protein L17 rplQ GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 36764 JCVI ribosomal protein bL17 50S ribosomal protein L17 The bacterial 50S ribosomal protein L17 is a component of the macrolide binding site in the peptidyl transferase center. TIGR00063.1 TIGR00063 folE 181.6 181.6 180 equivalog Y Y N GTP cyclohydrolase I FolE folE 3.5.4.16 GO:0003934,GO:0046654 131567 cellular organisms no rank 44573 JCVI GTP cyclohydrolase I GTP cyclohydrolase I FolE alternate names: Punch (Drosophila), GTP cyclohydrolase I (EC 3.5.4.16) catalyzes the biosynthesis of formic acid and dihydroneopterin triphosphate from GTP. This reaction is the first step in the biosynthesis of tetrahydrofolate in prokaryotes, of tetrahydrobiopterin in vertebrates, and of pteridine-containing pigments in insects. TIGR00064.1 TIGR00064 ftsY 260.7 260.7 279 equivalog Y Y N signal recognition particle-docking protein FtsY ftsY GO:0003924,GO:0005047,GO:0006614,GO:0009306 24211265,29330529 131567 cellular organisms no rank 83703 JCVI signal recognition particle-docking protein FtsY signal recognition particle-docking protein FtsY FtsY, a GTPase, serves as a membrane receptor for the signal recognition particle. It belongs to a system that lets proteins with an N-terminal signal peptide to resume translation and insert into the membrane. In E.coli, ftsY is located near the similarly named genes ftsE and ftsX, but their products are involved instead in cell division. TIGR00065.1 TIGR00065 ftsZ 295.2 295.2 353 equivalog Y Y N cell division protein FtsZ ftsZ GO:0000910,GO:0003924,GO:0005525 8016071 131567 cellular organisms no rank 56137 JCVI cell division protein FtsZ cell division protein FtsZ FtsZ, a GTPase, is structurally similar to tubulin. It undergoes GTP-dependent polymerization into filaments that form a cytoskeleton involved in septum synthesis for cell division. Other proteins such as FtsA, ZipA, and ZapA, interact with and regulate FtsZ function. TIGR00066.1 TIGR00066 g_glut_trans 357.85 357.85 518 equivalog Y Y N gamma-glutamyltransferase ggt 2.3.2.2 GO:0006750,GO:0006751,GO:0036374 131567 cellular organisms no rank 74288 JCVI gamma-glutamyltransferase gamma-glutamyltransferase Also called gamma-glutamyltranspeptidase (ggt). Some members of this family have antibiotic synthesis or resistance activities. In the case of a cephalosporin acylase from Pseudomonas sp., the enzyme was shown to retain some gamma-glutamyltranspeptidase activity. Other, more distantly related proteins have ggt-related activities and score below the trusted cutoff. TIGR00067.1 TIGR00067 glut_race 146.65 146.65 251 equivalog Y Y N glutamate racemase murI 5.1.1.3 GO:0008881,GO:0009252 131567 cellular organisms no rank 58157 JCVI glutamate racemase glutamate racemase This family consists of glutamate racemase, a protein required for making the UDP-N-acetylmuramoyl-pentapeptide used as a precursor in bacterial peptidoglycan biosynthesis. The most closely related proteins differing in function are aspartate racemases. TIGR00069.1 TIGR00069 hisD 243.8 243.8 393 equivalog_domain Y Y N histidinol dehydrogenase hisD 1.1.1.23 GO:0000105,GO:0004399,GO:0046872,GO:0051287 131567 cellular organisms no rank 86805 JCVI histidinol dehydrogenase histidinol dehydrogenase This HMM describes a polypeptide sequence catalyzing the final step in histidine biosynthesis, found sometimes as an independent protein and sometimes as a part of a multifunctional protein. TIGR00070.1 TIGR00070 hisG 75.75 75.75 183 equivalog Y Y N ATP phosphoribosyltransferase hisG 2.4.2.17 GO:0000105,GO:0003879,GO:0005737 10430882,12269828,15660995 131567 cellular organisms no rank 50524 JCVI ATP phosphoribosyltransferase ATP phosphoribosyltransferase HisG, ATP phosphoribosyltransferase, is an enzyme of histidine biosynthesis. This HMM excludes a C-terminal extension region that is variably present. TIGR00071.1 TIGR00071 hisT_truA 142.85 142.85 228 equivalog Y Y N tRNA pseudouridine(38-40) synthase TruA truA 5.4.99.12 GO:0001522,GO:0003723,GO:0009451,GO:0009982 17114947,17466622 131567 cellular organisms no rank 73706 JCVI tRNA pseudouridine(38-40) synthase tRNA pseudouridine(38-40) synthase TruA Members of this family are the tRNA modification enzyme TruA, tRNA pseudouridine(38-40) synthase. In a few species (e.g. Bacillus anthracis), TruA is represented by two paralogs. TIGR00072.1 TIGR00072 hydrog_prot 47.45 47.45 145 superfamily Y Y N hydrogenase maturation protease GO:0008233 131567 cellular organisms no rank 27630 JCVI hydrogenase maturation protease hydrogenase maturation protease HycI and HoxM are well-characterized as responsible for C-terminal protease activity on their respective hydrogenase large chains. A large number of homologous proteins appear responsible for the maturation of various forms of hydrogenase. TIGR00073.1 TIGR00073 hypB 121.2 121.2 217 equivalog Y Y N hydrogenase nickel incorporation protein HypB hypB GO:0000166,GO:0003924,GO:0016151,GO:0016530,GO:0036211,GO:0051604 131567 cellular organisms no rank 22522 JCVI hydrogenase accessory protein HypB hydrogenase nickel incorporation protein HypB A GTP hydrolase for assembly of nickel metallocenter of hydrogenase. A similar protein, ureG, is an accessory protein for urease, which also uses nickel. hits scoring 75 and above are safe as orthologs. [SS 1/05/04 I changed the role_ID and process GO from protein folding to to protein modification, since a protein folding role has not been established, but HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.] TIGR00074.1 TIGR00074 hypC_hupF 48 48 80 subfamily Y Y N HypC/HybG/HupF family hydrogenase formation chaperone hypC GO:0016530,GO:0051082,GO:0065003 9485446 131567 cellular organisms no rank 18073 JCVI hydrogenase assembly chaperone HypC/HupF HypC/HybG/HupF family hydrogenase formation chaperone See Medline:98153179 for function. This protein is suggested by act as a chaperone for a hydrogenase large subunit, holding the precursor form before metallocenter nickel incorporation. [SS 12/31/03] More recently proposed additional function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PMID:12441107. Added metallochaperone and protein mod GO terms. TIGR00075.1 TIGR00075 hypD 192.8 192.8 372 equivalog Y Y N hydrogenase formation protein HypD hypD GO:0016530,GO:0036211 1849603 131567 cellular organisms no rank 24139 JCVI hydrogenase expression/formation protein HypD hydrogenase formation protein HypD HypD is involved in the hyp operon which is needed for the activity of the three hydrogenase isoenzymes in Escherichia coli. HypD is one of the genes needed for formation of these enzymes. This protein has been found in gram-negative and gram-positive bacteria and Archaea. TIGR00078.1 TIGR00078 nadC 198.4 198.4 269 equivalog Y Y N carboxylating nicotinate-nucleotide diphosphorylase nadC 2.4.2.19 GO:0004514,GO:0009435 8419294 131567 cellular organisms no rank 61761 JCVI nicotinate-nucleotide diphosphorylase (carboxylating) carboxylating nicotinate-nucleotide diphosphorylase Synonym: quinolinate phosphoribosyltransferase (decarboxylating) TIGR00079.1 TIGR00079 pept_deformyl 103.95 103.95 161 equivalog Y Y N peptide deformylase def 3.5.1.88 GO:0036211,GO:0042586 9126850 131567 cellular organisms no rank 88059 JCVI peptide deformylase peptide deformylase Peptide deformylase (EC 3.5.1.88), also called polypeptide deformylase, is a metalloenzyme that uses water to release formate from the N-terminal formyl-L-methionine of bacterial and chloroplast peptides. This enzyme should not be confused with formylmethionine deformylase (EC 3.5.1.31) which is active on free N-formyl methionine and has been reported from rat intestine. TIGR00080.1 TIGR00080 pimt 159.05 159.05 216 equivalog Y Y N protein-L-isoaspartate O-methyltransferase pcm 2.1.1.77 GO:0004719,GO:0036211 131567 cellular organisms no rank 27201 JCVI protein-L-isoaspartate O-methyltransferase protein-L-isoaspartate O-methyltransferase This is an all-kingdom (but not all species) full-length ortholog enzyme for repairing aging proteins. Among the prokaryotes, the gene name is pcm. Among eukaryotes, pimt. TIGR00081.1 TIGR00081 purC 189.9 189.9 279 equivalog Y Y N phosphoribosylaminoimidazolesuccinocarboxamide synthase purC 6.3.2.6 GO:0004639,GO:0006164 131567 cellular organisms no rank 47341 JCVI phosphoribosylaminoimidazolesuccinocarboxamide synthase phosphoribosylaminoimidazolesuccinocarboxamide synthase Alternate name: SAICAR synthetase. Involved in purine de novo biosynthesis. Note that longer members of this family may be multifunctional enzymes. TIGR00083.1 TIGR00083 ribF 184.35 184.35 290 equivalog Y Y N riboflavin biosynthesis protein RibF ribF 2.7.1.26,2.7.7.2 GO:0003919,GO:0005737,GO:0006747,GO:0009398 131567 cellular organisms no rank 66773 JCVI riboflavin biosynthesis protein RibF riboflavin biosynthesis protein RibF multifunctional enzyme: riboflavin kinase (EC 2.7.1.26) (flavokinase) / FMN adenylyltransferase (EC 2.7.7.2) (FAD pyrophosphorylase) (FAD synthetase). TIGR00084.2 TIGR00084 ruvA 85 85 202 equivalog Y Y N Holliday junction branch migration protein RuvA ruvA 3.6.4.12 GO:0003678,GO:0006281,GO:0006310,GO:0009378,GO:0009379 9047358,9442895 131567 cellular organisms no rank 58002 JCVI Holliday junction DNA helicase RuvA Holliday junction branch migration protein RuvA RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. TIGR00087.1 TIGR00087 surE 135.1 135.1 252 equivalog Y Y N 5'/3'-nucleotidase SurE surE 3.1.3.5,3.1.3.6 GO:0008253,GO:0008254 11709173,12595266,1423722,15489502,17561111 131567 cellular organisms no rank 40252 JCVI 5'/3'-nucleotidase SurE 5'/3'-nucleotidase SurE SurE, a metal-dependent phosphatase, is a stationary phase survival protein with activities against 3'-ribonucleotides, 5'-ribonucleotides, and polyphosphate. TIGR00089.1 TIGR00089 TIGR00089 251 251 429 subfamily Y Y N MiaB/RimO family radical SAM methylthiotransferase 2.8.4.- GO:0006400,GO:0008172,GO:0016782,GO:0051539 10572129,11313137,11882645 131567 cellular organisms no rank 146783 JCVI radical SAM methylthiotransferase, MiaB/RimO family MiaB/RimO family radical SAM methylthiotransferase This subfamily contains the tRNA-i(6)A37 modification enzyme, MiaB (TIGR01574). The phylogenetic tree indicates 4 distinct clades, one of which corresponds to MiaB. The other three clades are modelled by hypothetical equivalogs (TIGR01125, TIGR01579 and TIGR01578). Together, the four models hit every sequence hit by the subfamily model without any overlap between them. This subfamily is aparrently a part of a larger superfamily of enzymes utilizing both a 4Fe4S cluster and S-adenosyl methionine (SAM) to initiate radical reactions. MiaB acts on a particular isoprenylated Adenine base of certain tRNAs causing thiolation at an aromatic carbon, and probably also transferring a methyl grouyp from SAM to the thiol. The particular substrate of the three other clades is unknown but may be very closely related. TIGR00090.1 TIGR00090 rsfS_iojap_ybeB 56.9 56.9 99 equivalog Y Y N ribosome silencing factor rsfS GO:0017148,GO:0043022 17337586,22238375,22829778,9618584 131567 cellular organisms no rank 43695 JCVI ribosome silencing factor ribosome silencing factor This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes RsfS(YbeB) from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. The conserved function of this protein is to silence ribosomes by binding the ribosomal large subunit and impairing joining with the small subunit in response to nutrient stress. Note that RsfS (starvation) is an author-endorsed change from the published symbol RsfA, which conflicted with previously published gene symbols. TIGR00091.1 TIGR00091 TIGR00091 112.65 112.65 194 equivalog Y Y N tRNA (guanosine(46)-N7)-methyltransferase TrmB trmB 2.1.1.33 GO:0006400,GO:0008176 12403464,12730187 131567 cellular organisms no rank 55359 JCVI tRNA (guanine-N(7)-)-methyltransferase tRNA (guanosine(46)-N7)-methyltransferase TrmB This predicted S-adenosylmethionine-dependent methyltransferase is found in a single copy in most Bacteria. It is also found, with a short amino-terminal extension in eukaryotes. Its function is unknown. In E. coli, this protein flanks the DNA repair protein MutY, also called micA. TIGR00093.1 TIGR00093 TIGR00093 109.3 109.3 161 subfamily Y Y N pseudouridine synthase GO:0001522,GO:0003723,GO:0009451,GO:0009982,GO:0016866 131567 cellular organisms no rank 154091 JCVI pseudouridine synthase pseudouridine synthase This HMM identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc. TIGR00094.1 TIGR00094 tRNA_TruD_broad 172.2 172.2 413 equivalog Y Y N tRNA pseudouridine(13) synthase TruD truD 5.4.99.27 GO:0001522,GO:0003723,GO:0009451,GO:0009982 12756329 131567 cellular organisms no rank 12978 JCVI tRNA pseudouridine synthase, TruD family tRNA pseudouridine(13) synthase TruD an EGAD loading error caused one member to be called surE, but that's an adjacent gene. MJ11364 is a strong partial match from 50 to 230 aa. TIGR00097.1 TIGR00097 HMP-P_kinase 204.95 204.95 254 equivalog_domain Y Y N bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase thiD 2.7.1.49,2.7.4.7 GO:0008902,GO:0008972,GO:0009228 10075431 131567 cellular organisms no rank 69346 JCVI hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase This HMM represents a bifunctional enzyme, phosphomethylpyrimidine kinase (EC 2.7.4.7)/Hydroxymethylpyrimidine kinase (EC 2.7.1.49), the ThiD/J protein of thiamine biosynthesis. The protein is commonly observed within operons containing other thiamine biosynthesis genes. Numerous examples are fusion proteins with other thiamine-biosynthetic domains. Saccaromyces has three recent paralogs, two of which are isofunctional and score above the trusted cutoff. The third shows a longer branch length in a phylogenetic tree and scores below the trusted cutoff, as do putative second copies in a number of species. TIGR00100.1 TIGR00100 hypA 88.1 88.1 116 equivalog Y Y N hydrogenase maturation nickel metallochaperone HypA hypA GO:0008901,GO:0016151,GO:0036211 12081959 131567 cellular organisms no rank 9870 JCVI hydrogenase nickel insertion protein HypA hydrogenase maturation nickel metallochaperone HypA CXXC-~12X-CXXC and genetically seems a regulatory protein. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes. TIGR00101.1 TIGR00101 ureG 204.2 204.2 199 equivalog Y Y N urease accessory protein UreG ureG GO:0003924,GO:0016530,GO:0019627,GO:0046872 17309280 131567 cellular organisms no rank 27456 JCVI urease accessory protein UreG urease accessory protein UreG This HMM represents UreG, a GTP hydrolase that acts in the assembly of the nickel metallocenter of urease. It is found only in urease-positive species, although some urease-positive species (e.g. Bacillus subtilis) lack this protein. A similar protein, hypB, is an accessory protein for expression of hydrogenase, which also uses nickel. TIGR00104.1 TIGR00104 tRNA_TsaA 93.25 93.25 143 equivalog Y Y N tRNA (N6-threonylcarbamoyladenosine(37)-N6)-methyltransferase TrmO tsaA GO:0005737,GO:0006400,GO:0008757 17588214 131567 cellular organisms no rank 24795 JCVI tRNA-Thr(GGU) m(6)t(6)A37 methyltransferase TsaA tRNA (N6-threonylcarbamoyladenosine(37)-N6)-methyltransferase TrmO This protein has been characterized by crystallography in complex with S-Adenosylmethionine, making it a probable S-adenosylmethionine-dependent methyltransferase. Analysis in EcoGene links this protein to the enzyme characterization mapped to the tsaA gene in Escherichia coli. TIGR00106.1 TIGR00106 TIGR00106 54.7 54.7 97 hypoth_equivalog Y Y N MTH1187 family thiamine-binding protein 12866058 131567 cellular organisms no rank 11216 JCVI uncharacterized protein, MTH1187 family MTH1187 family thiamine-binding protein This protein has been crystallized in both Methanobacterium thermoautotrophicum and yeast, but its function remains unknown. Both crystal structures showed sulfate ions bound at the interface of two dimers to form a tetramer. TIGR00109.1 TIGR00109 hemH 124.6 124.6 322 equivalog Y Y N ferrochelatase hemH 4.98.1.1 GO:0004325,GO:0006779 10561552,8056770 131567 cellular organisms no rank 58317 JCVI ferrochelatase ferrochelatase This family includes proteins currently designated 4.98.1.1 (protoporphyrin ferrochelatase) and 4.99.1.9 (coproporphyrin ferrochelatase). The former occurs primarily in Gram-negative bacteria and in mitochondria, the latter primarily in Gram-positive bacteria. TIGR00110.1 TIGR00110 ilvD 618.15 618.15 543 equivalog Y Y N dihydroxy-acid dehydratase ilvD 4.2.1.9 GO:0004160,GO:0009082,GO:0051536 31315931 131567 cellular organisms no rank 74069 JCVI dihydroxy-acid dehydratase dihydroxy-acid dehydratase This protein, dihydroxy-acid dehydratase, catalyzes the fourth step in valine and isoleucine biosynthesis. Family members from spinach and from Mycobacterium tuberculosis were shown to contains catalytically essential [2Fe-2S] cluster, while in older work, the enzyme from Escherichia coli was interpreted as containing a [4Fe-4S] cluster. TIGR00112.1 TIGR00112 proC 196.75 196.75 263 equivalog Y Y N pyrroline-5-carboxylate reductase proC 1.5.1.2 GO:0004735,GO:0006561 11418582,28824574 131567 cellular organisms no rank 72775 JCVI pyrroline-5-carboxylate reductase pyrroline-5-carboxylate reductase This enzyme catalyzes the final step in proline biosynthesis, reduction from 1-pyrroline-5-carboxylate. TIGR00113.1 TIGR00113 queA 267.45 267.45 345 equivalog Y Y N tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA queA 2.4.99.17 GO:0005737,GO:0006400,GO:0008616,GO:0051075 131567 cellular organisms no rank 54612 JCVI S-adenosylmethionine:tRNA ribosyltransferase-isomerase tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA This model describes the enzyme for S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA). QueA synthesizes Queuosine which is usually in the first position of the anticodon of tRNAs specific for asparagine, aspartate, histidine, and tyrosine. TIGR00114.1 TIGR00114 lumazine-synth 84.6 84.6 138 equivalog Y Y N 6,7-dimethyl-8-ribityllumazine synthase ribH 2.5.1.78 GO:0000906,GO:0009349 7559556 131567 cellular organisms no rank 43216 JCVI 6,7-dimethyl-8-ribityllumazine synthase 6,7-dimethyl-8-ribityllumazine synthase This enzyme catalyzes the cyclo-ligation of 3,4-dihydroxy-2-butanone-4-P and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione to form 6,7-dimethyl-8-ribityllumazine, the immediate precursor of riboflavin. Sometimes referred to as riboflavin synthase, beta subunit, this should not be confused with the alpha subunit which carries out the subsequent reaction. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff. TIGR00118.1 TIGR00118 acolac_lg 538.35 538.35 557 equivalog Y Y N biosynthetic-type acetolactate synthase large subunit ilvB 2.2.1.6 GO:0000287,GO:0003984,GO:0009082,GO:0030976,GO:0050660 9099862,9655946 131567 cellular organisms no rank 83867 JCVI acetolactate synthase, large subunit, biosynthetic type biosynthetic-type acetolactate synthase large subunit Two groups of proteins form acetolactate from two molecules of pyruvate. The type of acetolactate synthase described in this model also catalyzes the formation of acetohydroxybutyrate from pyruvate and 2-oxobutyrate, an early step in the branched chain amino acid biosynthesis; it is therefore also termed acetohydroxyacid synthase. In bacteria, this catalytic chain is associated with a smaller regulatory chain in an alpha2/beta2 heterotetramer. Acetolactate synthase is a thiamine pyrophosphate enzyme. In this type, FAD and Mg++ are also found. Several isozymes of this enzyme are found in E. coli K12, one of which contains a frameshift in the large subunit gene and is not expressed. TIGR00119.1 TIGR00119 acolac_sm 56.9 56.9 158 equivalog Y Y N acetolactate synthase small subunit ilvN 2.2.1.6 GO:0005948,GO:0009082,GO:1990610 131567 cellular organisms no rank 33585 JCVI acetolactate synthase, small subunit acetolactate synthase small subunit Acetolactate synthase is a heterodimeric thiamine pyrophosphate enzyme with large and small subunits. One of the three isozymes in E. coli K12 contains a frameshift in the large subunit gene and is not expressed. acetohydroxyacid synthase is a synonym. TIGR00120.1 TIGR00120 ArgJ 298 298 405 equivalog Y Y N bifunctional ornithine acetyltransferase/N-acetylglutamate synthase argJ 2.3.1.1,2.3.1.35 GO:0004042,GO:0004358,GO:0006526,GO:0006592 131567 cellular organisms no rank 53879 JCVI glutamate N-acetyltransferase/amino-acid acetyltransferase bifunctional ornithine acetyltransferase/N-acetylglutamate synthase This enzyme can acetylate Glu to N-acetyl-Glu by deacetylating N-2-acetyl-ornithine into ornithine; the two halves of this reaction represent the first and fifth steps in the synthesis of Arg (or citrulline) from Glu by way of ornithine (EC 2.3.1.35). In Bacillus stearothermophilus, but not in Thermus thermophilus HB27, the enzyme is bifunctional and can also use acetyl-CoA to acetylate Glu (EC 2.3.1.1). TIGR00121.1 TIGR00121 birA_ligase 83.1 83.1 235 equivalog_domain Y Y N biotin--[acetyl-CoA-carboxylase] ligase 6.3.4.15 GO:0004077,GO:0036211 3536662 131567 cellular organisms no rank 77685 JCVI biotin--[acetyl-CoA-carboxylase] ligase biotin--[acetyl-CoA-carboxylase] ligase This model represents the biotin--acetyl-CoA-carboxylase ligase region of biotin--acetyl-CoA-carboxylase ligase. In Escherichia coli and some other species, this enzyme is part of a bifunction protein BirA that includes a small, N-terminal biotin operon repressor domain. Proteins identified by this model should not be called bifunctional unless they are also identified by birA_repr_reg (TIGR00122). The protein name suggests that this enzyme transfers biotin only to acetyl-CoA-carboxylase but it also transfers the biotin moiety to other proteins. The apparent orthologs among the eukaryotes are larger proteins that contain a single copy of this domain. TIGR00123.1 TIGR00123 cbiM 184.15 184.15 214 equivalog Y Y N cobalt ECF transporter S component CbiM cbiM GO:0006824,GO:0009236,GO:0016020,GO:0043190 8501034 131567 cellular organisms no rank 6789 JCVI cobalamin biosynthesis protein CbiM cobalt ECF transporter S component CbiM A cutoff of 200 bits for trusted orthologs of cbiM is suggested. Scores lower than 200 but higher than 20 may be considered sufficient to call a protein cobalamin biosynthesis protein CbiM-related. The seed alignment for this HMM is a cluster of very closely related proteins from Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, Methanococcus jannaschii, and Salmonella typhimurium, each of which has greater than 50% identity to all the others. The ortholog from Salmonella is the source of the gene symbol cbiM for this set. In Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, and Methanococcus jannaschii, a second homolog of cbiM is also found. These cbiM-related proteins appear to represent a distinct but less well-conserved orthologous group. Still more distant homologs include sll0383 from Synechocystis sp. and HI1621 from Haemophilus influenzae; the latter protein, from a species that does not synthesize cobalamin, is the most divergent member of the group. The functions of and relationships among the set of proteins homologous to cbiM have not been determined. TIGR00125.1 TIGR00125 cyt_tran_rel 27.7 27.7 65 domain Y Y N adenylyltransferase/cytidyltransferase family protein GO:0003824,GO:0009058 131567 cellular organisms no rank 227041 JCVI cytidyltransferase-like domain cytidyltransferase-like domain Protein families that contain at least one copy of this domain include citrate lyase ligase, pantoate-beta-alanine ligase, glycerol-3-phosphate cytidyltransferase, ADP-heptose synthase, phosphocholine cytidylyltransferase, lipopolysaccharide core biosynthesis protein KdtB, the bifunctional protein NadR, and a number whose function is unknown. Many of these proteins are known to use CTP or ATP and release pyrophosphate. TIGR00126.1 TIGR00126 deoC 117.3 117.3 211 equivalog Y Y N deoxyribose-phosphate aldolase deoC 4.1.2.4 GO:0004139,GO:0005737,GO:0009264 131567 cellular organisms no rank 57332 JCVI deoxyribose-phosphate aldolase deoxyribose-phosphate aldolase Involved in catabolism of nucleotides and deoxyribonucleotides; catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate. TIGR00129.1 TIGR00129 fdhD_narQ 140.9 140.9 237 equivalog Y Y N formate dehydrogenase accessory sulfurtransferase FdhD fdhD GO:0009061,GO:0009326,GO:0015942,GO:0016783 22194618,23765795 131567 cellular organisms no rank 48720 JCVI formate dehydrogenase family accessory protein FdhD formate dehydrogenase accessory sulfurtransferase FdhD FdhD in E. coli and NarQ in B. subtilis are required for the activity of formate dehydrogenase. The gene name in B. subtilis reflects the requirement of the neighboring gene narA for nitrate assimilation, for which NarQ is not required. In some species, the gene is associated not with a known formate dehydrogenase but with a related putative molybdopterin-binding oxidoreductase. A reasonable hypothesis is that this protein helps prepare a required cofactor for assembly into the holoenzyme. TIGR00131.1 TIGR00131 gal_kin 226.65 226.65 388 equivalog Y Y N galactokinase galK 2.7.1.6 GO:0004335,GO:0005524,GO:0006012,GO:0046835 131567 cellular organisms no rank 44893 JCVI galactokinase galactokinase Galactokinase is a member of the GHMP kinases (Galactokinase, Homoserine kinase, Mevalonate kinase, Phosphomevalonate kinase) and shares with them an amino-terminal domain probably related to ATP binding. The galactokinases found by this HMM are divided into two sets. Prokaryotic forms are generally shorter. The eukaryotic forms are longer because of additional central regions and in some cases are known to be bifunctional, with regulatory activities that are independent of galactokinase activity. TIGR00132.1 TIGR00132 gatA 481.1 481.1 466 equivalog Y Y N Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA gatA GO:0006412,GO:0006424,GO:0030956,GO:0050567 19520089,9342321 131567 cellular organisms no rank 59228 JCVI aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA Members of this family are GatA, the amidase chain (designated subunit A) of a heterotrimeric complex that converts Asp to Asn, and/or converts Glu to Gln, after misacylation of a tRNA(Asn) with Asp or of tRNA(Gln) with Glu. Where direct experimental evidence for an enzyme or a sufficiently close homolog is lacking, the fine specificity may best be inferred by genomic context. Where direct ligation of neither Gln not Asn to tRNA occurs, and only a single GatA family occurs, the amidase should contribute to both EC 6.3.5.6 and 6.3.5.7 activities. TIGR00133.1 TIGR00133 gatB 314.8 314.8 481 equivalog Y Y N Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB gatB GO:0006424,GO:0016884,GO:0030956,GO:0050567 17329242,19520089,29156229 131567 cellular organisms no rank 58646 JCVI aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB The heterotrimer GatABC is responsible for transferring the NH2 group that converts Glu to Gln, or Asp to Asn after the Glu or Asp has been ligated to the tRNA for Gln or Asn, respectively. In Lactobacillus, GatABC is responsible only for tRNA(Gln). In the Archaea, GatABC is responsible only for tRNA(Asn), while GatDE is responsible for tRNA(Gln). In lineages that include Thermus, Chlamydia, or Acidithiobacillus, the GatABC complex catalyzes both. TIGR00134.1 TIGR00134 gatE_arch 319.55 319.55 622 equivalog Y Y N Glu-tRNA(Gln) amidotransferase subunit GatE gatE GO:0006424,GO:0016884,GO:0050567 10993083 131567 cellular organisms no rank 1622 JCVI glutamyl-tRNA(Gln) amidotransferase, subunit E Glu-tRNA(Gln) amidotransferase subunit GatE This peptide is found only in the Archaea. It is paralogous to the gatB-encoded subunit of Glu-tRNA(Gln) amidotransferase. The GatABC system operates in many bacteria to convert Glu-tRNA(Gln) into Gln-tRNA(Gln). However, the homologous system in archaea instead converts Asp-tRNA(Asn) to Asn-tRNA(Asn). Glu-tRNA(Gln) is converted to Gln-tRNA(Gln) by a heterodimeric amidotransferase of GatE (this protein) and GatD. The Archaea have an Asp-tRNA(Asn) amidotransferase instead of an Asp--tRNA ligase, but the genes have not been identified. It is likely that this protein replaces gatB in Asp-tRNA(Asn) amidotransferase but that both enzymes share gatA. TIGR00135.1 TIGR00135 gatC 47.1 47.1 93 equivalog Y Y N Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC gatC GO:0006424,GO:0006450,GO:0030956,GO:0050567 131567 cellular organisms no rank 32650 JCVI aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC Archaea, organelles, and many bacteria charge Gln-tRNA by first misacylating it with Glu and then amidating Glu to Gln. This small protein is part of the amidotransferase heterotrimer and appears to be important to the stability of the amidase subunit encode by gatA, but its function may not be required in every organism that expresses gatA and gatB. The seed alignment for this HMM does not include any eukaryotic sequence and is not guaranteed to find eukaryotic examples, although it does find some. Saccharomyces cerevisiae, which expresses the amidotransferase for mitochondrial protein translation, seems to lack a gatC ortholog. This HMM has been revised to remove the candidate sequence from Methanococcus jannaschii, now part of a related model. TIGR00136.1 TIGR00136 mnmG_gidA 524.85 524.85 616 equivalog Y Y N tRNA uridine-5-carboxymethylaminomethyl(34) synthesis enzyme MnmG mnmG GO:0002098,GO:0008033 17062623 131567 cellular organisms no rank 63509 JCVI tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA tRNA uridine-5-carboxymethylaminomethyl(34) synthesis enzyme MnmG MnmG, a tRNA uridine-5-carboxymethylaminomethyl(34) synthesis enzyme, was previously known as GidA (glucose-inhibited division protein A). It partners with MnmE, in an alpha2/beta2 heterotetramer, in the 5-carboxymethylaminomethyl modification of uridine 34 in certain tRNAs. TIGR00138.1 TIGR00138 rsmG_gidB 99.5 99.5 183 equivalog Y Y N 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG rsmG 2.1.1.170 GO:0008168,GO:0031167,GO:0046118 12001236,17238915 131567 cellular organisms no rank 65967 JCVI 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG RsmG was previously called GidB (glucose-inhibited division protein B). It is present and a single copy in nearly all complete eubacterial genomes. It is missing only from some obligate intracellular species of various lineages (Chlamydiae, Ehrlichia, Wolbachia, Anaplasma, Buchnera, etc.). RsmG shows a methytransferase fold in its the crystal structure, and acts as a 7-methylguanosine (m(7)G) methyltransferase, apparently specific to 16S rRNA. TIGR00143.1 TIGR00143 hypF 466.1 466.1 741 equivalog Y Y N carbamoyltransferase HypF hypF 6.1.2.- GO:0003998,GO:0016743,GO:0036211,GO:0046872 11375153 131567 cellular organisms no rank 33325 JCVI carbamoyltransferase HypF carbamoyltransferase HypF A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression. TIGR00144.1 TIGR00144 beta_RFAP_syn 113.5 113.5 325 subfamily Y Y N beta-ribofuranosylaminobenzene 5'-phosphate synthase family protein 12142414,15262968,36629016 131567 cellular organisms no rank 3228 JCVI beta-ribofuranosylaminobenzene 5'-phosphate synthase family beta-ribofuranosylaminobenzene 5'-phosphate synthase family protein This protein family contains several archaeal examples of beta-ribofuranosylaminobenzene 5-prime-phosphate synthase (beta-RFAP synthase, MptG), an enzyme involved in methanopterin biosynthesis. In some species, two members of this family are found. It is unclear whether both act as beta-RFAP synthase. This family is related to the GHMP kinases (Galactokinase, Homoserine kinase, Mevalonate kinase, Phosphomevalonate kinase). Members are found so far only in the Archaea and in Methylobacterium extorquens. TIGR00147.1 TIGR00147 TIGR00147 118.65 118.65 296 subfamily Y Y N YegS/Rv2252/BmrU family lipid kinase GO:0001727,GO:0005524 10220166,16689792,17351295,7961792 131567 cellular organisms no rank 54876 JCVI lipid kinase, YegS/Rv2252/BmrU family YegS/Rv2252/BmrU family lipid kinase The E. coli member of this family, YegS has been purified [1] and shown to have phosphatidylglycerol kinase activity. The member from M. tuberculosis, Rv2252, has diacylglycerol kinase activity. BmrU from B. subtilis is in an operon with multidrug efflux transporter Bmr, but is uncharacterized. TIGR00148.1 TIGR00148 TIGR00148 244.85 244.85 438 subfamily Y Y N UbiD family decarboxylase GO:0016831 11029449,12799002 131567 cellular organisms no rank 44262 JCVI decarboxylase, UbiD family UbiD family decarboxylase The member of this family in E. coli is UbiD, 3-octaprenyl-4-hydroxybenzoate carboxy-lyase. The family described by this HMM, however, is broad enough that it is likely to contain several different decarboxylases. Found in bacteria, archaea, and yeast, with two members in A. fulgidus. No homologs were detected besides those classified as orthologs. The member from H. pylori has a C-terminal extension of just over 100 residues that is shared in part by the Aquifex aeolicus homolog. TIGR00149.1 TIGR00149 TIGR00149_YjbQ 67.75 67.75 132 hypoth_equivalog Y Y N secondary thiamine-phosphate synthase enzyme YjbQ GO:0003824,GO:0005737 18178222,21119630 131567 cellular organisms no rank 30718 JCVI secondary thiamine-phosphate synthase enzyme secondary thiamine-phosphate synthase enzyme YjbQ Members of this protein family, designated YjbQ in E. coli have been studied extensively by crystallography. Members from several different species have been shown to have sufficient thiamine phosphate synthase activity (EC 2.5.1.3) to complement thiE mutants. However, it is presumed that this is a secondary activity, and the primary function of the YjbQ family enzyme remains unknown. TIGR00150.1 TIGR00150 T6A_YjeE 60.1 60.1 135 equivalog Y Y N tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex ATPase subunit type 1 TsaE tsaE GO:0002949 12112691,17581233,22378793 131567 cellular organisms no rank 61637 JCVI tRNA threonylcarbamoyl adenosine modification protein YjeE tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex ATPase subunit type 1 TsaE This protein family belongs to a four-gene system responsible for the threonylcarbamoyl adenosine (t6A) tRNA modification. Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have (weak) ATPase activity. TIGR00152.1 TIGR00152 TIGR00152 65.55 65.55 188 equivalog Y Y N dephospho-CoA kinase coaE 2.7.1.24 GO:0004140,GO:0005524,GO:0005737,GO:0015937 131567 cellular organisms no rank 75919 JCVI dephospho-CoA kinase dephospho-CoA kinase CoaE catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A. CoaE is present, as encoded by a single copy gene, in the vast majority of bacterial genomes. Distantly related proteins include adenylate, guanylate, uridine, and thymidylate kinases. Dephospho-CoA kinase (CoaE) performs the final step in coenzyme A biosynthesis. TIGR00153.1 TIGR00153 TIGR00153 104.3 104.3 217 hypoth_equivalog Y Y N TIGR00153 family protein 131567 cellular organisms no rank 3351 JCVI TIGR00153 family protein TIGR00153 family protein An apparent homolog with a suggested function is Pit accessory protein from Sinorhizobium meliloti, which may be involved in phosphate (Pi) transport. TIGR00157.1 TIGR00157 TIGR00157 100 100 247 equivalog Y Y N ribosome small subunit-dependent GTPase A rsgA GO:0003924,GO:0005525,GO:0006412,GO:0043022 12220175,14973029,15466596 131567 cellular organisms no rank 78159 JCVI ribosome small subunit-dependent GTPase A ribosome small subunit-dependent GTPase A Members of this protein were designated YjeQ and are now designated RsgA (ribosome small subunit-dependent GTPase A). The strongest motif in the alignment of these proteins is GXSGVGKS[ST], a classic P-loop for nucleotide binding. This protein has been shown to cleave GTP and remain bound to GDP. A role as a regulator of translation has been suggested. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option). TIGR00160.1 TIGR00160 MGSA 146.9 146.9 143 equivalog Y Y N methylglyoxal synthase mgsA 4.2.3.3 GO:0006007,GO:0008929,GO:0019242 9489667 131567 cellular organisms no rank 14725 JCVI methylglyoxal synthase methylglyoxal synthase Methylglyoxal synthase (MGS) generates methylglyoxal (MG), a toxic metabolite (that may also be a regulatory metabolite and) that is detoxified, prinicipally, through a pathway involving glutathione and glyoxylase I. Totemeyer, et al. (MUID:98149311) propose that, during a loss of control over carbon flux, with accumulation of phosphorylated sugars and depletion of phosphate, as might happen during a rapid shift to a richer medium, MGS aids the cell by converting some dihydroxyacetone phosphate (DHAP) to MG and phosphate. This is therefore an alternative to triosephosphate isomerase and the remainder of the glycolytic pathway for the disposal of DHAP during the stress of a sudden increase in available sugars. TIGR00164.2 TIGR00164 AS_decarb 230 230 215 equivalog Y Y N archaetidylserine decarboxylase 4.1.1.65 16243780,18708506 131567 cellular organisms no rank 965 JCVI phosphatidylserine decarboxylase homolog archaetidylserine decarboxylase This HMM has been rebuilt. It originally included mostly (but now exclusively) archaeal sequences in the seed alignment. These sequences are archaetidylserine decarboxylase, related to bacterial phosphatidylserine decarboxylase. These enzymes are translated as a single chain precursor. Generation of the pyruvoyl active site from a Ser is coupled to cleavage of a Gly-Ser bond between the larger (beta) and smaller (alpha) subunits. TIGR00167.1 TIGR00167 cbbA 215.6 215.6 290 subfamily Y Y N ketose-bisphosphate aldolase GO:0005975,GO:0016832 131567 cellular organisms no rank 75711 JCVI ketose-bisphosphate aldolase ketose-bisphosphate aldolase This model is under revision. Proteins found by this model include fructose-bisphosphate and tagatose-bisphosphate aldolase. TIGR00170.1 TIGR00170 leuC 560.25 560.25 466 equivalog_domain Y Y N 3-isopropylmalate dehydratase large subunit leuC 4.2.1.33 GO:0003861,GO:0009098,GO:0009316,GO:0051539 131567 cellular organisms no rank 62735 JCVI 3-isopropylmalate dehydratase, large subunit 3-isopropylmalate dehydratase large subunit Members of this family are 3-isopropylmalate dehydratase, large subunit, or the large subunit domain of single-chain forms. Homoaconitase, aconitase, and 3-isopropylmalate dehydratase have similar overall structures. All are dehydratases (EC 4.2.1.-) and bind a Fe-4S iron-sulfur cluster. 3-isopropylmalate dehydratase is split into large (leuC) and small (leuD) chains in eubacteria. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain. These homologs are now described by a separate model of subfamily (rather than equivalog) homology type, and the priors and cutoffs for this model have been changed to focus this equivalog family more narrowly. TIGR00171.1 TIGR00171 leuD 116.25 116.25 188 equivalog_domain Y Y N 3-isopropylmalate dehydratase small subunit leuD 4.2.1.33 GO:0003861,GO:0009098,GO:0009316 131567 cellular organisms no rank 54913 JCVI 3-isopropylmalate dehydratase, small subunit 3-isopropylmalate dehydratase small subunit Homoaconitase, aconitase, and 3-isopropylmalate dehydratase have similar overall structures. All are dehydratases (EC 4.2.1.-) and bind a Fe-4S iron-sulfur cluster. 3-isopropylmalate dehydratase is split into large (leuC) and small (leuD) chains in eubacteria. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain. The candidate archaeal leuD proteins are not included in the seed alignment for this model and score below the trusted cutoff. TIGR00172.1 TIGR00172 maf 117.15 117.15 185 subfamily Y Y N Maf family nucleotide pyrophosphatase GO:0000917,GO:0030428,GO:0047429 24210219,25658941,8387996 131567 cellular organisms no rank 83057 JCVI septum formation protein Maf Maf family nucleotide pyrophosphatase Maf (for multicopy associated filamentation) is a large family of non-essential proteins active as nucleotide pyrophosphatases, with substrate ranges that include modified bases such as 5-methyl-UTP, pseudo-UTP, 5-methyl-CTP, and 7-methyl-GTP. Two members in Escherichia coli are YhdE (a dTTP/UTP pyrophosphatase) and YceF (m(7)GTP pyrophosphatase). The name Maf reflects an early study in Bacillus subtilis showing that overexpression causes inhibition of septum formation. TIGR00173.1 TIGR00173 menD 244.2 244.2 435 equivalog Y Y N 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase menD 2.2.1.9 GO:0009234,GO:0030976,GO:0070204 17760421 131567 cellular organisms no rank 38271 JCVI 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase MenD was once thought to act as SHCHC synthase, but was shown in 2007 to act instead as SEPHCHC synthase. Conversion of SEPHCHC into SHCHC and pyruvate may occur spontaneously but is catalyzed efficiently, at least in some organisms, by MenH (see TIGR03695). TIGR00176.1 TIGR00176 mobB 76.2 76.2 155 equivalog Y Y N molybdopterin-guanine dinucleotide biosynthesis protein B mobB GO:0003824,GO:0005525,GO:0006777 131567 cellular organisms no rank 26885 JCVI molybdopterin-guanine dinucleotide biosynthesis protein B molybdopterin-guanine dinucleotide biosynthesis protein B This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes. TIGR00177.1 TIGR00177 molyb_syn 85.35 85.35 148 domain Y Y N molybdenum cofactor synthesis domain-containing protein GO:0003824,GO:0006777 11525167,15159566,29717023 131567 cellular organisms no rank 164434 JCVI molybdenum cofactor synthesis domain molybdenum cofactor biosynthesis domain The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by this HMM. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine receptors and GABA receptors, rather than a protein of molybdenum cofactor biosynthesis. TIGR00178.1 TIGR00178 monomer_idh 950 950 744 equivalog Y Y N NADP-dependent isocitrate dehydrogenase 1.1.1.42 GO:0004450,GO:0006099 131567 cellular organisms no rank 33186 JCVI isocitrate dehydrogenase, NADP-dependent NADP-dependent isocitrate dehydrogenase The monomeric type of isocitrate dehydrogenase has been found so far in a small number of species, including Azotobacter vinelandii, Corynebacterium glutamicum, Rhodomicrobium vannielii, and Neisseria meningitidis. It is NADP-specific. TIGR00179.1 TIGR00179 murB 144.5 144.5 290 equivalog Y Y N UDP-N-acetylmuramate dehydrogenase murB 1.3.1.98 GO:0008762,GO:0009252 131567 cellular organisms no rank 76233 JCVI UDP-N-acetylenolpyruvoylglucosamine reductase UDP-N-acetylmuramate dehydrogenase This HMM describes MurB, UDP-N-acetylenolpyruvoylglucosamine reductase, which is also called UDP-N-acetylmuramate dehydrogenase. It is part of the pathway for the biosynthesis of the UDP-N-acetylmuramoyl-pentapeptide that is a precursor of bacterial peptidoglycan. TIGR00180.1 TIGR00180 parB_part 58.45 58.45 186 domain Y Y N ParB/RepB/Spo0J family partition protein GO:0000910,GO:0003677,GO:0007059 9506522 131567 cellular organisms no rank 119412 JCVI ParB/RepB/Spo0J family partition protein ParB/RepB/Spo0J family partition protein This HMM represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction. TIGR00181.1 TIGR00181 pepF 490.55 490.55 591 equivalog Y Y N oligoendopeptidase F pepF GO:0004222,GO:0006508 7798200,8757883 131567 cellular organisms no rank 28775 JCVI oligoendopeptidase F oligoendopeptidase F This family represents the oligoendopeptidase F clade of the family of larger M3 or thimet (for thiol-dependent metallopeptidase) oligopeptidase family. Lactococcus lactis PepF hydrolyzed peptides of 7 and 17 amino acids with fairly broad specificity. The homolog of lactococcal PepF in group B Streptococcus was named PepB (PMID:8757883), with the name difference reflecting a difference in species of origin rather activity; substrate profiles were quite similar. Differences in substrate specificity should be expected in other species. The gene is duplicated in Lactococcus lactis on the plasmid that bears it. A shortened second copy is found in Bacillus subtilis. TIGR00183.1 TIGR00183 prok_nadp_idh 567.3 567.3 417 equivalog Y Y N isocitrate dehydrogenase (NADP(+)) icd 1.1.1.42 GO:0004450,GO:0006099 131567 cellular organisms no rank 19305 JCVI isocitrate dehydrogenase, NADP-dependent isocitrate dehydrogenase (NADP(+)) Several NAD- or NADP-dependent dehydrogenases, including 3-isopropylmalate dehydrogenase, tartrate dehydrogenase, and the multimeric forms of isocitrate dehydrogenase, share a nucleotide binding domain unrelated to that of lactate dehydrogenase and its homologs. These enzymes dehydrogenate their substates at a H-C-OH site adjacent to a H-C-COOH site; Prokaryotic NADP-dependent isocitrate dehydrogenases resemble their NAD-dependent counterparts and 3-isopropylmalate dehydrogenase (an NAD-dependent enzyme) more closely than they resemble eukaryotic NADP-dependent isocitrate dehydrogenases. TIGR00184.1 TIGR00184 purA 395.55 395.55 425 equivalog Y Y N adenylosuccinate synthase purA 6.3.4.4 GO:0004019,GO:0009152 131567 cellular organisms no rank 58669 JCVI adenylosuccinate synthase adenylosuccinate synthase Catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis. TIGR00186.1 TIGR00186 rRNA_methyl_3 160.15 160.15 240 equivalog Y Y N 23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB rlmB GO:0006396,GO:0008173 8265370 131567 cellular organisms no rank 56166 JCVI RNA methyltransferase, TrmH family, group 3 23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB this is part of the trmH (spoU) family of rRNA methylases TIGR00187.1 TIGR00187 ribE 156.6 156.6 207 equivalog Y Y N riboflavin synthase ribE 2.5.1.9 GO:0004746 131567 cellular organisms no rank 63534 JCVI riboflavin synthase, alpha subunit riboflavin synthase This protein family consists almost entirely of two lumazine-binding domains, described in the HMM Lum_binding from PFAM. The model generates lower scores against other proteins that also have two lumazine-binding domains, including some involved in bioluminescence. The name ribE was selected, from among alternatives including ribB and ribC, to match the usage in EcoCyc. TIGR00190.1 TIGR00190 thiC 460 460 423 equivalog Y Y N phosphomethylpyrimidine synthase thiC 4.1.99.17 GO:0003824,GO:0009228,GO:0051536 131567 cellular organisms no rank 58300 JCVI phosphomethylpyrimidine synthase phosphomethylpyrimidine synthase The thiC ortholog is designated thiA in Bacillus subtilis. TIGR00191.1 TIGR00191 thrB 168.25 168.25 304 equivalog Y Y N homoserine kinase thrB 2.7.1.39 GO:0004413,GO:0005524,GO:0009088 131567 cellular organisms no rank 42092 JCVI homoserine kinase homoserine kinase Homoserine kinase is part of the threonine biosynthetic pathway. Homoserine kinase is a member of the GHMP kinases (Galactokinase, Homoserine kinase, Mevalonate kinase, Phosphomevalonate kinase) and shares with them an amino-terminal domain probably related to ATP binding. P.aeruginosa homoserine kinase seems not to be homologous (see PROSITE:PDOC0054) TIGR00192.1 TIGR00192 urease_beta 90.3 90.3 103 equivalog_domain Y Y N urease subunit beta ureB 3.5.1.5 GO:0009039,GO:0035550,GO:0043419 30608981 131567 cellular organisms no rank 28235 JCVI urease, beta subunit urease subunit beta In a number of species, including B.subtilis, Synechocystis, and Haemophilus influenzae, urease subunits beta and gamma are encoded as separate polypeptides. In Helicobacter pylori UreA and in the fission yeast Schizosaccharomyces pombe, beta subunit-like sequence follows gamma subunit-like sequence in a single chain; the fission yeast protein contains additional C-terminal regions. TIGR00193.1 TIGR00193 urease_gam 82.3 82.3 102 equivalog_domain Y Y N urease subunit gamma ureA 3.5.1.5 GO:0009039,GO:0016151,GO:0019627 131567 cellular organisms no rank 25120 JCVI urease, gamma subunit urease subunit gamma In a number of species, including B.subtilis, Synechocystis, and Haemophilus influenzae, urease subunits beta and gamma are encoded as separate polypeptides. In Helicobacter pylori UreA and in the fission yeast Schizosaccharomyces pombe, beta subunit-like sequence follows gamma subunit-like sequence in a single chain; the fission yeast protein contains additional C-terminal regions. Nomenclature for the various subunits of urease in Helicobacter differs from nomenclature in most other species. TIGR00194.1 TIGR00194 uvrC 285.45 285.45 574 equivalog Y Y N excinuclease ABC subunit UvrC uvrC GO:0006289,GO:0009380,GO:0009381 10671556 131567 cellular organisms no rank 82967 JCVI excinuclease ABC subunit C excinuclease ABC subunit UvrC The UvrABC repair system catalyzes the recognition and processing of helix-distorting DNA lesions, such as those caused by UV light, for Nucleotide Excision Repair (NER). UvrC cuts on both the 5' and the 3' side of the lesion. TIGR00195.1 TIGR00195 exoDNase_III 182.55 182.55 254 equivalog Y Y N exodeoxyribonuclease III xth 3.1.11.2 GO:0006281,GO:0008311 131567 cellular organisms no rank 88126 JCVI exodeoxyribonuclease III exodeoxyribonuclease III The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family TIGR00196.1 TIGR00196 yjeF_cterm 129.85 129.85 277 hypoth_equivalog_domain Y Y N NAD(P)H-hydrate dehydratase GO:0016836 131567 cellular organisms no rank 83422 JCVI YjeF family C-terminal domain NAD(P)H-hydrate dehydratase E. coli yjeF has full-length orthologs in a number of species, all of unknown function. However, yeast YNL200C is homologous and corresponds to the N-terminal region while yeast YKL151C and B. subtilis yxkO correspond to this C-terminal region only. With search program hmmsw, the present model hits hydroxyethylthiazole kinase, an enzyme associated with thiamine biosynthesis, with scores between 10 and 30. The noise cutoff for this family is set higher, at 40 bits. TIGR00197.1 TIGR00197 yjeF_nterm 88.6 88.6 206 hypoth_equivalog_domain Y Y N NAD(P)H-hydrate epimerase 5.1.99.6 131567 cellular organisms no rank 66949 JCVI YjeF family N-terminal domain NAD(P)H-hydrate epimerase The protein region corresponding to this HMM shows no clear homology to any protein of known function. This HMM is built on yeast protein YNL200C and the N-terminal regions of E. coli yjeF and its orthologs in various species. The C-terminal region of yjeF and its orthologs shows similarity to hydroxyethylthiazole kinase (thiM) and other enzymes involved in thiamine biosynthesis. Yeast YKL151C and B. subtilis yxkO match the yjeF C-terminal domain but lack this region. TIGR00198.1 TIGR00198 cat_per_HPI 770.25 770.25 716 equivalog Y Y N catalase/peroxidase HPI katG 1.11.1.21 GO:0004096,GO:0004601,GO:0006979,GO:0020037 27665757,30793344 131567 cellular organisms no rank 51381 JCVI catalase/peroxidase HPI catalase/peroxidase HPI As catalase, HPI (hydroperoxidase I, product of katG) catalyzes the dismutation of two molecules of hydrogen peroxide to dioxygen and two molecules of water. As a peroxidase, it uses hydrogen peroxide to oxidize donor compounds and produce water. The EC number 1.11.1.21 describes enzymes with both activities. HPI from E. coli is a homotetramer with two non-covalently associated iron protoheme IX groups per tetramer, but the ortholog from Synechococcus sp. is a homodimer with one protoheme. HPI is unrelated to HPII (hydroperoxidase II), a monofunctional catalase encoded by katE. TIGR00199.1 TIGR00199 PncC_domain 68.9 68.9 149 subfamily_domain Y Y N nicotinamide-nucleotide amidohydrolase family protein GO:0016810 21953451,24340054,24530526,28388636 131567 cellular organisms no rank 77263 JCVI amidohydrolase, PncC family nicotinamide-nucleotide amidohydrolase family protein The nicotinamide-nucleotide amidohydrolase domain family contains active enzymes and apparently inactive homologs as well. Member proteins in the family contain both extended forms with an additional fused ADP-ribose pyrophosphatase or a NUDIX hydrolase activity (MocF) domain. PMID:28388636 (2017) recommends using CinA for proteins consisting only of a functional nicotinamide-nucleotide amidohydrolase domain, and using PncC for the longer, fused forms. Note that E. coli encodes a paralog of the CinA/PncC enzyme, called YdeJ, that appears inactive and whose role and function are unknown. TIGR00203.1 TIGR00203 cydB 117.3 117.3 378 equivalog Y Y N cytochrome d ubiquinol oxidase subunit II cydB 7.1.1.- GO:0016682 131567 cellular organisms no rank 60786 JCVI cytochrome d ubiquinol oxidase, subunit II cytochrome d ubiquinol oxidase subunit II part of a two component cytochrome D terminal complex. Terminal reaction in the aerobic respiratory chain. TIGR00209.1 TIGR00209 galT_1 102.1 102.1 349 equivalog Y Y N galactose-1-phosphate uridylyltransferase galT 2.7.7.12 GO:0006012,GO:0008108,GO:0008270 131567 cellular organisms no rank 28528 JCVI galactose-1-phosphate uridylyltransferase galactose-1-phosphate uridylyltransferase This enzyme is involved in glucose and galactose interconversion. This model describes one of two extremely distantly related branches of the model PF01087 from PFAM. TIGR00210.1 TIGR00210 gltS 310.75 310.75 398 equivalog Y Y N sodium/glutamate symporter gltS GO:0015501,GO:0015813,GO:0016020 2017136 131567 cellular organisms no rank 16802 JCVI sodium/glutamate symporter sodium/glutamate symporter TIGR00211.2 TIGR00211 glyS 300 300 684 equivalog_domain Y Y N glycine--tRNA ligase subunit beta glyS 6.1.1.14 GO:0000166,GO:0004820,GO:0005524,GO:0005737,GO:0006426 9490048 131567 cellular organisms no rank 57524 JCVI glycine--tRNA ligase, beta subunit glycine--tRNA ligase subunit beta The glycyl-tRNA synthetases differ even among the eubacteria in oligomeric structure. In Escherichia coli and most others, it is a heterodimer of two alpha chains and two beta chains, encoded by tandem genes. The genes are similar, but fused, in Chlamydia trachomatis. By contrast, the glycyl-tRNA synthetases of Thermus thermophilus and of archaea and eukaryotes differ considerably; they are homodimeric, mutually similar, and not detected by this model. TIGR00212.1 TIGR00212 hemC 164 164 293 equivalog Y Y N hydroxymethylbilane synthase hemC 2.5.1.61 GO:0004418,GO:0033014 7665501,8436121,8727319 131567 cellular organisms no rank 69364 JCVI hydroxymethylbilane synthase hydroxymethylbilane synthase Catalyzes the transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis TIGR00214.1 TIGR00214 lipB 83.55 83.55 187 equivalog Y Y N lipoyl(octanoyl) transferase LipB lipB 2.3.1.181 GO:0009249,GO:0033819 12591875 131567 cellular organisms no rank 45298 JCVI lipoyl(octanoyl) transferase lipoyl(octanoyl) transferase LipB Catalyzes the transfer of the lipoyl/octanoyl moiety of lipoyl/octanoyl-ACP onto lipoate-dependent enzymes like pyruvate dehydrogenase and the glycine cleavage system H protein. TIGR00217.1 TIGR00217 malQ 205.65 205.65 587 equivalog Y Y N 4-alpha-glucanotransferase malQ 2.4.1.25 GO:0004134,GO:0005980 131567 cellular organisms no rank 54746 JCVI 4-alpha-glucanotransferase 4-alpha-glucanotransferase This enzyme is known as amylomaltase and disproportionating enzyme. TIGR00218.1 TIGR00218 manA 116.2 116.2 359 equivalog Y Y N mannose-6-phosphate isomerase, class I manA 5.3.1.8 GO:0004476,GO:0005975,GO:0008270 131567 cellular organisms no rank 41249 JCVI mannose-6-phosphate isomerase, class I mannose-6-phosphate isomerase, class I The names phosphomannose isomerase and mannose-6-phosphate isomerase are synonomous. This family contains two rather deeply branched groups. One group contains an experimentally determined phosphomannose isomerase of Streptococcus mutans as well as three uncharacterized paralogous proteins of Bacillus subtilis, all at more than 50 % identity to each other, plus a more distant homolog from Archaeoglobus fulgidus. The other group contains members from E. coli, budding yeast, Borrelia burgdorferi, etc. TIGR00220.1 TIGR00220 mscL 71 71 127 equivalog Y Y N large conductance mechanosensitive channel protein MscL mscL GO:0006810,GO:0008381,GO:0016020 8890153 131567 cellular organisms no rank 46200 JCVI large conductance mechanosensitive channel protein large conductance mechanosensitive channel protein MscL Protein encodes a channel which opens in response to a membrane stretch force. Probably serves as an osmotic gauge. Carboxy terminus tends to be more divergent across species with a high degree of sequence conservation found at the N-terminus. TIGR00221.1 TIGR00221 nagA 225.65 225.65 380 equivalog Y Y N N-acetylglucosamine-6-phosphate deacetylase nagA 3.5.1.25 GO:0006044,GO:0008448 17567047,17567048 131567 cellular organisms no rank 59190 JCVI N-acetylglucosamine-6-phosphate deacetylase N-acetylglucosamine-6-phosphate deacetylase TIGR00222.1 TIGR00222 panB 207.55 207.55 264 equivalog Y Y N 3-methyl-2-oxobutanoate hydroxymethyltransferase panB 2.1.2.11 GO:0003864,GO:0015940 8096212 131567 cellular organisms no rank 56468 JCVI 3-methyl-2-oxobutanoate hydroxymethyltransferase 3-methyl-2-oxobutanoate hydroxymethyltransferase Members of this family are 3-methyl-2-oxobutanoate hydroxymethyltransferase, the first enzyme of the pantothenate biosynthesis pathway. An alternate name is ketopantoate hydroxymethyltransferase. TIGR00223.1 TIGR00223 panD 106 106 126 equivalog Y Y N aspartate 1-decarboxylase panD 4.1.1.11 GO:0004068,GO:0006523 26038753,31953389 131567 cellular organisms no rank 29810 JCVI aspartate 1-decarboxylase aspartate 1-decarboxylase Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group. TIGR00224.1 TIGR00224 pckA 590.05 590.05 532 equivalog Y Y N phosphoenolpyruvate carboxykinase (ATP) pckA 4.1.1.49 GO:0004612,GO:0006094 131567 cellular organisms no rank 33535 JCVI phosphoenolpyruvate carboxykinase (ATP) phosphoenolpyruvate carboxykinase (ATP) Involved in the gluconeogenesis pathway. It converts oxaloacetic acid to phosphoenolpyruvate using ATP. Enzyme is a monomer. The reaction is also catalysed by phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32) using GTP instead of ATP, described in PROSITE:PDOC00421 TIGR00227.1 TIGR00227 ribD_Cterm 150.15 150.15 216 domain Y N N riboflavin-specific deaminase C-terminal domain GO:0008703,GO:0050661 131567 cellular organisms no rank 48341 JCVI riboflavin-specific deaminase C-terminal domain riboflavin-specific deaminase C-terminal domain Eubacterial riboflavin-specific deaminases have a zinc-binding domain recognized by the dCMP_cyt_deam HMM toward the N-terminus and this domain toward the C-terminus. Yeast HTP reductase, a riboflavin-biosynthetic enzyme, and several archaeal proteins believed related to riboflavin biosynthesis consist only of this domain and lack the dCMP_cyt_deam domain. TIGR00228.1 TIGR00228 ruvC 100.65 100.65 156 equivalog Y Y N crossover junction endodeoxyribonuclease RuvC ruvC 3.1.21.10 GO:0006310,GO:0008821 131567 cellular organisms no rank 42336 JCVI crossover junction endodeoxyribonuclease RuvC crossover junction endodeoxyribonuclease RuvC Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC. TIGR00229.1 TIGR00229 sensory_box 22.9 22.9 126 domain Y Y N PAS domain S-box protein 131567 cellular organisms no rank 1099831 JCVI PAS domain S-box protein PAS domain S-box protein The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. TIGR00230.1 TIGR00230 sfsA 126.45 126.45 234 equivalog Y Y N DNA/RNA nuclease SfsA sfsA GO:0003677 2013578 131567 cellular organisms no rank 22136 JCVI sugar fermentation stimulation protein DNA/RNA nuclease SfsA Members of this family are SfsA (sugar fermentation stimulation protein A), now recognized as a nuclease of the PD-(D/E)XK superfamily. TIGR00231.1 TIGR00231 small_GTP 42.5 42.5 164 domain Y Y N GTP-binding protein GO:0005525 131567 cellular organisms no rank 703242 JCVI small GTP-binding protein domain small GTP-binding protein domain Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once. This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. TIGR00233.1 TIGR00233 trpS 176.75 176.75 328 equivalog Y Y N tryptophan--tRNA ligase trpS 6.1.1.2 GO:0000166,GO:0004830,GO:0005524,GO:0006436 131567 cellular organisms no rank 85307 JCVI tryptophan--tRNA ligase tryptophan--tRNA ligase This HMM represents tryptophanyl-tRNA synthetase. Some members of the family have a PF00458 domain amino-terminal to the region described by this HMM. TIGR00234.1 TIGR00234 tyrS 113.8 113.8 406 equivalog Y Y N tyrosine--tRNA ligase tyrS 6.1.1.1 GO:0000166,GO:0004831,GO:0005524,GO:0006437 131567 cellular organisms no rank 80529 JCVI tyrosine--tRNA ligase tyrosine--tRNA ligase This HMM for tyrosine--tRNA ligase identifies proteins with a deep split between two groups. One group contains bacterial and organellar eukaryotic examples. The other contains archaeal and cytosolic eukaryotic examples. TIGR00235.1 TIGR00235 udk 220.3 220.3 207 equivalog Y Y N uridine kinase udk 2.7.1.48 GO:0004849,GO:0005737,GO:0046108 131567 cellular organisms no rank 13781 JCVI uridine kinase uridine kinase Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below TIGR00236.1 TIGR00236 wecB 210.15 210.15 366 equivalog Y Y N non-hydrolyzing UDP-N-acetylglucosamine 2-epimerase wecB 5.1.3.14 GO:0008761 131567 cellular organisms no rank 60044 JCVI UDP-N-acetylglucosamine 2-epimerase non-hydrolyzing UDP-N-acetylglucosamine 2-epimerase TIGR00237.1 TIGR00237 xseA 180 180 389 equivalog Y Y N exodeoxyribonuclease VII large subunit xseA 3.1.11.6 GO:0006308,GO:0008855,GO:0009318 22718974,6284744 131567 cellular organisms no rank 81937 JCVI exodeoxyribonuclease VII, large subunit exodeoxyribonuclease VII large subunit This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'->3' or 3'->5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits. TIGR00238.1 TIGR00238 TIGR00238 199.2 199.2 331 subfamily Y Y N KamA family radical SAM protein GO:0008152,GO:0016853,GO:0051539,GO:1904047 10839984 131567 cellular organisms no rank 25399 JCVI KamA family protein KamA family radical SAM protein This HMM represents essentially the whole of E. coli YjeK and of some of its apparent orthologs. YodO in Bacillus subtilis, a family member which is longer protein by an additional 100 residues, is characterized as a lysine 2,3-aminomutase with iron, sulphide and pyridoxal 5'-phosphate groups. The homolog MJ0634 from M. jannaschii is preceded by nearly 200 C-terminal residues. This family shows similarity to molybdenum cofactor biosynthesis protein MoaA and related proteins. Note that the E. coli homolog was expressed in E. coli and purified and found not to display display lysine 2,3-aminomutase activity. Active site residues are found in 100 residue extension in B. subtilis. Name changed to KamA family protein. TIGR00240.1 TIGR00240 ATCase_reg 148.55 148.55 150 equivalog Y Y N aspartate carbamoyltransferase regulatory subunit pyrI 2.1.3.2 GO:0006207,GO:0009347 131567 cellular organisms no rank 4541 JCVI aspartate carbamoyltransferase, regulatory subunit aspartate carbamoyltransferase regulatory subunit The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff. TIGR00241.1 TIGR00241 CoA_E_activ 125.4 125.4 248 domain Y Y N acyl-CoA dehydratase activase GO:0008047 11967068,22827463,7607244 131567 cellular organisms no rank 20791 JCVI putative CoA-substrate-specific enzyme activase acyl-CoA dehydratase activase domain This domain is found in a set of closely related [4Fe-4S]-containing ATPases, including activators of (R)-2-hydroxyglutaryl-CoA dehydratase, (R)-phenyllactate dehydratase, lactoyl-CoA dehydratase, and benzoyl-CoA reductase, as well as the uncharacterized protein YjiL of E. coli. Characterized members of this family provide a key reactive electron that their cognate enzyme requires for activity, and can use for multiple reaction cycles until the electron is lost and needs to be replaced. TIGR00244.1 TIGR00244 TIGR00244 124.65 124.65 147 equivalog Y Y N transcriptional regulator NrdR nrdR GO:0006355,GO:0008270,GO:0140110 15522084,15949864,16950922 131567 cellular organisms no rank 32119 JCVI transcriptional regulator NrdR transcriptional regulator NrdR Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes. TIGR00246.1 TIGR00246 tRNA_RlmH_YbeA 149.7 149.7 155 equivalog Y Y N 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH rlmH 2.1.1.177 GO:0005737,GO:0070037,GO:0070475 18755835 131567 cellular organisms no rank 18372 JCVI rRNA large subunit m3Psi methyltransferase RlmH 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH This protein, in the SPOUT methyltransferase family, previously designated YbeA in E. coli, was shown to be responsible for a further modification, a methylation, to a pseudouridine base in ribosomal large subunit RNA. TIGR00247.1 TIGR00247 TIGR00247 103.4 103.4 347 hypoth_equivalog Y Y N endolytic transglycosylase MltG mltG GO:0008932,GO:0009252,GO:0071555 26507882 131567 cellular organisms no rank 80625 JCVI conserved hypothetical protein, YceG family endolytic transglycosylase MltG This uncharacterized protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in E. coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC. TIGR00249.1 TIGR00249 sixA 74.5 74.5 154 equivalog Y Y N phosphohistidine phosphatase SixA sixA GO:0005737,GO:0036211,GO:0101006 10734219,17628145 131567 cellular organisms no rank 11018 JCVI phosphohistidine phosphatase SixA phosphohistidine phosphatase SixA TIGR00251.3 TIGR00251 TIGR00251 35 35 71 subfamily Y Y N DUF167 family protein 12975589 131567 cellular organisms no rank 17017 JCVI TIGR00251 family protein DUF167 family protein This family is conserved from E. coli K-12 (where the member is named YggU) to the archaea. The function of this small protein is unknown. This model has been revised to better agree with PF02594, which defines the DUF167 family. See HMM PRK05090.1 for YggU proteins within the DUF167 family. TIGR00253.1 TIGR00253 RNA_bind_YhbY 78.5 78.5 96 equivalog Y Y N ribosome assembly RNA-binding protein YhbY yhbY GO:0003723 12429100,27732863 131567 cellular organisms no rank 11959 JCVI putative RNA-binding protein, YhbY family ribosome assembly RNA-binding protein YhbY A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins. TIGR00256.1 TIGR00256 TIGR00256 101.5 101.5 146 equivalog Y Y N D-aminoacyl-tRNA deacylase dtd 3.1.1.96 GO:0004045,GO:0008152 11568181,27200345 131567 cellular organisms no rank 47384 JCVI D-tyrosyl-tRNA(Tyr) deacylase D-aminoacyl-tRNA deacylase This homodimeric enzyme, D-aminoacyl-tRNA deacylase, appears able to cleave any D-amino acid (and glycine, which does not have distinct D/L forms) from mis-charged tRNA molecules. The old name D-tyrosyl-tRNA(Tyr) deacylase reflects characterization with respect to D-Tyr on tRNA(Tyr) as established in the literature, but substrate specificity seems much broader. TIGR00257.1 TIGR00257 IMPACT_YIGZ 167.95 167.95 205 hypoth_equivalog Y Y N YigZ family protein 15103642 131567 cellular organisms no rank 29994 JCVI uncharacterized protein, YigZ family YigZ family protein This uncharacterized protein family includes YigZ, which has been crystallized, from E. coli. YigZ is homologous to the protein product of the mouse IMPACT gene. Crystallography shows a two-domain stucture, and the C-terminal domain is suggested to bind nucleic acids. The function is unknown. Note that the ortholog from E. coli was shown fused to the pepQ gene in GenBank entry X54687. This caused occasional misidentification of this protein as pepQ; this family is found in a number of species that lack pepQ. TIGR00258.1 TIGR00258 TIGR00258 117.1 117.1 168 equivalog Y Y N inosine/xanthosine triphosphatase yjjX 3.6.1.- GO:0005737,GO:0016462,GO:0046128 16216582 131567 cellular organisms no rank 5700 JCVI inosine/xanthosine triphosphatase inosine/xanthosine triphosphatase TIGR00259.1 TIGR00259 thylakoid_BtpA 153.4 153.4 257 subfamily Y Y N BtpA/SgcQ family protein 10806238,12651001,9045660 131567 cellular organisms no rank 5929 JCVI membrane complex biogenesis protein, BtpA family BtpA/SgcQ family protein Members of this family are found broadly, incuding Synechocystis sp. (BtpA), E. coli (SgcQ/YjhM), several of the Archaea, and the model round worm, C. elegans. Members in Cyanobacteria have been shown to play a role in protein complex biogenesis, and designated BtpA (biogenesis of thylakoid proteins A). Functions in non-photosynthetic species, where thylakoid intracytoplasmic membranes are lacking, are unknown, but a role in biogenesis of membrane protein complexes is possible. TIGR00260.1 TIGR00260 thrC 167.1 167.1 340 equivalog Y Y N threonine synthase thrC 4.2.3.1 GO:0004795,GO:0009088 3098560 131567 cellular organisms no rank 85246 JCVI threonine synthase threonine synthase Involved in threonine biosynthesis it catalyses the reaction O-PHOSPHO-L-HOMOSERINE + H(2)O = L-THREONINE + ORTHOPHOSPHATE using pyridoxal phosphate as a cofactor. the enzyme is distantly related to the serine/threonine dehydratases which are also pyridoxal-phosphate dependent enzymes. the pyridoxal-phosphate binding site is a Lys (K) residues present at residue 70 of the model. TIGR00261.1 TIGR00261 traB 178.35 178.35 380 subfamily Y Y N TraB family protein 131567 cellular organisms no rank 4609 JCVI TraB family protein TraB family protein traB is a plasmid encoded gene that functions in the shutdown of the peptide sex pheromone cPD1 which is produced by the plasmid free recipient cell prior to conjugative transfer in Enterococcus faecalis. Once the recipient acquires the plasmid, production of cPD1 is shut down. The gene product may play another role in the other species in the family. TIGR00262.1 TIGR00262 trpA 102.35 102.35 256 equivalog Y Y N tryptophan synthase subunit alpha trpA 4.2.1.20 GO:0000162,GO:0004834 22310642,3053720 131567 cellular organisms no rank 71575 JCVI tryptophan synthase, alpha subunit tryptophan synthase subunit alpha Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan. The alpha subunit performs the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. The beta subunit then combines the indole with L-serine to complete the biosynthesis. TIGR00263.1 TIGR00263 trpB 392.45 392.45 385 equivalog Y Y N tryptophan synthase subunit beta trpB 4.2.1.20 GO:0000162,GO:0004834 131567 cellular organisms no rank 72719 JCVI tryptophan synthase, beta subunit tryptophan synthase subunit beta Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan. the beta chain contains the functional domain for or the synthesis of tryptophan from indole and serine. The enzyme requires pyridoxal-phosphate as a cofactor. The pyridoxal-P attachment site is contained within the conserved region [LIVM]-x-H-x-G-[STA]-H-K-x-N] [K is the pyridoxal-P attachment site] which is present between residues 90-100 of the model. TIGR00266.1 TIGR00266 TIGR00266 96.6 96.6 222 hypoth_equivalog Y Y N TIGR00266 family protein 131567 cellular organisms no rank 14829 JCVI TIGR00266 family protein TIGR00266 family protein TIGR00268.1 TIGR00268 TIGR00268 166.5 166.5 253 equivalog Y Y N ATP-dependent sacrificial sulfur transferase LarE larE GO:0016783 16166538,27114550,28830089 131567 cellular organisms no rank 10455 JCVI TIGR00268 family protein ATP-dependent sacrificial sulfur transferase LarE LarE, a PP-loop ATPase, works with LarB and LarC to produce the pyridinium-3-thioamide-5-thiocarboxylic acid mononucleotide nickel cofactor required by the lactate racemase LarA in lactic acid bacteria such as Lactobacillus plantarum. TIGR00269.1 TIGR00269 TIGR00269 62.75 62.75 104 hypoth_equivalog Y Y N TIGR00269 family protein GO:0000049,GO:0002098,GO:0034227 131567 cellular organisms no rank 1956 JCVI TIGR00269 family protein TIGR00269 family protein TIGR00271.1 TIGR00271 TIGR00271 146.5 146.5 175 domain Y N N uncharacterized hydrophobic domain 131567 cellular organisms no rank 5135 JCVI uncharacterized hydrophobic domain uncharacterized hydrophobic domain This domain is in a family of archaeal proteins that includes AF0785 of Archaeoglobus fulgidus and in several eubacterial proteins, including the much longer protein sll1151 from Synechocystis PCC6803. TIGR00273.1 TIGR00273 TIGR00273 444.8 444.8 432 equivalog Y Y N LutB/LldF family L-lactate oxidation iron-sulfur protein GO:0006089,GO:0051536 19196979,19201793 131567 cellular organisms no rank 24441 JCVI iron-sulfur cluster-binding protein LutB/LldF family L-lactate oxidation iron-sulfur protein Members of this family, including LutB from Bacillus subtilis and LldF from Shewanella oneidensis, have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4fe-4S iron-sulfur clusters, and are involved in lactate utilization. TIGR00275.1 TIGR00275 TIGR00275 183.8 183.8 401 subfamily Y Y N aminoacetone oxidase family FAD-binding enzyme 25269103 131567 cellular organisms no rank 77878 JCVI flavoprotein, HI0933 family aminoacetone oxidase family FAD-binding enzyme The model when searched with a partial length search brings in proteins with a dinucleotide-binding motif (Rossman fold) over the initial 40 residues of the model, including oxidoreductases and dehydrogenases. Partially characterized members include an FAD-binding protein from Bacillus cereus and flavoprotein HI0933 from Haemophilus influenzae. TIGR00277.1 TIGR00277 HDIG 27.6 27.6 84 domain Y Y N HDIG domain-containing metalloprotein 34094591 131567 cellular organisms no rank 139003 JCVI HDIG domain HDIG domain This domain is found in a few known nucleotidyltransferes and in a large number of uncharacterized proteins. It contains four widely separated His residues, the second of which is part of an invariant dipeptide His-Asp in a region matched approximately by the motif HDIG. For proteins scoring above the trusted cutoff, confidence is high both that the domain is present and that the HMM produces an essentially correct alignment. Protein regions scoring between the trusted and noise cutoffs include correctly aligned domains, homologous domains in which one or more of the His residues is conserved but misaligned, and some probable false-positive hits indications of homology. TIGR00278.2 TIGR00278 TIGR00278 40 40 64 equivalog Y Y N membrane protein insertion efficiency factor YidD yidD 21803992 131567 cellular organisms no rank 49369 JCVI putative membrane protein insertion efficiency factor membrane protein insertion efficiency factor YidD This HMM describes a family, YidD, of usually small, non-essential proteins now suggested to improve YidC-dependent inner membrane protein insertion. A related protein is found in the temperature phage HP1 of Haemophilus influenzae. TIGR00279.1 TIGR00279 uL16_euk_arch 223.55 223.55 172 equivalog Y Y N 50S ribosomal protein L16 rplJ GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 330 JCVI ribosomal protein uL16 50S ribosomal protein L16 This model finds the archaeal and eukaryotic forms of ribosomal protein uL16, previously L10.e. The protein is encoded by multiple loci in some eukaryotes and has been assigned a number of extra-ribosomal functions, some of which will require re-evaluation in the context of identification as a ribosomal protein. L10.e is distantly related to eubacterial ribosomal protein L16. TIGR00280.1 TIGR00280 eL43_euk_arch 95.8 95.8 92 equivalog Y Y N 50S ribosomal protein L37Ae rpl37A GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 556 JCVI ribosomal protein eL43 ribosomal protein eL43 This HMM finds eukaryotic ribosomal protein eL43 (previously L37a) and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a. TIGR00281.1 TIGR00281 TIGR00281 89.2 89.2 186 equivalog Y Y N SMC-Scp complex subunit ScpB scpB GO:0005515,GO:0007059 12100548,12897137 131567 cellular organisms no rank 49176 JCVI segregation and condensation protein B SMC-Scp complex subunit ScpB Shown to be required for chromosome segregation and condensation in B. subtilis. [1] TIGR00283.1 TIGR00283 arch_pth2 82 82 115 equivalog Y Y N aminoacyl-tRNA hydrolase pth2 3.1.1.29 GO:0004045,GO:0006412 16251366 131567 cellular organisms no rank 1584 JCVI peptidyl-tRNA hydrolase aminoacyl-tRNA hydrolase This model describes an archaeal/eukaryotic form of peptidyl-tRNA hydrolase. Most bacterial forms are described by TIGR00447. TIGR00286.1 TIGR00286 TIGR00286 106.95 106.95 152 equivalog Y Y N pyruvoyl-dependent arginine decarboxylase 4.1.1.19 GO:0006527,GO:0008792 11980912 131567 cellular organisms no rank 993 JCVI arginine decarboxylase, pyruvoyl-dependent pyruvoyl-dependent arginine decarboxylase The three copies present in Archeoglobus fulgidus, one of which is only half-length and excluded from the seed alignment, are very closely related and clearly arose by duplication after the separation from well-studied species. The other completed archaeal genomes each contain a single copy. The lone, weak (below trusted cutoff) hit to a non-archaeal sequence is to an uncharacterized protein of Chlamydia, with the greatest similarity in the amino-terminal half of the model. TIGR00287.1 TIGR00287 cas1 71.7 71.7 327 equivalog Y Y N CRISPR-associated endonuclease Cas1 cas1 GO:0004520,GO:0043571,GO:0046872 11952905,19523907 131567 cellular organisms no rank 34927 JCVI CRISPR-associated endonuclease Cas1 CRISPR-associated endonuclease Cas1 This model identifies CRISPR-associated protein Cas1, the most universal CRISPR system protein. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, a system for heritable host defense by prokaryotic cells against phage and other foreign DNA. Cas1 is a metal-dependent DNA-specific endonuclease. TIGR00290.1 TIGR00290 MJ0570_dom 114.6 114.6 223 equivalog Y Y N diphthine--ammonia ligase 6.3.1.14 131567 cellular organisms no rank 7570 JCVI MJ0570-related uncharacterized domain diphthine--ammonia ligase Diphthine--ammonia ligase belongs to the adenine nucleotide alpha hydrolase family. In the course of amidating dipthine to complete the diphthamide post-translational modification of a translational elongation factor, it cleaves ATP to AMP and pyrophosphate. TIGR00292.1 TIGR00292 TIGR00292 148.3 148.3 254 equivalog Y Y N sulfide-dependent adenosine diphosphate thiazole synthase 2.4.2.59 GO:0003824,GO:0009228 26919468,26928142 131567 cellular organisms no rank 1547 JCVI thiazole biosynthesis enzyme sulfide-dependent adenosine diphosphate thiazole synthase Members of this family are archaeal homologs of eukaryotic THI4. They use sulfide (EC 2.4.2.59), rather than sulfur from cysteine from the enzyme itself such that the enzyme can act only once (EC 2.4.2.60). TIGR00293.1 TIGR00293 TIGR00293 53.9 53.9 129 equivalog Y Y N prefoldin subunit alpha pfdA GO:0005515,GO:0006457 131567 cellular organisms no rank 1318 JCVI prefoldin, alpha subunit prefoldin subunit alpha Members of this protein family, rich in coiled coil regions, are molecular chaperones in the class of the prefoldin (GimC) alpha subunit. Prefoldin is a hexamer of two alpha and four beta subunits. This protein appears universal in the archaea but is restricted to Aquifex aeolicus among bacteria so far. Eukaryotes have several related proteins; only prefoldin subunit 5, which appeared the most similar to archaeal prefoldin alpha, is included in this model. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and builds of HMMs for the seed alignment with less selective parameters lead to significant hits to large numbers of proteins that contain coiled coil regions. This model is built with a more selective usage of Dirichlet priors. TIGR00294.2 TIGR00294 TIGR00294 220 220 302 equivalog Y Y N GTP cyclohydrolase MptA mptA 3.5.4.39 GO:0003933 17032654,17497938 131567 cellular organisms no rank 1125 JCVI GTP cyclohydrolase GTP cyclohydrolase MptA This HMM has been narrowed in scope, to include the GTP cyclohydrolase MptA involved in methanopterin biosynthesis in archaea (EC 3.5.4.39), but to no longer include FolE2, involved in de novo tetrahydrofolate biosynthesis in some bacteria. TIGR00295.1 TIGR00295 TIGR00295 172.35 172.35 164 hypoth_equivalog Y Y N TIGR00295 family protein 131567 cellular organisms no rank 281 JCVI TIGR00295 family protein TIGR00295 family protein This set of orthologs is narrowly defined, comprising proteins found in three Archaea but not in Pyrococcus horikoshii. The closest homologs are other archaeal proteins that appear to be represent distinct orthologous clusters. TIGR00296.1 TIGR00296 TIGR00296 91.05 91.05 200 hypoth_equivalog Y Y N TIGR00296 family protein 15558565 131567 cellular organisms no rank 4696 JCVI uncharacterized protein, PH0010 family TIGR00296 family protein Members of this functionally uncharacterized protein family have been crystallized from Pyrococcus Horikoshii, Methanosarcina Mazei, and Sulfolobus Tokodaii. TIGR00297.1 TIGR00297 TIGR00297 205.85 205.85 237 hypoth_equivalog Y Y N TIGR00297 family protein GO:0016020 131567 cellular organisms no rank 1233 JCVI TIGR00297 family protein TIGR00297 family protein TIGR00298.1 TIGR00298 TIGR00298 175.05 175.05 216 equivalog Y Y N 2-phosphosulfolactate phosphatase comB 3.1.3.71 GO:0050532 11589710 131567 cellular organisms no rank 282 JCVI 2-phosphosulfolactate phosphatase 2-phosphosulfolactate phosphatase 2-phosphosulfolactate phosphatase catalyzes the sulfonation of phosphoenolpyruvate to form 2-phospho-3-sulfolactate, the second step in coenzyme M biosynthesis. Coenzyme M is the terminal methyl carrier in methanogenesis. TIGR00299.1 TIGR00299 TIGR00299 242.7 242.7 382 equivalog Y Y N nickel pincer cofactor biosynthesis protein LarC larC 4.99.1.12 16166538,24710389,28830089 131567 cellular organisms no rank 9576 JCVI TIGR00299 family protein nickel pincer cofactor biosynthesis protein LarC Members of this family are found in the Archaea and in several different bacteria lineages. The function in unknown and the genomic context is not well conserved. TIGR00300.1 TIGR00300 TIGR00300 410.8 410.8 407 hypoth_equivalog Y Y N TIGR00300 family protein 131567 cellular organisms no rank 2216 JCVI TIGR00300 family protein TIGR00300 family protein All members of the family come from genome projects. A partial length search brings in two plant lysine-ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzymes hitting the N-terminal region of the family. TIGR00302.1 TIGR00302 TIGR00302 39 39 80 equivalog Y Y N phosphoribosylformylglycinamidine synthase subunit PurS purS GO:0004642,GO:0009152 10784038 131567 cellular organisms no rank 19567 JCVI phosphoribosylformylglycinamidine synthase, purS protein phosphoribosylformylglycinamidine synthase subunit PurS In species such as Bacillus subtilis in which FGAM synthetase is split into two ORFs purL and purQ, this small protein, previously called yexA, is required for FGAM synthetase activity. Although the article does not make it clear whether this is a subunit or an accessory protein, it is encoded as part of the operon, which suggests stochiometric amounts, = subunit. TIGR00303.2 TIGR00303 TIGR00303 240 240 334 equivalog Y Y N nicotinate mononucleotide-dependent phosphoribosyltransferase CobT cobT 30640434 131567 cellular organisms no rank 2008 JCVI TIGR00303 family protein nicotinate mononucleotide-dependent phosphoribosyltransferase CobT Members of this family, archaeal and cyanobacterial counterparts to the distantly related CobT of most bacteria (nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase, EC 2.4.2.21), play a similar role if now identical role in cobamide biosynthesis and are likewise designated CobT. TIGR00305.1 TIGR00305 TIGR00305 29.15 29.15 115 equivalog Y Y N putative toxin-antitoxin system toxin component, PIN family GO:0004521,GO:0005515 19493340 131567 cellular organisms no rank 11095 JCVI putative toxin-antitoxin system toxin component, PIN family putative toxin-antitoxin system toxin component, PIN family This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems. TIGR00306.2 TIGR00306 apgM 320 320 403 subfamily Y Y N 2,3-bisphosphoglycerate-independent phosphoglycerate mutase apgM 5.4.2.12 GO:0006094,GO:0006096,GO:0046537 12062435,12076796,9127192 131567 cellular organisms no rank 5191 JCVI phosphoglycerate mutase (2,3-diphosphoglycerate-independent), archaeal form 2,3-bisphosphoglycerate-independent phosphoglycerate mutase This protein family includes two archaeal subfamilies of 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. TIGR00307.1 TIGR00307 eS8 78.25 78.25 127 equivalog Y Y N 30S ribosomal protein S8e GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 1178 JCVI ribosomal protein eS8 ribosomal protein eS8 Archaeal and eukaryotic ribosomal protein S8. This model could easily have been split into two models, one for eukaryotic S8 and one for archaeal S8; eukaryotic forms invariably have in insert of about 80 residues that archaeal forms of S8 do not. TIGR00308.1 TIGR00308 TRM1 280.65 280.65 375 equivalog Y Y N tRNA (guanine(10)-N(2))-dimethyltransferase 2.1.1.213 GO:0003723,GO:0008033,GO:0160102 131567 cellular organisms no rank 1210 JCVI N2,N2-dimethylguanosine tRNA methyltransferase tRNA (guanine(10)-N(2))-dimethyltransferase This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes. TIGR00309.1 TIGR00309 V_ATPase_subD 72.25 72.25 209 subfamily Y Y N V-type ATP synthase subunit D 7.1.2.2 GO:0008553,GO:1902600 131567 cellular organisms no rank 6439 JCVI V-type ATPase, D subunit V-type ATP synthase subunit D Although this ATPase can run backwards, using a proton gradient to synthesize ATP, the primary biological role is to acidify some compartment, such as yeast vacuole (a lysosomal homolog) or the interior of a prokaryote. TIGR00312.2 TIGR00312 cbiD 200 200 346 equivalog Y Y N cobalt-precorrin-5B (C(1))-methyltransferase CbiD cbiD 2.1.1.195 GO:0005737,GO:0009236 15741157,8550510,9742225 131567 cellular organisms no rank 23290 JCVI cobalamin biosynthesis protein CbiD cobalt-precorrin-5B (C(1))-methyltransferase CbiD The methyltransferase CbiD belongs to an anaerobic pathway for cobalamin biosynthesis, one in which cobalt is added early. TIGR00313.1 TIGR00313 cobQ 309.9 309.9 477 equivalog Y Y N cobyric acid synthase CobQ cobQ GO:0005737,GO:0009236,GO:0051921 8501034 131567 cellular organisms no rank 50018 JCVI cobyric acid synthase CobQ cobyric acid synthase CobQ TIGR00314.1 TIGR00314 cdhA 781.3 781.3 784 equivalog Y Y N CO dehydrogenase/acetyl-CoA synthase complex subunit alpha cdhA 1.2.7.4 GO:0006084,GO:0043885 20202935,8662887 131567 cellular organisms no rank 329 JCVI CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit CO dehydrogenase/acetyl-CoA synthase complex subunit alpha Anaerobic carbon-monoxide dehydrogenase (EC 1.2.7.4) is a nickel cofactor-containing enzyme that catalyzes the reversible reduction of CO(2) to CO (carbon monoxide). It typically occurs as part of a multienzyme complex with efficient transfer of CO. In methanogenic archaea, this subunit of EC 1.2.7.4, CdhA, is known as the alpha subunit of the CO dehydrogenase/acetyl-CoA synthase complex. TIGR00315.1 TIGR00315 cdhB 101.2 101.2 162 equivalog Y Y N CO dehydrogenase/acetyl-CoA synthase complex subunit epsilon cdhB GO:0006085,GO:0043885 20202935,8955306 131567 cellular organisms no rank 272 JCVI CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit CO dehydrogenase/acetyl-CoA synthase complex subunit epsilon Anaerobic carbon-monoxide dehydrogenase (EC 1.2.7.4) is a nickel cofactor-containing enzyme that catalyzes the reversible reduction of CO(2) to CO (carbon monoxide). It typically occurs as part of a multienzyme complex with efficient transfer of CO. In methanogenic archaea, this subunit of EC 1.2.7.4, CdhB, is known as the epsilon subunit of the CO dehydrogenase/acetyl-CoA synthase complex. TIGR00316.1 TIGR00316 cdhC 355.95 355.95 460 equivalog Y Y N CO dehydrogenase/CO-methylating acetyl-CoA synthase complex subunit beta cdhC 2.3.1.169 GO:0006084,GO:0043884,GO:0043885 8955306 131567 cellular organisms no rank 1257 JCVI CO dehydrogenase/CO-methylating acetyl-CoA synthase complex, beta subunit CO dehydrogenase/CO-methylating acetyl-CoA synthase complex subunit beta Nomenclature follows the description for Methanosarcina thermophila. The CO-methylating acetyl-CoA synthase is considered the defining enzyme of the Wood-Ljungdahl pathway, used for acetate catabolism by sulfate reducing bacteria but for acetate biosynthesis by acetogenic bacteria such as Moorella thermoacetica (f. Clostridium thermoaceticum). TIGR00317.1 TIGR00317 cobS 110 110 241 equivalog Y Y N adenosylcobinamide-GDP ribazoletransferase cobS 2.7.8.26 GO:0008818,GO:0009236,GO:0051073 8501034 131567 cellular organisms no rank 27655 JCVI cobalamin 5'-phosphate synthase adenosylcobinamide-GDP ribazoletransferase cobS is involved with cobalamin biosynthesis in part III of colbalmin biosynthesis. The enzyme catyalzes the reactions adenosylcobinamide-GDP + alpha-ribazole-5'-P = adenosylcobalamin-5'-phosphate + GMP and adenosylcobinamide-GDP + alpha-ribazole = adenosylcobalamin + GMP. The protein product is associated with a large complex of proteins and is induced by cobinamide. TIGR00318.1 TIGR00318 cyaB 57.95 57.95 174 equivalog Y Y N class IV adenylate cyclase cyaB 16905149,19568747 131567 cellular organisms no rank 4706 JCVI putative adenylyl cyclase CyaB class IV adenylate cyclase The protein CyaB from Aeromonas hydrophila is a second adenylyl cyclase from that species, as demonstrated by complementation in E. coli and by assay of the enzymatic properties of purified recombinant protein. It has no detectable homology to any other protein of known function, and has several unusual properties, including an optimal temperature of 65 degrees and an optimal pH of 9.5. A cluster of uncharaterized archaeal homologs may be orthologous and serve (under certain circumstances) to produce the regulatory metabolite cyclic AMP (cAMP). TIGR00319.1 TIGR00319 desulf_FeS4 36.05 36.05 34 domain Y Y N desulfoferrodoxin FeS4 iron-binding domain-containing protein 131567 cellular organisms no rank 2119 JCVI desulfoferrodoxin FeS4 iron-binding domain desulfoferrodoxin FeS4 iron-binding domain This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-heme iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-heme iron protein with 2 Fe atoms per monomer in different oxidation states.This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain. TIGR00320.1 TIGR00320 dfx_rbo 146.9 146.9 125 equivalog Y Y N desulfoferrodoxin GO:0004784,GO:0005506,GO:0019430 131567 cellular organisms no rank 1360 JCVI desulfoferrodoxin desulfoferrodoxin The short N-terminal domain contains four conserved Cys for binding of a ferric iron atom, and is homologous to the small protein desulforedoxin; this domain may also be responsible for dimerization. The remainder of the molecule binds a ferrous iron atom and is similar to neelaredoxin, a monomeric blue non-heme iron protein. The homolog from Treponema pallidum scores between the trusted cutoff for orthology and the noise cutoff. Although essentially a full length homolog, it lacks three of the four Cys residues in the N-terminal domain; the domain may have lost ferric binding ability but may have some conserved structural role such as dimerization, or some new function. This protein is described in some articles as rubredoxin oxidoreductase (rbo), and its gene shares an operon with the rubredoxin gene in Desulfovibrio vulgaris Hildenborough. TIGR00322.1 TIGR00322 diphth2_R 35 35 320 domain Y N N diphthamide biosynthesis enzyme Dph1/Dph2 domain GO:0017183,GO:0090560 20559380 131567 cellular organisms no rank 1440 JCVI diphthamide biosynthesis enzyme Dph1/Dph2 domain diphthamide biosynthesis enzyme Dph1/Dph2 domain Archaea and Eukaryotes, but not Eubacteria, share the property of having a covalently modified residue, 2'-[3-carboxamido-3-(trimethylammonio)propyl]histidine, as a part of a cytosolic protein. The modified His, termed diphthamide, is part of translation elongation factor EF-2 and is the site for ADP-ribosylation by diphtheria toxin. This model includes both Dph1 and Dph2 from Saccharomyces cerevisiae, although only Dph2 is found in the Archaea (see TIGR03682). Dph2 has been shown to act analogously to the radical SAM (rSAM) family (PF04055), with 4Fe-4S-assisted cleavage of S-adenosylmethionine to create a free radical, but a different organic radical than in rSAM. TIGR00326.1 TIGR00326 eubact_ribD 156.35 156.35 343 equivalog Y Y N bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD ribD 1.1.1.193,3.5.4.26 GO:0008703,GO:0008835 131567 cellular organisms no rank 74422 JCVI riboflavin biosynthesis protein RibD bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD This HMM describes the ribD protein as found in Escherichia coli. The N-terminal domain includes the conserved zinc-binding site region captured in the HMM dCMP_cyt_deam and shared by proteins such as cytosine deaminase, mammalian apolipoprotein B mRNA editing protein, blasticidin-S deaminase, and Bacillus subtilis competence protein comEB. The C-terminal domain is homologous to the full length of yeast HTP reductase, a protein required for riboflavin biosynthesis. A number of archaeal proteins believed related to riboflavin biosynthesis contain only this C-terminal domain and are not found as full-length matches to this model. TIGR00327.1 TIGR00327 secE_euk_arch 36.2 36.2 61 equivalog Y Y N protein translocase SEC61 complex subunit gamma GO:0006886,GO:0008320,GO:0016020 131567 cellular organisms no rank 960 JCVI protein translocase SEC61 complex gamma subunit, archaeal and eukaryotic protein translocase SEC61 complex subunit gamma This model describes archaeal SEC61-like and eukaryotic SEC61 but not bacterial secE proteins, for which a Pfam PF00584 (SecE) has been created. TIGR00329.1 TIGR00329 gcp_kae1 207.8 207.8 305 subfamily Y Y N tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex transferase subunit TsaD tsaD 11889100,17766251,1885539 131567 cellular organisms no rank 76024 JCVI metallohydrolase, glycoprotease/Kae1 family tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex transferase subunit TsaD This subfamily includes the well-studied secreted O-sialoglycoprotein endopeptidase (glycoprotease, EC 3.4.24.57) of Pasteurella haemolytica, a pathogen. A member from Riemerella anatipestifer, associated with cohemolysin activity, likewise is exported without benefit of a classical signal peptide and shows glycoprotease activity on the test substrate glycophorin. However, archaeal members of this subfamily show unrelated activities as demonstrated in Pyrococcus abyssi: DNA binding, iron binding, apurinic endonuclease activity, genomic association with a kinase domain, and no glycoprotease activity. This family thus pulls together a set of proteins as a homology group that appears to be near-universal in life, yet heterogeneous in assayed function between bacteria and archaea. TIGR00330.1 TIGR00330 glpX 259.3 259.3 334 equivalog Y Y N class II fructose-bisphosphatase glpX 3.1.3.11 GO:0006071,GO:0006094,GO:0042132 10986273,15470127 131567 cellular organisms no rank 29509 JCVI fructose-1,6-bisphosphatase, class II class II fructose-bisphosphatase This model represents GlpX, one of three classes of bacterial fructose-1,6-bisphosphatases. This form is homodimeric and Mn2+-dependent, and only very distantly related to the class I fructose-1,6-bisphosphatase, the product of the fbp gene, which is homotetrameric and Mg2+-dependent. A third class is found as one of two types in Bacillus subtilis. In E. coli, GlpX is found in the glpFKX operon together with a glycerol update protein and glycerol kinase. TIGR00332.1 TIGR00332 neela_ferrous 61.9 61.9 107 domain Y N N desulfoferrodoxin ferrous iron-binding domain 8001576,9914498 131567 cellular organisms no rank 3705 JCVI desulfoferrodoxin ferrous iron-binding domain desulfoferrodoxin ferrous iron-binding domain This domain comprises essentially the full length of neelaredoxin, a monomeric, blue, non-heme iron protein of Desulfovibrio gigas said to bind two iron atoms per monomer with identical spectral properties. Neelaredoxin was shown recently to have significant superoxide dismutase activity. This domain is also found (in a form in which the distance between the motifs H[HWYF]IXW and CN[IL]HGXW is somewhat shorter) as the C-terminal domain of desulfoferrodoxin, which is said to bind a single ferrous iron atom. The N-terminal domain of desulfoferrodoxin is described in a separate HMM, dfx_rbo (TIGR00320). TIGR00336.1 TIGR00336 pyrE 106.8 106.8 173 equivalog_domain Y Y N orotate phosphoribosyltransferase pyrE 2.4.2.10 GO:0004588,GO:0009220 131567 cellular organisms no rank 48690 JCVI orotate phosphoribosyltransferase orotate phosphoribosyltransferase Orotate phosphoribosyltransferase (OPRTase) is involved in the biosynthesis of pyrimidine nucleotides. Alpha-D-ribosyldiphosphate 5-phosphate (PRPP) and orotate are utilized to form pyrophosphate and orotidine 5'-monophosphate (OMP) in the presence of divalent cations, preferably Mg2+. In a number of eukaryotes, this protein is fused to a domain that catalyses the reaction (EC 4.1.1.23). The combined activity of EC 2.4.2.10 and EC 4.1.1.23 is termed uridine 5'-monophosphate synthase. The conserved Lys (K) residue at position 101 of the seed alignment has been proposed as the active site for the enzyme. TIGR00337.1 TIGR00337 PyrG 462.75 462.75 526 equivalog Y Y N glutamine hydrolyzing CTP synthase pyrG 6.3.4.2 GO:0003883,GO:0006221 131567 cellular organisms no rank 59678 JCVI CTP synthase glutamine hydrolyzing CTP synthase CTP synthase is involved in pyrimidine ribonucleotide/ribonucleoside metabolism. The enzyme catalyzes the reaction L-glutamine + H2O + UTP + ATP = CTP + phosphate + ADP + L-glutamate. The enzyme exists as a dimer of identical chains that aggregates as a tetramer. This gene has been found circa 500 bp 5' upstream of enolase in both beta (Nitrosomonas europaea) and gamma (E.coli) subdivisions of proteobacterium (FEMS Microbiol Lett 1998 Aug 1;165(1):153-7). TIGR00338.1 TIGR00338 serB 144.15 144.15 219 equivalog Y Y N phosphoserine phosphatase SerB serB 3.1.3.3 GO:0006564,GO:0036424 131567 cellular organisms no rank 46510 JCVI phosphoserine phosphatase SerB phosphoserine phosphatase SerB Phosphoserine phosphatase catalyzes the reaction 3-phospho-serine + H2O = L-serine + phosphate. It catalyzes the last of three steps in the biosynthesis of serine from D-3-phosphoglycerate. Note that this enzyme acts on free phosphoserine, not on phosphoserine residues of phosphoproteins. TIGR00339.1 TIGR00339 sopT 322.95 322.95 383 equivalog_domain Y Y N sulfate adenylyltransferase sat 2.7.7.4 GO:0000103,GO:0004781 7493984 131567 cellular organisms no rank 10540 JCVI sulfate adenylyltransferase sulfate adenylyltransferase This enzyme forms adenosine 5'-phosphosulfate (APS) from ATP and free sulfate, the first step in the formation of the activated sulfate donor 3'-phosphoadenylylsulfate (PAPS). In some cases, it is found in a bifunctional protein in which the other domain, APS kinase, catalyzes the second and final step, the phosphorylation of APS to PAPS; the combined ATP sulfurylase/APS kinase may be called PAPS synthase. Members of this family also include the dissimilatory sulfate adenylyltransferase (sat) of the sulfate reducer Archaeoglobus fulgidus. TIGR00341.1 TIGR00341 TIGR00341 94.75 94.75 325 hypoth_equivalog Y Y N TIGR00341 family protein 131567 cellular organisms no rank 6629 JCVI TIGR00341 family protein TIGR00341 family protein This conserved hypothetical protein is found so far only in three archaeal genomes and in Streptomyces coelicolor. It shares a hydrophobic uncharacterized domain (see HMM TIGR00271) of about 180 residues with several eubacterial proteins, including the much longer protein sll1151 of Synechocystis PCC6803. TIGR00342.1 TIGR00342 TIGR00342 264.5 264.5 373 equivalog_domain Y Y N tRNA uracil 4-sulfurtransferase ThiI thiI 2.8.1.4 GO:0006400,GO:0009228,GO:0140741 11443125,18604845,21724998,9209060 131567 cellular organisms no rank 27010 JCVI tRNA sulfurtransferase ThiI tRNA uracil 4-sulfurtransferase ThiI Members of this protein family are the sulfurtransferase ThiI, involved in 4-thiouridine modification of tRNA. This protein often is bifunctional, with genetically separable activities, where the C-terminal rhodanese-like domain (residues 385 to 482 in E. coli ThiI), a domain not included in this model, is sufficient to synthesize the thiazole moiety of thiamine (see TIGR04271). Note that ThiI, because of its role in tRNA modification, may occur in species (such as Mycoplasma genitalium) that lack de novo thiamine biosynthesis. TIGR00343.1 TIGR00343 TIGR00343 438.45 438.45 287 equivalog Y Y N pyridoxal 5'-phosphate synthase lyase subunit PdxS pdxS GO:0042819,GO:0042823 10430950,9660944 131567 cellular organisms no rank 19180 JCVI pyridoxal 5'-phosphate synthase, synthase subunit Pdx1 pyridoxal 5'-phosphate synthase lyase subunit PdxS This protein had been believed to be a singlet oxygen resistance protein. Subsequent work showed that it is a protein of pyridoxine (vitamin B6) biosynthesis, and that pyridoxine quenches the highly toxic singlet form of oxygen produced by light in the presence of certain chemicals. TIGR00344.1 TIGR00344 alaS 457.05 457.05 847 equivalog Y Y N alanine--tRNA ligase alaS 6.1.1.7 GO:0000166,GO:0004813,GO:0005737,GO:0006419 131567 cellular organisms no rank 93580 JCVI alanine--tRNA ligase alanine--tRNA ligase The model describes alanine--tRNA ligase. This enzyme catalyzes the reaction (tRNAala + L-alanine + ATP = L-alanyl-tRNAala + pyrophosphate + AMP). TIGR00345.1 TIGR00345 GET3_arsA_TRC40 135 135 299 subfamily Y Y N TRC40/GET3/ArsA family transport-energizing ATPase 7.3.2.- GO:0005524,GO:0015446,GO:0016887 20981284,22124326,8674982 131567 cellular organisms no rank 19816 JCVI transport-energizing ATPase, TRC40/GET3/ArsA family TRC40/GET3/ArsA family transport-energizing ATPase Members of this family are ATPases that energize transport, although with different partner proteins for different functions. Recent findings show that TRC40 (GET3 in yeast) in involved in the insertion of tail-anchored membrane proteins in eukaryotes. A similar function is expected for members of this family in archaea. However, the earliest discovery of a function for this protein family is ArsA, an arsenic resistance protein that partners with ArsB (see PF02040) for As(III) efflux. TIGR00347.1 TIGR00347 bioD 83.3 83.3 166 equivalog Y Y N dethiobiotin synthase bioD 6.3.3.3 GO:0000287,GO:0004141,GO:0005524,GO:0009102 9125495 131567 cellular organisms no rank 53514 JCVI dethiobiotin synthase dethiobiotin synthase Dethiobiotin synthase is involved in biotin biosynthesis and catalyses the reaction (CO2 + 7,8-diaminononanoate + ATP = dethiobiotin + phosphate + ADP). The enzyme binds ATP (see motif in first 12 residues of the SEED alignment) and requires magnesium as a co-factor. TIGR00348.1 TIGR00348 hsdR 284.55 284.55 674 subfamily Y Y N HsdR family type I site-specific deoxyribonuclease 3.1.21.3 GO:0003677,GO:0005524,GO:0009035,GO:0009307 131567 cellular organisms no rank 61019 JCVI type I site-specific deoxyribonuclease, HsdR family HsdR family type I site-specific deoxyribonuclease This gene is part of the type I restriction and modification system which is composed of three polypeptides R (restriction endonuclease), M (modification) and S (specificity). This group of enzymes recognize specific short DNA sequences and have an absolute requirement for ATP (or dATP) and S-adenosyl-L-methionine. They also catalyse the reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar site specificity.(J. Mol. Biol. 271 (3), 342-348 (1997)). Members of this family are assumed to differ from each other in DNA site specificity. TIGR00350.1 TIGR00350 lytR_cpsA_psr 62.3 62.3 152 domain Y N N cell envelope-related function transcriptional attenuator common domain 8996082 131567 cellular organisms no rank 164626 JCVI cell envelope-related function transcriptional attenuator common domain cell envelope-related function transcriptional attenuator common domain This HMM describes a domain of unknown function that is found in the predicted extracellular domain of a number of putative membrane-bound proteins. One of these is proteins psr, described as a penicillin binding protein 5 (PDP-5) synthesis repressor. Another is Bacillus subtilis LytR, described as a transcriptional attenuator of itself and the LytABC operon, where LytC is N-acetylmuramoyl-L-alanine amidase. A third is CpsA, a putative regulatory protein involved in exocellular polysaccharide biosynthesis. Besides the region of strong similarily represented by this HMM, these proteins share the property of having a short putative N-terminal cytoplasmic domain and transmembrane domain forming a signal-anchor. TIGR00355.1 TIGR00355 purH 528 528 511 equivalog Y Y N bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase purH 2.1.2.3,3.5.4.10 GO:0003937,GO:0004643,GO:0009152 131567 cellular organisms no rank 70479 JCVI phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase PurH is bifunctional: IMP cyclohydrolase (EC 3.5.4.10); phosphoribosylaminoimidazolecarboxamide formyltransferase (EC 2.1.2.3) Involved in purine ribonucleotide biosynthesis. The IMP cyclohydrolase activity is in the N-terminal region. TIGR00357.1 TIGR00357 TIGR00357 113.05 113.05 134 equivalog_domain Y Y N peptide-methionine (R)-S-oxide reductase MsrB msrB 1.8.4.12 GO:0006979,GO:0030091,GO:0033743 19040639,8755589,9927663 131567 cellular organisms no rank 76912 JCVI methionine-R-sulfoxide reductase peptide-methionine (R)-S-oxide reductase MsrB The stereospecific enzyme peptide-methionine (R)-S-oxide reductase MsrB co-occurs with MsrA, which reduces the (S) form, occasionally fused with MsrA in a bifunctional protein. It provides protection against oxidative stress. TIGR00362.1 TIGR00362 DnaA 343.9 343.9 437 equivalog Y Y N chromosomal replication initiator protein DnaA dnaA GO:0003677,GO:0003688,GO:0005524,GO:0006270,GO:0006275 16753031,1779750,21620858 131567 cellular organisms no rank 60683 JCVI chromosomal replication initiator protein DnaA chromosomal replication initiator protein DnaA DnaA binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication. It can also affect transcription of multiple genes including itself. is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006). TIGR00364.1 TIGR00364 TIGR00364 150.3 150.3 201 equivalog Y Y N 7-cyano-7-deazaguanine synthase QueC queC 6.3.4.20 GO:0008616 14660578,16199558,9045825,9367855 131567 cellular organisms no rank 39033 JCVI queuosine biosynthesis protein QueC 7-cyano-7-deazaguanine synthase QueC Members of this protein family are QueC, involved in synthesizing pre-Q0 from GTP en route to tRNA modification with queuosine. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In Rhizobium meliloti, the gene was designated exsB, possibly because of polar effects on exsA expression in a shared polycistronic mRNA. In Arthrobacter viscosus, the homologous gene was designated ALU1 and was associated with an aluminum tolerance phenotype. TIGR00367.1 TIGR00367 TIGR00367 179.65 179.65 312 hypoth_equivalog Y Y N calcium/sodium antiporter GO:0016020,GO:0098662 22287543,27183196,9461611 131567 cellular organisms no rank 28480 JCVI K+-dependent Na+/Ca+ exchanger homolog calcium/sodium antiporter This HMM models a family of bacterial and archaeal proteins that is homologous, except for lacking a central region of ~ 250 amino acids and an N-terminal region of > 100 residues, to a functionally proven potassium-dependent sodium-calcium exchanger of the rat. TIGR00369.1 TIGR00369 unchar_dom_1 36.6 36.6 117 domain Y Y N hotdog fold thioesterase GO:0016790 16464851,17675380 131567 cellular organisms no rank 133151 JCVI uncharacterized domain 1 hotdog fold thioesterase TIGR00369 describes a set of hotdog fold thioesterases, found either as stand-alone protein or as a domain of a multifunctional protein. Examples include EntH (the proofreading thioesterase of enterobactin biosynthesis), MenI (1,4-dihydroxy-2-naphthoyl-CoA hydrolase), and PaaI (hydroxyphenylacetyl-CoA thioesterase). TIGR00370.1 TIGR00370 TIGR00370 145.55 145.55 202 equivalog Y Y N 5-oxoprolinase subunit PxpB pxpB 3.5.2.9 GO:0005975,GO:0008152,GO:0017168 18459799,21245531,28830929 131567 cellular organisms no rank 26953 JCVI sensor histidine kinase inhibitor, KipI family 5-oxoprolinase subunit PxpB One member of this family, originally designated KipI, was called an inhibitor of B. subtilis sporulation kinase A (KinA) (see PMID: 9334321). However, the family occurs broadly, and members of this family are now recognized as 5-oxoprolinase subunit PxpB. Misannotation as a subunit of allophanate hydrolase has also occurred. TIGR00372.1 TIGR00372 cas4 65 65 180 equivalog Y Y N CRISPR-associated protein Cas4 cas4 3.1.12.1 GO:0043571 11788711,11952905 131567 cellular organisms no rank 11300 JCVI CRISPR-associated protein Cas4 CRISPR-associated protein Cas4 This HMM represents a family of proteins associated with CRISPR repeats in a wide set of prokaryotic genomes. This scope of this model has been broadened since it was first built to describe an archaeal subset only. The function of the protein is undefined. Distantly related proteins, excluded from this model, include ORFs from Mycobacteriophage D29 and Sulfolobus islandicus filamentous virus and a region of the Schizosaccharomyces pombe DNA replication helicase Dna2p. TIGR00374.1 TIGR00374 TIGR00374 43.2 43.2 323 subfamily_domain Y Y N flippase-like domain-containing protein 25583072 131567 cellular organisms no rank 34574 JCVI TIGR00374 family protein flippase-like domain Members of this family show sequence homology to the flippase region of lysylphosphatidylglycerol synthetase/flippase proteins. Characterized members include AglD (archaeal glycosylation protein) of Haloferax volcanii, which also has a glycosyltransferase domain and which is involved in biosynthesis of a pentasaccharide moiety for N-linked glycosylation of the S-layer-forming major cell surface glycoprotein. TIGR00375.1 TIGR00375 TIGR00375 326.6 326.6 374 hypoth_equivalog Y Y N TIGR00375 family protein 131567 cellular organisms no rank 1364 JCVI TIGR00375 family protein TIGR00375 family protein The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology. TIGR00376.1 TIGR00376 TIGR00376 348.9 348.9 639 hypoth_equivalog Y Y N IGHMBP2 family helicase 3.6.4.12 GO:0003677,GO:0005524 19299493,22965130,8349627 131567 cellular organisms no rank 619 JCVI putative DNA helicase IGHMBP2 family helicase This helicase may be involved in protein translation. TIGR00377.1 TIGR00377 ant_ant_sig 53.45 53.45 108 superfamily Y Y N anti-sigma factor antagonist GO:0006355,GO:0043856 12354223,7751305,8144446 131567 cellular organisms no rank 81627 JCVI anti-anti-sigma factor anti-sigma factor antagonist This superfamily includes small (105-125 residue) proteins related to SpoIIAA of Bacillus subtilis, an anti-anti-sigma factor. SpoIIAA can bind to and inhibit the anti-sigma F factor SpoIIAB. Also, it can be phosphorylated by SpoIIAB on a Ser residue at position 59 of the seed alignment. A similar arrangement is inferred for RsbV, an anti-anti-sigma factor for sigma B. This Ser is fairly well conserved within a motif resembling MXS[STA]G[VIL]X[VIL][VILF] among homologous known or predicted anti-anti-sigma factors. Regions similar to SpoIIAA and apparently homologous, but differing considerably near the phosphorlated Ser of SpoIIAA, appear in a single copy in several longer proteins, but score below the trusted cutoff currently set for this superfamily HMM. This anti-anti-sigma factor, or anti-sigma factor antagonist, belongs to a family that includes characterized members SpoIIAA, RsbV, RsfA, and RsfB. TIGR00378.1 TIGR00378 cax 211.15 211.15 349 equivalog Y Y N calcium/proton exchanger cax GO:0006816,GO:0015369 8710949 131567 cellular organisms no rank 5959 JCVI calcium/proton exchanger calcium/proton exchanger TIGR00379.1 TIGR00379 cobB 261.4 261.4 449 subfamily Y Y N cobyrinic/hydrogenobyrinic acid a,c-diamide synthase cobB 6.3.5.- GO:0009236,GO:0042242 131567 cellular organisms no rank 35181 JCVI cobyrinic acid a,c-diamide synthase cobyrinic/hydrogenobyrinic acid a,c-diamide synthase Members of this family are the cobyrinic acid a,c-diamide synthetase (EC 6.3.5.11) CbiA for anaerobic biosynthesis of cobalamin or the hydrogenobyrinic acid a,c-diamide synthase (EC 6.3.5.9) CobB for aerobic biosynthesis of the same. Some archaeal CbiA have a second function as Ni-sirohydrochlorin a,c-diamide synthase (EC 6.3.5.12) for F(430) biosynthesis. Each of these enzymes is responsible for the amidation of carboxylic groups at positions A and C of either cobyrinic acid or hydrogenobrynic acid. NH(2) groups are provided by glutamine and one molecule of ATP hydrogenolyzed for each amidation. TIGR00380.1 TIGR00380 cobal_cbiB 165.9 165.9 305 equivalog Y Y N adenosylcobinamide-phosphate synthase CbiB cbiB GO:0009236,GO:0016020,GO:0048472 17827296,7635831,8550510 131567 cellular organisms no rank 40521 JCVI cobalamin biosynthesis protein CobD adenosylcobinamide-phosphate synthase CbiB CbiB is adenosylcobinamide-phosphate synthase. It is part of the anaerobic cobalamin biosynthesis pathway, as found in Salmonella enterica. The name CobD had been associated with this family in other contexts, but that name now belongs more properly to threonine-phosphate decarboxylase (see model TIGR01140). TIGR00381.1 TIGR00381 cdhD 252.9 252.9 389 equivalog Y Y N CO dehydrogenase/acetyl-CoA synthase subunit delta cdhD GO:0006085,GO:0006730,GO:0008168,GO:0043885 8550451 131567 cellular organisms no rank 295 JCVI CO dehydrogenase/acetyl-CoA synthase, delta subunit CO dehydrogenase/acetyl-CoA synthase subunit delta This is the small subunit of a heterodimer which catalyzes the reaction CO + H2O + Acceptor = CO2 + Reduced acceptor and is involved in the synthesis of acetyl-CoA from CO2 and H2. TIGR00383.1 TIGR00383 corA 200.75 200.75 320 equivalog Y Y N magnesium/cobalt transporter CorA corA GO:0006824,GO:0015087,GO:0015095,GO:0015693,GO:0016020 9775386 131567 cellular organisms no rank 33638 JCVI magnesium and cobalt transport protein CorA magnesium/cobalt transporter CorA The article in Microb Comp Genomics 1998;3(3):151-69 (Medline:98448512) discusses this family and suggests that some members may have functions other than Mg2+ transport. TIGR00384.1 TIGR00384 dhsB 88 88 222 subfamily Y N N succinate dehydrogenase and fumarate reductase iron-sulfur protein GO:0000104,GO:0006099,GO:0009060,GO:0009061 131567 cellular organisms no rank 48795 JCVI succinate dehydrogenase and fumarate reductase iron-sulfur protein succinate dehydrogenase and fumarate reductase iron-sulfur protein Succinate dehydrogenase and fumarate reductase are reverse directions of the same enzymatic interconversion, succinate + FAD+ = fumarate + FADH2 (EC 1.3.11.1). In E. coli, the forward and reverse reactions are catalyzed by distinct complexes: fumarate reductase operates under anaerobic conditions and succinate dehydrogenase operates under aerobic conditions. This model also describes a region of the B subunit of a cytosolic archaeal fumarate reductase. TIGR00388.1 TIGR00388 glyQ 361.45 361.45 293 equivalog_domain Y Y N glycine--tRNA ligase subunit alpha glyQ 6.1.1.14 GO:0000166,GO:0004820,GO:0005524,GO:0005737,GO:0006426 131567 cellular organisms no rank 29314 JCVI glycine--tRNA ligase, alpha subunit glycine--tRNA ligase subunit alpha This tetrameric form of glycyl-tRNA synthetase (2 alpha, 2 beta) is found in the majority of completed eubacterial genomes, with the two genes fused in a few species. A substantially different homodimeric form (not recognized by this model) replaces this form in the Archaea, animals, yeasts, and some eubacteria. TIGR00389.1 TIGR00389 glyS_dimeric 243.3 243.3 565 equivalog Y Y N glycine--tRNA ligase glyS 6.1.1.14 GO:0000166,GO:0004820,GO:0005524,GO:0005737,GO:0006426 9490048 131567 cellular organisms no rank 26508 JCVI glycine--tRNA ligase glycine--tRNA ligase, homodimeric type This HMM describes a glycyl-tRNA synthetase distinct from the two alpha and two beta chains of the tetrameric E. coli glycyl-tRNA synthetase. This enzyme is a homodimeric class II tRNA synthetase and is recognized by pfam HMM tRNA-synt_2b, which recognizes His, Ser, Pro, and this set of glycyl-tRNA synthetases. TIGR00391.1 TIGR00391 hydA 179.5 179.5 365 subfamily Y Y N hydrogenase small subunit GO:0008901,GO:0009375,GO:0051536 131567 cellular organisms no rank 11435 JCVI hydrogenase (NiFe) small subunit (hydA) hydrogenase small subunit Members of this family are the small subunit of the enzyme hydrogenase, of which there are a number of different types. Members include HyaA, HybO, HupS, HoxK, etc. TIGR00392.1 TIGR00392 ileS 621.4 621.4 861 equivalog Y Y N isoleucine--tRNA ligase ileS 6.1.1.5 GO:0000166,GO:0004822,GO:0005524,GO:0006428 11584022,12672810,15388946 131567 cellular organisms no rank 100613 JCVI isoleucine--tRNA ligase isoleucine--tRNA ligase The isoleucyl tRNA synthetase (IleS) is a class I amino acyl-tRNA ligase and is particularly closely related to the valyl tRNA synthetase. It catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile). Since isoleucine and other amino acids such as valine are similar, there is additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile). There are two active sites, one for aminoacylation and one for editing. Some organisms carry two different copies of this enzyme TIGR00395.1 TIGR00395 leuS_arch 648.5 648.5 938 equivalog Y Y N leucine--tRNA ligase leuS 6.1.1.4 GO:0000166,GO:0004823,GO:0005524,GO:0006429 131567 cellular organisms no rank 1228 JCVI leucine--tRNA ligase leucine--tRNA ligase The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both archaeal and cytosolic eukaryotic leucyl-tRNA synthetases; the eubacterial and mitochondrial forms differ so substantially that some other tRNA ligases score higher by this model than does any eubacterial LeuS. TIGR00396.1 TIGR00396 leuS_bact 548.4 548.4 843 equivalog Y Y N leucine--tRNA ligase leuS 6.1.1.4 GO:0000166,GO:0004823,GO:0005524,GO:0006429 15775966,16155584,16277600 131567 cellular organisms no rank 90241 JCVI leucine--tRNA ligase bacterial-type leucine--tRNA ligase The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both eubacterial and mitochondrial leucyl-tRNA synthetases. It generates higher scores for some valyl-tRNA synthetases than for any archaeal or eukaryotic cytosolic leucyl-tRNA synthetase. Note that the enzyme from Aquifex aeolicus is split into alpha and beta chains; neither chain is long enough to score above the trusted cutoff, but the alpha chain scores well above the noise cutoff. The beta chain must be found by a model and search designed for partial length matches. TIGR00398.1 TIGR00398 metG 336.35 336.35 530 equivalog_domain Y Y N methionine--tRNA ligase metG 6.1.1.10 GO:0000166,GO:0004825,GO:0005524,GO:0006431 11233169,12792655,19015366 131567 cellular organisms no rank 91309 JCVI methionine--tRNA ligase methionine--tRNA ligase The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This HMM appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this HMM shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (small) subunit; this model does not include the C-terminal region corresponding to the beta chain. TIGR00399.1 TIGR00399 metG_C_term 116.65 116.65 139 equivalog_domain Y Y N methionine--tRNA ligase subunit beta metG 6.1.1.10 GO:0000166,GO:0004825,GO:0005524,GO:0006431 131567 cellular organisms no rank 54856 JCVI methionine--tRNA ligase, beta subunit methionine--tRNA ligase subunit beta The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This HMM describes a region of the methionyl-tRNA synthetase that is present at the C-terminus of MetG in some species (E. coli, B. subtilis, Thermotoga maritima, Methanobacterium thermoautotrophicum), and as a separate beta chain in Aquifex aeolicus. It is absent in a number of other species (e.g. Mycoplasma genitalium, Mycobacterium tuberculosis), while Pyrococcus horikoshii has both a full length MetG and a second protein homologous to the beta chain only. Proteins hit by this HMM should called methionyl-tRNA synthetase beta chain if and only if the HMM metG hits a separate protein not also hit by this HMM. TIGR00400.1 TIGR00400 mgtE 232.75 232.75 450 equivalog Y Y N magnesium transporter mgtE GO:0015095,GO:0015693,GO:0016020 7868596,9622348 131567 cellular organisms no rank 45237 JCVI magnesium transporter magnesium transporter This family of prokaryotic proteins models a class of Mg++ transporter first described in Bacillus firmus. May form a homodimer. TIGR00401.1 TIGR00401 msrA 108.1 108.1 153 equivalog_domain Y Y N peptide-methionine (S)-S-oxide reductase MsrA msrA 1.8.4.11 GO:0006979,GO:0008113,GO:0030091,GO:0033744 8755589 131567 cellular organisms no rank 100741 JCVI peptide-methionine (S)-S-oxide reductase peptide-methionine (S)-S-oxide reductase MsrA This HMM describes peptide methionine sulfoxide reductase (MsrA), a repair enzyme for proteins that have been inactivated by oxidation. The enzyme from E. coli is coextensive with this model and has enzymatic activity. However, in all completed genomes in which this module is present, a second protein module, described in TIGR00357, is also found, and in several cases as part of the same polypeptide chain: N-terminal to this module in Helicobacter pylori and Haemophilus influenzae (as in PilB of Neisseria gonorrhoeae) but C-terminal to it in Treponema pallidum. PilB, containing both domains, has been shown to be important for the expression of adhesins in certain pathogens. TIGR00405.1 TIGR00405 KOW_elon_Spt5 69.95 69.95 145 equivalog Y Y N transcription elongation factor Spt5 GO:0003746 20197319 131567 cellular organisms no rank 1022 JCVI transcription elongation factor Spt5 transcription elongation factor Spt5 This protein contains a KOW domain, shared by bacterial NusG and the uL24 (previously L24p/L26e) family of ribosomal proteins. The most recent papers and crystal structures make this a transcription elongation factor rather than a ribosomal protein. TIGR00407.1 TIGR00407 proA 317.45 317.45 398 equivalog_domain Y Y N glutamate-5-semialdehyde dehydrogenase proA 1.2.1.41 GO:0004350,GO:0006561 131567 cellular organisms no rank 72784 JCVI glutamate-5-semialdehyde dehydrogenase glutamate-5-semialdehyde dehydrogenase The related HMM TIGR01092 describes a full-length fusion protein delta l-pyrroline-5-carboxylate synthetase that includes a gamma-glutamyl phosphate reductase region as described by this model. Alternate name: glutamate-5-semialdehyde dehydrogenase. The prosite motif begins at residue 332 of the seed alignment although not all of the members of the family exactly obey the motif. TIGR00408.1 TIGR00408 proS_fam_I 437 437 475 equivalog Y Y N proline--tRNA ligase proS 6.1.1.15 GO:0004827,GO:0005524,GO:0005737,GO:0006433 131567 cellular organisms no rank 20797 JCVI proline--tRNA ligase proline--tRNA ligase Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam HMM tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi. The other family includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae. TIGR00412.2 TIGR00412 redox_disulf_2 62 62 75 subfamily Y Y N MTH895/ArsE family thioredoxin-like protein 11939770,22866991,31059239 131567 cellular organisms no rank 7006 JCVI redox-active disulfide protein 2 MTH895/ArsE family thioredoxin-like protein This small protein is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The original version of this HMM had a seed alignment of proteins from three early-sequenced archaeal genomes: Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum, and named proteins "redox-active disulfide protein 2". A newly described bacterial member, ArsE, is a small, thioredoxin-like component of a nitroreductase active in converting the nitro group of two different synthetic aromatic organoarsenical compounds to an amine. The model is now rebuilt to cover a broader set of related proteins. TIGR00414.1 TIGR00414 serS 301.65 301.65 418 equivalog Y Y N serine--tRNA ligase serS 6.1.1.11 GO:0000166,GO:0004828,GO:0005524,GO:0006434 131567 cellular organisms no rank 73558 JCVI serine--tRNA ligase serine--tRNA ligase This HMM represents the serine--tRNA ligase found in most organisms. It is a class II tRNA ligase. The seryl-tRNA synthetases of two model archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model. TIGR00417.1 TIGR00417 speE 249.55 249.55 271 equivalog Y Y N spermidine synthase speE 2.5.1.16 GO:0003824 131567 cellular organisms no rank 14602 JCVI spermidine synthase spermidine synthase the SpeE subunit of spermidine synthase catalysesthe reaction (putrescine + S-adenosylmethioninamine = spermidine + 5'-methylthioadenosine) and is involved in polyamine biosynthesis and in the biosynthesis of spermidine from arganine. The region between residues 77 and 120 of the seed alignment is thought to be involved in binding to decarboxylated SAM. TIGR00418.1 TIGR00418 thrS 383.65 383.65 565 equivalog Y Y N threonine--tRNA ligase thrS 6.1.1.3 GO:0004829,GO:0005524,GO:0005737,GO:0006435 11953757 131567 cellular organisms no rank 86634 JCVI threonine--tRNA ligase threonine--tRNA ligase This HMM represents the threonyl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam HMM tRNA-synt_2b. Note that B. subtilis has closely related isozymes thrS and thrZ. The N-terminal regions are quite dissimilar between archaeal and eubacterial forms, while some eukaryotic forms are missing sequence there altogether. . TIGR00419.1 TIGR00419 tim 130.6 130.6 228 equivalog Y Y N triose-phosphate isomerase tpiA 5.3.1.1 GO:0004807,GO:0006096 131567 cellular organisms no rank 62823 JCVI triose-phosphate isomerase triose-phosphate isomerase Triosephosphate isomerase (tim/TPIA) is the glycolytic enzyme that catalyzes the reversible interconversion of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. TIGR00420.1 TIGR00420 trmU 236.95 236.95 351 equivalog Y Y N tRNA 2-thiouridine(34) synthase MnmA mnmA trmU 2.8.1.13 GO:0002143,GO:0004808,GO:0005737,GO:0006396,GO:0016783 12549933,16871210 131567 cellular organisms no rank 73850 JCVI tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase tRNA 2-thiouridine(34) synthase MnmA tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (trmU, asuE, or mnmA) is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine (mnm5s2U34) present in the wobble position of some tRNAs. This enzyme appears not to occur in the Archaea. TIGR00421.1 TIGR00421 ubiX_pad 108.9 108.9 181 subfamily Y Y N UbiX family flavin prenyltransferase GO:0008152,GO:0016831 26083743 131567 cellular organisms no rank 36152 JCVI polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases UbiX family flavin prenyltransferase UbiX partners with UbiD for decarboxylation of the 3-octaprenyl-4-hydroxybenzoate precursor during ubiquinone biosynthesis, but the role of UbiX is as a flavin prenyltransferase that provides a cofactor UbiD requires. TIGR00422.1 TIGR00422 valS 612.1 612.1 863 equivalog Y Y N valine--tRNA ligase valS 6.1.1.9 GO:0000166,GO:0004832,GO:0005524,GO:0006438 131567 cellular organisms no rank 88737 JCVI valine--tRNA ligase valine--tRNA ligase The valyl-tRNA synthetase (ValS) is a class I amino acyl-tRNA ligase and is particularly closely related to the isoleucyl tRNA synthetase. TIGR00423.1 TIGR00423 TIGR00423 260.25 260.25 310 subfamily Y Y N CofH family radical SAM protein GO:0016765 131567 cellular organisms no rank 38767 JCVI radical SAM domain protein, CofH subfamily CofH family radical SAM protein This protein family includes the CofH protein of coenzyme F(420) biosynthesis from Methanocaldococcus jannaschii, but appears to hit genomes more broadly than just the subset that make coenzyme F(420), so that narrower group is being built as a separate family. TIGR00425.1 TIGR00425 CBF5 238.15 238.15 322 equivalog Y Y N RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5 5.4.99.25 GO:0006396 27539785 131567 cellular organisms no rank 1446 JCVI putative rRNA pseudouridine synthase RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5 This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both. TIGR00427.1 TIGR00427 TIGR00427 99.2 99.2 201 subfamily Y Y N NAAT family transporter GO:0005886 12761179,17954692,26546518 131567 cellular organisms no rank 36573 JCVI membrane protein, MarC family NAAT family transporter MarC from Escherichia coli belongs to the "6 transmembrane segment Neutral Amino Acid Transporter (NAAT) Family", according to tcdb.org. Its substrate is unknown. TIGR00430.1 TIGR00430 Q_tRNA_tgt 306.75 306.75 368 equivalog Y Y N tRNA guanosine(34) transglycosylase Tgt tgt 2.4.2.29 GO:0005737,GO:0006400,GO:0008479 12909636,12949492 131567 cellular organisms no rank 53090 JCVI tRNA-guanine transglycosylase tRNA guanosine(34) transglycosylase Tgt This tRNA-guanine transglycosylase (tgt) catalyzes an exchange for the guanine base at position 34 of many tRNAs; this nucleotide is subsequently modified to queuosine. The Archaea have a closely related enzyme that catalyzes a base exchange for guanine at position 15 in some tRNAs, a site that is subsequently converted to the archaeal-specific modified base archaeosine (7-formamidino-7-deazaguanosine), while Archaeoglobus fulgidus has both enzymes. TIGR00433.2 TIGR00433 bioB 225 225 307 equivalog Y Y N biotin synthase BioB bioB 2.8.1.6 GO:0004076,GO:0009102,GO:0051536,GO:1904047 131567 cellular organisms no rank 51456 JCVI biotin synthase biotin synthase BioB Catalyzes the last step of the biotin biosynthesis pathway. All members of the seed alignment are in the immediate gene neighborhood of a bioA gene. TIGR00434.1 TIGR00434 cysH 165.1 165.1 214 subfamily Y N N phosophoadenylyl-sulfate reductase cysH GO:0004604,GO:0019379 8917600 131567 cellular organisms no rank 36973 JCVI phosophoadenylyl-sulfate reductase phosophoadenylyl-sulfate reductase This enzyme, involved in the assimilation of inorganic sulfate, is designated cysH in Bacteria and MET16 in Saccharomyces cerevisiae. Synonyms include phosphoadenosine phosphosulfate reductase, PAPS reductase, and PAPS reductase, thioredoxin-dependent. In a reaction requiring reduced thioredoxin and NADPH, it converts 3(prime)-phosphoadenylylsulfate (PAPS) to sulfite and adenosine 3(prime),5(prime) diphosphate (PAP). A related family of plant enzymes, scoring below the trusted cutoff, differs in having a thioredoxin-like C-terminal domain, not requiring thioredoxin, and in having a preference for 5(prime)-adenylylsulfate (APS) over PAPS. TIGR00435.1 TIGR00435 cysS 340 340 466 equivalog Y Y N cysteine--tRNA ligase cysS 6.1.1.16 GO:0004817,GO:0005524,GO:0005737,GO:0006423 131567 cellular organisms no rank 81967 JCVI cysteine--tRNA ligase cysteine--tRNA ligase Cysteine--tRNA ligase charges a cysteine by linking its carboxyl group to the alpha-phosphate of ATP and then transfers the aminoacyl-adenylate to its tRNA. This HMM finds the cysteinyl-tRNA synthetase from most but not from all species. Many archaea instead and a few bacteria rely on the SepRS/SepCysS pathway, first ligating phosphoserine to tRNA(Cys), then replacing the phosphate with sulfide. TIGR00437.1 TIGR00437 feoB 315.65 315.65 594 equivalog Y Y N ferrous iron transport protein B feoB GO:0005525,GO:0006826,GO:0015093,GO:0016020 131567 cellular organisms no rank 50116 JCVI ferrous iron transport protein B ferrous iron transport protein B FeoB (773 amino acids in E. coli), a cytoplasmic membrane protein required for iron(II) update, is encoded in an operon with FeoA (75 amino acids), which is also required, and is regulated by Fur. There appear to be two copies in Archaeoglobus fulgidus and Clostridium acetobutylicum. TIGR00442.1 TIGR00442 hisS 286.75 286.75 406 equivalog Y Y N histidine--tRNA ligase hisS 6.1.1.21 GO:0004821,GO:0005524,GO:0005737,GO:0006427 131567 cellular organisms no rank 77504 JCVI histidine--tRNA ligase histidine--tRNA ligase This model finds a histidyl-tRNA synthetase in every completed genome. Apparent second copies from Bacillus subtilis, Synechocystis sp., and Aquifex aeolicus are slightly shorter, more closely related to each other than to other hisS proteins, and actually serve as regulatory subunits for an enzyme of histidine biosynthesis. They were excluded from the seed alignment and score much lower than do single copy histidyl-tRNA synthetases of other genomes not included in the seed alignment. These putative second copies of HisS score below the trusted cutoff. The regulatory protein kinase GCN2 of Saccharomyces cerevisiae (YDR283c), and related proteins from other species designated eIF-2 alpha kinase, have a domain closely related to histidyl-tRNA synthetase that may serve to detect and respond to uncharged tRNA(his), an indicator of amino acid starvation; these regulatory proteins are not orthologous and so score below the noise cutoff. TIGR00443.1 TIGR00443 hisZ_biosyn_reg 271.65 271.65 314 equivalog Y Y N ATP phosphoribosyltransferase regulatory subunit hisZ GO:0000105,GO:0003879,GO:0005737,GO:0030234 15660995 131567 cellular organisms no rank 15146 JCVI ATP phosphoribosyltransferase, regulatory subunit ATP phosphoribosyltransferase regulatory subunit Apparant second copies of histidyl-tRNA synthetase, found in Bacillus subtilis, Synechocystis sp., Aquifex aeolicus, and others, are in fact a regulatory subunit of ATP phosphoribosyltransferase, and usually encoded by a gene adjacent to that encoding the catalytic subunit. TIGR00444.1 TIGR00444 mazG 148.3 148.3 248 subfamily Y Y N MazG family protein 131567 cellular organisms no rank 46554 JCVI MazG family protein MazG family protein This family of prokaryotic proteins has no known function. It includes the uncharacterized protein MazG in E. coli. TIGR00446.1 TIGR00446 nop2p 210.45 210.45 264 subfamily_domain Y Y N NOL1/NOP2/sun family putative RNA methylase GO:0003723,GO:0006396,GO:0008757 131567 cellular organisms no rank 16426 JCVI NOL1/NOP2/sun family putative RNA methylase NOL1/NOP2/sun family putative RNA methylase TIGR00449.1 TIGR00449 tgt_general 47.6 47.6 367 superfamily Y Y N tRNA-guanine transglycosylase 2.4.2.- 131567 cellular organisms no rank 57204 JCVI tRNA-guanine family transglycosylase tRNA-guanine transglycosylase This tRNA-guanine transglycosylase includes enzymes that replace guanine at position 34 in bacteria with queuine (Tgt), and at position 15 in archaea with 7-cyano-7-carbaguanine. TIGR00451.1 TIGR00451 unchar_dom_2 27 27 107 domain Y N N uncharacterized domain 2 GO:0003723 131567 cellular organisms no rank 4768 JCVI uncharacterized domain 2 uncharacterized domain 2 This uncharacterized domain is found a number of enzymes and uncharacterized proteins, often at the C-terminus. It is found in some but not all members of a family of related tRNA-guanine transglycosylases (tgt), which exchange a guanine base for some modified base without breaking the phosphodiester backbone of the tRNA. It is also found in rRNA pseudouridine synthase, another enzyme of RNA base modification not otherwise homologous to tgt. It is found, again at the C-terminus, in two putative glutamate 5-kinases. It is also found in a family of small, uncharacterized archaeal proteins consisting mostly of this domain. TIGR00453.1 TIGR00453 ispD 181.3 181.3 219 equivalog_domain Y Y N 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase ispD 2.7.7.60 GO:0008299,GO:0019288,GO:0050518 131567 cellular organisms no rank 58625 JCVI 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase Members of this protein family are 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, the IspD protein of the deoxyxylulose pathway of IPP biosynthesis. In about twenty percent of bacterial genomes, this protein occurs as IspDF, a bifunctional fusion protein. TIGR00455.1 TIGR00455 apsK 138.7 138.7 184 equivalog_domain Y Y N adenylyl-sulfate kinase cysC 2.7.1.25 GO:0000103,GO:0004020,GO:0005524 131567 cellular organisms no rank 46977 JCVI adenylyl-sulfate kinase adenylyl-sulfate kinase This protein, adenylylsulfate kinase, is often found as a fusion protein with sulfate adenylyltransferase. Important residue (active site in E.coli) is residue 100 of the seed alignment. TIGR00456.1 TIGR00456 argS 261.65 261.65 569 equivalog Y Y N arginine--tRNA ligase argS 6.1.1.19 GO:0004814,GO:0005524,GO:0005737,GO:0006420 131567 cellular organisms no rank 86928 JCVI arginine--tRNA ligase arginine--tRNA ligase This HMM recognizes arginyl-tRNA synthetase in every completed genome to date. An interesting feature of the alignment of all arginyl-tRNA synthetases is a fairly deep split between two families. One family includes archaeal, eukaryotic and organellar, spirochete, E. coli, and Synechocystis sp. The second, sharing a deletion of about 25 residues in the central region relative to the first, includes Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas and Mycobacteria, and the Gram-negative bacterium Helicobacter pylori. TIGR00457.1 TIGR00457 asnS 342.6 342.6 455 equivalog Y Y N asparagine--tRNA ligase asnS 6.1.1.22 GO:0000166,GO:0004816,GO:0005524,GO:0006421 131567 cellular organisms no rank 28713 JCVI asparagine--tRNA ligase asparagine--tRNA ligase In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This HMM, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn. TIGR00458.1 TIGR00458 aspS_nondisc 368.4 368.4 428 equivalog Y Y N aspartate--tRNA(Asn) ligase aspS 6.1.1.23 GO:0000166,GO:0004815,GO:0005524,GO:0005737,GO:0006422 131567 cellular organisms no rank 5425 JCVI aspartate--tRNA(Asn) ligase aspartate--tRNA(Asn) ligase In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This HMM, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). TIGR00459.1 TIGR00459 aspS_bact 373.85 373.85 586 equivalog Y Y N aspartate--tRNA ligase aspS 6.1.1.- GO:0004815,GO:0005524,GO:0005737,GO:0006422 131567 cellular organisms no rank 75822 JCVI aspartate--tRNA ligase aspartate--tRNA ligase Asparate--tRNA ligases in this family may be discriminating (6.1.1.12) or nondiscriminating (6.1.1.23). In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This HMM, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences. TIGR00460.1 TIGR00460 fmt 201.5 201.5 315 equivalog Y Y N methionyl-tRNA formyltransferase fmt 2.1.2.9 GO:0004479,GO:0005737,GO:0071951 131567 cellular organisms no rank 77832 JCVI methionyl-tRNA formyltransferase methionyl-tRNA formyltransferase The top-scoring characterized proteins other than methionyl-tRNA formyltransferase (fmt) itself are formyltetrahydrofolate dehydrogenases. The mitochondrial methionyl-tRNA formyltransferases are so divergent that, in a multiple alignment of bacterial fmt, mitochondrial fmt, and formyltetrahydrofolate dehydrogenases, the mitochondrial fmt appears the most different. However, because both bacterial and mitochondrial fmt are included in the seed alignment, all credible fmt sequences score higher than any non-fmt sequence. This enzyme modifies Met on initiator tRNA to f-Met. TIGR00463.1 TIGR00463 gltX_arch 401.75 401.75 560 equivalog Y Y N glutamate--tRNA ligase gltX 6.1.1.17 GO:0000166,GO:0004818,GO:0005524,GO:0005737,GO:0006424 131567 cellular organisms no rank 1659 JCVI glutamate--tRNA ligase glutamate--tRNA ligase The glutamyl-tRNA synthetases of the eukaryotic cytosol and of the Archaea are more similar to glutaminyl-tRNA synthetases than to bacterial glutamyl-tRNA synthetases. This HMM models just the eukaryotic cytosolic and archaeal forms of the enzyme. In some eukaryotes, the glutamyl-tRNA synthetase is part of a longer, multifunctional aminoacyl-tRNA ligase. In many species, the charging of tRNA(gln) proceeds first through misacylation with Glu and then transamidation. For this reason, glutamyl-tRNA synthetases, including all known archaeal enzymes (as of 2010) may act on both tRNA(gln) and tRNA(glu). TIGR00465.1 TIGR00465 ilvC 226.15 226.15 314 equivalog Y Y N ketol-acid reductoisomerase ilvC 1.1.1.86 GO:0004455,GO:0009082,GO:0016491 131567 cellular organisms no rank 51580 JCVI ketol-acid reductoisomerase ketol-acid reductoisomerase Ketol-acid reductoisomerase is the second enzyme in the parallel isoleucine-valine biosynthetic pathway. Nearly all members of this family are designated EC 1.1.1.86, meaning specificity for NADPH, but a rare few are noted to be specific for NADH (EC 1.1.1.382) or for either (EC 1.1.1.383). TIGR00466.1 TIGR00466 kdsB 155.2 155.2 241 equivalog Y Y N 3-deoxy-manno-octulosonate cytidylyltransferase kdsB 2.7.7.38 GO:0008690,GO:0009244 131567 cellular organisms no rank 36895 JCVI 3-deoxy-D-manno-octulosonate cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase TIGR00467.1 TIGR00467 lysS_arch 147.55 147.55 515 equivalog Y Y N lysine--tRNA ligase lysS 6.1.1.6 GO:0004824,GO:0006430,GO:0017101 131567 cellular organisms no rank 16615 JCVI lysine--tRNA ligase lysine--tRNA ligase This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set. TIGR00468.1 TIGR00468 pheS 237.45 237.45 324 equivalog Y Y N phenylalanine--tRNA ligase subunit alpha pheS 6.1.1.20 GO:0000166,GO:0004826,GO:0005524,GO:0005737,GO:0006432 21082706,24936059 131567 cellular organisms no rank 58304 JCVI phenylalanine--tRNA ligase, alpha subunit phenylalanine--tRNA ligase subunit alpha Catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a heterotetramer of alpha(2)beta(2); binds two magnesium ions per tetramer. Most phenylalanyl-tRNA synthetases are heterodimeric, with 2 alpha (pheS) and 2 beta (pheT) subunits. This HMM describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. TIGR00471.1 TIGR00471 pheT_arch 282.65 282.65 551 equivalog Y Y N phenylalanine--tRNA ligase subunit beta pheT 6.1.1.20 GO:0000166,GO:0004826,GO:0005524,GO:0005737,GO:0006432 131567 cellular organisms no rank 1924 JCVI phenylalanine--tRNA ligase, beta subunit phenylalanine--tRNA ligase subunit beta Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This HMM represents the subfamily that includes the beta subunit from eukaryotic cytosol, the Archaea, and spirochetes. TIGR00473.1 TIGR00473 pssA 107 107 153 equivalog Y Y N CDP-diacylglycerol--serine O-phosphatidyltransferase pssA 2.7.8.8 GO:0003882,GO:0008654 131567 cellular organisms no rank 26947 JCVI CDP-diacylglycerol-serine O-phosphatidyltransferase CDP-diacylglycerol--serine O-phosphatidyltransferase This enzyme, CDP-diacylglycerol--serine O-phosphatidyltransferase, is involved in phospholipid biosynthesis catalyzing the reaction CDP-diacylglycerol + L-serine = CMP + L-1-phosphatidylserine. Members of this family do not bear any significant sequence similarity to the corresponding E.coli protein. TIGR00475.1 TIGR00475 selB 242.25 242.25 581 equivalog Y Y N selenocysteine-specific translation elongation factor selB GO:0001514,GO:0003723,GO:0003746,GO:0003924,GO:0005525,GO:0005737 12486046 131567 cellular organisms no rank 27292 JCVI selenocysteine-specific translation elongation factor selenocysteine-specific translation elongation factor In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This HMM describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes. TIGR00476.1 TIGR00476 selD 125 125 311 equivalog Y Y N selenide, water dikinase SelD selD 2.7.9.3 GO:0001887,GO:0004756,GO:0005524 131567 cellular organisms no rank 31839 JCVI selenide, water dikinase selenide, water dikinase SelD In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This HMM describes SelD, known as selenophosphate synthetase, selenium donor protein, and selenide,water dikinase. SelD provides reduced selenium for the selenium transferase SelA. This protein itself contains selenocysteine in many species; any sequence scoring above the trusted cutoff but not aligning to the beginning of the HMM is likely have selenocysteine residue incorrectly interpreted as a stop codon upstream of the given sequence. The SelD protein also provides selenophosphate for the enzyme tRNA 2-selenouridine synthase, which catalyzes a tRNA base modification, and SenB, a selenosugar-synthesizing enzyme in the pathway of selenoneine biosynthesis. It also contributes to selenium incorporation by selenium-dependent molybdenum hydroxylases (SDMH), in genomes with the marker TIGR03309. All genomes with SelD should make selenocysteine, selenouridine, selenoneine, SDMH, or some combination. TIGR00478.1 TIGR00478 tly 185.8 185.8 228 subfamily Y Y N TlyA family rRNA (cytidine-2'-O)-methyltransferase 1730486,22779429,9611795 131567 cellular organisms no rank 37404 JCVI TlyA family rRNA methyltransferase/putative hemolysin TlyA family rRNA (cytidine-2'-O)-methyltransferase Members of this family include TlyA from Mycobacterium tuberculosis, an rRNA methylase whose modifications are necessary to confer sensitivity to ribosome-targeting antibiotics capreomycin and viomycin. Homology supports identification as a methyltransferase. However, a parallel literature persists in calling some members hemolysins. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. A recent study (2013) on SCO1782 from Streptomyces coelicolor shows hemolysin activity as earlier described for a homolog from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. TIGR00479.1 TIGR00479 rumA 183.55 183.55 432 equivalog Y Y N 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD rlmD 2.1.1.190 GO:0008649 11779873 131567 cellular organisms no rank 76996 JCVI 23S rRNA (uracil-5-)-methyltransferase RumA 23S rRNA (uracil-5-)-methyltransferase RlmD This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. TIGR00481.1 TIGR00481 TIGR00481 57.75 57.75 142 subfamily Y Y N YbhB/YbcL family Raf kinase inhibitor-like protein 11439028,25183735 131567 cellular organisms no rank 47882 JCVI Raf kinase inhibitor-like protein, YbhB/YbcL family YbhB/YbcL family Raf kinase inhibitor-like protein TIGR00483.1 TIGR00483 EF-1_alpha 540.1 540.1 427 equivalog Y Y N translation elongation factor EF-1 subunit alpha tuf GO:0003746,GO:0005525,GO:0006414 131567 cellular organisms no rank 1415 JCVI translation elongation factor EF-1, subunit alpha translation elongation factor EF-1 subunit alpha This model represents the counterpart of bacterial EF-Tu for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1 alpha). The trusted cutoff is set fairly high so that incomplete sequences will score between suggested and trusted cutoff levels. TIGR00484.1 TIGR00484 EF-G 659.4 659.4 691 equivalog Y Y N elongation factor G fusA GO:0003746,GO:0005525,GO:0006414 15491605,9600930 131567 cellular organisms no rank 71999 JCVI translation elongation factor G elongation factor G After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. TIGR00485.1 TIGR00485 EF-Tu 522.4 522.4 394 equivalog Y Y N elongation factor Tu tuf GO:0003746,GO:0005525,GO:0006414 131567 cellular organisms no rank 57233 JCVI translation elongation factor Tu elongation factor Tu This HMM models orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts, one of several GTP-binding translation factors found by the more general pfam HMM GTP_EFTU. The eukaryotic conterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this model. EF-Tu is one of the most abundant proteins in bacteria, as well as one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation. TIGR00486.1 TIGR00486 YbgI_SA1388 130.55 130.55 250 equivalog Y Y N Nif3-like dinuclear metal center hexameric protein GO:0005737,GO:0051540 14519207,17187687,23825549,25243119,29625546 131567 cellular organisms no rank 61606 JCVI dinuclear metal center protein, YbgI/SA1388 family Nif3-like dinuclear metal center hexameric protein PMID:23825549 (2013) identifies HP0959 from Helicobacter pylori as a new type of GTP cyclohydrolase I. Other well-studied members of this family include YbgI from E. coli, SA1388 from Staphylococcus aureus, and MJ0927 from Methanocaldococcus jannaschii. Note that HP0959 showed activity only at low pH, and that HP0928 from the same organism is a member of family TIGR00063, GTP cyclohydrolase I type 1 (FolE). TIGR00492.1 TIGR00492 alr 168 168 369 equivalog Y Y N alanine racemase alr 5.1.1.1 GO:0006522,GO:0008784,GO:0009252 131567 cellular organisms no rank 101599 JCVI alanine racemase alanine racemase This enzyme interconverts L-alanine and D-alanine. Its primary function is to generate D-alanine for cell wall formation. With D-alanine-D-alanine ligase, it makes up the D-alanine branch of the peptidoglycan biosynthetic route. It is a monomer with one pyridoxal phosphate per subunit. In E. coli, the ortholog is duplicated so that a second isozyme, DadX, is present. DadX, a paralog of the biosynthetic Alr, is induced by D- or L-alanine and is involved in catabolism. TIGR00494.1 TIGR00494 crcB 80.45 80.45 117 equivalog Y Y N fluoride efflux transporter CrcB crcB GO:0016020,GO:1903424,GO:1903425 22194412 131567 cellular organisms no rank 49462 JCVI protein CrcB fluoride efflux transporter CrcB CrcB was previously annotated as camphor resistance protein, and linked to chromosome condensation. However, it confers resistance to fluoride ion, by acting as an efflux transporter, and usually is preceded by a fluoride-responsive riboswitch. TIGR00497.1 TIGR00497 hsdM 242.75 242.75 515 equivalog Y Y N type I restriction-modification system subunit M 2.1.1.72 GO:0003677,GO:0009007,GO:0009307 131567 cellular organisms no rank 34901 JCVI type I restriction-modification system, M subunit type I restriction-modification system subunit M Function: methylation of specific adenine residues; required for both restriction and modification activities. The ECOR124/3 I enzyme recognizes 5'GAA(N7)RTCG. for E.coli see (J. Mol. Biol. 257: 960-969 (1996)). TIGR00499.1 TIGR00499 lysS_bact 427.6 427.6 496 equivalog Y Y N lysine--tRNA ligase lysS 6.1.1.6 GO:0004824,GO:0005524,GO:0005737,GO:0006430 131567 cellular organisms no rank 63731 JCVI lysine--tRNA ligase lysine--tRNA ligase This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms. TIGR00501.1 TIGR00501 met_pdase_II 222.65 222.65 295 equivalog Y Y N type II methionyl aminopeptidase map 3.4.11.18 GO:0006508,GO:0070006 131567 cellular organisms no rank 1402 JCVI methionine aminopeptidase, type II type II methionyl aminopeptidase Methionine aminopeptidase (map) is a cobalt-binding enzyme. Bacterial and organellar examples (type I) differ from eukaroytic and archaeal (type II) examples in lacking a region of approximately 60 amino acids between the 4th and 5th cobalt-binding ligands. The role of this protein in general is to produce the mature amino end of cytosolic proteins by removing the N-terminal methionine. This model describes type II, among which the eukaryotic members typically have an N-terminal extension not present in archaeal members. It can act cotranslationally. The enzyme from rat has been shown to associate with translation initiation factor 2 (IF-2) and may have a role in translational regulation. TIGR00504.1 TIGR00504 pyro_pdase 201.75 201.75 213 equivalog Y Y N pyroglutamyl-peptidase I pcp 3.4.19.3 GO:0005829,GO:0006508,GO:0008234,GO:0016920 131567 cellular organisms no rank 15656 JCVI pyroglutamyl-peptidase I pyroglutamyl-peptidase I Alternate names include pyroglutamate aminopeptidase, pyrrolidone-carboxylate peptidase, and 5-oxoprolyl-peptidase. It removes pyroglutamate (pyrrolidone-carboxylate, a modified glutamine) that can otherwise block hydrolysis of a polypeptide at the amino end, and so can be extremely useful in the biochemical studies of proteins. The biological role in the various species in which it is found is not fully understood. The enzyme appears to be a homodimer. It does not closely resemble any other peptidases. TIGR00505.1 TIGR00505 ribA 205.85 205.85 191 equivalog_domain Y Y N GTP cyclohydrolase II ribA 3.5.4.25 GO:0003935 131567 cellular organisms no rank 48245 JCVI GTP cyclohydrolase II GTP cyclohydrolase II Several members of the family are bifunctional, involving both ribA and ribB function. In these cases, ribA tends to be on the C-terminal end of the protein and ribB tends to be on the N-terminal. The function of archaeal members of the family has not been demonstrated and is assigned tentatively. TIGR00506.1 TIGR00506 ribB 177.45 177.45 204 equivalog_domain Y Y N 3,4-dihydroxy-2-butanone-4-phosphate synthase ribB 4.1.99.12 GO:0008686 11342130,12200440,1597419 131567 cellular organisms no rank 70421 JCVI 3,4-dihydroxy-2-butanone-4-phosphate synthase 3,4-dihydroxy-2-butanone-4-phosphate synthase RibB (DHBP synthase) catalyzes the formation of 3,4-dihydroxy-2-butanone-4-phosphate synthase in riboflavin biosynthesis. Many members of the family are bifunctional, involving both ribA and ribB function. In these cases, ribA tends to be on the C-terminal end of the protein and ribB tends to be on the N-terminal. TIGR00507.1 TIGR00507 aroE 200.2 200.2 270 equivalog_domain Y Y N shikimate dehydrogenase aroE 1.1.1.25 GO:0004764,GO:0019632,GO:0050661 131567 cellular organisms no rank 54169 JCVI shikimate dehydrogenase shikimate dehydrogenase This HMM finds proteins from prokaryotes and functionally equivalent domains from larger, multifunctional proteins of fungi and plants. Below the trusted cutoff of 180, but above the noise cutoff of 20, are the putative shikimate dehydrogenases of Thermotoga maritima and Mycobacterium tuberculosis, and uncharacterized paralogs of shikimate dehydrogenase from E. coli and H. influenzae. The related enzyme quinate 5-dehydrogenase scores below the noise cutoff. A neighbor-joining tree, constructed with quinate 5-dehydrogenases as the outgroup, shows the Clamydial homolog as clustering among the shikimate dehydrogenases, although the sequence is unusual in the degree of sequence divergence and the presence of an additional N-terminal domain. TIGR00508.1 TIGR00508 bioA 405 405 419 equivalog Y Y N adenosylmethionine--8-amino-7-oxononanoate transaminase bioA 2.6.1.62 GO:0004015,GO:0009102 131567 cellular organisms no rank 58756 JCVI adenosylmethionine-8-amino-7-oxononanoate transaminase adenosylmethionine--8-amino-7-oxononanoate transaminase The biotin biosynthesis enzyme BioA (adenosylmethionine--8-amino-7-oxononanoate transaminase) catalyzes the formation of S-adenosyl-4-methylthionine-2-oxobutanoate and 7,8-diaminononanoate from S-adenosyl-L-methionine and 8-amino-7-oxononanoate. Alternate names include 7,8-diaminopelargonic acid aminotransferase, and DAPA aminotransferase. TIGR00510.1 TIGR00510 lipA 310.25 310.25 302 equivalog Y Y N lipoyl synthase lipA 2.8.1.8 GO:0009107,GO:0016992,GO:0051539,GO:1904047 10403368,8349643 131567 cellular organisms no rank 49406 JCVI lipoyl synthase lipoyl synthase This enzyme is an iron-sulfur protein. It is localized to mitochondria in yeast and Arabidopsis. It generates lipoic acid, a thiol antioxidant that is linked to a specific Lys as prosthetic group for the pyruvate and alpha-ketoglutarate dehydrogenase complexes and the glycine-cleavage system. The family shows strong sequence conservation. TIGR00512.1 TIGR00512 salvage_mtnA 279 279 335 equivalog Y Y N S-methyl-5-thioribose-1-phosphate isomerase mtnA 5.3.1.23 GO:0019509,GO:0046523 9520434 131567 cellular organisms no rank 32162 JCVI S-methyl-5-thioribose-1-phosphate isomerase S-methyl-5-thioribose-1-phosphate isomerase The delineation of this family was based in part on a discussion and neighbor-joining phylogenetic study, by Kyrpides and Woese, of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. This clade is now recognized to include the methionine salvage pathway enzyme MtnA. TIGR00514.1 TIGR00514 accC 626.5 626.5 449 equivalog Y Y N acetyl-CoA carboxylase biotin carboxylase subunit accC 6.3.4.14 GO:0004075,GO:0009317,GO:0016874 131567 cellular organisms no rank 46921 JCVI acetyl-CoA carboxylase, biotin carboxylase subunit acetyl-CoA carboxylase biotin carboxylase subunit This model represents the biotin carboxylase subunit found usually as a component of acetyl-CoA carboxylase. Acetyl-CoA carboxylase is designated EC 6.4.1.2 and this component, biotin carboxylase, has its own designation, EC 6.3.4.14. Homologous domains are found in eukaryotic forms of acetyl-CoA carboxylase and in a number of other carboxylases (e.g. pyruvate carboxylase), but seed members and trusted cutoff are selected so as to exclude these. In some systems, the biotin carboxyl carrier protein and this protein (biotin carboxylase) may be shared by different carboxyltransferases. However, this model is not intended to identify the biotin carboxylase domain of propionyl-coA carboxylase. The model should hit the full length of proteins, except for chloroplast transit peptides in plants. If it hits a domain only of a longer protein, there may be a problem with the identification. TIGR00516.1 TIGR00516 acpS 59.8 59.8 125 equivalog_domain Y Y N holo-ACP synthase acpS 2.7.8.7 GO:0008610,GO:0008897 7559576 131567 cellular organisms no rank 38061 JCVI holo-[acyl-carrier-protein] synthase holo-[acyl-carrier-protein] synthase Formerly dpj. This enzyme adds the prosthetic group, phosphopantethiene, to the acyl carrier protein (ACP) apo-enzyme to generate the holo-enzyme. Related phosphopantethiene--protein transferases also exist. There is an orthologous domain in eukaryotic proteins. TIGR00518.1 TIGR00518 alaDH 391.85 391.85 370 equivalog Y Y N alanine dehydrogenase ald 1.4.1.1 GO:0000286,GO:0042853 11888165 131567 cellular organisms no rank 42603 JCVI alanine dehydrogenase alanine dehydrogenase The family of known L-alanine dehydrogenases (EC 1.4.1.1) includes representatives from the Proteobacteria, Firmicutes, Cyanobacteria, and Actinobacteria, all with about 50 % identity or better. An outlier to this group in both sequence and gap pattern is the homolog from Helicobacter pylori, an epsilon division Proteobacteria, which must be considered a putative alanine dehydrogenase. In Mycobacterium smegmatis and M. tuberculosis, the enzyme doubles as a glycine dehydrogenase (1.4.1.10), running in the reverse direction (glyoxylate amination to glycine, with conversion of NADH to NAD+). Related proteins include saccharopine dehydrogenase and the N-terminal half of the NAD(P) transhydrogenase alpha subunit. All of these related proteins bind NAD and/or NADP. TIGR00519.1 TIGR00519 asnASE_I 260.5 260.5 337 subfamily Y Y N type I asparaginase 3.5.1.1 GO:0004067,GO:0006520 131567 cellular organisms no rank 15940 JCVI L-asparaginase, type I type I asparaginase Two related families of asparaginase are designated type I and type II according to the terminology in E. coli, which has both: L-asparaginase I is a low-affinity enzyme found in the cytoplasm, while L-asparaginase II is a high-affinity secreted enzyme synthesized with a cleavable signal sequence. This model describes L-asparaginases related to type I of E. coli. Archaeal putative asparaginases are of this type but contain an extra ~ 80 residues in a conserved N-terminal region. These archaeal homologs are included in this model. TIGR00521.1 TIGR00521 coaBC_dfp 219.7 219.7 392 equivalog Y Y N bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase CoaBC coaBC 4.1.1.36,6.3.2.5 GO:0004632,GO:0004633,GO:0010181,GO:0015937,GO:0015941 11278255,3123465 131567 cellular organisms no rank 74407 JCVI phosphopantothenoylcysteine decarboxylase / phosphopantothenate--cysteine ligase bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase CoaBC This HMM represents a bifunctional enzyme that catalyzes the second and third steps (cysteine ligation, EC 6.3.2.5, and decarboxylation, EC 4.1.1.36) in the biosynthesis of coenzyme A (CoA) from pantothenate in bacteria. In early descriptions of this flavoprotein, a ts mutation in one region of the protein appeared to cause a defect in DNA metaobolism rather than an increased need for the pantothenate precursor beta-alanine. This protein was then called dfp, for DNA/pantothenate metabolism flavoprotein. The authors responsible for detecting phosphopantothenate--cysteine ligase activity suggest renaming this bifunctional protein coaBC for its role in CoA biosynthesis. This enzyme contains the FMN cofactor, but no FAD or pyruvoyl group. The amino-terminal region contains the phosphopantothenoylcysteine decarboxylase activity. TIGR00524.1 TIGR00524 eIF-2B_rel 185.85 185.85 303 subfamily Y Y N S-methyl-5-thioribose-1-phosphate isomerase 5.3.1.23 GO:0009058 15215245,17690466,9520434 131567 cellular organisms no rank 33789 JCVI eIF-2B alpha/beta/delta-related uncharacterized proteins S-methyl-5-thioribose-1-phosphate isomerase This HMM, eIF-2B_rel, describes half of a superfamily, where the other half consists of eukaryotic translation initiation factor 2B (eIF-2B) subunits alpha, beta, and delta. It is unclear whether the eIF-2B_rel set is monophyletic, or whether they are all more closely related to each other than to any eIF-2B subunit because the eIF-2B clade is highly derived. Members of this branch of the family are all uncharacterized with respect to function and are found in the Archaea, Bacteria, and Eukarya, although a number are described as putative translation intiation factor components. Proteins found by eIF-2B_rel include at least three clades, including a set of uncharacterized eukaryotic proteins, a set found in some but not all Archaea, and a set universal so far among the Archaea and closely related to several uncharacterized bacterial proteins. TIGR00525.1 TIGR00525 folB 72.15 72.15 116 equivalog Y Y N dihydroneopterin aldolase folB 4.1.2.25 GO:0004150,GO:0006760 9651328 131567 cellular organisms no rank 39739 JCVI dihydroneopterin aldolase dihydroneopterin aldolase This model describes a bacterial dihydroneopterin aldolase, shown to form homo-octamers in E. coli. The equivalent activity is catalyzed by domains of larger folate biosynthesis proteins in other systems. The closely related parologous enzyme in E. coli, dihydroneopterin triphosphate epimerase, which is also homo-octameric, and dihydroneopterin aldolase domains of larger proteins, score below the trusted cutoff but may score well above the noise cutoff. TIGR00526.1 TIGR00526 folB_dom 45.05 45.05 122 domain Y Y N FolB domain-containing protein GO:0004150,GO:0006760 9651328,9709001 131567 cellular organisms no rank 50898 JCVI FolB domain FolB domain Two paralogous genes of E. coli, folB (dihydroneopterin aldolase) and folX (d-erythro-7,8-dihydroneopterin triphosphate epimerase) are homologous to each other and homo-octameric. In Pneumocystis carinii, a multifunctional enzyme of folate synthesis has an N-terminal region active as dihydroneopterin aldolase. This region consists of two tandem sequences each homologous to folB and forms tetramers. TIGR00527.1 TIGR00527 gcvH 115.85 115.85 129 equivalog Y Y N glycine cleavage system protein GcvH gcvH GO:0005960,GO:0019464 131567 cellular organisms no rank 45082 JCVI glycine cleavage system H protein glycine cleavage system protein GcvH This model represents the glycine cleavage system H protein, which shuttles the methylamine group of glycine from the P protein to the T protein. The mature protein is about 130 residues long and contains a lipoyl group covalently bound to a conserved Lys residue. The genome of Aquifex aeolicus contains one protein scoring above the trusted cutoff and clustering with other bacterial H proteins, and four more proteins clustering together and scoring below the trusted cutoff; it seems doubtful that all of these homologs are authentic H protein. The Chlamydial homolog of H protein is nearly as divergent as the Aquifex outgroup, is not accompanied by P and T proteins, is not included in the seed alignment, and consequently also scores below the trusted cutoff. TIGR00528.1 TIGR00528 gcvT 235.85 235.85 362 equivalog Y Y N glycine cleavage system aminomethyltransferase GcvT gcvT 2.1.2.10 GO:0004047,GO:0005737,GO:0019464 131567 cellular organisms no rank 63885 JCVI glycine cleavage system T protein glycine cleavage system aminomethyltransferase GcvT The glycine cleavage system T protein (GcvT) is also known as aminomethyltransferase (EC 2.1.2.10). It works with the H protein (GcvH), the P protein (GcvP), and lipoamide dehydrogenase. The reported sequence of the member from Aquifex aeolicus starts about 50 residues downstream of the start of other members of the family (perhaps in error); it scores below the trusted cutoff. Eukaryotic forms are mitochondrial and have an N-terminal transit peptide. TIGR00529.1 TIGR00529 AF0261 378.4 378.4 387 hypoth_equivalog Y Y N TIGR00529 family membrane protein 131567 cellular organisms no rank 61 JCVI integral membrane protein, TIGR00529 family TIGR00529 family membrane protein This protein is predicted to have 10 transmembrane regions. Members of this family are found so far in the Archaea (Archaeoglobus fulgidus and Pyrococcus horikoshii) and in a bacterial thermophile, Thermotoga maritima. In Pyrococcus, the gene is located between nadA and nadB, two components of an enzyme involved in de novo synthesis of NAD. By PSI-BLAST, this family shows similarity (but not necessarily homology) to gluconate permease and other transport proteins. TIGR00532.1 TIGR00532 HMG_CoA_R_NAD 259.95 259.95 395 equivalog Y Y N hydroxymethylglutaryl-CoA reductase, degradative 1.1.1.88 GO:0004420,GO:0015936,GO:0016616 2656635 131567 cellular organisms no rank 14052 JCVI hydroxymethylglutaryl-CoA reductase, degradative hydroxymethylglutaryl-CoA reductase, degradative Most known examples of hydroxymethylglutaryl-CoA reductase are NADP-dependent (EC 1.1.1.34) from eukaryotes and archaea, involved in the biosynthesis of mevalonate from 3-hydroxy-3-methylglutaryl-CoA. This model, in contrast, is built from the two examples in completed genomes of sequences closely related to the degradative, NAD-dependent hydroxymethylglutaryl-CoA reductase of Pseudomonas mevalonii, a bacterium that can use mevalonate as its sole carbon source. TIGR00533.1 TIGR00533 HMG_CoA_R_NADP 441.8 441.8 402 equivalog_domain Y Y N hydroxymethylglutaryl-CoA reductase (NADPH) hmgA 1.1.1.34 GO:0004420,GO:0005515,GO:0008299 131567 cellular organisms no rank 1264 JCVI hydroxymethylglutaryl-CoA reductase (NADPH) hydroxymethylglutaryl-CoA reductase (NADPH) This model represents archaeal examples of the enzyme hydroxymethylglutaryl-CoA reductase (NADP) (EC 1.1.1.34) and the catalytic domain of eukaryotic examples, which also contain a hydrophobic N-terminal domain. This enzyme synthesizes mevalonate, a precursor of isopentenyl pyrophosphate (IPP), a building block for the synthesis of cholesterol, isoprenoids, and other molecules. A related hydroxymethylglutaryl-CoA reductase, typified by an example from Pseudomonas mevalonii, is NAD-dependent and catabolic. TIGR00537.1 TIGR00537 hemK_rel_arch 87 87 179 hypoth_equivalog Y Y N HemK2/MTQ2 family protein methyltransferase 2.1.1.- GO:0008168 18539146,35621100 131567 cellular organisms no rank 9017 JCVI putative methylase HemK2/MTQ2 family protein methyltransferase Members of this family include the eukaryotic methyltransferase HemK2, which methylates translation termination factor eRF1, and archaeal homologs that may be similar in function. TIGR00543.1 TIGR00543 isochor_syn 224.75 224.75 349 subfamily Y Y N isochorismate synthase 5.4.4.2 GO:0005737,GO:0008909,GO:0009234 9795253 131567 cellular organisms no rank 47447 JCVI isochorismate synthase isochorismate synthase This enzyme interconverts chorismate and isochorismate. In E. coli, different loci encode isochorismate synthases for the pathways of menaquinone biosynthesis and enterobactin biosynthesis (via salicilate) and fail to complement each other. Among isochorismate synthases, the N-terminal domain is poorly conserved. TIGR00549.1 TIGR00549 mevalon_kin 163.05 163.05 276 equivalog Y Y N mevalonate kinase mvk 2.7.1.36 GO:0004496,GO:0005524,GO:0005737,GO:0016126,GO:0019287 10497066,12384294 131567 cellular organisms no rank 9349 JCVI mevalonate kinase mevalonate kinase This model represents mevalonate kinase, the third step in the mevalonate pathway of isopentanyl pyrophosphate (IPP) biosynthesis [1]. IPP is a common intermediate for a number of pathways including cholesterol biosynthesis. This model covers enzymes from eukaryotes, archaea and bacteria. The related enzyme from the same pathway, phosphmevalonate kinase, serves as an outgroup for this clade. Paracoccus exhibits two genes within the phosphomevalonate/mevalonate kinase family, one of which falls between trusted and noise cutoffs of this model. The degree of divergence is high, but if the trees created from this model are correct, the proper names of these genes have been swapped [2]. TIGR00550.1 TIGR00550 nadA 262.9 262.9 309 equivalog Y Y N quinolinate synthase nadA 2.5.1.72 GO:0008987,GO:0019363 131567 cellular organisms no rank 54795 JCVI quinolinate synthetase complex, A subunit quinolinate synthase This protein, termed NadA, plays a role in the synthesis of pyridine, a precursor to NAD. The quinolinate synthetase complex consists of A protein (this protein) and B protein. B protein converts L-aspartate to iminoaspartate, an unstable reaction product which in the absence of A protein is spontaneously hydrolyzed to form oxaloacetate. The A protein, NadA, converts iminoaspartate to quinolate. TIGR00551.1 TIGR00551 nadB 452.75 452.75 489 equivalog Y Y N L-aspartate oxidase nadB 1.4.3.16 GO:0008734,GO:0009435 131567 cellular organisms no rank 50293 JCVI L-aspartate oxidase L-aspartate oxidase L-aspartate oxidase is the B protein, NadB, of the quinolinate synthetase complex. Quinolinate synthetase makes a precursor of the pyridine nucleotide portion of NAD. This model identifies proteins that cluster as L-aspartate oxidase (a flavoprotein difficult to separate from the set of closely related flavoprotein subunits of succinate dehydrogenase and fumarate reductase) by both UPGMA and neighbor-joining trees. The most distant protein accepted as an L-aspartate oxidase (NadB), that from Pyrococcus horikoshii, not only clusters with other NadB but is just one gene away from NadA. TIGR00552.1 TIGR00552 nadE 63.65 63.65 251 equivalog_domain Y Y N NAD(+) synthase nadE 6.3.1.5 GO:0005737,GO:0008795,GO:0009435 9620974 131567 cellular organisms no rank 85144 JCVI NAD+ synthetase NAD(+) synthase NAD+ synthetase is a nearly ubiquitous enzyme for the final step in the biosynthesis of the essensial cofactor NAD. The member of this family from Bacillus subtilis is a strictly NH(3)-dependent NAD(+) synthetase of 272 amino acids. Proteins consisting only of the domain modeled here may be named as NH3-dependent NAD+ synthetase. Amidotransferase activity may reside in a separate protein, or not be present. Some other members of the family, such as from Mycobacterium tuberculosis, are considerably longer, contain an apparent amidotransferase domain, and show glutamine-dependent as well as NH(3)-dependent activity. TIGR00554.2 TIGR00554 panK_bact 235 235 310 equivalog Y Y N type I pantothenate kinase coaA 2.7.1.33 GO:0004594,GO:0015937 7929447 131567 cellular organisms no rank 22434 JCVI pantothenate kinase type I pantothenate kinase Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model. TIGR00556.1 TIGR00556 pantethn_trn 45.35 45.35 128 domain Y N N phosphopantetheine--protein transferase domain GO:0000287,GO:0006633,GO:0008897 131567 cellular organisms no rank 47931 JCVI phosphopantetheine--protein transferase domain phosphopantetheine--protein transferase domain This HMM models a domain active in transferring the phophopantetheine prosthetic group to its attachment site on enzymes and carrier proteins. Many members of this family are small proteins that act on the acyl carrier protein involved in fatty acid biosynthesis. Some members are domains of larger proteins involved specialized pathways for the synthesis of unusual molecules including polyketides, atypical fatty acids, and antibiotics. TIGR00557.1 TIGR00557 pdxA 290.35 290.35 320 equivalog Y Y N 4-hydroxythreonine-4-phosphate dehydrogenase PdxA pdxA 1.1.1.262 GO:0008615,GO:0050570 10225425 131567 cellular organisms no rank 53135 JCVI 4-hydroxythreonine-4-phosphate dehydrogenase PdxA 4-hydroxythreonine-4-phosphate dehydrogenase PdxA This HMM represents PdxA, an NAD+-dependent 4-hydroxythreonine 4-phosphate dehydrogenase (EC 1.1.1.262) active in pyridoxal phosphate biosynthesis. TIGR00558.3 TIGR00558 pdxH 180 180 190 equivalog Y Y N pyridoxamine 5'-phosphate oxidase pdxH 1.4.3.5 GO:0004733,GO:0008615,GO:0010181 9693059 131567 cellular organisms no rank 41676 JCVI pyridoxamine 5'-phosphate oxidase pyridoxamine 5'-phosphate oxidase This HMM is similar to Pyridox_oxidase from PFAM but is designed to find only true pyridoxamine-phosphate oxidase and to ignore the related protein PhzG involved in phenazine biosynthesis. This protein from E. coli was characterized as a homodimer with two FMN per dimer. TIGR00560.1 TIGR00560 pgsA 109.1 109.1 183 equivalog Y Y N CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase pgsA 2.7.8.5 GO:0008444,GO:0008654,GO:0016020 131567 cellular organisms no rank 46298 JCVI CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase Alternate names: phosphatidylglycerophosphate synthase; glycerophosphate phosphatidyltransferase; PGP synthase. A number of related enzymes are quite similar in both sequence and catalytic activity, including Saccharamyces cerevisiae YDL142c, now known to be a cardiolipin synthase. There may be problems with incorrect transitive annotation of near homologs as authentic CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase. TIGR00562.1 TIGR00562 proto_IX_ox 97.85 97.85 470 equivalog Y Y N protoporphyrinogen oxidase hemG 1.3.3.4 GO:0004729,GO:0006779 7713909,8621563,9784236 131567 cellular organisms no rank 28688 JCVI protoporphyrinogen oxidase protoporphyrinogen oxidase This enzyme oxidizes protoporphyrinogen IX to protoporphyrin IX, a precursor of heme and chlorophyll. Bacillus subtilis HemY also has coproporphyrinogen III to coproporphyrin III oxidase activity in a heterologous expression system, although the role for this activity in vivo is unclear. This protein is a flavoprotein and has a beta-alpha-beta dinucleotide binding motif near the amino end. TIGR00564.1 TIGR00564 trpE_most 517.7 517.7 455 equivalog Y Y N anthranilate synthase component I trpE 4.1.3.27 GO:0000162,GO:0004049 131567 cellular organisms no rank 40218 JCVI anthranilate synthase component I anthranilate synthase component I This enzyme resembles some other chorismate-binding enzymes, including para-aminobenzoate synthase (pabB) and isochorismate synthase. There is a fairly deep split between two sets, seen in the pattern of gaps as well as in amino acid sequence differences. Archaeal enzymes have been excluded from this model (and are now found in TIGR01820) as have a clade of enzymes which constitute a TrpE paralog which may have PabB activity (TIGR01824). This allows the B. subtilus paralog which has been shown to have PabB activity to score below trusted to this model. This model contains sequences from gram-positive bacteria, certain proteobacteria, cyanobacteria, plants, fungi and assorted other bacteria. A second family of TrpE enzymes is modelled by TIGR00565. The breaking of the TrpE family into these diverse models allows for the separation of the models for the related enzyme, PabB. TIGR00566.1 TIGR00566 trpG_papA 121.05 121.05 192 subfamily Y N N glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase GO:0016884 131567 cellular organisms no rank 83354 JCVI glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase This HMM describes the glutamine amidotransferase domain or peptide of the tryptophan-biosynthetic pathway enzyme anthranilate synthase or of the folate biosynthetic pathway enzyme para-aminobenzoate synthase. In at least one case, a single polypeptide from Bacillus subtilis was shown to have both functions. This model covers a subset of the sequences described by the PFAM HMM GATase. TIGR00567.1 TIGR00567 3mg 116.35 116.35 192 subfamily Y Y N DNA-3-methyladenine glycosylase GO:0003677,GO:0003905,GO:0006284 131567 cellular organisms no rank 31995 JCVI DNA-3-methyladenine glycosylase DNA-3-methyladenine glycosylase This families are based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). All proteins in this family for which the function is known are involved in the base excision repair of alkylation damage to DNA. The exact specificty of the type of alkylation damage repaired by each of these varies somewhat between species. Substrates include 3-methyl adenine, 7-methyl-guanaine, and 3-methyl-guanine. TIGR00571.1 TIGR00571 dam 114.85 114.85 267 subfamily Y Y N Dam family site-specific DNA-(adenine-N6)-methyltransferase 2.1.1.72 GO:0009007,GO:0009307 131567 cellular organisms no rank 27964 JCVI DNA adenine methylase Dam family site-specific DNA-(adenine-N6)-methyltransferase All proteins in this family for which functions are known are DNA-adenine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The DNA adenine methylase (dam) of E. coli and related species is instrumental in distinguishing the newly synthesized strand during DNA replication for methylation-directed mismatch repair. This family includes several phage methylases and a number of different restriction enzyme chromosomal site-specific modification systems. TIGR00573.1 TIGR00573 dnaq 71.5 71.5 217 subfamily_domain Y N N exonuclease, DNA polymerase III, epsilon subunit family GO:0003677,GO:0003887,GO:0006260 131567 cellular organisms no rank 111098 JCVI exonuclease, DNA polymerase III, epsilon subunit family exonuclease, DNA polymerase III, epsilon subunit family All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00574.1 TIGR00574 dnl1 217.8 217.8 527 superfamily Y Y N ATP-dependent DNA ligase 6.5.1.1 GO:0003910,GO:0005524,GO:0071897 131567 cellular organisms no rank 14510 JCVI DNA ligase I, ATP-dependent (dnl1) ATP-dependent DNA ligase All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00575.1 TIGR00575 dnlj 444.45 444.45 652 equivalog Y Y N NAD-dependent DNA ligase LigA ligA 6.5.1.2 GO:0003911,GO:0006260,GO:0006281,GO:0006310 131567 cellular organisms no rank 99184 JCVI DNA ligase, NAD-dependent DNA ligase (NAD(+)) LigA All proteins in this family with known functions are NAD-dependent DNA ligases. Functions of these proteins include DNA repair, DNA replication, and DNA recombination. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (PF00533) at the C-terminus. It is included in the seed. TIGR00576.1 TIGR00576 dut 102.55 102.55 143 superfamily Y Y N dUTP diphosphatase dut 3.6.1.23 GO:0000287,GO:0004170,GO:0006226,GO:0046081 1311056,14724274,17452782 131567 cellular organisms no rank 43820 JCVI dUTP diphosphatase dUTP diphosphatase The main function of these proteins is in maintaining the levels of dUTP in the cell to prevent dUTP incorporation into DNA during DNA replication. The enzyme occurs in bacteria, viruses including prophage regions, and eukaryotes. TIGR00577.1 TIGR00577 fpg 203.3 203.3 276 equivalog Y Y N DNA-formamidopyrimidine glycosylase mutM 3.2.2.23 GO:0005737,GO:0006281,GO:0008534,GO:0046872 19496823 131567 cellular organisms no rank 57464 JCVI DNA-formamidopyrimidine glycosylase DNA-formamidopyrimidine glycosylase All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00581.1 TIGR00581 moaC 141.5 141.5 148 equivalog Y Y N cyclic pyranopterin monophosphate synthase MoaC moaC 4.6.1.17 GO:0006777,GO:0061799 7890743 131567 cellular organisms no rank 48410 JCVI molybdenum cofactor biosynthesis protein C cyclic pyranopterin monophosphate synthase MoaC MoaC catalyzes an early step in molybdenum cofactor biosynthesis in E. coli. The Arabidopsis homolog Cnx3 complements MoaC deficiency in E. coli (MUID:95197640). Eukarotic members of this family branch within the bacterial branch, with the archaeal members as an apparent outgroup. This protein is absent in a number of the pathogens with smaller genomes, including Mycoplasmas, Chlamydias, and spirochetes, but is found in most other complete genomes to date. The homolog form Synechocystis sp. is fused to a MobA-homologous region and is an outlier to all other bacterial forms by both neighbor-joining and UPGMA analyses. Members of this family are well-conserved. The seed for this model excludes both archaeal sequences and the most divergent bacterial sequences, but still finds all candidate MoaC sequences easily between trusted and noise cutoffs. We suggest that sequences branching outside the set that contains all seed members be regarded only as putative functional equivalents of MoaC unless and until a member of the archaeal outgroup is shown to have equivalent function. TIGR00585.2 TIGR00585 mutl 180 180 555 equivalog Y Y N DNA mismatch repair endonuclease MutL mutL GO:0005524,GO:0006298,GO:0016887,GO:0030983 26283381 131567 cellular organisms no rank 73622 JCVI DNA mismatch repair protein MutL DNA mismatch repair endonuclease MutL All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00587.1 TIGR00587 nfo 129.65 129.65 279 subfamily Y Y N deoxyribonuclease IV 3.1.21.2 GO:0003677,GO:0006281,GO:0008270 131567 cellular organisms no rank 32593 JCVI apurinic endonuclease (APN1) deoxyribonuclease IV Deoxyribonuclease IV is a DNA repair enzyme that cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites). Members of this family include the AP endodeoxyribonucleases Nfo of Escherichia coli and Apn1 of yeast. TIGR00589.1 TIGR00589 ogt 46.4 46.4 80 superfamily Y Y N methylated-DNA--[protein]-cysteine S-methyltransferase 2.1.1.63 GO:0003908,GO:0006281 131567 cellular organisms no rank 141740 JCVI methylated-DNA--[protein]-cysteine S-methyltransferase methylated-DNA--[protein]-cysteine S-methyltransferase All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00590.1 TIGR00590 pcna 99.1 99.1 259 equivalog Y Y N proliferating cell nuclear antigen (pcna) pcn GO:0003677,GO:0006275,GO:0030337 131567 cellular organisms no rank 438 JCVI proliferating cell nuclear antigen (pcna) proliferating cell nuclear antigen (pcna) All proteins in this family for which functions are known form sliding DNA clamps that are used in DNA replication processes. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00591.1 TIGR00591 phr2 550.05 550.05 453 superfamily Y Y N deoxyribodipyrimidine photo-lyase phrB 4.1.99.3 GO:0003904,GO:0006281 131567 cellular organisms no rank 301 JCVI deoxyribodipyrimidine photolyase deoxyribodipyrimidine photo-lyase All proteins in this family for which functions are known are DNA-photolyases used for the direct repair of UV irradiation induced DNA damage. Some repair 6-4 photoproducts while others repair cyclobutane pyrimidine dimers. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00592.1 TIGR00592 pol2 239.95 239.95 1176 superfamily Y N N DNA polymerase (pol2) 131567 cellular organisms no rank 292 JCVI DNA polymerase (pol2) DNA polymerase (pol2) All proteins in this superfamily for which functions are known are DNA polymerases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00593.1 TIGR00593 pola 600 600 890 equivalog Y Y N DNA polymerase I polA 2.7.7.7 GO:0003887,GO:0006260 131567 cellular organisms no rank 95705 JCVI DNA polymerase I DNA polymerase I All proteins in this family for which functions are known are DNA polymerases Many also have an exonuclease motif. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00608.1 TIGR00608 radc 133.85 133.85 218 superfamily Y Y N DNA repair protein RadC radC GO:0006281 131567 cellular organisms no rank 61123 JCVI DNA repair protein RadC DNA repair protein RadC The genes in this family for which the functions are known have an as yet porrly defined role in determining sensitivity to DNA damaging agents such as UV irradiation. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00611.2 TIGR00611 recf 172 172 339 equivalog Y Y N DNA replication/repair protein RecF recF GO:0003697,GO:0005524,GO:0006260,GO:0006281,GO:0006310,GO:0009432 15186413,19451222,26874520,37081315,37125644 131567 cellular organisms no rank 60369 JCVI DNA replication and repair protein RecF DNA replication/repair protein RecF RecF forms a complex with RecO and RecR to form a complex with roles in both DNA repair and DNA replication. All proteins in this family for which functions are known are DNA-binding proteins that assist the filamentation of RecA onto DNA for the initiation of recombination or recombinational repair. TIGR00614.1 TIGR00614 recQ_fam 219.8 219.8 470 subfamily Y Y N RecQ family ATP-dependent DNA helicase 3.6.4.12 GO:0004386,GO:0006310 131567 cellular organisms no rank 117697 JCVI ATP-dependent DNA helicase, RecQ family RecQ family ATP-dependent DNA helicase All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00619.1 TIGR00619 sbcd 77.65 77.65 252 subfamily Y Y N exonuclease subunit SbcD sbcD 3.1.11.- GO:0004527,GO:0006260,GO:0006310 131567 cellular organisms no rank 54681 JCVI exonuclease SbcCD, D subunit exonuclease subunit SbcD All proteins in this family for which functions are known are double-stranded DNA exonuclease (as part of a complex with SbcC homologs). This complex functions in the initiation of recombination and recombinational repair and is particularly important in regulating the stability of DNA sections that can form secondary structures. This family is likely homologous to the MRE11 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00621.2 TIGR00621 ssb 53.95 53.95 165 subfamily Y Y N single-stranded DNA-binding protein ssb GO:0003697,GO:0006260,GO:0006281,GO:0006310,GO:0006351 131567 cellular organisms no rank 108994 JCVI single-stranded DNA-binding protein single-stranded DNA-binding protein All proteins in this family for which functions are known are single-stranded DNA binding proteins that function in many processes including transcription, repair, replication and recombination. Members encoded between genes for ribosomal proteins S6 and S18 should be annotated as primosomal protein N (PriB). Forms in gamma-protoeobacteria are much shorter and poorly recognized by this model. Additional members of this family include phage proteins. Eukaryotic members are organellar proteins. TIGR00624.1 TIGR00624 tag 232.5 232.5 179 subfamily Y Y N DNA-3-methyladenine glycosylase I tag 3.2.2.20 GO:0006284,GO:0008725 131567 cellular organisms no rank 26052 JCVI DNA-3-methyladenine glycosylase I DNA-3-methyladenine glycosylase I All proteins in this family are alkylation DNA glycosylases that function in base excision repair This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00628.1 TIGR00628 ung 185.75 185.75 210 equivalog Y Y N uracil-DNA glycosylase ung 3.2.2.27 GO:0004844,GO:0006281,GO:0006284 131567 cellular organisms no rank 53421 JCVI uracil-DNA glycosylase uracil-DNA glycosylase All proteins in this family for which functions are known are uracil-DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00629.1 TIGR00629 uvde 124.45 124.45 312 equivalog Y Y N UV DNA damage repair endonuclease UvsE uvsE GO:0004518,GO:0006281,GO:0009650 11807060,8614629 131567 cellular organisms no rank 8951 JCVI UV damage endonuclease UvdE UV DNA damage repair endonuclease UvsE All proteins in this family for which functions are known are UV dimer endonucleases that function in an alternative nucleotide excision repair process. TIGR00630.1 TIGR00630 uvra 729.8 729.8 924 equivalog Y Y N excinuclease ABC subunit UvrA uvrA GO:0003677,GO:0006289,GO:0009380,GO:0016887 131567 cellular organisms no rank 107182 JCVI excinuclease ABC subunit A excinuclease ABC subunit UvrA This family is a member of the ABC transporter superfamily of proteins of which all members for which functions are known except the UvrA proteins are involved in the transport of material through membranes. UvrA orthologs are involved in the recognition of DNA damage as a step in nucleotide excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00631.1 TIGR00631 uvrb 750.1 750.1 658 equivalog Y Y N excinuclease ABC subunit UvrB uvrB GO:0003677,GO:0005524,GO:0006289,GO:0009380,GO:0016887 131567 cellular organisms no rank 75655 JCVI excinuclease ABC subunit B excinuclease ABC subunit UvrB All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) TIGR00632.1 TIGR00632 vsr 97.85 97.85 119 subfamily Y Y N DNA mismatch endonuclease Vsr vsr GO:0004520,GO:0006298 20511499,2198248 131567 cellular organisms no rank 29579 JCVI DNA mismatch endonuclease Vsr DNA mismatch endonuclease Vsr All proteins in this family for which functions are known are G:T mismatch endonucleases that function in a specialized mismatch repair process used usually to repair G:T mismatches in specific sections of the genome. This family was based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Members of this family typically are found near to a DNA cytosine methyltransferase. TIGR00633.1 TIGR00633 xth 99.05 99.05 255 equivalog Y Y N exodeoxyribonuclease III 3.1.11.2 GO:0004518,GO:0006281 10540738,16936028,17012282 131567 cellular organisms no rank 103287 JCVI exodeoxyribonuclease III (xth) exodeoxyribonuclease III All proteins in this family for which functions are known are 5' AP endonucleases that function in base excision repair and the repair of abasic sites in DNA. Note that the member from Methanothermobacter thermautotrophicus functions additionally as a DNA uridine endonuclease. This family derived from the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00635.1 TIGR00635 ruvB 299.05 299.05 305 equivalog Y Y N Holliday junction branch migration DNA helicase RuvB ruvB 3.6.4.12 GO:0003677,GO:0005524,GO:0006281,GO:0006310,GO:0009378 9442895 131567 cellular organisms no rank 55351 JCVI Holliday junction DNA helicase RuvB Holliday junction DNA helicase RuvB All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. TIGR00636.1 TIGR00636 PduO_Nterm 108.45 108.45 171 equivalog_domain Y Y N cob(I)yrinic acid a,c-diamide adenosyltransferase 2.5.1.17 GO:0008817,GO:0009236 11160088,15687219 131567 cellular organisms no rank 45061 JCVI ATP:cob(I)alamin adenosyltransferase cob(I)yrinic acid a,c-diamide adenosyltransferase This HMM represents as ATP:cob(I)alamin adenosyltransferase family corresponding to the N-terminal half of Salmonella PduO, a 1,2-propanediol utilization protein that probably is bifunctional. PduO represents one of at least three families of ATP:corrinoid adenosyltransferase: others are CobA (which partially complements PduO) and EutT. It was not clear originally whether ATP:cob(I)alamin adenosyltransferase activity resides in the N-terminal region of PduO, modeled here, but this has now become clear from the characterization of MeaD from Methylobacterium extorquens. TIGR00638.1 TIGR00638 Mop 55 55 70 subfamily_domain Y N N molybdenum-pterin binding domain GO:0015689 2820842,8491722 131567 cellular organisms no rank 32280 JCVI molybdenum-pterin binding domain molybdenum-pterin binding domain This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins. TIGR00639.1 TIGR00639 PurN 150.1 150.1 192 equivalog Y Y N phosphoribosylglycinamide formyltransferase purN 2.1.2.2 GO:0004644,GO:0006189 3301838 131567 cellular organisms no rank 62009 JCVI phosphoribosylglycinamide formyltransferase phosphoribosylglycinamide formyltransferase This HMM describes phosphoribosylglycinamide formyltransferase (GAR transformylase), one of several proteins in formyl_transf (Pfam family PF00551). This enzyme uses formyl tetrahydrofolate as a formyl group donor to produce 5'-phosphoribosyl-N-formylglycinamide. PurT, a different GAR transformylase, uses ATP and formate rather than formyl tetrahydrofolate. Experimental proof includes complementation of E. coli purN mutants by orthologs from vertebrates (where it is a domain of a multifunctional protein), Bacillus subtilis, and Arabidopsis. No archaeal example was detected. In phylogenetic analyses, the member from Saccharomyces cerevisiae shows a long branch length but membership in the family, while the formyltetrahydrofolate deformylases form a closely related outgroup. TIGR00640.1 TIGR00640 acid_CoA_mut_C 57.45 57.45 132 subfamily_domain Y N N methylmalonyl-CoA mutase C-terminal domain GO:0016853 9242908 131567 cellular organisms no rank 54285 JCVI methylmalonyl-CoA mutase C-terminal domain methylmalonyl-CoA mutase C-terminal domain Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This HMM describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2. TIGR00641.1 TIGR00641 acid_CoA_mut_N 303.8 303.8 528 subfamily_domain Y N N methylmalonyl-CoA mutase N-terminal domain GO:0004494,GO:0031419 8868443,9242908,9497386 131567 cellular organisms no rank 69461 JCVI methylmalonyl-CoA mutase N-terminal domain methylmalonyl-CoA mutase N-terminal domain Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 abd AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This HMM describes the N-terminal domain subfamily. In a neighbor-joining tree, AF2215 branches with a bacterial isobutyryl-CoA mutase, which is also the same length. Scoring between the noise and trusted cutoffs are the non-catalytic, partially homologous beta chains from certain heterodimeric examples of 5.4.99.2. TIGR00643.1 TIGR00643 recG 659.4 659.4 629 equivalog Y Y N ATP-dependent DNA helicase RecG recG 3.6.4.12 GO:0003678,GO:0006281,GO:0006310 131567 cellular organisms no rank 64692 JCVI ATP-dependent DNA helicase RecG ATP-dependent DNA helicase RecG TIGR00645.1 TIGR00645 HI0507 144.4 144.4 167 hypoth_equivalog Y Y N TIGR00645 family protein 131567 cellular organisms no rank 10775 JCVI TIGR00645 family protein TIGR00645 family protein This conserved hypothetical protein with four predicted transmembrane regions includes uncharacterized proteins such as YqhA from Escherchia coli K-12, HI0507 and HP0189 from Haemophilus influenzae, and VC0208 from Vibrio cholerae. TIGR00649.1 TIGR00649 MG423 400 400 546 subfamily Y Y N RNase J family beta-CASP ribonuclease GO:0003723,GO:0008270,GO:0046872 15831787,23403287 131567 cellular organisms no rank 47347 JCVI beta-CASP ribonuclease, RNase J family RNase J family beta-CASP ribonuclease This family of metalloenzymes includes RNase J1 and RNase J2, involved in mRNA degradation in a wide range of organism. TIGR00651.1 TIGR00651 pta 311.2 311.2 304 equivalog Y Y N phosphate acetyltransferase pta 2.3.1.8 GO:0006086,GO:0008959 131567 cellular organisms no rank 47311 JCVI phosphate acetyltransferase phosphate acetyltransferase Alternate name: phosphotransacetylase Model contains a gene from E.coli coding for ethanolamine utilization protein (euti) and also contains similarity to malate oxidoreductases TIGR00652.1 TIGR00652 DapF 114.65 114.65 270 equivalog Y Y N diaminopimelate epimerase dapF 5.1.1.7 GO:0008837,GO:0009089 10194362,18269631,23426375 131567 cellular organisms no rank 70239 JCVI diaminopimelate epimerase diaminopimelate epimerase TIGR00653.1 TIGR00653 GlnA 429.15 429.15 462 equivalog Y Y N type I glutamate--ammonia ligase glnA 6.3.1.2 GO:0004356,GO:0006542 7700148,9865608 131567 cellular organisms no rank 50275 JCVI glutamine synthetase, type I glutamine synthetase, type I Alternate name: glutamate--ammonia ligase. This model represents the dodecameric form, which can be subdivided into 1-alpha and 1-beta forms. The phylogeny of the 1-alpha and 1-beta forms appears polyphyletic. E. coli, Synechocystis PCC6803, Aquifex aeolicus, and the crenarcheon Sulfolobus acidocaldarius have form 1-beta, while Bacillus subtilis, Thermotoga maritima, and various euryarchaea has form 1-alpha. The 1-beta dodecamer from the crenarcheon Sulfolobus acidocaldarius differs from that in E. coli in that it is not regulated by adenylylation. TIGR00654.1 TIGR00654 PhzF_family 76.2 76.2 298 subfamily Y Y N PhzF family phenazine biosynthesis isomerase GO:0003824,GO:0009058 28740244,8586283 131567 cellular organisms no rank 88302 JCVI phenazine biosynthesis protein, PhzF family PhzF family phenazine biosynthesis isomerase Members of this family show a distant global similarity to diaminopimelate epimerases, which can be taken as the outgroup. One member of this family has been shown to act as an enzyme in the biosynthesis of the antibiotic phenazine in Pseudomonas aureofaciens. The function in other species is unclear. TIGR00656.1 TIGR00656 asp_kin_monofn 402.25 402.25 407 equivalog Y Y N aspartate kinase, monofunctional class 2.7.2.4 GO:0004072,GO:0009089 131567 cellular organisms no rank 40587 JCVI aspartate kinase, monofunctional class aspartate kinase, monofunctional class This model describes a subclass of aspartate kinases. These are mostly Lys-sensitive and not fused to homoserine dehydrogenase, unlike some Thr-sensitive and Met-sensitive forms. Homoserine dehydrogenase is part of Thr and Met but not Lys biosynthetic pathways. Aspartate kinase catalyzes a first step in the biosynthesis from Asp of Lys (and its precursor diaminopimelate), Met, and Thr. In E. coli, a distinct isozyme is inhibited by each of the three amino acid products. The Met-sensitive (I) and Thr-sensitive (II) forms are bifunctional enzymes fused to homoserine dehydrogenases and form homotetramers, while the Lys-sensitive form (III) is a monofunctional homodimer. The Lys-sensitive enzyme of Bacillus subtilis resembles the E. coli form but is an alpha 2/beta 2 heterotetramer, where the beta subunit is translated from an in-phase alternative initiator at Met-246. The protein slr0657 from Synechocystis PCC6803 is extended by a duplication of the C-terminal region corresponding to the beta chain. Incorporation of a second copy of the C-terminal domain may be quite common in this subgroup of aspartokinases. TIGR00657.1 TIGR00657 asp_kinases 208.7 208.7 442 subfamily_domain Y Y N aspartate kinase 2.7.2.4 GO:0004072,GO:0008652 131567 cellular organisms no rank 105337 JCVI aspartate kinase aspartate kinase Aspartate kinase catalyzes a first step in the biosynthesis from Asp of Lys (and its precursor diaminopimelate), Met, and Thr. Prokaryotic genomes frequently encode multiple aspartate kinases. In E. coli, a distinct isozyme is inhibited by each of the three amino acid products. The Met-sensitive (I) and Thr-sensitive (II) forms are bifunctional enzymes fused to homoserine dehydrogenases and form homotetramers, while the Lys-sensitive form (III) is a monofunctional homodimer. TIGR00658.1 TIGR00658 orni_carb_tr 280.85 280.85 304 equivalog Y Y N ornithine carbamoyltransferase argF 2.1.3.3 GO:0004585,GO:0042450 9501170 131567 cellular organisms no rank 67859 JCVI ornithine carbamoyltransferase ornithine carbamoyltransferase This family of ornithine carbamoyltransferases (OTCase) is in a superfamily with the related enzyme aspartate carbamoyltransferase. Most known examples are anabolic, playing a role in arginine biosynthesis, but some are catabolic. Most OTCases are homotrimers, but the homotrimers are organized into dodecamers built from four trimers in at least two species; the catabolic OTCase of Pseudomonas aeruginosa is allosterically regulated, while OTCase of the extreme thermophile Pyrococcus furiosus shows both allostery and thermophily. TIGR00661.1 TIGR00661 MJ1255 195.9 195.9 321 subfamily Y Y N MJ1255/VC2487 family glycosyltransferase 2.4.-.- GO:0016757 15664940 131567 cellular organisms no rank 4278 JCVI conserved hypothetical protein MJ1255/VC2487 family glycosyltransferase This HMM represents nearly the full length of MJ1255 from Methanococcus jannaschii and of VC2487 from Vibrio cholerae, as well as the C-terminal half of a protein from Methanobacterium thermoautotrophicum. The most closely related characterized proteins all are glycosyltransferases. VC2487 is induced during infection of mice, and its deletion attenuates infection. TIGR00663.1 TIGR00663 dnan 137.65 137.65 367 equivalog Y Y N DNA polymerase III subunit beta dnaN 2.7.7.7 GO:0003677,GO:0003887,GO:0006260,GO:0009360 21219854,30366028 131567 cellular organisms no rank 61274 JCVI DNA polymerase III, beta subunit DNA polymerase III subunit beta The beta subunit of DNA polymerase III, known also as the beta sliding clamp, forms a ring-shaped homodimer that encircles double-stranded DNA. TIGR00666.1 TIGR00666 PBP4 107.8 107.8 397 equivalog Y Y N D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase dacB 3.4.16.4 GO:0004175,GO:0009002,GO:0009252 1554361,2040429 131567 cellular organisms no rank 54206 JCVI D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase In E. coli, this protein is known as penicillin binding protein 4 (dacB). A signal sequence is cleaved from a precursor form. The protein is described as periplasmic in E. coli (Gram-negative) and extracellular in Actinomadura R39 (Gram-positive). Unlike some other proteins with similar activity, it does not form transpeptidation. It is not essential for viability. This family is related to class A beta-lactamases. TIGR00670.1 TIGR00670 asp_carb_tr 236.95 236.95 304 equivalog Y Y N aspartate carbamoyltransferase pyrB 2.1.3.2 GO:0004070,GO:0006207 8757751 131567 cellular organisms no rank 59159 JCVI aspartate carbamoyltransferase aspartate carbamoyltransferase Aspartate transcarbamylase (ATCase) is an alternate name. PyrB encodes the catalytic chain of aspartate carbamoyltransferase, an enzyme of pyrimidine biosynthesis, which organizes into trimers. In some species, including E. coli and the Archaea but excluding Bacillus subtilis, a regulatory subunit PyrI is also present in an allosterically regulated hexameric holoenzyme. Several molecular weight classes of ATCase are described in MEDLINE:96303527 and often vary within taxa. PyrB and PyrI are fused in Thermotoga maritima. Ornithine carbamoyltransferases are in the same superfamily and form an outgroup. TIGR00671.1 TIGR00671 baf 58.2 58.2 243 subfamily Y Y N type III pantothenate kinase coaX 2.7.1.33 GO:0004594,GO:0015937 17323930,7601846 131567 cellular organisms no rank 44462 JCVI pantothenate kinase, type III type III pantothenate kinase This HMM describes a family of proteins found in a single copy in at least ten different early completed bacterial genomes. The only characterized member of the family is Bvg accessory factor (Baf), a protein required, in addition to the regulatory operon bvgAS, for heterologous transcription of the Bordetella pertussis toxin operon (ptx) in E. coli. TIGR00673.1 TIGR00673 cynS 113.3 113.3 150 equivalog Y Y N cyanase cynS 4.2.1.104 GO:0008824,GO:0009439 9294430 131567 cellular organisms no rank 10428 JCVI cyanase cyanase Alternate names include cyanate C-N-lyase, cyanate hydratase, and cyanate hydrolase. TIGR00674.1 TIGR00674 dapA 206.15 206.15 286 equivalog Y Y N 4-hydroxy-tetrahydrodipicolinate synthase dapA 4.3.3.7 GO:0008840,GO:0009089 131567 cellular organisms no rank 84629 JCVI 4-hydroxy-tetrahydrodipicolinate synthase 4-hydroxy-tetrahydrodipicolinate synthase Members of this family are 4-hydroxy-tetrahydrodipicolinate synthase, previously (incorrectly) called dihydrodipicolinate synthase. It is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment. TIGR00675.1 TIGR00675 dcm 100.65 100.65 329 superfamily Y Y N DNA (cytosine-5-)-methyltransferase dcm 2.1.1.37 GO:0003886,GO:0006304 131567 cellular organisms no rank 85883 JCVI DNA (cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). TIGR00680.1 TIGR00680 kdpA 387.7 387.7 563 equivalog Y Y N potassium-transporting ATPase subunit KdpA kdpA 7.2.2.6 GO:0006813,GO:0008556,GO:0031004 17536175,28636601,32955430 131567 cellular organisms no rank 49318 JCVI K+-transporting ATPase, A subunit potassium-transporting ATPase subunit KdpA Kdp, as found in Escherichia coli, is a high affinity ATP-driven K+ transport system. It is composed of three membrane-bound subunits, KdpA, KdpB and KdpC and one small peptide, KdpF. KdpA is the K+-transporting subunit of this complex. TIGR00681.1 TIGR00681 kdpC 152.55 152.55 187 equivalog Y Y N K(+)-transporting ATPase subunit C kdpC 7.2.2.6 GO:0006813,GO:0008556,GO:0031004 9858692 131567 cellular organisms no rank 34275 JCVI K+-transporting ATPase, C subunit K(+)-transporting ATPase subunit C This chain has a single predicted transmembrane region near the amino end. It is part of a K+-transport ATPase that contains two other membrane-bound subunits, KdpA and KdpB, and a small subunit KdpF. KdpA is the K+-translocating subunit, KdpB the ATP-hydrolyzing subunit. During assembly of the complex, KdpA and KdpC bind to each other. This interaction is thought to stabilize the complex [MEDLINE:9858692]. Data indicates that KdpC might connect the KdpA, the K+-transporting subunit, to KdpB, the ATP-hydrolyzing (energy providing) subunit [MEDLINE:9858692]. TIGR00684.1 TIGR00684 narJ 59.35 59.35 152 equivalog Y Y N nitrate reductase molybdenum cofactor assembly chaperone narJ GO:0051082,GO:0051131 9632249 131567 cellular organisms no rank 23260 JCVI nitrate reductase molybdenum cofactor assembly chaperone nitrate reductase molybdenum cofactor assembly chaperone This protein is termed NarJ in most species that have a single copy, and has been called the delta subunit of nitrate reductase. However, although it is required for correct assembly of active enzyme, it dissociates and is not part of the enzyme. Two hits to this HMM are found each in E. coli and in Mycobacterium tuberculosis, but in each case duplication to create paralogs appears to be recent. The NarX protein of Mycobacterium tuberculosis includes one of these paralogs as a domain, fused to structural domains of nitrate reductases before and after the NarJ-homologous region. TIGR00685.1 TIGR00685 T6PP 68.05 68.05 250 equivalog Y Y N trehalose-phosphatase otsB 3.1.3.12 GO:0004805,GO:0005992 11701378,11851922,15158675,8045430,8444170 131567 cellular organisms no rank 34934 JCVI trehalose-phosphatase trehalose-phosphatase Trehalose, a neutral disaccharide of two glucose residues, is an important osmolyte for dessication and/or salt tolerance in a number of prokaryotic and eukaryotic species, including E. coli, Saccharomyces cerevisiae, and Arabidopsis thaliana. Many bacteria also utilize trehalose in the synthesis of trehalolipids, specialized cell wall constituents believed to be involved in the uptake of hydrophobic substances. Trehalose dimycolate (TDM, cord factor) and related substances are important constituents of the mycobacterial waxy coat and responsible for various clinically important immunological interactions with host organism [5]. This enzyme, trehalose-phosphatase, removes a phosphate group in the final step of trehalose biosynthesis. The trehalose-phosphatase from Saccharomyces cerevisiae is fused to the synthase. At least 18 distinct sequences from Arabidopsis have been identified, roughly half of these are of the fungal type, with a fused synthase and half are like the bacterial members having only the phosphatase domain. It has been suggested [3,4] that trehalose is being used in Arabidopsis as a regulatory molecule in development and possibly other processes. TIGR00689.1 TIGR00689 rpiB_lacA_lacB 88.3 88.3 145 subfamily Y Y N RpiB/LacA/LacB family sugar-phosphate isomerase GO:0005975,GO:0016853 8576032 131567 cellular organisms no rank 46875 JCVI sugar-phosphate isomerase, RpiB/LacA/LacB family RpiB/LacA/LacB family sugar-phosphate isomerase Proteins of known function in this family act as sugar (pentose and/or hexose)-phosphate isomerases, including the LacA and LacB subunits of galactose-6-phosphate isomerases from Gram-positive bacteria and RpiB. RpiB is the second ribose phosphate isomerase of E. coli. It lacks homology to RpiA, its inducer is unknown (but is not ribose), and it can be replaced by the homologous galactose-6-phosphate isomerase of Streptococcus mutans, all of which suggests that the ribose phosphate isomerase activity of RpiB is a secondary function. On the other hand, there appear to be a significant number of species which contain rpiB, lack rpiA and seem to require rpi activity in order to complete the pentose phosphate pathway. TIGR00692.1 TIGR00692 tdh 458.35 458.35 340 equivalog Y Y N L-threonine 3-dehydrogenase tdh 1.1.1.103 GO:0006567,GO:0008270,GO:0008743 9500838 131567 cellular organisms no rank 12756 JCVI L-threonine 3-dehydrogenase L-threonine 3-dehydrogenase This protein is a tetrameric, zinc-binding, NAD-dependent enzyme of threonine catabolism. Closely related proteins include sorbitol dehydrogenase, xylitol dehydrogenase, and benzyl alcohol dehydrogenase. Eukaryotic examples of this enzyme have been demonstrated experimentally but do not appear in database search results. E. coli His-90 modulates substrate specificity and is believed part of the active site. TIGR00693.1 TIGR00693 thiE 145.1 145.1 197 equivalog_domain Y Y N thiamine phosphate synthase thiE 2.5.1.3 GO:0004789,GO:0009228 9700068 131567 cellular organisms no rank 68677 JCVI thiamine-phosphate diphosphorylase thiamine phosphate synthase This model represents the thiamine-phosphate pyrophosphorylase, ThiE, of a number of bacteria, and N-terminal domains of bifunctional thiamine proteins of Saccharomyces cerevisiae and Schizosaccharomyces pombe, in which the C-terminal domain corresponds to the bacterial hydroxyethylthiazole kinase (EC 2.7.1.50), ThiM. This model includes ThiE from Bacillus subtilis but excludes its paralog, the regulatory protein TenI (SP:P25053), and neighbors of TenI. TIGR00694.1 TIGR00694 thiM 256.4 256.4 249 equivalog_domain Y Y N hydroxyethylthiazole kinase thiM 2.7.1.50 GO:0000287,GO:0004417,GO:0005524,GO:0009228 2542220,8394314 131567 cellular organisms no rank 20577 JCVI hydroxyethylthiazole kinase hydroxyethylthiazole kinase This model represents the hydoxyethylthiazole kinase, ThiM, of a number of bacteria, and C-terminal domains of bifunctional thiamine biosynthesis proteins of Saccharomyces cerevisiae and Schizosaccharomyces pombe, in which the N-terminal domain corresponds to the bacterial thiamine-phosphate pyrophosphorylase (EC 2.5.1.3), ThiE. TIGR00697.1 TIGR00697 TIGR00697 50.95 50.95 201 equivalog Y Y N queuosine precursor transporter GO:1990397 28208705 131567 cellular organisms no rank 29479 JCVI conserved hypothetical integral membrane protein queuosine precursor transporter YhhQ from Escherichia coli became the first characterized member of the TIGR00697 family of integral membrane proteins when it was shown to be able to import the queuosine precursor 7-cyano-7-deazaguanine (preQ0), and to a lesser extent 7-aminomethyl-7-deazaguanine (preQ1). The activity was suspected, prior to its experimental degradation, because this family of transporters is regularly found in bacteria that have an incomplete (salvage-only) queuosine biosynthetic pathway instead of the full biosynthetic pathway. TIGR00702.1 TIGR00702 TIGR00702 75.65 75.65 377 domain Y N N YcaO-type kinase domain GO:0016301 22522320 131567 cellular organisms no rank 28032 JCVI YcaO-type kinase domain YcaO-type kinase domain This protein family includes YcaO and homologs that can phosphorylate a peptide amide backbone (rather than side chains), as during heterocycle-forming modifications during maturation of the TOMM class (Thiazole/Oxazole-Modified Microcins) of bacteriocins. However, YcaO domain proteins also occur in contexts that do not suggest peptide modification. TIGR00703.1 TIGR00703 TIGR00703 155.4 155.4 223 hypoth_equivalog Y Y N TIGR00703 family protein 131567 cellular organisms no rank 93 JCVI TIGR00703 family protein TIGR00703 family protein The function of this family is unknown. These proteins are from 222 to 233 residues in length, lack hydrophobic stretches, and are found so far only in thermophiles. TIGR00704.1 TIGR00704 NaPi_cotrn_rel 210.1 210.1 308 hypoth_equivalog Y N N Na/Pi-cotransporter II-related protein GO:0016020 131567 cellular organisms no rank 23949 JCVI Na/Pi-cotransporter II-related protein Na/Pi-cotransporter II-related protein This HMM describes essentially the full length of an uncharacterized protein from Bacillus subtilis and correponding lengths of longer proteins from E. coli and Treponema pallidum. PSI-BLAST analysis converges to demonstrate homology to one other group of proteins, type II sodium/phosphate (Na/Pi) cotransporters. A well-conserved repeated domain in this family, approximately 60 residues in length, is also repeated in the Na/Pi cotransporters, although with greater spacing between the repeats. The two families share additional homology in the region after the first repeat, share the properly of having extensive hydrophobic regions, and may be similar in function. TIGR00706.1 TIGR00706 SppA_dom 155.45 155.45 208 equivalog_domain Y Y N signal peptide peptidase SppA sppA GO:0004252,GO:0006465 10455123 131567 cellular organisms no rank 43889 JCVI signal peptide peptidase SppA, 36K type signal peptide peptidase SppA The related but duplicated, double-length protein SppA (protease IV) of E. coli was shown experimentally to degrade signal peptides as are released by protein processing and secretion. This protein shows stronger homology to the C-terminal region of SppA than to the N-terminal domain or to the related putative protease SuhB. The member of this family from Bacillus subtilis was shown to have properties consistent with a role in degrading signal peptides after cleavage from precursor proteins, although it was not demonstrated conclusively. TIGR00707.1 TIGR00707 argD 410.05 410.05 381 subfamily Y Y N acetylornithine/succinylornithine family transaminase GO:0006525,GO:0008483 10074354,2199330,9696779 131567 cellular organisms no rank 72797 JCVI transaminase, acetylornithine/succinylornithine family acetylornithine/succinylornithine family transaminase This family of proteins, for which ornithine aminotransferases form an outgroup, consists mostly of proteins designated acetylornithine aminotransferase. However, the two very closely related members from E. coli are assigned different enzymatic activities. One is acetylornithine aminotransferase (EC 2.6.1.11), ArgD, an enzyme of arginine biosynthesis, while another is succinylornithine aminotransferase, an enzyme of the arginine succinyltransferase pathway, an ammonia-generating pathway of arginine catabolism (See MEDLINE:98361920). Members of this family may also act on ornithine, like ornithine aminotransferase (EC 2.6.1.13) (see MEDLINE:90337349) and on succinyldiaminopimelate, like N-succinyldiaminopmelate-aminotransferase (EC 2.6.1.17, DapC, an enzyme of lysine biosynthesis) (see MEDLINE:99175097) TIGR00708.1 TIGR00708 cobA 167.75 167.75 177 equivalog Y Y N cob(I)yrinic acid a,c-diamide adenosyltransferase cobO 2.5.1.17 GO:0008817,GO:0009236 7860601 131567 cellular organisms no rank 29205 JCVI cob(I)yrinic acid a,c-diamide adenosyltransferase cob(I)yrinic acid a,c-diamide adenosyltransferase Alternate name: corrinoid adenosyltransferase. TIGR00709.1 TIGR00709 dat 401.6 401.6 442 subfamily Y Y N diaminobutyrate--2-oxoglutarate transaminase family protein GO:0008483,GO:0019491 9260954,9514614 131567 cellular organisms no rank 32768 JCVI 2,4-diaminobutyrate 4-transaminase diaminobutyrate--2-oxoglutarate transaminase family protein This family consists of L-diaminobutyric acid transaminases. This general designation covers both 2.6.1.76 (diaminobutyrate-2-oxoglutarate transaminase, which uses glutamate as the amino donor in DABA biosynthesis), and 2.6.1.46 (diaminobutyrate--pyruvate transaminase, which uses alanine as the amino donor). A related enzyme is 4-aminobutyrate aminotransferase (EC 2.6.1.19), also called GABA transaminase. These enzymes all are pyridoxal phosphate-containing class III aminotransferase. TIGR00710.1 TIGR00710 efflux_Bcr_CflA 200.9 200.9 385 subfamily Y Y N Bcr/CflA family efflux MFS transporter GO:0016020,GO:0042908,GO:0042910 8486276 131567 cellular organisms no rank 105299 JCVI drug resistance transporter, Bcr/CflA subfamily Bcr/CflA family efflux MFS transporter This subfamily of drug efflux proteins, a part of the major faciliator family, is predicted to have 12 membrane-spanning regions. Members with known activity include Bcr (bicyclomycin resistance protein) in E. coli, Flor (chloramphenicol and florfenicol resistance) in Salmonella typhimurium DT104, and CmlA (chloramphenicol resistance) in Pseudomonas sp. plasmid R1033. TIGR00711.1 TIGR00711 efflux_EmrB 230.2 230.2 485 subfamily Y Y N DHA2 family efflux MFS transporter permease subunit GO:0006855,GO:0016020,GO:0022857 1409590,9466256 131567 cellular organisms no rank 341354 JCVI drug resistance MFS transporter, drug:H+ antiporter-2 (14 Spanner) (DHA2) family DHA2 family efflux MFS transporter permease subunit This subfamily of drug efflux proteins, a part of the major faciliator family, is predicted to have 14 potential membrane-spanning regions. Members with known activities include EmrB (multiple drug resistance efflux pump) in E. coli, FarB (antibacterial fatty acid resistance) in Neisseria gonorrhoeae, TcmA (tetracenomycin C resistance) in Streptomyces glaucescens, etc. In most cases, the efflux pump is described as having a second component encoded in the same operon, such as EmrA of E. coli. TIGR00713.1 TIGR00713 hemL 527.3 527.3 423 equivalog Y Y N glutamate-1-semialdehyde 2,1-aminomutase hemL 5.4.3.8 GO:0033014,GO:0042286 131567 cellular organisms no rank 60341 JCVI glutamate-1-semialdehyde-2,1-aminomutase glutamate-1-semialdehyde 2,1-aminomutase This enzyme, glutamate-1-semialdehyde-2,1-aminomutase (glutamate-1-semialdehyde aminotransferase, GSA aminotransferase), contains a pyridoxal phosphate attached at a Lys residue at position 283 of the seed alignment. It is in the family of class III aminotransferases. TIGR00715.1 TIGR00715 precor6x_red 129.85 129.85 256 equivalog Y Y N precorrin-6A reductase cobK 1.3.1.54 GO:0009236,GO:0016994 1732193 131567 cellular organisms no rank 26088 JCVI precorrin-6x reductase precorrin-6A reductase This enzyme catalyzes a step in cobalamin biosynthesis. It has been identified experimentally in Pseudomonas denitrificans and has been shown to be part of cobalamin biosynthetic operons in several other species. This enzyme was found to be a monomer by gel filtration. TIGR00720.1 TIGR00720 sda_mono 345.1 345.1 450 equivalog Y Y N L-serine ammonia-lyase 4.3.1.17 GO:0003941,GO:0006094 15498577,8436113 131567 cellular organisms no rank 57618 JCVI L-serine ammonia-lyase L-serine ammonia-lyase This enzyme is also called serine deaminase and L-serine dehydratase 1. L-serine ammonia-lyase converts serine into pyruvate in the gluconeogenesis pathway from serine. This enzyme is comprised of a single chain in Escherichia coli, Mycobacterium tuberculosis, and several other species, but has separate alpha and beta chains in Bacillus subtilis and related species. The beta and alpha chains are homologous to the N-terminal and C-terminal regions, respectively, but are rather deeply branched in a UPGMA tree. This enzyme requires iron and dithiothreitol for activation in vitro, and is a predicted 4Fe-4S protein. Escherichia coli Pseudomonas aeruginosa have two copies of this protein. TIGR00722.1 TIGR00722 ttdA_fumA_fumB 100.65 100.65 273 subfamily_domain Y N N hydrolyase, tartrate alpha subunit/fumarate domain protein, Fe-S type GO:0016829 131567 cellular organisms no rank 46100 JCVI hydrolyase, tartrate alpha subunit/fumarate domain protein, Fe-S type hydrolyase, tartrate alpha subunit/fumarate domain protein, Fe-S type A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see PROSITE:PDOC00147). This model represents a subset of closely related proteins or modules, including the E. coli tartrate dehydratase alpha chain and the N-terminal region of the class I fumarase (where the C-terminal region is homologous to the tartrate dehydratase beta chain). The activity of archaeal proteins in this subfamily has not been established. TIGR00723.1 TIGR00723 ttdB_fumA_fumB 145.15 145.15 169 subfamily_domain Y Y N FumA C-terminus/TtdB family hydratase beta subunit GO:0016836 131567 cellular organisms no rank 46934 JCVI hydrolyase, tartrate beta subunit/fumarate domain protein, Fe-S type FumA C-terminus/TtdB family hydratase beta subunit A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see PROSITE:PDOC00147). This model represents a subset of closely related proteins or modules, including the E. coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of archaeal proteins in this subfamily has not been established. TIGR00724.1 TIGR00724 urea_amlyse_rel 230.2 230.2 315 domain Y Y N 5-oxoprolinase/urea amidolyase family protein 6124544 131567 cellular organisms no rank 70698 JCVI biotin-dependent carboxylase uncharacterized domain biotin-dependent carboxylase uncharacterized domain Urea amidolyase of Saccharomyces cerevisiae is a 1835 amino acid protein with an amidase domain, a biotin/lipoyl cofactor attachment domain, a carbamoyl-phosphate synthase L chain-like domain, and uncharacterized regions. It has both urea carboxylase and allophanate hydrolase activities. This HMM models a domain that represents uncharacterized prokaryotic proteins of about 300 amino acids, regions of prokaryotic urea carboxylase and of the urea carboxylase region of yeast urea amidolyase, and regions of other biotin-containing proteins. TIGR00725.1 TIGR00725 TIGR00725 106.9 106.9 159 hypoth_equivalog Y Y N TIGR00725 family protein 131567 cellular organisms no rank 3004 JCVI TIGR00725 family protein TIGR00725 family protein This model represents one branch of a subfamily of uncharacterized proteins. Both PSI-BLAST and weak hits by this HMM show a low level of similarity and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting the branches may have distinct functions. This family is one of several families within the scope of PFAM model PF03641, several members of which are annotated as lysine decarboxylases. That larger family, and the branch described by this model, have a well-conserved motif PGGXGTXXE. TIGR00728.1 TIGR00728 OPT_sfam 128.35 128.35 659 superfamily Y Y N OPT family oligopeptide transporter GO:0035673 9643541 131567 cellular organisms no rank 12716 JCVI oligopeptide transporter, OPT superfamily OPT family oligopeptide transporter This superfamily has two main branches. One branch contains a tetrapeptide transporter demonstrated experimentally in three different species of yeast. The other family contains EspB of Myxococcus xanthus, a protein required for normal rather than delayed sporulation after cellular aggregation; its role is unknown but is compatible with transport of a signalling molecule. Homology between the two branches of the superfamily is seen most easily at the ends of the protein. The central regions are poorly conserved within each branch and may not be homologous between branches. TIGR00729.1 TIGR00729 TIGR00729 123.3 123.3 207 equivalog Y Y N ribonuclease HII rnhB GO:0004523,GO:0006401 20047562,9789007,9829929 131567 cellular organisms no rank 1422 JCVI ribonuclease HII ribonuclease HII This enzyme cleaves RNA from DNA-RNA hybrids. Archaeal members of this subfamily of RNase H are designated RNase HII and one has been shown to be active as a monomer. A member from Homo sapiens was characterized as RNase HI, large subunit. TIGR00730.1 TIGR00730 TIGR00730 96.35 96.35 178 hypoth_equivalog Y Y N TIGR00730 family Rossman fold protein GO:0009691,GO:0016787 15459330 131567 cellular organisms no rank 67706 JCVI TIGR00730 family protein Rossman fold protein, TIGR00730 family This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this HMM show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions. TIGR00732.1 TIGR00732 dprA 191.15 191.15 220 equivalog Y Y N DNA-processing protein DprA dprA GO:0009294 10482496,12123453,14617176,7768823 131567 cellular organisms no rank 81025 JCVI DNA protecting protein DprA DNA-processing protein DprA Disruption of this gene in both Haemophilus influenzae and Helicobacter pylori drastically reduces the efficiency of transformation with exogenous DNA, but with different levels of effect on chromosomal (linear) and plasmid (circular) DNA [1][2]. This difference suggests the DprA is not active in recombination, and it has been shown not to affect DNA binding, leaving the intermediate step in natural transformation, DNA processing. In Strep. pneumoniae, inactivation of dprA had no effect on the uptake of DNA [3]. All of these data indicated that DprA is required at a later stage in transformation. Subsequently DprA and RecA were both shown in S. pneumoniae to be required to protect incoming ssDNA from immediate degradation. [4]. Role of DprA in non-transformable species is not known. The gene symbol smf was assigned in E. coli, but without assignment of function. TIGR00733.1 TIGR00733 TIGR00733 182.5 182.5 589 equivalog Y Y N OPT family oligopeptide transporter GO:0006857,GO:0016020,GO:0035673 9643541 131567 cellular organisms no rank 13963 JCVI oligopeptide transporter, OPT family OPT family oligopeptide transporter This protein represents a small family of integral membrane proteins from Gram-negative bacteria, a Gram-positive bacteria, and an archaeal species. Members of this family contain 15 to 18 GES predicted transmembrane regions, and this family has extensive homology to a family of yeast tetrapeptide transporters, including isp4 (Schizosaccharomyces pombe) and Opt1 (Candida albicans). EspB, an apparent equivalog from Myxococcus xanthus, shares an operon with a two component system regulatory protein, and is required for the normal timing of sporulation after the aggregation of cells. This is consistent with a role in transporting oligopeptides as signals across the membrane. TIGR00735.1 TIGR00735 hisF 294.55 294.55 254 equivalog_domain Y Y N imidazole glycerol phosphate synthase subunit HisF hisF 4.3.2.10 GO:0000105,GO:0000107 12795595,8366040,9654139 131567 cellular organisms no rank 55113 JCVI imidazoleglycerol phosphate synthase, cyclase subunit imidazole glycerol phosphate synthase subunit HisF TIGR00737.1 TIGR00737 nifR3_yhdG 293.3 293.3 319 equivalog Y Y N tRNA dihydrouridine synthase DusB dusB 1.3.1.- GO:0008033,GO:0017150,GO:0050660 9738943 131567 cellular organisms no rank 60115 JCVI putative TIM-barrel protein, nifR3 family tRNA dihydrouridine synthase DusB This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). This branch includes NifR3 itself, from Rhodobacter capsulatus. It excludes a broadly distributed but more sparsely populated subfamily that contains sll0926 from Synechocystis PCC6803, HI0634 from Haemophilus influenzae, and BB0225 from Borrelia burgdorferi. It also excludes a shorter and more distant archaeal subfamily. The function of nifR3, a member of this family, is unknown, but it is found in an operon with nitrogen-sensing two component regulators in Rhodobacter capsulatus. Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. TIGR00738.1 TIGR00738 rrf2_super 73.3 73.3 132 superfamily Y Y N Rrf2 family transcriptional regulator 9148780 131567 cellular organisms no rank 86943 JCVI Rrf2 family protein Rrf2 family transcriptional regulator This HMM represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency. TIGR00745.1 TIGR00745 apbA_panE 141.35 141.35 305 subfamily Y Y N 2-dehydropantoate 2-reductase 1.1.1.169 GO:0008677,GO:0015940 18391442,9721324 131567 cellular organisms no rank 76946 JCVI 2-dehydropantoate 2-reductase 2-dehydropantoate 2-reductase This HMM describes enzymes that perform as 2-dehydropantoate 2-reductase, one of four enzymes required for the de novo biosynthesis of pantothenate (vitamin B5) from Asp and 2-oxoisovalerate. Although few members of the seed alignment are characterized experimentally, nearly all from complete genomes are found in a genome-wide (but not local) context of all three other pantothenate-biosynthetic enzymes. Note that this family includes both NADH and NADPH-dependent enzymes, and enzymes with broad specificity, such as a D-mandelate dehydrogease that is also a 2-dehydropantoate 2-reductase. TIGR00746.1 TIGR00746 arcC 358.25 358.25 309 equivalog Y Y N carbamate kinase arcC 2.7.2.2 GO:0006520,GO:0008804 10347186,20188742 131567 cellular organisms no rank 19670 JCVI carbamate kinase carbamate kinase In most species, carbamate kinase works in arginine catabolism and consumes carbamoyl phosphate to convert ADP into ATP. In the pathway in Pyrococcus furiosus, the enzyme acts instead to generate carbamoyl phosphate. The seed alignment for this model includes experimentally confirmed examples from a set of phylogenetically distinct species. In a neighbor-joining tree constructed from an alignment of candidate carbamate kinases and several acetylglutamate kinases, the latter group forms a clear outgroup which roots the tree of carbamate kinase-like proteins. This analysis suggests that in E. coli, the ArcC paralog YqeA may be a second isozyme, while the paralog YahI branches as an outlier and is less likely to be an authentic carbamate kinase. The homolog from Mycoplasma pneumoniae likewise branches outside the set containing known carbamate kinases and also scores below the trusted cutoff. TIGR00747.1 TIGR00747 fabH 292.1 292.1 322 subfamily Y Y N beta-ketoacyl-ACP synthase III fabH 2.3.1.180 GO:0004315,GO:0006633 20096678,8020746 131567 cellular organisms no rank 75389 JCVI 3-oxoacyl-[acyl-carrier-protein] synthase III beta-ketoacyl-ACP synthase III FabH in general initiate elongation in type II fatty acid synthase systems found in bacteria and plants. The two members of this subfamily from Bacillus subtilis differ from each other, and from FabH from E. coli, in acyl group specificity. Active site residues include Cys112, His244 and Asn274 of E. coli FabH. Cys-112 is the site of acyl group attachment. TIGR00748.1 TIGR00748 HMG_CoA_syn_Arc 353.35 353.35 345 equivalog Y Y N hydroxymethylglutaryl-CoA synthase 2.3.3.10 GO:0004315,GO:0006633 10322017,12107122 131567 cellular organisms no rank 768 JCVI putative hydroxymethylglutaryl-CoA synthase hydroxymethylglutaryl-CoA synthase This family of archaeal proteins shows considerable homology and identical active site residues to the bacterial hydroxymethylglutaryl-CoA synthase (HMG-CoA synthase, modeled by TIGR01835) which is the second step in the mevalonate pathway of IPP biosynthesis [1]. An enzyme from Pseudomonas fluorescens involved in the biosynthesis of the polyketide diacetyl-phloroglucinol is more closely related, but lacks the active site residues [2]. In each of the genomes containing a member of this family there is no other recognized HMG-CoA synthase, although other elements of the mevalonate pathway are in evidence. The only archaeon currently sequenced which lacks a homolog in this pathway is Halobacterium, which _does_ contain a separate HMG-CoA synthase. Thus, although there is no experimental evidence supporting this name, the bioinformatics-based conclusion appears to be sound. TIGR00750.1 TIGR00750 lao 240.75 240.75 300 equivalog Y Y N methylmalonyl Co-A mutase-associated GTPase MeaB meaB GO:0003924,GO:0005525,GO:0015819,GO:0015822,GO:0016772,GO:1903826 2104851,2136858 131567 cellular organisms no rank 34948 JCVI LAO/AO transport system ATPase methylmalonyl Co-A mutase-associated GTPase MeaB In E. coli, mutation of this kinase blocks phosphorylation of two transporter system periplasmic binding proteins and consequently inhibits those transporters. This kinase is also found in Gram-positive bacteria, archaea, and the roundworm C. elegans. It may have a more general, but still unknown function. Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however. TIGR00751.1 TIGR00751 menA 102.15 102.15 284 equivalog Y Y N 1,4-dihydroxy-2-naphthoate octaprenyltransferase menA 2.5.1.74 GO:0009234,GO:0046428 9573170 131567 cellular organisms no rank 27437 JCVI 1,4-dihydroxy-2-naphthoate octaprenyltransferase 1,4-dihydroxy-2-naphthoate octaprenyltransferase This membrane-associated enzyme converts 1,4-dihydroxy-2-naphthoic acid (DHNA) to demethylmenaquinone, a step in menaquinone biosynthesis. TIGR00753.1 TIGR00753 undec_PP_bacA 217.5 217.5 255 equivalog Y Y N undecaprenyl-diphosphatase UppP uppP 3.6.1.27 GO:0016020,GO:0016311,GO:0046677,GO:0050380 15138271,8389741 131567 cellular organisms no rank 49475 JCVI undecaprenyl-diphosphatase UppP undecaprenyl-diphosphatase UppP This is a family of small, highly hydrophobic proteins. Overexpression of this protein in Escherichia coli is associated with bacitracin resistance, and the protein was originally proposed to be an undecaprenol kinase and called bacA. It is now known to be an undecaprenyl pyrophosphate phosphatase (EC 3.6.1.27) and is renamed UppP. TIGR00754.1 TIGR00754 bfr 125.55 125.55 157 equivalog Y Y N bacterioferritin bfr 1.16.3.1 GO:0004322,GO:0006879,GO:0006880,GO:0008199 33460502,9409768,9867433 131567 cellular organisms no rank 23735 JCVI bacterioferritin bacterioferritin Bacterioferritin, predominantly an iron-storage protein restricted to Bacteria, has also been designated cytochrome b1 and cytochrome b-557. Its di-iron ferroxidase center site is catalytically active for iron mineralisation by conversion of Fe(2+) to Fe(3+), while the heme group is involved in the reverse reaction. Bacterioferritin is a homomultimer most species. In Neisseria gonorrhoeae, Synechocystis PCC6803, Magnetospirillum magnetotacticum, and Pseudomonas aeruginosa, two types of subunit are found in a heteromultimeric complex, with each species having one member of each type. At present, both types of subunit are including in this single model. TIGR00755.1 TIGR00755 ksgA 171 171 256 equivalog Y Y N 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA rsmA 2.1.1.182 GO:0000179,GO:0006364 8064863 131567 cellular organisms no rank 69208 JCVI ribosomal RNA small subunit methyltransferase A 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA RsmA (ribosomal RNA small subunit methyltransferase A) performs dimethylation of two adjacent adenosine residues in a conserved hairpin of 16S rRNA in bacteria, 18S rRNA in eukaryotes. This adjacent dimethylation is the only rRNA modification shared by bacteria and eukaryotes. This protein is essential in yeast, but not in E. coli, where its deletion leads to resistance to the antibiotic kasugamycin. TIGR00758.1 TIGR00758 UDG_fam4 125.3 125.3 173 subfamily Y N N uracil-DNA glycosylase, family 4 GO:0004844,GO:0006281 1324872,14556741 131567 cellular organisms no rank 30694 JCVI uracil-DNA glycosylase, family 4 uracil-DNA glycosylase, family 4 This well-conserved family of proteins is about 200 residues in length and homologous to the N-terminus of the DNA polymerase of phage SPO1 of Bacillus subtilis. The member from Thermus thermophilus HB8 is known to act as uracil-DNA glycosylase, an enzyme of DNA base excision repair. Its appearance as a domain of phage DNA polymerases could be consistent with uracil-DNA glycosylase activity. TIGR00761.1 TIGR00761 argB 151.3 151.3 231 equivalog_domain Y Y N acetylglutamate kinase argB 2.7.2.8 GO:0003991,GO:0005737,GO:0006592 1649049 131567 cellular organisms no rank 56195 JCVI acetylglutamate kinase acetylglutamate kinase This HMM describes N-acetylglutamate kinases (ArgB) of many prokaryotes and the N-acetylglutamate kinase domains of multifunctional proteins from yeasts. This enzyme is the second step in the "acetylated" ornithine biosynthesis pathway. A related group of enzymes representing the first step of the pathway contain a homologous domain and are excluded from this model. TIGR00763.1 TIGR00763 lon 608.05 608.05 795 equivalog Y Y N endopeptidase La lon 3.4.21.53 GO:0004252,GO:0005524,GO:0006508,GO:0016887 131567 cellular organisms no rank 66411 JCVI endopeptidase La endopeptidase La This protein, the ATP-dependent serine endopeptidase La, is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock. TIGR00764.1 TIGR00764 lon_rel 516.6 516.6 608 equivalog Y Y N ATP-dependent protease LonB lonB 3.4.21.- GO:0004176,GO:0005524,GO:0006508 15560777 131567 cellular organisms no rank 1256 JCVI putative ATP-dependent protease ATP-dependent protease LonB This HMM represents a set of proteins with extensive C-terminal homology to the ATP-dependent protease La, product of the lon gene of E. coli. The model is based on a seed alignment containing only archaeal members, but several bacterial proteins match the model well. Because several species, including Thermotoga maritima and Treponema pallidum, contain both a close homolog of the lon protease and nearly full-length homolog of the members of this family, we suggest there may also be a functional division between the two families. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein. TIGR00765.1 TIGR00765 yihY_not_rbn 73.15 73.15 259 subfamily_domain Y Y N YihY family inner membrane protein GO:0005886 1400219,15764599,20092870 131567 cellular organisms no rank 79573 JCVI YihY family inner membrane protein YihY family inner membrane protein Initial identification of members of this protein family was based on characterization of the yihY gene product as ribonuclease BN in Escherichia coli. This identification has been withdrawn, as the group now finds the homolog in E. coli of RNase Z is the true ribonuclease BN rather than a strict functional equivalent of RNase Z. Members of this subfamily include the largely uncharacterized BrkB (Bordetella resist killing by serum B) from Bordetella pertussis. Some members have an additional C-terminal domain. Paralogs from E. coli (yhjD) and Mycobactrium tuberculosis (Rv3335c) are part of a smaller, related subfamily that form their own cluster. TIGR00767.1 TIGR00767 rho 509.45 509.45 415 equivalog Y Y N transcription termination factor Rho rho GO:0003723,GO:0005524,GO:0006353,GO:0008186 16946247 131567 cellular organisms no rank 51263 JCVI transcription termination factor Rho transcription termination factor Rho This RNA helicase, the transcription termination factor Rho, occurs in nearly all bacteria but is missing from the Cyanobacteria, the Mollicutes (Mycoplasmas), and various Lactobacillales including Streptococcus. It is also missing, of course, from the Archaea, which also lack Nus factors. Members of this family from Micrococcus luteus, Mycobacterium tuberculosis, and related species have a related but highly variable long, highly charged insert near the amino end. Members of this family differ in the specificity of RNA binding. TIGR00768.1 TIGR00768 rimK_fam 143.4 143.4 276 subfamily Y Y N RimK family alpha-L-glutamate ligase GO:0016881 2570347,9416615 131567 cellular organisms no rank 21866 JCVI alpha-L-glutamate ligase, RimK family RimK family alpha-L-glutamate ligase This family, related to bacterial glutathione synthetases, contains at least three different alpha-L-glutamate ligases. One is RimK, as in E. coli, which adds additional Glu residues to the native Glu-Glu C-terminus of ribosomal protein S6, but not to Lys-Glu mutants. Most species with a member of this subfamily lack an S6 homolog ending in Glu-Glu, however. Members in Methanococcus jannaschii act instead as a tetrahydromethanopterin:alpha-l-glutamate ligase (MJ0620) and a gamma-F420-2:alpha-l-glutamate ligase (MJ1001). TIGR00778.1 TIGR00778 ahpD_dom 27.8 27.8 51 domain Y N N alkylhydroperoxidase AhpD family core domain GO:0051920 131567 cellular organisms no rank 136795 JCVI alkylhydroperoxidase AhpD family core domain alkylhydroperoxidase AhpD family core domain This HMM represents a 51-residue core region of homology among a family of mostly uncharacterized proteins of 110 to 227 amino acids. Most members of this family contain the motif EXXXXXX[SA]XXXXXC[VIL]XCXXXH. Members of the family include the alkylhydroperoxidase AhpD of Mycobacterium tuberculosis, a macrophage infectivity potentiator peptide of Legionella pneumophila, and an uncharacterized peptide in the tetrachloroethene reductive dehalogenase operon of Dehalospirillum multivorans. We suggest that many peptides containing this domain may have alkylhydroperoxidase or related antioxidant activity. TIGR00784.1 TIGR00784 citMHS 259.7 259.7 431 subfamily Y Y N citrate:proton symporter GO:0015137,GO:0015746,GO:0016020 131567 cellular organisms no rank 22476 JCVI citrate transporter citrate:proton symporter This family includes two characterized citrate/proton symporters from Bacillus subtilis. CitM transports citrate complexed to Mg2+, while the CitH apparently transports citrate without Mg2+. The family also includes uncharacterized transporters, including a third paralog in Bacillus subtilis. TIGR00785.1 TIGR00785 dass 198.6 198.6 444 subfamily Y Y N DASS family sodium-coupled anion symporter GO:0006820,GO:0008509,GO:0016020 19840771,26546518,28436435 131567 cellular organisms no rank 51865 JCVI transporter, divalent anion:Na+ symporter (DASS) family DASS family sodium-coupled anion symporter DASS (Divalent Anion:Sodium(+) Symporter) transporters include Na(+)-coupled transporters of organic di- and tricarboxylates, inorganic phosphate, and inorganic sulfate. The family is designated 2.A.47 by the Transporter Classification Database. TIGR00786.1 TIGR00786 dctM 268.45 268.45 405 subfamily Y Y N TRAP transporter large permease subunit GO:0015556,GO:0015740,GO:0016020,GO:0031317 131567 cellular organisms no rank 116704 JCVI TRAP transporter, DctM subunit TRAP transporter large permease subunit The Tripartite ATP-independent Periplasmic Transporter (TRAP-T) Family (TC 2.A.56)- DctM subunit TRAP-T family permeases generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. Only one member of the family has been both sequenced and functionally characterized. This system is the DctPQM system of Rhodobacter capsulatus (Forward et al., 1997). DctP is a periplasmic dicarboxylate (malate, fumarate, succinate) binding receptor that is biochemically well-characterized. DctQ is an integral cytoplasmic membrane protein with 4 putative transmembrane a-helical spanners (TMSs). DctM is a second integral cytoplasmic membrane protein with 12 putative TMSs. These proteins have been shown to be both necessary and sufficient for the proton motive force-dependent uptake of dicarboxylates into R. capsulatus. TIGR00790.1 TIGR00790 fnt 232.3 232.3 239 subfamily Y Y N formate/nitrite family transporter GO:0006820,GO:0008509,GO:0016020 131567 cellular organisms no rank 12581 JCVI formate/nitrite transporter formate/nitrite family transporter The Formate-Nitrite Transporter (FNT) Family (TC 2.A.44) The prokaryotic proteins of the FNT family probably function in the transport of the structurally related compounds, formate and nitrite. The homologous yeast protein may function as a short chain aliphatic carboxylate H+ symporter, transporting formate, acetate and propionate, and functioning primarily as an acetate uptake permease. The putative formate efflux transporters (FocA) of bacteria associated with pyruvate-formate lyase (pfl) comprise cluster I; the putative formate uptake permeases (FdhC) of bacteria and archaea associated with formate dehydrogenase comprise cluster II; the putative nitrite uptake permeases (NirC) of bacteria comprise cluster III, and the single yeast protein, the putative acetate:H+ symporter alone comprises cluster IV. The energy coupling mechanisms for proteins of the FNT family have not been extensively characterized. HCO2 -, CH3CO2 - and NO2 - uptakes are probably coupled to H+ symport. HCO2 - efflux may be driven by the membrane potential by a uniport mechanism or by H+ antiport. TIGR00795.1 TIGR00795 lctP 341.15 341.15 530 subfamily Y Y N lactate permease LctP family transporter GO:0005886,GO:0008028,GO:0015718 131567 cellular organisms no rank 38446 JCVI transporter, lactate permease (LctP) family lactate permease LctP family transporter This HMM is derived from TCDB family 2.A.14, the Lactate Permease (LctP) Family. The originally characterized member of this family, from E. coli, appears to catalyze lactate:H+ uptake. Members of this family have 12 probable TMS. TIGR00797.1 TIGR00797 matE 147.4 147.4 396 subfamily Y Y N MATE family efflux transporter GO:0015297,GO:0016020,GO:0042910,GO:0055085 131567 cellular organisms no rank 265420 JCVI MATE efflux family protein MATE family efflux transporter The Multi Antimicrobial Extrusion (MATE) Family (TC 2.A.66) The MATE family consists of probable efflux proteins including a functionally characterized multi drug efflux system from Vibrio parahaemolyticus, a putative ethionine resistance protein of Saccharomyces cerevisiae, and the functionally uncharacterized DNA damage-inducible protein F (DinF) of E. coli. These proteins have 12 probable TMS. TIGR00801.1 TIGR00801 ncs2 291.8 291.8 415 superfamily Y Y N NCS2 family nucleobase:cation symporter GO:0015205,GO:0015851,GO:0016020 131567 cellular organisms no rank 100207 JCVI uracil-xanthine permease NCS2 family nucleobase:cation symporter The Nucleobase:Cation Symporter-2 (NCS2) Family (TC 2.A.40) Most of the functionally characterized members of the NCS2 family are transporters specific for nucleobases including both purines and pyrimidines. However, two closely related rat members of the family, SVCT1 and SVCT2, localized to different tissues of the body, cotransport L-ascorbate and Na+ with a high degree of specificity and high affinity for the vitamin. The NCS2 family appears to be distantly related to the NCS1 family (TC #2.A.39). TIGR00802.1 TIGR00802 nico 333.05 333.05 281 subfamily Y Y N HoxN/HupN/NixA family nickel/cobalt transporter GO:0005886,GO:0035444 131567 cellular organisms no rank 13719 JCVI transition metal uptake transporter, Ni2+-Co2+ transporter (NiCoT) family HoxN/HupN/NixA family nickel/cobalt transporter This family is found in both Gram-negative and Gram-positive bacteria. The functionally characterized members of the family catalyze uptake of either Ni2+ or Co2+ in a proton motive force-dependent process. Topological analyses with the HoxN Ni2+ transporter of Ralstonia eutropha (Alcaligenes eutrophus) suggest that it possesses 8 TMSs with its N- and C-termini in the cytoplasm. TIGR00813.1 TIGR00813 sss 184 184 411 superfamily Y Y N sodium/solute symporter GO:0005886,GO:0006810,GO:0015370 131567 cellular organisms no rank 106541 JCVI transporter, solute:sodium symporter (SSS) family sodium/solute symporter Members of the SSS family have been identified in bacteria, archaea and animals, and all functionally well characterized members catalyze solute uptake via Na+ symport. Proteins of the SSS generally share a core of 13 TMSs, but different members of the family may have different numbers of TMSs. A 13 TMS topology with a periplasmic N-terminus and a cytoplasmic C-terminus has been experimentally determined for the proline:Na+ symporter, PutP, of E. coli. Members of the Solute:Sodium Symporter (SSS), TC 2.A.21 as described in tcdb.org, catalyze solute:Na+ symport. Known solutes for members of the family include sugars, amino acids, nucleosides, inositols, vitamins, urea or anions, depending on the system. TIGR00815.1 TIGR00815 sulP 380.45 380.45 565 subfamily Y Y N sulfate permease sulP GO:0015116,GO:0016020,GO:1902358 131567 cellular organisms no rank 27429 JCVI sulfate permease sulfate permease The SulP family is a large and ubiquitous family with over 30 sequenced members derived from bacteria and eukaryotes. Many have multiple SulP family paralogues. Characterized members are sulfate uptake transporters, but with varied affinities. These proteins exhibit 10-13 putative transmembrane alpha-helical segments. TIGR00829.1 TIGR00829 FRU 76.85 76.85 85 subfamily_domain Y Y N fructose PTS transporter subunit IIB 2.7.1.202 GO:0009401,GO:0022877 131567 cellular organisms no rank 72666 JCVI PTS system, Fru family, IIB component fructose PTS transporter subunit IIB Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Fru family is a large and complex family which includes several sequenced fructose and mannitol-specific permeases as well as several PTS components of unknown specificities. The fructose components of this family phosphorylate fructose on the 1-position. The Fru family PTS systems typically have 3 domains, IIA, IIB and IIC, which may be found as 1 or more proteins. The fructose and mannitol transporters form separate phylogenetic clusters in this family. This family is specific for the IIB domain of the fructose PTS transporters. TIGR00831.1 TIGR00831 a_cpa1 279.6 279.6 525 equivalog Y Y N Na+/H+ antiporter GO:0006814,GO:0006885,GO:0015385,GO:0016020,GO:1902600 131567 cellular organisms no rank 41244 JCVI Na+/H+ antiporter Na+/H+ antiporter The Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36) The CPA1 family is a large family of proteins derived from Gram-positive and Gram-negative bacteria, blue green bacteria, yeast, plants and animals. Transporters from eukaryotes have been functionally characterized, and all of these catalyze Na+:H+ exchange. Their primary physiological functions may be in (1) cytoplasmic pH regulation, extruding the H+ generated during metabolism, and (2) salt tolerance (in plants), due to Na+ uptake into vacuoles. This Hmm is specific for the bacterial members of this family. TIGR00832.1 TIGR00832 acr3 282.8 282.8 327 equivalog Y Y N ACR3 family arsenite efflux transporter arsB GO:0008490,GO:0015103,GO:0015297,GO:0015700,GO:0016020,GO:0046685 131567 cellular organisms no rank 36934 JCVI arsenical-resistance protein ACR3 family arsenite efflux transporter The Arsenical Resistance-3 (ACR3) Family (TC 2.A.59) The first protein of the ACR3 family functionally characterized was the ACR3 protein of Saccharomyces cerevisiae. It is present in the yeast plasma membrane and pumps arsenite out of the cell in response to the pmf. Similar proteins are found in bacteria, often as part of a four gene operon with an regulatory protein ArsR, a protein of unknown function ArsH, and an arsenate reductase that converts arsenate to arsenite to facilitate transport. TIGR00835.1 TIGR00835 agcS 272.65 272.65 424 subfamily Y Y N amino acid carrier protein GO:0005416,GO:0006865,GO:0016020 131567 cellular organisms no rank 82869 JCVI amino acid carrier protein amino acid carrier protein The Alanine or Glycine: Cation Symporter (AGCS) Family (TC 2.A.25) Members of the AGCS family transport alanine and/or glycine in symport with Na+ and or H+. TIGR00836.1 TIGR00836 amt 343.3 343.3 406 subfamily Y Y N ammonium transporter amt GO:0008519,GO:0016020,GO:0072488 131567 cellular organisms no rank 73678 JCVI ammonium transporter ammonium transporter The Ammonium Transporter (Amt) Family (TC 2.A.49) All functionally characterized members of the Amt family are ammonia or ammonium uptake transporters. Some, but not others, also transport methylammonium. The mechanism of energy coupling, if any, to methyl-NH2 or NH3 uptake by the AmtB protein of E. coli is not entirely clear. NH4+ uniport driven by the pmf, energy independent NH3 facilitation, and NH4+/K+ antiport have been proposed as possible transport mechanisms. In Corynebacterium glutamicum and Arabidopsis thaliana, uptake via the Amt1 homologues of AmtB has been reported to be driven by the pmf. TIGR00838.1 TIGR00838 argH 279.5 279.5 455 equivalog Y Y N argininosuccinate lyase argH 4.3.2.1 GO:0004056,GO:0042450 131567 cellular organisms no rank 78061 JCVI argininosuccinate lyase argininosuccinate lyase This model describes argininosuccinate lyase, but may include examples of avian delta crystallins, in which argininosuccinate lyase activity may or may not be present and the biological role is to provide the optically clear cellular protein of the eye lens. TIGR00842.1 TIGR00842 bcct 407.55 407.55 452 subfamily Y Y N BCCT family transporter GO:0015652,GO:0015697,GO:0016020 131567 cellular organisms no rank 73969 JCVI transporter, betaine/carnitine/choline transporter (BCCT) family BCCT family transporter The Betaine/Carnitine/Choline Transporter (BCCT) Family (TC 2.A.15) Proteins of the BCCT family share the common functional feature of transporting molecules with a quaternary ammonium group [R-N+(CH3)3]. The BCCT family includes transporters for carnitine, choline and glycine betaine. BCCT transporters have 12 putative TMS, and are energized by pmf-driven proton symport. Some of these permeases exhibit osmosensory and osmoregulatory properties inherent to their polypeptide chains. TIGR00847.1 TIGR00847 ccoS 28.35 28.35 51 equivalog Y Y N cbb3-type cytochrome oxidase assembly protein CcoS ccoS GO:0008535 20171584,8661920 131567 cellular organisms no rank 16549 JCVI cytochrome oxidase maturation protein, cbb3-type cytochrome oxidase maturation protein, cbb3-type CcoS from Rhodobacter capsulatus has been shown essential for incorporation of redox-active prosthetic groups (heme, Cu) into cytochrome cbb(3) oxidase. FixS of Bradyrhizobium japonicum appears to have the same function. Members of this family are found so far in organisms with a cbb3-type cytochrome oxidase, including Neisseria meningitidis, Helicobacter pylori, Campylobacter jejuni, Caulobacter crescentus, Bradyrhizobium japonicum, and Rhodobacter capsulatus. TIGR00848.1 TIGR00848 fruA 103.5 103.5 129 subfamily_domain Y Y N fructose PTS transporter subunit IIA 2.7.1.202 GO:0008982,GO:0009401,GO:0016020 131567 cellular organisms no rank 51467 JCVI PTS system, fructose subfamily, IIA component fructose PTS transporter subunit IIA 4.A.2 The PTS Fructose-Mannitol (Fru) Family Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Fru family is a large and complex family which includes several sequenced fructose and mannitol-specific permeases as well as several putative PTS permeases of unknown specificities. The fructose permeases of this family phosphorylate fructose on the 1-position. Those of family 4.6 phosphorylate fructose on the 6-position. The Fru family PTS systems typically have 3 domains, IIA, IIB and IIC, which may be found as 1 or more proteins. The fructose and mannitol transporters form separate phylogenetic clusters in this family. This Hmm is specific for the IIA domain of the fructose PTS transporters. Also similar to the Enzyme IIA Fru subunits of the PTS, but included in TIGR01419 rather than this model, is enzyme IIA Ntr (nitrogen), also called PtsN, found in E. coli and other organisms, which may play a solely regulatory role. TIGR00857.1 TIGR00857 pyrC_multi 279.05 279.05 412 subfamily_domain Y Y N dihydroorotase pyrC 3.5.2.3 GO:0004151,GO:0009220 131567 cellular organisms no rank 68335 JCVI dihydroorotase, multifunctional complex type dihydroorotase, multifunctional complex type In contrast to the homodimeric type of dihydroorotase found in E. coli, this class tends to appear in a large, multifunctional complex with aspartate transcarbamoylase. Homologous domains appear in multifunctional proteins of higher eukaryotes. In some species, including Pseudomonas putida and P. aeruginosa, this protein is inactive but is required as a non-catalytic subunit of aspartate transcarbamoylase (ATCase). In these species, a second, active dihydroorotase is also present. The seed for this model does not include any example of the dihydroorotase domain of eukaryotic multidomain pyrimidine synthesis proteins. All proteins described by this HMM should represent active and inactive dihydroorotase per se and functionally equivalent domains of multifunctional proteins from higher eukaryotes, but the model excludes related proteins such as allantoinase. TIGR00858.1 TIGR00858 bioF 426.45 426.45 365 equivalog Y Y N 8-amino-7-oxononanoate synthase bioF 2.3.1.47 GO:0008710,GO:0009102 131567 cellular organisms no rank 27856 JCVI 8-amino-7-oxononanoate synthase 8-amino-7-oxononanoate synthase 7-keto-8-aminopelargonic acid synthetase is an alternate name. This model represents 8-amino-7-oxononanoate synthase, the BioF protein of biotin biosynthesis. This model is based on a careful phylogenetic analysis to separate members of this family from 2-amino-3-ketobutyrate and other related pyridoxal phosphate-dependent enzymes. In several species, including Staphylococcus and Coxiella, a candidate 8-amino-7-oxononanoate synthase is confirmed by location in the midst of a biotin biosynthesis operon but scores below the trusted cutoff of this model. TIGR00861.1 TIGR00861 MIP 171.25 171.25 224 subfamily Y Y N MIP family channel protein GO:0015267,GO:0016020,GO:0055085 131567 cellular organisms no rank 45133 JCVI MIP family channel proteins MIP family channel protein 1.A.8 The Major Intrinsic Protein (MIP) Family The MIP family is large and diverse, possessing over 100 members that all form transmembrane channels. These channel proteins function in water, small carbohydrate (e.g., glycerol), urea, NH3, CO2 and possibly ion transport by an energy independent mechanism. They are found ubiquitously in bacteria, archaea and eukaryotes. The MIP family contains two major groups of channels: aquaporins and glycerol facilitators. The known aquaporins cluster loosely together as do the known glycerol facilitators. MIP family proteins are believed to form aqueous pores that selectively allow passive transport of their solute(s) across the membrane with minimal apparent recognition. Aquaporins selectively transport water (but not glycerol) while glycerol facilitators selectively transport glycerol but not water. Some aquaporins can transport NH3 and CO2. Glycerol facilitators function as solute nonspecific channels, and may transport glycerol, dihydroxyacetone, propanediol, urea and other small neutral molecules in physiologically important processes. Some members of the family, including the yeast FPS protein (TC #1.A.8.5.1) and tobacco NtTIPA may transport both water and small solutes. TIGR00872.1 TIGR00872 gnd_rel 297.2 297.2 299 equivalog Y Y N phosphogluconate dehydrogenase (NAD(+)-dependent, decarboxylating) gnd 1.1.1.343 GO:0006098,GO:0016616 10658669 131567 cellular organisms no rank 26561 JCVI 6-phosphogluconate dehydrogenase (decarboxylating) phosphogluconate dehydrogenase (NAD(+)-dependent, decarboxylating) This family resembles the larger family (gnd) of bacterial and eukaryotic NADP+-dependent 6-phosphogluconate dehydrogenase (EC 1.1.1.44), but differs from it by a deep split in a UPGMA similarity clustering tree and the lack of a central region of about 140 residues. It differs also in being NAD+-dependent, making this family EC 1.1.1.343. Among complete genomes, it is found is found in Bacillus subtilis and Mycobacterium tuberculosis, both of which also contain gnd, and in Aquifex aeolicus. The protein from Methylobacillus flagellatus KT has been characterized as a decarboxylating 6-phosphogluconate dehydrogenase as part of an unusual formaldehyde oxidation cycle In some sequenced organisms members of this family are the sole 6-phosphogluconate dehydrogenase present and are probably active in the pentose phosphate cycle. TIGR00875.1 TIGR00875 fsa_talC_mipB 245.95 245.95 213 equivalog Y Y N fructose-6-phosphate aldolase fsa GO:0005975,GO:0016832 11120740 131567 cellular organisms no rank 22386 JCVI fructose-6-phosphate aldolase fructose-6-phosphate aldolase This HMM represents a family that includes the E. coli transaldolase homologs TalC and MipB, both shown to be fructose-6-phosphate aldolases rather than transaldolases as previously thought. It is related to but distinct from the transaldolase family of E. coli TalA and TalB. The member from Bacillus subtilis becomes phosphorylated during early stationary phase but not during exponential growth. TIGR00877.1 TIGR00877 purD 288 288 425 equivalog_domain Y Y N phosphoribosylamine--glycine ligase purD 6.3.4.13 GO:0004637,GO:0009113 9843369 131567 cellular organisms no rank 82385 JCVI phosphoribosylamine--glycine ligase phosphoribosylamine--glycine ligase Phosphoribosylamine--glycine ligase catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis. It is also called glycinamide ribonucleotide synthetase (GARS). This enzyme appears as a monofunctional protein in prokaryotes but as part of a larger, multidomain protein in eukaryotes. TIGR00878.1 TIGR00878 purM 236.35 236.35 332 equivalog_domain Y Y N phosphoribosylformylglycinamidine cyclo-ligase purM 6.3.3.1 GO:0004641,GO:0006189 131567 cellular organisms no rank 61636 JCVI phosphoribosylformylglycinamidine cyclo-ligase phosphoribosylformylglycinamidine cyclo-ligase Alternate name: phosphoribosylformylglycinamidine cyclo-ligase; AIRS; AIR synthase This enzyme is found as a homodimeric monofunctional protein in prokaryotes and as part of a larger, multifunctional protein, sometimes with two copies of this enzyme in tandem, in eukaryotes. TIGR00879.1 TIGR00879 SP 237.8 237.8 510 subfamily Y Y N sugar porter family MFS transporter GO:0008643,GO:0016020,GO:0051119 131567 cellular organisms no rank 56138 JCVI MFS transporter, sugar porter (SP) family sugar porter family MFS transporter This HMM represent the sugar porter subfamily of the major facilitator superfamily (PF00083) TIGR00884.1 TIGR00884 guaA_Cterm 338.75 338.75 310 equivalog_domain Y Y N glutamine-hydrolyzing GMP synthase guaA 6.3.5.2 GO:0003922,GO:0005524,GO:0009152 131567 cellular organisms no rank 69144 JCVI GMP synthase (glutamine-hydrolyzing), C-terminal domain glutamine-hydrolyzing GMP synthase, C-terminal domain This protein of purine de novo biosynthesis is well-conserved. However, it appears to split into two separate polypeptide chains in most of the Archaea. This C-terminal region would be the larger subunit TIGR00888.1 TIGR00888 guaA_Nterm 172.15 172.15 188 equivalog_domain Y Y N glutamine-hydrolyzing GMP synthase guaA 6.3.5.2 GO:0003922,GO:0005524,GO:0006177 131567 cellular organisms no rank 68559 JCVI GMP synthase (glutamine-hydrolyzing), N-terminal domain glutamine-hydrolyzing GMP synthase, N-terminal domain This protein of purine de novo biosynthesis is well-conserved. However, it appears to split into two separate polypeptide chains in most of the Archaea. This N-terminal region would be the smaller subunit. TIGR00900.1 TIGR00900 2A0121 319.6 319.6 364 subfamily Y N N H+ Antiporter protein 131567 cellular organisms no rank 1503 JCVI H+ Antiporter protein H+ Antiporter protein TIGR00908.1 TIGR00908 2A0305 381.75 381.75 442 equivalog Y Y N ethanolamine permease eat GO:0006865,GO:0015171,GO:0016020 131567 cellular organisms no rank 14656 JCVI ethanolamine permease ethanolamine permease The three genes used as the seed for this model (from Burkholderia pseudomallei, Pseudomonas aeruginosa and Clostridium acetobutylicum are all adjacent to genes for the catabolism of ethanolamine. Most if not all of the hits to this model have a similar arrangement of genes. This group is a member of the Amino Acid-Polyamine-Organocation (APC) Superfamily. TIGR00909.1 TIGR00909 2A0306 556.8 556.8 429 subfamily Y Y N amino acid transporter 131567 cellular organisms no rank 3648 JCVI amino acid transporter amino acid transporter TIGR00921.1 TIGR00921 2A067 351.9 351.9 733 subfamily Y Y N hydrophobe/amphiphile efflux-3 (HAE3) family transporter 10941792 131567 cellular organisms no rank 891 JCVI efflux transporter, putative, hydrophobe/amphiphile efflux-3 (HAE3) family hydrophobe/amphiphile efflux-3 (HAE3) family transporter Characterized members of the RND superfamily all probably catalyze substrate efflux via an H+ antiport mechanism. These proteins are found ubiquitously in bacteria, archaea and eukaryotes. They fall into seven phylogenetic families, this family (2.A.6.7) consists of uncharacterised putative transporters, largely in the Archaea. TIGR00922.1 TIGR00922 nusG 135.7 135.7 172 equivalog Y Y N transcription termination/antitermination protein NusG nusG GO:0032784 12198166,20281307,8763936 131567 cellular organisms no rank 40157 JCVI transcription termination/antitermination factor NusG transcription termination/antitermination protein NusG NusG proteins are transcription factors which are aparrently universal in prokaryotes (archaea and eukaryotes have homologs that may have related functions). The essential components of these factors include an N-terminal RNP-like (ribonucleoprotein) domain and a C-terminal KOW motif (PF00467) believed to be a nucleic acid binding domain [3]. In E. coli, NusA has been shown to interact with RNA polymerase and termination factor Rho. This model covers a wide variety of bacterial species but excludes mycoplasmas which are covered by a separate model (TIGR01956). The function of all of these NusG proteins is likely to be the same at the level of interaction with RNA and other protein factors to affect termination; however different species may utilize NusG towards different processes and in combination with different suites of affector proteins. In E. coli, NusG promotes rho-dependent termination. It is an essential gene. In Streptomyces virginiae and related species, an additional N-terminal sequence is also present and is suggested to play a role in butyrolactone-mediated autoregulation. In Thermotoga maritima, NusG has a long insert, fails to substitute for E. coli NusG (with or without the long insert), is a large 0.7 % of total cellular protein, and has a general, sequence non-specific DNA and RNA binding activity that blocks ethidium staining, yet permits transcription. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405). TIGR00924.1 TIGR00924 yjdL_sub1_fam 130.2 130.2 475 subfamily Y Y N oligopeptide:H+ symporter GO:0015333,GO:0015833,GO:0016020 131567 cellular organisms no rank 63604 JCVI amino acid/peptide transporter (Peptide:H+ symporter) oligopeptide:H+ symporter The model describes proton-dependent oligopeptide transporters in bacteria. This model is restricted in its range in recognizing bacterial proton-dependent oligopeptide transporters, although they are found in yeast, plants and animals. They function by proton symport in a 1:1 stoichiometry, which is variable in different species. All of them are predicted to contain 12 transmembrane domains, for which limited experimental evidence exists. TIGR00928.1 TIGR00928 purB 326.2 326.2 436 equivalog Y Y N adenylosuccinate lyase purB 4.3.2.2 GO:0004018,GO:0009152 131567 cellular organisms no rank 69003 JCVI adenylosuccinate lyase adenylosuccinate lyase This family consists of adenylosuccinate lyase, the enzyme that catalyzes step 8 in the purine biosynthesis pathway for de novo synthesis of IMP and also the final reaction in the two-step sequence from IMP to AMP. TIGR00931.1 TIGR00931 antiport_nhaC 370 370 454 equivalog Y Y N Na+/H+ antiporter NhaC nhaC GO:0006814,GO:0015297,GO:0015385,GO:0016020,GO:1902600 131567 cellular organisms no rank 23337 JCVI Na+/H+ antiporter NhaC Na+/H+ antiporter NhaC A single member of the NhaC family, a protein from Bacillus firmus, has been functionally characterized.It is involved in pH homeostasis and sodium extrusion. Members of the NhaC family are found in both Gram-negative bacteria and Gram-positive bacteria. Intriguingly, archaeal homolog ArcD (just outside boundaries of family) has been identified as an arginine/ornithine antiporter. TIGR00933.1 TIGR00933 2a38 331.15 331.15 391 subfamily Y Y N TrkH family potassium uptake protein GO:0015379,GO:0016020 131567 cellular organisms no rank 25155 JCVI potassium uptake protein, TrkH family TrkH family potassium uptake protein The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. TIGR00936.1 TIGR00936 ahcY 497.6 497.6 416 equivalog Y Y N adenosylhomocysteinase ahcY 3.13.2.1 GO:0004013,GO:0006730 131567 cellular organisms no rank 41306 JCVI adenosylhomocysteinase adenosylhomocysteinase This enzyme hydrolyzes adenosylhomocysteine as part of a cycle for the regeneration of the methyl donor S-adenosylmethionine. Species that lack this enzyme are likely to have adenosylhomocysteine nucleosidase (EC 3.2.2.9), an enzyme which also acts as 5'-methyladenosine nucleosidase (see TIGR01704). TIGR00937.1 TIGR00937 2A51 171.7 171.7 368 subfamily Y Y N chromate efflux transporter chrA GO:0015109,GO:0015703 18776016 131567 cellular organisms no rank 40705 JCVI chromate efflux transporter chromate efflux transporter Members of this family probably act as chromate transporters, and are found in Pseudomonas aeruginosa, Alcaligenes eutrophus, Vibrio cholerae, Bacillus subtilis, Ochrobactrum tritici, cyanobacteria and archaea. The protein reduces chromate accumulation and is essential for chromate resistance. TIGR00945.1 TIGR00945 tatC 132.7 132.7 215 equivalog Y Y N twin-arginine translocase subunit TatC tatC GO:0005886,GO:0015628 12634324,25416690 131567 cellular organisms no rank 55354 JCVI twin arginine-targeting protein translocase TatC twin-arginine translocase subunit TatC This model represents the TatC translocase component of the Sec-independent protein translocation system. This system is responsible for translocation of folded proteins, often with bound cofactors across the periplasmic membrane [1]. A related model (TIGR01912) represents the archaeal clade of this family. TatC is often found in a gene cluster with the two other components of the system, TatA/E (TIGR01411) and TatB (TIGR01410). A model also exists for the Twin-arginine signal sequence (TIGR01409). TIGR00962.1 TIGR00962 atpA 484.45 484.45 503 equivalog Y Y N F0F1 ATP synthase subunit alpha atpA 7.1.2.2 GO:0015986,GO:0045261,GO:0046933 131567 cellular organisms no rank 52308 JCVI ATP synthase F1, alpha subunit F0F1 ATP synthase subunit alpha The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. The alpha-subunit contains a highly conserved adenine-specific noncatalytic nucleotide-binding domain. The conserved amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton translocating ATP synthase F1, alpha subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), B subunit. TIGR00964.1 TIGR00964 secE_bact 27.55 27.55 57 equivalog Y Y N preprotein translocase subunit SecE secE GO:0005886,GO:0009306,GO:0015450,GO:0043952 131567 cellular organisms no rank 35952 JCVI preprotein translocase, SecE subunit preprotein translocase subunit SecE This HMM represents exclusively the bacterial (and some organellar) SecE protein. SecE is part of the core heterotrimer, SecYEG, of the Sec preprotein translocase system. Other components are the ATPase SecA, a cytosolic chaperone SecB, and an accessory complex of SecDF and YajC. TIGR00966.2 TIGR00966 transloc_SecF 160 160 279 equivalog_domain Y Y N protein translocase subunit SecF secF GO:0006886,GO:0015450,GO:0031522,GO:0043952 131567 cellular organisms no rank 70643 JCVI protein-export membrane protein SecF protein translocase subunit SecF This bacterial protein is always found with the homologous protein-export membrane protein SecD. In numerous lineages, this protein occurs as a SecDF fusion protein. TIGR00967.1 TIGR00967 3a0501s007 253.6 253.6 414 equivalog Y Y N preprotein translocase subunit SecY secY GO:0015031,GO:0016020,GO:0043952 131567 cellular organisms no rank 47195 JCVI preprotein translocase, SecY subunit preprotein translocase subunit SecY Members of this protein family are the SecY component of the SecYEG translocon, or protein translocation pore, which is driven by the ATPase SecA. This model does not discriminate bacterial from archaeal forms. TIGR00972.1 TIGR00972 3a0107s01c2 343.2 343.2 248 equivalog Y Y N phosphate ABC transporter ATP-binding protein PstB pstB 7.3.2.1 GO:0005524,GO:0006817,GO:0009898,GO:0015415,GO:0055052 29351743 131567 cellular organisms no rank 53002 JCVI phosphate ABC transporter, ATP-binding protein phosphate ABC transporter ATP-binding protein PstB This HMM represents the ATP-binding protein of a family of ABC transporters for inorganic phosphate. In the model species Escherichia coli, a constitutive transporter for inorganic phosphate, with low affinity, is also present. The high affinity transporter that includes this polypeptide is induced when extracellular phosphate concentrations are low. The proteins most similar to the members of this family but not included appear to be amino acid transporters. TIGR00973.1 TIGR00973 leuA_bact 598.7 598.7 494 equivalog Y Y N 2-isopropylmalate synthase leuA 2.3.3.13 GO:0003852,GO:0009098 131567 cellular organisms no rank 31166 JCVI 2-isopropylmalate synthase 2-isopropylmalate synthase This is the first enzyme of leucine biosynthesis. A larger family of homologous proteins includes homocitrate synthase, distinct lineages of 2-isopropylmalate synthase, several distinct, uncharacterized, orthologous sets in the Archaea, and other related enzymes. This model describes a family of 2-isopropylmalate synthases found primarily in Bacteria. The homologous families in the Archaea may represent isozymes and/or related enzymes. TIGR00974.1 TIGR00974 3a0107s02c 193.45 193.45 272 equivalog Y Y N phosphate ABC transporter permease PstA pstA GO:0005886,GO:0006817,GO:0015415,GO:0055052 131567 cellular organisms no rank 66525 JCVI phosphate ABC transporter, permease protein PstA phosphate ABC transporter permease PstA This HMM describes PtsA, one of a pair of permease proteins in the ABC (high affinity) phosphate transporter. In a number of species, this permease is fused with the PtsC protein (TIGR02138). In the model bacterium Escherichia coli, this transport system is induced when the concentration of extrallular inorganic phosphate is low. A constitutive, lower affinity transporter operates otherwise. TIGR00975.1 TIGR00975 3a0107s03 205 205 315 equivalog Y Y N phosphate ABC transporter substrate-binding protein PstS pstS GO:0006817,GO:0015415,GO:0035435,GO:0042301,GO:0043190 131567 cellular organisms no rank 34622 JCVI phosphate ABC transporter, phosphate-binding protein PstS phosphate ABC transporter substrate-binding protein PstS This family represents one type of (periplasmic, in Gram-negative bacteria) phosphate-binding protein found in phosphate ABC (ATP-binding cassette) transporters. This protein is accompanied, generally in the same operon, by an ATP binding protein and (usually) two permease proteins. TIGR00976.1 TIGR00976 CocE_NonD 66.3 66.3 550 subfamily Y Y N CocE/NonD family hydrolase GO:0016787 10698749,11772629 131567 cellular organisms no rank 71673 JCVI hydrolase CocE/NonD family protein CocE/NonD family hydrolase This model represents a protein subfamily that includes the cocaine esterase CocE, several glutaryl-7-ACA acylases, and the putative diester hydrolase NonD of Streptomyces griseus (all hydrolases). This family shows extensive, low-level similarity to a family of xaa-pro dipeptidyl-peptidases, and local similarity by PSI-BLAST to many other hydrolases. TIGR00977.1 TIGR00977 citramal_synth 450 450 526 equivalog Y Y N citramalate synthase cimA 2.3.3.21 GO:0009097,GO:0019752,GO:0043714,GO:0046912 18245290 131567 cellular organisms no rank 19166 JCVI citramalate synthase citramalate synthase This model includes GSU1798 and is now known to represent citramalate synthase. Members are related to 2-isopropylmalate synthases and homocitrate synthases but phylogenetically distinct. The role is isoleucine biosynthesis, the first dedicated step. TIGR00978.1 TIGR00978 asd_EA 301.2 301.2 342 equivalog Y Y N aspartate-semialdehyde dehydrogenase asd 1.2.1.11 GO:0004073,GO:0009089,GO:0050661 131567 cellular organisms no rank 5320 JCVI aspartate-semialdehyde dehydrogenase aspartate-semialdehyde dehydrogenase Two closely related families of aspartate-semialdehyde dehydrogenase are found. They differ by a deep split in phylogenetic and percent identity trees and in gap patterns. Separate models are built for the two types in order to exclude the USG-1 protein, found in several species, which is specifically related to the Bacillus subtilis type of aspartate-semialdehyde dehydrogenase. Members of this type are found primarily in organisms that lack peptidoglycan. TIGR00979.1 TIGR00979 fumC_II 664.75 664.75 458 equivalog Y Y N class II fumarate hydratase fumC 4.2.1.2 GO:0004333,GO:0006106,GO:0045239 131567 cellular organisms no rank 38756 JCVI fumarate hydratase, class II class II fumarate hydratase Putative fumarases from several species (Mycobacterium tuberculosis, Streptomyces coelicolor, Pseudomonas aeruginosa) branch deeply, although within the same branch of a phylogenetic tree rooted by aspartate ammonia-lyase sequences, and score between the trusted and noise cutoffs. TIGR00982.1 TIGR00982 uS12_E_A 140.2 140.2 139 equivalog Y Y N 30S ribosomal protein S12 GO:0003735,GO:0006412,GO:0015935 131567 cellular organisms no rank 631 JCVI ribosomal protein uS12 30S ribosomal protein S12 This model represents eukaryotic and archaeal forms of ribosomal protein uS12. This protein was known previously as S23 in eukaryotes and as either S12 or S23 in the Archaea. TIGR01001.1 TIGR01001 metA 315.4 315.4 301 equivalog Y Y N homoserine O-succinyltransferase metA 2.3.1.46 GO:0005737,GO:0008899,GO:0019281 131567 cellular organisms no rank 18518 JCVI homoserine O-succinyltransferase homoserine O-succinyltransferase The apparent equivalog from Bacillus subtilis is broken into two tandem reading frames. TIGR01003.1 TIGR01003 PTS_HPr_family 47.9 47.9 82 subfamily Y Y N HPr family phosphocarrier protein GO:0008982,GO:0009401 131567 cellular organisms no rank 74290 JCVI phosphocarrier, HPr family HPr family phosphocarrier protein The HPr family are bacterial proteins (or domains of proteins) which function in phosphoryl transfer system (PTS) systems. They include energy-coupling components which catalyze sugar uptake via a group translocation mechanism. The functions of most of these proteins are not known, but they presumably function in PTS-related regulatory capacities. All seed members are stand-alone HPr proteins, although the model also recognizes HPr domains of PTS fusion proteins. This family includes the related NPr protein. TIGR01007.1 TIGR01007 eps_fam 108.05 108.05 204 subfamily_domain Y Y N polysaccharide biosynthesis tyrosine autokinase 2.7.10.2 GO:0000271 25666613,8626297 131567 cellular organisms no rank 92313 JCVI capsular exopolysaccharide family polysaccharide biosynthesis tyrosine autokinase Wzc family tyrosine kinases, such as CpsD of Streptococcus agalactiae, work together with cognate proteins to regulate chain length and attachment of exported polysaccharides involved in capsule formation, O-antigen biosynthesis, colanic acid biosynthesis, and similar pathways. TIGR01008.1 TIGR01008 uS3_euk_arch 150.25 150.25 195 equivalog Y Y N 30S ribosomal protein S3 rpsC GO:0003735,GO:0006412,GO:0015935 131567 cellular organisms no rank 1253 JCVI ribosomal protein uS3 30S ribosomal protein S3 This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly. TIGR01009.1 TIGR01009 rpsC_bact 114.5 114.5 212 equivalog Y Y N 30S ribosomal protein S3 rpsC GO:0003735,GO:0006412 131567 cellular organisms no rank 32332 JCVI ribosomal protein uS3 30S ribosomal protein S3 This model describes the bacterial type of ribosomal protein S3, which forms a complex with S10 and S14. It binds the lower part of the 30S subunit head and the mRNA in the complete ribosome to position it for translation. Note that chloroplast and mitochondrial forms have large, variable inserts between conserved N-terminal and C-terminal domains, and may score below cutoffs. TIGR01012.1 TIGR01012 uS2_euk_arch 211.5 211.5 196 equivalog Y Y N 30S ribosomal protein S2 rpsB GO:0003735,GO:0006412,GO:0015935 131567 cellular organisms no rank 1170 JCVI ribosomal protein uS2 30S ribosomal protein S2 This HMM describes the ribosomal protein of Archaea and the eukaryotic cytosol, homologous to S2 of bacteria. It is designated typically as Sa in eukaryotes and Sa or S2 in the archaea. S2 is one of the last subunits in the assembly of the 30S subunit; absence of S2 does not inhibit assembly but results in an inactive subunit. TIGR01016.1 TIGR01016 sucCoAbeta 375.55 375.55 386 subfamily Y Y N succinate-CoA ligase subunit beta sucC GO:0004774,GO:0006099 131567 cellular organisms no rank 45692 JCVI succinate-CoA ligase, beta subunit succinate-CoA ligase subunit beta This model is designated subfamily because it does not discriminate the ADP-forming enzyme ((EC 6.2.1.5) from the GDP_forming (EC 6.2.1.4) enzyme. The N-terminal half is described by the CoA-ligases HMM (PF00549). The C-terminal half is described by the ATP-grasp HMM (PF02222). This family contains a split seen both in a maximum parsimony tree (which ignores gaps) and in the gap pattern near position 85 of the seed alignment. Eukaryotic and most bacterial sequences are longer and contain a region similar to TXQTXXXG. Sequences from Deinococcus radiodurans, Mycobacterium tuberculosis, Streptomyces coelicolor, and the Archaea are 6 amino acids shorter in that region and contain a motif resembling [KR]G TIGR01018.1 TIGR01018 uS4_arch 82.25 82.25 162 equivalog Y Y N 30S ribosomal protein S4 rpsD GO:0003735,GO:0006412,GO:0015935 131567 cellular organisms no rank 1157 JCVI ribosomal protein uS4 30S ribosomal protein S4 This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4. TIGR01019.1 TIGR01019 sucCoAalpha 353.2 353.2 286 subfamily Y Y N succinate--CoA ligase subunit alpha sucD GO:0003824,GO:0004775,GO:0004776,GO:0009361 131567 cellular organisms no rank 41733 JCVI succinate-CoA ligase, alpha subunit succinate--CoA ligase subunit alpha This model describes succinyl-CoA synthetase alpha subunits but does not discriminate between GTP-specific and ATP-specific reactions. The model is designated as subfamily rather than equivalog for that reason. ATP citrate lyases appear to form an outgroup. TIGR01020.1 TIGR01020 uS5_euk_arch 181.65 181.65 212 equivalog Y Y N 30S ribosomal protein S5 rpsE GO:0003735,GO:0006412,GO:0015935 131567 cellular organisms no rank 1112 JCVI ribosomal protein uS5 30S ribosomal protein S5 This model finds eukaryotic ribosomal protein uS5 (previously S2 in yeast and human) as well as archaeal ribosomal protein uS5. TIGR01025.1 TIGR01025 uS19_arch 139 139 135 equivalog Y Y N 30S ribosomal protein S19 rpsS GO:0003735,GO:0006412,GO:0015935 131567 cellular organisms no rank 1073 JCVI ribosomal protein uS19 30S ribosomal protein S19 This HMM represents eukaryotic ribosomal protein uS19 (previously S15) and its archaeal equivalent. It excludes bacterial and organellar ribosomal protein S19. The nomenclature for the archaeal members is unresolved and given variously as S19 (after the more distant bacterial homologs) or S15. TIGR01027.1 TIGR01027 proB 186 186 363 equivalog_domain Y Y N glutamate 5-kinase proB 2.7.2.11 GO:0004349,GO:0005737,GO:0006561 17321544,23770122 131567 cellular organisms no rank 59550 JCVI glutamate 5-kinase glutamate 5-kinase The glutamate 5-kinase ProB has an N-terminal kinase domain and a dispensable C-terminal PUA domain. ProB catalyzes the first step in proline biosynthesis from glutamate, and typically is subject to feedback inhibition by proline. TIGR01028.1 TIGR01028 uS7_euk_arch 200 200 186 equivalog Y Y N 30S ribosomal protein S7 rpsG GO:0003735,GO:0006412,GO:0015935 131567 cellular organisms no rank 1173 JCVI ribosomal protein uS7 30S ribosomal protein S7 This HMM describes the members from the eukaryotic cytosol and the Archaea of the family that includes ribosomal protein uS7 (previously S5 in yeast and human). A separate model describes bacterial and organellar S7. TIGR01034.1 TIGR01034 metK 309.4 309.4 377 equivalog Y Y N methionine adenosyltransferase metK 2.5.1.6 GO:0004478,GO:0005524,GO:0006556 8611562,8755891 131567 cellular organisms no rank 64280 JCVI methionine adenosyltransferase methionine adenosyltransferase Methionine adenosyltransferase (S-adenosylmethionine synthetase) catalyzes the formation of S-adenosylmethionine from methionine and ATP. TIGR01035.1 TIGR01035 hemA 209.55 209.55 416 equivalog Y Y N glutamyl-tRNA reductase hemA 1.2.1.70 GO:0008883,GO:0050661 131567 cellular organisms no rank 50910 JCVI glutamyl-tRNA reductase glutamyl-tRNA reductase This enzyme, together with glutamate-1-semialdehyde-2,1-aminomutase (TIGR00713), leads to the production of delta-amino-levulinic acid from Glu-tRNA. TIGR01036.1 TIGR01036 pyrD_sub2 200 200 356 equivalog Y Y N dihydroorotate dehydrogenase (quinone) pyrD 1.3.5.2 GO:0004152,GO:0006207,GO:0016020 131567 cellular organisms no rank 56236 JCVI dihydroorotate dehydrogenase (fumarate) dihydroorotate dehydrogenase (quinone) This model describes enzyme protein dihydroorotate dehydrogenase exclusively for subfamily 2. It includes members from bacteria, yeast, plants etc. The subfamilies 1 and 2 share extensive homology, particularly toward the C-terminus. This subfamily has a longer N-terminal region. TIGR01037.2 TIGR01037 pyrD_sub1_fam 270 270 300 subfamily Y Y N dihydroorotate dehydrogenase 131567 cellular organisms no rank 19758 JCVI dihydroorotate dehydrogenase family protein dihydroorotate dehydrogenase This family includes dihydroorotate dehydrogenases EC 1.3.1.14, which uses NAD(+) as an acceptor, and EC 1.3.98.1, which uses fumarate as an acceptor, as the enzyme converts dihydroorotate to orotate during pyrimidine nucleotide biosynthesis. TIGR01038.1 TIGR01038 uL22_arch_euk 79.85 79.85 148 equivalog Y Y N 50S ribosomal protein L22 rplV GO:0003735,GO:0006412,GO:0015934 131567 cellular organisms no rank 1144 JCVI ribosomal protein uL22 50S ribosomal protein L22 This model describes the ribosomal protein uL22 of the eukaryotic cytosol and of the Archaea, previously designated as L17, L22, and L23. The corresponding bacterial form of uL22 is described by a separate model. TIGR01039.1 TIGR01039 atpD 462.85 462.85 462 equivalog Y Y N F0F1 ATP synthase subunit beta atpD 7.1.2.2 GO:0015986,GO:0045261,GO:0046933 131567 cellular organisms no rank 47871 JCVI ATP synthase F1, beta subunit F0F1 ATP synthase subunit beta The F0F1 ATP synthase can produce ATP in the presence of a proton gradient across the membrane. Members of this family are the beta subunit of the F1 sector. The alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. Catalytic sites belong primarily to the beta-subunit. TIGR01043.1 TIGR01043 ATP_syn_A_arch 972.15 972.15 580 equivalog Y Y N ATP synthase subunit A 7.1.2.2 GO:0015986,GO:0033178,GO:0046961 131567 cellular organisms no rank 1064 JCVI ATP synthase archaeal, A subunit ATP synthase archaeal, A subunit Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases. TIGR01044.1 TIGR01044 rplV_bact 73.65 73.65 103 equivalog Y Y N 50S ribosomal protein L22 rplV GO:0003735,GO:0006412,GO:0015934 12225755,13130133,9862810 131567 cellular organisms no rank 25023 JCVI ribosomal protein uL22 50S ribosomal protein L22 L22 binds specifically to 23S rRNA during the early stages of 50S assembly; makes contact with all 6 domains of the 23S rRNA in the assembled 50S subunit and ribosome; mutations in this gene result in erythromycin resistance; located near peptidyl-transferase center. This model describes bacterial and chloroplast forms of ribosomal protein L22. TIGR01046.1 TIGR01046 uS10_euk_arch 96.25 96.25 99 equivalog Y Y N 30S ribosomal protein S10 rpsJ GO:0003735,GO:0006412,GO:0015935 131567 cellular organisms no rank 609 JCVI ribosomal protein uS10 30S ribosomal protein S10 This model describes the archaeal version of ribosomal protein uS10 and its equivalents (previously called S20) in eukaryotes. It is involved in assembly of the 30S subunit and in the ribosome binding to tRNA. TIGR01047.1 TIGR01047 nspC 409.05 409.05 380 equivalog Y Y N carboxynorspermidine decarboxylase nspC 4.1.1.96 GO:0016831,GO:0045312 1955861 131567 cellular organisms no rank 14508 JCVI carboxynorspermidine decarboxylase carboxynorspermidine decarboxylase This protein is related to diaminopimelate decarboxylase. It is the last enzyme in norspermidine biosynthesis by an unusual pathway shown in Vibrio alginolyticus. TIGR01048.1 TIGR01048 lysA 297.9 297.9 417 equivalog Y Y N diaminopimelate decarboxylase lysA 4.1.1.20 GO:0008836,GO:0009089 131567 cellular organisms no rank 78980 JCVI diaminopimelate decarboxylase diaminopimelate decarboxylase This family consists of diaminopimelate decarboxylase, an enzyme which catalyzes the conversion of diaminopimelic acid into lysine during the last step of lysine biosynthesis. TIGR01050.1 TIGR01050 rpsS_bact 89.35 89.35 92 equivalog Y Y N 30S ribosomal protein S19 rpsS GO:0003735,GO:0006412,GO:0015935 10512703 131567 cellular organisms no rank 17997 JCVI ribosomal protein uS19 30S ribosomal protein S19 Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. This HMM represents bacterial forms. TIGR01051.1 TIGR01051 topA_bact 456.4 456.4 632 equivalog Y Y N type I DNA topoisomerase topA 5.6.2.1 GO:0003677,GO:0003917,GO:0005737,GO:0006260,GO:0006265 131567 cellular organisms no rank 79646 JCVI DNA topoisomerase I type I DNA topoisomerase This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events. TIGR01052.1 TIGR01052 top6b 380.7 380.7 488 equivalog Y Y N DNA topoisomerase VI subunit B top6B 5.6.2.2 GO:0003677,GO:0003918,GO:0005524,GO:0006265 9121560 131567 cellular organisms no rank 1396 JCVI DNA topoisomerase VI, B subunit DNA topoisomerase VI subunit B This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase). TIGR01053.1 TIGR01053 LSD1 15.5 15.5 31 subfamily_domain Y Y N zinc finger domain-containing protein 9054508 131567 cellular organisms no rank 950 JCVI zinc finger domain, LSD1 subclass zinc finger domain, LSD1 subclass This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC TIGR01054.1 TIGR01054 rgy 471.7 471.7 1172 equivalog Y Y N reverse gyrase rgy 3.6.4.12,5.6.2.2 GO:0003677,GO:0003916,GO:0006265 12359215,25013168,9440516 131567 cellular organisms no rank 540 JCVI reverse gyrase reverse gyrase Reverse gyrase, a combination of a type I DNA topoisomerase and an ATP-dependent DNA helicase, introduces positive supercoils that raise the melting (strand dissociation) temperature of circular DNA. It is the quintessential marker of hyperthermophiles, for both bacteria and archaea. TIGR01057.1 TIGR01057 topA_arch 458 458 618 equivalog Y Y N DNA topoisomerase I topA 5.6.2.1 GO:0003677,GO:0003916,GO:0003917,GO:0006265 131567 cellular organisms no rank 859 JCVI DNA topoisomerase I DNA topoisomerase I This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent. TIGR01059.1 TIGR01059 gyrB 882.4 882.4 639 equivalog Y Y N DNA topoisomerase (ATP-hydrolyzing) subunit B gyrB 5.6.2.2 GO:0003677,GO:0003918,GO:0005524,GO:0005694,GO:0006265 131567 cellular organisms no rank 65589 JCVI DNA gyrase, B subunit DNA gyrase subunit B This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB. TIGR01060.1 TIGR01060 eno 443.85 443.85 425 equivalog Y Y N phosphopyruvate hydratase eno 4.2.1.11 GO:0000015,GO:0000287,GO:0004634,GO:0006096 131567 cellular organisms no rank 62731 JCVI phosphopyruvate hydratase phosphopyruvate hydratase Alternate name: enolase TIGR01063.1 TIGR01063 gyrA 877 877 800 equivalog Y Y N DNA topoisomerase (ATP-hydrolyzing) subunit A gyrA 5.6.2.2 GO:0003916,GO:0003918,GO:0006265,GO:0009330 131567 cellular organisms no rank 82764 JCVI DNA gyrase, A subunit DNA gyrase subunit A This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. TIGR01064.1 TIGR01064 pyruv_kin 306.4 306.4 476 equivalog Y Y N pyruvate kinase pyk 2.7.1.40 GO:0000287,GO:0004743,GO:0006096,GO:0030955 23999300 131567 cellular organisms no rank 76706 JCVI pyruvate kinase pyruvate kinase This enzyme is a homotetramer. Some forms are active only in the presence of fructose-1,6-bisphosphate or similar phosphorylated sugars. TIGR01068.1 TIGR01068 thioredoxin 96.8 96.8 101 equivalog Y Y N thioredoxin trxA GO:0015035 23229911 131567 cellular organisms no rank 87341 JCVI thioredoxin thioredoxin Several proteins, such as protein disulfide isomerase, have two or more copies of a domain closely related to thioredoxin. This model is designed to recognize authentic thioredoxin, a small protein that should be hit exactly once by this HMM. Any protein that hits once with a score greater than the second (per domain) trusted cutoff may be taken as thioredoxin. TIGR01070.1 TIGR01070 mutS1 641.7 641.7 840 equivalog Y Y N DNA mismatch repair protein MutS mutS GO:0005524,GO:0006298,GO:0030983 16026761,9722651 131567 cellular organisms no rank 72204 JCVI DNA mismatch repair protein MutS DNA mismatch repair protein MutS TIGR01071.1 TIGR01071 rplO_bact 77.95 77.95 144 equivalog Y Y N 50S ribosomal protein L15 rplO GO:0003735,GO:0006412,GO:0015934 2204629 131567 cellular organisms no rank 36278 JCVI ribosomal protein uL15 50S ribosomal protein L15 TIGR01076.1 TIGR01076 sortase_fam 39.35 39.35 136 subfamily Y Y N sortase 3.4.22.70 GO:0004197,GO:0016485,GO:0045184 10427003,11371637 131567 cellular organisms no rank 64669 JCVI sortase sortase This family includes Staphylococcus aureus sortase A, a housekeeping transpeptidase that attaches surface proteins by the Thr of an LPXTG motif to the cell wall. The family also includes special purpose sortases required for correct assembly of LPXTG-containing fimbrial proteins. It excludes the sortase B family, for which the recognition site NPXTN is typical. TIGR01077.1 TIGR01077 L13_A_E 98.9 98.9 141 equivalog Y Y N 50S ribosomal protein L13 rplM GO:0003735,GO:0006412,GO:0015934 131567 cellular organisms no rank 1187 JCVI ribosomal protein uL13 50S ribosomal protein L13 This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol. Bacterial and organellar forms are represented by HMM TIGR01066. TIGR01080.1 TIGR01080 rplX_A_E 47.65 47.65 116 equivalog Y Y N 50S ribosomal protein L24 rplX GO:0003735,GO:0006412,GO:0015934 131567 cellular organisms no rank 1175 JCVI ribosomal protein uL24 50S ribosomal protein L24 Assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by related HMM TIGR01079. TIGR01083.1 TIGR01083 nth 211.7 211.7 192 equivalog Y Y N endonuclease III nth 4.2.99.18 GO:0006281,GO:0140078 131567 cellular organisms no rank 60936 JCVI endonuclease III endonuclease III This equivalog HMM identifes nth members of the PF00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY. TIGR01084.1 TIGR01084 mutY 286.5 286.5 277 equivalog Y Y N A/G-specific adenine glycosylase mutY 3.2.2.31 GO:0006284,GO:0019104 12483591,2682664,9846876 131567 cellular organisms no rank 52991 JCVI A/G-specific adenine glycosylase A/G-specific adenine glycosylase This equivalog HMM identifies mutY members of the PF00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY. TIGR01085.1 TIGR01085 murE 257.3 257.3 472 subfamily Y Y N UDP-N-acetylmuramyl-tripeptide synthetase murE GO:0005524,GO:0005737,GO:0008360,GO:0016881,GO:0051301 10498701 131567 cellular organisms no rank 92719 JCVI UDP-N-acetylmuramyl-tripeptide synthetase UDP-N-acetylmuramyl-tripeptide synthetase This model is equivalog because it does not distinguish lysine-adding (EC 6.3.2.7) from diaminopimelate-adding forms of MurE (EC 6.3.2.13). TIGR01087.1 TIGR01087 murD 211.95 211.95 441 equivalog Y Y N UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase murD 6.3.2.9 GO:0005524,GO:0005737,GO:0008360,GO:0008764,GO:0009252,GO:0051301 10356330,25130693,9218784 131567 cellular organisms no rank 83378 JCVI UDP-N-acetylmuramoylalanine--D-glutamate ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase Involved in peptidoglycan biosynthesis; catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine during cell wall formation TIGR01088.1 TIGR01088 aroQ 169.85 169.85 141 equivalog Y Y N type II 3-dehydroquinate dehydratase aroQ 4.2.1.10 GO:0003855,GO:0009423 131567 cellular organisms no rank 44962 JCVI 3-dehydroquinate dehydratase, type II 3-dehydroquinate dehydratase, type II This HMM specifies the type II enzyme. The type I enzyme, often found as part of a multifunctional protein, is described by TIGR01093. TIGR01090.1 TIGR01090 apt 185.85 185.85 169 equivalog Y Y N adenine phosphoribosyltransferase apt 2.4.2.7 GO:0003999,GO:0005737,GO:0006168 131567 cellular organisms no rank 35715 JCVI adenine phosphoribosyltransferase adenine phosphoribosyltransferase A phylogenetic analysis suggested omitting the bi-directional best hit homologs from the spirochetes from the seed for this HMM and making only tentative predictions of adenine phosphoribosyltransferase function for this lineage. The trusted cutoff score is made high for this reason. Most proteins scoring between the trusted and noise cutoffs are likely to act as adenine phosphotransferase. TIGR01091.1 TIGR01091 upp 208.35 208.35 207 equivalog Y Y N uracil phosphoribosyltransferase upp 2.4.2.9 GO:0004845,GO:0006223 131567 cellular organisms no rank 34012 JCVI uracil phosphoribosyltransferase uracil phosphoribosyltransferase A fairly deep split in phylogenetic and UPGMA trees separates this mostly prokaryotic set of uracil phosphoribosyltransferases from a mostly eukaryotic set that includes uracil phosphoribosyltransferase, uridine kinases, and other, uncharacterized proteins. TIGR01093.1 TIGR01093 aroD 139.3 139.3 229 equivalog_domain Y Y N type I 3-dehydroquinate dehydratase aroD 4.2.1.10 GO:0003855,GO:0009423 21087925 131567 cellular organisms no rank 14052 JCVI 3-dehydroquinate dehydratase, type I type I 3-dehydroquinate dehydratase 3-dehydroquinate dehydratase catalyzes the dehydration of 3-dehydroquinate to form 3-dehydroshikimate in aromatic amino acid biosynthesis. This model detects 3-dehydroquinate dehydratase of type I (AroD), either as a monofunctional protein or as a domain of a larger, multifunctional protein. It is often found fused to shikimate 5-dehydrogenase (EC 1.1.1.25), and sometimes additional domains. Type II 3-dehydroquinate dehydratase, designated AroQ, is described by the HMM TIGR01088. TIGR01097.1 TIGR01097 PhnE 216.7 216.7 252 equivalog Y Y N phosphonate ABC transporter, permease protein PhnE phnE 7.3.2.2 GO:0005886,GO:0015416,GO:0015716,GO:0055052 131567 cellular organisms no rank 40297 JCVI phosphonate ABC transporter, permease protein PhnE phosphonate ABC transporter, permease protein PhnE Phosphonates are a class of compound analogous to organic phosphates, but in which the C-O-P linkage is replaced by a direct, stable C-P bond. Some bacteria can utilize phosphonates as a source of phosphorus. This family consists of permease proteins of known or predicted phosphonate ABC transporters. Often this protein is found as a duplicated pair, occasionally as a fused pair. Certain "second" copies score in between the trusted and noise cutoff and should be considered true hits (by context). TIGR01098.1 TIGR01098 3A0109s03R 112.05 112.05 253 subfamily Y Y N phosphate/phosphite/phosphonate ABC transporter substrate-binding protein phnD GO:0043168,GO:0043190,GO:0043225,GO:0055085 15317793,16751609,17074913,8335257 131567 cellular organisms no rank 32183 JCVI phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein phosphate/phosphite/phosphonate ABC transporter substrate-binding protein Phosphonates are a varied class of phosphorus-containing organic compound in which a direct C-P bond is found, rather than a C-O-P linkage of the phosphorus through an oxygen atom. They may be toxic but also may be used as sources of phosphorus and energy by various bacteria. Phosphonate utilization systems typically are encoded in 14 or more genes, including a three gene ABC transporter. This family includes the periplasmic binding protein component of ABC transporters for phosphonates [1] as well as other, related binding components for closely related substances such as phosphate [2] and phosphite [3]. A number of members of this family are found in genomic contexts with components of selenium metabolic processes suggestive of a role in selenate or other selenium-compound transport. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system (GenProp0232, [4]) has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates. TIGR01099.1 TIGR01099 galU 326.8 326.8 261 equivalog Y Y N UTP--glucose-1-phosphate uridylyltransferase GalU galU 2.7.7.9 GO:0003983,GO:0006011 131567 cellular organisms no rank 53137 JCVI UTP--glucose-1-phosphate uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase GalU Built to distinquish between the highly similar genes galU and galF TIGR01104.1 TIGR01104 V_PPase 651.9 651.9 697 equivalog Y Y N V-type H(+)-translocating pyrophosphatase 3.6.1.1 GO:0004427,GO:0005886,GO:0009678,GO:1902600 10556526 131567 cellular organisms no rank 27684 JCVI V-type H(+)-translocating pyrophosphatase V-type H(+)-translocating pyrophosphatase This model describes proton pyrophosphatases from eukaryotes (predominantly plants), archaea and bacteria. It is an integral membrane protein and is suggested to have about 15 membrane spanning domains. Proton translocating inorganic pyrophosphatase, like H(+)-ATPase, acidifies the vacuoles and is pivotal to the vacuolar secondary active transport systems in plants. TIGR01108.1 TIGR01108 oadA 756.5 756.5 582 equivalog Y Y N sodium-extruding oxaloacetate decarboxylase subunit alpha oadA 7.2.4.2 GO:0006814,GO:0008948,GO:0015081 131567 cellular organisms no rank 16982 JCVI oxaloacetate decarboxylase alpha subunit sodium-extruding oxaloacetate decarboxylase subunit alpha This model describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea. The oxaloacetate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases that present in bacteria and archaea. It a multi subunit enzyme consisting of a peripheral alpha-subunit and integral membrane subunits beta and gamma. The energy released by the decarboxylation reaction of oxaloacetate is coupled to Na+ ion pumping across the membrane. TIGR01109.1 TIGR01109 Na_pump_decarbB 190.6 190.6 354 subfamily Y Y N sodium ion-translocating decarboxylase subunit beta 7.2.4.- GO:0006814,GO:0016829 11248185 131567 cellular organisms no rank 21773 JCVI sodium ion-translocating decarboxylase, beta subunit sodium ion-translocating decarboxylase subunit beta This model describes the beta subunits of sodium pump decarboxylases that include oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, and glutaconyl-CoA decarboxylase. Beta and gammma-subunits are integral membrane proteins, while alpha is membrane bound. Catalytically, the energy released by the decarboxylation reaction is coupled to the extrusion of Na+ ions across the membrane. TIGR01116.1 TIGR01116 ATPase-IIA1_Ca 703.4 703.4 799 equivalog Y Y N calcium-translocating P-type ATPase, SERCA-type 7.2.2.10 GO:0005388,GO:0005524,GO:0006816,GO:0016020,GO:0016887 131567 cellular organisms no rank 4539 JCVI calcium-translocating P-type ATPase, SERCA-type calcium-translocating P-type ATPase, SERCA-type This model describes the P-type ATPase responsible for translocating calcium ions across the endoplasmic reticulum membrane of eukaryotes [1], and is of particular importance in the sarcoplasmic reticulum of skeletal and cardiac muscle in vertebrates [2]. These pumps transfer Ca2+ from the cytoplasm to the lumen of the endoplasmic reticulum. In humans and mice, at least, there are multiple isoforms of the SERCA pump with overlapping but not redundant functions. Defects in SERCA isoforms are associated with diseases in humans [3]. The calcium P-type ATPases have been characterized as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump [4] modelled by TIGR01517. A separate analysis divides Type IIA into sub-types, SERCA and PMR1 [5] the latter of which is modelled by TIGR01522. TIGR01117.1 TIGR01117 mmdA 998.8 998.8 512 subfamily Y Y N methylmalonyl-CoA decarboxylase subunit alpha mmdA 7.2.4.3 131567 cellular organisms no rank 25 JCVI methylmalonyl-CoA decarboxylase alpha subunit methylmalonyl-CoA decarboxylase subunit alpha This model describes methylmalonyl-CoA decarboxylase alpha subunit in archaea and bacteria. Methylmalonyl-CoA decarboxylase Na+ pump is a representative of a class of Na+ transport decarboxylases that couples the energy derived by decarboxylation of carboxylic acid substrates to drive the extrusion of Na+ ion across the membrane. TIGR01120.1 TIGR01120 rpiB 138.65 138.65 143 equivalog Y Y N ribose 5-phosphate isomerase B rpiB 5.3.1.6 GO:0004751,GO:0009052 131567 cellular organisms no rank 21673 JCVI ribose 5-phosphate isomerase B ribose 5-phosphate isomerase B Involved in the non-oxidative branch of the pentose phospate pathway. TIGR01122.1 TIGR01122 ilvE_I 245.55 245.55 298 equivalog Y Y N branched-chain-amino-acid transaminase ilvE 2.6.1.42 GO:0004084,GO:0009081 131567 cellular organisms no rank 25131 JCVI branched-chain amino acid aminotransferase branched-chain-amino-acid transaminase Among the class IV aminotransferases are two phylogenetically separable groups of branched-chain amino acid aminotransferase (IlvE). The last common ancestor of the two lineages appears also to have given rise to a family of D-amino acid aminotransferases (DAAT). This model represents the IlvE family more strongly similar to the DAAT family. TIGR01123.1 TIGR01123 ilvE_II 250.05 250.05 313 equivalog Y Y N branched-chain-amino-acid transaminase ilvE 2.6.1.42 GO:0004084,GO:0009081 131567 cellular organisms no rank 43328 JCVI branched-chain amino acid aminotransferase branched-chain-amino-acid transaminase Among the class IV aminotransferases are two phylogenetically separable groups of branched-chain amino acid aminotransferase (IlvE). The last common ancestor of the two lineages appears also to have given rise to a family of D-amino acid aminotransferases (DAAT). This model represents the IlvE family less similar to the DAAT family. TIGR01127.1 TIGR01127 ilvA_1Cterm 378.75 378.75 380 equivalog Y Y N threonine ammonia-lyase ilvA 4.3.1.19 GO:0004794,GO:0006567 131567 cellular organisms no rank 27011 JCVI threonine ammonia-lyase threonine ammonia-lyase A form of threonine dehydratase with two copies of the C-terminal domain Pfam:PF00585 is described by TIGR01124. This model describes a phylogenetically distinct form with a single copy of PF00585. This form branches with the catabolic threonine dehydratase of E. coli; many members are designated as catabolic for this reason. However, the catabolic form lacks any PF00585 domain. Many members of this model are found in species with other Ile biosynthetic enzymes. TIGR01129.1 TIGR01129 secD 244.4 244.4 397 equivalog_domain Y Y N protein translocase subunit SecD secD GO:0006886,GO:0015450,GO:0031522,GO:0043952 131567 cellular organisms no rank 76714 JCVI protein-export membrane protein SecD protein translocase subunit SecD Members of this family are highly variable in length immediately after the well-conserved motif LGLGLXGG at the amino-terminal end of this model. Archaeal homologs are not included in the seed and score between the trusted and noise cutoffs. SecD from Mycobacterium tuberculosis has a long Pro-rich insert. TIGR01131.1 TIGR01131 ATP_synt_6_or_A 102.6 102.6 227 equivalog Y Y N F0F1 ATP synthase subunit A atpB 7.1.2.2 GO:0015986,GO:0045263,GO:0046933 131567 cellular organisms no rank 48051 JCVI ATP synthase F0, A subunit F0F1 ATP synthase subunit A Bacterial forms should be designated ATP synthase, F0 subunit A; eukaryotic (chloroplast and mitochondrial) forms should be designated ATP synthase, F0 subunit 6. The F1/F0 ATP synthase is a multisubunit, membrane associated enzyme found in bacteria and mitochondria and chloroplast. This enzyme is principally involved in the synthesis of ATP from ADP and inorganic phosphate by coupling the energy derived from the proton electrochemical gradient across the biological membrane. A brief description of this multisubunit enzyme complex: F1 and F0 represent two major clusters of subunits. Individual subunits in each of these clusters are named differently in prokaryotes and in organelles e.g., mitochondria and chloroplast. The bacterial equivalent of subunit 6 is named subunit 'A'. It has been shown that proton is conducted though this subunit. Typically, deprotonation and reprotonation of the acidic amino acid side-chains are implicated in the process. TIGR01134.1 TIGR01134 purF 350 350 432 equivalog Y Y N amidophosphoribosyltransferase purF 2.4.2.14 GO:0004044,GO:0009113 131567 cellular organisms no rank 53957 JCVI amidophosphoribosyltransferase amidophosphoribosyltransferase Alternate name: glutamine phosphoribosylpyrophosphate (PRPP) amidotransferase. TIGR01135.1 TIGR01135 glmS 418.05 418.05 607 equivalog Y Y N glutamine--fructose-6-phosphate transaminase (isomerizing) glmS 2.6.1.16 GO:0004360,GO:1901137 131567 cellular organisms no rank 88167 JCVI glutamine-fructose-6-phosphate transaminase (isomerizing) glutamine--fructose-6-phosphate transaminase (isomerizing) The member from Methanococcus jannaschii contains an intein. TIGR01136.1 TIGR01136 cysKM 344.15 344.15 299 subfamily Y Y N cysteine synthase 2.5.1.47 GO:0004124,GO:0006535 131567 cellular organisms no rank 75671 JCVI cysteine synthase cysteine synthase This model discriminates cysteine synthases (EC 2.5.1.47) (both CysK and CysM) from cystathionine beta-synthase, a protein found primarily in eukaryotes and carrying a C-terminal CBS domain lacking from this protein. Bacterial proteins lacking the CBS domain but otherwise showing resemblamnce to cystathionine beta-synthases and considerable phylogenetic distance from known cysteine synthases were excluded from the seed and score below the trusted cutoff. TIGR01137.1 TIGR01137 cysta_beta 510.25 510.25 457 equivalog Y Y N cystathionine beta-synthase 4.2.1.22 GO:0004122,GO:0005737,GO:0019343 131567 cellular organisms no rank 11171 JCVI cystathionine beta-synthase cystathionine beta-synthase Members of this family closely resemble cysteine synthase but contain an additional C-terminal CBS domain. The function of any bacterial member included in this family is proposed but not proven. TIGR01139.1 TIGR01139 cysK 350.95 350.95 298 equivalog Y Y N cysteine synthase A cysK 2.5.1.47 GO:0004124,GO:0006535 131567 cellular organisms no rank 51743 JCVI cysteine synthase A cysteine synthase A This model distinguishes cysteine synthase A (CysK) from cysteine synthase B (CysM). CysM differs in having a broader specificity that also allows the use of thiosulfate to produce cysteine thiosulfonate. TIGR01140.1 TIGR01140 L_thr_O3P_dcar 290.55 290.55 331 equivalog Y Y N threonine-phosphate decarboxylase CobD cobD 4.1.1.81 GO:0003824,GO:0009236 11939774,12119022,9446573 131567 cellular organisms no rank 20805 JCVI threonine-phosphate decarboxylase threonine-phosphate decarboxylase CobD Members of this family are CobD, a threonine-phosphate decarboxylase involved in an anaerobic pathway for cobalamin biosynthesis, as found in Salmonella enterica. The enzyme is a pyridoxal phosphate-binding class II aminotransferases (see PFAM:PF00222) closely related to, yet distinct from, histidinol-phosphate aminotransferase (HisC). Note that the term CobD has been used previously to refer to the cobalamin biosynthesis enzyme now known as CbiB. TIGR01141.1 TIGR01141 hisC 276.55 276.55 349 equivalog Y Y N histidinol-phosphate transaminase hisC 2.6.1.9 GO:0000105,GO:0004400 131567 cellular organisms no rank 101361 JCVI histidinol-phosphate transaminase histidinol-phosphate transaminase Alternate names: histidinol-phosphate transaminase; imidazole acetol-phosphate transaminase Histidinol-phosphate aminotransferase is a pyridoxal-phosphate dependent enzyme. TIGR01142.1 TIGR01142 purT 502.15 502.15 380 equivalog Y Y N phosphoribosylglycinamide formyltransferase 2 purT GO:0000287,GO:0004644,GO:0005524,GO:0009152,GO:0016742 131567 cellular organisms no rank 25893 JCVI phosphoribosylglycinamide formyltransferase 2 phosphoribosylglycinamide formyltransferase 2 This enzyme is an alternative to PurN (TIGR00639) TIGR01158.1 TIGR01158 SUI1_rel 111.65 111.65 102 equivalog Y Y N stress response translation initiation inhibitor YciH yciH GO:0003743 10497266 131567 cellular organisms no rank 7931 JCVI putative translation initiation factor SUI1 stress response translation initiation inhibitor YciH This family of archaeal and bacterial proteins is homologous to the eukaryotic translation intiation factor SUI1 involved in directing the ribosome to the proper start site of translation by functioning in concert with eIF-2 and the initiator tRNA-Met. TIGR01161.1 TIGR01161 purK 318.4 318.4 362 equivalog_domain Y Y N 5-(carboxyamino)imidazole ribonucleotide synthase purK 6.3.4.18 GO:0009152,GO:0009320,GO:0034028 10569930 131567 cellular organisms no rank 65972 JCVI phosphoribosylaminoimidazole carboxylase, ATPase subunit 5-(carboxyamino)imidazole ribonucleotide synthase Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This model represents PurK, N5-carboxyaminoimidazole ribonucleotide synthetase (EC 6.3.4.18), which hydrolyzes ATP and converts AIR to N5-CAIR. PurE converts N5-CAIR to CAIR. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. TIGR01162.1 TIGR01162 purE 149.6 149.6 156 equivalog_domain Y Y N 5-(carboxyamino)imidazole ribonucleotide mutase purE 4.1.1.21,5.4.99.18 GO:0004638,GO:0006189,GO:0009152,GO:0009320 10074353 131567 cellular organisms no rank 52529 JCVI phosphoribosylaminoimidazole carboxylase, catalytic subunit 5-(carboxyamino)imidazole ribonucleotide mutase Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This model represents PurK, an N5-CAIR mutase. TIGR01163.1 TIGR01163 rpe 212.6 212.6 211 equivalog Y Y N ribulose-phosphate 3-epimerase rpe 5.1.3.1 GO:0004750,GO:0006098 15333955,21402925 131567 cellular organisms no rank 62857 JCVI ribulose-phosphate 3-epimerase ribulose-phosphate 3-epimerase Members of this family are ribulose-phosphate 3-epimerase, also known as pentose-5-phosphate 3-epimerase (PPE). PPE converts D-ribulose 5-phosphate into D-xylulose 5-phosphate in Calvin's reductive pentose phosphate cycle. It has been found in a wide range of bacteria, archaea, fungi, and plants. TIGR01165.1 TIGR01165 cbiN 104.85 104.85 91 subfamily Y Y N cobalt ECF transporter S component CbiN cbiN 131567 cellular organisms no rank 3875 JCVI cobalt transport protein cobalt ECF transporter S component CbiN This model describes the cobalt transporter in bacteria and its equivalents in archaea. It principally functions in the ion uptake mechanism. It is a multisubunit transporter with two integral membrane proteins and two closely associated cytoplasmic subunits. This transporter belongs to the ABC transporter superfamily (ATP stands for ATP Binding Cassette). This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux. TIGR01166.1 TIGR01166 cbiO 211.8 211.8 190 subfamily Y N N cobalt ABC transporter, ATP-binding protein GO:0005524,GO:0006824,GO:0032778,GO:0043190 131567 cellular organisms no rank 14847 JCVI cobalt ABC transporter, ATP-binding protein cobalt ABC transporter, ATP-binding protein This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux. TIGR01167.1 TIGR01167 LPXTG_anchor 15.9 15.9 34 domain Y Y N LPXTG cell wall anchor domain-containing protein GO:0009986 10754567 131567 cellular organisms no rank 359035 JCVI LPXTG cell wall anchor domain LPXTG cell wall anchor domain This model describes the LPXTG motif-containing region found at the C-terminus of many surface proteins of Streptococcus and Streptomyces species. Cleavage between the Thr and Gly by sortase or a related enzyme leads to covalent anchoring at the new C-terminal Thr to the cell wall. Hits that do not lie at the C-terminus or are not found in Gram-positive bacteria are probably false-positive. A common feature of this proteins containing this domain appears to be a high proportion of charged and zwitterionic residues immediatedly upstream of the LPXTG motif. This model differs from other descriptions of the LPXTG region by including a portion of that upstream charged region. TIGR01171.1 TIGR01171 rplB_bact 174.5 174.5 275 equivalog Y Y N 50S ribosomal protein L2 rplB GO:0003723,GO:0003735,GO:0006412,GO:0015934,GO:0016740 131567 cellular organisms no rank 35001 JCVI ribosomal protein uL2 50S ribosomal protein L2 L2 is one of the primary rRNA-binding proteins; required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. This HMM is specific for bacterial and organellar forms of ribosomal protein L2. TIGR01172.1 TIGR01172 cysE 210.65 210.65 162 equivalog Y Y N serine O-acetyltransferase cysE 2.3.1.30 GO:0005737,GO:0006535,GO:0009001 131567 cellular organisms no rank 35269 JCVI serine O-acetyltransferase serine O-acetyltransferase Cysteine biosynthesis TIGR01178.1 TIGR01178 ade 472.5 472.5 552 equivalog Y Y N adenine deaminase ade 3.5.4.2 GO:0000034,GO:0006146,GO:0006168 131567 cellular organisms no rank 19809 JCVI adenine deaminase adenine deaminase The family described by this model includes an experimentally characterized adenine deaminase of Bacillus subtilis. It also include a member from Methanobacterium thermoautotrophicum, in which adenine deaminase activity has been detected. TIGR01179.1 TIGR01179 galE 262.3 262.3 332 equivalog Y Y N UDP-glucose 4-epimerase GalE galE 5.1.3.2 GO:0003978,GO:0006012 131567 cellular organisms no rank 98082 JCVI UDP-glucose 4-epimerase GalE UDP-glucose 4-epimerase GalE Alternate name: UDPgalactose 4-epimerase This enzyme interconverts UDP-glucose and UDP-galactose. A set of related proteins, some of which are tentatively identified as UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus halodurans, and several archaea, but deeply branched from this set and lacking experimental evidence, are excluded from this HMM and described by a separate model. TIGR01181.1 TIGR01181 dTDP_gluc_dehyt 365.1 365.1 321 equivalog Y Y N dTDP-glucose 4,6-dehydratase rfbB 4.2.1.46 GO:0008460,GO:0009225,GO:0019305 131567 cellular organisms no rank 77507 JCVI dTDP-glucose 4,6-dehydratase dTDP-glucose 4,6-dehydratase This protein is related to UDP-glucose 4-epimerase (GalE) and likewise has an NAD cofactor. TIGR01182.1 TIGR01182 eda 156.05 156.05 204 subfamily Y Y N bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase eda 4.1.2.14,4.1.3.16 GO:0008675,GO:0008700,GO:0009255 131567 cellular organisms no rank 54366 JCVI 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase 2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida TIGR01186.1 TIGR01186 proV 326.6 326.6 363 subfamily Y Y N betaine/proline/choline family ABC transporter ATP-binding protein GO:0005524,GO:0015837,GO:0016020,GO:0043190 131567 cellular organisms no rank 59262 JCVI glycine betaine/L-proline transport ATP binding subunit betaine/proline/choline family ABC transporter ATP-binding protein This model describes the ATP binding subunit of a subfamily of ABC transporters, including ProV (for glycine betaine and proline betaine transport), OpuBA (choline), OpuCA (carnitine), GbuA (glycine betaine and carnitine), OusV (glycine betaine and choline), etc. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system includes an ATP binding (and hydrolyzing) subunit; a hydrophilic polypeptide that forms a channel through the membrane, and a substrate binding protein; any of these subunits may be represented by two paralogs instead of just one. Substrates for many members of this transport system, such as glycine betaine (a glycine with its N trimethylated, often simply called betaine), serve as osmoprotectants , although they also may serve as nutrients. Members of the family are the ATP-binding subunit of ABC transporters for substrates such as betaine, L-proline or other amino acids, choline, carnitine, etc. The substrate specificity is best determined from the substrate-binding subunit, rather than this subunit, as it interacts with the permease subunit and not with substrate directly. TIGR01187.1 TIGR01187 potA 355.6 355.6 325 subfamily Y Y N polyamine ABC transporter ATP-binding protein potA 7.6.2.11 GO:0005524,GO:0015417,GO:0015846,GO:0043190 131567 cellular organisms no rank 61877 JCVI polyamine ABC transporter, ATP-binding protein polyamine ABC transporter ATP-binding protein This model describes spermidine/putrescine ABC transporter, ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. Polyamines like spermidine and putrescine play vital role in cell proliferation, differentiation, and ion homeostasis. The concentration of polyamines within the cell are regulated by biosynthesis, degradation and transport (uptake and efflux included). TIGR01188.1 TIGR01188 drrA 312.45 312.45 302 subfamily Y N N daunorubicin resistance ABC transporter, ATP-binding protein GO:0005524,GO:0043190,GO:0043215 131567 cellular organisms no rank 69425 JCVI daunorubicin resistance ABC transporter, ATP-binding protein daunorubicin resistance ABC transporter, ATP-binding protein This model describes daunorubicin resistance ABC transporter, ATP binding subunit in bacteria and archaea. This model is restricted in its scope to preferentially recognize the ATP binding subunit associated with effux of the drug, daunorubicin. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. In eukaryotes proteins of similar function include p-gyco proteins, multidrug resistance protein etc. TIGR01189.1 TIGR01189 ccmA 131.6 131.6 198 equivalog Y Y N heme ABC exporter ATP-binding protein CcmA ccmA 7.6.2.5 GO:0015439,GO:0015886,GO:0017004,GO:0022857,GO:0043190 131567 cellular organisms no rank 25475 JCVI heme ABC exporter, ATP-binding protein CcmA heme ABC exporter ATP-binding protein CcmA This model describes the cyt c biogenesis protein encoded by ccmA in bacteria. An exception is, an arabidopsis protein. Quite likely this is encoded by an organelle. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c. TIGR01195.1 TIGR01195 oadG_fam 36.05 36.05 84 subfamily Y N N sodium pump decarboxylases, gamma subunit GO:0015081,GO:0016020,GO:0036376 131567 cellular organisms no rank 8376 JCVI sodium pump decarboxylases, gamma subunit sodium pump decarboxylases, gamma subunit This model finds the subfamily of distantly related, low complexity, hydrophobic small subunits of several related sodium ion-pumping decarboxylases. These include oxaloacetate decarboxylase gamma subunit and methylmalonyl-CoA decarboxylase delta subunit. Most sequences scoring between the noise and trusted cutoffs are eukaryotic sodium channel proteins. TIGR01197.1 TIGR01197 nramp 272.5 272.5 390 subfamily Y N N metal ion transporter, metal ion (Mn2+/Fe2+) transporter (Nramp) family GO:0016020 11027260 131567 cellular organisms no rank 31078 JCVI metal ion transporter, metal ion (Mn2+/Fe2+) transporter (Nramp) family metal ion transporter, metal ion (Mn2+/Fe2+) transporter (Nramp) family This model describes the Nramp metal ion transporter family. Historically, in mammals these proteins have been functionally characterized as proteins involved in the host pathogen resistance, hence the name - NRAMP. At least two isoforms Nramp1 and Nramp2 have been identified. However the exact mechanism of pathogen resistance was unclear, until it was demonstrated by expression cloning and electrophysiological techniques that this protein was a metal ion transporter. It was also independently demonstrated that a microcytic anemia (mk) locus in mouse, encodes a metal ion transporter (DCT1 or Nramp2). The transporter has a broad range of substrate specificity that include Fe+2, Zn+2, Mn+2, Co+2, Cd+2, Cu+2, Ni+2 and Pb+2. The uptake of these metal ions is coupled to proton symport. Metal ions are essential cofactors in a number of biological process including, oxidative phosphorylation, gene regulation and metal ion homeostasis. Nramp1 could confer resistance to infection in one of the two ways. (1) The uptake of Fe+2 can produce toxic hydroxyl radicals via Fenton reaction killing the pathogens in phagosomes or (2) Deplete the metal ion pools in the phagosome and deprive the pathogens of metal ions, which is critical for its survival. TIGR01204.1 TIGR01204 bioW 193.55 193.55 232 equivalog Y Y N 6-carboxyhexanoate--CoA ligase bioW 6.2.1.14 GO:0009102,GO:0042410 1445232 131567 cellular organisms no rank 1588 JCVI 6-carboxyhexanoate--CoA ligase 6-carboxyhexanoate--CoA ligase Alternate name: pimeloyl-CoA synthase. TIGR01205.1 TIGR01205 D_ala_D_alaTIGR 245.65 245.65 318 subfamily Y Y N D-alanine--D-alanine ligase 6.3.2.4 GO:0005524,GO:0005737,GO:0008716,GO:0009252 131567 cellular organisms no rank 83512 JCVI D-alanine--D-alanine ligase D-alanine--D-alanine ligase This model describes D-Ala--D-Ala ligase, an enzyme that makes a required precursor of the bacterial cell wall. It also describes some closely related proteins responsible for resistance to glycopeptide antibiotics such as vancomycin. The mechanism of glyopeptide antibiotic resistance involves the production of D-alanine-D-lactate (VanA and VanB families) or D-alanine-D-serine (VanC). The seed alignment contains only chromosomally encoded D-ala--D-ala ligases, but a number of antibiotic resistance proteins score above the trusted cutoff of this model. TIGR01206.1 TIGR01206 lysW 53.2 53.2 54 equivalog Y Y N lysine biosynthesis protein LysW lysW GO:0019878 11238076 131567 cellular organisms no rank 806 JCVI lysine biosynthesis protein LysW lysine biosynthesis protein LysW This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway. TIGR01207.1 TIGR01207 rmlA 360.65 360.65 286 equivalog Y Y N glucose-1-phosphate thymidylyltransferase RfbA rfbA 2.7.7.24 GO:0000271,GO:0008879,GO:0019305 9084178 131567 cellular organisms no rank 59604 JCVI glucose-1-phosphate thymidylyltransferase glucose-1-phosphate thymidylyltransferase RfbA Alternate name: dTDP-D-glucose synthase homotetramer This HMM describes a tightly conserved but broadly distributed subfamily (here designated as short form) of known and putative bacterial glucose-1-phosphate thymidylyltransferases. It is well characterized in several species as the first of four enzymes involved in the biosynthesis of dTDP-L-rhamnose, a cell wall constituent and a feedback inhibitor of the enzyme. TIGR01208.1 TIGR01208 rmlA_long 320.25 320.25 353 equivalog Y Y N glucose-1-phosphate thymidylyltransferase 2.7.7.24 GO:0000271,GO:0008879 131567 cellular organisms no rank 6805 JCVI glucose-1-phosphate thymidylyltransferase glucose-1-phosphate thymidylyltransferase The family of known and putative glucose-1-phosphate thymidyltransferase (also called dTDP-glucose synthase) shows a deep split into a short form (see TIGR01207) and a long form described by this model. The homotetrameric short form is found in numerous bacterial species that incorporate dTDP-L-rhamnose, which it helps synthesize, into the cell wall. It is subject to feedback inhibition. This form, in contrast, is found in many species for which it serves as a sugar-activating enzyme for antibiotic biosynthesis and or other, unknown pathways, and in which dTDP-L-rhamnose is not necessarily produced. Alternate name: dTDP-D-glucose synthase TIGR01209.1 TIGR01209 TIGR01209 136.9 136.9 375 hypoth_equivalog Y Y N RNA ligase GO:0005737,GO:0008452,GO:0016070 18511537 131567 cellular organisms no rank 678 JCVI RNA ligase, Pab1020 family RNA ligase Members of this family are found, so far, in a single copy per genome and largely in thermophiles, of which only Aquifex aeolicus is bacterial rather than archaeal. PSI-BLAST converges after a single iteration to the whole of this family and reveals no convincing similarity to any other protein. The member protein Pab1020 has been characterized as an RNA ligase with circularization activity. TIGR01210.1 TIGR01210 TIGR01210 212.15 212.15 313 equivalog Y Y N archaeosine biosynthesis radical SAM protein RaSEA 31740832 131567 cellular organisms no rank 1344 JCVI radical SAM enzyme, TIGR01210 family archaeosine biosynthesis radical SAM protein RaSEA This exclusively archaeal radical SAM enzyme contributes to archaeosine biosynthesis for tRNA maturation. It partners with the lysine transferase ArcS and may be considered an archaeosine synthase beta-subunit. The reported designation RaSEA signifies RAdical Sam Enzyme for Archaeosine formation. TIGR01211.1 TIGR01211 ELP3 350 350 522 subfamily Y Y N tRNA uridine(34) 5-carboxymethylaminomethyl modification radical SAM/GNAT enzyme Elp3 GO:0016407,GO:1904047 10445034,20054296,25151136 131567 cellular organisms no rank 1920 JCVI radical SAM enzyme/protein acetyltransferase, ELP3 family tRNA uridine(34) 5-carboxymethylaminomethyl modification radical SAM/GNAT enzyme Elp3 This protein performs a tRNA modification at C5 of U34, and archaea and bacteria with this protein lack genes encoding MnmE and MnmG. TIGR01212.1 TIGR01212 TIGR01212 180 180 302 equivalog Y Y N TIGR01212 family radical SAM protein GO:0051536,GO:1904047 20054296 131567 cellular organisms no rank 23242 JCVI radical SAM protein, TIGR01212 family TIGR01212 family radical SAM protein Members of this family are apparent radical-SAM enzymes, related to the N-terminal region of the bifunctional ELP3, whose C-terminal region is part of the elongator complex and appears to acetylate histones and other proteins. ELP3 binds S-adenosylmethionine (SAM) and was recently shown to be involved in a DNA demethylation process in eukaryotes. Close sequence similarity of this family (with lacks the GNAT family acetyltransferase domain) to the ELP3 N-terminal region and a strong match to the Pfam model PF04055 support identification of this family as radical SAM despite the atypical spacing between first and second Cys residues in the 4Fe4S-binding motif. This family includes YhcC from E. coli K-12, an uncharacterized radical SAM protein. TIGR01213.2 TIGR01213 pseudo_Pus10arc 200 200 402 equivalog Y Y N tRNA pseudouridine(54/55) synthase Pus10 5.4.99.25 GO:0009982,GO:0031119 21628430,23898217,29349599 131567 cellular organisms no rank 1475 JCVI tRNA pseudouridine(54/55) synthase tRNA pseudouridine(54/55) synthase Pus10 Members of this family selected for the seed alignment are archaeal tRNA pseudouridine(54/55) synthases called Pus10. Related proteins are found in eukaryotic genomes. TIGR01214.1 TIGR01214 rmlD 224.05 224.05 285 equivalog Y Y N dTDP-4-dehydrorhamnose reductase rfbD 1.1.1.133 GO:0008831,GO:0009243,GO:0019305 131567 cellular organisms no rank 59593 JCVI dTDP-4-dehydrorhamnose reductase dTDP-4-dehydrorhamnose reductase This enzyme catalyzes the last of 4 steps in making dTDP-rhamnose, a precursor of LPS core antigen, O-antigen, etc. TIGR01217.1 TIGR01217 ac_ac_CoA_syn 520.9 520.9 652 equivalog Y Y N acetoacetate--CoA ligase 6.2.1.16 GO:0019287,GO:0030729 131567 cellular organisms no rank 33257 JCVI acetoacetate-CoA ligase acetoacetate--CoA ligase This enzyme catalyzes the first step of the mevalonate pathway of IPP biosynthesis. Most bacteria do not use this pathway, but rather the deoxyxylulose pathway. TIGR01221.1 TIGR01221 rmlC 155.75 155.75 176 equivalog Y Y N dTDP-4-dehydrorhamnose 3,5-epimerase rfbC 5.1.3.13 GO:0008830,GO:0019305 131567 cellular organisms no rank 52940 JCVI dTDP-4-dehydrorhamnose 3,5-epimerase dTDP-4-dehydrorhamnose 3,5-epimerase This enzyme participates in the biosynthesis of dTDP-L-rhamnose, often as a precursor to LPS O-antigen TIGR01224.1 TIGR01224 hutI 298.15 298.15 377 equivalog Y Y N imidazolonepropionase hutI 3.5.2.7 GO:0005737,GO:0016812,GO:0019556,GO:0050480 16990261,17640072 131567 cellular organisms no rank 52141 JCVI imidazolonepropionase imidazolonepropionase Catalyzes the hydrolysis of 4-imidazolone-5-propionate to N-formimidoyl-L-glutamate, the third step in the histidine degradation pathway. TIGR01225.1 TIGR01225 hutH 539.15 539.15 506 equivalog Y Y N histidine ammonia-lyase hutH 4.3.1.3 GO:0004397,GO:0005737,GO:0006548 131567 cellular organisms no rank 48125 JCVI histidine ammonia-lyase histidine ammonia-lyase This enzyme deaminates histidine to urocanic acid, the first step in histidine degradation. It is closely related to phenylalanine ammonia-lyase. TIGR01227.1 TIGR01227 hutG 229.15 229.15 307 equivalog Y Y N formimidoylglutamase hutG 3.5.3.8 GO:0019556,GO:0050415 2842309 131567 cellular organisms no rank 17562 JCVI formimidoylglutamase formimidoylglutamase Formimidoylglutamase (formiminoglutamase), the fourth enzyme of histidine degradation, is similar to arginases and agmatinases. It catalyzes the formation of glutamate and formamide from N-formimidoyl-L-glutamate. It is often encoded near other enzymes of the histidine degradation pathway: histidine ammonia-lyase, urocanate hydratase, and imidazolonepropionase. TIGR01228.1 TIGR01228 hutU 422.2 422.2 545 equivalog Y Y N urocanate hydratase hutU 4.2.1.49 GO:0006548,GO:0016153 131567 cellular organisms no rank 46335 JCVI urocanate hydratase urocanate hydratase This model represents the second of four enzymes involved in the degradation of histidine to glutamate. TIGR01229.1 TIGR01229 rocF_arginase 227.6 227.6 300 equivalog Y Y N arginase rocF 3.5.3.1 GO:0004053,GO:0019547,GO:0046872 10931887 131567 cellular organisms no rank 15599 JCVI arginase arginase This model helps resolve arginases from known and putative agmatinases, formiminoglutamases, and other related proteins of unknown specifity. The pathway from arginine to the polyamine putrescine may procede by hydrolysis to remove urea (arginase) followed by decarboxylation (ornithine decarboxylase), or by decarboxylation first (arginine decarboxylase) followed by removal of urea (agmatinase). TIGR01230.1 TIGR01230 agmatinase 174.3 174.3 275 equivalog Y Y N agmatinase speB 3.5.3.11 GO:0008295,GO:0008783 10931887 131567 cellular organisms no rank 43328 JCVI agmatinase agmatinase Members of this family include known and predicted examples of agmatinase (agmatine ureohydrolase). The seed includes members of archaea, for which no definitive agmatinase sequence has yet been made available. However, archaeal sequences are phylogenetically close to the experimentally verified B. subtilis sequence. One species of Halobacterium has been demonstrated in vitro to produce agmatine from arginine, but no putrescine from ornithine, suggesting that arginine decarboxylase and agmatinase, rather than arginase and ornithine decarboxylase, lead from Arg to polyamine biosynthesis. Note: a history of early misannotation of members of this family is detailed in PUBMED:10931887. TIGR01236.1 TIGR01236 D1pyr5carbox1 613.6 613.6 533 equivalog Y Y N L-glutamate gamma-semialdehyde dehydrogenase pruA 1.2.1.88 GO:0003842,GO:0010133 131567 cellular organisms no rank 16709 JCVI 1-pyrroline-5-carboxylate dehydrogenase L-glutamate gamma-semialdehyde dehydrogenase This model represents one of two related branches of delta-1-pyrroline-5-carboxylate dehydrogenase. The two branches are not as closely related to each other as some aldehyde dehydrogenases are to this branch, and separate models are built for this reason. The enzyme is the second of two in the degradation of proline to glutamate. TIGR01240.1 TIGR01240 mevDPdecarb 171.35 171.35 305 equivalog Y Y N diphosphomevalonate decarboxylase mvaD 4.1.1.33 GO:0004163,GO:0005829,GO:0019287 131567 cellular organisms no rank 9432 JCVI diphosphomevalonate decarboxylase diphosphomevalonate decarboxylase This enzyme catalyzes the last step in the synthesis of isopentenyl diphosphate (IPP) in the mevalonate pathway. Alternate names: mevalonate diphosphate decarboxylase; pyrophosphomevalonate decarboxylase TIGR01243.1 TIGR01243 CDC48 802.65 802.65 733 subfamily Y Y N CDC48 family AAA ATPase GO:0005524,GO:0016887 131567 cellular organisms no rank 4756 JCVI AAA family ATPase, CDC48 subfamily CDC48 family AAA ATPase This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. TIGR01245.1 TIGR01245 trpD 199.05 199.05 330 equivalog_domain Y Y N anthranilate phosphoribosyltransferase trpD 2.4.2.18 GO:0000162,GO:0004048 131567 cellular organisms no rank 69582 JCVI anthranilate phosphoribosyltransferase anthranilate phosphoribosyltransferase In many widely different species, including E. coli, Thermotoga maritima, and Archaeoglobus fulgidus, this enzymatic domain (anthranilate phosphoribosyltransferase) is found C-terminal to glutamine amidotransferase; the fusion protein is designated anthranilate synthase component II (EC 4.1.3.27) TIGR01247.1 TIGR01247 drrB 223.05 223.05 236 subfamily Y N N daunorubicin resistance ABC transporter membrane protein GO:0005886,GO:0043190,GO:0043215 131567 cellular organisms no rank 358 JCVI daunorubicin resistance ABC transporter membrane protein daunorubicin resistance ABC transporter membrane protein This model describes daunorubicin resistance ABC transporter, membrane associated protein in bacteria and archaea. The protein associated with effux of the drug, daunorubicin. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. In eukaryotes proteins of similar function include p-gyco proteins, multidrug resistance protein etc. TIGR01249.1 TIGR01249 pro_imino_pep_1 259.75 259.75 307 equivalog Y Y N prolyl aminopeptidase pip 3.4.11.5 GO:0004177,GO:0005737,GO:0030163 131567 cellular organisms no rank 29568 JCVI prolyl aminopeptidase prolyl aminopeptidase This HMM represents one of two related families of proline iminopeptidase in the alpha/beta fold hydrolase family. The fine specificities of the various members, including both the range of short peptides from which proline can be removed and whether other amino acids such as alanine can be also removed, may vary among members. TIGR01250.1 TIGR01250 pro_imino_pep_2 167.65 167.65 288 subfamily Y Y N proline iminopeptidase-family hydrolase GO:0006508,GO:0008233 9572959 131567 cellular organisms no rank 12764 JCVI proline-specific peptidase proline iminopeptidase-family hydrolase This HMM describes a subfamily of the alpha/beta fold family of hydrolases. Characterized members include prolinases (Pro-Xaa dipeptidase, EC 3.4.13.8), prolyl aminopeptidases (EC 3.4.11.5), and a leucyl aminopeptidase TIGR01251.1 TIGR01251 ribP_PPkin 113 113 309 subfamily Y Y N ribose-phosphate diphosphokinase prs 2.7.6.1 GO:0000287,GO:0004749,GO:0009165 8132556 131567 cellular organisms no rank 59412 JCVI ribose-phosphate diphosphokinase ribose-phosphate diphosphokinase Alternate name: phosphoribosylpyrophosphate synthetase In some systems, close homologs lacking enzymatic activity exist and perform regulatory functions. The model is designated subfamily rather than equivalog for this reason. TIGR01252.1 TIGR01252 acetolac_decarb 180.65 180.65 232 equivalog Y Y N acetolactate decarboxylase budA 4.1.1.5 GO:0045151,GO:0047605 131567 cellular organisms no rank 10504 JCVI alpha-acetolactate decarboxylase acetolactate decarboxylase Puruvate can be fermented to 2,3-butanediol. It is first converted to alpha-acetolactate by alpha-acetolactate synthase, then decarboxylated to acetoin by this enzyme. Acetoin can be reduced in some species to 2,3-butanediol by acetoin reductase. TIGR01254.1 TIGR01254 sfuA 93.4 93.4 306 subfamily Y Y N thiamine ABC transporter substrate-binding protein GO:0015888,GO:0030288,GO:0030975,GO:0048502,GO:0055052 131567 cellular organisms no rank 23784 JCVI ABC transporter periplasmic binding protein, thiB subfamily thiamine ABC transporter substrate-binding protein The model describes thiamine ABC transporter, periplasmic protein in bacteria and archae. The protein belongs to the larger ABC transport system. It consists of at least three components: the thiamine binding periplasmic protein; an inner membrane permease; an ATP-binding subunit. It has been experimentally demonstrated that the mutants in the various steps in the de novo synthesis of the thiamine and the biologically active form, namely thiamine pyrophosphate can be exogenously supplemented with thiamine, thiamine monophosphate (TMP) or thiamine pyrophosphate (TPP). TIGR01256.1 TIGR01256 modA 62.5 62.5 217 equivalog Y Y N molybdate ABC transporter substrate-binding protein modA GO:0015412,GO:0015689,GO:0030288,GO:0030973,GO:0055052 131567 cellular organisms no rank 68763 JCVI molybdate ABC transporter, periplasmic molybdate-binding protein molybdate ABC transporter substrate-binding protein The model describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represent hydrophylioc periplasmic-binding protein in gram-negative organisms and its counterpart in gram-positive organisms is a lipoprotein. The other components of the system include the ModB, an integral membrane protein and ModC the ATP-binding subunit. Invariably almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains. TIGR01258.1 TIGR01258 pgm_1 81.7 81.7 245 subfamily Y Y N 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase 5.4.2.11 GO:0004619,GO:0006096,GO:0016868 9544241 131567 cellular organisms no rank 33412 JCVI phosphoglycerate mutase 1 family 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase Most members of this family are phosphoglycerate mutase (EC 5.4.2.11). This enzyme interconverts 2-phosphoglycerate and 3-phosphoglycerate. The enzyme is transiently phosphorylated on an active site histidine by 2,3-diphosphoglyerate, which is both substrate and product. Some members of this family have phosphoglycerate mutase as a minor activity and act primarily as a bisphoglycerate mutase, interconverting 2,3-diphosphoglycerate and 1,3-diphosphoglycerate (EC 5.4.2.4). This HMM is designated as a subfamily for this reason. The second and third paralogs in S. cerevisiae are somewhat divergent and apparently inactive (see PUBMED:9544241) but are also part of this subfamily phylogenetically. TIGR01260.1 TIGR01260 ATP_synt_c 43.95 43.95 58 equivalog Y Y N ATP synthase F0 subunit C atpE 7.1.2.2 GO:0015078,GO:0015986,GO:0045263 131567 cellular organisms no rank 16781 JCVI ATP synthase F0, C subunit ATP synthase F0 subunit C This model describes the subunit c in F1/F0-ATP synthase, a membrane associated multisubunit complex found in bacteria and organelles of higher eukaryotes, namely, mitochondria and chloroplast. This enzyme is principally involved in the synthesis of ATP from ADP and inorganic phosphate by coupling the energy derived from the proton electrochemical gradient across the biological membrane. A brief description of this multisubunit enzyme complex: F1 and F0 represent two major clusters of subunits. The functional role of subunit c, which is the part of F0 cluster, has been delineated in-vitro reconstitution experiments. Overall experimental proof exists that demonstrate the electrochemical gradient is converted into a rotational torque that leads to ATP synthesis. TIGR01263.1 TIGR01263 4HPPD 277 277 353 equivalog Y Y N 4-hydroxyphenylpyruvate dioxygenase hppD 1.13.11.27 GO:0003868,GO:0006559,GO:0006572 131567 cellular organisms no rank 33360 JCVI 4-hydroxyphenylpyruvate dioxygenase 4-hydroxyphenylpyruvate dioxygenase This protein oxidizes 4-hydroxyphenylpyruvate, a tyrosine and phenylalanine catabolite, to homogentisate. Homogentisate can undergo a further non-enzymatic oxidation and polymerization into brown pigments that protect some bacterial species from light. A similar process occurs spontaneously in blood and is hemolytic (see PMID:8000039). In some bacterial species, this enzyme has been studied as a hemolysin. TIGR01265.1 TIGR01265 tyr_nico_aTase 292.45 292.45 403 subfamily Y N N tyrosine/nicotianamine family aminotransferase GO:0006520,GO:0008483,GO:0030170 131567 cellular organisms no rank 23 JCVI tyrosine/nicotianamine family aminotransferase tyrosine/nicotianamine family aminotransferase This subfamily of pyridoxal phosphate-dependent enzymes includes known examples of both tyrosine aminotransferase from animals and nicotianamine aminotransferase from barley. TIGR01273.1 TIGR01273 speA 624.1 624.1 624 equivalog Y Y N arginine decarboxylase speA 4.1.1.19 GO:0006527,GO:0008295,GO:0008792 131567 cellular organisms no rank 15359 JCVI arginine decarboxylase arginine decarboxylase Two alternative pathways can convert arginine to putrescine. One is decarboxylation by this enzyme followed by removal of the urea moeity by agmatinase. In the other, the ureohydrolase (arginase) acts first, followed by ornithine decarboxylase. This pathway leads to spermidine biosynthesis, hence the gene symbol speA. A distinct biodegradative form is also pyridoxal phosphate-dependent but is not similar in sequence. TIGR01275.1 TIGR01275 ACC_deam_rel 289.4 289.4 321 subfamily Y N N pyridoxal phosphate-dependent enzymes, D-cysteine desulfhydrase family GO:0003824 11527960 131567 cellular organisms no rank 11142 JCVI pyridoxal phosphate-dependent enzymes, D-cysteine desulfhydrase family pyridoxal phosphate-dependent enzymes, D-cysteine desulfhydrase family This HMM represents a family of pyridoxal phosphate-dependent enzymes closely related to (and often designated as putative examples of) 1-aminocyclopropane-1-carboxylate deaminase. It appears that members of this family include both D-cysteine desulfhydrase (EC 4.4.1.15) and 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7). TIGR01280.1 TIGR01280 xseB 35 35 57 equivalog Y Y N exodeoxyribonuclease VII small subunit xseB 3.1.11.6 GO:0006308,GO:0008855,GO:0009318 131567 cellular organisms no rank 41899 JCVI exodeoxyribonuclease VII, small subunit exodeoxyribonuclease VII small subunit This protein is the small subunit for exodeoxyribonuclease VII. Exodeoxyribonuclease VII is made of a complex of four small subunits to one large subunit. The complex degrades single-stranded DNA into large acid-insoluble oligonucleotides. These nucleotides are then degraded further into acid-soluble oligonucleotides. TIGR01282.1 TIGR01282 nifD 653.55 653.55 466 equivalog Y Y N nitrogenase molybdenum-iron protein alpha chain nifD 1.18.6.1 GO:0009399,GO:0016163,GO:0016612 131567 cellular organisms no rank 4025 JCVI nitrogenase molybdenum-iron protein alpha chain nitrogenase molybdenum-iron protein alpha chain Nitrogenase consists of alpha (NifD) and beta (NifK) subunits of the molybdenum-iron protein and an ATP-binding iron-sulfur protein (NifH). This HMM describes a large clade of NifD proteins, but excludes a lineage that contains putative NifD and NifD homologs from species with vanadium-dependent nitrogenases. TIGR01283.1 TIGR01283 nifE 505.1 505.1 459 equivalog Y Y N nitrogenase iron-molybdenum cofactor biosynthesis protein NifE nifE GO:0009399,GO:0065003 131567 cellular organisms no rank 5315 JCVI nitrogenase MoFe cofactor biosynthesis protein NifE nitrogenase iron-molybdenum cofactor biosynthesis protein NifE This protein is part of the NifEN complex involved in biosynthesis of the molybdenum-iron cofactor used by the homologous NifDK complex of nitrogenase. In a few species, the protein is found as a NifEN fusion protein. TIGR01284.1 TIGR01284 alt_nitrog_alph 512.8 512.8 457 subfamily Y Y N nitrogenase subunit alpha 1.18.6.1 GO:0009399,GO:0016163,GO:0051536 131567 cellular organisms no rank 564 JCVI nitrogenase alpha chain nitrogenase subunit alpha This model represents the alpha chains of various forms of the nitrogen-fixing enzyme nitrogenase: vanadium-iron, iron-iron, and molybdenum-iron. Most examples of NifD, the molybdenum-iron type nitrogenase alpha chain, are excluded from this model and described instead by equivalog model TIGR01282. It appears by phylogenetic and UPGMA trees that this model represents a distinct clade of NifD homologs, in which arose several molybdenum-independent forms. TIGR01285.1 TIGR01285 nifN 326.8 326.8 433 equivalog Y Y N nitrogenase iron-molybdenum cofactor biosynthesis protein NifN nifN GO:0009399,GO:0065003 17050696 131567 cellular organisms no rank 4543 JCVI nitrogenase molybdenum-iron cofactor biosynthesis protein NifN nitrogenase iron-molybdenum cofactor biosynthesis protein NifN This protein forms a complex with NifE, and appears as a NifEN in some species. NifEN is a required for producing the molybdenum-iron cofactor of molybdenum-requiring nitrogenases. NifN is closely related to the nitrogenase molybdenum-iron protein beta chain NifK. TIGR01286.1 TIGR01286 nifK 427.3 427.3 516 equivalog Y Y N nitrogenase molybdenum-iron protein subunit beta nifK 1.18.6.1 GO:0009399,GO:0016163,GO:0016612 131567 cellular organisms no rank 4424 JCVI nitrogenase molybdenum-iron protein beta chain nitrogenase molybdenum-iron protein subunit beta This HMM represents the majority of known sequences of the nitrogenase molybdenum-iron protein beta subunit. A distinct clade in a phylogenetic tree contains molybdenum-iron, vanadium-iron, and iron-iron forms of nitrogenase beta subunit and is excluded from this model. Nitrogenase, also called dinitrogenase, is responsible for nitrogen fixation. Note: the trusted cutoff score has recently been lowered to include an additional family in which the beta subunit is shorter by about 50 amino acids at the N-terminus. In species with the shorter form of the beta subunit, the alpha subunit has a novel insert of similar length. TIGR01287.1 TIGR01287 nifH 394.35 394.35 275 equivalog Y Y N nitrogenase iron protein nifH 1.18.6.1 GO:0009399,GO:0016163,GO:0016610 131567 cellular organisms no rank 4356 JCVI nitrogenase iron protein nitrogenase iron protein This HMM describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase. TIGR01290.1 TIGR01290 nifB 343.65 343.65 441 equivalog Y Y N nitrogenase cofactor biosynthesis protein NifB nifB GO:0009399,GO:0051539,GO:1904047 10364262,16567617,7592933 131567 cellular organisms no rank 5157 JCVI nitrogenase cofactor biosynthesis protein NifB nitrogenase cofactor biosynthesis protein NifB This HMM describes NifB, a protein required for the biosynthesis of the iron-molybdenum (or iron-vanadium) cofactor used by the nitrogen-fixing enzyme nitrogenase. NifB belongs to the radical SAM family, and the FeMo cluster biosynthesis process requires S-adenosylmethionine. Archaeal homologs lack the most C-terminal region and score between the trusted and noise cutoffs of this model. TIGR01291.1 TIGR01291 nodJ 206.65 206.65 253 subfamily Y N N ABC-2 type transporter, NodJ family GO:0015772,GO:0016020,GO:0022857 131567 cellular organisms no rank 2804 JCVI ABC-2 type transporter, NodJ family ABC-2 type transporter, NodJ family Nearly all members of this subfamily are NodJ which, together with NodI (TIGR01288), acts to export a variety of modified carbohydrate molecules as signals to plant hosts to establish root nodules. The seed alignment includes a highly divergent member from Azorhizobium caulinodans that is, nonetheless, associated with nodulation. This HMM is designated as subfamily in part because not all sequences derived from the last common ancestral sequence of Rhizobium sp. and Azorhizobium caulinodans NodJ are necessarily nodulation proteins. TIGR01292.1 TIGR01292 TRX_reduct 343.45 343.45 300 equivalog Y Y N thioredoxin-disulfide reductase trxB 1.8.1.9 GO:0004791,GO:0005737,GO:0019430,GO:0071949 14522589,2644268,27249779 131567 cellular organisms no rank 65214 JCVI thioredoxin-disulfide reductase thioredoxin-disulfide reductase This HMM describes thioredoxin-disulfide reductase, a member of the pyridine nucleotide-disulphide oxidoreductases (PFAM:PF00070). TIGR01296.1 TIGR01296 asd_B 324.2 324.2 339 equivalog Y Y N aspartate-semialdehyde dehydrogenase asd 1.2.1.11 GO:0004073,GO:0009086,GO:0009088,GO:0009089,GO:0009097,GO:0050661 131567 cellular organisms no rank 55045 JCVI aspartate-semialdehyde dehydrogenase aspartate-semialdehyde dehydrogenase Two closely related families of aspartate-semialdehyde dehydrogenase are found. They differ by a deep split in phylogenetic and percent identity trees and in gap patterns. This model represents a branch more closely related to the USG-1 protein than to the other aspartate-semialdehyde dehydrogenases represented in model TIGR00978. TIGR01297.1 TIGR01297 CDF 82.35 82.35 285 superfamily Y Y N cation diffusion facilitator family transporter GO:0006812,GO:0008324,GO:0015562,GO:0016020 9075641 131567 cellular organisms no rank 175539 JCVI cation diffusion facilitator family transporter cation diffusion facilitator family transporter This HMM describes a broadly distributed family of transporters, a number of which have been shown to transport divalent cations of cobalt, cadmium and/or zinc. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence. TIGR01300.1 TIGR01300 CPA3_mnhG_phaG 63.1 63.1 97 equivalog Y Y N monovalent cation/H(+) antiporter subunit G mnhG GO:0015297,GO:0051139,GO:0098662 131567 cellular organisms no rank 25353 JCVI monovalent cation/proton antiporter, MnhG/PhaG subunit monovalent cation/H(+) antiporter subunit G This HMM represents a subfamily of small, transmembrane proteins believed to be components of Na+/H+ and K+/H+ antiporters. Members, including proteins designated MnhG from Staphylococcus aureus and PhaG from Rhizobium meliloti, show some similarity to chain L of the NADH dehydrogenase I, which also translocates protons. TIGR01302.1 TIGR01302 IMP_dehydrog 481.5 481.5 450 equivalog Y Y N IMP dehydrogenase guaB 1.1.1.205 GO:0003938,GO:0006164 10200156,18312263,25706619 131567 cellular organisms no rank 51011 JCVI inosine-5'-monophosphate dehydrogenase IMP dehydrogenase This HMM describes IMP dehydrogenase, an enzyme of GMP biosynthesis. This form contains two CBS domains. This HMM describes a rather tightly conserved cluster of IMP dehydrogenase sequences, many of which are characterized. The model excludes two related families of proteins proposed also to be IMP dehydrogenases, but without characterized members. These are related families are the subject of separate models. TIGR01307.1 TIGR01307 pgm_bpd_ind 330.65 330.65 504 equivalog Y Y N 2,3-bisphosphoglycerate-independent phosphoglycerate mutase gpmI 5.4.2.12 GO:0006096,GO:0046537 131567 cellular organisms no rank 43626 JCVI phosphoglycerate mutase (2,3-diphosphoglycerate-independent) 2,3-bisphosphoglycerate-independent phosphoglycerate mutase This form of phosphoglycerate mutase (EC 5.4.2.12) is unrelated to forms that use 2,3-bisphosphoglycerate as a cofactor (EC 5.4.2.11), and is about double in length. TIGR01311.1 TIGR01311 glycerol_kin 590.35 590.35 496 equivalog Y Y N glycerol kinase GlpK glpK 2.7.1.30 GO:0004370,GO:0006072 8358828,9930671 131567 cellular organisms no rank 69083 JCVI glycerol kinase glycerol kinase GlpK This HMM describes glycerol kinase, a member of the FGGY family of carbohydrate kinases. TIGR01312.1 TIGR01312 XylB 380.25 380.25 481 equivalog Y Y N xylulokinase xylB 2.7.1.17 GO:0004856,GO:0005997 131567 cellular organisms no rank 49923 JCVI xylulokinase xylulokinase This HMM describes D-xylulose kinases, a subfamily of the FGGY family of carbohydrate kinases. The member from Klebsiella pneumoniae, designated DalK (see PMID:9324246), was annotated erroneously in GenBank as D-arabinitol kinase but is authentic D-xylulose kinase. D-xylulose kinase (XylB) generally is found with xylose isomerase (XylA) and acts in xylose utilization. TIGR01316.1 TIGR01316 gltA 471.75 471.75 449 equivalog Y Y N NADPH-dependent glutamate synthase gltA 1.4.1.13 GO:0004355,GO:0006537 9202379 131567 cellular organisms no rank 8739 JCVI glutamate synthase (NADPH), homotetrameric NADPH-dependent glutamate synthase This protein is homologous to the small subunit of NADPH and NADH forms of glutamate synthase as found in eukaryotes and some bacteria. This protein is found in numerous species having no homolog of the glutamate synthase large subunit. The prototype of the family, from Pyrococcus sp. KOD1, was shown to be active as a homotetramer and to require NADPH. TIGR01317.1 TIGR01317 GOGAT_sm_gam 447.7 447.7 485 subfamily_domain Y Y N glutamate synthase small subunit gltD 1.4.1.- GO:0006537,GO:0009342 131567 cellular organisms no rank 43168 JCVI glutamate synthase, NADH/NADPH, small subunit glutamate synthase small subunit This HMM represents one of three built for the NADPH-dependent or NADH-dependent glutamate synthase (EC 1.4.1.13 and 1.4.1.14, respectively) small subunit or homologous region. TIGR01316 describes a family in several archaeal and deeply branched bacterial lineages of a homotetrameric form for which there is no large subunit. Another model describes glutamate synthase small subunit from gamma and some alpha subdivision Proteobacteria plus paralogs of unknown function. This model describes the small subunit, or homologous region of longer forms proteins, of eukaryotes, Gram-positive bacteria, cyanobacteria, and some other lineages. All members with known function participate in NADH or NADPH-dependent reactions to interconvert between glutamine plus 2-oxoglutarate and two molecules of glutamate. TIGR01323.1 TIGR01323 nitrile_alph 249.85 249.85 189 equivalog Y Y N nitrile hydratase subunit alpha nthA 4.2.1.84 GO:0018822,GO:0046914,GO:0050898 131567 cellular organisms no rank 6988 JCVI nitrile hydratase, alpha subunit nitrile hydratase subunit alpha This model describes both iron- and cobalt-containing nitrile hydratase alpha chains. It excludes the thiocyanate hydrolase gamma subunit of Thiobacillus thioparus, a sequence that appears to have evolved from within the family of nitrile hydratase alpha subunits but which differs by several indels and a more rapid accumulation of point mutations. TIGR01326.1 TIGR01326 OAH_OAS_sulfhy 495.1 495.1 418 subfamily Y N N O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase GO:0003961,GO:0004124,GO:0009086,GO:0016765,GO:0019344,GO:0019413 131567 cellular organisms no rank 61168 JCVI O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase This HMM describes a distinct clade of the Cys/Met metabolism pyridoxal phosphate-dependent enzyme superfamily. Members include examples of OAH/OAS sulfhydrylase, an enzyme with activity both as O-acetylhomoserine (OAH) sulfhydrylase (EC 2.5.1.49) and O-acetylserine (OAS) sulphydrylase (EC 2.5.1.47). An alternate name for OAH sulfhydrylase is homocysteine synthase. This HMM is designated subfamily because it may or may not have both activities. TIGR01327.1 TIGR01327 PGDH 454 454 525 equivalog Y Y N phosphoglycerate dehydrogenase serA 1.1.1.95 GO:0004617,GO:0006564 131567 cellular organisms no rank 29961 JCVI phosphoglycerate dehydrogenase phosphoglycerate dehydrogenase This HMM represents a long form of D-3-phosphoglycerate dehydrogenase, the serA gene of one pathway of serine biosynthesis. Shorter forms, scoring between trusted and noise cutoff, include SerA from E. coli. TIGR01331.1 TIGR01331 bisphos_cysQ 228.8 228.8 250 equivalog Y Y N 3'(2'),5'-bisphosphate nucleotidase CysQ cysQ 3.1.3.7 GO:0000287,GO:0006790,GO:0008441 131567 cellular organisms no rank 23090 JCVI 3'(2'),5'-bisphosphate nucleotidase 3'(2'),5'-bisphosphate nucleotidase CysQ Sulfate is incorporated into 3-phosphoadenylylsulfate, PAPS, for utilization in pathways such as methionine biosynthesis. Transfer of sulfate from PAPS to an acceptor leaves adenosine 3'-5'-bisphosphate, APS. This HMM describes a form found in bacteria of the enzyme 3'(2'),5'-bisphosphate nucleotidase, which removes the 3'-phosphate from APS to regenerate AMP and help drive the cycle. TIGR01334.1 TIGR01334 modD 178.85 178.85 277 hypoth_equivalog Y Y N ModD protein modD GO:0004514 8491722 131567 cellular organisms no rank 3739 JCVI modD protein ModD protein The gene modD for a member of this family is found with molybdenum transport genes modABC in Rhodobacter capsulatus. However, disruption of modD causes only a 4-fold (rather than 500-fold for modA, modB, modC) change in the external molybdenum concentration required to suppress an alternative nitrogenase. ModD proteins are highly similar to nicotinate-nucleotide pyrophosphorylase (also called quinolinate phosphoribosyltransferase). The function unknown. TIGR01340.1 TIGR01340 aconitase_mito 825.35 825.35 745 equivalog Y Y N aconitate hydratase 4.2.1.3 GO:0003994,GO:0006099,GO:0051539 131567 cellular organisms no rank 6506 JCVI aconitate hydratase, mitochondrial aconitate hydratase, mitochondrial type This HMM represents mitochondrial forms of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. TIGR01341.1 TIGR01341 aconitase_1 945 945 876 equivalog Y Y N aconitate hydratase AcnA acnA 4.2.1.3 GO:0003994,GO:0006099 10748225 131567 cellular organisms no rank 58334 JCVI aconitate hydratase 1 aconitate hydratase AcnA This HMM represents one form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It is found in bacteria, archaea, and eukaryotic cytosol. It has been shown to act also as an iron-responsive element binding protein in animals and may have the same role in other eukaryotes. TIGR01342.1 TIGR01342 acon_putative 719.15 719.15 655 hypoth_equivalog Y N N putative aconitate hydratase GO:0003994,GO:0006099 131567 cellular organisms no rank 6169 JCVI putative aconitate hydratase putative aconitate hydratase This model represents a small family of proteins homologous (and likely functionally equivalent to) aconitase 1. Members are found, so far in the anaerobe Clostridium acetobutylicum, in the microaerophilic, early-branching bacterium Aquifex aeolicus, and in the halophilic archaeon Halobacterium sp. NRC-1. No member is experimentally characterized. TIGR01343.1 TIGR01343 hacA_fam 385.7 385.7 412 subfamily Y Y N homoaconitate hydratase family protein GO:0008652,GO:0016836,GO:0051539 131567 cellular organisms no rank 11642 JCVI homoaconitate hydratase family protein homoaconitate hydratase family protein This HMM represents a subfamily of proteins consisting of aconitase, homoaconitase, 3-isopropylmalate dehydratase, and uncharacterized proteins. The majority of the members of this family have been designated as 3-isopropylmalate dehydratase large subunit (LeuC) in microbial genome annotation, but the only characterized member is Thermus thermophilus homoaconitase, an enzyme of a non-aspartate pathway of Lys biosynthesis. TIGR01346.1 TIGR01346 isocit_lyase 275.9 275.9 527 equivalog Y Y N isocitrate lyase aceA 4.1.3.1 GO:0004451,GO:0006099,GO:0019752 131567 cellular organisms no rank 21955 JCVI isocitrate lyase isocitrate lyase Isocitrate lyase and malate synthase are the enzymes of the glyoxylate shunt, a pathway associated with the TCA cycle. TIGR01350.1 TIGR01350 lipoamide_DH 408.8 408.8 461 equivalog Y Y N dihydrolipoyl dehydrogenase lpdA 1.8.1.4 GO:0004148,GO:0050660 131567 cellular organisms no rank 114643 JCVI dihydrolipoyl dehydrogenase dihydrolipoyl dehydrogenase This HMM describes dihydrolipoamide dehydrogenase, a flavoprotein that acts in a number of ways. It is the E3 component of dehydrogenase complexes for pyruvate, 2-oxoglutarate, 2-oxoisovalerate, and acetoin. It can also serve as the L protein of the glycine cleavage system. This family includes a few members known to have distinct functions (ferric leghemoglobin reductase and NADH:ferredoxin oxidoreductase) but that may be predicted by homology to act as dihydrolipoamide dehydrogenase as well. The motif GGXCXXXGCXP near the N-terminus contains a redox-active disulfide. TIGR01351.1 TIGR01351 adk 168 168 212 subfamily Y Y N adenylate kinase 2.7.4.- GO:0004017,GO:0005524,GO:0016776 131567 cellular organisms no rank 38746 JCVI adenylate kinase adenylate kinase Members of this family have adenylate kinase activity (EC 2.7.4.3), interconverting ATP + AMP with 2 ADP, although for some members, that activity falls within the broader activity of EC 2.7.4.10 (NTP + AMP = NDP + ADP). TIGR01353.1 TIGR01353 dGTP_triPase 152.35 152.35 389 subfamily Y Y N dGTP triphosphohydrolase dgt GO:0008832,GO:0015949 2826481,36067314,9422594 131567 cellular organisms no rank 64508 JCVI putative dGTPase dGTP triphosphohydrolase dGTP triphosphohydrolase (dgt) releases inorganic triphosphate, an unusual activity reaction product, from GTP. Its activity has been called limited to the Enterobacteriaceae, although homologous sequences are detected elsewhere. This finding casts doubt on whether the activity is shared in other species. In several of these other species, the homologous gene is found in an apparent operon with dnaG, the DNA primase gene. The enzyme from E. coli was shown to bind coopertatively to single stranded DNA. The biological role of dgt is unknown. TIGR01354.1 TIGR01354 cyt_deam_tetra 113.65 113.65 126 equivalog Y Y N cytidine deaminase cdd 3.5.4.5 GO:0004126,GO:0005737,GO:0008270,GO:0008655,GO:0009972 10493793 131567 cellular organisms no rank 27617 JCVI cytidine deaminase cytidine deaminase This small, homotetrameric zinc metalloprotein is found in humans and most bacteria. A related, homodimeric form with a much larger subunit is found in E. coli and in Arabidopsis. Both types may act on deoxycytidine as well as cytidine. TIGR01356.1 TIGR01356 aroA 287.25 287.25 415 equivalog Y Y N 3-phosphoshikimate 1-carboxyvinyltransferase aroA 2.5.1.19 GO:0003866,GO:0009073 131567 cellular organisms no rank 83262 JCVI 3-phosphoshikimate 1-carboxyvinyltransferase 3-phosphoshikimate 1-carboxyvinyltransferase This model represents 3-phosphoshikimate-1-carboxyvinyltransferase (aroA), which catalyzes the sixth of seven steps in the shikimate pathway of the biosynthesis of chorimate. Chorismate is last common precursor of all three aromatic amino acids. Sequences scoring between the trusted and noise cutoffs include fragmentary and aberrant sequences in which generally well-conserved motifs are missing or altererd, but no example of a protein known to have a different function. TIGR01357.1 TIGR01357 aroB 305 305 344 equivalog Y Y N 3-dehydroquinate synthase aroB 4.2.3.4 GO:0003856,GO:0005737,GO:0009073,GO:0009423 131567 cellular organisms no rank 73530 JCVI 3-dehydroquinate synthase 3-dehydroquinate synthase This HMM represents 3-dehydroquinate synthase, the enzyme catalyzing the second of seven steps in the shikimate pathway of chorismate biosynthesis. Chorismate is the last common intermediate in the biosynthesis of all three aromatic amino acids. TIGR01361.1 TIGR01361 DAHP_synth_Bsub 267.75 267.75 260 equivalog_domain Y Y N 3-deoxy-7-phosphoheptulonate synthase aroF 2.5.1.54 GO:0003849,GO:0009423 131567 cellular organisms no rank 18345 JCVI 3-deoxy-7-phosphoheptulonate synthase 3-deoxy-7-phosphoheptulonate synthase This model describes one of at least three types of phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthase). This enzyme catalyzes the first of 7 steps in the biosynthesis of chorismate, that last common precursor of all three aromatic amino acids and of PABA, ubiquinone and menaquinone. Some members of this family, including an experimentally characterized member from Bacillus subtilis, are bifunctional, with a chorismate mutase domain N-terminal to this region. The member of this family from Synechocystis PCC 6803, CcmA, was shown to be essential for carboxysome formation. However, no other candidate for this enzyme is present in that species, chorismate biosynthesis does occur, other species having this protein lack carboxysomes but appear to make chorismate, and a requirement of CcmA for carboxysome formation does not prohibit a role in chorismate biosynthesis. TIGR01362.1 TIGR01362 KDO8P_synth 314 314 258 equivalog Y Y N 3-deoxy-8-phosphooctulonate synthase kdsA 2.5.1.55 GO:0005737,GO:0008676,GO:0019294 131567 cellular organisms no rank 32605 JCVI 3-deoxy-8-phosphooctulonate synthase 3-deoxy-8-phosphooctulonate synthase This HMM describes 3-deoxy-8-phosphooctulonate synthase. Alternate names include 2-dehydro-3-deoxyphosphooctonate aldolase, 3-deoxy-d-manno-octulosonic acid 8-phosphate and KDO-8 phosphate synthetase. It catalyzes the aldol condensation of phosphoenolpyruvate with D-arabinose 5-phosphate: phosphoenolpyruvate + D-arabinose 5-phosphate + H2O = 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate In Gram-negative bacteria, this is the first step in the biosynthesis of 3-deoxy-D-manno-octulosonate, part of the oligosaccharide core of lipopolysaccharide. TIGR01365.1 TIGR01365 serC_2 448.2 448.2 374 equivalog Y Y N phosphoserine transaminase 2.6.1.52 GO:0004648,GO:0006564 131567 cellular organisms no rank 9398 JCVI phosphoserine aminotransferase phosphoserine transaminase This HMM represents a variant form of the serine biosynthesis enzyme phosphoserine aminotransferase, as found in a small number of distantly related species, including Caulobacter crescentus, Mesorhizobium loti, and the archaeon Methanosarcina barkeri. TIGR01368.1 TIGR01368 CPSaseIIsmall 307.35 307.35 361 equivalog_domain Y Y N glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit carA 6.3.5.5 GO:0004088,GO:0006207,GO:0006541 10089390,11729189,15322282,9174345 131567 cellular organisms no rank 71701 JCVI carbamoyl-phosphate synthase, small subunit glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit Catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways. This HMM represents the whole of the small chain of the glutamine-dependent form (EC 6.3.5.5) of carbamoyl phosphate synthase, CPSase II. The C-terminal domain has glutamine amidotransferase activity. Note that the sequence from the mammalian urea cycle form has lost the active site Cys, resulting in an ammonia-dependent form, CPSase I (EC 6.3.4.16). CPSases of pyrimidine biosynthesis, arginine biosynthesis, and the urea cycle may be encoded by one or by several genes, depending on the species. TIGR01369.1 TIGR01369 CPSaseII_lrg 1027 1027 1052 equivalog_domain Y Y N carbamoyl-phosphate synthase (glutamine-hydrolyzing) large subunit carB 6.3.5.5 GO:0004088,GO:0005951,GO:0009220 131567 cellular organisms no rank 87732 JCVI carbamoyl-phosphate synthase, large subunit carbamoyl-phosphate synthase (glutamine-hydrolyzing) large subunit Carbamoyl-phosphate synthase (CPSase) catalyzes the first committed step in pyrimidine, arginine, and urea biosynthesis. In general, it is a glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II in eukaryotes. An exception is the mammalian mitochondrial urea-cycle form, CPSase I, in which the glutamine amidotransferase domain active site Cys on the small subunit has been lost, and the enzyme is ammonia-dependent. In both CPSase I and the closely related, glutamine-dependent CPSase III (allosterically activated by acetyl-glutamate) demonstrated in some other vertebrates, the small and large chain regions are fused in a single polypeptide chain. This HMM represents the large chain of glutamine-hydrolysing carbamoyl-phosphate synthases, or the corresponding regions of larger, multifunctional proteins, as found in all domains of life, and CPSase I forms are considered exceptions within the family. In several thermophilic species (Methanobacterium thermoautotrophicum, Methanococcus jannaschii, Aquifex aeolicus), the large subunit appears split, at different points, into two separate genes. TIGR01370.1 TIGR01370 TIGR01370 181.25 181.25 315 hypoth_equivalog Y Y N MJ1477/TM1410 family putative glycoside hydrolase GO:0016798 11333988,11790254,14679218 131567 cellular organisms no rank 311 JCVI extracellular protein MJ1477/TM1410 family putative glycoside hydrolase Original assignment of this protein family as cysteinyl-tRNA synthetase is controversial, supported by PMID:11333988 but challenged by PMID:14679218 and by subsequent discovery of the actual mechanism for synthesizing Cys-tRNA in species where a direct Cys--tRNA ligase was not found. Lingering legacy annotations of members of this family probably should be removed. Evidence against the role includes a signal peptide. This family as been renamed "extracellular protein" to facilitate correction. Members of this family occur in Deinococcus radiodurans (bacterial) and Methanococcus jannaschii (archaeal). A number of homologous but more distantly related proteins are annotated as alpha-1,4 polygalactosaminidases. The function remains unknown. TIGR01371.1 TIGR01371 met_syn_B12ind 929.95 929.95 754 equivalog Y Y N 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase metE 2.1.1.14 GO:0003871,GO:0008270,GO:0009086 131567 cellular organisms no rank 48456 JCVI 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase This HMM describes the cobalamin-independent methionine synthase. A family of uncharacterized archaeal proteins is homologous to the C-terminal region of this family. That family is excluded from this model but, along with this family, belongs to Pfam HMM PF01717. TIGR01376.1 TIGR01376 POMP_repeat 15 15 28 repeat Y N N polymorphic outer membrane protein 10587946 131567 cellular organisms no rank 11717 JCVI chlamydial polymorphic outer membrane protein repeat chlamydial polymorphic outer membrane protein repeat This HMM represents a repeat region of about 27 residues that appears from twice to over twenty times in Chlamydial polymorphic outer membrane proteins (POMP). Characteristic motifs in the repeat are FXXN and GGAI. Except for a few apparently truncated examples, Chlamydial proteins have this repeat region if and only if they also have the autotransporter beta-domain (PF03797) at the C-terminus, with Phe as the C-terminal residue. This repeat is observed, but is very rare, outside the Chlamydias. TIGR01379.1 TIGR01379 thiL 184.15 184.15 320 equivalog Y Y N thiamine-phosphate kinase thiL 2.7.4.16 GO:0009030,GO:0009228 131567 cellular organisms no rank 52840 JCVI thiamine-phosphate kinase thiamine-phosphate kinase This HMM describes thiamine-monophosphate kinase, an enzyme that converts thiamine monophosphate into thiamine pyrophosphate (TPP, coenzyme B1), an enzyme cofactor. Thiamine monophosphate may be derived from de novo synthesis or from unphosphorylated thiamine, known as vitamin B1. Proteins scoring between the trusted and noise cutoff for this model include short forms from the Thermoplasmas (which lack the N-terminal region) and a highly derived form from Campylobacter jejuni. Eukaryotes lack this enzyme, and add pyrophosphate from ATP to unphosphorylated thiamine in a single step. TIGR01382.1 TIGR01382 PfpI 139.05 139.05 169 subfamily Y Y N DJ-1/PfpI/YhbO family deglycase/protease GO:0006508,GO:0008234 11114201 131567 cellular organisms no rank 47764 JCVI intracellular protease, PfpI family DJ-1/PfpI/YhbO family deglycase/protease The member of this family from Pyrococcus horikoshii has been solved to 2 Angstrom resolution. It is an ATP-independent intracellular protease that crystallizes as a hexameric ring. Cys-101 is proposed as the active site residue in a catalytic triad with the adjacent His-102 and a Glu residue from an adjacent monomer. A member of this family from Bacillus subtilis, GSP18, has been shown to be expressed in response to several forms of stress. A role in the degradation of small peptides has been suggested. A closely related family consists of the thiamine biosynthesis protein ThiJ and its homologs. TIGR01383.1 TIGR01383 not_thiJ 131.25 131.25 180 equivalog Y Y N DJ-1 family glyoxalase III 24758716,33922426,36820886,37060572,37884446,9070310 131567 cellular organisms no rank 16678 JCVI DJ-1 family protein DJ-1 family glyoxalase III Members of this family, found in bacteria and eukaryotes, include human DJ-1, product of the PARK7 (Parkinson disease protein 7) gene, previously called a deglycase but now called a glyoxalase III. Many members of the DJ-1 clade have been annotated (apparently incorrectly) as ThiJ, a protein of thiamine biosynthesis. However, published reports of ThiJ activity and identification of a ThiJ/ThiD bifunctional protein describe an unrelated locus mapping near ThiM, rather than the DJ-1 homolog of E. coli. Glyoxalase III detoxifies methylglyoxal by a one-step conversion to D-lactate, and does not require glutathione. TIGR01384.1 TIGR01384 TFS_arch 64.75 64.75 101 equivalog Y Y N transcription factor S GO:0006355 20239876 131567 cellular organisms no rank 1752 JCVI transcription factor S transcription factor S This model describes archaeal transcription factor S, a protein related in size and sequence to certain eukaryotic RNA polymerase small subunits, and in sequence and function to the much larger eukaryotic transcription factor IIS (TFIIS). Although originally suggested to be a subunit of the archaeal RNA polymerase, it elutes separately from active polymerase in gel filtration experiments and acts, like TFIIs, as an induction factor for RNA cleavage by RNA polymerase. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae. TIGR01389.1 TIGR01389 recQ 640.2 640.2 591 equivalog Y Y N DNA helicase RecQ recQ 5.6.2.4 GO:0003678,GO:0006310,GO:0009432 131567 cellular organisms no rank 63026 JCVI ATP-dependent DNA helicase RecQ DNA helicase RecQ The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ. TIGR01392.1 TIGR01392 homoserO_Ac_trn 276.85 276.85 351 equivalog Y Y N homoserine O-acetyltransferase metX 2.3.1.31 GO:0004414,GO:0009086 131567 cellular organisms no rank 32809 JCVI homoserine O-acetyltransferase homoserine O-acetyltransferase This family describes homoserine-O-acetyltransferase, an enzyme of methionine biosynthesis. This model has been rebuilt to identify sequences more broadly, including a number of sequences suggested to be homoserine O-acetyltransferase based on proximity to other Met biosynthesis genes. TIGR01394.1 TIGR01394 TypA_BipA 757.3 757.3 594 equivalog Y Y N translational GTPase TypA typA GO:0003924,GO:0005525,GO:0006412,GO:0006950 23570569,9622352 131567 cellular organisms no rank 52175 JCVI GTP-binding protein TypA/BipA translational GTPase TypA/BipA This bacterial (and Arabidopsis) protein, termed TypA or BipA, a GTP-binding protein, is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown. TIGR01409.1 TIGR01409 TAT_signal_seq 16.7 16.7 29 domain Y Y N twin-arginine translocation signal domain-containing protein 10652088,8939424 131567 cellular organisms no rank 207625 JCVI Tat (twin-arginine translocation) pathway signal sequence twin-arginine translocation signal domain Many proteins that fold in the cytosol because a required cofactor is available there only, or because cytosolic chaperones assist in folding, or because high salt in the extracellular milieu would interfere with folding there, cannot rely on the standard general secretory (Sec) pathway for secretion across the plasma membrane. This model describes a family of predicted long, non-Sec signal sequences and signal-anchor sequences (uncleaved signal sequences). All contain a typically invariant pair of arginine residues, in a motif approximated by (S/T)-R-R-X-F-L-K, followed by a membrane-spanning hydrophobic region. The system that secretes pre-folded proteins with this motif is known as twin-arginine translocation, or TAT. Note that some variant forms, often lineage-specific ones such as the RKxFL version found in Leptospira, do occur but typically fall outside the scope of this HMM. Twin-arginine signal domains with small amino acid side chains at the -1 and -3 positions from the C-terminus of the model should be predicted to be cleaved as are Sec pathway signal sequences. The system, although far from universal in prokaryotes, is widespread in bacteria and present also in many archaea. TIGR01411.1 TIGR01411 tatAE 53.9 53.9 47 subfamily Y Y N twin-arginine translocase TatA/TatE family subunit tatA GO:0016020,GO:0043953 131567 cellular organisms no rank 46755 JCVI twin arginine-targeting protein translocase, TatA/E family twin-arginine translocase TatA/TatE family subunit This HMM distinguishes TatA/E from the related TatB, but does not distinguish TatA from TatE. The Tat (twin-arginine translocation) system is a Sec-independent exporter for folded proteins, often with a redox cofactor already bound, across the bacterial inner membrane. Functionally equivalent systems are found in the chloroplast and some in archaeal species. The signal peptide recognized by the Tat system is modeled by TIGR01409. TIGR01415.1 TIGR01415 trpB_rel 518.85 518.85 419 hypoth_equivalog Y Y N TrpB-like pyridoxal phosphate-dependent enzyme GO:0000162,GO:0004834,GO:0030170 131567 cellular organisms no rank 7475 JCVI pyridoxal-phosphate dependent TrpB-like enzyme TrpB-like pyridoxal phosphate-dependent enzyme This HMM represents a family of pyridoxal-phosphate dependent enzyme (PF00291) closely related to the beta subunit of tryptophan synthase (TIGR00263). However, the only case in which a member of this family replaces a member of TIGR00263 is in Sulfolobus species which contain two sequences which hit this model, one of which is proximal to the alpha subunit. In every other case so far, either the species appears not to make tryptophan (there is no trp synthase alpha subunit), or a trp synthase beta subunit matching TIGR00263 is also found. TIGR01417.1 TIGR01417 PTS_I_fam 341.7 341.7 565 equivalog_domain Y Y N phosphoenolpyruvate--protein phosphotransferase ptsP 2.7.3.9 GO:0008965,GO:0009401 131567 cellular organisms no rank 92756 JCVI phosphoenolpyruvate-protein phosphotransferase phosphoenolpyruvate--protein phosphotransferase This HMM recognizes a distinct clade of phophoenolpyruvate (PEP)-dependent enzymes. Most members are known or deduced to function as the phosphoenolpyruvate-protein phosphotransferase (or enzyme I) of PTS sugar transport systems. However, some species with both a member of this family and a homolog of the phosphocarrier protein HPr lack a IIC component able to serve as a permease. An HPr homolog designated NPr has been implicated in the regulation of nitrogen assimilation, which demonstrates that not all phosphotransferase system components are associated directly with PTS transport. TIGR01418.1 TIGR01418 PEP_synth 739.75 739.75 784 equivalog Y Y N pyruvate, water dikinase ppsA 2.7.9.2 GO:0006090,GO:0008986 131567 cellular organisms no rank 30598 JCVI phosphoenolpyruvate synthase pyruvate, water dikinase Also called pyruvate,water dikinase and PEP synthase. The member from Methanococcus jannaschii contains a large intein. This enzyme generates phosphoenolpyruvate (PEP) from pyruvate, hydrolyzing ATP to AMP and releasing inorganic phosphate in the process. The enzyme shows extensive homology to other enzymes that use PEP as substrate or product. This enzyme may provide PEP for gluconeogenesis, for PTS-type carbohydrate transport systems, or for other processes. TIGR01426.2 TIGR01426 MGT 260 260 393 subfamily Y Y Y macrolide family glycosyltransferase GO:0016758 10658660,17376874,21987796,8244027 131567 cellular organisms no rank 19284 JCVI glycosyltransferase, MGT family macrolide family glycosyltransferase This model describes the MGT (macrolide glycosyltransferase) subfamily of the UDP-glucuronosyltransferase family. Members include a number of glucosyl transferases for macrolide antibiotic inactivation, but also include transferases of glucose-related sugars for macrolide antibiotic production. TIGR01427.1 TIGR01427 PTS_IIC_fructo 157.55 157.55 346 subfamily_domain Y Y N fructose-specific PTS transporter subunit EIIC GO:0009401,GO:0016020,GO:0022877 131567 cellular organisms no rank 76273 JCVI PTS system, Fru family, IIC component fructose-specific PTS transporter subunit EIIC This model represents the IIC component, or IIC region of a IIABC or IIBC polypeptide of a phosphotransferase system for carbohydrate transport. Members of this family belong to the fructose-specific subfamily of the broader family (PF02378) of PTS IIC proteins. Members should be found as part of the same chain or in the same operon as fructose family IIA (TIGR00848) and IIB (TIGR00829) protein regions. A number of bacterial species have members in two different branches of this subfamily, suggesting some diversity in substrate specificity of its members. TIGR01428.1 TIGR01428 HAD_type_II 125.4 125.4 197 equivalog Y Y N haloacid dehalogenase type II GO:0019120 10198020,10498712,11404103,1744048 131567 cellular organisms no rank 30837 JCVI haloacid dehalogenase, type II haloacid dehalogenase, type II Catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids. Belongs to the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases (PF00702), class (subfamily) I. Note that the Type I HAD enzymes have not yet been fully characterized, but clearly utilize a substantially different catalytic mechanism and are thus unlikely to be related. TIGR01439.1 TIGR01439 lp_hng_hel_AbrB 28.3 28.3 44 domain Y N N transcriptional regulator, AbrB family GO:0003700,GO:0006355 11101897 131567 cellular organisms no rank 32783 JCVI transcriptional regulator, AbrB family transcriptional regulator, AbrB family This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609. TIGR01443.1 TIGR01443 intein_Cterm 15.6 14.8 24 domain Y N N intein C-terminal splicing region GO:0016539 131567 cellular organisms no rank 27317 JCVI intein C-terminal splicing region intein C-terminal splicing region This HMM represents the well-conserved C-terminal region of a large number of inteins. It is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. Inteins are regions encoded within proteins from which they remove themselves after translation in a self-splicing reaction, leaving the remainder of the coding region to form a complete, functional protein as if the intein were never there. Proteins with inteins include RecA, GyrA, ribonucleotide reductase, and others. Most inteins have a central region with putative endonuclease activity. TIGR01444.1 TIGR01444 fkbM_fam 37.7 37.7 143 subfamily_domain Y Y N FkbM family methyltransferase GO:0016740 8752344 131567 cellular organisms no rank 60625 JCVI methyltransferase, FkbM family FkbM family methyltransferase Members of this family are characterized by two well-conserved short regions separated by a variable in both sequence and length. The first of the two regions is found in a large number of proteins outside this subfamily, a number of which have been characterized as methyltransferases. One member of the present family, FkbM, was shown to be required for a specific methylation in the biosynthesis of the immunosuppressant FK506 in Streptomyces strain MA6548. TIGR01445.1 TIGR01445 intein_Nterm 24.5 24.5 83 domain Y N N intein N-terminal splicing region GO:0016539 131567 cellular organisms no rank 11576 JCVI intein N-terminal splicing region intein N-terminal splicing region This model is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. It is designed to recognize inteins but not the related region of the sonic hedgehog protein. TIGR01451.2 TIGR01451 B_ant_repeat 24 20 53 repeat Y N N DUF11 type repeat protein 21821775 131567 cellular organisms no rank 68701 JCVI conserved repeat domain DUF11 family repeat This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically diverse prokaryotes. The model overlaps significantly in coverage with DUF11 (PF01345). Examples of the domain occur within longer repeats in three of the five longest proteins of Bacillus anthracis, in a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins. TIGR01452.1 TIGR01452 PGP_euk 201.95 201.95 279 subfamily Y Y N phosphoglycolate/pyridoxal phosphate family phosphatase GO:0008967,GO:0009853,GO:0015671 11581250,11601995,14522954,2164460,3015949 131567 cellular organisms no rank 15 JCVI phosphoglycolate/pyridoxal phosphate phosphatase family phosphoglycolate/pyridoxal phosphate family phosphatase This subfamily belongs to the Haloacid dehalogenase (HAD) superfamily of hydrolase enzymes (PF00702). Members include both phosphoglycolate phosphatase, which is an essential enzyme in the glycolate salvage pathway in higher organisms (photorespiration in plants), and pyridoxal phosphatase. TIGR01453.1 TIGR01453 grpIintron_endo 56.05 56.05 215 subfamily Y N N group I intron endonuclease GO:0004519,GO:0006316 131567 cellular organisms no rank 1298 JCVI group I intron endonuclease group I intron endonuclease This HMM represents one subfamily of endonucleases containing the endo/excinuclease amino terminal domain, Pfam:PF01541 at its amino end. A distinct subfamily includes excinuclease abc subunit c (uvrC). Members of PF01541 are often termed GIY-YIG endonucleases after conserved motifs near the amino end. This subfamily in this HMM is found in open reading frames of group I introns in both phage and mitochondria. The closely related endonucleases of phage T4: segA, segB, segC, segD and segE, score below the trusted cutoff for the family. TIGR01458.1 TIGR01458 HAD-SF-IIA-hyp3 175.95 175.95 257 hypoth_equivalog Y Y N TIGR01458 family HAD-type hydrolase GO:0008152,GO:0016787 131567 cellular organisms no rank 2086 JCVI HAD hydrolase, TIGR01458 family TIGR01458 family HAD-type hydrolase This hypothetical equivalog is a member of the IIA subfamily (TIGR01460) of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. One sequence (GP|10716807) has been annotated as a "phospholysine phosphohistidine inorganic pyrophosphatase," probably in reference to studies on similarly described (but unsequenced) enzymes from bovine and rat tissues [1,2]. However, the supporting information for this annotation has never been published. TIGR01460.1 TIGR01460 HAD-SF-IIA 100.15 100.15 246 subfamily Y Y N HAD-IIA family hydrolase GO:0008152,GO:0016787 10956028,11601995,2190615,7966317,9084180 131567 cellular organisms no rank 53123 JCVI HAD hydrolase, family IIA HAD-IIA family hydrolase This HMM represents one structural subclass of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The classes are defined based on the location and the observed or predicted fold of a so-called "capping domain", or the absence of such a domain. Class II consists of sequences in which the capping domain is found between the second and third motifs. The Class IIA capping domain is predicted by PSI-PRED to consist of a mixed alpha-beta fold with the basic pattern: Helix-Helix-Helix-Sheet-Helix-Loop-Sheet-Helix-Sheet-Helix. Presently, this subfamily encompasses a single equivalog model (TIGR01452) for the eukaryotic phosphoglycolate phosphatase, as well as four hypothetical equivalogs covering closely related sequences (TIGR01456 and TIGR01458 in eukaryotes, TIGR01457 in Gram-positive bacteria and TIGR01459 in Gram-negative bacteria), and the Escherishia coli NagD gene and the Bacillus subtilus AraL proteins. TIGR01463.1 TIGR01463 mtaA_cmuA 235.4 235.4 340 subfamily Y Y N MtaA/CmuA family methyltransferase 2.1.1.- GO:0006730,GO:0008168 11133460,8654414 131567 cellular organisms no rank 1180 JCVI methyltransferase, MtaA/CmuA family MtaA/CmuA family methyltransferase This subfamily is closely related to, yet is distinct from, uroporphyrinogen decarboxylase (EC 4.1.1.37). It includes two isozymes from Methanosarcina barkeri of methylcobalamin--coenzyme M methyltransferase. It also includes a chloromethane utilization protein, CmuA, which transfers the methyl group of chloromethane to a corrinoid protein. TIGR01464.1 TIGR01464 hemE 302.95 302.95 338 equivalog Y Y N uroporphyrinogen decarboxylase hemE 4.1.1.37 GO:0004853,GO:0006779 131567 cellular organisms no rank 56695 JCVI uroporphyrinogen decarboxylase uroporphyrinogen decarboxylase This HMM represents uroporphyrinogen decarboxylase (HemE), which converts uroporphyrinogen III to coproporphyrinogen III. This step takes the pathway toward protoporphyrin IX, a common precursor of both heme and chlorophyll, rather than toward precorrin 2 and its products. TIGR01465.1 TIGR01465 cobM_cbiF 259.65 259.65 247 equivalog Y Y N precorrin-4 C(11)-methyltransferase cobM 2.1.1.133 GO:0009236,GO:0046026 131567 cellular organisms no rank 30187 JCVI precorrin-4 C11-methyltransferase precorrin-4 C(11)-methyltransferase This HMM represents precorrin-4 C11-methyltransferase, one of two methyltransferases commonly referred to as precorrin-3 methylase (the other is precorrin-3B C17-methyltransferase, EC 2.1.1.131). This enzyme participates in the pathway toward the biosynthesis of cobalamin and related products. TIGR01466.1 TIGR01466 cobJ_cbiH 246.35 246.35 239 equivalog_domain Y Y N precorrin-3B C(17)-methyltransferase cobJ 2.1.1.131 GO:0009236,GO:0030789 131567 cellular organisms no rank 36678 JCVI precorrin-3B C17-methyltransferase precorrin-3B C(17)-methyltransferase This HMM represents precorrin-3B C17-methyltransferase, one of two methyltransferases commonly referred to as precorrin-3 methylase (the other is precorrin-4 C11-methyltransferase, EC 2.1.1.133). This enzyme participates in the pathway toward the biosynthesis of cobalamin and related products. Members of this family may appear as fusion proteins with other enzymes of cobalamin biosynthesis. TIGR01467.1 TIGR01467 cobI_cbiL 163.25 163.25 230 equivalog Y Y N precorrin-2 C(20)-methyltransferase cobI 2.1.1.130 GO:0009236,GO:0030788 131567 cellular organisms no rank 29947 JCVI precorrin-2 C(20)-methyltransferase precorrin-2 C(20)-methyltransferase This HMM represents precorrin-2 C(20)-methyltransferase, one of several closely related S-adenosylmethionine-dependent methyltransferases involved in cobalamin (vitamin B12) biosynthesis. TIGR01469.1 TIGR01469 cobA_cysG_Cterm 185 185 238 equivalog_domain Y Y N uroporphyrinogen-III C-methyltransferase cobA 2.1.1.107 GO:0004851,GO:0019354 131567 cellular organisms no rank 96254 JCVI uroporphyrinogen-III C-methyltransferase uroporphyrinogen-III C-methyltransferase This HMM represents enzymes, or enzyme domains, with uroporphyrin-III C-methyltransferase activity. This enzyme catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). Cobalamin contains cobalt while siroheme contains iron. Siroheme is a cofactor for nitrite and sulfite reductases and therefore plays a role in cysteine biosynthesis; many members of this family are CysG, siroheme synthase, with an additional N-terminal domain and with additional oxidation and iron insertion activities. TIGR01470.1 TIGR01470 cysG_Nterm 62.3 62.3 205 subfamily_domain Y N N siroheme synthase, N-terminal domain GO:0019354,GO:0043115,GO:0051266 11114933 131567 cellular organisms no rank 56210 JCVI siroheme synthase, N-terminal domain siroheme synthase, N-terminal domain This HMM represents a subfamily of CysG N-terminal region-related sequences. All sequences in the seed alignment for this model are N-terminal regions of known or predicted siroheme synthases. The C-terminal region of each is uroporphyrin-III C-methyltransferase (EC 2.1.1.107), which catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). The region represented by this model completes the process of oxidation and iron insertion to yield siroheme. Siroheme is a cofactor for nitrite and sulfite reductases, so siroheme synthase is CysG of cysteine biosynthesis in some organisms. TIGR01472.1 TIGR01472 gmd 415 415 342 equivalog Y Y N GDP-mannose 4,6-dehydratase gmd 4.2.1.47 GO:0000271,GO:0008446,GO:0019673 9525924 131567 cellular organisms no rank 31518 JCVI GDP-mannose 4,6-dehydratase GDP-mannose 4,6-dehydratase Alternate name: GDP-D-mannose dehydratase. This enzyme converts GDP-mannose to GDP-4-dehydro-6-deoxy-D-mannose, the first of three steps for the conversion of GDP-mannose to GDP-fucose in animals, plants, and bacteria. In bacteria, GDP-L-fucose acts as a precursor of surface antigens such as the extracellular polysaccharide colanic acid of E. coli. Excluded from this model are members of the clade that score poorly because of highly dervied (phylogenetically long-branch) sequences, e.g. Aneurinibacillus thermoaerophilus Gmd, described as a bifunctional GDP-mannose 4,6-dehydratase/GDP-6-deoxy-D-lyxo-4-hexulose reductase (PUBMED:11096116). TIGR01473.1 TIGR01473 cyoE_ctaB 210.3 210.3 281 equivalog Y Y N heme o synthase cyoE 2.5.1.141 GO:0006783,GO:0008495,GO:0016020 1336371,8118433,9378722 131567 cellular organisms no rank 50737 JCVI protoheme IX farnesyltransferase heme o synthase This HMM describes protoheme IX farnesyltransferase, also called heme O synthase, an enzyme that creates an intermediate in the biosynthesis of heme A. Prior to the description of its enzymatic function, this protein was often called a cytochrome o ubiquinol oxidase assembly factor. TIGR01475.1 TIGR01475 ubiA_other 180.8 180.8 282 subfamily Y Y N UbiA-like polyprenyltransferase GO:0006744,GO:0008412 24558159 131567 cellular organisms no rank 13620 JCVI putative 4-hydroxybenzoate polyprenyltransferase UbiA-like polyprenyltransferase A fairly deep split separates this UbiA-like polyprenyltransferase subfamily from the set of mitochondrial and proteobacterial 4-hydroxybenzoate polyprenyltransferases, described in TIGR01474. Protoheme IX farnesyltransferase (heme O synthase) (TIGR01473) is more distantly related. Species with a member of this family, from lineages such as the Actinobacteria, Epsilonproteobacteria, Deinococcus/Thermus, and some Archaea, generally do not also have a member of UbiA family TIGR01474, suggesting 4-hydroxybenzoate polyprenyltransferase (UbiA) activity for this family. However, overlap is also strong with species that synthesize menaquinone by the (alternate) futalosine pathway, suggesting MqnP activity. This model is therefore designated subfamily. TIGR01479.1 TIGR01479 GMP_PMI 372.95 372.95 467 equivalog Y Y N mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase 2.7.7.13,5.3.1.8 GO:0000271,GO:0016779 131567 cellular organisms no rank 39119 JCVI mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase This enzyme is known to be bifunctional, as both mannose-6-phosphate isomerase (EC 5.3.1.8) (PMI) and mannose-1-phosphate guanylyltransferase (EC 2.7.7.22) in Pseudomonas aeruginosa, Xanthomonas campestris, and Gluconacetobacter xylinus. The literature on the enzyme from E. coli attributes mannose-6-phosphate isomerase activity to an adjacent gene, but the present sequence has not been shown to lack the activity. The PMI domain is C-terminal. TIGR01482.1 TIGR01482 SPP-subfamily 107.15 107.15 225 subfamily Y N N sucrose-phosphate phosphatase subfamily 131567 cellular organisms no rank 2536 JCVI sucrose-phosphate phosphatase subfamily sucrose-phosphate phosphatase subfamily This HMM includes both the members of the SPP equivalog model (TIGR01485), encompassing plants and cyanobacteria, as well as those archaeal sequences which are the closest relatives (TIGR01487). It remains to be shown whether these archaeal sequences catalyze the same reaction as SPP. TIGR01484.1 TIGR01484 HAD-SF-IIB 41.8 41.8 221 subfamily Y Y N HAD-IIB family hydrolase GO:0008152,GO:0016787 131567 cellular organisms no rank 229822 JCVI HAD hydrolase, family IIB HAD-IIB family hydrolase This subfamily falls within the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The Class II subfamilies are characterized by a domain that is located between the second and third conserved catalytic motifs of the superfamily domain. The IIB subfamily is distinguished from the IIA subfamily (TIGR01460) by homology and the predicted secondary structure of this domain by PSI-PRED. The IIB subfamily's Class II domain has the following predicted structure: Helix-Sheet-Sheet-(Helix or Sheet)-Helix-Sheet-(variable)-Helix-Sheet-Sheet. The IIB subfamily consists of Trehalose-6-phosphatase (TIGR00685), plant and cyanobacterial Sucrose-phosphatase and a closely related group of bacterial and archaeal sequences, eukaryotic phosphomannomutase (PF03332), a large subfamily ("Cof-like hydrolases", TIGR00099) containing many closely related bacterial sequences, a hypothetical equivalog containing the E. coli YedP protein, as well as two small clusters containing OMNI|TC0379 and OMNI|SA2196 whose relationship to the other groups is unclear. TIGR01486.1 TIGR01486 HAD-SF-IIB-MPGP 164.75 164.75 257 subfamily Y N N mannosyl-3-phosphoglycerate phosphatase family GO:0005737,GO:0050531,GO:0051479 12788726 131567 cellular organisms no rank 6909 JCVI mannosyl-3-phosphoglycerate phosphatase family mannosyl-3-phosphoglycerate phosphatase family This small group of proteins is a member of the IIB subfamily (TIGR01484) of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. Several members of this family from thermophiles (and from Dehalococcoides ethenogenes) are now known to act as mannosyl-3-phosphoglycerate (MPG) phosphatase. In these cases, the enzyme acts after MPG synthase to make the compatible solute mannosylglycerate. We propose that other mesophilic members of this family do not act as mannosyl-3-phosphoglycerate phosphatase. A member of this family is found in Escherichia coli, which appears to lack MPG synthase. Mannosylglycerate is imported in E. coli by phosphoenolpyruvate-dependent transporter (PMID:14645248), but it appears the phosphorylation is not on the glycerate moiety, that the phosphorylated import is degraded by an alpha-mannosidase from an adjacent gene, and that E. coli would have no pathway to obtain MPG. TIGR01487.1 TIGR01487 Pglycolate_arch 122.75 122.75 215 equivalog Y Y N phosphoglycolate phosphatase 3.1.3.18 GO:0008967 14555659 131567 cellular organisms no rank 1148 JCVI phosphoglycolate phosphatase, TA0175-type phosphoglycolate phosphatase, TA0175-type This group of Archaeal sequences, now known to be phosphoglycolate phosphatases, is most closely related to the sucrose-phosphate phosphatases from plants and cyanobacteria (TIGR01485). Together, these two models comprise a subfamily model (TIGR01482). TIGR01482, in turn, is a member of the IIB subfamily (TIGR01484) of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. TIGR01488.1 TIGR01488 HAD-SF-IB 45 45 177 subfamily Y Y N HAD-IB family phosphatase GO:0008152,GO:0016787 131567 cellular organisms no rank 120127 JCVI HAD phosphoserine phosphatase-like hydrolase, family IB HAD-IB family phosphatase This HMM represents a subfamily of the Haloacid Dehalogenase superfamily of aspartate-nucleophile hydrolases. Subfamily IA, B, C and D are distinguished from the rest of the superfamily by the presence of a variable domain between the first and second conserved catalytic motifs. In subfamilies IA and IB, this domain consists of an alpha-helical bundle. It was necessary to model these two subfamilies separately, breaking them at a an apparent phylogenetic bifurcation, so that the resulting model(s) are not so broadly defined that members of subfamily III (which lack the variable domain) are included. Subfamily IA includes the enzyme phosphoserine phosphatase (TIGR00338) as well as three hypothetical equivalogs. Many members of these hypothetical equivalogs have been annotated as PSPase-like or PSPase-family proteins. In particular, the hypothetical equivalog which appears to be most closely related to PSPase contains only Archaea (while TIGR00338 contains only eukaryotes and bacteria) of which some are annotated as PSPases. Although this is a reasonable conjecture, none of these sequences has sufficient evidence for this assignment. If such should be found, this model should be retired while the PSPase model should be broadened to include these sequences. TIGR01491.1 TIGR01491 HAD-SF-IB-PSPlk 151.9 151.9 201 hypoth_equivalog Y N N phosphoserine phosphatase-like hydrolase, archaeal 131567 cellular organisms no rank 142 JCVI phosphoserine phosphatase-like hydrolase, archaeal phosphoserine phosphatase-like hydrolase, archaeal This hypothetical equivalog is a member of the IB subfamily (TIGR01488) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this HMM are all from archaeal species. The phylogenetically closest group of sequences to these are phosphoserine phosphatases (TIGR00338). There are no known archaeal phosphoserine phosphatases, and no archaea fall within TIGR00338. It is likely, then, that this HMM represents the archaeal branch of the PSPase equivalog. TIGR01493.1 TIGR01493 HAD-SF-IA-v2 39 39 161 subfamily Y Y N HAD-IA family hydrolase 131567 cellular organisms no rank 33173 JCVI HAD hydrolase, family IA, variant 2 HAD-IA family hydrolase This HMM represents part of one structural subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs (PMID:7966317). The subfamilies are defined (PMID:11601995) based on the location and the observed or predicted fold of a so-called 'capping domain' (PMID:10956028), or the absence of such a domain. Subfamily I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. The Subfamily IA and IB capping domains are predicted by PSI-PRED to consist of an alpha helical bundle. This model represents the variant 2 form of the still very broad HAD-IA family. In it, the third of the three defining catalytic motifs takes the form hhhhssxxx(x)D, where _s_ refers to a small amino acid and _h_ to a hydrophobic one. TIGR01494.1 TIGR01494 ATPase_P-type 62.3 62.3 478 subfamily Y Y N HAD-IC family P-type ATPase GO:0005215,GO:0005524,GO:0016020,GO:0016887 131567 cellular organisms no rank 523165 JCVI HAD ATPase, P-type, family IC HAD-IC family P-type ATPase The P-type ATPases are a large family of trans-membrane transporters acting on charged substances. The distinguishing feature of the family is the formation of a phosphorylated intermediate (aspartyl-phosphate) during the course of the reaction. P-type ATPases typically consist of only a single subunit encompassing the ATPase and ion translocation pathway, but these functions are split in some systems. The catalytic core of a P-type ATPase is a haloacid dehalogenase(HAD)-type aspartate-nucleophile hydrolase. The location of the ATP-binding loop in between the first and second HAD conserved catalytic motifs defines these enzymes as members of subfamily I of the HAD superfamily (see also TIGR01493, TIGR01509, TIGR01549, TIGR01544 and TIGR01545). Based on these classifications, the P-type ATPase _superfamily_ corresponds to the IC subfamily of the HAD superfamily. TIGR01496.1 TIGR01496 DHPS 162.6 162.6 258 equivalog Y Y N dihydropteroate synthase folP 2.5.1.15 GO:0004156,GO:0009396 131567 cellular organisms no rank 90971 JCVI dihydropteroate synthase dihydropteroate synthase This HMM represents dihydropteroate synthase, the enzyme that catalyzes the second to last step in folic acid biosynthesis. The gene is usually designated folP (folic acid biosynthsis) or sul (sulfanilamide resistance). This model represents one branch of the family of pterin-binding enzymes (PF00809) and of a cluster of dihydropteroate synthase and related enzymes (COG0294). Other members of PF00809 and COG0294 are represented by HMM TIGR00284. TIGR01497.1 TIGR01497 kdpB 527.9 527.9 675 equivalog Y Y N potassium-transporting ATPase subunit KdpB kdpB 7.2.2.6 GO:0005524,GO:0006813,GO:0008556,GO:0016020,GO:0031004 28636601,30478378 131567 cellular organisms no rank 50361 JCVI K+-transporting ATPase, B subunit potassium-transporting ATPase subunit KdpB KdpB is a component of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions. TIGR01498.1 TIGR01498 folK 54.1 54.1 128 equivalog Y Y N 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase folK 2.7.6.3 GO:0003848,GO:0009396 131567 cellular organisms no rank 73261 JCVI 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase This HMM describes the folate biosynthesis enzyme 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase. Alternate names include 6-hydroxymethyl-7,8-dihydropterin diphosphokinase and 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase (HPPK). The extreme C-terminal region, of typically eight to thirty residues, is not included in the model. This enzyme may be found as a fusion protein with other enzymes of folate biosynthesis. TIGR01499.1 TIGR01499 folC 162.65 162.65 400 subfamily Y N N bifunctional protein FolC folC GO:0004326,GO:0005524,GO:0005737,GO:0006760,GO:0008841,GO:0046654 1989505 131567 cellular organisms no rank 94825 JCVI bifunctional protein FolC bifunctional protein FolC This HMM represents the FolC family of folate pathway proteins. Most examples are bifunctional, active as both folylpolyglutamate synthetase (EC 6.3.2.17) and dihydrofolate synthetase (EC 6.3.2.12). The two activities are similar - ATP + glutamate + dihydropteroate or tetrahydrofolyl-[Glu](n) = ADP + orthophosphate + dihydrofolate or tetrahydrofolyl-[Glu](n+1). A mutation study of the FolC gene of E. coli suggests that both activities belong to the same active site. Because some examples are monofunctional (and these cannot be separated phylogenetically), the model is treated as subfamily, not equivalog. TIGR01501.1 TIGR01501 MthylAspMutase 135.8 135.8 134 equivalog Y Y N methylaspartate mutase subunit S mamA 5.4.99.1 GO:0016866,GO:0019670,GO:0050097 131567 cellular organisms no rank 1193 JCVI methylaspartate mutase, S subunit methylaspartate mutase subunit S This HMM represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation. TIGR01502.1 TIGR01502 B_methylAsp_ase 286.15 286.15 408 equivalog Y Y N methylaspartate ammonia-lyase 4.3.1.2 GO:0019670,GO:0050096 131567 cellular organisms no rank 2178 JCVI methylaspartate ammonia-lyase methylaspartate ammonia-lyase This HMM describes methylaspartate ammonia-lyase, also called beta-methylaspartase (EC 4.3.1.2). It follows methylaspartate mutase (composed of S and E subunits) in one of several possible pathways of glutamate fermentation. TIGR01503.1 TIGR01503 MthylAspMut_E 390.1 390.1 480 equivalog Y Y N methylaspartate mutase subunit E 5.4.99.1 GO:0019670,GO:0050097 131567 cellular organisms no rank 1750 JCVI methylaspartate mutase, E subunit methylaspartate mutase subunit E This HMM represents the E (epsilon) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation. TIGR01506.1 TIGR01506 ribC_arch 100.55 100.55 151 equivalog Y Y N riboflavin synthase ribC 2.5.1.9 GO:0004746 131567 cellular organisms no rank 484 JCVI riboflavin synthase riboflavin synthase This archaeal protein catalyzes the same reaction, the final step in riboflavin biosynthesis, as bacterial riboflavin biosynthesis alpha chain. However, it is more similar in sequence to 6,7-dimethyl-8-ribityllumazine synthase, which catalyzes the previous reaction and which (in bacteria) is called the riboflavin synthase beta chain. TIGR01508.1 TIGR01508 rib_reduct_arch 186.45 186.45 210 equivalog Y Y N 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase 1.1.1.302 GO:0016491 11889103 131567 cellular organisms no rank 1434 JCVI diaminohydroxyphosphoribosylaminopyrimidine reductase 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase This HMM represents a specific reductase of riboflavin biosynthesis in the Archaea, diaminohydroxyphosphoribosylaminopyrimidine reductase. It should not be confused with bacterial 5-amino-6-(5-phosphoribosylamino)uracil reductase. The intermediate 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine in riboflavin biosynthesis is reduced first, and then deaminated, in both Archaea and Fungi, opposite the order in Bacteria. The subsequent deaminase is not presently known and is not closely homologous to the deaminase domain (3.5.4.26) fused to the reductase domain (1.1.1.193) similar to this protein but found in most bacteria. TIGR01509.1 TIGR01509 HAD-SF-IA-v3 29.4 29.4 154 subfamily Y Y N HAD-IA family hydrolase GO:0008152,GO:0016787 131567 cellular organisms no rank 386531 JCVI HAD hydrolase, family IA, variant 3 HAD-IA family hydrolase This HMM represents part of one structural subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs (PMID:7966317). HAD subfamilies are defined (PMID:11601995) based on the location and the observed or predicted fold of a so-called "capping domain" (PMID:10956028), or the absence of such a domain. Subfamily I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. The Subfamily IA and IB capping domains are predicted by PSI-PRED to consist of an alpha helical bundle. This model represents variant 3 of subfamily IA, in which the HAD superfamily's third catalytic motif takes the form hhhhDDxxx(x)s, where _s_ refers to a small amino acid and _h_ to a hydrophobic one. TIGR01511.1 TIGR01511 ATPase-IB1_Cu 397 397 542 subfamily Y Y N copper-translocating P-type ATPase 3.6.3.- GO:0005375,GO:0006825,GO:0043682 131567 cellular organisms no rank 190406 JCVI copper-translocating P-type ATPase copper-translocating P-type ATPase Members of this P-type ATPase family apparently include both Cu(+) (EC 3.6.3.54) and Cu(2+) (EC 3.6.3.4) copper efflux transporters. TIGR01512.1 TIGR01512 ATPase-IB2_Cd 313.5 313.5 494 subfamily Y Y N cadmium family heavy metal-translocating P-type ATPase cadA 7.2.2.21 GO:0015434,GO:0015691 23344975 131567 cellular organisms no rank 103845 JCVI cadmium-translocating P-type ATPase cadmium family heavy metal-translocating P-type ATPase This model describes the P-type ATPase primarily responsible for translocating cadmium ions (and other closely-related divalent heavy metals such as cobalt, mercury, lead and zinc) across biological membranes. These transporters are found in prokaryotes and plants. Experimentally characterized members of the seed alignment include: SP|P37617 from E. coli, SP|Q10866 from Mycobacterium tuberculosis and SP|Q59998 from Synechocystis PCC6803. The cadmium P-type ATPases have been characterized as Type IB based on a phylogenetic analysis which combines the copper-translocating ATPases with the cadmium-translocating species [1]. This HMM and that describing the copper-ATPases (TIGR01511) are well separated, and thus we further type the copper-ATPases as IB1 and the cadmium-ATPases as IB2. Several sequences which have not been characterized experimentally fall just below trusted cutoff for both of these models (SP|Q9CCL1 from Mycobacterium leprae, GP|13816263 from Sulfolobus solfataricus, OMNI|NTL01CJ01098 from Campylobacter jejuni, OMNI|NTL01HS01687 from Halobacterium sp., GP|6899169 from Ureaplasma urealyticum and OMNI|HP1503 from Helicobacter pylori). TIGR01513.1 TIGR01513 NAPRTase_put 297.4 297.4 452 equivalog Y Y N nicotinate phosphoribosyltransferase pncB 6.3.4.21 GO:0004516,GO:0009435 131567 cellular organisms no rank 39249 JCVI nicotinate phosphoribosyltransferase nicotinate phosphoribosyltransferase A deep split separates two related families of proteins, one of which includes experimentally characterized examples of nicotinate phosphoribosyltransferase, an the first enzyme of NAD salvage biosynthesis. This HMM represents the other family. Members have a different (longer) spacing of several key motifs and have an additional C-terminal domain of up to 100 residues. One argument suggesting that this family represents the same enzyme is that no species has a member of both families. Another is that the gene encoding this protein is located near other NAD salvage biosynthesis genes in Nostoc and in at least four different Gram-positive bacteria. NAD and NADP are ubiquitous in life. Most members of this family are Gram-positive bacteria. An additional set of mutually closely related archaeal sequences score between the trusted and noise cutoffs. TIGR01514.1 TIGR01514 NAPRTase 269.55 269.55 399 equivalog Y Y N nicotinate phosphoribosyltransferase pncB 6.3.4.21 GO:0004516,GO:0009435 131567 cellular organisms no rank 22663 JCVI nicotinate phosphoribosyltransferase nicotinate phosphoribosyltransferase This HMM represents nicotinate phosphoribosyltransferase, the first enzyme in the salvage pathway of NAD biosynthesis from nicontinate (niacin). Members are primary proteobacterial but also include yeasts and Methanosarcina acetivorans. A related family, apparently non-overlapping in species distribution, is TIGR01513. Members of that family differ in substantially in sequence and have a long C-terminal extension missing from this family, but are proposed also to act as nicotinate phosphoribosyltransferase (see model TIGR01513). TIGR01515.1 TIGR01515 branching_enzym 463.95 463.95 607 equivalog Y Y N 1,4-alpha-glucan branching enzyme glgB 2.4.1.18 GO:0003844,GO:0005978 11257505,407932 131567 cellular organisms no rank 69925 JCVI 1,4-alpha-glucan branching enzyme 1,4-alpha-glucan branching enzyme This HMM describes the glycogen branching enzymes which are responsible for the transfer of chains of approx. 7 alpha(1--4)-linked glucosyl residues to other similar chains (in new alpha(1--6) linkages) in the biosynthesis of glycogen. This enzyme is a member of the broader amylase family of starch hydrolases which fold as (beta/alpha)8 barrels, the so-called TIM-barrel structure [1,2]. All of the sequences comprising the seed of this model have been experimentally characterized. (For instance, [3]). This model encompasses both bacterial and eukaryotic species. No archaea have this enzyme, although Aquifex aolicus does. Two species, Bacillus thuringiensis and Clostridium perfringens have two sequences each which are annotated as amylases. These annotations are aparrently in error. GP|18143720 from C. perfringens, for instance, contains the note "674 aa, similar to gp:A14658_1 amylase (1,4-alpha-glucan branching enzyme (EC 2.4.1.18) ) from Bacillus thuringiensis (648 aa); 51.1% identity in 632 aa overlap." A branching enzyme from Porphyromonas gingivales, OMNI|PG1793, appears to be more closely related to the eukaryotic species (across a deep phylogenetic split) and may represent an instance of lateral transfer from this species' host. A sequence from Arabidopsis thaliana, GP|9294564, scores just above trusted, but appears either to contain corrupt sequence or, more likely, to be a pseudogene as some of the conserved catalytic residues common to the alpha amylase family are not conserved here. TIGR01517.1 TIGR01517 ATPase-IIB_Ca 507.05 507.05 882 equivalog Y Y N calcium-translocating P-type ATPase, PMCA-type 7.2.2.10 GO:0005388,GO:0005524,GO:0006816,GO:0016020 10433975,10434059,10802325,11779702,9419228 131567 cellular organisms no rank 9263 JCVI calcium-translocating P-type ATPase, PMCA-type calcium-translocating P-type ATPase, PMCA-type This model describes the P-type ATPase responsible for translocating calcium ions across the plasma membrane of eukaryotes [1], out of the cell. In some organisms, this type of pump may also be found in vacuolar membranes [2]. In humans and mice, at least, there are multiple isoforms of the PMCA pump with overlapping but not redundant functions. Accordingly, there are no human diseases linked to PMCA defects, although alterations of PMCA function do elicit physiological effects [3]. The calcium P-type ATPases have been characterized as Type IIB based on a phylogenetic analysis which distinguishes this group from the Type IIA SERCA calcium pump [4]. A separate analysis divides Type IIA into sub-types (SERCA and PMR1) [5] which are modelled by two corresponding HMMs (TIGR01116 and TIGR01522). This HMM is well separated from those. TIGR01522.1 TIGR01522 ATPase-IIA2_Ca 798.3 798.3 854 equivalog Y Y N calcium-transporting P-type ATPase, PMR1-type 7.2.2.10 GO:0005388,GO:0006816,GO:0016020 10433975,2526682 131567 cellular organisms no rank 591 JCVI calcium-transporting P-type ATPase, PMR1-type calcium-transporting P-type ATPase, PMR1-type This model describes the P-type ATPase responsible for translocating calcium ions across the golgi membrane of fungi and animals [1,2], and is of particular importance in the sarcoplasmic reticulum of skeletal and cardiac muscle in vertebrates [2]. The calcium P-type ATPases have been characterized as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump [3] modelled by TIGR01517. A separate analysis divides Type IIA into sub-types, SERCA and PMR1 [2] the former of which is modelled by TIGR01116. TIGR01524.1 TIGR01524 ATPase-IIIB_Mg 610.75 610.75 867 equivalog Y Y N magnesium-translocating P-type ATPase mgtA 7.2.2.14 GO:0015444,GO:0015693,GO:0016020 1328179,9419228 131567 cellular organisms no rank 34242 JCVI magnesium-translocating P-type ATPase magnesium-translocating P-type ATPase This HMM describes the magnesium translocating P-type ATPase found in a limited number of bacterial species and best described in Salmonella typhimurium, which contains two isoforms [1]. These transporters are active in low external Mg2+ concentrations and pump the ion into the cytoplasm. The magnesium ATPases have been classified as type IIIB by a phylogenetic analysis [2]. TIGR01525.1 TIGR01525 ATPase-IB_hvy 346.25 346.25 560 subfamily Y Y N heavy metal translocating P-type ATPase GO:0006812,GO:0016020,GO:0042625 131567 cellular organisms no rank 299303 JCVI heavy metal translocating P-type ATPase heavy metal translocating P-type ATPase This HMM encompasses two equivalog models for the copper and cadmium-type heavy metal transporting P-type ATPases (TIGR01511 and TIGR01512) as well as those species which score ambiguously between both models. For more comments and references, see the files on TIGR01511 and 01512. TIGR01527.1 TIGR01527 arch_NMN_Atrans 181.2 181.2 167 equivalog Y Y N nicotinamide-nucleotide adenylyltransferase 2.7.7.1 GO:0000309,GO:0005737,GO:0009435 9401030 131567 cellular organisms no rank 1243 JCVI nicotinamide-nucleotide adenylyltransferase nicotinamide-nucleotide adenylyltransferase This HMM describes a family of archaeal proteins with the activity of the NAD salvage biosynthesis enzyme nicotinamide-nucleotide adenylyltransferase (EC 2.7.7.1). In some cases, the enzyme was tested and found also to have the activity of nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18), an enzyme of NAD de novo biosynthesis, although with a higher Km. In some archaeal species, a lower-scoring paralog, uncharacterized with respect to activity, is also present. These score between trusted and noise cutoffs. TIGR01528.1 TIGR01528 NMN_trans_PnuC 42.45 42.45 187 equivalog Y Y N nicotinamide riboside transporter PnuC pnuC GO:0015663,GO:0015890,GO:0016020 1991724 131567 cellular organisms no rank 37428 JCVI nicotinamide mononucleotide transporter PnuC nicotinamide riboside transporter PnuC The PnuC protein of E. coli is membrane protein responsible for nicotinamide mononucleotide transport, subject to regulation by interaction with the NadR (also called NadI) protein (see TIGR01526). This HMM defines a region corresponding to most of the length of PnuC, found primarily in pathogens. The extreme N- and C-terminal regions are poorly conserved and not included in the alignment and model. TIGR01534.1 TIGR01534 GAPDH-I 367.2 367.2 330 equivalog Y Y N type I glyceraldehyde-3-phosphate dehydrogenase gap GO:0006006,GO:0016620,GO:0050661,GO:0051287 10799476,11200221,7751290,9182530 131567 cellular organisms no rank 92113 JCVI glyceraldehyde-3-phosphate dehydrogenase, type I glyceraldehyde-3-phosphate dehydrogenase, type I This HMM represents glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the enzyme responsible for the interconversion of 1,3-diphosphoglycerate and glyceraldehyde-3-phosphate, a central step in glycolysis and gluconeogenesis. Forms exist which utilize NAD (EC 1.2.1.12), NADP (EC 1.2.1.13) or either (1.2.1.59). In some species, distinct NAD- and NADP- utilizing forms exist, typically being responsible for reactions in the anabolic and catabolic directions respectively [1]. TIGR01536.1 TIGR01536 asn_synth_AEB 267.1 267.1 517 equivalog Y Y N asparagine synthase (glutamine-hydrolyzing) asnB 6.3.5.4 GO:0004066,GO:0006529 10498721 131567 cellular organisms no rank 88250 JCVI asparagine synthase (glutamine-hydrolyzing) asparagine synthase (glutamine-hydrolyzing) This HMM describes the glutamine-hydrolysing asparagine synthase. A poorly conserved C-terminal extension was removed from the model. Bacterial members of the family tend to have a long, poorly conserved insert lacking from archaeal and eukaryotic sequences. Multiple isozymes have been demonstrated, such as in Bacillus subtilis. Long-branch members of the phylogenetic tree (which typically were also second or third candidate members from their genomes) were removed from the seed alignment and score below trusted cutoff. TIGR01537.1 TIGR01537 portal_HK97 112.05 112.05 343 equivalog Y Y N phage portal protein GO:0005198,GO:0019068,GO:0044423 7723020 131567 cellular organisms no rank 46576 JCVI phage portal protein, HK97 family phage portal protein This HMM represents one of several distantly related families of phage portal protein. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average mol. wt. of 40-90 KDa. TIGR01543.1 TIGR01543 proheadase_HK97 59 59 142 equivalog Y Y N HK97 family phage prohead protease GO:0005198,GO:0008233,GO:0019068,GO:0019082 7723020 131567 cellular organisms no rank 23940 JCVI phage prohead protease, HK97 family HK97 family phage prohead protease This HMM describes the prohead protease of HK97 and related phage. It is generally encoded next to the gene for the capsid protein that it processes, and in some cases may be fused to it. This family does not show similarity to the prohead protease of phage T4 (see PF03420). TIGR01546.1 TIGR01546 GAPDH-II_archae 232.9 232.9 333 equivalog Y Y N phosphorylating glyceraldehyde-3-phosphate dehydrogenase 1.2.1.59 GO:0005737,GO:0006096,GO:0016620,GO:0050661,GO:0051287 2165475 131567 cellular organisms no rank 2227 JCVI glyceraldehyde-3-phosphate dehydrogenase, type II phosphorylating glyceraldehyde-3-phosphate dehydrogenase This HMM describes the type II glyceraldehyde-3-phosphate dehydrogenases which are limited to archaea. These enzymes catalyze the interconversion of 1,3-diphosphoglycerate and glyceraldehyde-3-phosphate, a central step in glycolysis and gluconeogenesis. In archaea, either NAD or NADP may be utilized as the cofactor. The class I GAPDH's from bacteria and eukaryotes are covered by TIGR01534. All of the members of the seed are characterized. See, for instance [1]. This model is very solid, there are no species falling between trusted and noise at this time. The closest relatives scoring in the noise are the class I GAPDH's. TIGR01547.1 TIGR01547 phage_term_2 105.05 105.05 396 equivalog Y Y N PBSX family phage terminase large subunit 131567 cellular organisms no rank 23655 JCVI phage terminase, large subunit, PBSX family PBSX family phage terminase large subunit This HMM detects members of a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from PF03354. TIGR01548.1 TIGR01548 HAD-SF-IA-hyp1 140.2 140.2 197 hypoth_equivalog Y Y N TIGR01548 family HAD-type hydrolase 7966317 131567 cellular organisms no rank 1626 JCVI HAD hydrolase, TIGR01548 family TIGR01548 family HAD-type hydrolase This HMM represents a small and phylogenetically curious clade of sequences. Sequences are found from Halobacterium (an archaeon), Nostoc and Synechococcus (cyanobacteria) and Phytophthora (a stramenophile eukaryote). These appear to be members of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases by general homology and the conservation of all of the recognized catalytic motifs [1]. The variable domain is found in between motifs 1 and 2, indicating membership in subfamily I and phylogeny and prediction of the alpha helical nature of the variable domain (by PSI-PRED) indicate membership in subfamily IA. All but the Halobacterium sequence currently found are annotated as "Imidazoleglycerol-phosphate dehydratase", however, the source of the annotation could not be traced and significant homology could not be found between any of these sequences and known IGPD's. TIGR01549.1 TIGR01549 HAD-SF-IA-v1 23.3 23.3 149 subfamily Y Y N HAD-IA family hydrolase GO:0008152,GO:0016787 131567 cellular organisms no rank 293169 JCVI HAD hydrolase, family IA, variant 1 HAD-IA family hydrolase This HMM represents part of one structural subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs [PMID:7966317]. The subfamilies are defined [PMID:11601995] based on the location and the observed or predicted fold of a so-called "capping domain" [PMID:10956028], or the absence of such a domain. Subfamily I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Subfamily II consists of sequences in which the capping domain is found between the second and third motifs. Subfamily III sequences have no capping domain in either of these positions. TIGR01550.1 TIGR01550 DOC_P1 38.65 38.65 122 subfamily Y Y N type II toxin-antitoxin system death-on-curing family toxin GO:0016301 8411153 131567 cellular organisms no rank 18997 JCVI death-on-curing family protein type II toxin-antitoxin system death-on-curing family toxin The characterized member of this family is the death-on-curing (DOC) protein of phage P1. It is part of a two protein operon with prevents-host-death (phd) that forms an addiction module. DOC lacks homology to analogous addiction module post-segregational killing proteins involved in plasmid maintenance. These modules work as a combination of a long lived poison (e.g. this protein) and a more abundant but shorter lived antidote. Members of this family have a well-conserved central motif HxFx[ND][AG]NKR. A similar region, with K replaced by G, is found in the huntingtin interacting protein (HYPE) family. TIGR01552.1 TIGR01552 phd_fam 20.8 20.8 53 subfamily Y Y N type II toxin-antitoxin system prevent-host-death family antitoxin GO:0008219 131567 cellular organisms no rank 76594 JCVI prevent-host-death family protein type II toxin-antitoxin system prevent-host-death family antitoxin This HMM recognizes a region of about 55 amino acids toward the N-terminal end of bacterial proteins of about 85 amino acids in length. The best-characterized member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (TIGR01550) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family. TIGR01554.3 TIGR01554 major_cap_HK97 27.5 27.5 385 equivalog Y Y N phage major capsid protein GO:0005198,GO:0019068,GO:0044423 131567 cellular organisms no rank 67964 JCVI phage major capsid protein, HK97 family phage major capsid protein, HK97 family This HMM family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. TIGR01561.1 TIGR01561 gde_arch 364.15 364.15 569 hypoth_equivalog Y N N putative glycogen debranching enzyme, archaeal type GO:0004133,GO:0005980 131567 cellular organisms no rank 2658 JCVI putative glycogen debranching enzyme, archaeal type putative glycogen debranching enzyme, archaeal type The seed for this model is composed of two uncharacterized archaeal proteins from Methanosarcina acetivorans and Sulfolobus solfataricus. Trusted cutoff is set so that essentially only archaeal members hit the model. The notable exceptions to archaeal membership are the Gram positive Clostridium perfringens which scores much better than some other archaea and the Cyanobacterium Nostoc sp. which scores just above the trusted cutoff. Noise cutoff is set to exclude the characterized eukaryotic glycogen debranching enzyme in S. cerevisiae. These cutoffs leave the prokaryotes Porphyromonas gingivalis and Deinococcus radiodurans below trusted but above noise. Multiple alignments including these last two species exhibit sequence divergence which may suggest a subtly different function for these prokaryotic proteins. TIGR01564.1 TIGR01564 S_layer_MJ 25 25 571 subfamily Y Y N S-layer protein 131567 cellular organisms no rank 268 JCVI S-layer protein S-layer protein This HMM represents one of several families of proteins associated with the formation of prokaryotic S-layers. Members of this family are found in archaeal species, including Pyrococcus horikoshii (split into two tandem reading frames), Methanococcus jannaschii, and related species. Some local similarity can be found to other S-layer protein families. TIGR01573.1 TIGR01573 cas2 24.5 24.5 96 equivalog Y Y N CRISPR-associated endonuclease Cas2 cas2 GO:0004521,GO:0043571 11952905,18482976,22942283 131567 cellular organisms no rank 19371 JCVI CRISPR-associated endonuclease Cas2 CRISPR-associated endonuclease Cas2 This model describes most members of the family of Cas2, one of the first four protein families found to mark prokaryotic genomes that contain multiple CRISPR elements. CRISPR systems protect against invasive nucleic acid sequences, including phage. Cas2 proteins have been characterized as either endoribonuclease (for ssRNA) or endodeoxyribonuclease (for dsDNA), depending on the system to which the Cas2 belongs. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. The cas genes usually are found near the repeats. A distinct branch of the Cas2 family shows a very low level of sequence identity and is modeled by TIGR01873 instead of by this HMM (TIGR01573). TIGR01574.1 TIGR01574 miaB-methiolase 355.3 355.3 437 equivalog Y Y N tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB miaB 2.8.4.3 GO:0006400,GO:0016782,GO:0051539,GO:1904047 10572129,11313137,11882645,12766153 131567 cellular organisms no rank 66641 JCVI tRNA-i(6)A37 thiotransferase enzyme MiaB tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB This model represents homologs of the MiaB enzyme responsible for the modification of the isopentenylated adenine-37 base of most bacterial and eukaryotic tRNAs that read codons beginning with uracil. Adenine-37 is next to the anticodon on the 3' side in these tRNA's. TIGR01575.1 TIGR01575 rimI 86.4 86.4 132 equivalog Y Y N ribosomal protein S18-alanine N-acetyltransferase rimI 2.3.1.266 GO:0008999,GO:0036211,GO:0042254 2828880,6806564 131567 cellular organisms no rank 48384 JCVI ribosomal-protein-alanine acetyltransferase ribosomal protein S18-alanine N-acetyltransferase Members of this model belong to the GCN5-related N-acetyltransferase (GNAT) superfamily. This model covers prokarotes and the archaea. The seed contains a characterized accession for Gram negative E. coli [1]. An untraceable characterized accession (PIR|S66013) for Gram positive B. subtilis scores well (205.0) in the full alignment. Characterized members are lacking in the archaea. Noise cutoff (72.4) was set to exclude M. loti paralog of rimI. Trusted cutoff (80.0) was set at next highest scoring member in the mini-database. TIGR01578.1 TIGR01578 MiaB-like-B 314.7 314.7 421 hypoth_equivalog Y Y N tRNA (N(6)-L-threonylcarbamoyladenosine(37)-C(2))-methylthiotransferase 2.8.4.5 GO:0035598,GO:0035600 10572129,11313137,11882645 131567 cellular organisms no rank 1482 JCVI MiaB-like tRNA modifying enzyme, archaeal-type tRNA (N(6)-L-threonylcarbamoyladenosine(37)-C(2))-methylthiotransferase This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see TIGR01574 [1,2,3]). Sequence alignments suggest that this equivalog performs the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade is a member of a subfamily (TIGR00089) and spans the archaea and eukaryotes. The only archaeal miaB-like genes are in this clade, while eukaryotes have sequences described by this HMM as well as ones falling within the scope of the MiaB equivalog model. TIGR01580.1 TIGR01580 narG 1084.15 1084.15 1235 equivalog Y Y N nitrate reductase subunit alpha 1.7.99.4 GO:0008940,GO:0009325,GO:0042126 131567 cellular organisms no rank 38742 JCVI nitrate reductase, alpha subunit nitrate reductase subunit alpha The Nitrate reductase enzyme complex allows bacteria to use nitrate as an electron acceptor during anaerobic growth. The enzyme complex consists of a tetramer that has an alpha, beta and 2 gamma subunits. The alpha and beta subunits have catalytic activity and the gamma subunits attach the enzyme to the membrane and is a b-type cytochrome that receives electrons from the quinone pool and transfers them to the beta subunit. This model is specific for the alpha subunit for nitrate reductase I (narG) and nitrate reductase II (narZ) for gram positive and gram negative bacteria.A few thermophiles and archaea also match the model The seed members used to make the model include Nitrate reductases from Pseudomonas fluorescens (GP:11344601), E.coli (SP:P09152) and B.subtilis (SP:P42175). All seed members are experimentally characterized. Some unpublished nitrate reductases, that are shorter sequences, and probably fragments fall in between the noise and trusted cutoffs. Pfam models PF00384 (Molybdopterin oxidoreductase) and PF01568(Molydopterin dinucleotide binding domain) will also match the nitrate reductase, alpha subunit. TIGR01581.1 TIGR01581 Mo_ABC_porter 210.3 210.3 225 hypoth_equivalog Y Y N ABC transporter permease GO:0016020,GO:0042626,GO:0043190,GO:0055085 2194453 131567 cellular organisms no rank 16314 JCVI NifC-like ABC-type porter ABC transporter permease This model describes a clade of ABC porter genes with relatively weak homology compared to its neighbor clades, the molybdate (TIGR02141) and sulfate (TIGR00969) porters. Neighbor-Joining, PAM-distance phylogenetic trees support the separation of the clades in this way. Included in this group is a gene designated NifC in Clostridium pasturianum [1]. It would be reasonable to presume that NifC acts as a molybdate porter since the most common form of nitrogenase is a molybdoenzyme. Several other sequences falling within the scope of this model are annotated as molybdate porters and one, from Halobacterium, is annotated as a sulfate porter. There is presently no experimental evidence to support annotations with this degree of specificity. TIGR01587.1 TIGR01587 cas3_core 102.45 102.45 358 equivalog_domain Y Y N CRISPR-associated helicase Cas3' cas3 GO:0004386,GO:0043571 11788711,11952905 131567 cellular organisms no rank 26784 JCVI CRISPR-associated helicase Cas3 CRISPR-associated helicase Cas3' This HMM represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by PF00270 (DEAD/DEAH box helicase) and PF00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (PF01966) that is not included within this model. TIGR01591.1 TIGR01591 Fdh-alpha 666.25 666.25 672 equivalog Y Y N formate dehydrogenase subunit alpha fdhF 1.17.1.9 GO:0008863,GO:0009326,GO:0015942 131567 cellular organisms no rank 43368 JCVI formate dehydrogenase, alpha subunit formate dehydrogenase subunit alpha TIGR01595.1 TIGR01595 cas_CT1132 125.8 125.8 268 subfamily Y Y N CRISPR-associated protein GO:0043571 131567 cellular organisms no rank 7184 JCVI CRISPR-associated protein, CT1132 family CRISPR-associated protein, CT1132 family This protein is found in at least five widely species that contain CRISPR loci. Four cas (CRISPR-associated) proteins that are widely distributed and found near the CRISPR repeats. This protein is found exclusively next to other cas proteins. Its function is unknown. TIGR01596.1 TIGR01596 cas3_HD 43.45 43.45 178 equivalog_domain Y Y N CRISPR-associated endonuclease Cas3'' GO:0004521,GO:0043571 11952905,19174159 131567 cellular organisms no rank 29245 JCVI CRISPR-associated endonuclease Cas3-HD CRISPR-associated endonuclease Cas3'' CRISPR/Cas systems are widespread, mobile systems for host defense against invasive elements such as phage. In these systems, Cas3 designates one of the core proteins shared widely by multiple types of CRISPR/Cas system. This HMM represents an HD-like endonuclease that occurs either separately or as the N-terminal region of Cas3, the helicase-containing CRISPR-associated protein. TIGR01613.1 TIGR01613 primase_Cterm 108.7 108.7 304 subfamily_domain Y Y N phage/plasmid primase, P4 family GO:0003896,GO:0006260 131567 cellular organisms no rank 27889 JCVI phage/plasmid primase, P4 family, C-terminal domain phage/plasmid primase, P4 family, C-terminal domain This HMM represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus. TIGR01617.1 TIGR01617 arsC_related 75.05 75.05 117 subfamily Y Y N Spx/MgsR family RNA polymerase-binding regulatory protein 18643936,18687074,19580872 131567 cellular organisms no rank 38332 JCVI transcriptional regulator, Spx/MgsR family Spx/MgsR family RNA polymerase-binding regulatory protein Members of this family regulate transcription by binding the alpha subunit of RNA polymerase, and affecting its binding of DNA, rather than by binding DNA directly. Characterized members of this family include Spx and MgsR from Bacillus subtili. Spx is a global regulator for response to thiol-specific oxidative stress. MgsR (modulator of the general stress response, also called YqgZ) provides a second level of regulation for more than a third of the proteins in the B. subtilis general stress regulon controlled by Sigma-B. Members are related to the arsenate reductase ArsC. TIGR01630.1 TIGR01630 psiM2_ORF9 41.65 41.65 142 equivalog_domain Y Y N phage terminase large subunit terL 17615066,9791169 131567 cellular organisms no rank 14820 JCVI phage uncharacterized protein, C-terminal domain phage terminase large subunit C-terminal domain This HMM represents the C-terminal region of a set of phage proteins typically about 400-500 amino acids in length, although some members are considerably shorter. Most proteins in this family have an apparent P-loop nucleotide-binding sequence toward the N-terminus, consistent with the ATPase activity of phage terminase large subunit (TerL). The assignment as TerL is suggested by gene context in numerous phage as well as by homology to better characterized families of TerL. TIGR01633.1 TIGR01633 phi3626_gp14_N 23.65 23.65 123 hypoth_equivalog Y Y N distal tail protein Dit GO:0005198,GO:0016032,GO:0044423 20843802 131567 cellular organisms no rank 11508 JCVI putative phage tail component, N-terminal domain distal tail protein Dit This HMM represents the best-conserved region of about 125 amino acids, toward the N-terminus, of a family of proteins from temperate phage of a number of Gram-positive bacteria. These phage proteins range in length from 230 to 525 amino acids. TIGR01641.1 TIGR01641 phageSPP1_gp7 39.65 39.65 109 domain Y Y N minor capsid protein GO:0016032,GO:0019068,GO:0044423 16899078 131567 cellular organisms no rank 28566 JCVI phage head morphogenesis protein, SPP1 gp7 family minor capsid protein This HMM describes a region of about 110 amino acids found exclusively in phage-related proteins, internally or toward the C-terminus. One member, gp7 of phage SPP1, appears involved in head morphogenesis. TIGR01643.1 TIGR01643 YD_repeat_2x 15.8 15.8 42 repeat N N N YD repeat-containing protein 10341219,2403547,7934896 131567 cellular organisms no rank 197436 JCVI YD repeat (two copies) YD repeat (two copies) This HMM describes two tandem copies of a 21-residue extracellular repeat found in Gram-negative, Gram-positive, and animal proteins. The repeat is named for a YD dipeptide, the most strongly conserved motif of the repeat. These repeats appear in general to be involved in binding carbohydrate; the chicken teneurin-1 YD-repeat region has been shown to bind heparin. TIGR01647.1 TIGR01647 ATPase-IIIA_H 615.5 615.5 755 equivalog Y Y N plasma-membrane proton-efflux P-type ATPase 7.1.2.1 GO:0008553,GO:0016020,GO:0120029 1288321 131567 cellular organisms no rank 1824 JCVI plasma-membrane proton-efflux P-type ATPase plasma-membrane proton-efflux P-type ATPase This model describes the plasma membrane proton efflux P-type ATPase found in plants, fungi, protozoa, slime molds and archaea. The best studied representative is from yeast [1]. TIGR01656.1 TIGR01656 Histidinol-ppas 84.15 84.15 149 subfamily_domain Y N N histidinol-phosphate phosphatase domain GO:0016791 131567 cellular organisms no rank 51913 JCVI histidinol-phosphate phosphatase domain histidinol-phosphate phosphatase domain This domain is found in authentic histidinol-phosphate phosphatases which are sometimes found as stand-alone entities and sometimes as fusions with imidazoleglycerol-phosphate dehydratase (TIGR01261). Additionally, a family of proteins including YaeD from E. coli (TIGR00213) and various other proteins are closely related but may not have the same substrate specificity. This domain is a member of the haloacid-dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. This superfamily is distinguished by the presence of three motifs: an N-terminal motif containing the nucleophilic aspartate, a central motif containing an conserved serine or threonine, and a C-terminal motif containing a conserved lysine (or arginine) and conserved aspartates. More specifically, the domian modelled here is a member of subfamily III of the HAD-superfamily by virtue of lacking a "capping" domain in either of the two common positions, between motifs 1 and 2, or between motifs 2 and 3. TIGR01660.1 TIGR01660 narH 524.05 524.05 492 equivalog Y Y N nitrate reductase subunit beta narH 1.7.99.4 GO:0008940,GO:0009325,GO:0042126 131567 cellular organisms no rank 24090 JCVI nitrate reductase, beta subunit nitrate reductase subunit beta The Nitrate reductase enzyme complex allows bacteria to use nitrate as an electron acceptor during anaerobic growth. The enzyme complex consists of a tetramer that has an alpha, beta and 2 gamma subunits. The alpha and beta subunits have catalytic activity and the gamma subunits attach the enzyme to the membrane and is a b-type cytochrome that receives electrons from the quinone pool and transfers them to the beta subunit. This model is specific for the beta subunit for nitrate reductase I (narH) and nitrate reductase II (narY) for gram positive and gram negative bacteria.A few thermophiles and archaea also match the model.The seed members used in this model are all experimentally characterized and include the following:SP:P11349, and SP:P19318, both E.Coli (NarH and NarY respectively), SP:P42176 from B. Subtilis, GP:11344602 from Psuedomonas fluorescens,GP:541762 from Paracoccus denitrificans, and GP:18413622 from Halomonas halodenitrificans. This HMM also matches PFAM PF00037 for 4Fe-4S binding domain. TIGR01662.1 TIGR01662 HAD-SF-IIIA 44.6 44.6 141 subfamily_domain Y Y N HAD-IIIA family hydrolase GO:0016787 3007936 131567 cellular organisms no rank 81221 JCVI HAD hydrolase, family IIIA HAD-IIIA family hydrolase This subfamily falls within the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The Class III subfamilies are characterized by the lack of any domains located between either between the first and second conserved catalytic motifs (as in the Class I subfamilies, TIGR01493, TIGR01509, TIGR01488 and TIGR01494) or between the second and third conserved catalytic motifs (as in the Class II subfamilies, TIGR01460 and TIGR01484) of the superfamily domain. The IIIA subfamily contains five major clades: histidinol-phosphatase (TIGR01261, [3]) and histidinol-phosphatase-related protein (TIGR00213) which together form a subfamily (TIGR01656), DNA 3'-phosphatase (TIGR01663, TIGR01664), YqeG (TIGR01668) and YrbI (TIGR01670). In the case of histidinol phosphatase and PNK-3'-phosphatase, this model represents a domain of a bifunctional system. In the histidinol phosphatase HisB, a C-terminal domain is an imidazoleglycerol-phosphate dehydratase which catalyzes a related step in histidine biosynthesis. In PNK-3'-phosphatase, N- and C-terminal domains constitute the polynucleotide kinase and DNA-binding components of the enzyme. TIGR01670.1 TIGR01670 KdsC-phosphatas 106.95 106.95 154 subfamily Y N N 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family GO:0009103,GO:0019143 11835514,12639950 131567 cellular organisms no rank 25655 JCVI 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family This family of proteins is a member of the IIIA subfamily of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterized members of this subfamily (TIGR01662) and most characterized members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs [1], all of which are found conserved here. One member of this family, the YrbI protein from H. influenzae has been cloned, expressed, purified and found to be an active 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase[2]. Furthermore, its crystal structure has been determined [3]. This family consists of sequences from beta, gamma and epsilon proteobacteria, Aquifex, Fusobacterium, Porphyromonas and Methanosarcina. The Methanosarcina sequence is distinctive in that it is linked to an N-terminal cytidylyltransferase domain (PF02348) and is annotated as acylneuraminate cytidylyltransferase. This may give some clue as the function of these phosphatases. Several eukaryotic sequences scoring between trusted and noise are also closely related to this function such as the CMP-N-acetylneuraminic acid synthetase from mouse, but in these cases the phosphatase domain is clearly inactive as many of the active site residues are not conserved. TIGR01679.1 TIGR01679 bact_FAD_ox 292.25 292.25 419 subfamily Y N N FAD-linked oxidoreductase 131567 cellular organisms no rank 19187 JCVI FAD-linked oxidoreductase FAD-linked oxidoreductase This HMM represents a family of bacterial oxidoreductases with covalently linked FAD, closely related to two different eukaryotic oxidases, L-gulonolactone oxidase (EC 1.1.3.8) from rat and D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) from Saccharomyces cerevisiae. TIGR01681.1 TIGR01681 HAD-SF-IIIC 35.75 35.75 132 subfamily_domain Y Y N HAD-IIIC family phosphatase 11601995,7966317 131567 cellular organisms no rank 15113 JCVI HAD phosphatase, family IIIC HAD-IIIC family phosphatase This model represents the IIIC subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate nucleophile hydrolases. Subfamily III (also including IIIA - TIGR01662 and IIIB - PF03767) contains sequences which do not contain either of the insert domains (between the 1st and 2nd conserved catalytic motifs, subfamily I - TIGR01493, TIGR01509, TIGR01549, TIGR01488, TIGR01494, TIGR01658, TIGR01544 and TIGR01545, or between the 2nd and 3rd, subfamily II - TIGR01460 and TIGR01484). Subfamily IIIC contains five relatively distantly related clades: a family of viral proteins (TIGR01684), a family of eukaryotic proteins called MDP-1 and a family of archaeal proteins most closely related to MDP-1 (TIGR01685), a family of bacteria including the Streptomyces FkbH protein (TIGR01686), and a small clade including the Pasteurella BcbF and EcbF proteins. The overall lack of species overlap among these clades may indicate a conserved function, but the degree of divergence between the clades and the differences in archetecture outside of the domain in some clades warns against such a conclusion. No member of this subfamily is characterized with respect to function, however the MDP-1 protein [1] is a characterized phosphatase. All of the characterized enzymes within subfamily III are phosphatases, and all of the active site residues characteristic of HAD-superfamily phosphatases [2] are present in subfamily IIIC. TIGR01682.1 TIGR01682 moaD 66.15 66.15 80 equivalog Y Y N molybdopterin converting factor subunit 1 moaD GO:0003824,GO:0006777 131567 cellular organisms no rank 17376 JCVI molybdopterin converting factor, subunit 1 molybdopterin converting factor subunit 1 This HMM describes MoaD. It excludes archaeal homologs, since many Archaea have two MoaD-like proteins, suggesting two different functions. The Pfam HMM PF02597 describes both the thiamine biosynthesis protein ThiS and this protein, MoaD, a subunit (together with MoaE, Pfam:PF02391) of the molybdopterin converting factor. Both ThiS and MoaD are involved in sulfur transfer reactions. Distribution of this family appears limited to species that also have a member of PF02391, but a number of Archaea have two different members, suggesting functionally distinct subtypes. The C-terminal Gly-Gly of this model is critical to function. TIGR01683.1 TIGR01683 thiS 37.45 37.45 64 equivalog Y Y N sulfur carrier protein ThiS thiS GO:0003824,GO:0009228 10781607 131567 cellular organisms no rank 36769 JCVI thiamine biosynthesis protein ThiS sulfur carrier protein ThiS This HMM represents ThiS, a small, ubiquitin-like thiamine biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis. TIGR01685.1 TIGR01685 MDP-1 53.75 53.75 174 equivalog Y Y N magnesium-dependent phosphatase-1 10889041,11601995 131567 cellular organisms no rank 236 JCVI magnesium-dependent phosphatase-1 magnesium-dependent phosphatase-1 This model represents two closely related clades of sequences from eukaryotes and archaea. The mouse enzyme has been characterized as a phosphatase and has been positively identified as a member of the haloacid dehalogenase (HAD) superfamily by site-directed mutagenesis of the active site residues [1,2]. TIGR01686.1 TIGR01686 FkbH 146.65 146.65 323 subfamily_domain Y N N FkbH domain 10863099,7966317 131567 cellular organisms no rank 14226 JCVI FkbH domain FkbH domain This model describes a domain of a family of proteins of unknown overall function. One of these, however, is a modular polyketide synthase 4800 amino acids in length from Streptomyces avermilitis in which this domain is the C-terminal segment. By contrast, the FkbH protein from Streptomyces hygroscopicus aparently contains only this domain. The remaining members of the family all contain an additional N-terminal domain of between 200 and 275 amino acids which show less than 20% identity to one another. It seems likely then that these proteins are involved in disparate functions, probably the biosynthesis of different natural products. For instance, the FkbH gene is found in a gene cluster believed to be responsible for the biosynthesis of unususal "PKS extender units" in the ascomycin pathway [2]. This domain is composed of two parts, the first of which is a member of subfamily IIIC (TIGR01681) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. All of the characterized enzymes within subfamily III are phosphatases, and all of the active site residues characteristic of HAD-superfamily phosphatases [1] are present in this domain. The C-terminal portion of this domain is unique to this family (by BLAST). TIGR01687.1 TIGR01687 moaD_arch 49.5 49.5 88 subfamily Y Y N MoaD family protein GO:0003824,GO:0006777 131567 cellular organisms no rank 5294 JCVI MoaD family protein MoaD family protein Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable. TIGR01689.1 TIGR01689 EcbF-BcbF 162 162 126 subfamily Y N N capsule biosynthesis phosphatase 10699509,7966317 131567 cellular organisms no rank 938 JCVI capsule biosynthesis phosphatase capsule biosynthesis phosphatase This model describes a small family of highly conserved proteins (>60% ID). Two of these, BcbF and EcbF of Pasteurella multocida are believed to be part of the capsule polysaccharide biosynthesis machinery because they are cotranscribed from a locus devoted to that purpose [1]. In pasteurella there are six different variant capsules (A-F), and these proteins are found only in B and E. The other two species in which this gene is (currently) found are both also pathogenic. These proteins are also members of the IIIC (TIGR01681) subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. All of the characterized enzymes within subfamily III are phosphatases, and all of the active site residues characteristic of HAD-superfamily phosphatases [2] are present in this subfamily. Due to the likelihood that the substrates of these enzymes are different depending on the nature of the particular polysaccharides associated with each species, this model has been classified as a subfamily despite the close homology. TIGR01691.1 TIGR01691 enolase-ppase 128.1 128.1 224 equivalog Y Y N acireductone synthase mtnC 3.1.3.77 GO:0000287,GO:0019509,GO:0043874 131567 cellular organisms no rank 10183 JCVI 2,3-diketo-5-methylthio-1-phosphopentane phosphatase acireductone synthase This enzyme is the enolase-phosphatase of methionine salvage, a pathway that regenerates methionine from methylthioadenosine (MTA). Adenosylmethionine (AdoMet) is a donor of different moieties for various processes, including methylation reactions. Use of AdoMet for spermidine biosynthesis, which leads to polyamine biosynthesis, leaves MTA as a by-product that must be cleared. In Bacillus subtilis and related species, this single protein is replaced by separate enzymes with enolase and phosphatase activities. TIGR01694.1 TIGR01694 MTAP 274.85 274.85 240 equivalog Y Y N S-methyl-5'-thioadenosine phosphorylase mtnP 2.4.2.28 GO:0006168,GO:0017061,GO:0019509 10404592,11489901,7929153,8687427 131567 cellular organisms no rank 20381 JCVI methylthioadenosine phosphorylase S-methyl-5'-thioadenosine phosphorylase This model represents the methylthioadenosine phosphorylase found in metazoa, cyanobacteria and a limited number of archaea such as Sulfolobus, Aeropyrum, Pyrobaculum, Pyrococcus, and Thermoplasma. This enzyme is responsible for the first step in the methionine salvage pathway after the transfer of the amino acid moiety from S-adenosylmethionine. TIGR01697.1 TIGR01697 PNPH-PUNA-XAPA 197.1 197.1 247 subfamily Y N N inosine/guanosine/xanthosine phosphorylase family GO:0004731,GO:0006139 131567 cellular organisms no rank 34114 JCVI inosine/guanosine/xanthosine phosphorylase family inosine/guanosine/xanthosine phosphorylase family This model is a subset of the subfamily represented by PF00896 (phosphorylase family 2). This model excludes the methylthioadenosine phosphorylases (MTAP, TIGR01684) which are believed toplay a specific role in the recycling of methionine from methylthioadenosine. In this subfamily is found three clades of purine phosphorylases based on a neighbor-joining tree using the MTAP family as an outgroup. The highest-branching clade (TIGR01698) consists of a group of sequences from both gram positive and gram negative bacteria which have been annotated as purine nucleotide phosphorylases but have not been further characterized as to substrate specificity. Of the two remaining clades, one is xanthosine phosphorylase (XAPA, TIGR01699), is limited to certain gamma proteobacteria and constitutes a special purine phosphorylase found in a specialized operon for xanthosine catabolism. The enzyme also acts on the same purines (inosine and guanosine) as the other characterized members of this subfamily, but is only induced when xanthosine must be degraded. The remaining and largest clade consists of purine nucleotide phosphorylases (PNPH, TIGR01700) from metazoa and bacteria which act primarily on guanosine and inosine (and do not act on adenosine). Sequences from Clostridium (GP:15025051) and Thermotoga (OMNI:TM1596) fall between these last two clades and are uncharacterized with respect to substrate range and operon. TIGR01701.1 TIGR01701 Fdhalpha-like 582.15 582.15 744 subfamily Y Y N FdhF/YdeP family oxidoreductase GO:0016491,GO:0030151,GO:0051539 16313621,22767548,8824147 131567 cellular organisms no rank 54525 JCVI oxidoreductase alpha (molybdopterin) subunit FdhF/YdeP family oxidoreductase This model represents a well-defined clade of oxidoreductase alpha subunits most closely related to a group of formate dehydrogenases including the E. coli FdhH protein (TIGR01591). These alpha subunits contain a molybdopterin cofactor and generally associate with two other subunits which contain iron-sulfur clusters and cytochromes. The particular subunits with which this enzyme interacts and the substrate which is reduced is unknown at this time. In Ralstonia, the gene is associated with the cbb operon [1], but is not essential for CO2 fixation. TIGR01702.1 TIGR01702 CO_DH_cata 478 478 621 equivalog Y Y N anaerobic carbon-monoxide dehydrogenase catalytic subunit cooS 1.2.7.4 GO:0006091,GO:0016151,GO:0043885,GO:0051539 11509720,1644755,1748656 131567 cellular organisms no rank 3467 JCVI carbon-monoxide dehydrogenase, catalytic subunit anaerobic carbon-monoxide dehydrogenase catalytic subunit This HMM represents the carbon-monoxide dehydrogenase catalytic subunit. This protein is related to prismane (also called hybrid cluster protein), a complex whose activity is not yet fully described; the two share similar sets of ligands to unusual metal-containing clusters. TIGR01703.1 TIGR01703 hybrid_clust 360.8 360.8 522 equivalog Y Y N hydroxylamine reductase hcp 1.7.99.1 GO:0005737,GO:0016661,GO:0050418,GO:0051536 10651802,12374823,1318832,30670550 131567 cellular organisms no rank 21312 JCVI hydroxylamine reductase hydroxylamine reductase This HMM represents a family of proteins containing an unusual 4Fe-2S-2O hydrid cluster. Earlier reports had proposed a 6Fe-6S prismane cluster. This subfamily is heterogeneous with respect to the presence or absence of a region of about 100 amino acids not far from the N-terminus of the protein. Members have been described as monomeric. The general function is unknown, although members from E. coli and several other species have hydroxylamine reductase activity. Members are found in various bacteria, in Archaea, and in several parasitic eukaryotes: Giardia intestinalis, Trichomonas vaginalis, and Entamoeba histolytica. TIGR01722.1 TIGR01722 MMSDH 448.5 448.5 477 subfamily Y Y N CoA-acylating methylmalonate-semialdehyde dehydrogenase mmsA 1.2.1.27 GO:0004491 1339433,1527093,16332250,8550471,9226270 131567 cellular organisms no rank 69611 JCVI methylmalonate-semialdehyde dehydrogenase (acylating) CoA-acylating methylmalonate-semialdehyde dehydrogenase Involved in valine catabolism, methylmalonate-semialdehyde dehydrogenase catalyzes the irreversible NAD+- and CoA-dependent oxidative decarboxylation of methylmalonate semialdehyde to propionyl-CoA [1]. Methylmalonate-semialdehyde dehydrogenase has been characterized in both prokaryotes [1,2] and eukaryotes [3], functioning as a mammalian tetramer and a bacterial homodimer. Although similar in monomeric molecular mass and enzymatic activity, the N-terminal sequence in P.aeruginosa does not correspond with the N-terminal sequence predicted for rat liver [1]. Sequence homology to a variety of prokaryotic and eukaryotic aldehyde dehydrogenases places MMSDH in the aldehyde dehydrogenase (NAD+) superfamily (PF00171), making MMSDH's CoA requirement unique among known ALDHs. Methylmalonate semialdehyde dehydrogenase is closely related to betaine aldehyde dehydrogenase, 2-hydroxymuconic semialdehyde dehydrogenase, and class 1 and 2 aldehyde dehydrogenase [3]. In Bacillus, a highly homologous protein to methylmalonic acid semialdehyde dehydrogenase, groups out from the main MMSDH clade with Listeria and Sulfolobus. This Bacillus protein has been suggested to be located in an iol operon and/or involved in myo-inositol catabolism, converting malonic semialdehyde to acetyl CoA ad CO2 [4]. The preceeding enzymes responsible for valine catabolism are present in Bacillus, Listeria, and Sulfolobus. TIGR01724.1 TIGR01724 hmd_rel 167.2 167.2 341 subfamily Y N N H2-forming N(5),N(10)-methenyltetrahydromethanopterin dehydrogenase-related protein 11081790 131567 cellular organisms no rank 101 JCVI H2-forming N(5),N(10)-methenyltetrahydromethanopterin dehydrogenase-related protein H2-forming N(5),N(10)-methenyltetrahydromethanopterin dehydrogenase-related protein This HMM represents a sister clade to the authenticated coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin reductase (HMD) of TIGR01723. Two members, designated HmdII and HmdIII, are found. Members are restricted to methanogens, but the function is unknown. TIGR01725.1 TIGR01725 phge_HK97_gp10 30.8 30.8 120 equivalog Y Y N HK97-gp10 family putative phage morphogenesis protein 131567 cellular organisms no rank 20987 JCVI phage protein, HK97 gp10 family HK97-gp10 family putative phage morphogenesis protein This HMM represents an uncharacterized, highly divergent bacteriophage family. The family includes gp10 from HK022 and HK97. It appears related to TIGR01635, a phage morphogenesis family believed to be involved in tail completion. TIGR01726.1 TIGR01726 HEQRo_perm_3TM 42.2 42.2 99 subfamily_domain Y Y N ABC transporter permease subunit GO:0015837,GO:0016020,GO:0022857 131567 cellular organisms no rank 388517 JCVI amino ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family ABC transporter permease subunit, His/Glu/Gln/Arg/opine family, N-terminal region This HMM represents one of several classes of multiple membrane spanning regions found immediately N-terminal to the domain described by PF00528, binding-protein-dependent transport systems inner membrane component. The N-terminal region of this protein, as described by TIGR01726, is a three transmembrane segment that identifies a subfamily of ABC transporter permease subunits, which specificities that include histidine, arginine, glutamine, glutamate, L-cystine (sic), the opines (in Agrobacterium) octopine and nopaline, etc. TIGR01727.1 TIGR01727 oligo_HPY 37.6 37.6 87 subfamily_domain Y Y N oligopeptide/dipeptide ABC transporter ATP-binding protein GO:0005524,GO:0009898,GO:0015440,GO:0015833,GO:0043190 131567 cellular organisms no rank 353457 JCVI oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain oligopeptide/dipeptide ABC transporter ATP-binding protein , C-terminal domain This HMM represents a domain found in the C-terminal regions of ABC transporter ATP binding proteins, immediately following the ATP-binding domain (PF00005). Many are involved in the transport of oligopeptides or dipeptides, including E. coli K-12 proteins DppD (dipeptide/heme), OppD and OppF (oligopeptide), DdpD and DdpF (D,D-dipeptide), etc. TIGR01728.1 TIGR01728 SsuA_fam 163.5 163.5 290 subfamily Y Y N aliphatic sulfonate ABC transporter substrate-binding protein GO:0016020,GO:0042626,GO:0042918,GO:0043190 10506196 131567 cellular organisms no rank 67786 JCVI ABC transporter, substrate-binding protein, aliphatic sulfonates family aliphatic sulfonate ABC transporter substrate-binding protein Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this HMM include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins. TIGR01733.1 TIGR01733 AA-adenyl-dom 317.4 317.4 409 subfamily_domain Y Y N amino acid adenylation domain-containing protein 10021423 131567 cellular organisms no rank 470951 JCVI amino acid adenylation domain amino acid adenylation domain This model represents a domain responsible for the specific recognition of amino acids and activation as adenylyl amino acids. The reaction catalyzed is aa + ATP -> aa-AMP + PPi. These domains are usually found as components of multi-domain non-ribosomal peptide synthetases and are usually called "A-domains" in that context (for a review, see [1]). A-domains are almost invariably followed by "T-domains" (thiolation domains, PF00550) to which the amino acid adenylate is transferred as a thiol-ester to a bound pantetheine cofactor with the release of AMP (these are also called peptide carrier proteins, or PCPs. When the A-domain does not represent the first module (corresponding to the first amino acid in the product molecule) it is usually preceded by a "C-domain" (condensation domain, PF00668) which catalyzes the ligation of two amino acid thiol-esters from neighboring modules. This domain is a subset of the AMP-binding domain found in Pfam (PF00501) which also hits substrate--CoA ligases and luciferases. Sequences scoring in between trusted and noise for this model may be ambiguous as to whether they activate amino acids or other molecules lacking an alpha amino group. TIGR01736.1 TIGR01736 FGAM_synth_II 525.75 525.75 718 equivalog Y Y N phosphoribosylformylglycinamidine synthase subunit PurL purL 6.3.5.3 GO:0004642,GO:0006189 2531746 131567 cellular organisms no rank 42607 JCVI phosphoribosylformylglycinamidine synthase II phosphoribosylformylglycinamidine synthase subunit PurL Phosphoribosylformylglycinamidine synthase is a single, long polypeptide in most Proteobacteria and eukarotes. Three proteins are required in Bacillus subtilis and many other species. This is the longest of the three and is designated PurL, phosphoribosylformylglycinamidine synthase II, or FGAM synthase II. TIGR01737.1 TIGR01737 FGAM_synth_I 177.8 177.8 228 equivalog Y Y N phosphoribosylformylglycinamidine synthase I purQ 6.3.5.3 GO:0004642,GO:0006189 131567 cellular organisms no rank 30658 JCVI phosphoribosylformylglycinamidine synthase I phosphoribosylformylglycinamidine synthase I In some species, phosphoribosylformylglycinamidine synthase is composed of a single polypeptide chain. This HMM describes the PurQ protein of Bacillus subtilis (where PurL, PurQ, and PurS are required for phosphoribosylformylglycinamidine synthase activity) and functionally equivalent proteins from other bacteria and archaea. TIGR01740.1 TIGR01740 pyrF 92.3 92.3 216 equivalog_domain Y Y N orotidine-5'-phosphate decarboxylase pyrF 4.1.1.23 GO:0004590,GO:0044205 131567 cellular organisms no rank 42313 JCVI orotidine 5'-phosphate decarboxylase orotidine-5'-phosphate decarboxylase This model represents orotidine 5'-monophosphate decarboxylase, the PyrF protein of pyrimidine nucleotide biosynthesis. In many eukaryotes, the region hit by this model is part of a multifunctional protein. TIGR01746.1 TIGR01746 Thioester-redct 213.35 213.35 371 subfamily_domain Y Y N thioester reductase domain-containing protein 10320345,11029592,11254122,29916519 131567 cellular organisms no rank 30059 JCVI thioester reductase domain thioester reductase domain This model describes a thioester reductase domain that occurs invariably at the C-terminus of proteins that contain it. Most proteins with the domain are non-ribosomal peptide synthetases (NRPS), but the domain also occurs in some polyketide synthases (PKS). The domain participates in biosynthetic pathways in which substrate is activated by adenylation, then transferred as a thioester to a protein's covalently linked pantetheine cofactor. The thioester bond is then reduced, breaking the bond to release the product, and to regenerate the pantetheine thiol (PMID:11254122). Examples of this domain include the terminal domain from the fungal alpha aminoadipate reductase enzyme (also known as aminoadipate semialdehyde dehydrogenase) which is involved in the biosynthesis of lysine (PMID:10320345), as well as the reductase-containing component of the myxochelin biosynthetic gene cluster, MxcG (PMID:11029592). The activity of this domain is fundamentally different from the more common beta-ketoreductase domains of PKS, which act at a carbonyl two carbons removed from the thioester and form an alcohol as a product. TIGR01755.1 TIGR01755 flav_wrbA 132.5 132.5 197 equivalog Y Y N NAD(P)H:quinone oxidoreductase type IV wrbA 1.6.5.2 GO:0003955,GO:0010181 16672604,8516330,9694845 131567 cellular organisms no rank 26818 JCVI NAD(P)H:quinone oxidoreductase, type IV NAD(P)H:quinone oxidoreductase, type IV This HMM represents a protein, WrbA, related to and slightly larger than flavodoxin. It was just shown, in E. coli and Archaeoglobus fulgidus (and previously for some eukaryotic homologs) to act as fourth type of NAD(P)H:quinone oxidoreductase. In E. coli, this protein was earlier reported to be produced during stationary phase, bind to the trp repressor, and make trp operon repression more efficient. WrbA does not interact with the trp operator by itself. Members are found in species in which homologs of the E. coli trp operon repressor TrpR (SP:P03032) are not detected. TIGR01760.1 TIGR01760 tape_meas_TP901 28.8 28.8 349 equivalog_domain Y Y N phage tail tape measure protein GO:0005198,GO:0016032 11040123 131567 cellular organisms no rank 86183 JCVI phage tail tape measure protein, TP901 family, core region phage tail tape measure protein This HMM represents a reasonably well conserved core region of a family of phage tail proteins. The member from phage TP901-1 was characterized as a tail length tape measure protein in that a shortened form of the protein leads to phage with proportionately shorter tails. TIGR01763.1 TIGR01763 MalateDH_bact 351.85 351.85 305 equivalog Y Y N malate dehydrogenase mdh 1.1.1.37 GO:0005975,GO:0016616 11021970 131567 cellular organisms no rank 16042 JCVI malate dehydrogenase, NAD-dependent malate dehydrogenase This enzyme converts malate into oxaloacetate in the citric acid cycle. The critical residues which discriminate malate dehydrogenase from lactate dehydrogenase have been characterized [1], and have been used to set the cutoffs for this model. Sequences showing [aflimv][ap]R[rk]pgM[st] and [ltv][ilm]gGhgd were kept above trusted, while those in which the capitalized residues in the patterns were found to be Q, E and E were kept below the noise cutoff. Some sequences in the grey zone have been annotated as malate dehydrogenases, but none have been characterized. Phylogenetically, a clade of sequences from eukaryotes such as Toxoplasma and Plasmodium which include a characterized lactate dehydrogenase and show abiguous critical residue patterns appears to be more closely related to these bacterial sequences than other eukaryotic sequences. These are relatively long branch and have been excluded from the model. All other sequences falling below trusted appear to be phylogenetically outside of the clade including the trusted hits. The annotation of Botryococcus braunii as lactate dehydrogenase appears top be in error. This was initially annotated as MDH by Swiss-Prot and then changed. The rationale for either of these annotations is not traceable. TIGR01764.1 TIGR01764 excise 28.8 28.8 49 domain Y Y N excisionase family DNA-binding protein GO:0003677 131567 cellular organisms no rank 108949 JCVI DNA binding domain, excisionase family DNA binding domain, excisionase family An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This HMM represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This HMM identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (PF00376). TIGR01765.1 TIGR01765 tspaseT_teng_N 47.25 47.25 73 subfamily_domain Y N N transposase, putative, N-terminal domain GO:0004803,GO:0006313 131567 cellular organisms no rank 863 JCVI transposase, putative, N-terminal domain transposase, putative, N-terminal domain This HMM represents the N-terminal region of a family of putative transposases found in the largest copy number in Thermoanaerobacter tengcongensis. The three homologs in Bacillus anthracis are each split into two ORFs and this HMM represents the upstream ORF. TIGR01766.2 TIGR01766 TIGR01766 32 32 82 domain Y Y N IS200/IS605 family accessory protein TnpB-related protein GO:0004803,GO:0006313 131567 cellular organisms no rank 106422 JCVI transposase, IS605 OrfB family IS200/IS605 family accessory protein TnpB-like domain This HMM represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposases described by Pfam HMM PF01385, some type V CRISPR system effectors, and other proteins. TIGR01768.1 TIGR01768 GGGP-family 113.25 113.25 224 subfamily Y Y N geranylgeranylglyceryl phosphate synthase family protein 11732904 131567 cellular organisms no rank 9093 JCVI geranylgeranylglyceryl phosphate synthase family protein geranylgeranylglyceryl phosphate synthase family protein This model represents a family of sequences including geranylgeranylglyceryl phosphate synthase which catalyzes the first committed step in the synthesis of ether-linked membrane lipids in archaea [1]. The clade of bacterial sequences may have the same function or a closely related function. This model supercedes TIGR00265, which has been retired. TIGR01769.1 TIGR01769 GGGP 161.55 161.55 205 equivalog Y Y N phosphoglycerol geranylgeranyltransferase 2.5.1.41 GO:0000287,GO:0005737,GO:0006650,GO:0047294 11732904,12801917 131567 cellular organisms no rank 2906 JCVI phosphoglycerol geranylgeranyltransferase phosphoglycerol geranylgeranyltransferase This model represents geranylgeranylglyceryl phosphate synthase which catalyzes the first committed step in the synthesis of ether-linked membrane lipids in archaea [1]. The active enzyme is reported to be a homopentamer in Methanobacterium thermoautotrophicum but is reported to be a homodimer in Thermoplasma acidophilum. TIGR01770.1 TIGR01770 NDH_I_N 332.6 332.6 472 subfamily Y Y N NADH-quinone oxidoreductase subunit NuoN nuoN 7.1.1.2 GO:0008137,GO:0042773 131567 cellular organisms no rank 46410 JCVI proton-translocating NADH-quinone oxidoreductase, chain N NADH-quinone oxidoreductase subunit NuoN This HMM describes the 14th (based on E. coli) structural gene, N, of bacterial and chloroplast energy-transducing NADH (or NADPH) dehydrogenases. This model does not describe any subunit of the mitochondrial complex I (for which the subunit composition is very different), nor NADH dehydrogenases that are not coupled to ion transport. For chloroplast members, the name NADH-plastoquinone oxidoreductase is used for the complex and this protein is designated as subunit 2 or B. This model also includes a subunit of a related complex in the archaeal methanogen, Methanosarcina mazei, in which F420H2 replaces NADH and 2-hydroxyphenazine replaces the quinone. TIGR01771.1 TIGR01771 L-LDH-NAD 303.55 303.55 299 equivalog Y Y N L-lactate dehydrogenase 1.1.1.27 GO:0004459,GO:0005737,GO:0006096 11021970,19465534 131567 cellular organisms no rank 20381 JCVI L-lactate dehydrogenase L-lactate dehydrogenase This model represents the NAD-dependent L-lactate dehydrogenases from bacteria and eukaryotes. This enzyme function as as the final step in anaerobic glycolysis. Although lactate dehydrogenases have in some cases been mistaken for malate dehydrogenases due to the similarity of these two substrates and the apparent ease with which evolution can toggle these activities, critical residues have been identified [1] which can discriminate between the two activities. At the time of the creation of this model no hits above the trusted cutoff contained critical residues typical of malate dehydrogenases. TIGR01777.1 TIGR01777 yfcH 207.35 207.35 292 hypoth_equivalog Y Y N TIGR01777 family oxidoreductase GO:0003824 131567 cellular organisms no rank 55996 JCVI TIGR01777 family protein TIGR01777 family oxidoreductase This model represents a clade of proteins of unknown function including the E. coli yfcH protein. TIGR01788.1 TIGR01788 Glu-decarb-GAD 380.4 380.4 431 equivalog Y Y N glutamate decarboxylase 4.1.1.15 GO:0004351,GO:0006540,GO:0030170 131567 cellular organisms no rank 20511 JCVI glutamate decarboxylase glutamate decarboxylase This model represents the pyridoxal phosphate-dependent glutamate (alpha) decarboxylase found in bacteria (low and hi-GC gram positive, proteobacteria and cyanobacteria), plants, fungi and at least one archaon (Methanosarcina). The product of the enzyme is gamma-aminobutyrate (GABA). TIGR01791.2 TIGR01791 CM_archaeal 66.95 66.95 83 equivalog_domain Y Y N chorismate mutase 5.4.99.5 131567 cellular organisms no rank 476 JCVI chorismate mutase chorismate mutase This model represents a clade of archaeal chorismate mutases. Chorismate mutase catalyzes the conversion of chorismate into prephenate which is subsequently converted into either phenylalanine or tyrosine. In Sulfolobus this gene is found as a fusion with prephenate dehydrogenase (although the non-TIGR annotation contains a typographical error indicating it as a dehydratase OMNI|NTL02SS0274) which is the next enzyme in the tyrosine biosynthesis pathway. The Archaeoglobus gene contains an N-terminal prephenate dehydrogenase domain and a C-terminal prephenate dehydratase domain followed by a regulatory amino acid-binding ACT domain. The Thermoplasma volcanium gene is adjacent to prephenate dehydratase. TIGR01792.1 TIGR01792 urease_alph 680 680 568 equivalog Y Y N urease subunit alpha ureC 3.5.1.5 GO:0009039,GO:0016151,GO:0019627 131567 cellular organisms no rank 38277 JCVI urease, alpha subunit urease subunit alpha This HMM describes the urease alpha subunit UreC (designated beta or B chain, UreB in Helicobacter species). Accessory proteins for incorporation of the nickel cofactor are usually found in addition to the urease alpha, beta, and gamma subunits. The trusted cutoff is set above the scores of many reported fragments and of a putative second urease alpha chain in Streptomyces coelicolor. TIGR01800.1 TIGR01800 cit_synth_II 421.3 421.3 368 subfamily Y N N 2-methylcitrate synthase/citrate synthase II GO:0005737,GO:0046912 9579066 131567 cellular organisms no rank 29096 JCVI 2-methylcitrate synthase/citrate synthase II 2-methylcitrate synthase/citrate synthase II Members of this family are dimeric enzymes with activity as 2-methylcitrate synthase, citrate synthase, or both. Many Gram-negative species have a hexameric citrate synthase, termed citrate synthase I (TIGR01798). Members of this family (TIGR01800) appear as a second citrate synthase isozyme but typically are associated with propionate metabolism and synthesize 2-methylcitrate from propionyl-CoA; citrate synthase activity may be incidental. A number of species, including Thermoplasma acidophilum, Pyrococcus furiosus, and the Antarctic bacterium DS2-3R have a bifunctional member of this family as the only citrate synthase isozyme. TIGR01808.1 TIGR01808 CM_M_hiGC-arch 52.15 52.15 74 equivalog_domain Y Y N chorismate mutase 5.4.99.5 131567 cellular organisms no rank 6021 JCVI chorismate mutase chorismate mutase This model represents the monofunctional chorismate mutase from high GC gram-positive bacteria and archaea. Trusted annotations from Corynebacterium and Pyrococcus are aparrently the sole chorismate mutase enzymes in their respective genomes. This is coupled with the presence in those genomes of the enzymes of the chorismate pathways both up- and downstream of chorismate mutase. TIGR01812.1 TIGR01812 sdhA_frdA_Gneg 567.3 567.3 568 subfamily Y N N succinate dehydrogenase or fumarate reductase, flavoprotein subunit GO:0000104,GO:0006099,GO:0009060,GO:0009061,GO:0022900,GO:0050660 131567 cellular organisms no rank 40570 JCVI succinate dehydrogenase or fumarate reductase, flavoprotein subunit succinate dehydrogenase or fumarate reductase, flavoprotein subunit This HMM represents the succinate dehydrogenase flavoprotein subunit as found in Gram-negative bacteria, mitochondria, and some Archaea. Mitochondrial forms interact with ubiquinone and are designated EC 1.3.5.1, but can be degraded to 1.3.99.1. Some isozymes in E. coli and other species run primarily in the opposite direction and are designated fumarate reductase. TIGR01814.1 TIGR01814 kynureninase 246.4 246.4 400 equivalog Y Y N kynureninase kynU 3.7.1.3 GO:0005737,GO:0006569,GO:0009435,GO:0030170,GO:0030429 131567 cellular organisms no rank 29938 JCVI kynureninase kynureninase This HMM describes kynureninase, a pyridoxal-phosphate enzyme. Kynurinine is a Trp breakdown product and a precursor for NAD. In Chlamydia psittaci, an obligate intracellular pathogen, kynureninase makes anthranilate, a Trp precursor, from kynurenine. This counters the tryptophan hydrolysis that occurs in the host cell in response to the pathogen. TIGR01816.1 TIGR01816 sdhA_forward 727.35 727.35 584 equivalog Y Y N succinate dehydrogenase flavoprotein subunit sdhA GO:0006099,GO:0016627,GO:0050660 12560550 131567 cellular organisms no rank 29502 JCVI succinate dehydrogenase, flavoprotein subunit succinate dehydrogenase flavoprotein subunit Succinate dehydrogenase and fumarate reductase are homologous enzymes reversible in principle but favored under different circumstances. This HMM represents a narrowly defined clade of the succinate dehydrogenase flavoprotein subunit as found in mitochondria, in Rickettsia, in E. coli and other Proteobacteria, and in a few other lineages. However, this HMM excludes all known fumarate reductases. It also excludes putative succinate dehydrogenases that appear to diverged before the split between E. coli succinate dehydrogenase and fumarate reductase. TIGR01819.1 TIGR01819 F420_cofD 257.45 257.45 301 equivalog Y Y N 2-phospho-L-lactate transferase cofD 2.7.8.28 GO:0000287,GO:0043743 11888293 131567 cellular organisms no rank 13518 JCVI 2-phospho-L-lactate transferase 2-phospho-L-lactate transferase This HMM represents LPPG:Fo 2-phospho-L-lactate transferase, which catalyses the fourth step in the biosynthesis of coenzyme F420, a flavin derivative found in methanogens, the Mycobacteria, and several other lineages. This enzyme is characterized so far in Methanococcus jannaschii but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. The clade represented by this HMM is one of two major divisions of proteins in Pfam HMM PF01933. TIGR01820.1 TIGR01820 TrpE-arch 512.05 512.05 449 equivalog Y Y N anthranilate synthase component I trpE 4.1.3.27 GO:0000162,GO:0004049 8416906 131567 cellular organisms no rank 938 JCVI anthranilate synthase component I anthranilate synthase component I This model represents an archaeal clade of anthranilate synthase component I enzymes. This enzyme is responsible for the first step of tryptophan biosynthesis from chorismate. The Sulfolobus enzyme has been reported to be part of a gene cluster for Trp biosynthesis [1] TIGR01821.1 TIGR01821 5aminolev_synth 338.55 338.55 402 equivalog_domain Y Y N 5-aminolevulinate synthase hemA 2.3.1.37 GO:0003870,GO:0030170,GO:0033014 16121195,29551290,8468290 131567 cellular organisms no rank 12580 JCVI 5-aminolevulinic acid synthase 5-aminolevulinate synthase This HMM represents 5-aminolevulinic acid synthase, an enzyme for one of two routes to the heme precursor 5-aminolevulinate. The protein is a pyridoxal phosphate-dependent enzyme related to 2-amino-3-ketobutyrate CoA tranferase and 8-amino-7-oxononanoate synthase. This enzyme appears restricted to the alpha Proteobacteria and mitochondrial derivatives. TIGR01824.1 TIGR01824 PabB-clade2 408.55 408.55 355 equivalog Y Y N aminodeoxychorismate synthase, component I pabB 2.6.1.85 8409921 131567 cellular organisms no rank 2986 JCVI aminodeoxychorismate synthase, component I aminodeoxychorismate synthase, component I This clade of sequences is more closely related to TrpE (anthranilate synthase, TIGR00564/TIGR01820/TIGR00565) than to the better characterized group of PabB enzymes (TIGR00553/TIGR01823). This clade includes one characterized enzyme from Lactococcus [1] and the conserved function across the clade is supported by these pieces of evidence: 1) all genomes with a member in this clade also have a separate TrpE gene, 2) none of these genomes contain an aparrent PabB from any of the other PabB clades, 3) none of these sequences are found in a region of the genome in association with other Trp biosynthesis genes, 4) all of these genomes aparrently contain most if not all of the steps of the folate biosynthetic pathway (for which PABA is a precursor). Many of the sequences hit by this model are annotated as TrpE enzymes, however, we believe that all members of this clade are, in fact, PabB. The sequences from Bacillus halodurans and subtilus which score below the trusted cutoff for this model are also likely to be PabB enzymes, but are too closely related to TrpE to be separated at this time. TIGR01825.1 TIGR01825 gly_Cac_T_rel 535.4 535.4 385 subfamily Y Y N BioF/Kbl family PLP-dependent acyltransferase 2.3.1.- 18071260 131567 cellular organisms no rank 5261 JCVI putative pyridoxal phosphate-dependent acyltransferase BioF/Kbl family PLP-dependent acyltransferase This HMM represents a family of pyridoxal phosphate-dependent acyltransferases, including a bifunctional protein from Thermus thermophilus shown to act both as a BioF (8-amino-7-oxononanoate synthase, EC 2.3.1.47) and as glycine C-acetyltransferase (EC 2.3.1.29). This enzyme family is also similar to 5-aminolevulinate synthase (EC 2.3.1.37). All those enzymes transfer an R-group (acetyl, succinyl, or 6-carboxyhexanoyl) from coenzyme A to an amino acid (Gly or Ala), in two cases with release of CO2. Because of uncertainties about which member proteins will carry which activities, the functional name is deliberately left somewhat vague. TIGR01828.1 TIGR01828 pyru_phos_dikin 843.45 843.45 865 equivalog Y Y N pyruvate, phosphate dikinase ppdK 2.7.9.1 GO:0006090,GO:0050242 131567 cellular organisms no rank 33299 JCVI pyruvate, phosphate dikinase pyruvate, phosphate dikinase This HMM represents pyruvate,phosphate dikinase, also called pyruvate,orthophosphate dikinase. It is similar in sequence to other PEP-utilizing enzymes. TIGR01830.1 TIGR01830 3oxo_ACP_reduc 297.75 297.75 239 equivalog Y Y N 3-oxoacyl-[acyl-carrier-protein] reductase fabG 1.1.1.100 GO:0004316,GO:0006633,GO:0051287 131567 cellular organisms no rank 47078 JCVI 3-oxoacyl-[acyl-carrier-protein] reductase 3-oxoacyl-[acyl-carrier-protein] reductase This HMM represents 3-oxoacyl-[ACP] reductase, also called 3-ketoacyl-acyl carrier protein reductase, an enzyme of fatty acid biosynthesis. TIGR01836.1 TIGR01836 PHA_synth_III_C 365.3 365.3 350 subfamily Y Y N class III poly(R)-hydroxyalkanoic acid synthase subunit PhaC phaC GO:0016746,GO:0042619 11418564 131567 cellular organisms no rank 3069 JCVI poly(R)-hydroxyalkanoic acid synthase, class III, PhaC subunit class III poly(R)-hydroxyalkanoic acid synthase subunit PhaC This HMM represents the PhaC subunit of a heterodimeric form of polyhydroxyalkanoic acid (PHA) synthase. Excepting the PhaC of Bacillus megaterium (which needs PhaR), all members require PhaE (TIGR01834) for activity and are designated class III. This enzyme builds ester polymers for carbon and energy storage that accumulate in inclusions, and both this enzyme and the depolymerase associate with the inclusions. Class III enzymes polymerize short-chain-length hydroxyalkanoates. TIGR01840.1 TIGR01840 esterase_phb 107.85 107.85 213 subfamily Y Y N PHB depolymerase family esterase GO:0016787 131567 cellular organisms no rank 23408 JCVI esterase, PHB depolymerase family PHB depolymerase family esterase This HMM describes a subfamily among lipases of the ab-hydrolase family. This subfamily includes bacterial depolymerases for poly(3-hydroxybutyrate) (PHB) and related polyhydroxyalkanoates (PHA), as well as acetyl xylan esterases, feruloyl esterases, and others from fungi. TIGR01850.1 TIGR01850 argC 233.6 233.6 345 equivalog Y Y N N-acetyl-gamma-glutamyl-phosphate reductase argC 1.2.1.38 GO:0003942,GO:0006526,GO:0006592,GO:0070401 131567 cellular organisms no rank 60088 JCVI N-acetyl-gamma-glutamyl-phosphate reductase N-acetyl-gamma-glutamyl-phosphate reductase This HMM represents the more common of two related families of N-acetyl-gamma-glutamyl-phosphate reductase, an enzyme catalyzing the third step or Arg biosynthesis from Glu. The two families differ by phylogeny, similarity clustering, and the gap architecture in a multiple sequence alignment. Bacterial members of this family tend to be found within Arg biosynthesis operons. TIGR01851.1 TIGR01851 argC_other 229.85 229.85 310 equivalog Y Y N N-acetyl-gamma-glutamyl-phosphate reductase argC 1.2.1.38 GO:0003942,GO:0005737,GO:0006526 1406250,21075924 131567 cellular organisms no rank 14021 JCVI N-acetyl-gamma-glutamyl-phosphate reductase N-acetyl-gamma-glutamyl-phosphate reductase This HMM represents the less common of two related families of N-acetyl-gamma-glutamyl-phosphate reductase, an enzyme catalyzing the third step of Arg biosynthesis from Glu. The two families differ by phylogeny, similarity clustering, and gap architecture in a multiple sequence alignment. TIGR01855.1 TIGR01855 IMP_synth_hisH 105.4 105.4 198 equivalog Y Y N imidazole glycerol phosphate synthase subunit HisH hisH 4.3.2.10 GO:0000105,GO:0000107 11208798,11264293 131567 cellular organisms no rank 63223 JCVI imidazole glycerol phosphate synthase, glutamine amidotransferase subunit imidazole glycerol phosphate synthase subunit HisH This HMM represents HisH, the glutamine amidotransferase subunit (or domain, in eukaryotic systems) of imidazole glycerol phosphate synthase. IGPS catalyzes the conversion of phosphoribulosyl-formimino-5-aminoimidazole-4-carboxamide ribonucleotide phosphate and glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamide ribonucleotide, and glutamate during histidine biosynthesis. TIGR01856.1 TIGR01856 hisJ_fam 90.2 90.2 252 subfamily Y Y N histidinol-phosphatase HisJ family protein GO:0000105,GO:0004401 10322033 131567 cellular organisms no rank 20833 JCVI histidinol phosphate phosphatase, HisJ family histidinol-phosphatase HisJ family protein This HMM represents the histidinol phosphate phosphatase HisJ of Bacillus subtilis, and related proteins from a number of species within a larger family of phosphatases in the PHP hydrolase family. HisJ catalyzes the penultimate step of histidine biosynthesis but shows no homology to the functionally equivalent sequence in E. coli, a domain of the bifunctional HisB protein. Note, however, that many species have two members and that Clostridium perfringens, predicted not to make histidine, has five members of this family; this family is designated subfamily rather than equivalog to indicate that members may not all act as HisJ. TIGR01857.1 TIGR01857 FGAM-synthase 1057.05 1057.05 1239 equivalog Y Y N phosphoribosylformylglycinamidine synthase 6.3.5.3 GO:0004642,GO:0006189 131567 cellular organisms no rank 14807 JCVI phosphoribosylformylglycinamidine synthase phosphoribosylformylglycinamidine synthase This HMM represents a single-molecule form of phosphoribosylformylglycinamidine synthase, also called FGAM synthase, an enzyme of purine de novo biosynthesis. This model represents a second clade of these enzymes found in Clostridia, Bifidobacteria and Streptococcus species. This enzyme performs the fourth step in IMP biosynthesis (the precursor of all purines) from PRPP. TIGR01860.1 TIGR01860 VNFD 823.1 823.1 461 equivalog Y Y N nitrogenase vanadium-iron protein, alpha chain vnfD 1.18.6.1 GO:0009399,GO:0016163,GO:0016613,GO:0051212,GO:0051536 131567 cellular organisms no rank 157 JCVI nitrogenase vanadium-iron protein, alpha chain nitrogenase vanadium-iron protein, alpha chain This HMM represents the alpha chain of the vanadium-containing component of the vanadium-iron nitrogenase compound I. The complex also includes a second alpha chain, two beta chains and two delta chains. Compount I interacts with compound II also known as the iron-protein which transfers electrons to compound I where the catalysis occurs. TIGR01861.1 TIGR01861 ANFD 873.8 873.8 513 equivalog Y Y N nitrogenase iron-iron protein, alpha chain anfD 1.18.6.1 GO:0009399,GO:0016163,GO:0016611,GO:0051536 131567 cellular organisms no rank 277 JCVI nitrogenase iron-iron protein, alpha chain nitrogenase iron-iron protein, alpha chain This model represents the all-iron variant of the nitrogenase component I alpha chain. Molybdenum-iron and vanadium iron forms are also found. The complete complex contains two alpha chains, two beta chains and two delta chains. The component I associates with component II also known as the iron protein which serves to provide electrons for component I. TIGR01862.1 TIGR01862 N2-ase-Ialpha 486.05 486.05 444 subfamily Y Y N nitrogenase component I subunit alpha 1.18.6.1 GO:0016163,GO:0051536 131567 cellular organisms no rank 4754 JCVI nitrogenase component I, alpha chain nitrogenase component I subunit alpha This model represents the alpha chain of all three varieties (Mo-Fe, V-Fe, and Fe-Fe) of component I of nitrogenase. TIGR01863.1 TIGR01863 cas_Csd1 218.65 218.65 588 equivalog Y Y N type I-C CRISPR-associated protein Cas8c/Csd1 cas8c GO:0043571 131567 cellular organisms no rank 6805 JCVI CRISPR-associated protein Cas8c/Csd1, subtype I-C/DVULG type I-C CRISPR-associated protein Cas8c/Csd1 CRISPR loci appear to be mobile elements with a wide host range. This HMM represents a protein that tends to be found near CRISPR repeats of the DVULG subtype of CRISPR/Cas locus. We designate this family Csd1 (CRISPR/Cas Subtype DVULG protein 1). The species range for this subtype, so far, is exclusively bacterial and mesophilic, although CRISPR loci in general are particularly common among archaea and thermophilic bacteria. In a few species (Xanthomonas axonopodis pv. citri str. 306 and Streptococcus mutans UA159), homology to this protein family is split across two tandem genes; the trusted cutoff to this family is set low enough to capture at least the longer of the two. TIGR01865.2 TIGR01865 cas_Csn1 100 100 1070 equivalog Y Y N type II CRISPR RNA-guided endonuclease Cas9 cas9 csn1 GO:0004520,GO:0043571 16292354 131567 cellular organisms no rank 12983 JCVI CRISPR subtype II RNA-guided endonuclease Cas9 type II CRISPR RNA-guided endonuclease Cas9 Cas9, originally named Csn1, is the large, multifunctional signature protein of type II CRISPR/Cas systems. It is well known even to general audiences because its RNA-guided endonuclease activity has made it a popular tool for custom editing of eukaryotic genomes. Cas9, originally named Csn1, is the large, multifunctional signature protein of type II CRISPR/Cas systems. It is well known even to general audiences because its RNA-guided endonuclease activity has made it a popular tool for custom editing of eukaryotic genomes. TIGR01866.1 TIGR01866 cas_Csn2 35 35 222 equivalog Y Y N type II-A CRISPR-associated protein Csn2 csn2 GO:0043571 16292354,22479393 131567 cellular organisms no rank 2389 JCVI CRISPR type II-A/NMEMI-associated protein Csn2 type II-A CRISPR-associated protein Csn2 Csn2 belongs to type II-A CRISPR systems, original called the NMENI subtype. The neighboring protein originally named Csn1 is now called Cas9. TIGR01868.1 TIGR01868 casD_Cas5e 68.95 68.95 230 equivalog Y Y N type I-E CRISPR-associated protein Cas5/CasD cas5e GO:0003723,GO:0043571,GO:0051607 131567 cellular organisms no rank 11299 JCVI CRISPR-associated protein Cas5/CasD, subtype I-E/ECOLI type I-E CRISPR-associated protein Cas5/CasD CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family is part of the ECOLI subtype CRISPR/Cas locus, and now characterized as part of the CASCADE complex of that system. It shares a small N-terminal homology region with members of several other CRISPR/Cas subtypes, and we view the families that share this region as being Cas5. TIGR01869.1 TIGR01869 casC_Cse4 178.05 178.05 325 exception Y Y N type I-E CRISPR-associated protein Cas7/Cse4/CasC cas7e GO:0043571 18703739 131567 cellular organisms no rank 10725 JCVI CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI type I-E CRISPR-associated protein Cas7/Cse4/CasC CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family is represented by CT1975 of Chlorobium tepidum and is part of the Ecoli subtype of CRISPR/Cas locis. It is designated Cse4, for CRISPR/Cas Subtype Ecoli protein 4. TIGR01870.1 TIGR01870 cas_TM1810_Csm2 30.6 30.6 96 hypoth_equivalog_domain Y Y N type III-A CRISPR-associated protein Csm2 csm2 GO:0043571 131567 cellular organisms no rank 1878 JCVI CRISPR type III-A/MTUBE-associated protein Csm2 type III-A CRISPR-associated protein Csm2 These proteins are found adjacent to a characteristic short, palidromic repeat cluster termed CRISPR, a probable mobile DNA element. This HMM represents the C-terminal domain of a minor family of CRISPR-associated protein from the Mtube subtype of CRISPR/Cas locus. The family is designated Csm2, for CRISPR/Cas Subtype Mtube Protein 2. TIGR01873.1 TIGR01873 cas_CT1978 33.15 33.15 87 equivalog Y Y N type I-E CRISPR-associated endoribonuclease Cas2e cas2e GO:0004521,GO:0043571 18482976 131567 cellular organisms no rank 7619 JCVI CRISPR-associated endoribonuclease Cas2, subtype I-E/ECOLI type I-E CRISPR-associated endoribonuclease Cas2e CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This HMM represents a minor branch of the Cas2 family of CRISPR-associated endonuclease, whereas most Cas2 proteins are modeled instead by TIGR01573. This form of Cas2 is characteristic for the Ecoli subtype of CRISPR/Cas locus. TIGR01874.1 TIGR01874 cas_cas5a 23.05 23.05 173 exception Y Y N type I-A CRISPR-associated protein Cas5a cas5a GO:0043571 11788711 131567 cellular organisms no rank 152 JCVI CRISPR-associated protein Cas5, subtype I-A/APERN type I-A CRISPR-associated protein Cas5a This HMM represents a minor family of CRISPR-associated (Cas) protein. These proteins are found adjacent to a characteristic short, palidromic repeat cluster termed CRISPR, a probable mobile DNA element. This family belongs to a set of several Cas proteins, one each for a number of different CRISPR/Cas subtypes, that share a region of N-terminal sequence similarity modeled by TIGR02593. The family is designated Cas5a, for CRISPR-associated protein Cas5, Apern subtype. TIGR01875.1 TIGR01875 cas_MJ0381 67.3 67.3 240 subfamily Y Y N DevR family CRISPR-associated autoregulator GO:0043571 7693658 131567 cellular organisms no rank 3055 JCVI CRISPR-associated autoregulator DevR family DevR family CRISPR-associated autoregulator CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This HMM represents one such family, represented by MJ0381 of Methanococcus jannaschii. This family includes the DevR protein of Myxococcus xanthus, a protein whose expression appears to regulated through a number of means, including both location and autorepression; DevR mutants are incapable of fruiting body development. TIGR01876.1 TIGR01876 cas_Cas5d 85 85 203 exception Y Y N type I-C CRISPR-associated protein Cas5c cas5c GO:0004519,GO:0043571,GO:0051607 131567 cellular organisms no rank 6040 JCVI CRISPR-associated protein Cas5, subtype I-C/DVULG type I-C CRISPR-associated protein Cas5c CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This small Cas family is represented by CT1134 of Chlorobium tepidum. This family belongs to a set of several Cas protein families, one each for a number of different CRISPR/Cas subtypes, that share a region of N-terminal sequence similarity modeled by TIGR02593. This family represents the Dvulg subtype of CRISPR/Cas locus. TIGR01877.1 TIGR01877 cas_cas6 58.65 58.65 200 equivalog Y Y N CRISPR-associated endoribonuclease Cas6 cas6 GO:0004521,GO:0043571 19141480 131567 cellular organisms no rank 7159 JCVI CRISPR-associated endoribonuclease Cas6 CRISPR-associated endoribonuclease Cas6 CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This broadly distributed, highly divergent Cas family is now characterized as an endoribonuclease that generates guide RNAs for host defense against phage and other invaders. The family contains a C-terminal motif GXGXXXXXGXG, where the each X between two Gly is hydrophobic and the spacer XXXXX contains (usually) one Arg or Lys. The seed alignment for the current version of this model has gappy columns removed. Members of this protein family are found associated with several different CRISPR/cas system subtypes, and consequently we designate this family Cas6. TIGR01878.1 TIGR01878 cas_Csa5 53.35 53.35 107 equivalog Y Y N type I-A CRISPR-associated protein Csa5 csa5 GO:0043571 11788711 131567 cellular organisms no rank 73 JCVI CRISPR type I-A/APERN-associated protein Csa5 type I-A CRISPR-associated protein Csa5 CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This HMM represents a minor family of Cas protein found in the (all archaeal) APERN subtype of CRISPR/Cas locus, so the family is designated Csa5, for CRISPR/Cas Subtype Protein 5. TIGR01879.1 TIGR01879 hydantase 204 204 401 subfamily Y Y N hydantoinase/carbamoylase family amidase 3.5.-.- GO:0016813 131567 cellular organisms no rank 75623 JCVI amidase, hydantoinase/carbamoylase family hydantoinase/carbamoylase family amidase Enzymes in this subfamily hydrolize the amide bonds of compounds containing carbamoyl groups or hydantoin rings. These enzymes are members of the broader family of amidases represented by PF01546. TIGR01881.1 TIGR01881 cas_Cmr5 27.9 27.9 143 equivalog Y Y N type III-B CRISPR module-associated protein Cmr5 cmr5 GO:0043571 11788711 131567 cellular organisms no rank 1227 JCVI CRISPR type III-B/RAMP module-associated protein Cmr5 type III-B CRISPR module-associated protein Cmr5 CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This HMM family, represented by TM1791.1 of Thermotoga maritima, is found in both archaeal and bacterial species as part of the 6-gene CRISPR RAMP module. TIGR01883.1 TIGR01883 PepT-like 274.25 274.25 361 hypoth_equivalog Y N N peptidase T-like protein 131567 cellular organisms no rank 10190 JCVI peptidase T-like protein peptidase T-like protein This model represents a clade of enzymes closely related to Peptidase T, an aminotripeptidase found in bacteria. This clade consists of gram positive bacteria of which several additionally contain a Peptidase T gene. TIGR01884.1 TIGR01884 cas_HTH 60.2 60.2 202 subfamily Y Y N CRISPR-associated CARF protein Csa3 csa3 GO:0043571 16292354,21093452 131567 cellular organisms no rank 428 JCVI CRISPR locus-related DNA-binding protein CRISPR-associated CARF protein Csa3 Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity. TIGR01885.1 TIGR01885 Orn_aminotrans 378.4 378.4 402 equivalog Y Y N ornithine--oxo-acid transaminase rocD 2.6.1.13 GO:0004587 131567 cellular organisms no rank 25280 JCVI ornithine--oxo-acid transaminase ornithine--oxo-acid transaminase This HMM describes the final step in the biosynthesis of ornithine from glutamate via the non-acetylated pathway. Ornithine amino transferase takes L-glutamate 5-semialdehyde and makes it into ornithine, which is used in the urea cycle, as well as in the biosynthesis of arginine. This model includes low-GC bacteria and eukaryotic species. The genes from two species are annotated as putative acetylornithine aminotransferases - one from Porphyromonas gingivalis (OMNI|PG1271), and the other from Staphylococcus aureus (OMNI|SA0170). After homology searching using BLAST it was determined that these two sequences were most closely related to ornithine aminotransferases. This model's seed includes one characterized hit, from Bacillus subtilis (SP|P38021). TIGR01888.1 TIGR01888 cas_cmr3 100.4 100.4 346 equivalog Y Y N type III-B CRISPR module-associated protein Cmr3 cmr3 GO:0043571 11788711 131567 cellular organisms no rank 626 JCVI CRISPR type III-B/RAMP module-associated protein Cmr3 type III-B CRISPR module-associated protein Cmr3 CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This highly divergent family is found in at least ten different archaeal and bacterial species as part of the CRISPR RAMP modulue but is not a member of the RAMP superfamily itself. A typical example is TM1793 from Thermotoga maritima. TIGR01891.1 TIGR01891 amidohydrolases 153.75 153.75 366 subfamily Y Y N amidohydrolase GO:0004180 131567 cellular organisms no rank 215475 JCVI amidohydrolase amidohydrolase This model represents a subfamily of amidohydrolases which are a subset of those sequences detected by PF01546. Included within this group are hydrolases of hippurate (N-benzylglycine), indoleacetic acid (IAA) N-conjugates of amino acids, N-acetyl-L-amino acids and aminobenzoylglutamate. These hydrolases are of the carboxypeptidase-type, most likely utilizing a zinc ion in the active site. TIGR01893.1 TIGR01893 aa-his-dipept 343.75 343.75 478 subfamily Y Y N beta-Ala-His dipeptidase pepD 3.4.13.20 GO:0006508,GO:0016787 11157967,20819954,7988883 131567 cellular organisms no rank 26515 JCVI Xaa-His dipeptidase beta-Ala-His dipeptidase This model represents a clade of dipeptidase enzymes, many of which are specific for carnosine (beta-alanyl-histidine). This enzymes is found broadly in bacteria and at least one archaeon (Methanosarcina). In most species there is only one sequence hitting this model, while Bacteroides thetaiotaomicron, Chlorobium tepidum and Clostridium perfringens have two each and Fusobacterium nucleatum has three. These may indicate that there is a broader substrate range than just carnosine in these (and other) species. 8/19/03 GO terms added [SS] TIGR01894.1 TIGR01894 cas_TM1795_cmr1 28.65 28.65 167 hypoth_equivalog_domain Y Y N type III-B CRISPR module RAMP protein Cmr1 cmr1 GO:0043571 11788711 131567 cellular organisms no rank 1601 JCVI CRISPR type III-B/RAMP module RAMP protein Cmr1 type III-B CRISPR module RAMP protein Cmr1 CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This HMM represents the region of stongest conservation, the N-terminal half, of one such family, represented by TM1795 from Thermotoga maritima. This protein is the first of a set of six genes, mostly from the RAMP superfamily, that we designated the CRISPR-associated RAMP module. TIGR01895.1 TIGR01895 cas_Cas5t 96.7 96.7 217 exception Y Y N type I-B CRISPR-associated protein Cas5b cas5b GO:0043571 131567 cellular organisms no rank 1001 JCVI CRISPR-associated protein Cas5, subtype I-B/TNEAP type I-B CRISPR-associated protein Cas5b CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This family is represented by TM1800 from Thermotoga maritima. It is related to TIGR01868 (CRISPR-associated protein, CT1976 family). TIGR01896.1 TIGR01896 cas_AF1879 103.35 103.35 273 equivalog Y Y N type I-A CRISPR-associated protein Cas4/Csa1 cas4a GO:0043571 11788711 131567 cellular organisms no rank 181 JCVI CRISPR-associated protein Cas4/Csa1, subtype I-A/APERN type I-A CRISPR-associated protein Cas4/Csa1 CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This HMM describes a particularly strongly conserved family found so only in the APERN subtype of CRISPR/Cas loci and represented by AF1879 from Archaeoglobus fulgidus. This family has four perfectly preserved Cys residues. This subfamily is found in a CRISPR/Cas locus we designate APERN, so the family is designated Csa1, for CRISPR/Cas Subtype Protein 1. TIGR01897.1 TIGR01897 cas_MJ1666 110 110 417 equivalog Y Y N CRISPR-associated CARF protein Csx1 csx1 GO:0043571 16292354,31541109 131567 cellular organisms no rank 174 JCVI CRISPR-associated protein, MJ1666 family CRISPR-associated CARF protein Csx1, MJ1666-like Csx1 is a CRISPR-associated Rossman fold (CARF) superfamily protein. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This HMM describes a Cas protein about 400 residues in length, found mostly in the Archaea but also in Aquifex. TIGR01898.1 TIGR01898 cas_TM1791_cmr6 51.1 51.1 195 equivalog Y Y N type III-B CRISPR module RAMP protein Cmr6 cmr6 GO:0043571 11788711 131567 cellular organisms no rank 1920 JCVI CRISPR type III-B/RAMP module RAMP protein Cmr6 type III-B CRISPR module RAMP protein Cmr6 CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This family, represented by TM1791 of Thermotoga maritima, is designated Cmr6 [sic], for CRISPR/Cas Ramp Module protein 6. This family is both closely related to and frequently encoded next to the TM1792 family of Cas proteins described by TIGR01867. The two proteins are fused in an example from Methanopyrus kandleri. TIGR01899.1 TIGR01899 cas_TM1807_csm5 38.3 38.3 364 equivalog Y Y N type III-A CRISPR-associated RAMP protein Csm5 csm5 GO:0043571 11788711 131567 cellular organisms no rank 2015 JCVI CRISPR type III-A/MTUBE-associated RAMP protein Csm5 type III-A CRISPR-associated RAMP protein Csm5 CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. Members of this cas gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm5, for CRISPR/cas Subtype Mtube, protein 5. TIGR01902.1 TIGR01902 dapE-lys-deAc 163.1 163.1 340 subfamily Y N N N-acetyl-ornithine/N-acetyl-lysine deacetylase GO:0008270,GO:0009085,GO:0016811,GO:0050897 11852094 131567 cellular organisms no rank 2450 JCVI N-acetyl-ornithine/N-acetyl-lysine deacetylase N-acetyl-ornithine/N-acetyl-lysine deacetylase This clade of mainly archaeal and related bacterial species contains two characterized enzymes, an deacetylase with specificity for both N-acetyl-ornithine and N-acetyl-lysine from Thermus [1] which is found within a lysine biosynthesis operon, and a fusion protein with acetyl-glutamate kinase (an enzyme of ornithine biosynthesis) from Lactobacillus. It is possible that all of the sequences within this clade have dual specificity, or that a mix of specificities have evolved within this clade. TIGR01903.2 TIGR01903 cas5_csm4 55 55 304 equivalog Y Y N type III-A CRISPR-associated RAMP protein Csm4 csm4 GO:0043571 11788711 131567 cellular organisms no rank 2296 JCVI CRISPR type III-A/MTUBE-associated RAMP protein Csm4 type III-A CRISPR-associated RAMP protein Csm4 CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. Members of this cas gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm4, for CRISPR/cas Subtype Mtube, protein 4. TIGR01907.1 TIGR01907 casE_Cse3 45.2 45.2 208 equivalog Y Y N type I-E CRISPR-associated protein Cas6/Cse3/CasE cas6e GO:0043571 16672237,18703739 131567 cellular organisms no rank 10452 JCVI CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI type I-E CRISPR-associated protein Cas6/Cse3/CasE CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This HMM family, represented by CT1974 from Chlorobium tepidum, is found in the Ecoli subtype of CRISPR/Cas regions and is designated Cse3 (CRISPR/Cas Subtype Ecoli protein 3). The representative of this family from Thermus thermophilus HB8 (TTHB192) has been crystallized [2] and found to have a structure consisting of two domains with opposing parallel beta-sheets known as a beta-sheet platform. This structure is similar to those found in the Sex-lethal protein and poly(A)-binding protein. This structure is consistent with an RNA-binding function. TIGR01908.1 TIGR01908 cas_CXXC_CXXC 19.4 19.4 308 equivalog_domain Y Y N type I-B CRISPR-associated protein Cas8b1/Cst1 cas8a1 GO:0043571 131567 cellular organisms no rank 1429 JCVI CRISPR-associated protein Cas8b1/Cst1, subtype I-B/TNEAP type I-B CRISPR-associated protein Cas8b1/Cst1 CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This (revised) HMM describes a conserved region from an otherwise highly divergent protein found in the Tneap subtype of CRISPR/Cas regions. This Cys-rich region features two motifs of CXXC. TIGR01909.1 TIGR01909 C_GCAxxG_C_C 47.4 47.4 120 subfamily Y Y N C-GCAxxG-C-C family (seleno)protein 131567 cellular organisms no rank 7557 JCVI C_GCAxxG_C_C family protein C-GCAxxG-C-C family (seleno)protein This HMM represents a putative redox-active protein of about 140 residues, with four perfectly conserved Cys residues. It includes a CGAXXG motif. Most members are found within one or two loci of transporter or oxidoreductase genes. A member from Geobacter sulfurreducens, located in a molybdenum transporter operon, has a TAT (twin-arginine translocation) signal sequence for Sec-independent transport across the plasma membrane, a hallmark of bound prosthetic groups such as FeS clusters. TIGR01910.1 TIGR01910 DapE-ArgE 217.6 217.6 373 subfamily Y Y N ArgE/DapE family deacylase GO:0016787 131567 cellular organisms no rank 29111 JCVI peptidase, ArgE/DapE family ArgE/DapE family deacylase This group of sequences contains annotations for both acetylornithine deacetylase and succinyl-diaminopimelate desuccinylase, but does not contain any members with experimental characterization. Bacillus, Staphylococcus and Sulfolobus species contain multiple hits to this subfamily and each may have a separate activity. Determining which is which must await further laboratory research. TIGR01911.1 TIGR01911 HesB_rel_seleno 66.35 66.35 92 subfamily Y Y N HesB-like protein 131567 cellular organisms no rank 364 JCVI HesB-like selenoprotein HesB-like selenoprotein This HMM represents a family of small proteins related to HesB and its close homologs, which are likely to be invovlved in iron-sulfur cluster assembly (See TIGR00049 and PF01521). Several members are selenoproteins, with a TGA codon and Sec residue that aligns to the conserved Cys of the HesB domain. A variable Cys/Ser/Gly-rich C-terminal region is not included in the seed alignment and model. TIGR01912.1 TIGR01912 TatC-Arch 192.6 192.6 234 equivalog Y Y N Sec-independent protein translocase TatC tatC GO:0033281,GO:0043953 12634324 131567 cellular organisms no rank 74 JCVI Sec-independent protein translocase TatC Sec-independent protein translocase TatC This model represents the TatC translocase component of the Sec-independent protein translocation system. This system is responsible for translocation of folded proteins, often with bound cofactors across the periplasmic membrane [1]. A related model (TIGR00945) represents the bacterial clade of this family. TatC is often found (in bacteria) in a gene cluster with the two other components of the system, TatA/E (TIGR01411) and TatB (TIGR01410). A model also exists for the Twin-arginine signal sequence (TIGR01409). TIGR01915.1 TIGR01915 npdG 149.8 149.8 220 equivalog Y Y N NADPH-dependent F420 reductase npdG GO:0006740,GO:0016651,GO:0050661,GO:0070967 131567 cellular organisms no rank 9534 JCVI NADPH-dependent F420 reductase NADPH-dependent F420 reductase This HMM represents a subset of a parent family described by Pfam model PF03807. Unlike the parent family, members of this family are found only in species with evidence of coenzyme F420. All members of this family are believed to act as NADPH-dependent F420 reductase. TIGR01916.1 TIGR01916 F420_cofE 180.65 180.65 244 equivalog Y Y N coenzyme F420-0:L-glutamate ligase cofE 6.3.2.31 GO:0043773,GO:0046872 11717263,12911320 131567 cellular organisms no rank 16174 JCVI coenzyme F420-0:L-glutamate ligase coenzyme F420-0:L-glutamate ligase This model represents an enzyme of coenzyme F(420) biosynthesis, as catalyzed by MJ0768 of Methanococcus jannaschii and by the N-terminal half of FbiB of Mycobacterium bovis strain BCG. Note that only two glutamates are ligated in M. jannaschii, but five to six in the Mycobacterium lineage. In M. jannaschii, CofE catalyzes the GTP-dependent addition of two L-glutamates. TIGR01920.1 TIGR01920 Shik_kin_archae 126.85 126.85 266 equivalog Y Y N shikimate kinase 2.7.1.71 GO:0004765,GO:0005737,GO:0009073,GO:0009423 11114929 131567 cellular organisms no rank 1271 JCVI shikimate kinase shikimate kinase This HMM represents the shikimate kinase (SK) gene found in archaea which is only distantly related to homoserine kinase (thrB) and not atr all to the bacterial SK enzyme. The SK from M. janaschii has been overexpressed in E. coli and characterized [1]. SK catalyzes the fifth step of the biosynthesis of chorismate from D-erythrose-4-phosphate and phosphoenolpyruvate. TIGR01921.1 TIGR01921 DAP-DH 180.6 180.6 324 equivalog Y Y N diaminopimelate dehydrogenase 1.4.1.16 GO:0009089,GO:0047850 8885833 131567 cellular organisms no rank 7086 JCVI diaminopimelate dehydrogenase diaminopimelate dehydrogenase This model represents the diaminopimelate dehydrogenase enzyme which provides an alternate (shortcut) route of lysine buiosynthesis in Corynebacterium, Bacterioides, Porphyromonas and scattered other species. The enzyme from Corynebacterium glutamicum has been crystallized and characterized [1]. TIGR01922.1 TIGR01922 purO_arch 158.35 158.35 199 equivalog Y Y N IMP cyclohydrolase purO 3.5.4.10 GO:0003937,GO:0006164,GO:0006188 11844782 131567 cellular organisms no rank 901 JCVI IMP cyclohydrolase IMP cyclohydrolase This model represents IMP cyclohydrolase, the final step in the biosynthesis of inosine monophosphate (IMP) in archaea [1]. In bacteria this step is catalyzed by a bifunctional enzyme (purH). TIGR01923.1 TIGR01923 menE 330.15 330.15 442 equivalog Y Y N o-succinylbenzoate--CoA ligase menE 6.2.1.26 GO:0005524,GO:0008756,GO:0009234 131567 cellular organisms no rank 22350 JCVI O-succinylbenzoate-CoA ligase o-succinylbenzoate--CoA ligase This model represents an enzyme, O-succinylbenzoate-CoA ligase, which is involved in the fourth step of the menaquinone biosynthesis pathway. O-succinylbenzoate-CoA ligase, together with menB - naphtoate synthase, take 2-succinylbenzoate and convert it into 1,4-di-hydroxy-2- naphtoate. TIGR01926.1 TIGR01926 peroxid_rel 81.8 81.8 178 subfamily Y Y N peroxidase-related enzyme GO:0051920 131567 cellular organisms no rank 22967 JCVI uncharacterized peroxidase-related enzyme peroxidase-related enzyme Homology through a core region (see TIGR00778) shared with alkylhydroperoxidase AhpD, with the motif CxxCxxxHxxxxxxxG, suggests a peroxidase function. A number of homologs to this family are known to act as peroxidases or to correlate with resistance to oxidative stress. At least one member, from Myxococcus xanthus, is a selenoprotein, with an otherwise conserved Cys replaced by Sec. This protein belongs to a clade of uncharacterized proteins related to peroxidases such as the alkylhydroperoxidase AhpD. TIGR01928.1 TIGR01928 menC_lowGC_arch 200.65 200.65 325 equivalog Y Y N o-succinylbenzoate synthase menC 4.2.1.113 GO:0009234,GO:0016829 10194342 131567 cellular organisms no rank 15049 JCVI o-succinylbenzoate synthase o-succinylbenzoate synthase This model describes the enzyme o-succinylbenzoic acid synthetase (menC) that is involved in one of the steps of the menaquinone biosynthesis pathway. It takes SHCHC and makes it into 2-succinylbenzoate. Included in this model are low GC gram positive bacteria and archaea. Also included in the seed and in the model are enzymes with the com-name of N-acylamino acid racemase (or the more general term, racemase / racemase family), which refers to the enzyme's industrial application as racemases, and not to its biological function as o-succinylbenzoic acid synthetase. TIGR01929.1 TIGR01929 menB 342.7 342.7 259 equivalog Y Y N 1,4-dihydroxy-2-naphthoyl-CoA synthase menB 4.1.3.36 GO:0008935,GO:0009234 131567 cellular organisms no rank 20521 JCVI naphthoate synthase 1,4-dihydroxy-2-naphthoyl-CoA synthase This model represents an enzyme, naphthoate synthase (dihydroxynaphthoic acid synthetase), which is involved in the fifth step of the menaquinone biosynthesis pathway. Together with o-succinylbenzoate-CoA ligase (menE: TIGR01923), this enzyme takes 2-succinylbenzoate and converts it into 1,4-di-hydroxy-2-naphthoate. Included above the trusted cutoff are two enzymes from Arabadopsis thaliana and one from Staphylococcus aureus which are identified as putative enoyl-CoA hydratase/isomerases. These enzymes group with the naphthoate synthases when building a tree and when doing BLAST searches. TIGR01930.1 TIGR01930 AcCoA-C-Actrans 240.55 240.55 385 subfamily Y Y N acetyl-CoA C-acyltransferase 2.3.1.16 GO:0003985,GO:0006631 131567 cellular organisms no rank 324802 JCVI acetyl-CoA C-acyltransferase acetyl-CoA C-acyltransferase This model represents a large family of enzymes which catalyze the thiolysis of a linear fatty acid CoA (or acetoacetyl-CoA) using a second CoA molecule to produce acetyl-CoA and a CoA-ester product two carbons shorter (or, alternatively, the condensation of two molecules of acetyl-CoA to produce acetoacetyl-CoA and CoA). This enzyme is also known as "thiolase", "3-ketoacyl-CoA thiolase", "beta-ketothiolase" and "Fatty oxidation complex beta subunit". When catalyzing the degradative reaction on fatty acids the corresponding EC number is 2.3.1.16. The condensation reaction corresponds to 2.3.1.9. Note that the enzymes which catalyze the condensation are generally not involved in fatty acid biosynthesis, which is carried out by a decarboxylating condensation of acetyl and malonyl esters of acyl carrier proteins. Rather, this activity may produce acetoacetyl-CoA for pathways such as IPP biosynthesis in the absence of sufficient fatty acid oxidation. TIGR01934.1 TIGR01934 MenG_MenH_UbiE 158.35 158.35 223 subfamily Y Y N ubiquinone/menaquinone biosynthesis methyltransferase 2.1.1.- GO:0008168,GO:0008299 8340421,9045837 131567 cellular organisms no rank 50131 JCVI ubiquinone/menaquinone biosynthesis methyltransferase ubiquinone/menaquinone biosynthesis methyltransferase null TIGR01944.1 TIGR01944 rnfB 68.7 68.7 190 subfamily Y Y N RnfABCDGE type electron transport complex subunit B GO:0009055,GO:0022900,GO:0051536 12773378,9154934 131567 cellular organisms no rank 22715 JCVI electron transport complex, RnfABCDGE type, B subunit RnfABCDGE type electron transport complex subunit B The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the B subunit. TIGR01945.1 TIGR01945 rnfC 245.95 245.95 435 subfamily Y Y N RnfABCDGE type electron transport complex subunit C GO:0009055,GO:0016020,GO:0051539 12773378,9154934 131567 cellular organisms no rank 42995 JCVI electron transport complex, RnfABCDGE type, C subunit RnfABCDGE type electron transport complex subunit C The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the C subunit. TIGR01947.1 TIGR01947 rnfG 102 102 187 subfamily Y Y N RnfABCDGE type electron transport complex subunit G GO:0005886,GO:0009055,GO:0010181,GO:0022900 12773378,9154934 131567 cellular organisms no rank 16020 JCVI electron transport complex, RnfABCDGE type, G subunit RnfABCDGE type electron transport complex subunit G The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the A subunit. TIGR01948.1 TIGR01948 rnfE 213.4 213.4 196 subfamily Y Y N RnfABCDGE type electron transport complex subunit E GO:0016020,GO:0022900 12773378,9154934 131567 cellular organisms no rank 12903 JCVI electron transport complex, RnfABCDGE type, E subunit RnfABCDGE type electron transport complex subunit E The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the E subunit. TIGR01949.1 TIGR01949 ADH_synth 299.45 299.45 255 equivalog Y Y N 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase 2.2.1.10 GO:0009073,GO:0016836 15182204,17713928,18318840 131567 cellular organisms no rank 1800 JCVI predicted phospho-2-dehydro-3-deoxyheptonate aldolase 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase ADH synthase, found mostly in Archaea, belongs an alternate pathway for the biosynthesis of 3-dehydroquinate (DHQ), an intermediate in the biosynthesis of aromatic amino acids. The enzyme also can cleave fructose-1,6-bisphosphate to glyceraldehyde-3-phosphate and dihydroxyacetone phosphate. TIGR01952.1 TIGR01952 nusA_arch 74.35 74.35 141 equivalog Y Y N NusA-like transcription termination signal-binding factor 17288993 131567 cellular organisms no rank 1239 JCVI NusA family KH domain protein, archaeal NusA-like transcription termination signal-binding factor This NusA-like archaeal protein resembles the KH domain-containing C-terminal region of bacterial NusA, a transcription termination/antitermination factor. The particulars of transcription termination are likely to differ profoundly from what is seen in bacteria, so this protein should not be called NusA per se. TIGR01957.1 TIGR01957 nuoB_fam 142.7 142.7 145 subfamily Y Y N NADH-quinone oxidoreductase subunit B GO:0030964,GO:0048038,GO:0050136,GO:0051539 131567 cellular organisms no rank 31981 JCVI NADH-quinone oxidoreductase, B subunit NADH-quinone oxidoreductase subunit B This HMM describes the B chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. The quinone is plastoquinone in Synechocystis (where the chain is designated K) and in chloroplast, where NADH may be replaced by NADPH. In the methanogenic archaeal genus Methanosarcina, NADH is replaced by F420H2. TIGR01958.1 TIGR01958 nuoE_fam 142.4 142.4 148 subfamily Y Y N NADH-quinone oxidoreductase subunit NuoE nuoE GO:0016491 131567 cellular organisms no rank 28112 JCVI NADH-quinone oxidoreductase, E subunit NADH-quinone oxidoreductase subunit NuoE This HMM describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria. TIGR01961.1 TIGR01961 NuoC_fam 122.45 122.45 122 subfamily Y N N NADH (or F420H2) dehydrogenase, subunit C nuoC GO:0016651 131567 cellular organisms no rank 37245 JCVI NADH (or F420H2) dehydrogenase, subunit C NADH (or F420H2) dehydrogenase, subunit C This model describes the C subunit of the NADH dehydrogenase complex I in bacteria, as well as many instances of the corresponding mitochondrial subunit (NADH dehydrogenase subunit 9) and of the F420H2 dehydrogenase in Methanosarcina. Complex I contains subunits designated A-N. This C subunit often occurs as a fusion protein with the D subunit. This model excludes the NAD(P)H and plastoquinone-dependent form of chloroplasts and TIGR01962.1 TIGR01962 NuoD 459.35 459.35 386 equivalog_domain Y Y N NADH dehydrogenase (quinone) subunit D nuoD 7.1.1.- GO:0050136 131567 cellular organisms no rank 33387 JCVI NADH dehydrogenase (quinone), D subunit NADH dehydrogenase (quinone) subunit D This model recognizes specificially the D subunit of NADH dehydrogenase I complex. It excludes the related chain of NAD(P)H-quinone oxidoreductases from chloroplast and Synechocystis, where the quinone may be plastoquinone rather than ubiquinone. This subunit often appears as a C/D fusion. TIGR01965.1 TIGR01965 VCBS_repeat 15.5 15.5 99 domain Y Y N VCBS domain-containing protein 131567 cellular organisms no rank 56116 JCVI VCBS repeat VCBS domain This domain of about 100 residues was found originally in multiple (up to 35) copies in long proteins from several species of Vibrio, Colwellia, Bradyrhizobium, and Shewanella (hence the name VCBS) and in smaller copy numbers in proteins from several other bacteria. The large protein size and repeat copy numbers, species distribution, and suggested activities of several member proteins suggests a role for this domain in adhesion. This HMM for a repeated domain overlaps substantially (shifted by half its length) with newer Pfam model PF17803 (bacterial cadherin-like domain). TIGR01966.1 TIGR01966 RNasePH 141.5 141.5 236 equivalog Y Y N ribonuclease PH rph 2.7.7.56 GO:0000049,GO:0008033,GO:0009022 14767080,1512253 131567 cellular organisms no rank 39215 JCVI ribonuclease PH ribonuclease PH This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans. TIGR01969.1 TIGR01969 minD_arch 201.75 201.75 251 subfamily Y Y N cell division ATPase MinD minD 11248256,11296216,12694607 131567 cellular organisms no rank 791 JCVI cell division ATPase MinD cell division ATPase MinD This HMM represents the archaeal branch of the MinD family. MinD, a weak ATPase, works in bacteria with MinC as a generalized cell division inhibitor and, through interaction with MinE, prevents septum placement inappropriate sites. Often several members of this family are found in archaeal genomes, and the function is uncharacterized. More distantly related proteins ParA chromosome partitioning proteins. The exact roles of the various archaeal MinD homologs are unknown. TIGR01971.1 TIGR01971 NuoI 113.05 113.05 121 subfamily Y N N NADH-quinone oxidoreductase, chain I 7.1.1.- GO:0016020,GO:0050136,GO:0051539 131567 cellular organisms no rank 27319 JCVI NADH-quinone oxidoreductase, chain I NADH-quinone oxidoreductase, chain I This HMM represents the I subunit (one of 14: A->N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This HMM excludes "I" subunits from the closely related F420H2 dehydrogenase and formate hydrogenlyase complexes. TIGR01972.1 TIGR01972 NDH_I_M 263.8 263.8 486 subfamily Y Y N NADH-quinone oxidoreductase subunit M 1.6.5.- GO:0008137,GO:0042773 131567 cellular organisms no rank 64208 JCVI proton-translocating NADH-quinone oxidoreductase, chain M NADH-quinone oxidoreductase subunit M TIGR01972 describes the 13th (based on E. coli) structural gene, M, of bacterial NADH dehydrogenase I, as well as chain 4 of the corresponding mitochondrial complex I and of the chloroplast NAD(P)H dehydrogenase complex. The complex to which this protein belongs may rely on ubiquinone as electron acceptor (EC 1.6.5.3), or allow more general use of other quinones such as menaquinone (EC 1.6.5.11). TIGR01974.1 TIGR01974 NDH_I_L 407.5 407.5 630 subfamily Y Y N NADH-quinone oxidoreductase subunit L 1.6.5.- GO:0050136 131567 cellular organisms no rank 63417 JCVI proton-translocating NADH-quinone oxidoreductase, chain L NADH-quinone oxidoreductase subunit L TIGR01972 describes the 12th (based on E. coli) structural gene, L, of bacterial NADH dehydrogenase I, as well as chain 5 of the corresponding mitochondrial complex I and subunit 5 (or F) of the chloroplast NAD(P)H-plastoquinone dehydrogenase complex.. The complex to which this protein belongs may rely on ubiquinone as electron acceptor (EC 1.6.5.3), or allow more general use of other quinones such as menaquinone (EC 1.6.5.11). TIGR01976.1 TIGR01976 am_tr_V_VC1184 352.35 352.35 401 hypoth_equivalog Y Y N cysteine desulfurase-like protein GO:0003824 131567 cellular organisms no rank 14618 JCVI cysteine desulfurase family protein cysteine desulfurase-like protein This HMM describes a subfamily of probable pyridoxal phosphate-dependent enzymes in the aminotransferase class V family (PF00266). The most closely related characterized proteins are active as cysteine desulfurases, selenocysteine lyases, or both; some are involved in FeS cofactor biosynthesis and are designated NifS. An active site Cys residue present in those sequences, in motifs resembling GHHC or GSAC, is not found in this family. The function of members of this family is unknown, but seems unlike to be as an aminotransferase. TIGR01977.1 TIGR01977 am_tr_V_EF2568 377 377 376 hypoth_equivalog Y N N cysteine desulfurase family protein GO:0031071 131567 cellular organisms no rank 7650 JCVI cysteine desulfurase family protein cysteine desulfurase family protein This HMM describes a subfamily of probable pyridoxal phosphate-dependent enzymes in the aminotransferase class V family. Related families contain members active as cysteine desulfurases, selenocysteine lyases, or both. The members of this family form a distinct clade and all are shorter at the N-terminus. The function of this subfamily is unknown. TIGR01978.1 TIGR01978 sufC 212.8 212.8 243 equivalog Y Y N Fe-S cluster assembly ATPase SufC sufC GO:0005524,GO:0016226 131567 cellular organisms no rank 38219 JCVI FeS assembly ATPase SufC Fe-S cluster assembly ATPase SufC SufC is part of the SUF system, shown in E. coli to consist of six proteins and believed to act in Fe-S cluster formation during oxidative stress. SufC forms a complex with SufB and SufD. SufC belongs to the ATP-binding cassette transporter family (PF00005) but is no longer thought to be part of a transporter. The complex is reported as cytosolic (PMID:12554644) or associated with the membrane (PMID:11943156). The SUF system also includes a cysteine desulfurase (SufS, enhanced by SufE) and a probable iron-sulfur cluster assembly scaffold protein, SufA. TIGR01979.1 TIGR01979 sufS 475.1 475.1 403 subfamily Y Y N SufS family cysteine desulfurase 2.8.1.7 GO:0006534,GO:0016226,GO:0030170,GO:0031071 131567 cellular organisms no rank 67534 JCVI cysteine desulfurase, SufS family SufS family cysteine desulfurase This model represents a subfamily of NifS-related cysteine desulfurases involved in FeS cluster formation needed for nitrogen fixation among other vital functions. Many cysteine desulfurases are also active as selenocysteine lyase and/or cysteine sulfinate desulfinase. This subfamily is associated with the six-gene SUF system described in E. coli and Erwinia as an FeS cluster formation system during oxidative stress. The active site Cys is this subfamily resembles GHHC with one or both His conserved. TIGR01980.1 TIGR01980 sufB 346.4 346.4 448 equivalog Y Y N Fe-S cluster assembly protein SufB sufB GO:0016226 16109955 131567 cellular organisms no rank 42692 JCVI FeS assembly protein SufB Fe-S cluster assembly protein SufB This protein, SufB, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component. TIGR01981.1 TIGR01981 sufD 222 221.5 275 equivalog Y Y N Fe-S cluster assembly protein SufD sufD GO:0016226 131567 cellular organisms no rank 50735 JCVI FeS assembly protein SufD Fe-S cluster assembly protein SufD This protein, SufD, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. SufB and SufD are homologous. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component. TIGR01987.1 TIGR01987 HI0074 55.8 55.8 123 subfamily Y Y N HI0074 family nucleotidyltransferase substrate-binding subunit GO:0016779 12486719 131567 cellular organisms no rank 5544 JCVI nucleotidyltransferase substrate binding protein, HI0074 family HI0074 family nucleotidyltransferase substrate-binding subunit The member of this family from Haemophilus influenzae, HI0074, has been shown by crystal structure to resemble nucleotidyltransferase substrate binding proteins. It forms a complex with HI0073, encoded by the adjacent gene and containing a nucleotidyltransferase nucleotide binding domain (PF01909). TIGR01994.1 TIGR01994 SUF_scaf_2 92.5 92.5 137 equivalog Y Y N Fe-S cluster assembly sulfur transfer protein SufU sufU GO:0005198,GO:0016226 24321018,29292548 131567 cellular organisms no rank 21886 JCVI SUF system FeS assembly protein, NifU family Fe-S cluster assembly sulfur transfer protein SufU Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. SUF is important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents SufU from the SUF system, a homolog of IscU and NifU. It is now understood to be a sulfur transfer protein, although previously it was called a scaffold protein. TIGR02008.1 TIGR02008 fdx_plant 81.15 81.15 97 subfamily Y N N ferredoxin [2Fe-2S] GO:0009055,GO:0022900,GO:0051537 131567 cellular organisms no rank 3806 JCVI ferredoxin [2Fe-2S] ferredoxin [2Fe-2S] This model represents single domain 2Fe-2S (also called plant type) ferredoxins. In general, these occur as a single domain proteins or with a chloroplast transit peptide. Species tend to be photosynthetic, but several forms may occur in one species and individually may not be associated with photocynthesis. Halobacterial forms differ somewhat in architecture; they score between trusted and noise cutoffs. Sequences scoring below the noise cutoff tend to be ferredoxin-related domains of larger proteins. TIGR02013.1 TIGR02013 rpoB 801.15 801.15 1238 equivalog Y Y N DNA-directed RNA polymerase subunit beta rpoB 2.7.7.6 GO:0003677,GO:0003899,GO:0006351 131567 cellular organisms no rank 64183 JCVI DNA-directed RNA polymerase, beta subunit DNA-directed RNA polymerase subunit beta This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. TIGR02024.1 TIGR02024 FtcD 221.25 221.25 298 equivalog Y Y N glutamate formimidoyltransferase ftcD 2.1.2.5 GO:0019556,GO:0030409,GO:0030412 10673422,12815595 131567 cellular organisms no rank 3799 JCVI glutamate formiminotransferase glutamate formimidoyltransferase This HMM represents the tetrahydrofolate (THF) dependent glutamate formiminotransferase involved in the histidine utilization pathway. This enzyme interconverts L-glutamate and N-formimino-L-glutamate. The enzyme is bifunctional as it also catalyzes the cyclodeaminase reaction on N-formimino-THF, converting it to 5,10-methenyl-THF and releasing ammonia - part of the process of regenerating THF. This model covers enzymes from metazoa as well as gram-positive bacteria and archaea. In humans, deficiency of this enzyme results in a disease phenotype [1]. The crystal structure of the enzyme has been studied in the context of the catalytic mechanism [2]. TIGR02025.1 TIGR02025 BchH 829 829 1271 equivalog Y Y N magnesium chelatase subunit H bchH 6.6.1.1 GO:0010007,GO:0015995,GO:0016851 12828371 131567 cellular organisms no rank 3746 JCVI magnesium chelatase, H subunit magnesium chelatase subunit H This HMM represents the H subunit of the magnesium chelatase complex responsible for magnesium insertion into the protoporphyrin IX ring in the biosynthesis of both chlorophyll and bacteriochlorophyll. In chlorophyll-utilizing species, this gene is known as ChlH, while in bacteriochlorophyll-utilizing spoecies it is called BchH. Subunit H is the largest (~140kDa) of the three subunits (the others being BchD/ChlD and BchI/ChlI), and is known to bind protoporphyrin IX. Subunit H is homologous to the CobN subunit of cobaltochelatase and by anology with that enzyme, subunit H is believed to also bind the magnesium ion which is inserted into the ring. In conjunction with the hydrolysis of ATP by subunits I and D, a conformation change is believed to happen in subunit H causing the magnesium ion insertion into the distorted protoporphyrin ring [1]. TIGR02030.1 TIGR02030 BchI-ChlI 466.95 466.95 337 equivalog Y Y N magnesium chelatase ATPase subunit I bchI 6.6.1.1 GO:0005524,GO:0010007,GO:0015995,GO:0016851,GO:0016887 7892204 131567 cellular organisms no rank 2650 JCVI magnesium chelatase ATPase subunit I magnesium chelatase ATPase subunit I This HMM represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll [1]. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. TIGR02031.1 TIGR02031 BchD-ChlD 499.55 499.55 608 equivalog Y Y N magnesium chelatase ATPase subunit D bchD 6.6.1.1 GO:0005524,GO:0010007,GO:0015995,GO:0016851,GO:0016887 7892204 131567 cellular organisms no rank 1473 JCVI magnesium chelatase ATPase subunit D magnesium chelatase ATPase subunit D This HMM represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll [1]. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea. TIGR02032.1 TIGR02032 GG-red-SF 158.8 158.8 297 subfamily Y Y N geranylgeranyl reductase family protein GO:0015995,GO:0030494,GO:0045550 131567 cellular organisms no rank 32316 JCVI geranylgeranyl reductase family geranylgeranyl reductase family protein This HMM represents a subfamily which includes geranylgeranyl reductases involved in chlorophyll and bacteriochlorophyll biosynthesis as well as other related enzymes which may also act on geranylgeranyl groups or related substrates. TIGR02033.1 TIGR02033 D-hydantoinase 393.25 393.25 454 equivalog Y Y N dihydropyrimidinase hydA 3.5.2.2 GO:0004157,GO:0005737,GO:0008152 7765480 131567 cellular organisms no rank 31246 JCVI dihydropyrimidinase dihydropyrimidinase This HMM represents the D-hydantoinase (dihydropyrimidinase) which primarily converts 5,6-dihydrouracil to 3-ureidopropanoate but also acts on dihydrothymine and hydantoin. The enzyme is a metalloenzyme [1]. TIGR02034.1 TIGR02034 CysN 336.1 336.1 406 subfamily Y N N sulfate adenylyltransferase, large subunit cysN 2.7.7.4 GO:0000103,GO:0004781 12676676,2828368,7961471 131567 cellular organisms no rank 55283 JCVI sulfate adenylyltransferase, large subunit sulfate adenylyltransferase, large subunit Metabolic assimilation of sulfur from inorganic sulfate, requires sulfate activation by coupling to a nucleoside, for the production of high-energy nucleoside phosphosulfates. This pathway appears to be similar in all prokaryotic organisms. Activation is first achieved through sulfation of sulfate with ATP by sulfate adenylyltransferase (ATP sulfurylase) to produce 5'-phosphosulfate (APS), coupled by GTP hydrolysis. Subsequently, APS is phosphorylated by an APS kinase to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) [1]. In Escherichia coli, ATP sulfurylase is a heterodimer composed of two subunits encoded by cysD and cysN, with APS kinase encoded by cysC. These genes are located in a unidirectionally transcribed gene cluster, and have been shown to be required for the synthesis of sulfur-containing amino acids [1]. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules [2]. With members of the Rhizobiaceae family, nodQ often appears as a fusion of cysN (large subunit of ATP sulfurase) and cysC (APS kinase) [2,3]. TIGR02039.1 TIGR02039 CysD 396.6 396.6 294 subfamily Y N N sulfate adenylyltransferase, small subunit cysD 2.7.7.4 GO:0000103,GO:0004781 12676676,2828368 131567 cellular organisms no rank 37414 JCVI sulfate adenylyltransferase, small subunit sulfate adenylyltransferase, small subunit Metabolic assimilation of sulfur from inorganic sulfate, requires sulfate activation by coupling to a nucleoside, for the production of high-energy nucleoside phosphosulfates. This pathway appears to be similar in all prokaryotic organisms. Activation is first achieved through sulfation of sulfate with ATP by sulfate adenylyltransferase (ATP sulfurylase) to produce 5'-phosphosulfate (APS), coupled by GTP hydrolysis. Subsequently, APS is phosphorylated by an APS kinase to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) [1]. In Escherichia coli, ATP sulfurylase is a heterodimer composed of two subunits encoded by cysD and cysN, with APS kinase encoded by cysC. These genes are located in a unidirectionally transcribed gene cluster, and have been shown to be required for the synthesis of sulfur-containing amino acids [1]. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules [2]. TIGR02050.1 TIGR02050 gshA_cyan_rel 176.4 176.4 287 subfamily Y Y N YbdK family carboxylate-amine ligase GO:0016879 15211520,18719892,22059487 131567 cellular organisms no rank 40929 JCVI carboxylate-amine ligase, YbdK family YbdK family carboxylate-amine ligase This family represents a division of a larger family, the other branch of which is predicted to act as glutamate--cysteine ligase (the first of two enzymes in glutathione biosynthesis) in the cyanobacteria. Species containing this protein, however, are generally not believe to make glutathione, and the function is unknown. TIGR02053.1 TIGR02053 MerA 454.45 454.45 465 equivalog Y Y Y mercury(II) reductase merA 1.16.1.1 GO:0016152,GO:0045340,GO:0046689,GO:0050660,GO:0050661,GO:0050787 8467420 131567 cellular organisms no rank 5786 JCVI mercury(II) reductase mercury(II) reductase This HMM represents the mercuric reductase found in the mer operon for the detoxification of mercury compounds. MerA is a FAD-containing flavoprotein which reduces Hg(II) to Hg(0) utilizing NADPH [1]. TIGR02055.1 TIGR02055 APS_reductase 235.3 235.3 194 subfamily Y N N adenylylsulfate reductase, thioredoxin dependent GO:0009973,GO:0010134,GO:0019344 10464198,10613872,11940598,12072441 131567 cellular organisms no rank 17078 JCVI adenylylsulfate reductase, thioredoxin dependent adenylylsulfate reductase, thioredoxin dependent This model describes recently identified adenosine 5'-phosphosulfate (APS) reductase activity found in sulfate-assimilatory prokaryotes, thus separating it from the traditionally described phosphoadenosine 5'-phosphosulfate (PAPS) reductases found in bacteria and fungi [1]. Homologous to PAPS reductase in enterobacteria, cyanobacteria, and yeast, APS reductase here clusters with, and demonstrates greater homology to plant APS reductase. Additionally, the presence of two conserved C-terminal motifs (CCXXRKXXPL & SXGCXXCT) distinguishes APS substrate specificity and serves as a FeS cluster [2]. TIGR02058.1 TIGR02058 lin0512_fam 56.85 56.85 117 subfamily Y Y N Lin0512 family protein 131567 cellular organisms no rank 2924 JCVI conserved hypothetical protein Lin0512 family protein This family is named for a founding member from Listeria innocua (in the Firmicutes) but is broadly distributed in bacteria. The species range includes some Cyanobacteria, and member proteins also found also in green plants. The alignment includes a perfectly conserved motif GxGxDxHG near the N-terminus. The function remains unknown. TIGR02059.1 TIGR02059 swm_rep_I 40.1 15 101 domain Y N N cyanobacterial long protein repeat 131567 cellular organisms no rank 2683 JCVI cyanobacterial long protein repeat cyanobacterial long protein repeat This domain appears in 29 copies in a large (>10000 amino protein in Synechococcus sp. WH8102 associated with a novel flagellar system, as one of three different repeats. Similar domains are found in two different large (4)-alpha-D-glucan 1-alpha-D-glucosylmutase, is the TreY enzyme of the TreYZ pathway of trehalose biosynthesis, an alternative to the OtsAB pathway. Trehalose may be incorporated into more complex compounds but is best known as compatible solute. It is one of the most effective osmoprotectants, and unlike the various betaines does not require nitrogen for its synthesis. TIGR02402.1 TIGR02402 trehalose_TreZ 538.8 538.8 545 equivalog Y Y N malto-oligosyltrehalose trehalohydrolase treZ 3.2.1.141 GO:0005992,GO:0033942 10926520 131567 cellular organisms no rank 33156 JCVI malto-oligosyltrehalose trehalohydrolase malto-oligosyltrehalose trehalohydrolase Members of this family are the trehalose biosynthetic enzyme malto-oligosyltrehalose trehalohydrolase, formally known as 4-alpha-D-{(1->4)-alpha-D-glucano}trehalose trehalohydrolase (EC 3.2.1.141). It is the TreZ protein of the TreYZ pathway for trehalose biosynthesis, and alternative to the OtsAB system. TIGR02406.1 TIGR02406 ectoine_EctA 120.6 120.6 157 equivalog Y Y N diaminobutyrate acetyltransferase ectA 2.3.1.178 GO:0019491,GO:0033816 131567 cellular organisms no rank 11174 JCVI diaminobutyrate acetyltransferase diaminobutyrate acetyltransferase This enzyme family is the EctA of ectoine biosynthesis. Ectoine is a compatible solute, analagous to trehalose, betaines, etc., found often in halotolerant organisms. EctA is L-2,4-diaminobutyric acid acetyltransferase, also called DABA acetyltransferase. TIGR02407.1 TIGR02407 ectoine_ectB 552.2 552.2 412 equivalog Y Y N diaminobutyrate--2-oxoglutarate transaminase ectB 2.6.1.76 GO:0019491,GO:0030170,GO:0047307 131567 cellular organisms no rank 14863 JCVI diaminobutyrate--2-oxoglutarate aminotransferase diaminobutyrate--2-oxoglutarate transaminase Members of this family of class III pyridoxal-phosphate-dependent aminotransferases are diaminobutyrate--2-oxoglutarate aminotransferase (EC 2.6.1.76) that catalyze the first step in ectoine biosynthesis from L-aspartate beta-semialdehyde. This family is readily separated phylogenetically from enzymes with the same substrate and product but involved in other process such as siderophore (SP|Q9Z3R2) or 1,3-diaminopropane (SP|P44951) biosynthesis. The family TIGR00709 previously included both groups but has now been revised to exclude the ectoine biosynthesis proteins of this family. Ectoine is a compatible solute particularly effective in conferring salt tolerance. TIGR02408.1 TIGR02408 ectoine_ThpD 336.5 336.5 277 equivalog Y Y N ectoine hydroxylase thpD 1.14.11.55 GO:0016706 15128576 131567 cellular organisms no rank 9200 JCVI ectoine hydroxylase ectoine hydroxylase Both ectoine and hydroxyectoine are compatible solvents that serve as protectants against osmotic and thermal stresses. A number of genomes synthesize ectoine. This enzyme allows conversion of ectoine to hydroxyectoine, which may be more effective for some purposes, and is found in a subset of ectoine-producing organisms. TIGR02416.1 TIGR02416 CO_dehy_Mo_lg 991.15 991.15 770 equivalog Y Y N aerobic carbon-monoxide dehydrogenase large subunit 1.2.5.3 GO:0005507,GO:0030151,GO:0043885 28161485,31358912 131567 cellular organisms no rank 3409 JCVI carbon-monoxide dehydrogenase, large subunit aerobic carbon-monoxide dehydrogenase large subunit This model represents the large subunits of group of aerobic carbon-monoxide dehydrogenases that include molybdenum as part of the enzymatic cofactor. There are various forms of carbon-monoxide dehydrogenase; Salicibacter pomeroyi DSS-3, for example, has two forms. Note that, at least in some species, the active site Cys is modified with a selenium attached to (rather than replacing) the sulfur atom. This is termed selanylcysteine, and created post-translationally, in contrast to selenocysteine incorporation during translation as for many other selenoproteins. TIGR02442.1 TIGR02442 Cob-chelat-sub 779.45 779.45 641 hypoth_equivalog Y Y N putative cobaltochelatase GO:0005524 131567 cellular organisms no rank 8743 JCVI cobaltochelatase subunit putative cobaltochelatase Cobaltochelatase is responsible for the insertion of cobalt into the corrin ring of coenzyme B12 during its biosynthesis. Two versions have been well described. CbiK/CbiX is a monomeric, anaerobic version which acts ealy in the biosynthesis (PF06180). CobNST is a trimeric, ATP-dependent, aerobic version which acts late in the biosynthesis (TIGR02257/TIGR01650/TIGR01651). A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis. TIGR02452.1 TIGR02452 TIGR02452 50 50 266 hypoth_equivalog Y Y N TIGR02452 family protein 131567 cellular organisms no rank 10325 JCVI TIGR02452 family protein TIGR02452 family protein Members of this uncharacterized protein family are found in Streptomyces, Nostoc sp. PCC 7120, Clostridium acetobutylicum, Lactobacillus johnsonii NCC 533, Deinococcus radiodurans, and Pirellula sp. for a broad but sparse phylogenetic distibution that at least suggests lateral gene transfer. TIGR02454.1 TIGR02454 ECF_T_CbiQ 111.8 111.8 200 equivalog Y Y N cobalt ECF transporter T component CbiQ cbiQ GO:0005886,GO:0006824,GO:0032778,GO:0043190 18931129 131567 cellular organisms no rank 18798 JCVI cobalt ECF transporter T component CbiQ cobalt ECF transporter T component CbiQ This model represents the CbiQ component of the cobalt-specific ECF-type. CbiQ is now recognized as the T component of energy-coupling factor (ECF)-type transporters. The S component confers specificity (CbiM-N for cobalt systems), which CbiO is the ABC-family ATPase. In general, proteins found by this model reside next to the other putative subunits of the complex, identified as CbiN, CbiO, or CbiM. Note that the designation of cobalt transporter has been spread excessively among ECF system transporters with many other specificities. TIGR02456.1 TIGR02456 treS_nterm 678.35 678.35 539 equivalog_domain Y Y N maltose alpha-D-glucosyltransferase treS 5.4.99.16 GO:0005991,GO:0047471 15378530,8829531 131567 cellular organisms no rank 22720 JCVI trehalose synthase maltose alpha-D-glucosyltransferase Trehalose synthase interconverts maltose and alpha, alpha-trehalose by transglucosylation. This is one of at least three mechanisms for biosynthesis of trehalose, an important and widespread compatible solute. However, it is not driven by phosphate activation of sugars and its physiological role may tend toward trehalose degradation. This view is accentuated by numerous examples of fusion to a probable maltokinase domain. The sequence region described by this model is found both as the whole of a trehalose synthase and as the N-terminal region of a larger fusion protein that includes trehalose synthase activity. Several of these fused trehalose synthases have a domain homologous to proteins with maltokinase activity from Actinoplanes missouriensis and Streptomyces coelicolor (PMID:15378530). TIGR02460.1 TIGR02460 osmo_MPGsynth 351.2 351.2 383 equivalog Y Y N mannosyl-3-phosphoglycerate synthase mpgS 2.4.1.217 GO:0005737,GO:0050504,GO:0051479 12788726 131567 cellular organisms no rank 270 JCVI mannosyl-3-phosphoglycerate synthase mannosyl-3-phosphoglycerate synthase This family consists of examples of mannosyl-3-phosphoglycerate synthase (MPGS), which together mannosyl-3-phosphoglycerate phosphatase (MPGP) comprises a two-step pathway for mannosylglycerate biosynthesis. Mannosylglycerate is a compatible solute that tends to be restricted to extreme thermophiles of archaea and bacteria. Note that in Rhodothermus marinus, this pathway is one of two; the other is condensation of GDP-mannose with D-glycerate by mannosylglycerate synthase. TIGR02461.1 TIGR02461 osmo_MPG_phos 244.35 244.35 227 equivalog Y Y N mannosyl-3-phosphoglycerate phosphatase mpgP 3.1.3.70 GO:0050531,GO:0051479 11562374 131567 cellular organisms no rank 157 JCVI mannosyl-3-phosphoglycerate phosphatase mannosyl-3-phosphoglycerate phosphatase Members of this family are mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70). It acts sequentially after mannosyl-3-phosphoglycerate synthase (EC 2.4.1.217) in a two-step pathway of biosynthesis of the compatible solute mannosylglycerate, a typical osmolyte of thermophiles. TIGR02464.1 TIGR02464 ribofla_fusion 73.7 73.7 153 subfamily_domain Y N N conserved hypothetical protein 131567 cellular organisms no rank 19334 JCVI conserved hypothetical protein conserved hypothetical protein This model describes a sequence region that occurs in at least three different polypeptide contexts. It is found fused to GTP cyclohydrolase II, the RibA of riboflavin biosynthesis (TIGR00505), as in Vibrio vulnificus. It is found fused to riboflavin biosynthesis protein RibD (TIGR00326) in rice and Arabidopsis. It occurs as a standalone protein in a number of bacterial species in varied contexts, including single gene operons and bacteriophage genomes. The member from E. coli currently is named YbiA. The function(s) of members of this family is unknown. TIGR02467.1 TIGR02467 CbiE 92.9 92.9 204 equivalog_domain Y Y N precorrin-6y C5,15-methyltransferase (decarboxylating) subunit CbiE cbiE GO:0009236,GO:0046025,GO:0046140 131567 cellular organisms no rank 43762 JCVI precorrin-6y C5,15-methyltransferase (decarboxylating), CbiE subunit precorrin-6y C5,15-methyltransferase (decarboxylating) subunit CbiE This model recognizes the CbiE methylase which is responsible, in part (along with CbiT), for methylating precorrin-6y (or cobalt-precorrin-6y) at both the 5 and 15 positions as well as the concomitant decarbozylation at C-12. In many organisms, this protein is fused to the CbiT subunit. The fused protein, when found in organisms catalyzing the oxidative version of the cobalamin biosynthesis pathway, is called CobL. TIGR02469.1 TIGR02469 CbiT 78.3 78.3 124 equivalog_domain Y Y N precorrin-6Y C5,15-methyltransferase (decarboxylating) subunit CbiT cbiT GO:0009236,GO:0046025,GO:0046140 131567 cellular organisms no rank 38028 JCVI precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit precorrin-6Y C5,15-methyltransferase (decarboxylating) subunit CbiT This model recognizes the CbiT methylase which is responsible, in part (along with CbiE), for methylating precorrin-6y (or cobalt-precorrin-6y) at both the 5 and 15 positions as well as the concomitant decarbozylation at C-12. In many organisms, this protein is fused to the CbiE subunit. The fused protein, when found in organisms catalyzing the oxidative version of the cobalamin biosynthesis pathway, is called CobL. TIGR02476.1 TIGR02476 BluB 150 150 205 equivalog Y Y N 5,6-dimethylbenzimidazole synthase bluB 1.13.11.79 GO:0009236,GO:0016722,GO:0032363 12869542,17301238,17377583,7635831 131567 cellular organisms no rank 26003 JCVI 5,6-dimethylbenzimidazole synthase 5,6-dimethylbenzimidazole synthase A previously published hypothesis that BluB, involved in cobalamin biosynthesis, is EC 1.16.8.1 (cob(II)yrinic acid a,c-diamide reductase) is now contradicted by newer work ascribing a role in 5,6-dimethylbenzimidazole (DMB) biosynthesis. The BluB protein is related to the nitroreductase family (PF0881). TIGR02481.1 TIGR02481 hemeryth_dom 51.75 51.75 126 domain Y Y N hemerythrin domain-containing protein GO:0046872 15885093,22484247,27336621 131567 cellular organisms no rank 20468 JCVI hemerythrin-like metal-binding domain hemerythrin-like metal-binding domain This model describes both members of the hemerythrin (TIGR00058) family of marine invertebrates and a broader collection of bacterial and archaeal homologs. Many of the latter group are multidomain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (TIGR00254, PF00990) and methyl-accepting chemotaxis protein signaling domain (PF00015). Most hemerythrins are oxygen-carriers with a bound non-heme iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. Patterns of conserved residues suggest that all prokaryotic instances of this domain bind iron or another heavy metal, but the exact function is unknown. Not surprisingly, the prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium. TIGR02482.1 TIGR02482 PFKA_ATP 371.35 371.35 301 equivalog Y Y N 6-phosphofructokinase pfkA 2.7.1.11 GO:0005524,GO:0006002,GO:0006096 1828763,2953977,8436141 131567 cellular organisms no rank 17510 JCVI 6-phosphofructokinase 6-phosphofructokinase 6-phosphofructokinase (EC 2.7.1.11) catalyzes the addition of phosphate from ATP to fructose 6-phosphate to give fructose 1,6-bisphosphate. This represents a key control step in glycolysis. This model hits bacterial ATP-dependent 6-phosphofructokinases which lack a beta-hairpin loop present in TIGR02483 family members. TIGR02483 contains members that are ATP-dependent as well as members that are pyrophosphate-dependent. TIGR02477 represents the pyrophosphate-dependent phosphofructokinase, diphosphate--fructose-6-phosphate 1-phosphotransferase (EC 2.7.1.90). TIGR02483.1 TIGR02483 PFK_mixed 430.55 430.55 325 subfamily Y N N phosphofructokinase GO:0006096,GO:0016773 8550409,9055413,9555897 131567 cellular organisms no rank 18475 JCVI phosphofructokinase phosphofructokinase Members of this family that are characterized, save one, are phosphofructokinases dependent on pyrophosphate (EC 2.7.1.90) rather than ATP (EC 2.7.1.11). The exception is one of three phosphofructokinases from Streptomyces coelicolor. Family members are both bacterial and archaeal. TIGR02485.1 TIGR02485 CobZ_N-term 372.55 372.55 437 equivalog Y Y N FAD-dependent tricarballylate dehydrogenase TcuA tcuA GO:0009236 15525640 131567 cellular organisms no rank 6047 JCVI precorrin 3B synthase CobZ FAD-dependent tricarballylate dehydrogenase TcuA CobZ is essential for cobalamin biosynthesis (by knockout of the R. capsulatus gene [1]) and is complemented by the characterized precorrin 3B synthase CobG. The enzyme has been shown to contain flavin, heme and Fe-S cluster cofactors and is believed to require dioxygen as a substrate. This model identifies the N-terminal portion of the R. capsulatus gene which, in other species exists as a separate protein. The C-terminal portion is homologous to the 2-component signal transduction system protein CitB (TIGR02484). TIGR02486.1 TIGR02486 RDH 160.35 160.35 314 subfamily Y Y N reductive dehalogenase 11097881,9224702 131567 cellular organisms no rank 1585 JCVI reductive dehalogenase reductive dehalogenase This model represents a family of corrin and 8-iron Fe-S cluster-containing reductive dehalogenases [1] found primarily in halorespiring microorganisms such as dehalococcoides ethenogenes which contains as many as 17 enzymes of this type with varying substrate ranges. One example of a characterized species is the tetrachloroethene reductive dehalogenase [2] (1.97.1.8) which also acts on trichloroethene converting it to dichloroethene. TIGR02487.1 TIGR02487 NrdD 326.35 326.35 581 equivalog Y Y N anaerobic ribonucleoside-triphosphate reductase nrdD 1.17.4.2 GO:0006260,GO:0008998,GO:0009265,GO:0016491 10066165,11526118,12655046 131567 cellular organisms no rank 32707 JCVI anaerobic ribonucleoside-triphosphate reductase anaerobic ribonucleoside-triphosphate reductase This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical [1], a C-terminal zinc binding site [2], and a set of conserved active site cysteines and asparagines [3]. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer. TIGR02492.1 TIGR02492 flgK_ends 170.75 170.75 437 equivalog Y Y N flagellar hook-associated protein FlgK flgK GO:0005198,GO:0009424,GO:0044780 131567 cellular organisms no rank 45225 JCVI flagellar hook-associated protein FlgK flagellar hook-associated protein FlgK The flagellar hook-associated protein FlgK of bacterial flagella has conserved N- and C-terminal domains. The central region is highly variable in length and sequence, and often contains substantial runs of low-complexity sequence. This model is built from an alignment of FlgK sequences with the central region excised. Note that several other proteins of the flagellar apparatus also are homologous in the N- and C-terminal regions to FlgK, but are excluded from this model. TIGR02495.1 TIGR02495 NrdG2 131.15 131.15 193 equivalog Y Y N anaerobic ribonucleoside-triphosphate reductase activating protein GO:0009265,GO:0051353,GO:0051539 11297442,11389585 131567 cellular organisms no rank 7867 JCVI anaerobic ribonucleoside-triphosphate reductase activating protein anaerobic ribonucleoside-triphosphate reductase activating protein This enzyme is a member of the radical-SAM family (PF04055). It is often gene clustered with the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487) and presumably fulfills the identical function as NrdG [1,2] which utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in NrdD. TIGR02504.1 TIGR02504 NrdJ_Z 399.95 399.95 606 equivalog Y Y N adenosylcobalamin-dependent ribonucleoside-diphosphate reductase 1.17.4.1 GO:0000166,GO:0004748,GO:0031419 6986368,8990160,9012808,9391052 131567 cellular organisms no rank 36384 JCVI ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent adenosylcobalamin-dependent ribonucleoside-diphosphate reductase This model represents a group of adenosylcobalamin(B12)-dependent ribonucleotide reductases (Class II RNRs) related to the characterized species from Pyrococcus [1], Thermoplasma [2], Corynebacterium [3] and Deinococcus [3]. RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA biosynthesis. This model identifies genes in a wide range of deeply branching bacteria. All are structurally related to the class I (non-heme iron dependent) RNRs. In most species this gene is known as NrdJ, while in mycobacteria it is called NrdZ. TIGR02506.1 TIGR02506 NrdE_NrdA 341.05 341.05 616 equivalog Y Y N ribonucleoside-diphosphate reductase subunit alpha 1.17.4.1 GO:0004748,GO:0005971,GO:0009265 11807048,8052308,8820648 131567 cellular organisms no rank 70025 JCVI ribonucleoside-diphosphate reductase, alpha subunit ribonucleoside-diphosphate reductase subunit alpha This model represents the alpha (large) chain of the class I ribonucleotide reductase (RNR). RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA biosynthesis. Class I RNR's generate the required radical (on tyrosine) via a "non-heme" iron cofactor which resides in the beta (small) subunit. The alpha subunit contains the catalytic and allosteric regulatory sites. The mechanism of this enzyme requires molecular oxygen [1]. E. Coli contains two versions of this enzyme which are regulated independently (NrdAB and NrdEF, where NrdA and NrdE are the large chains [2,3]). Most organisms contain only one, but the application of the gene symbols NrdA and NrdE are somewhat arbitrary. This model identifies RNR's in diverse clades of bacteria, eukaryotes as well as numerous DNA viruses and phage. TIGR02510.1 TIGR02510 NrdE-prime 602.25 602.25 560 equivalog Y Y N ribonucleoside-diphosphate reductase subunit alpha 1.17.4.1 GO:0004748 131567 cellular organisms no rank 1722 JCVI ribonucleoside-diphosphate reductase, alpha chain ribonucleoside-diphosphate reductase subunit alpha This model represents a small clade of ribonucleoside-diphosphate reductase, alpha chains which are sufficiently divergent from the usual Class I RNR alpha chains (NrdE or NrdA, TIGR02506) as to warrant their own model. The genes from Thermus thermophilus, Dichelobacter and Salinibacter are adjacent to the usual RNR beta chain. TIGR02535.1 TIGR02535 hyp_Hser_kinase 446.3 446.3 397 hypoth_equivalog Y N N proposed homoserine kinase GO:0046537 131567 cellular organisms no rank 3318 JCVI proposed homoserine kinase cofactor-independent phosphoglycerate mutase The genes in this family are largely adjacent to genes involved in the biosynthesis of threonine (aspartate kinase, homoserine dehydrogenase and threonine synthase) in genomes which are lacking any other known homoserine kinase, and in which the presence of a homoserine kinase would indicate a complete pathway for the biosynthesis of threonine. These genes are a member of the (now subfamily, formerly equivalog) TIGR00306 model describing the archaeal form of 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. All of these are members of a superfamily (PF01676) of metalloenzyme also including phosphopentomutase alkaline phosphatases and sulfatases. The proposal that this family encodes a kinase is based on analogy to phosphomutases which are intramolecular phosphotransferases. A mutase active site could evolve to bring together homoserine and a phosphate donor such as phosphoenolpyruvate resulting in a kinase activity. TIGR02537.2 TIGR02537 arch_flag_Nterm 20 19.5 33 domain Y Y N archaellin/type IV pilin N-terminal domain-containing protein 12813086,15723834,23794623 131567 cellular organisms no rank 7225 JCVI archaeal flagellin N-terminal-like domain archaellin/type IV pilin N-terminal domain-containing protein This model describes a hydrophobic N-terminal sequence of archaeal flagellins (archaellin) archaeal type IV pilins, which share some processing machinery. The sequence is directly analogous to bacterial sequences recognized by TIGR02532, which has cleavage motif resembling G^FxxxE followed by strongly hydrophobic sequence. Such sequences are the recognized for cleavage and methylation, and include pilins and other pilus components and competence and type II secretion secretion proteins. In the present family, the E is not conversed and sequence differs enough that there is no overlap between this family and TIGR02532. TIGR02543.1 TIGR02543 List_Bact_rpt 20.95 20.95 44 repeat Y N N TIGR02543 family repeat protein 131567 cellular organisms no rank 24955 JCVI repeat, TIGR02543 family TIGR02543 family repeat This model describes a conserved core region, about 43 residues in length, of at least two families of tandem repeats. These include 78-residue repeats from 2 to 15 in number, in some proteins of Bacteroides forsythus ATCC 43037, and 70-residue repeats in families of internalins of Listeria species. Single copies are found in proteins of Fibrobacter succinogenes, Geobacter sulfurreducens, and a few bacteria. TIGR02547.1 TIGR02547 casA_cse1 70.05 70.05 504 equivalog Y Y N type I-E CRISPR-associated protein Cse1/CasA casA cse1 GO:0043571 16292354,18703739 131567 cellular organisms no rank 11626 JCVI CRISPR type I-E/ECOLI-associated protein CasA/Cse1 type I-E CRISPR-associated protein Cse1/CasA CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This HMM family is found in type I-E (originally the Ecoli subtype of) CRISPR/Cas regions in many bacteria, most of which are mesophiles, and not in Archaea. It is designated either Cse1 or CasA. TIGR02548.2 TIGR02548 casB_cse2 28.5 28.5 167 equivalog Y Y N type I-E CRISPR-associated protein Cse2/CasB casB cse2 GO:0043571 16292354,18703739 131567 cellular organisms no rank 10402 JCVI CRISPR type I-E/ECOLI-associated protein CasB/Cse2 type I-E CRISPR-associated protein Cse2/CasB CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This HMM family is found in type I-E (originally the Ecoli subtype) CRISPR/Cas regions of many bacteria, most of which are mesophiles, and not in Archaea. It was designated Cse2 originally, and renamed CasB based on its characterization in the CASCADE complex. TIGR02549.2 TIGR02549 CRISPR_DxTHG 21 21 26 domain Y Y N CRISPR-associated DxTHG motif protein GO:0043571 131567 cellular organisms no rank 1550 JCVI CRISPR-associated DxTHG motif protein CRISPR-associated DxTHG motif protein This model describes a short region highly conserved between several substantially different CRISPR-associated (cas) proteins, including Csx1, Csx16, Csx20, etc. This region includes the motif [VIL]-D-x-[ST]-H-[GS]. TIGR02556.1 TIGR02556 cas_TM1802 156.95 156.95 571 equivalog Y Y N TIGR02556 family CRISPR-associated protein GO:0043571 131567 cellular organisms no rank 512 JCVI CRISPR-associated protein, TM1802 family TIGR02556 family CRISPR-associated protein This minor cas protein is found in CRISPR/cas regions of at least five prokaryotic genomes: Methanosarcina mazei, Sulfurihydrogenibium azorense, Thermotoga maritima, Carboxydothermus hydrogenoformans, and Dictyoglomus thermophilum, the first of which is archaeal while the rest are bacterial. TIGR02563.1 TIGR02563 cas_Csy4 36.25 36.25 184 equivalog Y Y N type I-F CRISPR-associated endoribonuclease Cas6/Csy4 cas6f GO:0004521,GO:0043571 22522703 131567 cellular organisms no rank 4487 JCVI CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST type I-F CRISPR-associated endoribonuclease Cas6/Csy4 CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family, typified by YPO2462 of Yersinia pestis, is a CRISPR-associated (Cas) family strictly associated with the Ypest subtype of CRISPR/Cas locus. This family is designated Csy4, for CRISPR/Cas Subtype Ypest protein 4. TIGR02570.1 TIGR02570 cas7_GSU0053 38 38 178 equivalog_domain Y Y N type I-U CRISPR-associated RAMP protein Csb1/Cas7u cas7u GO:0043571 16292354,21552286 131567 cellular organisms no rank 1251 JCVI CRISPR-associated protein GSU0053/csb1, Dpsyc system type I-U CRISPR-associated RAMP protein Csb1/Cas7u Members of this family, previously called Csx4 and now called Csb1 or Cas7u, are found in association with CRISPR repeats and other CRISPR-associated (cas) genes. Its CRISPR/Cas type, now called type I-U, originally was designated Dpsych. It was first seen in the genomes of Geobacter sulfurreducens PCA and Desulfotalea psychrophila LSv54 (both Desulfobacterales from the Deltaproteobacteria), Gemmata obscuriglobus (Planctomycete), and Actinomyces naeslundii MG1 (Actinobacteria). TIGR02577.1 TIGR02577 cas_TM1794_Cmr2 79.4 79.4 510 equivalog Y Y N type III-B CRISPR-associated protein Cas10/Cmr2 cas10 GO:0043571 11788711 131567 cellular organisms no rank 2255 JCVI CRISPR-associated protein Cas10/Cmr2, subtype III-B type III-B CRISPR-associated protein Cas10/Cmr2 This model represent a Crm2 family of the CRISPR-associated RAMP module, a set of six genes recurring found together in prokaryotic genomes. This gene cluster is found only in species with CRISPR repeats, usually near the repeats themselves. Because most of the six (but not this family) contain RAMP domains, and because its appearance in a genome appears to depend on other CRISPR-associated Cas genes, the set is designated the CRISPR RAMP module. This protein, typified by TM1794 from Thermotoga maritima, is designated Crm2, for CRISPR RAMP Module protein 2. TIGR02578.2 TIGR02578 cas_TM1811_Csm1 170 170 753 equivalog Y Y N type III-A CRISPR-associated protein Cas10/Csm1 cas10 GO:0043571 131567 cellular organisms no rank 2732 JCVI CRISPR-associated protein Cas10/Csm1, subtype III-A/MTUBE type III-A CRISPR-associated protein Cas10/Csm1 The family is designated Csm2, for CRISPR/Cas Subtype Mtube Protein 2. A typical example is TM1811 from Thermotoga maritima. CRISPR are Clustered Regularly Interspaced Short Palindromic Repeats. This protein family belongs to a conserved gene cluster regularly found near CRISPR repeats. TIGR02579.1 TIGR02579 cas_csx3 55.4 55.4 83 equivalog Y Y N CRISPR-associated ring nuclease Crn3/Csx3 crn3 GO:0043571 16292354,26106927,32597755 131567 cellular organisms no rank 271 JCVI CRISPR-associated protein, Csx3 family CRISPR-associated ring nuclease Crn3/Csx3 Members of this family, originally Csx3 and now Crn3, are ring nucleases that cleave and degrade cyclic tetra-adenylate (cA4), a second messenger generated by Cas10 in type III CRISPR systems. Founding members of the family were noted in a number thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). TIGR02580.1 TIGR02580 cas_RAMP_Cmr4 87 87 283 equivalog Y Y N type III-B CRISPR module RAMP protein Cmr4 cmr4 GO:0043571 11788711 131567 cellular organisms no rank 2249 JCVI CRISPR type III-B/RAMP module RAMP protein Cmr4 type III-B CRISPR module RAMP protein Cmr4 This model represents a CRISPR-associated protein from the family that includes TM1792 of Thermotoga maritima. This family is part of the broad RAMP superfamily (PF03787) collection of CRISPR-associated proteins. It is the fourth of a recurring set of six proteins, four of are in the RAMP superfamily, that we designate the CRISPR RAMP module. TIGR02581.1 TIGR02581 cas_cyan_RAMP 108.05 108.05 216 equivalog Y Y N CRISPR-associated RAMP protein Csx7 csx7 GO:0043571 16292354 131567 cellular organisms no rank 475 JCVI CRISPR-associated RAMP protein, SSO1426 family CRISPR-associated RAMP protein Csx7 This CRISPR-associated RAMP protein family, which includes representative protein SSO1426 from Saccharolobus solfataricus P2, was designated Csx7 in PMID:16292354 (2005). TIGR02582.1 TIGR02582 cas7_TM1809 90 80 203 equivalog Y Y N type III-A CRISPR-associated RAMP protein Csm3 csm3 GO:0043571 11788711 131567 cellular organisms no rank 2142 JCVI CRISPR type III-A/MTUBE-associated RAMP protein Csm3 type III-A CRISPR-associated RAMP protein Csm3 Members of this CRISPR-associated (cas) gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm3, for CRISPR/cas Subtype Mtube, protein 3. TIGR02585.1 TIGR02585 cas_Cst2_DevR 72.75 72.75 321 exception Y Y N type I-B CRISPR-associated protein Cas7/Cst2/DevR cas7i GO:0043571 131567 cellular organisms no rank 2500 JCVI CRISPR-associated protein Cas7/Cst2/DevR, subtype I-B/TNEAP type I-B CRISPR-associated protein Cas7/Cst2/DevR CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This clade is a member of the DevR family (TIGR01875) and includes the DevR protein of Myxococcus xanthus, a protein whose expression appears to be regulated through a number of means, including both location and autorepression; DevR mutants are incapable of fruiting body development [1]. TIGR02589.1 TIGR02589 cas_Csd2 182.25 182.25 284 exception Y Y N type I-C CRISPR-associated protein Cas7/Csd2 cas7c GO:0043571 131567 cellular organisms no rank 5981 JCVI CRISPR-associated protein Cas7/Csd2, subtype I-C/DVULG type I-C CRISPR-associated protein Cas7/Csd2 This model represents one of two closely related CRISPR-associated proteins that belong to the larger family of TIGR01595. Members are the Csd2 protein of the Dvulg subtype of CRISPR/cas system. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. The related model is TIGR02590, the Csh2 protein of the Hmari CRISPR subtype. TIGR02590.1 TIGR02590 cas_Csh2 171.55 171.55 286 exception Y Y N type I-B CRISPR-associated protein Cas7/Csh2 cas7b GO:0043571 131567 cellular organisms no rank 1139 JCVI CRISPR-associated protein Cas7/Csh2, subtype I-B/HMARI type I-B CRISPR-associated protein Cas7/Csh2 This model represents one of two closely related CRISPR-associated proteins that belong to the larger family of TIGR01595. Members are the Csh2 protein of the Hmari subtype of CRISPR/cas system. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. The related model is TIGR02589, the Csd3 protein of the Dvulg CRISPR subtype. TIGR02591.1 TIGR02591 cas_Csh1 104.05 104.05 395 hypoth_equivalog_domain Y Y N type I-B CRISPR-associated protein Cas8b/Csh1 cas8b GO:0043571 131567 cellular organisms no rank 800 JCVI CRISPR-associated protein Cas8b/Csh1, subtype I-B/HMARI type I-B CRISPR-associated protein Cas8b/Csh1 This domain is found in the C-terminal 2/3 of a family of CRISPR associated proteins of the Hmari subtype [1]. Except for the two sequences from halophilic archaea this domain contains a pair of CXXC motifs. TIGR02592.1 TIGR02592 cas_Cas5h 97 97 241 exception Y Y N type I-B CRISPR-associated protein Cas5b cas5b GO:0043571 131567 cellular organisms no rank 1596 JCVI CRISPR-associated protein Cas5, subtype I-B/HMARI type I-B CRISPR-associated protein Cas5b This is a CRISPR-associated protein unique to the hmari subtype of cas genes and CRISPR repeat, which is the only subtype present in Haloarcula marismortui ATCC 43049. The hmari type, though uncommon, is also found in the Aquificae, Thermotogae, Firmicutes, and Dictyoglomi. TIGR02593.1 TIGR02593 CRISPR_cas5 17.8 15 43 subfamily_domain Y Y N CRISPR-associated protein Cas5 cas5 GO:0043571 131567 cellular organisms no rank 22671 JCVI CRISPR-associated protein Cas5 CRISPR-associated protein Cas5 This model represents a shared N-terminal domain, about 43 amino acids in length, common to a number of related protein families each of which is associated with a distinct subtype of CRISPR/cas system, where CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeat and Cas is an abbreviation for CRISPR-associated. Members of this family are widely distributed enough that we designated the family Cas5. Homology appears remote, or absent, between the more C-terminal regions different subfamilies of these proteins, which typically are 210 to 265 amino acids in total length. Cas5 proteins of six different CRISPR/cas subtypes so far defined are described by respective full-length models TIGR01868, TIGR01876, TIGR01895, TIGR01874, TIGR02586, and TIGR02592. The best characterized protein in this family is DevS or Myxococcus xanthus, a Cas protein that appears to participate in a species-specific developmental pathway. TIGR02602.1 TIGR02602 8TM_EpsH 105.55 105.55 241 subfamily Y Y N exosortase xrt 3.4.22.- GO:0004197,GO:0006605,GO:0016020,GO:0043687 12624205,16930487,29473278 131567 cellular organisms no rank 7164 JCVI exosortase exosortase This family is designated exosortase, and it is the predicted protein-sorting transpeptidase for the PEP-CTERM protein-sorting signal of many biofilm-producing Gram-negative bacteria. This system is analogous to the sortase/LPXTG system found mostly in Gram-positive bacteria. Members of this family are integral membrane proteins with eight predicted transmembrane helices in common, and with a triad of invariant residues that matches the catalytic triad of sortases. Some members of this family have long trailing sequences past the region described by this model, which in other species is a separate protein EpsI. This model does not include the region of the first predicted transmembrane region. The only partially characterized member is EpsH of Methylobacillus sp. 12S, part of a locus associated with biosynthesis of the exopolysaccharide methanolan but itself not involved in polysaccharide biosynthesis. TIGR02604.1 TIGR02604 Piru_Ver_Nterm 122.2 122.2 367 subfamily_domain Y Y N PVC-type heme-binding CxxCH protein 19133117,37343709 131567 cellular organisms no rank 8285 JCVI putative membrane-bound dehydrogenase domain PVC-type heme-binding CxxCH domain This model represents a domain limited to few species but expanded into large paralogous families in some species that contain it. We find at least 15 member proteins per proteome in PVC superphylum members such as Rhodopirellula baltica SH 1 (phylum Planctomycetota), Gemmata obscuriglobus (phylum Planctomycetota), Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobiota), and Chthoniobacter flavus (phylum Verrucomicrobiota), all of which have a compartmentalized cell structure with internal membranes that most bacteria lack. These proteins typically contain, in addition to this domain, several hundred residues of highly variable sequence, and then a well-conserved C-terminal domain (TIGR02603) that features a putative cytochrome c-type heme binding motif CXXCH. The membrane-bound L-sorbosone dehydrogenase from Acetobacter liquefaciens (Gluconacetobacter liquefaciens) (SP|Q44091) is homologous to this domain but lacks additional sequence regions shared by members of this family and belongs to a different clade of the larger family of homologs. It and its closely related homologs are excluded from the this model by scoring between the trusted (45) and noise (18) cutoffs. TIGR02605.1 TIGR02605 CxxC_CxxC_SSSS 31.3 31.3 52 subfamily_domain Y Y N FmdB family zinc ribbon protein 131567 cellular organisms no rank 35853 JCVI putative regulatory protein, FmdB family FmdB family zinc ribbon protein This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (SP:Q50229, PMID:8841393 ). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors. TIGR02606.1 TIGR02606 antidote_CC2985 46.2 46.2 70 hypoth_equivalog Y Y N type II toxin-antitoxin system ParD family antitoxin GO:0051983 20143871 131567 cellular organisms no rank 18160 JCVI putative addiction module antidote protein, CC2985 family type II toxin-antitoxin system ParD family antitoxin This bacterial protein family has a very similar seed alignment to that of Pfam model PF03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (PF05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15. TIGR02608.1 TIGR02608 delta_60_rpt 76.5 14 55 domain Y N N delta-60 repeat domain 131567 cellular organisms no rank 9599 JCVI delta-60 repeat domain delta-60 repeat domain This domain occurs in tandem repeats, as many as 13, in proteins from Bdellovibrio bacteriovorus, Azotobacter vinelandii, Geobacter sulfurreducens, Pirellula sp. 1, Myxococcus xanthus, and others, many of which are Deltaproteobacteria. The periodicity of the repeat ranges from about 57 to 61 amino acids, and a core region of about 54 is represented by this model and seed alignment. TIGR02619.1 TIGR02619 TIGR02619 37.45 37.45 149 domain Y Y N putative CRISPR-associated protein GO:0043571 131567 cellular organisms no rank 574 JCVI putative CRISPR-associated protein, APE2256 family putative CRISPR-associated protein, APE2256 family This model represents a conserved domain of about 150 amino acids found in at least five archaeal species and three bacterial species, exclusively in species with CRISPR (Clustered Regularly Interspaced Short Palidromic Repeats). In six of eight species, the member of this family is in the vicinity of a CRISPR/Cas locus. TIGR02620.1 TIGR02620 cas_VVA1548 46.35 46.35 93 hypoth_equivalog_domain Y Y N CRISPR-associated protein Csx16 csx16 GO:0043571 131567 cellular organisms no rank 567 JCVI putative CRISPR-associated protein, VVA1548 family CRISPR-associated protein Csx16 This model represents a conserved domain of about 95 amino acids exclusively in species with CRISPR (Clustered Regularly Interspaced Short Palidromic Repeats). In all bacterial species with members so far (Vibrio vulnificus YJ016, Mannheimia succiniciproducens MBEL55E, and Nitrosomonas europaea ATCC 19718) and but not in the archaeon Methanothermobacter thermautotrophicus str. Delta H, the gene for this protein is in the midst of a cluster of Cas protein gene near CRISPR repeats. TIGR02621.1 TIGR02621 cas3_GSU0051 218.25 218.25 864 exception Y Y N type I-U CRISPR-associated helicase/endonuclease Cas3 cas3u GO:0004386,GO:0043571 131567 cellular organisms no rank 1001 JCVI CRISPR-associated helicase Cas3, subtype Dpsyc type I-U CRISPR-associated helicase/endonuclease Cas3 This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs. TIGR02622.1 TIGR02622 CDP_4_6_dhtase 278.45 278.45 352 equivalog Y Y N CDP-glucose 4,6-dehydratase rfbG 4.2.1.45 GO:0009243,GO:0047733 15023057,9367902 131567 cellular organisms no rank 11601 JCVI CDP-glucose 4,6-dehydratase CDP-glucose 4,6-dehydratase Members of this protein family are CDP-glucose 4,6-dehydratase from a variety of Gram-negative and Gram-positive bacteria. Members typically are encoded next to a gene that encodes a glucose-1-phosphate cytidylyltransferase, which produces the substrate, CDP-D-glucose, used by this enzyme to produce CDP-4-keto-6-deoxyglucose. TIGR02623.1 TIGR02623 G1P_cyt_trans 300.25 300.25 255 equivalog Y Y N glucose-1-phosphate cytidylyltransferase rfbF 2.7.7.33 GO:0009243,GO:0047343 15292268,15634670,1710759 131567 cellular organisms no rank 11351 JCVI glucose-1-phosphate cytidylyltransferase glucose-1-phosphate cytidylyltransferase Members of this family are the enzyme glucose-1-phosphate cytidylyltransferase, also called CDP-glucose pyrophosphorylase, the product of the rfbF gene. TIGR02640.1 TIGR02640 gas_vesic_GvpN 266.8 266.8 262 equivalog Y Y N gas vesicle protein GvpN gvpN GO:0000166,GO:0005524,GO:0031411,GO:0031412 131567 cellular organisms no rank 1227 JCVI gas vesicle protein GvpN gas vesicle protein GvpN Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (PF07728). TIGR02644.1 TIGR02644 Y_phosphoryl 409.05 409.05 417 subfamily Y Y N pyrimidine-nucleoside phosphorylase pdp GO:0006213,GO:0016154 131567 cellular organisms no rank 43593 JCVI pyrimidine-nucleoside phosphorylase pyrimidine-nucleoside phosphorylase In general, members of this protein family are designated pyrimidine-nucleoside phosphorylase, enzyme family EC 2.4.2.2, as in Bacillus subtilis, and more narrowly as the enzyme family EC 2.4.2.4, thymidine phosphorylase (alternate name: pyrimidine phosphorylase), as in Escherichia coli. The set of proteins encompassed by this model is designated subfamily rather than equivalog for this reason; the protein name from this model should be used when TIGR02643 does not score above trusted cutoff. TIGR02645.1 TIGR02645 ARCH_P_rylase 434.6 434.6 493 hypoth_equivalog Y N N putative thymidine phosphorylase GO:0016763 131567 cellular organisms no rank 3976 JCVI putative thymidine phosphorylase putative thymidine phosphorylase Members of this family are closely related to characterized examples of thymidine phosphorylase (EC 2.4.2.4) and pyrimidine nucleoside phosphorylase (RC 2.4.2.2). Most examples are found in the archaea, but other examples in Legionella pneumophila str. Paris and Rhodopseudomonas palustris CGA009. TIGR02646.1 TIGR02646 TIGR02646 52.15 52.15 144 subfamily Y Y N retron system putative HNH endonuclease GO:0051607 33157039 131567 cellular organisms no rank 3621 JCVI TIGR02646 family protein retron system putative HNH endonuclease Members of this uncharacterized protein family are found exclusively in bacteria. Neighboring genes in various genomes are also uncharacterized or may annotated as similar to restriction system proteins. TIGR02651.1 TIGR02651 RNase_Z 292.95 292.95 302 equivalog Y Y N ribonuclease Z rnz 3.1.26.11 GO:0016891,GO:0042780 131567 cellular organisms no rank 23260 JCVI ribonuclease Z ribonuclease Z Processing of the 3-prime end of tRNA precursors may be the result of endonuclease or exonuclease activity, and differs in different species. Member of this family are ribonuclease Z, a tRNA 3-prime endonuclease that processes tRNAs to prepare for addition of CCA. In species where all tRNA sequences already have the CCA tail, such as E. coli, the need for such an enzyme is unclear. Protein similar to the E. coli enzyme, matched by TIGRFAMs HMM TIGR02649, are designated ribonuclease BN. TIGR02653.1 TIGR02653 Lon_rel_chp 628.25 628.25 675 hypoth_equivalog Y Y N protease Lon-related BREX system protein BrxL brxL 25452498 131567 cellular organisms no rank 3840 JCVI conserved hypothetical protein protease Lon-related BREX system protein BrxL This model describes a protein family of unknown function, about 690 residues in length, in which some members show C-terminal sequence similarity to Pfam model PF05362, which is the Lon protease C-terminal proteolytic domain, from MEROPS family S16. However, the annotated catalytic sites of E. coli Lon protease are not conserved in members of this family. Members have a motif GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif GxxGxGK[ST]. TIGR02660.1 TIGR02660 nifV_homocitr 462.9 462.9 365 equivalog Y Y N homocitrate synthase nifV 2.3.3.14 GO:0004410 9294461 131567 cellular organisms no rank 3742 JCVI homocitrate synthase homocitrate synthase This family consists of the NifV clade of homocitrate synthases, most of which are found in operons for nitrogen fixation. Members are closely homologous to enzymes that include 2-isopropylmalate synthase, (R)-citramalate synthase, and homocitrate synthases associated with other processes. The homocitrate made by this enzyme becomes a part of the iron-molybdenum cofactor of nitrogenase. TIGR02666.1 TIGR02666 moaA 284.05 284.05 336 equivalog Y Y N GTP 3',8-cyclase MoaA moaA 4.1.99.22 GO:0006777,GO:0046872,GO:0051539 31235512 131567 cellular organisms no rank 65890 JCVI molybdenum cofactor biosynthesis protein A GTP 3',8-cyclase MoaA The model for this family describes molybdenum cofactor biosynthesis protein A, or MoaA, as found in bacteria. It does not include the family of probable functional equivalent proteins from the archaea. MoaA works together with MoaC to synthesize precursor Z from guanine. TIGR02682.1 TIGR02682 cas_csx11 248.95 248.95 1007 equivalog Y Y N CRISPR-associated protein Csx11 GO:0043571 131567 cellular organisms no rank 178 JCVI CRISPR-associated protein, Csx11 family CRISPR-associated protein Csx11 Members of this uncommon, sporadically distributed protein family are large (>900 amino acids) and strictly associated, so far, with CRISPR-associated (Cas) gene clusters. Nearby Cas genes always include members of the RAMP superfamily and the six-gene CRISPR-associated RAMP module. Species in which it is found, so far, include three archaea (Methanosarcina mazei, M. barkeri and Methanobacterium thermoautotrophicum) and two bacteria (Thermodesulfovibrio yellowstonii DSM 11347 and Sulfurihydrogenibium azorense). TIGR02683.1 TIGR02683 upstrm_HI1419 62.85 62.85 95 hypoth_equivalog Y Y N type II toxin-antitoxin system RelE/ParE family toxin GO:0004540,GO:0008219 27455323 131567 cellular organisms no rank 11751 JCVI putative addiction module killer protein type II toxin-antitoxin system RelE/ParE family toxin Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the upstream member of a gene pair, where the downstream member is a predicted DNA-binding protein from a clade within Pfam helix-turn-helix family PF01381. These gene pairs, when found on the bacterial chromosome, often are located with prophage regions, but also in both integrated plasmid regions and near housekeeping genes. Ssl7039 was characterized as a ribonuclease toxin. TIGR02684.1 TIGR02684 dnstrm_HI1420 53.7 53.7 89 hypoth_equivalog Y Y N addiction module antidote protein GO:0003677 131567 cellular organisms no rank 10716 JCVI probable addiction module antidote protein addiction module antidote protein Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the downstream member of a gene pair. It is a predicted DNA-binding protein from a clade within Pfam helix-turn-helix family PF01381. These gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module. TIGR02687.1 TIGR02687 TIGR02687 270.35 270.35 844 equivalog Y Y N BREX-1 system phosphatase PglZ type A pglZ GO:0003824 25452498 131567 cellular organisms no rank 6085 JCVI TIGR02687 family protein BREX-1 system phosphatase PglZ type A Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 880 amino acids in length. This protein is repeatedly found upstream of another uncharacterized protein of about 470 amino acids in length, modeled by TIGR02688. TIGR02688.1 TIGR02688 TIGR02688 329.3 329.3 449 equivalog Y Y N BREX system Lon protease-like protein BrxL brxL GO:0004176,GO:0030163 25452498 131567 cellular organisms no rank 6746 JCVI TIGR02688 family protein BREX system Lon protease-like protein BrxL Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or PF02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687. TIGR02693.1 TIGR02693 arsenite_ox_L 359.05 359.05 806 equivalog Y Y N arsenate reductase (azurin) large subunit 1.20.9.1 GO:0050611 12679550 131567 cellular organisms no rank 1043 JCVI arsenite oxidase, large subunit arsenate reductase (azurin) large subunit This model represents the large subunit of an arsenite oxidase complex. The small subunit is a Rieske protein. Homologs to both large and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7. This enzyme acts in energy metabolim by arsenite oxidation, rather than detoxification by reduction of arsenate to arsenite prior to export. TIGR02694.1 TIGR02694 arsenite_ox_S 95.65 95.65 129 equivalog Y Y N arsenate reductase (azurin) small subunit 1.20.9.1 GO:0050611 12679550 131567 cellular organisms no rank 1019 JCVI arsenite oxidase, small subunit arsenate reductase (azurin) small subunit This model represents the small subunit of an arsenite oxidase complex. It is a Rieske protein and appears to rely on the Tat (twin-arginine translocation) system to cross the membrane. Although this enzyme could run in the direction of arsenate reduction to arsenite in principle, the relevant biological function is arsenite oxidation for energy metabolism, not arsenic resistance. Homologs to both large (TIGR02693) and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7. TIGR02699.1 TIGR02699 archaeo_AfpA 192.45 192.45 174 hypoth_equivalog Y Y N archaeoflavoprotein AfpA afpA 14679228 131567 cellular organisms no rank 228 JCVI archaeoflavoprotein AfpA archaeoflavoprotein AfpA The prototypical member of this archaeal protein family is AF1518 from Archaeoglobus fulgidus. This homodimer with two non-covalently bound FMN cofactors can receive electrons from ferredoxin, but not from a number of other electron donors such as NADH or rubredoxin. It can then donate electrons to various reductases. TIGR02710.1 TIGR02710 TIGR02710 83.9 83.9 384 equivalog Y Y N TIGR02710 family CRISPR-associated CARF protein GO:0043571 16292354,24817877 131567 cellular organisms no rank 687 JCVI CRISPR-associated protein, TIGR02710 family TIGR02710 family CRISPR-associated CARF protein Members of this family are found, exclusively in the vicinity of CRISPR repeats and other CRISPR-associated (cas) genes, in Methanothermobacter thermautotrophicus (Archaea), Thermus thermophilus (Deinococcus-Thermus), Chloroflexus aurantiacus (Chloroflexi), and Thermomicrobium roseum (Thermomicrobia). TIGR02713.1 TIGR02713 allophanate_hyd 511.05 511.05 563 equivalog Y Y N allophanate hydrolase atzF 3.5.1.54 GO:0004039,GO:0019627 15090492,15901697 131567 cellular organisms no rank 20282 JCVI allophanate hydrolase allophanate hydrolase Allophanate hydrolase catalyzes the second reaction in an ATP-dependent two-step degradation of urea to ammonia and C02, following the action of the biotin-containing urea carboxylase. The yeast enzyme, a fusion of allophanate hydrolase to urea carboxylase, is designated urea amidolyase. TIGR02717.1 TIGR02717 AcCoA-syn-alpha 567.15 567.15 447 equivalog_domain Y Y N acetate--CoA ligase alpha subunit acs GO:0003985,GO:0046356 10375639,11069669,8830684 131567 cellular organisms no rank 739 JCVI acetyl coenzyme A synthetase (ADP forming), alpha domain acetate--CoA ligase alpha subunit/domain Although technically reversible, it is believed that this group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which it has been characterized [1,2,3]. In most species this protein exists as a fused alpha-beta domain polypeptide. In Pyrococcus and related species, however the domains exist as separate polypeptides. This model represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. In reference [1], one of these (along with its beta-domain partner) was characterized as ACS-II showing specificity for phenylacetyl-CoA. This model has been constructed to exclude these non-ACS-I paralogs. This may result in new, authentic ACS-I sequences falling below the trusted cutoff. TIGR02724.1 TIGR02724 phenyl_P_beta 468.95 468.95 472 equivalog Y Y N phenylphosphate carboxylase subunit beta ppcB 15231788 131567 cellular organisms no rank 59 JCVI phenylphosphate carboxylase, beta subunit phenylphosphate carboxylase subunit beta Members of this protein family are the beta subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. This beta subunit is homologous to the alpha subunit and, more broadly, to UbiD family decarboxylases. TIGR02727.1 TIGR02727 MTHFS_bact 84.9 84.9 182 equivalog Y Y N 5-formyltetrahydrofolate cyclo-ligase 6.3.3.2 GO:0006730,GO:0030272 16104022 131567 cellular organisms no rank 75309 JCVI 5-formyltetrahydrofolate cyclo-ligase 5-formyltetrahydrofolate cyclo-ligase This enzyme, 5,10-methenyltetrahydrofolate synthetase, is also called 5-formyltetrahydrofolate cycloligase. Function of bacterial proteins in this family was inferred originally from the known activity of eukaryotic homologs. Recently, activity was shown explicitly for the member from Mycoplasma pneumonia. Members of this family from alpha- and gamma-proteobacteria, designated ygfA, are often found in an operon with 6S structural RNA, and show a similar pattern of high expression during stationary phase. The function may be to deplete folate to slow 1-carbon biosynthetic metabolism. TIGR02734.1 TIGR02734 crtI_fam 238.1 238.1 504 subfamily Y Y N phytoene desaturase family protein crtI 1.-.-.- GO:0016117,GO:0016166 131567 cellular organisms no rank 41016 JCVI phytoene desaturase phytoene desaturase family protein Phytoene is converted to lycopene by desaturation at four (two symmetrical pairs of) sites. This is achieved by two enzymes (crtP and crtQ) in cyanobacteria (Gloeobacter being an exception) and plants, but by a single enzyme in most other bacteria and in fungi. This single enzyme is called the bacterial-type phytoene desaturase, or CrtI. Most members of this family, part of the larger Pfam family PF01593, which also contains amino oxidases, are CrtI itself; it is likely that all members act on either phytoene or on related compounds such as dehydrosqualene, for carotenoid biosynthesis. TIGR02751.1 TIGR02751 PEPCase_arch 146.05 146.05 506 equivalog Y Y N phosphoenolpyruvate carboxylase ppcA 4.1.1.31 GO:0008964 15262949,15516590 131567 cellular organisms no rank 830 JCVI phosphoenolpyruvate carboxylase phosphoenolpyruvate carboxylase This family is the archaeal-type phosphoenolpyruvate carboxylase, although not every host species is archaeal. These sequences bear little resemblance to the bacterial/eukaryotic type. The members from Sulfolobus solfataricus and Methanothermobacter thermautotrophicus were verified experimentally, while the activity is known to be present in a number of other archaea. TIGR02753.1 TIGR02753 sodN 90 90 145 equivalog Y Y N superoxide dismutase, Ni sodN 1.15.1.1 GO:0004784,GO:0016151,GO:0019430 15516600 131567 cellular organisms no rank 3988 JCVI superoxide dismutase, Ni superoxide dismutase, Ni This superoxide dismutase uses nickel, rather than iron, manganese, copper, or zinc. Its gene is always accompanied by a gene for a required protease. TIGR02754.1 TIGR02754 sod_Ni_protease 63.25 63.25 90 equivalog Y Y N nickel-type superoxide dismutase maturation protease sodX GO:0004252,GO:0016485,GO:0019430 15516600 131567 cellular organisms no rank 4817 JCVI nickel-type superoxide dismutase maturation protease nickel-type superoxide dismutase maturation protease Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model PF00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad. TIGR02765.1 TIGR02765 crypto_DASH 317.05 317.05 431 subfamily Y Y N DASH family cryptochrome GO:0003913,GO:0006281 10871367,15147276 131567 cellular organisms no rank 7976 JCVI cryptochrome, DASH family DASH family cryptochrome Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes. TIGR02772.1 TIGR02772 Ku_bact 204.3 204.3 259 equivalog Y Y N Ku protein GO:0006303,GO:0045027 15499016,25767122 131567 cellular organisms no rank 45039 JCVI Ku protein Ku protein Members of this protein family are Ku proteins of non-homologous end joining (NHEJ) DNA repair in bacteria and in at least one member of the archaea (Archaeoglobus fulgidus). Most members are encoded by a gene adjacent to the gene for the DNA ligase that completes the repair. The NHEJ system is broadly but rather sparsely distributed, being present in about one fifth of the first 250 completed prokarytotic genomes. A few species (e.g. Archaeoglobus fulgidus and Bradyrhizobium japonicum) have multiple copies that appear to represent recent paralogous family expansion. TIGR02776.1 TIGR02776 NHEJ_ligase_prk 373.2 373.2 587 equivalog Y Y N DNA ligase D ligD 6.5.1.1 GO:0006303 16046407 131567 cellular organisms no rank 25206 JCVI DNA ligase D DNA ligase D Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this HMM. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; this HMM models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku. TIGR02777.1 TIGR02777 LigD_PE_dom 144 144 156 equivalog_domain Y N N DNA ligase D, 3'-phosphoesterase domain ligD 16046407 131567 cellular organisms no rank 31801 JCVI DNA ligase D, 3'-phosphoesterase domain DNA ligase D, 3'-phosphoesterase domain Most sequences in this family are the 3'-phosphoesterase domain of a multidomain, multifunctional DNA ligase, LigD, involved, along with bacterial Ku protein, in non-homologous end joining, the less common of two general mechanisms of repairing double-stranded breaks in DNA sequences. LigD is variable in architecture, as it lacks this domain in Bacillus subtilis, is permuted in Mycobacterium tuberculosis, and occasionally is encoded by tandem ORFs rather than as a multifuntional protein. In a few species (Dehalococcoides ethenogenes and the archaeal genus Methanosarcina), sequences corresponding to the ligase and polymerase domains of LigD are not found, and the role of this protein is unclear. TIGR02778.1 TIGR02778 ligD_pol 214.7 214.7 245 equivalog_domain Y Y N non-homologous end-joining DNA ligase ligD 6.5.1.1 131567 cellular organisms no rank 62859 JCVI DNA ligase D, polymerase domain non-homologous end-joining DNA ligase, polymerase domain DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide designated LigD in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain of LigD. Many species have multiple forms of LigD. TIGR02779.1 TIGR02779 NHEJ_ligase_lig 227.75 227.75 302 equivalog_domain Y Y N non-homologous end-joining DNA ligase ligD GO:0003910,GO:0005524,GO:0006281,GO:0006310 16046407 131567 cellular organisms no rank 41741 JCVI DNA ligase D, ligase domain non-homologous end-joining DNA ligase, ligase domain DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the ligase domain. TIGR02822.1 TIGR02822 adh_fam_2 283.5 283.5 329 subfamily Y Y N zinc-binding alcohol dehydrogenase family protein 1.-.-.- GO:0004022,GO:0006113,GO:0008270 131567 cellular organisms no rank 11836 JCVI zinc-binding alcohol dehydrogenase family protein zinc-binding alcohol dehydrogenase family protein Members of this model form a distinct subset of the larger family of oxidoreductases that includes zinc-binding alcohol dehydrogenases and NADPH:quinone reductases (PF00107). The gene neighborhood of members of this family is not conserved and it appears that no members are characterized. The sequence of the family includes 6 invariant cysteine residues and one invariant histidine. It appears that no member is characterized. TIGR02824.1 TIGR02824 quinone_pig3 296.8 296.8 325 subfamily Y N N putative NAD(P)H quinone oxidoreductase, PIG3 family GO:0008152,GO:0016655 131567 cellular organisms no rank 44524 JCVI putative NAD(P)H quinone oxidoreductase, PIG3 family putative NAD(P)H quinone oxidoreductase, PIG3 family Members of this family are putative quinone oxidoreductases that belong to the broader superfamily (modeled by Pfam PF00107) of zinc-dependent alcohol (of medium chain length) dehydrogenases and quinone oxiooreductases. The alignment shows no motif of conserved Cys residues as are found in zinc-binding members of the superfamily, and members are likely to be quinone oxidoreductases instead. A member of this family in Homo sapiens, PIG3, is induced by p53 but is otherwise uncharacterized. TIGR02826.1 TIGR02826 RNR_activ_nrdG3 151.7 151.7 148 equivalog Y Y N anaerobic ribonucleoside-triphosphate reductase activating protein nrdG GO:0008998,GO:0009265,GO:0043364,GO:0051536 15949864 131567 cellular organisms no rank 1340 JCVI anaerobic ribonucleoside-triphosphate reductase activating protein anaerobic ribonucleoside-triphosphate reductase activating protein Members of this family represent a set of radical SAM enzymes related to, yet architecturally different from, the activating protein for the glycine radical-containing, oxygen-sensitive ribonucleoside-triphosphate reductase (RNR) as described in model TIGR02491. Members of this family are found paired with members of a similarly divergent set of anaerobic ribonucleoside-triphosphate reductases. Identification of this protein as an RNR activitating protein is partly from pairing with a candidate RNR. It is further supported by our finding that upstream of these operons are examples of a conserved regulatory element (described Rodionov and Gelfand) that is found in nearly all bacteria and that occurs specifically upstream of operons for all three classes of RNR genes. TIGR02827.1 TIGR02827 RNR_anaer_Bdell 568.3 568.3 596 equivalog Y Y N anaerobic ribonucleoside-triphosphate reductase nrdD GO:0006260,GO:0008998,GO:0016491 15949864 131567 cellular organisms no rank 1906 JCVI anaerobic ribonucleoside-triphosphate reductase anaerobic ribonucleoside-triphosphate reductase Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons. TIGR02832.1 TIGR02832 spo_yunB 111.9 111.9 204 equivalog Y Y N sporulation protein YunB yunB GO:0030436 12662922,16311624 131567 cellular organisms no rank 5363 JCVI sporulation protein YunB sporulation protein YunB A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. Mutation of this sigma E-regulated gene, designated yunB, has been shown to cause a sporulation defect. TIGR02862.1 TIGR02862 spore_BofA 53.35 53.35 83 subfamily Y Y N pro-sigmaK processing inhibitor BofA bofA GO:0016020,GO:0030436 11959848 131567 cellular organisms no rank 2328 JCVI pro-sigmaK processing inhibitor BofA pro-sigmaK processing inhibitor BofA Members of this protein family are found only in endospore-forming bacteria, such as Bacillus subtilis and Clostridium tetani. Among such bacteria, it appears only Symbiobacterium thermophilum lacks a member of this family. The protein, designated BofA, is an integral membrane protein that regulates the proteolytic activation of the RNA polymerase sigma factor K. TIGR02866.1 TIGR02866 CoxB 147.7 147.7 202 equivalog Y Y N cytochrome c oxidase subunit II coxB 7.1.1.9 GO:0004129,GO:0016020 9380672 131567 cellular organisms no rank 40851 JCVI cytochrome c oxidase, subunit II cytochrome c oxidase subunit II Cytochrome c oxidase is the terminal electron acceptor of mitochondria (and one of several possible acceptors in prokaryotes) in the electron transport chain of aerobic respiration. The enzyme couples the oxidation of reduced cytochrome c with the reduction of molecular oxygen to water. This process results in the pumping of four protons across the membrane which are used in the proton gradient powered synthesis of ATP. The oxidase contains two heme a cofactors and three copper atoms as well as other bound ions [1]. TIGR02868.1 TIGR02868 CydC 329.05 329.05 530 equivalog Y Y N thiol reductant ABC exporter subunit CydC cydC GO:0005524,GO:0016020,GO:0033228,GO:0033230,GO:0045454,GO:0050456,GO:0055051 12393891,16040611,32900959,9335308 131567 cellular organisms no rank 47045 JCVI thiol reductant ABC exporter, CydC subunit thiol reductant ABC exporter subunit CydC The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (PF00664) and a C-terminal ATP-binding domain (PF00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione [1,2]. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex. Recently, it has been shown that CydDC also function as a cytoplasmic cystine reductase (PMID: 32900959). TIGR02891.1 TIGR02891 CtaD_CoxA 670.75 670.75 504 equivalog Y Y N cytochrome c oxidase subunit I ctaD 7.1.1.9 GO:0004129,GO:0015990 131567 cellular organisms no rank 55557 JCVI cytochrome c oxidase, subunit I cytochrome c oxidase subunit I This large family represents subunit I's (CtaD, CoxA, CaaA) of cytochrome c oxidases of bacterial origin. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Subunits I-III form the functional core of the enzyme complex. Subunit I is the catalytic subunit of the enzyme. Electrons originating in cytochrome c are transferred via the copper A center of subunit II and heme a of subunit I to the bimetallic center formed by heme a3 and copper B. This cytochrome c oxidase shows proton pump activity across the membrane in addition to the electron transfer. In the bacilli an apparent split (paralogism) has created a sister clade (TIGR02882) encoding subunits (QoxA) of the aa3-type quinone oxidase complex which reacts directly with quinones, bypassing the interaction with soluble cytochrome c. This model attempts to exclude these sequences, placing them between the trusted and noise cutoffs. These families, as well as archaeal and eukaryotic cytochrome c subunit I's are included within the superfamily model, PF00115. TIGR02913.1 TIGR02913 HAF_rpt 22.65 22.65 39 repeat Y N N HAF repeat protein 131567 cellular organisms no rank 5506 JCVI probable extracellular repeat, HAF family HAF repeat The HMM for this family detects a homology domain of about 40 amino acids. Member proteins always have a least two tandem copies and as many as seven. The spacing between repeats as defined here usually is four residues exactly. This repeat is named for a tripeptide motif HAF found in most members. Some members proteins are found in species with no outer membrane (archaea and Gram-positive bacteria) while others have C-terminal autotransporter domains that suggest that the repeat region is transported across the outer membrane. This domain seems likely to be an extracellular protein repeat. TIGR02923.1 TIGR02923 AhaC 240.5 240.5 348 equivalog Y Y N ATP synthase A1 subunit C ahaC GO:0033179,GO:0046961 8702544 131567 cellular organisms no rank 1142 JCVI ATP synthase A1, C subunit ATP synthase A1 subunit C The A1/A0 ATP synthase is homologous to the V-type (V1/V0, vacuolar) ATPase, but functions in the ATP synthetic direction as does the F1/F0 ATPase of bacteria. The C subunit is part of the hydrophilic A1 "stalk" complex (AhaABCDEFG) [1] which is the site of ATP generation and is coupled to the membrane-embedded proton translocating A0 complex. TIGR02926.1 TIGR02926 AhaH 48.5 48.5 85 equivalog Y Y N ATP synthase archaeal subunit H ahaH 7.1.2.2 131567 cellular organisms no rank 818 JCVI ATP synthase archaeal, H subunit ATP synthase archaeal subunit H he A1/A0 ATP synthase is homologous to the V-type (V1/V0, vacuolar) ATPase, but functions in the ATP synthetic direction as does the F1/F0 ATPase of bacteria. The hydrophilic A1 "stalk" complex (AhaABCDEFG) [1] is the site of ATP generation and is coupled to the membrane-embedded proton translocating A0 complex. It is unclear precisely where AhaH fits into these complexes. TIGR02928.1 TIGR02928 TIGR02928 181.3 181.3 366 subfamily Y N N orc1/cdc6 family replication initiation protein 16179962 131567 cellular organisms no rank 6673 JCVI orc1/cdc6 family replication initiation protein orc1/cdc6 family replication initiation protein Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other. TIGR02929.1 TIGR02929 anfG_nitrog 124.7 124.7 109 equivalog Y Y N Fe-only nitrogenase subunit delta anfG 1.18.6.1 GO:0005506,GO:0009399,GO:0016163,GO:0051536 131567 cellular organisms no rank 259 JCVI Fe-only nitrogenase, delta subunit Fe-only nitrogenase subunit delta Nitrogenase, also called dinitrogenase, is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, AnfG, represents the delta subunit of the Fe-only alternative nitrogenase. It is homologous to VnfG, the delta subunit of the V-containing (vanadium) nitrogenase. TIGR02930.1 TIGR02930 vnfG_nitrog 141.7 141.7 109 equivalog Y Y N V-containing nitrogenase subunit delta vnfG 1.18.6.1 GO:0009399,GO:0016163,GO:0046872 131567 cellular organisms no rank 156 JCVI V-containing nitrogenase, delta subunit V-containing nitrogenase subunit delta Nitrogenase is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, VnfG, represents the delta subunit of the V-containing (vanadium) alternative nitrogenase. It is homologous to AnfG, the delta subunit of the Fe-only nitrogenase. TIGR02931.1 TIGR02931 anfK_nitrog 853.85 853.85 461 equivalog Y Y N Fe-only nitrogenase subunit beta anfK 1.18.6.1 GO:0009399,GO:0016163 131567 cellular organisms no rank 279 JCVI Fe-only nitrogenase, beta subunit Fe-only nitrogenase subunit beta Nitrogenase is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, AnfK, represents the beta subunit of the iron-only alternative nitrogenase. It is homologous to NifK and VnfK, of the molybdenum-containing and the vanadium (V)-containing types, respectively. TIGR02932.1 TIGR02932 vnfK_nitrog 873.95 873.95 457 equivalog Y Y N V-containing nitrogenase subunit beta vnfK 1.18.6.1 GO:0009399,GO:0016163,GO:0016613,GO:0051536 131567 cellular organisms no rank 149 JCVI V-containing nitrogenase, beta subunit V-containing nitrogenase subunit beta Nitrogenase is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, VnfK, represents the beta subunit of the vanadium (V)-containing alternative nitrogenase. It is homologous to NifK and AnfK, of the molybdenum-containing and the iron (Fe)-only types, respectively. TIGR02940.1 TIGR02940 anfO_nitrog 129.15 129.15 214 equivalog Y Y N Fe-only nitrogenase accessory protein AnfO anfO 15601692 131567 cellular organisms no rank 221 JCVI Fe-only nitrogenase accessory protein AnfO Fe-only nitrogenase accessory protein AnfO Members of this protein family, called Anf1 in Rhodobacter capsulatus and AnfO in Azotobacter vinelandii, are found only in species with the Fe-only nitrogenase and are encoded immediately downstream of the structural genes in the above named species. TIGR02953.1 TIGR02953 penta_MxKDx 41 41 78 subfamily Y Y N pentapeptide MXKDX repeat protein 131567 cellular organisms no rank 3117 JCVI pentapeptide MXKDX repeat protein pentapeptide MXKDX repeat protein Members of this protein family are small bacterial proteins, each with an N-terminal signal sequence followed by up to 11 imperfect repeats of a pentapeptide. The pentapeptide repeat usually follows the form Met-Xaa-Lys-Asp-Xaa. TIGR02962.1 TIGR02962 hdxy_isourate 87.45 87.45 113 equivalog Y Y N hydroxyisourate hydrolase uraH 3.5.2.17 GO:0006144,GO:0033971 16098976,17085964,21795808 131567 cellular organisms no rank 28626 JCVI hydroxyisourate hydrolase hydroxyisourate hydrolase Members of this family, hydroxyisourate hydrolase, represent a distinct clade of transthyretin-related proteins. Bacterial members typically are encoded next to ureidoglycolate hydrolase and often near either xanthine dehydrogenase or xanthine/uracil permease genes and have been demonstrated to have hydroxyisourate hydrolase activity [1]. In eukaryotes, a clade separate from the transthyretins (a family of thyroid-hormone binding proteins) has also been shown to have HIU hydrolase activity in urate catabolizing organisms [2]. Transthyretin, then, would appear to be the recently diverged paralog of the more ancient HIUH family. TIGR02967.1 TIGR02967 guan_deamin 375.4 375.4 401 equivalog Y Y N guanine deaminase guaD 3.5.4.3 GO:0006147,GO:0008270,GO:0008892 10913105 131567 cellular organisms no rank 25663 JCVI guanine deaminase guanine deaminase This model describes guanine deaminase, which hydrolyzes guanine to xanthine and ammonia. Xanthine can then be converted to urate by xanthine dehydrogenase, and urate subsequently degraded. In some bacteria, the guanine deaminase gene is found near the xdhABC genes for xanthine dehydrogenase. Non-homologous forms of guanine deaminase also exist, as well as distantly related forms outside the scope of this model. TIGR02970.1 TIGR02970 succ_dehyd_cytB 52.3 52.3 120 equivalog Y Y N succinate dehydrogenase, cytochrome b556 subunit sdhC GO:0000104,GO:0006099,GO:0009055,GO:0045273 131567 cellular organisms no rank 23351 JCVI succinate dehydrogenase, cytochrome b556 subunit succinate dehydrogenase, cytochrome b556 subunit In E. coli and many other bacteria, two small, hydrophobic, mutually homologous subunits of succinate dehydrogenase, a TCA cycle enzyme, are SdhC and SdhD. This family is the SdhC, the cytochrome b subunit, called b556 in bacteria and b560 in mitochondria. SdhD (see TIGR02968) is called the hydrophobic membrane anchor subunit, although both SdhC and SdhD participate in anchoring the complex. In some bacteria, this cytochrome b subunit is replaced my a member of the cytochrome b558 family (see TIGR02046). TIGR03006.1 TIGR03006 pepcterm_polyde 276.2 276.2 272 equivalog Y Y N XrtA system polysaccharide deacetylase 16930487 131567 cellular organisms no rank 3739 JCVI polysaccharide deacetylase family protein, PEP-CTERM locus subfamily XrtA system polysaccharide deacetylase Members of this protein family belong to the family of polysaccharide deacetylases (PF01522). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. The highest scoring homologs below the trusted cutoff for this model are found in several species of Methanosarcina, an archaeal genus. TIGR03011.1 TIGR03011 sulf_tusB_dsrH 49.2 49.2 95 equivalog_domain Y Y N sulfurtransferase complex subunit TusB tusB GO:0002098,GO:0016782 16387657,9695921 131567 cellular organisms no rank 8335 JCVI sulfur relay protein TusB/DsrH sulfurtransferase complex subunit TusB The three proteins TusB, TusC, and TusD form a heterohexamer responsible for a sulfur relay reaction. In large numbers of proteobacterial species, this complex acts on a Cys-derived persulfide moiety, delivered by the cysteine desulfurase IscS to TusA, then to TusBCD. The activated sulfur group is then transferred to TusE (DsrC), then by MnmA (TrmU) for modification of an anticodon nucleotide in tRNAs for Glu, Lys, and Gln. The sulfur relay complex TusBCD is also found, under the designation DsrEFH, in phototrophic and chemotrophic sulfur bacteria, such as Chromatium vinosum. In these organisms, it seems the primary purpose is related to sulfur flux, such as oxidation from sulfide to molecular sulfur to sulfate. TIGR03019.1 TIGR03019 pepcterm_femAB 260.35 260.35 330 equivalog Y Y N FemAB family XrtA/PEP-CTERM system-associated protein 16930487,29473278 131567 cellular organisms no rank 3380 JCVI FemAB-related protein, PEP-CTERM system-associated FemAB family XrtA/PEP-CTERM system-associated protein Members of this protein family are found always as part of extended exopolysaccharide biosynthesis loci in bacteria. In nearly every case, these loci contain determinants for the processing of the PEP-CTERM proposed C-terminal protein sorting signal. This family shows remote, local sequence similarity to the FemA and FemB family of cell wall peptidyl transferases (see PF02388). TIGR03023.1 TIGR03023 WcaJ_sugtrans 410.75 410.75 453 equivalog Y Y N undecaprenyl-phosphate glucose phosphotransferase 2.7.8.31 GO:0016780 12624205,318640,8626328,9537354 131567 cellular organisms no rank 27289 JCVI undecaprenyl-phosphate glucose phosphotransferase undecaprenyl-phosphate glucose phosphotransferase This family of proteins encompasses the E. coli WcaJ protein involved in colanic acid biosynthesis [1], the Methylobacillus EpsB protein involved in methanolan biosynthesis [2], as well as the GumD protein involved in the biosynthesis of xanthan [3]. All of these are closely related to the well-characterized WbaP (formerly RfbP) protein [4] which is the first enzyme in O-antigen biosynthesis in Salmonella typhimurium. The enzyme transfers galactose from UDP-galactose (NOTE: not glucose) to a polyprenyl carrier (utilizing the highly conserved C-terminal sugar transferase domain, PF02397) a reaction which takes place at the cytoplasmic face of the inner membrane. The N-terminal hydrophobic domain is then believed to facilitate the "flippase" function of transferring the liposaccharide unit from the cytoplasmic face to the periplasmic face of the inner membrane. Most of these genes are found within large operons dedicated to the production of complex exopolysaccharides such as the enterobacterial O-antigen. Colanic acid biosynthesis utilizes a glucose-undecaprenyl carrier [1], knockout of EpsB abolishes incorporation of UDP-glucose into the lipid phase [2] and the C-terminal portion of GumD has been shown to be responsible for the glucosyl-1-transferase activity [3]. TIGR03025.1 TIGR03025 EPS_sugtrans 295.55 295.55 445 subfamily Y Y N exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase GO:0003677,GO:0003678,GO:0005524,GO:0006260,GO:0032508 10085014,10515924,12624205,12949095,14769477,318640,7596293,8355611,8626328,9537354 131567 cellular organisms no rank 85897 JCVI exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase Members of this family are generally found near other genes involved in the biosynthesis of a variety of exopolysaccharides. These proteins consist of two fused domains, an N-terminal hydrophobic domain of generally low conservation and a highly conserved C-terminal sugar transferase domain (PF02397). Characterized and partially characterized members of this subfamily include Salmonella WbaP (originally RfbP) [1], E. coli WcaJ [2], Methylobacillus EpsB [3], Xanthomonas GumD [4], Vibrio CpsA [5], Erwinia AmsG [6], Group B Streptococcus CpsE (originally CpsD) [7], and Streptococcus suis Cps2E [8]. Each of these is believed to act in transferring the sugar from, for instance, UDP-glucose or UDP-galactose, to a lipid carrier such as undecaprenyl phosphate as the first (priming) step in the synthesis of an oligosaccharide "block". This function is encoded in the C-terminal domain. The liposaccharide is believed to be subsequently transferred through a "flippase" function from the cytoplasmic to the periplasmic face of the inner membrane by the N-terminal domain. Certain closely related transferase enzymes such as Sinorhizobium ExoY [9] and Lactococcus EpsD [10] lack the N-terminal domain and are not found by this model. TIGR03026.1 TIGR03026 NDP-sugDHase 189.8 189.8 413 subfamily Y Y N nucleotide sugar dehydrogenase GO:0000271,GO:0016616,GO:0051287 10376820,10931835,15226302,2166030,8606150 131567 cellular organisms no rank 167364 JCVI nucleotide sugar dehydrogenase nucleotide sugar dehydrogenase Enzymes in this family catalyze the NAD-dependent alcohol-to-acid oxidation of nucleotide-linked sugars. Examples include UDP-glucose 6-dehydrogenase (1.1.1.22) [1], GDP-mannose 6-dehydrogenase (1.1.1.132) [2], UDP-N-acetylglucosamine 6-dehydrogenase (1.1.1.136) [3], UDP-N-acetyl-D-galactosaminuronic acid dehydrogenase [4] and UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase [5]. These enzymes are most often involved in the biosynthesis of polysaccharides and are often found in operons devoted to that purpose. All of these enzymes contain three Pfam domains, PF03721, PF00984, and PF03720 for the N-terminal, central, and C-terminal regions respectively. TIGR03033.1 TIGR03033 phage_rel_nuc 68.05 68.05 153 subfamily_domain Y Y N lambda-exonuclease family protein 21893587,32556263,9295273 131567 cellular organisms no rank 15794 JCVI putative phage-type endonuclease lambda-exonuclease family protein Members of this protein family are found often in phage genomes and in prokaryotic genomes in uncharacterized regions that resemble integrated prophage regions. TIGR03057.1 TIGR03057 xxxLxxG_by_4 18.6 18.6 28 repeat Y N N X-X-X-Leu-X-X-Gly heptad repeat protein 131567 cellular organisms no rank 40448 JCVI X-X-X-Leu-X-X-Gly heptad repeats X-X-X-Leu-X-X-Gly heptad repeat (four copies) This model represents a 28-column alignment, comprising four tandem sets of seven residues each, in which the fourth residue tends to be Leu and the seventh tends to be Gly in each set. This heptad periodicity, corresponding to two turns of an alpha helix, suggests alpha-helical structure; in many proteins this 28-region model hits many times in tandem. Arrangement of these sequences on a helical wheel would show a strict alternation of Leu and Gly residues on one side of the helix, that is, an extremely bulky side chain alternating with the virtual absence of one. This suggests an extended zippering of one alpha helix to another, analogous to the shorter leucine zippers found in many dimerizing transcription factors. Proteins in which these heptad repeats occur often have higher order repeats of a unit comprised of several heptads. TIGR03061.1 TIGR03061 pip_yhgE_Nterm 96.15 96.15 164 subfamily_domain Y Y N YhgE/Pip family protein 8366036 131567 cellular organisms no rank 51462 JCVI YhgE/Pip N-terminal domain YhgE/Pip N-terminal domain This family contains the N-terminal domain of a family of multiple membrane-spanning proteins of Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called "phage infection protein". A separate model, TIGR03062, represents the conserved C-terminal domain. The domains are separated by regions highly variable in both length and sequence, often containing extended heptad repeats as described in model TIGR03057. TIGR03062.1 TIGR03062 pip_yhgE_Cterm 102.2 102.2 208 subfamily_domain Y Y N YhgE/Pip family protein 8366036 131567 cellular organisms no rank 48068 JCVI YhgE/Pip C-terminal domain YhgE/Pip C-terminal domain This family contains the C-terminal domain of a family of multiple membrane-spanning proteins of Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called "phage infection protein". A separate model, TIGR03061, represents the conserved N-terminal domain. The domains are separated by regions highly variable in both length and sequence, often containing extended heptad repeats as described in model TIGR03057. TIGR03070.1 TIGR03070 couple_hipB 71.65 71.65 58 subfamily Y Y N type II toxin-antitoxin system Y4mF family antitoxin 131567 cellular organisms no rank 2865 JCVI transcriptional regulator, y4mF family type II toxin-antitoxin system Y4mF family antitoxin Members of this family, including the DNA-binding transcriptional repressor Y4mF that serves as the antitoxin component of an addiction module in a plasmid of Sinorhizobium fredii NGR234, are related to the HibB antitoxin of E. coli's HipAB toxin-antitoxin pair. TIGR03071.1 TIGR03071 couple_hipA 27.8 27.8 101 domain Y N N HipA N-terminal domain 131567 cellular organisms no rank 29719 JCVI HipA N-terminal domain HipA N-terminal domain Although Pfam models PF07805 and PF07804 currently are called HipA-like N-terminal domain and HipA-like C-terminal domain, respectively, those models hit the central and C-terminal regions of E. coli HipA but not the N-terminal region. This model hits the N-terminal region of HipA and its homologs, and also identifies proteins that lack match regions for PF07804 and PF07805. TIGR03081.1 TIGR03081 metmalonyl_epim 114.95 114.95 129 equivalog Y Y N methylmalonyl-CoA epimerase mce 5.1.99.1 11470438,11481338 131567 cellular organisms no rank 23090 JCVI methylmalonyl-CoA epimerase methylmalonyl-CoA epimerase Members of this protein family are the enzyme methylmalonyl-CoA epimerase (EC 5.1.99.1), also called methylmalonyl-CoA racemase. This enzyme converts (2R)-methylmalonyl-CoA to (2S)-methylmalonyl-CoA, which is then a substrate for methylmalonyl-CoA mutase (TIGR00642). It is known in bacteria, archaea, and as a mitochondrial protein in animals. It is closely related to lactoylglutathione lyase (TIGR00068), which is also called glyoxylase I, and is also a homodimer. TIGR03095.1 TIGR03095 rusti_cyanin 146.7 146.7 148 equivalog Y Y N rusticyanin GO:0005507,GO:0009055 15256554,15357880 131567 cellular organisms no rank 43 JCVI rusticyanin rusticyanin Rusticyanin is a blue copper protein, described in an obligate acidophilic chemolithoautroph, Acidithiobacillus ferrooxidans, as an electron transfer protein. It can constitute up to 5 percent of protein in cells grown on Fe(II) and is thought to be part of an electron chain for Fe(II) oxidation, with two c-type cytochromes, an aa3-type cytochrome oxidase, and 02 as terminal electron acceptor. It is rather closely related to sulfocyanin (TIGR03094). TIGR03102.1 TIGR03102 halo_cynanin 93.8 93.8 115 subfamily_domain Y Y N halocyanin domain-containing protein 131567 cellular organisms no rank 2096 JCVI halocyanin domain halocyanin domain Halocyanins are blue (type I) copper redox proteins found in halophilic archaea such as Natronobacterium pharaonis. This model represents a domain duplicated in some halocyanins, while appearing once in others. This domain includes the characteristic copper ligand residues. This family does not include plastocyanins, and does not include certain divergent paralogs of halocyanin. TIGR03105.1 TIGR03105 gln_synth_III 469.6 469.6 435 equivalog Y Y N type III glutamate--ammonia ligase glnT 6.3.1.2 GO:0004356,GO:0006542 8093245 131567 cellular organisms no rank 6306 JCVI glutamine synthetase, type III glutamine synthetase, type III This family consists of the type III isozyme of glutamine synthetase, originally described in Rhizobium meliloti, where types I and II also occur. TIGR03119.1 TIGR03119 one_C_fhcD 292.6 292.6 288 equivalog Y Y N formylmethanofuran--tetrahydromethanopterin N-formyltransferase fhcD 2.3.1.101 GO:0006730,GO:0030270 16011764,16466742 131567 cellular organisms no rank 2159 JCVI formylmethanofuran--tetrahydromethanopterin N-formyltransferase formylmethanofuran--tetrahydromethanopterin N-formyltransferase Members of this protein family are the FhcD protein of tetrahydromethanopterin (H4MPT)-dependent C-1 carrier metabolism. In the archaea, FhcD is designated formylmethanofuran--tetrahydromethanopterin N-formyltransferase, while in bacteria it is commonly designated as formyltransferase/hydrolase complex subunit D. FhcD is essential for one-carbon metabolism in at least three groups of prokaryotes: methanogenic archaea, sulfate-reducing archaea, and methylotrophic bacteria. TIGR03120.1 TIGR03120 one_C_mch 228.8 228.8 313 equivalog Y Y N methenyltetrahydromethanopterin cyclohydrolase mch 3.5.4.27 GO:0006730,GO:0018759 131567 cellular organisms no rank 2834 JCVI methenyltetrahydromethanopterin cyclohydrolase methenyltetrahydromethanopterin cyclohydrolase Members of this protein family are the enzyme methenyltetrahydromethanopterin cyclohydrolase, a key enzyme for tetrahydromethanopterin (H4MPT)-linked C1 transfer metabolism. It catalyzes the reversible formation of methenyl-H(4)methanopterin from N(5)-formyl-H(4)methanopterin. TIGR03121.1 TIGR03121 one_C_dehyd_A 392.75 392.75 556 equivalog Y Y N formylmethanofuran dehydrogenase subunit A 1.2.7.12 GO:0016810 8954165 131567 cellular organisms no rank 2629 JCVI formylmethanofuran dehydrogenase subunit A formylmethanofuran dehydrogenase subunit A Members of this largely archaeal protein family are subunit A of the formylmethanofuran dehydrogenase. Nomenclature in some bacteria may reflect inclusion of the formyltransferase described by TIGR03119 as part of the complex, and therefore call this protein formyltransferase/hydrolase complex Fhc subunit A. Note that this model does not distinguish tungsten (FwdA) from molybdenum-containing (FmdA) forms of this enzyme; a single gene from this family is expressed constitutively in Methanobacterium thermoautotrophicum, which has both tungsten and molybdenum forms and may work interchangeably. TIGR03122.1 TIGR03122 one_C_dehyd_C 130.65 130.65 260 equivalog Y Y N formylmethanofuran dehydrogenase subunit C 1.2.7.12 GO:0015948,GO:0018493,GO:0046914 8954165 131567 cellular organisms no rank 2428 JCVI formylmethanofuran dehydrogenase subunit C formylmethanofuran dehydrogenase subunit C Members of this largely archaeal protein family are subunit C of the formylmethanofuran dehydrogenase. Nomenclature in some bacteria may reflect inclusion of the formyltransferase described by TIGR03119 as part of the complex, and therefore call this protein formyltransferase/hydrolase complex Fhc subunit C. Note that this model does not distinguish tungsten (FwdC) from molybdenum-containing (FmdC) forms of this enzyme. TIGR03123.1 TIGR03123 one_C_unchar_1 244.1 244.1 327 hypoth_equivalog Y N N probable H4MPT-linked C1 transfer pathway protein 131567 cellular organisms no rank 2340 JCVI probable H4MPT-linked C1 transfer pathway protein probable H4MPT-linked C1 transfer pathway protein This protein family was identified, by the method of partial phylogenetic profiling, as related to the use of tetrahydromethanopterin (H4MPT) as a C-1 carrier. Characteristic markers of the H4MPT-linked C1 transfer pathway include formylmethanofuran dehydrogenase subunits, methenyltetrahydromethanopterin cyclohydrolase, etc. Tetrahydromethanopterin, a tetrahydrofolate analog, occurs in methanogenic archaea, bacterial methanotrophs, planctomycetes, and a few other lineages. TIGR03126.1 TIGR03126 one_C_fae 118.05 118.05 160 equivalog_domain Y Y N formaldehyde-activating enzyme fae GO:0016051,GO:0016840 131567 cellular organisms no rank 3883 JCVI formaldehyde-activating enzyme formaldehyde-activating enzyme This family consists of formaldehyde-activating enzyme, or the corresponding domain of longer, bifunctional proteins. It links formaldehyde to the C1 carrier tetrahydromethanopterin (H4MPT), an analog of tetrahydrofolate, and is common among species with H4MPT. The ribulose monophosphate (RuMP) pathway, which removes the toxic metabolite formaldehyde by assimilation, runs in the opposite direction in some species to produce ribulose 5-phosphate for nucleotide biosynthesis, leaving formaldehyde as an additional metabolite. In these species, formaldehyde activating enzyme may occur as a fusion protein with D-arabino 3-hexulose 6-phosphate formaldehyde lyase from the RuMP pathway. TIGR03127.2 TIGR03127 RuMP_HxlB 160 160 178 equivalog_domain Y Y N 6-phospho-3-hexuloisomerase hxlB 5.3.1.27 GO:0016853,GO:0043800,GO:1901135 10418139,11468398,15901685 131567 cellular organisms no rank 9290 JCVI 6-phospho 3-hexuloisomerase 6-phospho-3-hexuloisomerase Members of this protein family are 6-phospho 3-hexuloisomerase (PHI), or the PHI domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin. TIGR03128.2 TIGR03128 RuMP_HxlA 200 200 205 equivalog_domain Y Y N 3-hexulose-6-phosphate synthase hxlA 4.1.2.43 GO:0005975,GO:0019647,GO:0043801 15697207,15978081 131567 cellular organisms no rank 6004 JCVI 3-hexulose-6-phosphate synthase 3-hexulose-6-phosphate synthase Members of this protein family are 3-hexulose-6-phosphate synthase (HPS), or the HPS domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin. In these species, the enzyme is viewed as a lyase rather than a synthase and is called D-arabino 3-hexulose 6-phosphate formaldehyde lyase. Note that there is some overlap in specificity with the Escherichia coli enzyme 3-keto-L-gulonate 6-phosphate decarboxylase. TIGR03129.1 TIGR03129 one_C_dehyd_B 327.8 327.8 421 equivalog Y Y N formylmethanofuran dehydrogenase subunit B 1.2.7.12 GO:0015948,GO:0018493 8954165 131567 cellular organisms no rank 1137 JCVI formylmethanofuran dehydrogenase subunit B formylmethanofuran dehydrogenase subunit B Members of this largely archaeal protein family are subunit B of the formylmethanofuran dehydrogenase. Nomenclature in some bacteria may reflect inclusion of the formyltransferase described by TIGR03119 as part of the complex, and therefore call this protein formyltransferase/hydrolase complex Fhc subunit C. Note that this model does not distinguish tungsten (FwdB) from molybdenum-containing (FmdB) forms of this enzyme. TIGR03139.1 TIGR03139 QueF-II 86.9 86.9 115 equivalog Y Y N preQ(1) synthase queF 1.7.1.13 GO:0005737,GO:0008616,GO:0033739,GO:0046857 15767583 131567 cellular organisms no rank 16648 JCVI 7-cyano-7-deazaguanine reductase preQ(1) synthase This enzyme catalyzes the 4-electron reduction of the cyano group of 7-cyano-7-deazaguanine (proQ1) to an amine [1]. Although related to a large family of GTP cyclohydrolases (PF01227), the relationship is structural and not germane to the catalytic mechanism. This mode represents the shorter, gram-positive version of the enzyme as found in B. subtilis. The enzymatic step represents the first point at which the biosynthesis of queuosine in bacteria and eukaryotes is distinguished from the biosynthesis of archaeosine in archaea. TIGR03144.1 TIGR03144 cytochr_II_ccsB 187.6 187.6 252 equivalog Y Y N c-type cytochrome biogenesis protein CcsB ccsB GO:0017004,GO:0020037 15937156 131567 cellular organisms no rank 25151 JCVI cytochrome c-type biogenesis protein CcsB c-type cytochrome biogenesis protein CcsB Members of this protein family represent one of two essential proteins of system II for c-type cytochrome biogenesis. Additional proteins tend to be part of the system but can be replaced by chemical reductants such as dithiothreitol. This protein is designated CcsB in Bordetella pertussis and some other bacteria, resC in Bacillus (where there is additional N-terminal sequence), and CcsA in chloroplast. We use the CcsB designation here. Member sequences show regions of strong sequence conservation and variable-length, poorly conserved regions in between; sparsely filled columns were removed from the seed alignment prior to model construction. TIGR03153.1 TIGR03153 cytochr_NrfH 134.2 134.2 138 equivalog Y Y N cytochrome c nitrite reductase small subunit nrfH 1.7.2.2 GO:0016020,GO:0022900 10672190,11722563 131567 cellular organisms no rank 2247 JCVI cytochrome c nitrite reductase, small subunit cytochrome c nitrite reductase small subunit Members of this protein family are NrfH, a tetraheme cytochrome c. NrfH is the cytochrome c nitrite reductase small subunit, and forms a heterodimer with NrfA, the catalytic subunit. While NrfA can act as a monomer, NrfH can bind to and anchor NrfA in the membrane and enables electron transfer to NrfA from quinones. TIGR03156.1 TIGR03156 GTP_HflX 216.75 216.75 351 equivalog Y Y N GTPase HflX hflX GO:0005525 8248183,9466997 131567 cellular organisms no rank 69892 JCVI GTP-binding protein HflX GTPase HflX This protein family is one of a number of homologous small, well-conserved GTP-binding proteins with pleiotropic effects. Bacterial members are designated HflX, following the naming convention in Escherichia coli where HflX is encoded immediately downstream of the RNA chaperone Hfq, and immediately upstream of HflKC, a membrane-associated protease pair with an important housekeeping function. Over large numbers of other bacterial genomes, the pairing with hfq is more significant than with hflK and hlfC. The gene from Homo sapiens in this family has been named PGPL (pseudoautosomal GTP-binding protein-like). TIGR03157.1 TIGR03157 cas_Csc2 38 38 282 equivalog Y Y N type I-D CRISPR-associated protein Cas7/Csc2 cas7d 131567 cellular organisms no rank 934 JCVI CRISPR type I-D/CYANO-associated protein Csc2 type I-D CRISPR-associated protein Cas7/Csc2 CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family is a CRISPR-associated (Cas) family strictly associated with the Cyano subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. This family is designated Csc2 for CRISPR/Cas Subtype Cyano protein 2, as it is often the second gene upstream of the core cas genes, cas3-cas4-cas1-cas2. TIGR03158.1 TIGR03158 cas3_cyano 69.1 69.1 357 exception Y Y N type I-D CRISPR-associated helicase Cas3' cas3 GO:0004386,GO:0043571 131567 cellular organisms no rank 908 JCVI CRISPR-associated helicase Cas3, subtype CYANO type I-D CRISPR-associated helicase Cas3' CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family is a CRISPR-associated (Cas) family strictly associated with the Cyano subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system. TIGR03159.1 TIGR03159 cas_Csc1 41.4 41.4 225 equivalog Y Y N type I-D CRISPR-associated protein Cas5/Csc1 cas5d 131567 cellular organisms no rank 811 JCVI CRISPR type I-D/CYANO-associated protein Csc1 type I-D CRISPR-associated protein Cas5/Csc1 CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family is a CRISPR-associated (Cas) family strictly associated with the Cyano subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. This family is designated Csc1 for CRISPR/Cas Subtype Cyano protein 1, as it is often the first gene upstream of the core cas genes, cas3-cas4-cas1-cas2. TIGR03160.1 TIGR03160 cobT_DBIPRT 319.3 319.3 334 equivalog Y Y N nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase cobT 2.4.2.21 GO:0008939,GO:0009236 11441022 131567 cellular organisms no rank 54475 JCVI nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase Members of this family are nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase, an enzyme of cobalamin biosynthesis. TIGR03164.1 TIGR03164 UHCUDC 96.25 96.25 157 equivalog_domain Y Y N 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase uraD 4.1.1.97 GO:0000255 16462750 131567 cellular organisms no rank 15753 JCVI OHCU decarboxylase 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus [1]. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model. TIGR03165.1 TIGR03165 F1F0_chp_2 55.5 55.5 83 hypoth_equivalog Y N N F1/F0 ATPase, Methanosarcina type, subunit 2 9425287 131567 cellular organisms no rank 858 JCVI F1/F0 ATPase, Methanosarcina type, subunit 2 F1/F0 ATPase, Methanosarcina type, subunit 2 Members of this protein family are uncharacterized, highly hydrophobic proteins encoded in the middle of apparent F1/F0 ATPase operons. We note, however, that this protein is both broadly and sparsely distributed. It is found in about only about two percent of microbial genomes sequenced, with the first ten examples found coming from the Euryarchaeota, Chlorobia, Betaproteobacteria, Deltaproteobacteria, and Planctomycetes. In most of these species, surrounding operon appears to represent a second F1/F0 ATPase system, and the member proteins belong to subfamilies with the same phylogenetic distribution as the current protein family. TIGR03166.1 TIGR03166 alt_F1F0_F1_eps 100.1 100.1 122 hypoth_equivalog Y N N alternate F1F0 ATPase, F1 subunit epsilon 21262962,9425287 131567 cellular organisms no rank 1854 JCVI alternate F1F0 ATPase, F1 subunit epsilon alternate F1F0 ATPase, F1 subunit epsilon A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 epsilon subunit of this apparent second ATP synthase. One member of this family belongs to an ATPase known to translocate Na+ instead of H+. TIGR03168.1 TIGR03168 1-PFK 216.4 216.4 305 subfamily Y Y N hexose kinase 2.7.1.- GO:0005975,GO:0016773 131567 cellular organisms no rank 64740 JCVI hexose kinase, 1-phosphofructokinase family hexose kinase, FruK/PfkB/LacC family This family consists largely of 1-phosphofructokinases, but also includes tagatose-6-kinases and 6-phosphofructokinases. TIGR03172.2 TIGR03172 TIGR03172 73.05 73.05 209 equivalog Y Y N selenium cofactor biosynthesis protein YqeC yqeC 18289380,18510720 131567 cellular organisms no rank 6539 JCVI putative selenium-dependent hydroxylase accessory protein YqeC selenium cofactor biosynthesis protein YqeC This family describes YqeC, TIGR03309 describes the C-terminal portion of YqeB from E. coli, and the pair predicts the presence of variant forms of molybdenum cofactor enzymes that contain a labile (non-selenocysteine) selenium replacing the more typical sulfur atom. TIGR03173.1 TIGR03173 pbuX 414.15 414.15 407 subfamily Y N N xanthine permease pbuX GO:0015851,GO:0016020,GO:0022857 9098051 131567 cellular organisms no rank 53014 JCVI xanthine permease xanthine permease All the seed members of this model are observed adjacent to genes for either xanthine phosphoribosyltransferase (for the conversion of xanthine to guanine, GenProp0696, [1]) or genes for the conversion of xanthine to urate and its concomitant catabolism (GenProp0640, GenProp0688, GenProp0686 and GenProp0687). A number of sequences scoring higher than trusted to this model are found in different genomic contexts, and the possibility exist that these transport related compounds in addition to or instead of xanthine itself. The outgroup to this family are sequences which are characterized as uracil permeases or are adjacent to established uracil phosphoribosyltransferases. TIGR03174.1 TIGR03174 cas_Csc3 60 40 946 equivalog Y Y N type I-D CRISPR-associated protein Cas10d/Csc3 cas10d 131567 cellular organisms no rank 728 JCVI CRISPR type I-D/CYANO-associated protein Csc3/Cas10d type I-D CRISPR-associated protein Cas10d/Csc3 CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family is a CRISPR-associated (Cas) family strictly associated with the Cyano subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. This family is designated Csc3 for CRISPR/Cas Subtype Cyano protein 3, as it is often the third gene upstream of the core cas genes, cas3-cas4-cas1-cas2. TIGR03178.1 TIGR03178 allantoinase 357.85 357.85 441 equivalog Y Y N allantoinase AllB allB 3.5.2.5 GO:0000256,GO:0004038,GO:0008270,GO:0050897 131567 cellular organisms no rank 19314 JCVI allantoinase allantoinase AllB Members of this family are AllB, an allantoinase unrelated to PuuE, described by TIGR03212. TIGR03181.1 TIGR03181 PDH_E1_alph_x 411.35 411.35 341 equivalog Y Y N pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha pdhA GO:0004739,GO:0006086,GO:0045254 131567 cellular organisms no rank 32928 JCVI pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha Members of this protein family are the alpha subunit of the E1 component of pyruvate dehydrogenase (PDH). This model represents one branch of a larger family that E1-alpha proteins from 2-oxoisovalerate dehydrogenase, acetoin dehydrogenase, another PDH clade, etc. TIGR03183.1 TIGR03183 DNA_S_dndC 290.4 290.4 447 equivalog Y Y N DNA phosphorothioation system sulfurtransferase DndC dndC 16102010,26539172 131567 cellular organisms no rank 4276 JCVI putative sulfurtransferase DndC DNA phosphorothioation system sulfurtransferase DndC Members of this protein family are the DndC protein from the dnd (degradation during electrophoresis) operon. The dnd phenotype reflects a sulfur-containing modification to DNA. This operon is sparsely and sporadically distributed among bactera; among the first eight examples are members from the Actinobacteria, Firmicutes, Gammaproteobacteria, Cyanobacteria. DndC is suggested to be a sulfurtransferase. TIGR03184.1 TIGR03184 DNA_S_dndE 71.85 71.85 104 equivalog Y Y N DNA sulfur modification protein DndE dndE 16102010 131567 cellular organisms no rank 2794 JCVI DNA sulfur modification protein DndE DNA sulfur modification protein DndE This model describes the DndE protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndE is a putative carboxylase homologous to NCAIR synthetases. TIGR03185.1 TIGR03185 DNA_S_dndD 245.85 245.85 650 equivalog Y Y N DNA sulfur modification protein DndD dndD 16102010,22070167 131567 cellular organisms no rank 4606 JCVI DNA sulfur modification protein DndD DNA sulfur modification protein DndD This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. TIGR03187.1 TIGR03187 DGQHR 58.85 58.85 276 domain Y Y N DGQHR domain-containing protein 131567 cellular organisms no rank 12471 JCVI DGQHR domain DGQHR domain This highly divergent, uncharacterized domain has several absolutely conserved residues, including a QR pair and FxxxN motif. Its most striking feature, however, is a near invariant pentapeptide motif DGQHR. Several different subfamilies occur specifically as a part of DNA phosphorothioation systems, previously called DND (DNA instability during electrophoresis), while others (e.g. CPS_2936) occur in other contexts suggestive of lateral gene transfer (sporadic distribution of helicase-containing cassettes). The region described by this model is about 280 amino acids in length; additional sequences show local sequence similarity. TIGR03188.1 TIGR03188 histidine_hisI 42.7 42.7 84 equivalog_domain Y Y N phosphoribosyl-ATP diphosphatase hisE 3.6.1.31 GO:0000105,GO:0004636 131567 cellular organisms no rank 48939 JCVI phosphoribosyl-ATP diphosphatase phosphoribosyl-ATP diphosphatase This enzyme, phosphoribosyl-ATP pyrophosphohydrolase, catalyses the second step in the histidine biosynthesis pathway. It often occurs as a fusion protein. This model a somewhat narrower scope than Pfam model PF01503, as some paralogs that appear to be functionally distinct are excluded from this model. TIGR03191.1 TIGR03191 benz_CoA_bzdO 448.6 448.6 430 equivalog Y Y N benzoyl-CoA reductase, bzd-type, subunit O bzdO 1.3.7.8 GO:0018522 131567 cellular organisms no rank 51 JCVI benzoyl-CoA reductase, bzd-type, O subunit benzoyl-CoA reductase, bzd-type, subunit O Members of this family are the O subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene. TIGR03192.1 TIGR03192 benz_CoA_bzdQ 380.2 380.2 293 equivalog Y Y N benzoyl-CoA reductase, bzd-type, subunit Q bzdQ 1.3.7.8 GO:0018522 131567 cellular organisms no rank 55 JCVI benzoyl-CoA reductase, bzd-type, Q subunit benzoyl-CoA reductase, bzd-type, subunit Q Members of this family are the Q subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene. TIGR03211.1 TIGR03211 catechol_2_3 320.2 320.2 303 equivalog Y Y N catechol 2,3-dioxygenase 1.13.11.2 GO:0008198,GO:0009712,GO:0018577 9973359 131567 cellular organisms no rank 4438 JCVI catechol 2,3 dioxygenase catechol 2,3-dioxygenase Members of this family all are enzymes active as catechol 2,3 dioxygenase (1.13.11.2), although some members have highly significant activity on catechol derivatives such as 3-methylcatechol, 3-chlorocatechol, and 4-chlorocatechol (see Mars, et al.). This enzyme is also called metapyrocatechase, as it performs a meta-cleavage (an extradiol ring cleavage), in contrast to the ortho-cleavage (intradiol ring cleavage)performed by catechol 1,2-dioxygenase (EC 1.13.11.1), also called pyrocatechase. TIGR03215.1 TIGR03215 ac_ald_DH_ac 282.25 282.25 285 equivalog Y Y N acetaldehyde dehydrogenase (acetylating) 1.2.1.10 GO:0008774,GO:0009056 1732207 131567 cellular organisms no rank 19072 JCVI acetaldehyde dehydrogenase (acetylating) acetaldehyde dehydrogenase (acetylating) Members of this protein family are acetaldehyde dehydrogenase (acetylating), EC 1.2.1.10. This enzyme oxidizes acetaldehyde, using NAD(+), and attaches coenzyme A (CoA), yielding acetyl-CoA. It occurs as a late step in the meta-cleavage pathways of a variety of compounds, including catechol, biphenyl, toluene, salicylate, etc. TIGR03217.1 TIGR03217 4OH_2_O_val_ald 286 286 334 equivalog Y Y N 4-hydroxy-2-oxovalerate aldolase dmpG 4.1.3.39 GO:0008701,GO:0009056 12764229,7496535 131567 cellular organisms no rank 19522 JCVI 4-hydroxy-2-oxovalerate aldolase 4-hydroxy-2-oxovalerate aldolase Members of this protein family are 4-hydroxy-2-oxovalerate aldolase, also called 4-hydroxy-2-ketovalerate aldolase and 2-oxo-4-hydroxypentanoate aldolase. This enzyme, part of the pathway for the meta-cleavage of catechol, produces pyruvate and acetaldehyde. Acetaldehyde is then converted by acetaldehyde dehydrogenase (acylating) (DmpF; EC 1.2.1.10) to acetyl-CoA. The two enzymes are tightly associated. TIGR03233.1 TIGR03233 DNA_S_dndB 328 328 355 equivalog Y Y N DNA sulfur modification protein DndB dndB 16102010 131567 cellular organisms no rank 2454 JCVI DNA sulfur modification protein DndB DNA sulfur modification protein DndB This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndB is described as a putative ATPase. TIGR03236.1 TIGR03236 dnd_assoc_1 20 20 363 equivalog Y Y N DNA phosphorothioation-dependent restriction protein DptG dptG GO:0009307 20627870,22070167 131567 cellular organisms no rank 2066 JCVI DNA phosphorothioation-dependent restriction protein DptG DNA phosphorothioation-dependent restriction protein DptG A DNA sulfur modification (phosphorothioation) system, dnd (degradation during electrophoresis), is sparsely and sporadically distributed among the bacteria. This protein is one member of a three-gene restriction enzyme cassette that depends on DNA phosphorothioation. TIGR03237.1 TIGR03237 dnd_assoc_2 620.65 620.65 1256 equivalog Y Y N DNA phosphorothioation-dependent restriction protein DptH dptH GO:0009307 20627870,22070167 131567 cellular organisms no rank 2219 JCVI DNA phosphorothioation-dependent restriction protein DptH DNA phosphorothioation-dependent restriction protein DptH A DNA sulfur modification (phosphorothioation) system, dnd (degradation during electrophoresis), is sparsely and sporadically distributed among the bacteria. This protein is one member of a three-gene restriction enzyme cassette that depends on DNA phosphorothioation. TIGR03238.1 TIGR03238 dnd_assoc_3 50 50 504 equivalog Y Y N DNA phosphorothioation-dependent restriction protein DptF dptF GO:0009307 20627870,22070167 131567 cellular organisms no rank 2449 JCVI DNA phosphorothioation-dependent restriction protein DptF DNA phosphorothioation-dependent restriction protein DptF A DNA sulfur modification (phosphorothioation) system, dnd (degradation during electrophoresis), is sparsely and sporadically distributed among the bacteria. This protein is one member of a three-gene restriction enzyme cassette that depends on DNA phosphorothioation. TIGR03251.1 TIGR03251 LAT_fam 520.8 520.8 433 equivalog Y Y N L-lysine 6-transaminase lat 2.6.1.36 GO:0017000,GO:0030170,GO:0045484 12005058,9355735 131567 cellular organisms no rank 3820 JCVI L-lysine 6-transaminase L-lysine 6-transaminase Characterized members of this protein family are L-lysine 6-transaminase, also called lysine epsilon-aminotransferase (LAT). The immediate product of the reaction of this enzyme on lysine, 2-aminoadipate 6-semialdehyde, becomes 1-piperideine 6-carboxylate, or P6C. This product may be converted subsequently to pipecolate or alpha-aminoadipate, lysine catabolites that may be precursors of certain seconary metabolites. TIGR03266.1 TIGR03266 methan_mark_1 365 365 376 equivalog Y Y N YcaO-related McrA-glycine thioamidation protein 16930487,22070167,28880150 131567 cellular organisms no rank 594 JCVI putative methanogenesis marker protein 1 YcaO-related McrA-glycine thioamidation protein This protein, previously designated "methanogenesis marker protein 1", is universal in and restricted to methanogenic archaea. It shares homology with YcaO (ribosomal protein S12 methylthiotransferase) and its homologs involved in ATP-dependent formation of heterocycles in thiazole/oxazole-modified peptide antibiotics. TIGR03284.1 TIGR03284 thym_sym 108.35 108.35 296 equivalog Y Y N thymidylate synthase thyA 2.1.1.45 GO:0004799,GO:0006231 131567 cellular organisms no rank 49545 JCVI thymidylate synthase thymidylate synthase Members of this protein family are thymidylate synthase, an enzyme that produces dTMP from dUMP. In prokaryotes, its gene usually is found close to that for dihydrofolate reductase, and in some systems the two enzymes are found as a fusion protein. This model excludes a set of related proteins (TIGR03283) that appears to replace this family in archaeal methanogens, where tetrahydrofolate is replaced by tetrahydromethanopterin. TIGR03287.1 TIGR03287 methan_mark_16 363.95 363.95 391 hypoth_equivalog Y Y N methanogenesis marker 16 metalloprotein 131567 cellular organisms no rank 546 JCVI putative methanogenesis marker 16 metalloprotein methanogenesis marker 16 metalloprotein Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. This protein is a predicted to bind FeS clusters, based on the presence of two copies of the Fer4 domain (PF00037), with each copy having four Cys residues invariant across all members. TIGR03292.1 TIGR03292 PhnH_redo 91.5 91.5 184 equivalog Y Y N phosphonate C-P lyase system protein PhnH phnH GO:0019634 1840580,2155230 131567 cellular organisms no rank 12277 JCVI phosphonate C-P lyase system protein PhnH phosphonate C-P lyase system protein PhnH PhnH is a component of the C-P lyase system (GenProp0232) for the catabolism of phosphonate compounds. The specific function of this component is unknown. This model is based on Pfam model PF05845.2, and has been broadened to include sequences missed by that model which are clearly true positive hits based on genome context. TIGR03293.1 TIGR03293 PhnG_redo 89 89 144 equivalog Y Y N phosphonate C-P lyase system protein PhnG phnG GO:0015716,GO:0019634 9882650 131567 cellular organisms no rank 10826 JCVI phosphonate C-P lyase system protein PhnG phosphonate C-P lyase system protein PhnG PhnH is a component of the C-P lyase system (GenProp0232) for the catabolism of phosphonate compounds. The specific function of this component is unknown. This model is based on Pfam model PF06754.2, and has been broadened to include sequences missed by that model which are clearly true positive hits based on genome context. TIGR03294.1 TIGR03294 FrhG 245.5 245.5 228 equivalog Y Y N coenzyme F420 hydrogenase subunit gamma frhG 1.12.98.1 GO:0016151,GO:0050454,GO:0050660,GO:0051536 2207102 131567 cellular organisms no rank 361 JCVI coenzyme F420 hydrogenase, subunit gamma coenzyme F420 hydrogenase subunit gamma This model represents that clade of F420-dependent hydrogenases (FRH) beta subunits [1] found exclusively and universally in methanogenic archaea. This protein contains two 4Fe-4S cluster binding domains (PF00037) and scores above the trusted cutoff to model PF01058 for the "NADH ubiquinone oxidoreductase, 20 Kd subunit" family. TIGR03296.1 TIGR03296 M6dom_TIGR03296 110.8 110.8 286 domain Y Y N M6 family metalloprotease domain-containing protein GO:0006508,GO:0008233 131567 cellular organisms no rank 39903 JCVI M6 family metalloprotease domain M6 family metalloprotease domain This model describes a metalloproteinase domain, with a characteristic HExxH motif. Examples of this domain are found in proteins in the family of immune inhibitor A, which cleaves antibacterial peptides, and in other, only distantly related proteases. This model is built to be broader and more inclusive than Pfam model PF05547. TIGR03297.1 TIGR03297 Ppyr-DeCO2ase 312.5 312.5 360 equivalog Y Y N phosphonopyruvate decarboxylase aepY 4.1.1.82 GO:0032923,GO:0033980 11035722,12672809,1337066,1547241,9673017 131567 cellular organisms no rank 4386 JCVI phosphonopyruvate decarboxylase phosphonopyruvate decarboxylase This family consists of examples of phosphonopyruvate an decarboxylase enzyme that produces phosphonoacetaldehyde (Pald), the second step in the biosynthesis phosphonate-containing compounds. Since the preceding enzymate step, PEP phosphomutase (AepX, TIGR02320) favors the substrate PEP energetically, the decarboxylase is required to drive the reaction in the direction of phosphonate production. Pald is a precursor of natural products including antibiotics like bialaphos [1] and phosphonothricin [2] in Streptomyces species, phosphonate-modified molecules such as the polysaccharide B of Bacteroides fragilis [3], the phosphonolipids of Tetrahymena pyroformis [4], the glycosylinositolphospholipids of Trypanosoma cruzi [5]. This gene generally occurs in prokaryotic organisms adjacent to the gene for AepX. Most often an aminotansferase (aepZ) is also present which leads to the production of the most common phosphonate compound, 2-aminoethylphosphonate (AEP). TIGR03299.1 TIGR03299 LGT_TIGR03299 110.7 110.7 312 subfamily Y N N phage/plasmid-like protein TIGR03299 131567 cellular organisms no rank 9693 JCVI phage/plasmid-like protein TIGR03299 phage/plasmid-like protein TIGR03299 Members of this uncharacterized protein family are found in various Mycobacterium phage genomes, in Streptomyces coelicolor plasmid SCP1, and in bacterial genomes near various markers that suggest lateral gene transfer. The function is unknown. TIGR03305.1 TIGR03305 alt_F1F0_F1_bet 752 752 449 exception Y N N alternate F1F0 ATPase, F1 subunit beta 7.1.2.2 GO:0015986,GO:0045261,GO:0046933,GO:0046961 9425287 131567 cellular organisms no rank 892 JCVI alternate F1F0 ATPase, F1 subunit beta alternate F1F0 ATPase, F1 subunit beta A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase. TIGR03306.1 TIGR03306 altF1_A 302.1 302.1 217 exception Y N N alternate F1F0 ATPase, F0 subunit A 9425287 131567 cellular organisms no rank 968 JCVI alternate F1F0 ATPase, F0 subunit A alternate F1F0 ATPase, F0 subunit A A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F0 subunit A of this apparent second ATP synthase. TIGR03308.1 TIGR03308 phn_thr-fam 201.65 201.65 204 hypoth_equivalog Y N N phosphonate metabolim protein, transferase hexapeptide repeat family 131567 cellular organisms no rank 7290 JCVI phosphonate metabolim protein, transferase hexapeptide repeat family phosphonate metabolim protein, transferase hexapeptide repeat family This family of proteins contains copies of the Bacterial transferase hexapeptide repeat family (PF00132) and is only found in operons encoding the phosphonate C-P lyase system (GenProp0232). Many C-P lyase operons, however, lack a homolog of this protein. TIGR03317.1 TIGR03317 ygfZ_signature 34.4 34.4 67 signature Y N N folate-binding protein YgfZ ygfZ GO:0005542,GO:0006400 16359333 131567 cellular organisms no rank 52370 JCVI folate-binding protein YgfZ folate-binding protein YgfZ YgfZ is a protein from Escherichia coli, homologous to the glycine cleavage system T protein, or aminomethyltransferase, GcvT (TIGR00528). Homologs of YgfZ other than members of the GcvT family share a well-conserved signature region that includes the motif, KGCYxGQE. Elsewhere, sequence diverge and length variation are substantial. Members of this family are mostly bacterial, largely absent from the Firmicutes and otherwise usually present. A few eukaryotic examples are found among the Apicomplexa, and a few archaeal sequences are found. Two functions implicated for this folate-binding protein are RNA modification (a function likely to be conserved) and replication initiation (a function likely to be highly variable). Many members of this family are, at the time of construction of this model, misnamed as the glycine cleavage system T protein. TIGR03321.1 TIGR03321 alt_F1F0_F0_B 224.7 224.7 246 exception Y N N alternate F1F0 ATPase, F0 subunit B 9425287 131567 cellular organisms no rank 786 JCVI alternate F1F0 ATPase, F0 subunit B alternate F1F0 ATPase, F0 subunit B A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, CC and in principle may run in either direction. This model represents the F0 subunit B of this apparent second ATP synthase. TIGR03322.1 TIGR03322 alt_F1F0_F0_C 130.85 130.85 86 exception Y N N alternate F1F0 ATPase, F0 subunit C 9425287 131567 cellular organisms no rank 909 JCVI alternate F1F0 ATPase, F0 subunit C alternate F1F0 ATPase, F0 subunit C A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F0 subunit C of this apparent second ATP synthase. TIGR03323.1 TIGR03323 alt_F1F0_F1_gam 282.35 282.35 285 exception Y N N alternate F1F0 ATPase, F1 subunit gamma 9425287 131567 cellular organisms no rank 842 JCVI alternate F1F0 ATPase, F1 subunit gamma alternate F1F0 ATPase, F1 subunit gamma A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 gamma subunit of this apparent second ATP synthase. TIGR03324.1 TIGR03324 alt_F1F0_F1_al 750.5 750.5 497 exception Y Y N alternate F1F0 ATPase, F1 subunit alpha 7.1.2.2 GO:0015986,GO:0045261,GO:0046933 9425287 131567 cellular organisms no rank 963 JCVI alternate F1F0 ATPase, F1 subunit alpha alternate F1F0 ATPase, F1 subunit alpha A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase. TIGR03326.1 TIGR03326 rubisco_III 497.45 497.45 426 equivalog Y Y N type III ribulose-bisphosphate carboxylase rbcL 4.1.1.39 GO:0015977,GO:0016984 12730164,17303759 131567 cellular organisms no rank 483 JCVI ribulose bisphosphate carboxylase, type III ribulose bisphosphate carboxylase, type III Members of this protein family are the archaeal, single chain, type III form of ribulose bisphosphate carboxylase, or RuBisCO. Members act is a three-step pathway for conversion of the sugar moiety of AMP to two molecules of 3-phosphoglycerate. Many of these species use ADP-dependent sugar kinases, which form AMP, for glycolysis. TIGR03328.1 TIGR03328 salvage_mtnB 137.05 137.05 194 equivalog Y Y N methylthioribulose 1-phosphate dehydratase mtnB 4.2.1.109 GO:0005737,GO:0019509,GO:0046872 15102328 131567 cellular organisms no rank 12000 JCVI methylthioribulose-1-phosphate dehydratase methylthioribulose 1-phosphate dehydratase Members of this family are the methylthioribulose-1-phosphate dehydratase of the methionine salvage pathway. This pathway allows methylthioadenosine, left over from polyamine biosynthesis, to be recycled to methionine. TIGR03330.1 TIGR03330 SAM_DCase_Bsu 75.65 75.65 112 equivalog Y Y N adenosylmethionine decarboxylase speD 4.1.1.50 GO:0004014,GO:0008295 10844697,11073910 131567 cellular organisms no rank 9606 JCVI S-adenosylmethionine decarboxylase proenzyme adenosylmethionine decarboxylase Members of this protein family are the single chain precursor of the two chains of the mature S-adenosylmethionine decarboxylase as found in Methanocaldococcus jannaschii, Bacillus subtilis, and a wide range of other species. It differs substantially in architecture from the form as found in Escherichia coli, and lacks any extended homology to the eukaryotic form (TIGR00535). TIGR03334.1 TIGR03334 IOR_beta 205.8 205.8 189 equivalog Y Y N indolepyruvate ferredoxin oxidoreductase subunit beta iorB 1.2.7.8 GO:0043805 15262931,8206994 131567 cellular organisms no rank 480 JCVI indolepyruvate ferredoxin oxidoreductase, beta subunit indolepyruvate ferredoxin oxidoreductase subunit beta This model represents the beta subunit of indolepyruvate ferredoxin oxidoreductase, an alpha(2)/beta(2) tetramer, as found in Pyrococcus furiosus and Methanobacterium thermoautotrophicum. Cofactors for the tetramer include TPP, 4Fe4S, and 3Fe-4S. It shows considerable sequence similarity to subunits of several other ketoacid oxidoreductases. TIGR03336.1 TIGR03336 IOR_alpha 650.9 650.9 595 equivalog Y Y N indolepyruvate ferredoxin oxidoreductase subunit alpha iorA 1.2.7.8 GO:0043805 15262931 131567 cellular organisms no rank 4334 JCVI indolepyruvate ferredoxin oxidoreductase, alpha subunit indolepyruvate ferredoxin oxidoreductase subunit alpha Indolepyruvate ferredoxin oxidoreductase (IOR) is an alpha 2/beta 2 tetramer related to ketoacid oxidoreductases for pyruvate (1.2.7.1, POR), 2-ketoglutarate (1.2.7.3, KOR), and 2-oxoisovalerate (1.2.7.7, VOR). These multi-subunit enzymes typically are found in anaerobes and are inactiviated by oxygen. IOR in Pyrococcus acts in fermentation of all three aromatic amino acids, following removal of the amino group by transamination. In Methanococcus maripaludis, by contrast, IOR acts in the opposite direction, in pathways of amino acid biosynthesis from phenylacetate, indoleacetate, and p-hydroxyphenylacetate. In M. maripaludis and many other species, iorA and iorB are found next to an apparent phenylacetate-CoA ligase. TIGR03342.1 TIGR03342 dsrC_tusE_dsvC 53.5 53.5 108 subfamily Y Y N TusE/DsrC/DsvC family sulfur relay protein tusE 16387657 131567 cellular organisms no rank 11103 JCVI sulfur relay protein, TusE/DsrC/DsvC family TusE/DsrC/DsvC family sulfur relay protein Members of this protein family may be described as TusE, a partner to TusBCD in a sulfur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Other members are DsrC, a functionally similar protein in species where the sulfur relay system exists primarily for sulfur metabolism rather than tRNA base modification. Some members of this family are known explicitly as the gamma subunit of sulfite reductases. TIGR03346.1 TIGR03346 chaperone_ClpB 1232.1 1232.1 853 equivalog Y Y N ATP-dependent chaperone ClpB clpB GO:0005737,GO:0009408,GO:0042026 15037241 131567 cellular organisms no rank 67859 JCVI ATP-dependent chaperone protein ClpB ATP-dependent chaperone ClpB Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (PF00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins. TIGR03367.1 TIGR03367 queuosine_QueD 89.25 89.25 92 equivalog Y Y N 6-carboxytetrahydropterin synthase QueD queD 4.1.2.50 GO:0003824,GO:0008616 14660578 131567 cellular organisms no rank 16058 JCVI queuosine biosynthesis protein QueD 6-carboxytetrahydropterin synthase QueD Members of this protein family, closely related to eukaryotic 6-pyruvoyl tetrahydrobiopterin synthase enzymes, are the QueD protein of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble position of tRNAs for Tyr, His, Asp, and Asn in many species. This modification, although widespread, appears not to be important for viability. The queuosine precursor made by this enzyme may be converted instead to archeaosine as in some Archaea. TIGR03378.1 TIGR03378 glycerol3P_GlpB 174.15 174.15 419 equivalog Y Y N anaerobic glycerol-3-phosphate dehydrogenase subunit GlpB glpB 1.1.5.3 GO:0004368,GO:0006071,GO:0009331 3286606 131567 cellular organisms no rank 10364 JCVI glycerol-3-phosphate dehydrogenase, anaerobic, B subunit anaerobic glycerol-3-phosphate dehydrogenase subunit GlpB Members of this protein family are the B subunit, product of the glpB gene, of a three-subunit, membrane-anchored, FAD-dependent anaerobic glycerol-3-phosphate dehydrogenase. TIGR03379.1 TIGR03379 glycerol3P_GlpC 279.9 279.9 397 equivalog Y Y N anaerobic glycerol-3-phosphate dehydrogenase subunit GlpC glpC 1.1.5.3 GO:0004368,GO:0006071,GO:0009061,GO:0009331,GO:0016020,GO:0051536 3286606 131567 cellular organisms no rank 7076 JCVI glycerol-3-phosphate dehydrogenase, anaerobic, C subunit anaerobic glycerol-3-phosphate dehydrogenase subunit GlpC Members of this protein family are the membrane-anchoring, non-catalytic C subunit, product of the glpC gene, of a three-subunit, FAD-dependent, anaerobic glycerol-3-phosphate dehydrogenase. GlpC lasks classical hydrophobic transmembrane helices; Cole, et al suggest interaction with the membrane may involve amphipathic helices. GlcC has conserved Cys-containing motifs suggestive of iron-sulfur binding. This complex is found mostly in Escherichia coli and closely related species. TIGR03382.1 TIGR03382 GC_trans_RRR 15.85 15.85 27 domain Y Y N MYXO-CTERM sorting domain-containing protein GO:0031240 131567 cellular organisms no rank 3074 JCVI Myxococcales GC_trans_RRR domain MYXO-CTERM domain This model largely duplicates TIGR03901, but differs somewhat in coverage. The domain described here, now called MYXO-CTERM, is small (about 30 amino acids), hydrophobic, only moderately conserved, and similar to numerous other transmembrane helix-containing sequence regions from convergent evolution. The trusted cutoff for the HMM therefore must be set fairly high. This domain is found, once per protein but in many proteins per genome in several bacteria of the order Myxococcales. It begins with a signature Gly-Cys motif. Its other features, including a hydrophobic transmembrane helix, Arg-rich cluster, and location at the protein C-terminus, resemble the PEP-CTERM proposed protein targeting domain. MYXO-CTERM domains occur in species with the processing endopeptidase myxosortase. It is likely that lipid is attached to the Cys side chain prior to a cleavage of the sorting domain distal to the GC site. TIGR03383.1 TIGR03383 urate_oxi 168.4 168.4 283 equivalog Y Y N factor-independent urate hydroxylase pucL 1.7.3.3 GO:0004846,GO:0019628 25314114,9360612 131567 cellular organisms no rank 12020 JCVI urate oxidase factor-independent urate hydroxylase Members of this protein family are urate oxidase, also called uricase. This protein contains two copies of the domain described by the uricase model PF01014. In animals, this enzyme has been lost from primates and birds. TIGR03399.1 TIGR03399 RNA_3prim_cycl 250.05 250.05 326 equivalog Y Y N RNA 3'-terminal phosphate cyclase rtcA 6.5.1.4 GO:0003963,GO:0006396 22074260 131567 cellular organisms no rank 6806 JCVI RNA 3'-phosphate cyclase RNA 3'-terminal-phosphate cyclase Members of this protein family are RNA 3'-phosphate cyclase (6.5.1.4), an enzyme whose function is conserved from E. coli to human. The modification this enzyme performs enables certain RNA ligations to occur, although the full biological roll for this enzyme is not fully described. This model separates this enzyme from a related protein, present only in eukaryotes, localized to the nucleolus, and involved in ribosomal modification. TIGR03402.1 TIGR03402 FeS_nifS 530.75 530.75 379 equivalog Y Y N cysteine desulfurase NifS nifS 2.8.1.7 GO:0006520,GO:0030170,GO:0031071 10639125,15667274 131567 cellular organisms no rank 6928 JCVI cysteine desulfurase NifS cysteine desulfurase NifS Members of this protein family are NifS, one of several related families of cysteine desulfurase involved in iron-sulfur (FeS) cluster biosynthesis. NifS is part of the NIF system, usually associated with other nif genes involved in nitrogenase expression and nitrogen fixation. The protein family is given a fairly broad interpretation here. It includes a clade nearly always found in extended nitrogen fixation genomic regions, plus a second clade more closely related to the first than to IscS and also part of NifS-like/NifU-like systems. This model does not extend to a more distantly clade found in the epsilon proteobacteria such as Helicobacter pylori, also named NifS in the literature, built instead in TIGR03403. TIGR03404.1 TIGR03404 bicupin_oxalic 254.2 254.2 367 subfamily Y N N bicupin, oxalate decarboxylase family GO:0033609 16000768 131567 cellular organisms no rank 6723 JCVI bicupin, oxalate decarboxylase family bicupin, oxalate decarboxylase family Members of this protein family are defined as bicupins as they have two copies of the cupin domain (PF00190). Two different known activities for members of this family are oxalate decarboxylase (EC 4.1.1.2) and oxalate oxidase (EC 1.2.3.4), although the latter activity has more often been found in distantly related monocupin (germin) proteins. TIGR03419.1 TIGR03419 NifU_clost 187.9 187.9 121 equivalog Y Y N Fe-S cluster assembly scaffold protein NifU nifU GO:0005198,GO:0016226 131567 cellular organisms no rank 2502 JCVI FeS cluster assembly scaffold protein NifU Fe-S cluster assembly scaffold protein NifU NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not. TIGR03438.1 TIGR03438 egtD_ergothio 290.9 290.9 301 equivalog Y Y N L-histidine N(alpha)-methyltransferase egtD 2.1.1.44 GO:0052699,GO:0052706 20420449 131567 cellular organisms no rank 23886 JCVI dimethylhistidine N-methyltransferase L-histidine N(alpha)-methyltransferase This model represents a distinct set of uncharacterized proteins found in the bacteria. Analysis by PSI-BLAST shows remote sequence homology to methyltransferases TIGR03439.1 TIGR03439 methyl_EasF 205.55 205.55 321 subfamily_domain Y Y N EasF family methyltransferase 2.1.1.- 1880714 131567 cellular organisms no rank 59 JCVI probable methyltransferase domain, EasF family EasF family methyltransferase This model represents an uncharacterized domain of about 300 amino acids with homology to S-adenosylmethionine-dependent methyltransferases. Proteins with this domain are exclusively fungal. A few, such as EasF from Neotyphodium lolii, are associated with the biosynthesis of ergot alkaloids, a class of fungal secondary metabolites. EasF may, in fact, be the AdoMet:dimethylallyltryptophan N-methyltransferase, the enzyme that follows tryptophan dimethylallyltransferase (DMATS) in ergot alkaloid biosynthesis. Several other members of this family, including mug158 (meiotically up-regulated gene 158 protein) from Schizosaccharomyces pombe, contain an additional uncharacterized domain DUF323 (PF03781). TIGR03440.2 TIGR03440 egtB_TIGR03440 360 360 413 equivalog Y Y N ergothioneine biosynthesis protein EgtB egtB GO:0052699 20420449 131567 cellular organisms no rank 25290 JCVI ergothioneine biosynthesis protein EgtB ergothioneine biosynthesis protein EgtB Members of this family include EgtB, and enzyme of the ergothioneine biosynthesis, as found in numerous Actinobacteria. Characterized homologs to this family include a formylglycine-generating enzyme that serves as a maturase for an aerobic sulfatase (cf. the radical SAM enzymes that serve as anaerobic sulfatase maturases). TIGR03455.1 TIGR03455 HisG_C-term 40.05 40.05 100 equivalog_domain Y Y N ATP phosphoribosyltransferase hisG GO:0000105,GO:0000287,GO:0003879,GO:0005737 131567 cellular organisms no rank 25934 JCVI ATP phosphoribosyltransferase, C-terminal domain ATP phosphoribosyltransferase, C-terminal domain This domain corresponds to the C-terminal third of the HisG protein. It is absent in many lineages. TIGR03457.1 TIGR03457 sulphoacet_xsc 676.4 676.4 579 equivalog Y Y N sulfoacetaldehyde acetyltransferase xsc 2.3.3.15 GO:0000287,GO:0005737,GO:0019529,GO:0030976,GO:0050487 131567 cellular organisms no rank 3952 JCVI sulfoacetaldehyde acetyltransferase sulfoacetaldehyde acetyltransferase Members of this protein family are sulfoacetaldehyde acetyltransferase, an enzyme of taurine utilization. Taurine, or 2-aminoethanesulfonate, can be used by bacteria as a source of carbon, nitrogen, and sulfur. TIGR03460.1 TIGR03460 crt_membr_arch 154.7 154.7 248 equivalog Y Y N bisanhydrobacterioruberin hydratase CruF cruF 4.2.1.161 25712483 131567 cellular organisms no rank 673 JCVI carotene biosynthesis associated membrane protein bisanhydrobacterioruberin hydratase CruF TIGR03462.1 TIGR03462 CarR_dom_SF 39.4 39.4 89 subfamily_domain Y Y N lycopene cyclase domain-containing protein GO:0016872 10951210,16625353 131567 cellular organisms no rank 11554 JCVI lycopene cyclase domain lycopene cyclase domain This domain is often repeated twice within the same polypeptide, as is observed in Archaea, Thermus, Sphingobacteria [1] and Fungi. In the fungal sequences, this tandem domain pair is observed as the N-terminal half of a bifunctional protein [2], where it has been characterized as a lycopene beta-cyclase and the C-terminal half is a phytoene synthetase. In Myxococcus and Actinobacterial genomes this domain appears as a single polypeptide, tandemly repeated and usually in a genomic context consistent with a role in carotenoid biosynthesis. It is unclear whether any of the sequences in this family truly encode lycopene epsilon cyclases. However a number are annotated as such. The domain is generally hydrophobic with a number of predicted membrane spanning segments and contains a distinctive motif (hPhEEhhhhhh). In certain sequences one of either the proline or glutamates may vary, but always one of the tandem pair appear to match this canonical sequence exactly. TIGR03477.1 TIGR03477 DMSO_red_II_gam 169.85 169.85 206 subfamily Y N N DMSO reductase family type II enzyme, heme b subunit GO:0020037,GO:0042597 11294876,12067345,15866716 131567 cellular organisms no rank 286 JCVI DMSO reductase family type II enzyme, heme b subunit DMSO reductase family type II enzyme, heme b subunit This model represents a heme b-binding subunit, typically called the gamma subunit, of various proteins that also contain a molybdopterin subunit and an iron-sulfur protein. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase and ethylbenzene dehydrogenase. TIGR03478.1 TIGR03478 DMSO_red_II_bet 480.7 480.7 321 subfamily Y N N DMSO reductase family type II enzyme, iron-sulfur subunit GO:0009061,GO:0042597,GO:0051536 12067345 131567 cellular organisms no rank 385 JCVI DMSO reductase family type II enzyme, iron-sulfur subunit DMSO reductase family type II enzyme, iron-sulfur subunit This model represents the iron-sulfur subunit, typically called the beta subunit, of various proteins that also contain a molybdopterin subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase and ethylbenzene dehydrogenase. TIGR03479.1 TIGR03479 DMSO_red_II_alp 984.75 984.75 913 subfamily Y Y N molybdopterin-dependent oxidoreductase GO:0016491 10826693,11443088,12067345,16030201,25512066 131567 cellular organisms no rank 326 JCVI DMSO reductase family type II enzyme, molybdopterin subunit DMSO reductase family type II enzyme, molybdopterin subunit This model represents the molybdopterin subunit, typically called the alpha subunit, of various proteins that also contain an iron-sulfur subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase, ethylbenzene dehydrogenase, and an archaeal respiratory nitrate reductase. This alpha subunit has a twin-arginine translocation (TAT) signal for Sec-independent translocation across the plasma membrane. TIGR03482.1 TIGR03482 DMSO_red_II_cha 152.3 152.3 197 subfamily Y N N DMSO reductase family type II enzyme chaperone 12067345 131567 cellular organisms no rank 215 JCVI DMSO reductase family type II enzyme chaperone DMSO reductase family type II enzyme chaperone Type II members of the DMSO reductase family are heterotrimeric proteins with bis(molybdopterin guanine dinucleotide)Mo, iron-sulfur, and heme b prosthetic groups bound by the alpha, beta, and gamma subunits respectively. Members of this protein family are not part of the mature protein, although they are the product of a fourth clustered gene. Proteins in this family are interpreted as a chaperone, analogous to NarJ of nitrate reductases. TIGR03491.1 TIGR03491 TIGR03491 97.45 97.45 462 subfamily_domain Y Y N TM0106 family RecB-like putative nuclease 131567 cellular organisms no rank 12070 JCVI putative RecB family nuclease, TM0106 family TM0106 family RecB-like putative nuclease Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats. TIGR03510.1 TIGR03510 XapX 27.8 27.8 49 domain Y Y N XapX domain-containing protein GO:0016020 131567 cellular organisms no rank 8777 JCVI XapX domain XapX domain This HMM describes an uncharacterized small, hydrophobic protein of about 50 amino acids, found between the xapB and xapR genes of the E. coli xanthosine utilization system, and homologous regions in other small proteins, such as the N-terminal region of DUF1427 (Pfam model PF07235). We name this domain XapX, as it comprises the full length of the protein encoded between the genes for the well-studied XapB and XapR proteins. TIGR03540.1 TIGR03540 DapC_direct 593.25 593.25 383 equivalog Y Y N LL-diaminopimelate aminotransferase 2.6.1.83 GO:0009089,GO:0010285 17093042,17583737 131567 cellular organisms no rank 574 JCVI LL-diaminopimelate aminotransferase LL-diaminopimelate aminotransferase This clade of the PF00155 superfamily of aminotransferases includes several which are adjacent to elements of the lysine biosynthesis via diaminopimelate pathway (GenProp0125). Every member of this clade is from a genome which possesses most of the lysine biosynthesis pathway but lacks any of the known aminotransferases, succinylases, desuccinylases, acetylases or deacetylases typical of the acylated versions of this pathway nor do they have the direct, NADPH-dependent enzyme (ddh). Although there is no experimental characterization of any of the sequences in this clade, a direct pathway is known in plants and Chlamydia [1, 2] and the clade containing the Chlamydia gene is a neighboring one in the same PF00155 superfamily so it seems quite reasonable that these enzymes catalyze the same transformation. TIGR03542.1 TIGR03542 DAPAT_plant 364.7 364.7 402 equivalog Y Y N LL-diaminopimelate aminotransferase 2.6.1.83 GO:0008483 17093042,17583737 131567 cellular organisms no rank 6850 JCVI LL-diaminopimelate aminotransferase LL-diaminopimelate aminotransferase This clade of the PF00155 superfamily of aminotransferases includes several which are adjacent to elements of the lysine biosynthesis via diaminopimelate pathway (GenProp0125). This clade includes characterized species in plants and Chlamydia [1, 2]. Every member of this clade is from a genome which possesses most of the lysine biosynthesis pathway but lacks any of the known succinylases, desuccinylases, acetylases or deacetylases typical of the acylated versions of this pathway nor do they have the direct, NADPH-dependent enzyme (ddh). TIGR03550.1 TIGR03550 F420_cofG 213.35 213.35 322 equivalog_domain Y Y N 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase CofG cofG 4.3.1.32 GO:0016765,GO:0051539 14593448 131567 cellular organisms no rank 16617 JCVI 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase CofG This model represents either a subunit or a domain, depending on whether or not the genes are fused, of a bifunctional protein that completes the synthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin, or FO. FO is the chromophore of coenzyme F(420), involved in methanogenesis in methanogenic archaea but found in certain other lineages as well. The chromophore also occurs as a cofactor in DNA photolyases in Cyanobacteria. TIGR03551.1 TIGR03551 F420_cofH 374.1 374.1 345 equivalog_domain Y Y N 5-amino-6-(D-ribitylamino)uracil--L-tyrosine 4-hydroxyphenyl transferase CofH cofH 2.5.1.147 GO:0016765 14593448 131567 cellular organisms no rank 15341 JCVI 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit 5-amino-6-(D-ribitylamino)uracil--L-tyrosine 4-hydroxyphenyl transferase CofH This enzyme, together with CofG, complete the biosynthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, the chromophore of coenzyme F420. The chromophore is also used in cyanobacteria DNA photolyases. TIGR03552.1 TIGR03552 F420_cofC 105 105 196 equivalog Y Y N 2-phospho-L-lactate guanylyltransferase cofC 2.7.7.68 GO:0043814 18260642 131567 cellular organisms no rank 13644 JCVI 2-phospho-L-lactate guanylyltransferase 2-phospho-L-lactate guanylyltransferase Members of this protein family are the CofC enzyme of coenzyme F420 biosynthesis. TIGR03557.1 TIGR03557 F420_G6P_family 210.4 210.4 316 subfamily Y Y N TIGR03557 family F420-dependent LLM class oxidoreductase 1.-.-.- GO:0016491 20675471,23110042 131567 cellular organisms no rank 23743 JCVI F420-dependent oxidoreductase, G6PDH family TIGR03557 family F420-dependent LLM class oxidoreductase Members of this protein family include F420-dependent glucose-6-phosphate dehydrogenases (TIGR03554) and related proteins. All members of this family come from species that synthesize coenzyme F420, with the exception of those that belong to TIGR03885, a clade within this family in which cofactor binding may instead be directed to FMN. TIGR03558.1 TIGR03558 oxido_grp_1 166.95 166.95 325 subfamily Y Y N MsnO8 family LLM class oxidoreductase 1.-.-.- GO:0010181,GO:0016491 24554499 131567 cellular organisms no rank 83553 JCVI luciferase family oxidoreductase, group 1 MsnO8 family LLM class oxidoreductase The Pfam domain family PF00296 is named for luciferase-like monooxygenases, but the family also contains several coenzyme F420-dependent enzymes. This protein family represents a well-resolved clade within family PF00296 and shows no restriction to coenzyme F420-positive species, unlike some other clades within PF00296. TIGR03560.1 TIGR03560 F420_Rv1855c 231.4 231.4 227 subfamily Y Y N TIGR03560 family F420-dependent LLM class oxidoreductase GO:0016491,GO:0070967 20675471 131567 cellular organisms no rank 23693 JCVI probable F420-dependent oxidoreductase, Rv1855c family TIGR03560 family F420-dependent LLM class oxidoreductase Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea 34H, Rhodopseudomonas palustris HaA2, and others. Partial phylogenetic profiling identifies protein subfamilies, within the larger family called luciferase-like monooxygenanases (PF00296), that appear only in F420-positive genomes and are likely to be F420-dependent. This model describes one such subfamily, exemplified by Rv1855c from Mycobacterium tuberculosis. TIGR03562.1 TIGR03562 osmo_induc_OsmC 85.8 85.8 137 subfamily Y Y N OsmC family peroxiredoxin GO:0004601,GO:0006979 18084893 131567 cellular organisms no rank 22269 JCVI peroxiredoxin, OsmC subfamily OsmC family peroxiredoxin Pfam model PF02566, OsmC-like protein, contains several deeply split clades of homologous proteins. The clade modeled here includes the protein OsmC, or osmotically induced protein C. The member from Thermus thermophilus was shown to have hydroperoxide peroxidase activity. In many species, this protein is induced by stress and helps resist oxidative stress. TIGR03568.1 TIGR03568 NeuC_NnaA 235.9 235.9 365 equivalog Y Y N UDP-N-acetylglucosamine 2-epimerase neuC 3.2.1.183 GO:0006047,GO:0008761 14729696 131567 cellular organisms no rank 9641 JCVI UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing UDP-N-acetylglucosamine 2-epimerase (hydrolyzing) This family of enzymes catalyzes the combined epimerization and UDP-hydrolysis of UDP-N-acetylglucosamine to N-acetylmannosamine [1]. This is in contrast to the related enzyme WecB (TIGR00236) which retains the UDP moiety. NeuC acts in concert with NeuA and NeuB to synthesize CMP-N5-acetyl-neuraminate. TIGR03569.1 TIGR03569 NeuB_NnaB 399.65 399.65 329 equivalog Y Y N N-acetylneuraminate synthase neuB 2.5.1.56 GO:0003824,GO:0016051 131567 cellular organisms no rank 6478 JCVI N-acetylneuraminate synthase N-acetylneuraminate synthase This family is a subset of the Pfam model PF03102 and is believed to include only authentic NeuB N-acetylneuraminate (sialic acid) synthase enzymes. The majority of the genes identified by this model are observed adjacent to both the NeuA and NeuC genes which together effect the biosynthesis of CMP-N-acetylneuraminate from UDP-N-acetylglucosamine. TIGR03570.1 TIGR03570 NeuD_NnaD 160.8 160.8 202 subfamily Y Y N NeuD/PglB/VioB family sugar acetyltransferase GO:0016740 16490781,16923886,19787374,30314705,7814319 131567 cellular organisms no rank 24759 JCVI sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family NeuD/PglB/VioB family sugar acetyltransferase This family of proteins includes the characterized NeuD sialic acid O-acetyltransferase enzymes from E. coli and Streptococcus agalactiae. It also includes UDP-N-acetylbacillosamine N-acetyltransferases, GDP-perosamine N-acetyltransferases, and dTDP-4-amino-4,6-dideoxy-D-glucose acetyltransferases. TIGR03571.1 TIGR03571 lucif_BA3436 303.9 303.9 304 subfamily Y Y N TIGR03571 family LLM class oxidoreductase 1.-.-.- GO:0010181,GO:0016491 131567 cellular organisms no rank 9755 JCVI luciferase-type oxidoreductase, BA3436 family TIGR03571 family LLM class oxidoreductase This family is a distinct subgroup among members of the luciferase monooxygenase domain family. The larger family contains both FMN-binding enzymes (luciferase, alkane monooxygenase) and F420-binding enzymes (methylenetetrahydromethanopterin reductase, secondary alcohol dehydrogenase, glucose-6-phosphate dehydrogenase). Although some members of the domain family bind coenzyme F420 rather than FMN, members of this family are from species that lack the genes for F420 biosynthesis. A crystal structure, but not function, is known (but unpublished) for the member from Bacillus cereus, PDB|2B81. TIGR03572.1 TIGR03572 WbuZ 299.7 299.7 232 equivalog Y Y N glycosyl amidation-associated protein WbuZ wbuZ GO:0016833 15629947,16684771,18156256 131567 cellular organisms no rank 480 JCVI glycosyl amidation-associated protein WbuZ glycosyl amidation-associated protein WbuZ This clade of sequences is highly similar to the HisF protein, but generally represents the second HisF homolog in the genome where the other is an authentic HisF observed in the context of a complete histidine biosynthesis operon. The similarity between these WbuZ sequences and true HisFs is such that often the closest match by BLAST of a WbuZ is a HisF. Only by making a multiple sequence alignment is the homology relationship among the WbuZ sequences made apparent. WbuZ genes are invariably observed in the presence of a homolog of the HisH protein (designated WbuY) and a proposed N-acetyl sugar amidotransferase designated in WbuX in E. coli [1], IfnA in P. aeriginosa [2] and PseA in C. jejuni [3]. Similarly, this trio of genes is invariably found in the context of saccharide biosynthesis loci. It has been shown that the WbuYZ homologs are not essential components of the activity expressed by WbuX, leading to the proposal that these to proteins provide ammonium ions to the amidotransferase when these are in low concentration [1]. WbuY (like HisH) is proposed to act as a glutaminase to release ammonium. In histidine biosynthesis this is also dispensible in the presence of exogenous ammonium ion. HisH and HisF form a complex such that the ammonium ion is passed directly to HisF where it is used in an amidation reaction causing a subsequent cleavage and cyclization. In the case of WbuYZ, the ammonium ion would be passed from WbuY to WbuZ. WbuZ, being non-essential and so similar to HisF that a sugar substrate is unlikely, would function instead as a amoonium channel to the WbuX protein which does the enzymatic work. TIGR03573.1 TIGR03573 WbuX 203.2 203.2 344 subfamily Y Y N N-acetyl sugar amidotransferase 15629947,16684771,18156256 131567 cellular organisms no rank 5808 JCVI N-acetyl sugar amidotransferase N-acetyl sugar amidotransferase This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid [1]. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation [2]. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an invariable contextual association with homologs of the HisH and HisF proteins known as WbuY and WbuZ, respectively. These two proteins are believed to supply the enzyme with ammonium by hydrolysis of glutamine and delivery through an ammonium conduit [3]. TIGR03584.1 TIGR03584 PseF 205.7 205.7 222 equivalog Y Y N pseudaminic acid cytidylyltransferase pseF 2.7.7.81 GO:0070567 16684771 131567 cellular organisms no rank 7826 JCVI pseudaminic acid cytidylyltransferase pseudaminic acid cytidylyltransferase The sequences in this family include the PF02348 (cytidyltransferase) domain and are homologous to the NeuA protein responsible for the transfer of CMP to neuraminic acid. According to [1], this gene is responsible for the transfer of CMP to the structurally related sugar, pseudaminic acid which is observed as a component of sugar modifications of flagellin in Campylobacter species. This gene is commonly observed in apparent operons with other genes responsible for the biosynthesis of pseudaminic acid and as a component of flagellar and exopolysaccharide biosynthesis loci. TIGR03585.1 TIGR03585 PseH 93.1 93.1 156 equivalog Y Y N UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase pseH 2.3.1.202 GO:0008080,GO:0009058 16684771,19483088 131567 cellular organisms no rank 5620 JCVI UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase Sequences in this family are members of the PF00583 (GNAT) superfamily of acetyltransferases and are proposed to perform a N-acetylation step in the process of pseudaminic acid biosynthesis in Campylobacter species [1]. This gene is commonly observed in apparent operons with other genes responsible for the biosynthesis of pseudaminic acid and as a component of flagellar and exopolysaccharide biosynthesis loci. Significantly, many genomes containing other components of this pathway lack this gene, indicating that some other N-acetyl transferases may be incolved and/or the step is optional, resulting in a non-acetylated pseudaminic acid variant sugar. TIGR03586.1 TIGR03586 PseI 340.25 340.25 327 equivalog Y Y N pseudaminic acid synthase pseI 2.5.1.97 GO:0016765 16684771 131567 cellular organisms no rank 13015 JCVI pseudaminic acid synthase pseudaminic acid synthase Members of this family are included within the larger PF03102 (NeuB) family. NeuB itself (TIGR03569) is involved in the biosynthesis of neuraminic acid by the condensation of phosphoenolpyruvate (PEP) with N-Acetyl-D-Mannosamine. In an analagous reaction, this enzyme, PseI [1], condenses PEP with 6-deoxy-beta-L-AltNAc4NAc to generate pseudaminic acid. TIGR03587.1 TIGR03587 Pse_Me-ase 112.05 112.05 204 hypoth_equivalog Y Y N pseudaminic acid biosynthesis-associated methylase 16684771 131567 cellular organisms no rank 1039 JCVI pseudaminic acid biosynthesis-associated methylase pseudaminic acid biosynthesis-associated methylase Members of this small clade are methyltransferases of the PF08241 family and are observed within operons for the biosynthesis of pseudaminic acid, a component of exopolysaccharide and flagellin glycosyl modifications [1]. Notable among these genomes is Pseudomonas fluorescens PfO-1. Possibly one of the two hydroxyl groups of pseudaminic acid, at positions 4 and 8 is converted to a methoxy group by this enzyme TIGR03588.1 TIGR03588 PseC 423.5 423.5 380 equivalog Y Y N UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine transaminase pseC 2.6.1.92 GO:0003824 15790564,16286454,16421095,16684771 131567 cellular organisms no rank 12731 JCVI UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine transaminase UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine transaminase This family of enzymes are aminotransferases of the PF01041 family involved in the biosynthesis of pseudaminic acid [1,2,3]. They convert UDP-4-keto-6-deoxy-N-acetylglucosamine into UDP-4-amino-4,6-dideoxy-N-acetylgalactose. Pseudaminic acid has a role in surface polysaccharide in Pseudomonas as well as in the modification of flagellin in Campylobacter and Helicobacter species [4]. TIGR03589.1 TIGR03589 PseB 407.75 407.75 324 equivalog Y Y N UDP-N-acetylglucosamine 4,6-dehydratase (inverting) pseB 4.2.1.115 14617187,14960321,16286454,16684771,17893902 131567 cellular organisms no rank 10591 JCVI UDP-N-acetylglucosamine 4,6-dehydratase (inverting) UDP-N-acetylglucosamine 4,6-dehydratase (inverting) This enzyme catalyzes the first step in the biosynthesis of pseudaminic acid, the conversion of UDP-N-acetylglucosamine to UDP-4-keto-6-deoxy-N-acetylglucosamine. These sequences are members of the broader PF01073 (3-beta hydroxysteroid dehydrogenase/isomerase family) family. TIGR03590.1 TIGR03590 PseG 153.55 153.55 280 equivalog Y Y N UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase pseG 3.6.1.57 GO:0016758 16684771,19483088 131567 cellular organisms no rank 8748 JCVI UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase This protein is found in association with enzymes involved in the biosynthesis of pseudaminic acid [1], a component of polysaccharide in certain Pseudomonas strains as well as a modification of flagellin in Campylobacter and Hellicobacter [1]. The role of this protein is unclear, although it may participate in N-acetylation in conjunction with, or in the absence of PseH (TIGR03585) as it often scores above the trusted cutoff to PF00583 representing a family of acetyltransferases. TIGR03591.1 TIGR03591 polynuc_phos 525.05 525.05 689 equivalog Y Y N polyribonucleotide nucleotidyltransferase pnp 2.7.7.8 GO:0003723,GO:0004654,GO:0006402 17965156 131567 cellular organisms no rank 66416 JCVI polyribonucleotide nucleotidyltransferase polyribonucleotide nucleotidyltransferase Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family). TIGR03598.1 TIGR03598 GTPase_YsxC 124.45 124.45 186 equivalog Y Y N ribosome biogenesis GTP-binding protein YihA/YsxC yihA GO:0003924,GO:0005525,GO:0005737,GO:0042254,GO:0043022 17981968,20021644,21636901,32057832 131567 cellular organisms no rank 40739 JCVI ribosome biogenesis GTP-binding protein YsxC ribosome biogenesis GTP-binding protein YihA/YsxC Members of this protein family are a GTPase associated with ribosome biogenesis, currently named YihA in Escherichia coli and YsxC in Gram-positive bacteria. The family is widely but not universally distributed among bacteria. Some members previously were named EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic organellar sequences. This protein is found in about 80 percent of bacterial genomes. TIGR03604.1 TIGR03604 TOMM_cyclo_SagD 219.25 219.25 377 subfamily_domain Y N N thiazole/oxazole-forming peptide maturase, SagD family component 18375757,22522320 131567 cellular organisms no rank 17883 JCVI thiazole/oxazole-forming peptide maturase, SagD family component thiazole/oxazole-forming peptide maturase, SagD family component Members of this protein family include enzymes related to SagD, previously referred to as a scaffold or docking protein involved in the biosynthesis of streptolysin S in Streptococcus pyogenes from the protoxin polypeptide (product of the sagA gene). Newer evidence describes an enzymatic activity, an ATP-dependent cyclodehydration reaction, previously ascribed to the SagC component. This protein family serves as a marker for widely distributed prokaryotic systems for making a general class of heterocycle-containing bacteriocins. TIGR03605.1 TIGR03605 antibiot_sagB 78.4 78.4 173 domain Y Y N SagB family peptide dehydrogenase GO:0016491 18375757,27841750 131567 cellular organisms no rank 18400 JCVI SagB-type dehydrogenase domain SagB family peptide dehydrogenase SagB of Sterptococcus pyogenes participates in the maturation of streptolysin S from a ribosomally produced precursor polypeptide. Chemically similar systems operate on highly diverse sets of bacteriocin precursors in numerous other bacteria. The cyanobactin oxidase ThcOx likewise participates in peptide modification for form a natural product. TIGR03605 describes a domain within SgaB and homologous regions from other proteins, many of which appear to be involved in biosynthesis of secondary metabolites. While some substrates may be intermediates in non-ribosomal peptide syntheses, others are involved in heterocycle-containing bacteriocin biosynthesis, and can be found near SgaC-like (see TIGR03603) and SgaD-like (see TIGR03604) proteins. Members of this domain family are heterogeneous in length, as many have a partial second copy of the domain represented here. The incomplete second domain scores below the cutoffs to this model in most cases. TIGR03609.1 TIGR03609 S_layer_CsaB 213.1 213.1 301 equivalog Y Y N polysaccharide pyruvyl transferase CsaB csaB GO:0042545,GO:0046919 10970841 131567 cellular organisms no rank 5126 JCVI polysaccharide pyruvyl transferase CsaB polysaccharide pyruvyl transferase CsaB The CsaB protein (cell surface anchoring B) of Bacillus anthracis adds a pyruvoyl group to peptidoglycan-associated polysaccharide. This addition is required for proteins with an S-layer homology domain (PF00395) to bind. Within the larger group of proteins described by Pfam model PF04230, this model represents a distinct clade that nearly exactly follows the phylogenetic distribution of the S-layer homology domain (PF00395). TIGR03617.1 TIGR03617 F420_MSMEG_2256 278.15 278.15 318 subfamily Y Y N TIGR03617 family F420-dependent LLM class oxidoreductase 1.-.-.- GO:0016491,GO:0070967 20675471 131567 cellular organisms no rank 5607 JCVI probable F420-dependent oxidoreductase, MSMEG_2256 family TIGR03617 family F420-dependent LLM class oxidoreductase Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea 34H, Rhodopseudomonas palustris HaA2, and others. Partial phylogenetic profiling identifies protein subfamilies, within the larger family called luciferase-like monooxygenanases (PF00296), that appear only in F420-positive genomes and are likely to be F420-dependent. This model describes one such subfamily, exemplified by MSMEG_2256 from Mycobacterium smegmatis. TIGR03618.1 TIGR03618 Rv1155_F420 79.05 79.05 127 subfamily Y Y N TIGR03618 family F420-dependent PPOX class oxidoreductase GO:0016491,GO:0070967 15620716,20675471 131567 cellular organisms no rank 50569 JCVI PPOX class probable F420-dependent enzyme TIGR03618 family F420-dependent PPOX class oxidoreductase Members of this family are F420-dependent oxidoreductases, and occur strictly in lineages that synthesize F420. The family is distantly related to pyridoxine/pyridoxamine phosphate oxidases (PPOX), which depend on the related flavonoid cofactor FMN. A characterized member of this family is Rv2074, an F420-dependent biliverdin reductase. TIGR03619.1 TIGR03619 F420_Rv2161c 166.9 166.9 247 subfamily_domain Y Y N TIGR03619 family F420-dependent LLM class oxidoreductase 1.-.-.- GO:0016491,GO:0070967 20675471 131567 cellular organisms no rank 41488 JCVI probable F420-dependent oxidoreductase, Rv2161c family TIGR03619 family F420-dependent LLM class oxidoreductase Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea 34H, Rhodopseudomonas palustris HaA2, and others. Partial phylogenetic profiling identifies protein subfamilies, within the larger family called luciferase-like monooxygenanases (PF00296), that appear only in F420-positive genomes and are likely to be F420-dependent. This model describes a domain found in a distinctive subset of bacterial luciferase homologs, found only in F420-biosynthesizing members of the Actinobacteria. TIGR03624.1 TIGR03624 TIGR03624 136.05 136.05 346 subfamily Y N N putative hydrolase 131567 cellular organisms no rank 28820 JCVI putative hydrolase putative hydrolase Members of this protein family have a phylogenetic distribution skewed toward the Actinobacteria (high GC Gram-positive bacteria), but with a few members occuring in the Archaea and Chloroflexi. The function is unknown. TIGR03630.1 TIGR03630 uS17_arch 105 105 102 equivalog Y Y N 30S ribosomal protein S17 GO:0003735,GO:0006412,GO:0022627 131567 cellular organisms no rank 996 JCVI ribosomal protein uS17 30S ribosomal protein S17 This model describes exclusively the archaeal ribosomal protein S17P. It excludes the homologous ribosomal protein S17 from bacteria, and is not intended for use on eukaryotic sequences, where some instances of ribosomal proteins S11 score above the trusted cutoff. TIGR03632.1 TIGR03632 uS11_bact 154.5 154.5 117 equivalog Y Y N 30S ribosomal protein S11 rpsK GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 17596 JCVI ribosomal protein uS11 30S ribosomal protein S11 This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected. TIGR03633.1 TIGR03633 arc_protsome_A 287.35 287.35 230 equivalog Y Y N archaeal proteasome endopeptidase complex subunit alpha psmA 3.4.25.1 GO:0000502,GO:0004175,GO:0010498 131567 cellular organisms no rank 1596 JCVI proteasome endopeptidase complex, archaeal, alpha subunit archaeal proteasome endopeptidase complex subunit alpha This protein family describes the archaeal proteasome alpha subunit, homologous to both the beta subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated. TIGR03636.1 TIGR03636 uL23_arch 94.95 94.95 77 equivalog Y Y N 50S ribosomal protein L23 GO:0003735,GO:0005840,GO:0006412 131567 cellular organisms no rank 985 JCVI ribosomal protein uL23 50S ribosomal protein L23 This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts. TIGR03638.1 TIGR03638 cas1_ECOLI 215.6 215.6 269 exception Y Y N type I-E CRISPR-associated endonuclease Cas1e cas1e GO:0003676,GO:0004520,GO:0043571,GO:0046872,GO:0051607 16292354 131567 cellular organisms no rank 8864 JCVI CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI type I-E CRISPR-associated endonuclease Cas1e The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 protein particular to the ECOLI subtype of CRISPR/Cas system. TIGR03639.1 TIGR03639 cas1_NMENI 120 120 278 exception Y Y N type II CRISPR-associated endonuclease Cas1 cas1 GO:0003676,GO:0004520,GO:0043571,GO:0046872,GO:0051607 16292354 131567 cellular organisms no rank 8009 JCVI CRISPR-associated endonuclease Cas1, subtype II/NMENI type II CRISPR-associated endonuclease Cas1 The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is a prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 variant of the NMENI subtype of CRISPR/Cas system. TIGR03640.1 TIGR03640 cas1_DVULG 385 385 340 exception Y Y N type I-C CRISPR-associated endonuclease Cas1c cas1c GO:0003676,GO:0004519,GO:0043571,GO:0046872,GO:0051607 16292354 131567 cellular organisms no rank 5337 JCVI CRISPR-associated endonuclease Cas1, subtype I-C/DVULG type I-C CRISPR-associated endonuclease Cas1c The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 protein particular to the DVULG subtype of CRISPR/Cas system. TIGR03641.1 TIGR03641 cas1_HMARI 304.1 304.1 324 exception Y Y N type I-B CRISPR-associated endonuclease Cas1b cas1b GO:0004520,GO:0043571,GO:0046872 16292354 131567 cellular organisms no rank 3708 JCVI CRISPR-associated endonuclease Cas1, subtype I-B/HMARI/TNEAP type I-B CRISPR-associated endonuclease Cas1b The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes Cas1 subgroup that includes Cas1 proteins of the related HMARI and TNEAP subtypes of CRISPR/Cas system. TIGR03642.1 TIGR03642 cas_csx14 90.35 90.35 124 hypoth_equivalog_domain Y Y N CRISPR-associated protein Csx14 131567 cellular organisms no rank 58 JCVI CRISPR-associated protein, Csx14 family CRISPR-associated protein Csx14 This model describes a protein N-terminal protein sequence domain strictly associated with CRISPR and CRISPR-associated protein systems. This model and TIGR02584 identify two separate clades from a larger homology domain family, both CRISPR-associated, while other homologs are found that may not be. Members are found in bacteria that include Pelotomaculum thermopropionicum SI, Thermoanaerobacter tengcongensis MB4, and Roseiflexus sp. RS-1, and in archaea that include Thermoplasma volcanium, Picrophilus torridus, and Methanospirillum hungatei. The molecular function is unknown. TIGR03647.1 TIGR03647 Na_symport_sm 26.05 26.05 77 subfamily_domain Y Y N sodium/substrate symporter small subunit 33343547 131567 cellular organisms no rank 10189 JCVI putative solute:sodium symporter small subunit sodium/substrate symporter small subunit Members of this family are highly hydrophobic bacterial proteins of about 90 amino acids in length. Members usually are found immediately upstream (sometimes fused to) a member of the solute:sodium symporter family, and therefore are a putative sodium:solute symporter small subunit. Members tend to be found in aquatic species, especially those from marine or other high salt environments. Substrates identified for various members include acetate, pyruvate, D-alanine, L-lactate and L-malate. TIGR03648.1 TIGR03648 Na_symport_lg 320.75 320.75 547 subfamily Y Y N VC_2705 family sodium/solute symporter GO:0016020,GO:0022857,GO:0055085 131567 cellular organisms no rank 13146 JCVI probable sodium:solute symporter, VC_2705 subfamily VC_2705 family sodium/solute symporter This family belongs to a larger family of transporters of the sodium:solute symporter (SSS) superfamily, TC 2.A.21, as defined by the Transporter Classification DataBase (TCDB). Members of this strictly bacterial protein subfamily are found almost invariably immediately downstream from a member of family TIGR03647. Occasionally, the two genes are fused. The best characterized member of the larger SSS superfamily, to which this subfamily belongs, is the acetate permease ActP found in E. coli, and many members of this family have received that annotation. TIGR03661.1 TIGR03661 T1SS_VCA0849 17.6 17.6 91 domain Y Y N type I secretion C-terminal target domain-containing protein 131567 cellular organisms no rank 48104 JCVI type I secretion C-terminal target domain (VC_A0849 subclass) type I secretion C-terminal target domain (VC_A0849 subclass) This model represents a C-terminal domain associated with secretion by type 1 secretion systems (T1SS). Members of this subclass do not include the RtxA toxin of Vibrio cholerae and its homologs, although the two classes of proteins share large size, occurrence in genomes with T1SS, regions with long tandem repeats, and regions with the glycine-rich repeat modeled by PF00353. TIGR03662.1 TIGR03662 Chlor_Arch_YYY 300.25 300.25 727 subfamily_domain Y N N chlor_Arch_YYY domain 131567 cellular organisms no rank 1353 JCVI chlor_Arch_YYY domain chlor_Arch_YYY domain Members of this highly hydrophobic probable integral membrane family belong to two classes. In one, a single copy of the region modeled by this HMM represents essentially the full length of a strongly hydrophobic protein of about 700 to 900 residues (variable because of long inserts in some). The domain architecture of the other class consists of an additional N-terminal region, two copies of the region represented by this model, and three to four repeats of TPR, or tetratricopeptide repeat. The unusual species range includes several Archaea, several Chloroflexi, and Clostridium phytofermentans. An unusual motif YYYxG is present, and we suggest the name Chlor_Arch_YYY protein. The function is unknown. TIGR03663.1 TIGR03663 TIGR03663 126.25 126.25 435 subfamily Y Y N flippase activity-associated protein Agl23 32706435 131567 cellular organisms no rank 1272 JCVI TIGR03663 family protein flippase activity-associated protein Agl23 Members of this protein family, uncommon and rather sporadically distributed, are found almost always in the same genomes as members of family TIGR03662, and frequently as a nearby gene. Members show some N-terminal sequence similarity with Pfam family PF02366, dolichyl-phosphate-mannose-protein mannosyltransferase. The few invariant residues in this family, found toward the N-terminus, include a dipeptide DE, a tripeptide HGP, and two different Arg residues. Up to three members may be found in a genome. A member of this family, HAH_2016 from the halophilic archaeaon Haloarcula hispanica, was renamed Agl23. Agl23 was shown to be required for both N-linked and O-linked glycosylation of the S-layer glycoprotein in whole cells, but not in lysates, suggesting a flippase-like or flippase-associated function. TIGR03664.1 TIGR03664 fut_nucase 124.7 124.7 228 equivalog Y Y N futalosine hydrolase mqnB 3.2.2.26 GO:0009234,GO:0016799 18801996,19420717 131567 cellular organisms no rank 10731 JCVI futalosine hydrolase futalosine hydrolase This enzyme catalyzes the conversion of futalosine to de-hypoxanthine futalosine in a pathway for the biosynthesis of menaquinone [1] distinct from the pathway observed in E. coli. TIGR03666.1 TIGR03666 Rv2061_F420 84.9 84.9 132 subfamily Y Y N PPOX class F420-dependent oxidoreductase 1.-.-.- GO:0016491,GO:0070967 20675471 131567 cellular organisms no rank 11510 JCVI PPOX class probable F420-dependent enzyme, Rv2061 family PPOX class F420-dependent oxidoreductase A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme pyridoxamine phosphate oxidase (PPOX) binds FMN. TIGR03668.1 TIGR03668 Rv0121_F420 119.15 119.15 141 hypoth_equivalog Y Y N TIGR03668 family PPOX class F420-dependent oxidoreductase GO:0016491,GO:0070967 16930487,20675471 131567 cellular organisms no rank 4633 JCVI PPOX class probable F420-dependent enzyme, Rv0121 family TIGR03668 family PPOX class F420-dependent oxidoreductase A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme pyridoxamine phosphate oxidase (PPOX) binds FMN. TIGR03669.1 TIGR03669 urea_ABC_arch 494.8 494.8 375 equivalog Y Y N urea ABC transporter substrate-binding protein GO:0015840,GO:0033219,GO:0033221,GO:0055052 131567 cellular organisms no rank 882 JCVI urea ABC transporter, substrate-binding protein urea ABC transporter substrate-binding protein Members of this protein family are identified as the substrate-binding protein of a urea ABC transport system by similarity to a known urea transporter from Corynebacterium glutamicum, operon structure, proximity of its operons to urease (urea-utilization protein) operons, and by Partial Phylogenetic Profiling vs. urea utilization. TIGR03674.1 TIGR03674 fen_arch 351.95 351.95 338 equivalog Y Y N flap endonuclease-1 fen GO:0016788 12147694 131567 cellular organisms no rank 1459 JCVI flap structure-specific endonuclease flap endonuclease-1 Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA TIGR03675.1 TIGR03675 arCOG00543 580.2 580.2 631 equivalog Y Y N beta-CASP ribonuclease aCPSF1 GO:0003723 18042280,21565697,23222134 131567 cellular organisms no rank 1471 JCVI arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein beta-CASP ribonuclease aCPSF1 This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (PF00013) a central beta-lactamase-domain (PF00753) with a C-terminal motif associated with RNA metabolism (PF07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in [1] as arCOG01782. TIGR03677.1 TIGR03677 eL8_ribo 134.6 134.6 117 equivalog Y Y N 50S ribosomal protein L7Ae rpl7ae GO:0003723,GO:0003735,GO:0005840,GO:0006412 16008351 131567 cellular organisms no rank 946 JCVI ribosomal protein eL8 ribosomal protein eL8 This model specifically identifies the archaeal version of the large ribosomal complex protein eL8, previously designated L8 in yeast and L7Ae in the archaea. The family is a narrower version of the PF01248 model which also recognizes the L30 protein. TIGR03684.1 TIGR03684 arCOG00985 120.6 120.6 154 hypoth_equivalog Y N N arCOG04150 universal archaeal PUA-domain protein 18042280 131567 cellular organisms no rank 1239 JCVI arCOG04150 universal archaeal PUA-domain protein arCOG04150 universal archaeal PUA-domain protein This universal archaeal protein [1] contains a domain possibly associated with RNA binding (PF01472, TIGR00451). TIGR03685.1 TIGR03685 ribo_P1_arch 100 100 105 equivalog Y Y N 50S ribosomal protein P1 rpl12p GO:0003735,GO:0005840,GO:0006414 10328820,28042029 131567 cellular organisms no rank 1217 JCVI 50S ribosomal protein P1 50S ribosomal protein P1 This model represents aP1, the L12P protein of the large (50S) subunit of the archaeal ribosome. TIGR03696.1 TIGR03696 Rhs_assc_core 32.5 32.5 76 domain Y Y N RHS repeat-associated core domain-containing protein 15194482,16406038 131567 cellular organisms no rank 262872 JCVI RHS repeat-associated core domain RHS repeat-associated core domain This model represents a conserved unique core sequence shared by large numbers of proteins. It is occasional in the Archaea Methanosarcina barkeri) but common in bacteria and eukaryotes. Most fall into two large classes. One class consists of long proteins in which two classes of repeats are abundant: an FG-GAP repeat (PF01839) class, and an RHS repeat (PF05593) or YD repeat (TIGR01643). This class includes secreted bacterial insecticidal toxins and intercellular signalling proteins such as the teneurins in animals. The other class consists of uncharacterized proteins shorter than 400 amino acids, where this core domain of about 75 amino acids tends to occur in the N-terminal half. Over twenty such proteins are found in Pseudomonas putida alone; little sequence similarity or repeat structure is found among these proteins outside the region modeled by this domain. TIGR03698.1 TIGR03698 clan_AA_DTGF 57.35 57.35 107 subfamily Y Y N clan AA aspartic protease 3.4.23.- GO:0004190 19173708 131567 cellular organisms no rank 806 JCVI clan AA aspartic protease, AF_0612 family clan AA aspartic protease Members of this protein family are clan AA aspartic proteases, related to family TIGR02281. These proteins resemble retropepsins, pepsin-like proteases of retroviruses such as HIV. Members of this family are found in archaea and bacteria. TIGR03699.1 TIGR03699 menaquin_MqnC 428.1 428.1 342 equivalog Y Y N cyclic dehypoxanthinyl futalosine synthase mqnC 1.21.98.1 GO:0009234 18801996,23763543 131567 cellular organisms no rank 11010 JCVI dehypoxanthine futalosine cyclase cyclic dehypoxanthinyl futalosine synthase Members of this protein family are involved in menaquinone biosynthesis by an alternate pathway via futalosine. TIGR03700.1 TIGR03700 mena_SCO4494 434.55 434.55 351 equivalog Y Y N aminofutalosine synthase MqnE mqnE GO:0009234 18801996 131567 cellular organisms no rank 10933 JCVI putative menaquinone biosynthesis radical SAM enzyme, SCO4494 family aminofutalosine synthase MqnE Members of this protein family appear to be involved in menaquinone biosynthesis by an alternate pathway via futalosine, based on close phylogenetic correlation with known markers of the futalosine pathway, gene clustering in many organisms, and paralogy with the SCO4550 protein. TIGR03701.1 TIGR03701 mena_SCO4490 495.9 495.9 433 equivalog Y Y N menaquinone biosynthesis decarboxylase GO:0009234,GO:0016831 18801996 131567 cellular organisms no rank 10969 JCVI menaquinone biosynthesis decarboxylase, SCO4490 family menaquinone biosynthesis decarboxylase Members of this protein family are putative decarboxylases involved in a late stage of the alternative pathway for menaquinone, via futalosine, as in Streptomyces coelicolor and Helicobacter pylori. TIGR03705.1 TIGR03705 poly_P_kin 465.85 465.85 673 equivalog Y Y N polyphosphate kinase 1 ppk1 2.7.4.1 GO:0006799,GO:0008976,GO:0009358 15520374,2164013 131567 cellular organisms no rank 65143 JCVI polyphosphate kinase 1 polyphosphate kinase 1 Members of this protein family are the enzyme polyphosphate kinase 1 (PPK1). This family is found in many prokaryotes and also in Dictyostelium. Sequences in the seed alignment were taken from prokaryotic consecutive two-gene pairs in which the other gene encodes an exopolyphosphatase. It synthesizes polyphosphate from the terminal phosphate of ATP but not GTP, in contrast to PPK2. TIGR03707.1 TIGR03707 PPK2_P_aer 301.8 301.8 230 equivalog Y Y N polyphosphate kinase 2 ppk2 2.7.4.1 GO:0006793,GO:0008976 12482933 131567 cellular organisms no rank 38585 JCVI polyphosphate kinase 2 polyphosphate kinase 2 Members of this protein family are designated polyphosphate kinase 2 (PPK2) after the characterized protein in Pseudomonas aeruginosa. This family comprises one of three well-separated clades in the larger family described by Pfam model PF03976. PA0141 from this family has been shown capable of operating in reverse, with GDP preferred (over ADP) as a substrate, producing GTP (or ATP) by transfer of a phosphate residue from polyphosphate. Most species with a member of this family also encode a polyphosphate kinase 1 (PPK1). TIGR03708.1 TIGR03708 poly_P_AMP_trns 547.65 547.65 493 equivalog Y Y N polyphosphate:AMP phosphotransferase pap 2.7.4.33 GO:0006797,GO:0043751 15262957 131567 cellular organisms no rank 5978 JCVI polyphosphate:AMP phosphotransferase polyphosphate:AMP phosphotransferase Members of this protein family contain a domain duplication. The characterized member from Acinetobacter johnsonii is polyphosphate:AMP phosphotransferase (PAP), which can transfer the terminal phosphate from poly(P) to AMP, yielding ADP. In the opposite direction, this enzyme can synthesize poly(P). Each domain of this protein family is homologous to polyphosphate kinase, an enzyme that can run in the forward direction to extend a polyphosphate chain with a new terminal phosphate from ATP, or in reverse to make ATP (or GTP) from ADP (or GDP). TIGR03709.1 TIGR03709 PPK2_rel_1 247.2 247.2 264 subfamily Y Y N PPK2 family polyphosphate kinase GO:0006797,GO:0016776 19001261,24532069,29531036 131567 cellular organisms no rank 22572 JCVI polyphosphate:nucleotide phosphotransferase, PPK2 family PPK2 family polyphosphate kinase Members of this protein family belong to the polyphosphate kinase 2 (PPK2) family, which is not related in sequence to PPK1. While PPK1 tends to act in the biosynthesis of polyphosphate, or poly(P), members of the PPK2 family tend to use the terminal phosphate of poly(P) to regenerate ATP or GTP from the corresponding nucleoside diphosphate, or ADP from AMP as is the case with polyphosphate:AMP phosphotransferase (PAP). Members of this protein family most likely transfer the terminal phosphate between poly(P) and some nucleotide, but it is not clear which. TIGR03710.1 TIGR03710 OAFO_sf 482.75 482.75 561 subfamily Y Y N 2-oxoacid:acceptor oxidoreductase subunit alpha 11401501,15184674,8655524,8902625 131567 cellular organisms no rank 24821 JCVI 2-oxoacid:acceptor oxidoreductase, alpha subunit 2-oxoacid:acceptor oxidoreductase subunit alpha This family of proteins contains a C-terminal thiamine diphosphate (TPP) binding domain typical of flavodoxin/ferredoxin oxidoreductases (PF01855) as well as an N-terminal domain similar to the gamma subunit of the same group of oxidoreductases (PF01558). The genes represented by this model are always found in association with a neighboring gene for a beta subunit (TIGR02177) which also occurs in a 4-subunit (alpha/beta/gamma/ferredoxin) version of the system. This alpha/gamma plus beta structure was used to define the set of sequences to include in this model. TIGR03718.1 TIGR03718 R_switched_Alx 246.4 246.4 303 subfamily Y Y N TerC/Alx family metal homeostasis membrane protein GO:0016020 12724390,23044854,25794618,26778143,29440394,3049247 131567 cellular organisms no rank 45342 JCVI integral membrane protein, TerC family TerC/Alx family metal homeostasis membrane protein Members of this family include the tellurium resistance protein TerC (a probable efflux transporter) and the manganese homeostasis protein Alx from Escherichia coli K-12. TIGR03725.1 TIGR03725 T6A_YeaZ 69.3 69.3 212 equivalog Y Y N tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex dimerization subunit type 1 TsaB tsaB 2.3.1.234 GO:0002949 16617437,22378793 131567 cellular organisms no rank 73809 JCVI tRNA threonylcarbamoyl adenosine modification protein YeaZ tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex dimerization subunit type 1 TsaB This family describes a protein family, YeaZ, now associated with the threonylcarbamoyl adenosine (t6A) tRNA modification. Members of this family may occur as fusions with ygjD (previously gcp) or the ribosomal protein N-acetyltransferase rimI, and is frequently encoded next to rimI. TIGR03730.1 TIGR03730 tungstate_WtpA 242.75 242.75 275 equivalog Y Y N tungstate ABC transporter substrate-binding protein WtpA wtpA GO:1901359 16952940 131567 cellular organisms no rank 463 JCVI tungstate ABC transporter binding protein WtpA tungstate ABC transporter substrate-binding protein WtpA Members of this protein family are tungstate (and, more weakly, molybdate) binding proteins of tungstate(/molybdate) ABC transporters, as first characterized in Pyrococcus furiosus. Model seed members and cutoffs, pending experimental evidence for more distant homologs, were chosen such that this model identifies select archaeal proteins, excluding weaker archaeal and all bacterial homologs. Note that this family is homologous to molybdate transporters, and that at least one other family of tungstate transporter binding protein, TupA, also exists. TIGR03753.1 TIGR03753 blh_monoox 95.25 95.25 260 subfamily Y Y N beta-carotene 15,15'-dioxygenase, Brp/Blh family 1.13.11.63 GO:0016702 19366683 131567 cellular organisms no rank 2683 JCVI beta-carotene 15,15'-monooxygenase, Brp/Blh family beta-carotene 15,15'-dioxygenase, Brp/Blh family This integral membrane protein family includes Brp (bacterio-opsin related protein) and Blh (Brp-like protein). Bacteriorhodopsin is a light-driven proton pump with a covalently bound retinal cofactor that appears to be derived beta-carotene. Blh has been shown to cleave beta-carotene to product two all-trans retinal molecules. Mammalian enzymes with similar enzymatic function are not multiple membrane spanning proteins and are not homologous. TIGR03768.1 TIGR03768 RPA4764 387.4 387.4 547 hypoth_equivalog Y Y N TIGR03768 family metallophosphoesterase 131567 cellular organisms no rank 124 JCVI metallophosphoesterase, RPA4764 family TIGR03768 family metallophosphoesterase This HMM describes a small collection of probable metallophosphoresterases, related to PF00149. Members of this protein family usually have a Sec-independent TAT (twin-arginine translocation) signal sequence, N-terminal to the region modeled by this HMM. This model and TIGR03767 divide a narrow clade of PF00149-related enzymes. TIGR03783.1 TIGR03783 Bac_Flav_CT_G 261.55 261.55 829 subfamily Y Y N TraG family conjugative transposon ATPase GO:0016887,GO:0032196,GO:0032991 131567 cellular organisms no rank 9408 JCVI Bacteroides conjugation system ATPase, TraG family TraG family conjugative transposon ATPase Members of this family include the predicted ATPase, TraG, encoded by transfer region genes of conjugative transposons of Bacteroides, such as CTnDOT, found on the main chromosome. Members also include TraG homologs borne on plasmids in Bacteroides. The protein family is related to the conjugative transfer system ATPase VirB4. TIGR03790.1 TIGR03790 TIGR03790 67 67 316 subfamily Y Y N TIGR03790 family protein 131567 cellular organisms no rank 1275 JCVI TIGR03790 family protein TIGR03790 family protein Despite a broad and sporadic distribution (Cyanobacteria, Verrucomicrobia, Acidobacteria, beta and delta Proteobacteria, and Planctomycetes), this uncharacterized protein family occurs only among the roughly 8 percent of prokarotyic species that carry homologs of the integral membrane protein exosortase (see TIGR02602), a proposed protein-sorting system transpeptidase. TIGR03793.1 TIGR03793 leader_NHLP 50.9 50.9 77 domain Y Y N NHLP leader peptide family RiPP precursor 20500830,22983711 131567 cellular organisms no rank 1973 JCVI NHLP leader peptide domain NHLP family RiPP leader peptide This HMM represents a domain that is conserved among a large number of ribosomally synthesized and post-translationally modified peptide natural product (RiPP) precursors, including thiazole/oxazole-modified microcins (TOMMs), lantibiotics, and radical SAM/SPASM-modified peptides. As a leader peptide domain, likely to be removed from the mature product, this domain is unusual in several ways. First, it is longer than most previously described RiPP leader peptides. Second, most of the domain is homologous to nitrile hydratase alpha subunits, hence NHLP, for Nitrile Hydratase-like Leader Peptide. The variety of types of modification associated with RiPPs with this one family of leader peptide suggests additional modification chemistries may be discovered for some family members. This family is expanded especially in Pelotomaculum thermopropionicum SI. TIGR03796.1 TIGR03796 NHLM_micro_ABC1 853.3 853.3 710 equivalog Y Y N NHLP family bacteriocin export ABC transporter peptidase/permease/ATPase subunit GO:0005524,GO:0006508,GO:0008233,GO:0055085,GO:0140359 131567 cellular organisms no rank 6826 JCVI NHLM bacteriocin system ABC transporter, peptidase/ATP-binding protein NHLP family bacteriocin export ABC transporter peptidase/permease/ATPase subunit This protein describes a multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHLM, Nitrile Hydratase Leader Microcin. TIGR03797.1 TIGR03797 NHLM_micro_ABC2 709.4 709.4 686 equivalog Y Y N NHLP bacteriocin export ABC transporter permease/ATPase subunit GO:0015440,GO:0043213 131567 cellular organisms no rank 7219 JCVI NHLM bacteriocin system ABC transporter, ATP-binding protein NHLP bacteriocin export ABC transporter permease/ATPase subunit Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal leader sequence cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, members of protein families related to nitrile hydratase alpha subunit or to nif11 have undergone paralogous family expansions, with members possessing a putative bacteriocin cleavage region ending with a classic Gly-Gly motif. Those sets of putative bacteriocins, members of this protein family and its partners TIGR03794 and TIGR03796, and cyclodehydratase/docking scaffold fusion proteins of thiazole/oxazole biosynthesis frequently show correlated species distribution and co-clustering within many of those genomes. TIGR03798.1 TIGR03798 leader_Nif11 32.3 32.3 68 subfamily Y Y N Nif11-like leader peptide family RiPP precursor 20479271,20500830,22574919 131567 cellular organisms no rank 3393 JCVI nif11-like leader peptide domain Nif11-like RiPP leader peptide This model describes a conserved, fairly long (about 65 residue) leader peptide region for a family of ribosomally synthesized and post-translationally modified peptide natural products (RiPPs) of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain. Members include the prochlorosins, lanthipeptides from Prochlorococcus. TIGR03800.1 TIGR03800 PLP_synth_Pdx2 105.55 105.55 184 equivalog Y Y N pyridoxal 5'-phosphate synthase glutaminase subunit PdxT pdxT 3.5.1.2,4.3.3.6 GO:0004359,GO:0016884,GO:0042823 131567 cellular organisms no rank 24995 JCVI pyridoxal 5'-phosphate synthase, glutaminase subunit Pdx2 pyridoxal 5'-phosphate synthase glutaminase subunit PdxT Pyridoxal 5'-phosphate (PLP) is synthesized by the PdxA/PdxJ pathway in some species (mostly within the gamma subdivision of the proteobacteria) and by the Pdx1/Pdx2 pathway in most other organisms. This family describes Pdx2, the glutaminase subunit of the PLP synthase. TIGR03801.1 TIGR03801 asp_4_decarbox 435.1 435.1 521 equivalog Y Y N aspartate 4-decarboxylase aspD 4.1.1.12 GO:0006531,GO:0047688 12003930,19265705 131567 cellular organisms no rank 7244 JCVI aspartate 4-decarboxylase aspartate 4-decarboxylase This enzyme, aspartate 4-decarboxylase (EC 4.1.1.12), removes the side-chain carboxylate from L-aspartate, converting it to L-alanine plus carbon dioxide. It is a PLP-dependent enzyme, homologous to aspartate aminotransferase (EC 2.6.1.1). TIGR03804.1 TIGR03804 para_beta_helix 19.45 19.45 44 repeat Y N N parallel beta-helix repeat protein 11852237 131567 cellular organisms no rank 25590 JCVI parallel beta-helix repeat parallel beta-helix repeat (two copies) This model represents a tandem pair of an approximately 22-amino acid (each) repeat homologous to the beta-strand repeats that stack in a right-handed parallel beta-helix in the periplasmic C-5 mannuronan epimerase, AlgA, of Pseudomonas aeruginosa. A homology domain consisting of a longer tandem array of these repeats is described in the SMART database as CASH (SM00722), and is found in many carbohydrate-binding proteins and sugar hydrolases. A single repeat is represented by SM00710. This TIGRFAMs model represents a flavor of the parallel beta-helix-forming repeat based on prokaryotic sequences only in its seed alignment, although it also finds many eukaryotic sequences. TIGR03812.1 TIGR03812 tyr_de_CO2_Arch 299.4 299.4 375 equivalog Y Y N tyrosine decarboxylase MfnA mfnA 4.1.1.25 GO:0004837 15715981 131567 cellular organisms no rank 1408 JCVI tyrosine decarboxylase MnfA tyrosine decarboxylase MfnA Members of this protein family are the archaeal form, MnfA, of tyrosine decarboxylase, and are involved in methanofuran biosynthesis. Members show clear homology to the Enterococcus form, Tdc, that is involved in tyrosine decarboxylation for resistance to acidic conditions. TIGR03820.1 TIGR03820 lys_2_3_AblA 525.4 525.4 417 equivalog Y Y N lysine 2,3-aminomutase ablA 5.4.3.2 GO:0046440,GO:0050066,GO:0051539,GO:1904047 14532061 131567 cellular organisms no rank 3559 JCVI lysine-2,3-aminomutase lysine 2,3-aminomutase This model describes lysine-2,3-aminomutase, which can occur in multiple pathways. It is designated AblA when paired with beta-lysine acetyltransferase in a two-enzyme pathway for making the compatible solute N-epsilon-acetyl-beta-lysine. This compatible solute, or osmolyte, is known to protect a number of methanogenic archaea against salt stress. Lysine-2,3-aminomutase is belongs to lysine degradation pathways, where it is known as KamA. The enzyme belongs to the radical SAM superfamily. TIGR03827.1 TIGR03827 GNAT_ablB 205.1 205.1 266 equivalog Y Y N putative beta-lysine N-acetyltransferase ablB GO:0008080 14532061 131567 cellular organisms no rank 3678 JCVI putative beta-lysine N-acetyltransferase putative beta-lysine N-acetyltransferase Members of this protein family are GNAT family acetyltransferases, based on a seed alignment in which every member is associated with a lysine 2,3-aminomutase family protein, usually as the adjacent gene. This family includes AblB, the enzyme beta-lysine acetyltransferase that completes the two-step synthesis of the osmolyte (compatible solute) N-epsilon-acetyl-beta-lysine; all members of the family may have this function. Note that N-epsilon-acetyl-beta-lysine has been observed only in methanogenic archaea (e.g. Methanosarcina) but that this model, paired with TIGR03820, suggests a much broader distribution. TIGR03828.1 TIGR03828 pfkB 292 292 305 equivalog Y Y N 1-phosphofructokinase pfkB 2.7.1.56 GO:0008662 131567 cellular organisms no rank 33640 JCVI 1-phosphofructokinase 1-phosphofructokinase This enzyme acts in concert with the fructose-specific phosphotransferase system (PTS) which imports fructose as fructose-1-phosphate. The action of 1-phosphofructokinase results in beta-D-fructose-1,6-bisphosphate and is an entry point into glycolysis (GenProp0688). TIGR03831.1 TIGR03831 YgiT_finger 20.2 20.2 46 domain Y Y N YgiT-type zinc finger protein 19636869 131567 cellular organisms no rank 6517 JCVI YgiT-type zinc finger domain YgiT-type zinc finger domain This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by PF01381. TIGR03833.1 TIGR03833 TIGR03833 63.4 63.4 62 hypoth_equivalog Y Y N YwbE family protein 131567 cellular organisms no rank 5484 JCVI conserved hypothetical protein YwbE family protein A pair of adjacent genes, ablAB (acetyl-beta-lysine biosynthesis) encodes lysine 2,3-aminomutase and beta-lysine acetyltransferase in methanogenic archaea. Homologous pairs, possibly with identical function, occur in a wide range of species, including Bacillus subtilis. This model describes a conserved hypothetical protein, small in size, with a phylogenetic distribution moderately well correlated to that of the acetyltransferase family. This protein family is also described as DUF2196 and COG4895. The function is unknown. TIGR03842.1 TIGR03842 F420_CPS_4043 295.45 295.45 329 hypoth_equivalog Y Y N TIGR03842 family LLM class F420-dependent oxidoreductase GO:0016491,GO:0070967 20675471 131567 cellular organisms no rank 8791 JCVI F420-dependent oxidoreductase, CPS_4043 family TIGR03842 family LLM class F420-dependent oxidoreductase This HMM represents a family of putative F420-dependent oxidoreductases, fairly closely related to 5,10-methylenetetrahydromethanopterin reductase (mer, TIGR03555), both within the bacterial luciferase-like monoxygenase (LLM) family. A fairly deep split (to about 40 % sequence identity) in the present family separates a strictly Actinobacterial clade from an alpha/beta/gamma-proteobacterial clade, in which the member is often the only apparent F420-dependent LLM family member. The specific function, and whether Actinobacterial and Proteobacterial clades differ in function, are unknown. TIGR03844.1 TIGR03844 cysteate_syn 324.9 324.9 398 equivalog Y Y N cysteate synthase 2.5.1.76 GO:0030170,GO:0044686 19761441 131567 cellular organisms no rank 964 JCVI cysteate synthase cysteate synthase Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M. TIGR03845.1 TIGR03845 sulfopyru_alph 147.95 147.95 160 equivalog_domain Y Y N sulfopyruvate decarboxylase subunit alpha comD 4.1.1.79 GO:0030976 10940029,19581363 131567 cellular organisms no rank 809 JCVI sulfopyruvate decarboxylase, alpha subunit sulfopyruvate decarboxylase subunit alpha This HMM represents the alpha subunit, or the N-terminal region, of sulfopyruvate decarboxylase, an enzyme of coenzyme M biosynthesis. Coenzyme M is found almost exclusively in the methanogenic archaea. However, the enzyme also occurs in Roseovarius nubinhibens ISM in a degradative pathway, where the resulting sulfoacetaldehyde is desulfonated to acetyl phosphate, then converted to acetyl-CoA (see PMID:19581363). TIGR03846.1 TIGR03846 sulfopy_beta 221.5 221.5 182 equivalog Y Y N sulfopyruvate decarboxylase subunit beta comE 4.1.1.79 GO:0003824,GO:0030976 10940029,19581363 131567 cellular organisms no rank 982 JCVI sulfopyruvate decarboxylase, beta subunit sulfopyruvate decarboxylase subunit beta Nearly every member of this protein family is the beta subunit, or else the C-terminal region, of sulfopyruvate decarboxylase, in an archaeal species capable of coenzyme M biosynthesis. However, the enzyme also occurs in Roseovarius nubinhibens ISM in a degradative pathway, where the resulting sulfoacetaldehyde is desulfonated to acetyl phosphate, then converted to acetyl-CoA (see PMID:19581363). TIGR03855.1 TIGR03855 NAD_NadX 206.55 206.55 229 equivalog Y Y N aspartate dehydrogenase nadX 1.4.1.21 GO:0033735 131567 cellular organisms no rank 1340 JCVI aspartate dehydrogenase aspartate dehydrogenase Members of this protein family are L-aspartate dehydrogenase, as shown for the NADP-dependent enzyme TM_1643 of Thermotoga maritima. Members lack homology to NadB, the aspartate oxidase (EC 1.4.3.16) of most mesophilic bacteria (described by TIGR00551), which this enzyme replaces in the generation of oxaloacetate from aspartate for the NAD biosynthetic pathway. All members of the seed alignment are found adjacent to other genes of NAD biosynthesis, although other uses of L-aspartate dehydrogenase may occur. TIGR03858.1 TIGR03858 LLM_2I7G 462.25 462.25 337 subfamily Y Y N Atu2307/SP_0267 family LLM class monooxygenase 1.-.-.- GO:0010181 131567 cellular organisms no rank 16487 JCVI probable oxidoreductase, LLM family Atu2307/SP_0267 family LLM class monooxygenase This HMM describes a highly conserved, somewhat broadly distributed family withing the luciferase-like monooxygenase (LLM) superfamily. Most members are from species incapable of synthesizing coenzyme F420, bound by some members of the LLM superfamily. Members, therefore, are more likely to use FMN as a cofactor. Member protein Atu2307 from Agrobacterium tumefaciens has a solved crystal structure. TIGR03859.1 TIGR03859 PQQ_PqqD 46 46 81 equivalog Y Y N pyrroloquinoline quinone biosynthesis peptide chaperone PqqD pqqD GO:0018189,GO:0048038 17223081 131567 cellular organisms no rank 10302 JCVI coenzyme PQQ biosynthesis protein PqqD pyrroloquinoline quinone biosynthesis peptide chaperone PqqD This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ. TIGR03860.1 TIGR03860 FMN_nitrolo 279.7 279.7 422 subfamily Y Y N NtaA/DmoA family FMN-dependent monooxygenase 1.14.-.- GO:0008152,GO:0010181,GO:0016491 18164311,21216999,9023192 131567 cellular organisms no rank 92573 JCVI FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family NtaA/DmoA family FMN-dependent monooxygenase Characterized members of this FMN-dependent monooxygenase family include nitrilotriacetate (which is a chelating agent used in detergents) monooxygenase subunit NtaA from Aminobacter aminovorans, dimethyl-sulfide monooxygenase DmoA from Hyphomicrobium sulfonivorans, a long-chain alkane monooxygenase from Geobacillus thermodenitrificans, etc. This protein belongs to a clade of FMN-dependent monooxygenases, within a broader family of flavin-dependent oxidoreductases, the luciferase-like monooxygenase (LMM) family, some of whose members use coenzyme F420 rather than FMN. TIGR03875.1 TIGR03875 RNA_lig_partner 95.3 95.3 206 hypoth_equivalog Y Y N RNA ligase partner protein 131567 cellular organisms no rank 671 JCVI RNA ligase partner, MJ_0950 family RNA ligase partner protein This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown. TIGR03877.1 TIGR03877 thermo_KaiC_1 307.25 307.25 238 hypoth_equivalog Y Y N KaiC domain-containing protein 131567 cellular organisms no rank 186 JCVI KaiC domain protein, Ph0284 family KaiC domain-containing protein, Ph0284 family Members of this family contain a single copy of the KaiC domain (PF06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga. TIGR03878.1 TIGR03878 thermo_KaiC_2 232.2 232.2 259 hypoth_equivalog Y Y N KaiC domain-containing protein 131567 cellular organisms no rank 162 JCVI KaiC domain protein, AF_0795 family KaiC domain protein, AF_0795 family This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles. TIGR03879.1 TIGR03879 near_KaiC_dom 65.1 65.1 91 domain Y N N probable regulatory domain 131567 cellular organisms no rank 315 JCVI probable regulatory domain probable regulatory domain This HMM describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation. TIGR03882.1 TIGR03882 cyclo_dehyd_2 36.9 36.9 164 equivalog_domain Y Y N TOMM precursor leader peptide-binding protein 18375757,26024319 131567 cellular organisms no rank 24223 JCVI bacteriocin biosynthesis cyclodehydratase domain TOMM precursor leader peptide-binding domain Proteins/domains belonging to this ThiF-related family were originally thought to be the cyclodehydratase domain of thiazole/oxazole modified microcin (TOMM)-type peptide natural product biosynthesis. The family is now recognized instead to be involved in leader peptide-binding. TIGR03883.1 TIGR03883 DUF2342_F420 171.35 171.35 346 subfamily Y N N uncharacterized protein, coenzyme F420 biosynthesis associated 131567 cellular organisms no rank 12038 JCVI uncharacterized protein, coenzyme F420 biosynthesis associated uncharacterized protein, coenzyme F420 biosynthesis associated A phylogenetic tree of the DUF2342 family (TIGR03624) consists of two major branches. One of these branches, modeled here, is observed almost entirely to be found in coenzyme F420 biosynthesizing species of the Actinobacterial, Chloroflexi and Archaeal lineages. The few organisms having genes within this family and lacking F420 biosynthesis may either have an undiscovered F420 transporter, or may represent F420-to-FMN revertants. This family includes a Chloroflexus Aurantiacus protein whose crystal structure has been determined (PDB:3CMN_A). This has been annotated as a putative hydrolase, but the support for that assertion is untraceable. There is no cofactor present in the structure. TIGR03885.1 TIGR03885 flavin_revert 398.7 398.7 315 hypoth_equivalog Y Y N TIGR03885 family FMN-dependent LLM class oxidoreductase 1.-.-.- GO:0016491 20675471 131567 cellular organisms no rank 4049 JCVI probable non-F420 flavinoid oxidoreductase TIGR03885 family FMN-dependent LLM class oxidoreductase This model represents a clade of proteins within the larger subfamily TIGR03557. The parent model includes the F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554) and many other proteins. Excepting the members of this family, all members of TIGR03557 occur in species capable of synthesizing coenzyme F420. All members of the seed alignment for this model are from species that lack F420 biosynthesis. It is suggested that members of this family bind FMN, or FO, or a novel flavinoid cofactor, but not F420 per se. TIGR03888.1 TIGR03888 nitrile_beta 152.2 152.2 226 equivalog Y Y N nitrile hydratase subunit beta nthB 4.2.1.84 GO:0018822,GO:0046914,GO:0050898 131567 cellular organisms no rank 6372 JCVI nitrile hydratase, beta subunit nitrile hydratase subunit beta Members of this protein family are the beta subunit of nitrile hydratase. The alpha subunit is represented by model TIGR01323. While nitrile hydratase is given the specific EC number 4.2.1.84, nitriles are a class of compounds, and one genome may carry more than one nitrile hydratase. The enzyme occurs in both non-heme iron and non-corrin cobalt forms. TIGR03889.1 TIGR03889 nitrile_acc 46 46 74 equivalog Y Y N nitrile hydratase accessory protein GO:0050898 131567 cellular organisms no rank 5564 JCVI nitrile hydratase accessory protein nitrile hydratase accessory protein Members of this protein family are found in operons with the alpha and beta subunits of nitrile hydratase, an enzyme with Fe(III) or Co(III) at the active site, and appear to be accessory proteins for maturation or activation of the enzyme. This protein is homologous to the beta subunit (see TIGR03888). TIGR03895.1 TIGR03895 protease_PatA 421.05 421.05 606 subfamily_domain Y Y N PatA/PatG family cyanobactin maturation protease 15883371,18425112 131567 cellular organisms no rank 764 JCVI cyanobactin maturation protease, PatA/PatG family PatA/PatG family cyanobactin maturation protease This model describes a protease domain associated with the maturation of various members of the cyanobactin family of ribosomally produced, heavily modified bioactive metabolites. Members include the PatA protein and C-terminal domain of the PatG protein of Prochloron didemni, TenA and a region of TenG from Nostoc spongiaeforme var. tenue, etc. TIGR03897.1 TIGR03897 lanti_2_LanM 304 304 932 subfamily Y Y N type 2 lanthipeptide synthetase LanM lanM GO:0009403,GO:0018193 19561184 131567 cellular organisms no rank 10893 JCVI type 2 lantibiotic biosynthesis protein LanM type 2 lanthipeptide synthetase LanM Members of this family are known generally as LanM, a multifunctional enzyme of lanthipeptide (usually lantibiotic) biosynthesis. This catalysis by LanM distinguishes the type 2 lantibiotics, such as mersacidin, cinnamycin, and lichenicidin, from LanBC-produced type 1 lantibiotics such as nisin and subtilin. The N-terminal domain contains regions associated with Ser and Thr dehydration. The C-terminal region contains a PF05147 domain, which catalyzes the formation of the lanthionine bridge. TIGR03901.2 TIGR03901 MYXO-CTERM 20 20 34 domain Y Y N MYXO-CTERM sorting domain-containing protein GO:0031240 22511878,31975447,38084967 131567 cellular organisms no rank 3017 JCVI MYXO-CTERM domain MYXO-CTERM protein-sorting domain This model describes MYXO-CTERM, a C-terminal putative protein sorting domain, analogous to LPXTG (TIGR01167) and PEP-CTERM (TIGR02595). It is restricted to the Myxococcales, a division of the Deltaproteobacteria, with over 60 members occurring in Plesiocystis pacifica SIR-1. An example protein is TraA, involved in outer membrane exchange (lipids and proteins) through which one strain of Myxococcus can repair a mobility defect in another. Users of this model should be aware that the short length, great diversity, and lineage-specific differences in the protein regions recognized by this model guarantee that this model has some false-positive hits (e.g. anything in the Firmicutes) and many false-negatives. Researchers interested in getting a full census of MYXO-CTERM in any member of the Myxococcales are advised to use this model to find lineage-specific sequences and the improve the model iteratively. TIGR03904.1 TIGR03904 SAM_YgiQ 462.35 462.35 558 equivalog Y Y N YgiQ family radical SAM protein GO:1904047 131567 cellular organisms no rank 26457 JCVI uncharacterized radical SAM protein YgiQ YgiQ family radical SAM protein Members of this family are fairly widespread uncharacterized radical SAM family proteins, many of which are designated YgiQ. TIGR03909.1 TIGR03909 pyrrolys_PylC 248.3 248.3 374 equivalog Y Y N 3-methylornithine--L-lysine ligase PylC pylC GO:0005737,GO:0071524 17204561 131567 cellular organisms no rank 301 JCVI pyrrolysine biosynthesis protein PylC 3-methylornithine--L-lysine ligase PylC This protein is PylC, part of a three-gene cassette that is sufficient to direct the biosynthesis of pyrrolysine, the twenty-second amino acid, incorporated in some species at a UAG canonical stop codon. TIGR03910.1 TIGR03910 pyrrolys_PylB 348.2 348.2 347 equivalog Y Y N methylornithine synthase PylB pylB GO:0005737,GO:0071524,GO:1904047 17204561 131567 cellular organisms no rank 300 JCVI pyrrolysine biosynthesis radical SAM protein methylornithine synthase PylB This model describes a radical SAM protein, PylB, that is part of the three-gene cassette sufficient for the biosynthesis of pyrrolysine (the twenty-second amino acid) when expressed heterologously in E. coli. The pyrrolysine next is ligated to its own tRNA and incorporated at special UAG codons. TIGR03911.1 TIGR03911 pyrrolys_PylD 150.05 150.05 266 equivalog Y Y N 3-methylornithyl-N6-L-lysine dehydrogenase PylD pylD GO:0005737,GO:0008652 17204561 131567 cellular organisms no rank 251 JCVI pyrrolysine biosynthesis protein PylD 3-methylornithyl-N6-L-lysine dehydrogenase PylD This protein is PylD, part of a three-gene cassette that is sufficient to direct the biosynthesis of pyrrolysine, the twenty-second amino acid, incorporated in some species at a UAG canonical stop codon. TIGR03912.1 TIGR03912 PylS_Nterm 51.15 51.15 89 equivalog_domain Y Y N pyrrolysine--tRNA(Pyl) ligase small subunit pylSn GO:0006418,GO:0043767 15314242,15329732 131567 cellular organisms no rank 257 JCVI pyrrolysine--tRNA ligase, N-terminal region pyrrolysine--tRNA(Pyl) ligase, N-terminal region or small subunit PylS is the enzyme responsible for charging the pyrrolysine tRNA, PylT, by ligating a free molecule of pyrrolysine. Pyrrolysine is encoded at an in-frame UAG (amber) at least in several corrinoid-dependent methyltransferases of the archaeal genera Methanosarcina and Methanococcoides, such as trimethylamine methyltransferase. This protein occurs as a fusion protein in Methanosarcina but as split genes in Desulfitobacterium hafniense and other bacteria. This model describes the small, N-terminal region. TIGR03916.1 TIGR03916 rSAM_link_UDG 343.5 343.5 415 hypoth_equivalog_domain Y Y N putative DNA modification/repair radical SAM protein GO:0051539,GO:1904047 131567 cellular organisms no rank 17123 JCVI putative DNA modification/repair radical SAM protein putative DNA modification/repair radical SAM protein This uncharacterized protein of about 400 amino acids in length contains a radical SAM protein in the N-terminal half. Members are present in about twenty percent of prokaryotic genomes, always paired with a member of the conserved hypothetical protein TIGR03915. Roughly forty percent of the members of that family exist as fusions with a uracil-DNA glycosylase-like region, TIGR03914. In DNA, uracil results from deamidation of cytosine, forming U/G mismatches that lead to mutation, and so uracil-DNA glycosylase is a DNA repair enzyme. This indirect connection, and the recurring role or radical SAM protein in modification chemistries, suggest that this protein may act in DNA modification, repair, or both. TIGR03957.1 TIGR03957 rSAM_HmdB 320.9 320.9 317 equivalog Y Y N 5,10-methenyltetrahydromethanopterin hydrogenase cofactor biosynthesis protein HmdB hmdB GO:0015948,GO:0051539,GO:1904047 19897660 131567 cellular organisms no rank 198 JCVI 5,10-methenyltetrahydromethanopterin hydrogenase cofactor biosynthesis protein HmdB 5,10-methenyltetrahydromethanopterin hydrogenase cofactor biosynthesis protein HmdB Members of this archaeal protein family are HmdB, a partially characterized radical SAM protein with an unusual CX5CX2C motif. Its gene flanks the H2-forming methylene-H4-methanopterin dehydrogenase gene hmdA, found in hydrogenotrophic methanogens. HmdB appears to act in in biosynthesis of the novel cofactor of HmdA. TIGR03958.1 TIGR03958 monoFe_hyd_HmdC 407 407 505 equivalog Y Y N 5,10-methenyltetrahydromethanopterin hydrogenase cofactor biosynthesis protein HmdC hmdC GO:0015948 19897660 131567 cellular organisms no rank 226 JCVI 5,10-methenyltetrahydromethanopterin hydrogenase cofactor biosynthesis protein HmdC 5,10-methenyltetrahydromethanopterin hydrogenase cofactor biosynthesis protein HmdC Members of this protein family are HmdC, whose gene regularly occurs in the context of genes for HmdA (5,10-methenyltetrahydromethanopterin hydrogenase) and the radical SAM protein HmdB involved in biosynthesis of the HmdA cofactor. Bioinformatics suggests this protein, a homolog of eukaryotic fibrillarin, may be involved in biosynthesis of the guanylyl pyridinol cofactor in HmdA. TIGR03962.1 TIGR03962 mycofact_rSAM 265 265 339 equivalog Y Y N mycofactocin radical SAM maturase mftC 1.3.98.7,4.1.99.26 GO:0031179,GO:0051539,GO:0140604 21223593,27158836,27312813,28634235,31113891 131567 cellular organisms no rank 3524 JCVI mycofactocin radical SAM maturase mycofactocin radical SAM maturase The mycofactocin maturase MftC is found broadly in Mycobacterium tuberculosis and many other Actinomycetota, but also in some Thermodesulfobacteriota (e.g. Geotalea uraniireducens), Bacillota (Pelotomaculum thermopropionicum and Desulfotomaculum acetoxidans), and Chloroflexia (e.g. Thermomicrobium roseum DSM 5159). The protein contains both an N-terminal radical SAM domain and a C-terminal SPASM domain (TIGR04085), and is one of the founding members of the SPASM (modification of Subtilosin, PQQ, Anaerobic Sulfatase, and Mycofactocin) family. MftC performs the first two modifications to the C-terminal Val-Tyr dipeptide of the precursor peptide MftA. MftC is a radical SAM/SPASM enzyme that catalyzes the first two steps in biosynthesis of the electron carrier mycofactocin from the terminal Val-Tyr dipeptide of the precursor peptide MftA. TIGR03964.1 TIGR03964 mycofact_creat 172 172 228 equivalog Y Y N mycofactocin biosynthesis peptidyl-dipeptidase MftE mftE GO:0140604 21223593,28077628,31113891 131567 cellular organisms no rank 3424 JCVI mycofactocin system creatininase family protein mycofactocin biosynthesis peptidyl-dipeptidase MftE This creatininase homolog from the mycofactocin biosynthesis system, MftE, is now known to be a peptidyl-dipeptidase for the twice-modified C-terminal Val-Tyr dipeptide. Mature mycofactocin is a redox carrier involved involved in redox homeostasis and metabolism of various alcohols and aldehydes. TIGR03965.1 TIGR03965 mycofact_glyco 280 280 467 equivalog Y Y N mycofactocin biosynthesis glycosyltransferase MftF mftF GO:0016740,GO:0140604 21223593,30778644,33014324 131567 cellular organisms no rank 3626 JCVI mycofactocin system glycosyltransferase mycofactocin biosynthesis glycosyltransferase MftF MftF was shown, through a metabolomics study in Mycolicibacterium smegmatis published by the Lackner group in 2020, to perform oligo-glycosylation as the final step in mycofactocin biosynthesis. Up to nine glucose residues (or 2-O-methylglucose) are added, with beta-1-4 linkages, to the small molecule derived from the Val-Tyr terminal dipeptide of the mycofactocin precursor, MftA. Other proteins involved in mycofactocin biosynthesis include the radical SAM enzyme MftC, the modification chaperone MftB, the dipeptidase MftE, and the FMN dependent protein MftD. Members of this protein family, MftF, are glycosyltransferases, members of PF00535 (glycosyl transferase family 2). The encoding gene is found as part of the mycofactocin cassette, in Mycobacterium tuberculosis, many other Actinobacteria, and occasional members of other lineages. Mycofactocin itself, a putative redox carrier, is a heavily modified derivative of the C-terminal Val-Tyr dipeptide of the mycofactocin precursor MftA (TIGR03969). TIGR03969.1 TIGR03969 mycofactocin 25 25 23 equivalog Y Y N mycofactocin precursor MftA mftA GO:0009055,GO:0140604 21223593,27158836,27312813,31113891,31381312 131567 cellular organisms no rank 2191 JCVI mycofactocin precursor mycofactocin precursor MftA The first two steps of mycofactocin maturation are both performed by the radical SAM enzyme MftC. This step is followed by separation of the twice-modified Val-Tyr from the rest of the precursor. MftD converts the VY-derived dipeptide to premycofactocin, which has a biologically active redox center. And finally, MftF performs oligoglycosylation, to a variable degree, so mycofactocin is actually a mix of variably glycosylated forms. The mycofactocin system, with its modification of a ribosomally translated precursor by a radical SAM enzyme in order to create a redox-active product, and its inevitable co-occurence with certain families of enzymes dependent on that product, is closely analogous to the previously described PQQ system. A number of families of oxidoreductases discovered to occur only in mycofactocin-producing species feature non-exchangeable NAD(P) molecules, suggesting that mycofactocin can mediate electron transfers to couple the oxidation reaction by one mycofactocin-linked enzyme with a reduction reaction by another. Mycofactocin systems are common within the Actinobacteria, but are found also in some delta-Proteobacteria (e.g. Geobacter uraniireducens), Firmicutes (Pelotomaculum thermopropionicum and Desulfotomaculum acetoxidans), and Chloroflexi (Thermomicrobium roseum DSM 5159 and Sphaerobacter thermophilus DSM 20745). Mycofactocin is a small molecule electron carrier derived from the final two amino acids, Val-Tyr, of MftA, the mycofactocin precursor. It plays a role in redox homeostasis and the metabolism of alcohols and aldehydes in Actinobacteria, including Mycobacterium tuberculosis. TIGR03971.1 TIGR03971 SDR_subfam_1 300 300 271 subfamily Y Y N mycofactocin-coupled SDR family oxidoreductase 1.1.99.- GO:0016491 21223593,28120876,31113891 131567 cellular organisms no rank 16946 JCVI SDR family mycofactocin-dependent oxidoreductase mycofactocin-coupled SDR family oxidoreductase Characterized members of this family are described as NDMA-dependent, meaning that a blue aniline dye serving as an artificial electron acceptor is required for members of this family to cycle in vitro, since the bound NAD residue is not exchangeable (see EC 1.1.99.36). DCPIP (dichlorophenolindophenol) may be used in such assays instead of NDMA. Characterized members of the family include the stereoselective carveol dehydrogenase LimC from Rhodococcus erythropolis DCL14. The SDR family (PF00106) is one of three families of oxidoreductases with predicted mycofactocin-dependent branches. The others are the zinc-binding dehydrogenase family (PF00107) and the iron-activated oxidoreductase (PF00465) family. This oxidoreductase belongs to a branch of the SDR family in which the NAD cofactor is especially deeply buried and is non-exchangeable. Members of this branch occur only in species that product mycofactocin, a small molecule electron carrier derived from the final two residues of the mycofactocin precursor protein, MftA. Mycofactocin is thought to mediate transfers of electrons between such non-exchangeable NAD cofactors from different enzymes acting on different substates, and has been shown to play a role in the metabolism of alcohols and aldehydes in Mycolicibacterium smegmatis and in Mycobacterium tuberculosis. TIGR03975.1 TIGR03975 rSAM_ocin_1 281.85 281.85 606 subfamily Y Y N RiPP maturation radical SAM C-methyltransferase GO:0003824 22983711,22984777 131567 cellular organisms no rank 3997 JCVI ribosomal peptide maturation radical SAM protein 1 RiPP maturation radical SAM C-methyltransferase Members of this family of peptide-modifying radical SAM proteins include BstC, BstF, and BstJ, three enzymes involved in the biosynthesis of the antibiotic bottromycin D from a ribosomally translated peptide precursor that lacks a leader peptide. They appear to perform methylations of carbon atoms. Other members of the family occur in genomic contexts with RiPP family precursors in the Nif11-like and NHLP families, as well as other peptide maturases from the lanthionine synthase and cyclodehydratase families. TIGR03980.1 TIGR03980 prismane_assoc 44.95 44.95 58 subfamily_domain Y N N hybrid cluster protein-associated redox disulfide domain 131567 cellular organisms no rank 4837 JCVI hybrid cluster protein-associated redox disulfide domain hybrid cluster protein-associated redox disulfide domain Members of this protein family resemble the domain of unknown function DUF1858 described by PF08984, but all members contain an apparent redox-active disulfide. In at least one member protein, a cysteine in the CXXC motif is substituted by a selenocysteine. Most member proteins consist of this domain only, but a few members are fused to or adjacent to members of the hybrid-cluster (prismane) family or the nitrite/sulfite reductase family. TIGR03984.2 TIGR03984 TIGR03984 35 35 170 equivalog Y Y N CRISPR-associated protein Csx19 csx19 28698278 131567 cellular organisms no rank 743 JCVI CRISPR-associated protein, TIGR03984 family CRISPR-associated protein Csx19 Members of this protein family are found exclusively in CRISPR-containing organisms, in operon contexts with RAMP (repeat-associated mystery protein) proteins also linked to CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats). The Csx19 family previously was known as the TIGR03984 family CRISPR-associated protein. TIGR03986.1 TIGR03986 TIGR03986 161.35 161.35 568 hypoth_equivalog Y Y N TIGR03986 family CRISPR-associated RAMP protein 131567 cellular organisms no rank 1735 JCVI CRISPR-associated protein TIGR03986 family CRISPR-associated RAMP protein Members of this protein family, part of the larger RAMP family, are found exclusively in species with CRISPR systems, in local contexts containing other RAMP (Repeat-Associated Mystery Proteins). TIGR03990.1 TIGR03990 Arch_GlmM 439 439 444 equivalog Y Y N phosphoglucosamine mutase glmM 5.4.2.10 GO:0008966,GO:0009252 16930487,18263721 131567 cellular organisms no rank 10064 JCVI phosphoglucosamine mutase phosphoglucosamine mutase The MMP1680 protein from Methanococcus maripaludis has been characterized as the archaeal protein responsible for the second step of UDP-GlcNAc biosynthesis [1]. This GlmM protein catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate. The first-characterized bacterial GlmM protein is modeled by TIGR01455. These two families are members of the larger phosphoglucomutase/phosphomannomutase family (characterized by three domains: PF02878, PF02879 and PF02880), but are not nearest neighbors to each other. This model also includes a number of sequences from non-archaea in the Bacteroides, Chlorobi, Chloroflexi, Planctomycetes and Spirochaetes lineages. Evidence supporting their inclusion in this equivalog as having the same activity comes from genomic context and phylogenetic profiling. A large number of these organisms are known to produce exo-polysaccharide and yet only appeared to contain the GlmS enzyme of the GlmSMU pathway for UDP-GlcNAc biosynthesis (GenProp0750). In some organisms including Leptospira, this archaeal GlmM is found adjacent to the GlmS as well as a putative GlmU non-orthologous homolog. Phylogenetic profiling of the GlmS-only pattern using PPP [2] identifies members of this archaeal GlmM family as the highest-scoring result. TIGR03991.1 TIGR03991 alt_bact_glmU 225.3 225.3 394 hypoth_equivalog Y N N UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase glmU 2.3.1.157,2.7.7.23 GO:0003977,GO:0009252,GO:0019134 16930487,18263721 131567 cellular organisms no rank 5356 JCVI UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase The MJ_1101 protein from Methanococcus jannaschii has been characterized as the GlmU enzyme catalyzing the final two steps of UDP-GlcNAc biosynthesis [1]. Homologs of this enzyme are identified in a number of bacterial organisms and modeled here. A number of these are observed in proximity to the GlmS and GlmM genes, and phylogenetic profiling by PPP [2] identifies the LEPBI_I0518 gene in Leptospira biflexa as a likely Glm-system candidate. Multiple sequence alignments of these bacterial homologs with their archaeal counterparts reveals significant structural differences, necessitating the construction of separate models. TIGR03992.1 TIGR03992 Arch_glmU 292.1 292.1 393 subfamily Y Y N bifunctional sugar-1-phosphate nucleotidylyltransferase/acetyltransferase glmU 2.3.1.157,2.7.7.23 GO:0003977,GO:0019134 15598657,18263721 131567 cellular organisms no rank 1802 JCVI UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase bifunctional sugar-1-phosphate nucleotidylyltransferase/acetyltransferase The MJ_1101 protein from Methanococcus jannaschii has been characterized as the GlmU enzyme catalyzing the final two steps of UDP-GlcNAc biosynthesis, glucosamine-1-phosphate N-acetyltransferase and UDP-N-acetylglucosamine diphosphorylase. Many more proteins identified by this model are encoded near GlmS and GlmM genes and likewise presumed to be GlmU. However, some archaeal genomes contain multiple closely-related homologs from this family and it is not clear what the substrate specificity is for each of them. TIGR03995.1 TIGR03995 target_X_rSAM 87.6 87.6 84 equivalog Y Y N CGCGG family rSAM-modified RiPP protein 131567 cellular organisms no rank 644 JCVI putative rSAM target protein, CGCGG family CGCGG family rSAM-modified RiPP protein Members of this family of small proteins, approx. 100 amino acids in length, co-occur with a subfamily of radical SAM protein in several species in the Halobacteria and in Bacillus. The radical SAM protein belongs to a branch in which most characterized members act on peptide substrates. The lack of homology of this family to any known enzyme and the distinctive C-terminal region motif, with the common modification target residue Cys flanked by sterically permissive Gly residues. TIGR04001.1 TIGR04001 thiol_BshB1 182.5 182.5 226 equivalog Y Y N bacillithiol biosynthesis deacetylase BshB1 bshB1 GO:0019213,GO:0071793 20308541 131567 cellular organisms no rank 8184 JCVI bacillithiol biosynthesis deacetylase BshB1 bacillithiol biosynthesis deacetylase BshB1 Members of this protein family are BshB1 (YpjG), an enzyme of bacillithiol biosynthesis; either BshB1 or BshB2 (YojG) must be present, and often both are present. Bacillithiol is a low-molecular-weight thiol, an analog of glutathione and mycothiol, and is found largely in the Firmicutes. TIGR04013.1 TIGR04013 B12_SAM_MJ_1487 251 251 382 hypoth_equivalog Y Y N TIGR04013 family B12-binding domain/radical SAM domain-containing protein GO:0003824,GO:0046500,GO:0051539 131567 cellular organisms no rank 961 JCVI B12-binding domain/radical SAM domain protein, MJ_1487 family TIGR04013 family B12-binding domain/radical SAM domain-containing protein Members of this family have both a B12 binding homology domain (PF02310) and a radical SAM domain (PF04055), and occur only once per genome. Some species with members of this family have a related protein with similar domain architecture. This protein is occurs largely in archaeal methanogens but also in a few bacteria, including Thermotoga maritima and Myxococcus xanthus. TIGR04021.1 TIGR04021 LLM_DMSO2_sfnG 382.95 382.95 350 equivalog Y Y N dimethylsulfone monooxygenase SfnG sfnG 1.14.14.35 GO:0004497,GO:0006790,GO:0010181 17768252 131567 cellular organisms no rank 8758 JCVI dimethyl sulfone monooxygenase SfnG dimethylsulfone monooxygenase SfnG This family of FMNH2-dependent members of the luciferase-like monooxygenase (LLM) family includes SfnG, a monooxygenase that converts dimethylsulphone (DMSO2) to methanesulphonate. This step can be followed immediately by methanesulfonate sulfonatase (an alkanesulfonate monooxygenase - see TIGR03565) for the FMNH2-dependent conversion an inorganic form. TIGR04023.1 TIGR04023 PPOX_MSMEG_5819 85.6 85.6 115 subfamily Y Y N PPOX class F420-dependent oxidoreductase 1.-.-.- GO:0016491,GO:0070967 20675471,23621493 131567 cellular organisms no rank 5108 JCVI PPOX class F420-dependent enzyme, MSMEG_5819/OxyR family PPOX class F420-dependent oxidoreductase A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. This subfamily within the PPOX family occurs in at least 19 distinct species of F420 producers and is likely to bind F420 rather than FMN. The member OxyR was shown to use F420 to catalyze a C5a-C11a reduction in oxytetracycline biosynthesis. TIGR04038.1 TIGR04038 tatD_link_rSAM 129.7 129.7 192 subfamily_domain Y Y N TatD family nuclease-associated radical SAM protein 131567 cellular organisms no rank 2394 JCVI radical SAM protein, TatD family-associated TatD family nuclease-associated radical SAM protein Members of this family are radical SAM proteins found in about 5 percent of microbial genomes. A portion occur as gene fusions with, or adjacent to, members of the TatD family of metallo-hydrolases (PF01026), some of which are known to cleave DNA or RNA. TIGR04043.1 TIGR04043 rSAM_MSMEG_0568 303.7 303.7 354 hypoth_equivalog Y Y N MSMEG_0568 family radical SAM protein GO:0009058,GO:0046500,GO:0051539 131567 cellular organisms no rank 4241 JCVI radical SAM protein, MSMEG_0568 family MSMEG_0568 family radical SAM protein Members of this protein family are radical SAM proteins related to MSMEG_0568 from Mycobacterium smegmatis. Members occur within 8-gene operons in species as diverse as M. smegmatis, Rhizobium leguminosarum, Synechococcus elongatus, and Sorangium cellulosum. The function of the operon is unknown, but similarity of MSMEG_0568 to some cofactor biosynthesis radical SAM proteins suggests a similar biosynthetic function. TIGR04053.2 TIGR04053 TIGR04053 395 395 366 equivalog Y Y N TIGR04053 family radical SAM/SPASM domain-containing protein GO:0003824 21478363 131567 cellular organisms no rank 3737 JCVI radical SAM protein, BA_1875 family TIGR04053 family radical SAM/SPASM domain-containing protein Members of this subfamily of the radical SAM domain superfamily show closer sequence relationships to peptide-modifying proteins of bacteriocin and PQQ biosynthesis than to other characterized radical SAM proteins. Within this subfamily, targets are likely to be diverse. See TIGR03995 for a family of peptides that may be targets for post-translational modification by this enzyme. TIGR04070.1 TIGR04070 photo_TT_lyase 400 400 338 equivalog Y Y N spore photoproduct lyase splB 4.1.99.14 GO:0006290,GO:0016830,GO:0046500,GO:0051539 19178276 131567 cellular organisms no rank 4271 JCVI spore photoproduct lyase spore photoproduct lyase DNA damage to bacterial spores from ultraviolet light accumulates in the form of 5-thyminyl-5,6-dihydrothymine, spore photoproduct. The damage is repaired by spore photoproduct lyase, a member of the radical SAM family of enzymes. The score of this model is set to restrict itself to spore-forming members of the Firmicutes, but additional homologs scoring below the trusted cutoff tend to occur in radioresistant organisms (e.g. Kineococcus radiotolerans) and may be functionally equivalent. A related family in the Mycobacterium lineage is described by family TIGR03886, and may or may not be equivalent in function. TIGR04076.1 TIGR04076 TIGR04076 33 33 91 subfamily Y Y N TIGR04076 family protein GO:0046500,GO:0051539 131567 cellular organisms no rank 4875 JCVI TIGR04076 family protein TIGR04076 family protein Members of this protein family are uncharacterized. The only invariant residue, and one of three other residues better than 90 percent conserved are both Cys. Phylogenetic profiling results and occasional fusion genes suggest a role for members of this family in redox reactions or iron cluster metabolism. Species occasionally have two or three copies. TIGR04083.1 TIGR04083 rSAM_pep_methan 300 300 376 hypoth_equivalog Y Y N TIGR04083 family peptide-modifying radical SAM enzyme 131567 cellular organisms no rank 416 JCVI putative peptide-modifying radical SAM enzyme, Mhun_1560 family TIGR04083 family peptide-modifying radical SAM enzyme Members of this family are radical SAM enzymes, homologous to a variety of other peptide-modifying radical SAM, and found primarily in methanogenic archaea. TIGR04084.1 TIGR04084 rSAM_AF0577 225 225 347 subfamily Y Y N TIGR04084 family radical SAM/SPASM domain-containing protein GO:0046500,GO:0051539,GO:1904047 20218986 131567 cellular organisms no rank 242 JCVI putative peptide-modifying radical SAM enzyme, AF0577 family TIGR04084 family radical SAM/SPASM domain-containing protein This radical SAM family contains a C-terminal region motif CXXCX5CX3C that is found in PqqE and other radical SAM enzymes that act on peptide substrates. Members of this family are found primarily in the Archaea, but also several eukaryotes (Trichomonas vaginalis G3, Entamoeba dispar SAW760, Giardia intestinalis ATCC 50581, etc.). The function is unknown. TIGR04085.1 TIGR04085 rSAM_more_4Fe4S 27 27 93 domain Y Y N SPASM domain-containing protein 20218986,21223593,21478363,25477505 131567 cellular organisms no rank 71181 JCVI radical SAM additional 4Fe4S-binding SPASM domain SPASM domain The SPASM domain usually occurs as a C-terminal extension to a radical SAM domain (see Pfam model PF04055)-containing protein, although some proteins with free-standing SPASM domains do occur. A radical SAM protein binds a 4Fe-4S cluster, and the SPASM domain binds two additional 4Fe-4S clusters. Radical SAM enzymes with an additional SPASM domain tend to be involved in protein modification. The acronym SPASM derives from the protein-modifying radical SAM enzymes of the Subtilosin, PQQ, Anaerobic Sulfatase, and Mycofactocin systems. Additional radical SAM/SPASM domain proteins participate in the maturation of quinohemoprotein amine dehydrogenase, the natural product Pep1357, SCIFF, sporulation killing factor, thurincin H, thuricin CD, etc. The motif CxxCxxxxxCxxxC is nearly invariant for members of this family, although PqqE has a variant form. An incomplete SPASM domain that binds one 4Fe-4S cluster, instead of two, is called a TWITCH domain. This domain contains regions binding additional 4Fe4S clusters found in various radical SAM proteins C-terminal to the domain described by model PF04055. Radical SAM enzymes with this domain tend to be involved in protein modification, including anaerobic sulfatase maturation proteins, a quinohemoprotein amine dehydrogenase biogenesis protein, the Pep1357-cyclizing radical SAM enzyme, and various bacteriocin biosynthesis proteins. The motif CxxCxxxxxCxxxC is nearly invariant for members of this family, although PqqE has a variant form. We name this domain SPASM for Subtilosin, PQQ, Anaerobic Sulfatase, and Mycofactocin. TIGR04088.1 TIGR04088 cognate_SipW 19 19 34 domain Y Y N SipW-dependent-type signal peptide-containing protein 131567 cellular organisms no rank 11644 JCVI SipW-cognate class signal peptide SipW-dependent-type signal peptide This HMM describes a protein N-terminal domain found regularly in proteins encoded near a variant form of signal peptidase I such as the SipW protein found in Bacillus subtilis but with homologs in endoplasmic reticulum and some archaea. Members of this family include camelysin (a casein-cleaving metalloprotease) and TasA (CotN), a metalloprotease that is secreted, along with extracellular polysaccharide (EPS), to be the major protein constituent of the Bacillus subtilis biofilm matrix. Sequencing from several known TasA/CotN proteins shows the cleavage location to be near the center of the alignment and typical of type I signal peptidases, with small residues at -3 and -1. This domain, therefore, appears to be a special subclass of signal peptide. TIGR04093.1 TIGR04093 cas1_CYANO 385 385 334 exception Y Y N type I-D CRISPR-associated endonuclease Cas1d cas1d GO:0004520,GO:0043571,GO:0046872 131567 cellular organisms no rank 662 JCVI CRISPR-associated endonuclease Cas1, subtype CYANO type I-D CRISPR-associated endonuclease Cas1d The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes a clade of Cas1 limited to the CYANO subtype of CRISPR/Cas system and most often the type found there. TIGR04113.1 TIGR04113 cas_csx17 150 150 718 equivalog Y Y N type I-U CRISPR-associated protein Csx17 csx17 131567 cellular organisms no rank 353 JCVI CRISPR-associated protein Csx17, subtype Dpsyc type I-U CRISPR-associated protein Csx17 Members of this protein family are found exclusively in CRISPR-associated (cas) type I system gene clusters of the Dpsyc subtype. Markers for that type include a variant form of cas3 (model TIGR02621) and the GSU0054-like protein family (model TIGR02165). This family occurs in less than half of known Dpsyc clusters. TIGR04141.1 TIGR04141 TIGR04141 35 35 516 subfamily Y Y N TIGR04141 family sporadically distributed protein 131567 cellular organisms no rank 6359 JCVI sporadically distributed protein, TIGR04141 family TIGR04141 family sporadically distributed protein This HMM describes a sporadically distributed conserved hypothetical protein in which complete members average over 500 amino acids in length, although matching sequences frequently are truncated or broken into tandem ORFs. Regular co-clustering with known markers of mobility (integrases, transposases, phage proteins, restriction enzymes, etc.) suggests this family also is part of the mobilome. The function is unknown. TIGR04154.1 TIGR04154 archaeo_STT3 450 450 831 subfamily Y Y N oligosaccharyl transferase, archaeosortase A system-associated GO:0004576,GO:0006487 22037399 131567 cellular organisms no rank 1207 JCVI oligosaccharyl transferase, archaeosortase A system-associated oligosaccharyl transferase, archaeosortase A system-associated Members of this protein family occur, one to three members per genome, in the same species of Euryarchaeota as contain the predicted protein-sorting enzyme archaeosortase (TIGR04125) and its cognate protein-sorting signal PGF-CTERM (TIGR04126). TIGR04163.1 TIGR04163 rSAM_cobopep 375 375 428 equivalog Y Y N peptide-modifying radical SAM enzyme CbpB cbpB 131567 cellular organisms no rank 115 JCVI peptide-modifying radical SAM enzyme CbpB peptide-modifying radical SAM enzyme CbpB Members of this family are radical SAM enzymes that modify a short peptide encoded by an upstream gene. A role in metal chelation is suggested. TIGR04164.1 TIGR04164 cobo_pep 35 35 25 equivalog Y Y N modified peptide precursor CbpA cbpA 131567 cellular organisms no rank 80 JCVI modified peptide precursor CbpA modified peptide precursor CbpA Members of this family are short peptides predicted to reach mature form after modification by a radical SAM enzyme (TIGR04163). TIGR04178.1 TIGR04178 exo_archaeo 23 23 97 signature Y N N exosortase/archaeosortase family protein GO:0004197,GO:0006605,GO:0016020,GO:0043687 22037399 131567 cellular organisms no rank 16148 JCVI exosortase/archaeosortase family protein exosortase/archaeosortase domain This model represents the most conserved region of the multitransmembrane protein family of exosortases and archaeosortases. The region includes nearly invariant motifs at the ends of three predicted transmembrane helices on the extracytoplasmic face: a Cys (often Cys-Xaa-Gly), Asn-Xaa-Xaa-Arg, and His. This model is much broader than the bacterial exosortase model (TIGR02602), and has in intended scope similar to (or broader than) Pfam model PF09721. TIGR04180.1 TIGR04180 EDH_00030 475 475 297 hypoth_equivalog Y Y N NAD-dependent 4,6-dehydratase LegB 27986835 131567 cellular organisms no rank 2695 JCVI NAD dependent epimerase/dehydratase, LLPSF_EDH_00030 family NAD-dependent 4,6-dehydratase LegB This clade within the NAD dependent epimerase/dehydratase superfamily (PF01370) is characterized by inclusion of its members within a cassette of seven distinctive enzymes. These include four genes homologous to the elements of the neuraminic (sialic) acid biosynthesis cluster (NeuABCD), an aminotransferase and a nucleotidyltransferase in addition to the epimerase/dehydratase. Together it is very likely that these enzymes direct the biosynthesis of a nine-carbon sugar analagous to CMP-neuraminic acid. Family member BFO_1074 from Tannerella forsythia was shown to act on GDP-GlcNAc at the start of a legionaminic acid biosynthesis pathway. TIGR04181.1 TIGR04181 NHT_00031 420 420 359 hypoth_equivalog Y Y N LegC family aminotransferase 19282391,27689684 131567 cellular organisms no rank 5724 JCVI aminotransferase, LLPSF_NHT_00031 family LegC family aminotransferase LegC from Campylobacter jejuni is an enzyme in the biosynthesis pathway for CMP-legionaminic acid, the activated form of a 9-carbon sugar related to sialic acid and pseudominic acid. TIGR04190.1 TIGR04190 B12_SAM_Ta0216 500 500 554 equivalog Y Y N TIGR04190 family B12-binding domain/radical SAM domain protein 131567 cellular organisms no rank 360 JCVI B12-binding domain/radical SAM domain protein, Ta0216 family TIGR04190 family B12-binding domain/radical SAM domain protein Members of this family are enzymes with an N-terminal B12-binding domain and central radical SAM domain. Families TIGR03975, TIGR04013 and TIGR04014 exhibit a similar architecture, which may be associated with lipid metabolism. TIGR04207.1 TIGR04207 halo_sig_pep 24.6 24.6 30 domain Y Y N surface glycoprotein 131567 cellular organisms no rank 1029 JCVI surface glycoprotein signal peptide surface glycoprotein signal peptide This N-terminal homology domain appears to be a specialized class of signal peptide. It occurs mostly in the halophilic archaea, primarily on proteins with the C-terminal PGF-CTERM domain, including the S-layer-forming major surface glycoprotein of several species. The PGF-CTERM domain is the putative archaeosortase A recognition sequence. However, this N-terminal domain occurs also in several archaeal proteins that lack PGF-CTERM. TIGR04213.1 TIGR04213 PGF_pre_PGF 28 28 153 domain Y Y N PGF-pre-PGF domain-containing protein 26712937,28069824 131567 cellular organisms no rank 2813 JCVI PGF-pre-PGF domain PGF-pre-PGF domain This domain occurs in archaeal species. Most domains in this family end with a motif PGF, after which the member sequences change in character to low-complexity sequence (usually Thr-rich) for about 40 residues. The low complexity region usually is followed by a PGF-CTERM domain (TIGR04126), which is the recognition sequence for archaeosortase A (TIGR04125), involved in replacement of the C-terminal region by a membrane-anchoring lipid moiety (see PMID:26712937). The similarity between the PGF motif in this domain and in the PGF-CTERM domain is highly suggestive. Note that investigation of a different case of PGF in the middle of an archaeal protein, HVO_0405, confirmed that cleavage by ArtA at internal sites can indeed occur (see PMID:28069824). TIGR04215.1 TIGR04215 choice_anch_A 29 29 255 domain Y Y N choice-of-anchor A family protein 15456768 131567 cellular organisms no rank 15066 JCVI choice-of-anchor A domain choice-of-anchor A domain This domain may occur as essentially the full length of a protein, except for an N-terminal sequence and a C-terminal protein-sorting signal such as PEP-CTERM or LPXTG. Most often, the putative surface protein is longer and contains repetitive sequence regions. This is one of very few domains for which both anchoring domains occur, and designated choice-of-anchor A domain. The best characterized member is Bacillus anthracis protein BA0871, a collagen-binding protein with five CNA-family protein B-type repeats toward the C-terminus and an LPXTG cell wall attachment motif. TIGR04223.1 TIGR04223 quorum_AgrD 19 19 38 subfamily Y Y N AgrD family cyclic lactone autoinducer peptide 12122003,15001569,19520867 131567 cellular organisms no rank 3932 JCVI cyclic lactone autoinducer peptide AgrD family cyclic lactone autoinducer peptide Members of this family of short peptides are precursors to thiolactone (unless Cys is replaced by Ser) cyclic autoinducer peptides, used in quorum-sensing systems in Gram-positive bacteria. The best characterized is the AgrD precursor, processed by the AgrB protein. Nearby proteins regularly encountered include a histidine kinase and a response regulator. This model is related to PF05931 but is newer and currently broader in scope. TIGR04226.1 TIGR04226 RrgB_K2N_iso_D2 30 30 123 domain Y Y N isopeptide-forming domain-containing fimbrial protein GO:0018262 20559564,2900829 131567 cellular organisms no rank 31128 JCVI fimbrial isopeptide formation D2 domain fimbrial isopeptide formation D2 domain The Streptococcus Pneumoniae pilus backbone protein, RrgB, has three tandem domains with Lys-to-Asn isopeptide bonds, but these three regions are extremely divergent in sequence. This model represents the homology domain family of the D2 domain. It occurs just once in many surface proteins but up to twenty times in some pilin subunit proteins. Three of every four members have the typical Gram-positive C-terminal motif, LPXTG, although in many cases this motif may be involved in pilin subunit cross-linking rather than cell wall attachment. Proteins with this domain include fimbrial proteins with lectin-like adhesion functions, and the majority of characterized members are involved in surface adhesion to host structures. TIGR04244.1 TIGR04244 nitrous_NosZ_RR 625 625 627 equivalog Y Y N TAT-dependent nitrous-oxide reductase nosZ 1.7.2.4 GO:0005507,GO:0005509,GO:0019333,GO:0050304 11160097 131567 cellular organisms no rank 4351 JCVI nitrous-oxide reductase, TAT-dependent TAT-dependent nitrous-oxide reductase Members of this family are the nitrous-oxide reductase structural protein, NosZ, with an N-terminal twin-arginine translocation (TAT) signal sequence (see TIGR01409). The TAT system replaces the Sec system for export of proteins with bound cofactor. TIGR04246.1 TIGR04246 nitrous_NosZ_Gp 625 625 578 equivalog_domain Y Y N Sec-dependent nitrous-oxide reductase nosZ 1.7.2.4 GO:0019333,GO:0050304 19054093 131567 cellular organisms no rank 2677 JCVI nitrous-oxide reductase, Sec-dependent Sec-dependent nitrous-oxide reductase This model represents the nitrous-oxide reductase protein NosZ as characterized in Geobacillus thermodenitrificans. In contrast to the related form in Pseudomonas stutzeri, this version lacks a recognizable twin-arginine translocation (TAT) signal at the N-terminus. Consequently, its accessory protein may differ. Some members of this family have an additional cytochrome c-like domain at the C-terminus. TIGR04247.1 TIGR04247 NosD_copper_fam 300 300 377 subfamily Y Y N nitrous oxide reductase family maturation protein NosD nosD GO:0071941 12533464 131567 cellular organisms no rank 8846 JCVI nitrous oxide reductase family maturation protein NosD nitrous oxide reductase family maturation protein NosD Members of this family include NosD, a repetitive periplasmic protein required for the maturation of the copper-containing enzyme nitrous-oxide reductase. NosD appears to be part of a complex with NosF (an ABC transporter family ATP-binding protein) and NosY (a six-helix transmembrane protein in the ABC-2 permease family). However, NosDFY-like complexes appear to occur also in species whose copper requiring enzymes are something other than nitrous-oxide reductase. TIGR04248.1 TIGR04248 SCM_PqqD_rel 100 100 84 equivalog Y Y N SynChlorMet cassette protein ScmD scmD 20737074 131567 cellular organisms no rank 8 JCVI SynChlorMet cassette protein ScmD SynChlorMet cassette protein ScmD A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Members of this family are the PqqD-like protein. TIGR04249.1 TIGR04249 SCM_chp_ScmC 125 125 292 equivalog Y Y N SynChlorMet cassette protein ScmC scmC 131567 cellular organisms no rank 18 JCVI SynChlorMet cassette protein ScmC SynChlorMet cassette protein ScmC A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Members of this family are designated ScmC. TIGR04250.1 TIGR04250 SCM_rSAM_ScmE 400 400 358 equivalog Y Y N SynChlorMet cassette radical SAM/SPASM protein ScmE scmE GO:0009058,GO:0051539,GO:1904047 131567 cellular organisms no rank 17 JCVI SynChlorMet cassette radical SAM/SPASM protein ScmE SynChlorMet cassette radical SAM/SPASM protein ScmE A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Of the two PqqE homologs of the cassette, this family is the closer in sequence. TIGR04251.1 TIGR04251 SCM_rSAM_ScmF 400 400 353 equivalog Y Y N SynChlorMet cassette radical SAM/SPASM protein ScmF scmF GO:0009058,GO:0051539,GO:1904047 131567 cellular organisms no rank 15 JCVI SynChlorMet cassette radical SAM/SPASM protein ScmF SynChlorMet cassette radical SAM/SPASM protein ScmF A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Of the two PqqE homologs of the cassette, this family is the more distant in sequence. TIGR04252.1 TIGR04252 SCM_precur_ScmA 35 35 49 equivalog Y Y N SynChlorMet cassette protein ScmA scmA GO:0009058 131567 cellular organisms no rank 3 JCVI SynChlorMet cassette protein ScmA SynChlorMet cassette protein ScmA A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. This HMM identifies a conserved open reading frame that was identified as a predicted gene in only one of those species (Chlorobium), but that may represent the ribosomally produced peptide precursor of the system. As with most other radical SAM enzyme-modified ribosomal natural products, these polypeptides are Cys-rich in the C-terminal half. TIGR04255.1 TIGR04255 sporadTIGR04255 30 30 252 subfamily Y Y N TIGR04255 family protein 131567 cellular organisms no rank 4117 JCVI TIGR04255 family protein TIGR04255 family protein Members of this uncharacterized protein family are found broadly but sporadically among bacteria and archaea, including members of the genera Mycobacterium, Nostoc, Acinetobacter, Planctomyces, Geobacter, Streptomyces, Methanospirillum, etc. The function is unknown. TIGR04256.1 TIGR04256 GxxExxY 35 35 116 subfamily Y Y N GxxExxY protein 131567 cellular organisms no rank 13126 JCVI GxxExxY protein GxxExxY protein Members of this protein family average about 130 residues in length and include an almost perfectly conserved motif GxxExxY. Members occur in a wide range of prokaryotes, including Proteobacteria, Perrucomicrobia, Cyanobacteria, Bacteriodetes, Archaea, etc. TIGR04261.1 TIGR04261 rSAM_GlyRichRpt 310 310 363 subfamily Y Y N cyclophane-forming radical SAM/SPASM peptide maturase GrrM/OscB grrM GO:0051539,GO:1904047 32807886 131567 cellular organisms no rank 605 JCVI radical SAM/SPASM domain protein, GRRM system cyclophane-forming radical SAM/SPASM peptide maturase GrrM/OscB Members of this protein family are peptide-modifying radical SAM/SPASM domain proteins (see PF04055 and TIGR04085) discovered bioinformatically by TIGRFAMs and named GrrM (Glycine-rich peptide radical SAM maturase). The modifications introduced by the radical SAM enzyme are now understood to be cyclophane formations, that is, the crosslinking of an aromatic amino acid side chain to another side chain two residues away to form a strained cyclophane moiety. Work by the Morinaka lab uses a more species-specific gene symbol, OscB, based on the study of a system in an Oscillatoriales cyanobacterium strain, and a convention of treating the radical SAM gene as the B gene in biosynthetic gene clusters. TIGR04265.1 TIGR04265 bac_cardiolipin 290 290 483 equivalog Y Y N cardiolipin synthase cls GO:0008808,GO:0016780,GO:0032049 9370333 131567 cellular organisms no rank 56891 JCVI cardiolipin synthase cardiolipin synthase This model is based on experimentally characterized bacterial cardiolipin synthases (cls) from E. coli, Staphylococcus aureus (two), and Bacillus pseudofirmus OF4. This model describes just one of several homologous but non-orthologous forms of cls. The cutoff score is set arbitrarily high to avoid false-positives. Note that there are two enzymatic activites called cardiolipin synthase. This model represents type 1, which does not rely on a CDP-linked donor, but instead does a reversible transfer of a phosphatidyl group from one phosphatidylglycerol molecule to another. TIGR04267.2 TIGR04267 mod_HExxH 40 40 177 domain Y Y N aKG-HExxH-type peptide beta-hydroxylase 39294420 131567 cellular organisms no rank 15346 JCVI HEXXH motif domain aKG-HExxH-type peptide beta-hydroxylase domain Sequences belonging to this family include C-terminal extension regions shared by members of the FxsB family of radical SAM/SPASM proteins that perform post-translational modifications to FxSxx-COOH family RiPP precursor proteins, but also additional proteins from bacteria that lack an FxSxx-COOH modification system. All seed alignment members, and all family members that are not fused to a radical SAM domain, have a HEXXH motif that hinted at metalloprotease activity. However, the domain recently was shown instead to function as an alpha-ketoglutarate (aKG)-dependent non-heme iron beta-hydroxylase ('H') domain. Note that this HMM has been shortened to a new length of 177 residues, from its original definition as a domain of length 399. TIGR04269.1 TIGR04269 SAM_SPASM_FxsB 370 370 363 subfamily_domain Y Y N FxsB family cyclophane-forming radical SAM/SPASM peptide maturase GO:0051539,GO:1904047 32807886 131567 cellular organisms no rank 10209 JCVI radical SAM/SPASM domain protein, FxsB family FxsB family cyclophane-forming radical SAM/SPASM peptide maturase This HMM describes a radical SAM (PF04055)/SPASM domain (TIGR04085) fusion subfamily distinct from PqqE, MftC, anaerobic sulfatase maturases, and other peptide maturases. The combined region described in this model can itself be fused to another domain, such as TIGR04267, or stand alone. Members occurring in the same cassette as a member of family TIGR04268 should be designated FxsB. TIGR04270.1 TIGR04270 Rama_corrin_act 500 500 534 subfamily Y Y N methylamine methyltransferase corrinoid protein reductive activase GO:0015948,GO:0051539 19043046 131567 cellular organisms no rank 480 JCVI methylamine methyltransferase corrinoid protein reductive activase methylamine methyltransferase corrinoid protein reductive activase Members of this family occur as paralogs in species capable of generating methane from mono-, di-, and tri-methylamine. Members include RamA (Reductive Activation of Methyltransfer, Amines) from Methanosarcina barkeri MS (DSM 800). Member proteins have two C-terminal motifs with four Cys each, likely to bind one 4Fe-4S cluster per motif. TIGR04272.1 TIGR04272 cxxc_cxxc_Mbark 36 36 37 domain Y Y N CxxC-x17-CxxC domain-containing protein 131567 cellular organisms no rank 1791 JCVI CxxC-x17-CxxC domain CxxC-x17-CxxC domain This domain, with a pair of CXXC motifs separated by 17 amino acids, is a candidate zinc finger domain based on these motifs. Some proteins have two copies of the domain, while others are fused to another probable zinc-binding domain, described by Pfam model PF13451. TIGR04274.1 TIGR04274 hypoxanDNAglyco 80 80 150 equivalog Y Y N DNA-deoxyinosine glycosylase 3.2.2.15 GO:0006285,GO:0033958 21642431 131567 cellular organisms no rank 13536 JCVI DNA-deoxyinosine glycosylase DNA-deoxyinosine glycosylase Members of this protein family represent family 6 of the uracil-DNA glycosylase superfamily, where the five previously described families all act as uracil-DNA glycosylase (EC 3.2.2.27) per se. This family, instead, acts as a hypoxanthine-DNA glycosylase, where hypoxanthine results from deamination of adenine. Activity was shown directly for members from Methanosarcina barkeri and Methanosarcina acetivorans. TIGR04275.1 TIGR04275 beta_prop_Msarc 85 30 40 repeat Y N N beta-propeller repeat protein 131567 cellular organisms no rank 1030 JCVI beta propeller repeat beta-propeller repeat This model describes a repeat region found mostly in cell surface proteins of various methanogens. Methanosarcina barkeri, for example, has twenty such proteins, often with either seven or fourteen repeats. These repeats resemble the beta propeller repeats of the TolB periplasmic protein of Gram-negative bacteria, part of a complex associated with various functions including biopolymer transport (see TIGR02800). TIGR04282.1 TIGR04282 glyco_like_cofC 134 134 189 hypoth_equivalog Y Y N TIGR04282 family arsenosugar biosynthesis glycosyltransferase GO:0009058,GO:0016740 30525501 131567 cellular organisms no rank 8793 JCVI transferase 1, rSAM/selenodomain-associated TIGR04282 family arsenosugar biosynthesis glycosyltransferase Members of this protein family show strongly correlated phylogenetic distribution, and in most cases co-clustering, with an unusual radical SAM enzyme (TIGR04167) whose C-terminal PF12345 domain often contains a selenocysteine residue. Other members of the conserved gene neighborhood include another putative glycosyltransferase, an alkylhydroperoxidase family protein (TIGR04169), and a phosphoesterase family protein (TIGR04168). The radical SAM enzyme is now known to participate in arsenosugar biosynthesis. TIGR04283.1 TIGR04283 glyco_like_mftF 182 182 221 equivalog Y Y N TIGR04283 family arsenosugar biosynthesis glycosyltransferase GO:0009058,GO:0016740 30525501 131567 cellular organisms no rank 7926 JCVI transferase 2, rSAM/selenodomain-associated TIGR04283 family arsenosugar biosynthesis glycosyltransferase This enzyme, a putative glycosyltransferase, co-occurs with a radical SAM enzyme, now characterized as an enzyme of arsenosugar biosynthesis (TIGR04167), whose C-terminal domain (PF12345) frequently contains a selenocysteine. Other proposed members of the pathway include another transferase (TIGR04282), a methyltransferase, and a phosphoesterase. TIGR04289.1 TIGR04289 heavy_Cys 50 50 52 domain Y Y N eight-cysteine-cluster domain-containing protein 131567 cellular organisms no rank 86 JCVI eight-cysteine-cluster domain eight-cysteine-cluster domain In this domain of about 50 residues, eight of twelve invariant residues are Cys. Proteins with this domain tend to have N-terminal signal sequences, suggesting an extracytoplasmic location for this domain. TIGR04291.1 TIGR04291 arsen_driv_ArsA 650 650 565 equivalog Y Y N arsenical pump-driving ATPase arsA 7.3.2.7 GO:0005524,GO:0015446,GO:0016887,GO:0071722 131567 cellular organisms no rank 8568 JCVI arsenical pump-driving ATPase arsenical pump-driving ATPase The broader family (TIGR00345) to which the current family belongs consists of transport-energizing ATPases, including to TRC40/GET3 family involved in post-translational insertion of protein C-terminal transmembrane anchors into membranes from the cyotosolic face. This family, however, is restricted to ATPases that energize pumps that export arsenite (or antimonite). TIGR04306.1 TIGR04306 salvage_TenA 130 130 208 equivalog Y Y N thiaminase II tenA 3.5.99.2 GO:0006772,GO:0050334 15709744,18028398,21206023 131567 cellular organisms no rank 20209 JCVI thiaminase II thiaminase II The TenA protein of Bacillus subtilis and Staphylococcus aurues, and the C-terminal region of trifunctional protein Thi20p from Saccharomyces cerevisiae, perform cleavages on thiamine and related compounds to produce 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), a substrate a salvage pathway for thiamine biosynthesis. The gene symbol tenA, for Transcription ENhancement A, reflects a misleading early characterization as a regulatory protein. This family is related to PqqC from the PQQ biosynthesis system (see TIGR02111), heme oxygenase (PF01126), and CADD (Chlamydia protein Associating with Death Domains), a putative folate metabolism enzyme (see TIGR04305). TIGR04315.1 TIGR04315 octaheme_Shew 375 375 440 subfamily Y Y N tetrathionate reductase family octaheme c-type cytochrome GO:0020037,GO:0022904 15361860 131567 cellular organisms no rank 1727 JCVI octaheme c-type cytochrome, tetrathionate reductase family tetrathionate reductase family octaheme c-type cytochrome Members of this protein family bind heme covalently and contain eight (at least) CXXCH heme-binding motifs. A characterized member is the respiratory enzyme octaheme tetrathionate reductase from Shewanella. Some members of this family are selenoproteins. TIGR04317.1 TIGR04317 W_rSAM_matur 380 380 349 equivalog Y Y N tungsten cofactor oxidoreductase radical SAM maturase 131567 cellular organisms no rank 232 JCVI tungsten cofactor oxidoreducase radical SAM maturase tungsten cofactor oxidoreductase radical SAM maturase Members of this family are radical SAM enzymes involved in the maturation of tungsten (W)-containing cofactors in the enzymes aldehyde ferredoxin oxidoreductase, formaldehyde ferredoxin oxidoreductase, and others, and tend to be encoded by an adjacent gene. TIGR04325.1 TIGR04325 MTase_LIC12133 80 80 234 subfamily Y Y N methyltransferase, TIGR04325 family 2.1.1.- 131567 cellular organisms no rank 1565 JCVI putative methyltransferase, LIC12133 family methyltransferase, TIGR04325 family Members of this family tend to occur next to glycosyltransferases and other characteristic enzymes of O-antigen biosynthetic regions. The founding member is LIC12133 from Leptospira interrogans serovar Copenhageni. PSI-BLAST reveals distant homology to known SAM-dependent methyltransferases, as in Pfam family PF13489. TIGR04328.1 TIGR04328 cas4_PREFRAN 70 70 178 exception Y Y N type V CRISPR-associated protein Cas4 cas4 GO:0004518 131567 cellular organisms no rank 205 JCVI CRISPR-associated protein Cas4, subtype PREFRAN type V CRISPR-associated protein Cas4 Members of this family are the Cas4 protein of a novel CRISPR subtype, PREFRAN, found in Prevotella bryantii B14, Prevotella disiens FB035-09AN, Francisella tularensis subsp. novicida, Francisella philomiragia, Butyrivibrio proteoclasticus B316, Helcococcus kunzii ATCC 51366, etc. TIGR04329.1 TIGR04329 cas1_PREFRAN 300 300 317 exception Y Y N type V CRISPR-associated endonuclease Cas1 cas1 GO:0004520,GO:0043571,GO:0046872 131567 cellular organisms no rank 178 JCVI CRISPR-associated endonuclease Cas1, subtype PREFRAN type V CRISPR-associated endonuclease Cas1 Members of this family are the Cas1 endonuclease of a novel CRISPR subtype, PREFRAN, found in Prevotella bryantii B14, Prevotella disiens FB035-09AN, Francisella tularensis subsp. novicida, Francisella philomiragia, Butyrivibrio proteoclasticus B316, Helcococcus kunzii ATCC 51366, etc. TIGR04330.1 TIGR04330 cas_Cpf1 300 300 1288 equivalog Y Y N type V CRISPR-associated protein Cas12a/Cpf1 cas12a 131567 cellular organisms no rank 335 JCVI CRISPR-associated protein Cpf1, subtype PREFRAN type V CRISPR-associated protein Cas12a/Cpf1 This family is the long protein of a novel CRISPR subtype, PREFRAN, which is most common in Prevotella and Francisella, although widely distributed. The PREFRAN type has Cas1, Cas2, and Cas4, but lacks the helicase Cas3 and endonuclease Cas3-HD. TIGR04331.1 TIGR04331 o_ant_LIC12162 225 225 585 subfamily Y Y N LIC12162 family transferase 131567 cellular organisms no rank 425 JCVI putative transferase, LIC12162 family LIC12162 family transferase This protein family shows C-terminal sequence similarity to various surface carbohydrate biosynthesis enzymes: spore coat polysaccharide biosynthesis protein SpsB, UDP-N-acetyl-D-glucosamine 2-epimerase, lipid A disaccharide synthetase LpxB, etc. It may occur in O-antigen biosythesis regions. TIGR04335.1 TIGR04335 AmmeMemoSam_A 99 99 175 hypoth_equivalog Y Y N AmmeMemoRadiSam system protein A amrA 17715145 131567 cellular organisms no rank 6813 JCVI AmmeMemoRadiSam system protein A AmmeMemoRadiSam system protein A Members of this protein family belong to the same domain family as AMMECR1, a mammalian protein named for AMME - Alport syndrome, Mental Retardation, Midface hypoplasia, and Elliptocytosis. Members of the present family occur as part of a three gene system with a homolog of the mammalian protein Memo (Mediator of ErbB2-driven cell MOtility), and an uncharacterized radical SAM enzyme. TIGR04336.1 TIGR04336 AmmeMemoSam_B 26 26 270 hypoth_equivalog Y Y N AmmeMemoRadiSam system protein B amrB 18045866 131567 cellular organisms no rank 6872 JCVI AmmeMemoRadiSam system protein B AmmeMemoRadiSam system protein B Members of this protein family belong to the same domain family as the mammalian protein Memo (Mediator of ErbB2-driven cell MOtility). Members of the present family occur as part of a three gene system with an uncharacterized radical SAM enzyme and a homolog of the mammalian protein AMMECR1, a mammalian protein named for AMME - Alport syndrome, Mental Retardation, Midface hypoplasia, and Elliptocytosis. Memo in humans has protein-protein interaction activity with binding of phosphorylated Try, but members of this family may be active as enzymes, as suggested by homology to a class of nonheme iron dioxygenases. TIGR04337.1 TIGR04337 AmmeMemoSam_rS 220 220 349 hypoth_equivalog Y Y N AmmeMemoRadiSam system radical SAM enzyme amrS GO:0051536 131567 cellular organisms no rank 7161 JCVI AmmeMemoRadiSam system radical SAM enzyme AmmeMemoRadiSam system radical SAM enzyme Members of this protein family are uncharacterized radical SAM enzymes that occur in a prokaryotic three-gene system along with homologs of mammalian proteins Memo (Mediator of ErbB2-driven cell MOtility) and AMMERCR1 (Alport syndrome, Mental Retardation, Midface hypoplasia, and Elliptocytosis). Among radical SAM enzymes that have been experimentally characterized, the most closely related in sequence include activases of pyruvate formate-lyase and of benzylsuccinate synthase. TIGR04340.1 TIGR04340 rSAM_ACGX 400 400 341 hypoth_equivalog Y Y N radical SAM/SPASM domain protein, ACGX system acgM 131567 cellular organisms no rank 382 JCVI radical SAM/SPASM domain protein, ACGX system radical SAM/SPASM domain protein, ACGX system Members of this protein family are radical SAM/SPASM domain proteins likely to be involved in the modification of small, Cys-rich peptides. Members of the family of proposed target sequences, TIGR04341, average 75 amino acids in length and average six instances of the motif ACGX, where X is A, S, or T. TIGR04350.1 TIGR04350 C_S_lyase_PatB 340 340 384 subfamily Y Y N PatB family C-S lyase GO:0003824,GO:0009058,GO:0030170 10880431,15760717,21247153,32719469 131567 cellular organisms no rank 45729 JCVI putative C-S lyase PatB family C-S lyase Characterized members of this subfamily are known or probable C-S lyases from a family of pyridoxal phosphate-dependent enzymes that tend to be (mis)annotated as probable aminotransferases. One member is PatB of Bacillus subtilis, a proven C-S-lyase. Another is the virulence factor cystalysin from Treponema denticola, whose hemolysin activity may stem from H2S production. Members of the seed alignment occur next to examples of the enzyme 5-histidylcysteine sulfoxide synthase, from ovothiol A biosynthesis, and would be expected to perform a C-S cleavage of 5-histidylcysteine sulfoxide to leave 1-methyl-4-mercaptohistidine (ovothiol A). The PatB from Staphylococcus hominis (ShPatB) is a C-S lyase active on aliphatic cysteine-S-conjugates; its release of the thioalcohol 3-methyl-3-sulfanylhexan-1-ol (3M3SH) from the odourless precursor Cys-Gly-3M3SH secreted from human skin is a major contributor to body odor. TIGR04353.1 TIGR04353 PqqD_rel_X 35 35 74 equivalog Y Y N HPr-rel-A system PqqD family peptide chaperone 131567 cellular organisms no rank 1606 JCVI PqqD family protein, HPr-rel-A system HPr-rel-A system PqqD family peptide chaperone Members of this protein show distant homology to PqqD, and belong to a three-gene cassette that included the HPr kinase related protein family of TIGR04352. The role of the cassette, and of this protein, are unknown. TIGR04354.1 TIGR04354 amphi-Trp 31 31 67 subfamily Y Y N amphi-Trp domain-containing protein 131567 cellular organisms no rank 5881 JCVI amphi-Trp domain amphi-Trp domain This domain usually comprises most of the span of bacterial or archaeal proteins with a length of about 90 amino acids. Some members, however, are extended by one or two copies of domain PF07411 in the C-terminal region. No residue in this domain is invariant. A striking feature of this domain is a C-terminal region that alternates strongly charged with strongly hydrophobic residues and usually ends with a Trp residue, e.g. LEIEIEW or FEIKVRW, suggesting an amphipathic beta strand structure. We suggest the name amphi-Trp for this domain. Some members of this function occur regularly in genomic contexts that include putative kinases of unknown specificity related to (but distinct from) HPr kinase, a Ser-specific protein kinase. The function is unknown. TIGR04362.1 TIGR04362 choice_anch_C 120 120 157 subfamily_domain Y Y N choice-of-anchor C family protein 131567 cellular organisms no rank 967 JCVI choice-of-anchor C domain choice-of-anchor C domain This family describes an extracellular bacterial domain that occurs on a number of proteins with PEP-CTERM (exosortase recognition site) sequences at the C-terminus, as well some with an apparent alternate anchor sequence. Note that related Pfam model PF04862 (DUF642) belongs to a Pfam clan called the galactose-binding domain-like superfamily. TIGR04370.1 TIGR04370 glyco_rpt_poly 40 40 396 subfamily Y Y N oligosaccharide repeat unit polymerase GO:0000271,GO:0016757 131567 cellular organisms no rank 9857 JCVI oligosaccharide repeat unit polymerase oligosaccharide repeat unit polymerase Members of this subfamily of highly hydrophobic proteins, with few highly conserved residues, all may act to polymerize the oligosaccharide repeat units of surface polysaccharides, including O-antigen in Gram-negative bacteria such as Leptospira (assign gene symbol wzy) and capsular polysaccharide in Gram-positive bacteria such as Streptococcus. O-antigen biosynthesis enzymes produce a repeat unit, usually an oligosaccharide, which itself is polymerized. O-antigen polymerase, usually designated Wzy. This family bears homology to the O-antigen ligase WaaL, but known examples of WaaL fall outside the bounds defined here. This model is much broader than Pfam model PF14296. TIGR04371.1 TIGR04371 methyltran_NanM 44 42 273 subfamily Y Y N putative sugar O-methyltransferase 2.1.1.- GO:0008171,GO:0016051 12770825 131567 cellular organisms no rank 1146 JCVI putative sugar O-methyltransferase putative sugar O-methyltransferase Members of this family appear to be SAM-dependent O-methyltransferases acting on sugars, based on iterated sequence searches and gene context. Members occur in Leptospira O-antigen regions, as well NanM from the biosynthesis cluster for nanchangmycin, which produces 4-O-methyl-L-rhodinose as an intermediate. TIGR04378.1 TIGR04378 myo_inos_iolB 205 205 247 equivalog Y Y N 5-deoxy-glucuronate isomerase iolB 5.3.1.30 GO:0016861,GO:0019310 18310071,19011032 131567 cellular organisms no rank 24129 JCVI 5-deoxy-glucuronate isomerase 5-deoxy-glucuronate isomerase Members of this protein family, 5-deoxy-glucuronate isomerase (iolB), represent one of eight enzymes in a pathway converting myo-inositol to acetyl-CoA. TIGR04380.1 TIGR04380 myo_inos_iolG 355 355 330 equivalog Y Y N inositol 2-dehydrogenase iolG 1.1.1.18 GO:0019310,GO:0050112 131567 cellular organisms no rank 13462 JCVI inositol 2-dehydrogenase inositol 2-dehydrogenase All members of the seed alignment for this model are known or predicted inositol 2-dehydrogenase sequences co-clustered with other enzymes for catabolism of myo-inositol or closely related compounds. Inositol 2-dehydrogenase catalyzes the first step in inositol catabolism. Members of this family may vary somewhat in their ranges of acceptable substrates and some may act on analogs to myo-inositol rather than myo-inositol per se. TIGR04382.1 TIGR04382 myo_inos_iolC_N 300 300 309 equivalog_domain Y Y N 5-dehydro-2-deoxygluconokinase iolC 2.7.1.92 GO:0019310,GO:0047590 131567 cellular organisms no rank 28724 JCVI 5-dehydro-2-deoxygluconokinase 5-dehydro-2-deoxygluconokinase All members of the seed alignment for this model are translated from the iolC gene of known or putative inositol catabolism operons. Members with characterized function are 5-dehydro-2-deoxygluconokinase, the enzyme catalyzing the fifth step in degradation from myo-inositol or closely related compounds. Note that many members of this family are fusion proteins with an additional C-terminal domain, of unknown function, described by Pfam model PF09863. TIGR04387.1 TIGR04387 capsid_maj_N4 60 50 324 equivalog Y Y N N4-gp56 family major capsid protein GO:0019028 18374942 131567 cellular organisms no rank 3901 JCVI major capsid protein, N4-gp56 family N4-gp56 family major capsid protein Members of this family are phage major capsid proteins as found in phage N4 (a double-stranded DNA virus) plus many additional lytic phage and integrated prophage regions. TIGR04391.1 TIGR04391 CcmD_alt_fam 24 24 36 subfamily Y Y N CcmD family protein GO:0005886 18326572 131567 cellular organisms no rank 1044 JCVI CcmD family protein CcmD family protein Members of this protein family are small (typically less than 50 amino acids in length), with the first half highly hydrophobic like transmembrane alpha helices and containing a nearly invariant tyrosine residue. Members from the Desulfovibrionales appear in the position of ccmD of system I c-type cytochrome biogenesis operons (see PF04995). This family and PF04995 appear very similar in sequence properties, but the very low level of actual sequence identify makes it unclear that the similarity reflects homology per se. TIGR04396.2 TIGR04396 surf_polysacc 125 125 427 subfamily Y Y N surface carbohydrate biosynthesis protein GO:0000271,GO:0003824 131567 cellular organisms no rank 885 JCVI surface carbohydrate biosynthesis protein surface carbohydrate biosynthesis protein This model describes an uncharacterized homology region found broadly in proteins of surface carbohydrate biosynthesis regions. This family shows distant homology to a variety of carbohydrate-active enzymes such as UDP-N-acetylglucosamine 2-epimerase and teichoic acid glycerol-phosphate transferase. TIGR04416.1 TIGR04416 group_II_RT_mat 300 300 353 equivalog Y Y N group II intron reverse transcriptase/maturase ltrA 2.7.7.49 GO:0000373,GO:0003964 131567 cellular organisms no rank 42098 JCVI group II intron reverse transcriptase/maturase group II intron reverse transcriptase/maturase Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (PF00078) followed by an RNA-binding maturase domain (PF08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. TIGR04417.1 TIGR04417 PFTS_polysacc 100 100 522 subfamily Y Y N polysaccharide biosynthesis PFTS motif protein 131567 cellular organisms no rank 75 JCVI polysaccharide biosynthesis PFTS motif protein polysaccharide biosynthesis PFTS motif protein Members of this protein family are found in O-antigen biosynthesis loci in Leptospira, two tandem homologs in a polysaccharide biosynthesis region in the archaeon Methanoregula formicicum, in Rhizobium leguminosarum bv. trifolii WSM2297, etc. Members are more strongly conserved in the C-terminal region, where an invariant sequence PFTS is found. TIGR04440.1 TIGR04440 glyco_TIGR04440 70 70 215 domain Y Y N TIGR00180 family glycosyltransferase 131567 cellular organisms no rank 1850 JCVI glycosyltransferase domain TIGR00180 family glycosyltransferase This model describes a putative glycotransferase domain, related to the group 2 family glycosyltransferases of PF00535. TIGR04448.1 TIGR04448 creatininase 235 235 246 equivalog Y Y N creatininase 3.5.2.10 GO:0006601,GO:0046449,GO:0047789 9563845 131567 cellular organisms no rank 2004 JCVI creatininase creatininase Members of this family are creatininase (EC 3.5.2.10), an amidohydrolase that interconverts creatinine + H(2)O with creatine. It should not be confused with creatinase (EC 3.5.3.3), which hydrolyzes creatine to sarcosine plus urea. TIGR04449.1 TIGR04449 halocin_C8_dom 24 24 69 subfamily_domain Y Y N halocin C8-like domain-containing protein 18658263 131567 cellular organisms no rank 297 JCVI halocin C8-like bacteriocin domain bacteriocin halocin C8-like domain This HMM describes the 76-amino C-terminal domain of the halocin C8 precursor that actually becomes the mature bacteriocin halocin C8 after export and cleavage, as well as homologous C-terminal regions from many other archaea. Surprisingly, this Cys-rich region occurs also in many strains of Staphylococcus epidermidis. Gene regions do not provide evidence for post-translational modification other than cleavage. Halocin C8 is active against a broad range of archaea; the region N-terminal to the bacteriocin domain modeled here serves as the immunity protein for the cell secreting the bacteriocin. TIGR04463.1 TIGR04463 rSAM_vs_C_rich 525 525 438 equivalog Y Y N TIGR04463 family radical SAM/SPASM RiPP maturase 131567 cellular organisms no rank 17 JCVI radical SAM/SPASM domain protein maturase TIGR04463 family radical SAM/SPASM RiPP maturase Members of this family are probable protein/peptide-modifying radical SAM/SPASM domain proteins. The majority of members of this family seem to target Cys-rich repetitive regions of large proteins rather than of bacteriocin-sized small precursors. This arrangement suggests the modification target may be multifunctional, with the C-terminal domain behaving like a bacteriocin but other parts of the same precursor serving an immunity function, as occurs for the halocin C8 precursor. TIGR04470.1 TIGR04470 rSAM_mob_pairB 410 410 285 equivalog Y Y N radical SAM mobile pair protein B 131567 cellular organisms no rank 1224 JCVI radical SAM mobile pair protein B radical SAM mobile pair protein B Members of this family are the downstream member (B) of a pair of tandem-encoded radical SAM enzymes. Most of these radical SAM gene pairs have an additional upstream regulatory gene in the MarR family. Examples of high sequence identity (over 96 percent) from cassettes in several Treponema species of the oral cavity to those in multiple Firmicutes in the gut microbiome suggest recent lateral gene transfer, as might be expected for antibiotic resistance genes. The function is unknown. TIGR04471.1 TIGR04471 rSAM_mob_pairA 355 355 220 equivalog Y Y N radical SAM mobile pair protein A 131567 cellular organisms no rank 821 JCVI radical SAM mobile pair protein A radical SAM mobile pair protein A Members of this family are the upstream member (A) of a pair of tandem-encoded radical SAM enzymes. Most of these radical SAM gene pairs have an additional upstream regulatory gene in the MarR family. Examples of high sequence identity (over 96 percent) from cassettes in several Treponema species of the oral cavity to those in multiple Firmicutes in the gut microbiome suggest recent lateral gene transfer, as might be expected for antibiotic resistance genes. The function is unknown. TIGR04474.1 TIGR04474 tcm_partner 53 53 263 subfamily Y Y N three-Cys-motif partner protein TcmP tcmP 131567 cellular organisms no rank 6204 JCVI three-Cys-motif partner protein three-Cys-motif partner protein TcmP Members of this family occur regularly as a partner to as a member of family PF07505, which has been called a phage protein but which seems to occur also in other contexts. Members average about 400 residues in length, but the conserved region covered by the model averages 260 residues and excludes the C-terminus. Conserved motifs suggest enzymatic activity. Note that its frequent partner protein (see PF07505) has a three-cysteine motif that resembles the Cx3CxxC motif of radical SAM proteins, and that in one branch (see TIGR04471) actually becomes Cx3CxxC. We suggest the name three-Cys-motif partner protein (tcmP), and renaming PF07505 to three-Cys-motif family protein TIGR04498.1 TIGR04498 AbiV_defense 27 26 143 subfamily Y Y N AbiV family abortive infection protein 20851990 131567 cellular organisms no rank 2006 JCVI abortive infection protein, AbiV family AbiV family abortive infection protein This family includes AbiV (abortive infection system V) from Lactococcus lactis, a phage resistance protein that causes certain phage infections to fail to lead to successful phage replication. Abortive infection mechanisms differ greatly. AbiV interacts directly with the protein SaV in phage p2 and blocks translation of phage proteins. TIGR04499.1 TIGR04499 abortive_AbiA 250 250 615 subfamily Y Y N AbiA family abortive infection protein 12450864 131567 cellular organisms no rank 225 JCVI abortive infection protein, AbiA family AbiA family abortive infection protein Members of this protein family average about 650 amino acids in length, with an N-terminal region related to reverse transcriptases. The only characterized member is AbiA, with reported activity as an abortive infection protein for phage defense in Lactococcus lactis and (heterologously) in Streptococcus thermophilus. TIGR04520.1 TIGR04520 ECF_ATPase_1 315 315 269 equivalog Y Y N energy-coupling factor transporter ATPase GO:0005524,GO:0006810,GO:0009898,GO:0042626 18931129 131567 cellular organisms no rank 13195 JCVI energy-coupling factor transporter ATPase energy-coupling factor transporter ATPase Members of this family are ATP-binding cassette (ABC) proteins by homology, but belong to energy coupling factor (ECF) transport systems. The architecture in general is two ATPase subunits (or a double-length fusion protein), a T component, and a substrate capture (S) component that is highly variable, and may be interchangeable in genomes with only one T component. This model identifies many but not examples of the upstream member of the pair of ECF ATPases in Firmicutes and Mollicutes. TIGR04534.2 TIGR04534 ELWxxDGT_rpt 65 65 47 domain Y Y N ELWxxDGT repeat protein 131567 cellular organisms no rank 2615 JCVI ELWxxDGT repeat ELWxxDGT repeat This model describes protein repeat with a well-conserved motif ELWxxDGT, and a periodicity of about 48. A single protein may have as many as 18 repeats. It may consist nearly entirely of this repeat, or may have other repeats as well (e.g. hyalin repeat). It is most common in the Deltaproteobacteria. TIGR04545.1 TIGR04545 rSAM_ahbD_hemeb 500 500 339 equivalog Y Y N heme b synthase ahbD 1.3.98.6 GO:0006785,GO:0051539,GO:1904047 24713144 131567 cellular organisms no rank 485 JCVI heme b synthase AdoMet-dependent heme b synthase Members of this family are AhbD (alternative heme biosynthetic protein D), a radical SAM enzyme in sulfate-reducing bacteria and methanogens that performs the last decarboxylations to synthesize heme b from Fe-coproporphyrin III. Members include DVU_0855, previously included in error in TIGR04055, the NirJ2 family thought to be involved in heme d1 biosynthesis. TIGR04546.1 TIGR04546 rSAM_ahbC_deAc 650 650 390 equivalog Y Y N 12,18-didecarboxysiroheme deacetylase ahbC GO:0006785,GO:1904047 131567 cellular organisms no rank 463 JCVI 12,18-didecarboxysiroheme deacetylase 12,18-didecarboxysiroheme deacetylase This model describes one of a pair of radical SAM enzymes involved in the alternative heme biosynthesis (ahb) pathway for heme b biosynthesis from siroheme. This anaerobic pathway occurs in sulfate-reducing bacteria and methanogens. A very similar pair of radical SAM enzymes (TIGR04054, TIGR04055) is involved in heme d1 biosynthesis in species such as Heliobacillus mobilis and Heliophilum fasciatum. NF018940.5 PF07289.16 BBL5 23.8 23.8 334 domain Y Y N Bardet-Biedl syndrome 5 protein GO:0034464 15137946,17574030,21344540 1325932 Robertmurraya andreesenii species 1 EBI-EMBL Bardet-Biedl syndrome 5 protein Bardet-Biedl syndrome 5 protein BBS5 is part of the BBSome complex that may function as a coat complex required for sorting of specific membrane proteins to the primary cilia [1]. Mutations in the BBS5 gene cause Bardet-Biedl syndrome 5 [2, 3]. [1]. 17574030. A core complex of BBS proteins cooperates with the GTPase Rab8 to promote ciliary membrane biogenesis. Nachury MV, Loktev AV, Zhang Q, Westlake CJ, Peranen J, Merdes A, Slusarski DC, Scheller RH, Bazan JF, Sheffield VC, Jackson PK;. Cell. 2007;129:1201-1213. [2]. 15137946. Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene. Li JB, Gerdes JM, Haycraft CJ, Fan Y, Teslovich TM, May-Simera H, Li H, Blacque OE, Li L, Leitch CC, Lewis RA, Green JS, Parfrey PS, Leroux MR, Davidson WS, Beales PL, Guay-Woodford LM, Yoder BK, Stormo GD, Katsanis N, Dutcher SK;. Cell. 2004;117:541-552. [3]. 21344540. BBS genotype-phenotype assessment of a multiethnic patient cohort calls for a revision of the disease definition. Deveault C, Billingsley G, Duncan JL, Bin J, Theal R, Vincent A, Fieggen KJ, Gerth C, Noordeh N, Traboulsi EI, Fishman GA, Chitayat D, Knueppel T, Millan JM, Munier FL, Kennedy D, Jacobson SG, Innes AM, Mitchell GA, Boycott K, Heon E;. Hum Mutat. 2011;32:610-619. (from Pfam) NF040705.1 sigma_mbnA 350 350 272 exception Y Y N methanobactin precursor domain-containing sigma factor 23442874,23682956 133 Methylocystis genus 17 NCBIFAM methanobactin precursor domain-containing sigma factor This variant form of sigma factor is found exclusively with a C-terminal methanobactin precursor domain. NF005259.0 PRK06762 PRK06762.3-4 349 349 170 equivalog Y N N hypothetical protein 1334 Streptococcus dysgalactiae species 16 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF024378.5 PF12976.12 DUF3860 27 27 93 domain Y Y N DUF3860 domain-containing protein 133814 Candidatus Poseidoniales order 9 EBI-EMBL Domain of Unknown Function with PDB structure (DUF3860) Domain of Unknown Function with PDB structure (DUF3860) A protein family created to cover PDB:2OD5. 2OD5 is a hypothetical protein (JCVI_PEP_1096688149193) from an environmental metagenome (unidentified marine microbe). (from Pfam) NF041740.1 choice_anch_T 70 70 259 equivalog Y Y N choice-of-anchor T family protein coaT 133814 Candidatus Poseidoniales order 10 NCBIFAM choice-of-anchor T family protein Members of this family are found almost exclusively the predicted proteins of archaeal genomes from metagenome-derived assemblies. Multiple sequence alignment shows that members contains several different classes of short C-terminal putative sorting signals, although currently defined HMMs for sorting signal detection, such as NF033507 (an archaeosortase-dependent sorting signal) and NF041738 may score members below their cutoffs. NF045872.1 urea_MBA 305 305 147 equivalog Y Y N multiple banded antigen mba 19220471,22253806,28451522 134821 Ureaplasma parvum species 14 NCBIFAM multiple banded antigen, N-terminal domain This HMM describes the N-terminal domain of the Ureaplasma surface-exposed lipoprotein known as MBA (multiple banded antigen, UU375). It distinguishes MBA from at least 5 paralogs that share a homologous N-terminal region, described by model NF045871. NF000036.1 D_ala_D_ser_VanE 700 700 352 exception Y Y Y D-alanine--D-serine ligase VanE vanE 6.3.2.35 1350 Enterococcus genus 3 NCBIFAM D-alanine--D-serine ligase VanE D-alanine--D-serine ligase VanE NF000093.1 D_ala_D_ser_VanN 700 700 343 exception Y Y Y D-alanine--D-serine ligase VanN vanN 6.3.2.35 1350 Enterococcus genus 6 NCBIFAM D-alanine--D-serine ligase VanN D-alanine--D-serine ligase VanN NF000165.3 AAC_6p_Entco 300 300 178 exception Y Y Y aminoglycoside N-acetyltransferase AAC(6')-Ii aac(6') GO:0008080 1350 Enterococcus genus 142 NCBIFAM AAC(6')-Ii family aminoglycoside 6'-N-acetyltransferase aminoglycoside 6'-N-acetyltransferase NF000371.1 vanH_Agroup 700 700 322 exception Y Y Y VanH-A/VanH-Pt family D-lactate dehydrogenase vanH 1.1.1.28 1350 Enterococcus genus 14 NCBIFAM D-lactate dehydrogenase, VanH-A/VanH-Pt group VanH-A/VanH-Pt family D-lactate dehydrogenase NF000402.1 vanR-B 480 480 219 exception Y Y Y vancomycin resistance response regulator transcription factor VanR-B vanR-B 1350 Enterococcus genus 20 NCBIFAM VanB-type vancomycin resistance DNA-binding response regulator VanR vancomycin resistance response regulator transcription factor VanR-B Members of this family are the response regulator VanR of VanB-type vancomycin resistance systems. NF000403.1 vanR-C 480 480 231 exception Y Y Y vancomycin resistance response regulator transcription factor VanR-C vanR-C 1350 Enterococcus genus 45 NCBIFAM VanC-type vancomycin resistance DNA-binding response regulator VanR vancomycin resistance response regulator transcription factor VanR-C Members of this family are the response regulator VanR of VanC-type vancomycin resistance systems. NF000473.1 vanY_BG 400 400 274 exception Y Y Y VanY-B/VanY-G family D-Ala-D-Ala carboxypeptidase vanY GO:0006508 1350 Enterococcus genus 14 NCBIFAM VanY-B/VanY-G family D-Ala-D-Ala carboxypeptidase VanY-B/VanY-G family D-Ala-D-Ala carboxypeptidase NF003637.0 PRK05270 PRK05270.3-2 860 860 404 equivalog Y Y N UDP-glucose--hexose-1-phosphate uridylyltransferase 2.7.7.12 1350 Enterococcus genus 187 NCBI Protein Cluster (PRK) galactose-1-phosphate uridylyltransferase UDP-glucose--hexose-1-phosphate uridylyltransferase NF006361.0 PRK08581 PRK08581.1-3 839 839 652 equivalog Y Y N amidase domain-containing protein 1350 Enterococcus genus 240 NCBI Protein Cluster (PRK) N-acetylmuramoyl-L-alanine amidase amidase domain-containing protein NF012213.0 VanC1_ser_lig 775 775 343 exception Y Y Y D-alanine--D-serine ligase VanC1 vanC1 1350 Enterococcus genus 25 NCBIFAM D-alanine--D-serine ligase VanC1 D-alanine--D-serine ligase VanC1 This model describes VanC1, one of two recognized subfamilies of the VanC type D-alanine--D-serine ligase involved in vancomycin resistance. The other type is VanC2/3. NF012214.1 D_ala_D_ser_VanC 650 650 350 exception Y Y Y D-alanine--D-serine ligase VanC vanC 6.3.2.35 1350 Enterococcus genus 93 NCBIFAM D-alanine--D-serine ligase VanC D-alanine--D-serine ligase VanC NF021166.5 PF09627.15 PrgU 25 25 106 subfamily Y Y N PrgU family protein 17302827,27785854 1350 Enterococcus genus 264 EBI-EMBL PrgU-like protein PrgU family protein PrgU is a protein of plasmid in origin expressed mainly in Enterococcus bacteria. It forms a six beta-strand barrel with three accompanying alpha helices and is probably a homo-dimer in the cell [1]. PrgU probably acts as a RNA-binding regulator that mitigates toxicity accompanying overproduction of PrgB-like adhesins, which are involved in conjugative transfer [2]. [1]. 17302827. Specificity determinants of conjugative DNA processing in the Enterococcus faecalis plasmid pCF10 and the Lactococcus lactis plasmid pRS01. Chen Y, Staddon JH, Dunny GM;. Mol Microbiol. 2007;63:1549-1564. [2]. 27785854. PrgU: a suppressor of sex pheromone toxicity in Enterococcus faecalis. Bhatty M, Camacho MI, Gonzalez-Rivera C, Frank KL, Dale JL, Manias DA, Dunny GM, Christie PJ;. Mol Microbiol. 2017;103:398-412. (from Pfam) NF021682.5 PF10179.14 NDNF 27.3 27.3 127 domain Y Y N fibronectin domain-containing protein 20969804,24706764 1350 Enterococcus genus 50 EBI-EMBL Neuron-derived neurotrophic factor, first Fn(III) domain Neuron-derived neurotrophic factor, first Fn(III) domain This domain is found towards the N-terminal of Neuron-derived neurotrophic factor (NDNF) which contains the first fibronectin type III domain and one of the predicted N-linked glycosylation sites [1,2]. NDNF is a glycosylated and disulfide-bonded secreted protein expressed in brain and spinal cord that promotes migration and neurite growth. It also promotes endothelial cell survival, vessel formation and plays an important role in the process of revascularization. [1]. 20969804. Spatio-temporal expression of a novel neuron-derived neurotrophic factor (NDNF) in mouse brains during development. Kuang XL, Zhao XM, Xu HF, Shi YY, Deng JB, Sun GT;. BMC Neurosci. 2010;11:137. [2]. 24706764. Neuron-derived neurotrophic factor functions as a novel modulator that enhances endothelial cell function and revascularization processes. Ohashi K, Enomoto T, Joki Y, Shibata R, Ogura Y, Kataoka Y, Shimizu Y, Kambara T, Uemura Y, Yuasa D, Matsuo K, Hayakawa S, Hiramatsu-Ito M, Murohara T, Ouchi N;. J Biol Chem. 2014;289:14132-14144. (from Pfam) NF022911.5 PF11472.13 DUF3206 23.7 23.7 128 PfamAutoEq Y Y N DUF3206 domain-containing protein 1350 Enterococcus genus 91 EBI-EMBL Protein of unknown function (DUF3206) Protein of unknown function (DUF3206) This bacterial family of proteins has no known function. (from Pfam) NF027393.5 PF16067.10 DUF4809 27 27 130 subfamily Y Y N DUF4809 family protein 1350 Enterococcus genus 573 EBI-EMBL Domain of unknown function (DUF4809) DUF4809 family protein This family of proteins is found in bacteria. Proteins in this family are typically between 120 and 137 amino acids in length. There is a conserved GGCNAC sequence motif. (from Pfam) NF027632.5 PF16308.10 DUF4950 25 25 191 domain Y Y N DUF4950 domain-containing protein 1350 Enterococcus genus 219 EBI-EMBL Domain of unknown function (DUF4950) Domain of unknown function (DUF4950) This family consists of several uncharacterized proteins around 250 residues in length and is mainly found in various Enterococcus faecalis species. The function of this family is unknown. (from Pfam) NF033090.1 HK_VanS_B 920 920 447 exception Y Y Y vancomycin resistance histidine kinase VanS-B vanS-B GO:0000155,GO:0007165,GO:0016020 1350 Enterococcus genus 44 NCBIFAM VanB-type vancomycin resistance histidine kinase VanS vancomycin resistance histidine kinase VanS-B NF033122.1 vanW-B 610 610 275 exception Y Y Y glycopeptide resistance accessory protein VanW-B vanW-B 1350 Enterococcus genus 32 NCBIFAM glycopeptide resistance accessory protein VanW-B glycopeptide resistance accessory protein VanW-B VanW family proteins are found in vancomycin resistance systems of types VanB, VanG, and VanPt. The function is unknown. It is not certain that all members of the minimal family that includes VanW-B, VanW-G, and VanW-Pt are involved in resistance to glycopeptide antibiotics, so separate HMMs are created for each. This model identifies VanW-B proteins. NF033385.1 enterocin_LsbB 33 33 35 subfamily Y Y N LsbB family leaderless bacteriocin 24993828 1350 Enterococcus genus 24 NCBIFAM LsbB family leaderless bacteriocin LsbB family leaderless bacteriocin Members of this family are leaderless peptide components of bacteriocins with a conserved motif KXXXGXXPWE. NF033875.1 Agg_substance 1500 1500 1306 equivalog Y Y N LPXTG-anchored aggregation substance 1350 Enterococcus genus 1303 NCBIFAM LPXTG-anchored aggregation substance LPXTG-anchored aggregation substance Aggregation substances, as described in Enterococcus, are LPXTG-anchored large surface proteins that contribute to virulence. Several closely related paralogs may be found in a single strain. NF033898.1 QWxxN_dom 55 35 127 domain Y Y N QWxxN domain 1350 Enterococcus genus 342 NCBIFAM QWxxN domain QWxxN domain-containing protein The QWxxN domain is about 125 amino acids long, and appears typically as the conserved core region in up to 9 tandem repeats, each about 200 amino acids long. Proteins with this domain are known so far only in the genus Enterococcus, and may reach over 3000 amino acids in length. NF036645.5 PF17436.7 DUF5415 25 25 66 domain Y Y N DUF5415 family protein 1350 Enterococcus genus 126 EBI-EMBL Family of unknown function (DUF5415) DUF5415 family protein This is a family of unknown function found in Enterococcus. (from Pfam) NF037790.5 PF18333.6 ssDNA_DBD 25 25 106 domain Y N N Non-canonical single-stranded DNA-binding domain 22106294 1350 Enterococcus genus 652 EBI-EMBL Non-canonical single-stranded DNA-binding domain Non-canonical single-stranded DNA-binding domain This domain is found in ThermoDBP, a non-canonical single-stranded DNA-binding protein in Thermoproteales. Single-stranded DNA-binding proteins are needed for DNA metabolism, sequestering and protecting transiently formed ssDNA during DNA replication and recombination, detecting DNA damage and recruiting repair proteins. The outer edge of the ssDNA-binding cleft, formed by this domain, has a strongly positive electrostatic surface potential because of the conserved basic residues R49, K54, R65, R80, R86, R90, K97, and R112 [1]. [1]. 22106294. Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales. Paytubi S, McMahon SA, Graham S, Liu H, Botting CH, Makarova KS, Koonin EV, Naismith JH, White MF;. Proc Natl Acad Sci U S A. 2012;109:E398-E405. (from Pfam) NF037933.1 EpaQ_fam 100 100 377 subfamily Y Y N EpaQ family protein 30910809 1350 Enterococcus genus 672 NCBIFAM EpaQ family protein EpaQ, as described in the Gram-positive bacterium Enterococcus faecalis, is encoded with the enterococcal polysaccharide antigen (epa) operon. It is distantly related to some O-antigen ligases of Gram-negative bacteria, and may have a similar molecular function. EpaQ contributes to biofilm formation and resistance to certain antibiotics. NF038240.1 fibro_bind_EfbA 1025 1025 567 exception Y Y N fibronectin-binding protein EfbA efbA 22782954,26351286 1350 Enterococcus genus 750 NCBIFAM fibronectin-binding protein EfbA The virulence factor EfbA (enterococcal fibronectin-binding protein A), like its close homolog PavA from Streptococcus pneumoniae, is an anchorless adhesin, meaning it has no site for processing by sortase and covalent attachment to the cell surface, but still contributes to adhesion that contributes to pathogenesis. NF040768.1 Epx 400 400 297 equivalog Y Y N enterococcus pore-forming toxin Epx epx GO:0046930 35259335 1350 Enterococcus genus 12 NCBIFAM enterococcus pore-forming toxin Epx NF040779.1 Sec_lyase_SclA 525 525 378 exception Y Y N selenocysteine lyase SclA sclA 4.4.1.16 GO:0001887,GO:0009000 33444662 1350 Enterococcus genus 230 NCBIFAM selenocysteine lyase SclA In bacteria, selenocysteine lyase activity (EC 4.4.1.16) usually is seen as a secondary activity of a cysteine desulfurase (EC 2.8.1.7). However, SclA, as studied in Enterococcus faecalis, acts primary on selenocysteine, binding cysteine just as well but acting on cysteine with much lower catalytic efficiency. NF041439.1 TraE_Enteroc 100 100 99 subfamily Y Y N type IV conjugative transfer system protein TraE traE 1315730 1350 Enterococcus genus 232 NCBIFAM type IV conjugative transfer system protein TraE NF041508.1 BacL2 200 200 202 equivalog Y Y N BacL2 family protein bacL2 18203826 1350 Enterococcus genus 84 NCBIFAM BacL2 family protein NF046671.1 PF22459.1 PrgX_C_TPR 27 27 190 domain Y N N Pheromone cCF10 receptor, C-terminal TPR region 16339309,17038121 1350 Enterococcus genus 124 EBI-EMBL Pheromone cCF10 receptor, C-terminal TPR region Pheromone cCF10 receptor, C-terminal TPR region This entry represents the C-terminal tetratrico peptide repeat region (TPR) of the pheromone cCF10 receptor from Enterococcus faecalis (PrgX), which serves as a molecular switch controlling expression of conjugation and virulence genes encoded by the conjugative plasmid pCF10. This region includes two domains: a large central dimerisation (and pheromone-binding) domain, and a C-terminal regulatory domain that is important for structural integrity [1,2]. Paper describing PDB structure 2aw6. [1]. 16339309. Structure of peptide sex pheromone receptor PrgX and PrgX/pheromone complexes and regulation of conjugation in Enterococcus faecalis. Shi K, Brown CK, Gu ZY, Kozlowicz BK, Dunny GM, Ohlendorf DH, Earhart CA;. Proc Natl Acad Sci U S A. 2005;102:18596-18601. Paper describing PDB structure 2grm. [2]. 17038121. Molecular basis for control of conjugation by bacterial pheromone and inhibitor peptides. Kozlowicz BK, Shi K, Gu ZY, Ohlendorf DH, Earhart CA, Dunny GM;. Mol Microbiol. 2006;62:958-969. (from Pfam) NF046731.1 PF22312.1 SgrA_ig-like 27 27 110 domain Y N N SgrA, immunoglobulin-like 27334767 1350 Enterococcus genus 317 EBI-EMBL SgrA, immunoglobulin-like SgrA, immunoglobulin-like This entry represents a Immunoglobulin-like domain present in the Serine-glutamate repeat protein A (SgrA), also known as LPXTG family cell surface protein Fms2 [1]. Paper describing PDB structure 5fce. [1]. 27334767. The crystal structure of the ligand-binding region of serine-glutamate repeat containing protein A (SgrA) of Enterococcus faecium reveals a new protein fold: functional characterization and insights into its adhesion function. Nagarajan R, Hendrickx AP, Ponnuraj K;. FEBS J. 2016;283:3039-3055. (from Pfam) NF046883.1 PF22652.1 DUF7006 27 27 112 subfamily Y Y N DUF7006 family protein 1350 Enterococcus genus 986 EBI-EMBL Family of unknown function (DUF7006) DUF7006 family protein Proteins in this family are found in Firmicutes. They are approximately 120 amino acids in length and are predicted to adopt an alpha helical structure. Members of this family contain two highly conserved acid residues aspartate and glutamate. (from Pfam) NF047405.1 SensHisKinSapS 550 550 341 equivalog Y Y N two-component system sensor histidine kinase SapS sapS GO:0000155,GO:0003677,GO:0007165,GO:0016310,GO:0016772 24342648,38646792 1350 Enterococcus genus 406 NCBIFAM two-component system sensor histidine kinase SapS TIGR02709.1 TIGR02709 branched_ptb 475.15 475.15 271 equivalog Y Y N branched-chain phosphotransacylase ptb 1350 Enterococcus genus 130 JCVI branched-chain phosphotransacylase branched-chain phosphotransacylase This model distinguishes branched-chain phosphotransacylases like that of Enterococcus faecalis from closely related subfamilies of phosphate butyryltransferase (EC 2.3.1.19) (TIGR02706) and phosphate acetyltransferase (EC 2.3.1.8) (TIGR00651). Members of this family and of TIGR02706 show considerable crossreactivity, and the occurrence of a member of either family near an apparent leucine dehydrogenase will suggest activity on branched chain-acyl-CoA compounds. NF000478.2 linco_LnuE 350 350 160 exception Y Y Y lincosamide nucleotidyltransferase Lnu(E) lnu(E) 1351 Enterococcus faecalis species 1 NCBIFAM lincosamide nucleotidyltransferase Lnu(E) lincosamide nucleotidyltransferase Lnu(E) NF033473.1 trim_sens_DfrEf 350 350 164 exception Y Y N trimethoprim-sensitive dihydrofolate reductase dfr 1.5.1.3 GO:0004146 9869579 1351 Enterococcus faecalis species 65 NCBIFAM trimethoprim-resistant dihydrofolate reductase DfrE trimethoprim-sensitive dihydrofolate reductase This dihydrofolate reductase was originally described as the intrinsic dihydrofolate reductase of Enterococcus faecalis, sensitive to trimethoprim and incapable of conferring resistance to that antibiotic. Although the protein was referred to as DfrE by Coque, et al. (1999, PMID:9869579), to contrast it with the much rarer, resistance-conferring enzyme DfrF, we do not use the term DfrE, as a name in that series suggests a TMP-resistant form. Instead, we reserve the name DfrE for the trimethoprim-resistant enzyme WP_012655890.1 and close homologs, as described in PMID:34374564. NF033893.1 pheromone_ipd 33 33 21 equivalog Y Y N peptide pheromone inhibitor Ipd ipd 7559344 1351 Enterococcus faecalis species 3 NCBIFAM peptide pheromone inhibitor Ipd peptide pheromone inhibitor Ipd The pheromone inhibitor iPD1, in mature form, is the last 8 amino acids of the product of the ipd gene. It was described in conjugative plasmids of Enterococcus faecalis. NF039878.4 PF19159.5 DUF5841 25 25 48 domain Y Y N EntF family bacteriocin induction factor 1352 Enterococcus faecium species 66 EBI-EMBL Family of unknown function (DUF5841) EntF family bacteriocin induction factor See family NF033383 for more information. NF003397.0 PRK04612 PRK04612.1 735 735 408 equivalog Y Y N acetylornithine transaminase 2.6.1.11 135614 Lysobacterales order 938 NCBI Protein Cluster (PRK) acetylornithine transaminase protein acetylornithine transaminase Catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine in the arginine biosynthetic pathway NF006443.0 PRK08760 PRK08760.1 741 741 476 equivalog Y Y N replicative DNA helicase 3.6.4.12 135614 Lysobacterales order 764 NCBI Protein Cluster (PRK) replicative DNA helicase replicative DNA helicase Unwinds double stranded DNA NF006455.0 PRK08813 PRK08813.1 489 489 374 equivalog Y Y N threonine dehydratase 4.3.1.19 135614 Lysobacterales order 890 NCBI Protein Cluster (PRK) threonine dehydratase threonine dehydratase NF006457.0 PRK08818 PRK08818.1 411 411 373 equivalog Y Y N prephenate dehydrogenase 135614 Lysobacterales order 1093 NCBI Protein Cluster (PRK) prephenate dehydrogenase prephenate dehydrogenase NF008910.0 PRK12274 PRK12274.1 372 372 219 equivalog Y N N serine/threonine protein kinase 135614 Lysobacterales order 772 NCBI Protein Cluster (PRK) serine/threonine protein kinase serine/threonine protein kinase NF009637.0 PRK13159 PRK13159.1 247 247 156 equivalog Y Y N cytochrome c maturation protein CcmE ccmE 135614 Lysobacterales order 422 NCBI Protein Cluster (PRK) cytochrome c-type biogenesis protein CcmE cytochrome c maturation protein CcmE CycJ; periplasmic heme chaperone that binds heme transiently via a histidine residue and delivers it to newly synthesized and exported c-type cytochromes; requires the ATP hydrolysis activity of the CcmA protein in order to transfer the heme to the apocytochrome; part of the cytochrome c maturation system; periplasmic protein anchored to the inner membrane NF011018.0 PRK14446 PRK14446.1 101 101 88 equivalog Y Y N acylphosphatase 135614 Lysobacterales order 441 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF047335.1 T3SS_XAC0095 34 34 62 domain Y Y N XAC0095 family protein 15342589 135614 Lysobacterales order 1589 NCBIFAM XAC0095 domain XAC0095 from the plant pathogen Xanthomonas axonopodis pv. citri, a founding member of this protein family, was shown to interact with HrpG, a response regulator transcription factor responsible for type III secretion system (T3SS) hrp gene expression. Homologs of XAC0095 include both proteins of similar lengths and substantially longer proteins that contain additional domains. NF037299.5 PF18252.6 Cu_bind_CorA 27 27 184 PfamEq Y Y N copper(I)-binding protein CorA corA 18348978,24498370 135618 Methylococcales order 43 EBI-EMBL Copper(I)-binding protein CorA-like copper(I)-binding protein CorA This domain is found in CorA present in Methylomicrobium album. CorA is a copper repressible surface associated copper(I)-binding protein. CorA can bind one copper ion per protein molecule. The overall fold of CorA is similar to M. capsulatus protein MopE [2], including the unique copper(I)-binding site and most of the secondary structure elements [1]. [1]. 24498370. CorA is a copper repressible surface-associated copper(I)-binding protein produced in Methylomicrobium album BG8. Johnson KA, Ve T, Larsen O, Pedersen RB, Lillehaug JR, Jensen HB, Helland R, Karlsen OA;. PLoS One. 2014;9:e87750. [2]. 18348978. An oxidized tryptophan facilitates copper binding in Methylococcus capsulatus-secreted protein MopE. Helland R, Fjellbirkeland A, Karlsen OA, Ve T, Lillehaug JR, Jensen HB;. J Biol Chem. 2008;283:13897-13904. (from Pfam) NF041628.1 NaLiK_antip_UmpB 500 500 252 equivalog Y Y N Na,Li,K/H(+) antiporter subunit UmpB umpB GO:0006813,GO:0006814,GO:0015297 28652569 135619 Oceanospirillales order 48 NCBIFAM Na,Li,K/H(+) antiporter subunit UmpB NF000438.2 blaPOM 610 610 286 exception Y Y Y POM family subclass B3 metallo-beta-lactamase blaPOM 3.5.2.6 GO:0008800 135621 Pseudomonadaceae family 14 NCBIFAM POM family subclass B3 metallo-beta-lactamase POM family subclass B3 metallo-beta-lactamase NF000445.2 blaDIM 560 560 251 exception Y Y Y DIM family subclass B1 metallo-beta-lactamase blaDIM 3.5.2.6 GO:0008800 135621 Pseudomonadaceae family 2 NCBIFAM DIM family subclass B1 metallo-beta-lactamase DIM family subclass B1 metallo-beta-lactamase NF001247.0 PRK00218 PRK00218.1-3 334 334 207 equivalog Y Y N high frequency lysogenization protein HflD hflD 135621 Pseudomonadaceae family 1371 NCBI Protein Cluster (PRK) putative lysogenization regulator high frequency lysogenization protein HflD NF001421.0 PRK00295 PRK00295.1 95 95 68 equivalog Y N N hypothetical protein 135621 Pseudomonadaceae family 1179 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF001681.0 PRK00442 PRK00442.1 102 102 92 equivalog Y Y N twin-arginine translocase TatA/TatE family subunit 135621 Pseudomonadaceae family 1000 NCBI Protein Cluster (PRK) twin arginine translocase protein A twin-arginine translocase TatA/TatE family subunit NF004318.0 PRK05714 PRK05714.1 653 653 407 equivalog Y Y N 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase GO:0006744,GO:0016709,GO:0071949 135621 Pseudomonadaceae family 3085 NCBI Protein Cluster (PRK) 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase Catalyzes the formation of 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinol from 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol NF006982.0 PRK09450 PRK09450.2-2 1547 1547 951 equivalog Y Y N class I adenylate cyclase 4.6.1.1 135621 Pseudomonadaceae family 1502 NCBI Protein Cluster (PRK) adenylate cyclase class I adenylate cyclase NF007222.0 PRK09640 PRK09640.1 194 194 188 equivalog Y Y N RNA polymerase sigma factor SigX sigX 10438740 135621 Pseudomonadaceae family 914 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigX RNA polymerase sigma factor SigX Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription NF021129.5 PF09589.15 HrpA_pilin 25 25 96 domain Y N N HrpA pilus formation protein GO:0005615 11953310 135621 Pseudomonadaceae family 189 EBI-EMBL HrpA pilus formation protein HrpA pilus formation protein HrpA is an essential component of the type III secretion system (TTSS) which pathogens use to inject virulence factors directly into their host cells, and to cause disease. The TTSS has an Hrp pilus appendage for channelling effector proteins through the plant cell wall and this pilus elongates by the addition of HrpA pilin subunits at the distal end [1]. [1]. 11953310. The Hrp pilus of Pseudomonas syringae elongates from its tip and acts as a conduit for translocation of the effector protein HrpZ. Li CM, Brown I, Mansfield J, Stevens C, Boureau T, Romantschuk M, Taira S;. EMBO J. 2002;21:1909-1915. (from Pfam) NF023446.5 PF12021.13 DUF3509 25 25 87 domain Y Y N DUF3509 domain-containing protein 135621 Pseudomonadaceae family 3914 EBI-EMBL Protein of unknown function (DUF3509) Protein of unknown function (DUF3509) This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 92 to 110 amino acids in length. This protein has two completely conserved residues (G and R) that may be functionally important. (from Pfam) NF028013.5 PF16703.10 DUF5064 27 27 117 subfamily Y Y N DUF5064 family protein 135621 Pseudomonadaceae family 2099 EBI-EMBL Domain of unknown function (DUF5064) DUF5064 family protein This is found in Pseudomonas species. Several members are annotated as being acetyl-CoA carboxylase alpha subunit, but his could not be confirmed. (from Pfam) NF036935.5 PF17525.7 DUF5447 25 25 106 PfamEq Y Y N lysogeny maintenance protein PflM pflM 38687034 135621 Pseudomonadaceae family 1899 EBI-EMBL Family of unknown function (DUF5447) Pf prophage lysogeny maintenance protein PflM PflM is identified as a lysogeny maintenance protein in Pf prophages such as Pf1 in Pseudomonas aeruginosa PAO1. NF037295.5 PF18226.6 QslA 25 25 71 subfamily Y Y N LasR-specific antiactivator QslA 24319092 135621 Pseudomonadaceae family 930 EBI-EMBL LasR-specific antiactivator QslA LasR-specific antiactivator QslA This domain is found in QslA from Pseudomonas aeruginosa. QslA is an antiactivator which binds to the transcription factor LasR, disrupting its dimerization and preventing LasR from binding to target DNA. QslA forms a dimer that interacts with the ligand-binding domain in LasR [1]. [1]. 24319092. QsIA disrupts LasR dimerization in antiactivation of bacterial quorum sensing. Fan H, Dong Y, Wu D, Bowler MW, Zhang L, Song H;. Proc Natl Acad Sci U S A. 2013;110:20765-20770. (from Pfam) NF038194.1 AlgK_TPR_lipo 700 700 448 equivalog Y Y N alginate biosynthesis TPR repeat lipoprotein AlgK algK 17565185,20159471,23503314,25968647 135621 Pseudomonadaceae family 2705 NCBIFAM alginate biosynthesis TPR repeat lipoprotein AlgK NF038359.1 blaPRC 820 820 379 exception Y Y Y PRC family class C beta-lactamase blaPRC 3.5.2.6 GO:0008800 34975778 135621 Pseudomonadaceae family 23 NCBIFAM PRC family class C beta-lactamase PRC (PDC-Related class C beta-lactamase) is found in some members of the genus Pseudomonas, apparently as an AmpC-like chromosomally encoded class C beta-lactamase. Such enzymes typical act as cephalosporinases. PRC is more closely to PDC than to any other previously named beta-lactamase family, at about 73 percent identity. NF040644.1 blaPAM 615 615 287 exception Y Y Y PAM family subclass B3 metallo-beta-lactamase blaPAM 3.5.2.6 GO:0008800 24356301,33577996 135621 Pseudomonadaceae family 12 NCBIFAM PAM family subclass B3 metallo-beta-lactamase Expression of PAM-1 (Pseudomonas alcaligenes metallo-beta-lactamase 1) in P. aeruginosa PAO1 or in E. coli reduced sensitivity to ceftazidime, meropenem, imipenem, and doripenem (the latter two only in P. aeruginosa), while having no effect on aztreonam resistance. NF040858.1 condensinMksE 400 400 232 equivalog Y Y N Mks condensin complex protein MksE mksE 35072315 135621 Pseudomonadaceae family 1586 NCBIFAM Mks condensin complex protein MksE NF041250.1 VI_TagQ 300 300 301 equivalog Y Y N type VI secretion system-associated lipoprotein TagQ tagQ 22765374 135621 Pseudomonadaceae family 853 NCBIFAM type VI secretion system-associated lipoprotein TagQ NF041604.1 CSP_NTE_dom 45 45 112 subfamily_domain Y Y N cold shock domain-containing protein membrane protein 135621 Pseudomonadaceae family 1435 NCBIFAM cold shock protein N-terminal extension domain Members of this family have a C-terminal cold shock domain, but also a longer, hydrophobic N-terminal domain. Members are found primarily in the genus Pseudomonas, including in P. aeruginosa. NF041831.1 NO_HK_NahK 1500 1500 854 exception Y Y N hybrid sensor histidine kinase/response regulator NahK/ErcS' nahK 28238256 135621 Pseudomonadaceae family 1591 NCBIFAM hybrid sensor histidine kinase/response regulator NahK/ErcS' NahK (also called ErcS'), including PA1976 from Pseudomonas aeruginosa, is a cytosolic hybrid histidine kinase/response regulator protein with multiple PAS sensor domains but no apparent transmembrane or DNA-binding domain. It is regularly found encoded next to the nitric oxide-sensing protein NosP. NahK is a paralog of ErcS (PA1992). NF041860.1 silencer_MvaT 180 180 125 exception Y Y N histone-like nucleoid-structuring protein MvaT mvaT GO:0003677,GO:0071824 22798496,26068099,30782629 135621 Pseudomonadaceae family 828 NCBIFAM histone-like nucleoid-structuring protein MvaT Paralogs MvaT and MvaU from Pseudomonas aeruginosa previously were viewed (or at least annotated) as transcription factors based on changes they mediated in the expression of various genes. However, like other histone-like nucleoid structuring proteins, MvaT, MvaU, and their homologs are considered to be largely non-specific in their DNA-binding. A preference for binding AT-rich regions makes MvaT, like its paralog MvaU, effective as silencer of xenogeneic DNA, including phage DNA. Members of this family are MvaT itself. NF041714.1 arsenate_red_ArrA 1600 1600 848 equivalog Y Y N arsenate respiratory reductase molybdopterin-containing subunit ArrA arrA 1.20.99.1 GO:0016491,GO:0043546,GO:0051539 17951391,30104376 135622 Alteromonadales order 52 NCBIFAM arsenate respiratory reductase molybdopterin-containing subunit ArrA NF041715.1 arsenate_red_ArrB 450 450 233 equivalog Y Y N arsenate respiratory reductase iron-sulfur subunit ArrB arrB GO:0046872,GO:0051539 17951391,30104376 135622 Alteromonadales order 43 NCBIFAM arsenate respiratory reductase iron-sulfur subunit ArrB NF007058.0 PRK09505 PRK09505.2-3 897 897 742 equivalog Y Y N alpha-amylase 3.2.1.1 135624 Aeromonadales order 895 NCBI Protein Cluster (PRK) alpha-amylase alpha-amylase NF001131.0 PRK00139 PRK00139.2-5 1000 1000 483 equivalog Y Y N UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase 6.3.2.13 1357 Lactococcus genus 94 NCBI Protein Cluster (PRK) UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase NF003634.0 PRK05270 PRK05270.2-3 1021 1021 493 equivalog Y Y N UDP-glucose--hexose-1-phosphate uridylyltransferase 2.7.7.12 1357 Lactococcus genus 112 NCBI Protein Cluster (PRK) galactose-1-phosphate uridylyltransferase UDP-glucose--hexose-1-phosphate uridylyltransferase NF006362.0 PRK08581 PRK08581.1-4 620 620 541 equivalog Y Y N amidase domain-containing protein 1357 Lactococcus genus 250 NCBI Protein Cluster (PRK) N-acetylmuramoyl-L-alanine amidase amidase domain-containing protein NF011130.0 PRK14553 PRK14553.2-3 189 189 111 equivalog Y Y N ribosomal-processing cysteine protease Prp 1357 Lactococcus genus 34 NCBI Protein Cluster (PRK) hypothetical protein ribosomal-processing cysteine protease Prp NF011134.0 PRK14553 PRK14553.3-3 185 185 95 equivalog Y Y N ribosomal-processing cysteine protease Prp 1357 Lactococcus genus 71 NCBI Protein Cluster (PRK) hypothetical protein ribosomal-processing cysteine protease Prp NF018030.5 PF06275.16 DUF1031 25 25 80 domain Y Y N DUF1031 family protein 1357 Lactococcus genus 336 EBI-EMBL Protein of unknown function (DUF1031) DUF1031 family protein This family consists of several Lactococcus lactis bacteriophage and Lactococcus lactis proteins of unknown function. (from Pfam) NF018614.5 PF06926.16 Rep_Org_C 27 27 95 PfamEq Y Y N phage replisome organiser protein 11157223 1357 Lactococcus genus 246 EBI-EMBL Putative replisome organiser protein C-terminus phage replisome organiser protein This family represents the C-terminus (approximately 100 residues) of a putative replisome organiser protein in Lactococcus bacteriophages [1]. [1]. 11157223. Improvement and optimization of two engineered phage resistance mechanisms in Lactococcus lactis. McGrath S, Fitzgerald GF, van Sinderen D;. Appl Environ Microbiol 2001;67:608-616. (from Pfam) NF018764.5 PF07097.16 DUF1359 25 25 104 domain Y Y N DUF1359 domain-containing protein 1357 Lactococcus genus 104 EBI-EMBL Protein of unknown function (DUF1359) Protein of unknown function (DUF1359) This family consists of several hypothetical bacterial and phage proteins of around 100 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this species. The function of this family is unknown. (from Pfam) NF018850.5 PF07193.16 DUF1408 27 27 71 domain Y Y N DUF1408 domain-containing protein 1357 Lactococcus genus 129 EBI-EMBL Protein of unknown function (DUF1408) Protein of unknown function (DUF1408) This family consists of several hypothetical Lactococcus lactis and related phage proteins of around 75 residues in length. The function of this family is unknown. (from Pfam) NF019030.5 PF07384.16 DUF1497 27 27 59 domain Y Y N DUF1497 domain-containing protein 1357 Lactococcus genus 114 EBI-EMBL Protein of unknown function (DUF1497) Protein of unknown function (DUF1497) This family consists of several phage and bacterial proteins of around 59 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this organism. The function of this family is unknown. (from Pfam) NF042958.1 phage_res_AbiGII 275 275 396 equivalog Y Y N abortive phage resistance protein AbiGII abiGII 8795193,9872803 1357 Lactococcus genus 10 NCBIFAM abortive phage resistance protein AbiGII NF044804.2 PF21470.2 BppU-like_C 27 27 59 domain Y N N Minor structural protein 5-like, C-terminal domain 26814179 1357 Lactococcus genus 124 EBI-EMBL Minor structural protein 5-like, C-terminal domain Minor structural protein 5-like, C-terminal domain This domain is found at the C-terminal end of Minor structural protein 5 from Lactococcus phage Tuc2009 (BppU) and similar proteins from tailed bacteriophages and prophages found mostly in firmicutes. BppU is a viral baseplate component. This domain folds into a structure formed mostly by beta-strands [1]. Paper describing PDB structure 5e7t. [1]. 26814179. The Atomic Structure of the Phage Tuc2009 Baseplate Tripod Suggests that Host Recognition Involves Two Different Carbohydrate Binding Modules. Legrand P, Collins B, Blangy S, Murphy J, Spinelli S, Gutierrez C, Richet N, Kellenberger C, Desmyter A, Mahony J, van Sinderen D, Cambillau C;. mBio. 2016;7:e01781-e01715. (from Pfam) NF000945.0 PRK00094 PRK00094.2-3 491 491 352 equivalog Y Y N NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 1.1.1.94 136 Spirochaetales order 154 NCBI Protein Cluster (PRK) NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NF002424.0 PRK01558 PRK01558.1 241 241 203 equivalog Y Y N V-type ATP synthase subunit E 7.1.2.2 136 Spirochaetales order 144 NCBI Protein Cluster (PRK) V-type ATP synthase subunit E V-type ATP synthase subunit E NF004429.0 PRK05771 PRK05771.2-2 799 799 608 equivalog Y Y N V-type ATP synthase subunit I 7.1.2.2 136 Spirochaetales order 151 NCBI Protein Cluster (PRK) V-type ATP synthase subunit I V-type ATP synthase subunit I NF005173.0 PRK06647 PRK06647.1 623 623 568 equivalog Y N N DNA polymerase III subunits gamma and tau 2.7.7.7 136 Spirochaetales order 370 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunits gamma and tau NF005175.0 PRK06654 PRK06654.1 218 218 181 equivalog Y N N flagellar basal body-associated protein FliL 136 Spirochaetales order 76 NCBI Protein Cluster (PRK) flagellar basal body-associated protein FliL flagellar basal body-associated protein FliL NF009345.0 PRK12705 PRK12705.1-2 904 904 509 equivalog Y N N hypothetical protein 136 Spirochaetales order 87 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF011089.0 PRK14512 PRK14512.1 251 251 200 equivalog Y N N ATP-dependent Clp protease proteolytic subunit 136 Spirochaetales order 238 NCBI Protein Cluster (PRK) ATP-dependent Clp protease proteolytic subunit ATP-dependent Clp protease proteolytic subunit NF017444.5 PF05628.17 Borrelia_P13 25 25 138 subfamily Y Y N P13 family porin 11292755 136 Spirochaetales order 310 EBI-EMBL Borrelia membrane protein P13 P13 family porin This family consists of P13 proteins from Borrelia species. P13 is a 13kDa integral membrane protein which is post-translationally processed at both ends and modified by an unknown mechanism [1]. [1]. 11292755. P13, an integral membrane protein of Borrelia burgdorferi, is C-terminally processed and contains surface-exposed domains. Noppa L, Ostberg Y, Lavrinovicha M, Bergstrom S;. Infect Immun 2001;69:3323-3334. (from Pfam) NF033751.1 pallilysin_like 150 150 385 subfamily Y Y N pallilysin-related adhesin 26283341 136 Spirochaetales order 371 NCBIFAM pallilysin-related adhesin pallilysin-related adhesin In contrast to pallilysin itself (a bifunctional adhesin and protease), members of the pallilysin-related adhesin family average twice the length, lack the HEXXH motif essential to pallilysin's metalloprotease activity, and are likely to function in virulence only as an adhesin. Typical members of this family include TDE0840 from Treponema denticola and BB0038 from Borrelia burgdorferi, which share less than 20% pairwise amino acid sequence identity. NF041606.1 dguan_cyc_DgcA 370 370 340 equivalog Y Y N diguanylate cyclase DgcA dgcA 2.7.7.65 GO:0052621 33452878 136 Spirochaetales order 136 NCBIFAM diguanylate cyclase DgcA NF042739.3 PF20424.3 PilZN3 27.4 27.4 135 domain Y Y N PilZN3 domain-containing protein 31740493 136 Spirochaetales order 296 EBI-EMBL PilZN3 domain PilZN3 domain This is a noncanonical PilZ domain found in spirochaetes, such as B. burgdorferi BB0733 and Treponema denticola TDE0214 proteins. They have a PilZN3-PilZ domain architecture and affect the motility and virulence of these organisms. Secondary structure predictions suggest that this domain retains the C-terminal alpha-helix of PilZ and three additional alpha helices [1]. [1]. 31740493. Structural Conservation and Diversity of PilZ-Related Domains. Galperin MY, Chou SH;. J Bacteriol. 2020; [Epub ahead of print] (from Pfam) NF047328.1 OMP_TP0733 130 130 202 subfamily Y Y N TP0733 family outer membrane beta-barrel protein 33972353 136 Spirochaetales order 212 NCBIFAM TP0733 family outer membrane beta-barrel protein Members of this family, including founding protein TP0733, are OmpW-like outer membrane beta-barrel proteins from Treponema and other spirochetes. NF047372.1 FlcA_NTERM 28 28 39 equivalog_domain Y Y N periplasmic-type flagellar collar protein FlcA flcA 31743518 136 Spirochaetales order 414 NCBIFAM periplasmic-type flagellar collar protein FlcA, N-terminal domain In spirochetes, flagella are located within the periplasm. FlcA is one of several structural proteins involved in formation of the flagellar collar. Conserved N-terminal domain of about 40 amino acids and C-terminal region domain of about 650 amino acids are separated by a long and variable length stretch of low-complexity sequence. NF000519.2 blaPDC_var 900 900 397 exception Y Y Y PDC variant family class C beta-lactamase blaPDC 3.5.2.6 GO:0008800,GO:0030288 136841 Pseudomonas aeruginosa group species group 13 NCBIFAM blaPDC_var: PDC variant family class C beta-lactamase PDC variant family class C beta-lactamase PDC (Pseudomonas-Derived Cephalosporinase) is a chromosomal AmpC, or class C beta-lactamase. NF047495.1 blaOXA-50-var 600 600 262 exception Y Y Y OXA-50-var family class D beta-lactamase blaOXA 3.5.2.6 15155197 136841 Pseudomonas aeruginosa group species group 9 NCBIFAM OXA-50-var family class D beta-lactamase Members of this family of chromosomal class D beta-lactamase share about 88% identity with OXA-50 of Pseudomonas aeruginosa, and can be found in the closely related species Pseudomonas paraeruginosa. The family is named OXA-50-var to signify its close relationship with but also its difference from the closely related OXA-50 family. NF047534.1 lipo_BTA121_dup 45 30 134 subfamily_domain Y Y N BTA121 domain-containing protein surface lipoprotein 29127407 138 Borrelia genus 546 NCBIFAM lipoprotein BTA121 duplicated domain This HMM describes a domain of about 135 amino acids that appears limited to the genus Borrelia, and that appears from 2 to 14 times in surface lipoproteins such as BTA121 of Borrelia turicatae. NF000089.1 qac_MFS_AB 900 900 514 exception Y Y Y QacA/B family quaternary ammonium compound efflux MFS transporter qac 1385 Bacillales order 130 NCBIFAM QacA/B family quaternary ammonium compound efflux MFS transporter QacA/B family quaternary ammonium compound efflux MFS transporter NF000096.1 stregra_B_VgbB 600 600 295 exception Y Y Y streptogramin B lyase Vgb(B) vgb(B) 1385 Bacillales order 2 NCBIFAM streptogramin B lyase Vgb(B) streptogramin B lyase Vgb(B) NF000097.1 stregram_VatC 425 425 212 exception Y Y Y streptogramin A O-acetyltransferase Vat(C) vat(C) 1385 Bacillales order 2 NCBIFAM streptogramin A O-acetyltransferase Vat(C) streptogramin A O-acetyltransferase Vat(C) NF000145.1 vanZ-F 375 375 206 exception Y Y Y glycopeptide resistance protein VanZ-F vanZ-F 1385 Bacillales order 16 NCBIFAM glycopeptide resistance protein VanZ-F glycopeptide resistance protein VanZ-F Members of this family are the glycopeptide resistance protein VanZ of VanF-type vancomycin resistance systems. NF000256.1 MsrSA 1100 1100 488 exception Y Y Y ABC-F type ribosomal protection protein Msr(A) msr(A) 1385 Bacillales order 110 NCBIFAM macrolide efflux ABC transporter Msr(A) ABC-F type ribosomal protection protein Msr(A) NF000411.1 Erm45 525 525 245 exception Y Y Y 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(45) erm(45) 1385 Bacillales order 3 NCBIFAM 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(45) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(45) NF000493.1 Fos_BSH 240 240 137 exception Y Y Y FosB/FosD family fosfomycin resistance bacillithiol transferase fosB 23256780 1385 Bacillales order 777 NCBIFAM FosB/FosD family fosfomycin resistance thiol transferase FosB/FosD family fosfomycin resistance bacillithiol transferase NF001682.0 PRK00443 PRK00443.1-1 528 528 262 equivalog Y Y N glucosamine-6-phosphate deaminase 3.5.99.6 1385 Bacillales order 217 NCBI Protein Cluster (PRK) glucosamine-6-phosphate deaminase glucosamine-6-phosphate deaminase NF002466.0 PRK01699 PRK01699.1 101 101 99 equivalog Y Y N flagellar hook-basal body complex protein FliE fliE 1385 Bacillales order 252 NCBI Protein Cluster (PRK) flagellar hook-basal body protein FliE flagellar hook-basal body complex protein FliE Forms a junction between the M-ring and FlgB during flagella biosynthesis NF002843.0 PRK03081 PRK03081.1 84 84 51 equivalog Y Y N small, acid-soluble spore protein K 1385 Bacillales order 565 NCBI Protein Cluster (PRK) acid-soluble spore protein K small, acid-soluble spore protein K NF002902.0 PRK03501 PRK03501.1 219 219 266 equivalog Y Y N NAD kinase GO:0003951,GO:0019674 1385 Bacillales order 2063 NCBI Protein Cluster (PRK) inorganic polyphosphate/ATP-NAD kinase NAD kinase Catalyzes the phosphorylation of NAD to NADP NF003813.0 PRK05406 PRK05406.1-2 392 392 252 equivalog Y Y N 5-oxoprolinase subunit PxpA pxpA 3.5.2.9 GO:0003824 28830929 1385 Bacillales order 2027 NCBI Protein Cluster (PRK) LamB/YcsF family protein 5-oxoprolinase subunit PxpA NF004446.0 PRK05777 PRK05777.2-4 590 590 502 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoN nuoN 1.6.5.9 1385 Bacillales order 2023 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit N NADH-quinone oxidoreductase subunit NuoN NF005093.0 PRK06522 PRK06522.2-4 308 308 304 equivalog Y Y N 2-dehydropantoate 2-reductase 1.1.1.169 GO:0008677,GO:0015940 1385 Bacillales order 2899 NCBI Protein Cluster (PRK) 2-dehydropantoate 2-reductase 2-dehydropantoate 2-reductase NF005156.0 PRK06635 PRK06635.1-5 594 594 411 equivalog Y Y N aspartate kinase 2.7.2.4 GO:0004072 1385 Bacillales order 2868 NCBI Protein Cluster (PRK) aspartate kinase aspartate kinase NF005161.0 PRK06635 PRK06635.2-5 586 586 402 equivalog Y Y N aspartate kinase 2.7.2.4 1385 Bacillales order 1174 NCBI Protein Cluster (PRK) aspartate kinase aspartate kinase NF005194.1 PRK06666 PRK06666.1-5 206 206 327 equivalog Y Y N flagellar motor switch protein FliM fliM GO:0003774,GO:0009425,GO:0071973 29487588 1385 Bacillales order 395 NCBI Protein Cluster (PRK) flagellar motor switch protein FliM flagellar motor switch protein FliM NF005210.0 PRK06683 PRK06683.1 140 140 82 equivalog Y N N hypothetical protein 1385 Bacillales order 123 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005212.0 PRK06690 PRK06690.1 498 498 363 equivalog Y Y N acetyl-CoA C-acyltransferase 1385 Bacillales order 1983 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA C-acyltransferase NF005222.0 PRK06718 PRK06718.1 204 204 203 equivalog Y Y N NAD(P)-binding protein 1385 Bacillales order 1800 NCBI Protein Cluster (PRK) precorrin-2 dehydrogenase NAD(P)-binding protein NF005239.0 PRK06748 PRK06748.1 111 111 84 subfamily Y N N hypothetical protein 1385 Bacillales order 219 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005246.0 PRK06756 PRK06756.1 130 130 148 subfamily Y N N flavodoxin 1385 Bacillales order 2212 NCBI Protein Cluster (PRK) flavodoxin flavodoxin NF005263.0 PRK06767 PRK06767.1 617 617 392 equivalog Y Y N methionine gamma-lyase megL 4.4.1.11 GO:0018826,GO:0019346 1385 Bacillales order 1961 NCBI Protein Cluster (PRK) methionine gamma-lyase methionine gamma-lyase Catalyzes the formation of methanethiol and 2-ocobutanoate from L-methionine NF005275.1 PRK06782 PRK06782.1 681 681 516 equivalog Y Y N flagellar motor switch protein 20003186,29487588 1385 Bacillales order 757 NCBI Protein Cluster (PRK) flagellar motor switch protein flagellar motor switch protein This family includes flagellar motor switch protein FliY from Listeria monocytogenes. NF005276.0 PRK06788 PRK06788.1 98 98 119 equivalog Y N N flagellar motor switch protein 1385 Bacillales order 229 NCBI Protein Cluster (PRK) flagellar motor switch protein flagellar motor switch protein NF005277.0 PRK06789 PRK06789.1 81 81 74 equivalog Y N N flagellar motor switch protein 1385 Bacillales order 78 NCBI Protein Cluster (PRK) flagellar motor switch protein flagellar motor switch protein NF005280.0 PRK06797 PRK06797.1 106 106 135 equivalog Y N N flagellar basal body rod protein FlgB 1385 Bacillales order 422 NCBI Protein Cluster (PRK) flagellar basal body rod protein FlgB flagellar basal body rod protein FlgB NF005281.0 PRK06798 PRK06798.1 375 375 440 equivalog Y Y N flagellar hook-associated protein 2 1385 Bacillales order 925 NCBI Protein Cluster (PRK) flagellar capping protein flagellar hook-associated protein 2 Involved in flagellin assembly NF005283.0 PRK06800 PRK06800.1 192 192 228 equivalog Y N N flagellar assembly protein H 1385 Bacillales order 661 NCBI Protein Cluster (PRK) flagellar assembly protein H flagellar assembly protein H NF005384.0 PRK06928 PRK06928.1 301 301 277 exception Y Y N pyrroline-5-carboxylate reductase ProG proG 1.5.1.2 11418582 1385 Bacillales order 949 NCBI Protein Cluster (PRK) pyrroline-5-carboxylate reductase pyrroline-5-carboxylate reductase ProG Catalyzes the formation of L-proline from pyrroline-5-carboxylate. ProG is one of several isozymes found in Bacillus subtilis. NF005814.0 PRK07680 PRK07680.1 278 278 275 equivalog Y Y N late competence protein ComER comER GO:0004735,GO:0006561 11418582,27446060,28824574 1385 Bacillales order 3035 NCBI Protein Cluster (PRK) late competence protein ComER late competence protein ComER ComER, as found in Bacillus subtilis, resembles pyrroline-5-carboxylate reductase, but in contrast to paralogs ProG, ProH, and ProI, appears not to contribute to proline biosynthesis. NF005819.0 PRK07695 PRK07695.1 251 251 205 equivalog Y Y N thiazole tautomerase TenI tenI 1385 Bacillales order 1594 NCBI Protein Cluster (PRK) transcriptional regulator TenI thiazole tautomerase TenI NF005823.0 PRK07709 PRK07709.1 545 545 285 equivalog Y Y N class II fructose-bisphosphate aldolase 4.1.2.13 GO:0004332,GO:0006096 1385 Bacillales order 702 NCBI Protein Cluster (PRK) fructose-bisphosphate aldolase class II fructose-bisphosphate aldolase Catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate NF005824.0 PRK07710 PRK07710.1 976 976 573 equivalog Y Y N acetolactate synthase large subunit ilvB GO:0003984 1385 Bacillales order 2483 NCBI Protein Cluster (PRK) acetolactate synthase catalytic subunit acetolactate synthase large subunit NF005836.0 PRK07740 PRK07740.1 261 261 244 equivalog Y N N hypothetical protein 1385 Bacillales order 1672 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005980.0 PRK08073 PRK08073.1 291 291 287 equivalog Y Y N flagellar hook-associated protein 3 1385 Bacillales order 548 NCBI Protein Cluster (PRK) flagellar hook-associated protein FlgL flagellar hook-associated protein 3 With FlgK acts as a hook filament junction protein to join the flagellar filament to the hook NF006146.0 PRK08295 PRK08295.1-3 414 414 218 equivalog Y Y N RNA polymerase factor sigma-70 2.7.7.6 1385 Bacillales order 82 NCBI Protein Cluster (PRK) RNA polymerase factor sigma-70 RNA polymerase factor sigma-70 NF006366.0 PRK08589 PRK08589.1 386 386 272 equivalog Y Y N SDR family oxidoreductase 1385 Bacillales order 1369 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006369.0 PRK08594 PRK08594.1 378 378 257 equivalog Y Y N enoyl-ACP reductase FabI fabI 1.3.1.- GO:0004318,GO:0006633 1385 Bacillales order 3281 NCBI Protein Cluster (PRK) enoyl-(acyl carrier protein) reductase enoyl-ACP reductase FabI NF006373.0 PRK08601 PRK08601.1 377 377 510 equivalog Y Y N NADH dehydrogenase subunit 5 1.6.5.9 1385 Bacillales order 2851 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit 5 NADH dehydrogenase subunit 5 NF006376.0 PRK08610 PRK08610.1 527 527 286 equivalog Y Y N class II fructose-bisphosphate aldolase 4.1.2.13 GO:0004332,GO:0006096 10658656 1385 Bacillales order 1883 NCBI Protein Cluster (PRK) fructose-bisphosphate aldolase class II fructose-bisphosphate aldolase Catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate NF006904.0 PRK09398 PRK09398.1 64 64 47 equivalog Y Y N acid-soluble spore protein N 1385 Bacillales order 615 NCBI Protein Cluster (PRK) acid-soluble spore protein N acid-soluble spore protein N Found in the forespore compartment NF006905.0 PRK09399 PRK09399.1 63 63 48 equivalog Y Y N small acid-soluble spore protein P 1385 Bacillales order 628 NCBI Protein Cluster (PRK) acid-soluble spore protein P small acid-soluble spore protein P SASP P; found in forespore compartment NF006931.0 PRK09416 PRK09416.1 112 112 135 equivalog Y Y N PadR family transcriptional regulator 1385 Bacillales order 1192 NCBI Protein Cluster (PRK) lineage-specific thermal regulator protein PadR family transcriptional regulator NF007220.0 PRK09639 PRK09639.1-5 260 260 181 equivalog Y Y N RNA polymerase sigma factor SigX sigX 1385 Bacillales order 974 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigX RNA polymerase sigma factor SigX NF007871.0 PRK10577 PRK10577.2-2 899 899 679 equivalog Y Y N Fe(3+)-hydroxamate ABC transporter permease FhuB fhuB 1385 Bacillales order 254 NCBI Protein Cluster (PRK) iron-hydroxamate transporter permease subunit Fe(3+)-hydroxamate ABC transporter permease FhuB NF009081.0 PRK12416 PRK12416.1 702 702 466 equivalog Y Y N protoporphyrinogen oxidase 1.3.3.4 1385 Bacillales order 1636 NCBI Protein Cluster (PRK) protoporphyrinogen oxidase protoporphyrinogen oxidase NF009107.0 PRK12452 PRK12452.1 787 787 509 equivalog Y Y N cardiolipin synthase 2.7.8.- 1385 Bacillales order 619 NCBI Protein Cluster (PRK) cardiolipin synthetase cardiolipin synthase Catalyzes the transfer of a phosphatidyl group to phosphodidylglycerol to form cardiolipin (diphosphatidylglycerol) NF009195.0 PRK12543 PRK12543.1 197 197 192 subfamily Y N N RNA polymerase sigma factor 1385 Bacillales order 1639 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009236.0 PRK12586 PRK12586.1 156 156 145 equivalog Y Y N Na+/H+ antiporter subunit G 1385 Bacillales order 905 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit G Na+/H+ antiporter subunit G Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF009499.0 PRK12859 PRK12859.1 366 366 258 subfamily Y Y N SDR family oxidoreductase 1385 Bacillales order 1714 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase SDR family oxidoreductase NF009584.0 PRK13024 PRK13024.1-4 1171 1171 759 equivalog Y Y N protein translocase subunit SecDF secDF 21486434 1385 Bacillales order 1566 NCBI Protein Cluster (PRK) bifunctional preprotein translocase subunit SecD/SecF protein translocase subunit SecDF NF009755.0 PRK13261 PRK13261.2-1 223 223 150 equivalog Y Y N urease accessory protein UreE ureE 1385 Bacillales order 1039 NCBI Protein Cluster (PRK) urease accessory protein UreE urease accessory protein UreE NF009839.0 PRK13314 PRK13314.1 115 115 107 equivalog Y Y N heme oxygenase isdG 1.14.14.18 16428411 1385 Bacillales order 638 NCBI Protein Cluster (PRK) heme-degrading monooxygenase IsdG heme oxygenase Iron regulated; catalyzes the release of heme from hemoglobin allowing bacterial pathogens to use the host heme as an iron source NF009924.0 PRK13385 PRK13385.1 342 342 230 subfamily Y Y N 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2.7.7.60 1385 Bacillales order 464 NCBI Protein Cluster (PRK) 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 4-diphosphocytidyl-2C-methyl-D-erythritol synthase; MEP cytidylyltransferase; catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis NF009987.0 PRK13453 PRK13453.1 172 172 173 equivalog Y Y N F0F1 ATP synthase subunit B 1385 Bacillales order 749 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit B F0F1 ATP synthase subunit B Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B is part of the membrane proton channel NF010066.0 PRK13546 PRK13546.1 320 320 264 equivalog Y Y N teichoic acids export ABC transporter ATP-binding subunit TagH tagH GO:0005524,GO:0016020,GO:0140359 7565096 1385 Bacillales order 2681 NCBI Protein Cluster (PRK) teichoic acids export protein ATP-binding subunit teichoic acids export ABC transporter ATP-binding subunit TagH NF010189.0 PRK13668 PRK13668.1 221 221 267 equivalog Y N N hypothetical protein 1385 Bacillales order 4063 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010198.0 PRK13673 PRK13673.1-5 116 116 118 equivalog Y N N hypothetical protein 1385 Bacillales order 359 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010219.0 PRK13678 PRK13678.2-2 147 147 93 equivalog Y N N hypothetical protein 1385 Bacillales order 476 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010241.0 PRK13688 PRK13688.1 194 194 159 equivalog Y Y N N-acetyltransferase GO:0008080 1385 Bacillales order 1901 NCBI Protein Cluster (PRK) hypothetical protein N-acetyltransferase NF010498.0 PRK13917 PRK13917.1 417 417 344 equivalog Y N N plasmid segregation protein ParM 1385 Bacillales order 118 NCBI Protein Cluster (PRK) plasmid segregation protein ParM plasmid segregation protein ParM NF010558.0 PRK13953 PRK13953.1 197 197 128 equivalog Y Y N large conductance mechanosensitive channel protein MscL mscL 1385 Bacillales order 182 NCBI Protein Cluster (PRK) large-conductance mechanosensitive channel large conductance mechanosensitive channel protein MscL Channel that opens in response to pressure or hypoosmotic shock NF010666.0 PRK14063 PRK14063.1 111 111 78 equivalog Y Y N exodeoxyribonuclease VII small subunit 3.1.11.6 1385 Bacillales order 868 NCBI Protein Cluster (PRK) exodeoxyribonuclease VII small subunit exodeoxyribonuclease VII small subunit Catalyzes the bidirectional exonucleolytic cleavage of DNA NF010723.0 PRK14125 PRK14125.1 105 105 105 equivalog Y Y N cell division suppressor protein YneA yneA 1385 Bacillales order 384 NCBI Protein Cluster (PRK) cell division suppressor protein YneA cell division suppressor protein YneA NF010801.0 PRK14205 PRK14205.1 119 119 118 equivalog Y Y N fluoride efflux transporter CrcB crcB 1385 Bacillales order 1070 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter CrcB NF011327.0 PRK14741 PRK14741.1 55 55 26 equivalog Y Y N stage V sporulation protein SpoVM spoVM 1385 Bacillales order 478 NCBI Protein Cluster (PRK) stage V sporulation protein M stage V sporulation protein SpoVM NF011543.0 PRK14975 PRK14975.2-3 1139 1139 853 equivalog Y Y N bifunctional 3'-5' exonuclease/DNA polymerase 1385 Bacillales order 6 NCBI Protein Cluster (PRK) bifunctional 3'-5' exonuclease/DNA polymerase bifunctional 3'-5' exonuclease/DNA polymerase NF012167.0 classA_firm 427 427 255 exception Y Y Y class A beta-lactamase bla 3.5.2.6 GO:0008800,GO:0030655 1385 Bacillales order 3240 NCBIFAM classA_firm: class A beta-lactamase class A beta-lactamase NF012184.0 tet_MFS_45 975 975 458 exception Y Y Y tetracycline efflux MFS transporter Tet(45) tet(45) GO:0008493,GO:0015904 1385 Bacillales order 1 NCBIFAM tetracycline efflux MFS transporter Tet(45) tetracycline efflux MFS transporter Tet(45) NF012201.1 WIAG-tail 33 33 80 domain Y Y N WIAG-tail domain 1385 Bacillales order 1647 NCBIFAM WIAG-tail domain WIAG-tail domain This 80-amino acid domain occurs in proteins in a single copy at the C-terminus. In most proteins, the domain immediately follows a long, variable run of tandem 10-amino acid repeats. The domain is named for its C-terminal motif, WIAxGx, hence the name WIAG-tail. NF018906.5 PF07252.16 DUF1433 30.8 30.8 88 domain Y Y N DUF1433 domain-containing protein 1385 Bacillales order 5521 EBI-EMBL Protein of unknown function (DUF1433) Protein of unknown function (DUF1433) This family contains a number of hypothetical bacterial proteins of unknown function approximately 100 residues in length. (from Pfam) NF019516.5 PF07901.16 DUF1672 25 25 276 subfamily Y Y N DUF1672 family protein 1385 Bacillales order 7291 EBI-EMBL Protein of unknown function (DUF1672) DUF1672 family protein This family is composed of hypothetical bacterial proteins of unknown function. (from Pfam) NF019669.5 PF08057.16 Ery_res_leader2 25 25 14 PfamEq Y Y N erythromycin resistance leader peptide GO:0046677 1713206 1385 Bacillales order 62 EBI-EMBL Erythromycin resistance leader peptide erythromycin resistance leader peptide This family consists of erythromycin resistance gene leader peptides. These leader peptides are involved in the transcriptional attenuation control of the synthesis of the macrolide-lincosamide -streptogramin B resistance protein. It acts as a transcriptional attenuator, in contrast to other inducible erm genes. The mRNA leader sequence can fold in either of two mutually exclusive conformations, one of which is postulated to form in the absence of induction, and to contain two rho factor-independent terminators. [1]. [1]. 1713206. Transcriptional attenuation control of ermK, a macrolide-lincosamide-streptogramin B resistance determinant from Bacillus licheniformis. Kwak JH, Choi EC, Weisblum B;. J Bacteriol 1991;173:4725-4735. (from Pfam) NF019740.5 PF08130.16 Antimicrobial18 25 25 60 subfamily Y Y N type A lantibiotic 2253617,9726851 1385 Bacillales order 44 EBI-EMBL Type A lantibiotic family type A lantibiotic This family consists of the type A lantibiotic peptides. Both Pep5 and epicidin-280 are ribosomally-synthesised antimicrobial peptides produced by Gram-positive bacteria that are characterised by the presence of lanthionine and/or methyllanthionine residues. The lantibiotics family has a highly specific activity against multi- drug resistant bacteria and has potential to be utilised in a wide range of medical applications [1,2]. [1]. 2253617. Biosynthesis of the lantibiotic Pep5. Isolation and characterization of a prepeptide containing dehydroamino acids. Weil HP, Beck-Sickinger AG, Metzger J, Stevanovic S, Jung G, Josten M, Sahl HG;. Eur J Biochem 1990;194:217-223. [2]. 9726851. Isolation, characterization, and heterologous expression of the novel lantibiotic epicidin 280 and analysis of its biosynthetic gene cluster. Heidrich C, Pag U, Josten M, Metzger J, Jack RW, Bierbaum G, Jung G, Sahl HG;. Appl Environ Microbiol 1998;64:3140-3146. (from Pfam) NF019785.5 PF08177.16 SspN 25 25 46 PfamEq Y Y N small acid-soluble spore protein N sspN GO:0030436,GO:0042601 10333516 1385 Bacillales order 693 EBI-EMBL Small acid-soluble spore protein N family small acid-soluble spore protein N This family consists of the small acid-soluble spore protein (SASP) N type (sspN). SspN is a 48 residues protein that is expressed only in the forespore compartment of sporulating Bacillus subtilis. The sspN gene is recognised equally by both sigma-G and sigma-F. The role of SspN is still not well-defined [1]. [1]. 10333516. Regulation of four genes encoding small, acid-soluble spore proteins in Bacillus subtilis. Cabrera-Hernandez A, Sanchez-Salas JL, Paidhungat M, Setlow P;. Gene 1999;232:1-10. (from Pfam) NF020389.5 PF08810.15 KapB 26.3 26.3 112 PfamEq Y Y N sporulation phosphorelay system protein KapB kapB 29314743,8497199,9426145 1385 Bacillales order 2963 EBI-EMBL Kinase associated protein B sporulation phosphorelay system protein KapB KapB was reported to be a lipoprotein in Bacillus subtilis, but we note that the putative lipoprotein signal peptide seems insufficiently hydrophobic, which the critical Cys residue for cleavage and lipid attachment is not conserved. NF020547.5 PF08977.15 BOFC_N 25 25 51 domain Y Y N BofC N-terminal domain-containing protein 16049010 1385 Bacillales order 1882 EBI-EMBL Bypass of Forespore C, N terminal Bypass of Forespore C, N terminal The N-terminal domain of 'bypass of forespore C' is composed of a four-stranded beta-sheet covered by an alpha-helix. The beta-sheet has a beta2-beta1-beta4-beta3 topology, where strands beta1 and beta2 and strands beta3 and beta4 are connected by beta-turns, whereas strands beta2 and beta3 are joined by an alpha-helix that runs across one face of the beta-sheet. This domain is similar to the third immunoglobulin G-binding domain of protein G from Streptococcus, the latter belonging to a large and diverse group of cell surface-associated proteins that bind to immunoglobulins. It has been hypothesised that this domain may be a mediator of protein-protein interactions involved in proteolytic events at the cell surface [1]. [1]. 16049010. The structure of bypass of forespore C, an intercompartmental signaling factor during sporulation in Bacillus. Patterson HM, Brannigan JA, Cutting SM, Wilson KS, Wilkinson AJ, Ab E, Diercks T, de Jong RN, Truffault V, Folkers GE, Kaptein R;. J Biol Chem. 2005;280:36214-36220. (from Pfam) NF020695.5 PF09131.15 Endotoxin_mid 22 22 206 domain Y N N Bacillus thuringiensis delta-Endotoxin, middle domain 11377201 1385 Bacillales order 40 EBI-EMBL Bacillus thuringiensis delta-Endotoxin, middle domain Bacillus thuringiensis delta-Endotoxin, middle domain Members of this family adopt a structure consisting of three four-stranded beta-sheets, each with a Greek key fold, with internal pseudo threefold symmetry. Thus they act as a receptor binding beta-prism, binding to insect-specific receptors of gut epithelial cells [1]. [1]. 11377201. Structure of Cry2Aa suggests an unexpected receptor binding epitope. Morse RJ, Yamamoto T, Stroud RM;. Structure. 2001;9:409-417. (from Pfam) NF021017.5 PF09467.15 Yopt 25.5 25.5 71 subfamily Y Y N YopT family protein 1385 Bacillales order 65 EBI-EMBL Hypothetical protein Yopt YopT family protein This hypothetical protein is expressed in bacteria, particularly Bacillus subtilis. It forms homo-dimers, with each monomer consisting of one alpha helix and three beta strands. (from Pfam) NF021167.5 PF09628.15 YvfG 25 25 67 PfamEq Y Y N protein YvfG yvfG 1385 Bacillales order 240 EBI-EMBL YvfG protein protein YvfG Yvfg is a hypothetical protein of 71 residues expressed in some bacteria. The monomer consists of two parallel alpha helices, and the protein crystallises as a homo-dimer. (from Pfam) NF022211.5 PF10751.14 DUF2535 25 25 83 PfamAutoEq Y Y N DUF2535 family protein 1385 Bacillales order 824 EBI-EMBL Protein of unknown function (DUF2535) DUF2535 family protein This family of proteins with unknown function appears to be restricted to Bacillus spp. (from Pfam) NF022212.5 PF10752.14 DUF2533 25 25 83 PfamAutoEq Y Y N DUF2533 family protein 1385 Bacillales order 1181 EBI-EMBL Protein of unknown function (DUF2533) DUF2533 family protein This family of proteins with unknown function appears to be restricted to Bacillus spp. (from Pfam) NF022272.5 PF10815.13 ComZ 22.2 22.2 55 PfamEq Y Y N ComZ family protein 10940045 1385 Bacillales order 725 EBI-EMBL ComZ ComZ family protein ComZ is part of a two gene operon. It affects competence regulation by negatively affecting the transcription of the ComG operon. ComZ contains a leucine zipper motif [1]. [1]. 10940045. Bacillus subtilis comZ (yjzA) negatively affects expression of comG but not comK. Ogura M, Tanaka T;. J Bacteriol. 2000;182:4992-4994. (from Pfam) NF022276.5 PF10819.13 DUF2564 26.3 26.3 79 PfamAutoEq Y Y N DUF2564 family protein 1385 Bacillales order 669 EBI-EMBL Protein of unknown function (DUF2564) DUF2564 family protein This family of proteins with unknown function appears to be restricted to Bacillus spp. (from Pfam) NF023603.5 PF12181.13 MogR_DNAbind 25 25 151 domain Y Y N DNA-binding domain-containing protein 19446532 1385 Bacillales order 1034 EBI-EMBL DNA binding domain of the motility gene repressor (MogR) DNA binding domain of the motility gene repressor (MogR) This domain family is found in bacteria, and is approximately 150 amino acids in length. MogR is involved in repression of transcription of the flagellar gene in Listeria bacteria. This allows a phenotypical switch from an extracellular bacterium to an intracellular pathogen. MogR binds AT rich flagellar gene promoter regions upstream of the flagellar gene. These regions follow the pattern 5'-TTTTNNNNNAAAA-3'. This domain is the DNA binding domain of MogR. [1]. 19446532. Recognition of AT-rich DNA binding sites by the MogR repressor. Shen A, Higgins DE, Panne D;. Structure. 2009;17:769-777. (from Pfam) NF023628.5 PF12207.13 DUF3600 26.5 26.5 160 PfamAutoEq Y Y N DUF3600 domain-containing protein 1385 Bacillales order 1234 EBI-EMBL Domain of unknown function (DUF3600) Domain of unknown function (DUF3600) This family of proteins is found in bacteria. Proteins in this family are approximately 230 amino acids in length. This domain is the C terminal of the putative ecf-type sigma factor negative effector. (from Pfam) NF023854.5 PF12438.13 DUF3679 22 22 56 PfamAutoEq Y Y N DUF3679 domain-containing protein 1385 Bacillales order 1620 EBI-EMBL Protein of unknown function (DUF3679) Protein of unknown function (DUF3679) This domain family is found in bacteria, and is approximately 60 amino acids in length. (from Pfam) NF023952.5 PF12538.13 FtsK_SpoIIIE_N 27 27 115 PfamEq Y Y N FtsK/SpoIIIE N-terminal domain-containing protein 18593879 1385 Bacillales order 5443 EBI-EMBL DNA transporter DNA transporter This domain family is found in bacteria, and is typically between 107 and 121 amino acids in length. The family is found in association with Pfam:PF01580. The FtsK/SpoIIIE family of DNA transporters are responsible for translocating missegregated chromosomes after the completion of cell division. [1]. 18593879. SpoIIIE strips proteins off the DNA during chromosome translocation. Marquis KA, Burton BM, Nollmann M, Ptacin JL, Bustamante C, Ben-Yehuda S, Rudner DZ;. Genes Dev. 2008;22:1786-1795. (from Pfam) NF024446.5 PF13046.11 DUF3906 25 25 64 PfamAutoEq Y Y N DUF3906 family protein 1385 Bacillales order 751 EBI-EMBL Protein of unknown function (DUF3906) DUF3906 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved EKK sequence motif. (from Pfam) NF024447.5 PF13047.11 DUF3907 27 27 147 PfamAutoEq Y Y N DUF3907 family protein 1385 Bacillales order 1800 EBI-EMBL Protein of unknown function (DUF3907) DUF3907 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length. There is a conserved AYTG sequence motif. (from Pfam) NF024456.5 PF13056.11 DUF3918 21.3 21.3 43 PfamAutoEq Y Y N DUF3918 family protein 1385 Bacillales order 636 EBI-EMBL Protein of unknown function (DUF3918) DUF3918 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There are two completely conserved residues (G and R) that may be functionally important. (from Pfam) NF024470.5 PF13070.11 DUF3934 25 25 42 PfamAutoEq Y Y N DUF3934 family protein 1385 Bacillales order 890 EBI-EMBL Protein of unknown function (DUF3934) DUF3934 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There are two conserved sequence motifs: GTG and SKG. (from Pfam) NF024507.5 PF13107.11 DUF3964 27 27 109 PfamAutoEq Y Y N DUF3964 family protein 1385 Bacillales order 351 EBI-EMBL Protein of unknown function (DUF3964) DUF3964 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. There are two conserved sequence motifs: FYF and AFW. (from Pfam) NF024519.5 PF13119.11 DUF3973 25 25 40 domain Y Y N DUF3973 domain-containing protein 1385 Bacillales order 462 EBI-EMBL Domain of unknown function (DUF3973) Domain of unknown function (DUF3973) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 40 amino acids in length. There is a conserved YCI sequence motif. (from Pfam) NF024528.5 PF13128.11 DUF3954 23.7 23.7 49 domain Y Y N DUF3954 domain-containing protein 1385 Bacillales order 1166 EBI-EMBL Protein of unknown function (DUF3954) Protein of unknown function (DUF3954) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 60 amino acids in length. (from Pfam) NF024531.5 PF13131.11 DUF3951 26.3 26.3 52 domain Y Y N DUF3951 domain-containing protein 1385 Bacillales order 1072 EBI-EMBL Protein of unknown function (DUF3951) Protein of unknown function (DUF3951) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 56 and 71 amino acids in length. There is a conserved YTP sequence motif. (from Pfam) NF024537.5 PF13137.11 DUF3983 25 25 34 domain Y Y N DUF3983 domain-containing protein 1385 Bacillales order 736 EBI-EMBL Protein of unknown function (DUF3983) Protein of unknown function (DUF3983) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 40 amino acids in length. There is a conserved AWRN sequence motif. (from Pfam) NF024557.5 PF13158.11 DUF3993 22.4 22.4 118 PfamAutoEq Y Y N DUF3993 domain-containing protein 1385 Bacillales order 965 EBI-EMBL Protein of unknown function (DUF3993) Protein of unknown function (DUF3993) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length. (from Pfam) NF024717.5 PF13321.11 DUF4084 22.4 22.4 304 PfamAutoEq Y Y N DUF4084 domain-containing protein 1385 Bacillales order 951 EBI-EMBL Domain of unknown function (DUF4084) Domain of unknown function (DUF4084) This family of Firmicute proteins is frequently associated with the EAL, GGDEF and PAS families, Pfam:PF00563, Pfam:PF00990, and Pfam:PF00989. The exact function is not known. (from Pfam) NF025410.5 PF14044.11 NETI 27 27 56 PfamEq Y Y N NETI motif-containing protein 1385 Bacillales order 2123 EBI-EMBL NETI protein NETI protein This family includes the B. subtilis YebG protein Swiss:O34700, which is functionally uncharacterised. This is not a homologue of E. coli YebG, which belongs to Pfam:PF07130. This family of proteins is found in bacteria. Proteins in this family are typically between 42 and 66 amino acids in length and contain a conserved NETI motif. (from Pfam) NF025440.5 PF14074.11 DUF4257 27 27 81 domain Y Y N DUF4257 domain-containing protein 1385 Bacillales order 588 EBI-EMBL Protein of unknown function (DUF4257) Protein of unknown function (DUF4257) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. (from Pfam) NF025483.5 PF14118.11 YfzA 27 27 90 subfamily Y Y N YfzA family protein 1385 Bacillales order 1028 EBI-EMBL YfzA-like protein YfzA family protein The YfzA-like protein family includes the B. subtilis YfzA protein Swiss:C0H3X6 which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. (from Pfam) NF025527.5 PF14162.11 YozD 27.5 27.5 56 PfamEq Y Y N YozD family protein 1385 Bacillales order 531 EBI-EMBL YozD-like protein YozD family protein The YozD-like protein family includes the B. subtilis YozD protein Swiss:O31863, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. (from Pfam) NF025529.5 PF14164.11 YqzH 30 30 64 PfamEq Y Y N YqzH family protein 1385 Bacillales order 835 EBI-EMBL YqzH-like protein YqzH family protein The YqzH-like protein family includes the B. subtilis YqzH protein Swiss:O32014, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. (from Pfam) NF025531.5 PF14166.11 YueH 27 27 79 PfamEq Y Y N YueH family protein 1385 Bacillales order 1179 EBI-EMBL YueH-like protein YueH family protein The YueH-like protein family includes the B. subtilis YueH protein Swiss:O32093, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. (from Pfam) NF025535.5 PF14171.11 SpoIISA_toxin 27 27 243 PfamEq Y Y N type II toxin-antitoxin system SpoIISA family toxin GO:0016020 21147767 1385 Bacillales order 1193 EBI-EMBL Toxin SpoIISA, type II toxin-antitoxin system type II toxin-antitoxin system SpoIISA family toxin SpoIISA is a toxin which causes lysis of vegetatively growing cells. It forms part of a type II toxin-antitoxin system, where the SpoIISB protein, Pfam:PF14185, acts as an antitoxin. It is a transmembrane protein, with a cytoplasmic domain accounting for approximately two-thirds of the protein. The structure of the cytoplasmic domain resembles that of the GAF domains, Pfam: PF01590. SpoIISB binds to the cytoplasmic domain of SpoIISA with high affinity [1]. [1]. 21147767. The structure and interactions of SpoIISA and SpoIISB, a toxin-antitoxin system in Bacillus subtilis. Florek P, Levdikov VM, Blagova E, Lebedev AA, Skrabana R, Resetarova S, Pavelcikova P, Barak I, Wilkinson AJ;. J Biol Chem. 2011;286:6808-6819. (from Pfam) NF025545.5 PF14182.11 YgaB 27 27 77 PfamEq Y Y N YgaB family protein 9202460 1385 Bacillales order 925 EBI-EMBL YgaB-like protein YgaB family protein The YgaB-like protein family includes the B. subtilis YgaB protein Swiss:P71080, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. (from Pfam) NF025548.5 PF14185.11 SpoIISB_antitox 27 27 57 PfamEq Y Y N type II toxin-antitoxin system SpoIISB family antitoxin 21147767 1385 Bacillales order 141 EBI-EMBL Antitoxin SpoIISB, type II toxin-antitoxin system type II toxin-antitoxin system SpoIISB family antitoxin Members of this family act as antitoxins. They bind to the SpoIISA toxin, Pfam:PF14171. They are disordered proteins which adopt structure only when bound to SpoIISA [1]. [1]. 21147767. The structure and interactions of SpoIISA and SpoIISB, a toxin-antitoxin system in Bacillus subtilis. Florek P, Levdikov VM, Blagova E, Lebedev AA, Skrabana R, Resetarova S, Pavelcikova P, Barak I, Wilkinson AJ;. J Biol Chem. 2011;286:6808-6819. (from Pfam) NF026079.5 PF14729.11 DUF4467 25 25 94 domain Y Y N cystatin-like fold lipoprotein 1385 Bacillales order 1396 EBI-EMBL Domain of unknown function with cystatin-like fold (DUF4467) cystatin-like fold lipoprotein Large family of predicted lipoproteins from Gram-positive bacteria Experimentally determined structure shows a cystatitin-like fold, allowing us to classify this family in the NFT2 clan, despite lack of any detectable sequence similarity between members of this family and other families in this clan (from Pfam) NF026831.5 PF15493.12 YrpD 26.4 25.5 214 subfamily Y Y N YrpD family protein 1385 Bacillales order 617 EBI-EMBL Domain of unknown function, YrpD YrpD family protein This family of proteins is found in bacteria. Proteins in this family are typically between 236 and 351 amino acids in length. The member from Bacillus subtilis, UniProtKB:O05411, is named YrpD. (from Pfam) NF027493.5 PF16167.10 DUF4871 25 25 128 PfamAutoEq Y Y N DUF4871 domain-containing protein 1385 Bacillales order 971 EBI-EMBL Domain of unknown function (DUF4871) Domain of unknown function (DUF4871) This family consists of uncharacterized proteins around 170 residues in length and is mainly found in various Bacillus species (B. cereus, B. thuringiensis and B. anthracis). The solved structure of B. anthracis homologs has a variant of the Greek-key beta barrel fold, making the DUF4870 family a member of a large group of bacterial immunoglobulin like domains, but the functional consequences of this classification remain unknown. (from Pfam) NF027626.5 PF16302.10 DUF4944 23 23 128 domain Y Y N DUF4944 domain-containing protein 1385 Bacillales order 771 EBI-EMBL Domain of unknown function (DUF4944) Domain of unknown function (DUF4944) This family consists of uncharacterized proteins around 160 residues in length and is mainly found in various Bacillus species. The function of this family is unknown. (from Pfam) NF028197.5 PF16887.10 DUF5081 27 27 231 PfamAutoEq Y Y N DUF5081 family protein 1385 Bacillales order 1002 EBI-EMBL Domain of unknown function (DUF5081) DUF5081 family protein This protein is believed to be involved in the type VII secretion system. (from Pfam) NF033193.2 lipo_NDxxF 60 60 199 hypoth_equivalog Y Y N NDxxF motif lipoprotein 1385 Bacillales order 2035 NCBIFAM NDxxF motif lipoprotein NDxxF motif lipoprotein Members of this family are lipoproteins, about 200 amino acids long in precursor form, found in Staphylococcus aureus, Bacillus cereus, and various other Firmicutes. The protein family is named for one of its several highly conserved motifs. NF033202.0 GW_glycos_SH3 50 50 81 domain Y Y N GW domain-containing glycosaminoglycan-binding protein 12411480 1385 Bacillales order 4368 NCBIFAM GW domain-containing glycosaminoglycan-binding protein GW domain The GW domain of Listeria belongs to the clan of SH3-like domains. A similar but broader model (PF13457) occurs in Pfam. The GW domain occurs as repeats on surface proteins of the cell-invading pathogenic bacterium Listeria monocytogenes, and is involved in binding to glycosaminoglycans. Members of this family include the GW-type internalin InlB and several paralogs. NF033468.1 stregram_VatI 415 415 208 exception Y Y Y streptogramin A O-acetyltransferase Vat(I) vat(I) 1385 Bacillales order 68 NCBIFAM streptogramin A O-acetyltransferase Vat(I) streptogramin A O-acetyltransferase Vat(I) NF033472.1 AAC_2p_IIb 390 390 228 exception Y Y Y kasugamycin N-acetyltransferase AAC(2')-IIb aac(2')-IIb 27929110 1385 Bacillales order 119 NCBIFAM kasugamycin N-acetyltransferase AAC(2')-IIb kasugamycin N-acetyltransferase AAC(2')-IIb The characterized member of this family, and presumably also the well-conserved homologs also used in the seed alignment for the definition of this family, perform a modification a distinctive sugar found in the agricultural antibiotic kasugamycin. While the modification position is described as 2-prime, the sugar itself is different, and in fact, neither AAC(2')-IIb (this family) nor its homolog AAC(2')-IIa confer resistance to any aminoglycoside other than kasugamycin. NF033491.1 BA3454_fam 40 40 43 equivalog Y Y N BA3454 family stress response protein 25231235 1385 Bacillales order 690 NCBIFAM BA3454 family stress response protein BA3454 family stress response protein BA3454, a protein less than 45 amino acids long, is up-regulated strongly by SpxA2 during stress conditions. Related proteins are found widely in the genus Bacillus, although not in Bacillus subtilis. NF033560.1 merT_RC607 130 130 97 exception Y Y Y mercuric transport protein MerT merT 10559175,2536669 1385 Bacillales order 58 NCBIFAM mercuric transport protein MerT mercuric transport protein MerT NF033714.1 blaBBI 625 625 304 exception Y Y Y BBI family class A beta-lactamase blaBBI 3.5.2.6 GO:0008800,GO:0030655,GO:0046677 29259290 1385 Bacillales order 41 NCBIFAM BBI family class A beta-lactamase BBI family class A beta-lactamase The BBI family of class A beta-lactamase is found typically in Brevibacillus brevis, a member of the Firmicutes. NF033802.1 AimP_fam 35 35 43 subfamily Y Y N lysogeny pheromone AimP family peptide 28099413 1385 Bacillales order 129 NCBIFAM lysogeny pheromone AimP family peptide lysogeny pheromone AimP family peptide AimP is the quorum signaling-like peptide pheromone of a phage system, called the arbitrium system, that detects environmental evidence of predecessor phage activity, in order to direct a lysis/lysogeny decision. NF036626.5 PF17368.7 YwcE 25 25 85 domain Y Y N spore morphogenesis/germination protein YwcE 16159778,25225273 1385 Bacillales order 266 EBI-EMBL Spore morphogenesis and germination YwcE spore morphogenesis/germination protein YwcE The ywcE gene codes for a holin-like protein that localizes to the cell and spore membranes [1]. It is expressed at the onset of sporulation and transcription is repressed during growth by the transition-state regulator AbrB. YwcE is an 83-residue protein with three trans-membrane regions and a highly charged C-terminal tail. Moreover, YwcE has a dual start motif, which plays a role in the regulation of class I or class II holins. It is likely to have the N terminus on the outside of the membrane and the C terminus in the cytoplasm [2]. This family is found in YwcE proteins in Bacilli. [1]. 25225273. Sporulation during growth in a gut isolate of Bacillus subtilis. Serra CR, Earl AM, Barbosa TM, Kolter R, Henriques AO;. J Bacteriol. 2014;196:4184-4196. [2]. 16159778. A gene encoding a holin-like protein involved in spore morphogenesis and spore germination in Bacillus subtilis. Real G, Pinto SM, Schyns G, Costa T, Henriques AO, Moran CP Jr;. J Bacteriol. 2005;187:6443-6453. (from Pfam) NF036696.5 PF18058.6 SbsC_C 27 27 131 domain Y N N SbsC C-terminal domain 18682224 1385 Bacillales order 1376 EBI-EMBL SbsC C-terminal domain SbsC C-terminal domain This is the C-terminal domain found in Bacterial Cell Surface Layer Protein SbsC which can be found in species such as Geobacillus stearothermophilus. The C-terminal domain is the third and last triple-helical bundle and adopts a canonical coiled-coil structure. A similar overall arrangement of antiparallel triple-helical bundles has been found in the cytoskeletal protein spectrin (2SPC)[1]. [1]. 18682224. The structure and binding behavior of the bacterial cell surface layer protein SbsC. Pavkov T, Egelseer EM, Tesarz M, Svergun DI, Sleytr UB, Keller W;. Structure. 2008;16:1226-1237. (from Pfam) NF036963.5 PF17637.7 DUF5516 25 25 37 domain Y Y N DUF5516 domain-containing protein 1385 Bacillales order 21 EBI-EMBL Family of unknown function (DUF5516) DUF5516 domain This is a family of unknown function found in T7 viruses. (from Pfam). This protein family is known from T7 phage. NF037391.5 PF18698.6 HisK_sensor 27.3 27.3 126 domain Y N N Histidine kinase sensor domain 14996800,27512901 1385 Bacillales order 4631 EBI-EMBL Histidine kinase sensor domain Histidine kinase sensor domain The Bacillus subtilis ResD-ResE two-component (TC) regulatory system activates genes involved in nitrate respiration in response to oxygen limitation or nitric oxide (NO). The sensor kinase ResE activates the response regulator ResD through phosphorylation, which then binds to the regulatory region of genes involved in anaerobiosis to activate their transcription. In other words, ResE is involved in sensing signals related to the redox state of the cells. ResE is composed of an N-terminal signal input domain and a C-terminal catalytic domain. The N-terminal domain contains two transmembrane subdomains and a large extra-cytoplasmic loop. Mutational analysis indicate that cytoplasmic ResE lacking the transmembrane segments and the extra-cytoplasmic loop retains the ability to sense oxygen limitation and NO, which leads to transcriptional activation of ResDE-dependent genes. Having said that, it is also proposed that the extra-cytoplasmic region may serve as a second signal-sensing subdomain. This suggests that the extracytoplasmic region could contribute to amplification of ResE activity leading to the robust activation of genes required for anaerobic metabolism in B. subtilis. This entry represents the extracytoplasmic subdomain [1]. Family members also include SrrB found in S. aureus that is similar to ResE of B. subtilis [2]. [1]. 14996800. Mutational analysis of the signal-sensing domain of ResE histidine kinase from Bacillus subtilis. Baruah A, Lindsey B, Zhu Y, Nakano MM;. J Bacteriol. 2004;186:1694-1704. [2]. 27512901. Bacterial Stress Responses during Host Infection. Fang FC, Frawley ER, Tapscott T, Vazquez-Torres A;. TRUNCATED at 1650 bytes (from Pfam) NF037879.5 PF18681.6 DUF5634 30.4 30.4 98 domain Y Y N DUF5634 family protein 1385 Bacillales order 366 EBI-EMBL Family of unknown function (DUF5634) DUF5634 family protein This is a domain of unknown function mostly found in bacilli. (from Pfam) NF038165.1 garvicinKS_B 35 35 31 subfamily Y Y N GatB family leaderless bacteriocin 27316965 1385 Bacillales order 46 NCBIFAM GatB family leaderless bacteriocin GatB is one component of the multipeptide leaderless bacteriocin designated garvicin KS, as found in Lactococcus garvieae KS1546. NF039548.4 PF19140.5 DUF5823 25 25 178 subfamily Y Y N DUF5823 family protein 1385 Bacillales order 540 EBI-EMBL Family of unknown function (DUF5823) DUF5823 family protein This is a family of uncharacterised proteins. (from Pfam) NF039663.4 PF19618.4 DUF6123 27 27 89 subfamily Y Y N DUF6123 family protein 1385 Bacillales order 857 EBI-EMBL Family of unknown function (DUF6123) DUF6123 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. (from Pfam) NF039958.4 PF19482.4 DUF6018 25 25 117 subfamily Y Y N DUF6018 family natural product bioysynthesis protein 15640177,16512902 1385 Bacillales order 273 EBI-EMBL Family of unknown function (DUF6018) DUF6018 family natural product bioysynthesis protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000320) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This family includes a protein from the cereulide biosynthetic gene cluster from Bacillus cereus and appears to be predominantly found in Bacilli [1,2]. [1]. 15640177. Identification and partial characterization of the nonribosomal peptide synthetase gene responsible for cereulide production in emetic Bacillus cereus. Ehling-Schulz M, Vukov N, Schulz A, Shaheen R, Andersson M, Martlbauer E, Scherer S;. Appl Environ Microbiol. 2005;71:105-113. [2]. 16512902. Cereulide synthetase gene cluster from emetic Bacillus cereus: structure and location on a mega virulence plasmid related to Bacillus anthracis toxin plasmid pXO1. Ehling-Schulz M, Fricker M, Grallert H, Rieck P, Wagner M, Scherer S;. BMC Microbiol. 2006;6:20. (from Pfam) NF040280.4 PF19395.4 DUF5970 25 25 77 subfamily Y Y N DUF5970 family protein 1385 Bacillales order 117 EBI-EMBL Family of unknown function (DUF5970) DUF5970 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000616) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide). (from Pfam) NF040841.1 AMEP412_fam 45 45 74 subfamily Y Y N AMEP412 family response elicitor 31352630,31912374 1385 Bacillales order 24 NCBIFAM AMEP412 family response elicitor AMEP412 (WP_017418614.1) from Bacillus subtilis strain BU412, a 76-amino acid protein that is the founding member of this family, has been shown both to elicit a hypersensitive response in tobacco and have antimicrobial activity against Streptomyces scabiei. Members of this family are found regularly in the context of an apparent ABC transporter ATP-binding protein and a large (about 520 amino acid) protein whose hydrophobic nature suggest transporter permease function. NF040842.1 elici_assc_perm 250 250 513 equivalog Y Y N elicitor-associated permease-like protein 1385 Bacillales order 52 NCBIFAM AMEP412-like elicitor-associated permease-like protein Members of this family are found as part of a conserved bacterial gene neighborhood, along with AMEP412 family proteins and an apparent ABC transporter ATP-binding protein. The hydrophobic nature of this protein suggests the protein is a transporter subunit associated with AMEP412 family protein export. Members of the AMEP412 family (see NF040841) are about 76 amino acids in length, and affect both plant cells (hypersensitive response in tobacco) and other bacterial cells (antimicrobial activity vs. the plant pathogen Streptomyces scabiei). NF041108.1 RQC_minor_2 300 300 465 equivalog Y Y N RQC-minor-2 family DNA-binding protein 1385 Bacillales order 375 NCBIFAM RQC-minor-2 family DNA-binding protein The DNA-binding RQC domain (PF09382) appears primarily in RecQ, a DNA helicase involved in recombination, replication, and repair. However, it appears also in this long, uncharacterized protein family, to which we give the name "RQC-minor-2 family DNA-binding protein." NF041669.1 GvpT 80 80 123 domain Y Y N GvpT/GvpP family gas vesicle accessory protein gvpT GO:0031411,GO:0031412 9573198 1385 Bacillales order 682 NCBIFAM GvpT/GvpP family gas vesicle accessory protein NF041670.1 GvpQ 100 100 137 equivalog Y Y N gas vesicle protein GvpQ gvpQ GO:0031411,GO:0031412 9573198 1385 Bacillales order 400 NCBIFAM gas vesicle protein GvpQ NF042993.1 AlphKGSA_gudD 770 770 481 equivalog Y Y N alpha-ketoglutaric semialdehyde dehydrogenase GucD gucD 1.2.1.26 17202142 1385 Bacillales order 1980 NCBIFAM alpha-ketoglutaric semialdehyde dehydrogenase GucD NF044363.2 PF20971.2 MASE12 27 27 165 domain Y N N MASE12 34928179 1385 Bacillales order 2485 EBI-EMBL MASE12 MASE12 This is the membrane-associated sensor domain 12 (MASE12), found in (predicted) c-di-GMP phosphodiesterases and histidine kinases [1]. This domain has conserved aromatic residues in the transmembrane segments, which suggests that its ligand could be a molecule with one or more aromatic rings [1]. [1]. 34928179. Sequence Conservation, Domain Architectures, and Phylogenetic Distribution of the HD-GYP Type c-di-GMP Phosphodiesterases. Galperin MY, Chou SH;. J Bacteriol. 2021; [Epub ahead of print] (from Pfam) NF044483.2 PF21469.2 BH1974-like_central 27 27 74 domain Y N N BH1974-like, central domain 1385 Bacillales order 75 EBI-EMBL BH1974-like, central domain BH1974-like, central domain This domain is located centrally in BH1974 protein from Alkalihalobacillus halodurans and similar bacterial proteins. It is found C-terminal to Pfam:PF02625 and N-terminal to Pfam:PF13478 and shows an alpha-beta structure. (from Pfam) NF045699.1 AHLLactAiiA 375 375 251 equivalog Y Y N N-acyl homoserine lactonase AiiA aiiA 3.1.1.81 GO:0102007 10716724,11459062 1385 Bacillales order 800 NCBIFAM N-acyl homoserine lactonase AiiA NF046109.1 RNaseH_Halikb 320 320 211 equivalog Y Y N ribonuclease H rnhA 3.1.26.4 GO:0003676,GO:0004523,GO:0046872 15989951 1385 Bacillales order 774 NCBIFAM ribonuclease H NF046278.1 PF22440.1 SirC_C 27 27 47 domain Y N N SirC C-terminal domain 18588505 1385 Bacillales order 2447 EBI-EMBL SirC C-terminal domain SirC C-terminal domain This entry represents the C-terminal helical domain of SirC from Bacillus megaterium and related sequences [1]. This domain contains Arg159 which contributes to the active site from the alternate molecule of the homodimer. Paper describing PDB structure 3dfz. [1]. 18588505. Structure and function of SirC from Bacillus megaterium: a metal-binding precorrin-2 dehydrogenase. Schubert HL, Rose RS, Leech HK, Brindley AA, Hill CP, Rigby SE, Warren MJ;. Biochem J. 2008;415:257-263. (from Pfam) NF046899.1 PF22713.1 SNaCT6 27 27 119 domain Y N N Short NACHT-associated C-Terminal domain, family 6 37160116 1385 Bacillales order 12 EBI-EMBL Short NACHT-associated C-Terminal domain, family 6 Short NACHT-associated C-Terminal domain, family 6 The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors [1]. [1]. 37160116. Bacterial NLR-related proteins protect against phage. Kibby EM, Conte AN, Burroughs AM, Nagy TA, Vargas JA, Whalen LA, Aravind L, Whiteley AT;. Cell. 2023;186:2410-2424. (from Pfam) NF047231.1 PF22644.1 BsNagA_N 27.4 27.4 50 domain Y N N BsNagA composite domain 14557261 1385 Bacillales order 815 EBI-EMBL BsNagA composite domain BsNagA composite domain This entry represents the composite domain of NagA from Bacillus subtilis [1], a N-acetylglucosamine-6-phosphate deacetylase, similar to that from E.coli. However, they have some sequence differences [1]. Paper describing PDB structure 2vhl. [1]. 14557261. The three-dimensional structure of the N-acetylglucosamine-6-phosphate deacetylase, NagA, from Bacillus subtilis: a member of the urease superfamily. Vincent F, Yates D, Garman E, Davies GJ, Brannigan JA;. J Biol Chem. 2004;279:2809-2816. (from Pfam) NF047520.1 trans_act_CidR 415 415 292 equivalog Y Y N cidABC operon transcriptional activator CidR cidR 16109930,31501288 1385 Bacillales order 1815 NCBIFAM cidABC operon transcriptional activator CidR NF047574.1 opine_export_Sa 235 235 388 equivalog Y Y N staphylopine family metallophore export MFS transporter CntE cntE 27230378 1385 Bacillales order 1590 NCBIFAM staphylopine family metallophore export MFS transporter CntE NF047578.1 opine_ATP_CntD 380 380 266 equivalog Y Y N staphylopine uptake ABC transporter ATP-binding protein CntD cntD 27230378,29089427 1385 Bacillales order 1045 NCBIFAM staphylopine uptake ABC transporter ATP-binding protein CntD NF047673.2 TeichurnBiosyTuaD 700 700 439 equivalog Y Y N UDP-glucose 6-dehydrogenase TuaD tuaD 1.1.1.22 GO:0003979,GO:0006065,GO:0051287 10048024,12970183 1385 Bacillales order 841 NCBIFAM UDP-glucose 6-dehydrogenase TuaD NF047830.1 lanti_ElxA 75 75 55 subfamily Y Y N epilancin family lantibiotic 21802007 1385 Bacillales order 12 NCBIFAM epilancin family lantibiotic TIGR00555.1 TIGR00555 panK_eukar 247.6 247.6 304 equivalog Y Y N type II pantothenate kinase coaA 2.7.1.33 GO:0004594,GO:0006085 12760898,9890959 1385 Bacillales order 1329 JCVI pantothenate kinase type II pantothenate kinase This model describes a eukaryotic form of pantothenate kinase, characterized from the fungus Aspergillus nidulans and with similar forms known in several other eukaryotes. It also includes forms from several Gram-positive bacteria suggested to have originated from the eukaryotic form by lateral transfer. It differs in a number of biochemical properties (such as inhibition by acetyl-CoA) from most bacterial CoaA and lacks sequence similarity. This enzyme is the key regulatory step in the biosynthesis of coenzyme A (CoA). TIGR01002.1 TIGR01002 hlyII 245.6 245.6 313 subfamily Y Y N beta-channel forming cytolysin GO:0005576 10547438 1385 Bacillales order 2926 JCVI beta-channel forming cytolysin beta-channel forming cytolysin This family of cytolytic pore-forming proteins includes alpha toxin and leukocidin F and S subunits from Staphylococcus aureus, hemolysin II of Bacillus cereus, and related toxins. TIGR01377.1 TIGR01377 soxA_mon 479.65 479.65 381 subfamily Y Y N amino oxidase GO:0008115 10220347,10642506 1385 Bacillales order 15 JCVI sarcosine oxidase, monomeric form amino oxidase Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) forms TIGR01741.1 TIGR01741 staph_tand_hypo 82.05 82.05 157 subfamily Y Y N TIGR01741 family protein 1385 Bacillales order 9080 JCVI conserved hypothetical protein TIGR01741 family protein This HMM represents a tandem array of 10 proteins in Staphylococcus aureus and the C-terminal region of one protein each in Bacillus subtilis and Bacillus halodurans. TIGR02705.1 TIGR02705 nudix_YtkD 154.4 154.4 156 equivalog Y Y N RNA deprotection pyrophosphohydrolase ytkD GO:0006139,GO:0017111 14761999,15576788,23610407 1385 Bacillales order 2712 JCVI nucleoside triphosphatase YtkD RNA deprotection pyrophosphohydrolase The functional assignment to the proteins of this family has been contentious. PMID:15576788 (2004) challenges the findings of reference PMID:14761999 (2004), both in interpretation and in enzyme assay results. This protein belongs to the Nudix family and shares some sequence identity with E. coli MutT but appears not to be functionally interchangeable with it. PMID:23610407 (23610407) TIGR02752.1 TIGR02752 MenG_heptapren 419.85 419.85 231 equivalog Y Y N demethylmenaquinone methyltransferase menG 2.1.1.163 GO:0008168,GO:0009234 9139683 1385 Bacillales order 1707 JCVI demethylmenaquinone methyltransferase demethylmenaquinone methyltransferase MenG is a generic term for a methyltransferase that catalyzes the last step in menaquinone biosynthesis; the exact enzymatic activity differs for different MenG because the menaquinone differ in their prenoid side chains in different species. Members of this MenG protein family are 2-heptaprenyl-1,4-naphthoquinone methyltransferase, and are found together in operons with the two subunits of the heptaprenyl diphosphate synthase in Bacillus subtilis and related species. TIGR02878.1 TIGR02878 spore_ypjB 229.15 229.15 233 equivalog Y Y N sporulation protein YpjB ypjB GO:0030436 1385 Bacillales order 1468 JCVI sporulation protein YpjB sporulation protein YpjB Members of this protein, YpjB, family are restricted to a subset of endospore-forming bacteria, including Bacillus species but not CLostridium or some others. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon, where sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect. This protein family is not, however, a part of the endospore formation minimal gene set. TIGR02904.1 TIGR02904 spore_ysxE 263.55 263.55 309 equivalog Y Y N spore coat protein YsxE ysxE GO:0030436 16371471,8449878 1385 Bacillales order 2109 JCVI spore coat protein YsxE spore coat protein YsxE Members of this family are homologs of the Bacillus subtilis spore coat protein CotS. Members of this family, designated YsxE, are found only in the family Bacillaceae, from among the endospore-forming members of the Firmicutes branch of the Bacteria. As a rule, the ysxE gene is found immediately downstream of spoVID, a gene necessary for spore coat assembly. The protein has been shown to be part of the spore coat. TIGR03601.1 TIGR03601 B_an_ocin 35 35 88 subfamily Y Y N heterocycloanthracin/sonorensin family bacteriocin 19383135,24610839 1385 Bacillales order 1817 JCVI bacteriocin, heterocycloanthracin/sonorensin family heterocycloanthracin family bacteriocin Numerous bacteria encode systems for producing bacteriocins by extensive modification of ribosomally synthesized precursors. Members of the TOMM class (thiazole/oxazole-modified microcins) are recognizable by association with cyclodehydratase (and often dehydrogenase) maturation proteins. This family consists of a special subclass, the heterocycloanthracin family, that share a homologous leader peptide region and then a repeat region with Cys as every third residue. In Bacillus anthracis and Bacillus cereus, the RiPP (ribosomally translated and post-translationally modified natural product) precursor is encoded far from its maturase genes, and every strain has the system. In other species (e.g. B. licheniformis, B. sorenensis), precursor and maturase genes are close together. Sonorensin, from B. sonorensis MT93, was shown to have broad spectrum antimicrobial activity, affecting Gram-positive and Gram-negative bacteria. TIGR03656.1 TIGR03656 IsdC 155.85 155.85 219 equivalog Y Y N heme uptake protein IsdC isdC GO:0009274,GO:0015886,GO:0030492 17012401,18676371,18715872 1385 Bacillales order 1817 JCVI heme uptake protein IsdC heme uptake protein IsdC Isd proteins are iron-regulated surface proteins found in Bacillus, Staphylococcus and Listeria species and are responsible for heme scavenging from hemoproteins [1]. The IsdC protein consists of an N-terminal hydrophobic signal sequence, a central NEAT (NEAr Transporter, PF05031) domain which confers the ability to bind heme [2] and a C-terminal SrtB processing signal which targets the protein to the cell wall [3]. IsdC is believed to make a direct contact with, and transfer heme to, the heme-binding component (IsdE) of an ABC transporter in the cytoplasmic membrane, and to receive heme from other NEAT-containing heme-binding proteins also localized in the cell wall. TIGR03829.1 TIGR03829 YokU_near_AblA 90.85 90.85 89 hypoth_equivalog Y Y N YokU family protein 1385 Bacillales order 1194 JCVI uncharacterized protein, YokU family YokU family protein Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by PF01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context. TIGR03933.1 TIGR03933 PIA_icaB 248.35 248.35 245 equivalog Y Y N intercellular adhesin biosynthesis polysaccharide N-deacetylase icaB GO:0000271,GO:0019213 1385 Bacillales order 795 JCVI intercellular adhesin biosynthesis polysaccharide N-deacetylase intercellular adhesin biosynthesis polysaccharide N-deacetylase A common motif in bacterial biosynthesis of polysaccharide for export is modification that follows polymerization. This HMM describes a subfamily of polysaccharide N-deacetylases that acts on poly-beta-1,6-N-acetyl-D-glyscosamine as produced by Staphylococcus epidermidis and S. aureus. The end product in these species is designated polysaccharide intercellular adhesin (PIA), and this gene designated icaB (intercellular adhesion protein B). TIGR04195.1 TIGR04195 S_glycosyl_SunS 350 350 421 equivalog Y Y N SunS family peptide S-glycosyltransferase GO:0018240 21196935 1385 Bacillales order 76 JCVI peptide S-glycosyltransferase, SunS family SunS family peptide S-glycosyltransferase Members of this family include SunS, the S-glycosyltransferase that transfers a sugar (substrate is variable in reconstitution assays) onto the precursor of the glycopeptide sublancin, which once was thought to be a lantibiotic. TIGR04404.1 TIGR04404 RiPP_SkfA 45 45 53 equivalog Y Y N sporulation killing factor skfA 16816204 1385 Bacillales order 35 JCVI sporulation killing factor sporulation killing factor Members of this family are ribosomally synthesized and post-translationally modified peptide natural products, modified by sulfur-to-alpha-carbon cross-link introduced by a radical SAM enzyme, SkfB (TIGR04403). TIGR04536.1 TIGR04536 geobac_encap 100 100 194 equivalog Y Y N IMEF encapsulin system ferritin-like cargo protein GO:0006880,GO:0140315,GO:0140737 28263314,31194509,31282860 1385 Bacillales order 294 JCVI encapsulated protein IMEF encapsulin system ferritin-like cargo protein Members of this family are lineage-restricted proteins found mostly in Brevibacillus and Geobacillus. Members are encoded next to the gene for encapsulin (which once was called a bacteriocin), and have the C-terminal motif for associating with encapsulin. The type of encapsulin system to which they belong is now referred to as Iron-Mineralizing Encapsulin-Associated Firmicute (IMEF). NF000098.1 Fos_BSH_Bcer 295 295 138 exception Y Y Y FosB family fosfomycin resistance bacillithiol transferase fosB 1386 Bacillus genus 48 NCBIFAM fosfomycin resistance thiol transferase FosB FosB family fosfomycin resistance bacillithiol transferase NF000312.1 ANT_6_aadK 600 600 284 exception Y Y Y aminoglycoside 6-adenylyltransferase AadK aadK 1386 Bacillus genus 137 NCBIFAM aminoglycoside 6-adenylyltransferase AadK aminoglycoside 6-adenylyltransferase AadK NF000992.0 PRK00104 PRK00104.1-1 417 417 247 equivalog Y Y N segregation/condensation protein A 1386 Bacillus genus 169 NCBI Protein Cluster (PRK) segregation and condensation protein A segregation/condensation protein A NF001254.0 PRK00220 PRK00220.2-1 199 199 182 equivalog Y Y N glycerol-3-phosphate 1-O-acyltransferase PlsY plsY 2.3.1.15 1386 Bacillus genus 467 NCBI Protein Cluster (PRK) putative glycerol-3-phosphate acyltransferase PlsY glycerol-3-phosphate 1-O-acyltransferase PlsY NF002046.0 PRK00872 PRK00872.1-2 184 184 95 equivalog Y N N hypothetical protein 1386 Bacillus genus 174 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002297.0 PRK01222 PRK01222.1-3 259 259 204 equivalog Y Y N phosphoribosylanthranilate isomerase 5.3.1.24 1386 Bacillus genus 610 NCBI Protein Cluster (PRK) N-(5'-phosphoribosyl)anthranilate isomerase phosphoribosylanthranilate isomerase NF002452.0 PRK01631 PRK01631.1 144 144 76 equivalog Y N N hypothetical protein 1386 Bacillus genus 172 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002585.0 PRK02234 PRK02234.1-6 396 396 200 equivalog Y Y N Holliday junction resolvase RecU recU 3.1.21.10 1386 Bacillus genus 166 NCBI Protein Cluster (PRK) Holliday junction-specific endonuclease Holliday junction resolvase RecU NF002641.0 PRK02315 PRK02315.1-1 411 411 227 equivalog Y Y N adaptor protein MecA mecA 1386 Bacillus genus 171 NCBI Protein Cluster (PRK) adaptor protein adaptor protein MecA NF002692.0 PRK02487 PRK02487.1-1 297 297 158 equivalog Y Y N heme-degrading domain-containing protein 1386 Bacillus genus 394 NCBI Protein Cluster (PRK) hypothetical protein heme-degrading domain-containing protein NF002824.0 PRK02998 PRK02998.1 360 360 283 subfamily Y N N peptidylprolyl isomerase 1386 Bacillus genus 743 NCBI Protein Cluster (PRK) peptidylprolyl isomerase peptidylprolyl isomerase NF002827.0 PRK03002 PRK03002.1 343 343 285 equivalog Y Y N peptidylprolyl isomerase PrsA prsA 12606539,14976191 1386 Bacillus genus 510 NCBI Protein Cluster (PRK) peptidylprolyl isomerase peptidylprolyl isomerase PrsA Cis/trans isomerase of peptidylprolyl NF002846.0 PRK03095 PRK03095.1 361 361 287 equivalog Y Y N peptidylprolyl isomerase PrsA prsA 12606539,14976191 1386 Bacillus genus 457 NCBI Protein Cluster (PRK) peptidylprolyl isomerase peptidylprolyl isomerase PrsA Cis/trans isomerase of peptidylprolyl NF003193.0 PRK04164 PRK04164.1-4 351 351 182 equivalog Y N N hypothetical protein 1386 Bacillus genus 131 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003411.0 PRK04778 PRK04778.1-5 1073 1073 570 equivalog Y Y N septation ring formation regulator EzrA ezrA 1386 Bacillus genus 352 NCBI Protein Cluster (PRK) septation ring formation regulator EzrA septation ring formation regulator EzrA NF004443.0 PRK05777 PRK05777.2-1 626 626 506 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoN nuoN 1.6.5.9 1386 Bacillus genus 1041 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit N NADH-quinone oxidoreductase subunit NuoN NF004502.0 PRK05846 PRK05846.2-1 791 791 500 equivalog Y Y N NADH-quinone oxidoreductase subunit M 1.6.5.9 1386 Bacillus genus 887 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit M NADH-quinone oxidoreductase subunit M NF004583.0 PRK05928 PRK05928.1-5 432 432 250 equivalog Y Y N uroporphyrinogen-III synthase hemD 4.2.1.75 1386 Bacillus genus 488 NCBI Protein Cluster (PRK) uroporphyrinogen-III synthase uroporphyrinogen-III synthase NF005090.0 PRK06522 PRK06522.2-1 496 496 296 equivalog Y Y N 2-dehydropantoate 2-reductase panE 1.1.1.169 1386 Bacillus genus 492 NCBI Protein Cluster (PRK) 2-dehydropantoate 2-reductase 2-dehydropantoate 2-reductase NF005104.0 PRK06545 PRK06545.1-1 713 713 366 equivalog Y Y N prephenate dehydrogenase tyrA 1.3.1.12 1386 Bacillus genus 486 NCBI Protein Cluster (PRK) prephenate dehydrogenase prephenate dehydrogenase NF005166.0 PRK06638 PRK06638.2-1 284 284 174 equivalog Y Y N NADH-quinone oxidoreductase subunit J 1.6.5.9 1386 Bacillus genus 301 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit J NADH-quinone oxidoreductase subunit J NF005206.0 PRK06672 PRK06672.1 416 416 341 equivalog Y N N hypothetical protein 1386 Bacillus genus 225 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005213.0 PRK06698 PRK06698.1 768 768 459 equivalog Y N N bifunctional 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/phosphatase 1386 Bacillus genus 250 NCBI Protein Cluster (PRK) bifunctional 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/phosphatase bifunctional 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/phosphatase NF005215.0 PRK06702 PRK06702.1 709 709 432 equivalog Y Y N bifunctional O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase 2.5.1.47 1386 Bacillus genus 463 NCBI Protein Cluster (PRK) O-acetylhomoserine aminocarboxypropyltransferase bifunctional O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase NF005217.0 PRK06704 PRK06704.1 256 256 228 equivalog Y Y N RNA polymerase subunit sigma-70 1386 Bacillus genus 545 NCBI Protein Cluster (PRK) RNA polymerase factor sigma-70 RNA polymerase subunit sigma-70 NF005218.0 PRK06705 PRK06705.1 883 883 502 equivalog Y Y N argininosuccinate lyase argH 4.3.2.1 1386 Bacillus genus 695 NCBI Protein Cluster (PRK) argininosuccinate lyase argininosuccinate lyase Catalyzes the formation of arginine and fumarate from arginosuccinate NF005220.0 PRK06710 PRK06710.1 1116 1116 563 equivalog Y Y N long-chain-fatty-acid--CoA ligase 6.2.1.3 1386 Bacillus genus 556 NCBI Protein Cluster (PRK) long-chain-fatty-acid--CoA ligase long-chain-fatty-acid--CoA ligase Activates fatty acids by binding to coenzyme A NF005221.0 PRK06714 PRK06714.1 218 218 236 equivalog Y N N S-adenosylhomocysteine nucleosidase 1386 Bacillus genus 458 NCBI Protein Cluster (PRK) S-adenosylhomocysteine nucleosidase S-adenosylhomocysteine nucleosidase NF005223.0 PRK06719 PRK06719.1 223 223 157 equivalog Y Y N precorrin-2 dehydrogenase 1386 Bacillus genus 414 NCBI Protein Cluster (PRK) precorrin-2 dehydrogenase precorrin-2 dehydrogenase Catalyzes the formation of siroheme from precorrin-2 NF005224.0 PRK06720 PRK06720.1 207 207 169 equivalog Y N N hypothetical protein 1386 Bacillus genus 224 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005226.0 PRK06722 PRK06722.1 290 290 281 equivalog Y Y N exonuclease 1386 Bacillus genus 550 NCBI Protein Cluster (PRK) exonuclease exonuclease NF005227.0 PRK06724 PRK06724.1 146 146 128 equivalog Y N N hypothetical protein 1386 Bacillus genus 248 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005228.0 PRK06725 PRK06725.1 991 991 571 equivalog Y Y N acetolactate synthase large subunit ilvB 1386 Bacillus genus 738 NCBI Protein Cluster (PRK) acetolactate synthase 3 catalytic subunit acetolactate synthase large subunit NF005229.0 PRK06728 PRK06728.1 628 628 347 equivalog Y Y N aspartate-semialdehyde dehydrogenase 1.2.1.11 1386 Bacillus genus 578 NCBI Protein Cluster (PRK) aspartate-semialdehyde dehydrogenase aspartate-semialdehyde dehydrogenase Catalyzes the formation of aspartate semialdehyde from aspartyl phosphate NF005230.0 PRK06731 PRK06731.1 553 553 281 equivalog Y N N flagellar biosynthesis regulator FlhF 1386 Bacillus genus 652 NCBI Protein Cluster (PRK) flagellar biosynthesis regulator FlhF flagellar biosynthesis regulator FlhF NF005233.0 PRK06737 PRK06737.1 102 102 76 equivalog Y Y N ACT domain-containing protein 1386 Bacillus genus 133 NCBI Protein Cluster (PRK) acetolactate synthase 1 regulatory subunit ACT domain-containing protein NF005236.0 PRK06742 PRK06742.1 312 312 225 equivalog Y N N flagellar motor protein MotS 1386 Bacillus genus 247 NCBI Protein Cluster (PRK) flagellar motor protein MotS flagellar motor protein MotS NF005237.0 PRK06743 PRK06743.1 373 373 277 equivalog Y N N flagellar motor protein MotP 1386 Bacillus genus 341 NCBI Protein Cluster (PRK) flagellar motor protein MotP flagellar motor protein MotP NF005240.0 PRK06749 PRK06749.1 686 686 428 subfamily Y N N replicative DNA helicase 1386 Bacillus genus 1852 NCBI Protein Cluster (PRK) replicative DNA helicase replicative DNA helicase NF005242.0 PRK06752 PRK06752.1 189 189 112 equivalog Y Y N single-stranded DNA-binding protein 1386 Bacillus genus 362 NCBI Protein Cluster (PRK) single-stranded DNA-binding protein single-stranded DNA-binding protein NF005245.0 PRK06755 PRK06755.1 322 322 209 equivalog Y N N hypothetical protein 1386 Bacillus genus 183 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005247.0 PRK06758 PRK06758.1 233 233 128 equivalog Y N N hypothetical protein 1386 Bacillus genus 176 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005249.0 PRK06760 PRK06760.1 287 287 223 subfamily Y N N hypothetical protein 1386 Bacillus genus 550 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005260.0 PRK06763 PRK06763.1 226 226 213 subfamily Y N N F0F1 ATP synthase subunit alpha 1386 Bacillus genus 787 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit alpha F0F1 ATP synthase subunit alpha NF005261.0 PRK06764 PRK06764.1 176 176 105 equivalog Y N N hypothetical protein 1386 Bacillus genus 204 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005265.0 PRK06770 PRK06770.1-1 257 257 161 equivalog Y N N hypothetical protein 1386 Bacillus genus 452 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005266.0 PRK06770 PRK06770.1-2 396 396 201 equivalog Y N N hypothetical protein 1386 Bacillus genus 426 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005267.0 PRK06770 PRK06770.1-3 168 168 170 subfamily Y N N hypothetical protein 1386 Bacillus genus 188 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005268.0 PRK06770 PRK06770.1-4 277 277 188 subfamily Y N N hypothetical protein 1386 Bacillus genus 497 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005269.0 PRK06771 PRK06771.1 90 90 97 equivalog Y N N hypothetical protein 1386 Bacillus genus 394 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005289.0 PRK06807 PRK06807.1 335 335 313 equivalog Y Y N 3'-5' exonuclease 1386 Bacillus genus 615 NCBI Protein Cluster (PRK) DNA polymerase III subunit epsilon 3'-5' exonuclease NF005317.0 PRK06851 PRK06851.1-1 689 689 369 equivalog Y N N hypothetical protein 1386 Bacillus genus 515 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005524.0 PRK07168 PRK07168.1 603 603 474 equivalog Y Y N uroporphyrin-III C-methyltransferase 2.1.1.107 1386 Bacillus genus 724 NCBI Protein Cluster (PRK) bifunctional uroporphyrinogen-III methyltransferase/uroporphyrinogen-III synthase uroporphyrinogen-III C-methyltransferase NF005808.0 PRK07668 PRK07668.1 232 232 254 subfamily Y N N hypothetical protein 1386 Bacillus genus 1328 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006171.0 PRK08311 PRK08311.1-2 451 451 239 equivalog Y Y N RNA polymerase sigma factor SigI sigI 1386 Bacillus genus 333 NCBI Protein Cluster (PRK) putative RNA polymerase sigma factor SigI RNA polymerase sigma factor SigI NF006748.0 PRK09272 PRK09272.1-1 181 181 109 equivalog Y N N hypothetical protein 1386 Bacillus genus 315 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006933.0 PRK09418 PRK09418.1 1419 1419 780 equivalog Y Y N bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase cpdB 1386 Bacillus genus 1138 NCBI Protein Cluster (PRK) bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precursor protein bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase Functions during ribonucleic acid degradation; 2',3'-cyclic nucleotides are first converted to 3'-nucleotide and then cleaved to yield a ribonucleotide and a phosphate NF006935.0 PRK09419 PRK09419.1-2 2801 2801 1445 equivalog Y Y N multifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase/5'-nucleotidase 3.1.3.5,3.1.3.6,3.1.4.16 1386 Bacillus genus 177 NCBI Protein Cluster (PRK) bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precursor protein multifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase/5'-nucleotidase NF006937.0 PRK09419 PRK09419.1-4 2554 2554 1411 equivalog Y Y N multifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase/5'-nucleotidase 3.1.3.5,3.1.3.6,3.1.4.16 1386 Bacillus genus 1429 NCBI Protein Cluster (PRK) bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precursor protein multifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase/5'-nucleotidase NF007219.0 PRK09639 PRK09639.1-4 276 276 176 subfamily Y Y N RNA polymerase sigma factor SigX sigX 1386 Bacillus genus 323 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigX RNA polymerase sigma factor SigX NF007221.0 PRK09639 PRK09639.1-6 322 322 176 subfamily Y Y N RNA polymerase sigma factor SigX sigX 1386 Bacillus genus 265 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigX RNA polymerase sigma factor SigX NF007224.0 PRK09642 PRK09642.1 212 212 160 equivalog Y Y N RNA polymerase sigma factor 15126472 1386 Bacillus genus 365 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigW RNA polymerase sigma factor NF007870.0 PRK10577 PRK10577.2-1 1355 1355 678 equivalog Y Y N Fe(3+)-hydroxamate ABC transporter permease FhuB fhuB 1386 Bacillus genus 409 NCBI Protein Cluster (PRK) iron-hydroxamate transporter permease subunit Fe(3+)-hydroxamate ABC transporter permease FhuB NF008938.0 PRK12292 PRK12292.1-6 833 833 420 equivalog Y Y N ATP phosphoribosyltransferase regulatory subunit 1386 Bacillus genus 436 NCBI Protein Cluster (PRK) ATP phosphoribosyltransferase regulatory subunit ATP phosphoribosyltransferase regulatory subunit NF009066.0 PRK12400 PRK12400.1 538 538 290 equivalog Y Y N D-amino-acid transaminase 2.6.1.21 7592528,9003455 1386 Bacillus genus 430 NCBI Protein Cluster (PRK) D-amino acid aminotransferase D-amino-acid transaminase NF009113.0 PRK12463 PRK12463.1 799 799 390 equivalog Y Y N chorismate synthase aroC 4.2.3.5 1386 Bacillus genus 420 NCBI Protein Cluster (PRK) chorismate synthase chorismate synthase Catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis NF009121.0 PRK12473 PRK12473.1 241 241 198 subfamily Y N N hypothetical protein 1386 Bacillus genus 678 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF009126.0 PRK12479 PRK12479.1 518 518 299 equivalog Y Y N branched-chain-amino-acid transaminase ilvE 2.6.1.42 1386 Bacillus genus 341 NCBI Protein Cluster (PRK) branched-chain amino acid aminotransferase branched-chain-amino-acid transaminase Catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids NF009387.0 PRK12746 PRK12746.1 363 363 254 equivalog Y Y N SDR family oxidoreductase 1386 Bacillus genus 493 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF009388.0 PRK12747 PRK12747.1 376 376 252 equivalog Y N N short chain dehydrogenase 1386 Bacillus genus 399 NCBI Protein Cluster (PRK) short chain dehydrogenase short chain dehydrogenase NF009419.0 PRK12784 PRK12784.1 135 135 84 equivalog Y N N hypothetical protein 1386 Bacillus genus 198 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF009449.0 PRK12807 PRK12807.1 347 347 287 subfamily Y N N flagellin 1386 Bacillus genus 344 NCBI Protein Cluster (PRK) flagellin flagellin NF009450.0 PRK12808 PRK12808.1 476 0 476 equivalog Y N N flagellin 1386 Bacillus genus 678 NCBI Protein Cluster (PRK) flagellin flagellin NF009533.0 PRK12897 PRK12897.1 488 488 248 equivalog Y Y N type I methionyl aminopeptidase 16207374 1386 Bacillus genus 527 NCBI Protein Cluster (PRK) methionine aminopeptidase type I methionyl aminopeptidase Catalyzes the removal of N-terminal amino acids from peptides and arylamides NF009646.0 PRK13182 PRK13182.1-1 262 262 180 equivalog Y Y N chromosome-anchoring protein RacA racA 1386 Bacillus genus 254 NCBI Protein Cluster (PRK) polar chromosome segregation protein chromosome-anchoring protein RacA NF009649.0 PRK13182 PRK13182.1-5 265 265 186 equivalog Y Y N chromosome-anchoring protein RacA racA 1386 Bacillus genus 46 NCBI Protein Cluster (PRK) polar chromosome segregation protein chromosome-anchoring protein RacA NF009994.0 PRK13463 PRK13463.1 277 277 203 equivalog Y Y N phosphoserine phosphatase 1 3.1.3.3 1386 Bacillus genus 450 NCBI Protein Cluster (PRK) phosphatase PhoE phosphoserine phosphatase 1 NF010074.0 PRK13555 PRK13555.1 432 432 230 equivalog Y Y N FMN-dependent NADH-azoreductase 1.7.1.17 1386 Bacillus genus 388 NCBI Protein Cluster (PRK) azoreductase FMN-dependent NADH-azoreductase FMN-dependent; requires NADH; catalyzes the cleavage of azo bond in aromatic azo compounds NF010194.0 PRK13673 PRK13673.1-1 192 192 121 equivalog Y N N hypothetical protein 1386 Bacillus genus 180 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010211.0 PRK13676 PRK13676.1-4 200 200 118 equivalog Y Y N YlbF/YmcA family competence regulator 1386 Bacillus genus 149 NCBI Protein Cluster (PRK) hypothetical protein YlbF/YmcA family competence regulator NF010216.0 PRK13678 PRK13678.1-3 109 109 92 equivalog Y N N hypothetical protein 1386 Bacillus genus 74 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010482.0 PRK13907 PRK13907.1 231 231 128 equivalog Y N N ribonuclease H 1386 Bacillus genus 183 NCBI Protein Cluster (PRK) ribonuclease H ribonuclease H NF010601.0 PRK13997 PRK13997.1 319 319 193 equivalog Y Y N K(+)-transporting ATPase subunit C kdpC 1386 Bacillus genus 509 NCBI Protein Cluster (PRK) potassium-transporting ATPase subunit C K(+)-transporting ATPase subunit C Component of the high-affinity ATP-driven potassium transport (or KDP)system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions; the C subunit may be involved in assembly of the KDP complex NF012037.0 PRK15493 PRK15493.1 779 779 435 equivalog Y Y N bifunctional S-methyl-5'-thioadenosine deaminase/S-adenosylhomocysteine deaminase 1386 Bacillus genus 678 NCBI Protein Cluster (PRK) 5-methylthioadenosine/S-adenosylhomocysteine deaminase bifunctional S-methyl-5'-thioadenosine deaminase/S-adenosylhomocysteine deaminase NF012098.1 blaBPU 525 525 262 exception Y Y Y BPU family class D beta-lactamase blaBPU 3.5.2.6 GO:0008800 1386 Bacillus genus 358 NCBIFAM blaBPU: BPU family class D beta-lactamase BPU family class D beta-lactamase Toth, et al. (PMID:26551395) characterized BPU-1 as the founding member of a family of class D beta-lactamases native to Gram-positive bacteria. BPU-1 was characterized as an extended-spectrum beta-lactamase, with activity against penicillins, ceftazidime, and aztreonam. NF012156.1 blaP 660 660 307 exception Y Y Y class A beta-lactamase BlaP blaP 3.5.2.6 GO:0008800 1386 Bacillus genus 49 NCBIFAM blaP: class A beta-lactamase BlaP class A beta-lactamase BlaP NF017381.5 PF05560.16 Bt_P21 25 25 182 domain Y Y N P21 chaperone 2644205,9023925 1386 Bacillus genus 3 EBI-EMBL Bacillus thuringiensis P21 molecular chaperone protein P21 chaperone This family contains several Bacillus thuringiensis P21 proteins. These proteins are thought to be molecular chaperones and have mosquitocidal properties [1,2]. [1]. 2644205. A 20-kilodalton protein is required for efficient production of the Bacillus thuringiensis subsp. israelensis 27-kilodalton crystal protein in Escherichia coli. Adams LF, Visick JE, Whiteley HR;. J Bacteriol 1989;171:521-530. [2]. 9023925. Identification of a gene for Cyt1A-like hemolysin from Bacillus thuringiensis subsp. medellin and expression in a crystal-negative B. thuringiensis strain. Thiery I, Delecluse A, Tamayo MC, Orduz S;. Appl Environ Microbiol 1997;63:468-473. (from Pfam) NF017752.5 PF05968.16 Bacillus_PapR 27 27 48 PfamEq Y Y N quorum-sensing peptide PapR 12198157 1386 Bacillus genus 117 EBI-EMBL Bacillus PapR protein quorum-sensing peptide PapR This family consists of the Bacillus species specific PapR protein. The papR gene belongs to the PlcR regulon and is located 70 bp downstream from plcR. It encodes a 48-amino-acid peptide. Disruption of the papR gene abolishes expression of the PlcR regulon, resulting in a large decrease in haemolysis and virulence in insect larvae. A processed form of PapR activates the PlcR regulon by allowing PlcR to bind to its DNA target. This activating mechanism is strain specific [1]. [1]. 12198157. A cell-cell signaling peptide activates the PlcR virulence regulon in bacteria of the Bacillus cereus group. Slamti L, Lereclus D;. EMBO J 2002;21:4550-4559. (from Pfam) NF023545.5 PF12123.13 CBD_PlyG 28.2 28.2 44 domain Y Y N N-acetylmuramoyl-L-alanine amidase C-terminal domain-containing protein 17888883 1386 Bacillus genus 2193 EBI-EMBL PlyG Cell wall binding domain PlyG Cell wall binding domain This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is thought to be a cell wall binding domain [1]. [1]. 17888883. Identification of the amino acid residues critical for specific binding of the bacteriolytic enzyme of gamma-phage, PlyG, to Bacillus anthracis. Kikkawa H, Fujinami Y, Suzuki S, Yasuda J;. Biochem Biophys Res Commun. 2007;363:531-535. (from Pfam) NF024433.5 PF13033.11 DUF3894 25 25 54 PfamAutoEq Y Y N DUF3894 domain-containing protein 1386 Bacillus genus 149 EBI-EMBL Protein of unknown function (DUF3894) Protein of unknown function (DUF3894) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 66 and 79 amino acids in length. There are two conserved sequence motifs: FNIC and MALLNLT. (from Pfam) NF024442.5 PF13042.11 DUF3902 25 25 161 PfamAutoEq Y Y N DUF3902 family protein 1386 Bacillus genus 1056 EBI-EMBL Protein of unknown function (DUF3902) DUF3902 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 170 amino acids in length. There is a conserved LGI sequence motif. (from Pfam) NF024443.5 PF13043.11 DUF3903 26.4 26.4 40 PfamAutoEq Y Y N DUF3903 domain-containing protein 1386 Bacillus genus 189 EBI-EMBL Domain of unknown function (DUF3903) Domain of unknown function (DUF3903) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 40 amino acids in length. (from Pfam) NF024449.5 PF13049.11 DUF3910 37.8 37.8 95 PfamAutoEq Y Y N DUF3910 family protein 1386 Bacillus genus 455 EBI-EMBL Protein of unknown function (DUF3910) DUF3910 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. (from Pfam) NF024450.5 PF13050.11 DUF3911 25 25 78 PfamAutoEq Y Y N DUF3911 family protein 1386 Bacillus genus 160 EBI-EMBL Protein of unknown function (DUF3911) DUF3911 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. (from Pfam) NF024452.5 PF13052.11 DUF3913 25 25 57 PfamAutoEq Y Y N DUF3913 family protein 1386 Bacillus genus 85 EBI-EMBL Protein of unknown function (DUF3913) DUF3913 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. (from Pfam) NF024453.5 PF13053.11 DUF3914 25 25 89 PfamAutoEq Y Y N DUF3914 domain-containing protein 1386 Bacillus genus 434 EBI-EMBL Protein of unknown function (DUF3914) Protein of unknown function (DUF3914) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. There are two conserved sequence motifs: KFDIR and DLW. (from Pfam) NF024454.5 PF13054.11 DUF3915 26.9 26.9 126 PfamAutoEq Y Y N DUF3915 family protein 1386 Bacillus genus 307 EBI-EMBL Protein of unknown function (DUF3915) DUF3915 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. (from Pfam) NF024455.5 PF13055.11 DUF3917 25.1 25.1 71 PfamAutoEq Y Y N DUF3917 domain-containing protein 1386 Bacillus genus 148 EBI-EMBL Protein of unknown function (DUF3917) Protein of unknown function (DUF3917) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. (from Pfam) NF024459.5 PF13059.11 DUF3922 25 25 79 PfamAutoEq Y Y N DUF3992 domain-containing protein 1386 Bacillus genus 350 EBI-EMBL Protein of unknown function (DUF3992) Protein of unknown function (DUF3992) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 87 and 98 amino acids in length. (from Pfam) NF024460.5 PF13060.11 DUF3921 25 25 58 PfamAutoEq Y Y N DUF3921 family protein 1386 Bacillus genus 142 EBI-EMBL Protein of unknown function (DUF3921) DUF3921 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. (from Pfam) NF024463.5 PF13063.11 DUF3925 25 25 65 PfamAutoEq Y Y N DUF3925 family protein 1386 Bacillus genus 188 EBI-EMBL Protein of unknown function (DUF3925) DUF3925 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. (from Pfam) NF024465.5 PF13065.11 DUF3928 30.3 30.3 95 PfamAutoEq Y Y N DUF3928 family protein 1386 Bacillus genus 153 EBI-EMBL Protein of unknown function (DUF3928) DUF3928 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. (from Pfam) NF024466.5 PF13066.11 DUF3929 25 25 64 PfamAutoEq Y Y N DUF3929 family protein 1386 Bacillus genus 73 EBI-EMBL Protein of unknown function (DUF3929) DUF3929 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. (from Pfam) NF024467.5 PF13067.11 DUF3930 25 25 51 PfamAutoEq Y Y N DUF3930 family protein 1386 Bacillus genus 141 EBI-EMBL Protein of unknown function (DUF3930) DUF3930 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 51 and 67 amino acids in length. (from Pfam) NF024468.5 PF13068.11 DUF3932 25 25 81 PfamAutoEq Y Y N DUF3932 family protein 1386 Bacillus genus 153 EBI-EMBL Protein of unknown function (DUF3932) DUF3932 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. (from Pfam) NF024473.5 PF13073.11 DUF3937 22.5 22.5 72 PfamAutoEq Y Y N DUF3937 family protein 1386 Bacillus genus 363 EBI-EMBL Protein of unknown function (DUF3937) DUF3937 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. (from Pfam) NF024474.5 PF13074.11 DUF3938 25 25 98 PfamAutoEq Y Y N DUF3938 domain-containing protein 1386 Bacillus genus 208 EBI-EMBL Protein of unknown function (DUF3938) Protein of unknown function (DUF3938) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. (from Pfam) NF024478.5 PF13078.11 DUF3942 25 25 137 PfamAutoEq Y Y N DUF3942 family protein 1386 Bacillus genus 327 EBI-EMBL Protein of unknown function (DUF3942) DUF3942 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. (from Pfam) NF024480.5 PF13080.11 DUF3926 26.4 26.4 43 PfamAutoEq Y Y N DUF3926 domain-containing protein 1386 Bacillus genus 282 EBI-EMBL Protein of unknown function (DUF3926) Protein of unknown function (DUF3926) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 46 and 63 amino acids in length. There is a single completely conserved residue P that may be functionally important. (from Pfam) NF024482.5 PF13082.11 DUF3931 25 25 66 PfamAutoEq Y Y N DUF3931 domain-containing protein 1386 Bacillus genus 59 EBI-EMBL Protein of unknown function (DUF3931) Protein of unknown function (DUF3931) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. (from Pfam) NF024504.5 PF13104.11 DUF3956 22.3 22.3 45 domain Y Y N DUF3956 family protein 1386 Bacillus genus 182 EBI-EMBL Protein of unknown function (DUF3956) DUF3956 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. (from Pfam) NF024505.5 PF13105.11 DUF3959 25 25 238 PfamAutoEq Y Y N DUF3959 family protein 1386 Bacillus genus 621 EBI-EMBL Protein of unknown function (DUF3959) DUF3959 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 260 amino acids in length. (from Pfam) NF024506.5 PF13106.11 DUF3961 25 25 39 PfamAutoEq Y Y N DUF3961 domain-containing protein 1386 Bacillus genus 499 EBI-EMBL Domain of unknown function (DUF3961) Domain of unknown function (DUF3961) This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 40 amino acids in length. (from Pfam) NF024512.5 PF13112.11 DUF3965 22.1 22.1 291 PfamAutoEq Y Y N DUF3965 domain-containing protein 1386 Bacillus genus 391 EBI-EMBL Protein of unknown function (DUF3965) Protein of unknown function (DUF3965) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 380 amino acids in length. (from Pfam) NF024520.5 PF13120.11 DUF3974 25 25 126 PfamAutoEq Y Y N DUF3974 domain-containing protein 1386 Bacillus genus 380 EBI-EMBL Domain of unknown function (DUF3974) Domain of unknown function (DUF3974) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 130 amino acids in length. (from Pfam) NF024521.5 PF13121.11 DUF3976 25 25 40 PfamAutoEq Y Y N DUF3976 domain-containing protein 1386 Bacillus genus 152 EBI-EMBL Domain of unknown function (DUF3976) Domain of unknown function (DUF3976) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 40 amino acids in length. (from Pfam) NF024523.5 PF13123.11 DUF3978 25 25 144 PfamAutoEq Y Y N DUF3978 family protein 1386 Bacillus genus 224 EBI-EMBL Protein of unknown function (DUF3978) DUF3978 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length. (from Pfam) NF024524.5 PF13124.11 DUF3963 25 25 40 PfamAutoEq Y Y N DUF3963 domain-containing protein 1386 Bacillus genus 274 EBI-EMBL Protein of unknown function (DUF3963) Protein of unknown function (DUF3963) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 42 and 85 amino acids in length. There is a conserved DIQKW sequence motif. (from Pfam) NF024526.5 PF13126.11 DUF3975 25 25 80 PfamAutoEq Y Y N DUF3975 family protein 1386 Bacillus genus 373 EBI-EMBL Protein of unknown function (DUF3975) DUF3975 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. (from Pfam) NF024530.5 PF13130.11 DUF3952 25 25 101 domain Y Y N DUF3952 domain-containing protein 1386 Bacillus genus 1258 EBI-EMBL Domain of unknown function (DUF3952) Domain of unknown function (DUF3952) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 110 amino acids in length. There is a conserved VMSAS sequence motif. (from Pfam) NF024539.5 PF13139.11 DUF3981 25 25 115 PfamAutoEq Y Y N DUF3981 domain-containing protein 1386 Bacillus genus 541 EBI-EMBL Domain of unknown function (DUF3981) Domain of unknown function (DUF3981) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 110 amino acids in length. (from Pfam) NF024540.5 PF13140.11 DUF3980 25 25 87 PfamAutoEq Y Y N DUF3980 domain-containing protein 1386 Bacillus genus 490 EBI-EMBL Domain of unknown function (DUF3980) Domain of unknown function (DUF3980) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 90 amino acids in length. (from Pfam) NF024541.5 PF13141.11 DUF3979 25 25 115 PfamAutoEq Y Y N DUF3979 family protein 1386 Bacillus genus 270 EBI-EMBL Protein of unknown function (DUF3979) DUF3979 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. (from Pfam) NF024542.5 PF13142.11 DUF3960 22.9 22.9 89 PfamAutoEq Y Y N DUF3960 domain-containing protein 1386 Bacillus genus 377 EBI-EMBL Domain of unknown function (DUF3960) Domain of unknown function (DUF3960) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically between 72 and 89 amino acids in length. (from Pfam) NF024608.5 PF13210.11 DUF4018 25 25 198 PfamAutoEq Y Y N DUF4018 domain-containing protein 1386 Bacillus genus 927 EBI-EMBL Domain of unknown function (DUF4018) Domain of unknown function (DUF4018) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 190 amino acids in length. (from Pfam) NF024612.5 PF13214.11 DUF4022 25 25 77 PfamAutoEq Y Y N DUF4022 family protein 1386 Bacillus genus 223 EBI-EMBL Protein of unknown function (DUF4022) DUF4022 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 73 and 85 amino acids in length. (from Pfam) NF024618.5 PF13220.11 DUF4028 25 25 65 PfamAutoEq Y Y N DUF4028 family protein 1386 Bacillus genus 257 EBI-EMBL Protein of unknown function (DUF4028) DUF4028 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 67 and 93 amino acids in length. There are two conserved sequence motifs: IVKI and YVKKWF. (from Pfam) NF024619.5 PF13221.11 DUF4029 25 25 96 PfamAutoEq Y Y N DUF4029 domain-containing protein 1386 Bacillus genus 372 EBI-EMBL Protein of unknown function (DUF4029) Protein of unknown function (DUF4029) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 95 and 119 amino acids in length. (from Pfam) NF024658.5 PF13261.11 DUF4052 25 25 217 PfamAutoEq Y Y N DUF4052 family protein 1386 Bacillus genus 526 EBI-EMBL Protein of unknown function (DUF4052) DUF4052 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 220 amino acids in length. (from Pfam) NF024690.5 PF13294.11 DUF4075 25 25 79 PfamAutoEq Y Y N DUF4075 domain-containing protein 1386 Bacillus genus 234 EBI-EMBL Domain of unknown function (DUF4075) Domain of unknown function (DUF4075) The members of this family are putative mature parasite-infected erythrocyte surface antigen protein from Bacillus spp. (from Pfam) NF024691.5 PF13295.11 DUF4077 25 25 172 PfamAutoEq Y Y N DUF4077 domain-containing protein 1386 Bacillus genus 667 EBI-EMBL Domain of unknown function (DUF4077) Domain of unknown function (DUF4077) This is the N-terminal region of methyl-accepting chemotaxis proteins from Bacillus spp. The function is not known. (from Pfam) NF025522.5 PF14157.11 YmzC 27 27 62 domain Y Y N YmzC family protein 1386 Bacillus genus 649 EBI-EMBL YmzC-like protein YmzC family protein The YmzC-like protein family includes the B. subtilis YmzC protein Swiss:O31797, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 91 amino acids in length. There is a conserved ELR sequence motif. (from Pfam) NF025804.5 PF14448.11 Nuc_N 25 25 58 domain Y N N Nuclease N terminal 21306995 1386 Bacillus genus 1103 EBI-EMBL Nuclease N terminal Nuclease N terminal This is a conserved short region that is found in many bacterial polymorphic toxin proteins [1]. It is often located before C-terminal nuclease domains [1]. [1]. 21306995. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Zhang D, Iyer LM, Aravind L;. Nucleic Acids Res. 2011;39:4532-4552. (from Pfam) NF028033.5 PF16723.10 DUF5065 26.8 26.8 156 subfamily Y Y N DUF5065 family protein 1386 Bacillus genus 892 EBI-EMBL Domain of unknown function (DUF5065) DUF5065 family protein This family is found in found in Bacillus species. The function is not known. (from Pfam) NF033095.1 bla_Bc_2 500 500 255 exception Y Y Y BcII family subclass B1 metallo-beta-lactamase bla2 3.5.2.6 GO:0008800 1386 Bacillus genus 523 NCBIFAM BcII family subclass B1 metallo-beta-lactamase BcII family subclass B1 metallo-beta-lactamase NF033096.1 bla1 630 630 307 exception Y Y Y class A beta-lactamase Bla1 bla 3.5.2.6 GO:0008800 1386 Bacillus genus 789 NCBIFAM class A beta-lactamase Bla1 class A beta-lactamase Bla1 Member of this family are class A beta-lactamases in Bacillus cereus (where it was named beta-lactamase 1, or bla1), B. anthracis, B. thuringiensis, and other closely related species from the genus Bacillus. The enzyme may be poorly expressed in B. anthracis and fail to confer penicillin resistance. Protein heterologously expressed in E. coli confers strong resistance to a variety of penicillins, but not to the cephalosporins or carbapenems tested. NF033190.2 inl_like_NEAT_1 1275 1275 754 exception Y Y N NEAT domain-containing leucine-rich repeat protein 1386 Bacillus genus 767 NCBIFAM NEAT domain-containing leucine-rich repeat protein NEAT domain-containing leucine-rich repeat protein Members of this family have an N-terminal NEAT (near transporter) domain often associated with iron transport, followed by a leucine-rich repeat region with significant sequence similarity to the internalins of Listeria monocytogenes. However, since Bacillus cereus (from which this protein was described, in PMID:16978259) is not considered an intracellular pathogen, and the function may be iron transport rather than internalization, applying the name "internalin" to this family probably would be misleading. NF033800.1 quorum_NprX 75 75 43 equivalog Y Y N quorum-signaling peptide NprX nprX 23388036,29075240 1386 Bacillus genus 28 NCBIFAM quorum-signaling peptide NprX quorum-signaling peptide NprX NprX, also called NprRB, belongs to the NprR-NprX quorum-sensing system in Bacillus. The mature form of the peptide pheromone is the SKPDIVG heptapeptide. NF033801.3 NprX_fam 33 33 42 subfamily Y Y N NprX family peptide pheromone 23388036,29075240 1386 Bacillus genus 145 NCBIFAM NprX family peptide pheromone NprX family peptide pheromone NF036962.5 PF17633.7 DUF5514 27 27 142 subfamily Y Y N DUF5514 family protein 1386 Bacillus genus 178 EBI-EMBL Family of unknown function (DUF5514) DUF5514 family protein This is a family of unknown function found in Bacillus. (from Pfam) NF037599.5 PF17631.7 DUF5512 27 27 139 domain Y Y N DUF5512 family protein 1386 Bacillus genus 134 EBI-EMBL Family of unknown function (DUF5512) DUF5512 family protein This is a family of unknown function found in Bacillus. (from Pfam) NF038057.1 macrolide_MphL 612 612 298 exception Y Y Y macrolide 2'-phosphotransferase MphL mphL 1386 Bacillus genus 149 NCBIFAM macrolide 2'-phosphotransferase MphL NF040670.1 wall_bind_EntA 560 560 291 exception Y Y N cell wall-binding protein EntA 27757102 1386 Bacillus genus 579 NCBIFAM cell wall-binding protein EntA This HMM describes the cell wall-binding protein EntA, as found in Bacillus cereus. EntA is related to EntB, EntC, and EndD, but it lacks the central region of KAXEXX repeats that EntB and EndC have. EntD also lacks those repeats. Ent proteins have a signal peptide, an N-terminal SH3 domain and a C-terminal 3D (Asp-Asp-Asp) domain. NF040675.1 wall_bind_EntD 590 590 310 exception Y Y N cell wall-binding protein EntD entD 26500610,27757102 1386 Bacillus genus 435 NCBIFAM cell wall-binding protein EntD This HMM describes the cell wall-binding protein EntD, as found in Bacillus cereus. EntD, like its close homolog EntA, is related to EntB and EntC, but lacks the central region of KAXEXX repeats that EntB and EndC share. Ent proteins have a signal peptide, an N-terminal SH3 domain and a C-terminal 3D (Asp-Asp-Asp) domain. They may play a role in maintenance of cell wall structure and stress responses that support virulence, and probably lack any direct role as enterotoxins. NF040676.1 wall_bind_EntB 780 400 490 exception Y Y N cell wall-binding protein EntB entB 27757102 1386 Bacillus genus 1301 NCBIFAM cell wall-binding protein EntB This HMM describes the cell wall-binding protein EntB, as found in Bacillus cereus. EntB is related to EntA, EntC, and EndD. All Ent family proteins have a signal peptide, an N-terminal SH3 domain and a C-terminal 3D (Asp-Asp-Asp) domain. EntB and EndC have a central region with a highly variable number of repeats resembling KAXEXX. The gene symbol derives from the notion that at least some members of the family function as enterotoxins, but more recent descriptions focus on roles in stress response and cell wall integrity. NF040677.1 wall_bind_EntC 770 440 422 exception Y Y N cell wall-binding protein EntC entC 27757102 1386 Bacillus genus 1284 NCBIFAM cell wall-binding protein EntC This HMM describes the cell wall-binding protein EntC, as found in Bacillus cereus. EntC is related to EntA, EntB, and EndD. All Ent family proteins have a signal peptide, an N-terminal SH3 domain and a C-terminal 3D (Asp-Asp-Asp) domain. EntB and EndC have a central region with a highly variable number of repeats resembling KAXEXX. The gene symbol derives from the notion that at least some members of the family function as enterotoxins, but more recent descriptions focus on roles in stress response and cell wall integrity. NF040678.1 EntFM_CwpFM 720 720 430 equivalog Y Y Y enterotoxin EntFM entFM 18068844,20233921,9055420 1386 Bacillus genus 682 NCBIFAM enterotoxin EntFM EntFM (enterotoxin FM), originally described in Bacillus cereus strain FM-1, has repeated been shown to function as a toxin for eukaryotic cell lines, although the mechanism is not clearly described. The C-terminal region contains a NlpC/P60 domain, suggesting bacterial cell wall peptidase activity. NF041270.1 bla_Bcer_III 670 670 314 exception Y Y Y class A beta-lactamase BlaIII blaIII 3.5.2.6 GO:0008800 26511485,3027036,6414514 1386 Bacillus genus 426 NCBIFAM class A beta-lactamase BlaIII Members of this family of class A beta-lactamases, including the founding member from Bacillus cereus, are now referred to as BlaIII (or Bla3) in both name and gene symbo, as the symbol blaZ now far refers much more frequently to a distantly related class A enzyme from Staphylococcus. BlaIII has a lipoprotein-type signal peptide and is membrane-associated. NF041469.1 spor_prot_SB 110 110 58 equivalog Y Y N stage II sporulation protein SB spoIISB 18096016 1386 Bacillus genus 256 NCBIFAM stage II sporulation protein SB NF041541.1 fosBx1_fam 290 290 138 exception Y Y Y FosBx1 family fosfomycin resistance bacillithiol transferase fosB 24004181,34989942 1386 Bacillus genus 298 NCBIFAM FosBx1 family fosfomycin resistance bacillithiol transferase Members of this family, found in Bacillus cereus and related species that synthesis bacillithiol rather than glutathione, are VOC family thiol transferases. They provide resistance to the antibiotic fosfomycin by transferring either bacillithiol or cysteine (but not glutathione) to fosfomycin, leaving it inactive. Note that this family is drawn rather narrowly, and several such families, all non-overlapping, appear in B. cereus and its close relatives. This family includes proteins that have been named FosBx1 (although the original source of that name is hard to trace), and the protein studied crystallographically by Thompson, et al. (see PMID:24004181). NF041643.1 EAxFAS_anti 27 27 35 domain N N N EAxFAS motif-containing spurious protein 1386 Bacillus genus 836 NCBIFAM EAxFAS motif-containing spurious protein Spurious proteins belonging to this family occur in the Bacillus genus, in an intergenic region with a variable number of repeats. Translations in the frame of this AntiFam-type HMM typically contain an EAxFAS motif. NF041752.4 sbcc_Bac 1420 1420 1130 equivalog Y Y N exonuclease subunit SbcC sbcC 3.1.11.- GO:0004527,GO:0006260,GO:0006310 16780573,19906728 1386 Bacillus genus 1203 NCBIFAM exonuclease subunit SbcC NF041883.1 RNase_A_lipo 200 200 168 exception Y Y N RNase A-like domain-containing lipoprotein 28398546 1386 Bacillus genus 284 NCBIFAM RNase A-like domain-containing lipoprotein The RNase domain that constitutes the majority of the length of proteins in this family was described originally as the C-terminal effector domain of large CDI (contact-dependent growth inhibition) toxins in Gram-negative bacteria, some several thousand amino acids long. However, the members of this family are small lipoproteins, about 170 amino acids in length, found in Gram-positive bacteria. NF044506.2 PF21567.2 Gp22 27 27 117 domain Y N N Gp22 20506290 1386 Bacillus genus 171 EBI-EMBL Gp22 Gp22 This protein family includes Gp22 from Bacillus phage SPP1 (Swiss:O48465), an protein that shows a significant structural similarity with the N-terminal shoulder domain (Pfam:PF20747) of Receptor binding protein from Lactococcus phage p2 (RBP). It folds into two small three-stranded antiparallel beta-sheets and one large five-stranded mixed beta-sheet forming a pseudo-beta-sandwich [1]. Paper describing PDB structure 2xc8. [1]. 20506290. Crystal structure of Bacillus subtilis SPP1 phage gp22 shares fold similarity with a domain of lactococcal phage p2 RBP. Veesler D, Blangy S, Spinelli S, Tavares P, Campanacci V, Cambillau C;. Protein Sci. 2010;19:1439-1443. (from Pfam) NF045821.1 PgAcgDacpgdA1_Bac 400 400 282 equivalog Y Y N peptidoglycan-N-acetylglucosamine deacetylase 3.5.1.104 GO:0005975,GO:0016810 15961396,18323609,29983281 1386 Bacillus genus 600 NCBIFAM peptidoglycan-N-acetylglucosamine deacetylase NF045822.1 PgAcgDacpgdA2_Bac 400 400 274 equivalog Y Y N peptidoglycan-N-acetylglucosamine deacetylase 3.5.1.104 GO:0005975,GO:0016810 29983281 1386 Bacillus genus 1290 NCBIFAM peptidoglycan-N-acetylglucosamine deacetylase NF046032.1 TransRegSlrRBacil 250 250 149 equivalog Y Y N HTH-type transcriptional regulator SlrR slrR GO:0006355 18430133,18647168 1386 Bacillus genus 235 NCBIFAM HTH-type transcriptional regulator SlrR NF046066.1 BioflmMtrxTasA 450 450 264 equivalog Y Y N biofilm matrix protein TasA tasA GO:0030435,GO:0042802 10368135,16430696,29531041 1386 Bacillus genus 282 NCBIFAM biofilm matrix protein TasA NF046200.1 PF22146.1 LicP_NPro 27 27 61 domain Y N N LicP N-terminal prodomain 30090246 1386 Bacillus genus 11 EBI-EMBL LicP N-terminal prodomain LicP N-terminal prodomain LicP is a class II LanP protease that is involved in the biosynthesis of the lantibiotic lichenicidin. This enzyme is an extracellularly located serine protease expressed by some strains of Bacillus licheniformis and undergoes a self-cleavage maturation resulting in two fragments, the N-terminal prodomain and the C-terminal catalytic protease domain. The prodomain folds into a single compact domain consisting of four antiparallel beta-strands interconnected with two helices [1]. Paper describing PDB structure 4zoq. [1]. 30090246. Applications of the class II lanthipeptide protease LicP for sequence-specific, traceless peptide bond cleavage. Tang W, Dong SH, Repka LM, He C, Nair SK, van der Donk WA;. Chem Sci. 2015;6:6270-6279. (from Pfam) NF046515.1 PF22127.1 NtdA_N 27 27 66 domain Y N N NTD biosynthesis operon protein NtdA, N-terminal domain 24097983 1386 Bacillus genus 353 EBI-EMBL NTD biosynthesis operon protein NtdA, N-terminal domain NTD biosynthesis operon protein NtdA, N-terminal domain This entry represents the N-terminal domain of NtdA, which is not found in other aminotransferases and consists of two-stranded parallel beta-sheet flanked by two alpha-helices [1]. This domain may be involved in protein-protein interactions. NtdA is a sugar aminotransferase involved in the biosynthesis of kanosamine. Paper describing PDB structure 4k2b. [1]. 24097983. The structure of NtdA, a sugar aminotransferase involved in the kanosamine biosynthetic pathway in Bacillus subtilis, reveals a new subclass of aminotransferases. van Straaten KE, Ko JB, Jagdhane R, Anjum S, Palmer DRJ, Sanders DAR;. J Biol Chem. 2013;288:34121-34130. (from Pfam) NF046649.1 PF22372.1 BA_2335-like 27 27 59 domain Y N N BA_2335-like 1386 Bacillus genus 243 EBI-EMBL BA_2335-like BA_2335-like This protein family includes the uncharacterised protein BA_2335 from Bacillus anthracis and similar sequences from Bacilli. It adopts a beta-sandwich configuration. (from Pfam) NF046755.1 PF22501.1 DUF6991 26 26 66 domain Y Y N DUF6991 domain-containing protein 1386 Bacillus genus 1173 EBI-EMBL Domain of unknown function (DUF6991) Domain of unknown function (DUF6991) This entry represents a C-terminal domain of a functionally unknown conserved protein from Bacillus anthracis (PDB:4fca). (from Pfam) NF046992.1 PF22872.1 DUF7018 27.8 27.8 116 domain Y Y N DUF7018 domain-containing (lipo)protein 1386 Bacillus genus 1730 EBI-EMBL Domain of unknown function (DUF7018) DUF7018 domain Most members of this family appear to be lipoproteins. NF047535.1 small_SR7P 45 45 42 equivalog Y Y N small protein SR7P sr7p 32752915,34066298,37994189 1386 Bacillus genus 102 NCBIFAM small protein SR7P SR7P is a small protein, about 40 amino acids in length, translated from a reading frame in the dual-function antisense RNA SR7 of Bacillus subtilis and many other Bacillus species. SR7P interacts with enolase, which serves as a scaffolding protein in the Bacillus form of the RNA degradosome, and increases the amount of RNase Y bound to enolase. TIGR01631.1 TIGR01631 Trypano_RHS 89.75 89.75 761 paralog N N N trypanosome RHS family 1386 Bacillus genus 1 JCVI trypanosome RHS family trypanosome RHS family This fragment-mode HMM describes full-length and part-length members of the RHS (retrotransposon hot spot) family in Trypanosoma brucei and Trypanosoma cruzi. Members of this family are frequently interrupted by non-LTR retrotransposons inserted at exactly the same relative position. TIGR04196.1 TIGR04196 glycopep_SunS 40 40 80 subfamily Y Y N sublancin family glycopeptide sunA 21196935 1386 Bacillus genus 19 JCVI glycopeptide, sublancin family sublancin family glycopeptide Members of this family, including sublancin, are post-ribosomal natural products (PRNP) with an S-linked glycosylation. Sublancin itself also has two disulfide bonds. A related gene cluster in Bacillus cereus E33L includes the four Cys involved in the disulfide cluster but lacks the region with the glycosylated Cys. These score ~ 27 by this HMMER3 model and are excluded. NF044919.2 PF20835.2 PA_Ig-like 27 27 155 domain Y N N Anthrax protective antigen, immunoglobulin-like domain 15243628,15326297,19361425,19627991,19722284,9039918 1392 Bacillus anthracis species 35 EBI-EMBL Anthrax protective antigen, immunoglobulin-like domain Anthrax protective antigen, immunoglobulin-like domain Anthrax protective antigen (PA) is one of the three proteins forming the anthrax toxin. It is involved in the first step of toxin entry into host cells, enabling lethal factor (LF) and oedema factor (EF) to cross to the cytosol. PA undergoes cleavage by Furin to generate PA20 and PA63. The latter, which adopts a ring-shaped heptameric assembly, shows four distinct domains. The fourth domain, a carboxy- terminal receptor-binding domain, shows an initial hairpin and helix, followed by a beta-sandwich with an immunoglobulin-like fold (this entry) [1-5]. Paper describing PDB structure 1acc. [1]. 9039918. Crystal structure of the anthrax toxin protective antigen. Petosa C, Collier RJ, Klimpel KR, Leppla SH, Liddington RC;. Nature. 1997;385:833-838. Paper describing PDB structure 1t6b. [2]. 15243628. Crystal structure of a complex between anthrax toxin and its host cell receptor. Santelli E, Bankston LA, Leppla SH, Liddington RC;. Nature. 2004;430:905-908. Paper describing PDB structure 1tzn. [3]. 15326297. Structure of heptameric protective antigen bound to an anthrax toxin receptor: a role for receptor in pH-dependent pore formation. Lacy DB, Wigelsworth DJ, Melnyk RA, Harrison SC, Collier RJ;. Proc Natl Acad Sci U S A. 2004;101:13147-13151. Paper describing PDB structure 3etb. [4]. 19361425. Crystal structure of the engineered neutralizing antibody M18 complexed to domain 4 of the anthrax protective antigen. Leysath CE, Monzingo AF, Maynard JA, Barnett J, Georgiou G, Iverson BL, Robertus JD;. J Mol Biol. 2009;387:680-693. Paper describing PDB structure 3hvd. [5]. 19627991. The protective antigen component of anthrax toxin fo. TRUNCATED at 1650 bytes (from Pfam) NF023285.5 PF11857.13 DUF3377 26.5 26.5 72 domain Y Y N DUF3377 domain-containing protein GO:0004222 1392758 Rhizocola hellebori species 1 EBI-EMBL Domain of unknown function (DUF3377) Domain of unknown function (DUF3377) This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is about 70 amino acids in length. (from Pfam) TIGR01678.1 TIGR01678 FAD_lactone_ox 396.8 396.8 438 subfamily Y Y N sugar 1,4-lactone oxidase 1396 Bacillus cereus species 2 JCVI sugar 1,4-lactone oxidases sugar 1,4-lactone oxidase This HMM represents a family of at least two different sugar 1,4 lactone oxidases, both involved in synthesizing ascorbic acid or a derivative. These include L-gulonolactone oxidase (EC 1.1.3.8) from rat and D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) from Saccharomyces cerevisiae. Members are proposed to have the cofactor FAD covalently bound at a site specified by Prosite motif PS00862; OX2_COVAL_FAD; 1. TIGR00860.1 TIGR00860 LIC 280.2 280.2 462 subfamily N N N cation transporter family protein 1401 Paenibacillus lautus species 1 JCVI cation transporter family protein cation transporter family protein The Ligand-gated Ion Channel (LIC) Family of Neurotransmitter Receptors TC 1.A.9) Members of the LIC family of ionotropic neurotransmitter receptors are found only in vertebrate and invertebrate animals. They exhibit receptor specificity for (1) acetylcholine, (2) serotonin, (3) glycine, (4) glutamate and (5) g-aminobutyric acid (GABA). All of these receptor channels are probably hetero- or homopentameric. The best characterized are the nicotinic acetyl-choline receptors which are pentameric channels of a2bgd subunit composition. All subunits are homologous. The three dimensional structures of the protein complex in both the open and closed configurations have been solved at 0.9 nm resolution. The channel protein complexes of the LIC family preferentially transport cations or anions depending on the channel (e.g., the acetylcholine receptors are cation selective while glycine receptors are anion selective). NF002178.0 PRK01022 PRK01022.2-1 351 351 178 equivalog Y N N hypothetical protein 145260 Methanothermobacter genus 13 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002180.0 PRK01022 PRK01022.2-5 268 268 166 equivalog Y N N hypothetical protein 145260 Methanothermobacter genus 13 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004932.0 PRK06287 PRK06287.1-3 191 191 105 equivalog Y N N cobalt transport protein CbiN 145260 Methanothermobacter genus 10 NCBI Protein Cluster (PRK) cobalt transport protein CbiN cobalt transport protein CbiN TIGR00588.1 TIGR00588 ogg 397.85 397.85 310 subfamily N N N 8-oxoguanine DNA-glycosylase (ogg) GO:0006284 21220122,30442810 145260 Methanothermobacter genus 4 JCVI 8-oxoguanine DNA-glycosylase (ogg) 8-oxoguanine DNA-glycosylase (ogg) All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily. NF046629.1 PF22291.1 DUF6964 24.5 24.5 36 domain Y Y N DUF6964 domain-containing protein 146918 Salinibacter genus 81 EBI-EMBL Family of unknown function (DUF6964) Family of unknown function (DUF6964) This short helical domain is found in a small set of ribosomal S1 proteins. It's function is unknown. (from Pfam) NF001074.0 PRK00118 PRK00118.2-4 186 186 110 equivalog Y Y N putative DNA-binding protein 1485 Clostridium genus 14 NCBI Protein Cluster (PRK) putative DNA-binding protein putative DNA-binding protein NF002052.0 PRK00886 PRK00886.1-1 440 440 239 equivalog Y Y N 2-phosphosulfolactate phosphatase family protein 1485 Clostridium genus 37 NCBI Protein Cluster (PRK) 2-phosphosulfolactate phosphatase 2-phosphosulfolactate phosphatase family protein This bacterial enzyme is related to archaeal 2-phosphosulfolactate phosphatase, involved in biosynthesis of coenzyme M, a cofactor involved in methanogenesis in the archaea. It may differ in function. NF005320.0 PRK06851 PRK06851.1-6 556 556 363 equivalog Y N N hypothetical protein 1485 Clostridium genus 78 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006062.0 PRK08207 PRK08207.1-5 1007 1007 476 equivalog Y Y N coproporphyrinogen III oxidase 1485 Clostridium genus 55 NCBI Protein Cluster (PRK) coproporphyrinogen III oxidase coproporphyrinogen III oxidase NF008891.0 PRK11924 PRK11924.1-5 259 259 171 subfamily Y N N RNA polymerase sigma factor 1485 Clostridium genus 38 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009984.0 PRK13450 PRK13450.1 164 164 133 equivalog Y Y N F0F1 ATP synthase subunit epsilon 7.1.2.2 1485 Clostridium genus 162 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit epsilon F0F1 ATP synthase subunit epsilon Produces ATP from ADP in the presence of a proton gradient across the membrane; the epsilon subunit is part of the catalytic core of the ATP synthase complex NF010732.0 PRK14134 PRK14134.1 351 351 283 equivalog Y Y N recombination regulator RecX recX 1485 Clostridium genus 114 NCBI Protein Cluster (PRK) recombination regulator RecX recombination regulator RecX Binds RecA and inhibits RecA-mediated DNA strand exchange and ATP hydrolysis and coprotease activities NF011444.0 PRK14869 PRK14869.1-6 1105 1105 547 equivalog Y Y N putative manganese-dependent inorganic diphosphatase 3.6.1.1 1485 Clostridium genus 64 NCBI Protein Cluster (PRK) putative manganese-dependent inorganic pyrophosphatase putative manganese-dependent inorganic diphosphatase NF011978.0 PRK15443 PRK15443.2-5 261 261 141 subfamily Y Y N diol dehydratase small subunit 1485 Clostridium genus 39 NCBI Protein Cluster (PRK) propanediol dehydratase small subunit diol dehydratase small subunit NF013870.5 PF01742.22 Peptidase_M27 27 27 423 domain Y Y N tetanus/botulinum neurotoxin GO:0004222,GO:0006508,GO:0008270 7901925,8897436 1485 Clostridium genus 253 EBI-EMBL Clostridial neurotoxin zinc protease tetanus/botulinum neurotoxin These toxins are zinc proteases that block neurotransmitter release by proteolytic cleavage of synaptic proteins such as synaptobrevins, syntaxin and SNAP-25. [1]. 8897436. Botulinum neurotoxins: mechanism of action and therapeutic applications. Montecucco C, Schiavo G, Tugnoli V, de Grandis D;. Mol Med Today 1996;2:418-424. [2]. 7901925. Tetanus and botulism neurotoxins: a new group of zinc proteases. Montecucco C, Schiavo G;. Trends Biochem Sci 1993;18:324-327. (from Pfam) NF019563.5 PF07951.17 Toxin_R_bind_C 25 25 222 domain Y N N Clostridium neurotoxin, C-terminal receptor binding 9783750 1485 Clostridium genus 105 EBI-EMBL Clostridium neurotoxin, C-terminal receptor binding Clostridium neurotoxin, C-terminal receptor binding The Clostridium neurotoxin family is composed of tetanus neurotoxins and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (Pfam:PF01742), the central translocation domains and two receptor binding domains [1]. This domains is the C-terminal receptor binding domain, which adopts a modified beta-trefoil fold with a six stranded beta-barrel and a beta-hairpin triplet capping the domain [1]. The first step in the intoxication process is a binding event between this domains and the pre-synaptic nerve ending [1]. [1]. 9783750. Crystal structure of botulinum neurotoxin type A and implications for toxicity. Lacy DB, Tepp W, Cohen AC, DasGupta BR, Stevens RC;. Nat Struct Biol 1998;5:898-902. (from Pfam) NF019564.5 PF07952.17 Toxin_trans 25 25 323 domain Y Y N botulinum/tetanus neurotoxin translocation domain-containing protein GO:0008320 9783750 1485 Clostridium genus 115 EBI-EMBL Clostridium neurotoxin, Translocation domain Clostridium neurotoxin, Translocation domain The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (Pfam:PF01742), the central translocation domains and two receptor binding domains [1]. Subsequent to cell surface binding and receptor mediated endocytosis of the neurotoxin, an acid induced conformational change in the neurotoxin translocation domain is believed to allow the domain to penetrate the endosome and from a pore, thereby facilitating the passage of the catalytic domain across the membrane into the cytosol [1]. The structure of the translocation reveals a pair of helices that are 105 Angstroms long and is structurally distinct from other pore forming toxins [1]. [1]. 9783750. Crystal structure of botulinum neurotoxin type A and implications for toxicity. Lacy DB, Tepp W, Cohen AC, DasGupta BR, Stevens RC;. Nat Struct Biol 1998;5:898-902. (from Pfam) NF020059.5 PF08470.15 NTNH_C 23.9 23.9 162 domain Y Y N nontoxic nonhemagglutinin C-terminal domain-containing protein 11233171,11595633 1485 Clostridium genus 135 EBI-EMBL Nontoxic nonhaemagglutinin C-terminal Nontoxic nonhaemagglutinin C-terminal Bacteria of the Clostridium genus produce protein neurotoxins, which are complexes consisting of neurotoxin (NT), haemagglutinin (HA), nontoxic nonhaemagglutinin (NTNH), and RNA [1, 2]. The domain described here is found at the C-terminus of the NTNH component. [1]. 11595633. Clostridium botulinum and its neurotoxins: a metabolic and cellular perspective. Johnson EA, Bradshaw M;. Toxicon 2001;39:1703-1722. [2]. 11233171. Characterization of nicking of the nontoxic-nonhemagglutinin components of Clostridium botulinum types C and D progenitor toxin. Sagane Y, Watanabe T, Kouguchi H, Sunagawa H, Inoue K, Fujinaga Y, Oguma K, Ohyama T;. J Protein Chem 2000;19:575-581. (from Pfam) NF026218.5 PF14868.11 DUF4487 25 25 583 domain Y Y N DUF4487 domain-containing protein 1485 Clostridium genus 3 EBI-EMBL Domain of unknown function (DUF4487) Domain of unknown function (DUF4487) This family of proteins is found in eukaryotes. Proteins in this family are typically between 209 and 938 amino acids in length. There is a conserved WCF sequence motif. There is a single completely conserved residue W that may be functionally important. (from Pfam) NF033911.1 botu_NTNH 800 800 1164 equivalog Y Y N non-toxic nonhemagglutinin NTNH ntnH GO:0004222,GO:0005576,GO:0006508,GO:0008270 22363010,25592073 1485 Clostridium genus 134 NCBIFAM non-toxic nonhemagglutinin NTNH non-toxic nonhemagglutinin NTNH The botulinum neurotoxin (BoNT) is always encoded together with associated non-toxic proteins (ANTPs) that are co-produced with it and form a complex that protects the toxin. Often, NtnH (non-toxic nonhemagglutinin) is one of these ANTPs, with the ntnh gene lying immediately upstream of the bont gene. NF036538.5 PF17993.6 HA70_C 25 25 135 PfamEq Y Y N botulinum neurotoxin hemagglutinin HA70 subunit 22684008,24130488,24948737 1485 Clostridium genus 47 EBI-EMBL Haemagglutinin 70 C-terminal domain botulinum neurotoxin hemagglutinin HA70 subunit C-terminal region This is the C-terminal domain found in hemagglutinin component such as HA70 found in Clostridium botulinum. HA is a component of the large botulinum neurotoxin complex and is critical for its oral toxicity. HA plays multiple roles in toxin penetration in the gastrointestinal tract, including protection from the digestive environment, binding to the intestinal mucosal surface, and disruption of the epithelial barrier [1]. HA consists of three different proteins, designated HA70 (also known as HA3), HA33 (HA1), and HA17 (HA2) based on molecular mass [2]. HA70 consists of three domains (D1-3). The D1 and D2 domains, which adopt similar structures, mediate the trimerization of HA70 with each protomer. The D3 domain, sitting at the tip of the trimer, is composed of two similar jelly-roll-like beta-sandwich structures [3]. Furthermore, crystal structures of HA70 in a complex with alpha2,3- or alpha2,6-SiaLac (alpha2,6-sialyllactose), show that alpha2,3- and alpha2,6-SiaLac bound to the same region in the D3 domain of HA70. This domain is the D3 domain found in HA3/HA70 which has been shown to be involved in binding to carbohydrate of glycoproteins from epithelial cells in the infection process [2]. [1]. 24948737. Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin A complex. Lee K, Zhong X, Gu S, Kruel AM, Dorner MB, Perry K, Rummel A, Dong M, Jin R;. Science. 2014;344:1405-1410. [2]. 22684008. Carbohydrate recognition mechanism of HA70 from Clostridium botulinum deduced from X-ray structures in complexes with sialylated oligosaccharides. Yamashita S, Yoshida H, Uchiyama N, Nakakita Y, Nakakita S, Tonoz. TRUNCATED at 1650 bytes (from Pfam) NF046596.1 PF22133.1 Toxin_BN_H 27 27 276 domain Y N N Botulinum neurotoxin, helical domain 22363010,22828508,26639353 1485 Clostridium genus 142 EBI-EMBL Botulinum neurotoxin, helical domain Botulinum neurotoxin, helical domain This entry represents an elongated helical domain present in Clostridium neurotoxins. The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin [1,2,3]. Paper describing PDB structure 3v0a. [1]. 22363010. Botulinum neurotoxin is shielded by NTNHA in an interlocked complex. Gu S, Rumpel S, Zhou J, Strotmeier J, Bigalke H, Perry K, Shoemaker CB, Rummel A, Jin R;. Science. 2012;335:977-981. Paper describing PDB structure 3vuo. [2]. 22828508. Small-angle X-ray scattering reveals structural dynamics of the botulinum neurotoxin associating protein, nontoxic nonhemagglutinin. Sagane Y, Miyashita S, Miyata K, Matsumoto T, Inui K, Hayashi S, Suzuki T, Hasegawa K, Yajima S, Yamano A, Niwa K, Watanabe T;. Biochem Biophys Res Commun. 2012;425:256-260. Paper describing PDB structure 4zkt. [3]. 26639353. Molecular Assembly of Clostridium botulinum progenitor M complex of type E. Eswaramoorthy S, Sun J, Li H, Singh BR, Swaminathan S;. Sci Rep. 2015;5:17795. (from Pfam) NF047168.1 PF22374.1 Clospo_01618-like 27 27 127 domain Y N N Clospo_01618-like 1485 Clostridium genus 30 EBI-EMBL Clospo_01618-like Clospo_01618-like This domain is found in Lipoprotein from Clostridium sporogenes (Clospo_01618) and similar bacterial proteins. It shows a two -layered alpha/beta configuration, displaying structural similarity to the N-terminal domain of YycH, which plays a role in signal transduction. (from Pfam) TIGR02806.2 TIGR02806 clostrip 550 550 472 equivalog Y Y N clostripain cloSI 3.4.22.8 GO:0004197,GO:0006508 11976286,20940055,762145 1485 Clostridium genus 334 JCVI clostripain clostripain Clostripain is a cysteine protease characterized from Clostridium histolyticum (now called Hathewaya histolytica) and Clostridium perfringens, and observed in related species. It is a heterodimer processed from a single precursor polypeptide, specific for Arg-|-Xaa peptide bonds. The older term alpha-clostripain refers to the most active, most reduced form, rather than to the product of one of several different genes. Clostripain belongs to the peptidase family C11, or clostripain family (see PF03415). TIGR03209.1 TIGR03209 P21_Cbot 138.35 138.35 142 equivalog Y Y N botulinum neurotoxin transcription-activating sigma factor BotR botR 15158256,16677313,16701505 1485 Clostridium genus 52 JCVI transcriptional regulator BotR, P-21 botulinum neurotoxin transcription-activating sigma factor BotR Clostridium botulinum neurotoxin production is regulated by a regulatory sigma-70 protein, BotR transcription regulator. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo [3]. NF000517.2 blaCBP 650 650 308 exception Y Y Y CBP family penicillin-hydrolyzing class A beta-lactamase blaCBP 3.5.2.6 GO:0008800 1491 Clostridium botulinum species 7 NCBIFAM blaCBP: CBP family penicillin-hydrolyzing class A beta-lactamase CBP family penicillin-hydrolyzing class A beta-lactamase NF006063.0 PRK08207 PRK08207.2-1 1074 1074 518 equivalog Y Y N coproporphyrinogen III oxidase 1496 Clostridioides difficile species 74 NCBI Protein Cluster (PRK) coproporphyrinogen III oxidase coproporphyrinogen III oxidase NF023632.5 PF12211.13 LMWSLP_N 27 27 262 domain Y N N Low molecular weight S layer protein N terminal 19183279 1496 Clostridioides difficile species 226 EBI-EMBL Low molecular weight S layer protein N terminal Low molecular weight S layer protein N terminal This family of proteins is found in bacteria. Proteins in this family are typically between 328 and 381 amino acids in length. There is a conserved LGDG sequence motif. Clostridial species have a layer of surface proteins surrounding their membrane. This layer is comprised of a high molecular weight protein and a low molecular weight protein. This domain is the N terminal domain of the low molecular weight protein. It is a structural domain. [1]. 19183279. Structural insights into the molecular organization of the S-layer from Clostridium difficile. Fagan RP, Albesa-Jove D, Qazi O, Svergun DI, Brown KA, Fairweather NF;. Mol Microbiol. 2009;71:1308-1322. (from Pfam) NF033435.1 S-layer_Clost 650 600 728 equivalog Y Y N S-layer protein SlpA slpA 12081960,19183279 1496 Clostridioides difficile species 282 NCBIFAM S-layer protein SlpA S-layer protein SlpA In Clostridiodes difficile, the S-layer protein precursor, SlpA, is one member of a large paralogous family of protein that share several cell wall-binding repeats. SlpA is cleaved into a larger and smaller protein. The S-layer protein itself is important to adhesion, and portions of it are highly variable, and then N-terminal and C-terminal are well-conserved. NF033866.1 blaCDD 600 600 310 exception Y Y Y CDD family class D beta-lactamase blaCDD 3.5.2.6 GO:0008658,GO:0008800 30563905 1496 Clostridioides difficile species 75 NCBIFAM CDD family class D beta-lactamase CDD family class D beta-lactamase CDD is an unusual beta-lactamase, most similar to class D beta-lactamases and called that by Toth, et al. It was described originally in Clostridioides difficile as intrinsic. It appears more similar to BlaR1 than to most known class D beta-lactamases. CDD joins a small family of class D beta-lactamases from Gram-positive sequences, where names other than OXA tend to be used. NF041444.1 SASP_CD1290 50 50 61 equivalog Y Y N CD1290 family small acid-soluble spore protein 1496 Clostridioides difficile species 48 NCBIFAM CD1290 family small acid-soluble spore protein CD1290 (CD630_12900) from Clostridioides difficile 630 is the founding member group of small acid-soluble spore proteins (SASP). Members are related to the alpha/beta family described by Pfam model PF00269, but are shorter on average and typically score below thresholds for that model. Sequences that resemble germination protease GPR cleavage motifs are EIAx[D/E] and [E/D]IIEN. NF044788.2 PF21398.2 PG_binding_5 24.1 24.1 67 domain Y N N Putative peptidoglycan-binding domain 1496 Clostridioides difficile species 633 EBI-EMBL Putative peptidoglycan-binding domain Putative peptidoglycan-binding domain This entry represents a putative peptidoglycan binding domain. (from Pfam) NF044803.2 PF21465.2 Cwp6_N 27 27 108 domain Y N N Putative N-acetylmuramoyl-L-alanine amidase cwp6, N-terminal domain 28132783 1496 Clostridioides difficile species 1115 EBI-EMBL Putative N-acetylmuramoyl-L-alanine amidase cwp6, N-terminal domain Putative N-acetylmuramoyl-L-alanine amidase cwp6, N-terminal domain This domain is found in the putative N-acetylmuramoyl-L-alanine amidase cwp6 from Clostridioides difficile and similar proteins from firmicutes. Cwp6, which is involved in cell wall remodelling, consists of five domains: an N-terminal (this entry), a trimer of CWB2 (Pfam:PF04122) and a C-terminal (Pfam:PF01520). This domain, which locates at the bottom of the molecule, folds into a seven-stranded beta-barrel with one alpha-helix and with two additional short beta-strands [1]. Paper describing PDB structure 5j72. [1]. 28132783. The CWB2 Cell Wall-Anchoring Module Is Revealed by the Crystal Structures of the Clostridium difficile Cell Wall Proteins Cwp8 and Cwp6. Usenik A, Renko M, Mihelic M, Lindic N, Borisek J, Perdih A, Pretnar G, Muller U, Turk D;. Structure. 2017;25:514-521. (from Pfam) NF046189.1 PF22093.1 Cwp8_D2 27 27 79 domain Y N N Cell wall binding protein Cwp8 domain 2 28132783 1496 Clostridioides difficile species 97 EBI-EMBL Cell wall binding protein Cwp8 domain 2 Cell wall binding protein Cwp8 domain 2 Cwp8 is a member of the C. difficile cell wall protein (CWP) family. It consists of several domains. This entry represents the domain 2 that is a part of the N-terminal elongated part of the molecule [1]. This domain is composed of a three-stranded antiparallel beta-sheet, an alpha-helix packed on it and a short beta-hairpin located at the edge of the sheet. Paper describing PDB structure 5j6q. [1]. 28132783. The CWB2 Cell Wall-Anchoring Module Is Revealed by the Crystal Structures of the Clostridium difficile Cell Wall Proteins Cwp8 and Cwp6. Usenik A, Renko M, Mihelic M, Lindic N, Borisek J, Perdih A, Pretnar G, Muller U, Turk D;. Structure. 2017;25:514-521. (from Pfam) NF046518.1 PF22135.1 Cwp8_D3 27 27 94 domain Y N N Cell wall binding protein Cwp8 domain 3 28132783 1496 Clostridioides difficile species 89 EBI-EMBL Cell wall binding protein Cwp8 domain 3 Cell wall binding protein Cwp8 domain 3 This entry represents the third domain (D3) of cell wall protein Cwp8 found in C. difficile. This domain folds into an alpha/beta structure consisting of a four-stranded antiparallel beta-sheet packed on one side with alpha-helices [1]. This domain is related to domain 1 (D1) of the cell wall protein Cwp2 from the same organism. Paper describing PDB structure 5j6q. [1]. 28132783. The CWB2 Cell Wall-Anchoring Module Is Revealed by the Crystal Structures of the Clostridium difficile Cell Wall Proteins Cwp8 and Cwp6. Usenik A, Renko M, Mihelic M, Lindic N, Borisek J, Perdih A, Pretnar G, Muller U, Turk D;. Structure. 2017;25:514-521. (from Pfam) NF046829.1 PF22434.1 PilW_C 27 27 128 domain Y N N PilW, C-terminal 25599642 1496 Clostridioides difficile species 130 EBI-EMBL PilW, C-terminal PilW, C-terminal This domain is found at the C-terminal end of the putative pilin protein from Clostridioides difficile (PilW) and similar sequences mainly found in Clostidia, which plays a role in biofilm formation. PilW shows a single transmembrane helix followed by a soluble domain and a central alpha-helix with a beta-sheet packed against it [1]. This long domain is found associated with Pfam:PF07963. Paper describing PDB structure 4ogm. [1]. 25599642. Structural and evolutionary analyses show unique stabilization strategies in the type IV pili of Clostridium difficile. Piepenbrink KH, Maldarelli GA, Martinez de la Pena CF, Dingle TC, Mulvey GL, Lee A, von Rosenvinge E, Armstrong GD, Donnenberg MS, Sundberg EJ;. Structure. 2015;23:385-396. (from Pfam) NF046839.1 PF22473.1 PilJ_Pilin 26 26 81 domain Y N N PilJ, Pilin domain 24362261 1496 Clostridioides difficile species 74 EBI-EMBL PilJ, Pilin domain PilJ, Pilin domain This entry represents a N-terminal Pilin-like domain of PilJ from Clostridium difficile [1]. Paper describing PDB structure 4ixj. [1]. 24362261. Structure of Clostridium difficile PilJ exhibits unprecedented divergence from known type IV pilins. Piepenbrink KH, Maldarelli GA, de la Pena CF, Mulvey GL, Snyder GA, De Masi L, von Rosenvinge EC, Gunther S, Armstrong GD, Donnenberg MS, Sundberg EJ;. J Biol Chem. 2014;289:4334-4345. (from Pfam) NF047374.1 CD_typeI_toxin 60 60 51 equivalog Y Y N type I toxin-antitoxin system toxin GO:0090729,GO:0110001 29529286,33247281 1496 Clostridioides difficile species 121 NCBIFAM type I toxin-antitoxin system toxin A type I toxin-antitoxin system typically consists of a small hydrophobic toxic protein and an antisense RNA, which forms RNA duplex with the toxin-encoding mRNA to inhibit toxin translation. Members of this family are small type I toxin-antitoxin system toxin proteins found in Clostridium difficile. Their encoding genes are usually adjacent to CRISPR arrays. NF040765.1 adhesion_FAF 500 500 632 equivalog Y Y N adhesion factor FAF faf 18808384 150022 Finegoldia genus 46 NCBIFAM adhesion factor FAF FAF (Finegoldia adhesion factor) has firstly been identified and characterized in the opportunistic pathogen Finegoldia magna. FAF mediate bacterial adhesion to hosts through interactions with the basement membrane protein BM-40. NF005318.0 PRK06851 PRK06851.1-2 734 734 353 equivalog Y N N hypothetical protein 1502 Clostridium perfringens species 75 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006934.0 PRK09419 PRK09419.1-1 1646 1646 1174 subfamily Y Y N multifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase/5'-nucleotidase 3.1.3.5,3.1.3.6,3.1.4.16 1502 Clostridium perfringens species 489 NCBI Protein Cluster (PRK) bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precursor protein multifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase/5'-nucleotidase NF010220.0 PRK13678 PRK13678.2-3 111 111 84 equivalog Y N N hypothetical protein 1502 Clostridium perfringens species 12 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF040685.1 conju_mem_TcpD 100 100 114 equivalog Y Y N conjugal transfer membrane protein TcpD tcpD 16788202,25488300 1502 Clostridium perfringens species 85 NCBIFAM conjugal transfer membrane protein TcpD NF043009.1 Cyt554Puf2C_Caul 800 800 416 equivalog Y Y N cytochrome c-554 Puf2C puf2C GO:0009055,GO:0019684,GO:0020037 1660302,7535995 1508594 Chloroflexineae suborder 21 NCBIFAM cytochrome c-554 Puf2C NF020861.5 PF09301.15 DUF1970 25 25 112 domain Y Y N DUF1970 domain-containing protein 1514971 Haloprofundus marisrubri species 1 EBI-EMBL Domain of unknown function (DUF1970) Domain of unknown function (DUF1970) Members of this family consist of various uncharacterised viral hypothetical proteins. (from Pfam) NF005258.0 PRK06762 PRK06762.3-3 344 344 164 equivalog Y N N hypothetical protein 1520 Clostridium beijerinckii species 10 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein TIGR01639.1 TIGR01639 P_fal_TIGR01639 25.75 25.75 61 paralog_domain N N N Plasmodium falciparum uncharacterized domain TIGR01639 1526574 Psychroflexus salis species 1 JCVI Plasmodium falciparum uncharacterized domain TIGR01639 Plasmodium falciparum uncharacterized domain TIGR01639 This HMM represents a conserved sequence region of about 60 amino acids found in over 40 predicted proteins of Plasmodium falciparum. It is not found elsewhere, including closely related species such as Plasmodium yoelii. No member of this family is characterized. NF000440.2 blaTHIN 700 700 316 exception Y Y Y THIN family subclass B3 metallo-beta-lactamase blaTHIN 3.5.2.6 GO:0008800 1528773 Janthinobacterium sp. AD80 species 1 NCBIFAM THIN family subclass B3 metallo-beta-lactamase THIN family subclass B3 metallo-beta-lactamase NF047176.1 PF22388.1 DUF6974 26 26 104 subfamily Y Y N DUF6974 family protein 1538529 uncultured Planktomarina sp. species 1 EBI-EMBL Domain of unknown function (DUF6974) DUF6974 family protein This entry represents a dimeric alpha/beta barrel domain from an uncultured marine organism (PDB:2op5). The function of this family is unknown. (from Pfam) NF025207.5 PF13837.11 Myb_DNA-bind_4 27 27 89 domain Y Y N myb/SANT-like DNA-binding domain-containing protein 155567 uncultured Rhizobium sp. species 1 EBI-EMBL Myb/SANT-like DNA-binding domain Myb/SANT-like DNA-binding domain This presumed domain appears to be related to other Myb/SANT-like DNA binding domains. In particular Pfam:PF10545 seems most related. This family is greatly expanded in plants and appears in several proteins annotated as transposon proteins. (from Pfam) NF012710.5 PF00500.23 Late_protein_L1 27 27 497 domain Y Y N L1 family major capsid protein GO:0005198,GO:0019028 1561003 Candidatus Ichthyocystis hellenicum species 2 EBI-EMBL L1 (late) protein L1 family major capsid protein NF012721.5 PF00511.22 PPV_E2_C 25 25 80 domain Y Y N E2 DNA-binding domain-containing protein GO:0003677,GO:0003700,GO:0006275,GO:0006355,GO:0042025 17915949,9878365 1561003 Candidatus Ichthyocystis hellenicum species 1 EBI-EMBL E2 (early) protein, C terminal E2 (early) protein, C terminal NF045731.1 blaDYB 550 550 250 exception Y Y Y DYB family subclass B1 metallo-beta-lactamase blaDYB 3.5.2.6 GO:0008800 156973 Dysgonomonas genus 6 NCBIFAM DYB family subclass B1 metallo-beta-lactamase DYB (Dysgonomonas class B) is a family of subclass B1 metallo-beta-lactamases, found in the genus Dysgonomonas. NF002355.0 PRK01318 PRK01318.2-2 891 891 602 equivalog Y Y N membrane protein insertase YidC yidC 157 Treponema genus 38 NCBI Protein Cluster (PRK) membrane protein insertase membrane protein insertase YidC NF006859.0 PRK09358 PRK09358.3-6 549 549 299 equivalog Y Y N adenosine deaminase 3.5.4.4 157 Treponema genus 27 NCBI Protein Cluster (PRK) adenosine deaminase adenosine deaminase NF007042.0 PRK09496 PRK09496.3-5 467 467 466 equivalog Y Y N Trk system potassium transporter TrkA trkA 157 Treponema genus 58 NCBI Protein Cluster (PRK) potassium transporter peripheral membrane component Trk system potassium transporter TrkA NF008708.0 PRK11713 PRK11713.7-3 380 380 294 equivalog Y Y N 16S rRNA (uracil(1498)-N(3))-methyltransferase 2.1.1.193 157 Treponema genus 15 NCBI Protein Cluster (PRK) 16S ribosomal RNA methyltransferase RsmE 16S rRNA (uracil(1498)-N(3))-methyltransferase NF009800.0 PRK13285 PRK13285.2-3 226 226 149 equivalog Y N N flagellar assembly protein FliW 157 Treponema genus 38 NCBI Protein Cluster (PRK) flagellar assembly protein FliW flagellar assembly protein FliW NF011108.0 PRK14536 PRK14536.1 780 780 490 equivalog Y Y N cysteine--tRNA ligase 6.1.1.16 157 Treponema genus 53 NCBI Protein Cluster (PRK) cysteinyl-tRNA synthetase cysteine--tRNA ligase Catalyzes a two-step reaction; charges a cysteine by linking its carboxyl group to the alpha-phosphate of ATP then transfers the aminoacyl-adenylate to its tRNA NF011230.0 PRK14637 PRK14637.1 159 159 152 equivalog Y Y N ribosome maturation factor RimP rimP 157 Treponema genus 43 NCBI Protein Cluster (PRK) hypothetical protein ribosome maturation factor RimP NF014733.5 PF02707.21 MOSP_N 25.1 25.1 196 domain Y Y N major outer sheath N-terminal domain-containing protein 9023187 157 Treponema genus 464 EBI-EMBL Major Outer Sheath Protein N-terminal region Major Outer Sheath Protein N-terminal region This is a family of spirochete major outer sheath protein N-terminal regions. These proteins are present on the bacterial cell surface. In T. denticola the major outer sheath protein (Msp) binds immobilised laminin and fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola [1]. [1]. 9023187. Conservation of msp, the gene encoding the major outer membrane protein of oral Treponema spp. Fenno JC, Wong GW, Hannam PM, Muller KH, Leung WK, McBride BC;. J Bacteriol 1997;179:1082-1089. (from Pfam) NF014743.5 PF02722.20 MOSP_C 25 25 205 domain Y Y N major outer sheath C-terminal domain-containing protein 23457251,9023187 157 Treponema genus 514 EBI-EMBL Major Outer Sheath Protein C-terminal domain Major Outer Sheath Protein C-terminal domain This is a family of spirochete major outer sheath protein C-terminal regions. These proteins are present on the bacterial cell surface. In T. denticola the major outer sheath protein (Msp) binds immobilised laminin and fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola [1]. This domain forms an amphipathic beta rich structure with channel forming activity [2]. [1]. 9023187. Conservation of msp, the gene encoding the major outer membrane protein of oral Treponema spp. Fenno JC, Wong GW, Hannam PM, Muller KH, Leung WK, McBride BC;. J Bacteriol 1997;179:1082-1089. [2]. 23457251. The major outer sheath protein (Msp) of Treponema denticola has a bipartite domain architecture and exists as periplasmic and outer membrane-spanning conformers. Anand A, Luthra A, Edmond ME, Ledoyt M, Caimano MJ, Radolf JD;. J Bacteriol. 2013;195:2060-2071. (from Pfam) NF021244.5 PF09710.15 Trep_dent_lipo 25.3 25.3 397 domain Y N N Treponema clustered lipoprotein (Trep_dent_lipo) 157 Treponema genus 174 EBI-EMBL Treponema clustered lipoprotein (Trep_dent_lipo) Treponema clustered lipoprotein (Trep_dent_lipo) This entry represents a family of six predicted lipoproteins from a region of about 20 tandemly arranged genes in the Treponema denticola genome. Two other neighbouring genes share the lipoprotein signal peptide region but do not show more extensive homology. The function of this locus is unknown. (from Pfam) NF033595.1 denti_PrtP 300 300 606 equivalog Y Y N dentilisin complex serine proteinase subunit PrtP prtP 23253337 157 Treponema genus 62 NCBIFAM dentilisin complex serine proteinase subunit PrtP dentilisin complex serine proteinase subunit PrtP PrtP, a chymotrypsin-like protease known as dentilisin, forms a complex with PrcB and PrcA. It is found in Treponema denticola and in numerous other Treponema species. Dentilisin from T. denticola plays a significant role in pathogen-host interactions in periodontal disease. NF033596.1 denti_PrcB 125 125 176 equivalog Y Y N dentilisin complex subunit PrcB prcB 157 Treponema genus 48 NCBIFAM dentilisin complex subunit PrcB dentilisin complex subunit PrcB NF033597.1 denti_PrcA 200 200 611 equivalog Y Y N dentilisin complex subunit PrcA prcA 157 Treponema genus 63 NCBIFAM dentilisin complex subunit PrcA dentilisin complex subunit PrcA PrcA is a lipoprotein that, together with PrcB and the serine proteinase subunit PrtP, form a chymotrypsin-like surface complex that is also known as dentilisin, after its discovery and characterization in Treponema denticola. Dentilisin is an important virulence factor in periodontal disease. NF033926.0 msp_porin 200 200 522 subfamily Y Y N MSP porin GO:0046930 22661689,25225245,8626313 157 Treponema genus 147 NCBIFAM MSP porin MSP porin Members of this HMM are MSP porins (major outer sheath proteins) in Treponema. They may play a role in immune evasion and persistence. NF044299.2 PF20740.2 TP0453 27 27 252 domain Y N N Outer membrane-associated lipoprotein TP0453 21965687 157 Treponema genus 183 EBI-EMBL Outer membrane-associated lipoprotein TP0453 Outer membrane-associated lipoprotein TP0453 This domain is found in TP0453, a lipoprotein associated with the inner leaflet of the outer membrane of Treponema pallidum. This protein consists of an alpha/beta/alpha-fold and includes five stably folded amphipathic helices and may function as a carrier of lipids, glycolipids, and/or derivatives during the biogenesis of the outer membrane [1]. Paper describing PDB structure 3k8g. [1]. 21965687. The transition from closed to open conformation of Treponema pallidum outer membrane-associated lipoprotein TP0453 involves membrane sensing and integration by two amphipathic helices. Luthra A, Zhu G, Desrosiers DC, Eggers CH, Mulay V, Anand A, McArthur FA, Romano FB, Caimano MJ, Heuck AP, Malkowski MG, Radolf JD;. J Biol Chem. 2011;286:41656-41668. (from Pfam) NF045225.2 PF20813.2 FhbB 27 27 80 domain Y N N Factor H binding protein B 22371503 157 Treponema genus 65 EBI-EMBL Factor H binding protein B Factor H binding protein B Treponema denticola, a human pathogen that contributes to periodontitis, survives by binding factor H (FH) to its surface through its Factor H binding protein B (FhbB). The structure of this protein is highly ordered consisting of an alpha-beta fold. This highly thermostable protein forms a weak dimer with an interface occurring along one alpha helix from each subunit in an anti-parallel alignment with no direct hydrogen bonding between the subunits [1]. Paper describing PDB structure 3qz0. [1]. 22371503. Structure of factor H-binding protein B (FhbB) of the periopathogen, Treponema denticola: insights into progression of periodontal disease. Miller DP, Bell JK, McDowell JV, Conrad DH, Burgner JW, Heroux A, Marconi RT;. J Biol Chem. 2012;287:12715-12722. (from Pfam) TIGR01781.1 TIGR01781 Trep_dent_lipo 294.45 294.45 412 paralog Y Y N clustered-type lipoprotein 157 Treponema genus 90 JCVI Treponema denticola clustered lipoprotein clustered-type lipoprotein This HMM represents a family of six predicted lipoproteins from a region of about 20 tandemly arranged genes in the Treponema denticola genome. Two other neighboring genes share the lipoprotein signal peptide region but do not show more extensive homology. The function of this locus is unknown. NF014317.5 PF02246.20 B1 25 25 69 domain Y N N Protein L b1 domain 1618782 1570339 Peptoniphilaceae family 23 EBI-EMBL Protein L b1 domain Protein L b1 domain Protein L is a bacterial protein with immunoglobulin (Ig) light chain-binding properties. It contains a number of homologous b1 repeats towards the N-terminus. These repeats have been found to be responsible for the interaction of protein L with Ig light chains [1]. [1]. 1618782. Structure of peptostreptococcal protein L and identification of a repeated immunoglobulin light chain-binding domain. Kastern W, Sjobring U, Bjorck L;. J Biol Chem 1992;267:12820-12825. (from Pfam) NF001127.0 PRK00139 PRK00139.2-1 997 997 520 equivalog Y Y N UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase 6.3.2.13 1578 Lactobacillus genus 292 NCBI Protein Cluster (PRK) UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase NF005257.0 PRK06762 PRK06762.3-2 202 202 170 equivalog Y N N hypothetical protein 1578 Lactobacillus genus 106 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010391.0 PRK13818 PRK13818.1 206 206 121 equivalog Y Y N ribosome-binding factor A 1578 Lactobacillus genus 114 NCBI Protein Cluster (PRK) ribosome-binding factor A ribosome-binding factor A Associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA NF010987.0 PRK14411 PRK14411.1 243 243 204 equivalog Y N N membrane protein 1578 Lactobacillus genus 260 NCBI Protein Cluster (PRK) membrane protein membrane protein NF046822.1 PF22796.1 SlpA_N 27 27 166 domain Y N N SlpA N-terminal domain 1578 Lactobacillus genus 545 EBI-EMBL SlpA N-terminal domain SlpA N-terminal domain This entry represents the N-terminal domain of S-layer protein SlpA from Lactobacillus amylovorus and related proteins. This domain adopts unusual topology composed of beta-strands arranged in a barrel-sandwich fold. (from Pfam) NF046823.1 PF22797.1 SlpA_D2 24.5 24.5 102 domain Y N N SlpA domain II 1578 Lactobacillus genus 735 EBI-EMBL SlpA domain II SlpA domain II This domain is found in homologues of SlpA protein from Lactobacillus acidophilus. This domain is involved in the self-assembly and dimerization of the S-layer. It adopts an alpha/beta structure consisting of a curved mixed beta-sheet and two alpha-helices packed on it. It has a partial structural similarity to the cadherin ectodomains comprising the curved beta-sheet and differs significantly in the central part that adopts an alpha-helical conformation instead of extended beta. (from Pfam) NF045489.1 XrtG_Nterm_ext 125 125 176 equivalog Y Y N exosortase XrtG N-terminal extension domain-like protein 1579 Lactobacillus acidophilus species 11 NCBIFAM exosortase XrtG N-terminal extension domain This domain appears as an N-terminal extension, or an accompanying protein, for a minority of exosortase XrtG family putative protein-sorting intramembrane endopeptidases. NF027193.5 PF15860.10 DUF4728 26.7 26.7 91 domain Y Y N DUF4728 domain-containing protein 1586242 Luteimonas arsenica species 1 EBI-EMBL Domain of unknown function (DUF4728) Domain of unknown function (DUF4728) This family of arthropod proteins is functionally uncharacterised. (from Pfam) NF016755.5 PF04884.19 UVB_sens_prot 28.3 28.3 241 domain Y Y N RUS1 family protein 19515790,20562234,21511809 1587 Lactobacillus helveticus species 9 EBI-EMBL Vitamin B6 photo-protection and homoeostasis RUS1 family protein In plants, this domain plays a role in auxin-transport, plant growth and development [1,2] and appears to be expressed by all cells in the plant as well as in plastids. The family has been shown to play a role in vitamin B6 photo-protection and homoeostasis in plants [3]. [1]. 19515790. ROOT UV-B SENSITIVE2 acts with ROOT UV-B SENSITIVE1 in a root ultraviolet B-sensing pathway. Leasure CD, Tong H, Yuen G, Hou X, Sun X, He ZH;. Plant Physiol. 2009;150:1902-1915. [2]. 20562234. Arabidopsis ROOT UVB SENSITIVE2/WEAK AUXIN RESPONSE1 is required for polar auxin transport. Ge L, Peer W, Robert S, Swarup R, Ye S, Prigge M, Cohen JD, Friml J, Murphy A, Tang D, Estelle M;. Plant Cell. 2010;22:1749-1761. [3]. 21511809. root uv-b sensitive mutants are suppressed by specific mutations in ASPARTATE AMINOTRANSFERASE2 and by exogenous vitamin B6. Leasure CD, Tong HY, Hou XW, Shelton A, Minton M, Esquerra R, Roje S, Hellmann H, He ZH;. Mol Plant. 2011;4:759-770. (from Pfam) NF007327.0 PRK09814 PRK09814.3-1 792 792 364 equivalog Y N N beta-1,6-galactofuranosyltransferase 1597 Lacticaseibacillus paracasei species 4 NCBI Protein Cluster (PRK) beta-1,6-galactofuranosyltransferase beta-1,6-galactofuranosyltransferase NF007328.0 PRK09814 PRK09814.3-2 450 450 208 equivalog Y N N beta-1,6-galactofuranosyltransferase 1597 Lacticaseibacillus paracasei species 12 NCBI Protein Cluster (PRK) beta-1,6-galactofuranosyltransferase beta-1,6-galactofuranosyltransferase NF040719.1 Lar0958_adhesin 1200 1200 1222 exception Y Y N Lar_0958 family LPXTG-anchored mucus adhesin 24593252 1598 Limosilactobacillus reuteri species 48 NCBIFAM Lar_0958 family LPXTG-anchored mucus adhesin NF001062.0 PRK00117 PRK00117.5-2 336 336 164 equivalog Y Y N recombination regulator RecX recX 160 Treponema pallidum species 3 NCBI Protein Cluster (PRK) recombination regulator RecX recombination regulator RecX NF011242.0 PRK14648 PRK14648.1 426 426 354 equivalog Y Y N UDP-N-acetylmuramate dehydrogenase 1.3.1.98 160 Treponema pallidum species 10 NCBI Protein Cluster (PRK) UDP-N-acetylenolpyruvoylglucosamine reductase UDP-N-acetylmuramate dehydrogenase NF011266.0 PRK14672 PRK14672.1 1504 1504 691 equivalog Y N N excinuclease ABC subunit C 160 Treponema pallidum species 8 NCBI Protein Cluster (PRK) excinuclease ABC subunit C excinuclease ABC subunit C NF046300.1 PF22496.1 SOR_N 27 27 37 domain Y Y N superoxide reductase domain-containing protein 16791639 160 Treponema pallidum species 2 EBI-EMBL Class III superoxide reductase, N-terminal superoxide reductase domain-containing protein This short domain is found at the N-terminal end of class III superoxide reductase from Treponema pallidum (SOR, [swissprot:O83795]), a small protein that catalyse the one -electron reduction of superoxide to hydrogen peroxide, having rubredoxin as their putative electron donor. It is organised into two distinct domains: an N-terminal (this entry) that shows four beta-strands and a C-terminal that harbours the catalytic site and displays an immunoglobulin-like fold [1]. Paper describing PDB structure 1y07. [1]. 16791639. The first crystal structure of class III superoxide reductase from Treponema pallidum. Santos-Silva T, Trincao J, Carvalho AL, Bonifacio C, Auchere F, Raleiras P, Moura I, Moura JJ, Romao MJ;. J Biol Inorg Chem. 2006;11:548-558. (from Pfam) NF000275.2 blaPLA_ORN_TER 550 550 291 exception Y Y Y PLA/ORN/TER family class A beta-lactamase bla 3.5.2.6 GO:0008800 160674 Raoultella genus 73 NCBIFAM PLA/ORN/TER family class A beta-lactamase PLA/ORN/TER family class A beta-lactamase NF021657.5 PF10154.14 DUF2362 25.8 25.8 498 domain Y Y N DUF2362 domain-containing protein 31106069 160674 Raoultella genus 18 EBI-EMBL Uncharacterised conserved protein (DUF2362) Uncharacterised conserved protein (DUF2362) This is a family of proteins conserved from nematodes to humans. The function is not known. [1]. 31106069. A novel conserved family of Macro-like domains-putative new players in ADP-ribosylation signaling. Dudkiewicz M, Pawlowski K;. PeerJ. 2019;7:e6863. (from Pfam) NF038400.1 blaTER 620 620 284 exception Y Y Y TER family class A beta-lactamase blaTER 3.5.2.6 GO:0008800 160674 Raoultella genus 31 NCBIFAM TER family class A beta-lactamase NF025075.5 PF13695.11 zf-3CxxC 23 23 97 domain Y Y N 3CxxC-type zinc finger protein 1609546 endosymbiont DhMRE of Dentiscutata heterogama species 1 EBI-EMBL Zinc-binding domain Zinc-binding domain This is a family with several pairs of CxxC motifs possibly representing a multiple zinc-binding region. Only one pair of cysteines is associated with a highly conserved histidine residue. (from Pfam) NF003723.0 PRK05329 PRK05329.2-1 680 680 436 equivalog Y Y N glycerol-3-phosphate dehydrogenase subunit GlpB glpB 1.1.5.3 161492 Anaeromyxobacter genus 4 NCBI Protein Cluster (PRK) anaerobic glycerol-3-phosphate dehydrogenase subunit B glycerol-3-phosphate dehydrogenase subunit GlpB NF005730.0 PRK07546 PRK07546.1-4 222 222 207 equivalog Y N N hypothetical protein 161492 Anaeromyxobacter genus 4 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010779.0 PRK14182 PRK14182.1 537 537 282 equivalog Y N N bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase 161492 Anaeromyxobacter genus 9 NCBI Protein Cluster (PRK) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase NF011088.0 PRK14511 PRK14511.1-6 1877 1877 1009 equivalog Y Y N malto-oligosyltrehalose synthase 5.4.99.15 161492 Anaeromyxobacter genus 9 NCBI Protein Cluster (PRK) maltooligosyl trehalose synthase malto-oligosyltrehalose synthase NF042642.3 PF20224.3 DUF6583 27 27 473 subfamily Y Y N DUF6583 family protein 1623490 uncultured Gemmiger sp. species 1 EBI-EMBL Family of unknown function (DUF6583) DUF6583 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, mainly in Firmicutes. Proteins in this family are typically between 454 and 596 amino acids in length. There are two highly conserved residues, a Tyr and an Asp. (from Pfam) NF040211.4 PF19154.5 DUF5836 25 25 38 subfamily Y Y N induction peptide AbpIP family protein 11932444,19591924 1624 Ligilactobacillus salivarius species 13 EBI-EMBL Family of unknown function (DUF5836) induction peptide AbpIP family protein This family represents the induction peptide AbpIP, which regulates the biosynthesis of the bacteriocin ABP-118 in Lactobacillus salivarius subsp. salivarius UCC118 [1,2]. [1]. 11932444. Characterization of the genetic locus responsible for the production of ABP-118, a novel bacteriocin produced by the probiotic bacterium Lactobacillus salivarius subsp. salivarius UCC118. Flynn S, van Sinderen D, Thornton GM, Holo H, Nes IF, Collins JK;. Microbiology. 2002;148:973-984. [2]. 19591924. Characterization of salivaricin CRL 1328, a two-peptide bacteriocin produced by Lactobacillus salivarius CRL 1328 isolated from the human vagina. Vera Pingitore E, Hebert EM, Nader-Macias ME, Sesma F;. Res Microbiol. 2009;160:401-408. (from Pfam) NF012811.5 PF00604.22 Flu_PB2_5th 25 25 210 domain Y Y N polymerase basic protein 2 domain-containing protein GO:0003723,GO:0039694 26503046,8806170 163604 Nocardiopsis exhalans species 1 EBI-EMBL Influenza RNA polymerase PB2 CAP binding domain Influenza RNA polymerase PB2 CAP binding domain Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding [1] and endonuclease domains required for transcription initiation by cap-snatching [2]. This entry represents the CAP binding domain [2]. [1]. 8806170. Recombinant-baculovirus-expressed PB2 subunit of the influenza A virus RNA polymerase binds cap groups as an isolated subunit. Shi L, Galarza JM, Summers DF;. Virus Res 1996;42:1-9. [2]. 26503046. Crystal structure of the RNA-dependent RNA polymerase from influenza C virus. Hengrung N, El Omari K, Serna Martin I, Vreede FT, Cusack S, Rambo RP, Vonrhein C, Bricogne G, Stuart DI, Grimes JM, Fodor E;. Nature. 2015;527:114-117. (from Pfam) NF045258.2 PF20948.2 Flu_PB2_2nd 25 25 68 domain Y N N Influenza RNA polymerase PB2 second domain 26503046,8806170 163604 Nocardiopsis exhalans species 1 EBI-EMBL Influenza RNA polymerase PB2 second domain Influenza RNA polymerase PB2 second domain Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding [1] and endonuclease domains required for transcription initiation by cap-snatching [2]. This entry represents the domain of the Flu PB protein that follows the N-terminal extended region. [1]. 8806170. Recombinant-baculovirus-expressed PB2 subunit of the influenza A virus RNA polymerase binds cap groups as an isolated subunit. Shi L, Galarza JM, Summers DF;. Virus Res 1996;42:1-9. [2]. 26503046. Crystal structure of the RNA-dependent RNA polymerase from influenza C virus. Hengrung N, El Omari K, Serna Martin I, Vreede FT, Cusack S, Rambo RP, Vonrhein C, Bricogne G, Stuart DI, Grimes JM, Fodor E;. Nature. 2015;527:114-117. (from Pfam) NF045259.2 PF20949.2 Flu_PB2_3rd 27 27 143 domain Y N N Influenza RNA polymerase PB2 middle domain 26503046,8806170 163604 Nocardiopsis exhalans species 1 EBI-EMBL Influenza RNA polymerase PB2 middle domain Influenza RNA polymerase PB2 middle domain Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding [1] and endonuclease domains required for transcription initiation by cap-snatching [2]. This entry represents the middle domain in Flu PB2 protein. [1]. 8806170. Recombinant-baculovirus-expressed PB2 subunit of the influenza A virus RNA polymerase binds cap groups as an isolated subunit. Shi L, Galarza JM, Summers DF;. Virus Res 1996;42:1-9. [2]. 26503046. Crystal structure of the RNA-dependent RNA polymerase from influenza C virus. Hengrung N, El Omari K, Serna Martin I, Vreede FT, Cusack S, Rambo RP, Vonrhein C, Bricogne G, Stuart DI, Grimes JM, Fodor E;. Nature. 2015;527:114-117. (from Pfam) NF045260.2 PF20950.2 Flu_PB2_4th 25 25 70 domain Y N N Influenza RNA polymerase PB2 helical domain 26503046,8806170 163604 Nocardiopsis exhalans species 1 EBI-EMBL Influenza RNA polymerase PB2 helical domain Influenza RNA polymerase PB2 helical domain Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding [1] and endonuclease domains required for transcription initiation by cap-snatching [2]. This entry represents the helical domain of Flu PB2 protein. [1]. 8806170. Recombinant-baculovirus-expressed PB2 subunit of the influenza A virus RNA polymerase binds cap groups as an isolated subunit. Shi L, Galarza JM, Summers DF;. Virus Res 1996;42:1-9. [2]. 26503046. Crystal structure of the RNA-dependent RNA polymerase from influenza C virus. Hengrung N, El Omari K, Serna Martin I, Vreede FT, Cusack S, Rambo RP, Vonrhein C, Bricogne G, Stuart DI, Grimes JM, Fodor E;. Nature. 2015;527:114-117. (from Pfam) NF000217.1 MATE_multi_FepA 900 900 443 equivalog Y Y N multidrug efflux MATE transporter FepA fepA 1637 Listeria genus 156 NCBIFAM multidrug efflux MATE transporter FepA multidrug efflux MATE transporter FepA NF001069.0 PRK00118 PRK00118.1-5 194 194 110 equivalog Y Y N putative DNA-binding protein 1637 Listeria genus 39 NCBI Protein Cluster (PRK) putative DNA-binding protein putative DNA-binding protein NF002192.0 PRK01059 PRK01059.1-2 679 679 340 equivalog Y Y N protein arginine kinase 2.7.14.1 1637 Listeria genus 184 NCBI Protein Cluster (PRK) ATP:guanido phosphotransferase protein arginine kinase NF002210.0 PRK01100 PRK01100.1 282 282 210 equivalog Y Y N accessory gene regulator ArgB-like protein 1637 Listeria genus 92 NCBI Protein Cluster (PRK) putative accessory gene regulator protein accessory gene regulator ArgB-like protein NF002582.0 PRK02234 PRK02234.1-3 348 348 201 equivalog Y Y N Holliday junction resolvase RecU recU 3.1.21.10 1637 Listeria genus 79 NCBI Protein Cluster (PRK) Holliday junction-specific endonuclease Holliday junction resolvase RecU NF002766.0 PRK02833 PRK02833.1-4 247 247 137 equivalog Y Y N phosphate-starvation-inducible protein PsiE psiE 1637 Listeria genus 35 NCBI Protein Cluster (PRK) phosphate-starvation-inducible protein PsiE phosphate-starvation-inducible protein PsiE NF003192.0 PRK04164 PRK04164.1-3 341 341 174 equivalog Y N N hypothetical protein 1637 Listeria genus 44 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003408.0 PRK04778 PRK04778.1-2 1122 1122 571 equivalog Y Y N septation ring formation regulator EzrA ezrA 1637 Listeria genus 173 NCBI Protein Cluster (PRK) septation ring formation regulator EzrA septation ring formation regulator EzrA NF004586.0 PRK05928 PRK05928.2-4 401 401 240 equivalog Y Y N uroporphyrinogen-III synthase 4.2.1.75 1637 Listeria genus 241 NCBI Protein Cluster (PRK) uroporphyrinogen-III synthase uroporphyrinogen-III synthase NF004974.0 PRK06347 PRK06347.1 701 701 592 equivalog Y Y N 1,4-beta-N-acetylmuramoylhydrolase 1637 Listeria genus 665 NCBI Protein Cluster (PRK) autolysin 1,4-beta-N-acetylmuramoylhydrolase NF007994.0 PRK10719 PRK10719.1-5 952 952 473 equivalog Y Y N ethanolamine ammonia-lyase reactivating factor EutA eutA 1637 Listeria genus 186 NCBI Protein Cluster (PRK) reactivating factor for ethanolamine ammonia lyase ethanolamine ammonia-lyase reactivating factor EutA NF008875.0 PRK11911 PRK11911.1 274 274 140 equivalog Y N N flagellar basal body rod modification protein 1637 Listeria genus 38 NCBI Protein Cluster (PRK) flagellar basal body rod modification protein flagellar basal body rod modification protein NF009235.0 PRK12585 PRK12585.1 273 273 197 equivalog Y N N putative monovalent cation/H+ antiporter subunit G 1637 Listeria genus 89 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit G putative monovalent cation/H+ antiporter subunit G NF009368.0 PRK12726 PRK12726.1 832 832 407 equivalog Y N N flagellar biosynthesis regulator FlhF 1637 Listeria genus 132 NCBI Protein Cluster (PRK) flagellar biosynthesis regulator FlhF flagellar biosynthesis regulator FlhF NF009447.0 PRK12805 PRK12805.1 404 404 287 equivalog Y Y N FliC/FljB family flagellin 1637 Listeria genus 33 NCBI Protein Cluster (PRK) flagellin FliC/FljB family flagellin NF009643.0 PRK13169 PRK13169.1-4 249 249 129 equivalog Y Y N DNA replication initiation control protein YabA yabA 1637 Listeria genus 36 NCBI Protein Cluster (PRK) DNA replication intiation control protein YabA DNA replication initiation control protein YabA NF009841.0 PRK13316 PRK13316.1 156 156 121 equivalog Y Y N heme oxygenase IsdG isdG 1637 Listeria genus 73 NCBI Protein Cluster (PRK) heme-degrading monooxygenase IsdG heme oxygenase IsdG Iron regulated; catalyzes the release of heme from hemoglobin allowing bacterial pathogens to use the host heme as an iron source NF010197.0 PRK13673 PRK13673.1-4 210 210 120 equivalog Y N N hypothetical protein 1637 Listeria genus 89 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010210.0 PRK13676 PRK13676.1-2 223 223 117 equivalog Y Y N YlbF/YmcA family competence regulator 1637 Listeria genus 28 NCBI Protein Cluster (PRK) hypothetical protein YlbF/YmcA family competence regulator NF010495.0 PRK13914 PRK13914.1 647 647 481 equivalog Y Y N invasion associated endopeptidase 14527997 1637 Listeria genus 313 NCBI Protein Cluster (PRK) invasion associated secreted endopeptidase invasion associated endopeptidase iap; p60; autolytic enzyme; can cleave bacterial peptidoglycan; secreted by SecA2 system NF010667.0 PRK14064 PRK14064.1 134 134 75 equivalog Y Y N exodeoxyribonuclease VII small subunit 1637 Listeria genus 28 NCBI Protein Cluster (PRK) exodeoxyribonuclease VII small subunit exodeoxyribonuclease VII small subunit Catalyzes the bidirectional exonucleolytic cleavage of DNA NF010767.0 PRK14170 PRK14170.1 559 559 284 equivalog Y Y N bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD folD 1637 Listeria genus 175 NCBI Protein Cluster (PRK) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD Catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate NF010810.0 PRK14214 PRK14214.1 132 132 118 equivalog Y Y N fluoride efflux transporter CrcB crcB 1637 Listeria genus 132 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter CrcB NF010827.0 PRK14231 PRK14231.1 143 143 129 equivalog Y Y N fluoride efflux transporter CrcB crcB 1637 Listeria genus 139 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter CrcB NF011015.0 PRK14443 PRK14443.1 131 131 93 equivalog Y Y N acylphosphatase 3.6.1.7 1637 Listeria genus 61 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011125.0 PRK14553 PRK14553.1-5 201 201 105 equivalog Y Y N ribosomal-processing cysteine protease Prp 1637 Listeria genus 57 NCBI Protein Cluster (PRK) hypothetical protein ribosomal-processing cysteine protease Prp NF011973.0 PRK15443 PRK15443.1-4 334 334 170 subfamily Y Y N diol dehydratase small subunit 1637 Listeria genus 83 NCBI Protein Cluster (PRK) propanediol dehydratase small subunit diol dehydratase small subunit NF012136.0 SecA2_Lm 1100 1100 776 equivalog Y Y N accessory Sec system translocase SecA2 secA2 1637 Listeria genus 210 NCBIFAM SecA2_Lm: accessory Sec system translocase SecA2 accessory Sec system translocase SecA2 Members of this family are SecA2, part of a Sec-like preprotein translocase called accessory Sec. This SecA2 family is characteristic of Listeria species. NF016916.5 PF05058.17 ActA 23.8 23.8 633 PfamEq Y Y N actin assembly-inducing protein ActA actA 11854187,11886549 1637 Listeria genus 628 EBI-EMBL ActA Protein actin assembly-inducing protein ActA The ActA family is found in Listeria and is associated with motility. ActA protein acts as a scaffold to assemble and activate host cell actin cytoskeletal factors at the bacterial surface, resulting in directional actin polymerisation and propulsion of the bacterium through the cytoplasm of the host cell [1,2]. [1]. 11886549. Systematic mutational analysis of the amino-terminal domain of the Listeria monocytogenes ActA protein reveals novel functions in actin-based motility. Lauer P, Theriot JA, Skoble J, Welch MD, Portnoy DA;. Mol Microbiol 2001;42:1163-1177. [2]. 11854187. Intracellular induction of Listeria monocytogenes actA expression. Shetron-Rama LM, Marquis H, Bouwer HG, Freitag NE;. Infect Immun 2002;70:1087-1096. (from Pfam) NF017615.5 PF05814.16 Ac76 22.5 22.5 83 PfamAutoEq Y Y N AC76 family protein 20484514 1637 Listeria genus 76 EBI-EMBL Orf76 (Ac76) AC76 family protein This family consists mainly of baculovirus proteins. Family members include Autographa californica multiple nucleopolyhedrovirus (AcMNPV), protein AC76. Ac76 has been shown to be involved in intranuclear microvesicle formation. Functional studies suggest that ac76 is essential for both BV (budded virus) and ODV (occlusion-derived virus) development but is not required for viral DNA synthesis [1]. [1]. 20484514. Autographa californica multiple nucleopolyhedrovirus ac76 is involved in intranuclear microvesicle formation. Hu Z, Yuan M, Wu W, Liu C, Yang K, Pang Y;. J Virol. 2010;84:7437-7447. (from Pfam) NF022119.5 PF10653.14 Phage-A118_gp45 27 27 62 PfamEq Y Y N gp45 family putative tail fiber system protein 1637 Listeria genus 156 EBI-EMBL Protein gp45 of Bacteriophage A118 gp45 family putative tail fiber system protein This domain is found in bacteriophage and is thought to have a gp45 function within the phage tail-fibre system. (from Pfam) NF022120.5 PF10654.14 DUF2481 25.1 25.1 126 domain Y Y N DUF2481 family protein 1637 Listeria genus 203 EBI-EMBL Protein of unknown function (DUF2481) DUF2481 family protein This is a hypothetical protein family homologous to Lmo2305 in Bacteriophage A118 systems. (from Pfam) NF022131.5 PF10666.14 Phage_TAC_8 33.7 33.7 140 PfamEq Y Y N phage tail assembly chaperone 14507382,23542344 1637 Listeria genus 105 EBI-EMBL Phage tail assembly chaperone protein Gp14 ()A118 phage tail assembly chaperone This phage protein family is expressed from within a cluster of tail- and base plate-producing genes [1]. It is a family of tail assembly chaperone proteins [2]. [1]. 14507382. Genome and proteome of Listeria monocytogenes phage PSA: an unusual case for programmed + 1 translational frameshifting in structural protein synthesis. Zimmer M, Sattelberger E, Inman RB, Calendar R, Loessner MJ;. Mol Microbiol. 2003;50:303-317. [2]. 23542344. A conserved spiral structure for highly diverged phage tail assembly chaperones. Pell LG, Cumby N, Clark TE, Tuite A, Battaile KP, Edwards AM, Chirgadze NY, Davidson AR, Maxwell KL;. J Mol Biol. 2013;425:2436-2449. (from Pfam) NF022134.5 PF10669.14 Phage_Gp23 29.3 29.3 120 subfamily Y Y N Gp23 family protein 10652093 1637 Listeria genus 171 EBI-EMBL Protein gp23 (Bacteriophage A118) Gp23 (Bacteriophage A118) family protein Members of this family resemble the uncharacterized protein Gp23 of bacteriophage A118 of Listeria monocytogenes. Note that terms such as Gp23 have different meanings in different lineages. This model once previously cited PMID:11123671, and consequently ascribed a role as a major tail subunit protein based on the Gp23 of an unrelated virus. NF022757.5 PF11313.13 DUF3116 25.9 25.9 84 domain Y Y N DUF3116 family protein 1637 Listeria genus 359 EBI-EMBL Protein of unknown function (DUF3116) DUF3116 family protein This family of proteins with unknown function appears to be restricted to Bacillales. (from Pfam) NF022772.5 PF11328.13 DUF3130 25 25 89 subfamily Y Y N DUF3130 family protein 1637 Listeria genus 1176 EBI-EMBL Protein of unknown function (DUF3130 DUF3130 family protein This bacterial family of proteins has no known function. (from Pfam) NF025722.5 PF14364.11 DUF4408 22 22 33 domain Y Y N DUF4408 domain-containing protein 1637 Listeria genus 3 EBI-EMBL Domain of unknown function (DUF4408) Domain of unknown function (DUF4408) This domain is found at the N-terminus of member of the DUF761 family Pfam:PF05553. Many members are plant proteins. (from Pfam) NF033932.1 LapB_rpt_80 45 30 83 domain Y Y N LapB repeat-containing protein 20617901,27613687 1637 Listeria genus 8137 NCBIFAM LapB repeat-containing protein LapB C-terminal region repeat This model describes a tandem repeat about 80 amino acids in length per repeat, found in at least 12 different surface-exposed proteins of the pathogen Listeria monocytogenes, and in particular found 10 times in tandem in the surface protein LapB, for which the repeat is named. NF033945.1 AcrIIA2_fam 40 40 118 subfamily Y Y N AcrIIA2 family anti-CRISPR protein 28041849 1637 Listeria genus 117 NCBIFAM AcrIIA2 family anti-CRISPR protein AcrIIA2 family anti-CRISPR protein Anti-CRISPR proteins are phage proteins that defeat CRISPR-Cas systems for immunity based on phage-derived spacers found in arrays between CRISPR repeats. The founding member of this family, AcrIIA2, works against a CRISPR-Cas class II system. NF033946.1 AcrIIA4_fam 40 40 86 subfamily Y Y N AcrIIA4 family anti-CRISPR protein 28448066 1637 Listeria genus 41 NCBIFAM AcrIIA4 family anti-CRISPR protein AcrIIA4 family anti-CRISPR protein AcrIIA4 is an anti-CRISPR protein that affects Cas9, a class II CRISPR system protein used in biotechnology applications for targeted genome editing. NF037793.5 PF18341.6 PSA_CBD 27 27 60 domain Y N N PSA endolysin C-terminal cell wall binding domain 17010991 1637 Listeria genus 337 EBI-EMBL PSA endolysin C-terminal cell wall binding domain PSA endolysin C-terminal cell wall binding domain This is the C-terminal domain of bacteriophage PSA endolysin. The C-terminal domain is the cell wall-binding domain (CBD) which is composed of two structurally homologous subdomains. CBD comprises two copies of a beta-barrel-like folds, which are held together by means of swapped beta-strands. The observed structure of the CBD sub-domains from Listeriaphage endolysin (N-acetyl-muramoyl-l-alanine amidase), could be the result of either a gene duplication during evolution of the CBD or the pick-up of another functionally equivalent coding sequence, followed by swapping of the respective ancestral leading beta-strands [1]. [1]. 17010991. The crystal structure of the bacteriophage PSA endolysin reveals a unique fold responsible for specific recognition of Listeria cell walls. Korndorfer IP, Danzer J, Schmelcher M, Zimmer M, Skerra A, Loessner MJ;. J Mol Biol. 2006;364:678-689. (from Pfam) NF040158.4 PF18981.5 InlK_D3 25 25 75 domain Y N N Internalin K domain (D3/D4) 23958637 1637 Listeria genus 8649 EBI-EMBL Internalin K domain (D3/D4) Internalin K domain (D3/D4) This domain is found at the elbow of internalin surface proteins, used by the bacteria to invade mammalian cells. This domain has an Ig-like fold [1]. [1]. 23958637. Structure of internalin InlK from the human pathogen Listeria monocytogenes. Neves D, Job V, Dortet L, Cossart P, Dessen A;. J Mol Biol. 2013;425:4520-4529. (from Pfam) NF041209.1 resp_regPieR 450 450 231 equivalog Y Y N two component system response regulator PieR pieR GO:0000160,GO:0003677,GO:0006355 35943959 1637 Listeria genus 146 NCBIFAM two component system response regulator PieR NF041210.1 his_kin_PieS 850 850 474 equivalog Y Y N two component system sensor histidine kinase PieS pieS GO:0000155,GO:0007165,GO:0016310,GO:0016772 35943959 1637 Listeria genus 221 NCBIFAM two component system sensor histidine kinase PieS NF041889.1 Lmo0654_fam 75 75 61 equivalog Y Y N Lmo0654 family protein 18564909 1637 Listeria genus 79 NCBIFAM Lmo0654 family protein Members of this family of small proteins (about 67 amino acids long) are found in multiple species of the genus Listeria. The function is unknown, but Lmo0654 was shown to be regulated by sigma factor SigB. The family shows apparent homology to SE1832 family proteins (see HMM NF040877), whose members are also found in Gram-positive bacteria. NF046114.1 DA_rpt_lmo1799 200 200 227 equivalog_domain Y Y N Lmo1799 family Asp-Ala repeat surface protein 21444667 1637 Listeria genus 2066 NCBIFAM Lmo1799 family Asp-Ala repeat surface protein N-terminal domain Members of this family, including Lmo1799 from Listeria monocytogenes EGD-e, are sortase-dependent (LPXTG motif-containing) surface proteins of L. monocytogenes, present in some lineages only, and thought to contribute to stress survival and to virulence. A notable feature of this family is a variable length run of Asp-Ala (DA) repeats averaging over 300 amino acids in length. Lmo1799 has often been called a putative peptidoglycan-binding protein. This model represents family a non-repetitive region from the N-terminus to the start of the start of the DA repeats. Lmo1799 is encoded downstream of LipA (Lmo1800). NF047159.1 PF22350.1 Int_EF-hand 29 29 37 domain Y N N Internalin, EF-hand domain 18343406 1637 Listeria genus 1148 EBI-EMBL Internalin, EF-hand domain Internalin, EF-hand domain This entry represents the N-terminal EF-hand domain present in the internalin family [1]. Internalin is a virulence-associated surface protein of Listeria monocytogenes and related bacteria. Paper describing PDB structure 3bz5. [1]. 18343406. Crystal structure and standardized geometric analysis of InlJ, a listerial virulence factor and leucine-rich repeat protein with a novel cysteine ladder. Bublitz M, Holland C, Sabet C, Reichelt J, Cossart P, Heinz DW, Bierne H, Schubert WD;. J Mol Biol. 2008;378:87-96. (from Pfam) NF047192.1 PF22508.1 InlJ_IG 26 26 81 domain Y N N Internalin J, Immunoglobulin-like domain 18343406 1637 Listeria genus 1269 EBI-EMBL Internalin J, Immunoglobulin-like domain Internalin J, Immunoglobulin-like domain This entry represents a immunoglobulin-like domain present in the Internalin J (InlJ) protein from Listeria monocytogenes [1]. Paper describing PDB structure 3bz5. [1]. 18343406. Crystal structure and standardized geometric analysis of InlJ, a listerial virulence factor and leucine-rich repeat protein with a novel cysteine ladder. Bublitz M, Holland C, Sabet C, Reichelt J, Cossart P, Heinz DW, Bierne H, Schubert WD;. J Mol Biol. 2008;378:87-96. (from Pfam) NF047325.1 lmo0673_fam 80 80 69 equivalog Y Y N lmo0673 family protein 32185833 1637 Listeria genus 25 NCBIFAM lmo0673 family protein In Listeria monocytogenes, lmo0673 is encoded immediately downstream of mogR in a bicistronic operon encoded divergently from flagellar genes. MogR is a transcriptional repressor essential for temperature-dependent transcription of flagellar genes. The gene lmo0673 is therefore the treated as the end gene of a large flagellar biosynthesis and motility region from lmo0673 to lmo0718. Lmo0673 is commonly cited as a biofilm formation-associated protein. NF047425.1 MenI_Listeria 185 185 122 exception Y Y N 1,4-dihydroxy-2-naphthoyl-CoA hydrolase MenI menI GO:0009234 28325762,33619030 1637 Listeria genus 146 NCBIFAM 1,4-dihydroxy-2-naphthoyl-CoA hydrolase MenI, Listeria type 1,4-dihydroxy-2-naphthoyl-CoA hydrolase (DHNA hydrolase, EC 3.1.2.28) enzymes have very different sequences in Escherichia coli, Listeria, and Staphylococcus aureus, but all are called MenI. This exception-level model describes the form of this menaquinone biosynthesis enzyme found in Listeria species. NF047857.1 LipGcvHLiptaseLipL 450 450 277 equivalog Y Y N lipoyl-[GcvH]:protein N-lipoyltransferase lipL 2.3.1.200 GO:0009107,GO:0017118 20937762,21768091 1637 Listeria genus 233 NCBIFAM lipoyl-[GcvH]:protein N-lipoyltransferase NF008874.0 PRK11910 PRK11910.1 680 680 615 equivalog Y N N amidase 1639 Listeria monocytogenes species 269 NCBI Protein Cluster (PRK) amidase amidase NF033186.1 internalin_K 1100 1100 604 exception Y Y Y class 1 internalin InlK inlK 17764999,21829365,22082958,23958637 1639 Listeria monocytogenes species 315 NCBIFAM internalin K class 1 internalin InlK Internalins, as found in the intracellular human pathogen Listeria monocytogenes, are paralogous surface-anchored proteins with an N-terminal signal peptide, leucine-rich repeats, and a C-terminal LPXTG processing and cell surface anchoring site. Members of this family are internalin K (InlK), a virulence factor. See articles PMID:17764999. for a general discussion of internalins, and PMID:21829365, PMID:22082958, and PMID:23958637 for more information about internalin K. NF033187.0 internalin_J 1700 1700 846 exception Y Y N class 1 internalin InlJ inlJ 17764999 1639 Listeria monocytogenes species 250 NCBIFAM internalin J class 1 internalin InlJ Internalins, as found in the intracellular human pathogen Listeria monocytogenes, are paralogous surface-anchored proteins with an N-terminal signal peptide, leucine-rich repeats, and a C-terminal LPXTG processing and cell surface anchoring site. See PMID:17764999 for a general discussion of internalins. Members of this family are internalin J (InlJ). NF033188.1 internalin_H 1050 1050 548 exception Y Y N InlH/InlC2 family class 1 internalin inlH 17764999 1639 Listeria monocytogenes species 296 NCBIFAM internalin H InlH/InlC2 family class 1 internalin Internalins, as found in the intracellular human pathogen Listeria monocytogenes, are paralogous surface or secreted proteins with an N-terminal signal peptide, leucine-rich repeats, and usually a C-terminal LPXTG processing and cell surface anchoring site. See PMID:17764999 for a general discussion of internalins. Members of this family are internalin H (InlH), or internalin C2, two class 1 (LPXTG-type) internalins that are closely related, one apparently derived from the other through a recombination event. NF033189.1 internalin_A 1600 1600 799 exception Y Y Y class 1 internalin InlA inlA 17764999 1639 Listeria monocytogenes species 292 NCBIFAM internalin A class 1 internalin InlA Internalins, as found in the intracellular human pathogen Listeria monocytogenes, are paralogous surface or secreted proteins with an N-terminal signal peptide, leucine-rich repeats, and usually a C-terminal LPXTG processing and cell surface anchoring site. See PMID:17764999 for a general discussion of internalins. Members of this family are internalin A (InlA), a class 1 (LPXTG-type) internalin. NF033201.1 Vip_LPXTG_Lm 600 400 414 exception Y Y Y cell invasion LPXTG protein Vip vip 16015374 1639 Listeria monocytogenes species 149 NCBIFAM cell invasion LPXTG protein Vip cell invasion LPXTG protein Vip Vip (Virulence protein), like the LPXTG-type internalins, is an LPXTG-anchored surface protein of the mammalian cell-invading pathogen Listeria monocytogenes, but absent from the related species Listeria innocua. For certain cell types, Vip is required for Listeria's ability to invade. It appears to bind the endoplasmic reticulum (ER) resident chaperone Gp96 as its receptor. NF036383.5 PF17606.7 DUF5502 27 27 87 PfamEq Y Y N DUF5502 family protein 1639 Listeria monocytogenes species 96 EBI-EMBL Family of unknown function (DUF5502) DUF5502 family protein This is a family of unknown function found in Listeria. (from Pfam). This small protein, a possible lipoprotein, is found in Listeria monocytogenes. NF046256.1 PF22390.1 LntA_helical 26 26 133 domain Y N N LntA, four-helical up-and-down bundle 21252314,24449750 1639 Listeria monocytogenes species 195 EBI-EMBL LntA, four-helical up-and-down bundle LntA, four-helical up-and-down bundle This entry represents an helical domain present in LntA protein, a virulence factor from Listeria monocytogenes [1,2]. LntA target the chromatin repressor BAHD1 in the host cell nucleus to activate interferon-stimulated genes. Paper describing PDB structure 2xl4. [1]. 21252314. A bacterial protein targets the BAHD1 chromatin complex to stimulate type III interferon response. Lebreton A, Lakisic G, Job V, Fritsch L, Tham TN, Camejo A, Mattei PJ, Regnault B, Nahori MA, Cabanes D, Gautreau A, Ait-Si-Ali S, Dessen A, Cossart P, Bierne H;. Science. 2011;331:1319-1321. Paper describing PDB structure 4cih. [2]. 24449750. Structural basis for the inhibition of the chromatin repressor BAHD1 by the bacterial nucleomodulin LntA. Lebreton A, Job V, Ragon M, Le Monnier A, Dessen A, Cossart P, Bierne H;. mBio. 2014;5:e00775-e00713. (from Pfam) NF046266.1 PF22416.1 Lmo2445-like_C 27 27 94 domain Y N N Lmo2445-like, C-terminal domain 1639 Listeria monocytogenes species 156 EBI-EMBL Lmo2445-like, C-terminal domain Lmo2445-like, C-terminal domain This domain is found at the C-terminal end of the Lmo2445 protein from Listeria monocytogenes. This domain shows a immunoglobulin -like fold. (from Pfam) NF022301.5 PF10845.13 DUF2576 20.4 20.4 48 domain Y Y N DUF2576 domain-containing protein 1643443 Microbacterium sp. Ag1 species 1 EBI-EMBL Protein of unknown function (DUF2576) Protein of unknown function (DUF2576) The function of this viral family of proteins is unknown. (from Pfam) NF001396.0 PRK00281 PRK00281.3-3 382 382 264 equivalog Y Y N undecaprenyl-diphosphate phosphatase 3.6.1.27 1643685 Borreliaceae family 110 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate phosphatase undecaprenyl-diphosphate phosphatase NF001538.0 PRK00364 PRK00364.3-4 142 142 92 equivalog Y Y N co-chaperone GroES groES 1643685 Borreliaceae family 38 NCBI Protein Cluster (PRK) co-chaperonin GroES co-chaperone GroES NF002358.0 PRK01318 PRK01318.2-5 605 605 545 equivalog Y Y N membrane protein insertase YidC yidC 1643685 Borreliaceae family 136 NCBI Protein Cluster (PRK) membrane protein insertase membrane protein insertase YidC NF008698.0 PRK11713 PRK11713.4-5 393 393 242 equivalog Y Y N 16S rRNA (uracil(1498)-N(3))-methyltransferase 2.1.1.193 1643685 Borreliaceae family 120 NCBI Protein Cluster (PRK) 16S ribosomal RNA methyltransferase RsmE 16S rRNA (uracil(1498)-N(3))-methyltransferase NF009265.0 PRK12622 PRK12622.1 145 145 135 equivalog Y N N flagellar basal body rod protein FlgB 1643685 Borreliaceae family 92 NCBI Protein Cluster (PRK) flagellar basal body rod protein FlgB flagellar basal body rod protein FlgB NF009348.0 PRK12706 PRK12706.1 444 444 328 equivalog Y N N flagellar basal body P-ring protein 1643685 Borreliaceae family 139 NCBI Protein Cluster (PRK) flagellar basal body P-ring protein flagellar basal body P-ring protein NF009366.0 PRK12723 PRK12723.1 585 585 388 equivalog Y N N flagellar biosynthesis regulator FlhF 1643685 Borreliaceae family 54 NCBI Protein Cluster (PRK) flagellar biosynthesis regulator FlhF flagellar biosynthesis regulator FlhF NF009445.0 PRK12803 PRK12803.1 450 450 335 equivalog Y N N flagellin 1643685 Borreliaceae family 65 NCBI Protein Cluster (PRK) flagellin flagellin NF009863.0 PRK13326 PRK13326.1 412 412 264 equivalog Y Y N type III pantothenate kinase 1643685 Borreliaceae family 117 NCBI Protein Cluster (PRK) pantothenate kinase type III pantothenate kinase Catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP NF009950.0 PRK13414 PRK13414.1 306 306 209 equivalog Y N N flagellar biosynthesis protein FliZ 1643685 Borreliaceae family 96 NCBI Protein Cluster (PRK) flagellar biosynthesis protein FliZ flagellar biosynthesis protein FliZ NF010017.0 PRK13494 PRK13494.1 285 285 163 equivalog Y N N chemoreceptor glutamine deamidase CheD 1643685 Borreliaceae family 76 NCBI Protein Cluster (PRK) chemoreceptor glutamine deamidase CheD chemoreceptor glutamine deamidase CheD NF010878.0 PRK14285 PRK14285.1 551 551 365 equivalog Y N N chaperone protein DnaJ 1643685 Borreliaceae family 99 NCBI Protein Cluster (PRK) chaperone protein DnaJ chaperone protein DnaJ NF010930.0 PRK14350 PRK14350.1 652 652 669 equivalog Y N N NAD-dependent DNA ligase LigA 1643685 Borreliaceae family 157 NCBI Protein Cluster (PRK) NAD-dependent DNA ligase LigA NAD-dependent DNA ligase LigA NF011006.0 PRK14432 PRK14432.1 105 105 92 equivalog Y Y N acylphosphatase 3.6.1.7 1643685 Borreliaceae family 69 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011107.0 PRK14534 PRK14534.1 744 744 481 equivalog Y Y N cysteine--tRNA ligase 6.1.1.16 1643685 Borreliaceae family 139 NCBI Protein Cluster (PRK) cysteinyl-tRNA synthetase cysteine--tRNA ligase Catalyzes a two-step reaction; charges a cysteine by linking its carboxyl group to the alpha-phosphate of ATP then transfers the aminoacyl-adenylate to its tRNA NF011115.0 PRK14543 PRK14543.1 287 287 169 equivalog Y Y N nucleoside-diphosphate kinase 2.7.4.6 1643685 Borreliaceae family 87 NCBI Protein Cluster (PRK) nucleoside diphosphate kinase nucleoside-diphosphate kinase Catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate NF011123.0 PRK14553 PRK14553.1-3 178 178 110 equivalog Y Y N ribosomal-processing cysteine protease Prp 1643685 Borreliaceae family 95 NCBI Protein Cluster (PRK) hypothetical protein ribosomal-processing cysteine protease Prp NF011168.0 PRK14570 PRK14570.1 505 505 364 equivalog Y N N D-alanyl-alanine synthetase A 1643685 Borreliaceae family 125 NCBI Protein Cluster (PRK) D-alanyl-alanine synthetase A D-alanyl-alanine synthetase A NF011188.0 PRK14594 PRK14594.1 174 174 166 equivalog Y N N 16S rRNA-processing protein RimM 1643685 Borreliaceae family 111 NCBI Protein Cluster (PRK) 16S rRNA-processing protein RimM 16S rRNA-processing protein RimM NF011223.0 PRK14630 PRK14630.1 143 143 145 equivalog Y Y N ribosome maturation factor RimP rimP 1643685 Borreliaceae family 91 NCBI Protein Cluster (PRK) hypothetical protein ribosome maturation factor RimP NF011264.0 PRK14670 PRK14670.1 1021 1021 602 equivalog Y N N excinuclease ABC subunit C 1643685 Borreliaceae family 164 NCBI Protein Cluster (PRK) excinuclease ABC subunit C excinuclease ABC subunit C NF011400.0 PRK14825 PRK14825.1 246 246 199 equivalog Y N N putative deoxyribonucleotide triphosphate pyrophosphatase 1643685 Borreliaceae family 113 NCBI Protein Cluster (PRK) putative deoxyribonucleotide triphosphate pyrophosphatase putative deoxyribonucleotide triphosphate pyrophosphatase NF011410.0 PRK14837 PRK14837.1 342 342 230 equivalog Y N N undecaprenyl pyrophosphate synthase 1643685 Borreliaceae family 118 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate synthase undecaprenyl pyrophosphate synthase NF013114.5 PF00921.22 Lipoprotein_2 22.6 22.6 298 subfamily Y Y N variable large family protein GO:0016020 1643685 Borreliaceae family 3142 EBI-EMBL Borrelia lipoprotein variable large family protein This family of lipoproteins is found in Borrelia spirochetes. The function of these proteins is uncertain. (from Pfam) NF013808.5 PF01672.21 Plasmid_parti 22.1 22.1 85 domain Y Y N plasmid partition family protein 8655548,9695920 1643685 Borreliaceae family 1350 EBI-EMBL Putative plasmid partition protein plasmid partition family protein This family consists of conserved hypothetical proteins from Borrelia burgdorferi the lyme disease spirochaete, some of which are putative plasmid partition proteins [1]. [1]. 9695920. Evidence of past recombination events among the genes encoding the Erp antigens of Borrelia burgdorferi. Stevenson B, Casjens S, Rosa P;. Microbiology 1998;144:1869-1879. [2]. 8655548. A family of genes located on four separate 32-kilobase circular plasmids in Borrelia burgdorferi B31. Stevenson B, Tilly K, Rosa PA;. J Bacteriol 1996;178:3508-3516. (from Pfam) NF014468.5 PF02414.20 Borrelia_orfA 25.8 25.8 288 subfamily Y Y N plasmid maintenance protein 8636030 1643685 Borreliaceae family 2919 EBI-EMBL Borrelia ORF-A plasmid maintenance protein This protein is encoded by an open reading frame in plasmid borne DNA repeats of Borrelia species. This protein is known as ORF-A [1]. The function of this putative protein is unknown. [1]. 8636030. Circular and linear plasmids of Lyme disease spirochetes have extensive homology: characterization of a repeated DNA element. Zuckert WR, Meyer J;. J Bacteriol 1996;178:2287-2298. (from Pfam) NF014889.5 PF02890.19 DUF226 25 25 139 domain Y Y N DUF226 domain-containing protein 1643685 Borreliaceae family 1519 EBI-EMBL Borrelia family of unknown function DUF226 Borrelia family of unknown function DUF226 This family of proteins are found in Borrelia. The proteins are about 190 amino acids long and have no known function. (from Pfam) NF014983.5 PF02989.19 DUF228 25 25 182 subfamily Y Y N DUF228 domain-containing protein 1643685 Borreliaceae family 1385 EBI-EMBL Lyme disease proteins of unknown function Lyme disease proteins of unknown function NF014992.5 PF02999.19 Borrelia_orfD 27 27 100 subfamily Y Y N BBA14 family lipoprotein 8655511 1643685 Borreliaceae family 604 EBI-EMBL Borrelia orf-D family BBA14 family lipoprotein Borrelia burgdorferi supercoiled plasmids encode multicopy tandem open reading frames called Orf-A, Orf-B, Orf-C and Orf-D. This family corresponds to Orf-D. The putative product of this gene has no known function. [1]. 8655511. Borrelia burgdorferi supercoiled plasmids encode multicopy tandem open reading frames and a lipoprotein gene family. Porcella SF, Popova TG, Akins DR, Li M, Radolf JD, Norgard MV;. J Bacteriol 1996;178:3293-3307. (from Pfam) NF015096.5 PF03112.19 DUF244 22 22 161 domain Y Y N DUF244 domain-containing protein 10672174 1643685 Borreliaceae family 690 EBI-EMBL Uncharacterized protein family (ORF7) DUF Uncharacterized protein family (ORF7) DUF Several members of this family are Borrelia burgdorferi plasmid proteins of uncharacterized function. [1]. 10672174. A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi. Casjens S, Palmer N, van Vugt R, Huang WM, Stevenson B, Rosa P, Lathigra R, Sutton G, Peterson J, Dodson RJ, Haft D, Hickey E, Gwinn M, White O, Fraser CM;. Mol Microbiol 2000;35:490-516. (from Pfam) NF015173.5 PF03196.18 DUF261 26.1 26.1 137 subfamily Y Y N DUF261 family protein 1643685 Borreliaceae family 792 EBI-EMBL Protein of unknown function, DUF261 DUF261 family protein NF015275.5 PF03304.18 Mlp 21 21 121 subfamily Y Y N Mlp family lipoprotein 10531261,9488385 1643685 Borreliaceae family 839 EBI-EMBL Mlp lipoprotein family Mlp family lipoprotein The Mlp (for Multicopy Lipoprotein) family of lipoproteins is found in Borrelia species [1]. This family were previously known as 2.9 lipoprotein genes [2]. These surface expressed genes may represent new candidate vaccinogens for Lyme disease [1]. Members of this family generally are downstream of four ORFs called A,B,C and D that are involved in hemolytic activity. [1]. 9488385. A monoclonal antibody generated by antigen inoculation via tick bite is reactive to the Borrelia burgdorferi Rev protein, a member of the 2.9 gene family locus. Gilmore RD Jr, Mbow ML;. Infect Immun 1998;66:980-986. [2]. 10531261. Identification, characterization, and expression of three new members of the Borrelia burgdorferi Mlp (2.9) lipoprotein gene family. Yang X, Popova TG, Hagman KE, Wikel SK, Schoeler GB, Caimano MJ, Radolf JD, Norgard MV;. Infect Immun 1999;67:6008-6018. (from Pfam) NF015399.5 PF03434.18 DUF276 25 25 291 subfamily Y Y N DUF276 domain-containing protein 1643685 Borreliaceae family 707 EBI-EMBL DUF276 DUF276 family protein This family is specific to Borrelia burgdorferi. The protein is encoded on extra-chromosomal DNA. This domain has no known function. (from Pfam). DUF276 is restricted to Borreliella and related spirochetes. NF016941.5 PF05085.17 DUF685 25 25 265 domain Y Y N DUF685 domain-containing protein 1643685 Borreliaceae family 701 EBI-EMBL Protein of unknown function (DUF685) Protein of unknown function (DUF685) This family consists of several uncharacterised proteins from Borrelia burgdorferi (Lyme disease spirochete). There is some evidence to suggest that the proteins may be outer surface proteins. (from Pfam) NF016958.5 PF05102.17 Holin_BlyA 27 27 61 subfamily Y Y N BlyA family holin 11073925,17897882 1643685 Borreliaceae family 234 EBI-EMBL holin, BlyA family BlyA family holin BlyA, a small holin found in Borrelia circular plasmids that is encoded by a prophage. BlyA contains two largely hydrophobic helices and a highly charged C-terminus and has two transmembrane segments [1]. [1]. 11073925. Characterization of Borrelia burgdorferi BlyA and BlyB proteins: a prophage-encoded holin-like system. Damman CJ, Eggers CH, Samuels DS, Oliver DB;. J Bacteriol 2000;182:6791-6797. [2]. 17897882. Release of latent ClyA cytolysin from Escherichia coli mediated by a bacteriophage-associated putative holin (BlyA) from Borrelia burgdorferi. Ludwig A, von Rhein C, Mischke A, Brade V;. Int J Med Microbiol. 2008;298:473-481. (from Pfam) NF016969.5 PF05113.18 DUF693 25 25 313 subfamily Y Y N DUF693 family protein 1643685 Borreliaceae family 637 EBI-EMBL Protein of unknown function (DUF693) DUF693 family protein This family consists of several uncharacterised proteins from Borrelia burgdorferi (Lyme disease spirochete). (from Pfam) NF017093.5 PF05246.16 DUF735 23.4 23.4 211 subfamily Y Y N DUF735 family protein 1643685 Borreliaceae family 522 EBI-EMBL Protein of unknown function (DUF735) DUF735 family protein This family consists of several uncharacterised Borrelia burgdorferi (Lyme disease spirochete) proteins of unknown function. (from Pfam) NF017132.5 PF05289.16 BLYB 25 25 120 subfamily Y Y N BlyB family putative holin accessory protein 11073925,8655511 1643685 Borreliaceae family 828 EBI-EMBL Borrelia hemolysin accessory protein BlyB family putative holin accessory protein This family consists of several borrelia hemolysin accessory proteins (BLYB). BLYB was thought to be an accessory protein, which was proposed to comprise a hemolysis system but it is now thought that BlyA and BlyB function instead as a prophage-encoded holin or holin-like system [1]. [1]. 11073925. Characterization of Borrelia burgdorferi BlyA and BlyB proteins: a prophage-encoded holin-like system. Damman CJ, Eggers CH, Samuels DS, Oliver DB;. J Bacteriol 2000;182:6791-6797. [2]. 8655511. Borrelia burgdorferi supercoiled plasmids encode multicopy tandem open reading frames and a lipoprotein gene family. Porcella SF, Popova TG, Akins DR, Li M, Radolf JD, Norgard MV;. J Bacteriol 1996;178:3293-3307. (from Pfam) NF017358.5 PF05537.16 DUF759 27 27 429 subfamily Y Y N DUF759 family protein 1643685 Borreliaceae family 616 EBI-EMBL Borrelia burgdorferi protein of unknown function (DUF759) DUF759 family protein This family consists of several uncharacterised proteins from the Lyme disease spirochete Borrelia burgdorferi. (from Pfam) NF017382.5 PF05561.16 DUF764 25 25 182 subfamily Y Y N DUF764 family protein 1643685 Borreliaceae family 531 EBI-EMBL Borrelia burgdorferi protein of unknown function (DUF764) DUF764 family protein This family consists of proteins of unknown function from Borrelia burgdorferi (Lyme disease spirochete). (from Pfam) NF017423.5 PF05606.16 DUF777 25 25 135 subfamily Y Y N DUF777 family protein 1643685 Borreliaceae family 527 EBI-EMBL Borrelia burgdorferi protein of unknown function (DUF777) DUF777 family protein This family consists of several hypothetical proteins of unknown function from Borrelia burgdorferi (Lyme disease spirochete). (from Pfam) NF017435.5 PF05619.16 DUF787 25 25 369 subfamily Y Y N DUF787 family protein 1643685 Borreliaceae family 750 EBI-EMBL Borrelia burgdorferi protein of unknown function (DUF787) DUF787 family protein This family consists of several hypothetical proteins of unknown function from Borrelia burgdorferi (Lyme disease spirochete). (from Pfam) NF017448.5 PF05632.16 DUF792 25 25 184 subfamily Y Y N DUF792 family protein 1643685 Borreliaceae family 482 EBI-EMBL Borrelia burgdorferi protein of unknown function (DUF792) DUF792 family protein This family consists of several hypothetical proteins from the Lyme disease spirochete Borrelia burgdorferi. (from Pfam) NF017525.5 PF05714.16 PFam54_60 27 27 185 domain Y Y N CRASP family complement regulator-acquiring lipoprotein 10456881,15711564,32135236 1643685 Borreliaceae family 2374 EBI-EMBL Borrelia Bbcrasp-1 domain containing protein CRASP family complement regulator-acquiring lipoprotein This family contains lipoproteins from the Lyme disease spirochete Borrelia burgdorferi and related bacteria. This entry contains proteins from Paralogous family 54 (PFam54) and 60 and (PFam60). The first crystal structure of B. burgdorferi PFam54 member BBA68 revealed a previously unseen novel fold, which, according to the CATH protein domain classification, was named the Bbcrasp-1 fold because of the common name used for the protein BBA68 [2]. [1]. 10456881. Cloning and molecular characterization of plasmid-encoded antigens of Borrelia burgdorferi. Skare JT, Foley DM, Hernandez SR, Moore DC, Blanco DR, Miller JN, Lovett MA;. Infect Immun 1999;67:4407-4417. [2]. 15711564. A novel fold for the factor H-binding protein BbCRASP-1 of Borrelia burgdorferi. Cordes FS, Roversi P, Kraiczy P, Simon MM, Brade V, Jahraus O, Wallis R, Skerka C, Zipfel PF, Wallich R, Lea SM;. Nat Struct Mol Biol. 2005;12:276-277. [3]. 32135236. Structural analysis of the outer surface proteins from Borrelia burgdorferi paralogous gene family 54 that are thought to be the key players in the pathogenesis of Lyme disease. Brangulis K, Akopjana I, Petrovskis I, Kazaks A, Tars K;. J Struct Biol. 2020; [Epub ahead of print] (from Pfam) NF018761.5 PF07094.16 DUF1357 22 22 223 subfamily Y Y N DUF1357 family protein 1643685 Borreliaceae family 579 EBI-EMBL Protein of unknown function (DUF1357) DUF1357 family protein This family consists of several hypothetical bacterial proteins of around 225 residues in length. Members of this family appear to be specific Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown. (from Pfam) NF018920.5 PF07268.16 EppA_BapA 29.1 29.1 138 PfamEq Y N N Exported protein precursor (EppA/BapA) 12724373 1643685 Borreliaceae family 143 EBI-EMBL Exported protein precursor (EppA/BapA) Exported protein precursor (EppA/BapA) This family consists of a number of exported protein precursor (EppA and BapA) sequences which seem to be specific to Borrelia burgdorferi (Lyme disease spirochete). bapA gene sequences are quite stable but the encoded proteins do not provoke a strong immune response in most individuals. Conversely, EppA proteins are much more antigenic but are more variable in sequence. It is thought that BapA and EppA play important roles during the Borrelia burgdorferi infectious cycle [1]. [1]. 12724373. Immunological and genetic characterization of Borrelia burgdorferi BapA and EppA proteins. Miller JC, Stevenson B;. Microbiology 2003;149:1113-1125. (from Pfam) NF018966.5 PF07316.16 DUF1463 25 25 137 domain Y Y N DUF1463 family protein 1643685 Borreliaceae family 342 EBI-EMBL Protein of unknown function (DUF1463) DUF1463 family protein This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be found exclusively in Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown. (from Pfam) NF018989.5 PF07341.16 DUF1473 25 25 163 subfamily Y Y N DUF1473 family protein 1643685 Borreliaceae family 406 EBI-EMBL Protein of unknown function (DUF1473) DUF1473 family protein This family consists of several hypothetical bacterial proteins of around 150 residues in length. Members of this family seem to be found exclusively in Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown. (from Pfam) NF019051.5 PF07405.16 DUF1506 25 25 127 domain Y Y N DUF1506 family protein 1643685 Borreliaceae family 374 EBI-EMBL Protein of unknown function (DUF1506) DUF1506 family protein This family consists of several bacterial proteins of around 130 residues in length. Members of this family seem to be specific to Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown. (from Pfam) NF022707.5 PF11263.13 Attachment_P66 25.2 25.2 253 subfamily Y Y N integrin-binding adhesin P66 family protein 12748384 1643685 Borreliaceae family 175 EBI-EMBL Borrelia burgdorferi attachment protein P66 integrin-binding adhesin P66 family protein P66 is an outer membrane protein in Borrelia burgdorferi, the agent of Lyme disease. P66 has a role in the attachment of Borrelia burgdorferi to human cell-surface receptors [1]. [1]. 12748384. Targeted mutation of the outer membrane protein P66 disrupts attachment of the Lyme disease agent, Borrelia burgdorferi, to integrin alphavbeta3. Coburn J, Cugini C;. Proc Natl Acad Sci U S A. 2003;100:7301-7306. (from Pfam) NF024429.5 PF13029.11 DUF3890 22.8 22.8 84 domain Y Y N DUF3890 domain-containing protein 1643685 Borreliaceae family 442 EBI-EMBL Domain of unknown function (DUF3890) Domain of unknown function (DUF3890) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 70 amino acids in length. (from Pfam) NF024560.5 PF13161.11 DUF3996 22 22 154 subfamily Y Y N BAPKO_0422 family outer member beta-barrel protein 26181365 1643685 Borreliaceae family 535 EBI-EMBL Protein of unknown function (DUF3996) BAPKO_0422 family outer member beta-barrel protein Members of this family of spirochete outer membrane beta-barrel proteins include BAPKO_0422 from Borrelia afzelii, which was shown to bind human factor H, a regulator of complement activation. NF028354.5 PF17044.10 BPTA 27 27 196 domain Y N N Borrelial persistence in ticks protein A 1643685 Borreliaceae family 210 EBI-EMBL Borrelial persistence in ticks protein A Borrelial persistence in ticks protein A BPTA is a family of proteins that are found in Borrelia species. The function is not known. (from Pfam) NF033721.0 P12_lipo 50 50 294 equivalog Y Y N P12 family lipoprotein 19936201 1643685 Borreliaceae family 495 NCBIFAM P12 family lipoprotein P12 family lipoprotein NF033723.0 S2_P23 150 150 179 equivalog Y Y N S2/P23 family protein 1643685 Borreliaceae family 451 NCBIFAM S2/P23 family protein S2/P23 family protein NF033724.0 P13_porin 100 100 178 equivalog Y Y N P13 family porin 24825899 1643685 Borreliaceae family 215 NCBIFAM P13 family porin P13 family porin NF033725.0 borfam_49 60 60 150 equivalog Y Y N chromosome replication/partitioning protein 15150244 1643685 Borreliaceae family 1285 NCBIFAM chromosome replication/partitioning protein chromosome replication/partitioning protein NF033728.0 borfam54_1 30 30 377 equivalog Y Y N complement regulator-acquiring protein 16824109,23630963 1643685 Borreliaceae family 658 NCBIFAM complement regulator-acquiring protein complement regulator-acquiring protein NF033729.0 borfam54_2 30 30 226 equivalog Y Y N complement regulator-acquiring protein 23219363,28453837 1643685 Borreliaceae family 1329 NCBIFAM complement regulator-acquiring protein complement regulator-acquiring protein NF033730.0 borfam54_3 30 30 292 equivalog Y Y N complement regulator-acquiring protein 23618869,28453837 1643685 Borreliaceae family 474 NCBIFAM complement regulator-acquiring protein complement regulator-acquiring protein NF033732.0 borfam95 60 60 176 equivalog Y Y N exported protein A EppA eppA 22544270 1643685 Borreliaceae family 125 NCBIFAM exported protein A EppA exported protein A EppA NF040499.1 Bdr_N_group1 40 40 52 subfamily Y Y N Bdr family repetitive protein bdr 10644495 1643685 Borreliaceae family 1056 NCBIFAM Bdr protein N-terminal domain Bdr (Borrelia direct repeat) proteins have an N-terminal domain, a variable length region of repeats, typically 11 amino acids long with a KID repeat, and a non-repetitive C-terminal domain. This HMM describes the conserved N-terminal domain of families designated BdrA, BdrB, and BdrC. A related but non-overlapping model, NF040500, describes the N-terminal domain of additional Bdr families. NF040500.1 Bdr_N_group2 40 40 47 subfamily Y Y N Bdr family repetitive protein bdr 1643685 Borreliaceae family 495 NCBIFAM Bdr protein N-terminal domain Bdr (Borrelia direct repeat) proteins have an N-terminal domain, a variable length region of repeats, typically 11 amino acids long with a KID repeat, and a non-repetitive C-terminal domain. This HMM describes the conserved N-terminal domain of families other than BdrA, BdrB, and BdrC, which are described by sister model NF040499. NF041829.1 Borr_BB0208 600 600 558 equivalog Y Y N BB_0208 family protein 1643685 Borreliaceae family 130 NCBIFAM BB_0208 family protein This family is named for uncharacterized protein BB_0208 from the Lyme disease spirochete Borrelia burgdorferi. Members average about 570 amino acids in length and are found in over twenty species of Borrelia and Borreliella. NF045885.1 PhCholSynBorr 400 400 234 equivalog Y Y N phosphatidylcholine synthase pcsA 2.7.8.24 GO:0008654,GO:0050520 14663079,14766917 1643685 Borreliaceae family 108 NCBIFAM phosphatidylcholine synthase NF046295.1 PF22487.1 CRASP-2 27 27 206 domain Y N N Complement regulator-acquiring surface protein 2 24702793 1643685 Borreliaceae family 112 EBI-EMBL Complement regulator-acquiring surface protein 2 Complement regulator-acquiring surface protein 2 This protein family includes Complement regulator-acquiring surface protein 2 from Borreliella burgdorferi (CRASP-2, also known as CspZ), the causative agent of Lyme disease. CRASP-2 can bind both the major alternative pathway complement regulator factor H (CFH) and factor H-like protein 1 (CFHL-1), contributing to the resistance of the bacteria to the host's immune response. This protain consists of a single domain almost entirely formed by alpha-helices [1]. Paper describing PDB structure 4bg0. [1]. 24702793. Structural characterization of CspZ, a complement regulator factor H and FHL-1 binding protein from Borrelia burgdorferi. Brangulis K, Petrovskis I, Kazaks A, Bogans J, Otikovs M, Jaudzems K, Ranka R, Tars K;. FEBS J. 2014;281:2613-2622. (from Pfam) NF047327.1 OMP_BB0027 300 300 211 subfamily Y Y N BB0027 family outer member beta-barrel protein 26181365 1643685 Borreliaceae family 84 NCBIFAM BB0027 family outer member beta-barrel protein Members of this family, including founding protein BB0027, are OmpW-like outer membrane beta-barrel proteins from Borrelia burgdorferi and related spirochetes. NF047404.1 cdiGMPrecepPlzA 450 450 261 equivalog Y Y N c-di-GMP-binding receptor PlzA plzA 20030712,21357718,30050868 1643685 Borreliaceae family 94 NCBIFAM c-di-GMP-binding receptor PlzA TIGR01606.1 TIGR01606 holin_BlyA 52.85 52.85 63 equivalog Y Y N BlyA family holin GO:0140911 11073925 1643685 Borreliaceae family 179 JCVI holin, BlyA family holin, BlyA family This family represents a BlyA, a small holin found in Borrelia circular plasmids that prove to be temperate phage. This protein was previously proposed to be an hemolysin. BlyA is small (67 residues) and contains two largely hydrophobic helices and a highly charged C-terminus. TIGR04419.1 TIGR04419 no_iron_rSAM 300 300 378 equivalog Y Y N HemN-related non-iron pseudo-SAM protein PsgB psgB 10834845 1643685 Borreliaceae family 150 JCVI HemN-related non-iron pseudo-SAM protein PsgB HemN-related non-iron pseudo-SAM protein PsgB Members of this protein family are related to radical SAM enzymes HemN (oxygen-independent coproporphyrinogen III oxidase) and HutW (a putative heme utilization enzyme) but lack the signature CxxxCxxC motif for 4Fe-4S binding. Members occur exclusively in Borrelia, which appears to live without iron, as the only radical SAM enzyme homolog in any Borrelia genome. We designate this enzyme PsgB (Pseudo-SAM, Genus Borrelia). NF041661.1 Cycl_ph_dihydrol 500 500 259 equivalog Y Y N phosphoribosyl 1,2-cyclic phosphate 1,2-diphosphodiesterase phnPP 3.1.4.57 GO:0102561 24147537 1643826 Eggerthellaceae family 46 NCBIFAM phosphoribosyl 1,2-cyclic phosphate 1,2-diphosphodiesterase NF041913.1 HVO_2142 90 90 48 equivalog Y Y N HVO_2142 family zinc finger protein GO:0008270 31083437 1644056 Haloferacaceae family 56 NCBIFAM HVO_2142 family zinc finger protein Short proteins of this family are important for stress adaptation, biofilm formation, and swarming. NF005445.0 PRK07034 PRK07034.1 703 703 536 equivalog Y N N hypothetical protein 1649845 Yersinia pseudotuberculosis complex species group 34 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006774.0 PRK09290 PRK09290.2-4 897 897 427 equivalog Y Y N allantoate amidohydrolase 1649845 Yersinia pseudotuberculosis complex species group 37 NCBI Protein Cluster (PRK) allantoate amidohydrolase allantoate amidohydrolase NF008225.0 PRK10993 PRK10993.1-5 654 654 311 equivalog Y Y N omptin family outer membrane protease 3.4.23.49 1649845 Yersinia pseudotuberculosis complex species group 26 NCBI Protein Cluster (PRK) outer membrane protease omptin family outer membrane protease NF008679.0 PRK11700 PRK11700.1-2 391 391 191 equivalog Y Y N VOC family protein 1649845 Yersinia pseudotuberculosis complex species group 11 NCBI Protein Cluster (PRK) hypothetical protein VOC family protein NF009108.0 PRK12456 PRK12456.1 398 398 199 equivalog Y N N Na(+)-translocating NADH-quinone reductase subunit E 1649845 Yersinia pseudotuberculosis complex species group 5 NCBI Protein Cluster (PRK) Na(+)-translocating NADH-quinone reductase subunit E Na(+)-translocating NADH-quinone reductase subunit E NF009836.0 PRK13311 PRK13311.1 551 551 256 equivalog Y N N N-acetyl-D-glucosamine kinase 1649845 Yersinia pseudotuberculosis complex species group 10 NCBI Protein Cluster (PRK) N-acetyl-D-glucosamine kinase N-acetyl-D-glucosamine kinase NF011173.0 PRK14575 PRK14575.1 850 850 406 equivalog Y N N putative peptidase 1649845 Yersinia pseudotuberculosis complex species group 13 NCBI Protein Cluster (PRK) putative peptidase putative peptidase NF011800.0 PRK15265 PRK15265.1 195 195 141 equivalog Y N N subtilase cytotoxin subunit B-like protein 1649845 Yersinia pseudotuberculosis complex species group 24 NCBI Protein Cluster (PRK) subtilase cytotoxin subunit B-like protein subtilase cytotoxin subunit B-like protein NF011915.0 PRK15386 PRK15386.1-4 872 872 410 equivalog Y Y N EspK/GogB family type III secretion system effector 15843015,16958848 1649845 Yersinia pseudotuberculosis complex species group 13 NCBI Protein Cluster (PRK) type III secretion protein GogB EspK/GogB family type III secretion system effector Members of this family, typically found in the genus Yersinia, are probably type III secretion system (T3SS) effectors homologous to the EspK from enterohaemorrhagic Escherichia coli (EHEC) and the anti-inflammatory effector GogB from Salmonella enterica. NF020708.5 PF09144.15 YpM 25 25 117 PfamEq Y Y N superantigen YpM 14725774 1649845 Yersinia pseudotuberculosis complex species group 4 EBI-EMBL Yersinia pseudo-tuberculosis mitogen superantigen YpM Members of this family of Yersinia pseudo-tuberculosis mitogens adopt a sandwich structure consisting of nine strands in two beta sheets, in a jelly-roll topology. As with other super-antigens, they are able to excessively activate T cells by binding to the T cell receptor [1]. [1]. 14725774. Crystal and solution structures of a superantigen from Yersinia pseudotuberculosis reveal a jelly-roll fold. Donadini R, Liew CW, Kwan AH, Mackay JP, Fields BA;. Structure. 2004;12:145-156. (from Pfam) NF040979.1 Ve_Ilp_Nterm 1125 1125 550 equivalog_domain Y Y N inverse autotransporter adhesin Ilp ilp 22851752 1649845 Yersinia pseudotuberculosis complex species group 186 NCBIFAM inverse autotransporter adhesin Ilp N-terminal domain Ilp (Intimin/invasin-Like Protein), as found in Yersinia, is an inverse autotransporter (type Ve secretion protein) that can have over 40 repeats of the Bacterial Ig-like (BIG) domain (PF02369) and has an average length over 4000 amino acids. This HMM describes the non-repetitive N-terminal domain. NF020139.5 PF08550.15 DUF1752 20.9 20.9 28 domain Y Y N DUF1752 domain-containing protein 1652133 Halobacteriovorax genus 2 EBI-EMBL Fungal protein of unknown function (DUF1752) Fungal protein of unknown function (DUF1752) This is a family of fungal proteins of unknown function. This short section domain is bounded by two highly conserved tryptophans. The family contains Swiss:P34072 that is thought to be a negative regulator of RAS-cAMP pathway in S.cerevisiae. the Sch.pombe member is a GAF1 transcription factor Swiss:Q10280 that is also associated with the zinc finger family GATA Pfam:PF00320. (from Pfam) NF009294.0 PRK12651 PRK12651.1-5 303 303 162 equivalog Y Y N Na+/H+ antiporter subunit E 1653176 Cereibacter genus 10 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit E Na+/H+ antiporter subunit E NF033575.1 blaRHO 825 825 380 exception Y Y Y RHO family class C beta-lactamase blaRHO 3.5.2.6 GO:0008800,GO:0030288 1653176 Cereibacter genus 10 NCBIFAM RHO family class C beta-lactamase RHO family class C beta-lactamase The class C beta-lactamase of Rhodobacter sphaeroides, here renamed RHO because the term AmpC is too generic, confers resistance to a number of cephalosporins (cephalothin, cephapirin, cephalosporin C), and to penicillin G, but not to ampicillin, carbenicillin, oxacillin, cloxacillin, or methicillin. NF038043.1 act_def_assoc_A 250 250 379 equivalog Y Y N actinodefensin-associated protein A adfA 1654 Actinomyces genus 30 NCBIFAM actinodefensin-associated protein A Actinodefensin (see family NF038042) is a bacterial branch of the arthropod defensin family. Members of that family occur in the Actinomyes lineage, have a distinctive N-terminal region that may reflect how processing and transport occur, and are found in a conserved gene neighborhood. Actinodefensin-associated protein A is found exclusively in these conserved gene neighborhoods. NF033149.0 CHL_hydrolase 500 500 310 equivalog Y Y Y chloramphenicol hydrolase estDL136 165696 Novosphingobium genus 34 NCBIFAM chloramphenicol hydrolase chloramphenicol hydrolase NF012810.5 PF00603.22 Flu_PA 23 23 694 domain Y Y N polymerase PA GO:0003723,GO:0039694 22638584,8709268 1673 Rhizobium viscosum species 2 EBI-EMBL Influenza RNA-dependent RNA polymerase subunit PA polymerase PA NF025969.5 PF14618.11 DUF4452 27 27 170 domain Y Y N DUF4452 domain-containing protein 167481 Companilactobacillus mindensis species 1 EBI-EMBL Domain of unknown function (DUF4452) Domain of unknown function (DUF4452) This fungal family has no known function. However, it is rich in paired, as CXXC, cysteines and histidines, but these do not fall in the conformation that might suggest zinc-binding. (from Pfam) NF003632.0 PRK05270 PRK05270.2-1 865 865 515 equivalog Y Y N UDP-glucose--hexose-1-phosphate uridylyltransferase 2.7.7.12 1678 Bifidobacterium genus 256 NCBI Protein Cluster (PRK) galactose-1-phosphate uridylyltransferase UDP-glucose--hexose-1-phosphate uridylyltransferase NF005843.0 PRK07764 PRK07764.1-1 1190 1190 964 equivalog Y Y N DNA polymerase III subunit gamma and tau 2.7.7.7 1678 Bifidobacterium genus 290 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunit gamma and tau NF010375.0 PRK13802 PRK13802.1 1386 1386 695 equivalog Y Y N bifunctional indole-3-glycerol phosphate synthase/tryptophan synthase subunit beta 1678 Bifidobacterium genus 585 NCBI Protein Cluster (PRK) bifunctional indole-3-glycerol phosphate synthase/tryptophan synthase subunit beta bifunctional indole-3-glycerol phosphate synthase/tryptophan synthase subunit beta Catalyzes ring closure to form indole-3-glycerol phosphate; Catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate NF011002.0 PRK14428 PRK14428.1 120 120 97 equivalog Y Y N acylphosphatase 1678 Bifidobacterium genus 61 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011274.0 PRK14681 PRK14681.1 207 207 158 equivalog Y N N hypothetical protein 1678 Bifidobacterium genus 153 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF011451.0 PRK14873 PRK14873.1-1 1147 1147 764 equivalog Y N N primosome assembly protein PriA 1678 Bifidobacterium genus 527 NCBI Protein Cluster (PRK) primosome assembly protein PriA primosome assembly protein PriA NF041578.1 betaarabinsidaseHypBA2 3200 3200 1709 equivalog Y Y N beta-L-arabinobiosidase HypBA2 hypBA2 3.2.1.187 GO:0000272,GO:0016798 21149454 1678 Bifidobacterium genus 541 NCBIFAM beta-L-arabinobiosidase HypBA2 NF017424.5 PF05608.17 DUF778 28 28 149 domain Y Y N DUF778 domain-containing protein 167968 uncultured Desulfovibrio sp. species 1 EBI-EMBL Domain of unknown function (DUF778) Domain of unknown function (DUF778) This domain is present in several eukaryotic proteins of unknown function. This domain has been identified as structurally similar to peptidase C97 domain (Pfam:PF05903). (from Pfam) NF033569.1 blaLHK 850 850 390 exception Y Y Y LHK family class C beta-lactamase blaLHK 3.5.2.6 GO:0008800,GO:0030288 15855519 168471 Laribacter hongkongensis species 24 NCBIFAM LHK family class C beta-lactamase LHK family class C beta-lactamase NF022831.5 PF11389.13 Porin_OmpL1 27 27 272 PfamEq Y Y N porin OmpL1 GO:0005886,GO:0015288,GO:0055085 12183539 170 Leptospiraceae family 244 EBI-EMBL Leptospira porin protein OmpL1 porin OmpL1 OmpL1 is a member of the outer membrane (OM) proteins in the mammalian pathogen Leptospira. Specifically, it is a porin [1]. [1]. 12183539. Characterization of the leptospiral outer membrane and description of three novel leptospiral membrane proteins. Haake DA, Matsunaga J;. Infect Immun. 2002;70:4936-4945. (from Pfam) NF047475.1 GDSL_LA_2490 325 325 431 hypoth_equivalog Y Y N LA_2490 family SGNH/GDSL-type esterase 170 Leptospiraceae family 190 NCBIFAM LA_2490 family SGNH/GDSL-type esterase NF047479.1 LIC10729_fam 125 125 190 subfamily Y Y N LIC10729 family protein 170 Leptospiraceae family 146 NCBIFAM LIC10729 family protein NF047486.1 LA_1737_Cterm 60 60 158 subfamily_domain Y Y N LA_1737 family protein 170 Leptospiraceae family 319 NCBIFAM LA_1737 C-terminal domain This HMM represents a well-conserved C-terminal block of aligned sequence, about 160 amino acids long, from LA_1737 and homologs, all from Leptospira. Most full-length members of this family are between 1200 and 1800 amino acids in length. NF047497.1 HK_LIC_12097 500 500 367 equivalog Y Y N LIC_12097 family sensor histidine kinase 170 Leptospiraceae family 115 NCBIFAM LIC_12097 family sensor histidine kinase Members of this somewhat NtrB-like family of sensor histidine kinases are universal in and restricted to the genera Leptospira and Leptonema. Together with LIC_12098, its response regulator, it may have a role as a regulator of nitrogen metabolism, but this is not yet shown. NF047513.1 LIC_13246_fam 70 70 116 equivalog Y Y N LIC_13246 family protein 170 Leptospiraceae family 251 NCBIFAM LIC_13246 family protein NF047613.1 LIC11625_fam 160 160 140 exception Y Y N LIC11625 family surface-exposed protein 28352257 170 Leptospiraceae family 115 NCBIFAM LIC11625 family surface-exposed protein NF047672.1 LIC11274_fam 360 360 357 subfamily Y Y N LIC11274 family protein 28141801,29670056,33021995 170 Leptospiraceae family 143 NCBIFAM LIC11274 family protein NF047700.1 LIC10415_fam 180 180 169 equivalog Y Y N LIC10415 family protein 24626166 170 Leptospiraceae family 121 NCBIFAM LIC10415 family protein NF047715.1 LIC12298_fam 100 100 70 subfamily Y Y N LIC12298 family protein 26762976 170 Leptospiraceae family 63 NCBIFAM LIC12298 family protein NF047760.1 LIC10042_TonB 100 100 156 equivalog Y Y N LIC_10042 family TonB-like protein 170 Leptospiraceae family 151 NCBIFAM LIC_10042 family TonB-like protein Members of this family are restricted to the spirochete lineages Leptospira and Leptonema, one to a species, and are the only energy transducer TonB-like protein in those species. NF047770.1 LBF_2127_lipo 150 150 183 equivalog Y Y N LBF_2127 family putative lipoprotein 170 Leptospiraceae family 135 NCBIFAM LBF_2127 family putative lipoprotein Members of this family of putative lipoproteins occur in more than half the known species of Leptospira and Leptonema. The function is unknown. NF047799.1 LIC11874_lipo 250 250 204 equivalog Y Y N LIC11874 family lipoprotein 170 Leptospiraceae family 115 NCBIFAM LIC11874 family lipoprotein NF047805.1 LIC13255_lipo 90 90 77 equivalog Y Y N LIC13255 family lipoprotein 28352257 170 Leptospiraceae family 125 NCBIFAM LIC13255 family lipoprotein NF047814.1 LIC20211_lipo 130 130 95 equivalog Y Y N LIC20211 family lipoprotein 170 Leptospiraceae family 130 NCBIFAM LIC20211 family lipoprotein NF047817.1 LIC13411_adhesin 150 150 210 equivalog Y Y N LIC13411 family adhesin 25275630,35937702 170 Leptospiraceae family 188 NCBIFAM LIC13411 family adhesin TIGR04410.1 TIGR04410 Spiro_T2SS_lipo 50 50 117 equivalog Y Y N type II secretion system-associated lipoprotein 170 Leptospiraceae family 116 JCVI type II secretion system-associated lipoprotein type II secretion system-associated lipoprotein Members of this family occur only in spirochetes (Leptospira, Leptonema, Turneriella), as part of a type II secretion system (T2SS) cassette. Properly extended gene models always include an N-terminal signal sequence ending with a Cys residue, suggesting this small protein (about 100 amino acids) is a lipoprotein. TIGR04453.1 TIGR04453 Lepto_8Cys 34 33 85 subfamily Y Y N Cys-rich protein 170 Leptospiraceae family 243 JCVI Cys-rich protein, LA_1312 family Cys-rich protein Members of this protein family occur, so far, exclusively in the genus Leptospira. Members, although small (about 90 amino acids), have a predicted signal peptide followed by a region with eight invariant Cys residues. Some members have an additional Cys in the signal peptide region that suggests handling as a lipoprotein, but this Cys is not well conserved. TIGR04457.1 TIGR04457 lipo_LenA_lepto 50 50 224 equivalog Y Y N lipoprotein LenA lenA 20160016 170 Leptospiraceae family 91 JCVI lipoprotein LenA lipoprotein LenA Members of this family are LenA (Leptospira Endostatin-like protein A), found in pathogenic and intermediate species of Leptospira but not in saprophytes. LenA binds plasminogen, laminin, and complement regulator factor H. Behavior during outer membrane solubilization by low concentrations of Triton X-114 and conservation in all family members of an apparent lipoprotein signal sequence, with invariant Cys residue, strongly suggest that LenA is a lipoprotein. Just outside this family is a full-length homolog found in another spirochete, Turneriella parva DSM 21527. NF008894.0 PRK11924 PRK11924.3-1 258 258 188 equivalog Y N N RNA polymerase sigma factor 1706369 Cellvibrionales order 10 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF041611.1 exoglucan_CbhB 1950 1950 997 equivalog Y Y N exoglucanase CbhB cbhB 3.2.1.91 GO:0016162,GO:0030245 7575482 1707 Cellulomonas genus 6 NCBIFAM exoglucanase CbhB NF000777.0 PRK00052 PRK00052.3-2 558 558 310 equivalog Y Y N prolipoprotein diacylglyceryl transferase 2.4.99.- 171 Leptospira genus 112 NCBI Protein Cluster (PRK) prolipoprotein diacylglyceryl transferase prolipoprotein diacylglyceryl transferase NF001956.0 PRK00733 PRK00733.3-1 1321 1321 704 equivalog Y Y N sodium-translocating pyrophosphatase 3.6.1.1 171 Leptospira genus 199 NCBI Protein Cluster (PRK) membrane-bound proton-translocating pyrophosphatase sodium-translocating pyrophosphatase NF003388.0 PRK04531 PRK04531.1-4 819 819 385 equivalog Y N N acetylglutamate kinase 171 Leptospira genus 5 NCBI Protein Cluster (PRK) acetylglutamate kinase acetylglutamate kinase NF003389.0 PRK04531 PRK04531.1-5 741 741 371 equivalog Y N N acetylglutamate kinase 171 Leptospira genus 78 NCBI Protein Cluster (PRK) acetylglutamate kinase acetylglutamate kinase NF004369.0 PRK05738 PRK05738.3-5 177 177 104 equivalog Y Y N 50S ribosomal protein L23 171 Leptospira genus 61 NCBI Protein Cluster (PRK) 50S ribosomal protein L23 50S ribosomal protein L23 NF004944.0 PRK06292 PRK06292.2-2 619 619 460 equivalog Y Y N dihydrolipoyl dehydrogenase 1.8.1.4 171 Leptospira genus 220 NCBI Protein Cluster (PRK) dihydrolipoamide dehydrogenase dihydrolipoyl dehydrogenase NF008944.0 PRK12292 PRK12292.3-2 374 374 341 equivalog Y Y N ATP phosphoribosyltransferase regulatory subunit 171 Leptospira genus 159 NCBI Protein Cluster (PRK) ATP phosphoribosyltransferase regulatory subunit ATP phosphoribosyltransferase regulatory subunit NF009156.0 PRK12497 PRK12497.4-2 162 162 114 equivalog Y Y N YraN family protein 171 Leptospira genus 46 NCBI Protein Cluster (PRK) hypothetical protein YraN family protein NF009157.0 PRK12497 PRK12497.4-3 152 152 116 equivalog Y Y N YraN family protein 171 Leptospira genus 50 NCBI Protein Cluster (PRK) hypothetical protein YraN family protein NF009267.0 PRK12624 PRK12624.1 241 241 143 equivalog Y N N flagellar basal body rod protein FlgB 171 Leptospira genus 68 NCBI Protein Cluster (PRK) flagellar basal body rod protein FlgB flagellar basal body rod protein FlgB NF009367.0 PRK12724 PRK12724.1 718 718 433 equivalog Y N N flagellar biosynthesis regulator FlhF 171 Leptospira genus 131 NCBI Protein Cluster (PRK) flagellar biosynthesis regulator FlhF flagellar biosynthesis regulator FlhF NF009371.0 PRK12729 PRK12729.1 145 145 127 equivalog Y N N flagellar hook-basal body protein FliE 171 Leptospira genus 85 NCBI Protein Cluster (PRK) flagellar hook-basal body protein FliE flagellar hook-basal body protein FliE NF009412.0 PRK12773 PRK12773.1 886 886 649 equivalog Y N N flagellar biosynthesis protein FlhB 171 Leptospira genus 116 NCBI Protein Cluster (PRK) flagellar biosynthesis protein FlhB flagellar biosynthesis protein FlhB NF009892.0 PRK13351 PRK13351.1-3 640 640 623 equivalog Y Y N elongation factor G-like protein 171 Leptospira genus 235 NCBI Protein Cluster (PRK) elongation factor G elongation factor G-like protein NF009952.0 PRK13417 PRK13417.1 531 531 352 equivalog Y N N F0F1 ATP synthase subunit A 171 Leptospira genus 150 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit A F0F1 ATP synthase subunit A NF009969.0 PRK13434 PRK13434.1 179 179 186 equivalog Y N N F0F1 ATP synthase subunit delta 171 Leptospira genus 125 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit delta F0F1 ATP synthase subunit delta NF009979.0 PRK13444 PRK13444.1 163 163 127 equivalog Y N N F0F1 ATP synthase subunit epsilon 171 Leptospira genus 99 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit epsilon F0F1 ATP synthase subunit epsilon NF009991.0 PRK13460 PRK13460.1 183 183 173 equivalog Y Y N F0F1 ATP synthase subunit B 171 Leptospira genus 96 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit B F0F1 ATP synthase subunit B Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B is part of the membrane proton channel NF010508.0 PRK13922 PRK13922.11-1 648 648 369 equivalog Y Y N rod shape-determining protein MreC mreC 171 Leptospira genus 117 NCBI Protein Cluster (PRK) rod shape-determining protein MreC rod shape-determining protein MreC NF010562.0 PRK13957 PRK13957.1 414 414 252 equivalog Y Y N indole-3-glycerol-phosphate synthase 171 Leptospira genus 107 NCBI Protein Cluster (PRK) indole-3-glycerol-phosphate synthase indole-3-glycerol-phosphate synthase Involved in tryptophan biosynthesis; amino acid biosynthesis; converts 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate to C(1)-(3-indolyl)-glycerol 3-phosphate NF010608.0 PRK14004 PRK14004.1 216 216 210 equivalog Y N N imidazole glycerol phosphate synthase subunit HisH hisH 171 Leptospira genus 111 NCBI Protein Cluster (PRK) imidazole glycerol phosphate synthase subunit HisH imidazole glycerol phosphate synthase subunit HisH NF010672.0 PRK14069 PRK14069.1 123 123 95 equivalog Y Y N exodeoxyribonuclease VII small subunit 171 Leptospira genus 68 NCBI Protein Cluster (PRK) exodeoxyribonuclease VII small subunit exodeoxyribonuclease VII small subunit Catalyzes the bidirectional exonucleolytic cleavage of DNA NF010744.0 PRK14146 PRK14146.1 201 201 215 equivalog Y Y N nucleotide exchange factor GrpE grpE 171 Leptospira genus 126 NCBI Protein Cluster (PRK) heat shock protein GrpE nucleotide exchange factor GrpE With DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins NF010774.0 PRK14177 PRK14177.1 515 515 284 equivalog Y Y N bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD folD 171 Leptospira genus 155 NCBI Protein Cluster (PRK) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD Catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate NF010879.0 PRK14286 PRK14286.1 626 626 372 equivalog Y N N chaperone protein DnaJ 171 Leptospira genus 108 NCBI Protein Cluster (PRK) chaperone protein DnaJ chaperone protein DnaJ NF011114.0 PRK14542 PRK14542.1 250 250 137 equivalog Y Y N nucleoside-diphosphate kinase 2.7.4.6 171 Leptospira genus 58 NCBI Protein Cluster (PRK) nucleoside diphosphate kinase nucleoside-diphosphate kinase Catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate NF011170.0 PRK14572 PRK14572.1 489 489 351 equivalog Y N N D-alanyl-alanine synthetase A 6.3.2.4 171 Leptospira genus 153 NCBI Protein Cluster (PRK) D-alanyl-alanine synthetase A D-alanyl-alanine synthetase A NF011184.0 PRK14590 PRK14590.1 189 189 176 equivalog Y N N 16S rRNA-processing protein RimM 171 Leptospira genus 121 NCBI Protein Cluster (PRK) 16S rRNA-processing protein RimM 16S rRNA-processing protein RimM NF011207.0 PRK14613 PRK14613.1 359 359 297 equivalog Y Y N 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase 2.7.1.148 171 Leptospira genus 136 NCBI Protein Cluster (PRK) 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase Catalyzes the phosphorylation of 4-diphosphocytidyl-2-C-methyl-D-erythritol in the nonmevalonate pathway of isoprenoid biosynthesis NF011228.0 PRK14635 PRK14635.1 137 137 162 equivalog Y Y N ribosome maturation factor RimP rimP 171 Leptospira genus 97 NCBI Protein Cluster (PRK) hypothetical protein ribosome maturation factor RimP NF011324.0 PRK14737 PRK14737.1 318 318 187 equivalog Y Y N guanylate kinase 2.7.4.8 171 Leptospira genus 100 NCBI Protein Cluster (PRK) guanylate kinase guanylate kinase Essential for recycling GMP and indirectly, cGMP NF011364.0 PRK14783 PRK14783.1 212 212 182 equivalog Y Y N lipoprotein signal peptidase 3.4.23.36 171 Leptospira genus 93 NCBI Protein Cluster (PRK) lipoprotein signal peptidase lipoprotein signal peptidase Integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis NF011379.0 PRK14804 PRK14804.1 373 373 311 equivalog Y Y N ornithine carbamoyltransferase 2.1.3.3 171 Leptospira genus 122 NCBI Protein Cluster (PRK) ornithine carbamoyltransferase ornithine carbamoyltransferase Catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation NF011389.0 PRK14814 PRK14814.1 285 285 186 equivalog Y N N NADH dehydrogenase subunit B 1.6.5.9 171 Leptospira genus 69 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit B NADH dehydrogenase subunit B NF011415.0 PRK14842 PRK14842.1 360 360 241 equivalog Y Y N isoprenyl transferase 171 Leptospira genus 138 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate synthase isoprenyl transferase Catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate NF011517.0 PRK14956 PRK14956.1 654 654 486 equivalog Y N N DNA polymerase III subunits gamma and tau 171 Leptospira genus 180 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunits gamma and tau NF018503.5 PF06797.16 DUF1229 25 25 164 PfamAutoEq Y Y N DUF1229 domain-containing protein 171 Leptospira genus 100 EBI-EMBL Protein of unknown function (DUF1229) Protein of unknown function (DUF1229) This family consists of several hypothetical proteins of around 415 residues in length which seem to be specific to the bacterium Leptospira interrogans. (from Pfam) NF019234.5 PF07599.16 DUF1563 21 21 43 domain Y Y N DUF1563 domain-containing protein 171 Leptospira genus 223 EBI-EMBL Protein of unknown function (DUF1563) Protein of unknown function (DUF1563) A small family of short hypothetical proteins in Leptospira interrogans. (from Pfam) NF019235.5 PF07600.16 DUF1564 25 25 167 subfamily Y Y N DUF1564 family protein 171 Leptospira genus 3421 EBI-EMBL Protein of unknown function (DUF1564) DUF1564 family protein A family of paralogous proteins in Leptospira interrogans. Several (e.g. Swiss:Q8F4V2) have been annotated as possible CopG-like transcriptional regulators (see Pfam:PF01402). (from Pfam) NF019245.5 PF07614.16 DUF1577 25 25 256 domain Y Y N DUF1577 domain-containing protein 171 Leptospira genus 695 EBI-EMBL Protein of unknown function (DUF1577) Protein of unknown function (DUF1577) A family of hypothetical proteins in Leptospira interrogans. (from Pfam) NF026306.5 PF14956.11 DUF4505 27.3 27.3 177 PfamAutoEq Y Y N DUF4505 family protein 171 Leptospira genus 93 EBI-EMBL Domain of unknown function (DUF4505) DUF4505 family protein This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 166 and 225 amino acids in length. (from Pfam) NF033160.0 lipo_LipL36 400 400 383 equivalog Y Y N lipoprotein LipL36 171 Leptospira genus 142 NCBIFAM lipoprotein LipL36 lipoprotein LipL36 Members of this family are lipoprotein LipL36, as described in Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 but found broadly in the genus Leptospira. Close homologs that are not lipoproteins by sequence are likely defective in their reported coding region. NF033161.1 lipo_LipL41 400 400 358 equivalog Y Y N lipoprotein LipL41 171 Leptospira genus 98 NCBIFAM lipoprotein LipL41 lipoprotein LipL41 Members of this family are lipoprotein LipL41, as described in Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 but found broadly in the genus Leptospira. Close homologs that are not lipoproteins by sequence are likely defective in their reported coding region. NF033162.1 lipo_LipL21 200 200 191 equivalog Y Y N lipoprotein LipL21 171 Leptospira genus 71 NCBIFAM lipoprotein LipL21 lipoprotein LipL21 Members of this family are lipoprotein LipL21, as described in Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 but found broadly in the genus Leptospira. Close homologs that are not lipoproteins by sequence are likely defective in their reported coding region. NF033163.1 lipo_LipL71 600 600 471 equivalog Y Y N lipoprotein LipL71 171 Leptospira genus 217 NCBIFAM lipoprotein LipL71 lipoprotein LipL71 Members of this family are lipoprotein LipL71, also known as LruA, as described in Leptospira interrogans but found broadly in the genus Leptospira. Close homologs that are not lipoproteins by sequence are likely defective in their reported coding region. NF033164.1 lipo_LipL46 400 400 413 equivalog Y Y N lipoprotein LipL46 171 Leptospira genus 114 NCBIFAM lipoprotein LipL46 lipoprotein LipL46 Members of this family are lipoprotein LipL46, as described in Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 but found broadly in the genus Leptospira. Close homologs that are not lipoproteins by sequence are likely defective in their reported coding region. NF033165.1 lipo_LipL45 350 350 391 exception Y Y N lipoprotein LipL45 171 Leptospira genus 156 NCBIFAM lipoprotein LipL45 lipoprotein LipL45 Members of this family are lipoprotein LipL45, as described in Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 but found broadly in the genus Leptospira. Close homologs that are not lipoproteins by sequence are likely defective in their reported coding region. NF033166.1 lipo_LipL31 250 250 210 equivalog Y Y N lipoprotein LipL31 171 Leptospira genus 109 NCBIFAM lipoprotein LipL31 lipoprotein LipL31 Members of this family are lipoprotein LipL31, as described in Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 but found broadly in the genus Leptospira. Close homologs that are not lipoproteins by sequence are likely defective in their reported coding region. NF033167.1 lipo_LIC11695 100 100 186 subfamily Y Y N LIC_11695 family lipoprotein 17371863 171 Leptospira genus 101 NCBIFAM lipoprotein LIC_11695/LIC_11696 family lipoprotein Members of this family are lipoproteins found broadly in the genus Leptospira. Two paralogs, LIC_11695 and LIC_11696 are found in Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (a well-studied reference strain), where they are encoded by tandem genes, and are among the 25 proteins whose expression is up-regulated the most by the increase in osmolarity that signals entry into a host species. NF033168.1 lipo_LIC10766 150 150 142 hypoth_equivalog Y Y N lipoprotein 171 Leptospira genus 117 NCBIFAM lipoprotein LIC_10766 family lipoprotein Members of this family are lipoproteins found broadly in the genus Leptospira. NF033169.1 lipo_LIC10494 70 70 223 subfamily Y Y N lipoprotein 171 Leptospira genus 162 NCBIFAM lipoprotein LIC_10494 family lipoprotein Members of this family are lipoproteins found broadly in the genus Leptospira. NF033566.1 adhes_LIC20035 250 250 434 equivalog Y Y N LIC20035 family adhesin 29269501 171 Leptospira genus 185 NCBIFAM LIC20035 family adhesin LIC20035 family adhesin LIC20035 of Leptospira interrogans was characterized as a surface exposed adhesin that binds host extracellular matrix components. Orthologs appear restricted to the genus Leptospira. Member proteins average about 430 residues in length, much of which consists of repeats. All members are predicted lipoproteins. NF038097.1 KCGN_DNA_rpt 26 24 21 domain N N N KCGN motif-containing spurious repeat 171 Leptospira genus 30 NCBIFAM KCGN motif-containing spurious repeat This AntiFam-type HMM recognizes spurious protein translations, often with the motif KCGN, of a DNA repeat widespread in the genus Leptospira. NF038294.1 lipo_LIC11966 200 200 158 equivalog Y Y N ErpY-like lipoprotein 30776321,31548314 171 Leptospira genus 53 NCBIFAM ErpY-like lipoprotein Members of this family are surface-exposed lipoproteins from the genus Leptospira. Members include the founding member LIC11966, reported to be a fibrinogen-binding protein. NF038383.1 lipo_LIC12048 700 700 1441 equivalog Y Y N LIC12048 family lipoprotein 28496441 171 Leptospira genus 337 NCBIFAM LIC12048 family lipoprotein NF038393.1 lipo_LIC_10705 100 100 178 subfamily Y Y N LIC_10705 family lipoprotein 171 Leptospira genus 272 NCBIFAM LIC_10705 family lipoprotein The LIC_10705 family of lipoproteins, found in the genus Leptospira, includes tandem-encoded paralogs such as LIC_10705 and LIC_10706 in L. interrogans serovar Copenhageni str. Fiocruz L1-130. NF038394.1 lipo_LipL32 300 300 269 equivalog Y Y N major surface lipoprotein LipL32 lipL32 19236879,19477185,22147698 171 Leptospira genus 67 NCBIFAM major surface lipoprotein LipL32 LipL32, a surface lipoprotein, is found in the genus Leptospira only in pathogenic species, where it is the most abundant surface protein. LipL32 belongs to a broader family of surface lipoproteins (see PF12103) found also in other host-colonizing bacteria such as Pseudoalteromonas tunicata. NF042433.1 CitmalDyn_Leptosp 950 950 514 equivalog Y Y N (R)-citramalate synthase CimA cimA 2.3.3.21 GO:0003852,GO:0009097,GO:0009098,GO:0043714 15292141,18498255 171 Leptospira genus 160 NCBIFAM (R)-citramalate synthase CimA NF047432.1 LA_3334_fam 200 200 280 equivalog Y Y N LA_3334 family protein 171 Leptospira genus 365 NCBIFAM LA_3334 family protein This uncharacterized protein family is restricted to the genus Leptospira, and is named for LA_3334 (AAN50532.1) from Leptospira interrogans serovar Lai str. 56601 NF047433.1 Lepto_7_Nterm 43 43 63 domain Y Y N LA_0442/LA_0875 N-terminal domain-containing protein 171 Leptospira genus 1557 NCBIFAM LA_0442/LA_0875 N-terminal domain This HMM described a 65-amino acid conserved N-terminal region largely restricted to the genus Leptospira, and shared by seven otherwise mostly unrelated proteins in the model strain Leptospira interrogans serovar Lai str. 56601 (LA_0442, LA_0875, LA_1192, LA_1904, LA_2672, LA_3334, and LA_3681). A signal-anchor-like region is followed by the most strongly conserved motif in the domain, [LVI][LVI][LF]KXG. NF047434.1 LA_0364_fam_lipo 40 40 94 equivalog Y Y N LA_0364 family Cys-rich lipoprotein 28352257 171 Leptospira genus 59 NCBIFAM LA_0364 family Cys-rich lipoprotein NF047435.1 LA_2272_fam_lipo 30 30 59 equivalog_domain Y Y N LA_2272/LA_2273 family lipoprotein 28352257 171 Leptospira genus 407 NCBIFAM LA_2272/LA_2273 family lipoprotein, N-terminal domain Tandem lipoproteins from LA_2272 and LA_2273 Leptospira interrogans serovar Lai str. 56601 share both an N-terminal unique domain, modeled by this HMM. Those lipoproteins also have a novel family 15 amino-acid repeats that is now modeled by NF047436. These 15 amino-acid repeats are found much more broadly, including in VC2662 from Vibrio cholerae. NF047439.1 prenyl_LA_0991 300 300 275 equivalog Y Y N LA_0991 family prenyltransferase-like protein 171 Leptospira genus 139 NCBIFAM LA_0991 family prenyltransferase-like protein Members of this family are apparent membrane proteins averaging about 285 miles long. This family shows very distant homology to the family of UbiA-like prenyltransferases described by Pfam model PF01040. NF047441.1 Lepto_OmpL47 250 250 336 equivalog Y Y N multi-beta-barrel domain surface protein OmpL47 ompL47 19562037 171 Leptospira genus 154 NCBIFAM multi-beta-barrel domain surface protein OmpL47 Members of this family are found only in the genus Leptospira. They average about 370 amino acids in length, and this length includes three tandem repeats of a region of about 92 amino acids that corresponds to repetitive regions of surface proteins in many other lineages (see NF047446). Each repeat from member protein Q04PQ5 is modeled with very high confidence by AlphaFold as a beta-barrel domain. The founding member, Lic13050 from Leptospira interrogans serovar Copenhageni strain Fiocruz L1-130, demonstrated experimentally to be a surface-exposed protein. The function is unknown. NF047442.1 SaltregLepto 220 220 140 equivalog Y Y N LA_1841 family salt-regulated protein 17371863 171 Leptospira genus 81 NCBIFAM LA_1841 family salt-regulated protein NF047443.1 CompRegAqLcpA 300 300 189 equivalog Y Y N complement regulator-acquiring protein LcpA lcpA 20404075,31443566 171 Leptospira genus 85 NCBIFAM complement regulator-acquiring protein LcpA NF047444.1 Sig54regLepto 240 240 149 equivalog Y Y N LEPBI_I1174 family sigma 54-regulated protein 29633391 171 Leptospira genus 47 NCBIFAM LEPBI_I1174 family sigma 54-regulated protein NF047445.1 PeroxupregLepto 140 140 92 equivalog Y Y N LA_1064 family peroxide-responsive upregulated protein 33021995 171 Leptospira genus 54 NCBIFAM LA_1064 family peroxide-responsive upregulated protein NF047447.1 Lepto_OmpL37 150 150 228 subfamily Y Y N adhesin OmpL37 family surface protein GO:0019867 19562037,20844573,36555188 171 Leptospira genus 362 NCBIFAM adhesin OmpL37 family surface protein Members of this family of major outer membrane proteins are found strictly within spirochetes, and almost entirely in the genus Leptospira, where from one to three paralogs are seen per proteome. In Leptospira interrogans, the family includes two paralogs, LA_1495, which is the adhesin OmpL37, and LA_0306, which is uncharacterized. OmpL37 interacts with host elastin, laminin, plasma fibronectin, and fibrinogen. NF047448.1 flagella_FcpA 400 400 302 equivalog Y Y N flagellar coiling protein FcpA fcpA GO:0055040,GO:0071977 27113476,28291747,29634754 171 Leptospira genus 64 NCBIFAM flagellar coiling protein FcpA FcpA (flagellar-coiling protein A) is unique Leptospira, Leptonema and Turneriella. It is part of the filament sheath of the spirochete periplasmic flagellum. NF047449.1 Lepto_FcpA_rel 200 200 266 equivalog Y Y N FcpA-related putative periplasmic flagellar protein 171 Leptospira genus 158 NCBIFAM FcpA-related putative periplasmic flagellar protein Model NF047448 (flagella_FcpA) describes flagellar coiling protein FcpA, a sheath protein of the Leptospira-like subclass of the spirochete periplasmic flagellum. Members of this family are paralogs to FcpA, likewise a single copy protein when present, and not yet characterized. We name this protein as an FcpA-related putative periplasmic flagellar protein. NF047452.1 PerABupregLA3478 400 400 218 equivalog Y Y N LA_3478 family PerA/PerB upregulated protein 34855918 171 Leptospira genus 31 NCBIFAM LA_3478 family PerA/PerB upregulated protein NF047453.1 PerABupregLA3781 160 160 100 equivalog Y Y N LA_3781 family PerA/PerB upregulated protein 34855918 171 Leptospira genus 52 NCBIFAM LA_3781 family PerA/PerB upregulated protein NF047454.1 SphinmyaseLepto 400 400 235 equivalog Y Y N sphingomyelinase sph 15780195 171 Leptospira genus 71 NCBIFAM sphingomyelinase NF047459.1 LA_3150_fam_lipo 70 70 144 equivalog Y Y N LA_3150 family lipoprotein 171 Leptospira genus 81 NCBIFAM LA_3150 family lipoprotein Members of this lipoprotein family average 150 amino acids in length, and occur only in the genus Leptospira. In addition to the conserved Cys residue of the lipoprotein signal peptide, four additional invariant Cys residues are found. NF047461.1 FUR_perox_PerRB 250 250 143 exception Y Y N peroxide-responsive transcriptional repressor PerRB perRB GO:0000302 34855911,34855918,37372003 171 Leptospira genus 65 NCBIFAM peroxide-responsive transcriptional repressor PerRB PerRB is a FUR family transcriptional regulator found in all pathogenic species of Leptospira, and involved in the response to hydrogen peroxide. NF047462.1 FUR_perox_PerRA 200 200 142 exception Y Y N peroxide-responsive transcriptional repressor PerRA perRA GO:0000302 34855911,34855918,37372003 171 Leptospira genus 93 NCBIFAM peroxide-responsive transcriptional repressor PerRA PerRA is a FUR family transcriptional regulator restricted to species of Leptospira, and involved in the response to hydrogen peroxide. It has a paralog PerRB, which has a different distribution within the genus. NF047463.1 CllEntPrLepto 400 400 250 equivalog Y Y N mammalian cell entry protein Mce mce 22329803,27468683 171 Leptospira genus 108 NCBIFAM mammalian cell entry protein Mce NF047464.1 FibnectbindLIC11051 1000 1000 685 equivalog Y Y N LIC_11051 family fibronectin-binding protein GO:0005515 22961849 171 Leptospira genus 96 NCBIFAM LIC_11051 family fibronectin-binding protein NF047465.1 hybrid_HK_LvrA 1200 1200 819 exception Y Y N hybrid histidine kinase/response regulator LvrA lvrA 29600195 171 Leptospira genus 134 NCBIFAM hybrid histidine kinase/response regulator LvrA LvrA and LvrB (Leptospira virulence regulator system A and B) are hybrid histidine kinase/response regulators encoded by tandem genes. Neither protein has either a transmembrane domain or a DNA-binding domain. From N-terminus toward C-terminus, LvrA has a PAS-like sensor domain, a histidine kinase (HK) region, a response regulator domain, and then another HK region, and it is described as the hybrid histidine kinase component of a two-component system. LvrB has a domain architecture similar to the C-terminal region of LvrA, from the response regulator domain to the C-terminus. NF047466.1 hybrid_RR_LvrB 500 500 377 exception Y Y N hybrid histidine kinase/response regulator LvrB lvrB 29600195 171 Leptospira genus 107 NCBIFAM hybrid histidine kinase/response regulator LvrB LvrA and LvrB (Leptospira virulence regulator system A and B) are hybrid histidine kinase/response regulators encoded by tandem genes. Neither protein has either a transmembrane domain or a DNA-binding domain. From N-terminus toward C-terminus, LvrA has a PAS-like sensor domain, a histidine kinase (HK) region, a response regulator domain, and then another HK region, and it is described as the hybrid histidine kinase component of a two-component system. LvrB has a domain architecture similar to the C-terminal region of LvrA, from the response regulator domain to the C-terminus. NF047467.1 PlasmgnRcptrLp30 450 450 279 equivalog Y Y N plasminogen-binding receptor Lp30 lp30 21755014 171 Leptospira genus 65 NCBIFAM plasminogen-binding receptor Lp30 NF047468.1 PerABupregLA1694 420 420 241 equivalog Y Y N LA_1694 family PerA/PerB upregulated protein 34855918 171 Leptospira genus 54 NCBIFAM LA_1694 family PerA/PerB upregulated protein NF047469.2 UVExpRegProtLA1448 100 100 77 equivalog Y Y N LA_1448 family UV-C exposure upregulated protein 24098496 171 Leptospira genus 111 NCBIFAM LA_1448 family UV-C exposure upregulated protein NF047470.1 PerABupregLA3241 350 350 201 equivalog Y Y N LA3241 family PerA/PerB upregulated protein 34855918 171 Leptospira genus 115 NCBIFAM LA3241 family PerA/PerB upregulated protein NF047471.1 LamininBindLsa27 300 300 208 equivalog Y Y N laminin-binding protein Lsa27 lsa27 19541787 171 Leptospira genus 44 NCBIFAM laminin-binding protein Lsa27 NF047473.1 lipo_LIC11755 300 300 699 subfamily Y Y N LIC11755 family lipoprotein 28496441 171 Leptospira genus 332 NCBIFAM LIC11755 family lipoprotein LIC11755 family proteins are predicted to be surface-exposed outer membrane lipoproteins of the genus Leptospira. Shorter members of this family average about 700 amino acids, while longer versions have an additional C-terminal region of 250 to 300 amino acids. NF047474.1 GDSL_LA_2486 300 300 326 hypoth_equivalog Y Y N LA_2486 family SGNH/GDSL-type esterase 171 Leptospira genus 193 NCBIFAM LA_2486 family SGNH/GDSL-type esterase NF047476.1 LA_2168_fam 250 250 470 subfamily Y Y N LA_2168 family protein 171 Leptospira genus 235 NCBIFAM LA_2168 family protein NF047480.1 Lepto_Lp29 75 75 212 subfamily Y Y N Lp29 family lipoprotein 17609931,20582320,23118516 171 Leptospira genus 273 NCBIFAM Lp29 family lipoprotein NF047481.1 lipo_LIC12587 200 200 213 subfamily Y Y N LIC12587 family lipoprotein 31422744,38204132 171 Leptospira genus 115 NCBIFAM LIC12587 family lipoprotein LIC12587 is a surface-exposed lipoprotein from Leptospira interrogans. It was shown to bind E-cadherin and laminin, suggesting a role in adhesion to host epithelial cells. NF047482.1 OM_LenAB_fam 300 300 230 equivalog Y Y N endostatin-like outer membrane protein, LenA/LenB family len 171 Leptospira genus 123 NCBIFAM endostatin-like outer membrane protein, LenA/LenB family LenA and LenB are two of the most closely related members of the family of Leptospira endostatin-like (Len) outer membrane proteins, all of which have at least one copy of the DUF1554 domain. This model covers LenA, LenB, and unnamed additional close homologs within the Len family. BlastRules NBR016752 and NBR016751 identify LenA and LenB, respectively. NF047483.1 OM_LenF_fam 400 400 267 equivalog Y Y N endostatin-like outer membrane lipoprotein LenF lenF 18000555,25201075 171 Leptospira genus 192 NCBIFAM endostatin-like outer membrane lipoprotein LenF LenF belongs to the family of Leptospira endostatin-like (Len) outer membrane proteins, all of which have at least one copy of the DUF1554 domain. LenF family members have either one or two copies. NF047484.1 LA1326_LA4305 100 100 205 subfamily Y Y N LA_1326/LA_4305 family lipoprotein 171 Leptospira genus 355 NCBIFAM LA_1326/LA_4305 family lipoprotein NF047487.2 MPL17FamLepto 180 180 129 equivalog Y Y N cell surface protein MPL17 mpl17 18799647 171 Leptospira genus 130 NCBIFAM cell surface protein MPL17 NF047488.1 Sig54regLEPBII2431 175 175 112 equivalog Y Y N LEPBI_I2431 family sigma-54 regulated protein GO:0035438 29633391 171 Leptospira genus 41 NCBIFAM LEPBI_I2431 family sigma-54 regulated protein NF047489.2 adhesinLsa23 270 270 202 equivalog Y Y N surface adhesion protein Lsa23 lsa23 23958908,26614523 171 Leptospira genus 144 NCBIFAM surface adhesion protein Lsa23 NF047490.1 LamCadPlsmbinLA2219 285 285 188 equivalog Y Y N LA_2219 family laminin/E-cadherin/plasminogen-binding protein 31422744 171 Leptospira genus 132 NCBIFAM LA_2219 family laminin/E-cadherin/plasminogen-binding protein NF047493.1 LB_053_fam 200 200 273 equivalog Y Y N LB_053 family protein 24366253 171 Leptospira genus 193 NCBIFAM LB_053 family protein NF047494.1 Lepto_SBBP_lipo 400 400 466 equivalog Y Y N SBBP repeat beta-propeller lipoprotein, LipL53 family 171 Leptospira genus 886 NCBIFAM SBBP repeat beta-propeller lipoprotein, LipL53 family This lipoprotein family, limited to the genus Leptospira, has multiple copies of the SBBP (Seven Bladed Beta Propeller) repeat. It occurs as a paralogous family. Member proteins from the model strain Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 include LIC12208, LIC12209, LIC12099 (LipL53), LIC13066, etc. NF047496.1 HK_LIC11548 750 750 589 equivalog Y Y N LIC_11548 family sensor histidine kinase 2.7.13.3 171 Leptospira genus 183 NCBIFAM LIC_11548 family sensor histidine kinase The two-component system of sensor histidine kinase LIC_11548 and response regulator LIC_11549 is conserved across the genus Leptospira. It resembles the system of nitrate sensor histitdine kinase NtrY and response regulator NtrX, but the actual role has not been established. A full-length homolog exists in Leptonema, but cutoffs are set such that it scores in the gray zone between the gathering threshold and the noise cutoff in case the specific function differs. NF047499.1 LIC_11026_fam 325 325 1006 hypoth_equivalog Y Y N LIC_11026 family protein 171 Leptospira genus 279 NCBIFAM LIC_11026 family protein NF047501.1 lipo_LIC_13215 200 200 194 equivalog Y Y N LIC_13215 family putative lipoprotein 171 Leptospira genus 93 NCBIFAM LIC_13215 family putative lipoprotein NF047502.1 LIC_13346_fam 200 200 279 equivalog Y Y N LIC_13346 family putative lipoprotein 171 Leptospira genus 157 NCBIFAM LIC_13346 family putative lipoprotein Members of this family, broadly distributed in the genus Leptospira, are uncharacterized, but appear to be lipoproteins. NF047503.1 LB_137_fam 200 200 288 subfamily Y Y N LB_137 family protein 171 Leptospira genus 188 NCBIFAM LB_137 family protein Members of this family occur in the genus Leptospira, and include LB_137 from chromosome II of Leptospira interrogans serovar Lai str. 56601. The function is unknown. NF047504.1 LIC_10030_fam 250 250 301 equivalog Y Y N LIC_10030 family protein 171 Leptospira genus 147 NCBIFAM LIC_10030 family protein NF047505.1 LIC_10177_fam 100 100 130 equivalog Y Y N LIC_10177 family protein 24626166 171 Leptospira genus 88 NCBIFAM LIC_10177 family protein NF047506.1 VWA_BatB_Lepto 350 350 324 exception Y Y N VWA domain-containing protein BatB batB 23234440,32078713 171 Leptospira genus 207 NCBIFAM VWA domain-containing protein BatB, Leptospira type Bat (Bacteriodes aerotolerance)-related operons are found broadly in bacteria, but differ in their makeup in different lineages. This HMM describes the family of the von Willebrand factor A (VWA) domain-containing protein BatB, as found in the genus Leptospira, or the N-terminal domain of a BatBC fusion protein. The function may not actually be related to tolerance of oxidative stress. Recombinant Leptospira BatB is reported to function as a serine protease active on thrombin, fibrin, fibrinogen, gelatin and casein. NF047507.1 TPR_BatC_Lepto 175 175 214 exception Y Y N TPR repeat-containing protein BatC batC 23234440,32078713 171 Leptospira genus 213 NCBIFAM TPR repeat-containing protein BatC, Leptospira type Bat (Bacteriodes aerotolerance) operons are found broadly in bacteria, but differ in their makeup in different lineages. This HMM describes the family of the tetratricopeptide repeat (TPR)-containing protein BatC, as found in the genus Leptospira, or the C-terminal domain of a BatBC fusion protein. The function may not actually be related to tolerance of oxidative stress. NF047508.1 VWA_BatA_Lepto 380 380 315 exception Y Y N VWA domain-containing protein BatA batA 23234440,32078713 171 Leptospira genus 154 NCBIFAM VWA domain-containing protein BatA, Leptospira type Bat (Bacteriodes aerotolerance)-related operons are found broadly in bacteria, but differ in their makeup in different lineages. This HMM describes the family of the von Willebrand factor A (VWA) domain-containing protein BatA, as found in the genus Leptospira The function may not actually be related to tolerance of oxidative stress. Recombinant Leptospira BatA is reported to function as a serine protease. NF047511.1 LIC_11959_fam 125 125 156 equivalog Y Y N LIC_11959 family protein 171 Leptospira genus 172 NCBIFAM LIC_11959 family protein NF047517.1 LIC_12586_fam 800 800 702 equivalog Y Y N LIC_12586 family protein 171 Leptospira genus 269 NCBIFAM LIC_12586 family protein NF047518.1 LIC_10091_fam 350 350 325 equivalog Y Y N LIC_10091 family lipoprotein 21221970,38204132 171 Leptospira genus 237 NCBIFAM LIC_10091 family lipoprotein NF047519.1 LIC_11366_fam 300 300 239 subfamily Y Y N LIC_11366 family protein 36275031 171 Leptospira genus 159 NCBIFAM LIC_11366 family protein NF047521.1 LIC_11904_fam 400 400 398 equivalog Y Y N LIC_11904 family protein 171 Leptospira genus 95 NCBIFAM LIC_11904 family protein NF047522.1 LIC_12613_fam 200 200 129 equivalog Y Y N LIC_12613 family protein 171 Leptospira genus 56 NCBIFAM LIC_12613 family protein NF047523.1 LIC_20245_fam 190 190 222 equivalog Y Y N LIC_20245 family lipoprotein 171 Leptospira genus 263 NCBIFAM LIC_20245 family lipoprotein NF047524.1 LIC_10461_domain 60 60 83 domain Y Y N LIC_10461 domain-containing protein 171 Leptospira genus 139 NCBIFAM LIC_10461 domain NF047525.1 LIMLP_04285_fam 100 100 136 equivalog Y Y N LIMLP_04285 family protein 171 Leptospira genus 91 NCBIFAM LIMLP_04285 family protein NF047526.1 LIC_10421_fam 90 90 111 subfamily Y Y N LIC_10421 family protein 171 Leptospira genus 253 NCBIFAM LIC_10421 family protein NF047527.1 LIC_12337_fam 270 270 389 subfamily Y Y N LIC_12337 family protein 171 Leptospira genus 198 NCBIFAM LIC_12337 family protein NF047528.1 LIMLP_03685_anti-sigma 200 200 347 equivalog Y Y N LIMLP_03685 family anti-sigma factor rsx 33301041 171 Leptospira genus 208 NCBIFAM LIMLP_03685 family anti-sigma factor In Leptospira interrogans serovar Manilae, LIMLP_03680 encodes a putative extracytoplasmic function (ECF) sigma factor, which is in an operon with its cognate trans-membrane anti-sigma factor (LIMLP_03685). NF047529.1 SrpA 240 240 390 subfamily Y Y N sigma factor sigX-regulated lipoprotein SrpA srpA 33301041 171 Leptospira genus 301 NCBIFAM sigma factor sigX-regulated lipoprotein SrpA It has been reported that the expression of three genes, including srpA (LIMLP_06130), srpB (LIMLP_15890), and srpC, (LIMLP_03790), was regulated by the sigma factor SigX (LIMLP_03680) and anti-sigma factor Rsx (LIMLP_03685) in pathogenic species of Leptospira. NF047530.1 SrpBC 200 200 236 subfamily Y Y N sigma factor SigX-regulated lipoprotein srp 33301041 171 Leptospira genus 204 NCBIFAM sigma factor SigX-regulated lipoprotein It has been reported that the expression of three genes, including srpA (LIMLP_06130), srpB (LIMLP_15890), and srpC, (LIMLP_03790), was regulated by the sigma factor SigX (LIMLP_03680) and anti-sigma factor Rsx (LIMLP_03685) in pathogenic species of Leptospira. SrpB and SrpC are paralogs. NF047531.1 LIC_10730_fam 170 170 162 equivalog Y Y N LIC_10730 family protein 171 Leptospira genus 93 NCBIFAM LIC_10730 family protein NF047532.1 LIC_20087_fam 300 300 293 subfamily Y Y N LIC_20087 family outer membrane protein 24147173,28496441 171 Leptospira genus 99 NCBIFAM LIC_20087 family outer membrane protein NF047533.1 LBL_2463_fam 110 110 177 subfamily Y Y N LBL_2463 family protein 171 Leptospira genus 356 NCBIFAM LBL_2463 family protein NF047538.1 LIC_11321_fam 60 60 45 equivalog Y Y N LIC_11321 family protein 171 Leptospira genus 119 NCBIFAM LIC_11321 family protein This protein family appears restricted to the genus Leptospira, but is nearly always present in that lineage. Most members of the family appear to have either a type I (regular) or type II (lipoprotein) signal peptide. The HMM built for this family omits the signal peptide region and an adjacent short region of low-complexity sequence. An invariant GCC[RK]I[KR] motif is notable in the short region (46 amino acids) that is the most highly conserved. The function is unknown. NF047540.1 LIC_13241_dom 50 50 85 domain Y Y N LIC_13241 domain-containing protein 171 Leptospira genus 148 NCBIFAM LIC_13241 domain NF047543.1 CytMemPImpL63 1000 1000 525 equivalog Y Y N cytoplasmic membrane protein ImpL63 impL63 12183539 171 Leptospira genus 116 NCBIFAM cytoplasmic membrane protein ImpL63 NF047544.1 AdhsnLsa30Lept 500 500 292 equivalog Y Y N laminin/fibronectin-binding adhesin Lsa30 lsa30 22732096 171 Leptospira genus 83 NCBIFAM laminin/fibronectin-binding adhesin Lsa30 NF047545.1 EndstnLikeLenA 350 350 210 equivalog Y Y N endostatin-like outer membrane lipoprotein LenA lenA lsa24 16954400,20160016 171 Leptospira genus 109 NCBIFAM endostatin-like outer membrane lipoprotein LenA NF047546.1 PhIPhlseLepto 184 184 131 equivalog Y Y N phosphatidylinositol phospholipase 24124502 171 Leptospira genus 119 NCBIFAM phosphatidylinositol phospholipase NF047547.1 LIC_12096_fam 200 200 201 equivalog Y Y N LIC_12096 family protein 171 Leptospira genus 174 NCBIFAM LIC_12096 family protein NF047548.1 LIC_10183_fam 140 140 119 equivalog Y Y N LIC_10183 family protein 171 Leptospira genus 102 NCBIFAM LIC_10183 family protein NF047549.1 LIC_20196_fam 230 230 136 equivalog Y Y N LIC_20196 family exoprotein 25987703 171 Leptospira genus 78 NCBIFAM LIC_20196 family exoprotein NF047550.1 LIC_12071_fam 350 350 337 equivalog Y Y N LIC_12071 family protein 171 Leptospira genus 208 NCBIFAM LIC_12071 family protein NF047552.1 LIC_20245_11074_fam 190 190 221 subfamily Y Y N LIC_20245/LIC_11074 family protein 171 Leptospira genus 264 NCBIFAM LIC_20245/LIC_11074 family protein NF047553.1 LBBP_01157_fam 270 270 243 equivalog Y Y N LBBP_01157 family protein 29236926 171 Leptospira genus 167 NCBIFAM LBBP_01157 family protein NF047554.1 LIC_10463_fam 150 150 138 equivalog Y Y N LIC_10463 family lipoprotein 171 Leptospira genus 117 NCBIFAM LIC_10463 family lipoprotein NF047555.1 LIMLP_16695_fam 100 100 57 equivalog Y Y N LIMLP_16695 family PerRB-regulated protein 34855911 171 Leptospira genus 47 NCBIFAM LIMLP_16695 family PerRB-regulated protein NF047557.1 LIC_11826_fam 240 240 246 subfamily Y Y N LIC_11826 family putative surface polysaccharide biosynthesis enzyme 171 Leptospira genus 169 NCBIFAM LIC_11826 family putative surface polysaccharide biosynthesis enzyme Members of this family occur exclusively in the genus Leptospira, and regularly occur in a locus that includes proteins annotated as D-sedoheptulose 7-phosphate isomerase (an LPS biosynthesis enzyme), glycosyltransferase, O-antigen ligase. NF047559.1 LIC_12238_fam 170 170 156 equivalog Y Y N LIC_12238 family plasminogen-binding lipoprotein 20582320,30166455 171 Leptospira genus 152 NCBIFAM LIC_12238 family plasminogen-binding lipoprotein NF047562.1 LIC_14007_fam 130 130 113 domain Y Y N LIC_14007 family protein 171 Leptospira genus 67 NCBIFAM LIC_14007 family protein NF047569.1 LIC10421_LIC12816_fam 100 100 111 subfamily Y Y N LIC10421/LIC12816 family protein 23118516,34855918 171 Leptospira genus 198 NCBIFAM LIC10421/LIC12816 family protein This HMM hits two paralogs (LIC12816 and LIC10421) in the genome of Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130. They are putative plasminogen-binding proteins (PMID: 23118516) and/or PerRA/PerRB-regulated proteins (PMID: 34855918). NF047571.1 LIC13212_fam 250 250 269 equivalog Y Y N LIC13212 family protein 171 Leptospira genus 115 NCBIFAM LIC13212 family protein NF047579.1 LIC_13029_fam 250 250 282 subfamily Y Y N LIC_13029 family protein 171 Leptospira genus 71 NCBIFAM LIC_13029 family protein NF047582.1 LIC13081_fam 185 185 154 equivalog Y Y N LIC13081 family protein 171 Leptospira genus 81 NCBIFAM LIC13081 family protein NF047583.1 LIC10604_fam 200 200 161 equivalog Y Y N LIC10604 family protein 171 Leptospira genus 88 NCBIFAM LIC10604 family protein NF047584.1 LIC11612_FN_binding 260 260 323 equivalog Y Y N LIC11612 family fibronectin-binding protein 22961849 171 Leptospira genus 100 NCBIFAM LIC11612 family fibronectin-binding protein NF047585.2 LIC10012_fam 400 400 513 equivalog Y Y N LIC10012 family protein 28352257 171 Leptospira genus 251 NCBIFAM LIC10012 family protein Members of this family of putative surface-exposed proteins are found broadly throughout the genus Leptospira, and appear to have a VWA (von Willibrand factor type A) domain. NF047586.1 LIC11270_fam 490 490 404 equivalog Y Y N LIC11270 family surface protein 28352257 171 Leptospira genus 164 NCBIFAM LIC11270 family surface protein NF047587.1 lipo_LIC11073 150 150 223 equivalog Y Y N LIC11073 family putative lipoprotein 171 Leptospira genus 127 NCBIFAM LIC11073 family putative lipoprotein Members of this family, found broadly in the genus Leptospira, are probable lipoproteins with an average length of about 250 amino acids. The C-terminal 100 residues contain 12 invariant Cys residues. The function is unknown. NF047592.1 LA_1883_fam 400 400 499 equivalog Y Y N LIC12015 family putative lipoprotein 171 Leptospira genus 171 NCBIFAM LIC12015 family putative lipoprotein This uncharacterized protein family occurs broadly in the genus Leptospira. An apparent signal peptide and an invariant Cys residue at about position 21 suggests that members of this family may be lipoproteins. NF047594.1 LIC10707_fam 380 380 406 equivalog Y Y N LIC10707 family hydrolase 171 Leptospira genus 117 NCBIFAM LIC10707 family hydrolase NF047596.1 LIMLP_15305_fam 210 210 175 equivalog Y Y N LIMLP_15305 family protein 171 Leptospira genus 137 NCBIFAM LIMLP_15305 family protein NF047597.1 LIMLP_12425_fam 200 200 171 equivalog Y Y N LIMLP_12425 family protein 171 Leptospira genus 125 NCBIFAM LIMLP_12425 family protein NF047604.1 LIC14007_fam 140 140 110 equivalog Y Y N LIC14007 family protein 171 Leptospira genus 64 NCBIFAM LIC14007 family protein NF047605.1 LIC10235_fam 160 160 92 equivalog Y Y N LIC10235 family protein 34855918 171 Leptospira genus 55 NCBIFAM LIC10235 family protein NF047606.1 LIC11177_fam 190 190 154 equivalog Y Y N LIC11177 family protein 171 Leptospira genus 124 NCBIFAM LIC11177 family protein NF047607.1 LBF_2017_Nterm 50 50 124 subfamily_domain Y Y N LBF_2017 N-terminal domain-containing protein 171 Leptospira genus 121 NCBIFAM LBF_2017 N-terminal domain This HMM describes an N-terminal domain restricted to the genus Leptospira, and shared by two homolgous proteins in Leptospira biflexa, LBF_1751 and LBF_2017. The domain is followed in Leptospira by two tandem copies of a domain about 90 amino acids long that can be repeated 10 or more times in homologs from other lineages, such as WP_165822350.1 from Paenibacillus. NF047608.1 LIC13292_fam 200 200 166 subfamily Y Y N LIC13292 family transcriptional regulator 171 Leptospira genus 91 NCBIFAM LIC13292 family transcriptional regulator NF047610.1 LIMLP_18675_fam 125 125 196 equivalog Y Y N LIMLP_18675 family protein 171 Leptospira genus 174 NCBIFAM LIMLP_18675 family protein NF047611.1 LIC20162_fam 200 200 198 equivalog Y Y N LIC20162 family protein 171 Leptospira genus 173 NCBIFAM LIC20162 family protein NF047612.1 LIC_10740_fam 150 150 266 equivalog Y Y N LIC_10740 family protein 171 Leptospira genus 175 NCBIFAM LIC_10740 family protein NF047614.1 LIC11469_fam 150 150 191 equivalog Y Y N LIC11469 family lipoprotein adhesin Lsa20 lsa20 21844229 171 Leptospira genus 171 NCBIFAM LIC11469 family lipoprotein adhesin Lsa20 It has been reported that the Lsa20 protein from L. interrogans serovar Copenhageni strain M20 bound to laminin and human plasminogen. It is predicted to be a lipoprotein. NF047615.1 LIC13259_LIC11441_fam 100 100 144 subfamily Y Y N LIC13259/LIC11441 family protein 171 Leptospira genus 213 NCBIFAM LIC13259/LIC11441 family protein NF047616.1 LIC10183_fam 140 140 118 exception Y Y N LIC10183 family protein 171 Leptospira genus 102 NCBIFAM LIC10183 family protein NF047617.1 LIC12077_fam 110 110 68 equivalog Y Y N LIC12077 family protein 171 Leptospira genus 39 NCBIFAM LIC12077 family protein NF047618.1 LIC11086_fam 350 350 280 exception Y Y N LIC11086 family outer membrane transporter 36275031 171 Leptospira genus 197 NCBIFAM LIC11086 family outer membrane transporter NF047624.1 LIC_13076_fam 110 90 214 equivalog Y Y N LIC_13076 family protein 28352257 171 Leptospira genus 169 NCBIFAM LIC_13076 family protein This family occurs in the genus Leptospira. Members are predicted to be surface-exposed proteins and are possible lipoproteins. NF047627.1 LIC_10230_fam 150 150 327 equivalog Y Y N LIC_10230 family protein 171 Leptospira genus 153 NCBIFAM LIC_10230 family protein NF047653.1 OMPLoa22Lepto 300 300 183 equivalog Y Y N OmpA family outer membrane lipoprotein Loa22 loa22 GO:0042834 14553914,33441663 171 Leptospira genus 99 NCBIFAM OmpA family outer membrane lipoprotein Loa22 Members of this family are lipoproteins with a C-terminal OmpA domain. They are highly conserved among pathogenic leptospires. It has been reported that Loa22 interacts with Toll-Like Receptor 2 (TLR2) through Leptospira peptidoglycan (LPGN), inducing downstream signals to trigger inflammatory responses. NF047654.1 DiguCycDgcRLepto 500 500 295 equivalog Y Y N diguanylate cyclase DgcR dgcR 2.7.7.65 GO:0052621 33846343 171 Leptospira genus 57 NCBIFAM diguanylate cyclase DgcR NF047655.1 ImlysnLruBLepto 850 850 441 equivalog Y Y N imelysin LruB lruB 37227474 171 Leptospira genus 143 NCBIFAM imelysin LruB NF047656.1 ColgnaseColALepto 1550 1550 880 equivalog Y Y N collagenase ColA colA GO:0004222,GO:0006508,GO:0008270 34673004 171 Leptospira genus 110 NCBIFAM collagenase ColA NF047657.1 CellWlHdaseLepto 400 400 221 equivalog Y N N hypothetical protein GO:0004222 37517629 171 Leptospira genus 75 NCBIFAM NF047661.1 LIC_10907 100 100 102 equivalog Y Y N LIC_10907 family protein 171 Leptospira genus 37 NCBIFAM LIC_10907 family protein NF047662.1 LEPBI_I2678_fam 240 240 247 subfamily Y Y N LEPBI_I2678 family protein 29633391 171 Leptospira genus 45 NCBIFAM LEPBI_I2678 family protein NF047663.1 LEPBI_I0682_fam 220 220 158 subfamily Y Y N LEPBI_I0682 family protein 29633391 171 Leptospira genus 17 NCBIFAM LEPBI_I0682 family protein NF047664.1 LIMLP_16025_fam 140 140 80 subfamily Y Y N LIMLP_16025 family protein 33021995 171 Leptospira genus 58 NCBIFAM LIMLP_16025 family protein NF047665.1 LIC10362_fam 90 90 95 subfamily Y Y N LIC10362 family protein 24098496 171 Leptospira genus 125 NCBIFAM LIC10362 family protein NF047669.1 LIC13354_fam 130 130 174 subfamily Y Y N LIC13354 family exoprotein 24626166,25987703,28352257 171 Leptospira genus 114 NCBIFAM LIC13354 family exoprotein NF047670.1 LIC10816_fam 150 150 94 subfamily Y Y N LIC10816 family protein 33826628 171 Leptospira genus 22 NCBIFAM LIC10816 family protein NF047678.1 LIC10486_fam 500 500 363 equivalog Y Y N LIC10486 family protein 24147173,28141801 171 Leptospira genus 140 NCBIFAM LIC10486 family protein NF047679.1 LIC10906_fam 200 200 283 subfamily Y Y N LIC10906 family membrane protein 33826628,34855918 171 Leptospira genus 453 NCBIFAM LIC10906 family membrane protein NF047680.1 LIC13197_LIC10919_LIC10469_fam 280 280 207 subfamily Y Y N LIC13197/LIC10919/LIC10469 family protein 33021995 171 Leptospira genus 65 NCBIFAM LIC13197/LIC10919/LIC10469 family protein NF047681.1 LIC10775_fam 400 400 331 subfamily Y Y N LIC10775 family protein 24626166 171 Leptospira genus 210 NCBIFAM LIC10775 family protein NF047682.1 LIC12628_fam 65 65 42 subfamily Y Y N LIC12628 family protein 33021995 171 Leptospira genus 41 NCBIFAM LIC12628 family protein NF047687.1 LIC10173_fam 230 230 198 subfamily Y Y N LIC10173 family protein 24626166 171 Leptospira genus 131 NCBIFAM LIC10173 family protein NF047688.1 LIMLP_19325_fam 70 70 54 subfamily Y Y N LIMLP_19325 family protein 34855911 171 Leptospira genus 129 NCBIFAM LIMLP_19325 family protein NF047689.1 LIC10907_fam 100 100 99 subfamily Y Y N LIC10907 family protein 33021995 171 Leptospira genus 37 NCBIFAM LIC10907 family protein NF047690.1 LIC20036_fam 250 250 195 subfamily Y Y N LIC20036 family protein 17109759,33021995 171 Leptospira genus 104 NCBIFAM LIC20036 family protein NF047691.1 LIC13344_fam 140 140 84 subfamily Y Y N LIC13344 family protein 20113507,25063661 171 Leptospira genus 77 NCBIFAM LIC13344 family protein NF047692.1 LIC11631_fam 185 185 209 subfamily Y Y N LIC11631 family protein 33021995 171 Leptospira genus 150 NCBIFAM LIC11631 family protein NF047693.1 LIC11113_fam 270 270 240 subfamily Y Y N LIC11113 family protein 33260771 171 Leptospira genus 174 NCBIFAM LIC11113 family protein NF047701.1 B9T54_RS14040_fam 120 120 70 subfamily Y Y N B9T54_RS14040 family protein 33826628 171 Leptospira genus 19 NCBIFAM B9T54_RS14040 family protein NF047702.1 LIC10965_fam 130 130 104 subfamily Y Y N LIC10965 family protein 24626166 171 Leptospira genus 49 NCBIFAM LIC10965 family protein NF047704.1 Lsa16_fam_lipo 80 80 158 subfamily Y Y N Lsa16 family lipoprotein adhesin 28600123 171 Leptospira genus 149 NCBIFAM Lsa16 family lipoprotein adhesin NF047706.1 LIC12611_phage_tail 480 480 628 subfamily Y Y N LIC12611 family phage tail protein 24098822,26762976 171 Leptospira genus 189 NCBIFAM LIC12611 family phage tail protein NF047707.1 LIC13341_fam 550 550 353 subfamily Y Y N LIC13341 family surface-exposed protein 29969088,31548314 171 Leptospira genus 186 NCBIFAM LIC13341 family surface-exposed protein NF047708.1 LIC20153_fam 120 120 164 subfamily Y Y N LIC20153 family lipoprotein 23813276,23895271,28352257 171 Leptospira genus 145 NCBIFAM LIC20153 family lipoprotein NF047716.1 LIC10260_fam 100 100 109 subfamily Y Y N LIC10260 family lipoprotein 28352257,36853003 171 Leptospira genus 49 NCBIFAM LIC10260 family lipoprotein NF047717.1 LIC10244_fam 475 475 252 exception Y Y N LIC10244 family PerRA/PerRB upregulated protein 34855918 171 Leptospira genus 57 NCBIFAM LIC10244 family PerRA/PerRB upregulated protein NF047735.1 MPL36 430 430 305 exception Y Y N RlpA family plasminogen-binding lipoprotein MPL36 mpl36 GO:0005515 37486929 171 Leptospira genus 135 NCBIFAM RlpA family plasminogen-binding lipoprotein MPL36 Proteins of this family are homologs of rare lipoprotein A (RlpA) with a C-terminal Sporulation related (SPOR) domain. They bind to plasminogen (PLG) and convert bound-PLG to active plasmin. Therefore, they are important virulence factors in pathogenic Leptospira. NF047736.1 LIC_10202_fam 50 50 339 equivalog Y Y N LIC_10202 family protein 171 Leptospira genus 137 NCBIFAM LIC_10202 family protein NF047755.1 LIC_10271_M23 180 180 207 exception Y Y N LIC_10271 family cell wall hydrolase 37517629 171 Leptospira genus 159 NCBIFAM LIC_10271 family cell wall hydrolase Members of this family of cell wall hydrolases, restricted to the genus Leptospira, have an N-terminal LysM domain and a C-terminal M23 murein hydrolase domain. NF047756.1 LIC11435_fam 380 380 360 equivalog Y Y N LIC11435 family protein 28352257 171 Leptospira genus 200 NCBIFAM LIC11435 family protein Members of this family of putative surface-exposed proteins include LIC11435 from Leptospira interrogans and, it appears, one ortholog from every other species in the genus. Some members score just above the cutoff to Pfam model PF18935.5 and were therefore named as DUF5683 domain-containing proteins. The signal peptide region is not well conserved in this protein family and is not included in the seed alignment. NF047757.1 LBF_1011_fam 350 350 402 equivalog Y Y N LBF_1011 family protein 171 Leptospira genus 60 NCBIFAM LBF_1011 family protein This family is named for member protein LBF_1011 from Leptospira biflexa, a saprophytic (non-pathogenic) species of Leptospira. NF047758.1 LIC12936_fam 250 250 229 equivalog Y Y N LIC_12936 family protein 171 Leptospira genus 114 NCBIFAM LIC_12936 family protein Members of this family are named after LIC_12936 from Leptospira interrogans, and found in all three clades of Leptospira (Pathogenic, Intermediate, and Saprophytic). Members have a conserved signal peptide region. The function is unknown. NF047759.1 LBF_1134_fam 200 200 196 equivalog Y Y N LBF_1134 family protein 171 Leptospira genus 56 NCBIFAM LBF_1134 family protein This family is named for member protein LBF_1134 from Leptospira biflexa, a saprophytic (non-pathogenic) species of Leptospira. NF047761.1 LBF_4227_fam 75 75 96 equivalog Y Y N LBF_4227 family protein 171 Leptospira genus 138 NCBIFAM LBF_4227 family protein Members of this family are found in most species of Leptospira. NF047763.1 LIC_10572_fam 200 200 205 equivalog Y Y N LIC_10572 family protein 171 Leptospira genus 96 NCBIFAM LIC_10572 family protein NF047764.1 LIC_11883_fam 150 150 195 equivalog Y Y N LIC_11883 family protein 171 Leptospira genus 169 NCBIFAM LIC_11883 family protein NF047769.1 LIC10067_lipo 200 200 239 equivalog Y Y N LIC10067 family putative lipoprotein 28352257 171 Leptospira genus 143 NCBIFAM LIC10067 family putative lipoprotein NF047771.1 LIC_11490_fam 100 100 235 equivalog Y Y N LIC_11490 family protein 171 Leptospira genus 192 NCBIFAM LIC_11490 family protein NF047772.1 LBF0736_ABC_LP 250 250 203 equivalog Y Y N ABC-type transport auxiliary lipoprotein, LBF_0736 family 171 Leptospira genus 47 NCBIFAM ABC-type transport auxiliary lipoprotein, LBF_0736 family Members of this family are related to the ABC-type transport auxiliary lipoproteins of Pfam family PF03886, although mostly not detected by that model. NF047774.1 LBF_1199_fam 200 200 296 equivalog Y Y N LBF_1199 family protein 171 Leptospira genus 74 NCBIFAM LBF_1199 family protein NF047775.1 LIC_11090_fam 75 75 141 subfamily Y Y N LIC_11090 family protein 171 Leptospira genus 262 NCBIFAM LIC_11090 family protein Members of this family average about 150 amino acids in length, and share five invariant Cys residues, including two CxC motifs. The family is found in Leptospira, and named for LIC_11090 from the model strain Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130. NF047776.1 LIC11485_Nterm 80 80 105 subfamily_domain Y Y N LIC_11485 family protein 171 Leptospira genus 148 NCBIFAM LIC_11485 family protein N-terminal domain NF047777.1 LIC_11502_fam 75 75 82 equivalog_domain Y Y N LIC_11502 family protein 171 Leptospira genus 136 NCBIFAM LIC_11502 family protein NF047778.1 LIC_10450_fam 150 150 367 equivalog Y Y N LIC_10450 family protein 24626166 171 Leptospira genus 171 NCBIFAM LIC_10450 family protein NF047781.1 LB099_fam 200 200 170 equivalog Y Y N LB099 family protein 21049008 171 Leptospira genus 51 NCBIFAM LB099 family protein NF047800.1 LIC12353_lipo 350 350 298 equivalog Y Y N LIC12353 family lipoprotein 24626166,25987703 171 Leptospira genus 132 NCBIFAM LIC12353 family lipoprotein NF047801.1 LIC10301_lipo 130 130 124 equivalog Y Y N LIC10301 family lipoprotein 33240263 171 Leptospira genus 75 NCBIFAM LIC10301 family lipoprotein NF047802.1 LIC11661_lipo 150 150 144 equivalog Y Y N LIC11661 family lipoprotein 171 Leptospira genus 127 NCBIFAM LIC11661 family lipoprotein NF047803.1 LIC12338_lipo 90 90 66 equivalog Y Y N LIC12338 family lipoprotein 17371863,24626166 171 Leptospira genus 35 NCBIFAM LIC12338 family lipoprotein NF047804.1 LIC13305_lipo 250 250 274 equivalog Y Y N LIC13305 family lipoprotein 21221970 171 Leptospira genus 361 NCBIFAM LIC13305 family lipoprotein NF047806.1 LIC10025_lipo 420 420 377 equivalog Y Y N LIC10025 family lipoprotein 171 Leptospira genus 207 NCBIFAM LIC10025 family lipoprotein NF047807.1 LIC10920_lipo 210 210 217 equivalog Y Y N LIC10920 family plasminogen-binding lipoprotein 30713004 171 Leptospira genus 169 NCBIFAM LIC10920 family plasminogen-binding lipoprotein NF047808.1 LIC11299_lipo 170 170 119 equivalog Y Y N LIC11299 family lipoprotein 171 Leptospira genus 82 NCBIFAM LIC11299 family lipoprotein NF047809.1 LIC12806_lipo 100 100 94 equivalog Y Y N LIC12806 family lipoprotein 171 Leptospira genus 117 NCBIFAM LIC12806 family lipoprotein NF047810.1 LIC11742_lipo 210 210 125 equivalog Y Y N LIC11742 family lipoprotein 171 Leptospira genus 74 NCBIFAM LIC11742 family lipoprotein NF047811.1 LIC10647_lipo 340 340 295 equivalog Y Y N LIC10647 family lipoprotein 18423054 171 Leptospira genus 112 NCBIFAM LIC10647 family lipoprotein NF047812.1 LIC11213_lipo 100 100 118 equivalog Y Y N LIC11213 family lipoprotein 28352257 171 Leptospira genus 90 NCBIFAM LIC11213 family lipoprotein NF047813.1 LIC13410_lipo 180 180 123 equivalog Y Y N LIC13410 family lipoprotein 171 Leptospira genus 114 NCBIFAM LIC13410 family lipoprotein NF047815.1 LIC10124_lipo 650 650 516 equivalog Y Y N LIC10124 family lipoprotein 21423275,35185824 171 Leptospira genus 191 NCBIFAM LIC10124 family lipoprotein NF047818.1 LIC11996_lipo 350 350 422 equivalog Y Y N LIC11996 family lipoprotein 18423054 171 Leptospira genus 111 NCBIFAM LIC11996 family lipoprotein NF047844.1 FlgcoilFcpBLepto 400 400 277 equivalog Y Y N flagellar-coiling protein FcpB fcpB 29868490 171 Leptospira genus 97 NCBIFAM flagellar-coiling protein FcpB NF047845.1 FlagFilOutFlaA1Lepto 500 500 306 equivalog Y Y N flagellar filament outer layer protein FlaA1 flaA1 22451522 171 Leptospira genus 125 NCBIFAM flagellar filament outer layer protein FlaA1 NF047846.1 FlagFilOutFlaA2Lepto 440 440 231 equivalog Y Y N flagellar filament outer layer protein FlaA2 flaA2 22451522 171 Leptospira genus 73 NCBIFAM flagellar filament outer layer protein FlaA2 NF047849.1 Lsa33 420 420 310 exception Y Y N surface adhesin Lsa33 lsa33 22463075 171 Leptospira genus 90 NCBIFAM surface adhesin Lsa33 NF047850.1 Lsa25 260 260 207 exception Y Y N surface adhesin Lsa25 lsa25 22463075 171 Leptospira genus 143 NCBIFAM surface adhesin Lsa25 NF047854.1 LIC10774_LIC10365_LIC10821_LIC11207_LIC11030_fam 380 380 358 equivalog Y Y N LIC10774 family surface protein 23092690,23173023,25987703,27129366,32247916 171 Leptospira genus 383 NCBIFAM LIC10774 family surface protein Proteins of this family are paralogous surface proteins found in pathogenic Leptosprial species. They are annotated from five loci (LIC10774, LIC10365, LIC10821, LIC11207, and LIC11030) on the genome of Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130. They have similar length (340-370aa) and share high sequence identity (~>40%), therefore, they may have similar function. TIGR04142.1 TIGR04142 PCisTranLspir 250 250 316 hypoth_equivalog Y Y N putative peptidyl-prolyl cis-trans isomerase 171 Leptospira genus 135 JCVI putative peptidyl-prolyl cis-trans isomerase, LIC12922 family putative peptidyl-prolyl cis-trans isomerase Members of this protein family have a known crystal structure (3NRK) showing similarity to the peptidyl-prolyl cis-trans isomerase SurA. Members are found in Leptospira species next to an uncharacterized radical SAM enzyme and a cytidylyltransferase family protein. TIGR04327.1 TIGR04327 OMP_LA_2444 120 120 291 subfamily Y Y N LA_2444/LA_4059 family outer membrane protein 171 Leptospira genus 425 JCVI outer membrane protein, LA_2444/LA_4059 family LA_2444/LA_4059 family outer membrane protein Members of this family are predicted outer membrane proteins, apparently restricted to the Leptospiraceae (Leptospira and Leptonema). TIGR04388.1 TIGR04388 Lepto_longest 45 45 1693 subfamily Y Y N TIGR04388 family protein 171 Leptospira genus 2083 JCVI putative large structural protein TIGR04388 family protein Members of this family are restricted so far to the lineage Leptospira, where they may be the longest protein encoded by the genome. Two or three paralogs are often found. The seed alignment for this model includes sequences with significant length variability, and stops adjacent to an intein feature most full-length members of this family share. Oddly, members closely related in sequence up to the start of the intein (see TIGR01445) usually show very little sequence similarity C-terminal to the end of the intein (see TIGR01443). TIGR04389.1 TIGR04389 Lepto_lipo_1 100 100 201 subfamily Y Y N lipoprotein, tandem type 18778767,26657108 171 Leptospira genus 157 JCVI lipoprotein, tandem type lipoprotein, tandem type Members of this family are lipoproteins restricted (so far) to the genus Leptospira, sometimes with several paralogs clustered with each other, such as four in a row (out of six) in Leptospira interrogans str. UI 13372. The tandem set may be co-clustered with a putative structural protein that is usually the longest encoded by the leptospiral genome (and that often is an intein-containing protein). Members of this family discussed in the literature include LIC10507, LIC10508, and LIC10509. TIGR04400.1 TIGR04400 RK_trnsloc_Pase 200 200 358 equivalog Y Y N Arg-Lys translocation region protein phosphatase RktP rktP GO:0004722 26890609 171 Leptospira genus 170 JCVI Arg-Lys translocation region protein phosphatase Arg-Lys translocation region protein phosphatase RktP The Sec-independent protein export system TAT, or twin-arginine translocation, is unusual in Leptospira, with Lys replacing Arg in the second position of the twin-Arg motif. This protein, restricted to Leptospira and showing distant homology to the phosphoserine phosphatases RsbU and SpoIIE, is always encoded immediately downstream of the tatC gene and appears to be part of the variant TAT system. It lacks a TAT signal itself, and so is more likely to be part of the Sec-independent translocation machinery than to be a substrate. The suggested symbol is rktP, for RK-Translocation Phosphatase. TIGR04420.1 TIGR04420 Sec_Non_Glob 90 90 243 hypoth_equivalog Y Y N SRP-less Sec system protein 26890609 171 Leptospira genus 177 JCVI Sec region non-globular protein SRP-less Sec system protein Members of this family, TIGR04420, occur only in the genus Leptospira, always encoded between genes for the YajC and SecD components of the Sec preprotein translocase. Sequences have an N-terminal signal peptide and a C-terminal transmembrane segment. Between these are regions of non-globular, low-complexity sequence including Lys-rich and Ser/Thr/Asn/Glu-rich regions. The Leptospira lineage is remarkable for its lack of signal recognition particle (SRP) RNA as well as signal recognition system proteins Ffh and FtsY. Thus, TIGR04420 family proteins belong to the Sec system locus in a lineage that lacks SRP and may be hypothesized to fill a role necessitated by that lack. TIGR04441.1 TIGR04441 lept_O_ant_chp1 150 150 373 subfamily Y Y N LA_1612 family putative O-antigen biosynthesis protein 171 Leptospira genus 81 JCVI surface carbohydrate biosynthesis protein LA_1612 family putative O-antigen biosynthesis protein Members of this protein family occur only in a subset of Leptospira species, and in those species occur only in O-antigen biosynthesis regions. Members average about 375 amino acids in length. The function is unknown. TIGR04452.1 TIGR04452 Lepto_Lipo_YY_C 28 28 116 subfamily Y Y N TIGR04452 family lipoprotein 171 Leptospira genus 487 JCVI small lipoprotein, LA_3946 family TIGR04452 family lipoprotein Members of this family of small lipoproteins that occur in at least nineteen species of Leptospira, but not so far anywhere outside that genus. Notable features include the putative lipoprotein modification Cys and an additional Cys near the C-terminus, both invariant, plus a well-conserved (although not invariant) Tyr-Tyr pair. From one to four paralogs occur in most Leptospira species. Members include LA_3946. TIGR04454.1 TIGR04454 Lepto_4Cys 35 35 92 hypoth_equivalog Y Y N TIGR04454 family lipoprotein 171 Leptospira genus 76 JCVI small lipoprotein, LB_250 family TIGR04454 family lipoprotein Members of this family average about 92 amino acids in length, including an apparent lipoprotein signal peptide and a mature portion with four additional invariant Cys residues. This family is universal, so far, across at least twenty species of Leptospira but unknown outside the genus. TIGR04464.1 TIGR04464 chaper_lep 60 60 114 equivalog Y Y N LipL41-expression chaperone Lep lep 23690405 171 Leptospira genus 81 JCVI LipL41-expression chaperone Lep LipL41-expression chaperone Lep Members of this protein family are Lep, an outer membrane lipoprotein LipL41-binding protein that appears to function as a chaperone important to its expression. LipL41 is the third most abundant lipoprotein in the pathogen Leptospira interrogans, but is found in saprophytic Leptospira species as well and is not essential for virulence. TIGR04571.1 TIGR04571 LmtA_Leptospira 325 325 252 exception Y Y N lipid A Kdo2 1-phosphate O-methyltransferase lmtA GO:0008171,GO:0009245 15994324 171 Leptospira genus 131 JCVI lipid A Kdo2 1-phosphate O-methyltransferase lipid A Kdo2 1-phosphate O-methyltransferase This family describes LmtA, which methylates a phosphate on the Kdo2 sugar of lipid A. The model is classified as exception (more specific than equivalog) to reflect that its scope is limited to the genus Leptospira, whereas homologs with matching activity might exist more broadly. Members of this family belong to the broader family of PF04191, phospholipid methyltransferase, which includes a characterized yeast enzyme that acts on a range of unsaturated phospholipids. NF000261.1 NimABCDEF 260 260 153 equivalog Y Y Y NimABCDEF family 5-nitroimidazole reductase nim 30315962 171549 Bacteroidales order 18 NCBIFAM NimABCDEF family nitroimidazole resistance protein NimABCDEF family 5-nitroimidazole reductase Nim proteins are 5-nitroimidazole reductase enzymes, typically associated with markers of mobility, that inactivate and provide resistance to the antibiotic metronidazole (MTZ). NF000262.1 NimIJ 270 270 151 equivalog Y Y Y NimIJ family nitroimidazole resistance protein 171549 Bacteroidales order 23 NCBIFAM NimIJ family nitroimidazole resistance protein NimIJ family nitroimidazole resistance protein NF001483.0 PRK00326 PRK00326.3-5 239 239 155 equivalog Y Y N division/cell wall cluster transcriptional repressor MraZ mraZ 171549 Bacteroidales order 421 NCBI Protein Cluster (PRK) cell division protein MraZ division/cell wall cluster transcriptional repressor MraZ NF002534.0 PRK02048 PRK02048.1 886 886 613 equivalog Y Y N 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 1.17.7.3 171549 Bacteroidales order 1891 NCBI Protein Cluster (PRK) 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase NF002547.0 PRK02101 PRK02101.2-5 392 392 255 equivalog Y Y N peroxide stress protein YaaA yaaA 171549 Bacteroidales order 622 NCBI Protein Cluster (PRK) hypothetical protein peroxide stress protein YaaA NF002553.0 PRK02113 PRK02113.1 386 386 252 equivalog Y Y N MBL fold metallo-hydrolase 171549 Bacteroidales order 718 NCBI Protein Cluster (PRK) putative hydrolase MBL fold metallo-hydrolase NF003750.0 PRK05346 PRK05346.2-1 352 352 225 equivalog Y Y N Na(+)-translocating NADH-quinone reductase subunit C 171549 Bacteroidales order 299 NCBI Protein Cluster (PRK) Na(+)-translocating NADH-quinone reductase subunit C Na(+)-translocating NADH-quinone reductase subunit C NF003923.0 PRK05443 PRK05443.3-1 1116 1116 692 equivalog Y Y N RNA degradosome polyphosphate kinase 2.7.4.1 171549 Bacteroidales order 778 NCBI Protein Cluster (PRK) polyphosphate kinase RNA degradosome polyphosphate kinase NF009959.0 PRK13426 PRK13426.1 394 394 291 equivalog Y Y N F0F1 ATP synthase subunit gamma 7.1.2.2 171549 Bacteroidales order 1156 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit gamma F0F1 ATP synthase subunit gamma Produces ATP from ADP in the presence of a proton gradient across the membrane; the gamma chain is a regulatory subunit NF009964.0 PRK13429 PRK13429.1-3 154 154 180 equivalog Y Y N F0F1 ATP synthase subunit delta 7.1.2.2 171549 Bacteroidales order 985 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit delta F0F1 ATP synthase subunit delta NF010634.0 PRK14031 PRK14031.1 822 822 444 equivalog Y Y N NADP-specific glutamate dehydrogenase 171549 Bacteroidales order 798 NCBI Protein Cluster (PRK) glutamate dehydrogenase NADP-specific glutamate dehydrogenase Converts 2-oxoglutarate to glutamate NF011391.0 PRK14816 PRK14816.1 283 283 196 equivalog Y Y N NADH-quinone oxidoreductase subunit B 1.6.5.9 171549 Bacteroidales order 785 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit B NADH-quinone oxidoreductase subunit B NF011411.0 PRK14838 PRK14838.1 417 417 244 equivalog Y Y N isoprenyl transferase 171549 Bacteroidales order 756 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate synthase isoprenyl transferase NF018072.5 PF06321.16 P_gingi_FimA 21.4 21.4 153 domain Y Y N fimbrial protein 11748193,17906122 171549 Bacteroidales order 6685 EBI-EMBL Major fimbrial subunit protein (FimA) Porphyromonas gingivalis FimA family fimbrial protein N-terminal domain This HMM describes a domain shared by various fimbrial major and minor subunit proteins, including FimA, FimC, Mfa3, and MfA4 in Porphyromonas gingivalis, typically found about 40 amino acids from the N-terminus and representing about a quarter of the total length of the protein. NF020418.5 PF08842.15 Mfa2 21.2 21.2 277 domain Y Y N FimB/Mfa2 family fimbrial subunit 15972485,19589838 171549 Bacteroidales order 9847 EBI-EMBL Fimbrillin-A associated anchor proteins Mfa1 and Mfa2 FimB/Mfa2 family fimbrial subunit This family of proteins may be lipoproteins principally from bacilli. They are between 300 and 400 residues. Many Bacteroides-like bacterial species, including Porphyromonas gingivalis, the causal agent of periodontal infection, carry at least two types of fimbriae, namely FimA and Mfa1 fimbriae, following the names of their major subunit proteins [1]. Normally, FimA fimbriae are long filaments that are easily detached from cells, whereas Mfa1 fimbriae are short filaments that are tightly bound to cells; however, in the absence of Mfa2 protein, the Mfa1 fimbriae are also very long and are not attached. Mfa2 and Mfa1 are associated with each other in whole P. gingivalis cells to the extent that Mfa2 is located on the cell surface and probably associated with Mfa1 fimbriae in such a way that it anchors the Mfa1 fimbriae to the cell surface and regulates Mfa1 filament length [2]. [1]. 15972485. Short fimbriae of Porphyromonas gingivalis and their role in coadhesion with Streptococcus gordonii. Park Y, Simionato MR, Sekiya K, Murakami Y, James D, Chen W, Hackett M, Yoshimura F, Demuth DR, Lamont RJ;. Infect Immun. 2005;73:3983-3989. [2]. 19589838. Anchoring and length regulation of Porphyromonas gingivalis Mfa1 fimbriae by the downstream gene product Mfa2. Hasegawa Y, Iwami J, Sato K, Park Y, Nishikawa K, Atsumi T, Moriguchi K, Murakami Y, Lamont RJ, Nakamura H, Ohno N, Yoshimura F;. Microbiology. 2009;155:3333-3347. (from Pfam) NF021851.5 PF10365.14 DUF2436 25 25 164 domain Y Y N DUF2436 domain-containing protein 171549 Bacteroidales order 380 EBI-EMBL Domain of unknown function (DUF2436) Domain of unknown function (DUF2436) This domain is found on peptidase C25 proteins and has no known function. (from Pfam) NF023074.5 PF11644.13 DUF3256 25 25 195 PfamAutoEq Y Y N DUF3256 family protein 171549 Bacteroidales order 1557 EBI-EMBL Protein of unknown function (DUF3256) DUF3256 family protein This family of proteins with unknown function appears to be restricted to Bacteroidales. (from Pfam) NF024332.5 PF12930.12 DUF3836 25 25 127 domain Y Y N DUF3836 domain-containing protein 171549 Bacteroidales order 1500 EBI-EMBL Family of unknown function (DUF3836) Family of unknown function (DUF3836) Family of uncharacterised proteins found in Bacteroidales species. (from Pfam) NF024386.5 PF12984.12 DUF3868 27 27 105 domain Y Y N DUF3868 domain-containing protein 15790854,16735464 171549 Bacteroidales order 4069 EBI-EMBL Domain of unknown function (DUF3868) Domain of unknown function (DUF3868) Based on Bacteroides thetaiotaomicron gene BT_1065, a putative uncharacterized protein As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), It appears to be upregulated in the presence of host or other bacterial species vs when in culture [1,2]. [1]. 15790854. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Sonnenburg JL, Xu J, Leip DD, Chen CH et al. Science 2005 Mar 25;307(5717):1955-9. [2]. 16735464. A hybrid two-component system protein of a prominent human gut symbiont couples glycan sensing in vivo to carbohydrate metabolism. Sonnenburg ED, Sonnenburg JL, Manchester JK, Hansen EE et al. Proc Natl Acad Sci U S A 2006 Jun 6;103(23):8834-9. (from Pfam) NF024392.5 PF12990.12 DUF3874 28.3 28.3 71 domain Y Y N DUF3874 domain-containing protein 15790854,16735464 171549 Bacteroidales order 5528 EBI-EMBL Domain of unknonw function from B. Theta Gene description (DUF3874) DUF3874 domain-containing protein Based on Bacteroides thetaiotaomicron gene BT_4228, a putative uncharacterized protein As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), It appears to be upregulated in the presence of host or other bacterial species vs when in culture [1,2]. [1]. 15790854. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Sonnenburg JL, Xu J, Leip DD, Chen CH et al. Science 2005 Mar 25;307(5717):1955-9. [2]. 16735464. A hybrid two-component system protein of a prominent human gut symbiont couples glycan sensing in vivo to carbohydrate metabolism. Sonnenburg ED, Sonnenburg JL, Manchester JK, Hansen EE et al. Proc Natl Acad Sci U S A 2006 Jun 6;103(23):8834-9. (from Pfam) NF025419.5 PF14053.11 DUF4248 27 27 68 domain Y Y N DUF4248 domain-containing protein 171549 Bacteroidales order 2685 EBI-EMBL Domain of unknown function (DUF4248) Domain of unknown function (DUF4248) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 73 and 86 amino acids in length. (from Pfam) NF025421.5 PF14055.11 NVEALA 27 27 62 subfamily Y Y N NVEALA domain-containing protein 171549 Bacteroidales order 2502 EBI-EMBL NVEALA protein NVEALA domain-containing protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 75 and 92 amino acids in length. There is a conserved NVEALA sequence motif. (from Pfam) NF026011.5 PF14660.11 DUF4458 22.4 22.4 114 domain Y Y N DUF4458 domain-containing protein 171549 Bacteroidales order 750 EBI-EMBL Domain of unknown function (DUF4458) Domain of unknown function (DUF4458) this domain is found in tandem repeats on the N-terminus of secreted LRR proteins from human associated Bacteroidetes domain boundaries are based on the JCSG solved 3D structure of JCSG target SP16667A (BT_0210) (from Pfam) NF026754.5 PF15414.11 DUF4621 27 27 329 subfamily Y Y N DUF4621 domain-containing protein 171549 Bacteroidales order 77 EBI-EMBL Protein of unknown function (DUF4621) Protein of unknown function (DUF4621) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 350 amino acids in length. (from Pfam) NF026755.5 PF15415.11 Mfa_like_2 20 20 303 subfamily Y Y N BF2992 family fimbrillin-A clan protein 171549 Bacteroidales order 676 EBI-EMBL Fimbrillin-like BF2992 family fimbrillin-A clan protein PDB has a crystral structure with unpublished and untraceable annotation, suggesting the protein is a probable adhesin, from locus BF2867 in Bacteroides fragilis. But the crystal structure appears to match the protein from locus tag BF2992, not BF2867. Pfam places the protein in the fimbrillin-A clan. NF026833.5 PF15495.11 Fimbrillin_C 27 27 84 domain Y Y N fimbria major subunit 11748193 171549 Bacteroidales order 4439 EBI-EMBL Major fimbrial subunit protein type IV, Fimbrillin, C-terminal fimbria major subunit Fimbrillin_C is a C-terminal family of major fimbrial subunit protein type IV proteins largely from Bacillus species. The family is associated with family P_gingi_FimA, Pfam:PF06321. [1]. 11748193. Functional differences among FimA variants of Porphyromonas gingivalis and their effects on adhesion to and invasion of human epithelial cells. Nakagawa I, Amano A, Kuboniwa M, Nakamura T, Kawabata S, Hamada S;. Infect Immun 2002;70:277-285. (from Pfam) NF027221.5 PF15889.10 DUF4738 23.9 23.9 146 domain Y Y N DUF4738 domain-containing protein 171549 Bacteroidales order 1905 EBI-EMBL Domain of unknown function (DUF4738) Domain of unknown function (DUF4738) Family of uncharacterized proteins found in CFB group of bacteria, mostly from Bacteroides and Prevotella genera present in human gut and oral cavity, respectively. JCSG target SP13584B, the experimentally determined structure consists of two WD40-like beta sheet repeats forming a beta sandwich (from Pfam) NF027350.5 PF16023.10 DUF4784 25 25 304 PfamAutoEq Y Y N WD40-like domain containing protein 171549 Bacteroidales order 421 EBI-EMBL DUF4784 WD40-like domain DUF4784 WD40-like domain This is a family of uncharacterised proteins from Bacteroidetes. This entry adopts a 6-bladed beta propeller structure. (from Pfam) NF027435.5 PF16109.10 DUF4827 29.4 29.4 183 PfamAutoEq Y Y N DUF4827 family protein 171549 Bacteroidales order 1403 EBI-EMBL Domain of unknown function (DUF4827) DUF4827 family protein This family consists of uncharacterized proteins around 200 residues in length and is mainly found in various Bacteroides species. Distant homology prediction algorithms consistently suggest a homology between this family and FKBP-type peptidyl-prolyl cis-trans isomerases (PF00254), but this relation is as yet not confirmed. The function of this family is unknown. (from Pfam) NF027465.5 PF16139.10 DUF4847 25 25 147 PfamAutoEq Y Y N DUF4847 family protein 171549 Bacteroidales order 445 EBI-EMBL Domain of unknown function (DUF4847) DUF4847 family protein This uncharacterized domain has a lipocalin fold. (from Pfam) NF027466.5 PF16140.10 DUF4848 22.8 22.8 216 domain Y Y N DUF4848 domain-containing protein 171549 Bacteroidales order 283 EBI-EMBL Domain of unknown function (DUF4848) Domain of unknown function (DUF4848) A small family of uncharacterized proteins around 310 residues in length and found in various Bacteroides species. The function of this family is unknown. (from Pfam) NF027476.5 PF16150.10 DUF4858 22 22 188 domain Y Y N DUF4858 domain-containing protein 171549 Bacteroidales order 591 EBI-EMBL Domain of unknown function (DUF4858) Domain of unknown function (DUF4858) This family consists of uncharacterized proteins around 190 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. (from Pfam) NF027574.5 PF16249.10 DUF4906 28.7 28.7 225 domain Y Y N DUF4906 domain-containing protein 171549 Bacteroidales order 448 EBI-EMBL Domain of unknown function (DUF4906) Domain of unknown function (DUF4906) A family of uncharacterised proteins around 300 residues in length and found in various Bacteroides species. The function of this family is unknown. (from Pfam) NF027597.5 PF16272.10 DUF4925 28.5 28.5 324 domain Y Y N DUF4925 domain-containing protein 171549 Bacteroidales order 1167 EBI-EMBL Domain of unknown function (DUF4925) Domain of unknown function (DUF4925) This family consists of uncharacterized proteins around 400 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. (from Pfam) NF027611.5 PF16287.10 DUF4933 26 26 396 domain Y Y N DUF4933 domain-containing protein 171549 Bacteroidales order 333 EBI-EMBL Domain of unknown function (DUF4933) Domain of unknown function (DUF4933) This family consists of uncharacterized proteins around 450 residues in length and is mainly found in various species, such as Bacteroides and Parabacteroides. Several members are annotated as putative transmembrane proteins, but the specific function of this family is unknown. (from Pfam) NF027661.5 PF16341.10 DUF4971 31.3 31.3 141 domain Y Y N DUF4971 domain-containing protein 171549 Bacteroidales order 141 EBI-EMBL Domain of unknown function (DUF4971) Domain of unknown function (DUF4971) This small family consists of uncharacterised proteins around 370 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. (from Pfam) NF027690.5 PF16372.10 DUF4984 25 25 164 domain Y Y N DUF4984 domain-containing protein 171549 Bacteroidales order 400 EBI-EMBL Domain of unknown function (DUF4984) Domain of unknown function (DUF4984) This domain is around 150 residues long and is located in the C-terminal of some uncharacterized proteins in various Bacteroides and Prevotella species. The function of this domain remains unknown. (from Pfam) NF027695.5 PF16377.10 DUF4987 28.7 28.7 154 domain Y N N Domain of unknown function 171549 Bacteroidales order 366 EBI-EMBL Domain of unknown function Domain of unknown function This family around 150 residues locates in the C-terminal of some uncharacterized proteins in various Bacteroides and Prevotella species. The function of this family remains unknown. (from Pfam) NF027697.5 PF16379.10 DUF4989 22.8 22.8 293 domain Y Y N DUF4989 domain-containing protein 171549 Bacteroidales order 267 EBI-EMBL Domain of unknown function (DUF4989) Domain of unknown function (DUF4989) This family around 300 residues locates in the N-terminal of some uncharacterized proteins in various Bacteroides and Alistipes species. The function of this family remains unknown. This entry contains a duplication of a DUF1735-like domain. (from Pfam) NF027700.5 PF16383.10 DUF4992 29 29 183 subfamily_domain Y Y N DUF4992 family lipoprotein 171549 Bacteroidales order 376 EBI-EMBL Domain of unknown function DUF4992 domain This family around 150 residues locates in the N-terminal of some uncharacterized proteins in various Bacteroides and Prevotella species. The function of this family remains unknown. (from Pfam) NF027703.5 PF16386.10 DUF4995 28.4 28.4 73 domain Y Y N DUF4995 domain-containing protein 171549 Bacteroidales order 541 EBI-EMBL Domain of unknown function DUF4995 domain This family around 100 residues locates in the N-terminal of some uncharacterized proteins and glucuronyl hydrolases in various Bacteroides species. The function of this family remains unknown. (from Pfam) NF027706.5 PF16390.10 DUF4999 25 25 76 domain Y Y N DUF4999 domain-containing protein 171549 Bacteroidales order 327 EBI-EMBL Domain of unknown function DUF4999 domain This family around 75 residues locates in the N-terminal of F5/8 type C domain proteins and some uncharacterized proteins in various Bacteroides species. The function of this family remains unknown. (from Pfam) NF027709.5 PF16394.10 DUF5003 25 25 341 domain Y Y N DUF5003 domain-containing protein 171549 Bacteroidales order 437 EBI-EMBL Domain of unknown function (DUF5003) Domain of unknown function (DUF5003) This small family of proteins is functionally uncharacterised. This family is found in bacteroides. Proteins in this family are typically between 500 and 650 amino acids in length. (from Pfam) NF027742.5 PF16427.10 DUF5024 25 25 104 PfamAutoEq Y Y N DUF5024 domain-containing protein 171549 Bacteroidales order 173 EBI-EMBL Domain of unknown function (DUF5024) Domain of unknown function (DUF5024) This family consists of several uncharacterized proteins around 150 or 200 in length and is mainly found in various Bacteroides and Parabacteroides species. The function of this family is unknown. (from Pfam) NF027748.5 PF16433.10 DUF5030 25 25 314 domain Y Y N DUF5030 domain-containing protein 171549 Bacteroidales order 163 EBI-EMBL Domain of unknown function (DUF5030) Domain of unknown function (DUF5030) This family consists of several uncharacterized proteins around 300 in length and is mainly found in various Bacteroides species. The function of this family is unknown. (from Pfam) NF027749.5 PF16434.10 DUF5031 25 25 362 PfamAutoEq Y Y N DUF5031 domain-containing protein 171549 Bacteroidales order 131 EBI-EMBL Domain of unknown function (DUF5031) Domain of unknown function (DUF5031) This family consists of several uncharacterized proteins around 380 in length and is mainly found in Bacteroides fragilis and sp. The function of this family is unknown. (from Pfam) NF027754.5 PF16439.10 DUF5036 25 25 238 PfamAutoEq Y Y N DUF5036 family protein 171549 Bacteroidales order 287 EBI-EMBL Domain of unknown function (DUF5036) DUF5036 family protein This family consists of several uncharacterized proteins around 240 residues in length and is mainly found in various Bacteroides and Parabacteroides species. The function of this family is unknown. (from Pfam) NF027757.5 PF16442.10 DUF5039 25 25 203 PfamAutoEq Y Y N DUF5039 family protein 171549 Bacteroidales order 125 EBI-EMBL Domain of unknown function (DUF5039) DUF5039 family protein This family consists of several uncharacterized proteins around 240 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. (from Pfam) NF027759.5 PF16444.10 DUF5041 28.2 28.2 192 domain Y Y N DUF5041 domain-containing protein 171549 Bacteroidales order 173 EBI-EMBL Domain of unknown function (DUF5041) Domain of unknown function (DUF5041) This family consists of several uncharacterized proteins around 230 residues in length and is mainly found in various Bacteroidales species. The function of this family is unknown. (from Pfam) NF027760.5 PF16445.10 DUF5042 25 25 434 domain Y Y N DUF5042 domain-containing protein 171549 Bacteroidales order 92 EBI-EMBL Domain of unknown function (DUF5042) Domain of unknown function (DUF5042) This family consists of several uncharacterized proteins around 460 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. (from Pfam) NF027779.5 PF16464.10 DUF5045 29.9 29.9 85 domain Y Y N DUF5045 domain-containing protein 171549 Bacteroidales order 899 EBI-EMBL Domain of unknown function (DUF5045) Domain of unknown function (DUF5045) This family consists of N-terminal of several uncharacterised proteins around 260 residues in length and is mainly found in various Bacteroides and Parabacteroides species. The function of this family is unknown. (from Pfam) NF027794.5 PF16479.10 DUF5056 28 28 93 PfamAutoEq Y Y N DUF5056 domain-containing protein 171549 Bacteroidales order 730 EBI-EMBL Domain of unknown function (DUF5056) Domain of unknown function (DUF5056) This family consists of uncharacterized proteins around 360 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. (from Pfam) NF027899.5 PF16585.10 Lipocalin_8 27.2 27.2 135 domain Y Y N lipocalin-like domain-containing protein 171549 Bacteroidales order 1485 EBI-EMBL Lipocalin-like domain Lipocalin-like domain NF028449.5 PF17139.9 DUF5112 29.4 29.4 266 PfamAutoEq Y Y N DUF5112 domain-containing protein 171549 Bacteroidales order 2193 EBI-EMBL Domain of unknown function (DUF5112) Domain of unknown function (DUF5112) This domain is frequently found upstream of family HATPase_c Pfam:PF000251. (from Pfam) NF028450.5 PF17140.9 DUF5113 27.1 27.1 161 PfamAutoEq Y Y N DUF5113 domain-containing protein 171549 Bacteroidales order 2254 EBI-EMBL Domain of unknown function (DUF5113) Domain of unknown function (DUF5113) This domain is frequently found downstream of family HATPase_c Pfam:PF000251 in duplicate. (from Pfam) NF028452.5 PF17142.9 DUF5115 28 28 276 PfamAutoEq Y Y N DUF5115 domain-containing protein 171549 Bacteroidales order 816 EBI-EMBL Domain of unknown function (DUF5115) Domain of unknown function (DUF5115) NF028454.5 PF17145.9 DUF5119 27 27 191 domain Y Y N DUF5119 domain-containing protein 171549 Bacteroidales order 2737 EBI-EMBL Domain of unknown function (DUF5119) Domain of unknown function (DUF5119) This is a family of uncharacterised Bacteroidia sequences. (from Pfam) NF028469.5 PF17160.9 DUF5124 27 27 100 PfamAutoEq Y Y N DUF5124 domain-containing protein 171549 Bacteroidales order 82 EBI-EMBL Domain of unknown function (DUF5124) Domain of unknown function (DUF5124) NF033071.0 SusD 725 725 558 exception Y Y N starch-binding outer membrane lipoprotein SusD susD 171549 Bacteroidales order 348 NCBIFAM starch-binding outer membrane lipoprotein SusD starch-binding outer membrane lipoprotein SusD SusD (Starch Uptake System D) is an outer membrane lipoprotein that binds starch and participates in a TonB-dependent nutrient uptake complex. Related proteins from similar TonB-dependent complexes that import other, usually multimeric nutrient substrates include RagB and NanU. NF033879.1 smalltalk 24.7 24.3 29 hypoth_equivalog Y Y N smalltalk protein 31402174 171549 Bacteroidales order 1735 NCBIFAM smalltalk protein smalltalk protein Smalltalk is a membrane-associated protein of very small size (less than 35 amino acids), found broadly in Bacteroides and Prevotella, both of which are prevalent in human gut microbiomes. Genomic context suggests a role in crosstalk in the gut microbiome, whether that involve toxins and immunity, signaling, or some other form of interaction. The family was identified and discussed by Sberro, et al., in a screen for overlooked small proteins encoded within human microbiomes, and named smalltalk here for its small size and cross-talk role. NF037871.5 PF18630.6 Peptidase_M60_C 26.2 26.2 65 domain Y N N Peptidase M60 C-terminal domain 27005013,28096352 171549 Bacteroidales order 880 EBI-EMBL Peptidase M60 C-terminal domain Peptidase M60 C-terminal domain This is C-terminal domain (CTD) of M60-peptidases Pfam:PF13402 [1]. It Can also be found at the C-terminal region of gingipain B (RgpB) from P. gingivalis. It was found to possess a typical Ig-like fold encompassing seven antiparallel beta-strands organized in two beta-sheets, packed into a beta-sandwich structure that can spontaneously dimerise through C-terminal strand swapping. Translocation of gingipains from the periplasm across the OM is dependent on the conserved CTD, which appears to be important for secretion of the proteins and in particular, truncation of the last few C-terminal residues of this domain leads to accumulation of gingipains in the periplasm. Subsequently, the T9SS targeting signal was demonstrated to reside within the last 22 residues at the C-terminus of the CTD. During gingipain translocation across the OM, the CTD is cleaved off by PorU [2]. [1]. 28096352. Recognition of protein-linked glycans as a determinant of peptidase activity. Noach I, Ficko-Blean E, Pluvinage B, Stuart C, Jenkins ML, Brochu D, Buenbrazo N, Wakarchuk W, Burke JE, Gilbert M, Boraston AB;. Proc Natl Acad Sci U S A. 2017;114:E679. [2]. 27005013. The outer-membrane export signal of Porphyromonas gingivalis type IX secretion system (T9SS) is a conserved C-terminal beta-sandwich domain. de Diego I, Ksiazek M, Mizgalska D, Koneru L, Golik P, Szmigielski B, Nowak M, Nowakowska Z, Potempa B, Houston JA, Enghild JJ, Thogersen IB, Gao J, Kwan AH, Trewhella J, Dubin G, Gomis-Ruth FX, Nguyen KA, Potempa J;. Sci Rep. 2016;6:23123. (from Pfam) NF037914.5 PF18805.6 LRR_10 30 20 67 domain Y N N Leucine-rich repeat 171549 Bacteroidales order 711 EBI-EMBL Leucine-rich repeat Leucine-rich repeat This Pfam entry includes some LRRs that fail to be detected with the Pfam:PF00560 model. This entry represents two repeat units. (from Pfam) NF037923.5 PF18827.6 LPD14 27 27 136 domain Y N N Large polyvalent protein-associated domain 14 28559295 171549 Bacteroidales order 138 EBI-EMBL Large polyvalent protein-associated domain 14 Large polyvalent protein-associated domain 14 This is an alpha-helical domain with a conserved glutamate residue that is mainly found in polyvalent proteins of prophages [1]. [1]. 28559295. Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. Iyer LM, Burroughs AM, Anand S, de Souza RF, Aravind L;. J Bacteriol. 2017; [Epub ahead of print] (from Pfam) NF038041.1 fim_Mfa1_fam 130 130 495 subfamily Y Y N Mfa1 family fimbria major subunit GO:0009418 18973529,29379120 171549 Bacteroidales order 3745 NCBIFAM Mfa1 family fimbria major subunit Members of this family are fimbrial shaft proteins (major subunit proteins), found in the Bacteriodetes. The family is named for Mfa1 from Porphyromonas gingivalis, and is related to but distinct from the family of FimA from the species. NF039660.4 PF19603.4 DUF6108 23.9 23.9 138 subfamily Y Y N DUF6108 family protein 171549 Bacteroidales order 456 EBI-EMBL Family of unknown function (DUF6108) DUF6108 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in Bacteroidetes. Proteins in this family are typically between 148 and 173 amino acids in length. (from Pfam) NF039965.4 PF19513.4 DUF6047 27 27 190 subfamily Y Y N DUF6047 family protein 171549 Bacteroidales order 1470 EBI-EMBL Family of unknown function (DUF6047) DUF6047 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in Bacteroidetes bacteria. Proteins in this family are typically between 238 and 400 amino acids in length. (from Pfam) NF040440.4 PF20096.4 DUF6486 22.7 22.7 31 subfamily Y Y N DUF6486 family protein 171549 Bacteroidales order 1645 EBI-EMBL Family of unknown function (DUF6486) DUF6486 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 30 amino acids in length. There is a conserved IAVASA sequence motif. (from Pfam) NF041944.1 Xylase_Ferestase 1200 1200 694 equivalog Y Y N bifunctional endo-1,4-beta-xylanase/feruloyl esterase xyn10D/fae1 3.1.1.73,3.2.1.8 GO:0030600,GO:0045493 19304844 171549 Bacteroidales order 125 NCBIFAM bifunctional endo-1,4-beta-xylanase/feruloyl esterase NF042455.3 PF20200.3 DUF6562 25 25 304 domain Y Y N DUF6562 domain-containing protein 171549 Bacteroidales order 1622 EBI-EMBL Family of unknown function (DUF6562) DUF6562 domain This family of proteins is functionally uncharacterised. This family of proteins is found in Bacteroidetes. Proteins in this family are typically between 340 and 430 amino acids in length and have the conserved motifs WAD, RP and TxxG. Some members are hypothetical Fimbrillin-A associated anchor protein Mfa1/Mfa2 and related to Pfam:PF08842. (from Pfam) NF042535.3 PF20264.3 DUF4784_N 24.2 24.2 107 domain Y N N DUF4784 N-terminal Ig-like domain 171549 Bacteroidales order 421 EBI-EMBL DUF4784 N-terminal Ig-like domain DUF4784 N-terminal Ig-like domain This is a family of uncharacterised proteins from Bacteroidetes. This domain is found to the N-terminus of a WD40-like domain in DUF4784 family protein. (from Pfam) NF042670.3 PF20326.3 DUF6621 27 27 190 subfamily Y Y N DUF6621 family protein 171549 Bacteroidales order 1000 EBI-EMBL Family of unknown function (DUF6621) DUF6621 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 200 amino acids in length. (from Pfam) NF042801.3 PF20558.3 DUF6769 27 27 130 subfamily Y Y N DUF6769 family protein 171549 Bacteroidales order 692 EBI-EMBL Family of unknown function (DUF6769) DUF6769 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically 136 amino acids in length. (from Pfam) NF044611.2 PF20756.2 SusG_CBM58 24 24 117 domain Y N N Alpha-amylase SusG, CBM58 domain 20159465,27137179,29603462 171549 Bacteroidales order 404 EBI-EMBL Alpha-amylase SusG, CBM58 domain Alpha-amylase SusG, CBM58 domain Enzymes of the Glycoside hydrolase family 13 typically show three domains A, B and C. In addition to these, Alpha-amylase SusG from Bacteroides thetaiotaomicron (Swiss:Q8A1G3) includes the insertion of a unique carbohydrate binding module (CBM) family 58 (this entry), which gives the protein an elongated shape. SusG, located on the outer membrane of the cell, cleaves starch into oligosaccharides before internalisation for degradation. CBM58 is approximately 120 residues in length. This domain folds into a beta sandwich and adopts an immunoglobulin-like topology with a flat five-stranded antiparallel beta sheet opposing a four-stranded antiparallel beta sheet which features three protruding loops. Y260, W287, and W299 form the starch-binding site [1, 2, 3]. Paper describing PDB structure 3k8k. [1]. 20159465. SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules. Koropatkin NM, Smith TJ;. Structure. 2010;18:200-215. Paper describing PDB structure 6bs6. [2]. 29603462. Structural basis for the flexible recognition of alpha-glucan substrates by Bacteroides thetaiotaomicron SusG. Arnal G, Cockburn DW, Brumer H, Koropatkin NM;. Protein Sci. 2018;27:1093-1101. [3]. 27137179. The Sus operon: a model system for starch uptake by the human gut Bacteroidetes. Foley MH, Cockburn DW, Koropatkin NM;. Cell Mol Life Sci. 2016;73:2603-2617. (from Pfam) NF045083.2 PF21514.2 FimA-like_C 27 27 189 domain Y N N FimA-like major fimbrial subunit protein, C-terminal domain 27062925 171549 Bacteroidales order 233 EBI-EMBL FimA-like major fimbrial subunit protein, C-terminal domain FimA-like major fimbrial subunit protein, C-terminal domain This domain is found at the C-terminal end of FimA-like major fimbrial subunit protein from Bacteroides stercoris and similar proteins found predominately in bacteroidetes [1]. It is normally found associated with Pfam:PF06321. Paper describing PDB structure 4gpv. [1]. 27062925. A Distinct Type of Pilus from the Human Microbiome. Xu Q, Shoji M, Shibata S, Naito M, Sato K, Elsliger MA, Grant JC, Axelrod HL, Chiu HJ, Farr CL, Jaroszewski L, Knuth MW, Deacon AM, Godzik A, Lesley SA, Curtis MA, Nakayama K, Wilson IA;. Cell. 2016;165:690-703. (from Pfam) NF045387.2 PF21489.2 Fim1C-like_C 27 27 181 domain Y N N Fimbrium tip subunit Fim1C-like, C-terminal domain 27062925 171549 Bacteroidales order 176 EBI-EMBL Fimbrium tip subunit Fim1C-like, C-terminal domain Fimbrium tip subunit Fim1C-like, C-terminal domain This domain is found at the C-terminal end of the putative fimbrium tip subunit Fim1C from Parabacteroides distasonis, and similar proteins from bacteroidetes. Fim1C is thought to be a component of the fimbrium tip that plays a role on the mediation of cell adhesion and biofilm formation. This domain shows transthyretin-like fold that contains seven core beta- strands arranged in two beta-sheets [1]. Paper describing PDB structure 4jg5. [1]. 27062925. A Distinct Type of Pilus from the Human Microbiome. Xu Q, Shoji M, Shibata S, Naito M, Sato K, Elsliger MA, Grant JC, Axelrod HL, Chiu HJ, Farr CL, Jaroszewski L, Knuth MW, Deacon AM, Godzik A, Lesley SA, Curtis MA, Nakayama K, Wilson IA;. Cell. 2016;165:690-703. (from Pfam) NF045572.1 Hepsulflyase_bctds 600 600 706 equivalog Y Y N heparin-sulfate lyase HepC hepC 4.2.2.8 GO:0015021 23011846 171549 Bacteroidales order 418 NCBIFAM heparin-sulfate lyase HepC NF046589.1 PF22095.1 BT_3535-like 27 27 182 domain Y N N BT_3535-like 171549 Bacteroidales order 80 EBI-EMBL BT_3535-like BT_3535-like This family represents the functionally uncharacterised protein BT_3535 from Bacteroides thetaiotaomicron (Swiss:Q8A1X3) and similar sequences found in bacteroidetes. This protein is organised into two domains. (from Pfam) NF046741.1 PF22358.1 MfA4_C 27 27 137 domain Y N N Minor fimbrium tip subunit MfA4, C-terminal 26972441,27062925 171549 Bacteroidales order 95 EBI-EMBL Minor fimbrium tip subunit MfA4, C-terminal Minor fimbrium tip subunit MfA4, C-terminal This domain is found at the C-terminal end of Minor fimbrium tip subunit MfA4 from Porphyromonas gingivalis and similar sequences mainly found in bacteroidales. MfA4 is involved in biofilm formation, adhesion onto host cells and onto other bacteria that are part of the oral microbiome. This domain adopts a transthyretin-like fold that contains seven core beta-strands arranged in two beta-sheets [1]. Paper describing PDB structure 4rdb. [1]. 27062925. A Distinct Type of Pilus from the Human Microbiome. Xu Q, Shoji M, Shibata S, Naito M, Sato K, Elsliger MA, Grant JC, Axelrod HL, Chiu HJ, Farr CL, Jaroszewski L, Knuth MW, Deacon AM, Godzik A, Lesley SA, Curtis MA, Nakayama K, Wilson IA;. Cell. 2016;165:690-703. Paper describing PDB structure 5dhm. [2]. 26972441. Structure of the fimbrial protein Mfa4 from Porphyromonas gingivalis in its precursor form: implications for a donor-strand complementation mechanism. Kloppsteck P, Hall M, Hasegawa Y, Persson K;. Sci Rep. 2016;6:22945. (from Pfam) NF046844.1 PF22492.1 FimA4_C 27 27 208 domain Y N N FimA4 pilin C-terminal domain 27062925,32284566 171549 Bacteroidales order 357 EBI-EMBL FimA4 pilin C-terminal domain FimA4 pilin C-terminal domain This entry represents the C-terminal domain of FimA4 pilin. It folds into a Ig-like beta-sandwich having the characteristic features of the FimA superfamily. Paper describing PDB structure 3liu. [1]. 27062925. A Distinct Type of Pilus from the Human Microbiome. Xu Q, Shoji M, Shibata S, Naito M, Sato K, Elsliger MA, Grant JC, Axelrod HL, Chiu HJ, Farr CL, Jaroszewski L, Knuth MW, Deacon AM, Godzik A, Lesley SA, Curtis MA, Nakayama K, Wilson IA;. Cell. 2016;165:690-703. Paper describing PDB structure 6jzj. [2]. 32284566. Structure of polymerized type V pilin reveals assembly mechanism involving protease-mediated strand exchange. Shibata S, Shoji M, Okada K, Matsunami H, Matthews MM, Imada K, Nakayama K, Wolf M;. Nat Microbiol. 2020;5:830-837. (from Pfam) TIGR03952.1 TIGR03952 metzin_BF0631 208.1 208.1 351 equivalog Y Y N zinc-dependent metalloproteinase lipoprotein GO:0006508,GO:0008237,GO:0008270 171549 Bacteroidales order 866 JCVI zinc-dependent metalloproteinase lipoprotein, BF0631 family zinc-dependent metalloproteinase lipoprotein, BF0631 family Members of this protein family are zinc-dependent metalloproteinases, related to ulilysin and other members of the pappalysin family. Members occur as predicted lipoproteins and occur mostly in the genera Bacteriodes and Prevotella. TIGR04134.1 TIGR04134 lipo_with_rSAM 39.8 39 150 hypoth_equivalog Y Y N radical SAM-associated putative lipoprotein 21478363 171549 Bacteroidales order 652 JCVI putative lipoprotein, rSAM/lipoprotein system radical SAM-associated putative lipoprotein Members of this family are Bacteroidetes lineage putative lipoproteins that always occur in pairs with a radical SAM enzyme, TIGR04133, which has a C-terminal SPASM domain. Many radical SAM/SPASM proteins perform peptide or protein modifications. In some members of this protein family, the region distal to the Cys of the putative lipoprotein cleavage motif is duplicated. TIGR04148.1 TIGR04148 GG_samocin_CFB 300 300 411 equivalog Y Y N radical SAM peptide maturase GO:0031179,GO:0051539,GO:1904047 21478363 171549 Bacteroidales order 520 JCVI radical SAM peptide maturase, GG-Bacteroidales family radical SAM peptide maturase Members of this protein family are radical SAM enzymes (PF04055) with the additional C-terminal region (TIGR04085) that is frequently a marker of peptide modification. Many members of this family are found in the vicinity of one or several ORFs encoding short polypeptides with a Gly-Gly motif (common for bacteriocin leader peptide cleavage), followed by a Cys-rich patch and then poorly conserved sequences. TIGR04150.1 TIGR04150 pseudo_rSAM_GG 250 250 407 subfamily Y Y N TIGR04150 pseudo-rSAM protein 21478363 171549 Bacteroidales order 389 JCVI pseudo-rSAM protein, GG-Bacteroidales system TIGR04150 pseudo-rSAM protein Many peptide-modifying radical SAM enzymes have two 4Fe4S-binding regions, an N-terminal one recognized by Pfam radical SAM domain-defining model PF04055 and a C-terminal one recognized by TIGR04085. Members of this protein family occur in cassettes with such a radical SAM family (TIGR04148) and with a peptide modification target (TIGR04149). Surprisingly, members of this family show full-length homology to each other, with several scoring at least borderline hits to both PF04055 and TIGR04085, and yet differ in the presence/absence of a signature CX(3)CX(2)CX(9)C motif. Instead, members are best-conserved in the TIGR04085-like C-terminal region. Therefore, this protein family is designated a pseudo-radical-SAM protein, which likely works in partnership with a TIGR04148 family protein. TIGR04157.1 TIGR04157 glyco_rSAM_CFB 400 400 406 subfamily Y Y N TIGR04157 family glycosyltransferase 21478363 171549 Bacteroidales order 306 JCVI glycosyltransferase, GG-Bacteroidales peptide system TIGR04157 glycosyltransferase Members of this protein family are predicted glycosyltransferases that occur in conserved gene neighborhoods in various members of the Bacteroidales. These neighborhoods feature a radical SAM enzyme predicted to act in peptide modification (family TIGR04148), peptides from family TIGR04149 with a characteristic GG cleavage motif, and several other proteins. NF042968.1 AcxylEst_AxeA1 700 700 459 equivalog Y Y N acetylxylan esterase AxeA1 axeA1 3.1.1.72 GO:0045493,GO:0046555 21742923 171552 Prevotellaceae family 119 NCBIFAM acetylxylan esterase AxeA1 NF000738.0 PRK00043 PRK00043.3-1 445 445 221 equivalog Y Y N thiamine phosphate synthase 2.5.1.3 1716 Corynebacterium genus 13 NCBI Protein Cluster (PRK) thiamine-phosphate pyrophosphorylase thiamine phosphate synthase NF001031.0 PRK00111 PRK00111.1 293 293 180 equivalog Y N N hypothetical protein 1716 Corynebacterium genus 55 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF001059.0 PRK00117 PRK00117.4-3 253 253 206 equivalog Y Y N recombination regulator RecX recX 1716 Corynebacterium genus 469 NCBI Protein Cluster (PRK) recombination regulator RecX recombination regulator RecX NF001101.0 PRK00134 PRK00134.1 95 95 104 equivalog Y Y N fluoride efflux transporter family protein 1716 Corynebacterium genus 271 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter family protein NF001212.0 PRK00182 PRK00182.1 195 195 165 equivalog Y Y N Sec-independent protein translocase subunit TatB tatB 1716 Corynebacterium genus 87 NCBI Protein Cluster (PRK) sec-independent translocase Sec-independent protein translocase subunit TatB NF001265.0 PRK00227 PRK00227.1 799 799 693 equivalog Y Y N [protein-PII] uridylyltransferase 2.7.7.59 1716 Corynebacterium genus 527 NCBI Protein Cluster (PRK) PII uridylyl-transferase [protein-PII] uridylyltransferase Uridylylates and de-uridylylates the small trimeric nitrogen regulatory protein PII NF001282.0 PRK00235 PRK00235.2-4 342 342 286 equivalog Y Y N adenosylcobinamide-GDP ribazoletransferase 2.7.8.26 1716 Corynebacterium genus 87 NCBI Protein Cluster (PRK) cobalamin synthase adenosylcobinamide-GDP ribazoletransferase NF001300.0 PRK00247 PRK00247.1 375 375 429 equivalog Y Y N membrane protein insertase YidC yidC 1716 Corynebacterium genus 283 NCBI Protein Cluster (PRK) putative inner membrane protein translocase component YidC membrane protein insertase YidC NF002546.0 PRK02101 PRK02101.2-4 321 321 245 equivalog Y Y N peroxide stress protein YaaA yaaA 1716 Corynebacterium genus 553 NCBI Protein Cluster (PRK) hypothetical protein peroxide stress protein YaaA NF004110.0 PRK05599 PRK05599.1 362 362 246 equivalog Y Y N SDR family oxidoreductase 1716 Corynebacterium genus 457 NCBI Protein Cluster (PRK) hypothetical protein SDR family oxidoreductase NF004112.0 PRK05601 PRK05601.1 550 550 407 equivalog Y N N DNA polymerase III subunit epsilon 1716 Corynebacterium genus 197 NCBI Protein Cluster (PRK) DNA polymerase III subunit epsilon DNA polymerase III subunit epsilon NF004125.0 PRK05613 PRK05613.1 765 765 437 equivalog Y Y N O-acetylhomoserine/O-acetylserine sulfhydrylase 2.5.1.47 1716 Corynebacterium genus 736 NCBI Protein Cluster (PRK) O-acetylhomoserine aminocarboxypropyltransferase O-acetylhomoserine/O-acetylserine sulfhydrylase NF004169.0 PRK05637 PRK05637.1 332 332 210 equivalog Y Y N anthranilate synthase component II 1716 Corynebacterium genus 433 NCBI Protein Cluster (PRK) anthranilate synthase component II anthranilate synthase component II With component I catalyzes the formation of anthranilate and glutamate from chorismate and glutamine NF005622.0 PRK07375 PRK07375.2-1 185 185 179 equivalog Y N N putative monovalent cation/H+ antiporter subunit C 1716 Corynebacterium genus 107 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit C putative monovalent cation/H+ antiporter subunit C NF005625.0 PRK07375 PRK07375.2-4 165 165 141 equivalog Y N N putative monovalent cation/H+ antiporter subunit C 1716 Corynebacterium genus 201 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit C putative monovalent cation/H+ antiporter subunit C NF005783.0 PRK07597 PRK07597.9-4 127 127 109 equivalog Y Y N preprotein translocase subunit SecE secE 1716 Corynebacterium genus 310 NCBI Protein Cluster (PRK) preprotein translocase subunit SecE preprotein translocase subunit SecE NF005844.0 PRK07764 PRK07764.1-3 964 964 841 equivalog Y Y N DNA polymerase III subunit gamma and tau 2.7.7.7 1716 Corynebacterium genus 371 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunit gamma and tau NF006239.0 PRK08375 PRK08375.1-5 760 760 511 equivalog Y N N putative monovalent cation/H+ antiporter subunit D 1716 Corynebacterium genus 580 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit D putative monovalent cation/H+ antiporter subunit D NF009187.0 PRK12535 PRK12535.1 290 290 197 equivalog Y Y N RNA polymerase sigma factor 1716 Corynebacterium genus 566 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009238.0 PRK12592 PRK12592.1 170 170 126 equivalog Y N N putative monovalent cation/H+ antiporter subunit G 1716 Corynebacterium genus 225 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit G putative monovalent cation/H+ antiporter subunit G NF009255.0 PRK12612 PRK12612.1-3 112 112 92 equivalog Y N N putative monovalent cation/H+ antiporter subunit F 1716 Corynebacterium genus 39 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit F putative monovalent cation/H+ antiporter subunit F NF009256.0 PRK12612 PRK12612.1-4 136 136 90 equivalog Y N N putative monovalent cation/H+ antiporter subunit F 1716 Corynebacterium genus 57 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit F putative monovalent cation/H+ antiporter subunit F NF009297.0 PRK12654 PRK12654.1 116 116 151 equivalog Y Y N monovalent cation/H+ antiporter subunit E 1716 Corynebacterium genus 379 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit E monovalent cation/H+ antiporter subunit E Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF009318.0 PRK12674 PRK12674.2-3 97 97 102 equivalog Y Y N Na+/H+ antiporter subunit G 1716 Corynebacterium genus 347 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit G Na+/H+ antiporter subunit G NF009319.0 PRK12674 PRK12674.2-4 149 149 140 equivalog Y Y N Na+/H+ antiporter subunit G 1716 Corynebacterium genus 66 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit G Na+/H+ antiporter subunit G NF010631.0 PRK14027 PRK14027.1 515 515 283 equivalog Y Y N quinate/shikimate dehydrogenase (NAD+) 1716 Corynebacterium genus 18 NCBI Protein Cluster (PRK) quinate/shikimate dehydrogenase quinate/shikimate dehydrogenase (NAD+) Catalyzes the NAD-dependent formation of 3-dehydroquinate and 3-dehydroshikimate from quinate and shikimate NF011455.0 PRK14873 PRK14873.1-5 969 969 675 equivalog Y Y N primosomal protein N' 3.6.1.- 1716 Corynebacterium genus 727 NCBI Protein Cluster (PRK) primosome assembly protein PriA primosomal protein N' NF013489.5 PF01324.24 Diphtheria_R 25 25 167 PfamEq Y N N Diphtheria toxin, R domain 7833808,8573568 1716 Corynebacterium genus 19 EBI-EMBL Diphtheria toxin, R domain Diphtheria toxin, R domain C-terminal receptor binding (R) domain - binds to cell surface receptor, permitting the toxin to enter the cell by receptor mediated endocytosis. [1]. 7833808. Refined structure of monomeric diphtheria toxin at 2.3 A resolution. Bennett MJ, Eisenberg D;. Protein Sci 1994;3:1464-1475. [2]. 8573568. Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide. Bell CE, Eisenberg D;. Biochemistry 1996;35:1137-1149. (from Pfam) NF022997.5 PF11565.13 PorB 22.5 22.5 99 domain Y N N Alpha helical Porin B 18462756 1716 Corynebacterium genus 252 EBI-EMBL Alpha helical Porin B Alpha helical Porin B Porin B is a porin from Corynebacterium glutamicum which allows the exchange of material across the mycolic acid layer which is the protective nonpolar barrier. Porin B has an alpha helical core structure consisting of four alpha-helices surrounding a nonpolar interior. There is a disulphide bridge between helices 1 and 4 to form a stable covalently bound ring [1]. The channel of PorB is oligomeric [1]. [1]. 18462756. A putative alpha-helical porin from Corynebacterium glutamicum. Ziegler K, Benz R, Schulz GE;. J Mol Biol. 2008;379:482-491. (from Pfam) NF033494.1 NSS_import_MetS 70 70 53 equivalog Y Y N methionine/alanine import NSS transporter subunit MetS metS 18991398 1716 Corynebacterium genus 186 NCBIFAM methionine/alanine import NSS transporter subunit MetS methionine/alanine import NSS transporter subunit MetS NF033925.0 pora_1 50 50 42 subfamily Y Y N PorA family porin GO:0015288 1716 Corynebacterium genus 26 NCBIFAM PorA family porin PorA family porin This HMM hits Corynebacterial Porin A (PorA) family porins, which are short membrane proteins. NF033938.0 porH_2 30 30 63 subfamily Y Y N PorH family porin GO:0015288 16000733,24100136 1716 Corynebacterium genus 154 NCBIFAM PorH family porin PorH family porin Proteins of this HMM family form major outer membrane hetero-oligomeric pores on the cell wall of Corynebacterium with PorA family porins. NF038023.1 S_layer_PS2 300 300 499 exception Y Y N S-layer protein PS2 cspB 12948629,15288952,9044282 1716 Corynebacterium genus 21 NCBIFAM S-layer protein PS2 NF038152.1 TrpL_Coryne 30 30 17 equivalog Y Y N trp operon leader peptide trpL GO:0031556 3609747,3667535,7683184 1716 Corynebacterium genus 6 NCBIFAM trp operon leader peptide, Corynebacterium type Member of this family are tryptophan biosynthesis operon leader peptide TrpL, as found in the genus Corynebacterium. It differs substantially from Trp-rich leader peptides documented in other lineages, such as in the gammaproteobacteria. NF040480.1 CGLAU_01105_fam 45 45 179 hypoth_equivalog Y Y N CGLAU_01105 family protein 1716 Corynebacterium genus 329 NCBIFAM CGLAU_01105 family protein Members of this family are found, so far, almost entirely in the genus Corynebacterium. The function is unknown. The model was built, in part, to prevent misannotations that might result from a now-corrected improper inclusion of a family member in the seed alignment of Pfam model PF05407, which represents an endopeptidase of Rubella virus, MEROPS family C27. NF040633.1 FadD32_Coryne 875 875 614 exception Y Y N FadD32-like long-chain-fatty-acid--AMP ligase GO:0071768 1716 Corynebacterium genus 759 NCBIFAM FadD32-like long-chain-fatty-acid--AMP ligase Members of this family are found in the genus Corynebacterium, are most similar to the key mycolic acid biosynthesis protein FadD32 of any fatty acid--AMP ligase in Mycobacterium tuberculosis, and are likewise encoded next to Pks13. However, as the mycolic acids produced in Corynebacterium and in Mycobacterium differ substantially, it is not clear that assigning the same name in Corynebacterium is appropriate. NF041660.1 oxygluDhInhib_OdhI 250 250 141 equivalog Y Y N oxoglutarate dehydrogenase inhibitor Odhl odhI 16522631 1716 Corynebacterium genus 312 NCBIFAM oxoglutarate dehydrogenase inhibitor Odhl NF044828.2 PF21575.2 DsbA_N 27 27 61 domain Y N N DsbA, N-terminal domain 1716 Corynebacterium genus 68 EBI-EMBL DsbA, N-terminal domain DsbA, N-terminal domain This domain is found at the N-terminal end of Putative secreted protein from Corynebacterium diphtheriae (DsbA, Swiss:Q6NJK4). It is usually found associated with Pfam:PF13462 and Pfam:PF01323.\ Its specific function is unknown. (from Pfam) NF046504.1 PF22089.1 DIP2116-like_N 27 27 165 domain Y N N DIP2116-like, N-terminal domain 1716 Corynebacterium genus 144 EBI-EMBL DIP2116-like, N-terminal domain DIP2116-like, N-terminal domain This domain is found at the N-terminal end of the putative membrane anchored protein DIP2116 from Corynebacterium diphtheriae (Swiss:Q6NEZ3). It shows an immunoglobulin-like fold. (from Pfam) NF046634.1 PF22313.1 DIP0205-like_N 27 27 57 domain Y N N DIP0205-like, N-terminal domain 1716 Corynebacterium genus 25 EBI-EMBL DIP0205-like, N-terminal domain DIP0205-like, N-terminal domain This domain is found at the N-terminal end of DIP0205 from Corynebacterium diphtheriae and other putative phage capsid proteins found in tailed bacteriophages and bacterial prophages. This domain shows an alpha-helical configuration. It is often found associated to Pfam:PF05065. (from Pfam) NF046710.1 PF22242.1 6PGD_like 27 27 98 domain Y N N 6-phosphogluconate dehydrogenase C-terminal domain-like 1716 Corynebacterium genus 368 EBI-EMBL 6-phosphogluconate dehydrogenase C-terminal domain-like 6-phosphogluconate dehydrogenase C-terminal domain-like This alpha helical domain is found at the C-terminus of proteins that contain an N-terminal Rossmann domain. This domain belongs to the 6-phosphogluconate dehydrogenase C-terminal domain-like superfamily. (from Pfam) NF047720.1 ThrSerExpThrE 550 550 468 equivalog Y Y N threonine/serine exporter ThrE thrE GO:0006865,GO:0022857 11514515,11881894 1716 Corynebacterium genus 881 NCBIFAM threonine/serine exporter ThrE NF033937.0 porH_1 100 100 97 subfamily Y Y N PorH family porin GO:0015288 19966008 1717 Corynebacterium diphtheriae species 23 NCBIFAM PorH family porin PorH family porin Proteins of this HMM family form major outer membrane hetero-oligomeric pores on the cell wall of Corynebacterium with PorA family porins. NF022528.5 PF11077.13 DUF2616 25 25 171 domain Y Y N DUF2616 domain-containing protein 1737063 Brumimicrobium aurantiacum species 1 EBI-EMBL Protein of unknown function (DUF2616) Protein of unknown function (DUF2616) This cysteine-rich family is expressed by the double-stranded Nucleopolyhedrovirus, a member of the Baculoviridae family of dsDNA viruses. The function is not known. (from Pfam) NF013330.5 PF01151.23 ELO 27 27 242 domain Y Y N elongation of very long chain fatty acids protein GO:0009922,GO:0016020 8027068,9211877 1740721 Neobacillus cucumis species 2 EBI-EMBL GNS1/SUR4 family elongation of very long chain fatty acids protein Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis [1]. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 (Swiss:P40319) affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1 [2]. [1]. 9211877. ELO2 and ELO3, homologues of the Saccharomyces cerevisiae ELO1 gene, function in fatty acid elongation and are required for sphingolipid formation. Oh CS, Toke DA, Mandala S, Martin CE;. J Biol Chem 1997;272:17376-17384. [2]. 8027068. Transcriptional control of yeast plasma membrane H(+)-ATPase by glucose. Cloning and characterization of a new gene involved in this regulation. Garcia-Arranz M, Maldonado AM, Mazon MJ, Portillo F;. J Biol Chem 1994;269:18076-18082. (from Pfam) NF005845.0 PRK07764 PRK07764.1-5 1897 1897 957 equivalog Y Y N DNA polymerase III subunit gamma and tau 2.7.7.7 1747 Cutibacterium acnes species 42 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunit gamma and tau NF015601.5 PF03645.18 Tctex-1 22.8 22.8 95 domain Y Y N dynein light chain Tctex-type family protein 10399916,2570638 174713 uncultured Tenacibaculum sp. species 1 EBI-EMBL Tctex-1 family dynein light chain Tctex-type family protein Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction. [1]. 2570638. tctex-1: a candidate gene family for a mouse t complex sterility locus. Lader E, Ha HS, O'Neill M, Artzt K, Bennett D;. Cell 1989;58:969-979. [2]. 10399916. Rhodopsin's carboxy-terminal cytoplasmic tail acts as a membrane receptor for cytoplasmic dynein by binding to the dynein light chain Tctex-1. Tai AW, Chuang JZ, Bode C, Wolfrum U, Sung CH;. Cell 1999;97:877-887. (from Pfam) TIGR01680.1 TIGR01680 Veg_Stor_Prot 375.8 375.8 270 equivalog Y Y N vegetative storage protein 1639823 1749036 Dyadobacter endophyticus species 1 JCVI vegetative storage protein vegetative storage protein The proteins represented by this model are close relatives of the plant acid phosphatases (TIGR01675), are limited to members of the Phaseoleae including Glycine max (soybean) and Phaseolus vulgaris (kidney bean). These proteins are highly expressed in the leaves of repeatedly depodded plants [1]. VSP differs most strinkingly from the acid phosphatases in the lack of the conserved nucleophilic aspartate residue in the N-terminus, thus, they should be inactive as phosphatases. This issue was confused by the publication in 1992 of an article claiming activity for the Glycine max VSP [2]. In 1994 this assertion was refuted by the separation of the activity from the VSP [3]. NF000086.1 vanY_far 250 250 196 exception Y Y Y D,D-peptidase/D,D-carboxypeptidase VanY-N vanY-N GO:0006508 22788848 1760 Actinomycetes class 336 NCBIFAM VanY-like protein D,D-peptidase/D,D-carboxypeptidase VanY-N NF000088.1 viomycin_Vph 400 400 293 equivalog Y Y Y viomycin phosphotransferase vph 1760 Actinomycetes class 508 NCBIFAM viomycin phosphotransferase viomycin phosphotransferase NF000120.3 47473_otr 900 900 608 exception Y Y Y tetracycline resistance ribosomal protection protein Otr(A) otr(A) 1760 Actinomycetes class 1323 NCBIFAM tetracycline resistance ribosomal protection protein Otr(A) tetracycline resistance ribosomal protection protein Otr(A) NF000166.1 ABCF_CarA 1050 1050 556 exception Y Y Y ABC-F type ribosomal protection protein Car(A) car(A) 1612454 1760 Actinomycetes class 63 NCBIFAM CarA family ABC-F type ribosomal protection protein ABC-F type ribosomal protection protein Car(A) NF000171.1 ABCF_producer 800 800 541 exception Y Y Y TlrC/CarA/OleB/SrmB family ABC-F type ribosomal protection protein 1612454 1760 Actinomycetes class 1439 NCBIFAM TlrC/CarA/OleB/SrmB family ABC-F type ribosomal protection protein TlrC/CarA/OleB/SrmB family ABC-F type ribosomal protection protein NF000225.3 AAC_6p_Strep 250 250 156 exception Y Y Y aminoglycoside 6'-N-acetyltransferase aac(6') 2.3.1.82 GO:0008080 1760 Actinomycetes class 346 NCBIFAM aminoglycoside 6'-N-acetyltransferase aminoglycoside 6'-N-acetyltransferase Members of this family are GNAT family N-acetyltranfersases that are found in the genus Streptomyces. These enzyme modify the 6'-position of aminoglycosides such as amikacin and kanamycin, and thereby provide resistance to those antibiotics. NF000318.1 rifampin_ARR_Ms 250 250 143 exception Y Y Y NAD(+)--rifampin ADP-ribosyltransferase arr 1760 Actinomycetes class 228 NCBIFAM NAD(+)--rifampin ADP-ribosyltransferase NAD(+)--rifampin ADP-ribosyltransferase NF000337.1 erm_SHROVE 320 320 248 exception Y Y Y ErmE/ErmH/ErmO/ErmR family 23S rRNA (adenine(2058)-N(6))-methyltransferase erm 1760 Actinomycetes class 1974 NCBIFAM ErmE/ErmH/ErmO/ErmR family 23S rRNA (adenine(2058)-N(6))-methyltransferase ErmE/ErmH/ErmO/ErmR family 23S rRNA (adenine(2058)-N(6))-methyltransferase NF000361.1 self_FomB_kinase 400 400 325 exception Y Y Y FomB family phosphonate monophosphate kinase 1760 Actinomycetes class 140 NCBIFAM FomB family phosphonate monophosphate kinase FomB family phosphonate monophosphate kinase NF000363.1 self_KamB 350 350 216 exception Y Y Y 16S rRNA (adenine(1408)-N(1))-methyltransferase KamB kamB GO:0006400 1760 Actinomycetes class 38 NCBIFAM 16S rRNA (adenine(1408)-N(1))-methyltransferase KamB 16S rRNA (adenine(1408)-N(1))-methyltransferase KamB NF000374.1 D_ala_D_lac_VanO 750 750 346 exception Y Y Y D-alanine--(R)-lactate ligase VanO vanO 6.1.2.1 GO:0005737,GO:0008716,GO:0046872 1760 Actinomycetes class 12 NCBIFAM D-alanine--(R)-lactate ligase VanO D-alanine--(R)-lactate ligase VanO NF000482.1 AAC_3_XI 300 300 148 exception Y Y Y aminoglycoside N-acetyltransferase AAC(3)-XI aac(3)-XI 1760 Actinomycetes class 8 NCBIFAM aminoglycoside N-acetyltransferase AAC(3)-XI aminoglycoside N-acetyltransferase AAC(3)-XI NF000506.1 tet_ABC_AB_A 1025 1000 513 exception Y Y Y tetracycline efflux ABC transporter TetAB subunit A tetA GO:0008493,GO:0015904 1760 Actinomycetes class 62 NCBIFAM tet_ABC_A: tetracycline efflux ABC transporter TetAB subunit A tetracycline efflux ABC transporter TetAB subunit A NF000598.1 PRK00015 PRK00015.2-2 273 273 203 equivalog Y Y N ribonuclease HII 3.1.26.4 1760 Actinomycetes class 4699 NCBI Protein Cluster (PRK) ribonuclease HII ribonuclease HII NF000600.1 PRK00015 PRK00015.2-4 364 364 212 equivalog Y Y N ribonuclease HII 3.1.26.4 1760 Actinomycetes class 1214 NCBI Protein Cluster (PRK) ribonuclease HII ribonuclease HII NF000741.0 PRK00043 PRK00043.3-5 350 350 217 equivalog Y Y N thiamine phosphate synthase 2.5.1.3 1760 Actinomycetes class 82 NCBI Protein Cluster (PRK) thiamine-phosphate pyrophosphorylase thiamine phosphate synthase NF000930.0 PRK00092 PRK00092.2-2 150 150 179 equivalog Y Y N ribosome maturation factor RimP rimP GO:0042274 1760 Actinomycetes class 9694 NCBI Protein Cluster (PRK) ribosome maturation protein RimP ribosome maturation factor RimP NF001061.0 PRK00117 PRK00117.5-1 264 264 246 equivalog Y Y N recombination regulator RecX recX GO:0006282 1760 Actinomycetes class 6235 NCBI Protein Cluster (PRK) recombination regulator RecX recombination regulator RecX NF001064.0 PRK00117 PRK00117.5-4 217 217 194 equivalog Y Y N recombination regulator RecX recX 1760 Actinomycetes class 586 NCBI Protein Cluster (PRK) recombination regulator RecX recombination regulator RecX NF001194.0 PRK00159 PRK00159.1 102 102 87 equivalog Y Y N cell division protein CrgA crgA 21531798,23002219,25548160 1760 Actinomycetes class 1645 NCBI Protein Cluster (PRK) putative septation inhibitor protein cell division protein CrgA Involved in inhibition of the Z-ring formation NF001269.0 PRK00228 PRK00228.2-1 278 278 201 equivalog Y Y N YqgE/AlgH family protein 1760 Actinomycetes class 1228 NCBI Protein Cluster (PRK) hypothetical protein YqgE/AlgH family protein NF001272.0 PRK00228 PRK00228.2-4 241 241 198 equivalog Y Y N YqgE/AlgH family protein 1760 Actinomycetes class 2220 NCBI Protein Cluster (PRK) hypothetical protein YqgE/AlgH family protein NF002374.0 PRK01371 PRK01371.1-1 162 162 152 equivalog Y Y N sec-independent translocase GO:0015031 1760 Actinomycetes class 4552 NCBI Protein Cluster (PRK) sec-independent translocase sec-independent translocase NF002544.0 PRK02101 PRK02101.2-1 339 339 248 equivalog Y Y N peroxide stress protein YaaA yaaA 1760 Actinomycetes class 2039 NCBI Protein Cluster (PRK) hypothetical protein peroxide stress protein YaaA NF002545.0 PRK02101 PRK02101.2-3 324 324 265 equivalog Y Y N peroxide stress protein YaaA yaaA 1760 Actinomycetes class 7667 NCBI Protein Cluster (PRK) hypothetical protein peroxide stress protein YaaA NF002595.0 PRK02251 PRK02251.2-1 109 109 84 equivalog Y Y N cell division protein CrgA crgA 1760 Actinomycetes class 2099 NCBI Protein Cluster (PRK) putative septation inhibitor protein cell division protein CrgA NF002821.0 PRK02983 PRK02983.1 742 742 1102 equivalog Y Y N bifunctional lysylphosphatidylglycerol synthetase/lysine--tRNA ligase LysX lysX 2.3.2.3,6.1.1.6 GO:0000166,GO:0003676,GO:0004824,GO:0005524,GO:0006430 19649276 1760 Actinomycetes class 8189 NCBI Protein Cluster (PRK) lysyl-tRNA synthetase bifunctional lysylphosphatidylglycerol synthetase/lysine--tRNA ligase LysX LysX, as found in Mycobacterium tuberculosis, is a bifunctional protein that produces lysinylated phosphatidylglycerol, which improves resistance to cationic antimicrobial peptides. Its two functional domains are lysyltransferase (EC 2.3.2.3) and lysine--tRNA ligase (EC 6.1.1.6). NF002871.0 PRK03195 PRK03195.1 246 246 187 equivalog Y Y N DUF721 family protein 1760 Actinomycetes class 1435 NCBI Protein Cluster (PRK) hypothetical protein DUF721 family protein NF002873.0 PRK03204 PRK03204.1 466 466 286 equivalog Y Y N haloalkane dehalogenase 3.8.1.5 1760 Actinomycetes class 602 NCBI Protein Cluster (PRK) haloalkane dehalogenase haloalkane dehalogenase NF002899.0 PRK03449 PRK03449.1 276 276 359 equivalog Y Y N membrane protein insertase YidC yidC GO:0016020,GO:0032977 1760 Actinomycetes class 3569 NCBI Protein Cluster (PRK) putative inner membrane protein translocase component YidC membrane protein insertase YidC NF003724.0 PRK05329 PRK05329.2-3 327 327 426 equivalog Y Y N glycerol-3-phosphate dehydrogenase subunit GlpB glpB 1.1.5.3 1760 Actinomycetes class 443 NCBI Protein Cluster (PRK) anaerobic glycerol-3-phosphate dehydrogenase subunit B glycerol-3-phosphate dehydrogenase subunit GlpB NF004111.0 PRK05600 PRK05600.1 437 437 371 equivalog Y Y N ThiF family adenylyltransferase 1760 Actinomycetes class 514 NCBI Protein Cluster (PRK) thiamine biosynthesis protein ThiF ThiF family adenylyltransferase NF004351.0 PRK05731 PRK05731.1-4 324 324 321 equivalog Y Y N thiamine-phosphate kinase 2.7.4.16 GO:0009030,GO:0009228 1760 Actinomycetes class 9641 NCBI Protein Cluster (PRK) thiamine monophosphate kinase thiamine-phosphate kinase NF004511.1 PRK05852 PRK05852.1 650 650 505 equivalog Y Y N FadD7 family fatty acid--CoA ligase 1760 Actinomycetes class 1027 NCBI Protein Cluster (PRK) acyl-CoA synthetase FadD7 family fatty acid--CoA ligase NF004528.0 PRK05875 PRK05875.1 334 334 280 equivalog Y Y N SDR family oxidoreductase GO:0016491 1760 Actinomycetes class 950 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF004548.0 PRK05892 PRK05892.1 126 126 158 equivalog Y N N nucleoside diphosphate kinase regulator 1760 Actinomycetes class 1697 NCBI Protein Cluster (PRK) nucleoside diphosphate kinase regulator nucleoside diphosphate kinase regulator NF004560.0 PRK05901 PRK05901.1-1 711 711 516 equivalog Y Y N RNA polymerase sigma factor GO:0003677,GO:0003700,GO:0006352,GO:0016987 1760 Actinomycetes class 3784 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF004719.0 PRK06063 PRK06063.1 389 389 331 equivalog Y Y N DEDDh family exonuclease GO:0003677,GO:0006260 1760 Actinomycetes class 6291 NCBI Protein Cluster (PRK) DNA polymerase III subunit epsilon DEDDh family exonuclease NF004828.0 PRK06183 PRK06183.1-2 853 853 568 equivalog Y Y N bifunctional 3-(3-hydroxy-phenyl)propionate/3-hydroxycinnamic acid hydroxylase 1.14.13.127 1760 Actinomycetes class 737 NCBI Protein Cluster (PRK) 3-(3-hydroxyphenyl)propionate hydroxylase bifunctional 3-(3-hydroxy-phenyl)propionate/3-hydroxycinnamic acid hydroxylase NF004838.1 PRK06188 PRK06188.1 875 875 524 equivalog Y Y N fatty-acid--CoA ligase FadD8 fadD8 30997306 1760 Actinomycetes class 1398 NCBI Protein Cluster (PRK) acyl-CoA synthetase fatty-acid--CoA ligase FadD8 NF005108.0 PRK06545 PRK06545.1-6 327 327 321 equivalog Y Y N prephenate dehydrogenase 1.3.1.12 GO:0004665,GO:0006571,GO:0008977 1760 Actinomycetes class 3492 NCBI Protein Cluster (PRK) prephenate dehydrogenase prephenate dehydrogenase NF005109.0 PRK06545 PRK06545.2-1 397 397 361 equivalog Y Y N prephenate dehydrogenase 1.3.1.12 1760 Actinomycetes class 6175 NCBI Protein Cluster (PRK) prephenate dehydrogenase prephenate dehydrogenase NF005512.0 PRK07121 PRK07121.1-5 812 812 489 subfamily Y Y N FAD-binding protein 1760 Actinomycetes class 1533 NCBI Protein Cluster (PRK) hypothetical protein FAD-binding protein NF005514.0 PRK07122 PRK07122.1 372 372 264 subfamily Y N N RNA polymerase sigma factor SigF 1760 Actinomycetes class 1677 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigF RNA polymerase sigma factor SigF NF005857.1 PRK07786 PRK07786.1 733 733 513 exception Y Y N fatty-acid--CoA ligase FadD5 fadD5 20214478 1760 Actinomycetes class 1999 NCBI Protein Cluster (PRK) long-chain-fatty-acid--CoA ligase fatty-acid--CoA ligase FadD5 NF005862.0 PRK07792 PRK07792.1 414 414 307 equivalog Y Y N 3-oxoacyl-ACP reductase GO:0016491 1760 Actinomycetes class 6721 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase 3-oxoacyl-ACP reductase NF005877.1 PRK07824 PRK07824.1 345 345 362 equivalog Y Y N o-succinylbenzoate--CoA ligase menE 6.2.1.26 1760 Actinomycetes class 4063 NCBI Protein Cluster (PRK) O-succinylbenzoic acid--CoA ligase o-succinylbenzoate--CoA ligase NF005891.0 PRK07854 PRK07854.1 237 237 243 equivalog Y Y N enoyl-CoA hydratase 4.2.1.17 1760 Actinomycetes class 1982 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF005894.0 PRK07857 PRK07857.1 73 73 106 equivalog Y Y N chorismate mutase 5.4.99.5 GO:0046417 1760 Actinomycetes class 7422 NCBI Protein Cluster (PRK) hypothetical protein chorismate mutase NF005900.0 PRK07874 PRK07874.1 114 114 80 equivalog Y Y N ATP synthase F0 subunit C 1760 Actinomycetes class 541 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit C ATP synthase F0 subunit C Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit C is part of the membrane proton channel F0 NF005904.0 PRK07883 PRK07883.1-2 969 969 584 equivalog Y Y N DEDD exonuclease domain-containing protein 1760 Actinomycetes class 655 NCBI Protein Cluster (PRK) hypothetical protein DEDD exonuclease domain-containing protein NF005916.1 PRK07910 PRK07910.1 560 560 418 equivalog Y Y N KasA/KasB family beta-ketoacyl-ACP synthase GO:0071768 1760 Actinomycetes class 3310 NCBI Protein Cluster (PRK) 3-oxoacyl-(acyl carrier protein) synthase II KasA/KasB family beta-ketoacyl-ACP synthase NF005918.0 PRK07914 PRK07914.1 420 420 321 equivalog Y N N hypothetical protein 1760 Actinomycetes class 1984 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005920.0 PRK07921 PRK07921.1 464 464 328 subfamily Y Y N RNA polymerase sigma factor SigB sigB 10580156,9882660 1760 Actinomycetes class 13529 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigB RNA polymerase sigma factor SigB Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma factors in this cluster are active during stationary phase NF006103.0 PRK08257 PRK08257.1-1 757 757 495 equivalog Y Y N acetyl-CoA acetyltransferase GO:0016746 21795802 1760 Actinomycetes class 1035 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA acetyltransferase NF006501.0 PRK08937 PRK08937.3-1 310 310 191 equivalog Y Y N adenylosuccinate lyase 4.3.2.2 1760 Actinomycetes class 3273 NCBI Protein Cluster (PRK) adenylosuccinate lyase adenylosuccinate lyase NF007070.0 PRK09517 PRK09517.1 761 761 755 equivalog Y N N multifunctional thiamine-phosphate pyrophosphorylase/synthase/phosphomethylpyrimidine kinase 1760 Actinomycetes class 142 NCBI Protein Cluster (PRK) multifunctional thiamine-phosphate pyrophosphorylase/synthase/phosphomethylpyrimidine kinase multifunctional thiamine-phosphate pyrophosphorylase/synthase/phosphomethylpyrimidine kinase NF007071.0 PRK09518 PRK09518.1 953 953 706 equivalog Y Y N bifunctional cytidylate kinase/GTPase Der der 1760 Actinomycetes class 1169 NCBI Protein Cluster (PRK) bifunctional cytidylate kinase/GTPase Der bifunctional cytidylate kinase/GTPase Der NF007230.0 PRK09648 PRK09648.1 209 209 195 subfamily Y Y N RNA polymerase sigma factor ShbA shbA 10027986,15659067 1760 Actinomycetes class 6262 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigD RNA polymerase sigma factor ShbA Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this protein is involved in expression of ribosome-associated gene products in stationary phase NF008167.0 PRK10917 PRK10917.2-1 995 995 744 equivalog Y Y N ATP-dependent DNA helicase RecG recG 3.6.4.12 GO:0003678,GO:0006281,GO:0006310 1760 Actinomycetes class 10382 NCBI Protein Cluster (PRK) ATP-dependent DNA helicase RecG ATP-dependent DNA helicase RecG NF008341.1 PRK11127 PRK11127.1-1 145 145 80 equivalog Y Y N autonomous glycyl radical cofactor GrcA2 grcA2 1760 Actinomycetes class 326 NCBI Protein Cluster (PRK) autonomous glycyl radical cofactor GrcA autonomous glycyl radical cofactor GrcA2 Members of this family are a lineage-specific form of the autonomous glycyl radical cofactor that substitutes for damaged parts of formate C-acetyltransferase, more similar to a region of that enzyme itself than to GrcA fo Escherichia coli. Lineages with members of this family include Corynebacterium, Actinomyces, Mobiluncus, and related members of the Actinobacteria. NF008496.0 PRK11408 PRK11408.1-3 260 260 238 equivalog Y N N hypothetical protein 1760 Actinomycetes class 1212 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF008527.1 PRK11463 PRK11463.1-1 150 150 191 exception Y Y N FxsA family membrane protein fxsA 1760 Actinomycetes class 5969 NCBI Protein Cluster (PRK) phage T7 F exclusion suppressor FxsA FxsA family membrane protein, extended form NF008841.0 PRK11883 PRK11883.1-1 517 517 453 equivalog Y Y N protoporphyrinogen oxidase 1.3.3.4 GO:0004729,GO:0006779 1760 Actinomycetes class 2453 NCBI Protein Cluster (PRK) protoporphyrinogen oxidase protoporphyrinogen oxidase NF008882.0 PRK11914 PRK11914.1 302 302 306 equivalog Y Y N diacylglycerol kinase 2.7.1.107 GO:0016301 16689792 1760 Actinomycetes class 5869 NCBI Protein Cluster (PRK) diacylglycerol kinase diacylglycerol kinase NF008976.0 PRK12324 PRK12324.1-1 474 474 306 equivalog Y Y N decaprenyl-phosphate phosphoribosyltransferase 2.4.2.45 1760 Actinomycetes class 1424 NCBI Protein Cluster (PRK) phosphoribose diphosphate:decaprenyl-phosphate phosphoribosyltransferase decaprenyl-phosphate phosphoribosyltransferase NF008988.0 PRK12334 PRK12334.1-4 501 501 335 equivalog Y Y N nucleoside triphosphate pyrophosphohydrolase 3.6.1.9 1760 Actinomycetes class 6037 NCBI Protein Cluster (PRK) nucleoside triphosphate pyrophosphohydrolase nucleoside triphosphate pyrophosphohydrolase NF008989.0 PRK12334 PRK12334.2-1 494 494 328 equivalog Y Y N nucleoside triphosphate pyrophosphohydrolase 3.6.1.9 1760 Actinomycetes class 704 NCBI Protein Cluster (PRK) nucleoside triphosphate pyrophosphohydrolase nucleoside triphosphate pyrophosphohydrolase NF009097.0 PRK12438 PRK12438.1 1254 1254 991 subfamily Y N N hypothetical protein 1760 Actinomycetes class 2911 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF009473.0 PRK12835 PRK12835.1 837 837 585 subfamily Y Y N FAD-binding protein 1760 Actinomycetes class 1501 NCBI Protein Cluster (PRK) 3-ketosteroid-delta-1-dehydrogenase FAD-binding protein NF009476.0 PRK12839 PRK12839.1 940 940 572 equivalog Y Y N FAD-dependent oxidoreductase 1760 Actinomycetes class 539 NCBI Protein Cluster (PRK) hypothetical protein FAD-dependent oxidoreductase NF009483.0 PRK12846 PRK12846.1-4 267 267 193 equivalog Y Y N peptide deformylase 3.5.1.88 GO:0042586 1760 Actinomycetes class 2708 NCBI Protein Cluster (PRK) peptide deformylase peptide deformylase NF009915.0 PRK13375 PRK13375.1 413 413 425 equivalog Y Y N mannosyltransferase 16803893 1760 Actinomycetes class 1951 NCBI Protein Cluster (PRK) mannosyltransferase mannosyltransferase NF009927.1 PRK13388 PRK13388.1 800 800 523 exception Y Y N fatty-acid--CoA ligase FadD1 fadD1 1760 Actinomycetes class 1631 NCBI Protein Cluster (PRK) acyl-CoA synthetase fatty-acid--CoA ligase FadD1 Member of this family are the fatty-acid--CoA ligase FadD1 as the term is used in Mycobacterium tuberculosis. Note that the same name is used in other lineages, with different meanings. NF009961.0 PRK13428 PRK13428.1 328 328 445 equivalog Y Y N F0F1 ATP synthase subunit B/delta 7.1.2.2 1760 Actinomycetes class 945 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit delta F0F1 ATP synthase subunit B/delta Produces ATP from ADP in the presence of a proton gradient across the membrane; the delta subunit is part of the catalytic core of the ATP synthase complex NF009993.0 PRK13462 PRK13462.1 226 226 203 equivalog Y Y N acid phosphatase 3.1.3.2 16672613 1760 Actinomycetes class 1681 NCBI Protein Cluster (PRK) acid phosphatase acid phosphatase NF010141.1 PRK13616 PRK13616.1 602 602 584 equivalog Y Y N MtrAB system accessory lipoprotein LpqB lpqB 20233304 1760 Actinomycetes class 2262 NCBI Protein Cluster (PRK) lipoprotein LpqB MtrAB system accessory lipoprotein LpqB NF010238.0 PRK13685 PRK13685.1 432 432 335 subfamily Y N N hypothetical protein 1760 Actinomycetes class 2383 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010246.0 PRK13693 PRK13693.1 203 203 142 equivalog Y Y N (3R)-hydroxyacyl-ACP dehydratase subunit HadB hadB GO:0071768 17804795,17906131,18048930 1760 Actinomycetes class 1074 NCBI Protein Cluster (PRK) (3R)-hydroxyacyl-ACP dehydratase subunit HadB (3R)-hydroxyacyl-ACP dehydratase subunit HadB Functions as a heterodimer along with HadA or HadC in fatty acid biosynthesis; fatty acid synthase type II; FAS-II NF010374.0 PRK13800 PRK13800.1 1196 1196 898 equivalog Y Y N fumarate reductase/succinate dehydrogenase flavoprotein subunit GO:0016491 1760 Actinomycetes class 4479 NCBI Protein Cluster (PRK) putative oxidoreductase/HEAT repeat-containing protein fumarate reductase/succinate dehydrogenase flavoprotein subunit NF010510.0 PRK13922 PRK13922.11-5 415 415 334 equivalog Y Y N rod shape-determining protein MreC mreC GO:0008360 1760 Actinomycetes class 4826 NCBI Protein Cluster (PRK) rod shape-determining protein MreC rod shape-determining protein MreC NF010573.0 PRK13966 PRK13966.1 661 661 324 equivalog Y Y N ribonucleotide-diphosphate reductase subunit beta 1760 Actinomycetes class 1452 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit beta ribonucleotide-diphosphate reductase subunit beta NF010599.0 PRK13994 PRK13994.1 355 355 226 equivalog Y Y N potassium-transporting ATPase subunit C 7.2.2.6 1760 Actinomycetes class 5148 NCBI Protein Cluster (PRK) potassium-transporting ATPase subunit C potassium-transporting ATPase subunit C Component of the high-affinity ATP-driven potassium transport (or KDP)system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions NF010664.0 PRK14059 PRK14059.1-2 226 226 257 equivalog Y Y N pyrimidine reductase family protein 1760 Actinomycetes class 1309 NCBI Protein Cluster (PRK) hypothetical protein pyrimidine reductase family protein NF010760.0 PRK14163 PRK14163.1 240 240 217 equivalog Y Y N nucleotide exchange factor GrpE grpE GO:0000774,GO:0006457,GO:0042803,GO:0051087 1760 Actinomycetes class 4427 NCBI Protein Cluster (PRK) heat shock protein GrpE nucleotide exchange factor GrpE With DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins NF010871.0 PRK14278 PRK14278.1 502 502 378 equivalog Y Y N molecular chaperone DnaJ dnaJ GO:0006457,GO:0051082 1760 Actinomycetes class 8165 NCBI Protein Cluster (PRK) chaperone protein DnaJ molecular chaperone DnaJ Chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion NF010872.0 PRK14279 PRK14279.1 556 556 394 equivalog Y Y N molecular chaperone DnaJ dnaJ 1760 Actinomycetes class 2647 NCBI Protein Cluster (PRK) chaperone protein DnaJ molecular chaperone DnaJ Chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion NF010888.0 PRK14295 PRK14295.1 592 592 389 equivalog Y Y N molecular chaperone DnaJ dnaJ GO:0005524,GO:0006457,GO:0009408,GO:0031072,GO:0051082 1760 Actinomycetes class 5042 NCBI Protein Cluster (PRK) chaperone protein DnaJ molecular chaperone DnaJ Chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion NF011351.0 PRK14769 PRK14769.1 216 216 156 subfamily Y N N lipoprotein signal peptidase 1760 Actinomycetes class 64 NCBI Protein Cluster (PRK) lipoprotein signal peptidase lipoprotein signal peptidase NF011362.0 PRK14781 PRK14781.1 177 177 170 subfamily Y N N lipoprotein signal peptidase 1760 Actinomycetes class 137 NCBI Protein Cluster (PRK) lipoprotein signal peptidase lipoprotein signal peptidase NF011452.0 PRK14873 PRK14873.1-2 980 980 708 equivalog Y Y N primosomal protein N' 3.6.1.- GO:0003677,GO:0003678,GO:0006260,GO:0032508 1760 Actinomycetes class 7772 NCBI Protein Cluster (PRK) primosome assembly protein PriA primosomal protein N' NF011453.0 PRK14873 PRK14873.1-3 812 812 653 equivalog Y N N primosome assembly protein PriA 1760 Actinomycetes class 262 NCBI Protein Cluster (PRK) primosome assembly protein PriA primosome assembly protein PriA NF011513.0 PRK14952 PRK14952.1 737 737 596 equivalog Y Y N DNA polymerase III subunits gamma/tau 2.7.7.7 1760 Actinomycetes class 3129 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunits gamma/tau Catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA NF012139.0 exosort_XrtP 200 200 159 exception Y Y N exosortase P xrtP GO:0004197,GO:0006605,GO:0016020,GO:0043687 22037399 1760 Actinomycetes class 254 NCBIFAM exosort_XrtP: exosortase P exosortase P NF012178.0 tet_MFS_V 640 640 409 exception Y Y Y tetracycline efflux MFS transporter Tet(V) tet(V) GO:0008493,GO:0015904 1760 Actinomycetes class 301 NCBIFAM tetracycline efflux MFS transporter Tet(V) tetracycline efflux MFS transporter Tet(V) Tet(V) is described as a tetracycline efflux MFS transporter found in a subset of species in the genus Mycobacterium, including M. smegmatis and M. fortuitum, but exclusing M. tuberculosis, M. avium, M. chelonae, M. gordonae, M. xenopi, M. terrae, M. kansasii, etc. NF012197.0 lonely_Cys 200 200 707 domain Y Y N lonely Cys domain-containing protein 1760 Actinomycetes class 1971 NCBIFAM lonely Cys domain-containing protein lonely Cys domain This model describes an unusual domain, over 700 amino acids long, that is largely restricted to the Streptomyces (prodigious producers of natural products) and that may occur ten or more times in giant proteins. The most striking feature is an extremely low cysteine composition, one residue per domain, and that in an essentially invariant position. NF015696.5 PF03752.18 ALF 25.4 25.4 42 repeat Y N N ALF repeat protein 12625841 1760 Actinomycetes class 12004 EBI-EMBL Short repeats of unknown function ALF repeat This set of repeats is found in a small family of secreted proteins of no known function, though they are possibly involved in signal transduction. ALF stands for Alanine-rich (AL) - conserved Phenylalanine (F). [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF015713.5 PF03771.21 SPDY 25 25 61 domain Y Y N DUF317 domain-containing protein 12625841 1760 Actinomycetes class 14708 EBI-EMBL Domain of unknown function (DUF317) Domain of unknown function (DUF317) This a sequence family found in a set of bacterial proteins with no known function. This domain is currently only found in streptomyces bacteria. Most proteins contain two copies of this domain. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF016375.5 PF04486.17 SchA_CurD 24.2 24.2 119 domain Y Y N SchA/CurD-like domain-containing protein 8344517 1760 Actinomycetes class 5385 EBI-EMBL SchA/CurD like domain SchA/CurD like domain Members of this family have only been identified in species of the Streptomyces genus. Two family members are known to be part of gene clusters involved in the synthesis of polyketide-based spore pigments, homologous to clusters involved in the synthesis of polyketide antibiotics. The function of this protein is unknown, but it has been speculated to contain a NAD(P) binding site [1]. Many of these proteins contain two copies of this presumed domain. [1]. 8344517. Hybridization and DNA sequence analyses suggest an early evolutionary divergence of related biosynthetic gene sets encoding polyketide antibiotics and spore pigments in Streptomyces spp. Blanco G, Brian P, Pereda A, Mendez C, Salas JA, Chater KF;. Gene 1993;130:107-116. (from Pfam) NF016484.5 PF04602.17 Arabinose_trans 25 25 459 domain Y Y N arabinosyltransferase domain-containing protein GO:0052636,GO:0071766 8876238 1760 Actinomycetes class 10922 EBI-EMBL Mycobacterial cell wall arabinan synthesis protein Mycobacterial cell wall arabinan synthesis protein Arabinosyltransferase is involved in arabinogalactan (AG) biosynthesis pathway in mycobacteria. AG is a component of the macromolecular assembly of the mycolyl-AG-peptidoglycan complex of the cell wall. This enzyme has important clinical applications as it is believed to be the target of the antimycobacterial drug Ethambutol [1]. [1]. 8876238. The embAB genes of Mycobacterium avium encode an arabinosyl transferase involved in cell wall arabinan biosynthesis that is the target for the antimycobacterial drug ethambutol. Belanger AE, Besra GS, Ford ME, Mikusova K, Belisle JT, Brennan PJ, Inamine JM;. Proc Natl Acad Sci U S A 1996;93:11919-11924. (from Pfam) NF016564.5 PF04686.17 SsgA 25 25 98 domain Y Y N SsgA family sporulation/cell division regulator GO:0051301 11004161 1760 Actinomycetes class 26716 EBI-EMBL Streptomyces sporulation and cell division protein, SsgA SsgA family sporulation/cell division regulator The precise function of SsgA is unknown. It has been found to be essential for spore formation, and to stimulate cell division [1]. [1]. 11004161. ssgA is essential for sporulation of Streptomyces coelicolor A3(2) and affects hyphal development by stimulating septum formation. van Wezel GP, van der Meulen J, Kawamoto S, Luiten RG, Koerten HK, Kraal B;. J Bacteriol 2000;182:5653-5662. (from Pfam) NF016978.5 PF05122.18 SpdB 25 25 50 domain Y Y N mobile element transfer protein 12625841,8366038 1760 Actinomycetes class 5103 EBI-EMBL Mobile element transfer protein mobile element transfer protein This proteins are involved in transferring a group of integrating conjugative DNA elements, such as pSAM2 from Streptomyces ambofaciens ([1]). Their precise role is not known. [1]. 8366038. Transfer functions of the conjugative integrating element pSAM2 from Streptomyces ambofaciens: characterization of a kil-kor system associated with transfer. Hagege J, Pernodet JL, Sezonov G, Gerbaud C, Friedmann A, Guerineau M;. J Bacteriol 1993;175:5529-5538. [2]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF017148.5 PF05305.19 DUF732 22.4 22.4 72 domain Y Y N DUF732 domain-containing protein 1760 Actinomycetes class 13627 EBI-EMBL Protein of unknown function (DUF732) Protein of unknown function (DUF732) This family consists of several uncharacterised Mycobacterium tuberculosis and leprae proteins of unknown function. (from Pfam) NF017309.5 PF05481.17 Myco_19_kDa 23 23 117 domain Y Y N lipoprotein LpqH GO:0016020 2230723,8454357 1760 Actinomycetes class 3864 EBI-EMBL Mycobacterium 19 kDa lipoprotein antigen lipoprotein LpqH Most of the antigens of Mycobacterium leprae and M. tuberculosis that have been identified are members of stress protein families, which are highly conserved throughout many diverse species. Of the M. leprae and M. tuberculosis antigens identified by monoclonal antibodies, all except the 18-kDa M. leprae antigen and the 19-kDa M. tuberculosis antigen are strongly cross-reactive between these two species and are coded within very similar genes [1,2]. [1]. 8454357. Homologs of Mycobacterium leprae 18-kilodalton and Mycobacterium tuberculosis 19-kilodalton antigens in other mycobacteria. Booth RJ, Williams DL, Moudgil KD, Noonan LC, Grandison PM, McKee JJ, Prestidge RL, Watson JD;. Infect Immun 1993;61:1509-1515. [2]. 2230723. Cloning and characterization of the gene for the '19 kDa' antigen of Mycobacterium bovis. Collins ME, Patki A, Wall S, Nolan A, Goodger J, Woodward MJ, Dale JW;. J Gen Microbiol 1990;136:1429-1436. (from Pfam) NF018832.5 PF07174.16 FAP 27.9 27.9 300 subfamily Y Y N APA family fibronectin-binding glycoprotein GO:0005576,GO:0050840 9988684 1760 Actinomycetes class 1686 EBI-EMBL Fibronectin-attachment protein (FAP) APA family fibronectin-binding glycoprotein APA (Alanine and Proline-rich Antigenic glycoprotein), a mannosylated glycoprotein of Mycobacterium tuberculosis and M. bovis BCG, also called the 45/47-kDa protein complex, is secreted from cells, but is suggested to have adhesin activity transiently prior to its release from the cell. Homologs are found in related species such as Mycobacterium avium, Mycobacterium leprae, Mycolicibacterium gilvum, and Mycolicibacterium smegmatis. NF019018.5 PF07371.17 DUF1490 28.4 28.4 88 subfamily Y Y N DUF1490 family protein 1760 Actinomycetes class 1107 EBI-EMBL Protein of unknown function (DUF1490) DUF1490 family protein This family consists of several hypothetical bacterial proteins of around 90 residues in length. Members of the family seem to be found exclusively in Mycobacterium species. The function of this family is unknown. (from Pfam) NF019667.5 PF08055.16 Trp_leader1 25 25 18 PfamEq Y Y N trp operon leader peptide 15262409 1760 Actinomycetes class 974 EBI-EMBL Tryptophan leader peptide trp operon leader peptide This family consists of the tryptophan (trp) leader peptides. Tryptophan accumulation is the principal event resulting in downregulation of transcription of the structural genes of the trp operon. The leader peptide of the trp operon forms mutually exclusive secondary structures that would either result in the termination of transcription of the trp operon when tryptophan is in plentiful supply or vice versa [1]. [1]. 15262409. The different roles of tryptophan transfer RNA in regulating trp operon expression in E. coli versus B. subtilis. Yanofsky C;. Trends Genet 2004;20:367-374. (from Pfam) NF019842.5 PF08237.16 PE-PPE 21 21 228 domain Y Y N PE-PPE domain-containing protein 12711809 1760 Actinomycetes class 10325 EBI-EMBL PE-PPE domain PE-PPE domain This domain is found C terminal to the PE (Pfam:PF00934) and PPE (Pfam:PF00823) domains. The secondary structure of this domain is predicted to be a mixture of alpha helices and beta strands [1]. [1]. 12711809. Sequence analysis corresponding to the PPE and PE proteins in Mycobacterium tuberculosis and other genomes. Adindla S, Guruprasad L;. J Biosci 2003;28:169-179. (from Pfam) NF020729.5 PF09167.16 DUF1942 22.4 22.4 123 domain Y Y N DUF1942 domain-containing protein GO:0005615 12441386 1760 Actinomycetes class 1938 EBI-EMBL Domain of unknown function (DUF1942) Domain of unknown function (DUF1942) Members of this family of bacterial proteins assume a beta-sandwich structure consisting of two antiparallel beta-sheets similar to an immunoglobulin-like fold, with an additional small, antiparallel beta-sheet. The longer-stranded beta-sheet is made up of four antiparallel beta-strands. The shorter-stranded beta-sheet consists of five beta-strands, four of these beta-strands form an antiparallel beta-sheet. The exact function of this family of proteins is unknown, though a putative role includes involvement in host-bacterial interactions involved in endocytosis or phagocytosis, possibly during bacterial internalisation [1]. [1]. 12441386. Crystal structure of a major secreted protein of Mycobacterium tuberculosis-MPT63 at 1.5-A resolution. Goulding CW, Parseghian A, Sawaya MR, Cascio D, Apostol MI, Gennaro ML, Eisenberg D;. Protein Sci. 2002;11:2887-2893. (from Pfam) NF020765.5 PF09203.16 MspA 22.9 22.9 179 domain Y Y N MspA family porin 14976314 1760 Actinomycetes class 9395 EBI-EMBL MspA MspA family porin MspA is a membrane porin produced by Mycobacteria, allowing hydrophilic nutrients to enter the bacterium. The protein forms a tightly interconnected octamer with eightfold rotation symmetry that resembles a goblet and contains a central channel. Each subunit fold contains a beta-sandwich of Ig-like topology and a beta-ribbon arm that forms an oligomeric transmembrane barrel [1]. [1]. 14976314. The structure of a mycobacterial outer-membrane channel. Faller M, Niederweis M, Schulz GE;. Science. 2004;303:1189-1192. (from Pfam) NF020805.5 PF09244.15 Suc_Porlyase_C 23 23 67 PfamAutoEq Y Y N sucrose phosphorylase domain-containing protein 14756551,16990265,32260541 1760 Actinomycetes class 752 EBI-EMBL Sucrose phosphorylase, C-terminal Sucrose phosphorylase, C-terminal This domain is C-terminal to the catalytic sucrose phosphorylase beta/alpha barrel domain which adopts a beta-sandwich fold with Greek-key topology [1,2,3]. [1]. 14756551. Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis. Sprogoe D, van den Broek LA, Mirza O, Kastrup JS, Voragen AG, Gajhede M, Skov LK;. Biochemistry. 2004;43:1156-1162. [2]. 16990265. Structural rearrangements of sucrose phosphorylase from Bifidobacterium adolescentis during sucrose conversion. Mirza O, Skov LK, Sprogoe D, van den Broek LA, Beldman G, Kastrup JS, Gajhede M;. J Biol Chem. 2006;281:35576-35584. [3]. 32260541. Sucrose Phosphorylase and Related Enzymes in Glycoside Hydrolase Family 13: Discovery, Application and Engineering. Franceus J, Desmet T;. Int J Mol Sci. 2020; [Epub ahead of print] (from Pfam) NF020851.5 PF09291.15 DUF1968 22.1 22.1 81 domain Y Y N DUF1968 domain-containing protein 1760 Actinomycetes class 2 EBI-EMBL Domain of unknown function (DUF1968) Domain of unknown function (DUF1968) Members of this family are found in mammalian T-cell antigen receptor, and adopt an immunoglobulin-like beta-sandwich fold, with seven strands in two beta-sheets in a Greek-key topology. Their exact function has not, as yet, been determined. (from Pfam) NF021000.5 PF09449.15 DUF2020 25 25 144 PfamAutoEq Y Y N DUF2020 domain-containing protein 1760 Actinomycetes class 1116 EBI-EMBL Domain of unknown function (DUF2020) Domain of unknown function (DUF2020) Protein of unknown function found in bacteria. (from Pfam) NF021959.5 PF10476.14 DUF2448 24.5 24.5 205 domain Y Y N DUF2448 domain-containing protein GO:0005637 1760 Actinomycetes class 3 EBI-EMBL Protein of unknown function C-terminus (DUF2448) Protein of unknown function C-terminus (DUF2448) The family DUF2349 is the N-terminal part of this family. This protein is found in eukaryotes but its function is not known. (from Pfam) NF022198.5 PF10738.14 Lpp-LpqN 22.4 22.4 174 domain Y Y N LpqN/LpqT family lipoprotein 15539077 1760 Actinomycetes class 4020 EBI-EMBL Probable lipoprotein LpqN LpqN/LpqT family lipoprotein This family is conserved in Mycobacteriaceae and is likely to be a lipoprotein [1]. [1]. 15539077. Lipoproteins of Mycobacterium tuberculosis: an abundant and functionally diverse class of cell envelope components. Sutcliffe IC, Harrington DJ;. FEMS Microbiol Rev. 2004;28:645-659. (from Pfam) NF022258.5 PF10801.13 DUF2537 23.2 23.2 80 PfamAutoEq Y Y N DUF2537 domain-containing protein 1760 Actinomycetes class 1880 EBI-EMBL Protein of unknown function (DUF2537) Protein of unknown function (DUF2537) This bacterial family of proteins has no known function. (from Pfam) NF022271.5 PF10814.13 CwsA 26.7 26.7 134 PfamEq Y Y N cell wall synthesis protein CwsA cwsA 23002219 1760 Actinomycetes class 724 EBI-EMBL Cell wall synthesis protein CwsA cell wall synthesis protein CwsA Cell wall synthesis protein CwsA is required for cell division, cell wall synthesis and cell shape maintenance [1]. [1]. 23002219. Mycobacterium tuberculosis CwsA interacts with CrgA and Wag31, and the CrgA-CwsA complex is involved in peptidoglycan synthesis and cell shape determination. Plocinski P, Arora N, Sarva K, Blaszczyk E, Qin H, Das N, Plocinska R, Ziolkiewicz M, Dziadek J, Kiran M, Gorla P, Cross TA, Madiraju M, Rajagopalan M;. J Bacteriol. 2012;194:6398-6409. (from Pfam) NF022274.5 PF10817.13 DUF2563 21.2 21.2 104 PfamAutoEq Y Y N DUF2563 family protein 1760 Actinomycetes class 726 EBI-EMBL Protein of unknown function (DUF2563) DUF2563 family protein This family of proteins with unknown function appears to be restricted to Mycobacterium. (from Pfam) NF022344.5 PF10888.13 DUF2742 22.7 22.7 97 domain Y Y N DUF2742 domain-containing protein 1760 Actinomycetes class 737 EBI-EMBL Protein of unknown function (DUF2742) Protein of unknown function (DUF2742) Members in this family of phage proteins are the product of the gene phiRv1, however no function is known. (from Pfam) NF022422.5 PF10969.13 DUF2771 23.8 23.8 128 PfamAutoEq Y Y N DUF2771 family protein 1760 Actinomycetes class 2813 EBI-EMBL Protein of unknown function (DUF2771) DUF2771 family protein This bacterial family of proteins has no known function. (from Pfam) NF023502.5 PF12079.13 DUF3558 34.1 34.1 173 domain Y Y N DUF3558 family protein 1760 Actinomycetes class 21231 EBI-EMBL Protein of unknown function (DUF3558) DUF3558 family protein This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 177 to 195 amino acids in length. (from Pfam) NF024145.5 PF12734.12 CYSTM 25.2 25.2 37 domain Y Y N cysteine-rich/transmembrane domain-containing protein 19933165 1760 Actinomycetes class 180 EBI-EMBL Cysteine-rich TM module stress tolerance Cysteine-rich TM module stress tolerance The members of this family are short cysteine-rich membrane proteins that most probably dimerise together to form a transmembrane sulfhydryl-lined pore. The CYSTM module is always present at the extreme C-terminus of the protein in which it is present. Furthermore, like the yeast prototypes, the majority of the proteins also possess a proline/glutamine-rich segment upstream of the CYSTM module that is likely to form a polar, disordered head in the cytoplasm. The presence of an atypical well-conserved acidic residue at the C-terminal end of the TM helix suggests that this might interact with a positively charged moiety in the lipid head group. Consistently across the eukaryotes, the different versions of the CYSTM module appear to have roles in stress-response or stress-tolerance, and, more specifically, in resistance to deleterious substances, implying that these might be general functions of the whole family. [1]. 19933165. CYSTM, a novel cysteine-rich transmembrane module with a role in stress tolerance across eukaryotes. Venancio TM, Aravind L;. Bioinformatics. 2010;26:149-152. (from Pfam) NF025377.5 PF14011.11 ESX-1_EspG 27 27 245 domain Y Y N ESX secretion-associated protein EspG 16368961,17433643 1760 Actinomycetes class 15675 EBI-EMBL EspG family ESX secretion-associated protein EspG This family of proteins contains the the EspG1, EspG2 and EspG3 proteins from M. tuberculosis. These proteins are involved in the ESAT-6 secretion system 1 (ESX-1) of Mycobacterium tuberculosis which is important for virulence and intercellular spread [2]. Proteins in this family are typically between 254 and 295 amino acids in length. [1]. 16368961. Dissection of ESAT-6 system 1 of Mycobacterium tuberculosis and impact on immunogenicity and virulence. Brodin P, Majlessi L, Marsollier L, de Jonge MI, Bottai D, Demangel C, Hinds J, Neyrolles O, Butcher PD, Leclerc C, Cole ST, Brosch R;. Infect Immun. 2006;74:88-98. [2]. 17433643. A protein linkage map of the ESAT-6 secretion system 1 (ESX-1) of Mycobacterium tuberculosis. Teutschbein J, Schumann G, Mollmann U, Grabley S, Cole ST, Munder T;. Microbiol Res. 2009;164:253-259. (from Pfam) NF025398.5 PF14032.11 PknH_C 27 27 187 domain Y Y N sensor domain-containing protein 14690440 1760 Actinomycetes class 8763 EBI-EMBL PknH-like extracellular domain PknH-like extracellular domain This domain is functionally uncharacterised. It is found as the periplasmic domain of the bacterial protein kinase PknH [1]. The domain is also found in isolation in numerous proteins, for example the lipoproteins lpqQ, lprH, lppH and lpqA from M. tuberculosis. This family of proteins is found in bacteria. Proteins in this family are typically between 214 and 268 amino acids in length. There are two completely conserved C residues that are likely to form a disulphide bond. A second pair of cysteines are less well conserved probably form a second disulphide bond. It seems likely that this domain functions to bind some as yet unknown ligand. [1]. 14690440. An FHA phosphoprotein recognition domain mediates protein EmbR phosphorylation by PknH, a Ser/Thr protein kinase from Mycobacterium tuberculosis. Molle V, Kremer L, Girard-Blanc C, Besra GS, Cozzone AJ, Prost JF;. Biochemistry. 2003;42:15300-15309. (from Pfam) NF025762.5 PF14404.11 Strep_pep 25 25 63 domain Y N N Ribosomally synthesized peptide in Streptomyces species 20023723 1760 Actinomycetes class 1254 EBI-EMBL Ribosomally synthesized peptide in Streptomyces species Ribosomally synthesized peptide in Streptomyces species A ribosomally synthesized peptide related to microviridin and marinostatin, usually in the gene neighborhood of one or more RimK-like ATP-grasp. The gene-context suggests that it is further modified by the ATP-grasp. The peptide is predicted to function in a defensive or developmental role, or as an antibiotic [1]. [1]. 20023723. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L;. Mol Biosyst. 2009;5:1636-1660. (from Pfam) NF025765.5 PF14408.11 Actino_peptide 25 25 58 domain Y Y N putative ATP-grasp-modified RiPP 20023723 1760 Actinomycetes class 3114 EBI-EMBL Ribosomally synthesised peptide in actinomycetes putative ATP-grasp-modified RiPP Ribosomally synthesised peptide that is usually in the gene neighbourhood of a RimK-like ATP-grasp and an aspartyl-O-methylase. Gene contexts suggest that it is further modified by the ATP-grasp and the methylase. It might function in defence or development, or as a peptide antibiotic [1]. [1]. 20023723. Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L;. Mol Biosyst. 2009;5:1636-1660. (from Pfam) NF026246.5 PF14896.11 Arabino_trans_C 25 25 385 domain Y Y N arabinosyltransferase C-terminal domain-containing protein 21383969,8876238 1760 Actinomycetes class 10862 EBI-EMBL EmbC C-terminal domain EmbC C-terminal domain Arabinosyltransferase is involved in arabinogalactan (AG) biosynthesis pathway in mycobacteria. AG is a component of the macromolecular assembly of the mycolyl-AG-peptidoglycan complex of the cell wall. This enzyme has important clinical applications as it is believed to be the target of the antimycobacterial drug Ethambutol [1]. This domain represents the C-terminal extracellular domain that is likely to bind to carbohydrate [2]. [1]. 8876238. The embAB genes of Mycobacterium avium encode an arabinosyl transferase involved in cell wall arabinan biosynthesis that is the target for the antimycobacterial drug ethambutol. Belanger AE, Besra GS, Ford ME, Mikusova K, Belisle JT, Brennan PJ, Inamine JM;. Proc Natl Acad Sci U S A 1996;93:11919-11924. [2]. 21383969. The C-terminal domain of the Arabinosyltransferase Mycobacterium tuberculosis EmbC is a lectin-like carbohydrate binding module. Alderwick LJ, Lloyd GS, Ghadbane H, May JW, Bhatt A, Eggeling L, Futterer K, Besra GS;. PLoS Pathog. 2011;7:e1001299. (from Pfam) NF026869.5 PF15531.11 Ntox27 24 24 130 domain Y Y N polymorphic toxin type 27 domain-containing protein 22731697 1760 Actinomycetes class 626 EBI-EMBL Bacterial toxin 27 polymorphic toxin type 27 domain (predicted RNase) A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold and conserved aspartate and glutamate residues, and an RxW motif. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 7 secretion systems [1]. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF026936.5 PF15598.11 Imm61 25 25 157 PfamEq Y Y N Imm61 family immunity protein 22731697 1760 Actinomycetes class 576 EBI-EMBL Immunity protein 61 Imm61 family immunity protein A predicted immunity protein with an alpha+beta fold and a conserved arginine. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Ntox40 family [1]. [1]. 22731697. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;. Biol Direct. 2012;7:18. (from Pfam) NF027471.5 PF16145.10 DUF4853 34.8 34.8 135 domain Y Y N DUF4853 domain-containing protein 1760 Actinomycetes class 246 EBI-EMBL Domain of unknown function (DUF4853) Domain of unknown function (DUF4853) This family consists of uncharacterized proteins around 220 residues in length and is mainly found in various Actinomyces species. The function of this family is unknown. (from Pfam) NF027839.5 PF16525.10 MHB 27.4 27.4 77 domain Y Y N heme-binding protein GO:0020037 21383189 1760 Actinomycetes class 3496 EBI-EMBL Haemophore, haem-binding heme-binding protein MHB is a coiled-coil molecule that binds free haem in mycobacterial cytoplasm to deliver it to membrane proteins for shuttling through the membrane [1]. [1]. 21383189. Discovery and characterization of a unique mycobacterial heme acquisition system. Tullius MV, Harmston CA, Owens CP, Chim N, Morse RP, McMath LM, Iniguez A, Kimmey JM, Sawaya MR, Whitelegge JP, Horwitz MA, Goulding CW;. Proc Natl Acad Sci U S A. 2011;108:5051-5056. (from Pfam) NF028018.5 PF16708.10 LppA 26.4 26.4 153 subfamily Y Y N LppA family lipoprotein 19899167 1760 Actinomycetes class 2607 EBI-EMBL Lipoprotein confined to pathogenic Mycobacterium LppA family lipoprotein This is a family of lipoproteins found only in pathogenic mycobacteria. These pathogenic lipoproteins may play a role in host-pathogen interactions. Lipoproteins localised to the cell-envelope of pathogenic bacteria are major determinants of virulence. The proteins are localised to the cell-surface via an N-terminal lipidation carried out by a transferase - pro-lipoprotein diacylglyceryl transferase Lgt - which attaches a diacylglyceride molecule to a sulfur atom from a crucial cysteine, and a consecutively acting lipoprotein signal peptidase LspA that cleaves the signal peptide just before the modified cysteine. When the peptidase is inactivated the pathogen has difficulty in replicating inside macrophages [1]. [1]. 19899167. Crystal structure of Mycobacterium tuberculosis LppA, a lipoprotein confined to pathogenic mycobacteria. Grana M, Bellinzoni M, Bellalou J, Haouz A, Miras I, Buschiazzo A, Winter N, Alzari PM;. Proteins. 2010;78:769-772. (from Pfam) NF028061.5 PF16751.10 RsdA_SigD_bd 26.7 26.7 46 subfamily_domain Y Y N anti-sigma-D factor RsdA GO:0016989 23314154 1760 Actinomycetes class 2720 EBI-EMBL Anti-sigma-D factor RsdA to sigma factor binding region anti-sigma-D factor RsdA RsdA_SigD_bd is a domain at the N-terminus of anti-sigma-D factor RsdA proteins. It binds to the -35 promoter binding domain of sigma-D. The complex formed regulates the transcriptional expression of the bacterium [1]. [1]. 23314154. Mycobacterium tuberculosis RsdA provides a conformational rationale for selective regulation of sigma-factor activity by proteolysis. Jaiswal RK, Prabha TS, Manjeera G, Gopal B;. Nucleic Acids Res. 2013;41:3414-3423. (from Pfam) NF028137.5 PF16827.10 zf-HC3 25 25 67 domain Y Y N zinc finger protein 1760 Actinomycetes class 1119 EBI-EMBL zinc-finger zinc finger protein This is a family of putative zinc-fingers from Actinobacteriales. (from Pfam) NF028187.5 PF16877.10 DUF5078 27 27 118 PfamAutoEq Y Y N DUF5078 domain-containing protein 1760 Actinomycetes class 1014 EBI-EMBL Domain of unknown function (DUF5078) Domain of unknown function (DUF5078) This family of unknown function is found in Mycobacterium spp. (from Pfam) NF028505.5 PF17196.9 DUF5133 25 25 65 domain Y Y N DUF5133 domain-containing protein 15112998,15186422 1760 Actinomycetes class 10669 EBI-EMBL Protein of unknown function (DUF5133) Protein of unknown function (DUF5133) This protein of unknown function is part of the Borrelidin synthesis genomic cluster. Borrelidin is a polyketide antibiotic [1,2]. [1]. 15186422. Biosynthesis of the angiogenesis inhibitor borrelidin by Streptomyces parvulus Tu4055: insights into nitrile formation. Olano C, Moss SJ, Brana AF, Sheridan RM, Math V, Weston AJ, Mendez C, Leadlay PF, Wilkinson B, Salas JA;. Mol Microbiol. 2004;52:1745-1756. [2]. 15112998. Biosynthesis of the angiogenesis inhibitor borrelidin by Streptomyces parvulus Tu4055: cluster analysis and assignment of functions. Olano C, Wilkinson B, Sanchez C, Moss SJ, Sheridan R, Math V, Weston AJ, Brana AF, Martin CJ, Oliynyk M, Mendez C, Leadlay PF, Salas JA;. Chem Biol. 2004;11:87-97. (from Pfam) NF032897.1 APH_3p_V 450 450 264 exception Y Y Y APH(3')-V family aminoglycoside O-phosphotransferase 1760 Actinomycetes class 30 NCBIFAM APH(3')-V family aminoglycoside O-phosphotransferase APH(3')-V family aminoglycoside O-phosphotransferase NF033070.1 rSAM_AprD4 500 500 456 equivalog Y Y N AprD4 family radical SAM diol-dehydratase 27599765,33784078 1760 Actinomycetes class 15 NCBIFAM AprD4 family radical SAM diol-dehydratase AprD4 family radical SAM diol-dehydratase AprD4, as described originally in Streptoalloteichus hindustanus, is a radical SAM enzyme involved in C3-deoxygenation of the intermediate paromamine during biosynthesis of the aminoglycoside apramycin. It acts as a diol-dehydratase, and works with the partner protein, AprD3, a reductase. NF033129.1 macro_glyco_Mgt 700 700 393 subfamily Y Y Y macrolide-inactivating glycosyltransferase mgt 1760 Actinomycetes class 3325 NCBIFAM macrolide-inactivating glycosyltransferase macrolide-inactivating glycosyltransferase NF033403.1 linaridin_rel 40 40 64 subfamily Y Y N linaridin-like RiPP 1760 Actinomycetes class 21 NCBIFAM linaridin-like RiPP linaridin-like RiPP Members of this family share N-terminal (leader peptide) sequence with the linaridin family of ribosomally translated, post-translationally modified natural product precursors. NF033407.1 SnoaL_meth_ester 200 200 144 subfamily Y Y N SnoaL/DnrD family polyketide biosynthesis methyl ester cyclase 7836284 1760 Actinomycetes class 267 NCBIFAM SnoaL/DnrD family polyketide biosynthesis methyl ester cyclase SnoaL/DnrD family polyketide biosynthesis methyl ester cyclase This HMM represents mutually closely related methyl ester cyclases from a number of polyketide biosynthesis pathways. Examples include proteins designated SnoaL (nogalamycin biosynthesis), DnrD (doxorubicin biosynthesis), RdmA (rhodomycin biosynthesis), etc. NF033414.0 bottro_RiPP 40 40 44 subfamily Y Y N bottromycin family RiPP peptide botA 22984777,27653442 1760 Actinomycetes class 22 NCBIFAM bottromycin family RiPP peptide bottromycin family RiPP peptide Bottromycins are one of the rarer known classes of ribosomally translated, post-translationally modified peptide (RiPP) antibiotics. NF033415.1 thiovirid_RiPP 40 40 72 subfamily Y Y N thioviridamide family RiPP peptide tvaA 23995943,28981254 1760 Actinomycetes class 44 NCBIFAM thioviridamide family RiPP peptide thioviridamide family RiPP peptide Thioviridamide represents one of the rarer known classes of ribosomally translated, post-translationally modified peptide (RiPP) antibiotics. NF033485.1 small_SCO1431 35 35 47 equivalog Y Y N SCO1431 family membrane protein 21573234 1760 Actinomycetes class 2810 NCBIFAM SCO1431 family membrane protein SCO1431 family membrane protein Members of this family, including SCO1431 from Streptomyces coelicolor A3(2), are small and extremely hydrophobic proteins that lack an N-terminal signal peptide. Known members are restricted to the genus Streptomyces, where the protein family is widespread. NF033490.1 small_SPW0924 33 33 44 hypoth_equivalog Y Y N SPW_0924 family protein 1760 Actinomycetes class 1973 NCBIFAM SPW_0924 family protein SPW_0924 family protein Members of this family average less than 44 amino acids in length, and are found exclusively in the Actinobacteria (mostly Streptomyces). The N-terminal half is organized like a signal peptide, beginning Met-Arg and then continuing with a hydrophobic stretch that is unusually rich in alanine. The C-terminal region has a nearly invariant motif TSPxPLLTTVP. The function is unknown. NF033525.2 lasso_albusnod 30 30 44 subfamily Y Y N albusnodin family lasso peptide 1760 Actinomycetes class 417 NCBIFAM albusnodin family lasso peptide albusnodin family lasso peptide Members of this family are lasso peptides in the family of albusnodin, and appear limited so far to the Actinobacteria. Members are more strongly conserved in the core peptide region than in the leader peptide region, which is unusual for ribosomally produced, post-translationally modified natural products. The founding member of this family is not only circularized by the formation of an isopeptide bond, but also acetylated. NF033533.1 lone7_assoc_B 35 35 136 subfamily Y Y N type VII secretion system-associated protein 1760 Actinomycetes class 1271 NCBIFAM type VII secretion system-associated protein type VII secretion system-associated protein Members of this family are found almost entirely in the genus Streptomyces, and are associated with a type VII secretion system (T7SS). NF033628.1 snapalysin 300 300 207 exception Y Y N snapalysin snpA 3.4.24.77 12746556,19201757 1760 Actinomycetes class 4737 NCBIFAM snapalysin snapalysin Snapalysin (SnpA, or Small Neutral Protease A) belongs to the metzincin family of zinc-dependent metalloendopeptidases. NF033629.0 RiPP_CPAC 60 60 52 subfamily Y Y N RiPP peptide 1760 Actinomycetes class 12 NCBIFAM RiPP peptide RiPP peptide null NF033638.1 RNase_AS 200 200 155 equivalog Y Y N polyadenylate-specific 3'-exoribonuclease AS GO:0000287,GO:0008408 24311791,24704253,25882544 1760 Actinomycetes class 2992 NCBIFAM polyadenylate-specific 3'-exoribonuclease AS polyadenylate-specific 3'-exoribonuclease AS RNase AS is a 3'-exoribonuclease, found in Mycobacterium tuberculosis and other Actinobacteria, that acts specifically to degrade polyadenylate sequences from the 3'-end of RNA. NF033649.1 LipDrop_Rv1109c 110 110 198 equivalog Y Y N lipid droplet-associated protein 21731490,22180631 1760 Actinomycetes class 2285 NCBIFAM lipid droplet-associated protein lipid droplet-associated protein RHA1_ro05869 from Rhodococcus jostii RHA1, an ortholog of Rv1109c from Mycobacterium tuberculosis, has been shown specifically with lipid droplets that consist of a neutral lipid core enveloped by a phospholipid monolayer and surface proteins. Lipid droplets of triacylglycerol can be especially prominent in members of the genus Rhodococcus, but occur also in Mycobacterium tuberculosis and can support dormancy of that pathogen. NF033703.1 transcr_KstR 280 280 185 equivalog Y Y N cholesterol catabolism transcriptional regulator KstR kstR GO:0003677 17635188,20167624,24802756,26858250 1760 Actinomycetes class 1379 NCBIFAM cholesterol catabolism transcriptional regulator KstR cholesterol catabolism transcriptional regulator KstR KstR, a protein characterized in Mycobacterium tuberculosis (MTB) and M. smegmatis is a TetR family transcriptional regulator that is essential for pathogenesis in MTB. In controls the expression of about 80 proteins involved in the earlier stages of cholesterol catabolism. KstR binds not to cholesterol itself, but to catabolites found early in the degradation pathway. NF033752.1 linaridin_CypA 35 35 52 subfamily Y Y N cypemycin family RiPP 20805503,7802859 1760 Actinomycetes class 70 NCBIFAM cypemycin family RiPP cypemycin family RiPP The cypemycin precursor CypA belongs to the linaridin class (linear "arid" peptide, following dehydration modifications) of RiPP natural product precursors. The signature terminal motif CL[VI]C is modified by decarboxylation of the C-terminal Cys residue, followed by cyclization. NF033753.1 RiPP_decarbCypD 215 215 182 equivalog Y Y N CypD family RiPP peptide-cysteine decarboxylase GO:0003824 1760 Actinomycetes class 76 NCBIFAM CypD family RiPP peptide-cysteine decarboxylase CypD family RiPP peptide-cysteine decarboxylase CypD, a Cys decarboxylase flavoprotein, oxidatively removes the carboxyl moiety from the C-terminal Cys residue of CypA, the precursor of the RiPP natural product cypemycin. NF033896.2 MFS_LfrA 825 825 504 equivalog Y Y N efflux MFS transporter LfrA lfrA GO:0022857,GO:0055085 8552639 1760 Actinomycetes class 182 NCBIFAM efflux MFS transporter LfrA efflux MFS transporter LfrA This efflux transporter, as characterized in Mycolicibacterium (Mycobacterium) smegmatis, provides low-level fluoroquinolone resistance (lfr) when overexpressed. NF035932.1 lectin_4 300 300 320 subfamily Y Y N lectin 1760 Actinomycetes class 20 NCBIFAM lectin Lectins are important adhesin proteins, which bind carbohydrate structures on host cell surface. The carbohydrate specificity of diverse lectins to a large extent dictates bacteria tissue tropism by mediating specific attachment to unique host sites expressing the corresponding carbohydrate receptor. NF035935.1 ESAT6_3 100 100 98 subfamily Y Y N pore-forming ESAT-6 family protein 1760 Actinomycetes class 1563 NCBIFAM pore-forming ESAT-6 family protein NF035953.1 integrity_Cei 150 150 212 equivalog Y Y N envelope integrity protein Cei cei 31285241 1760 Actinomycetes class 2084 NCBIFAM envelope integrity protein Cei Cei (cell envelope integrity), as described for the founding member Rv2700 from Mycobacterium tuberculosis, is a transmembrane protein with an extracellular LytR_C domain. It lacks any DNA-binding domain and is not a transcriptional regulator. It shares homology to C-terminal regions present in some members of the LytR-CpsA-Psr family, a family in which some characterized members transfer teichoic acids to from carriers to mature peptidoglycan. NF036291.5 PF17230.7 DUF5304 26.8 26.8 143 domain Y Y N DUF5304 family protein 1760 Actinomycetes class 5311 EBI-EMBL Family of unknown function (DUF5304) DUF5304 family protein This family of unknown function is found in Actinobacteria. (from Pfam) NF036306.5 PF17301.7 LpqV 25 25 113 PfamEq Y Y N lipoprotein LpqV lpqV 21504606 1760 Actinomycetes class 758 EBI-EMBL Putative lipoprotein LpqV lipoprotein LpqV This is a family of cell surface proteins found in Mycobacterium with no known function [1]. [1]. 21504606. Mycobacterium tuberculosis septum site determining protein, Ssd encoded by rv3660c, promotes filamentation and elicits an alternative metabolic and dormancy stress response. England K, Crew R, Slayden RA;. BMC Microbiol. 2011;11:79. (from Pfam) NF036408.5 PF17240.7 DUF5313 27.4 27.4 123 domain Y Y N DUF5313 family protein 1760 Actinomycetes class 3716 EBI-EMBL Family of unknown function (DUF5313) DUF5313 family protein This is a family of unknown function, found mostly in Actinobacteria and composed of trans-membrane proteins. (from Pfam) NF036596.5 PF17468.7 GP52 25 25 61 domain Y N N Phage gene product 52 1760 Actinomycetes class 71 EBI-EMBL Phage gene product 52 Phage gene product 52 This is a family of unknown function found in Mycobacterium phage. (from Pfam) NF036975.5 PF17689.7 Arabino_trans_N 25 25 156 domain Y N N Arabinosyltransferase concanavalin like domain 8876238 1760 Actinomycetes class 10583 EBI-EMBL Arabinosyltransferase concanavalin like domain Arabinosyltransferase concanavalin like domain Arabinosyltransferase is involved in arabinogalactan (AG) biosynthesis pathway in mycobacteria. AG is a component of the macromolecular assembly of the mycolyl-AG-peptidoglycan complex of the cell wall. This enzyme has important clinical applications as it is believed to be the target of the antimycobacterial drug Ethambutol [1]. [1]. 8876238. The embAB genes of Mycobacterium avium encode an arabinosyl transferase involved in cell wall arabinan biosynthesis that is the target for the antimycobacterial drug ethambutol. Belanger AE, Besra GS, Ford ME, Mikusova K, Belisle JT, Brennan PJ, Inamine JM;. Proc Natl Acad Sci U S A 1996;93:11919-11924. (from Pfam) NF037166.5 PF18007.6 Rv3651-like_N 25 25 93 domain Y Y N GAF domain-containing protein 29119630 1760 Actinomycetes class 2603 EBI-EMBL Rv3651-like, N-terminal Rv3651-like, N-terminal This domain is found in Rv3651 from Mycobacterium tuberculosis (Swiss:I6YCP0) and similar proteins from Actinobacteria. Rv3651 adopts a three-domain configuration. This entry represents the N-terminal domain, a GAF domain that shows a central antiparallel beta-sheet of six beta-strands [1]. [1]. 29119630. Mycobacterium tuberculosis Rv3651 is a triple sensor-domain protein. Abendroth J, Frando A, Phan IQ, Staker BL, Myler PJ, Edwards TE, Grundner C;. Protein Sci. 2018;27:568-572. (from Pfam) NF037234.5 PF18407.6 GNAT_like 26.3 26.3 61 domain Y N N GCN5-related N-acetyltransferase like domain 23801751 1760 Actinomycetes class 10278 EBI-EMBL GCN5-related N-acetyltransferase like domain GCN5-related N-acetyltransferase like domain This is a domain with a GCN5-related N-acetyltransferase (GNAT) fold which can be found in Rv1692 phophatases. Crystal structure of Rv1692 indicates that this C-temrinal extension, which is absent in other characterized HADSF members, resembles a small GCN5-related N-acetyltransferase (GNAT) fold. Furthermore, it is fused to the HADSF catalytic domain Pfam:PF13242 . Functional studies indicate that this GNAT region is not likely to be involved in acetyl group transfer using AcCoA and SucCoA, it could nonetheless be a regulatory domain. Furthermore, it is suggested that this GNAT domain is required for the solubility of the HADSF fold of Rv1692 and is potentially needed for the structural integrity of this enzyme [1]. [1]. 23801751. Discovery of a glycerol 3-phosphate phosphatase reveals glycerophospholipid polar head recycling in Mycobacterium tuberculosis. Larrouy-Maumus G, Biswas T, Hunt DM, Kelly G, Tsodikov OV, de Carvalho LP;. Proc Natl Acad Sci U S A. 2013;110:11320-11325. (from Pfam) NF037650.5 PF17843.6 MycE_N 27.3 27.3 111 domain Y N N MycE methyltransferase N-terminal 21884704 1760 Actinomycetes class 697 EBI-EMBL MycE methyltransferase N-terminal MycE methyltransferase N-terminal This is the N-terminal domain found in MycE from the mycinamicin biosynthetic pathway. MycE is a tetramer of a two-domain polypeptide, comprising a C-terminal catalytic MT domain and an N-terminal auxiliary domain, which is important for quaternary assembly and for substrate binding [1]. [1]. 21884704. A new structural form in the SAM/metal-dependent omethyltransferase family: MycE from the mycinamicin biosynthetic pathway. Akey DL, Li S, Konwerski JR, Confer LA, Bernard SM, Anzai Y, Kato F, Sherman DH, Smith JL;. J Mol Biol. 2011;413:438-450. (from Pfam) NF037941.1 PKS_NbtC 1150 1150 1027 equivalog Y Y N nocobactin polyketide synthase NbtC nbtC 21097631 1760 Actinomycetes class 742 NCBIFAM nocobactin polyketide synthase NbtC NF037944.1 holin_2 50 50 64 subfamily Y Y N bacteriophage holin 1760 Actinomycetes class 402 NCBIFAM bacteriophage holin Proteins of this family are homologs of the mycobacterial phage holin Gp29. They can cause host cell lysis to release progeny phage particles. NF037950.1 spanin2_1 100 100 130 subfamily Y Y N bacteriophage spanin2 family protein 1760 Actinomycetes class 180 NCBIFAM bacteriophage spanin2 family protein A number of bacteriophage proteins cause lysis of host cells. Holins and endolysins induce the disruption of inner membrane by degrading peptidoglycans. Then, spanin2 family proteins are involved in the final step in host cell lysis by disrupting the outer membrane. NF037967.1 SemiSWEET_1 200 200 196 subfamily Y Y N SemiSWEET transporter 29872447 1760 Actinomycetes class 102 NCBIFAM SemiSWEET transporter The SWEET (Sugars Will Eventually be Exported Transporter) is a superfamily of sugar transporters found in both eukaryotes and prokaryotes. Eukaryotic SWEETs usually have seven transmembrane helices (TMHs), but most prokaryotic SWEETs (SemiSWEETs) have only three TMHs. Proteins of this family have 7 TMHs. NF037996.1 B-4DMT 100 100 139 subfamily Y Y N B-4DMT family transporter 1760 Actinomycetes class 1853 NCBIFAM B-4DMT family transporter Proteins of this family usually have four transmembrane regions. They are classified as a new transporter family (9.B.148) by TCDB. TMSs per polypeptide chain. Homology with SMR-like proteins has not yet been established. Archaeal homologues may be found in the A-4DMT Family (TC# 9.B.54). NF038016.1 sporang_Gsm 240 240 316 equivalog Y Y N sporangiospore maturation cell wall hydrolase GsmA gsmA 31570527 1760 Actinomycetes class 280 NCBIFAM sporangiospore maturation cell wall hydrolase GsmA The peptidoglycan-hydrolyzing enzyme GsmA occurs in some sporangia-forming members of the Actinobacteria, such as Actinoplanes missouriensis, and is required for proper separation of spores. GsmA proteins have one or two SH3 domains N-terminal to the hydrolase domain. NF038022.1 PorACj_fam 28 28 32 subfamily Y Y N PorACj family cell wall channel-forming small protein 24116064 1760 Actinomycetes class 61 NCBIFAM PorACj family cell wall channel-forming small protein Members of this unusual protein family are small (often 40 amino acids or shorter), variable, and detected so far only in the genus Corynebacterium. Despite its small size, the founding member reported to form into homooligomeric channels in the cell wall (not the plasma membrane). This family, as built, may also include PorA subunits of PorA/PorH heterooligomeric cell wall channels. NF038042.1 actinodefensin 65 65 69 subfamily Y Y N actinodefensin 1760 Actinomycetes class 68 NCBIFAM actinodefensin The actinodefensin family is named (here) as an Actinomyces-specific branch of the (otherwise eukaryotic) arthropod defensin family described by Pfam model PF01097. NF038044.1 act_def_assoc_B 45 45 63 subfamily Y Y N actinodefensin-associated protein B adfB 1760 Actinomycetes class 147 NCBIFAM actinodefensin-associated protein B Members of this family are small proteins, averaging about 70 amino acids in length, restricted to the Actinomycetes. Member proteins typically occur in the vicinity of actinodefensin, which represents and Actinomycetes-restricted branch of the arthropod defensin family. The function of this protein is unknown. NF038047.1 not_Tcp10 70 70 399 subfamily_domain Y Y N AAWKG family protein 1760 Actinomycetes class 2781 NCBIFAM AAWKG family protein Members of this family are found primarily in Streptomyces. The family is notable in part because a region outside of the N-terminal region modeled here contains 9-residue repeats that resemble the 18-residue repeats found by PF07202 in the C-terminal region of eukaryotic T-complex protein 10. The family is uncharacterized. This model was constructed, and named for family's most prominent motif, AAWKG, to head off any possible confusion with Tcp10. Members of this family are unrelated to eukaryotic Tcp10, although some members contain a repetitive region similar to a C-terminal repeat region of Tcp10. NF038081.1 BN159_2729_fam 80 80 242 subfamily Y Y N BN159_2729 family protein 1760 Actinomycetes class 854 NCBIFAM BN159_2729 family protein This uncharacterized protein family occurs in Streptomyces and related species. Some members have insertions of long stretches of low-complexity sequences. NF038082.1 phiSA1p31 30 30 60 domain Y Y N phiSA1p31-related protein 1760 Actinomycetes class 1618 NCBIFAM phiSA1p31 domain This domain occurs in Streptomyces and related lineages, in proteins with highly variable architectures, typically at or near the C-terminus. Member proteins include at least two from known temperate phage of Streptomyces, including phiSA1p31, for which it is named, from Streptomyces phage phiSASD1. NF038098.1 GyrA_w_intein 1850 1550 1232 exception Y Y N intein-containing DNA gyrase subunit A gyrA 1760 Actinomycetes class 585 NCBIFAM intein-containing DNA gyrase subunit A NF038139.1 Reg_Aceta_RamB 700 700 465 equivalog Y Y N acetate metabolism transcriptional regulator RamB ramB 15090522,19767422,26021728 1760 Actinomycetes class 1832 NCBIFAM acetate metabolism transcriptional regulator RamB RamB (Regulator of Acetate Metabolism B), as described in Mycobacterium tuberculosis and Corynebacterium glutamicum, is a transcription factor with multiple targets connected to acetate metabolism. It features an N-terminal XRE (Xenobiotic Response Element) family DNA-binding domain and a DUF2083 (PF09856) domain-containing C-terminal region. NF038147.1 lanti_IV_venA 35 35 49 subfamily Y Y N VenA family class IV lanthipeptide 20351769 1760 Actinomycetes class 357 NCBIFAM VenA family class IV lanthipeptide Members of this family include VenA, precursor of the class IV lanthipeptide venezuelin, and all detectable homologs. NF038148.1 lanti_IV_SflA 25 25 52 subfamily Y Y N SflA family class IV lanthipeptide 32356655 1760 Actinomycetes class 381 NCBIFAM SflA family class IV lanthipeptide SflA is the precursor peptide of a RiPP biosynthetic gene cluster (BGC) designated “sfl”, for the Second-most abundant class Four (IV) Lanthipeptide. NF038156.1 lant_syn_V_LxmK 315 315 347 equivalog Y Y N class V lanthionine synthetase subunit LxmK lxmK 32648341 1760 Actinomycetes class 1226 NCBIFAM class V lanthionine synthetase subunit LxmK NF038175.1 IniB_NTERM 40 40 49 domain Y Y N IniB N-terminal domain-containing protein 1760 Actinomycetes class 5538 NCBIFAM IniB N-terminal domain This domain is found as the N-terminal fifty amino acids of a number low-complexity proteins that often bear little or no similarity to each other elsewhere in the protein. The domain occurs twice in Mycobacterium tuberculosis strain H37Rv, in two adjacent proteins, Rv0340 and the isoniazid inducible protein IniB (Rv0341). NF038206.1 RGCVC_fam 35 35 54 equivalog Y Y N RGCVC family protein 1760 Actinomycetes class 585 NCBIFAM RGCVC family protein This family of small proteins, averaging just over 60 amino acids in length, has conspicuous motifs CxxCxH, HD, and RGCVC. The last motif, for which the family is named, is distinctive. The family appears in GC-rich bacteria. The function is unknown. NF038339.3 FAAL_FadD32 975 975 625 equivalog Y Y N long-chain-fatty-acid--AMP ligase FadD32 fadD32 GO:0071768 19182784,19436070 1760 Actinomycetes class 1848 NCBIFAM long-chain-fatty-acid--AMP ligase FAAL32/FadD32 FadD32, also called FAAL32, is a marker enzyme for the biosynthesis of the type of mycolic acids, the very large “eumycolic acids”, found in Mycobacterium. NF038343.1 ligase_FadD11 950 950 585 exception Y Y N fatty acid--CoA ligase FadD11 fadD11 1760 Actinomycetes class 940 NCBIFAM fatty acid--CoA ligase FadD11 The fatty-acid-coA ligase FadD11 is disrupted in multiple strains of Mycobacterium tuberculosis, including the type strain H37Rv. This HMM represents full-length versions. NF038357.1 BN6_48550_fam 90 90 344 domain Y Y N BN6_48550 family protein 1760 Actinomycetes class 1130 NCBIFAM BN6_48550 family protein This uncharacterized domain, named for its occurrence in the arbitrarily chosen protein BN6_48550, seems restricted to the Actinobacteria. This domain tends to be N-terminal in longer proteins that contain additional domains, such TIR-like (PF10137) or glycosyltransferase domains. The function is unknown. NF038391.1 streptophobe 60 45 408 domain Y Y N streptophobe family protein 28761057 1760 Actinomycetes class 10330 NCBIFAM streptophobe family protein Members of this family of uncharacterized probably membrane proteins are restricted almost entirely to the genus Streptomyces, and are highly hydrophobic through the aligned region, hence our coinage of the name streptophobe. Member SCO7274 from Streptomyces coelicolor A3(2) was shown to be expressed as protein. NF038395.1 nocathioamide 30 30 49 subfamily Y Y N nocathioamide family RiPP precursor ntaA 33991039,36682862 1760 Actinomycetes class 2 NCBIFAM nocathioamide family RiPP precursor NF039301.4 PF19374.4 DUF5949 22.7 22.7 167 subfamily Y Y N DUF5949 family protein 1760 Actinomycetes class 3242 EBI-EMBL Family of unknown function (DUF5949) DUF5949 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide. (from Pfam) NF039361.4 PF19655.4 DUF6158 26.8 26.8 66 subfamily Y Y N DUF6158 family protein 16766657 1760 Actinomycetes class 3231 EBI-EMBL Family of unknown function (DUF6158) DUF6158 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus and appears to be predominantly found in actinobacteria [1]. [1]. 16766657. Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Yanai K, Murakami T, Bibb M;. Proc Natl Acad Sci U S A. 2006;103:9661-9666. (from Pfam) NF039370.4 PF19685.4 DUF6187 25 25 141 subfamily Y Y N DUF6187 family protein 29090939 1760 Actinomycetes class 215 EBI-EMBL Family of unknown function (DUF6187) DUF6187 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001503) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the amycolamycin A biosynthetic gene cluster from Amycolatopsis sp. [1]. This family appears to be predominantly found in Actinobacteria. [1]. 29090939. Amycolamycins A and B, Two Enediyne-Derived Compounds from a Locust-Associated Actinomycete. Ma SY, Xiao YS, Zhang B, Shao FL, Guo ZK, Zhang JJ, Jiao RH, Sun Y, Xu Q, Tan RX, Ge HM;. Org Lett. 2017;19:6208-6211. (from Pfam) NF039372.4 PF19690.4 DUF6191 27.4 27.4 42 domain Y Y N DUF6191 domain-containing protein 30694017 1760 Actinomycetes class 8523 EBI-EMBL Family of unknown function (DUF6191) Family of unknown function (DUF6191) This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0002014) is described by MIBiG as an example of the following biosynthetic classes, polyketide and NRP (non-ribosomal peptide). It includes a member of the pepticinnamin E biosynthetic gene cluster from Actinobacteria bacterium OK006 [1]. This family appears to be predominantly found in Actinobacteria. [1]. 30694017. Targeted Rediscovery and Biosynthesis of the Farnesyl-Transferase Inhibitor Pepticinnamin E. Santa Maria KC, Chan AN, O'Neill EM, Li B;. Chembiochem. 2019;20:1387-1393. (from Pfam) NF039373.4 PF19691.4 DUF6192 27 27 248 subfamily Y Y N DUF6192 family protein 16258246 1760 Actinomycetes class 2311 EBI-EMBL Family of unknown function (DUF6192) DUF6192 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000713) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from from the ribostamycin biosynthetic gene cluster from Streptomyces ribosidificus [1]. This family appears to be predominantly found in bacteria. [1]. 16258246. The ribostamycin biosynthetic gene cluster in Streptomyces ribosidificus: comparison with butirosin biosynthesis. Subba B, Kharel MK, Lee HC, Liou K, Kim BG, Sohng JK;. Mol Cells. 2005;20:90-96. (from Pfam) NF039379.4 PF19726.4 DUF6218 26.8 26.8 229 subfamily Y Y N DUF6218 family protein 15376556,19362651 1760 Actinomycetes class 177 EBI-EMBL Family of unknown function (DUF6218) DUF6218 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000696) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the gentamicin biosynthetic gene cluster from Micromonospora echinospora [1,2]. [1]. 15376556. Gene cluster in Micromonospora echinospora ATCC15835 for the biosynthesis of the gentamicin C complex. Unwin J, Standage S, Alexander D, Hosted T Jr, Horan AC, Wellington EM;. J Antibiot (Tokyo). 2004;57:436-445. [2]. 19362651. Enzymology of aminoglycoside biosynthesis-deduction from gene clusters. Wehmeier UF, Piepersberg W;. Methods Enzymol. 2009;459:459-491. (from Pfam) NF039383.4 PF19735.4 DUF6225 26.5 26.5 87 subfamily Y Y N DUF6225 family protein 20086163 1760 Actinomycetes class 785 EBI-EMBL Family of unknown function (DUF6225) DUF6225 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000896) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the cycloserine biosynthetic gene cluster from Streptomyces lavendulae subsp. lavendulae [1]. [1]. 20086163. Molecular cloning and heterologous expression of a biosynthetic gene cluster for the antitubercular agent D-cycloserine produced by Streptomyces lavendulae. Kumagai T, Koyama Y, Oda K, Noda M, Matoba Y, Sugiyama M;. Antimicrob Agents Chemother. 2010;54:1132-1139. (from Pfam) NF039386.4 PF19748.4 DUF6235 25 25 96 subfamily Y Y N DUF6235 family protein 29090939 1760 Actinomycetes class 203 EBI-EMBL Family of unknown function (DUF6235) DUF6235 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001503) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the amycolamycin A biosynthetic gene cluster from Amycolatopsis sp. [1]. This family appears to be predominantly found in Actinobacteria. [1]. 29090939. Amycolamycins A and B, Two Enediyne-Derived Compounds from a Locust-Associated Actinomycete. Ma SY, Xiao YS, Zhang B, Shao FL, Guo ZK, Zhang JJ, Jiao RH, Sun Y, Xu Q, Tan RX, Ge HM;. Org Lett. 2017;19:6208-6211. (from Pfam) NF039387.4 PF19756.4 DUF6243 25 25 67 subfamily Y Y N DUF6243 family protein 1760 Actinomycetes class 4851 EBI-EMBL Family of unknown function (DUF6243) DUF6243 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001931) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the carrimycin biosynthetic gene cluster from unidentified unclassified sequences. This family appears to be predominantly found in Actinobacteria. (from Pfam) NF039414.4 PF19870.4 DUF6343 27.2 27.2 82 subfamily Y Y N DUF6343 family protein 28333450 1760 Actinomycetes class 7032 EBI-EMBL Family of unknown function (DUF6343) DUF6343 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001558) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the cosmomycin C biosynthetic gene cluster from Streptomyces sp. CNT302 [1]. This family appears to be predominantly found in Actinobacteria. [1]. 28333450. PCR-Independent Method of Transformation-Associated Recombination Reveals the Cosmomycin Biosynthetic Gene Cluster in an Ocean Streptomycete. Larson CB, Crusemann M, Moore BS;. J Nat Prod. 2017;80:1200-1204. (from Pfam) NF039415.4 PF19873.4 DUF6346 25 25 145 domain Y Y N DUF6346 domain-containing protein 20690632 1760 Actinomycetes class 553 EBI-EMBL Family of unknown function (DUF6346) DUF6346 domain This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000223) is described by MIBiG as an example of the following biosynthetic class, polyketide, rabelomycin biosynthetic gene cluster from uncultured bacterium BAC AB649/1850 [1]. This family appears to be predominantly found in Actinobacteria. [1]. 20690632. Fluostatins produced by the heterologous expression of a TAR reassembled environmental DNA derived type II PKS gene cluster. Feng Z, Kim JH, Brady SF;. J Am Chem Soc. 2010;132:11902-11903. (from Pfam) NF039420.4 PF19907.4 DUF6380 27 27 46 subfamily Y Y N DUF6380 family protein 8843436 1760 Actinomycetes class 1613 EBI-EMBL Family of unknown function (DUF6380) DUF6380 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000663) is described by MIBiG as an example of the following biosynthetic class, terpene, in particular the hopene biosynthetic gene cluster from Streptomyces coelicolor A3(2) [1]. [1]. 8843436. A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome. Redenbach M, Kieser HM, Denapaite D, Eichner A, Cullum J, Kinashi H, Hopwood DA;. Mol Microbiol. 1996;21:77-96. (from Pfam) NF039435.4 PF19969.4 VMAP-M8 27 27 97 domain Y N N vWA-MoxR associated protein middle region (VMAP-M) 8 32101166 1760 Actinomycetes class 225 EBI-EMBL vWA-MoxR associated protein middle region (VMAP-M) 8 vWA-MoxR associated protein middle region (VMAP-M) 8 Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. [1]. 32101166. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. Kaur G, Burroughs AM, Iyer LM, Aravind L;. Elife. 2020; [Epub ahead of print] (from Pfam) NF039464.4 PF20070.4 DUF6466 25 25 146 subfamily Y Y N DUF6466 family protein 1760 Actinomycetes class 573 EBI-EMBL Family of unknown function (DUF6466) DUF6466 family protein This family of proteins is functionally uncharacterised. This family of proteins is mainly found in Bifidobacteria. Proteins in this family are approximately 190 amino acids in length. They contain the conserved motifs QQQQ, SxxLT and KPW. Members in this family are probably cell surface proteins, some of them are likely elastin binding proteins. (from Pfam) NF039509.4 PF18966.5 Lipoprotein_23 25 25 179 subfamily Y Y N lipoprotein 1760 Actinomycetes class 3171 EBI-EMBL Uncharacterised lipoprotein PF18966 family actinobacterial lipoprotein This entry includes members found in Actinobacteria (mostly streptomycetaceae, micromonosporales and pseudonocardiales). Some members are annotated as lipoproteins. (from Pfam) NF039603.4 PF19379.4 DUF5954 22.8 22.8 297 subfamily Y Y N DUF5954 family protein 1760 Actinomycetes class 3357 EBI-EMBL Family of unknown function (DUF5954) DUF5954 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001973) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). (from Pfam) NF039627.4 PF19487.4 DUF6023 26.8 26.8 150 subfamily Y Y N DUF6023 family protein 21264995 1760 Actinomycetes class 184 EBI-EMBL Family of unknown function (DUF6023) DUF6023 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001077) is described by MIBiG as an example of the following biosynthetic classes, polyketide and terpene. This family includes a protein from the alkyl-O-dihydrogeranyl- methoxyhydroquinones biosynthetic gene cluster from Actinoplanes missouriensis 431 and appears to be predominantly found in Actinobacteria [1]. [1]. 21264995. Characterization of the biosynthesis gene cluster for alkyl-O-dihydrogeranyl-methoxyhydroquinones in Actinoplanes missouriensis. Awakawa T, Fujita N, Hayakawa M, Ohnishi Y, Horinouchi S;. Chembiochem. 2011;12:439-448. (from Pfam) NF039655.4 PF19594.4 DUF6099 25 25 142 subfamily Y Y N DUF6099 family protein 21102601 1760 Actinomycetes class 4352 EBI-EMBL Family of unknown function (DUF6099) DUF6099 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000222) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the FD-594 biosynthetic gene cluster from Streptomyces sp. TA-0256 and it appears to be predominantly found in actinobacteria [1]. [1]. 21102601. Cloning of the biosynthetic gene cluster for naphthoxanthene antibiotic FD-594 from Streptomyces sp. TA-0256. Kudo F, Yonezawa T, Komatsubara A, Mizoue K, Eguchi T;. J Antibiot (Tokyo). 2011;64:123-132. (from Pfam) NF039687.4 PF19711.4 DUF6207 25 25 67 subfamily Y Y N DUF6207 family protein 30405594 1760 Actinomycetes class 4257 EBI-EMBL Family of unknown function (DUF6207) DUF6207 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001709) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the nystatin biosynthetic gene cluster from Streptomyces albulus [1]. This family appears to be predominantly found in Actinobacteria. [1]. 30405594. Identification of wysPII as an Activator of Morphological Development in Streptomyces albulus CK-15. Liu B, Ge B, Ma J, Wei Q, Khan AA, Shi L, Zhang K;. Front Microbiol. 2018;9:2550. (from Pfam) NF039690.4 PF19721.4 DUF6215 27.1 27.1 135 domain Y Y N DUF6215 domain-containing protein 30806648 1760 Actinomycetes class 3002 EBI-EMBL Family of unknown function (DUF6215) Family of unknown function (DUF6215) This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001856) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the caniferolide A biosynthetic gene cluster from Streptomyces caniferus [1]. This family appears to be predominantly found in Actinobacteria. [1]. 30806648. Structure elucidation and biosynthetic gene cluster analysis of caniferolides A-D, new bioactive 36-membered macrolides from the marine-derived Streptomyces caniferus CA-271066. Perez-Victoria I, Oves-Costales D, Lacret R, Martin J, Sanchez-Hidalgo M, Diaz C, Cautain B, Vicente F, Genilloud O, Reyes F;. Org Biomol Chem. 2019;17:2954-2971. (from Pfam) NF039699.4 PF19757.4 DUF6244 31.6 31.6 87 domain Y Y N DUF6244 family protein 19384899 1760 Actinomycetes class 726 EBI-EMBL Family of unknown function (DUF6244) DUF6244 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000267) is described by MIBiG as an example of the following biosynthetic classes, polyketide and saccharide. This entry includes a member from the saquayamycin Z biosynthetic gene cluster from Micromonospora sp. Tu 6368 [1]. This family appears to be predominantly found in Actinobacteria. [1]. 19384899. Cloning and sequencing of the biosynthetic gene cluster for saquayamycin Z and galtamycin B and the elucidation of the assembly of their saccharide chains. Erb A, Luzhetskyy A, Hardter U, Bechthold A;. Chembiochem. 2009;10:1392-1401. (from Pfam) NF039703.4 PF19764.4 DUF6251 26.5 26.5 126 subfamily Y Y N DUF6251 family protein 19362651 1760 Actinomycetes class 1714 EBI-EMBL Family of unknown function (DUF6251) DUF6251 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis [1]. [1]. 19362651. Enzymology of aminoglycoside biosynthesis-deduction from gene clusters. Wehmeier UF, Piepersberg W;. Methods Enzymol. 2009;459:459-491. (from Pfam) NF039706.4 PF19771.4 DUF6257 26.2 26.2 61 subfamily Y Y N DUF6257 family protein 19362651 1760 Actinomycetes class 1261 EBI-EMBL Family of unknown function (DUF6257) DUF6257 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis [1]. [1]. 19362651. Enzymology of aminoglycoside biosynthesis-deduction from gene clusters. Wehmeier UF, Piepersberg W;. Methods Enzymol. 2009;459:459-491. (from Pfam) NF039712.4 PF19790.4 DUF6274 25 25 77 subfamily Y Y N DUF6274 family protein 17827660,19670201,23521145 1760 Actinomycetes class 4240 EBI-EMBL Family of unknown function (DUF6274) DUF6274 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000119) is described by MIBiG as an example of the following biosynthetic classes, polyketide and saccharide, in particular the 7-deoxypactamycin biosynthetic gene cluster from Streptomyces pactum [1,2,3]. This family appears to be predominantly found in Actinobacteria. [1]. 17827660. Cloning of the pactamycin biosynthetic gene cluster and characterization of a crucial glycosyltransferase prior to a unique cyclopentane ring formation. Kudo F, Kasama Y, Hirayama T, Eguchi T;. J Antibiot (Tokyo). 2007;60:492-503. [2]. 19670201. Deciphering pactamycin biosynthesis and engineered production of new pactamycin analogues. Ito T, Roongsawang N, Shirasaka N, Lu W, Flatt PM, Kasanah N, Miranda C, Mahmud T;. Chembiochem. 2009;10:2253-2265. [3]. 23521145. Mutasynthesis of fluorinated pactamycin analogues and their antimalarial activity. Almabruk KH, Lu W, Li Y, Abugreen M, Kelly JX, Mahmud T;. Org Lett. 2013;15:1678-1681. (from Pfam) NF039717.4 PF19809.4 DUF6292 27.1 27.1 88 subfamily Y Y N DUF6292 family protein 25831524 1760 Actinomycetes class 3142 EBI-EMBL Family of unknown function (DUF6292) DUF6292 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001203) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the clarexpoxcin biosynthetic gene cluster from uncultured bacterium AR_456 [1]. This family appears to be predominantly found in Actinobacteria. [1]. 25831524. Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors. Owen JG, Charlop-Powers Z, Smith AG, Ternei MA, Calle PY, Reddy BV, Montiel D, Brady SF;. Proc Natl Acad Sci U S A. 2015;112:4221-4226. (from Pfam) NF039732.4 PF19859.4 DUF6333 31.4 31.4 234 subfamily Y Y N DUF6333 family protein 23157252 1760 Actinomycetes class 1186 EBI-EMBL Family of unknown function (DUF6333) DUF6333 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000274) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the tetarimycin A biosynthetic gene cluster from uncultured bacterium [1]. [1]. 23157252. Tetarimycin A, an MRSA-active antibiotic identified through induced expression of environmental DNA gene clusters. Kallifidas D, Kang HS, Brady SF;. J Am Chem Soc. 2012;134:19552-19555. (from Pfam) NF039742.4 PF19899.4 DUF6372 27.4 27.4 68 subfamily Y Y N DUF6372 family protein 19362651 1760 Actinomycetes class 157 EBI-EMBL Family of unknown function (DUF6372) DUF6372 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis [1]. [1]. 19362651. Enzymology of aminoglycoside biosynthesis-deduction from gene clusters. Wehmeier UF, Piepersberg W;. Methods Enzymol. 2009;459:459-491. (from Pfam) NF039764.4 PF19979.4 DUF6415 27.5 27.5 95 subfamily Y Y N DUF6415 family natural product biosynthesis protein 16766657 1760 Actinomycetes class 7462 EBI-EMBL Family of unknown function (DUF6415) DUF6415 family natural product biosynthesis protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [1]. This family appears to be predominantly found in Actinobacteria. [1]. 16766657. Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Yanai K, Murakami T, Bibb M;. Proc Natl Acad Sci U S A. 2006;103:9661-9666. (from Pfam) NF039922.4 PF19354.4 DUF5931 27 27 175 domain Y Y N DUF5931 domain-containing protein 1760 Actinomycetes class 10505 EBI-EMBL Family of unknown function (DUF5931) Family of unknown function (DUF5931) This presumed domain is functionally uncharacterised. This domain family is found in actinobacteria, and is approximately 170 amino acids in length. This domain is found at the N-terminus of 2 component signalling proteins which also contain Pfam:PF07730, and Pfam:PF02518. This domain presumably binds an as yet unknown ligand. (from Pfam) NF039952.4 PF19450.4 DUF5988 27 27 70 subfamily Y Y N DUF5988 family protein 1760 Actinomycetes class 3214 EBI-EMBL Family of unknown function (DUF5988) DUF5988 family protein This family of proteins is found in bacteria. Proteins in this family are typically between 68 and 82 amino acids in length. There are two conserved sequence motifs: GGP and YEHF. (from Pfam) NF039972.4 PF19534.4 DUF6059 27.3 27.3 56 subfamily Y Y N DUF6059 family protein 30080389 1760 Actinomycetes class 1887 EBI-EMBL Family of unknown function (DUF6059) DUF6059 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001922) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the isoindolinomycin biosynthetic gene cluster from Streptomyces sp. SoC090715LN-16 and appears to be predominantly found in Actinobacteria [1]. [1]. 30080389. Discovery of an Antibacterial Isoindolinone-Containing Tetracyclic Polyketide by Cryptic Gene Activation and Characterization of Its Biosynthetic Gene Cluster. Thong WL, Shin-Ya K, Nishiyama M, Kuzuyama T;. ACS Chem Biol. 2018;13:2615-2622. (from Pfam) NF040025.4 PF19719.4 DUF6213 27.7 27.7 66 subfamily Y Y N DUF6213 family protein 29255990 1760 Actinomycetes class 1195 EBI-EMBL Family of unknown function (DUF6213) DUF6213 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001916) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the lavendiol biosynthetic gene cluster from Streptomyces lavendulae [1]. This family appears to be predominantly found in Actinobacteria. [1]. 29255990. Discovery of a new diol-containing polyketide by heterologous expression of a silent biosynthetic gene cluster from Streptomyces lavendulae FRI-5. Pait IGU, Kitani S, Roslan FW, Ulanova D, Arai M, Ikeda H, Nihira T;. J Ind Microbiol Biotechnol. 2018;45:77-87. (from Pfam) NF040033.4 PF19751.4 DUF6238 29.1 29.1 152 subfamily Y Y N DUF6238 family protein 16766657 1760 Actinomycetes class 2567 EBI-EMBL Family of unknown function (DUF6238) DUF6238 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [1]. This family appears to be predominantly found in bacteria. [1]. 16766657. Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Yanai K, Murakami T, Bibb M;. Proc Natl Acad Sci U S A. 2006;103:9661-9666. (from Pfam) NF040036.4 PF19761.4 DUF6248 26.7 26.7 155 subfamily Y Y N DUF6248 family natural product biosynthesis protein 16766657 1760 Actinomycetes class 488 EBI-EMBL Family of unknown function (DUF6248) DUF6248 family natural product biosynthesis protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [1]. [1]. 16766657. Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Yanai K, Murakami T, Bibb M;. Proc Natl Acad Sci U S A. 2006;103:9661-9666. (from Pfam) NF040038.4 PF19768.4 DUF6255 25 25 70 subfamily Y Y N DUF6255 family natural product biosynthesis protein 29349495 1760 Actinomycetes class 498 EBI-EMBL Family of unknown function (DUF6255) DUF6255 family natural product biosynthesis protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001662) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the mediomycin A biosynthetic gene cluster from Kitasatospora mediocidica [1]. [1]. 29349495. Genomic-driven discovery of an amidinohydrolase involved in the biosynthesis of mediomycin A. Sun F, Xu S, Jiang F, Liu W;. Appl Microbiol Biotechnol. 2018;102:2225-2234. (from Pfam) NF040045.4 PF19801.4 DUF6284 27.4 27.4 86 subfamily Y Y N DUF6284 family protein 19362651 1760 Actinomycetes class 6609 EBI-EMBL Family of unknown function (DUF6284) DUF6284 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis [1]. This family appears to be predominantly found in Actinoabactteria. [1]. 19362651. Enzymology of aminoglycoside biosynthesis-deduction from gene clusters. Wehmeier UF, Piepersberg W;. Methods Enzymol. 2009;459:459-491. (from Pfam) NF040047.4 PF19813.4 DUF6296 27.2 27.2 78 subfamily Y Y N DUF6296 family protein 25489112 1760 Actinomycetes class 2476 EBI-EMBL Family of unknown function (DUF6296) DUF6296 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000187) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the asukamycin biosynthetic gene cluster from Streptomyces nodosus subsp. asukaensis [1]. This family appears to be predominantly found in actinobacteria. [1]. 25489112. Microbial biosynthesis of medium-chain 1-alkenes by a nonheme iron oxidase. Rui Z, Li X, Zhu X, Liu J, Domigan B, Barr I, Cate JH, Zhang W;. Proc Natl Acad Sci U S A. 2014;111:18237-18242. (from Pfam) NF040050.4 PF19819.4 DUF6302 27.2 27.2 135 subfamily Y Y N DUF6302 family protein 16766657 1760 Actinomycetes class 908 EBI-EMBL Family of unknown function (DUF6302) DUF6302 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [1]. [1]. 16766657. Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Yanai K, Murakami T, Bibb M;. Proc Natl Acad Sci U S A. 2006;103:9661-9666. (from Pfam) NF040051.4 PF19820.4 DUF6303 25 25 93 subfamily Y Y N DUF6303 family protein 19362651 1760 Actinomycetes class 1834 EBI-EMBL Family of unknown function (DUF6303) DUF6303 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis [1]. This family appears to be predominantly found in actinobacteria. [1]. 19362651. Enzymology of aminoglycoside biosynthesis-deduction from gene clusters. Wehmeier UF, Piepersberg W;. Methods Enzymol. 2009;459:459-491. (from Pfam) NF040053.4 PF19826.4 DUF6307 25 25 43 subfamily Y Y N DUF6307 family protein 1760 Actinomycetes class 482 EBI-EMBL Family of unknown function (DUF6307) DUF6307 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000202) is described by MIBiG as an example of the following biosynthetic class, polyketide. (from Pfam) NF040056.4 PF19836.4 DUF6315 29.7 29.7 174 subfamily Y Y N DUF6315 family protein 23360970 1760 Actinomycetes class 107 EBI-EMBL Family of unknown function (DUF6315) DUF6315 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000081) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650 [1]. [1]. 23360970. Cloning and sequencing of the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650 revealing new insights into biosynthesis of the enediyne family of antitumor antibiotics. Lohman JR, Huang SX, Horsman GP, Dilfer PE, Huang T, Chen Y, Wendt-Pienkowski E, Shen B;. Mol Biosyst. 2013;9:478-491. (from Pfam) NF040061.4 PF19844.4 DUF6319 23.9 23.9 115 subfamily Y Y N DUF6319 family protein 1760 Actinomycetes class 2151 EBI-EMBL Family of unknown function (DUF6319) DUF6319 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 251 amino acids in length. (from Pfam) NF040083.4 PF19938.4 DUF6400 27.1 27.1 69 subfamily Y Y N DUF6400 family protein 22156425 1760 Actinomycetes class 2373 EBI-EMBL Family of unknown function (DUF6400) DUF6400 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000144) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the salinomycin biosynthetic gene cluster from Streptomyces albus [1]. This family appears to be predominantly found in Actinobacteria. [1]. 22156425. Cloning and characterization of the polyether salinomycin biosynthesis gene cluster of Streptomyces albus XM211. Jiang C, Wang H, Kang Q, Liu J, Bai L;. Appl Environ Microbiol. 2012;78:994-1003. (from Pfam) NF040084.4 PF19939.4 DUF6401 29.2 29.2 82 subfamily Y Y N DUF6401 family natural product biosynthesis protein 27829923 1760 Actinomycetes class 2537 EBI-EMBL Family of unknown function (DUF6401) DUF6401 family natural product biosynthesis protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001580) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the ebelactone biosynthetic gene cluster from Kitasatospora aburaviensis [1]. This family appears to be predominantly found in actinobacteria. [1]. 27829923. Evidence for an iterative module in chain elongation on the azalomycin polyketide synthase. Hong H, Sun Y, Zhou Y, Stephens E, Samborskyy M, Leadlay PF;. Beilstein J Org Chem. 2016;12:2164-2172. (from Pfam) NF040087.4 PF19948.4 DUF6410 25 25 189 domain Y Y N DUF6410 domain-containing protein 19680283 1760 Actinomycetes class 76 EBI-EMBL Family of unknown function (DUF6410) DUF6410 domain This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001062) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the TLN-05220 biosynthetic gene cluster from Micromonospora echinospora subsp. challisensis [1]. [1]. 19680283. TLN-05220, TLN-05223, new Echinosporamicin-type antibiotics, and proposed revision of the structure of bravomicins(*). Banskota AH, Aouidate M, Sorensen D, Ibrahim A, Piraee M, Zazopoulos E, Alarco AM, Gourdeau H, Mellon C, Farnet CM, Falardeau P, McAlpine JB;. J Antibiot (Tokyo). 2009;62:565-570. (from Pfam) NF040092.4 PF19968.4 VMAP-M7 27 27 160 domain Y Y N VMAP-related conflict system protein 32101166 1760 Actinomycetes class 30 EBI-EMBL vWA-MoxR associated protein middle region (VMAP-M) 7 VMAP-related conflict system protein Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. [1]. 32101166. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. Kaur G, Burroughs AM, Iyer LM, Aravind L;. Elife. 2020; [Epub ahead of print] (from Pfam) NF040183.4 PF19054.5 DUF5753 23.4 23.4 178 subfamily Y Y N Scr1 family TA system antitoxin-like transcriptional regulator 30524403 1760 Actinomycetes class 194597 EBI-EMBL Domain of unknown function (DUF5753) Scr1 family TA system antitoxin-like transcriptional regulator This entry represents a putative ligand binding domain found in bacterial transcription regulators that have an N-terminal HTH domain Pfam:PF13560. (from Pfam) NF040285.4 PF19410.4 DUF5980 27.1 27.1 97 subfamily Y Y N DUF5980 family protein 1760 Actinomycetes class 301 EBI-EMBL Family of unknown function (DUF5980) DUF5980 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000666) is described by MIBiG as an example of the following biosynthetic class, terpene. (from Pfam) NF040297.4 PF19466.4 DUF6003 35.4 35.4 140 subfamily Y Y N DUF6003 family protein 12940979 1760 Actinomycetes class 1476 EBI-EMBL Family of unknown function (DUF6003) DUF6003 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000100) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from monensin biosynthetic gene cluster from Streptomyces cinnamonensis [1]. [1]. 12940979. Analysis of the biosynthetic gene cluster for the polyether antibiotic monensin in Streptomyces cinnamonensis and evidence for the role of monB and monC genes in oxidative cyclization. Oliynyk M, Stark CB, Bhatt A, Jones MA, Hughes-Thomas ZA, Wilkinson C, Oliynyk Z, Demydchuk Y, Staunton J, Leadlay PF;. Mol Microbiol. 2003;49:1179-1190. (from Pfam) NF040316.4 PF19565.4 DUF6087 27.1 27.1 99 subfamily Y Y N DUF6087 family protein 16766657 1760 Actinomycetes class 2402 EBI-EMBL Family of unknown function (DUF6087) DUF6087 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a protein from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [1]. [1]. 16766657. Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Yanai K, Murakami T, Bibb M;. Proc Natl Acad Sci U S A. 2006;103:9661-9666. (from Pfam) NF040345.4 PF19679.4 DUF6181 25 25 134 subfamily Y Y N DUF6181 family protein 16766657 1760 Actinomycetes class 158 EBI-EMBL Family of unknown function (DUF6181) DUF6181 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [1]. [1]. 16766657. Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Yanai K, Murakami T, Bibb M;. Proc Natl Acad Sci U S A. 2006;103:9661-9666. (from Pfam) NF040349.4 PF19698.4 DUF6197 28.5 28.5 165 subfamily Y Y N DUF6197 family protein 16766657 1760 Actinomycetes class 454 EBI-EMBL Family of unknown function (DUF6197) DUF6197 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [1]. [1]. 16766657. Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Yanai K, Murakami T, Bibb M;. Proc Natl Acad Sci U S A. 2006;103:9661-9666. (from Pfam) NF040353.4 PF19716.4 DUF6211 25 25 92 subfamily Y Y N DUF6211 family protein 16766657 1760 Actinomycetes class 250 EBI-EMBL Family of unknown function (DUF6211) DUF6211 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [1]. [1]. 16766657. Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Yanai K, Murakami T, Bibb M;. Proc Natl Acad Sci U S A. 2006;103:9661-9666. (from Pfam) NF040358.4 PF19731.4 DUF6222 26.9 26.9 62 subfamily Y Y N DUF6222 family protein 29090939 1760 Actinomycetes class 126 EBI-EMBL Family of unknown function (DUF6222) DUF6222 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001503) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the amycolamycin A biosynthetic gene cluster from Amycolatopsis sp. [1]. [1]. 29090939. Amycolamycins A and B, Two Enediyne-Derived Compounds from a Locust-Associated Actinomycete. Ma SY, Xiao YS, Zhang B, Shao FL, Guo ZK, Zhang JJ, Jiao RH, Sun Y, Xu Q, Tan RX, Ge HM;. Org Lett. 2017;19:6208-6211. (from Pfam) NF040360.4 PF19738.4 DUF6227 25 25 227 subfamily Y Y N DUF6227 family protein 17827660 1760 Actinomycetes class 4733 EBI-EMBL Family of unknown function (DUF6227) DUF6227 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000118) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the pactamycin biosynthetic gene cluster from Streptomyces pactum [1]. This family appears to be predominantly found in Actinobacteria. [1]. 17827660. Cloning of the pactamycin biosynthetic gene cluster and characterization of a crucial glycosyltransferase prior to a unique cyclopentane ring formation. Kudo F, Kasama Y, Hirayama T, Eguchi T;. J Antibiot (Tokyo). 2007;60:492-503. (from Pfam) NF040373.4 PF19816.4 DUF6299 26.8 26.8 114 subfamily Y Y N DUF6299 family protein 25041948 1760 Actinomycetes class 3681 EBI-EMBL Family of unknown function (DUF6299) DUF6299 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000376) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular JBIR-34 biosynthetic gene cluster from Streptomyces sp. Sp080513GE-23 [1]. This family appears to be predominantly found in actinobacteria. [1]. 25041948. Biosynthesis of the 4-methyloxazoline-containing nonribosomal peptides, JBIR-34 and -35, in Streptomyces sp. Sp080513GE-23. Muliandi A, Katsuyama Y, Sone K, Izumikawa M, Moriya T, Hashimoto J, Kozone I, Takagi M, Shin-ya K, Ohnishi Y;. Chem Biol. 2014;21:923-934. (from Pfam) NF040377.4 PF19832.4 DUF6313 25.8 25.8 182 subfamily Y Y N DUF6313 family protein 16766657 1760 Actinomycetes class 627 EBI-EMBL Family of unknown function (DUF6313) DUF6313 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [1]. [1]. 16766657. Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Yanai K, Murakami T, Bibb M;. Proc Natl Acad Sci U S A. 2006;103:9661-9666. (from Pfam) NF040379.4 PF19840.4 DUF6317 27.4 27.4 100 subfamily Y Y N DUF6317 family protein 29324854 1760 Actinomycetes class 469 EBI-EMBL Family of unknown function (DUF6317) DUF6317 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001740) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the phthoxazolin biosynthetic gene cluster from Streptomyces avermitilis [1]. [1]. 29324854. Characterization of the biosynthetic gene cluster for cryptic phthoxazolin A in Streptomyces avermitilis. Suroto DA, Kitani S, Arai M, Ikeda H, Nihira T;. PLoS One. 2018;13:e0190973. (from Pfam) NF040382.4 PF19871.4 DUF6344 35.6 35.6 34 domain Y Y N DUF6344 domain-containing protein 15644894,22435762 1760 Actinomycetes class 4840 EBI-EMBL Family of unknown function (DUF6344) Family of unknown function (DUF6344) This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000843) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular the alanylclavam biosynthetic gene cluster from Streptomyces clavuligerus ATCC 27064 [1,2]. This family appears to be predominantly found in Actinobacteria. [1]. 22435762. A comparison of the clavam biosynthetic gene clusters in Streptomyces antibioticus Tu1718 and Streptomyces clavuligerus. Goomeshi Nobary S, Jensen SE;. Can J Microbiol. 2012;58:413-425. [2]. 15644894. Three unlinked gene clusters are involved in clavam metabolite biosynthesis in Streptomyces clavuligerus. Tahlan K, Park HU, Jensen SE;. Can J Microbiol. 2004;50:803-810. (from Pfam) NF040401.4 PF19934.4 DUF6397 25 25 243 subfamily Y Y N DUF6397 family protein 15574905 1760 Actinomycetes class 6921 EBI-EMBL Family of unknown function (DUF6397) DUF6397 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000406) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the phosphinothricintripeptide biosynthetic gene cluster from Streptomyces viridochromogenes [1]. This family appears to be predominantly found in Actinobacteria. [1]. 15574905. Biosynthetic gene cluster of the herbicide phosphinothricin tripeptide from Streptomyces viridochromogenes Tu494. Schwartz D, Berger S, Heinzelmann E, Muschko K, Welzel K, Wohlleben W;. Appl Environ Microbiol. 2004;70:7093-7102. (from Pfam) NF040402.4 PF19947.4 DUF6409 27.2 27.2 122 subfamily Y Y N DUF6409 family protein 16766657 1760 Actinomycetes class 283 EBI-EMBL Family of unknown function (DUF6409) DUF6409 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [1]. [1]. 16766657. Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Yanai K, Murakami T, Bibb M;. Proc Natl Acad Sci U S A. 2006;103:9661-9666. (from Pfam) NF040407.4 PF19965.4 VMAP-M2 27.7 27.7 214 domain Y N N vWA-MoxR associated protein middle region (VMAP-M) 2 32101166 1760 Actinomycetes class 903 EBI-EMBL vWA-MoxR associated protein middle region (VMAP-M) 2 vWA-MoxR associated protein middle region (VMAP-M) 2 Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. [1]. 32101166. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. Kaur G, Burroughs AM, Iyer LM, Aravind L;. Elife. 2020; [Epub ahead of print] (from Pfam) NF040464.1 SCO3374_fam 110 110 165 subfamily Y Y N SCO3374 family protein 1760 Actinomycetes class 5939 NCBIFAM SCO3374 family protein This HMM describes a family restricted to the genus Streptomyces. The HMM produces scores that are significant, although below the cutoffs set for this model, to about 10 percent of the proteins in the seed alignment of Pfam model PF09250.11, designated "bifunctional DNA primase/polymerase, N-terminal" NF040526.1 SCO0930_lipo 275 275 311 equivalog Y Y N SCO0930 family lipoprotein 12625841 1760 Actinomycetes class 5180 NCBIFAM SCO0930 family lipoprotein Members of this family are full-length homologs to the lipoprotein SCO0930, Streptomyces coelicolor A3(2). SCO0930 contains four copies of the repeat described by Pfam model PF03640. By comparison, PA5359 from Pseudomonas aeruginosa PAO1 has only two copies of the repeat, differs substantially in several regions, and is excluded from this family. NF040555.1 Pro-rich_NTERM 40 40 99 subfamily_domain Y Y N Pro-rich N-terminal domain-containing protein 1760 Actinomycetes class 3377 NCBIFAM AAA family ATPase Pro-rich N-terminal domain This HMM describes an extremely rich N-terminal domain that is well-conserved for a family of AAA family ATPases seen in Streptomyces. The HMM was built to support correct structural annotation of this unusual, low-complexity domain. NF040564.1 SCO2523_fam 200 200 305 equivalog Y Y N SCO2523 family variant P-loop protein 1760 Actinomycetes class 1625 NCBIFAM SCO2523 family variant P-loop protein The family of proteins related to SCO2523 of Streptomyces coelicolor is limited to the Acintobacteria, and part of a conserved gene neighborhood encoding proteins SCO2521-SCO2524. The N-terminal half shows homology to P-loop-containing regions of multiple protein families, but the key motif differs substantially from the P-loop consensus, DKGGTGRS when GxxGxGK[ST] is typical. NF040565.1 SCO2521_fam 150 150 302 equivalog Y Y N SCO2521 family protein 1760 Actinomycetes class 2123 NCBIFAM SCO2521 family protein The family of proteins related to SCO2521 of Streptomyces coelicolor is limited to the Acintobacteria, and part of a conserved gene neighborhood encoding proteins SCO2521-SCO2524. NF040566.1 SCO2522_fam 200 200 314 equivalog Y Y N SCO2522 family protein 1760 Actinomycetes class 2096 NCBIFAM SCO2522 family protein The family of proteins related to SCO2522 of Streptomyces coelicolor is limited to the Acintobacteria, and part of a conserved gene neighborhood encoding proteins SCO2521-SCO2524. NF040567.1 SCO2524_fam 300 300 612 equivalog Y Y N SCO2524 family protein 1760 Actinomycetes class 1934 NCBIFAM SCO2524 family protein The family of proteins related to SCO2524 of Streptomyces coelicolor is limited to the Acintobacteria, and part of a conserved gene neighborhood encoding proteins SCO2521-SCO2524. NF040568.1 SCO2525_fam 240 240 242 equivalog Y Y N SCO2525 family SAM-dependent methyltransferase 15150245 1760 Actinomycetes class 1404 NCBIFAM SCO2525 family SAM-dependent methyltransferase The founding member of this strictly actinobacterial family of class I SAM-dependent methyltransferases, SCO2525, appears to affect development, as inferred by mutant phenotype in Streptomyces coelicolor. SCO2525 belongs to a conserved gene neighborhood that also includes SCO2521-SCO2524. NF040605.2 mycolic_FabG1 420 420 233 exception Y Y N 3-oxoacyl-ACP reductase FabG1 fabG1 GO:0071768 11932442 1760 Actinomycetes class 1219 NCBIFAM 3-oxoacyl-ACP reductase FabG1 NF040607.1 mycolic_Pks13 2100 1500 1680 equivalog Y Y N polyketide synthase Pks13 pks13 GO:0071768 19436070,29072327,29761048 1760 Actinomycetes class 3345 NCBIFAM polyketide synthase Pks13 Pks13 is a key enzyme in mycolic acid biosynthesis. NF040620.1 fused_HadA_HadB 350 350 329 exception Y Y N fused (3R)-hydroxyacyl-ACP dehydratase subunits HadA/HadB GO:0071768 17804795,26104214 1760 Actinomycetes class 2663 NCBIFAM fused (3R)-hydroxyacyl-ACP dehydratase subunits HadA/HadB NF040624.1 HadA 180 180 144 equivalog Y Y N (3R)-hydroxyacyl-ACP dehydratase subunit HadA hadA GO:0071768 17804795,26104214 1760 Actinomycetes class 1561 NCBIFAM (3R)-hydroxyacyl-ACP dehydratase subunit HadA NF040631.2 InhA 430 430 257 exception Y Y N NADH-dependent enoyl-ACP reductase InhA inhA GO:0071768 10336454,10521269,10708367 1760 Actinomycetes class 1196 NCBIFAM NADH-dependent enoyl-ACP reductase InhA NF040636.1 AcpM 146 146 93 exception Y Y N meromycolate extension acyl carrier protein AcpM acpM GO:0071768 11373295,11825906,9694888 1760 Actinomycetes class 781 NCBIFAM meromycolate extension acyl carrier protein AcpM NF040672.1 SCO2322_fam 85 85 144 subfamily Y Y N SCO2322 family protein 1760 Actinomycetes class 7233 NCBIFAM SCO2322 family protein NF040681.1 GPS-CTERM 31 31 30 domain Y Y N GPS-CTERM domain-containing protein 1760 Actinomycetes class 6190 NCBIFAM GPS-CTERM domain The GPS-CTERM domain, defined by this HMM, is found in Actinobacteria such as Nocardia and Streptomyces, at the C-terminus of at least two otherwise unrelated protein families. It is an apparent novel protein-sorting domain. NF040690.1 mycolate_SDR 380 380 265 equivalog Y Y N mycolate reductase cmrA 1.1.1.- GO:0071768 17308303,18804030,31785114 1760 Actinomycetes class 2163 NCBIFAM mycolate reductase Catalyzes the final step in mycolic acid biosynthesis. Catalyzes the final step in mycolic acid biosynthesis. NF040714.1 streptamidine 40 40 28 equivalog Y Y N streptamidine family RiPP amiA 34659714 1760 Actinomycetes class 408 NCBIFAM streptamidine family RiPP Streptamidine is a ribosomally translated, post-translationally modified peptide (RiPP) whose modification depends on a YcaO family maturase. The mature product derives from the central hexapeptide HLSATH, or a similar peptide. See related model NF040715 for a similar family in which a related RiPP precursor domain occurs typically in two or more tandem repeats. NF040715.1 AmiA_rel_RiPP2x 45 45 35 subfamily Y Y N streptamidine-related RiPP repeat protein 34659714 1760 Actinomycetes class 95 NCBIFAM streptamidine-related RiPP repeat This HMM represents a family of streptamidine-related RiPP precursor proteins, most of which have two or more repeats of the 35 amino-acid long domain that contains the modification site. Modification is performed by a YcaO family peptide maturase. The related model NF040714 describes the family of RiPP precursor proteins that includes streptamidine (AmiA) itself and close homologs. While in the streptamidine precursor AmiA itself and its homologs, the core peptide is HLSATH or something similar, the six residues from this family that align are typically APQGPG, suggesting a very different mature product. NF040912.1 SGM_5486_fam 35 35 37 subfamily Y Y N SGM_5486 family transporter-associated protein 1760 Actinomycetes class 1987 NCBIFAM SGM_5486 family transporter-associated protein Members of this family, found in the genus Streptomyces, regularly are found encoded next to an MFS transporter gene. Proteins average about 40 amino acids in length, with the last 25 extremely hydrophobic. NF040918.1 LPFR_fam 40 40 35 subfamily Y Y N LPFR motif small protein 1760 Actinomycetes class 1426 NCBIFAM LPFR motif small protein This HMM describes an uncharacterized small, hydrophobic protein that is widespread in the genus Streptomyces. Multiple sequence alignment shows a well-conserved start site, patterns of conservative substitution of amino acids, and a best-conserved motif VTLPFRxxARLF. Coding regions for this protein have been systematically underreported previously because of small size, often less than 45 amino acids, and the lack of supporting evidence such as this HMM. NF041021.1 SCO5717_Nterm 35 35 48 equivalog_domain Y Y N SCO5717 family growth-regulating ATPase 19470379 1760 Actinomycetes class 8064 NCBIFAM SCO5717 family growth-regulating ATPase N-terminal domain Members of this unusual protein family have a short domain described by this HMM at the N-terminus, then (typically) a long, low-complexity, typically Pro-rich region, then a AAA+ family ATPase domain, and then another region of low-complexity sequence. NF041169.1 f2_encap_cargo4 450 450 334 exception Y Y N family 2 encapsulin nanocompartment cargo protein polyprenyl transferase GO:0008299,GO:0140737 34362927 1760 Actinomycetes class 6295 NCBIFAM family 2 encapsulin nanocompartment cargo protein polyprenyl transferase NF041258.1 motor_HelR_2 1100 1100 713 exception Y Y N RNA polymerase recycling motor ATPase HelR helR 34964291 1760 Actinomycetes class 1643 NCBIFAM RNA polymerase recycling motor ATPase HelR group 2 This HMM describes the second of at least two "HelR" subclasses of the RNA polymerase recycling motor protein HelD for which at least a few members have genes preceded by a Rifamycin Associated Element (RAE) and are known or predicted to be induced by rifampicin, a rifamycin-type antibiotic. HelD proteins, including HelR, are helicase-like motor proteins that play a role in transcription, removing and recycling stalled transcription complexes that could interfere with normal transcription or with DNA replication. NF041273.1 GlcN_kinase 550 550 391 equivalog Y Y N glucosamine kinase GO:0005975,GO:0047931 31088917 1760 Actinomycetes class 130 NCBIFAM glucosamine kinase NF041280.1 mem_Micro_34 37.5 37.5 34 equivalog Y Y N small membrane protein MtfM mtfM 1760 Actinomycetes class 181 NCBIFAM small membrane protein MtfM Members of this family are typically 34 amino acids in length, consisting largely of one highly hydrophobic predicted transmembrane segment. Many are from the genera Micromonospora and Actinoplanes. Note that many annotation pipelines are unable to predict a bacterial protein this small without supporting homology evidence as from this HMM. We suggest the symbol MtfM (Membrane protein of length Thirty-Four from Micromonospora). NF041413.1 ArsR_Rv2640c_fam 155 155 118 equivalog Y Y N Rv2640c family ArsR-like transcriptional regulator 1760 Actinomycetes class 1200 NCBIFAM Rv2640c family ArsR-like transcriptional regulator Mycobacterium tuberculosis has several ArsR-related transcriptional regulators, including Rv2640c, a member of this family, and Rv2642, encoded nearby. Members of the Rv2640c family have two invariant CC motifs, one at (or a single amino acid away from) the C-terminus. NF041465.1 HelD_MYCSM 1051 1051 719 equivalog Y Y N RNA polymerase recycling motor HelD helD 33339823 1760 Actinomycetes class 1647 NCBIFAM RNA polymerase recycling motor HelD (Actinomycetota-type) NF041480.1 flag_mot_ctl_ZomB 410 410 641 equivalog Y Y N flagellar motor control protein ZomB zomB 29995998 1760 Actinomycetes class 2395 NCBIFAM flagellar motor control protein ZomB NF041482.1 ADPrt_Strmyces 250 250 208 equivalog Y Y N ADP-ribosyltransferase 22752904 1760 Actinomycetes class 1376 NCBIFAM ADP-ribosyltransferase NF041483.1 growth_prot_Scy 1040 1040 1293 equivalog Y Y N polarized growth protein Scy scy 23297235,23536551 1760 Actinomycetes class 6897 NCBIFAM polarized growth protein Scy NF041509.1 paralog_Rho2 628 628 360 exception Y Y N transcription termination factor Rho, short form 1760 Actinomycetes class 184 NCBIFAM transcription termination factor Rho, short form In genera such as Nocardia, Amycolatopsis, and Kutzneria, members of this family appear as a shorter second paralog of transcription termination factor Rho NF041510.1 AMED_5909_fam 35 35 69 subfamily Y Y N AMED_5909 family protein 1760 Actinomycetes class 502 NCBIFAM AMED_5909 family protein Most members of this family of uncharacterized proteins are about 80 amino acids in length, and are found in members of the Actinomycetota, such as the genera Amycolatopsis, Lentzea, Pseudonocardiales, Saccharomonospora, and Saccharothrix. The family is named for one of its members, AMED_5909 from Amycolatopsis mediterranei (ADJ47652). NF041527.1 SCO1860_LAETG 200 200 306 equivalog Y Y N SCO1860 family LAETG-anchored protein 22347508 1760 Actinomycetes class 6488 NCBIFAM SCO1860 family LAETG-anchored protein Members of this poorly characterized family, including SCO1860 from Streptomyces coelicolor, are surface proteins whose C-terminus contains a variant type sortase recognition and cleavage sorting signal. The sorting signal motif, LAETG, is compatible with processing by a SrtE family sortase enzyme. NF041528.1 strep_LAETG 30 30 35 domain Y Y N LAETG motif-containing sortase-dependent surface protein 31155711 1760 Actinomycetes class 30940 NCBIFAM LAETG motif sortase-processing domain This HMM describes a Streptomyces-specific variant of the widespread LPXTG motif-containing sortase recognition and processing domain. NF041565.1 selin_dien_syn 450 450 345 equivalog Y Y N selina-4(15),7(11)-diene synthase 4.2.3.181 GO:0000287,GO:0010333,GO:0016114 23307484,24890698 1760 Actinomycetes class 416 NCBIFAM selina-4(15),7(11)-diene synthase NF041573.1 rhamnosid_Stmyc 1720 1720 1028 equivalog Y Y N alpha-L-rhamnosidase 3.2.1.40 GO:0005975,GO:0030596 23291751 1760 Actinomycetes class 1950 NCBIFAM alpha-L-rhamnosidase NF041584.1 MqnP_SCO4491 420 420 285 exception Y Y N menaquinone biosynthesis prenyltransferase MqnP mqnP 30447488 1760 Actinomycetes class 6164 NCBIFAM menaquinone biosynthesis prenyltransferase MqnP, SCO4491 family This model is one of three built to describe UbiA-like prenyltransferases thought to be menaquinone biosynthesis prenyltransferase MqnP. This family contains the founding protein SCO4491. NF041588.1 AQJ64_40280_fam 70 70 116 hypoth_equivalog Y Y N AQJ64_40280 family protein 1760 Actinomycetes class 683 NCBIFAM AQJ64_40280 family protein Members of this family occur almost exclusively in the genus Streptomyces. The function is unknown. Some members, such as AQJ64_40280 (KUN75916.1) for which we name the family, previously were annotated as amine oxidase, but the source of that annotation could not be traced during model construction. NF041673.1 transregRamA 500 500 280 equivalog Y Y N acetate metabolism transcriptional regulator RamA ramA GO:0003677,GO:0006083,GO:0006355 16547043,18355281,19095019 1760 Actinomycetes class 375 NCBIFAM acetate metabolism transcriptional regulator RamA NF041717.1 HaaA_phane_TPR 1125 1125 882 equivalog Y Y N cyclophane-containing RiPP biosynthesis TPR protein HaaT haaT 35729768 1760 Actinomycetes class 414 NCBIFAM cyclophane-containing RiPP biosynthesis TPR protein HaaT Members of this family are tetratricopeptide repeat (TPR) proteins with multiple TPR repeats. Members appear to occur strictly as part of biosynthetic gene clusters (BGC) for the production of cyclophane-containing RiPP peptides in which the predicted cyclized tripeptide is HAA (see NF041708 for the precursor peptide). The composition of the BGC is similar to that of FxSxx-COOH family cyclophane-containing RiPP peptides. NF041721.1 phane_AmcA_1 40 40 54 equivalog Y Y N multiple cyclophane-containing RiPP AmcA amcA 36454686 1760 Actinomycetes class 676 NCBIFAM Actinobacterial multiple cyclophane triceptide AmcA, group 1 Members of this family belong to one of several classes of peptide natural product synthesized on the ribosome and then post-translationally modified (RiPP), where the modfication begins with the Actinobacterial multiple cyclophane-forming radical SAM peptide maturase AmcB (NF041718). NF041722.1 phane_AmcA_3a 65 65 58 equivalog Y Y N multiple cyclophane-containing RiPP AmcA amcA 36454686 1760 Actinomycetes class 574 NCBIFAM Actinobacterial multiple cyclophane triceptide AmcA, group 3a Members of this family belong to one of several classes of peptide natural product synthesized on the ribosome and then post-translationally modified (RiPP), where the modfication begins with the Actinobacterial multiple cyclophane-forming radical SAM peptide maturase AmcB (NF041718). NF041725.1 phane_AmcA_5 40 40 55 equivalog Y Y N multiple cyclophane-containing RiPP AmcA amcA 36454686 1760 Actinomycetes class 341 NCBIFAM Actinobacterial multiple cyclophane triceptide AmcA, group 5 Members of this family belong to one of several classes of peptide natural product synthesized on the ribosome and then post-translationally modified (RiPP), where the modfication begins with the Actinobacterial multiple cyclophane-forming radical SAM peptide maturase AmcB (NF041718). NF041732.1 hist_kin_CseC 700 700 424 equivalog Y Y N two-component system sensor histidine kinase CseC cseC 2.7.13.3 GO:0000155,GO:0005524 10411727,12068806 1760 Actinomycetes class 4781 NCBIFAM two-component system sensor histidine kinase CseC NF041733.1 resp_reg_CseB 350 350 228 equivalog Y Y N two-component system response regulator CseB cseB GO:0000156,GO:0000976,GO:0006355 10411727,12068806 1760 Actinomycetes class 6214 NCBIFAM two-component system response regulator CseB NF041805.1 daptide_Mpa1 40 40 44 equivalog Y Y N MpaA1 family daptide-type RiPP mpaA1 36959188 1760 Actinomycetes class 79 NCBIFAM MpaA1 family daptide-type RiPP Daptides are RiPPs (ribosomally synthesized and post-translationally modified peptide natural products) that feature an unusual conversion of the C-terminal Thr residue to the daptide signature (S)-N2,N2-dimethyl-1,2-propanediamine (Dmp) moiety. Sequential motifications to create the Dmp are catalyzed by a an oxidative decarboxylase, an aminotransferase, and a methyltransferase. The founding member of this family, from Microbacterium paraoxydans DSM 15019 (mpa), is designated MpaA1. NF041806.1 daptide_Mpa2 40 40 41 equivalog Y Y N MpaA2 family daptide-type RiPP mpaA2 36959188 1760 Actinomycetes class 67 NCBIFAM MpaA2 family daptide-type RiPP Daptides are RiPPs (ribosomally synthesized and post-translationally modified peptide natural products) that feature an unusual conversion of the C-terminal Thr residue to the daptide signature (S)-N2,N2-dimethyl-1,2-propanediamine (Dmp) moiety. Sequential motifications to create the Dmp are catalyzed by a an oxidative decarboxylase, an aminotransferase, and a methyltransferase. The founding member of this family, from Microbacterium paraoxydans DSM 15019 (mpa), is designated MpaA2. NF041822.1 daptide_DH 300 300 363 equivalog Y Y N daptide-type RiPP biosynthesis dehydogenase mpaC 36959188 1760 Actinomycetes class 669 NCBIFAM daptide-type RiPP biosynthesis dehydogenase Members of this family are the dehydrogenase, or C protein, of Actinomycetota-type daptide biosynthesis operons. Bacillota-type counterparts are not found by this model. The gene symbol mpaC is based on the system prototype from Microbacterium paraoxydans DSM 15019 (mpa). NF041851.1 cyc_nuc_deg_phdiest 400 400 253 equivalog Y Y N cyclic nucleotide-degrading phosphodiesterase 36760076 1760 Actinomycetes class 1336 NCBIFAM cyclic nucleotide-degrading phosphodiesterase NF042451.3 PF20177.3 DUF6542 27 27 123 domain Y Y N DUF6542 domain-containing protein 1760 Actinomycetes class 11824 EBI-EMBL Domain of unknown function (DUF6542) Domain of unknown function (DUF6542) This entry represents an integral membrane domain composed of four predicted transmembrane helices. The function of this region is unknown. (from Pfam) NF042457.3 PF20211.3 DUF6571 27 27 729 subfamily Y Y N DUF6571 family protein 1760 Actinomycetes class 2483 EBI-EMBL Family of unknown function (DUF6571) DUF6571 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in Actinobacteria. Proteins in this family are typically between 547 and 730 amino acids in length. (from Pfam) NF042470.3 PF20271.3 CATASP 29 29 86 hypoth_equivalog Y Y N CATRA system-associated protein 32868406 1760 Actinomycetes class 995 EBI-EMBL CATRA-Associated Small Protein CATRA system-associated protein Small, rapidly-evolving domain predicted to possess a compact, four-helix structure. Along with a gene encoding a TPR repeat region fused to a CASPASE domain and a gene encoding the CATRA module (CATRA-N+CATRA-C) C-terminally fused to a diverse range of conflict effector domains, forms the three gene island making up the CATRA conflict systems. Plays a possible inhibitory role in the CATRA system which is relieved upon sensing of an invasive molecule or is directly cleaved by the CASPASE domain. [1]. 32868406. Identification of Uncharacterized Components of Prokaryotic Immune Systems and Their Diverse Eukaryotic Reformulations. Burroughs AM, Aravind L;. J Bacteriol. 2020; [Epub ahead of print] (from Pfam) NF042653.3 PF20269.3 CATRA-N 27 27 203 equivalog_domain Y Y N CATRA conflict system CASPASE/TPR repeat-associated protein 32868406 1760 Actinomycetes class 1124 EBI-EMBL CASPASE and TPR Repeat-Associated N-terminal domain CASPASE and TPR Repeat-Associated N-terminal domain One of two constant domains forming the CATRA module which is in turn C-terminally fused to a diverse range of conflict effector domains. This gene, along with a gene encoding the CATASP domain and a gene encoding a TPR repeat region fused to a CASPASE domain, forms the three gene island making up the CATRA conflict systems. This alpha/beta domain is predicted to be involved in recognition of invasive molecules or in the transmitting of a signal through conformational change, enabling CASPASE-mediated proteolysis to free the fused effector domains. [1]. 32868406. Identification of Uncharacterized Components of Prokaryotic Immune Systems and Their Diverse Eukaryotic Reformulations. Burroughs AM, Aravind L;. J Bacteriol. 2020; [Epub ahead of print] (from Pfam) NF042676.3 PF20348.3 DUF6643 27 27 150 subfamily Y Y N DUF6643 family protein 1760 Actinomycetes class 4392 EBI-EMBL Family of unknown function (DUF6643) DUF6643 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 144 and 171 amino acids in length. (from Pfam) NF042829.3 PF20550.3 DUF6764 27 27 164 subfamily Y Y N DUF6764 family protein 1760 Actinomycetes class 1051 EBI-EMBL Family of unknown function (DUF6764) DUF6764 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically 165 and 195 amino acids in length. (from Pfam) NF042880.3 PF20486.3 DUF6725 27 27 83 subfamily Y Y N DUF6725 family protein 1760 Actinomycetes class 411 EBI-EMBL Family of unknown function (DUF6725) DUF6725 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. (from Pfam) NF042893.3 PF20544.3 DUF6758 27 27 208 subfamily Y Y N DUF6758 family protein 1760 Actinomycetes class 5838 EBI-EMBL Family of unknown function (DUF6758) DUF6758 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 215 amino acids in length. (from Pfam) NF042914.1 SAV915_dom 40 40 58 domain Y Y N SAV_915 family protein 25822496,31409675 1760 Actinomycetes class 6041 NCBIFAM SAV_915 family protein Members of this family of uncharacterized proteins from include SAV_915 from the paulomycin biosynthetic gene cluster (BGC) of Streptomyces paulus, FevO from the iron chelator ferroverdin BGC, and WP_122618374.1 from a bagremycin antibiotic BGC. Some members of this family have two separated copies of the domain. NF042918.1 PAGG_Syn_BesB 800 800 491 equivalog Y Y N L-2-amino-4-chloropent-4-enoate dechlorinase/desaturase BesB besB 4.5.1.- GO:0062142,GO:0062143,GO:0062144 30867596 1760 Actinomycetes class 64 NCBIFAM L-2-amino-4-chloropent-4-enoate dechlorinase/desaturase BesB NF042919.1 ChlAlygly_Syn_BesC 500 500 257 equivalog Y Y N 4-chloro-allylglycine synthase BesC besC 1.14.99.- GO:0062142,GO:0062143,GO:0062146 30867596 1760 Actinomycetes class 43 NCBIFAM 4-chloro-allylglycine synthase BesC NF042920.1 Lys_halognase_BesD 450 450 229 equivalog Y Y N L-lysine 4-chlorinase BesD besD 1.14.20.- GO:0062142,GO:0062143,GO:0062147 30867596 1760 Actinomycetes class 51 NCBIFAM L-lysine 4-chlorinase BesD NF042933.1 leader_Ms5788A 45 45 27 equivalog Y Y N Ms5788A family Cys-rich leader peptide 32181921 1760 Actinomycetes class 560 NCBIFAM Ms5788A family Cys-rich leader peptide Found members of this family are apparent leader peptides, that is, cis-regulatory features whose ability to be translated on the ribosome into peptide controls whether or not the translation of downstream proteins occurs. NF042936.1 leader_Ms4527A 45 45 21 exception Y Y N Ms4527A family Cys-rich leader peptide 32181921 1760 Actinomycetes class 352 NCBIFAM Ms4527A family Cys-rich leader peptide NF042937.1 leader_Ms4533A 31 31 30 equivalog Y Y N Ms4533A family Cys-rich leader peptide 32181921 1760 Actinomycetes class 1464 NCBIFAM Ms4533A family Cys-rich leader peptide Ms4533A belongs to a recently class of small peptides in various Actinobacteria, generally Cys-rich at the C-terminus, whose rate of translation and then translational termination controls whether or not transcription of various mRNAs for sulfur metabolism operons will continue. NF042988.1 Erm46 503 503 255 exception Y Y Y 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(46) erm(46) 26377866 1760 Actinomycetes class 17 NCBIFAM 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(46) Erm(46), a 23S RNA-modifying enzyme, confers high-level resistance to macrolides, lincosamides and streptogramins B, including Azithromycin, Clarithromycin, Erythromycin, Tildipirosin, Gamithromycin, Clindamycin, and Virginiamycin S. NF042989.1 AldDh_AldH_Clos 800 800 458 equivalog Y Y N aldehyde dehydrogenase AldH aldh 1.2.1.3,1.2.1.4 GO:0004030,GO:0042843 23063486 1760 Actinomycetes class 62 NCBIFAM aldehyde dehydrogenase AldH NF043016.1 DigluglyOctase 250 250 224 equivalog Y Y N diglucosylglycerate octanoyltransferase octT 2.3.1.273 GO:0016414 26324178 1760 Actinomycetes class 2136 NCBIFAM diglucosylglycerate octanoyltransferase NF044639.2 PF20859.2 RHA1_ro05818_N 27 27 58 domain Y N N Hypothetical protein RHA1_ro05818, N-terminal helical domain 23024343 1760 Actinomycetes class 629 EBI-EMBL Hypothetical protein RHA1_ro05818, N-terminal helical domain Hypothetical protein RHA1_ro05818, N-terminal helical domain This domain is found at the N terminus of Hypothetical protein RHA1_ro05818 from Rhodococcus jostii (Swiss:Q0S4E1). This protein is thought to be a thioesterase involved in the metabolism of cholate [1]. This protein has a 4HBT domain (Pfam:PF03061) at the C-terminal. The N-terminal domain shows an helical fold. [1]. 23024343. Gene cluster encoding cholate catabolism in Rhodococcus spp. Mohn WW, Wilbrink MH, Casabon I, Stewart GR, Liu J, van der Geize R, Eltis LD;. J Bacteriol. 2012;194:6712-6719. (from Pfam) NF044662.2 PF20947.2 Flu_PB2_1st 27 27 36 domain Y N N Influenza RNA polymerase PB2 N-terminal region 26503046,8806170 1760 Actinomycetes class 3 EBI-EMBL Influenza RNA polymerase PB2 N-terminal region Influenza RNA polymerase PB2 N-terminal region Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding [1] and endonuclease domains required for transcription initiation by cap-snatching [2]. This entry represents the N-terminal extended region of Flu PB2 protein, which is the N-terminal PB1 interaction domain. [1]. 8806170. Recombinant-baculovirus-expressed PB2 subunit of the influenza A virus RNA polymerase binds cap groups as an isolated subunit. Shi L, Galarza JM, Summers DF;. Virus Res 1996;42:1-9. [2]. 26503046. Crystal structure of the RNA-dependent RNA polymerase from influenza C virus. Hengrung N, El Omari K, Serna Martin I, Vreede FT, Cusack S, Rambo RP, Vonrhein C, Bricogne G, Stuart DI, Grimes JM, Fodor E;. Nature. 2015;527:114-117. (from Pfam) NF044842.2 PF21666.2 DUF4246_N 27.4 27.4 75 domain Y N N Domain of unknown function DUF4246, N-terminal 1760 Actinomycetes class 2364 EBI-EMBL Domain of unknown function DUF4246, N-terminal Domain of unknown function DUF4246, N-terminal This presumed domain is found N-terminal of Pfam:PF14033) which may consist of four helices. (from Pfam) NF045279.2 PF21043.2 Rv3651-like_C 31.1 31.1 118 domain Y N N Rv3651-like, C-terminal domain 29119630 1760 Actinomycetes class 1642 EBI-EMBL Rv3651-like, C-terminal domain Rv3651-like, C-terminal domain This domain is found in Rv3651 from Mycobacterium tuberculosis (Swiss: I6YCP0) and similar proteins from Actinobacteria. Rv3651 adopts a three-domain configuration. This entry represents the C-terminal domain, a PAS domain that shows a central antiparallel beta-sheet of five beta-strands [1]. [1]. 29119630. Mycobacterium tuberculosis Rv3651 is a triple sensor-domain protein. Abendroth J, Frando A, Phan IQ, Staker BL, Myler PJ, Edwards TE, Grundner C;. Protein Sci. 2018;27:568-572. (from Pfam) NF045483.1 IsozizSyn 675 675 361 equivalog Y Y N epi-isozizaene synthase cyc1 4.2.3.37 GO:0052680 16669656 1760 Actinomycetes class 2474 NCBIFAM epi-isozizaene synthase NF045516.1 GlpR 120 120 330 equivalog Y Y N gephyrin-like molybdotransferase receptor GlpR glpR GO:1990586 37679597 1760 Actinomycetes class 9227 NCBIFAM gephyrin-like molybdotransferase receptor GlpR Eukaryotic gephyrin-like molybdotransferase Glp and its membrane receptor GlpR bind to FtsZ and Wag31 to form a tight protein complex, which plays an important role in divisome-elongasome transition during cytokinesis in Corynebacteriales. NF045554.1 AmiPhnlOxPhsA 950 950 581 equivalog Y Y N O-aminophenol oxidase PhsA phsA 1.10.3.4 GO:0005507,GO:0017000,GO:0050149 10770769,19268377 1760 Actinomycetes class 1086 NCBIFAM O-aminophenol oxidase PhsA NF045558.1 StsA_sacti_RiPP 42 42 38 equivalog Y Y N StsA family sactipeptide RiPP stsA 37363077 1760 Actinomycetes class 37 NCBIFAM StsA family sactipeptide RiPP Members of this family are encoded next to the radical SAM enzyme StsB, average about 40 amino acids in length. Maturation involves the introduction of three sulfur-to-alpha carbon thioether (sactionine) crosslinks, from the Cys residues in the motif CxCxC to glycines in a nearby motif GxGxG that runs antiparallel in a hairpin structure. NF045559.1 sacti_RiPP_CxC 75 75 87 equivalog Y Y N StsA-related sactipeptide RiPP 37363077 1760 Actinomycetes class 97 NCBIFAM StsA-related sactipeptide RiPP The members of this family are more than twice as long as the sactipeptide StsA, but the C-terminal region resembles StsA. However, members of this family have only two Cys side-chains cross-linked through the sulfur atom to the alpha carbons of Gly residues, as compared to three in StsA. Post-translation modification is performed by a radical SAM enzyme similar to StsB. NF045603.1 diiron_AurF 620 620 334 exception Y Y N 4-aminobenzoate N-oxygenase 1.14.99.68 17763486,18458342 1760 Actinomycetes class 45 NCBIFAM 4-aminobenzoate N-oxygenase AurF and NorF are examples of closely related di-iron oxygenases encoded in polyketide synthase-type biosynthetic gene clusters that produce aureothin and neoaureothin, respectively. Both are 4-aminobenzoate N-oxygenase (EC 1.14.99.68) enzymes. NF045629.1 monooxsub_HsaA 450 450 383 equivalog Y Y N 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygenase oxygenase subunit hsaA 1.14.14.12 GO:0009056,GO:0016042,GO:0036383 17264217,20448045 1760 Actinomycetes class 3730 NCBIFAM 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygenase oxygenase subunit NF045630.1 monooxsub_HsaB 230 230 186 equivalog Y Y N 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygenase reductase subunit hsaB 1.5.1.36 GO:0009056,GO:0016042,GO:0036382 17264217,20448045 1760 Actinomycetes class 1853 NCBIFAM 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygenase reductase subunit NF045631.1 exdiol_diox_HsaC 450 450 296 equivalog Y Y N iron-dependent extradiol dioxygenase HsaC hsaC bphC 1.13.11.25 GO:0009056,GO:0016042,GO:0047071 16233225,17264217,19300498 1760 Actinomycetes class 2010 NCBIFAM iron-dependent extradiol dioxygenase HsaC NF045632.1 hydroxlase_HsaD 400 400 290 equivalog Y Y N 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase hsaD bphD 3.7.1.17,3.7.1.8 GO:0009056,GO:0016042,GO:0102296 16233225,17264217,18097091,19875455 1760 Actinomycetes class 2324 NCBIFAM 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase NF045652.1 ProlPCPDhRedW 650 650 376 equivalog Y Y N L-prolyl-[peptidyl-carrier protein] dehydrogenase redW 1.3.8.14 GO:0003995,GO:0033539,GO:0050660 11514230,11880032 1760 Actinomycetes class 256 NCBIFAM L-prolyl-[peptidyl-carrier protein] dehydrogenase NF045684.1 tet_MFS_65 800 800 383 exception Y Y Y tetracycline efflux MFS transporter Tet(65) tet(65) GO:0008493,GO:0015904 38497972 1760 Actinomycetes class 10 NCBIFAM tetracycline efflux MFS transporter Tet(65) NF045736.1 PaDhStyDRhodo 800 800 479 equivalog Y Y N phenylacetaldehyde dehydrogenase StyD styD 1.2.1.39 GO:0008957,GO:0042207 25187627,9172343 1760 Actinomycetes class 246 NCBIFAM phenylacetaldehyde dehydrogenase StyD NF045811.1 PentlnSynPtlA 675 675 336 equivalog Y Y N pentalenene synthase ptlA penA,pntA 4.2.3.7 GO:0017000,GO:0050467 16681390,21284395,8180213,9295272 1760 Actinomycetes class 139 NCBIFAM pentalenene synthase NF045812.1 PentlenOxigase 800 800 444 equivalog Y Y N pentalenene oxygenase ptlI penI,pntI 1.14.15.32 GO:0004497,GO:0016705,GO:0017000,GO:0050467 17017767,21250661,21284395 1760 Actinomycetes class 170 NCBIFAM pentalenene oxygenase NF045813.1 DxPntBtaHylase 550 550 285 equivalog Y Y N 1-deoxypentalenic acid 11-beta-hydroxylase ptlH penH,pntH 1.14.11.35 GO:0017000,GO:0051213 16704250,21250661,21284395 1760 Actinomycetes class 144 NCBIFAM 1-deoxypentalenic acid 11-beta-hydroxylase NF045814.1 HdxpentlteDhPtlF 450 450 247 equivalog Y Y N 1-deoxy-11-beta-hydroxypentalenate dehydrogenase ptlF penF,pntF 1.1.1.340 GO:0016491,GO:0016616,GO:0017000 17178094,21250661,21284395 1760 Actinomycetes class 151 NCBIFAM 1-deoxy-11-beta-hydroxypentalenate dehydrogenase NF045815.1 Neo-PentlctneFsynPtlD 550 550 301 equivalog Y Y N neopentalenolactone/pentalenolactone F synthase ptlD penD,pntD 1.14.11.-,1.14.11.36 GO:0016706,GO:0017000 21250661,21284395 1760 Actinomycetes class 145 NCBIFAM neopentalenolactone/pentalenolactone F synthase NF045816.1 PentlenlactSyn 700 700 396 equivalog Y Y N pentalenolactone synthase penM pntM 1.14.19.8 GO:0004497,GO:0016636,GO:0017000 21284395 1760 Actinomycetes class 114 NCBIFAM pentalenolactone synthase NF045818.1 Neo-PentlctneDsynPtlE 1100 1100 587 equivalog Y Y N neopentalenolactone/pentalenolactone D synthase ptlE penE,pntE 1.14.13.170,1.14.13.171 GO:0016709,GO:0017000 21250661,21284395 1760 Actinomycetes class 170 NCBIFAM neopentalenolactone/pentalenolactone D synthase NF045898.1 ArgS_rel_codon 340 190 327 equivalog Y Y N ArgS-related anticodon-binding protein NrtL nrtL 1760 Actinomycetes class 7122 NCBIFAM ArgS-related anticodon-binding protein NrtL NrtL (Not aRginine tRNA Ligase), named here and still uncharacterized, is a paralog of arginine--tRNA ligase. It is widespread in the genus Streptomyces but rare outside of it. NF046068.1 AkvoneHdxseDnrF 650 650 439 equivalog Y Y N aklavinone 12-hydroxylase DnrF dnrF 1.14.13.180 GO:0017000,GO:0071949 7773378,7961477 1760 Actinomycetes class 308 NCBIFAM aklavinone 12-hydroxylase DnrF NF046069.1 AkvoneHdxseRdmE 700 700 521 equivalog Y Y N aklavinone 12-hydroxylase RdmE rdmE 1.14.13.180 GO:0017000,GO:0071949 10082933,19744497,7751313 1760 Actinomycetes class 349 NCBIFAM aklavinone 12-hydroxylase RdmE NF046120.1 lipo_SCO0607 80 80 86 equivalog Y Y N SCO0607 family lipoprotein 30530707 1760 Actinomycetes class 1632 NCBIFAM SCO0607 family lipoprotein The lipoprotein SCO0607 of Streptomyces coelicolor, along with a number of morphogenic membrane proteins, is regulated by the response regulator transcription factor MarR (SCO2120). Related lipoproteins are found in a large number of Streptomyces species NF046121.1 lipo_SCO7460 300 300 326 subfamily Y Y N SCO7460 family lipoprotein 30530707 1760 Actinomycetes class 824 NCBIFAM SCO7460 family lipoprotein NF046122.1 morpho_MmpA 32 32 47 equivalog Y Y N morphogenic membrane protein MmpA mmpA 30530707 1760 Actinomycetes class 1779 NCBIFAM morphogenic membrane protein MmpA NF046665.1 PF22447.1 EEP_ig-like 26 26 105 domain Y Y N ig-like domain-containing protein 1760 Actinomycetes class 15 EBI-EMBL Endonuclease/exonuclease/phosphatase family, ig-like domain ig-like domain-containing protein This entry corresponds to the C-terminal immunoglobulin-like domain of a putative endonuclease/exonuclease/phosphatase from Beutenbergia cavernae (PDB:4ruw). (from Pfam) NF046857.1 PF22554.1 Chap-C 27 27 91 domain Y N N TY-Chap C-terminal domain 36146784,36968434 1760 Actinomycetes class 963 EBI-EMBL TY-Chap C-terminal domain TY-Chap C-terminal domain This entry represents a domain observed in host systems predicted to counter the action of viral ribosylating toxins. It is found C-terminal to the TY-Chap1 (Pfam:PF22551) and TY-Chap3 (Pfam:PF22552) domains [1,2]. [1]. 36146784. Apprehending the NAD(+)-ADPr-Dependent Systems in the Virus World. Iyer LM, Burroughs AM, Anantharaman V, Aravind L;. Viruses. 2022;14:1977. [2]. 36968434. Separating Inner and Outer Membranes of Escherichia coli by EDTA-free Sucrose Gradient Centrifugation. Shu S, Mi W;. Bio Protoc. 2023;13:e4638. (from Pfam) NF047320.1 morpho_MmpB 34 34 39 equivalog Y Y N morphogenic membrane protein MmpB mmpB 30530707 1760 Actinomycetes class 2513 NCBIFAM morphogenic membrane protein MmpB NF047322.1 HK_morpho_MacS 300 300 367 equivalog Y Y N MacS family sensor histidine kinase macS GO:0004673,GO:0007165 30530707 1760 Actinomycetes class 10327 NCBIFAM MacS family sensor histidine kinase Members of this family are histidine kinases with an amino-terminal DUF5931 (PF19354) domain. The family occurs in the Actinomycetes, including the genera Streptomyces, Micromonospora, Nocardia, Mycobacterium, etc. The best described example is MacS from Streptomyces coelicolor, a partner to the response regulator MacR, which directly regulates a number of morphogenic membrane proteins and indirectly regulates the biosynthesis of some secondary metabolites. Because members of this family appear limited to one per proteome, and the relationship to the response regulator is expected to be conserved, this family is designated equivalog-level, and the gene symbol macS is assigned to all members. NF047334.1 modulat_TrpM 50 50 43 equivalog Y Y N tryptophan biosynthesis modulator TrpM trpM trpX 10361288,27669158,32140146 1760 Actinomycetes class 3599 NCBIFAM tryptophan biosynthesis modulator TrpM TrpM (tryptophan biosynthesis modulator) is a predicted small protein encoded between trpC and trpB in many Streptomyces genomes. NF047431.1 hiber_recruit 375 375 402 equivalog Y Y N ribosome hibernation factor-recruiting GTPase MRF mrf 30038002 1760 Actinomycetes class 2233 NCBIFAM ribosome hibernation factor-recruiting GTPase MRF NF047631.1 SodCMycob 230 230 236 equivalog Y Y N superoxide dismutase[Cu-Zn] sodC 1.15.1.1 GO:0004784,GO:0005507 11549243,11563965,15155722 1760 Actinomycetes class 1498 NCBIFAM superoxide dismutase[Cu-Zn] NF047724.1 TrhSuTaseStf0 400 400 261 equivalog Y Y N trehalose 2-sulfotransferase stf0 2.8.2.37 GO:0016740 15258569,15866533,22360425 1760 Actinomycetes class 774 NCBIFAM trehalose 2-sulfotransferase NF047783.1 VWA_dom_MadC 600 600 498 equivalog Y Y N MadC family VWA domain-containing protein madC 38837369 1760 Actinomycetes class 553 NCBIFAM MadC family VWA domain-containing protein NF047784.1 MadB_ATPase 475 475 298 equivalog Y Y N MadB family AAA-type ATPase 38837369 1760 Actinomycetes class 489 NCBIFAM MadB family AAA-type ATPase NF047785.1 respo_reg_MadR 300 300 209 equivalog Y Y N MadR family response regulator transcription factor 38837369 1760 Actinomycetes class 799 NCBIFAM MadR family response regulator transcription factor NF047786.1 his_kin_MadS 500 500 434 equivalog Y Y N MadS family sensor histidine kinase 38837369 1760 Actinomycetes class 880 NCBIFAM MadS family sensor histidine kinase NF047833.1 TyroCdyMelC1 120 120 127 equivalog Y Y N apotyrosinase chaperone MelC1 melC1 29133199,8360164 1760 Actinomycetes class 2969 NCBIFAM apotyrosinase chaperone MelC1 NF047834.1 TyrosinaseMelC2 450 450 272 equivalog Y Y N tyrosinase MelC2 melC2 1.14.18.1 GO:0004503,GO:0042438 29133199,3932128 1760 Actinomycetes class 2750 NCBIFAM tyrosinase MelC2 NF047839.1 PspM_Rv2743c 80 80 220 equivalog Y Y N phage shock envelope stress response protein PspM pspM 25899163,38809013 1760 Actinomycetes class 2751 NCBIFAM phage shock envelope stress response protein PspM NF047860.1 Tet-DihydfolSynFolCMyb 700 700 468 equivalog Y Y N bifunctional tetrahydrofolate synthase/dihydrofolate synthase folC 6.3.2.12,6.3.2.17 GO:0004326,GO:0008841,GO:0009396,GO:0046654 16754987,18566510,24366731,27082669 1760 Actinomycetes class 8817 NCBIFAM bifunctional tetrahydrofolate synthase/dihydrofolate synthase TIGR00025.1 TIGR00025 Mtu_efflux 146.9 146.9 238 paralog Y N N ABC transporter efflux protein, DrrB family GO:0043215,GO:0046677,GO:1900753 1760 Actinomycetes class 4066 JCVI ABC transporter efflux protein, DrrB family ABC transporter efflux protein, DrrB family The seed members for this model are a paralogous family of Mycobacterium tuberculosis. Nearly all proteins scoring above the noise cutoff are from high-GC Gram-positive organisms. The members of this paralogous family of efflux proteins are all found in operons with ATP-binding chain partners. They are related to a putative daunorubicin resistance efflux protein of Streptomyces peucetius. This model represents a branch of a larger superfamily that also includes NodJ, a part of the NodIJ pair of nodulation-triggering signal efflux proteins. The members of this branch may all act in antibiotic resistance. TIGR01454.1 TIGR01454 AHBA_synth_RP 246.65 246.65 205 hypoth_equivalog Y N N AHBA synthesis associated protein 1760 Actinomycetes class 976 JCVI AHBA synthesis associated protein AHBA synthesis associated protein The enzymes in this equivalog are all located in the operons for the biosynthesis of 3-amino-5-hydroxybenoic acid (AHBA), which is a precursor of several antibiotics including ansatrienin [1], naphthomycin [1], rifamycin [2] and mitomycin [3]. The role that this enzyme plays in this biosynthesis has not been elucidated. This enzyme is a member of the Haloacid dehalogenase superfamily (PF00702) of aspartate-nucleophile hydrolases. This enzyme is closely related to phosphoglycolate phosphatase (TIGR01449), but it is unclear what purpose a PGPase or PGPase-like activity would serve in these biosyntheses. This model is limited to the Gram positive Actinobacteria. The most closely related enzyme below the noise cutoff is IndB which is involved in the biosynthesis of Indigoidine in Pectobacterium (Erwinia) chrysanthemi, a gamma proteobacter [4]. This enzyme is similarly related to PGP. In this case, too it is unclear what role would be be played by a PGPase activity. TIGR01809.1 TIGR01809 Shik-DH-AROM 196 196 282 equivalog_domain Y Y N shikimate dehydrogenase aroE 1.1.1.25 GO:0004764,GO:0005737,GO:0009423 1760 Actinomycetes class 3699 JCVI shikimate-5-dehydrogenase shikimate dehydrogenase This model represents a clade of shikimate-5-dehydrogenases found in Corynebacterium, Mycobacteria and fungi. The fungal sequences are pentafunctional proteins known as AroM which contain the central five seven steps in the chorismate biosynthesis pathway. The Corynebacterium and Mycobacterial sequences represent the sole shikimate-5-dehydrogenases in species which otherwise have every enzyme of the chorismate biosynthesis pathway. TIGR02234.1 TIGR02234 trp_oprn_chp 71.15 71.15 202 hypoth_equivalog Y Y N TIGR02234 family membrane protein 1760 Actinomycetes class 7966 JCVI membrane protein, TIGR02234 family TIGR02234 family membrane protein Members of this family are predicted transmembrane proteins with four membrane-spanning helices. Members are found in the Actinobacteria (Mycobacterium, Corynebacterium, Streptomyces), always associated with genes for tryptophan biosynthesis. TIGR02319.1 TIGR02319 CPEP_Pphonmut 420.05 420.05 294 equivalog Y Y N carboxyvinyl-carboxyphosphonate phosphorylmutase bcpA 2.7.8.23 GO:0008807 2160937 1760 Actinomycetes class 28 JCVI carboxyvinyl-carboxyphosphonate phosphorylmutase carboxyvinyl-carboxyphosphonate phosphorylmutase This family consists of carboxyvinyl-carboxyphosphonate phosphorylmutase (CPEP phosphonomutase), an unusual enzyme involved in the biosynthesis of the antibiotic bialaphos. So far, it is known only in that pathway and only in Streptomyces hygroscopicus. Some related proteins annotated as being functionally equivalent are likely misannotated examples of methylisocitrate lyase, an enzyme of priopionate utilization. TIGR03428.1 TIGR03428 ureacarb_perm 740.45 740.45 475 hypoth_equivalog Y N N permease, urea carboxylase system 1760 Actinomycetes class 1207 JCVI permease, urea carboxylase system permease, urea carboxylase system A number of bacteria obtain nitrogen by biotin- and ATP-dependent urea degradation system distinct from urease. The two characterized proteins of this system are the enzymes urea carboxylase and allophanate hydrolase, but other, uncharacterized proteins co-occur as genes encoded nearby in multiple organisms. This family includes predicted permeases of the amino acid permease family, likely to transport either urea or a compound from which urea is derived. It is found so far only Actinobacteria, whereas a number of other species with the urea carboxylase have an adjacent ABC transporter operon. TIGR03452.1 TIGR03452 mycothione_red 635.65 635.65 452 equivalog Y Y N mycothione reductase mtr 1.8.1.15 GO:0010126,GO:0050627,GO:0070402 10512639 1760 Actinomycetes class 3245 JCVI mycothione reductase mycothione reductase Mycothiol, a glutathione analog in Mycobacterium tuberculosis and related species, can form a disulfide-linked dimer called mycothione. This enzyme can reduce mycothione to regenerate two mycothiol molecules. The enzyme shows some sequence similarity to glutathione-disulfide reductase, trypanothione-disulfide reductase, and dihydrolipoamide dehydrogenase. The characterized protein from M. tuberculosis, a homodimer, has FAD as a cofactor, one per monomer, and uses NADPH as a substrate. TIGR03459.1 TIGR03459 crt_membr 439.4 439.4 470 equivalog Y Y N alpha-(1->6)-mannopyranosyltransferase A 17714444 1760 Actinomycetes class 2587 JCVI carotene biosynthesis associated membrane protein alpha-(1->6)-mannopyranosyltransferase A This model represents a family of hydrophobic and presumed membrane proteins found in the Actinobacteria. The genes encoding these proteins are syntenically associated with (found proximal to) genes of carotene biosynthesis ususally including phytoene synthase (crtB), phytoene dehydrogenase (crtI) and geranylgeranyl pyrophosphate synthase (ispA). TIGR03919.1 TIGR03919 T7SS_EccB 154 154 457 equivalog Y Y N type VII secretion protein EccB eccB GO:0009306 19876390 1760 Actinomycetes class 20221 JCVI type VII secretion protein EccB type VII secretion protein EccB This model represents the transmembrane protein EccB of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccB1, EccB2, etc. This model does not identify functionally related proteins in the Firmicutes such as Staphylococcus aureus and Bacillus anthracis. TIGR03920.1 TIGR03920 T7SS_EccD 94.95 94.95 455 equivalog Y Y N type VII secretion integral membrane protein EccD eccD GO:0009306 19876390 1760 Actinomycetes class 22584 JCVI type VII secretion integral membrane protein EccD type VII secretion integral membrane protein EccD Members of this family are EccD, a component of actinobacterial type VII secretion systems (T7SS) with ten to eleven predicted transmembrane helix regions. TIGR03921.1 TIGR03921 T7SS_mycosin 278.75 278.75 353 equivalog Y Y N type VII secretion-associated serine protease mycosin mycP GO:0008236,GO:0009306 19876390 1760 Actinomycetes class 26631 JCVI type VII secretion-associated serine protease mycosin type VII secretion-associated serine protease mycosin Members of this family are subtilisin-related serine proteases, found strictly in the Actinobacteria and associated with type VII secretion operons. The designation mycosin is used for members from Mycobacterium. TIGR03923.1 TIGR03923 T7SS_EccE 108 108 344 equivalog_domain Y Y N type VII secretion protein EccE eccE GO:0009306 19876390 1760 Actinomycetes class 11682 JCVI type VII secretion protein EccE type VII secretion protein EccE This model represents the transmembrane protein EccB of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccE1, EccE2, etc. This model represents a conserved core region, and many members have 200 or more additional C-terminal residues. TIGR03931.1 TIGR03931 T7SS_Rv3446c 47.6 47.6 194 hypoth_equivalog_domain Y Y N type VII secretion-associated protein GO:0009306 1760 Actinomycetes class 3697 JCVI type VII secretion-associated protein, Rv3446c family type VII secretion-associated protein Members of this protein family occur as part of the ESX-4 cluster of type VII secretion system (T7SS) proteins in Mycobacterium tuberculosis and in similar T7SS clusters in other Actinobacteria genera, including Corynebacterium, Nocardia, Rhodococcus, and Saccharopolyspora. This HMM describes the better-conserved C-terminal region. TIGR04188.1 TIGR04188 methyltr_grsp 380 380 363 subfamily Y Y N ATP-grasp peptide maturase system methyltransferase tgmC 1760 Actinomycetes class 3947 JCVI methyltransferase, ATP-grasp peptide maturase system ATP-grasp peptide maturase system methyltransferase Members of this protein family are predicted SAM-dependent methyltransferases that regularly occur in the context of a putative peptide modification ATP-grasp enzyme (TIGR04187, related to enzymes of microviridin maturation) and a putative ribosomal peptide modification target (TIGR04186). TIGR04268.1 TIGR04268 FxSxx-COOH 28 28 44 equivalog Y Y N FxSxx-COOH cyclophane-containing RiPP peptide fxsA 32101166,34164914 1760 Actinomycetes class 2969 JCVI FXSXX-COOH protein FxSxx-COOH cyclophane-containing RiPP peptide Members of this family are very short (~60 residue) polypeptides, among which the fifth and third to last residues are nearly always Phe and Ser, respectively. Because members occur in a conserved context with a putative peptide-modifying radical SAM/SPASM domain protein, we suggested that members of this family are the modification target. The gene symbol fxsA was given to reflect both the FXA motif and the proposed role as a ribosomal natural product. Work on modification of SjiA, from a branch of the FxSxx-COOH (FxsA) family that scores below the original (and current) cutoffs of this model, has now demonstrated radical SAM enzyme-catalyzed cyclization of the Phe and Ser to produce a cyclophane moiety. Variety within the FxsA family iwithin the FxSxx motif, and oxidations of the cyclophane group observed in vitro to form aminomalonate suggest great plasticity in the generation of FxsA RiPP family products. Kaur, et al. find bioinformatic evidence that FxSxx-COOH systems in play a role in biological conflict systems. TIGR04338.1 TIGR04338 HEXXH_Rv0185 90 90 161 hypoth_equivalog Y Y N TIGR04338 family metallohydrolase 1760 Actinomycetes class 1759 JCVI putative metallohydrolase, TIGR04338 family TIGR04338 family metallohydrolase This protein family is restricted to the Actinomycetales, including Mycobacterium, Rhodococcus, Nocardia, Gordonii, and others. The invariant motif HEXXH, at the core of the best conserved region in the protein, suggests metallohydrolase activity, as does local sequence similarity in this region to other metallohydrolases. TIGR04343.1 TIGR04343 egtE_PLP_lyase 400 400 370 equivalog Y Y N ergothioneine biosynthesis PLP-dependent enzyme EgtE egtE GO:0016829,GO:0052699 20420449 1760 Actinomycetes class 1156 JCVI ergothioneine biosynthesis PLP-dependent enzyme EgtE ergothioneine biosynthesis PLP-dependent enzyme EgtE Members of this protein family are the pyridoxal phosphate-dependent enzyme EgtE, which catalyzes the final step in the biosynthesis of ergothioneine. TIGR04351.1 TIGR04351 TOMM_nitrile_2 65 65 48 subfamily Y Y N TIGR04351 family putative TOMM peptide 1760 Actinomycetes class 70 JCVI putative TOMM peptide TIGR04351 family putative TOMM peptide Members of this family of short peptides average about 110 amino acids in length, with greatest variability in the last thirty. The conserved region resembles the alpha subunit of nitrile hydratase, as with the NHLP leader peptide domain (TIGR03793), and members usually are found near a cyclodehydratase (maturase) enzyme, marking these as like thiazole/oxazole-modified microcins (TOMM), but these precursor forms lack the GlyGly cleavage motif that marks the clear end of a leader peptide region. Genomes with this system include Streptomyces clavuligerus ATCC 27064, Verrucosispora maris AB-18-032, and Kitasatospora setae KM-6054. TIGR04363.1 TIGR04363 LD_lanti_pre 30 30 37 subfamily Y Y N FxLD family lanthipeptide fxlA 1760 Actinomycetes class 3156 JCVI FxLD family lantipeptide FxLD family lanthipeptide Members of this protein family occur with a cassette of lanthionine-type peptide modification enzymes. Members are small (about 60 amino acids long), rich in Cys, and variable in copy number per genome (from one to three). These features suggest that members of this family are modified to become lanthipeptides, although not necessarily a lantibiotic. There is no GlyGly cleavage motif to separate a leader peptide from core region. The considerable abundance in Streptomyces and relatively strong conservation hints at a non-antibiotic function. The motif FxLD in the N-terminal region is nearly invariant. TIGR04426.1 TIGR04426 rSAM_desII 450 450 468 equivalog Y Y N dTDP-4-amino-4,6-dideoxy-D-glucose ammonia-lyase desII 4.3.1.30 GO:0016841,GO:0033068,GO:0051539 19746907 1760 Actinomycetes class 195 JCVI TDP-4-amino-4,6-dideoxy-D-glucose deaminase dTDP-4-amino-4,6-dideoxy-D-glucose ammonia-lyase Members of this protein family, including DesII, are radical SAM enzymes that deaminate TDP-4-amino-4,6-dideoxy-D-glucose to TDP-3-keto-4,6-dideoxy-D-glucose. This is the fourth step of the six step pathway in Streptomyces venezuelae for synthesizing D-desosamine, or 3-(dimethylamino)-3,4,6-trideoxyglucose, a precursor for many macrolide antibiotics. TIGR04427.1 TIGR04427 PLP_DesI 650 650 390 equivalog Y Y N dTDP-4-dehydro-6-deoxyglucose aminotransferase 17630700 1760 Actinomycetes class 156 JCVI dTDP-4-dehydro-6-deoxyglucose aminotransferase dTDP-4-dehydro-6-deoxyglucose aminotransferase Members of this family are pyridoxal phosphate-dependent aminotransferases that convert TDP-4-keto-6-deoxy-D-glucose to the 4-amino sugar form, TDP-4-amino-4,6-dideoxy-D-glucose. In Streptomyces venezuelae, this enzyme is designated DesI, catalyzing the third of six steps in the biosynthesis of TDP-D-desosamine, a component of a number of different macrolide antibiotics made by that organism. Related proteins, scoring below the trusted cutoff, include sugar aminotranferases in O-antigen biosynthesis regions. TIGR04428.1 TIGR04428 B12_rSAM_trp_MT 500 500 558 equivalog Y Y N tryptophan 2-C-methyltransferase tsrT 2.1.1.106 GO:0006568,GO:0017000,GO:0030772 23064318 1760 Actinomycetes class 272 JCVI tryptophan 2-C-methyltransferase tryptophan 2-C-methyltransferase Members of this family are the B12-binding domain/radical SAM domain enzyme tryptophan methyltransferase, named TsrT in the cassette for thiostrepton biosynthesis. Thiostrepton and related thiopeptides are synthesized by extensive modification of a ribosomally translated product, but this enzyme is involved in a pathway that converts a free Trp residue to a quinaldic acid moiety before it is appended. TIGR04451.1 TIGR04451 lanti_SCO0268 40 40 53 equivalog Y Y N SCO0268 family class II lanthipeptide lanA 21672958 1760 Actinomycetes class 78 JCVI lantipeptide, SCO0268 family SCO0268 family class II lanthipeptide Members of this family are putative lanthipeptide (most likely lantibiotic) precursors, about 53 amino acids long, found in a lantibiotic-type biosynthetic cluster in several species of Streptomyces (S. coelicolor, S. griseoflavus, S. ambofaciens, etc.). This family is described in AntiSMASH as Streptomyces PEQAXS motif lanthipeptide precursor. TIGR04458.1 TIGR04458 CYP450_TxtE 500 500 403 equivalog Y Y N 4-nitrotryptophan synthase txtE 22941045 1760 Actinomycetes class 94 JCVI 4-nitrotryptophan synthase 4-nitrotryptophan synthase Members of this family are cytochrome P450 enzymes that convert L-tryptophan into L-4-nitrotryptophan. In thaxtomin gene clusters, this enzyme (TxtE) uses nitric acid (NO) derived from arginine by the nitric oxide synthase TxtD, and O2, to perform the tryptophan nitration. L-4-nitrotryptophan is then used as a non-proteinogenic amino acid by non-ribosomal peptide synthases (NRPS). TIGR04460.1 TIGR04460 endura_MppR 380 380 257 equivalog Y Y N enduracididine biosynthesis enzyme MppR mppR 23758195 1760 Actinomycetes class 197 JCVI enduracididine biosynthesis enzyme MppR enduracididine biosynthesis enzyme MppR Members of this family are MppR, one of three enzymes involved in synthesizing enduracididine, a non-proteinogenic amino acid used in non-ribosomal peptide synthases to make natural products such as enduracidin from Streptomyces fungicidicus ATCC 21013. MppR is belongs to the acetoacetate decarboxylase-like superfamily. MppR catalyzes an aldol condensation and a dehydration, not a decarboxylation. TIGR04461.1 TIGR04461 endura_MppQ 540 540 392 equivalog Y Y N enduracididine biosynthesis enzyme MppQ mppQ 23758195 1760 Actinomycetes class 78 JCVI enduracididine biosynthesis enzyme MppQ enduracididine biosynthesis enzyme MppQ Members of this family are MppQ, one of three enzymes involved in synthesizing enduracididine, a non-proteinogenic amino acid used in non-ribosomal peptide synthases to make natural products such as enduracidin from Streptomyces fungicidicus ATCC 21013. MppQ is a PLP-dependent enzyme, predicted by homology to be an aminotransferase. TIGR04462.1 TIGR04462 endura_MppP 450 450 289 equivalog Y Y N enduracididine biosynthesis enzyme MppP mppP 23758195 1760 Actinomycetes class 175 JCVI enduracididine biosynthesis enzyme MppP enduracididine biosynthesis enzyme MppP Members of this family are MppP, one of three enzymes involved in synthesizing enduracididine, a non-proteinogenic amino acid used in non-ribosomal peptide synthases to make natural products such as enduracidin from Streptomyces fungicidicus ATCC 21013. MppP is a PLP-dependent enzyme, predicted by homology to be an aminotransferase. TIGR04466.1 TIGR04466 rSAM_BlsE 400 400 327 equivalog Y Y N cytosylglucuronate decarboxylase blsE GO:0016831,GO:0017000,GO:1904047 23874663 1760 Actinomycetes class 260 JCVI cytosylglucuronate decarboxylase cytosylglucuronate decarboxylase BlsE, part of the blasticidin S biosynthetic pathway, is a radical SAM enzyme that performs a decarboxylation at C5 of the glucoside residue. MilG in mildiomycin biosynthesis is equivalent. This enzyme follows CGA synthase and makes the pyranoside core moiety of a class of peptidyl nucleoside antibiotics. TIGR04469.1 TIGR04469 CGA_synth_rel 150 150 297 equivalog Y Y N CGA synthase-related protein blsF GO:0017000 23377931 1760 Actinomycetes class 283 JCVI CGA synthase-related protein CGA synthase-related protein Members of this family are related to cytosylglucuronate (CGA) synthase (TIGR04466), and found in the same clusters as CGA synthase and CGA decarboxylase. These clusters produce peptidyl nucleoside antibiotics with a pyranoside core moiety, found in a number of Streptomyces species. Removal of the S. griseochromogenes member of this family, BlsF, from a heterologous expression system caused an increase, not blockage, of blasticidin S. TIGR04497.1 TIGR04497 GRASP_targ_2 32 32 50 subfamily Y Y N putative ATP-grasp target RiPP 1760 Actinomycetes class 135 JCVI putative ATP-grasp target RiPP putative ATP-grasp target RiPP Members of this small family are putative RiPP (Ribosomally translated, Post-translationally modified Peptides) precursors, modified by RimK-like ATP-grasp proteins. Members are encoded near both an ATP-grasp protein and C39 peptidase domain-containing transporter. Members are short polypeptides that contain the GG motif expected for cleavage on export. TIGR04506.1 TIGR04506 F_threo_transal 650 650 609 equivalog Y Y N fluorothreonine transaldolase 2.2.1.8 GO:0033806,GO:0090346 22858315 1760 Actinomycetes class 31 JCVI fluorothreonine transaldolase fluorothreonine transaldolase Members of this family are fluorothreonine transaldolase, and enzyme involved in biosynthesis of 4-fluorothreonine, one of the few known known naturally occurring organofluorine compounds. TIGR04507.1 TIGR04507 fluorinase 400 400 286 equivalog Y Y N adenosyl-fluoride synthase 2.5.1.63 GO:0033846,GO:0090346 16604208 1760 Actinomycetes class 35 JCVI adenosyl-fluoride synthase adenosyl-fluoride synthase Members of this family are fluorinase (adenosyl-fluoride synthase, EC 2.5.1.63), an enzyme involved in the first committed step in the biosynthesis of at least two different organofluorine compounds. Few organofluorine natural products are known. Related enzymes include chlorinases (EC 2.5.1.94) that lack fluorinase activity, although a fluorinase may show chlorinase activity. TIGR04515.1 TIGR04515 P450_rel_GT_act 343 343 386 subfamily Y Y N P450-derived glycosyltransferase activator 22056329 1760 Actinomycetes class 781 JCVI P450-derived glycosyltranferase activator P450-derived glycosyltransferase activator Members of this family resemble cytochrome P450 by homolog, but lack a critical heme-binding Cys residue. Members in general are encoded next to a glycosyltransferase gene in a natural products biosynthesis cluster, physically interact with it, and help the glycosyltransferase achieve high specificity while retaining high activity. Many members of this family assist in the attachment of a sugar moiety to a natural product such as a polyketide. TIGR04516.1 TIGR04516 glycosyl_450act 440 440 418 subfamily Y Y N activator-dependent family glycosyltransferase GO:0016757 1760 Actinomycetes class 3977 JCVI glycosyltransferase, activator-dependent family activator-dependent family glycosyltransferase Many biosynthesis clusters for secondary metabolites feature a glycosyltransferase gene next to a P450 homolog, often with the P450 lacking a critical heme-binding Cys. These P540-derived sequences seem to be allosteric activators of glycosyltransferases such as the member of this family. This HMM describes a set of related glycosyltransferases, many of which can be recognized as activator-dependent from genomic context. TIGR04529.1 TIGR04529 MTB_hemophore 32 32 77 subfamily Y Y N hemophore-related protein GO:0005488,GO:0005576,GO:0006810 11101579,16828326,21383189,23760277 1760 Actinomycetes class 5005 JCVI hemophore-related protein, Rv0203/Rv1174c family hemophore-related protein Members of this family occur as paralogs in most Mycobacterium strains, including 2 in M. tuberculosis, 6 in M. avium, and 9 in M. smegmatis. Members have a cleaved N-terminal signal peptide and exactly two Cys residues in the mature protein, both at invariant positions. The best characterized member, Rv0203, is a hemophore, that is, a secreted polypeptide that binds heme and delivers it to a transport system for import. Hemophores are protein analogs of siderophores, natural products that chelate non-heme iron and deliver it to receptors for transport. The unrelated HasA family of hemophores has been described in Gram-negative bacteria such as Yersinia pestis and Pseudomonas aeruginosa. TIGR04531.1 TIGR04531 nonproteo_OH 300 300 277 subfamily Y Y N putative nonproteinogenic amino acid hydroxylase 20710026,24506891 1760 Actinomycetes class 170 JCVI putative nonproteinogenic amino acid hydroxylase putative nonproteinogenic amino acid hydroxylase This extremely rare protein family, a branch of the 2-oxoglutarate dependent oxygenase family related to proline 3-hydroxylase, appears only in natural product biosynthetic clusters that include nonribosomal peptide synthases. One members is PlyP from the polyoxypeptin A cluster, suggested to hydroxylate 3-methylproline. Another, GetF from the GE81112 biosynthetic gene cluster, is a proposed to hydroxylate pipecolic acid. TIGR04542.1 TIGR04542 GMC_mycofac_2 400 400 425 equivalog Y Y N mycofactocin system GMC family oxidoreductase MftG mftG 1.-.-.- 21223593 1760 Actinomycetes class 195 JCVI GMC family mycofactocin-associated oxidreductase mycofactocin system GMC family oxidoreductase MftG This model describes a set of dehydrogenases belonging to the glucose-methanol-choline oxidoreductase (GMC oxidoreductase) family. Members of the present family are restricted to the bacterial genus Gordonia, and seem to replace the related family TIGR03970, which occurs in Actinobacteria generally but not in the genus Gordonia. Members of both this family and TIGR03970 are associated with the mycofactocin biosynthesis operon in Actinobacteria. NF000010.1 AAC_2p_Ib 400 400 195 exception Y Y Y aminoglycoside N-acetyltransferase AAC(2')-Ib aac(2')-Ib GO:0008080 9159528 1762 Mycobacteriaceae family 36 NCBIFAM aminoglycoside N-acetyltransferase AAC(2')-Ib aminoglycoside N-acetyltransferase AAC(2')-Ib NF001056.0 PRK00117 PRK00117.3-1 237 237 181 equivalog Y Y N recombination regulator RecX recX 12218174 1762 Mycobacteriaceae family 716 NCBI Protein Cluster (PRK) recombination regulator RecX recombination regulator RecX NF001855.0 PRK00576 PRK00576.1 205 205 197 equivalog Y Y N molybdenum cofactor guanylyltransferase mobA 2.7.7.77 GO:0006777,GO:0061603 1762 Mycobacteriaceae family 730 NCBI Protein Cluster (PRK) molybdopterin-guanine dinucleotide biosynthesis protein A molybdenum cofactor guanylyltransferase Links a guanosine 5'-phosphate to molydopterin to form molybdopterin guanine dinucleotide; involved in molybdenum cofactor biosynthesis NF002366.0 PRK01346 PRK01346.1-3 624 624 405 equivalog Y N N hypothetical protein 1762 Mycobacteriaceae family 302 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002615.0 PRK02268 PRK02268.1-1 264 264 145 equivalog Y N N hypothetical protein 1762 Mycobacteriaceae family 139 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004509.1 PRK05850 PRK05850.1 775 775 578 subfamily Y Y N fatty-acid--AMP ligase 19182784 1762 Mycobacteriaceae family 2732 NCBI Protein Cluster (PRK) acyl-CoA synthetase fatty-acid--AMP ligase This HMM describes a paralogous family of fatty-acid--AMP ligases (FAAL), including proteins from Mycobacterium tuberculosis previously known as FadD21, FadD23, FadD24, FadD25, FadD26, FadD28, and FadD29. These proteins are involved in biosynthesis, so the gene symbol FadD (fatty acid degradation D) is somewhat misleading. NF004512.0 PRK05853 PRK05853.1 215 215 168 equivalog Y N N hypothetical protein 1762 Mycobacteriaceae family 656 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004515.0 PRK05857 PRK05857.1 726 726 532 equivalog Y Y N fatty acid--CoA ligase FadD10 fadD10 23625916 1762 Mycobacteriaceae family 445 NCBI Protein Cluster (PRK) acyl-CoA synthetase fatty acid--CoA ligase FadD10 NF004524.0 PRK05869 PRK05869.1 326 326 254 equivalog Y Y N enoyl-CoA hydratase 4.2.1.17 1762 Mycobacteriaceae family 645 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF004529.0 PRK05876 PRK05876.1 338 338 275 equivalog Y N N short chain dehydrogenase 1762 Mycobacteriaceae family 439 NCBI Protein Cluster (PRK) short chain dehydrogenase short chain dehydrogenase NF004534.0 PRK05884 PRK05884.1 244 244 224 equivalog Y Y N SDR family oxidoreductase 1762 Mycobacteriaceae family 721 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005859.1 PRK07788 PRK07788.1 875 875 560 exception Y Y N long-chain-fatty-acid--CoA ligase FadD2 fadD2 6.2.1.3 16544254,22283817,27855077 1762 Mycobacteriaceae family 790 NCBI Protein Cluster (PRK) acyl-CoA synthetase long-chain-fatty-acid--CoA ligase FadD2 Disruption of FadD2 (as the term is used in Mycobacterium tuberculosis) was shown to greatly increase susceptibility to the first-line tuberculosis drug pyrazinamide (PZA). NF005897.1 PRK07867 PRK07867.1 850 850 496 exception Y Y N long-chain-fatty-acid--CoA ligase FadD17 fadD17 6.2.1.3 15042094 1762 Mycobacteriaceae family 838 NCBI Protein Cluster (PRK) acyl-CoA synthetase long-chain-fatty-acid--CoA ligase FadD17 NF005903.0 PRK07883 PRK07883.1-1 1038 1038 642 equivalog Y Y N DEDD exonuclease domain-containing protein 1762 Mycobacteriaceae family 42 NCBI Protein Cluster (PRK) hypothetical protein DEDD exonuclease domain-containing protein NF006789.0 PRK09294 PRK09294.1-3 873 873 410 equivalog Y N N acyltransferase PapA5 1762 Mycobacteriaceae family 3 NCBI Protein Cluster (PRK) acyltransferase PapA5 acyltransferase PapA5 NF006790.0 PRK09294 PRK09294.1-4 716 716 418 equivalog Y Y N phthiocerol/phthiodiolone dimycocerosyl transferase 1762 Mycobacteriaceae family 60 NCBI Protein Cluster (PRK) acyltransferase PapA5 phthiocerol/phthiodiolone dimycocerosyl transferase NF007213.0 PRK09635 PRK09635.1 317 317 290 equivalog Y Y N RNA polymerase sigma factor SigI sigI 1762 Mycobacteriaceae family 568 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigI RNA polymerase sigma factor SigI Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription NF008987.0 PRK12334 PRK12334.1-1 375 375 326 equivalog Y Y N nucleoside triphosphate pyrophosphohydrolase 3.6.1.9 20529853 1762 Mycobacteriaceae family 826 NCBI Protein Cluster (PRK) nucleoside triphosphate pyrophosphohydrolase nucleoside triphosphate pyrophosphohydrolase NF009153.0 PRK12497 PRK12497.3-1 171 171 125 equivalog Y Y N YraN family protein 1762 Mycobacteriaceae family 570 NCBI Protein Cluster (PRK) hypothetical protein YraN family protein NF009921.1 PRK13382 PRK13382.1 850 850 529 exception Y Y N acyl-CoA ligase FadD12 fadD12 22283817 1762 Mycobacteriaceae family 885 NCBI Protein Cluster (PRK) acyl-CoA synthetase acyl-CoA ligase FadD12 NF010244.0 PRK13691 PRK13691.1 221 221 166 exception Y Y N (3R)-hydroxyacyl-ACP dehydratase subunit HadC hadC 17804795,17906131,18048930 1762 Mycobacteriaceae family 556 NCBI Protein Cluster (PRK) (3R)-hydroxyacyl-ACP dehydratase subunit HadC (3R)-hydroxyacyl-ACP dehydratase subunit HadC Functions as a heterodimer along with HadB in fatty acid biosynthesis; fatty acid synthase type II; FAS-II NF010245.0 PRK13692 PRK13692.1 232 232 159 equivalog Y Y N (3R)-hydroxyacyl-ACP dehydratase subunit HadA hadA 17804795,17906131,18048930 1762 Mycobacteriaceae family 589 NCBI Protein Cluster (PRK) (3R)-hydroxyacyl-ACP dehydratase subunit HadA (3R)-hydroxyacyl-ACP dehydratase subunit HadA Functions as a heterodimer along with HadB in fatty acid biosynthesis; fatty acid synthase type II; FAS-II NF010665.0 PRK14059 PRK14059.1-4 274 274 260 equivalog Y Y N pyrimidine reductase family protein 1762 Mycobacteriaceae family 693 NCBI Protein Cluster (PRK) hypothetical protein pyrimidine reductase family protein NF011402.0 PRK14827 PRK14827.1 535 535 296 equivalog Y Y N decaprenyl diphosphate synthase 1762 Mycobacteriaceae family 588 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate synthase decaprenyl diphosphate synthase Catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate NF011974.0 PRK15443 PRK15443.2-1 171 171 110 subfamily Y Y N diol dehydratase small subunit 1762 Mycobacteriaceae family 150 NCBI Protein Cluster (PRK) propanediol dehydratase small subunit diol dehydratase small subunit NF013021.5 PF00823.24 PPE 28.2 28.2 158 domain Y Y N PPE domain-containing protein 16690741,9634230 1762 Mycobacteriaceae family 54878 EBI-EMBL PPE family PPE family This family named after a PPE motif near to the amino terminus of the domain. The PPE family of proteins all contain an amino-terminal region of about 180 amino acids. The carboxyl terminus of this family are variable, and on the basis of this region fall into at least three groups. The MPTR subgroup has tandem copies of a motif NXGXGNXG. The second subgroup contains a conserved motif at about position 350. The third group are only related in the amino terminal region. The function of these proteins is uncertain but it has been suggested that they may be related to antigenic variation of Mycobacterium tuberculosis [1]. [1]. 9634230. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE 3rd, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jage. Nature 1998;393:537-544. [2]. 16690741. Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Strong M, Sawaya MR, Wang S, Phillips M, Cascio D, Eisenberg D;. Proc Natl Acad Sci U S A. 2006;103:8060-8065. (from Pfam) NF013127.5 PF00934.25 PE 22 22 91 domain Y Y N PE domain-containing protein 16690741,9634230 1762 Mycobacteriaceae family 80332 EBI-EMBL PE family PE family This family named after a PE motif near to the amino terminus of the domain. The PE family of proteins all contain an amino-terminal region of about 110 amino acids. The carboxyl terminus of this family are variable and fall into several classes. The largest class of PE proteins is the highly repetitive PGRS class which have a high glycine content. The function of these proteins is uncertain but it has been suggested that they may be related to antigenic variation of Mycobacterium tuberculosis [1]. The C-terminus of this domain contains the type VII secretion signal that has a YXXXD/E motif. [1]. 9634230. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE 3rd, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jage. Nature 1998;393:537-544. [2]. 16690741. Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Strong M, Sawaya MR, Wang S, Phillips M, Cascio D, Eisenberg D;. Proc Natl Acad Sci U S A. 2006;103:8060-8065. (from Pfam) NF022374.5 PF10921.13 DUF2710 29.6 29.6 104 PfamAutoEq Y Y N DUF2710 family protein 1762 Mycobacteriaceae family 302 EBI-EMBL Protein of unknown function (DUF2710) DUF2710 family protein This family of proteins with unknown function appears to be restricted to Mycobacteriaceae. (from Pfam) NF028246.5 PF16936.10 Holin_9 25.3 25.3 78 PfamEq Y Y N putative holin 1762 Mycobacteriaceae family 495 EBI-EMBL Putative holin putative holin This is a family of putative holins from Actinobacteria with three TM regions. (from Pfam) NF033741.1 NlpC_p60_RipA 625 625 457 exception Y Y N NlpC/P60 family peptidoglycan endopeptidase RipA ripA 26977111,29722065 1762 Mycobacteriaceae family 839 NCBIFAM NlpC/P60 family peptidoglycan endopeptidase RipA NlpC/P60 family peptidoglycan endopeptidase RipA NF033742.1 NlpC_p60_RipB 335 335 206 exception Y Y N NlpC/P60 family peptidoglycan endopeptidase RipB ripB 21864539,26977111 1762 Mycobacteriaceae family 802 NCBIFAM NlpC/P60 family peptidoglycan endopeptidase RipB NlpC/P60 family peptidoglycan endopeptidase RipB NF033743.1 NlpC_inact_RipD 215 215 181 exception Y Y N NlpC/P60 family peptidoglycan-binding protein RipD ripD 24107184 1762 Mycobacteriaceae family 575 NCBIFAM NlpC/P60 family peptidoglycan-binding protein RipD NlpC/P60 family peptidoglycan-binding protein RipD RipD proteins, such as founding member Rv1566c from Mycobacterium tuberculosis, is a catalytically inactive paralog of the peptidoglycan endopeptidases RipA and RipB. A catalytically important Cys and His pair is replaced by Ala-83 and Ser-132. NF037478.5 PF18621.6 Rv3651-like_middle 31.1 31.1 110 domain Y Y N PAS domain-containing protein 29119630 1762 Mycobacteriaceae family 834 EBI-EMBL Rv3651-like, middle domain Rv3651-like, middle domain This domain is found in Rv3651 from Mycobacterium tuberculosis (Swiss:I6YCP0) and similar proteins from Actinobacteria. Rv3651 adopts a three-domain configuration. This entry represents the middle domain, a PAS domain that shows a central antiparallel beta-sheet of five beta-strands [1]. [1]. 29119630. Mycobacterium tuberculosis Rv3651 is a triple sensor-domain protein. Abendroth J, Frando A, Phan IQ, Staker BL, Myler PJ, Edwards TE, Grundner C;. Protein Sci. 2018;27:568-572. (from Pfam) NF037560.5 PF17471.7 GP63 25 25 73 domain Y N N Gene product 63 1762 Mycobacteriaceae family 31 EBI-EMBL Gene product 63 Gene product 63 This is a family of unknown function found in Mycobacterium. (from Pfam) NF037868.5 PF18625.6 EspB_PE 29 29 77 domain Y N N ESX-1 secreted protein B PE domain 26051906 1762 Mycobacteriaceae family 843 EBI-EMBL ESX-1 secreted protein B PE domain ESX-1 secreted protein B PE domain The ESX-1 secretion system is an important virulence determinant in Mycobacterium tuberculosis. ESX-1 secreted protein B (EspB) contains putative PE (Pro-Glu) and PPE (Pro-Pro-Glu) domains, and a C-terminal domain, which is processed by MycP1 protease during secretion. This domain represents the PE domain located at the N-terminal region of EspB which carries the conserved YxxxD/E secretion motif [1]. [1]. 26051906. Structure of EspB, a secreted substrate of the ESX-1 secretion system of Mycobacterium tuberculosis. Korotkova N, Piton J, Wagner JM, Boy-Rottger S, Japaridze A, Evans TJ, Cole ST, Pojer F, Korotkov KV;. J Struct Biol. 2015;191:236-244. (from Pfam) NF037940.1 PKS_MbtD 1150 1150 978 equivalog Y Y N mycobactin polyketide synthase MbtD mbtD 9831524 1762 Mycobacteriaceae family 742 NCBIFAM mycobactin polyketide synthase MbtD NF037942.1 ac_ACP_DH_MbtN 700 700 376 equivalog Y Y N mycobactin biosynthesis acyl-ACP dehydrogenase MbtN mbtN 25849397 1762 Mycobacteriaceae family 402 NCBIFAM mycobactin biosynthesis acyl-ACP dehydrogenase MbtN MbtN belongs to a family of dehydrogenases that in most cases act on acyl groups carried on CoA. However, MbtN appears to act on an acyl group carried instead on the mycobactin biosynthesis acyl carrier protein MbtL. NF038021.1 mannan_LmeA 325 325 264 exception Y Y N mannan chain length control protein LmeA lmeA 28855252 1762 Mycobacteriaceae family 696 NCBIFAM mannan chain length control protein LmeA NF038176.1 Rv0340_fam 100 100 178 equivalog Y Y N Rv0340 family IniB-related protein 12654653 1762 Mycobacteriaceae family 560 NCBIFAM Rv0340 family IniB-related protein Homologs of Rv0340 from Mycobacterium tuberculosis H37Rv are regularly found encoded upstream of the genes for IniB, IniA, and IniC. As with those families, mutation in this family can contribute to resistance to isoniazid, a front-line treatment for Mycobacterium tuberculosis that works by inhibiting cell wall biosynthesis. Rv0340 and glycine-rich repetive protein IniB are homologous across the N-terminal 50 amino acids of each, but otherwise dissimilar. NF038181.1 reg_ATPase_IniR 750 750 827 equivalog Y Y N isoniazid response ATPase/transcriptional regulator IniR iniR 29281637 1762 Mycobacteriaceae family 842 NCBIFAM isoniazid response ATPase/transcriptional regulator IniR Two unrelated first-line drugs for the treatment of tuberculosis, isoniazid and ethambutol, block different steps in the biosynthesis of the Mycobacterial cell envelope, and induce expression of the iniBAC operon, mutations in which often lead to adaptive resistance to those drugs. IniR (iniBAC Regulator), an ATPase but also a transcriptional regulator, with an N-terminal P-loop motif GGxGxGK[ST] and a C-terminal LuxR-like helix-turn-helix DNA-binding domain, responds to the envelope stress signal and induces IniB, IniA, and IniC. NF038269.1 lipase_LipE 750 750 407 equivalog Y Y N lipase LipE lipE 3.1.1.1 31636137 1762 Mycobacteriaceae family 845 NCBIFAM lipase LipE NF038341.1 ligase_FadD4 850 850 506 exception Y Y N fatty-acid--CoA ligase FadD4 fadD4 31911463 1762 Mycobacteriaceae family 905 NCBIFAM fatty-acid--CoA ligase FadD4 NF038342.1 FACL_FadD6 975 975 584 exception Y Y N long-chain-acyl-CoA synthetase FadD6 fadD6 6.2.1.3 25490545 1762 Mycobacteriaceae family 796 NCBIFAM long-chain-acyl-CoA synthetase FadD6 NF038345.1 wall_hydro_RipC 425 425 362 exception Y Y N peptidoglycan hydrolase RipC ripC 24843173 1762 Mycobacteriaceae family 850 NCBIFAM peptidoglycan hydrolase RipC RipC is a peptidoglycan hydrolase, found in species such as Mycobacterium tuberculosis, that is activated by conformation change sent as a signal by the cell division-regulating transporter-like complex FtsEX. Members of this family are distinguished from more distant homologs by a Pro/Gly-rich region. NF039174.4 PF18878.5 PPE-PPW 27 27 48 domain Y N N PPE-PPW subfamily C-terminal region 12711809,17105670 1762 Mycobacteriaceae family 6059 EBI-EMBL PPE-PPW subfamily C-terminal region PPE-PPW subfamily C-terminal region This entry represents the C-terminal region of a subfamily of PPE proteins known as the PPW subfamily [1,2]. The PPW refers to three conserved residues found in the sequence alignment. The region also contains a second conserved motif GFGT. [1]. 17105670. Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. Gey van Pittius NC, Sampson SL, Lee H, Kim Y, van Helden PD, Warren RM;. BMC Evol Biol. 2006;6:95. [2]. 12711809. Sequence analysis corresponding to the PPE and PE proteins in Mycobacterium tuberculosis and other genomes. Adindla S, Guruprasad L;. J Biosci 2003;28:169-179. (from Pfam) NF039175.4 PF18879.5 EspA_EspE 27 27 84 domain Y Y N EspA/EspE family type VII secretion system effector 24078612,30571761 1762 Mycobacteriaceae family 2367 EBI-EMBL EspA/EspE family EspA/EspE family type VII secretion system effector This family of proteins includes Mycobacterium tuberculosis EspA and EspE proteins. (from Pfam) NF040775.1 endonuc_Nei2 400 400 252 equivalog Y Y N endonuclease VIII Nei2 nei2 4.2.99.18 GO:0006284,GO:0019104,GO:0140078 28955788,34820919 1762 Mycobacteriaceae family 817 NCBIFAM endonuclease VIII Nei2 NF041183.1 Pks2_ls1_myc 2400 2400 2086 equivalog Y Y N sulfolipid-1 biosynthesis phthioceranic/hydroxyphthioceranic acid synthase pks2 11278910 1762 Mycobacteriaceae family 2982 NCBIFAM sulfolipid-1 biosynthesis phthioceranic/hydroxyphthioceranic acid synthase NF041247.1 UsfY 100 100 95 equivalog Y Y N protein UsfY usfY 9666957 1762 Mycobacteriaceae family 778 NCBIFAM protein UsfY Proteins of this family are encoded by the usfY gene on Mycobacterium genomes. The usfY gene is tightly linked with the anti-sigma B factor rsbW (usfX). However, the function of UsfY is unknown. NF041276.1 treh_trans_TtfA 450 450 283 equivalog Y Y N trehalose monomycolate transport factor TtfA ttfA GO:0071555 31239378,31833106 1762 Mycobacteriaceae family 734 NCBIFAM trehalose monomycolate transport factor TtfA NF041460.1 kinGactiv_GlnX 780 780 439 equivalog Y Y N protein kinase G-activating protein GlnX glnX 30065086 1762 Mycobacteriaceae family 568 NCBIFAM protein kinase G-activating protein GlnX NF041468.1 anti_sig_RseA 165 165 135 equivalog Y Y N anti-sigma E factor RseA rseA GO:0016989 18606740,20025669,25999340 1762 Mycobacteriaceae family 578 NCBIFAM anti-sigma E factor RseA NF041481.1 beta_arabfuran_tase 1050 1050 633 equivalog Y Y N terminal beta-(1->2)-arabinofuranosyltransferase aftB 17387176 1762 Mycobacteriaceae family 910 NCBIFAM terminal beta-(1->2)-arabinofuranosyltransferase NF041570.1 acyltasePE 580 580 351 equivalog Y Y N acyltransferase PE pe 2.3.1.- GO:0006629,GO:0016746 27028886,32554804 1762 Mycobacteriaceae family 467 NCBIFAM acyltransferase PE NF041677.1 trans_regClgR 170 170 113 equivalog Y Y N transcriptional regulator ClgR clgR GO:0003677 20025669,20661284,20688819,24705585,25422323 1762 Mycobacteriaceae family 511 NCBIFAM transcriptional regulator ClgR NF042416.1 GFPPS_Mycobact 600 600 350 equivalog Y Y N bifunctional (2E,6E)-farnesyl/geranyl diphosphate synthase idsA2 2.5.1.1,2.5.1.10 GO:0004161,GO:0004337,GO:0004659,GO:0008299,GO:0033384 32495977 1762 Mycobacteriaceae family 709 NCBIFAM bifunctional (2E,6E)-farnesyl/geranyl diphosphate synthase NF042417.1 NPPPS_Mycobact 600 600 335 equivalog Y Y N nonaprenyl/(2E,6E)-farnesyl/geranylgeranyl diphosphat synthase grcC1 2.5.1.10,2.5.1.29,2.5.1.85 GO:0004311,GO:0004337,GO:0004659,GO:0008299,GO:0033384,GO:0052924 32495977 1762 Mycobacteriaceae family 636 NCBIFAM nonaprenyl/(2E,6E)-farnesyl/geranylgeranyl diphosphat synthase NF042938.1 Erm55 525 525 270 exception Y Y Y 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(55) erm(55) 37347171 1762 Mycobacteriaceae family 1 NCBIFAM 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(55) The three defining alleles of Erm(55) were discovered in a single, highly clarithromycin resistant isolate of Mycobacterium chelonae. One was found in a plasmid, one as part of transposon, and one simply chromosomal. This HMM is based on all three. NF043015.1 DibenthMonoxDszC 850 850 415 equivalog Y Y N dibenzothiophene monooxygenase dszC 1.14.14.21 GO:0004497,GO:0016627,GO:0018896 19144512,8824615,9308179 1762 Mycobacteriaceae family 10 NCBIFAM dibenzothiophene monooxygenase NF043047.1 EstaseRv3036c 200 200 231 equivalog Y Y N esterase 3.1.1.- GO:0006629,GO:0008126 25224799,27690385 1762 Mycobacteriaceae family 951 NCBIFAM esterase NF043060.1 MAP_0585_fam 170 170 319 equivalog Y Y N MAP_0585 family protein 31683552,35455267 1762 Mycobacteriaceae family 317 NCBIFAM MAP_0585 family protein Members of this family, found in Mycobacterium avium and related species, average about 310 amino acids in length, including a signal peptide-containing N-terminal region of about 30 amino acids, a conserved C-terminal region of about 130 amino acids, intrinsically disordered region of about 150 amino acids, rich in Pro, Gly, and hydrophilic residues. The protein has been studied as a vaccine component but is otherwise uncharacterized. NF045548.1 GDSL_lipase 300 300 231 equivalog Y Y N Rv0518 family GDSL lipase 3.1.1.- GO:0016042,GO:0052689 31125644 1762 Mycobacteriaceae family 619 NCBIFAM Rv0518 family GDSL lipase NF045655.1 MkRedMenJ 700 700 406 equivalog Y Y N menaquinone reductase menJ 1.3.99.38 GO:0009234,GO:0016627,GO:0016628 26436137 1762 Mycobacteriaceae family 811 NCBIFAM menaquinone reductase NF045823.1 PthPhpthDimycoMt 300 300 256 equivalog Y Y N phthiotriol/phenolphthiotriol dimycocerosates methyltransferase 2.1.1.- GO:0008757,GO:0071770 15292265 1762 Mycobacteriaceae family 660 NCBIFAM phthiotriol/phenolphthiotriol dimycocerosates methyltransferase NF045825.1 FAmtase_mtf2 400 400 248 equivalog Y Y N fatty-acid O-methyltransferase Mtf2 mtf2 2.1.1.15 GO:0030733 12368441 1762 Mycobacteriaceae family 147 NCBIFAM fatty-acid O-methyltransferase Mtf2 TIGR00833.1 TIGR00833 actII 874.7 874.7 910 subfamily Y Y N MMPL family RND transporter GO:0016020 1762 Mycobacteriaceae family 10994 JCVI transport protein MMPL family RND transporter The Resistance-Nodulation-Cell Division (RND) Superfamily- MmpL sub family (TC 2.A.6.5) Characterized members of the RND superfamily all probably catalyze substrate efflux via an H+ antiport mechanism. These proteins are found ubiquitously in bacteria, archaea and eukaryotes. This sub-family includes the S. coelicolor ActII3 protein, which may play a role in drug resistance, and the M. tuberculosis MmpL7 protein, which catalyzes export of an outer membrane lipid, phthiocerol dimycocerosate. TIGR04530.1 TIGR04530 hemophoreRv0203 120 120 118 equivalog Y Y N hemophore GO:0015886,GO:0020037 23760277 1762 Mycobacteriaceae family 637 JCVI hemophore hemophore Members of this family, including Rv0203 from Mycobacterium tuberculosis, are secreted heme-binding proteins used in heme acquisition. Such proteins are called hemophores. Members have a cleavable N-terminal signal peptide, and a mature region just over 100 amino acids long with a pair of invariant Cys residues. An unrelated hemophore, HasA, occurs in Gram-negative pathogens such as Yersinia pestis. NF002365.0 PRK01346 PRK01346.1-2 788 788 412 subfamily Y N N hypothetical protein 1763 Mycobacterium genus 80 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004520.0 PRK05865 PRK05865.1 1509 1509 854 equivalog Y Y N sugar epimerase family protein 1763 Mycobacterium genus 417 NCBI Protein Cluster (PRK) hypothetical protein sugar epimerase family protein NF004522.0 PRK05867 PRK05867.1 447 447 255 equivalog Y Y N SDR family oxidoreductase 1763 Mycobacterium genus 286 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF004523.0 PRK05868 PRK05868.1 536 536 372 equivalog Y Y N FAD-binding protein 1763 Mycobacterium genus 305 NCBI Protein Cluster (PRK) hypothetical protein FAD-binding protein NF004527.0 PRK05874 PRK05874.1 308 308 218 equivalog Y Y N L-fuculose-phosphate aldolase 1763 Mycobacterium genus 339 NCBI Protein Cluster (PRK) L-fuculose-phosphate aldolase L-fuculose-phosphate aldolase Catalyzes the formation of glycerone phosphate and (S)-lactaldehyde from L-fuculose 1-phosphate NF005782.0 PRK07597 PRK07597.9-1 201 201 164 equivalog Y Y N preprotein translocase subunit SecE secE 1763 Mycobacterium genus 234 NCBI Protein Cluster (PRK) preprotein translocase subunit SecE preprotein translocase subunit SecE NF008883.0 PRK11915 PRK11915.1 698 698 621 equivalog Y Y N lysophospholipid acyltransferase 1763 Mycobacterium genus 446 NCBI Protein Cluster (PRK) glycerol-3-phosphate acyltransferase lysophospholipid acyltransferase NF008972.0 PRK12320 PRK12320.1 792 792 699 equivalog Y N N hypothetical protein 1763 Mycobacterium genus 463 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF009922.0 PRK13383 PRK13383.1 987 987 528 equivalog Y N N acyl-CoA synthetase 1763 Mycobacterium genus 144 NCBI Protein Cluster (PRK) acyl-CoA synthetase acyl-CoA synthetase NF013623.5 PF01469.23 Pentapeptide_2 26.4 26.4 40 repeat Y N N pentapeptide repeat-containing protein 9634230,9655353 1763 Mycobacterium genus 21897 EBI-EMBL Pentapeptide repeats (8 copies) Pentapeptide repeats (8 copies) These repeats are found in many mycobacterial proteins. These repeats are most common in the Pfam:PF00823 family of proteins, where they are found in the MPTR subfamily of PPE proteins. The function of these repeats is unknown. The repeat can be approximately described as XNXGX, where X can be any amino acid. These repeats are similar to Pfam:PF00805 [1], however it is not clear if these two families are structurally related. [1]. 9655353. Structure and distribution of pentapeptide repeats in bacteria. Bateman A, Murzin A, Teichmann SA;. Protein Sci 1998;7:1477-1480. [2]. 9634230. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE 3rd, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jage. Nature 1998;393:537-544. (from Pfam) NF023900.5 PF12484.13 PPE-SVP 23 23 80 subfamily_domain Y Y N PPE family protein, SVP subgroup 17105670,19144814 1763 Mycobacterium genus 16722 EBI-EMBL PPE-SVP subfamily C-terminal region SVP domain This domain family is found in bacteria, and is approximately 90 amino acids in length. The family is found to the C-terminus of Pfam:PF00823. There is a conserved SVP sequence motif which is diagnostic of this subfamily [2]. There is a single completely conserved residue W that may be functionally important. The proteins in this family are PPE proteins implicated in immunostimulation and virulence. [1]. 19144814. Genomic comparison of PE and PPE genes in the Mycobacterium avium complex. Mackenzie N, Alexander DC, Turenne CY, Behr MA, De Buck JM;. J Clin Microbiol. 2009;47:1002-1011. [2]. 17105670. Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. Gey van Pittius NC, Sampson SL, Lee H, Kim Y, van Helden PD, Warren RM;. BMC Evol Biol. 2006;6:95. (from Pfam) NF036921.5 PF18646.6 DUF5632 25 25 81 domain Y Y N DUF5632 domain-containing protein 27487929 1763 Mycobacterium genus 2108 EBI-EMBL Family of unknown function (DUF5632) DUF5632 domain This an alpha-beta-alpha domain found at the N-terminal region of Rv3899c, a hypothetical protein from Mycobacterium tuberculosis which is conserved across mycobacteria [1]. [1]. 27487929. Crystal structure of Rv3899c(184-410), a hypothetical protein from Mycobacterium tuberculosis. Liu Y, Gao Y, Li D, Fleming J, Li H, Bi L;. Acta Crystallogr F Struct Biol Commun. 2016;72:642-645. (from Pfam) NF037368.5 PF18645.6 DUF5631 25 25 96 domain Y Y N DUF5631 domain-containing protein 27487929 1763 Mycobacterium genus 2121 EBI-EMBL Family of unknown function (DUF5631) DUF5631 domain-containing protein This is an alpha helical domain found at the C-terminal region of the hypothetical protein Rv3899c from Mycobacterium tuberculosis which is conserved across mycobacteria [1]. [1]. 27487929. Crystal structure of Rv3899c(184-410), a hypothetical protein from Mycobacterium tuberculosis. Liu Y, Gao Y, Li D, Fleming J, Li H, Bi L;. Acta Crystallogr F Struct Biol Commun. 2016;72:642-645. (from Pfam) NF038019.1 PE_process_PecA 150 150 278 equivalog_domain Y Y N PecA family PE domain-processing aspartic protease GO:0004190 23923105,31662454 1763 Mycobacterium genus 1872 NCBIFAM PecA family PE domain-processing aspartic protease PecA from Mycobacterium marinum, and by homology, three related paralogs from Mycobacterium tuberculosis (PE26, PE_PGRS35, and PE_PGRS16) are all PE domain-containing proteins secreted by a type VII secretion system (T7SS, also called ESX in Mycobacterium), and all share a C-terminal aspartic protease-like domain. PecA itself is now known to be a functional aspartic protease that cleaves within the PE domain of T7SS secretion substrates that have the domain, including itself. Members of this family typically contain a long, variable, low-complexity region. This HMM represents the aspartic protease region C-terminal to the low-complexity region. NF038337.1 FAAL_FadD21 1100 1100 579 exception Y Y N fatty-acid--AMP ligase FAAL21/FadD21 fadD21 19182784,25124040 1763 Mycobacterium genus 215 NCBIFAM fatty-acid--AMP ligase FAAL21/FadD21 NF040652.1 Mbox_reg_Rv1535 62 62 77 equivalog Y Y N Rv1535 family protein 16573683 1763 Mycobacterium genus 411 NCBIFAM Rv1535 family protein Members of this family include Rv1535 from Mycobacterium tuberculosis, regulated in response to changes in Mg(2+) leves and encoded immediately downstream from an Mbox Mg(2+)-sensing riboswitch. NF044496.2 PF21526.2 PGRS 27 27 73 domain Y Y N PGRS repeat-containing protein 36048802 1763 Mycobacterium genus 54963 EBI-EMBL PGRS repeats PGRS repeat PE_PGRSs are a large family of Mtb proteins implicated in tuberculosis (TB) pathogenesis that show a modular structure: the N-terminal PE domain, highly homologous to the domain found in tens of others PE proteins and whose structure has been already solved by crystallography; a C-terminal domain that is unique for each protein; the polymorphic glycine-rich domain (PGRS) that varies in length from few tens to more than 1,000 amino acids [1]. [1]. 36048802. PGRS domain structures: Doomed to sail the mycomembrane. Berisio R, Delogu G;. PLoS Pathog. 2022;18:e1010760. (from Pfam) NF045549.1 GGPPsyn_IdsB 475 475 346 equivalog Y Y N geranylgeranyl diphosphate synthase IdsB idsB 2.5.1.29 GO:0004311,GO:0004659,GO:0008299,GO:0033386 23091471 1763 Mycobacterium genus 166 NCBIFAM geranylgeranyl diphosphate synthase IdsB NF046107.1 ResusProRpfC 200 200 136 equivalog Y Y N resuscitation-promoting factor RpfC rpfC GO:0009372,GO:0016787,GO:0042127 15723078,16034419,20545848 1763 Mycobacterium genus 177 NCBIFAM resuscitation-promoting factor RpfC TIGR04465.1 TIGR04465 ArgArg_F420 470 470 364 equivalog Y Y N F420-dependent hydroxymycolic acid dehydrogenase 23110042 1763 Mycobacterium genus 368 JCVI TAT-translocated F420-dependent dehydrogenase, FGD2 family F420-dependent hydroxymycolic acid dehydrogenase Members of this family are F420-binding enzymes with a proven functional N-terminal twin-arginine translocation (TAT) signal. Members are homologous to the cytosolic F420-dependent glucose-6-phosphate dehydrogenase but do not share the same function. NF041658.1 ornithlipidmtase_OlsG 350 350 191 equivalog Y Y N ornithine lipid N-methyltransferase olsG 2.1.1.344 GO:0000179 25925947 1763524 Isosphaeraceae family 16 NCBIFAM ornithine lipid N-methyltransferase NF020878.5 PF09320.16 DUF1977 23.4 23.4 108 domain Y Y N DUF1977 domain-containing protein 1763998 Rheinheimera sp. F8 species 1 EBI-EMBL Domain of unknown function (DUF1977) Domain of unknown function (DUF1977) Members of this family of functionally uncharacterised domains are predominantly found in dnaj-like proteins. (from Pfam) NF017925.5 PF06159.18 DUF974 25.3 25.3 242 domain Y Y N DUF974 domain-containing protein 1766256 uncultured Agathobacter sp. species 1 EBI-EMBL Protein of unknown function (DUF974) Protein of unknown function (DUF974) Family of uncharacterised eukaryotic proteins. (from Pfam) NF021761.5 PF10265.14 Miga 25 25 540 domain Y Y N mitoguardin GO:0008053 26711011,26716412 1767027 Flavobacterium suaedae species 1 EBI-EMBL Mitoguardin mitoguardin Mitoguardin (Miga) was first identified in flies as a mitochondrial outer-membrane protein that promotes mitochondrial fusion. Later, the mammalian Miga homologues, Miga1 and Miga2, were identified. They are found to promote mitochondrial fusion by regulating mitochondrial phospholipid metabolism via MitoPLD [1, 2]. [1]. 26711011. Mitoguardin Regulates Mitochondrial Fusion through MitoPLD and Is Required for Neuronal Homeostasis. Zhang Y, Liu X, Bai J, Tian X, Zhao X, Liu W, Duan X, Shang W, Fan HY, Tong C;. Mol Cell. 2016;61:111-124. [2]. 26716412. Mitoguardin-1 and -2 promote maturation and the developmental potential of mouse oocytes by maintaining mitochondrial dynamics and functions. Liu XM, Zhang YP, Ji SY, Li BT, Tian X, Li D, Tong C, Fan HY;. Oncotarget. 2016;7:1155-1167. (from Pfam) NF000054.1 AAC_2p_Ie 400 400 182 exception Y Y Y aminoglycoside N-acetyltransferase AAC(2')-Ie aac(2')-Ie 1769 Mycobacterium leprae species 1 NCBIFAM aminoglycoside N-acetyltransferase AAC(2')-Ie aminoglycoside N-acetyltransferase AAC(2')-Ie NF000042.1 AAC_2p_Id 400 400 210 exception Y Y Y aminoglycoside N-acetyltransferase AAC(2')-Id aac(2')-Id 2163027 1772 Mycolicibacterium smegmatis species 3 NCBIFAM aminoglycoside 2'-N-acetyltransferase AAC(2')-Id aminoglycoside N-acetyltransferase AAC(2')-Id NF011977.0 PRK15443 PRK15443.2-4 230 230 119 subfamily Y Y N diol dehydratase small subunit 1772 Mycolicibacterium smegmatis species 2 NCBI Protein Cluster (PRK) propanediol dehydratase small subunit diol dehydratase small subunit NF000034.1 AAC_2p_Ic 375 375 181 exception Y Y Y aminoglycoside N-acetyltransferase AAC(2')-Ic aac(2')-Ic 9159528 1773 Mycobacterium tuberculosis species 27 NCBIFAM aminoglycoside 2'-N-acetyltransferase AAC(2')-Ic aminoglycoside N-acetyltransferase AAC(2')-Ic NF000349.1 mfpA_AE000516.2 360 360 183 equivalog Y Y N pentapeptide repeat protein MfpA mfpA 21605934 1773 Mycobacterium tuberculosis species 38 NCBIFAM pentapeptide repeat protein MfpA pentapeptide repeat protein MfpA NF000468.1 Erm37 350 350 179 exception Y Y Y 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(37) erm(37) 1773 Mycobacterium tuberculosis species 35 NCBIFAM 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(37) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(37) NF002364.0 PRK01346 PRK01346.1-1 701 701 408 equivalog Y Y N enhanced intracellular survival protein Eis 17259625 1773 Mycobacterium tuberculosis species 129 NCBI Protein Cluster (PRK) hypothetical protein enhanced intracellular survival protein Eis NF003982.0 PRK05471 PRK05471.1-1 441 441 262 equivalog Y Y N CDP-diacylglycerol diphosphatase 3.6.1.26 1773 Mycobacterium tuberculosis species 62 NCBI Protein Cluster (PRK) CDP-diacylglycerol pyrophosphatase CDP-diacylglycerol diphosphatase NF004716.0 PRK06060 PRK06060.1 1228 1228 705 equivalog Y Y N p-hydroxybenzoic acid--AMP ligase FadD22 1773 Mycobacterium tuberculosis species 166 NCBI Protein Cluster (PRK) acyl-CoA synthetase p-hydroxybenzoic acid--AMP ligase FadD22 NF006116.0 PRK08264 PRK08264.1-2 459 459 235 equivalog Y Y N SDR family oxidoreductase 1773 Mycobacterium tuberculosis species 49 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006788.0 PRK09294 PRK09294.1-2 539 539 422 equivalog Y Y N phthiocerol/phthiodiolone dimycocerosyl transferase 1773 Mycobacterium tuberculosis species 111 NCBI Protein Cluster (PRK) acyltransferase PapA5 phthiocerol/phthiodiolone dimycocerosyl transferase NF007072.0 PRK09519 PRK09519.1 1024 1024 790 equivalog Y Y N intein-containing recombinase RecA recA 11850426,12853636 1773 Mycobacterium tuberculosis species 117 NCBI Protein Cluster (PRK) DNA recombination protein RecA intein-containing recombinase RecA Catalyzes the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs NF009674.0 PRK13195 PRK13195.1 382 382 222 equivalog Y N N pyrrolidone-carboxylate peptidase 1773 Mycobacterium tuberculosis species 70 NCBI Protein Cluster (PRK) pyrrolidone-carboxylate peptidase pyrrolidone-carboxylate peptidase NF009681.0 PRK13202 PRK13202.1 204 204 104 equivalog Y Y N urease subunit beta 3.5.1.5 7559354 1773 Mycobacterium tuberculosis species 16 NCBI Protein Cluster (PRK) urease subunit beta urease subunit beta NF010126.0 PRK13603 PRK13603.1 234 234 126 equivalog Y Y N fumarate reductase subunit C 1773 Mycobacterium tuberculosis species 36 NCBI Protein Cluster (PRK) fumarate reductase subunit C fumarate reductase subunit C Part of four member fumarate reductase enzyme complex FrdABCD which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdCD are the membrane components which interact with quinone and are involved in electron transfer; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; the catalytic subunits are similar to succinate dehydrogenase SdhAB NF010547.0 PRK13938 PRK13938.1 320 320 196 equivalog Y Y N D-sedoheptulose 7-phosphate isomerase 5.3.1.28 1773 Mycobacterium tuberculosis species 73 NCBI Protein Cluster (PRK) phosphoheptose isomerase D-sedoheptulose 7-phosphate isomerase Catalyzes the isomerization of sedoheptulose 7-phosphate to D-glycero-D-manno-heptose 7-phosphate NF010574.0 PRK13967 PRK13967.1 687 687 322 equivalog Y Y N ribonucleotide-diphosphate reductase subunit beta 1773 Mycobacterium tuberculosis species 38 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit beta ribonucleotide-diphosphate reductase subunit beta NF010605.0 PRK14001 PRK14001.1 369 369 189 equivalog Y Y N K(+)-transporting ATPase subunit C 1773 Mycobacterium tuberculosis species 43 NCBI Protein Cluster (PRK) potassium-transporting ATPase subunit C K(+)-transporting ATPase subunit C Component of the high-affinity ATP-driven potassium transport (or KDP)system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions; the C subunit may be involved in assembly of the KDP complex NF010864.0 PRK14271 PRK14271.1 561 561 276 equivalog Y Y N phosphate ABC transporter ATP-binding protein 1773 Mycobacterium tuberculosis species 82 NCBI Protein Cluster (PRK) phosphate ABC transporter ATP-binding protein phosphate ABC transporter ATP-binding protein Part of an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation NF021868.5 PF10382.14 ZGRF1-like_N 23 23 80 domain Y Y N DNA helicase ZGRF1 domain-containing protein 15161972,16169489,26920759,26966246,26966248,32640219,34552057 1773 Mycobacterium tuberculosis species 1 EBI-EMBL DNA helicase ZGRF1-like, N-terminal domain DNA helicase ZGRF1-like, N-terminal domain This domain can be found in human 5'-3' DNA helicase ZGRF1 and similar eukaryotic proteins. ZGRF1 promotes repair of replication -blocking DNA lesions through stimulation of homologous recombination (HR) [6,7]. This domain can also be found in Mte1 (Mph1-associated telomere maintenance protein 1) from Saccharomyces cerevisiae, which is involved in telomere maintenance [1] and in and fission yeast Dbl2, involved in meiotic chromosome segregation. However, there is no evidence to suggest that this domain, which is predicted to adopt an all-beta structure, is implicated in DNA damage resistance or nuclear focus formation [2-5]. [1]. 15161972. A genome-wide screen for Saccharomyces cerevisiae deletion mutants that affect telomere length. Askree SH, Yehuda T, Smolikov S, Gurevich R, Hawk J, Coker C, Krauskopf A, Kupiec M, McEachern MJ;. Proc Natl Acad Sci U S A. 2004;101:8658-8663. [2]. 16169489. Novel genes required for meiotic chromosome segregation are identified by a high-throughput knockout screen in fission yeast. Gregan J, Rabitsch PK, Sakem B, Csutak O, Latypov V, Lehmann E, Kohli J, Nasmyth K;. Curr Biol. 2005;15:1663-1669. [3]. 26920759. MTE1 Functions with MPH1 in Double-Strand Break Repair. Yimit A, Kim T, Anand RP, Meister S, Ou J, Haber JE, Zhang Z, Brown GW;. Genetics. 2016;203:147-157. [4]. 26966248. Mte1 interacts with Mph1 and promotes crossover recombination and telomere maintenance. Silva S, Altmannova V, Luke-Glaser S, Henriksen P, Gallina I, Yang X, Choudhary C, Luke B, Krejci L, Lisby M;. Genes Dev. 2016;30:700-717. [5]. 26966246. Differential regulation of the anti-crossover and replication fork regressi. TRUNCATED at 1650 bytes (from Pfam) NF038338.1 FAAL_FadD28 1100 1100 580 exception Y Y N fatty-acid--AMP ligase FAAL28/FadD28 fadD28 12446629,19182784 1773 Mycobacterium tuberculosis species 125 NCBIFAM fatty-acid--AMP ligase FAAL28/FadD28 NF040165.4 PF18993.5 Rv0078B 27.1 27.1 63 domain Y N N Rv0078B-related antitoxin 31022176 1773 Mycobacterium tuberculosis species 195 EBI-EMBL Rv0078B-related antitoxin Rv0078B-related antitoxin Putative antitoxin protein according to TASmania database [1]. [1]. 31022176. TASmania: A bacterial Toxin-Antitoxin Systems database. Akarsu H, Bordes P, Mansour M, Bigot DJ, Genevaux P, Falquet L;. PLoS Comput Biol. 2019;15:e1006946. (from Pfam) NF041154.1 MTB_classA_BlaC 685 685 307 exception Y Y Y class A beta-lactamase BlaC blaC 3.5.2.6 GO:0008800 25492589,35196121 1773 Mycobacterium tuberculosis species 42 NCBIFAM class A beta-lactamase BlaC NF041649.1 ceramidase_neut 1200 1200 636 equivalog Y Y N neutral ceramidase 3.5.1.23 GO:0017040,GO:0046514 20139604 1773 Mycobacterium tuberculosis species 163 NCBIFAM neutral ceramidase NF042939.1 leader_Rv2334A 35 35 22 equivalog Y Y N Rv2334A family Cys-rich leader peptide 32181921 1773 Mycobacterium tuberculosis species 9 NCBIFAM Rv2334A family Cys-rich leader peptide Zero WPs at creation, it seemed. Model will need a rebuild once some become available. Manually created WP_306921051. NF045824.1 RhmsylMtase 400 400 226 equivalog Y Y N rhamnosyl O-methyltransferase 2.1.1.- GO:0008757,GO:0071770 15292265 1773 Mycobacterium tuberculosis species 148 NCBIFAM rhamnosyl O-methyltransferase TIGR01147.1 TIGR01147 V_ATP_synt_G 56.95 56.95 113 equivalog Y Y N V-type ATPase subunit G 7.1.2.2 GO:0008553,GO:0016471,GO:1902600 1773 Mycobacterium tuberculosis species 1 JCVI V-type ATPase, G subunit V-type ATPase subunit G This model describes the vacuolar ATP synthase G subunit in eukaryotes and includes members from diverse groups e.g., fungi, plants, parasites etc. V-ATPases are multi-subunit enzymes composed of two functional domains: A transmembrane Vo domain and a peripheral catalytic domain V1. The G subunit is one of the subunits of the catalytic domain. V-ATPases are responsible for the acidification of endosomes and lysosomes, which are part of the central vacuolar system. NF017244.5 PF05407.17 Peptidase_C27 26.3 26.3 164 equivalog Y Y N C27 family endopeptidase GO:0004197 10466783,10823845,10846076 1775132 Streptomyces mesophilus species 2 EBI-EMBL Rubella virus endopeptidase Rubella virus endopeptidase Corresponds to Merops family C27. Required for processing of the rubella virus replication protein. [1]. 10823845. Rubella virus nonstructural protein protease domains involved in trans- and cis-cleavage activities. Liang Y, Yao J, Gillam S;. J Virol 2000;74:5412-5423. [2]. 10846076. Characterization of the zinc binding activity of the rubella virus nonstructural protease. Liu X, Yang J, Ghazi AM, Frey TK;. J Virol 2000;74:5949-5956. [3]. 10466783. Virus-encoded proteinases of the Togaviridae. ten Dam E, Flint M, Ryan MD;. J Gen Virol 1999;80:1879-1888. (from Pfam) NF040671.1 PLuB_AAA 999 999 1256 exception Y Y N PLuB system helicase-like protein plbH 1779134 Bradymonadales order 7 NCBIFAM PLuB system helicase-like protein The PLuB system is found in the genera Persicimonas, Lujinxingia, and Bradymonas, all members of the Deltaproteobacteria. This protein, with an AAA+ domain, shows strong local homology to various helicases. The system also includes a CPBP family intramembrane glutamic endopeptidase and a PQQ-binding-like beta-propeller repeat protein. NF040673.1 PLuB_PQQ_rpt 250 250 395 exception Y Y N PLuB system PQQ-binding repeat protein plbQ 1779134 Bradymonadales order 7 NCBIFAM PLuB system PQQ-binding repeat protein Members of this family contain a region similar to the PQQ-binding repeats domain (see PF13360), and occur in a conserved gene neighborhood together with a helicase-like protein and a CPBP family intramembrane protease. This system, designated PLuB, is found in the genera Persicimonas, Lujinxingia, and Bradymonas, all members of the Deltaproteobacteria. NF040674.1 PLuB_CAAX 250 250 354 equivalog Y Y N myxosortase MrtP mrtP 3.4.26.- GO:0005886,GO:0006605,GO:0070007 1779134 Bradymonadales order 7 NCBIFAM myxosortase MrtP NF009029.0 PRK12365 PRK12365.1 1350 1350 1046 equivalog Y Y N ribonucleoside-diphosphate reductase subunit alpha 1783257 PVC group no rank 93 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit alpha ribonucleoside-diphosphate reductase subunit alpha NF011448.0 PRK14869 PRK14869.2-4 562 562 563 equivalog Y Y N putative manganese-dependent inorganic diphosphatase 3.6.1.1 1783257 PVC group no rank 160 NCBI Protein Cluster (PRK) putative manganese-dependent inorganic pyrophosphatase putative manganese-dependent inorganic diphosphatase NF042425.1 Amuc_1099_fam 50 50 321 equivalog Y Y N Amuc_1099 family pilus-like system protein 1783257 PVC group no rank 128 NCBIFAM Amuc_1099 family pilus-like system protein NF045322.2 PF21223.2 TPPII_Ig-like-1 27 27 117 domain Y N N Tripeptidyl-peptidase II, first Ig-like domain 20676100 1783257 PVC group no rank 31 EBI-EMBL Tripeptidyl-peptidase II, first Ig-like domain Tripeptidyl-peptidase II, first Ig-like domain Tripeptidyl peptidase II (TPPII) is a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides. This protein adopts a dimeric assembly. Each monomer is organised into three main parts: the N-terminal subtilisine-like domain (Pfam:PF00082) a central domain and C-terminal domain (Pfam:PF12583). The central domain can be subdivided into two Ig-like domains and a GBD-like domain (Pfam:PF21316). This entry represents the first Ig-like domain, while Pfam:PF12580 represents the second one [1]. Paper describing PDB structure 3lxu. [1]. 20676100. Hybrid molecular structure of the giant protease tripeptidyl peptidase II. Chuang CK, Rockel B, Seyit G, Walian PJ, Schonegge AM, Peters J, Zwart PH, Baumeister W, Jap BK;. Nat Struct Mol Biol. 2010;17:990-996. (from Pfam) TIGR02597.1 TIGR02597 TIGR02597 50 45 363 paralog Y Y N TIGR02597 family protein 1783257 PVC group no rank 83 JCVI TIGR02597 family protein TIGR02597 family protein This model describes a paralogous family with at least ten members in Verrucomicrobium spinosum. Two additional predicted proteins match more weakly and score between the trusted and noise cutoffs, while a third contains a point mutation. Eleven of the thirteen genes are found in a single tandem array. NF002082.0 PRK00913 PRK00913.3-4 552 552 504 equivalog Y Y N leucyl aminopeptidase 3.4.11.1 1783270 FCB group no rank 43 NCBI Protein Cluster (PRK) multifunctional aminopeptidase A leucyl aminopeptidase NF011388.0 PRK14813 PRK14813.1 294 294 189 equivalog Y N N NADH dehydrogenase subunit B 1783270 FCB group no rank 373 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit B NADH dehydrogenase subunit B NF019592.5 PF07980.16 SusD_RagB 23.1 23.1 297 domain Y Y N RagB/SusD family nutrient uptake outer membrane protein 22819666,26441291 1783270 FCB group no rank 193217 EBI-EMBL SusD family RagB/SusD family nutrient uptake outer membrane protein This domain is found in bacterial cell surface proteins such SusD Swiss:Q8A1G2 and SusD-like proteins Swiss:A7LXT5 as as well RagB, outer membrane surface receptor antigen. Bacteroidetes, one of the two dominant bacterial phyla in the human gut, are Gram-negative saccharolytic microorganisms that utilize a diverse array of glycans. Hence, they express starch-utilization system (Sus) for glycan uptake. SusD has 551 amino acids, and is almost entirely alpha-helical, with 22 alpha-helices, eight of which form 4 tetra-trico peptide repeats (TPRs: helix-turn-helix motifs involved in protein-protein interactions). The four TPRs pack together to create a right-handed super-helix. This is predicted to mediate the formation of SusD and SusC porin complex at the cell surface. The interaction between SusC and TPR1/TPR2 region of SusD is predicted to be of functional importance since it allows SusD to be in position for oligosaccharide capture from other Sus lipoproteins and delivery of these glycans to the SusC porin. The non-TPR containing portion of SusD is where starch binding occurs. The binding site is a shallow surface cavity located on top of TPR1. SusD homologs such as SusD-like proteins have a critical role in carbohydrate acquisition. Both SusD and its homologs, contain 15-20 residues at the N-terminus that might be a flexible linker region, anchoring the protein to the membrane and the glycan-binding domain [1]. Other homologs to SusD have been examined in Porphyromonas gingivalis such as RagB, an immunodominant outer-membrane surface receptor antigen. Structural characterization of RagB shows substantial similarity with . TRUNCATED at 1650 bytes (from Pfam) NF024152.5 PF12741.12 SusD-like 27 27 495 domain Y Y N SusD/RagB family nutrient-binding outer membrane lipoprotein 19191477 1783270 FCB group no rank 38789 EBI-EMBL Susd and RagB outer membrane lipoprotein SusD/RagB family nutrient-binding outer membrane lipoprotein This is a family of SusD-like proteins, one member of which, BT1043 (Swiss:Q8A8X4), is an outer membrane lipoprotein involved in host glycan metabolism. The structures of this and SusD-homologues in the family are dominated by tetratrico peptide repeats that may facilitate association with outer membrane beta-barrel transporters required for glycan uptake. The structure of BT1043 complexed with N-acetyllactosamine reveals that recognition is mediated via hydrogen bonding interactions with the reducing end of beta-N-acetylglucosamine, suggesting a role in binding glycans liberated from the mucin polypeptide. Mammalian distal gut bacteria have an expanded capacity to utilize glycans. In the absence of dietary sources, some species rely on host-derived mucosal glycans. The ability of Bacteroides thetaiotaomicron, a prominent human gut symbiont, to forage host glycans contributes to both its ability to persist within an individual host and its ability to be transmitted naturally to new hosts at birth. [1]. 19191477. Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont. Koropatkin N, Martens EC, Gordon JI, Smith TJ;. Biochemistry. 2009;48:1532-1542. (from Pfam) NF024181.5 PF12771.12 SusD-like_2 27 27 415 domain Y Y N SusD/RagB family nutrient-binding outer membrane lipoprotein 19191477 1783270 FCB group no rank 51225 EBI-EMBL Starch-binding associating with outer membrane SusD/RagB family nutrient-binding outer membrane lipoprotein SusD is a secreted starch-binding protein with an N-terminal lipid tail that allows it to associate with the outer membrane. (from Pfam) NF024599.5 PF13201.11 PCMD 28 28 234 domain Y Y N PCMD domain-containing protein 20944224 1783270 FCB group no rank 7664 EBI-EMBL Putative carbohydrate metabolism domain Putative carbohydrate metabolism domain This domain has been suggested to participate in carbohydrate metabolism [1]. Structural evidence indicates that it might be a carbohydrate binding domain, with or without enzymatic activity. In particular, it has been hypothesised that it might act as a glycoside hydrolase [1]. [1]. 20944224. Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 A resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism. Yeh AP, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:1287-1296. (from Pfam) NF027573.5 PF16248.10 DUF4905 29.6 29.6 83 PfamAutoEq Y Y N DUF4905 domain-containing protein 1783270 FCB group no rank 542 EBI-EMBL Domain of unknown function (DUF4905) Domain of unknown function (DUF4905) A small family of uncharacterized proteins around 270 residues in length and found in various Cytophagales, Sphingobacteriaceae and Ignavibacteriaceae species. The function of this family is unknown. (from Pfam) NF047600.1 SerpalmtaseCFB 640 640 395 equivalog Y Y N serine palmitoyltransferase spt 2.3.1.50 GO:0004758,GO:0030170,GO:0046513 17557831 1783270 FCB group no rank 1506 NCBIFAM serine palmitoyltransferase TIGR04056.1 TIGR04056 OMP_RagA_SusC 368.25 368.25 981 subfamily Y Y N SusC/RagA family TonB-linked outer membrane protein GO:0009279,GO:0022857 11553542,11717282,15972517 1783270 FCB group no rank 268726 JCVI TonB-linked outer membrane protein, SusC/RagA family SusC/RagA family TonB-linked outer membrane protein This model describes a distinctive clade among the TonB-linked outer membrane proteins (OMP). Members of this family are restricted to the Bacteriodetes lineage (except for Gemmatimonas aurantiaca T-27 from the novel phylum Gemmatimonadetes) and occur in high copy numbers, with over 100 members from Bacteroides thetaiotaomicron VPI-5482 alone. Published descriptions of members of this family are available for RagA from Porphyromonas gingivalis, SusC from Bacteroides thetaiotaomicron, and OmpW from Bacteroides caccae. Members form pairs with members of the SusD/RagB family (PF07980). Transporter complexes including these outer membrane proteins are likely to import large degradation products of proteins (e.g. RagA) or carbohydrates (e.g. SusC) as nutrients, rather than siderophores. TIGR04057.1 TIGR04057 SusC_RagA_signa 46.2 46.2 31 signature Y N N SusC/RagA subfamily TonB-dependent outer membrane receptor 1783270 FCB group no rank 258967 JCVI TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region SusC/RagA subfamily TonB-dependent outer membrane receptor, signature region This model describes a 31-residue signature region of the SusC/RagA family of outer membrane proteins from the Bacteriodetes. While many TonB-dependent outer membrane receptors are associated with siderophore import, this family seems to include generalized nutrient receptors that may convey fairly large oligomers of protein or carbohydrate. This family occurs in high copy numbers in the most abundant species of the human gut microbiome. NF000049.1 tet_MFS_40 800 800 406 exception Y Y Y tetracycline efflux MFS transporter Tet(40) tet(40) GO:0008493,GO:0015904 1783272 Bacillati kingdom 107 NCBIFAM tetracycline efflux MFS transporter Tet(40) tetracycline efflux MFS transporter Tet(40) NF000091.3 D_ala_D_ser_VanG 495 495 344 exception Y Y Y D-alanine--D-serine ligase VanG vanG 6.3.2.35 1783272 Bacillati kingdom 630 NCBIFAM D-alanine--D-serine ligase VanG D-alanine--D-serine ligase VanG This model describes the VanG family of D-alanine--D-serine ligase, including both characterized examples and additional proteins from similar genomic contexts next to other signature vancomycin resistance genes. NF000129.1 D_ala_D_lac_Sc 650 650 346 exception Y Y Y D-alanine--(R)-lactate ligase VanA-Sc vanA-Sc 6.1.2.1 GO:0005737,GO:0008716,GO:0046872 1783272 Bacillati kingdom 255 NCBIFAM D-alanine--(R)-lactate ligase VanA-Sc D-alanine--(R)-lactate ligase VanA-Sc NF000477.1 NshR_TsnR 425 360 266 equivalog Y Y Y NshR/TsnR family 23S rRNA methyltransferase nshR GO:0006396,GO:0046677 1783272 Bacillati kingdom 243 NCBIFAM NshR/TsnR family 23S rRNA methyltransferase NshR/TsnR family 23S rRNA methyltransferase NF000671.1 PRK00033 PRK00033.1-4 107 107 91 equivalog Y Y N ATP-dependent Clp protease adapter ClpS clpS 1783272 Bacillati kingdom 666 NCBI Protein Cluster (PRK) ATP-dependent Clp protease adaptor protein ClpS ATP-dependent Clp protease adapter ClpS NF000825.0 PRK00068 PRK00068.1 995 995 973 subfamily Y N N hypothetical protein 1783272 Bacillati kingdom 7053 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF000994.0 PRK00104 PRK00104.1-3 234 234 246 equivalog Y Y N segregation/condensation protein A 1783272 Bacillati kingdom 1325 NCBI Protein Cluster (PRK) segregation and condensation protein A segregation/condensation protein A NF001900.0 PRK00654 PRK00654.1-3 509 509 481 equivalog Y Y N glycogen synthase GlgA glgA 2.4.1.21 1783272 Bacillati kingdom 1019 NCBI Protein Cluster (PRK) glycogen synthase glycogen synthase GlgA NF002605.0 PRK02260 PRK02260.2-3 306 306 164 equivalog Y Y N S-ribosylhomocysteine lyase 4.4.1.21 1783272 Bacillati kingdom 311 NCBI Protein Cluster (PRK) S-ribosylhomocysteinase S-ribosylhomocysteine lyase NF002608.0 PRK02260 PRK02260.3-1 272 272 158 equivalog Y Y N S-ribosylhomocysteine lyase 4.4.1.21 1783272 Bacillati kingdom 1601 NCBI Protein Cluster (PRK) S-ribosylhomocysteinase S-ribosylhomocysteine lyase NF002707.0 PRK02509 PRK02509.1 949 949 983 equivalog Y N N hypothetical protein 1783272 Bacillati kingdom 906 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003299.0 PRK04296 PRK04296.1-4 284 284 191 equivalog Y Y N thymidine kinase 2.7.1.21 GO:0004797 1783272 Bacillati kingdom 3104 NCBI Protein Cluster (PRK) thymidine kinase thymidine kinase NF003356.0 PRK04405 PRK04405.1 339 339 299 subfamily Y Y N peptidylprolyl isomerase 5.2.1.8 1783272 Bacillati kingdom 1324 NCBI Protein Cluster (PRK) peptidylprolyl isomerase peptidylprolyl isomerase Cis/trans isomerase of peptidylprolyl NF004368.0 PRK05738 PRK05738.3-4 122 122 100 equivalog Y Y N 50S ribosomal protein L23 1783272 Bacillati kingdom 558 NCBI Protein Cluster (PRK) 50S ribosomal protein L23 50S ribosomal protein L23 NF005219.0 PRK06707 PRK06707.1 498 498 536 equivalog Y N N amidase 1783272 Bacillati kingdom 1284 NCBI Protein Cluster (PRK) amidase amidase NF005253.0 PRK06762 PRK06762.1-4 159 159 166 equivalog Y N N hypothetical protein 1783272 Bacillati kingdom 1985 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005255.0 PRK06762 PRK06762.2-2 140 140 163 equivalog Y N N hypothetical protein 1783272 Bacillati kingdom 2453 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005832.0 PRK07735 PRK07735.1 431 431 430 equivalog Y Y N NADH-quinone oxidoreductase subunit C 1.6.5.9 GO:0008137 1783272 Bacillati kingdom 2806 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit C NADH-quinone oxidoreductase subunit C NF006087.0 PRK08236 PRK08236.1 213 213 219 equivalog Y Y N futalosine hydrolase 3.2.2.26 GO:0009234,GO:0016799 1783272 Bacillati kingdom 8762 NCBI Protein Cluster (PRK) hypothetical protein futalosine hydrolase NF006365.0 PRK08588 PRK08588.1 289 289 383 subfamily Y N N succinyl-diaminopimelate desuccinylase 1783272 Bacillati kingdom 6155 NCBI Protein Cluster (PRK) succinyl-diaminopimelate desuccinylase succinyl-diaminopimelate desuccinylase NF006380.0 PRK08621 PRK08621.1 164 164 142 equivalog Y Y N galactose-6-phosphate isomerase subunit LacA lacA 5.3.1.26 1400164,15466549 1783272 Bacillati kingdom 1800 NCBI Protein Cluster (PRK) galactose-6-phosphate isomerase subunit LacA galactose-6-phosphate isomerase subunit LacA Catalyzes the interconversion of galactose 6-phosphate to tagatose 6-phosphate; tagatose pathway for galactose utilization NF006382.0 PRK08624 PRK08624.1 440 440 373 equivalog Y N N hypothetical protein 1783272 Bacillati kingdom 258 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF009104.0 PRK12449 PRK12449.1 70 70 80 equivalog Y N N acyl carrier protein 1783272 Bacillati kingdom 1690 NCBI Protein Cluster (PRK) acyl carrier protein acyl carrier protein NF009975.0 PRK13436 PRK13436.1 129 129 180 equivalog Y Y N F0F1 ATP synthase subunit delta 7.1.2.2 1783272 Bacillati kingdom 398 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit delta F0F1 ATP synthase subunit delta Produces ATP from ADP in the presence of a proton gradient across the membrane; the delta subunit is part of the catalytic core of the ATP synthase complex NF010036.0 PRK13511 PRK13511.1 610 610 469 subfamily Y Y N 6-phospho-beta-galactosidase 3.2.1.85 1783272 Bacillati kingdom 4898 NCBI Protein Cluster (PRK) 6-phospho-beta-galactosidase 6-phospho-beta-galactosidase Catalyzes the formation of 6-phospho-galactose from a 6-phospho-beta-galactoside NF010724.0 PRK14126 PRK14126.1 80 80 87 equivalog Y Y N cell division protein ZapA zapA GO:0051301 12368265 1783272 Bacillati kingdom 1824 NCBI Protein Cluster (PRK) cell division protein ZapA cell division protein ZapA NF010741.0 PRK14143 PRK14143.1 184 184 258 equivalog Y Y N nucleotide exchange factor GrpE grpE 1783272 Bacillati kingdom 992 NCBI Protein Cluster (PRK) heat shock protein GrpE nucleotide exchange factor GrpE With DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins NF010824.0 PRK14228 PRK14228.1 99 99 122 equivalog Y Y N fluoride efflux transporter CrcB crcB 1783272 Bacillati kingdom 1465 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter CrcB NF011021.0 PRK14450 PRK14450.1 109 109 91 equivalog Y Y N acylphosphatase 3.6.1.7 1783272 Bacillati kingdom 19 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011092.0 PRK14515 PRK14515.1 876 876 479 subfamily Y Y N aspartate ammonia-lyase 4.3.1.1 1783272 Bacillati kingdom 2777 NCBI Protein Cluster (PRK) aspartate ammonia-lyase aspartate ammonia-lyase Catalyzes the formation of fumarate from aspartate NF011109.0 PRK14537 PRK14537.1 187 187 232 equivalog Y N N 50S ribosomal protein L20/unknown domain fusion protein 1783272 Bacillati kingdom 67 NCBI Protein Cluster (PRK) 50S ribosomal protein L20/unknown domain fusion protein 50S ribosomal protein L20/unknown domain fusion protein NF011449.0 PRK14869 PRK14869.2-5 411 411 451 equivalog Y Y N putative manganese-dependent inorganic diphosphatase 3.6.1.1 1783272 Bacillati kingdom 94 NCBI Protein Cluster (PRK) putative manganese-dependent inorganic pyrophosphatase putative manganese-dependent inorganic diphosphatase NF011547.0 PRK14976 PRK14976.1-4 305 305 291 equivalog Y N N 5'-3' exonuclease 1783272 Bacillati kingdom 433 NCBI Protein Cluster (PRK) 5'-3' exonuclease 5'-3' exonuclease NF012162.2 surf_Nterm_1 40 40 234 domain Y Y N thioester-forming surface-anchored protein 26032562 1783272 Bacillati kingdom 2841 NCBIFAM surf_Nterm_1: surface protein N-terminal domain surface-anchored protein thioester-forming domain This model describes a conserved region, fairly rich in insertions and deletions, located just past the signal peptide region in long, variable, and typically highly repetitive and sortase-dependent surface proteins. Members are found in a broad range of taxa, including many strains of Streptococcus pneumoniae. A conserved Cys forms a thioester bond, often to a host protein for covalent attachment. NF012712.5 PF00502.24 Phycobilisome 22.2 22.2 155 domain Y N N Phycobilisome protein GO:0015979,GO:0030089 1783272 Bacillati kingdom 7759 EBI-EMBL Phycobilisome protein Phycobilisome protein NF013518.5 PF01356.24 A_amylase_inhib 25 25 68 PfamEq Y N N Alpha amylase inhibitor GO:0015066 3489104 1783272 Bacillati kingdom 1100 EBI-EMBL Alpha amylase inhibitor Alpha amylase inhibitor NF013627.5 PF01473.25 Choline_bind_1 20.5 9.8 19 repeat Y N N choline-binding repeat-containing protein 11040428,14527392,1830357,2307516,3040686,3422470,7860591 1783272 Bacillati kingdom 56664 EBI-EMBL Putative cell wall binding repeat choline-binding repeat These repeats are characterised by conserved aromatic residues and glycines are found in multiple tandem copies in a number of proteins. The CW repeat is 20 amino acid residues long. The exact domain boundaries may not be correct. It has been suggested that these repeats in Swiss:P15057 might be responsible for the specific recognition of choline-containing cell walls [1]. Similar but longer repeats are found in the glucosyltransferases and glucan-binding proteins of oral streptococci and shown to be involved in glucan binding [2] as well as in the related dextransucrases of Leuconostoc mesenteroides. Repeats also occur in toxins of Clostridium difficile and other clostridia, though the ligands are not always known. [1]. 3422470. Molecular evolution of lytic enzymes of Streptococcus pneumoniae and its bacteriophages. Garcia E, Garcia JL, Garcia P, Arraras A, Sanchez-Puelles JM, Lopez R;. Proc Natl Acad Sci U S A 1988;85:914-918. [2]. 14527392. Structural basis for selective recognition of pneumococcal cell wall by modular endolysin from phage Cp-1. Hermoso JA, Monterroso B, Albert A, Galan B, Ahrazem O, Garcia P, Martinez-Ripoll M, Garcia JL, Menendez M;. Structure (Camb) 2003;11:1239-1249. [3]. 7860591. Tracking the evolution of the bacterial choline-binding domain: molecular characterization of the Clostridium acetobutylicum NCIB 8052 cspA gene. Sanchez-Beato AR, Ronda C, Garcia JL;. J Bacteriol 1995;177:1098-1103. [4]. 1830357. A family of clostridial and streptococcal ligand-binding proteins with conserved C-terminal repeat sequences. Wren BW;. Mol Microbiol 1991;5:797-803. [5]. 2307516. Sequence analysis of the gene. TRUNCATED at 1650 bytes (from Pfam) NF014145.5 PF02052.20 Gallidermin 21 21 52 subfamily Y Y N gallidermin family lantibiotic GO:0005576,GO:0042742 1783272 Bacillati kingdom 467 EBI-EMBL Gallidermin gallidermin family lantibiotic NF014580.5 PF02533.20 PsbK 25 25 41 PfamEq Y N N Photosystem II 4 kDa reaction centre component GO:0009523,GO:0009539,GO:0015979 8193302 1783272 Bacillati kingdom 323 EBI-EMBL Photosystem II 4 kDa reaction centre component Photosystem II 4 kDa reaction centre component This family consists of various photosystem II 4 kDa reaction centre components (PsbK) from plant and Cyanobacteria. The photosystem II reaction centre is responsible for catalysing the core photosynthesis reaction the light-induced splitting of water and the consequential release of dioxygen. In C. reinhardtii the psbK product is required for the stable assembly and/or stability of the photosystem II complex [1]. [1]. 8193302. Directed disruption of the Chlamydomonas chloroplast psbK gene destabilizes the photosystem II reaction center complex. Takahashi Y, Matsumoto H, Goldschmidt-Clermont M, Rochaix JD;. Plant Mol Biol 1994;24:779-788. (from Pfam) NF015533.5 PF03574.20 Peptidase_S48 22.5 22.5 149 domain Y N N Peptidase family S48 GO:0003677,GO:0004252,GO:0043158 1783272 Bacillati kingdom 489 EBI-EMBL Peptidase family S48 Peptidase family S48 NF016047.5 PF04122.17 CW_binding_2 24.9 22.3 73 domain Y Y N cell wall-binding repeat-containing protein 25649385,28132783 1783272 Bacillati kingdom 28130 EBI-EMBL Cell wall binding domain 2 (CWB2) Cell wall binding domain 2 (CWB2) This domain is found in 1 to 3 tandem copies in a wide variety of bacterial cell surface proteins. It has been show the three tandem repeats of the CWB2 domain are essential for correct anchoring to the cell wall [1]. It was shown that in SlpA and Cwp2 that these domains were essential for the binding of PSII an anionic teichoic acid-like component of the cell wall [1]. The structure of the Cwp8 and Cwp6 proteins shows that this domain forms a trimeric arrangement with each domain adopting a structure with some similarity to the Toprim fold [2]. A groove containing many conserved residues was predicted to be the site of the PSII molecule [2]. [1]. 25649385. Clostridium difficile surface proteins are anchored to the cell wall using CWB2 motifs that recognise the anionic polymer PSII. Willing SE, Candela T, Shaw HA, Seager Z, Mesnage S, Fagan RP, Fairweather NF;. Mol Microbiol. 2015;96:596-608. [2]. 28132783. The CWB2 Cell Wall-Anchoring Module Is Revealed by the Crystal Structures of the Clostridium difficile Cell Wall Proteins Cwp8 and Cwp6. Usenik A, Renko M, Mihelic M, Lindic N, Borisek J, Perdih A, Pretnar G, Muller U, Turk D;. Structure. 2017;25:514-521. (from Pfam) NF016070.5 PF04149.17 DUF397 24 24 55 domain Y Y N DUF397 domain-containing protein 1783272 Bacillati kingdom 184078 EBI-EMBL Domain of unknown function (DUF397) Domain of unknown function (DUF397) The function of this family is unknown. (from Pfam) NF016402.5 PF04513.17 Baculo_PEP_C 38 38 140 domain Y Y N polyhedral envelope protein GO:0005198,GO:0019028,GO:0019031 8176372 1783272 Bacillati kingdom 21 EBI-EMBL Baculovirus polyhedron envelope protein, PEP, C terminus polyhedral envelope protein Polyhedra are large crystalline occlusion bodies containing nucleopolyhedrovirus virions, and surrounded by an electron-dense structure called the polyhedron envelope or polyhedron calyx. The polyhedron envelope (associated) protein PEP is thought to be an integral part of the polyhedron envelope. PEP is concentrated at the surface of polyhedra, and is thought to be important for the proper formation of the periphery of polyhedra. It is thought that PEP may stabilise polyhedra and protect them from fusion or aggregation [1]. [1]. 8176372. Orgyia pseudotsugata baculovirus p10 and polyhedron envelope protein genes: analysis of their relative expression levels and role in polyhedron structure. Gross CH, Russell RL, Rohrmann GF;. J Gen Virol 1994;75:1115-1123. (from Pfam) NF016617.5 PF04740.17 LXG 26.5 26.5 202 domain Y Y N T7SS effector LXG polymorphic toxin 21306995 1783272 Bacillati kingdom 23535 EBI-EMBL LXG domain of WXG superfamily polymorphic toxin LXG domain This domain is present is the N-terminal region of a group of polymorphic toxin proteins in bacteria. It is predicted to use Type VII secretion pathway to mediate export of bacterial toxins [1]. [1]. 21306995. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Zhang D, Iyer LM, Aravind L;. Nucleic Acids Res. 2011;39:4532-4552. (from Pfam) NF016636.5 PF04761.17 Phage_Treg 25 25 61 domain Y Y N putative transcriptional regulator 11337471 1783272 Bacillati kingdom 229 EBI-EMBL Lactococcus bacteriophage putative transcription regulator putative transcriptional regulator This family represents a number of putative transcription repressor proteins found in several Lactococcus bacteriophages. Horizontal transfer may account for the presence of similar proteins in Lactococcus [1]. [1]. 11337471. The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, Weissenbach J, Ehrlich SD, Sorokin A;. Genome Res 2001;11:731-753. (from Pfam) NF016653.5 PF04778.17 LMP 26 26 158 domain Y N N LMP repeated region 7543881 1783272 Bacillati kingdom 309 EBI-EMBL LMP repeated region LMP repeated region This family consists of a repeated sequence element found in the LMP group of surface-located membrane proteins of Mycoplasma hominis. The the number of repeats in the protein affects the tendency of cells to spontaneously aggregate. Agglutination may be an important factor in colonisation. Non-agglutinating microorganisms might easily be distributed whereas aggregation might provide a better chance to avoid an antibody response since some of the epitopes may be buried [1]. [1]. 7543881. Selection of Mycoplasma hominis PG21 deletion mutants by cultivation in the presence of monoclonal antibody 552. Jensen LT, Ladefoged S, Birkelund S, Christiansen G;. Infect Immun 1995;63:3336-3347. (from Pfam) NF016964.5 PF05108.18 T7SS_ESX1_EccB 27 27 474 domain Y Y N type VII secretion protein EccB 22140496,22411983,23541477 1783272 Bacillati kingdom 21606 EBI-EMBL Type VII secretion system ESX-1, transport TM domain B type VII secretion protein EccB EccB is a family of largely Gram-positive bacterial transmembrane componenets of the type VII secretion system characterised in Mycobacterium tuberculosis, systems ESX1-5. Translocation of virulent peptides through the membranes is thought to be mediated via a complex that includes EccB, EccC, EccD, EccE, and MycP [1,2]. EccB, EccC, EccD, and EccE form a stable complex in the mycobacterial cell envelope [3]. [1]. 22140496. Computational analysis of the ESX-1 region of Mycobacterium tuberculosis: insights into the mechanism of type VII secretion system. Das C, Ghosh TS, Mande SS;. PLoS One. 2011;6:e27980. [2]. 22411983. Protein secretion and surface display in Gram-positive bacteria. Schneewind O, Missiakas DM;. Philos Trans R Soc Lond B Biol Sci. 2012;367:1123-1139. [3]. 23541477. Leaving home ain't easy: protein export systems in Gram-positive bacteria. Freudl R;. Res Microbiol. 2013;164:664-674. (from Pfam) NF017004.5 PF05151.17 PsbM 24 24 31 PfamEq Y N N Photosystem II reaction centre M protein (PsbM) GO:0009523,GO:0015979,GO:0016020,GO:0019684 12069591 1783272 Bacillati kingdom 367 EBI-EMBL Photosystem II reaction centre M protein (PsbM) Photosystem II reaction centre M protein (PsbM) This family consists of several Photosystem II reaction centre M proteins (PsbM) from plants and cyanobacteria. During the photosynthetic light reactions in the thylakoid membranes of cyanobacteria, algae, and plants, photosystem II (PSII), a multi-subunit membrane protein complex, catalyses oxidation of water to molecular oxygen and reduction of plastoquinon [1]. [1]. 12069591. Proteomic analysis of a highly active photosystem II preparation from the cyanobacterium Synechocystis sp. PCC 6803 reveals the presence of novel polypeptides. Kashino Y, Lauber WM, Carroll JA, Wang Q, Whitmarsh J, Satoh K, Pakrasi HB;. Biochemistry 2002;41:8004-8012. (from Pfam) NF017172.5 PF05334.18 DUF719 22.4 22.4 182 domain Y Y N DUF719 domain-containing protein 1783272 Bacillati kingdom 2 EBI-EMBL Protein of unknown function (DUF719) Protein of unknown function (DUF719) This family consists of several eukaryotic proteins of unknown function. (from Pfam) NF017180.5 PF05342.19 Peptidase_M26_N 27.7 27.7 250 domain Y Y N ZmpA/ZmpB/ZmpC family metallo-endopeptidase-related protein GO:0004222,GO:0008270,GO:0016020 10189832,8057925,8703438,9423856 1783272 Bacillati kingdom 7124 EBI-EMBL M26 IgA1-specific Metallo-endopeptidase N-terminal region ZmpA/ZmpB/ZmpC family metallo-endopeptidase-related protein This domain occurs primarily in LPXTG sorting signal-containing streptococcal surface-anchored proteins that have the HEXXH motif of paralogous zinc-dependent metalloproteases such as Iga/ZmpA (which cleaves human IgA1), ZmpC (which cleaves human matrix metalloproteinase 9), and ZmpB. The HEXXH site essential to catalysis occurs in a more C-terminal domain described by PF07580. NF017471.5 PF05657.16 DUF806 25 25 121 subfamily Y Y N DUF806 family protein 1783272 Bacillati kingdom 1687 EBI-EMBL Protein of unknown function (DUF806) DUF806 family protein This family consists of several Siphovirus and Lactococcus proteins of unknown function. The viral sequences are thought to be tail component proteins. (from Pfam) NF017926.5 PF06160.17 EzrA 39.6 39.6 557 PfamEq Y Y N septation ring formation regulator EzrA GO:0000921,GO:0005940,GO:0016020 10449747,25403286 1783272 Bacillati kingdom 10344 EBI-EMBL Septation ring formation regulator, EzrA septation ring formation regulator EzrA During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [1]. The structure contains 5 spectrin like alpha helical repeats [2]. [1]. 10449747. Identification and characterization of a negative regulator of FtsZ ring formation in Bacillus subtilis. Levin PA, Kurtser IG, Grossman AD;. Proc Natl Acad Sci U S A 1999;96:9642-9647. Paper describing PDB structure 4uxv. [2]. 25403286. Structure and function of a spectrin-like regulator of bacterial cytokinesis. Cleverley RM, Barrett JR, Basle A, Bui NK, Hewitt L, Solovyova A, Xu ZQ, Daniel RA, Dixon NE, Harry EJ, Oakley AJ, Vollmer W, Lewis RJ;. Nat Commun. 2014;5:5421. (from Pfam) NF018090.5 PF06341.16 DUF1056 22.2 22.2 64 PfamAutoEq Y Y N DUF1056 family protein 1783272 Bacillati kingdom 703 EBI-EMBL Protein of unknown function (DUF1056) DUF1056 family protein This family consists of several putative head-tail joining bacteriophage proteins. (from Pfam) NF018196.5 PF06458.17 MucBP 23 10 63 domain Y Y N MucBP domain-containing protein 1783272 Bacillati kingdom 38356 EBI-EMBL MucBP domain MucBP domain The MucBP (MUCin-Binding Protein) domain is found in a wide variety of bacterial proteins, in several repeats. The domain is found in bacterial peptidoglycan bound proteins and is often found in conjunction with Pfam:PF00746 and Pfam:PF00560. (from Pfam) NF018289.5 PF06563.16 DUF1125 25 25 55 PfamAutoEq Y Y N DUF1125 domain-containing protein 1783272 Bacillati kingdom 132 EBI-EMBL Protein of unknown function (DUF1125) Protein of unknown function (DUF1125) This family consists of several short Lactococcus lactis and bacteriophage proteins. The function of this family is unknown. (from Pfam) NF018367.5 PF06646.16 CypI 27 27 332 domain Y Y N p37/Cypl family ABC transporter substrate-binding protein 19233924,3208756 1783272 Bacillati kingdom 685 EBI-EMBL Extracytoplasmic thiamine-binding lipoprotein p37/Cypl family ABC transporter substrate-binding protein Thiamine-binding lipoprotein (Cypl) and related proteins are specific to Mycoplasma species [1]. Cypl, also known as p37, whose gene is part of an operon encoding two additional proteins, which are highly similar to components of the periplasmic binding-protein-dependent transport systems of Gram-negative bacteria. It has been suggested that p37 is part of a homologous, high-affinity transport system in Mycoplasma hyorhinis, a Gram-positive bacterium [1]. Its structure indicates that it is a thiamine pyrophosphate-binding protein [2]. The monomer is a mixed alpha/beta fold split into two globular domains (domains I and II) connected by two linker regions and the C-terminal helix. [1]. 3208756. A mycoplasma high-affinity transport system and the in vitro invasiveness of mouse sarcoma cells. Dudler R, Schmidhauser C, Parish RW, Wettenhall RE, Schmidt T;. EMBO J 1988;7:3963-3970. [2]. 19233924. Structural insights into the extracytoplasmic thiamine-binding lipoprotein p37 of Mycoplasma hyorhinis. Sippel KH, Robbins AH, Reutzel R, Boehlein SK, Namiki K, Goodison S, Agbandje-McKenna M, Rosser CJ, McKenna R;. J Bacteriol. 2009;191:2585-2592. (from Pfam) NF018401.5 PF06686.16 SpoIIIAC 24 24 56 domain Y Y N SpoIIIAC/SpoIIIAD family protein 8969508 1783272 Bacillati kingdom 6330 EBI-EMBL Stage III sporulation protein AC/AD protein family SpoIIIAC/SpoIIIAD domain This family consists of several bacterial stage III sporulation protein AC (SpoIIIAC) and SpoIIIAD sequences. The exact function of this family is unknown. SpoIIIAD is the an uncharacterised protein which is part of the spoIIIA operon that acts at sporulation stage III as part of a cascade of events leading to endospore formation. The operon is regulated by sigmaG [1]. [1]. 8969508. Systematic sequencing of the 283 kb 210 degrees-232 degrees region of the Bacillus subtilis genome containing the skin element and many sporulation genes. Mizuno M, Masuda S, Takemaru K, Hosono S, Sato T, Takeuchi M, Kobayashi Y;. Microbiology 1996;142:3103-3111. (from Pfam) NF018459.5 PF06749.17 DUF1218 25.3 25.3 95 domain Y Y N DUF1218 domain-containing protein 1783272 Bacillati kingdom 2 EBI-EMBL Protein of unknown function (DUF1218) Protein of unknown function (DUF1218) This family contains hypothetical plant proteins of unknown function. Family members contain a number of conserved cysteine residues. (from Pfam) NF018631.5 PF06946.16 Phage_holin_5_1 22.4 22.4 93 PfamEq Y Y N holin 11459934,8577256 1783272 Bacillati kingdom 1810 EBI-EMBL Bacteriophage A118-like holin, Hol118 Hol118 family holin This family consists of several Listeria bacteriophage holin proteins and related bacterial sequences. Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis. It is thought that the temporal precision of holin-mediated lysis may occur through the build up of a holin oligomer which causes the lysis [1]. [1]. 11459934. Holins kill without warning. Grundling A, Manson MD, Young R;. Proc Natl Acad Sci U S A 2001;98:9348-9352. [2]. 8577256. Heterogeneous endolysins in Listeria monocytogenes bacteriophages: a new class of enzymes and evidence for conserved holin genes within the siphoviral lysis cassettes. Loessner MJ, Wendlinger G, Scherer S;. Mol Microbiol 1995;16:1231-1241. (from Pfam) NF018855.5 PF07198.16 DUF1410 25.5 17.2 61 domain Y Y N DUF1410 domain-containing protein 1783272 Bacillati kingdom 1206 EBI-EMBL Protein of unknown function (DUF1410) Protein of unknown function (DUF1410) This family represents a conserved domain approximately 100 residues long, multiple copies of which are found within hypothetical Ureaplasma parvum proteins of unknown function, as well as related species. (from Pfam) NF018868.5 PF07212.16 Hyaluronidase_1 25 25 273 domain Y N N Hyaluronidase protein (HylP) GO:0004415,GO:0045227 7622224 1783272 Bacillati kingdom 807 EBI-EMBL Hyaluronidase protein (HylP) Hyaluronidase protein (HylP) This family consists of several phage associated hyaluronidase proteins (EC:3.2.1.35) which seem to be specific to Streptococcus pyogenes and Streptococcus pyogenes bacteriophages. The substrate of hyaluronidase is hyaluronic acid, a sugar polymer composed of alternating N-acetylglucosamine and glucuronic acid residues. Hyaluronic acid is found in the ground substance of human connective tissue and the vitreous of the eye and also is the sole component of the capsule of group A streptococci. The capsule has been shown to be an important virulence factor of this organism by virtue of its ability to resist phagocytosis. Production by S. pyogenes of both a hyaluronic acid capsule and hyaluronidase enzymatic activity capable of destroying the capsule is an interesting, yet-unexplained, phenomenon [1]. [1]. 7622224. Analysis of a second bacteriophage hyaluronidase gene from Streptococcus pyogenes: evidence for a third hyaluronidase involved in extracellular enzymatic activity. Hynes WL, Hancock L, Ferretti JJ;. Infect Immun 1995;63:3015-3020. (from Pfam) NF019020.5 PF07373.16 CAMP_factor 23.3 23.3 219 subfamily Y Y N CAMP factor family pore-forming toxin 10456923 1783272 Bacillati kingdom 703 EBI-EMBL CAMP factor (Cfa) CAMP factor family pore-forming toxin This family consists of several bacterial CAMP factor (Cfa) proteins which seem to be specific to Streptococcus species. The CAMP reaction is a synergistic lysis of erythrocytes by the interaction of an extracellular protein (CAMP factor) produced by some streptococcal species with the Staphylococcus aureus sphingomyelinase C (beta-toxin) [1]. [1]. 10456923. Identification, cloning, and expression of the CAMP factor gene (cfa) of group A streptococci. Gase K, Ferretti JJ, Primeaux C, McShan WM;. Infect Immun 1999;67:4725-4731. (from Pfam). The term CAMP (Christie, Atkins, Munch-Petersen) factor is used for toxins encoded in group A and B Streptococcus, but expressed well enough to give a positive CAMP test only in GBS. Related toxins are found in Propionibacterium acnes and other bacterial species. NF019192.5 PF07554.18 FIVAR 29.2 11.1 71 repeat Y N N FIVAR domain-containing protein 10896508,12438356,14759609 1783272 Bacillati kingdom 34959 EBI-EMBL FIVAR domain FIVAR domain This domain is found in a wide variety of contexts, but mostly occurring in cell wall associated proteins. A lack of conserved catalytic residues suggests that it is a binding domain. From context, possible substrates are hyaluronate or fibronectin (personal obs: C Yeats). This is further evidenced by [1]. Possibly the exact substrate is N-acetyl glucosamine. Finding it in the same protein as Pfam:PF05089 further supports this proposal. It is found in the C-terminal part of Swiss:O82833, which is removed during maturation ([2]). Some of the proteins it is found in (e.g. Swiss:Q9RL69) are involved in methicillin resistance ([3]). The name FIVAR derives from Found In Various Architectures. [1]. 12438356. Identification of a fibronectin-binding protein from Staphylococcus epidermidis. Williams RJ, Henderson B, Sharp LJ, Nair SP;. Infect Immun 2002;70:6805-6810. [2]. 14759609. Posttranslational processing of polysaccharide lyase: maturation route for gellan lyase in Bacillus sp. GL1. Miyake O, Kobayashi E, Nankai H, Hashimoto W, Mikami B, Murata K;. Arch Biochem Biophys 2004;422:211-220. [3]. 10896508. Tn551-mediated insertional inactivation of the fmtB gene encoding a cell wall-associated protein abolishes methicillin resistance in Staphylococcus aureus. Komatsuzawa H, Ohta K, Sugai M, Fujiwara T, Glanzmann P, Berger-BachiB, Suginaka H;. J Antimicrob Chemother 2000;45:421-431. (from Pfam) NF019216.5 PF07580.19 Peptidase_M26_C 22 22 792 domain Y Y N ZmpA/ZmpB/ZmpC family metallo-endopeptidase GO:0004222,GO:0005576,GO:0008270 10189832,8057925,8703438,9423856 1783272 Bacillati kingdom 8432 EBI-EMBL M26 IgA1-specific Metallo-endopeptidase C-terminal region M26 family metallo-endopeptidase catalytic domain Members of this family include several paralogous, LPXTG-anchored surface zinc-dependent metallo-endopeptidases of Streptococcus, including ZmpA (Iga), ZmpB, and ZmpC, the first of which contributes to pathgenesis by cleaving host Iga1. Most family members also contain a domain described by PF05342 upstream of this domain. NF019381.5 PF07761.17 DUF1617 22 22 143 subfamily Y Y N DUF1617 family protein 1783272 Bacillati kingdom 1387 EBI-EMBL Protein of unknown function (DUF1617) DUF1617 family protein This is a family of sequences from hypothetical bacterial and bacteriophage proteins. The region in question is approximately 150 residues long and is highly conserved throughout the family. (from Pfam) NF019483.5 PF07868.16 DUF1655 20.1 20.1 55 domain Y Y N DUF1655 domain-containing protein 11160885 1783272 Bacillati kingdom 314 EBI-EMBL Protein of unknown function (DUF1655) Protein of unknown function (DUF1655) This protein is found in some prophages found in Lactobacillales lactis ([1]). [1]. 11160885. Analysis of six prophages in Lactococcus lactis IL1403: different genetic structure of temperate and virulent phage populations. Chopin A, Bolotin A, Sorokin A, Ehrlich SD, Chopin M;. Nucleic Acids Res 2001;29:644-651. (from Pfam) NF019618.5 PF08006.16 HAAS_TM 28.3 28.3 117 domain Y Y N HAAS domain-containing protein 1783272 Bacillati kingdom 2288 EBI-EMBL HAAS transmembrane region HAAS transmembrane region This entry represents the transmembrane region fused to HAAS (HTH-associated alpha-helical signaling) domain (Preprint https://doi.org/10.1101/2020.09.24.301986). (from Pfam) NF019962.5 PF08363.15 GbpC 27.2 27.2 307 domain Y Y N GbpC/Spa domain-containing protein 9009329 1783272 Bacillati kingdom 6099 EBI-EMBL Glucan-binding protein C GbpC/Spa domain This domain is found in the Streptococcus Glucan-binding protein C (GbpC) and also in surface protein antigen (Spa)-family proteins which show sequence similarity to GbpC [1]. [1]. 9009329. Cloning and sequence analysis of the gbpC gene encoding a novel glucan-binding protein of Streptococcus mutans. Sato Y, Yamamoto Y, Kizaki H;. Infect Immun 1997;65:668-675. (from Pfam) NF020049.5 PF08460.15 SH3_5 22 22 68 domain Y Y N SH3 domain-containing protein 1783272 Bacillati kingdom 12635 EBI-EMBL Bacterial SH3 domain Bacterial SH3 domain NF020070.5 PF08481.15 GBS_Bsp-like 31.6 31.6 92 domain Y Y N GBS Bsp-like repeat-containing protein 12368458 1783272 Bacillati kingdom 8274 EBI-EMBL GBS Bsp-like repeat GBS Bsp-like repeat This domain is found as a repeat in a number of Streptococcus proteins including some hypothetical proteins and Bsp. Bsp is a protein of group B Streptococcus (GBS) which might control cell morphology [1]. [1]. 12368458. Influence of proteins Bsp and FemH on cell shape and peptidoglycan composition in group B streptococcus. Reinscheid DJ, Stosser C, Ehlert K, Jack RW, Moller K, Eikmanns BJ, Chhatwal GS;. Microbiology 2002;148:3245-3254. (from Pfam) NF020450.5 PF08876.16 DUF1836 27 27 105 domain Y Y N DUF1836 domain-containing protein 1783272 Bacillati kingdom 9252 EBI-EMBL Domain of unknown function (DUF1836) Domain of unknown function (DUF1836) This family of proteins are functionally uncharacterised. (from Pfam) NF020642.5 PF09076.15 Crystall_2 25 25 70 domain Y Y N beta/gamma crystallin domain-containing protein 10601197,11114251,11350173 1783272 Bacillati kingdom 1744 EBI-EMBL Beta/Gamma crystallin Beta/Gamma crystallin Members of this family assume a beta-gamma-crystallin fold [1,2], wherein nine beta-strands are connected by loop, and are separated into two sheets, each sheet forming the Greek key motif. The two Greek key motifs face each other in the global topology. The three-dimensional structure of the molecule is a 'sandwich'-shaped beta-barrel structure: hydrophobic side-chains are packed in the large interface area of the beta-sheets. In Streptomyces killer toxin-like protein domain confers a cytocidal effect to the toxin, causing cell death in both budding and fission yeasts, and morphological changes in yeasts and filamentous fungi [1]. This family also includes chitin-biding antifungal proteins [2-3]. [1]. 11114251. NMR structure of Streptomyces killer toxin-like protein, SKLP: further evidence for the wide distribution of single-domain betagamma-crystallin superfamily proteins. Ohki SY, Kariya E, Hiraga K, Wakamiya A, Isobe T, Oda K, Kainosho M;. J Mol Biol. 2001;305:109-120. [2]. 11350173. Solution structure, backbone dynamics and chitin binding of the anti-fungal protein from Streptomyces tendae TU901. Campos-Olivas R, Horr I, Bormann C, Jung G, Gronenborn AM;. J Mol Biol. 2001;308:765-782. [3]. 10601197. Characterization of a novel, antifungal, chitin-binding protein from Streptomyces tendae Tu901 that interferes with growth polarity. Bormann C, Baier D, Horr I, Raps C, Berger J, Jung G, Schwarz H;. J Bacteriol. 1999;181:7421-7429. (from Pfam) NF020782.5 PF09221.15 Bacteriocin_IId 23.6 23.6 67 subfamily Y Y N uberolysin/carnocyclin family circular bacteriocin 12620847,14623193,15544534,17464077,19692336 1783272 Bacillati kingdom 630 EBI-EMBL Bacteriocin class IId cyclical uberolysin-like uberolysin/carnocyclin family circular bacteriocin Members of this family are membrane-interacting peptides, produced by Firmicutes that display a broad anti-microbial spectrum against Gram-positive and Gram-negative bacteria. They adopt a helical structure, with four or five alpha helices forming a Saposin-like fold [2,5]. The structure has been found to be cyclical [1, 3, 5]. It should be pointed out that one reference [4] implies that both circularin A and gassericin A are class V or IIc-type bacteriocins; however we find that these two proteins fall into different Pfam families families, this one and BacteriocIIc_cy, Pfam:PF12173. [1]. 12620847. Identification and characterization of two novel clostridial bacteriocins, circularin A and closticin 574. Kemperman R, Kuipers A, Karsens H, Nauta A, Kuipers O, Kok J;. Appl Environ Microbiol. 2003;69:1589-1597. [2]. 14623193. Structure of bacteriocin AS-48: from soluble state to membrane bound state. Sanchez-Barrena MJ, Martinez-Ripoll M, Galvez A, Valdivia E, Maqueda M, Cruz V, Albert A;. J Mol Biol. 2003;334:541-549. [3]. 17464077. Uberolysin: a novel cyclic bacteriocin produced by Streptococcus uberis. Wirawan RE, Swanson KM, Kleffmann T, Jack RW, Tagg JR;. Microbiology. 2007;153:1619-1630. [4]. 15544534. The circular bacteriocins gassericin A and circularin A. Kawai Y, Kemperman R, Kok J, Saito T;. Curr Protein Pept Sci. 2004;5:393-398. [5]. 19692336. The three-dimensional structure of carnocyclin A reveals that many circular bacteriocins share a common structural motif. Martin-Visscher LA, Gong X, Duszyk M, Vederas JC;. J Biol Chem. 2009;284:28674-28681. (from Pfam) NF021168.5 PF09629.15 YorP 25 25 71 subfamily Y Y N YorP family protein 1783272 Bacillati kingdom 111 EBI-EMBL YorP protein YorP family protein YorP is a 71 residue protein found in bacteria. As it is also found in a bacteriophage it might be of viral origin. The structure is of an alpha helix between two of five beta strands. The function is unknown. (from Pfam) NF021191.5 PF09654.15 DUF2396 21 21 157 PfamAutoEq Y Y N DUF2396 family protein 1783272 Bacillati kingdom 588 EBI-EMBL Protein of unknown function (DUF2396) DUF2396 family protein These conserved hypothetical proteins have so far been found only in the Cyanobacteria. They are about 170 amino acids long and contain a CxxCx(14)CxxH motif near the N-terminus. (from Pfam) NF021585.5 PF10078.14 DUF2316 26 26 89 PfamAutoEq Y Y N DUF2316 family protein 1783272 Bacillati kingdom 1393 EBI-EMBL Uncharacterized protein conserved in bacteria (DUF2316) DUF2316 family protein Members of this family of hypothetical bacterial proteins have no known function. (from Pfam) NF021643.5 PF10140.14 YukC 27.4 27.4 357 subfamily Y Y N type VII secretion protein EssB/YukC 15657139,19299134,19674902,20852931 1783272 Bacillati kingdom 4978 EBI-EMBL WXG100 protein secretion system (Wss), protein YukC type VII secretion protein EssB/YukC Members of this family of type VII secretion systems as found in the Firmicutes (T7SSa) are called EssB in Staphylococcus aureus, YukC in Bacillus subtilis, and are the counterpart to EssB from T7SSb systems in Actinobacteria such as Mycobacterium tuberculosis. NF022139.5 PF10674.14 Ycf54 25 25 92 PfamAutoEq Y Y N MgPME-cyclase complex family protein 17932292,28008132 1783272 Bacillati kingdom 814 EBI-EMBL Ycf54 protein DUF2488 family protein Ycf54 is found encoded in the chloroplast genomes of algae, also found in plants and cyanobacteria. It is a component of the MgPME-cyclase complex and plays two roles: first, it plays a critical role in the assembly/stability of the Mg-cyclase complex and its constituents; secondly, it is required for normal Pchlide formation [1,2]. This protein is required for optimal MgPME-cyclase activity, although it is not absolutely essential. [1]. 17932292. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Gr. Science. 2007;318:245-250. [2]. 28008132. Conserved residues in Ycf54 are required for protochlorophyllide formation in Synechocystis sp. PCC 6803. Hollingshead S, Bliss S, Baker PJ, Neil Hunter C;. Biochem J. 2017;474:667-681. (from Pfam) NF022192.5 PF10732.14 DUF2524 25 25 84 PfamAutoEq Y Y N DUF2524 family protein 1783272 Bacillati kingdom 1104 EBI-EMBL Protein of unknown function (DUF2524) DUF2524 family protein This family of proteins with unknown function appears to be restricted to Bacillaceae bacteria. (from Pfam) NF022222.5 PF10763.14 DUF2584 25 25 80 PfamAutoEq Y Y N DUF2584 family protein 1783272 Bacillati kingdom 1186 EBI-EMBL Protein of unknown function (DUF2584) DUF2584 family protein This bacterial family of proteins have no known function. (from Pfam) NF022351.5 PF10896.13 DUF2714 23.9 23.9 143 PfamEq Y Y N MSC_0623 family F1-like ATPase-associated protein 22685606 1783272 Bacillati kingdom 367 EBI-EMBL Protein of unknown function (DUF2714) MSC_0623 family F1-like ATPase-associated protein The protein previously known as DUF2714 is now described as protein 2 of a seven-gene system unique to Mycoplasma-like species. In this system, four of the proteins are related to the alpha, beta, gamma, and epsilon subunits of the F1F0 ATPase, which those species also have. NF022370.5 PF10916.13 DUF2712 22 22 111 domain Y Y N DUF2712 domain-containing protein 1783272 Bacillati kingdom 388 EBI-EMBL Protein of unknown function (DUF2712) Protein of unknown function (DUF2712) This family of proteins with unknown function appear to be restricted to Bacillales. (from Pfam) NF022474.5 PF11021.13 DUF2613 22.1 22.1 55 PfamAutoEq Y Y N DUF2613 family protein 1783272 Bacillati kingdom 1220 EBI-EMBL Protein of unknown function (DUF2613) DUF2613 family protein This is a family of putative small secreted proteins expressed by Actinobacteria. The function is not known. (from Pfam) NF022650.5 PF11203.13 EccE 23.7 23.7 97 domain Y Y N type VII secretion protein EccE 22140496,22411983,23541477 1783272 Bacillati kingdom 13769 EBI-EMBL Putative type VII ESX secretion system translocon, EccE type VII secretion protein EccE EccE is a family of largely Gram-positive bacterial transmembrane componenets of the type VII secretion system characterised in Mycobacterium tuberculosis, systems ESX1-5. Translocation of virulent peptides through the membranes is thought to be mediated via a complex that includes EccB, EccC, EccD, EccE, and MycP [1,2]. EccB, EccC, EccD, and EccE form a stable complex in the mycobacterial cell envelope [3]. [1]. 22140496. Computational analysis of the ESX-1 region of Mycobacterium tuberculosis: insights into the mechanism of type VII secretion system. Das C, Ghosh TS, Mande SS;. PLoS One. 2011;6:e27980. [2]. 22411983. Protein secretion and surface display in Gram-positive bacteria. Schneewind O, Missiakas DM;. Philos Trans R Soc Lond B Biol Sci. 2012;367:1123-1139. [3]. 23541477. Leaving home ain't easy: protein export systems in Gram-positive bacteria. Freudl R;. Res Microbiol. 2013;164:664-674. (from Pfam) NF022668.5 PF11222.13 DUF3017 25 25 74 domain Y Y N DUF3017 domain-containing protein 1783272 Bacillati kingdom 10840 EBI-EMBL Protein of unknown function (DUF3017) Protein of unknown function (DUF3017) This bacterial family of proteins with unknown function appear to be restricted to Actinobacteria. (from Pfam) NF022788.5 PF11344.13 DUF3146 22 22 80 PfamAutoEq Y Y N DUF3146 family protein 1783272 Bacillati kingdom 604 EBI-EMBL Protein of unknown function (DUF3146) DUF3146 family protein This family of proteins with unknown function appear to be restricted to Cyanobacteria. (from Pfam) NF022826.5 PF11384.13 DUF3188 24.6 24.6 50 PfamAutoEq Y Y N DUF3188 domain-containing protein 1783272 Bacillati kingdom 675 EBI-EMBL Protein of unknown function (DUF3188) Protein of unknown function (DUF3188) This bacterial family of proteins has no known function. (from Pfam) NF022942.5 PF11506.13 DUF3217 26.4 26.4 104 PfamAutoEq Y Y N DUF3217 domain-containing protein 17348019 1783272 Bacillati kingdom 35 EBI-EMBL Protein of unknown function (DUF3217) Protein of unknown function (DUF3217) This family of proteins with unknown function appears to be restricted to Mycoplasma and Ruminococcus spp. The structure of Uncharacterized protein MG376 homolog from Mycoplasma pneumoniae shows an OB fold with six beta-strands and three loops forming a beta-barrel that is capped by one alpha-helix [1]. Its specific function is still unknown. [1]. 17348019. Crystal structure of a novel single-stranded DNA binding protein from Mycoplasma pneumoniae. Das D, Hyun H, Lou Y, Yokota H, Kim R, Kim SH;. Proteins. 2007;67:776-782. (from Pfam) NF022979.5 PF11545.13 HemeBinding_Shp 26.4 26.4 148 domain Y Y N heme-binding Shp domain-containing protein GO:0020037 17920629 1783272 Bacillati kingdom 1679 EBI-EMBL Cell surface heme-binding protein Shp Cell surface heme-binding protein Shp Shp is part of a complex which functions in heme uptake in Streptococcus pyogenes. During which, Shp transfers its heme to HtsA which is a component of an ABC transporter. The heme binding region of Shp contains an immunoglobulin-like beta-sandwich fold and has a unique heme-iron coordination with the axial ligands being two methionine residues from the same Shp molecule [1]. Surrounding the heme pocket, there is a negative surface which may serve as a docking interface for heme transfer [1]. [1]. 17920629. Bis-methionyl coordination in the crystal structure of the heme-binding domain of the streptococcal cell surface protein Shp. Aranda R 4th, Worley CE, Liu M, Bitto E, Cates MS, Olson JS, Lei B, Phillips GN Jr;. J Mol Biol. 2007;374:374-383. (from Pfam) NF023186.5 PF11758.13 Bacteriocin_IIi 25 25 51 subfamily Y Y N aureocin A53 family class IId bacteriocin 12054867,12406714 1783272 Bacillati kingdom 234 EBI-EMBL Aureocin-like type II bacteriocin aureocin A53 family class IId bacteriocin This is a small family of type II bacteriocins usually encoded on a plasmid. Characteristically the members are small, cationic, rich in Lys and Try, and bring about a generalised membrane permeabilisation leading to leakage of ions. The family includes aureocin A, lacticins Q and Z, and BhtB as well as an archaeal member. [1]. 12054867. Biochemical characterisation and genetic analysis of aureocin A53, a new, atypical bacteriocin from Staphylococcus aureus. Netz DJ, Pohl R, Beck-Sickinger AG, Selmer T, Pierik AJ, Bastos Mdo C, Sahl HG;. J Mol Biol. 2002;319:745-756. [2]. 12406714. Mode of action of the antimicrobial peptide aureocin A53 from Staphylococcus aureus. Netz DJ, Bastos Mdo C, Sahl HG;. Appl Environ Microbiol. 2002;68:5274-5280. (from Pfam) NF023194.5 PF11766.13 Candida_ALS_N 25 25 247 PfamEq Y N N Agglutinin-like protein, N-terminal domain 11292808,17554046,17870620,21896717,24802757,8455628 1783272 Bacillati kingdom 1676 EBI-EMBL Agglutinin-like protein, N-terminal domain Agglutinin-like protein, N-terminal domain This entry represents the N-terminal domain of yeast alpha-agglutinin [1, 2] and agglutinin-like (ALS) proteins. The ALS glycoproteins have been associated with binding of host-cell surface proteins and small peptides of random sequence, the formation of biofilms and amyloid fibers. The N-terminal domains of Candida albicans ALS3 and ALS9 were shown to be involved in peptide binding [3, 4]. The ligand recognition of these domains relies on a motif capable of binding the flexible C terminus of peptides in extended conformation. In baker's yeast alpha-agglutinin, this domain was implicated in high affinity binding to a-agglutinin that mediates cell-cell contact during mating [5, 6]. [1]. 17554046. A biochemical guide to yeast adhesins: glycoproteins for social and antisocial occasions. Dranginis AM, Rauceo JM, Coronado JE, Lipke PN;. Microbiol Mol Biol Rev. 2007;71:282-294. [2]. 17870620. Molecular phylogenetics of ascomycotal adhesins-A novel family of putative cell-surface adhesive proteins in fission yeasts. Linder T, Gustafsson CM;. Fungal Genet Biol. 2007; [Epub ahead of print]. [3]. 21896717. Structural basis for the broad specificity to host-cell ligands by the pathogenic fungus Candida albicans. Salgado PS, Yan R, Taylor JD, Burchell L, Jones R, Hoyer LL, Matthews SJ, Simpson PJ, Cota E;. Proc Natl Acad Sci U S A. 2011;108:15775-15779. [4]. 24802757. The peptide-binding cavity is essential for Als3-mediated adhesion of Candida albicans to human cells. Lin J, Oh SH, Jones R, Garnett JA, Salgado PS, Rusnakova S, Matthews SJ, Hoyer LL, Cota E;. J Biol Chem. 2014;289:18401-18412. [5]. 11292808. Interaction of alpha-agg. TRUNCATED at 1650 bytes (from Pfam) NF023341.5 PF11914.13 DUF3432 26.7 26.7 98 domain Y Y N DUF3432 domain-containing protein 1783272 Bacillati kingdom 5 EBI-EMBL Domain of unknown function (DUF3432) Domain of unknown function (DUF3432) This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 100 amino acids in length. This domain is found associated with Pfam:PF00096. This domain has two conserved sequence motifs: YPSPV and PSP. (from Pfam) NF023587.5 PF12165.13 Alfin 21 21 127 domain Y Y N alfin GO:0006355,GO:0042393 10364398,10750899 1783272 Bacillati kingdom 10 EBI-EMBL Alfin alfin The Alfin family includes PHD finger protein Alfin1 and Alfin1-like proteins. Alfin1 is a histone-binding component that specifically recognises H3 tails trimethylated on 'Lys-4' (H3K4me3), which marks transcription start sites of virtually all active genes [1, 2]. [1]. 10364398. Transgenic overexpression of the transcription factor alfin1 enhances expression of the endogenous MsPRP2 gene in alfalfa and improves salinity tolerance of the plants. Winicov I I, Bastola DR;. Plant Physiol. 1999;120:473-480. [2]. 10750899. Alfin1 transcription factor overexpression enhances plant root growth under normal and saline conditions and improves salt tolerance in alfalfa. Winicov I;. Planta. 2000;210:416-422. (from Pfam) NF023670.5 PF12249.13 AftA_C 25 25 177 PfamEq Y Y N arabinofuranosyltransferase GO:0005886,GO:0016020,GO:0016757,GO:0044038 16595677 1783272 Bacillati kingdom 3786 EBI-EMBL Arabinofuranosyltransferase A C terminal arabinofuranosyltransferase This domain family is found in bacteria, and is typically between 179 and 190 amino acids in length. This family is the C terminal region of AftA. The enzyme catalyses the addition of the first key arabinofuranosyl residue from the sugar donor beta-D-arabinofuranosyl-1-monophosphoryldecaprenol to the galactan domain of the cell wall, thus priming the galactan for further elaboration by the arabinofuranosyltransferases. The C terminal region is predicted to be directed towards the periplasm. [1]. 16595677. Identification of a novel arabinofuranosyltransferase (AftA) involved in cell wall arabinan biosynthesis in Mycobacterium tuberculosis. Alderwick LJ, Seidel M, Sahm H, Besra GS, Eggeling L;. J Biol Chem. 2006;281:15653-15661. (from Pfam) NF023671.5 PF12250.13 AftA_N 26.7 26.7 429 PfamEq Y Y N arabinofuranosyltransferase GO:0005886,GO:0016020,GO:0016757,GO:0044038 16595677 1783272 Bacillati kingdom 3930 EBI-EMBL Arabinofuranosyltransferase N terminal arabinofuranosyltransferase This domain family is found in bacteria, and is typically between 430 and 441 amino acids in length. This family is the N terminal region of AftA. The enzyme catalyses the addition of the first key arabinofuranosyl residue from the sugar donor beta-D-arabinofuranosyl-1-monophosphoryldecaprenol to the galactan domain of the cell wall, thus priming the galactan for further elaboration by the arabinofuranosyltransferases. The N terminal region has been predicted to span 11 transmembrane regions. [1]. 16595677. Identification of a novel arabinofuranosyltransferase (AftA) involved in cell wall arabinan biosynthesis in Mycobacterium tuberculosis. Alderwick LJ, Seidel M, Sahm H, Besra GS, Eggeling L;. J Biol Chem. 2006;281:15653-15661. (from Pfam) NF023719.5 PF12299.13 DUF3627 20.9 10 93 domain Y Y N DUF3627 domain-containing protein 1783272 Bacillati kingdom 234 EBI-EMBL Protein of unknown function (DUF3627) Protein of unknown function (DUF3627) This domain family is found in bacteria and viruses, and is approximately 90 amino acids in length. The family is found in association with Pfam:PF02498. (from Pfam) NF023941.5 PF12527.13 DUF3727 23.8 23.8 97 PfamAutoEq Y Y N DUF3727 domain-containing protein 1783272 Bacillati kingdom 817 EBI-EMBL Protein of unknown function (DUF3727) Protein of unknown function (DUF3727) This domain family is found in bacteria and eukaryotes, and is approximately 100 amino acids in length. (from Pfam) NF024088.5 PF12676.12 DUF3796 24.8 24.8 120 domain Y Y N DUF3796 domain-containing protein 1783272 Bacillati kingdom 1572 EBI-EMBL Protein of unknown function (DUF3796) Protein of unknown function (DUF3796) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. (from Pfam) NF024296.5 PF12892.12 FctA 22.1 18.9 120 domain Y Y N Spy0128 family protein 17012387,17501921,18063798 1783272 Bacillati kingdom 11093 EBI-EMBL Spy0128-like isopeptide containing domain Spy0128-like isopeptide containing domain The FCT and equivalent region genes of Streptococcus pyogenes and other related bacteria encode surface proteins that include fibronectin- and collagen-binding proteins and the serological markers known as T antigens. Some of these proteins give rise to pilus-like appendages [1]. The FctA family is found in many Firmicutes and related bacteria. In S. pyogenes, the pili have a role in bacterial adherence and colonisation of human tissues [2]. Members of this family have a conserved N-terminal lysine and C-terminal asparagine that can form a covalent isopeptide bond [3]. [1]. 17012387. Role of streptococcal T antigens in superficial skin infection. Lizano S, Luo F, Bessen DE;. J Bacteriol. 2007;189:1426-1434. [2]. 17501921. Streptococcus pyogenes pili promote pharyngeal cell adhesion and biofilm formation. Manetti AG, Zingaretti C, Falugi F, Capo S, Bombaci M, Bagnoli F, Gambellini G, Bensi G, Mora M, Edwards AM, Musser JM, Graviss EA, Telford JL, Grandi G, Margarit I;. Mol Microbiol. 2007;64:968-983. [3]. 18063798. Stabilizing isopeptide bonds revealed in gram-positive bacterial pilus structure. Kang HJ, Coulibaly F, Clow F, Proft T, Baker EN;. Science. 2007;318:1625-1628. (from Pfam) NF024445.5 PF13045.11 DUF3905 27 27 84 PfamAutoEq Y Y N DUF3905 domain-containing protein 1783272 Bacillati kingdom 1272 EBI-EMBL Protein of unknown function (DUF3905) Protein of unknown function (DUF3905) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. (from Pfam) NF024461.5 PF13061.11 DUF3923 25 25 65 PfamAutoEq Y Y N DUF3923 family protein 1783272 Bacillati kingdom 1563 EBI-EMBL Protein of unknown function (DUF3923) DUF3923 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. (from Pfam) NF024722.5 PF13326.11 PSII_Pbs27 25 25 140 PfamEq Y N N Photosystem II Pbs27 GO:0009523,GO:0010206,GO:0010207 19697958 1783272 Bacillati kingdom 809 EBI-EMBL Photosystem II Pbs27 Photosystem II Pbs27 This family of proteins contains Pbs27, a highly conserved component of photosystem II. Pbs27 is comprised of four helices arranged in a right handed up-down-up-down fold, with a less ordered region located at the N-terminus [1]. [1]. 19697958. Solution structure of Psb27 from cyanobacterial photosystem II. Mabbitt PD, Rautureau GJ, Day CL, Wilbanks SM, Eaton-Rye JJ, Hinds MG;. Biochemistry. 2009;48:8771-8773. (from Pfam) NF025153.5 PF13780.11 DUF4176 25 25 74 domain Y Y N DUF4176 domain-containing protein 1783272 Bacillati kingdom 4498 EBI-EMBL Domain of unknown function (DUF4176) Domain of unknown function (DUF4176) NF025159.5 PF13786.11 DUF4179 30.1 30.1 94 domain Y Y N DUF4179 domain-containing protein 1783272 Bacillati kingdom 18503 EBI-EMBL Domain of unknown function (DUF4179) Domain of unknown function (DUF4179) NF025487.5 PF14122.11 YokU 27 27 87 domain Y Y N YokU family protein 1783272 Bacillati kingdom 1393 EBI-EMBL YokU-like protein, putative antitoxin YokU family protein The YokU-like protein family includes the B. subtilis YokU protein Swiss:C0H434 which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two conserved CXXC sequence motifs. This is likely to be a family of bacterial antitoxins, as the sequence bears remote homology to the RelE fold family. (from Pfam) NF025547.5 PF14184.11 YrvL 27 27 127 subfamily Y Y N YrvL family regulatory protein 18573182,19047353 1783272 Bacillati kingdom 2359 EBI-EMBL Regulatory protein YrvL YrvL family regulatory protein YrvL prevents expression and activity of the YrvI sigma factor. It may function as an anti-sigma factor [1,2] [1]. 18573182. A previously unidentified sigma factor and two accessory proteins regulate oxalate decarboxylase expression in Bacillus subtilis. MacLellan SR, Wecke T, Helmann JD;. Mol Microbiol. 2008;69:954-967. [2]. 19047353. The YvrI alternative sigma factor is essential for acid stress induction of oxalate decarboxylase in Bacillus subtilis. MacLellan SR, Helmann JD, Antelmann H;. J Bacteriol. 2009;191:931-939. (from Pfam) NF025628.5 PF14270.11 DUF4358 25 25 102 domain Y Y N DUF4358 domain-containing protein 1783272 Bacillati kingdom 3706 EBI-EMBL Domain of unknown function (DUF4358) Domain of unknown function (DUF4358) This domain family is found in bacteria, and is approximately 110 amino acids in length. (from Pfam) NF025634.5 PF14276.11 DUF4363 27.5 27.5 107 subfamily Y Y N DUF4363 family protein 1783272 Bacillati kingdom 2272 EBI-EMBL Domain of unknown function (DUF4363) DUF4363 family protein This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. (from Pfam) NF026217.5 PF14867.11 Lantibiotic_a 27 27 29 subfamily Y Y N lichenicidin alpha family lanthipeptide GO:0050830 10971756,20578714 1783272 Bacillati kingdom 359 EBI-EMBL Lantibiotic alpha lichenicidin alpha family lanthipeptide Lantibiotics are two-component lanthionine-containing peptide antibiotics active on Gram-positive bacteria [1-2]. [1]. 20578714. Isolation, structure elucidation, and synergistic antibacterial activity of a novel two-component lantibiotic lichenicidin from Bacillus licheniformis VK21. Shenkarev ZO, Finkina EI, Nurmukhamedova EK, Balandin SV, Mineev KS, Nadezhdin KD, Yakimenko ZA, Tagaev AA, Temirov YV, Arseniev AS, Ovchinnikova TV;. Biochemistry. 2010;49:6462-6472. [2]. 10971756. Biological and molecular characterization of a two-peptide lantibiotic produced by Lactococcus lactis IFPL105. Martinez-Cuesta MC, Buist G, Kok J, Hauge HH, Nissen-Meyer J, Pelaez C, Requena T;. J Appl Microbiol. 2000;89:249-260. (from Pfam) NF027472.5 PF16146.10 DUF4854 28 28 102 domain Y Y N DUF4854 domain-containing protein 1783272 Bacillati kingdom 672 EBI-EMBL Domain of unknown function (DUF4854) Domain of unknown function (DUF4854) This family consists of uncharacterized proteins found in firmicutes and high GC Gram+ bacteria associated with human and animal guts. The function of this family is unknown. (from Pfam) NF027478.5 PF16152.10 DUF4860 25 25 98 PfamAutoEq Y Y N DUF4860 domain-containing protein 1783272 Bacillati kingdom 1223 EBI-EMBL Domain of unknown function (DUF4860) Domain of unknown function (DUF4860) This family consists of uncharacterized proteins around 160 residues in length and is mainly found in various Eubacterium and Clostridium species. The function of this family is unknown. (from Pfam) NF027682.5 PF16364.10 Antigen_C 29.5 29.5 172 domain Y Y N LPXTG cell wall anchor domain-containing protein 12485987,20138058,21505225 1783272 Bacillati kingdom 7348 EBI-EMBL Cell surface antigen C-terminus Cell surface antigen C-terminus This repeated domain is found at the C-terminus of cell surface antigens [1-3]. In the Streptococcus mutans antigen I/II there are three repeats of this domain, a cleft between the first two of these forms a binding site for the human salivary agglutinin (SAG) [3]. [1]. 12485987. A novel variant of the immunoglobulin fold in surface adhesins of Staphylococcus aureus: crystal structure of the fibrinogen-binding MSCRAMM, clumping factor A. Deivanayagam CC, Wann ER, Chen W, Carson M, Rajashankar KR, Hook M, Narayana SV;. EMBO J. 2002;21:6660-6672. [2]. 20138058. Two intramolecular isopeptide bonds are identified in the crystal structure of the Streptococcus gordonii SspB C-terminal domain. Forsgren N, Lamont RJ, Persson K;. J Mol Biol. 2010;397:740-751. [3]. 21505225. Crystal structure of the C-terminal region of Streptococcus mutans antigen I/II and characterization of salivary agglutinin adherence domains. Larson MR, Rajashankar KR, Crowley PJ, Kelly C, Mitchell TJ, Brady LJ, Deivanayagam C;. J Biol Chem. 2011;286:21657-21666. (from Pfam) NF027745.5 PF16430.10 DUF5027 25 25 159 domain Y Y N DUF5027 family lipoprotein 1783272 Bacillati kingdom 89 EBI-EMBL Domain of unknown function (DUF5027) DUF5027 family lipoprotein This family consists of several uncharacterised proteins around 180 in length and is mainly found in various Clostridiales species. The function of this family is unknown. (from Pfam) NF027746.5 PF16431.10 DUF5028 29.9 29.9 166 PfamAutoEq Y Y N DUF5028 domain-containing protein 1783272 Bacillati kingdom 83 EBI-EMBL Domain of unknown function (DUF5028) Domain of unknown function (DUF5028) This family consists of several uncharacterized proteins around 200 in length and is mainly found in Eubacterium and Clostridium. The function of this family is unknown. (from Pfam) NF027755.5 PF16440.10 DUF5037 25 25 247 domain Y Y N DUF5037 domain-containing protein 1783272 Bacillati kingdom 46 EBI-EMBL Domain of unknown function (DUF5037) Domain of unknown function (DUF5037) This family consists of several uncharacterized proteins around 270 residues in length and is mainly found in various Clostridiales species. The function of this family is unknown. (from Pfam) NF027795.5 PF16480.10 DUF5057 27.9 27.9 378 PfamAutoEq Y Y N DUF5057 domain-containing protein 1783272 Bacillati kingdom 968 EBI-EMBL Domain of unknown function (DUF5057) Domain of unknown function (DUF5057) This family consists of C-terminal of uncharacterized proteins and F5/8 type C domain proteins around 360 residues in length and is mainly found in various Firmicutes species. The function of this family is unknown. (from Pfam) NF028160.5 PF16850.10 Inhibitor_I66 27 27 146 subfamily Y Y N I66 family serine proteinase inhibitor GO:0004867 10411656,22167196 1783272 Bacillati kingdom 147 EBI-EMBL Peptidase inhibitor I66 I66 family serine proteinase inhibitor This family of serine protease inhibitors has a beta-trefoil fold and inhibits trypsin and chymotrypsin [1-2]. [1]. 22167196. Structural basis of trypsin inhibition and entomotoxicity of cospin, serine protease inhibitor involved in defense of Coprinopsis cinerea fruiting bodies. Sabotic J, Bleuler-Martinez S, Renko M, Avanzo Caglic P, Kallert S, Strukelj B, Turk D, Aebi M, Kos J, Kunzler M;. J Biol Chem. 2012;287:3898-3907. [2]. 10411656. The inhibitory properties and primary structure of a novel serine proteinase inhibitor from the fruiting body of the basidiomycete, Lentinus edodes. Odani S, Tominaga K, Kondou S, Hori H, Koide T, Hara S, Isemura M, Tsunasawa S;. Eur J Biochem. 1999;262:915-923. (from Pfam) NF028183.5 PF16873.10 AbiGii_2 25 25 397 PfamEq Y Y N abortive infection system toxin AbiGii family protein 12023079 1783272 Bacillati kingdom 322 EBI-EMBL Putative abortive phage resistance protein AbiGii toxin abortive infection system toxin AbiGii family protein AbiGii is a family of putative type IV toxin-antitoxin system toxins. The AbiG abortive phage resistance protein affects lactococcal bacteriophages phiP335 and phiQ30 but not the other P335 phage species. AbiGii toxin appears to confer resistance to phages by a mechanism of abortive infection that acts by interfering with phage RNA synthesis [1]. The cognate anti-toxin is found in Pfam:PF10899. [1]. 12023079. Effectiveness of the lactococcal abortive infection systems AbiA, AbiE, AbiF and AbiG against P335 type phages. Tangney M, Fitzgerald GF;. FEMS Microbiol Lett. 2002;210:67-72. (from Pfam) NF028198.5 PF16888.10 DUF5082 33.7 33.7 123 domain Y Y N DUF5082 family protein 1783272 Bacillati kingdom 2697 EBI-EMBL Domain of unknown function (DUF5082) DUF5082 family protein This entry contains proteins that are uncharacterised. (from Pfam) NF028303.5 PF16993.10 Asp1 26 26 522 PfamEq Y Y N accessory Sec system glycosyltransferase Asp1 asp1 GO:0015031 16549667,23000954 1783272 Bacillati kingdom 4936 EBI-EMBL Accessory Sec system protein Asp1 accessory Sec system glycosyltransferase Asp1 Asp1, along with SecY2, SecA2, and other proteins forms part of the accessory secretory protein system. The system is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus. This protein family is assigned to transport rather than glycosylation function, but the specific molecular role is unknown [1]. Asp1 is predicted to be cytosolic [2]. [1]. 16549667. A unique serine-rich repeat protein (Srr-2) and novel surface antigen (epsilon) associated with a virulent lineage of serotype III Streptococcus agalactiae. Seifert KN, Adderson EE, Whiting AA, Bohnsack JF, Crowley PJ, Brady LJ;. Microbiology. 2006;152:1029-1040. [2]. 23000954. Emerging themes in SecA2-mediated protein export. Feltcher ME, Braunstein M;. Nat Rev Microbiol. 2012;10:779-789. (from Pfam) NF028459.5 PF17150.9 CHASE6_C 27 27 80 domain Y N N C-terminal domain of two-partite extracellular sensor domain 12486065 1783272 Bacillati kingdom 1662 EBI-EMBL C-terminal domain of two-partite extracellular sensor domain C-terminal domain of two-partite extracellular sensor domain CHASE6 was originally described as a two-partite extracellular (periplasmic) sensor domain found in histidine kinases and HD-GYP-type c-di-GMP-specific phosphodiesterases [1] and assigned to COG4250 in the COG database. Subsequently, its N-terminal part has been described as a separate DICT (DIguanylate Cyclases and Two-component systems) domain (PF10069) (Aravind L., Iyer LM, Anantharaman V. (2010) Natural history of sensor domains in the bacterial signalling systems. In: Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition ((Spiro S, Dixon R, eds)), pp. 1-38. Caister Academic Press, Norfolk, UK). The current entry contains only the C-terminal part of the original CHASE6 domain described in [1], which is found primarily in cyanobacteria. [1]. 12486065. Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea. Zhulin IB, Nikolskaya AN, Galperin MY;. J Bacteriol 2003;185:285-294. (from Pfam) NF033128.2 vanW-gen 365 365 271 equivalog Y Y Y glycopeptide resistance accessory protein VanW vanW 1783272 Bacillati kingdom 140 NCBIFAM glycopeptide resistance accessory protein VanW glycopeptide resistance accessory protein VanW Members of this family are VanW, an accessory protein of unknown function found in many types of glycopeptide resistance systems, including cryptic and/or uncharacterized systems as was as those giving strong active clinical resistance to the vancomycin. NF033131.1 vanT-G-Cterm 460 460 368 exception Y Y Y serine racemase VanT catalytic subunit vanT GO:0016747 1783272 Bacillati kingdom 742 NCBIFAM serine racemase VanT catalytic subunit serine racemase VanT catalytic subunit This HMM describes serine racemase, usually found as the C-terminal region of the serine bound serine racemase enzyme VanT. In some systems, such as VanL, the N-terminal membrane-binding region and the C-terminal catalytic region are encoded as separate subunits. Members of this family should occur in gene neighborhoods that also encode a VanG-like D-alanine--D-serine ligase. NF033401.1 thiazolyl_BerA 37.5 37.5 42 subfamily Y Y N thiocillin/thiostrepton family thiazolyl peptide 23650400 1783272 Bacillati kingdom 130 NCBIFAM thiocillin/thiostrepton family thiazolyl peptide thiocillin/thiostrepton family thiazolyl peptide Members of this family include the precursor peptides for the antibiotics thiostrepton, nosiheptide, thiocillin, and berninamycin. NF033431.1 cinnamycin_RiPP 35 35 81 subfamily Y Y N cinnamycin family lantibiotic 21770392,28576760,30177849 1783272 Bacillati kingdom 98 NCBIFAM cinnamycin family lantibiotic cinnamycin family lantibiotic Members of this family are RiPP precursor peptides from which the lantibiotic cinnamycin is the most heavily studied. Mature cinnamycin is 19 amino acids long with nine post-translational modifications, including lanthionine, methyllanthionine, and lysinoalanine bridge modifications. NF033433.1 NisI_immun_dup 35 25 105 domain Y Y N NisI/SpaI family lantibiotic immunity lipoprotein 22904324,26459561 1783272 Bacillati kingdom 871 NCBIFAM NisI/SpaI family lantibiotic immunity lipoprotein NisI/SpaI lantibiotic immunity lipoprotein domain This HMM describes a domain that occurs twice in the nisin lantibiotic self-immunity lipoprotein NisI, and once in the subtilin lantibiotic self-immunity lipoprotein SpaI, and once or twice in numerous other known or putative lantibiotic resistance lipoproteins. NF033561.1 macrolact_Ik_Al 300 300 561 subfamily Y Y N albusnodin/ikarugamycin family macrolactam cyclase 24706593,29350227 1783272 Bacillati kingdom 1083 NCBIFAM albusnodin/ikarugamycin family macrolactam cyclase albusnodin/ikarugamycin family macrolactam cyclase Members of this family show homology enzymes known to form the lactam bond of the isopeptide linkage of lasso peptides. This family includes the peptide cyclase involved in biosynthesis of the lasso peptide albusnodin. However, another member of this family belongs to the biosynthesis cassette for ikarugamycin, a macrolactam whose biosynthesis relies on a hybrid PKS/NRPS system, not a ribosomally produced peptide. NF033562.2 BH0509_fam 30 30 43 subfamily Y Y N BH0509 family protein 1783272 Bacillati kingdom 696 NCBIFAM BH0509 family protein BH0509 family protein This family of unknown function appears restricted to the Firmicutes. Proteomics evidence for expression was provided for the member from Bacillus cereus by Dr. Samuel Payne, Pacific Northwest National Labs. The family is named, for now, after BH0509 from Bacillus halodurans. NF033688.1 MG406_fam 40 40 118 hypoth_equivalog Y Y N MG406 family protein 16407165 1783272 Bacillati kingdom 110 NCBIFAM MG406 family protein MG406 family protein Homologs to MG406 from Mycoplasma genitalium and MPN605 from Mycoplasma pneumoniae are about 150 amino acids long on average, highly hydrophobic, widespread in but restricted to the Mollicutes, and highly divergent there. MG406 itself appears to be an essential gene. NF033717.2 HPDL_rSAM_activ 420 420 311 equivalog Y Y N 4-hydroxyphenylacetate decarboxylase activase hpdA GO:0003824,GO:0016491,GO:0051536,GO:0051539 23716017 1783272 Bacillati kingdom 286 NCBIFAM 4-hydroxyphenylacetate decarboxylase activase 4-hydroxyphenylacetate decarboxylase activase 4-hydroxyphenylacetate decarboxylase activase is a radical SAM enzyme, found in anaerobic bacteria where 4-hydroxyphenylacetate decarboxylase occurs and required to prepare the glycyl radical active site of the enzyme. NF033718.1 indole_decarb 1100 1100 868 equivalog Y Y N indoleacetate decarboxylase GO:0003824 30310076 1783272 Bacillati kingdom 34 NCBIFAM indoleacetate decarboxylase indoleacetate decarboxylase Indoleacetate decarboxylase is a single subunit glycyl radical enzyme that depends on a cognate radical SAM enzyme for its activation. It performs the final step in the anaerobic fermentation of tryptophan to skatole, a malodorous volatile compound. NF033719.1 ind_deCO2_activ 425 425 302 equivalog Y Y N indoleacetate decarboxylase activase GO:0003824,GO:0016491,GO:0051536,GO:0051539 1783272 Bacillati kingdom 32 NCBIFAM indoleacetate decarboxylase activase indoleacetate decarboxylase activase NF033878.1 thiovarsolin 35 35 89 subfamily Y Y N thiovarsolin family RiPP 30916321 1783272 Bacillati kingdom 13 NCBIFAM thiovarsolin family RiPP thiovarsolin family RiPP The thiovarsolins, named for a founding member from Streptomyces varsoviensis, are RiPPs (ribosomally synthesized and post-translationally modified peptide). As with the thioviridamides, thiovarsolin precursors are encoded in loci that encode YcaO and TfuA family proteins, suggesting post-translational modification by thioamidation. NF033881.1 aureocin_A53 27 27 48 equivalog Y Y N aureocin A53 family class IId bacteriocin 12054867,26771761,29107139 1783272 Bacillati kingdom 261 NCBIFAM aureocin A53 family class IId bacteriocin aureocin A53 family class IId bacteriocin Members of this family include leaderless, unmodified class IId bacteriocins such as lacticin Q, BacSp222, and the founding member aureocin A53. NF033904.1 LlsX_fam 29 29 90 subfamily Y Y N LlsX family protein 30888475 1783272 Bacillati kingdom 275 NCBIFAM LlsX family protein LlsX family protein LlsX, as found in Listeria monocytogenes, is a small protein of unknown function, encoded in the island responsible for listeriolysin S biosynthesis and processing. Related proteins are found in additional Gram-positive lineages, such as Streptococcus sobrinus and Lactobacillus sp. NF035929.1 lectin_1 800 800 886 subfamily Y Y N lectin 1783272 Bacillati kingdom 1560 NCBIFAM lectin Lectins are important adhesin proteins, which bind carbohydrate structures on host cell surface. The carbohydrate specificity of diverse lectins to a large extent dictates bacteria tissue tropism by mediating specific attachment to unique host sites expressing the corresponding carbohydrate receptor. NF036334.5 PF17424.7 DUF5411 30 30 134 subfamily Y Y N DUF5411 family protein 1783272 Bacillati kingdom 110 EBI-EMBL Family of unknown function (DUF5411) DUF5411 family protein This is a family of unknown function found in Bacteria. (from Pfam) NF036363.5 PF17534.7 DUF5453 25 25 186 subfamily Y Y N DUF5453 family protein 1783272 Bacillati kingdom 31 EBI-EMBL Family of unknown function (DUF5453) DUF5453 family protein This is a family of unknown function found in Mycoplasma. Family members have 4 predicted trans-membrane regions. (from Pfam) NF036459.5 PF17260.7 DUF5326 27 27 70 domain Y Y N DUF5326 family protein 1783272 Bacillati kingdom 2788 EBI-EMBL Family of unknown function (DUF5326) DUF5326 family protein This is a family of unknown function mostly found in Actinobacteria. Many of the family members are predicted to contain two trans-membrane domains. (from Pfam) NF036540.5 PF18008.6 Bac_RepA_C 25 25 95 domain Y N N Replication initiator protein A C-terminal domain 24927575 1783272 Bacillati kingdom 4289 EBI-EMBL Replication initiator protein A C-terminal domain Replication initiator protein A C-terminal domain This is the C-terminal domain (CTD) that can be found in the conserved replication initiator, RepA,essential for staphylococcal propagation. RepA CTD shared the strongest structural homology to the Enterococcus faecalis DnaD CTD, yet perform distinct functions. RepA CTD shows strong sequence homology between RepA_N plasmids in genus-specific clusters, suggesting that it may perform host-specific functions necessary for replication. The RepA CTD interacts with the host DnaG primase, which binds the replicative helicase. Structural data indicate that the RepA CTD exists as a monomeric entity, flexibly tethered to the DNA-bound NTD [1]. [1]. 24927575. Mechanism of staphylococcal multiresistance plasmid replication origin assembly by the RepA protein. Schumacher MA, Tonthat NK, Kwong SM, Chinnam NB, Liu MA, Skurray RA, Firth N;. Proc Natl Acad Sci U S A. 2014;111:9121-9126. (from Pfam) NF036572.5 PF17359.7 DUF5385 25 25 217 subfamily Y Y N DUF5385 family protein 1783272 Bacillati kingdom 56 EBI-EMBL Family of unknown function (DUF5385) DUF5385 family protein This is a family of unknown function found in Mycoplasmataceae. Family members are predicted to have one trans-membrane region. (from Pfam) NF036647.5 PF17440.7 Thiol_cytolys_C 23 23 102 domain Y Y N thiol-activated cytolysin C-terminal domain-containing protein 1783272 Bacillati kingdom 2993 EBI-EMBL Thiol-activated cytolysin beta sandwich domain Thiol-activated cytolysin beta sandwich domain This domain has an immunoglobulin like fold. It is found at the C-terminus of the thiol-activated cytolsin protein. (from Pfam) NF036738.5 PF18218.6 Spa1_C 26.4 26.4 99 domain Y N N Lantibiotic immunity protein Spa1 C-terminal domain 22904324 1783272 Bacillati kingdom 492 EBI-EMBL Lantibiotic immunity protein Spa1 C-terminal domain Lantibiotic immunity protein Spa1 C-terminal domain This is the C-terminal domain found in SpaI present in Bacillus subtilis. SpaI is an immunity lipoprotein that protects the Gram-positive bacteria against their own lantibiotics, in this case subtilin. SpaI together with the ABC transporter SpaFEG protects the membrane from subtilin insertion [1]. [1]. 22904324. The First structure of a lantibiotic immunity protein, SpaI from Bacillus subtilis, reveals a novel fold. Christ NA, Bochmann S, Gottstein D, Duchardt-Ferner E, Hellmich UA, Dusterhus S, Kotter P, Guntert P, Entian KD, Wohnert J;. J Biol Chem. 2012;287:35286-35298. (from Pfam) NF036924.5 PF18674.6 TarS_C1 26.3 26.3 147 domain Y N N TarS beta-glycosyltransferase C-terminal domain 1 27973583 1783272 Bacillati kingdom 2577 EBI-EMBL TarS beta-glycosyltransferase C-terminal domain 1 TarS beta-glycosyltransferase C-terminal domain 1 Beta-glycosyltransferase TarS is an enzyme responsible for the glycosylation of wall teichoic acid polymers of the S. aureus cell wall, a process that has been shown to be specifically responsible for methicillin resistance in MRSA. It contains a trimerization domain composed of tandem carbohydrate binding motifs.The two C-terminally localized regions composed of a series of beta-sheets participate in an extensive trimerization interface and they assume an immunoglobulin-like fold. It is suggested that both carbohydrate binding domains may be involved in polyRboP binding, however unlike pullulanase, the CBMs of TarS are involved in the formation of an extensive trimerization interface [1]. [1]. 27973583. Structure and Mechanism of Staphylococcus aureus TarS, the Wall Teichoic Acid beta-glycosyltransferase Involved in Methicillin Resistance. Sobhanifar S, Worrall LJ, King DT, Wasney GA, Baumann L, Gale RT, Nosella M, Brown ED, Withers SG, Strynadka NC;. PLoS Pathog. 2016;12:e1006067. (from Pfam) NF037164.5 PF17998.6 AgI_II_C2 27.1 27.1 148 domain Y N N Cell surface antigen I/II C2 terminal domain 24918040 1783272 Bacillati kingdom 11986 EBI-EMBL Cell surface antigen I/II C2 terminal domain Cell surface antigen I/II C2 terminal domain This is the second domain (C2) located in the C-terminal region found in antigen I/II type adhesin protein AspA from S. pyogenes. Together with C3, these two domains form an elongated structure, each domain adopts the DEv-IgG fold. Similar to the classical IgG folds, it is comprised of two major antiparallel beta-sheets, designated ABED and CFG. For the C2-domain, there are two additional strands on the CFG sheet. Furthermore, sheets ABED and CFG are interconnected by several cross-connecting loops and one alpha-helix (DH1). The side chains of D982 and N996 in the C2-domain are involved in hydrogen bonding with the side chains of R1264 and N1295 in the C3 domain. Main chain hydrogen bonding can also be observed between S992 in C2 and N1189/G1191 in C3, furthermore stabilizing the interaction between the domains. The C2 domain contains one bound metal ion, modelled as Ca2+, and both the C2- and C3-domains are stabilized by conserved isopeptide bonds, which connect the beta-sheets of the central DEv-IgG motifs [1].Other members of this family include Major cell-surface adhesin PAc from Streptococcus mutans and SspB from Streptococcus gordonii. [1]. 24918040. Structure of the C-terminal domain of AspA (antigen I/II-family) protein from Streptococcus pyogenes. Hall M, Nylander S, Jenkinson HF, Persson K;. FEBS Open Bio. 2014;4:283-289. (from Pfam) NF037188.5 PF18094.6 DNA_pol_B_N 25 25 104 domain Y N N DNA polymerase beta N-terminal domain 16615916 1783272 Bacillati kingdom 6394 EBI-EMBL DNA polymerase beta N-terminal domain DNA polymerase beta N-terminal domain This is the N-terminal domain of DNA polymerase beta present in Homo sapiens. DNA polymerase beta is a repair enzyme that has a key role in the base excision repair of simple DNA lesions [1]. [1]. 16615916. Magnesium-induced assembly of a complete DNA polymerase catalytic complex. Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC, Wilson SH;. Structure. 2006;14:757-766. (from Pfam) NF037264.5 PF18524.6 HPIP_like 28.1 28.1 40 domain Y N N High potential iron-sulfur protein like 21823587 1783272 Bacillati kingdom 184 EBI-EMBL High potential iron-sulfur protein like High potential iron-sulfur protein like This is a C-terminal domain found in 4-hydroxyphenylacetate decarboxylase small subunit (EC:4.1.1.83), which catalyzes the last reaction in the fermentative production of p-cresol from tyrosine. The C-terminal domain [4F-4S] cluster bears structural similarity to high-potential iron-sulfur proteins (HiPIPs). HiPIPs have an N-terminal extension of 20-40 residues, so the structural similarity is limited to their Fe/S cluster-binding scaffold. Furthermore, despite of the weak amino acid sequence identity, the cluster binding motifs are remarkably similar to H/CX2CX12-13CX16-17C for the gamma-subunit and CX2CX13-19CX14-19C for HiPIPs [1]. [1]. 21823587. Structural basis for a Kolbe-type decarboxylation catalyzed by a glycyl radical enzyme. Martins BM, Blaser M, Feliks M, Ullmann GM, Buckel W, Selmer T;. J Am Chem Soc. 2011;133:14666-14674. (from Pfam) NF037372.5 PF18655.6 SHIRT 22.4 15 82 domain Y Y N SHIRT domain-containing protein 34074781 1783272 Bacillati kingdom 2829 EBI-EMBL SHIRT domain SHIRT domain The SHIRT domain is found in a range of presumed bacterial adhesin proteins. (from Pfam) NF037561.5 PF17475.7 Binary_toxB_2 25 25 218 domain Y N N Clostridial binary toxin B/anthrax toxin PA domain 2 GO:0051260 1783272 Bacillati kingdom 677 EBI-EMBL Clostridial binary toxin B/anthrax toxin PA domain 2 Clostridial binary toxin B/anthrax toxin PA domain 2 This domain forms the middle beta sandwish domain in anthrax toxin. (from Pfam) NF037562.5 PF17476.7 Binary_toxB_3 28.4 28.4 102 domain Y N N Clostridial binary toxin B/anthrax toxin PA domain 3 1783272 Bacillati kingdom 653 EBI-EMBL Clostridial binary toxin B/anthrax toxin PA domain 3 Clostridial binary toxin B/anthrax toxin PA domain 3 This entry represents the beta-grasp domain in anthrax protective antigen. (from Pfam) NF037678.5 PF17934.6 TetR_C_26 25 25 109 domain Y N N Tetracyclin repressor-like, C-terminal domain 1783272 Bacillati kingdom 1450 EBI-EMBL Tetracyclin repressor-like, C-terminal domain Tetracyclin repressor-like, C-terminal domain This entry represents the C-terminal domain present in putative HTH-type transcriptional regulator. Family members are found in bacilli. (from Pfam) NF037690.5 PF17961.6 Big_8 22.9 22.9 103 domain Y Y N Ig-like domain-containing protein 17392280,19043557,21280131,24627488 1783272 Bacillati kingdom 62046 EBI-EMBL Bacterial Ig domain Ig-like domain This entry represents a bacterial Ig-fold domain that is found in a wide range of bacterial cell surface adherence proteins. [1]. 21280131. Crystal structure of the functional region of Uro-adherence factor A from Staphylococcus saprophyticus reveals participation of the B domain in ligand binding. Matsuoka E, Tanaka Y, Kuroda M, Shouji Y, Ohta T, Tanaka I, Yao M;. Protein Sci. 2011;20:406-416. [2]. 19043557. A structural model of the Staphylococcus aureus ClfA-fibrinogen interaction opens new avenues for the design of anti-staphylococcal therapeutics. Ganesh VK, Rivera JJ, Smeds E, Ko YP, Bowden MG, Wann ER, Gurusiddappa S, Fitzgerald JR, Hook M;. PLoS Pathog. 2008;4:e1000226. [3]. 17392280. The Enterococcus faecalis MSCRAMM ACE binds its ligand by the Collagen Hug model. Liu Q, Ponnuraj K, Xu Y, Ganesh VK, Sillanpaa J, Murray BE, Narayana SV, Hook M;. J Biol Chem. 2007;282:19629-19637. [4]. 24627488. Evidence for steric regulation of fibrinogen binding to Staphylococcus aureus fibronectin-binding protein A (FnBPA). Stemberk V, Jones RP, Moroz O, Atkin KE, Edwards AM, Turkenburg JP, Leech AP, Massey RC, Potts JR;. J Biol Chem. 2014;289:12842-12851. (from Pfam) NF037692.5 PF17966.6 Muc_B2 23.5 23.5 67 domain Y Y N mucin-binding protein 19758995 1783272 Bacillati kingdom 15848 EBI-EMBL Muc B2-like domain Muc B2-like domain This entry corresponds to the Muc B2 domain [1]. This domain is related to the Muc B1 domain Pfam:PF17965. This domain may be involved in mucin binding. This domain is often found associated with the related Pfam:PF17965 in bacterial cell surface proteins. [1]. 19758995. Crystal structure of a mucus-binding protein repeat reveals an unexpected functional immunoglobulin binding activity. MacKenzie DA, Tailford LE, Hemmings AM, Juge N;. J Biol Chem. 2009;284:32444-32453. (from Pfam) NF037700.5 PF17995.7 GH101_N 25 25 180 domain Y N N Endo-alpha-N-acetylgalactosaminidase N-terminal domain 18784084 1783272 Bacillati kingdom 2551 EBI-EMBL Endo-alpha-N-acetylgalactosaminidase N-terminal domain Endo-alpha-N-acetylgalactosaminidase N-terminal domain This is the N-terminal domain found in Streptococcus pneumoniae endo-alpha-N-acetylgalactosaminidase (EC:3.2.1.97) , a cell surface-anchored glycoside hydrolase from family GH101 involved in the breakdown of mucin type O-linked glycans. This is a twisted beta-sandwich domain composed of two sheets of six and seven antiparallel beta-strands. The domain appears to be missing the extended metal and carbohydrate-binding loops [1]. Paper describing PDB structure 3ecq. [1]. 18784084. The structural basis for T-antigen hydrolysis by Streptococcus pneumoniae: a target for structure-based vaccine design. Caines ME, Zhu H, Vuckovic M, Willis LM, Withers SG, Wakarchuk WW, Strynadka NC;. J Biol Chem. 2008;283:31279-31283. (from Pfam) NF037702.5 PF17999.6 PulA_N1 27 27 85 domain Y N N Pullulanase N1-terminal domain 24375572 1783272 Bacillati kingdom 3727 EBI-EMBL Pullulanase N1-terminal domain Pullulanase N1-terminal domain This is the N-terminal domain found in debranching enzyme such as Pullulanase (PulA)from Anoxybacillus sp. LM18-11. The PulA structure comprises four domains (N1, N2, A, and C). This is the N1 domain which has been identified as a carbohydrate-binding motif. Two maltotriose or maltotetraose molecules were found between the N1 domain and a loop of the A domain in the PulA-maltotriose or PulA-maltotetraose structures. These carbohydrates are bound in a parallel binding mode close to each other and form hydrogen bonds. The sugar moieties bound to the N1 domain are not immediately adjacent to the active site, but the enzyme might use N1 binding to attract and grab the substrate. Functional analysis indicate that N1 is important for catalytic activity and thermostability in addition to assisting substrate binding. The structure of the N1 domain reveals a classic distorted beta-jelly roll fold consisting of two anti-parallel beta-sheets, forming a concave and a convex surface. On the concave side of N1 domain there is a cleft to accommodate two molecules of maltotriose or maltotetraose [1]. [1]. 24375572. Functional and structural studies of pullulanase from Anoxybacillus sp. LM18-11. Xu J, Ren F, Huang CH, Zheng Y, Zhen J, Sun H, Ko TP, He M, Chen CC, Chan HC, Guo RT, Song H, Ma Y;. Proteins. 2014;82:1685-1693. (from Pfam) NF037874.5 PF18652.6 Adhesin_P1_N 27.1 27.1 106 domain Y N N Adhesin P1 N-terminal domain 25331888 1783272 Bacillati kingdom 6533 EBI-EMBL Adhesin P1 N-terminal domain Adhesin P1 N-terminal domain The cariogenic bacterium Streptococcus mutans uses adhesin P1 to adhere to tooth surfaces, extracellular matrix components, and other bacteria. The N terminus forms a stabilizing scaffold by wrapping behind the base of P1's elongated stalk and physically 'locking' it into place. It is suggested that the N-terminal has such a pronounced impact on P1 immunogenicity, antigenicity, folding, stability, and adherent function [1]. [1]. 25331888. An intramolecular lock facilitates folding and stabilizes the tertiary structure of Streptococcus mutans adhesin P1. Heim KP, Crowley PJ, Long JR, Kailasan S, McKenna R, Brady LJ;. Proc Natl Acad Sci U S A. 2014;111:15746-15751. (from Pfam) NF037898.5 PF18768.6 RNPP_C 26.5 26.5 213 domain Y N N RNPP family C-terminal domain 23277548 1783272 Bacillati kingdom 5063 EBI-EMBL RNPP family C-terminal domain RNPP family C-terminal domain The bacterial PIcR helix-turn-helix transcription factor includes five TPR units of different lengths [1]. This entry represents the TPR containing domain as a whole. This family is called RNPP after (Rapm NprR, PrgX, and PlcR). [1]. 23277548. Structural basis for the activation mechanism of the PlcR virulence regulator by the quorum-sensing signal peptide PapR. Grenha R, Slamti L, Nicaise M, Refes Y, Lereclus D, Nessler S;. Proc Natl Acad Sci U S A. 2013;110:1047-1052. (from Pfam) NF037945.1 holin_3 80 80 37 subfamily Y Y N bacteriophage holin 1783272 Bacillati kingdom 82 NCBIFAM bacteriophage holin Bacteriophage holin can cause host cell lysis to release progeny phage particles. Proteins of this family have about 60 amino acids, and a transmembrane domain is usually found on the C-terminal. NF038040.1 phero_PhrK_fam 35 35 40 equivalog Y Y N PhrK family phosphatase-inhibitory pheromone 1783272 Bacillati kingdom 154 NCBIFAM PhrK family phosphatase-inhibitory pheromone NF038080.1 PG_bind_siph 55 55 76 domain Y Y N peptidoglycan-binding protein 12923110 1783272 Bacillati kingdom 13049 NCBIFAM peptidoglycan-binding domain This domain occurs shows apparent homology to known or putative peptidoglycan-binding domains in families such as PF01471. The domain occurs once, or twice, at the C-terminus of proteins such as cell wall amidases. In particular, member proteins can be found among putative lysins of phage of Streptomyces from the Siphoviridae family, such as phiBT1. NF038146.1 LxmA_leader 25 25 31 domain Y Y N LxmA leader domain family RiPP 32648341 1783272 Bacillati kingdom 834 NCBIFAM LxmA family RiPP leader domain LxmA is the founding member of a family of ribosomally synthesized and post-translationally modified lanthipeptides whose lanthionine moiety is created by a novel class of enzyme. This HMM represents the leader domain, and the first four residues of the core peptide, of LxmA, its full-length homologs, and a number of other RiPPs that much lower sequence similarity outside the leader peptide region. NF038155.1 lanthi_I_FDLD 20 20 34 domain Y Y N FDLD family class I lanthipeptide 1783272 Bacillati kingdom 786 NCBIFAM FDLD family class I lanthipeptide This HMM finds a broad collection of putative class I lanthipeptides with a well-conserved motif FDLD near the N-terminus, and poorly conserved but typically Cys-rich core peptide regions. Some members belong to the more narrowly defined family of gallidermin/nisin-like lanthipeptides. NF038186.1 YPDG_rpt 40 40 98 domain Y Y N YPDG domain-containing protein 1783272 Bacillati kingdom 8375 NCBIFAM YPDG domain The YPDG domain may occur once in a protein, or up to 22 times in tandem repeats. It is common in proteins of Gram-positive bacteria with C-terminal LPXTG sites for anchoring on the cell surface. NF038340.1 SAR2788_fam 50 50 177 subfamily Y Y N SAR2788 family putative toxin 1783272 Bacillati kingdom 793 NCBIFAM SAR2788 family putative toxin NF038360.1 rad_fix_GrcA3 158 158 78 exception Y Y N autonomous glycyl radical cofactor GrcA3 grcA3 1783272 Bacillati kingdom 312 NCBIFAM autonomous glycyl radical cofactor GrcA3 This small protein, like GrcA and GrcA2, is a lineage-specific small protein related to the glycyl radical active site-containing C-terminal region of pyruvate formate-lyase (PFL, also called formate C-acetyltransferase) from similar species. Because PFL is prone to damage and inactivation, this protein is made as a spare part that fills in for the portion of the protein that was damaged and lost. The distinct families we now call GrcA, GrcA2, and GrcA3 all have the surprising property of being much more closely related to some full length PFL than to members of the other GrcA-series families. NF039172.4 PF18873.5 Sgo0707_N1 25 25 269 domain Y N N Sgo0707 N-terminal domain 23691093 1783272 Bacillati kingdom 423 EBI-EMBL Sgo0707 N-terminal domain Sgo0707 N-terminal domain This domain found at the N-terminus of the cell surface Sgo0707 protein. This domain is called the N1 domain and is involved in host colonisation.The largest domain, N1, comprises a putative binding cleft with a single cysteine located in its centre and exhibits an unexpected structural similarity to the variable domains of the streptococcal Antigen I/II adhesins [1]. [1]. 23691093. Structural and functional analysis of the N-terminal domain of the Streptococcus gordonii adhesin Sgo0707. Nylander A, Svensater G, Senadheera DB, Cvitkovitch DG, Davies JR, Persson K;. PLoS One. 2013;8:e63768. (from Pfam) NF039231.4 PF19085.5 Choline_bind_2 27 27 38 repeat Y N N choline-binding repeat-containing protein 27917891 1783272 Bacillati kingdom 17202 EBI-EMBL Choline-binding repeat Choline-binding repeat this entry contains a pair of presumed choline-binding repeats that are often found adjacent to Pfam:PF01473. [1]. 27917891. Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L (CbpL) Contributing to Pneumococcal Pathogenesis. Gutierrez-Fernandez J, Saleh M, Alcorlo M, Gomez-Mejia A, Pantoja-Uceda D, Trevino MA, Voss F, Abdullah MR, Galan-Bartual S, Seinen J, Sanchez-Murcia PA, Gago F, Bruix M, Hammerschmidt S, Hermoso JA;. Sci Rep. 2016;6:38094. (from Pfam) NF039246.4 PF19158.5 DUF5840 25 25 49 subfamily Y Y N anacyclamide/piricyclamide family prenylated cyclic peptide 20008171,30266955 1783272 Bacillati kingdom 304 EBI-EMBL Family of unknown function (DUF5840) anacyclamide/piricyclamide family prenylated cyclic peptide This family contains uncharacterised proteins. It also contains the anacyclamide synthesis protein AcyE. Cyanobactins are small, cyclic peptides found in cyanobacteria. They are ribosomally synthesised and post-translationally modified. Cyanobactin biosynthesis clusters contain 7-12 genes [1]. Anaclyclamides are a type of cyanobactin produced in strains of the cyanobacteria Anabaena [1]. AcyE is a 49-amino-acid protein with N-terminal homology to the peptide precursor proteins in the other cyanobactin pathways [2]. The core peptide of AcyE is cleaved during post-translational processing of the precursor peptide [2]. [1]. 20008171. Highly diverse cyanobactins in strains of the genus Anabaena. Leikoski N, Fewer DP, Jokela J, Wahlsten M, Rouhiainen L, Sivonen K;. Appl Environ Microbiol. 2010;76:701-709. [2]. 30266955. Sphaerocyclamide, a prenylated cyanobactin from the cyanobacterium Sphaerospermopsis sp. LEGE 00249. Martins J, Leikoski N, Wahlsten M, Azevedo J, Antunes J, Jokela J, Sivonen K, Vasconcelos V, Fewer DP, Leao PN;. Sci Rep. 2018;8:14537. (from Pfam) NF039316.4 PF19462.4 DUF5999 27.5 27.5 57 subfamily Y Y N DUF5999 family protein 16766657 1783272 Bacillati kingdom 7745 EBI-EMBL Family of unknown function (DUF5999) DUF5999 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a protein from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [1]. This family appears to be predominantly found in Actinobacteria. [1]. 16766657. Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Yanai K, Murakami T, Bibb M;. Proc Natl Acad Sci U S A. 2006;103:9661-9666. (from Pfam) NF039332.4 PF19508.4 DUF6042 26.8 26.8 219 subfamily Y Y N DUF6042 family protein 16208464 1783272 Bacillati kingdom 973 EBI-EMBL Family of unknown function (DUF6042) DUF6042 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000291) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This family includes a protein from the A54145 biosynthetic gene cluster from Streptomyces fradiae [1]. [1]. 16208464. The lipopeptide antibiotic A54145 biosynthetic gene cluster from Streptomyces fradiae. Miao V, Brost R, Chapple J, She K, Gal MF, Baltz RH;. J Ind Microbiol Biotechnol. 2006;33:129-140. (from Pfam) NF039604.4 PF19380.4 DUF5955 27.1 27.1 88 subfamily Y Y N DUF5955 family protein 1783272 Bacillati kingdom 4085 EBI-EMBL Family of unknown function (DUF5955) DUF5955 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001731) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). (from Pfam) NF039637.4 PF19522.4 DUF6052 25 25 61 subfamily Y Y N DUF6052 family protein 26853480 1783272 Bacillati kingdom 148 EBI-EMBL Family of unknown function (DUF6052) DUF6052 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001397) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the lidamycin biosynthetic gene cluster from Streptomyces globisporus C-1027 and appears to be predominantly present in bacteria [1]. [1]. 26853480. Complete genome sequence of Streptomyces globisporus C-1027, the producer of an enediyne antibiotic lidamycin. Li X, Lei X, Zhang C, Jiang Z, Shi Y, Wang S, Wang L, Hong B;. J Biotechnol. 2016;222:9-10. (from Pfam) NF039647.4 PF19561.4 DUF6083 27.1 27.1 112 domain Y Y N DUF6083 domain-containing protein 28111097 1783272 Bacillati kingdom 4474 EBI-EMBL Family of unknown function (DUF6083) DUF6083 domain This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC00001735) is described by MIBiG as an example of the following biosynthetic class, other. This family includes a protein from the pentostatine biosynthetic gene cluster from Streptomyces antibioticus and appears to be predominantly found in Streptomyces [1]. [1]. 28111097. An Unusual Protector-Protege Strategy for the Biosynthesis of Purine Nucleoside Antibiotics. Wu P, Wan D, Xu G, Wang G, Ma H, Wang T, Gao Y, Qi J, Chen X, Zhu J, Li YQ, Deng Z, Chen W;. Cell Chem Biol. 2017;24:171-181. (from Pfam) NF039695.4 PF19746.4 DUF6233 27.6 27.6 59 domain Y Y N DUF6233 domain-containing protein 30565634 1783272 Bacillati kingdom 10571 EBI-EMBL Family of unknown function (DUF6233) Family of unknown function (DUF6233) This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001973) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the fervenulin biosynthetic gene cluster from Streptomyces hiroshimensis [1]. This family appears to be predominantly found in Actinoabacteria. [1]. 30565634. Characterization of the N-methyltransferases involved in the biosynthesis of toxoflavin, fervenulin and reumycin from Streptomyces hiroshimensis ATCC53615. Su C, Yan Y, Guo X, Luo J, Liu C, Zhang Z, Xiang WS, Huang SX;. Org Biomol Chem. 2019;17:477-481. (from Pfam) NF039700.4 PF19760.4 DUF6247 26.9 26.9 99 subfamily Y Y N DUF6247 family protein 2106503,24168704 1783272 Bacillati kingdom 5395 EBI-EMBL Family of unknown function (DUF6247) DUF6247 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000345) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the eponemycin biosynthetic gene cluster from Streptomyces hygroscopicus [1,2]. This family appears to be predominantly found in Actinobacteria. [1]. 24168704. Genetic basis for the biosynthesis of the pharmaceutically important class of epoxyketone proteasome inhibitors. Schorn M, Zettler J, Noel JP, Dorrestein PC, Moore BS, Kaysser L;. ACS Chem Biol. 2014;9:301-309. [2]. 2106503. Eponemycin, a new antibiotic active against B16 melanoma. I. Production, isolation, structure and biological activity. Sugawara K, Hatori M, Nishiyama Y, Tomita K, Kamei H, Konishi M, Oki T;. J Antibiot (Tokyo). 1990;43:8-18. (from Pfam) NF039758.4 PF19949.4 DUF6411 25 25 63 subfamily Y Y N DUF6411 family protein 29324854 1783272 Bacillati kingdom 977 EBI-EMBL Family of unknown function (DUF6411) DUF6411 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001740) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the phthoxazolin biosynthetic gene cluster from Streptomyces avermitilis [1]. [1]. 29324854. Characterization of the biosynthetic gene cluster for cryptic phthoxazolin A in Streptomyces avermitilis. Suroto DA, Kitani S, Arai M, Ikeda H, Nihira T;. PLoS One. 2018;13:e0190973. (from Pfam) NF039771.4 PF19990.4 DUF6426 25 25 203 subfamily Y Y N DUF6426 family protein 27191535 1783272 Bacillati kingdom 217 EBI-EMBL Family of unknown function (DUF6426) DUF6426 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001396) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the aldgamycin J biosynthetic gene cluster from Streptomyces sp. A1(2016) [1]. [1]. 27191535. A Single Gene Cluster for Chalcomycins and Aldgamycins: Genetic Basis for Bifurcation of Their Biosynthesis. Tang XL, Dai P, Gao H, Wang CX, Chen GD, Hong K, Hu D, Yao XS;. Chembiochem. 2016;17:1241-1249. (from Pfam) NF039775.4 PF20006.4 fvmYukDl_N 27 27 85 domain Y N N YukD-like N-terminal domain 32101166 1783272 Bacillati kingdom 89 EBI-EMBL YukD-like N-terminal domain YukD-like N-terminal domain Uncharacterized domain found N-terminal to YukD-like Ubiquitin domain in FtsH ternary systems, a class of NTP-dependent biological conflict systems. [1]. 32101166. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. Kaur G, Burroughs AM, Iyer LM, Aravind L;. Elife. 2020; [Epub ahead of print] (from Pfam) NF039813.4 PF18877.5 SSSPR-51 27 27 48 domain Y N N SSSPR-51 domain 1783272 Bacillati kingdom 3126 EBI-EMBL SSSPR-51 domain SSSPR-51 domain This repeat domain is designated SSSPR-51, Streptococcal and Staphylococcal Surface Protein Repeat of size 51. These repeats are homologous to the listerial repeats of Pfam:PF06458, but shorter on average by about 8 amino acids. (from Pfam) NF039816.4 PF18892.5 DUF5651 27 27 53 domain Y Y N DUF5651 domain-containing protein 1783272 Bacillati kingdom 229 EBI-EMBL Family of unknown function (DUF5651) Family of unknown function (DUF5651) This entry represents a probable zinc binding domain found at the C-terminus of some Firmicute bacteria. The function of these proteins is unknown. (from Pfam) NF039929.4 PF19375.4 DurN 23.9 23.9 103 subfamily Y Y N DurN family substrate-assisted peptide maturase 30177849 1783272 Bacillati kingdom 88 EBI-EMBL DurN substrate-assisted peptide maturase DurN family substrate-assisted peptide maturase The peptide maturase DurN, a substrate-assisted lysinoalanine synthase, forms a Lys-Ala crosslink in the RiPP peptide duramycin. NF040000.4 PF19621.4 DUF6126 25 25 40 subfamily Y Y N DUF6126 family protein 12000953,8843436 1783272 Bacillati kingdom 4735 EBI-EMBL Family of unknown function (DUF6126) DUF6126 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000663) is described by MIBiG as an example of the following biosynthetic class, terpene. It includes a member from the hopene biosynthetic gene cluster from Streptomyces coelicolor A3(2) and appears to be predominantly found in actinobacteria [1,2]. [1]. 12000953. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA;. Nature. 2002;417:141-147. [2]. 8843436. A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome. Redenbach M, Kieser HM, Denapaite D, Eichner A, Cullum J, Kinashi H, Hopwood DA;. Mol Microbiol. 1996;21:77-96. (from Pfam) NF040018.4 PF19688.4 DUF6189 25 25 102 subfamily Y Y N DUF6189 family protein 24584498 1783272 Bacillati kingdom 24 EBI-EMBL Family of unknown function (DUF6189) DUF6189 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000807) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member of the phosphonoglycans biosynthetic gene cluster from Stackebrandtia nassauensis DSM 44728 [1]. [1]. 24584498. Purification and characterization of phosphonoglycans from Glycomyces sp. strain NRRL B-16210 and Stackebrandtia nassauensis NRRL B-16338. Yu X, Price NP, Evans BS, Metcalf WW;. J Bacteriol. 2014;196:1768-1779. (from Pfam) NF040063.4 PF19848.4 DUF6323 30.6 30.6 127 subfamily Y Y N DUF6323 family protein 27806569 1783272 Bacillati kingdom 1256 EBI-EMBL Family of unknown function (DUF6323) DUF6323 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001520) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the aurantinin B biosynthetic gene cluster from Bacillus subtilis [1]. This family appears to be predominantly present in Firmicutes. [1]. 27806569. Genomics-Inspired Discovery of Three Antibacterial Active Metabolites, Aurantinins B, C, and D from Compost-Associated Bacillus subtilis fmb60. Yang J, Zhu X, Cao M, Wang C, Zhang C, Lu Z, Lu F;. J Agric Food Chem. 2016;64:8811-8820. (from Pfam) NF040112.4 PF20069.4 DUF6465 26 26 130 subfamily Y Y N DUF6465 family protein 1783272 Bacillati kingdom 1831 EBI-EMBL Family of unknown function (DUF6465) DUF6465 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 117 and 173 amino acids in length. These proteins have a highly charged N-terminus. (from Pfam) NF040203.4 PF19127.5 Choline_bind_3 27 27 47 repeat Y N N choline-binding repeat-containing protein 1783272 Bacillati kingdom 53266 EBI-EMBL Choline-binding repeat choline-binding repeat Pair of presumed choline-binding repeats often found adjacent to Pfam:PF01473. (from Pfam) NF040270.4 PF19369.4 DUF5944 25 25 243 subfamily Y Y N DUF5944 family protein 1783272 Bacillati kingdom 70 EBI-EMBL Family of unknown function (DUF5944) DUF5944 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001797) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide). (from Pfam) NF040328.4 PF19608.4 DUF6113 27 27 129 subfamily Y Y N DUF6113 family protein 1783272 Bacillati kingdom 6373 EBI-EMBL Family of unknown function (DUF6113) DUF6113 family protein This family of putative integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 136 and 154 amino acids in length. (from Pfam) NF040335.4 PF19644.4 DUF6147 24 24 138 subfamily Y Y N DUF6147 family protein 1783272 Bacillati kingdom 442 EBI-EMBL Family of unknown function (DUF6147) DUF6147 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 155 and 173 amino acids in length. (from Pfam) NF040348.4 PF19695.4 DUF6195 25 25 139 subfamily Y Y N DUF6195 family protein 16766657 1783272 Bacillati kingdom 173 EBI-EMBL Family of unknown function (DUF6195) DUF6195 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus [1]. [1]. 16766657. Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus. Yanai K, Murakami T, Bibb M;. Proc Natl Acad Sci U S A. 2006;103:9661-9666. (from Pfam) NF040352.4 PF19708.4 DUF6205 27.3 27.3 141 subfamily Y Y N DUF6205 family protein 23921821 1783272 Bacillati kingdom 133 EBI-EMBL Family of unknown function (DUF6205) DUF6205 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000078) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the incednine biosynthetic gene cluster from Streptomyces sp. ML694-90F3 [1]. [1]. 23921821. Identification of the incednine biosynthetic gene cluster: characterization of novel beta-glutamate-beta-decarboxylase IdnL3. Takaishi M, Kudo F, Eguchi T;. J Antibiot (Tokyo). 2013;66:691-699. (from Pfam) NF040359.4 PF19736.4 DUF6226 26.8 26.8 205 subfamily Y Y N DUF6226 family protein 20690632 1783272 Bacillati kingdom 1651 EBI-EMBL Family of unknown function (DUF6226) DUF6226 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000223) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the rabelomycin biosynthetic gene cluster from uncultured bacterium BAC AB649/1850 [1]. This family appears to be predominantly found in Actinobacteria. [1]. 20690632. Fluostatins produced by the heterologous expression of a TAR reassembled environmental DNA derived type II PKS gene cluster. Feng Z, Kim JH, Brady SF;. J Am Chem Soc. 2010;132:11902-11903. (from Pfam) NF040364.4 PF19758.4 DUF6245 25 25 171 subfamily Y Y N DUF6245 family protein 19362651 1783272 Bacillati kingdom 254 EBI-EMBL Family of unknown function (DUF6245) DUF6245 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis [1]. [1]. 19362651. Enzymology of aminoglycoside biosynthesis-deduction from gene clusters. Wehmeier UF, Piepersberg W;. Methods Enzymol. 2009;459:459-491. (from Pfam) NF040664.1 HEC_x9_TCC_lant 46 46 39 equivalog Y Y N lacticin 481 family lantibiotic 17096664,30272026 1783272 Bacillati kingdom 161 NCBIFAM lacticin 481 family lantibiotic The lacticin 481 group exert their antimicrobial action by disrupting the cytoplasmic membrane. This model contains a lipid II-binding motif. The docking of the lantibiotic with lipid II is part of the mechanism by which family members form a membrane-disrupting structure. The lacticin 481 group includes lacticin 481, mutacin H-29B, variacin, nukacin ISK-1, butyrivibriocin OR79A, streptococcin A-FF2, ruminococcin A, mutacin II, and salivaricin A. NF040680.1 chromo_anti 86 86 133 equivalog Y Y N enediyne antibiotic chromoprotein 12183628,8226326,8235619 1783272 Bacillati kingdom 474 NCBIFAM enediyne antibiotic chromoprotein Members of this family are the apoprotein polypeptides of chromophore-containing antibiotics such as neocarzinostatin and actinoxanthin, interesting in part for the roles as anticancer therapeutics. NF041022.1 rodlin_AB 75 75 134 equivalog Y Y N rodlin 12832397,22309453,28211492 1783272 Bacillati kingdom 8092 NCBIFAM rodlin NF041045.1 RsbA_anti_sig 210 210 303 subfamily Y Y N anti-sigma factor RsbA family regulatory protein 15576799,28484446 1783272 Bacillati kingdom 9881 NCBIFAM anti-sigma factor RsbA family regulatory protein Members of this family have MEDS sensory domain in the N-terminal region and a histidine kinase-like ATPase domain in the C-terminal region. RsbA of Streptomyces coelicolor, the founding member of this family, was suggested as an anti-sigma factor by genomic location preceding sigB, by homology to RsbW of Bacillus subtilis, and by binding to SigmaB and effects on its activity. Members of this family include full-length homologs, but it appears members they may perform different regulatory functions in different lineages. Therefore, the symbol RsbA will be inappropriate for some family members, such as PrsR from Streptomyces avermitilis. NF041213.1 plasmid_TraA 80 80 165 equivalog Y Y N plasmid transfer protein TraA traA 7991673 1783272 Bacillati kingdom 1264 NCBIFAM plasmid transfer protein TraA NF041214.1 plasmid_TraB 800 800 639 equivalog Y Y N plasmid transfer protein TraB traB GO:0003677,GO:0005524 7991673 1783272 Bacillati kingdom 1207 NCBIFAM plasmid transfer protein TraB NF041256.1 GntI_guanitoxin 357 357 282 equivalog Y Y N guanitoxin biosynthesis pre-guanitoxin N-oxide kinase GntI gntI 35583956 1783272 Bacillati kingdom 7 NCBIFAM guanitoxin biosynthesis pre-guanitoxin N-oxide kinase GntI NF041486.1 rep_init_RepSA 700 700 443 equivalog Y Y N replication initiator protein RepSA repSA 8029324 1783272 Bacillati kingdom 6506 NCBIFAM replication initiator protein RepSA NF041501.1 cola_mem 150 150 312 domain Y Y N FGLLP motif-containing membrane protein 1783272 Bacillati kingdom 217 NCBIFAM FGLLP motif-containing membrane domain Members of this family average about 700 amino acids in length, with variable N-terminal regions but a shared hydrophobic C-domain, modeled by this HMM, about 300 amino acids in length. NF041554.1 SA1362_fam 42 42 70 subfamily Y Y N SA1362 family protein 1783272 Bacillati kingdom 2188 NCBIFAM SA1362 family protein Members of this family include SA1362 from Staphylococcus aureus. The N-terminal 50 amino acids are highly hydrophobic and suggest two transmembrane alpha-helical regions. The C-terminal region rich in basic residues, variable in length, and often somewhat repetitive. The family is widespread in Gram-positive species. NF041638.1 QRL_CxxC_CxxC 65 65 102 subfamily Y Y N RRQRL motif-containing zinc-binding protein GO:0008270 1783272 Bacillati kingdom 11004 NCBIFAM RRQRL motif-containing zinc-binding protein Members of this family, found in multiple species of Streptomyces, are judged by be zinc-binding by the pair of CxxC motifs in the C-terminal region. The family is named for a near-invariant QRL motif (usually RRQRL) closer to the N-terminus. NF041644.1 CBO0543_fam 35 35 116 subfamily Y Y N CBO0543 family protein 1783272 Bacillati kingdom 10446 NCBIFAM CBO0543 family protein This family is named for an uncharacterized founding protein from Clostridium botulinum. The family is rather hydrophobic, about 165 amino acids in length, and found in genera such as Bacillus, Paenibacillus, Desulfosporosinus, and Weizmannia. The function is unknown. NF041824.1 daptide_HExxH 300 300 379 equivalog Y Y N daptide biosynthesis intramembrane metalloprotease mpaP GO:0004222,GO:0031179 36959188 1783272 Bacillati kingdom 816 NCBIFAM daptide biosynthesis intramembrane metalloprotease Members of this family are intramembrane metalloendopeptidases with a typical HExxH motif, found in biosynthetic gene clusters for daptide-type RiPP peptide biosynthesis and probably performing export-related cleavage. They are related to the site-2-proteases. NF042446.3 PF20164.3 GspA_SrpA_N 27.4 27.4 117 domain Y Y N sialoglycan-binding domain-containing protein 26833566 1783272 Bacillati kingdom 711 EBI-EMBL GspA/SrpA SigLec-like domain GspA/SrpA SigLec-like domain This domain is an adhesive domain that binds to sialoglycan [1]. A Thr-Arg motif conserved across homologous carbohydrate-binding adhesins that may orient the sialic acid moiety of carbohydrate ligands [1]. [1]. 26833566. Structural Basis for Sialoglycan Binding by the Streptococcus sanguinis SrpA Adhesin. Bensing BA, Loukachevitch LV, McCulloch KM, Yu H, Vann KR, Wawrzak Z, Anderson S, Chen X, Sullam PM, Iverson TM;. J Biol Chem. 2016;291:7230-7240. (from Pfam) NF042520.3 PF20214.3 DUF6574 27.1 27.1 265 domain Y Y N DUF6574 domain-containing protein 1783272 Bacillati kingdom 1968 EBI-EMBL Family of unknown function (DUF6574) DUF6574 domain Many protein with this DUF6574 domain contain an additional N-terminal putative zinc ribbon region (PF12773). NF042612.3 PF20592.3 pAdhesive_10 27 27 167 domain Y Y N adhesin domain containing protein 1783272 Bacillati kingdom 691 EBI-EMBL Putative adhesin domain (group 10) Putative adhesin domain (group 10) This domain is found N-terminal to repeating stalk domains in bacterial surface proteins. The structure model of this domain consists out of seven beta-strands within two beta-sheets, similar to the RrgB pilus backbone, which was again described to correspond to the collagen binding domain. The position of this domain at the tip of bacterial surface proteins suggests an adhesive function. (from Pfam) NF042679.3 PF20357.3 DUF6652 27 27 183 domain Y Y N DUF6652 family protein 1783272 Bacillati kingdom 64 EBI-EMBL Family of unknown function (DUF6652) DUF6652 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 189 and 210 amino acids in length. (from Pfam) NF042845.3 PF20595.3 pAdhesive_6 27 27 165 domain Y Y N adhesive domain-containing protein 1783272 Bacillati kingdom 30 EBI-EMBL Putative adhesive domain (group 6) Putative adhesive domain (group 6) This domain resembles the SdrG_C_C adhesive domain, known to bind within a supra-domain with the Big_8 domain (Pfam:PF17961) to fibrinogen. It is found N-terminal to repeating stalk domains in bacterial surface proteins. (from Pfam) NF042856.3 PF20623.3 Sgo0707_N2 27 27 141 domain Y Y N Sgo0707 family adhesin 23691093 1783272 Bacillati kingdom 1335 EBI-EMBL Sgo0707 N2 domain Sgo0707 N2 domain This domain represents the N2 domain found in the Sgo0707 adhesin protein [1]. This domain is closely related to Pfam:PF16569. Paper describing PDB structure 4igb. [1]. 23691093. Structural and functional analysis of the N-terminal domain of the Streptococcus gordonii adhesin Sgo0707. Nylander A, Svensater G, Senadheera DB, Cvitkovitch DG, Davies JR, Persson K;. PLoS One. 2013;8:e63768. (from Pfam) NF042897.3 PF20568.3 DUF6777 27 27 163 domain Y Y N DUF6777 domain-containing protein 1783272 Bacillati kingdom 10827 EBI-EMBL Domain of unknown function (DUF6777) DUF6777 domain This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 160 amino acids in length. (from Pfam) NF043012.1 LacAcidTportLarD 390 390 237 equivalog Y Y N D/L-lactic acid transporter LarD larD GO:0015267 23799297 1783272 Bacillati kingdom 717 NCBIFAM D/L-lactic acid transporter LarD NF043075.1 MMSYN1_0197 550 550 341 equivalog Y Y N spermidine/putrescine ABC transporter ATP-binding protein potA GO:0005524,GO:1902047 20488990,31308405 1783272 Bacillati kingdom 1284 NCBIFAM spermidine/putrescine ABC transporter ATP-binding protein NF043079.1 MMSYN1_0167 740 740 561 equivalog Y Y N oligopeptide ABC transporter ATP-binding protein OppD oppD GO:0006810,GO:0042626 20488990,31308405 1783272 Bacillati kingdom 137 NCBIFAM oligopeptide ABC transporter ATP-binding protein OppD NF044357.2 PF20956.2 DUF4931_C 28.6 28.6 119 domain Y N N Domain of unknown function (DUF4931) C-terminal domain 1783272 Bacillati kingdom 2925 EBI-EMBL Domain of unknown function (DUF4931) C-terminal domain Domain of unknown function (DUF4931) C-terminal domain This family consists of uncharacterized proteins around 270 residues in length and is mainly found in various Bacillus cereus species. Some members of this family are annotated as Galactose-1-phosphate uridylyltransferases, but the specific function of this family is unknown. (from Pfam) NF044517.2 PF21606.2 BgaA-like_CBM 27 27 160 domain Y N N Beta-galactosidase-like, Galactose-binding domain 25210925 1783272 Bacillati kingdom 2617 EBI-EMBL Beta-galactosidase-like, Galactose-binding domain Beta-galactosidase-like, Galactose-binding domain This domain is found in Beta-galactosidase from Streptococcus pneumoniae (BgaA) and similar bacterial sequences. BgaA is specific for terminal galactose residues beta-1-4 linked to glucose or N-acetylglucosamine. It is involved in pneumococcal growth, resistance to opsonophagocytic killing, and adherence. This entry represents two non-enzymatic carbohydrate-binding modules (CBMs) that mediate adherence to the host cell surface displayed lactose or N-acetyllactosamine. Each of these CBMs folds into a beta-sandwich fold comprising opposing sheets of 4- and 5-antiparallel beta-strands [1]. Paper describing PDB structure 4cu9. [1]. 25210925. Unravelling the multiple functions of the architecturally intricate Streptococcus pneumoniae beta-galactosidase, BgaA. Singh AK, Pluvinage B, Higgins MA, Dalia AB, Woodiga SA, Flynn M, Lloyd AR, Weiser JN, Stubbs KA, Boraston AB, King SJ;. PLoS Pathog. 2014;10:e1004364. (from Pfam) NF044707.2 PF21110.2 GlxA 27 27 105 domain Y N N GlxA beta barrel domain 26205496,28093470 1783272 Bacillati kingdom 6820 EBI-EMBL GlxA beta barrel domain GlxA beta barrel domain This entry represents the second domain of the GlxA protein. GlxA contains a beta propeller domain and this beta sandwich domain is inserted within it [1]. Paper describing PDB structure 4unm. [1]. 26205496. GlxA is a new structural member of the radical copper oxidase family and is required for glycan deposition at hyphal tips and morphogenesis of Streptomyces lividans. Chaplin AK, Petrus ML, Mangiameli G, Hough MA, Svistunenko DA, Nicholls P, Claessen D, Vijgenboom E, Worrall JA;. Biochem J. 2015;469:433-444. Paper describing PDB structure 5lqi. [2]. 28093470. Active-site maturation and activity of the copper-radical oxidase GlxA are governed by a tryptophan residue. Chaplin AK, Svistunenko DA, Hough MA, Wilson MT, Vijgenboom E, Worrall JA;. Biochem J. 2017;474:809-825. (from Pfam) NF044929.2 PF20880.2 G1_gp67_N 27 27 77 domain Y N N Phage G1 gp67, N-terminal domain 23178120 1783272 Bacillati kingdom 6 EBI-EMBL Phage G1 gp67, N-terminal domain Phage G1 gp67, N-terminal domain gp67 from Staphylococcus virus G1 binds to the sigma(A)-subunit of the RNA polymerase (RNAP) of its host to block cell growth by inhibiting transcription. This protein is organized in two domains, an N-terminal beta-sheet-rich domain (this entry) and a C-terminal alpha-helical domain, which are connected by a linker-alpha-helix on the surface of gp67 opposite the interaction surface [1]. Paper describing PDB structure 4g6d. [1]. 23178120. Promoter-specific transcription inhibition in Staphylococcus aureus by a phage protein. Osmundson J, Montero-Diez C, Westblade LF, Hochschild A, Darst SA;. Cell. 2012;151:1005-1016. (from Pfam) NF044939.2 PF20909.2 SpGH101_helical 27 27 60 domain Y N N Endo-alpha-N-acetylgalactosaminidase, helical bundle domain 16141207,18784084 1783272 Bacillati kingdom 503 EBI-EMBL Endo-alpha-N-acetylgalactosaminidase, helical bundle domain Endo-alpha-N-acetylgalactosaminidase, helical bundle domain This domain is found in Endo-alpha-N-acetylgalactosaminidase (SpGH101) from Streptococcus pneumoniae and similar bacterial proteins. This protein, which belongs to the Glycoside Hydrolase Family 101 (GH101), is a virulence factor. It hydrolyses the T-antigen disaccharide from extracellular host glycoproteins to aid colonization. SpGH101 has seven domains. This entry represents the helical bundle domain, which consists of three alpha-helices that form an interface [1,2]. [1]. 18784084. The structural basis for T-antigen hydrolysis by Streptococcus pneumoniae: a target for structure-based vaccine design. Caines ME, Zhu H, Vuckovic M, Willis LM, Withers SG, Wakarchuk WW, Strynadka NC;. J Biol Chem. 2008;283:31279-31283. [2]. 16141207. Identification and molecular cloning of a novel glycoside hydrolase family of core 1 type O-glycan-specific endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum. Fujita K, Oura F, Nagamine N, Katayama T, Hiratake J, Sakata K, Kumagai H, Yamamoto K;. J Biol Chem. 2005;280:37415-37422. (from Pfam) NF044982.2 PF21124.2 VinK_C 27 27 62 domain Y N N VinK acyltransferase small domain 26831085,34473106 1783272 Bacillati kingdom 1713 EBI-EMBL VinK acyltransferase small domain VinK acyltransferase small domain This family includes the VinK acyltransferase. VinK transfers a dipeptide group between two ACPs, VinL and VinP1LdACP, in vicenistatin biosynthesis [1]. This entry represents the small C-terminal domain [1]. VinK has two conserved catalytic residues, Ser-106 and His-216, at the interface between the large domain and small domain [1]. Paper describing PDB structure 5czc. [1]. 26831085. Structure-based analysis of the molecular interactions between acyltransferase and acyl carrier protein in vicenistatin biosynthesis. Miyanaga A, Iwasawa S, Shinohara Y, Kudo F, Eguchi T;. Proc Natl Acad Sci U S A. 2016;113:1802-1807. Paper describing PDB structure 7f2r. [2]. 34473106. Complex structure of the acyltransferase VinK and the carrier protein VinL with a pantetheine cross-linking probe. Miyanaga A, Ouchi R, Kudo F, Eguchi T;. Acta Crystallogr F Struct Biol Commun. 2021;77:294-302. (from Pfam) NF045077.2 PF21493.2 TubZ_C 27 27 133 domain Y N N Tubulin-like protein TubZ, C-terminal domain 22847006 1783272 Bacillati kingdom 178 EBI-EMBL Tubulin-like protein TubZ, C-terminal domain Tubulin-like protein TubZ, C-terminal domain Tubulin-like protein TubZ is a tubulin-like, filament forming GTPase, the motor component of the type III plasmid partition system which ensures correct segregation of the pXO1 plasmid. This entry represents the C-terminal GTPase-activating domain of TubZ [1]. Paper describing PDB structure 4ei7. [1]. 22847006. Filament formation of the FtsZ/tubulin-like protein TubZ from the Bacillus cereus pXO1 plasmid. Hoshino S, Hayashi I;. J Biol Chem. 2012;287:32103-32112. (from Pfam) NF045556.1 TbtD_PbtD_pyrid 325 325 354 equivalog Y Y N thiopeptide maturation pyridine synthase 26675417,30653303,36351243 1783272 Bacillati kingdom 589 NCBIFAM thiopeptide maturation pyridine synthase Pyridine synthase synthases for thiopeptide (thiazolyl peptide) maturation, including TbtD in thiomuracin biosynthesis and PbtD in GE2270A biosynthesis, resemble the elimination domain (C-terminal domain) of class I lanthipeptide dehydratases, but those dehydratases convert Ser and Thr residues to dehydroamino acids. NF045770.1 MPN403_MG284_C 37.3 37 57 domain Y Y N MG284/MPN403 family protein 1783272 Bacillati kingdom 364 NCBIFAM MG284/MPN403 family protein C-terminal domain NF045848.1 MMCAP2_0566_fam 90 90 322 domain Y Y N MMCAP2_0566 family conjugal transfer protein 21324191 1783272 Bacillati kingdom 763 NCBIFAM MMCAP2_0566 domain This HMM describes the hydrophobic N-terminal half of MMCAP2_0566, found within an Integrative Conjugal Element (ICE) of Mycoplasma mycoides subsp. capri str. GM12. The domain shows distant sequence similarity to conjugal transfer protein TrbL (see PF19597). NF045889.1 ICE_Mbov_0396_TM 70 60 306 equivalog Y Y N Mbov_0396 family ICE element transmembrane protein 22693604 1783272 Bacillati kingdom 788 NCBIFAM Mbov_0396 family ICE element transmembrane protein This HMM describes a 300-amino acid hydrophobic domain presumed to be embedded bacterial membranes. Proteins with this domain have additional C-terminal regions that are poorly conserved, low complexity, and variable in length, but averaging about 150 amino acids. Family members Mbov_0396 and MMCAP2_0566 both are discussed in publications as proteins encoded in Integrating Conjugal Elements (ICE elements). The protein appears to act in a VirB-like conjugal DNA transfer system. NF045941.1 PropMonoxMimD 150 150 108 equivalog Y Y N propane 2-monooxygenase effector subunit MimD mimD prmD GO:0004497,GO:0008152 14645271,17873074,21183637 1783272 Bacillati kingdom 740 NCBIFAM propane 2-monooxygenase effector subunit MimD NF045944.1 ResRegRpaBCyano 330 330 229 equivalog Y Y N response regulator transcription factor RpaB rpaB GO:0000160,GO:0003677 10585546,22665493 1783272 Bacillati kingdom 964 NCBIFAM response regulator transcription factor RpaB NF045964.1 RNAP_delt_plasma 72 72 77 equivalog Y Y N DNA-directed RNA polymerase subunit delta rpoE 2.7.7.6 GO:0003899,GO:0006351 1783272 Bacillati kingdom 174 NCBIFAM DNA-directed RNA polymerase subunit delta, Mycoplasma variant time Members of this family are variant forms of DNA-directed RNA polymerase subunit delta that are typical in Mycoplasmas and related species. Most members of this family score below cutoffs for the more general model TIGR04567 for detection of that protein in low-GC Gram-positive species and some of the Mycoplasmas. NF045980.1 MAG6410_fam_LP 450 450 622 equivalog Y Y N MAG6410 family transglutaminase-related lipoprotein 1783272 Bacillati kingdom 274 NCBIFAM MAG6410 family transglutaminase-related lipoprotein This HMM describes the C-terminal 625 amino acid transglutaminase-related domain of the MAG6410 family of lipoproteins. The additional N-terminal region of family members, averaging about 145 residues in length, begins with a lipoprotein signal peptide, but then is highly variable in both length and sequence. NF046071.1 B1-4RhmsylTfaseCps2T 500 500 384 equivalog Y Y N beta 1-4 rhamnosyltransferase Cps2T cps2T wchF GO:0016757 16707704,23002227 1783272 Bacillati kingdom 3774 NCBIFAM beta 1-4 rhamnosyltransferase Cps2T NF046124.1 PF21835.1 YIEGIA_cap 24.1 24.1 58 domain Y Y N capping complex subunit for YIEGIA 1783272 Bacillati kingdom 1621 EBI-EMBL Capping complex subunit for YIEGIA capping complex subunit for YIEGIA This entry contains a family of small protein of unknown function. Proteins in this family are found in Firmicutes. These proteins adopt a beta sheet structure with four strands with an alpha helix packed on one face between the second and third strands. Using AlphaFold we can identify a likely hexameric ring complex. Additionally these proteins likely form a cap on a goblet like hexameric complex of Pfam:PF14045. Analysis of genomic context suggests this larger complex is involved in spore germination and possibly phospholipid synthesis or regulation (pers.obs. Alex Bateman). (from Pfam) NF046208.1 PF22206.1 Cas_Csm6_6H 23.4 23.4 53 domain Y N N CRISPR-associated protein Csm6 6H domain 32221291 1783272 Bacillati kingdom 432 EBI-EMBL CRISPR-associated protein Csm6 6H domain CRISPR-associated protein Csm6 6H domain This entry includes Csm6 from bacteria (i.e Enterococcus italicus), a Cas (CRISPR-associated) protein from type III-A CRISPR-Cas system. It consists of a CARF domain at the N-terminal, a six-helix (6H) domain and a C-terminal HEPN domain at the C-terminal, which has RNase activity [1]. This is the 6H domain [1]. [1]. 32221291. Activation and self-inactivation mechanisms of the cyclic oligoadenylate-dependent CRISPR ribonuclease Csm6. Garcia-Doval C, Schwede F, Berk C, Rostol JT, Niewoehner O, Tejero O, Hall J, Marraffini LA, Jinek M;. Nat Commun. 2020;11:1596. (from Pfam) NF046400.1 PF22905.1 Hydro_N_hd 27 27 195 domain Y N N Hydrolase N-terminal helical domain 15688435 1783272 Bacillati kingdom 1651 EBI-EMBL Hydrolase N-terminal helical domain Hydrolase N-terminal helical domain This entry represents a N-terminal domain found in a family of alpha/beta hydrolases (Pfam:PF06259) [1]. [1]. 15688435. Protein domain of unknown function DUF1023 is an alpha/beta hydrolase. Zheng M, Ginalski K, Rychlewski L, Grishin NV;. Proteins. 2005;59:1-6. (from Pfam) NF046444.1 PF21826.1 DUF6887 24.2 24.2 62 subfamily Y Y N DUF6887 family protein 1783272 Bacillati kingdom 2318 EBI-EMBL Family of unknown function (DUF6887) DUF6887 family protein This entry represents a family of uncharacterised cyanobacterial proteins. (from Pfam) NF046687.1 PF22181.1 TarS_linker 27 27 100 domain Y N N Glycosyl transferase TarS linker domain 27973583,30464342 1783272 Bacillati kingdom 13080 EBI-EMBL Glycosyl transferase TarS linker domain Glycosyl transferase TarS linker domain TarS is an enzyme responsible for the glycosylation of wall teichoic acid polymers of the S. aureus cell wall, a process that has been shown to contribute for methicillin resistance in MRSA. TarS consist of three domains: catalytic, linker and trimerisation [1]. This entry represents the linker domain that bridges the catalytic and trimerisation domains. Paper describing PDB structure 5tz8. [1]. 27973583. Structure and Mechanism of Staphylococcus aureus TarS, the Wall Teichoic Acid beta-glycosyltransferase Involved in Methicillin Resistance. Sobhanifar S, Worrall LJ, King DT, Wasney GA, Baumann L, Gale RT, Nosella M, Brown ED, Withers SG, Strynadka NC;. PLoS Pathog. 2016;12:e1006067. Paper describing PDB structure 6h1j. [2]. 30464342. Methicillin-resistant Staphylococcus aureus alters cell wall glycosylation to evade immunity. Gerlach D, Guo Y, De Castro C, Kim SH, Schlatterer K, Xu FF, Pereira C, Seeberger PH, Ali S, Codee J, Sirisarn W, Schulte B, Wolz C, Larsen J, Molinaro A, Lee BL, Xia G, Stehle T, Peschel A;. Nature. 2018;563:705-709. (from Pfam) NF046900.1 PF22717.1 SNaCT10 27 27 42 domain Y N N Short NACHT-associated C-Terminal domain, family 10 37160116 1783272 Bacillati kingdom 14 EBI-EMBL Short NACHT-associated C-Terminal domain, family 10 Short NACHT-associated C-Terminal domain, family 10 The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors [1]. [1]. 37160116. Bacterial NLR-related proteins protect against phage. Kibby EM, Conte AN, Burroughs AM, Nagy TA, Vargas JA, Whalen LA, Aravind L, Whiteley AT;. Cell. 2023;186:2410-2424. (from Pfam) NF047156.1 PF22343.1 Surface-like_ins_dom 27 27 100 domain Y N N Pilus-presented adhesin helical insertion domain 26032562 1783272 Bacillati kingdom 293 EBI-EMBL Pilus-presented adhesin helical insertion domain Pilus-presented adhesin helical insertion domain This entry represents the helical insertion domain found in surface proteins in certain pathogens, such as Streptococcus pneumoniae [1]. Paper describing PDB structure 5a0n. [1]. 26032562. An internal thioester in a pathogen surface protein mediates covalent host binding. Walden M, Edwards JM, Dziewulska AM, Bergmann R, Saalbach G, Kan SY, Miller OK, Weckener M, Jackson RJ, Shirran SL, Botting CH, Florence GJ, Rohde M, Banfield MJ, Schwarz-Linek U;. Elife. 2015; [Epub ahead of print] (from Pfam) NF047163.1 PF22360.1 SbsC_spectrin-like 26 26 62 domain Y N N SbsC,spectrin-like repeat 18682224 1783272 Bacillati kingdom 155 EBI-EMBL SbsC,spectrin-like repeat SbsC,spectrin-like repeat This entry represents a Spectrin-like domain present in the bacterial S-layer protein SbsC from Geobacillus stearothermophilus [1]. This domain shows structural similarity to the Spectrin domain (Pfam:PF00435). Paper describing PDB structure 2ra1. [1]. 18682224. The structure and binding behavior of the bacterial cell surface layer protein SbsC. Pavkov T, Egelseer EM, Tesarz M, Svergun DI, Sleytr UB, Keller W;. Structure. 2008;16:1226-1237. (from Pfam) NF047244.1 PF22724.1 NCAB1 27 27 140 domain Y N N NACHT C-terminal Alpha/Beta 1 37160116 1783272 Bacillati kingdom 650 EBI-EMBL NACHT C-terminal Alpha/Beta 1 NACHT C-terminal Alpha/Beta 1 This domain contains alpha-helices and beta-strands, found at the C-terminus of certain bacterial NACHT conflict systems [1]. [1]. 37160116. Bacterial NLR-related proteins protect against phage. Kibby EM, Conte AN, Burroughs AM, Nagy TA, Vargas JA, Whalen LA, Aravind L, Whiteley AT;. Cell. 2023;186:2410-2424. (from Pfam) NF047537.1 YonT_type_I_tox 45 45 59 equivalog Y Y N type I TA system toxin YonT yonT 29414903 1783272 Bacillati kingdom 114 NCBIFAM type I TA system toxin YonT YonT, encoded in a prophage region in Bacillus subtilis, is type I toxin-antitoxin (TA) system about 59 amino acids in length. NF047542.1 telomere_Tap 600 600 695 equivalog Y Y N telomere-associated protein Tap tap 12651895,28369604 1783272 Bacillati kingdom 7780 NCBIFAM telomere-associated protein Tap (Streptomyces) TIGR00534.1 TIGR00534 OpcA 256.25 256.25 313 equivalog Y Y N glucose-6-phosphate dehydrogenase assembly protein OpcA opcA GO:0006098,GO:0065003 9639925 1783272 Bacillati kingdom 11559 JCVI glucose-6-phosphate dehydrogenase assembly protein OpcA glucose-6-phosphate dehydrogenase assembly protein OpcA The opcA gene is found immediately downstream of zwf, the glucose-6-phosphate dehydrogenase (G6PDH) gene, in a number of species, including Mycobacterium tuberculosis, Streptomyces coelicolor, Nostoc punctiforme, and Synechococcus sp. PCC 7942. In the latter, disruption of opcA was shown to block assembly of G6PDH into active oligomeric forms. TIGR01153.1 TIGR01153 psbC 603.05 603.05 432 equivalog Y Y N photosystem II reaction center protein CP43 psbC GO:0009523,GO:0009772,GO:0015979,GO:0016020,GO:0016168,GO:0045156 1903653,2105233 1783272 Bacillati kingdom 798 JCVI photosystem II 44 kDa subunit reaction center protein photosystem II reaction center protein CP43 This model describes the Photosystem II, 44kDa subunit (also called P6 protein, CP43) in bacterial and its equivalents in chloroplast of algae and higher plants. Photosystem II is in many ways functionally equivalent to bacterial reaction center. At the core of Photosystem II are several light harvesting cofactors including plastoquinones, pheophytins, phyloquinones etc. These cofactors are intimately associated with the polypeptides, which principally including subunits 44 kDa protein,DI, DII, Cyt.b, Cyt.f, iron-sulphur protein and others. Functinally 44 kDa subunit is imlicated in chlorophyll binding. Together they participate in the electron transfer reactions that lead to the net production of the reducting equivalents in the form of NADPH, which are used for reduction of CO2 to carbohydrates(C6H1206). Phosystem II operates during oxygenic photosynthesis and principal electron donor is H2O. Although no high resolution X-ray structural data is presently available, recently a 3D structure of the supercomplex has been described by cryo-electron microscopy. Besides a huge body of literature exits that describes function using a variety of biochemical and biophysical techniques. TIGR01233.1 TIGR01233 lacG 561.2 561.2 472 equivalog Y Y N 6-phospho-beta-galactosidase lacG 3.2.1.85 GO:0019512,GO:0033920 1783272 Bacillati kingdom 4910 JCVI 6-phospho-beta-galactosidase 6-phospho-beta-galactosidase This enzyme is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation. TIGR01627.1 TIGR01627 A_thal_3515 149.85 149.85 225 domain Y Y N TIGR01627 domain-containing protein GO:0045492 1783272 Bacillati kingdom 11 JCVI uncharacterized plant-specific domain TIGR01627 TIGR01627 domain This HMM represents an uncharacterized domain found in both Arabidopsis thaliana (at least 10 copies) and Oryza sativa. Most member proteins have only a short stretch of sequence N-terminal to this domain, but one has a long N-terminal extension that includes a protein kinase domain (PF00069). TIGR01653.1 TIGR01653 lactococcin_972 32.1 32.1 97 subfamily Y Y N lactococcin 972 family bacteriocin 10589723 1783272 Bacillati kingdom 1840 JCVI bacteriocin, lactococcin 972 family lactococcin 972 family bacteriocin This HMM represents bacteriocins related to lactococcin 972. Members tend to be found in association with a seven transmembrane putative immunity protein. TIGR01673.1 TIGR01673 holin_LLH 34.75 34.75 108 equivalog Y Y N phage holin GO:0140911 1783272 Bacillati kingdom 1910 JCVI phage holin, LL-H family phage holin This HMM represents a putative phage holin from a number of phage and prophage regions of Gram-positive bacteria. Like other holins, it is small (about 100 amino acids) with stretches of hydrophobic sequence and is encoded adjacent to lytic enzymes. TIGR01956.2 TIGR01956 NusG_myco 150 120 239 equivalog Y Y N transcription termination/antitermination protein NusG nusG GO:0006355 25101070 1783272 Bacillati kingdom 1244 JCVI NusG family protein transcription termination/antitermination protein NusG This model is designed to find, in the Mollicutes lineage (Mycoplasmas and related species), variant forms of NusG that may be missed by the general bacterial NusG model TIGR00922. All members of the seed alignment are from the Mollicutes (Mycoplasmas and related species), but the divergent nature of some members necessitated cutoffs for the model such that many NusG from outside the Mollicutes are also detected. In some of the target organisms, although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent, and its absence calls into question how the putative NusG found there by this model may function. TIGR02331.1 TIGR02331 rib_alpha 35.25 35.25 80 repeat Y N N Rib/alpha/Esp repeat surface protein 8702550 1783272 Bacillati kingdom 12628 JCVI Rib/alpha/Esp surface antigen repeat Rib/alpha/Esp surface antigen repeat Sequences in this family are tandem repeats of about 79 amino acids, present in up to 14 copies in a protein and highly identical, even at the DNA level, within each protein. Sequences with these repeats are found in the Rib and alpha surface antigens of group B Streptococcus, Esp of Enterococcus faecalis, and related proteins of Lactobacillus. The repeat lacks Cys residues. Most members of this protein family also have the cell wall anchor motif LPXTG shared by many staphyloccal and streptococcal surface antigens. TIGR02366.1 TIGR02366 DHAK_reg 129 129 176 equivalog Y Y N dihydroxyacetone kinase transcriptional activator DhaS dhaS 1783272 Bacillati kingdom 1449 JCVI probable dihydroxyacetone kinase regulator dihydroxyacetone kinase transcriptional activator DhaS The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (PF00440) at the N-terminus and sequence homology throughout. TIGR02719.1 TIGR02719 repress_PhaQ 139.35 139.35 138 equivalog Y Y N poly-beta-hydroxybutyrate-responsive repressor phaQ 15126462 1783272 Bacillati kingdom 473 JCVI poly-beta-hydroxybutyrate-responsive repressor poly-beta-hydroxybutyrate-responsive repressor Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see PF03551). TIGR02720.1 TIGR02720 pyruv_oxi_spxB 637.85 637.85 575 equivalog Y Y N pyruvate oxidase spxB 1.2.3.3 GO:0047112 15175288 1783272 Bacillati kingdom 4003 JCVI pyruvate oxidase pyruvate oxidase Members of this family are examples of pyruvate oxidase (EC 1.2.3.3), an enzyme with FAD and TPP as cofactors that catalyzes the reaction pyruvate + phosphate + O2 + H2O = acetyl phosphate + CO2 + H2O2. It should not be confused with pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2) as in E. coli PoxB, although the E. coli enzyme is closely homologous and has pyruvate oxidase as an alternate name. TIGR02830.1 TIGR02830 spore_III_AG 147.7 147.7 186 equivalog Y Y N stage III sporulation protein AG spoIIIAG GO:0030436 16311624 1783272 Bacillati kingdom 3362 JCVI stage III sporulation protein AG stage III sporulation protein AG CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG. TIGR02846.1 TIGR02846 spore_sigmaK 298.65 298.65 227 equivalog Y Y N RNA polymerase sporulation sigma factor SigK sigK GO:0003677,GO:0003700,GO:0006352,GO:0006355,GO:0016987 1783272 Bacillati kingdom 2662 JCVI RNA polymerase sigma-K factor RNA polymerase sporulation sigma factor SigK The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K. TIGR02860.1 TIGR02860 spore_IV_B 305.25 305.25 402 equivalog Y Y N SpoIVB peptidase spoIVB 3.4.21.116 GO:0008236,GO:0030436 10931284 1783272 Bacillati kingdom 6384 JCVI stage IV sporulation protein B SpoIVB peptidase SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase, expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else. TIGR02900.1 TIGR02900 spore_V_B 372.3 372.3 488 equivalog Y Y N stage V sporulation protein B spoVB GO:0030436 1744050 1783272 Bacillati kingdom 4970 JCVI stage V sporulation protein B stage V sporulation protein B SpoVB is the stage V sporulation protein B of the bacterial endopore formation program in Bacillus subtilis and various other Firmcutes. It is nearly universal among endospore-formers. Paralogs with rather high sequence similarity to SpoVB exist, including YkvU in B. subtilis and a number of proteins in the genus Clostridium. Member sequences for the seed alignment and cutoff scores for the resulting HMM were chosen to select those proteins, no more than one to a genome, closest to B. subtilis SpoVB in a neighbor joining tree. TIGR02919.1 TIGR02919 TIGR02919 338.3 338.3 438 equivalog Y Y N accessory Sec system glycosylation chaperone GtfB gtfB GO:0031647 15901716 1783272 Bacillati kingdom 3510 JCVI accessory Sec system glycosyltransferase GtfB accessory Sec system glycosylation chaperone GtfB Members of this protein family are found only in Gram-positive bacteria of the Firmicutes lineage, including several species of Staphylococcus, Streptococcus, and Lactobacillus. TIGR02952.1 TIGR02952 Sig70_famx2 206.45 206.45 170 equivalog Y Y N ECF subfamily RNA polymerase sigma factor, BldN family 10913095,29905823 1783272 Bacillati kingdom 4025 JCVI RNA polymerase sigma-70 factor, TIGR02952 family ECF subfamily RNA polymerase sigma factor, BldN family This group of sigma factors are members of the sigma-70 family (TIGR02937). They appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages. TIGR03038.1 TIGR03038 PS_II_psbM 35.05 35.05 33 equivalog Y Y N photosystem II reaction center protein PsbM psbM GO:0009538,GO:0009539 1783272 Bacillati kingdom 365 JCVI photosystem II reaction center protein PsbM photosystem II reaction center protein PsbM Members of this protein family are the photosystem II reaction center M protein, product of the psbM gene, in Cyanobacteria and their derived organelles in plants. This model resembles Pfam model PF05151 but has cutoffs set to avoid false-positive matches to similar (not necessarily homologous) sequences in species that are not photosynthetic. TIGR03042.1 TIGR03042 PS_II_psbQ_bact 106.9 106.9 142 equivalog Y Y N photosystem II protein PsbQ psbQ GO:0009654,GO:0030096 12069591 1783272 Bacillati kingdom 780 JCVI photosystem II protein PsbQ photosystem II protein PsbQ This protein through the member sll1638 from Synechocystis sp. PCC 6803, was shown to be part of the cyanobacteria photosystem II. It is homologous to (but quite diverged from) the chloroplast PsbQ protein, called oxygen-evolving enhancer protein 3 (OEE3). We designate this cyanobacteria protein PsbQ by homology. TIGR03069.1 TIGR03069 PS_II_S4 201.55 201.55 257 equivalog Y Y N photosystem II S4 domain protein GO:0015979,GO:0030095,GO:0030096 12069591 1783272 Bacillati kingdom 1027 JCVI photosystem II S4 domain protein photosystem II S4 domain protein Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium. TIGR03111.1 TIGR03111 glyc2_xrt_Gpos1 363.95 363.95 439 hypoth_equivalog Y Y N TIGR03111 family XrtG-associated glycosyltransferase 22037399 1783272 Bacillati kingdom 724 JCVI putative glycosyltransferase, exosortase G-associated TIGR03111 family XrtG-associated glycosyltransferase Members of this protein family are probable glycosyltransferases of family 2, whose genes are near those for the exosortase homolog XrtG (TIGR03110), which is restricted to Gram-positive bacteria. Other genes in the conserved gene neighborhood include a 6-pyruvoyl tetrahydropterin synthase homolog (TIGR03112) and an uncharacterized intergral membrane protein (TIGR03766). TIGR03445.1 TIGR03445 mycothiol_MshB 224.35 224.35 284 equivalog Y Y N N-acetyl-1-D-myo-inositol-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase mshB 3.5.1.103 GO:0010125,GO:0035595 11092856,16630724 1783272 Bacillati kingdom 12390 JCVI N-acetyl-1-D-myo-inositol-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase N-acetyl-1-D-myo-inositol-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase Members of this protein family are N-acetyl-1-D-myo-inositol-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase, also called 1D-myo-inosityl-2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase, the MshB protein of mycothiol biosynthesis in Mycobacterium tuberculosis and related species. TIGR03693.1 TIGR03693 ocin_ThiF_like 561.9 561.9 637 hypoth_equivalog Y Y N putative thiazole-containing bacteriocin maturation protein GO:0030152 1783272 Bacillati kingdom 2224 JCVI putative thiazole-containing bacteriocin maturation protein putative thiazole-containing bacteriocin maturation protein Members of this protein family are found in a three-gene operon in Bacillus anthracis and related Bacillus species, where the other two genes are clearly identified with maturation of a putative thiazole-containing bacteriocin precursor. While there is no detectable pairwise sequence similarity between members of this family and the proposed cyclodehydratases such as SagC of Streptococcus pyogenes (see family TIGR03603), both families show similarity through PSI-BLAST to ThiF, a protein involved in biosynthesis of the thiazole moiety for thiamine biosynthesis. This family, therefore, may contribute to cyclodehydratase function in heterocycle-containing bacteriocin biosyntheses. In Bacillus licheniformis ATCC 14580, the bacteriocin precursor gene is adjacent to the gene for this protein. TIGR03713.1 TIGR03713 acc_sec_asp1 136.1 136.1 519 equivalog Y Y N accessory Sec system protein Asp1 asp1 GO:0006886 18621893 1783272 Bacillati kingdom 3602 JCVI accessory Sec system protein Asp1 accessory Sec system protein Asp1 This protein is designated Asp1 because, along with SecY2, SecA2, and other proteins it is part of the accessory secretory protein system. The system is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus. This protein family is assigned to transport rather than glycosylation function, but the specific molecular role is unknown. TIGR03714.1 TIGR03714 secA2 930 928 762 equivalog Y Y N accessory Sec system translocase SecA2 secA2 GO:0015031,GO:0015450 18621893 1783272 Bacillati kingdom 3600 JCVI accessory Sec system translocase SecA2 accessory Sec system translocase SecA2 Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii. TIGR03731.1 TIGR03731 lantibio_gallid 29.3 29.3 48 subfamily Y Y N gallidermin/nisin family lantibiotic GO:0005576,GO:0042742 19009315 1783272 Bacillati kingdom 514 JCVI lantibiotic, gallidermin/nisin family gallidermin/nisin family lantibiotic Members of this family are lantibiotic precursors in the family that includes gallidermin, nisin, mutacin, epidermin, and streptin. TIGR03786.1 TIGR03786 strep_pil_rpt 31.85 31.85 70 domain Y N N streptococcal pilin isopeptide linkage domain GO:0018262 19497855 1783272 Bacillati kingdom 9292 JCVI streptococcal pilin isopeptide linkage domain streptococcal pilin isopeptide linkage domain This HMM describes a domain that occurs once in the major pilin of Streptococcus pyogenes, Spy0128, but in higher copy numbers in other streptococcal proteins. The domain occurs nine times in a surface-anchored protein of Bifidobacterium longum. All members of this family have LPXTG-type sortase target sequences. The S. pyogenes major pilin has been shown to undergo isopeptide bond cross-linking, mediated by sortases, that are critical to maintaining pilus structural integrity. One such Lys-to-Asn isopeptide bond is to a near-invariant Asn near the C-terminal end of this domain (column 81 of the seed alignment). A Glu in the S. pyogenes major pilin (column 25 of the seed alignment), invariant as Glu or Gln, is described as catalytic for isopeptide bond formation. TIGR03893.1 TIGR03893 lant_SP_1948 32.95 32.95 61 subfamily Y Y N lichenicidin A2 family type 2 lantibiotic GO:0005488,GO:0005576,GO:0019835 19477413 1783272 Bacillati kingdom 735 JCVI type 2 lantibiotic, SP_1948 family lichenicidin A2 family type 2 lantibiotic This HMM recognizes a number of type 2 lantibiotic-type bacteriocins, related to but distinct from the family that includes lichenicidin and mersacidin. Sequence similarity among members consists largely of a 20-residue block of conserved sequence that covers most of the leader peptide region, absent from the mature lantibiotic. This is followed by a region with characteristic composition for lantibiotic precursor regions, rich in Ser and Thr and including a near-invariant Cys near or at the C-terminus, involved in cyclization. Members of this family typically are shorter than 70 amino acids. TIGR03924.1 TIGR03924 T7SS_EccC_a 509.15 509.15 673 equivalog_domain Y Y N type VII secretion protein EccCa eccCa GO:0009306 19876390 1783272 Bacillati kingdom 25898 JCVI type VII secretion protein EccCa type VII secretion protein EccCa This model represents the N-terminal domain or EccCa subunit of the type VII secretion protein EccC as found in the Actinobacteria. Type VII secretion is defined more broadly as including secretion systems for ESAT-6-like proteins in the Firmicutes as well as in the Actinobacteria, but this family does not show close homologs in the Firmicutes. TIGR03925.1 TIGR03925 T7SS_EccC_b 346.55 346.55 564 equivalog_domain Y Y N type VII secretion protein EccCb eccCb GO:0009306 19876390 1783272 Bacillati kingdom 27045 JCVI type VII secretion protein EccCb type VII secretion protein EccCb This model represents the C-terminal domain or EccCb subunit of the type VII secretion protein EccC as found in the Actinobacteria. Type VII secretion is defined more broadly as including secretion systems for ESAT-6-like proteins in the Firmicutes as well as in the Actinobacteria, but this family does not show close homologs in the Firmicutes. TIGR03926.1 TIGR03926 T7_EssB 229.75 229.75 377 equivalog Y Y N type VII secretion protein EssB essB GO:0009306 18554323,23098276 1783272 Bacillati kingdom 3886 JCVI type VII secretion protein EssB type VII secretion protein EssB Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This protein is designated YukC in Bacillus subtilis and EssB is Staphylococcus aureus. TIGR03928.1 TIGR03928 T7_EssCb_Firm 778.4 778.4 1296 equivalog Y Y N type VII secretion protein EssC essC GO:0009306 18554323 1783272 Bacillati kingdom 9549 JCVI type VII secretion protein EssC type VII secretion protein EssC This HMM describes the C-terminal domain, or longer subunit, of the Firmicutes type VII secretion protein EssC. This protein (homologous to EccC in Actinobacteria) and the WXG100 target proteins are the only homologous parts of type VII secretion between Firmicutes and Actinobacteria. TIGR03929.1 TIGR03929 T7_esaA_Nterm 122 122 193 equivalog_domain Y Y N type VII secretion protein EsaA esaA GO:0016020 18554323 1783272 Bacillati kingdom 7628 JCVI type VII secretion protein EsaA type VII secretion protein EsaA Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This model represents the conserved N-terminal domain. TIGR04091.1 TIGR04091 LTA_dltB 375 375 380 equivalog Y Y N D-alanyl-lipoteichoic acid biosynthesis protein DltB dltB GO:0016746,GO:0070395 9158726 1783272 Bacillati kingdom 7137 JCVI D-alanyl-lipoteichoic acid biosynthesis protein DltB D-alanyl-lipoteichoic acid biosynthesis protein DltB Members of this protein family are DltB, part of a four-gene operon for D-alanyl-lipoteichoic acid biosynthesis that is present in the vast majority of low-GC Gram-positive organisms. This protein may be involved in transport of D-alanine across the plasma membrane. TIGR04158.1 TIGR04158 rSAM_MIA_synth 400 400 368 equivalog Y Y N 3-methyl-2-indolic acid synthase nocL 21240261,21454624 1783272 Bacillati kingdom 38 JCVI 3-methyl-2-indolic acid synthase 3-methyl-2-indolic acid synthase Members are a radical SAM enzyme that converts L-Trp to 3-methyl-2-indolic acid synthase through a complex rearrangement. This enzyme is closest to ThiH, which also does a complex rearrangement, among other characterized radical SAM enzymes. TIGR04168.1 TIGR04168 TIGR04168 200 200 269 hypoth_equivalog Y Y N TIGR04168 family protein 1783272 Bacillati kingdom 1034 JCVI TIGR04168 family protein TIGR04168 family protein Members of this uncharacterized protein family are restricted, in 49 of 50 genomes, to organisms with a family TIGR04167 radical SAM protein, which occasionally is a selenoprotein. TIGR04228.1 TIGR04228 isopep_sspB_C2 36 34 173 domain Y Y N SspB-related isopeptide-forming adhesin GO:0005509,GO:0018262 20138058 1783272 Bacillati kingdom 8596 JCVI adhesin isopeptide-forming adherence domain adhesin isopeptide-forming adherence domain This domain has a conserved Lys (position 3 in seed alignment) and Asn at 177 that form an intramolecular isopeptide bond. The Asp (or Glu) at position 59, first position of the motif DDYDQ, forms hydrogen bonds to moieties in the isopeptide bond. TIGR04308.1 TIGR04308 repeat_SSSPR51 35 27.5 49 repeat Y N N SSSPR51 repeat surface protein 1783272 Bacillati kingdom 3461 JCVI surface protein repeat SSSPR-51 SSSPR51 repeat This repeat domain is designated SSRS51, Streptococcal and Staphylococcal Surface Protein Repeat of size 51. These repeats are homologous to the listerial repeats of Pfam model PF13461, but shorter on average by about 8 amino acids. Up to twelve tandem repeats can occur, on some of the longest proteins of their respective species. Nearly all member proteins carry the C-terminal sortase target sequence, LPXTG, recognizable by model TIGR01167. The repeat structure and probable surface location suggest a possible adhesion function. A protein with this class of repeats may have other classes as well. TIGR04403.1 TIGR04403 rSAM_skfB 300 300 402 equivalog Y Y N sporulation killing factor system radical SAM maturase skfB 23282011 1783272 Bacillati kingdom 153 JCVI sporulation killing factor system radical SAM maturase sporulation killing factor system radical SAM maturase Members of this family are a radical SAM enzyme of post-translational modification of ribosomally translated peptides. In Bacillus subtilis, the enzyme SkfB creates a sactipeptide (sulfur-to-alpha-carbon) crosslink of Cys-4 to Met-12 of the mature form of sporulation killing factor (SkfA). In Paenibacillus larvae subsp. larvae B-3650, the Met is replaced by Leu, so the modification must be different. SkfB has 2 4Fe-4S clusters, one in its radical SAM domain (PF04055) and one in a region that somewhat resembles the SPASM domain (TIGR04085). TIGR04429.1 TIGR04429 Phr_nterm 25 25 28 subfamily_domain Y Y N Phr family secreted Rap phosphatase inhibitor 9689219 1783272 Bacillati kingdom 843 JCVI Phr family secreted Rap phosphatase inhibitor Phr family secreted Rap phosphatase inhibitor Phr peptides are short peptides, best conserved in their amino-terminal regions, that are almost always encoded immediately downstream of a Rap phosphatase. A portion of the Phr peptide is secreted, enters another cell, and forms a quorum-sensing system by inhibiting its Rap phosphatase partner. The set of Phr peptides recognized by this N-terminal region model is disjoint from the PhrC/PhrF set recognized by Pfam model PF11131. TIGR04446.1 TIGR04446 pren_cyc_PirE 35 35 51 subfamily Y Y N anacyclamide/piricyclamide family prenylated cyclic peptide 20195859,21766822 1783272 Bacillati kingdom 321 JCVI prenylated cyclic peptide, anacyclamide/piricyclamide family anacyclamide/piricyclamide family prenylated cyclic peptide Members of this protein family occur primarily in Cyanobacteria. They average about 50 residues in length and are the ribosomally translated precursors of peptide natural products whose modifications include cleavage, cyclization, and prenylation. Sequences are well-conserved in the N-terminal region. They are nearly invariant over the last eight residues, but hypervariable just before that stretch. A related family, often in a similar genome context, is TIGR03678. TIGR04447.1 TIGR04447 PatC_TenC_TruC 30 30 34 domain Y Y N cyanobactin biosynthesis PatC/TenC/TruC family protein 15883371 1783272 Bacillati kingdom 193 JCVI cyanobactin cluster PatC/TenC/TruC protein cyanobactin biosynthesis PatC/TenC/TruC family protein Members of this family usually are small proteins (PatC, TenC, TruC) of unknown function in cyanobactin (prenylated cyclic peptide) biosynthesis clusters, where a different small protein is a known cyanobactin precursor (patellamide, anacyclamide, piricyclamide, etc). They may instead be the C-terminal domain of a longer protein that otherwise consists mostly of lectin-like or VWF type A domains, in similar context. Similar to the cyanobactin precursors, members of this family have two very strongly conserved regions separated by a hypervariable region, suggesting these proteins may undergo a similar maturation. TIGR04467.1 TIGR04467 CGA_synthase 300 300 382 equivalog Y Y N hydroxymethylcytosylglucuronate/cytosylglucuronate synthase 22753012 1783272 Bacillati kingdom 347 JCVI hydroxymethylcytosylglucuronate/cytosylglucuronate synthase hydroxymethylcytosylglucuronate/cytosylglucuronate synthase Members of this family synthesize cytosylglucuronate (or hydroxymethylcytosylglucuronate) from UDP-glucuronate and free cytosine (or hydroxymethylcytosine). This reaction is followed by a decarboxylation at C5 of the glucoside residue. The net reaction makes the pyranoside core moiety of a class of peptidyl nucleoside antibiotics. TIGR04522.1 TIGR04522 EcfS_MSC_0063 60 60 152 hypoth_equivalog Y N N putative energy coupling factor transporter S component GO:0005215,GO:0006810 1783272 Bacillati kingdom 141 JCVI putative energy coupling factor transporter S component putative energy coupling factor transporter S component This family of proteins is restricted to the Mollicutes (including Mycoplasma, Spiroplasma, and Ureaplasma). Members belong to a superfamily of multiple membrane-spanning proteins, among which those with assigned activities function as the S component (the specificity component) of ECF transporters. However, members fail to score better than the trusted cutoffs to previously built models for S component proteins (see Pfam family PF07155). NF001556.0 PRK00377 PRK00377.1 238 238 198 equivalog Y N N cobalt-precorrin-6Y C(15)-methyltransferase 1783275 Thermoproteati kingdom 42 NCBI Protein Cluster (PRK) cobalt-precorrin-6Y C(15)-methyltransferase cobalt-precorrin-6Y C(15)-methyltransferase NF002446.0 PRK01611 PRK01611.3-3 399 399 636 equivalog Y Y N arginine--tRNA ligase 6.1.1.19 1783275 Thermoproteati kingdom 112 NCBI Protein Cluster (PRK) arginyl-tRNA synthetase arginine--tRNA ligase NF003134.0 PRK04046 PRK04046.3-2 360 360 222 equivalog Y N N translation initiation factor IF-6 1783275 Thermoproteati kingdom 11 NCBI Protein Cluster (PRK) translation initiation factor IF-6 translation initiation factor IF-6 NF004417.0 PRK05761 PRK05761.1-3 780 780 858 equivalog Y Y N DNA-directed DNA polymerase I 2.7.7.7 1783275 Thermoproteati kingdom 178 NCBI Protein Cluster (PRK) DNA polymerase I DNA-directed DNA polymerase I NF004546.0 PRK05888 PRK05888.3-3 260 260 196 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoI nuoI 1.6.5.9 1783275 Thermoproteati kingdom 8 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit I NADH-quinone oxidoreductase subunit NuoI NF004729.0 PRK06073 PRK06073.1-5 94 94 134 equivalog Y N N NADH dehydrogenase subunit A 1783275 Thermoproteati kingdom 17 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit A NADH dehydrogenase subunit A NF006816.0 PRK09335 PRK09335.1 118 118 96 equivalog Y Y N 30S ribosomal protein S26e 1783275 Thermoproteati kingdom 121 NCBI Protein Cluster (PRK) 30S ribosomal protein S26e 30S ribosomal protein S26e NF006817.0 PRK09336 PRK09336.1 75 75 52 equivalog Y Y N 30S ribosomal protein S30e 1783275 Thermoproteati kingdom 79 NCBI Protein Cluster (PRK) 30S ribosomal protein S30e 30S ribosomal protein S30e NF017729.5 PF05942.16 PaREP1 24.4 24.4 115 domain Y Y N PaREP1 family protein 1783275 Thermoproteati kingdom 1438 EBI-EMBL Archaeal PaREP1/PaREP8 family PaREP1 family protein This family consists of several archaeal PaREP1 and PaREP8 proteins the function of this family is unknown. (from Pfam) NF026244.5 PF14894.11 Lsm_C 27 27 63 subfamily_domain Y Y N Lsm family RNA-binding protein 12668760 1783275 Thermoproteati kingdom 104 EBI-EMBL Lsm C-terminal Lsm family RNA-binding protein This domain is found at the C-terminus of archaeal Lsm (like-Sm) proteins [1]. [1]. 12668760. Structure and assembly of an augmented Sm-like archaeal protein 14-mer. Mura C, Phillips M, Kozhukhovsky A, Eisenberg D;. Proc Natl Acad Sci U S A. 2003;100:4539-4544. (from Pfam) NF037370.5 PF18653.6 Arcadin_1 25 25 111 PfamEq Y Y N arcadin 1 27852434 1783275 Thermoproteati kingdom 43 EBI-EMBL Arcadin 1 arcadin 1 Arcadin-1 is encoded by arcade gene cluster which also encodes cernactin. Crenactin is a filament-forming protein from the crenarchaeon Pyrobaculum calidifontis which shows exceptional similarity to eukaryotic F-actin. Arcadin-1 on the other hand does not seem to be related to any known eukaryotic actin binding proteins nor does it affect crenactin polymerisation [1]. [1]. 27852434. Crenactin forms actin-like double helical filaments regulated by arcadin-2. Izore T, Kureisaite-Ciziene D, McLaughlin SH, Lowe J;. Elife. 2016; [Epub ahead of print] (from Pfam) NF037920.5 PF18822.6 CdvA 30 30 123 domain Y Y N CdvA-like protein 29670199 1783275 Thermoproteati kingdom 132 EBI-EMBL CdvA-like coiled-coil domain CdvA coiled-coil domain A coiled coil region domain related to the CdvA-like proteins [1]. [1]. 29670199. Evolutionary convergence and divergence in archaeal chromosomal proteins and Chromo-like domains from bacteria and eukaryotes. Kaur G, Iyer LM, Subramanian S, Aravind L;. Sci Rep. 2018;8:6196. (from Pfam) NF038049.1 SelD_rel_HyperS 250 250 465 equivalog Y Y N SelD-related putative sulfur metabolism protein 25326317 1783275 Thermoproteati kingdom 84 NCBIFAM SelD-related putative sulfur metabolism protein NF040947.1 trans_reg_LysM 180 180 136 equivalog Y Y N HTH-type transcriptional regulator LysM lysM GO:0019878,GO:0043565 12042311 1783275 Thermoproteati kingdom 82 NCBIFAM HTH-type transcriptional regulator LysM NF046075.1 UpsF 400 400 484 equivalog Y Y N membrane pilin protein UpsF upsF GO:0009289 24106028 1783275 Thermoproteati kingdom 46 NCBIFAM membrane pilin protein UpsF Proteins of this family are encoded by the archaeal upsF gene on the UV-inducible pili operon (ups operon), which is involved in UV-induced pili assembly, cellular aggregation, and subsequent DNA exchange between cells. The ATPase UpsE and the membrane protein UpsF are essential for the formation of ups pili. TIGR03881.1 TIGR03881 KaiC_arch_4 247.8 247.8 231 hypoth_equivalog Y Y N KaiC domain-containing protein 1783275 Thermoproteati kingdom 93 JCVI KaiC domain protein, PAE1156 family KaiC domain protein, PAE1156 family Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain. NF033864.1 cytochrome579 280 280 179 equivalog Y Y N cytochrome 579 GO:0009055,GO:0020037 18469132,22518111 179 Leptospirillum genus 8 NCBIFAM cytochrome 579 cytochrome 579 Cytochrome 579, as described originally in Leptospirillum from acid mine drainage, is an abundant red cytochrome that acts as an electron transfer protein involved in Fe(II) oxidation. NF045219.2 PF20786.2 DUF6840 26.8 26.8 92 domain Y Y N DUF6840 family protein 179 Leptospirillum genus 3 EBI-EMBL Family of unknown function (DUF6840) DUF6840 family protein This uncharacterised protein family is predominantly found in Leptospirillum sp. Its function is unknown. There are some conserved motifs: SRD, AGGL and some highly conserved Y, H and W residues. (from Pfam) NF045342.2 PF21308.2 C3_CUB2 26.7 26.7 62 domain Y N N Complement component 3, CUB domain, second segment 16177781,16831446,17051150,17051160,17412383,21205667 1795 Mycolicibacterium neoaurum species 1 EBI-EMBL Complement component 3, CUB domain, second segment Complement component 3, CUB domain, second segment Complement C3 is major component in the both the classical and alternative complement activation pathways. C3 is cleaved into two chains (alpha and beta) by C3 convertases. This entry represents the second segment of the CUB domain, which is completed by Pfam:PF21406 [2]. The CUB domain is interrupted by the TE domain. The CUB, TE and MG8 domains form a massive, tightly packed super domain. This entry also includes venom factors, also known as Complement C3 homologues. These are complement-activating proteins with structural and functional similarities to complement component C3b, the activated form of C3 [6]. Paper describing PDB structure 2a73. [1]. 16177781. Structures of complement component C3 provide insights into the function and evolution of immunity. Janssen BJ, Huizinga EG, Raaijmakers HC, Roos A, Daha MR, Nilsson-Ekdahl K, Nilsson B, Gros P;. Nature. 2005;437:505-511. Paper describing PDB structure 2b39. [2]. 16831446. The structure of bovine complement component 3 reveals the basis for thioester function. Fredslund F, Jenner L, Husted LB, Nyborg J, Andersen GR, Sottrup-Jensen L;. J Mol Biol. 2006;361:115-127. Paper describing PDB structure 2i07. [3]. 17051160. Structure of C3b reveals conformational changes that underlie complement activity. Janssen BJ, Christodoulidou A, McCarthy A, Lambris JD, Gros P;. Nature. 2006;444:213-216. Paper describing PDB structure 2icf. [4]. 17051150. Structure of C3b in complex with CRIg gives insights into regulation of complement activation. Wiesmann C, Katschke KJ, Yin J, Helmy KY, Steffek M, Fairbrother WJ, McCallum SA, Embuscado L, DeForge L, Hass PE, van Lookeren Campagne M;. TRUNCATED at 1650 bytes (from Pfam) NF017703.5 PF05915.17 TMEM_230_134 26.8 26.8 119 domain Y Y N transmembrane domain-containing protein 27270108,27899274 1796652 Turicimonas muris species 1 EBI-EMBL Transmembrane proteins 230/134 Transmembrane proteins 230/134 This family consists of the eukaryotic transmembrane proteins 230 and 134 (TMEM230 and 134). TMEM134 function is unknown, but it has been shown to interact with E virus ORF2 [1]. TMEM 230 is involved in trafficking and recycling of synaptic vesicles [2]. [1]. 27899274. Systematic identification of hepatitis E virus ORF2 interactome reveals that TMEM134 engages in ORF2-mediated NF-kappaB pathway. Tian Y, Huang W, Yang J, Wen Z, Geng Y, Zhao C, Zhang H, Wang Y;. Virus Res. 2017;228:102-108. [2]. 27270108. Identification of TMEM230 mutations in familial Parkinson's disease. Deng HX, Shi Y, Yang Y, Ahmeti KB, Miller N, Huang C, Cheng L, Zhai H, Deng S, Nuytemans K, Corbett NJ, Kim MJ, Deng H, Tang B, Yang Z, Xu Y, Chan P, Huang B, Gao XP, Song Z, Liu Z, Fecto F, Siddique N, Foroud T, Jankovic J, Ghetti B, Nicholson DA, Krainc D, Melen O, Vance JM, Pericak-Vance MA, Ma YC, Rajput AH, Siddique T;. Nat Genet. 2016;48:733-739. (from Pfam) TIGR02387.1 TIGR02387 rpoC1_cyan 975.9 975.9 619 equivalog Y Y N DNA-directed RNA polymerase subunit gamma rpoC1 2.7.7.6 GO:0003677,GO:0003899,GO:0006351 2495268 1798711 Cyanobacteriota/Melainabacteria group no rank 791 JCVI DNA-directed RNA polymerase, gamma subunit DNA-directed RNA polymerase subunit gamma The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''. NF000092.1 D_ala_D_lac_Ao2 700 700 348 exception Y Y Y D-alanine--(R)-lactate ligase VanA-Ao2 vanA-Ao2 6.1.2.1 1813 Amycolatopsis genus 34 NCBIFAM D-alanine--(R)-lactate ligase VanA-Ao2 D-alanine--(R)-lactate ligase VanA-Ao2 NF040074.4 PF19901.4 DUF6374 25 25 59 subfamily Y Y N DUF6374 family protein 30867595 1817 Nocardia genus 329 EBI-EMBL Family of unknown function (DUF6374) DUF6374 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0002024) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the nargenicin biosynthetic gene cluster from Nocardia argentinensis [1]. [1]. 30867595. Enzyme-catalysed [6+4] cycloadditions in the biosynthesis of natural products. Zhang B, Wang KB, Wang W, Wang X, Liu F, Zhu J, Shi J, Li LY, Han H, Xu K, Qiao HY, Zhang X, Jiao RH, Houk KN, Liang Y, Tan RX, Ge HM;. Nature. 2019;568:122-126. (from Pfam) NF033094.0 HK_VanS_O 720 720 345 exception Y Y Y vancomycin resistance histidine kinase VanS-O vanS-O 1827 Rhodococcus genus 10 NCBIFAM VanO-type vancomycin resistance histidine kinase VanS vancomycin resistance histidine kinase VanS-O NF033118.1 vanR-O 505 505 233 exception Y Y Y vancomycin resistance response regulator transcription factor VanR-O vanR-O GO:0000160,GO:0006355 1827 Rhodococcus genus 5 NCBIFAM VanO-type vancomycin resistance DNA-binding response regulator VanR vancomycin resistance response regulator transcription factor VanR-O Members of this family are the DNA-binding response regulator designated VanR from the VanO-type vancomycin resistance system known in Rhodococcus equi and perhaps to be found elsewhere. No homolog is closer than 90% identity to the founding member and none is known to be part of another VanO-type system. NF016391.5 PF04502.18 Saf4_Yju2 27.8 27.8 332 PfamAutoEq Y Y N Saf4/Yju2 family protein GO:0000398 11884590,17515604 1828640 Nostoc sp. LEGE 12447 species 1 EBI-EMBL Saf4/Yju2 protein Saf4/Yju2 family protein This is a family of eukaryotic proteins that includes CCDC130 and CCDC94 from humans, Saf4 from fission yeasts and Yju2 from budding yeasts. Saf4 (also known as cwc16) is involved in mRNA splicing where it associates with cdc5 and the other cwf proteins as part of the spliceosome [1]. Yju2 is a splicing factor that is associated with the Prp 19-associated complex and acts after Prp2 in promoting the first catalytic reaction of pre-mRNA splicing [2]. [1]. 11884590. Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs. Ohi MD, Link AJ, Ren L, Jennings JL, McDonald WH, Gould KL;. Mol Cell Biol 2002;22:2011-2024. [2]. 17515604. A novel splicing factor, Yju2, is associated with NTC and acts after Prp2 in promoting the first catalytic reaction of pre-mRNA splicing. Liu YC, Chen HC, Wu NY, Cheng SC;. Mol Cell Biol. 2007;27:5403-5413. (from Pfam) NF009716.0 PRK13244 PRK13244.1-2 197 197 138 subfamily Y N N protease inhibitor protein 1835 Saccharopolyspora genus 6 NCBI Protein Cluster (PRK) protease inhibitor protein protease inhibitor protein NF002672.0 PRK02395 PRK02395.1-4 435 435 486 subfamily Y N N hypothetical protein 183710 Deinococcaceae family 139 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003790.0 PRK05379 PRK05379.2-2 403 403 354 equivalog Y N N bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase 183710 Deinococcaceae family 121 NCBI Protein Cluster (PRK) bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase NF011359.0 PRK14777 PRK14777.1 187 187 191 subfamily Y N N lipoprotein signal peptidase 183710 Deinococcaceae family 138 NCBI Protein Cluster (PRK) lipoprotein signal peptidase lipoprotein signal peptidase NF001398.0 PRK00281 PRK00281.3-5 354 354 278 equivalog Y Y N undecaprenyl-diphosphate phosphatase 3.6.1.27 183924 Thermoprotei class 57 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate phosphatase undecaprenyl-diphosphate phosphatase NF001541.2 PRK00369 PRK00369.1 310 310 400 equivalog Y Y N dihydroorotase pyrC 3.5.2.3 GO:0004151,GO:0008270,GO:0044205 12142413 183924 Thermoprotei class 68 NCBI Protein Cluster (PRK) dihydroorotase dihydroorotase NF001544.0 PRK00373 PRK00373.1-3 253 253 216 equivalog Y Y N V-type ATP synthase subunit D 7.1.2.2 183924 Thermoprotei class 51 NCBI Protein Cluster (PRK) V-type ATP synthase subunit D V-type ATP synthase subunit D NF001592.0 PRK00394 PRK00394.1-1 270 270 194 equivalog Y Y N TATA-box-binding protein 183924 Thermoprotei class 86 NCBI Protein Cluster (PRK) transcription factor TATA-box-binding protein NF001647.0 PRK00420 PRK00420.1-4 108 108 130 equivalog Y N N hypothetical protein 183924 Thermoprotei class 64 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF001667.0 PRK00431 PRK00431.2-3 252 252 182 equivalog Y Y N ADP-ribose-binding protein 183924 Thermoprotei class 74 NCBI Protein Cluster (PRK) RNase III inhibitor ADP-ribose-binding protein NF001747.0 PRK00466 PRK00466.1 288 288 346 equivalog Y Y N N-acetyl-lysine deacetylase 183924 Thermoprotei class 56 NCBI Protein Cluster (PRK) acetyl-lysine deacetylase N-acetyl-lysine deacetylase Catalyzes N(2)-acetyl-L-lysine + H(2)O = acetate + L-lysine NF002218.0 PRK01115 PRK01115.1-1 267 267 249 equivalog Y Y N DNA polymerase sliding clamp 183924 Thermoprotei class 58 NCBI Protein Cluster (PRK) DNA polymerase sliding clamp DNA polymerase sliding clamp NF002233.0 PRK01146 PRK01146.1-1 79 79 92 equivalog Y Y N DNA-directed RNA polymerase subunit L 2.7.7.6 183924 Thermoprotei class 33 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit L DNA-directed RNA polymerase subunit L NF003095.0 PRK04019 PRK04019.1-1 381 381 339 equivalog Y Y N 50S ribosomal protein L10 183924 Thermoprotei class 79 NCBI Protein Cluster (PRK) acidic ribosomal protein P0 50S ribosomal protein L10 NF003126.0 PRK04046 PRK04046.1-1 283 283 223 equivalog Y N N translation initiation factor IF-6 183924 Thermoprotei class 55 NCBI Protein Cluster (PRK) translation initiation factor IF-6 translation initiation factor IF-6 NF003135.0 PRK04046 PRK04046.3-3 320 320 226 equivalog Y N N translation initiation factor IF-6 183924 Thermoprotei class 12 NCBI Protein Cluster (PRK) translation initiation factor IF-6 translation initiation factor IF-6 NF003208.0 PRK04171 PRK04171.2-3 305 305 222 equivalog Y N N ribosome biogenesis protein 183924 Thermoprotei class 8 NCBI Protein Cluster (PRK) ribosome biogenesis protein ribosome biogenesis protein NF003263.0 PRK04235 PRK04235.1-1 237 237 219 equivalog Y N N hypothetical protein 183924 Thermoprotei class 67 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003292.0 PRK04290 PRK04290.1-1 253 253 216 equivalog Y Y N 30S ribosomal protein S6e 183924 Thermoprotei class 64 NCBI Protein Cluster (PRK) 30S ribosomal protein S6e 30S ribosomal protein S6e NF003336.0 PRK04342 PRK04342.1-5 531 531 386 equivalog Y Y N DNA topoisomerase IV subunit A 5.6.2.2 183924 Thermoprotei class 102 NCBI Protein Cluster (PRK) DNA topoisomerase VI subunit A DNA topoisomerase IV subunit A NF004062.0 PRK05576 PRK05576.1-5 194 194 219 equivalog Y Y N cobalt-factor II C(20)-methyltransferase 2.1.1.151 183924 Thermoprotei class 49 NCBI Protein Cluster (PRK) cobalt-precorrin-2 C(20)-methyltransferase cobalt-factor II C(20)-methyltransferase NF004419.0 PRK05761 PRK05761.1-5 1285 1285 932 equivalog Y Y N DNA-directed DNA polymerase I 2.7.7.7 183924 Thermoprotei class 29 NCBI Protein Cluster (PRK) DNA polymerase I DNA-directed DNA polymerase I NF004423.0 PRK05765 PRK05765.1 332 332 247 equivalog Y Y N precorrin-3B C(17)-methyltransferase 2.1.1.131 183924 Thermoprotei class 55 NCBI Protein Cluster (PRK) precorrin-3B C17-methyltransferase precorrin-3B C(17)-methyltransferase Catalyzes the formation of precorrin-4 from precorrin-3B and S-adenosyl-L-methionine NF004436.0 PRK05772 PRK05772.1 521 521 363 equivalog Y Y N S-methyl-5-thioribose-1-phosphate isomerase 5.3.1.23 183924 Thermoprotei class 67 NCBI Protein Cluster (PRK) translation initiation factor IF-2B subunit alpha S-methyl-5-thioribose-1-phosphate isomerase NF004437.0 PRK05773 PRK05773.1 262 262 219 equivalog Y N N 3,4-dihydroxy-2-butanone 4-phosphate synthase 183924 Thermoprotei class 78 NCBI Protein Cluster (PRK) 3,4-dihydroxy-2-butanone 4-phosphate synthase 3,4-dihydroxy-2-butanone 4-phosphate synthase NF004449.0 PRK05782 PRK05782.1 298 298 333 equivalog Y N N bifunctional sirohydrochlorin cobalt chelatase/precorrin-8X methylmutase 4.99.1.3,5.4.99.61 183924 Thermoprotei class 48 NCBI Protein Cluster (PRK) bifunctional sirohydrochlorin cobalt chelatase/precorrin-8X methylmutase bifunctional sirohydrochlorin cobalt chelatase/precorrin-8X methylmutase NF004450.0 PRK05783 PRK05783.1 96 96 84 equivalog Y N N hypothetical protein 183924 Thermoprotei class 52 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004455.0 PRK05787 PRK05787.1-3 258 258 221 equivalog Y Y N cobalt-precorrin-7 (C(5))-methyltransferase 2.1.1.289 183924 Thermoprotei class 39 NCBI Protein Cluster (PRK) cobalt-precorrin-6Y C(5)-methyltransferase cobalt-precorrin-7 (C(5))-methyltransferase NF004467.0 PRK05788 PRK05788.1-5 376 376 326 equivalog Y Y N cobalt-precorrin 5A hydrolase cbiG 3.7.1.12 183924 Thermoprotei class 43 NCBI Protein Cluster (PRK) cobalamin biosynthesis protein CbiG cobalt-precorrin 5A hydrolase NF004541.0 PRK05888 PRK05888.2-2 217 217 168 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoI nuoI 1.6.5.9 183924 Thermoprotei class 45 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit I NADH-quinone oxidoreductase subunit NuoI NF004888.0 PRK06251 PRK06251.1 101 101 102 equivalog Y N N V-type ATP synthase subunit K 183924 Thermoprotei class 46 NCBI Protein Cluster (PRK) V-type ATP synthase subunit K V-type ATP synthase subunit K NF006398.0 PRK08651 PRK08651.1-1 439 439 403 equivalog Y N N succinyl-diaminopimelate desuccinylase 183924 Thermoprotei class 23 NCBI Protein Cluster (PRK) succinyl-diaminopimelate desuccinylase succinyl-diaminopimelate desuccinylase NF006422.0 PRK08674 PRK08674.1-1 317 317 302 subfamily Y N N bifunctional phosphoglucose/phosphomannose isomerase 183924 Thermoprotei class 48 NCBI Protein Cluster (PRK) bifunctional phosphoglucose/phosphomannose isomerase bifunctional phosphoglucose/phosphomannose isomerase NF006813.0 PRK09334 PRK09334.1-3 83 83 97 equivalog Y Y N 30S ribosomal protein S25e 183924 Thermoprotei class 26 NCBI Protein Cluster (PRK) 30S ribosomal protein S25e 30S ribosomal protein S25e NF008914.0 PRK12277 PRK12277.1 96 96 83 equivalog Y Y N 50S ribosomal protein L13e 183924 Thermoprotei class 38 NCBI Protein Cluster (PRK) 50S ribosomal protein L13e 50S ribosomal protein L13e NF009621.0 PRK13125 PRK13125.1 234 234 244 equivalog Y Y N tryptophan synthase subunit alpha trpA 4.2.1.20 183924 Thermoprotei class 73 NCBI Protein Cluster (PRK) tryptophan synthase subunit alpha tryptophan synthase subunit alpha Catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis. The indole is then used in the final step of the biosynthesis, performed by the beta subunit. This HMM describes a variant form found in genera such as Sulfolobus in the Thermoprotei class of the Crenarchaeota. NF009787.0 PRK13280 PRK13280.2-1 383 383 290 equivalog Y N N N-glycosylase/DNA lyase 183924 Thermoprotei class 6 NCBI Protein Cluster (PRK) N-glycosylase/DNA lyase N-glycosylase/DNA lyase NF010544.0 PRK13934 PRK13934.1 325 325 266 equivalog Y N N stationary phase survival protein SurE 3.1.3.6 183924 Thermoprotei class 32 NCBI Protein Cluster (PRK) stationary phase survival protein SurE stationary phase survival protein SurE NF011084.0 PRK14511 PRK14511.1-1 1021 1021 728 equivalog Y Y N malto-oligosyltrehalose synthase 5.4.99.15 183924 Thermoprotei class 27 NCBI Protein Cluster (PRK) maltooligosyl trehalose synthase malto-oligosyltrehalose synthase NF011157.0 PRK14562 PRK14562.1-2 238 238 191 equivalog Y N N haloacid dehalogenase superfamily protein 183924 Thermoprotei class 23 NCBI Protein Cluster (PRK) haloacid dehalogenase superfamily protein haloacid dehalogenase superfamily protein NF011460.0 PRK14879 PRK14879.1-1 199 199 232 equivalog Y Y N Kae1-associated kinase Bud32 183924 Thermoprotei class 58 NCBI Protein Cluster (PRK) serine/threonine protein kinase Kae1-associated kinase Bud32 NF011478.0 PRK14889 PRK14889.1-1 182 182 152 equivalog Y N N VKOR family protein 183924 Thermoprotei class 25 NCBI Protein Cluster (PRK) VKOR family protein VKOR family protein NF011480.0 PRK14889 PRK14889.1-4 120 120 132 equivalog Y N N VKOR family protein 183924 Thermoprotei class 24 NCBI Protein Cluster (PRK) VKOR family protein VKOR family protein NF011482.0 PRK14892 PRK14892.1 109 109 101 equivalog Y N N putative transcription elongation factor Elf1 183924 Thermoprotei class 61 NCBI Protein Cluster (PRK) putative transcription elongation factor Elf1 putative transcription elongation factor Elf1 NF020637.5 PF09071.15 Alpha-amyl_C 27 27 67 domain Y N N Alpha-amylase, C terminal 10926520 183924 Thermoprotei class 35 EBI-EMBL Alpha-amylase, C terminal Alpha-amylase, C terminal Members of this family, which are found in the prokaryotic protein glycosyltrehalose trehalohydrolase, assume a gamma-crystallin-type fold with a five-stranded anti-parallel beta-sheet that packs against the C-terminal side of a beta-alpha barrel. This domain is common to family 13 glycosidases and typically contains a five to ten strand beta-sheet, however its precise fold varies [1]. [1]. 10926520. Crystal structure of glycosyltrehalose trehalohydrolase from the hyperthermophilic archaeum Sulfolobus solfataricus. Feese MD, Kato Y, Tamada T, Kato M, Komeda T, Miura Y, Hirose M, Hondo K, Kobayashi K, Kuroki R;. J Mol Biol. 2000;301:451-464. (from Pfam) NF021562.5 PF10051.14 DUF2286 24 24 138 PfamAutoEq Y Y N DUF2286 domain-containing protein 183924 Thermoprotei class 80 EBI-EMBL Uncharacterized protein conserved in archaea (DUF2286) Uncharacterized protein conserved in archaea (DUF2286) Members of this family of hypothetical archaeal proteins have no known function. (from Pfam) NF022955.5 PF11520.13 Cren7 25 25 58 PfamEq Y Y N chromatin protein Cren7 GO:0003690,GO:0005737 18096617 183924 Thermoprotei class 105 EBI-EMBL Chromatin protein Cren7 chromatin protein Cren7 Cren7 is a chromatin protein found in Crenarchaeota and has a higher affinity for double-stranded DNA than for single-stranded DNA. The protein contains negative DNA supercoils and is associated with genomic DNA in vivo.Cren7 interacts with duplex DNA through a beta-sheet and a long flexible loop. The function has not been completely determined but it is thought that the protein may have a role similar to that of archaeal proteins in Euryarchaea [1]. [1]. 18096617. Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea. Guo L, Feng Y, Zhang Z, Yao H, Luo Y, Wang J, Huang L;. Nucleic Acids Res. 2008;36:1129-1137. (from Pfam) NF023558.5 PF12136.13 RNA_pol_Rpo13 25 25 43 PfamEq Y Y N RNA polymerase subunit Rpo13 19419240 183924 Thermoprotei class 49 EBI-EMBL RNA polymerase Rpo13 subunit HTH domain RNA polymerase Rpo13 subunit HTH domain This domain is found in archaea, and is about 40 amino acids in length. It has a single completely conserved residue E that may be functionally important. It is found in the archaeal DNA dependent RNA polymerase. The domain is a 'helix-turn-helix' (HTH) domain in the Rpo13 subunit of the RNA polymerase. This domain is involved in downstream DNA binding, and the entire subunit has also been implicated in contacting transcription factor II B. [1]. 19419240. Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure. Korkhin Y, Unligil UM, Littlefield O, Nelson PJ, Stuart DI, Sigler PB, Bell SD, Abrescia NG;. PLoS Biol. 2009;7:e102. (from Pfam) NF028302.5 PF16992.10 RNA_pol_RpbG 27 27 119 PfamEq Y Y N DNA-directed RNA polymerase subunit G 2.7.7.6 183924 Thermoprotei class 72 EBI-EMBL DNA-directed RNA polymerase, subunit G DNA-directed RNA polymerase subunit G RNA_pol_RpbG is a family of archaeal and fungal subunit G of DNA-directed RNA polymerase. (from Pfam) NF037451.5 PF18533.6 DUF5622 25 25 66 domain Y Y N DUF5622 domain-containing protein 24875358 183924 Thermoprotei class 61 EBI-EMBL Domain of unknown function (DUF5622) Domain of unknown function (DUF5622) This is a domain of unknown function found in archaea-specific ribosomal proteins such as L46a which is suggested to directly bind to rRNA in the ribosome [1]. [1]. 24875358. Structure determination of archaea-specific ribosomal protein L46a reveals a novel protein fold. Feng Y, Song X, Lin J, Xuan J, Cui Q, Wang J;. Biochem Biophys Res Commun. 2014;450:67-72. (from Pfam) NF037687.5 PF17952.6 Cas6_N 27 27 115 domain Y N N Cas6 N-terminal domain 16545108,17379808,17442114,21699496,23454186,23527601,24459147 183924 Thermoprotei class 112 EBI-EMBL Cas6 N-terminal domain Cas6 N-terminal domain The CRISPR-Cas system is a prokaryotic defense mechanism against foreign genetic elements. The key elements of this defense system are the Cas proteins and the CRISPR RNA.Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes [1]. CRISPRs appear to provide acquired resistance against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA).The defense reaction is divided into three stages. In the adaptation stage, the invader DNA is cleaved, and a piece of it is selected to be integrated as a new spacer into the CRISPR locus, where it is stored as an identity tag for future attacks by this invader. During the second stage (the expression stage), the CRISPR RNA (pre-crRNA) is transcribed and subsequently processed into the mature crRNAs. In the third stage (the interference stage), Cas proteins, together with crRNAs, identify and degrade the invader [2, 3, 4].The CRISPR-Cas systems have been sorted into three major classes. In CRISPR-Cas types I and III, the mature crRNA is generally generated by a member of the Cas6 protein family. Whereas in system III the Cas6 protein acts alone, in some class I systems it is part of a complex of Cas proteins known as Cascade (CRISPR-associated complex for antiviral defense). This entry represents the N-terminal domain of C. TRUNCATED at 1650 bytes (from Pfam) NF040938.1 KDG_KDGal_kin 400 400 305 equivalog Y Y N bifunctional 2-dehydro-3-deoxygluconokinase/2-dehydro-3-deoxygalactonokinase kdgK 2.7.1.178 GO:0008671,GO:0008673 16794308,19018105 183924 Thermoprotei class 53 NCBIFAM bifunctional 2-dehydro-3-deoxygluconokinase/2-dehydro-3-deoxygalactonokinase NF040939.1 trans_reg_lrs14 158 158 118 equivalog Y Y N HTH-type transcriptional regulator Lrs14 lrs14 GO:0003677,GO:0003700 10049378 183924 Thermoprotei class 82 NCBIFAM HTH-type transcriptional regulator Lrs14 NF040952.1 Arch_mtprotase_TldD 635 635 443 equivalog Y Y N zinc metalloprotease TldD tldD 3.4.-.- GO:0006508,GO:0008237,GO:0008270 22950735 183924 Thermoprotei class 54 NCBIFAM zinc metalloprotease TldD NF040954.1 Arch_KDGaldase 390 390 288 equivalog Y Y N bifunctional 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase 4.1.2.55 GO:0005975,GO:0008674,GO:0008675 10527934,12824170,29812914 183924 Thermoprotei class 51 NCBIFAM bifunctional 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase NF041006.2 cell_div_CdvC 650 650 370 equivalog Y Y N cell division protein CdvC cdvC GO:0051301 18987308,19008417 183924 Thermoprotei class 38 NCBIFAM cell division protein CdvC NF041011.1 dihydoor_dh_Arch 330 330 289 equivalog Y Y N dihydroorotate dehydrogenase PyrD pyrD 1.3.1.14 GO:0004152,GO:0004589,GO:0006207 12142413 183924 Thermoprotei class 69 NCBIFAM dihydroorotate dehydrogenase PyrD NF041019.1 glyceraldDH_beta 350 350 280 equivalog Y Y N glyceraldehyde dehydrogenase subunit beta cutB 1.2.99.8 GO:0005506,GO:0016903,GO:0043795 10095793 183924 Thermoprotei class 103 NCBIFAM glyceraldehyde dehydrogenase subunit beta NF041020.1 glyceraldDH_gamma 290 290 164 equivalog Y Y N glyceraldehyde dehydrogenase subunit gamma cutC 1.2.99.8 GO:0005506,GO:0016903,GO:0043795 10095793 183924 Thermoprotei class 76 NCBIFAM glyceraldehyde dehydrogenase subunit gamma NF041069.1 IPMS_Sufob 600 600 371 equivalog Y Y N isopropylmalate synthase 2.3.3.13 GO:0003852,GO:0009098 31330039 183924 Thermoprotei class 43 NCBIFAM isopropylmalate synthase NF041071.1 Trm10_mtase_Thprot 330 330 296 equivalog Y Y N tRNA (adenine(9)-N1)-methyltransferase Trm10 trm10 2.1.1.218 GO:0030488 20525789 183924 Thermoprotei class 60 NCBIFAM tRNA (adenine(9)-N1)-methyltransferase Trm10 NF041080.1 DGGGPL_reductase 580 580 447 equivalog Y Y N digeranylgeranylglycerophospholipid reductase GO:0008654,GO:0016628 18375567,21515284 183924 Thermoprotei class 81 NCBIFAM digeranylgeranylglycerophospholipid reductase NF041081.1 prot_lys_mtase_Arch 200 200 142 equivalog Y Y N protein-lysine N-methyltransferase 2.1.1.- GO:0016279 23086207 183924 Thermoprotei class 48 NCBIFAM protein-lysine N-methyltransferase NF041172.1 AcrlCoa_red_Thmprot 500 500 334 equivalog Y Y N acryloyl-coenzyme A reductase 1.3.1.84 GO:0043957 19429610 183924 Thermoprotei class 79 NCBIFAM acryloyl-coenzyme A reductase NF041797.1 Ced_CedA1 100 100 75 equivalog Y Y N DNA import protein CedA1 cedA1 26884154,36750723 183924 Thermoprotei class 52 NCBIFAM DNA import protein CedA1 NF044800.2 PF21437.2 CbiG-like_linker 27 27 78 domain Y N N CbiG-like, linker domain 183924 Thermoprotei class 40 EBI-EMBL CbiG-like, linker domain CbiG-like, linker domain This domain is found once in the putative Cobalamin biosynthesis protein G homolog from the archaea Saccharolobus solfataricus (CbiG-like), C-terminal to Pfam:PF11760 and N-terminal to Pfam:PF01890. It is also found several times in uncharacterised proteins from lower eukaryotes, some of which also contain ankyrin repeats (Pfam:PF00023, Pfam:PF12796, Pfam:PF13637, Pfam:PF13857, Pfam:PF13606). (from Pfam) NF045238.2 PF20873.2 PriS_C 27 27 50 domain Y N N Primase chain A, C-terminal domain 16273105,29167441 183924 Thermoprotei class 47 EBI-EMBL Primase chain A, C-terminal domain Primase chain A, C-terminal domain This domain is found at the C-terminal end of the small subunit (PriS) of the core primase from the archaeon Sulfolobus solfataricus, an RNA polymerase that catalyzes the synthesis of the RNA primers required by the DNA polymerases. PriS is the catalytic subunit, with the active site located within an exposed groove in the concave side of two divergent beta-sheets, surrounded on the outside by alpha-helices This C-terminal domain, which is not found in other homologues, shows a mixed alpha-beta fold. It seems to support and position the elongated hairpin structure leading into the zinc-binding motif (PriS-Zn) [1,2]. Paper describing PDB structure 1zt2. [1]. 16273105. Structure of the heterodimeric core primase. Lao-Sirieix SH, Nookala RK, Roversi P, Bell SD, Pellegrini L;. Nat Struct Mol Biol. 2005;12:1137-1144. Paper describing PDB structure 5of3. [2]. 29167441. Primer synthesis by a eukaryotic-like archaeal primase is independent of its Fe-S cluster. Holzer S, Yan J, Kilkenny ML, Bell SD, Pellegrini L;. Nat Commun. 2017;8:1718. (from Pfam) NF003083.0 PRK04012 PRK04012.1-2 130 130 94 subfamily Y Y N translation initiation factor aIF-1A 183963 Halobacteria class 799 NCBI Protein Cluster (PRK) translation initiation factor IF-1A translation initiation factor aIF-1A NF003341.0 PRK04358 PRK04358.1-2 353 353 224 equivalog Y N N hypothetical protein 183963 Halobacteria class 254 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003713.0 PRK05325 PRK05325.2-5 467 467 441 equivalog Y N N hypothetical protein 183963 Halobacteria class 549 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005561.0 PRK07234 PRK07234.1-1 718 718 569 equivalog Y N N putative monovalent cation/H+ antiporter subunit D 183963 Halobacteria class 509 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit D putative monovalent cation/H+ antiporter subunit D NF007124.0 PRK09565 PRK09565.1 446 0 637 equivalog Y Y N heme-binding protein 183963 Halobacteria class 650 NCBI Protein Cluster (PRK) hypothetical protein heme-binding protein NF009160.0 PRK12505 PRK12505.1 140 140 179 equivalog Y N N putative monovalent cation/H+ antiporter subunit B 183963 Halobacteria class 453 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit B putative monovalent cation/H+ antiporter subunit B NF009244.0 PRK12599 PRK12599.1-3 90 90 92 equivalog Y N N putative monovalent cation/H+ antiporter subunit F 183963 Halobacteria class 426 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit F putative monovalent cation/H+ antiporter subunit F NF009295.0 PRK12652 PRK12652.1 290 290 368 equivalog Y Y N monovalent cation/H+ antiporter subunit E 183963 Halobacteria class 492 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit E monovalent cation/H+ antiporter subunit E Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF009401.0 PRK12766 PRK12766.1 239 239 238 equivalog Y Y N 50S ribosomal protein L32e 183963 Halobacteria class 566 NCBI Protein Cluster (PRK) 50S ribosomal protein L32e 50S ribosomal protein L32e Contacts helix 25 of domain III of the 23S rRNA NF010045.0 PRK13518 PRK13518.1 395 395 360 equivalog Y Y N glutamate--cysteine ligase 6.3.2.2 183963 Halobacteria class 617 NCBI Protein Cluster (PRK) carboxylate-amine ligase glutamate--cysteine ligase NF027817.5 PF16502.10 DUF5059 25 25 619 PfamAutoEq Y Y N DUF5059 domain-containing protein 183963 Halobacteria class 232 EBI-EMBL Domain of unknown function (DUF5059) Domain of unknown function (DUF5059) This domain is found fused to a copper-binding protein at the C-terminus, family Copper-bind, Pfam:PF00127. Its function is not known, and it is found in the Halobacteriaceae family in Archaea. (from Pfam) NF037148.5 PF17909.6 Htr2 25 25 61 subfamily_domain Y Y N sensory rhodopsin II transducer 23619282,28165484 183963 Halobacteria class 19 EBI-EMBL Htr2 transmembrane domain Htr2 transmembrane domain Archaebacterial photoreceptors mediate phototaxis by regulating cell motility through two-component signaling cascades like those found in chemotaxis signaling chains of enteric bacteria. The photoreceptor sensory rhodopsin II from N. pharaonis (NpSRII) in complex with its cognate transducer NpHtrII serves as a system for transmembrane signal transfer. This entry is for the transmembrane domain of the transducer HtrII. Studies suggest that conformation changes of the NpSRII/NpHtrII complex may be crucial for the mechanism of signal propagation spanning the membrane domain and feeding into the HAMP domain [1]. Furthermore, HtrII in H. salinarum not only transmits the signal from the photoreceptor SRII but also operates as a chemoreceptor [2]. [1]. 28165484. New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex. Ishchenko A, Round E, Borshchevskiy V, Grudinin S, Gushchin I, Klare JP, Remeeva A, Polovinkin V, Utrobin P, Balandin T, Engelhard M, Buldt G, Gordeliy V;. Sci Rep. 2017;7:41811. [2]. 23619282. Ground state structure of D75N mutant of sensory rhodopsin II in complex with its cognate transducer. Ishchenko A, Round E, Borshchevskiy V, Grudinin S, Gushchin I, Klare JP, Balandin T, Remeeva A, Engelhard M, Buldt G, Gordeliy V;. J Photochem Photobiol B. 2013;123:55-58. (from Pfam) NF038088.1 anchor_synt_D 240 240 194 exception Y Y N protein sorting system archaetidylserine decarboxylase 32209681 183963 Halobacteria class 526 NCBIFAM protein sorting system archaetidylserine decarboxylase Members of this family, including founding member HVO_0146 from Haloferax volcanii, are archaeal homologs of bacterial phosphatidylserine decarboxylases (PssD). HVO_0146, and the PssA homolog HVO_1143, were shown be required for archaeosortase A (ArtA)-mediated removal of the PGF-CTERM protein-sorting signal and replacement with a large, prenyl-derived, C-terminal anchoring lipid moiety that is proposed to be archaetidylethanolamine. NF039232.4 PF19096.5 DUF5784 36.3 36.3 328 subfamily Y Y N DUF5784 family protein 183963 Halobacteria class 603 EBI-EMBL Family of unknown function (DUF5784) DUF5784 family protein Family of unknown function predominantly found in Halobacteria. (from Pfam) NF039233.4 PF19099.5 DUF5786 26.9 26.9 55 subfamily Y Y N DUF5786 family protein 183963 Halobacteria class 1378 EBI-EMBL Family of unknown function (DUF5786) DUF5786 family protein Family of unknown function predominantly found in Halobacteria. (from Pfam) NF039866.4 PF19115.5 DUF5800 26.8 26.8 64 subfamily Y Y N DUF5800 family protein 183963 Halobacteria class 470 EBI-EMBL Family of unknown function (DUF5800) DUF5800 family protein This is a family of proteins of unknown function predominantly found in Halobacteria. (from Pfam) NF039868.4 PF19118.5 DUF5802 28.9 28.9 113 subfamily Y Y N DUF5802 family protein 183963 Halobacteria class 575 EBI-EMBL Family of unknown function (DUF5802) DUF5802 family protein Family of unknown function predominantly found in Halobacteria. (from Pfam) NF039871.4 PF19137.5 DUF5820 33.7 33.7 117 subfamily Y Y N DUF5820 family protein 183963 Halobacteria class 589 EBI-EMBL Family of unknown function (DUF5820) DUF5820 family protein This is a family of unknown function predominantly found in Halobacteria. (from Pfam) NF040010.4 PF19646.4 DUF6149 27 27 200 subfamily Y Y N DUF6149 family protein 183963 Halobacteria class 590 EBI-EMBL Family of unknown function (DUF6149) DUF6149 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in archaea. Proteins in this family are typically between 191 and 204 amino acids in length. (from Pfam) NF041313.1 UDPGP_AglF_Halo 400 400 234 equivalog Y Y N UTP--glucose-1-phosphate uridylyltransferase AglF aglF 2.7.7.9 GO:0003983 18631242,20487296,22730124 183963 Halobacteria class 786 NCBIFAM UTP--glucose-1-phosphate uridylyltransferase AglF NF041315.1 malate_syn_AceB_Halo 780 780 429 equivalog Y Y N malate synthase AceB aceB 2.3.3.9 GO:0004474,GO:0006097,GO:0006099 11513957,9738442 183963 Halobacteria class 294 NCBIFAM malate synthase AceB NF041370.1 desamp_Halo 130 130 133 equivalog Y Y N desampylase 3.4.19.15 GO:0006508,GO:0008237 22970855,24097257 183963 Halobacteria class 461 NCBIFAM desampylase NF041389.1 dodecin_Halo 100 100 65 equivalog Y Y N dodecin GO:1902444 12679016,17027852,19224924 183963 Halobacteria class 486 NCBIFAM dodecin Dodecin is a dodecameric protein able to bind riboflavin and related molecules. NF041391.1 DPhHxTase_Halo 375 375 213 equivalog Y Y N dolichyl-phosphate hexose transferase 2.4.1.- GO:0016757 20802039 183963 Halobacteria class 495 NCBIFAM dolichyl-phosphate hexose transferase NF041394.1 GtaseAglG_Halo 440 440 304 equivalog Y Y N glucosyl-dolichyl phosphate glucuronosyltransferase aglG 2.4.1.356 GO:0016757,GO:0045232 18631242,28809486 183963 Halobacteria class 448 NCBIFAM glucosyl-dolichyl phosphate glucuronosyltransferase NF041396.1 TranRegLrp_Halo 190 190 149 equivalog Y Y N HTH-type transcriptional regulator Lrp lrp GO:0043565 20509863 183963 Halobacteria class 746 NCBIFAM HTH-type transcriptional regulator Lrp NF041398.1 GluDhGdhB_Halo 620 620 410 equivalog Y Y N glutamate dehydrogenase GdhB gdhB 1.4.1.- GO:0016639 15780999 183963 Halobacteria class 820 NCBIFAM glutamate dehydrogenase GdhB NF047393.1 TransRegTbspHalo 300 300 270 equivalog Y Y N transcriptional regulator TbsP tbsP 38204420 183963 Halobacteria class 686 NCBIFAM transcriptional regulator TbsP NF047750.1 SAMPActivE1UbaA 450 450 270 equivalog Y Y N SAMP-activating enzyme E1 ubaA 2.7.7.- GO:0005524,GO:0008641,GO:0016779 21368171,24097257,24906001 183963 Halobacteria class 638 NCBIFAM SAMP-activating enzyme E1 NF027124.5 PF15788.10 DUF4705 27 6.8 52 domain Y Y N DUF4705 domain-containing protein 1848904 Capnocytophaga stomatis species 1 EBI-EMBL Domain of unknown function (DUF4705) Domain of unknown function (DUF4705) DUF4705 is a family of repeated domains that is found in eukaryotes. It can occur up to 10 times in any one sequence. The repeat is rich in glycine and proline residues. (from Pfam) NF041192.2 encap_f4c 90 90 97 exception Y Y N family 4C encapsulin nanocompartment shell protein GO:0140737 34362927,35146412 1853224 Rhodothermales order 13 NCBIFAM family 4C encapsulin nanocompartment shell protein Capsid-like encapsulin nanocompartments are commonly found in bacteria and archaea. Encapsulin nanocompartments, which are assembled from shell proteins, encapsulate various cargo proteins, typically peroxidases or ferritin-like proteins, to protect cells from oxidative stress caused by peroxide. NF008991.0 PRK12334 PRK12334.2-3 696 696 454 equivalog Y Y N nucleoside triphosphate pyrophosphohydrolase 3.6.1.9 1854 Frankia genus 8 NCBI Protein Cluster (PRK) nucleoside triphosphate pyrophosphohydrolase nucleoside triphosphate pyrophosphohydrolase NF040470.1 blaEAM 660 660 318 exception Y Y Y EAM family subclass B3 metallo-beta-lactamase blaEAM 3.5.2.6 GO:0008800 22850693 1855416 Qipengyuania genus 5 NCBIFAM EAM family subclass B3 metallo-beta-lactamase EAM (Erythrobacter aquimaris metallo-beta-lactamase), a subclass B3 enzyme, is one of five related chromosomal subclass B3 metallo-beta-lactamases from various species of Erythrobacter spp., (EAM, ECM, EFM, ELM, EVM). Erythrobacter aquimaris is also called Qipengyuania aquimaris. EAM-1 showed small to negligible activity against three tested carbapenems (IPM, MEM, ETP), but significant activity against piperacillin (PIP) and various cephalosporins. NF043078.1 MMSYN1_0168 800 800 649 equivalog Y Y N oligopeptide ABC transporter ATP-binding protein OppF oppF GO:0006810,GO:0042626 20488990,31308405 186328 Entomoplasmatales order 59 NCBIFAM oligopeptide ABC transporter ATP-binding protein OppF NF009929.0 PRK13390 PRK13390.1 951 951 501 equivalog Y N N acyl-CoA synthetase 1866885 Mycolicibacterium genus 17 NCBI Protein Cluster (PRK) acyl-CoA synthetase acyl-CoA synthetase NF012218.0 erm_38_23S_MT 800 800 386 exception Y Y Y 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(38) erm(38) 16127056 1866885 Mycolicibacterium genus 10 NCBIFAM 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(38) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(38) Members of this family are Erm(38), a 23S rRNA methyltransferase that confers intrinsic resistance to erythromycin in species that include Mycobacterium smegmatis and Mycobacterium goodii. NF000779.0 PRK00052 PRK00052.3-5 405 405 257 equivalog Y Y N prolipoprotein diacylglyceryl transferase 2.4.99.- 186801 Clostridia class 50 NCBI Protein Cluster (PRK) prolipoprotein diacylglyceryl transferase prolipoprotein diacylglyceryl transferase NF000809.0 PRK00059 PRK00059.1 303 303 336 equivalog Y Y N peptidylprolyl isomerase 5.2.1.8 186801 Clostridia class 573 NCBI Protein Cluster (PRK) peptidylprolyl isomerase peptidylprolyl isomerase Cis/trans isomerase of peptidylprolyl NF000867.0 PRK00078 PRK00078.1 249 249 192 equivalog Y Y N Maf-like protein 186801 Clostridia class 495 NCBI Protein Cluster (PRK) Maf-like protein Maf-like protein NF000934.0 PRK00092 PRK00092.3-1 175 175 153 equivalog Y Y N ribosome maturation factor RimP rimP 186801 Clostridia class 386 NCBI Protein Cluster (PRK) ribosome maturation protein RimP ribosome maturation factor RimP NF001775.0 PRK00513 PRK00513.1-6 292 292 210 equivalog Y Y N septum site-determining protein MinC minC 186801 Clostridia class 367 NCBI Protein Cluster (PRK) septum formation inhibitor septum site-determining protein MinC NF002329.0 PRK01286 PRK01286.1-4 494 494 342 equivalog Y Y N deoxyguanosinetriphosphate triphosphohydrolase 186801 Clostridia class 520 NCBI Protein Cluster (PRK) deoxyguanosinetriphosphate triphosphohydrolase-like protein deoxyguanosinetriphosphate triphosphohydrolase NF004047.0 PRK05564 PRK05564.1 282 282 313 equivalog Y Y N DNA polymerase III subunit delta' 2.7.7.7 186801 Clostridia class 497 NCBI Protein Cluster (PRK) DNA polymerase III subunit delta' DNA polymerase III subunit delta' Catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA NF004057.0 PRK05575 PRK05575.1 311 311 207 equivalog Y Y N precorrin-8X methylmutase 5.4.99.61 186801 Clostridia class 399 NCBI Protein Cluster (PRK) precorrin-8X methylmutase precorrin-8X methylmutase Catalyzes the interconversion of precorrin-8X and cobyrinic acid NF004109.0 PRK05595 PRK05595.1 737 737 444 equivalog Y Y N replicative DNA helicase 3.6.4.12 186801 Clostridia class 373 NCBI Protein Cluster (PRK) replicative DNA helicase replicative DNA helicase Unwinds double stranded DNA NF004473.0 PRK05807 PRK05807.1 178 178 136 equivalog Y Y N S1 domain-containing RNA-binding protein 186801 Clostridia class 349 NCBI Protein Cluster (PRK) hypothetical protein S1 domain-containing RNA-binding protein NF004484.0 PRK05815 PRK05815.3-2 234 234 226 equivalog Y Y N F0F1 ATP synthase subunit A 7.1.2.2 186801 Clostridia class 390 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit A F0F1 ATP synthase subunit A NF006060.0 PRK08207 PRK08207.1-3 653 653 477 equivalog Y Y N coproporphyrinogen III oxidase 186801 Clostridia class 688 NCBI Protein Cluster (PRK) coproporphyrinogen III oxidase coproporphyrinogen III oxidase NF006170.0 PRK08311 PRK08311.1-1 271 271 221 equivalog Y Y N RNA polymerase sigma factor SigI sigI 186801 Clostridia class 55 NCBI Protein Cluster (PRK) putative RNA polymerase sigma factor SigI RNA polymerase sigma factor SigI NF006178.0 PRK08311 PRK08311.2-6 306 306 236 equivalog Y Y N RNA polymerase sigma factor SigI sigI 186801 Clostridia class 24 NCBI Protein Cluster (PRK) putative RNA polymerase sigma factor SigI RNA polymerase sigma factor SigI NF009411.0 PRK12772 PRK12772.1 739 739 610 equivalog Y Y N fused FliR family export protein/FlhB family type III secretion system protein 186801 Clostridia class 663 NCBI Protein Cluster (PRK) bifunctional flagellar biosynthesis protein FliR/FlhB fused FliR family export protein/FlhB family type III secretion system protein NF010122.0 PRK13599 PRK13599.1 456 456 220 equivalog Y Y N peroxiredoxin 1.11.1.24 186801 Clostridia class 13 NCBI Protein Cluster (PRK) putative peroxiredoxin peroxiredoxin Alkyl hydroperoxidase; catalyze the reduction of hydrogen peroxide to water and the reduction of alkyl hydroperoxides to the corresponding alcohols NF010157.0 PRK13636 PRK13636.1 463 463 285 equivalog Y N N cobalt transporter ATP-binding subunit 186801 Clostridia class 77 NCBI Protein Cluster (PRK) cobalt transporter ATP-binding subunit cobalt transporter ATP-binding subunit NF010218.0 PRK13678 PRK13678.2-1 96 96 83 equivalog Y N N hypothetical protein 186801 Clostridia class 177 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010586.0 PRK13979 PRK13979.1 1475 1475 957 equivalog Y Y N DNA topoisomerase IV subunit A 186801 Clostridia class 850 NCBI Protein Cluster (PRK) DNA topoisomerase IV subunit A DNA topoisomerase IV subunit A NF010743.0 PRK14145 PRK14145.1 186 186 200 equivalog Y Y N nucleotide exchange factor GrpE grpE 186801 Clostridia class 39 NCBI Protein Cluster (PRK) heat shock protein GrpE nucleotide exchange factor GrpE With DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins NF010769.0 PRK14172 PRK14172.1 392 392 278 equivalog Y N N bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase 186801 Clostridia class 436 NCBI Protein Cluster (PRK) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase NF010890.0 PRK14297 PRK14297.1 569 569 382 equivalog Y Y N molecular chaperone DnaJ dnaJ 186801 Clostridia class 478 NCBI Protein Cluster (PRK) chaperone protein DnaJ molecular chaperone DnaJ Chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion NF011127.0 PRK14553 PRK14553.1-7 122 122 123 equivalog Y Y N ribosomal-processing cysteine protease Prp 186801 Clostridia class 247 NCBI Protein Cluster (PRK) hypothetical protein ribosomal-processing cysteine protease Prp NF022939.5 PF11503.13 YNR034W-A-like 25 25 72 domain Y Y N YNR034W-A-like family protein 26206314,31579828 186801 Clostridia class 3 EBI-EMBL YNR034W-A-like YNR034W-A-like family protein This family of proteins is predominantly found in Saccharomycetales, including YNR034W-A (also known as Ego4) and YCR075W-A (Ego2) from Saccharomyces cerevisiae. Ego2 is a component of the yeast EGO complex (EGOC), which is responsible for the amino acid-dependent activation of the target of rapamycin complex 1 (TORC1). Ego2 adopts a Roadblock domain fold that consists of a central core beta-sheet of five anti-parallel beta-strands flanked by a long alpha-helix on the bottom side. Ego4 shows a similar configuration. It interacts with the GTPase Gtr2, but its specific function remains unknown [1,2]. [1]. 31579828. Structural insights into the EGO-TC-mediated membrane tethering of the TORC1-regulatory Rag GTPases. Zhang T, Peli-Gulli MP, Zhang Z, Tang X, Ye J, De Virgilio C, Ding J;. Sci Adv. 2019;5:eaax8164. [2]. 26206314. Crystal structure of the Ego1-Ego2-Ego3 complex and its role in promoting Rag GTPase-dependent TORC1 signaling. Powis K, Zhang T, Panchaud N, Wang R, De Virgilio C, Ding J;. Cell Res. 2015;25:1043-1059. (from Pfam) NF024066.5 PF12653.12 DUF3785 27 27 136 PfamAutoEq Y Y N DUF3785 family protein 186801 Clostridia class 463 EBI-EMBL Protein of unknown function (DUF3785) DUF3785 family protein This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. These proteins share two CXXC motifs suggesting these are zinc binding proteins. This protein is found in clostridia in an operon with three signalling proteins, suggesting this protein may be a DNA-binding transcription regulator downstream of an as yet unknown signalling pathway (Bateman A pers obs). (from Pfam) NF024385.5 PF12983.12 DUF3867 27 27 185 PfamAutoEq Y Y N DUF3867 family protein 186801 Clostridia class 519 EBI-EMBL Protein of unknown function (DUF3867) DUF3867 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 190 amino acids in length. (from Pfam) NF024395.5 PF12993.12 DUF3877 27 27 173 PfamAutoEq Y Y N DUF3877 family protein 19321416 186801 Clostridia class 763 EBI-EMBL Domain of unknown function, E. rectale Gene description (DUF3877) DUF3877 family protein Based on Eubacterium rectale gene EUBREC_0237. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14737), it appears to be upregulated in the presence of Bacteroides thetaiotaomicron vs when isolated in culture [1]. [1]. 19321416. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ et al. Proc Natl Acad Sci U S A 2009 Apr 7;106(14):5859-64. (from Pfam) NF025979.5 PF14628.11 DUF4454 25 25 210 domain Y Y N DUF4454 domain-containing protein 186801 Clostridia class 182 EBI-EMBL Domain of unknown function (DUF4454) Domain of unknown function (DUF4454) This C-terminal domain is found only on a small subgroup of proteins from Gram-positive Clostridiales that also carry a YARHG domain, Pfam:PF13308. (from Pfam) NF026757.5 PF15417.11 DUF4624 25 25 132 PfamAutoEq Y Y N DUF4624 family lipoprotein 186801 Clostridia class 122 EBI-EMBL Domain of unknown function (DUF4624) DUF4624 family lipoprotein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length. (from Pfam) NF027549.5 PF16224.10 DUF4883 27.1 27.1 119 PfamAutoEq Y Y N DUF4883 family protein 186801 Clostridia class 555 EBI-EMBL DOmain of unknown function (DUF4883) DUF4883 family protein This family consists of several uncharacterized proteins around 160 residues in length and is mainly found in various Clostridium species. The function of this family is unknown. (from Pfam) NF033850.1 LCxxNW 40 40 61 subfamily Y Y N mobility-associated LCxxNW protein 186801 Clostridia class 126 NCBIFAM mobility-associated LCxxNW protein mobility-associated LCxxNW protein This protein belongs to a family of small proteins, about 65 amino acids long, with three invariant Cys residues, including one in the motif LCxxNW, for which the family is named. Member proteins are found in contexts that suggests they are accessory proteins of mobile elements. The context includes members of families PF01695, PF01610, and PF00665, all associated with transposition and/or integration. NF035950.1 RumC_sactiRiPP 40 40 64 subfamily Y Y N RumC family sactipeptide 31337708 186801 Clostridia class 44 NCBIFAM RumC family sactipeptide The founding member of this family of radical SAM/SPASM-modified sactipeptide bacteriocins is ruminococcin C1, AEC03333.1 from Ruminococcus gnavus. This bacteriocin, from a human gut bacterium, is interesting because of its anti-clostridial activity. Known homologs to RumC1 average about 65 amino acids in length and have four invariant Cys residues. This RiPP (ribosomally translated, post-translationally modified peptide natural product), in the ruminococcin C family, is modified by a radical SAM/SPASM domain protein to have several cross-bridges from Cys sulfur atoms to alpha carbons of another amino acids. It is therefore defined as a sactipeptide. NF035954.1 ocin_CA_C0660 60 60 64 subfamily Y Y N CA_C0660 family putative sactipeptide bacteriocin 186801 Clostridia class 26 NCBIFAM CA_C0660 family putative sactipeptide bacteriocin Members of this family are Cys-rich peptides about 65 amino acids in length, regularly found in the vicinity of the radical SAM/SPASM domain enzymes. The most closely related such radical SAM enzyme is the RiPP modification enzyme that introduces sulfur-to-alpha-carbon peptide (sactipeptide) modification in ruminococcin C, whose precursor is very similar in length and in Cys content and arrangement. NF037345.5 PF18425.6 CspB_prodomain 25 25 89 domain Y N N Csp protease B prodomain 23408892 186801 Clostridia class 2663 EBI-EMBL Csp protease B prodomain Csp protease B prodomain Csp proteases (Csps) and the subtilase protease family Subtilases are serine proteases that contain a catalytic triad in the order of Asp, His and Ser. Structure analysis reveals that Csps are subtilisin-like proteases with two distinctive functional features: a central jellyroll domain and a retained prodomain. The prodomain adopts a similar fold to the prodomains of related subtilisin-like proteases with the C-terminal region extending deep into the catalytic cleft. However, unlike the majority of subtilisin-like proteases, the prodomain stays bound to the subtilase domain via a network of interactions that result in tighter prodomain binding relative to other subtilases. Finally the prodomain acts as both an intramolecular chaperone and an inhibitor of CspB protease activity [1]. [1]. 23408892. Structural and functional analysis of the CspB protease required for Clostridium spore germination. Adams CM, Eckenroth BE, Putnam EE, Doublie S, Shen A;. PLoS Pathog. 2013;9:e1003165. (from Pfam) NF038344.1 bile_CoA_BaiB 650 650 504 exception Y Y N bile acid--CoA ligase BaiB baiB 6.2.1.7 1551828 186801 Clostridia class 35 NCBIFAM bile acid--CoA ligase BaiB NF040732.3 DsrE_rel_SaoD 169 169 110 equivalog Y Y N DsrE-related protein SaoD saoD GO:0018942 36598231 186801 Clostridia class 105 NCBIFAM DsrE-related protein SaoD NF040756.1 corr_regen_AcsV 800 800 632 exception Y Y N corrinoid activation/regeneration protein AcsV acsV 21966917,22479398,32967909 186801 Clostridia class 588 NCBIFAM corrinoid activation/regeneration protein AcsV NF040758.1 CODH_ACS_meth 370 370 261 exception Y Y N carbon monoxide dehydrogenase/acetyl-CoA synthase methytransferase subunit acsE 32967909 186801 Clostridia class 258 NCBIFAM carbon monoxide dehydrogenase/acetyl-CoA synthase methytransferase subunit NF040759.1 WLP_AcsD 430 430 312 exception Y Y N acetyl-CoA decarbonylase/synthase complex subunit delta acsD 22479398,32967909 186801 Clostridia class 333 NCBIFAM acetyl-CoA decarbonylase/synthase complex subunit delta This component of the acetyl-CoA decarbonylase/synthase complex, as found in acetogens with the Wood-Ljungdahl pathway, is the corrinoid iron-sulfur protein small subunit, AcsD. NF040762.1 Hydr_FeFe_Clost 900 900 572 exception Y Y N ferredoxin hydrogenase 1.12.7.2 17681007,9836629 186801 Clostridia class 334 NCBIFAM ferredoxin hydrogenase, clostridial type Members of this family of hydrogenases share full-length homology with many other iron-only hydrogenases, but differ in transferrring electrons only to ferredoxins (EC 1.12.7.2) and not to NAD(P)+. NF040794.1 sarcosine_GrdF 800 800 435 exception Y Y N sarcosine reductase complex component B subunit beta grdF 24926057 186801 Clostridia class 199 NCBIFAM sarcosine reductase complex component B subunit beta NF040919.1 Clostri_philic 40 40 38 subfamily Y Y N clostri-philic family protein 186801 Clostridia class 156 NCBIFAM clostri-philic family protein Members of this unusual, uncharacterized protein family are small in size (about 45 amino acids), rich in charged residues and therefore highly hydrophilic, and largely restricted to the genus Clostridium. We propose the name clostri-philic. The function is unknown. NF041287.1 lipo_GerS_rel 100 100 201 equivalog Y Y N germination lipoprotein GerS-related protein 29950380 186801 Clostridia class 482 NCBIFAM germination lipoprotein GerS-related protein Members of this family are related to the lipoprotein GerS that is found in the spore cortex of bacterial such as Clostridium difficile, and that regulates the activity of other spore cortex proteins. Similar between members of this family and GerS family lipoproteins NF041552.1 TF_PrdR 795 795 577 equivalog Y Y N sigma-54 dependent transcriptional regulator PrdR prdR 186801 Clostridia class 228 NCBIFAM sigma-54 dependent transcriptional regulator PrdR NF042606.3 PF20574.3 DUF6783 22.8 22.8 60 domain Y Y N DUF6783 domain-containing protein 186801 Clostridia class 4395 EBI-EMBL Family of unknown function (DUF6783) Family of unknown function (DUF6783) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 61 and 97 amino acids in length. (from Pfam) NF042675.3 PF20342.3 DUF6637 27 27 103 subfamily Y Y N DUF6637 family protein 186801 Clostridia class 119 EBI-EMBL Family of unknown function (DUF6637) DUF6637 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. (from Pfam) NF042803.3 PF20564.3 DUF6774 25 25 28 domain Y Y N DUF6774 domain-containing protein 186801 Clostridia class 341 EBI-EMBL Family of unknown function (DUF6774) Family of unknown function (DUF6774) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 57 and 70 amino acids in length. There is a conserved sequence motif QLGDTL. (from Pfam) NF043038.1 ABCF_CplR 780 780 544 exception Y Y Y ABC-F type ribosomal protection protein CplR cplR 36951104 186801 Clostridia class 490 NCBIFAM ABC-F type ribosomal protection protein CplR CplR (Clostridial pleuromutilin and lincosamide resistance) is an intrinsic member of the ABC-F type ribosomal protection protein family in multiple species of Clostridium and Clostridioides, including Clostridium perfringens and Clostridioides difficile. Contributes to intrinsic pleuromutilin, lincosamide and streptogramin A resistance. NF045111.2 PF21615.2 CBM-like_2 27 27 126 domain Y N N Carbohydrate binding module-like 186801 Clostridia class 12 EBI-EMBL Carbohydrate binding module-like Carbohydrate binding module-like This domain is found in a a group of bacterial proteins, including the uncharacterised Fibronectin type-III domain-containing protein from Agathobacter rectalis (Swiss:C4ZEB7). It adopts a jelly roll structure. (from Pfam) NF045114.2 PF21640.2 LytM_N 27 27 88 domain Y N N LytM, N-terminal domain 186801 Clostridia class 138 EBI-EMBL LytM, N-terminal domain LytM, N-terminal domain This domain is found at the N-terminal end of the peptidase from the M23 family LytM found in Ruminococcus gnavus and similar proteins predominantly found in firmicutes. This protein is predicted to have glycyl-glycine endopeptidase activity. This domain shows an all-alpha structure. (from Pfam) NF046218.1 PF22239.1 DUF6947 27 27 134 domain Y Y N DUF6947 domain-containing protein 186801 Clostridia class 13 EBI-EMBL Domain of unknown function (DUF6947) Domain of unknown function (DUF6947) This is a domain found in a group of uncharacterised bacterial sequences whose function is unknown. This domain adopts a galactose-binding-like structure (PDBe:4lr4). (from Pfam) NF046779.1 PF22609.1 Fe_hydrogense_Fe-S_bd 27 27 41 domain Y N N Iron hydrogenase 1-like, iron-sulfur centre-binding domain 10529166,28722011,29896366,30413719,32796105 186801 Clostridia class 350 EBI-EMBL Iron hydrogenase 1-like, iron-sulfur centre-binding domain Iron hydrogenase 1-like, iron-sulfur centre-binding domain This entry represents a Fe-S centre binding domain found in iron hydrogenases [1-5]. Paper describing PDB structure 1c4a. [1]. 10529166. Binding of exogenously added carbon monoxide at the active site of the iron-only hydrogenase (CpI) from Clostridium pasteurianum. Lemon BJ, Peters JW;. Biochemistry. 1999;38:12969-12973. Paper describing PDB structure 4xdc. [2]. 29896366. A structural view of synthetic cofactor integration into [FeFe]-hydrogenases. Esselborn J, Muraki N, Klein K, Engelbrecht V, Metzler-Nolte N, Apfel UP, Hofmann E, Kurisu G, Happe T;. Chem Sci. 2016;7:959-968. Paper describing PDB structure 5la3. [3]. 28722011. Accumulating the hydride state in the catalytic cycle of [FeFe]-hydrogenases. Winkler M, Senger M, Duan J, Esselborn J, Wittkamp F, Hofmann E, Apfel UP, Stripp ST, Happe T;. Nat Commun. 2017;8:16115. Paper describing PDB structure 6gly. [4]. 30413719. Crystallographic and spectroscopic assignment of the proton transfer pathway in [FeFe]-hydrogenases. Duan J, Senger M, Esselborn J, Engelbrecht V, Wittkamp F, Apfel UP, Hofmann E, Stripp ST, Happe T, Winkler M;. Nat Commun. 2018;9:4726. Paper describing PDB structure 6yf4. [5]. 32796105. The roles of long-range proton-coupled electron transfer in the directionality and efficiency of [FeFe]-hydrogenases. Lampret O, Duan J, Hofmann E, Winkler M, Armstrong FA, Happe T;. Proc Natl Acad Sci U S A. 2020;117:20520-20529. (from Pfam) TIGR02828.1 TIGR02828 TIGR02828 154.4 154.4 188 hypoth_equivalog_domain Y N N putative membrane fusion protein 186801 Clostridia class 29 JCVI putative membrane fusion protein putative membrane fusion protein Members of this family show similarity to the members of TIGR00999, the membrane fusion protein (MFP) cluster 2 family, which is linked to RND transport systems. TIGR04333.1 TIGR04333 Clo7Bot_mod_Cys 31 31 34 subfamily Y Y N Clo7bot family Cys-rich peptide 186801 Clostridia class 154 JCVI Cys-rich peptide, Clo7bot family Clo7bot family Cys-rich peptide Members of this protein family range in size from 34 to 53 residues, including from four to seven Cys residues. Multiple strains of Clostridium botulinum show seven tandem members upstream of a radical SAM/SPASM domain protein likely to act as a ribosomal natural product maturase. By analogy to subtilosin A, the Cys residues are likely targets for modifications that may introduce new crosslinks. Across multiple strains of Clostridium botulinum and C. sporogenes, the adjacent radical SAM enzyme is nearly invariant. TIGR04334.1 TIGR04334 rSAM_Clo7bot 600 600 440 equivalog Y Y N radical SAM/SPASM domain Clo7bot peptide maturase ctpM GO:0031179,GO:0051539,GO:1904047 186801 Clostridia class 99 JCVI radical SAM/SPASM domain Clo7bot peptide maturase radical SAM/SPASM domain Clo7bot peptide maturase In multiple strains of Clostridium botulinum, this single radical SAM domain protein occurs next to a tandem array of seven homologous Cys-rich small peptides (see TIGR04333). Because this radical SAM enzyme contains the SPASM domain, associated with peptide modification, it is proposed to modify all seven C. botulinum targets, hence the name Clo7bot for this system. Suggested gene symbol is ctpM (Clostridial Tandem Peptide Maturase). NF000372.1 D_ala_D_lac_VanI 700 700 341 exception Y Y Y D-alanine--(R)-lactate ligase VanI vanI 6.1.2.1 GO:0005737,GO:0008716,GO:0046872 186802 Eubacteriales order 15 NCBIFAM D-alanine--(R)-lactate ligase VanI D-alanine--(R)-lactate ligase VanI NF002055.0 PRK00886 PRK00886.1-4 345 345 236 equivalog Y Y N 2-phosphosulfolactate phosphatase family protein 186802 Eubacteriales order 487 NCBI Protein Cluster (PRK) 2-phosphosulfolactate phosphatase 2-phosphosulfolactate phosphatase family protein This bacterial enzyme is related to archaeal 2-phosphosulfolactate phosphatase, involved in biosynthesis of coenzyme M, a cofactor involved in methanogenesis in the archaea. It may differ in function. NF006173.0 PRK08311 PRK08311.2-1 287 287 251 subfamily Y Y N RNA polymerase sigma factor SigI sigI 186802 Eubacteriales order 119 NCBI Protein Cluster (PRK) putative RNA polymerase sigma factor SigI RNA polymerase sigma factor SigI NF007035.0 PRK09496 PRK09496.2-2 521 521 455 equivalog Y Y N Trk system potassium transporter TrkA trkA 186802 Eubacteriales order 112 NCBI Protein Cluster (PRK) potassium transporter peripheral membrane component Trk system potassium transporter TrkA NF010681.0 PRK14081 PRK14081.1 842 842 667 equivalog Y Y N triple tyrosine motif-containing protein 186802 Eubacteriales order 660 NCBI Protein Cluster (PRK) triple tyrosine motif-containing protein triple tyrosine motif-containing protein NF011133.0 PRK14553 PRK14553.3-2 171 171 113 equivalog Y Y N ribosomal-processing cysteine protease Prp 186802 Eubacteriales order 10 NCBI Protein Cluster (PRK) hypothetical protein ribosomal-processing cysteine protease Prp NF038189.1 VI_Cas13d 150 150 882 equivalog Y Y N type VI-D CRISPR-associated RNA-guided ribonuclease Cas13d cas13d 29551514,31857715 186802 Eubacteriales order 79 NCBIFAM type VI-D CRISPR-associated RNA-guided ribonuclease Cas13d NF040492.1 not_ScfB 855 855 450 exception Y Y N ScfB-related radical SAM/SPASM orphan maturase nscfB 186802 Eubacteriales order 7 NCBIFAM ScfB-related radical SAM/SPASM orphan maturase Members of this rare protein family are SPASM domain-containing radical SAM enzymes that closely resembly ScfB, the thioether bridge-forming peptide modification enzyme of the SCIFF (Six Cysteines in Forty-Five residues) RiPP precursor. However, they form their own, distinctive clade within is ScfB-like family, are noticeably different toward the N-terminus, and are found in genomic contexts in which no ScfA-like encoded protein can be found. The protein is designated an orphan maturase because no substrate has been identified. NF047660.1 HUIPC_Trx_selen 105 105 91 equivalog Y Y N HUIPC motif thioredoxin-like (seleno)protein 186802 Eubacteriales order 6 NCBIFAM HUIPC motif thioredoxin-like (seleno)protein NF028533.5 PF17224.8 DUF5300 27 27 99 subfamily Y Y N DUF5300 family protein 186803 Lachnospiraceae family 44 EBI-EMBL Domain of unknown function (DUF5300) DUF5300 family protein This small family of proteins found in Clostridiales is functionally uncharacterized. Proteins in this family are around 130 amino acids in length. Based on NMR structure 2MCA, it forms a beta-sandwich structure consisting of two 4-stranded antiparallel b-strands. The structure is very similar to glutamine glutamyltransferases (1l9n) and peptide transporters (5a9h). (from Pfam) NF035951.1 rSAM_RumMC 720 720 510 equivalog Y Y N RumMC family radical SAM sactipeptide maturase 31337708 186803 Lachnospiraceae family 24 NCBIFAM RumMC family radical SAM sactipeptide maturase The RumMC family of radical SAM/SPASM domain peptide modification enzymes creates sulfur-to-alpha-carbon (sactipeptide) linages in RiPP peptide natural products in the family of ruminococcin C. NF040282.4 PF19400.4 DUF5975 25 25 125 subfamily Y Y N DUF5975 family protein 186803 Lachnospiraceae family 12 EBI-EMBL Family of unknown function (DUF5975) DUF5975 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000486) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide). (from Pfam) NF011350.0 PRK14768 PRK14768.1 210 210 148 equivalog Y N N lipoprotein signal peptidase 186804 Peptostreptococcaceae family 87 NCBI Protein Cluster (PRK) lipoprotein signal peptidase lipoprotein signal peptidase NF040808.2 CspC_non_triad 675 650 556 exception Y Y N bile acid germinant receptor pseudoprotease CspC cspC 23675301,24814671,27573580,32781028 186804 Peptostreptococcaceae family 390 NCBIFAM bile acid germinant receptor pseudoprotease CspC Members of this family share homology with MEROPS S8 family serine proteases, but with substitutions that replace key catalytic residues, as seen in CD2246 from Clostridium difficile. The related germination-specific protease CspC of Clostridium perfringens, outside the scope of this model, retains its serine protease catalytic triad residues. Adjacent to CD2246 is the fusion protein CD2247, CspBA, in which the CspB region retains its subtilisin-like catalytic triad while the CspA, like CspC, has lost it. NF040809.1 germ_prot_CspBA 1250 1250 1099 exception Y Y N bifunctional germination protease/germinant receptor pseudoprotease CspBA cspBA 3.4.21.- 24814671 186804 Peptostreptococcaceae family 295 NCBIFAM bifunctional germination protease/germinant receptor pseudoprotease CspBA CspBA, as found in Clostridium difficile, is translated as a fusion protein, but cleaved into separate homologous CspB and CspA proteins during spore formation. CspB is a protease, required to active SleC by cleaving it in order to trigger germination. CspA, like the bile salt germinant receptor CspC (encoded by the adjacent gene), has lost the catalytic residues necessary for subtilisin-like serine protease activity. NF041286.1 lipo_GerS 175 175 196 equivalog Y Y N germination lipoprotein GerS gerS 29950380,31858953 186804 Peptostreptococcaceae family 133 NCBIFAM germination lipoprotein GerS NF041648.1 spore_exo_CotA 75 75 215 equivalog Y Y N CotA family spore coat protein 23335421,32714296 186804 Peptostreptococcaceae family 128 NCBIFAM CotA family spore coat protein CotA, as the term is used in Clostridium difficile, is a spore coat protein also reportedly detected also in exosporium. Homologs are found in a number of related endospore-forming bacteria. NF001071.0 PRK00118 PRK00118.2-1 160 160 117 equivalog Y Y N putative DNA-binding protein 186814 Thermoanaerobacteraceae family 11 NCBI Protein Cluster (PRK) putative DNA-binding protein putative DNA-binding protein NF004141.0 PRK05618 PRK05618.4-4 309 309 201 equivalog Y Y N 50S ribosomal protein L25/general stress protein Ctc 186814 Thermoanaerobacteraceae family 26 NCBI Protein Cluster (PRK) 50S ribosomal protein L25/general stress protein Ctc 50S ribosomal protein L25/general stress protein Ctc NF006405.0 PRK08652 PRK08652.1-3 455 455 367 equivalog Y N N acetylornithine deacetylase 186814 Thermoanaerobacteraceae family 9 NCBI Protein Cluster (PRK) acetylornithine deacetylase acetylornithine deacetylase NF006843.0 PRK09357 PRK09357.2-4 786 786 431 equivalog Y Y N dihydroorotase 3.5.2.3 186814 Thermoanaerobacteraceae family 35 NCBI Protein Cluster (PRK) dihydroorotase dihydroorotase NF010124.0 PRK13601 PRK13601.1 124 124 84 equivalog Y N N putative L7Ae-like ribosomal protein 186814 Thermoanaerobacteraceae family 16 NCBI Protein Cluster (PRK) putative L7Ae-like ribosomal protein putative L7Ae-like ribosomal protein NF047601.1 MscSThanab 500 500 280 equivalog Y Y N small-conductance mechanosensitive channel MscS mscS GO:0008381,GO:0042802 23074248 186814 Thermoanaerobacteraceae family 23 NCBIFAM small-conductance mechanosensitive channel MscS NF000060.1 MFS_efflux_LmrB 800 800 479 exception Y Y N lincomycin efflux MFS transporter Lmr(B) lmr(B) 12499232 186817 Bacillaceae family 250 NCBIFAM lincomycin efflux MFS transporter Lmr(B) lincomycin efflux MFS transporter Lmr(B) The lin-2 mutant, described in PMID:12499232, alters Lmr(B) expression in Bacillus subtilis and allows Lmr(B) to confer resistance to lincomycin. NF002435.0 PRK01581 PRK01581.1 537 537 374 equivalog Y Y N polyamine aminopropyltransferase 2.5.1.16 186817 Bacillaceae family 1188 NCBI Protein Cluster (PRK) spermidine synthase polyamine aminopropyltransferase NF002603.0 PRK02260 PRK02260.1-3 267 267 157 equivalog Y Y N S-ribosylhomocysteine lyase 4.4.1.21 186817 Bacillaceae family 813 NCBI Protein Cluster (PRK) S-ribosylhomocysteinase S-ribosylhomocysteine lyase NF002836.0 PRK03057 PRK03057.1 258 258 183 equivalog Y N N hypothetical protein 186817 Bacillaceae family 62 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005234.0 PRK06739 PRK06739.1 564 564 352 equivalog Y Y N pyruvate kinase 2.7.1.40 186817 Bacillaceae family 777 NCBI Protein Cluster (PRK) pyruvate kinase pyruvate kinase Catalyzes the formation of phosphoenolpyruvate from pyruvate NF005241.0 PRK06751 PRK06751.1 313 313 173 equivalog Y N N single-stranded DNA-binding protein 186817 Bacillaceae family 144 NCBI Protein Cluster (PRK) single-stranded DNA-binding protein single-stranded DNA-binding protein NF005248.0 PRK06759 PRK06759.1 133 133 156 equivalog Y N N RNA polymerase factor sigma-70 186817 Bacillaceae family 817 NCBI Protein Cluster (PRK) RNA polymerase factor sigma-70 RNA polymerase factor sigma-70 NF005377.0 PRK06920 PRK06920.1 1806 1806 1108 equivalog Y Y N DNA polymerase III subunit alpha dnaE 186817 Bacillaceae family 2036 NCBI Protein Cluster (PRK) DNA polymerase III DnaE DNA polymerase III subunit alpha NF005813.0 PRK07679 PRK07679.1 404 404 279 exception Y Y N pyrroline-5-carboxylate reductase ProI proI 1.5.1.2 11418582 186817 Bacillaceae family 642 NCBI Protein Cluster (PRK) pyrroline-5-carboxylate reductase pyrroline-5-carboxylate reductase ProI Catalyzes the formation of L-proline from pyrroline-5-carboxylate. ProI is one of several isozymes found in Bacillus subtilis. NF006059.0 PRK08207 PRK08207.1-1 1012 1012 496 equivalog Y Y N coproporphyrinogen III oxidase 186817 Bacillaceae family 322 NCBI Protein Cluster (PRK) coproporphyrinogen III oxidase coproporphyrinogen III oxidase NF007226.0 PRK09644 PRK09644.1 199 199 166 equivalog Y N N RNA polymerase sigma factor SigM 186817 Bacillaceae family 298 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigM RNA polymerase sigma factor SigM NF009193.0 PRK12541 PRK12541.1 171 171 161 equivalog Y Y N RNA polymerase sigma factor 186817 Bacillaceae family 525 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor Bacteria have multiple sigma factors which are active under specific conditions; the sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs Bacterial core RNA polymerase to specific promoter elements to initiate transcription NF009495.0 PRK12855 PRK12855.1 180 180 103 subfamily Y N N hypothetical protein 186817 Bacillaceae family 359 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF009496.0 PRK12856 PRK12856.1 177 177 103 subfamily Y N N hypothetical protein 186817 Bacillaceae family 362 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF009546.0 PRK12935 PRK12935.1 418 418 247 equivalog Y N N acetoacetyl-CoA reductase 186817 Bacillaceae family 240 NCBI Protein Cluster (PRK) acetoacetyl-CoA reductase acetoacetyl-CoA reductase NF009647.0 PRK13182 PRK13182.1-2 165 165 176 equivalog Y Y N chromosome-anchoring protein RacA racA 186817 Bacillaceae family 72 NCBI Protein Cluster (PRK) polar chromosome segregation protein chromosome-anchoring protein RacA NF009648.0 PRK13182 PRK13182.1-4 170 170 184 equivalog Y Y N chromosome-anchoring protein RacA racA 186817 Bacillaceae family 474 NCBI Protein Cluster (PRK) polar chromosome segregation protein chromosome-anchoring protein RacA NF009951.1 PRK13415 PRK13415.1 242 242 219 equivalog Y Y N flagella biosynthesis regulatory protein FliZ fliZ GO:0044781 1597417 186817 Bacillaceae family 518 NCBI Protein Cluster (PRK) flagella biosynthesis protein FliZ flagella biosynthesis regulatory protein FliZ NF010065.0 PRK13545 PRK13545.1 538 538 549 equivalog Y N N teichoic acids export protein ATP-binding subunit 186817 Bacillaceae family 228 NCBI Protein Cluster (PRK) teichoic acids export protein ATP-binding subunit teichoic acids export protein ATP-binding subunit NF010135.0 PRK13609 PRK13609.1 500 500 388 equivalog Y Y N diglucosyl diacylglycerol synthase 186817 Bacillaceae family 703 NCBI Protein Cluster (PRK) diacylglycerol glucosyltransferase diglucosyl diacylglycerol synthase Processive; catalyzes the formation of mono-, di- and tri-glucosyldiacylglycerol by the progressive transfer of glucosyl residues to diacylglycerol; involved in the formation of membrane glycolipids NF010196.0 PRK13673 PRK13673.1-3 141 141 117 equivalog Y N N hypothetical protein 186817 Bacillaceae family 151 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010534.0 PRK13923 PRK13923.1-2 345 345 212 equivalog Y N N putative spore coat protein regulator protein YlbO 186817 Bacillaceae family 16 NCBI Protein Cluster (PRK) putative spore coat protein regulator protein YlbO putative spore coat protein regulator protein YlbO NF010535.0 PRK13923 PRK13923.1-3 257 257 193 equivalog Y Y N sporulation-specific transcriptional regulator GerR gerR 15621419,20435725 186817 Bacillaceae family 286 NCBI Protein Cluster (PRK) putative spore coat protein regulator protein YlbO sporulation-specific transcriptional regulator GerR NF010809.0 PRK14213 PRK14213.1 126 126 118 equivalog Y N N camphor resistance protein CrcB 186817 Bacillaceae family 305 NCBI Protein Cluster (PRK) camphor resistance protein CrcB camphor resistance protein CrcB NF010880.0 PRK14287 PRK14287.1 737 737 371 equivalog Y N N chaperone protein DnaJ 186817 Bacillaceae family 94 NCBI Protein Cluster (PRK) chaperone protein DnaJ chaperone protein DnaJ NF010995.0 PRK14420 PRK14420.1 110 110 91 equivalog Y Y N acylphosphatase 186817 Bacillaceae family 400 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF012164.0 AlbA 850 850 442 equivalog Y Y N subtilosin maturase AlbA albA 186817 Bacillaceae family 173 NCBIFAM AlbA: subtilosin maturase AlbA subtilosin maturase AlbA AlbA is a radical SAM/SPASM domain-containing protein responsible for introducing thioether crosslinks during that maturation of bacteriocins such subtilosin A. NF012764.5 PF00555.24 Endotoxin_M 25 25 204 domain Y Y N insecticidal delta-endotoxin GO:0005102 1658659,9729609 186817 Bacillaceae family 902 EBI-EMBL delta endotoxin insecticidal delta-endotoxin This family contains insecticidal toxins produced by Bacillus species of bacteria. During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins they are activated by proteolytic cleavage. The N terminus is cleaved in all of the proteins and a C terminal extension is cleaved in some members. Once activated the endotoxin binds to the gut epithelium and causes cell lysis leading to death. This activated region of the delta endotoxin is composed of three structural domains. The N-terminal helical domain is involved in membrane insertion and pore formation. The second and third domains are involved in receptor binding. [1]. 1658659. Crystal structure of insecticidal delta-endotoxin from Bacillus thuringiensis at 2.5 angstroms resolution. Li J, Carroll J, Ellar DJ;. Nature 1991;353:815-821. [2]. 9729609. Bacillus thuringiensis and its pesticidal crystal proteins. Schnepf E, Crickmore N, Van Rie J, Lereclus D, Baum J, Feitelson J, Zeigler DR, Dean DH;. Microbiol Mol Biol Rev 1998;62:775-806. (from Pfam) NF016665.5 PF04791.21 LMBR1 31.9 31.9 510 PfamEq Y Y N LMBR1 domain-containing protein 11090342,11287427,12032320,19136951,25535791 186817 Bacillaceae family 193 EBI-EMBL LMBR1-like membrane protein LMBR1-like membrane protein Members of this family are integral membrane proteins that are around 500 residues in length. LMBR1 is not involved in preaxial polydactyly, as originally thought [1]. Vertebrate members of this family may play a role in limb development [2]. Lysosomal cobalamin transport escort protein LMBD1 is a lysosomal membrane chaperone required to export cobalamin from lysosome to the cytosol, allowing its conversion to cofactors [3,4]. A member of this family has been shown to be a lipocalin membrane receptor [5]. [1]. 12032320. Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly. Lettice LA, Horikoshi T, Heaney SJ, van Baren MJ, van der Linde HC, Breedveld GJ, Joosse M, Akarsu N, Oostra BA, Endo N, Shibata M, Suzuki M, Takahashi E, Shinka T, Nakahori Y, Ayusawa D, Nakabayashi K, Scherer SW, Heutink P, Hill RE, Noji S;. Proc Natl Acad Sci U S A 2002;99:7548-7553. [2]. 11090342. Acheiropodia is caused by a genomic deletion in C7orf2, the human orthologue of the Lmbr1 gene. Ianakiev P, van Baren MJ, Daly MJ, Toledo SP, Cavalcanti MG, Neto JC, Silveira EL, Freire-Maia A, Heutink P, Kilpatrick MW, Tsipouras P;. Am J Hum Genet 2001;68:38-45. [3]. 19136951. Identification of a putative lysosomal cobalamin exporter altered in the cblF defect of vitamin B12 metabolism. Rutsch F, Gailus S, Miousse IR, Suormala T, Sagne C, Toliat MR, Nurnberg G, Wittkampf T, Buers I, Sharifi A, Stucki M, Becker C, Baumgartner M, Robenek H, Marquardt T, Hohne W, Gasnier B, Rosenblatt DS, Fowler B, Nurnberg P;. Nat Genet. 2009;41:234-239. [4]. 25535791. Purification and interaction analyses of two human lysosomal vitamin B12 tra. TRUNCATED at 1650 bytes (from Pfam) NF019789.5 PF08181.16 DegQ 22 22 46 PfamEq Y Y N DegQ family regulator GO:1900192 1688843 186817 Bacillaceae family 93 EBI-EMBL DegQ (SacQ) family DegQ family regulator This family consists of the DegQ (formerly sacQ) regulatory peptides. The DegQ family of peptides control the rates of synthesis of a class of both secreted and intracellular degradative enzymes in Bacillus subtilis. DegQ is 46 amino acids long and activates the synthesis of degradative enzymes. The expression of this peptide was shown to be subjected both to catabolite repression and DegS-DegU-mediated control. Thus allowing an increase in the rate of synthesis of degQ under conditions of nitrogen starvation [1]. [1]. 1688843. Signal transduction pathway controlling synthesis of a class of degradative enzymes in Bacillus subtilis: expression of the regulatory genes and analysis of mutations in degS and degU. Msadek T, Kunst F, Henner D, Klier A, Rapoport G, Dedonder R;. J Bacteriol 1990;172:824-834. (from Pfam) NF021050.5 PF09501.15 Bac_small_YrzI 23 23 45 subfamily Y Y N YrzI family small protein 186817 Bacillaceae family 2543 EBI-EMBL Probable sporulation protein (Bac_small_yrzI) YrzI family small protein Members of this family are very small proteins, about 47 residues each, in the genus Bacillus. Single members are found in Bacillus subtilis and Bacillus halodurans, while arrays of six members in tandem are found in Bacillus cereus and Bacillus anthracis. An EIxxE motif present in most members of this family resembles cleavage sites by the germination protease GPR in a number of small acid-soluble spore proteins (SASP). A role in sporulation is possible. (from Pfam) NF021116.5 PF09575.15 Spore_SspJ 25 25 47 PfamEq Y Y N small acid-soluble spore protein SspJ sspJ 9852018 186817 Bacillaceae family 98 EBI-EMBL Small spore protein J (Spore_SspJ) small acid-soluble spore protein SspJ Spore_SspJ represents a group of small acid-soluble proteins (SASP) from Bacillus sp., which are present in spores but not in growing cells. The sspJ gene is transcribed in the forespore compartment by RNA polymerase with the forespore-specific sigmaG. Loss of SspJ causes a slight decrease in the rate of spore outgrowth in an otherwise wild-type background. (from Pfam) NF022251.5 PF10794.14 DUF2606 25.4 25.4 134 PfamAutoEq Y Y N DUF2606 family protein 16220534 186817 Bacillaceae family 423 EBI-EMBL Protein of unknown function (DUF2606) DUF2606 family protein Family of bacterial proteins with unknown function. These proteins have been classified as membrane proteins [1]. 16220534. Proteomics-based consensus prediction of protein retention in a bacterial membrane. Tjalsma H, van Dijl JM;. Proteomics. 2005;5:4472-4482. (from Pfam) NF022283.5 PF10827.13 DUF2552 27 27 79 PfamAutoEq Y Y N DUF2552 family protein 186817 Bacillaceae family 335 EBI-EMBL Protein of unknown function (DUF2552) DUF2552 family protein This bacterial family of proteins has no known function. (from Pfam) NF022581.5 PF11131.13 PhrC_PhrF 25 25 38 subfamily Y Y N PhrC/PhrF family phosphatase-inhibitory pheromone 12456319,16816200 186817 Bacillaceae family 125 EBI-EMBL Rap-phr extracellular signalling PhrC/PhrF family phosphatase-inhibitory pheromone PhrC and PhrF stimulate ComA-dependent gene expression to different levels and are both required for full expression of genes activated by ComA, which activates the expression of genes involved in competence development and the production of several secreted products [1]. [1]. 16816200. Modulation of the ComA-dependent quorum response in Bacillus subtilis by multiple Rap proteins and Phr peptides. Auchtung JM, Lee CA, Grossman AD;. J Bacteriol. 2006;188:5273-5285. [2]. 12456319. The extracellular Phr peptide-Rap phosphatase signaling circuit of Bacillus subtilis. Pottathil M, Lazazzera BA;. Front Biosci. 2003;8:32-45. (from Pfam) NF022923.5 PF11486.13 DUF3212 27 27 121 PfamAutoEq Y Y N DUF3212 family protein 186817 Bacillaceae family 256 EBI-EMBL Protein of unknown function (DUF3212) DUF3212 family protein Members in this family of proteins are annotated as YfmB however currently no function for this protein is known. (from Pfam) NF023062.5 PF11631.13 DUF3255 25 25 123 domain Y Y N DUF3255 family protein 186817 Bacillaceae family 279 EBI-EMBL Protein of unknown function (DUF3255) DUF3255 family protein Members in this family of proteins are annotated as YxeF however no function is currently known. The family appears to be restricted to Bacillus. (from Pfam) NF024435.5 PF13035.11 DUF3896 25 25 61 PfamAutoEq Y Y N DUF3896 family protein 186817 Bacillaceae family 343 EBI-EMBL Protein of unknown function (DUF3896) DUF3896 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. (from Pfam) NF024458.5 PF13058.11 DUF3920 27.3 27.3 126 PfamAutoEq Y Y N DUF3920 family protein 186817 Bacillaceae family 496 EBI-EMBL Protein of unknown function (DUF3920) DUF3920 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. (from Pfam) NF024469.5 PF13069.11 DUF3933 25 25 52 PfamAutoEq Y Y N DUF3933 family protein 186817 Bacillaceae family 148 EBI-EMBL Protein of unknown function (DUF3933) DUF3933 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. (from Pfam) NF024481.5 PF13081.11 DUF3941 25 25 24 PfamAutoEq Y Y N DUF3941 domain-containing protein 186817 Bacillaceae family 230 EBI-EMBL Domain of unknown function (DUF3941) Domain of unknown function (DUF3941) This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 30 amino acids in length. There is a conserved YSK sequence motif. (from Pfam) NF024510.5 PF13110.11 DUF3966 25 25 42 PfamAutoEq Y Y N DUF3966 domain-containing protein 186817 Bacillaceae family 99 EBI-EMBL Protein of unknown function (DUF3966) Protein of unknown function (DUF3966) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 86 amino acids in length. (from Pfam) NF024513.5 PF13113.11 DUF3970 21.1 21.1 55 PfamAutoEq Y Y N DUF3970 family protein 186817 Bacillaceae family 459 EBI-EMBL Protein of unknown function (DUF3970) DUF3970 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved NPKY sequence motif. (from Pfam) NF024535.5 PF13135.11 DUF3947 25 25 91 subfamily Y Y N DUF3947 family protein 186817 Bacillaceae family 781 EBI-EMBL Protein of unknown function (DUF3947) DUF3947 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. (from Pfam) NF024558.5 PF13159.11 DUF3994 25 25 123 domain Y Y N DUF3994 domain-containing protein 186817 Bacillaceae family 1218 EBI-EMBL Domain of unknown function (DUF3994) Domain of unknown function (DUF3994) This presumed domain is functionally uncharacterised. This domain is found in bacteria, and is typically between 97 and 111 amino acids in length, found at the C-terminal in most instances. According to structure predictions, it might have a beta-barrel fold. (from Pfam) NF024611.5 PF13213.11 DUF4021 25 25 46 PfamAutoEq Y Y N DUF4021 domain-containing protein 186817 Bacillaceae family 451 EBI-EMBL Protein of unknown function (DUF4021) Protein of unknown function (DUF4021) This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved YGM sequence motif. (from Pfam) NF024617.5 PF13219.11 DUF4027 25 25 36 PfamAutoEq Y Y N DUF4027 family protein 186817 Bacillaceae family 174 EBI-EMBL Protein of unknown function (DUF4027) DUF4027 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There is a conserved CLGGF sequence motif. (from Pfam) NF024780.5 PF13388.11 DUF4106 27 27 431 domain Y Y N DUF4106 domain-containing protein 186817 Bacillaceae family 5 EBI-EMBL Protein of unknown function (DUF4106) Protein of unknown function (DUF4106) This family of proteins are found in large numbers in the Trichomonas vaginalis proteome. The function of this protein is unknown. (from Pfam) NF025403.5 PF14037.11 YoqO 27 27 116 subfamily Y Y N YoqO family protein 186817 Bacillaceae family 1277 EBI-EMBL YoqO-like protein YoqO family protein The YoqO-like protein family includes the B. subtilis YoqO protein Swiss:O31923, which is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 120 amino acids in length. There are two completely conserved residues (I and Y) that may be functionally important. (from Pfam) NF025507.5 PF14142.11 YrzO 27 27 46 PfamEq Y Y N YrzO family protein 186817 Bacillaceae family 199 EBI-EMBL YrzO-like protein YrzO family protein The YrzO-like protein family includes the B. subtilis YrzO protein Swiss:C0H458 which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. (from Pfam) NF025521.5 PF14156.11 AbbA_antirepres 27 27 63 PfamEq Y Y N antirepressor AbbA abbA 18840696 186817 Bacillaceae family 316 EBI-EMBL Antirepressor AbbA antirepressor AbbA This family inactivates the repressor AbrB, which represses genes switched on during the transition from the exponential to the stationary phase of growth. It binds to AbrB and prevents it from binding to DNA [1]. [1]. 18840696. Parallel pathways of repression and antirepression governing the transition to stationary phase in Bacillus subtilis. Banse AV, Chastanet A, Rahn-Lee L, Hobbs EC, Losick R;. Proc Natl Acad Sci U S A. 2008;105:15547-15552. (from Pfam) NF025904.5 PF14553.11 YqbF 27 27 43 domain Y Y N YqbF domain-containing protein 186817 Bacillaceae family 616 EBI-EMBL YqbF, hypothetical protein domain YqbF, hypothetical protein domain This N-terminal domain is found in Bacillus and related spp. The function is not known. (from Pfam) NF027621.5 PF16297.10 DUF4939 29 29 112 domain Y Y N DUF4939 domain-containing protein 10403563,12712434,21310924,21547351 186817 Bacillaceae family 2 EBI-EMBL Domain of unknown function (DUF4939) Domain of unknown function (DUF4939) This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases [1,2,3,4]. But the specific function of this family is still unknown. [1]. 10403563. Identification of a novel gene, LDOC1, down-regulated in cancer cell lines. Nagasaki K, Manabe T, Hanzawa H, Maass N, Tsukada T and Yamaguchi K;. Cancer Lett. 140 (1-2), 227-234 (1999). [2]. 12712434. Leucine-zipper protein, LDOC1, inhibits NF-kappaB activation and sensitizes pancreatic cancer cells to apoptosis. Nagasaki K, Schem C, von Kaisenberg C, Biallek M, Rosel F, Jonat W and Maass N;. Int. J. Cancer 105 (4), 454-458 (2003). [3]. 21547351. Over expression of LDOC1 and PARP1, two pro-apoptotic genes, in a patient with cryptorchidism and DiGeorge anomaly. Salemi M, Castiglione R, La Vignera S, Condorelli RA, Bosco P, Vicari E and Calogero AE;. Hum. Cell 24 (2), 112-113 (2011). [4]. 21310924. LDOC1 mRNA is differentially expressed in chronic lymphocytic leukemia and predicts overall survival in untreated patients. Duzkale H, Schweighofer CD, Coombes KR, Barron LL, Ferrajoli A, O'Brien S, Wierda WG, Pfeifer J, Majewski T, Czerniak BA, Jorgensen JL, Medeiros LJ, Freireich EJ, Keating MJ and Abruzzo LV;. Blood 117 (15), 4076-4084 (2011). (from Pfam) NF028404.5 PF17094.10 UPF0715 27 27 119 domain Y Y N UPF0715 family protein 186817 Bacillaceae family 1503 EBI-EMBL Uncharacterised protein family (UPF0715) UPF0715 family protein This is a family of Bacilli transmembrane proteins. The function is unknown. (from Pfam) NF033173.0 anticapsin_BacC 525 525 252 exception Y Y N dihydroanticapsin 7-dehydrogenase bacC 1.1.1.385 186817 Bacillaceae family 225 NCBIFAM dihydroanticapsin 7-dehydrogenase dihydroanticapsin 7-dehydrogenase Members of this family are dihydroanticapsin 7-dehydrogenase (EC 1.1.1.385), one of seven key molecular markers for biosynthesis of the non-cognate amino acid anticapsin, a building block for the dipeptide antibiotic natural product bacilysin. NF033217.1 Fur_reg_FbpC 60 60 29 equivalog Y Y N Fur-regulated basic protein FbpC fbpC 18697947,8396117 186817 Bacillaceae family 45 NCBIFAM Fur-regulated basic protein FbpC Fur-regulated basic protein FbpC Members of this family are FbpC, Fur-regulated basic protein C. This protein has also been described as MrgC (metal-regulated gene C). Members of this family are found so far only in the genus Bacillus, although the small size may have interferred in gene-finding. NF036335.5 PF17431.7 YpmT 25 25 60 PfamEq Y Y N protein YpmT ypmT 186817 Bacillaceae family 183 EBI-EMBL Uncharacterized YmpT-like protein YpmT This is a family of unknown function found in Bacillus. (from Pfam) NF036340.5 PF17447.7 YkpC 27.7 27.7 42 PfamEq Y Y N protein YkpC 186817 Bacillaceae family 84 EBI-EMBL Uncharacterized YkpC-like protein YkpC This is a family of unknown function found in Bacillus. (from Pfam). YkpC, a protein of only 43 or 44 amino acids, is found broadly in the genus Bacillus. NF036341.5 PF17448.7 YqaH 31 31 88 subfamily Y Y N YqaH family protein 186817 Bacillaceae family 647 EBI-EMBL Uncharacterized YqaH-like YqaH family protein This is a family of unknown function found in Bacillus. (from Pfam) NF036342.5 PF17449.7 YrzK 27.8 27.8 54 subfamily Y Y N YrzK family protein 186817 Bacillaceae family 93 EBI-EMBL Uncharacterized YrzK-like YrzK family protein This is a family of unknown function found in Bacillus. (from Pfam) NF036344.5 PF17452.7 YnfE 25 25 78 subfamily Y Y N YnfE family protein 186817 Bacillaceae family 231 EBI-EMBL Uncharacterized YnfE-like YnfE family protein This is a family of unknown function found in Bacillus. (from Pfam) NF036360.5 PF17522.7 DUF5446 26.2 26.2 72 domain Y Y N DUF5446 family protein 186817 Bacillaceae family 260 EBI-EMBL Family of unknown function (DUF5446) DUF5446 family protein This is a family of unknown function found in Bacillales. (from Pfam) NF036390.5 PF17632.7 DUF5513 27 27 91 subfamily Y Y N DUF5513 family protein 186817 Bacillaceae family 83 EBI-EMBL Family of unknown function (DUF5513) DUF5513 family protein This is a family of unknown function found in Bacillus. (from Pfam) NF036587.5 PF17423.7 SwrA 25 25 116 domain Y Y N swarming motility protein SwrAA 22496484,24386445,25538299 186817 Bacillaceae family 126 EBI-EMBL Swarming motility protein swarming motility protein SwrAA This domain family is found in Bacillus. Members of this family are Swra proteins involved in swarming motility (a multicellular movement of hyper-flagellated cells on a surface). SwrA is a key transcription factor facilitating this cascade. It acts synergistically with DegU to drive the fla/che operon encoding flagella components, chemotaxis constituents and the alternative sigma factor sigmaD, which is regarded as the primary event in the development of motility [1]. LonA protease of Bacillus subtilis inhibits SwrA by proteolytically restricting its accumulation [2]. SwrA does not contain any known DNA binding domain, and it has been shown to interact with the N-terminal domain of DegU. Anecdotally, in most laboratory strains, e.g. 168, the swrA coding sequence contains a nucleotide insertion that prematurely interrupts its reading frame, causing a non-swarming phenotype strain [3]. [1]. 22496484. SwrA regulates assembly of Bacillus subtilis DegU via its interaction with N-terminal domain of DegU. Ogura M, Tsukahara K;. J Biochem. 2012;151:643-655. [2]. 25538299. Adaptor-mediated Lon proteolysis restricts Bacillus subtilis hyperflagellation. Mukherjee S, Bree AC, Liu J, Patrick JE, Chien P, Kearns DB;. Proc Natl Acad Sci U S A. 2015;112:250-255. [3]. 24386445. The role of SwrA, DegU and P(D3) in fla/che expression in B. subtilis. Mordini S, Osera C, Marini S, Scavone F, Bellazzi R, Galizzi A, Calvio C;. PLoS One. 2013;8:e85065. (from Pfam) NF036592.5 PF17453.7 Sigma_M_inh 25 25 96 domain Y N N Sigma-M inhibitor 10216858,14993308 186817 Bacillaceae family 93 EBI-EMBL Sigma-M inhibitor Sigma-M inhibitor This family includes members such as Sigma M inhibitor proteins YhdK. In Bacillus subtilis, sigM (yhdM) gene, is required for growth and survival after salt stress. Expression of sigM is positively autoregulated and is controlled by growth phase and medium composition. SigM-dependent transcription is regulated by the products of both the yhdL and the yhdK genes, which are co-transcribed with the sigM gene [1]. The small hydrophobic protein YhdK, appears to interact with the trans-membrane domain of YhdL, suggesting some specific role for YhdK in the anti-sigma function of YhdL [2]. [1]. 10216858. Sigma M, an ECF RNA polymerase sigma factor of Bacillus subtilis 168, is essential for growth and survival in high concentrations of salt. Horsburgh MJ, Moir A;. Mol Microbiol. 1999;32:41-50. [2]. 14993308. Interaction of Bacillus subtilis extracytoplasmic function (ECF) sigma factors with the N-terminal regions of their potential anti-sigma factors. Yoshimura M, Asai K, Sadaie Y, Yoshikawa H;. Microbiology. 2004;150:591-599. (from Pfam) NF036673.5 PF17584.7 ComS 27 27 44 subfamily Y Y N competence protein ComS comS 25520171 186817 Bacillaceae family 79 EBI-EMBL Bacillus competence protein S competence protein ComS ComS, a protein 46 amino acids in length, is described as the product of a gene fully embedded in the much longer gene srfAB, which encodes a non-ribosomal peptide synthetase subunit involved in surfactin biosynthesis. The gene is encoded on the same strand, allowing ComS to be produced from the same mRNA as SrfAB. ComS is seen as crucial for competence development as it prevents proteolytic degradation of ComK, the key transcriptional activator of all genes required for the uptake and integration of DNA. Note that many annotation prokaryotic genome annotation pipelines currently will not make the gene call for the fully embedded smaller gene when two genes overlap extensively in different reading frames. NF036792.5 PF17735.6 BslA 38.7 38.7 121 domain Y Y N BslA/BslB family hydrophobin 23904481 186817 Bacillaceae family 716 EBI-EMBL Biofilm surface layer A BslA/BslB family hydrophobin BslA (biofilm-surface layer protein A), as found in Bacillus subtillis, is classified as a hydrophobin, a bacterial counterpart to small amphiphilic proteins of filamentous fungi. BlsA self-assembles into a monolayer that coats biofilm and presents a hydrophobic surface. NF037163.5 PF17997.6 Cry1Ac_D5 25 25 173 domain Y N N Insecticidal delta-endotoxin CryIA(c) domain 5 25139047 186817 Bacillaceae family 740 EBI-EMBL Insecticidal delta-endotoxin CryIA(c) domain 5 Insecticidal delta-endotoxin CryIA(c) domain 5 This domain is found in the protoxins portion of insecticidal proteins (parasporins, or Cry proteins) such as those from Bacillus thuringiensis (Bt) Cry1Ac. The protoxin portion comprise a proteolytically labile C-terminal segment (sometimes referred to as the protoxin domain). This is domain V in Cry1Ac from B. thuringiensis. One of the four protoxin domains (D-IV through D-VII). Domains V and VII are beta-rolls (similar to D-II or D-III) that closely resemble carbohydrate-binding modules (CBM) found in sugar hydrolases, however, it is difficult to guess which particular carbohydrates (if any) may serve as their ligands because residues on the putative sugar-binding interfaces are conserved neither in sequence nor in local structure. Structural analysis indicate that there are putative disulfide crosslinking at the dimer interface mediated by cysteines within 783-823 region of this domain which together with other cysteines creates a three-dimensional network of cross-links across the crystal which may play a role in stabilizing mature Bt Cry1Ac [1]. [1]. 25139047. Structure of the full-length insecticidal protein Cry1Ac reveals intriguing details of toxin packaging into in vivo formed crystals. Evdokimov AG, Moshiri F, Sturman EJ, Rydel TJ, Zheng M, Seale JW, Franklin S;. Protein Sci. 2014;23:1491-1497. (from Pfam) NF037554.5 PF17444.7 YhdX 25 25 33 subfamily Y Y N YhdX family protein 186817 Bacillaceae family 73 EBI-EMBL Uncharacterized YhdX-like YhdX family protein This is a family of unknown function found in Bacillus. (from Pfam) NF037912.5 PF18801.6 RapH_N 27 25 62 domain Y N N response regulator aspartate phosphatase H, N terminal 21346797 186817 Bacillaceae family 14122 EBI-EMBL response regulator aspartate phosphatase H, N terminal response regulator aspartate phosphatase H, N terminal Rap proteins consist of a N-terminal 3-helix bundle and a tetratricopeptide domain [1]. This entry represents the conserved region of the C-terminal bundle. [1]. 21346797. Structural basis of response regulator dephosphorylation by Rap phosphatases. Parashar V, Mirouze N, Dubnau DA, Neiditch MB;. PLoS Biol. 2011;9:e1000589. (from Pfam) NF038056.1 macrolide_MphM 610 610 298 exception Y Y Y macrolide 2'-phosphotransferase MphM mphM 186817 Bacillaceae family 81 NCBIFAM macrolide 2'-phosphotransferase MphM NF038334.1 malate_HK_MalK 800 800 533 exception Y Y N malate sensor histidine kinase MalK malK 2.7.13.3 186817 Bacillaceae family 451 NCBIFAM malate sensor histidine kinase MalK NF039429.4 PF19945.4 DUF6407 25 25 96 subfamily Y Y N DUF6407 family protein 20142038 186817 Bacillaceae family 214 EBI-EMBL Family of unknown function (DUF6407) DUF6407 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000926) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular the rhizocticin A biosynthetic gene cluster from Bacillus subtilis subsp. spizizenii ATCC 6633 [1]. [1]. 20142038. Biosynthesis of rhizocticins, antifungal phosphonate oligopeptides produced by Bacillus subtilis ATCC6633. Borisova SA, Circello BT, Zhang JK, van der Donk WA and Metcalf WW;. Chem. Biol. 2007; 17 (1): 28-37. (from Pfam) NF040516.1 CapE_47_fam 35 35 39 domain Y Y N CapE family protein 16267300 186817 Bacillaceae family 173 NCBIFAM CapE family protein Known members of this family are full-length homologs of CapE, a 47-amino acid linked to polyglutamate synthesis in Bacillus, or longer proteins sharing N-terminal homology with CapE. NF040668.1 regulator_TseB 200 200 161 equivalog Y Y N cell wall elongation/penicillin-binding protein regulator TseB tseB 25954268,34411374 186817 Bacillaceae family 349 NCBIFAM cell wall elongation/penicillin-binding protein regulator TseB NF040827.1 CotZ_rel 90 90 212 equivalog Y Y N CotZ-related putative spore coat protein 186817 Bacillaceae family 140 NCBIFAM CotZ-related putative spore coat protein Members of this appear only in endospore-forming bacteria, and are distantly related to spore coat protein CotZ. NF041202.1 StoA_CxxC 210 210 163 exception Y Y N endospore biogenesis thiol-disulfide oxidoreductase StoA stoA 15342593,19144642,19919673,28383125 186817 Bacillaceae family 482 NCBIFAM endospore biogenesis thiol-disulfide oxidoreductase StoA StoA (originally YkvV in Bacillus subtilis) is a paralog of ResA. It is involved in proper formation of the peptidoglycan cortex of the endospore, while ResA is involved in cytochrome c maturation. Both are membrane-bound and outside of the cytoplasm. This HMM separates StoA from the much larger set of ResA proteins. NF041457.1 reg_protDegQ_Bacil 80 80 46 equivalog Y Y N degradation enzyme regulation protein DegQ degQ GO:1900192 17827323,26302846 186817 Bacillaceae family 52 NCBIFAM degradation enzyme regulation protein DegQ gene synonym sacQ NF041458.1 antiadapt_SpxO 107 107 54 equivalog Y Y N anti-adapter protein SpxO spxO 21378193,30001325 186817 Bacillaceae family 54 NCBIFAM anti-adapter protein SpxO NF041478.1 spor_prot_SspM 40 40 34 equivalog Y Y N acid-soluble spore protein SspM sspM GO:0034301 10806362,9852018 186817 Bacillaceae family 77 NCBIFAM acid-soluble spore protein SspM NF041485.2 spor_mat_CgeC 110 110 101 equivalog Y Y N spore maturation protein CgeC cgeC 10066829,1729246,21665972 186817 Bacillaceae family 213 NCBIFAM spore maturation protein CgeC NF041489.1 sigO_reg_RsoA 100 100 77 equivalog Y Y N sigma-O factor regulator RsoA rsoA 18573182,19047353,27558998 186817 Bacillaceae family 238 NCBIFAM sigma-O factor regulator RsoA NF041754.1 sbcd_Bac 750 750 390 equivalog Y Y N exonuclease subunit SbcD sbcD 3.1.11.- GO:0004527,GO:0006260,GO:0006310 16780573,8493111 186817 Bacillaceae family 638 NCBIFAM exonuclease subunit SbcD NF041825.1 hydrophobin_BslA 250 250 178 equivalog Y Y N biofilm surface layer hydrophobin BslA bslA 22571672,23904481,28701036 186817 Bacillaceae family 223 NCBIFAM biofilm surface layer hydrophobin BslA BslA (biofilm-surface layer protein A), as found in Bacillus subtillis, is classified as a hydrophobin, a bacterial counterpart to small amphiphilic proteins of filamentous fungi. BlsA self-assembles into a monolayer that coats biofilm and presents a hydrophobic surface. NF041828.1 hydrophobin_BslB 225 225 157 equivalog Y Y N biofilm surface layer hydrophobin BslB bslB 15187182,28751732 186817 Bacillaceae family 223 NCBIFAM biofilm surface layer hydrophobin BslB BslB (biofilm-surface layer protein A), as found in Bacillus subtillis, is a paralog of the better characterized BslA, which forms a hydrophobic surface on biofilms. Both are classified as hydrophobins, a bacterial counterpart to small amphiphilic proteins of filamentous fungi. NF044482.2 PF21463.2 Cry1Ac_dom-VII 27 27 79 domain Y N N Cry1Ac, domain VII 25139047 186817 Bacillaceae family 483 EBI-EMBL Cry1Ac, domain VII Cry1Ac, domain VII This entry includes insecticidal protein Cry1Ac from Bacillus thuringiensis, which contains a proteolytically labile protoxin segment (in the C-terminal region) and a three-domain toxic core at the N terminus (domains I-III) [1]. The protoxin segment consists of domains IV-VII. This entry represents domain VII, which is a beta-roll that closely resembles carbohydrate-binding modules. Paper describing PDB structure 4w8j. [1]. 25139047. Structure of the full-length insecticidal protein Cry1Ac reveals intriguing details of toxin packaging into in vivo formed crystals. Evdokimov AG, Moshiri F, Sturman EJ, Rydel TJ, Zheng M, Seale JW, Franklin S;. Protein Sci. 2014;23:1491-1497. (from Pfam) NF045775.1 acetoin_reg_AlsR 430 430 290 exception Y Y N acetoin biosynthesis transcriptional regulator AlsR alsR 23695583,7685336 186817 Bacillaceae family 529 NCBIFAM acetoin biosynthesis transcriptional regulator AlsR NF045984.1 StressProtLiaH 380 380 225 equivalog Y Y N stress responsive protein LiaH liaH 20639339,32302670 186817 Bacillaceae family 394 NCBIFAM stress responsive protein LiaH NF046031.1 AntRepSinIBacil 80 80 58 equivalog Y Y N anti-repressor SinI sinI GO:0006355,GO:0046983 8422983,9799632 186817 Bacillaceae family 73 NCBIFAM anti-repressor SinI NF047193.1 PF22510.1 FlhF_N 27 27 54 domain Y N N Flagellar biosynthesis protein FlhF, N domain 17699634,22223736,22223738,23022487,23999294 186817 Bacillaceae family 384 EBI-EMBL Flagellar biosynthesis protein FlhF, N domain Flagellar biosynthesis protein FlhF, N domain This domain is found in Flagellar biosynthesis protein FlhF from Bacillus subtilis, a protein that is necessary for flagellar biosynthesis. FlhF contains a basic N-terminal domain followed by the conserved NG domain, which can be divided into two segments: the N domain (this entry) and the G domain (Pfam:PF00448) [1]. Paper describing PDB structure 2px0. [1]. 17699634. The crystal structure of the third signal-recognition particle GTPase FlhF reveals a homodimer with bound GTP. Bange G, Petzold G, Wild K, Parlitz RO, Sinning I;. Proc Natl Acad Sci U S A. 2007;104:13621-13625. Paper describing PDB structure 2ypf. [2]. 23999294. Structure of the AvrBs3-DNA complex provides new insights into the initial thymine-recognition mechanism. Stella S, Molina R, Yefimenko I, Prieto J, Silva G, Bertonati C, Juillerat A, Duchateau P, Montoya G;. Acta Crystallogr D Biol Crystallogr. 2013;69:1707-1716. Paper describing PDB structure 3ugm. [3]. 22223736. The crystal structure of TAL effector PthXo1 bound to its DNA target. Mak AN, Bradley P, Cernadas RA, Bogdanove AJ, Stoddard BL;. Science. 2012;335:716-719. Paper describing PDB structure 3v6p. [4]. 22223738. Structural basis for sequence-specific recognition of DNA by TAL effectors. Deng D, Yan C, Pan X, Mahfouz M, Wang J, Zhu JK, Shi Y, Yan N;. Science. 2012;335:720-723. Paper describing PDB structure 4gg4. [5]. 23022487. Specific DNA-RNA hybrid recognition by TAL effectors. Yin P, Deng D, Yan C, Pan X, Xi JJ, Yan N, Shi Y;. Cell Rep. 2012;2:707-713. (from Pfam) NF047410.1 CotG_ExsB_Nterm 28 28 26 domain Y Y N CotG/ExsB N-terminal domain-containing protein 186817 Bacillaceae family 2046 NCBIFAM CotG/ExsB N-terminal domain NF047411.1 spore_coat_G 99 80 197 equivalog Y Y N spore coat protein CotG cotG GO:0043593 36354330 186817 Bacillaceae family 731 NCBIFAM spore coat protein CotG CotG is a lysine-rich repetitive endospore coat protein that is among the most highly charged proteins known. It is reported to mediate spore surface permeability. NF047674.1 TeichurnBiosyTuaB 580 580 469 equivalog Y Y N teichuronic acid biosynthesis protein TuaB tuaB GO:0050845 10048024 186817 Bacillaceae family 905 NCBIFAM teichuronic acid biosynthesis protein TuaB NF047675.1 TeichurnBiosyTuaE 400 400 488 equivalog Y Y N teichuronic acid biosynthesis protein TuaE tuaE GO:0050845 10048024 186817 Bacillaceae family 1045 NCBIFAM teichuronic acid biosynthesis protein TuaE NF047676.1 TeichurnBiosyTuaH 550 550 384 equivalog Y Y N teichuronic acid biosynthesis protein TuaH tuaH GO:0050845 10048024,30498236 186817 Bacillaceae family 979 NCBIFAM teichuronic acid biosynthesis protein TuaH NF047683.1 TeichurnBiosyTuaG 400 400 252 equivalog Y Y N teichuronic acid biosynthesis protein TuaG tuaG GO:0050845 10048024 186817 Bacillaceae family 492 NCBIFAM teichuronic acid biosynthesis protein TuaG NF047684.1 TeichurnBiosyTuaC 550 550 391 equivalog Y Y N teichuronic acid biosynthesis protein TuaC tuaC GO:0050845 10048024 186817 Bacillaceae family 1029 NCBIFAM teichuronic acid biosynthesis protein TuaC NF047685.1 TeichurnBiosyTuaF 340 340 225 equivalog Y Y N teichuronic acid biosynthesis protein TuaF tuaF GO:0050845 10048024 186817 Bacillaceae family 531 NCBIFAM teichuronic acid biosynthesis protein TuaF TIGR00841.1 TIGR00841 bass 326.3 326.3 321 subfamily Y Y N bile acid:sodium symporter family transporter GO:0008508,GO:0015721 186817 Bacillaceae family 593 JCVI bile acid transporter bile acid:sodium symporter family transporter The Bile Acid:Na+ Symporter (BASS) Family (TC 2.A.28) Functionally characterized members of the BASS family catalyze Na+:bile acid symport. These systems have been identified in intestinal, liver and kidney tissues of animals. These symporters exhibit broad specificity, taking up a variety of non bile organic compounds as well as taurocholate and other bile salts. Functionally uncharacterised homologues are found in plants, yeast, archaea and bacteria. TIGR02131.1 TIGR02131 phaP_Bmeg 109.3 109.3 165 equivalog Y Y N polyhydroxyalkanoic acid inclusion protein PhaP phaP 9882674 186817 Bacillaceae family 222 JCVI polyhydroxyalkanoic acid inclusion protein PhaP polyhydroxyalkanoic acid inclusion protein PhaP This HMM describes a protein found in polyhydroxyalkanoic acid (PHA) gene regions and incorporated into PHA inclusions in Bacillus cereus and Bacillus megaterium. The role of the protein may include amino acid storage (see McCool,G.J. and Cannon,M.C, 1999). TIGR02132.1 TIGR02132 phaR_Bmeg 148.4 148.4 189 equivalog Y Y N polyhydroxyalkanoic acid synthase subunit PhaR phaR 11418564 186817 Bacillaceae family 275 JCVI polyhydroxyalkanoic acid synthase, PhaR subunit polyhydroxyalkanoic acid synthase subunit PhaR This HMM describes a protein, PhaR, localized to polyhydroxyalkanoic acid (PHA) inclusion granules in Bacillus cereus and related species. PhaR is required for PHA biosynthesis along with PhaC and may be a regulatory subunit. TIGR02413.1 TIGR02413 Bac_small_yrzI 47.05 47.05 46 paralog Y Y N YrzI family small protein 186817 Bacillaceae family 1468 JCVI Bacillus tandem small hypothetical protein YrzI family small protein Members of this family are very small proteins, about 47 residues each, in the genus Bacillus. Single members are found in Bacillus subtilis and Bacillus halodurans, but arrays of six in tandem in Bacillus cereus and Bacillus anthracis. An EIxxE motif present in most members of this family resembles cleavage sites by the germination protease GPR in a number small, acid-soluble spore proteins (SASP). A role in sporulation is possible. TIGR02863.1 TIGR02863 spore_sspJ 37.85 37.85 47 equivalog Y Y N small acid-soluble spore protein SspJ sspJ GO:0030436 9852018 186817 Bacillaceae family 93 JCVI small, acid-soluble spore protein, SspJ family small acid-soluble spore protein SspJ TIGR03198.1 TIGR03198 pucE 254.3 254.3 151 equivalog Y Y N xanthine dehydrogenase subunit E pucE 1.17.1.4 11344136 186817 Bacillaceae family 231 JCVI xanthine dehydrogenase E subunit xanthine dehydrogenase subunit E This gene has been characterized in B. subtilis [1] as the Iron-sulfur cluster binding-subunit of xanthine dehydrogenase (pucE), acting in conjunction with pucC, the FAD-binding subunit and pucD, the molybdopterin binding subunit. The more common XDH complex (GenProp0640) includes the xdhA gene as the Fe-S cluster binding component. TIGR03199.1 TIGR03199 pucC 306.05 306.05 264 equivalog Y Y N xanthine dehydrogenase subunit C pucC 1.17.1.4 11344136 186817 Bacillaceae family 293 JCVI xanthine dehydrogenase C subunit xanthine dehydrogenase subunit C This gene has been characterized in B. subtilis [1] as the FAD binding-subunit of xanthine dehydrogenase (pucC), acting in conjunction with pucD, the molybdopterin-binding subunit and pucE, the FeS-binding subunit. TIGR03202.1 TIGR03202 pucB 235.05 235.05 192 equivalog Y Y N xanthine dehydrogenase accessory protein PucB pucB 11344136 186817 Bacillaceae family 320 JCVI xanthine dehydrogenase accessory protein pucB xanthine dehydrogenase accessory protein PucB In Bacillus subtilis [1] the expression of this protein, located in an operon with the structural subunits of xanthine dehydrogenase, has been found to be essential for XDH activity. Some members of this family appear to have a distant relationship to the MobA protein involved in molybdopterin biosynthesis, although this may be coincidental. NF000017.1 linco_LnuD 325 325 164 exception Y Y Y lincosamide nucleotidyltransferase Lnu(D) lnu(D) 186826 Lactobacillales order 1 NCBIFAM lincosamide nucleotidyltransferase Lnu(D) lincosamide nucleotidyltransferase Lnu(D) NF000020.1 stregram_VatE 450 450 214 exception Y Y Y streptogramin A O-acetyltransferase Vat(E) vat(E) 186826 Lactobacillales order 8 NCBIFAM streptogramin A O-acetyltransferase Vat(E) streptogramin A O-acetyltransferase Vat(E) NF000504.1 stregram_VatH 475 425 216 exception Y Y Y streptogramin A O-acetyltransferase Vat(H) vat(H) GO:0016740 186826 Lactobacillales order 1 NCBIFAM vatH: streptogramin A O-acetyltransferase Vat(H) streptogramin A O-acetyltransferase Vat(H) NF001066.0 PRK00118 PRK00118.1-1 147 147 110 equivalog Y Y N putative DNA-binding protein 186826 Lactobacillales order 664 NCBI Protein Cluster (PRK) putative DNA-binding protein putative DNA-binding protein NF001260.0 PRK00226 PRK00226.1-1 234 234 160 equivalog Y Y N transcription elongation factor GreA greA 186826 Lactobacillales order 702 NCBI Protein Cluster (PRK) transcription elongation factor GreA transcription elongation factor GreA NF001382.0 PRK00279 PRK00279.1-4 334 334 212 equivalog Y Y N adenylate kinase 2.7.4.3 186826 Lactobacillales order 912 NCBI Protein Cluster (PRK) adenylate kinase adenylate kinase NF002529.0 PRK01966 PRK01966.1-5 472 472 348 equivalog Y Y N D-alanine--D-alanine ligase 6.3.2.4 186826 Lactobacillales order 2396 NCBI Protein Cluster (PRK) D-alanyl-alanine synthetase A D-alanine--D-alanine ligase NF002686.0 PRK02458 PRK02458.1 506 506 323 equivalog Y Y N ribose-phosphate diphosphokinase 2.7.6.1 186826 Lactobacillales order 1269 NCBI Protein Cluster (PRK) ribose-phosphate pyrophosphokinase ribose-phosphate diphosphokinase Catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP NF002698.0 PRK02491 PRK02491.1 301 301 328 equivalog Y Y N nucleoside-triphosphate diphosphatase GO:0009143,GO:0047429 186826 Lactobacillales order 2347 NCBI Protein Cluster (PRK) putative deoxyribonucleotide triphosphate pyrophosphatase/unknown domain fusion protein nucleoside-triphosphate diphosphatase NF002711.0 PRK02539 PRK02539.1 112 112 85 equivalog Y Y N DUF896 family protein 186826 Lactobacillales order 804 NCBI Protein Cluster (PRK) hypothetical protein DUF896 family protein NF002714.0 PRK02551 PRK02551.1 190 190 157 equivalog Y Y N class Ib ribonucleoside-diphosphate reductase assembly flavoprotein NrdI nrdI GO:0010181 186826 Lactobacillales order 2152 NCBI Protein Cluster (PRK) flavoprotein NrdI class Ib ribonucleoside-diphosphate reductase assembly flavoprotein NrdI Has a stimulatory effect on the ribonucleotide reductase activity of NrdH with NrdEF NF002763.0 PRK02833 PRK02833.1-1 138 138 143 equivalog Y Y N phosphate-starvation-inducible protein PsiE psiE 186826 Lactobacillales order 283 NCBI Protein Cluster (PRK) phosphate-starvation-inducible protein PsiE phosphate-starvation-inducible protein PsiE NF003410.0 PRK04778 PRK04778.1-4 754 754 575 equivalog Y Y N septation ring formation regulator EzrA ezrA 186826 Lactobacillales order 1846 NCBI Protein Cluster (PRK) septation ring formation regulator EzrA septation ring formation regulator EzrA NF003631.0 PRK05270 PRK05270.1-5 765 765 493 subfamily Y Y N UDP-glucose--hexose-1-phosphate uridylyltransferase 2.7.7.12 186826 Lactobacillales order 3120 NCBI Protein Cluster (PRK) galactose-1-phosphate uridylyltransferase UDP-glucose--hexose-1-phosphate uridylyltransferase NF004361.0 PRK05738 PRK05738.2-1 144 144 98 equivalog Y Y N 50S ribosomal protein L23 186826 Lactobacillales order 318 NCBI Protein Cluster (PRK) 50S ribosomal protein L23 50S ribosomal protein L23 NF004401.0 PRK05758 PRK05758.2-1 116 116 178 equivalog Y Y N F0F1 ATP synthase subunit delta 7.1.2.2 186826 Lactobacillales order 1254 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit delta F0F1 ATP synthase subunit delta NF004748.0 PRK06079 PRK06079.1 362 362 252 equivalog Y Y N enoyl-ACP reductase FabI fabI 1.3.1.9 186826 Lactobacillales order 1137 NCBI Protein Cluster (PRK) enoyl-(acyl carrier protein) reductase enoyl-ACP reductase FabI NF005117.0 PRK06549 PRK06549.1 159 159 130 equivalog Y Y N acetyl-CoA carboxylase biotin carboxyl carrier protein subunit 186826 Lactobacillales order 659 NCBI Protein Cluster (PRK) acetyl-CoA carboxylase biotin carboxyl carrier protein subunit acetyl-CoA carboxylase biotin carboxyl carrier protein subunit Composes the biotin carboxyl carrier protein subunit of the acetyl-CoA carboxylase complex NF005231.0 PRK06732 PRK06732.1 265 265 229 equivalog Y Y N phosphopantothenate--cysteine ligase 6.3.2.5 186826 Lactobacillales order 2162 NCBI Protein Cluster (PRK) phosphopantothenate--cysteine ligase phosphopantothenate--cysteine ligase NF005580.0 PRK07275 PRK07275.1 254 254 162 subfamily Y N N single-stranded DNA-binding protein 186826 Lactobacillales order 862 NCBI Protein Cluster (PRK) single-stranded DNA-binding protein single-stranded DNA-binding protein NF005588.0 PRK07309 PRK07309.1 576 576 391 equivalog Y Y N pyridoxal phosphate-dependent aminotransferase 2.6.1.- GO:0003824,GO:0009058,GO:0030170 186826 Lactobacillales order 2754 NCBI Protein Cluster (PRK) aromatic amino acid aminotransferase pyridoxal phosphate-dependent aminotransferase NF005590.0 PRK07315 PRK07315.1 443 443 293 equivalog Y Y N class II fructose-bisphosphate aldolase 4.1.2.13 GO:0004332,GO:0006096 186826 Lactobacillales order 798 NCBI Protein Cluster (PRK) fructose-bisphosphate aldolase class II fructose-bisphosphate aldolase Catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate NF008846.0 PRK11886 PRK11886.1-1 353 353 312 equivalog Y Y N bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA birA 6.3.4.15 186826 Lactobacillales order 1683 NCBI Protein Cluster (PRK) bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA NF008971.0 PRK12319 PRK12319.1 406 406 256 equivalog Y Y N acetyl-CoA carboxylase carboxyl transferase subunit alpha 186826 Lactobacillales order 1666 NCBI Protein Cluster (PRK) acetyl-CoA carboxylase subunit alpha acetyl-CoA carboxylase carboxyl transferase subunit alpha NF009257.0 PRK12613 PRK12613.1 243 243 141 equivalog Y Y N galactose-6-phosphate isomerase subunit LacA lacA 186826 Lactobacillales order 428 NCBI Protein Cluster (PRK) galactose-6-phosphate isomerase subunit LacA galactose-6-phosphate isomerase subunit LacA Catalyzes the interconversion of galactose 6-phosphate to tagatose 6-phosphate; tagatose pathway for galactose utilization NF009642.0 PRK13169 PRK13169.1-3 142 142 112 equivalog Y Y N DNA replication initiation control protein YabA yabA 186826 Lactobacillales order 134 NCBI Protein Cluster (PRK) DNA replication intiation control protein YabA DNA replication initiation control protein YabA NF009885.0 PRK13344 PRK13344.1 152 152 132 equivalog Y Y N transcriptional regulator Spx spx 186826 Lactobacillales order 476 NCBI Protein Cluster (PRK) transcriptional regulator Spx transcriptional regulator Spx NF010714.0 PRK14116 PRK14116.1 401 401 229 equivalog Y Y N 2,3-diphosphoglycerate-dependent phosphoglycerate mutase 5.4.2.11 186826 Lactobacillales order 575 NCBI Protein Cluster (PRK) phosphoglyceromutase 2,3-diphosphoglycerate-dependent phosphoglycerate mutase Catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate; 2,3-diphosphoglycerate-dependent NF010753.0 PRK14156 PRK14156.1 172 172 180 equivalog Y Y N nucleotide exchange factor GrpE grpE 186826 Lactobacillales order 1662 NCBI Protein Cluster (PRK) heat shock protein GrpE nucleotide exchange factor GrpE With DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins NF010776.0 PRK14179 PRK14179.1 445 445 284 equivalog Y Y N bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase GO:0004488 186826 Lactobacillales order 1966 NCBI Protein Cluster (PRK) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase Catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate NF013537.5 PF01378.22 IgG_binding_B 25 25 68 domain Y N N B domain 8161530 186826 Lactobacillales order 225 EBI-EMBL B domain B domain This domain is found as a tandem repeat in Streptococcal cell surface proteins, such as the IgG binding protein G. [1]. 8161530. Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR. Gallagher T, Alexander P, Bryan P, Gilliland GL;. Biochemistry 1994;33:4721-4729. (from Pfam) NF015035.5 PF03047.19 ComC 20.4 20.4 31 domain Y Y N ComC/BlpC family leader-containing pheromone/bacteriocin GO:0005186 7479953,9352904 186826 Lactobacillales order 1451 EBI-EMBL COMC family ComC/BlpC family leader peptide This family consists exclusively of streptococcal competence stimulating peptide precursors, which are generally up to 50 amino acid residues long. In all the members of this family, the leader sequence is cleaved after two conserved glycine residues; thus the leader sequence is of the double- glycine type [2]. Competence stimulating peptides (CSP) are small (less than 25 amino acid residues) cationic peptides. The N-terminal amino acid residue is negatively charged, either glutamate or aspartate. The C-terminal end is positively charged. The third residue is also positively charged: a highly conserved arginine [2]. A few COMC proteins and their precursors (not included in this family) do not fully follow the above description. In particular: the leader sequence in the CSP precursor from Streptococcus sanguis NCTC 7863 Swiss:O33758 is not of the double-glycine type; the CSP from Streptococcus gordonii NCTC 3165 Swiss:O33645 does not have a negatively charged N-terminus residue and has a lysine instead of arginine at the third position. Functionally, CSP act as pheromones, stimulating competence for genetic transformation in streptococci. In streptococci, the (CSP mediated) competence response requires exponential cell growth at a critical density, a relatively simple requirement when compared to the stationary-phase requirement of Haemophilus, or the late-logarithmic- phase of Bacillus [1]. All bacteria induced to competence by a particular CSP are said to belong to the same pherotype, because each CSP is recognised by a specific receptor (the signalling domain of a histidine kinase ComD). Pherotypes are not necessarily s. TRUNCATED at 1650 bytes (from Pfam) NF015193.5 PF03217.19 SlpA 23 15.6 63 domain Y Y N SLAP domain-containing protein 8522531 186826 Lactobacillales order 10179 EBI-EMBL Surface layer protein A domain Surface layer protein A domain This short domain is found in a variety of bacterial cell surface proteins. The domain is about 60 residues in length (although previously defined as 2 copies of this domain). It usually occurs in tandem pairs. It may be distantly related to the SH3 domain [1]. [1]. 8522531. Identification, cloning, and nucleotide sequence of a silent S-layer protein gene of Lactobacillus acidophilus ATCC 4356 which has extensive similarity with the S-layer protein gene of this species. Boot HJ, Kolen CP, Pouwels PH;. J Bacteriol 1995;177:7222-7230. (from Pfam) NF016182.5 PF04270.18 Strep_his_triad 27 5 52 domain Y Y N pneumococcal-type histidine triad protein 11349048,18632116,24312273 186826 Lactobacillales order 12063 EBI-EMBL Streptococcal histidine triad protein pneumococcal-type histidine triad protein All members of this family are proteins from Streptococcal species. The proteins are characterised by having a HxxHxH motif that usually occurs multiple times throughout the protein [1]. The histidine triad is predicted to bind metal cations, in particular Zn2+. The zinc is transferred, on the surface of the streptococcus from the Strep_his_triad protein, a zinc scavenger, to apo-ADCAII, a cell-surface lipoprotein transporter [3] that leads to Zn2+ uptake [2] into the bacterium. [1]. 11349048. Recombinant PhpA protein, a unique histidine motif-containing protein from Streptococcus pneumoniae, protects mice against intranasal pneumococcal challenge. Zhang Y, Masi AW, Barniak V, Mountzouros K, Hostetter MK, Green BA;. Infect Immun 2001;69:3827-3836. [2]. 24312273. New insights into histidine triad proteins: solution structure of a Streptococcus pneumoniae PhtD domain and zinc transfer to AdcAII. Bersch B, Bougault C, Roux L, Favier A, Vernet T, Durmort C;. PLoS One. 2013;8:e81168. [3]. 18632116. AdcAII, a new pneumococcal Zn-binding protein homologous with ABC transporters: biochemical and structural analysis. Loisel E, Jacquamet L, Serre L, Bauvois C, Ferrer JL, Vernet T, Di Guilmi AM, Durmort C;. J Mol Biol. 2008;381:594-606. (from Pfam) NF018273.5 PF06543.17 Lac_bphage_repr 21 21 49 domain Y N N Lactococcus bacteriophage repressor 186826 Lactobacillales order 546 EBI-EMBL Lactococcus bacteriophage repressor Lactococcus bacteriophage repressor This family represents the C-terminus of Lactococcus bacteriophage repressor proteins. (from Pfam) NF019739.5 PF08129.16 Antimicrobial17 25 25 57 PfamEq Y Y N enterocin 1071A family bacteriocin 10742203 186826 Lactobacillales order 18 EBI-EMBL Alpha/beta enterocin family enterocin 1071A family bacteriocin This family consists of the alpha and beta enterocins and lactococcin G peptides. These peptides have some antimicrobial properties; they inhibit the growth of Enterococcus spp. and a few other gram-positive bacteria. These peptides act as pore- forming toxins that create cell membrane channels through a barrel-stave mechanism and thus produce an ionic imbalance in the cell. These family of antimicrobial peptides belong to the class II group of bacteriocin [1]. [1]. 10742203. Characterization and cloning of the genes encoding enterocin 1071A and enterocin 1071B, two antimicrobial peptides produced by Enterococcus faecalis BFE 1071. Balla E, Dicks LM, Du Toit M, Van Der Merwe MJ, Holzapfel WH;. Appl Environ Microbiol 2000;66:1298-1304. (from Pfam) NF019875.5 PF08270.16 PRD_Mga 23 23 220 domain Y Y N M protein trans-acting positive regulator PRD domain-containing protein 11952907 186826 Lactobacillales order 3042 EBI-EMBL M protein trans-acting positive regulator (MGA) PRD domain M protein trans-acting positive regulator (MGA) PRD domain Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [1]. This corresponds to the PRD like region. [1]. 11952907. Two DNA-binding domains of Mga are required for virulence gene activation in the group A streptococcus. McIver KS, Myles RL;. Mol Microbiol 2002;43:1591-1601. (from Pfam) NF020399.5 PF08820.15 DUF1803 32.2 32.2 91 PfamAutoEq Y Y N DUF1803 domain-containing protein 186826 Lactobacillales order 2372 EBI-EMBL Domain of unknown function (DUF1803) Domain of unknown function (DUF1803) This small domain is found in one or two copies in proteins from bacteria. The function of this domain is unknown. (from Pfam) NF020441.5 PF08866.15 DUF1831 25 25 111 PfamEq Y N N Putative amino acid metabolism 20944212 186826 Lactobacillales order 2050 EBI-EMBL Putative amino acid metabolism Putative amino acid metabolism Solution of the structure of the Lactobacillus plantarum protein from this family has indicated a potential new fold with remote similarities to TBP-like (TATA-binding protein) structures. This similarity, in combination with genomic context analysis, leads us to propose an involvement in amino-acid metabolism. The potentially novel fold is an alpha + beta fold comprising two beta sheets packed against a single helix. The enzyme is present in the cytosol. [1]. 20944212. Structure of LP2179, the first representative of Pfam family PF08866, suggests a new fold with a role in amino-acid metabolism. Bakolitsa C, Kumar A, Carlton D, Miller MD, Krishna SS, Abdubek P, Astakhova T, Axelrod HL, Chiu HJ, Clayton T, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Grant JC, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Tien HJ, Trout CV, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:1205-1210. (from Pfam) NF020730.5 PF09168.15 PepX_N 25 25 157 PfamEq Y N N X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal GO:0006508,GO:0008239 12377124 186826 Lactobacillales order 5954 EBI-EMBL X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal Members of this family adopt a secondary structure consisting of a helical bundle of eight alpha helices and three beta strands, the last alpha helix connecting to the first strand of the catalytic domain. The first strand of the N-terminus also forms a small parallel beta sheet with strand 5' of catalytic domain. The domain mediates dimerisation of the protein, with two proline residues present in the domain being critical for interaction [1]. [1]. 12377124. The structural basis for catalysis and specificity of the X-prolyl dipeptidyl aminopeptidase from Lactococcus lactis. Rigolet P, Mechin I, Delage MM, Chich JF;. Structure. 2002;10:1383-1394. (from Pfam) NF022534.5 PF11083.13 Relaxase_C 30 30 125 domain Y Y N helical hairpin domain-containing protein 31039174 186826 Lactobacillales order 2337 EBI-EMBL C-terminal helical hairpin domain from relaxase conjugative relaxase C-terminal region This Pfam HMM is based on an open reading frame originally proposed to be SrtI, an immunity protein of the streptin biosynthesis locus, but the region is actually a pseudogene fragment of a conjugative relaxase. NF022632.5 PF11184.13 DUF2969 25 25 71 PfamAutoEq Y Y N DUF2969 family protein 186826 Lactobacillales order 1583 EBI-EMBL Protein of unknown function (DUF2969) DUF2969 family protein This family of proteins with unknown function appears to be restricted to Lactobacillales. (from Pfam) NF022663.5 PF11217.13 DUF3013 25 25 160 PfamAutoEq Y Y N DUF3013 family protein 186826 Lactobacillales order 2432 EBI-EMBL Protein of unknown function (DUF3013) DUF3013 family protein This bacterial family of proteins with unknown function appear to be restricted to Firmicutes. (from Pfam) NF022685.5 PF11240.13 DUF3042 25 25 54 PfamAutoEq Y Y N DUF3042 family protein 186826 Lactobacillales order 975 EBI-EMBL Protein of unknown function (DUF3042) DUF3042 family protein This family of proteins with unknown function appears to be restricted to Firmicutes. (from Pfam) NF023604.5 PF12182.13 DUF3642 22.7 22.7 93 domain Y Y N DUF3642 domain-containing protein 186826 Lactobacillales order 1258 EBI-EMBL Bacterial lipoprotein DUF3642 domain This domain family is found in bacteria, and is approximately 60 amino acids in length. There is a single completely conserved Y residue that may be functionally important. This domain is from a bacterial lipoprotein, a major virulence factor in Gram negative bacteria. (from Pfam) NF025860.5 PF14507.11 CppA_C 23.5 23.5 103 domain Y Y N CppA C-terminal domain-containing protein 21234750,8077717 186826 Lactobacillales order 2402 EBI-EMBL CppA C-terminal CppA C-terminal This is the C-terminal domain of the CppA protein found in species of Streptococcus. CppA is a putative C3-glycoprotein degrading proteinase, involved in pathogenicity [1,2]. It is often found associated with Pfam:PF14506. [1]. 8077717. Degradation of C3 by Streptococcus pneumoniae. Angel CS, Ruzek M, Hostetter MK;. J Infect Dis. 1994;170:600-608. [2]. 21234750. In silico prediction of horizontal gene transfer in Streptococcus thermophilus. Eng C, Thibessard A, Danielsen M, Rasmussen TB, Mari JF, Leblond P;. Arch Microbiol. 2011;193:287-297. (from Pfam) NF027313.5 PF15983.10 DUF4767 27 27 139 domain Y Y N DUF4767 domain-containing protein 186826 Lactobacillales order 3764 EBI-EMBL Domain of unknown function (DUF4767) Domain of unknown function (DUF4767) This domain family is found in bacteria, and is approximately 140 amino acids in length. There is a single completely conserved residue Q that may be functionally important. (from Pfam) NF027436.5 PF16110.10 DUF4828 23.3 23.3 79 PfamAutoEq Y Y N DUF4828 domain-containing protein 186826 Lactobacillales order 891 EBI-EMBL Domain of unknown function (DUF4828) Domain of unknown function (DUF4828) This family consists of uncharacterized proteins around 120 residues in length and is mainly found in various Enterococcus and Lactobacillus species. The function of this family is unknown. (from Pfam) NF027629.5 PF16305.10 DUF4947 25 25 169 PfamAutoEq Y Y N DUF4947 domain-containing protein 186826 Lactobacillales order 415 EBI-EMBL Domain of unknown function (DUF4947) Domain of unknown function (DUF4947) This small family consists of uncharacterized proteins around 220 residues in length and is mainly found in various Streptococcus mutans species. The function of this family is unknown. (from Pfam) NF033461.1 glycerol3P_ox_1 840 840 607 equivalog Y Y N type 1 glycerol-3-phosphate oxidase glpO GO:0004368,GO:0006072 18154320 186826 Lactobacillales order 3128 NCBIFAM type 1 glycerol-3-phosphate oxidase type 1 glycerol-3-phosphate oxidase Glycerol-3-phosphate oxidase, also called alpha-glycerophosphate oxidase (GlpO), is an FAD-dependent enzyme related to the glycerol-3-phosphate dehydrogenase GlpD. Notably, GlpO releases hydrogen peroxide, which can contribute to virulence. NF033794.2 chaper_CopZ_Eh 95 95 68 exception Y Y N copper chaperone CopZ copZ GO:0005507,GO:0046872 19903200 186826 Lactobacillales order 233 NCBIFAM copper chaperone CopZ copper chaperone CopZ Copper chaperone CopZ, as the name is used in Enterococcus hirae and related species, is a small copper-binding protein with close homology to domains found, sometimes in multiple copies, in various copper-translocating copper-translocating P-type ATPases, and to distinct families of other small copper chaperones that also named CopZ. NF036413.5 PF17255.7 EbsA 25.9 25.9 133 domain Y Y N EbsA family protein 8226689 186826 Lactobacillales order 2116 EBI-EMBL EbsA-like protein EbsA family protein This is a family of unknown function which contains the EbsA protein Swiss:P36920 from Enterococcus faecalis. The uncharacterized family is mainly found in lactobacilli and consists of two N-terminal transmembrane helices followed by a bacterial PH domain. (from Pfam) NF036837.5 PF17883.6 MBG 23.3 19.7 97 domain Y Y N MBG domain-containing protein 24593252 186826 Lactobacillales order 3333 EBI-EMBL MBG domain MBG domain This domain is found in a variety of bacterial extracellular proteins. Although initially described as having a divergent Ig fold this domain has a novel topology that is like a mirror image of the beta grasp fold. Hence the name of Mirror Beta Grasp (MBG) domain. [1]. 24593252. Structural and molecular insights into novel surface-exposed mucus adhesins from Lactobacillus reuteri human strains. Etzold S, MacKenzie DA, Jeffers F, Walshaw J, Roos S, Hemmings AM, Juge N;. Mol Microbiol. 2014;92:543-556. (from Pfam) NF037171.5 PF18041.6 MapZ_EC1 33.1 33.1 129 subfamily_domain Y Y N cell division site-positioning protein MapZ family protein 27346279 186826 Lactobacillales order 4283 EBI-EMBL MapZ extracellular domain 1 MapZ extracellular domain 1 This is the extracellular domain 1 (MapZextra1) found in Streptococcus pneumoniae cell division site positioning protein MapZ. MapZ ensures accurate placement of the bacterial division site. The domain is a rigid four alpha-helices with two flexible linkers. The N-terminal end of MapZextra1 is connected to the trans-membrane segment of MapZ whilst the C-terminal is linked to MapZextra2 via a serine rich linker (SRL).The highly conserved residues are not accessible at the surface but are directly involved in many inter-helices interactions allowing for rigidity [1]. [1]. 27346279. Structure-function analysis of the extracellular domain of the pneumococcal cell division site positioning protein MapZ. Manuse S, Jean NL, Guinot M, Lavergne JP, Laguri C, Bougault CM, VanNieuwenhze MS, Grangeasse C, Simorre JP;. Nat Commun. 2016;7:12071. (from Pfam) NF037394.5 PF18708.6 MapZ_C2 27.6 27.6 94 subfamily Y Y N cell division site-positioning protein MapZ family protein 25470041,27346279 186826 Lactobacillales order 4250 EBI-EMBL MapZ extracellular C-terminal domain 2 MapZ extracellular C-terminal domain 2 In the pneumococcus cell division, MapZ (Midcell Anchored Protein Z) locates at the division site before FtsZ and guides septum positioning. MapZ forms ring structures at the cell equator and moves apart as the cell elongates, therefore behaving as a permanent beacon of division sites. MapZ then positions the FtsZ-ring through direct protein-protein interactions [1]. Structural analysis indicate that it displays a bi-modular structure composed of two subdomains separated by a flexible serine-rich linker. The extracellular C-terminal domain carries a conserved patch of amino acids which plays a crucial function in binding peptidoglycan and positioning MapZ at the cell equator [2]. [1]. 25470041. MapZ marks the division sites and positions FtsZ rings in Streptococcus pneumoniae. Fleurie A, Lesterlin C, Manuse S, Zhao C, Cluzel C, Lavergne JP, Franz-Wachtel M, Macek B, Combet C, Kuru E, VanNieuwenhze MS, Brun YV, Sherratt D, Grangeasse C;. Nature. 2014;516:259-262. [2]. 27346279. Structure-function analysis of the extracellular domain of the pneumococcal cell division site positioning protein MapZ. Manuse S, Jean NL, Guinot M, Lavergne JP, Laguri C, Bougault CM, VanNieuwenhze MS, Grangeasse C, Simorre JP;. Nat Commun. 2016;7:12071. (from Pfam) NF037495.5 PF18710.6 ComR_TPR 26.5 26.5 222 domain Y N N ComR tetratricopeptide 27907154,27907189 186826 Lactobacillales order 2492 EBI-EMBL ComR tetratricopeptide ComR tetratricopeptide In Gram-positive bacteria, cell-to-cell communication mainly relies on extracellular signaling peptides. ComR is a member of the RNPP family, which positively controls competence for natural DNA transformation in streptococci. It is directly activated by the binding of its associated pheromone XIP [1]. The crystal structure analysis of ComR shows that it contains an N-terminal helix-turn-helix (HTH), DNA binding domain (DBD) and a C-terminal tetratricopeptide repeat (TPR) domain. The TPR domain is composed of 11 alpha-helices forming 5 TPR motifs followed by an additional C-terminal alpha-helix 16 called CAP. The pheromone XIP binding site is found in the TPR region. Biochemical and mutational analysis indicate that, if the interacting XIP is accepted it can then trigger the conformational change of the TPR domain to open the DBD-TPR interface to allow dimer formation that is required to bind DNA [2]. [1]. 27907189. Structural Insights into Streptococcal Competence Regulation by the Cell-to-Cell Communication System ComRS. Talagas A, Fontaine L, Ledesma-Garcia L, Mignolet J, Li de la Sierra-Gallay I, Lazar N, Aumont-Nicaise M, Federle MJ, Prehna G, Hols P, Nessler S;. PLoS Pathog. 2016;12:e1005980. [2]. 27907154. Pheromone Recognition and Selectivity by ComR Proteins among Streptococcus Species. Shanker E, Morrison DA, Talagas A, Nessler S, Federle MJ, Prehna G;. PLoS Pathog. 2016;12:e1005979. (from Pfam) NF038025.1 dapto_LiaX 350 350 512 exception Y Y N daptomycin-sensing surface protein LiaX liaX 31818937 186826 Lactobacillales order 1074 NCBIFAM daptomycin-sensing surface protein LiaX LiaX (lipid-II–interacting antibiotics X), as described in Enterococcus faecalis, is expressed under control of the the LiaR response regulator, and is involved in the process of resistance to daptomycin and to antimicrobial peptides of the innate immune response. NF038277.1 accessory_MacP 45 45 98 equivalog Y Y N cell wall synthase accessory phosphoprotein MacP macP 29487215 186826 Lactobacillales order 1107 NCBIFAM cell wall synthase accessory phosphoprotein MacP MacP was characterized in Streptococcus pneumoniae as a partner protein to the cell wall synthase PBP2a, required for its activity. NF039609.4 PF19405.4 DUF5978 25 15 73 domain Y N N Family of unknown function (DUF5978) 186826 Lactobacillales order 56 EBI-EMBL Family of unknown function (DUF5978) Family of unknown function (DUF5978) This presumed domain is found as highly identical tandem repeats in bacterial cell surface proteins associated with Bact_lectin. (from Pfam) NF039932.4 PF19387.4 DUF5962 25 25 99 subfamily Y Y N DUF5962 family protein 186826 Lactobacillales order 633 EBI-EMBL Family of unknown function (DUF5962) DUF5962 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000498) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide). (from Pfam) NF040278.4 PF19390.4 DUF5965 25 25 74 subfamily Y Y N DUF5965 family protein 186826 Lactobacillales order 361 EBI-EMBL Family of unknown function (DUF5965) DUF5965 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000561) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide). (from Pfam) NF040897.1 SPJ_0845_Nterm 24 24 25 domain Y Y N SPJ_0845 family protein 186826 Lactobacillales order 1523 NCBIFAM SPJ_0845 N-terminal domain NF040927.1 ABC_perm_SloB 460 460 271 subfamily Y Y N metal ABC transporter permease subunit 14526007 186826 Lactobacillales order 964 NCBIFAM metal ABC transporter permease subunit Members of this family are metal ABC transporter permease subunits, including SloB from Streptococcus mutans and a number of others, closely related but characterized as acting on different panels of metals, and named in a variety of ways. The SloABC transporter, for example, is characterized as acting on manganese and iron, but its regulator SloR responds only to manganese. NF041014.1 pilin_ComGG_2 40 40 101 equivalog Y Y N competence type IV pilus minor pilin ComGG comGG 186826 Lactobacillales order 2028 NCBIFAM competence type IV pilus minor pilin ComGG ComGG is an especially variable protein of ComG-like DNA binding/uptake type IV pilus formation systems. This HMM identifies ComGG proteins as found in Streptococcus pneumoniae, not Bacillus subtilis. NF041284.1 PrgO 100 100 90 equivalog Y Y N DNA segregation protein PrgO prgO 18245388 186826 Lactobacillales order 73 NCBIFAM DNA segregation protein PrgO NF041547.1 GntR_LSA1692 275 275 233 equivalog Y Y N GntR family transcriptional regulator, LSA1692 subfamily 186826 Lactobacillales order 445 NCBIFAM GntR family transcriptional regulator, LSA1692 subfamily NF041575.1 antitoxPezA_Strep 290 290 158 equivalog Y Y N type II toxin-antitoxin system antitoxin PezA pezA GO:0003677 17488720 186826 Lactobacillales order 679 NCBIFAM type II toxin-antitoxin system antitoxin PezA NF042930.1 EF0163_fam 65 65 165 equivalog Y Y N EF0163 family protein 26322633 186826 Lactobacillales order 533 NCBIFAM EF0163 family protein Members of this family, most of which are predicted to be lipoproteins, have an N-terminal lipoprotein signal peptide-like region, then a nearly 50 amino acid stretch rich in Glu, Asp, Gln, Asn, Ser, and Thr, and average about 170 amino acids in length. The founding member, EF0163 from Enterococcus faecalis, was found to be upregulated more than six-fold in a mice peritonitis model. NF042931.1 SAG1386_EF1546 80 80 158 equivalog Y Y N SAG1386/EF1546 family surface-associated protein 31801066 186826 Lactobacillales order 1729 NCBIFAM SAG1386/EF1546 family surface-associated protein Members of this family, which occur in Gram-positive bacteria such as Streptococcus pyogenes, Enterococcus faecalis, Lactococcus lactis, Lactobacillus acidophilus, average about 170 amino acids in length, and include a C-terminal region Lysin Motif (LysM) domain, a peptidoglycan-binding domain for surface-associated proteins. The family member SPy_0802 has been called a virulence factor capable of binding host red blood cells to block immune response by white cells, and was named S protein. NF042957.1 phage_res_AbiGI 300 300 249 equivalog Y Y N abortive phage resistance protein AbiGI abiGI 8795193,9872803 186826 Lactobacillales order 58 NCBIFAM abortive phage resistance protein AbiGI NF044928.2 PF20874.2 Relaxase_M 27 27 86 domain Y N N Relaxase central domain 186826 Lactobacillales order 3030 EBI-EMBL Relaxase central domain Relaxase central domain This domain is found in some relaxase proteins. (from Pfam) NF046452.1 PF21869.2 Dit-like_CBM2 27 27 228 domain Y N N Distal tail component, second carbohydrate binding domain 28196397 186826 Lactobacillales order 337 EBI-EMBL Distal tail component, second carbohydrate binding domain Distal tail component, second carbohydrate binding domain This domain is found in the distal tail component from Lactobacillus phage J-1 (Dit), which is involved in host recognition. This entry represents the second putative carbohydrate binding domain (CBM2). It folds into a beta-sandwich with two beta-sheets gathering 12 beta-strands [1]. This domain usually appears associated to Pfam:PF05709. Paper describing PDB structure 5ly8. [1]. 28196397. Evolved distal tail carbohydrate binding modules of Lactobacillus phage J-1: a novel type of anti-receptor widespread among lactic acid bacteria phages. Dieterle ME, Spinelli S, Sadovskaya I, Piuri M, Cambillau C;. Mol Microbiol. 2017;104:608-620. (from Pfam) NF047588.1 GlcsyltransPgfSStrep 500 500 308 equivalog Y Y N glycosyltransferase PgfS pgfS 24837294,29549320 186826 Lactobacillales order 222 NCBIFAM glycosyltransferase PgfS TIGR01000.1 TIGR01000 bacteriocin_acc 258.85 258.85 457 subfamily Y Y N bacteriocin secretion accessory protein 186826 Lactobacillales order 2433 JCVI bacteriocin secretion accessory protein bacteriocin secretion accessory protein This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193. TIGR01363.1 TIGR01363 strep_his_triad 33 33 348 subfamily_domain Y Y N pneumococcal-type histidine triad protein 11349048 186826 Lactobacillales order 11670 JCVI streptococcal histidine triad protein pneumococcal-type histidine triad protein This HMM represents the N-terminal half of a family of Streptococcal proteins that contain a signal peptide and then up to five repeats of a region that includes a His-X-X-His-X-His (histidine triad) motif. Three repeats are found in the seed alignment. Additional copies in more poorly conserved regions can be detected because this is a fragment-mode HMM. Members of this family from Streptococcus pneumoniae are suggested to cleave human C3, and the member PhpA has been shown in vaccine studies to be a protective antigen in mice. TIGR01886.1 TIGR01886 dipeptidase 632 632 466 equivalog Y Y N dipeptidase PepV pepV 3.4.13.- GO:0004151,GO:0006221,GO:0046872 12176387,9171382 186826 Lactobacillales order 3518 JCVI dipeptidase PepV dipeptidase PepV This model represents a small clade of dipeptidase enzymes which are members of the larger M25 subfamily of metalloproteases. Two characterized enzymes are included in the seed. One, from Lactococcus lactis has been shown to act on a wide range of dipeptides, but not larger peptides. The enzyme from Lactobacillus delbrueckii was originally characterized as a Xaa-His dipeptidase, specifically a carnosinase (beta-Ala-His) by complementation of an E. coli mutant. Further study, including the crystallization of the enzyme [1], has shown it to also be a non-specific dipeptidase. This group also includes enzymes from Streptococcus and Enterococcus. TIGR02113.1 TIGR02113 coaC_strep 261.4 261.4 177 equivalog Y Y N phosphopantothenoylcysteine decarboxylase coaC 4.1.1.36 GO:0004633,GO:0015937 11278255 186826 Lactobacillales order 1862 JCVI phosphopantothenoylcysteine decarboxylase phosphopantothenoylcysteine decarboxylase In most bacteria, a single bifunctional protein catalyses phosphopantothenoylcysteine decarboxylase and phosphopantothenate--cysteine ligase activities, sequential steps in coenzyme A biosynthesis (see TIGR00521). These activities reside in separate proteins encoded by tandem genes in some bacterial lineages. This model describes proteins from the genera Streptococcus and Enterococcus homologous to the N-terminal region of TIGR00521, corresponding to phosphopantothenoylcysteine decarboxylase activity. TIGR02114.1 TIGR02114 coaB_strep 217.2 217.2 228 equivalog Y Y N phosphopantothenate--cysteine ligase coaB 6.3.2.5 GO:0004632,GO:0015937 11278255 186826 Lactobacillales order 2347 JCVI phosphopantothenate--cysteine ligase phosphopantothenate--cysteine ligase In most bacteria, a single bifunctional protein catalyses phosphopantothenoylcysteine decarboxylase and phosphopantothenate--cysteine ligase activities, sequential steps in coenzyme A biosynthesis (see TIGR00521). These activities reside in separate proteins encoded by tandem genes in some bacterial lineages. This model describes proteins from the genera Streptococcus and Enterococcus homologous to the C-terminal region of TIGR00521, corresponding to phosphopantothenate--cysteine ligase activity. TIGR03107.1 TIGR03107 glu_aminopep 469.7 469.7 350 equivalog Y Y N glutamyl aminopeptidase pepA 3.4.11.7 8535515 186826 Lactobacillales order 2720 JCVI glutamyl aminopeptidase glutamyl aminopeptidase This model represents the M42.001 clade within MEROPS family M42. M42 includes glutamyl aminopeptidase as in the present model, deblocking aminopeptidases as from Pyrococcus horikoshii and related species, and endo-1,4-beta-glucanase (cellulase M) as from Clostridium thermocellum. The current family includes TIGR03766.2 TIGR03766 TIGR03766 500 500 496 equivalog Y Y N TIGR03766 family XrtG-associated glycosyltransferase 22037399 186826 Lactobacillales order 552 JCVI conserved hypothetical integral membrane protein TIGR03766 family XrtG-associated glycosyltransferase Models TIGR03110, TIGR03111, and TIGR03112 describe a three-gene system found in several Gram-positive bacteria, where TIGR03110 (XrtG) is distantly related to a putative transpeptidase, exosortase (TIGR02602). This HMM (rebuilt in 2023) describes a small clade that correlates by both gene clustering and phyletic pattern, although imperfectly, to the three gene system. Both this narrow clade, and the larger set of full-length homologous integral membrane proteins, have an especially well-conserved region near the C-terminus with an invariant tyrosine. Homology suggests glycosyltransferase activity. TIGR04035.1 TIGR04035 glucan_65_rpt 147.7 45 64 repeat Y N N glucan-binding repeat-containing protein GO:0030246 15576779 186826 Lactobacillales order 5091 JCVI glucan-binding repeat glucan-binding repeat This model describes a region of about 63 amino acids that is composed of three repeats of a more broadly distributed family of shorter repeats modeled by Pfam model PF01473. While the shorter repeats are often associated with choline binding (and therefore with cell wall binding), the longer repeat described here represents a subgroup of repeat sequences associated with glucan binding, as found in a number glycosylhydrolases. Shah, et al. describe a repeat consensus, WYYFDANGKAVTGAQTINGQTLYFDQDGKQVKG, that corresponds to half of the repeat as modeled here and one and a half copies of the repeat as modeled by PF01473. NF016725.5 PF04852.17 ALOG_dom 26.6 26.6 126 domain Y Y N ALOG domain-containing protein 19901325,23146749 1869181 Chitinophaga sp. species 1 EBI-EMBL ALOG domain ALOG domain The 125-residue ALOG (Arabidopsis LSH1 and oryza G1) domain is rich in basic amino acids, especially arginine, and is highly conserved among land plants. Members of the ALOG family of proteins function as key developmental regulators. It has been proposed that the ALOG domain originated from the N-terminal DNA-binding domains of integrases belonging to the tyrosine recombinase superfamily encoded by a distinct type of DIRS1-like LTR retrotransposon found in several eukaryotes. Secondary structure predictions revealed an all-alpha helical domain with four conserved helices [1,2]. Some proteins known to contain an ALOG domain are Arabidopsis thaliana LIGHT_DEPENDENT SHORT HYPOCOTYLS1 (LSH1),involved in phytochrome- dependent light signalling; Oryza G1, involved in the specification of sterile lemma identity and Plant defence proteins. [1]. 19901325. The homeotic gene long sterile lemma (G1) specifies sterile lemma identity in the rice spikelet. Yoshida A, Suzaki T, Tanaka W, Hirano HY;. Proc Natl Acad Sci U S A. 2009;106:20103-20108. [2]. 23146749. ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons. Iyer LM, Aravind L;. Biol Direct. 2012;7:39. (from Pfam) NF019525.5 PF07911.18 DUF1677 25 25 94 domain Y Y N DUF1677 domain-containing protein 1870990 Paenibacillus bouchesdurhonensis species 1 EBI-EMBL Protein of unknown function (DUF1677) Protein of unknown function (DUF1677) The sequences found in this family are all derived from hypothetical plant proteins of unknown function. The region features a number of highly conserved cysteine residues. (from Pfam) NF044811.2 PF21507.2 V18-19 27 27 380 domain Y Y N phage minor capsid protein 23091035 1871086 Brevundimonas sp. species 1 EBI-EMBL Sputnik minor capsid protein V18/19 phage minor capsid protein This entry includes Sputnik virus minor capsid proteins, such V19. Sputnik is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba [1]. It is an icosahedral virus and its capsid contains a major protein (V20) and two minor proteins (V18/19). Proteins in this entry have a single jelly-roll structure [1]. Paper describing PDB structure 3j26. [1]. 23091035. Structure of Sputnik, a virophage, at 3.5-A resolution. Zhang X, Sun S, Xiang Y, Wong J, Klose T, Raoult D, Rossmann MG;. Proc Natl Acad Sci U S A. 2012;109:18431-18436. (from Pfam) NF000476.1 myrA 625 625 295 exception Y Y Y 23S rRNA (guanine(748)-N(1))-methyltransferase MyrA myrA 1873 Micromonospora genus 4 NCBIFAM 23S rRNA (guanine(748)-N(1))-methyltransferase MyrA 23S rRNA (guanine(748)-N(1))-methyltransferase MyrA NF000024.1 ErmS 675 675 319 exception Y Y Y 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(S) erm(S) 1883 Streptomyces genus 5 NCBIFAM 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(S) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(S) NF000025.1 MFS_efflux_tcmA 999 999 538 exception Y Y Y tetracenomycin C efflux MFS transporter tcmA GO:0022857,GO:0055085 1883 Streptomyces genus 9 NCBIFAM tetracenomycin C efflux MFS transporter tetracenomycin C efflux MFS transporter NF000029.2 APH_9_Ib 675 675 330 exception Y Y Y aminoglycoside O-phosphotransferase APH(9)-Ib aph(9)-Ib 1883 Streptomyces genus 2 NCBIFAM aminoglycoside O-phosphotransferase APH(9)-Ib aminoglycoside O-phosphotransferase APH(9)-Ib NF000031.1 MFS_efflux_LmrA 850 850 484 exception Y Y N lincomycin efflux MFS transporter Lmr(A) lmr(A) 1883 Streptomyces genus 17 NCBIFAM lincomycin efflux MFS transporter Lmr(A) lincomycin efflux MFS transporter Lmr(A) NF000035.1 nosihep_NshR 500 500 274 exception Y Y Y NshR family nosiheptide/thiostrepton resistance 23S rRNA methyltransferase GO:0006396,GO:0046677 1883 Streptomyces genus 10 NCBIFAM NshR family nosiheptide/thiostrepton resistance 23S rRNA methyltransferase NshR family nosiheptide/thiostrepton resistance 23S rRNA methyltransferase NF000047.1 ErmV 500 500 259 exception Y Y Y 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(V) erm(V) 1883 Streptomyces genus 34 NCBIFAM 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(V) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(V) NF000087.1 ErmO 450 450 259 exception Y Y Y 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(O) erm(O) 1883 Streptomyces genus 306 NCBIFAM 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(O) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(O) NF000095.1 tet_MFS_OtrB 999 999 563 exception Y Y Y oxytetracycline resistance efflux MFS transporter OtrB otr(B) GO:0022857,GO:0055085 1883 Streptomyces genus 36 NCBIFAM oxytetracycline resistance efflux MFS transporter OtrB oxytetracycline resistance efflux MFS transporter OtrB NF000128.1 vanH-Sc 650 650 337 exception Y Y Y D-lactate dehydrogenase VanH-Sc vanH-Sc 1.1.1.28 1883 Streptomyces genus 33 NCBIFAM D-lactate dehydrogenase VanH D-lactate dehydrogenase VanH-Sc NF000133.1 Erm32 550 550 280 exception Y Y Y 23S rRNA (guanine(748)-N(1))-methyltransferase Erm(32) erm(32) 1883 Streptomyces genus 1 NCBIFAM 23S rRNA (guanine(748)-N(1))-methyltransferase Erm(32) 23S rRNA (guanine(748)-N(1))-methyltransferase Erm(32) NF000157.1 fusid_est_FusH 999 999 520 equivalog Y Y Y fusidic acid esterase FusH fusH GO:0006508 1883 Streptomyces genus 34 NCBIFAM fusidic acid esterase FusH fusidic acid esterase FusH NF000283.1 RPH_KJ151292.1 1700 1700 865 equivalog Y Y Y rifamycin-inactivating phosphotransferase Rph rph GO:0016310 1883 Streptomyces genus 17 NCBIFAM rifamycin-inactivating phosphotransferase Rph rifamycin-inactivating phosphotransferase Rph NF000338.1 fomA_AB016934.1.gene6 550 550 266 equivalog Y Y Y fosfomycin resistance kinase FomA fomA GO:0016301 1883 Streptomyces genus 4 NCBIFAM fosfomycin resistance kinase FomA fosfomycin resistance kinase FomA NF000362.1 self_GT_OleI 700 700 424 exception Y Y Y OleI family self-immunity macrolide glycosyltransferase 1883 Streptomyces genus 4 NCBIFAM OleI family self-immunity macrolide glycosyltransferase OleI family self-immunity macrolide glycosyltransferase NF000373.1 vanJ 700 700 330 equivalog Y Y Y teicoplanin resistance protein VanJ vanJ 1883 Streptomyces genus 26 NCBIFAM teicoplanin resistance protein VanJ teicoplanin resistance protein VanJ NF000487.1 stat 420 420 189 exception Y Y Y streptothricin N-acetyltransferase STAT sta GO:0008080 1883 Streptomyces genus 1 NCBIFAM streptothricin N-acetyltransferase STAT streptothricin N-acetyltransferase STAT NF000488.1 chrB 620 620 280 exception Y Y Y 23S rRNA (guanine(748)-N(1))-methyltransferase ChrB chrB 15561847 1883 Streptomyces genus 4 NCBIFAM 23S rRNA (guanine(748)-N(1))-methyltransferase ChrB 23S rRNA (guanine(748)-N(1))-methyltransferase ChrB ChrB, as the term is used for Streptomyces bikiniensis, is a 23S rRNA modification methyltransferase that provides self-protection during production of the 16-membered macrolide antibiotic chalcomycin. Note that the same gene symbol is also given to certain unrelated proteins involved in chromate resistance. NF009715.0 PRK13244 PRK13244.1-1 242 242 144 equivalog Y Y N protease inhibitor 1883 Streptomyces genus 1169 NCBI Protein Cluster (PRK) protease inhibitor protein protease inhibitor NF009717.0 PRK13244 PRK13244.1-3 292 292 147 equivalog Y N N protease inhibitor protein 1883 Streptomyces genus 54 NCBI Protein Cluster (PRK) protease inhibitor protein protease inhibitor protein NF012199.0 cml_V_MFS 830 830 412 exception Y Y Y chloramphenicol efflux MFS transporter CmlV cmlV 1883 Streptomyces genus 4 NCBIFAM chloramphenicol efflux MFS transporter CmlV chloramphenicol efflux MFS transporter CmlV NF022098.5 PF10631.14 DUF2477 20.6 20.6 142 domain Y Y N DUF2477 domain-containing protein 1883 Streptomyces genus 4 EBI-EMBL Protein of unknown function (DUF2477) Protein of unknown function (DUF2477) This is a family of proteins with no known function. The family is rich in proline residues. (from Pfam) NF024011.5 PF12597.13 Cox20 25 25 101 domain Y Y N cytochrome c oxidase assembly protein COX20 family protein GO:0005743,GO:0033617 10671482,23125284,24403053 1883 Streptomyces genus 10 EBI-EMBL Cytochrome c oxidase assembly protein COX20 cytochrome c oxidase assembly protein COX20 family protein Complex IV (CIV) is a copper-heme oxidase that couples electron transfer from cytochrome c to oxygen with proton extrusion across the inner membrane to contribute to the proton gradient required for ATP generation. This entry includes fungal mitochondrial complex IV assembly factor Cox20 [1] and its homologues (also known as FAM36A in metazoa [2]. Human CIV is formed by three catalytic core subunits (COX1/2/3). COX20 has been found to form a complex with SCO1, SCO2, and newly synthesized COX2. It may act as a chaperone in the early steps of COX2 maturation [3]. [1]. 10671482. Identification of Cox20p, a novel protein involved in the maturation and assembly of cytochrome oxidase subunit 2. Hell K, Tzagoloff A, Neupert W, Stuart RA;. J Biol Chem. 2000;275:4571-4578. [2]. 23125284. A mutation in the FAM36A gene, the human ortholog of COX20, impairs cytochrome c oxidase assembly and is associated with ataxia and muscle hypotonia. Szklarczyk R, Wanschers BF, Nijtmans LG, Rodenburg RJ, Zschocke J, Dikow N, van den Brand MA, Hendriks-Franssen MG, Gilissen C, Veltman JA, Nooteboom M, Koopman WJ, Willems PH, Smeitink JA, Huynen MA, van den Heuvel LP;. Hum Mol Genet. 2013;22:656-667. [3]. 24403053. Human COX20 cooperates with SCO1 and SCO2 to mature COX2 and promote the assembly of cytochrome c oxidase. Bourens M, Boulet A, Leary SC, Barrientos A;. Hum Mol Genet. 2014;23:2901-2913. (from Pfam) NF032894.1 APH_3pp_Ia 600 600 272 exception Y Y Y aminoglycoside O-phosphotransferase APH(3'')-Ia aph(3'')-Ia GO:0046677 1883 Streptomyces genus 16 NCBIFAM aminoglycoside O-phosphotransferase APH(3'')-Ia aminoglycoside O-phosphotransferase APH(3'')-Ia Members of this family are aminoglycoside O-phosphotransferases. They modify the 3'' site found in streptomycin, and therefore confer resistance to streptomycin. NF033066.0 APH_3p_VIIIa 520 520 267 exception Y Y Y aminoglycoside O-phosphotransferase APH(3')-VIIIa aph(3')-VIIIa 2.7.1.95 1883 Streptomyces genus 13 NCBIFAM aminoglycoside O-phosphotransferase APH(3')-VIII aminoglycoside O-phosphotransferase APH(3')-VIIIa NF033099.1 bla_Exo 650 650 312 exception Y Y Y Exo family class A beta-lactamase bla2a 3.5.2.6 GO:0008800 1883 Streptomyces genus 77 NCBIFAM Exo family class A beta-lactamase Exo family class A beta-lactamase The founding member of this family of class A beta-lactamases is named Exo because it is an exocellular protein from Streptomyces albus, that is, it can be recovered from the culture medium (see PMID:6975618). The exocellular trait is common for beta-lactamases of Gram-positive bacteria, but the name Exo is applied only to this narrow family. NF033101.0 blaL 650 650 325 exception Y Y Y BlaL family class A beta-lactamase 3.5.2.6 GO:0008800 1883 Streptomyces genus 6 NCBIFAM BlaL family class A beta-lactamase BlaL family class A beta-lactamase NF033180.1 AAC_3_VIII 560 560 286 exception Y Y Y aminoglycoside N-acetyltransferase AAC(3)-VIII aac(3)-VIII GO:0046677 1883 Streptomyces genus 23 NCBIFAM aminoglycoside N-acetyltransferase AAC(3)-VIII aminoglycoside N-acetyltransferase AAC(3)-VIII NF033402.1 linaridin_RiPP 35 35 63 subfamily Y Y N linaridin family RiPP 26256511 1883 Streptomyces genus 50 NCBIFAM linaridin family RiPP linaridin family RiPP Linaridins are ribosomally translated, post-translationally modified peptide natural products, or RiPPs. Examples include cypemycin, SGR-1832, and legonaridin. NF033416.1 YM-216391_RiPP 35 35 35 subfamily Y Y N YM-216391 family RiPP peptide 22248379 1883 Streptomyces genus 6 NCBIFAM YM-216391 family RiPP peptide YM-216391 family RiPP peptide YM-216391 represents one of the rarer known classes of ribosomally translated, post-translationally modified peptide (RiPP) antibiotics. NF038371.1 phegan_RiPP_fam 28 28 37 subfamily Y Y N pheganomycin family RiPP precursor 25402768 1883 Streptomyces genus 15 NCBIFAM pheganomycin family RiPP precursor NF039766.4 PF19981.4 DUF6417 28.4 28.4 69 subfamily Y Y N DUF6417 family protein 19025863 1883 Streptomyces genus 1419 EBI-EMBL Family of unknown function (DUF6417) DUF6417 family protein This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000087) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the lasalocid biosynthetic gene cluster from Streptomyces lasaliensis [1]. This family appears to be predominantly found in Actinobacteria. [1]. 19025863. Analysis of specific mutants in the lasalocid gene cluster: evidence for enzymatic catalysis of a disfavoured polyether ring closure. Smith L, Hong H, Spencer JB, Leadlay PF;. Chembiochem. 2008;9:2967-2975. (from Pfam) NF041217.1 BagE_FevW 800 800 424 exception Y Y N bagremycin/ferroverdin synthetase BagE/FevW bagE 22065278,30526412,31409675 1883 Streptomyces genus 67 NCBIFAM bagremycin/ferroverdin synthetase BagE/FevW NF041218.1 BagM_FevK 420 420 215 exception Y Y N bagremycin/ferroverdin biosynthesis UbiX family decarboxylase BagM/FevK bagM GO:0003824 22065278,30526412,31409675 1883 Streptomyces genus 56 NCBIFAM bagremycin/ferroverdin biosynthesis UbiX family decarboxylase BagM/FevK NF041219.1 BagN_FevL 1000 1000 502 exception Y Y N bagremycin/ferroverdin biosynthesis UbiD family decarboxylase BagN/FevL bagN GO:0016831 22065278,30526412,31409675 1883 Streptomyces genus 76 NCBIFAM bagremycin/ferroverdin biosynthesis UbiD family decarboxylase BagN/FevL NF041220.1 BagH_FevF 630 630 305 exception Y Y N bagremycin/ferroverdin biosynthesis o-aminophenol oxidase BagH/FevF bagH 22065278,30526412,31409675 1883 Streptomyces genus 51 NCBIFAM bagremycin/ferroverdin biosynthesis o-aminophenol oxidase BagH/FevF NF041221.1 BagZ_FevE 200 200 122 exception Y Y N bagremycin/ferroverdin biosynthesis copper chaperon BagZ/FevE bagZ 22065278,30526412,31409675 1883 Streptomyces genus 43 NCBIFAM bagremycin/ferroverdin biosynthesis copper chaperon BagZ/FevE NF041222.1 BagA_FevW 1000 1000 529 exception Y Y N bagremycin/ferroverdin biosynthesis tyrosine ammonia-lyase BagA/FevW bagA 22065278,30526412,31409675 1883 Streptomyces genus 66 NCBIFAM bagremycin/ferroverdin biosynthesis tyrosine ammonia-lyase BagA/FevW NF041223.1 BagB_FevI 500 500 257 exception Y Y N bagremycin/ferroverdin biosynthesis DhnA-type aldolase BagB/FevI bagB 22065278,30526412,31409675 1883 Streptomyces genus 42 NCBIFAM bagremycin/ferroverdin biosynthesis DhnA-type aldolase BagB/FevI NF041224.1 BagC_FevH 750 750 368 exception Y Y N bagremycin/ferroverdin biosynthesis 3,4-AHBA synthase BagC/FevH bagC 22065278,30526412,31409675 1883 Streptomyces genus 39 NCBIFAM bagremycin/ferroverdin biosynthesis 3,4-AHBA synthase BagC/FevH NF041226.1 BagK_FevA1 800 800 453 equivalog Y Y N bagremycin/ferroverdin biosynthesis FAD-dependent oxygenase BagK/FevA1 bagK 22065278,30526412,31409675 1883 Streptomyces genus 68 NCBIFAM bagremycin/ferroverdin biosynthesis FAD-dependent oxygenase BagK/FevA1 NF041227.1 BagG_FevA2 850 850 455 exception Y Y N bagremycin/ferroverdin biosynthesis FAD-dependent oxygenase BagG/FevA2 bagG 22065278,30526412,31409675 1883 Streptomyces genus 65 NCBIFAM bagremycin/ferroverdin biosynthesis FAD-dependent oxygenase BagG/FevA2 NF041228.1 BagJ_FevB 800 800 452 exception Y Y N bagremycin/ferroverdin transporter BagJ/FevB bagJ 22065278,30526412,31409675 1883 Streptomyces genus 48 NCBIFAM bagremycin/ferroverdin transporter BagJ/FevB NF041229.1 BagF_FevY 700 700 340 exception Y Y N phospho-2-dehydro-3-deoxyheptonate aldolase BagF/FevY bagF 22065278,30526412,31409675 1883 Streptomyces genus 37 NCBIFAM phospho-2-dehydro-3-deoxyheptonate aldolase BagF/FevY NF041230.1 BagL_FevM 230 230 145 exception Y Y N MarR family transcriptional regulator BagL/FevM bagL 22065278,30526412,31409675 1883 Streptomyces genus 50 NCBIFAM MarR family transcriptional regulator BagL/FevM NF041231.1 BagI_FevR 500 500 315 exception Y Y N AfsR/SARP family transcriptional regulator BagI/FevR bagI 22065278,30526412,31409675 1883 Streptomyces genus 58 NCBIFAM AfsR/SARP family transcriptional regulator BagI/FevR NF041232.1 BagY_FevT 700 700 367 exception Y Y N LuxR family transcriptional regulator BagY/FevT bagY 22065278,30526412,31409675 1883 Streptomyces genus 50 NCBIFAM LuxR family transcriptional regulator BagY/FevT NF041563.1 amorph_syn 540 540 304 equivalog Y Y N (-)-alpha-amorphene synthase 4.2.3.162 GO:0016114,GO:0016829,GO:0046872 23307484,27666571,27829890 1883 Streptomyces genus 610 NCBIFAM (-)-alpha-amorphene synthase NF041564.1 eudesmol_syn 680 680 341 equivalog Y Y N 7-epi-alpha-eudesmol synthase 4.2.3.169 GO:0016114,GO:0016829,GO:0046872 23307484,27829890 1883 Streptomyces genus 604 NCBIFAM 7-epi-alpha-eudesmol synthase NF047623.1 Stavidin 300 300 183 equivalog Y Y N streptavidin GO:0009374 33708394,3951999 1883 Streptomyces genus 74 NCBIFAM streptavidin NF009246.0 PRK12599 PRK12599.1-5 92 92 83 equivalog Y N N putative monovalent cation/H+ antiporter subunit F 188708 Thermotogae class 54 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit F putative monovalent cation/H+ antiporter subunit F NF009999.0 PRK13471 PRK13471.1 124 124 85 equivalog Y Y N F0F1 ATP synthase subunit C 188708 Thermotogae class 45 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit C F0F1 ATP synthase subunit C Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit C is part of the membrane proton channel F0 NF010545.0 PRK13935 PRK13935.1 365 365 254 equivalog Y N N stationary phase survival protein SurE 3.1.3.6 188708 Thermotogae class 76 NCBI Protein Cluster (PRK) stationary phase survival protein SurE stationary phase survival protein SurE NF010556.0 PRK13951 PRK13951.1 560 560 492 equivalog Y Y N bifunctional shikimate kinase AroK/3-dehydroquinate synthase AroB aroB 2.7.1.71,4.2.3.4 188708 Thermotogae class 39 NCBI Protein Cluster (PRK) bifunctional shikimate kinase/3-dehydroquinate synthase bifunctional shikimate kinase AroK/3-dehydroquinate synthase AroB Catalyzes the formation of shikimate 3-phosphate from shikimate and the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate in aromatic amino acid biosynthesis NF010598.0 PRK13992 PRK13992.1 183 183 205 equivalog Y Y N septum site-determining protein MinC minC 188708 Thermotogae class 52 NCBI Protein Cluster (PRK) septum formation inhibitor septum site-determining protein MinC Blocks the formation of polar Z-ring septums NF010736.0 PRK14138 PRK14138.1 395 395 244 equivalog Y N N NAD-dependent deacetylase 188708 Thermotogae class 12 NCBI Protein Cluster (PRK) NAD-dependent deacetylase NAD-dependent deacetylase NF010937.0 PRK14357 PRK14357.1 658 658 448 equivalog Y Y N bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU glmU 2.7.7.23 188708 Thermotogae class 67 NCBI Protein Cluster (PRK) bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU Catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis NF011106.0 PRK14533 PRK14533.1 128 128 91 equivalog Y N N co-chaperonin GroES 188708 Thermotogae class 56 NCBI Protein Cluster (PRK) co-chaperonin GroES co-chaperonin GroES NF027560.5 PF16235.10 DUF4894 28 28 122 PfamAutoEq Y Y N DUF4894 domain-containing protein 188708 Thermotogae class 67 EBI-EMBL Domain of unknown function (DUF4894) Domain of unknown function (DUF4894) A small family of uncharacterized proteins around 180 residues in length and found in various Thermotoga species. The function of this family is unknown. (from Pfam) NF027561.5 PF16236.10 DUF4895 25 25 218 PfamAutoEq Y Y N DUF4895 domain-containing protein 188708 Thermotogae class 83 EBI-EMBL Domain of unknown function (DUF4895) Domain of unknown function (DUF4895) A small family of uncharacterized proteins around 250 residues in length and found in various Thermotoga species. The function of this family is unknown. (from Pfam) NF028499.5 PF17190.9 RecG_N 23.1 23.1 89 PfamEq Y N N RecG N-terminal helical domain 11595187 188708 Thermotogae class 89 EBI-EMBL RecG N-terminal helical domain RecG N-terminal helical domain This four helical bundle domain is found at the N-terminus of bacterial RecG proteins [1]. [1]. 11595187. Structural analysis of DNA replication fork reversal by RecG. Singleton MR, Scaife S, Wigley DB;. Cell. 2001;107:79-89. (from Pfam) NF037082.5 PF18298.6 NusG_add 27 27 109 domain Y N N NusG additional domain 23415559 188708 Thermotogae class 82 EBI-EMBL NusG additional domain NusG additional domain This domain is found in Thermotoga maritima NusG, which interacts with RNA polymerase and other proteins to form multi-component complexes that modulate transcription. This domain is referred to as Domain II and is an additional domain inserted into the N-terminal domain [1]. [1]. 23415559. An autoinhibited state in the structure of Thermotoga maritima NusG. Drogemuller J, Stegmann CM, Mandal A, Steiner T, Burmann BM, Gottesman ME, Wohrl BM, Rosch P, Wahl MC, Schweimer K;. Structure. 2013;21:365-375. (from Pfam) NF041090.1 Cyc-maltodext_AglB 540 540 470 equivalog Y Y N cyclomaltodextrinase aglB 3.2.1.54 GO:0005975,GO:0047798 12127967 188708 Thermotogae class 46 NCBIFAM cyclomaltodextrinase NF041091.1 asp_aminotase_Arch 550 550 376 equivalog Y Y N aspartate aminotransferase aspC 2.6.1.1 GO:0004069 15103638 188708 Thermotogae class 88 NCBIFAM aspartate aminotransferase NF041093.1 CheC_Thtogales 250 250 201 equivalog Y Y N CheY-P phosphatase CheC cheC GO:0006935,GO:0016787 15546616,16469702 188708 Thermotogae class 53 NCBIFAM CheY-P phosphatase CheC NF041096.1 esterase_EstD 600 600 421 equivalog Y Y N esterase EstD estD 3.1.1.1 GO:0052689 17466017 188708 Thermotogae class 19 NCBIFAM esterase EstD NF041101.1 manno_glu_gly_synth 640 640 431 equivalog Y Y N mannosylglucosylglycerate synthase mggS 2.4.1.- GO:0016757 20061481 188708 Thermotogae class 41 NCBIFAM mannosylglucosylglycerate synthase NF041119.1 CheD_Thtga 240 240 160 equivalog Y Y N chemoreceptor glutamine deamidase/glutamate methylesterase CheD cheD 3.1.1.61,3.5.1.44 GO:0006935,GO:0008984,GO:0050568 16469702 188708 Thermotogae class 59 NCBIFAM chemoreceptor glutamine deamidase/glutamate methylesterase CheD NF046519.1 PF22136.1 MpAgo_N-like 27 27 65 domain Y N N Bacterial argonaute protein N-terminal domain 27035975,28520746 188708 Thermotogae class 14 EBI-EMBL Bacterial argonaute protein N-terminal domain Bacterial argonaute protein N-terminal domain Argonaute proteins are key effectors of eukaryotic RNA interference and, in prokaryotes, function in host genome defense. This entry represents a domain found at the N-terminus of the Marinitoga piezophila Argonaute (MpAgo) protein that uses 5'-hydroxylated guide RNAs to recognise and cleave single-stranded target sequences rather than the 5'-phosphorylated guides used by all known Argonautes [1]. This domain adopts alpha/beta structure consisting of four-stranded beta-sheet and two helices. Compared to other Argonaute proteins, this domain differs in both its secondary structure and its orientation relative to the MID/PIWI lobe. Paper describing PDB structure 5i4a. [1]. 27035975. A bacterial Argonaute with noncanonical guide RNA specificity. Kaya E, Doxzen KW, Knoll KR, Wilson RC, Strutt SC, Kranzusch PJ, Doudna JA;. Proc Natl Acad Sci U S A. 2016;113:4057-4062. Paper describing PDB structure 5ux0. [2]. 28520746. DNA recognition by an RNA-guided bacterial Argonaute. Doxzen KW, Doudna JA;. PLoS One. 2017;12:e0177097. (from Pfam) NF046644.1 PF22362.1 Ago_MID_bact 27 27 172 domain Y N N Argonaute, middle domain, bacteria 27035975,28520746 188708 Thermotogae class 15 EBI-EMBL Argonaute, middle domain, bacteria Argonaute, middle domain, bacteria This entry represents the middle domain of bacterial argonaute (Ago) [1,2]. Ago bind small RNA or DNA guides which provide base-pairing specificity for recognition and cleavage of complementary nucleic acid targets. Bacterial Ago adopt a bilobed structure; an N-terminal and a PAZ domain constitute one lobe, the second one consists of a middle (MID) domain and the catalytic PIWI domain. This domain mediates the recognition of the 5' end of the guide [1,2]. Paper describing PDB structure 5i4a. [1]. 27035975. A bacterial Argonaute with noncanonical guide RNA specificity. Kaya E, Doxzen KW, Knoll KR, Wilson RC, Strutt SC, Kranzusch PJ, Doudna JA;. Proc Natl Acad Sci U S A. 2016;113:4057-4062. Paper describing PDB structure 5ux0. [2]. 28520746. DNA recognition by an RNA-guided bacterial Argonaute. Doxzen KW, Doudna JA;. PLoS One. 2017;12:e0177097. (from Pfam) NF005563.0 PRK07234 PRK07234.1-3 454 454 454 equivalog Y N N putative monovalent cation/H+ antiporter subunit D 188709 Thermotogaceae family 12 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit D putative monovalent cation/H+ antiporter subunit D NF010550.0 PRK13943 PRK13943.1 359 359 322 equivalog Y Y N protein-L-isoaspartate O-methyltransferase 2.1.1.77 11080641 188709 Thermotogaceae family 16 NCBI Protein Cluster (PRK) protein-L-isoaspartate O-methyltransferase protein-L-isoaspartate O-methyltransferase Catalyzes the methyl esterification of L-isoaspartyl residues that are formed in damaged proteins NF010943.0 PRK14363 PRK14363.1 273 273 204 equivalog Y N N Maf-like protein 188709 Thermotogaceae family 10 NCBI Protein Cluster (PRK) Maf-like protein Maf-like protein NF011231.0 PRK14638 PRK14638.1 188 188 150 equivalog Y Y N ribosome maturation factor RimP rimP 188709 Thermotogaceae family 16 NCBI Protein Cluster (PRK) hypothetical protein ribosome maturation factor RimP NF011270.0 PRK14677 PRK14677.1 124 124 108 equivalog Y N N hypothetical protein 188709 Thermotogaceae family 16 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF033413.1 RiPP_TM1316 35 35 31 equivalog Y Y N Cys-rich RiPP peptide 23974142 188709 Thermotogaceae family 2 NCBIFAM Cys-rich RiPP peptide Cys-rich RiPP peptide Member of this family include the small, Cys-rich peptide TM1316 of Thermotoga maritima, encoded near the peptide-modifying radical SAM/SPASM protein TM1317 (AE000512.1). TM1316 is expressed at very high levels in stationary phase. NF010500.0 PRK13919 PRK13919.1 226 226 186 subfamily Y N N putative RNA polymerase sigma E protein 188786 Thermaceae family 45 NCBI Protein Cluster (PRK) putative RNA polymerase sigma E protein putative RNA polymerase sigma E protein NF010892.0 PRK14299 PRK14299.1 392 392 291 equivalog Y N N chaperone protein DnaJ 188786 Thermaceae family 99 NCBI Protein Cluster (PRK) chaperone protein DnaJ chaperone protein DnaJ NF023004.5 PF11572.13 DUF3234 23.7 23.7 95 PfamAutoEq Y Y N DUF3234 domain-containing protein 188786 Thermaceae family 54 EBI-EMBL Protein of unknown function (DUF3234) Protein of unknown function (DUF3234) This bacterial family of proteins has no known function. Some members in this family of proteins are annotated as TTHA0547 however this cannot be confirmed. (from Pfam) NF026145.5 PF14795.11 Leucyl-specific 25 25 56 PfamEq Y N N Leucine-tRNA synthetase-specific domain 10811626 188786 Thermaceae family 109 EBI-EMBL Leucine-tRNA synthetase-specific domain Leucine-tRNA synthetase-specific domain This short region is found only in leucyl-tRNA synthetases. It is flexibly linked to the enzyme-core by beta-ribbons structures [1] [1]. 10811626. The 2 A crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue. Cusack S, Yaremchuk A, Tukalo M;. EMBO J. 2000;19:2351-2361. (from Pfam) NF036755.5 PF18274.6 V_ATPase_prox 27 27 52 domain Y N N Vacuolar ATPase Subunit I N-terminal proximal lobe 21787787 188786 Thermaceae family 115 EBI-EMBL Vacuolar ATPase Subunit I N-terminal proximal lobe Vacuolar ATPase Subunit I N-terminal proximal lobe This domain is found in the cytoplasmic N-terminal domain of vacuolar ATP synthase subunit I present in Meiothermus ruber. Subunit I is a homolog of subunit A which associates with the membrane-bound complex of eukaryotic vacuolar H+-ATPase (V-ATPase) acidification machinery. The domain forms the proximal lobe that caps one end of the alpha helix bundle, with the distal lobe capping the other end. Although the two lobes exhibit a similar motif, the molecular nature of the coupling with the identical stalks is thought to be dissimilar [1]. [1]. 21787787. Crystal structure of the cytoplasmic N-terminal domain of subunit I, a homolog of subunit a, of V-ATPase. Srinivasan S, Vyas NK, Baker ML, Quiocho FA;. J Mol Biol. 2011;412:14-21. (from Pfam) NF041566.1 branchenz_Thermus 920 920 527 equivalog Y Y N 1,4-alpha-glucan branching protein 2.4.1.18 GO:0003844,GO:0030979 21097495 188786 Thermaceae family 91 NCBIFAM 1,4-alpha-glucan branching protein NF041567.1 mtaseRsmF_Thermus 690 690 443 equivalog Y Y N 16S rRNA (cytosine(1407)-C(5))-methyltransferase RsmF rsmF 2.1.1.178 GO:0001510,GO:0008168 20558545 188786 Thermaceae family 106 NCBIFAM 16S rRNA (cytosine(1407)-C(5))-methyltransferase RsmF NF042418.1 LysJ_Th_th 700 700 386 equivalog Y Y N [LysW]-aminoadipate semialdehyde transaminase LysJ lysJ 2.6.1.118 GO:0006525,GO:0008483,GO:0019878 11489859,19620981 188786 Thermaceae family 74 NCBIFAM [LysW]-aminoadipate semialdehyde transaminase LysJ NF042921.1 HpaC_Thermus 200 200 150 equivalog Y Y N 4-hydroxyphenylacetate 3-monooxygenase reductase subunit hpaC 1.5.1.36 GO:0009056,GO:0010181,GO:0036382 17729270 188786 Thermaceae family 85 NCBIFAM 4-hydroxyphenylacetate 3-monooxygenase reductase subunit NF044631.2 PF20814.2 CAA3_Cox_suIV 27.5 27.5 64 domain Y N N CAA3-type cytochrome c oxidase subunit IV 22763450 188786 Thermaceae family 75 EBI-EMBL CAA3-type cytochrome c oxidase subunit IV CAA3-type cytochrome c oxidase subunit IV Cytochrome c oxidase plays a key role in the respiratory chain of mitochondria and aerobic prokaryotes. This electron transfer complex consists of three subunits, SU I/III, IIc and IV, which together form a bundle of 23 transmembrane (TM) helices and a bulky extra-membrane cytochrome c/cupredoxin domain. This family represents subunit IV, which shows two connected TM helices [1]. It is predominantly found in Deinococcus-Thermus. Paper describing PDB structure 2yev. [1]. 22763450. Structural insights into electron transfer in caa3-type cytochrome oxidase. Lyons JA, Aragao D, Slattery O, Pisliakov AV, Soulimane T, Caffrey M;. Nature. 2012;487:514-518. (from Pfam) NF044832.2 PF21591.2 Hera_DD 27 27 52 domain Y N N RNA helicase Hera, dimerization domain 19050012,19710183 188786 Thermaceae family 104 EBI-EMBL RNA helicase Hera, dimerization domain RNA helicase Hera, dimerization domain This domain is found at the C-terminal region of Heat resistant RNA dependent ATPase from Thermus thermophilus (also known as Hera) the first DEAD box helicase that forms a stable dimer in the absence of ligands. This dimerization domain (DD) folds into a single turn of a left-handed super-helix [1,2]. Paper describing PDB structure 3eaq. [1]. 19050012. A novel dimerization motif in the C-terminal domain of the Thermus thermophilus DEAD box helicase Hera confers substantial flexibility. Klostermeier D, Rudolph MG;. Nucleic Acids Res. 2009;37:421-430. Paper describing PDB structure 3i32. [2]. 19710183. The Thermus thermophilus DEAD box helicase Hera contains a modified RNA recognition motif domain loosely connected to the helicase core. Rudolph MG, Klostermeier D;. RNA. 2009;15:1993-2001. (from Pfam) NF045947.1 ProDh_Thermus 500 500 307 equivalog Y Y N proline dehydrogenase 1.5.5.2 GO:0004657,GO:0006562 17344208,18426222 188786 Thermaceae family 88 NCBIFAM proline dehydrogenase NF046492.1 PF22047.1 RecJ_C 30 30 110 domain Y N N Single-stranded-DNA-specific exonuclease RecJ C-terminal domain 10633092,20129927 188786 Thermaceae family 110 EBI-EMBL Single-stranded-DNA-specific exonuclease RecJ C-terminal domain Single-stranded-DNA-specific exonuclease RecJ C-terminal domain This entry represents a C-terminal domain present in a set of RecJ proteins, such as RecJ from Thermus thermophilus. The RecJ protein of Escherichia coli plays an important role in a number of DNA repair and recombination pathways. RecJ catalyses processive degradation of single-stranded DNA in a 5'-to-3' direction. Sequences highly related to those encoding RecJ can be found in many of the eubacterial genomes sequenced to date [1,2]. Paper describing PDB structure 2zxo. [1]. 20129927. Structure of RecJ exonuclease defines its specificity for single-stranded DNA. Wakamatsu T, Kitamura Y, Kotera Y, Nakagawa N, Kuramitsu S, Masui R;. J Biol Chem. 2010;285:9762-9769. [2]. 10633092. A thermostable single-strand DNase from Methanococcus jannaschii related to the RecJ recombination and repair exonuclease from Escherichia coli. Rajman LA, Lovett ST;. J Bacteriol. 2000;182:607-612. (from Pfam) NF047406.1 TransRegPerRTherm 200 200 130 equivalog Y Y N manganese-dependent transcriptional regulator PerR perR GO:0003677,GO:0006355 38735869 188786 Thermaceae family 79 NCBIFAM manganese-dependent transcriptional regulator PerR NF047407.1 TransRegMntRTherm 350 350 227 equivalog Y Y N manganese-dependent transcriptional regulator MntR mntR GO:0003677,GO:0003700,GO:0006355,GO:0046914,GO:0046983 38735869 188786 Thermaceae family 79 NCBIFAM manganese-dependent transcriptional regulator MntR NF000784.0 PRK00052 PRK00052.4-5 409 409 298 subfamily Y Y N prolipoprotein diacylglyceryl transferase 2.4.99.- 188787 Deinococci class 242 NCBI Protein Cluster (PRK) prolipoprotein diacylglyceryl transferase prolipoprotein diacylglyceryl transferase NF001790.0 PRK00517 PRK00517.3-3 269 269 262 equivalog Y Y N 50S ribosomal protein L11 methyltransferase 188787 Deinococci class 228 NCBI Protein Cluster (PRK) ribosomal protein L11 methyltransferase 50S ribosomal protein L11 methyltransferase NF006841.0 PRK09357 PRK09357.2-2 640 640 421 equivalog Y Y N dihydroorotase 3.5.2.3 188787 Deinococci class 235 NCBI Protein Cluster (PRK) dihydroorotase dihydroorotase NF007150.0 PRK09585 PRK09585.3-5 585 585 393 equivalog Y Y N anhydro-N-acetylmuramic acid kinase 2.7.1.170 188787 Deinococci class 69 NCBI Protein Cluster (PRK) anhydro-N-acetylmuramic acid kinase anhydro-N-acetylmuramic acid kinase NF008706.0 PRK11713 PRK11713.7-1 273 273 232 equivalog Y Y N 16S rRNA (uracil(1498)-N(3))-methyltransferase 2.1.1.193 188787 Deinococci class 211 NCBI Protein Cluster (PRK) 16S ribosomal RNA methyltransferase RsmE 16S rRNA (uracil(1498)-N(3))-methyltransferase NF008945.0 PRK12292 PRK12292.3-3 409 409 368 equivalog Y Y N ATP phosphoribosyltransferase regulatory subunit 188787 Deinococci class 100 NCBI Protein Cluster (PRK) ATP phosphoribosyltransferase regulatory subunit ATP phosphoribosyltransferase regulatory subunit NF008986.0 PRK12333 PRK12333.1 292 292 204 equivalog Y N N nucleoside triphosphate pyrophosphohydrolase 188787 Deinococci class 197 NCBI Protein Cluster (PRK) nucleoside triphosphate pyrophosphohydrolase nucleoside triphosphate pyrophosphohydrolase NF008994.0 PRK12337 PRK12337.1 603 603 492 equivalog Y N N 2-phosphoglycerate kinase 188787 Deinococci class 202 NCBI Protein Cluster (PRK) 2-phosphoglycerate kinase 2-phosphoglycerate kinase NF009344.0 PRK12705 PRK12705.1-1 831 831 572 equivalog Y N N hypothetical protein 188787 Deinococci class 238 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010403.0 PRK13829 PRK13829.1 145 145 177 equivalog Y N N 16S rRNA-processing protein RimM 188787 Deinococci class 192 NCBI Protein Cluster (PRK) 16S rRNA-processing protein RimM 16S rRNA-processing protein RimM NF010499.0 PRK13918 PRK13918.1 274 274 205 equivalog Y N N CRP/FNR family transcriptional regulator 188787 Deinococci class 172 NCBI Protein Cluster (PRK) CRP/FNR family transcriptional regulator CRP/FNR family transcriptional regulator NF010501.0 PRK13920 PRK13920.1 225 225 213 subfamily Y N N putative anti-sigmaE protein 188787 Deinococci class 62 NCBI Protein Cluster (PRK) putative anti-sigmaE protein putative anti-sigmaE protein NF010520.0 PRK13922 PRK13922.13-5 343 343 263 equivalog Y Y N rod shape-determining protein MreC mreC 188787 Deinococci class 91 NCBI Protein Cluster (PRK) rod shape-determining protein MreC rod shape-determining protein MreC NF010538.0 PRK13926 PRK13926.1 285 285 213 equivalog Y N N ribonuclease HII 188787 Deinococci class 212 NCBI Protein Cluster (PRK) ribonuclease HII ribonuclease HII NF010554.0 PRK13948 PRK13948.1 217 217 192 equivalog Y Y N shikimate kinase 2.7.1.71 188787 Deinococci class 198 NCBI Protein Cluster (PRK) shikimate kinase shikimate kinase Catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis NF010680.0 PRK14079 PRK14079.1 386 386 349 equivalog Y N N recombination protein F 188787 Deinococci class 219 NCBI Protein Cluster (PRK) recombination protein F recombination protein F NF010700.0 PRK14100 PRK14100.1 332 332 237 equivalog Y Y N 2-phosphosulfolactate phosphatase 188787 Deinococci class 180 NCBI Protein Cluster (PRK) 2-phosphosulfolactate phosphatase 2-phosphosulfolactate phosphatase Catalyzes the formation of (2R)-3-sulfolactate from (2R)-2-phospho-3-sulfolactate NF010770.0 PRK14173 PRK14173.1 411 411 287 equivalog Y N N bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase 188787 Deinococci class 191 NCBI Protein Cluster (PRK) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase NF010885.0 PRK14292 PRK14292.1 585 585 371 equivalog Y N N chaperone protein DnaJ 188787 Deinococci class 118 NCBI Protein Cluster (PRK) chaperone protein DnaJ chaperone protein DnaJ NF010978.0 PRK14401 PRK14401.1 163 163 187 equivalog Y N N membrane protein 188787 Deinococci class 203 NCBI Protein Cluster (PRK) membrane protein membrane protein NF011090.0 PRK14513 PRK14513.1 347 347 201 equivalog Y N N ATP-dependent Clp protease proteolytic subunit 188787 Deinococci class 103 NCBI Protein Cluster (PRK) ATP-dependent Clp protease proteolytic subunit ATP-dependent Clp protease proteolytic subunit NF011211.0 PRK14618 PRK14618.1 489 489 328 equivalog Y Y N NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 1.1.1.94 188787 Deinococci class 195 NCBI Protein Cluster (PRK) NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NAD(P)H-dependent glycerol-3-phosphate dehydrogenase Catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate NF011239.0 PRK14645 PRK14645.1 149 149 154 equivalog Y Y N ribosome maturation factor RimP rimP 188787 Deinococci class 180 NCBI Protein Cluster (PRK) hypothetical protein ribosome maturation factor RimP NF011256.0 PRK14662 PRK14662.1 150 150 123 equivalog Y N N 4'-phosphopantetheinyl transferase 188787 Deinococci class 204 NCBI Protein Cluster (PRK) 4'-phosphopantetheinyl transferase 4'-phosphopantetheinyl transferase NF011386.0 PRK14811 PRK14811.1 414 414 269 equivalog Y Y N DNA-formamidopyrimidine glycosylase 3.2.2.23 188787 Deinococci class 194 NCBI Protein Cluster (PRK) formamidopyrimidine-DNA glycosylase DNA-formamidopyrimidine glycosylase Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents; acts as DNA glycosylase that recognizes and removes damaged bases NF011409.0 PRK14835 PRK14835.1 425 425 279 equivalog Y Y N isoprenyl transferase 188787 Deinococci class 192 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate synthase isoprenyl transferase NF011524.0 PRK14963 PRK14963.1 601 601 647 equivalog Y N N DNA polymerase III subunits gamma and tau 2.7.7.7 188787 Deinococci class 247 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunits gamma and tau NF022920.5 PF11482.13 DUF3208 25 25 108 PfamAutoEq Y Y N DUF3208 family protein 188787 Deinococci class 182 EBI-EMBL Protein of unknown function (DUF3208) DUF3208 family protein This bacterial family of proteins has no known function. (from Pfam) NF022934.5 PF11497.13 NADH_Oxid_Nqo15 25 25 123 PfamEq Y Y N NADH-quinone oxidoreductase subunit 15 1.6.5.9 16469879 188787 Deinococci class 180 EBI-EMBL NADH-quinone oxidoreductase chain 15 NADH-quinone oxidoreductase subunit 15 This protein, Nqo15, is a part of respiratory complex 1 which is a complex that plays a central role in cellular energy production in both bacteria and mitochondria. Nqo15 has a similar fold to Frataxin, the mitochondrial iron chaperone. This protein may have a role in iron-sulphur cluster regeneration in the complex. This domain represents more than half the molecular mass of the entire complex [1]. [1]. 16469879. Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. Sazanov LA, Hinchliffe P;. Science. 2006;311:1430-1436. (from Pfam) NF023041.5 PF11609.13 DUF3248 27 27 63 PfamAutoEq Y Y N DUF3248 domain-containing protein 188787 Deinococci class 164 EBI-EMBL Protein of unknown function (DUF3248) Protein of unknown function (DUF3248) This family of proteins is thought to be the product of the gene TT1592 from Thermus thermophilus however this cannot be confirmed. Currently there is no known function. (from Pfam) NF024134.5 PF12723.12 DUF3809 25 25 137 PfamAutoEq Y Y N DUF3809 family protein 188787 Deinococci class 219 EBI-EMBL Protein of unknown function (DUF3809) DUF3809 family protein This family of proteins is functionally uncharacterised. This family of proteins is found in Deinococci bacteria. Proteins in this family are typically between 117 and 157 amino acids in length. (from Pfam) NF033622.1 repair_DdrC 150 150 223 equivalog Y Y N DNA damage response protein DdrC ddrC 28542368 188787 Deinococci class 132 NCBIFAM DNA damage response protein DdrC DNA damage response protein DdrC DdrC is a DNA-binding protein that seems restricted to the genus Deinococcus, and that plays a role in the ability of members of that genus to recover from fragmentation of their DNA. Note that the region where DdrC is found in Deinococcus radiodurans R1 originally had incorrect structural annotation, with a feature designated DR_0003 shown on the opposite strand. NF037069.5 PF18222.6 PilN_bio_d 25 25 102 domain Y N N PilN biogenesis protein dimerization domain 24218553 188787 Deinococci class 211 EBI-EMBL PilN biogenesis protein dimerization domain PilN biogenesis protein dimerization domain This domain is found in PilN type IV pilus biogenesis protein present in Thermus thermophiles. PilN is an integral inner membrane protein needed for the formation of type IV pilus. This domain forms a dimer which is mediated by symmetric contacts between residues in alpha-1, beta-1, beta-3 and alpha-3 [1]. [1]. 24218553. Structure and assembly of an inner membrane platform for initiation of type IV pilus biogenesis. Karuppiah V, Collins RF, Thistlethwaite A, Gao Y, Derrick JP;. Proc Natl Acad Sci U S A. 2013;110:E4638-E4647. (from Pfam) NF037490.5 PF18690.6 DUF5639 25 25 81 domain Y Y N DUF5639 domain-containing protein 188787 Deinococci class 232 EBI-EMBL Family of unknown function (DUF5639) Family of unknown function (DUF5639) This is a domain of unknown function which is mainly found in Deinococcus-Thermus. Some family members can be found in the C-terminal region of Pfam:PF01565. (from Pfam) NF041586.1 MqnP_DT 430 430 277 exception Y Y N menaquinone biosynthesis prenyltransferase MqnP mqnP 30447488 188787 Deinococci class 201 NCBIFAM menaquinone biosynthesis prenyltransferase MqnP, Deinococcus/Thermus-type NF044835.2 PF21620.2 SlpA_C 27 13.5 878 domain Y N N S-layer protein SlpA, beta-barrel 26074883,26909071 188787 Deinococci class 197 EBI-EMBL S-layer protein SlpA, beta-barrel S-layer protein SlpA, beta-barrel This entry represents the beta-barrel found at the C-terminal of S-layer protein SlpA and similar S-layer proteins. SlpA plays an important role in the structural organisation and integrity of the S-layer [1,2]. In Deinococcus radiodurans, SlpA binds the carotenoid deinoxanthin, a strong protective antioxidant specific of this bacterium suggested to be part of the first lane of defense against UV radiation, especially under desiccation [2]. [1]. 26074883. Purification and characterization of DR_2577 (SlpA) a major S-layer protein from Deinococcus radiodurans. Farci D, Bowler MW, Esposito F, McSweeney S, Tramontano E, Piano D;. Front Microbiol. 2015;6:414. [2]. 26909071. The S-layer Protein DR_2577 Binds Deinoxanthin and under Desiccation Conditions Protects against UV-Radiation in Deinococcus radiodurans. Farci D, Slavov C, Tramontano E, Piano D;. Front Microbiol. 2016;7:155. (from Pfam) NF046210.1 PF22210.1 VP17_central_barrel 27 27 82 domain Y N N Large MCP VP17 central beta-barrel 23623731 188787 Deinococci class 37 EBI-EMBL Large MCP VP17 central beta-barrel Large MCP VP17 central beta-barrel This entry represents the central beta-barrel of VP17, the large major capsid protein of of bacteriophage P23-77 [1]. [1]. 23623731. Bacteriophage P23-77 capsid protein structures reveal the archetype of an ancient branch from a major virus lineage. Rissanen I, Grimes JM, Pawlowski A, Mantynen S, Harlos K, Bamford JK, Stuart DI;. Structure. 2013;21:718-726. (from Pfam) NF046706.1 PF22231.1 Hera_RBD 27 27 74 domain Y N N DEAD box helicase Hera, RNA-binding domain 19710183,23625962 188787 Deinococci class 206 EBI-EMBL DEAD box helicase Hera, RNA-binding domain DEAD box helicase Hera, RNA-binding domain This domain is found at the C-terminal end DEAD box helicase Hera from Thermus thermophilus. This entry represents the RNA binding domain, which is located C-terminal to the dimerisation domain Pfam:PF21591. This domain is responsible for binding of Hera to 23S rRNA. It consists of a central four-stranded beta-sheet, flanked by an alpha-helix, and a long loop connecting beta-strands 3 and 4 that replaces helix alpha2 present in canonical RNA recognition motif (RRM) [1,2]. Paper describing PDB structure 3i31. [1]. 19710183. The Thermus thermophilus DEAD box helicase Hera contains a modified RNA recognition motif domain loosely connected to the helicase core. Rudolph MG, Klostermeier D;. RNA. 2009;15:1993-2001. Paper describing PDB structure 4i67. [2]. 23625962. Recognition of two distinct elements in the RNA substrate by the RNA-binding domain of the T. thermophilus DEAD box helicase Hera. Steimer L, Wurm JP, Linden MH, Rudolph MG, Wohnert J, Klostermeier D;. Nucleic Acids Res. 2013;41:6259-6272. (from Pfam) NF047377.1 heat_HspR_dupli 300 300 214 exception Y Y N heat shock protein transcriptional repressor HspR, fused homodimer type hspR GO:0003700,GO:0009408 188787 Deinococci class 184 NCBIFAM heat shock protein transcriptional repressor HspR, fused homodimer type Members of this family are a tandem-duplicated, double-length version of the heat shock gene transcriptional represssor HspR. The duplication architecture is most common in the genus Deinococcus. NF001217.0 PRK00192 PRK00192.1-4 373 373 265 equivalog Y N N mannosyl-3-phosphoglycerate phosphatase 1890424 Synechococcales order 87 NCBI Protein Cluster (PRK) mannosyl-3-phosphoglycerate phosphatase mannosyl-3-phosphoglycerate phosphatase NF001929.0 PRK00704 PRK00704.1-6 316 316 163 equivalog Y Y N photosystem I reaction center protein subunit XI 1890424 Synechococcales order 24 NCBI Protein Cluster (PRK) photosystem I reaction center protein subunit XI photosystem I reaction center protein subunit XI NF003369.0 PRK04447 PRK04447.1-2 420 420 394 equivalog Y N N hypothetical protein 1890424 Synechococcales order 173 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003607.0 PRK05257 PRK05257.2-3 734 734 497 equivalog Y Y N malate:quinone oxidoreductase 1.1.5.4 1890424 Synechococcales order 144 NCBI Protein Cluster (PRK) malate:quinone oxidoreductase malate:quinone oxidoreductase NF009565.0 PRK13019 PRK13019.1-5 158 158 98 equivalog Y Y N ATP-dependent Clp protease adapter ClpS clpS 1890424 Synechococcales order 61 NCBI Protein Cluster (PRK) ATP-dependent Clp protease adaptor ATP-dependent Clp protease adapter ClpS NF011227.0 PRK14634 PRK14634.1 203 203 155 equivalog Y Y N ribosome maturation factor RimP rimP 1890424 Synechococcales order 119 NCBI Protein Cluster (PRK) hypothetical protein ribosome maturation factor RimP NF019479.5 PF07864.16 DUF1651 22 22 74 domain Y Y N DUF1651 domain-containing protein 1890424 Synechococcales order 942 EBI-EMBL Protein of unknown function (DUF1651) Protein of unknown function (DUF1651) This is a family containing bacterial proteins of unknown function. (from Pfam) NF022746.5 PF11302.13 DUF3104 27 27 69 domain Y Y N DUF3104 domain-containing protein 1890424 Synechococcales order 366 EBI-EMBL Protein of unknown function (DUF3104) Protein of unknown function (DUF3104) This family of proteins with unknown function appears to be restricted to Cyanobacteria. (from Pfam) TIGR03894.1 TIGR03894 chp_P_marinus_1 67.75 67.75 95 hypoth_equivalog Y Y N TIGR03894 family protein 1890424 Synechococcales order 97 JCVI conserved hypothetical protein, TIGR03894 family TIGR03894 family protein This protein family is restricted to the Prochlorococcus and Synechococcus lineages of the Cyanobacteria, and is sporadic in those lineages. Members average 100 amino acids in length, including a 30-residue, highly polar, low complexity region sandwiched between an N-terminal region of about 60 residues and a C-terminal [KR]VVR[KR]RS motif, both well-conserved. The function is unknown. NF023848.5 PF12432.13 INTS1_RP2B-bd 25 25 156 domain Y Y N RP2B-binding domain-containing protein 33243860,34762484 1891207 Thaumasiovibrio subtropicus species 1 EBI-EMBL Integrator complex subunit 1, RP2B-binding domain Integrator complex subunit 1, RP2B-binding domain Integrator (INT) complex is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. It binds the C-terminal domain (CTD) of RNA polymerase II (Pol II) and functions as an RNA endonuclease to cleave different classes of RNAs, regulating the transcription of both protein-coding genes and noncoding elements [1,2]. Integrator also associates with protein phosphatase 2A (PP2A) core enzyme to form the INTAC complex [1] which regulates transcription through dephosphorylation of Pol II CTD. This entry includes the Integrator complex subunit 1 (INTS1) which forms the backbone module of the complex (it consists of four modules: backbone, shoulder, phosphatase and endonuclease) through the association with INTS2 and INTS7 to form a rigid scaffold. The backbone and shoulder modules form a central cruciform scaffold. INTS1 is an all-alpha helical protein with four repetitive helix hairpin domains towards the C-terminal (R1-R4) [1]. This entry represents a domain found at the N-terminal of INTS1, which interacts with Pol II subunit RPB2 and form interface A [2]. [1]. 33243860. Identification of Integrator-PP2A complex (INTAC), an RNA polymerase II phosphatase. Zheng H, Qi Y, Hu S, Cao X, Xu C, Yin Z, Chen X, Li Y, Liu W, Li J, Wang J, Wei G, Liang K, Chen FX, Xu Y;. Science. 2020; [Epub ahead of print]. [2]. 34762484. Structural basis of Integrator-mediated transcription regulation. Fianu I, Chen Y, Dienemann C, Dybkov O, Linden A, Urlaub H, Cramer P;. Science. 2021;374:883-887. (from Pfam) NF007888.0 PRK10591 PRK10591.2-2 109 109 93 equivalog Y N N hypothetical protein 1903409 Erwiniaceae family 19 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF041896.1 pecestase_PemA 700 700 365 equivalog Y Y N pectinesterase PemA pemA 3.1.1.11 GO:0030599,GO:0045490 11162105,17717531,8370537 1903410 Pectobacteriaceae family 221 NCBIFAM pectinesterase PemA NF041897.1 pecacetest_PaeY 1000 1000 549 equivalog Y Y N pectin acetylesterase PaeY paeY GO:0016787 9218776 1903410 Pectobacteriaceae family 330 NCBIFAM pectin acetylesterase PaeY NF041898.1 pec_ly_PelI 620 620 349 equivalog Y Y N pectate lyase PelI pelI 4.2.2.2 GO:0030570,GO:0045490 18430740,9393696 1903410 Pectobacteriaceae family 154 NCBIFAM pectate lyase PelI NF041899.1 pec_ly_PelN 740 740 437 equivalog Y Y N pectate lyase PelN pelN 4.2.2.2 GO:0030570,GO:0045490 23475966 1903410 Pectobacteriaceae family 175 NCBIFAM pectate lyase PelN NF041900.1 pec_ly_PelZ 840 840 422 equivalog Y Y N pectate lyase PelZ pelZ 4.2.2.2 GO:0030570,GO:0045490 8955401 1903410 Pectobacteriaceae family 206 NCBIFAM pectate lyase PelZ NF041901.1 pecestase_PemB 700 700 379 equivalog Y Y N pectinesterase PemB pemB 3.1.1.11 GO:0030599,GO:0045490 8830237 1903410 Pectobacteriaceae family 344 NCBIFAM pectinesterase PemB NF041903.1 exo-PATE_PelX 1490 1490 734 equivalog Y Y N pectate disaccharide-lyase PelX pelX 4.2.2.9 GO:0045490,GO:0047489 10049400 1903410 Pectobacteriaceae family 328 NCBIFAM pectate disaccharide-lyase PelX NF041904.1 exo-PATE_PelW 1000 1000 543 equivalog Y Y N pectate disaccharide-lyase PelW pelW 4.2.2.9 GO:0045490,GO:0047489 10383957,1766386 1903410 Pectobacteriaceae family 258 NCBIFAM pectate disaccharide-lyase PelW NF003984.0 PRK05471 PRK05471.1-3 423 423 265 equivalog Y Y N CDP-diacylglycerol diphosphatase 3.6.1.26 1903411 Yersiniaceae family 216 NCBI Protein Cluster (PRK) CDP-diacylglycerol pyrophosphatase CDP-diacylglycerol diphosphatase NF007053.0 PRK09505 PRK09505.1-3 1269 1269 687 equivalog Y Y N alpha-amylase 3.2.1.1 1903411 Yersiniaceae family 820 NCBI Protein Cluster (PRK) alpha-amylase alpha-amylase NF008664.0 PRK11667 PRK11667.1-2 232 232 163 equivalog Y N N hypothetical protein 1903411 Yersiniaceae family 211 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF011334.0 PRK14750 PRK14750.1 53 53 29 equivalog Y Y N K(+)-transporting ATPase subunit F 1903411 Yersiniaceae family 50 NCBI Protein Cluster (PRK) potassium-transporting ATPase subunit F K(+)-transporting ATPase subunit F Component of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions NF041433.1 UmoA 200 200 178 subfamily Y Y N UmoA family flagellar biogenesis regulator umoA 9723914 1903414 Morganellaceae family 114 NCBIFAM UmoA family flagellar biogenesis regulator NF041435.1 UmoD 150 150 158 subfamily Y Y N UmoD family flagellar biogenesis regulator umoD 9723914 1903414 Morganellaceae family 232 NCBIFAM UmoD family flagellar biogenesis regulator NF003682.0 PRK05305 PRK05305.2-2 284 284 212 equivalog Y Y N phosphatidylserine decarboxylase 4.1.1.65 191411 Chlorobiales order 38 NCBI Protein Cluster (PRK) phosphatidylserine decarboxylase phosphatidylserine decarboxylase NF005506.0 PRK07118 PRK07118.1-5 388 388 279 equivalog Y Y N Fe-S cluster domain-containing protein 191411 Chlorobiales order 22 NCBI Protein Cluster (PRK) ferredoxin Fe-S cluster domain-containing protein NF006842.0 PRK09357 PRK09357.2-3 695 695 440 equivalog Y Y N dihydroorotase 3.5.2.3 191411 Chlorobiales order 35 NCBI Protein Cluster (PRK) dihydroorotase dihydroorotase NF008705.0 PRK11713 PRK11713.6-4 343 343 248 equivalog Y Y N 16S rRNA (uracil(1498)-N(3))-methyltransferase 2.1.1.193 191411 Chlorobiales order 28 NCBI Protein Cluster (PRK) 16S ribosomal RNA methyltransferase RsmE 16S rRNA (uracil(1498)-N(3))-methyltransferase NF009058.0 PRK12392 PRK12392.1 494 494 333 subfamily Y N N bacteriochlorophyll c synthase 191411 Chlorobiales order 51 NCBI Protein Cluster (PRK) bacteriochlorophyll c synthase bacteriochlorophyll c synthase NF009852.0 PRK13320 PRK13320.1-4 439 439 270 equivalog Y Y N pantothenate kinase 2.7.1.33 191411 Chlorobiales order 4 NCBI Protein Cluster (PRK) pantothenate kinase pantothenate kinase NF009958.0 PRK13425 PRK13425.1 501 501 292 equivalog Y Y N F0F1 ATP synthase subunit gamma 191411 Chlorobiales order 31 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit gamma F0F1 ATP synthase subunit gamma Produces ATP from ADP in the presence of a proton gradient across the membrane; the gamma chain is a regulatory subunit NF010542.0 PRK13932 PRK13932.1 436 436 261 equivalog Y N N stationary phase survival protein SurE 191411 Chlorobiales order 33 NCBI Protein Cluster (PRK) stationary phase survival protein SurE stationary phase survival protein SurE NF010771.0 PRK14174 PRK14174.1 530 530 295 equivalog Y N N bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase 191411 Chlorobiales order 28 NCBI Protein Cluster (PRK) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase NF010874.0 PRK14281 PRK14281.1 619 619 397 equivalog Y N N chaperone protein DnaJ 191411 Chlorobiales order 34 NCBI Protein Cluster (PRK) chaperone protein DnaJ chaperone protein DnaJ NF011042.0 PRK14472 PRK14472.1 198 198 175 equivalog Y Y N F0F1 ATP synthase subunit B 191411 Chlorobiales order 33 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit B F0F1 ATP synthase subunit B Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B is part of the membrane proton channel NF011368.0 PRK14787 PRK14787.1 177 177 167 equivalog Y N N lipoprotein signal peptidase 191411 Chlorobiales order 33 NCBI Protein Cluster (PRK) lipoprotein signal peptidase lipoprotein signal peptidase NF011401.0 PRK14826 PRK14826.1 268 268 226 equivalog Y N N putative deoxyribonucleotide triphosphate pyrophosphatase 191411 Chlorobiales order 33 NCBI Protein Cluster (PRK) putative deoxyribonucleotide triphosphate pyrophosphatase putative deoxyribonucleotide triphosphate pyrophosphatase NF011516.0 PRK14955 PRK14955.1 560 560 397 equivalog Y N N DNA polymerase III subunits gamma and tau 191411 Chlorobiales order 34 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunits gamma and tau NF001063.0 PRK00117 PRK00117.5-3 186 186 165 equivalog Y Y N recombination regulator RecX recX 191412 Chlorobiaceae family 20 NCBI Protein Cluster (PRK) recombination regulator RecX recombination regulator RecX NF002507.0 PRK01903 PRK01903.1-1 225 225 150 equivalog Y N N ribonuclease P 3.1.26.5 191412 Chlorobiaceae family 7 NCBI Protein Cluster (PRK) ribonuclease P ribonuclease P NF002511.0 PRK01903 PRK01903.2-2 227 227 140 equivalog Y N N ribonuclease P 191412 Chlorobiaceae family 5 NCBI Protein Cluster (PRK) ribonuclease P ribonuclease P NF006193.0 PRK08324 PRK08324.2-1 1213 1213 705 subfamily Y Y N bifunctional aldolase/short-chain dehydrogenase 191412 Chlorobiaceae family 40 NCBI Protein Cluster (PRK) short chain dehydrogenase short-chain dehydrogenase NF009454.0 PRK12814 PRK12814.1 916 916 657 equivalog Y N N putative NADPH-dependent glutamate synthase small subunit 191412 Chlorobiaceae family 31 NCBI Protein Cluster (PRK) putative NADPH-dependent glutamate synthase small subunit putative NADPH-dependent glutamate synthase small subunit NF009849.0 PRK13320 PRK13320.1-1 354 354 267 equivalog Y Y N type III pantothenate kinase 2.7.1.33 191412 Chlorobiaceae family 19 NCBI Protein Cluster (PRK) pantothenate kinase type III pantothenate kinase NF010698.0 PRK14098 PRK14098.1 754 754 489 equivalog Y Y N starch synthase 2.4.1.21 191412 Chlorobiaceae family 33 NCBI Protein Cluster (PRK) glycogen synthase starch synthase Catalyzes the formation of alpha-1,4-glucan chains from ADP-glucose NF011059.0 PRK14490 PRK14490.1 354 354 374 equivalog Y Y N bifunctional molybdenum cofactor guanylyltransferase MobA/molybdopterin-guanine dinucleotide biosynthesis adaptor protein MobB mobAB 191412 Chlorobiaceae family 33 NCBI Protein Cluster (PRK) putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MobA bifunctional molybdenum cofactor guanylyltransferase MobA/molybdopterin-guanine dinucleotide biosynthesis adaptor protein MobB MobA links a guanosine 5'-phosphate to molydopterin to form molybdopterin guanine dinucleotide during molybdenum cofactor biosynthesis; MobB is not essential but has been found to interact with multiple proteins involved in the molybdopterin guanine dinucleotide cofactor biosynthesis pathway NF011234.0 PRK14641 PRK14641.1 151 151 173 equivalog Y Y N ribosome maturation factor RimP rimP 191412 Chlorobiaceae family 21 NCBI Protein Cluster (PRK) hypothetical protein ribosome maturation factor RimP NF011515.0 PRK14954 PRK14954.1 1117 1117 620 equivalog Y N N DNA polymerase III subunits gamma and tau 191412 Chlorobiaceae family 7 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunits gamma and tau TIGR03058.1 TIGR03058 rpt_csmH 60 10 27 equivalog_domain Y Y N chlorosome envelope protein H csmH GO:0015979 191412 Chlorobiaceae family 23 JCVI chlorosome envelope protein H chlorosome envelope protein H CsmH, as studied in Chlorobium tepidum, is one of at least ten surface-exposed proteins of the chloroplast, a bacteriochlorophyll-rich structure with a lipid-protein envelope. CsmH contain typically three copies of a repeated sequence, modeled by this HMM. TIGR03066.1 TIGR03066 Gem_osc_para_1 93.25 93.25 121 paralog_domain Y Y N TIGR03066 family protein 1914233 Gemmataceae family 49 JCVI Gemmata obscuriglobus paralogous family TIGR03066 TIGR03066 family protein This model represents an uncharacterized paralogous family in Gemmata obscuriglobus UQM 2246, a member of the Planctomycetes. This family shows sequence similarity to TIGR03067, which is also found in Gemmata obscuriglobus as well as in a few other species. TIGR01408.1 TIGR01408 Ube1 750.05 750.05 1008 subfamily N N N ubiquitin-activating enzyme E1 1915473 Methanobrevibacter sp. UBA188 species 1 JCVI ubiquitin-activating enzyme E1 ubiquitin-activating enzyme E1 This HMM represents the full length, over a thousand amino acids, of a multicopy family of eukaryotic proteins, many of which are designated ubiquitin-activating enzyme E1. Members have two copies of the ThiF family domain (PF00899), a repeat found in ubiquitin-activating proteins (PF02134), and other regions. NF017863.5 PF06088.16 TLP-20 23.5 23.5 164 domain Y Y N TLP20 family protein 7517434 191579 Fluviicola taffensis species 1 EBI-EMBL Nucleopolyhedrovirus telokin-like protein-20 (TLP20) TLP20 family protein This family consists of several Nucleopolyhedrovirus telokin-like protein-20 (TLP20) sequences. The function of this family is unknown but TLP20 is known to shares some antigenic similarities to the smooth muscle protein telokin although the amino acid sequence shows no homologies to telokin [1]. [1]. 7517434. Sequence and expression of a baculovirus protein with antigenic similarity to telokin. Raynes DA, Hartshorne DJ, Guerriero V Jr;. J Gen Virol 1994;75:1807-1809. (from Pfam) TIGR04513.1 TIGR04513 VPAMP_CTERM 32 32 28 subfamily_domain Y Y N VPAMP-CTERM sorting domain-containing protein 191863 Chthoniobacter flavus species 4 JCVI VPAMP-CTERM protein sorting domain VPAMP-CTERM protein-sorting domain This rare protein-sorting domain is found as the extreme C-terminal region of four extracellular protein (mostly protease) precursor sequences the genus Chthoniobacter, from the Spartobacteria class of phylum Verrucomicrobia. This domain contains the cognate signal for one of several exosortase family enzymes in the typical C. flavus genome, and coexists with the more common PEP-CTERM domain, found on more than 50 proteins. A suggestion of which exosortase acts on VPAMP-CTERM proteins comes from the pair of adjacent proteins WP_083805188.1 (an XrtH-like exosortase) and WP_083805187.1 (a VPAMP-CTERM protein). The VPAMP-CTERM sorting signal appears to derive from the XrtH-dependent IPTL-CTERM sorting signal. NF040469.1 blaEFM 610 610 302 exception Y Y Y EFM family subclass B3 metallo-beta-lactamase blaEFM 3.5.2.6 GO:0008800 22850693 192812 Qipengyuania flava species 11 NCBIFAM EFM family subclass B3 metallo-beta-lactamase EFM (Erythrobacter flavus metallo-beta-lactamase), a subclass B3 enzyme, is one of five related chromosomal subclass B3 metallo-beta-lactamases from various species of Erythrobacter spp., (EAM, ECM, EFM, ELM, EVM). Erythrobacter flavus is also called Qipengyuania flava. EFM-1 increased MICs for three tested carbapenems, imipenem in particular, and showed strong activity against piperacillin (PIP) and various cephalosporins. NF000435.2 blaOXA-61_like 540 540 252 exception Y Y Y OXA-61 family class D beta-lactamase blaOXA 3.5.2.6 GO:0008658,GO:0008800 194 Campylobacter genus 75 NCBIFAM OXA-61 family class D beta-lactamase OXA-61 family class D beta-lactamase NF000461.2 blaOXA-184_like 475 475 248 exception Y Y Y OXA-184 family class D beta-lactamase blaOXA 3.5.2.6 GO:0008658,GO:0008800 27736787 194 Campylobacter genus 80 NCBIFAM OXA-184 family class D beta-lactamase OXA-184 family class D beta-lactamase NF000462.2 blaOXA-493_like 475 475 248 exception Y Y Y OXA-493 family class D beta-lactamase blaOXA 3.5.2.6 GO:0008800 194 Campylobacter genus 87 NCBIFAM OXA-493 family class D beta-lactamase OXA-493 family class D beta-lactamase NF000463.2 blaOXA_Campylobacter 390 390 248 exception Y Y Y class D beta-lactamase blaOXA 3.5.2.6 GO:0008658,GO:0008800 194 Campylobacter genus 296 NCBIFAM class D beta-lactamase class D beta-lactamase NF000665.1 PRK00031 PRK00031.2-3 202 202 169 equivalog Y Y N outer membrane lipoprotein chaperone LolA lolA 194 Campylobacter genus 213 NCBI Protein Cluster (PRK) lipoprotein chaperone outer membrane lipoprotein chaperone LolA NF000666.0 PRK00031 PRK00031.2-4 157 157 170 equivalog Y Y N outer membrane lipoprotein chaperone LolA lolA 194 Campylobacter genus 597 NCBI Protein Cluster (PRK) lipoprotein chaperone outer membrane lipoprotein chaperone LolA NF001805.0 PRK00521 PRK00521.3-3 202 202 121 equivalog Y Y N 30S ribosome-binding factor RbfA rbfA 194 Campylobacter genus 212 NCBI Protein Cluster (PRK) ribosome-binding factor A 30S ribosome-binding factor RbfA NF004590.0 PRK05928 PRK05928.3-2 330 330 209 equivalog Y Y N uroporphyrinogen-III synthase 4.2.1.75 194 Campylobacter genus 171 NCBI Protein Cluster (PRK) uroporphyrinogen-III synthase uroporphyrinogen-III synthase NF006264.0 PRK08411 PRK08411.1 729 729 572 subfamily Y Y N flagellin GO:0005198 194 Campylobacter genus 2942 NCBI Protein Cluster (PRK) flagellin flagellin NF006298.0 PRK08487 PRK08487.1-1 530 530 321 equivalog Y N N DNA polymerase III subunit delta 16417636 194 Campylobacter genus 488 NCBI Protein Cluster (PRK) DNA polymerase III subunit delta hypothetical protein NF006301.0 PRK08487 PRK08487.1-4 485 485 330 equivalog Y N N DNA polymerase III subunit delta 194 Campylobacter genus 178 NCBI Protein Cluster (PRK) DNA polymerase III subunit delta hypothetical protein NF006502.0 PRK08937 PRK08937.3-2 259 259 275 equivalog Y Y N adenylosuccinate lyase 4.3.2.2 194 Campylobacter genus 330 NCBI Protein Cluster (PRK) adenylosuccinate lyase adenylosuccinate lyase NF006504.0 PRK08937 PRK08937.3-4 256 256 268 equivalog Y Y N adenylosuccinate lyase 4.3.2.2 194 Campylobacter genus 315 NCBI Protein Cluster (PRK) adenylosuccinate lyase adenylosuccinate lyase NF006782.0 PRK09293 PRK09293.2-3 457 457 280 equivalog Y Y N class 1 fructose-bisphosphatase 3.1.3.11 194 Campylobacter genus 815 NCBI Protein Cluster (PRK) fructose-1,6-bisphosphatase class 1 fructose-bisphosphatase NF008885.0 PRK11917 PRK11917.1 373 373 259 equivalog Y N N bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein 194 Campylobacter genus 223 NCBI Protein Cluster (PRK) bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein NF009400.1 PRK12765 PRK12765.1 448 448 596 equivalog Y Y N flagellar filament capping protein FliD fliD GO:0007155,GO:0009421 24445509 194 Campylobacter genus 1293 NCBI Protein Cluster (PRK) flagellar capping protein flagellar filament capping protein FliD NF009452.0 PRK12812 PRK12812.1 258 258 289 equivalog Y Y N flagellar basal body rod modification protein 11298288,14617189 194 Campylobacter genus 532 NCBI Protein Cluster (PRK) flagellar basal body rod modification protein flagellar basal body rod modification protein Acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod NF009519.0 PRK12880 PRK12880.1 436 436 353 equivalog Y Y N beta-ketoacyl-ACP synthase III 194 Campylobacter genus 477 NCBI Protein Cluster (PRK) 3-oxoacyl-(acyl carrier protein) synthase III beta-ketoacyl-ACP synthase III NF010116.0 PRK13589 PRK13589.1 983 983 576 subfamily Y Y N flagellin A GO:0005198 194 Campylobacter genus 2020 NCBI Protein Cluster (PRK) flagellin flagellin A NF010486.0 PRK13909 PRK13909.1-3 1109 1109 921 equivalog Y Y N RecB-like helicase 194 Campylobacter genus 693 NCBI Protein Cluster (PRK) putative recombination protein RecB RecB-like helicase NF010487.0 PRK13909 PRK13909.1-4 759 759 924 equivalog Y Y N RecB-like helicase 194 Campylobacter genus 1377 NCBI Protein Cluster (PRK) putative recombination protein RecB RecB-like helicase NF010679.0 PRK14077 PRK14077.1 343 343 287 equivalog Y Y N NAD(+) kinase 2.7.1.23 194 Campylobacter genus 606 NCBI Protein Cluster (PRK) inorganic polyphosphate/ATP-NAD kinase NAD(+) kinase Catalyzes the phosphorylation of NAD to NADP NF010756.0 PRK14159 PRK14159.1 171 171 176 equivalog Y Y N nucleotide exchange factor GrpE grpE 194 Campylobacter genus 382 NCBI Protein Cluster (PRK) heat shock protein GrpE nucleotide exchange factor GrpE With DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins NF010763.0 PRK14166 PRK14166.1 501 501 282 equivalog Y N N bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase 194 Campylobacter genus 322 NCBI Protein Cluster (PRK) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase NF011232.0 PRK14639 PRK14639.1 193 193 141 equivalog Y Y N ribosome maturation factor RimP rimP 194 Campylobacter genus 693 NCBI Protein Cluster (PRK) hypothetical protein ribosome maturation factor RimP NF011282.0 PRK14692 PRK14692.1 878 878 749 equivalog Y Y N flagellar hook-associated protein FlgL flgL 194 Campylobacter genus 963 NCBI Protein Cluster (PRK) lagellar hook-associated protein FlgL flagellar hook-associated protein FlgL NF014718.5 PF02689.19 Herpes_Helicase 27 27 808 domain Y N N Helicase GO:0004386,GO:0005524 8030256 194 Campylobacter genus 561 EBI-EMBL Helicase Helicase This family consists of Helicases from the Herpes viruses. Helicases are responsible for the unwinding of DNA and are essential for replication and completion of the viral life cycle. [1]. 8030256. Identification of the pseudorabies virus UL4 and UL5 (helicase) genes. Dean HJ, Cheung AK;. Virology 1994;202:962-967. (from Pfam) NF027978.5 PF16668.10 JLPA 27 27 352 PfamEq Y Y N JlpA family lipoprotein adhesin GO:0007155 22245776,24303031 194 Campylobacter genus 492 EBI-EMBL Adhesin from Campylobacter JlpA family lipoprotein adhesin This HMM describes a family of lipoprotein adhesins found in multiple species of Campylobacter. The founding member, from Campylobacter jejuni, in named JlpA (jejuni lipoprotein A). NF033602.0 campy_sm_acidic 24 24 51 equivalog Y Y N highly acidic protein 194 Campylobacter genus 181 NCBIFAM highly acidic protein highly acidic protein This highly acidic protein, usually between 50 and 55 amino acids long, is found so far in Campylobacter jejuni and Campylobacter coli. A reanalysis of proteomics data, performed by Dr. Samuel Payne of Pacific Northwest National Labs, shows strong evidence for expression of AIW09513.1, founding member of the family. NF033603.1 mini-MOMP_1 75 75 63 subfamily Y Y N mini-MOMP protein 194 Campylobacter genus 121 NCBIFAM mini-MOMP protein mini-MOMP protein Mini-MOMP proteins, found in several species of Campylobacter, are small proteins (about 63 amino acids long before removal of the signal peptide) with strong homology to the N-terminal region of MOMP, the major outer membrane protein that is Campylobacter's major porin. NF036646.5 PF17437.7 DUF5416 25 25 173 subfamily Y Y N DUF5416 family protein 194 Campylobacter genus 600 EBI-EMBL Family of unknown function (DUF5416) DUF5416 family protein This is a family of unknown function found in Campylobacteria. (from Pfam) NF038205.1 Campy_LoFi_RPT 25 18 23 repeat Y N N LOFI repeat protein 194 Campylobacter genus 904 NCBIFAM LOFI repeat This weakly conserved (low-fidelity, or LOFI) repeat appears primarily in Campylobacteria, but not exclusively, in proteins such as Cj0967, Cj0736, and Cj0735. The HMM models a core region about 23 residues in length of repeats whose lengths vary typically between 35 and 50 residues in length. NF041051.1 SelTWH_Campy 88 88 70 equivalog Y Y N SelT/SelW/SelH family (seleno)protein 35883471 194 Campylobacter genus 377 NCBIFAM SelT/SelW/SelH family (seleno)protein, Campylobacterial type Members of this family are primarily (perhaps exclusively) selenoproteins, found in Campylobacter species such as C. lari, but also in members of several other lineages. The protein family is related to SelT, SelW, and SelH, and features a CXXU motif. NF041252.1 outer_memb_MapA 300 300 213 equivalog Y Y N outer membrane lipoprotein MapA mapA 7790451 194 Campylobacter genus 245 NCBIFAM outer membrane lipoprotein MapA NF041329.1 CmeU 80 80 75 subfamily Y Y N CmeU family protein cmeU 12069964,16359189 194 Campylobacter genus 293 NCBIFAM CmeU family protein NF041446.1 APH_2pp_Ii 625 625 297 exception Y Y Y aminoglycoside O-phosphotransferase APH(2'')-Ii aph(2'')-Ii 2.7.1.190 29976591 194 Campylobacter genus 1 NCBIFAM aminoglycoside O-phosphotransferase APH(2'')-Ii NF041454.1 FspA 120 120 138 equivalog Y Y N flagellum-secreted nonflagellar protein FspA fspA 17517862 194 Campylobacter genus 123 NCBIFAM flagellum-secreted nonflagellar protein FspA NF041456.1 surv_prot_CiaI 290 290 186 equivalog Y Y N intracellular survival protein CiaI ciaI 21435039 194 Campylobacter genus 301 NCBIFAM intracellular survival protein CiaI NF041772.1 tung_bind_TupA 400 400 266 equivalog Y Y N tungstate ABC transporter substrate-binding protein TupA tupA GO:1901238 19818021 194 Campylobacter genus 460 NCBIFAM tungstate ABC transporter substrate-binding protein TupA NF041773.1 tung_perm_TupB 320 320 230 equivalog Y Y N tungstate ABC transporter permease TupB tupB GO:1901238 19818021 194 Campylobacter genus 435 NCBIFAM tungstate ABC transporter permease TupB NF041774.1 tung_ATPbind_TupC 400 400 319 equivalog Y Y N tungstate ABC transporter ATP-binding protein TupC tupC 7.3.2.6 GO:0005524,GO:0016887,GO:1901238 19818021 194 Campylobacter genus 623 NCBIFAM tungstate ABC transporter ATP-binding protein TupC NF042952.1 MFR_FeS_SdhB 600 600 320 equivalog Y Y N 8-methylmenaquinol:fumarate reductase iron-sulfur subunit sdhB 1.3.5.- GO:0006099,GO:0009055 19170876 194 Campylobacter genus 364 NCBIFAM 8-methylmenaquinol:fumarate reductase iron-sulfur subunit NF042965.1 MFR_anch_SdhE 500 500 282 equivalog Y Y N 8-methylmenaquinol:fumarate reductase membrane anchor subunit sdhE 1.3.5.- GO:0016491 19170876 194 Campylobacter genus 388 NCBIFAM 8-methylmenaquinol:fumarate reductase membrane anchor subunit NF042982.1 MFR_Fp_SdhA 1100 1100 612 equivalog Y Y N 8-methylmenaquinol:fumarate reductase flavoprotein subunit sdhA 1.3.5.- GO:0016627,GO:0022900,GO:0050660 19170876 194 Campylobacter genus 508 NCBIFAM 8-methylmenaquinol:fumarate reductase flavoprotein subunit NF045377.2 PF21464.2 flgE_D3 27 27 179 domain Y N N Flagellar hook protein FlgE, D3 domain 27759043,27811912 194 Campylobacter genus 2006 EBI-EMBL Flagellar hook protein FlgE, D3 domain Flagellar hook protein FlgE, D3 domain This domain is found in Flagellar hook protein FlgE from Campylobacter jejuni and similar proteins found in Epsilonproteobacteria. Around 100 copies of FlgE polymerise to form a tubular helical structure: the bacterial flagellar hook. This protein is organised into five domains. This entry represents domain D3, which is made of two discontinuous segments. It shows a set of eight beta-strands separated into two groups by two alpha-helices that form an alpha-beta barrel. This domain is not conserved in other bacterial FlgE proteins [1,2]. Paper describing PDB structure 5az4. [1]. 27759043. Structural insights into bacterial flagellar hooks similarities and specificities. Yoon YH, Barker CS, Bulieris PV, Matsunami H, Samatey FA;. Sci Rep. 2016;6:35552. Paper describing PDB structure 5jxl. [2]. 27811912. Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions. Matsunami H, Barker CS, Yoon YH, Wolf M, Samatey FA;. Nat Commun. 2016;7:13425. (from Pfam) NF046756.1 PF22506.1 Cj1289-like_C 27 27 91 domain Y N N Cj1289-like, C-terminal domain 194 Campylobacter genus 714 EBI-EMBL Cj1289-like, C-terminal domain Cj1289-like, C-terminal domain This domain is found at the C-terminal end of the possible periplasmic protein Swiss:Q0P8W8 from Campylobacter jejuni (Cj1289) and similar sequences mainly found in epsilonproteobacteria. This domain is normally associated to Pfam:PF09312. It shows an alpha-beta configuration. Its specific function is unknown. (from Pfam) NF047367.1 redox_TF_RrpA 185 185 101 exception Y Y N MarR family transcription factor RrpA rrpA 26257713,34606373 194 Campylobacter genus 112 NCBIFAM MarR family transcription factor RrpA RrpA, as described in Campylobacter jejuni, is a MarR family helix-turn-helix transcription factor with about 45 percent identity its paralog RrpB. RrpA has invariant Cys residues at positions 8, 13, and 33 that participate in thiol-based detection of redox state and regulating the expression of reductases that contribute to stress adaptation. NF046837.1 PF22464.1 Spike_JR1 26 26 78 domain Y N N Spike protein P1, first jelly-roll domain 18775333 194690 unclassified Pseudoalteromonas no rank 4 EBI-EMBL Spike protein P1, first jelly-roll domain Spike protein P1, first jelly-roll domain This entry represents the first jelly-roll domain of Spike protein P1 from Pseudoalteromonas phage PM2 [1]. Paper describing PDB structure 2w0c. [1]. 18775333. Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2. Abrescia NG, Grimes JM, Kivela HM, Assenberg R, Sutton GC, Butcher SJ, Bamford JK, Bamford DH, Stuart DI;. Mol Cell. 2008;31:749-761. (from Pfam) NF010670.0 PRK14067 PRK14067.1 107 107 81 equivalog Y Y N exodeoxyribonuclease VII small subunit 194924 Desulfovibrionaceae family 35 NCBI Protein Cluster (PRK) exodeoxyribonuclease VII small subunit exodeoxyribonuclease VII small subunit Catalyzes the bidirectional exonucleolytic cleavage of DNA NF010942.0 PRK14362 PRK14362.1 290 290 210 equivalog Y N N Maf-like protein 194924 Desulfovibrionaceae family 27 NCBI Protein Cluster (PRK) Maf-like protein Maf-like protein NF011260.0 PRK14666 PRK14666.1 649 649 698 equivalog Y N N excinuclease ABC subunit C 194924 Desulfovibrionaceae family 44 NCBI Protein Cluster (PRK) excinuclease ABC subunit C excinuclease ABC subunit C NF011273.0 PRK14680 PRK14680.1 199 199 134 equivalog Y N N hypothetical protein 194924 Desulfovibrionaceae family 30 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF011520.0 PRK14959 PRK14959.1 798 798 624 equivalog Y N N DNA polymerase III subunits gamma and tau 194924 Desulfovibrionaceae family 30 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunits gamma and tau NF027469.5 PF16143.10 DUF4851 25 25 189 domain Y Y N DUF4851 domain-containing protein 194924 Desulfovibrionaceae family 251 EBI-EMBL Domain of unknown function (DUF4851) Domain of unknown function (DUF4851) This family consists of several uncharacterized proteins around 250 residues in length and is mainly found in various Desulfovibrio species. The function of this family is unknown. (from Pfam) NF033221.1 ANT_6_Ig 620 620 299 exception Y Y Y aminoglycoside nucleotidyltransferase ANT(6)-Ig ant(6)-Ig 27154456,29976591 195 Campylobacter coli species 10 NCBIFAM aminoglycoside 6-adenylyltransferase AadE-Cc aminoglycoside nucleotidyltransferase ANT(6)-Ig Article PMID:27154456 describes a streptomycin resistance protein, "Campylobacter ANT-like protein A", highly similar to WP_002785795.1, and reports internal primers that match exactly to genes encoding WP_002785795.1. Campylobacter ANT-like protein A was shown to confer resistance to streptomycin. This model identifies proteins from this family, including WP_002785795.1. The most closely related sequence found by database search was the family of "Campylobacter ANT-like protein B", such as WP_038855261.1, which also is found in Campylobacter coli but which could not be shown to confer resistance to streptomycin. NF009031.0 PRK12366 PRK12366.1-2 767 767 647 equivalog Y N N replication factor A 196117 Methanocaldococcaceae family 9 NCBI Protein Cluster (PRK) replication factor A replication factor A NF046264.1 PF22413.1 OGT_N 27 27 72 domain Y N N Methylated DNA-protein cysteine MeTransferase OGT N-terminal domain 16826543 196117 Methanocaldococcaceae family 11 EBI-EMBL Methylated DNA-protein cysteine MeTransferase OGT N-terminal domain Methylated DNA-protein cysteine MeTransferase OGT N-terminal domain This entry represents the N-terminal of methylated DNA-protein cysteine methyltransferase (MGMT, also known as 6-O- methylguanine-DNA methyltransferase and MJ1529/OGT) from Methanocaldococcus jannaschii and similar sequences [1]. This entry corresponds to the ribonuclease-like domain associated with 6-O-methylguanine DNA methyltransferase activity. Paper describing PDB structure 2g7h. [1]. 16826543. Structural studies of MJ1529, an O6-methylguanine-DNA methyltransferase. Roberts A, Pelton JG, Wemmer DE;. Magn Reson Chem. 2006;44:S71-S82. (from Pfam) NF046620.1 PF22226.1 Mre11_C 27 27 44 domain Y Y N Rad50-binding domain-containing protein 26717941 196117 Methanocaldococcaceae family 8 EBI-EMBL Mre11 C-terminal Rad50-binding domain Rad50-binding domain-containing protein Communication between Mre11 and Rad50 in the MR complex is critical for the sensing, damage signaling, and repair of DNA double-strand breaks. Mre11 protein consists of an N-terminal core domain and a C-terminal domain linked by an extended connecting loop. The C-terminal domain of Mre11 is composed of three helices and binds to the C-terminal part of the Rad50 coiled-coil [1]. Paper describing PDB structure 5dny. [1]. 26717941. ATP-dependent DNA binding, unwinding, and resection by the Mre11/Rad50 complex. Liu Y, Sung S, Kim Y, Li F, Gwon G, Jo A, Kim AK, Kim T, Song OK, Lee SE, Cho Y;. EMBO J. 2016;35:743-758. (from Pfam) NF002094.0 PRK00933 PRK00933.1-4 300 300 169 equivalog Y Y N rRNA maturation protein 196118 Methanocaldococcus genus 9 NCBI Protein Cluster (PRK) ribosomal biogenesis protein rRNA maturation protein NF003289.0 PRK04286 PRK04286.1-3 526 526 292 equivalog Y N N hypothetical protein 196118 Methanocaldococcus genus 8 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004928.0 PRK06286 PRK06286.1-3 150 150 91 equivalog Y N N putative monovalent cation/H+ antiporter subunit G 196118 Methanocaldococcus genus 9 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit G putative monovalent cation/H+ antiporter subunit G NF009147.0 PRK12496 PRK12496.1-4 311 311 170 equivalog Y N N hypothetical protein 196118 Methanocaldococcus genus 7 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF046198.1 PF22138.1 MjAgo_N-like 27 27 69 domain Y Y N argonaute domain-containing protein 28319084 196118 Methanocaldococcus genus 2 EBI-EMBL Archaeal argonaute protein N-terminal domain argonaute domain-containing protein Argonaute (Ago) proteins are found in all three domains of life. They share a common molecular architecture, with the C-terminal lobe consisting of the middle (Mid) and PIWI (P element wimpy testis) domains and the N-terminal lobe containing the N-terminal and PIWI-Argonaute-Zwille (PAZ) domains. Archaeal argonaute proteins are guided by 5'-phosphorylated DNA strands and exclusively process cognate DNA targets. This entry represents the N-terminal domain of the archaeal argonaute protein found in M.jannaschii. This domain consists of a four stranded antiparallel beta-sheet and an alpha-helix [1]. Paper describing PDB structure 5g5s. [1]. 28319084. Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein. Willkomm S, Oellig CA, Zander A, Restle T, Keegan R, Grohmann D, Schneider S;. Nat Microbiol. 2017;2:17035. (from Pfam) NF047155.1 PF22333.1 Ago_PAZ_arc 27 27 96 domain Y Y N PAZ domain-containing protein 28319081,28319084 196118 Methanocaldococcus genus 2 EBI-EMBL Argonaute, PAZ domain, archaea PAZ domain-containing protein This entry represents the PAZ domain of archaeal argonaute (Ago) [1]. Ago is a DNA-guided ssDNA endonuclease that may play a role in defense against invading genetic elements that uses short ssDNA sequences as guides (gDNA) to bind complementary target strands resulting in slicing of the target DNA (tDNA) [1,2]. Paper describing PDB structure 5g5s. [1]. 28319084. Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein. Willkomm S, Oellig CA, Zander A, Restle T, Keegan R, Grohmann D, Schneider S;. Nat Microbiol. 2017;2:17035. [2]. 28319081. Guide-independent DNA cleavage by archaeal Argonaute from Methanocaldococcus jannaschii. Zander A, Willkomm S, Ofer S, van Wolferen M, Egert L, Buchmeier S, Stockl S, Tinnefeld P, Schneider S, Klingl A, Albers SV, Werner F, Grohmann D;. Nat Microbiol. 2017;2:17034. (from Pfam) NF046749.1 PF22415.1 PSV_ORF131-like_dom 27 27 80 domain Y N N PSV_Hypothetical protein ORF131-like domain 20419351 1961369 Thermofilum sp. species 2 EBI-EMBL PSV_Hypothetical protein ORF131-like domain PSV_Hypothetical protein ORF131-like domain This domain is found in the uncharacterised protein Swiss:Q6ZYH1 from Pyrobaculum spherical virus (PSV), also known as ORF131, and similar viral sequences. It adopts a two-layered alpha-beta configuration [1]. Paper describing PDB structure 2x5c. [1]. 20419351. The Scottish Structural Proteomics Facility: targets, methods and outputs. Oke M, Carter LG, Johnson KA, Liu H, McMahon SA, Yan X, Kerou M, Weikart ND, Kadi N, Sheikh MA, Schmelz S, Dorward M, Zawadzki M, Cozens C, Falconer H, Powers H, Overton IM, van Niekerk CA, Peng X, Patel P, Garrett RA, Prangishvili D, Botting CH, Coote PJ, Dryden DT, Barton GJ, Schwarz-Linek U, Challis GL, Taylor GL, White MF, Naismith JH;. J Struct Funct Genomics. 2010;11:167-180. (from Pfam) NF047169.1 PF22376.1 PSV_trans_reg_dom 27 27 81 domain Y Y N winged-helix domain-containing protein 20419351 1961369 Thermofilum sp. species 1 EBI-EMBL PSV, transcriptional regulator domain winged-helix domain-containing protein This domain is found in Transcriptional regulator from Pyrobaculum spherical virus (PSV) and similar viral proteins. It shows a winged-helix configuration [1]. Paper describing PDB structure 2vxz. [1]. 20419351. The Scottish Structural Proteomics Facility: targets, methods and outputs. Oke M, Carter LG, Johnson KA, Liu H, McMahon SA, Yan X, Kerou M, Weikart ND, Kadi N, Sheikh MA, Schmelz S, Dorward M, Zawadzki M, Cozens C, Falconer H, Powers H, Overton IM, van Niekerk CA, Peng X, Patel P, Garrett RA, Prangishvili D, Botting CH, Coote PJ, Dryden DT, Barton GJ, Schwarz-Linek U, Challis GL, Taylor GL, White MF, Naismith JH;. J Struct Funct Genomics. 2010;11:167-180. (from Pfam) NF003020.0 PRK03879 PRK03879.2-1 154 154 100 equivalog Y N N ribonuclease P protein component 1 3.1.26.5 1963268 Haloarculaceae family 10 NCBI Protein Cluster (PRK) ribonuclease P protein component 1 ribonuclease P protein component 1 NF006785.0 PRK09293 PRK09293.3-2 477 477 291 equivalog Y Y N class 1 fructose-bisphosphatase 3.1.3.11 1963268 Haloarculaceae family 63 NCBI Protein Cluster (PRK) fructose-1,6-bisphosphatase class 1 fructose-bisphosphatase NF009143.0 PRK12495 PRK12495.1-4 372 372 244 equivalog Y N N hypothetical protein 1963268 Haloarculaceae family 6 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003755.0 PRK05346 PRK05346.2-6 563 563 310 equivalog Y Y N Na(+)-translocating NADH-quinone reductase subunit C 1963360 Parachlamydiales order 5 NCBI Protein Cluster (PRK) Na(+)-translocating NADH-quinone reductase subunit C Na(+)-translocating NADH-quinone reductase subunit C NF033613.1 blaOXA-576_like 530 530 248 exception Y Y Y OXA-576 family class D beta-lactamase blaOXA 3.5.2.6 GO:0008800 197 Campylobacter jejuni species 2 NCBIFAM OXA-576 family class D beta-lactamase OXA-576 family class D beta-lactamase The OXA-576 family of class D beta-lactamase is known so far only in Campylobacter jejuni. NF038379.2 amino_Aden_PurZ 300 300 293 exception Y Y N succino-amino-deoxyadenylate synthase PurZ purZ 33926955 1971902 Zhongshania sp. species 1 NCBIFAM succino-amino-deoxyadenylate synthase PurZ PurZ, so far found only in viruses in bacteria, belongs to a pathway through which novel purine aminoadenine (Z), rather than adenine (A), in incorporated into DNA. The substitution gives resistance to typical restriction enzymes to those rare viruses . NF038380.1 phage_DpoZ_1 500 500 607 exception Y Y N aminoadenine-incorporating DNA polymerase DpoZ dpoZ 33926956 1971902 Zhongshania sp. species 1 NCBIFAM aminoadenine-incorporating DNA polymerase DpoZ NF020499.5 PF08925.16 DUF1907 25 25 285 domain Y Y N DUF1907 domain-containing protein GO:0005634 16522806 198251 Candidatus Pelagibacter genus 6 EBI-EMBL Domain of Unknown Function (DUF1907) Domain of Unknown Function (DUF1907) The structure of this domain displays an alpha-beta-beta-alpha four layer topology, with an HxHxxxxxxxxxH motif that coordinates a zinc ion, and an acetate anion at a site that likely supports the enzymatic activity of an ester hydrolase [1]. [1]. 16522806. Crystal structure of Homo sapiens PTD012 reveals a zinc-containing hydrolase fold. Manjasetty BA, Bussow K, Fieber-Erdmann M, Roske Y, Gobom J, Scheich C, Gotz F, Niesen FH, Heinemann U;. Protein Sci. 2006;15:914-920. (from Pfam) NF013726.5 PF01579.23 DUF19 23.2 23.2 157 domain Y Y N DUF19 domain-containing protein 1982626 Faecalibacillus intestinalis species 1 EBI-EMBL Domain of unknown function (DUF19) Domain of unknown function (DUF19) This presumed domain has no known function. It is found in one or two copies in several Caenorhabditis elegans proteins. It is roughly 130 amino acids long. The domain contains 12 conserved cysteines which suggests that the domain is an extracellular domain and that these cysteines form six intradomain disulphide bridges. The GO annotation for this protein indicates that it has a function in nematode larval development and has a positive regulation of growth rate. (from Pfam) NF025275.5 PF13907.11 CHD1-like_C 28.3 28.3 96 domain Y Y N chromodomain-helicase-DNA-binding domain-containing protein 18042460,27591891,28866611 199441 Halalkalibacter krulwichiae species 1 EBI-EMBL Chromodomain-helicase-DNA-binding protein 1-like, C-terminal Chromodomain-helicase-DNA-binding protein 1-like, C-terminal This domain is found at the C-terminus of chromodomain-helicase-DNA-binding proteins, including Chromodomain-helicase-DNA-binding protein 1 from humans (CHD1), an ATP-dependent chromatin-remodeling factor which acts as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. This helical domain consists of five alpha-helices organised in a variant helical bundle topology. Its surface is positively charged and can bind dsDNA and nucleosomes, but its specific function remains unknown [1,2,3]. [1]. 18042460. Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. Sims RJ 3rd, Millhouse S, Chen CF, Lewis BA, Erdjument-Bromage H, Tempst P, Manley JL, Reinberg D;. Mol Cell. 2007;28:665-676. [2]. 28866611. Missense variants in the chromatin remodeler CHD1 are associated with neurodevelopmental disability. Pilarowski GO, Vernon HJ, Applegate CD, Boukas L, Cho MT, Gurnett CA, Benke PJ, Beaver E, Heeley JM, Medne L, Krantz ID, Azage M, Niyazov D, Henderson LB, Wentzensen IM, Baskin B, Sacoto MJG, Bowman GD, Bjornsson HT;. J Med Genet. 2018;55:561-566. [3]. 27591891. The Chromatin Remodelling Protein CHD1 Contains a Previously Unrecognised C-Terminal Helical Domain. Mohanty B, Helder S, Silva AP, Mackay JP, Ryan DP;. J Mol Biol. 2016;428:4298-4314. (from Pfam) NF000015.3 APH_2pp_IIa 625 625 299 exception Y Y Y aminoglycoside O-phosphotransferase APH(2'')-IIa aph(2'')-IIa 2 Bacteria superkingdom 10 NCBIFAM aminoglycoside O-phosphotransferase APH(2'')-IIa aminoglycoside O-phosphotransferase APH(2'')-IIa NF000016.1 AAC_6p_Im 350 350 178 exception Y Y Y aminoglycoside N-acetyltransferase AAC(6')-Im aac(6')-Im 2 Bacteria superkingdom 8 NCBIFAM aminoglycoside N-acetyltransferase AAC(6')-Im aminoglycoside N-acetyltransferase AAC(6')-Im NF000023.1 qac_SMR_C 200 200 107 exception Y Y Y quaternary ammonium compound efflux SMR transporter QacC qacC 2 Bacteria superkingdom 42 NCBIFAM quaternary ammonium compound efflux SMR transporter QacC quaternary ammonium compound efflux SMR transporter QacC NF000027.1 156720500_bleO 275 275 134 exception Y Y Y bleomycin binding protein bleO 2 Bacteria superkingdom 75 NCBIFAM bleomycin binding protein bleomycin binding protein NF000030.1 16S_rRNA_NpmA 450 450 219 exception Y Y Y 16S rRNA (adenine(1408)-N(1))-methyltransferase NpmA npmA GO:0006400 2 Bacteria superkingdom 2 NCBIFAM 16S rRNA (adenine(1408)-N(1))-methyltransferase NpmA 16S rRNA (adenine(1408)-N(1))-methyltransferase NpmA NF000043.1 tet_MFS_P_a 750 750 420 exception Y Y Y tetracycline efflux MFS transporter TetA(P) tetA(P) GO:0008493,GO:0015904,GO:0022857,GO:0055085 2 Bacteria superkingdom 97 NCBIFAM tetracycline efflux MFS transporter TetA(P) tetracycline efflux MFS transporter TetA(P) NF000044.2 APH_2pp_IIIa 625 625 306 exception Y Y Y aminoglycoside O-phosphotransferase APH(2'')-IIIa aph(2'')-IIIa 2 Bacteria superkingdom 9 NCBIFAM aminoglycoside O-phosphotransferase APH(2'')-IIIa aminoglycoside O-phosphotransferase APH(2'')-IIIa NF000061.1 linco_LnuP 300 300 166 exception Y Y Y lincosamide nucleotidyltransferase Lnu(P) lnu(P) 2 Bacteria superkingdom 1 NCBIFAM lincosamide nucleotidyltransferase Lnu(P) lincosamide nucleotidyltransferase Lnu(P) NF000062.1 ANT_6_str 500 500 282 exception Y Y Y streptomycin adenylyltransferase Str str 2 Bacteria superkingdom 57 NCBIFAM streptomycin adenylyltransferase Str streptomycin adenylyltransferase Str NF000064.3 ANT_2pp_Ia 350 350 177 exception Y Y Y aminoglycoside nucleotidyltransferase ANT(2'')-Ia aadB 2 Bacteria superkingdom 70 NCBIFAM aminoglycoside nucleotidyltransferase ANT(2'')-Ia aminoglycoside nucleotidyltransferase ANT(2'')-Ia NF000085.1 Fos_BSH_Saur 260 260 139 exception Y Y Y FosB1/FosB3 family fosfomycin resistance bacillithiol transferase fosB 2 Bacteria superkingdom 17 NCBIFAM fosfomycin resistance thiol transferase FosB FosB1/FosB3 family fosfomycin resistance bacillithiol transferase NF000107.2 APH_4_Ia 725 725 341 exception Y Y Y aminoglycoside O-phosphotransferase APH(4)-Ia aph(4)-Ia 2 Bacteria superkingdom 48 NCBIFAM aminoglycoside O-phosphotransferase APH(4)-Ia aminoglycoside O-phosphotransferase APH(4)-Ia NF000132.2 APH_2pp_Ig 620 620 306 exception Y Y Y aminoglycoside O-phosphotransferase APH(2'')-Ig aph(2'')-Ig 2 Bacteria superkingdom 6 NCBIFAM aminoglycoside O-phosphotransferase APH(2'')-Ig aminoglycoside O-phosphotransferase APH(2'')-Ig NF000137.2 APH_7pp_Ia 640 640 332 exception Y Y Y aminoglycoside O-phosphotransferase APH(7'')-Ia aph(7'')-Ia 2 Bacteria superkingdom 24 NCBIFAM aminoglycoside O-phosphotransferase APH(7'')-Ia aminoglycoside O-phosphotransferase APH(7'')-Ia NF000139.2 penta_rpt_QnrD 425 425 214 exception Y Y Y QnrD family quinolone resistance pentapeptide repeat protein 2 Bacteria superkingdom 64 NCBIFAM QnrD family quinolone resistance pentapeptide repeat protein QnrD family quinolone resistance pentapeptide repeat protein NF000141.1 linco_LnuC 300 300 164 exception Y Y Y lincosamide nucleotidyltransferase Lnu(C) lnu(C) 2 Bacteria superkingdom 32 NCBIFAM lincosamide nucleotidyltransferase Lnu(C) lincosamide nucleotidyltransferase Lnu(C) NF000167.2 ABCF_Lsa_all 750 750 492 exception Y Y Y Lsa family ABC-F type ribosomal protection protein GO:0005524,GO:0016887 29415157 2 Bacteria superkingdom 2689 NCBIFAM Lsa family ABC-F type ribosomal protection protein Lsa family ABC-F type ribosomal protection protein NF000168.2 ABCF_Msr_all 680 680 487 exception Y Y Y Msr family ABC-F type ribosomal protection protein GO:0005524 29712846 2 Bacteria superkingdom 1298 NCBIFAM Msr family ABC-F type ribosomal protection protein Msr family ABC-F type ribosomal protection protein NF000206.1 D_ala_D_lac 550 550 342 equivalog Y Y Y D-alanine--(R)-lactate ligase vanA 6.1.2.1 GO:0005737,GO:0008716,GO:0046872 2 Bacteria superkingdom 1334 NCBIFAM D-alanine--(R)-lactate ligase D-alanine--(R)-lactate ligase NF000208.1 EreA 750 750 408 exception Y Y Y EreA family erythromycin esterase ere(A) 2 Bacteria superkingdom 17 NCBIFAM EreA family erythromycin esterase EreA family erythromycin esterase NF000218.1 FexA 900 900 475 exception Y Y Y chloramphenicol/florfenicol efflux MFS transporter FexA fexA GO:0022857,GO:0055085 2 Bacteria superkingdom 130 NCBIFAM chloramphenicol/florfenicol efflux MFS transporter FexA chloramphenicol/florfenicol efflux MFS transporter FexA NF000222.1 FosX 170 170 127 equivalog Y Y Y FosX/FosE/FosI family fosfomycin resistance hydrolase fosX 17567049,26552984,32952996 2 Bacteria superkingdom 1070 NCBIFAM fosfomycin inactivation enzyme FosX FosX/FosE/FosI family fosfomycin resistance hydrolase Both FosX and FosI (more recently called FosM, although that we regard a different protein as the proper FosM) have been shown to use water as a substrate, not a thiol, in the modification of the epoxide ring of the antibiotic fosfomycin. The enzyme is Mn2+-dependent, and belongs to the VOC (vicinal oxygen chelate) family. It is related to FosA and FosB, which use glutathione and bacillithiol, respectively. NF000235.3 linco_LnuB 525 525 267 exception Y Y Y lincosamide nucleotidyltransferase Lnu(B) lnu(B) 2 Bacteria superkingdom 42 NCBIFAM LinB family lincosamide nucleotidyltransferase lincosamide nucleotidyltransferase Lnu(B) NF000236.1 linco_LnuA 300 300 161 exception Y Y Y lincosamide nucleotidyltransferase Lnu(A) lnu(A) 2 Bacteria superkingdom 64 NCBIFAM lincosamide nucleotidyltransferase Lnu(A) lincosamide nucleotidyltransferase Lnu(A) NF000242.2 macrolide_MphB 615 615 299 exception Y Y Y Mph(B) family macrolide 2'-phosphotransferase 2 Bacteria superkingdom 53 NCBIFAM macrolide 2'-phosphotransferase Mph(B) family macrolide 2'-phosphotransferase NF000245.1 macrolide_MefA 675 675 405 exception Y Y Y macrolide efflux MFS transporter Mef(A) mef(A) 2 Bacteria superkingdom 333 NCBIFAM macrolide efflux MFS transporter Mef(A) macrolide efflux MFS transporter Mef(A) NF000267.2 blaOXA-2_like 590 590 275 exception Y Y Y OXA-2 family class D beta-lactamase blaOXA 3.5.2.6 GO:0008658,GO:0008800 2 Bacteria superkingdom 27 NCBIFAM class D beta-lactamase OXA-2 family class D beta-lactamase NF000276.2 SMR_qac_E 185 185 101 exception Y Y Y quaternary ammonium compound efflux SMR transporter QacE qacE GO:0016020 2 Bacteria superkingdom 235 NCBIFAM QacE family quaternary ammonium compound efflux SMR transporter quaternary ammonium compound efflux SMR transporter QacE NF000277.1 qac_SMR_G 200 200 107 exception Y Y Y quaternary ammonium compound efflux SMR transporter QacG qacG 2 Bacteria superkingdom 25 NCBIFAM quaternary ammonium compound efflux SMR transporter QacG quaternary ammonium compound efflux SMR transporter QacG NF000279.1 qac_SMR_H 205 205 107 exception Y Y Y quaternary ammonium compound efflux SMR transporter QacH qacH GO:0016020 2 Bacteria superkingdom 13 NCBIFAM quaternary ammonium compound efflux SMR transporter QacH quaternary ammonium compound efflux SMR transporter QacH NF000280.1 SMR_efflux_smr 200 200 105 exception Y Y Y multidrug efflux SMR transporter Smr smr GO:0016020 2 Bacteria superkingdom 12 NCBIFAM quaternary ammonium compound efflux SMR transporter QacK multidrug efflux SMR transporter Smr NF000282.2 RND_permease_1 1250 1250 1029 subfamily Y Y Y multidrug efflux RND transporter permease subunit GO:0015562,GO:0016020,GO:0042908,GO:0055085 2 Bacteria superkingdom 106713 NCBIFAM multidrug efflux RND transporter permease subunit HAE1 family multidrug efflux RND transporter permease subunit Multidrug efflux RND transporter permease subunits that belong to this family include OqxB, AcrB, AcrD, AcrF, MdtF, AdeE, AdeJ, MexB, etc. NF000294.1 Sul1 600 600 278 exception Y Y Y sulfonamide-resistant dihydropteroate synthase Sul1 sul1 2 Bacteria superkingdom 459 NCBIFAM sulfonamide-resistant dihydropteroate synthase Sul1 sulfonamide-resistant dihydropteroate synthase Sul1 NF000311.1 Vat_ABCDEFH 300 300 201 equivalog Y Y Y Vat family streptogramin A O-acetyltransferase GO:0016740 2 Bacteria superkingdom 3585 NCBIFAM Vat family streptogramin A O-acetyltransferase Vat family streptogramin A O-acetyltransferase NF000330.1 trim_DfrA1_like 250 250 157 exception Y Y Y trimethoprim-resistant dihydrofolate reductase DfrA dfrA 1.5.1.3 GO:0004146 2 Bacteria superkingdom 307 NCBIFAM trimethoprim-resistant dihydrofolate reductase DfrA trimethoprim-resistant dihydrofolate reductase DfrA NF000333.1 trim_DfrF 320 320 164 exception Y Y Y trimethoprim-resistant dihydrofolate reductase DfrF dfrF 1.5.1.3 GO:0004146 2 Bacteria superkingdom 11 NCBIFAM trimethoprim-resistant dihydrofolate reductase DfrF trimethoprim-resistant dihydrofolate reductase DfrF NF000360.1 sat4 380 380 180 exception Y Y Y streptothricin N-acetyltransferase Sat4 sat4 2 Bacteria superkingdom 99 NCBIFAM streptothricin N-acetyltransferase Sat4 streptothricin N-acetyltransferase Sat4 NF000384.1 QacCGHJ 160 160 107 equivalog Y Y Y QacCGHJ group quaternary ammonium compound efflux SMR transporter qac GO:0016020 2 Bacteria superkingdom 136 NCBIFAM QacCGHJ group quaternary ammonium compound efflux SMR transporter QacCGHJ group quaternary ammonium compound efflux SMR transporter NF000424.4 CfrAB 530 530 338 exception Y Y Y Cfr family 23S rRNA (adenine(2503)-C(8))-methyltransferase 2.1.1.224 25762794 2 Bacteria superkingdom 694 NCBIFAM Cfr family 23S ribosomal RNA methyltransferase Cfr family 23S rRNA (adenine(2503)-C(8))-methyltransferase NF000470.1 D_ala_D_lac_VanM 760 760 343 exception Y Y Y D-alanine--(R)-lactate ligase VanM vanM 6.1.2.1 2 Bacteria superkingdom 5 NCBIFAM D-alanine--(R)-lactate ligase VanM D-alanine--(R)-lactate ligase VanM NF000472.1 vanY_AFMPt 425 425 283 exception Y Y Y VanY-A/VanY-F/VanY-M family D-Ala-D-Ala carboxypeptidase vanY 2 Bacteria superkingdom 475 NCBIFAM VanY-A/VanY-F/VanY-M family D-Ala-D-Ala carboxypeptidase VanY-A/VanY-F/VanY-M family D-Ala-D-Ala carboxypeptidase NF000489.1 ble_Sh 260 260 124 exception Y Y Y phleomycin/bleomycin binding protein Ble-Sh ble-Sh 2 Bacteria superkingdom 6 NCBIFAM phleomycin/bleomycin binding protein Ble-Sh phleomycin/bleomycin binding protein Ble-Sh NF000491.1 chloram_CatA 270 270 208 equivalog Y Y Y type A chloramphenicol O-acetyltransferase catA 2.3.1.28 2 Bacteria superkingdom 3894 NCBIFAM type A chloramphenicol O-acetyltransferase type A chloramphenicol O-acetyltransferase NF000492.1 vanH_gen 540 500 312 exception Y Y Y D-lactate dehydrogenase VanH vanH 1.1.1.28 2 Bacteria superkingdom 507 NCBIFAM D-lactate dehydrogenase VanH D-lactate dehydrogenase VanH NF000498.2 APH_2pp_If_Ih 600 600 297 exception Y Y Y APH(2'')-If/Ih family aminoglycoside O-phosphotransferase aph(2'')-I 2 Bacteria superkingdom 19 NCBIFAM APH(2'')-If/Ih family aminoglycoside O-phosphotransferase APH(2'')-If/Ih family aminoglycoside O-phosphotransferase NF000499.1 Erm23S_rRNA_broad 215 215 244 equivalog Y Y Y 23S ribosomal RNA methyltransferase Erm erm 2 Bacteria superkingdom 5846 NCBIFAM 23S ribosomal RNA methyltransferase Erm 23S ribosomal RNA methyltransferase Erm NF000502.2 blaOXA-85_like 550 500 261 exception Y Y Y OXA-85 family oxacillin-hydrolyzing class D beta-lactamase blaOXA 3.5.2.6 GO:0008800 2 Bacteria superkingdom 5 NCBIFAM blaOXA-85_like: OXA-85 family oxacillin-hydrolyzing class D beta-lactamase OXA-85 family oxacillin-hydrolyzing class D beta-lactamase NF000507.1 AAC_6p_Ie 450 420 201 exception Y Y Y aminoglycoside N-acetyltransferase AAC(6')-Ie aac(6')-Ie GO:0008080 2 Bacteria superkingdom 338 NCBIFAM AAC6_pr_Ie: aminoglycoside N-acetyltransferase AAC(6')-Ie aminoglycoside N-acetyltransferase AAC(6')-Ie NF000508.1 APH_2pp_Ia 600 570 277 exception Y Y Y aminoglycoside O-phosphotransferase APH(2'')-Ia aph(2'')-Ia 2 Bacteria superkingdom 265 NCBIFAM APH2pr_pr_Ia: aminoglycoside O-phosphotransferase APH(2'')-Ia aminoglycoside O-phosphotransferase APH(2'')-Ia NF000510.1 efflux_Cmx 800 700 391 exception Y Y Y chloramphenicol efflux MFS transporter Cmx cmx GO:0022857,GO:0055085 2 Bacteria superkingdom 51 NCBIFAM efflux_Cmx: Cmx family chloramphenicol efflux MFS transporter chloramphenicol efflux MFS transporter Cmx NF000514.1 ABCF_OptrA 1450 1000 655 exception Y Y Y ABC-F type ribosomal protection protein OptrA optrA GO:0005524,GO:0016887 2 Bacteria superkingdom 168 NCBIFAM ABCF_OptrA: ABC-F type ribosomal protection protein OptrA ABC-F type ribosomal protection protein OptrA NF000539.0 plantaricin 29 27 69 subfamily Y Y N plantaricin C family lantibiotic 2 Bacteria superkingdom 776 NCBIFAM plantaricin: plantaricin.SEED plantaricin C family lantibiotic This family describes plantaricin C-like lantibiotic precursors. The seed alignment straddles the cleavage motif (typically GG), and includes both an extended leader peptide region and a Cys-rich core peptide region. Because of the mosaic structure of lantibiotic precursors, this family can be expected to overlap other lantibiotic precursor families in the same clan. NF000540.1 alt_ValS 900 900 827 exception Y Y N valine--tRNA ligase valS 6.1.1.9 GO:0000166,GO:0002161,GO:0004832,GO:0005524,GO:0006438 2 Bacteria superkingdom 9022 NCBIFAM alt_ValS: valine--tRNA ligase valine--tRNA ligase NF000582.1 PRK00006 PRK00006.1 113 113 137 equivalog Y Y N 3-hydroxyacyl-ACP dehydratase FabZ fabZ 4.2.1.59 15371447,15980063 2 Bacteria superkingdom 33863 NCBI Protein Cluster (PRK) (3R)-hydroxymyristoyl-ACP dehydratase 3-hydroxyacyl-ACP dehydratase FabZ Essential for membrane formation; performs third step of type II fatty acid biosynthesis; catalyzes dehydration of (3R)-hydroxyacyl-ACP to trans-2-acyl-ACP NF000585.0 PRK00010 PRK00010.1 186 186 181 equivalog Y Y N 50S ribosomal protein L5 rplE GO:0003735,GO:0005840,GO:0006412 11866091 2 Bacteria superkingdom 31759 NCBI Protein Cluster (PRK) 50S ribosomal protein L5 50S ribosomal protein L5 Part of 50S and 5S/L5/L18/L25 subcomplex; contacts 5S rRNA and P site tRNA; forms a bridge to the 30S subunit in the ribosome by binding to S13 NF000594.1 PRK00015 PRK00015.1-1 243 243 251 equivalog Y Y N ribonuclease HII 3.1.26.4 GO:0003723,GO:0004523 2 Bacteria superkingdom 25622 NCBI Protein Cluster (PRK) ribonuclease HII ribonuclease HII NF000595.1 PRK00015 PRK00015.1-3 167 167 188 equivalog Y Y N ribonuclease HII 3.1.26.4 GO:0003723,GO:0004523 2 Bacteria superkingdom 70054 NCBI Protein Cluster (PRK) ribonuclease HII ribonuclease HII NF000596.1 PRK00015 PRK00015.1-4 251 251 186 equivalog Y Y N ribonuclease HII rnhB 3.1.26.4 GO:0003723,GO:0004523 2 Bacteria superkingdom 15834 NCBI Protein Cluster (PRK) ribonuclease HII ribonuclease HII NF000612.0 PRK00019 PRK00019.1 70 70 72 equivalog Y Y N 50S ribosomal protein L31 rpmE GO:0003735,GO:0005840,GO:0006412 11574053,15049826,16547061 2 Bacteria superkingdom 14520 NCBI Protein Cluster (PRK) 50S ribosomal protein L31 50S ribosomal protein L31 NF000648.1 PRK00026 PRK00026.1 220 220 221 equivalog Y Y N tRNA (guanosine(37)-N1)-methyltransferase TrmD trmD 2.1.1.228 GO:0008033,GO:0052906 12773376 2 Bacteria superkingdom 62036 NCBI Protein Cluster (PRK) tRNA (guanine-N(1)-)-methyltransferase tRNA (guanosine(37)-N1)-methyltransferase TrmD Methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA NF000668.1 PRK00033 PRK00033.1-1 86 86 77 equivalog Y Y N ATP-dependent Clp protease adapter ClpS clpS GO:0006508 2 Bacteria superkingdom 8542 NCBI Protein Cluster (PRK) ATP-dependent Clp protease adaptor protein ClpS ATP-dependent Clp protease adapter ClpS NF000669.1 PRK00033 PRK00033.1-2 149 149 94 equivalog Y Y N ATP-dependent Clp protease adapter ClpS clpS GO:0006508 2 Bacteria superkingdom 7500 NCBI Protein Cluster (PRK) ATP-dependent Clp protease adaptor protein ClpS ATP-dependent Clp protease adapter ClpS NF000672.0 PRK00033 PRK00033.1-5 112 112 104 equivalog Y Y N ATP-dependent Clp protease adapter ClpS clpS 2 Bacteria superkingdom 13415 NCBI Protein Cluster (PRK) ATP-dependent Clp protease adaptor protein ClpS ATP-dependent Clp protease adapter ClpS NF000689.1 PRK00035 PRK00035.2-1 408 408 311 equivalog Y Y N ferrochelatase 4.98.1.1 GO:0004325,GO:0006783 2 Bacteria superkingdom 15957 NCBI Protein Cluster (PRK) ferrochelatase ferrochelatase NF000722.0 PRK00042 PRK00042.2-1 293 293 256 equivalog Y Y N triose-phosphate isomerase 5.3.1.1 GO:0004807 2 Bacteria superkingdom 2841 NCBI Protein Cluster (PRK) triosephosphate isomerase triose-phosphate isomerase NF000734.0 PRK00043 PRK00043.1-5 252 252 201 equivalog Y Y N thiamine phosphate synthase 2.5.1.3 GO:0004789,GO:0009228 2 Bacteria superkingdom 4012 NCBI Protein Cluster (PRK) thiamine-phosphate pyrophosphorylase thiamine phosphate synthase NF000740.0 PRK00043 PRK00043.3-4 202 202 218 equivalog Y Y N thiamine phosphate synthase 2.5.1.3 2 Bacteria superkingdom 873 NCBI Protein Cluster (PRK) thiamine-phosphate pyrophosphorylase thiamine phosphate synthase NF000744.0 PRK00045 PRK00045.1-3 429 429 447 equivalog Y Y N glutamyl-tRNA reductase 1.2.1.70 GO:0008883 2 Bacteria superkingdom 15599 NCBI Protein Cluster (PRK) glutamyl-tRNA reductase glutamyl-tRNA reductase NF000750.0 PRK00045 PRK00045.3-4 289 289 439 equivalog Y Y N glutamyl-tRNA reductase 1.2.1.70 GO:0008883,GO:0033014,GO:0050661 2 Bacteria superkingdom 3763 NCBI Protein Cluster (PRK) glutamyl-tRNA reductase glutamyl-tRNA reductase NF000755.0 PRK00046 PRK00046.1 277 277 343 equivalog Y Y N UDP-N-acetylmuramate dehydrogenase murB 1.3.1.98 GO:0008762,GO:0071949 12492849,7920261,8805513,9020778 2 Bacteria superkingdom 30996 NCBI Protein Cluster (PRK) UDP-N-acetylenolpyruvoylglucosamine reductase UDP-N-acetylmuramate dehydrogenase Catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis NF000797.0 PRK00054 PRK00054.1-2 270 270 267 equivalog Y Y N dihydroorotate dehydrogenase electron transfer subunit GO:0006221,GO:0016491,GO:0050660,GO:0051537 2 Bacteria superkingdom 4713 NCBI Protein Cluster (PRK) dihydroorotate dehydrogenase electron transfer subunit dihydroorotate dehydrogenase electron transfer subunit NF000798.0 PRK00054 PRK00054.1-3 219 219 244 equivalog Y Y N dihydroorotate dehydrogenase electron transfer subunit GO:0006221,GO:0016491,GO:0050660,GO:0051537 2 Bacteria superkingdom 2489 NCBI Protein Cluster (PRK) dihydroorotate dehydrogenase electron transfer subunit dihydroorotate dehydrogenase electron transfer subunit NF000799.0 PRK00054 PRK00054.1-4 314 314 258 equivalog Y Y N dihydroorotate dehydrogenase electron transfer subunit GO:0016491 2 Bacteria superkingdom 3962 NCBI Protein Cluster (PRK) dihydroorotate dehydrogenase electron transfer subunit dihydroorotate dehydrogenase electron transfer subunit NF000800.0 PRK00055 PRK00055.1-1 398 398 305 equivalog Y Y N ribonuclease Z rnz 3.1.26.11 GO:0016891,GO:0042780 2 Bacteria superkingdom 5523 NCBI Protein Cluster (PRK) ribonuclease Z ribonuclease Z Ribonuclease Z from E. coli is sometimes called RNase BN. NF000805.0 PRK00055 PRK00055.2-3 416 416 307 equivalog Y Y N ribonuclease Z 3.1.26.11 2 Bacteria superkingdom 9089 NCBI Protein Cluster (PRK) ribonuclease Z ribonuclease Z NF000812.0 PRK00061 PRK00061.1-4 194 194 156 equivalog Y Y N 6,7-dimethyl-8-ribityllumazine synthase ribE 2.5.1.78 GO:0000906,GO:0009349 2 Bacteria superkingdom 11770 NCBI Protein Cluster (PRK) 6,7-dimethyl-8-ribityllumazine synthase 6,7-dimethyl-8-ribityllumazine synthase NF000814.0 PRK00061 PRK00061.2-2 174 174 160 equivalog Y Y N 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 GO:0000906,GO:0009349 2 Bacteria superkingdom 2393 NCBI Protein Cluster (PRK) 6,7-dimethyl-8-ribityllumazine synthase 6,7-dimethyl-8-ribityllumazine synthase NF000831.0 PRK00070 PRK00070.3-1 124 124 130 equivalog Y Y N holo-ACP synthase 2.7.8.7 2 Bacteria superkingdom 1591 NCBI Protein Cluster (PRK) 4'-phosphopantetheinyl transferase holo-ACP synthase NF000832.0 PRK00070 PRK00070.3-2 107 107 116 equivalog Y Y N holo-ACP synthase 2.7.8.7 GO:0006633,GO:0008897 2 Bacteria superkingdom 8505 NCBI Protein Cluster (PRK) 4'-phosphopantetheinyl transferase holo-ACP synthase NF000839.0 PRK00071 PRK00071.1-1 187 187 219 equivalog Y Y N nicotinate-nucleotide adenylyltransferase nadD 2.7.7.18 GO:0009435,GO:0016779 2 Bacteria superkingdom 11529 NCBI Protein Cluster (PRK) nicotinic acid mononucleotide adenylyltransferase nicotinate-nucleotide adenylyltransferase gene synonym: fusB NF000840.1 PRK00071 PRK00071.1-3 150 150 201 equivalog Y Y N nicotinate-nucleotide adenylyltransferase nadD 2.7.7.18 GO:0009435,GO:0016779 2 Bacteria superkingdom 34822 NCBI Protein Cluster (PRK) nicotinic acid mononucleotide adenylyltransferase nicotinate-nucleotide adenylyltransferase NF000841.0 PRK00071 PRK00071.1-4 197 197 194 equivalog Y Y N nicotinate-nucleotide adenylyltransferase 2.7.7.18 GO:0009435,GO:0016779 2 Bacteria superkingdom 6921 NCBI Protein Cluster (PRK) nicotinic acid mononucleotide adenylyltransferase nicotinate-nucleotide adenylyltransferase NF000843.0 PRK00071 PRK00071.2-2 240 240 212 equivalog Y Y N nicotinate-nucleotide adenylyltransferase 2.7.7.18 2 Bacteria superkingdom 7660 NCBI Protein Cluster (PRK) nicotinic acid mononucleotide adenylyltransferase nicotinate-nucleotide adenylyltransferase NF000845.0 PRK00071 PRK00071.2-4 210 210 197 equivalog Y Y N nicotinate-nucleotide adenylyltransferase 2.7.7.18 GO:0009435,GO:0016779 2 Bacteria superkingdom 5152 NCBI Protein Cluster (PRK) nicotinic acid mononucleotide adenylyltransferase nicotinate-nucleotide adenylyltransferase NF000907.0 PRK00087 PRK00087.1 624 624 671 equivalog Y Y N bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1 1.17.7.4 GO:0019288,GO:0050992,GO:0051745 2 Bacteria superkingdom 2818 NCBI Protein Cluster (PRK) 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1 NF000908.1 PRK00089 PRK00089.1 237 237 291 equivalog Y Y N GTPase Era era GO:0003723,GO:0005525 31465450 2 Bacteria superkingdom 54829 NCBI Protein Cluster (PRK) GTPase Era GTPase Era NF000928.0 PRK00092 PRK00092.1-2 163 163 158 equivalog Y Y N ribosome maturation factor RimP rimP GO:0042274 2 Bacteria superkingdom 5593 NCBI Protein Cluster (PRK) ribosome maturation protein RimP ribosome maturation factor RimP NF000932.0 PRK00092 PRK00092.2-5 185 185 200 equivalog Y Y N ribosome maturation factor RimP rimP 2 Bacteria superkingdom 5997 NCBI Protein Cluster (PRK) ribosome maturation protein RimP ribosome maturation factor RimP NF000941.0 PRK00094 PRK00094.1-3 423 423 336 equivalog Y Y N NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 1.1.1.94 GO:0009331,GO:0046168,GO:0047952,GO:0051287 7592341 2 Bacteria superkingdom 11265 NCBI Protein Cluster (PRK) NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NF000950.0 PRK00095 PRK00095.1-3 756 756 641 equivalog Y Y N DNA mismatch repair endonuclease MutL mutL GO:0005524,GO:0006298,GO:0016887,GO:0030983,GO:0032300 2 Bacteria superkingdom 11917 NCBI Protein Cluster (PRK) DNA mismatch repair protein DNA mismatch repair endonuclease MutL NF000953.0 PRK00095 PRK00095.2-4 693 693 611 equivalog Y Y N DNA mismatch repair endonuclease MutL mutL GO:0005524,GO:0006298,GO:0016887,GO:0030983,GO:0032300 2 Bacteria superkingdom 9122 NCBI Protein Cluster (PRK) DNA mismatch repair protein DNA mismatch repair endonuclease MutL NF000955.1 PRK00099 PRK00099.1-1 85 85 168 equivalog Y Y N 50S ribosomal protein L10 rplJ GO:0003735,GO:0006412,GO:0015934 2 Bacteria superkingdom 38596 NCBI Protein Cluster (PRK) 50S ribosomal protein L10 50S ribosomal protein L10 This model describes bacterial forms of the 50S ribosomal protein L10. NF000986.0 PRK00103 PRK00103.1-4 141 141 156 equivalog Y Y N 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH rlmH GO:0006364,GO:0008168 2 Bacteria superkingdom 11726 NCBI Protein Cluster (PRK) rRNA large subunit methyltransferase 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH NF000989.0 PRK00103 PRK00103.2-3 169 169 160 equivalog Y Y N 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH rlmH GO:0006364,GO:0008168 2 Bacteria superkingdom 5431 NCBI Protein Cluster (PRK) rRNA large subunit methyltransferase 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH NF000995.0 PRK00104 PRK00104.1-4 315 315 251 equivalog Y Y N segregation/condensation protein A 2 Bacteria superkingdom 2484 NCBI Protein Cluster (PRK) segregation and condensation protein A segregation/condensation protein A NF001030.0 PRK00110 PRK00110.1 243 243 245 equivalog Y Y N YebC/PmpR family DNA-binding transcriptional regulator 2 Bacteria superkingdom 44556 NCBI Protein Cluster (PRK) hypothetical protein YebC/PmpR family DNA-binding transcriptional regulator NF001033.0 PRK00114 PRK00114.1 244 244 297 equivalog Y Y N Hsp33 family molecular chaperone HslO hslO GO:0006457,GO:0051082 2 Bacteria superkingdom 25751 NCBI Protein Cluster (PRK) Hsp33-like chaperonin Hsp33 family molecular chaperone HslO NF001058.0 PRK00117 PRK00117.4-1 194 194 214 equivalog Y Y N recombination regulator RecX recX 2 Bacteria superkingdom 878 NCBI Protein Cluster (PRK) recombination regulator RecX recombination regulator RecX NF001065.0 PRK00117 PRK00117.5-5 175 175 149 equivalog Y Y N recombination regulator RecX recX 2 Bacteria superkingdom 21 NCBI Protein Cluster (PRK) recombination regulator RecX recombination regulator RecX NF001068.0 PRK00118 PRK00118.1-4 125 125 113 equivalog Y Y N putative DNA-binding protein 2 Bacteria superkingdom 2875 NCBI Protein Cluster (PRK) putative DNA-binding protein putative DNA-binding protein NF001070.0 PRK00118 PRK00118.1-6 117 117 110 equivalog Y Y N putative DNA-binding protein 2 Bacteria superkingdom 3774 NCBI Protein Cluster (PRK) putative DNA-binding protein putative DNA-binding protein NF001095.0 PRK00124 PRK00124.1 139 139 150 equivalog Y Y N YaiI/YqxD family protein 2 Bacteria superkingdom 24046 NCBI Protein Cluster (PRK) hypothetical protein YaiI/YqxD family protein NF001099.0 PRK00132 PRK00132.1 112 112 130 equivalog Y Y N 30S ribosomal protein S9 rpsI GO:0003735,GO:0005840,GO:0006412 3884974 2 Bacteria superkingdom 32256 NCBI Protein Cluster (PRK) 30S ribosomal protein S9 30S ribosomal protein S9 Forms a direct contact with the tRNA during translation NF001109.0 PRK00136 PRK00136.1 119 119 131 equivalog Y Y N 30S ribosomal protein S8 rpsH GO:0003735,GO:0005840,GO:0006412 9061793 2 Bacteria superkingdom 26825 NCBI Protein Cluster (PRK) 30S ribosomal protein S8 30S ribosomal protein S8 Binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit NF001124.0 PRK00139 PRK00139.1-2 476 476 500 equivalog Y Y N UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase 6.3.2.13 GO:0005524,GO:0008360,GO:0009058,GO:0016881,GO:0051301 2 Bacteria superkingdom 51224 NCBI Protein Cluster (PRK) UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase NF001133.0 PRK00142 PRK00142.1-1 254 254 350 equivalog Y Y N rhodanese-related sulfurtransferase 2 Bacteria superkingdom 7084 NCBI Protein Cluster (PRK) putative rhodanese-related sulfurtransferase rhodanese-related sulfurtransferase NF001134.0 PRK00142 PRK00142.1-2 320 320 304 equivalog Y Y N rhodanese-related sulfurtransferase 2 Bacteria superkingdom 3776 NCBI Protein Cluster (PRK) putative rhodanese-related sulfurtransferase rhodanese-related sulfurtransferase NF001135.0 PRK00142 PRK00142.1-3 255 255 319 equivalog Y Y N rhodanese-related sulfurtransferase 2 Bacteria superkingdom 9863 NCBI Protein Cluster (PRK) putative rhodanese-related sulfurtransferase rhodanese-related sulfurtransferase NF001136.0 PRK00142 PRK00142.1-4 303 303 327 equivalog Y Y N rhodanese-related sulfurtransferase 2 Bacteria superkingdom 15637 NCBI Protein Cluster (PRK) putative rhodanese-related sulfurtransferase rhodanese-related sulfurtransferase NF001154.0 PRK00149 PRK00149.3-3 410 410 462 equivalog Y Y N chromosomal replication initiator protein DnaA dnaA 2 Bacteria superkingdom 293 NCBI Protein Cluster (PRK) chromosomal replication initiation protein chromosomal replication initiator protein DnaA NF001186.0 PRK00155 PRK00155.2-3 253 253 224 equivalog Y Y N 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2.7.7.60 2 Bacteria superkingdom 3252 NCBI Protein Cluster (PRK) 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase NF001211.0 PRK00179 PRK00179.1 492 492 544 equivalog Y Y N glucose-6-phosphate isomerase pgi 5.3.1.9 GO:0004347,GO:0006094,GO:0006096 2 Bacteria superkingdom 55530 NCBI Protein Cluster (PRK) glucose-6-phosphate isomerase glucose-6-phosphate isomerase NF001222.0 PRK00199 PRK00199.1 115 115 95 equivalog Y Y N integration host factor subunit beta GO:0003677,GO:0005694,GO:0006310,GO:0006355 9171434 2 Bacteria superkingdom 11411 NCBI Protein Cluster (PRK) integration host factor subunit beta integration host factor subunit beta One of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control NF001236.0 PRK00203 PRK00203.1 160 160 151 equivalog Y Y N ribonuclease HI rnhA 3.1.26.4 GO:0003676,GO:0004523 10788800,25965344 2 Bacteria superkingdom 31635 NCBI Protein Cluster (PRK) ribonuclease H ribonuclease HI Specifically degrades the RNA strand of RNA-DNA hybrids NF001238.0 PRK00211 PRK00211.1 79 79 119 equivalog Y Y N sulfurtransferase complex subunit TusC tusC 2.8.1.- 2 Bacteria superkingdom 8768 NCBI Protein Cluster (PRK) sulfur relay protein TusC sulfurtransferase complex subunit TusC The TusBCD complex is involved in sulfur related that results in thiouridation to U34 position in some tRNAs NF001241.0 PRK00216 PRK00216.1-2 327 327 231 equivalog Y Y N demethylmenaquinone methyltransferase 2.1.1.163 GO:0008168 2 Bacteria superkingdom 11336 NCBI Protein Cluster (PRK) ubiquinone/menaquinone biosynthesis methyltransferase demethylmenaquinone methyltransferase NF001261.0 PRK00226 PRK00226.1-2 167 167 157 equivalog Y Y N transcription elongation factor GreA greA GO:0003677,GO:0032784,GO:0070063 2 Bacteria superkingdom 22157 NCBI Protein Cluster (PRK) transcription elongation factor GreA transcription elongation factor GreA NF001262.0 PRK00226 PRK00226.1-3 161 161 165 equivalog Y Y N transcription elongation factor GreA greA GO:0003677,GO:0032784,GO:0070063 2 Bacteria superkingdom 8914 NCBI Protein Cluster (PRK) transcription elongation factor GreA transcription elongation factor GreA NF001263.0 PRK00226 PRK00226.1-4 145 145 160 equivalog Y Y N transcription elongation factor GreA greA GO:0003677,GO:0032784,GO:0070063 2 Bacteria superkingdom 30356 NCBI Protein Cluster (PRK) transcription elongation factor GreA transcription elongation factor GreA NF001264.0 PRK00226 PRK00226.1-5 180 180 158 equivalog Y Y N transcription elongation factor GreA greA GO:0003677,GO:0032784,GO:0070063 2 Bacteria superkingdom 15660 NCBI Protein Cluster (PRK) transcription elongation factor GreA transcription elongation factor GreA NF001268.0 PRK00228 PRK00228.1-4 216 216 201 equivalog Y Y N YqgE/AlgH family protein 2 Bacteria superkingdom 4176 NCBI Protein Cluster (PRK) hypothetical protein YqgE/AlgH family protein NF001270.0 PRK00228 PRK00228.2-2 225 225 193 equivalog Y Y N YqgE/AlgH family protein 2 Bacteria superkingdom 5377 NCBI Protein Cluster (PRK) hypothetical protein YqgE/AlgH family protein NF001273.0 PRK00230 PRK00230.1 193 193 233 equivalog Y Y N orotidine-5'-phosphate decarboxylase pyrF 4.1.1.23 GO:0004590,GO:0006207,GO:0044205 11749542 2 Bacteria superkingdom 40343 NCBI Protein Cluster (PRK) orotidine 5'-phosphate decarboxylase orotidine-5'-phosphate decarboxylase Type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide NF001310.0 PRK00258 PRK00258.1-2 221 221 279 equivalog Y Y N shikimate dehydrogenase aroE 1.1.1.25 GO:0004764,GO:0019632 2 Bacteria superkingdom 23753 NCBI Protein Cluster (PRK) shikimate 5-dehydrogenase shikimate dehydrogenase NF001311.0 PRK00258 PRK00258.1-3 235 235 279 equivalog Y Y N shikimate dehydrogenase 1.1.1.25 GO:0004764 2 Bacteria superkingdom 14743 NCBI Protein Cluster (PRK) shikimate 5-dehydrogenase shikimate dehydrogenase NF001312.0 PRK00258 PRK00258.1-4 295 295 285 equivalog Y Y N shikimate dehydrogenase 1.1.1.25 GO:0004764,GO:0019632 2 Bacteria superkingdom 6823 NCBI Protein Cluster (PRK) shikimate 5-dehydrogenase shikimate dehydrogenase NF001313.0 PRK00258 PRK00258.2-1 431 431 290 equivalog Y Y N shikimate dehydrogenase 1.1.1.25 GO:0004764,GO:0019632,GO:0050661 2 Bacteria superkingdom 1901 NCBI Protein Cluster (PRK) shikimate 5-dehydrogenase shikimate dehydrogenase NF001323.0 PRK00259 PRK00259.1-1 196 196 198 equivalog Y Y N septation protein A 2 Bacteria superkingdom 3791 NCBI Protein Cluster (PRK) intracellular septation protein A septation protein A NF001369.0 PRK00278 PRK00278.1-1 329 329 271 equivalog Y Y N indole-3-glycerol phosphate synthase TrpC trpC 4.1.1.48 GO:0004425,GO:0006568 2 Bacteria superkingdom 11899 NCBI Protein Cluster (PRK) indole-3-glycerol-phosphate synthase indole-3-glycerol phosphate synthase TrpC NF001375.0 PRK00278 PRK00278.2-2 360 360 255 equivalog Y Y N indole-3-glycerol phosphate synthase TrpC trpC 4.1.1.48 2 Bacteria superkingdom 1144 NCBI Protein Cluster (PRK) indole-3-glycerol-phosphate synthase indole-3-glycerol phosphate synthase TrpC NF001379.0 PRK00279 PRK00279.1-1 268 268 216 equivalog Y Y N adenylate kinase adk 2.7.4.3 GO:0004017,GO:0005524,GO:0006139 2 Bacteria superkingdom 11844 NCBI Protein Cluster (PRK) adenylate kinase adenylate kinase NF001388.0 PRK00281 PRK00281.1-1 362 362 273 equivalog Y Y N undecaprenyl-diphosphate phosphatase bacA 3.6.1.27 GO:0016020,GO:0016311,GO:0050380 2 Bacteria superkingdom 3202 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate phosphatase undecaprenyl-diphosphate phosphatase NF001391.0 PRK00281 PRK00281.1-5 293 293 279 equivalog Y Y N undecaprenyl-diphosphate phosphatase 3.6.1.27 GO:0016020,GO:0016311,GO:0050380 2 Bacteria superkingdom 5672 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate phosphatase undecaprenyl-diphosphate phosphatase NF001392.0 PRK00281 PRK00281.2-1 308 308 280 equivalog Y Y N undecaprenyl-diphosphate phosphatase 3.6.1.27 GO:0016020,GO:0016311,GO:0050380 2 Bacteria superkingdom 16087 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate phosphatase undecaprenyl-diphosphate phosphatase NF001393.0 PRK00281 PRK00281.2-4 284 284 266 equivalog Y Y N undecaprenyl-diphosphate phosphatase 3.6.1.27 GO:0016020,GO:0016311,GO:0050380 2 Bacteria superkingdom 5920 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate phosphatase undecaprenyl-diphosphate phosphatase NF001394.0 PRK00281 PRK00281.2-5 311 311 281 equivalog Y Y N undecaprenyl-diphosphate phosphatase 3.6.1.27 2 Bacteria superkingdom 1724 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate phosphatase undecaprenyl-diphosphate phosphatase NF001399.0 PRK00283 PRK00283.1 279 279 300 subfamily Y Y N tyrosine recombinase 10361305,11114887,12050668,9311978 2 Bacteria superkingdom 71575 NCBI Protein Cluster (PRK) site-specific tyrosine recombinase XerD tyrosine recombinase NF001415.0 PRK00292 PRK00292.1-2 333 333 346 equivalog Y Y N glucokinase 2.7.1.2 GO:0004340,GO:0005524,GO:0005536,GO:0006096,GO:0051156 2 Bacteria superkingdom 3793 NCBI Protein Cluster (PRK) glucokinase glucokinase NF001422.0 PRK00296 PRK00296.1 58 58 87 equivalog Y Y N cell division topological specificity factor MinE minE GO:0032955 14569005 2 Bacteria superkingdom 8452 NCBI Protein Cluster (PRK) cell division topological specificity factor MinE cell division topological specificity factor MinE works in conjunction with MinC and MinD to enable cell division at the midpoint of the long axis of the cell NF001492.0 PRK00346 PRK00346.2-2 271 271 261 equivalog Y Y N 5'/3'-nucleotidase SurE surE 3.1.3.6 GO:0008252 2 Bacteria superkingdom 7507 NCBI Protein Cluster (PRK) 5'(3')-nucleotidase/polyphosphatase 5'/3'-nucleotidase SurE NF001493.0 PRK00346 PRK00346.2-3 230 230 269 equivalog Y Y N 5'/3'-nucleotidase SurE surE 3.1.3.6 2 Bacteria superkingdom 804 NCBI Protein Cluster (PRK) 5'(3')-nucleotidase/polyphosphatase 5'/3'-nucleotidase SurE NF001527.0 PRK00364 PRK00364.1-2 120 120 96 subfamily Y Y N co-chaperone GroES groES 2 Bacteria superkingdom 18999 NCBI Protein Cluster (PRK) co-chaperonin GroES co-chaperone GroES NF001529.0 PRK00364 PRK00364.1-5 133 133 95 subfamily Y Y N co-chaperone GroES groES 2 Bacteria superkingdom 10314 NCBI Protein Cluster (PRK) co-chaperonin GroES co-chaperone GroES NF001530.0 PRK00364 PRK00364.1-6 136 136 104 equivalog Y Y N co-chaperone GroES groES GO:0005524,GO:0006457,GO:0016887 2 Bacteria superkingdom 6219 NCBI Protein Cluster (PRK) co-chaperonin GroES co-chaperone GroES NF001531.0 PRK00364 PRK00364.2-2 96 96 94 subfamily Y Y N co-chaperone GroES groES 2 Bacteria superkingdom 29166 NCBI Protein Cluster (PRK) co-chaperonin GroES co-chaperone GroES NF001533.0 PRK00364 PRK00364.2-4 99 99 98 subfamily Y Y N co-chaperone GroES groES 2 Bacteria superkingdom 26461 NCBI Protein Cluster (PRK) co-chaperonin GroES co-chaperone GroES NF001534.0 PRK00364 PRK00364.2-5 120 120 94 equivalog Y Y N co-chaperone GroES groES GO:0005524,GO:0006457,GO:0016887 2 Bacteria superkingdom 16438 NCBI Protein Cluster (PRK) co-chaperonin GroES co-chaperone GroES NF001540.0 PRK00366 PRK00366.1 345 345 364 equivalog Y Y N flavodoxin-dependent (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase ispG gcpE 1.17.7.1 GO:0008152,GO:0046429 11752431 2 Bacteria superkingdom 48822 NCBI Protein Cluster (PRK) 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase Catalyzes the conversion of 2C-methyl-D-erythritol 2,4-cyclodiphosphate into 4-hydroxy-3-methyl-2-en-1-yl diphosphate; involved in isoprenoid synthesis NF001543.0 PRK00373 PRK00373.1-2 290 290 212 equivalog Y Y N V-type ATP synthase subunit D 7.1.2.2 2 Bacteria superkingdom 1716 NCBI Protein Cluster (PRK) V-type ATP synthase subunit D V-type ATP synthase subunit D NF001588.0 PRK00392 PRK00392.8-5 76 76 63 equivalog Y Y N DNA-directed RNA polymerase subunit omega 2.7.7.6 2 Bacteria superkingdom 81 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit omega DNA-directed RNA polymerase subunit omega NF001589.0 PRK00392 PRK00392.8-6 84 84 86 equivalog Y Y N DNA-directed RNA polymerase subunit omega 2.7.7.6 2 Bacteria superkingdom 186 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit omega DNA-directed RNA polymerase subunit omega NF001602.0 PRK00395 PRK00395.1 95 95 79 equivalog Y Y N RNA chaperone Hfq hfq GO:0003723,GO:0006355 15681864,20647674,24454955 2 Bacteria superkingdom 13575 NCBI Protein Cluster (PRK) RNA-binding protein Hfq RNA chaperone Hfq NF001610.0 PRK00400 PRK00400.1-1 104 104 93 equivalog Y Y N phosphoribosyl-ATP diphosphatase 3.6.1.31 GO:0004636 2 Bacteria superkingdom 6638 NCBI Protein Cluster (PRK) phosphoribosyl-ATP pyrophosphatase phosphoribosyl-ATP diphosphatase NF001613.0 PRK00400 PRK00400.1-5 120 120 107 equivalog Y Y N phosphoribosyl-ATP diphosphatase 3.6.1.31 GO:0000105,GO:0004636 2 Bacteria superkingdom 6628 NCBI Protein Cluster (PRK) phosphoribosyl-ATP pyrophosphatase phosphoribosyl-ATP diphosphatase NF001684.0 PRK00443 PRK00443.1-4 326 326 260 subfamily Y Y N glucosamine-6-phosphate deaminase 3.5.99.6 2 Bacteria superkingdom 10580 NCBI Protein Cluster (PRK) glucosamine-6-phosphate deaminase glucosamine-6-phosphate deaminase NF001688.0 PRK00448 PRK00448.1 873 873 1445 equivalog Y Y N PolC-type DNA polymerase III 2.7.7.7 GO:0003677,GO:0003887,GO:0006260,GO:0008408 2 Bacteria superkingdom 23725 NCBI Protein Cluster (PRK) DNA polymerase III PolC PolC-type DNA polymerase III NF001729.0 PRK00455 PRK00455.1-3 245 245 231 equivalog Y Y N orotate phosphoribosyltransferase 2.4.2.10 GO:0004588,GO:0009116 2 Bacteria superkingdom 3873 NCBI Protein Cluster (PRK) orotate phosphoribosyltransferase orotate phosphoribosyltransferase NF001748.0 PRK00468 PRK00468.1 106 106 75 equivalog Y Y N KH domain-containing protein 2 Bacteria superkingdom 1794 NCBI Protein Cluster (PRK) hypothetical protein KH domain-containing protein NF001754.0 PRK00481 PRK00481.1-4 252 252 244 equivalog Y Y N NAD-dependent protein deacylase 2.3.1.286 2 Bacteria superkingdom 1843 NCBI Protein Cluster (PRK) NAD-dependent deacetylase NAD-dependent protein deacylase NF001764.0 PRK00504 PRK00504.1 40 40 50 subfamily Y Y N 50S ribosomal protein L33 15049826 2 Bacteria superkingdom 12759 NCBI Protein Cluster (PRK) 50S ribosomal protein L33 50S ribosomal protein L33 NF001772.0 PRK00513 PRK00513.1-3 271 271 226 equivalog Y Y N septum site-determining protein MinC minC 2 Bacteria superkingdom 541 NCBI Protein Cluster (PRK) septum formation inhibitor septum site-determining protein MinC NF001785.0 PRK00517 PRK00517.2-2 188 188 282 equivalog Y Y N 50S ribosomal protein L11 methyltransferase prmA GO:0006479,GO:0008276 2 Bacteria superkingdom 6885 NCBI Protein Cluster (PRK) ribosomal protein L11 methyltransferase 50S ribosomal protein L11 methyltransferase NF001802.0 PRK00521 PRK00521.2-5 142 142 144 equivalog Y Y N 30S ribosome-binding factor RbfA rbfA GO:0006364 2 Bacteria superkingdom 6649 NCBI Protein Cluster (PRK) ribosome-binding factor A 30S ribosome-binding factor RbfA NF001808.0 PRK00522 PRK00522.1 123 123 167 equivalog Y Y N thiol peroxidase tpx 1.11.1.- GO:0008379,GO:0016684 2 Bacteria superkingdom 25255 NCBI Protein Cluster (PRK) lipid hydroperoxide peroxidase thiol peroxidase NF001809.0 PRK00528 PRK00528.1 70 70 75 equivalog Y Y N 50S ribosomal protein L31 rpmE GO:0003735,GO:0006412 2 Bacteria superkingdom 16516 NCBI Protein Cluster (PRK) 50S ribosomal protein L31 50S ribosomal protein L31 NF001813.0 PRK00549 PRK00549.1 379 379 414 equivalog Y Y N competence/damage-inducible protein A 2 Bacteria superkingdom 19592 NCBI Protein Cluster (PRK) competence damage-inducible protein A competence/damage-inducible protein A NF001842.0 PRK00567 PRK00567.1-3 146 146 147 equivalog Y Y N large-conductance mechanosensitive channel protein MscL mscL GO:0008381,GO:0016020,GO:0034220 2 Bacteria superkingdom 2114 NCBI Protein Cluster (PRK) large-conductance mechanosensitive channel large-conductance mechanosensitive channel protein MscL NF001846.0 PRK00571 PRK00571.1-3 132 132 137 equivalog Y Y N F0F1 ATP synthase subunit epsilon 7.1.2.2 GO:0015986,GO:0045261,GO:0046933 2 Bacteria superkingdom 4992 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit epsilon F0F1 ATP synthase subunit epsilon NF001847.0 PRK00571 PRK00571.1-4 135 135 139 equivalog Y Y N F0F1 ATP synthase subunit epsilon 7.1.2.2 GO:0015986,GO:0046933 2 Bacteria superkingdom 8314 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit epsilon F0F1 ATP synthase subunit epsilon NF001851.0 PRK00571 PRK00571.2-4 131 131 135 equivalog Y Y N F0F1 ATP synthase subunit epsilon 7.1.2.2 GO:0015986,GO:0045261,GO:0046933 2 Bacteria superkingdom 2544 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit epsilon F0F1 ATP synthase subunit epsilon NF001852.0 PRK00571 PRK00571.2-5 145 145 124 equivalog Y Y N F0F1 ATP synthase subunit epsilon 7.1.2.2 2 Bacteria superkingdom 1355 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit epsilon F0F1 ATP synthase subunit epsilon NF001854.0 PRK00575 PRK00575.1 72 72 94 equivalog Y Y N Sec-independent protein translocase subunit TatA tatA GO:0016020,GO:0043953 2 Bacteria superkingdom 13103 NCBI Protein Cluster (PRK) twin arginine translocase protein A Sec-independent protein translocase subunit TatA Part of system that translocates proteins with a conserved twin arginine motif across the inner membrane; capable of translocating folded substrates typically those with bound cofactors NF001859.2 PRK00591 PRK00591.1 400 400 347 equivalog Y Y N peptide chain release factor 1 prfA GO:0006415,GO:0016149 2 Bacteria superkingdom 55583 NCBI Protein Cluster (PRK) peptide chain release factor 1 peptide chain release factor 1 Recognizes the termination signals UAG and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF1 NF001860.2 PRK00595 PRK00595.1 50 50 49 subfamily Y Y N 50S ribosomal protein L33 9044258 2 Bacteria superkingdom 21482 NCBI Protein Cluster (PRK) 50S ribosomal protein L33 50S ribosomal protein L33 NF001861.0 PRK00596 PRK00596.1 85 85 102 equivalog Y Y N 30S ribosomal protein S10 rpsJ GO:0003723,GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 10582 NCBI Protein Cluster (PRK) 30S ribosomal protein S10 30S ribosomal protein S10 NusE; involved in assembly of the 30S subunit; in the ribosome, this protein is involved in the binding of tRNA; in Escherichia coli this protein was also found to be involved in transcription antitermination; NusB/S10 heterodimers bind boxA sequences in the leader RNA of rrn operons which is required for antitermination; binding of NusB/S10 to boxA nucleates assembly of the antitermination complex NF001886.0 PRK00642 PRK00642.1 247 247 208 equivalog Y Y N inorganic pyrophosphatase 3.6.1.1 2 Bacteria superkingdom 1202 NCBI Protein Cluster (PRK) inorganic pyrophosphatase inorganic pyrophosphatase Catalyzes the hydrolysis of pyrophosphate to phosphate NF001898.0 PRK00654 PRK00654.1-1 603 603 477 equivalog Y Y N glycogen synthase GlgA glgA 2.4.1.21 GO:0004373 2 Bacteria superkingdom 10618 NCBI Protein Cluster (PRK) glycogen synthase glycogen synthase GlgA NF001899.0 PRK00654 PRK00654.1-2 459 459 478 equivalog Y Y N glycogen synthase GlgA glgA 2.4.1.21 GO:0004373 2 Bacteria superkingdom 20940 NCBI Protein Cluster (PRK) glycogen synthase glycogen synthase GlgA NF001902.0 PRK00654 PRK00654.2-1 845 845 492 equivalog Y Y N glycogen synthase GlgA glgA 2.4.1.21 2 Bacteria superkingdom 465 NCBI Protein Cluster (PRK) glycogen synthase glycogen synthase GlgA NF001905.0 PRK00654 PRK00654.2-4 560 560 489 subfamily Y Y N glycogen synthase GlgA glgA 2.4.1.21 2 Bacteria superkingdom 705 NCBI Protein Cluster (PRK) glycogen synthase glycogen synthase GlgA NF001907.1 PRK00665 PRK00665.1 60 60 31 equivalog Y Y N cytochrome b6-f complex subunit V petG GO:0015979,GO:0017004,GO:0045158 14526088 2 Bacteria superkingdom 335 NCBI Protein Cluster (PRK) cytochrome b6-f complex subunit PetG cytochrome b6-f complex subunit V Cytochrome b6-f complex subunit 5; plastohydroquinone/plastocyanin oxidoreductase; with PetL, PetM and PetN makes up the small subunit of the cytochrome b6-f complex; cytochrome b6-f mediates electron transfer between photosystem II and photosystem I NF001933.0 PRK00711 PRK00711.1 383 383 429 subfamily Y Y N D-amino acid dehydrogenase 1.4.99.- GO:0008718,GO:0019478 2 Bacteria superkingdom 30867 NCBI Protein Cluster (PRK) D-amino acid dehydrogenase small subunit D-amino acid dehydrogenase NF001936.0 PRK00714 PRK00714.1-3 118 118 155 equivalog Y Y N RNA pyrophosphohydrolase 3.6.1.- 2 Bacteria superkingdom 4699 NCBI Protein Cluster (PRK) RNA pyrophosphohydrolase RNA pyrophosphohydrolase NF001938.0 PRK00714 PRK00714.1-5 116 116 172 equivalog Y Y N RNA pyrophosphohydrolase 3.6.1.- GO:0016787 2 Bacteria superkingdom 19169 NCBI Protein Cluster (PRK) RNA pyrophosphohydrolase RNA pyrophosphohydrolase NF001939.1 PRK00719 PRK00719.1 510 510 373 subfamily Y Y N alkanesulfonate monooxygenase ssuD 10480865 2 Bacteria superkingdom 17262 NCBI Protein Cluster (PRK) alkanesulfonate monooxygenase alkanesulfonate monooxygenase NF001940.0 PRK00720 PRK00720.1 83 83 78 equivalog Y Y N twin-arginine translocase TatA/TatE family subunit GO:0016020,GO:0043953 2 Bacteria superkingdom 3370 NCBI Protein Cluster (PRK) twin arginine translocase protein A twin-arginine translocase TatA/TatE family subunit NF001941.0 PRK00723 PRK00723.1 371 371 297 equivalog Y Y N phosphatidylserine decarboxylase 4.1.1.65 2 Bacteria superkingdom 1174 NCBI Protein Cluster (PRK) phosphatidylserine decarboxylase phosphatidylserine decarboxylase Catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine NF001947.0 PRK00725 PRK00725.1 470 470 426 subfamily Y Y N glucose-1-phosphate adenylyltransferase 2.7.7.27 2 Bacteria superkingdom 19320 NCBI Protein Cluster (PRK) glucose-1-phosphate adenylyltransferase glucose-1-phosphate adenylyltransferase Catalyzes the formation of ADP-glucose and diphosphate from ATP and alpha-D-glucose 1-phosphate NF001952.0 PRK00733 PRK00733.1-4 912 912 782 equivalog Y Y N sodium-translocating pyrophosphatase 3.6.1.1 2 Bacteria superkingdom 9174 NCBI Protein Cluster (PRK) membrane-bound proton-translocating pyrophosphatase sodium-translocating pyrophosphatase NF001955.0 PRK00733 PRK00733.2-4 1059 1059 736 equivalog Y Y N sodium-translocating pyrophosphatase 3.6.1.1 GO:0004427,GO:0009678,GO:0016020,GO:1902600 2 Bacteria superkingdom 4035 NCBI Protein Cluster (PRK) membrane-bound proton-translocating pyrophosphatase sodium-translocating pyrophosphatase NF001957.0 PRK00733 PRK00733.3-2 945 945 651 equivalog Y Y N sodium-translocating pyrophosphatase 3.6.1.1 2 Bacteria superkingdom 69 NCBI Protein Cluster (PRK) membrane-bound proton-translocating pyrophosphatase sodium-translocating pyrophosphatase NF001958.0 PRK00733 PRK00733.3-3 1055 1055 680 equivalog Y Y N sodium-translocating pyrophosphatase 3.6.1.1 2 Bacteria superkingdom 52 NCBI Protein Cluster (PRK) membrane-bound proton-translocating pyrophosphatase sodium-translocating pyrophosphatase NF001961.0 PRK00733 PRK00733.3-6 926 926 671 equivalog Y Y N sodium-translocating pyrophosphatase 3.6.1.1 2 Bacteria superkingdom 702 NCBI Protein Cluster (PRK) membrane-bound proton-translocating pyrophosphatase sodium-translocating pyrophosphatase NF001964.0 PRK00741 PRK00741.1 473 473 529 equivalog Y Y N peptide chain release factor 3 GO:0003924,GO:0006415 2 Bacteria superkingdom 45170 NCBI Protein Cluster (PRK) peptide chain release factor 3 peptide chain release factor 3 Stimulates the release of release factors 1 and 2 from the ribosome after hydrolysis of the ester bond in peptidyl-tRNA has occurred; GDP/GTP-binding protein NF001966.0 PRK00745 PRK00745.1 80 80 62 equivalog Y Y N 4-oxalocrotonate tautomerase 5.3.2.6 2 Bacteria superkingdom 1554 NCBI Protein Cluster (PRK) 4-oxalocrotonate tautomerase 4-oxalocrotonate tautomerase NF001968.0 PRK00750 PRK00750.1-2 648 648 528 equivalog Y Y N lysine--tRNA ligase 6.1.1.6 GO:0000049,GO:0004824,GO:0005524,GO:0006430 2 Bacteria superkingdom 8195 NCBI Protein Cluster (PRK) lysyl-tRNA synthetase lysine--tRNA ligase NF001972.0 PRK00753 PRK00753.1 74 74 39 equivalog Y Y N photosystem II reaction center protein L 2 Bacteria superkingdom 318 NCBI Protein Cluster (PRK) photosystem II reaction center L photosystem II reaction center protein L NF001979.0 PRK00768 PRK00768.1 249 249 275 equivalog Y Y N ammonia-dependent NAD(+) synthetase nadE 6.3.1.5 GO:0003952,GO:0004359,GO:0008795,GO:0009435 12077433,15699042,15748981,8895556,9620974 2 Bacteria superkingdom 25196 NCBI Protein Cluster (PRK) NAD synthetase ammonia-dependent NAD(+) synthetase Catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia as the amide donor and ATP forms homodimers NF001995.1 PRK00794 PRK00794.1-1 125 125 125 equivalog Y Y N flagellar biosynthesis repressor FlbT flbT GO:0006402,GO:0048027,GO:1902209 11029689,1699845,21273249 2 Bacteria superkingdom 3100 NCBI Protein Cluster (PRK) flagellar biosynthesis repressor FlbT flagellar biosynthesis repressor FlbT NF002002.0 PRK00802 PRK00802.1-2 249 249 197 equivalog Y Y N DNA-3-methyladenine glycosylase 3.2.2.- GO:0003677,GO:0003905,GO:0006284 2 Bacteria superkingdom 1926 NCBI Protein Cluster (PRK) 3-methyladenine DNA glycosylase DNA-3-methyladenine glycosylase NF002014.0 PRK00819 PRK00819.1-4 239 239 182 equivalog Y Y N RNA 2'-phosphotransferase 2.7.1.- GO:0003950 2 Bacteria superkingdom 12542 NCBI Protein Cluster (PRK) RNA 2'-phosphotransferase RNA 2'-phosphotransferase NF002021.1 PRK00831 PRK00831.1 70 70 41 exception Y Y N type B 50S ribosomal protein L36 ykgO GO:0003735,GO:0005840,GO:0006412 32559334 2 Bacteria superkingdom 4720 NCBI Protein Cluster (PRK) 50S ribosomal protein L36 type B 50S ribosomal protein L36 The typical 50S ribosomal protein L36, encoded by rpmJ, is about 38 amino acids long, with a zinc-binding CxxC motif. This protein, a paralog of rpmJ encoded by ykgO (as named in Escherichia coli), lacks the zinc-binding site and replaces RpmJ when zinc availability is low. NF002023.0 PRK00844 PRK00844.1 458 458 408 subfamily Y Y N glucose-1-phosphate adenylyltransferase 2.7.7.27 2 Bacteria superkingdom 22409 NCBI Protein Cluster (PRK) glucose-1-phosphate adenylyltransferase glucose-1-phosphate adenylyltransferase Catalyzes the formation of ADP-glucose and diphosphate from ATP and alpha-D-glucose 1-phosphate NF002033.0 PRK00861 PRK00861.1 293 293 328 subfamily Y N N putative lipid kinase 2 Bacteria superkingdom 789 NCBI Protein Cluster (PRK) putative lipid kinase putative lipid kinase NF002035.0 PRK00865 PRK00865.1-3 328 328 267 equivalog Y Y N glutamate racemase racE 5.1.1.3 GO:0008152,GO:0008881 2 Bacteria superkingdom 6668 NCBI Protein Cluster (PRK) glutamate racemase glutamate racemase NF002047.0 PRK00872 PRK00872.1-4 286 286 181 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 11 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002056.0 PRK00886 PRK00886.1-5 323 323 243 equivalog Y Y N 2-phosphosulfolactate phosphatase family protein 2 Bacteria superkingdom 733 NCBI Protein Cluster (PRK) 2-phosphosulfolactate phosphatase 2-phosphosulfolactate phosphatase family protein This bacterial enzyme is related to archaeal 2-phosphosulfolactate phosphatase, involved in biosynthesis of coenzyme M, a cofactor involved in methanogenesis in the archaea. It may differ in function. NF002059.0 PRK00889 PRK00889.1 244 244 177 subfamily Y Y N adenylyl-sulfate kinase 2.7.1.25 2 Bacteria superkingdom 1065 NCBI Protein Cluster (PRK) adenylylsulfate kinase adenylyl-sulfate kinase Converts ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate NF002063.0 PRK00893 PRK00893.1-3 171 171 142 equivalog Y Y N aspartate carbamoyltransferase regulatory subunit 2 Bacteria superkingdom 1811 NCBI Protein Cluster (PRK) aspartate carbamoyltransferase regulatory subunit aspartate carbamoyltransferase regulatory subunit NF002075.0 PRK00913 PRK00913.2-2 468 468 502 equivalog Y Y N leucyl aminopeptidase 3.4.11.1 2 Bacteria superkingdom 9286 NCBI Protein Cluster (PRK) multifunctional aminopeptidase A leucyl aminopeptidase NF002076.0 PRK00913 PRK00913.2-3 491 491 494 equivalog Y Y N leucyl aminopeptidase 3.4.11.1 2 Bacteria superkingdom 1229 NCBI Protein Cluster (PRK) multifunctional aminopeptidase A leucyl aminopeptidase NF002077.0 PRK00913 PRK00913.2-4 471 471 501 equivalog Y Y N leucyl aminopeptidase 3.4.11.1 GO:0006508,GO:0030145,GO:0070006 2 Bacteria superkingdom 17304 NCBI Protein Cluster (PRK) multifunctional aminopeptidase A leucyl aminopeptidase NF002087.0 PRK00915 PRK00915.1-4 729 729 516 equivalog Y Y N 2-isopropylmalate synthase 2.3.3.13 GO:0003852 2 Bacteria superkingdom 9612 NCBI Protein Cluster (PRK) 2-isopropylmalate synthase 2-isopropylmalate synthase NF002091.1 PRK00924 PRK00924.1 250 250 277 equivalog Y Y N 5-dehydro-4-deoxy-D-glucuronate isomerase kduI 5.3.1.17 GO:0008697,GO:0045490 16152643,17322190,23437267,31285597 2 Bacteria superkingdom 16770 NCBI Protein Cluster (PRK) 5-keto-4-deoxyuronate isomerase 5-dehydro-4-deoxy-D-glucuronate isomerase Catalyzes the interconversion of 4-deoxy-L-threo-5-hexosulose uronate to 3-deoxy-D-glycero-2,5-hexodiulosonate ketol-isomerase NF002098.0 PRK00943 PRK00943.1 299 299 347 equivalog Y Y N selenide, water dikinase SelD selD 2.7.9.3 GO:0004756,GO:0016260 2 Bacteria superkingdom 26279 NCBI Protein Cluster (PRK) selenophosphate synthetase selenide, water dikinase SelD Catalyzes the formation of selenophosphate from selenide and ATP NF002099.0 PRK00944 PRK00944.1 241 241 195 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 3170 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002106.0 PRK00951 PRK00951.1-1 283 283 197 equivalog Y Y N imidazoleglycerol-phosphate dehydratase HisB hisB 4.2.1.19 GO:0000105,GO:0004424 2 Bacteria superkingdom 6677 NCBI Protein Cluster (PRK) imidazoleglycerol-phosphate dehydratase imidazoleglycerol-phosphate dehydratase HisB NF002109.0 PRK00951 PRK00951.1-5 278 278 196 equivalog Y Y N imidazoleglycerol-phosphate dehydratase HisB hisB 4.2.1.19 GO:0000105,GO:0004424 2 Bacteria superkingdom 12712 NCBI Protein Cluster (PRK) imidazoleglycerol-phosphate dehydratase imidazoleglycerol-phosphate dehydratase HisB NF002110.2 PRK00951 PRK00951.1-6 266 266 199 equivalog Y Y N imidazoleglycerol-phosphate dehydratase HisB hisB 4.2.1.19 GO:0000105,GO:0004424 2 Bacteria superkingdom 10008 NCBI Protein Cluster (PRK) imidazoleglycerol-phosphate dehydratase imidazoleglycerol-phosphate dehydratase HisB NF002115.0 PRK00951 PRK00951.2-5 289 289 195 equivalog Y Y N imidazoleglycerol-phosphate dehydratase HisB hisB 4.2.1.19 GO:0000105,GO:0004424 2 Bacteria superkingdom 2871 NCBI Protein Cluster (PRK) imidazoleglycerol-phosphate dehydratase imidazoleglycerol-phosphate dehydratase HisB NF002132.0 PRK00971 PRK00971.1-1 381 381 308 equivalog Y Y N glutaminase B glsB 3.5.1.2 GO:0004359,GO:0006541 2 Bacteria superkingdom 11493 NCBI Protein Cluster (PRK) glutaminase glutaminase B NF002133.0 PRK00971 PRK00971.1-2 368 368 305 equivalog Y Y N glutaminase 3.5.1.2 GO:0004359,GO:0006541 2 Bacteria superkingdom 17820 NCBI Protein Cluster (PRK) glutaminase glutaminase NF002134.0 PRK00971 PRK00971.1-4 557 557 429 equivalog Y Y N glutaminase 3.5.1.2 GO:0004359,GO:0006541 2 Bacteria superkingdom 2530 NCBI Protein Cluster (PRK) glutaminase glutaminase NF002147.0 PRK00982 PRK00982.1-1 84 84 83 equivalog Y Y N acyl carrier protein 2 Bacteria superkingdom 5298 NCBI Protein Cluster (PRK) acyl carrier protein acyl carrier protein NF002148.0 PRK00982 PRK00982.1-2 71 71 79 subfamily Y Y N acyl carrier protein 2 Bacteria superkingdom 21690 NCBI Protein Cluster (PRK) acyl carrier protein acyl carrier protein NF002149.0 PRK00982 PRK00982.1-3 106 106 78 equivalog Y Y N acyl carrier protein acpP GO:0006633 2 Bacteria superkingdom 9518 NCBI Protein Cluster (PRK) acyl carrier protein acyl carrier protein NF002150.0 PRK00982 PRK00982.1-4 66 66 80 subfamily Y Y N acyl carrier protein 2 Bacteria superkingdom 22678 NCBI Protein Cluster (PRK) acyl carrier protein acyl carrier protein NF002151.0 PRK00982 PRK00982.1-5 92 92 78 equivalog Y Y N acyl carrier protein GO:0006633 2 Bacteria superkingdom 11820 NCBI Protein Cluster (PRK) acyl carrier protein acyl carrier protein NF002187.0 PRK01045 PRK01045.1-1 276 276 282 equivalog Y Y N 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 1.17.7.4 GO:0019288,GO:0046872,GO:0050992,GO:0051745 2 Bacteria superkingdom 11017 NCBI Protein Cluster (PRK) 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 4-hydroxy-3-methylbut-2-enyl diphosphate reductase NF002188.0 PRK01045 PRK01045.1-2 420 420 315 equivalog Y Y N 4-hydroxy-3-methylbut-2-enyl diphosphate reductase ispH lytB 1.17.7.4 GO:0019288,GO:0046872,GO:0050992,GO:0051745 2 Bacteria superkingdom 30287 NCBI Protein Cluster (PRK) 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 4-hydroxy-3-methylbut-2-enyl diphosphate reductase NF002189.0 PRK01045 PRK01045.1-3 444 444 326 equivalog Y Y N 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 1.17.7.4 GO:0019288,GO:0046872,GO:0051745 2 Bacteria superkingdom 14673 NCBI Protein Cluster (PRK) 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 4-hydroxy-3-methylbut-2-enyl diphosphate reductase NF002190.0 PRK01045 PRK01045.1-4 389 389 321 subfamily Y Y N 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 1.17.7.4 2 Bacteria superkingdom 38675 NCBI Protein Cluster (PRK) 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 4-hydroxy-3-methylbut-2-enyl diphosphate reductase NF002191.0 PRK01059 PRK01059.1-1 381 381 358 equivalog Y Y N protein arginine kinase 2.7.14.1 2 Bacteria superkingdom 235 NCBI Protein Cluster (PRK) ATP:guanido phosphotransferase protein arginine kinase NF002194.0 PRK01059 PRK01059.1-4 385 385 345 equivalog Y Y N protein arginine kinase 2.7.14.1 GO:0016301,GO:0046314 2 Bacteria superkingdom 5128 NCBI Protein Cluster (PRK) ATP:guanido phosphotransferase protein arginine kinase NF002195.0 PRK01059 PRK01059.1-5 499 499 354 equivalog Y Y N protein arginine kinase 2.7.14.1 GO:0016301,GO:0046314 2 Bacteria superkingdom 2840 NCBI Protein Cluster (PRK) ATP:guanido phosphotransferase protein arginine kinase NF002196.0 PRK01060 PRK01060.1-1 333 333 297 equivalog Y Y N deoxyribonuclease IV 3.1.21.2 GO:0003677,GO:0006281,GO:0008270 2 Bacteria superkingdom 7891 NCBI Protein Cluster (PRK) endonuclease IV deoxyribonuclease IV NF002198.0 PRK01060 PRK01060.1-3 244 244 253 equivalog Y Y N deoxyribonuclease IV 3.1.21.2 GO:0003677,GO:0006281,GO:0008270 2 Bacteria superkingdom 4436 NCBI Protein Cluster (PRK) endonuclease IV deoxyribonuclease IV NF002201.0 PRK01064 PRK01064.1 85 85 78 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 242 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002203.0 PRK01076 PRK01076.1 572 572 419 equivalog Y Y N L-rhamnose isomerase 5.3.1.14 GO:0008740,GO:0019299,GO:0030145 2 Bacteria superkingdom 8557 NCBI Protein Cluster (PRK) L-rhamnose isomerase L-rhamnose isomerase Catalyzes the formation of L-rhamnulose from L-rhamnose NF002205.0 PRK01096 PRK01096.1 439 439 444 equivalog Y Y N deoxyguanosinetriphosphate triphosphohydrolase GO:0006203,GO:0008832 2 Bacteria superkingdom 8747 NCBI Protein Cluster (PRK) deoxyguanosinetriphosphate triphosphohydrolase-like protein deoxyguanosinetriphosphate triphosphohydrolase NF002224.0 PRK01119 PRK01119.1 169 169 110 equivalog Y Y N putative heavy metal-binding protein 2 Bacteria superkingdom 635 NCBI Protein Cluster (PRK) hypothetical protein putative heavy metal-binding protein NF002231.0 PRK01130 PRK01130.1 189 189 230 subfamily Y Y N putative N-acetylmannosamine-6-phosphate 2-epimerase 5.1.3.9 2 Bacteria superkingdom 18306 NCBI Protein Cluster (PRK) N-acetylmannosamine-6-phosphate 2-epimerase putative N-acetylmannosamine-6-phosphate 2-epimerase NF002266.0 PRK01198 PRK01198.1-2 270 270 333 equivalog Y Y N V-type ATP synthase subunit C 7.1.2.2 2 Bacteria superkingdom 1122 NCBI Protein Cluster (PRK) V-type ATP synthase subunit C V-type ATP synthase subunit C NF002293.0 PRK01220 PRK01220.1 115 115 99 equivalog Y Y N malonate decarboxylase subunit delta 2 Bacteria superkingdom 2531 NCBI Protein Cluster (PRK) malonate decarboxylase subunit delta malonate decarboxylase subunit delta NF002295.0 PRK01222 PRK01222.1-1 216 216 219 equivalog Y Y N phosphoribosylanthranilate isomerase 5.3.1.24 GO:0000162,GO:0004640 2 Bacteria superkingdom 8141 NCBI Protein Cluster (PRK) N-(5'-phosphoribosyl)anthranilate isomerase phosphoribosylanthranilate isomerase NF002298.0 PRK01222 PRK01222.1-4 215 215 209 equivalog Y Y N phosphoribosylanthranilate isomerase 5.3.1.24 GO:0000162,GO:0004640 2 Bacteria superkingdom 12581 NCBI Protein Cluster (PRK) N-(5'-phosphoribosyl)anthranilate isomerase phosphoribosylanthranilate isomerase NF002299.0 PRK01222 PRK01222.1-6 231 231 231 equivalog Y Y N phosphoribosylanthranilate isomerase 5.3.1.24 GO:0000162,GO:0004640 2 Bacteria superkingdom 9059 NCBI Protein Cluster (PRK) N-(5'-phosphoribosyl)anthranilate isomerase phosphoribosylanthranilate isomerase NF002300.0 PRK01222 PRK01222.1-7 212 212 195 equivalog Y Y N phosphoribosylanthranilate isomerase 5.3.1.24 2 Bacteria superkingdom 2758 NCBI Protein Cluster (PRK) N-(5'-phosphoribosyl)anthranilate isomerase phosphoribosylanthranilate isomerase NF002301.0 PRK01222 PRK01222.2-1 232 232 217 equivalog Y Y N phosphoribosylanthranilate isomerase 5.3.1.24 2 Bacteria superkingdom 1414 NCBI Protein Cluster (PRK) N-(5'-phosphoribosyl)anthranilate isomerase phosphoribosylanthranilate isomerase NF002315.0 PRK01237 PRK01237.1 280 280 291 equivalog Y Y N triphosphoribosyl-dephospho-CoA synthase 2.4.2.52 GO:0005524,GO:0016310,GO:0046917 2 Bacteria superkingdom 7975 NCBI Protein Cluster (PRK) triphosphoribosyl-dephospho-CoA synthase triphosphoribosyl-dephospho-CoA synthase Catalyzes the reversible formation of 2'-(5''-triphosphoribosyl)-3'dephospho-CoA from 3-dephospho-CoA NF002320.0 PRK01259 PRK01259.1 297 297 316 subfamily Y Y N ribose-phosphate diphosphokinase 2.7.6.1 GO:0004749,GO:0009156 2 Bacteria superkingdom 47538 NCBI Protein Cluster (PRK) ribose-phosphate pyrophosphokinase ribose-phosphate diphosphokinase Catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP NF002326.0 PRK01286 PRK01286.1-1 390 390 379 equivalog Y Y N deoxyguanosinetriphosphate triphosphohydrolase GO:0016793 2 Bacteria superkingdom 13228 NCBI Protein Cluster (PRK) deoxyguanosinetriphosphate triphosphohydrolase-like protein deoxyguanosinetriphosphate triphosphohydrolase NF002327.0 PRK01286 PRK01286.1-2 393 393 345 equivalog Y Y N deoxyguanosinetriphosphate triphosphohydrolase GO:0016793 2 Bacteria superkingdom 4016 NCBI Protein Cluster (PRK) deoxyguanosinetriphosphate triphosphohydrolase-like protein deoxyguanosinetriphosphate triphosphohydrolase NF002328.0 PRK01286 PRK01286.1-3 467 467 404 equivalog Y Y N deoxyguanosinetriphosphate triphosphohydrolase GO:0016793 2 Bacteria superkingdom 7411 NCBI Protein Cluster (PRK) deoxyguanosinetriphosphate triphosphohydrolase-like protein deoxyguanosinetriphosphate triphosphohydrolase NF002331.0 PRK01287 PRK01287.1 371 371 365 subfamily Y Y N site-specific tyrosine recombinase XerC xerC 2 Bacteria superkingdom 1186 NCBI Protein Cluster (PRK) site-specific tyrosine recombinase XerC site-specific tyrosine recombinase XerC Site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation NF002332.0 PRK01293 PRK01293.1 126 126 209 equivalog Y Y N malonate decarboxylase holo-ACP synthase GO:0016779 2 Bacteria superkingdom 7822 NCBI Protein Cluster (PRK) phosphoribosyl-dephospho-CoA transferase malonate decarboxylase holo-ACP synthase NF002342.0 PRK01305 PRK01305.1-3 205 205 239 equivalog Y Y N arginyltransferase 2.3.2.8 GO:0004057,GO:0008914,GO:0016598 2 Bacteria superkingdom 16344 NCBI Protein Cluster (PRK) arginyl-tRNA-protein transferase arginyltransferase NF002343.0 PRK01305 PRK01305.1-4 267 267 256 equivalog Y Y N arginyltransferase 2.3.2.8 GO:0004057,GO:0016598 2 Bacteria superkingdom 6994 NCBI Protein Cluster (PRK) arginyl-tRNA-protein transferase arginyltransferase NF002346.0 PRK01305 PRK01305.2-3 170 170 247 equivalog Y Y N arginyltransferase 2.3.2.8 2 Bacteria superkingdom 18557 NCBI Protein Cluster (PRK) arginyl-tRNA-protein transferase arginyltransferase NF002350.0 PRK01315 PRK01315.1 282 282 329 equivalog Y Y N membrane protein insertase YidC yidC GO:0032977 2 Bacteria superkingdom 9998 NCBI Protein Cluster (PRK) putative inner membrane protein translocase component YidC membrane protein insertase YidC NF002353.0 PRK01318 PRK01318.1-4 365 365 596 equivalog Y Y N membrane protein insertase YidC yidC GO:0016020,GO:0032977 2 Bacteria superkingdom 16193 NCBI Protein Cluster (PRK) membrane protein insertase membrane protein insertase YidC NF002363.0 PRK01345 PRK01345.1 422 422 318 equivalog Y Y N zinc metalloprotease HtpX htpX 3.4.24.- 2 Bacteria superkingdom 6154 NCBI Protein Cluster (PRK) heat shock protein HtpX zinc metalloprotease HtpX NF002367.0 PRK01346 PRK01346.1-4 259 259 411 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 22273 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002369.0 PRK01346 PRK01346.1-6 463 463 434 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 808 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002377.0 PRK01371 PRK01371.1-4 96 96 119 equivalog Y Y N sec-independent translocase GO:0015031 2 Bacteria superkingdom 6598 NCBI Protein Cluster (PRK) sec-independent translocase sec-independent translocase NF002381.0 PRK01388 PRK01388.1 414 414 405 subfamily Y Y N arginine deiminase 3.5.3.6 GO:0006527,GO:0016990 2 Bacteria superkingdom 25369 NCBI Protein Cluster (PRK) arginine deiminase arginine deiminase Catalyzes the degradation of arginine to citruline and ammonia NF002383.0 PRK01392 PRK01392.1 158 158 185 subfamily Y Y N citrate lyase holo-ACP synthase 2 Bacteria superkingdom 3153 NCBI Protein Cluster (PRK) 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA:apo-citrate lyase citrate lyase holo-ACP synthase NF002384.0 PRK01395 PRK01395.1 114 114 104 equivalog Y Y N V-type ATP synthase subunit F 7.1.2.2 2 Bacteria superkingdom 1609 NCBI Protein Cluster (PRK) V-type ATP synthase subunit F V-type ATP synthase subunit F NF002449.0 PRK01617 PRK01617.1 141 141 154 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 8703 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002451.0 PRK01625 PRK01625.1 106 106 59 equivalog Y Y N acid-soluble spore protein H 2 Bacteria superkingdom 143 NCBI Protein Cluster (PRK) acid-soluble spore protein H acid-soluble spore protein H Spore coat; expressed in forespore compartment NF002459.0 PRK01655 PRK01655.1 123 123 132 subfamily Y Y N transcriptional regulator Spx spx 2 Bacteria superkingdom 5944 NCBI Protein Cluster (PRK) transcriptional regulator Spx transcriptional regulator Spx NF002460.0 PRK01658 PRK01658.1 112 112 122 subfamily Y Y N CidA/LrgA family holin-like protein 2 Bacteria superkingdom 2957 NCBI Protein Cluster (PRK) holin-like protein CidA/LrgA family holin-like protein NF002461.0 PRK01663 PRK01663.1 513 513 428 subfamily Y Y N C4-dicarboxylate transporter DctA dctA GO:0006835,GO:0015293,GO:0016020 14659885,1617199 2 Bacteria superkingdom 27844 NCBI Protein Cluster (PRK) C4-dicarboxylate transporter DctA C4-dicarboxylate transporter DctA Involved in the transport of C4-dicarboxylates across the membrane NF002462.1 PRK01678 PRK01678.1 86 86 80 exception Y Y N type B 50S ribosomal protein L31 GO:0003735,GO:0005840,GO:0006412 11574053,15049826,16547061,32559334 2 Bacteria superkingdom 22462 NCBI Protein Cluster (PRK) 50S ribosomal protein L31 type B type B 50S ribosomal protein L31 This form of the bacterial 50S ribosomal protein L31 lacks the Zn-binding Cys pattern found in zinc-binding homologs such as RpmE of Escherichia coli or Bacillus subtilis. Many bacteria encode both forms of L31. NF002469.0 PRK01712 PRK01712.1 73 73 65 equivalog Y Y N carbon storage regulator CsrA csrA GO:0003723,GO:0006109,GO:0006402 26305456 2 Bacteria superkingdom 12598 NCBI Protein Cluster (PRK) carbon storage regulator carbon storage regulator CsrA Affects carbohydrate metabolism; has regulatory role in many processes NF002470.0 PRK01713 PRK01713.1 545 545 334 equivalog Y Y N ornithine carbamoyltransferase 2.1.3.3 GO:0004585,GO:0006520,GO:0006591,GO:0016597 2 Bacteria superkingdom 3605 NCBI Protein Cluster (PRK) ornithine carbamoyltransferase ornithine carbamoyltransferase NF002486.0 PRK01752 PRK01752.1 120 120 157 equivalog Y Y N YchJ family protein 2 Bacteria superkingdom 8926 NCBI Protein Cluster (PRK) hypothetical protein YchJ family protein NF002492.0 PRK01810 PRK01810.1 399 399 412 equivalog Y Y N DNA polymerase IV 2.7.7.7 GO:0003684,GO:0003887,GO:0006281 2 Bacteria superkingdom 4502 NCBI Protein Cluster (PRK) DNA polymerase IV DNA polymerase IV Involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function NF002496.0 PRK01827 PRK01827.1-2 325 325 318 equivalog Y Y N thymidylate synthase 2.1.1.45 GO:0004799,GO:0006231 2 Bacteria superkingdom 5484 NCBI Protein Cluster (PRK) thymidylate synthase thymidylate synthase NF002503.0 PRK01844 PRK01844.1 135 135 73 equivalog Y Y N YneF family protein 2 Bacteria superkingdom 584 NCBI Protein Cluster (PRK) hypothetical protein YneF family protein NF002524.0 PRK01964 PRK01964.1 86 86 64 equivalog Y Y N 4-oxalocrotonate tautomerase 5.3.2.6 2 Bacteria superkingdom 654 NCBI Protein Cluster (PRK) 4-oxalocrotonate tautomerase 4-oxalocrotonate tautomerase NF002526.0 PRK01966 PRK01966.1-2 449 449 362 equivalog Y Y N D-alanine--D-alanine ligase 6.3.2.4 GO:0005524,GO:0008716,GO:0046872 2 Bacteria superkingdom 5077 NCBI Protein Cluster (PRK) D-alanyl-alanine synthetase A D-alanine--D-alanine ligase NF002527.0 PRK01966 PRK01966.1-3 310 310 332 equivalog Y Y N D-alanine--D-alanine ligase 6.3.2.4 GO:0005524,GO:0008716,GO:0046872 2 Bacteria superkingdom 11236 NCBI Protein Cluster (PRK) D-alanyl-alanine synthetase A D-alanine--D-alanine ligase NF002528.0 PRK01966 PRK01966.1-4 262 262 366 subfamily Y Y N D-alanine--D-alanine ligase 6.3.2.4 2 Bacteria superkingdom 42324 NCBI Protein Cluster (PRK) D-alanyl-alanine synthetase A D-alanine--D-alanine ligase NF002542.0 PRK02101 PRK02101.1-3 278 278 258 equivalog Y Y N peroxide stress protein YaaA yaaA 2 Bacteria superkingdom 24020 NCBI Protein Cluster (PRK) hypothetical protein peroxide stress protein YaaA NF002543.0 PRK02101 PRK02101.1-4 204 204 244 equivalog Y Y N peroxide stress protein YaaA yaaA 2 Bacteria superkingdom 6625 NCBI Protein Cluster (PRK) hypothetical protein peroxide stress protein YaaA NF002555.0 PRK02118 PRK02118.1 431 431 436 equivalog Y Y N V-type ATP synthase subunit B 7.1.2.2 2 Bacteria superkingdom 1790 NCBI Protein Cluster (PRK) V-type ATP synthase subunit B V-type ATP synthase subunit B NF002557.0 PRK02122 PRK02122.1 384 384 653 subfamily Y N N glucosamine-6-phosphate deaminase-like protein 2 Bacteria superkingdom 5477 NCBI Protein Cluster (PRK) glucosamine-6-phosphate deaminase-like protein glucosamine-6-phosphate deaminase-like protein NF002558.0 PRK02126 PRK02126.1 315 315 345 subfamily Y N N ribonuclease Z 2 Bacteria superkingdom 892 NCBI Protein Cluster (PRK) ribonuclease Z ribonuclease Z NF002559.0 PRK02134 PRK02134.1 227 227 249 equivalog Y Y N chitin disaccharide deacetylase chbG 3.5.1.105 GO:0000272,GO:0016811 2 Bacteria superkingdom 6940 NCBI Protein Cluster (PRK) hypothetical protein chitin disaccharide deacetylase NF002564.0 PRK02190 PRK02190.1 302 302 307 subfamily Y Y N agmatinase 3.5.3.11 2 Bacteria superkingdom 19262 NCBI Protein Cluster (PRK) agmatinase agmatinase Catalyzes the formation of putrescine from agmatine NF002565.0 PRK02195 PRK02195.1 189 189 204 equivalog Y Y N V-type ATP synthase subunit D 7.1.2.2 2 Bacteria superkingdom 1272 NCBI Protein Cluster (PRK) V-type ATP synthase subunit D V-type ATP synthase subunit D NF002571.1 PRK02220 PRK02220.1 55 55 61 equivalog Y Y N 2-hydroxymuconate tautomerase 5.3.2.6 GO:0008152,GO:0016862 17902707 2 Bacteria superkingdom 5283 NCBI Protein Cluster (PRK) 4-oxalocrotonate tautomerase 2-hydroxymuconate tautomerase 2-hydroxymuconate tautomerase is also known as 4-oxalocrotonate tautomerase. NF002581.0 PRK02234 PRK02234.1-2 154 154 170 equivalog Y Y N Holliday junction resolvase RecU recU 3.1.21.10 2 Bacteria superkingdom 3516 NCBI Protein Cluster (PRK) Holliday junction-specific endonuclease Holliday junction resolvase RecU NF002584.0 PRK02234 PRK02234.1-5 236 236 206 equivalog Y Y N Holliday junction resolvase RecU recU 3.1.21.10 GO:0003676,GO:0004518,GO:0006281 2 Bacteria superkingdom 5953 NCBI Protein Cluster (PRK) Holliday junction-specific endonuclease Holliday junction resolvase RecU NF002601.0 PRK02259 PRK02259.1 180 180 293 equivalog Y Y N aspartoacylase 3.5.1.15 2 Bacteria superkingdom 2222 NCBI Protein Cluster (PRK) aspartoacylase aspartoacylase Catalyzes the conversion of N-acetyl_L-aspartic acid (NAA) to aspartate and acetate NF002602.0 PRK02260 PRK02260.1-2 197 197 171 equivalog Y Y N S-ribosylhomocysteine lyase luxS 4.4.1.21 2 Bacteria superkingdom 4464 NCBI Protein Cluster (PRK) S-ribosylhomocysteinase S-ribosylhomocysteine lyase NF002604.0 PRK02260 PRK02260.1-4 158 158 161 equivalog Y Y N S-ribosylhomocysteine lyase 4.4.1.21 GO:0005506,GO:0009372,GO:0043768 2 Bacteria superkingdom 8329 NCBI Protein Cluster (PRK) S-ribosylhomocysteinase S-ribosylhomocysteine lyase NF002606.0 PRK02260 PRK02260.2-4 208 208 153 equivalog Y Y N S-ribosylhomocysteine lyase 4.4.1.21 2 Bacteria superkingdom 1817 NCBI Protein Cluster (PRK) S-ribosylhomocysteinase S-ribosylhomocysteine lyase NF002617.0 PRK02268 PRK02268.1-3 220 220 137 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 395 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002618.0 PRK02269 PRK02269.1 460 460 321 equivalog Y Y N ribose-phosphate diphosphokinase 2.7.6.1 GO:0004749,GO:0009156 2 Bacteria superkingdom 5413 NCBI Protein Cluster (PRK) ribose-phosphate pyrophosphokinase ribose-phosphate diphosphokinase Catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP NF002625.0 PRK02290 PRK02290.1-3 375 375 369 subfamily Y Y N 3-dehydroquinate synthase II family protein 2 Bacteria superkingdom 1838 NCBI Protein Cluster (PRK) 3-dehydroquinate synthase 3-dehydroquinate synthase II family protein NF002640.0 PRK02308 PRK02308.1-4 456 456 308 equivalog Y Y N UV DNA damage repair endonuclease UvsE uvsE 2 Bacteria superkingdom 430 NCBI Protein Cluster (PRK) putative UV damage endonuclease UV DNA damage repair endonuclease UvsE NF002644.0 PRK02315 PRK02315.1-5 214 214 220 equivalog Y Y N adaptor protein MecA mecA 2 Bacteria superkingdom 2710 NCBI Protein Cluster (PRK) adaptor protein adaptor protein MecA NF002646.0 PRK02318 PRK02318.1-2 368 368 382 equivalog Y Y N mannitol-1-phosphate 5-dehydrogenase 1.1.1.17 GO:0008926,GO:0019594 2 Bacteria superkingdom 12185 NCBI Protein Cluster (PRK) mannitol-1-phosphate 5-dehydrogenase mannitol-1-phosphate 5-dehydrogenase NF002647.0 PRK02318 PRK02318.1-3 357 357 384 equivalog Y Y N mannitol-1-phosphate 5-dehydrogenase 1.1.1.17 2 Bacteria superkingdom 12202 NCBI Protein Cluster (PRK) mannitol-1-phosphate 5-dehydrogenase mannitol-1-phosphate 5-dehydrogenase NF002649.0 PRK02318 PRK02318.2-1 422 422 386 equivalog Y Y N mannitol-1-phosphate 5-dehydrogenase 1.1.1.17 2 Bacteria superkingdom 3042 NCBI Protein Cluster (PRK) mannitol-1-phosphate 5-dehydrogenase mannitol-1-phosphate 5-dehydrogenase NF002650.0 PRK02318 PRK02318.2-2 359 359 388 equivalog Y Y N mannitol-1-phosphate 5-dehydrogenase 1.1.1.17 2 Bacteria superkingdom 6874 NCBI Protein Cluster (PRK) mannitol-1-phosphate 5-dehydrogenase mannitol-1-phosphate 5-dehydrogenase NF002652.0 PRK02318 PRK02318.2-5 356 356 377 equivalog Y Y N mannitol-1-phosphate 5-dehydrogenase 1.1.1.17 GO:0008926,GO:0019594 2 Bacteria superkingdom 15761 NCBI Protein Cluster (PRK) mannitol-1-phosphate 5-dehydrogenase mannitol-1-phosphate 5-dehydrogenase NF002673.0 PRK02399 PRK02399.1-1 520 520 404 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 4296 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002696.0 PRK02487 PRK02487.1-5 146 146 160 equivalog Y Y N heme-degrading domain-containing protein 2 Bacteria superkingdom 11150 NCBI Protein Cluster (PRK) hypothetical protein heme-degrading domain-containing protein NF002700.0 PRK02496 PRK02496.1 262 262 184 equivalog Y Y N adenylate kinase 2 Bacteria superkingdom 658 NCBI Protein Cluster (PRK) adenylate kinase adenylate kinase NF002702.0 PRK02506 PRK02506.1 301 301 313 equivalog Y Y N dihydroorotate oxidase 1.3.98.1 GO:0004152,GO:0006221 12732650,9032071,9655329 2 Bacteria superkingdom 3438 NCBI Protein Cluster (PRK) dihydroorotate dehydrogenase 1A dihydroorotate oxidase NF002722.0 PRK02565 PRK02565.1 57 57 48 equivalog Y Y N photosystem II reaction center protein J 2 Bacteria superkingdom 381 NCBI Protein Cluster (PRK) photosystem II reaction center protein J photosystem II reaction center protein J NF002727.0 PRK02615 PRK02615.1 335 335 349 equivalog Y Y N thiamine phosphate synthase 2.5.1.3 2 Bacteria superkingdom 1348 NCBI Protein Cluster (PRK) thiamine-phosphate pyrophosphorylase thiamine phosphate synthase NF002728.1 PRK02624 PRK02624.1 65 65 60 equivalog Y Y N photosystem II reaction center phosphoprotein PsbH psbH GO:0009523,GO:0015979 15970599,2106663,26164101 2 Bacteria superkingdom 496 NCBI Protein Cluster (PRK) photosystem II reaction center protein H photosystem II reaction center phosphoprotein PsbH NF002730.0 PRK02628 PRK02628.1 473 473 677 equivalog Y Y N NAD(+) synthase 6.3.1.5 GO:0003952,GO:0004359,GO:0005524,GO:0008152,GO:0009435 15748981,9620974 2 Bacteria superkingdom 16932 NCBI Protein Cluster (PRK) NAD synthetase NAD(+) synthase Catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP NF002735.0 PRK02655 PRK02655.1 73 73 38 equivalog Y Y N photosystem II reaction center protein I 2 Bacteria superkingdom 327 NCBI Protein Cluster (PRK) photosystem II reaction center I protein I photosystem II reaction center protein I NF002739.0 PRK02714 PRK02714.1 259 259 320 equivalog Y Y N o-succinylbenzoate synthase 4.2.1.113 2 Bacteria superkingdom 852 NCBI Protein Cluster (PRK) O-succinylbenzoate synthase o-succinylbenzoate synthase Catalyzes the dehydration of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid to form O-succinylbenzoate NF002745.0 PRK02749 PRK02749.1 88 88 71 equivalog Y Y N photosystem I reaction center subunit IV 2 Bacteria superkingdom 617 NCBI Protein Cluster (PRK) photosystem I reaction center subunit IV photosystem I reaction center subunit IV Stabilizes the interaction between PsaC and the photosystem I core NF002748.0 PRK02769 PRK02769.1 305 305 382 equivalog Y Y N histidine decarboxylase 4.1.1.22 2 Bacteria superkingdom 2476 NCBI Protein Cluster (PRK) histidine decarboxylase histidine decarboxylase Catalyzes the formation of histamine from L-histidine NF002751.0 PRK02794 PRK02794.1 371 371 425 equivalog Y Y N DNA polymerase IV 2.7.7.7 GO:0003684,GO:0003887,GO:0006281 2 Bacteria superkingdom 7968 NCBI Protein Cluster (PRK) DNA polymerase IV DNA polymerase IV Involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function NF002756.0 PRK02797 PRK02797.1-5 457 457 351 equivalog Y Y N TDP-N-acetylfucosamine:lipid II N-acetylfucosaminyltransferase 2.4.1.325 2 Bacteria superkingdom 28 NCBI Protein Cluster (PRK) 4-alpha-L-fucosyltransferase TDP-N-acetylfucosamine:lipid II N-acetylfucosaminyltransferase NF002760.0 PRK02816 PRK02816.1 206 206 243 equivalog Y Y N phycocyanobilin:ferredoxin oxidoreductase 1.3.7.5 16380422 2 Bacteria superkingdom 1078 NCBI Protein Cluster (PRK) phycocyanobilin:ferredoxin oxidoreductase phycocyanobilin:ferredoxin oxidoreductase Catalyzes the reduction of biliverdin IX-alpha producing (3Z)-phycocyanobilin and oxidized ferredoxin NF002761.0 PRK02821 PRK02821.1 106 106 77 equivalog Y Y N RNA-binding protein GO:0003723 2 Bacteria superkingdom 3875 NCBI Protein Cluster (PRK) hypothetical protein RNA-binding protein NF002765.0 PRK02833 PRK02833.1-3 145 145 136 equivalog Y Y N phosphate-starvation-inducible protein PsiE psiE 2 Bacteria superkingdom 2431 NCBI Protein Cluster (PRK) phosphate-starvation-inducible protein PsiE phosphate-starvation-inducible protein PsiE NF002768.0 PRK02842 PRK02842.1 324 324 423 equivalog Y Y N ferredoxin:protochlorophyllide reductase (ATP-dependent) subunit N 1.3.7.7 GO:0015995,GO:0016730 2 Bacteria superkingdom 2810 NCBI Protein Cluster (PRK) light-independent protochlorophyllide reductase subunit N ferredoxin:protochlorophyllide reductase (ATP-dependent) subunit N Light-independent reduction of protochlorophyllide to form chlorophyllide a NF002769.0 PRK02853 PRK02853.1 162 162 161 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 6206 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002772.0 PRK02862 PRK02862.1 537 537 429 equivalog Y Y N glucose-1-phosphate adenylyltransferase 2.7.7.27 GO:0005978,GO:0008878 2 Bacteria superkingdom 3797 NCBI Protein Cluster (PRK) glucose-1-phosphate adenylyltransferase glucose-1-phosphate adenylyltransferase Catalyzes the formation of ADP-glucose and diphosphate from ATP and alpha-D-glucose 1-phosphate NF002777.0 PRK02886 PRK02886.1 115 115 90 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 1238 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002781.0 PRK02899 PRK02899.1 224 224 198 equivalog Y Y N genetic competence negative regulator 2 Bacteria superkingdom 1988 NCBI Protein Cluster (PRK) adaptor protein genetic competence negative regulator NF002782.0 PRK02901 PRK02901.1 288 288 328 equivalog Y Y N o-succinylbenzoate synthase 4.2.1.113 2 Bacteria superkingdom 9713 NCBI Protein Cluster (PRK) O-succinylbenzoate synthase o-succinylbenzoate synthase Catalyzes the dehydration of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid to form O-succinylbenzoate NF002789.0 PRK02910 PRK02910.1-3 509 509 535 equivalog Y Y N ferredoxin:protochlorophyllide reductase (ATP-dependent) subunit B 1.3.7.7 2 Bacteria superkingdom 116 NCBI Protein Cluster (PRK) light-independent protochlorophyllide reductase subunit B ferredoxin:protochlorophyllide reductase (ATP-dependent) subunit B NF002791.0 PRK02913 PRK02913.1 152 152 152 equivalog Y Y N DUF986 family protein 2 Bacteria superkingdom 3557 NCBI Protein Cluster (PRK) hypothetical protein DUF986 family protein This family of membrane proteins, named DUF986 by PF06173, includes YobD from Escherichia coli. NF002796.0 PRK02935 PRK02935.1 108 108 118 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 2535 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002797.0 PRK02936 PRK02936.1 496 496 385 equivalog Y Y N acetylornithine transaminase 2.6.1.11 GO:0006525,GO:0008483,GO:0030170 2 Bacteria superkingdom 6620 NCBI Protein Cluster (PRK) acetylornithine aminotransferase acetylornithine transaminase NF002813.0 PRK02958 PRK02958.1 83 83 73 equivalog Y Y N Sec-independent protein translocase subunit TatA tatA GO:0016020,GO:0043953 2 Bacteria superkingdom 5943 NCBI Protein Cluster (PRK) twin arginine translocase protein A Sec-independent protein translocase subunit TatA Part of system that translocates proteins with a conserved twin arginine motif across the inner membrane; capable of translocating folded substrates typically those with bound cofactors NF002814.1 PRK02963 PRK02963.1 333 333 311 equivalog Y Y N glutarate dioxygenase GlaH glaH 1.14.11.64 GO:0050498 30498244,9512707 2 Bacteria superkingdom 3362 NCBI Protein Cluster (PRK) carbon starvation induced protein glutarate dioxygenase GlaH NF002823.0 PRK02991 PRK02991.1 246 246 444 equivalog Y Y N D-serine ammonia-lyase 4.3.1.18 GO:0008721,GO:0030170,GO:0046416 7592420 2 Bacteria superkingdom 19315 NCBI Protein Cluster (PRK) D-serine dehydratase D-serine ammonia-lyase Catalyzes the formation of pyruvate from serine NF002825.0 PRK02999 PRK02999.1 565 565 726 equivalog Y Y N malate synthase G 2.3.3.9 GO:0004474,GO:0006097 2 Bacteria superkingdom 27079 NCBI Protein Cluster (PRK) malate synthase G malate synthase G Catalyzes the formation of malate from glyoxylate and acetyl-CoA NF002828.0 PRK03003 PRK03003.1 631 631 477 equivalog Y Y N ribosome biogenesis GTPase Der der GO:0005525 2 Bacteria superkingdom 13562 NCBI Protein Cluster (PRK) GTP-binding protein Der ribosome biogenesis GTPase Der NF002829.0 PRK03007 PRK03007.1 385 385 425 equivalog Y Y N deoxyguanosinetriphosphate triphosphohydrolase GO:0000287,GO:0006203,GO:0008832,GO:0016793 2 Bacteria superkingdom 16067 NCBI Protein Cluster (PRK) deoxyguanosinetriphosphate triphosphohydrolase-like protein deoxyguanosinetriphosphate triphosphohydrolase NF002834.0 PRK03011 PRK03011.1-5 222 222 357 subfamily Y Y N butyrate kinase 2.7.2.7 2 Bacteria superkingdom 8867 NCBI Protein Cluster (PRK) butyrate kinase butyrate kinase NF002838.0 PRK03065 PRK03065.1 201 201 148 equivalog Y Y N hut operon transcriptional regulator HutP hutP 15242603,15758992 2 Bacteria superkingdom 967 NCBI Protein Cluster (PRK) anti-terminator HutP hut operon transcriptional regulator HutP Regulates expression of hut operon by antitermination mechanism; forms a homohexamer; binds both magnesium and L-histidine and then binds RNA sequences within the terminator region and destabilizes the terminator structure NF002839.0 PRK03072 PRK03072.1 412 412 291 equivalog Y Y N zinc metalloprotease HtpX htpX 3.4.24.- GO:0004222,GO:0006508 2 Bacteria superkingdom 9840 NCBI Protein Cluster (PRK) heat shock protein HtpX zinc metalloprotease HtpX NF002844.0 PRK03092 PRK03092.1 438 438 326 equivalog Y Y N ribose-phosphate diphosphokinase 2.7.6.1 GO:0000287,GO:0004749,GO:0009058 2 Bacteria superkingdom 9986 NCBI Protein Cluster (PRK) ribose-phosphate pyrophosphokinase ribose-phosphate diphosphokinase Catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP NF002845.0 PRK03094 PRK03094.1 102 102 80 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 1275 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF002848.0 PRK03103 PRK03103.1 381 381 410 subfamily Y Y N DNA polymerase IV 2.7.7.7 2 Bacteria superkingdom 4318 NCBI Protein Cluster (PRK) DNA polymerase IV DNA polymerase IV Involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function NF002849.0 PRK03113 PRK03113.1 124 124 139 subfamily Y Y N disulfide oxidoreductase GO:0006457,GO:0015035,GO:0016020 2 Bacteria superkingdom 4431 NCBI Protein Cluster (PRK) putative disulfide oxidoreductase disulfide oxidoreductase NF002850.0 PRK03114 PRK03114.1 199 199 169 equivalog Y Y N DUF84 family protein 2 Bacteria superkingdom 2263 NCBI Protein Cluster (PRK) NTPase DUF84 family protein NF002852.0 PRK03137 PRK03137.1 648 648 514 subfamily Y Y N L-glutamate gamma-semialdehyde dehydrogenase 1.2.1.88 2 Bacteria superkingdom 8216 NCBI Protein Cluster (PRK) 1-pyrroline-5-carboxylate dehydrogenase L-glutamate gamma-semialdehyde dehydrogenase Catalyzes the conversion of 1-proline-5-carboxylate dehydrogenase to L-glutamate NF002853.0 PRK03140 PRK03140.1 307 307 262 equivalog Y Y N phosphatidylserine decarboxylase 4.1.1.65 GO:0004609,GO:0008654 2 Bacteria superkingdom 2224 NCBI Protein Cluster (PRK) phosphatidylserine decarboxylase phosphatidylserine decarboxylase Catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine NF002854.0 PRK03147 PRK03147.1 170 170 176 subfamily Y Y N thiol-disulfide oxidoreductase ResA resA GO:0015036,GO:0016020,GO:0017004 2 Bacteria superkingdom 3177 NCBI Protein Cluster (PRK) thiol-disulfide oxidoreductase thiol-disulfide oxidoreductase ResA Catalyzes the reduction of the disulfide bonds in the heme binding site of apocytochrome c NF002868.0 PRK03180 PRK03180.1 641 641 509 equivalog Y Y N ATP-dependent DNA ligase 6.5.1.1 GO:0003677,GO:0003910,GO:0005524,GO:0006281,GO:0006310,GO:0071897 14985346 2 Bacteria superkingdom 12580 NCBI Protein Cluster (PRK) ATP-dependent DNA ligase ATP-dependent DNA ligase Catalyzes the ATP-dependent formation of a phosphodiester at the site of a single-strand break in duplex DNA NF002869.0 PRK03187 PRK03187.1 307 307 276 equivalog Y Y N protein-glutamine gamma-glutamyltransferase 2.3.2.13 GO:0003810 12501297,15317760 2 Bacteria superkingdom 2178 NCBI Protein Cluster (PRK) transglutaminase protein-glutamine gamma-glutamyltransferase NF002870.0 PRK03188 PRK03188.1 286 286 310 equivalog Y Y N 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase 2.7.1.148 GO:0005524,GO:0016114,GO:0050515 2 Bacteria superkingdom 15693 NCBI Protein Cluster (PRK) 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase Catalyzes the phosphorylation of 4-diphosphocytidyl-2-C-methyl-D-erythritol in the nonmevalonate pathway of isoprenoid biosynthesis NF002876.0 PRK03298 PRK03298.1 252 252 224 equivalog Y Y N endonuclease NucS nucS GO:0004519 2 Bacteria superkingdom 10940 NCBI Protein Cluster (PRK) hypothetical protein endonuclease NucS NF002877.0 PRK03317 PRK03317.1 409 409 374 equivalog Y Y N histidinol-phosphate transaminase 2.6.1.9 GO:0000105,GO:0004400,GO:0030170 2 Bacteria superkingdom 16292 NCBI Protein Cluster (PRK) histidinol-phosphate aminotransferase histidinol-phosphate transaminase Catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis NF002878.0 PRK03321 PRK03321.1 374 374 352 subfamily Y Y N histidinol-phosphate transaminase 2.6.1.9 GO:0016740 2 Bacteria superkingdom 18345 NCBI Protein Cluster (PRK) putative aminotransferase histidinol-phosphate transaminase NF002879.0 PRK03333 PRK03333.1 215 215 395 equivalog Y Y N dephospho-CoA kinase coaE 2.7.1.24 GO:0004140,GO:0005524,GO:0015937 19876400 2 Bacteria superkingdom 15600 NCBI Protein Cluster (PRK) dephospho-CoA kinase/protein folding accessory domain-containing protein dephospho-CoA kinase, long form Long form Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis. This HMM describes a long form of dephospho-CoA kinase with an accessory C-terminal GrpB domain (see PF04229) that assists in protein folding. NF002880.0 PRK03341 PRK03341.1 200 200 170 equivalog Y Y N arginine repressor GO:0003700,GO:0006355,GO:0006525 2 Bacteria superkingdom 7637 NCBI Protein Cluster (PRK) arginine repressor arginine repressor Regulates arginine biosynthesis when complexed with arginine by binding at site that overlap the promotors of the arginine biosynthesis genes NF002881.0 PRK03343 PRK03343.1 367 367 370 subfamily Y Y N transaldolase 2.2.1.2 2 Bacteria superkingdom 23552 NCBI Protein Cluster (PRK) transaldolase transaldolase NF002882.0 PRK03348 PRK03348.1 389 389 461 equivalog Y Y N DNA polymerase IV 2.7.7.7 GO:0003887,GO:0006260 2 Bacteria superkingdom 13629 NCBI Protein Cluster (PRK) DNA polymerase IV DNA polymerase IV Involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function NF002883.0 PRK03352 PRK03352.1 330 330 347 equivalog Y Y N DNA polymerase IV 2.7.7.7 GO:0003684,GO:0003887,GO:0006281 21795801 2 Bacteria superkingdom 4178 NCBI Protein Cluster (PRK) DNA polymerase IV DNA polymerase IV Involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function NF002886.0 PRK03355 PRK03355.1 721 721 787 equivalog Y Y N glycerol-3-phosphate 1-O-acyltransferase 2.3.1.15 GO:0004366,GO:0008654 2 Bacteria superkingdom 2108 NCBI Protein Cluster (PRK) glycerol-3-phosphate acyltransferase glycerol-3-phosphate 1-O-acyltransferase Catalyzes the formation of 1-acyl-sn-glycerol 3-phosphate by transfering the acyl moiety from acyl-CoA NF002892.0 PRK03372 PRK03372.1 299 299 312 equivalog Y Y N NAD kinase 2.7.1.23 GO:0003951,GO:0006741,GO:0019674 11006082,15269221 2 Bacteria superkingdom 11934 NCBI Protein Cluster (PRK) inorganic polyphosphate/ATP-NAD kinase NAD kinase Catalyzes the phosphorylation of NAD to NADP NF002895.0 PRK03381 PRK03381.1 631 631 782 equivalog Y Y N [protein-PII] uridylyltransferase 2.7.7.59 GO:0008152,GO:0008773 12406211 2 Bacteria superkingdom 12503 NCBI Protein Cluster (PRK) PII uridylyl-transferase [protein-PII] uridylyltransferase Uridylylates and de-uridylylates the small trimeric nitrogen regulatory protein PII NF002909.0 PRK03522 PRK03522.2-1 553 553 374 equivalog Y Y N 23S rRNA (uracil(747)-C(5))-methyltransferase RlmC rlmC 2 Bacteria superkingdom 1545 NCBI Protein Cluster (PRK) 23S rRNA methyluridine methyltransferase 23S rRNA (uracil(747)-C(5))-methyltransferase RlmC NF002910.0 PRK03522 PRK03522.2-3 558 558 383 equivalog Y Y N 23S rRNA (uracil(747)-C(5))-methyltransferase RlmC rlmC 2 Bacteria superkingdom 201 NCBI Protein Cluster (PRK) 23S rRNA methyluridine methyltransferase 23S rRNA (uracil(747)-C(5))-methyltransferase RlmC NF002917.0 PRK03537 PRK03537.1-3 264 264 267 equivalog Y Y N molybdate ABC transporter substrate-binding protein 2 Bacteria superkingdom 755 NCBI Protein Cluster (PRK) molybdate ABC transporter periplasmic molybdate-binding protein molybdate ABC transporter substrate-binding protein NF002918.0 PRK03537 PRK03537.1-4 288 288 246 equivalog Y Y N molybdate ABC transporter substrate-binding protein 2 Bacteria superkingdom 632 NCBI Protein Cluster (PRK) molybdate ABC transporter periplasmic molybdate-binding protein molybdate ABC transporter substrate-binding protein NF002921.0 PRK03545 PRK03545.1 401 401 396 equivalog Y Y N sugar transporter GO:0022857,GO:0055085 2 Bacteria superkingdom 11058 NCBI Protein Cluster (PRK) putative arabinose transporter sugar transporter NF002952.0 PRK03606 PRK03606.2-3 260 260 164 equivalog Y Y N ureidoglycolate lyase 4.3.2.3 2 Bacteria superkingdom 1325 NCBI Protein Cluster (PRK) ureidoglycolate hydrolase ureidoglycolate lyase NF002955.0 PRK03609 PRK03609.1 431 431 422 subfamily Y Y N translesion error-prone DNA polymerase V subunit UmuC umuC 2.7.7.7 GO:0003684,GO:0006281 15276832,16199565 2 Bacteria superkingdom 20485 NCBI Protein Cluster (PRK) DNA polymerase V subunit UmuC translesion error-prone DNA polymerase V subunit UmuC NF002956.0 PRK03612 PRK03612.1 472 472 522 equivalog Y Y N polyamine aminopropyltransferase 2.5.1.16 GO:0003824 2 Bacteria superkingdom 15422 NCBI Protein Cluster (PRK) spermidine synthase polyamine aminopropyltransferase NF002958.0 PRK03620 PRK03620.1 278 278 307 subfamily Y Y N 5-dehydro-4-deoxyglucarate dehydratase 4.2.1.41 2 Bacteria superkingdom 19723 NCBI Protein Cluster (PRK) 5-dehydro-4-deoxyglucarate dehydratase 5-dehydro-4-deoxyglucarate dehydratase Catalyzes the formation of 2,5-dioxopentanoate from 5-dehydro-4-deoxy-D-glucarate NF002959.0 PRK03624 PRK03624.1 124 124 147 equivalog Y Y N GNAT family acetyltransferase 2.3.1.- GO:0008080 2 Bacteria superkingdom 7185 NCBI Protein Cluster (PRK) putative acetyltransferase GNAT family acetyltransferase NF002963.0 PRK03634 PRK03634.1 170 170 274 equivalog Y Y N rhamnulose-1-phosphate aldolase rhaD 4.1.2.19 2 Bacteria superkingdom 6944 NCBI Protein Cluster (PRK) rhamnulose-1-phosphate aldolase rhamnulose-1-phosphate aldolase NF002964.0 PRK03635 PRK03635.1 197 197 297 subfamily Y Y N ArgP/LysG family DNA-binding transcriptional regulator GO:0003700,GO:0006355 2 Bacteria superkingdom 26600 NCBI Protein Cluster (PRK) chromosome replication initiation inhibitor protein ArgP/LysG family DNA-binding transcriptional regulator NF002965.0 PRK03636 PRK03636.1 182 182 181 equivalog Y Y N ReoY family proteolytic degradation factor GO:0005515 32469310 2 Bacteria superkingdom 2079 NCBI Protein Cluster (PRK) hypothetical protein ReoY family proteolytic degradation factor ReoY was shown in Listeria monocytogenes to be secondary factor required for proteolytic degradation of ClpCP substrates. NF002966.0 PRK03640 PRK03640.1 556 556 483 equivalog Y Y N o-succinylbenzoate--CoA ligase 6.2.1.26 GO:0005524,GO:0008756,GO:0009234 2 Bacteria superkingdom 5652 NCBI Protein Cluster (PRK) O-succinylbenzoic acid--CoA ligase o-succinylbenzoate--CoA ligase Converts O-succinylbenzoate to O-succinylbenzoyl-CoA NF002968.0 PRK03642 PRK03642.1 385 385 432 equivalog Y Y N penicillin binding protein PBP4B pbp4b 2 Bacteria superkingdom 3898 NCBI Protein Cluster (PRK) putative periplasmic esterase penicillin binding protein PBP4B NF002969.0 PRK03643 PRK03643.1 359 359 482 subfamily Y Y N tagaturonate reductase 1.1.1.58 GO:0016491 2 Bacteria superkingdom 16552 NCBI Protein Cluster (PRK) altronate oxidoreductase tagaturonate reductase NF002971.0 PRK03655 PRK03655.1 312 312 414 equivalog Y Y N ion channel protein GO:0005247 2 Bacteria superkingdom 8175 NCBI Protein Cluster (PRK) putative ion channel protein ion channel protein NF002985.0 PRK03715 PRK03715.1 568 568 395 equivalog Y Y N acetylornithine transaminase 2.6.1.11 2 Bacteria superkingdom 2517 NCBI Protein Cluster (PRK) acetylornithine transaminase protein acetylornithine transaminase Catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine in the arginine biosynthetic pathway NF002990.0 PRK03735 PRK03735.1 325 325 223 subfamily Y Y N cytochrome b6 GO:0009055,GO:0016020,GO:0016491,GO:0022904 7737998 2 Bacteria superkingdom 1987 NCBI Protein Cluster (PRK) cytochrome b6 cytochrome b6 NF002991.1 PRK03739 PRK03739.1 455 455 550 subfamily Y Y N 2-isopropylmalate synthase 2.3.3.13 2 Bacteria superkingdom 43330 NCBI Protein Cluster (PRK) 2-isopropylmalate synthase 2-isopropylmalate synthase NF002992.0 PRK03743 PRK03743.1 470 470 333 equivalog Y Y N 4-hydroxythreonine-4-phosphate dehydrogenase PdxA pdxA 2 Bacteria superkingdom 1475 NCBI Protein Cluster (PRK) 4-hydroxythreonine-4-phosphate dehydrogenase 4-hydroxythreonine-4-phosphate dehydrogenase PdxA Catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate) NF003009.0 PRK03826 PRK03826.1 122 122 197 equivalog Y Y N 5'-deoxynucleotidase yfbR 3.1.3.89 GO:0002953 2 Bacteria superkingdom 6342 NCBI Protein Cluster (PRK) 5'-nucleotidase 5'-deoxynucleotidase NF003015.0 PRK03858 PRK03858.1 367 367 399 subfamily Y N N DNA polymerase IV 2.7.7.7 2 Bacteria superkingdom 10143 NCBI Protein Cluster (PRK) DNA polymerase IV DNA polymerase IV NF003024.0 PRK03893 PRK03893.1 604 604 497 subfamily Y Y N sialate:H+ symport family MFS transporter 2 Bacteria superkingdom 3801 NCBI Protein Cluster (PRK) putative sialic acid transporter sialate:H+ symport family MFS transporter NF003027.0 PRK03906 PRK03906.1 191 191 385 subfamily Y Y N mannonate dehydratase 4.2.1.8 2 Bacteria superkingdom 25470 NCBI Protein Cluster (PRK) mannonate dehydratase mannonate dehydratase Catalyzes the formation of 2-dehydro-3-deoxy-D-gluconate from mannonate NF003031.0 PRK03910 PRK03910.1-4 401 401 335 equivalog Y Y N D-cysteine desulfhydrase 4.4.1.15 GO:0003824 2 Bacteria superkingdom 4196 NCBI Protein Cluster (PRK) D-cysteine desulfhydrase D-cysteine desulfhydrase NF003144.0 PRK04069 PRK04069.1 145 145 161 equivalog Y Y N anti-sigma B factor RsbW rsbW 2.7.11.1 2 Bacteria superkingdom 3101 NCBI Protein Cluster (PRK) serine-protein kinase RsbW anti-sigma B factor RsbW Binds to sigma-B preventing the formation of an RNA polymerase holoenzyme NF003145.0 PRK04073 PRK04073.1 656 656 396 equivalog Y Y N ornithine--oxo-acid transaminase GO:0004587,GO:0030170 2 Bacteria superkingdom 4710 NCBI Protein Cluster (PRK) ornithine--oxo-acid transaminase ornithine--oxo-acid transaminase NF003152.0 PRK04101 PRK04101.1 171 171 139 equivalog Y Y N metallothiol transferase FosB fosB 11244082 2 Bacteria superkingdom 3161 NCBI Protein Cluster (PRK) fosfomycin resistance protein FosB metallothiol transferase FosB Catalyzes resistance to fosfomycin by the addition of a thiol cofactor NF003154.0 PRK04123 PRK04123.1 428 428 554 equivalog Y Y N ribulokinase 2.7.1.16 GO:0005524,GO:0008741,GO:0019569 2 Bacteria superkingdom 19599 NCBI Protein Cluster (PRK) ribulokinase ribulokinase Catalyzes the phosphorylation of ribulose to ribulose 5-phosphate NF003160.0 PRK04135 PRK04135.1 468 468 403 equivalog Y Y N 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 5.4.2.12 2 Bacteria superkingdom 622 NCBI Protein Cluster (PRK) cofactor-independent phosphoglycerate mutase 2,3-bisphosphoglycerate-independent phosphoglycerate mutase Catalyzes the interconversion of 3-phosphoglycerate and 2-phosphoglycerate; this enzyme does not require the cofactor 2,3-bisphosphoglycerate as a phosphate donor NF003164.0 PRK04147 PRK04147.1 281 281 294 equivalog Y Y N N-acetylneuraminate lyase 4.1.3.3 GO:0005975,GO:0008747 14617154 2 Bacteria superkingdom 3832 NCBI Protein Cluster (PRK) N-acetylneuraminate lyase N-acetylneuraminate lyase Catalyzes the formation of pyruvate and N-acetylmannosamine from N-acetylneuraminic acid NF003168.0 PRK04155 PRK04155.1 365 365 287 equivalog Y Y N glyoxalase III HchA hchA 3.5.1.124 GO:0036524 21696459,28235098,35483971 2 Bacteria superkingdom 4794 NCBI Protein Cluster (PRK) chaperone protein HchA glyoxalase III HchA HchA (Hsp31), a DJ-1 family protein, previously was thought to be a deglycase, but now is thought to be a one-step, glutathione-independent glyoxalase (glyoxalase III) that prevents glycation by reducing levels of the toxic metabolic byproduct methylglyoxal. NF003170.0 PRK04158 PRK04158.1 255 255 259 equivalog Y Y N GTP-sensing pleiotropic transcriptional regulator CodY codY GO:0003700,GO:0045892 29357354,29378891 2 Bacteria superkingdom 5498 NCBI Protein Cluster (PRK) transcriptional repressor CodY GTP-sensing pleiotropic transcriptional regulator CodY NF003194.0 PRK04164 PRK04164.1-5 160 160 178 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 3554 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003197.0 PRK04169 PRK04169.1-1 296 296 229 equivalog Y Y N heptaprenylglyceryl phosphate synthase 2.5.1.n9 GO:0016765 2 Bacteria superkingdom 4502 NCBI Protein Cluster (PRK) geranylgeranylglyceryl phosphate synthase-like protein heptaprenylglyceryl phosphate synthase NF003281.1 PRK04280 PRK04280.1 182 182 148 equivalog Y Y N transcriptional regulator AhrC/ArgR ahrC argR GO:0003700,GO:0006355,GO:0034618 11856827,35938859,38299858,9851988 2 Bacteria superkingdom 2364 NCBI Protein Cluster (PRK) arginine repressor transcriptional regulator AhrC/ArgR Regulates arginine biosynthesis when complexed with arginine by binding at site that overlap the promotors of the arginine biosynthesis genes NF003286.0 PRK04284 PRK04284.1 515 515 332 subfamily Y Y N ornithine carbamoyltransferase 2.1.3.3 2 Bacteria superkingdom 10336 NCBI Protein Cluster (PRK) ornithine carbamoyltransferase ornithine carbamoyltransferase Catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation NF003297.0 PRK04296 PRK04296.1-2 252 252 216 equivalog Y Y N thymidine kinase 2.7.1.21 GO:0004797,GO:0005524 2 Bacteria superkingdom 6973 NCBI Protein Cluster (PRK) thymidine kinase thymidine kinase NF003300.0 PRK04296 PRK04296.1-5 195 195 194 equivalog Y Y N thymidine kinase 2.7.1.21 GO:0004797,GO:0005524 2 Bacteria superkingdom 17139 NCBI Protein Cluster (PRK) thymidine kinase thymidine kinase NF003315.0 PRK04323 PRK04323.1 87 87 91 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 3298 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003322.0 PRK04334 PRK04334.1-2 290 290 295 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 2699 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003323.0 PRK04334 PRK04334.1-3 271 271 250 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 409 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003339.0 PRK04351 PRK04351.1 113 113 149 equivalog Y Y N SprT family protein 2 Bacteria superkingdom 8597 NCBI Protein Cluster (PRK) hypothetical protein SprT family protein NF003348.0 PRK04375 PRK04375.1-1 285 285 292 equivalog Y Y N heme o synthase cyoE 2.5.1.141 GO:0008495,GO:0016020,GO:0048034 2 Bacteria superkingdom 7608 NCBI Protein Cluster (PRK) protoheme IX farnesyltransferase heme o synthase NF003353.0 PRK04387 PRK04387.1 90 90 92 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 4499 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003354.0 PRK04388 PRK04388.1 168 168 172 equivalog Y Y N disulfide bond formation protein B 2 Bacteria superkingdom 860 NCBI Protein Cluster (PRK) disulfide bond formation protein B disulfide bond formation protein B Disulfide oxidoreductase; integral membrane protein; required for perioplasmic disulfide bond formation; oxidizes DsbA protein NF003359.0 PRK04424 PRK04424.1 183 183 190 equivalog Y Y N transcription factor FapR fapR GO:0003700,GO:0045717,GO:0045892 2 Bacteria superkingdom 3764 NCBI Protein Cluster (PRK) fatty acid biosynthesis transcriptional regulator transcription factor FapR Negative regulator of genes involved in fatty acid and phospholipid biosynthesis NF003361.0 PRK04435 PRK04435.1 131 131 148 equivalog Y Y N ACT domain-containing protein 2 Bacteria superkingdom 4351 NCBI Protein Cluster (PRK) hypothetical protein ACT domain-containing protein NF003377.0 PRK04452 PRK04452.1-3 527 527 432 subfamily Y Y N acetyl-CoA decarbonylase/synthase complex subunit delta 2 Bacteria superkingdom 93 NCBI Protein Cluster (PRK) acetyl-CoA decarbonylase/synthase complex subunit delta acetyl-CoA decarbonylase/synthase complex subunit delta NF003385.0 PRK04527 PRK04527.1 603 603 401 equivalog Y Y N argininosuccinate synthase 6.3.4.5 2 Bacteria superkingdom 1182 NCBI Protein Cluster (PRK) argininosuccinate synthase argininosuccinate synthase Catalyzes the formation of arginosuccinate from citrulline and aspartate in arginine biosynthesis NF003386.0 PRK04531 PRK04531.1-1 417 417 442 equivalog Y Y N acetylglutamate kinase 2.7.2.8 2 Bacteria superkingdom 1299 NCBI Protein Cluster (PRK) acetylglutamate kinase acetylglutamate kinase NF003387.0 PRK04531 PRK04531.1-2 426 426 441 equivalog Y Y N acetylglutamate kinase 2.7.2.8 2 Bacteria superkingdom 1302 NCBI Protein Cluster (PRK) acetylglutamate kinase acetylglutamate kinase NF003406.0 PRK04761 PRK04761.1 211 211 257 equivalog Y Y N NAD kinase 2.7.1.23 GO:0003951,GO:0006741,GO:0019674 2 Bacteria superkingdom 8265 NCBI Protein Cluster (PRK) inorganic polyphosphate/ATP-NAD kinase NAD kinase Catalyzes the phosphorylation of NAD to NADP NF003424.0 PRK04885 PRK04885.1 220 220 265 equivalog Y Y N NAD kinase 2.7.1.23 GO:0003951,GO:0006741 28828348 2 Bacteria superkingdom 5879 NCBI Protein Cluster (PRK) inorganic polyphosphate/ATP-NAD kinase NAD kinase Catalyzes the phosphorylation of NAD to NADP NF003462.0 PRK05084 PRK05084.1 267 267 360 equivalog Y Y N tyrosine recombinase XerS xerS GO:0003677,GO:0006310,GO:0015074 10361305,11114887,11763967,12050668,17630835 2 Bacteria superkingdom 6009 NCBI Protein Cluster (PRK) site-specific tyrosine recombinase XerS tyrosine recombinase XerS Site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation; cell division protein FtsK may regulate the XerS; NF003464.0 PRK05087 PRK05087.1 68 68 78 equivalog Y Y N D-alanine--poly(phosphoribitol) ligase subunit DltC dltC 6.1.1.13 GO:0019350,GO:0036370 8682792 2 Bacteria superkingdom 2215 NCBI Protein Cluster (PRK) D-alanine--poly(phosphoribitol) ligase subunit 2 D-alanine--poly(phosphoribitol) ligase subunit DltC D-alanyl carrier protein subunit; involved in the incorporation of D-alanine into membrane-associated D-alanyl-lipoteichoic acid; D-alanyl carrier protein is the acceptor of activated D-alanine which it donates to a membrane acceptor(D-alanyl transferase) for incorporation into membrane lipoteichoic acid NF003465.0 PRK05089 PRK05089.1 162 162 189 equivalog Y Y N cytochrome c oxidase assembly protein 2 Bacteria superkingdom 16215 NCBI Protein Cluster (PRK) cytochrome C oxidase assembly protein cytochrome c oxidase assembly protein Involved in the insertion of copper into subunit I of cytochrome C oxidase NF003467.0 PRK05092 PRK05092.1 959 959 940 equivalog Y Y N [protein-PII] uridylyltransferase 2.7.7.59 GO:0008152,GO:0008773 11274131,12384297 2 Bacteria superkingdom 8241 NCBI Protein Cluster (PRK) PII uridylyl-transferase [protein-PII] uridylyltransferase Uridylylates and de-uridylylates the small trimeric nitrogen regulatory protein PII NF003481.0 PRK05151 PRK05151.1 240 240 193 equivalog Y Y N electron transport complex subunit RsxA rsxA GO:0016020,GO:0022900 2 Bacteria superkingdom 7007 NCBI Protein Cluster (PRK) electron transport complex protein RsxA electron transport complex subunit RsxA NF003501.0 PRK05170 PRK05170.1-5 167 167 160 equivalog Y Y N YcgN family cysteine cluster protein 2 Bacteria superkingdom 14829 NCBI Protein Cluster (PRK) hypothetical protein YcgN family cysteine cluster protein NF003507.0 PRK05170 PRK05170.2-5 170 170 146 equivalog Y Y N YcgN family cysteine cluster protein 2 Bacteria superkingdom 14443 NCBI Protein Cluster (PRK) hypothetical protein YcgN family cysteine cluster protein NF003513.0 PRK05182 PRK05182.1-2 302 302 338 equivalog Y Y N DNA-directed RNA polymerase subunit alpha 2.7.7.6 GO:0003899,GO:0006351 2 Bacteria superkingdom 31214 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit alpha DNA-directed RNA polymerase subunit alpha NF003514.0 PRK05182 PRK05182.1-4 434 434 338 equivalog Y Y N DNA-directed RNA polymerase subunit alpha 2.7.7.6 GO:0003677,GO:0003899,GO:0006351,GO:0046983 2 Bacteria superkingdom 6079 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit alpha DNA-directed RNA polymerase subunit alpha NF003515.0 PRK05182 PRK05182.2-1 406 406 314 equivalog Y Y N DNA-directed RNA polymerase subunit alpha 2.7.7.6 GO:0003677,GO:0003899,GO:0006351,GO:0046983 2 Bacteria superkingdom 6307 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit alpha DNA-directed RNA polymerase subunit alpha NF003516.0 PRK05182 PRK05182.2-2 353 353 315 equivalog Y Y N DNA-directed RNA polymerase subunit alpha 2.7.7.6 GO:0003677,GO:0003899,GO:0006351,GO:0046983 2 Bacteria superkingdom 7358 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit alpha DNA-directed RNA polymerase subunit alpha NF003519.0 PRK05182 PRK05182.2-5 277 277 320 equivalog Y Y N DNA-directed RNA polymerase subunit alpha 2.7.7.6 GO:0003677,GO:0003899,GO:0006351,GO:0046983 2 Bacteria superkingdom 32986 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit alpha DNA-directed RNA polymerase subunit alpha NF003520.0 PRK05183 PRK05183.1 620 620 621 subfamily Y Y N Fe-S protein assembly chaperone HscA hscA 2 Bacteria superkingdom 51117 NCBI Protein Cluster (PRK) chaperone protein HscA Fe-S protein assembly chaperone HscA Involved in the maturation of iron-sulfur cluster-containing proteins NF003544.0 PRK05201 PRK05201.1 394 394 445 equivalog Y Y N ATP-dependent protease ATPase subunit HslU hslU 3.4.25.2 GO:0005524,GO:0008233,GO:0009376,GO:0016887 2 Bacteria superkingdom 33019 NCBI Protein Cluster (PRK) ATP-dependent protease ATP-binding subunit HslU ATP-dependent protease ATPase subunit HslU Heat shock protein involved in degradation of misfolded proteins NF003545.0 PRK05205 PRK05205.1-1 140 140 171 equivalog Y Y N bifunctional pyr operon transcriptional regulator/uracil phosphoribosyltransferase PyrR pyrR 2.4.2.9 GO:0009116 2 Bacteria superkingdom 10214 NCBI Protein Cluster (PRK) bifunctional pyrimidine regulatory protein PyrR uracil phosphoribosyltransferase bifunctional pyr operon transcriptional regulator/uracil phosphoribosyltransferase PyrR NF003547.0 PRK05205 PRK05205.1-3 230 230 194 equivalog Y Y N bifunctional pyr operon transcriptional regulator/uracil phosphoribosyltransferase PyrR pyrR 2.4.2.9 GO:0009116 2 Bacteria superkingdom 14156 NCBI Protein Cluster (PRK) bifunctional pyrimidine regulatory protein PyrR uracil phosphoribosyltransferase bifunctional pyr operon transcriptional regulator/uracil phosphoribosyltransferase PyrR NF003548.0 PRK05205 PRK05205.1-4 218 218 173 equivalog Y Y N bifunctional pyr operon transcriptional regulator/uracil phosphoribosyltransferase PyrR pyrR 2.4.2.9 2 Bacteria superkingdom 8186 NCBI Protein Cluster (PRK) bifunctional pyrimidine regulatory protein PyrR uracil phosphoribosyltransferase bifunctional pyr operon transcriptional regulator/uracil phosphoribosyltransferase PyrR NF003558.0 PRK05231 PRK05231.1 271 271 322 equivalog Y Y N homoserine kinase 2.7.1.39 GO:0004413,GO:0009088 2 Bacteria superkingdom 16370 NCBI Protein Cluster (PRK) homoserine kinase homoserine kinase Catalyzes the formation of O-phospho-L-homoserine from L-homoserine NF003573.0 PRK05246 PRK05246.1 272 272 316 equivalog Y Y N glutathione synthase gshB 6.3.2.3 GO:0004363,GO:0005524,GO:0006750,GO:0046872 2 Bacteria superkingdom 27342 NCBI Protein Cluster (PRK) glutathione synthetase glutathione synthase Catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione NF003585.0 PRK05249 PRK05249.1 465 465 464 equivalog Y Y N Si-specific NAD(P)(+) transhydrogenase sthA 1.6.1.1 GO:0003957,GO:0045454,GO:0050660 2 Bacteria superkingdom 12860 NCBI Protein Cluster (PRK) soluble pyridine nucleotide transhydrogenase Si-specific NAD(P)(+) transhydrogenase NF003603.0 PRK05257 PRK05257.1-1 563 563 548 subfamily Y Y N malate:quinone oxidoreductase 1.1.5.4 2 Bacteria superkingdom 26542 NCBI Protein Cluster (PRK) malate:quinone oxidoreductase malate:quinone oxidoreductase NF003604.0 PRK05257 PRK05257.1-3 737 737 500 subfamily Y Y N malate:quinone oxidoreductase 1.1.5.4 2 Bacteria superkingdom 6348 NCBI Protein Cluster (PRK) malate:quinone oxidoreductase malate:quinone oxidoreductase NF003605.0 PRK05257 PRK05257.1-4 666 666 545 subfamily Y Y N malate:quinone oxidoreductase 1.1.5.4 2 Bacteria superkingdom 26765 NCBI Protein Cluster (PRK) malate:quinone oxidoreductase malate:quinone oxidoreductase NF003606.0 PRK05257 PRK05257.2-1 425 425 497 subfamily Y Y N malate:quinone oxidoreductase 1.1.5.4 2 Bacteria superkingdom 31544 NCBI Protein Cluster (PRK) malate:quinone oxidoreductase malate:quinone oxidoreductase NF003608.0 PRK05257 PRK05257.2-4 733 733 498 subfamily Y Y N malate:quinone oxidoreductase 1.1.5.4 2 Bacteria superkingdom 9685 NCBI Protein Cluster (PRK) malate:quinone oxidoreductase malate:quinone oxidoreductase NF003609.0 PRK05257 PRK05257.2-5 586 586 488 equivalog Y Y N malate:quinone oxidoreductase 1.1.5.4 2 Bacteria superkingdom 5383 NCBI Protein Cluster (PRK) malate:quinone oxidoreductase malate:quinone oxidoreductase NF003610.0 PRK05257 PRK05257.3-1 745 745 495 equivalog Y Y N malate:quinone oxidoreductase 1.1.5.4 GO:0006099,GO:0008924 2 Bacteria superkingdom 8650 NCBI Protein Cluster (PRK) malate:quinone oxidoreductase malate:quinone oxidoreductase NF003611.0 PRK05257 PRK05257.3-2 499 499 497 subfamily Y Y N malate:quinone oxidoreductase 1.1.5.4 2 Bacteria superkingdom 31488 NCBI Protein Cluster (PRK) malate:quinone oxidoreductase malate:quinone oxidoreductase NF003612.0 PRK05257 PRK05257.3-3 742 742 498 equivalog Y Y N malate:quinone oxidoreductase 1.1.5.4 2 Bacteria superkingdom 2795 NCBI Protein Cluster (PRK) malate:quinone oxidoreductase malate:quinone oxidoreductase NF003613.0 PRK05257 PRK05257.3-4 728 728 494 subfamily Y Y N malate:quinone oxidoreductase 1.1.5.4 2 Bacteria superkingdom 4428 NCBI Protein Cluster (PRK) malate:quinone oxidoreductase malate:quinone oxidoreductase NF003616.0 PRK05261 PRK05261.1-1 777 777 788 subfamily Y Y N phosphoketolase 2 Bacteria superkingdom 7842 NCBI Protein Cluster (PRK) putative phosphoketolase phosphoketolase NF003617.0 PRK05261 PRK05261.1-2 1143 1143 797 subfamily Y Y N phosphoketolase 2 Bacteria superkingdom 19690 NCBI Protein Cluster (PRK) putative phosphoketolase phosphoketolase NF003618.0 PRK05261 PRK05261.1-3 1199 1199 789 subfamily Y Y N phosphoketolase 2 Bacteria superkingdom 4204 NCBI Protein Cluster (PRK) putative phosphoketolase phosphoketolase NF003619.0 PRK05261 PRK05261.1-4 962 962 799 subfamily Y Y N phosphoketolase 2 Bacteria superkingdom 26468 NCBI Protein Cluster (PRK) putative phosphoketolase phosphoketolase NF003621.0 PRK05261 PRK05261.1-6 1295 1295 801 subfamily Y Y N phosphoketolase 2 Bacteria superkingdom 17129 NCBI Protein Cluster (PRK) putative phosphoketolase phosphoketolase NF003623.0 PRK05265 PRK05265.1-1 347 347 243 equivalog Y Y N pyridoxine 5'-phosphate synthase pdxJ 2.6.99.2 GO:0008615,GO:0033856 2 Bacteria superkingdom 13201 NCBI Protein Cluster (PRK) pyridoxine 5'-phosphate synthase pyridoxine 5'-phosphate synthase NF003624.0 PRK05265 PRK05265.1-2 331 331 252 equivalog Y Y N pyridoxine 5'-phosphate synthase 2.6.99.2 GO:0008615,GO:0033856 2 Bacteria superkingdom 12722 NCBI Protein Cluster (PRK) pyridoxine 5'-phosphate synthase pyridoxine 5'-phosphate synthase NF003625.0 PRK05265 PRK05265.1-3 190 190 242 equivalog Y Y N pyridoxine 5'-phosphate synthase 2.6.99.2 GO:0008615,GO:0033856 2 Bacteria superkingdom 28625 NCBI Protein Cluster (PRK) pyridoxine 5'-phosphate synthase pyridoxine 5'-phosphate synthase NF003626.0 PRK05265 PRK05265.1-4 222 222 246 equivalog Y Y N pyridoxine 5'-phosphate synthase 2.6.99.2 GO:0008615,GO:0033856 2 Bacteria superkingdom 12476 NCBI Protein Cluster (PRK) pyridoxine 5'-phosphate synthase pyridoxine 5'-phosphate synthase NF003627.0 PRK05265 PRK05265.1-5 207 207 240 equivalog Y Y N pyridoxine 5'-phosphate synthase 2.6.99.2 2 Bacteria superkingdom 23970 NCBI Protein Cluster (PRK) pyridoxine 5'-phosphate synthase pyridoxine 5'-phosphate synthase NF003629.0 PRK05270 PRK05270.1-2 628 628 508 subfamily Y Y N UDP-glucose--hexose-1-phosphate uridylyltransferase 2.7.7.12 2 Bacteria superkingdom 13898 NCBI Protein Cluster (PRK) galactose-1-phosphate uridylyltransferase UDP-glucose--hexose-1-phosphate uridylyltransferase NF003642.0 PRK05282 PRK05282.1 156 156 233 equivalog Y Y N dipeptidase PepE pepE 3.4.13.21 GO:0006508,GO:0008236 10762256 2 Bacteria superkingdom 9949 NCBI Protein Cluster (PRK) (alpha)-aspartyl dipeptidase dipeptidase PepE Peptidase E; catalyzes the hydrolysis of dipeptides with an N-terminal aspartate residue; belongs to peptidase S51 family NF003650.0 PRK05286 PRK05286.2-3 477 477 393 equivalog Y Y N quinone-dependent dihydroorotate dehydrogenase 1.3.5.2 2 Bacteria superkingdom 410 NCBI Protein Cluster (PRK) dihydroorotate dehydrogenase 2 quinone-dependent dihydroorotate dehydrogenase NF003651.0 PRK05286 PRK05286.2-4 448 448 377 equivalog Y Y N quinone-dependent dihydroorotate dehydrogenase 1.3.5.2 2 Bacteria superkingdom 1388 NCBI Protein Cluster (PRK) dihydroorotate dehydrogenase 2 quinone-dependent dihydroorotate dehydrogenase NF003657.0 PRK05289 PRK05289.1 226 226 264 equivalog Y Y N acyl-ACP--UDP-N-acetylglucosamine O-acyltransferase lpxA 2.3.1.129 GO:0008610,GO:0008780 9197543 2 Bacteria superkingdom 31656 NCBI Protein Cluster (PRK) UDP-N-acetylglucosamine acyltransferase acyl-ACP--UDP-N-acetylglucosamine O-acyltransferase Catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis NF003661.0 PRK05291 PRK05291.1-3 380 380 448 equivalog Y Y N tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE mnmE 3.6.-.- GO:0003924,GO:0005515,GO:0005525,GO:0006400 2 Bacteria superkingdom 50487 NCBI Protein Cluster (PRK) tRNA modification GTPase TrmE tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE NF003670.0 PRK05293 PRK05293.1 470 470 382 equivalog Y Y N glucose-1-phosphate adenylyltransferase 2.7.7.27 GO:0005978,GO:0008878 2 Bacteria superkingdom 9978 NCBI Protein Cluster (PRK) glucose-1-phosphate adenylyltransferase glucose-1-phosphate adenylyltransferase Catalyzes the formation of ADP-glucose and diphosphate from ATP and alpha-D-glucose 1-phosphate NF003672.0 PRK05297 PRK05297.1 783 783 1290 equivalog Y Y N phosphoribosylformylglycinamidine synthase purL purI 6.3.5.3 GO:0004642 2 Bacteria superkingdom 40741 NCBI Protein Cluster (PRK) phosphoribosylformylglycinamidine synthase phosphoribosylformylglycinamidine synthase NF003676.1 PRK05303 PRK05303.1 300 300 344 subfamily Y Y N flagellar basal body P-ring protein FlgI flgI 2 Bacteria superkingdom 25542 NCBI Protein Cluster (PRK) flagellar basal body P-ring protein flagellar basal body P-ring protein FlgI Part of the basal body which consists of four rings L, P, S, and M mounted on a central rod NF003677.0 PRK05305 PRK05305.1-1 315 315 232 equivalog Y Y N phosphatidylserine decarboxylase 4.1.1.65 2 Bacteria superkingdom 4050 NCBI Protein Cluster (PRK) phosphatidylserine decarboxylase phosphatidylserine decarboxylase NF003678.0 PRK05305 PRK05305.1-2 225 225 218 equivalog Y Y N phosphatidylserine decarboxylase family protein 4.1.1.65 GO:0004609,GO:0008654 2 Bacteria superkingdom 13881 NCBI Protein Cluster (PRK) phosphatidylserine decarboxylase phosphatidylserine decarboxylase family protein NF003679.0 PRK05305 PRK05305.1-3 252 252 234 equivalog Y Y N phosphatidylserine decarboxylase 4.1.1.65 GO:0004609,GO:0008654 2 Bacteria superkingdom 8006 NCBI Protein Cluster (PRK) phosphatidylserine decarboxylase phosphatidylserine decarboxylase NF003699.0 PRK05312 PRK05312.1 378 378 340 equivalog Y Y N 4-hydroxythreonine-4-phosphate dehydrogenase PdxA pdxA 1.1.1.262 GO:0042823,GO:0050570,GO:0051287 2 Bacteria superkingdom 8849 NCBI Protein Cluster (PRK) 4-hydroxythreonine-4-phosphate dehydrogenase 4-hydroxythreonine-4-phosphate dehydrogenase PdxA Catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate) NF003701.1 PRK05318 PRK05318.1 383 383 426 subfamily Y Y N anti-phage deoxyguanosine triphosphatase 35817891 2 Bacteria superkingdom 5109 NCBI Protein Cluster (PRK) deoxyguanosinetriphosphate triphosphohydrolase-like protein anti-phage deoxyguanosine triphosphatase NF003703.0 PRK05320 PRK05320.1 331 331 280 equivalog Y Y N sulfurtransferase 2 Bacteria superkingdom 4541 NCBI Protein Cluster (PRK) rhodanese superfamily protein sulfurtransferase NF003711.0 PRK05325 PRK05325.2-3 388 388 369 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 389 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003717.0 PRK05327 PRK05327.1 116 116 202 equivalog Y Y N 30S ribosomal protein S4 rpsD GO:0003735,GO:0006412,GO:0015935,GO:0019843 11401563,11447122,1400226,1699930,1906866,4587210,7559430,9707415 2 Bacteria superkingdom 36181 NCBI Protein Cluster (PRK) 30S ribosomal protein S4 30S ribosomal protein S4 Primary rRNA binding protein; nucleates 30S assembly; involved in translational accuracy with proteins S5 and S12; interacts with protein S5; involved in autogeneously regulating ribosomal proteins by binding to pseudoknot structures in the polycistronic mRNA; interacts with transcription complex and functions similar to protein NusA in antitermination NF003727.1 PRK05330 PRK05330.1 297 297 294 equivalog Y Y N oxygen-dependent coproporphyrinogen oxidase hemF 1.3.3.3 GO:0004109,GO:0006779 2 Bacteria superkingdom 33629 NCBI Protein Cluster (PRK) coproporphyrinogen III oxidase oxygen-dependent coproporphyrinogen oxidase Catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis NF003738.0 PRK05333 PRK05333.1 305 305 295 equivalog Y Y N NAD-dependent protein deacetylase GO:0070403 2 Bacteria superkingdom 15916 NCBI Protein Cluster (PRK) NAD-dependent deacetylase NAD-dependent protein deacetylase NF003739.0 PRK05335 PRK05335.1 262 262 441 equivalog Y Y N methylenetetrahydrofolate--tRNA-(uracil(54)-C(5))-methyltransferase (FADH(2)-oxidizing) TrmFO trmFO GO:0008033,GO:0050660 2 Bacteria superkingdom 22305 NCBI Protein Cluster (PRK) tRNA (uracil-5-)-methyltransferase Gid methylenetetrahydrofolate--tRNA-(uracil(54)-C(5))-methyltransferase (FADH(2)-oxidizing) TrmFO NF003742.0 PRK05339 PRK05339.1 225 225 270 subfamily Y Y N pyruvate, phosphate dikinase/phosphoenolpyruvate synthase regulator ppsR 2 Bacteria superkingdom 25766 NCBI Protein Cluster (PRK) PEP synthetase regulatory protein pyruvate, phosphate dikinase/phosphoenolpyruvate synthase regulator NF003745.1 PRK05342 PRK05342.1 359 359 418 equivalog Y Y N ATP-dependent Clp protease ATP-binding subunit ClpX clpX GO:0005524,GO:0008270,GO:0016887,GO:0046983 2 Bacteria superkingdom 49970 NCBI Protein Cluster (PRK) ATP-dependent protease ATP-binding subunit ClpX ATP-dependent Clp protease ATP-binding subunit ClpX Binds and unfolds substrates as part of the ClpXP protease NF003756.0 PRK05349 PRK05349.1 414 414 406 equivalog Y Y N NADH:ubiquinone reductase (Na(+)-transporting) subunit B GO:0010181,GO:0016020,GO:0016655,GO:0022904,GO:0055085 2 Bacteria superkingdom 11180 NCBI Protein Cluster (PRK) Na(+)-translocating NADH-quinone reductase subunit B NADH:ubiquinone reductase (Na(+)-transporting) subunit B NF003757.0 PRK05350 PRK05350.1 65 65 83 equivalog Y Y N acyl carrier protein GO:0006633 2 Bacteria superkingdom 4184 NCBI Protein Cluster (PRK) acyl carrier protein acyl carrier protein NF003759.0 PRK05352 PRK05352.1-2 505 505 447 equivalog Y Y N Na(+)-translocating NADH-quinone reductase subunit A GO:0006814,GO:0016655 2 Bacteria superkingdom 9176 NCBI Protein Cluster (PRK) Na(+)-translocating NADH-quinone reductase subunit A Na(+)-translocating NADH-quinone reductase subunit A NF003764.0 PRK05355 PRK05355.1 253 253 357 equivalog Y Y N 3-phosphoserine/phosphohydroxythreonine transaminase serC 2.6.1.52 GO:0003824,GO:0004648,GO:0006564 2 Bacteria superkingdom 38290 NCBI Protein Cluster (PRK) 3-phosphoserine/phosphohydroxythreonine aminotransferase 3-phosphoserine/phosphohydroxythreonine transaminase NF003765.0 PRK05359 PRK05359.1 106 106 189 equivalog Y Y N oligoribonuclease orn 3.1.-.- GO:0000175,GO:0003676 2 Bacteria superkingdom 26217 NCBI Protein Cluster (PRK) oligoribonuclease oligoribonuclease NF003766.0 PRK05362 PRK05362.1 256 256 396 equivalog Y Y N phosphopentomutase 5.4.2.7 GO:0000287,GO:0008973,GO:0009117,GO:0043094 2 Bacteria superkingdom 29131 NCBI Protein Cluster (PRK) phosphopentomutase phosphopentomutase Catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose NF003767.0 PRK05363 PRK05363.1 207 207 320 equivalog Y Y N protein-methionine-sulfoxide reductase catalytic subunit MsrP msrP 1.8.5.- GO:0016667,GO:0030091,GO:0043546 15355966,16042411 2 Bacteria superkingdom 21421 NCBI Protein Cluster (PRK) TMAO/DMSO reductase protein-methionine-sulfoxide reductase catalytic subunit MsrP Encodes the periplasmic catalytic subunit of an oxidoreductase; requires inner membrane anchor protein YedZ NF003776.0 PRK05368 PRK05368.1-3 358 358 353 equivalog Y Y N homoserine O-succinyltransferase 2.3.1.46 2 Bacteria superkingdom 960 NCBI Protein Cluster (PRK) homoserine O-succinyltransferase homoserine O-succinyltransferase NF003779.0 PRK05370 PRK05370.1 657 657 448 equivalog Y Y N argininosuccinate synthase argG 6.3.4.5 GO:0004055,GO:0005524,GO:0006526,GO:0042803 10666579,11738042 2 Bacteria superkingdom 12502 NCBI Protein Cluster (PRK) argininosuccinate synthase argininosuccinate synthase Catalyzes the formation of arginosuccinate from citrulline and aspartate in arginine biosynthesis NF003784.0 PRK05377 PRK05377.1 392 392 297 equivalog Y Y N fructose bisphosphate aldolase GO:0004332,GO:0006096 2 Bacteria superkingdom 7794 NCBI Protein Cluster (PRK) fructose-1,6-bisphosphate aldolase fructose bisphosphate aldolase Catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate in glycolysis NF003786.0 PRK05379 PRK05379.1-2 397 397 354 equivalog Y Y N bifunctional nicotinamide-nucleotide adenylyltransferase/Nudix hydroxylase 2.7.7.1,3.6.1.- 2 Bacteria superkingdom 1814 NCBI Protein Cluster (PRK) bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase bifunctional nicotinamide-nucleotide adenylyltransferase/Nudix hydroxylase NF003788.0 PRK05379 PRK05379.1-5 354 354 351 equivalog Y Y N bifunctional nicotinamide-nucleotide adenylyltransferase/Nudix hydroxylase 2.7.7.1,3.6.1.- 2 Bacteria superkingdom 1684 NCBI Protein Cluster (PRK) bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase bifunctional nicotinamide-nucleotide adenylyltransferase/Nudix hydroxylase NF003791.0 PRK05379 PRK05379.2-3 409 409 340 equivalog Y Y N bifunctional nicotinamide-nucleotide adenylyltransferase/Nudix hydroxylase 2.7.7.1,3.6.1.- 2 Bacteria superkingdom 59 NCBI Protein Cluster (PRK) bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase bifunctional nicotinamide-nucleotide adenylyltransferase/Nudix hydroxylase NF003804.0 PRK05395 PRK05395.1-1 195 195 151 subfamily Y Y N type II 3-dehydroquinate dehydratase 4.2.1.10 2 Bacteria superkingdom 14319 NCBI Protein Cluster (PRK) 3-dehydroquinate dehydratase type II 3-dehydroquinate dehydratase NF003809.0 PRK05398 PRK05398.1 442 442 416 subfamily Y Y N formyl-CoA transferase 2.8.3.16 2 Bacteria superkingdom 7916 NCBI Protein Cluster (PRK) formyl-coenzyme A transferase formyl-CoA transferase Catalyzes the formation of oxalyl-CoA from oxalate and formyl-CoA NF003818.1 PRK05409 PRK05409.1 157 157 265 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 34268 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF003819.0 PRK05412 PRK05412.1 146 146 164 equivalog Y Y N YajQ family cyclic di-GMP-binding protein 2 Bacteria superkingdom 23233 NCBI Protein Cluster (PRK) putative nucleotide-binding protein YajQ family cyclic di-GMP-binding protein NF003828.1 PRK05416 PRK05416.1 244 244 278 equivalog Y Y N RNase adapter RapZ rapZ GO:0005524 2 Bacteria superkingdom 39709 NCBI Protein Cluster (PRK) glmZ(sRNA)-inactivating NTPase RNase adapter RapZ Inactivates the glmS upregulator glmZ NF003829.0 PRK05417 PRK05417.1 249 249 191 subfamily Y N N glutathione-dependent formaldehyde-activating enzyme 2 Bacteria superkingdom 2940 NCBI Protein Cluster (PRK) glutathione-dependent formaldehyde-activating enzyme glutathione-dependent formaldehyde-activating enzyme NF003840.0 PRK05421 PRK05421.1-2 163 163 282 equivalog Y Y N endonuclease/exonuclease/phosphatase family protein 2 Bacteria superkingdom 5132 NCBI Protein Cluster (PRK) hypothetical protein endonuclease/exonuclease/phosphatase family protein NF003842.0 PRK05421 PRK05421.1-4 144 144 259 equivalog Y Y N endonuclease/exonuclease/phosphatase family protein 2 Bacteria superkingdom 5410 NCBI Protein Cluster (PRK) hypothetical protein endonuclease/exonuclease/phosphatase family protein NF003843.0 PRK05422 PRK05422.1 130 130 156 equivalog Y Y N SsrA-binding protein SmpB smpB GO:0003723 15699355,15860775,15958166,15972795,15978085 2 Bacteria superkingdom 41755 NCBI Protein Cluster (PRK) SsrA-binding protein SsrA-binding protein SmpB Binds to ssrA RNA (tmRNA) and is required for its successful binding to ribosomes; also appears to function in the trans-translation step by promoting accommodation of tmRNA into the ribosomal A site; both the tmRNA and SmpB are regulated in cell cycle-dependent manner; functions in release of stalled ribosomes from damaged mRNAs and targeting proteins for degradation NF003844.0 PRK05423 PRK05423.1 122 122 110 equivalog Y Y N DUF496 family protein 2 Bacteria superkingdom 1540 NCBI Protein Cluster (PRK) hypothetical protein DUF496 family protein NF003916.0 PRK05442 PRK05442.1 271 271 328 equivalog Y Y N malate dehydrogenase 1.1.1.37 GO:0006108,GO:0016615 2 Bacteria superkingdom 17258 NCBI Protein Cluster (PRK) malate dehydrogenase malate dehydrogenase Catalyzes the oxidation of malate to oxaloacetate NF003919.0 PRK05443 PRK05443.1-4 908 908 730 equivalog Y Y N RNA degradosome polyphosphate kinase 2.7.4.1 GO:0006799,GO:0008976,GO:0009358 2 Bacteria superkingdom 7751 NCBI Protein Cluster (PRK) polyphosphate kinase RNA degradosome polyphosphate kinase NF003920.0 PRK05443 PRK05443.2-1 935 935 719 equivalog Y Y N RNA degradosome polyphosphate kinase 2.7.4.1 GO:0006799,GO:0008976,GO:0009358 2 Bacteria superkingdom 5705 NCBI Protein Cluster (PRK) polyphosphate kinase RNA degradosome polyphosphate kinase NF003922.0 PRK05443 PRK05443.2-3 981 981 735 equivalog Y Y N RNA degradosome polyphosphate kinase 2.7.4.1 GO:0006799,GO:0008976,GO:0009358 2 Bacteria superkingdom 13736 NCBI Protein Cluster (PRK) polyphosphate kinase RNA degradosome polyphosphate kinase NF003933.0 PRK05444 PRK05444.2-2 395 395 606 equivalog Y Y N 1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 GO:0008661,GO:0016114 2 Bacteria superkingdom 83575 NCBI Protein Cluster (PRK) 1-deoxy-D-xylulose-5-phosphate synthase 1-deoxy-D-xylulose-5-phosphate synthase NF003936.2 PRK05445 PRK05445.1 90 90 166 equivalog Y Y N YfbU family protein 2 Bacteria superkingdom 2929 NCBI Protein Cluster (PRK) hypothetical protein YfbU family protein NF003937.0 PRK05446 PRK05446.1 443 443 355 equivalog Y Y N bifunctional histidinol-phosphatase/imidazoleglycerol-phosphate dehydratase HisB hisB 3.1.3.15,4.2.1.19 GO:0000105,GO:0004401,GO:0004424 2 Bacteria superkingdom 16285 NCBI Protein Cluster (PRK) imidazole glycerol-phosphate dehydratase/histidinol phosphatase bifunctional histidinol-phosphatase/imidazoleglycerol-phosphate dehydratase HisB Catalyzes the formation of 3-(imidazol-4-yl)-2-oxopropyl phosphate from D-ethythro-1-(imidazol-4-yl)glycerol 3-phosphate and histidinol from histidinol phosphate NF003948.0 PRK05450 PRK05450.1-1 281 281 248 equivalog Y Y N 3-deoxy-manno-octulosonate cytidylyltransferase 2.7.7.38 GO:0008690 2 Bacteria superkingdom 4705 NCBI Protein Cluster (PRK) 3-deoxy-manno-octulosonate cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase NF003950.0 PRK05450 PRK05450.1-3 234 234 248 subfamily Y Y N 3-deoxy-manno-octulosonate cytidylyltransferase kdsB 2.7.7.38 2 Bacteria superkingdom 21786 NCBI Protein Cluster (PRK) 3-deoxy-manno-octulosonate cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase NF003958.0 PRK05454 PRK05454.2-1 419 419 704 equivalog Y Y N glucans biosynthesis glucosyltransferase MdoH mdoH 2.4.1.- 2 Bacteria superkingdom 17176 NCBI Protein Cluster (PRK) glucosyltransferase MdoH glucans biosynthesis glucosyltransferase MdoH NF003962.0 PRK05454 PRK05454.2-5 328 328 641 equivalog Y Y N glucans biosynthesis glucosyltransferase MdoH mdoH 2.4.1.- 2 Bacteria superkingdom 17373 NCBI Protein Cluster (PRK) glucosyltransferase MdoH glucans biosynthesis glucosyltransferase MdoH NF003964.0 PRK05456 PRK05456.1 137 137 179 equivalog Y Y N ATP-dependent protease subunit HslV hslV 3.4.25.2 GO:0004298,GO:0009376,GO:0051603 2 Bacteria superkingdom 21273 NCBI Protein Cluster (PRK) ATP-dependent protease subunit HslV ATP-dependent protease subunit HslV Heat shock protein involved in degradation of misfolded proteins NF003965.0 PRK05457 PRK05457.1 245 245 285 equivalog Y Y N protease HtpX htpX 3.4.24.- GO:0004222,GO:0006508 2 Bacteria superkingdom 12755 NCBI Protein Cluster (PRK) heat shock protein HtpX protease HtpX NF003966.0 PRK05458 PRK05458.1 344 344 327 equivalog Y Y N GMP reductase 1.7.1.7 GO:0003920,GO:0006163,GO:1902560 2 Bacteria superkingdom 8875 NCBI Protein Cluster (PRK) guanosine 5'-monophosphate oxidoreductase GMP reductase NF003967.1 PRK05461 PRK05461.1 106 106 123 equivalog Y Y N Co2+/Mg2+ efflux protein ApaG apaG 2670894,3031429 2 Bacteria superkingdom 16681 NCBI Protein Cluster (PRK) CO2+/MG2+ efflux protein ApaG Co2+/Mg2+ efflux protein ApaG ApaG, also known as CorD, is one of three proteins whose presence lets the magnesium import transporter CorA function also for efflux. NF003969.0 PRK05463 PRK05463.1 324 324 266 equivalog Y Y N putative hydro-lyase GO:0003824 2 Bacteria superkingdom 15458 NCBI Protein Cluster (PRK) hypothetical protein putative hydro-lyase NF003971.0 PRK05465 PRK05465.1 230 230 261 equivalog Y Y N ethanolamine ammonia-lyase subunit EutC eutC 4.3.1.7 GO:0006520,GO:0008851 2 Bacteria superkingdom 19524 NCBI Protein Cluster (PRK) ethanolamine ammonia-lyase small subunit ethanolamine ammonia-lyase subunit EutC Catalyzes the formation of acetaldehyde from ethanolamine NF003973.0 PRK05467 PRK05467.1-2 336 336 227 equivalog Y Y N Fe2+-dependent dioxygenase GO:0016705 2 Bacteria superkingdom 4172 NCBI Protein Cluster (PRK) Fe(II)-dependent oxygenase superfamily protein Fe2+-dependent dioxygenase NF003974.0 PRK05467 PRK05467.1-3 143 143 221 equivalog Y Y N Fe2+-dependent dioxygenase 2 Bacteria superkingdom 15365 NCBI Protein Cluster (PRK) Fe(II)-dependent oxygenase superfamily protein Fe2+-dependent dioxygenase NF003975.0 PRK05467 PRK05467.1-4 180 180 226 equivalog Y Y N Fe2+-dependent dioxygenase GO:0005506,GO:0016706,GO:0031418 2 Bacteria superkingdom 14945 NCBI Protein Cluster (PRK) Fe(II)-dependent oxygenase superfamily protein Fe2+-dependent dioxygenase NF003976.0 PRK05469 PRK05469.1 255 255 409 subfamily Y Y N tripeptide aminopeptidase PepT pepT 3.4.11.4 2 Bacteria superkingdom 38923 NCBI Protein Cluster (PRK) peptidase T tripeptide aminopeptidase PepT Catalyzes the release of the N-terminal amino acid from a tripeptide NF003977.1 PRK05470 PRK05470.1-1 60 60 117 equivalog Y Y N fumarate reductase subunit FrdD frdD 1.3.5.1 2 Bacteria superkingdom 3584 NCBI Protein Cluster (PRK) fumarate reductase subunit D fumarate reductase subunit FrdD NF003989.0 PRK05472 PRK05472.1-3 177 177 215 equivalog Y Y N redox-sensing transcriptional repressor Rex GO:0045892,GO:0051775 2 Bacteria superkingdom 14770 NCBI Protein Cluster (PRK) redox-sensing transcriptional repressor Rex redox-sensing transcriptional repressor Rex NF003991.0 PRK05472 PRK05472.1-5 198 198 211 equivalog Y Y N redox-sensing transcriptional repressor Rex 2 Bacteria superkingdom 4568 NCBI Protein Cluster (PRK) redox-sensing transcriptional repressor Rex redox-sensing transcriptional repressor Rex NF003992.0 PRK05472 PRK05472.2-1 226 226 249 equivalog Y Y N redox-sensing transcriptional repressor Rex GO:0045892,GO:0051775 2 Bacteria superkingdom 9571 NCBI Protein Cluster (PRK) redox-sensing transcriptional repressor Rex redox-sensing transcriptional repressor Rex NF003993.0 PRK05472 PRK05472.2-2 217 217 212 equivalog Y Y N redox-sensing transcriptional repressor Rex 2 Bacteria superkingdom 10783 NCBI Protein Cluster (PRK) redox-sensing transcriptional repressor Rex redox-sensing transcriptional repressor Rex NF003994.0 PRK05472 PRK05472.2-3 130 130 217 equivalog Y Y N redox-sensing transcriptional repressor Rex 2 Bacteria superkingdom 18899 NCBI Protein Cluster (PRK) redox-sensing transcriptional repressor Rex redox-sensing transcriptional repressor Rex NF003995.0 PRK05472 PRK05472.2-4 126 126 213 subfamily Y Y N redox-sensing transcriptional repressor Rex 2 Bacteria superkingdom 19121 NCBI Protein Cluster (PRK) redox-sensing transcriptional repressor Rex redox-sensing transcriptional repressor Rex NF003996.0 PRK05472 PRK05472.2-5 138 138 209 equivalog Y Y N redox-sensing transcriptional repressor Rex 2 Bacteria superkingdom 18647 NCBI Protein Cluster (PRK) redox-sensing transcriptional repressor Rex redox-sensing transcriptional repressor Rex NF003997.2 PRK05473 PRK05473.1 91 91 81 equivalog Y Y N IreB family regulatory phosphoprotein 24080657,28551334 2 Bacteria superkingdom 4716 NCBI Protein Cluster (PRK) hypothetical protein IreB family regulatory phosphoprotein IreB (EF1202) was characterized in Enterococcus faecalis as a small alpha-helical protein (PDB: 5US5), well-conserved in the Firmicutes. It belongs to a system that includes the Ser/Thr protein kinase IreK, and phosphatase IreP, undergoes phosphorylation on threonine residues, and is involved in regulating cephalosporin resistance. This family was previously named DUF965 by Pfam model PF06135. The gene symbol Ire signifies Intrinsic Resistance of Enterococci. NF003998.0 PRK05474 PRK05474.1 459 459 439 subfamily Y Y N xylose isomerase 5.3.1.5 2 Bacteria superkingdom 21104 NCBI Protein Cluster (PRK) xylose isomerase xylose isomerase Catalyzes the interconversion of D-xylose to D-xylulose NF004010.0 PRK05476 PRK05476.3-3 512 512 432 equivalog Y Y N adenosylhomocysteinase 3.13.2.1 2 Bacteria superkingdom 22 NCBI Protein Cluster (PRK) S-adenosyl-L-homocysteine hydrolase adenosylhomocysteinase NF004011.0 PRK05477 PRK05477.1-1 732 732 476 equivalog Y Y N Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB gatB 6.3.5.- GO:0016884 2 Bacteria superkingdom 8036 NCBI Protein Cluster (PRK) aspartyl/glutamyl-tRNA amidotransferase subunit B Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB NF004013.0 PRK05477 PRK05477.1-3 653 653 501 equivalog Y Y N Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB gatB GO:0016884 2 Bacteria superkingdom 14690 NCBI Protein Cluster (PRK) aspartyl/glutamyl-tRNA amidotransferase subunit B Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB NF004015.0 PRK05477 PRK05477.1-5 628 628 488 equivalog Y Y N Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB gatB GO:0016884 2 Bacteria superkingdom 19761 NCBI Protein Cluster (PRK) aspartyl/glutamyl-tRNA amidotransferase subunit B Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB NF004035.0 PRK05506 PRK05506.1 715 715 632 subfamily Y Y N bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase 2.7.1.25,2.7.7.4 2 Bacteria superkingdom 18685 NCBI Protein Cluster (PRK) bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase Catalyzes formation of activated sulfate intermediate; converts ATP and sulfate to diphosphate and adenylylsulfate and then ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate NF004038.0 PRK05528 PRK05528.1 200 200 157 equivalog Y Y N peptide-methionine (S)-S-oxide reductase 1.8.4.11 GO:0008113 2 Bacteria superkingdom 3065 NCBI Protein Cluster (PRK) methionine sulfoxide reductase A peptide-methionine (S)-S-oxide reductase Stereospecific enzyme reduces the S isomer of methionine sulfoxide while MsrB reduces the R form NF004040.0 PRK05537 PRK05537.1 669 669 572 equivalog Y Y N bifunctional sulfate adenylyltransferase/adenylylsulfate kinase 2 Bacteria superkingdom 2023 NCBI Protein Cluster (PRK) bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein bifunctional sulfate adenylyltransferase/adenylylsulfate kinase Catalyzes formation of activated sulfate intermediate; converts ATP and sulfate to diphosphate and adenylylsulfate and then ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate NF004046.0 PRK05563 PRK05563.1 413 413 562 equivalog Y Y N DNA polymerase III subunit gamma/tau dnaX 2.7.7.7 GO:0003677,GO:0003887,GO:0005524,GO:0006260,GO:0009360 2 Bacteria superkingdom 58597 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunit gamma/tau Catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA NF004052.0 PRK05572 PRK05572.1 311 311 252 subfamily Y Y N SigF/SigG family RNA polymerase sporulation sigma factor 2 Bacteria superkingdom 4783 NCBI Protein Cluster (PRK) sporulation sigma factor SigF RNA polymerase sporulation sigma factor, SigF/SigG family NF004061.0 PRK05576 PRK05576.1-4 265 265 237 equivalog Y Y N cobalt-factor II C(20)-methyltransferase 2.1.1.151 2 Bacteria superkingdom 1503 NCBI Protein Cluster (PRK) cobalt-precorrin-2 C(20)-methyltransferase cobalt-factor II C(20)-methyltransferase NF004066.1 PRK05580 PRK05580.1-3 813 813 788 equivalog Y Y N primosomal protein N' priA 3.6.1.- GO:0003678,GO:0006260,GO:0032508 2 Bacteria superkingdom 17541 NCBI Protein Cluster (PRK) primosome assembly protein PriA primosomal protein N' NF004070.0 PRK05580 PRK05580.2-2 921 921 729 equivalog Y Y N primosomal protein N' 3.6.1.- GO:0003677,GO:0003678,GO:0005524,GO:0006260,GO:0032508 2 Bacteria superkingdom 9221 NCBI Protein Cluster (PRK) primosome assembly protein PriA primosomal protein N' NF004079.0 PRK05584 PRK05584.1 169 169 232 equivalog Y Y N 5'-methylthioadenosine/adenosylhomocysteine nucleosidase 3.2.2.9 GO:0008782,GO:0008930,GO:0009116,GO:0009164,GO:0019509 2 Bacteria superkingdom 28722 NCBI Protein Cluster (PRK) 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase 5'-methylthioadenosine/adenosylhomocysteine nucleosidase Enables the cleavage of the glycosidic bond in both 5'-methylthioadenosine and S-adenosylhomocysteine NF004085.0 PRK05586 PRK05586.1 723 723 448 equivalog Y Y N acetyl-CoA carboxylase biotin carboxylase subunit GO:0005524,GO:0016874 2 Bacteria superkingdom 4362 NCBI Protein Cluster (PRK) biotin carboxylase acetyl-CoA carboxylase biotin carboxylase subunit NF004113.0 PRK05602 PRK05602.1 208 208 211 equivalog Y Y N RNA polymerase sigma factor 2 Bacteria superkingdom 3254 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF004114.0 PRK05605 PRK05605.1 766 766 575 equivalog Y Y N long-chain-fatty-acid--CoA ligase GO:0016874 2 Bacteria superkingdom 5425 NCBI Protein Cluster (PRK) long-chain-fatty-acid--CoA ligase long-chain-fatty-acid--CoA ligase NF004126.0 PRK05614 PRK05614.1 505 505 430 equivalog Y Y N citrate synthase 2.3.3.16 GO:0046912 11325948,11683626,12741811,12824188,15995199 2 Bacteria superkingdom 35875 NCBI Protein Cluster (PRK) type II citrate synthase citrate synthase Forms citrate from oxaloacetate and acetyl-CoA; functions in TCA cycle, glyoxylate cycle and respiration NF004127.0 PRK05617 PRK05617.1 274 274 356 subfamily Y Y N 3-hydroxyisobutyryl-CoA hydrolase GO:0003860 2 Bacteria superkingdom 43160 NCBI Protein Cluster (PRK) 3-hydroxyisobutyryl-CoA hydrolase 3-hydroxyisobutyryl-CoA hydrolase NF004128.0 PRK05618 PRK05618.1-2 174 174 210 equivalog Y Y N 50S ribosomal protein L25/general stress protein Ctc GO:0003735,GO:0006412,GO:0008097 2 Bacteria superkingdom 14217 NCBI Protein Cluster (PRK) 50S ribosomal protein L25/general stress protein Ctc 50S ribosomal protein L25/general stress protein Ctc NF004129.0 PRK05618 PRK05618.1-4 164 164 178 equivalog Y Y N 50S ribosomal protein L25/general stress protein Ctc 2 Bacteria superkingdom 1266 NCBI Protein Cluster (PRK) 50S ribosomal protein L25/general stress protein Ctc 50S ribosomal protein L25/general stress protein Ctc NF004130.0 PRK05618 PRK05618.1-5 199 199 212 equivalog Y Y N 50S ribosomal protein L25/general stress protein Ctc GO:0003735,GO:0006412,GO:0008097 2 Bacteria superkingdom 8176 NCBI Protein Cluster (PRK) 50S ribosomal protein L25/general stress protein Ctc 50S ribosomal protein L25/general stress protein Ctc NF004131.0 PRK05618 PRK05618.2-1 189 189 207 equivalog Y Y N 50S ribosomal protein L25/general stress protein Ctc GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 13184 NCBI Protein Cluster (PRK) 50S ribosomal protein L25/general stress protein Ctc 50S ribosomal protein L25/general stress protein Ctc NF004133.0 PRK05618 PRK05618.2-4 197 197 210 equivalog Y Y N 50S ribosomal protein L25/general stress protein Ctc GO:0003735,GO:0005840,GO:0006412,GO:0008097 2 Bacteria superkingdom 3596 NCBI Protein Cluster (PRK) 50S ribosomal protein L25/general stress protein Ctc 50S ribosomal protein L25/general stress protein Ctc NF004137.0 PRK05618 PRK05618.3-3 270 270 241 equivalog Y Y N 50S ribosomal protein L25/general stress protein Ctc 2 Bacteria superkingdom 227 NCBI Protein Cluster (PRK) 50S ribosomal protein L25/general stress protein Ctc 50S ribosomal protein L25/general stress protein Ctc NF004139.0 PRK05618 PRK05618.4-2 195 195 202 equivalog Y Y N 50S ribosomal protein L25/general stress protein Ctc 2 Bacteria superkingdom 528 NCBI Protein Cluster (PRK) 50S ribosomal protein L25/general stress protein Ctc 50S ribosomal protein L25/general stress protein Ctc NF004145.0 PRK05621 PRK05621.1-2 317 317 306 equivalog Y Y N F0F1 ATP synthase subunit gamma 7.1.2.2 GO:0015986,GO:0045261,GO:0046933 2 Bacteria superkingdom 13059 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit gamma F0F1 ATP synthase subunit gamma NF004146.0 PRK05621 PRK05621.1-4 342 342 296 equivalog Y Y N F0F1 ATP synthase subunit gamma 7.1.2.2 GO:0015986,GO:0046933 2 Bacteria superkingdom 6977 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit gamma F0F1 ATP synthase subunit gamma NF004159.0 PRK05627 PRK05627.1-2 306 306 326 equivalog Y Y N bifunctional riboflavin kinase/FAD synthetase 2.7.1.26,2.7.7.2 2 Bacteria superkingdom 17250 NCBI Protein Cluster (PRK) bifunctional riboflavin kinase/FMN adenylyltransferase bifunctional riboflavin kinase/FAD synthetase NF004161.0 PRK05627 PRK05627.1-4 461 461 324 equivalog Y Y N bifunctional riboflavin kinase/FAD synthetase ribF 2.7.1.26,2.7.7.2 2 Bacteria superkingdom 1872 NCBI Protein Cluster (PRK) bifunctional riboflavin kinase/FMN adenylyltransferase bifunctional riboflavin kinase/FAD synthetase NF004162.0 PRK05627 PRK05627.1-5 241 241 304 equivalog Y Y N bifunctional riboflavin kinase/FAD synthetase 2.7.1.26,2.7.7.2 GO:0003919 2 Bacteria superkingdom 31142 NCBI Protein Cluster (PRK) bifunctional riboflavin kinase/FMN adenylyltransferase bifunctional riboflavin kinase/FAD synthetase NF004167.0 PRK05632 PRK05632.1 418 418 708 equivalog Y Y N phosphate acetyltransferase pta 2.3.1.8 GO:0016407 2 Bacteria superkingdom 32532 NCBI Protein Cluster (PRK) phosphate acetyltransferase phosphate acetyltransferase NF004196.0 PRK05650 PRK05650.1 297 297 272 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 3050 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF004197.0 PRK05653 PRK05653.1-1 332 332 249 equivalog Y Y N 3-oxoacyl-ACP reductase FabG fabG 1.1.1.100 GO:0004316,GO:0006633,GO:0051287 2 Bacteria superkingdom 16836 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase 3-oxoacyl-ACP reductase FabG NF004199.0 PRK05653 PRK05653.1-4 301 301 247 equivalog Y Y N 3-oxoacyl-ACP reductase FabG fabG 1.1.1.100 GO:0016491 2 Bacteria superkingdom 6817 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase 3-oxoacyl-ACP reductase FabG NF004200.0 PRK05653 PRK05653.1-5 273 273 242 equivalog Y Y N 3-oxoacyl-ACP reductase FabG fabG 1.1.1.100 GO:0016491 2 Bacteria superkingdom 14665 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase 3-oxoacyl-ACP reductase FabG NF004201.0 PRK05653 PRK05653.2-1 288 288 231 equivalog Y Y N 3-oxoacyl-ACP reductase FabG fabG 1.1.1.100 2 Bacteria superkingdom 240 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase 3-oxoacyl-ACP reductase FabG NF004203.0 PRK05653 PRK05653.2-4 313 313 260 subfamily Y Y N 3-oxoacyl-ACP reductase FabG fabG 1.1.1.100 2 Bacteria superkingdom 3463 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase 3-oxoacyl-ACP reductase FabG NF004208.0 PRK05658 PRK05658.1 555 555 631 equivalog Y Y N RNA polymerase sigma factor RpoD rpoD GO:0003700,GO:0006355,GO:0016987 2 Bacteria superkingdom 27397 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RpoD RNA polymerase sigma factor RpoD Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this is the primary sigma factor of bacteria NF004225.0 PRK05672 PRK05672.1 939 939 1047 subfamily Y Y N error-prone DNA polymerase 2.7.7.7 GO:0003887,GO:0006260,GO:0008408 2 Bacteria superkingdom 38415 NCBI Protein Cluster (PRK) error-prone DNA polymerase error-prone DNA polymerase DNA polymerase involved in damage-induced mutagenesis and translesion synthesis NF004231.0 PRK05679 PRK05679.1 129 129 213 subfamily Y Y N pyridoxal 5'-phosphate synthase 1.4.3.5 GO:0004733,GO:0008615,GO:0010181 2 Bacteria superkingdom 53219 NCBI Protein Cluster (PRK) pyridoxamine 5'-phosphate oxidase pyridoxal 5'-phosphate synthase Catalyzes the formation of pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate NF004241.1 PRK05682 PRK05682.1-5 469 469 446 equivalog Y Y N flagellar hook protein FlgE flgE 8206841,8755894 2 Bacteria superkingdom 721 NCBI Protein Cluster (PRK) flagellar hook protein FlgE flagellar hook protein FlgE NF004284.0 PRK05693 PRK05693.1 326 326 274 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 3252 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF004309.0 PRK05704 PRK05704.1 449 449 408 equivalog Y Y N 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase odhB 2.3.1.61 GO:0004149,GO:0006099,GO:0045252 2 Bacteria superkingdom 36532 NCBI Protein Cluster (PRK) dihydrolipoamide succinyltransferase 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase NF004314.0 PRK05710 PRK05710.1-3 256 256 297 equivalog Y Y N tRNA glutamyl-Q(34) synthetase GluQRS gluQRS 6.1.1.- GO:0004812,GO:0043039 2 Bacteria superkingdom 30504 NCBI Protein Cluster (PRK) glutamyl-Q tRNA(Asp) synthetase tRNA glutamyl-Q(34) synthetase GluQRS NF004315.1 PRK05710 PRK05710.1-4 250 250 274 equivalog Y Y N tRNA glutamyl-Q(34) synthetase GluQRS gluQRS 6.1.1.- GO:0000166,GO:0004812,GO:0005524,GO:0006418 2 Bacteria superkingdom 21428 NCBI Protein Cluster (PRK) glutamyl-Q tRNA(Asp) synthetase tRNA glutamyl-Q(34) synthetase GluQRS NF004316.1 PRK05711 PRK05711.1 196 196 234 equivalog Y Y N DNA polymerase III subunit epsilon dnaQ 2.7.7.7 GO:0003677,GO:0003887,GO:0006260 2 Bacteria superkingdom 24748 NCBI Protein Cluster (PRK) DNA polymerase III subunit epsilon DNA polymerase III subunit epsilon 3'-5' exonuclease of DNA polymerase III NF004325.0 PRK05718 PRK05718.1 241 241 213 subfamily Y N N keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase 4.1.2.14,4.1.3.16 2 Bacteria superkingdom 32143 NCBI Protein Cluster (PRK) keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase NF004344.0 PRK05724 PRK05724.1 357 357 319 equivalog Y Y N acetyl-CoA carboxylase carboxyltransferase subunit alpha 6.4.1.2 GO:0003989,GO:0006633,GO:0009317 2 Bacteria superkingdom 37302 NCBI Protein Cluster (PRK) acetyl-CoA carboxylase carboxyltransferase subunit alpha acetyl-CoA carboxylase carboxyltransferase subunit alpha NF004347.0 PRK05728 PRK05728.1-4 132 132 150 equivalog Y Y N DNA polymerase III subunit chi 2.7.7.7 GO:0003677,GO:0003887,GO:0006260 2 Bacteria superkingdom 6574 NCBI Protein Cluster (PRK) DNA polymerase III subunit chi DNA polymerase III subunit chi NF004349.1 PRK05729 PRK05729.1 704 704 860 equivalog Y Y N valine--tRNA ligase 6.1.1.9 GO:0000166,GO:0004812,GO:0004832,GO:0005524,GO:0006438 11114335,12475234,12554880,14970394,15970591,3275660,3317277 2 Bacteria superkingdom 87876 NCBI Protein Cluster (PRK) valyl-tRNA synthetase valine--tRNA ligase ValRS; converts valine ATP and tRNA(Val) to AMP PPi and valyl-tRNA(Val); class-I aminoacyl-tRNA synthetase type 1 subfamily; has a posttransfer editing process to hydrolyze mischarged Thr-tRNA(Val) which is done by the editing domain NF004359.0 PRK05738 PRK05738.1-3 94 94 99 equivalog Y Y N 50S ribosomal protein L23 rplW GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 13005 NCBI Protein Cluster (PRK) 50S ribosomal protein L23 50S ribosomal protein L23 NF004360.0 PRK05738 PRK05738.1-5 118 118 99 equivalog Y Y N 50S ribosomal protein L23 GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 4509 NCBI Protein Cluster (PRK) 50S ribosomal protein L23 50S ribosomal protein L23 NF004363.0 PRK05738 PRK05738.2-4 81 81 96 equivalog Y Y N 50S ribosomal protein L23 rplW GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 26554 NCBI Protein Cluster (PRK) 50S ribosomal protein L23 50S ribosomal protein L23 NF004364.0 PRK05738 PRK05738.2-5 117 117 101 equivalog Y Y N 50S ribosomal protein L23 rplW GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 5701 NCBI Protein Cluster (PRK) 50S ribosomal protein L23 50S ribosomal protein L23 NF004366.0 PRK05738 PRK05738.3-2 111 111 96 equivalog Y Y N 50S ribosomal protein L23 2 Bacteria superkingdom 2955 NCBI Protein Cluster (PRK) 50S ribosomal protein L23 50S ribosomal protein L23 NF004371.0 PRK05740 PRK05740.1-1 109 109 126 equivalog Y Y N preprotein translocase subunit SecE secE 2 Bacteria superkingdom 2604 NCBI Protein Cluster (PRK) preprotein translocase subunit SecE preprotein translocase subunit SecE NF004384.0 PRK05748 PRK05748.1 525 525 452 equivalog Y Y N replicative DNA helicase dnaB 3.6.4.12 GO:0003677,GO:0003678,GO:0005524,GO:0006260 2 Bacteria superkingdom 28589 NCBI Protein Cluster (PRK) replicative DNA helicase replicative DNA helicase Unwinds double stranded DNA NF004392.0 PRK05751 PRK05751.1-3 143 143 160 equivalog Y Y N protein-export chaperone SecB secB GO:0015031,GO:0051082,GO:0051262 2 Bacteria superkingdom 8074 NCBI Protein Cluster (PRK) preprotein translocase subunit SecB protein-export chaperone SecB NF004396.0 PRK05753 PRK05753.1 109 109 137 equivalog Y Y N nucleoside diphosphate kinase regulator rnk GO:0003677,GO:0032784,GO:0070063 2 Bacteria superkingdom 9283 NCBI Protein Cluster (PRK) nucleoside diphosphate kinase regulator nucleoside diphosphate kinase regulator NF004398.0 PRK05756 PRK05756.1 292 292 287 equivalog Y Y N pyridoxal kinase PdxY pdxY 2.7.1.35 GO:0008478,GO:0009443 2 Bacteria superkingdom 15106 NCBI Protein Cluster (PRK) pyridoxamine kinase pyridoxal kinase PdxY Catalyzes the formation of pyridoxal 5'-phosphate from pyridoxal NF004402.0 PRK05758 PRK05758.2-2 115 115 179 equivalog Y Y N F0F1 ATP synthase subunit delta 7.1.2.2 GO:0015986,GO:0046933 2 Bacteria superkingdom 16658 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit delta F0F1 ATP synthase subunit delta NF004403.0 PRK05758 PRK05758.2-4 148 148 180 equivalog Y Y N F0F1 ATP synthase subunit delta 7.1.2.2 GO:0015986,GO:0016020,GO:0046933 2 Bacteria superkingdom 4330 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit delta F0F1 ATP synthase subunit delta NF004406.0 PRK05758 PRK05758.3-2 172 172 186 equivalog Y Y N F0F1 ATP synthase subunit delta 7.1.2.2 GO:0015986,GO:0016020,GO:0046933 2 Bacteria superkingdom 6615 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit delta F0F1 ATP synthase subunit delta NF004412.0 PRK05759 PRK05759.1-3 156 156 185 equivalog Y Y N F0F1 ATP synthase subunit B 7.1.2.2 GO:0015078,GO:0015986,GO:0045263 2 Bacteria superkingdom 10722 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit B F0F1 ATP synthase subunit B NF004440.0 PRK05777 PRK05777.1-3 519 519 477 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoN nuoN 7.1.1.2 GO:0008137,GO:0042773 2 Bacteria superkingdom 7716 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit N NADH-quinone oxidoreductase subunit NuoN NF004441.0 PRK05777 PRK05777.1-4 477 477 524 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoN nuoN 7.1.1.2 GO:0008137,GO:0042773 2 Bacteria superkingdom 11320 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit N NADH-quinone oxidoreductase subunit NuoN NF004442.0 PRK05777 PRK05777.1-5 523 523 483 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoN nuoN 7.1.1.2 GO:0008137,GO:0042773 2 Bacteria superkingdom 5828 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit N NADH-quinone oxidoreductase subunit NuoN NF004456.0 PRK05787 PRK05787.1-4 247 247 201 equivalog Y Y N cobalt-precorrin-7 (C(5))-methyltransferase 2.1.1.289 2 Bacteria superkingdom 946 NCBI Protein Cluster (PRK) cobalt-precorrin-6Y C(5)-methyltransferase cobalt-precorrin-7 (C(5))-methyltransferase NF004466.0 PRK05788 PRK05788.1-4 326 326 335 equivalog Y Y N cobalt-precorrin 5A hydrolase cbiG 3.7.1.12 2 Bacteria superkingdom 1399 NCBI Protein Cluster (PRK) cobalamin biosynthesis protein CbiG cobalt-precorrin 5A hydrolase NF004469.0 PRK05800 PRK05800.1 161 161 173 equivalog Y Y N bifunctional adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase cobU 2.7.1.156,2.7.7.62 GO:0000166,GO:0009236,GO:0043752 2 Bacteria superkingdom 26377 NCBI Protein Cluster (PRK) adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase bifunctional adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase Catalyzes ATP-dependent phosphorylation of adenosylcobinamide to form adenosylcobinamide phosphate and the addition of guanosine monophosphate to adenosylcobinamide phosphate to form adenosylcobinamide-GDP NF004470.0 PRK05802 PRK05802.1 313 313 330 equivalog Y Y N sulfide/dihydroorotate dehydrogenase-like FAD/NAD-binding protein 2 Bacteria superkingdom 710 NCBI Protein Cluster (PRK) hypothetical protein sulfide/dihydroorotate dehydrogenase-like FAD/NAD-binding protein NF004471.0 PRK05803 PRK05803.1 252 252 235 subfamily Y Y N RNA polymerase sporulation sigma factor SigK sigK 12694623,7961408 2 Bacteria superkingdom 8035 NCBI Protein Cluster (PRK) sporulation sigma factor SigK RNA polymerase sporulation sigma factor SigK Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this sigma factor is responsible for the expression of sporulation specific genes and is expressed in the mother cell after engulfment NF004472.0 PRK05805 PRK05805.1 399 399 302 subfamily Y Y N phosphate butyryltransferase 2.3.1.19 2 Bacteria superkingdom 1489 NCBI Protein Cluster (PRK) phosphate butyryltransferase phosphate butyryltransferase Catalyzes the synthesis of butanoylphosphate from butanoyl-CoA and inorganic phosphate NF004475.0 PRK05809 PRK05809.1 394 394 260 subfamily Y Y N short-chain-enoyl-CoA hydratase 4.2.1.150 2 Bacteria superkingdom 874 NCBI Protein Cluster (PRK) 3-hydroxybutyryl-CoA dehydratase short-chain-enoyl-CoA hydratase NF004476.0 PRK05813 PRK05813.1 171 171 219 equivalog Y Y N single-stranded DNA-binding protein 2 Bacteria superkingdom 1600 NCBI Protein Cluster (PRK) single-stranded DNA-binding protein single-stranded DNA-binding protein NF004479.0 PRK05815 PRK05815.1-4 268 268 238 equivalog Y Y N F0F1 ATP synthase subunit A atpB 7.1.2.2 GO:0015078,GO:0015986 2 Bacteria superkingdom 4176 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit A F0F1 ATP synthase subunit A NF004482.0 PRK05815 PRK05815.2-4 225 225 252 equivalog Y Y N F0F1 ATP synthase subunit A 7.1.2.2 GO:0015078,GO:0015986 2 Bacteria superkingdom 6773 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit A F0F1 ATP synthase subunit A NF004489.0 PRK05819 PRK05819.1 230 230 236 subfamily Y Y N DeoD-type purine-nucleoside phosphorylase 2.4.2.1 2 Bacteria superkingdom 21265 NCBI Protein Cluster (PRK) purine nucleoside phosphorylase DeoD-type purine-nucleoside phosphorylase Catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate NF004499.0 PRK05846 PRK05846.1-3 585 585 502 equivalog Y Y N NADH-quinone oxidoreductase subunit M 1.6.5.9 GO:0008137,GO:0042773 2 Bacteria superkingdom 13656 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit M NADH-quinone oxidoreductase subunit M NF004500.0 PRK05846 PRK05846.1-4 550 550 525 equivalog Y Y N NADH-quinone oxidoreductase subunit M 1.6.5.9 GO:0008137,GO:0042773 2 Bacteria superkingdom 12949 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit M NADH-quinone oxidoreductase subunit M NF004501.0 PRK05846 PRK05846.1-5 598 598 492 subfamily Y Y N NADH-quinone oxidoreductase subunit M 1.6.5.9 2 Bacteria superkingdom 12685 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit M NADH-quinone oxidoreductase subunit M NF004514.1 PRK05855 PRK05855.1 455 455 578 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 11378 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF004516.0 PRK05858 PRK05858.1 587 587 548 equivalog Y Y N acetolactate synthase 2.2.1.6 2 Bacteria superkingdom 2366 NCBI Protein Cluster (PRK) hypothetical protein acetolactate synthase NF004517.0 PRK05862 PRK05862.1 396 396 257 equivalog Y Y N enoyl-CoA hydratase 4.2.1.17 2 Bacteria superkingdom 16450 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF004519.0 PRK05864 PRK05864.1 337 337 276 equivalog Y Y N enoyl-CoA hydratase 4.2.1.17 2 Bacteria superkingdom 1196 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF004525.0 PRK05870 PRK05870.1 285 285 249 equivalog Y Y N enoyl-CoA hydratase 4.2.1.17 2 Bacteria superkingdom 1542 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF004526.0 PRK05872 PRK05872.1 276 276 297 subfamily Y Y N short-chain dehydrogenase/reductase GO:0016491 2 Bacteria superkingdom 12716 NCBI Protein Cluster (PRK) short chain dehydrogenase short-chain dehydrogenase/reductase NF004537.0 PRK05888 PRK05888.1-3 163 163 204 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoI nuoI 1.6.5.9 GO:0016651 2 Bacteria superkingdom 10447 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit I NADH-quinone oxidoreductase subunit NuoI NF004538.0 PRK05888 PRK05888.1-4 135 135 162 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoI nuoI 1.6.5.9 GO:0016651,GO:0051539 2 Bacteria superkingdom 8887 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit I NADH-quinone oxidoreductase subunit NuoI NF004539.0 PRK05888 PRK05888.1-5 225 225 162 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoI nuoI 1.6.5.9 GO:0016651,GO:0051539 2 Bacteria superkingdom 8045 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit I NADH-quinone oxidoreductase subunit NuoI NF004540.0 PRK05888 PRK05888.2-1 215 215 139 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoI nuoI 1.6.5.9 2 Bacteria superkingdom 875 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit I NADH-quinone oxidoreductase subunit NuoI NF004547.1 PRK05889 PRK05889.1 75 75 71 equivalog Y Y N biotin/lipoyl-binding carrier protein 2 Bacteria superkingdom 4278 NCBI Protein Cluster (PRK) putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit biotin/lipoyl-binding carrier protein This protein, averaging about 71 amino acids in length, likely binds either a lipoyl or biotin group at a conserved Lys residue, and that prosthetic group in turn likely allows this protein to act as a carrier subunit for some compound. However, the protein and any system to which it may belong has not yet been characterized. NF004556.0 PRK05899 PRK05899.2-2 575 575 639 equivalog Y Y N transketolase 2.2.1.1 2 Bacteria superkingdom 243 NCBI Protein Cluster (PRK) transketolase transketolase NF004561.0 PRK05901 PRK05901.1-3 582 582 537 equivalog Y Y N RNA polymerase sigma factor GO:0003677,GO:0006352,GO:0006355,GO:0016987 2 Bacteria superkingdom 14854 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF004584.0 PRK05928 PRK05928.2-1 233 233 269 equivalog Y Y N uroporphyrinogen-III synthase 4.2.1.75 GO:0004852,GO:0006780 2 Bacteria superkingdom 2776 NCBI Protein Cluster (PRK) uroporphyrinogen-III synthase uroporphyrinogen-III synthase NF004593.0 PRK05928 PRK05928.4-2 275 275 247 equivalog Y Y N uroporphyrinogen-III synthase 4.2.1.75 2 Bacteria superkingdom 70 NCBI Protein Cluster (PRK) uroporphyrinogen-III synthase uroporphyrinogen-III synthase NF004596.0 PRK05932 PRK05932.1-3 499 499 515 subfamily Y Y N RNA polymerase factor sigma-54 2.7.7.6 2 Bacteria superkingdom 7165 NCBI Protein Cluster (PRK) RNA polymerase factor sigma-54 RNA polymerase factor sigma-54 NF004612.1 PRK05943 PRK05943.1 67 67 93 equivalog Y Y N 50S ribosomal protein L25 rplY GO:0003735,GO:0005840,GO:0006412 10696113,11418764,15718233,2034228,9799245 2 Bacteria superkingdom 15807 NCBI Protein Cluster (PRK) 50S ribosomal protein L25 50S ribosomal protein L25 NF004621.0 PRK05957 PRK05957.1 498 498 389 equivalog Y Y N pyridoxal phosphate-dependent aminotransferase 2.6.1.- 2 Bacteria superkingdom 727 NCBI Protein Cluster (PRK) aspartate aminotransferase pyridoxal phosphate-dependent aminotransferase NF004627.0 PRK05968 PRK05968.1 508 508 389 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 2284 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004628.0 PRK05972 PRK05972.1 895 895 870 subfamily Y Y N ATP-dependent DNA ligase 6.5.1.1 2 Bacteria superkingdom 13535 NCBI Protein Cluster (PRK) ATP-dependent DNA ligase ATP-dependent DNA ligase Catalyzes the ATP dependent formation of a phosphodiester at the site of a single-strand break in duplex DNA NF004629.0 PRK05973 PRK05973.1 156 156 237 equivalog Y Y N DNA helicase GO:0003678,GO:0006260 2 Bacteria superkingdom 1512 NCBI Protein Cluster (PRK) replicative DNA helicase DNA helicase NF004631.0 PRK05975 PRK05975.1 371 371 352 equivalog Y Y N 3-carboxy-cis,cis-muconate cycloisomerase 5.5.1.2 GO:0047472 2 Bacteria superkingdom 2588 NCBI Protein Cluster (PRK) 3-carboxy-cis,cis-muconate cycloisomerase 3-carboxy-cis,cis-muconate cycloisomerase Catalyzes the cycloisomerization of cis,cis-muconate NF004634.0 PRK05980 PRK05980.1 375 375 263 equivalog Y Y N crotonase/enoyl-CoA hydratase family protein 2 Bacteria superkingdom 1251 NCBI Protein Cluster (PRK) enoyl-CoA hydratase crotonase/enoyl-CoA hydratase family protein NF004635.0 PRK05981 PRK05981.1 351 351 266 equivalog Y Y N enoyl-CoA hydratase/isomerase 2 Bacteria superkingdom 781 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase/isomerase NF004636.0 PRK05985 PRK05985.1 408 408 398 subfamily Y Y N amidohydrolase GO:0016810 2 Bacteria superkingdom 9951 NCBI Protein Cluster (PRK) cytosine deaminase amidohydrolase NF004638.0 PRK05988 PRK05988.1 198 198 159 equivalog Y Y N formate dehydrogenase subunit gamma GO:0016491 2 Bacteria superkingdom 6475 NCBI Protein Cluster (PRK) formate dehydrogenase subunit gamma formate dehydrogenase subunit gamma Catalyzes the oxidation of formate to carbon dioxide and hydrogen using NAD or NADP as the acceptor NF004647.0 PRK05990 PRK05990.1 271 271 245 equivalog Y Y N precorrin-2 C(20)-methyltransferase 2.1.1.130 GO:0009236,GO:0030788 2 Bacteria superkingdom 15460 NCBI Protein Cluster (PRK) precorrin-2 C(20)-methyltransferase precorrin-2 C(20)-methyltransferase Catalyzes the formation of precorrin-3 from precorrin-2 NF004650.0 PRK05994 PRK05994.1 667 667 427 equivalog Y Y N O-acetylhomoserine aminocarboxypropyltransferase 2.5.1.49 GO:0006520,GO:0016765,GO:0019346,GO:0030170 2 Bacteria superkingdom 3582 NCBI Protein Cluster (PRK) O-acetylhomoserine aminocarboxypropyltransferase O-acetylhomoserine aminocarboxypropyltransferase Catalyzes the formation of L-methionine and acetate from O-acetyl-L-homoserine and methanethiol NF004669.0 PRK06008 PRK06008.1 230 230 348 equivalog Y Y N flagellar hook-associated family protein GO:0005198 2 Bacteria superkingdom 2308 NCBI Protein Cluster (PRK) flagellar hook-associated protein FlgL flagellar hook-associated family protein NF004671.0 PRK06010 PRK06010.1 104 104 88 subfamily Y N N flagellar biosynthesis protein FliQ 2 Bacteria superkingdom 2233 NCBI Protein Cluster (PRK) flagellar biosynthesis protein FliQ flagellar biosynthesis protein FliQ NF004674.0 PRK06018 PRK06018.1 766 766 544 subfamily Y Y N long-chain-fatty-acid--CoA ligase 2 Bacteria superkingdom 5488 NCBI Protein Cluster (PRK) putative acyl-CoA synthetase long-chain-fatty-acid--CoA ligase NF004677.0 PRK06019 PRK06019.1-3 441 441 389 equivalog Y Y N 5-(carboxyamino)imidazole ribonucleotide synthase 6.3.4.18 GO:0004638,GO:0005524,GO:0006189,GO:0046872 2 Bacteria superkingdom 6334 NCBI Protein Cluster (PRK) phosphoribosylaminoimidazole carboxylase ATPase subunit 5-(carboxyamino)imidazole ribonucleotide synthase NF004681.0 PRK06023 PRK06023.1 282 282 250 equivalog Y Y N crotonase/enoyl-CoA hydratase family protein GO:0003824 2 Bacteria superkingdom 2270 NCBI Protein Cluster (PRK) enoyl-CoA hydratase crotonase/enoyl-CoA hydratase family protein NF004682.0 PRK06025 PRK06025.1 568 568 417 subfamily Y Y N acetyl-CoA C-acetyltransferase 2 Bacteria superkingdom 1864 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA C-acetyltransferase Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A NF004689.0 PRK06031 PRK06031.1 175 175 233 equivalog Y Y N phosphoribosyltransferase GO:0009116 2 Bacteria superkingdom 1620 NCBI Protein Cluster (PRK) phosphoribosyltransferase phosphoribosyltransferase NF004713.0 PRK06057 PRK06057.1 404 404 257 equivalog Y Y N 3-oxoacyl-ACP reductase 1.1.1.100 GO:0016491 2 Bacteria superkingdom 8206 NCBI Protein Cluster (PRK) short chain dehydrogenase 3-oxoacyl-ACP reductase NF004714.0 PRK06058 PRK06058.1 639 639 447 subfamily Y Y N 4-aminobutyrate--2-oxoglutarate transaminase 2.6.1.19 2 Bacteria superkingdom 12932 NCBI Protein Cluster (PRK) 4-aminobutyrate aminotransferase 4-aminobutyrate--2-oxoglutarate transaminase Catalyzes the formation of succinate semialdehyde and glutamate from 4-aminobutanoate and 2-oxoglutarate NF004715.0 PRK06059 PRK06059.1 424 424 399 equivalog Y Y N lipid-transfer protein GO:0016747 2 Bacteria superkingdom 5771 NCBI Protein Cluster (PRK) lipid-transfer protein lipid-transfer protein NF004730.0 PRK06074 PRK06074.1-1 193 193 200 equivalog Y Y N NADH-quinone oxidoreductase subunit C 1.6.5.9 GO:0008137 2 Bacteria superkingdom 7407 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit C NADH-quinone oxidoreductase subunit C NF004733.0 PRK06074 PRK06074.1-5 225 225 203 equivalog Y Y N NADH-quinone oxidoreductase subunit C 1.6.5.9 GO:0008137 2 Bacteria superkingdom 7333 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit C NADH-quinone oxidoreductase subunit C NF004743.0 PRK06076 PRK06076.1-4 494 494 433 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoH nuoH 1.6.5.9 GO:0016020,GO:0016651,GO:0051539 2 Bacteria superkingdom 10826 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit H NADH-quinone oxidoreductase subunit NuoH NF004745.0 PRK06076 PRK06076.1-6 450 450 341 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoH nuoH 1.6.5.9 GO:0016651 2 Bacteria superkingdom 6950 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit H NADH-quinone oxidoreductase subunit NuoH NF004747.0 PRK06078 PRK06078.1 559 559 434 equivalog Y Y N pyrimidine-nucleoside phosphorylase 2.4.2.2 GO:0006213,GO:0016154 9817849 2 Bacteria superkingdom 12134 NCBI Protein Cluster (PRK) pyrimidine-nucleoside phosphorylase pyrimidine-nucleoside phosphorylase Catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway NF004749.0 PRK06080 PRK06080.1-1 277 277 311 equivalog Y Y N 1,4-dihydroxy-2-naphthoate polyprenyltransferase 2.5.1.74 GO:0009234,GO:0016020,GO:0046428 2 Bacteria superkingdom 4011 NCBI Protein Cluster (PRK) 1,4-dihydroxy-2-naphthoate octaprenyltransferase 1,4-dihydroxy-2-naphthoate polyprenyltransferase NF004752.0 PRK06080 PRK06080.1-4 289 289 300 subfamily Y Y N 1,4-dihydroxy-2-naphthoate polyprenyltransferase 2.5.1.74 2 Bacteria superkingdom 3591 NCBI Protein Cluster (PRK) 1,4-dihydroxy-2-naphthoate octaprenyltransferase 1,4-dihydroxy-2-naphthoate polyprenyltransferase NF004755.0 PRK06082 PRK06082.1 467 467 459 equivalog Y Y N aspartate aminotransferase family protein GO:0008483,GO:0030170 2 Bacteria superkingdom 4339 NCBI Protein Cluster (PRK) 4-aminobutyrate aminotransferase aspartate aminotransferase family protein NF004760.0 PRK06091 PRK06091.1 433 433 555 subfamily Y Y N acyl-CoA synthetase FdrA fdrA GO:0003824 2 Bacteria superkingdom 11196 NCBI Protein Cluster (PRK) membrane protein FdrA acyl-CoA synthetase FdrA NF004767.0 PRK06105 PRK06105.1 517 517 460 subfamily Y Y N aminotransferase GO:0008483,GO:0030170 2 Bacteria superkingdom 16309 NCBI Protein Cluster (PRK) aminotransferase aminotransferase NF004769.0 PRK06107 PRK06107.1 617 617 402 equivalog Y Y N aspartate transaminase 2.6.1.1 2 Bacteria superkingdom 1751 NCBI Protein Cluster (PRK) aspartate aminotransferase aspartate transaminase Catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate NF004770.0 PRK06108 PRK06108.1 422 422 396 subfamily Y Y N pyridoxal phosphate-dependent aminotransferase 2.6.1.- 2 Bacteria superkingdom 5768 NCBI Protein Cluster (PRK) aspartate aminotransferase pyridoxal phosphate-dependent aminotransferase NF004771.0 PRK06110 PRK06110.1 317 317 323 equivalog Y Y N threonine dehydratase 4.3.1.19 2 Bacteria superkingdom 3626 NCBI Protein Cluster (PRK) hypothetical protein threonine dehydratase NF004772.0 PRK06112 PRK06112.1 673 673 578 subfamily Y Y N acetolactate synthase catalytic subunit GO:0000287,GO:0003824,GO:0030976 2 Bacteria superkingdom 1253 NCBI Protein Cluster (PRK) acetolactate synthase catalytic subunit acetolactate synthase catalytic subunit NF004776.0 PRK06116 PRK06116.1 480 480 450 equivalog Y Y N glutathione-disulfide reductase gorA 1.8.1.7 GO:0004362,GO:0006749,GO:0045454,GO:0050660,GO:0050661 2 Bacteria superkingdom 31934 NCBI Protein Cluster (PRK) glutathione reductase glutathione-disulfide reductase NF004777.0 PRK06123 PRK06123.1 383 383 249 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 4872 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF004778.0 PRK06124 PRK06124.1 303 303 256 equivalog Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 1894 NCBI Protein Cluster (PRK) gluconate 5-dehydrogenase SDR family oxidoreductase NF004779.0 PRK06125 PRK06125.1 261 261 259 subfamily Y Y N short-chain dehydrogenase/reductase GO:0016491 2 Bacteria superkingdom 2029 NCBI Protein Cluster (PRK) short chain dehydrogenase short-chain dehydrogenase/reductase NF004781.0 PRK06127 PRK06127.1 291 291 269 subfamily Y Y N enoyl-CoA hydratase GO:0003824 2 Bacteria superkingdom 1869 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF004782.0 PRK06128 PRK06128.1 481 481 300 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 2827 NCBI Protein Cluster (PRK) oxidoreductase SDR family oxidoreductase NF004783.0 PRK06129 PRK06129.1 347 347 315 equivalog Y Y N 3-hydroxyacyl-CoA dehydrogenase 1.1.1.35 2 Bacteria superkingdom 2861 NCBI Protein Cluster (PRK) 3-hydroxyacyl-CoA dehydrogenase 3-hydroxyacyl-CoA dehydrogenase NF004784.0 PRK06131 PRK06131.1 539 539 576 subfamily Y Y N dihydroxy-acid dehydratase GO:0003824 2 Bacteria superkingdom 34623 NCBI Protein Cluster (PRK) dihydroxy-acid dehydratase dihydroxy-acid dehydratase NF004785.0 PRK06132 PRK06132.1-2 169 169 353 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 5756 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004788.0 PRK06133 PRK06133.1 349 349 417 subfamily Y Y N glutamate carboxypeptidase GO:0016787 19911261 2 Bacteria superkingdom 5044 NCBI Protein Cluster (PRK) glutamate carboxypeptidase glutamate carboxypeptidase NF004789.0 PRK06134 PRK06134.1 747 747 581 subfamily Y Y N FAD-dependent oxidoreductase 2 Bacteria superkingdom 6244 NCBI Protein Cluster (PRK) putative FAD-binding dehydrogenase FAD-dependent oxidoreductase NF004791.0 PRK06138 PRK06138.1 312 312 252 equivalog Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 825 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF004792.0 PRK06139 PRK06139.1 308 308 327 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 2715 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF004793.0 PRK06141 PRK06141.1 322 322 314 equivalog Y Y N ornithine cyclodeaminase family protein 2 Bacteria superkingdom 6753 NCBI Protein Cluster (PRK) ornithine cyclodeaminase ornithine cyclodeaminase family protein NF004794.0 PRK06142 PRK06142.1 308 308 273 equivalog Y Y N crotonase/enoyl-CoA hydratase family protein 2 Bacteria superkingdom 6549 NCBI Protein Cluster (PRK) enoyl-CoA hydratase crotonase/enoyl-CoA hydratase family protein NF004795.0 PRK06143 PRK06143.1 283 283 260 subfamily Y Y N enoyl-CoA hydratase GO:0003824 2 Bacteria superkingdom 1472 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF004796.0 PRK06144 PRK06144.1 272 272 262 subfamily Y Y N enoyl-CoA hydratase GO:0003824 2 Bacteria superkingdom 3459 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF004800.0 PRK06149 PRK06149.1 973 973 972 equivalog Y Y N aminotransferase GO:0008483,GO:0030170 2 Bacteria superkingdom 5862 NCBI Protein Cluster (PRK) hypothetical protein aminotransferase NF004802.0 PRK06153 PRK06153.1-1 601 601 391 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 375 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004803.0 PRK06153 PRK06153.1-2 419 419 400 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 144 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004808.0 PRK06155 PRK06155.1 722 722 542 equivalog Y Y N ATP-dependent acyl-CoA ligase GO:0004467,GO:0005324,GO:0006633 2 Bacteria superkingdom 1076 NCBI Protein Cluster (PRK) crotonobetaine/carnitine-CoA ligase ATP-dependent acyl-CoA ligase NF004812.0 PRK06161 PRK06161.1 93 93 92 equivalog Y Y N K+/H+ antiporter subunit F GO:0015075,GO:0034220 16030218 2 Bacteria superkingdom 6260 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit F K+/H+ antiporter subunit F NF004814.0 PRK06164 PRK06164.1 677 677 540 equivalog Y N N acyl-CoA synthetase 2 Bacteria superkingdom 756 NCBI Protein Cluster (PRK) acyl-CoA synthetase acyl-CoA synthetase NF004815.0 PRK06169 PRK06169.1 506 506 471 equivalog Y Y N amidase 3.5.1.4 GO:0003824 2 Bacteria superkingdom 8446 NCBI Protein Cluster (PRK) putative amidase amidase NF004816.0 PRK06170 PRK06170.1 503 503 493 equivalog Y Y N amidase 3.5.1.4 2 Bacteria superkingdom 5010 NCBI Protein Cluster (PRK) amidase amidase NF004817.0 PRK06171 PRK06171.1 304 304 265 subfamily Y Y N sorbitol-6-phosphate dehydrogenase subunit 1.1.1.140 GO:0016491 2 Bacteria superkingdom 2604 NCBI Protein Cluster (PRK) sorbitol-6-phosphate 2-dehydrogenase sorbitol-6-phosphate dehydrogenase subunit Catalyzes the conversion of sorbitol 6-phosphate into fructose 6-phosphate NF004820.0 PRK06175 PRK06175.1 472 472 433 equivalog Y Y N L-aspartate oxidase 1.4.3.16 GO:0008734,GO:0009435 2 Bacteria superkingdom 2762 NCBI Protein Cluster (PRK) L-aspartate oxidase L-aspartate oxidase Catalyzes the formation of oxaloacetate from L-aspartate NF004821.0 PRK06176 PRK06176.1 642 642 380 equivalog Y Y N cystathionine gamma-synthase 2.5.1.48 GO:0003824,GO:0019346 2 Bacteria superkingdom 2599 NCBI Protein Cluster (PRK) cystathionine gamma-synthase/cystathionine beta-lyase cystathionine gamma-synthase Catalyzes the formation of cystathionine from L-cysteine and O-succinyl-L-homoserine NF004822.0 PRK06178 PRK06178.1 782 782 571 equivalog Y N N acyl-CoA synthetase 2 Bacteria superkingdom 1025 NCBI Protein Cluster (PRK) acyl-CoA synthetase acyl-CoA synthetase NF004823.0 PRK06179 PRK06179.1 310 310 271 subfamily Y Y N oxidoreductase GO:0016491 2 Bacteria superkingdom 6439 NCBI Protein Cluster (PRK) short chain dehydrogenase oxidoreductase NF004824.0 PRK06180 PRK06180.1 298 298 279 subfamily Y Y N oxidoreductase GO:0016491 2 Bacteria superkingdom 24106 NCBI Protein Cluster (PRK) short chain dehydrogenase oxidoreductase NF004829.0 PRK06183 PRK06183.1-3 390 390 520 subfamily Y Y N bifunctional 3-(3-hydroxy-phenyl)propionate/3-hydroxycinnamic acid hydroxylase 1.14.13.127 GO:0071949 2 Bacteria superkingdom 19576 NCBI Protein Cluster (PRK) 3-(3-hydroxyphenyl)propionate hydroxylase bifunctional 3-(3-hydroxy-phenyl)propionate/3-hydroxycinnamic acid hydroxylase NF004831.0 PRK06183 PRK06183.1-5 546 546 568 equivalog Y Y N bifunctional 3-(3-hydroxy-phenyl)propionate/3-hydroxycinnamic acid hydroxylase 1.14.13.127 2 Bacteria superkingdom 5955 NCBI Protein Cluster (PRK) 3-(3-hydroxyphenyl)propionate hydroxylase bifunctional 3-(3-hydroxy-phenyl)propionate/3-hydroxycinnamic acid hydroxylase NF004832.0 PRK06184 PRK06184.1 476 476 506 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 11665 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004833.1 PRK06185 PRK06185.1-1 488 488 403 subfamily Y Y N FAD-dependent oxidoreductase 2 Bacteria superkingdom 6662 NCBI Protein Cluster (PRK) hypothetical protein FAD-dependent oxidoreductase NF004834.1 PRK06185 PRK06185.1-3 500 500 420 subfamily Y Y N FAD-dependent oxidoreductase 2 Bacteria superkingdom 7512 NCBI Protein Cluster (PRK) hypothetical protein FAD-dependent oxidoreductase NF004836.0 PRK06186 PRK06186.1 219 219 238 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 8207 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004839.0 PRK06189 PRK06189.1 631 631 451 equivalog Y Y N allantoinase 3.5.2.5 2 Bacteria superkingdom 1732 NCBI Protein Cluster (PRK) allantoinase allantoinase NF004840.0 PRK06190 PRK06190.1 253 253 260 equivalog Y Y N enoyl-CoA hydratase 4.2.1.17 GO:0003824 2 Bacteria superkingdom 2400 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF004841.0 PRK06193 PRK06193.1-1 178 178 232 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 152 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004843.0 PRK06194 PRK06194.1 308 308 295 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 4780 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004844.0 PRK06195 PRK06195.1 373 373 309 equivalog Y N N DNA polymerase III subunit epsilon 2 Bacteria superkingdom 386 NCBI Protein Cluster (PRK) DNA polymerase III subunit epsilon DNA polymerase III subunit epsilon NF004847.0 PRK06198 PRK06198.1 240 240 269 subfamily Y Y N oxidoreductase GO:0016491 2 Bacteria superkingdom 5215 NCBI Protein Cluster (PRK) short chain dehydrogenase oxidoreductase NF004848.0 PRK06199 PRK06199.1 362 362 379 subfamily Y Y N tyramine oxidase subunit B 20482587 2 Bacteria superkingdom 2204 NCBI Protein Cluster (PRK) ornithine cyclodeaminase tyramine oxidase subunit B NF004849.1 PRK06200 PRK06200.1 330 330 269 equivalog Y Y N 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate dehydrogenase hcaB 1.3.1.87 GO:0016491 2 Bacteria superkingdom 2652 NCBI Protein Cluster (PRK) 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate dehydrogenase Catalyzes the formation of 3-(2,3-dihydroxylphenyl)propionate from cis-3-(3-carboxyethyl)-3,5-cyclohexadiene-1,2-diol (PP-dihydrodiol) NF004851.0 PRK06202 PRK06202.1 243 243 237 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 2422 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004852.0 PRK06203 PRK06203.1 333 333 407 equivalog Y Y N 3-dehydroquinate synthase 4.2.3.4 2 Bacteria superkingdom 2684 NCBI Protein Cluster (PRK) 3-dehydroquinate synthase 3-dehydroquinate synthase Catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis NF004853.0 PRK06205 PRK06205.1 551 551 404 subfamily Y Y N acetyl-CoA C-acetyltransferase 2 Bacteria superkingdom 7722 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA C-acetyltransferase Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A NF004854.0 PRK06207 PRK06207.1 464 464 405 subfamily Y Y N pyridoxal phosphate-dependent aminotransferase 2.6.1.- 2 Bacteria superkingdom 702 NCBI Protein Cluster (PRK) aspartate aminotransferase pyridoxal phosphate-dependent aminotransferase NF004855.0 PRK06208 PRK06208.1 255 255 274 subfamily Y Y N class II aldolase/adducin family protein 2 Bacteria superkingdom 10257 NCBI Protein Cluster (PRK) hypothetical protein class II aldolase/adducin family protein NF004856.0 PRK06209 PRK06209.1 486 486 450 equivalog Y Y N glutamate-1-semialdehyde 2,1-aminomutase 5.4.3.8 2 Bacteria superkingdom 4496 NCBI Protein Cluster (PRK) glutamate-1-semialdehyde 2,1-aminomutase glutamate-1-semialdehyde 2,1-aminomutase Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway NF004857.0 PRK06210 PRK06210.1 341 341 275 equivalog Y Y N enoyl-CoA hydratase 4.2.1.17 2 Bacteria superkingdom 1520 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF004858.0 PRK06213 PRK06213.1 171 171 230 equivalog Y Y N crotonase/enoyl-CoA hydratase family protein GO:0003824 2 Bacteria superkingdom 3919 NCBI Protein Cluster (PRK) enoyl-CoA hydratase crotonase/enoyl-CoA hydratase family protein NF004859.0 PRK06214 PRK06214.1 432 432 539 equivalog Y Y N sulfite reductase subunit alpha 1.8.1.2 GO:0016491,GO:0051536 2 Bacteria superkingdom 11261 NCBI Protein Cluster (PRK) sulfite reductase sulfite reductase subunit alpha Catalyzes the reduction of sulfite to sulfide, an essential step in the anaerobic sulfate-respiration pathway NF004860.0 PRK06215 PRK06215.1 319 319 238 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 3054 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF004864.0 PRK06224 PRK06224.1-1 261 261 278 equivalog Y Y N citryl-CoA lyase 4.1.3.34 GO:0046912 2 Bacteria superkingdom 2999 NCBI Protein Cluster (PRK) citrate synthase citryl-CoA lyase NF004876.0 PRK06234 PRK06234.1 666 666 400 subfamily Y Y N methionine gamma-lyase 4.4.1.11 2 Bacteria superkingdom 778 NCBI Protein Cluster (PRK) methionine gamma-lyase methionine gamma-lyase Catalyzes the formation of methanethiol and 2-ocobutanoate from L-methionine NF004879.0 PRK06241 PRK06241.1-4 976 976 868 equivalog Y Y N phosphoenolpyruvate synthase ppsA 2.7.9.2 GO:0005524,GO:0016301,GO:0016310 2 Bacteria superkingdom 10340 NCBI Protein Cluster (PRK) phosphoenolpyruvate synthase phosphoenolpyruvate synthase NF004881.0 PRK06241 PRK06241.2-2 883 883 898 equivalog Y Y N phosphoenolpyruvate synthase 2.7.9.2 2 Bacteria superkingdom 680 NCBI Protein Cluster (PRK) phosphoenolpyruvate synthase phosphoenolpyruvate synthase NF004886.0 PRK06247 PRK06247.1 623 623 476 subfamily Y Y N pyruvate kinase 2.7.1.40 2 Bacteria superkingdom 28066 NCBI Protein Cluster (PRK) pyruvate kinase pyruvate kinase Catalyzes the formation of phosphoenolpyruvate from pyruvate NF004887.0 PRK06249 PRK06249.1 360 360 316 equivalog Y Y N putative 2-dehydropantoate 2-reductase 1.1.1.169 GO:0008677,GO:0015940 2 Bacteria superkingdom 3709 NCBI Protein Cluster (PRK) 2-dehydropantoate 2-reductase putative 2-dehydropantoate 2-reductase NF004903.0 PRK06265 PRK06265.1-3 193 193 211 equivalog Y Y N cobalt transporter CbiM cbiM 2 Bacteria superkingdom 550 NCBI Protein Cluster (PRK) cobalt transport protein CbiM cobalt transporter CbiM NF004904.0 PRK06265 PRK06265.1-4 172 172 206 equivalog Y Y N cobalt transporter CbiM cbiM 2 Bacteria superkingdom 780 NCBI Protein Cluster (PRK) cobalt transport protein CbiM cobalt transporter CbiM NF004906.0 PRK06265 PRK06265.2-1 205 205 212 equivalog Y Y N cobalt transporter CbiM cbiM 2 Bacteria superkingdom 250 NCBI Protein Cluster (PRK) cobalt transport protein CbiM cobalt transporter CbiM NF004907.0 PRK06265 PRK06265.2-2 200 200 221 subfamily Y Y N cobalt transporter CbiM cbiM 2 Bacteria superkingdom 80 NCBI Protein Cluster (PRK) cobalt transport protein CbiM cobalt transporter CbiM NF004909.0 PRK06265 PRK06265.2-5 172 172 196 equivalog Y Y N cobalt transporter CbiM cbiM 2 Bacteria superkingdom 573 NCBI Protein Cluster (PRK) cobalt transport protein CbiM cobalt transporter CbiM NF004935.0 PRK06288 PRK06288.1 343 343 270 equivalog Y Y N RNA polymerase sigma factor WhiG whiG GO:0003677,GO:0003700,GO:0003899,GO:0006352,GO:0016987 2 Bacteria superkingdom 3796 NCBI Protein Cluster (PRK) RNA polymerase sigma factor WhiG RNA polymerase sigma factor WhiG Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this sigma factor is involved in the initiation of sporulation and glycogen biosynthesis NF004936.0 PRK06289 PRK06289.1 375 375 405 equivalog Y Y N acetyl-CoA acetyltransferase GO:0016746 2 Bacteria superkingdom 2099 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA acetyltransferase NF004939.0 PRK06292 PRK06292.1-1 435 435 476 equivalog Y Y N dihydrolipoyl dehydrogenase 1.8.1.4 2 Bacteria superkingdom 8413 NCBI Protein Cluster (PRK) dihydrolipoamide dehydrogenase dihydrolipoyl dehydrogenase NF004952.0 PRK06299 PRK06299.1-2 524 524 580 equivalog Y Y N 30S ribosomal protein S1 2 Bacteria superkingdom 19423 NCBI Protein Cluster (PRK) 30S ribosomal protein S1 30S ribosomal protein S1 NF004955.0 PRK06299 PRK06299.1-5 878 878 566 equivalog Y Y N 30S ribosomal protein S1 rpsA GO:0003723,GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 5719 NCBI Protein Cluster (PRK) 30S ribosomal protein S1 30S ribosomal protein S1 NF004970.0 PRK06333 PRK06333.1 525 525 424 subfamily Y Y N beta-ketoacyl-ACP synthase 2.3.1.179 2 Bacteria superkingdom 35932 NCBI Protein Cluster (PRK) 3-oxoacyl-(acyl carrier protein) synthase II beta-ketoacyl-ACP synthase NF004973.0 PRK06342 PRK06342.1 159 159 160 equivalog Y Y N transcription elongation factor GreA greA GO:0003677,GO:0032784,GO:0070063 2 Bacteria superkingdom 2864 NCBI Protein Cluster (PRK) transcription elongation factor regulatory protein transcription elongation factor GreA Activates RNA polymerase to cleave back-tracked RNA during elongational pausing NF004991.0 PRK06370 PRK06370.1-3 620 620 509 subfamily Y Y N FAD-containing oxidoreductase 2 Bacteria superkingdom 1374 NCBI Protein Cluster (PRK) mercuric reductase FAD-containing oxidoreductase NF004992.0 PRK06370 PRK06370.1-4 629 629 459 equivalog Y Y N FAD-containing oxidoreductase GO:0016491,GO:0045454,GO:0050660 2 Bacteria superkingdom 4794 NCBI Protein Cluster (PRK) mercuric reductase FAD-containing oxidoreductase NF005043.0 PRK06458 PRK06458.1-3 533 533 483 equivalog Y Y N hydrogenase 4 subunit F 2 Bacteria superkingdom 1653 NCBI Protein Cluster (PRK) hydrogenase 4 subunit F hydrogenase 4 subunit F NF005061.0 PRK06474 PRK06474.1 121 121 178 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 1314 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005063.0 PRK06476 PRK06476.1 254 254 258 equivalog Y Y N pyrroline-5-carboxylate reductase GO:0004735,GO:0006561 2 Bacteria superkingdom 1524 NCBI Protein Cluster (PRK) pyrroline-5-carboxylate reductase pyrroline-5-carboxylate reductase NF005064.0 PRK06481 PRK06481.1 542 542 506 equivalog Y Y N flavocytochrome c GO:0010181,GO:0016491 2 Bacteria superkingdom 7517 NCBI Protein Cluster (PRK) fumarate reductase flavoprotein subunit flavocytochrome c NF005065.0 PRK06482 PRK06482.1 291 291 276 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 3869 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005068.0 PRK06486 PRK06486.1 269 269 262 equivalog Y Y N aldolase 4.1.2.- 2 Bacteria superkingdom 2789 NCBI Protein Cluster (PRK) hypothetical protein aldolase NF005071.0 PRK06489 PRK06489.1 305 305 362 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 3000 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005072.0 PRK06490 PRK06490.1 339 339 251 equivalog Y Y N glutamine amidotransferase 2 Bacteria superkingdom 2967 NCBI Protein Cluster (PRK) glutamine amidotransferase glutamine amidotransferase Catalyzes the transfer of the ammonia group from glutamine to a new carbon-nitrogen group NF005073.0 PRK06495 PRK06495.1 296 296 257 subfamily Y Y N enoyl-CoA hydratase/isomerase family protein 2 Bacteria superkingdom 1122 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase/isomerase family protein NF005074.0 PRK06498 PRK06498.1 446 446 531 equivalog Y Y N isocitrate lyase 4.1.3.1 GO:0004451,GO:0019752 2 Bacteria superkingdom 7482 NCBI Protein Cluster (PRK) isocitrate lyase isocitrate lyase Catalyzes the reversible formation of glyoxylate and succinate from isocitrate; glyoxylate bypass pathway NF005075.0 PRK06500 PRK06500.1 336 336 249 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 3523 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005077.0 PRK06504 PRK06504.1 590 590 390 subfamily Y Y N acetyl-CoA C-acetyltransferase GO:0016746 2 Bacteria superkingdom 2827 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA C-acetyltransferase Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A NF005078.0 PRK06505 PRK06505.1 446 446 271 equivalog Y Y N enoyl-ACP reductase FabI fabI 1.3.1.9 2 Bacteria superkingdom 2742 NCBI Protein Cluster (PRK) enoyl-(acyl carrier protein) reductase enoyl-ACP reductase FabI NF005085.0 PRK06520 PRK06520.1 313 313 368 subfamily Y Y N 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase 2.1.1.14 GO:0003871,GO:0008270,GO:0009086 2 Bacteria superkingdom 17477 NCBI Protein Cluster (PRK) 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase Catalyzes the formation of tetrahydropteroyl-L-glutamate and methionine from L-homocysteine and 5-methyltetrahydropteroyltri-L-glutamate NF005086.0 PRK06521 PRK06521.1 667 667 669 equivalog Y Y N hydrogenase 4 subunit B hyfB GO:0008137,GO:0042773 2 Bacteria superkingdom 5205 NCBI Protein Cluster (PRK) hydrogenase 4 subunit B hydrogenase 4 subunit B NF005088.0 PRK06522 PRK06522.1-2 371 371 308 subfamily Y Y N 2-dehydropantoate 2-reductase 1.1.1.169 2 Bacteria superkingdom 2832 NCBI Protein Cluster (PRK) 2-dehydropantoate 2-reductase 2-dehydropantoate 2-reductase NF005094.0 PRK06522 PRK06522.2-5 382 382 307 equivalog Y Y N 2-dehydropantoate 2-reductase panE 1.1.1.169 GO:0008677,GO:0015940 2 Bacteria superkingdom 5194 NCBI Protein Cluster (PRK) 2-dehydropantoate 2-reductase 2-dehydropantoate 2-reductase NF005095.0 PRK06523 PRK06523.1 231 231 261 subfamily Y Y N oxidoreductase GO:0016491 2 Bacteria superkingdom 11949 NCBI Protein Cluster (PRK) short chain dehydrogenase oxidoreductase NF005096.0 PRK06524 PRK06524.1 684 684 493 equivalog Y Y N biotin carboxylase GO:0005524,GO:0046872 2 Bacteria superkingdom 1491 NCBI Protein Cluster (PRK) biotin carboxylase-like protein biotin carboxylase NF005098.0 PRK06526 PRK06526.1 296 296 266 subfamily Y N N transposase 2 Bacteria superkingdom 2330 NCBI Protein Cluster (PRK) transposase transposase NF005101.0 PRK06539 PRK06539.1 988 988 822 equivalog Y Y N ribonucleoside-diphosphate reductase subunit alpha 2 Bacteria superkingdom 500 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit alpha ribonucleoside-diphosphate reductase subunit alpha NF005102.0 PRK06541 PRK06541.1 574 574 460 equivalog Y Y N aspartate aminotransferase family protein GO:0008483,GO:0030170 2 Bacteria superkingdom 9638 NCBI Protein Cluster (PRK) hypothetical protein aspartate aminotransferase family protein NF005107.0 PRK06545 PRK06545.1-5 414 414 367 equivalog Y Y N prephenate dehydrogenase 1.3.1.12 2 Bacteria superkingdom 7695 NCBI Protein Cluster (PRK) prephenate dehydrogenase prephenate dehydrogenase NF005111.0 PRK06545 PRK06545.2-3 344 344 371 equivalog Y Y N prephenate dehydrogenase 1.3.1.12 GO:0004665,GO:0006571,GO:0008977 2 Bacteria superkingdom 10666 NCBI Protein Cluster (PRK) prephenate dehydrogenase prephenate dehydrogenase NF005112.0 PRK06545 PRK06545.2-4 294 294 356 subfamily Y Y N prephenate dehydrogenase 2 Bacteria superkingdom 11926 NCBI Protein Cluster (PRK) prephenate dehydrogenase prephenate dehydrogenase NF005114.0 PRK06546 PRK06546.1 893 893 578 equivalog Y Y N pyruvate dehydrogenase 2 Bacteria superkingdom 8437 NCBI Protein Cluster (PRK) pyruvate dehydrogenase pyruvate dehydrogenase Catalyzes the formation of acetate from pyruvate NF005115.0 PRK06547 PRK06547.1 173 173 172 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 2110 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005119.0 PRK06552 PRK06552.1 238 238 213 subfamily Y Y N bifunctional 2-keto-4-hydroxyglutarate aldolase/2-keto-3-deoxy-6-phosphogluconate aldolase 4.1.2.14,4.1.3.16 GO:0016829 2 Bacteria superkingdom 5035 NCBI Protein Cluster (PRK) keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase bifunctional 2-keto-4-hydroxyglutarate aldolase/2-keto-3-deoxy-6-phosphogluconate aldolase Catalyzes the formation of pyruvate and glyoxylate from 4-hydroxy-2-oxoglutarate; or pyruvate and D-glyceraldehyde 3-phosphate from 2-dehydro-3-deoxy-D-glyconate 6-phosphate NF005122.0 PRK06556 PRK06556.1 859 859 960 equivalog Y Y N vitamin B12-dependent ribonucleotide reductase 1.17.4.1 GO:0004748,GO:0006260 2 Bacteria superkingdom 10500 NCBI Protein Cluster (PRK) vitamin B12-dependent ribonucleotide reductase vitamin B12-dependent ribonucleotide reductase Catalyzes the reduction of ribonucleotides to deoxyribonucleotides; the rate-limiting step in dNTP synthesis NF005123.0 PRK06557 PRK06557.1 251 251 223 subfamily Y Y N L-ribulose-5-phosphate 4-epimerase 2 Bacteria superkingdom 5559 NCBI Protein Cluster (PRK) L-ribulose-5-phosphate 4-epimerase L-ribulose-5-phosphate 4-epimerase NF005124.0 PRK06558 PRK06558.1 127 127 159 equivalog Y Y N V-type ATP synthase subunit K 7.1.2.2 2 Bacteria superkingdom 1608 NCBI Protein Cluster (PRK) V-type ATP synthase subunit K V-type ATP synthase subunit K NF005126.0 PRK06563 PRK06563.1 261 261 263 subfamily Y Y N crotonase/enoyl-CoA hydratase family protein 2 Bacteria superkingdom 5559 NCBI Protein Cluster (PRK) enoyl-CoA hydratase crotonase/enoyl-CoA hydratase family protein NF005127.0 PRK06565 PRK06565.1 575 575 570 equivalog Y Y N amidase 3.5.1.4 2 Bacteria superkingdom 7666 NCBI Protein Cluster (PRK) amidase amidase NF005140.0 PRK06589 PRK06589.1 470 470 489 equivalog Y N N putative monovalent cation/H+ antiporter subunit D 2 Bacteria superkingdom 251 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit D putative monovalent cation/H+ antiporter subunit D NF005143.0 PRK06596 PRK06596.1 241 241 285 subfamily Y Y N RNA polymerase factor sigma-32 2.7.7.6 11254138,15470124 2 Bacteria superkingdom 21922 NCBI Protein Cluster (PRK) RNA polymerase factor sigma-32 RNA polymerase factor sigma-32 Binds with the catalytic core of RNA polymerase to produce the holoenzyme; this sigma factor is responsible for the expression of heat shock promoters NF005144.0 PRK06598 PRK06598.1 198 198 369 subfamily Y Y N aspartate-semialdehyde dehydrogenase 1.2.1.11 12071715,12493825,15272161,15288787,8100567,8936306 2 Bacteria superkingdom 16365 NCBI Protein Cluster (PRK) aspartate-semialdehyde dehydrogenase aspartate-semialdehyde dehydrogenase Catalyzes the formation of aspartate semialdehyde from aspartyl phosphate NF005153.0 PRK06635 PRK06635.1-1 585 585 421 equivalog Y Y N aspartate kinase 2.7.2.4 GO:0004072,GO:0008652 2 Bacteria superkingdom 10151 NCBI Protein Cluster (PRK) aspartate kinase aspartate kinase NF005154.0 PRK06635 PRK06635.1-2 376 376 407 equivalog Y Y N aspartate kinase 2.7.2.4 GO:0004072,GO:0009089 2 Bacteria superkingdom 38250 NCBI Protein Cluster (PRK) aspartate kinase aspartate kinase NF005155.0 PRK06635 PRK06635.1-4 346 346 407 equivalog Y Y N aspartate kinase 2.7.2.4 GO:0004072,GO:0009089 2 Bacteria superkingdom 40700 NCBI Protein Cluster (PRK) aspartate kinase aspartate kinase NF005164.0 PRK06638 PRK06638.1-4 154 154 211 equivalog Y Y N NADH-quinone oxidoreductase subunit J 1.6.5.9 GO:0008137 2 Bacteria superkingdom 11567 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit J NADH-quinone oxidoreductase subunit J NF005165.0 PRK06638 PRK06638.1-5 192 192 282 equivalog Y Y N NADH-quinone oxidoreductase subunit J 1.6.5.9 GO:0008137 2 Bacteria superkingdom 10485 NCBI Protein Cluster (PRK) NADH:ubiquinone oxidoreductase subunit J NADH-quinone oxidoreductase subunit J NF005174.0 PRK06649 PRK06649.1 127 127 143 equivalog Y N N V-type ATP synthase subunit K 2 Bacteria superkingdom 282 NCBI Protein Cluster (PRK) V-type ATP synthase subunit K V-type ATP synthase subunit K NF005208.0 PRK06676 PRK06676.1 368 368 391 equivalog Y Y N 30S ribosomal protein S1 rpsA GO:0003676 2 Bacteria superkingdom 22259 NCBI Protein Cluster (PRK) 30S ribosomal protein S1 30S ribosomal protein S1 Involved in binding to the leader sequence of mRNAs and is itself bound to the 30S subunit; autoregulates expression via a C-terminal domain; in most gram negative organisms this protein is composed of 6 repeats of the S1 domain while in gram positive there are 4 repeats; the S1 nucleic acid-binding domain is found associated with other proteins NF005209.0 PRK06680 PRK06680.1 320 320 286 subfamily Y Y N D-amino-acid transaminase 2.6.1.21 GO:0003824 16461714,7592528,9003455 2 Bacteria superkingdom 9700 NCBI Protein Cluster (PRK) D-amino acid aminotransferase D-amino-acid transaminase NF005232.0 PRK06733 PRK06733.1 93 93 151 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 1800 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005235.0 PRK06740 PRK06740.1 442 442 335 equivalog Y Y N histidinol phosphate phosphatase domain-containing protein 2 Bacteria superkingdom 1077 NCBI Protein Cluster (PRK) histidinol-phosphatase histidinol phosphate phosphatase domain-containing protein NF005243.0 PRK06753 PRK06753.1 365 365 374 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 2079 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005244.0 PRK06754 PRK06754.1 281 281 214 equivalog Y Y N methylthioribulose 1-phosphate dehydratase 4.2.1.109 GO:0019509 11545674,12022921,14551435,15102328 2 Bacteria superkingdom 2278 NCBI Protein Cluster (PRK) methylthioribulose-1-phosphate dehydratase methylthioribulose 1-phosphate dehydratase Converts methylthioribulose-1-phosphate into 2,3-diketo-5-methylthiopentyl-1-phosphate; involved in methionine salvage NF005250.0 PRK06761 PRK06761.1 270 270 282 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 1069 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005252.0 PRK06762 PRK06762.1-3 258 258 189 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 356 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005262.0 PRK06765 PRK06765.1 363 363 394 equivalog Y Y N homoserine O-acetyltransferase 2.3.1.31 GO:0009058,GO:0016747 2 Bacteria superkingdom 2187 NCBI Protein Cluster (PRK) homoserine O-acetyltransferase homoserine O-acetyltransferase Catalyzes the formation of O-acetyl -L-homoserine from L-homoserine and acetyl-CoA NF005288.0 PRK06806 PRK06806.1 396 396 281 equivalog Y Y N class II fructose-bisphosphate aldolase 4.1.2.13 GO:0004332,GO:0006096 2 Bacteria superkingdom 895 NCBI Protein Cluster (PRK) fructose-bisphosphate aldolase class II fructose-bisphosphate aldolase NF005291.0 PRK06814 PRK06814.1 1349 1349 1140 equivalog Y Y N acyl-[ACP]--phospholipid O-acyltransferase GO:0016746 2 Bacteria superkingdom 2567 NCBI Protein Cluster (PRK) acylglycerophosphoethanolamine acyltransferase acyl-[ACP]--phospholipid O-acyltransferase NF005293.2 PRK06816 PRK06816.1 450 450 378 subfamily Y Y N StlD/DarB family beta-ketosynthase 2 Bacteria superkingdom 3093 NCBI Protein Cluster (PRK) 3-oxoacyl-(acyl carrier protein) synthase III StlD/DarB family beta-ketosynthase NF005297.0 PRK06824 PRK06824.1 145 145 121 equivalog Y Y N translation initiation factor Sui1 GO:0003743,GO:0006413 2 Bacteria superkingdom 3644 NCBI Protein Cluster (PRK) translation initiation factor Sui1 translation initiation factor Sui1 NF005298.0 PRK06826 PRK06826.1 1260 1260 1151 equivalog Y Y N DNA polymerase III subunit alpha 2.7.7.7 GO:0006260,GO:0008408 2 Bacteria superkingdom 11738 NCBI Protein Cluster (PRK) DNA polymerase III DnaE DNA polymerase III subunit alpha Catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time. Proposed to be responsible for the synthesis of the lagging strand. In the low GC gram positive bacteria this enzyme is less processive and more error prone than its counterpart in other bacteria. NF005299.0 PRK06827 PRK06827.1 327 327 383 subfamily Y N N phosphoribosylpyrophosphate synthetase 2.7.6.1 2 Bacteria superkingdom 2345 NCBI Protein Cluster (PRK) phosphoribosylpyrophosphate synthetase phosphoribosylpyrophosphate synthetase NF005300.0 PRK06828 PRK06828.1 494 494 491 subfamily Y N N amidase 2 Bacteria superkingdom 4485 NCBI Protein Cluster (PRK) amidase amidase NF005301.0 PRK06830 PRK06830.1 400 400 445 equivalog Y Y N ATP-dependent 6-phosphofructokinase 2.7.1.11 2 Bacteria superkingdom 1816 NCBI Protein Cluster (PRK) diphosphate--fructose-6-phosphate 1-phosphotransferase ATP-dependent 6-phosphofructokinase NF005302.0 PRK06833 PRK06833.1 264 264 214 equivalog Y Y N L-fuculose-phosphate aldolase 4.1.2.17 2 Bacteria superkingdom 1373 NCBI Protein Cluster (PRK) L-fuculose phosphate aldolase L-fuculose-phosphate aldolase Catalyzes the formation of glycerone phosphate and (S)-lactaldehyde from L-fuculose 1-phosphate NF005303.0 PRK06834 PRK06834.1 625 625 488 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 2445 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005304.0 PRK06835 PRK06835.1 215 215 330 equivalog Y Y N ATP-binding protein GO:0005524 2 Bacteria superkingdom 3167 NCBI Protein Cluster (PRK) DNA replication protein DnaC ATP-binding protein NF005305.0 PRK06836 PRK06836.1 376 376 396 equivalog Y Y N pyridoxal phosphate-dependent aminotransferase 2.6.1.- GO:0003824,GO:0009058,GO:0030170 2 Bacteria superkingdom 5184 NCBI Protein Cluster (PRK) aspartate aminotransferase pyridoxal phosphate-dependent aminotransferase NF005309.0 PRK06841 PRK06841.1 286 286 255 subfamily Y Y N GolD/DthD family dehydrogenase 1.1.1.- GO:0016491 22773791,26560079 2 Bacteria superkingdom 3134 NCBI Protein Cluster (PRK) short chain dehydrogenase GolD/DthD family dehydrogenase NF005310.0 PRK06842 PRK06842.1 238 238 185 equivalog Y Y N Fe-S-containing hydro-lyase GO:0016836 2 Bacteria superkingdom 3793 NCBI Protein Cluster (PRK) fumarate hydratase Fe-S-containing hydro-lyase NF005312.0 PRK06846 PRK06846.1 447 447 412 subfamily Y Y N amidohydrolase GO:0016810 2 Bacteria superkingdom 10341 NCBI Protein Cluster (PRK) putative deaminase amidohydrolase NF005313.0 PRK06847 PRK06847.1 372 372 375 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 7626 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005315.0 PRK06849 PRK06849.1 406 406 389 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 1611 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005322.0 PRK06853 PRK06853.1-2 237 237 197 equivalog Y Y N indolepyruvate oxidoreductase subunit beta 2 Bacteria superkingdom 759 NCBI Protein Cluster (PRK) indolepyruvate oxidoreductase subunit beta indolepyruvate oxidoreductase subunit beta NF005363.0 PRK06876 PRK06876.1 71 71 80 equivalog Y Y N F0F1 ATP synthase subunit C atpE 7.1.2.2 GO:0015078,GO:0015986 2 Bacteria superkingdom 5923 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit C F0F1 ATP synthase subunit C Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit C is part of the membrane proton channel F0 NF005372.1 PRK06914 PRK06914.1 320 320 279 subfamily Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 3204 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005373.0 PRK06915 PRK06915.1 428 428 422 equivalog Y Y N peptidase GO:0016787 2 Bacteria superkingdom 2714 NCBI Protein Cluster (PRK) acetylornithine deacetylase peptidase NF005375.0 PRK06917 PRK06917.1 535 535 448 equivalog Y Y N aspartate aminotransferase family protein GO:0008483,GO:0030170 2 Bacteria superkingdom 2494 NCBI Protein Cluster (PRK) hypothetical protein aspartate aminotransferase family protein NF005376.0 PRK06918 PRK06918.1 676 676 451 equivalog Y Y N 4-aminobutyrate--2-oxoglutarate transaminase gabT 2.6.1.19 12123465 2 Bacteria superkingdom 2590 NCBI Protein Cluster (PRK) 4-aminobutyrate aminotransferase 4-aminobutyrate--2-oxoglutarate transaminase Catalyzes the formation of succinate semialdehyde and glutamate from 4-aminobutanoate and 2-oxoglutarate NF005378.0 PRK06921 PRK06921.1 207 207 266 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 1537 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005380.0 PRK06923 PRK06923.1 486 486 399 equivalog Y Y N isochorismate synthase DhbC dhbC 2 Bacteria superkingdom 3413 NCBI Protein Cluster (PRK) isochorismate synthase DhbC isochorismate synthase DhbC Synthesizes isochorismate from chorismate as part of the biosynthesis of the siderophore 2,3-dihydroxybenzoate NF005381.0 PRK06924 PRK06924.1 258 258 251 equivalog Y Y N (S)-benzoin forming benzil reductase 1.1.1.320 GO:0016491 2 Bacteria superkingdom 2358 NCBI Protein Cluster (PRK) short chain dehydrogenase (S)-benzoin forming benzil reductase NF005385.0 PRK06930 PRK06930.1 136 136 170 subfamily Y N N positive control sigma-like factor 2 Bacteria superkingdom 1673 NCBI Protein Cluster (PRK) positive control sigma-like factor positive control sigma-like factor NF005389.0 PRK06934 PRK06934.1 172 172 221 equivalog Y Y N flavodoxin 2 Bacteria superkingdom 960 NCBI Protein Cluster (PRK) flavodoxin flavodoxin An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group NF005390.0 PRK06935 PRK06935.1 369 369 258 equivalog Y Y N 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD kduD 1.1.1.127 24509771,27028675 2 Bacteria superkingdom 1793 NCBI Protein Cluster (PRK) 2-deoxy-D-gluconate 3-dehydrogenase 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD NF005400.0 PRK06947 PRK06947.1 367 367 252 equivalog Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 1466 NCBI Protein Cluster (PRK) glucose-1-dehydrogenase SDR family oxidoreductase NF005413.0 PRK06986 PRK06986.1 201 201 241 subfamily Y Y N RNA polymerase sigma factor FliA fliA 2 Bacteria superkingdom 22029 NCBI Protein Cluster (PRK) flagellar biosynthesis sigma factor RNA polymerase sigma factor FliA Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this sigma factor directs late flagellar biosynthesis genes NF005414.0 PRK06988 PRK06988.1 316 316 311 equivalog Y Y N formyltransferase GO:0016742 2 Bacteria superkingdom 10573 NCBI Protein Cluster (PRK) putative formyltransferase formyltransferase NF005415.0 PRK06991 PRK06991.1 281 281 284 equivalog Y Y N electron transport complex subunit RsxB rsxB GO:0009055,GO:0022900,GO:0051536 2 Bacteria superkingdom 3695 NCBI Protein Cluster (PRK) ferredoxin electron transport complex subunit RsxB NF005426.0 PRK07008 PRK07008.1 822 822 545 equivalog Y Y N 3-(methylthio)propionyl-CoA ligase GO:0016874 2 Bacteria superkingdom 4701 NCBI Protein Cluster (PRK) long-chain-fatty-acid--CoA ligase 3-(methylthio)propionyl-CoA ligase NF005436.0 PRK07023 PRK07023.1 292 292 248 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 2077 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005440.0 PRK07027 PRK07027.1-4 395 395 257 equivalog Y N N cobalamin biosynthesis protein CbiG 2 Bacteria superkingdom 270 NCBI Protein Cluster (PRK) cobalamin biosynthesis protein CbiG cobalamin biosynthesis protein CbiG NF005447.0 PRK07036 PRK07036.1 618 618 468 equivalog Y Y N aminotransferase 2 Bacteria superkingdom 2865 NCBI Protein Cluster (PRK) hypothetical protein aminotransferase NF005449.0 PRK07041 PRK07041.1 257 257 240 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 3646 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005450.0 PRK07042 PRK07042.1 458 458 464 equivalog Y Y N amidase 3.5.1.4 GO:0003824 2 Bacteria superkingdom 5405 NCBI Protein Cluster (PRK) amidase amidase NF005451.0 PRK07044 PRK07044.1 207 207 256 subfamily Y N N aldolase II superfamily protein 2 Bacteria superkingdom 19930 NCBI Protein Cluster (PRK) aldolase II superfamily protein aldolase II superfamily protein NF005453.0 PRK07046 PRK07046.1 425 425 453 subfamily Y Y N transaminase GO:0008483,GO:0030170 2 Bacteria superkingdom 6137 NCBI Protein Cluster (PRK) aminotransferase transaminase NF005455.0 PRK07049 PRK07049.1 504 504 427 equivalog Y Y N cystathionine gamma-synthase family protein GO:0019346,GO:0030170 2 Bacteria superkingdom 4922 NCBI Protein Cluster (PRK) methionine gamma-lyase cystathionine gamma-synthase family protein NF005458.0 PRK07053 PRK07053.1 250 250 234 equivalog Y Y N glutamine amidotransferase 2 Bacteria superkingdom 5630 NCBI Protein Cluster (PRK) glutamine amidotransferase glutamine amidotransferase Catalyzes the transfer of the ammonia group from glutamine to a new carbon-nitrogen group NF005460.0 PRK07056 PRK07056.1 447 447 457 subfamily Y Y N amidase GO:0003824 2 Bacteria superkingdom 7525 NCBI Protein Cluster (PRK) amidase amidase NF005468.0 PRK07062 PRK07062.1 266 266 265 equivalog Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 4838 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005470.0 PRK07064 PRK07064.1 495 495 552 equivalog Y Y N thiamine pyrophosphate-binding protein GO:0030976 2 Bacteria superkingdom 7064 NCBI Protein Cluster (PRK) hypothetical protein thiamine pyrophosphate-binding protein NF005471.0 PRK07066 PRK07066.1 414 414 321 equivalog Y Y N L-carnitine dehydrogenase 1.1.1.108 GO:0006631,GO:0016616,GO:0070403 2 Bacteria superkingdom 3642 NCBI Protein Cluster (PRK) 3-hydroxybutyryl-CoA dehydrogenase L-carnitine dehydrogenase Converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA NF005472.0 PRK07067 PRK07067.1 338 338 257 equivalog Y Y N L-iditol 2-dehydrogenase 1.1.1.14 GO:0016491 2 Bacteria superkingdom 5253 NCBI Protein Cluster (PRK) sorbitol dehydrogenase L-iditol 2-dehydrogenase NF005473.0 PRK07069 PRK07069.1 339 339 262 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 1466 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005475.0 PRK07075 PRK07075.1 126 126 105 equivalog Y Y N isochorismate lyase 4.2.99.21 2 Bacteria superkingdom 1052 NCBI Protein Cluster (PRK) isochorismate-pyruvate lyase isochorismate lyase NF005477.0 PRK07078 PRK07078.1 1014 1014 759 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 568 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005478.0 PRK07079 PRK07079.1 330 330 469 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 7716 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005479.0 PRK07080 PRK07080.1 357 357 318 equivalog Y Y N amino acid--[acyl-carrier-protein] ligase 6.2.1.n2 2 Bacteria superkingdom 3263 NCBI Protein Cluster (PRK) hypothetical protein amino acid--[acyl-carrier-protein] ligase NF005480.0 PRK07081 PRK07081.1 72 72 83 equivalog Y Y N acyl carrier protein 2 Bacteria superkingdom 1891 NCBI Protein Cluster (PRK) acyl carrier protein acyl carrier protein NF005481.0 PRK07084 PRK07084.1 511 511 324 equivalog Y Y N class II fructose-bisphosphate aldolase GO:0004332,GO:0006096 2 Bacteria superkingdom 1361 NCBI Protein Cluster (PRK) fructose-bisphosphate aldolase class II fructose-bisphosphate aldolase Catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate NF005482.0 PRK07085 PRK07085.1 446 446 558 subfamily Y Y N diphosphate--fructose-6-phosphate 1-phosphotransferase 2.7.1.90 2 Bacteria superkingdom 2157 NCBI Protein Cluster (PRK) diphosphate--fructose-6-phosphate 1-phosphotransferase diphosphate--fructose-6-phosphate 1-phosphotransferase Catalyzes the formation of fructose 1,6-bisphosphate from fructose 6-phosphate and diphosphate NF005484.0 PRK07090 PRK07090.1 261 261 260 equivalog Y Y N aldolase 4.1.2.- 2 Bacteria superkingdom 3930 NCBI Protein Cluster (PRK) class II aldolase/adducin domain protein aldolase NF005485.1 PRK07092 PRK07092.1 493 493 523 equivalog Y Y N benzoylformate decarboxylase mdlC 4.1.1.7 GO:0000287,GO:0030976 12590569 2 Bacteria superkingdom 8264 NCBI Protein Cluster (PRK) benzoylformate decarboxylase benzoylformate decarboxylase Catalyzes the formation of benzaldehyde from benzoylformate NF005486.0 PRK07093 PRK07093.1 275 275 323 equivalog Y Y N aminodeoxychorismate synthase component I 2.6.1.85 GO:0009058 2 Bacteria superkingdom 4201 NCBI Protein Cluster (PRK) para-aminobenzoate synthase component I aminodeoxychorismate synthase component I Catalyzes the formation of 4-amino-4-deoxychorismate from chorismate and glutamine in para-aminobenzoate synthesis NF005488.0 PRK07097 PRK07097.1 369 369 266 equivalog Y Y N gluconate 5-dehydrogenase 1.1.1.69 GO:0016491 2 Bacteria superkingdom 4365 NCBI Protein Cluster (PRK) gluconate 5-dehydrogenase gluconate 5-dehydrogenase Involved in the nonphosphorylative, ketogenic oxidation of glucose and oxidizes gluconate to 5-ketogluconate NF005489.0 PRK07102 PRK07102.1 267 267 243 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 3284 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005490.0 PRK07103 PRK07103.1 445 445 414 equivalog Y N N polyketide beta-ketoacyl:acyl carrier protein synthase 2 Bacteria superkingdom 1232 NCBI Protein Cluster (PRK) polyketide beta-ketoacyl:acyl carrier protein synthase polyketide beta-ketoacyl:acyl carrier protein synthase NF005492.0 PRK07106 PRK07106.1 415 415 390 equivalog Y Y N phosphoribosylaminoimidazolecarboxamide formyltransferase 2.1.2.3 GO:0003937,GO:0004643,GO:0006164 2 Bacteria superkingdom 4530 NCBI Protein Cluster (PRK) 5-aminoimidazole-4-carboxamide ribonucleotide transformylase phosphoribosylaminoimidazolecarboxamide formyltransferase NF005493.0 PRK07107 PRK07107.1 585 585 502 equivalog Y Y N IMP dehydrogenase 1.1.1.205 GO:0003938 2 Bacteria superkingdom 3309 NCBI Protein Cluster (PRK) inosine 5-monophosphate dehydrogenase IMP dehydrogenase Catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate NF005494.0 PRK07108 PRK07108.1 615 615 392 equivalog Y Y N acetyl-CoA C-acyltransferase 2.3.1.16 GO:0016747 2 Bacteria superkingdom 4195 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA C-acyltransferase NF005496.0 PRK07110 PRK07110.1 215 215 249 domain Y Y N polyketide synthase GO:0006633,GO:0016746 2 Bacteria superkingdom 2016 NCBI Protein Cluster (PRK) polyketide biosynthesis enoyl-CoA hydratase polyketide synthase NF005497.0 PRK07111 PRK07111.1 764 764 746 equivalog Y Y N anaerobic ribonucleoside triphosphate reductase 1.17.4.2 GO:0006260,GO:0008998 2 Bacteria superkingdom 4493 NCBI Protein Cluster (PRK) anaerobic ribonucleoside triphosphate reductase anaerobic ribonucleoside triphosphate reductase Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates NF005498.0 PRK07112 PRK07112.1 250 250 258 equivalog Y Y N enoyl-CoA hydratase/isomerase 4.2.1.17 2 Bacteria superkingdom 1009 NCBI Protein Cluster (PRK) polyketide biosynthesis enoyl-CoA hydratase enoyl-CoA hydratase/isomerase NF005500.0 PRK07115 PRK07115.1 264 264 261 equivalog Y Y N AMP nucleosidase 3.2.2.4 GO:0008714,GO:0009116,GO:0044209 2 Bacteria superkingdom 2624 NCBI Protein Cluster (PRK) AMP nucleosidase AMP nucleosidase Catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate using water as the nucleophile NF005502.0 PRK07117 PRK07117.1 79 79 82 equivalog Y Y N acyl carrier protein 2 Bacteria superkingdom 576 NCBI Protein Cluster (PRK) acyl carrier protein acyl carrier protein NF005503.0 PRK07118 PRK07118.1-2 252 252 292 equivalog Y Y N RnfABCDGE type electron transport complex subunit B rnfB 2 Bacteria superkingdom 704 NCBI Protein Cluster (PRK) ferredoxin RnfABCDGE type electron transport complex subunit B NF005508.0 PRK07121 PRK07121.1-1 537 537 497 equivalog Y Y N FAD-binding protein 2 Bacteria superkingdom 1535 NCBI Protein Cluster (PRK) hypothetical protein FAD-binding protein NF005510.0 PRK07121 PRK07121.1-3 481 481 492 subfamily Y Y N FAD-binding protein 2 Bacteria superkingdom 4562 NCBI Protein Cluster (PRK) hypothetical protein FAD-binding protein NF005511.0 PRK07121 PRK07121.1-4 466 466 553 equivalog Y Y N FAD-binding protein 2 Bacteria superkingdom 2532 NCBI Protein Cluster (PRK) hypothetical protein FAD-binding protein NF005513.0 PRK07121 PRK07121.1-6 608 608 533 equivalog Y Y N FAD-binding protein 2 Bacteria superkingdom 158 NCBI Protein Cluster (PRK) hypothetical protein FAD-binding protein NF005519.0 PRK07152 PRK07152.1 315 315 361 equivalog Y Y N nicotinate-nucleotide adenylyltransferase 2.7.7.18 2 Bacteria superkingdom 896 NCBI Protein Cluster (PRK) putative nicotinate-nucleotide adenylyltransferase nicotinate-nucleotide adenylyltransferase NF005526.0 PRK07179 PRK07179.1 428 428 407 equivalog Y Y N alpha-hydroxyketone-type quorum-sensing autoinducer synthase cqsA GO:0030170 15466044,18004304,18411263,31686391 2 Bacteria superkingdom 2493 NCBI Protein Cluster (PRK) hypothetical protein alpha-hydroxyketone-type quorum-sensing autoinducer synthase The PLP-dependent enzymes CAI-1 synthase from Vibrio cholerae and LAI-1 synthase from Legionella pneumophila produce alpha-hydroxyketone family quorum-sensing autoinducers. These autoinducers differ from the N-acyl-homoserine lactones of the AI-1 family, and are distinct enough that the two quorum-sensing systems can operate independently in the same organism. CqsA in V. cholerae (Cholerae Quorum-Sensing Autoinducer synthase produces (S)-3-hydroxytridecan-4-one, while LqsA in Legionella produces 3-hydroxypentadecan-4-one. NF005529.0 PRK07188 PRK07188.1 378 378 358 equivalog Y Y N nicotinate phosphoribosyltransferase 6.3.4.21 2 Bacteria superkingdom 1673 NCBI Protein Cluster (PRK) nicotinate phosphoribosyltransferase nicotinate phosphoribosyltransferase Catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate NF005530.0 PRK07189 PRK07189.1 228 228 303 equivalog Y Y N biotin-independent malonate decarboxylase subunit beta 4.1.1.88 GO:0003989,GO:0005975,GO:0006633,GO:0009317,GO:0016831 10339824,10561613 2 Bacteria superkingdom 10292 NCBI Protein Cluster (PRK) malonate decarboxylase subunit beta biotin-independent malonate decarboxylase subunit beta NF005536.0 PRK07198 PRK07198.1 403 403 419 equivalog Y Y N GTP cyclohydrolase II 3.5.4.25 GO:0003935 2 Bacteria superkingdom 2325 NCBI Protein Cluster (PRK) hypothetical protein GTP cyclohydrolase II NF005537.0 PRK07199 PRK07199.1 322 322 301 subfamily Y Y N ribose-phosphate diphosphokinase 2.7.6.1 2 Bacteria superkingdom 2989 NCBI Protein Cluster (PRK) phosphoribosylpyrophosphate synthetase ribose-phosphate diphosphokinase NF005538.0 PRK07200 PRK07200.1 453 453 396 equivalog Y Y N knotted carbamoyltransferase YgeW ygeW 2.1.3.- 2 Bacteria superkingdom 2628 NCBI Protein Cluster (PRK) aspartate/ornithine carbamoyltransferase family protein knotted carbamoyltransferase YgeW NF005539.0 PRK07201 PRK07201.1 549 549 657 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 4814 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005540.0 PRK07203 PRK07203.1 444 444 444 equivalog Y Y N putative aminohydrolase SsnA ssnA GO:0016810 2 Bacteria superkingdom 4782 NCBI Protein Cluster (PRK) putative chlorohydrolase/aminohydrolase putative aminohydrolase SsnA NF005541.0 PRK07204 PRK07204.1 402 402 329 equivalog Y Y N beta-ketoacyl-ACP synthase III 2 Bacteria superkingdom 789 NCBI Protein Cluster (PRK) 3-oxoacyl-(acyl carrier protein) synthase III beta-ketoacyl-ACP synthase III NF005547.0 PRK07208 PRK07208.1-3 380 380 465 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 2541 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005564.0 PRK07234 PRK07234.1-4 439 439 478 subfamily Y N N putative monovalent cation/H+ antiporter subunit D 2 Bacteria superkingdom 790 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit D putative monovalent cation/H+ antiporter subunit D NF005567.0 PRK07238 PRK07238.1 326 326 378 equivalog Y Y N bifunctional RNase H/acid phosphatase GO:0003676,GO:0004523 2 Bacteria superkingdom 12565 NCBI Protein Cluster (PRK) bifunctional RNase H/acid phosphatase bifunctional RNase H/acid phosphatase NF005568.0 PRK07239 PRK07239.1 273 273 381 equivalog Y Y N uroporphyrinogen-III synthase 4.2.1.75 GO:0004852,GO:0006780 2 Bacteria superkingdom 12733 NCBI Protein Cluster (PRK) bifunctional uroporphyrinogen-III synthetase/response regulator domain protein uroporphyrinogen-III synthase Catalyzes the formation of uroporphyrinogen-III from hydroxymethylbilane NF005572.0 PRK07251 PRK07251.1 537 537 438 equivalog Y Y N FAD-containing oxidoreductase GO:0016668,GO:0045454,GO:0050660 2 Bacteria superkingdom 4837 NCBI Protein Cluster (PRK) pyridine nucleotide-disulfide oxidoreductase FAD-containing oxidoreductase NF005585.0 PRK07283 PRK07283.1 107 107 100 equivalog Y Y N YlxQ-related RNA-binding protein 2 Bacteria superkingdom 1386 NCBI Protein Cluster (PRK) hypothetical protein YlxQ-related RNA-binding protein NF005591.0 PRK07318 PRK07318.1 435 435 466 equivalog Y Y N dipeptidase PepV pepV 3.4.13.- GO:0008270,GO:0016805 12176387,15664976,16962986,9171382 2 Bacteria superkingdom 13618 NCBI Protein Cluster (PRK) dipeptidase PepV dipeptidase PepV Divalent metal ion-dependent extracellular dipeptidase; able to hydrolyze a broad range of dipeptides but no tri-, tetra-, or larger oligopeptides NF005593.0 PRK07324 PRK07324.1 476 476 373 equivalog Y Y N aminotransferase GO:0003824,GO:0009058,GO:0030170 2 Bacteria superkingdom 3690 NCBI Protein Cluster (PRK) transaminase aminotransferase NF005594.0 PRK07326 PRK07326.1 271 271 237 equivalog Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 2069 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005595.0 PRK07327 PRK07327.1 292 292 271 subfamily Y Y N enoyl-CoA hydratase/isomerase family protein 2 Bacteria superkingdom 4332 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase/isomerase family protein NF005596.0 PRK07328 PRK07328.1 202 202 269 subfamily Y N N histidinol-phosphatase 3.1.3.15 2 Bacteria superkingdom 5882 NCBI Protein Cluster (PRK) histidinol-phosphatase histidinol-phosphatase NF005597.0 PRK07329 PRK07329.1 303 303 257 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 1069 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005600.0 PRK07334 PRK07334.1 496 496 408 equivalog Y Y N threonine ammonia-lyase 4.3.1.19 2 Bacteria superkingdom 5521 NCBI Protein Cluster (PRK) threonine dehydratase threonine ammonia-lyase Catalyzes the formation of 2-oxobutanoate from L-threonine NF005601.0 PRK07337 PRK07337.1 496 496 394 equivalog Y Y N pyridoxal phosphate-dependent aminotransferase 2.6.1.- GO:0003824,GO:0009058,GO:0030170 2 Bacteria superkingdom 6732 NCBI Protein Cluster (PRK) aminotransferase pyridoxal phosphate-dependent aminotransferase NF005602.0 PRK07338 PRK07338.1 357 357 409 equivalog Y Y N hydrolase GO:0016787 2 Bacteria superkingdom 2564 NCBI Protein Cluster (PRK) hypothetical protein hydrolase NF005603.0 PRK07340 PRK07340.1 266 266 307 equivalog Y Y N delta(1)-pyrroline-2-carboxylate reductase family protein 2 Bacteria superkingdom 2955 NCBI Protein Cluster (PRK) ornithine cyclodeaminase delta(1)-pyrroline-2-carboxylate reductase family protein NF005610.0 PRK07362 PRK07362.1 585 585 474 equivalog Y Y N NADP-dependent isocitrate dehydrogenase 2 Bacteria superkingdom 1065 NCBI Protein Cluster (PRK) isocitrate dehydrogenase NADP-dependent isocitrate dehydrogenase Catalyzes the formation of 2-oxoglutarate from isocitrate NF005613.0 PRK07366 PRK07366.1 486 486 391 equivalog Y Y N LL-diaminopimelate aminotransferase 2.6.1.83 2 Bacteria superkingdom 875 NCBI Protein Cluster (PRK) succinyldiaminopimelate transaminase LL-diaminopimelate aminotransferase NF005620.0 PRK07375 PRK07375.1-5 91 91 113 equivalog Y N N putative monovalent cation/H+ antiporter subunit C 2 Bacteria superkingdom 547 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit C putative monovalent cation/H+ antiporter subunit C NF005628.0 PRK07377 PRK07377.1-4 151 151 195 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 528 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005630.0 PRK07377 PRK07377.1-6 149 149 187 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 533 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005637.0 PRK07396 PRK07396.1 380 380 273 equivalog Y Y N 1,4-dihydroxy-2-naphthoyl-CoA synthase menB 4.1.3.36 GO:0008935,GO:0009234 2 Bacteria superkingdom 11490 NCBI Protein Cluster (PRK) dihydroxynaphthoic acid synthetase 1,4-dihydroxy-2-naphthoyl-CoA synthase Catalyzes the formation of 1,4-dihydroxy-2-naphthoate from O-succinylbenzoyl-CoA NF005656.0 PRK07431 PRK07431.1 657 657 587 equivalog Y Y N aspartate kinase 2.7.2.4 2 Bacteria superkingdom 1309 NCBI Protein Cluster (PRK) aspartate kinase aspartate kinase Catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP NF005657.0 PRK07432 PRK07432.1 453 453 291 equivalog Y Y N S-methyl-5'-thioadenosine phosphorylase 2.4.2.28 2 Bacteria superkingdom 848 NCBI Protein Cluster (PRK) 5'-methylthioadenosine phosphorylase S-methyl-5'-thioadenosine phosphorylase Catalyzes the reversible phosphorolysis of 5'-deoxy-5'- methylthioadenosine (MTA) to adenine and 5-methylthio-D-ribose-1- phosphate NF005660.0 PRK07445 PRK07445.1-2 525 525 397 equivalog Y N N O-succinylbenzoic acid--CoA ligase 2 Bacteria superkingdom 43 NCBI Protein Cluster (PRK) O-succinylbenzoic acid--CoA ligase O-succinylbenzoic acid--CoA ligase NF005676.0 PRK07470 PRK07470.1 774 774 544 equivalog Y Y N acyl-CoA synthetase 2 Bacteria superkingdom 2468 NCBI Protein Cluster (PRK) acyl-CoA synthetase acyl-CoA synthetase NF005677.0 PRK07471 PRK07471.1 252 252 366 equivalog Y Y N DNA polymerase III subunit delta' 2.7.7.7 2 Bacteria superkingdom 7252 NCBI Protein Cluster (PRK) DNA polymerase III subunit delta' DNA polymerase III subunit delta' Catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA NF005680.0 PRK07476 PRK07476.1 413 413 326 equivalog Y Y N hydroxyectoine utilization dehydratase EutB eutB 2 Bacteria superkingdom 4184 NCBI Protein Cluster (PRK) threonine dehydratase hydroxyectoine utilization dehydratase EutB NF005682.0 PRK07480 PRK07480.1 510 510 459 subfamily Y Y N aminotransferase GO:0008483,GO:0030170 2 Bacteria superkingdom 16846 NCBI Protein Cluster (PRK) putative aminotransferase aminotransferase NF005683.0 PRK07481 PRK07481.1 575 575 453 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 2978 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005684.0 PRK07482 PRK07482.1 687 687 464 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 6204 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005685.0 PRK07483 PRK07483.1 485 485 444 equivalog Y Y N aspartate aminotransferase family protein 2 Bacteria superkingdom 8494 NCBI Protein Cluster (PRK) hypothetical protein aspartate aminotransferase family protein NF005686.0 PRK07486 PRK07486.1 465 465 486 subfamily Y Y N amidase GO:0003824 2 Bacteria superkingdom 9720 NCBI Protein Cluster (PRK) amidase amidase NF005687.0 PRK07487 PRK07487.1 428 428 468 subfamily Y Y N amidase GO:0003824 2 Bacteria superkingdom 6319 NCBI Protein Cluster (PRK) amidase amidase NF005688.0 PRK07488 PRK07488.1 532 532 474 equivalog Y Y N indoleacetamide hydrolase iaaH 2 Bacteria superkingdom 2701 NCBI Protein Cluster (PRK) indole acetimide hydrolase indoleacetamide hydrolase Catalyzes the formation of indole-3-acetic acid from indole-3-acetamide NF005689.0 PRK07490 PRK07490.1 260 260 248 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 3205 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005691.0 PRK07494 PRK07494.1 459 459 404 equivalog Y Y N UbiH/UbiF family hydroxylase 2 Bacteria superkingdom 5177 NCBI Protein Cluster (PRK) 2-octaprenyl-6-methoxyphenyl hydroxylase UbiH/UbiF family hydroxylase NF005693.0 PRK07500 PRK07500.1 315 315 289 equivalog Y Y N RNA polymerase factor sigma-32 2.7.7.6 GO:0003700,GO:0006352 11254138,15470124 2 Bacteria superkingdom 3276 NCBI Protein Cluster (PRK) RNA polymerase factor sigma-32 RNA polymerase factor sigma-32 Binds with the catalytic core of RNA polymerase to produce the holoenzyme; this sigma factor is responsible for the expression of heat shock promoters NF005694.0 PRK07502 PRK07502.1 409 409 310 equivalog Y Y N prephenate/arogenate dehydrogenase family protein 2 Bacteria superkingdom 7310 NCBI Protein Cluster (PRK) cyclohexadienyl dehydrogenase prephenate/arogenate dehydrogenase family protein NF005697.0 PRK07505 PRK07505.1 342 342 405 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 3003 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005699.0 PRK07509 PRK07509.1 249 249 267 equivalog Y Y N crotonase/enoyl-CoA hydratase family protein GO:0003824 2 Bacteria superkingdom 8869 NCBI Protein Cluster (PRK) enoyl-CoA hydratase crotonase/enoyl-CoA hydratase family protein NF005700.0 PRK07511 PRK07511.1 274 274 260 subfamily Y Y N enoyl-CoA hydratase family protein GO:0003824 2 Bacteria superkingdom 3276 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase family protein NF005701.0 PRK07512 PRK07512.1 528 528 516 equivalog Y Y N L-aspartate oxidase 1.4.3.16 GO:0008734,GO:0009435 2 Bacteria superkingdom 7728 NCBI Protein Cluster (PRK) L-aspartate oxidase L-aspartate oxidase Catalyzes the formation of oxaloacetate from L-aspartate NF005702.0 PRK07514 PRK07514.1 558 558 506 subfamily Y N N malonyl-CoA synthase 2 Bacteria superkingdom 8726 NCBI Protein Cluster (PRK) malonyl-CoA synthase malonyl-CoA synthase NF005703.0 PRK07515 PRK07515.1 304 304 373 equivalog Y Y N beta-ketoacyl-ACP synthase III GO:0004315,GO:0006633 2 Bacteria superkingdom 9687 NCBI Protein Cluster (PRK) 3-oxoacyl-(acyl carrier protein) synthase III beta-ketoacyl-ACP synthase III NF005704.0 PRK07516 PRK07516.1 412 412 389 subfamily Y Y N thiolase domain-containing protein 2 Bacteria superkingdom 5019 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase thiolase domain-containing protein NF005710.0 PRK07522 PRK07522.1 412 412 391 subfamily Y Y N acetylornithine deacetylase 3.5.1.16 2 Bacteria superkingdom 19414 NCBI Protein Cluster (PRK) acetylornithine deacetylase acetylornithine deacetylase Catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine NF005711.0 PRK07523 PRK07523.1 413 413 255 subfamily Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 2439 NCBI Protein Cluster (PRK) gluconate 5-dehydrogenase SDR family oxidoreductase NF005714.0 PRK07529 PRK07529.1 632 632 640 subfamily Y Y N acyl-CoA synthetase 2 Bacteria superkingdom 6767 NCBI Protein Cluster (PRK) AMP-binding domain protein acyl-CoA synthetase NF005715.0 PRK07530 PRK07530.1 420 420 292 equivalog Y Y N 3-hydroxybutyryl-CoA dehydrogenase 1.1.1.157 GO:0006631,GO:0016616,GO:0070403 2 Bacteria superkingdom 7392 NCBI Protein Cluster (PRK) 3-hydroxybutyryl-CoA dehydrogenase 3-hydroxybutyryl-CoA dehydrogenase Converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA NF005718.0 PRK07534 PRK07534.1 338 338 337 equivalog Y Y N betaine--homocysteine S-methyltransferase bmt 2.1.1.5 17015658 2 Bacteria superkingdom 3003 NCBI Protein Cluster (PRK) methionine synthase I betaine--homocysteine S-methyltransferase Like its methionine synthase, betaine--homocysteine S-methyltransferase can make methionine from homocysteine by transferring a methyl group. However, it uses glycine-betaine as the methyl donor. This betaine--homocysteine S-methyltransferase is homologous to eukaryotic enzymes, and to the bacterial methionine synthase MetH, but lack homology to some other, previously described bacterial betaine methyl transferases. NF005720.0 PRK07538 PRK07538.1 400 400 418 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 8293 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005721.0 PRK07539 PRK07539.1-1 308 308 292 equivalog Y Y N NADH-quinone oxidoreductase subunit NuoE nuoE 1.6.5.9 GO:0016491 2 Bacteria superkingdom 10473 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit E NADH-quinone oxidoreductase subunit NuoE NF005726.0 PRK07544 PRK07544.1 396 396 295 equivalog Y Y N branched-chain amino acid aminotransferase 2.6.1.42 GO:0004084,GO:0009081 2 Bacteria superkingdom 4877 NCBI Protein Cluster (PRK) branched-chain amino acid aminotransferase branched-chain amino acid aminotransferase Catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids NF005732.0 PRK07550 PRK07550.1 366 366 389 equivalog Y Y N aminotransferase GO:0003824,GO:0009058,GO:0030170 2 Bacteria superkingdom 3588 NCBI Protein Cluster (PRK) hypothetical protein aminotransferase NF005733.0 PRK07558 PRK07558.1 85 85 75 equivalog Y Y N F0F1 ATP synthase subunit C 7.1.2.2 GO:0015078,GO:0015986,GO:0045263 2 Bacteria superkingdom 2057 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit C F0F1 ATP synthase subunit C Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit C is part of the membrane proton channel F0 NF005734.0 PRK07559 PRK07559.1 283 283 368 equivalog Y Y N 2'-deoxycytidine 5'-triphosphate deaminase 3.5.4.13 GO:0008829,GO:0009394 2 Bacteria superkingdom 5322 NCBI Protein Cluster (PRK) 2'-deoxycytidine 5'-triphosphate deaminase 2'-deoxycytidine 5'-triphosphate deaminase Catalyzes the deamination of dCTP to form dUTP NF005736.0 PRK07562 PRK07562.1 1737 1737 1222 equivalog Y Y N vitamin B12-dependent ribonucleotide reductase 1.17.4.1 GO:0004748,GO:0006260 2 Bacteria superkingdom 6632 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit alpha vitamin B12-dependent ribonucleotide reductase Catalyzes the reduction of ribonucleotides to deoxyribonucleotides; the rate-limiting step in dNTP synthesis NF005737.0 PRK07564 PRK07564.1-1 378 378 543 equivalog Y Y N alpha-D-glucose phosphate-specific phosphoglucomutase 5.4.2.2 GO:0005975,GO:0016868 2 Bacteria superkingdom 6809 NCBI Protein Cluster (PRK) phosphoglucomutase alpha-D-glucose phosphate-specific phosphoglucomutase NF005741.0 PRK07565 PRK07565.1 303 303 335 subfamily Y Y N dihydroorotate dehydrogenase-like protein 2 Bacteria superkingdom 3411 NCBI Protein Cluster (PRK) dihydroorotate dehydrogenase 2 dihydroorotate dehydrogenase-like protein NF005742.0 PRK07566 PRK07566.1 313 313 315 equivalog Y Y N chlorophyll synthase ChlG chlG 2.5.1.62 2 Bacteria superkingdom 2832 NCBI Protein Cluster (PRK) bacteriochlorophyll/chlorophyll a synthase chlorophyll synthase ChlG NF005743.0 PRK07567 PRK07567.1 264 264 245 equivalog Y Y N glutamine amidotransferase 2 Bacteria superkingdom 3678 NCBI Protein Cluster (PRK) glutamine amidotransferase glutamine amidotransferase Catalyzes the transfer of the ammonia group from glutamine to a new carbon-nitrogen group NF005744.0 PRK07568 PRK07568.1 389 389 398 subfamily Y Y N pyridoxal phosphate-dependent aminotransferase 2.6.1.- 2 Bacteria superkingdom 6423 NCBI Protein Cluster (PRK) aspartate aminotransferase pyridoxal phosphate-dependent aminotransferase NF005745.0 PRK07569 PRK07569.1 333 333 238 equivalog Y Y N bidirectional hydrogenase complex protein HoxU hoxU 2 Bacteria superkingdom 636 NCBI Protein Cluster (PRK) bidirectional hydrogenase complex protein HoxU bidirectional hydrogenase complex protein HoxU With HoxF and HoxE catalyzes H2-dependent NAD(P)+-reduction as well as NAD(P)H-dependent H2-evolution NF005746.0 PRK07570 PRK07570.1 243 243 250 subfamily Y Y N succinate dehydrogenase/fumarate reductase iron-sulfur subunit 2 Bacteria superkingdom 14457 NCBI Protein Cluster (PRK) succinate dehydrogenase/fumarate reductase iron-sulfur subunit succinate dehydrogenase/fumarate reductase iron-sulfur subunit NF005747.0 PRK07571 PRK07571.1 224 224 173 equivalog Y Y N bidirectional hydrogenase complex protein HoxE hoxE 2 Bacteria superkingdom 527 NCBI Protein Cluster (PRK) bidirectional hydrogenase complex protein HoxE bidirectional hydrogenase complex protein HoxE With HoxF and HoxU catalyzes H2-dependent NAD(P)+-reduction as well as NAD(P)H-dependent H2-evolution NF005748.0 PRK07572 PRK07572.1 438 438 426 subfamily Y Y N cytosine deaminase GO:0016810 2 Bacteria superkingdom 18352 NCBI Protein Cluster (PRK) cytosine deaminase cytosine deaminase NF005749.0 PRK07573 PRK07573.1 866 866 641 subfamily Y Y N fumarate reductase/succinate dehydrogenase flavoprotein subunit 2 Bacteria superkingdom 18488 NCBI Protein Cluster (PRK) succinate dehydrogenase flavoprotein subunit fumarate reductase/succinate dehydrogenase flavoprotein subunit Part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol NF005750.0 PRK07574 PRK07574.1 329 329 386 equivalog Y Y N NAD-dependent formate dehydrogenase GO:0008863,GO:0051287 2 Bacteria superkingdom 3858 NCBI Protein Cluster (PRK) formate dehydrogenase NAD-dependent formate dehydrogenase Catalyzes the reversible two-electron oxidation of formate to carbon dioxide NF005752.0 PRK07576 PRK07576.1 321 321 271 subfamily Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 2039 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005753.0 PRK07577 PRK07577.1 310 310 237 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 2012 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005754.0 PRK07578 PRK07578.1 167 167 200 equivalog Y Y N short chain dehydrogenase GO:0016491 2 Bacteria superkingdom 11384 NCBI Protein Cluster (PRK) short chain dehydrogenase short chain dehydrogenase NF005755.0 PRK07579 PRK07579.1 238 238 245 equivalog Y Y N dTDP-4-amino-4,6-dideoxyglucose formyltransferase 2 Bacteria superkingdom 232 NCBI Protein Cluster (PRK) hypothetical protein dTDP-4-amino-4,6-dideoxyglucose formyltransferase NF005758.0 PRK07582 PRK07582.1 440 440 372 equivalog Y Y N cystathionine gamma-lyase 4.4.1.1 GO:0003824,GO:0019346,GO:0030170 2 Bacteria superkingdom 9675 NCBI Protein Cluster (PRK) cystathionine gamma-lyase cystathionine gamma-lyase Catalyzes the formation of cysteine and 2-oxobutanoate from cystathionine NF005759.0 PRK07583 PRK07583.1 403 403 438 equivalog Y Y N cytosine deaminase 3.5.4.1 GO:0016810 2 Bacteria superkingdom 2764 NCBI Protein Cluster (PRK) cytosine deaminase-like protein cytosine deaminase NF005760.0 PRK07586 PRK07586.1 363 363 514 equivalog Y Y N acetolactate synthase large subunit GO:0003824,GO:0030976 2 Bacteria superkingdom 7664 NCBI Protein Cluster (PRK) hypothetical protein acetolactate synthase large subunit NF005761.0 PRK07588 PRK07588.1 454 454 392 equivalog Y Y N FAD-binding domain 2 Bacteria superkingdom 804 NCBI Protein Cluster (PRK) hypothetical protein FAD-binding domain NF005796.0 PRK07636 PRK07636.1 337 337 275 subfamily Y N N ATP-dependent DNA ligase 2 Bacteria superkingdom 1107 NCBI Protein Cluster (PRK) ATP-dependent DNA ligase ATP-dependent DNA ligase NF005797.0 PRK07638 PRK07638.1 518 518 487 equivalog Y N N acyl-CoA synthetase 2 Bacteria superkingdom 2197 NCBI Protein Cluster (PRK) acyl-CoA synthetase acyl-CoA synthetase NF005798.0 PRK07639 PRK07639.1 100 100 91 equivalog Y Y N petrobactin biosynthesis protein AsbD asbD 2 Bacteria superkingdom 400 NCBI Protein Cluster (PRK) acyl carrier protein petrobactin biosynthesis protein AsbD NF005799.0 PRK07649 PRK07649.1 327 327 195 equivalog Y Y N aminodeoxychorismate/anthranilate synthase component II pabA 2 Bacteria superkingdom 2591 NCBI Protein Cluster (PRK) para-aminobenzoate/anthranilate synthase glutamine amidotransferase component II aminodeoxychorismate/anthranilate synthase component II NF005800.0 PRK07650 PRK07650.1 308 308 290 equivalog Y Y N aminodeoxychorismate lyase pabC 4.1.3.38 GO:0003824 2 Bacteria superkingdom 3057 NCBI Protein Cluster (PRK) 4-amino-4-deoxychorismate lyase aminodeoxychorismate lyase Catalyzes the formation of 4-aminobenzoate and pyruvate from 4-amino-4-deoxychorismate NF005801.1 PRK07656 PRK07656.1 657 657 500 equivalog Y Y N FadD3 family acyl-CoA ligase 2 Bacteria superkingdom 11427 NCBI Protein Cluster (PRK) long-chain-fatty-acid--CoA ligase FadD3 family acyl-CoA ligase NF005802.0 PRK07657 PRK07657.1 363 363 260 equivalog Y Y N enoyl-CoA hydratase 4.2.1.17 GO:0003824 2 Bacteria superkingdom 2223 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF005803.0 PRK07658 PRK07658.1 313 313 257 equivalog Y Y N enoyl-CoA hydratase 4.2.1.17 2 Bacteria superkingdom 2738 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF005804.0 PRK07659 PRK07659.1 311 311 260 equivalog Y Y N enoyl-CoA hydratase 4.2.1.17 GO:0003824 2 Bacteria superkingdom 2390 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF005805.0 PRK07661 PRK07661.1 633 633 391 equivalog Y Y N acetyl-CoA C-acetyltransferase 2.3.1.9 2 Bacteria superkingdom 2763 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA C-acetyltransferase Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A NF005806.0 PRK07666 PRK07666.1 286 286 239 equivalog Y Y N 3-ketoacyl-ACP reductase GO:0016491 2 Bacteria superkingdom 4482 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase 3-ketoacyl-ACP reductase NF005809.0 PRK07670 PRK07670.1 326 326 255 equivalog Y Y N FliA/WhiG family RNA polymerase sigma factor 2 Bacteria superkingdom 1798 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigD FliA/WhiG family RNA polymerase sigma factor NF005810.0 PRK07671 PRK07671.1 594 594 377 equivalog Y Y N bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase GO:0019346,GO:0030170 2 Bacteria superkingdom 5335 NCBI Protein Cluster (PRK) cystathionine beta-lyase bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase Catalyzes the formation of L-homocysteine from cystathionine NF005811.0 PRK07677 PRK07677.1 318 318 254 equivalog Y Y N 2,4-dienoyl-CoA reductase fadH 1.3.1.34 GO:0008670,GO:0009062 17189250 2 Bacteria superkingdom 2205 NCBI Protein Cluster (PRK) short chain dehydrogenase 2,4-dienoyl-CoA reductase NF005812.0 PRK07678 PRK07678.1 488 488 451 subfamily Y Y N aminotransferase GO:0008483,GO:0030170 2 Bacteria superkingdom 4323 NCBI Protein Cluster (PRK) aminotransferase aminotransferase NF005816.0 PRK07682 PRK07682.1 620 620 390 equivalog Y Y N aminotransferase 2 Bacteria superkingdom 2460 NCBI Protein Cluster (PRK) hypothetical protein aminotransferase NF005818.0 PRK07691 PRK07691.1 586 586 496 equivalog Y Y N Na+/H+ antiporter subunit D GO:0008137,GO:0015297,GO:0042773 2 Bacteria superkingdom 5354 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit D Na+/H+ antiporter subunit D Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF005822.0 PRK07708 PRK07708.1 175 175 220 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 2674 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005825.0 PRK07714 PRK07714.1 113 113 102 equivalog Y Y N YlxQ family RNA-binding protein GO:0003723,GO:0003735 22355167 2 Bacteria superkingdom 1909 NCBI Protein Cluster (PRK) hypothetical protein YlxQ family RNA-binding protein NF005826.1 PRK07718 PRK07718.1 140 140 143 equivalog Y Y N flagellar basal body-associated protein FliL fliL GO:0006935,GO:0071973 1828465 2 Bacteria superkingdom 1519 NCBI Protein Cluster (PRK) flagellar basal body-associated protein FliL flagellar basal body-associated protein FliL Interacts with the cytoplasmic MS ring of the basal body and may act to stabilize the MotAB complexes which surround the MS ring NF005829.0 PRK07726 PRK07726.1 597 597 669 subfamily Y Y N DNA topoisomerase 3 GO:0003677,GO:0003916,GO:0006265 2 Bacteria superkingdom 56095 NCBI Protein Cluster (PRK) DNA topoisomerase III DNA topoisomerase 3 NF005830.0 PRK07729 PRK07729.1 546 546 343 equivalog Y Y N glyceraldehyde-3-phosphate dehydrogenase GO:0006006,GO:0016620 2 Bacteria superkingdom 2835 NCBI Protein Cluster (PRK) glyceraldehyde-3-phosphate dehydrogenase glyceraldehyde-3-phosphate dehydrogenase NF005831.1 PRK07734 PRK07734.1 301 301 250 equivalog Y Y N flagellar motor protein MotB motB 15306009,16095621 2 Bacteria superkingdom 2530 NCBI Protein Cluster (PRK) flagellar motor protein MotB flagellar motor protein MotB With MotA forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine NF005833.0 PRK07737 PRK07737.1 444 444 501 equivalog Y Y N flagellar hook-associated protein 2 2 Bacteria superkingdom 1966 NCBI Protein Cluster (PRK) flagellar capping protein flagellar hook-associated protein 2 Involved in flagellin assembly NF005834.1 PRK07738 PRK07738.1 107 107 117 equivalog Y Y N flagellar protein FlaG flaG 2 Bacteria superkingdom 1750 NCBI Protein Cluster (PRK) flagellar protein FlaG flagellar protein FlaG NF005839.0 PRK07756 PRK07756.1 163 163 122 equivalog Y Y N NADH-quinone oxidoreductase subunit A 2 Bacteria superkingdom 1068 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit A NADH-quinone oxidoreductase subunit A NF005841.0 PRK07758 PRK07758.1 115 115 95 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 1796 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005846.3 PRK07764 PRK07764.1-6 625 625 628 equivalog Y Y N DNA polymerase III subunit gamma and tau 2.7.7.7 GO:0003677,GO:0003887,GO:0005524,GO:0006260,GO:0009360 2 Bacteria superkingdom 21394 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunit gamma and tau This clade of the DNA polymerase III gene that gives rise to the gamma and tau subunits comes from GC-rich organisms such as Streptomyces. Both a central region and a C-terminal region have long, variable-length low-complexity sequences that are not well-conserved, and therefore not matched effectively by BLAST or HMM searches. The C-terminal low-complexity region has been removed from the seed alignment. NF005849.0 PRK07765 PRK07765.1 308 308 219 equivalog Y Y N aminodeoxychorismate/anthranilate synthase component II 2 Bacteria superkingdom 8445 NCBI Protein Cluster (PRK) para-aminobenzoate synthase component II aminodeoxychorismate/anthranilate synthase component II NF005850.0 PRK07768 PRK07768.1 572 572 545 subfamily Y Y N long-chain-fatty-acid--CoA ligase 2 Bacteria superkingdom 2730 NCBI Protein Cluster (PRK) long-chain-fatty-acid--CoA ligase long-chain-fatty-acid--CoA ligase NF005851.0 PRK07772 PRK07772.1 194 194 191 subfamily Y N N single-stranded DNA-binding protein 2 Bacteria superkingdom 15130 NCBI Protein Cluster (PRK) single-stranded DNA-binding protein single-stranded DNA-binding protein NF005852.0 PRK07773 PRK07773.1 780 780 886 equivalog Y Y N replicative DNA helicase 3.6.4.12 2 Bacteria superkingdom 1631 NCBI Protein Cluster (PRK) replicative DNA helicase replicative DNA helicase Unwinds double stranded DNA NF005853.0 PRK07774 PRK07774.1 303 303 250 equivalog Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 2082 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005855.0 PRK07777 PRK07777.1 553 553 391 equivalog Y Y N pyridoxal phosphate-dependent aminotransferase 2.6.1.- GO:0003824,GO:0009058,GO:0030170 2 Bacteria superkingdom 12315 NCBI Protein Cluster (PRK) aminotransferase pyridoxal phosphate-dependent aminotransferase NF005856.0 PRK07785 PRK07785.1 224 224 246 equivalog Y Y N NADH-quinone oxidoreductase subunit C 1.6.5.9 GO:0008137 2 Bacteria superkingdom 10442 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit C NADH-quinone oxidoreductase subunit C NF005858.0 PRK07787 PRK07787.1 575 575 471 subfamily Y N N acyl-CoA synthetase 2 Bacteria superkingdom 11443 NCBI Protein Cluster (PRK) acyl-CoA synthetase acyl-CoA synthetase NF005860.0 PRK07789 PRK07789.1 881 881 615 equivalog Y Y N acetolactate synthase large subunit GO:0000287,GO:0003984,GO:0009082,GO:0030976,GO:0050660 2 Bacteria superkingdom 14771 NCBI Protein Cluster (PRK) acetolactate synthase 1 catalytic subunit acetolactate synthase large subunit NF005863.0 PRK07798 PRK07798.1 543 543 540 subfamily Y N N acyl-CoA synthetase 2 Bacteria superkingdom 13270 NCBI Protein Cluster (PRK) acyl-CoA synthetase acyl-CoA synthetase NF005864.0 PRK07799 PRK07799.1 316 316 266 equivalog Y Y N crotonase/enoyl-CoA hydratase family protein 2 Bacteria superkingdom 6472 NCBI Protein Cluster (PRK) enoyl-CoA hydratase crotonase/enoyl-CoA hydratase family protein NF005865.0 PRK07801 PRK07801.1 591 591 382 equivalog Y Y N acetyl-CoA C-acetyltransferase 2.3.1.9 GO:0016747 2 Bacteria superkingdom 10312 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA C-acetyltransferase Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A NF005867.0 PRK07804 PRK07804.1 639 639 548 equivalog Y Y N L-aspartate oxidase 1.4.3.16 GO:0008734,GO:0009435 2 Bacteria superkingdom 11792 NCBI Protein Cluster (PRK) L-aspartate oxidase L-aspartate oxidase Catalyzes the formation of oxaloacetate from L-aspartate NF005868.0 PRK07806 PRK07806.1 162 162 248 subfamily Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 3546 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005869.0 PRK07807 PRK07807.1 549 549 479 equivalog Y Y N GuaB1 family IMP dehydrogenase-related protein GO:0003938 2 Bacteria superkingdom 12608 NCBI Protein Cluster (PRK) inosine 5-monophosphate dehydrogenase GuaB1 family IMP dehydrogenase-related protein NF005870.0 PRK07810 PRK07810.1 618 618 406 equivalog Y Y N O-succinylhomoserine sulfhydrylase 4.2.99.- 2 Bacteria superkingdom 2778 NCBI Protein Cluster (PRK) O-succinylhomoserine sulfhydrylase O-succinylhomoserine sulfhydrylase NF005872.0 PRK07812 PRK07812.1 703 703 439 equivalog Y Y N bifunctional o-acetylhomoserine/o-acetylserine sulfhydrylase 2.5.1.47 GO:0016765,GO:0019346 2 Bacteria superkingdom 8516 NCBI Protein Cluster (PRK) O-acetylhomoserine aminocarboxypropyltransferase bifunctional o-acetylhomoserine/o-acetylserine sulfhydrylase Catalyzes the formation of L-methionine and acetate from O-acetyl-L-homoserine and methanethiol NF005873.0 PRK07814 PRK07814.1 346 346 263 equivalog Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 1892 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005878.0 PRK07825 PRK07825.1 287 287 278 subfamily Y N N short chain dehydrogenase 2 Bacteria superkingdom 5039 NCBI Protein Cluster (PRK) short chain dehydrogenase short chain dehydrogenase NF005879.0 PRK07827 PRK07827.1 283 283 261 equivalog Y Y N enoyl-CoA hydratase family protein 2 Bacteria superkingdom 8531 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase family protein NF005880.0 PRK07831 PRK07831.1 336 336 263 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 8147 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005881.0 PRK07832 PRK07832.1 296 296 287 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 2133 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005882.1 PRK07843 PRK07843.1 788 788 547 equivalog Y Y N 3-oxosteroid 1-dehydrogenase kstD 1.3.99.4 GO:0006694,GO:0016042,GO:0047571 10788377,11230432,11750802,16000729 2 Bacteria superkingdom 5029 NCBI Protein Cluster (PRK) 3-ketosteroid-delta-1-dehydrogenase 3-oxosteroid 1-dehydrogenase NF005883.0 PRK07845 PRK07845.1 479 479 466 equivalog Y Y N NAD(P)H-quinone dehydrogenase GO:0016491,GO:0045454,GO:0050660 15456792 2 Bacteria superkingdom 11831 NCBI Protein Cluster (PRK) flavoprotein disulfide reductase NAD(P)H-quinone dehydrogenase Catalyzes the reduction of nonspecific electron acceptors such as 2,6-dimethyl-1,4-benzoquinone and 5-hydroxy-1,4-naphthaquinone NF005884.0 PRK07846 PRK07846.1 501 501 454 equivalog Y Y N mycothione reductase 1.8.1.15 10512639 2 Bacteria superkingdom 6013 NCBI Protein Cluster (PRK) mycothione reductase mycothione reductase Catalyzes the reduction of mycothione or glutathione to mycothione or glutathione disulfide NF005886.0 PRK07849 PRK07849.1-1 253 253 291 equivalog Y Y N aminodeoxychorismate lyase 4.1.3.38 2 Bacteria superkingdom 4527 NCBI Protein Cluster (PRK) 4-amino-4-deoxychorismate lyase aminodeoxychorismate lyase NF005887.0 PRK07849 PRK07849.1-2 278 278 291 equivalog Y Y N aminodeoxychorismate lyase 4.1.3.38 2 Bacteria superkingdom 2688 NCBI Protein Cluster (PRK) 4-amino-4-deoxychorismate lyase aminodeoxychorismate lyase NF005888.0 PRK07849 PRK07849.1-3 273 273 298 equivalog Y Y N aminodeoxychorismate lyase 4.1.3.38 2 Bacteria superkingdom 864 NCBI Protein Cluster (PRK) 4-amino-4-deoxychorismate lyase aminodeoxychorismate lyase NF005889.0 PRK07850 PRK07850.1 515 515 387 equivalog Y Y N steroid 3-ketoacyl-CoA thiolase 19822655,25482540,28786661 2 Bacteria superkingdom 6921 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase steroid 3-ketoacyl-CoA thiolase NF005890.0 PRK07851 PRK07851.1 580 580 406 equivalog Y Y N acetyl-CoA C-acetyltransferase 2.3.1.9 GO:0016747 2 Bacteria superkingdom 11337 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA C-acetyltransferase Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A NF005892.0 PRK07855 PRK07855.1 469 469 390 subfamily Y N N lipid-transfer protein 2 Bacteria superkingdom 12485 NCBI Protein Cluster (PRK) lipid-transfer protein lipid-transfer protein NF005893.0 PRK07856 PRK07856.1 255 255 255 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 9011 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF005895.0 PRK07860 PRK07860.1 802 802 811 equivalog Y Y N NADH-quinone oxidoreductase subunit G 1.6.5.9 GO:0008137,GO:0016020,GO:0042773,GO:0043546,GO:0051536 2 Bacteria superkingdom 13895 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit G NADH-quinone oxidoreductase subunit G NF005898.0 PRK07868 PRK07868.1 925 925 994 equivalog Y N N acyl-CoA synthetase 2 Bacteria superkingdom 2297 NCBI Protein Cluster (PRK) acyl-CoA synthetase acyl-CoA synthetase NF005899.0 PRK07869 PRK07869.1 418 418 471 equivalog Y Y N amidase 3.5.1.4 GO:0003824 2 Bacteria superkingdom 4261 NCBI Protein Cluster (PRK) amidase amidase NF005901.0 PRK07877 PRK07877.1 476 476 722 equivalog Y Y N Rv1355c family protein GO:0016491 2 Bacteria superkingdom 2202 NCBI Protein Cluster (PRK) hypothetical protein Rv1355c family protein NF005902.0 PRK07878 PRK07878.1 647 647 392 equivalog Y Y N adenylyltransferase/sulfurtransferase MoeZ moeZ GO:0008641 2 Bacteria superkingdom 7552 NCBI Protein Cluster (PRK) molybdopterin biosynthesis-like protein MoeZ adenylyltransferase/sulfurtransferase MoeZ NF005905.0 PRK07883 PRK07883.1-3 508 508 581 equivalog Y Y N DEDD exonuclease domain-containing protein 2 Bacteria superkingdom 5588 NCBI Protein Cluster (PRK) hypothetical protein DEDD exonuclease domain-containing protein NF005906.0 PRK07883 PRK07883.1-4 495 495 563 equivalog Y Y N DEDD exonuclease domain-containing protein 2 Bacteria superkingdom 58 NCBI Protein Cluster (PRK) hypothetical protein DEDD exonuclease domain-containing protein NF005907.0 PRK07883 PRK07883.1-5 454 454 584 equivalog Y Y N DEDD exonuclease domain-containing protein GO:0000027,GO:0003724,GO:0005524 2 Bacteria superkingdom 5951 NCBI Protein Cluster (PRK) hypothetical protein DEDD exonuclease domain-containing protein NF005908.0 PRK07889 PRK07889.1 299 299 256 equivalog Y Y N enoyl-ACP reductase FabI fabI 1.3.1.9 GO:0004318,GO:0006633 2 Bacteria superkingdom 9136 NCBI Protein Cluster (PRK) enoyl-(acyl carrier protein) reductase enoyl-ACP reductase FabI NF005909.0 PRK07890 PRK07890.1 258 258 260 subfamily Y N N short chain dehydrogenase 2 Bacteria superkingdom 7183 NCBI Protein Cluster (PRK) short chain dehydrogenase short chain dehydrogenase NF005911.0 PRK07899 PRK07899.1 691 691 486 equivalog Y Y N 30S ribosomal protein S1 rpsA GO:0003676 2 Bacteria superkingdom 8899 NCBI Protein Cluster (PRK) 30S ribosomal protein S1 30S ribosomal protein S1 Involved in binding to the leader sequence of mRNAs and is itself bound to the 30S subunit; autoregulates expression via a C-terminal domain; in most gram negative organisms this protein is composed of 6 repeats of the S1 domain while in gram positive there are 4 repeats; the S1 nucleic acid-binding domain is found associated with other proteins NF005912.0 PRK07904 PRK07904.1 242 242 253 equivalog Y Y N decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose 2-reductase 1.1.1.333 GO:0016491 16291675 2 Bacteria superkingdom 6348 NCBI Protein Cluster (PRK) short chain dehydrogenase decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose 2-reductase NF005919.0 PRK07920 PRK07920.1 209 209 311 equivalog Y Y N phosphatidylinositol mannoside acyltransferase GO:0016740 2 Bacteria superkingdom 12589 NCBI Protein Cluster (PRK) lipid A biosynthesis lauroyl acyltransferase phosphatidylinositol mannoside acyltransferase NF005921.0 PRK07922 PRK07922.1 180 180 170 equivalog Y Y N amino-acid N-acetyltransferase 2.3.1.1 GO:0006526,GO:0008080 2 Bacteria superkingdom 9463 NCBI Protein Cluster (PRK) N-acetylglutamate synthase amino-acid N-acetyltransferase NF005922.0 PRK07928 PRK07928.1 155 155 119 equivalog Y Y N NADH-quinone oxidoreductase subunit A 1.6.5.9 GO:0008137 2 Bacteria superkingdom 3967 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit A NADH-quinone oxidoreductase subunit A NF005923.0 PRK07933 PRK07933.1 193 193 213 equivalog Y Y N dTMP kinase 2.7.4.9 GO:0004798,GO:0005524,GO:0006233 2 Bacteria superkingdom 3089 NCBI Protein Cluster (PRK) thymidylate kinase dTMP kinase Catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP) NF005924.0 PRK07937 PRK07937.1 419 419 353 subfamily Y N N lipid-transfer protein 2 Bacteria superkingdom 7156 NCBI Protein Cluster (PRK) lipid-transfer protein lipid-transfer protein NF005925.0 PRK07938 PRK07938.1 260 260 252 equivalog Y Y N enoyl-CoA hydratase family protein GO:0003824 2 Bacteria superkingdom 8099 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase family protein NF005926.0 PRK07940 PRK07940.1 300 300 394 equivalog Y Y N DNA polymerase III subunit delta' 2.7.7.7 GO:0003677,GO:0003887,GO:0006260,GO:0008408,GO:0009360 2 Bacteria superkingdom 16126 NCBI Protein Cluster (PRK) DNA polymerase III subunit delta' DNA polymerase III subunit delta' Catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA NF005927.0 PRK07942 PRK07942.1 186 186 232 subfamily Y N N DNA polymerase III subunit epsilon 2 Bacteria superkingdom 15509 NCBI Protein Cluster (PRK) DNA polymerase III subunit epsilon DNA polymerase III subunit epsilon NF005929.0 PRK07946 PRK07946.1 157 157 204 equivalog Y Y N Na(+)/H(+) antiporter subunit C 2 Bacteria superkingdom 6722 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit C Na(+)/H(+) antiporter subunit C Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF005930.0 PRK07948 PRK07948.1 82 82 86 equivalog Y Y N monovalent cation/H+ antiporter complex subunit F GO:0015075,GO:0016020,GO:0034220 2 Bacteria superkingdom 1129 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit F monovalent cation/H+ antiporter complex subunit F NF005940.0 PRK07986 PRK07986.1 625 625 429 equivalog Y Y N adenosylmethionine--8-amino-7-oxononanoate transaminase bioA 2.6.1.62 GO:0004015,GO:0009102,GO:0030170 2 Bacteria superkingdom 17105 NCBI Protein Cluster (PRK) adenosylmethionine--8-amino-7-oxononanoate transaminase adenosylmethionine--8-amino-7-oxononanoate transaminase Catalyzes the formation of S-adenosyl-4-methylthionine-2-oxobutanoate and 7,8-diaminononanoate from S-adenosyl-L-methionine and 8-amino-7-oxononanoate NF005943.0 PRK07998 PRK07998.1 364 364 283 equivalog Y Y N class II aldolase 4.1.2.13 2 Bacteria superkingdom 661 NCBI Protein Cluster (PRK) putative fructose-1,6-bisphosphate aldolase class II aldolase NF005960.0 PRK08044 PRK08044.1 688 688 453 equivalog Y Y N allantoinase AllB allB GO:0000256,GO:0004038 2 Bacteria superkingdom 2336 NCBI Protein Cluster (PRK) allantoinase allantoinase AllB NF005968.0 PRK08057 PRK08057.1-2 231 231 248 equivalog Y Y N cobalt-precorrin-6A reductase 1.3.1.106 GO:0009236,GO:0016994 2 Bacteria superkingdom 21683 NCBI Protein Cluster (PRK) cobalt-precorrin-6x reductase cobalt-precorrin-6A reductase NF005970.0 PRK08057 PRK08057.1-4 245 245 256 equivalog Y Y N cobalt-precorrin-6A reductase 1.3.1.106 2 Bacteria superkingdom 955 NCBI Protein Cluster (PRK) cobalt-precorrin-6x reductase cobalt-precorrin-6A reductase NF005972.0 PRK08058 PRK08058.1 364 364 330 equivalog Y Y N DNA polymerase III subunit delta' holB 2.7.7.7 GO:0003887,GO:0006260,GO:0008408 2 Bacteria superkingdom 3972 NCBI Protein Cluster (PRK) DNA polymerase III subunit delta' DNA polymerase III subunit delta' Catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA NF005973.0 PRK08059 PRK08059.1 148 148 123 equivalog Y Y N S1 domain-containing post-transcriptional regulator GSP13 yugI 17163968,19152054,9298659 2 Bacteria superkingdom 1614 NCBI Protein Cluster (PRK) general stress protein 13 S1 domain-containing post-transcriptional regulator GSP13 GSP13 (YugI in Bacillus subtilis) was described originally as general stress protein 13. It is an RNA-binding protein, by means of its single copy of the S1 domain, which is found in several tandem copies in ribosomal small subunit protein S1. A related protein, CvfD, was shown to be a post-transcriptional regulator (see PMID:32601068). GSP13 is induced by heat shock, salt stress, oxidative stress, glucose limitation and oxygen limitation NF005974.0 PRK08061 PRK08061.1 77 77 61 equivalog Y Y N type Z 30S ribosomal protein S14 GO:0003735,GO:0005840,GO:0006412 11574053,12904577,15049826,9746356 2 Bacteria superkingdom 5891 NCBI Protein Cluster (PRK) 30S ribosomal protein S14 type Z 30S ribosomal protein S14 Located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit NF005975.0 PRK08063 PRK08063.1 328 328 250 equivalog Y Y N enoyl-[acyl-carrier-protein] reductase FabL fabL 1.3.1.104 2 Bacteria superkingdom 1624 NCBI Protein Cluster (PRK) enoyl-(acyl carrier protein) reductase enoyl-[acyl-carrier-protein] reductase FabL NF005976.0 PRK08064 PRK08064.1 627 627 390 equivalog Y Y N cystathionine beta-lyase metC 4.4.1.13 11832514 2 Bacteria superkingdom 2714 NCBI Protein Cluster (PRK) cystathionine beta-lyase cystathionine beta-lyase Catalyzes the formation of L-homocysteine from cystathionine NF005977.0 PRK08068 PRK08068.1 494 494 391 subfamily Y N N transaminase 2 Bacteria superkingdom 7240 NCBI Protein Cluster (PRK) transaminase transaminase NF005978.0 PRK08071 PRK08071.1 621 621 514 equivalog Y Y N L-aspartate oxidase nadB 1.4.3.16 GO:0008734,GO:0009435 2 Bacteria superkingdom 3696 NCBI Protein Cluster (PRK) L-aspartate oxidase L-aspartate oxidase Catalyzes the formation of oxaloacetate from L-aspartate NF005981.0 PRK08074 PRK08074.1 789 789 931 equivalog Y Y N ATP-dependent DNA helicase DinG dinG 3.6.4.12 GO:0006260,GO:0008408 2 Bacteria superkingdom 6343 NCBI Protein Cluster (PRK) bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon ATP-dependent DNA helicase DinG Helicase involved in DNA repair NF005988.0 PRK08099 PRK08099.1 201 201 411 equivalog Y Y N multifunctional transcriptional regulator/nicotinamide-nucleotide adenylyltransferase/ribosylnicotinamide kinase NadR nadR 2.7.1.22,2.7.7.1 GO:0000309,GO:0003677,GO:0009058,GO:0050262 2 Bacteria superkingdom 3942 NCBI Protein Cluster (PRK) bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase multifunctional transcriptional regulator/nicotinamide-nucleotide adenylyltransferase/ribosylnicotinamide kinase NadR Catalyzes the formation of NAD(+) from nicotinamide ribonucleotide; Catalyzes the formation of nicotinamide mononucleotide from nicotinamide riboside; also has a regulatory function NF005991.0 PRK08115 PRK08115.1 854 854 858 equivalog Y Y N vitamin B12-dependent ribonucleotide reductase GO:0000166,GO:0004748,GO:0005524,GO:0006260,GO:0031419 2 Bacteria superkingdom 1883 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit alpha vitamin B12-dependent ribonucleotide reductase Catalyzes the reduction of ribonucleotides to deoxyribonucleotides; the rate-limiting step in dNTP synthesis NF005992.0 PRK08116 PRK08116.1 189 189 269 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 3490 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF005993.0 PRK08117 PRK08117.1 574 574 433 subfamily Y Y N aspartate aminotransferase family protein 2 Bacteria superkingdom 1282 NCBI Protein Cluster (PRK) 4-aminobutyrate aminotransferase aspartate aminotransferase family protein NF005994.0 PRK08118 PRK08118.1 215 215 172 equivalog Y Y N DNA topology modulation protein 2 Bacteria superkingdom 1891 NCBI Protein Cluster (PRK) topology modulation protein DNA topology modulation protein NF005995.1 PRK08119 PRK08119.1 218 218 376 equivalog Y Y N flagellar motor switch phosphatase FliY fliY GO:0003774,GO:0006935,GO:0009425,GO:0016020,GO:0071973 1447979,14749334 2 Bacteria superkingdom 6245 NCBI Protein Cluster (PRK) flagellar motor switch protein flagellar motor switch phosphatase FliY One of three proteins involved in switching the direction of the flagellar rotation NF005996.1 PRK08123 PRK08123.1 133 133 262 equivalog Y Y N histidinol-phosphatase HisJ hisJ 3.1.3.15 GO:0000105,GO:0004401 10322033 2 Bacteria superkingdom 5674 NCBI Protein Cluster (PRK) histidinol-phosphatase histidinol-phosphatase HisJ Catalyzes the formation of L-histidinol from L-histidinol phosphate NF005997.1 PRK08124 PRK08124.1 340 340 259 equivalog Y Y N flagellar motor stator protein MotA motA 1624413,32929189 2 Bacteria superkingdom 2731 NCBI Protein Cluster (PRK) flagellar motor protein MotA flagellar motor stator protein MotA With MotB forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine NF006000.0 PRK08130 PRK08130.1 233 233 214 equivalog Y Y N aldolase 4.1.2.- 2 Bacteria superkingdom 9852 NCBI Protein Cluster (PRK) putative aldolase aldolase NF006002.0 PRK08132 PRK08132.1 416 416 552 subfamily Y N N FAD-dependent oxidoreductase 2 Bacteria superkingdom 10918 NCBI Protein Cluster (PRK) FAD-dependent oxidoreductase FAD-dependent oxidoreductase NF006003.0 PRK08133 PRK08133.1 522 522 396 equivalog Y Y N O-succinylhomoserine sulfhydrylase 4.2.99.- GO:0003824,GO:0019346,GO:0030170,GO:0071268 2 Bacteria superkingdom 10563 NCBI Protein Cluster (PRK) O-succinylhomoserine sulfhydrylase O-succinylhomoserine sulfhydrylase Catalyzes the conversion of O-succinylhomoserine into homocysteine NF006004.0 PRK08134 PRK08134.1 636 636 433 equivalog Y Y N O-acetylhomoserine aminocarboxypropyltransferase 2.5.1.49 2 Bacteria superkingdom 2988 NCBI Protein Cluster (PRK) O-acetylhomoserine aminocarboxypropyltransferase O-acetylhomoserine aminocarboxypropyltransferase Catalyzes the formation of L-methionine and acetate from O-acetyl-L-homoserine and methanethiol NF006006.0 PRK08137 PRK08137.1 534 534 529 equivalog Y Y N amidase 3.5.1.4 2 Bacteria superkingdom 6394 NCBI Protein Cluster (PRK) amidase amidase NF006008.0 PRK08139 PRK08139.1 313 313 266 equivalog Y Y N enoyl-CoA hydratase 4.2.1.17 GO:0003824 2 Bacteria superkingdom 9617 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF006013.0 PRK08150 PRK08150.1 232 232 259 subfamily Y Y N crotonase/enoyl-CoA hydratase family protein 2 Bacteria superkingdom 3886 NCBI Protein Cluster (PRK) enoyl-CoA hydratase crotonase/enoyl-CoA hydratase family protein NF006014.0 PRK08153 PRK08153.1 510 510 370 equivalog Y Y N pyridoxal phosphate-dependent aminotransferase GO:0016740,GO:0030170 2 Bacteria superkingdom 4161 NCBI Protein Cluster (PRK) histidinol-phosphate aminotransferase pyridoxal phosphate-dependent aminotransferase NF006015.0 PRK08154 PRK08154.1 204 204 314 subfamily Y N N anaerobic benzoate catabolism transcriptional regulator 2 Bacteria superkingdom 2776 NCBI Protein Cluster (PRK) anaerobic benzoate catabolism transcriptional regulator anaerobic benzoate catabolism transcriptional regulator NF006019.0 PRK08159 PRK08159.1 452 452 272 equivalog Y Y N enoyl-ACP reductase FabI fabI GO:0004318,GO:0006633 2 Bacteria superkingdom 5792 NCBI Protein Cluster (PRK) enoyl-(acyl carrier protein) reductase enoyl-ACP reductase FabI NF006020.0 PRK08162 PRK08162.1 677 677 545 subfamily Y N N acyl-CoA synthetase 2 Bacteria superkingdom 14768 NCBI Protein Cluster (PRK) acyl-CoA synthetase acyl-CoA synthetase NF006021.0 PRK08163 PRK08163.1 459 459 398 equivalog Y Y N 3-hydroxybenzoate 6-monooxygenase 1.14.13.24 GO:0071949 2 Bacteria superkingdom 4252 NCBI Protein Cluster (PRK) salicylate hydroxylase 3-hydroxybenzoate 6-monooxygenase NF006038.0 PRK08181 PRK08181.1 317 317 271 subfamily Y N N transposase 2 Bacteria superkingdom 1295 NCBI Protein Cluster (PRK) transposase transposase NF006039.0 PRK08182 PRK08182.1 70 70 150 subfamily Y N N single-stranded DNA-binding protein 2 Bacteria superkingdom 2058 NCBI Protein Cluster (PRK) single-stranded DNA-binding protein single-stranded DNA-binding protein NF006040.0 PRK08183 PRK08183.1 135 135 134 equivalog Y Y N NADH:ubiquinone oxidoreductase subunit NDUFA12 GO:0010257,GO:0016020 2 Bacteria superkingdom 6212 NCBI Protein Cluster (PRK) NADH dehydrogenase NADH:ubiquinone oxidoreductase subunit NDUFA12 NF006042.0 PRK08185 PRK08185.1 405 405 287 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 2139 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006047.0 PRK08193 PRK08193.1 257 257 231 subfamily Y Y N L-ribulose-5-phosphate 4-epimerase AraD araD 5.1.3.4 10769139,11741871,2251150,4879898,9548961 2 Bacteria superkingdom 20523 NCBI Protein Cluster (PRK) L-ribulose-5-phosphate 4-epimerase L-ribulose-5-phosphate 4-epimerase AraD Catalyzes the isomerization of L-ribulose 5-phosphate to D-xylulose 5-phosphate in the anaerobic catabolism of L-ascorbate; links the arabinose metabolic pathway to the pentose phosphate pathway and allows the bacteria to use arabinose as an energy source NF006048.0 PRK08194 PRK08194.1 501 501 352 equivalog Y Y N tartrate dehydrogenase 1.1.1.93 2 Bacteria superkingdom 3695 NCBI Protein Cluster (PRK) tartrate dehydrogenase tartrate dehydrogenase Catalyzes the formation of oxaloglycolate from tartrate; also Catalyzes the formation of pyruvate from malate and glycerate from tartrate NF006052.0 PRK08199 PRK08199.1 539 539 559 subfamily Y N N thiamine pyrophosphate protein 2 Bacteria superkingdom 15206 NCBI Protein Cluster (PRK) thiamine pyrophosphate protein thiamine pyrophosphate protein NF006055.0 PRK08203 PRK08203.1 532 532 455 equivalog Y Y N 8-oxoguanine deaminase 3.5.4.32 GO:0016810 9055410 2 Bacteria superkingdom 22004 NCBI Protein Cluster (PRK) hydroxydechloroatrazine ethylaminohydrolase 8-oxoguanine deaminase NF006058.0 PRK08206 PRK08206.1 276 276 402 equivalog Y Y N diaminopropionate ammonia-lyase 4.3.1.15 GO:0008838,GO:0030170 2 Bacteria superkingdom 13177 NCBI Protein Cluster (PRK) diaminopropionate ammonia-lyase diaminopropionate ammonia-lyase Catalyzes the formation of pyruvate from 2,3-diaminopropionate NF006061.0 PRK08207 PRK08207.1-4 702 702 501 equivalog Y Y N coproporphyrinogen III oxidase GO:0003824,GO:0051536 2 Bacteria superkingdom 2695 NCBI Protein Cluster (PRK) coproporphyrinogen III oxidase coproporphyrinogen III oxidase NF006064.0 PRK08207 PRK08207.2-2 504 504 465 equivalog Y Y N coproporphyrinogen III oxidase 2 Bacteria superkingdom 488 NCBI Protein Cluster (PRK) coproporphyrinogen III oxidase coproporphyrinogen III oxidase NF006067.1 PRK08208 PRK08208.1 380 380 427 equivalog Y Y N STM4012 family radical SAM protein GO:0051536 2 Bacteria superkingdom 7002 NCBI Protein Cluster (PRK) coproporphyrinogen III oxidase STM4012 family radical SAM protein Members of this family are radical SAM enzymes, related to coproporphyrinogen III oxidase but very likely differing in function. The family is named for a protein found in the Salmonella enterica model strain LT2, but the family and its conserved genome neighborhood is common in Streptomyces and related species, while rare in the Proteobacteria. NF006068.0 PRK08210 PRK08210.1 474 474 405 equivalog Y Y N aspartate kinase dapG 2.7.2.4 GO:0004072,GO:0009089 8098035 2 Bacteria superkingdom 4589 NCBI Protein Cluster (PRK) aspartate kinase I aspartate kinase Catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP; diaminopimelate sensitive NF006071.0 PRK08215 PRK08215.1 372 372 258 equivalog Y Y N RNA polymerase sporulation sigma factor SigG sigG 10419957 2 Bacteria superkingdom 3641 NCBI Protein Cluster (PRK) sporulation sigma factor SigG RNA polymerase sporulation sigma factor SigG Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this factor is involved in the transcription of small acid-soluble proteins involved in protecting the forespore chromatin NF006073.0 PRK08219 PRK08219.1 218 218 227 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 10981 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006074.0 PRK08220 PRK08220.1 312 312 251 equivalog Y Y N 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase dhbA 1.3.1.28 GO:0008667,GO:0019290 2 Bacteria superkingdom 11753 NCBI Protein Cluster (PRK) 2,3-dihydroxybenzoate-2,3-dehydrogenase 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase Catalyzes the formation of 2,3-dihydroxybenzoate from 2,3-dihydro-2,3-dihydroxybenzoate; involved in the biosynthesis of siderophores, enterobactin, bacillibactin or vibriobactin NF006077.0 PRK08223 PRK08223.1 266 266 296 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 1374 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006078.0 PRK08224 PRK08224.1 296 296 350 equivalog Y Y N ATP-dependent DNA ligase 6.5.1.1 GO:0003910,GO:0005524,GO:0006281,GO:0006310 14985346 2 Bacteria superkingdom 15826 NCBI Protein Cluster (PRK) ATP-dependent DNA ligase ATP-dependent DNA ligase Catalyzes the ATP-dependent formation of a phosphodiester at the site of a single-strand break in duplex DNA; in mycobacteria LigC has weak intrinsic nick joining activities and is not essential for growth NF006079.0 PRK08225 PRK08225.1 95 95 70 equivalog Y Y N acetyl-CoA carboxylase biotin carboxyl carrier protein subunit 2 Bacteria superkingdom 1604 NCBI Protein Cluster (PRK) acetyl-CoA carboxylase biotin carboxyl carrier protein subunit acetyl-CoA carboxylase biotin carboxyl carrier protein subunit Composes the biotin carboxyl carrier protein subunit of the acetyl-CoA carboxylase complex NF006081.0 PRK08227 PRK08227.1 297 297 291 equivalog Y Y N 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase lsrF 2.3.1.245 GO:0016829 2 Bacteria superkingdom 3560 NCBI Protein Cluster (PRK) autoinducer 2 aldolase 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase Involved in the degradation of autoinducer 2 NF006082.0 PRK08228 PRK08228.1 264 264 205 equivalog Y Y N L(+)-tartrate dehydratase subunit beta ttdB 4.2.1.32 GO:0016836 2 Bacteria superkingdom 2149 NCBI Protein Cluster (PRK) L(+)-tartrate dehydratase subunit beta L(+)-tartrate dehydratase subunit beta Involved in the tartrate degradation pathway NF006083.0 PRK08229 PRK08229.1 371 371 341 equivalog Y Y N 2-dehydropantoate 2-reductase 1.1.1.169 GO:0008677,GO:0015940 2 Bacteria superkingdom 4715 NCBI Protein Cluster (PRK) 2-dehydropantoate 2-reductase 2-dehydropantoate 2-reductase Catalyzes the formation of 2-dehydropantoate from (R)-pantoate NF006084.0 PRK08230 PRK08230.1 365 365 303 equivalog Y Y N L(+)-tartrate dehydratase subunit alpha ttdA GO:0008730 2 Bacteria superkingdom 2668 NCBI Protein Cluster (PRK) tartrate dehydratase subunit alpha L(+)-tartrate dehydratase subunit alpha Involved in the tartrate degradation pathway NF006085.0 PRK08233 PRK08233.1 198 198 184 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 1003 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006086.0 PRK08235 PRK08235.1 526 526 393 equivalog Y Y N acetyl-CoA C-acetyltransferase 2.3.1.9 GO:0016747 2 Bacteria superkingdom 4018 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA C-acetyltransferase Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A NF006089.0 PRK08241 PRK08241.1 240 240 343 subfamily Y Y N RNA polymerase subunit sigma-70 2.7.7.6 GO:0003677,GO:0003700,GO:0006355,GO:0016987 2 Bacteria superkingdom 24025 NCBI Protein Cluster (PRK) RNA polymerase factor sigma-70 RNA polymerase subunit sigma-70 NF006090.0 PRK08242 PRK08242.1 514 514 402 equivalog Y Y N acetyl-CoA C-acetyltransferase 2.3.1.9 GO:0016747 2 Bacteria superkingdom 20635 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA C-acetyltransferase Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A NF006091.0 PRK08243 PRK08243.1 351 351 393 subfamily Y Y N 4-hydroxybenzoate 3-monooxygenase 1.14.13.2 GO:0071949 2 Bacteria superkingdom 29777 NCBI Protein Cluster (PRK) 4-hydroxybenzoate 3-monooxygenase 4-hydroxybenzoate 3-monooxygenase Catalyzes the formation of protocatechuate from 4-hydroxybenzoate NF006092.0 PRK08244 PRK08244.1 644 644 494 equivalog Y Y N monooxygenase 2 Bacteria superkingdom 1679 NCBI Protein Cluster (PRK) hypothetical protein monooxygenase NF006093.0 PRK08245 PRK08245.1 208 208 240 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 11620 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006094.0 PRK08246 PRK08246.1 331 331 310 subfamily Y Y N serine/threonine dehydratase GO:0006520 2 Bacteria superkingdom 8220 NCBI Protein Cluster (PRK) threonine dehydratase serine/threonine dehydratase NF006095.0 PRK08247 PRK08247.1 585 585 369 equivalog Y Y N methionine biosynthesis PLP-dependent protein 2 Bacteria superkingdom 3283 NCBI Protein Cluster (PRK) cystathionine gamma-synthase methionine biosynthesis PLP-dependent protein NF006096.0 PRK08248 PRK08248.1 726 726 431 equivalog Y Y N homocysteine synthase GO:0016765,GO:0019346,GO:0030170 2 Bacteria superkingdom 2281 NCBI Protein Cluster (PRK) O-acetylhomoserine aminocarboxypropyltransferase homocysteine synthase NF006097.0 PRK08249 PRK08249.1 600 600 402 equivalog Y Y N cystathionine gamma-synthase family protein 2 Bacteria superkingdom 1443 NCBI Protein Cluster (PRK) cystathionine gamma-synthase cystathionine gamma-synthase family protein NF006098.0 PRK08250 PRK08250.1 301 301 239 equivalog Y N N glutamine amidotransferase 2 Bacteria superkingdom 4398 NCBI Protein Cluster (PRK) glutamine amidotransferase glutamine amidotransferase NF006099.0 PRK08251 PRK08251.1 253 253 250 equivalog Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 5052 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006100.0 PRK08252 PRK08252.1 282 282 254 subfamily Y Y N crotonase/enoyl-CoA hydratase family protein GO:0003824 2 Bacteria superkingdom 8841 NCBI Protein Cluster (PRK) enoyl-CoA hydratase crotonase/enoyl-CoA hydratase family protein NF006101.0 PRK08255 PRK08255.1 1078 1078 768 equivalog Y Y N bifunctional salicylyl-CoA 5-hydroxylase/oxidoreductase GO:0003959,GO:0010181,GO:0050661,GO:0071949 15006746 2 Bacteria superkingdom 14481 NCBI Protein Cluster (PRK) salicylyl-CoA 5-hydroxylase bifunctional salicylyl-CoA 5-hydroxylase/oxidoreductase Catalyzes the conversion of salicylyl-CoA to gentisyl-CoA NF006102.0 PRK08256 PRK08256.1 436 436 394 subfamily Y N N lipid-transfer protein 2 Bacteria superkingdom 9224 NCBI Protein Cluster (PRK) lipid-transfer protein lipid-transfer protein NF006104.0 PRK08257 PRK08257.1-3 654 654 512 equivalog Y N N acetyl-CoA acetyltransferase 2 Bacteria superkingdom 240 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA acetyltransferase NF006105.0 PRK08257 PRK08257.1-4 683 683 510 equivalog Y Y N acetyl-CoA acetyltransferase GO:0016746 2 Bacteria superkingdom 1253 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA acetyltransferase NF006107.0 PRK08258 PRK08258.1 330 330 277 equivalog Y Y N enoyl-CoA hydratase family protein 2 Bacteria superkingdom 9550 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase family protein NF006109.0 PRK08260 PRK08260.1 320 320 296 subfamily Y N N enoyl-CoA hydratase 2 Bacteria superkingdom 5924 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF006110.0 PRK08261 PRK08261.1 410 410 454 equivalog Y Y N 3-oxoacyl-ACP reductase 1.1.1.100 GO:0016491 2 Bacteria superkingdom 16089 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase 3-oxoacyl-ACP reductase NF006113.0 PRK08262 PRK08262.1-4 503 503 510 equivalog Y Y N M20 family peptidase 2 Bacteria superkingdom 789 NCBI Protein Cluster (PRK) hypothetical protein M20 family peptidase NF006114.0 PRK08263 PRK08263.1 290 290 280 subfamily Y N N short chain dehydrogenase 2 Bacteria superkingdom 16677 NCBI Protein Cluster (PRK) short chain dehydrogenase short chain dehydrogenase NF006117.0 PRK08264 PRK08264.1-3 299 299 234 equivalog Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 1816 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006118.0 PRK08264 PRK08264.1-4 279 279 244 subfamily Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 706 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006119.0 PRK08264 PRK08264.1-5 249 249 233 subfamily Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 14452 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006120.0 PRK08264 PRK08264.1-6 274 274 246 subfamily Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 469 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006121.0 PRK08265 PRK08265.1 294 294 263 subfamily Y N N short chain dehydrogenase 2 Bacteria superkingdom 3020 NCBI Protein Cluster (PRK) short chain dehydrogenase short chain dehydrogenase NF006122.0 PRK08266 PRK08266.1 571 571 543 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 1874 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006123.0 PRK08267 PRK08267.1 261 261 261 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 5475 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006124.0 PRK08268 PRK08268.1 508 508 507 subfamily Y Y N 3-hydroxyacyl-CoA dehydrogenase 1.1.1.35 GO:0006631,GO:0016491,GO:0070403 2 Bacteria superkingdom 19737 NCBI Protein Cluster (PRK) 3-hydroxy-acyl-CoA dehydrogenase 3-hydroxyacyl-CoA dehydrogenase NF006125.0 PRK08269 PRK08269.1 427 427 334 equivalog Y Y N 3-hydroxybutyryl-CoA dehydrogenase 1.1.1.157 GO:0006631,GO:0016616,GO:0070403 2 Bacteria superkingdom 2228 NCBI Protein Cluster (PRK) 3-hydroxybutyryl-CoA dehydrogenase 3-hydroxybutyryl-CoA dehydrogenase Converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA NF006129.0 PRK08273 PRK08273.1 724 724 598 equivalog Y Y N thiamine pyrophosphate-requiring protein GO:0000287,GO:0030976 2 Bacteria superkingdom 12312 NCBI Protein Cluster (PRK) thiamine pyrophosphate protein thiamine pyrophosphate-requiring protein NF006131.0 PRK08275 PRK08275.1 587 587 577 equivalog Y Y N fumarate reductase/succinate dehydrogenase flavoprotein subunit GO:0016491 2 Bacteria superkingdom 8776 NCBI Protein Cluster (PRK) putative oxidoreductase fumarate reductase/succinate dehydrogenase flavoprotein subunit NF006134.1 PRK08279 PRK08279.1 625 625 605 equivalog Y Y N long-chain-acyl-CoA synthetase 6.2.1.3 25490545 2 Bacteria superkingdom 7940 NCBI Protein Cluster (PRK) long-chain-acyl-CoA synthetase long-chain-acyl-CoA synthetase, FadD6 family Members of this family include Rv1206 (FACL6, FadD6), which has a preference for oleic acid. NF006136.0 PRK08285 PRK08285.1 276 276 209 equivalog Y Y N precorrin-8X methylmutase 5.4.99.61 GO:0009236,GO:0016993 11470433 2 Bacteria superkingdom 15724 NCBI Protein Cluster (PRK) precorrin-8X methylmutase precorrin-8X methylmutase Catalyzes the interconversion of precorrin-8X and cobyrinic acid NF006137.0 PRK08286 PRK08286.1 294 294 214 equivalog Y Y N cobalt-precorrin-8 methylmutase 5.4.99.60 2 Bacteria superkingdom 1690 NCBI Protein Cluster (PRK) cobalt-precorrin-8X methylmutase cobalt-precorrin-8 methylmutase Catalyzes the interconversion of cobalt-precorrin-8X and cobyrinic acid in the anaerobic biosynthesis of cobalamin NF006138.0 PRK08287 PRK08287.1 210 210 189 equivalog Y Y N decarboxylating cobalt-precorrin-6B (C(15))-methyltransferase GO:0008276,GO:0009236 2 Bacteria superkingdom 1826 NCBI Protein Cluster (PRK) cobalt-precorrin-6Y C(15)-methyltransferase decarboxylating cobalt-precorrin-6B (C(15))-methyltransferase Catalyzes the methylation of either C-15 or C-5 in cobalt-precorrin-6Y to form cobalt-precorrin-7W NF006139.0 PRK08289 PRK08289.1 431 431 480 equivalog Y Y N glyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 GO:0006006,GO:0016620,GO:0050661,GO:0051287 15925900 2 Bacteria superkingdom 16511 NCBI Protein Cluster (PRK) glyceraldehyde-3-phosphate dehydrogenase glyceraldehyde-3-phosphate dehydrogenase NF006140.0 PRK08290 PRK08290.1 280 280 292 subfamily Y Y N enoyl-CoA hydratase 4.2.1.17 2 Bacteria superkingdom 7560 NCBI Protein Cluster (PRK) enoyl-CoA hydratase enoyl-CoA hydratase NF006141.0 PRK08291 PRK08291.1 408 408 330 equivalog Y Y N cyclodeaminase 2 Bacteria superkingdom 4214 NCBI Protein Cluster (PRK) ectoine utilization protein EutC cyclodeaminase Cyclodeaminase NF006142.0 PRK08292 PRK08292.1 307 307 492 equivalog Y Y N AMP nucleosidase 3.2.2.4 GO:0008714,GO:0009116,GO:0044209 2 Bacteria superkingdom 15629 NCBI Protein Cluster (PRK) AMP nucleosidase AMP nucleosidase Catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate using water as the nucleophile NF006144.0 PRK08294 PRK08294.1 560 560 637 subfamily Y N N phenol 2-monooxygenase 2 Bacteria superkingdom 5538 NCBI Protein Cluster (PRK) phenol 2-monooxygenase phenol 2-monooxygenase NF006145.0 PRK08295 PRK08295.1-2 212 212 213 equivalog Y Y N RNA polymerase sporulation sigma factor SigH sigH 2 Bacteria superkingdom 3957 NCBI Protein Cluster (PRK) RNA polymerase factor sigma-70 RNA polymerase sporulation sigma factor SigH NF006147.0 PRK08295 PRK08295.1-4 212 212 201 equivalog Y Y N RNA polymerase factor sigma-70 2.7.7.6 2 Bacteria superkingdom 3889 NCBI Protein Cluster (PRK) RNA polymerase factor sigma-70 RNA polymerase factor sigma-70 NF006148.0 PRK08295 PRK08295.1-5 208 208 218 equivalog Y Y N RNA polymerase sporulation sigma factor SigH sigH GO:0003677,GO:0003700,GO:0006352,GO:0016987 2 Bacteria superkingdom 4375 NCBI Protein Cluster (PRK) RNA polymerase factor sigma-70 RNA polymerase sporulation sigma factor SigH NF006150.0 PRK08296 PRK08296.1-2 650 650 633 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 856 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006151.0 PRK08296 PRK08296.1-3 693 693 604 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 295 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006152.0 PRK08296 PRK08296.1-4 723 723 609 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 82 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006155.0 PRK08298 PRK08298.1 129 129 136 equivalog Y Y N cytidine deaminase 3.5.4.5 2 Bacteria superkingdom 1951 NCBI Protein Cluster (PRK) cytidine deaminase cytidine deaminase Reclaims exogenous and endogenous cytidine and 2'-deoxycytidine molecules for UMP synthesis NF006156.0 PRK08299 PRK08299.1 335 335 403 equivalog Y Y N NADP-dependent isocitrate dehydrogenase 1.1.1.42 GO:0000287,GO:0004450,GO:0006102,GO:0051287 2 Bacteria superkingdom 15162 NCBI Protein Cluster (PRK) isocitrate dehydrogenase NADP-dependent isocitrate dehydrogenase Catalyzes the formation of 2-oxoglutarate from isocitrate NF006158.0 PRK08301 PRK08301.1 339 339 241 equivalog Y Y N RNA polymerase sporulation sigma factor SigE sigE GO:0003677,GO:0003700,GO:0006352,GO:0016987 15028683 2 Bacteria superkingdom 3792 NCBI Protein Cluster (PRK) sporulation sigma factor SigE RNA polymerase sporulation sigma factor SigE Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this sigma factor is responsible for the expression of sporulation specific genes and is expressed in the mother cell at the onset of sporulation NF006159.0 PRK08303 PRK08303.1 364 364 305 subfamily Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 11769 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006161.0 PRK08305 PRK08305.1 156 156 196 equivalog Y Y N dipicolinate synthase subunit B GO:0003824 10986255,8098035,8345520 2 Bacteria superkingdom 4007 NCBI Protein Cluster (PRK) dipicolinate synthase subunit B dipicolinate synthase subunit B Involved in production of dipicolinic acid (pyridine-2,6-dicarboxylic acid, DPA) which is synthesized late in sporulation in the mother cell and accumulates in the spore NF006162.0 PRK08306 PRK08306.1 261 261 297 equivalog Y Y N dipicolinate synthase subunit DpsA dpsA 8098035,8345520 2 Bacteria superkingdom 3731 NCBI Protein Cluster (PRK) dipicolinate synthase subunit A dipicolinate synthase subunit DpsA Catalyzes the synthesis of dipicolinic acid from dihydroxydipicolinic acid; plays a role in spore heat resistance NF006167.0 PRK08308 PRK08308.1 513 513 414 equivalog Y N N acyl-CoA synthetase 2 Bacteria superkingdom 1199 NCBI Protein Cluster (PRK) acyl-CoA synthetase acyl-CoA synthetase NF006168.0 PRK08309 PRK08309.1 168 168 182 equivalog Y N N short chain dehydrogenase 2 Bacteria superkingdom 1147 NCBI Protein Cluster (PRK) short chain dehydrogenase short chain dehydrogenase NF006169.0 PRK08310 PRK08310.1 391 391 395 equivalog Y Y N amidase 3.5.1.4 2 Bacteria superkingdom 5058 NCBI Protein Cluster (PRK) amidase amidase NF006172.0 PRK08311 PRK08311.1-3 318 318 248 equivalog Y Y N RNA polymerase sigma factor SigI sigI 2 Bacteria superkingdom 980 NCBI Protein Cluster (PRK) putative RNA polymerase sigma factor SigI RNA polymerase sigma factor SigI NF006179.0 PRK08312 PRK08312.1 348 348 514 subfamily Y Y N indolepyruvate oxidoreductase subunit beta family protein 2 Bacteria superkingdom 3877 NCBI Protein Cluster (PRK) putative indolepyruvate oxidoreductase subunit B indolepyruvate oxidoreductase subunit beta family protein NF006188.0 PRK08324 PRK08324.1-1 1152 1152 679 equivalog Y Y N bifunctional aldolase/short-chain dehydrogenase GO:0016491 2 Bacteria superkingdom 9214 NCBI Protein Cluster (PRK) short chain dehydrogenase short-chain dehydrogenase NF006189.0 PRK08324 PRK08324.1-3 634 634 701 equivalog Y Y N bifunctional rhamnulose-1-phosphate aldolase/short-chain dehydrogenase GO:0016491 2 Bacteria superkingdom 16964 NCBI Protein Cluster (PRK) short chain dehydrogenase short-chain dehydrogenase NF006190.0 PRK08324 PRK08324.1-4 1014 1014 689 equivalog Y Y N bifunctional aldolase/short-chain dehydrogenase 2 Bacteria superkingdom 2053 NCBI Protein Cluster (PRK) short chain dehydrogenase short-chain dehydrogenase NF006192.0 PRK08324 PRK08324.1-6 639 639 685 equivalog Y Y N bifunctional aldolase/short-chain dehydrogenase 2 Bacteria superkingdom 1449 NCBI Protein Cluster (PRK) short chain dehydrogenase short-chain dehydrogenase NF006196.0 PRK08324 PRK08324.2-4 831 831 657 equivalog Y Y N bifunctional aldolase/short-chain dehydrogenase 2 Bacteria superkingdom 332 NCBI Protein Cluster (PRK) short chain dehydrogenase short-chain dehydrogenase NF006202.0 PRK08326 PRK08326.1-5 315 315 297 equivalog Y Y N R2-like ligand-binding oxidase 2 Bacteria superkingdom 457 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit beta R2-like ligand-binding oxidase NF006236.0 PRK08375 PRK08375.1-1 663 663 493 equivalog Y N N putative monovalent cation/H+ antiporter subunit D 2 Bacteria superkingdom 691 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit D putative monovalent cation/H+ antiporter subunit D NF006238.0 PRK08375 PRK08375.1-4 626 626 531 equivalog Y N N putative monovalent cation/H+ antiporter subunit D 2 Bacteria superkingdom 542 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit D putative monovalent cation/H+ antiporter subunit D NF006263.0 PRK08410 PRK08410.1 389 389 311 equivalog Y Y N D-2-hydroxyacid dehydrogenase GO:0016616 2 Bacteria superkingdom 4653 NCBI Protein Cluster (PRK) 2-hydroxyacid dehydrogenase D-2-hydroxyacid dehydrogenase NF006363.0 PRK08582 PRK08582.1 171 171 140 equivalog Y Y N S1 domain-containing RNA-binding protein GO:0003676 2 Bacteria superkingdom 3629 NCBI Protein Cluster (PRK) hypothetical protein S1 domain-containing RNA-binding protein Members of this family, such as Lmo0218 from Listeria monocytogenes, are probable RNA-binding proteins with a single copy of the RNA-binding domain found repeated in ribosomal small subunit protein S1. NF006370.0 PRK08596 PRK08596.1 412 412 425 equivalog Y Y N acetylornithine deacetylase 3.5.1.16 GO:0016787 2 Bacteria superkingdom 2811 NCBI Protein Cluster (PRK) acetylornithine deacetylase acetylornithine deacetylase Catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine NF006372.0 PRK08600 PRK08600.1 127 127 113 equivalog Y Y N Na(+)/H(+) antiporter subunit C GO:0006812,GO:0008324 2 Bacteria superkingdom 3150 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit C Na(+)/H(+) antiporter subunit C Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF006378.0 PRK08617 PRK08617.1 510 510 556 equivalog Y Y N acetolactate synthase AlsS alsS 2.2.1.6 GO:0000287,GO:0003984,GO:0030976,GO:0034077 23199739 2 Bacteria superkingdom 11144 NCBI Protein Cluster (PRK) acetolactate synthase acetolactate synthase AlsS NF006379.0 PRK08618 PRK08618.1 417 417 326 equivalog Y Y N ornithine cyclodeaminase family protein 2 Bacteria superkingdom 2369 NCBI Protein Cluster (PRK) ornithine cyclodeaminase ornithine cyclodeaminase family protein NF006381.0 PRK08622 PRK08622.1 234 234 171 equivalog Y Y N galactose-6-phosphate isomerase subunit LacB lacB 5.3.1.26 1400164,15466549 2 Bacteria superkingdom 2038 NCBI Protein Cluster (PRK) galactose-6-phosphate isomerase subunit LacB galactose-6-phosphate isomerase subunit LacB Catalyzes the interconversion of galactose 6-phosphate to tagatose 6-phosphate NF006383.0 PRK08626 PRK08626.1 663 663 657 equivalog Y Y N fumarate reductase flavoprotein subunit GO:0016491,GO:0022900,GO:0050660 2 Bacteria superkingdom 3180 NCBI Protein Cluster (PRK) fumarate reductase flavoprotein subunit fumarate reductase flavoprotein subunit Part of four member fumarate reductase enzyme complex FrdABCD which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdCD are the membrane components which interact with quinone and are involved in electron transfer; the catalytic subunits are similar to succinate dehydrogenase SdhAB NF006384.0 PRK08628 PRK08628.1 307 307 258 equivalog Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 4719 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF006385.0 PRK08629 PRK08629.1 355 355 439 equivalog Y Y N coproporphyrinogen III oxidase family protein 2 Bacteria superkingdom 1824 NCBI Protein Cluster (PRK) coproporphyrinogen III oxidase coproporphyrinogen III oxidase family protein NF006386.0 PRK08633 PRK08633.1 1221 1221 1147 equivalog Y Y N acyl-[ACP]--phospholipid O-acyltransferase 2 Bacteria superkingdom 2444 NCBI Protein Cluster (PRK) 2-acyl-glycerophospho-ethanolamine acyltransferase acyl-[ACP]--phospholipid O-acyltransferase NF006388.0 PRK08637 PRK08637.1 301 301 433 equivalog Y N N hypothetical protein 17565195,20419351 2 Bacteria superkingdom 3054 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006389.0 PRK08638 PRK08638.1 453 453 333 equivalog Y Y N bifunctional threonine ammonia-lyase/L-serine ammonia-lyase TdcB tdcB GO:0004794,GO:0006567,GO:0030170 2 Bacteria superkingdom 3112 NCBI Protein Cluster (PRK) threonine dehydratase bifunctional threonine ammonia-lyase/L-serine ammonia-lyase TdcB Catalyzes the formation of 2-oxobutanoate from L-threonine; catabolic NF006390.0 PRK08639 PRK08639.1 421 421 418 equivalog Y Y N threonine ammonia-lyase IlvA ilvA 4.3.1.19 GO:0004794,GO:0006520 30226377 2 Bacteria superkingdom 17044 NCBI Protein Cluster (PRK) threonine dehydratase threonine ammonia-lyase IlvA Catalyzes the formation of 2-oxobutanoate from L-threonine; biosynthetic NF006391.0 PRK08640 PRK08640.1 244 244 254 equivalog Y Y N succinate dehydrogenase iron-sulfur subunit sdhB GO:0006099,GO:0009055,GO:0016491,GO:0051536 2 Bacteria superkingdom 3822 NCBI Protein Cluster (PRK) succinate dehydrogenase iron-sulfur subunit succinate dehydrogenase iron-sulfur subunit NF006392.0 PRK08641 PRK08641.1 855 855 593 equivalog Y Y N succinate dehydrogenase flavoprotein subunit sdhA 2 Bacteria superkingdom 4400 NCBI Protein Cluster (PRK) succinate dehydrogenase flavoprotein subunit succinate dehydrogenase flavoprotein subunit NF006393.0 PRK08642 PRK08642.1 292 292 254 equivalog Y Y N 3-oxoacyl-ACP reductase 1.1.1.100 GO:0016491 2 Bacteria superkingdom 3818 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase 3-oxoacyl-ACP reductase NF006394.0 PRK08643 PRK08643.1 381 381 257 equivalog Y Y N (S)-acetoin forming diacetyl reductase 1.1.1.304 GO:0019152,GO:0045150 2 Bacteria superkingdom 2982 NCBI Protein Cluster (PRK) acetoin reductase (S)-acetoin forming diacetyl reductase NF006396.0 PRK08645 PRK08645.1 453 453 611 equivalog Y Y N bifunctional homocysteine S-methyltransferase/methylenetetrahydrofolate reductase 1.5.1.20,2.1.1.10 10094622 2 Bacteria superkingdom 7981 NCBI Protein Cluster (PRK) bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein bifunctional homocysteine S-methyltransferase/methylenetetrahydrofolate reductase Catalyzes the formation of 5,10-methylenetetrahydrofolate from 5-methyltetrahydrofolate and S-adenosyl-L-homocysteine and methionine from S-adenosyl-L-methionine and L-homocysteine; expressed in B. subtilis under methionine starvation conditions NF006425.0 PRK08674 PRK08674.1-5 471 471 358 equivalog Y Y N bifunctional phosphoglucose/phosphomannose isomerase 5.3.1.9 2 Bacteria superkingdom 105 NCBI Protein Cluster (PRK) bifunctional phosphoglucose/phosphomannose isomerase bifunctional phosphoglucose/phosphomannose isomerase NF006439.0 PRK08737 PRK08737.1 345 345 364 equivalog Y Y N acetylornithine deacetylase 3.5.1.16 2 Bacteria superkingdom 1432 NCBI Protein Cluster (PRK) acetylornithine deacetylase acetylornithine deacetylase Catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine NF006444.0 PRK08762 PRK08762.1 449 449 387 equivalog Y Y N molybdopterin-synthase adenylyltransferase MoeB moeB 2 Bacteria superkingdom 2166 NCBI Protein Cluster (PRK) molybdopterin biosynthesis protein MoeB molybdopterin-synthase adenylyltransferase MoeB ATP-dependent adenylate transferase, transfers adenyl moiety to the MoeD subunit of molybdopterin synthase NF006449.0 PRK08775 PRK08775.1 296 296 344 equivalog Y Y N homoserine O-succinyltransferase 2.3.1.46 2 Bacteria superkingdom 1640 NCBI Protein Cluster (PRK) homoserine O-acetyltransferase homoserine O-succinyltransferase NF006452.0 PRK08788 PRK08788.1 177 177 291 equivalog Y Y N crotonase/enoyl-CoA hydratase family protein 2 Bacteria superkingdom 3516 NCBI Protein Cluster (PRK) enoyl-CoA hydratase crotonase/enoyl-CoA hydratase family protein NF006477.0 PRK08881 PRK08881.1 77 77 101 equivalog Y Y N 30S ribosomal protein S14 rpsN GO:0003735,GO:0005840,GO:0006412 11574053,12904577,15049826,9746356 2 Bacteria superkingdom 24768 NCBI Protein Cluster (PRK) 30S ribosomal protein S14 30S ribosomal protein S14 Located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group do not appear to have the zinc-binding motif NF006486.0 PRK08903 PRK08903.1-6 307 307 222 equivalog Y Y N DnaA regulatory inactivator Hda hda 2 Bacteria superkingdom 223 NCBI Protein Cluster (PRK) DnaA regulatory inactivator Hda DnaA regulatory inactivator Hda NF006488.0 PRK08912 PRK08912.1 498 498 387 equivalog Y Y N aminotransferase 2 Bacteria superkingdom 3400 NCBI Protein Cluster (PRK) hypothetical protein aminotransferase NF006492.0 PRK08931 PRK08931.1 437 437 291 equivalog Y Y N S-methyl-5'-thioadenosine phosphorylase 2.4.2.28 GO:0009116,GO:0017061 2 Bacteria superkingdom 4045 NCBI Protein Cluster (PRK) 5'-methylthioadenosine phosphorylase S-methyl-5'-thioadenosine phosphorylase Catalyzes the reversible phosphorolysis of 5'-deoxy-5'- methylthioadenosine (MTA) to adenine and 5-methylthio-D-ribose-1- phosphate NF006493.1 PRK08936 PRK08936.1 420 420 261 subfamily Y Y N glucose-1-dehydrogenase 1.1.1.47 2 Bacteria superkingdom 2070 NCBI Protein Cluster (PRK) glucose-1-dehydrogenase glucose-1-dehydrogenase Converts glucose to D-glucono-1,5 lactone NF006505.0 PRK08939 PRK08939.1 228 228 306 equivalog Y Y N primosomal protein DnaI dnaI 11842108,16002087 2 Bacteria superkingdom 7791 NCBI Protein Cluster (PRK) primosomal protein DnaI primosomal protein DnaI Primosomal protein that may act to load helicase DnaC during DNA replication NF006506.0 PRK08942 PRK08942.1 178 178 182 equivalog Y Y N D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase gmhB 3.1.3.82 GO:0005975,GO:0016791 2 Bacteria superkingdom 14551 NCBI Protein Cluster (PRK) D,D-heptose 1,7-bisphosphate phosphatase D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase Converts the D-glycero-beta-D-manno-heptose 1,7-bisphosphate intermediate into D-glycero-beta-D-manno-heptose 1-phosphate NF006515.0 PRK08961 PRK08961.1 802 802 861 equivalog Y Y N bifunctional aspartate kinase/diaminopimelate decarboxylase 2.7.2.4,4.1.1.20 2 Bacteria superkingdom 1959 NCBI Protein Cluster (PRK) bifunctional aspartate kinase/diaminopimelate decarboxylase protein bifunctional aspartate kinase/diaminopimelate decarboxylase Catalyzes the 4-phospho-L-aspartate from L-aspartate and the formation of lysine from meso-2,6-diaminoheptanedioate NF006517.0 PRK08965 PRK08965.1-1 180 180 161 equivalog Y Y N Na+/H+ antiporter subunit E 2 Bacteria superkingdom 1413 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit E Na+/H+ antiporter subunit E NF006518.0 PRK08965 PRK08965.1-2 159 159 166 equivalog Y Y N Na+/H+ antiporter subunit E GO:0006812,GO:0008324,GO:0016020 2 Bacteria superkingdom 6466 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit E Na+/H+ antiporter subunit E NF006519.0 PRK08965 PRK08965.1-3 190 190 158 equivalog Y Y N Na+/H+ antiporter subunit E 2 Bacteria superkingdom 1054 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit E Na+/H+ antiporter subunit E NF006521.0 PRK08965 PRK08965.1-5 141 141 180 equivalog Y Y N Na+/H+ antiporter subunit E GO:0006812,GO:0008324 2 Bacteria superkingdom 7603 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit E Na+/H+ antiporter subunit E NF006530.0 PRK08999 PRK08999.1 245 245 315 equivalog Y Y N Nudix family hydrolase GO:0008413 2 Bacteria superkingdom 7348 NCBI Protein Cluster (PRK) hypothetical protein Nudix family hydrolase NF006540.0 PRK09034 PRK09034.1 434 434 454 equivalog Y Y N aspartate kinase 2.7.2.4 GO:0004072,GO:0009089 11471740 2 Bacteria superkingdom 10903 NCBI Protein Cluster (PRK) aspartate kinase aspartate kinase Catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP; lysine and threonine sensitive NF006543.0 PRK09039 PRK09039.1-2 305 305 350 equivalog Y Y N peptidoglycan -binding protein 2 Bacteria superkingdom 3858 NCBI Protein Cluster (PRK) hypothetical protein peptidoglycan -binding protein NF006549.0 PRK09045 PRK09045.1 540 540 444 equivalog Y Y N TRZ/ATZ family hydrolase GO:0016810 2 Bacteria superkingdom 6429 NCBI Protein Cluster (PRK) N-ethylammeline chlorohydrolase TRZ/ATZ family hydrolase NF006550.0 PRK09047 PRK09047.1 173 173 194 equivalog Y Y N RNA polymerase sigma factor 2.7.7.6 GO:0003677,GO:0006352,GO:0006355,GO:0016987 2 Bacteria superkingdom 4189 NCBI Protein Cluster (PRK) RNA polymerase factor sigma-70 RNA polymerase sigma factor NF006551.0 PRK09050 PRK09050.1 605 605 401 subfamily Y Y N 3-oxoadipyl-CoA thiolase 2.3.1.174 2 Bacteria superkingdom 28116 NCBI Protein Cluster (PRK) beta-ketoadipyl CoA thiolase 3-oxoadipyl-CoA thiolase NF006552.0 PRK09051 PRK09051.1 565 565 395 subfamily Y Y N beta-ketothiolase BktB bktB 9555876 2 Bacteria superkingdom 8023 NCBI Protein Cluster (PRK) beta-ketothiolase beta-ketothiolase BktB Catalyzes the formation of beta-ketovaleryl-CoA from acetyl-CoA and propionyl-CoA NF006553.0 PRK09052 PRK09052.1 567 567 399 equivalog Y Y N acetyl-CoA C-acyltransferase 2.3.1.16 GO:0016746 2 Bacteria superkingdom 4729 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA C-acyltransferase NF006559.0 PRK09060 PRK09060.1 482 482 444 equivalog Y Y N dihydroorotase 3.5.2.3 GO:0016810 2 Bacteria superkingdom 5620 NCBI Protein Cluster (PRK) dihydroorotase dihydroorotase NF006562.0 PRK09065 PRK09065.1 205 205 242 equivalog Y Y N glutamine amidotransferase 2 Bacteria superkingdom 5426 NCBI Protein Cluster (PRK) glutamine amidotransferase glutamine amidotransferase Catalyzes the transfer of the ammonia group from glutamine to a new carbon-nitrogen group NF006563.0 PRK09070 PRK09070.1 514 514 447 equivalog Y Y N aminodeoxychorismate synthase component I 2.6.1.85 2 Bacteria superkingdom 2077 NCBI Protein Cluster (PRK) hypothetical protein aminodeoxychorismate synthase component I NF006567.0 PRK09077 PRK09077.1 629 629 537 equivalog Y Y N L-aspartate oxidase nadB 1.4.3.16 GO:0008734,GO:0009435 2 Bacteria superkingdom 19235 NCBI Protein Cluster (PRK) L-aspartate oxidase L-aspartate oxidase Catalyzes the formation of oxaloacetate from L-aspartate NF006569.0 PRK09082 PRK09082.1 420 420 386 subfamily Y Y N methionine aminotransferase GO:0030170 2 Bacteria superkingdom 23957 NCBI Protein Cluster (PRK) methionine aminotransferase methionine aminotransferase NF006573.0 PRK09094 PRK09094.1 105 105 114 equivalog Y Y N Na+/H+ antiporter subunit C 2 Bacteria superkingdom 8630 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit C Na+/H+ antiporter subunit C Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF006581.0 PRK09107 PRK09107.1 974 974 595 equivalog Y Y N acetolactate synthase 3 large subunit 2.2.1.6 GO:0000287,GO:0003984,GO:0009082,GO:0030976,GO:0050660 2 Bacteria superkingdom 6646 NCBI Protein Cluster (PRK) acetolactate synthase 3 catalytic subunit acetolactate synthase 3 large subunit NF006583.0 PRK09109 PRK09109.1 237 237 246 equivalog Y Y N flagellar motor protein 15629949 2 Bacteria superkingdom 6638 NCBI Protein Cluster (PRK) flagellar motor protein flagellar motor protein NF006585.0 PRK09111 PRK09111.1 604 604 616 equivalog Y Y N DNA polymerase III subunit gamma/tau 2.7.7.7 GO:0003887,GO:0006260 2 Bacteria superkingdom 9325 NCBI Protein Cluster (PRK) DNA polymerase III subunits gamma and tau DNA polymerase III subunit gamma/tau Catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA NF006589.0 PRK09121 PRK09121.1 392 392 342 equivalog Y Y N methionine synthase 2.1.1.13 GO:0003871,GO:0008270,GO:0009086 18319726 2 Bacteria superkingdom 10312 NCBI Protein Cluster (PRK) 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase methionine synthase NF006591.0 PRK09124 PRK09124.1 792 792 574 equivalog Y Y N ubiquinone-dependent pyruvate dehydrogenase poxB 1.2.5.1 GO:0000287,GO:0006090,GO:0030976,GO:0052737 2 Bacteria superkingdom 17783 NCBI Protein Cluster (PRK) pyruvate dehydrogenase ubiquinone-dependent pyruvate dehydrogenase NF006592.0 PRK09125 PRK09125.1 200 200 283 equivalog Y Y N DNA ligase 6.5.1.1 GO:0003910,GO:0005524,GO:0006281,GO:0006310 2 Bacteria superkingdom 7791 NCBI Protein Cluster (PRK) DNA ligase DNA ligase Catalyzes the formation of a phosphodiester at the site of a single-strand break in duplex DNA NF006593.0 PRK09126 PRK09126.1 420 420 393 equivalog Y Y N 5-demethoxyubiquinol-8 5-hydroxylase UbiM ubiM GO:0006744,GO:0016709,GO:0071949 27822549 2 Bacteria superkingdom 3616 NCBI Protein Cluster (PRK) hypothetical protein 5-demethoxyubiquinol-8 5-hydroxylase UbiM NF006596.0 PRK09133 PRK09133.1 349 349 474 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 3684 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006598.0 PRK09135 PRK09135.1 288 288 249 equivalog Y Y N pteridine reductase 1.5.1.33 GO:0016491 2 Bacteria superkingdom 3492 NCBI Protein Cluster (PRK) pteridine reductase pteridine reductase Involved in pteridine salvage and antifolate resistance NF006600.0 PRK09140 PRK09140.1 207 207 210 subfamily Y Y N 2-dehydro-3-deoxy-6-phosphogalactonate aldolase 4.1.2.21 211976,324806 2 Bacteria superkingdom 14455 NCBI Protein Cluster (PRK) 2-dehydro-3-deoxy-6-phosphogalactonate aldolase 2-dehydro-3-deoxy-6-phosphogalactonate aldolase Catalyzes the formation of D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-galactonate 6-phosphate; functions in galactonate metabolism NF006604.0 PRK09148 PRK09148.1 648 648 406 equivalog Y Y N LL-diaminopimelate aminotransferase 2.6.1.83 GO:0030170 2 Bacteria superkingdom 4988 NCBI Protein Cluster (PRK) aminotransferase LL-diaminopimelate aminotransferase NF006606.0 PRK09165 PRK09165.1 540 540 497 equivalog Y Y N replicative DNA helicase 3.6.4.12 GO:0003678,GO:0006260 2 Bacteria superkingdom 7321 NCBI Protein Cluster (PRK) replicative DNA helicase replicative DNA helicase Unwinds double stranded DNA NF006613.0 PRK09177 PRK09177.1 138 138 159 equivalog Y Y N xanthine phosphoribosyltransferase gpt 2.4.2.22 GO:0000310,GO:0009116 2 Bacteria superkingdom 6682 NCBI Protein Cluster (PRK) xanthine-guanine phosphoribosyltransferase xanthine phosphoribosyltransferase NF006614.0 PRK09181 PRK09181.1 536 536 476 equivalog Y Y N aspartate kinase 2.7.2.4 2 Bacteria superkingdom 3595 NCBI Protein Cluster (PRK) aspartate kinase aspartate kinase Catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP NF006615.0 PRK09182 PRK09182.1 207 207 307 subfamily Y Y N 3'-5' exonuclease GO:0003676 2 Bacteria superkingdom 3753 NCBI Protein Cluster (PRK) DNA polymerase III subunit epsilon 3'-5' exonuclease NF006617.0 PRK09184 PRK09184.1 70 70 96 subfamily Y Y N phosphopantetheine-binding protein 2 Bacteria superkingdom 7083 NCBI Protein Cluster (PRK) acyl carrier protein phosphopantetheine-binding protein NF006618.0 PRK09185 PRK09185.1 407 407 394 subfamily Y Y N beta-ketoacyl-ACP synthase 2.3.1.179 GO:0004315,GO:0006633 2 Bacteria superkingdom 15166 NCBI Protein Cluster (PRK) 3-oxoacyl-(acyl carrier protein) synthase I beta-ketoacyl-ACP synthase NF006622.0 PRK09190 PRK09190.1 184 184 227 equivalog Y Y N RNA-binding protein 2 Bacteria superkingdom 5852 NCBI Protein Cluster (PRK) hypothetical protein RNA-binding protein NF006623.1 PRK09191 PRK09191.1 240 240 258 subfamily Y Y N PhyR family response regulator anti-anti-sigma factor 26724735,29052909 2 Bacteria superkingdom 6007 NCBI Protein Cluster (PRK) two-component response regulator PhyR family response regulator anti-anti-sigma factor PhyR, which has a response regulator receiver domain, transduces signals via interaction with the NepR anti-sigma factor rather than through DNA-binding activity. NF006625.0 PRK09194 PRK09194.1 558 558 559 equivalog Y Y N proline--tRNA ligase 6.1.1.15 GO:0000166,GO:0002161,GO:0004812,GO:0004827,GO:0005524,GO:0006418,GO:0006433 2 Bacteria superkingdom 57969 NCBI Protein Cluster (PRK) prolyl-tRNA synthetase proline--tRNA ligase Catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro) NF006626.0 PRK09195 PRK09195.1 384 384 284 subfamily Y N N tagatose-bisphosphate aldolase 2 Bacteria superkingdom 5853 NCBI Protein Cluster (PRK) tagatose-bisphosphate aldolase tagatose-bisphosphate aldolase NF006628.0 PRK09197 PRK09197.1 297 297 359 equivalog Y Y N class II fructose-bisphosphate aldolase fbaA 4.1.2.13 GO:0004332,GO:0005975,GO:0006096,GO:0008270 2 Bacteria superkingdom 21158 NCBI Protein Cluster (PRK) fructose-bisphosphate aldolase class II fructose-bisphosphate aldolase Catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate NF006630.0 PRK09200 PRK09200.1 862 862 789 subfamily Y Y N preprotein translocase subunit SecA secA 2 Bacteria superkingdom 23288 NCBI Protein Cluster (PRK) preprotein translocase subunit SecA preprotein translocase subunit SecA Functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimer NF006631.0 PRK09201 PRK09201.1 461 461 466 equivalog Y Y N AtzE family amidohydrolase GO:0003824 2 Bacteria superkingdom 7584 NCBI Protein Cluster (PRK) amidase AtzE family amidohydrolase Catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia NF006664.0 PRK09206 PRK09206.1 686 686 470 equivalog Y Y N pyruvate kinase PykF pykF 2.7.1.40 GO:0004743,GO:0006096 28686591 2 Bacteria superkingdom 3531 NCBI Protein Cluster (PRK) pyruvate kinase pyruvate kinase PykF Catalyzes the formation of phosphoenolpyruvate from pyruvate NF006665.0 PRK09209 PRK09209.1 1057 1057 761 equivalog Y Y N ribonucleoside-diphosphate reductase subunit alpha 1.17.4.1 GO:0004748,GO:0005524,GO:0006260 2 Bacteria superkingdom 3642 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit alpha ribonucleoside-diphosphate reductase subunit alpha NF006666.0 PRK09210 PRK09210.1 572 572 370 equivalog Y Y N RNA polymerase sigma factor RpoD rpoD GO:0003677,GO:0006355,GO:0016987 2 Bacteria superkingdom 7041 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RpoD RNA polymerase sigma factor RpoD Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this is the primary sigma factor of bacteria NF006670.0 PRK09218 PRK09218.1 162 162 136 equivalog Y Y N peptide deformylase 3.5.1.88 2 Bacteria superkingdom 4810 NCBI Protein Cluster (PRK) peptide deformylase peptide deformylase Cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins NF006671.0 PRK09219 PRK09219.1 177 177 192 equivalog Y Y N xanthine phosphoribosyltransferase 2.4.2.22 GO:0016763,GO:0043101,GO:0046110 2 Bacteria superkingdom 13692 NCBI Protein Cluster (PRK) xanthine phosphoribosyltransferase xanthine phosphoribosyltransferase NF006672.0 PRK09220 PRK09220.1 226 226 209 equivalog Y Y N methylthioribulose 1-phosphate dehydratase 4.2.1.109 GO:0019509,GO:0046872 2 Bacteria superkingdom 5882 NCBI Protein Cluster (PRK) methylthioribulose-1-phosphate dehydratase methylthioribulose 1-phosphate dehydratase Converts methylthioribulose-1-phosphate into 2,3-diketo-5-methylthiopentyl-1-phosphate; involved in methionine salvage NF006673.0 PRK09222 PRK09222.1 509 509 482 equivalog Y Y N NADP-dependent isocitrate dehydrogenase 1.1.1.42 2 Bacteria superkingdom 2212 NCBI Protein Cluster (PRK) isocitrate dehydrogenase NADP-dependent isocitrate dehydrogenase Catalyzes the formation of 2-oxoglutarate from isocitrate NF006674.0 PRK09224 PRK09224.1 577 577 508 subfamily Y Y N threonine ammonia-lyase IlvA ilvA 4.3.1.19 2005118 2 Bacteria superkingdom 21829 NCBI Protein Cluster (PRK) threonine dehydratase threonine ammonia-lyase IlvA Catalyzes the formation of 2-oxobutanoate from L-threonine; biosynthetic NF006681.0 PRK09229 PRK09229.1-2 362 362 451 equivalog Y Y N formimidoylglutamate deiminase 3.5.3.13 GO:0016810 2 Bacteria superkingdom 24851 NCBI Protein Cluster (PRK) N-formimino-L-glutamate deiminase formimidoylglutamate deiminase NF006684.0 PRK09229 PRK09229.1-5 525 525 456 equivalog Y Y N formimidoylglutamate deiminase 3.5.3.13 GO:0016810 2 Bacteria superkingdom 15792 NCBI Protein Cluster (PRK) N-formimino-L-glutamate deiminase formimidoylglutamate deiminase NF006685.0 PRK09230 PRK09230.1 483 483 426 subfamily Y Y N cytosine deaminase codA GO:0016810 2 Bacteria superkingdom 14592 NCBI Protein Cluster (PRK) cytosine deaminase cytosine deaminase Catalyzes the deamination of cytosine to uracil and ammonia NF006686.0 PRK09231 PRK09231.1 854 854 598 equivalog Y Y N fumarate reductase (quinol) flavoprotein subunit frdA 1.3.5.1 GO:0009061,GO:0016491,GO:0022900,GO:0050660 2 Bacteria superkingdom 6121 NCBI Protein Cluster (PRK) fumarate reductase flavoprotein subunit fumarate reductase (quinol) flavoprotein subunit Part of four member fumarate reductase enzyme complex FrdABCD which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdCD are the membrane components which interact with quinone and are involved in electron transfer; the catalytic subunits are similar to succinate dehydrogenase SdhAB NF006687.0 PRK09234 PRK09234.1 1018 1018 849 equivalog Y Y N bifunctional FO biosynthesis protein CofGH 2.5.1.147,4.3.1.32 GO:0016765,GO:0051539 11948155,14593448 2 Bacteria superkingdom 12223 NCBI Protein Cluster (PRK) FO synthase bifunctional FO biosynthesis protein CofGH 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase; catalyzes radical-mediated transfer of hydroxybenzyl group from 4-hydroxyphenylpyruvate (HPP) to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione to form 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO); functions in F420 biosynthesis NF006688.0 PRK09236 PRK09236.1 535 535 444 equivalog Y Y N dihydroorotase 3.5.2.3 GO:0016812 15278241 2 Bacteria superkingdom 11843 NCBI Protein Cluster (PRK) dihydroorotase dihydroorotase NF006689.0 PRK09237 PRK09237.1 371 371 383 equivalog Y Y N amidohydrolase/deacetylase family metallohydrolase GO:0016810,GO:0019213 2 Bacteria superkingdom 12969 NCBI Protein Cluster (PRK) dihydroorotase amidohydrolase/deacetylase family metallohydrolase NF006691.0 PRK09239 PRK09239.1 120 120 108 equivalog Y Y N chorismate mutase 5.4.99.5 GO:0046417 2 Bacteria superkingdom 11781 NCBI Protein Cluster (PRK) chorismate mutase chorismate mutase Catalyzes the interconversion of chorismate to prephenate NF006693.0 PRK09242 PRK09242.1 328 328 258 equivalog Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 1463 NCBI Protein Cluster (PRK) tropinone reductase SDR family oxidoreductase NF006694.0 PRK09243 PRK09243.1-1 663 663 485 equivalog Y Y N nicotinate phosphoribosyltransferase 6.3.4.21 GO:0004516,GO:0009435 2 Bacteria superkingdom 8866 NCBI Protein Cluster (PRK) nicotinate phosphoribosyltransferase nicotinate phosphoribosyltransferase NF006697.0 PRK09243 PRK09243.1-4 776 776 488 equivalog Y Y N nicotinate phosphoribosyltransferase 6.3.4.21 GO:0004516,GO:0009435 2 Bacteria superkingdom 7560 NCBI Protein Cluster (PRK) nicotinate phosphoribosyltransferase nicotinate phosphoribosyltransferase NF006698.0 PRK09243 PRK09243.1-5 531 531 440 equivalog Y Y N nicotinate phosphoribosyltransferase 6.3.4.21 GO:0004514,GO:0004516,GO:0009435 18490451 2 Bacteria superkingdom 16189 NCBI Protein Cluster (PRK) nicotinate phosphoribosyltransferase nicotinate phosphoribosyltransferase NF006699.0 PRK09245 PRK09245.1 354 354 266 subfamily Y Y N crotonase/enoyl-CoA hydratase family protein 2 Bacteria superkingdom 3846 NCBI Protein Cluster (PRK) enoyl-CoA hydratase crotonase/enoyl-CoA hydratase family protein NF006701.0 PRK09247 PRK09247.1 543 543 540 equivalog Y Y N ATP-dependent DNA ligase 6.5.1.1 GO:0003677,GO:0003910,GO:0005524,GO:0006281,GO:0006310 2 Bacteria superkingdom 16096 NCBI Protein Cluster (PRK) ATP-dependent DNA ligase ATP-dependent DNA ligase Catalyzes the ATP-dependent formation of a phosphodiester at the site of a single strand break in duplex DNA NF006702.0 PRK09248 PRK09248.1 264 264 246 domain Y Y N PHP domain-containing protein 2 Bacteria superkingdom 8311 NCBI Protein Cluster (PRK) putative hydrolase PHP domain-containing protein NF006704.0 PRK09250 PRK09250.1-1 277 277 308 equivalog Y Y N class I fructose-bisphosphate aldolase 4.1.2.13 GO:0004332,GO:0006096 2 Bacteria superkingdom 1885 NCBI Protein Cluster (PRK) fructose-bisphosphate aldolase class I fructose-bisphosphate aldolase NF006707.0 PRK09250 PRK09250.1-4 327 327 355 equivalog Y Y N class I fructose-bisphosphate aldolase 4.1.2.13 GO:0004332 2 Bacteria superkingdom 5196 NCBI Protein Cluster (PRK) fructose-bisphosphate aldolase class I fructose-bisphosphate aldolase NF006718.0 PRK09256 PRK09256.1 100 100 140 equivalog Y Y N alternative ribosome rescue aminoacyl-tRNA hydrolase ArfB arfB 3.1.1.29 GO:0003747,GO:0006415 33815344 2 Bacteria superkingdom 31940 NCBI Protein Cluster (PRK) hypothetical protein alternative ribosome rescue aminoacyl-tRNA hydrolase ArfB ArfB (alternative ribosome rescue factor B), a peptidyl-tRNA hydrolase, represents a separate ribosome rescue system from the tmRNA-mediated trans-translation system and the ArfA and PrfB alternative ribosome rescue system. In some species, ArfB enables survival when both the tmRNA and ArfA systems are disabled. NF006719.0 PRK09257 PRK09257.1 377 377 397 subfamily Y Y N aromatic amino acid transaminase GO:0006520,GO:0008483,GO:0030170 2 Bacteria superkingdom 38434 NCBI Protein Cluster (PRK) aromatic amino acid aminotransferase aromatic amino acid transaminase Catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate NF006720.0 PRK09258 PRK09258.1 285 285 338 equivalog Y Y N 3-oxoacyl-ACP synthase III GO:0004315,GO:0006633 22524624 2 Bacteria superkingdom 3240 NCBI Protein Cluster (PRK) 3-oxoacyl-(acyl carrier protein) synthase III 3-oxoacyl-ACP synthase III NF006721.0 PRK09259 PRK09259.1 557 557 574 equivalog Y Y N oxalyl-CoA decarboxylase oxc 4.1.1.8 GO:0000287,GO:0008949,GO:0030976,GO:0033611 2 Bacteria superkingdom 5102 NCBI Protein Cluster (PRK) putative oxalyl-CoA decarboxylase oxalyl-CoA decarboxylase NF006722.0 PRK09260 PRK09260.1 429 429 289 equivalog Y Y N 3-hydroxyacyl-CoA dehydrogenase 2 Bacteria superkingdom 1365 NCBI Protein Cluster (PRK) 3-hydroxybutyryl-CoA dehydrogenase 3-hydroxyacyl-CoA dehydrogenase NF006732.0 PRK09263 PRK09263.1 657 657 712 equivalog Y Y N anaerobic ribonucleoside-triphosphate reductase nrdD 1.17.4.2 GO:0006260,GO:0008998 2 Bacteria superkingdom 17852 NCBI Protein Cluster (PRK) anaerobic ribonucleoside triphosphate reductase anaerobic ribonucleoside-triphosphate reductase Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates NF006734.0 PRK09266 PRK09266.1 202 202 270 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 9020 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006738.0 PRK09267 PRK09267.1-4 172 172 171 equivalog Y Y N flavodoxin FldA fldA 2 Bacteria superkingdom 3185 NCBI Protein Cluster (PRK) flavodoxin FldA flavodoxin FldA NF006739.0 PRK09267 PRK09267.1-5 175 175 168 subfamily Y Y N flavodoxin FldA fldA 2 Bacteria superkingdom 9960 NCBI Protein Cluster (PRK) flavodoxin FldA flavodoxin FldA NF006740.0 PRK09268 PRK09268.1 539 539 431 equivalog Y Y N acetyl-CoA C-acetyltransferase 2.3.1.9 GO:0016746 2 Bacteria superkingdom 16718 NCBI Protein Cluster (PRK) acetyl-CoA acetyltransferase acetyl-CoA C-acetyltransferase Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A NF006741.0 PRK09269 PRK09269.1 158 158 194 equivalog Y Y N chorismate mutase 5.4.99.5 GO:0046417 15654876,17965159 2 Bacteria superkingdom 5824 NCBI Protein Cluster (PRK) chorismate mutase chorismate mutase Catalyzes the interconversion of chorismate to prephenate NF006743.0 PRK09270 PRK09270.1-2 227 227 217 equivalog Y Y N nucleoside/nucleotide kinase family protein GO:0005524,GO:0016301 2 Bacteria superkingdom 12400 NCBI Protein Cluster (PRK) nucleoside triphosphate hydrolase domain-containing protein nucleoside/nucleotide kinase family protein NF006747.0 PRK09271 PRK09271.1 104 104 160 equivalog Y Y N flavodoxin 2 Bacteria superkingdom 1202 NCBI Protein Cluster (PRK) flavodoxin flavodoxin An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group NF006749.0 PRK09272 PRK09272.1-2 119 119 116 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 1483 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006750.0 PRK09272 PRK09272.1-3 101 101 112 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 1055 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006751.0 PRK09272 PRK09272.1-4 154 154 116 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 1351 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006753.0 PRK09273 PRK09273.1 137 137 211 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 4721 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF006754.0 PRK09274 PRK09274.1 478 478 555 equivalog Y Y N fatty acid CoA ligase family protein GO:0006631,GO:0031956 2 Bacteria superkingdom 3670 NCBI Protein Cluster (PRK) peptide synthase fatty acid CoA ligase family protein NF006765.0 PRK09287 PRK09287.1 413 413 476 equivalog Y Y N NADP-dependent phosphogluconate dehydrogenase gndA 1.1.1.44 GO:0004616,GO:0006098,GO:0050661 2 Bacteria superkingdom 43763 NCBI Protein Cluster (PRK) 6-phosphogluconate dehydrogenase NADP-dependent phosphogluconate dehydrogenase Catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate NF006768.0 PRK09290 PRK09290.1-1 532 532 411 equivalog Y Y N allantoate deiminase allC 3.5.3.9 GO:0000256,GO:0009442,GO:0047652 17362992 2 Bacteria superkingdom 4337 NCBI Protein Cluster (PRK) allantoate amidohydrolase allantoate deiminase NF006770.0 PRK09290 PRK09290.1-4 372 372 403 equivalog Y Y N allantoate amidohydrolase GO:0016813 2 Bacteria superkingdom 11585 NCBI Protein Cluster (PRK) allantoate amidohydrolase allantoate amidohydrolase NF006772.0 PRK09290 PRK09290.2-1 424 424 430 subfamily Y Y N allantoate amidohydrolase 2 Bacteria superkingdom 2279 NCBI Protein Cluster (PRK) allantoate amidohydrolase allantoate amidohydrolase NF006775.0 PRK09290 PRK09290.2-5 479 479 419 equivalog Y Y N allantoate amidohydrolase GO:0016813 2 Bacteria superkingdom 9323 NCBI Protein Cluster (PRK) allantoate amidohydrolase allantoate amidohydrolase NF006777.0 PRK09292 PRK09292.1 235 235 209 equivalog Y Y N NADH:ubiquinone reductase (Na(+)-transporting) subunit D GO:0016020,GO:0016655 2 Bacteria superkingdom 7251 NCBI Protein Cluster (PRK) Na(+)-translocating NADH-quinone reductase subunit D NADH:ubiquinone reductase (Na(+)-transporting) subunit D NF006778.0 PRK09293 PRK09293.1-1 368 368 335 equivalog Y Y N class 1 fructose-bisphosphatase fbp 3.1.3.11 GO:0005975,GO:0042132 2 Bacteria superkingdom 13219 NCBI Protein Cluster (PRK) fructose-1,6-bisphosphatase class 1 fructose-bisphosphatase NF006779.0 PRK09293 PRK09293.1-3 349 349 334 equivalog Y Y N class 1 fructose-bisphosphatase 3.1.3.11 GO:0005975,GO:0042132 2 Bacteria superkingdom 17236 NCBI Protein Cluster (PRK) fructose-1,6-bisphosphatase class 1 fructose-bisphosphatase NF006780.0 PRK09293 PRK09293.1-4 358 358 343 equivalog Y Y N class 1 fructose-bisphosphatase 3.1.3.11 GO:0005975,GO:0042132 2 Bacteria superkingdom 11879 NCBI Protein Cluster (PRK) fructose-1,6-bisphosphatase class 1 fructose-bisphosphatase NF006819.0 PRK09344 PRK09344.1-1 745 745 538 subfamily Y Y N phosphoenolpyruvate carboxykinase 4.1.1.49 2 Bacteria superkingdom 12000 NCBI Protein Cluster (PRK) phosphoenolpyruvate carboxykinase phosphoenolpyruvate carboxykinase NF006822.0 PRK09344 PRK09344.1-4 806 806 537 equivalog Y Y N phosphoenolpyruvate carboxykinase 4.1.1.49 GO:0004612,GO:0006094 2 Bacteria superkingdom 6888 NCBI Protein Cluster (PRK) phosphoenolpyruvate carboxykinase phosphoenolpyruvate carboxykinase NF006823.0 PRK09344 PRK09344.1-5 815 815 513 equivalog Y Y N phosphoenolpyruvate carboxykinase 4.1.1.49 GO:0004611,GO:0005524,GO:0006094,GO:0017076 2 Bacteria superkingdom 3901 NCBI Protein Cluster (PRK) phosphoenolpyruvate carboxykinase phosphoenolpyruvate carboxykinase NF006829.0 PRK09352 PRK09352.1 249 249 322 subfamily Y Y N beta-ketoacyl-ACP synthase 3 2.3.1.180 GO:0004315 2 Bacteria superkingdom 87849 NCBI Protein Cluster (PRK) 3-oxoacyl-(acyl carrier protein) synthase III beta-ketoacyl-ACP synthase 3 NF006836.0 PRK09357 PRK09357.1-1 538 538 432 equivalog Y Y N dihydroorotase 3.5.2.3 2 Bacteria superkingdom 14936 NCBI Protein Cluster (PRK) dihydroorotase dihydroorotase NF006837.0 PRK09357 PRK09357.1-2 575 575 428 equivalog Y Y N dihydroorotase 3.5.2.3 GO:0004151,GO:0006221,GO:0046872 2 Bacteria superkingdom 9189 NCBI Protein Cluster (PRK) dihydroorotase dihydroorotase NF006847.0 PRK09358 PRK09358.1-2 412 412 364 equivalog Y Y N adenosine deaminase 3.5.4.4 GO:0004000,GO:0009168 2 Bacteria superkingdom 16443 NCBI Protein Cluster (PRK) adenosine deaminase adenosine deaminase NF006848.0 PRK09358 PRK09358.1-3 426 426 325 equivalog Y Y N adenosine deaminase 3.5.4.4 GO:0000034,GO:0006146 2 Bacteria superkingdom 3270 NCBI Protein Cluster (PRK) adenosine deaminase adenosine deaminase NF006849.0 PRK09358 PRK09358.1-5 494 494 350 equivalog Y Y N adenosine deaminase 3.5.4.4 GO:0009168,GO:0019239 2 Bacteria superkingdom 7359 NCBI Protein Cluster (PRK) adenosine deaminase adenosine deaminase NF006854.0 PRK09358 PRK09358.3-1 530 530 344 equivalog Y Y N adenosine deaminase 3.5.4.4 GO:0019239 2 Bacteria superkingdom 6577 NCBI Protein Cluster (PRK) adenosine deaminase adenosine deaminase NF006860.0 PRK09360 PRK09360.1 394 394 414 subfamily Y Y N maltoporin LamB lamB 2 Bacteria superkingdom 5400 NCBI Protein Cluster (PRK) maltoporin maltoporin LamB Porin involved in the transport of maltose and maltodextrins NF006875.0 PRK09372 PRK09372.1 136 136 161 equivalog Y Y N ribonuclease E activity regulator RraA rraA GO:0008428,GO:0051252 14499605 2 Bacteria superkingdom 17696 NCBI Protein Cluster (PRK) ribonuclease activity regulator protein RraA ribonuclease E activity regulator RraA Regulator of RNase E; increases half-life and abundance of RNAs; interacts with RNase E NF006880.0 PRK09375 PRK09375.2-1 556 556 368 equivalog Y Y N quinolinate synthase NadA nadA 2.5.1.72 GO:0008987,GO:0009435,GO:0051539 2 Bacteria superkingdom 3924 NCBI Protein Cluster (PRK) quinolinate synthetase quinolinate synthase NadA NF006881.0 PRK09375 PRK09375.2-2 663 663 389 equivalog Y Y N quinolinate synthase NadA nadA 2.5.1.72 GO:0008987,GO:0009435,GO:0051539 2 Bacteria superkingdom 7156 NCBI Protein Cluster (PRK) quinolinate synthetase quinolinate synthase NadA NF006884.0 PRK09375 PRK09375.2-5 691 691 426 equivalog Y Y N quinolinate synthase NadA nadA 2.5.1.72 2 Bacteria superkingdom 3079 NCBI Protein Cluster (PRK) quinolinate synthetase quinolinate synthase NadA NF006897.0 PRK09379 PRK09379.1 441 441 308 equivalog Y Y N LytR family transcriptional regulator 2 Bacteria superkingdom 2896 NCBI Protein Cluster (PRK) membrane-bound transcriptional regulator LytR LytR family transcriptional regulator NF006898.0 PRK09381 PRK09381.1 138 138 109 equivalog Y Y N thioredoxin TrxA trxA GO:0006662,GO:0015035 2 Bacteria superkingdom 7014 NCBI Protein Cluster (PRK) thioredoxin thioredoxin TrxA NF006899.0 PRK09382 PRK09382.1 417 417 387 equivalog Y Y N bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase 2.7.7.60,4.6.1.12 GO:0008299,GO:0008685,GO:0016114,GO:0050518 2 Bacteria superkingdom 11810 NCBI Protein Cluster (PRK) bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate and 2-C-methyl-D-erythritol 2,4-cyclodiphosphate and CMP from 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis NF006900.1 PRK09390 PRK09390.1 255 255 203 equivalog Y Y N response regulator FixJ fixJ GO:0000160,GO:0001216,GO:0045893 1857213,2046550,8552028 2 Bacteria superkingdom 2530 NCBI Protein Cluster (PRK) response regulator FixJ response regulator FixJ NF006901.0 PRK09392 PRK09392.1 211 211 236 equivalog Y N N transcriptional activator FtrB 2 Bacteria superkingdom 1026 NCBI Protein Cluster (PRK) transcriptional activator FtrB transcriptional activator FtrB NF006902.0 PRK09393 PRK09393.1 425 425 327 equivalog Y Y N transcriptional regulator FtrA ftrA GO:0003700,GO:0006355,GO:0043565 15911751 2 Bacteria superkingdom 7810 NCBI Protein Cluster (PRK) transcriptional activator FtrA transcriptional regulator FtrA upregulated by FixLJ/FixK under oxygen limitation; involved in regulation of genes involved in carbon and amino acid metabolism NF006914.0 PRK09404 PRK09404.1 764 764 919 equivalog Y Y N 2-oxoglutarate dehydrogenase E1 component 1.2.4.2 GO:0004591,GO:0006099,GO:0030976 2 Bacteria superkingdom 59134 NCBI Protein Cluster (PRK) 2-oxoglutarate dehydrogenase E1 component 2-oxoglutarate dehydrogenase E1 component NF006920.0 PRK09410 PRK09410.1-2 410 410 432 subfamily Y Y N PTS ascorbate transporter subunit IIC 2 Bacteria superkingdom 13466 NCBI Protein Cluster (PRK) PTS system ascorbate-specific transporter subunit IIC PTS ascorbate transporter subunit IIC NF006921.0 PRK09410 PRK09410.1-3 648 648 454 equivalog Y Y N PTS ascorbate transporter subunit IIC 2 Bacteria superkingdom 1231 NCBI Protein Cluster (PRK) PTS system ascorbate-specific transporter subunit IIC PTS ascorbate transporter subunit IIC NF006922.0 PRK09410 PRK09410.1-5 561 561 445 equivalog Y Y N PTS ascorbate transporter subunit IIC GO:0009401 2 Bacteria superkingdom 7829 NCBI Protein Cluster (PRK) PTS system ascorbate-specific transporter subunit IIC PTS ascorbate transporter subunit IIC NF006923.0 PRK09410 PRK09410.2-1 548 548 504 equivalog Y Y N PTS ascorbate transporter subunit IIC GO:0009401,GO:0016020 2 Bacteria superkingdom 2228 NCBI Protein Cluster (PRK) PTS system ascorbate-specific transporter subunit IIC PTS ascorbate transporter subunit IIC NF006927.0 PRK09412 PRK09412.1 369 369 433 subfamily Y Y N anaerobic C4-dicarboxylate transporter family protein 2 Bacteria superkingdom 18139 NCBI Protein Cluster (PRK) anaerobic C4-dicarboxylate transporter anaerobic C4-dicarboxylate transporter family protein NF006932.0 PRK09417 PRK09417.1 158 158 193 equivalog Y Y N molybdopterin adenylyltransferase mog 2.7.7.75 GO:0006777 2 Bacteria superkingdom 11336 NCBI Protein Cluster (PRK) molybdenum cofactor biosynthesis protein MogA molybdopterin adenylyltransferase NF006938.0 PRK09420 PRK09420.1 486 486 648 equivalog Y Y N bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase GO:0000166,GO:0008663,GO:0009166,GO:0016788 3005231 2 Bacteria superkingdom 26622 NCBI Protein Cluster (PRK) bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase Functions during ribonucleic acid degradation; 2',3'-cyclic nucleotides are first converted to 3'-nucleotide and then cleaved to yield a ribonucleotide and a phosphate NF006939.0 PRK09421 PRK09421.1 262 262 230 equivalog Y Y N molybdate ABC transporter permease subunit modB 7.3.2.- GO:0015098,GO:0015689,GO:0016020 7665460,8564363 2 Bacteria superkingdom 11596 NCBI Protein Cluster (PRK) molybdate ABC transporter permease protein molybdate ABC transporter permease subunit NF006940.0 PRK09422 PRK09422.1 344 344 338 equivalog Y Y N alcohol dehydrogenase AdhP adhP 1.1.1.1 10406936,2185223 2 Bacteria superkingdom 16165 NCBI Protein Cluster (PRK) ethanol-active dehydrogenase/acetaldehyde-active reductase alcohol dehydrogenase AdhP NF006943.0 PRK09425 PRK09425.1 575 575 480 equivalog Y Y N bifunctional 2-methylcitrate dehydratase/aconitate hydratase 4.2.1.3,4.2.1.79 GO:0019679,GO:0047547,GO:0051537 11294638,11807258,12473114 2 Bacteria superkingdom 12680 NCBI Protein Cluster (PRK) 2-methylcitrate dehydratase bifunctional 2-methylcitrate dehydratase/aconitate hydratase Functions in propionate metabolism; involved in isomerization of (2S,3S)-methylcitrate to (2R,3S)-methylisocitrate; also encodes minor aconitase or dehydratase activity; aconitase C NF006945.0 PRK09427 PRK09427.1 380 380 461 equivalog Y Y N bifunctional indole-3-glycerol-phosphate synthase TrpC/phosphoribosylanthranilate isomerase TrpF trpCF 4.1.1.48,5.3.1.24 GO:0004425,GO:0004640,GO:0006568 2494074,3303031 2 Bacteria superkingdom 16544 NCBI Protein Cluster (PRK) bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase bifunctional indole-3-glycerol-phosphate synthase TrpC/phosphoribosylanthranilate isomerase TrpF NF006949.0 PRK09431 PRK09431.1 499 499 554 equivalog Y Y N asparagine synthase B asnB 6.3.5.4 GO:0004066,GO:0006529 2 Bacteria superkingdom 13730 NCBI Protein Cluster (PRK) asparagine synthetase B asparagine synthase B NF006959.0 PRK09436 PRK09436.1 726 726 819 equivalog Y Y N bifunctional aspartate kinase/homoserine dehydrogenase I thrA 1.1.1.3,2.7.2.4 GO:0004072,GO:0004412,GO:0008652,GO:0009067,GO:0050661 4148765 2 Bacteria superkingdom 20017 NCBI Protein Cluster (PRK) bifunctional aspartokinase I/homoserine dehydrogenase I bifunctional aspartate kinase/homoserine dehydrogenase I Catalyzes the phosphorylation of aspartate to form aspartyl-4-phosphate as well as conversion of aspartate semialdehyde to homoserine; functions in a number of amino acid biosynthetic pathways NF006967.0 PRK09440 PRK09440.1-5 402 402 424 equivalog Y Y N valine--pyruvate transaminase 2.6.1.66 2 Bacteria superkingdom 9461 NCBI Protein Cluster (PRK) valine--pyruvate transaminase valine--pyruvate transaminase NF006968.0 PRK09441 PRK09441.1-1 389 389 495 equivalog Y Y N alpha-amylase amyA 3.2.1.1 GO:0004553,GO:0005509,GO:0005975 2 Bacteria superkingdom 14116 NCBI Protein Cluster (PRK) cytoplasmic alpha-amylase alpha-amylase NF006969.0 PRK09441 PRK09441.1-2 382 382 483 equivalog Y Y N alpha-amylase 3.2.1.1 2 Bacteria superkingdom 14273 NCBI Protein Cluster (PRK) cytoplasmic alpha-amylase alpha-amylase NF006972.0 PRK09441 PRK09441.1-5 804 804 514 equivalog Y Y N alpha-amylase amyS 3.2.1.1 2 Bacteria superkingdom 1870 NCBI Protein Cluster (PRK) cytoplasmic alpha-amylase alpha-amylase NF006974.0 PRK09444 PRK09444.1 689 689 460 equivalog Y Y N Re/Si-specific NAD(P)(+) transhydrogenase subunit beta pntB GO:0008750,GO:0016020,GO:0050661 1551908,15863102,3891338,8100227 2 Bacteria superkingdom 11329 NCBI Protein Cluster (PRK) pyridine nucleotide transhydrogenase Re/Si-specific NAD(P)(+) transhydrogenase subunit beta Involved in catalyzing the transfer of hydride ion equivalents between NAD and NADP; stereospecific (AB-specific); functions as a proton pump by translocating protons from cytoplasm to periplasm NF006975.0 PRK09448 PRK09448.1 114 114 168 equivalog Y Y N DNA starvation/stationary phase protection protein Dps dps pexB GO:0016722 9546221 2 Bacteria superkingdom 4743 NCBI Protein Cluster (PRK) DNA starvation/stationary phase protection protein Dps DNA starvation/stationary phase protection protein Dps Binds DNA in a non-sequence-specific manner and is abundant during stationary phase; forms a DNA-protein crystal that protects DNA from damage; required for normal starvation response and long-term stationary viability; forms a homododecameric complex and sequesters iron which provides protection against oxidative damage NF006976.0 PRK09449 PRK09449.1 183 183 225 equivalog Y Y N pyrimidine 5'-nucleotidase yjjG 3.1.3.5 GO:0008253 2 Bacteria superkingdom 6986 NCBI Protein Cluster (PRK) dUMP phosphatase pyrimidine 5'-nucleotidase NF006988.0 PRK09453 PRK09453.1 117 117 183 equivalog Y Y N phosphodiesterase yfcE 3.1.4.- 2 Bacteria superkingdom 8488 NCBI Protein Cluster (PRK) phosphodiesterase phosphodiesterase NF007000.1 PRK09463 PRK09463.1 600 600 726 subfamily Y Y N acyl-CoA dehydrogenase 1.3.8.- 10206693,12057976 2 Bacteria superkingdom 28150 NCBI Protein Cluster (PRK) acyl-CoA dehydrogenase acyl-CoA dehydrogenase NF007014.0 PRK09478 PRK09478.1 386 386 336 equivalog Y Y N galactose/methyl galactoside ABC transporter permease MglC mglC GO:0008643,GO:0016020,GO:0022857,GO:0055085 18263746,6294056 2 Bacteria superkingdom 3236 NCBI Protein Cluster (PRK) beta-methylgalactoside transporter inner membrane component galactose/methyl galactoside ABC transporter permease MglC With MglAB transports galactose or methyl galactoside into the cell; contains 2 ATP binding domains NF007020.0 PRK09485 PRK09485.1 215 215 306 equivalog Y Y N homocysteine S-methyltransferase mmuM 2.1.1.10 GO:0009086,GO:0047150 10026151,9882684 2 Bacteria superkingdom 19626 NCBI Protein Cluster (PRK) homocysteine methyltransferase homocysteine S-methyltransferase Converts homocysteine and S-adenosyl-methionine to methionine and S-adenosyl-homocysteine NF007024.0 PRK09490 PRK09490.1 1497 1497 1234 equivalog Y Y N methionine synthase metH 2.1.1.13 GO:0008270,GO:0008705,GO:0009086,GO:0031419 1593636,2668277,8369296,8939751 2 Bacteria superkingdom 39875 NCBI Protein Cluster (PRK) B12-dependent methionine synthase methionine synthase NF007033.0 PRK09496 PRK09496.1-5 338 338 449 equivalog Y Y N Trk system potassium transporter TrkA trkA 2 Bacteria superkingdom 3858 NCBI Protein Cluster (PRK) potassium transporter peripheral membrane component Trk system potassium transporter TrkA NF007038.0 PRK09496 PRK09496.2-6 374 374 445 equivalog Y Y N Trk system potassium transporter TrkA trkA GO:0005886,GO:0006813,GO:0015079 2 Bacteria superkingdom 2882 NCBI Protein Cluster (PRK) potassium transporter peripheral membrane component Trk system potassium transporter TrkA NF007043.0 PRK09496 PRK09496.3-6 384 384 445 equivalog Y Y N Trk system potassium transporter TrkA trkA 2 Bacteria superkingdom 122 NCBI Protein Cluster (PRK) potassium transporter peripheral membrane component Trk system potassium transporter TrkA NF007067.0 PRK09512 PRK09512.1 398 398 321 equivalog Y Y N ribose ABC transporter permease rbsC GO:0016020,GO:0022857,GO:0055085 3011793,6327617,9922273 2 Bacteria superkingdom 3928 NCBI Protein Cluster (PRK) ribose ABC transporter permease protein ribose ABC transporter permease RbsABCD acts to import ribose into the cell NF007074.0 PRK09525 PRK09525.1 1221 1221 1027 subfamily Y Y N beta-galactosidase 3.2.1.23 8008071 2 Bacteria superkingdom 16270 NCBI Protein Cluster (PRK) beta-D-galactosidase beta-galactosidase Hydrolyzes lactose disaccharide to galactose and glucose; converts lactose to allolactose which is the natural inducer of the lac operon NF007077.0 PRK09528 PRK09528.1 429 429 421 subfamily Y N N galactoside permease 2 Bacteria superkingdom 11453 NCBI Protein Cluster (PRK) galactoside permease galactoside permease NF007080.0 PRK09533 PRK09533.1 712 712 949 equivalog Y Y N bifunctional transaldolase/phosoglucose isomerase 2.2.1.2,5.3.1.9 2 Bacteria superkingdom 1872 NCBI Protein Cluster (PRK) bifunctional transaldolase/phosoglucose isomerase bifunctional transaldolase/phosoglucose isomerase NF007088.0 PRK09542 PRK09542.1 618 618 456 equivalog Y Y N phosphomannomutase/phosphoglucomutase GO:0005975,GO:0016868 16238626 2 Bacteria superkingdom 14141 NCBI Protein Cluster (PRK) phosphomannomutase/phosphoglucomutase phosphomannomutase/phosphoglucomutase NF007094.0 PRK09548 PRK09548.1 687 687 598 equivalog Y Y N PTS ascorbate-specific subunit IIBC 2 Bacteria superkingdom 1352 NCBI Protein Cluster (PRK) PTS system ascorbate-specific transporter subunits IICB PTS ascorbate-specific subunit IIBC Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF007095.0 PRK09549 PRK09549.1 409 409 407 equivalog Y Y N 2,3-diketo-5-methylthiopentyl-1-phosphate enolase 5.3.2.5 11545674,12022921,14551435,15102328 2 Bacteria superkingdom 3791 NCBI Protein Cluster (PRK) 2,3-diketo-5-methylthiopentyl-1-phosphate enolase 2,3-diketo-5-methylthiopentyl-1-phosphate enolase Converts 2,3-diketo-5-methylthiopentyl-1-phosphate into 2-hydroxy 3-keto-5-methylthiopentenyl-1-phosphate; involved in methionine salvage NF007103.0 PRK09552 PRK09552.1 292 292 220 equivalog Y Y N 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase 3.1.3.87 GO:0016791,GO:0071267 11545674,12022921,14551435,15102328 2 Bacteria superkingdom 3137 NCBI Protein Cluster (PRK) 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase Converts 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate to 1,2-dihydroxy-3-keto-5-methylthiopentene; involved in methionine salvage NF007105.0 PRK09554 PRK09554.1 683 683 772 equivalog Y Y N Fe(2+) transporter permease subunit FeoB feoB GO:0005525,GO:0006826,GO:0015093,GO:0016020 12446835,8407793 2 Bacteria superkingdom 11256 NCBI Protein Cluster (PRK) ferrous iron transport protein B Fe(2+) transporter permease subunit FeoB Cytoplasmic membrane ferrous uptake system permease NF007107.0 PRK09556 PRK09556.1 497 497 469 equivalog Y Y N hexose-6-phosphate:phosphate antiporter uhpT GO:0022857,GO:0055085 2156798,2197272,3522583 2 Bacteria superkingdom 3421 NCBI Protein Cluster (PRK) sugar phosphate antiporter hexose-6-phosphate:phosphate antiporter Catalyzes the active transport of sugar-phosphates such as glucose-6-phosphate with the obligatory exchange of inorganic phosphate or organophosphate NF007111.0 PRK09560 PRK09560.1 423 423 389 subfamily Y Y N Na(+)/H(+) antiporter NhaA nhaA 2 Bacteria superkingdom 18799 NCBI Protein Cluster (PRK) pH-dependent sodium/proton antiporter Na(+)/H(+) antiporter NhaA Exports sodium by using the electrochemical proton gradient to allow protons into the cell; functions in adaptation to high salinity and alkaline pH; activity increases at higher pH; downregulated at acidic pH NF007112.0 PRK09561 PRK09561.1 408 408 389 subfamily Y Y N sodium/proton antiporter NhaA nhaA 12562793,15039449,15962009,15988517,16390457 2 Bacteria superkingdom 17969 NCBI Protein Cluster (PRK) pH-dependent sodium/proton antiporter sodium/proton antiporter NhaA Exports sodium by using the electrochemical proton gradient to allow protons into the cell; functions in adaptation to high salinity and alkaline pH; activity increases at higher pH; downregulated at acidic pH NF007123.0 PRK09564 PRK09564.1 458 458 444 equivalog Y Y N CoA-disulfide reductase 1.8.1.14 GO:0016491,GO:0045454 16390443 2 Bacteria superkingdom 3960 NCBI Protein Cluster (PRK) coenzyme A disulfide reductase CoA-disulfide reductase CoADR; specific for coenzyme A disulfide; requires NADH; involved in protecting cells against reactive oxygen species by recycling coenzyme A disulfide which can reduce hydrogen peroxide NF007126.0 PRK09567 PRK09567.1 523 523 595 equivalog Y Y N NirA family protein 2 Bacteria superkingdom 1403 NCBI Protein Cluster (PRK) ferredoxin-nitrite reductase NirA family protein NF007128.0 PRK09569 PRK09569.1 344 344 437 subfamily Y Y N citrate (Si)-synthase 2.3.3.1 2 Bacteria superkingdom 704 NCBI Protein Cluster (PRK) type I citrate synthase citrate (Si)-synthase NF007135.0 PRK09581 PRK09581.1 474 474 457 equivalog Y Y N PleD family two-component system response regulator GO:0000160 2 Bacteria superkingdom 4067 NCBI Protein Cluster (PRK) response regulator PleD PleD family two-component system response regulator NF007139.0 PRK09585 PRK09585.1-3 367 367 370 equivalog Y Y N anhydro-N-acetylmuramic acid kinase 2.7.1.170 GO:0005524,GO:0006040,GO:0009254,GO:0016773 2 Bacteria superkingdom 22906 NCBI Protein Cluster (PRK) anhydro-N-acetylmuramic acid kinase anhydro-N-acetylmuramic acid kinase NF007141.0 PRK09585 PRK09585.1-5 352 352 370 equivalog Y Y N anhydro-N-acetylmuramic acid kinase 2.7.1.170 GO:0005524,GO:0006040,GO:0008080,GO:0009254 2 Bacteria superkingdom 7755 NCBI Protein Cluster (PRK) anhydro-N-acetylmuramic acid kinase anhydro-N-acetylmuramic acid kinase NF007142.0 PRK09585 PRK09585.2-1 435 435 384 equivalog Y Y N anhydro-N-acetylmuramic acid kinase AnmK anmK 2.7.1.170 GO:0006040,GO:0009254,GO:0016773 2 Bacteria superkingdom 2209 NCBI Protein Cluster (PRK) anhydro-N-acetylmuramic acid kinase anhydro-N-acetylmuramic acid kinase AnmK NF007146.0 PRK09585 PRK09585.2-6 440 440 391 equivalog Y Y N anhydro-N-acetylmuramic acid kinase 2.7.1.170 2 Bacteria superkingdom 5334 NCBI Protein Cluster (PRK) anhydro-N-acetylmuramic acid kinase anhydro-N-acetylmuramic acid kinase NF007148.0 PRK09585 PRK09585.3-2 387 387 386 equivalog Y Y N anhydro-N-acetylmuramic acid kinase 2.7.1.170 2 Bacteria superkingdom 13398 NCBI Protein Cluster (PRK) anhydro-N-acetylmuramic acid kinase anhydro-N-acetylmuramic acid kinase NF007151.0 PRK09585 PRK09585.3-6 599 599 396 equivalog Y Y N anhydro-N-acetylmuramic acid kinase 2.7.1.170 2 Bacteria superkingdom 31 NCBI Protein Cluster (PRK) anhydro-N-acetylmuramic acid kinase anhydro-N-acetylmuramic acid kinase NF007153.0 PRK09588 PRK09588.1 407 407 379 equivalog Y Y N RNA ligase RtcB family protein GO:0006396,GO:0008452 2 Bacteria superkingdom 5277 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF007154.0 PRK09589 PRK09589.1 624 624 476 subfamily Y Y N 6-phospho-beta-glucosidase 3.2.1.86 GO:0004553,GO:0005975 2 Bacteria superkingdom 22798 NCBI Protein Cluster (PRK) 6-phospho-beta-glucosidase 6-phospho-beta-glucosidase NF007155.0 PRK09590 PRK09590.1 101 101 104 equivalog Y Y N PTS cellobiose transporter subunit IIB 16390337 2 Bacteria superkingdom 717 NCBI Protein Cluster (PRK) cellobiose phosphotransferase system IIB component PTS cellobiose transporter subunit IIB Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF007156.0 PRK09591 PRK09591.1 144 144 105 equivalog Y Y N PTS cellobiose transporter subunit IIA 16390337 2 Bacteria superkingdom 550 NCBI Protein Cluster (PRK) cellobiose phosphotransferase system IIA component PTS cellobiose transporter subunit IIA Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF007157.0 PRK09592 PRK09592.1 503 503 451 equivalog Y Y N PTS cellobiose transporter subunit IIC celB GO:0008982,GO:0009401,GO:0016020 16390337 2 Bacteria superkingdom 1919 NCBI Protein Cluster (PRK) cellobiose phosphotransferase system IIC component PTS cellobiose transporter subunit IIC Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF007158.0 PRK09593 PRK09593.1 639 639 478 subfamily Y Y N 6-phospho-beta-glucosidase GO:0004553,GO:0005975 2 Bacteria superkingdom 20568 NCBI Protein Cluster (PRK) 6-phospho-beta-glucosidase 6-phospho-beta-glucosidase NF007182.0 PRK09614 PRK09614.1-1 471 471 324 subfamily Y Y N ribonucleotide-diphosphate reductase subunit beta 1.17.4.1 2 Bacteria superkingdom 10642 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit beta ribonucleotide-diphosphate reductase subunit beta NF007183.0 PRK09614 PRK09614.1-2 320 320 327 subfamily Y Y N ribonucleotide-diphosphate reductase subunit beta 1.17.4.1 2 Bacteria superkingdom 14958 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit beta ribonucleotide-diphosphate reductase subunit beta NF007184.0 PRK09614 PRK09614.1-3 310 310 346 equivalog Y Y N ribonucleotide-diphosphate reductase subunit beta 1.17.4.1 GO:0009263,GO:0016491 2 Bacteria superkingdom 5773 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit beta ribonucleotide-diphosphate reductase subunit beta NF007197.1 PRK09618 PRK09618.1 129 129 138 equivalog Y Y N flagellar hook assembly protein FlgD flgD 10481082 2 Bacteria superkingdom 2422 NCBI Protein Cluster (PRK) flagellar basal body rod modification protein flagellar hook assembly protein FlgD Acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod NF007199.0 PRK09620 PRK09620.1 248 248 229 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 761 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF007200.0 PRK09621 PRK09621.1 108 108 141 equivalog Y Y N ATP synthase subunit C 2 Bacteria superkingdom 443 NCBI Protein Cluster (PRK) V-type ATP synthase subunit K ATP synthase subunit C NF007209.0 PRK09631 PRK09631.1 644 644 635 equivalog Y Y N DNA topoisomerase IV subunit A 5.6.2.2 2 Bacteria superkingdom 7912 NCBI Protein Cluster (PRK) DNA topoisomerase IV subunit A DNA topoisomerase IV subunit A NF007210.0 PRK09632 PRK09632.1 989 989 781 equivalog Y Y N ATP-dependent DNA ligase 6.5.1.1 GO:0003910,GO:0006281,GO:0006310 15499016 2 Bacteria superkingdom 4905 NCBI Protein Cluster (PRK) ATP-dependent DNA ligase ATP-dependent DNA ligase Catalyzes the ATP-dependent formation of a phosphodiester at the site of a single-strand break in duplex DNA and has been shown to have polymerase activity NF007211.0 PRK09633 PRK09633.1 774 774 610 equivalog Y Y N DNA ligase D 6.5.1.1 GO:0003910,GO:0005524,GO:0006281 11095673 2 Bacteria superkingdom 2414 NCBI Protein Cluster (PRK) ATP-dependent DNA ligase DNA ligase D Catalyzes the ATP-dependent formation of a phosphodiester at the site of a single-strand break in duplex DNA NF007214.0 PRK09636 PRK09636.1 271 271 293 subfamily Y Y N RNA polymerase sigma factor SigJ sigJ GO:0006352,GO:0006355,GO:0016987 2 Bacteria superkingdom 61886 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigJ RNA polymerase sigma factor SigJ Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription NF007215.0 PRK09637 PRK09637.1 212 212 181 equivalog Y Y N RNA polymerase sigma factor SigZ sigZ 2 Bacteria superkingdom 1184 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigZ RNA polymerase sigma factor SigZ Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription NF007216.0 PRK09638 PRK09638.1 194 194 180 equivalog Y Y N RNA polymerase sigma factor SigY sigY 12897008,14769884 2 Bacteria superkingdom 1512 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigY RNA polymerase sigma factor SigY Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription NF007217.0 PRK09639 PRK09639.1-1 239 239 194 equivalog Y Y N RNA polymerase sigma factor SigX sigX 2 Bacteria superkingdom 762 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigX RNA polymerase sigma factor SigX NF007223.0 PRK09641 PRK09641.1 209 209 187 equivalog Y Y N RNA polymerase sigma factor SigW sigW 2 Bacteria superkingdom 2123 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigW RNA polymerase sigma factor SigW Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription: this protein is involved in detoxification and protection against antimicrobial NF007225.0 PRK09643 PRK09643.1 190 190 204 equivalog Y Y N RNA polymerase sigma factor SigM sigM GO:0003700,GO:0006355,GO:0016987 11899704 2 Bacteria superkingdom 9793 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigM RNA polymerase sigma factor SigM Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription NF007227.0 PRK09645 PRK09645.1 202 202 177 subfamily Y Y N sigma-70 family RNA polymerase sigma factor GO:0003677,GO:0003700,GO:0006352,GO:0016987 2 Bacteria superkingdom 10073 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigL sigma-70 family RNA polymerase sigma factor NF007228.0 PRK09646 PRK09646.1 226 226 194 subfamily Y Y N ECF RNA polymerase sigma factor SigK sigK GO:0003700,GO:0006352,GO:0016987 15882422 2 Bacteria superkingdom 11515 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigK ECF RNA polymerase sigma factor SigK Member of the extracytoplasmic function sigma factors which are active under specific conditions; binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription NF007229.0 PRK09647 PRK09647.1 265 265 220 equivalog Y Y N RNA polymerase sigma factor SigE sigE GO:0003700,GO:0006355,GO:0016987 15049808,15102817 2 Bacteria superkingdom 8206 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigE RNA polymerase sigma factor SigE Sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription NF007231.0 PRK09649 PRK09649.1 219 219 185 equivalog Y Y N RNA polymerase sigma factor SigC sigC 15049808 2 Bacteria superkingdom 655 NCBI Protein Cluster (PRK) RNA polymerase sigma factor SigC RNA polymerase sigma factor SigC Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; the proteins in this cluster is involved expression of genes important stationary phase, nitrogen promoter recognition, and light/dark adaption NF007266.0 PRK09722 PRK09722.1 271 271 230 equivalog Y Y N D-allulose 6-phosphate 3-epimerase alsE 18700786,9401019 2 Bacteria superkingdom 2539 NCBI Protein Cluster (PRK) allulose-6-phosphate 3-epimerase D-allulose 6-phosphate 3-epimerase NF007280.0 PRK09739 PRK09739.1 162 162 199 equivalog Y Y N NAD(P)H oxidoreductase 1.6.99.- 2 Bacteria superkingdom 2990 NCBI Protein Cluster (PRK) hypothetical protein NAD(P)H oxidoreductase NF007284.0 PRK09751 PRK09751.1 1496 1496 1538 equivalog Y Y N ATP-dependent helicase 3.6.4.- GO:0003676,GO:0005524,GO:0016818 7559321 2 Bacteria superkingdom 17949 NCBI Protein Cluster (PRK) putative ATP-dependent helicase Lhr ATP-dependent helicase NF007288.1 PRK09756 PRK09756.1 180 180 153 equivalog Y Y N PTS galactosamine transporter subunit IIB agaB 10931310,8932697 2 Bacteria superkingdom 2953 NCBI Protein Cluster (PRK) PTS system N-acetylgalactosamine-specific transporter subunit IIB PTS galactosamine transporter subunit IIB Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF007289.1 PRK09757 PRK09757.1 300 300 241 equivalog Y Y N PTS galactosamine transporter subunit IIC agaC 2 Bacteria superkingdom 1089 NCBI Protein Cluster (PRK) PTS system N-acetylgalactosamine-specific transporter subunit IIC PTS galactosamine transporter subunit IIC Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF007293.0 PRK09765 PRK09765.1 763 763 639 equivalog Y Y N PTS 2-O-a-mannosyl-D-glycerate transporter subunit IIABC mngA 2.7.1.195 GO:0005351,GO:0009401,GO:0016020,GO:0022877 2 Bacteria superkingdom 4109 NCBI Protein Cluster (PRK) PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC PTS 2-O-a-mannosyl-D-glycerate transporter subunit IIABC Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF007311.0 PRK09796 PRK09796.1 722 722 485 equivalog Y Y N PTS cellobiose/arbutin/salicin transporter subunit IIBC ascF GO:0008982,GO:0009401,GO:0016020 2 Bacteria superkingdom 5486 NCBI Protein Cluster (PRK) PTS system cellobiose/arbutin/salicin-specific transporter subunits IIBC PTS cellobiose/arbutin/salicin transporter subunit IIBC Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF007321.0 PRK09813 PRK09813.1 247 247 261 equivalog Y Y N fructoselysine 6-kinase frlD 2.7.1.218 2 Bacteria superkingdom 1599 NCBI Protein Cluster (PRK) fructoselysine 6-kinase fructoselysine 6-kinase NF007326.0 PRK09814 PRK09814.2-3 420 420 349 equivalog Y N N beta-1,6-galactofuranosyltransferase 2 Bacteria superkingdom 49 NCBI Protein Cluster (PRK) beta-1,6-galactofuranosyltransferase beta-1,6-galactofuranosyltransferase NF007331.0 PRK09819 PRK09819.1 1138 1138 885 equivalog Y Y N mannosylglycerate hydrolase mngB 3.2.1.170 GO:0004559,GO:0006013 2 Bacteria superkingdom 6244 NCBI Protein Cluster (PRK) alpha-mannosidase mannosylglycerate hydrolase NF007332.0 PRK09821 PRK09821.1 524 524 454 equivalog Y Y N GntP family transporter GO:0015128,GO:0016020,GO:0035429 9119199 2 Bacteria superkingdom 3032 NCBI Protein Cluster (PRK) putative transporter GntP family transporter NF007351.0 PRK09846 PRK09846.1 296 296 275 equivalog Y Y N recombination protein RecT recT GO:0003677,GO:0006259 2 Bacteria superkingdom 2024 NCBI Protein Cluster (PRK) recombination and repair protein RecT recombination protein RecT NF007356.0 PRK09852 PRK09852.1 623 623 474 subfamily Y Y N 6-phospho-beta-glucosidase ascB 3.2.1.86 GO:0004553,GO:0005975 2 Bacteria superkingdom 23435 NCBI Protein Cluster (PRK) cryptic 6-phospho-beta-glucosidase 6-phospho-beta-glucosidase NF007359.1 PRK09855 PRK09855.1 400 400 259 equivalog Y Y N PTS galactosamine transporter subunit IID agaD 2 Bacteria superkingdom 960 NCBI Protein Cluster (PRK) PTS system N-acetylgalactosamine-specific transporter subunit IID PTS galactosamine transporter subunit IID Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF007363.0 PRK09860 PRK09860.1 581 581 383 equivalog Y Y N L-threonine dehydrogenase yiaY 1.1.1.103 GO:0016491 2 Bacteria superkingdom 6295 NCBI Protein Cluster (PRK) putative alcohol dehydrogenase L-threonine dehydrogenase NF007365.0 PRK09862 PRK09862.1 530 530 506 equivalog Y Y N YifB family Mg chelatase-like AAA ATPase GO:0005524 2 Bacteria superkingdom 18742 NCBI Protein Cluster (PRK) putative ATP-dependent protease YifB family Mg chelatase-like AAA ATPase NF007366.0 PRK09863 PRK09863.1 426 426 586 equivalog Y Y N putative frv operon regulatory protein GO:0022857,GO:0055085 2 Bacteria superkingdom 1895 NCBI Protein Cluster (PRK) putative frv operon regulatory protein putative frv operon regulatory protein NF007372.0 PRK09874 PRK09874.1 571 571 408 equivalog Y Y N multidrug efflux MFS transporter MdtG mdtG GO:0022857,GO:0055085 2 Bacteria superkingdom 3670 NCBI Protein Cluster (PRK) drug efflux system protein MdtG multidrug efflux MFS transporter MdtG NF007386.0 PRK09907 PRK09907.1 120 120 111 equivalog Y Y N endoribonuclease MazF mazF 3.1.27.- 2 Bacteria superkingdom 1537 NCBI Protein Cluster (PRK) toxin MazF endoribonuclease MazF ChpA; endoribonuclease; toxin of the MazF-MazE (ChpA-ChpR) toxin-antitoxin system NF007388.0 PRK09912 PRK09912.1 448 448 346 subfamily Y Y N L-glyceraldehyde 3-phosphate reductase mgrA 1.1.1.- GO:0047834 2 Bacteria superkingdom 27377 NCBI Protein Cluster (PRK) L-glyceraldehyde 3-phosphate reductase L-glyceraldehyde 3-phosphate reductase NF007399.1 PRK09928 PRK09928.1 695 695 675 subfamily Y Y N choline BCCT transporter BetT betT GO:0016020,GO:0022857,GO:0071705 2 Bacteria superkingdom 15155 NCBI Protein Cluster (PRK) choline transport protein BetT choline BCCT transporter BetT Proton-motive-force-driven choline transporter NF007421.0 PRK09961 PRK09961.1 412 412 345 equivalog Y Y N aminopeptidase ypdE 3.4.11.- 2 Bacteria superkingdom 2082 NCBI Protein Cluster (PRK) exoaminopeptidase aminopeptidase NF007422.0 PRK09965 PRK09965.1 113 113 106 equivalog Y Y N bifunctional 3-phenylpropionate/cinnamic acid dioxygenase ferredoxin subunit 1.14.12.19 GO:0051537 2 Bacteria superkingdom 5217 NCBI Protein Cluster (PRK) 3-phenylpropionate dioxygenase ferredoxin subunit bifunctional 3-phenylpropionate/cinnamic acid dioxygenase ferredoxin subunit NF007426.0 PRK09970 PRK09970.1 916 916 761 equivalog Y Y N xanthine dehydrogenase molybdenum-binding subunit XdhA xdhA 1.17.1.4 GO:0005506,GO:0016491 2 Bacteria superkingdom 4262 NCBI Protein Cluster (PRK) xanthine dehydrogenase subunit XdhA xanthine dehydrogenase molybdenum-binding subunit XdhA Molybdenum cofactor-binding protein; participates in purine salvage NF007427.0 PRK09971 PRK09971.1 287 287 292 equivalog Y Y N xanthine dehydrogenase FAD-binding subunit XdhB xdhB GO:0016491,GO:0071949 2 Bacteria superkingdom 2787 NCBI Protein Cluster (PRK) xanthine dehydrogenase subunit XdhB xanthine dehydrogenase FAD-binding subunit XdhB FAD-binding subunit; with XdhA and XdhC participates in purine salvage NF007431.0 PRK09977 PRK09977.1 214 214 215 equivalog Y Y N MgtC/SapB family protein 2 Bacteria superkingdom 1051 NCBI Protein Cluster (PRK) putative Mg(2+) transport ATPase MgtC/SapB family protein NF007440.0 PRK09987 PRK09987.1 308 308 299 equivalog Y Y N dTDP-4-dehydrorhamnose reductase rfbD 1.1.1.133 2 Bacteria superkingdom 8374 NCBI Protein Cluster (PRK) dTDP-4-dehydrorhamnose reductase dTDP-4-dehydrorhamnose reductase With dTDP-4-dehydrorhamnose 3,5-epimerase forms a complex known as dTDP-L-rhamnose synthetase; catalyzes the reduction of dTDP-4-dehydro-6-deoxy-L-mannose to dTDP-L-rhamnose NF007480.0 PRK10070 PRK10070.1 444 444 400 equivalog Y Y N glycine betaine/L-proline ABC transporter ATP-binding protein ProV proV GO:0005524,GO:0031460 2 Bacteria superkingdom 6092 NCBI Protein Cluster (PRK) glycine betaine transporter ATP-binding subunit glycine betaine/L-proline ABC transporter ATP-binding protein ProV With ProWX is involved in the high-affinity uptake of glycine betaine NF007484.0 PRK10077 PRK10077.1 608 608 480 equivalog Y Y N D-xylose transporter XylE xylE GO:0016020,GO:0022857,GO:0055085 2 Bacteria superkingdom 3329 NCBI Protein Cluster (PRK) D-xylose transporter XylE D-xylose transporter XylE Xylose/proton symporter; member of the major facilitator superfamily (MFS) of transporter NF007493.0 PRK10089 PRK10089.1-2 160 160 112 equivalog Y Y N tRNA-binding protein 2 Bacteria superkingdom 2863 NCBI Protein Cluster (PRK) tRNA-binding protein tRNA-binding protein NF007496.0 PRK10089 PRK10089.1-5 171 171 109 equivalog Y Y N chaperone CsaA csaA 2 Bacteria superkingdom 1829 NCBI Protein Cluster (PRK) tRNA-binding protein chaperone CsaA NF007497.0 PRK10090 PRK10090.1 500 500 480 equivalog Y Y N aldehyde dehydrogenase aldA 1.2.1.- GO:0016620 2 Bacteria superkingdom 10610 NCBI Protein Cluster (PRK) aldehyde dehydrogenase A aldehyde dehydrogenase NF007509.0 PRK10110 PRK10110.1 665 665 530 subfamily Y Y N PTS maltose transporter subunit IICB malX 2 Bacteria superkingdom 6462 NCBI Protein Cluster (PRK) bifunctional PTS system maltose and glucose-specific transporter subunits IICB PTS maltose transporter subunit IICB Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF007525.0 PRK10137 PRK10137.1 625 625 790 equivalog Y Y N alpha-glucosidase ygjK 3.2.1.20 GO:0004555,GO:0005991 2 Bacteria superkingdom 6903 NCBI Protein Cluster (PRK) alpha-glucosidase alpha-glucosidase NF007538.0 PRK10150 PRK10150.1 544 544 607 equivalog Y Y N beta-glucuronidase uidA 3.2.1.31 GO:0004553,GO:0005975 2 Bacteria superkingdom 5418 NCBI Protein Cluster (PRK) beta-D-glucuronidase beta-glucuronidase NF007570.0 PRK10201 PRK10201.1 144 144 168 equivalog Y Y N G/U mismatch-specific DNA glycosylase mug 3.2.2.28 GO:0000700,GO:0006285 2 Bacteria superkingdom 13442 NCBI Protein Cluster (PRK) G/U mismatch-specific DNA glycosylase G/U mismatch-specific DNA glycosylase NF007574.0 PRK10206 PRK10206.1 352 352 345 equivalog Y Y N oxidoreductase GO:0000166 2 Bacteria superkingdom 5341 NCBI Protein Cluster (PRK) putative oxidoreductase oxidoreductase NF007621.2 PRK10276 PRK10276.1 110 110 115 subfamily Y Y N translesion error-prone DNA polymerase V autoproteolytic subunit umuD 2.7.7.7 GO:0003677 2 Bacteria superkingdom 20058 NCBI Protein Cluster (PRK) DNA polymerase V subunit UmuD translesion error-prone DNA polymerase V autoproteolytic subunit Members of this protein family, including UmuD and MucA, are autoproteolytic proteins, homologous to LexA, that are triggered by RecA to self-cleave under certain conditions. Two subunits of the processed form, and one UmuC/MucB-family subunit, for a function DNA polymerase that can replicate DNA across the sites of lesions. However, that replication is error-prone, so these systems are mutagenic. NF007625.0 PRK10281 PRK10281.1 386 386 301 equivalog Y Y N PhzF family isomerase GO:0003824,GO:0009058 2 Bacteria superkingdom 3082 NCBI Protein Cluster (PRK) hypothetical protein PhzF family isomerase NF007640.0 PRK10307 PRK10307.1 276 276 411 subfamily Y Y N WcaI family glycosyltransferase 30821147 2 Bacteria superkingdom 7563 NCBI Protein Cluster (PRK) putative glycosyl transferase WcaI family glycosyltransferase Members of this family of proteins include WcaI (a fucosyltransferase required for an early step in the biosynthesis of the exopolysaccharide colanic acid) and related glycosyltransferases of unknown specific function. NF007662.0 PRK10334 PRK10334.1 321 321 286 subfamily Y Y N small-conductance mechanosensitive channel MscS mscS GO:0016020,GO:0055085 2 Bacteria superkingdom 3706 NCBI Protein Cluster (PRK) mechanosensitive channel MscS small-conductance mechanosensitive channel MscS NF007666.0 PRK10340 PRK10340.1 1284 1284 1030 equivalog Y Y N beta-galactosidase subunit alpha ebgA 3.2.1.23 GO:0004565 2 Bacteria superkingdom 8154 NCBI Protein Cluster (PRK) cryptic beta-D-galactosidase subunit alpha beta-galactosidase subunit alpha NF007680.0 PRK10355 PRK10355.1 504 504 331 equivalog Y Y N D-xylose ABC transporter substrate-binding protein xylF GO:0015753 2 Bacteria superkingdom 2659 NCBI Protein Cluster (PRK) D-xylose transporter subunit XylF D-xylose ABC transporter substrate-binding protein NF007697.0 PRK10378 PRK10378.1 297 297 375 subfamily Y Y N iron uptake system protein EfeO efeO 2 Bacteria superkingdom 11387 NCBI Protein Cluster (PRK) inactive ferrous ion transporter periplasmic protein EfeO iron uptake system protein EfeO NF007699.1 PRK10381 PRK10381.1 300 300 368 equivalog Y Y N LPS O-antigen length regulator Wzz(fepE) wzz(fepE) GO:0009103,GO:0016020 12603743,15049819,15941987,16027021,2956250 2 Bacteria superkingdom 3788 NCBI Protein Cluster (PRK) LPS O-antigen length regulator LPS O-antigen length regulator Wzz(fepE) The protein previously called FepE because it was through to be involved in ferric enterobactin transport is now recognized as a second O-antigen chain length determinant protein (that is, a polysaccharide co-polymerase), whose presence allow for a bimodal distribution of chain lengths. It is now called Wzz(fepE) to distinguish it from other Wzz proteins. NF007707.0 PRK10402 PRK10402.1 180 180 226 subfamily Y Y N transcriptional regulator YeiL yeiL GO:0003677,GO:0006355 2 Bacteria superkingdom 3153 NCBI Protein Cluster (PRK) DNA-binding transcriptional activator YeiL transcriptional regulator YeiL Activator of nucleoside metabolism NF007714.0 PRK10410 PRK10410.1-2 88 88 103 equivalog Y Y N nitrous oxide-stimulated promoter family protein 2 Bacteria superkingdom 6978 NCBI Protein Cluster (PRK) hypothetical protein nitrous oxide-stimulated promoter family protein NF007746.0 PRK10426 PRK10426.1 553 553 683 equivalog Y Y N alpha-glucosidase 3.2.1.20 GO:0004553 2 Bacteria superkingdom 5567 NCBI Protein Cluster (PRK) alpha-glucosidase alpha-glucosidase NF007749.0 PRK10429 PRK10429.1 456 456 473 equivalog Y Y N melibiose:sodium transporter MelB melB GO:0006814,GO:0008643,GO:0015293,GO:0016020,GO:0022857 2 Bacteria superkingdom 3959 NCBI Protein Cluster (PRK) melibiose:sodium symporter melibiose:sodium transporter MelB NF007758.0 PRK10439 PRK10439.1 222 222 418 equivalog Y Y N enterochelin esterase fes 3.1.1.- GO:0005506,GO:0008849 16076215 2 Bacteria superkingdom 10306 NCBI Protein Cluster (PRK) enterobactin/ferric enterobactin esterase enterochelin esterase NF007761.0 PRK10443 PRK10443.1 433 433 311 equivalog Y Y N pyrimidine-specific ribonucleoside hydrolase RihA rihA 3.2.2.3 GO:0006206,GO:0050263 2 Bacteria superkingdom 5307 NCBI Protein Cluster (PRK) ribonucleoside hydrolase 1 pyrimidine-specific ribonucleoside hydrolase RihA Hydrolyzes with equal efficiency cytidine or uridine to ribose and cytosine or uracil, respectively NF007763.0 PRK10445 PRK10445.1 252 252 263 equivalog Y Y N endonuclease VIII nei 4.2.99.18 GO:0000703,GO:0003677,GO:0006281,GO:0008270,GO:0140078 2 Bacteria superkingdom 5287 NCBI Protein Cluster (PRK) endonuclease VIII endonuclease VIII NF007773.0 PRK10459 PRK10459.1 273 273 492 equivalog Y Y N MOP flippase family protein 2 Bacteria superkingdom 6229 NCBI Protein Cluster (PRK) colanic acid exporter MOP flippase family protein NF007783.0 PRK10474 PRK10474.1 135 0 106 equivalog Y Y N PTS fructose-like transporter subunit IIB 2.7.1.202 GO:0009401,GO:0022877 2 Bacteria superkingdom 8401 NCBI Protein Cluster (PRK) putative PTS system fructose-like transporter subunit EIIB PTS fructose-like transporter subunit IIB Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF007784.0 PRK10475 PRK10475.1 318 318 290 equivalog Y Y N 23S rRNA pseudouridine(2604) synthase RluF rluF 5.4.99.21 GO:0001522,GO:0003723,GO:0009982 11720289,27551044 2 Bacteria superkingdom 12656 NCBI Protein Cluster (PRK) 23S rRNA pseudouridine synthase F 23S rRNA pseudouridine(2604) synthase RluF Catalyzes the synthesis of pseudouridine from U2604 in 23S ribosomal RNA NF007787.0 PRK10478 PRK10478.1 426 426 359 equivalog Y Y N PTS fructose transporter subunit EIIC GO:0008982,GO:0009401,GO:0016020 2 Bacteria superkingdom 2906 NCBI Protein Cluster (PRK) putative PTS system fructose-like transporter subunit EIIC PTS fructose transporter subunit EIIC NF007788.0 PRK10481 PRK10481.1 198 198 225 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 3373 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF007790.0 PRK10484 PRK10484.1 401 401 527 equivalog Y Y N solute:sodium symporter family transporter GO:0016020,GO:0022857,GO:0055085 8031825 2 Bacteria superkingdom 7388 NCBI Protein Cluster (PRK) putative transporter solute:sodium symporter family transporter NF007792.0 PRK10489 PRK10489.1 324 324 419 equivalog Y Y N enterobactin transporter EntS entS GO:0042930,GO:0042931 12068807,16166532,1787794,1838574 2 Bacteria superkingdom 6766 NCBI Protein Cluster (PRK) enterobactin exporter EntS enterobactin transporter EntS Inner membrane protein that exports enterobactin to the periplasmic space; member of the major facilitator superfamily (MFS) of transporters NF007797.0 PRK10502 PRK10502.1 192 192 183 subfamily Y Y N WcaF family extracellular polysaccharide biosynthesis acetyltransferase 30821147 2 Bacteria superkingdom 5120 NCBI Protein Cluster (PRK) putative acyl transferase WcaF family extracellular polysaccharide biosynthesis acetyltransferase NF007806.0 PRK10513 PRK10513.1 273 273 270 equivalog Y Y N sugar-phosphatase yidA 3.1.3.23 GO:0016787 2 Bacteria superkingdom 9291 NCBI Protein Cluster (PRK) sugar phosphate phosphatase sugar-phosphatase NF007807.0 PRK10514 PRK10514.1 134 134 147 equivalog Y Y N acetyltransferase GO:0008080 2 Bacteria superkingdom 7261 NCBI Protein Cluster (PRK) putative acetyltransferase acetyltransferase NF007810.0 PRK10518 PRK10518.1 540 540 482 equivalog Y Y N alkaline phosphatase phoA 3.1.3.1 GO:0016791 2 Bacteria superkingdom 6331 NCBI Protein Cluster (PRK) alkaline phosphatase alkaline phosphatase NF007811.0 PRK10519 PRK10519.1 111 111 155 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 2073 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF007812.0 PRK10520 PRK10520.1 209 209 206 equivalog Y Y N homoserine/homoserine lactone efflux protein rhtB GO:0006865,GO:0016020 2 Bacteria superkingdom 3633 NCBI Protein Cluster (PRK) homoserine/homoserine lactone efflux protein homoserine/homoserine lactone efflux protein NF007825.0 PRK10534 PRK10534.1 312 312 333 equivalog Y Y N low-specificity L-threonine aldolase ltaE 4.1.2.48 GO:0006520,GO:0016829 2 Bacteria superkingdom 16701 NCBI Protein Cluster (PRK) L-threonine aldolase low-specificity L-threonine aldolase Catalyzes the formation of acetaldehyde and glycine from L-threonine; acts on L-threonine, L-allo-threonine, L-threo-phenylserine, and L-erythro-phenylserine NF007831.0 PRK10542 PRK10542.1 198 198 201 equivalog Y Y N glutathione transferase GstA gstA 2.5.1.18 GO:0005515,GO:0006749 2 Bacteria superkingdom 10782 NCBI Protein Cluster (PRK) glutathionine S-transferase glutathione transferase GstA NF007853.0 PRK10562 PRK10562.1 125 125 146 equivalog Y Y N N-acetyltransferase 2.3.1.- GO:0008080 2 Bacteria superkingdom 6025 NCBI Protein Cluster (PRK) putative acetyltransferase N-acetyltransferase NF007857.0 PRK10566 PRK10566.1 201 201 249 equivalog Y Y N esterase yjfP GO:0006508,GO:0008236 15808744 2 Bacteria superkingdom 4922 NCBI Protein Cluster (PRK) esterase esterase NF007867.0 PRK10577 PRK10577.1-3 849 849 710 subfamily Y Y N Fe(3+)-hydroxamate ABC transporter permease FhuB fhuB 2 Bacteria superkingdom 5723 NCBI Protein Cluster (PRK) iron-hydroxamate transporter permease subunit Fe(3+)-hydroxamate ABC transporter permease FhuB NF007872.0 PRK10577 PRK10577.2-3 727 727 676 equivalog Y Y N Fe(3+)-hydroxamate ABC transporter permease FhuB fhuB 2 Bacteria superkingdom 941 NCBI Protein Cluster (PRK) iron-hydroxamate transporter permease subunit Fe(3+)-hydroxamate ABC transporter permease FhuB NF007899.0 PRK10605 PRK10605.1 403 403 365 subfamily Y Y N N-ethylmaleimide reductase nemA 1.3.1.- 2 Bacteria superkingdom 15602 NCBI Protein Cluster (PRK) N-ethylmaleimide reductase N-ethylmaleimide reductase FMN-linked; catalyzes the formation of N-ethylsuccinimide from N-ethylmaleimide NF007911.0 PRK10624 PRK10624.1 537 537 382 equivalog Y Y N lactaldehyde reductase fucO 1.1.1.77 GO:0016491 2 Bacteria superkingdom 7266 NCBI Protein Cluster (PRK) L-1,2-propanediol oxidoreductase lactaldehyde reductase NF007912.0 PRK10625 PRK10625.1 415 415 346 equivalog Y Y N NADP(H)-dependent aldo-keto reductase GO:0047834 11470487,14517983,9560382 2 Bacteria superkingdom 12984 NCBI Protein Cluster (PRK) putative aldo-keto reductase NADP(H)-dependent aldo-keto reductase NF007922.1 PRK10637 PRK10637.1 400 400 450 equivalog Y Y N siroheme synthase CysG cysG 1.3.1.76,2.1.1.107,4.99.1.4 GO:0004851,GO:0019354,GO:0043115,GO:0051266,GO:0051287 2 Bacteria superkingdom 25624 NCBI Protein Cluster (PRK) siroheme synthase siroheme synthase CysG Multifunctional enzyme consisting of uroporphyrin-III C-methyltransferase, precorrin-2 dehydrogenase and sirohydrochlorin ferrochelatase; catalyzes the methylation of uroporphyrinogen III to form precorrin-2, then catalyzes formation of sirohydrochlorin from precorrin-2 and finally catalyzed the formation of siroheme from sirohydrochlorin NF007927.0 PRK10642 PRK10642.1 544 544 500 equivalog Y Y N glycine betaine/L-proline transporter ProP proP GO:0016020,GO:0022857,GO:0055085 2 Bacteria superkingdom 12137 NCBI Protein Cluster (PRK) proline/glycine betaine transporter glycine betaine/L-proline transporter ProP NF007936.0 PRK10653 PRK10653.1 337 337 295 equivalog Y Y N ribose ABC transporter substrate-binding protein RbsB rbsB 2 Bacteria superkingdom 6836 NCBI Protein Cluster (PRK) D-ribose transporter subunit RbsB ribose ABC transporter substrate-binding protein RbsB RbsABCD acts to import ribose into the cell NF007938.0 PRK10655 PRK10655.1 409 409 438 equivalog Y Y N putrescine-ornithine antiporter potE GO:0015496,GO:0015822,GO:0015847,GO:0016020,GO:0055085 10931886,1584788,9045651 2 Bacteria superkingdom 5044 NCBI Protein Cluster (PRK) putrescine transporter putrescine-ornithine antiporter Catalyzes the uptake of putrescine via a proton symport mechanism, as well as the efflux of putrescine by a putrescine/ornithine antiport system NF007972.0 PRK10696 PRK10696.1 272 272 295 equivalog Y Y N tRNA 2-thiocytidine(32) synthetase TtcA ttcA 2.8.1.- GO:0008033 14729701 2 Bacteria superkingdom 21210 NCBI Protein Cluster (PRK) tRNA 2-thiocytidine biosynthesis protein TtcA tRNA 2-thiocytidine(32) synthetase TtcA YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs NF007980.0 PRK10707 PRK10707.1 134 134 192 equivalog Y Y N CoA pyrophosphatase GO:0000287,GO:0010945 2 Bacteria superkingdom 18815 NCBI Protein Cluster (PRK) putative NUDIX hydrolase CoA pyrophosphatase NF007989.0 PRK10717 PRK10717.1 387 387 334 equivalog Y Y N cysteine synthase A 2.5.1.47 2 Bacteria superkingdom 16072 NCBI Protein Cluster (PRK) cysteine synthase A cysteine synthase A Forms a complex with serine acetyltransferase CysE; functions in cysteine biosynthesis NF007992.0 PRK10719 PRK10719.1-3 598 598 478 equivalog Y Y N ethanolamine ammonia-lyase reactivating factor EutA eutA 2 Bacteria superkingdom 1511 NCBI Protein Cluster (PRK) reactivating factor for ethanolamine ammonia lyase ethanolamine ammonia-lyase reactivating factor EutA NF007995.0 PRK10720 PRK10720.1 477 477 429 equivalog Y Y N uracil permease uraA GO:0022857 2 Bacteria superkingdom 6190 NCBI Protein Cluster (PRK) uracil transporter uracil permease NF008006.0 PRK10735 PRK10735.1 513 513 481 equivalog Y Y N metalloprotease TldD tldD 3.4.24.- GO:0006508,GO:0008237 12029038,8604133 2 Bacteria superkingdom 24233 NCBI Protein Cluster (PRK) protease TldD metalloprotease TldD NF008022.0 PRK10752 PRK10752.1 288 288 329 subfamily Y Y N sulfate ABC transporter substrate-binding protein GO:0015419,GO:1902358 2 Bacteria superkingdom 33987 NCBI Protein Cluster (PRK) sulfate transporter subunit sulfate ABC transporter substrate-binding protein NF008024.0 PRK10754 PRK10754.1 348 348 327 subfamily Y Y N NADPH:quinone reductase 1.6.5.5 GO:0008270,GO:0016491 2 Bacteria superkingdom 18879 NCBI Protein Cluster (PRK) quinone oxidoreductase, NADPH-dependent NADPH:quinone reductase NF008030.0 PRK10762 PRK10762.1 745 745 501 equivalog Y Y N ribose ABC transporter ATP-binding protein RbsA rbsA GO:0005524 2 Bacteria superkingdom 6907 NCBI Protein Cluster (PRK) D-ribose transporter ATP binding protein ribose ABC transporter ATP-binding protein RbsA RbsABCD acts to import ribose into the cell NF008033.1 PRK10765 PRK10765.1 223 223 240 equivalog Y Y N oxygen-insensitive NADPH nitroreductase nfsA GO:0016491 2 Bacteria superkingdom 13672 NCBI Protein Cluster (PRK) nitroreductase A oxygen-insensitive NADPH nitroreductase NADPH-dependent; oxygen-insensitive; catalyzes the reduction of nitroaromatic compounds NF008036.0 PRK10768 PRK10768.1 382 382 304 equivalog Y Y N ribonucleoside hydrolase RihC rihC 3.2.2.- GO:0016799 2 Bacteria superkingdom 4930 NCBI Protein Cluster (PRK) ribonucleoside hydrolase RihC ribonucleoside hydrolase RihC Catalyzes the hydrolysis of both purine and pyrimidine ribonucleosides NF008037.0 PRK10769 PRK10769.1 168 168 160 equivalog Y Y N type 3 dihydrofolate reductase folA GO:0004146,GO:0046654 2 Bacteria superkingdom 6133 NCBI Protein Cluster (PRK) dihydrofolate reductase type 3 dihydrofolate reductase Catalyzes the reduction of dihydrofolate to tetrahydrofolate NF008040.0 PRK10772 PRK10772.1 96 96 109 equivalog Y Y N cell division protein FtsL ftsL 2 Bacteria superkingdom 1156 NCBI Protein Cluster (PRK) cell division protein FtsL cell division protein FtsL Membrane bound cell division protein at septum NF008049.0 PRK10782 PRK10782.1 212 212 217 subfamily Y Y N methionine ABC transporter permease MetI metI 7.2.2.- 12819857 2 Bacteria superkingdom 19809 NCBI Protein Cluster (PRK) DL-methionine transporter permease subunit methionine ABC transporter permease MetI Part of the MetNIQ methionine uptake system NF008053.0 PRK10787 PRK10787.1 891 891 784 equivalog Y Y N endopeptidase La lon 3.4.21.53 GO:0004176,GO:0004252,GO:0006508,GO:0016887,GO:0043565 2 Bacteria superkingdom 30447 NCBI Protein Cluster (PRK) DNA-binding ATP-dependent protease La endopeptidase La NF008094.0 PRK10836 PRK10836.1 735 735 489 subfamily Y Y N amino acid permease GO:0006865 2 Bacteria superkingdom 8285 NCBI Protein Cluster (PRK) lysine transporter amino acid permease NF008102.0 PRK10847 PRK10847.1 236 236 219 equivalog Y Y N DedA family protein 2 Bacteria superkingdom 9002 NCBI Protein Cluster (PRK) hypothetical protein DedA family protein NF008106.0 PRK10852 PRK10852.1 308 308 338 subfamily Y Y N thiosulfate ABC transporter substrate-binding protein CysP cysP GO:0015419,GO:1902358 2 Bacteria superkingdom 32382 NCBI Protein Cluster (PRK) thiosulfate transporter subunit thiosulfate ABC transporter substrate-binding protein CysP NF008113.2 PRK10860 PRK10860.1 150 150 165 equivalog Y Y N tRNA adenosine(34) deaminase TadA tadA 3.5.4.33 GO:0002100,GO:0008251,GO:0008270 2 Bacteria superkingdom 38603 NCBI Protein Cluster (PRK) tRNA-specific adenosine deaminase tRNA adenosine(34) deaminase TadA NF008121.0 PRK10869 PRK10869.1 418 418 553 equivalog Y Y N DNA repair protein RecN recN GO:0005524,GO:0006281,GO:0006310 2 Bacteria superkingdom 30506 NCBI Protein Cluster (PRK) recombination and repair protein DNA repair protein RecN NF008131.0 PRK10879 PRK10879.1 465 465 438 equivalog Y Y N Xaa-Pro aminopeptidase pepP 3.4.11.9 GO:0070006 2 Bacteria superkingdom 13291 NCBI Protein Cluster (PRK) proline aminopeptidase P II Xaa-Pro aminopeptidase NF008139.0 PRK10887 PRK10887.1 490 490 445 equivalog Y Y N phosphoglucosamine mutase glmM 5.4.2.10 GO:0000287,GO:0005975,GO:0008966,GO:0016868 2 Bacteria superkingdom 36957 NCBI Protein Cluster (PRK) phosphoglucosamine mutase phosphoglucosamine mutase Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate NF008164.0 PRK10917 PRK10917.1-2 785 785 704 equivalog Y Y N ATP-dependent DNA helicase RecG recG 3.6.4.12 GO:0003678,GO:0006310 2 Bacteria superkingdom 9392 NCBI Protein Cluster (PRK) ATP-dependent DNA helicase RecG ATP-dependent DNA helicase RecG NF008165.0 PRK10917 PRK10917.1-3 711 711 692 equivalog Y Y N ATP-dependent DNA helicase RecG recG 3.6.4.12 GO:0003676,GO:0003678,GO:0005524,GO:0006281,GO:0006310 2 Bacteria superkingdom 55919 NCBI Protein Cluster (PRK) ATP-dependent DNA helicase RecG ATP-dependent DNA helicase RecG NF008185.0 PRK10936 PRK10936.1 200 200 346 equivalog Y Y N TMAO reductase system periplasmic protein TorT torT 2 Bacteria superkingdom 5564 NCBI Protein Cluster (PRK) TMAO reductase system periplasmic protein TorT TMAO reductase system periplasmic protein TorT NF008187.0 PRK10939 PRK10939.1 528 528 521 equivalog Y Y N autoinducer-2 kinase lsrK 2.7.1.189 GO:0005975,GO:0009372,GO:0071518 2 Bacteria superkingdom 6586 NCBI Protein Cluster (PRK) autoinducer-2 (AI-2) kinase autoinducer-2 kinase NF008200.0 PRK10957 PRK10957.1 205 205 330 equivalog Y Y N Fe2+-enterobactin ABC transporter substrate-binding protein fepB 7.2.2.- 2 Bacteria superkingdom 7249 NCBI Protein Cluster (PRK) iron-enterobactin transporter periplasmic binding protein Fe2+-enterobactin ABC transporter substrate-binding protein With FepCDG is involved in the transport of ferric enterobactin NF008201.0 PRK10958 PRK10958.1 165 165 212 equivalog Y Y N leucine efflux protein LeuE leuE GO:0006865 2 Bacteria superkingdom 10752 NCBI Protein Cluster (PRK) leucine export protein LeuE leucine efflux protein LeuE NF008215.0 PRK10982 PRK10982.1 828 828 506 equivalog Y Y N galactose/methyl galactoside ABC transporter ATP-binding protein MglA mglA GO:0005524,GO:0008643,GO:0016020,GO:0043211 2 Bacteria superkingdom 3923 NCBI Protein Cluster (PRK) galactose/methyl galaxtoside transporter ATP-binding protein galactose/methyl galactoside ABC transporter ATP-binding protein MglA With MglBC transports galactose or methyl galactoside into the cell; contains 2 ATP binding domains NF008220.0 PRK10991 PRK10991.1 775 775 591 equivalog Y Y N L-fucose isomerase 5.3.1.25 GO:0005996,GO:0008736,GO:0019317,GO:0030145 2 Bacteria superkingdom 8277 NCBI Protein Cluster (PRK) L-fucose isomerase L-fucose isomerase Catalyzes the conversion of the aldose L-fucose into the corresponding ketose L-fuculose NF008229.0 PRK10996 PRK10996.1 125 125 141 equivalog Y Y N thioredoxin TrxC trxC GO:0006662,GO:0015035 2 Bacteria superkingdom 12803 NCBI Protein Cluster (PRK) thioredoxin 2 thioredoxin TrxC NF008236.0 PRK11007 PRK11007.1 409 409 473 equivalog Y Y N PTS trehalose transporter subunit IIBC treB 2.7.1.201 GO:0008982,GO:0009401,GO:0015574,GO:0015771,GO:0016020 2 Bacteria superkingdom 14761 NCBI Protein Cluster (PRK) PTS system trehalose(maltose)-specific transporter subunits IIBC PTS trehalose transporter subunit IIBC Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF008241.0 PRK11017 PRK11017.1 326 326 416 equivalog Y Y N cytosine permease codB GO:0015209,GO:0016020,GO:0055085 2 Bacteria superkingdom 8301 NCBI Protein Cluster (PRK) cytosine permease cytosine permease NF008272.0 PRK11049 PRK11049.1 732 732 470 equivalog Y Y N D-serine/D-alanine/glycine transporter cycA dagA GO:0006865,GO:0016020,GO:0055085 2 Bacteria superkingdom 5648 NCBI Protein Cluster (PRK) D-alanine/D-serine/glycine permease D-serine/D-alanine/glycine transporter Involved in the transport across the cytoplasmic membrane of D-alanine, D-serine and glycine NF008286.0 PRK11064 PRK11064.1 459 459 420 equivalog Y Y N UDP-N-acetyl-D-mannosamine dehydrogenase wecC 1.1.1.336 GO:0009246,GO:0051287,GO:0089714 2 Bacteria superkingdom 12873 NCBI Protein Cluster (PRK) UDP-N-acetyl-D-mannosamine dehydrogenase UDP-N-acetyl-D-mannosamine dehydrogenase Catalyzes the oxidation of UDP-N-acetyl-D-mannosamine to UDP-N-acetylmannosaminuronic acid NF008292.0 PRK11072 PRK11072.1 487 487 946 equivalog Y Y N bifunctional [glutamate--ammonia ligase]-adenylyl-L-tyrosine phosphorylase/[glutamate--ammonia-ligase] adenylyltransferase glnE 2.7.7.42,2.7.7.89 GO:0008882 1360007 2 Bacteria superkingdom 40499 NCBI Protein Cluster (PRK) bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase bifunctional [glutamate--ammonia ligase]-adenylyl-L-tyrosine phosphorylase/[glutamate--ammonia-ligase] adenylyltransferase Catalyzes the ATP-dependent addition of AMP to a subunit of glutamine synthetase; also Catalyzes the reverse reaction - deadenylation NF008295.0 PRK11081 PRK11081.1 227 227 230 equivalog Y Y N tRNA (guanosine(18)-2'-O)-methyltransferase TrmH trmH GO:0030488,GO:0141100 2 Bacteria superkingdom 5951 NCBI Protein Cluster (PRK) tRNA guanosine-2'-O-methyltransferase tRNA (guanosine(18)-2'-O)-methyltransferase TrmH Specifically modifies tRNA at position G18 NF008298.1 PRK11086 PRK11086.1 520 520 529 subfamily Y Y N DcuS/MalK family sensor histidine kinase dcuS 2.7.13.3 GO:0000155,GO:0000160,GO:0006355 12949159,33277358 2 Bacteria superkingdom 7188 NCBI Protein Cluster (PRK) sensory histidine kinase DcuS DcuS/MalK family sensor histidine kinase DcuS, as found in Escherichia coli, is a C4-dicarboxylate-sensing histidine kinase, part of a two-component regulatory system with DcuR. It regulates anaerobic fumarate respiration. MalK, as found in Bacillus subtilis, is a malate sensor histidine kinase. NF008313.0 PRK11101 PRK11101.1 425 425 548 equivalog Y Y N anaerobic glycerol-3-phosphate dehydrogenase subunit A glpA 1.1.5.3 GO:0004368,GO:0006072,GO:0009331,GO:0010181,GO:0046174,GO:0050660 2 Bacteria superkingdom 8968 NCBI Protein Cluster (PRK) sn-glycerol-3-phosphate dehydrogenase subunit A anaerobic glycerol-3-phosphate dehydrogenase subunit A Catalyzes the conversion of glycerol 3-phosphate to dihydroxyacetone using fumarate or nitrate as electron acceptor NF008314.0 PRK11102 PRK11102.1 303 303 396 equivalog Y Y N Bcr/CflA family multidrug efflux MFS transporter GO:0016020,GO:0042908,GO:0042910,GO:1990961 2 Bacteria superkingdom 11457 NCBI Protein Cluster (PRK) bicyclomycin/multidrug efflux system Bcr/CflA family multidrug efflux MFS transporter NF008315.0 PRK11103 PRK11103.1 365 365 283 subfamily Y Y N PTS mannose transporter subunit IID manZ 2.7.1.191 2 Bacteria superkingdom 3285 NCBI Protein Cluster (PRK) PTS system mannose-specific transporter subunit IID PTS mannose transporter subunit IID Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF008316.0 PRK11104 PRK11104.1 142 142 177 equivalog Y Y N menaquinone-dependent protoporphyrinogen IX dehydrogenase hemG 1.3.5.3 2 Bacteria superkingdom 6483 NCBI Protein Cluster (PRK) protoporphyrinogen oxidase menaquinone-dependent protoporphyrinogen IX dehydrogenase Catalyzes the oxidation of protoporphyrinogen IX to form protoporphyrin IX NF008333.0 PRK11118 PRK11118.1 103 103 101 equivalog Y Y N monooxygenase 2 Bacteria superkingdom 3969 NCBI Protein Cluster (PRK) putative monooxygenase monooxygenase NF008334.0 PRK11119 PRK11119.1 215 215 331 equivalog Y Y N glycine betaine/L-proline ABC transporter substrate-binding protein ProX proX GO:0022857,GO:0043190,GO:0055085 2 Bacteria superkingdom 7935 NCBI Protein Cluster (PRK) glycine betaine transporter periplasmic subunit glycine betaine/L-proline ABC transporter substrate-binding protein ProX With ProVW, part of the high-affinity transport system for the osmoprotectant glycine betaine NF008348.1 PRK11131 PRK11131.1 1400 1400 1287 equivalog Y Y N ATP-dependent RNA helicase HrpA hrpA 3.6.4.13 GO:0003676,GO:0003724,GO:0005524 2 Bacteria superkingdom 38818 NCBI Protein Cluster (PRK) ATP-dependent RNA helicase HrpA ATP-dependent RNA helicase HrpA Involved in the post-transcriptional processing of the daa operon mRNA NF008352.0 PRK11139 PRK11139.1 288 288 305 subfamily Y Y N transcriptional regulator GcvA gcvA GO:0003700,GO:0006355 2 Bacteria superkingdom 25788 NCBI Protein Cluster (PRK) DNA-binding transcriptional activator GcvA transcriptional regulator GcvA Glycine cleavage system transcriptional activator; activates the gcvTHP operon in the presence of glycine and represses the operon in its absence NF008353.0 PRK11142 PRK11142.1 341 341 307 equivalog Y Y N ribokinase rbsK 2.7.1.15 GO:0004747,GO:0006014 25408351 2 Bacteria superkingdom 8646 NCBI Protein Cluster (PRK) ribokinase ribokinase Catalyzes the formation of D-ribose 5-phosphate from ribose NF008354.0 PRK11143 PRK11143.1 254 254 359 equivalog Y Y N glycerophosphodiester phosphodiesterase glpQ 3.1.4.46 GO:0006629,GO:0008081 2 Bacteria superkingdom 8314 NCBI Protein Cluster (PRK) glycerophosphodiester phosphodiesterase glycerophosphodiester phosphodiesterase NF008359.0 PRK11148 PRK11148.1 225 225 275 equivalog Y Y N 3',5'-cyclic-AMP phosphodiesterase cpdA 3.1.4.53 GO:0004115 2 Bacteria superkingdom 10216 NCBI Protein Cluster (PRK) cyclic 3',5'-adenosine monophosphate phosphodiesterase 3',5'-cyclic-AMP phosphodiesterase NF008373.0 PRK11171 PRK11171.1-2 445 445 274 equivalog Y Y N (S)-ureidoglycine aminohydrolase 3.5.3.26 GO:0071522 2 Bacteria superkingdom 6124 NCBI Protein Cluster (PRK) hypothetical protein (S)-ureidoglycine aminohydrolase NF008376.0 PRK11171 PRK11171.1-5 338 338 278 equivalog Y Y N (S)-ureidoglycine aminohydrolase 3.5.3.26 GO:0071522 2 Bacteria superkingdom 6957 NCBI Protein Cluster (PRK) hypothetical protein (S)-ureidoglycine aminohydrolase NF008383.0 PRK11178 PRK11178.1 262 262 254 equivalog Y Y N uridine phosphorylase udp 2.4.2.3 GO:0009116,GO:0016763 2 Bacteria superkingdom 3595 NCBI Protein Cluster (PRK) uridine phosphorylase uridine phosphorylase NF008387.0 PRK11183 PRK11183.1 391 391 570 equivalog Y Y N D-lactate dehydrogenase dld 1.1.1.28 GO:0006089,GO:0016901 2 Bacteria superkingdom 13812 NCBI Protein Cluster (PRK) D-lactate dehydrogenase D-lactate dehydrogenase NF008397.0 PRK11195 PRK11195.1 297 297 414 equivalog Y Y N lysophospholipid transporter LplT lplT GO:0022857,GO:0055085 2 Bacteria superkingdom 9245 NCBI Protein Cluster (PRK) lysophospholipid transporter LplT lysophospholipid transporter LplT NF008398.0 PRK11197 PRK11197.1 376 376 381 subfamily Y Y N L-lactate dehydrogenase 1.1.1.27 2 Bacteria superkingdom 19497 NCBI Protein Cluster (PRK) L-lactate dehydrogenase L-lactate dehydrogenase NF008399.0 PRK11198 PRK11198.1 134 134 149 equivalog Y Y N peptidoglycan-binding protein LysM lysM 2 Bacteria superkingdom 7448 NCBI Protein Cluster (PRK) LysM domain/BON superfamily protein peptidoglycan-binding protein LysM NF008400.0 PRK11199 PRK11199.1 273 273 374 equivalog Y Y N bifunctional chorismate mutase/prephenate dehydrogenase tyrA 1.3.1.12,5.4.99.5 GO:0004106,GO:0004665,GO:0006571,GO:0008977,GO:0046417 20944228 2 Bacteria superkingdom 7812 NCBI Protein Cluster (PRK) bifunctional chorismate mutase/prephenate dehydrogenase bifunctional chorismate mutase/prephenate dehydrogenase Catalyzes the formation of prephenate from chorismate and the formation of 4-hydroxyphenylpyruvate from prephenate in tyrosine biosynthesis NF008405.0 PRK11207 PRK11207.1 218 218 198 equivalog Y Y N tellurite resistance methyltransferase TehB tehB 2.1.1.265 GO:0008757,GO:0046690 2 Bacteria superkingdom 7092 NCBI Protein Cluster (PRK) tellurite resistance protein TehB tellurite resistance methyltransferase TehB With TehA confers resistance to tellurite NF008410.0 PRK11233 PRK11233.1 309 309 305 equivalog Y Y N nitrogen assimilation transcriptional regulator NAC nac GO:0003700,GO:0006355 20693327,7768865,8458853 2 Bacteria superkingdom 3774 NCBI Protein Cluster (PRK) nitrogen assimilation transcriptional regulator nitrogen assimilation transcriptional regulator NAC NAC (nitrogen assimilation control protein) is a LysR family transcriptional activator for the hut, put and ure operons, and a repressor for the gdh and gltB operons in response to nitrogen limitation. NF008412.0 PRK11235 PRK11235.1 96 96 80 equivalog Y Y N type II toxin-antitoxin system RelB/DinJ family antitoxin 2 Bacteria superkingdom 1373 NCBI Protein Cluster (PRK) bifunctional antitoxin/transcriptional repressor RelB type II toxin-antitoxin system RelB/DinJ family antitoxin NF008416.0 PRK11242 PRK11242.1 277 277 300 equivalog Y Y N transcriptional regulator CynR cynR GO:0003700,GO:0006355 2 Bacteria superkingdom 8361 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator CynR transcriptional regulator CynR Controls the expression of the cynTSX operon involved in degrading and using cyanate as a sole nitrogen source NF008431.0 PRK11269 PRK11269.1 791 791 591 equivalog Y Y N glyoxylate carboligase gcl 4.1.1.47 GO:0009436 2 Bacteria superkingdom 16515 NCBI Protein Cluster (PRK) glyoxylate carboligase glyoxylate carboligase Catalyzes the formation of 2-hydroxy-3-oxopropanoate (tartronate semialdehyde) from two molecules of glyoxylate NF008434.0 PRK11274 PRK11274.1 333 333 409 equivalog Y Y N glycolate oxidase subunit GlcF glcF 1.1.99.14 GO:0051536 2 Bacteria superkingdom 16910 NCBI Protein Cluster (PRK) glycolate oxidase iron-sulfur subunit glycolate oxidase subunit GlcF NF008440.0 PRK11283 PRK11283.1 638 638 437 equivalog Y Y N glutamate/aspartate:proton symporter GltP gltP GO:0006835,GO:0015293,GO:0016020 2 Bacteria superkingdom 4572 NCBI Protein Cluster (PRK) glutamate/aspartate:proton symporter glutamate/aspartate:proton symporter GltP Carrier protein part of the Na(+)-independent, binding-protein-independent glutamate-aspartate transport system NF008455.0 PRK11320 PRK11320.1 353 353 295 equivalog Y Y N methylisocitrate lyase prpB 4.1.3.30 GO:0019629,GO:0046421 2 Bacteria superkingdom 11707 NCBI Protein Cluster (PRK) 2-methylisocitrate lyase methylisocitrate lyase Catalyzes the formation of pyruvate and succinate from 2-methylisocitrate NF008468.0 PRK11360 PRK11360.1 646 646 616 equivalog Y Y N two-component system sensor histidine kinase AtoS atoS 2.7.13.3 2 Bacteria superkingdom 1769 NCBI Protein Cluster (PRK) sensory histidine kinase AtoS two-component system sensor histidine kinase AtoS With AtoC is a member of a two-component regulatory system involved in the transcriptional regulation of the ato genes for acetoacetate metabolism NF008470.0 PRK11365 PRK11365.1 347 347 263 equivalog Y Y N aliphatic sulfonate ABC transporter permease SsuC ssuC 7.6.2.- GO:0016020,GO:0055085 2 Bacteria superkingdom 8841 NCBI Protein Cluster (PRK) alkanesulfonate transporter permease subunit aliphatic sulfonate ABC transporter permease SsuC Part of the ABC type transport system for alkanesulfonate SsuABC NF008476.1 PRK11375 PRK11375.1 620 620 467 equivalog Y Y N allantoin permease allW allP GO:0015720,GO:0016020,GO:0022857 37147430 2 Bacteria superkingdom 2772 NCBI Protein Cluster (PRK) allantoin permease allantoin permease NF008482.1 PRK11383 PRK11383.1 150 150 123 exception Y Y N inner membrane protein YiaA yiaA 2 Bacteria superkingdom 4624 NCBI Protein Cluster (PRK) hypothetical protein inner membrane protein YiaA This model distinguishes the inner membrane protein YiaA, found in Escherichia coli and related species, from its paralog YiaB (see PRK11403). YiaA is longer and has two copies of the two-transmembrane helix domain described by Pfam model PF05360. NF008484.0 PRK11387 PRK11387.1 716 716 471 equivalog Y Y N S-methylmethionine permease mmuP GO:0055085 2 Bacteria superkingdom 3776 NCBI Protein Cluster (PRK) S-methylmethionine transporter S-methylmethionine permease NF008491.0 PRK11402 PRK11402.1 269 269 243 subfamily Y Y N GntR family transcriptional regulator 2 Bacteria superkingdom 844 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator FrlR GntR family transcriptional regulator NF008493.0 PRK11404 PRK11404.1 806 806 483 equivalog Y Y N PTS fructose-like transporter subunit IIBC 2.7.1.202 2 Bacteria superkingdom 1444 NCBI Protein Cluster (PRK) putative PTS system transporter subunits IIBC PTS fructose-like transporter subunit IIBC NF008498.0 PRK11408 PRK11408.1-5 276 276 214 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 1460 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF008501.0 PRK11411 PRK11411.1 255 255 303 subfamily Y Y N Fe(3+) dicitrate ABC transporter substrate-binding protein 2 Bacteria superkingdom 4944 NCBI Protein Cluster (PRK) iron-dicitrate transporter substrate-binding subunit Fe(3+) dicitrate ABC transporter substrate-binding protein NF008503.0 PRK11413 PRK11413.1 641 641 753 equivalog Y Y N hydratase 2 Bacteria superkingdom 6639 NCBI Protein Cluster (PRK) putative hydratase hydratase NF008508.1 PRK11425 PRK11425.1 180 180 157 equivalog Y Y N PTS N-acetylgalactosamine transporter subunit IIB agaV 10931310,8932697 2 Bacteria superkingdom 2675 NCBI Protein Cluster (PRK) PTS system N-acetylgalactosamine-specific transporter subunit IIB PTS N-acetylgalactosamine transporter subunit IIB Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF008514.0 PRK11433 PRK11433.1 322 322 218 equivalog Y Y N aldehyde dehydrogenase iron-sulfur subunit PaoA paoA 1.2.99.6 GO:0046872,GO:0047770,GO:0051536 27622978 2 Bacteria superkingdom 5061 NCBI Protein Cluster (PRK) aldehyde oxidoreductase 2Fe-2S subunit aldehyde dehydrogenase iron-sulfur subunit PaoA PaoA is a 2Fe-2S-binding subunit of the periplasmic aldehyde oxidoreductase PaoABC. The enzyme is known formally as carboxylate reductase (EC 1.2.99.6). NF008517.0 PRK11440 PRK11440.1 195 195 188 equivalog Y Y N hydrolase 2 Bacteria superkingdom 5812 NCBI Protein Cluster (PRK) putative hydrolase hydrolase NF008519.0 PRK11445 PRK11445.1 303 303 355 equivalog Y Y N FAD-binding protein 2 Bacteria superkingdom 2107 NCBI Protein Cluster (PRK) putative oxidoreductase FAD-binding protein NF008551.0 PRK11478 PRK11478.1 148 148 129 equivalog Y Y N VOC family protein 2 Bacteria superkingdom 12819 NCBI Protein Cluster (PRK) putative lyase VOC family protein NF008556.0 PRK11492 PRK11492.1 136 136 216 equivalog Y Y N hydrogenase 4 membrane subunit hyfE 2 Bacteria superkingdom 1219 NCBI Protein Cluster (PRK) hydrogenase 4 membrane subunit hydrogenase 4 membrane subunit NF008570.0 PRK11522 PRK11522.1 612 612 464 equivalog Y Y N putrescine aminotransferase 2.6.1.82 2 Bacteria superkingdom 3732 NCBI Protein Cluster (PRK) putrescine--2-oxoglutarate aminotransferase putrescine aminotransferase Catalyzes the formation of 4-aminobutyraldehyde from putrescine and 2-oxoglutarate NF008572.0 PRK11524 PRK11524.1 292 292 294 equivalog Y Y N adenine-specific DNA-methyltransferase yhdJ GO:0003677,GO:0008170 2 Bacteria superkingdom 1836 NCBI Protein Cluster (PRK) putative methyltransferase adenine-specific DNA-methyltransferase NF008588.0 PRK11553 PRK11553.1 299 299 319 subfamily Y Y N aliphatic sulfonate ABC transporter substrate-binding protein GO:0016020,GO:0042626 2 Bacteria superkingdom 14904 NCBI Protein Cluster (PRK) alkanesulfonate transporter substrate-binding subunit aliphatic sulfonate ABC transporter substrate-binding protein Part of the ABC type transport system SsuABC for aliphatic sulfonates NF008592.0 PRK11559 PRK11559.1 397 397 296 equivalog Y Y N 2-hydroxy-3-oxopropionate reductase garR 1.1.1.60 GO:0008679,GO:0046487 2 Bacteria superkingdom 4398 NCBI Protein Cluster (PRK) tartronate semialdehyde reductase 2-hydroxy-3-oxopropionate reductase NF008594.0 PRK11561 PRK11561.1 545 545 540 equivalog Y Y N isovaleryl-CoA dehydrogenase 1.3.8.4 GO:0003995 2 Bacteria superkingdom 10061 NCBI Protein Cluster (PRK) isovaleryl CoA dehydrogenase isovaleryl-CoA dehydrogenase Catalyzes the formation of 3-methylcrotonyl-CoA from isovaleryl-CoA NF008607.0 PRK11579 PRK11579.1 330 330 346 subfamily Y Y N oxidoreductase GO:0000166 2 Bacteria superkingdom 16606 NCBI Protein Cluster (PRK) putative oxidoreductase oxidoreductase NF008611.1 PRK11588 PRK11588.1 500 500 492 equivalog Y Y N putative basic amino acid antiporter YfcC yfcC GO:0016020 2 Bacteria superkingdom 3892 NCBI Protein Cluster (PRK) hypothetical protein putative basic amino acid antiporter YfcC NF008623.0 PRK11609 PRK11609.1 174 174 213 equivalog Y Y N bifunctional nicotinamidase/pyrazinamidase pncA 3.5.1.-,3.5.1.19 27451449 2 Bacteria superkingdom 16207 NCBI Protein Cluster (PRK) nicotinamidase/pyrazinamidase bifunctional nicotinamidase/pyrazinamidase Catalyzes the formation of nicotinate from nicotinamide in NAD biosynthesis and the formation of pyrazinoate from pyrazinamide NF008630.0 PRK11618 PRK11618.1 363 363 331 equivalog Y Y N galactofuranose ABC transporter, permease protein YjfF yjfF 7.5.2.9 GO:0016020,GO:0042875,GO:0103116 30698741 2 Bacteria superkingdom 10104 NCBI Protein Cluster (PRK) inner membrane ABC transporter permease protein YjfF galactofuranose ABC transporter, permease protein YjfF NF008632.0 PRK11621 PRK11621.1 162 162 203 equivalog Y Y N Tat proofreading chaperone DmsD dmsD 18175314 2 Bacteria superkingdom 4472 NCBI Protein Cluster (PRK) twin-argninine leader-binding protein DmsD Tat proofreading chaperone DmsD Binds to the twin-arginine signal peptides of certain proteins NF008633.1 PRK11622 PRK11622.1 203 203 397 subfamily Y Y N ABC transporter substrate-binding protein 2 Bacteria superkingdom 13107 NCBI Protein Cluster (PRK) hypothetical protein ABC transporter substrate-binding protein NF008669.0 PRK11670 PRK11670.1 348 348 369 equivalog Y Y N iron-sulfur cluster carrier protein ApbC apbC GO:0005524,GO:0016226,GO:0016887,GO:0051536 2 Bacteria superkingdom 20458 NCBI Protein Cluster (PRK) antiporter inner membrane protein iron-sulfur cluster carrier protein ApbC NF008676.0 PRK11689 PRK11689.1 194 194 297 equivalog Y Y N aromatic amino acid DMT transporter YddG yddG GO:0016020 17784858,21042032,27281193 2 Bacteria superkingdom 10830 NCBI Protein Cluster (PRK) aromatic amino acid exporter aromatic amino acid DMT transporter YddG NF008687.0 PRK11706 PRK11706.1 375 375 375 equivalog Y Y N dTDP-4-amino-4,6-dideoxygalactose transaminase rffA fcnA,wecE 2.6.1.59 GO:0009246,GO:0019180 2 Bacteria superkingdom 10219 NCBI Protein Cluster (PRK) TDP-4-oxo-6-deoxy-D-glucose transaminase dTDP-4-amino-4,6-dideoxygalactose transaminase Catalyzes the formation of dTDP-D-fucosamine from dTDP-4-oxo-6-deoxy-D-glucose in enterobacterial common antigen biosynthesis NF008688.0 PRK11709 PRK11709.1 306 306 355 equivalog Y Y N L-ascorbate 6-phosphate lactonase ulaG 3.1.1.- GO:0019854,GO:0030145,GO:0035460 2 Bacteria superkingdom 4783 NCBI Protein Cluster (PRK) putative L-ascorbate 6-phosphate lactonase L-ascorbate 6-phosphate lactonase NF008692.0 PRK11713 PRK11713.1-5 196 196 246 equivalog Y Y N 16S rRNA (uracil(1498)-N(3))-methyltransferase 2.1.1.193 GO:0006364,GO:0008168 2 Bacteria superkingdom 24374 NCBI Protein Cluster (PRK) 16S ribosomal RNA methyltransferase RsmE 16S rRNA (uracil(1498)-N(3))-methyltransferase NF008693.0 PRK11713 PRK11713.2-3 210 210 246 equivalog Y Y N 16S rRNA (uracil(1498)-N(3))-methyltransferase 2.1.1.193 GO:0006364,GO:0008168 2 Bacteria superkingdom 16050 NCBI Protein Cluster (PRK) 16S ribosomal RNA methyltransferase RsmE 16S rRNA (uracil(1498)-N(3))-methyltransferase NF008696.0 PRK11713 PRK11713.3-5 234 234 248 equivalog Y Y N 16S rRNA (uracil(1498)-N(3))-methyltransferase 2.1.1.193 GO:0006364,GO:0008168 2 Bacteria superkingdom 8671 NCBI Protein Cluster (PRK) 16S ribosomal RNA methyltransferase RsmE 16S rRNA (uracil(1498)-N(3))-methyltransferase NF008700.0 PRK11713 PRK11713.5-4 252 252 237 equivalog Y Y N 16S rRNA (uracil(1498)-N(3))-methyltransferase 2.1.1.193 GO:0006364,GO:0008168 2 Bacteria superkingdom 5872 NCBI Protein Cluster (PRK) 16S ribosomal RNA methyltransferase RsmE 16S rRNA (uracil(1498)-N(3))-methyltransferase NF008701.0 PRK11713 PRK11713.5-5 215 215 228 equivalog Y Y N 16S rRNA (uracil(1498)-N(3))-methyltransferase 2.1.1.193 2 Bacteria superkingdom 471 NCBI Protein Cluster (PRK) 16S ribosomal RNA methyltransferase RsmE 16S rRNA (uracil(1498)-N(3))-methyltransferase NF008704.0 PRK11713 PRK11713.6-3 216 216 227 equivalog Y Y N 16S rRNA (uracil(1498)-N(3))-methyltransferase 2.1.1.193 2 Bacteria superkingdom 140 NCBI Protein Cluster (PRK) 16S ribosomal RNA methyltransferase RsmE 16S rRNA (uracil(1498)-N(3))-methyltransferase NF008709.0 PRK11713 PRK11713.7-4 292 292 246 equivalog Y Y N 16S rRNA (uracil(1498)-N(3))-methyltransferase 2.1.1.193 2 Bacteria superkingdom 109 NCBI Protein Cluster (PRK) 16S ribosomal RNA methyltransferase RsmE 16S rRNA (uracil(1498)-N(3))-methyltransferase NF008712.1 PRK11715 PRK11715.1-1 275 275 429 equivalog Y Y N cell envelope integrity protein CreD creD 31451505 2 Bacteria superkingdom 15873 NCBI Protein Cluster (PRK) inner membrane protein cell envelope integrity protein CreD NF008722.0 PRK11716 PRK11716.1 246 246 293 equivalog Y Y N HTH-type transcriptional activator IlvY ilvY GO:0003700,GO:0006355 2 Bacteria superkingdom 7281 NCBI Protein Cluster (PRK) DNA-binding transcriptional regulator IlvY HTH-type transcriptional activator IlvY Participates in controlling several genes involved in isoleucine and valine biosynthesis; activates the transcription of the ilvC gene in the presence of acetolactate or acetohydroxybutyrate NF008724.0 PRK11720 PRK11720.1 448 448 348 equivalog Y Y N UDP-glucose--hexose-1-phosphate uridylyltransferase 2.7.7.12 GO:0006012,GO:0008108 2 Bacteria superkingdom 12015 NCBI Protein Cluster (PRK) galactose-1-phosphate uridylyltransferase UDP-glucose--hexose-1-phosphate uridylyltransferase NF008725.1 PRK11727 PRK11727.1 302 302 293 equivalog Y Y N 23S rRNA (adenine(1618)-N(6))-methyltransferase RlmF rlmF 2.1.1.181 GO:0006364,GO:0008988 2 Bacteria superkingdom 16670 NCBI Protein Cluster (PRK) 23S rRNA mA1618 methyltransferase 23S rRNA (adenine(1618)-N(6))-methyltransferase RlmF NF008731.0 PRK11752 PRK11752.1 325 325 287 equivalog Y Y N glutathione-dependent disulfide-bond oxidoreductase yghU GO:0005515,GO:0006749 14635120 2 Bacteria superkingdom 17450 NCBI Protein Cluster (PRK) putative S-transferase glutathione-dependent disulfide-bond oxidoreductase NF008735.0 PRK11761 PRK11761.1 413 413 296 equivalog Y Y N cysteine synthase CysM cysM 2.5.1.47 GO:0004124,GO:0006535 2 Bacteria superkingdom 15287 NCBI Protein Cluster (PRK) cysteine synthase B cysteine synthase CysM Catalyzes the formation of cysteine from 3-O-acetyl-L-serine and hydrogen sulfide NF008738.0 PRK11768 PRK11768.1 194 194 327 equivalog Y Y N serine/threonine protein kinase 2.7.11.1 GO:0004674,GO:0006468 11594757,12511488,17302814,7881552,9159398 2 Bacteria superkingdom 15527 NCBI Protein Cluster (PRK) serine/threonine protein kinase serine/threonine protein kinase NF008740.0 PRK11770 PRK11770.1-2 123 123 124 equivalog Y Y N YccF domain-containing protein 2 Bacteria superkingdom 14922 NCBI Protein Cluster (PRK) hypothetical protein YccF domain-containing protein NF008741.0 PRK11770 PRK11770.1-3 140 140 133 equivalog Y Y N YccF domain-containing protein 2 Bacteria superkingdom 2578 NCBI Protein Cluster (PRK) hypothetical protein YccF domain-containing protein NF008742.0 PRK11770 PRK11770.1-4 155 155 147 equivalog Y Y N YccF domain-containing protein 2 Bacteria superkingdom 2026 NCBI Protein Cluster (PRK) hypothetical protein YccF domain-containing protein NF008745.0 PRK11778 PRK11778.1 259 259 345 equivalog Y Y N protease SohB sohB 3.4.21.- GO:0006508,GO:0008233 2 Bacteria superkingdom 13322 NCBI Protein Cluster (PRK) putative inner membrane peptidase protease SohB NF008746.0 PRK11779 PRK11779.1 260 260 477 equivalog Y Y N exodeoxyribonuclease I sbcB 3.1.11.1 GO:0000175,GO:0003676,GO:0006281,GO:0008310 2 Bacteria superkingdom 22106 NCBI Protein Cluster (PRK) exonuclease I exodeoxyribonuclease I Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates NF008748.0 PRK11783 PRK11783.1 466 466 704 equivalog Y Y N bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2))-methyltransferase RlmL rlmKL 2.1.1.173,2.1.1.264 GO:0003723,GO:0008990,GO:0031167 17010378,17337586,17389639 2 Bacteria superkingdom 20330 NCBI Protein Cluster (PRK) 23S rRNA m(2)G2445 methyltransferase bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2))-methyltransferase RlmL NF008750.0 PRK11784 PRK11784.1-2 241 241 346 equivalog Y Y N tRNA 2-selenouridine(34) synthase MnmH mnmH 2.5.1.- 2 Bacteria superkingdom 16147 NCBI Protein Cluster (PRK) tRNA 2-selenouridine synthase tRNA 2-selenouridine(34) synthase MnmH NF008751.0 PRK11784 PRK11784.1-3 361 361 367 equivalog Y Y N tRNA 2-selenouridine(34) synthase MnmH mnmH 2.5.1.- GO:0043828 2 Bacteria superkingdom 11432 NCBI Protein Cluster (PRK) tRNA 2-selenouridine synthase tRNA 2-selenouridine(34) synthase MnmH NF008752.0 PRK11784 PRK11784.1-4 266 266 357 equivalog Y Y N tRNA 2-selenouridine(34) synthase MnmH mnmH 2.5.1.- GO:0002098,GO:0043828 2 Bacteria superkingdom 7305 NCBI Protein Cluster (PRK) tRNA 2-selenouridine synthase tRNA 2-selenouridine(34) synthase MnmH NF008759.0 PRK11790 PRK11790.1 404 404 410 equivalog Y Y N phosphoglycerate dehydrogenase serA 1.1.1.95 GO:0016616,GO:0051287 2 Bacteria superkingdom 16121 NCBI Protein Cluster (PRK) D-3-phosphoglycerate dehydrogenase phosphoglycerate dehydrogenase Catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis NF008761.0 PRK11797 PRK11797.1 93 93 139 equivalog Y Y N D-ribose pyranase rbsD 5.4.99.62 GO:0016872 11320319,12738765,15060078,15876375 2 Bacteria superkingdom 16018 NCBI Protein Cluster (PRK) D-ribose pyranase D-ribose pyranase Cytoplasmic mutarotase that catalyzes the conversion between beta-pyran and beta-furan forms of D-ribose NF008773.0 PRK11814 PRK11814.1 717 717 484 equivalog Y Y N Fe-S cluster assembly protein SufB sufB GO:0016226 2 Bacteria superkingdom 21386 NCBI Protein Cluster (PRK) cysteine desulfurase activator complex subunit SufB Fe-S cluster assembly protein SufB NF008774.0 PRK11815 PRK11815.1 269 269 337 equivalog Y Y N tRNA dihydrouridine(20/20a) synthase DusA dusA 1.3.1.-,1.3.1.91 GO:0002943,GO:0017150,GO:0050660 2 Bacteria superkingdom 33557 NCBI Protein Cluster (PRK) tRNA-dihydrouridine synthase A tRNA dihydrouridine(20/20a) synthase DusA NF008775.0 PRK11819 PRK11819.1 599 599 556 equivalog Y Y N energy-dependent translational throttle protein EttA ettA GO:0005524,GO:0045900 11344138 2 Bacteria superkingdom 38699 NCBI Protein Cluster (PRK) putative ABC transporter ATP-binding protein energy-dependent translational throttle protein EttA NF008809.0 PRK11831 PRK11831.1 441 441 270 equivalog Y Y N phospholipid ABC transporter ATP-binding protein MlaF mlaF GO:0005524 2 Bacteria superkingdom 3526 NCBI Protein Cluster (PRK) putative ABC transporter ATP-binding protein YrbF phospholipid ABC transporter ATP-binding protein MlaF NF008814.0 PRK11854 PRK11854.1 722 722 637 equivalog Y Y N pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase aceF 2.3.1.12 GO:0004742,GO:0006096,GO:0045254 2 Bacteria superkingdom 14826 NCBI Protein Cluster (PRK) pyruvate dehydrogenase dihydrolipoyltransacetylase pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase E2 component of pyruvate dehydrogenase multienzyme complex NF008845.0 PRK11883 PRK11883.1-5 560 560 468 equivalog Y Y N protoporphyrinogen oxidase hemY 1.3.3.4 GO:0004729,GO:0006779 2 Bacteria superkingdom 5090 NCBI Protein Cluster (PRK) protoporphyrinogen oxidase protoporphyrinogen oxidase NF008847.0 PRK11886 PRK11886.1-2 293 293 320 equivalog Y Y N bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA birA 6.3.4.15 GO:0004077,GO:0006355,GO:0036211 2 Bacteria superkingdom 10472 NCBI Protein Cluster (PRK) bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA NF008848.0 PRK11886 PRK11886.1-3 362 362 319 equivalog Y Y N bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA birA 6.3.4.15 GO:0004077,GO:0006355,GO:0036211 2 Bacteria superkingdom 4082 NCBI Protein Cluster (PRK) bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA NF008852.0 PRK11890 PRK11890.1 413 413 315 subfamily Y Y N phosphate acetyltransferase 2.3.1.8 2 Bacteria superkingdom 7206 NCBI Protein Cluster (PRK) phosphate acetyltransferase phosphate acetyltransferase Catalyzes the formation of acetyl phosphate from acetyl-CoA and phosphate; can also act with other short-chain acyl-CoAs NF008853.0 PRK11891 PRK11891.1 560 560 430 equivalog Y Y N aspartate carbamoyltransferase 2.1.3.2 2 Bacteria superkingdom 1278 NCBI Protein Cluster (PRK) aspartate carbamoyltransferase aspartate carbamoyltransferase Catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis NF008854.0 PRK11892 PRK11892.1 454 454 464 equivalog Y Y N pyruvate dehydrogenase complex E1 component subunit beta 1.2.4.1 GO:0004739,GO:0006086 2 Bacteria superkingdom 12891 NCBI Protein Cluster (PRK) pyruvate dehydrogenase subunit beta pyruvate dehydrogenase complex E1 component subunit beta NF008863.0 PRK11893 PRK11893.2-5 551 551 531 equivalog Y Y N methionine--tRNA ligase 6.1.1.10 2 Bacteria superkingdom 173 NCBI Protein Cluster (PRK) methionyl-tRNA synthetase methionine--tRNA ligase NF008866.0 PRK11899 PRK11899.1 359 359 283 equivalog Y Y N prephenate dehydratase 4.2.1.51 GO:0004664,GO:0009094 2 Bacteria superkingdom 8727 NCBI Protein Cluster (PRK) prephenate dehydratase prephenate dehydratase Catalyzes the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis NF008868.0 PRK11903 PRK11903.1 444 444 521 equivalog Y Y N 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase 2 Bacteria superkingdom 17887 NCBI Protein Cluster (PRK) aldehyde dehydrogenase 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase NF008869.0 PRK11904 PRK11904.1 747 747 1042 equivalog Y Y N bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA putA 1.2.1.88,1.5.5.2 GO:0003700,GO:0003842,GO:0004657,GO:0006355,GO:0010133,GO:0016620 2 Bacteria superkingdom 41024 NCBI Protein Cluster (PRK) bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA Proline utilization protein A; multifunctional protein that functions in proline catabolism in the first two enzymatic steps resulting in the conversion of proline to glutamate NF008872.0 PRK11908 PRK11908.1 294 294 349 equivalog Y Y N bifunctional UDP-4-keto-pentose/UDP-xylose synthase GO:0003824 2 Bacteria superkingdom 10222 NCBI Protein Cluster (PRK) NAD-dependent epimerase/dehydratase family protein bifunctional UDP-4-keto-pentose/UDP-xylose synthase NF008877.0 PRK11913 PRK11913.1-2 247 247 264 equivalog Y Y N phenylalanine 4-monooxygenase 1.14.16.1 2 Bacteria superkingdom 14797 NCBI Protein Cluster (PRK) phenylalanine 4-monooxygenase phenylalanine 4-monooxygenase NF008899.0 PRK12266 PRK12266.1 360 360 508 equivalog Y Y N glycerol-3-phosphate dehydrogenase glpD 1.1.5.3 GO:0004368,GO:0006072,GO:0009331 2 Bacteria superkingdom 29731 NCBI Protein Cluster (PRK) glycerol-3-phosphate dehydrogenase glycerol-3-phosphate dehydrogenase NF008900.0 PRK12267 PRK12267.1 598 598 648 equivalog Y Y N methionine--tRNA ligase metG 6.1.1.10 GO:0000049,GO:0004825,GO:0005524,GO:0006431 16189106 2 Bacteria superkingdom 39830 NCBI Protein Cluster (PRK) methionyl-tRNA synthetase methionine--tRNA ligase MetRS; adds methionine to tRNA(Met) with cleavage of ATP to AMP and diphosphate; some MetRS enzymes form dimers depending on a C-terminal domain that is also found in other proteins such as Trbp111 in Aquifex aeolicus and the cold-shock protein CsaA from Bacillus subtilis while others do not; four subfamilies exist based on sequence motifs and zinc content NF008907.0 PRK12270 PRK12270.1 878 878 1241 equivalog Y Y N multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit 4.1.1.71 GO:0004591,GO:0006099,GO:0016746,GO:0030976 16027371 2 Bacteria superkingdom 58333 NCBI Protein Cluster (PRK) alpha-ketoglutarate decarboxylase multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit kgd; produces succinic semialdehyde; part of alternative pathway from alpha-ketoglutarate to succinate NF008911.0 PRK12275 PRK12275.1-2 137 137 118 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 3126 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF008912.0 PRK12275 PRK12275.1-6 124 124 117 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 1836 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF008922.0 PRK12283 PRK12283.1 572 572 400 equivalog Y Y N tryptophan--tRNA ligase 6.1.1.2 GO:0000166,GO:0004830,GO:0005524,GO:0006436 2 Bacteria superkingdom 2779 NCBI Protein Cluster (PRK) tryptophanyl-tRNA synthetase tryptophan--tRNA ligase Catalyzes a two-step reaction, first charging a tryptophan molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA NF008941.0 PRK12292 PRK12292.2-4 447 447 393 equivalog Y Y N ATP phosphoribosyltransferase regulatory subunit GO:0000105 2 Bacteria superkingdom 3279 NCBI Protein Cluster (PRK) ATP phosphoribosyltransferase regulatory subunit ATP phosphoribosyltransferase regulatory subunit NF008954.1 PRK12296 PRK12296.1 377 377 470 equivalog Y Y N GTPase ObgE obgE GO:0000166,GO:0000287,GO:0003924,GO:0005525 2 Bacteria superkingdom 31137 NCBI Protein Cluster (PRK) GTPase CgtA GTPase ObgE Essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication NF008955.0 PRK12297 PRK12297.1 406 406 429 equivalog Y Y N GTPase ObgE obgE GO:0003924 2 Bacteria superkingdom 61580 NCBI Protein Cluster (PRK) GTPase CgtA GTPase ObgE Essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication NF008956.1 PRK12299 PRK12299.1 300 300 327 equivalog Y Y N GTPase ObgE obgE GO:0000287,GO:0003924,GO:0005525 17578452,19555460,28223358 2 Bacteria superkingdom 62833 NCBI Protein Cluster (PRK) GTPase CgtA GTPase ObgE Essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication NF008965.0 PRK12309 PRK12309.1 550 550 392 equivalog Y Y N transaldolase 2 Bacteria superkingdom 979 NCBI Protein Cluster (PRK) transaldolase/EF-hand domain-containing protein transaldolase NF008968.0 PRK12315 PRK12315.1 510 510 582 subfamily Y Y N 1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 2 Bacteria superkingdom 6111 NCBI Protein Cluster (PRK) 1-deoxy-D-xylulose-5-phosphate synthase 1-deoxy-D-xylulose-5-phosphate synthase Catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate NF008970.0 PRK12318 PRK12318.1 267 267 291 equivalog Y Y N methionyl aminopeptidase 3.4.11.18 2 Bacteria superkingdom 9170 NCBI Protein Cluster (PRK) methionine aminopeptidase methionyl aminopeptidase NF008974.0 PRK12322 PRK12322.1 522 522 366 equivalog Y Y N NADH-quinone oxidoreductase subunit D 1.6.5.9 2 Bacteria superkingdom 1909 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit D NADH-quinone oxidoreductase subunit D NF008979.1 PRK12325 PRK12325.1 550 550 437 exception Y Y N proline--tRNA ligase proS 6.1.1.15 GO:0004827,GO:0006433 2 Bacteria superkingdom 7214 NCBI Protein Cluster (PRK) prolyl-tRNA synthetase proline--tRNA ligase, alphaproteobacterial type Catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro) NF008984.0 PRK12330 PRK12330.1 827 827 500 equivalog Y Y N methylmalonyl-CoA carboxytransferase subunit 5S 2.1.3.1 2 Bacteria superkingdom 427 NCBI Protein Cluster (PRK) oxaloacetate decarboxylase methylmalonyl-CoA carboxytransferase subunit 5S NF008992.0 PRK12335 PRK12335.1 303 303 289 equivalog Y Y N SAM-dependent methyltransferase TehB tehB 2.1.1.- GO:0008757,GO:0046690 2 Bacteria superkingdom 5142 NCBI Protein Cluster (PRK) tellurite resistance protein TehB SAM-dependent methyltransferase TehB With TehA confers resistance to tellurite NF009003.0 PRK12348 PRK12348.1 331 331 228 subfamily Y Y N L-ribulose-5-phosphate 4-epimerase 5.1.3.4 10769139,11741871,2251150,4879898,9548961 2 Bacteria superkingdom 15257 NCBI Protein Cluster (PRK) L-ribulose-5-phosphate 4-epimerase L-ribulose-5-phosphate 4-epimerase Catalyzes the isomerization of L-ribulose 5-phosphate to D-xylulose 5-phosphate in the anaerobic catabolism of L-ascorbate; links the arabinose metabolic pathway to the pentose phosphate pathway and allows the bacteria to use arabinose as an energy source NF009006.0 PRK12351 PRK12351.1 549 549 384 equivalog Y Y N 2-methylcitrate synthase prpC 2.3.3.16,2.3.3.5 GO:0050440 2 Bacteria superkingdom 15170 NCBI Protein Cluster (PRK) methylcitrate synthase 2-methylcitrate synthase Catalyzes the synthesis of 2-methylcitrate from propionyl-CoA and oxaloacetate NF009013.0 PRK12355 PRK12355.2-4 605 605 576 subfamily Y Y N type-F conjugative transfer system mating-pair stabilization protein TraN traN 2 Bacteria superkingdom 422 NCBI Protein Cluster (PRK) conjugal transfer mating pair stabilization protein TraN type-F conjugative transfer system mating-pair stabilization protein TraN NF009020.0 PRK12356 PRK12356.1 395 395 319 equivalog Y Y N glutaminase A glsA 3.5.1.2 GO:0004359,GO:0006541 2 Bacteria superkingdom 4628 NCBI Protein Cluster (PRK) glutaminase glutaminase A Catalyzes the formation of glutamate from glutamine NF009021.0 PRK12357 PRK12357.1 470 470 326 equivalog Y Y N glutaminase 3.5.1.2 2 Bacteria superkingdom 1303 NCBI Protein Cluster (PRK) glutaminase glutaminase Catalyzes the formation of glutamate from glutamine NF009022.0 PRK12358 PRK12358.1 247 247 239 equivalog Y Y N glucosamine-6-phosphate deaminase 3.5.99.6 GO:0004342,GO:0006044 2 Bacteria superkingdom 1973 NCBI Protein Cluster (PRK) putative 6-phosphogluconolactonase glucosamine-6-phosphate deaminase NF009028.0 PRK12364 PRK12364.1 1377 1377 842 equivalog Y Y N ribonucleoside-diphosphate reductase subunit alpha 2 Bacteria superkingdom 1669 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit alpha ribonucleoside-diphosphate reductase subunit alpha NF009044.0 PRK12378 PRK12378.1 196 196 239 subfamily Y Y N YebC/PmpR family DNA-binding transcriptional regulator 2 Bacteria superkingdom 53743 NCBI Protein Cluster (PRK) hypothetical protein YebC/PmpR family DNA-binding transcriptional regulator NF009049.0 PRK12383 PRK12383.1 254 254 408 equivalog Y Y N phosphopentomutase 5.4.2.7 GO:0008973 2 Bacteria superkingdom 3924 NCBI Protein Cluster (PRK) putative mutase phosphopentomutase NF009050.0 PRK12384 PRK12384.1 307 307 259 equivalog Y Y N sorbitol-6-phosphate dehydrogenase srlD 1.1.1.140 GO:0016491 2 Bacteria superkingdom 1879 NCBI Protein Cluster (PRK) sorbitol-6-phosphate dehydrogenase sorbitol-6-phosphate dehydrogenase Catalyzes the conversion of sorbitol 6-phosphate into fructose 6-phosphate NF009055.0 PRK12389 PRK12389.1 637 637 431 equivalog Y Y N glutamate-1-semialdehyde 2,1-aminomutase 5.4.3.8 GO:0030170,GO:0033014,GO:0042286 2 Bacteria superkingdom 5510 NCBI Protein Cluster (PRK) glutamate-1-semialdehyde aminotransferase glutamate-1-semialdehyde 2,1-aminomutase Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate NF009065.0 PRK12399 PRK12399.1 458 458 326 subfamily Y Y N tagatose 1,6-diphosphate aldolase 17371500 2 Bacteria superkingdom 6074 NCBI Protein Cluster (PRK) tagatose 1,6-diphosphate aldolase tagatose 1,6-diphosphate aldolase Catalyzes the reversible reaction of dihydroxyacetone phosphate with glyceraldehyde 3-phosphate to produce tagatose 1,6-bisphosphate NF009069.0 PRK12404 PRK12404.1 442 442 338 subfamily Y Y N stage V sporulation protein AD 2 Bacteria superkingdom 4911 NCBI Protein Cluster (PRK) stage V sporulation protein AD stage V sporulation protein AD NF009071.0 PRK12406 PRK12406.1 701 701 510 subfamily Y Y N acyl-CoA synthetase 2 Bacteria superkingdom 1317 NCBI Protein Cluster (PRK) long-chain-fatty-acid--CoA ligase acyl-CoA synthetase NF009073.0 PRK12408 PRK12408.1 240 240 338 subfamily Y Y N glucokinase 2.7.1.2 GO:0004340,GO:0006096 2 Bacteria superkingdom 5871 NCBI Protein Cluster (PRK) glucokinase glucokinase Catalyzes the conversion of ATP and D-glucose to ADP and D-glucose 6-phosphate NF009077.0 PRK12412 PRK12412.1 385 385 274 equivalog Y Y N pyridoxine/pyridoxal/pyridoxamine kinase pdxK GO:0008972,GO:0009228 14973012,17012797 2 Bacteria superkingdom 2528 NCBI Protein Cluster (PRK) pyridoxal kinase pyridoxine/pyridoxal/pyridoxamine kinase Catalyzes the phosphorylation of three vitamin B6 precursors, pyridoxal, pyridoxine and pyridoxamine NF009084.0 PRK12419 PRK12419.1 160 160 166 equivalog Y Y N 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 GO:0000906,GO:0009349 2 Bacteria superkingdom 5849 NCBI Protein Cluster (PRK) riboflavin synthase subunit beta 6,7-dimethyl-8-ribityllumazine synthase 6,7-diimethyl-8-ribityllumazine synthase; DMRL synthase; lumazine synthase; beta subunit of riboflavin synthase; condenses 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate to generate 6,6-dimethyl-8-lumazine (DMRL); involved in the last steps of riboflavin biosynthesis NF009085.0 PRK12420 PRK12420.1 540 540 426 equivalog Y Y N histidine--tRNA ligase 6.1.1.21 2 Bacteria superkingdom 1835 NCBI Protein Cluster (PRK) histidyl-tRNA synthetase histidine--tRNA ligase Catalyzes a two-step reaction, first charging a histidine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class II aminoacyl-tRNA synthetase; forms homodimers; some organisms have a paralogous gene, hisZ, that is similar to hisS and produces a protein that performs the first step in histidine biosynthesis along with HisG NF009086.0 PRK12421 PRK12421.1 318 318 389 equivalog Y Y N ATP phosphoribosyltransferase regulatory subunit 2 Bacteria superkingdom 9138 NCBI Protein Cluster (PRK) ATP phosphoribosyltransferase regulatory subunit ATP phosphoribosyltransferase regulatory subunit NF009092.0 PRK12428 PRK12428.1 242 242 261 subfamily Y Y N coniferyl-alcohol dehydrogenase 1.1.1.194 GO:0016491 2 Bacteria superkingdom 3406 NCBI Protein Cluster (PRK) 3-alpha-hydroxysteroid dehydrogenase coniferyl-alcohol dehydrogenase NF009093.0 PRK12429 PRK12429.1 258 258 259 subfamily Y Y N 3-hydroxybutyrate dehydrogenase 1.1.1.30 GO:0003858 2 Bacteria superkingdom 36932 NCBI Protein Cluster (PRK) 3-hydroxybutyrate dehydrogenase 3-hydroxybutyrate dehydrogenase Catalyzes the formation of acetoacetate from 3-hydroxybutyrate NF009095.0 PRK12435 PRK12435.1 455 455 311 subfamily Y Y N ferrochelatase 4.98.1.1 2 Bacteria superkingdom 5100 NCBI Protein Cluster (PRK) ferrochelatase ferrochelatase Protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis NF009098.0 PRK12439 PRK12439.1 436 436 341 equivalog Y Y N NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 1.1.1.94 2 Bacteria superkingdom 1159 NCBI Protein Cluster (PRK) NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NAD(P)H-dependent glycerol-3-phosphate dehydrogenase Catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate NF009102.0 PRK12446 PRK12446.1 339 339 352 equivalog Y Y N undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase GO:0050511 2 Bacteria superkingdom 6108 NCBI Protein Cluster (PRK) undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase Involved in cell wall formation; inner membrane-associated; last step of peptidoglycan synthesis NF009103.0 PRK12448 PRK12448.1 710 710 616 equivalog Y Y N dihydroxy-acid dehydratase ilvD 4.2.1.9 GO:0004160,GO:0009082 2 Bacteria superkingdom 37107 NCBI Protein Cluster (PRK) dihydroxy-acid dehydratase dihydroxy-acid dehydratase NF009110.0 PRK12458 PRK12458.1 408 408 349 subfamily Y Y N glutathione synthetase GO:0004363,GO:0005524,GO:0006750 12049666,20935175,23170977,26713511 2 Bacteria superkingdom 1764 NCBI Protein Cluster (PRK) glutathione synthetase glutathione synthetase NF009112.0 PRK12462 PRK12462.1 563 563 365 equivalog Y Y N phosphoserine transaminase 2.6.1.52 2 Bacteria superkingdom 265 NCBI Protein Cluster (PRK) phosphoserine aminotransferase phosphoserine transaminase Catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate NF009114.0 PRK12464 PRK12464.1 461 461 389 equivalog Y Y N 1-deoxy-D-xylulose-5-phosphate reductoisomerase 1.1.1.267 GO:0005515,GO:0008299,GO:0030604,GO:0046872,GO:0070402 2 Bacteria superkingdom 36916 NCBI Protein Cluster (PRK) 1-deoxy-D-xylulose 5-phosphate reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate NF009118.0 PRK12469 PRK12469.1 396 396 483 subfamily Y Y N RNA polymerase factor sigma-54 rpoN 2 Bacteria superkingdom 24879 NCBI Protein Cluster (PRK) RNA polymerase factor sigma-54 RNA polymerase factor sigma-54 NF009123.0 PRK12475 PRK12475.1 510 510 338 subfamily Y Y N MoeB/ThiF family adenylyltransferase GO:0008641 2 Bacteria superkingdom 4774 NCBI Protein Cluster (PRK) thiamine/molybdopterin biosynthesis MoeB-like protein MoeB/ThiF family adenylyltransferase NF009130.0 PRK12483 PRK12483.1 801 801 521 subfamily Y Y N threonine ammonia-lyase 2 Bacteria superkingdom 11726 NCBI Protein Cluster (PRK) threonine dehydratase threonine ammonia-lyase NF009134.0 PRK12487 PRK12487.1 196 196 161 equivalog Y Y N putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase 2 Bacteria superkingdom 4752 NCBI Protein Cluster (PRK) ribonuclease activity regulator protein RraA putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase NF009136.0 PRK12489 PRK12489.1 396 396 444 subfamily Y Y N anaerobic C4-dicarboxylate transporter 7961398,9733683,9852003 2 Bacteria superkingdom 17608 NCBI Protein Cluster (PRK) anaerobic C4-dicarboxylate transporter anaerobic C4-dicarboxylate transporter Functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate NF009140.0 PRK12493 PRK12493.1 1300 1300 1313 equivalog Y Y N magnesium chelatase subunit H 6.6.1.1 2 Bacteria superkingdom 1313 NCBI Protein Cluster (PRK) magnesium chelatase subunit H magnesium chelatase subunit H NF009150.0 PRK12497 PRK12497.1-3 81 81 118 equivalog Y Y N YraN family protein GO:0003676,GO:0004518 2 Bacteria superkingdom 30626 NCBI Protein Cluster (PRK) hypothetical protein YraN family protein NF009151.0 PRK12497 PRK12497.1-5 124 124 126 equivalog Y Y N YraN family protein GO:0003676,GO:0004518 2 Bacteria superkingdom 4336 NCBI Protein Cluster (PRK) hypothetical protein YraN family protein NF009152.0 PRK12497 PRK12497.2-4 111 111 114 equivalog Y Y N YraN family protein 2 Bacteria superkingdom 1656 NCBI Protein Cluster (PRK) hypothetical protein YraN family protein NF009154.0 PRK12497 PRK12497.3-3 109 109 123 equivalog Y Y N YraN family protein GO:0003676,GO:0004518 2 Bacteria superkingdom 17237 NCBI Protein Cluster (PRK) hypothetical protein YraN family protein NF009161.0 PRK12507 PRK12507.1 272 272 336 equivalog Y N N putative monovalent cation/H+ antiporter subunit B 2 Bacteria superkingdom 462 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit B putative monovalent cation/H+ antiporter subunit B NF009163.0 PRK12509 PRK12509.1 148 148 137 equivalog Y Y N Na+/H+ antiporter subunit B 2 Bacteria superkingdom 1705 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit B Na+/H+ antiporter subunit B Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF009164.0 PRK12511 PRK12511.1 185 185 182 equivalog Y N N RNA polymerase sigma factor 2 Bacteria superkingdom 1522 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009165.0 PRK12512 PRK12512.1 198 198 184 equivalog Y N N RNA polymerase sigma factor 2 Bacteria superkingdom 1672 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009166.1 PRK12513 PRK12513.1 206 206 193 equivalog Y Y N RNA polymerase sigma factor GO:0003677,GO:0006352,GO:0016987 2 Bacteria superkingdom 2349 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor Bacteria have multiple sigma factors which are active under specific conditions; the sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs Bacterial core RNA polymerase to specific promoter elements to initiate transcription NF009168.0 PRK12515 PRK12515.1 236 236 189 subfamily Y N N RNA polymerase sigma factor 2 Bacteria superkingdom 1247 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009199.0 PRK12547 PRK12547.1 219 219 184 subfamily Y N N RNA polymerase sigma factor 2 Bacteria superkingdom 2902 NCBI Protein Cluster (PRK) RNA polymerase sigma factor RNA polymerase sigma factor NF009201.0 PRK12549 PRK12549.1 235 235 286 subfamily Y Y N shikimate dehydrogenase 1.1.1.25 2 Bacteria superkingdom 12108 NCBI Protein Cluster (PRK) shikimate 5-dehydrogenase shikimate dehydrogenase Catalyzes the conversion of shikimate to 3-dehydroshikimate NF009202.0 PRK12550 PRK12550.1 306 306 272 equivalog Y Y N shikimate 5-dehydrogenase GO:0004764 12906820,15596430,15735308,16202245,16828913 2 Bacteria superkingdom 7650 NCBI Protein Cluster (PRK) shikimate 5-dehydrogenase shikimate 5-dehydrogenase Catalyzes the conversion of shikimate to 3-dehydroshikimate NF009207.0 PRK12556 PRK12556.1 479 479 332 equivalog Y Y N tryptophan--tRNA ligase 6.1.1.2 GO:0004830,GO:0006436 2 Bacteria superkingdom 2507 NCBI Protein Cluster (PRK) tryptophanyl-tRNA synthetase tryptophan--tRNA ligase Catalyzes a two-step reaction, first charging a tryptophan molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA NF009210.0 PRK12559 PRK12559.1 159 159 131 equivalog Y Y N transcriptional regulator SpxA spxA GO:0045892 28484046 2 Bacteria superkingdom 2662 NCBI Protein Cluster (PRK) transcriptional regulator Spx transcriptional regulator SpxA The anti-alpha factor Spx interacts with RNA polymerase alpha subunit C-terminal domain in a region that interacts with the sigma 70 subunit and may interfere with activation of promoters NF009218.0 PRK12567 PRK12567.1-2 184 184 200 equivalog Y N N putative monovalent cation/H+ antiporter subunit B 2 Bacteria superkingdom 16 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit B putative monovalent cation/H+ antiporter subunit B NF009219.0 PRK12567 PRK12567.1-3 179 179 220 equivalog Y N N putative monovalent cation/H+ antiporter subunit B 2 Bacteria superkingdom 612 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit B putative monovalent cation/H+ antiporter subunit B NF009223.0 PRK12573 PRK12573.1 152 152 140 subfamily Y Y N Na(+)/H(+) antiporter subunit B 2 Bacteria superkingdom 4218 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit B Na(+)/H(+) antiporter subunit B Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF009232.0 PRK12582 PRK12582.1 777 777 624 subfamily Y N N acyl-CoA synthetase 2 Bacteria superkingdom 1364 NCBI Protein Cluster (PRK) acyl-CoA synthetase acyl-CoA synthetase NF009243.0 PRK12599 PRK12599.1-2 95 95 91 equivalog Y N N putative monovalent cation/H+ antiporter subunit F 2 Bacteria superkingdom 672 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit F putative monovalent cation/H+ antiporter subunit F NF009248.0 PRK12600 PRK12600.1 97 97 94 equivalog Y Y N Na(+)/H(+) antiporter subunit F1 2 Bacteria superkingdom 2509 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit F Na(+)/H(+) antiporter subunit F1 NF009259.0 PRK12616 PRK12616.1 390 390 270 equivalog Y Y N bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase 2.7.1.49 2 Bacteria superkingdom 1833 NCBI Protein Cluster (PRK) pyridoxal kinase bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase NF009278.1 PRK12636 PRK12636.1 350 350 263 equivalog Y Y N flagellar basal body rod protein FlgG flgG 1905667 2 Bacteria superkingdom 2253 NCBI Protein Cluster (PRK) flagellar basal body rod protein FlgG flagellar basal body rod protein FlgG Makes up the distal portion of the flagellar basal body rod NF009280.2 PRK12640 PRK12640.1 210 210 246 subfamily Y Y N flagellar basal body rod protein FlgF flgF 15170400,15687208,9931471 2 Bacteria superkingdom 14251 NCBI Protein Cluster (PRK) flagellar basal body rod protein FlgF flagellar basal body rod protein FlgF With FlgB and C, makes up the proximal portion of the flagellar basal body rod NF009284.0 PRK12644 PRK12644.1 962 962 975 equivalog Y Y N Na+/H+ antiporter subunit A 2 Bacteria superkingdom 10161 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit A Na+/H+ antiporter subunit A Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF009285.0 PRK12645 PRK12645.1 1028 1028 804 equivalog Y Y N Na+/H+ antiporter subunit A GO:0051139,GO:0098662 2 Bacteria superkingdom 6517 NCBI Protein Cluster (PRK) monovalent cation/H+ antiporter subunit A Na+/H+ antiporter subunit A Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF009287.0 PRK12647 PRK12647.1 937 937 773 equivalog Y Y N putative monovalent cation/H+ antiporter subunit A 2 Bacteria superkingdom 3024 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit A putative monovalent cation/H+ antiporter subunit A NF009288.0 PRK12648 PRK12648.1 1104 1104 954 equivalog Y Y N monovalent cation/H+ antiporter subunit A GO:0051139,GO:0098662 2 Bacteria superkingdom 13774 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit A monovalent cation/H+ antiporter subunit A Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF009290.0 PRK12650 PRK12650.1 980 980 966 equivalog Y Y N DUF4040 family protein 2 Bacteria superkingdom 1764 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit A DUF4040 family protein NF009292.0 PRK12651 PRK12651.1-3 213 213 158 equivalog Y Y N Na+/H+ antiporter subunit E 2 Bacteria superkingdom 1687 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit E Na+/H+ antiporter subunit E NF009299.0 PRK12656 PRK12656.1 214 214 222 equivalog Y Y N fructose-6-phosphate aldolase 4.1.2.- GO:0005975,GO:0016832 2 Bacteria superkingdom 2582 NCBI Protein Cluster (PRK) fructose-6-phosphate aldolase fructose-6-phosphate aldolase NF009301.0 PRK12658 PRK12658.1 156 156 125 equivalog Y Y N Na+/H+ antiporter subunit C 2 Bacteria superkingdom 1505 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit C Na+/H+ antiporter subunit C Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF009302.0 PRK12659 PRK12659.1 154 154 117 equivalog Y Y N Na+/H+ antiporter subunit C 2 Bacteria superkingdom 839 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit C Na+/H+ antiporter subunit C Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF009303.0 PRK12660 PRK12660.1 132 132 114 subfamily Y N N putative monovalent cation/H+ antiporter subunit C 2 Bacteria superkingdom 2246 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit C putative monovalent cation/H+ antiporter subunit C NF009306.0 PRK12663 PRK12663.1 542 542 498 equivalog Y Y N Na+/H+ antiporter subunit D GO:0008137,GO:0042773 2 Bacteria superkingdom 6217 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit D Na+/H+ antiporter subunit D Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF009308.0 PRK12665 PRK12665.1 585 585 531 equivalog Y Y N Na+/H+ antiporter subunit D GO:0008137,GO:0042773 2 Bacteria superkingdom 8427 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit D Na+/H+ antiporter subunit D Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF009309.0 PRK12666 PRK12666.1 476 476 529 equivalog Y Y N monovalent cation/H+ antiporter subunit D 2 Bacteria superkingdom 13043 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit D monovalent cation/H+ antiporter subunit D Part of an antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali NF009316.0 PRK12674 PRK12674.1-5 122 122 121 equivalog Y Y N Na+/H+ antiporter subunit G GO:0051139,GO:0098662 2 Bacteria superkingdom 4524 NCBI Protein Cluster (PRK) putative monovalent cation/H+ antiporter subunit G Na+/H+ antiporter subunit G NF009374.0 PRK12737 PRK12737.1 383 383 284 subfamily Y Y N tagatose-bisphosphate aldolase subunit GatY gatY 4.1.2.40 2 Bacteria superkingdom 5991 NCBI Protein Cluster (PRK) tagatose-bisphosphate aldolase tagatose-bisphosphate aldolase subunit GatY NF009377.1 PRK12740 PRK12740.1-1 890 890 700 equivalog Y Y N elongation factor G-like protein EF-G2 GO:0003924,GO:0005525 2 Bacteria superkingdom 10783 NCBI Protein Cluster (PRK) elongation factor G elongation factor G-like protein EF-G2 NF009384.0 PRK12743 PRK12743.1 264 264 258 equivalog Y Y N SDR family oxidoreductase 1.1.1.- GO:0016491 2 Bacteria superkingdom 6221 NCBI Protein Cluster (PRK) oxidoreductase SDR family oxidoreductase NF009385.0 PRK12744 PRK12744.1 296 296 257 equivalog Y Y N SDR family oxidoreductase GO:0016491 2 Bacteria superkingdom 5967 NCBI Protein Cluster (PRK) short chain dehydrogenase SDR family oxidoreductase NF009386.0 PRK12745 PRK12745.1 250 250 259 equivalog Y Y N 3-ketoacyl-ACP reductase GO:0016491 2 Bacteria superkingdom 3966 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase 3-ketoacyl-ACP reductase NF009389.0 PRK12748 PRK12748.1 286 286 256 subfamily Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 5286 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase SDR family oxidoreductase NF009395.0 PRK12755 PRK12755.1 343 343 355 subfamily Y Y N 3-deoxy-7-phosphoheptulonate synthase 2.5.1.54 2 Bacteria superkingdom 48253 NCBI Protein Cluster (PRK) phospho-2-dehydro-3-deoxyheptonate aldolase 3-deoxy-7-phosphoheptulonate synthase Catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, tyrosine sensitive NF009396.0 PRK12756 PRK12756.1 463 463 349 subfamily Y Y N Trp-sensitive 3-deoxy-7-phosphoheptulonate synthase AroH aroH 2.5.1.54 2 Bacteria superkingdom 23322 NCBI Protein Cluster (PRK) phospho-2-dehydro-3-deoxyheptonate aldolase Trp-sensitive 3-deoxy-7-phosphoheptulonate synthase AroH Tryptophan sensitive; catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate NF009397.0 PRK12758 PRK12758.1 780 780 870 equivalog Y Y N DNA gyrase/topoisomerase IV subunit A GO:0003677,GO:0003918,GO:0005524,GO:0006259,GO:0006265 2 Bacteria superkingdom 7634 NCBI Protein Cluster (PRK) DNA topoisomerase IV subunit A DNA gyrase/topoisomerase IV subunit A Decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling NF009399.0 PRK12764 PRK12764.1 444 444 501 equivalog Y Y N fumarylacetoacetate hydrolase family protein 2 Bacteria superkingdom 3674 NCBI Protein Cluster (PRK) hypothetical protein fumarylacetoacetate hydrolase family protein NF009405.0 PRK12767 PRK12767.1-4 390 390 320 equivalog Y N N carbamoyl phosphate synthase-like protein 2 Bacteria superkingdom 203 NCBI Protein Cluster (PRK) carbamoyl phosphate synthase-like protein carbamoyl phosphate synthase-like protein NF009406.0 PRK12767 PRK12767.1-5 271 271 327 equivalog Y N N carbamoyl phosphate synthase-like protein 2 Bacteria superkingdom 854 NCBI Protein Cluster (PRK) carbamoyl phosphate synthase-like protein carbamoyl phosphate synthase-like protein NF009414.0 PRK12778 PRK12778.1 1103 1103 752 equivalog Y Y N bifunctional dihydroorotate dehydrogenase B NAD binding subunit/NADPH-dependent glutamate synthase 2 Bacteria superkingdom 1586 NCBI Protein Cluster (PRK) putative bifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta bifunctional dihydroorotate dehydrogenase B NAD binding subunit/NADPH-dependent glutamate synthase NF009415.0 PRK12779 PRK12779.1 1519 1519 944 equivalog Y N N putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase 2 Bacteria superkingdom 244 NCBI Protein Cluster (PRK) putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase NF009434.1 PRK12793 PRK12793.1 99 99 113 equivalog Y Y N flagellar biosynthesis regulator FlaF flaF GO:0044781 17098908 2 Bacteria superkingdom 1393 NCBI Protein Cluster (PRK) flagellar biosynthesis regulatory protein FlaF flagellar biosynthesis regulator FlaF Acts as an activator or flagellin translation and may be required for filament secretion or assembly NF009435.1 PRK12794 PRK12794.1 91 91 116 equivalog Y Y N flagellar biosynthesis regulator FlaF flaF GO:0044781 16091049,17098908 2 Bacteria superkingdom 2956 NCBI Protein Cluster (PRK) flagellar biosynthesis regulatory protein FlaF flagellar biosynthesis regulator FlaF Acts as an activator of flagellin translation and may be required for filament secretion or assembly NF009438.0 PRK12797 PRK12797.1 179 179 217 subfamily Y Y N EscR/YscR/HrcR family type III secretion system export apparatus protein 2 Bacteria superkingdom 35864 NCBI Protein Cluster (PRK) type III secretion system protein YscR EscR/YscR/HrcR family type III secretion system export apparatus protein NF009446.0 PRK12804 PRK12804.1 352 352 301 subfamily Y Y N flagellin Hag hag 12730172,14762011,15342569,21895793,22720735,28800172,29124898,8045886,9648743 2 Bacteria superkingdom 1612 NCBI Protein Cluster (PRK) flagellin flagellin Hag NF009463.0 PRK12823 PRK12823.1 322 322 260 equivalog Y Y N 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase 1.3.1.25 GO:0016491 2 Bacteria superkingdom 7801 NCBI Protein Cluster (PRK) 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase Catalyzes the degradation of 2-hydro-1,2-dihydroxy benzoate to catechol NF009468.0 PRK12826 PRK12826.1-4 318 318 256 equivalog Y Y N SDR family oxidoreductase 2 Bacteria superkingdom 4157 NCBI Protein Cluster (PRK) 3-ketoacyl-(acyl-carrier-protein) reductase SDR family oxidoreductase NF009470.0 PRK12830 PRK12830.1 552 552 417 equivalog Y Y N UDP-N-acetylglucosamine 1-carboxyvinyltransferase 2.5.1.7 GO:0008760,GO:0019277 10894720,13129913,14763982 2 Bacteria superkingdom 11442 NCBI Protein Cluster (PRK) UDP-N-acetylglucosamine 1-carboxyvinyltransferase UDP-N-acetylglucosamine 1-carboxyvinyltransferase Adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation NF009471.0 PRK12833 PRK12833.1 686 686 467 equivalog Y Y N acetyl-CoA carboxylase biotin carboxylase subunit GO:0005524,GO:0016874,GO:0046872 2 Bacteria superkingdom 2965 NCBI Protein Cluster (PRK) acetyl-CoA carboxylase biotin carboxylase subunit acetyl-CoA carboxylase biotin carboxylase subunit Catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA NF009472.0 PRK12834 PRK12834.1 476 476 550 equivalog Y Y N FAD-binding dehydrogenase GO:0016627 2 Bacteria superkingdom 19094 NCBI Protein Cluster (PRK) putative FAD-binding dehydrogenase FAD-binding dehydrogenase NF009474.0 PRK12837 PRK12837.1 675 675 513 equivalog Y Y N FAD-binding protein 2 Bacteria superkingdom 1220 NCBI Protein Cluster (PRK) 3-ketosteroid-delta-1-dehydrogenase FAD-binding protein NF009478.0 PRK12844 PRK12844.1 789 789 559 equivalog Y N N 3-ketosteroid-delta-1-dehydrogenase 2 Bacteria superkingdom 465 NCBI Protein Cluster (PRK) 3-ketosteroid-delta-1-dehydrogenase 3-ketosteroid-delta-1-dehydrogenase NF009479.0 PRK12845 PRK12845.1 793 793 566 equivalog Y Y N 3-ketosteroid-delta-1-dehydrogenase 10788377,11230432,11750802,15231778,16000729 2 Bacteria superkingdom 1187 NCBI Protein Cluster (PRK) 3-ketosteroid-delta-1-dehydrogenase 3-ketosteroid-delta-1-dehydrogenase NF009492.0 PRK12853 PRK12853.1-3 428 428 472 equivalog Y Y N glucose-6-phosphate dehydrogenase 1.1.1.49 GO:0004345,GO:0006006 2 Bacteria superkingdom 23608 NCBI Protein Cluster (PRK) glucose-6-phosphate 1-dehydrogenase glucose-6-phosphate dehydrogenase NF009498.0 PRK12858 PRK12858.1 184 184 342 subfamily Y Y N tagatose 1,6-diphosphate aldolase 2 Bacteria superkingdom 8197 NCBI Protein Cluster (PRK) tagatose 1,6-diphosphate aldolase tagatose 1,6-diphosphate aldolase Catalyzes the reversible reaction of dihydroxyacetone phosphate with glyceraldehyde 3-phosphate to produce tagatose 1,6-bisphosphate NF009502.0 PRK12863 PRK12863.1-1 137 137 96 equivalog Y Y N YciI-like protein 2 Bacteria superkingdom 1305 NCBI Protein Cluster (PRK) YciI-like protein YciI-like protein NF009503.0 PRK12863 PRK12863.1-3 145 145 98 equivalog Y N N YciI-like protein 2 Bacteria superkingdom 598 NCBI Protein Cluster (PRK) YciI-like protein YciI-like protein NF009508.0 PRK12866 PRK12866.1 108 108 97 equivalog Y Y N YciI-like protein 2 Bacteria superkingdom 1573 NCBI Protein Cluster (PRK) YciI-like protein YciI-like protein NF009525.0 PRK12887 PRK12887.1 226 226 310 equivalog Y Y N homogentisate phytyltransferase 2.5.1.115 11418103,15965015 2 Bacteria superkingdom 818 NCBI Protein Cluster (PRK) tocopherol phytyltransferase homogentisate phytyltransferase Phytyltransferase acting specifically in the tocopherol biosynthetic pathway; member of the UbiA prenyltransferase family which catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones, hemes, chlorophylls, vitamin E, and shikonin NF009526.0 PRK12888 PRK12888.1 364 364 301 equivalog Y Y N 4-hydroxybenzoate octaprenyltransferase 2.5.1.39 GO:0016765 2 Bacteria superkingdom 6171 NCBI Protein Cluster (PRK) prenyltransferase 4-hydroxybenzoate octaprenyltransferase NF009538.1 PRK12904 PRK12904.1 814 814 814 equivalog Y Y N preprotein translocase subunit SecA secA GO:0005524,GO:0006605,GO:0006886,GO:0017038 12873133,15272299,15488768,16120599 2 Bacteria superkingdom 60213 NCBI Protein Cluster (PRK) preprotein translocase subunit SecA preprotein translocase subunit SecA Functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimer NF009541.0 PRK12921 PRK12921.1-1 338 338 297 equivalog Y Y N oxidoreductase 2 Bacteria superkingdom 4541 NCBI Protein Cluster (PRK) 2-dehydropantoate 2-reductase oxidoreductase NF009551.0 PRK12997 PRK12997.1-3 657 657 433 equivalog Y Y N PTS sugar transporter subunit IIC 2 Bacteria superkingdom 1528 NCBI Protein Cluster (PRK) PTS system ascorbate-specific transporter subunit IIC PTS sugar transporter subunit IIC NF009553.0 PRK12997 PRK12997.1-5 423 423 426 subfamily Y Y N PTS sugar transporter subunit IIC 2 Bacteria superkingdom 12880 NCBI Protein Cluster (PRK) PTS system ascorbate-specific transporter subunit IIC PTS sugar transporter subunit IIC NF009554.0 PRK12999 PRK12999.1 965 965 1147 equivalog Y Y N pyruvate carboxylase 6.4.1.1 GO:0004736,GO:0005524,GO:0006090,GO:0006094,GO:0009374,GO:0046872 9579065 2 Bacteria superkingdom 29929 NCBI Protein Cluster (PRK) pyruvate carboxylase pyruvate carboxylase Biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate NF009555.0 PRK13004 PRK13004.1 321 321 399 equivalog Y Y N YgeY family selenium metabolism-linked hydrolase GO:0016787 2 Bacteria superkingdom 4810 NCBI Protein Cluster (PRK) peptidase YgeY family selenium metabolism-linked hydrolase NF009557.0 PRK13009 PRK13009.1 284 284 377 equivalog Y Y N succinyl-diaminopimelate desuccinylase dapE 3.5.1.18 GO:0009014,GO:0009089 12896993,12962500,16421726 2 Bacteria superkingdom 33696 NCBI Protein Cluster (PRK) succinyl-diaminopimelate desuccinylase succinyl-diaminopimelate desuccinylase Catalyzes the formation of succinate and diaminoheptanedioate from succinyldiaminoheptanedioate NF009558.0 PRK13013 PRK13013.1 428 428 429 equivalog Y Y N acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase family protein 2 Bacteria superkingdom 2117 NCBI Protein Cluster (PRK) succinyl-diaminopimelate desuccinylase acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase family protein NF009559.0 PRK13016 PRK13016.1 882 882 578 equivalog Y Y N L-arabinonate dehydratase araD 4.2.1.9 27102126 2 Bacteria superkingdom 10580 NCBI Protein Cluster (PRK) dihydroxy-acid dehydratase L-arabinonate dehydratase NF009560.0 PRK13017 PRK13017.1 684 684 595 subfamily Y Y N dihydroxy-acid dehydratase 2 Bacteria superkingdom 30226 NCBI Protein Cluster (PRK) dihydroxy-acid dehydratase dihydroxy-acid dehydratase NF009564.0 PRK13019 PRK13019.1-4 143 143 101 equivalog Y Y N ATP-dependent Clp protease adapter ClpS clpS 2 Bacteria superkingdom 1334 NCBI Protein Cluster (PRK) ATP-dependent Clp protease adaptor ATP-dependent Clp protease adapter ClpS NF009581.0 PRK13024 PRK13024.1-1 1058 1058 752 equivalog Y Y N protein translocase subunit SecDF secDF GO:0006886,GO:0015450 2 Bacteria superkingdom 4648 NCBI Protein Cluster (PRK) bifunctional preprotein translocase subunit SecD/SecF protein translocase subunit SecDF NF009583.0 PRK13024 PRK13024.1-3 721 721 755 subfamily Y Y N protein translocase subunit SecDF secDF 2 Bacteria superkingdom 9819 NCBI Protein Cluster (PRK) bifunctional preprotein translocase subunit SecD/SecF protein translocase subunit SecDF NF009586.0 PRK13026 PRK13026.1 608 608 777 subfamily Y Y N acyl-CoA dehydrogenase 1.3.8.- 2 Bacteria superkingdom 28099 NCBI Protein Cluster (PRK) acyl-CoA dehydrogenase acyl-CoA dehydrogenase NF009587.0 PRK13027 PRK13027.1 570 570 442 subfamily Y Y N C4-dicarboxylate transporter DctA dctA 14659885 2 Bacteria superkingdom 15200 NCBI Protein Cluster (PRK) C4-dicarboxylate transporter DctA C4-dicarboxylate transporter DctA Involved in the transport of C4-dicarboxylates across the membrane NF009588.0 PRK13029 PRK13029.1 952 952 1196 subfamily Y Y N indolepyruvate ferredoxin oxidoreductase family protein 2 Bacteria superkingdom 24853 NCBI Protein Cluster (PRK) 2-oxoacid ferredoxin oxidoreductase indolepyruvate ferredoxin oxidoreductase family protein NF009589.0 PRK13030 PRK13030.1 816 816 1170 subfamily Y Y N indolepyruvate ferredoxin oxidoreductase family protein 2 Bacteria superkingdom 25217 NCBI Protein Cluster (PRK) 2-oxoacid ferredoxin oxidoreductase indolepyruvate ferredoxin oxidoreductase family protein NF009603.0 PRK13055 PRK13055.1 342 342 335 subfamily Y Y N diacylglycerol kinase 2.7.1.107 2 Bacteria superkingdom 6097 NCBI Protein Cluster (PRK) putative lipid kinase diacylglycerol kinase NF009604.0 PRK13057 PRK13057.1 274 274 302 equivalog Y Y N lipid kinase 2.7.1.- GO:0016301 2 Bacteria superkingdom 2910 NCBI Protein Cluster (PRK) putative lipid kinase lipid kinase NF009605.0 PRK13059 PRK13059.1 313 313 295 equivalog Y N N putative lipid kinase 2 Bacteria superkingdom 778 NCBI Protein Cluster (PRK) putative lipid kinase putative lipid kinase NF009608.0 PRK13105 PRK13105.1 217 217 291 equivalog Y Y N prenyltransferase GO:0016765 2 Bacteria superkingdom 2846 NCBI Protein Cluster (PRK) prenyltransferase prenyltransferase NF009622.0 PRK13128 PRK13128.1 443 443 518 equivalog Y Y N D-aminopeptidase 3.4.11.19 16131658 2 Bacteria superkingdom 684 NCBI Protein Cluster (PRK) D-aminopeptidase D-aminopeptidase NF009625.0 PRK13145 PRK13145.1 369 369 235 equivalog Y Y N L-ribulose-5-phosphate 4-epimerase 5.1.3.4 2 Bacteria superkingdom 1762 NCBI Protein Cluster (PRK) L-ribulose-5-phosphate 4-epimerase L-ribulose-5-phosphate 4-epimerase NF009644.0 PRK13169 PRK13169.1-5 137 137 116 equivalog Y Y N DNA replication initiation control protein YabA yabA GO:0006260 2 Bacteria superkingdom 1985 NCBI Protein Cluster (PRK) DNA replication intiation control protein YabA DNA replication initiation control protein YabA NF009685.0 PRK13206 PRK13206.1 907 907 573 equivalog Y Y N urease subunit alpha GO:0008152,GO:0009039,GO:0016151 7559354 2 Bacteria superkingdom 27853 NCBI Protein Cluster (PRK) urease subunit alpha urease subunit alpha Catalyzes the hydrolysis of urea into ammonia and carbon dioxide; the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa NF009688.0 PRK13209 PRK13209.1 317 317 286 subfamily Y Y N L-ribulose-5-phosphate 3-epimerase 5.1.3.22 11741871,12644495,14996803 2 Bacteria superkingdom 8968 NCBI Protein Cluster (PRK) L-xylulose 5-phosphate 3-epimerase L-ribulose-5-phosphate 3-epimerase Catalyzes the epimerization of L-ribulose-5-phosphate into L-xylulose-5-phosphate; part of the anaerobic L-ascorbate degradation pathway NF009689.0 PRK13210 PRK13210.1 200 200 286 subfamily Y Y N L-ribulose-5-phosphate 3-epimerase 5.1.3.22 11741871,12644495,14996803 2 Bacteria superkingdom 9706 NCBI Protein Cluster (PRK) putative L-xylulose 5-phosphate 3-epimerase L-ribulose-5-phosphate 3-epimerase NF009710.0 PRK13239 PRK13239.1 193 193 210 equivalog Y Y N alkylmercury lyase MerB merB GO:0018942 2 Bacteria superkingdom 649 NCBI Protein Cluster (PRK) alkylmercury lyase alkylmercury lyase MerB Cleaves the carbon-mercury bond of organomercuric compounds NF009724.0 PRK13251 PRK13251.1 117 117 76 equivalog Y Y N trp RNA-binding attenuation protein MtrB mtrB GO:0003723,GO:0006353 2 Bacteria superkingdom 1908 NCBI Protein Cluster (PRK) transcription attenuation protein MtrB trp RNA-binding attenuation protein MtrB NF009725.0 PRK13252 PRK13252.1 593 593 488 equivalog Y Y N betaine-aldehyde dehydrogenase betB 1.2.1.8 GO:0008802,GO:0019285,GO:0046872 2 Bacteria superkingdom 18374 NCBI Protein Cluster (PRK) betaine aldehyde dehydrogenase betaine-aldehyde dehydrogenase Catalyzes the formation of betaine from betaine aldehyde NF009726.0 PRK13253 PRK13253.1 65 65 98 subfamily Y Y N citrate lyase subunit gamma 2 Bacteria superkingdom 4251 NCBI Protein Cluster (PRK) citrate lyase subunit gamma citrate lyase subunit gamma With CitE and CitF catalyzes the formation of oxaloacetate from citrate NF009727.0 PRK13254 PRK13254.1-1 126 126 144 equivalog Y Y N cytochrome c maturation protein CcmE ccmE 2 Bacteria superkingdom 16688 NCBI Protein Cluster (PRK) cytochrome c-type biogenesis protein CcmE cytochrome c maturation protein CcmE NF009731.0 PRK13254 PRK13254.1-5 152 152 155 equivalog Y Y N cytochrome c maturation protein CcmE ccmE GO:0017004,GO:0020037 2 Bacteria superkingdom 13423 NCBI Protein Cluster (PRK) cytochrome c-type biogenesis protein CcmE cytochrome c maturation protein CcmE NF009732.0 PRK13255 PRK13255.1 213 213 218 equivalog Y Y N thiopurine S-methyltransferase 2.1.1.67 GO:0008119,GO:0010038 12003960,12839745 2 Bacteria superkingdom 9222 NCBI Protein Cluster (PRK) thiopurine S-methyltransferase thiopurine S-methyltransferase Catalyzes the S-adenosylmethionine-dependent transmethylation of thiopurine compounds; may be involved in selenium cycling by forming dimethylselenide and/or dimethyldiselenide NF009749.0 PRK13259 PRK13259.1 108 108 96 equivalog Y Y N septation regulator SpoVG spoVG GO:0030435 15205410,17635871,27001809,30392856 2 Bacteria superkingdom 3673 NCBI Protein Cluster (PRK) regulatory protein SpoVG septation regulator SpoVG Stage V sporulation protein G; essential for spore formation and a negative regulator of asymmetric septation NF009750.0 PRK13260 PRK13260.1 316 316 332 equivalog Y Y N 3-dehydro-L-gulonate 2-dehydrogenase yiaK 1.1.1.130 GO:0047559,GO:0070403 2 Bacteria superkingdom 3866 NCBI Protein Cluster (PRK) 2,3-diketo-L-gulonate reductase 3-dehydro-L-gulonate 2-dehydrogenase NF009751.0 PRK13261 PRK13261.1-1 144 144 160 equivalog Y Y N urease accessory protein UreE ureE GO:0006457,GO:0016151,GO:0019627,GO:0065003 2 Bacteria superkingdom 10603 NCBI Protein Cluster (PRK) urease accessory protein UreE urease accessory protein UreE NF009754.0 PRK13261 PRK13261.1-6 171 171 169 equivalog Y Y N urease accessory protein UreE ureE 2 Bacteria superkingdom 1543 NCBI Protein Cluster (PRK) urease accessory protein UreE urease accessory protein UreE NF009756.0 PRK13261 PRK13261.2-2 138 138 153 equivalog Y Y N urease accessory protein UreE ureE 2 Bacteria superkingdom 331 NCBI Protein Cluster (PRK) urease accessory protein UreE urease accessory protein UreE NF009757.0 PRK13261 PRK13261.2-3 199 199 159 equivalog Y Y N urease accessory protein UreE ureE 2 Bacteria superkingdom 695 NCBI Protein Cluster (PRK) urease accessory protein UreE urease accessory protein UreE NF009763.0 PRK13264 PRK13264.1 220 220 178 equivalog Y Y N 3-hydroxyanthranilate 3,4-dioxygenase 1.13.11.6 GO:0000334,GO:0005506 2 Bacteria superkingdom 6991 NCBI Protein Cluster (PRK) 3-hydroxyanthranilate 3,4-dioxygenase 3-hydroxyanthranilate 3,4-dioxygenase Catalyzes the formation of 2-amino-3-carboxymuconate semialdehyde from 3-hydroxyanthranilate in quinolinate biosynthesis NF009793.2 PRK13285 PRK13285.1-1 130 130 132 equivalog Y Y N flagellar assembly protein FliW fliW GO:0006417,GO:0044780 23144244,23753623,27516547 2 Bacteria superkingdom 4407 NCBI Protein Cluster (PRK) flagellar assembly protein FliW flagellar assembly protein FliW NF009799.0 PRK13285 PRK13285.2-2 165 165 150 equivalog Y N N flagellar assembly protein FliW 2 Bacteria superkingdom 60 NCBI Protein Cluster (PRK) flagellar assembly protein FliW flagellar assembly protein FliW NF009801.0 PRK13285 PRK13285.2-4 223 223 152 equivalog Y N N flagellar assembly protein FliW 2 Bacteria superkingdom 16 NCBI Protein Cluster (PRK) flagellar assembly protein FliW flagellar assembly protein FliW NF009803.0 PRK13287 PRK13287.1 406 406 333 equivalog Y Y N formamidase 3.5.1.49 GO:0004328 2 Bacteria superkingdom 2848 NCBI Protein Cluster (PRK) formamidase formamidase Formamide amidohydrolase; catalyzes the hydrolysis of formamide to formate NF009804.0 PRK13288 PRK13288.1 218 218 215 equivalog Y Y N pyrophosphatase PpaX ppaX 3.6.1.1 2 Bacteria superkingdom 4589 NCBI Protein Cluster (PRK) pyrophosphatase PpaX pyrophosphatase PpaX NF009805.0 PRK13289 PRK13289.1 432 432 399 equivalog Y Y N NO-inducible flavohemoprotein hmpA 1.14.12.17 GO:0008941,GO:0019825,GO:0020037,GO:0051409,GO:0071949 2 Bacteria superkingdom 23806 NCBI Protein Cluster (PRK) bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2 NO-inducible flavohemoprotein gene synonym: fsrB NF009807.1 PRK13291 PRK13291.1 160 160 172 equivalog Y Y N YfiT family bacillithiol transferase GO:0016151,GO:0016765 15581359,22059487 2 Bacteria superkingdom 7602 NCBI Protein Cluster (PRK) metal-dependent hydrolase YfiT family bacillithiol transferase Members of this family encode the nickel-binding protein YfiT of Bacillus subtilis, a bacillithiol transferase that was give the name BstA, despite being only a low level of sequence identity with BstA of Staphylococcus aureus (see PMID:24821014). NF009810.0 PRK13294 PRK13294.1 304 304 449 equivalog Y Y N coenzyme F420-0:L-glutamate ligase 6.3.2.31 GO:0043773,GO:0046872 2 Bacteria superkingdom 12028 NCBI Protein Cluster (PRK) F420-0--gamma-glutamyl ligase coenzyme F420-0:L-glutamate ligase Catalyzes the addition of gamma linked glutamate to 7,8-didemethyl-8-hydroxy-5-deazariboflavin NF009814.0 PRK13299 PRK13299.1 290 290 396 equivalog Y Y N CCA tRNA nucleotidyltransferase 2.7.7.72 GO:0001680,GO:0016779 2 Bacteria superkingdom 15027 NCBI Protein Cluster (PRK) tRNA CCA-pyrophosphorylase CCA tRNA nucleotidyltransferase Catalyzes the addition and repair of the 3'-terminal CCA sequence in tRNA; these proteins belong to the CCA-adding enzyme subfamily 2 which does not have phosphohydrolase activity NF009832.1 PRK13306 PRK13306.1 250 250 215 subfamily Y Y N 3-dehydro-L-gulonate-6-phosphate decarboxylase 11741871 2 Bacteria superkingdom 6134 NCBI Protein Cluster (PRK) 3-keto-L-gulonate-6-phosphate decarboxylase 3-dehydro-L-gulonate-6-phosphate decarboxylase Catalyzes the formation of L-xylulose-5-phosphate from 3-keto-L-gulonate-6-phosphate in anaerobic L-ascorbate utilization NF009834.0 PRK13309 PRK13309.1 1001 1001 572 equivalog Y Y N urease subunit alpha 17101645,17578575 2 Bacteria superkingdom 906 NCBI Protein Cluster (PRK) urease subunit alpha urease subunit alpha Catalyzes the hydrolysis of urea into ammonia and carbon dioxide; the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa NF009840.0 PRK13315 PRK13315.1 119 119 107 equivalog Y Y N heme oxygenase 2 Bacteria superkingdom 687 NCBI Protein Cluster (PRK) heme-degrading monooxygenase IsdG heme oxygenase Iron regulated; catalyzes the release of heme from hemoglobin allowing bacterial pathogens to use the host heme as an iron source NF009842.0 PRK13317 PRK13317.1 234 234 277 equivalog Y Y N type II pantothenate kinase coaW 2.7.1.33 GO:0004594,GO:0005524,GO:0015937 2 Bacteria superkingdom 2881 NCBI Protein Cluster (PRK) pantothenate kinase type II pantothenate kinase Catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type II pantothenate kinases are not regulated by feedback inhibition by coenzyme A NF009843.0 PRK13318 PRK13318.1-1 426 426 259 equivalog Y Y N type III pantothenate kinase 2.7.1.33 2 Bacteria superkingdom 1766 NCBI Protein Cluster (PRK) pantothenate kinase type III pantothenate kinase NF009844.0 PRK13318 PRK13318.1-2 331 331 259 equivalog Y Y N type III pantothenate kinase 2.7.1.33 GO:0004594 2 Bacteria superkingdom 4192 NCBI Protein Cluster (PRK) pantothenate kinase type III pantothenate kinase NF009845.0 PRK13318 PRK13318.1-3 358 358 258 equivalog Y Y N type III pantothenate kinase 2.7.1.33 2 Bacteria superkingdom 5915 NCBI Protein Cluster (PRK) pantothenate kinase type III pantothenate kinase NF009847.0 PRK13318 PRK13318.1-5 381 381 256 equivalog Y Y N type III pantothenate kinase 2.7.1.33 GO:0004594 2 Bacteria superkingdom 3677 NCBI Protein Cluster (PRK) pantothenate kinase type III pantothenate kinase NF009848.0 PRK13318 PRK13318.1-6 248 248 256 equivalog Y Y N type III pantothenate kinase 2.7.1.33 2 Bacteria superkingdom 9064 NCBI Protein Cluster (PRK) pantothenate kinase type III pantothenate kinase NF009874.0 PRK13337 PRK13337.1 385 385 305 equivalog Y Y N diacylglycerol kinase 2.7.1.107 GO:0003951 2 Bacteria superkingdom 5106 NCBI Protein Cluster (PRK) putative lipid kinase diacylglycerol kinase NF009875.0 PRK13339 PRK13339.1 623 623 498 subfamily Y Y N malate:quinone oxidoreductase 1.1.5.4 2 Bacteria superkingdom 29386 NCBI Protein Cluster (PRK) malate:quinone oxidoreductase malate:quinone oxidoreductase NF009881.0 PRK13341 PRK13341.1-2 651 651 736 equivalog Y Y N AAA family ATPase 2 Bacteria superkingdom 1161 NCBI Protein Cluster (PRK) recombination factor protein RarA/unknown domain fusion protein AAA family ATPase NF009883.0 PRK13341 PRK13341.1-4 668 668 729 equivalog Y Y N AAA family ATPase 2 Bacteria superkingdom 755 NCBI Protein Cluster (PRK) recombination factor protein RarA/unknown domain fusion protein AAA family ATPase NF009888.0 PRK13348 PRK13348.1 297 297 302 subfamily Y Y N HTH-type transcriptional regulator ArgP argP 2 Bacteria superkingdom 22033 NCBI Protein Cluster (PRK) chromosome replication initiation inhibitor protein HTH-type transcriptional regulator ArgP NF009891.0 PRK13351 PRK13351.1-1 597 597 681 equivalog Y Y N elongation factor G fusA GO:0003746,GO:0006414 2 Bacteria superkingdom 11759 NCBI Protein Cluster (PRK) elongation factor G elongation factor G NF009896.0 PRK13356 PRK13356.1 262 262 287 equivalog Y Y N branched-chain amino acid aminotransferase 2.6.1.42 2 Bacteria superkingdom 4827 NCBI Protein Cluster (PRK) aminotransferase branched-chain amino acid aminotransferase NF009901.0 PRK13364 PRK13364.1 290 290 279 subfamily Y Y N class III extradiol dioxygenase family protein GO:0016491 2 Bacteria superkingdom 5085 NCBI Protein Cluster (PRK) protocatechuate 4,5-dioxygenase subunit beta class III extradiol dioxygenase family protein NF009902.0 PRK13365 PRK13365.1 299 299 298 subfamily Y Y N class III extradiol dioxygenase family protein GO:0016491 2 Bacteria superkingdom 6340 NCBI Protein Cluster (PRK) protocatechuate 4,5-dioxygenase subunit beta class III extradiol dioxygenase family protein NF009903.0 PRK13366 PRK13366.1 317 317 284 subfamily Y Y N class III extradiol dioxygenase subunit beta 2 Bacteria superkingdom 3419 NCBI Protein Cluster (PRK) protocatechuate 4,5-dioxygenase subunit beta class III extradiol dioxygenase subunit beta NF009904.0 PRK13367 PRK13367.1 412 412 426 equivalog Y Y N gallate dioxygenase 1.13.11.57 GO:0008152,GO:0016491 12501294,9244273 2 Bacteria superkingdom 2344 NCBI Protein Cluster (PRK) protocatechuate 4,5-dioxygenase gallate dioxygenase Extradiol catechol dioxygenase that catalyzes the oxidative cleavage of substituted catechols; part of the bacterial aromatic compound degradation pathway NF009906.0 PRK13369 PRK13369.1 352 352 502 equivalog Y Y N glycerol-3-phosphate dehydrogenase 1.1.5.3 GO:0004368,GO:0006072,GO:0009331 2 Bacteria superkingdom 28292 NCBI Protein Cluster (PRK) glycerol-3-phosphate dehydrogenase glycerol-3-phosphate dehydrogenase NF009909.0 PRK13370 PRK13370.1-3 286 286 286 subfamily Y Y N 3-carboxyethylcatechol 2,3-dioxygenase 1.13.11.16 2 Bacteria superkingdom 919 NCBI Protein Cluster (PRK) 3-(2,3-dihydroxyphenyl)propionate dioxygenase 3-carboxyethylcatechol 2,3-dioxygenase NF009910.0 PRK13370 PRK13370.1-4 291 291 312 equivalog Y Y N 3-carboxyethylcatechol 2,3-dioxygenase 1.13.11.16 GO:0008152,GO:0016491 2 Bacteria superkingdom 5204 NCBI Protein Cluster (PRK) 3-(2,3-dihydroxyphenyl)propionate dioxygenase 3-carboxyethylcatechol 2,3-dioxygenase NF009911.0 PRK13371 PRK13371.1 440 440 405 equivalog Y Y N 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 1.17.7.4 2 Bacteria superkingdom 1857 NCBI Protein Cluster (PRK) 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 4-hydroxy-3-methylbut-2-enyl diphosphate reductase Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP); functions in the nonmevalonate isoprenoid biosynthesis pathway NF009912.0 PRK13372 PRK13372.1 837 837 443 equivalog Y Y N protocatechuate 4,5-dioxygenase subunit alpha/beta 2 Bacteria superkingdom 134 NCBI Protein Cluster (PRK) protocatechuate 4,5-dioxygenase protocatechuate 4,5-dioxygenase subunit alpha/beta Extradiol catechol dioxygenase that catalyzes the oxidative cleavage of substituted catechols; part of the bacterial aromatic compound degradation pathway NF009914.0 PRK13374 PRK13374.1 338 338 235 subfamily Y Y N DeoD-type purine-nucleoside phosphorylase 2.4.2.1 2 Bacteria superkingdom 7992 NCBI Protein Cluster (PRK) purine nucleoside phosphorylase DeoD-type purine-nucleoside phosphorylase Catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate NF009916.0 PRK13376 PRK13376.1 800 800 525 equivalog Y Y N bifunctional aspartate carbamoyltransferase catalytic subunit/aspartate carbamoyltransferase regulatory subunit 2 Bacteria superkingdom 111 NCBI Protein Cluster (PRK) bifunctional aspartate carbamoyltransferase catalytic subunit/aspartate carbamoyltransferase regulatory subunit bifunctional aspartate carbamoyltransferase catalytic subunit/aspartate carbamoyltransferase regulatory subunit Catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis NF009917.0 PRK13377 PRK13377.1 173 173 129 subfamily Y Y N protocatechuate 4,5-dioxygenase subunit alpha 1.13.11.8 2 Bacteria superkingdom 2127 NCBI Protein Cluster (PRK) protocatechuate 4,5-dioxygenase subunit alpha protocatechuate 4,5-dioxygenase subunit alpha Extradiol catechol dioxygenase that catalyzes the oxidative cleavage of substituted catechols; part of the bacterial aromatic compound degradation pathway NF009918.0 PRK13378 PRK13378.1 161 161 118 equivalog Y Y N protocatechuate 4,5-dioxygenase subunit alpha 1.13.11.8 17645527 2 Bacteria superkingdom 848 NCBI Protein Cluster (PRK) protocatechuate 4,5-dioxygenase subunit alpha protocatechuate 4,5-dioxygenase subunit alpha Extradiol catechol dioxygenase that catalyzes the oxidative cleavage of substituted catechols; part of the bacterial aromatic compound degradation pathway NF009919.0 PRK13379 PRK13379.1 141 141 119 equivalog Y N N protocatechuate 4,5-dioxygenase subunit alpha 2 Bacteria superkingdom 418 NCBI Protein Cluster (PRK) protocatechuate 4,5-dioxygenase subunit alpha protocatechuate 4,5-dioxygenase subunit alpha NF009920.0 PRK13381 PRK13381.1 293 293 412 subfamily Y Y N peptidase T 2 Bacteria superkingdom 38642 NCBI Protein Cluster (PRK) peptidase T peptidase T Catalyzes the release of the N-terminal amino acid from a tripeptide NF009941.0 PRK13404 PRK13404.1 647 647 478 subfamily Y Y N dihydropyrimidinase 3.5.2.2 2 Bacteria superkingdom 4359 NCBI Protein Cluster (PRK) dihydropyrimidinase dihydropyrimidinase Catalyzes the hydrolytic cleavage of imides that range from linear to heterocyclic and that include hydantoins, dihydropyrimidines, and phthalimides NF009949.0 PRK13413 PRK13413.1 272 272 203 equivalog Y Y N master DNA invertase Mpi family serine-type recombinase 12915735 2 Bacteria superkingdom 1101 NCBI Protein Cluster (PRK) multiple promoter invertase master DNA invertase Mpi family serine-type recombinase NF009967.0 PRK13430 PRK13430.1 200 200 271 equivalog Y Y N F0F1 ATP synthase subunit delta 7.1.2.2 GO:0015986,GO:0016020,GO:0046933 2 Bacteria superkingdom 13617 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit delta F0F1 ATP synthase subunit delta Produces ATP from ADP in the presence of a proton gradient across the membrane; the delta subunit is part of the catalytic core of the ATP synthase complex NF009977.0 PRK13442 PRK13442.1 80 80 102 equivalog Y Y N F0F1 ATP synthase subunit epsilon 7.1.2.2 GO:0015986,GO:0045261,GO:0046933 2 Bacteria superkingdom 9778 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit epsilon F0F1 ATP synthase subunit epsilon Produces ATP from ADP in the presence of a proton gradient across the membrane; the epsilon subunit is part of the catalytic core of the ATP synthase complex NF009980.0 PRK13446 PRK13446.1 129 129 136 equivalog Y Y N F0F1 ATP synthase subunit epsilon 7.1.2.2 2 Bacteria superkingdom 3727 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit epsilon F0F1 ATP synthase subunit epsilon Produces ATP from ADP in the presence of a proton gradient across the membrane; the epsilon subunit is part of the catalytic core of the ATP synthase complex NF009983.0 PRK13449 PRK13449.1 106 106 88 equivalog Y Y N ATP synthase F1 subunit epsilon 2 Bacteria superkingdom 1855 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit epsilon ATP synthase F1 subunit epsilon Produces ATP from ADP in the presence of a proton gradient across the membrane; the epsilon subunit is part of the catalytic core of the ATP synthase complex NF009992.0 PRK13461 PRK13461.1 127 127 159 equivalog Y Y N F0F1 ATP synthase subunit B 7.1.2.2 2 Bacteria superkingdom 406 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit B F0F1 ATP synthase subunit B Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B is part of the membrane proton channel NF010000.0 PRK13473 PRK13473.1 615 615 475 subfamily Y Y N aminobutyraldehyde dehydrogenase 1.2.1.19 GO:0016620 2 Bacteria superkingdom 33788 NCBI Protein Cluster (PRK) gamma-aminobutyraldehyde dehydrogenase aminobutyraldehyde dehydrogenase NF010001.0 PRK13474 PRK13474.1 154 154 178 subfamily Y Y N cytochrome b6-f complex iron-sulfur subunit petC 7.1.1.6 2 Bacteria superkingdom 929 NCBI Protein Cluster (PRK) cytochrome b6-f complex iron-sulfur subunit cytochrome b6-f complex iron-sulfur subunit Rieske protein with cytochrome b6, cytochrome f, and subunit IV makes up the large subunit of the cytochrome b6-f complex; cytochrome b6-f mediates electron transfer between photosystem II and photosystem I NF010006.0 PRK13479 PRK13479.1 296 296 369 equivalog Y Y N 2-aminoethylphosphonate--pyruvate transaminase 2.6.1.37 GO:0019700,GO:0047304 2 Bacteria superkingdom 15883 NCBI Protein Cluster (PRK) 2-aminoethylphosphonate--pyruvate transaminase 2-aminoethylphosphonate--pyruvate transaminase Catalyzes the formation of phosphonoacetaldehyde from 2-aminoethylphosphonate and pyruvate NF010007.0 PRK13480 PRK13480.1 460 460 314 equivalog Y Y N 3'-5' exoribonuclease YhaM yhaM 2 Bacteria superkingdom 2575 NCBI Protein Cluster (PRK) 3'-5' exoribonuclease YhaM 3'-5' exoribonuclease YhaM Catalyzes the exonucleic cleavage of mRNA yielding nucleioside 5'-phosphates NF010009.0 PRK13482 PRK13482.1 201 201 357 equivalog Y Y N DNA integrity scanning diadenylate cyclase DisA disA 2.7.7.85 18439896,30916351 2 Bacteria superkingdom 10251 NCBI Protein Cluster (PRK) DNA integrity scanning protein DisA DNA integrity scanning diadenylate cyclase DisA Non-specific DNA-binding; scans chromosomes during sporulation for DNA-damage; delays initiation of sporulation; participates in a checkpoint signaling cascade for cell-cycle progression and DNA repair NF010024.0 PRK13499 PRK13499.1-4 468 468 347 equivalog Y Y N L-rhamnose/proton symporter RhaT rhaT 2 Bacteria superkingdom 2047 NCBI Protein Cluster (PRK) rhamnose-proton symporter L-rhamnose/proton symporter RhaT NF010029.0 PRK13504 PRK13504.1 457 457 575 equivalog Y Y N NADPH-dependent assimilatory sulfite reductase hemoprotein subunit GO:0004783,GO:0008652,GO:0051536 2 Bacteria superkingdom 18056 NCBI Protein Cluster (PRK) sulfite reductase subunit beta NADPH-dependent assimilatory sulfite reductase hemoprotein subunit NADPH dependent; with the alpha subunit (a flavoprotein) catalyzes the reduction of sulfite to sulfide NF010031.0 PRK13506 PRK13506.1 800 800 578 equivalog Y Y N formate--tetrahydrofolate ligase 6.3.4.3 GO:0004329,GO:0005524 2 Bacteria superkingdom 4354 NCBI Protein Cluster (PRK) formate--tetrahydrofolate ligase formate--tetrahydrofolate ligase Catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate NF010032.0 PRK13507 PRK13507.1 938 938 587 equivalog Y Y N formate--tetrahydrofolate ligase 2 Bacteria superkingdom 395 NCBI Protein Cluster (PRK) formate--tetrahydrofolate ligase formate--tetrahydrofolate ligase Catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate NF010037.0 PRK13512 PRK13512.1 394 394 438 equivalog Y Y N CoA-disulfide reductase 1.8.1.14 GO:0016491,GO:0045454 2 Bacteria superkingdom 4580 NCBI Protein Cluster (PRK) coenzyme A disulfide reductase CoA-disulfide reductase NADPH-dependent; catalyzes the reduction of coenzyme A disulfide NF010041.0 PRK13517 PRK13517.1-1 332 332 368 subfamily Y Y N glutamate--cysteine ligase 6.3.2.2 GO:0004357,GO:0042398 2 Bacteria superkingdom 18680 NCBI Protein Cluster (PRK) carboxylate-amine ligase glutamate--cysteine ligase NF010042.0 PRK13517 PRK13517.1-2 427 427 376 equivalog Y Y N glutamate--cysteine ligase 6.3.2.2 GO:0004357,GO:0042398 2 Bacteria superkingdom 6383 NCBI Protein Cluster (PRK) carboxylate-amine ligase glutamate--cysteine ligase NF010043.0 PRK13517 PRK13517.1-3 409 409 381 equivalog Y Y N glutamate--cysteine ligase 6.3.2.2 2 Bacteria superkingdom 5562 NCBI Protein Cluster (PRK) carboxylate-amine ligase glutamate--cysteine ligase NF010044.0 PRK13517 PRK13517.1-4 437 437 372 equivalog Y Y N glutamate--cysteine ligase 6.3.2.2 GO:0004357,GO:0042398 2 Bacteria superkingdom 6223 NCBI Protein Cluster (PRK) carboxylate-amine ligase glutamate--cysteine ligase NF010047.0 PRK13523 PRK13523.1 431 431 339 equivalog Y Y N NADPH dehydrogenase NamA namA 1.6.99.1 GO:0003959,GO:0010181,GO:0050661 2 Bacteria superkingdom 5047 NCBI Protein Cluster (PRK) NADPH dehydrogenase NamA NADPH dehydrogenase NamA NF010050.0 PRK13526 PRK13526.1 181 181 179 equivalog Y N N glutamine amidotransferase subunit PdxT 2 Bacteria superkingdom 72 NCBI Protein Cluster (PRK) glutamine amidotransferase subunit PdxT glutamine amidotransferase subunit PdxT NF010053.0 PRK13530 PRK13530.1 215 215 133 subfamily Y Y N arsenate reductase (thioredoxin) 2 Bacteria superkingdom 4423 NCBI Protein Cluster (PRK) arsenate reductase arsenate reductase (thioredoxin) Catalyzes the reduction of arsenate to arsenite; also can dephosphorylate tyrosine phosphorylated proteins, aryl phosphates, and acyl phosphates NF010055.0 PRK13532 PRK13532.1 904 904 830 equivalog Y Y N nitrate reductase catalytic subunit NapA napA GO:0008940,GO:0030151,GO:0043546,GO:0051539 2 Bacteria superkingdom 12001 NCBI Protein Cluster (PRK) nitrate reductase catalytic subunit nitrate reductase catalytic subunit NapA With NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC NF010069.0 PRK13549 PRK13549.1 699 699 513 equivalog Y Y N xylose ABC transporter ATP-binding protein GO:0005524 2 Bacteria superkingdom 7547 NCBI Protein Cluster (PRK) xylose transporter ATP-binding subunit xylose ABC transporter ATP-binding protein NF010070.0 PRK13551 PRK13551.1 483 483 365 subfamily Y Y N agmatine deiminase 2 Bacteria superkingdom 10120 NCBI Protein Cluster (PRK) agmatine deiminase agmatine deiminase Catalyzes the formation of carbamoylputrescine from agmatine in the arginine decarboxylase pathway of putrescine biosynthesis NF010071.0 PRK13552 PRK13552.1 264 264 241 equivalog Y Y N fumarate reductase iron-sulfur subunit 2 Bacteria superkingdom 1738 NCBI Protein Cluster (PRK) fumarate reductase iron-sulfur subunit fumarate reductase iron-sulfur subunit Part of four member fumarate reductase enzyme complex FrdABCD which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdCD are the membrane components which interact with quinone and are involved in electron transfer; the catalytic subunits are similar to succinate dehydrogenase SdhAB NF010075.0 PRK13556 PRK13556.1 188 188 208 subfamily Y Y N FMN-dependent NADH-azoreductase 1.7.1.17 2 Bacteria superkingdom 6514 NCBI Protein Cluster (PRK) azoreductase FMN-dependent NADH-azoreductase FMN-dependent; requires NADH; catalyzes the cleavage of azo bond in aromatic azo compounds NF010076.0 PRK13557 PRK13557.1 631 631 540 subfamily Y Y N histidine kinase famiy protein 2 Bacteria superkingdom 2282 NCBI Protein Cluster (PRK) histidine kinase histidine kinase famiy protein NF010079.0 PRK13564 PRK13564.1 471 471 521 equivalog Y Y N anthranilate synthase component 1 4.1.3.27 GO:0004049,GO:0009058 2 Bacteria superkingdom 15013 NCBI Protein Cluster (PRK) anthranilate synthase component I anthranilate synthase component 1 With component II catalyzes the formation of anthranilate and glutamate from chorismate and glutamine NF010081.0 PRK13566 PRK13566.1 645 645 729 equivalog Y Y N anthranilate synthase component I 4.1.3.27 GO:0000162,GO:0004049 2 Bacteria superkingdom 4653 NCBI Protein Cluster (PRK) anthranilate synthase anthranilate synthase component I With component II catalyzes the formation of anthranilate and glutamate from chorismate and glutamine NF010086.0 PRK13571 PRK13571.1 693 693 510 equivalog Y Y N anthranilate synthase component I 4.1.3.27 GO:0000162,GO:0004049 2 Bacteria superkingdom 11869 NCBI Protein Cluster (PRK) anthranilate synthase component I anthranilate synthase component I With component II catalyzes the formation of anthranilate and glutamate from chorismate and glutamine NF010092.0 PRK13578 PRK13578.1 794 794 720 subfamily Y Y N ornithine decarboxylase speC 4.1.1.17 2 Bacteria superkingdom 14132 NCBI Protein Cluster (PRK) ornithine decarboxylase ornithine decarboxylase NF010093.0 PRK13579 PRK13579.1 459 459 371 equivalog Y Y N glycine cleavage system aminomethyltransferase GcvT gcvT 2.1.2.10 GO:0004047,GO:0006546 2 Bacteria superkingdom 15739 NCBI Protein Cluster (PRK) glycine cleavage system aminomethyltransferase T glycine cleavage system aminomethyltransferase GcvT Catalyzes the transfer of a methylene carbon from the methylamine-loaded GcvH protein to tetrahydrofolate, causing the release of ammonia and the generation of reduced GcvH protein NF010094.0 PRK13580 PRK13580.1 735 735 496 equivalog Y Y N glycine hydroxymethyltransferase 2.1.2.1 GO:0004372,GO:0019264,GO:0035999 2 Bacteria superkingdom 5016 NCBI Protein Cluster (PRK) serine hydroxymethyltransferase glycine hydroxymethyltransferase NF010109.0 PRK13582 PRK13582.1 133 133 205 equivalog Y Y N bifunctional phosphoserine phosphatase/homoserine phosphotransferase ThrH thrH 3.1.3.3 2 Bacteria superkingdom 4416 NCBI Protein Cluster (PRK) phosphoserine phosphatase bifunctional phosphoserine phosphatase/homoserine phosphotransferase ThrH NF010119.0 PRK13595 PRK13595.1 248 248 292 equivalog Y N N prenyltransferase 2 Bacteria superkingdom 468 NCBI Protein Cluster (PRK) prenyltransferase prenyltransferase NF010125.0 PRK13602 PRK13602.1 113 113 82 equivalog Y Y N 50S ribosomal protein L7ae-like protein 2 Bacteria superkingdom 1188 NCBI Protein Cluster (PRK) putative ribosomal protein L7Ae-like 50S ribosomal protein L7ae-like protein NF010127.0 PRK13604 PRK13604.1 529 529 307 equivalog Y Y N acyl transferase 2 Bacteria superkingdom 170 NCBI Protein Cluster (PRK) acyl transferase acyl transferase NF010139.1 PRK13614 PRK13614.1 802 802 572 equivalog Y N N lipoprotein LpqB 2 Bacteria superkingdom 372 NCBI Protein Cluster (PRK) lipoprotein LpqB lipoprotein LpqB NF010148.0 PRK13625 PRK13625.1 340 340 245 equivalog Y Y N bis(5'-nucleosyl)-tetraphosphatase PrpE prpE 2 Bacteria superkingdom 2725 NCBI Protein Cluster (PRK) bis(5'-nucleosyl)-tetraphosphatase PrpE bis(5'-nucleosyl)-tetraphosphatase PrpE Catalyzes the formation of NTP and NMP from P(1),P(4)-bis(5'-nucleosyl) tetraphosphate; acts on bis(5'-guanosyl) tetraphosphate, bis(5'-xanthosyl)-tetraphosphate, on bis(5'-adenosyl)-tetraphosphate, and bis(5'-uridyl)-tetraphosphate NF010155.0 PRK13634 PRK13634.1 413 413 290 equivalog Y Y N energy-coupling factor ABC transporter ATP-binding protein GO:0005524,GO:0016020,GO:0055085 2 Bacteria superkingdom 4440 NCBI Protein Cluster (PRK) cobalt transporter ATP-binding subunit energy-coupling factor ABC transporter ATP-binding protein NF010156.0 PRK13635 PRK13635.1 392 392 279 equivalog Y Y N energy-coupling factor ABC transporter ATP-binding protein GO:0005524,GO:0016020,GO:0055085 2 Bacteria superkingdom 5163 NCBI Protein Cluster (PRK) cobalt transporter ATP-binding subunit energy-coupling factor ABC transporter ATP-binding protein NF010172.0 PRK13654 PRK13654.1 391 391 361 subfamily Y Y N magnesium-protoporphyrin IX monomethyl ester cyclase 1.14.13.81 2 Bacteria superkingdom 3235 NCBI Protein Cluster (PRK) magnesium-protoporphyrin IX monomethyl ester cyclase magnesium-protoporphyrin IX monomethyl ester cyclase Oxidative; catalyzes the formation of divinylprotochlorophyllide from magnesium-protoporphyrin IX 13-monomethyl ester in isocyclic ring formation in chlorophyll biosynthesis NF010177.0 PRK13656 PRK13656.1 403 403 398 subfamily Y Y N enoyl-[acyl-carrier-protein] reductase FabV fabV 17382934,18032386,20055482 2 Bacteria superkingdom 15841 NCBI Protein Cluster (PRK) trans-2-enoyl-CoA reductase enoyl-[acyl-carrier-protein] reductase FabV FabV is one of several classes of enoyl-[acyl-carrier-protein] reductase that are only very distantly related to each other. Other classes include FabI (as in E. coli K-12), FabK, and FabL. NF010181.0 PRK13660 PRK13660.1 165 165 182 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 7810 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010182.0 PRK13661 PRK13661.1 99 99 183 equivalog Y Y N ECF-type riboflavin transporter substrate-binding protein GO:0016020 2 Bacteria superkingdom 3763 NCBI Protein Cluster (PRK) hypothetical protein ECF-type riboflavin transporter substrate-binding protein NF010183.0 PRK13662 PRK13662.1 213 213 177 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 3081 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010186.0 PRK13665 PRK13665.1 393 393 328 equivalog Y Y N flotillin-like protein FloA floA 22753055,22882210 2 Bacteria superkingdom 5911 NCBI Protein Cluster (PRK) hypothetical protein flotillin-like protein FloA flotillin-like protein involved in membrane lipid rafts NF010187.0 PRK13666 PRK13666.1 108 108 93 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 2382 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010188.0 PRK13667 PRK13667.1 87 87 70 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 2876 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010190.0 PRK13669 PRK13669.1 96 96 78 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 2128 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010191.0 PRK13670 PRK13670.1 360 360 392 equivalog Y Y N nucleotidyltransferase 2 Bacteria superkingdom 14631 NCBI Protein Cluster (PRK) hypothetical protein nucleotidyltransferase NF010192.0 PRK13671 PRK13671.1 238 238 298 equivalog Y Y N nucleotidyltransferase 2 Bacteria superkingdom 752 NCBI Protein Cluster (PRK) hypothetical protein nucleotidyltransferase NF010200.1 PRK13674 PRK13674.1-1 215 215 270 equivalog Y Y N GTP cyclohydrolase FolE2 folE2 3.5.4.16 GO:0003933 23457054 2 Bacteria superkingdom 15236 NCBI Protein Cluster (PRK) putative GTP cyclohydrolase GTP cyclohydrolase FolE2 NF010217.0 PRK13678 PRK13678.1-4 88 88 102 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 2427 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010221.0 PRK13678 PRK13678.2-4 104 104 99 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 840 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010223.0 PRK13679 PRK13679.1 129 129 170 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 2742 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010226.0 PRK13682 PRK13682.1-1 59 59 53 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 6432 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010228.0 PRK13682 PRK13682.1-3 71 71 57 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 4043 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010235.0 PRK13682 PRK13682.2-6 83 83 61 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 234 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010247.0 PRK13694 PRK13694.1 94 94 83 subfamily Y N N hypothetical protein 2 Bacteria superkingdom 6595 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010277.0 PRK13720 PRK13720.1 110 110 71 equivalog Y N N modulator of post-segregation killing protein 2 Bacteria superkingdom 14 NCBI Protein Cluster (PRK) modulator of post-segregation killing protein modulator of post-segregation killing protein NF010285.0 PRK13725 PRK13725.1 143 143 132 subfamily Y Y N tRNA(fMet)-specific endonuclease VapC vapC GO:0004540 2 Bacteria superkingdom 2827 NCBI Protein Cluster (PRK) plasmid maintenance protein tRNA(fMet)-specific endonuclease VapC NF010308.0 PRK13745 PRK13745.1 484 484 412 equivalog Y Y N anaerobic sulfatase-maturation protein 2 Bacteria superkingdom 1574 NCBI Protein Cluster (PRK) anaerobic sulfatase-maturase anaerobic sulfatase-maturation protein Oxidizes both cysteine and serine residues to C-alpha-formylglycine in sulfatase enzyme protein substrates NF010309.0 PRK13746 PRK13746.1 193 193 263 subfamily Y Y N aminoglycoside adenylyltransferase family protein 2 Bacteria superkingdom 5245 NCBI Protein Cluster (PRK) aminoglycoside resistance protein aminoglycoside adenylyltransferase family protein NF010310.2 PRK13747 PRK13747.1 80 80 76 equivalog Y Y Y broad-spectrum mercury transporter MerE merE 19265693,29226085 2 Bacteria superkingdom 420 NCBI Protein Cluster (PRK) putative mercury resistance protein broad-spectrum mercury transporter MerE NF010311.1 PRK13748 PRK13748.1 600 600 560 subfamily Y Y N mercury(II) reductase 1.16.1.1 2 Bacteria superkingdom 2471 NCBI Protein Cluster (PRK) putative mercuric reductase mercury(II) reductase NF010314.2 PRK13751 PRK13751.2 150 150 116 equivalog Y Y N mercuric ion transporter MerT merT 2 Bacteria superkingdom 1178 NCBI Protein Cluster (PRK) mercuric ion transporter MerT mercuric ion transporter MerT NF010315.0 PRK13752 PRK13752.1 261 261 144 subfamily Y Y Y Hg(II)-responsive transcriptional regulator merR 2 Bacteria superkingdom 551 NCBI Protein Cluster (PRK) putative transcriptional regulator MerR Hg(II)-responsive transcriptional regulator NF010318.0 PRK13755 PRK13755.1 170 170 140 equivalog Y Y N organomercurial transporter MerC merC 28674257,6530603 2 Bacteria superkingdom 613 NCBI Protein Cluster (PRK) putative mercury transport protein MerC organomercurial transporter MerC NF010321.0 PRK13758 PRK13758.1 441 441 370 equivalog Y N N anaerobic sulfatase-maturase 2 Bacteria superkingdom 536 NCBI Protein Cluster (PRK) anaerobic sulfatase-maturase anaerobic sulfatase-maturase NF010349.0 PRK13777 PRK13777.1 153 153 190 equivalog Y Y N HTH-type transcriptional regulator Hpr 3131303 2 Bacteria superkingdom 1824 NCBI Protein Cluster (PRK) transcriptional regulator Hpr HTH-type transcriptional regulator Hpr hpr; ScoC; MarR family; protease production regulatory protein NF010352.0 PRK13780 PRK13780.1 110 110 88 equivalog Y Y N phosphocarrier protein HPr 2 Bacteria superkingdom 2957 NCBI Protein Cluster (PRK) phosphocarrier protein HPr phosphocarrier protein HPr NF010354.0 PRK13782 PRK13782.1 123 123 85 equivalog Y Y N HPr family phosphocarrier protein 2 Bacteria superkingdom 1829 NCBI Protein Cluster (PRK) phosphocarrier protein Chr HPr family phosphocarrier protein NF010355.0 PRK13783 PRK13783.1 445 445 404 equivalog Y Y N adenylosuccinate synthase 6.3.4.4 2 Bacteria superkingdom 331 NCBI Protein Cluster (PRK) adenylosuccinate synthetase adenylosuccinate synthase Catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis NF010371.0 PRK13797 PRK13797.1 814 814 521 equivalog Y Y N allantoicase 3.5.3.4 2 Bacteria superkingdom 58 NCBI Protein Cluster (PRK) putative bifunctional allantoicase/OHCU decarboxylase allantoicase NF010372.0 PRK13798 PRK13798.1 124 124 173 subfamily Y Y N 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase 4.1.1.97 2 Bacteria superkingdom 21094 NCBI Protein Cluster (PRK) putative OHCU decarboxylase 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase NF010376.0 PRK13803 PRK13803.1 819 819 600 equivalog Y Y N bifunctional phosphoribosylanthranilate isomerase/tryptophan synthase subunit beta 4.1.1.48,4.2.1.20 2 Bacteria superkingdom 162 NCBI Protein Cluster (PRK) bifunctional phosphoribosylanthranilate isomerase/tryptophan synthase subunit beta bifunctional phosphoribosylanthranilate isomerase/tryptophan synthase subunit beta Catalyzes the formation of 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate from N-(5-phospho-beta-D-ribosyl)-anthranilate; Catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate NF010378.0 PRK13805 PRK13805.1 951 951 872 equivalog Y Y N bifunctional acetaldehyde-CoA/alcohol dehydrogenase adhE adhC 1.1.1.1,1.2.1.10 GO:0004022,GO:0006066,GO:0015976,GO:0016620,GO:0046872 2 Bacteria superkingdom 21898 NCBI Protein Cluster (PRK) bifunctional acetaldehyde-CoA/alcohol dehydrogenase bifunctional acetaldehyde-CoA/alcohol dehydrogenase null NF010380.0 PRK13807 PRK13807.1 838 838 756 domain Y Y N family 65 glycosyl hydrolase domain-containing protein GO:0005975,GO:0030246 2 Bacteria superkingdom 9745 NCBI Protein Cluster (PRK) maltose phosphorylase family 65 glycosyl hydrolase domain-containing protein NF010381.0 PRK13808 PRK13808.1 426 426 335 equivalog Y Y N adenylate kinase 2.7.4.3 2 Bacteria superkingdom 580 NCBI Protein Cluster (PRK) adenylate kinase adenylate kinase NF010395.0 PRK13823 PRK13823.1 60 60 103 subfamily Y Y N conjugal transfer protein TrbD trbD 2 Bacteria superkingdom 1827 NCBI Protein Cluster (PRK) conjugal transfer protein TrbD conjugal transfer protein TrbD NF010396.0 PRK13824 PRK13824.1 390 390 404 domain Y Y N replication protein C domain-containing protein 2 Bacteria superkingdom 6924 NCBI Protein Cluster (PRK) replication initiation protein RepC replication protein C domain-containing protein NF010404.0 PRK13830 PRK13830.1 810 810 818 subfamily Y N N conjugal transfer protein TrbE 2 Bacteria superkingdom 2496 NCBI Protein Cluster (PRK) conjugal transfer protein TrbE conjugal transfer protein TrbE NF010411.0 PRK13837 PRK13837.1 647 647 828 equivalog Y Y N two-component system VirA-like sensor kinase 2 Bacteria superkingdom 795 NCBI Protein Cluster (PRK) two-component VirA-like sensor kinase two-component system VirA-like sensor kinase NF010446.0 PRK13872 PRK13872.1 152 152 228 equivalog Y Y N conjugal transfer protein TrbF trbF 2 Bacteria superkingdom 6415 NCBI Protein Cluster (PRK) conjugal transfer protein TrbF conjugal transfer protein TrbF NF010447.0 PRK13873 PRK13873.1 1020 1020 815 equivalog Y Y N conjugal transfer protein TrbE trbE 2 Bacteria superkingdom 6926 NCBI Protein Cluster (PRK) conjugal transfer ATPase TrbE conjugal transfer protein TrbE NF010448.0 PRK13874 PRK13874.1 225 225 246 subfamily Y N N conjugal transfer protein TrbJ 2 Bacteria superkingdom 6003 NCBI Protein Cluster (PRK) conjugal transfer protein TrbJ conjugal transfer protein TrbJ NF010449.0 PRK13875 PRK13875.1 442 442 443 subfamily Y N N conjugal transfer protein TrbL 2 Bacteria superkingdom 7039 NCBI Protein Cluster (PRK) conjugal transfer protein TrbL conjugal transfer protein TrbL NF010450.0 PRK13876 PRK13876.1 674 674 667 subfamily Y Y N IncP-type conjugal transfer protein TraG traG 2 Bacteria superkingdom 6698 NCBI Protein Cluster (PRK) conjugal transfer coupling protein TraG IncP-type conjugal transfer protein TraG NF010451.0 PRK13877 PRK13877.1 134 134 124 equivalog Y Y N conjugal transfer transcriptional regulator TraJ traJ 2 Bacteria superkingdom 1168 NCBI Protein Cluster (PRK) conjugal transfer relaxosome component TraJ conjugal transfer transcriptional regulator TraJ NF010452.0 PRK13879 PRK13879.1 286 286 255 equivalog Y Y N P-type conjugative transfer protein TrbJ trbJ 2 Bacteria superkingdom 1685 NCBI Protein Cluster (PRK) conjugal transfer protein TrbJ P-type conjugative transfer protein TrbJ NF010453.0 PRK13880 PRK13880.1 586 586 630 subfamily Y N N conjugal transfer coupling protein TraG 2 Bacteria superkingdom 1112 NCBI Protein Cluster (PRK) conjugal transfer coupling protein TraG conjugal transfer coupling protein TraG NF010455.0 PRK13883 PRK13883.1-1 296 296 162 equivalog Y N N conjugal transfer protein TrbH 2 Bacteria superkingdom 20 NCBI Protein Cluster (PRK) conjugal transfer protein TrbH conjugal transfer protein TrbH NF010459.0 PRK13884 PRK13884.1 156 156 178 subfamily Y N N conjugal transfer peptidase TraF 2 Bacteria superkingdom 549 NCBI Protein Cluster (PRK) conjugal transfer peptidase TraF conjugal transfer peptidase TraF NF010460.0 PRK13885 PRK13885.1 370 370 299 subfamily Y N N conjugal transfer protein TrbG 2 Bacteria superkingdom 512 NCBI Protein Cluster (PRK) conjugal transfer protein TrbG conjugal transfer protein TrbG NF010461.0 PRK13886 PRK13886.1 360 360 241 subfamily Y N N conjugal transfer protein TraL 2 Bacteria superkingdom 375 NCBI Protein Cluster (PRK) conjugal transfer protein TraL conjugal transfer protein TraL NF010462.0 PRK13887 PRK13887.1 332 332 250 subfamily Y N N conjugal transfer protein TrbF 2 Bacteria superkingdom 415 NCBI Protein Cluster (PRK) conjugal transfer protein TrbF conjugal transfer protein TrbF NF010463.0 PRK13888 PRK13888.1 246 246 211 equivalog Y N N conjugal transfer protein TrbN 2 Bacteria superkingdom 475 NCBI Protein Cluster (PRK) conjugal transfer protein TrbN conjugal transfer protein TrbN NF010464.0 PRK13889 PRK13889.1 1015 1015 992 subfamily Y N N conjugal transfer relaxase TraA 2 Bacteria superkingdom 2031 NCBI Protein Cluster (PRK) conjugal transfer relaxase TraA conjugal transfer relaxase TraA NF010465.0 PRK13890 PRK13890.1 96 96 121 equivalog Y N N conjugal transfer protein TrbA 2 Bacteria superkingdom 298 NCBI Protein Cluster (PRK) conjugal transfer protein TrbA conjugal transfer protein TrbA NF010466.0 PRK13891 PRK13891.1 1322 1322 852 subfamily Y N N conjugal transfer protein TrbE 2 Bacteria superkingdom 580 NCBI Protein Cluster (PRK) conjugal transfer protein TrbE conjugal transfer protein TrbE NF010467.0 PRK13892 PRK13892.1 179 179 145 equivalog Y Y N conjugal transfer system pilin TrbC trbC 11073921,20018208 2 Bacteria superkingdom 167 NCBI Protein Cluster (PRK) conjugal transfer protein TrbC conjugal transfer system pilin TrbC Processing of the pilin TrbC of conjugal transfer systems of IncP group broad host range plasmids such as RP4 involves multiple steps. A signal peptide is removed by host signal peptidase I, then additional N-terminal and C-terminal propeptides are removed, and the remaining sequence is cyclized by TraF. TrbC is homologous to the VirB2 pilin of type IV secretion systems (T4SS), which is similarly cyclized. NF010468.0 PRK13893 PRK13893.1 259 259 194 equivalog Y N N conjugal transfer protein TrbM 2 Bacteria superkingdom 138 NCBI Protein Cluster (PRK) conjugal transfer protein TrbM conjugal transfer protein TrbM NF010469.0 PRK13894 PRK13894.1 508 508 320 subfamily Y N N conjugal transfer ATPase TrbB 2 Bacteria superkingdom 476 NCBI Protein Cluster (PRK) conjugal transfer ATPase TrbB conjugal transfer ATPase TrbB NF010470.0 PRK13895 PRK13895.1 139 139 144 subfamily Y N N conjugal transfer protein TraM 2 Bacteria superkingdom 324 NCBI Protein Cluster (PRK) conjugal transfer protein TraM conjugal transfer protein TraM NF010478.0 PRK13903 PRK13903.1 231 231 362 equivalog Y Y N UDP-N-acetylmuramate dehydrogenase 1.3.1.98 GO:0008762,GO:0071949 2 Bacteria superkingdom 36376 NCBI Protein Cluster (PRK) UDP-N-acetylenolpyruvoylglucosamine reductase UDP-N-acetylmuramate dehydrogenase NF010496.0 PRK13915 PRK13915.1 262 262 307 equivalog Y Y N glucosyl-3-phosphoglycerate synthase 2.4.1.266 2 Bacteria superkingdom 10519 NCBI Protein Cluster (PRK) putative glucosyl-3-phosphoglycerate synthase glucosyl-3-phosphoglycerate synthase NF010513.0 PRK13922 PRK13922.12-3 380 380 305 equivalog Y Y N rod shape-determining protein MreC mreC 2 Bacteria superkingdom 402 NCBI Protein Cluster (PRK) rod shape-determining protein MreC rod shape-determining protein MreC NF010524.0 PRK13922 PRK13922.14-4 332 332 270 equivalog Y Y N rod shape-determining protein MreC mreC 2 Bacteria superkingdom 5 NCBI Protein Cluster (PRK) rod shape-determining protein MreC rod shape-determining protein MreC NF010539.0 PRK13927 PRK13927.1 293 293 339 subfamily Y Y N rod shape-determining protein MreB mreB 2 Bacteria superkingdom 36633 NCBI Protein Cluster (PRK) rod shape-determining protein MreB rod shape-determining protein MreB NF010540.1 PRK13929 PRK13929.1 515 515 334 exception Y Y N rod-share determining protein MreBH mreBH 19659933,21091501 2 Bacteria superkingdom 1406 NCBI Protein Cluster (PRK) rod-share determining protein MreBH rod-share determining protein MreBH NF010552.0 PRK13946 PRK13946.1 186 186 198 equivalog Y Y N shikimate kinase 2.7.1.71 2 Bacteria superkingdom 7717 NCBI Protein Cluster (PRK) shikimate kinase shikimate kinase Catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis NF010553.0 PRK13947 PRK13947.1 204 204 173 equivalog Y Y N shikimate kinase 2.7.1.71 2 Bacteria superkingdom 144 NCBI Protein Cluster (PRK) shikimate kinase shikimate kinase Catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis NF010560.0 PRK13955 PRK13955.1 180 180 132 equivalog Y Y N large conductance mechanosensitive channel protein MscL mscL 2 Bacteria superkingdom 1073 NCBI Protein Cluster (PRK) large-conductance mechanosensitive channel large conductance mechanosensitive channel protein MscL Channel that opens in response to pressure or hypoosmotic shock NF010569.0 PRK13962 PRK13962.1 883 883 645 equivalog Y N N bifunctional phosphoglycerate kinase/triosephosphate isomerase 2 Bacteria superkingdom 238 NCBI Protein Cluster (PRK) bifunctional phosphoglycerate kinase/triosephosphate isomerase bifunctional phosphoglycerate kinase/triosephosphate isomerase NF010572.0 PRK13965 PRK13965.1 486 486 337 subfamily Y Y N class 1b ribonucleoside-diphosphate reductase subunit beta nrdF 2 Bacteria superkingdom 10531 NCBI Protein Cluster (PRK) ribonucleotide-diphosphate reductase subunit beta class 1b ribonucleoside-diphosphate reductase subunit beta NF010578.0 PRK13971 PRK13971.1 376 376 333 equivalog Y Y N 4-hydroxyproline epimerase 5.1.1.8 2 Bacteria superkingdom 6968 NCBI Protein Cluster (PRK) hydroxyproline-2-epimerase 4-hydroxyproline epimerase NF010590.0 PRK13984 PRK13984.1 946 946 611 equivalog Y N N putative oxidoreductase 2 Bacteria superkingdom 72 NCBI Protein Cluster (PRK) putative oxidoreductase putative oxidoreductase NF010611.0 PRK14012 PRK14012.1 548 548 406 equivalog Y Y N IscS subfamily cysteine desulfurase 2.8.1.7 GO:0030170,GO:0031071,GO:0044571 2 Bacteria superkingdom 14571 NCBI Protein Cluster (PRK) cysteine desulfurase IscS subfamily cysteine desulfurase NF010623.0 PRK14016 PRK14016.1 877 877 871 subfamily Y Y N cyanophycin synthetase 2 Bacteria superkingdom 11177 NCBI Protein Cluster (PRK) cyanophycin synthetase cyanophycin synthetase Catalyzes the formation of cyanophycin which may act to store excess nitrogen NF010625.0 PRK14018 PRK14018.1 522 522 521 equivalog Y Y N bifunctional peptide-methionine (S)-S-oxide reductase MsrA/peptide-methionine (R)-S-oxide reductase MsrB msrAB 2 Bacteria superkingdom 1356 NCBI Protein Cluster (PRK) trifunctional thioredoxin/methionine sulfoxide reductase A/B protein bifunctional peptide-methionine (S)-S-oxide reductase MsrA/peptide-methionine (R)-S-oxide reductase MsrB NF010629.0 PRK14023 PRK14023.1 229 229 166 equivalog Y N N homoaconitate hydratase small subunit 2 Bacteria superkingdom 242 NCBI Protein Cluster (PRK) homoaconitate hydratase small subunit homoaconitate hydratase small subunit NF010636.0 PRK14033 PRK14033.1 479 479 376 equivalog Y Y N bifunctional 2-methylcitrate synthase/citrate synthase 2.3.3.16,2.3.3.5 GO:0046912 2 Bacteria superkingdom 5864 NCBI Protein Cluster (PRK) citrate synthase bifunctional 2-methylcitrate synthase/citrate synthase NF010637.0 PRK14034 PRK14034.1 594 594 372 equivalog Y Y N citrate synthase citZ 2.3.3.1 GO:0046912 2 Bacteria superkingdom 3350 NCBI Protein Cluster (PRK) citrate synthase citrate synthase Forms citrate from oxaloacetate and acetyl-CoA; functions in TCA cycle, glyoxylate cycle and respiration NF010638.0 PRK14035 PRK14035.1 572 572 372 equivalog Y Y N citrate synthase 2 Bacteria superkingdom 3475 NCBI Protein Cluster (PRK) citrate synthase citrate synthase Forms citrate from oxaloacetate and acetyl-CoA; functions in TCA cycle, glyoxylate cycle and respiration NF010639.0 PRK14036 PRK14036.1 502 502 379 equivalog Y Y N citrate synthase 2 Bacteria superkingdom 1181 NCBI Protein Cluster (PRK) citrate synthase citrate synthase Forms citrate from oxaloacetate and acetyl-CoA; functions in TCA cycle, glyoxylate cycle and respiration NF010647.0 PRK14046 PRK14046.1 604 604 392 equivalog Y Y N malate--CoA ligase subunit beta 2 Bacteria superkingdom 1404 NCBI Protein Cluster (PRK) malate--CoA ligase subunit beta malate--CoA ligase subunit beta Catalyzes the formation of malyl-CoA from malate and CoA NF010649.0 PRK14048 PRK14048.1 374 374 374 equivalog Y N N ferrichrome/ferrioxamine B periplasmic transporter 2 Bacteria superkingdom 284 NCBI Protein Cluster (PRK) ferrichrome/ferrioxamine B periplasmic transporter ferrichrome/ferrioxamine B periplasmic transporter NF010657.0 PRK14056 PRK14056.1 346 346 580 equivalog Y Y N aromatic amino acid hydroxylase 1.14.16.- GO:0004497,GO:0005506,GO:0009072 2 Bacteria superkingdom 3864 NCBI Protein Cluster (PRK) phenylalanine 4-monooxygenase aromatic amino acid hydroxylase NF010663.0 PRK14059 PRK14059.1-1 184 184 253 equivalog Y Y N pyrimidine reductase family protein 2 Bacteria superkingdom 2956 NCBI Protein Cluster (PRK) hypothetical protein pyrimidine reductase family protein NF010674.0 PRK14071 PRK14071.1 544 544 360 equivalog Y Y N ATP-dependent 6-phosphofructokinase 2.7.1.11 2 Bacteria superkingdom 726 NCBI Protein Cluster (PRK) 6-phosphofructokinase ATP-dependent 6-phosphofructokinase Catalyzes the formation of D-fructose 1,6-bisphosphate from D-fructose 6-phosphate in glycolysis NF010675.0 PRK14072 PRK14072.1 273 273 416 subfamily Y Y N diphosphate--fructose-6-phosphate 1-phosphotransferase 2.7.1.90 2 Bacteria superkingdom 9874 NCBI Protein Cluster (PRK) 6-phosphofructokinase diphosphate--fructose-6-phosphate 1-phosphotransferase NF010682.0 PRK14082 PRK14082.1 86 86 71 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 313 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF010683.0 PRK14083 PRK14083.1 455 455 604 equivalog Y Y N HSP90 family protein GO:0005524,GO:0006457,GO:0016887,GO:0051082 2 Bacteria superkingdom 9556 NCBI Protein Cluster (PRK) HSP90 family protein HSP90 family protein NF010686.0 PRK14086 PRK14086.1 508 508 637 equivalog Y Y N chromosomal replication initiator protein DnaA dnaA GO:0003688,GO:0005524,GO:0006275,GO:0043565 10095766 2 Bacteria superkingdom 19791 NCBI Protein Cluster (PRK) chromosomal replication initiation protein chromosomal replication initiator protein DnaA Binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication; can also affect transcription of multiple genes including itself NF010691.0 PRK14091 PRK14091.1 270 270 176 equivalog Y Y N RNA chaperone Hfq hfq 2 Bacteria superkingdom 1078 NCBI Protein Cluster (PRK) RNA-binding protein Hfq RNA chaperone Hfq NF010693.0 PRK14093 PRK14093.1 544 544 479 equivalog Y Y N UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanine ligase GO:0005524,GO:0009058,GO:0047480,GO:0071555 2 Bacteria superkingdom 3457 NCBI Protein Cluster (PRK) UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanine ligase UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanine ligase NF010695.0 PRK14095 PRK14095.1 703 703 536 equivalog Y Y N glucose-6-phosphate isomerase 5.3.1.9 2 Bacteria superkingdom 1177 NCBI Protein Cluster (PRK) glucose-6-phosphate isomerase glucose-6-phosphate isomerase Functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family NF010697.0 PRK14097 PRK14097.1 443 443 448 equivalog Y Y N glucose-6-phosphate isomerase 5.3.1.9 GO:0004347,GO:0006096 2 Bacteria superkingdom 14473 NCBI Protein Cluster (PRK) glucose-6-phosphate isomerase glucose-6-phosphate isomerase Functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family NF010703.0 PRK14103 PRK14103.1 320 320 256 equivalog Y Y N trans-aconitate 2-methyltransferase 2.1.1.144 GO:0030798 2 Bacteria superkingdom 10136 NCBI Protein Cluster (PRK) trans-aconitate 2-methyltransferase trans-aconitate 2-methyltransferase Catalyzes the formation of (E)-3-(methoxycarbonyl)pent-2-enedioate and S-adenosyl-L-homocysteine from S-adenosyl-L-methionine and trans-aconitate NF010706.0 PRK14108 PRK14108.1 724 724 986 equivalog Y Y N bifunctional [glutamine synthetase] adenylyltransferase/[glutamine synthetase]-adenylyl-L-tyrosine phosphorylase 2.7.7.89 GO:0008882 2 Bacteria superkingdom 7467 NCBI Protein Cluster (PRK) bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase bifunctional [glutamine synthetase] adenylyltransferase/[glutamine synthetase]-adenylyl-L-tyrosine phosphorylase NF010707.0 PRK14109 PRK14109.1 625 625 1010 equivalog Y Y N bifunctional [glutamine synthetase] adenylyltransferase/[glutamine synthetase]-adenylyl-L-tyrosine phosphorylase 2.7.7.42,2.7.7.89 GO:0008882 2 Bacteria superkingdom 19307 NCBI Protein Cluster (PRK) bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase bifunctional [glutamine synthetase] adenylyltransferase/[glutamine synthetase]-adenylyl-L-tyrosine phosphorylase NF010709.0 PRK14111 PRK14111.1 425 425 290 equivalog Y Y N F0F1 ATP synthase subunit gamma 2 Bacteria superkingdom 36 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit gamma F0F1 ATP synthase subunit gamma Produces ATP from ADP in the presence of a proton gradient across the membrane; the gamma chain is a regulatory subunit NF010716.0 PRK14118 PRK14118.1 409 409 227 equivalog Y Y N 2,3-diphosphoglycerate-dependent phosphoglycerate mutase 5.4.2.11 2 Bacteria superkingdom 452 NCBI Protein Cluster (PRK) phosphoglyceromutase 2,3-diphosphoglycerate-dependent phosphoglycerate mutase Catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate; 2,3-diphosphoglycerate-dependent NF010725.0 PRK14127 PRK14127.1 91 91 111 equivalog Y Y N cell division regulator GpsB gpsB 18363795,18776011 2 Bacteria superkingdom 3417 NCBI Protein Cluster (PRK) cell division protein GpsB cell division regulator GpsB Guides PBP1 shuttling NF010731.0 PRK14133 PRK14133.1 362 362 352 equivalog Y Y N DNA polymerase IV 2.7.7.7 2 Bacteria superkingdom 7821 NCBI Protein Cluster (PRK) DNA polymerase IV DNA polymerase IV Involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function NF010737.0 PRK14139 PRK14139.1 164 164 188 equivalog Y Y N nucleotide exchange factor GrpE grpE GO:0000774,GO:0006457,GO:0051087 2 Bacteria superkingdom 9441 NCBI Protein Cluster (PRK) heat shock protein GrpE nucleotide exchange factor GrpE With DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins NF010739.0 PRK14141 PRK14141.1 192 192 211 equivalog Y Y N nucleotide exchange factor GrpE grpE GO:0000774,GO:0006457,GO:0042803,GO:0051087 2 Bacteria superkingdom 3426 NCBI Protein Cluster (PRK) heat shock protein GrpE nucleotide exchange factor GrpE With DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins NF010761.0 PRK14164 PRK14164.1 167 167 220 equivalog Y Y N nucleotide exchange factor GrpE grpE GO:0000774,GO:0006457,GO:0042803,GO:0051087 2 Bacteria superkingdom 3565 NCBI Protein Cluster (PRK) heat shock protein GrpE nucleotide exchange factor GrpE With DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins NF010785.0 PRK14188 PRK14188.1 396 396 297 subfamily Y Y N bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD folD 1.5.1.5,3.5.4.9 2 Bacteria superkingdom 12712 NCBI Protein Cluster (PRK) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD Catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate NF010786.0 PRK14189 PRK14189.1 421 421 285 subfamily Y Y N bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase 1.5.1.5,3.5.4.9 2 Bacteria superkingdom 4749 NCBI Protein Cluster (PRK) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase Catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate NF010789.1 PRK14193 PRK14193.1 401 401 281 equivalog Y Y N bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase GO:0004488 2 Bacteria superkingdom 13357 NCBI Protein Cluster (PRK) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase Catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate NF010791.0 PRK14195 PRK14195.1 129 129 125 equivalog Y Y N fluoride efflux transporter CrcB crcB 2 Bacteria superkingdom 3924 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter CrcB NF010794.0 PRK14198 PRK14198.1 125 125 125 equivalog Y Y N fluoride efflux transporter CrcB crcB 2 Bacteria superkingdom 1709 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter CrcB NF010799.0 PRK14203 PRK14203.1 129 129 132 equivalog Y Y N fluoride efflux transporter CrcB crcB 2 Bacteria superkingdom 432 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter CrcB NF010802.0 PRK14206 PRK14206.1 140 140 131 equivalog Y Y N fluoride efflux transporter CrcB crcB 2 Bacteria superkingdom 520 NCBI Protein Cluster (PRK) camphor resistance protein CrcB fluoride efflux transporter CrcB NF010869.0 PRK14276 PRK14276.1 549 549 380 equivalog Y Y N molecular chaperone DnaJ dnaJ GO:0006457,GO:0051082 2 Bacteria superkingdom 5246 NCBI Protein Cluster (PRK) chaperone protein DnaJ molecular chaperone DnaJ Chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion NF010873.0 PRK14280 PRK14280.1 562 562 375 equivalog Y Y N molecular chaperone DnaJ dnaJ GO:0005524,GO:0006457,GO:0009408,GO:0031072,GO:0051082 2 Bacteria superkingdom 5211 NCBI Protein Cluster (PRK) chaperone protein DnaJ molecular chaperone DnaJ Chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion NF010921.0 PRK14341 PRK14341.1 230 230 230 equivalog Y Y N lipoyl(octanoyl) transferase LipB lipB 2.3.1.181 GO:0009249,GO:0033819 2 Bacteria superkingdom 8727 NCBI Protein Cluster (PRK) lipoate-protein ligase B lipoyl(octanoyl) transferase LipB Catalyzes the transfer of the lipoyl/octanoyl moiety of lipoyl/octanoyl-ACP onto lipoate-dependent enzymes like pyruvate dehydrogenase and the glycine cleavage system H protein NF010932.0 PRK14352 PRK14352.1 611 611 488 equivalog Y Y N bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU glmU 2.7.7.23 GO:0000287,GO:0000902,GO:0003977,GO:0006048,GO:0009252,GO:0019134 2 Bacteria superkingdom 15877 NCBI Protein Cluster (PRK) bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU Catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis NF010933.0 PRK14353 PRK14353.1 505 505 453 equivalog Y Y N bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU glmU 2.7.7.23 GO:0000287,GO:0000902,GO:0003977,GO:0006048,GO:0009252,GO:0019134 2 Bacteria superkingdom 10677 NCBI Protein Cluster (PRK) bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU Catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis NF010934.0 PRK14354 PRK14354.1 563 563 458 equivalog Y Y N bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU glmU 2.3.1.157,2.7.7.23 GO:0000287,GO:0003977,GO:0006048,GO:0009252,GO:0019134 2 Bacteria superkingdom 15260 NCBI Protein Cluster (PRK) bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU Catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis NF010938.0 PRK14358 PRK14358.1 500 500 481 equivalog Y N N bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase 2 Bacteria superkingdom 220 NCBI Protein Cluster (PRK) bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase NF010996.0 PRK14421 PRK14421.1 98 98 99 equivalog Y Y N acylphosphatase 2 Bacteria superkingdom 931 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF010997.0 PRK14422 PRK14422.1 95 95 93 equivalog Y Y N acylphosphatase 3.6.1.7 GO:0003998 2 Bacteria superkingdom 6814 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011001.0 PRK14427 PRK14427.1 100 100 105 equivalog Y Y N acylphosphatase 2 Bacteria superkingdom 468 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011003.0 PRK14429 PRK14429.1 90 90 91 equivalog Y Y N acylphosphatase 3.6.1.7 2 Bacteria superkingdom 153 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011004.0 PRK14430 PRK14430.1 101 101 92 equivalog Y Y N acylphosphatase 2 Bacteria superkingdom 144 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011017.0 PRK14445 PRK14445.1 97 97 92 equivalog Y Y N acylphosphatase 3.6.1.7 2 Bacteria superkingdom 33 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011019.0 PRK14448 PRK14448.1 100 100 90 equivalog Y Y N acylphosphatase 3.6.1.7 2 Bacteria superkingdom 405 NCBI Protein Cluster (PRK) acylphosphatase acylphosphatase NF011024.0 PRK14453 PRK14453.1 468 468 348 equivalog Y Y N 23S rRNA (adenine(2503)-C(8))-methyltransferase Cfr cfr 2.1.1.224 2 Bacteria superkingdom 702 NCBI Protein Cluster (PRK) chloramphenicol/florfenicol resistance protein 23S rRNA (adenine(2503)-C(8))-methyltransferase Cfr NF011044.0 PRK14474 PRK14474.1 339 339 258 equivalog Y Y N F0F1 ATP synthase subunit B 7.1.2.2 2 Bacteria superkingdom 16 NCBI Protein Cluster (PRK) F0F1 ATP synthase subunit B F0F1 ATP synthase subunit B Produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B is part of the membrane proton channel NF011047.0 PRK14477 PRK14477.1 1229 1229 917 equivalog Y Y N bifunctional nitrogenase iron-molybdenum cofactor biosynthesis protein NifEN 2 Bacteria superkingdom 145 NCBI Protein Cluster (PRK) bifunctional nitrogenase molybdenum-cofactor biosynthesis protein NifE/NifN bifunctional nitrogenase iron-molybdenum cofactor biosynthesis protein NifEN NF011049.0 PRK14479 PRK14479.1 492 492 568 subfamily Y Y N dihydroxyacetone kinase family protein 2 Bacteria superkingdom 13183 NCBI Protein Cluster (PRK) dihydroxyacetone kinase dihydroxyacetone kinase family protein NF011053.0 PRK14485 PRK14485.1 1080 1080 716 subfamily Y N N putative bifunctional cbb3-type cytochrome c oxidase subunit I/II 2 Bacteria superkingdom 4746 NCBI Protein Cluster (PRK) putative bifunctional cbb3-type cytochrome c oxidase subunit I/II putative bifunctional cbb3-type cytochrome c oxidase subunit I/II NF011055.0 PRK14487 PRK14487.1 218 218 212 subfamily Y N N cbb3-type cytochrome c oxidase subunit II 2 Bacteria superkingdom 20298 NCBI Protein Cluster (PRK) cbb3-type cytochrome c oxidase subunit II cbb3-type cytochrome c oxidase subunit II NF011056.0 PRK14489 PRK14489.1-1 379 379 363 equivalog Y Y N bifunctional molybdenum cofactor guanylyltransferase MobA/molybdopterin-guanine dinucleotide biosynthesis adaptor protein MobB mobAB 2 Bacteria superkingdom 26 NCBI Protein Cluster (PRK) putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB bifunctional molybdenum cofactor guanylyltransferase MobA/molybdopterin-guanine dinucleotide biosynthesis adaptor protein MobB NF011078.0 PRK14508 PRK14508.1-1 776 776 503 subfamily Y Y N 4-alpha-glucanotransferase 2.4.1.25 2 Bacteria superkingdom 2214 NCBI Protein Cluster (PRK) 4-alpha-glucanotransferase 4-alpha-glucanotransferase NF011087.0 PRK14511 PRK14511.1-5 1556 1556 996 equivalog Y Y N malto-oligosyltrehalose synthase 5.4.99.15 2 Bacteria superkingdom 63 NCBI Protein Cluster (PRK) maltooligosyl trehalose synthase malto-oligosyltrehalose synthase NF011093.0 PRK14520 PRK14520.1 165 165 156 equivalog Y Y N 30S ribosomal protein S16 rpsP GO:0003735,GO:0006412 2 Bacteria superkingdom 9413 NCBI Protein Cluster (PRK) 30S ribosomal protein S16 30S ribosomal protein S16 Binds to lower part of 30S body where it stabilizes two domains; required for efficient assembly of 30S; in Escherichia coli this protein has nuclease activity NF011104.0 PRK14531 PRK14531.1 160 160 183 equivalog Y Y N adenylate kinase 2.7.4.3 2 Bacteria superkingdom 16135 NCBI Protein Cluster (PRK) adenylate kinase adenylate kinase NF011116.0 PRK14545 PRK14545.1 217 217 139 equivalog Y Y N nucleoside-diphosphate kinase 2.7.4.6 2 Bacteria superkingdom 3042 NCBI Protein Cluster (PRK) nucleoside diphosphate kinase nucleoside-diphosphate kinase Catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate NF011202.0 PRK14608 PRK14608.1 204 204 294 equivalog Y Y N 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase 2.7.1.148 GO:0050515 2 Bacteria superkingdom 17170 NCBI Protein Cluster (PRK) 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase Catalyzes the phosphorylation of 4-diphosphocytidyl-2-C-methyl-D-erythritol in the nonmevalonate pathway of isoprenoid biosynthesis NF011229.0 PRK14636 PRK14636.1 230 230 176 equivalog Y Y N ribosome maturation protein RimP rimP 2 Bacteria superkingdom 1324 NCBI Protein Cluster (PRK) hypothetical protein ribosome maturation protein RimP NF011245.0 PRK14651 PRK14651.1 224 224 273 equivalog Y Y N UDP-N-acetylmuramate dehydrogenase 1.3.1.98 2 Bacteria superkingdom 229 NCBI Protein Cluster (PRK) UDP-N-acetylenolpyruvoylglucosamine reductase UDP-N-acetylmuramate dehydrogenase NF011254.0 PRK14660 PRK14660.1 195 195 125 equivalog Y Y N holo-[acyl-carrier-protein] synthase 2 Bacteria superkingdom 6 NCBI Protein Cluster (PRK) 4'-phosphopantetheinyl transferase holo-[acyl-carrier-protein] synthase Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids NF011281.0 PRK14689 PRK14689.1 122 122 128 equivalog Y N N hypothetical protein 2 Bacteria superkingdom 171 NCBI Protein Cluster (PRK) hypothetical protein hypothetical protein NF011291.0 PRK14703 PRK14703.1 681 681 769 equivalog Y Y N glutamine--tRNA ligase/YqeY domain fusion protein GO:0000166,GO:0004819,GO:0005524,GO:0006425 2 Bacteria superkingdom 34789 NCBI Protein Cluster (PRK) glutaminyl-tRNA synthetase/YqeY domain fusion protein glutamine--tRNA ligase/YqeY domain fusion protein NF011292.0 PRK14704 PRK14704.1 736 736 618 equivalog Y Y N anaerobic ribonucleoside triphosphate reductase 2 Bacteria superkingdom 1880 NCBI Protein Cluster (PRK) anaerobic ribonucleoside triphosphate reductase anaerobic ribonucleoside triphosphate reductase Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates NF011293.0 PRK14705 PRK14705.1 2376 2376 1224 equivalog Y Y N 1,4-alpha-glucan branching enzyme 2.4.1.18 2 Bacteria superkingdom 398 NCBI Protein Cluster (PRK) glycogen branching enzyme 1,4-alpha-glucan branching enzyme Catalyzes the transfer of a segment of a 1,4-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain NF011301.0 PRK14713 PRK14713.1 512 512 534 equivalog Y Y N bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase 2.7.1.49,2.7.4.7 2 Bacteria superkingdom 1942 NCBI Protein Cluster (PRK) multifunctional hydroxymethylpyrimidine phosphokinase/4-amino-5-aminomethyl-2-methylpyrimidine hydrolase bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase NF011307.0 PRK14716 PRK14716.1-5 431 431 464 equivalog Y Y N glycosyl transferase family protein 2 Bacteria superkingdom 1323 NCBI Protein Cluster (PRK) bacteriophage N4 adsorption protein B glycosyl transferase family protein NF011325.0 PRK14738 PRK14738.1 263 263 206 equivalog Y Y N guanylate kinase 2.7.4.8 2 Bacteria superkingdom 86 NCBI Protein Cluster (PRK) guanylate kinase guanylate kinase Essential for recycling GMP and indirectly, cGMP NF011335.0 PRK14751 PRK14751.1 71 71 28 equivalog Y Y N tetracycline resistance determinant leader peptide 2 Bacteria superkingdom 78 NCBI Protein Cluster (PRK) tetracycline resistance determinant leader peptide tetracycline resistance determinant leader peptide Regulates the transcription of tet(M) by attenuation NF011339.0 PRK14753 PRK14753.1 58 58 27 equivalog Y N N 30S ribosomal protein Thx 2 Bacteria superkingdom 19 NCBI Protein Cluster (PRK) 30S ribosomal protein Thx 30S ribosomal protein Thx NF011354.0 PRK14772 PRK14772.1 321 321 190 equivalog Y N N lipoprotein signal peptidase 2 Bacteria superkingdom 340 NCBI Protein Cluster (PRK) lipoprotein signal peptidase lipoprotein signal peptidase NF011358.0 PRK14776 PRK14776.1 285 285 170 equivalog Y N N lipoprotein signal peptidase 2 Bacteria superkingdom 280 NCBI Protein Cluster (PRK) lipoprotein signal peptidase lipoprotein signal peptidase NF011367.0 PRK14786 PRK14786.1 190 190 154 equivalog Y N N lipoprotein signal peptidase 2 Bacteria superkingdom 40 NCBI Protein Cluster (PRK) lipoprotein signal peptidase lipoprotein signal peptidase NF011392.0 PRK14817 PRK14817.1 271 271 182 equivalog Y Y N NADH-quinone oxidoreductase subunit B 1.6.5.9 2 Bacteria superkingdom 101 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit B NADH-quinone oxidoreductase subunit B NF011393.0 PRK14818 PRK14818.1 255 255 173 equivalog Y N N NADH dehydrogenase subunit B 1.6.5.9 2 Bacteria superkingdom 22 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit B NADH dehydrogenase subunit B NF011394.0 PRK14819 PRK14819.1 312 312 264 equivalog Y Y N NADH-quinone oxidoreductase subunit B 1.6.5.9 2 Bacteria superkingdom 66 NCBI Protein Cluster (PRK) NADH dehydrogenase subunit B NADH-quinone oxidoreductase subunit B NF011397.0 PRK14822 PRK14822.1 234 234 201 equivalog Y Y N XTP/dITP diphosphatase 3.6.1.66 GO:0009143,GO:0047429 2 Bacteria superkingdom 17084 NCBI Protein Cluster (PRK) nucleoside-triphosphatase XTP/dITP diphosphatase Hydrolyzes non-standard nucleotides such as xanthine and inosine NF011403.0 PRK14828 PRK14828.1 348 348 258 equivalog Y Y N isoprenyl transferase GO:0016765 2 Bacteria superkingdom 10752 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate synthase isoprenyl transferase Catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate NF011404.0 PRK14829 PRK14829.1 372 372 260 equivalog Y Y N isoprenyl transferase GO:0016765 2 Bacteria superkingdom 12796 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate synthase isoprenyl transferase Catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate NF011405.0 PRK14830 PRK14830.1 304 304 251 equivalog Y Y N isoprenyl transferase GO:0016765 2 Bacteria superkingdom 27223 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate synthase isoprenyl transferase Catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate NF011408.0 PRK14834 PRK14834.1 348 348 252 equivalog Y Y N isoprenyl transferase GO:0016765 2 Bacteria superkingdom 3618 NCBI Protein Cluster (PRK) undecaprenyl pyrophosphate synthase isoprenyl transferase Catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate NF011429.0 PRK14857 PRK14857.1 77 77 91 equivalog Y Y N TatA/E family twin arginine-targeting protein translocase 2 Bacteria superkingdom 868 NCBI Protein Cluster (PRK) twin arginine translocase protein A TatA/E family twin arginine-targeting protein translocase NF011440.0 PRK14869 PRK14869.1-2 746 746 541 equivalog Y Y N putative manganese-dependent inorganic diphosphatase 3.6.1.1 2 Bacteria superkingdom 196 NCBI Protein Cluster (PRK) putative manganese-dependent inorganic pyrophosphatase putative manganese-dependent inorganic diphosphatase NF011441.0 PRK14869 PRK14869.1-3 753 753 548 equivalog Y Y N putative manganese-dependent inorganic diphosphatase 3.6.1.1 2 Bacteria superkingdom 854 NCBI Protein Cluster (PRK) putative manganese-dependent inorganic pyrophosphatase putative manganese-dependent inorganic diphosphatase NF011445.0 PRK14869 PRK14869.2-1 483 483 548 equivalog Y Y N putative manganese-dependent inorganic diphosphatase 3.6.1.1 2 Bacteria superkingdom 217 NCBI Protein Cluster (PRK) putative manganese-dependent inorganic pyrophosphatase putative manganese-dependent inorganic diphosphatase NF011447.0 PRK14869 PRK14869.2-3 522 522 540 equivalog Y Y N putative manganese-dependent inorganic diphosphatase 3.6.1.1 2 Bacteria superkingdom 37 NCBI Protein Cluster (PRK) putative manganese-dependent inorganic pyrophosphatase putative manganese-dependent inorganic diphosphatase NF011457.0 PRK14875 PRK14875.1 307 307 372 equivalog Y Y N acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit 2.3.1.12 2 Bacteria superkingdom 3986 NCBI Protein Cluster (PRK) acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase acetoin dehydrogenase dihydrolipoyllysine-residue acetyltransferase subunit NF011494.0 PRK14902 PRK14902.1 319 319 444 equivalog Y Y N 16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB rsmB 2.1.1.176 GO:0001510,GO:0003723,GO:0006355,GO:0008168 2 Bacteria superkingdom 29613 NCBI Protein Cluster (PRK) 16S rRNA methyltransferase B 16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB Catalyzes the methylation of the C5 position of C967 of the 16S rRNA NF011498.0 PRK14906 PRK14906.1 1437 1437 1459 equivalog Y Y N DNA-directed RNA polymerase subunit beta' 2.7.7.6 GO:0003677,GO:0003899,GO:0006351 2 Bacteria superkingdom 13915 NCBI Protein Cluster (PRK) DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein DNA-directed RNA polymerase subunit beta' NF011499.0 PRK14908 PRK14908.1 1244 1244 998 equivalog Y Y N glycine--tRNA ligase 6.1.1.14 2 Bacteria superkingdom 1277 NCBI Protein Cluster (PRK) glycyl-tRNA synthetase glycine--tRNA ligase Catalyzes a two-step reaction, first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA NF011538.0 PRK14975 PRK14975.1-1 389 389 557 equivalog Y Y N bifunctional 3'-5' exonuclease/DNA polymerase GO:0003887,GO:0006261 2 Bacteria superkingdom 14247 NCBI Protein Cluster (PRK) bifunctional 3'-5' exonuclease/DNA polymerase bifunctional 3'-5' exonuclease/DNA polymerase NF011541.0 PRK14975 PRK14975.2-1 871 871 645 equivalog Y Y N bifunctional 3'-5' exonuclease/DNA polymerase 2 Bacteria superkingdom 130 NCBI Protein Cluster (PRK) bifunctional 3'-5' exonuclease/DNA polymerase bifunctional 3'-5' exonuclease/DNA polymerase NF011565.0 PRK14989 PRK14989.1 883 883 847 subfamily Y Y N nitrite reductase large subunit nirB 1.7.1.15 2 Bacteria superkingdom 41933 NCBI Protein Cluster (PRK) nitrite reductase subunit NirD nitrite reductase large subunit NF011589.0 PRK15014 PRK15014.1 686 686 477 subfamily Y Y N 6-phospho-beta-glucosidase 3.2.1.86 GO:0004553,GO:0005975 2 Bacteria superkingdom 13639 NCBI Protein Cluster (PRK) 6-phospho-beta-glucosidase BglA 6-phospho-beta-glucosidase NF011599.0 PRK15025 PRK15025.1 356 356 349 equivalog Y Y N ureidoglycolate dehydrogenase allD 1.1.1.154 GO:0016491 2 Bacteria superkingdom 4168 NCBI Protein Cluster (PRK) ureidoglycolate dehydrogenase ureidoglycolate dehydrogenase Catalyzes the formation of oxalurate from ureidoglycolate NF011616.0 PRK15042 PRK15042.1 248 248 219 subfamily Y Y N propanediol/glycerol family dehydratase medium subunit 2 Bacteria superkingdom 2431 NCBI Protein Cluster (PRK) propanediol dehydratase medium subunit propanediol/glycerol family dehydratase medium subunit NF011620.1 PRK15046 PRK15046.1 310 310 334 equivalog Y Y N 2-aminoethylphosphonate ABC transporter substrate-binding protein 2 Bacteria superkingdom 6582 NCBI Protein Cluster (PRK) 2-aminoethylphosphonate ABC transporter substrate-binding protein 2-aminoethylphosphonate ABC transporter substrate-binding protein NF011624.0 PRK15050 PRK15050.1 247 247 297 equivalog Y Y N 2-aminoethylphosphonate ABC transporter permease subunit 2 Bacteria superkingdom 6717 NCBI Protein Cluster (PRK) 2-aminoethylphosphonate transport system permease PhnU 2-aminoethylphosphonate ABC transporter permease subunit Involved in the transport of 2-aminoethylphosphonate into the cell NF011625.2 PRK15051 PRK15051.1 92 92 111 equivalog Y Y N 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE arnE 2 Bacteria superkingdom 3083 NCBI Protein Cluster (PRK) 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE NF011647.0 PRK15065 PRK15065.1 278 278 267 subfamily Y Y N mannose/fructose/sorbose family PTS transporter subunit IIC 2 Bacteria superkingdom 6631 NCBI Protein Cluster (PRK) PTS system mannose-specific transporter subunit IIC mannose/fructose/sorbose family PTS transporter subunit IIC NF011649.1 PRK15067 PRK15067.1 554 554 461 subfamily Y Y N ethanolamine ammonia-lyase subunit EutB eutB 4.3.1.7 2 Bacteria superkingdom 19096 NCBI Protein Cluster (PRK) ethanolamine ammonia lyase large subunit ethanolamine ammonia-lyase subunit EutB Catalyzes the formation of acetaldehyde and ammonia from ethanolamine NF011650.0 PRK15068 PRK15068.1 209 209 324 equivalog Y Y N tRNA 5-methoxyuridine(34)/uridine 5-oxyacetic acid(34) synthase CmoB cmoB 2.5.1.- GO:0002098,GO:0016765 2 Bacteria superkingdom 15864 NCBI Protein Cluster (PRK) tRNA mo(5)U34 methyltransferase tRNA 5-methoxyuridine(34)/uridine 5-oxyacetic acid(34) synthase CmoB NF011652.1 PRK15070 PRK15070.1 209 209 185 subfamily Y Y N phosphate propanoyltransferase pduL 2.3.1.222 17158662,25962918 2 Bacteria superkingdom 8648 NCBI Protein Cluster (PRK) propanediol utilization phosphotransacylase phosphate propanoyltransferase Catalyzes the formation of propionyl phosphate from propionyl-CoA in propanediol degradation NF011654.0 PRK15072 PRK15072.1 430 430 404 subfamily Y Y N D-galactonate dehydratase family protein 2 Bacteria superkingdom 12107 NCBI Protein Cluster (PRK) bifunctional D-altronate/D-mannonate dehydratase D-galactonate dehydratase family protein NF011660.0 PRK15080 PRK15080.1 182 182 277 equivalog Y Y N ethanolamine utilization protein EutJ eutJ GO:0005515,GO:0051301 2 Bacteria superkingdom 4769 NCBI Protein Cluster (PRK) ethanolamine utilization protein EutJ ethanolamine utilization protein EutJ NF011663.0 PRK15083 PRK15083.1 589 589 639 subfamily Y Y N PTS mannitol transporter subunit IICBA 2.7.1.197 GO:0009401,GO:0022872 2 Bacteria superkingdom 15722 NCBI Protein Cluster (PRK) PTS system mannitol-specific transporter subunit IICBA PTS mannitol transporter subunit IICBA Involved in the phosphorylation and transport of sugars across the cell membrane; protein IIA transfers a phosphoryl group to IIB which then transfers the phosphoryl group to the sugar; IIC forms the translocation channel for the sugar uptake NF011666.0 PRK15086 PRK15086.1-2 482 482 364 subfamily Y Y N ethanolamine utilization protein EutH eutH 2 Bacteria superkingdom 1685 NCBI Protein Cluster (PRK) ethanolamine utilization protein EutH ethanolamine utilization protein EutH NF011667.0 PRK15086 PRK15086.1-3 387 387 362 equivalog Y Y N ethanolamine utilization protein EutH eutH 2 Bacteria superkingdom 2027 NCBI Protein Cluster (PRK) ethanolamine utilization protein EutH ethanolamine utilization protein EutH NF011668.0 PRK15086 PRK15086.1-4 575 575 413 equivalog Y Y N ethanolamine utilization protein EutH eutH 2 Bacteria superkingdom 1456 NCBI Protein Cluster (PRK) ethanolamine utilization protein EutH ethanolamine utilization protein EutH NF011678.0 PRK15098 PRK15098.1 666 666 765 equivalog Y Y N beta-glucosidase BglX bglX 3.2.1.21 GO:0004553,GO:0005975 2 Bacteria superkingdom 20633 NCBI Protein Cluster (PRK) beta-D-glucoside glucohydrolase beta-glucosidase BglX Catalyzes the hydrolysis of terminal beta-D-glucosyl residues NF011702.0 PRK15122 PRK15122.1 975 975 907 subfamily Y Y N magnesium-translocating P-type ATPase 7.2.2.14 2 Bacteria superkingdom 25301 NCBI Protein Cluster (PRK) magnesium-transporting ATPase magnesium-translocating P-type ATPase NF011709.0 PRK15130 PRK15130.1 218 218 186 equivalog Y Y N spermidine N1-acetyltransferase speG 2.3.1.57 GO:0008080 2 Bacteria superkingdom 3636 NCBI Protein Cluster (PRK) spermidine N1-acetyltransferase spermidine N1-acetyltransferase Catalyzes the formation of N(1)- and N(8)-acetylspermidine from spermidine NF011729.0 PRK15182 PRK15182.1 592 592 425 equivalog Y Y N Vi polysaccharide biosynthesis UDP-N-acetylglucosamine C-6 dehydrogenase TviB tviB GO:0000271,GO:0016491,GO:0051287 2 Bacteria superkingdom 5946 NCBI Protein Cluster (PRK) Vi polysaccharide biosynthesis protein TviB Vi polysaccharide biosynthesis UDP-N-acetylglucosamine C-6 dehydrogenase TviB With TviC is involved in the synthesis of the Vi antigen monomer NF011765.0 PRK15219 PRK15219.1 221 221 245 subfamily Y Y N carbonic anhydrase family protein GO:0004089 2 Bacteria superkingdom 3637 NCBI Protein Cluster (PRK) carbonic anhydrase carbonic anhydrase family protein NF011775.0 PRK15238 PRK15238.1 400 400 500 equivalog Y Y N glutamate/gamma-aminobutyrate family transporter YjeM yjeM GO:0022857 2 Bacteria superkingdom 6409 NCBI Protein Cluster (PRK) inner membrane transporter YjeM glutamate/gamma-aminobutyrate family transporter YjeM NF011924.1 PRK15395 PRK15395.1 420 420 329 equivalog Y Y N galactose/glucose ABC transporter substrate-binding protein MglB mglB GO:0030246 2 Bacteria superkingdom 2955 NCBI Protein Cluster (PRK) methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB galactose/glucose ABC transporter substrate-binding protein MglB With MglAC is involved in the transport of beta-methylgalactoside NF011925.1 PRK15396 PRK15396.1 108 108 78 subfamily Y Y N major outer membrane lipoprotein 2 Bacteria superkingdom 690 NCBI Protein Cluster (PRK) murein lipoprotein major outer membrane lipoprotein NF011927.0 PRK15398 PRK15398.1 403 403 465 subfamily Y Y N aldehyde dehydrogenase 1.2.1.- 2 Bacteria superkingdom 8173 NCBI Protein Cluster (PRK) aldehyde dehydrogenase EutE aldehyde dehydrogenase NF011930.0 PRK15401 PRK15401.1 267 267 214 equivalog Y Y N DNA oxidative demethylase AlkB alkB 1.14.11.33 2 Bacteria superkingdom 10661 NCBI Protein Cluster (PRK) alpha-ketoglutarate-dependent dioxygenase AlkB DNA oxidative demethylase AlkB Oxidative demethylase of N1-methyladenine or N3-methylcytosine DNA lesions NF011934.0 PRK15405 PRK15405.1 198 198 217 equivalog Y Y N ethanolamine utilization microcompartment protein EutL eutL GO:0005198,GO:0031469 2 Bacteria superkingdom 2562 NCBI Protein Cluster (PRK) ethanolamine utilization protein EutL ethanolamine utilization microcompartment protein EutL Carboxysome structural protein involved in ethanolamine utilization NF011937.0 PRK15408 PRK15408.1 384 384 340 equivalog Y Y N autoinducer 2 ABC transporter substrate-binding protein LsrB lsrB 7.6.2.- 2 Bacteria superkingdom 3450 NCBI Protein Cluster (PRK) autoinducer 2-binding protein lsrB autoinducer 2 ABC transporter substrate-binding protein LsrB With lsrACD is involved in the transport of autoinducer 2 into the cell NF011944.0 PRK15415 PRK15415.1 173 173 269 equivalog Y Y N propanediol utilization microcompartment protein PduB pduB GO:0005198,GO:0031469 2 Bacteria superkingdom 2277 NCBI Protein Cluster (PRK) propanediol utilization protein PduB propanediol utilization microcompartment protein PduB Carboxysome shell protein; may be involved in the formation of the polyhedral organelles involved in propanediol degradation NF011949.0 PRK15420 PRK15420.1 141 141 140 equivalog Y Y N L-fucose mutarotase fucU 5.1.3.29 GO:0016854,GO:0042354,GO:0042806 2 Bacteria superkingdom 2180 NCBI Protein Cluster (PRK) L-fucose mutarotase L-fucose mutarotase Catalyzes the interconversion of alpha-L-fucose to beta-L-fucose NF011964.0 PRK15435 PRK15435.1 345 345 354 equivalog Y Y N bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada ada 2.1.1.- GO:0003700,GO:0006281,GO:0006355 2 Bacteria superkingdom 15058 NCBI Protein Cluster (PRK) bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada Regulates genes involved in the repair of alkylated DNA; repairs DNA containing 6-O-methylguanine NF011969.0 PRK15441 PRK15441.1 127 127 93 equivalog Y Y N peptidylprolyl isomerase PpiC ppiC 5.2.1.8 2 Bacteria superkingdom 2095 NCBI Protein Cluster (PRK) peptidyl-prolyl cis-trans isomerase C peptidylprolyl isomerase PpiC NF011972.0 PRK15443 PRK15443.1-3 183 183 174 subfamily Y Y N diol dehydratase small subunit 2 Bacteria superkingdom 2196 NCBI Protein Cluster (PRK) propanediol dehydratase small subunit diol dehydratase small subunit NF011979.0 PRK15444 PRK15444.1 788 788 555 subfamily Y Y N propanediol/glycerol family dehydratase large subunit 2 Bacteria superkingdom 3599 NCBI Protein Cluster (PRK) propanediol dehydratase large subunit propanediol/glycerol family dehydratase large subunit NF011980.0 PRK15445 PRK15445.1 457 457 430 subfamily Y Y N arsenical efflux pump membrane protein ArsB arsB 2 Bacteria superkingdom 19560 NCBI Protein Cluster (PRK) arsenical pump membrane protein arsenical efflux pump membrane protein ArsB NF011981.0 PRK15446 PRK15446.1-2 375 375 378 equivalog Y Y N alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase phnM 3.6.1.63 GO:0016810,GO:0019700 2 Bacteria superkingdom 9350 NCBI Protein Cluster (PRK) phosphonate metabolism protein PhnM alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase NF011983.0 PRK15446 PRK15446.1-4 486 486 379 equivalog Y Y N alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase 3.6.1.63 GO:0016787,GO:0019700 2 Bacteria superkingdom 4494 NCBI Protein Cluster (PRK) phosphonate metabolism protein PhnM alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase NF011988.0 PRK15446 PRK15446.2-4 369 369 389 equivalog Y Y N alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase 3.6.1.63 2 Bacteria superkingdom 798 NCBI Protein Cluster (PRK) phosphonate metabolism protein PhnM alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase NF011989.0 PRK15446 PRK15446.2-5 565 565 385 equivalog Y Y N alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase 3.6.1.63 2 Bacteria superkingdom 460 NCBI Protein Cluster (PRK) phosphonate metabolism protein PhnM alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase NF011997.0 PRK15453 PRK15453.1 362 362 290 equivalog Y Y N phosphoribulokinase 2.7.1.19 GO:0005524,GO:0005975,GO:0008974 2 Bacteria superkingdom 7425 NCBI Protein Cluster (PRK) phosphoribulokinase phosphoribulokinase NF012012.0 PRK15468 PRK15468.1 123 123 111 subfamily Y Y N ethanolamine utilization microcompartment protein EutS eutS 2 Bacteria superkingdom 1855 NCBI Protein Cluster (PRK) carboxysome structural protein EutS ethanolamine utilization microcompartment protein EutS Involved in the degredation of ethanolamine NF012017.0 PRK15473 PRK15473.1 408 408 257 equivalog Y Y N cobalt-precorrin-4 methyltransferase 2.1.1.271 2 Bacteria superkingdom 1539 NCBI Protein Cluster (PRK) cobalt-precorrin-4 C(11)-methyltransferase cobalt-precorrin-4 methyltransferase Catalyzes the formation of cobalt-precorrin-5 from cobalt-precorrin-4 NF012018.0 PRK15474 PRK15474.1 133 133 97 equivalog Y Y N ethanolamine utilization microcompartment protein EutM eutM 2 Bacteria superkingdom 1451 NCBI Protein Cluster (PRK) carboxysome structural protein EutM ethanolamine utilization microcompartment protein EutM Involved in the degredation of ethanolamine NF012027.0 PRK15483 PRK15483.1 564 564 986 equivalog Y Y N type III restriction-modification system endonuclease GO:0003677,GO:0016788 2 Bacteria superkingdom 2499 NCBI Protein Cluster (PRK) type III restriction-modification system StyLTI enzyme res type III restriction-modification system endonuclease NF012029.0 PRK15485 PRK15485.1 303 303 225 equivalog Y Y N energy-coupling factor ABC transporter transmembrane protein 2 Bacteria superkingdom 1405 NCBI Protein Cluster (PRK) cobalt transport protein CbiQ energy-coupling factor ABC transporter transmembrane protein NF012099.1 SubclassA2 320 320 275 equivalog Y Y Y class A beta-lactamase, subclass A2 bla 3.5.2.6 GO:0008800 26511485 2 Bacteria superkingdom 2317 NCBIFAM SubclassA2: class A beta-lactamase, subclass A2 class A beta-lactamase, subclass A2 NF012153.1 tet_protect 775 775 614 equivalog Y Y Y tetracycline resistance ribosomal protection protein tet GO:0003924,GO:0005525 2 Bacteria superkingdom 3335 NCBIFAM ribo_protect_tet: tetracycline resistance ribosomal protection protein tetracycline resistance ribosomal protection protein NF012155.1 tet_protect_M 1420 1420 639 exception Y Y Y tetracycline resistance ribosomal protection protein Tet(M) tet(M) GO:0003924,GO:0005525 2 Bacteria superkingdom 926 NCBIFAM tet_M: tetracycline resistance ribosomal protection protein Tet(M) tetracycline resistance ribosomal protection protein Tet(M) NF012157.0 ANT_3pp_I 375 375 256 equivalog Y Y Y AadA family aminoglycoside 3''-O-nucleotidyltransferase 2 Bacteria superkingdom 940 NCBIFAM aadA: AadA family aminoglycoside 3''-O-nucleotidyltransferase ANT(3'')-I family aminoglycoside nucleotidyltransferase NF012161.0 bla_class_D_main 250 250 236 equivalog Y Y Y class D beta-lactamase blaOXA 3.5.2.6 GO:0008800,GO:0030655 2 Bacteria superkingdom 6240 NCBIFAM ClassD_main: class D beta-lactamase class D beta-lactamase NF012171.0 APH_6 325 325 270 equivalog Y Y Y APH(6)-I family aminoglycoside O-phosphotransferase 2 Bacteria superkingdom 978 NCBIFAM APH_6: APH(6)-I family aminoglycoside O-phosphotransferase APH(6)-I family aminoglycoside O-phosphotransferase Characterized members of this family are aminoglycoside 6-O-phosphotransferases, that is, streptomycin 6-kinase, EC 2.7.1.72 NF012174.0 tet_MFS_A_B_C_D 475 475 382 equivalog Y Y Y Tet(A)/Tet(B)/Tet(C) family tetracycline efflux MFS transporter tet GO:0008493,GO:0015904 2 Bacteria superkingdom 2595 NCBIFAM Tet(A)/Tet(B)/Tet(C) family tetracycline efflux MFS transporter Tet(A)/Tet(B)/Tet(C) family tetracycline efflux MFS transporter NF012175.1 tet_MFS_L_K_45 650 650 444 equivalog Y Y Y Tet(L)/Tet(K)/Tet(45) family tetracycline efflux MFS transporter tet GO:0008493,GO:0015904,GO:0022857,GO:0055085 2 Bacteria superkingdom 943 NCBIFAM Tet(L)/Tet(K)/Tet(45) family tetracycline efflux MFS transporter Tet(L)/Tet(K)/Tet(45) family tetracycline efflux MFS transporter NF012185.0 tet_MFS_L 925 925 457 exception Y Y Y tetracycline efflux MFS transporter Tet(L) tet(L) GO:0008493,GO:0015904 2 Bacteria superkingdom 285 NCBIFAM tetracycline efflux MFS transporter Tet(L) tetracycline efflux MFS transporter Tet(L) NF012191.0 tet_MFS_C 850 850 396 exception Y Y Y tetracycline efflux MFS transporter Tet(C) tet(C) GO:0008493,GO:0015904 2 Bacteria superkingdom 37 NCBIFAM tetracycline efflux MFS transporter Tet(C) tetracycline efflux MFS transporter Tet(C) NF012196.1 Ig_like_ice 50 40 108 domain Y Y N Ig-like domain-containing protein 2 Bacteria superkingdom 23050 NCBIFAM Ig-like domain Ig-like domain This variant form of the Ig-like domain occurs as a repeat in a number of large adhesins, including a 1.5-MDa ice-binding adhesin, the Marinomonas primoryensis antifreeze protein. NF012204.1 adhes_FxxPxG 60 60 153 domain Y Y N leukotoxin LktA family filamentous adhesin 2 Bacteria superkingdom 1059 NCBIFAM leukotoxin LktA family filamentous adhesin leukotoxin LktA family filamentous adhesin N-terminal domain This model, related to TIGR01901, describes a conserved single-copy N-terminal domain found in repeat-rich, extremely long proteins such as the leukotoxin LktA of Fusobacterium necrophorum. NF012206.1 LktA_tand_53 50 20 53 repeat Y N N tandem repeat-containing filamentous protein 2 Bacteria superkingdom 1487 NCBIFAM tandem repeat-containing filamentous protein leukotoxin LktA-type filamentous protein tandem repeat This repeat, about 53 amino acids in length, may comprise most of the length of proteins over 3000 amino acids long. The best characterized protein with this repeat is the leukotoxin LktA of Fusobacterium necrophorum, where it is the major virulence factor. NF012208.0 SDR_dihy_bifunc 325 325 233 exception Y Y N bifunctional dihydropteridine reductase/dihydrofolate reductase TmpR tmpR GO:0004146 2 Bacteria superkingdom 237 NCBIFAM bifunctional dihydropteridine reductase/dihydrofolate reductase TmpR bifunctional dihydropteridine reductase/dihydrofolate reductase TmpR Members of this family are SDR family oxidoreductases, unrelated to previously known families of dihydrofolate reductase (DHFR), one of which was demonstrated to be a bifunctional dihydropteridine reductase/dihydrofolate reductase. The DHFR activity can give a heterologously expressed protein the ability to confer resistance to trimethoprim, an inhibitor of most forms of DHFR. NF012209.1 LEPR-8K 17 15 24 domain Y Y N LEPR-XLL domain-containing protein 2 Bacteria superkingdom 1884 NCBIFAM LEPR-XLL domain-containing protein LEPR-XLL family repeat protein signature domain This model, just 24 amino acids long, describes an N-terminal single-copy region that contains the most highly conserved motif in a collection of repeat-filled giant proteins. Member proteins average over 8000 amino acids and include at least one longer than 35,000 in length. The signature motif is LEPRxLL NF012212.1 ANT_9 340 340 249 subfamily Y Y Y aminoglycoside nucleotidyltransferase ANT(9) ant(9) 2.7.7.- 37039640 2 Bacteria superkingdom 318 NCBIFAM aminoglycoside nucleotidyltransferase ANT(9) ANT(9) family aminoglycoside nucleotidyltransferase Members of this family modify position 9 on spectinomycin by nucleotidyltransferase activity. Proteins with activity often modify the 3'' site on streptomycin as well. NF012219.1 erm_C_23S_MT 530 530 244 exception Y Y Y 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(C) erm(C) 2.1.1.184 2492520 2 Bacteria superkingdom 132 NCBIFAM 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(C) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(C) NF012220.1 erm_B_23S_MT 525 525 245 exception Y Y Y 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) erm(B) 2 Bacteria superkingdom 443 NCBIFAM 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) NF012222.1 erm_A_23S_MT 475 475 243 exception Y Y Y 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A) erm(A) 2 Bacteria superkingdom 124 NCBIFAM 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A) NF012223.0 erm_F_23S_MT 575 575 266 exception Y Y Y 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(F) erm(F) 2 Bacteria superkingdom 118 NCBIFAM 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(F) 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(F) NF012229.1 bla_class_B_core 100 100 139 domain Y Y Y metallo-beta-lactamase bla 3.5.2.6 GO:0008800 2 Bacteria superkingdom 8493 NCBIFAM metallo-beta-lactamase metallo-beta-lactamase core region This HMM finds the region of greatest sequence conservation shared by metallo-beta-lactamases of subclasses B1, B2, and B3. Note that proteins matched well by this HMM should be Zn-dependent metallo-hydrolases, but are not necessarily active principally as beta-lactamases. NF012231.5 PF00001.26 7tm_1 30.5 30.5 260 subfamily Y Y N 7 transmembrane receptor GO:0004930,GO:0007186,GO:0016020 15774036 2 Bacteria superkingdom 36 EBI-EMBL 7 transmembrane receptor (rhodopsin family) 7 transmembrane receptor This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins [1]. [1]. 15774036. The opsins. Terakita A;. Genome Biol 2005;6:213. (from Pfam) NF012232.5 PF00002.29 7tm_2 20.6 20.6 250 subfamily Y Y N 7 transmembrane receptor GO:0004930,GO:0007186,GO:0016020 11790261 2 Bacteria superkingdom 15 EBI-EMBL 7 transmembrane receptor (Secretin family) 7 transmembrane receptor This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs). They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 (Swiss:P48960); calcium-independent receptors for latrotoxin (such as Swiss:O94910), and brain-specific angiogenesis inhibitors (such as Swiss:O14514) amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins (e.g. Swiss:P83119). Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling [1]. [1]. 11790261. Family-B G-protein-coupled receptors. Harmar AJ;. Genome Biol 2001;2:REVIEWS3013. (from Pfam) NF012247.5 PF00017.29 SH2 21 21 77 domain Y Y N SH2 domain-containing protein 2 Bacteria superkingdom 36 EBI-EMBL SH2 domain SH2 domain NF012248.5 PF00018.33 SH3_1 22.9 22.9 48 domain Y Y N SH3 domain-containing protein GO:0005515 12169629 2 Bacteria superkingdom 784 EBI-EMBL SH3 domain SH3 domain SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase Swiss:P12931. The structure is a partly opened beta barrel. [1]. 12169629. Diverse recognition of non-PxxP peptide ligands by the SH3 domains from p67(phox), Grb2 and Pex13p. Kami K, Takeya R, Sumimoto H, Kohda D;. EMBO J 2002;21:4268-4276. (from Pfam) NF012256.5 PF00026.28 Asp 19.9 19.9 315 domain Y Y N pepsin-like aspartyl protease 2 Bacteria superkingdom 734 EBI-EMBL Eukaryotic aspartyl protease pepsin-like aspartyl protease Aspartyl (acid) proteases include pepsins, cathepsins, and renins. Two-domain structure, probably arising from ancestral duplication. This family does not include the retroviral nor retrotransposon proteases (Pfam:PF00077), which are much smaller and appear to be homologous to a single domain of the eukaryotic asp proteases. (from Pfam) NF012268.5 PF00038.26 Filament 40 40 313 domain Y N N Intermediate filament protein 8771189 2 Bacteria superkingdom 53 EBI-EMBL Intermediate filament protein Intermediate filament protein NF012276.5 PF00046.34 Homeodomain 22.9 22.9 57 domain Y Y N homeobox domain-containing protein GO:0003677 1357790 2 Bacteria superkingdom 61 EBI-EMBL Homeodomain Homeodomain NF012288.5 PF00058.22 Ldl_recept_b 21 21 42 repeat Y N N Low-density lipoprotein receptor repeat class B 6091915,9790844 2 Bacteria superkingdom 123 EBI-EMBL Low-density lipoprotein receptor repeat class B Low-density lipoprotein receptor repeat class B This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure [2]. [1]. 6091915. The human LDL receptor: a cysteine-rich protein with multiple Alu sequences in its mRNA. Yamamoto T, Davis CG, Brown MS, Schneider WJ, Casey ML, Goldstein JL, Russell DW;. Cell 1984;39:27-38. [2]. 9790844. An Extracellular beta-Propeller Module Predicted in Lipoprotein and Scavenger Receptors, Tyrosine Kinases, Epidermal Growth Factor Precursor, and Extracellular Matrix Components. Springer TA;. J Mol Biol 1998;283:837-862. (from Pfam) NF012291.5 PF00061.28 Lipocalin 23 23 145 domain Y Y N lipocalin/fatty-acid binding family protein 2 Bacteria superkingdom 12180 EBI-EMBL Lipocalin / cytosolic fatty-acid binding protein family lipocalin/fatty-acid binding family protein Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel. (from Pfam) NF012297.5 PF00068.24 Phospholip_A2_1 32.1 32.1 110 domain Y Y N phospholipase A2 family protein GO:0004623,GO:0006644,GO:0050482 2 Bacteria superkingdom 342 EBI-EMBL Phospholipase A2 phospholipase A2 family protein Phospholipase A2 releases fatty acids from the second carbon group of glycerol. Perhaps the best known members are secreted snake venoms, but also found in secreted pancreatic and membrane-associated forms. Structure is all-alpha, with two core disulfide-linked helices and a calcium-binding loop. This alignment represents the major family of PLA2s. A second minor family, defined by the honeybee venom PLA2 PDB:1POC and related sequences from Gila monsters (Heloderma), is not recognised. This minor family conserves the core helix pair but is substantially different elsewhere. The PROSITE pattern PA2_HIS, specific to the first core helix, recognises both families. (from Pfam) NF012315.5 PF00086.23 Thyroglobulin_1 20.6 20.6 67 domain Y Y N thyroglobulin type-1 repeat-containing protein 10022822,8797845 2 Bacteria superkingdom 21 EBI-EMBL Thyroglobulin type-1 repeat Thyroglobulin type-1 repeat Thyroglobulin type 1 repeats are thought to be involved in the control of proteolytic degradation [2]. The domain usually contains six conserved cysteines. These form three disulphide bridges. Cysteines 1 pairs with 2, 3 with 4 and 5 with 6. [1]. 10022822. Crystal structure of MHC class II-associated p41 Ii fragment bound to cathepsin L reveals the structural basis for differentiation between cathepsins L and S. Guncar G, Pungercic G, Klemencic I, Turk V, Turk D;. EMBO J 1999;18:793-803. [2]. 8797845. Characterization of the type-1 repeat from thyroglobulin, a cysteine- rich module found in proteins from different families. Molina F, Bouanani M, Pau B, Granier C;. Eur J Biochem 1996;240:125-133. (from Pfam) NF012329.5 PF00101.25 RuBisCO_small 27 27 97 domain Y Y N ribulose bisphosphate carboxylase small subunit 2 Bacteria superkingdom 5471 EBI-EMBL Ribulose bisphosphate carboxylase, small chain ribulose bisphosphate carboxylase small subunit NF012352.5 PF00124.24 Photo_RC 27 27 260 domain Y N N Photosynthetic reaction centre protein GO:0009772,GO:0019684,GO:0045156 6392571 2 Bacteria superkingdom 5578 EBI-EMBL Photosynthetic reaction centre protein Photosynthetic reaction centre protein NF012367.5 PF00140.25 Sigma70_r1_2 22 22 34 domain Y Y N sigma-70 factor domain-containing protein GO:0003677,GO:0003700,GO:0006352,GO:0006355,GO:0016987 8858155 2 Bacteria superkingdom 111637 EBI-EMBL Sigma-70 factor, region 1.2 Sigma-70 factor, region 1.2 NF012374.5 PF00147.23 Fibrinogen_C 22 22 221 domain Y Y N fibrinogen-related protein 9333233 2 Bacteria superkingdom 637 EBI-EMBL Fibrinogen beta and gamma chains, C-terminal globular domain fibrinogen beta/gamma C-terminal-like domain NF012380.5 PF00153.32 Mito_carr 22.3 22.3 96 domain Y Y N MC/SLC25 family protein 11083877,24745987 2 Bacteria superkingdom 125 EBI-EMBL Mitochondrial carrier protein MC/SLC25 family protein NF012384.5 PF00157.22 Pou 27 27 72 PfamEq Y N N Pou domain - N-terminal to homeobox domain GO:0003700,GO:0006355 2 Bacteria superkingdom 20 EBI-EMBL Pou domain - N-terminal to homeobox domain Pou domain - N-terminal to homeobox domain NF012388.5 PF00161.24 RIP 21 21 197 domain Y Y N ribosome-inactivating family protein GO:0017148,GO:0030598 27754366,27886256 2 Bacteria superkingdom 2834 EBI-EMBL Ribosome inactivating protein ribosome-inactivating family protein NF012394.5 PF00167.23 FGF 24 24 124 domain Y Y N fibroblast growth factor GO:0008083 11276432,7583099 2 Bacteria superkingdom 6 EBI-EMBL Fibroblast growth factor fibroblast growth factor Fibroblast growth factors are a family of proteins involved in growth and differentiation in a wide range of contexts. They are found in a wide range of organisms, from nematodes to humans [2]. Most share an internal core region of high similarity, conserved residues in which are involved in binding with their receptors. On binding, they cause dimerisation of their tyrosine kinase receptors leading to intracellular signalling. There are currently four known tyrosine kinase receptors for fibroblast growth factors. These receptors can each bind several different members of this family. Members of this family have a beta trefoil structure. Most have N-terminal signal peptides and are secreted. A few lack signal sequences but are secreted anyway; still others also lack the signal peptide but are found on the cell surface and within the extracellular matrix. A third group remain intracellular [2]. They have central roles in development, regulating cell proliferation, migration and differentiation. On the other hand, they are important in tissue repair following injury in adult organisms [2]. [1]. 7583099. Functions of fibroblast growth factors and their receptors. Wilkie AOM, Morriss-Kay GM, Jones EY, Heath JK;. Curr Biol 1995;5:500-507. [2]. 11276432. Fibroblast growth factors. Ornitz DM, Itoh N;. Genome Biol 2001;2:REVIEWS3005. (from Pfam) NF012409.5 PF00182.24 Glyco_hydro_19 25.5 25.5 232 domain Y Y N glycoside hydrolase family 19 protein GO:0004568,GO:0006032,GO:0016998 2 Bacteria superkingdom 34231 EBI-EMBL Chitinase class I glycoside hydrolase family 19 protein NF012418.5 PF00191.25 Annexin 25 25 66 domain Y N N Annexin GO:0005509,GO:0005544 10220891,15059252 2 Bacteria superkingdom 264 EBI-EMBL Annexin Annexin This family of annexins also includes giardin that has been shown to function as an annexin [1]. [1]. 10220891. Functional identification of alpha 1-giardin as an annexin of Giardia lamblia. Bauer B, Engelbrecht S, Bakker-Grunwald T, Scholze H;. FEMS Microbiol Lett 1999;173:147-153. [2]. 15059252. The annexins. Moss SE, Morgan RO;. Genome Biol 2004;5:219. (from Pfam) NF012420.5 PF00194.26 Carb_anhydrase 27 27 254 domain Y Y N carbonic anhydrase family protein 2 Bacteria superkingdom 15418 EBI-EMBL Eukaryotic-type carbonic anhydrase carbonic anhydrase family protein NF012421.5 PF00195.24 Chal_sti_synt_N 27 27 225 domain Y N N Chalcone and stilbene synthases, N-terminal domain 10426957 2 Bacteria superkingdom 39289 EBI-EMBL Chalcone and stilbene synthases, N-terminal domain Chalcone and stilbene synthases, N-terminal domain The C-terminal domain of Chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase. The differences in activity are accounted for by differences in this N-terminal domain. [1]. 10426957. Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis. Ferrer JL, Jez JM, Bowman ME, Dixon RA, Noel JP;. Nat Struct Biol 1999;6:775-784. (from Pfam) NF012423.5 PF00197.23 Kunitz_legume 25.9 25.9 176 domain Y Y N Kunitz family serine protease inhibitor GO:0004866 2 Bacteria superkingdom 62 EBI-EMBL Trypsin and protease inhibitor Kunitz family serine protease inhibitor NF012443.5 PF00217.24 ATP-gua_Ptrans 22.4 22.4 203 PfamEq Y N N ATP:guanido phosphotransferase, C-terminal catalytic domain GO:0016301,GO:0016772 8692275 2 Bacteria superkingdom 7894 EBI-EMBL ATP:guanido phosphotransferase, C-terminal catalytic domain ATP:guanido phosphotransferase, C-terminal catalytic domain The substrate binding site is located in the cleft between N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain. [1]. 8692275. Structure of mitochondrial creatine kinase. Fritz-Wolf K, Schnyder T, Wallimann T, Kabsch W;. Nature 1996;381:341-345. (from Pfam) NF012448.5 PF00223.24 PsaA_PsaB 23.3 23.3 711 subfamily Y N N Photosystem I psaA/psaB protein GO:0009579,GO:0015979,GO:0016020 2 Bacteria superkingdom 2006 EBI-EMBL Photosystem I psaA/psaB protein Photosystem I psaA/psaB protein NF012458.5 PF00233.24 PDEase_I 24.8 24.8 238 PfamEq Y N N 3'5'-cyclic nucleotide phosphodiesterase GO:0004114,GO:0007165 2 Bacteria superkingdom 168 EBI-EMBL 3'5'-cyclic nucleotide phosphodiesterase 3'5'-cyclic nucleotide phosphodiesterase NF012460.5 PF00235.24 Profilin 25 25 127 PfamEq Y Y N profilin family protein GO:0003779 8078936,8771785 2 Bacteria superkingdom 219 EBI-EMBL Profilin profilin family protein NF012480.5 PF00257.24 Dehydrin 30.6 30.6 154 PfamEq Y N N Dehydrin GO:0009415 2 Bacteria superkingdom 28 EBI-EMBL Dehydrin Dehydrin NF012485.5 PF00263.26 Secretin 27.5 27.5 169 domain Y N N Bacterial type II and III secretion system protein GO:0009306 2 Bacteria superkingdom 119341 EBI-EMBL Bacterial type II and III secretion system protein Bacterial type II and III secretion system protein NF012491.5 PF00269.25 SASP 22 22 59 subfamily Y Y N small, acid-soluble spore protein, alpha/beta type GO:0003690,GO:0006265 2 Bacteria superkingdom 16578 EBI-EMBL Small, acid-soluble spore proteins, alpha/beta type small, acid-soluble spore protein, alpha/beta type NF012501.5 PF00280.23 potato_inhibit 24.5 24.5 64 PfamEq Y N N Potato inhibitor I family GO:0004867,GO:0009611 2 Bacteria superkingdom 650 EBI-EMBL Potato inhibitor I family Potato inhibitor I family NF012504.5 PF00283.24 Cytochrom_B559 30 30 29 domain Y N N Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits GO:0015979 2 Bacteria superkingdom 878 EBI-EMBL Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits NF012505.5 PF00284.25 Cytochrom_B559a 25 25 39 PfamEq Y N N Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit GO:0009523,GO:0015979,GO:0016020,GO:0046872 2 Bacteria superkingdom 508 EBI-EMBL Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit This family is the lumenal portion of cytochrome b559 alpha chain, matches to this family should be accompanied by a match to the Pfam:PF00283 family also. The Prosite pattern pattern matches the transmembrane region of the cytochrome b559 alpha and beta subunits. (from Pfam) NF012526.5 PF00305.24 Lipoxygenase 23.6 23.6 673 domain Y Y N lipoxygenase family protein GO:0016702,GO:0046872 2 Bacteria superkingdom 2258 EBI-EMBL Lipoxygenase lipoxygenase family protein NF012530.5 PF00309.25 Sigma54_AID 23.8 23.8 46 domain Y N N Sigma-54 factor, Activator interacting domain (AID) GO:0001216,GO:0016987 11544185 2 Bacteria superkingdom 48242 EBI-EMBL Sigma-54 factor, Activator interacting domain (AID) Sigma-54 factor, Activator interacting domain (AID) The sigma-54 holoenzyme is an enhancer dependent form of the RNA polymerase. The AID is necessary for activator interaction [1]. In addition, the AID also inhibits transcription initiation in the sigma-54 holoenzyme prior to interaction with the activator [1]. [1]. 11544185. Binding of transcriptional activators to sigma 54 in the presence of the transition state analog ADP-aluminum fluoride: insights into activator mechanochemical action. Chaney M, Grande R, Wigneshweraraj SR, Cannon W, Casaz P, Gallegos MT, Schumacher J, Jones S, Elderkin S, Dago AE, Morett E, Buck M;. Genes Dev 2001;15:2282-2294. (from Pfam) NF012548.5 PF00328.27 His_Phos_2 23.6 23.6 354 domain Y Y N histidine-type phosphatase 10329192,18092946 2 Bacteria superkingdom 21447 EBI-EMBL Histidine phosphatase superfamily (branch 2) histidine-type phosphatase The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle. Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue. Structure and sequence analyses show that different families contribute different additional residues to the 'phosphate pocket' and, more surprisingly, differ in the position, in sequence and in three dimensions, of a catalytically essential acidic residue. The superfamily may be divided into two main branches.The smaller branch 2 contains predominantly eukaryotic proteins. The catalytic functions in members include phytase, glucose-1-phosphatase and multiple inositol polyphosphate phosphatase. The in vivo roles of the mammalian acid phosphatases in branch 2 are not fully understood, although activity against lysophosphatidic acid and tyrosine-phosphorylated proteins has been demonstrated. [1]. 10329192. Crystal structure of Aspergillus niger pH 2.5 acid phosphatase at 2.4 A resolution. Kostrewa D, Wyss M, D'Arcy A, van Loon AP;. J Mol Biol 1999;288:965-974. [2]. 18092946. The histidine phosphatase superfamily: structure and function. Rigden DJ;. Biochem J. 2008;409:333-348. (from Pfam) NF012569.5 PF00349.26 Hexokinase_1 24.3 24.3 201 domain Y N N Hexokinase GO:0005524,GO:0005975,GO:0016773 5133118,7001032 2 Bacteria superkingdom 1155 EBI-EMBL Hexokinase Hexokinase Hexokinase (EC:2.7.1.1) contains two structurally similar domains represented by this family and Pfam:PF03727. Some members of the family have two copies of each of these domains. [1]. 7001032. Structure of a complex between yeast hexokinase A and glucose. II. Detailed comparisons of conformation and active site configuration with the native hexokinase B monomer and dimer. Bennett WS Jr, Steitz TA;. J Mol Biol 1980;140:211-230. [2]. 5133118. Structure of yeast hexokinase-B. I. Preliminary x-ray studies and subunit structure. Steitz TA;. J Mol Biol 1971;61:695-700. (from Pfam) NF012571.5 PF00351.26 Biopterin_H 22.7 22.7 331 PfamEq Y N N Biopterin-dependent aromatic amino acid hydroxylase GO:0016714 1655752,3475690,8108417,9406548 2 Bacteria superkingdom 19854 EBI-EMBL Biopterin-dependent aromatic amino acid hydroxylase Biopterin-dependent aromatic amino acid hydroxylase This family includes phenylalanine-4-hydroxylase, the phenylketonuria disease protein. [1]. 3475690. Full-length cDNA for rabbit tryptophan hydroxylase: functional domains and evolution of aromatic amino acid hydroxylases. Grenett HE, Ledley FD, Reed LL, Woo SL;. Proc Natl Acad Sci U S A 1987;84:5530-5534. [2]. 1655752. Cloning and expression of Chromobacterium violaceum phenylalanine hydroxylase in Escherichia coli and comparison of amino acid sequence with mammalian aromatic amino acid hydroxylases. Onishi A, Liotta LJ, Benkovic SJ;. J Biol Chem 1991;266:18454-18459. [3]. 8108417. Pseudomonas aeruginosa possesses homologues of mammalian phenylalanine hydroxylase and 4 alpha-carbinolamine dehydratase/DCoH as part of a three-component gene cluster. Zhao G, Xia T, Song J, Jensen RA;. Proc Natl Acad Sci U S A 1994;91:1366-1370. [4]. 9406548. Crystal structure of the catalytic domain of human phenylalanine hydroxylase reveals the structural basis for phenylketonuria. Erlandsen H, Fusetti F, Martinez A, Hough E, Flatmark T, Stevens RC;. Nat Struct Biol 1997;4:995-1000. (from Pfam) NF012576.5 PF00356.26 LacI 27 27 46 domain Y Y N LacI family DNA-binding transcriptional regulator GO:0003677,GO:0006355 2 Bacteria superkingdom 700814 EBI-EMBL Bacterial regulatory proteins, lacI family LacI family DNA-binding transcriptional regulator NF012578.5 PF00358.25 PTS_EIIA_1 27.2 27.2 127 domain Y Y N PTS glucose transporter subunit IIA GO:0009401 2 Bacteria superkingdom 102819 EBI-EMBL phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 PTS glucose transporter subunit IIA NF012580.5 PF00360.25 PHY 27 27 183 domain Y N N Phytochrome region GO:0006355,GO:0009584 18799745 2 Bacteria superkingdom 20902 EBI-EMBL Phytochrome region Phytochrome region Phytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarities are low, this domain is structurally related to Pfam:PF01590 [1], which is generally located immediately N-terminal to this domain. Compared with Pfam:PF01590, this domain carries an additional tongue-like hairpin loop between the fifth beta-sheet and the sixth alpha-helix which functions to seal the chromophore pocket and stabilise the photoactivated far-red-absorbing state (Pfr) [1]. The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue [1]. [1]. 18799745. The structure of a complete phytochrome sensory module in the Pr ground state. Essen LO, Mailliet J, Hughes J;. Proc Natl Acad Sci U S A. 2008;105:14709-14714. (from Pfam) NF012587.5 PF00367.25 PTS_EIIB 27 27 34 domain Y Y N PTS transporter subunit EIIB GO:0008982 2 Bacteria superkingdom 180400 EBI-EMBL phosphotransferase system, EIIB PTS transporter subunit EIIB NF012590.5 PF00372.24 Hemocyanin_M 20.8 20.8 268 PfamEq Y N N Hemocyanin, copper containing domain 2341396,2808410,8518732 2 Bacteria superkingdom 155 EBI-EMBL Hemocyanin, copper containing domain Hemocyanin, copper containing domain This family includes arthropod hemocyanins and insect larval storage proteins. Contains some proteins not known to be hemocyanins, but are clearly similar. [1]. 2341396. Molecular cloning, regulation, and complete sequence of a hemocyanin-related, juvenile hormone-suppressible protein from insect hemolymph. Jones G, Brown N, Manczak M, Hiremath S, Kafatos FC;. J Biol Chem 1990;265:8596-8602. [2]. 2808410. cDNA and gene sequence of Manduca sexta arylphorin, an aromatic amino acid-rich larval serum protein. Homology to arthropod hemocyanins. Willott E, Wang XY, Wells MA;. J Biol Chem 1989;264:19052-19059. [3]. 8518732. Crystal structure of deoxygenated Limulus polyphemus subunit II hemocyanin at 2.18 A resolution: clues for a mechanism for allosteric regulation. Hazes B, Magnus KA, Bonaventura C, Bonaventura J, Dauter Z, Kalk KH, Hol WG;. Protein Sci 1993;2:597-619. (from Pfam) NF012597.5 PF00379.28 Chitin_bind_4 21.5 21.5 53 domain Y Y N chitin-binding domain-containing protein GO:0042302 11520687 2 Bacteria superkingdom 36 EBI-EMBL Insect cuticle protein Insect cuticle protein Many insect cuticular proteins include a 35-36 amino acid motif known as the R&R consensus. The extensive conservation of this region led to the suggestion that it functions to bind chitin. Provocatively, it has no sequence similarity to the well-known cysteine-containing chitin-binding domain found in chitinases and some peritrophic membrane proteins. Chitin binding has been shown experimentally for this region [1]. Thus arthropods have two distinct classes of chitin binding proteins, those with the chitin-binding domain found in lectins, chitinases and peritrophic membranes (cysCBD) and those with the cuticular protein chitin-binding domain (non-cysCBD) [1]. [1]. 11520687. A conserved domain in arthropod cuticular proteins binds chitin. Rebers JE, Willis JH;. Insect Biochem Mol Biol 2001;31:1083-1093. (from Pfam) NF012613.5 PF00395.25 SLH 20.8 14.5 44 domain Y Y N S-layer homology domain-containing protein 10970841 2 Bacteria superkingdom 141424 EBI-EMBL S-layer homology domain S-layer homology domain NF012619.5 PF00401.25 ATP-synt_DE 24.6 24.6 47 domain Y Y N ATP synthase delta/epsilon chain alpha-helix domain-containing protein 9331422 2 Bacteria superkingdom 16496 EBI-EMBL ATP synthase, Delta/Epsilon chain, long alpha-helix domain ATP synthase, Delta/Epsilon chain, long alpha-helix domain Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. This subunit is called epsilon in bacteria and delta in mitochondria. In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP (Pfam:PF00213). This entry includes the epsilon subunit from bacteria and plants. [1]. 9331422. Crystal structure of the epsilon subunit of the proton-translocating ATP synthase from Escherichia coli. Uhlin U, Cox GB, Guss JM;. Structure 1997;5:1219-1230. (from Pfam) NF012625.5 PF00407.24 Bet_v_1 22.4 22.4 151 PfamEq Y N N Pathogenesis-related protein Bet v 1 family GO:0006952 15447655,18922149,9417891,9874249 2 Bacteria superkingdom 147 EBI-EMBL Pathogenesis-related protein Bet v 1 family Pathogenesis-related protein Bet v 1 family This family is named after Bet v 1, the major birch pollen allergen. This protein belongs to family 10 of plant pathogenesis-related proteins (PR-10), cytoplasmic proteins of 15-17 kd that are wide-spread among dicotyledonous plants [1]. In recent years, a number of diverse plant proteins with low sequence similarity to Bet v 1 was identified. A classification by sequence similarity yielded several subfamilies related to PR-10 [2]: - Pathogenesis-related proteins PR-10: These proteins were identified as major tree pollen allergens in birch and related species (hazel, alder), as plant food allergens expressed in high levels in fruits, vegetables and seeds (apple, celery, hazelnut), and as pathogenesis-related proteins whose expression is induced by pathogen infection, wounding, or abiotic stress. Hyp-1 (Swiss:Q8H1L1), an enzyme involved in the synthesis of the bioactive naphthodianthrone hypericin in St. John's wort (Hypericum perforatum) also belongs to this family. Most of these proteins were found in dicotyledonous plants. In addition, related sequences were identified in monocots and conifers. - Cytokinin-specific binding proteins: These legume proteins bind cytokinin plant hormones [3]. - (S)-Norcoclaurine synthases are enzymes catalysing the condensation of dopamine and 4-hydroxyphenylacetaldehyde to (S)-norcoclaurine, the first committed step in the biosynthesis of benzylisoquinoline alkaloids such as morphine [4]. -Major latex proteins and ripening-related proteins are proteins of unknown biological function that were first discovered in the latex of opium poppy (Papaver somniferum) and later found to be upregulated. TRUNCATED at 1650 bytes (from Pfam) NF012637.5 PF00421.24 PSII 25 25 500 domain Y N N Photosystem II protein GO:0009521,GO:0009767,GO:0016020,GO:0016168,GO:0019684 2 Bacteria superkingdom 3000 EBI-EMBL Photosystem II protein Photosystem II protein NF012642.5 PF00427.26 PBS_linker_poly 28.7 28.7 126 domain Y Y N phycobilisome rod-core linker polypeptide GO:0015979,GO:0030089 2 Bacteria superkingdom 5848 EBI-EMBL Phycobilisome Linker polypeptide phycobilisome rod-core linker polypeptide NF012657.5 PF00443.34 UCH 23.9 23.9 254 domain Y N N Ubiquitin carboxyl-terminal hydrolase GO:0004843,GO:0016579 2 Bacteria superkingdom 364 EBI-EMBL Ubiquitin carboxyl-terminal hydrolase Ubiquitin carboxyl-terminal hydrolase NF012658.5 PF00444.23 Ribosomal_L36 26.1 26.1 38 domain Y Y N 50S ribosomal protein L36 GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 10535 EBI-EMBL Ribosomal protein L36 50S ribosomal protein L36 NF012659.5 PF00445.23 Ribonuclease_T2 26 26 188 subfamily Y Y N ribonuclease T2 family protein GO:0003723,GO:0033897 8551522 2 Bacteria superkingdom 15358 EBI-EMBL Ribonuclease T2 family ribonuclease T2 family protein NF012667.5 PF00453.23 Ribosomal_L20 30.8 30.8 107 PfamEq Y Y N 50S ribosomal protein L20 GO:0003735,GO:0005840,GO:0006412,GO:0019843 2 Bacteria superkingdom 27585 EBI-EMBL Ribosomal protein L20 50S ribosomal protein L20 NF012668.5 PF00454.32 PI3_PI4_kinase 27.1 27.1 241 PfamEq Y N N Phosphatidylinositol 3- and 4-kinase 12456783,12471243 2 Bacteria superkingdom 710 EBI-EMBL Phosphatidylinositol 3- and 4-kinase Phosphatidylinositol 3- and 4-kinase Some members of this family probably do not have lipid kinase activity and are protein kinases, e.g. Swiss:P42345 [1]. [1]. 12456783. Elucidating TOR signaling and rapamycin action: lessons from Saccharomyces cerevisiae. Crespo JL, Hall MN;. Microbiol Mol Biol Rev 2002;66:579-591. [2]. 12471243. The protein kinase complement of the human genome. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S;. Science 2002;298:1912-1934. (from Pfam) NF012674.5 PF00460.25 Flg_bb_rod 20.7 20.7 31 domain Y Y N flagellar basal body protein GO:0071973 2 Bacteria superkingdom 170733 EBI-EMBL Flagella basal body rod protein flagellar basal body protein N-terminal domain NF012681.5 PF00468.22 Ribosomal_L34 25 25 44 PfamEq Y Y N 50S ribosomal protein L34 GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 13464 EBI-EMBL Ribosomal protein L34 50S ribosomal protein L34 NF012683.5 PF00471.25 Ribosomal_L33 25 25 47 domain Y Y N 50S ribosomal protein L33 GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 23833 EBI-EMBL Ribosomal protein L33 50S ribosomal protein L33 NF012684.5 PF00472.25 RF-1 35 35 116 domain Y Y N peptide chain release factor-like protein GO:0003747,GO:0006415 10676813 2 Bacteria superkingdom 151999 EBI-EMBL RF-1 domain RF-1 domain This domain is found in peptide chain release factors such as RF-1 (Swiss:P07011) and RF-2 (Swiss:P07012), and a number of smaller proteins of unknown function such as Swiss:P40711. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis. [1]. 10676813. The crystal structure of human eukaryotic release factor eRF1--mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. Song H, Mugnier P, Das AK, Webb HM, Evans DR, Tuite MF, Hemmings BA, Barford D;. Cell 2000;100:311-321. (from Pfam) NF012691.5 PF00479.27 G6PD_N 22.1 22.1 183 domain Y N N Glucose-6-phosphate dehydrogenase, NAD binding domain GO:0006006,GO:0016614,GO:0050661 9485426 2 Bacteria superkingdom 74431 EBI-EMBL Glucose-6-phosphate dehydrogenase, NAD binding domain Glucose-6-phosphate dehydrogenase, NAD binding domain NF012698.5 PF00486.33 Trans_reg_C 26.2 26.2 77 domain Y Y N winged helix-turn-helix domain-containing protein GO:0000160,GO:0003677,GO:0006355 9016718,9350875 2 Bacteria superkingdom 998886 EBI-EMBL Transcriptional regulatory protein, C terminal OmpR family winged helix-turn-helix DNA-binding domain NF012714.5 PF00504.26 Chloroa_b-bind 22.3 22.3 162 domain Y Y N chlorophyll a/b-binding protein 2 Bacteria superkingdom 2937 EBI-EMBL Chlorophyll A-B binding protein chlorophyll a/b-binding protein NF012715.5 PF00505.24 HMG_box 25.4 25.4 69 domain Y N N HMG (high mobility group) box 2 Bacteria superkingdom 115 EBI-EMBL HMG (high mobility group) box HMG (high mobility group) box NF012719.5 PF00509.23 Hemagglutinin 31.8 31.8 550 domain Y Y N hemagglutinin GO:0019031,GO:0019064,GO:0046789 2 Bacteria superkingdom 39 EBI-EMBL Haemagglutinin hemagglutinin Haemagglutinin from influenza virus causes membrane fusion of the viral membrane with the host membrane. Fusion occurs after the host cell internalises the virus by endocytosis. The drop of pH causes release of a hydrophobic fusion peptide and a large conformational change leading to membrane fusion. (from Pfam) NF012726.5 PF00516.23 GP120 27 27 525 domain Y N N Envelope glycoprotein GP120 GO:0019031 9641677 2 Bacteria superkingdom 11 EBI-EMBL Envelope glycoprotein GP120 Envelope glycoprotein GP120 The entry of HIV requires interaction of viral GP120 with Swiss:P01730 and a chemokine receptor on the cell surface. [1]. 9641677. Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J, Hendrickson WA;. Nature 1998;393:648-659. (from Pfam) NF012729.5 PF00519.22 PPV_E1_C 26.5 26.5 289 domain Y N N Papillomavirus helicase GO:0003677,GO:0003678,GO:0005524,GO:0006260 10949036,15289463 2 Bacteria superkingdom 32 EBI-EMBL Papillomavirus helicase Papillomavirus helicase This is the C-terminal ATPase/helicase domain of Papillomavirus E1 protein, a DNA helicase that is required for initiation of viral DNA replication. This protein forms a complex with the E2 protein Pfam:PF00508 [1,2]. The domain architecture of E1 is similar to that of the SV40 T-antigen [1]. [1]. 15289463. The X-ray structure of the papillomavirus helicase in complex with its molecular matchmaker E2. Abbate EA, Berger JM, Botchan MR;. Genes Dev. 2004;18:1981-1996. [2]. 10949036. Crystal structure of the DNA binding domain of the replication initiation protein E1 from papillomavirus. Enemark EJ, Chen G, Vaughn DE, Stenlund A, Joshua-Tor L;. Mol Cell. 2000;6:149-158. (from Pfam) NF012739.5 PF00529.25 CusB_dom_1 26.2 26.2 80 domain Y Y N HlyD family secretion protein GO:0055085 11755084,12813074,15763404,19695261,22239833 2 Bacteria superkingdom 145488 EBI-EMBL Cation efflux system protein CusB domain 1 HlyD family secretion protein The cation efflux system protein CusB from E. coli can be divided into four different domains, the first three domains of the protein are mostly beta-strands and the fourth forms an all alpha-helical domain. This entry represents the first beta-domain (domain 1) of CusB and it is formed by the N and C-terminal ends of the polypeptide (residues 89-102 and 324-385) [1]. CusB is part of the copper-transporting efflux system CusCFBA [2]. This domain can also be found in other membrane-fusion proteins, such as HlyD, MdtN, MdtE and AaeA. HlyD is a component of the prototypical alpha-haemolysin (HlyA) bacterial type I secretion system, along with the other components HlyB and TolC. HlyD is anchored in the cytoplasmic membrane by a single transmembrane domain and has a large periplasmic domain within the carboxy-terminal 100 amino acids [3], HlyB and HlyD form a stable complex that binds the recombinant protein bearing a C-terminal HlyA signal sequence and ATP in the cytoplasm [4]. HlyD, HlyB and TolC combine to form the three-component ABC transporter complex that forms a trans-membrane channel or pore through which HlyA can be transferred directly to the extracellular medium. Cutinase has been shown to be transported effectively through this pore [5]. [1]. 19695261. Crystal structure of the membrane fusion protein CusB from Escherichia coli. Su CC, Yang F, Long F, Reyon D, Routh MD, Kuo DW, Mokhtari AK, Van Ornam JD, Rabe KL, Hoy JA, Lee YJ, Rajashankar KR, Yu EW;. J Mol Biol. 2009;393:342-355. [2]. 12813074. Molecular analysis of the copper-transporting efflux system CusCFBA of Escherichia coli. Franke S, Grass G, Rensing C, Ni. TRUNCATED at 1650 bytes (from Pfam) NF012742.5 PF00532.26 Peripla_BP_1 22.2 22.2 281 domain Y N N Periplasmic binding proteins and sugar binding domain of LacI family 1583688,8638105 2 Bacteria superkingdom 898091 EBI-EMBL Periplasmic binding proteins and sugar binding domain of LacI family Periplasmic binding proteins and sugar binding domain of LacI family This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (Pfam:PF00356). [1]. 1583688. 1.7 A X-ray structure of the periplasmic ribose receptor from Escherichia coli. Mowbray SL, Cole LB;. J Mol Biol 1992;225:155-175. [2]. 8638105. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Lewis M, Chang G, Horton NC, Kercher MA, Pace HC, Schumacher MA, Brennan RG, Lu P;. Science 1996;271:1247-1254. (from Pfam) NF012746.5 PF00536.36 SAM_1 23 23 64 domain Y N N SAM domain (Sterile alpha motif) GO:0005515 8528090,9007998,9886291 2 Bacteria superkingdom 4335 EBI-EMBL SAM domain (Sterile alpha motif) SAM domain (Sterile alpha motif) It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains. Discovery of sterile alpha motif. [1]. 8528090. SAM: a novel motif in yeast sterile and Drosophila polyhomeotic proteins. Ponting CP;. Protein Sci 1995;4:1928-1930. Extension of family. [2]. 9007998. SAM as a protein interaction domain involved in developmental regulation. Schultz J, Ponting CP, Hofmann K, Bork P;. Protein Sci 1997;6:249-253. [3]. 9886291. The crystal structure of an Eph receptor SAM domain reveals a mechanism for modular dimerization. Stapleton D, Balan I, Pawson T, Sicheri F;. Nat Struct Biol 1999;6:44-49. (from Pfam) NF012748.5 PF00538.24 Linker_histone 22.4 22.4 74 PfamEq Y Y N histone H1/H5 family protein GO:0000786,GO:0003677,GO:0006334 8384699 2 Bacteria superkingdom 31 EBI-EMBL linker histone H1 and H5 family histone H1/H5 family protein Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types. [1]. 8384699. Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Ramakrishnan V, Finch JT, Graziano V, Lee PL, Sweet RM;. Nature 1993;362:219-223. (from Pfam) NF012754.5 PF00544.24 Pectate_lyase_4 24 24 211 domain Y N N Pectate lyase 8502994 2 Bacteria superkingdom 30508 EBI-EMBL Pectate lyase Pectate lyase This enzyme forms a right handed beta helix structure. Pectate lyase is an enzyme involved in the maceration and soft rotting of plant tissue. [1]. 8502994. New domain motif: the structure of pectate lyase C, a secreted plant virulence factor. Yoder MD, Keen NT, Jurnak F;. Science 1993;260:1503-1507. (from Pfam) NF012761.5 PF00552.26 IN_DBD_C 21 21 45 domain Y N N Integrase DNA binding domain GO:0003676 7632683 2 Bacteria superkingdom 6 EBI-EMBL Integrase DNA binding domain Integrase DNA binding domain Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain Pfam:PF00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain [1]. [1]. 7632683. Solution structure of the DNA binding domain of HIV-1 integrase. Lodi PJ, Ernst JA, Kuszewski J, Hickman AB, Engelman A, Craigie R, Clore GM, Gronenborn AM;. Biochemistry 1995;34:9826-9833. (from Pfam) NF012765.5 PF00556.25 LHC 23 23 39 domain Y Y N light-harvesting protein GO:0016020,GO:0019684,GO:0030077,GO:0045156 8736556 2 Bacteria superkingdom 3620 EBI-EMBL Antenna complex alpha/beta subunit light-harvesting protein NF012767.5 PF00558.24 Vpu 24 24 81 PfamEq Y Y N Vpu GO:0005261,GO:0019076,GO:0032801,GO:0033644 7853484,9182993,9338017 2 Bacteria superkingdom 78 EBI-EMBL Vpu protein Vpu The Vpu protein contains an N-terminal transmembrane spanning region and a C-terminal cytoplasmic region. The HIV-1 Vpu protein stimulates virus production by enhancing the release of viral particles from infected cells. The VPU protein binds specifically to CD4. [1]. 9338017. Enhancement of retroviral production from packaging cell lines expressing the human immunodeficiency type 1 VPU gene. Kobinger GP, Mouland AJ, Lalonde JP, Forget J, Cohen EA;. Gene Ther 1997;4:868-874. [2]. 7853484. The human immunodeficiency virus type 1 Vpu protein specifically binds to the cytoplasmic domain of CD4: implications for the mechanism of degradation. Bour S, Schubert U, Strebel K;. J Virol 1995;69:1510-1520. [3]. 9182993. Secondary structure and tertiary fold of the human immunodeficiency virus protein U (Vpu) cytoplasmic domain in solution. Willbold D, Hoffmann S, Rosch P;. Eur J Biochem 1997;245:581-588. (from Pfam) NF012772.5 PF00563.25 EAL 31.3 31.3 236 domain Y Y N EAL domain-containing protein 11557134 2 Bacteria superkingdom 713566 EBI-EMBL EAL domain EAL domain This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues. The EAL domain is a good candidate for a diguanylate phosphodiesterase function [1]. The domain contains many conserved acidic residues that could participate in metal binding and might form the phosphodiesterase active site [1]. [1]. 11557134. Novel domains of the prokaryotic two-component signal transduction systems. Galperin MY, Nikolskaya AN, Koonin EV;. FEMS Microbiol Lett 2001;203:11-21. (from Pfam) NF012794.5 PF00585.23 Thr_dehydrat_C 27 27 91 PfamEq Y N N C-terminal regulatory domain of Threonine dehydratase 9562556 2 Bacteria superkingdom 39850 EBI-EMBL C-terminal regulatory domain of Threonine dehydratase C-terminal regulatory domain of Threonine dehydratase Threonine dehydratases Pfam:PF00291 all contain a carboxy terminal region. This region may have a regulatory role. Some members contain two copies of this region. This family is homologous to the Pfam:PF01842 domain. [1]. 9562556. Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase. Gallagher DT, Gilliland GL, Xiao G, Zondlo J, Fisher KE, Chinchilla D, Eisenstein E;. Structure 1998;6:465-475. (from Pfam) NF012816.5 PF00609.24 DAGK_acc 27 27 158 PfamEq Y N N Diacylglycerol kinase accessory domain GO:0004143,GO:0007200 2156169,2159661,2175712,8626538 2 Bacteria superkingdom 337 EBI-EMBL Diacylglycerol kinase accessory domain Diacylglycerol kinase accessory domain Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. This domain is assumed to be an accessory domain: its function is unknown. [1]. 2156169. Porcine diacylglycerol kinase sequence has zinc finger and E-F hand motifs. Sakane F, Yamada K, Kanoh H, Yokoyama C, Tanabe T;. Nature 1990;344:345-348. [2]. 8626538. Molecular cloning of a novel diacylglycerol kinase isozyme with a pleckstrin homology domain and a C-terminal tail similar to those of the EPH family of protein-tyrosine kinases. Sakane F, Imai S, Kai M, Wada I, Kanoh H;. J Biol Chem 1996;271:8394-8401. [3]. 2175712. Purification, cDNA-cloning and expression of human diacylglycerol kinase. Schaap D, de Widt J, van der Wal J, Vandekerckhove J, van Damme J, Gussow D, Ploegh HL, van Blitterswijk WJ, van der Bend RL;. FEBS Lett 1990;275:151-158. [4]. 2159661. Diacylglycerol kinase: a key modulator of signal transduction?. Kanoh H, Yamada K, Sakane F;. Trends Biochem Sci 1990;15:47-50. (from Pfam) NF012817.5 PF00610.26 DEP 32.7 32.7 72 domain Y N N Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) GO:0035556 14614075,14625292,15353129,15728856,16990133,17011483,8755244 2 Bacteria superkingdom 219 EBI-EMBL Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) The DEP domain [1] is responsible for mediating intracellular protein targeting and regulation of protein stability in the cell [2-3]. The DEP domain is present in a number of signaling molecules, including Regulator of G protein Signaling (RGS) proteins, and has been implicated in membrane targeting [4-5]. New findings in yeast, however, demonstrate a major role for a DEP domain in mediating the interaction of an RGS protein to the C-terminal tail of a GPCR, thus placing RGS in close proximity with its substrate G protein alpha subunit [6-7]. [1]. 8755244. Pleckstrin's repeat performance: a novel domain in G-protein signaling?. Ponting CP, Bork P. Trends Biochem Sci 1996;21:245-246. [2]. 14614075. The DEP domain determines subcellular targeting of the GTPase activating protein RGS9 in vivo. Martemyanov KA, Lishko PV, Calero N, Keresztes G, Sokolov M, Strissel KJ, Leskov IB, Hopp JA, Kolesnikov AV, Chen CK, Lem J, Heller S, Burns ME, Arshavsky VY;. J Neurosci 2003;23:10175-10181. [3]. 14625292. Absence of the RGS9.Gbeta5 GTPase-activating complex in photoreceptors of the R9AP knockout mouse. Keresztes G, Martemyanov KA, Krispel CM, Mutai H, Yoo PJ, Maison SF, Burns ME, Arshavsky VY, Heller S;. J Biol Chem 2004;279:1581-1584. [4]. 15353129. Characterization of function of three domains in dishevelled-1: DEP domain is responsible for membrane translocation of dishevelled-1. Pan WJ, Pang SZ, Huang T, Guo HY, Wu D, Li L;. Cell Res. 2004;14:324-330. [5]. 15728856. D2 dopamine receptors colocalize regulator of G-protein signaling 9-2 (RGS9-2) via the RGS9 DEP domain, and RGS9 knock-out mice develop dyskinesias associated with do. TRUNCATED at 1650 bytes (from Pfam) NF012829.5 PF00622.34 SPRY 26.3 21.9 121 domain Y Y N SPRY domain-containing protein GO:0005515 17189197,23139046,27812363,9204703 2 Bacteria superkingdom 575 EBI-EMBL SPRY domain SPRY domain SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of histone H3 methylation, innate immunity or embryonic development [1,2,3,4]. It can be divided into 11 subfamilies based on amino acid sequence similarity or the presence of additional protein domains. The greater SPRY family is divided into the SPRY/B30.2 (which contains a PRY extension at the N-terminal) and SPRY-only sub-families which are preceded by a subdomain that is structurally similar to the PRY region [2]. SPRY/B30.2 structures revealed a bent beta-sandwich fold comprised of two beta-sheets. Distant homologues are domains in butyrophilin/ marenostrin/pyrin [1]. [1]. 9204703. SPRY domains in ryanodine receptors (Ca(2+)-release channels). Ponting C, Schultz J, Bork P;. Trends Biochem Sci 1997;22:193-194. [2]. 17189197. Structural basis for protein recognition by B30.2/SPRY domains. Woo JS, Suh HY, Park SY, Oh BH;. Mol Cell. 2006;24:967-976. [3]. 23139046. Structure and function of the SPRY/B30.2 domain proteins involved in innate immunity. D'Cruz AA, Babon JJ, Norton RS, Nicola NA, Nicholson SE;. Protein Sci. 2013;22:1-10. [4]. 27812363. SPRYSEC Effectors: A Versatile Protein-Binding Platform to Disrupt Plant Innate Immunity. Diaz-Granados A, Petrescu AJ, Goverse A, Smant G;. Front Plant Sci. 2016;7:1575. (from Pfam) NF012836.5 PF00629.29 MAM 26.4 26.4 158 domain Y N N MAM domain, meprin/A5/mu GO:0016020 16456543,17761881,22988105,8387703 2 Bacteria superkingdom 2964 EBI-EMBL MAM domain, meprin/A5/mu MAM domain, meprin/A5/mu An extracellular domain found in many receptors [1]. The MAM domain along with the associated Ig domain in type IIB receptor protein tyrosine phosphatases forms a structural unit (termed MIg) with a seamless interdomain interface. It plays a major role in homodimerisation of the phosphatase ectoprotein and in cell adhesion [2,3]. MAM is a beta-sandwich consisting of two five-stranded antiparallel beta-sheets rotated away from each other by approx 25 degrees, and plays a similar role in meprin metalloproteinases [4]. [1]. 8387703. An adhesive domain detected in functionally diverse receptors. Beckmann G, Bork P;. Trends Biochem Sci. 1993;18:40-41. [2]. 17761881. Structure of a tyrosine phosphatase adhesive interaction reveals a spacer-clamp mechanism. Aricescu AR, Siebold C, Choudhuri K, Chang VT, Lu W, Davis SJ, van der Merwe PA, Jones EY;. Science. 2007;317:1217-1220. [3]. 16456543. Molecular analysis of receptor protein tyrosine phosphatase mu-mediated cell adhesion. Aricescu AR, Hon WC, Siebold C, Lu W, van der Merwe PA, Jones EY;. EMBO J. 2006;25:701-712. [4]. 22988105. Structural basis for the sheddase function of human meprin beta metalloproteinase at the plasma membrane. Arolas JL, Broder C, Jefferson T, Guevara T, Sterchi EE, Bode W, Stocker W, Becker-Pauly C, Gomis-Ruth FX;. Proc Natl Acad Sci U S A. 2012;109:16131-16136. (from Pfam) NF012842.5 PF00635.31 Motile_Sperm 25.9 25.9 109 domain Y Y N mobile sperm domain-containing protein 1527183,8913307 2 Bacteria superkingdom 16 EBI-EMBL MSP (Major sperm protein) domain MSP (Major sperm protein) domain Major sperm proteins are involved in sperm motility. These proteins oligomerise to form filaments. This family contains many other proteins. [1]. 8913307. 2.5 A resolution crystal structure of the motile major sperm protein (MSP) of Ascaris suum. Bullock TL, Roberts TM, Stewart M;. J Mol Biol 1996;263:284-296. [2]. 1527183. Structure and macromolecular assembly of two isoforms of the major sperm protein (MSP) from the amoeboid sperm of the nematode, Ascaris suum. King KL, Stewart M, Roberts TM, Seavy M;. J Cell Sci 1992;101:847-857. (from Pfam) NF012851.5 PF00644.25 PARP 26.7 26.7 198 PfamEq Y N N Poly(ADP-ribose) polymerase catalytic domain GO:0003950 8390463,8755499,9521710 2 Bacteria superkingdom 464 EBI-EMBL Poly(ADP-ribose) polymerase catalytic domain Poly(ADP-ribose) polymerase catalytic domain Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active [2]. [1]. 8755499. Structure of the catalytic fragment of poly(AD-ribose) polymerase from chicken. Ruf A, Mennissier de Murcia J, de Murcia G, Schulz GE;. Proc Natl Acad Sci U S A 1996;93:7481-7485. [2]. 8390463. The carboxyl-terminal domain of human poly(ADP-ribose) polymerase. Overproduction in Escherichia coli, large scale purification, and characterization. Simonin F, Hofferer L, Panzeter PL, Muller S, de Murcia G, Althaus FR;. J Biol Chem 1993;268:13454-13461. [3]. 9521710. Inhibitor and NAD+ binding to poly(ADP-ribose) polymerase as derived from crystal structures and homology modeling. Ruf A, de Murcia G, Schulz GE;. Biochemistry 1998;37:3893-3900. (from Pfam) NF012853.5 PF00646.38 F-box 20.5 15.6 43 domain Y Y N F-box protein GO:0005515 8706131,9346238 2 Bacteria superkingdom 1945 EBI-EMBL F-box domain F-box domain This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; Pfam:PF00560 and Pfam:PF07723) and the WD repeat (Pfam:PF00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression [1-2]. [1]. 8706131. SKP1 connects cell cycle regulators to the ubiquitin proteolysis machinery through a novel motif, the F-box. Bai C, Sen P, Hofmann K, Ma L, Goebl M, Harper JW, Elledge SJ;. Cell 1996;86:263-274. [2]. 9346238. F-box proteins are receptors that recruit phosphorylated substrates to the SCF ubiquitin-ligase complex. Skowyra D, Craig KL, Tyers M, Elledge SJ, Harper JW;. Cell. 1997;91:209-219. (from Pfam) NF012858.5 PF00651.36 BTB 20.5 20.5 110 domain Y Y N BTB/POZ domain-containing protein GO:0005515 16207353,7938017,7958847,9019154,9765306,9770450,9824158 2 Bacteria superkingdom 159 EBI-EMBL BTB/POZ domain BTB/POZ domain The BTB (for BR-C, ttk and bab) [1] or POZ (for Pox virus and Zinc finger) [2] domain is present near the N-terminus of a fraction of zinc finger (Pfam:PF00096) proteins and in proteins that contain the Pfam:PF01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation [2]. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule [3]. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [4,5,6]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN. [1]. 7938017. The BTB domain, found primarily in zinc finger proteins, defines an evolutionarily conserved family that includes several developmentally regulated genes in Drosophila. Zollman S, Godt D, Prive GG, Couderc JL, Laski FA;. Proc Natl Acad Sci U S A 1994;91:10717-10721. [2]. 7958847. The POZ domain: a conserved protein-protein interaction motif. Bardwell VJ, Treisman R;. Genes Dev 1994;8:1664-1677. [3]. 9770450. Crystal structure of the BTB domain from PLZF. Ahmad KF, Engel CK, Prive GG;. Proc Natl Acad Sci U S A 1998;95:12123-12128. [4]. 9019154. The LAZ3/BCL6 oncogene encodes a sequence-specific transcriptional inhibitor: a novel function for the BTB/POZ domain as an autonomous repressing domain. Deweindt C, Alb. TRUNCATED at 1650 bytes (from Pfam) NF012874.5 PF00669.25 Flagellin_N 26.6 26.6 139 domain Y N N Bacterial flagellin N-terminal helical region GO:0005198,GO:0071973 7648320 2 Bacteria superkingdom 120608 EBI-EMBL Bacterial flagellin N-terminal helical region Bacterial flagellin N-terminal helical region Flagellins polymerise to form bacterial flagella. This family includes flagellins and hook associated protein 3. Structurally this family forms an extended helix that interacts with Pfam:PF00700. [1]. 7648320. Spinning tails. DeRosier DJ;. Curr Opin Struct Biol 1995;5:187-193. (from Pfam) NF012894.5 PF00691.25 OmpA 27.2 27.2 98 domain Y Y N OmpA family protein 2 Bacteria superkingdom 342809 EBI-EMBL OmpA family OmpA family protein The Pfam entry also includes MotB and related proteins which are not included in the Prosite family. (from Pfam) NF012903.5 PF00700.26 Flagellin_C 23 23 86 domain Y Y N flagellin GO:0005198,GO:0071973 2190210,7648320 2 Bacteria superkingdom 107891 EBI-EMBL Bacterial flagellin C-terminal helical region flagellin C-terminal helical domain Flagellins polymerise to form bacterial flagella. There is some similarity between this family and Pfam:PF00669, particularly the motif NRFXSXIXXL. It has been suggested that these two regions associate [2] and this is shown to be correct as structurally this family forms an extended helix that interacts with Pfam:PF00700. [1]. 7648320. Spinning tails. DeRosier DJ;. Curr Opin Struct Biol 1995;5:187-193. [2]. 2190210. Flagellin as an object for supramolecular engineering. Fedorov OV, Efimov AV;. Protein Eng 1990;3:411-413. (from Pfam) NF012910.5 PF00707.27 IF3_C 34.8 34.8 86 PfamEq Y N N Translation initiation factor IF-3, C-terminal domain GO:0006413 2 Bacteria superkingdom 41817 EBI-EMBL Translation initiation factor IF-3, C-terminal domain Translation initiation factor IF-3, C-terminal domain NF012923.5 PF00720.22 SSI 23.9 23.9 92 subfamily Y Y N SSI family serine proteinase inhibitor GO:0004867 15838021,16116298 2 Bacteria superkingdom 17358 EBI-EMBL Subtilisin inhibitor-like SSI family serine proteinase inhibitor NF012940.5 PF00737.25 PsbH 24.6 24.6 52 PfamAutoEq Y Y N photosystem II reaction center phosphoprotein PsbH psbH GO:0009523,GO:0015979,GO:0016020,GO:0042301,GO:0050821 2 Bacteria superkingdom 500 EBI-EMBL Photosystem II 10 kDa phosphoprotein photosystem II reaction center phosphoprotein PsbH This protein is phosphorylated in a light dependent reaction. (from Pfam) NF012948.5 PF00746.26 Gram_pos_anchor 20 17 43 domain Y N N LPXTG cell wall anchor motif 2 Bacteria superkingdom 203548 EBI-EMBL LPXTG cell wall anchor motif LPXTG cell wall anchor motif NF012957.5 PF00755.25 Carn_acyltransf 22.3 22.3 574 PfamEq Y Y N choline/carnitine O-acyltransferase 2 Bacteria superkingdom 2588 EBI-EMBL Choline/Carnitine o-acyltransferase choline/carnitine O-acyltransferase NF012967.5 PF00765.22 Autoind_synth 24 24 183 domain Y Y N acyl-homoserine-lactone synthase GO:0016740 12736370,9781877 2 Bacteria superkingdom 14780 EBI-EMBL Autoinducer synthase acyl-homoserine-lactone synthase NF012970.5 PF00768.25 Peptidase_S11 27.6 27.6 239 domain Y N N D-alanyl-D-alanine carboxypeptidase GO:0006508,GO:0009002 2 Bacteria superkingdom 161265 EBI-EMBL D-alanyl-D-alanine carboxypeptidase D-alanyl-D-alanine carboxypeptidase NF012973.5 PF00771.25 FHIPEP 29.1 29.1 657 domain Y Y N FHIPEP family type III secretion protein GO:0009306,GO:0016020 2 Bacteria superkingdom 51978 EBI-EMBL FHIPEP family FHIPEP family type III secretion protein NF012974.5 PF00772.26 DnaB 23 23 103 domain Y Y N DnaB-like helicase N-terminal domain-containing protein GO:0003678,GO:0005524,GO:0006260 10404598 2 Bacteria superkingdom 92243 EBI-EMBL DnaB-like helicase N terminal domain DnaB-like helicase N terminal domain The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation of the N-terminal domain has been observed and may occur during the enzymatic cycle. This N-terminal domain is required both for interaction with other proteins in the primosome and for DnaB helicase activity [1]. [1]. 10404598. Crystal structure of the N-terminal domain of the DnaB hexameric helicase. Fass D, Bogden CE, Berger JM;. Structure Fold Des 1999;7:691-698. (from Pfam) NF012994.5 PF00796.23 PSI_8 19.8 19.8 25 PfamEq Y N N Photosystem I reaction centre subunit VIII GO:0009522,GO:0015979 2 Bacteria superkingdom 506 EBI-EMBL Photosystem I reaction centre subunit VIII Photosystem I reaction centre subunit VIII NF013011.5 PF00813.25 FliP 26.9 26.9 191 domain Y N N FliP family GO:0009306,GO:0016020 2 Bacteria superkingdom 37665 EBI-EMBL FliP family FliP family NF013025.5 PF00829.26 Ribosomal_L21p 27 27 99 PfamEq Y Y N bL21 family ribosomal protein GO:0005840 2 Bacteria superkingdom 30855 EBI-EMBL Ribosomal prokaryotic L21 protein bL21 family ribosomal protein NF013026.5 PF00830.24 Ribosomal_L28 27 27 60 domain Y Y N L28 family ribosomal protein GO:0003735 17696316,24524803 2 Bacteria superkingdom 28091 EBI-EMBL Ribosomal L28 family L28 family ribosomal protein The ribosomal 28 family includes L28 proteins from bacteria and chloroplasts. The L24 protein from yeast Swiss:P36525 also contains a region of similarity to prokaryotic L28 proteins. L24 from yeast is also found in the large ribosomal subunit (from Pfam) NF013035.5 PF00839.22 Cys_rich_FGFR 22 22 58 repeat Y N N cysteine-rich repeat protein GO:0016020 1448090 2 Bacteria superkingdom 2401 EBI-EMBL Cysteine rich repeat Cysteine rich repeat This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors [1]. The repeat is also found in MG160 and E-selectin ligand (ESL-1). [1]. 1448090. Identification of a cysteine-rich receptor for fibroblast growth factors. Burrus LW, Zuber ME, Lueddecke BA, Olwin BB;. Mol Cell Biol 1992;12:5600-5609. (from Pfam) NF013058.5 PF00862.24 Sucrose_synth 23 23 549 domain Y N N Sucrose synthase GO:0005985,GO:0016157 2 Bacteria superkingdom 3230 EBI-EMBL Sucrose synthase Sucrose synthase Sucrose synthases catalyse the synthesis of sucrose from UDP-glucose and fructose. This family includes the bulk of the sucrose synthase protein. However the carboxyl terminal region of the sucrose synthases belongs to the glycosyl transferase family Pfam:PF00534. (from Pfam) NF013070.5 PF00874.25 PRD 23 23 90 domain Y Y N PRD domain-containing protein GO:0006355 11447120,11733988,11751049,15699035 2 Bacteria superkingdom 120129 EBI-EMBL PRD domain PRD domain The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory domain found in bacterial transcriptional antiterminator such as BglG, SacY and LicT, as well as in activators such as MtlR and LevR. The PRD is phosphorylated on one or two conserved histidine residues. PRD-containing proteins are involved in the regulation of catabolic operons in Gram+ and Gram- bacteria and are often characterised by a short N-terminal effector domain that binds to either RNA (CAT-RBD for antiterminators Pfam:PF03123) or DNA (for activators), and a duplicated PRD module which is phosphorylated by the sugar phosphotransferase system (PTS) in response to the availability of carbon source. The phosphorylations modify the conformation and stability of the dimeric proteins and thereby the RNA- or DNA-binding activity of the effector domain. The structure of the LicT PRD domains has been solved in both the active (pdb:1h99, [2]) and inactive state (pdb:1tlv [4]), revealing massive structural rearrangements upon activation. [1]. 11751049. Structural insights into the regulation of bacterial signalling proteins containing PRDs. van Tilbeurgh H, Declerck N;. Curr Opin Struct Biol 2001;11:685-693. [2]. 11447120. Crystal structure of an activated form of the PTS regulation domain from the LicT transcriptional antiterminator. van Tilbeurgh H, Le Coq D, Declerck N;. EMBO J 2001;20:3789-3799. [3]. 11733988. Dimer stabilization upon activation of the transcriptional antiterminator LicT. Declerck N, Dutartre H, Receveur V, Dubois V, Royer C, Aymerich S, van Tilbeurgh H;. J Mol Biol 2001;314:671-681. [4]. 15699035. Activation of the LicT tran. TRUNCATED at 1650 bytes (from Pfam) NF013082.5 PF00886.24 Ribosomal_S16 27 27 62 PfamEq Y Y N 30S ribosomal protein S16 GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 35365 EBI-EMBL Ribosomal protein S16 30S ribosomal protein S16 NF013085.5 PF00889.24 EF_TS 27 27 204 PfamEq Y N N Elongation factor TS GO:0003746,GO:0006414 2 Bacteria superkingdom 52727 EBI-EMBL Elongation factor TS Elongation factor TS NF013100.5 PF00905.27 Transpeptidase 22.1 22.1 299 domain Y Y N penicillin-binding transpeptidase domain-containing protein GO:0008658 8605631 2 Bacteria superkingdom 528100 EBI-EMBL Penicillin binding protein transpeptidase domain penicillin-binding transpeptidase domain The active site serine (residue 337 in Swiss:P14677) is conserved in all members of this family. [1]. 8605631. X-ray structure of Streptococcus pneumoniae PBP2x, a primary penicillin target enzyme. Pares S, Mouz N, Petillot Y, Hakenbeck R, Dideberg O. Nat Struct Biol 1996;3:284-289. (from Pfam) NF013106.5 PF00912.27 Transgly 27 27 178 domain Y Y N transglycosylase domain-containing protein 12867450,8830253,9244263,9614972 2 Bacteria superkingdom 305345 EBI-EMBL Transglycosylase Transglycosylase The penicillin-binding proteins are bifunctional proteins consisting of transglycosylase and transpeptidase in the N- and C-terminus respectively [1]. The transglycosylase domain catalyses the polymerisation of murein glycan chains ([4]). [1]. 9244263. Topographical and functional investigation of Escherichia coli penicillin-binding protein 1b by alanine stretch scanning mutagenesis. F. Lefevre, M. H. Remy & J. M. Masson;. J Bacteriol 1997;179:4761-4767. [2]. 9614972. X-ray studies of enzymes that interact with penicillins. Kelly JA, Kuzin AP, Charlier P, Fonze E;. Cell Mol Life Sci 1998;54:353-358. [3]. 8830253. Monofunctional biosynthetic peptidoglycan transglycosylases. Spratt BG, Zhou J, Taylor M, Merrick MJ;. Mol Microbiol 1996;19:639-640. [4]. 12867450. The glycosyltransferase domain of penicillin-binding protein 2a from Streptococcus pneumoniae catalyzes the polymerization of murein glycan chains. Di Guilmi AM, Dessen A, Dideberg O, Vernet T;. J Bacteriol 2003;185:4418-4423. (from Pfam) NF013129.5 PF00936.24 BMC 24.5 24.5 75 domain Y Y N BMC domain-containing protein GO:0031469 16081736 2 Bacteria superkingdom 31616 EBI-EMBL BMC domain BMC domain Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure [1]. [1]. 16081736. Protein structures forming the shell of primitive bacterial organelles. Kerfeld CA, Sawaya MR, Tanaka S, Nguyen CV, Phillips M, Beeby M, Yeates TO;. Science 2005;309:936-938. (from Pfam) NF013142.5 PF00949.26 Peptidase_S7 20 20 131 domain Y N N Peptidase S7, Flavivirus NS3 serine protease GO:0003723,GO:0003724,GO:0005524 10026173,2174669,7642575,8269709 2 Bacteria superkingdom 3661 EBI-EMBL Peptidase S7, Flavivirus NS3 serine protease Peptidase S7, Flavivirus NS3 serine protease The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B (Pfam:PF01002) as a cofactor [4]. [1]. 7642575. Association between NS3 and NS5 proteins of dengue virus type 2 in the putative RNA replicase is linked to differential phosphorylation of NS5. Kapoor M, Zhang L, Ramachandra M, Kusukawa J, Ebner KE, Padmanabhan R;. J Biol Chem 1995;270:19100-19106. [2]. 2174669. Flavivirus genome organization, expression, and replication. Chambers TJ, Hahn CS, Galler R, Rice CM;. Annu Rev Microbiol 1990;44:649-688. [3]. 8269709. Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Koonin EV, Dolja VV;. Crit Rev Biochem Mol Biol 1993;28:375-430. [4]. 10026173. Dengue virus NS3 serine protease. Crystal structure and insights into interaction of the active site with substrates by molecular modeling and structural analysis of mutational effects. Murthy HM, Clum S, Padmanabhan R;. J Biol Chem 1999;274:5573-5580. (from Pfam) NF013148.5 PF00955.26 HCO3_cotransp 27 27 551 PfamEq Y N N HCO3- transporter integral membrane domain GO:0006820,GO:0016020 2 Bacteria superkingdom 71 EBI-EMBL HCO3- transporter integral membrane domain HCO3- transporter integral membrane domain This family contains Band 3 anion exchange proteins that exchange CL-/HCO3- such as Swiss:P48751. This family also includes cotransporters of Na+/HCO3- such as Swiss:O15153. (from Pfam) NF013149.5 PF00956.23 NAP 28.6 28.6 266 domain Y Y N NAP domain-containing protein GO:0005634,GO:0006334 16432217,8923009,9325046 2 Bacteria superkingdom 3 EBI-EMBL Nucleosome assembly protein (NAP) Nucleosome assembly protein (NAP) NAP proteins are involved in moving histones into the nucleus, nucleosome assembly and chromatin fluidity. They affect the transcription of many genes. [1]. 9325046. Functional characterization of human nucleosome assembly protein-2 (NAP1L4) suggests a role as a histone chaperone. Rodriguez P, Munroe D, Prawitt D, Chu LL, Bric E, Kim J, Reid LH, Davies C, Nakagama H, Loebbert R, Winterpacht A, Petruzzi MJ, Higgins MJ, Nowak N, Evans G, Shows T, Weissman BE, Zabel B, Housman DE, Pelletier J;. Genomics 1997;44:253-265. [2]. 8923009. Testis-specific protein, Y-encoded (TSPY) expression in testicular tissues. Schnieders F, Dork T, Arnemann J, Vogel T, Werner M, Schmidtke J;. Hum Mol Genet 1996;5:1801-1807. [3]. 16432217. The structure of nucleosome assembly protein 1. Park YJ, Luger K;. Proc Natl Acad Sci U S A. 2006;103:1248-1253. (from Pfam) NF013152.5 PF00959.24 Phage_lysozyme 22.3 22.3 125 domain Y Y N glycoside hydrolase family protein GO:0003796,GO:0009253,GO:0016998 3586019,8177878,8218201 2 Bacteria superkingdom 58883 EBI-EMBL Phage lysozyme glycoside hydrolase family protein This family includes lambda phage lysozyme and E. coli endolysin. [1]. 3586019. Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution. Weaver LH, Matthews BW;. J Mol Biol 1987;193:189-199. [2]. 8218201. Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala-->Ser and Val-->Thr substitutions in T4 lysozyme. Blaber M, Lindstrom JD, Gassner N, Xu J, Heinz DW, Matthews BW;. Biochemistry. 1993;32:11363-11373. [3]. 8177878. Rapid crystallization of T4 lysozyme by intermolecular disulfide cross-linking. Heinz DW, Matthews BW;. Protein Eng. 1994;7:301-307. (from Pfam) NF013153.5 PF00960.23 Neocarzinostat 25 25 110 domain Y Y N neocarzinostatin apoprotein domain-containing protein GO:0003677,GO:0006952 8235619 2 Bacteria superkingdom 2763 EBI-EMBL Neocarzinostatin family Neocarzinostatin family NF013159.5 PF00967.22 Barwin 21 21 119 PfamEq Y N N Barwin family GO:0042742,GO:0050832 2 Bacteria superkingdom 191 EBI-EMBL Barwin family Barwin family NF013180.5 PF00990.26 GGDEF 23.8 23.8 161 domain Y Y N diguanylate cyclase domain-containing protein 2.7.7.65 11119645,11557134,15063857,15075296,15142243,15569936,16923812,18366254,21757706 2 Bacteria superkingdom 1185343 EBI-EMBL Diguanylate cyclase, GGDEF domain Diguanylate cyclase, GGDEF domain This domain is found linked to a wide range of non-homologous domains in a variety of bacteria. It has been shown to be homologous to the adenylyl cyclase catalytic domain [1] and has diguanylate cyclase activity [4]. This observation correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. In the WspR protein of Pseudomonas aeruginosa, the GGDEF domain acts as a diguanylate cyclase, PDB:3bre, when the whole molecule appears to form a tetramer consisting of two symmetrically-related dimers representing a biological unit. The active site is the GGD/EF motif, buried in the structure, and the cyclic dimeric guanosine monophosphate (c-di-GMP) bind to the inhibitory-motif RxxD on the surface. The enzyme thus catalyses the cyclisation of two guanosine triphosphate (GTP) molecules to one c-di-GMP molecule [6,7,8]. [1]. 11119645. GGDEF domain is homologous to adenylyl cyclase. Pei J, Grishin NV;. Proteins 2001;42:210-216. [2]. 11557134. Novel domains of the prokaryotic two-component signal transduction systems. Galperin MY, Nikolskaya AN, Koonin EV;. FEMS Microbiol Lett 2001;203:11-21. [3]. 15063857. Cyclic di-guanosine-monophosphate comes of age: a novel secondary messenger involved in modulating cell surface structures in bacteria?. Jenal U;. Curr Opin Microbiol 2004;7:185-191. [4]. 15075296. Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain. Paul R, Weiser S, Amiot NC, Chan C, Sch. TRUNCATED at 1650 bytes (from Pfam) NF013181.5 PF00992.25 Troponin 26.2 26.2 134 PfamEq Y N N Troponin GO:0005861 3102969,7601340,7852318 2 Bacteria superkingdom 26 EBI-EMBL Troponin Troponin Troponin (Tn) contains three subunits, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). this Pfam contains members of the TnT subunit. Troponin is a complex of three proteins, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). The troponin complex regulates Ca++ induced muscle contraction. This family includes troponin T and troponin I. Troponin I binds to actin and troponin T binds to tropomyosin. [1]. 3102969. Structure of co-crystals of tropomyosin and troponin. White SP, Cohen C, Phillips GN Jr;. Nature 1987;325:826-828. [2]. 7852318. A direct regulatory role for troponin T and a dual role for troponin C in the Ca2+ regulation of muscle contraction. Potter JD, Sheng Z, Pan BS, Zhao J;. J Biol Chem 1995;270:2557-2562. [3]. 7601340. The troponin complex and regulation of muscle contraction. Farah CS, Reinach FC;. FASEB J 1995;9:755-767. (from Pfam) NF013196.5 PF01007.25 IRK 22.7 22.7 141 PfamEq Y N N Inward rectifier potassium channel transmembrane domain 7580148 2 Bacteria superkingdom 2166 EBI-EMBL Inward rectifier potassium channel transmembrane domain Inward rectifier potassium channel transmembrane domain NF013203.5 PF01016.24 Ribosomal_L27 20.5 20.5 79 PfamEq Y Y N 50S ribosomal protein L27 GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 26343 EBI-EMBL Ribosomal L27 protein 50S ribosomal protein L27 NF013205.5 PF01018.27 GTP1_OBG 27 27 155 PfamEq Y N N GTP1/OBG 2 Bacteria superkingdom 63287 EBI-EMBL GTP1/OBG GTP1/OBG The N-terminal domain of Swiss:P20964 has the OBG fold, which is formed by three glycine-rich regions inserted into a small 8-stranded beta-sandwich these regions form six left-handed collagen-like helices packed and H-bonded together. (from Pfam) NF013214.5 PF01027.25 Bax1-I 34.1 34.1 207 domain Y Y N Bax inhibitor-1 family protein 14671021,19704470,19742129,21673659,24904158 2 Bacteria superkingdom 49192 EBI-EMBL Inhibitor of apoptosis-promoting Bax1 Bax inhibitor-1 family protein Programmed cell-death involves a set of Bcl-2 family proteins, some of which inhibit apoptosis (Bcl-2 and Bcl-XL) and some of which promote it (Bax and Bak). Human Bax inhibitor, BI-1, is an evolutionarily conserved integral membrane protein containing multiple membrane-spanning segments predominantly localised to intracellular membranes. It has 6-7 membrane-spanning domains. The C termini of the mammalian BI-1 proteins are comprised of basic amino acids resembling some nuclear targeting sequences, but otherwise the predicted proteins lack motifs that suggest a function. As plant BI-1 appears to localise predominantly to the ER, we hypothesized that plant BI-1 could also regulate cell death triggered by ER stress [2]. BI-1 appears to exert its effect through an interaction with calmodulin [3]. The budding yeast member of this family has been found unexpectedly to encode a BH3 domain-containing protein (Ybh3p) that regulates the mitochondrial pathway of apoptosis in a phylogenetically conserved manner [4]. Examination of the crystal structure of a bacterial member of this family shows that these proteins mediate a calcium leak across the membrane that is pH-dependent. Calcium homoeostasis balances passive calcium leak with active calcium uptake. The structure exists in a pore-closed and pore-open conformation, at pHs of 8 and 6 respectively, and the pore can be opened by intracrystalline transition; together these findings suggest that pH controls the conformational transition [5]. [1]. 14671021. Dissection of Arabidopsis Bax inhibitor-1 suppressing Bax-, hydrogen peroxide-, and salicylic acid-induced cell death. Kawai-Yam. TRUNCATED at 1650 bytes (from Pfam) NF013217.5 PF01030.29 Recep_L_domain 21.8 21.8 112 domain Y N N Receptor L domain 9690478 2 Bacteria superkingdom 716 EBI-EMBL Receptor L domain Receptor L domain The L domains from these receptors make up the bilobal ligand binding site. Each L domain consists of a single-stranded right hand beta-helix [1]. This Pfam entry is missing the first 50 amino acid residues of the domain. [1]. 9690478. Crystal structure of the first three domains of the type-1 insulin-like growth factor receptor. Garrett TP, McKern NM, Lou M, Frenkel MJ, Bentley JD, Lovrecz GO, Elleman TC, Cosgrove LJ, Ward CW;. Nature 1998;394:395-399. (from Pfam) NF013229.5 PF01043.25 SecA_PP_bind 23.5 23.5 110 domain Y N N SecA preprotein cross-linking domain GO:0016020,GO:0017038 12242434 2 Bacteria superkingdom 89324 EBI-EMBL SecA preprotein cross-linking domain SecA preprotein cross-linking domain The SecA ATPase is involved in the insertion and retraction of preproteins through the plasma membrane. This domain has been found to cross-link to preproteins, thought to indicate a role in preprotein binding. The pre-protein cross-linking domain is comprised of two sub domains that are inserted within the ATPase domain [1]. [1]. 12242434. Nucleotide control of interdomain interactions in the conformational reaction cycle of SecA. Hunt JF, Weinkauf S, Henry L, Fak JJ, McNicholas P, Oliver DB, Deisenhofer J;. Science 2002;297:2018-2026. (from Pfam) NF013235.5 PF01051.26 Rep3_N 22.4 22.4 141 domain Y Y N RepB family plasmid replication initiator protein GO:0003887,GO:0006270 15336485,18000058,31063152,3949778,8320218,9180376,9618448 2 Bacteria superkingdom 37039 EBI-EMBL Initiator Replication protein, WH1 RepB family plasmid replication initiator protein This protein is an initiator of plasmid replication [1-6]. RepB possesses nicking-closing (topoisomerase I) like activity. It is also able to perform a strand transfer reaction on ssDNA that contains its target. This entry also includes RepA which is an E.coli protein involved in plasmid replication. The RepA protein binds to DNA repeats that flank the repA gene [3,4]. These proteins consist of two domains containing a winged helix-turn-helix motif, the N-terminal one, WH1, represented in this entry, is involved in the dimerization of RepE and an auxiliary binding to DNA. The C-terminal one, WH2, is related to a sequence-specific binding to the common 8 bp of the iteron [6]. [1]. 9618448. Replication and control of circular bacterial plasmids. del Solar G, Giraldo R, Ruiz-Echevarria MJ, Espinosa M, Diaz-Orejas R;. Microbiol Mol Biol Rev 1998;62:434-464. [2]. 9180376. Initiation of replication of plasmid pMV158: mechanisms of DNA strand-transfer reactions mediated by the initiator RepB protein. Moscoso M, Eritja R, Espinosa M;. J Mol Biol 1997;268:840-856. [3]. 8320218. Regulatory interactions between RepA, an essential replication protein, and the DNA repeats of RepFIB from plasmid P307. Spiers AJ, Bhana N, Bergquist PL;. J Bacteriol 1993;175:4016-4024. [4]. 3949778. P1 plasmid replication. Purification and DNA-binding activity of the replication protein RepA. Abeles AL;. J Biol Chem 1986;261:3548-3555. [5]. 15336485. Twenty years of the pPS10 replicon: insights on the molecular mechanism for the activation of DNA replication in iteron-containing bacterial plasmids. Giraldo R, Fernandez-Tresguerres ME;. Plasmid. 2004;52:69. TRUNCATED at 1650 bytes (from Pfam) NF013236.5 PF01052.25 FliMN_C 23.8 23.8 73 domain Y Y N FliM/FliN family flagellar motor switch protein 1447979,15805535,16547037,8885278 2 Bacteria superkingdom 73795 EBI-EMBL Type III flagellar switch regulator (C-ring) FliN C-term FliM/FliN family flagellar motor switch protein This family includes the C-terminal region of flagellar motor switch proteins FliN and FliM. It is associated with family FliM, Pfam:PF02154 and family FliN_N Pfam:PF16973. [1]. 1447979. Identification and characterization of FliY, a novel component of the Bacillus subtilis flagellar switch complex. Bischoff DS, Ordal GW;. Mol Microbiol 1992;6:2715-2723. [2]. 8885278. Salmonella spp. are cytotoxic for cultured macrophages. Chen LM, Kaniga K, Galan JE;. Mol Microbiol 1996;21:1101-1115. [3]. 15805535. Crystal structure of the flagellar rotor protein FliN from Thermotoga maritima. Brown PN, Mathews MA, Joss LA, Hill CP, Blair DF;. J Bacteriol. 2005;187:2890-2902. [4]. 16547037. Organization of FliN subunits in the flagellar motor of Escherichia coli. Paul K, Blair DF;. J Bacteriol. 2006;188:2502-2511. (from Pfam) NF013246.5 PF01062.26 Bestrophin 24.2 23.4 291 subfamily Y Y N bestrophin family ion channel GO:0005254 12032738,12058047,12907679,19398034 2 Bacteria superkingdom 25501 EBI-EMBL Bestrophin, RFP-TM, chloride channel bestrophin family ion channel Human bestrophin is a chloride channel, while the Klebsiella pneumoniae homolog KpBest1 is a sodium channel. NF013264.5 PF01082.25 Cu2_monooxygen 30 30 130 domain Y N N Copper type II ascorbate-dependent monooxygenase, N-terminal domain GO:0004497,GO:0005507,GO:0016715 2 Bacteria superkingdom 109 EBI-EMBL Copper type II ascorbate-dependent monooxygenase, N-terminal domain Copper type II ascorbate-dependent monooxygenase, N-terminal domain The N and C-terminal domains of members of this family adopt the same PNGase F-like fold. (from Pfam) NF013265.5 PF01083.27 Cutinase 25.9 25.9 173 domain Y Y N cutinase family protein GO:0016787 9175860 2 Bacteria superkingdom 22195 EBI-EMBL Cutinase cutinase family protein NF013266.5 PF01084.25 Ribosomal_S18 21 21 52 domain Y N N Ribosomal protein S18 GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 21857 EBI-EMBL Ribosomal protein S18 Ribosomal protein S18 NF013267.5 PF01085.23 HH_signal 22.1 22.1 161 PfamEq Y N N Hedgehog amino-terminal signalling domain GO:0007267 7477329 2 Bacteria superkingdom 68 EBI-EMBL Hedgehog amino-terminal signalling domain Hedgehog amino-terminal signalling domain For the carboxyl Hint module, see Pfam:PF01079. Hedgehog is a family of secreted signal molecules required for embryonic cell differentiation. [1]. 7477329. A potential catalytic site revealed by the 1.7-A crystal structure of the amino-terminal signalling domain of Sonic hedgehog. Hall TM, Porter JA, Beachy PA, Leahy DJ;. Nature 1995;378:212-216. (from Pfam) NF013279.5 PF01098.24 FTSW_RODA_SPOVE 26.4 26.4 356 domain Y Y N FtsW/RodA/SpoVE family cell cycle protein GO:0016020,GO:0051301 9622350 2 Bacteria superkingdom 157805 EBI-EMBL Cell cycle protein FtsW/RodA/SpoVE family cell cycle protein This entry includes the following members; FtsW, RodA, SpoVE (from Pfam) NF013283.5 PF01103.28 Omp85 24 24 325 domain Y Y N BamA/TamA family outer membrane protein GO:0019867 25101071 2 Bacteria superkingdom 126600 EBI-EMBL Omp85 superfamily domain Omp85 superfamily domain The Omp85 protein superfamily contains bacterial outer membrane proteins, which can function as protein translocases or as membrane protein assembly factors [1]. The family includes the membrane bound beta barrel of proteins such as BamA and TamA from E. coli. [1]. 25101071. A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution. Heinz E, Lithgow T;. Front Microbiol. 2014;5:370. (from Pfam) NF013297.5 PF01117.25 Aerolysin 24.3 24.3 365 domain Y Y N aerolysin family beta-barrel pore-forming toxin GO:0005576 2 Bacteria superkingdom 1660 EBI-EMBL Aerolysin toxin aerolysin family toxin beta-barrel pore-forming domain This family represents the pore forming lobe of aerolysin. (from Pfam) NF013304.5 PF01124.23 MAPEG 23.4 23.4 129 domain Y Y N MAPEG family protein GO:0016020 10091672 2 Bacteria superkingdom 37215 EBI-EMBL MAPEG family MAPEG family protein This family is has been called MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism). It includes proteins such as Prostaglandin E synthase. This enzyme catalyses the synthesis of PGE2 from PGH2 (produced by cyclooxygenase from arachidonic acid). Because of structural similarities in the active sites of FLAP, LTC4 synthase and PGE synthase, substrates for each enzyme can compete with one another and modulate synthetic activity. [1]. 10091672. Common structural features of MAPEG -- a widespread superfamily of membrane associated proteins with highly divergent functions in eicosanoid and glutathione metabolism. Jakobsson PJ, Morgenstern R, Mancini J, Ford-Hutchinson A, Persson B;. Protein Sci 1999;8:689-692. (from Pfam) NF013306.5 PF01126.25 Heme_oxygenase 23 23 204 domain Y Y N biliverdin-producing heme oxygenase GO:0004392,GO:0006788 2 Bacteria superkingdom 25533 EBI-EMBL Heme oxygenase biliverdin-producing heme oxygenase NF013342.5 PF01165.25 Ribosomal_S21 27 27 55 domain Y Y N 30S ribosomal protein S21 GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 14392 EBI-EMBL Ribosomal protein S21 30S ribosomal protein S21 NF013356.5 PF01182.25 Glucosamine_iso 27 27 225 domain Y Y N 6-phosphogluconolactonase 3.1.1.31 GO:0005975 8747459 2 Bacteria superkingdom 89254 EBI-EMBL Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase 6-phosphogluconolactonase NF013368.5 PF01195.24 Pept_tRNA_hydro 27 27 183 PfamEq Y N N Peptidyl-tRNA hydrolase GO:0004045 9303320 2 Bacteria superkingdom 61045 EBI-EMBL Peptidyl-tRNA hydrolase Peptidyl-tRNA hydrolase NF013370.5 PF01197.23 Ribosomal_L31 27 27 65 domain Y Y N 50S ribosomal protein L31 GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 42349 EBI-EMBL Ribosomal protein L31 50S ribosomal protein L31 NF013376.5 PF01203.24 T2SSN 29.6 29.6 211 PfamEq Y Y N type II secretion system protein N gspN GO:0015627,GO:0015628 14600218,15223057,19299134 2 Bacteria superkingdom 12369 EBI-EMBL Type II secretion system (T2SS), protein N type II secretion system protein GspN Members of the T2SN family are involved in the Type II protein secretion system. The precise function of these proteins is unknown. [1]. 15223057. The general secretory pathway: a general misnomer?. Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR;. Trends Microbiol. 2004;12:306-309. [2]. 14600218. Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella. Peabody CR, Chung YJ, Yen MR, Vidal-Ingigliardi D, Pugsley AP, Saier MH Jr;. Microbiology. 2003;149:3051-3072. [3]. 19299134. Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Desvaux M, Hebraud M, Talon R, Henderson IR;. Trends Microbiol. 2009;17:139-145. (from Pfam) NF013390.5 PF01218.23 Coprogen_oxidas 31.8 31.8 295 PfamEq Y Y N coproporphyrinogen III oxidase GO:0004109,GO:0006779 2 Bacteria superkingdom 34776 EBI-EMBL Coproporphyrinogen III oxidase coproporphyrinogen III oxidase NF013399.5 PF01228.26 Gly_radical 22.2 22.2 106 domain Y Y N glycine radical domain-containing protein GO:0003824 10574800 2 Bacteria superkingdom 78133 EBI-EMBL Glycine radical Glycine radical NF013403.5 PF01232.28 Mannitol_dh 27 27 199 domain Y N N Mannitol dehydrogenase Rossmann domain GO:0016491 2 Bacteria superkingdom 92765 EBI-EMBL Mannitol dehydrogenase Rossmann domain Mannitol dehydrogenase Rossmann domain NF013405.5 PF01234.22 NNMT_PNMT_TEMT 25 25 261 PfamEq Y N N NNMT/PNMT/TEMT family GO:0008168 2 Bacteria superkingdom 1508 EBI-EMBL NNMT/PNMT/TEMT family NNMT/PNMT/TEMT family NF013408.5 PF01238.26 PMI_typeI_C 21 21 48 domain Y N N Phosphomannose isomerase type I C-terminal GO:0004476,GO:0005975,GO:0008270 8612079 2 Bacteria superkingdom 8365 EBI-EMBL Phosphomannose isomerase type I C-terminal Phosphomannose isomerase type I C-terminal This is the C-terminal domain of Phosphomannose isomerase type I enzymes (EC 5.3.1.8), which contains antiparallel beta-strands in an extended jelly roll topology with short loops connecting the strands [1]. [1]. 8612079. The x-ray crystal structure of phosphomannose isomerase from Candida albicans at 1.7 angstrom resolution. Cleasby A, Wonacott A, Skarzynski T, Hubbard RE, Davies GJ, Proudfoot AE, Bernard AR, Payton MA, Wells TN;. Nat Struct Biol 1996;3:470-479. (from Pfam) NF013410.5 PF01241.23 PSI_PSAK 23.2 23.2 70 domain Y N N Photosystem I psaG / psaK GO:0009522,GO:0015979,GO:0016020 2 Bacteria superkingdom 1271 EBI-EMBL Photosystem I psaG / psaK Photosystem I psaG / psaK NF013414.5 PF01245.25 Ribosomal_L19 22 22 111 PfamEq Y Y N 50S ribosomal protein L19 GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 32440 EBI-EMBL Ribosomal protein L19 50S ribosomal protein L19 NF013418.5 PF01249.23 Ribosomal_S21e 25 25 79 domain Y Y N 40S ribosomal protein S21 GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 7 EBI-EMBL Ribosomal protein S21e 40S ribosomal protein S21 NF013419.5 PF01250.22 Ribosomal_S6 27 27 90 PfamEq Y Y N 30S ribosomal protein S6 GO:0003735,GO:0005840,GO:0006412,GO:0019843 8137808 2 Bacteria superkingdom 32146 EBI-EMBL Ribosomal protein S6 30S ribosomal protein S6 NF013421.5 PF01252.23 Peptidase_A8 25 25 142 domain Y Y N signal peptidase II 3.4.23.36 GO:0004190,GO:0006508,GO:0016020 2 Bacteria superkingdom 69545 EBI-EMBL Signal peptidase (SPase) II signal peptidase II NF013438.5 PF01270.22 Glyco_hydro_8 24 24 341 subfamily Y Y N glycosyl hydrolase family 8 GO:0004553,GO:0005975 8805535 2 Bacteria superkingdom 24060 EBI-EMBL Glycosyl hydrolases family 8 glycosyl hydrolase family 8 NF013440.5 PF01272.24 GreA_GreB 26.9 26.9 77 domain Y Y N GreA/GreB family elongation factor GO:0003677,GO:0032784 7854424 2 Bacteria superkingdom 87606 EBI-EMBL Transcription elongation factor, GreA/GreB, C-term GreA/GreB family elongation factor This domain has an FKBP-like fold. [1]. 7854424. Crystal structure of the GreA transcript cleavage factor from Escherichia coli. Stebbins CE, Borukhov S, Orlova M, Polyakov A, Goldfarb A, Darst SA;. Nature. 1995;373:636-640. (from Pfam) NF013446.5 PF01278.25 Omptin 22.6 22.6 283 domain Y Y N omptin family outer membrane protease 3.4.23.49 GO:0004175,GO:0006508,GO:0009279 2 Bacteria superkingdom 4461 EBI-EMBL Omptin family omptin family outer membrane protease The omptin family is a family of serine proteases. (from Pfam) NF013449.5 PF01281.24 Ribosomal_L9_N 20.7 20.7 47 PfamEq Y N N Ribosomal protein L9, N-terminal domain 8306963 2 Bacteria superkingdom 42213 EBI-EMBL Ribosomal protein L9, N-terminal domain Ribosomal protein L9, N-terminal domain NF013457.5 PF01289.24 Thiol_cytolysin 25 25 353 domain Y Y N thiol-activated cytolysin family protein GO:0015485 2 Bacteria superkingdom 5149 EBI-EMBL Thiol-activated cytolysin thiol-activated cytolysin family protein NF013466.5 PF01298.23 TbpB_B_D 26 26 126 domain Y Y N transferrin-binding protein-like solute binding protein 18186471,19716795,25800619 2 Bacteria superkingdom 9633 EBI-EMBL C-lobe and N-lobe beta barrels of Tf-binding protein B transferrin-binding protein-like solute binding protein Bacterial lipoproteins represent a large group of specialized membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis, and cell adherence [1]. Pathogenic Gram-negative bacteria within the Neisseriaceae and Pasteurellaceae families rely on a specialized uptake system, characterized by an essential surface receptor complex that acquires iron from host transferrin (Tf) and transports the iron across the outer membrane. They have an iron uptake system composed of surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), that together function to extract iron from the host iron binding glycoprotein (Tf). TbpB is a bilobed (N and C lobe) lipid-anchored protein with each lobe consisting of an eight-stranded beta barrel flanked by a "handle" domain made up of four (N lobe) or eight (C lobe) beta strands [2]. TbpB extends from the outer membrane surface by virtue of an N-terminal peptide region that is anchored to the outer membrane by fatty acyl chains on the N-terminal cysteine and is involved in the initial capture of iron-loaded Tf [3]. This domain family is found in C and N lobe eight stranded beta barrel region of TbpB proteins. The eight-stranded barrel domains in N and C lobe draw comparisons to eight-stranded beta barrel outer-membrane protein W (OmpW). However, the barrel domains of TbpB have the hydrophobic residues line the inner surface of the beta barrels to create a stable hydrophobic core [2]. [1]. 18186471. The solut. TRUNCATED at 1650 bytes (from Pfam) NF013478.5 PF01311.25 Bac_export_1 27.8 27.8 230 domain Y Y N flagellar biosynthetic protein FliR GO:0006605,GO:0016020 7814323 2 Bacteria superkingdom 43506 EBI-EMBL Bacterial export proteins, family 1 flagellar biosynthetic protein FliR This family includes the following members; FliR, MopE, SsaT, YopT, Hrp, HrcT and SpaR All of these members export proteins, that do not possess signal peptides, through the membrane. Although the proteins that these exporters move may be different, the exporters are thought to function in similar ways [1]. [1]. 7814323. Caulobacter FliQ and FliR membrane proteins, required for flagellar biogenesis and cell division, belong to a family of virulence factor export proteins. Zhuang WY, Shapiro L;. J Bacteriol 1995;177:343-356. (from Pfam) NF013479.5 PF01312.24 Bac_export_2 24.4 24.4 335 domain Y Y N EscU/YscU/HrcU family type III secretion system export apparatus switch protein GO:0009306,GO:0016020 8626302,9618447 2 Bacteria superkingdom 63308 EBI-EMBL FlhB HrpN YscU SpaS Family EscU/YscU/HrcU family type III secretion system export apparatus switch protein This family includes the following members: FlhB, HrpN, YscU, SpaS, HrcU SsaU and YopU. All of these proteins export peptides using the type III secretion system. The peptides exported are quite diverse. [1]. 9618447. Type III protein secretion systems in bacterial pathogens of animals and plants. Hueck CJ;. Microbiol Mol Biol Rev 1998;62:379-433. [2]. 8626302. Erwinia amylovora secretes harpin via a type III pathway and contains a homolog of yopN of Yersinia spp. Bogdanove AJ, Wei ZM, Zhao L, Beer SV;. J Bacteriol 1996;178:1720-1730. (from Pfam) NF013480.5 PF01313.24 Bac_export_3 25 25 74 domain Y Y N flagellar biosynthetic protein FliQ GO:0009306,GO:0016020 7814323 2 Bacteria superkingdom 23416 EBI-EMBL Bacterial export proteins, family 3 flagellar biosynthetic protein FliQ This family includes the following members; FliQ, MopD, HrcS, Hrp, YopS and SpaQ All of these members export proteins, that do not possess signal peptides, through the membrane. Although the proteins that these exporters move may be different, the exporters are thought to function in similar ways [1]. [1]. 7814323. Caulobacter FliQ and FliR membrane proteins, required for flagellar biogenesis and cell division, belong to a family of virulence factor export proteins. Zhuang WY, Shapiro L;. J Bacteriol 1995;177:343-356. (from Pfam) NF013483.5 PF01316.26 Arg_repressor 27 27 70 domain Y N N Arginine repressor, DNA binding domain GO:0003700,GO:0006355,GO:0006525 9334747 2 Bacteria superkingdom 23918 EBI-EMBL Arginine repressor, DNA binding domain Arginine repressor, DNA binding domain NF013485.5 PF01320.23 Colicin_Pyocin 21.2 21.2 82 domain Y Y N bacteriocin immunity protein GO:0015643,GO:0030153 8692833,8755730 2 Bacteria superkingdom 6029 EBI-EMBL Colicin immunity protein / pyocin immunity protein bacteriocin immunity protein NF013487.5 PF01322.25 Cytochrom_C_2 26.5 26.5 121 domain Y Y N cytochrome c GO:0005506,GO:0009055,GO:0020037 8230224,8676382 2 Bacteria superkingdom 15484 EBI-EMBL Cytochrome C' cytochrome c NF013497.5 PF01333.24 Apocytochr_F_C 30.4 30.4 118 PfamEq Y N N Apocytochrome F, C-terminal GO:0005506,GO:0009055,GO:0015979,GO:0020037,GO:0042651 8081747 2 Bacteria superkingdom 993 EBI-EMBL Apocytochrome F, C-terminal Apocytochrome F, C-terminal This is a sub-family of cytochrome C. See Pfam:PF00034. [1]. 8081747. Crystal structure of chloroplast cytochrome f reveals a novel cytochrome fold and unexpected heme ligation. Martinez SE, Huang D, Szczepaniak A, Cramer WA, Smith JL;. Structure 1994;2:95-105. (from Pfam) NF013501.5 PF01338.23 Bac_thur_toxin 25 25 230 domain Y N N Bacillus thuringiensis toxin GO:0005576 8632451 2 Bacteria superkingdom 950 EBI-EMBL Bacillus thuringiensis toxin Bacillus thuringiensis toxin NF013504.5 PF01341.22 Glyco_hydro_6 27 27 305 domain Y Y N glycoside hydrolase family 6 protein GO:0004553,GO:0030245 8875646 2 Bacteria superkingdom 30148 EBI-EMBL Glycosyl hydrolases family 6 glycoside hydrolase family 6 protein NF013509.5 PF01346.23 FKBP_N 22 22 97 domain Y Y N FKBP-type peptidyl-prolyl cis-trans isomerase N-terminal domain-containing protein GO:0006457 14672666 2 Bacteria superkingdom 38748 EBI-EMBL Domain amino terminal to FKBP-type peptidyl-prolyl isomerase Domain amino terminal to FKBP-type peptidyl-prolyl isomerase This family is only found at the amino terminus of Pfam:PF00254. This entry represents the N-terminal domain found in FKBP-type peptidylprolyl isomerases (PPIase). The N-terminal domain forms the dimer interface by the mutual exchange of two beta-strands between monomers [1]. [1]. 14672666. Structural and functional studies of FkpA from Escherichia coli, a cis/trans peptidyl-prolyl isomerase with chaperone activity. Saul FA, Arie JP, Vulliez-le Normand B, Kahn R, Betton JM, Bentley GA;. J Mol Biol. 2004;335:595-608. (from Pfam) NF013519.5 PF01357.26 Expansin_C 24.6 24.6 78 domain Y Y N expansin C-terminal domain-related protein 15604683,2605214 2 Bacteria superkingdom 979 EBI-EMBL Expansin C-terminal domain Expansin C-terminal domain This domain is found at the C-terminus of expansins, plant cell wall proteins involved in the non-enzymatic rearrangement of cell walls during cell growth. It contains the allergens lol PI, PII and PIII from Lolium perenne. [1]. 2605214. Complete primary structure of a Lolium perenne (perennial rye grass) pollen allergen, Lol p III: comparison with known Lol p I and II sequences. Ansari AA, Shenbagamurthi P, Marsh DG;. Biochemistry 1989;28:8665-8670. [2]. 15604683. Nomenclature for members of the expansin superfamily of genes and proteins. Kende H, Bradford K, Brummell D, Cho HT, Cosgrove D, Fleming A, Gehring C, Lee Y, McQueen-Mason S, Rose J, Voesenek LA;. Plant Mol Biol. 2004;55:311-314. (from Pfam) NF013521.5 PF01359.23 Transposase_1 24 24 80 domain Y N N Transposase (partial DDE domain) 8895590 2 Bacteria superkingdom 22 EBI-EMBL Transposase (partial DDE domain) Transposase (partial DDE domain) This family includes the mariner transposase [1]. [1]. 8895590. A purified mariner transposase is sufficient to mediate transposition in vitro. Lampe DJ, Churchill ME, Robertson HM;. EMBO J 1996;15:5470-5479. (from Pfam) NF013523.5 PF01363.26 FYVE 27.8 27.8 67 domain Y Y N FYVE zinc finger domain-containing protein GO:0046872 10564636,8798641,9697764 2 Bacteria superkingdom 60 EBI-EMBL FYVE zinc finger FYVE zinc finger domain The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn++ ions [1]. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. We have included members which do not conserve these histidine residues but are clearly related. Discovery of the FYVE finger. [1]. 8798641. Endosomal localization of the autoantigen EEA1 is mediated by a zinc-binding FYVE finger. Stenmark H, Aasland R, Toh BH, D'Arrigo A;. J Biol Chem 1996;271:24048-24054. [2]. 9697764. FYVE fingers bind PtdIns(3)P. Gaullier JM, Simonsen A, D'Arrigo A, Bremnes B, Stenmark H, Aasland R;. Nature 1998;394:432-433. [3]. 10564636. FYVE-finger proteins - effectors of an inositol lipid. Stenmark H, Aasland R;. J Cell Sci 1999;112:4175-4183. (from Pfam) NF013531.5 PF01371.24 Trp_repressor 27 27 88 domain Y Y N Trp family transcriptional regulator GO:0003700,GO:0006355 3419502 2 Bacteria superkingdom 9828 EBI-EMBL Trp repressor protein Trp family transcriptional regulator This protein binds to tryptophan and represses transcription of the Trp operon. [1]. 3419502. Crystal structure of trp repressor/operator complex at atomic resolution. Otwinowski Z, Schevitz RW, Zhang RG, Lawson CL, Joachimiak A, Marmorstein RQ, Luisi BF, Sigler PB. Nature 1988;335:321-329. (from Pfam) NF013535.5 PF01375.22 Enterotoxin_a 21 21 258 domain Y Y N enterotoxin A family protein GO:0005615,GO:0090729 8478941 2 Bacteria superkingdom 1210 EBI-EMBL Heat-labile enterotoxin alpha chain enterotoxin A family protein NF013541.5 PF01382.22 Avidin 24 24 116 subfamily Y Y N avidin/streptavidin family protein GO:0009374 2 Bacteria superkingdom 1602 EBI-EMBL Avidin family avidin/streptavidin family protein NF013545.5 PF01386.24 Ribosomal_L25p 23.6 23.6 82 PfamEq Y N N Ribosomal L25p family GO:0003735,GO:0005840,GO:0006412 10562563,9799245 2 Bacteria superkingdom 47485 EBI-EMBL Ribosomal L25p family Ribosomal L25p family Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis Swiss:P14194, which is induced by stress. [1]. 9799245. The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases. Stoldt M, Wohnert J, Gorlach M, Brown LR;. EMBO J 1998;17:6377-6384. [2]. 10562563. The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition. Stoldt M, Wohnert J, Ohlenschlager O, Gorlach M, Brown LR;. EMBO J 1999;18:6508-6521. (from Pfam) NF013548.5 PF01389.22 OmpA_membrane 21 21 180 domain Y N N OmpA-like transmembrane domain GO:0009279,GO:0016020 9808047 2 Bacteria superkingdom 41875 EBI-EMBL OmpA-like transmembrane domain OmpA-like transmembrane domain The structure of OmpA transmembrane domain shows that it consists of an eight stranded beta barrel [1]. This family includes some other distantly related outer membrane proteins with low scores. [1]. 9808047. Structure of the outer membrane protein A transmembrane domain. Pautsch A, Schulz GE;. Nat Struct Biol 1998;5:1013-1017. (from Pfam) NF013554.5 PF01395.27 PBP_GOBP 22 22 113 domain Y Y N pheromone/general odorant binding protein GO:0005549 2010751 2 Bacteria superkingdom 9 EBI-EMBL PBP/GOBP family pheromone/general odorant binding protein The olfactory receptors of terrestrial animals exist in an aqueous environment, yet detect odorants that are primarily hydrophobic. The aqueous solubility of hydrophobic odorants is thought to be greatly enhanced via odorant binding proteins which exist in the extracellular fluid surrounding the odorant receptors [1]. This family is composed of pheromone binding proteins (PBP), which are male-specific and associate with pheromone-sensitive neurons and general-odorant binding proteins (GOBP). [1]. 2010751. Odorant-binding-protein subfamilies associate with distinct classes of olfactory receptor neurons in insects. Vogt RG, Prestwich GD, Lerner MR;. J Neurobiol 1991;22:74-84. (from Pfam) NF013560.5 PF01401.23 Peptidase_M2 23 23 581 PfamEq Y Y N M2 family metallopeptidase GO:0006508,GO:0008237,GO:0008241,GO:0016020 7674927,9629165 2 Bacteria superkingdom 5438 EBI-EMBL Angiotensin-converting enzyme M2 family metallopeptidase Members of this family are dipeptidyl carboxydipeptidases (cleave carboxyl dipeptides) and most notably convert angiotensin I to angiotensin II. Many members of this family contain a tandem duplication of the 600 amino acid peptidase domain, both of these are catalytically active. Most members are secreted membrane bound ectoenzymes. [1]. 9629165. Toward a role for angiotensin-converting enzyme in insects. Isaac RE, Schoofs L, Williams TA, Corvol P, Veelaert D, Sajid M, Coates D;. Ann N Y Acad Sci 1998;839:288-292. [2]. 7674927. Peptidyl dipeptidase A: angiotensin I-converting enzyme. Corvol P, Williams TA, Soubrier F;. Methods Enzymol 1995;248:283-305. (from Pfam) NF013569.5 PF01410.23 COLFI 26.2 26.2 233 domain Y N N Fibrillar collagen C-terminal domain GO:0005201 1639194 2 Bacteria superkingdom 52 EBI-EMBL Fibrillar collagen C-terminal domain Fibrillar collagen C-terminal domain Found at C-termini of fibrillar collagens: Ephydatia muelleri procollagen EMF1 alpha, vertebrate collagens alpha(1)III, alpha(1)II, alpha(2)V etc. [1]. 1639194. The modular architecture of vertebrate collagens. Bork P;. FEBS Lett 1992;307:49-54. (from Pfam) NF013577.5 PF01418.22 HTH_6 28.3 28.3 77 domain Y N N Helix-turn-helix domain, rpiR family GO:0003700,GO:0006355 8576032 2 Bacteria superkingdom 138482 EBI-EMBL Helix-turn-helix domain, rpiR family Helix-turn-helix domain, rpiR family This domain contains a helix-turn-helix motif [1]. The best characterised member of this family is Swiss:P39266. RpiR is a regulator of the expression of rpiB gene. [1]. 8576032. Ribose catabolism of Escherichia coli: characterization of the rpiB gene encoding ribose phosphate isomerase B and of the rpiR gene, which is involved in regulation of rpiB expression. Sorensen KI, Hove-Jensen B;. J Bacteriol 1996;178:1003-1011. (from Pfam) NF013580.5 PF01421.24 Reprolysin 20.8 20.8 200 domain Y N N Reprolysin (M12B) family zinc metalloprotease GO:0004222,GO:0006508 12514095,7674922 2 Bacteria superkingdom 1302 EBI-EMBL Reprolysin (M12B) family zinc metalloprotease Reprolysin (M12B) family zinc metalloprotease The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family are also known as adamalysins. Most members of this family are snake venom endopeptidases, but there are also some mammalian proteins such as Swiss:P78325, and fertilin Swiss:Q28472. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes. [1]. 7674922. Evolutionary families of metallopeptidases. Rawlings ND, Barrett AJ;. Meth Enzymol 1995;248:183-228. [2]. 12514095. The ADAMs family of metalloproteases: multidomain proteins with multiple functions. Seals DF, Courtneidge SA;. Genes Dev 2003;17:7-30. (from Pfam) NF013589.5 PF01430.24 HSP33 21.4 21.4 273 PfamEq Y Y N Hsp33 family molecular chaperone HslO GO:0005737,GO:0006457,GO:0051082 10025400,11377197 2 Bacteria superkingdom 41008 EBI-EMBL Hsp33 protein Hsp33 family molecular chaperone HslO Hsp33 is a molecular chaperone, distinguished from all other known chaperones by its mode of functional regulation. Its activity is redox regulated. Hsp33 is a cytoplasmically localised protein with highly reactive cysteines that respond quickly to changes in the redox environment. Oxidising conditions like H2O2 cause disulfide bonds to form in Hsp33, a process that leads to the activation of its chaperone function [1]. [1]. 10025400. Chaperone activity with a redox switch. Jakob U, Muse W, Eser M, Bardwell JC;. Cell 1999;96:341-352. [2]. 11377197. The 2.2 A crystal structure of Hsp33: a heat shock protein with redox-regulated chaperone activity. Vijayalakshmi J, Mukhergee MK, Graumann J, Jakob U, Saper MA;. Structure (Camb) 2001;9:367-375. (from Pfam) NF013593.5 PF01434.23 Peptidase_M41 29.9 29.9 191 domain Y N N Peptidase family M41 GO:0004176,GO:0004222,GO:0005524,GO:0006508 2 Bacteria superkingdom 94427 EBI-EMBL Peptidase family M41 Peptidase family M41 NF013599.5 PF01441.24 Lipoprotein_6 27.8 27.8 170 subfamily Y Y N Vsp/OspC family lipoprotein GO:0009279 9403685 2 Bacteria superkingdom 571 EBI-EMBL Lipoprotein Vsp/OspC family lipoprotein Members of this family are lipoproteins that are probably involved in evasion of the host immune system by pathogens. This family is discussed briefly on page 585. [1]. 9403685. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Fraser CM, Casjens S, Huang WM, Sutton GG, Clayton R, Lathigra R, White O, Ketchum KA, Dodson R, Hickey EK, Gwinn M, Dougherty B, Tomb JF, Fleischmann RD, Richardson D, Peterson J, Kerlavage AR, Quackenbush J, Salzberg S, Hanson M, van Vugt R, Palmer N, A. Nature. 1997;390:580-586. (from Pfam) NF013600.5 PF01442.23 Apolipoprotein 90 12 190 PfamEq Y N N Apolipoprotein A1/A4/E domain GO:0005576,GO:0006869,GO:0008289,GO:0042157 2063194 2 Bacteria superkingdom 4575 EBI-EMBL Apolipoprotein A1/A4/E domain Apolipoprotein A1/A4/E domain These proteins contain several 22 residue repeats which form a pair of alpha helices. This family includes: Swiss:P02647 Apolipoprotein A-I. Swiss:P06727 Apolipoprotein A-IV. Swiss:P02649 Apolipoprotein E. [1]. 2063194. Three-dimensional structure of the LDL receptor-binding domain of human apolipoprotein E. Wilson C, Wardell MR, Weisgraber KH, Mahley RW, Agard DA;. Science 1991;252:1817-1822. (from Pfam) NF013603.5 PF01446.22 Rep_1 33.2 33.2 253 domain Y Y N protein rep GO:0003677,GO:0006260 9570403 2 Bacteria superkingdom 16853 EBI-EMBL Replication protein protein rep Replication proteins (rep) are involved in plasmid replication. The Rep protein binds to the plasmid DNA and nicks it at the double strand origin (dso) of replication. The 3'-hydroxyl end created is extended by the host DNA replicase, and the 5' end is displaced during synthesis. At the end of one replication round, Rep introduces a second single stranded break at the dso and ligates the ssDNA extremities generating one double-stranded plasmid and one circular ssDNA form. Complementary strand synthesis of the circular ssDNA is usually initiated at the single-stranded origin by the host RNA polymerase [1]. [1]. 9570403. A rolling circle replication initiator protein with a nucleotidyl-transferase activity encoded by the plasmid pGT5 from the hyperthermophilic archaeon Pyrococcus abyssi. Marsin S, Forterre P;. Mol Microbiol 1998;27:1183-1192. (from Pfam) NF013609.5 PF01453.29 B_lectin 32.4 32.4 105 domain Y Y N bulb-type lectin domain-containing protein 12533465,8939757 2 Bacteria superkingdom 115 EBI-EMBL D-mannose binding lectin D-mannose binding lectin These proteins include mannose-specific lectins from plants[1] as well as bacteriocins from bacteria [2]. [1]. 8939757. The 2.0 A structure of a cross-linked complex between snowdrop lectin and a branched mannopentaose: evidence for two unique binding modes. Wright CS, Hester G;. Structure 1996;4:1339-1352. [2]. 12533465. Plant lectin-like bacteriocin from a rhizosphere-colonizing Pseudomonas isolate. Parret AH, Schoofs G, Proost P, De Mot R;. J Bacteriol 2003;185:897-908. (from Pfam) NF013618.5 PF01464.25 SLT 21.3 21.3 117 domain Y Y N transglycosylase SLT domain-containing protein 14625683,7548026,8203016,8692991 2 Bacteria superkingdom 309099 EBI-EMBL Transglycosylase SLT domain Transglycosylase SLT domain This family is distantly related to Pfam:PF00062. Members are found in phages, type II, type III and type IV secretion systems (reviewed in [4]). [1]. 8203016. A conserved domain in putative bacterial and bacteriophage transglycosylases. Koonin EV, Rudd KE;. Trends Biochem Sci 1994;19:106-107. [2]. 8692991. A family of lysozyme-like virulence factors in bacterial pathogens of plants and animals. Mushegian AR, Fullner KJ, Koonin EV, Nester EW;. Proc Natl Acad Sci U S A 1996;93:7321-7326. [3]. 7548026. Structure of the 70-kDa soluble lytic transglycosylase complexed with bulgecin A. Implications for the enzymatic mechanism. Thunnissen AM, Rozeboom HJ, Kalk KH, Dijkstra BW;. Biochemistry 1995;34:12729-12737. [4]. 14625683. Lytic transglycosylases in macromolecular transport systems of Gram-negative bacteria. Koraimann G;. Cell Mol Life Sci 2003;60:2371-2388. (from Pfam) NF013628.5 PF01474.21 DAHP_synth_2 27 27 438 domain Y Y N 3-deoxy-7-phosphoheptulonate synthase 2.5.1.54 GO:0003849,GO:0009073 2 Bacteria superkingdom 36570 EBI-EMBL Class-II DAHP synthetase family 3-deoxy-7-phosphoheptulonate synthase Members of this family are aldolase enzymes that catalyse the first step of the shikimate pathway. (from Pfam) NF013630.5 PF01476.25 LysM 20.9 11.8 43 domain Y Y N LysM peptidoglycan-binding domain-containing protein 10843862,1352512 2 Bacteria superkingdom 360050 EBI-EMBL LysM domain LysM peptidoglycan-binding domain The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation [1]. This domain may have a general peptidoglycan binding function. The structure of this domain is known [2]. [1]. 1352512. Modular design of the Enterococcus hirae muramidase-2 and Streptococcus faecalis autolysin. Joris B, Englebert S, Chu CP, Kariyama R, Daneo-Moore L, Shockman GD, Ghuysen JM;. FEMS Microbiol Lett 1992;70:257-264. [2]. 10843862. The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD). Bateman A, Bycroft M;. J Mol Biol 2000;299:1113-1119. (from Pfam) NF013642.5 PF01490.23 Aa_trans 25.6 25.6 410 domain Y N N Transmembrane amino acid transporter protein 9349821 2 Bacteria superkingdom 16524 EBI-EMBL Transmembrane amino acid transporter protein Transmembrane amino acid transporter protein This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains Swiss:P34579 [1]. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance Swiss:P38680. Other members of this family include proline transporters and amino acid permeases. [1]. 9349821. Identification and characterization of the vesicular GABA transporter. McIntire SL, Reimer RJ, Schuske K, Edwards RH, Jorgensen EM;. Nature 1997;389:870-876. (from Pfam) NF013649.5 PF01498.23 HTH_Tnp_Tc3_2 31.5 31.5 72 domain Y N N Transposase GO:0003677,GO:0006313,GO:0015074 9312061 2 Bacteria superkingdom 122 EBI-EMBL Transposase Transposase Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of C.elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in [1]. Tc3 is a member of the Tc1/mariner family of transposable elements. [1]. 9312061. Crystal structure of the specific DNA-binding domain of Tc3 transposase of C.elegans in complex with transposon DNA. van Pouderoyen G, Ketting RF, Perrakis A, Plasterk RH, Sixma TK;. EMBO J 1997;16:6044-6054. (from Pfam) NF013656.5 PF01505.23 Vault 27 27 42 repeat Y N N major vault protein repeat-containing protein 10196123,23695250 2 Bacteria superkingdom 101 EBI-EMBL Major Vault Protein repeat domain major vault protein repeat The vault is a ubiquitous and highly conserved ribonucleoprotein particle of approximately 13 mDa of unknown function [1]. This family corresponds to a repeated domain found in the amino terminal half of the major vault protein. [1]. 10196123. Structure of the vault, a ubiquitous celular component. Kong LB, Siva AC, Rome LH, Stewart PL. Structure 1999;7:371-379. [2]. 23695250. New features of vault architecture and dynamics revealed by novel refinement using the deformable elastic network approach. Casanas A, Querol-Audi J, Guerra P, Pous J, Tanaka H, Tsukihara T, Verdaguer N, Fita I;. Acta Crystallogr D Biol Crystallogr. 2013;69:1054-1061. (from Pfam) NF013664.5 PF01514.22 YscJ_FliF 24.4 24.4 179 domain Y N N Secretory protein of YscJ/FliF family 10049798,1332940 2 Bacteria superkingdom 51230 EBI-EMBL Secretory protein of YscJ/FliF family Secretory protein of YscJ/FliF family This family includes proteins that are related to the YscJ lipoprotein, and the amino terminus of FliF, the flageller M-ring protein. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flageller proteins, based on the similarity to YscJ proteins [2]. [1]. 1332940. MxiJ, a lipoprotein involved in secretion of Shigella Ipa invasins, is homologous to YscJ, a secretion factor of the Yersinia Yop proteins. Allaoui A, Sansonetti PJ, Parsot C;. J Bacteriol 1992;174:7661-7669. [2]. 10049798. A structural feature in the central channel of the bacterial flagellar FliF ring complex is implicated in type III protein export. Suzuki H, Yonekura K, Murata K, Hirai T, Oosawa K, Namba K;. J Struct Biol 1998;124:104-114. (from Pfam) NF013676.5 PF01526.22 DDE_Tnp_Tn3 24 24 389 domain Y Y N Tn3 family transposase GO:0004803,GO:0006313 6262296,8932514 2 Bacteria superkingdom 44754 EBI-EMBL Tn3 transposase DDE domain Tn3 family transposase This family includes transposases of Tn3, Tn21, Tn1721, Tn2501, Tn3926 transposons from E-coli. The specific binding of the Tn3 transposase to DNA has been demonstrated. Sequence analysis has suggested that the invariant triad of Asp689, Asp765, Glu895 (numbering as in Tn3) may correspond to the D-D-35-E motif previously implicated in the catalysis of numerous transposases [2]. [1]. 6262296. Purification of the Tn3 transposase and analysis of its binding to DNA. Fennewald MA, Gerrard SP, Chou J, Casadaban MJ, Cozzarelli NR;. J Biol Chem 1981;256:4687-4690. [2]. 8932514. Catalytic center quest: comparison of transposases belonging to the Tn3 family reveals an invariant triad of acidic amino acid residues. Yurieva O, Nikiforov V;. Biochem Mol Biol Int 1996;38:15-20. (from Pfam) NF013686.5 PF01536.21 SAM_decarbox 22.2 22.2 343 PfamEq Y N N Adenosylmethionine decarboxylase GO:0004014,GO:0006597,GO:0008295 9435790 2 Bacteria superkingdom 557 EBI-EMBL Adenosylmethionine decarboxylase Adenosylmethionine decarboxylase This is a family of S-adenosylmethionine decarboxylase (SAMDC) proenzymes. In the biosynthesis of polyamines SAMDC produces decarboxylated S-adenosylmethionine, which serves as the aminopropyl moiety necessary for spermidine and spermine biosynthesis from putrescine [1]. The Pfam alignment contains both the alpha and beta chains that are cleaved to form the active enzyme. [1]. 9435790. Cloning, mapping and mutational analysis of the S-adenosylmethionine decarboxylase gene in Drosophila melanogaster. Larsson J, Rasmuson-Lestander A;. Mol Gen Genet 1997;256:652-660. (from Pfam) NF013702.5 PF01553.26 Acyltransferase 23 23 132 domain Y Y N 1-acyl-sn-glycerol-3-phosphate acyltransferase GO:0016746 8630491,9259571 2 Bacteria superkingdom 324833 EBI-EMBL Acyltransferase 1-acyl-sn-glycerol-3-phosphate acyltransferase This family contains acyltransferases involved in phospholipid biosynthesis and other proteins of unknown function [1]. This family also includes tafazzin Swiss:Q16635, the Barth syndrome gene [2]. [1]. 9259571. Barth syndrome may be due to an acyltransferase deficiency. Neuwald AF;. Curr Biol 1997;7:465-466. [2]. 8630491. A novel X-linked gene, G4.5. is responsible for Barth syndrome. Bione S, D'Adamo P, Maestrini E, Gedeon AK, Bolhuis PA, Toniolo D;. Nat Genet 1996;12:385-389. (from Pfam) NF013723.5 PF01576.24 Myosin_tail_1 38.1 38.1 1081 domain Y N N Myosin tail GO:0016459 3783701 2 Bacteria superkingdom 30 EBI-EMBL Myosin tail Myosin tail The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types [1]. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament [1]. The coiled-coil region provides the structural backbone the thick filament [1]. [1]. 3783701. Complete nucleotide and encoded amino acid sequence of a mammalian myosin heavy chain gene. Evidence against intron-dependent evolution of the rod. Strehler EE, Strehler-page M-A, Perriard JC, Periasamy M, Nadal-ginard B;. J MOL BIOL 1986;190:291-317. (from Pfam) NF013732.5 PF01585.28 G-patch 22 22 45 domain Y N N G-patch domain GO:0003676 10470032 2 Bacteria superkingdom 5 EBI-EMBL G-patch domain G-patch domain This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines. [1]. 10470032. G-patch: a new conserved domain in eukaryotic RNA-processing proteins and type D retroviral polyproteins. Aravind L, Koonin EV;. Trends Biochem Sci 1999;24:342-344. (from Pfam) NF013737.5 PF01591.23 6PF2K 27 27 223 domain Y Y N 6-phosphofructo-2-kinase domain-containing protein GO:0003873,GO:0005524,GO:0006000 8805587 2 Bacteria superkingdom 218 EBI-EMBL 6-phosphofructo-2-kinase 6-phosphofructo-2-kinase This enzyme occurs as a bifunctional enzyme with fructose-2,6-bisphosphatase. The bifunctional enzyme catalyses both the synthesis and degradation of fructose-2,6-bisphosphate, a potent regulator of glycolysis [1]. This enzyme contains a P-loop motif. [1]. 8805587. The crystal structure of the bifunctional enzyme 6-phosphofructo-2- kinase/fructose-2,6-bisphosphatase reveals distinct domain homologies. Hasemann CA, Istvan ES, Uyeda K, Deisenhofer J;. Structure 1996;4:1017-1029. (from Pfam) NF013759.5 PF01617.22 Surface_Ag_2 22 22 247 domain Y Y N P44/Msp2 family outer membrane protein 8294020,9573188 2 Bacteria superkingdom 7771 EBI-EMBL Surface antigen P44/Msp2 family outer membrane protein This family includes a number of bacterial surface antigens expressed on the surface of pathogens. [1]. 8294020. Derivation of the complete msp4 gene sequence of Anaplasma marginale without cloning. Oberle SM, Barbet AF;. Gene 1993;136:291-294. [2]. 9573188. Cloning and characterization of a gene encoding the major surface protein of the bacterial endosymbiont Wolbachia pipientis. Braig HR, Zhou W, Dobson SL, O'Neill SL;. J Bacteriol 1998;180:2373-2378. (from Pfam) NF013770.5 PF01630.23 Glyco_hydro_56 23.2 23.2 335 PfamEq Y N N Hyaluronidase GO:0004415,GO:0005975 8282124 2 Bacteria superkingdom 162 EBI-EMBL Hyaluronidase Hyaluronidase NF013771.5 PF01632.24 Ribosomal_L35p 28.9 28.9 61 PfamEq Y Y N 50S ribosomal protein L35 GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 20854 EBI-EMBL Ribosomal protein L35 50S ribosomal protein L35 NF013779.5 PF01640.22 Peptidase_C10 26 26 194 domain Y Y N C10 family peptidase GO:0006508,GO:0008234 2 Bacteria superkingdom 6977 EBI-EMBL Peptidase C10 family C10 family peptidase This family represents just the active peptide part of these proteins. Residues 1-120 are not part of the model as they form the pro-peptide, which before cleavage blocks the active site from the substrate. The catalytic residues of histidine and cysteine are brought close together at the active site by the folding of the active peptide. (from Pfam) NF013783.5 PF01644.22 Chitin_synth_1 25 25 163 PfamEq Y N N Chitin synthase GO:0004100,GO:0006031 1731323,7773595,9483806 2 Bacteria superkingdom 146 EBI-EMBL Chitin synthase Chitin synthase This region is found commonly in chitin synthases classes I, II and III. Chitin a linear homopolymer of GlcNAc residues, it is an important component of the cell wall of fungi and is synthesised on the cytoplasmic surface of the cell membrane by membrane bound chitin synthases [2]. [1]. 9483806. Molecular cloning and sequencing of a chitin synthase gene (CHS2) of Paracoccidioides brasiliensis. Nino-Vega GA, Buurman ET, Gooday GW, San-Blas G, Gow NA;. Yeast 1998;14:181-187. [2]. 7773595. The fungal cell wall as a drug target. Georgopapadakou NH, Tkacz JS;. Trends Microbiol 1995;3:98-104. [3]. 1731323. Classification of fungal chitin synthases. Bowen AR, Chen-Wu JL, Momany M, Young R, Szaniszlo PJ, Robbins PW;. Proc Natl Acad Sci U S A 1992;89:519-523. (from Pfam) NF013787.5 PF01649.23 Ribosomal_S20p 29.5 29.5 83 PfamEq Y Y N 30S ribosomal protein S20 GO:0003723,GO:0003735,GO:0005840,GO:0006412 3373529 2 Bacteria superkingdom 31975 EBI-EMBL Ribosomal protein S20 30S ribosomal protein S20 Bacterial ribosomal protein S20 interacts with 16S rRNA [1]. [1]. 3373529. Interaction of proteins S16, S17 and S20 with 16 S ribosomal RNA. Stern S, Changchien LM, Craven GR, Noller HF;. J Mol Biol 1988;200:291-299. (from Pfam) NF013804.5 PF01668.23 SmpB 27 27 143 PfamEq Y Y N SsrA-binding protein GO:0003723 2 Bacteria superkingdom 42487 EBI-EMBL SmpB protein SsrA-binding protein NF013814.5 PF01679.22 Pmp3 22.9 22.9 49 PfamEq Y Y N YqaE/Pmp3 family membrane protein GO:0016020 16603158 2 Bacteria superkingdom 8963 EBI-EMBL Proteolipid membrane potential modulator YqaE/Pmp3 family membrane domain Pmp3 is an evolutionarily conserved proteolipid in the plasma membrane which, in S. pombe, is transcriptionally regulated by the Spc1 stress MAPK (mitogen-activated protein kinases) pathway. It functions to modulate the membrane potential, particularly to resist high cellular cation concentration. In eukaryotic organisms, stress-activated mitogen-activated protein kinases play crucial roles in transmitting environmental signals that will regulate gene expression for allowing the cell to adapt to cellular stress. Pmp3-like proteins are highly conserved in bacteria, yeast, nematode and plants. [1]. 16603158. The fission yeast stress MAPK cascade regulates the pmp3+ gene that encodes a highly conserved plasma membrane protein. Wang LY, Shiozaki K;. FEBS Lett. 2006;580:2409-2413. (from Pfam) NF013834.5 PF01701.23 PSI_PsaJ 22.4 22.4 37 domain Y N N Photosystem I reaction centre subunit IX / PsaJ GO:0009522,GO:0015979 10220342,8486290 2 Bacteria superkingdom 611 EBI-EMBL Photosystem I reaction centre subunit IX / PsaJ Photosystem I reaction centre subunit IX / PsaJ This family consists of the photosystem I reaction centre subunit IX or PsaJ from various organisms including Synechocystis sp. (strain pcc 6803), Pinus thunbergii (green pine) and Zea mays (maize). PsaJ Swiss:P19443 is a small 4.4kDa, chloroplastal encoded, hydrophobic subunit of the photosystem I reaction complex its function is not yet fully understood [1]. PsaJ can be cross-linked to PsaF Swiss:P12356 and has a single predicted transmembrane domain it has a proposed role in maintaining PsaF in the correct orientation to allow for fast electron transfer from soluble donor proteins to P700+ [1]. [1]. 10220342. A large fraction of PsaF is nonfunctional in photosystem I complexes lacking the PsaJ subunit. Fischer N, Boudreau E, Hippler M, Drepper F, Haehnel W, Rochaix JD;. Biochemistry 1999;38:5546-5552. [2]. 8486290. Genes encoding eleven subunits of photosystem I from the thermophilic cyanobacterium Synechococcus sp. Muhlenhoff U, Haehnel W, Witt H, Herrmann RG;. Gene 1993;127:71-78. (from Pfam) NF013836.5 PF01704.23 UDPGP 22 22 413 PfamEq Y Y N UTP--glucose-1-phosphate uridylyltransferase 2.7.7.9 GO:0070569 3035502,8631325,9603950 2 Bacteria superkingdom 5592 EBI-EMBL UTP--glucose-1-phosphate uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase This family consists of UTP--glucose-1-phosphate uridylyltransferases, EC:2.7.7.9. Also known as UDP-glucose pyrophosphorylase (UDPGP) and Glucose-1-phosphate uridylyltransferase. UTP--glucose-1-phosphate uridylyltransferase catalyses the interconversion of MgUTP + glucose-1-phosphate and UDP-glucose + MgPPi [1]. UDP-glucose is an important intermediate in mammalian carbohydrate interconversion involved in various metabolic roles depending on tissue type [1]. In Dictyostelium (slime mold) mutants in this enzyme abort the development cycle [2]. Also within the family is UDP-N-acetylglucosamine Swiss:Q16222 or AGX1 [3] and two hypothetical proteins from Borrelia burgdorferi the lyme disease spirochaete Swiss:O51893 and Swiss:O51036. [1]. 8631325. Sequence differences between human muscle and liver cDNAs for UDPglucose pyrophosphorylase and kinetic properties of the recombinant enzymes expressed in Escherichia coli. Duggleby RG, Chao YC, Huang JG, Peng HL, Chang HY;. Eur J Biochem 1996;235:173-179. [2]. 3035502. Structure and sequence of a UDP glucose pyrophosphorylase gene of Dictyostelium discoideum. Ragheb JA, Dottin RP;. Nucleic Acids Res 1987;15:3891-3906. [3]. 9603950. The eukaryotic UDP-N-acetylglucosamine pyrophosphorylases. Gene cloning, protein expression, and catalytic mechanism. Mio T, Yabe T, Arisawa M, Yamada-Okabe H;. J Biol Chem 1998;273:14392-14397. (from Pfam) NF013838.5 PF01706.21 FliG_C 23.3 23.3 108 domain Y Y N FliG C-terminal domain-containing protein 10440379 2 Bacteria superkingdom 27414 EBI-EMBL FliG C-terminal domain FliG C-terminal domain FliG is a component of the flageller rotor, present in about 25 copies per flagellum. This domain functions specifically in motor rotation. [1]. 10440379. Structure of the C-terminal domain of FliG, a component of the rotor in the bacterial flagellar motor [In Process Citation]. Lloyd SA, Whitby FG, Blair DF, Hill CP;. Nature 1999;400:472-475. (from Pfam) NF013841.5 PF01709.25 Transcrip_reg 27 27 160 domain Y Y N YebC/PmpR family DNA-binding transcriptional regulator 12060744,18641136,19503089 2 Bacteria superkingdom 55084 EBI-EMBL TACO1/YebC second and third domain TACO1/YebC second and third domain This is a family of transcriptional regulators. In mammals, it activates the transcription of mitochondrially-encoded COX1 [2]. In bacteria, it negatively regulates the quorum-sensing response regulator by binding to its promoter region [3]. This entry represents the second and third domains in this protein, with one domain nested within the other. [1]. 12060744. Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus. Shin DH, Yokota H, Kim R, Kim SH;. Proc Natl Acad Sci U S A. 2002;99:7980-7985. [2]. 19503089. Mutation in TACO1, encoding a translational activator of COX I, results in cytochrome c oxidase deficiency and late-onset Leigh syndrome. Weraarpachai W, Antonicka H, Sasarman F, Seeger J, Schrank B, Kolesar JE, Lochmuller H, Chevrette M, Kaufman BA, Horvath R, Shoubridge EA;. Nat Genet. 2009;41:833-837. [3]. 18641136. The YebC family protein PA0964 negatively regulates the Pseudomonas aeruginosa quinolone signal system and pyocyanin production. Liang H, Li L, Dong Z, Surette MG, Duan K;. J Bacteriol. 2008;190:6217-6227. (from Pfam) NF013844.5 PF01713.26 Smr 25.7 25.7 77 domain Y Y N Smr/MutS family protein 10431172,12730195 2 Bacteria superkingdom 72014 EBI-EMBL Smr domain Smr domain This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 Swiss:P23909 protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2 Swiss:P94545 [1]. This domain exhibits nicking endonuclease activity that might have a role in mismatch repair or genetic recombination. It shows no significant double strand cleavage or exonuclease activity [2]. The full-length Swiss:Q86UW6 also has the polynucleotide kinase activity. [1]. 10431172. Smr: a bacterial and eukaryotic homologue of the C-terminal region of the MutS2 family. Moreira D, Philippe H;. Trends Biochem Sci 1999;24:298-300. [2]. 12730195. Identification and characterization of BCL-3-binding protein: implications for transcription and DNA repair or recombination. Watanabe N, Wachi S, Fujita T;. J Biol Chem. 2003;278:26102-26110. (from Pfam) NF013845.5 PF01715.22 IPPT 23.6 23.6 243 PfamEq Y N N IPP transferase 1850093,8139535,9294434 2 Bacteria superkingdom 82879 EBI-EMBL IPP transferase IPP transferase This is a family of IPP transferases EC:2.5.1.8 also known as tRNA delta(2)-isopentenylpyrophosphate transferase. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37) [2]. [1]. 9294434. The modified nucleoside 2-methylthio-N6-isopentenyladenosine in tRNA of Shigella flexneri is required for expression of virulence genes. Durand JM, Bjork GR, Kuwae A, Yoshikawa M, Sasakawa C;. J Bacteriol 1997;179:5777-5782. [2]. 8139535. Subcellular locations of MOD5 proteins: mapping of sequences sufficient for targeting to mitochondria and demonstration that mitochondrial and nuclear isoforms commingle in the cytosol. Boguta M, Hunter LA, Shen WC, Gillman EC, Martin NC, Hopper AK;. Mol Cell Biol 1994;14:2298-2306. [3]. 1850093. MOD5 translation initiation sites determine N6-isopentenyladenosine modification of mitochondrial and cytoplasmic tRNA. Gillman EC, Slusher LB, Martin NC, Hopper AK;. Mol Cell Biol 1991;11:2382-2390. (from Pfam) NF013846.5 PF01716.23 MSP 25 25 242 PfamEq Y Y N photosystem II manganese-stabilizing polypeptide psbO GO:0009654,GO:0010207,GO:0010242,GO:0042549 3138527 2 Bacteria superkingdom 872 EBI-EMBL Manganese-stabilising protein / photosystem II polypeptide photosystem II manganese-stabilizing polypeptide This family consists of the 33 KDa photosystem II polypeptide from the oxygen evolving complex (OEC) of plants and cyanobacteria. The protein is also known as the manganese-stabilising protein as it is associated with the manganese complex of the OEC and may provide the ligands for the complex [1]. [1]. 3138527. Cloning, nucleotide sequence and mutational analysis of the gene encoding the Photosystem II manganese-stabilizing polypeptide of Synechocystis 6803. Philbrick JB, Zilinskas BA;. Mol Gen Genet 1988;212:418-425. (from Pfam) NF013849.5 PF01719.22 Rep_OBD 24.6 24.6 121 domain Y Y N Rep family protein GO:0003677,GO:0003916,GO:0005727,GO:0006260 1904536,26875695,2695401,36688326 2 Bacteria superkingdom 4778 EBI-EMBL Plasmid replication protein, origin binding domain Plasmid replication protein, origin binding domain This entry includes of various bacterial plasmid replication (Rep) proteins. These proteins are essential for replication of plasmids, the Rep proteins are topoisomerases that nick the positive stand at the plus origin of replication and also at the single-strand conversion sequence [2]. They consist of a N-terminal origin binding domain (OBD) which is the DNA-binding/catalytic domain that belongs to the HUH endonuclease superfamily [3,4] and a C-terminal oligomerisation domain (OD), an helical domain responsible for the hexameric state of the protein [3,4]. [1]. 1904536. Genetic analysis of a lactococcal plasmid replicon. Xu FF, Pearce LE, Yu PL;. Mol Gen Genet 1991;227:33-39. [2]. 2695401. Characterization of a cryptic plasmid from Lactobacillus plantarum. Bates EE, Gilbert HJ;. Gene 1989;85:253-258. [3]. 36688326. Structures of pMV158 replication initiator RepB with and without DNA reveal a flexible dual-function protein. Machon C, Ruiz-Maso JA, Amodio J, Boer DR, Bordanaba-Ruiseco L, Bury K, Konieczny I, Del Solar G, Coll M;. Nucleic Acids Res. 2023;51:1458-1472. [4]. 26875695. Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158. Boer DR, Ruiz-Maso JA, Rueda M, Petoukhov MV, Machon C, Svergun DI, Orozco M, del Solar G, Coll M;. Sci Rep. 2016;6:20915. (from Pfam) NF013853.5 PF01724.21 DUF29 22.5 22.5 138 subfamily Y Y N DUF29 family protein 2 Bacteria superkingdom 14487 EBI-EMBL Domain of unknown function DUF29 DUF29 family protein This family consists of various hypothetical proteins from cyanobacteria, none of which are functionally described. The aligned region is approximately 120-140 amino acids long corresponding to almost the entire length of the proteins in the family. Swiss:Q2RPE2, PDB:3fcn, is a small protein that has a novel all-alpha fold. The N-terminal helical hairpin is likely to function as a dimerisation module. This protein is a member of PFam family PF01724. The function of this protein is unknown. One protein sequence contains a fusion of this protein and a DnaB domain, suggesting a possible role in DNA helicase activity (hypothetical). Dali hits have low Z and high rmsd, suggesting probably only topological similarities (not functional relevance) (details derived from TOPSAN). The family has several highly conserved sequence motifs, including YD/ExD, DxxNVxEEIE, and CPY/F/W, as well as conserved tryptophans. (from Pfam) NF013863.5 PF01735.23 PLA2_B 23 23 491 PfamEq Y N N Lysophospholipase catalytic domain GO:0004620,GO:0009395 8027085,8051052 2 Bacteria superkingdom 160 EBI-EMBL Lysophospholipase catalytic domain Lysophospholipase catalytic domain This family consists of Lysophospholipase / phospholipase B EC:3.1.1.5 and cytosolic phospholipase A2 EC:3.1.4 which also has a C2 domain Pfam:PF00168. Phospholipase B enzymes catalyse the release of fatty acids from lysophsopholipids and are capable in vitro of hydrolysing all phospholipids extractable form yeast cells [1]. Cytosolic phospholipase A2 associates with natural membranes in response to physiological increases in Ca2+ and selectively hydrolyses arachidonyl phospholipids [2], the aligned region corresponds the the carboxy-terminal Ca2+-independent catalytic domain of the protein as discussed in [2]. [1]. 8027085. Delineation of two functionally distinct domains of cytosolic phospholipase A2, a regulatory Ca(2+)-dependent lipid-binding domain and a Ca(2+)-independent catalytic domain. Nalefski EA, Sultzman LA, Martin DM, Kriz RW, Towler PS, Knopf JL, Clark JD;. J Biol Chem 1994;269:18239-18249. [2]. 8051052. The Saccharomyces cerevisiae PLB1 gene encodes a protein required for lysophospholipase and phospholipase B activity. Lee KS, Patton JL, Fido M, Hines LK, Kohlwein SD, Paltauf F, Henry SA, Levin DE;. J Biol Chem 1994;269:19725-19730. (from Pfam) NF013873.5 PF01745.21 IPT 20 20 233 domain Y Y N isopentenyl transferase family protein 1465104 2 Bacteria superkingdom 68402 EBI-EMBL Isopentenyl transferase isopentenyl transferase family protein Isopentenyl transferase / dimethylallyl transferase synthesises isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid [1]. [1]. 1465104. Organization and functional analysis of three T-DNAs from the vitopine Ti plasmid pTiS4. Canaday J, Gerad JC, Crouzet P, Otten L;. Mol Gen Genet 1992;235:292-303. (from Pfam) NF013874.5 PF01746.26 tRNA_m1G_MT 27.3 27.3 195 PfamEq Y N N tRNA (Guanine-1)-methyltransferase 6337136 2 Bacteria superkingdom 62464 EBI-EMBL tRNA (Guanine-1)-methyltransferase tRNA (Guanine-1)-methyltransferase This is a family of tRNA (Guanine-1)-methyltransferases EC:2.1.1.31. In E.coli K12 this enzyme catalyses the conversion of a guanosine residue to N1-methylguanine in position 37, next to the anticodon, in tRNA [1]. [1]. 6337136. Purification and characterization of transfer RNA (guanine- 1)methyltransferase from Escherichia coli. Hjalmarsson KJ, Bystrom AS, Bjork GR;. J Biol Chem 1983;258:1343-1351. (from Pfam) NF013879.5 PF01752.22 Peptidase_M9 26 26 289 domain Y Y N collagenase 3.4.24.3 GO:0004222,GO:0005576,GO:0006508,GO:0008270 7582017,8282691 2 Bacteria superkingdom 20374 EBI-EMBL Collagenase collagenase This family of enzymes break down collagens. [1]. 7582017. Molecular analysis of an extracellular protease gene from Vibrio parahaemolyticus. Lee CY, Su SC, Liaw RB;. Microbiology 1995;141:2569-2576. [2]. 8282691. Purification and characterization of Clostridium perfringens 120- kilodalton collagenase and nucleotide sequence of the corresponding gene. Matsushita O, Yoshihara K, Katayama S, Minami J, Okabe A;. J Bacteriol 1994;176:149-156. (from Pfam) NF013882.5 PF01755.22 Glyco_transf_25 24 24 199 domain Y Y N glycosyltransferase family 25 protein 1956289,7964493,8817494,9334165 2 Bacteria superkingdom 31065 EBI-EMBL Glycosyltransferase family 25 (LPS biosynthesis protein) glycosyltransferase family 25 protein Members of this family belong to Glycosyltransferase family 25 [1] This is a family of glycosyltransferases involved in lipopolysaccharide (LPS) biosynthesis. These enzymes catalyse the transfer of various sugars onto the growing LPS chain during its biosynthesis. [1]. 9334165. A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Campbell JA, Davies GJ, Bulone V, Henrissat B;. Biochem J 1997;326:929-939. [2]. 8817494. Molecular analysis of a locus for the biosynthesis and phase-variable expression of the lacto-N-neotetraose terminal lipopolysaccharide structure in Neisseria meningitidis. Jennings MP, Hood DW, Peak IR, Virji M, Moxon ER;. Mol Microbiol 1995;18:729-740. [3]. 7964493. Genetic locus for the biosynthesis of the variable portion of Neisseria gonorrhoeae lipooligosaccharide. Gotschlich EC;. J Exp Med 1994;180:2181-2190. [4]. 1956289. Molecular cloning of a gene involved in lipooligosaccharide biosynthesis and virulence expression by Haemophilus influenzae type B. Cope LD, Yogev R, Mertsola J, Latimer JL, Hanson MS, McCracken GH Jr, Hansen EJ;. Mol Microbiol 1991;5:1113-1124. (from Pfam) NF013883.5 PF01756.24 ACOX 22.1 22.1 181 domain Y Y N acyl-CoA dehydrogenase GO:0003997,GO:0005777,GO:0006635 9525937 2 Bacteria superkingdom 14351 EBI-EMBL Acyl-CoA oxidase acyl-CoA dehydrogenase This is a family of Acyl-CoA oxidases EC:1.3.3.6. Acyl-coA oxidase converts acyl-CoA into trans-2- enoyl-CoA [1]. [1]. 9525937. Molecular characterization of a glyoxysomal long chain acyl-CoA oxidase that is synthesized as a precursor of higher molecular mass in pumpkin. Hayashi H, De Bellis L, Yamaguchi K, Kato A, Hayashi M, Nishimura M;. J Biol Chem 1998;273:8301-8307. (from Pfam) NF013888.5 PF01762.26 Galactosyl_T 23 23 195 domain Y N N Galactosyltransferase GO:0006486,GO:0016020,GO:0016758 9417047,9417100 2 Bacteria superkingdom 337 EBI-EMBL Galactosyltransferase Galactosyltransferase This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltrans feras e Swiss:O43825 [1] and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase Swiss:O54904 [2]. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2 [1]. [1]. 9417100. Cloning of a human UDP-galactose:2-acetamido-2-deoxy-D-glucose 3beta- galactosyltransferase catalyzing the formation of type 1 chains. Kolbinger F, Streiff MB, Katopodis AG;. J Biol Chem 1998;273:433-440. [2]. 9417047. Genomic cloning and expression of three murine UDP-galactose: beta-N- acetylglucosamine beta1,3-galactosyltransferase genes. Hennet T, Dinter A, Kuhnert P, Mattu TS, Rudd PM, Berger EG;. J Biol Chem 1998;273:58-65. (from Pfam) NF013891.5 PF01765.24 RRF 29.7 29.7 164 PfamEq Y Y N ribosome recycling factor 8183897 2 Bacteria superkingdom 42245 EBI-EMBL Ribosome recycling factor ribosome recycling factor The ribosome recycling factor (RRF / ribosome release factor) dissociates the ribosome from the mRNA after termination of translation, and is essential bacterial growth [1]. Thus ribosomes are "recycled" and ready for another round of protein synthesis. [1]. 8183897. Ribosome recycling factor (ribosome releasing factor) is essential for bacterial growth. Janosi L, Shimizu I, Kaji A;. Proc Natl Acad Sci U S A 1994;91:4249-4253. (from Pfam) NF013898.5 PF01773.25 Nucleos_tra2_N 27 27 74 domain Y Y N Na+ dependent nucleoside transporter N-terminal domain-containing protein 7775409,8027026 2 Bacteria superkingdom 36682 EBI-EMBL Na+ dependent nucleoside transporter N-terminus Na+ dependent nucleoside transporter N-terminus This family consists of nucleoside transport proteins. Swiss:Q62773 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane [1]. Swiss:Q62674 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC [2]. This alignment covers the N terminus of this family [1]. 7775409. Primary structure and functional expression of a cDNA encoding the bile canalicular, purine-specific Na(+)-nucleoside cotransporter. Che M, Ortiz DF, Arias IM;. J Biol Chem 1995;270:13596-13599. [2]. 8027026. Cloning and functional expression of a complementary DNA encoding a mammalian nucleoside transport protein. Huang QQ, Yao SY, Ritzel MW, Paterson AR, Cass CE, Young JD;. J Biol Chem 1994;269:17757-17760. (from Pfam) NF013903.5 PF01778.22 Ribosomal_L28e 33.2 33.2 115 domain Y Y N 60S ribosomal protein L28 2 Bacteria superkingdom 12 EBI-EMBL Ribosomal L28e protein family 60S ribosomal protein L28 NF013904.5 PF01779.22 Ribosomal_L29e 27 27 40 domain Y N N Ribosomal L29e protein family GO:0003735,GO:0005840,GO:0006412 2 Bacteria superkingdom 6 EBI-EMBL Ribosomal L29e protein family Ribosomal L29e protein family NF013908.5 PF01783.28 Ribosomal_L32p 21.3 21.3 56 PfamEq Y Y N 50S ribosomal protein L32 GO:0003735,GO:0006412,GO:0015934 2 Bacteria superkingdom 25010 EBI-EMBL Ribosomal L32p protein family 50S ribosomal protein L32 NF013911.5 PF01786.22 AOX 22.7 22.7 216 PfamEq Y Y N alternative oxidase GO:0009916 8770590,9426242 2 Bacteria superkingdom 2031 EBI-EMBL Alternative oxidase alternative oxidase The alternative oxidase is used as a second terminal oxidase in the mitochondria, electrons are transfered directly from reduced ubiquinol to oxygen forming water [2]. This is not coupled to ATP synthesis and is not inhibited by cyanide, this pathway is a single step process [1]. In rice the transcript levels of the alternative oxidase are increased by low temperature [1]. [1]. 9426242. Transcript levels of tandem-arranged alternative oxidase genes in rice are increased by low temperature. Ito Y, Saisho D, Nakazono M, Tsutsumi N, Hirai A;. Gene 1997;203:121-129. [2]. 8770590. Cloning and analysis of the alternative oxidase gene of Neurospora crassa. Li Q, Ritzel RG, McLean LL, McIntosh L, Ko T, Bertrand H, Nargang FE;. Genetics 1996;142:129-140. (from Pfam) NF013913.6 PF01788.22 PsbJ 30 30 39 PfamEq Y Y N photosystem II reaction center protein J GO:0009523,GO:0009539,GO:0015979,GO:0016020 8420932 2 Bacteria superkingdom 387 EBI-EMBL PsbJ photosystem II reaction center protein J This family consists of the photosystem II reaction centre protein PsbJ from plants and Cyanobacteria. In Synechocystis sp. PCC 6803 PsbJ regulates the number of photosystem II centres in thylakoid membranes, it is a predicted 4kDa protein with one membrane spanning domain [1]. [1]. 8420932. Genetic and immunological analyses of the cyanobacterium Synechocystis sp. PCC 6803 show that the protein encoded by the psbJ gene regulates the number of photosystem II centers in thylakoid membranes. Lind LK, Shukla VK, Nyhus KJ, Pakrasi HB;. J Biol Chem 1993;268:1575-1579. (from Pfam) NF013915.5 PF01790.23 LGT 24.9 24.9 240 subfamily Y Y N prolipoprotein diacylglyceryl transferase family protein 2.4.99.- GO:0005886,GO:0008961,GO:0042158 2 Bacteria superkingdom 87831 EBI-EMBL Prolipoprotein diacylglyceryl transferase prolipoprotein diacylglyceryl transferase family protein Members of this family that score below the cutoffs of prolipoprotein diacylglyceryl transferase model TIGR00544 are likely to have a function other than the processing of the typical N-terminal lipoprotein signal peptide. NF013937.5 PF01815.21 Rop 25 25 57 subfamily Y Y N Rop family plasmid primer RNA-binding protein 3681971,6183660 2 Bacteria superkingdom 4324 EBI-EMBL Rop protein Rop family plasmid primer RNA-binding protein NF013940.5 PF01818.22 Translat_reg 25 25 122 PfamEq Y Y N translational repressor RegA regA GO:0003723 3120177,7761833 2 Bacteria superkingdom 24 EBI-EMBL Bacteriophage translational regulator translational repressor RegA The translational regulator protein regA is encoded by the T4 bacteriophage and binds to a region of messenger RNA (mRNA) that includes the initiator codon. RegA is unusual in that it represses the translation of about 35 early T4 mRNAs but does not affect nearly 200 other mRNAs [1]. [1]. 7761833. Crystal structure of the T4 regA translational regulator protein at 1.9 A resolution. Kang C, Chan R, Berger I, Lockshin C, Green L, Gold L, Rich A;. Science 1995;268:1170-1173. [2]. 3120177. Bacteriophage T4 regA protein binds to mRNAs and prevents translation initiation. Winter RB, Morrissey L, Gauss P, Gold L, Hsu T, Karam J;. Proc Natl Acad Sci U S A 1987;84:7822-7826. (from Pfam). RegA, a phage protein, has been characterized in phage T4 and RB69 as an RNA-binding protein that blocks the initiation of protein translation. NF013946.5 PF01824.23 MatK_N 31.4 31.4 331 domain Y N N MatK/TrnK amino terminal region 8255751 2 Bacteria superkingdom 42 EBI-EMBL MatK/TrnK amino terminal region MatK/TrnK amino terminal region The function of this region is unknown. [1]. 8255751. Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Mohr G, Perlman PS, Lambowitz AM;. Nucleic Acids Res 1993;21:4991-4997. (from Pfam) NF013954.5 PF01832.25 Glucosaminidase 30.2 30.2 123 domain Y Y N glucosaminidase domain-containing protein GO:0004040 10049388 2 Bacteria superkingdom 91528 EBI-EMBL Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase This family includes Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase EC:3.2.1.96. As well as the flageller protein J Swiss:P75942 that has been shown to hydrolyse peptidoglycan [1]. [1]. 10049388. Peptidoglycan-hydrolyzing activity of the FlgJ protein, essential for flagellar rod formation in Salmonella typhimurium. Nambu T, Minamino T, Macnab RM, Kutsukake K;. J Bacteriol 1999;181:1555-1561. (from Pfam) NF013965.5 PF01845.22 CcdB 28.6 28.6 101 domain Y Y N CcdB family protein GO:0006276,GO:0008657 9917404 2 Bacteria superkingdom 8069 EBI-EMBL CcdB protein CcdB family protein NF013967.5 PF01847.21 VHL 21 21 82 domain Y N N VHL beta domain 10205047 2 Bacteria superkingdom 880 EBI-EMBL VHL beta domain VHL beta domain VHL forms a ternary complex with the elonginB Swiss:O44226 and elonginC Swiss:O13292 proteins. This complex binds Cul2, which then is involved in regulation of vascular endothelial growth factor Swiss:P15692 mRNA. [1]. 10205047. Structure of the VHL-ElonginC-ElonginB Complex: Implications for VHL Tumor Suppressor Function. Stebbins CE, Kaelin WG Jr, Pavletich NP;. Science 1999;284:455-461. (from Pfam) NF014109.5 PF02011.20 Glyco_hydro_48 25 25 619 domain Y Y N glycoside hydrolase family 48 protein GO:0004553,GO:0008810,GO:0030245 12096911,23055526 2 Bacteria superkingdom 7475 EBI-EMBL Glycosyl hydrolase family 48 glycoside hydrolase family 48 protein Members of this family are endoglucanase EC:3.2.1.4 and exoglucanase EC:3.2.1.91 enzymes that cleave cellulose or related substrate. (from Pfam) NF014111.5 PF02013.21 CBM_10 23 23 36 domain Y Y N carbohydrate-binding domain-containing protein 10493932,11514516,11524680,7492333 2 Bacteria superkingdom 1289 EBI-EMBL Cellulose or protein binding domain Cellulose or protein binding domain This domain is found in two distinct sets of proteins with different functions. Those found in aerobic bacteria bind cellulose (or other carbohydrates); but in anaerobic fungi they are protein binding domains, referred to as dockerin domains or docking domains. They are believed to be responsible for the assembly of a multiprotein cellulase/hemicellulase complex, similar to the cellulosome found in certain anaerobic bacteria. [1]. 7492333. Novel cellulose-binding domains, NodB homologues and conserved modular architecture in xylanases from the aerobic soil bacteria Pseudomonas fluorescens subsp. cellulosa and Cellvibrio mixtus. Millward-Sadler SJ, Davidson K, Hazlewood GP, Black GW, Gilbert HJ, Clarke JH;. Biochem J 1995;312:39-48. [2]. 11524680. Characterization of a cellulosome dockerin domain from the anaerobic fungus Piromyces equi. Raghothama S, Eberhardt RY, Simpson P, Wigelsworth D, White P, Hazlewood GP, Nagy T, Gilbert HJ, Williamson MP;. Nat Struct Biol 2001;8:775-778. [3]. 10493932. A modular cinnamoyl ester hydrolase from the anaerobic fungus Piromyces equi acts synergistically with xylanase and is part of a multiprotein cellulose-binding cellulase-hemicellulase complex. Fillingham IJ, Kroon PA, Williamson G, Gilbert HJ, Hazlewood GP;. Biochem J 1999;343:215-224. [4]. 11514516. Noncatalytic docking domains of cellulosomes of anaerobic fungi. Steenbakkers PJ, Li XL, Ximenes EA, Arts JG, Chen H, Ljungdahl LG, Op Den Camp HJ;. J Bacteriol 2001;183:5325-5333. (from Pfam) NF014128.5 PF02030.20 Lipoprotein_8 20 20 493 domain Y N N Hypothetical lipoprotein (MG045 family) 2 Bacteria superkingdom 16204 EBI-EMBL Hypothetical lipoprotein (MG045 family) Hypothetical lipoprotein (MG045 family) This family includes hypothetical lipoproteins, the amino terminal part of this protein is related to Pfam:PF01547, a family of solute binding proteins. This suggests this family also has a solute binding function. (from Pfam) NF014129.5 PF02031.21 Peptidase_M7 25 25 133 subfamily Y Y N snapalysin family zinc-dependent metalloprotease 3.4.24.- GO:0004222,GO:0005576,GO:0006508,GO:0008270 2 Bacteria superkingdom 9637 EBI-EMBL Streptomyces extracellular neutral proteinase (M7) family snapalysin family zinc-dependent metalloprotease NF014130.5 PF02033.23 RBFA 34.7 34.7 105 PfamEq Y Y N ribosome-binding factor A GO:0006364 2 Bacteria superkingdom 44236 EBI-EMBL Ribosome-binding factor A ribosome-binding factor A NF014138.5 PF02043.22 Bac_chlorC 25 25 80 domain Y Y N bacteriochlorophyll c-binding family protein GO:0015979 22685072,27534696 2 Bacteria superkingdom 71 EBI-EMBL Bacteriochlorophyll C binding protein bacteriochlorophyll c-binding family protein NF014143.5 PF02049.23 FliE 22.4 22.4 89 domain Y Y N flagellar hook-basal body complex protein FliE GO:0003774,GO:0005198,GO:0009288,GO:0071973 2 Bacteria superkingdom 26637 EBI-EMBL Flagellar hook-basal body complex protein FliE flagellar hook-basal body complex protein FliE NF014144.5 PF02050.21 FliJ 28.4 28.4 123 domain Y Y N flagellar FliJ family protein GO:0009288,GO:0071973 2 Bacteria superkingdom 21965 EBI-EMBL Flagellar FliJ protein flagellar FliJ family protein NF014149.5 PF02057.20 Glyco_hydro_59 27 27 294 domain Y N N Glycosyl hydrolase family 59 GO:0004336,GO:0006683 2 Bacteria superkingdom 18020 EBI-EMBL Glycosyl hydrolase family 59 Glycosyl hydrolase family 59 NF014160.5 PF02069.21 Metallothio_Pro 33 33 51 domain Y N N Prokaryotic metallothionein GO:0046872 11493688,3137921 2 Bacteria superkingdom 1827 EBI-EMBL Prokaryotic metallothionein Prokaryotic metallothionein Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds. (from Pfam) NF014168.5 PF02077.20 SURF4 27 27 267 domain Y N N SURF4 family GO:0016020 2 Bacteria superkingdom 7555 EBI-EMBL SURF4 family SURF4 family NF014172.5 PF02081.20 TrpBP 21.3 21.3 69 PfamEq Y Y N trp RNA-binding attenuation protein MtrB mtrB 2 Bacteria superkingdom 1957 EBI-EMBL Tryptophan RNA-binding attenuator protein trp RNA-binding attenuation protein MtrB NF014195.5 PF02107.21 FlgH 27 27 172 domain Y Y N flagellar basal body L-ring protein FlgH GO:0003774,GO:0009427,GO:0071973 2 Bacteria superkingdom 24000 EBI-EMBL Flagellar L-ring protein flagellar basal body L-ring protein FlgH NF014196.5 PF02108.21 FliH 24.1 24.1 128 domain Y Y N FliH/SctL family protein 2 Bacteria superkingdom 36488 EBI-EMBL Flagellar assembly protein FliH FliH/SctL family protein Top-scoring members of this family are the flagellar assembly protein FliH, but the family also includes the stator protein SctL of the type III secretion system (T3SS) apparatus. Note that SctL proteins have a variety of lineage-specific names: YscL, VscL, PscL, etc. NF014199.5 PF02112.20 PDEase_II 23.7 23.7 340 PfamEq Y N N cAMP phosphodiesterases class-II GO:0004115,GO:0006198 2 Bacteria superkingdom 4940 EBI-EMBL cAMP phosphodiesterases class-II cAMP phosphodiesterases class-II NF014202.5 PF02115.22 Rho_GDI 26.5 26.5 193 domain Y N N RHO protein GDP dissociation inhibitor GO:0005094,GO:0005515,GO:0005737,GO:0007266 2 Bacteria superkingdom 243 EBI-EMBL RHO protein GDP dissociation inhibitor RHO protein GDP dissociation inhibitor NF014206.5 PF02119.21 FlgI 25.3 25.3 343 domain Y Y N flagellar basal body P-ring protein FlgI GO:0005198,GO:0009428,GO:0030288,GO:0071973 2 Bacteria superkingdom 27540 EBI-EMBL Flagellar P-ring protein flagellar basal body P-ring protein FlgI NF014207.5 PF02120.21 Flg_hook 29.8 29.8 85 domain Y Y N flagellar hook-length control protein FliK 17542929 2 Bacteria superkingdom 74552 EBI-EMBL Flagellar hook-length control protein FliK flagellar hook-length control protein FliK This is the C terminal domain of FliK. FliK controls the length of the flagellar hook by directly measuring the hook length as a molecular ruler [1]. This family also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. [1]. 17542929. FliK regulates flagellar hook length as an internal ruler. Shibata S, Takahashi N, Chevance FF, Karlinsey JE, Hughes KT, Aizawa S;. Mol Microbiol. 2007;64:1404-1415. (from Pfam) NF014216.5 PF02130.22 YbeY 25 25 129 PfamEq Y Y N rRNA maturation RNAse YbeY GO:0004222,GO:0006364 12832766,15965736,20807199,23273979,32605982 2 Bacteria superkingdom 57319 EBI-EMBL Endoribonuclease YbeY rRNA maturation RNAse YbeY YbeY is a single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. It acts together with the RNase R to eliminate defective 70S ribosomes, but not properly maturated 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. It is involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both the 5'-and 3'-ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs [2,3,4]. The crystal structure of the protein from Aquifex aeolicus showed an overall fold consisting of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices [5]. [1]. 15965736. NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure. Penhoat CH, Li Z, Atreya HS, Kim S, Yee A, Xiao R, Murray D, Arrowsmith CH, Szyperski T;. J Struct Funct Genomics. 2005;6:51-62. [2]. 23273979. Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. Jacob AI, Kohrer C, Davies BW, RajBhandary UL, Walker GC;. Mol Cell. 2013;49:427-438. [3]. 20807199. Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing. Davies BW, Kohrer C, Jacob AI, Simmons LA, Zhu J, Aleman LM, Rajbhandary UL, Walker GC;. Mol Microbiol. 2010;78:506-518. [4]. 32605982. Endoribonuclease YbeY Is Essential for RNA Processing and Virulence in Pseudomonas aeruginosa. Xia Y, Weng Y, Xu C, Wang D, Pan X, Tian Z, Xia B, Li H, Chen R, Liu C, Jin Y, Bai F, Ch. TRUNCATED at 1650 bytes (from Pfam) NF014235.5 PF02154.20 FliM 27 27 192 domain Y N N Flagellar motor switch protein FliM GO:0003774,GO:0009425,GO:0071973 2 Bacteria superkingdom 23689 EBI-EMBL Flagellar motor switch protein FliM Flagellar motor switch protein FliM NF014247.5 PF02167.20 Cytochrom_C1 22.8 22.8 219 domain Y Y N cytochrome c1 GO:0009055,GO:0020037 21996020,2536365 2 Bacteria superkingdom 19676 EBI-EMBL Cytochrome C1 family cytochrome c1 NF014248.5 PF02169.21 LPP20 25.9 25.9 97 domain Y Y N LPP20 family lipoprotein 7928954 2 Bacteria superkingdom 5344 EBI-EMBL LPP20 lipoprotein LPP20 family lipoprotein This family contains the LPP20 lipoprotein, which is a non-essential class of lipoprotein [1]. [1]. 7928954. Molecular characterization of a conserved 20-kilodalton membrane-associated lipoprotein antigen of Helicobacter pylori. Kostrzynska M, O'Toole PW, Taylor DE, Trust TJ;. J Bacteriol. 1994;176:5938-5948. (from Pfam) NF014279.5 PF02201.23 SWIB 25 25 74 domain Y Y N SWIB/MDM2 domain-containing protein GO:0005515 12016060,8875929 2 Bacteria superkingdom 4170 EBI-EMBL SWIB/MDM2 domain SWIB/MDM2 domain This family includes the SWIB domain and the MDM2 domain [1]. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2 [2]. [1]. 12016060. The SWIB and the MDM2 domains are homologous and share a common fold. Bennett-Lovsey R, Hart SE, Shirai H, Mizuguchi K;. Bioinformatics 2002;18:626-630. [2]. 8875929. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Kussie PH, Gorina S, Marechal V, Elenbaas B, Moreau J, Levine AJ, Pavletich NP;. Science. 1996;274:948-953. (from Pfam) NF014291.5 PF02213.21 GYF 25.7 25.7 45 domain Y Y N GYF domain-containing protein GO:0005515 10404223,9843987 2 Bacteria superkingdom 78 EBI-EMBL GYF domain GYF domain The GYF domain is named because of the presence of Gly-Tyr-Phe residues. The GYF domain is a proline-binding domain in CD2-binding protein Swiss:O95400. [1]. 10404223. The GYF domain is a novel structural fold that is involved in lymphoid signaling through proline-rich sequences. Freund C, Dotsch V, Nishizawa K, Reinherz EL, Wagner G;. Nat Struct Biol 1999;6:656-660. [2]. 9843987. Identification of a proline-binding motif regulating CD2-triggered T lymphocyte activation. Nishizawa K, Freund C, Li J, Wagner G, Reinherz EL;. Proc Natl Acad Sci U S A 1998;95:14897-14902. (from Pfam) NF014297.5 PF02221.20 E1_DerP2_DerF2 22.7 22.7 133 domain Y Y N ML domain-containing protein 9737847 2 Bacteria superkingdom 133 EBI-EMBL ML domain ML domain ML domain - MD-2-related lipid recognition domain. This family consists of proteins from plants, animals and fungi, including dust mite allergen Der P 2 (Swiss:P49278). It has been implicate in lipid recognition, particularly in the recognition of pathogen related products. A mutation in Npc2 (Swiss:Q15668) causes a rare form of Niemann-Pick type C2 disease. This domain has a similar topology to immunoglobulin domains. [1]. 9737847. Tertiary structure of the major house dust mite allergen Der p 2: sequential and structural homologies. Mueller GA, Benjamin DC, Rule GS;. Biochemistry 1998;37:12707-12714. (from Pfam) NF014326.5 PF02255.21 PTS_IIA 27 27 94 domain Y Y N PTS lactose/cellobiose transporter subunit IIA GO:0009401 9261069 2 Bacteria superkingdom 19244 EBI-EMBL PTS system, Lactose/Cellobiose specific IIA subunit PTS lactose/cellobiose transporter subunit IIA The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIA PTS system enzymes. This family of proteins normally function as a homotrimer, stabilised by a centrally located metal ion [1]. Separation into subunits is thought to occur after phosphorylation. [1]. 9261069. The structure of enzyme IIAlactose from Lactococcus lactis reveals a new fold and points to possible interactions of a multicomponent system. Sliz P, Engelmann R, Hengstenberg W, Pai EF;. Structure 1997;5:775-788. (from Pfam) NF014327.5 PF02256.22 Fe_hyd_SSU 24 24 56 domain Y Y N iron hydrogenase small subunit 10368269 2 Bacteria superkingdom 10564 EBI-EMBL Iron hydrogenase small subunit iron hydrogenase small subunit This family represents the small subunit of the Fe-only hydrogenases EC:1.18.99.1. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold [1]. [1]. 10368269. Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center. Nicolet Y, Piras C, Legrand P, Hatchikian CE, Fontecilla-Camps JC;. Structure Fold Des 1999;7:13-23. (from Pfam) NF014335.5 PF02264.20 LamB 25.1 25.1 378 subfamily Y Y N carbohydrate porin GO:0015288,GO:0016020,GO:0034219 7824948 2 Bacteria superkingdom 36211 EBI-EMBL LamB porin carbohydrate porin Maltoporin (LamB protein) forms a trimeric structure which facilitates the diffusion of maltodextrins across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an antiparallel beta-barrel [1]. [1]. 7824948. Structural basis for sugar translocation through maltoporin channels at 3.1 A resolution [see comments]. Schirmer T, Keller TA, Wang YF, Rosenbusch JP;. Science 1995;267:512-514. (from Pfam) NF014346.5 PF02276.23 CytoC_RC 22.4 22.4 310 subfamily Y Y N photosynthetic reaction center cytochrome c subunit family protein GO:0005506,GO:0009055,GO:0019684,GO:0020037,GO:0030077 9351808 2 Bacteria superkingdom 2247 EBI-EMBL Photosynthetic reaction centre cytochrome C subunit photosynthetic reaction center cytochrome c subunit family protein Photosynthesis in purple bacteria is dependent on light-induced electron transfer in the reaction centre (RC), coupled to the uptake of protons from the cytoplasm. The RC contains a cytochrome molecule which re-reduces the oxidised electron donor. [1]. 9351808. The coupling of light-induced electron transfer and proton uptake as derived from crystal structures of reaction centres from Rhodopseudomonas viridis modified at the binding site of the secondary quinone, QB. Lancaster CR, Michel H;. Structure 1997;5:1339-1359. (from Pfam) NF014349.5 PF02281.21 Dimer_Tnp_Tn5 26.7 26.7 99 domain Y Y N IS4 family transposase 10207011,6306482 2 Bacteria superkingdom 3027 EBI-EMBL Transposase Tn5 dimerisation domain IS4 family transposase dimerization domain Tn5 belongs to the IS4 family of mobile element. This HMM describes a dimerization domain found at the C-terminus of IS4 family transposases. NF014354.5 PF02286.20 Dehydratase_LU 25 25 552 domain Y Y N propanediol/glycerol family dehydratase large subunit GO:0016836,GO:0031419 9805380 2 Bacteria superkingdom 4118 EBI-EMBL Dehydratase large subunit propanediol/glycerol family dehydratase large subunit This family contains the large subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances. [1]. 9805380. Molecular cloning, sequencing and characterization of the genes for adenosylcobalamin-dependent diol dehydratase of Klebsiella pneumoniae. Tobimatsu T, Azuma M, Hayashi S, Nishimoto K, Toraya T;. Biosci Biotechnol Biochem 1998;62:1774-1777. (from Pfam) NF014355.5 PF02287.20 Dehydratase_SU 25 25 133 domain Y Y N diol dehydratase small subunit 9805380 2 Bacteria superkingdom 2934 EBI-EMBL Dehydratase small subunit diol dehydratase small subunit This family contains the small subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances. [1]. 9805380. Molecular cloning, sequencing and characterization of the genes for adenosylcobalamin-dependent diol dehydratase of Klebsiella pneumoniae. Tobimatsu T, Azuma M, Hayashi S, Nishimoto K, Toraya T;. Biosci Biotechnol Biochem 1998;62:1774-1777. (from Pfam) NF014356.5 PF02288.20 Dehydratase_MU 27 27 110 domain Y Y N glycerol dehydratase reactivase beta/small subunit family protein 9805380 2 Bacteria superkingdom 5669 EBI-EMBL Dehydratase medium subunit glycerol dehydratase reactivase beta/small subunit family protein This family contains the medium subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances. [1]. 9805380. Molecular cloning, sequencing and characterization of the genes for adenosylcobalamin-dependent diol dehydratase of Klebsiella pneumoniae. Tobimatsu T, Azuma M, Hayashi S, Nishimoto K, Toraya T;. Biosci Biotechnol Biochem 1998;62:1774-1777. (from Pfam) NF014366.5 PF02300.22 Fumarate_red_C 24.2 24.2 127 PfamEq Y N N Fumarate reductase subunit C GO:0016020 3308458 2 Bacteria superkingdom 4002 EBI-EMBL Fumarate reductase subunit C Fumarate reductase subunit C Fumarate reductase is a membrane-bound flavoenzyme consisting of four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centres to the electron-transport chain. This family consists of the 15kD hydrophobic subunit C. [1]. 3308458. Nucleotide sequence and comparative analysis of the frd operon encoding the fumarate reductase of Proteus vulgaris. Extensive sequence divergence of the membrane anchors and absence of an frd-linked ampC cephalosporinase gene. Cole ST;. Eur J Biochem 1987;167:481-488. (from Pfam) NF014368.5 PF02302.22 PTS_IIB 23.6 23.6 90 domain Y N N PTS system, Lactose/Cellobiose specific IIB subunit GO:0008982,GO:0009401 9041631 2 Bacteria superkingdom 152879 EBI-EMBL PTS system, Lactose/Cellobiose specific IIB subunit PTS system, Lactose/Cellobiose specific IIB subunit The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian tyrosine phosphatases. This family also contains the fructose specific IIB subunit. [1]. 9041631. The NMR side-chain assignments and solution structure of enzyme IIBcellobiose of the phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli. Ab E, Schuurman-Wolters G, Reizer J, Saier MH, Dijkstra K, Scheek RM, Robillard GT;. Protein Sci 1997;6:304-314. (from Pfam) NF014369.5 PF02303.22 Phage_DNA_bind 25 25 82 subfamily Y Y N single-stranded DNA-binding protein GO:0003697,GO:0006260 3270530 2 Bacteria superkingdom 1443 EBI-EMBL Helix-destabilising protein single-stranded DNA-binding protein This family contains the bacteriophage helix-destabilising protein, or single-stranded DNA binding protein, required for DNA synthesis. [1]. 3270530. A preliminary structure for the DNA binding protein from bacteriophage IKe. Brayer GD;. J Biomol Struct Dyn 1987;4:859-868. (from Pfam) NF014372.5 PF02306.20 Phage_G 25 25 175 PfamEq Y N N Major spike protein (G protein) GO:0019048 9305849 2 Bacteria superkingdom 20 EBI-EMBL Major spike protein (G protein) Major spike protein (G protein) This is a family of proteins from single-stranded DNA bacteriophages. Five G proteins, each a tight beta barrel, from twelve surface spikes. [1]. 9305849. Structure of a viral procapsid with molecular scaffolding. Dokland T, McKenna R, Ilag LL, Bowman BR, Incardona NL, Fane BA, Rossmann MG;. Nature 1997;389:308-313. (from Pfam) NF014378.5 PF02313.22 Fumarate_red_D 25 25 114 PfamEq Y N N Fumarate reductase subunit D GO:0006106,GO:0016020 3308458 2 Bacteria superkingdom 3800 EBI-EMBL Fumarate reductase subunit D Fumarate reductase subunit D Fumarate reductase is a membrane-bound flavoenzyme consisting of four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centres to the electron-transport chain. This family consists of the 13kD hydrophobic subunit D. [1]. 3308458. Nucleotide sequence and comparative analysis of the frd operon encoding the fumarate reductase of Proteus vulgaris. Extensive sequence divergence of the membrane anchors and absence of an frd-linked ampC cephalosporinase gene. Cole ST;. Eur J Biochem 1987;167:481-488. (from Pfam) NF014379.5 PF02315.21 MDH 27 27 87 PfamEq Y N N Methanol dehydrogenase beta subunit GO:0004022,GO:0015946 7735834 2 Bacteria superkingdom 519 EBI-EMBL Methanol dehydrogenase beta subunit Methanol dehydrogenase beta subunit Methanol dehydrogenase (MDH) is a bacterial periplasmic quinoprotein that oxidises methanol to formaldehyde. MDH is a tetramer of two alpha and two beta subunits. This family contains the small beta subunit. [1]. 7735834. The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 A. Ghosh M, Anthony C, Harlos K, Goodwin MG, Blake C;. Structure 1995;3:177-187. (from Pfam) NF014380.5 PF02316.21 HTH_Tnp_Mu_1 23.3 23.3 134 domain Y Y N DNA-binding protein GO:0003677 10387082,2999776 2 Bacteria superkingdom 9540 EBI-EMBL Mu DNA-binding domain Mu DNA-binding domain This family consists of MuA-transposase and repressor protein CI. These proteins contain homologous DNA-binding domains at their N-termini which compete for the same DNA site within the Mu bacteriophage genome. [1]. 2999776. Primary structure of phage mu transposase: homology to mu repressor. Harshey RM, Getzoff ED, Baldwin DL, Miller JL, Chaconas G;. Proc Natl Acad Sci U S A 1985;82:7676-7680. [2]. 10387082. NMR structure and functional studies of the Mu repressor DNA-binding domain. Ilangovan U, Wojciak JM, Connolly KM, Clubb RT;. Biochemistry 1999;38:8367-8376. (from Pfam) NF014385.5 PF02321.23 OEP 22 22 187 domain Y Y N TolC family protein GO:0015562,GO:0055085 10092468 2 Bacteria superkingdom 472969 EBI-EMBL Outer membrane efflux protein TolC family protein The OEP family (Outer membrane efflux protein) form trimeric channels that allow export of a variety of substrates in Gram negative bacteria. Each member of this family is composed of two repeats. The trimeric channel is composed of a 12 stranded all beta sheet barrel that spans the outer membrane, and a long all helical barrel that spans the periplasm. [1]. 10092468. Alignment and structure prediction of divergent protein families: periplasmic and outer membrane proteins of bacterial efflux pumps. Johnson JM, Church GM;. J Mol Biol 1999;287:695-715. (from Pfam) NF014389.5 PF02325.22 YGGT 27 27 70 PfamEq Y Y N YggT family protein GO:0016020 18593701 2 Bacteria superkingdom 35942 EBI-EMBL YGGT family YggT family protein This family includes subunit CCB3 of cofactor assembly complex C, involved in c-type cytochrome maturation in photosynthetic organisms [1]. This family also includes uncharacterised protein YggT, associated with bacteria outside the cyanobacteria. [1]. 18593701. A novel pathway of cytochrome c biogenesis is involved in the assembly of the cytochrome b6f complex in arabidopsis chloroplasts. Lezhneva L, Kuras R, Ephritikhine G, de Vitry C;. J Biol Chem. 2008;283:24608-24616. (from Pfam) NF014390.5 PF02326.20 YMF19 22.6 22.6 84 PfamEq Y N N Plant ATP synthase F0 12671689,8029019,9168110 2 Bacteria superkingdom 7182 EBI-EMBL Plant ATP synthase F0 Plant ATP synthase F0 This family corresponds to subunit 8 (YMF19) of the F0 complex of plant and algae mitochondrial F-ATPases (EC:3.6.1.34). [1]. 9168110. An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Lang BF, Burger G, O'Kelly CJ, Cedergren R, Golding GB, Lemieux C, Sankoff D, Turmel M, Gray MW;. Nature 1997;387:493-497. [2]. 8029019. RNA editing of transcripts of a chimeric mitochondrial gene associated with cytoplasmic male-sterility in Brassica. Stahl R, Sun S, L'Homme Y, Ketela T, Brown GG;. Nucleic Acids Res 1994;22:2109-2113. [3]. 12671689. ORFB is a subunit of F1F(O)-ATP synthase: insight into the basis of cytoplasmic male sterility in sunflower. Sabar M, Gagliardi D, Balk J, Leaver CJ;. EMBO Rep. 2003;4:381-386. (from Pfam) NF014392.5 PF02329.21 HDC 25 25 294 PfamEq Y Y N histidine decarboxylase, pyruvoyl type GO:0004398,GO:0006547 9633629 2 Bacteria superkingdom 429 EBI-EMBL Histidine carboxylase PI chain histidine decarboxylase, pyruvoyl type Histidine carboxylase catalyses the formation of histamine from histidine. Cleavage of the proenzyme PI chain yields two subunits, alpha and beta, which arrange as a hexamer (alpha beta)6. [1]. 9633629. Histidine carboxylase of Leuconostoc oenos 9204: purification, kinetic properties, cloning and nucleotide sequence of the hdc gene. Coton E, Rollan GC, Lonvaud-Funel A;. J Appl Microbiol 1998;84:143-151. (from Pfam) NF014398.5 PF02335.20 Cytochrom_C552 24.1 24.1 438 PfamEq Y Y N ammonia-forming cytochrome c nitrite reductase subunit c552 GO:0008152,GO:0042279,GO:0042597 10440380 2 Bacteria superkingdom 10933 EBI-EMBL Cytochrome c552 ammonia-forming cytochrome c nitrite reductase subunit c552 Cytochrome c552 (cytochrome c nitrite reductase) is a crucial enzyme in the nitrogen cycle catalysing the reduction of nitrite to ammonia. The crystal structure of cytochrome c552 reveals it to be a dimer, with with 10 close-packed type c haem groups. [1]. 10440380. Structure of cytochrome c nitrite reductase. Einsle O, Messerschmidt A, Stach P, Bourenkov GP, Bartunik HD, Huber R, Kroneck PM;. Nature 1999;400:476-480. (from Pfam) NF014401.5 PF02338.24 OTU 23.3 23.3 128 domain Y N N OTU-like cysteine protease 10664582 2 Bacteria superkingdom 571 EBI-EMBL OTU-like cysteine protease OTU-like cysteine protease This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases. [1]. 10664582. A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae. Makarova KS, Aravind L, Koonin EV;. Trends Biochem Sci 2000;25:50-52. (from Pfam) NF014404.5 PF02342.23 TerD 25.3 25.3 187 domain Y Y N TerD family protein 10203839,23044854 2 Bacteria superkingdom 111272 EBI-EMBL TerD domain TerD domain The TerD domain is found in TerD family proteins that include the paralogous TerD, TerA, TerE, TerF and TerZ proteins [1,2] It is found in a stress response operon with TerB and TerC. TerD has a maximum of two calcium-binding sites [2] depending on the conservation of aspartates [2]. It has various fusions to nuclease domains, RNA binding domains, ubiquitin related domains, and metal binding domains. The ter gene products lie at the centre of membrane-linked metal recognition complexes with regulatory ramifications encompassing phosphorylation-dependent signal transduction, RNA-dependent regulation, biosynthesis of nucleoside-like metabolites and DNA processing linked to novel pathways [2]. Review on Bacterial tellurite resistance. [1]. 10203839. Bacterial tellurite resistance. Taylor DE;. Trends Microbiol 1999;7:111-115. [2]. 23044854. Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing. Anantharaman V, Iyer LM, Aravind L;. Mol Biosyst. 2012;8:3142-3165. (from Pfam) NF014424.5 PF02365.20 NAM 27 27 122 domain Y Y N NAC family transcription factor GO:0003677,GO:0006355 8612269,9489703 2 Bacteria superkingdom 2 EBI-EMBL No apical meristem (NAM) protein NAC family transcription factor This is a family of no apical meristem (NAM) proteins these are plant development proteins. Mutations in NAM result in the failure to develop a shoot apical meristem in petunia embryos [2]. NAM is indicated as having a role in determining positions of meristems and primordial [2]. One member of this family NAP (NAC-like, activated by AP3/PI) is encoded by the target genes of the AP3/PI transcriptional activators and functions in the transition between growth by cell division and cell expansion in stamens and petals [1]. [1]. 9489703. A homolog of NO APICAL MERISTEM is an immediate target of the floral homeotic genes APETALA3/PISTILLATA. Sablowski RW, Meyerowitz EM;. Cell 1998;92:93-103. [2]. 8612269. The no apical meristem gene of Petunia is required for pattern formation in embryos and flowers and is expressed at meristem and primordia boundaries. Souer E, van Houwelingen A, Kloos D, Mol J, Koes R;. Cell 1996;85:159-170. (from Pfam) NF014432.5 PF02373.27 JmjC 24 24 114 domain Y N N JmjC domain, hydroxylase 10838566,11165500,12773576,15809658,20739293 2 Bacteria superkingdom 1679 EBI-EMBL JmjC domain, hydroxylase JmjC domain, hydroxylase The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation [5]. [1]. 10838566. Evidence of domain swapping within the jumonji family of transcription factors. Balciunas D, Ronne H;. Trends Biochem Sci 2000;25:274-276. [2]. 12773576. A novel jmjC domain protein modulates heterochromatization in fission yeast. Ayoub N, Noma K, Isaac S, Kahan T, Grewal SI, Cohen A;. Mol Cell Biol 2003;23:4356-4370. [3]. 11165500. JmjC: cupin metalloenzyme-like domains in jumonji, hairless and phospholipase A2beta. Clissold PM, Ponting CP;. Trends Biochem Sci 2001;26:7-9. [4]. 15809658. Methylation: lost in hydroxylation?. Trewick SC, McLaughlin PJ, Allshire RC;. EMBO Rep 2005;6:315-320. [5]. 20739293. Expanding role of the jumonji C domain as an RNA hydroxylase. Noma A, Ishitani R, Kato M, Nagao A, Nureki O, Suzuki T;. J Biol Chem. 2010;285:34503-34507. (from Pfam) NF014437.5 PF02378.23 PTS_EIIC 30.7 30.7 319 domain Y Y N PTS transporter subunit EIIC GO:0008982,GO:0009401,GO:0016020 9689210 2 Bacteria superkingdom 337384 EBI-EMBL Phosphotransferase system, EIIC PTS transporter subunit EIIC The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The sugar-specific permease of the PTS consists of three domains (IIA, IIB and IIC). The IIC domain catalyses the transfer of a phosphoryl group from IIB to the sugar substrate. [1]. 9689210. Novel phosphotransferase system genes revealed by bacterial genome analysis: the complete complement of pts genes in mycoplasma genitalium. Reizer J, Paulsen IT, Reizer A, Titgemeyer F, Saier MH Jr;. Microb Comp Genomics 1996;1:151-164. (from Pfam) NF014449.5 PF02392.21 Ycf4 34.7 34.7 170 PfamEq Y Y N photosystem I assembly protein Ycf4 GO:0009522,GO:0009579,GO:0015979,GO:0016020 9321389 2 Bacteria superkingdom 840 EBI-EMBL Ycf4 photosystem I assembly protein Ycf4 This family consists of hypothetical Ycf4 proteins from various chloroplast genomes. It has been suggested that Ycf4 is involved in the assembly and/or stability of the photosystem I complex in chloroplasts [1]. [1]. 9321389. The chloroplast ycf3 and ycf4 open reading frames of Chlamydomonas reinhardtii are required for the accumulation of the photosystem I complex. Boudreau E, Takahashi Y, Lemieux C, Turmel M, Rochaix JD;. EMBO J 1997;16:6095-6104. (from Pfam) NF014452.5 PF02395.21 Peptidase_S6 23 23 833 domain Y Y N S6 family peptidase GO:0004252,GO:0006508 3027577,9194704,9743528 2 Bacteria superkingdom 10326 EBI-EMBL Immunoglobulin A1 protease S6 family peptidase This family consists of immunoglobulin A1 protease proteins. The immunoglobulin A1 protease cleaves immunoglobulin IgA and is found in pathogenic bacteria such as Neisseria gonorrhoeae [3]. Not all of the members of this family are IgA proteases Swiss:O32555 from E. coli O157:H7 cleaves human coagulation factor V [2] and Swiss:O88093 is a hemoglobin protease from E. coli EB1 [1]. [1]. 9743528. Characterization of a hemoglobin protease secreted by the pathogenic Escherichia coli strain EB1. Otto BR, van Dooren SJ, Nuijens JH, Luirink J, Oudega B;. J Exp Med 1998;188:1091-1103. [2]. 9194704. EspP, a novel extracellular serine protease of enterohaemorrhagic Escherichia coli O157:H7 cleaves human coagulation factor V. Brunder W, Schmidt H, Karch H;. Mol Microbiol 1997;24:767-778. [3]. 3027577. Gene structure and extracellular secretion of Neisseria gonorrhoeae IgA protease. Pohlner J, Halter R, Beyreuther K, Meyer TF;. Nature 1987;325:458-462. (from Pfam) NF014456.5 PF02401.23 LYTB 24.5 24.5 267 domain Y N N LytB protein GO:0019288,GO:0046872,GO:0050992,GO:0051745 11004185,11418107,11717301,11741609,11818558,8432714 2 Bacteria superkingdom 58657 EBI-EMBL LytB protein LytB protein The mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis is essential in many eubacteria, plants, and the malaria parasite. The LytB gene is involved in the trunk line of the MEP pathway. [1]. 8432714. Identification of the Escherichia coli lytB gene, which is involved in penicillin tolerance and control of the stringent response. Gustafson CE, Kaul S, Ishiguro EE;. J Bacteriol 1993;175:1203-1205. [2]. 11818558. Studies on the nonmevalonate terpene biosynthetic pathway: metabolic role of IspH (LytB) protein. Rohdich F, Hecht S, Gartner K, Adam P, Krieger C, Amslinger S, Arigoni D, Bacher A, Eisenreich W. Proc Natl Acad Sci U S A 2002;99:1158-11563. [3]. 11741609. Identification of (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate as a major activator for human gammadelta T cells in Escherichia coli. Hintz M, Reichenberg A, Altincicek B, Bahr U, Gschwind RM, Kollas AK, Beck E, Wiesner J, Eberl M, Jomaa H. FEBS Lett 2001;509:317-322. [4]. 11717301. The lytB gene of Escherichia coli is essential and specifies a product needed for isoprenoid biosynthesis. McAteer S, Coulson A, McLennan N, Masters M. J Bacteriol 2001;183:7403-7407. [5]. 11418107. LytB, a novel gene of the 2-C-methyl-D-erythritol 4-phosphate pathway of isoprenoid biosynthesis in Escherichia coli. Altincicek B, Kollas A, Eberl M, Wiesner J, Sanderbrand S, Hintz M, Beck E, Jomaa H. FEBS Lett 2001;499:37-40. [6]. 11004185. Evidence of a role for LytB in the nonmevalonate pathway of isoprenoid biosynthesis. Cunningham FX Jr, Lafond TP, Gantt E. J Bacteriol 2000;182:5841-5848. (from Pfam) NF014457.5 PF02402.21 Lysis_col 25 25 49 subfamily Y Y N colicin release lysis protein GO:0019835,GO:0019867 3323826 2 Bacteria superkingdom 627 EBI-EMBL Lysis protein colicin release lysis protein These small bacterial proteins are required for colicin release and partial cell lysis. This family contains lysis proteins for several different forms of colicin. Swiss:Q02112 has been included in this family, the similarity is not highly significant, however it is also a short protein, that is involved in secretion of other proteins (Bateman A pers. obs.). This family includes a signal peptide motif and a lipid attachment site. [1]. 3323826. Nucleotide sequences from the colicin E8 operon: homology with plasmid ColE2-P9. Uchimura T, Lau PC;. Mol Gen Genet 1987;209:489-493. (from Pfam) NF014460.5 PF02405.21 MlaE 22.5 22.5 212 domain Y Y N ABC transporter permease GO:0043190 12743031,16495545,19383799 2 Bacteria superkingdom 75157 EBI-EMBL Permease MlaE ABC transporter permease MlaE is a permease which in E. coli is a component of the Mla pathway, an ABC transport system that functions to maintain the asymmetry of the outer membrane [1]. In Swiss:Q7DD59 it is involved in L-glutamate import into the cell [2]. In Swiss:Q8L4R0 it is involved in lipid transfer within the cell [2]. [1]. 19383799. An ABC transport system that maintains lipid asymmetry in the gram-negative outer membrane. Malinverni JC, Silhavy TJ;. Proc Natl Acad Sci U S A. 2009;106:8009-8014. [2]. 16495545. Identification of a meningococcal L-glutamate ABC transporter operon essential for growth in low-sodium environments. Monaco C, Tala A, Spinosa MR, Progida C, De Nitto E, Gaballo A, Bruni CB, Bucci C, Alifano P;. Infect Immun. 2006;74:1725-1740. [3]. 12743031. A permease-like protein involved in ER to thylakoid lipid transfer in Arabidopsis. Xu C, Fan J, Riekhof W, Froehlich JE, Benning C;. EMBO J. 2003;22:2370-2379. (from Pfam) NF014462.5 PF02407.21 Viral_Rep 26 26 82 domain Y N N Putative viral replication protein GO:0006260,GO:0016779,GO:0016888 2 Bacteria superkingdom 465 EBI-EMBL Putative viral replication protein Putative viral replication protein This is a family of viral ORFs from various plant and animal ssDNA circoviruses. Published evidence to support the annotated function "viral replication associated protein" has not be found. (from Pfam) NF014465.5 PF02411.20 MerT 32.9 32.9 116 subfamily Y Y N mercuric transporter MerT family protein GO:0016020 9159519,9274008,9479042 2 Bacteria superkingdom 4882 EBI-EMBL MerT mercuric transport protein mercuric transporter MerT family protein MerT is an mercuric transport integral membrane protein and is responsible for transport of the Hg2+ iron from periplasmic MerP (also part of the transport system) to mercuric reductase (MerE). [1]. 9479042. Two aberrant mercury resistance transposons in the Pseudomonas stutzeri plasmid pPB. Reniero D, Mozzon E, Galli E, Barbieri P;. Gene 1998;208:37-42. [2]. 9159519. Intercontinental spread of promiscuous mercury-resistance transposons in environmental bacteria. Yurieva O, Kholodii G, Minakhin L, Gorlenko Z, Kalyaeva E, Mindlin S, Nikiforov V;. Mol Microbiol 1997;24:321-329. [3]. 9274008. Tn5041: a chimeric mercury resistance transposon closely related to the toluene degradative transposon Tn4651. Kholodii GYa, Yurieva OV, Gorlenko ZhM, Mindlin SZ, Bass IA, Lomovskaya OL, Kopteva AV, Nikiforov VG;. Microbiology 1997;143:2549-2556. (from Pfam) NF014467.5 PF02413.22 Caudo_TAP 22.1 22.1 131 domain Y Y N tail fiber assembly protein 10629200,1531648,19251647 2 Bacteria superkingdom 50443 EBI-EMBL Caudovirales tail fibre assembly protein, lambda gpK tail fiber assembly protein This family contains bacterial and phage tail fibre assembly proteins [1]. E.coli contains several members of this family although the function of these proteins is uncertain. Using the lambda phage members as examples, there are both gptfa and gpK tail proteins here [2]. GpK forms part of the TTC or tail-tip complex that is located at the distal end of the tail. TTCs form the platform on which the tail-tube proteins self-assemble and are also the attachment point for fibres or receptor-binding proteins that mediate phage-adsorption to the surface of the host cell. TTC assembly starts with gpJ, which is also known as the central tail fibre and is involved in host-cell adsorption. It is the C-terminus of gpJ that interacts with the lamB receptor on host cells. A number of intermediates including gpK then interact with gpJ during tail morphogenesis [3]. [1]. 1531648. DNA sequences of the tail fiber genes of bacteriophage P2: evidence for horizontal transfer of tail fiber genes among unrelated bacteriophages. Haggard-Ljungquist E, Halling C, Calendar R;. J Bacteriol 1992;174:1462-1477. [2]. 19251647. The phage lambda major tail protein structure reveals a common evolution for long-tailed phages and the type VI bacterial secretion system. Pell LG, Kanelis V, Donaldson LW, Howell PL, Davidson AR;. Proc Natl Acad Sci U S A. 2009;106:4160-4165. [3]. 10629200. The C-terminal portion of the tail fiber protein of bacteriophage lambda is responsible for binding to LamB, its receptor at the surface of Escherichia coli K-12. Wang J, Hofnung M, Charbit A;. J Bacteriol. 2000;182:508-512. (from Pfam) NF014472.5 PF02419.22 PsbL 33 33 37 PfamEq Y N N PsbL protein GO:0009523,GO:0009539,GO:0015979,GO:0016020 1463853,1547774 2 Bacteria superkingdom 322 EBI-EMBL PsbL protein PsbL protein This family consists of the photosystem II reaction centre protein PsbJ from plants and Cyanobacteria. The function of this small protein is unknown. Interestingly the mRNA for this protein requires a post-transcriptional modification of an ACG triplet to form an AUG initiator codon [1,2]. [1]. 1463853. The psbL gene from bell pepper (Capsicum annuum): plastid RNA editing also occurs in non-photosynthetic chromoplasts. Kuntz M, Camara B, Weil JH, Schantz R;. Plant Mol Biol 1992;20:1185-1188. [2]. 1547774. RNA editing in tobacco chloroplasts leads to the formation of a translatable psbL mRNA by a C to U substitution within the initiation codon. Kudla J, Igloi GL, Metzlaff M, Hagemann R, Kossel H;. EMBO J 1992;11:1099-1103. (from Pfam) NF014480.5 PF02427.22 PSI_PsaE 27 27 60 PfamEq Y Y N photosystem I reaction center subunit IV psaE GO:0009522,GO:0009538,GO:0015979 8193119 2 Bacteria superkingdom 629 EBI-EMBL Photosystem I reaction centre subunit IV / PsaE photosystem I reaction center subunit IV PsaE is a 69 amino acid polypeptide from photosystem I present on the stromal side of the thylakoid membrane [1]. The structure is comprised of a well-defined five-stranded beta-sheet similar to SH3 domains [1]. [1]. 8193119. Three-dimensional solution structure of PsaE from the cyanobacterium Synechococcus sp. strain PCC 7002, a photosystem I protein that shows structural homology with SH3 domains. Falzone CJ, Kao YH, Zhao J, Bryant DA, Lecomte JT;. Biochemistry 1994;33:6052-6062. (from Pfam) NF014511.5 PF02458.20 Transferase 22.7 22.7 434 domain Y Y N acyltransferase GO:0016747 9426598,9681034 2 Bacteria superkingdom 1112 EBI-EMBL Transferase family acyltransferase domain This family includes a number of transferase enzymes. These include anthranilate N-hydroxycinnamoyl/benzoyltransferase that catalyses the first committed reaction of phytoalexin biosynthesis [1]. Deacetylvindoline 4-O-acetyltransferase EC:2.3.1.107 catalyses the last step in vindoline biosynthesis is also a member of this family [2]. The motif HXXXD is probably part of the active site. The family also includes trichothecene 3-O-acetyltransferase. [1]. 9426598. Characterization and heterologous expression of hydroxycinnamoyl/benzoyl-CoA:anthranilate N-hydroxycinnamoyl/benzoyltransferase from elicited cell cultures of carnation, Dianthus caryophyllus L. Yang Q, Reinhard K, Schiltz E, Matern U;. Plant Mol Biol 1997;35:777-789. [2]. 9681034. The terminal O-acetyltransferase involved in vindoline biosynthesis defines a new class of proteins responsible for coenzyme A-dependent acyl transfer. St-Pierre B, Laflamme P, Alarco AM, De Luca V;. Plant J 1998;14:703-713. (from Pfam) NF014514.5 PF02461.21 AMO 27.5 27.5 238 domain Y Y N methane monooxygenase/ammonia monooxygenase subunit A 8468301 2 Bacteria superkingdom 415 EBI-EMBL Ammonia monooxygenase methane monooxygenase/ammonia monooxygenase subunit A Ammonia monooxygenase plays a key role in the nitrogen cycle and degrades a wide range of hydrocarbons and halogenated hydrocarbons. [1]. 8468301. Sequence of the gene coding for ammonia monooxygenase in Nitrosomonas europaea. McTavish H, Fuchs JA, Hooper AB;. J Bacteriol 1993;175:2436-2444. (from Pfam) NF014515.5 PF02462.20 Opacity 21 21 126 domain Y Y N opacity family porin GO:0015288,GO:0016020 10036728,3093085 2 Bacteria superkingdom 25380 EBI-EMBL Opacity family porin protein opacity family porin Pathogenic Neisseria spp. possess a repertoire of phase-variable Opacity proteins that mediate various pathogen--host cell interactions [2]. These proteins are integral membrane proteins related to other porins. [1]. 3093085. Opacity genes in Neisseria gonorrhoeae: control of phase and antigenic variation. Stern A, Brown M, Nickel P, Meyer TF;. Cell 1986;47:61-71. [2]. 10036728. The role of neisserial Opa proteins in interactions with host cells. Dehio C, Gray-Owen SD, Meyer TF;. Trends Microbiol 1998;6:489-495. (from Pfam) NF014518.5 PF02465.23 FliD_N 24.8 24.8 97 domain Y Y N flagellar cap protein FliD N-terminal domain-containing protein GO:0009424 8195064,9488388 2 Bacteria superkingdom 43402 EBI-EMBL Flagellar hook-associated protein 2 N-terminus Flagellar hook-associated protein 2 N-terminus The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria [2]. This alignment covers the N-terminal region of this family of proteins. [1]. 8195064. The Bacillus subtilis sigma D-dependent operon encoding the flagellar proteins FliD, FliS, and FliT. Chen L, Helmann JD;. J Bacteriol 1994;176:3093-3101. [2]. 9488388. The Pseudomonas aeruginosa flagellar cap protein, FliD, is responsible for mucin adhesion. Arora SK, Ritchings BW, Almira EC, Lory S, Ramphal R;. Infect Immun 1998;66:1000-1007. (from Pfam) NF014520.5 PF02467.21 Whib 23.6 23.6 65 domain Y Y N WhiB family transcriptional regulator 8506145 2 Bacteria superkingdom 62104 EBI-EMBL Transcription factor WhiB WhiB family transcriptional regulator WhiB is a putative transcription factor in Actinobacteria, required for differentiation and sporulation. [1]. 8506145. Streptomyces aureofaciens whiB gene encoding putative transcription factor essential for differentiation. Kormanec J, Homerova D;. Nucleic Acid Res 1993;21:2512-2512. (from Pfam) NF014521.5 PF02468.20 PsbN 25 25 43 domain Y Y N photosystem II reaction center protein PsbN psbN GO:0015979,GO:0016020 9159184 2 Bacteria superkingdom 493 EBI-EMBL Photosystem II reaction centre N protein (psbN) photosystem II reaction center protein PsbN This is a family of small proteins encoded on the chloroplast genome. psbN is involved in photosystem II during photosynthesis, but its exact role is unknown. [1]. 9159184. Complete nucleotide sequence of the chloroplast genome from the green algae Chlorella vulgaris: the existence of genes possibly involved in chloroplast division. Wakasugi T, Nagai T, Kapoor M, Sugita M, Ito M, Ito S, Tsudzuki J, Nakashima K, Tsudzuki T, Suzuki Y, Hamada A, Ohta T, Inamura A, Yoshinaga K, Sugiura M;. Proc Natl Acad Sci U S A 1997;94:5967-5972. (from Pfam) NF014523.5 PF02470.25 MlaD 25.1 25.1 81 domain Y Y N MlaD family protein 10474190,19383799,8367727 2 Bacteria superkingdom 201740 EBI-EMBL MlaD protein MlaD family protein This family of proteins contains MlaD, which is a component of the Mla pathway, an ABC transport system that functions to maintain the asymmetry of the outer membrane [1]. The family also contains the mce (mammalian cell entry) proteins from Mycobacterium tuberculosis. The archetype (Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage [2]. This family contains proteins of unknown function from other bacteria. [1]. 19383799. An ABC transport system that maintains lipid asymmetry in the gram-negative outer membrane. Malinverni JC, Silhavy TJ;. Proc Natl Acad Sci U S A. 2009;106:8009-8014. [2]. 8367727. Cloning of an M. tuberculosis DNA fragment associated with entry and survival inside cells [see comments]. Arruda S, Bomfim G, Knights R, Huima-Byron T, Riley LW;. Science 1993;261:1454-1457. [3]. 10474190. Disruption of the mycobacterial cell entry gene of Mycobacterium bovis BCG results in a mutant that exhibits a reduced invasiveness for epithelial cells. Flesselles B, Anand NN, Remani J, Loosmore SM, Klein MH;. FEMS Microbiol Lett 1999;177:237-242. (from Pfam) NF014526.5 PF02474.20 NodA 22 22 195 domain Y N N Nodulation protein A (NodA) GO:0005829,GO:0009877,GO:0016746 9163424 2 Bacteria superkingdom 3097 EBI-EMBL Nodulation protein A (NodA) Nodulation protein A (NodA) Rhizobia nodulation (nod) genes control the biosynthesis of Nod factors required for infection and nodulation of their legume hosts. Nodulation protein A (NodA) is a N-acetyltransferase involved in production of Nod factors that stimulate mitosis in various plant protoplasts. [1]. 9163424. Molecular basis of symbiosis between Rhizobium and legumes. Freiberg C, Fellay R, Bairoch A, Broughton WJ, Rosenthal A, Perret X;. Nature 1997;387:394-401. (from Pfam) NF014537.5 PF02486.24 Rep_trans 29.6 29.6 201 domain Y Y N replication initiation factor domain-containing protein GO:0003677,GO:0003916,GO:0006270 2270231,7735128 2 Bacteria superkingdom 18337 EBI-EMBL Replication initiation factor Replication initiation factor Plasmid replication is initiated by the replication initiation factor (REP). This family represents a probable topoisomerase that makes a sequence-specific single-stranded nick in the plasmid DNA at the origin of replication. Human proteins also belong to this family, including myelin transcription factor 2 (Swiss:O15150) and cerebrin-50 (Swiss:Q16301) [2]. [1]. 2270231. Nucleotide sequence of the rep gene of staphylococcal plasmid pCW7. Balson DF, Shaw WV;. Plasmid 1990;24:74-80. [2]. 7735128. Cerebrin-50, a human cerebrospinal fluid protein whose mRNA is present in multiple tissues but predominantly expressed in the lymphoblastoid cells and the brain. Li AH, Silvestrini B, Leone MG, Giacomelli S, Cheng CY;. Biochem Mol Biol Int 1995;35:135-144. (from Pfam) NF014541.5 PF02491.25 SHS2_FTSA 25.4 25.4 79 PfamEq Y N N SHS2 domain inserted in FTSA GO:0005515,GO:0051301 15281131,9352931 2 Bacteria superkingdom 34806 EBI-EMBL SHS2 domain inserted in FTSA SHS2 domain inserted in FTSA FtsA is essential for bacterial cell division, and co-localises to the septal ring with FtsZ. The SHS2 domain is inserted in to the RNAseH fold of FtsA [2], and is involved in protein-protein interaction [1]. [1]. 9352931. Interactions between heterologous FtsA and FtsZ proteins at the FtsZ ring. Ma X, Sun Q, Wang R, Singh G, Jonietz EL, Margolin W;. J Bacteriol 1997;179:6788-6797. [2]. 15281131. The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies. Anantharaman V, Aravind L;. Proteins. 2004;56:795-807. (from Pfam) NF014554.5 PF02504.20 FA_synthesis 29.1 29.1 324 PfamEq Y N N Fatty acid synthesis protein GO:0003824,GO:0006633,GO:0016747 9642179 2 Bacteria superkingdom 45104 EBI-EMBL Fatty acid synthesis protein Fatty acid synthesis protein The plsX gene is part of the bacterial fab gene cluster which encodes several key fatty acid biosynthetic enzymes [1]. The exact function of the plsX protein in fatty acid synthesis is unknown. [1]. 9642179. Transcriptional analysis of essential genes of the Escherichia coli fatty acid biosynthesis gene cluster by functional replacement with the analogous Salmonella typhimurium gene cluster. Zhang Y, Cronan JE Jr;. J Bacteriol 1998;180:3295-3303. (from Pfam) NF014556.5 PF02507.20 PSI_PsaF 27 27 172 domain Y N N Photosystem I reaction centre subunit III GO:0009522,GO:0009538,GO:0015979 8443351 2 Bacteria superkingdom 840 EBI-EMBL Photosystem I reaction centre subunit III Photosystem I reaction centre subunit III Photosystem I (PSI) is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin. Subunit III (or PSI-F) is one of at least 14 different subunits that compose the PSI complex. [1]. 8443351. Subunit III (Psa-F) of photosystem I reaction center of the C4 dicotyledon Flaveria trinervia. Lotan O, Streubel M, Westhoff P, Nechushtai R;. Plant Mol Biol 1993;21:573-577. (from Pfam) NF014576.5 PF02529.20 PetG 23.7 23.7 36 PfamEq Y Y N cytochrome b6-f complex subunit PetG GO:0009512 7493961,7493968 2 Bacteria superkingdom 338 EBI-EMBL Cytochrome B6-F complex subunit 5 cytochrome b6-f complex subunit PetG This family consists of cytochrome B6-F complex subunit 5 (PetG). The cytochrome bf complex found in green plants, eukaryotic algae and cyanobacteria, connects photosystem I to photosystem II in the electron transport chain, functioning as a plastoquinol:plastocyanin/cytochrome c6 oxidoreductase [1]. PetG or subunit 5 is associated with the bf complex and the absence of PetG affects either the assembly or stability of the cytochrome bf complex in Chlamydomonas reinhardtii [1]. [1]. 7493961. The deletion of petG in Chlamydomonas reinhardtii disrupts the cytochrome bf complex. Berthold DA, Schmidt CL, Malkin R;. J Biol Chem 1995;270:29293-29298. [2]. 7493968. Purification and characterization of the cytochrome b6 f complex from Chlamydomonas reinhardtii. Pierre Y, Breyton C, Kramer D, Popot JL;. J Biol Chem 1995;270:29342-29349. (from Pfam) NF014577.5 PF02530.19 Porin_2 22 22 357 domain Y Y N porin GO:0015288,GO:0016020,GO:0055085 2 Bacteria superkingdom 22384 EBI-EMBL Porin subfamily porin This family consists of porins from the alpha subdivision of Proteobacteria the members of this family are related to Pfam:PF00267. The porins form large aqueous channels in the cell membrane allowing the selective entry of hydrophilic compounds this so called 'molecular sieve' is found in the cell walls of gram negative bacteria. (from Pfam) NF014578.5 PF02531.21 PsaD 22.4 22.4 136 PfamEq Y Y N photosystem I reaction center subunit II psaD GO:0009522,GO:0009538,GO:0015979 9692933 2 Bacteria superkingdom 720 EBI-EMBL PsaD photosystem I reaction center subunit II This family consists of PsaD from plants and cyanobacteria. PsaD is an extrinsic polypeptide of photosystem I (PSI) and is required for native assembly of PSI reaction clusters and is implicated in the electrostatic binding of ferredoxin within the reaction centre [1]. PsaD forms a dimer in solution which is bound by PsaE however PsaD is monomeric in its native complexed PSI environment [1]. [1]. 9692933. Structure and properties in solution of PsaD, an extrinsic polypeptide of photosystem I. Xia Z, Broadhurst RW, Laue ED, Bryant DA, Golbeck JH, Bendall DS;. Eur J Biochem 1998;255:309-316. (from Pfam) NF014579.5 PF02532.19 PsbI 27 27 36 PfamEq Y Y N photosystem II reaction center protein I psbI GO:0009523,GO:0009539,GO:0015979,GO:0016020 8544827,9632665 2 Bacteria superkingdom 350 EBI-EMBL Photosystem II reaction centre I protein (PSII 4.8 kDa protein) photosystem II reaction center protein I This family consists of various Photosystem II (PSII) reaction centre I proteins or PSII 4.8 kDa proteins, PsbI, from the chloroplast genome of many plants and Cyanobacteria. PsbI is a small, integral membrane component of PSII the role of which is not clear [2]. Synechocystis mutants lacking PsbI have 20-30% loss of PSII activity however the PSII complex is not destabilised [2]. [1]. 9632665. Isolation and characterization of monomeric and dimeric CP47-reaction center photosystem II complexes. Zheleva D, Sharma J, Panico M, Morris HR, Barber J;. J Biol Chem 1998;273:16122-16127. [2]. 8544827. Directed inactivation of the psbI gene does not affect photosystem II in the cyanobacterium Synechocystis sp. PCC 6803. Ikeuchi M, Shukla VK, Pakrasi HB, Inoue Y;. Mol Gen Genet 1995;249:622-628. (from Pfam) NF014588.5 PF02542.21 YgbB 26.7 26.7 155 PfamEq Y Y N 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase GO:0008685,GO:0016114 10694574 2 Bacteria superkingdom 55390 EBI-EMBL YgbB family 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase The ygbB protein is a putative enzyme of deoxy-xylulose pathway (terpenoid biosynthesis) [1]. [1]. 10694574. Biosynthesis of terpenoids: YgbB protein converts 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate to 2C-methyl-D-erythritol 2,4-cyclodiphosphate. Herz S, Wungsintaweekul J, Schuhr CA, Hecht S, Luttgen H, Sagner S, Fellermeier M, Eisenreich W, Zenk MH, Bacher A, Rohdich F;. Proc Natl Acad Sci U S A 2000;97:2486-2490. (from Pfam) NF014595.5 PF02551.20 Acyl_CoA_thio 21 21 132 domain Y N N Acyl-CoA thioesterase 1645722,9299485 2 Bacteria superkingdom 43169 EBI-EMBL Acyl-CoA thioesterase Acyl-CoA thioesterase This family represents the thioesterase II domain. Two copies of this domain are found in a number of acyl-CoA thioesterases. [1]. 9299485. A novel acyl-CoA thioesterase enhances its enzymatic activity by direct binding with HIV Nef. Watanabe H, Shiratori T, Shoji H, Miyatake S, Okazaki Y, Ikuta K, Sato T, Saito T;. Biochem Biophys Res Commun 1997;238:234-239. [2]. 1645722. Cloning, sequencing, and characterization of Escherichia coli thioesterase II. Naggert J, Narasimhan ML, DeVeaux L, Cho H, Randhawa ZI, Cronan JE Jr, Green BN, Smith S;. J Biol Chem 1991;266:11044-11050. (from Pfam) NF014600.5 PF02557.22 VanY 25 25 132 domain Y Y N D-alanyl-D-alanine carboxypeptidase family protein GO:0006508,GO:0008233 11171967,8631706 2 Bacteria superkingdom 57873 EBI-EMBL D-alanyl-D-alanine carboxypeptidase D-alanyl-D-alanine carboxypeptidase family protein NF014602.5 PF02559.21 CarD_TRCF_RID 23 23 57 domain Y Y N CarD family transcriptional regulator 11533063,16469698,16879646,20371514,23858468,24115125,7876261,8692912 2 Bacteria superkingdom 119726 EBI-EMBL CarD-like/TRCF RID domain CarD-like/TRCF RID domain This is the RNA polymerase interacting domain (RID) of transcription-repair-coupling factor (TRCF), CarD and CarD homologue in Myxococcus xanthus, called CdnL. In Myxococcus xanthus, CdnL is a protein required for the activation of light- and starvation-inducible genes [1]. It interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus [4]. CarD is widely distributed among bacteria and represents a distinct class of RNAP binding proteins that regulate transcription and essential processes [4-8]. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription [3]. [1]. 8692912. High mobility group I(Y)-like DNA-binding domains on a bacterial transcription factor. Nicolas FJ, Cayuela ML, Martinez-Argudo IM, Ruiz-Vazquez RM, Murillo FJ;. Proc Natl Acad Sci U S A 1996;93:6881-6885. [2]. 11533063. Domain architecture of a high mobility group A-type bacterial transcriptional factor. Padmanabhan S, Elias-Arnanz M, Carpio E, Aparicio P, Murillo FJ;. J Biol Chem 2001;276:41566-41575. [3]. 7876261. Structure and function of transcription-repair coupling factor. I. Structural domains and binding properties. Selby CP, Sancar A;. J Biol Chem 1995;270:4882-4889. [4]. 16879646. Recruitment of a novel zinc-bound transcriptional factor by a bacterial HMGA-type protein is required for regulating multiple processes in Myxococcus xanthus. Penalver-Mellado M, Garcia-Heras F, Padmanabhan S, Garcia-Moreno D, Murillo FJ, Elias-Arnanz M;. Mol Microbiol. 2006;61:910-926. [5]. 20371514. CdnL, . TRUNCATED at 1650 bytes (from Pfam) NF014604.5 PF02561.19 FliS 26.7 26.7 115 domain Y Y N flagellar protein FliS GO:0044780 8550529 2 Bacteria superkingdom 24782 EBI-EMBL Flagellar protein FliS flagellar protein FliS FliS is coded for by the FliD operon and is transcribed in conjunction with FliD and FliT, however this protein has no known function. [1]. 8550529. Negative regulation by fliD, fliS, and fliT of the export of the flagellum-specific anti-sigma factor, FlgM, in Salmonella typhimurium. Yokoseki T, Iino T, Kutsukake K;. J Bacteriol 1996;178:899-901. (from Pfam) NF014606.5 PF02563.21 Poly_export 28 28 77 domain Y Y N polysaccharide biosynthesis/export family protein GO:0015159,GO:0015774,GO:0016020 8759852 2 Bacteria superkingdom 85874 EBI-EMBL Polysaccharide biosynthesis/export protein polysaccharide biosynthesis/export family protein This is a family of periplasmic proteins involved in polysaccharide biosynthesis and/or export. [1]. 8759852. Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid. Stevenson G, Andrianopoulos K, Hobbs M, Reeves PR;. J Bacteriol 1996;178:4885-4893. (from Pfam) NF014607.5 PF02565.20 RecO_C 22.1 22.1 157 PfamEq Y Y N DNA repair protein RecO C-terminal domain-containing protein GO:0006281,GO:0006310 2544549 2 Bacteria superkingdom 59791 EBI-EMBL Recombination protein O C terminal Recombination protein O C terminal Recombination protein O (RecO) is involved in DNA repair and Pfam:PF00470 pathway recombination. [1]. 2544549. Molecular analysis of the Escherichia coli recO gene. Morrison PT, Lovett ST, Gilson LE, Kolodner R;. J Bacteriol 1989;171:3641-3649. (from Pfam) NF014616.5 PF02575.21 YbaB_DNA_bd 25.5 25.5 91 subfamily Y Y N YbaB/EbfC family nucleoid-associated protein GO:0003677 12486730,19208644,19594923 2 Bacteria superkingdom 55922 EBI-EMBL YbaB/EbfC DNA-binding family YbaB/EbfC family nucleoid-associated protein This is a family of DNA-binding proteins. Members of this family form homodimers which bind DNA via a tweezer-like structure [1-3]. The conformation of the DNA is changed when bound to these proteins [3]. In bacteria, these proteins may play a role in DNA replication-recovery following DNA damage [1]. [1]. 12486730. Crystal structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function coexpressed with the recombinational DNA repair protein RecR. Lim K, Tempczyk A, Parsons JF, Bonander N, Toedt J, Kelman Z, Howard A, Eisenstein E, Herzberg O;. Proteins. 2003;50:375-379. [2]. 19594923. DNA-binding by Haemophilus influenzae and Escherichia coli YbaB, members of a widely-distributed bacterial protein family. Cooley AE, Riley SP, Kral K, Miller MC, DeMoll E, Fried MG, Stevenson B;. BMC Microbiol. 2009;9:13. [3]. 19208644. Borrelia burgdorferi EbfC defines a newly-identified, widespread family of bacterial DNA-binding proteins. Riley SP, Bykowski T, Cooley AE, Burns LH, Babb K, Brissette CA, Bowman A, Rotondi M, Miller MC, DeMoll E, Lim K, Fried MG, Stevenson B;. Nucleic Acids Res. 2009;37:1973-1983. (from Pfam) NF014617.5 PF02576.22 RimP_N 22.7 22.7 73 PfamEq Y N N RimP N-terminal domain 11493012,19150615 2 Bacteria superkingdom 48446 EBI-EMBL RimP N-terminal domain RimP N-terminal domain This entry represents the N-terminal domain of the ribosome maturation factor RimP (also known as yhbC). RimP facilitates the maturation of the 30S ribosomal subunit [1]. The N-terminal domain contains two alpha-helices and a three-stranded beta-sheet. It is suggested that the N-terminal domain of SP14.3 (RimP orthologue) could function as a protein module that binds to other proteins, especially those that contain highly positively charged surfaces. [2]. [1]. 19150615. The RimP protein is important for maturation of the 30S ribosomal subunit. Nord S, Bylund GO, Lovgren JM, Wikstrom PM;. J Mol Biol. 2009;386:742-753. [2]. 11493012. Solution structure and function of a conserved protein SP14.3 encoded by an essential Streptococcus pneumoniae gene. Yu L, Gunasekera AH, Mack J, Olejniczak ET, Chovan LE, Ruan X, Towne DL, Lerner CG, Fesik SW;. J Mol Biol. 2001;311:593-604. (from Pfam) NF014619.5 PF02578.20 Cu-oxidase_4 22.9 22.9 238 domain Y Y N laccase domain-containing protein 16740638 2 Bacteria superkingdom 70145 EBI-EMBL Multi-copper polyphenol oxidoreductase laccase Multi-copper polyphenol oxidoreductase laccase Laccases are multi-copper oxidoreductases able to oxidise a wide variety of phenolic and non-phenolic compounds and are widely distributed among both prokaryotes and eukaryotes. There are two main active catalytic sites with conserved histidines that are capable of binding four copper atoms [1]. [1]. 16740638. Novel polyphenol oxidase mined from a metagenome expression library of bovine rumen: biochemical properties, structural analysis, and phylogenetic relationships. Beloqui A, Pita M, Polaina J, Martinez-Arias A, Golyshina OV, Zumarraga M, Yakimov MM, Garcia-Arellano H, Alcalde M, Fernandez VM, Elborough K, Andreu JM, Ballesteros A, Plou FJ, Timmis KN, Ferrer M, Golyshin PN;. J Biol Chem. 2006;281:22933-22942. (from Pfam) NF014623.5 PF02582.19 DUF155 27 27 174 PfamEq Y Y N RMD1 family protein 12586695,23022098,23022099 2 Bacteria superkingdom 2915 EBI-EMBL RMND1/Sif2-Sif3/Mrx10, DUF155 RMD1 family protein This entry represents a domain found in RMND1 from mammals, Sif2/Sif3 from fission yeasts and Rmd1/Rmd8/YDR282C (Mrx10) from budding yeasts. RMND1 and its yeast homologue, Mrx10, are mitochondrial proteins required for mitochondrial translation [1,2]. Rmd1 and Rmd8 are cytoplasmic proteins required for sporulation [3]. [1]. 23022098. An RMND1 Mutation causes encephalopathy associated with multiple oxidative phosphorylation complex deficiencies and a mitochondrial translation defect. Janer A, Antonicka H, Lalonde E, Nishimura T, Sasarman F, Brown GK, Brown RM, Majewski J, Shoubridge EA;. Am J Hum Genet. 2012;91:737-743. [2]. 23022099. Infantile encephaloneuromyopathy and defective mitochondrial translation are due to a homozygous RMND1 mutation. Garcia-Diaz B, Barros MH, Sanna-Cherchi S, Emmanuele V, Akman HO, Ferreiro-Barros CC, Horvath R, Tadesse S, El Gharaby N, DiMauro S, De Vivo DC, Shokr A, Hirano M, Quinzii CM;. Am J Hum Genet. 2012;91:729-736. [3]. 12586695. Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae. Enyenihi AH, Saunders WS;. Genetics. 2003;163:47-54. (from Pfam) NF014627.5 PF02588.20 YitT_membrane 24.3 24.3 205 domain Y Y N YitT family protein 2 Bacteria superkingdom 70930 EBI-EMBL Uncharacterised 5xTM membrane BCR, YitT family COG1284 YitT family protein This is probably a bacterial ABC transporter permease (personal obs:Yeats C). (from Pfam) NF014630.5 PF02591.20 zf-RING_7 29.1 29.1 33 domain Y Y N C4-type zinc ribbon domain-containing protein 20826163,21348639 2 Bacteria superkingdom 20136 EBI-EMBL C4-type zinc ribbon domain C4-type zinc ribbon domain Zn-ribbon_9 is a Zn-ribbon domain rich in aromatic and positively charged amino acid residues. This C-terminal Zn-ribbon domain consists of two beta-strands acting as a scaffold for the two Zn knuckles. Both pairs of cysteines making up the two Zn knuckles are situated at highly conserved sharp beta-turns, an arrangement that facilitates the tetrahedral coordination of the divalent Zn ion. The two Zn-knuckle cysteine motifs are separated by 20 residues, 9 of which form an alpha-helix (helix 4) [2].Structural modelling suggests this domain may bind nucleic acids [1]. The domain appears to bind flaA-mRNA, thus contributing to flagellum formation and motility [2]. [1]. 21348639. Ab Initio Modeling Led Annotation Suggests Nucleic Acid Binding Function for Many DUFs. Rigden DJ;. OMICS 2011;0:0-0. [2]. 20826163. The 2.2-A structure of the HP0958 protein from Helicobacter pylori reveals a kinked anti-parallel coiled-coil hairpin domain and a highly conserved ZN-ribbon domain. Caly DL, O'Toole PW, Moore SA;. J Mol Biol. 2010;403:405-419. (from Pfam) NF014634.5 PF02595.20 Gly_kinase 23.3 23.3 372 domain Y Y N glycerate kinase GO:0008887,GO:0031388 10601204 2 Bacteria superkingdom 77748 EBI-EMBL Glycerate kinase family glycerate kinase This is family of Glycerate kinases. [1]. 10601204. Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli. Cusa E, Obradors N, Baldoma L, Badia J, Aguilar J;. J Bacteriol 1999;181:7479-7484. (from Pfam) NF014638.5 PF02599.21 CsrA 27 27 53 domain Y Y N carbon storage regulator GO:0003723,GO:0006109,GO:0006402 7665490,9211896 2 Bacteria superkingdom 17617 EBI-EMBL Global regulator protein family carbon storage regulator This is a family of global regulator proteins. This protein is a RNA-binding protein and a global regulator of carbohydrate metabolism genes facilitating mRNA decay [1]. In E. coli CsrA binds the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [1]. In other bacteria such as Erwinia caratovara RmsA has been shown to regulate the production of virulence determinants, such extracellular enzymes [2]. RmsA binds to RmsB regulatory RNA. [1]. 9211896. The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli. Liu MY, Gui G, Wei B, Preston JF 3rd, Oakford L, Yuksel U, Giedroc DP, Romeo T;. J Biol Chem 1997;272:17502-17510. [2]. 7665490. Identification of a global repressor gene, rsmA, of Erwinia carotovora subsp. carotovora that controls extracellular enzymes, N-(3-oxohexanoyl)-L-homoserine lactone, and pathogenicity in soft-rotting Erwinia spp. Cui Y, Chatterjee A, Liu Y, Dumenyo CK, Chatterjee AK;. J Bacteriol 1995;177:5108-5115. (from Pfam) NF014642.5 PF02603.21 Hpr_kinase_N 24 24 125 PfamEq Y N N HPr Serine kinase N terminus GO:0000155,GO:0000160,GO:0004672,GO:0005524,GO:0006109 11904409,9570401 2 Bacteria superkingdom 14078 EBI-EMBL HPr Serine kinase N terminus HPr Serine kinase N terminus This family represents the N-terminal region of Hpr Serine/threonine kinase PtsK. This kinase is the sensor in a multicomponent phospho-relay system in control of carbon catabolic repression in bacteria [1]. This kinase in unusual in that it recognises the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes [1]. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The blades are formed by two N-terminal domains each, and the compact central hub assembles the C-terminal kinase domains [2]. [1]. 9570401. A novel protein kinase that controls carbon catabolite repression in bacteria. Reizer J, Hoischen C, Titgemeyer F, Rivolta C, Rabus R, Stulke J, Karamata D, Saier MH Jr, Hillen W;. Mol Microbiol 1998;27:1157-1169. [2]. 11904409. Structure of the full-length HPr kinase/phosphatase from Staphylococcus xylosus at 1.95 A resolution: Mimicking the product/substrate of the phospho transfer reactions. Marquez JA, Hasenbein S, Koch B, Fieulaine S, Nessler S, Russell RB, Hengstenberg W, Scheffzek K;. Proc Natl Acad Sci U S A 2002;99:3458-3463. (from Pfam) NF014644.5 PF02605.20 PsaL 25 25 150 domain Y Y N photosystem I reaction center subunit XI GO:0009522,GO:0009538,GO:0015979 8901876 2 Bacteria superkingdom 1164 EBI-EMBL Photosystem I reaction centre subunit XI photosystem I reaction center subunit XI This family consists of the photosystem I reaction centre subunit XI, PsaL, from plants and bacteria. PsaL is one of the smaller subunits in photosystem I with only two transmembrane alpha helices and interacts closely with PsaI [1]. [1]. 8901876. Photosystem I at 4 A resolution represents the first structural model of a joint photosynthetic reaction centre and core antenna system. Krauss N, Schubert WD, Klukas O, Fromme P, Witt HT, Saenger W;. Nat Struct Biol 1996;3:965-973. (from Pfam) NF014645.5 PF02606.19 LpxK 27 27 328 PfamEq Y Y N tetraacyldisaccharide 4'-kinase 2.7.1.130 GO:0005524,GO:0009029,GO:0009245 9575203 2 Bacteria superkingdom 46870 EBI-EMBL Tetraacyldisaccharide-1-P 4'-kinase tetraacyldisaccharide 4'-kinase This family consists of tetraacyldisaccharide-1-P 4'-kinase also known as Lipid-A 4'-kinase or Lipid A biosynthesis protein LpxK, EC:2.7.1.130. This enzyme catalyses the reaction: ATP + 2,3-bis(3-hydroxytetradecanoyl)-D -glucosaminyl-(beta-D-1,6)-2,3-bis(3-hydroxytetradecanoyl)-D-glu cosam inyl beta-phosphate ADP + 2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D- glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate. This enzyme is involved in the synthesis of lipid A portion of the bacterial lipopolysaccharide layer (LPS) [1]. The family contains a P-loop motif at the N terminus. [1]. 9575203. Accumulation of a lipid A precursor lacking the 4'-phosphate following inactivation of the Escherichia coli lpxK gene. Garrett TA, Que NL, Raetz CR;. J Biol Chem 1998;273:12457-12465. (from Pfam) NF014650.5 PF02611.20 CDH 25 25 224 PfamEq Y Y N CDP-diacylglycerol diphosphatase 3.6.1.26 GO:0008654,GO:0008715,GO:0016020 2995360 2 Bacteria superkingdom 8344 EBI-EMBL CDP-diacylglycerol pyrophosphatase CDP-diacylglycerol diphosphatase This is a family of CDP-diacylglycerol pyrophosphatases, EC:3.6.1.26. This enzyme catalyses the reaction CDP-diacylglycerol + H2O CMP + phosphatidate. [1]. 2995360. Molecular cloning and sequencing of the gene for CDP-diglyceride hydrolase of Escherichia coli. Icho T, Bulawa CE, Raetz CR;. J Biol Chem 1985;260:12092-12098. (from Pfam) NF014655.5 PF02617.22 ClpS 23 23 80 PfamEq Y Y N ATP-dependent Clp protease adaptor ClpS GO:0030163 11931773,12426582 2 Bacteria superkingdom 32128 EBI-EMBL ATP-dependent Clp protease adaptor protein ClpS ATP-dependent Clp protease adaptor ClpS In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins [1]. [1]. 11931773. ClpS, a substrate modulator of the ClpAP machine. Dougan DA, Reid BG, Horwich AL, Bukau B;. Mol Cell 2002;9:673-683. [2]. 12426582. Structural analysis of the adaptor protein ClpS in complex with the N-terminal domain of ClpA. Zeth K, Ravelli RB, Paal K, Cusack S, Bukau B, Dougan DA;. Nat Struct Biol 2002;9:906-911. (from Pfam) NF014656.5 PF02618.21 YceG 32.4 32.4 275 PfamEq Y Y N endolytic transglycosylase MltG 2 Bacteria superkingdom 84642 EBI-EMBL YceG-like family endolytic transglycosylase MltG This family of proteins is found in bacteria. Proteins in this family are typically between 332 and 389 amino acids in length. This family was previously incorrectly annotated and names as aminodeoxychorismate lyase. The structure of Swiss:P28306 was solved by X-ray crystallography. (from Pfam) NF014657.5 PF02620.22 YceD 33.2 33.2 119 PfamEq Y Y N YceD family protein 27574185 2 Bacteria superkingdom 51875 EBI-EMBL Large ribosomal RNA subunit accumulation protein YceD YceD family protein This family is nearly universally conserved in bacteria and plants except the Chlorophyceae algae. Thus far, mutantional analysis in bacteria have not established a function. In contrast, mutants have embryo lethal phenotypes in maize and Arabidopsis. In maize, the mutant embryos arrest at an early transition stage.It has been suggested that family members specifically affect 23S rRNA accumulation in plastids as well as bacteria [1]. [1]. 27574185. Essential role of conserved DUF177A protein in plastid 23S rRNA accumulation and plant embryogenesis. Yang J, Suzuki M, McCarty DR;. J Exp Bot. 2016;67:5447-5460. (from Pfam) NF014659.5 PF02622.20 DUF179 27 27 157 PfamEq Y Y N YqgE/AlgH family protein 2 Bacteria superkingdom 32812 EBI-EMBL Uncharacterized ACR, COG1678 YqgE/AlgH family protein NF014660.5 PF02623.20 FliW 25 25 122 domain Y Y N flagellar assembly protein FliW fliW GO:0044780 11196647,11895937,16936039,17555441,21895793 2 Bacteria superkingdom 10686 EBI-EMBL FliW protein flagellar assembly protein FliW The protein BSU35380 from Bacillus subtilis (renamed FliW) was characterised as being a flagellar assembly factor. Experimental characterisation was also carried out in Treponema pallidum (TP0658). In Campylobacter jejuni, Cj1075 has been shown to be involved in motility and flagellin biosynthesis. The two paralogues in Helicobacter pylori (HP1154 and HP1377) were found to be able to bind to flagellin. FliW proteins are involved in flagellar assembly [4]. FliW is part of a three-part feedback loop: in Bacillus subtilis FliW inhibits CsrA (an RNA-binding protein) which inhibits FliC translation; hence FliW is required for FliC (flagellin) production [5]. [1]. 16936039. Novel conserved assembly factor of the bacterial flagellum. Titz B, Rajagopala SV, Ester C, Hauser R, Uetz P;. J Bacteriol. 2006;188:7700-7706. [2]. 11895937. Identification of motility and autoagglutination Campylobacter jejuni mutants by random transposon mutagenesis. Golden NJ, Acheson DW;. Infect Immun. 2002;70:1761-1771. [3]. 11196647. The protein-protein interaction map of Helicobacter pylori. Rain JC, Selig L, De Reuse H, Battaglia V, Reverdy C, Simon S, Lenzen G, Petel F, Wojcik J, Schachter V, Chemama Y, Labigne A, Legrain P;. Nature. 2001;409:211-215. [4]. 17555441. CsrA of Bacillus subtilis regulates translation initiation of the gene encoding the flagellin protein (hag) by blocking ribosome binding. Yakhnin H, Pandit P, Petty TJ, Baker CS, Romeo T, Babitzke P;. Mol Microbiol. 2007;64:1605-1620. [5]. 21895793. CsrA-FliW interaction governs flagellin homeostasis and a checkpoint on flagellar morphogenesis in Bacillus subtilis. Mukherjee S, Yakhnin . TRUNCATED at 1650 bytes (from Pfam) NF014668.5 PF02631.21 RecX_HTH2 26 26 42 PfamEq Y Y N RecX family transcriptional regulator GO:0006282 18650935,23284295,35730924 2 Bacteria superkingdom 56247 EBI-EMBL RecX, second three-helix domain RecX, second three-helix domain This entry represents the second three-helix domain (HTH-like) found in RecX family of proteins. RecX functions as a regulator of DNA recombination and repair pathways in bacterial cells [1]. RecX protein is known to inhibit the activity of RecA protein in DNA recombination [2,3]. [1]. 23284295. RecX facilitates homologous recombination by modulating RecA activities. Cardenas PP, Carrasco B, Defeu Soufo C, Cesar CE, Herr K, Kaufenstein M, Graumann PL, Alonso JC;. PLoS Genet. 2012;8:e1003126. [2]. 35730924. A new insight into RecA filament regulation by RecX from the analysis of conformation-specific interactions. Alekseev A, Pobegalov G, Morozova N, Vedyaykin A, Cherevatenko G, Yakimov A, Baitin D, Khodorkovskii M;. Elife. 2022;11:e78409. [3]. 18650935. Structural basis for inhibition of homologous recombination by the RecX protein. Ragone S, Maman JD, Furnham N, Pellegrini L;. EMBO J. 2008;27:2259-2269. (from Pfam) NF014679.5 PF02645.21 DegV 27 27 280 subfamily Y Y N DegV family protein 12577257 2 Bacteria superkingdom 71793 EBI-EMBL Uncharacterised protein, DegV family COG1307 DegV family protein The structure of this protein revealed a bound fatty-acid molecule in a pocket between the two protein domains. The structure indicates that this family has the molecular function of fatty-acid binding and may play a role in the cellular functions of fatty acid transport or metabolism [1]. [1]. 12577257. Crystal structure of a hypothetical protein, TM841 of Thermotoga maritima, reveals its function as a fatty acid-binding protein. Schulze-Gahmen U, Pelaschier J, Yokota H, Kim R, Kim SH;. Proteins 2003;50:526-530. (from Pfam) NF014682.5 PF02650.19 HTH_WhiA 27 27 84 domain Y Y N helix-turn-helix domain-containing protein 10986251,17603302,19836336 2 Bacteria superkingdom 20097 EBI-EMBL WhiA C-terminal HTH domain WhiA C-terminal HTH domain This domain is found at the C-terminus of the sporulation regulator WhiA. It is predicted to form a DNA-binding helix-turn-helix structure [2]. The WhiA protein also contains two N-terminal domains that are distant homologues of LAGLIDADG homing endonucleases [2]. [1]. 10986251. WhiA, a protein of unknown function conserved among gram-positive bacteria, is essential for sporulation in Streptomyces coelicolor A3(2). Ainsa JA, Ryding NJ, Hartley N, Findlay KC, Bruton CJ, Chater KF;. J Bacteriol. 2000;182:5470-5478. [2]. 17603302. Bacterial DUF199/COG1481 Proteins Including Sporulation Regulator WhiA are Distant Homologs of LAGLIDADG Homing Endonucleases That Retained Only DNA Binding. Knizewski L, Ginalski K;. Cell Cycle. 2007;6:1666-1670. [3]. 19836336. The structure of a bacterial DUF199/WhiA protein: domestication of an invasive endonuclease. Kaiser BK, Clifton MC, Shen BW, Stoddard BL;. Structure. 2009;17:1368-1376. (from Pfam) NF014690.5 PF02660.20 G3P_acyltransf 24.1 24.1 164 PfamEq Y Y N glycerol-3-phosphate acyltransferase GO:0005886,GO:0008654,GO:0043772 16949372 2 Bacteria superkingdom 46289 EBI-EMBL Glycerol-3-phosphate acyltransferase glycerol-3-phosphate acyltransferase This family of enzymes catalyses the transfer of an acyl group from acyl-ACP to glycerol-3-phosphate to form lysophosphatidic acid [1]]. [1]. 16949372. Acyl-phosphates initiate membrane phospholipid synthesis in Gram-positive pathogens. Lu YJ, Zhang YM, Grimes KD, Qi J, Lee RE, Rock CO;. Mol Cell. 2006;23:765-772. (from Pfam) NF014694.5 PF02664.20 LuxS 27 27 154 PfamEq Y Y N S-ribosylhomocysteine lyase 4.4.1.21 GO:0005506,GO:0009372,GO:0043768 12705835,14583032,15287744,9990077 2 Bacteria superkingdom 17011 EBI-EMBL S-Ribosylhomocysteinase (LuxS) S-ribosylhomocysteine lyase This family consists of the LuxS protein involved in autoinducer AI2 synthesis and its hypothetical relatives. S-ribosylhomocysteinase (LuxS) catalyses the cleavage of the thioether bond in S-ribosylhomocysteine (SRH) to produce homocysteine and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor of type II bacterial quorum sensing molecule. [1]. 9990077. Quorum sensing in Escherichia coli, Salmonella typhimurium, and Vibrio harveyi: a new family of genes responsible for autoinducer production. Surette MG, Miller MB, Bassler BL;. Proc Natl Acad Sci U S A 1999;96:1639-1644. [2]. 15287744. Catalytic mechanism of S-ribosylhomocysteinase (LuxS): stereochemical course and kinetic isotope effect of proton transfer reactions. Zhu J, Patel R, Pei D;. Biochemistry 2004;43:10166-10172. [3]. 14583032. Catalytic mechanism of S-ribosylhomocysteinase (LuxS): direct observation of ketone intermediates by 13C NMR spectroscopy. Zhu J, Hu X, Dizin E, Pei D;. J Am Chem Soc 2003;125:13379-13381. [4]. 12705835. S-Ribosylhomocysteinase (LuxS) is a mononuclear iron protein. Zhu J, Dizin E, Hu X, Wavreille AS, Park J, Pei D;. Biochemistry 2003;42:4717-4726. (from Pfam) NF014698.5 PF02668.21 TauD 27 27 267 domain Y Y N TauD/TfdA family dioxygenase GO:0016491 3036764,8504802,8779585,9287300 2 Bacteria superkingdom 112617 EBI-EMBL Taurine catabolism dioxygenase TauD, TfdA family TauD/TfdA family dioxygenase This family consists of taurine catabolism dioxygenases of the TauD, TfdA family. TauD from E. coli Swiss:P37610 is a alpha-ketoglutarate-dependent taurine dioxygenase [1]. This enzyme catalyses the oxygenolytic release of sulfite from taurine [1]. TfdA from Burkholderia sp. Swiss:Q45423 is a 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase [2]. TfdA from Alcaligenes eutrophus JMP134 Swiss:P10088 is a 2,4-dichlorophenoxyacetate monooxygenase [3]. Also included are gamma-Butyrobetaine hydroxylase enzymes EC:1.14.11.1 [4]. [1]. 9287300. Characterization of alpha-ketoglutarate-dependent taurine dioxygenase from Escherichia coli. Eichhorn E, van der Ploeg JR, Kertesz MA, Leisinger T;. J Biol Chem 1997;272:23031-23036. [2]. 8779585. Characterization of a chromosomally encoded 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase from Burkholderia sp. strain RASC. Suwa Y, Wright AD, Fukimori F, Nummy KA, Hausinger RP, Holben WE, Forney LJ;. Appl Environ Microbiol 1996;62:2464-2469. [3]. 3036764. Analysis, cloning, and high-level expression of 2,4-dichlorophenoxyacetate monooxygenase gene tfdA of Alcaligenes eutrophus JMP134. Streber WR, Timmis KN, Zenk MH;. J Bacteriol 1987;169:2950-2955. [4]. 8504802. gamma-Butyrobetaine hydroxylase. Structural characterization of the Pseudomonas enzyme. Ruetschi U, Nordin I, Odelhog B, Jornvall H, Lindstedt S;. Eur J Biochem 1993;213:1075-1080. (from Pfam) NF014702.5 PF02672.20 CP12 22.7 22.7 70 domain Y Y N CP12 domain-containing protein 31570616,32102842 2 Bacteria superkingdom 1872 EBI-EMBL CP12 domain CP12 domain The function of this domain is unknown, it does contain three conserved cysteines and a histidine, that suggests this may be a zinc binding domain (Bateman A pers. observation). This domain is found associated with CBS domains in some proteins Pfam:PF00571. (from Pfam) NF014704.5 PF02674.21 Colicin_V 29.3 29.3 144 PfamEq Y Y N CvpA family protein GO:0009403,GO:0016020 2542219 2 Bacteria superkingdom 52455 EBI-EMBL Colicin V production protein CvpA family protein Colicin V production protein is required in E. Coli for colicin V production from plasmid pColV-K30 [1]. This protein is coded for in the purF operon. [1]. 2542219. Characterization of a purF operon mutation which affects colicin V production. Fath MJ, Mahanty HK, Kolter R;. J Bacteriol 1989;171:3158-3161. (from Pfam) NF014707.5 PF02677.19 QueH 23.5 23.5 175 PfamEq Y Y N epoxyqueuosine reductase QueH 28128549 2 Bacteria superkingdom 16859 EBI-EMBL Epoxyqueuosine reductase QueH epoxyqueuosine reductase QueH The reduction of epoxyqueuosine (oQ) is the last step in the synthesis of the tRNA modification queuosine (Q). members of this family were predicted to encode for an alternative epoxyqueuosine reductase. Furthermore, it has been suggested that family members are a non-orthologous replacement of queG, responsible for oQ to Q conversion. QueH contains conserved cysteines that could be involved in the coordination of a Fe/S center in a similar fashion to what has been identified in QueG. No cobalamin was identified associated with recombinant QueH protein, indicating that the reduction activity is independent from cobalamin [1]. [1]. 28128549. Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics. Zallot R, Ross R, Chen WH, Bruner SD, Limbach PA, de Crecy-Lagard V;. ACS Chem Biol. 2017;12:844-851. (from Pfam) NF014715.5 PF02685.21 Glucokinase 22.1 22.1 314 domain Y Y N glucokinase GO:0004340,GO:0005524,GO:0005536,GO:0006096,GO:0051156 9023215 2 Bacteria superkingdom 49588 EBI-EMBL Glucokinase glucokinase This is a family of glucokinases or glucose kinases EC:2.7.1.2. These enzymes phosphorylate glucose using ATP as a donor to give glucose-6-phosphate and ADP. [1]. 9023215. Molecular characterization of glucokinase from Escherichia coli K-12. Meyer D, Schneider-Fresenius C, Horlacher R, Peist R, Boos W;. J Bacteriol 1997;179:1298-1306. (from Pfam) NF014725.5 PF02699.20 YajC 28.2 28.2 78 domain Y Y N preprotein translocase subunit YajC 11051763 2 Bacteria superkingdom 43919 EBI-EMBL Preprotein translocase subunit preprotein translocase subunit YajC See [1]. [1]. 11051763. Protein traffic in bacteria: multiple routes from the ribosome to and across the membrane. Muller M, Koch HG, Beck K, Schafer U;. Prog Nucleic Acid Res Mol Biol 2001;66:107-157. (from Pfam) NF014741.5 PF02720.22 DUF222 24.4 24.4 306 domain Y Y N DUF222 domain-containing protein 12029045 2 Bacteria superkingdom 79324 EBI-EMBL Domain of unknown function (DUF222) Domain of unknown function (DUF222) This family is often found associated to the N-terminus of the HNH endonuclease domain Pfam:PF01844. The function of this domain is uncertain. This family has been called the 13E12 repeat family [1]. [1]. 12029045. Definition of the mycobacterial SOS box and use to identify LexA-regulated genes in Mycobacterium tuberculosis. Davis EO, Dullaghan EM, Rand L;. J Bacteriol. 2002;184:3287-3295. (from Pfam) NF014756.5 PF02736.24 Myosin_N 27 27 45 domain Y Y N myosin N-terminal SH3-like domain-containing protein GO:0003774,GO:0005524,GO:0016459 16982629,17597155 2 Bacteria superkingdom 7 EBI-EMBL Myosin N-terminal SH3-like domain Myosin N-terminal SH3-like domain This domain has an SH3-like fold. It is found at the N-terminus of many but not all myosins. The function of this domain is unknown. (from Pfam) NF014783.5 PF02763.19 Diphtheria_C 25 25 187 domain Y N N Diphtheria toxin, C domain 7833808,8573568 2 Bacteria superkingdom 69 EBI-EMBL Diphtheria toxin, C domain Diphtheria toxin, C domain N-terminal catalytic (C) domain - blocks protein synthesis by transfer of ADP-ribose from NAD to a diphthamide residue of EF-2. [1]. 7833808. Refined structure of monomeric diphtheria toxin at 2.3 A resolution. Bennett MJ, Eisenberg D;. Protein Sci 1994;3:1464-1475. [2]. 8573568. Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide. Bell CE, Eisenberg D;. Biochemistry 1996;35:1137-1149. (from Pfam) NF014784.5 PF02764.19 Diphtheria_T 27 27 166 PfamEq Y N N Diphtheria toxin, T domain 7833808,8573568 2 Bacteria superkingdom 102 EBI-EMBL Diphtheria toxin, T domain Diphtheria toxin, T domain Central domain of diphtheria toxin is the translocation (T) domain. pH induced conformational change in this domain triggers insertion into the endosomal membrane and facilitates the transfer of the catalytic domain into the cytoplasm. [1]. 7833808. Refined structure of monomeric diphtheria toxin at 2.3 A resolution. Bennett MJ, Eisenberg D;. Protein Sci 1994;3:1464-1475. [2]. 8573568. Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide. Bell CE, Eisenberg D;. Biochemistry 1996;35:1137-1149. (from Pfam) NF014787.5 PF02768.20 DNA_pol3_beta_3 27 27 121 PfamEq Y N N DNA polymerase III beta subunit, C-terminal domain GO:0003677,GO:0003887,GO:0006260,GO:0008408,GO:0009360 1349852 2 Bacteria superkingdom 61840 EBI-EMBL DNA polymerase III beta subunit, C-terminal domain DNA polymerase III beta subunit, C-terminal domain A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold. [1]. 1349852. Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. Kong XP, Onrust R, O'Donnell M, Kuriyan J;. Cell 1992;69:425-437. (from Pfam) NF014800.5 PF02781.21 G6PD_C 27 27 296 domain Y N N Glucose-6-phosphate dehydrogenase, C-terminal domain GO:0004345,GO:0006006,GO:0050661 9485426 2 Bacteria superkingdom 74202 EBI-EMBL Glucose-6-phosphate dehydrogenase, C-terminal domain Glucose-6-phosphate dehydrogenase, C-terminal domain NF014813.5 PF02794.21 HlyC 25 25 127 domain Y Y N toxin-activating lysine-acyltransferase GO:0005737,GO:0009404,GO:0016746 10079090 2 Bacteria superkingdom 4169 EBI-EMBL RTX toxin acyltransferase family toxin-activating lysine-acyltransferase Members of this family are enzymes EC:2.3.1.-. involved in fatty acylation of the protoxins (HlyA) at lysine residues, thereby converting them to the active toxin. Acyl-acyl carrier protein (ACP) is the essential acyl donor. This family show a number of conserved residues that are possible candidates for participation in acyl transfer. Site-directed mutagenesis of the single conserved histidine residue in Swiss:P06736 resulted in complete inactivation of the enzyme [1]. [1]. 10079090. HlyC, the internal protein acyltransferase that activates hemolysin toxin: role of conserved histidine, serine, and cysteine residues in enzymatic activity as probed by chemical modification and site-directed mutagenesis. Trent MS, Worsham LM, Ernst-Fonberg ML;. Biochemistry 1999;38:3433-3439. (from Pfam) NF014815.5 PF02797.20 Chal_sti_synt_C 27 27 151 domain Y N N Chalcone and stilbene synthases, C-terminal domain 10426957 2 Bacteria superkingdom 27759 EBI-EMBL Chalcone and stilbene synthases, C-terminal domain Chalcone and stilbene synthases, C-terminal domain This domain of chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase. The differences in activity are accounted for by differences in the N-terminal domain. [1]. 10426957. Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis. Ferrer JL, Jez JM, Bowman ME, Dixon RA, Noel JP;. Nat Struct Biol 1999;6:775-784. (from Pfam) NF014819.5 PF02801.27 Ketoacyl-synt_C 20.8 20.8 119 domain Y N N Beta-ketoacyl synthase, C-terminal domain 9482715 2 Bacteria superkingdom 483542 EBI-EMBL Beta-ketoacyl synthase, C-terminal domain Beta-ketoacyl synthase, C-terminal domain The structure of beta-ketoacyl synthase is similar to that of the thiolase family (Pfam:PF00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains. [1]. 9482715. Crystal structure of beta-ketoacyl-acyl carrier protein synthase II from E.coli reveals the molecular architecture of condensing enzymes. Huang W, Jia J, Edwards P, Dehesh K, Schneider G, Lindqvist Y;. EMBO J 1998;17:1183-1191. (from Pfam) NF014823.5 PF02807.20 ATP-gua_PtransN 25.7 25.7 67 PfamEq Y N N ATP:guanido phosphotransferase, N-terminal domain GO:0016301,GO:0016772 8692275 2 Bacteria superkingdom 130 EBI-EMBL ATP:guanido phosphotransferase, N-terminal domain ATP:guanido phosphotransferase, N-terminal domain The N-terminal domain has an all-alpha fold. [1]. 8692275. Structure of mitochondrial creatine kinase. Fritz-Wolf K, Schnyder T, Wallimann T, Kabsch W;. Nature 1996;381:341-345. (from Pfam) NF014830.5 PF02815.24 MIR 25.6 25.6 185 domain Y Y N MIR domain-containing protein GO:0016020 10664581 2 Bacteria superkingdom 64 EBI-EMBL MIR domain MIR domain The mostly fungal MIR domain, which may have a ligand transferase function, is also found in a number of bacterial proteins as the C-terminal domain of proteins with an N-terminal carbohydrate-binding domain. NF014846.5 PF02831.20 gpW 22.5 22.5 66 PfamEq Y Y N gpW family head-tail joining protein gpW GO:0019058 11302702 2 Bacteria superkingdom 2536 EBI-EMBL gpW gpW family head-tail joining protein Members of this family, including W from phage lambda, are head-tail joining proteins. NF014864.5 PF02863.23 Arg_repressor_C 25 25 68 domain Y N N Arginine repressor, C-terminal domain GO:0034618,GO:0051259 11856827,9334747 2 Bacteria superkingdom 23857 EBI-EMBL Arginine repressor, C-terminal domain Arginine repressor, C-terminal domain This is the C-terminal domain of the arginine repressor, responsible for arginine binding and multimerization [1,2]. It binds mainly Arg, but also ornithine, Pro and Tyr (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 9334747. Solution structure of the DNA-binding domain and model for the complex of multifunctional hexameric arginine repressor with DNA. Sunnerhagen M, Nilges M, Otting G, Carey J;. Nat Struct Biol 1997;4:819-826. [2]. 11856827. The structure of AhrC, the arginine repressor/activator protein from Bacillus subtilis. Dennis C CA, Glykos NM, Parsons MR, Phillips SE;. Acta Crystallogr D Biol Crystallogr. 2002;58:421-430. (from Pfam) NF014876.5 PF02877.19 PARP_reg 26.8 26.8 135 PfamEq Y N N Poly(ADP-ribose) polymerase, regulatory domain GO:0003950 8390463,8755499,9521710 2 Bacteria superkingdom 69 EBI-EMBL Poly(ADP-ribose) polymerase, regulatory domain Poly(ADP-ribose) polymerase, regulatory domain Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active [2]. [1]. 8755499. Structure of the catalytic fragment of poly(AD-ribose) polymerase from chicken. Ruf A, Mennissier de Murcia J, de Murcia G, Schulz GE;. Proc Natl Acad Sci U S A 1996;93:7481-7485. [2]. 8390463. The carboxyl-terminal domain of human poly(ADP-ribose) polymerase. Overproduction in Escherichia coli, large scale purification, and characterization. Simonin F, Hofferer L, Panzeter PL, Muller S, de Murcia G, Althaus FR;. J Biol Chem 1993;268:13454-13461. [3]. 9521710. Inhibitor and NAD+ binding to poly(ADP-ribose) polymerase as derived from crystal structures and homology modeling. Ruf A, de Murcia G, Schulz GE;. Biochemistry 1998;37:3893-3900. (from Pfam) NF014900.5 PF02901.20 PFL-like 24.3 24.3 647 domain Y Y N pyruvate formate lyase family protein GO:0003824 10504733,11231288,15096031,23151509,9632263 2 Bacteria superkingdom 58086 EBI-EMBL Pyruvate formate lyase-like pyruvate formate lyase family protein This family of enzymes includes pyruvate formate lyase [1], choline trimethylamine lyase [2], glycerol dehydratase [3], 4-hydroxyphenylacetate decarboxylase [4], and benzylsuccinate synthase [5]. [1]. 10504733. Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase. Becker A, Fritz-Wolf K, Kabsch W, Knappe J, Schultz S, Volker Wagner AF;. Nat Struct Biol 1999;6:969-975. [2]. 23151509. Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme. Craciun S, Balskus EP;. Proc Natl Acad Sci U S A. 2012;109:21307-21312. [3]. 15096031. Insight into the mechanism of the B12-independent glycerol dehydratase from Clostridium butyricum: preliminary biochemical and structural characterization. O'Brien JR, Raynaud C, Croux C, Girbal L, Soucaille P, Lanzilotta WN;. Biochemistry. 2004;43:4635-4645. [4]. 11231288. p-Hydroxyphenylacetate decarboxylase from Clostridium difficile. A novel glycyl radical enzyme catalysing the formation of p-cresol. Selmer T, Andrei PI;. Eur J Biochem. 2001;268:1363-1372. [5]. 9632263. Biochemical and genetic characterization of benzylsuccinate synthase from Thauera aromatica: a new glycyl radical enzyme catalysing the first step in anaerobic toluene metabolism. Leuthner B, Leutwein C, Schulz H, Horth P, Haehnel W, Schiltz E, Schagger H, Heider J;. Mol Microbiol 1998;28:615-628. (from Pfam) NF014905.5 PF02907.20 Peptidase_S29 25 25 149 PfamEq Y N N Hepatitis C virus NS3 protease GO:0006508,GO:0008236,GO:0019087 8861916,9083052,9568891 2 Bacteria superkingdom 19 EBI-EMBL Hepatitis C virus NS3 protease Hepatitis C virus NS3 protease Hepatitis C virus NS3 protein is a serine protease which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. NS2-3 proteinase, a zinc-dependent enzyme, performs a single proteolytic cut to release the N-terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4A. [1]. 9568891. Complex of NS3 protease and NS4A peptide of BK strain hepatitis C virus: a 2.2 A resolution structure in a hexagonal crystal form. Yan Y, Li Y, Munshi S, Sardana V, Cole JL, Sardana M, Steinkuehler C, Tomei L, De Francesco R, Kuo LC, Chen Z;. Protein Sci 1998;7:837-847. [2]. 8861916. The crystal structure of hepatitis C virus NS3 proteinase reveals a trypsin-like fold and a structural zinc binding site. Love RA, Parge HE, Wickersham JA, Hostomsky Z, Habuka N, Moomaw EW, Adachi T, Hostomska Z;. Cell 1996;87:331-342. [3]. 9083052. Substrate specificity of the hepatitis C virus serine protease NS3. Urbani A, Bianchi E, Narjes F, Tramontano A, De Francesco R, Steinkuhler C, Pessi A;. J Biol Chem 1997;272:9204-9209. (from Pfam) NF014906.5 PF02909.22 TetR_C_1 21 21 146 domain Y Y N TetR/AcrR family transcriptional regulator C-terminal domain-containing protein GO:0045892 8153629 2 Bacteria superkingdom 136705 EBI-EMBL Tetracyclin repressor-like, C-terminal domain Tetracyclin repressor-like, C-terminal domain NF014911.5 PF02914.20 DDE_2 23 23 221 domain Y Y N transposase domain-containing protein GO:0003677,GO:0004803,GO:0006313,GO:0015074 7628012 2 Bacteria superkingdom 2915 EBI-EMBL Bacteriophage Mu transposase Bacteriophage Mu transposase This transposase is essential for integration, replication-transposition and excision of Bacteriophage Mu DNA. The crystal structure of the core domain of Mu transposase, MuA, exhibits that the first of two subdomains contains the active site and, despite very limited sequence homology, exhibits a striking similarity to the core domain of Human immunodeficiency virus 1 integrase. The enzymatic activity of MuA is known to be activated by formation of a DNA-bound tetramer of the protein [1]. [1]. 7628012. Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration. Rice P, Mizuuchi K;. Cell. 1995;82:209-220. (from Pfam) NF014914.5 PF02917.19 Pertussis_S1 21.3 21.3 239 PfamEq Y N N Pertussis toxin, subunit 1 GO:0003950,GO:0005576 8637000 2 Bacteria superkingdom 1892 EBI-EMBL Pertussis toxin, subunit 1 Pertussis toxin, subunit 1 NF014917.5 PF02920.20 Integrase_DNA 27 27 70 domain Y Y N integrase DNA-binding domain-containing protein GO:0003677,GO:0008907,GO:0015074 9665166 2 Bacteria superkingdom 4910 EBI-EMBL DNA binding domain of tn916 integrase DNA binding domain of tn916 integrase NF014921.5 PF02924.19 HDPD 29.1 29.1 116 domain Y Y N head decoration protein 10700283 2 Bacteria superkingdom 10737 EBI-EMBL Bacteriophage lambda head decoration protein D head decoration protein NF014937.5 PF02941.20 FeThRed_A 25 25 67 PfamEq Y Y N ferredoxin-thioredoxin reductase variable chain GO:0015979 10649999 2 Bacteria superkingdom 737 EBI-EMBL Ferredoxin thioredoxin reductase variable alpha chain ferredoxin-thioredoxin reductase variable chain NF014944.5 PF02948.20 Amelogenin 27 27 179 PfamEq Y N N Amelogenin 11223334 2 Bacteria superkingdom 8 EBI-EMBL Amelogenin Amelogenin Amelogenins play a role in biomineralisation. They seem to regulate the formation of crystallites during the secretory stage of tooth enamel development. thought to play a major role in the structural organisation and mineralisation of developing enamel. They are found in the extracellular matrix. Mutations in X-chromosomal amelogenin can cause Amelogenesis imperfecta [1]. [1]. 11223334. Reduced hydrolysis of amelogenin may result in X-linked amelogenesis imperfecta. Li W, Gibson CW, Abrams WR, Andrews DW, DenBesten PK;. Matrix Biol 2001;19:755-760. (from Pfam) NF014947.5 PF02951.19 GSH-S_N 21.3 21.3 119 PfamEq Y N N Prokaryotic glutathione synthetase, N-terminal domain GO:0004363,GO:0006750 8445637 2 Bacteria superkingdom 29208 EBI-EMBL Prokaryotic glutathione synthetase, N-terminal domain Prokaryotic glutathione synthetase, N-terminal domain NF014958.5 PF02962.20 CHMI 26.5 26.5 124 domain Y N N 5-carboxymethyl-2-hydroxymuconate isomerase GO:0008704,GO:0009056 8547259 2 Bacteria superkingdom 17363 EBI-EMBL 5-carboxymethyl-2-hydroxymuconate isomerase 5-carboxymethyl-2-hydroxymuconate isomerase NF014960.5 PF02964.21 MeMO_Hyd_G 25 25 161 PfamEq Y N N Methane monooxygenase, hydrolase gamma chain GO:0015049,GO:0015947 8255292 2 Bacteria superkingdom 96 EBI-EMBL Methane monooxygenase, hydrolase gamma chain Methane monooxygenase, hydrolase gamma chain NF014962.5 PF02966.21 DIM1 27 27 133 PfamEq Y N N Mitosis protein DIM1 GO:0000398,GO:0046540 10610776 2 Bacteria superkingdom 55 EBI-EMBL Mitosis protein DIM1 Mitosis protein DIM1 NF014967.5 PF02973.22 Sialidase 26 26 189 domain Y Y N sialidase domain-containing protein GO:0004308,GO:0005975 9562562 2 Bacteria superkingdom 3532 EBI-EMBL Sialidase, N-terminal domain Sialidase, N-terminal domain NF014969.5 PF02975.19 Me-amine-dh_L 25 25 113 domain Y Y N methylamine dehydrogenase light chain GO:0009308,GO:0016638,GO:0042597 8140419 2 Bacteria superkingdom 1694 EBI-EMBL Methylamine dehydrogenase, L chain methylamine dehydrogenase light chain NF014974.5 PF02980.21 FokI_dom_2 25 25 136 domain Y Y N restriction endonuclease FokI catalytic domain-containing protein GO:0003677,GO:0009307 10508668,9214510,9724743 2 Bacteria superkingdom 361 EBI-EMBL FokI, recognition domain, subdomain 2 FokI, recognition domain, subdomain 2 Type IIS restriction endonuclease FokI is a member of an unusual class of bipartite restriction enzymes that recognises the double-stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand [1]. FokI contains amino- and carboxy-terminal domains corresponding to the DNA- recognition and cleavage functions, respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP [3]. This entry represents the subdomain D2 of FokI. D1 and D2 make almost all of the base-specific contacts with the DNA [3]. [1]. 9724743. Structure of FokI has implications for DNA cleavage. Wah DA, Bitinaite J, Schildkraut I, Aggarwal AK;. Proc Natl Acad Sci U S A. 1998;95:10564-10569. [2]. 10508668. Type II restriction endonucleases: structural, functional and evolutionary relationships. Kovall RA, Matthews BW;. Curr Opin Chem Biol 1999;3:578-583. [3]. 9214510. Structure of the multimodular endonuclease FokI bound to DNA. Wah DA, Hirsch JA, Dorner LF, Schildkraut I, Aggarwal AK;. Nature. 1997;388:97-100. (from Pfam) NF014975.5 PF02981.20 FokI_D1 25 25 156 domain Y Y N restriction endonuclease FokI recognition domain-containing protein GO:0003677,GO:0009307 10508668,9214510,9724743 2 Bacteria superkingdom 350 EBI-EMBL FokI, recognition domain, subdomain 1 FokI, recognition domain, subdomain 1 Type IIS restriction endonuclease FokI is a member of an unusual class of bipartite restriction enzymes that recognises the double-stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand [1]. FokI contains amino- and carboxy-terminal domains corresponding to the DNA- recognition and cleavage functions, respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix- containing DNA-binding domain of the catabolite gene activator protein CAP [3]. This entry represents the subdomain D1 of FokI. Subdomain D1 of the recognition domain covers the DNA major groove, recognizing base pairs at the 3' end of the recognition sequence (GGATG) [3]. [1]. 9724743. Structure of FokI has implications for DNA cleavage. Wah DA, Bitinaite J, Schildkraut I, Aggarwal AK;. Proc Natl Acad Sci U S A. 1998;95:10564-10569. [2]. 10508668. Type II restriction endonucleases: structural, functional and evolutionary relationships. Kovall RA, Matthews BW;. Curr Opin Chem Biol 1999;3:578-583. [3]. 9214510. Structure of the multimodular endonuclease FokI bound to DNA. Wah DA, Hirsch JA, Dorner LF, Schildkraut I, Aggarwal AK;. Nature. 1997;388:97-100. (from Pfam) NF014976.5 PF02982.19 Scytalone_dh 27 27 160 PfamEq Y N N Scytalone dehydratase GO:0006582,GO:0030411 9665698 2 Bacteria superkingdom 68 EBI-EMBL Scytalone dehydratase Scytalone dehydratase Scytalone dehydratases are structurally related to the NTF2 family (see Pfam:PF02136). [1]. 9665698. Cryogenic X-ray crystal structure analysis for the complex of scytalone dehydratase of a rice blast fungus and its tight-binding inhibitor, carpropamid: the structural basis of tight-binding inhibition. Nakasako M, Motoyama T, Kurahashi Y, Yamaguchi I;. Biochemistry 1998;37:9931-9939. (from Pfam) NF014977.5 PF02983.19 Pro_Al_protease 23.4 23.4 59 domain Y Y N alpha-lytic protease prodomain-containing protein GO:0005576,GO:0006508,GO:0008236 9808037 2 Bacteria superkingdom 37072 EBI-EMBL Alpha-lytic protease prodomain Alpha-lytic protease prodomain NF014981.5 PF02987.21 LEA_4 51.1 51.1 44 PfamEq Y N N Late embryogenesis abundant protein 7630968 2 Bacteria superkingdom 8 EBI-EMBL Late embryogenesis abundant protein Late embryogenesis abundant protein Different types of LEA proteins are expressed at different stages of late embryogenesis in higher plant seed embryos and under conditions of dehydration stress. The function of these proteins is unknown. [1]. 7630968. Sequence and regulation of a late embryogenesis abundant group 3 protein of maize. White CN, Rivin CJ;. Plant Physiol 1995;108:1337-1338. (from Pfam) NF014984.5 PF02990.21 EMP70 27 27 517 domain Y Y N transmembrane 9 family protein GO:0016020 9332367 2 Bacteria superkingdom 2 EBI-EMBL Endomembrane protein 70 transmembrane 9 family protein NF014988.5 PF02994.19 Transposase_22 22.4 22.4 98 domain Y Y N RBD-like domain-containing protein 18073200,19139409,9140393 2 Bacteria superkingdom 46 EBI-EMBL L1 transposable element RBD-like domain L1 transposable element RBD-like domain This entry represents the RBD-like domain. [1]. 9140393. Many human L1 elements are capable of retrotransposition. Sassaman DM, Dombroski BA, Moran JV, Kimberland ML, Naas TP, DeBerardinis RJ, Gabriel A, Swergold GD, Kazazian HH Jr;. Nat Genet 1997;16:37-43. [2]. 18073200. Functional endogenous LINE-1 retrotransposons are expressed and mobilized in rat chloroleukemia cells. Kirilyuk A, Tolstonog GV, Damert A, Held U, Hahn S, Lower R, Buschmann C, Horn AV, Traub P, Schumann GG;. Nucleic Acids Res. 2008;36:648-665. [3]. 19139409. Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame. Khazina E, Weichenrieder O;. Proc Natl Acad Sci U S A. 2009;106:731-736. (from Pfam) NF014997.5 PF03006.25 HlyIII 26.2 26.2 224 PfamEq Y Y N hemolysin III family protein GO:0016020 11916977,16044242,17082257,21733186,7495855 2 Bacteria superkingdom 49477 EBI-EMBL Haemolysin-III related hemolysin III family protein Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus [1]. It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism [2]. In eukaryotes, members are seven-transmembrane pass molecules found to encode functional receptors with a broad range of apparent ligand specificities, including progestin and adipoQ receptors, and hence have been named PAQR proteins [3]. The mammalian members include progesterone binding proteins [4]. Unlike the case with GPCR receptor proteins, the evolutionary ancestry of the members of this family can be traced back to the Archaea. This family belongs to the CREST superfamily [5], which are distantly related to GPCRs. [1]. 7495855. Cloning and primary structure of a new hemolysin gene from Bacillus cereus. Baida GE, Kuzmin NP;. Biochim Biophys Acta 1995;1264:151-154. [2]. 11916977. Multiple regulatory roles of a novel Saccharomyces cerevisiae protein, encoded by YOL002c, in lipid and phosphate metabolism. Karpichev IV, Cornivelli L, Small GM;. J Biol Chem 2002;0:0-1. [3]. 16044242. PAQR proteins: a novel membrane receptor family defined by an ancient 7-transmembrane pass motif. Tang YT, Hu T, Arterburn M, Boyle B, Bright JM, Emtage PC, Funk WD;. J Mol Evol. 2005;61:372-380. [4]. 17082257. Steroid and G protein binding characteristics of the seatrout and human progestin membrane receptor alpha subtypes and their evolutionary origins. Thomas P, Pang Y, Dong J, Groenen P, Kelder J, de Vlieg J, Zhu Y, Tubbs C;. Endocrino. TRUNCATED at 1650 bytes (from Pfam) NF015006.5 PF03015.24 Sterile 35.4 35.4 93 domain Y Y N acyl-CoA reductase C-terminal domain-containing protein 9351246 2 Bacteria superkingdom 637 EBI-EMBL Male sterility protein Male sterility protein This family represents the C-terminal region of the male sterility protein in a number of arabidopsis and drosophila. A sequence-related jojoba acyl CoA reductase is also included. [1]. 9351246. The Arabidopsis MALE STERILITY 2 protein shares similarity with reductases in elongation/condensation complexes. Aarts MG, Hodge R, Kalantidis K, Florack D, Wilson ZA, Mulligan BJ, Stiekema WJ, Scott R, Pereira A;. Plant J 1997;12:615-623. (from Pfam) NF015009.5 PF03018.19 Dirigent 29.1 29.1 148 PfamEq Y Y N dirigent protein 16463097,17590394,27756822 2 Bacteria superkingdom 255 EBI-EMBL Dirigent-like protein dirigent protein This family contains a number of proteins which are induced during disease response in plants. Members of this family are involved in lignification. (from Pfam) NF015029.5 PF03040.19 CemA 27.4 27.4 229 domain Y N N CemA family GO:0016020 2103453,8633006 2 Bacteria superkingdom 1577 EBI-EMBL CemA family CemA family Members of this family are probable integral membrane proteins. Their molecular function is unknown. CemA proteins are found in the inner envelope membrane of chloroplasts but not in the thylakoid membrane [1]. A cyanobacterial member of this family has been implicated in CO2 transport, but is probably not a CO2 transporter itself [1]. They are predicted to be haem-binding however this has not been proven experimentally [2]. [1]. 8633006. cemA homologue essential to CO2 transport in the cyanobacterium Synechocystis PCC6803. Katoh A, Lee KS, Fukuzawa H, Ohyama K, Ogawa T;. Proc Natl Acad Sci U S A 1996;93:4006-4010. [2]. 2103453. An open reading frame encoding a putative haem-binding polypeptide is cotranscribed with the pea chloroplast gene for apocytochrome f. Willey DL, Gray JC;. Plant Mol Biol 1990;15:347-356. (from Pfam) NF015039.5 PF03051.20 Peptidase_C1_2 22 22 438 domain Y Y N C1 family peptidase GO:0006508,GO:0070005 7925365,9546396 2 Bacteria superkingdom 18686 EBI-EMBL Peptidase C1-like family C1 family peptidase This family is closely related to the Peptidase_C1 family Pfam:PF00112, containing several prokaryotic and eukaryotic aminopeptidases and bleomycin hydrolases. [1]. 9546396. The unusual active site of Gal6/bleomycin hydrolase can act as a carboxypeptidase, aminopeptidase, and peptide ligase. Zheng W, Johnston SA, Joshua-Tor L;. Cell 1998;93:103-109. [2]. 7925365. Gene cloning and characterization of PepC, a cysteine aminopeptidase from Streptococcus thermophilus, with sequence similarity to the eucaryotic bleomycin hydrolase. Chapot-Chartier MP, Rul F, Nardi M, Gripon JC;. Eur J Biochem 1994;224:497-506. (from Pfam) NF015055.5 PF03068.20 PAD 25 25 395 domain Y Y N protein-arginine deiminase family protein GO:0004668,GO:0005509,GO:0005737 10092850,11166924,9129218 2 Bacteria superkingdom 1886 EBI-EMBL Protein-arginine deiminase (PAD) protein-arginine deiminase Protein-arginine deiminases, as characterized in mammals, perform post-translational modificiations that convert arginine to citrulline. Prokaryotic examples are found in bacterial genera such as Streptomyces and Myxococcus. NF015066.5 PF03080.21 Neprosin 22 21.5 214 subfamily Y Y N neprosin family prolyl endopeptidase 27481162 2 Bacteria superkingdom 821 EBI-EMBL Neprosin neprosin family prolyl endopeptidase Pitcher plants are insectivorous and secrete a digestive fluid into the pitcher. This fluid contains a mixture of enzymes including peptidases. One of these is neprosin, characterized from the pitcher plant Nepenthes ventrata. This peptidase is of unknown catalytic type and is unaffected by standard peptidase inhibitors. Unusually, activity is directed towards prolyl bonds, but unlike most peptidase that cleave after proline, there is no restriction on sequence length or position of the proline residue. The peptidase is secreted and is presumed to possess an N-terminal activation peptide. The neprosin domain corresponds to the mature peptidase [1]. It is not known if other proteins with this domain are peptidases. [1]. 27481162. Addressing proteolytic efficiency in enzymatic degradation therapy for celiac disease. Rey M, Yang M, Lee L, Zhang Y, Sheff JG, Sensen CW, Mrazek H, Halada P, Man P, McCarville JL, Verdu EF, Schriemer DC;. Sci Rep. 2016;6:30980. (from Pfam) NF015076.5 PF03090.22 Replicase 26 26 130 domain Y Y N replication initiation protein 11296251 2 Bacteria superkingdom 9644 EBI-EMBL Replicase family replication initiation protein This is a family of bacterial plasmid DNA replication initiator proteins. Pfam: PF01051 is a similar family. These RepA proteins exist as monomers and dimers in equilibrium: monomers bind directly to repeated DNA sequences and thus activate replication; dimers repress repA transcription by binding an inversely repeated DNA operator. Dimer dissociation can occur spontaneously or be mediated by Hsp70 chaperones. [1]. 11296251. Similarities between the DNA replication initiators of Gram-negative bacteria plasmids (RepA) and eukaryotes (Orc4p)/archaea (Cdc6p). Giraldo R, Diaz-Orejas R;. Proc Natl Acad Sci U S A 2001;98:4938-4943. (from Pfam) NF015102.5 PF03118.20 RNA_pol_A_CTD 23.8 23.8 67 domain Y Y N DNA-directed RNA polymerase subunit alpha C-terminal domain-containing protein GO:0003677,GO:0003899,GO:0006351 7491496,7613089,9050843 2 Bacteria superkingdom 40630 EBI-EMBL Bacterial RNA polymerase, alpha chain C terminal domain Bacterial RNA polymerase, alpha chain C terminal domain The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal [2]. NMR structure. [1]. 7491496. Solution structure of the activator contact domain of the RNA polymerase alpha subunit. Jeon YH, Negishi T, Shirakawa M, Yamazaki T, Fujita N, Ishihama A, Kyogoku Y;. Science 1995;270:1495-1497. [2]. 7613089. The Escherichia coli RNA polymerase alpha subunit: structure and function. Ebright RH, Busby S;. Curr Opin Genet Dev 1995;5:197-203. [3]. 9050843. The two alpha subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element. Murakami K, Kimura M, Owens JT, Meares CF, Ishihama A;. Proc Natl Acad Sci USA 1997;94:1709-1714. (from Pfam) NF015107.5 PF03123.20 CAT_RBD 25 25 57 domain Y Y N CAT RNA binding domain-containing protein GO:0003723 10610766,11953318,9305643,9305644 2 Bacteria superkingdom 29419 EBI-EMBL CAT RNA binding domain CAT RNA binding domain This RNA binding domain is found at the amino terminus of transcriptional antitermination proteins such as BglG, SacY and LicT. These proteins control the expression of sugar metabolising operons in Gram+ and Gram- bacteria. This domain has been called the CAT (Co-AntiTerminator) domain. It binds as a dimer [1] to short Ribonucleotidic Anti-Terminator (RAT) hairpin, each monomer interacting symmetrically with both strands of the RAT hairpin [4]. In the full-length protein, CAT is followed by two phosphorylatable PTS regulation domains (Pfam:PF00874) that modulate the RNA binding activity of CAT. Upon activation, the dimeric proteins bind to RAT targets in the nascent mRNA, thereby preventing abortive dissociation of the RNA polymerase from the DNA template [2]. [1]. 9305644. Crystal structure of a new RNA-binding domain from the antiterminator protein SacY of Bacillus subtilis. van Tilbeurgh H, Manival X, Aymerich S, Lhoste JM, Dumas C, Kochoyan M;. EMBO J 1997;16:5030-5036. [2]. 10610766. RNA recognition by transcriptional antiterminators of the BglG/SacY family: functional and structural comparison of the CAT domain from SacY and LicT. Declerck N, Vincent F, Hoh F, Aymerich S, van Tilbeurgh H;. J Mol Biol 1999;294:389-402. [3]. 9305643. From genetic to structural characterization of a new class of RNA-binding domain within the SacY/BglG family of antiterminator proteins. Manival X, Yang Y, Strub MP, Kochoyan M, Steinmetz M, Aymerich S;. EMBO J 1997;16:5019-5029. [4]. 11953318. Solution structure of the LicT-RNA antitermination complex: CAT clamping RAT. Yang Y, Declerck N, Manival X, Aymerich S, Kochoyan M;. EMBO J. 2002. TRUNCATED at 1650 bytes (from Pfam) NF015117.5 PF03134.24 TB2_DP1_HVA22 27.2 27.2 77 domain Y Y N TB2/DP1/HVA22 family protein 10805953,8226892 2 Bacteria superkingdom 3 EBI-EMBL TB2/DP1, HVA22 family TB2/DP1/HVA22 family protein This family includes members from a wide variety of eukaryotes. It includes the TB2/DP1 (deleted in polyposis) protein (e.g. Swiss:Q00765), which in humans is deleted in severe forms of familial adenomatous polyposis, an autosomal dominant oncological inherited disease. The family also includes the plant protein of known similarity to TB2/DP1, the HVA22 abscisic acid-induced protein (e.g. Swiss:Q07764), which is thought to be a regulatory protein. [1]. 10805953. Familial adenomatous polyposis. Lal G, Gallinger S;. Semin Surg Oncol 2000;18:314-323. [2]. 8226892. Hormone response complex in a novel abscisic acid and cycloheximide-inducible barley gene. Shen Q, Uknes SJ, Ho TH;. J Biol Chem 1993;268:23652-23660. (from Pfam) NF015119.5 PF03136.20 Pup_ligase 25 25 441 domain Y Y N proteasome accessory factor PafA2 family protein GO:0010498,GO:0019941 18832610,18980670 2 Bacteria superkingdom 23127 EBI-EMBL Pup-ligase protein proteasome accessory factor PafA2 family protein Pupylation is a novel protein modification system found in some bacteria [1]. This family of proteins are the enzyme that can conjugate proteins of the Pup family to lysine residues in target proteins marking them for degradation. The archetypal protein in this family is PafA (proteasome accessory factor) from Mycobacterium tuberculosis [2]. It has been suggested that these proteins are related to gamma-glutamyl-cysteine synthetases [1]. [1]. 18980670. Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination. Iyer LM, Burroughs AM, Aravind L;. Biol Direct. 2008;3:45. [2]. 18832610. Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis. Pearce MJ, Mintseris J, Ferreyra J, Gygi SP, Darwin KH;. Science. 2008;322:1104-1107. (from Pfam) NF015149.5 PF03170.18 BcsB 21 21 606 domain Y Y N cellulose biosynthesis cyclic di-GMP-binding regulatory protein BcsB GO:0006011,GO:0016020 10376842,2146681,7860585 2 Bacteria superkingdom 25344 EBI-EMBL Bacterial cellulose synthase subunit cellulose biosynthesis cyclic di-GMP-binding regulatory protein BcsB This family includes bacterial proteins involved in cellulose synthesis. Cellulose synthesis has been identified in several bacteria. In Agrobacterium tumefaciens, for instance, cellulose has a pathogenic role: it allows the bacteria to bind tightly to their host plant cells. While several enzymatic steps are involved in cellulose synthesis, potentially the only step unique to this pathway is that catalysed by cellulose synthase. This enzyme is a multi subunit complex. This family encodes a subunit that is thought to bind the positive effector cyclic di-GMP. This subunit is found in several different bacterial cellulose synthase enzymes. The first recognised sequence for this subunit is BcsB. In the AcsII cellulose synthase, this subunit and the subunit corresponding to BcsA are found in the same protein. Indeed, this alignment only includes the C-terminal half of the AcsAII synthase (Swiss:Q59167), which corresponds to BcsB. [1]. 2146681. Genetic organization of the cellulose synthase operon in Acetobacter xylinum. Wong HC, Fear AL, Calhoon RD, Eichinger GH, Mayer R, Amikam D, Benziman M, Gelfand DH, Meade JH, Emerick AW, et al.;. Proc Natl Acad Sci U S A 1990;87:8130-8134. [2]. 7860585. Genes required for cellulose synthesis in Agrobacterium tumefaciens. Matthysse AG, White S, Lightfoot R;. J Bacteriol 1995;177:1069-1075. [3]. 10376842. Structural and putative regulatory genes involved in cellulose synthesis in Rhizobium leguminosarum bv. trifolii. Ausmees N, Jonsson H, Hoglund S, Ljunggren H, Lindberg M;. Microbiology 1999;145:1253-1262. (from Pfam) NF015150.5 PF03171.25 2OG-FeII_Oxy 23 23 101 domain Y Y N 2OG-Fe(II) oxygenase family protein GO:0016491 11276424,7753822,7791906,9211872 2 Bacteria superkingdom 47085 EBI-EMBL 2OG-Fe(II) oxygenase superfamily 2OG-Fe(II) oxygenase family protein This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1]. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalysing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site [3]. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB. [1]. 11276424. The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. Aravind L, Koonin EV;. Genome Biol 2001;2:RESEARCH0007. [2]. 9211872. Cloning of the human prolyl 4-hydroxylase alpha subunit isoform alpha(II) and characterization of the type II enzyme tetramer. The alpha(I) and alpha(II) subunits do not form a mixed alpha(I)alpha(II)beta2 tetramer. Annunen P, Helaakoski T, Myllyharju J, Veijola J, Pihlajaniemi T, Kivirikko KI;. J Biol Chem 1997;272:17342-17348. [3]. 7753822. Cloning, baculovirus expression, and characterization of a second mouse prolyl 4-hydroxylase alpha-subunit isoform: formation of an alpha 2 beta 2 tetramer with the protein disulfide-isomerase/beta subunit. Helaakoski T, Annunen P, Vuori K, MacNeil IA, Pihlajaniemi T, Kivirikko KI;. Proc Natl Acad Sci U S A 1995;92:4427-4431. [4]. 7791906. Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes. Roach PL, Clifton IJ, Fulop V, Harlos K, Barton GJ, Hajdu J, Andersson I, Schofield CJ, Bal. TRUNCATED at 1650 bytes (from Pfam) NF015152.5 PF03173.18 CHB_HEX 25 25 160 domain Y Y N carbohydate-binding domain-containing protein 8673609 2 Bacteria superkingdom 10637 EBI-EMBL Putative carbohydrate binding domain Putative carbohydrate binding domain This domain represents the N terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi [1]. This suggests that this may be a carbohydrate binding domain. [1]. 8673609. Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay-Sachs disease. Tews I, Perrakis A, Oppenheim A, Dauter Z, Wilson KS, Vorgias CE;. Nat Struct Biol 1996;3:638-648. (from Pfam) NF015153.5 PF03174.18 CHB_HEX_C 23.6 23.6 76 domain Y Y N chitobiase/beta-hexosaminidase C-terminal domain-containing protein 8673609 2 Bacteria superkingdom 9715 EBI-EMBL Chitobiase/beta-hexosaminidase C-terminal domain Chitobiase/beta-hexosaminidase C-terminal domain This short domain represents the C terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure [1]. The function of this domain is unknown. [1]. 8673609. Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay-Sachs disease. Tews I, Perrakis A, Oppenheim A, Dauter Z, Wilson KS, Vorgias CE;. Nat Struct Biol 1996;3:638-648. (from Pfam) NF015175.5 PF03198.19 Glyco_hydro_72 25.9 25.9 314 PfamEq Y N N Glucanosyltransferase 10769178,1824714,7823929 2 Bacteria superkingdom 330 EBI-EMBL Glucanosyltransferase Glucanosyltransferase This is a family of glycosylphosphatidylinositol-anchored beta(1-3)glucanosyltransferases. The active site residues in the Aspergillus fumigatus example Swiss:B0XT72 are the two glutamate residues at 160 and 261 [3]. [1]. 1824714. Determinants for glycophospholipid anchoring of the Saccharomyces cerevisiae GAS1 protein to the plasma membrane. Nuoffer C, Jeno P, Conzelmann A, Riezman H;. Mol Cell Biol 1991;11:27-37. [2]. 7823929. PHR1, a pH-regulated gene of Candida albicans, is required for morphogenesis. Saporito-Irwin SM, Birse CE, Sypherd PS, Fonzi WA;. Mol Cell Biol 1995;15:601-613. [3]. 10769178. Identification of the catalytic residues of the first family of beta(1-3)glucanosyltransferases identified in fungi. Mouyna I, Monod M, Fontaine T, Henrissat B, Lechenne B, Latge JP;. Biochem J. 2000;347:741-747. (from Pfam) NF015180.5 PF03203.19 MerC 27.6 27.6 108 subfamily Y Y N MerC family mercury resistance protein GO:0016020 11116334 2 Bacteria superkingdom 8630 EBI-EMBL MerC mercury resistance protein MerC family mercury resistance protein NF015182.5 PF03206.19 NifW 23 23 99 PfamEq Y Y N nitrogenase-stabilizing/protective protein NifW GO:0009399 9514861 2 Bacteria superkingdom 3078 EBI-EMBL Nitrogen fixation protein NifW nitrogenase-stabilizing/protective protein NifW Nitrogenase is a complex metalloenzyme composed of two proteins designated the Fe-protein and the MoFe-protein. Apart from these two proteins, a number of accessory proteins are essential for the maturation and assembly of nitrogenase. Even though experimental evidence suggests that these accessory proteins are required for nitrogenase activity, the exact roles played by many of these proteins in the functions of nitrogenase are unclear [1]. Using yeast two-hybrid screening it has been shown that NifW can interact with itself as well as NifZ [1]. [1]. 9514861. Genetic analysis on the NifW by utilizing the yeast two-hybrid system revealed that the NifW of Azotobacter vinelandii interacts with the NifZ to form higher-order complexes. Lee SH, Pulakat L, Parker KC, Gavini N;. Biochem Biophys Res Commun 1998;244:498-504. (from Pfam) NF015187.5 PF03211.18 Pectate_lyase 25 25 202 domain Y Y N pectate lyase 4.2.2.2 GO:0005576,GO:0030570 9748456 2 Bacteria superkingdom 7572 EBI-EMBL Pectate lyase pectate lyase NF015188.5 PF03212.19 Pertactin 22 22 121 domain Y Y N pertactin-like passenger domain-containing protein 8609998 2 Bacteria superkingdom 48913 EBI-EMBL Pertactin Pertactin NF015194.5 PF03219.19 TLC 21 21 491 subfamily Y Y N Npt1/Npt2 family nucleotide transporter GO:0005471,GO:0006862,GO:0016020 9973346 2 Bacteria superkingdom 2495 EBI-EMBL TLC ATP/ADP transporter Npt1/Npt2 family nucleotide transporter Members of this family include both ATP/ADP antiporters for nucleotide exchange and NTP/proton symporters for net nucleotide import, and can be found in intracellular pathogens such as Chlamydia and Rickettsia, as well as in plants with chloroplasts. NF015197.5 PF03222.18 Trp_Tyr_perm 22 22 393 subfamily Y Y N aromatic amino acid transport family protein GO:0003333 9422600 2 Bacteria superkingdom 46322 EBI-EMBL Tryptophan/tyrosine permease family aromatic amino acid transport family protein NF015205.5 PF03230.18 Antirestrict 25 25 92 domain Y Y N antirestriction protein 8393008 2 Bacteria superkingdom 19558 EBI-EMBL Antirestriction protein antirestriction protein This family includes various protein that are involved in antirestriction. The ArdB protein Swiss:Q47057 efficiently inhibits restriction by members of the three known families of type I systems of E. coli [1]. [1]. 8393008. Plasmid pKM101 encodes two nonhomologous antirestriction proteins (ArdA and ArdB) whose expression is controlled by homologous regulatory sequences. Belogurov AA, Delver EP, Rodzevich OV;. J Bacteriol 1993;175:4843-4850. (from Pfam) NF015218.5 PF03245.18 Phage_lysis 25.4 25.4 126 subfamily Y Y N lysis system i-spanin subunit Rz GO:0019835,GO:0044659 10628848 2 Bacteria superkingdom 23885 EBI-EMBL Bacteriophage Rz lysis protein lysis system i-spanin subunit Rz This protein is involved in host lysis. This family is not considered to be a peptidase according to the MEROPs database. This family Rz and the Rz1 protein (Pfam:PF06085) represent a unique example of two genes located in different reading frames in the same nucleotide sequence, which encode different proteins that are both required in the same physiological pathway [1]. [1]. 10628848. Complementation and characterization of the nested Rz and Rz1 reading frames in the genome of bacteriophage lambda. Zhang N, Young R;. Mol Gen Genet. 1999;262:659-667. (from Pfam) NF015229.5 PF03256.21 ANAPC10 21 21 185 PfamEq Y N N Anaphase-promoting complex, subunit 10 (APC10) 10318877,11448992 2 Bacteria superkingdom 52 EBI-EMBL Anaphase-promoting complex, subunit 10 (APC10) Anaphase-promoting complex, subunit 10 (APC10) NF015237.5 PF03264.19 Cytochrom_NNT 24.1 24.1 174 domain Y Y N NapC/NirT family cytochrome c 11056172,7639719,8022286 2 Bacteria superkingdom 20798 EBI-EMBL NapC/NirT cytochrome c family, N-terminal region NapC/NirT family cytochrome c Within the NapC/NirT family of cytochrome c proteins, some members, such as NapC Swiss:P33932 and NirT Swiss:P24038, bind four haem groups, while others, such as TorC Swiss:P33226, bind five haems. This family aligns the common N-terminal region that contains four haem-binding C-X(2)-CH motifs. [1]. 11056172. Electron transfer and binding of the c-type cytochrome TorC to the trimethylamine N-oxide reductase in Escherichia coli. Gon S, Giudici-Orticoni MT, Mejean V, Iobbi-Nivol C;. J Biol Chem 2001;276:11545-11551. [2]. 7639719. The napEDABC gene cluster encoding the periplasmic nitrate reductase system of Thiosphaera pantotropha. Berks BC, Richardson DJ, Reilly A, Willis AC, Ferguson SJ;. Biochem J 1995;309:983-992. [3]. 8022286. TMAO anaerobic respiration in Escherichia coli: involvement of the tor operon. Mejean V, Iobbi-Nivol C, Lepelletier M, Giordano G, Chippaux M, Pascal MC;. Mol Microbiol 1994;11:1169-1179. (from Pfam) NF015242.5 PF03270.18 DUF269 25 25 121 domain Y Y N DUF269 domain-containing protein 2 Bacteria superkingdom 2960 EBI-EMBL Protein of unknown function, DUF269 Protein of unknown function, DUF269 Members of this family may be involved in nitrogen fixation, since they are found within nitrogen fixation operons. (from Pfam) NF015244.5 PF03272.18 Mucin_bdg 27 27 116 domain Y Y N putative mucin/carbohydrate-binding domain-containing protein 9192677 2 Bacteria superkingdom 8778 EBI-EMBL Putative mucin or carbohydrate-binding module Putative mucin or carbohydrate-binding module This family is the putative binding domain for the substrates of enhancin, and other similar metallopeptidases. This is not the enzymically active, peptidase, part of the proteins - see Pfam:PF13402. [1]. 9192677. An intestinal mucin is the target substrate for a baculovirus enhancin. Wang P, Granados RR;. Proc Natl Acad Sci U S A 1997;94:6977-6982. (from Pfam) NF015251.5 PF03279.18 Lip_A_acyltrans 22.3 22.3 295 domain Y N N Bacterial lipid A biosynthesis acyltransferase GO:0016020,GO:0016740 2 Bacteria superkingdom 96059 EBI-EMBL Bacterial lipid A biosynthesis acyltransferase Bacterial lipid A biosynthesis acyltransferase NF015255.5 PF03284.18 PHZA_PHZB 24 24 162 domain Y Y N PhzA/PhzB family protein GO:0017000 9573209 2 Bacteria superkingdom 3928 EBI-EMBL Phenazine biosynthesis protein A/B PhzA/PhzB family protein NF015285.5 PF03314.19 DUF273 30 30 219 domain Y Y N DUF273 domain-containing protein 2 Bacteria superkingdom 7 EBI-EMBL Protein of unknown function, DUF273 Protein of unknown function, DUF273 NF015288.5 PF03318.18 ETX_MTX2 22 22 228 domain Y Y N ETX/MTX2 family pore-forming toxin 11278669,8621095 2 Bacteria superkingdom 2433 EBI-EMBL Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 ETX/MTX2 family pore-forming toxin This family appears to be distantly related to Pfam:PF01117. [1]. 8621095. A Bacillus sphaericus gene encoding a novel type of mosquitocidal toxin of 31.8 kDa. Thanabalu T, Porter AG;. Gene 1996;170:85-89. [2]. 11278669. Clostridium perfringens epsilon toxin induces a rapid change of cell membrane permeability to ions and forms channels in artificial lipid bilayers. Petit L, Maier E, Gibert M, Popoff MR, Benz R;. J Biol Chem 2001;276:15736-15740. (from Pfam) NF015289.5 PF03319.18 EutN_CcmL 25 25 83 domain Y Y N EutN/CcmL family microcompartment protein GO:0031469 10464203,17588214 2 Bacteria superkingdom 7033 EBI-EMBL Ethanolamine utilisation protein EutN/carboxysome EutN/CcmL family microcompartment protein The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB:2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a hole in the center. this suggests that EutN forms a pore, with an opening of 26 Angstrom in diameter on one face and 14 Angstrom on the other face [2]. EutN is involved in the cobalamin-dependent degradation of ethanolamine [1]. [1]. 10464203. The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. Kofoid E, Rappleye C, Stojiljkovic I, Roth J;. J Bacteriol 1999;181:5317-5329. [2]. 17588214. Functional insights from structural genomics. Forouhar F, Kuzin A, Seetharaman J, Lee I, Zhou W, Abashidze M, Chen Y, Yong W, Janjua H, Fang Y, Wang D, Cunningham K, Xiao R, Acton TB, Pichersky E, Klessig DF, Porter CW, Montelione GT, Tong L;. J Struct Funct Genomics. 2007;8:37-44. (from Pfam) NF015292.5 PF03323.18 GerA 27 27 466 domain Y Y N spore germination protein GO:0009847,GO:0016020 10762253 2 Bacteria superkingdom 50522 EBI-EMBL Bacillus/Clostridium GerA spore germination protein spore germination protein NF015298.5 PF03330.23 DPBB_1 28.8 28.8 83 domain Y Y N RlpA-like double-psi beta-barrel domain-containing protein 10368289,10610264,24806796,3316191,8576052 2 Bacteria superkingdom 56732 EBI-EMBL Lytic transglycolase Lytic transglycolase Rare lipoprotein A (RlpA) contains a conserved region that has the double-psi beta-barrel (DPBB) fold [3,4]. The function of RlpA is not well understood, but it has been shown to act as a prc mutant suppressor in Escherichia coli [1]. The DPBB fold is often an enzymatic domain. The members of this family are quite diverse, and if catalytic this family may contain several different functions. Another example of this domain is found in the N terminus of pollen allergen. Recent studies show that the full-length RlpA protein from Pseudomonas Aeruginosa is an outer membrane protein that is a lytic transglycolase with specificity for peptidoglycan lacking stem peptides. Residue D157 in UniProtKB:Q9X6V6 is critical for lytic activity [5]. [1]. 8576052. Multicopy suppressors of prc mutant Escherichia coli include two HtrA (DegP) protease homologs (HhoAB), DksA, and a truncated R1pA. Bass S, Gu Q, Christen A;. J Bacteriol 1996;178:1154-1161. [2]. 3316191. Genes encoding two lipoproteins in the leuS-dacA region of the Escherichia coli chromosome. Takase I, Ishino F, Wachi M, Kamata H, Doi M, Asoh S, Matsuzawa H, Ohta T, Matsuhashi M;. J Bacteriol 1987;169:5692-5699. [3]. 10610264. N-ethylmaleimide-sensitive fusion protein (NSF) and CDC48 confirmed as members of the double-psi beta-barrel aspartate decarboxylase/formate dehydrogenase family. Mizuguchi K, Dhanaraj V, Blundell TL, Murzin AG;. Structure Fold Des. 1999;7:215-216. [4]. 10368289. A six-stranded double-psi beta barrel is shared by several protein superfamilies. Castillo RM, Mizuguchi K, Dhanaraj V, Albert A, Blundell TL, Murzin AG;. Structure Fold Des 1999;7:227-236. [5]. . TRUNCATED at 1650 bytes (from Pfam) NF015299.5 PF03331.18 LpxC 27 27 268 PfamEq Y Y N UDP-3-O-acyl-N-acetylglucosamine deacetylase 3.5.1.108 GO:0009245,GO:0103117 10753902 2 Bacteria superkingdom 30733 EBI-EMBL UDP-3-O-acyl N-acetylglycosamine deacetylase UDP-3-O-acyl-N-acetylglucosamine deacetylase The enzymes in this family catalyse the second step in the biosynthetic pathway for lipid A. [1]. 10753902. Antibacterial agents that target lipid A biosynthesis in gram-negative bacteria. Inhibition of diverse UDP-3-O-(r-3-hydroxymyristoyl)-n-acetylglucosamine deacetylases by substrate analogs containing zinc binding motifs. Jackman JE, Fierke CA, Tumey LN, Pirrung M, Uchiyama T, Tahir SH, Hindsgaul O, Raetz CR;. J Biol Chem 2000;275:11002-11009. (from Pfam) NF015304.5 PF03336.18 Pox_C4_C10 25 25 322 PfamEq Y N N Poxvirus C4/C10 protein 22791606 2 Bacteria superkingdom 189 EBI-EMBL Poxvirus C4/C10 protein Poxvirus C4/C10 protein This family represents proteins found in Poxvirus, including Protein C10 and Protein C4. Vaccinia virus protein C4 plays a role in the inhibition of host NF-kappa-B activation. It blocks the subunit p65/RELA translocation into the host nucleus [1]. [1]. 22791606. Vaccinia virus protein C4 inhibits NF-kappaB activation and promotes virus virulence. Ember SWJ, Ren H, Ferguson BJ, Smith GL;. J Gen Virol. 2012;93:2098-2108. (from Pfam) NF015316.5 PF03349.21 Toluene_X 29.7 29.7 421 domain Y Y N outer membrane protein transport protein 10671442,7535376,9150211 2 Bacteria superkingdom 52547 EBI-EMBL Outer membrane protein transport protein (OMPP1/FadL/TodX) outer membrane protein transport protein This family includes TodX from Pseudomonas putida F1 Swiss:Q51971 and TbuX from Ralstonia pickettii PKO1 Swiss:Q9RBW8. These are membrane proteins of uncertain function that are involved in toluene catabolism. Related proteins involved in the degradation of similar aromatic hydrocarbons are also in this family, such as CymD Swiss:O33458. This family also includes FadL involved in translocation of long-chain fatty acids across the outer membrane. It is also a receptor for the bacteriophage T2. [1]. 7535376. Identification of a membrane protein and a truncated LysR-type regulator associated with the toluene degradation pathway in Pseudomonas putida F1. Wang Y, Rawlings M, Gibson DT, Labbe D, Bergeron H, Brousseau R, Lau PC;. Mol Gen Genet 1995;246:570-579. [2]. 10671442. Characterization and role of tbuX in utilization of toluene by Ralstonia pickettii PKO1. Kahng HY, Byrne AM, Olsen RH, Kukor JJ;. J Bacteriol 2000;182:1232-1242. [3]. 9150211. p-Cymene catabolic pathway in Pseudomonas putida F1: cloning and characterization of DNA encoding conversion of p-cymene to p-cumate. Eaton RW;. J Bacteriol 1997;179:3171-3180. (from Pfam) NF015336.5 PF03370.18 CBM_21 28.9 28.9 113 domain Y N N Carbohydrate/starch-binding module (family 21) GO:0005515 9045612,9046081,9187237 2 Bacteria superkingdom 561 EBI-EMBL Carbohydrate/starch-binding module (family 21) Carbohydrate/starch-binding module (family 21) This family consists of several eukaryotic proteins that are thought to be involved in the regulation of glycogen metabolism. For instance, the mouse PTG protein Swiss:O08541 has been shown to interact with glycogen synthase, phosphorylase kinase, phosphorylase a: these three enzymes have key roles in the regulation of glycogen metabolism. PTG also binds the catalytic subunit of protein phosphatase 1 (PP1C) and localises it to glycogen. Subsets of similar interactions have been observed with several other members of this family, such as the yeast PIG1, PIG2, GAC1 and GIP2 proteins. While the precise function of these proteins is not known, they may serve a scaffold function, bringing together the key enzymes in glycogen metabolism. This family is a carbohydrate binding domain. [1]. 9045612. PTG, a protein phosphatase 1-binding protein with a role in glycogen metabolism. Printen JA, Brady MJ, Saltiel AR;. Science 1997;275:1475-1478. [2]. 9046081. Yeast PIG genes: PIG1 encodes a putative type 1 phosphatase subunit that interacts with the yeast glycogen synthase Gsy2p. Cheng C, Huang D, Roach PJ;. Yeast 1997;13:1-8. [3]. 9187237. Cloning and characterization of a protein phosphatase type 1-binding subunit from smooth muscle similar to the glycogen-binding subunit of liver. Hirano K, Hirano M, Hartshorne DJ;. Biochim Biophys Acta 1997;1339:177-180. (from Pfam) NF015340.5 PF03374.19 ANT 25.3 25.3 108 domain Y Y N phage antirepressor KilAC domain-containing protein GO:0003677 11897024,7669337 2 Bacteria superkingdom 32120 EBI-EMBL Phage antirepressor protein KilAC domain Phage antirepressor protein KilAC domain This domain was called the KilAC domain by Iyer and colleagues [2]. [1]. 7669337. The tripartite immunity system of phages P1 and P7. Heinrich J, Velleman M, Schuster H;. FEMS Microbiol Rev 1995;17:121-126. [2]. 11897024. Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors. Iyer LM, Koonin EV, Aravind L;. Genome Biol 2002;3:RESEARCH0012. (from Pfam) NF015349.5 PF03384.19 DUF287 21 21 55 domain Y Y N DUF287 domain-containing protein 2 Bacteria superkingdom 2 EBI-EMBL Drosophila protein of unknown function, DUF287 Drosophila protein of unknown function, DUF287 NF015355.5 PF03390.20 2HCT 26.2 26.2 415 domain Y Y N 2-hydroxycarboxylate transporter family protein GO:0008514,GO:0015711,GO:0016020 15853816,16339740 2 Bacteria superkingdom 12201 EBI-EMBL 2-hydroxycarboxylate transporter family 2-hydroxycarboxylate transporter family protein The 2-hydroxycarboxylate transporter family is a family of secondary transporters found exclusively in the bacterial kingdom. They function in the metabolism of the di- and tricarboxylates malate and citrate, mostly in fermentative pathways involving decarboxylation of malate or oxaloacetate [1]. [1]. 16339740. The 2-hydroxycarboxylate transporter family: physiology, structure, and mechanism. Sobczak I, Lolkema JS;. Microbiol Mol Biol Rev. 2005;69:665-695. [2]. 15853816. Secondary transporters of the 2HCT family contain two homologous domains with inverted membrane topology and trans re-entrant loops. Lolkema JS, Sobczak I, Slotboom DJ;. FEBS J. 2005;272:2334-2344. (from Pfam) NF015370.5 PF03405.19 FA_desaturase_2 22.7 22.7 325 subfamily Y Y N acyl-ACP desaturase 1.14.19.2 GO:0006631,GO:0045300 26224800 2 Bacteria superkingdom 18581 EBI-EMBL Fatty acid desaturase acyl-ACP desaturase NF015371.5 PF03406.18 Phage_fiber_2 22 22 42 domain Y Y N tail fiber protein GO:0019062,GO:0046718 7676622 2 Bacteria superkingdom 43961 EBI-EMBL Phage tail fibre repeat Phage tail fibre repeat This repeat is found in the tail fibres of phage. For example protein K Swiss:Q37842 [1]. The repeats are about 40 residues long. [1]. 7676622. DNA sequence of tail fiber genes of coliphage 186 and evidence for a common ancestor shared by dsDNA phage fiber genes. Xue Q, Egan JB;. Virology 1995;212:128-133. (from Pfam) NF015376.5 PF03411.18 Peptidase_M74 25 25 240 PfamEq Y Y N penicillin-insensitive murein endopeptidase GO:0004252,GO:0006508,GO:0030288 2 Bacteria superkingdom 13822 EBI-EMBL Penicillin-insensitive murein endopeptidase penicillin-insensitive murein endopeptidase NF015379.5 PF03414.18 Glyco_transf_6 25 25 313 PfamEq Y N N Glycosyltransferase family 6 GO:0005975,GO:0016020,GO:0016758 2 Bacteria superkingdom 607 EBI-EMBL Glycosyltransferase family 6 Glycosyltransferase family 6 NF015383.5 PF03418.19 Peptidase_A25 27.8 27.8 353 PfamEq Y Y N GPR endopeptidase GO:0006508,GO:0008233,GO:0009847 2 Bacteria superkingdom 6335 EBI-EMBL Germination protease GPR endopeptidase NF015384.5 PF03419.18 Peptidase_U4 28.4 28.4 284 PfamEq Y Y N sigma-E processing peptidase SpoIIGA 3.4.23.- GO:0004190,GO:0006508,GO:0030436 2 Bacteria superkingdom 7390 EBI-EMBL Sporulation factor SpoIIGA sigma-E processing peptidase SpoIIGA NF015388.5 PF03423.18 CBM_25 27.3 27.3 106 domain Y Y N carbohydrate binding domain-containing protein GO:2001070 2 Bacteria superkingdom 5063 EBI-EMBL Carbohydrate binding domain (family 25) Carbohydrate binding domain (family 25) NF015389.5 PF03424.19 CBM_17_28 25 25 176 domain Y Y N carbohydrate-binding domain-containing protein GO:0008810,GO:0030245 11733998,15136030 2 Bacteria superkingdom 156 EBI-EMBL Carbohydrate binding domain (family 17/28) Carbohydrate binding domain (family 17/28) This entry represents two tandem carbohydrate binding domains from CBM17 and CBM28 families. CBM17 binds to amorphous cellulose and soluble beta-1,4-glucans. CBM28 does not compete with CBM17 modules when binding to non-crystalline cellulose and it is closely related to CBM17, according to sequence and structural conservation which suggests that they have evolved through gene duplication and subsequent divergence. [1]. 15136030. X-ray crystal structure of a non-crystalline cellulose-specific carbohydrate-binding module: CBM28. Jamal S, Nurizzo D, Boraston AB, Davies GJ;. J Mol Biol. 2004;339:253-258. [2]. 11733998. Recognition of cello-oligosaccharides by a family 17 carbohydrate-binding module: an X-ray crystallographic, thermodynamic and mutagenic study. Notenboom V, Boraston AB, Chiu P, Freelove AC, Kilburn DG, Rose DR;. J Mol Biol. 2001;314:797-806. (from Pfam) NF015391.5 PF03426.19 CBM_15 22 22 166 domain Y Y N family 15 carbohydrate-binding domain-containing protein 2 Bacteria superkingdom 66 EBI-EMBL Carbohydrate binding domain (family 15) family 15 carbohydrate-binding domain NF015393.5 PF03428.18 RP-C 24.4 24.4 175 domain Y Y N helix-turn-helix domain-containing protein 15808743 2 Bacteria superkingdom 11733 EBI-EMBL Replication protein C N-terminal domain Replication protein C N-terminal domain Replication protein C is involved in the early stages of viral DNA replication. (from Pfam) NF015414.5 PF03449.20 GreA_GreB_N 24.5 24.5 71 domain Y N N Transcription elongation factor, N-terminal GO:0003677,GO:0032784 7854424 2 Bacteria superkingdom 58931 EBI-EMBL Transcription elongation factor, N-terminal Transcription elongation factor, N-terminal This domain adopts a long alpha-hairpin structure. [1]. 7854424. Crystal structure of the GreA transcript cleavage factor from Escherichia coli. Stebbins CE, Borukhov S, Orlova M, Polyakov A, Goldfarb A, Darst SA;. Nature. 1995;373:636-640. (from Pfam) NF015422.5 PF03457.19 HA 28.4 28.4 64 domain Y Y N Helicase associated domain protein 12625841 2 Bacteria superkingdom 21323 EBI-EMBL Helicase associated domain Helicase associated domain This short domain is found in multiple copies in bacterial helicase proteins. The domain is predicted to contain 3 alpha helices. The function of this domain may be to bind nucleic acid. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF015427.5 PF03462.23 PCRF 24 24 194 domain Y Y N PCRF domain-containing protein GO:0006415 19064930 2 Bacteria superkingdom 112886 EBI-EMBL PCRF domain PCRF domain This domain is found in peptide chain release factors. [1]. 19064930. Crystal structure of a translation termination complex formed with release factor RF2. Korostelev A, Asahara H, Lancaster L, Laurberg M, Hirschi A, Zhu J, Trakhanov S, Scott WG, Noller HF;. Proc Natl Acad Sci U S A. 2008;105:19684-19689. (from Pfam) NF015431.5 PF03466.25 LysR_substrate 28 28 209 domain Y Y N LysR substrate-binding domain-containing protein 9309218 2 Bacteria superkingdom 2147006 EBI-EMBL LysR substrate binding domain LysR-like substrate-binding domain The structure of this domain is known and is similar to the periplasmic binding proteins [1]. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 9309218. The structure of the cofactor-binding fragment of the LysR family member, CysB: a familiar fold with a surprising subunit arrangement. Tyrrell R, Verschueren KH, Dodson EJ, Murshudov GN, Addy C, Wilkinson AJ;. Structure 1997;5:1017-1032. (from Pfam) NF015437.5 PF03472.20 Autoind_bind 23 23 149 domain Y Y N autoinducer binding domain-containing protein 2 Bacteria superkingdom 36636 EBI-EMBL Autoinducer binding domain Autoinducer binding domain This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules (N-Acyl homoserine lactones, chlorolactone and rosmarinic acid) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). (from Pfam) NF015443.5 PF03478.23 DUF295 27 27 259 domain Y Y N DUF295 domain-containing protein 2 Bacteria superkingdom 4 EBI-EMBL Domain of unknown function (DUF295) Domain of unknown function (DUF295) This domain is found in plant proteins of unknown function. It can be found in association with F-box domain Pfam:PF00646. This domain adopts a beta propeller structure with 6 blades. (from Pfam) NF015462.5 PF03497.21 Anthrax_toxA 25 25 173 domain Y Y N anthrax toxin-like adenylyl cyclase domain-containing protein GO:0005576,GO:0008294 2 Bacteria superkingdom 2081 EBI-EMBL Anthrax toxin LF subunit anthrax toxin-like adenylyl cyclase domain NF015463.5 PF03498.19 CDtoxinA 22 22 149 domain Y N N Cytolethal distending toxin A/C domain 2 Bacteria superkingdom 7509 EBI-EMBL Cytolethal distending toxin A/C domain Cytolethal distending toxin A/C domain NF015476.5 PF03512.18 Glyco_hydro_52 25 25 413 domain Y Y N glycoside hydrolase family 52 protein GO:0005975,GO:0009044 11322943 2 Bacteria superkingdom 1060 EBI-EMBL Glycosyl hydrolase family 52 glycoside hydrolase family 52 protein NF015477.5 PF03513.19 Cloacin_immun 25 25 80 subfamily Y Y N colicin E3-like toxin immunity protein GO:0015643,GO:0030153 10986462 2 Bacteria superkingdom 1191 EBI-EMBL Cloacin immunity protein colicin E3-like toxin immunity protein NF015478.5 PF03514.19 GRAS 27 27 374 domain Y Y N GRAS family protein 10341448,10817761,19820314,22829623,27095838 2 Bacteria superkingdom 329 EBI-EMBL GRAS domain family GRAS family protein Proteins in the GRAS (GAI, RGA, SCR) family are known as major players in gibberellin (GA) signaling, which regulates various aspects of plant growth and development [1]. Mutation of the SCARECROW (SCR) gene results in a radial pattern defect, loss of a ground tissue layer, in the root. The PAT1 protein is involved in phytochrome A signal transduction [2]. A sequence, structure and evolutionary analysis showed that the GRAS family emerged in bacteria and belongs to the Rossmann-fold, AdoMET (SAM)-dependent methyltransferase superfamily [3]. All bacterial, and a subset of plant GRAS proteins, are predicted to be active and function as small-molecule methylases. Several plant GRAS proteins lack one or more AdoMet (SAM)-binding residues while preserving their substrate-binding residues. Although GRAS proteins are implicated to function as transcriptional factors, the above analysis suggests that they instead might either modify or bind small molecules [3]. [1]. 10341448. The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes. Pysh LD, Wysocka-Diller JW, Camilleri C, Bouchez D, Benfey PN;. Plant J 1999;18:111-119. [2]. 10817761. PAT1, a new member of the GRAS family, is involved in phytochrome A signal transduction. Bolle C, Koncz C, Chua NH;. Genes Dev 2000;14:1269-1278. [3]. 22829623. Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms. Zhang D, Iyer LM, Aravind L;. Bioinformatics. 2012;28:2407-2411. [4]. 27095838. A Structure for Plant-Specific Transcription Factors: The GRAS Domain Revealed. Hofma. TRUNCATED at 1650 bytes (from Pfam) NF015479.5 PF03515.19 Cloacin 25 25 277 domain Y Y N colicin-like bacteriocin tRNase domain-containing protein 11741540,12423786 2 Bacteria superkingdom 3176 EBI-EMBL Colicin-like bacteriocin tRNase domain Colicin-like bacteriocin tRNase domain The C-terminal region of colicin-like bacteriocins is either a pore-forming or an endonuclease-like domain. Cloacin and Pyocins have similar structures and activities to the colicins from E coli and the klebicins from Klebsiella spp. Colicins E5 and D cleave the anticodon loops of distinct tRNAs of Escherichia coli both in vivo and in vitro [1]. The full-length molecule has an N-terminal translocation domain and a middle, double alpha-helical region which is receptor-binding [2]. [1]. 12423786. The modes of action of colicins E5 and D, and related cytotoxic tRNases. Masaki H, Ogawa T;. Biochimie. 2002;84:433-438. [2]. 11741540. Crystal structure of colicin E3: implications for cell entry and ribosome inactivation. Soelaiman S, Jakes K, Wu N, Li C, Shoham M;. Mol Cell. 2001;8:1053-1062. (from Pfam) NF015481.5 PF03517.18 Voldacs 22.1 22.1 138 domain Y Y N Voldacs domain-containing protein 15760659,16734741,17138647,19471107,20573047 2 Bacteria superkingdom 7 EBI-EMBL Regulator of volume decrease after cellular swelling Regulator of volume decrease after cellular swelling ICln is a ubiquitously expressed multi-functional protein that plays a critical role in regulating volume decrease in cells after cellular swelling. In plants, ICln induces Cl- currents [1,4,5], thus regulating Cl- homoeostasis in eukaryotes [2,3]. Structurally, the fold resembles a pleckstrin homology fold, on of whose roles is to recruit and tether their host protein to the cell membrane; and although the surface charges of the ICln fold are not equivalent to those of the PH domain, ICln can be phosphorylated in vitro and the PH-nature of the domain may be the part involving it in the transposition from cytosol to cell membrane during cytotonic swelling [1]. [1]. 16734741. The ICln interactome. Furst J, Botta G, Saino S, Dopinto S, Gandini R, Dossena S, Vezzoli V, Rodighiero S, Bazzini C, Garavaglia ML, Meyer G, Jakab M, Ritter M, Wappl-Kornherr E, Paulmichl M;. Acta Physiol (Oxf). 2006;187:43-49. [2]. 17138647. Hypotonicity induces aquaporin-2 internalization and cytosol-to-membrane translocation of ICln in renal cells. Tamma G, Procino G, Strafino A, Bononi E, Meyer G, Paulmichl M, Formoso V, Svelto M, Valenti G;. Endocrinology. 2007;148:1118-1130. [3]. 19471107. Quaternary structure assessment of ICln by fluorescence resonance energy transfer (FRET) in vivo. Schmidt S, Jakab M, Costa I, Furst J, Ravasio A, Paulmichl M, Botta G, Ritter M;. Cell Physiol Biochem. 2009;23:397-406. [4]. 20573047. Cl- homeostasis in includer and excluder citrus rootstocks: transport mechanisms and identification of candidate genes. Brumos J, Talon M, Bouhlal R, Colmenero-Flores JM;. Plant Cell Environ. 2010;33:2012-2027. [5]. 15760659. Mole. TRUNCATED at 1650 bytes (from Pfam) NF015485.5 PF03522.20 SLC12 27 27 418 domain Y N N Solute carrier family 12 GO:0006811,GO:0016020,GO:0022857 2 Bacteria superkingdom 538 EBI-EMBL Solute carrier family 12 Solute carrier family 12 NF015487.5 PF03524.20 CagX 34.2 34.2 198 domain Y Y N TrbG/VirB9 family P-type conjugative transfer protein 17244707 2 Bacteria superkingdom 29322 EBI-EMBL Conjugal transfer protein TrbG/VirB9 family P-type conjugative transfer protein This family includes type IV secretion system CagX conjugation protein. Other members of this family are involved in conjugal transfer to plant cells of T-DNA. (from Pfam) NF015490.5 PF03527.19 RHS 27.9 27.9 38 domain Y Y N RHS domain-containing protein 2 Bacteria superkingdom 91987 EBI-EMBL RHS protein RHS protein NF015505.5 PF03543.19 Peptidase_C58 23 23 205 domain Y Y N YopT-type cysteine protease domain-containing protein GO:0004197 2 Bacteria superkingdom 3142 EBI-EMBL Yersinia/Haemophilus virulence surface antigen YopT-type cysteine protease domain-containing protein NF015506.5 PF03544.19 TonB_C 24.6 24.6 79 domain Y Y N energy transducer TonB GO:0055085 16741124,21277822 2 Bacteria superkingdom 159496 EBI-EMBL Gram-negative bacterial TonB protein C-terminal energy transducer TonB The TonB_C domain is the well-characterised C-terminal region of the TonB receptor molecule. This protein is bound to an inner membrane-bound protein ExbB via a globular domain and has a flexible middle region that is likely to help in positioning the C-terminal domain into the iron-transporter barrel in the outer membrane [1]. TonB_C interacts with the N-terminal TonB box of the outer membrane transporter that binds the Fe3+-siderophore complex. The barrel of the transporter, consisting of 22 beta-sheets and an inside plug, binds the iron complex in the barrel entrance [2]. [1]. 16741124. Outer membrane active transport: structure of the BtuB:TonB complex. Shultis DD, Purdy MD, Banchs CN, Wiener MC;. Science. 2006;312:1396-1399. [2]. 21277822. Recent insights into iron import by bacteria. Braun V, Hantke K;. Curr Opin Chem Biol. 2011;15:328-334. (from Pfam) NF015522.5 PF03561.20 Allantoicase 27 27 155 domain Y N N Allantoicase repeat GO:0000256,GO:0004037 2 Bacteria superkingdom 17882 EBI-EMBL Allantoicase repeat Allantoicase repeat This family is found in pairs in Allantoicases, forming the majority of the protein. These proteins allow the use of purines as secondary nitrogen sources in nitrogen-limiting conditions through the reaction: allantoate + H(2)0 = (-)-ureidoglycolate + urea. (from Pfam) NF015523.5 PF03562.22 MltA 24.3 24.3 163 PfamEq Y Y N MltA domain-containing protein GO:0004553 16139297 2 Bacteria superkingdom 25261 EBI-EMBL MltA specific insert domain MltA specific insert domain This beta barrel domain is found inserted in the MltA a murein degrading transglycosylase enzyme [1]. This domain may be involved in peptidoglycan binding. [1]. 16139297. Crystal structure of MltA from Escherichia coli reveals a unique lytic transglycosylase fold. van Straaten KE, Dijkstra BW, Vollmer W, Thunnissen AM;. J Mol Biol 2005;352:1068-1080. (from Pfam) NF015525.5 PF03564.20 DUF1759 25.4 25.4 148 PfamAutoEq Y Y N DUF1759 domain-containing protein 2 Bacteria superkingdom 28 EBI-EMBL Protein of unknown function (DUF1759) Protein of unknown function (DUF1759) This is a family of proteins of unknown function. Most of the members are gag-polyproteins. (from Pfam) NF015541.5 PF03583.19 LIP 23 23 286 domain Y Y N lipase family protein GO:0004806,GO:0016042 11131027 2 Bacteria superkingdom 44000 EBI-EMBL Secretory lipase lipase family protein These lipases are expressed and secreted during the infection cycle of these pathogens. In particular, C. albicans has a large number of different lipases, possibly reflecting broad lipolytic activity, which may contribute to the persistence and virulence of C. albicans in human tissue [1]. [1]. 11131027. Secreted lipases of Candida albicans: cloning, characterisation and expression analysis of a new gene family with at least ten members. Hube B, Stehr F, Bossenz M, Mazur A, Kretschmar M, Schafer W;. Arch Microbiol 2000;174:362-374. (from Pfam) NF015546.5 PF03588.19 Leu_Phe_trans 22.7 22.7 171 PfamEq Y N N Leucyl/phenylalanyl-tRNA protein transferase GO:0008914,GO:0030163 2 Bacteria superkingdom 37257 EBI-EMBL Leucyl/phenylalanyl-tRNA protein transferase Leucyl/phenylalanyl-tRNA protein transferase NF015547.5 PF03589.18 Antiterm 26.7 26.7 87 domain Y Y N antitermination protein GO:0003677,GO:0006355 1522593,6458514 2 Bacteria superkingdom 12927 EBI-EMBL Antitermination protein antitermination protein NF015548.5 PF03590.20 AsnA 27 27 228 PfamEq Y N N Aspartate-ammonia ligase GO:0004071,GO:0005737,GO:0006529 2 Bacteria superkingdom 12220 EBI-EMBL Aspartate-ammonia ligase Aspartate-ammonia ligase NF015550.5 PF03592.21 Terminase_2 26.1 26.1 141 domain Y Y N terminase small subunit GO:0051276 2679356 2 Bacteria superkingdom 27218 EBI-EMBL Terminase small subunit terminase small subunit Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [1]. [1]. 2679356. DNA packaging in dsDNA bacteriophages. Black LW;. Annu Rev Microbiol 1989;43:267-292. (from Pfam) NF015562.5 PF03605.19 DcuA_DcuB 27 27 368 domain Y Y N anaerobic C4-dicarboxylate transporter family protein GO:0015556,GO:0015740,GO:0016020 2 Bacteria superkingdom 20442 EBI-EMBL Anaerobic c4-dicarboxylate membrane transporter anaerobic C4-dicarboxylate transporter family protein NF015563.5 PF03606.20 DcuC 23.1 23.1 461 domain Y N N C4-dicarboxylate anaerobic carrier GO:0016020 2 Bacteria superkingdom 74675 EBI-EMBL C4-dicarboxylate anaerobic carrier C4-dicarboxylate anaerobic carrier NF015565.5 PF03608.18 EII-GUT 25 25 167 domain Y Y N PTS glucitol/sorbitol transporter subunit IIC GO:0009401,GO:0016020 1100608 2 Bacteria superkingdom 4359 EBI-EMBL PTS system enzyme II sorbitol-specific factor PTS glucitol/sorbitol transporter subunit IIC NF015566.5 PF03609.19 EII-Sor 26.3 26.3 233 domain Y Y N PTS sugar transporter subunit IIC GO:0009401,GO:0016020 2 Bacteria superkingdom 26120 EBI-EMBL PTS system sorbose-specific iic component PTS sugar transporter subunit IIC NF015568.5 PF03611.19 EIIC-GAT 24.2 24.2 394 domain Y Y N PTS transporter subunit IIC GO:0009401,GO:0016020 11741871 2 Bacteria superkingdom 39301 EBI-EMBL PTS system sugar-specific permease component PTS transporter subunit IIC This family includes bacterial transmembrane proteins with a putative sugar-specific permease function, including and analogous to the IIC component of the PTS system. It has been suggested that this permease may form part of an L-ascorbate utilisation pathway, with proposed specificity for 3-keto-L-gulonate (formed by hydrolysis of L-ascorbate)[1]. This family includes the IIC component of the galactitol specific GAT family PTS system. [1]. 11741871. Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons. Yew WS, Gerlt JA;. J Bacteriol 2002;184:302-306. (from Pfam) NF015569.5 PF03612.19 EIIBC-GUT_N 22.8 22.8 184 domain Y N N Sorbitol phosphotransferase enzyme II N-terminus GO:0008982,GO:0009401,GO:0016020 2 Bacteria superkingdom 7604 EBI-EMBL Sorbitol phosphotransferase enzyme II N-terminus Sorbitol phosphotransferase enzyme II N-terminus NF015570.5 PF03613.19 EIID-AGA 25 25 265 domain Y Y N PTS system mannose/fructose/sorbose family transporter subunit IID GO:0009401,GO:0016020 2 Bacteria superkingdom 26903 EBI-EMBL PTS system mannose/fructose/sorbose family IID component PTS system mannose/fructose/sorbose family transporter subunit IID NF015575.5 PF03618.19 Kinase-PPPase 23.5 23.5 256 domain Y Y N kinase/pyrophosphorylase GO:0005524,GO:0016772 16696949,17996018,20044937 2 Bacteria superkingdom 26828 EBI-EMBL Kinase/pyrophosphorylase kinase/pyrophosphorylase This family of regulatory proteins has ADP-dependent kinase and inorganic phosphate-dependent pyrophosphorylase activity [1-3]. [1]. 16696949. Cloning and expression of maize-leaf pyruvate, Pi dikinase regulatory protein gene. Burnell JN, Chastain CJ;. Biochem Biophys Res Commun. 2006;345:675-680. [2]. 17996018. The pyruvate, orthophosphate dikinase regulatory proteins of Arabidopsis possess a novel, unprecedented Ser/Thr protein kinase primary structure. Chastain CJ, Xu W, Parsley K, Sarath G, Hibberd JM, Chollet R;. Plant J. 2008;53:854-863. [3]. 20044937. Cloning and characterization of Escherichia coli DUF299: a bifunctional ADP-dependent kinase--Pi-dependent pyrophosphorylase from bacteria. Burnell JN;. BMC Biochem. 2010;11:1. (from Pfam) NF015578.5 PF03621.18 MbtH 27 27 53 domain Y Y N MbtH family NRPS accessory protein 12625841,17464054,17464055,17502378,22726990,9831524 2 Bacteria superkingdom 30476 EBI-EMBL MbtH-like protein MbtH family NRPS accessory protein This domain is found in the MbtH protein Swiss:O05821 as well as at the N terminus of the antibiotic synthesis protein NIKP1. MbtH and its homologues were first noted in gene clusters involved in non-ribosomal peptides and other secondary metabolites by Quadri et al [1]. This domain is about 70 amino acids long and contains 3 fully conserved tryptophan residues [2]. The structure of the PA2412 protein shows it adopts a beta-beta-beta-alpha-alpha topology with the short C-terminal helix forming the tip of an overall arrowhead shape [3]. MbtH proteins have been shown to be required for the synthesis of antibiotics, siderophores and glycopeptidolipids [3-6]. [1]. 9831524. Identification of a Mycobacterium tuberculosis gene cluster encoding the biosynthetic enzymes for assembly of the virulence-conferring siderophore mycobactin. Quadri LE, Sello J, Keating TA, Weinreb PH, Walsh CT;. Chem Biol. 1998;5:631-645. [2]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. [3]. 17502378. The 1.8 A crystal structure of PA2412, an MbtH-like protein from the pyoverdine cluster of Pseudomonas aeruginosa. Drake EJ, Cao J, Qu J, Shah MB, Straubinger RM, Gulick AM;. J Biol Chem. 2007;282:20425-20434. [4]. 17464055. Effects of deletions of mbtH-like genes on clorobiocin biosynthesis in Streptomyces coelicolor. Wolpert M, Gust B, Kammerer B, Heide L;. Microbiology. 2007;153:1413-1423. [5]. 17464054. MbtH-like protein-mediated cross-talk between non-ribosomal peptide antibiotic and siderophore biosynthetic pathways in Streptomyces c. TRUNCATED at 1650 bytes (from Pfam) NF015585.5 PF03629.23 SASA 24.8 24.8 226 domain Y Y N sialate O-acetylesterase 16301800,20555325 2 Bacteria superkingdom 48396 EBI-EMBL Carbohydrate esterase, sialic acid-specific acetylesterase sialate O-acetylesterase The catalytic triad of this esterase enzyme comprises residues Ser127, His403 and Asp391 in UniProtKB:P70665 [1,2]. [1]. 16301800. The structure at 1.6 Angstroms resolution of the protein product of the At4g34215 gene from Arabidopsis thaliana. Bitto E, Bingman CA, McCoy JG, Allard ST, Wesenberg GE, Phillips GN Jr;. Acta Crystallogr D Biol Crystallogr. 2005;61:1655-1661. [2]. 20555325. Functionally defective germline variants of sialic acid acetylesterase in autoimmunity. Surolia I, Pirnie SP, Chellappa V, Taylor KN, Cariappa A, Moya J, Liu H, Bell DW, Driscoll DR, Diederichs S, Haider K, Netravali I, Le S, Elia R, Dow E, Lee A, Freudenberg J, De Jager PL, Chretien Y, Varki A, MacDonald ME, Gillis T, Behrens TW, Bloch D, Collier D, Korzenik J, Podolsky DK, Hafler D, Murali M, Sands B, Stone JH, Gregersen PK, Pillai S;. Nature. 2010;466:243-247. (from Pfam) NF015586.5 PF03630.19 Fumble 28.5 28.5 334 PfamEq Y N N Fumble GO:0004594,GO:0005524,GO:0015937 11238410 2 Bacteria superkingdom 3228 EBI-EMBL Fumble Fumble Fumble is required for cell division in Drosophila. Mutants lacking fumble exhibit abnormalities in bipolar spindle organisation, chromosome segregation, and contractile ring formation. Analyses have demonstrated that encodes three protein isoforms, all of which contain a domain with high similarity to the pantothenate kinases of A. nidulans and mouse[1]. A role of fumble in membrane synthesis has been proposed[1]. [1]. 11238410. fumble encodes a pantothenate kinase homolog required for proper mitosis and meiosis in Drosophila melanogaster. Afshar K, Gonczy P, DiNardo S, Wasserman SA;. Genetics 2001;157:1267-1276. (from Pfam) NF015600.5 PF03644.18 Glyco_hydro_85 22.2 22.2 302 domain Y Y N endo-beta-N-acetylglucosaminidase GO:0005737,GO:0033925 19252736 2 Bacteria superkingdom 10531 EBI-EMBL Glycosyl hydrolase family 85 endo-beta-N-acetylglucosaminidase Family of endo-beta-N-acetylglucosaminidases. These enzymes work on a broad spectrum of substrates. (from Pfam) NF015602.5 PF03646.20 FlaG 23.8 23.8 101 PfamEq Y Y N flagellar protein FlaG 2 Bacteria superkingdom 16056 EBI-EMBL FlaG protein flagellar protein FlaG Although important for flagella the exact function of this protein is unknown. (from Pfam) NF015603.5 PF03647.18 Tmemb_14 24.8 24.8 92 domain Y Y N TMEM14 family protein GO:0016020 25646734 2 Bacteria superkingdom 592 EBI-EMBL Transmembrane proteins 14C TMEM14 family protein This family of short membrane proteins are as yet uncharacterised. (from Pfam) NF015607.5 PF03652.20 RuvX 29.2 29.2 134 PfamEq Y Y N Holliday junction resolvase RuvX ruvX 3.1.21.10 GO:0006364 10982859,1661673,26817626 2 Bacteria superkingdom 53414 EBI-EMBL Holliday junction resolvase Holliday junction resolvase RuvX The central intermediate formed during mitotic and meiotic recombination is a four stranded DNA structure, also known as the Holliday junction (HJ), and its efficient resolution is essential for proper segregation of chromosomes. Resolution of HJs is mediated by a diverse group of DNA structure specific endonucleases known as Holliday junction resolvases (HJR) [1]. This entry is specific for RuvX also known as YqgF a family of nucleases which resolves the Holliday junction intermediates in genetic recombination[2-3]. Studies carried out in M. tuberculosis, have shown that YqgF/RuvX is a genuine HJR analogous to RuvC from E. coli. Furthermore, a single cysteine present in M. tuberculosis RuvX was found to be required for disulfide-bond mediated intermolecular dimerization and HJ resolution activity, suggesting that M. tuberculosis RuvX has adapted its YqgF protein to function like a typical RuvC family HJR [1]. [1]. 26817626. Mycobacterium tuberculosis RuvX is a Holliday junction resolvase formed by dimerisation of the monomeric YqgF nuclease domain. Nautiyal A, Rani PS, Sharples GJ, Muniyappa K;. Mol Microbiol. 2016;100:656-674. [2]. 10982859. Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Aravind L, Makarova KS, Koonin EV;. Nucleic Acids Res. 2000;28:3417-3432. [3]. 1661673. Escherichia coli RuvC protein is an endonuclease that resolves the Holliday structure. Iwasaki H, Takahagi M, Shiba T, Nakata A, Shinagawa H;. EMBO J. 1991;10:4381-4389. (from Pfam) NF015608.5 PF03653.18 UPF0093 34.2 34.2 146 domain Y Y N CopD family protein 2 Bacteria superkingdom 26476 EBI-EMBL Uncharacterised protein family (UPF0093) CopD family protein NF015615.5 PF03662.19 Glyco_hydro_79n 23.1 23.1 318 PfamEq Y N N Glycosyl hydrolase family 79, N-terminal domain GO:0016020,GO:0016798 11530216 2 Bacteria superkingdom 838 EBI-EMBL Glycosyl hydrolase family 79, N-terminal domain Glycosyl hydrolase family 79, N-terminal domain Family of endo-beta-N-glucuronidase, or heparanase. Heparan sulfate proteoglycans (HSPGs) play a key role in the self- assembly, insolubility and barrier properties of basement membranes and extracellular matrices. Hence, cleavage of heparan sulfate (HS) affects the integrity and functional state of tissues and thereby fundamental normal and pathological phenomena involving cell migration and response to changes in the extracellular micro-environment. Heparanase degrades HS at specific intra-chain sites. The enzyme is synthesised as a latent approximately 65 kDa protein that is processed at the N-terminus into a highly active approximately 50 kDa form. Experimental evidence suggests that heparanase may facilitate both tumour cell invasion and neovascularization, both critical steps in cancer progression. The enzyme is also involved in cell migration associated with inflammation and autoimmunity [1]. [1]. 11530216. Molecular properties and involvement of heparanase in cancer progression and normal development. Vlodavsky I, Goldshmidt O, Zcharia E, Metzger S, Chajek-Shaul T, Atzmon R, Guatta-Rangini Z, Friedmann Y;. Biochimie 2001;83:831-839. (from Pfam) NF015617.5 PF03664.18 Glyco_hydro_62 22.1 22.1 272 subfamily Y Y N non-reducing end alpha-L-arabinofuranosidase family hydrolase GO:0046373,GO:0046556 2 Bacteria superkingdom 9854 EBI-EMBL Glycosyl hydrolase family 62 non-reducing end alpha-L-arabinofuranosidase family hydrolase Family of alpha -L-arabinofuranosidase (EC 3.2.1.55). This enzyme hydrolysed aryl alpha-L-arabinofuranosides and cleaves arabinosyl side chains from arabinoxylan and arabinan. (from Pfam) NF015620.5 PF03668.20 RapZ-like_N 25.4 25.4 158 PfamEq Y Y N RNase adapter RapZ GO:0005524 23475961,28977623,36968430 2 Bacteria superkingdom 40423 EBI-EMBL RapZ-like N-terminal domain RapZ-like N-terminal domain This entry represents the N-terminal P-loop kinase domain of RNase adapter protein RapZ and related proteins. RapZ plays a central role in RNA-mediated regulation of amino-sugar metabolism [1-3]. It is a RNA-binding protein that recruits the major endoribonuclease RNase E to sRNAs GlmZ [1,2]. [1]. 23475961. Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA. Gopel Y, Papenfort K, Reichenbach B, Vogel J, Gorke B;. Genes Dev. 2013;27:552-564. [2]. 28977623. Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism. Gonzalez GM, Durica-Mitic S, Hardwick SW, Moncrieffe MC, Resch M, Neumann P, Ficner R, Gorke B, Luisi BF;. Nucleic Acids Res. 2017;45:10845-10860. [3]. 36968430. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. Burroughs AM, Aravind L;. NAR Genom Bioinform. 2023;5:lqad029. (from Pfam) NF015624.5 PF03672.18 UPF0154 27.1 27.1 60 PfamEq Y Y N YneF family protein 2 Bacteria superkingdom 3728 EBI-EMBL Uncharacterised protein family (UPF0154) YneF family protein This family contains a set of short bacterial proteins of unknown function. (from Pfam) NF015627.5 PF03677.18 UPF0137 34 34 237 domain Y Y N CT583 family protein 2 Bacteria superkingdom 141 EBI-EMBL Uncharacterised protein family (UPF0137) CT583 family protein This family includes GP6-D a virulence plasmid encoded protein. (from Pfam) NF015634.5 PF03687.18 UPF0164 21.4 21.4 325 domain Y Y N UPF0164 family protein 2 Bacteria superkingdom 498 EBI-EMBL Uncharacterised protein family (UPF0164) UPF0164 family protein This family of uncharacterised proteins are only found in Treponema pallidum. These proteins belong to the membrane beta barrel superfamily. (from Pfam) NF015638.5 PF03691.19 UPF0167 25 25 174 PfamEq Y Y N CbrC family protein 2 Bacteria superkingdom 5613 EBI-EMBL Uncharacterised protein family (UPF0167) CbrC family protein The proteins in this family are about 200 amino acids long and each contain 3 CXXC motifs. (from Pfam) NF015642.5 PF03695.18 UPF0149 25 25 181 domain Y Y N UPF0149 family protein 15317022 2 Bacteria superkingdom 26515 EBI-EMBL Uncharacterised protein family (UPF0149) UPF0149 family protein The protein in this family are about 190 amino acids long. The function of these proteins is unknown. [1]. 15317022. X-ray structure of HI0817 from Haemophilus influenzae: protein of unknown function with a novel fold. Galkin A, Sarikaya E, Lehmann C, Howard A, Herzberg O;. Proteins. 2004;57:874-877. (from Pfam) NF015643.5 PF03698.18 UPF0180 25.4 25.4 77 PfamEq Y Y N YkuS family protein 2 Bacteria superkingdom 2426 EBI-EMBL Uncharacterised protein family (UPF0180) YkuS family protein The members of this family are small uncharacterised proteins. (from Pfam) NF015652.5 PF03707.21 MHYT 21 21 59 domain Y Y N MHYT domain-containing protein 11728710 2 Bacteria superkingdom 50373 EBI-EMBL Bacterial signalling protein N terminal repeat Bacterial signalling protein N terminal repeat Found as an N terminal triplet tandem repeat in bacterial signalling proteins. Family includes CoxC (Swiss:Q9KX27) and CoxH (Swiss:Q9KX23) from P.carboxydovorans. Each repeat contains two transmembrane helices. Domain is also described as the MHYT domain [1]. [1]. 11728710. MHYT, a new integral membrane sensor domain. Galperin MY, Gaidenko TA, Mulkidjanian AY, Nakano M, Price CW;. FEMS Microbiol Lett 2001;205:17-23. (from Pfam) NF015654.5 PF03709.20 OKR_DC_1_N 29.3 29.3 111 domain Y Y N Orn/Lys/Arg decarboxylase N-terminal domain-containing protein GO:0016831 7563080 2 Bacteria superkingdom 37330 EBI-EMBL Orn/Lys/Arg decarboxylase, N-terminal domain Orn/Lys/Arg decarboxylase, N-terminal domain This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure. [1]. 7563080. Crystallographic structure of a PLP-dependent ornithine decarboxylase from Lactobacillus 30a to 3.0 A resolution. Momany C, Ernst S, Ghosh R, Chang NL, Hackert ML;. J Mol Biol 1995;252:643-655. (from Pfam) NF015655.5 PF03710.20 GlnE 24 24 252 PfamEq Y N N Glutamate-ammonia ligase adenylyltransferase GO:0008882 2 Bacteria superkingdom 63544 EBI-EMBL Glutamate-ammonia ligase adenylyltransferase Glutamate-ammonia ligase adenylyltransferase Conserved repeated domain found in GlnE proteins. These proteins adenylate and deadenylate glutamine synthases: ATP + {L-Glutamate:ammonia ligase (ADP-forming)} = Diphosphate + Adenylyl-{L-Glutamate:Ammonia ligase (ADP-forming)}. The family is related to the Pfam:PF01909 domain. (from Pfam) NF015657.5 PF03712.20 Cu2_monoox_C 23 23 157 domain Y N N Copper type II ascorbate-dependent monooxygenase, C-terminal domain 2 Bacteria superkingdom 1485 EBI-EMBL Copper type II ascorbate-dependent monooxygenase, C-terminal domain Copper type II ascorbate-dependent monooxygenase, C-terminal domain The N and C-terminal domains of members of this family adopt the same PNGase F-like fold. (from Pfam) NF015659.5 PF03714.19 PUD 25 25 97 domain Y Y N pullulanase-associated domain-containing protein GO:0005975,GO:0030246 12625841 2 Bacteria superkingdom 25806 EBI-EMBL Bacterial pullanase-associated domain Bacterial pullanase-associated domain Domain is found in pullanase - carbohydrate de-branching - proteins. It is found both to the N or the C terminii of of the alpha-amylase active site region. This domain contains several conserved aromatic residues that are suggestive of a carbohydrate binding function. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF015662.5 PF03717.20 PBP_dimer 24.4 24.4 180 domain Y N N Penicillin-binding Protein dimerisation domain GO:0008658 2 Bacteria superkingdom 189116 EBI-EMBL Penicillin-binding Protein dimerisation domain Penicillin-binding Protein dimerisation domain This domain is found at the N terminus of Class B High Molecular Weight Penicillin-Binding Proteins. Its function has not been precisely defined, but is strongly implicated in PBP polymerisation. The domain forms a largely disordered 'sugar tongs' structure. (from Pfam) NF015663.5 PF03718.18 Glyco_hydro_49 27 27 118 domain Y Y N family 49 glycosyl hydrolase 2 Bacteria superkingdom 349 EBI-EMBL Glycosyl hydrolase family 49 family 49 glycosyl hydrolase Family of dextranase (EC 3.2.1.11) and isopullulanase (EC 3.2.1.57). Dextranase hydrolyses alpha-1,6-glycosidic bonds in dextran polymers. This domain corresponds to the C-terminal pectate lyase like domain. (from Pfam) NF015668.5 PF03723.19 Hemocyanin_C 26.4 26.4 249 PfamEq Y N N Hemocyanin, ig-like domain 2341396,2808410,8518732 2 Bacteria superkingdom 108 EBI-EMBL Hemocyanin, ig-like domain Hemocyanin, ig-like domain This family includes arthropod hemocyanins and insect larval storage proteins. Contains some proteins not known to be hemocyanins, but are clearly similar. [1]. 2341396. Molecular cloning, regulation, and complete sequence of a hemocyanin-related, juvenile hormone-suppressible protein from insect hemolymph. Jones G, Brown N, Manczak M, Hiremath S, Kafatos FC;. J Biol Chem 1990;265:8596-8602. [2]. 2808410. cDNA and gene sequence of Manduca sexta arylphorin, an aromatic amino acid-rich larval serum protein. Homology to arthropod hemocyanins. Willott E, Wang XY, Wells MA;. J Biol Chem 1989;264:19052-19059. [3]. 8518732. Crystal structure of deoxygenated Limulus polyphemus subunit II hemocyanin at 2.18 A resolution: clues for a mechanism for allosteric regulation. Hazes B, Magnus KA, Bonaventura C, Bonaventura J, Dauter Z, Kalk KH, Hol WG;. Protein Sci 1993;2:597-619. (from Pfam) NF015672.5 PF03727.21 Hexokinase_2 24 24 242 domain Y N N Hexokinase GO:0005524,GO:0005975,GO:0016773 5133118,7001032 2 Bacteria superkingdom 1163 EBI-EMBL Hexokinase Hexokinase Hexokinase (EC:2.7.1.1) contains two structurally similar domains represented by this family and Pfam:PF00349. Some members of the family have two copies of each of these domains. [1]. 7001032. Structure of a complex between yeast hexokinase A and glucose. II. Detailed comparisons of conformation and active site configuration with the native hexokinase B monomer and dimer. Bennett WS Jr, Steitz TA;. J Mol Biol 1980;140:211-230. [2]. 5133118. Structure of yeast hexokinase-B. I. Preliminary x-ray studies and subunit structure. Steitz TA;. J Mol Biol 1971;61:695-700. (from Pfam) NF015677.5 PF03732.22 Retrotrans_gag 24.1 24.1 97 domain Y N N Retrotransposon gag protein 11600699 2 Bacteria superkingdom 254 EBI-EMBL Retrotransposon gag protein Retrotransposon gag protein Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved [1]. [1]. 11600699. Pyret, a Ty3/Gypsy retrotransposon in Magnaporthe grisea contains an extra domain between the nucleocapsid and protease domains. Nakayashiki H, Matsuo H, Chuma I, Ikeda K, Betsuyaku S, Kusaba M, Tosa Y, Mayama S;. Nucleic Acids Res 2001;29:4106-4113. (from Pfam) NF015679.5 PF03734.19 YkuD 23.4 23.4 146 domain Y Y N L,D-transpeptidase family protein GO:0016740 16647082 2 Bacteria superkingdom 286256 EBI-EMBL L,D-transpeptidase catalytic domain L,D-transpeptidase catalytic domain This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking [1]. This gives bacteria resistance to beta-lactam antibiotics that inhibit PBPs which usually carry out the cross-linking reaction. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue. Several members of this family contain peptidoglycan binding domains. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure. [1]. 16647082. Crystal structure of a novel beta-lactam-insensitive peptidoglycan transpeptidase. Biarrotte-Sorin S, Hugonnet JE, Delfosse V, Mainardi JL, Gutmann L, Arthur M, Mayer C;. J Mol Biol. 2006;359:533-538. (from Pfam) NF015683.5 PF03738.19 GSP_synth 29.3 29.3 371 domain Y Y N glutathionylspermidine synthase family protein 17124497,7775463 2 Bacteria superkingdom 36326 EBI-EMBL Glutathionylspermidine synthase preATP-grasp glutathionylspermidine synthase family protein This region contains the Glutathionylspermidine synthase enzymatic activity EC:6.3.1.8. This is the C-terminal region in bi-enzymes such as Swiss:P43675. Glutathionylspermidine (GSP) synthetases of Trypanosomatidae and Escherichia coli couple hydrolysis of ATP (to ADP and Pi) with formation of an amide bond between spermidine and the glycine carboxylate of glutathione (gamma-Glu-Cys-Gly). In the pathogenic trypanosomatids, this reaction is the penultimate step in the biosynthesis of the antioxidant metabolite, trypanothione (N1,N8-bis-(glutathionyl)spermidine), and is a target for drug design [1]. This region, the pre-ATP grasp region, probably carries the substrate-binding site [2]. [1]. 7775463. Glutathionylspermidine metabolism in Escherichia coli. Purification, cloning, overproduction, and characterization of a bifunctional glutathionylspermidine synthetase/amidase. Bollinger JM Jr, Kwon DS, Huisman GW, Kolter R, Walsh CT;. J Biol Chem 1995;270:14031-14041. [2]. 17124497. Dual binding sites for translocation catalysis by Escherichia coli glutathionylspermidine synthetase. Pai CH, Chiang BY, Ko TP, Chou CC, Chong CM, Yen FJ, Chen S, Coward JK, Wang AH, Lin CH;. EMBO J. 2006;25:5970-5982. (from Pfam) NF015684.5 PF03739.19 LptF_LptG 27.9 27.9 353 subfamily Y Y N LptF/LptG family permease GO:0016020 18375759 2 Bacteria superkingdom 77342 EBI-EMBL Lipopolysaccharide export system permease LptF/LptG LptF/LptG family permease Members of this family are predicted integral membrane proteins of about 350 amino acids long and containing about 6 trans-membrane regions. Characterised members include LptF and LptG, two homologous tandem-encoded permeases of an export ATP transporter for lipopolysaccharide (LPS) assembly in most Gram-negative bacteria [1]. [1]. 18375759. Identification of two inner-membrane proteins required for the transport of lipopolysaccharide to the outer membrane of Escherichia coli. Ruiz N, Gronenberg LS, Kahne D, Silhavy TJ;. Proc Natl Acad Sci U S A. 2008;105:5537-5542. (from Pfam) NF015685.5 PF03740.18 PdxJ 24.5 24.5 234 PfamEq Y Y N pyridoxine 5'-phosphate synthase 2.6.99.2 GO:0005737,GO:0008615,GO:0033856 10225425 2 Bacteria superkingdom 35831 EBI-EMBL Pyridoxal phosphate biosynthesis protein PdxJ pyridoxine 5'-phosphate synthase Members of this family belong to the PdxJ family that catalyses the condensation of 1-deoxy-d-xylulose-5-phosphate (DXP) and 1-amino-3-oxo-4-(phosphohydroxy)propan-2-one to form pyridoxine 5'-phosphate (PNP). This reaction is involved in de novo synthesis of pyridoxine (vitamin B6) and pyridoxal phosphate [1]. [1]. 10225425. Vitamin B6 biosynthesis: formation of pyridoxine 5'-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein. Laber B, Maurer W, Scharf S, Stepusin K, Schmidt FS;. FEBS Lett 1999;449:45-48. (from Pfam) NF015687.5 PF03742.19 PetN 20.3 20.3 29 PfamEq Y Y N cytochrome b6-f complex subunit PetN GO:0009512,GO:0017004,GO:0045158 10545095 2 Bacteria superkingdom 288 EBI-EMBL PetN cytochrome b6-f complex subunit PetN PetN is a small hydrophobic protein, crucial for cytochrome b6-f complex assembly and/or stability. [1]. 10545095. Targeted inactivation of the smallest plastid genome-encoded open reading frame reveals a novel and essential subunit of the cytochrome b(6)f complex. Hager M, Biehler K, Illerhaus J, Ruf S, Bock R;. EMBO J 1999;18:5834-5842. (from Pfam) NF015688.5 PF03743.19 TrbI 35 35 188 domain Y Y N TrbI/VirB10 family protein 8763954 2 Bacteria superkingdom 42526 EBI-EMBL Bacterial conjugation TrbI-like protein TrbI/VirB10 family protein Although not essential for conjugation, the TrbI protein greatly increase the conjugational efficiency [1]. [1]. 8763954. The conjugal transfer system of Agrobacterium tumefaciens octopine-type Ti plasmids is closely related to the transfer system of an IncP plasmid and distantly related to Ti plasmid vir genes. Alt-Morbe J, Stryker JL, Fuqua C, Li PL, Farrand SK, Winans SC;. J Bacteriol 1996;178:4248-4257. (from Pfam) NF015693.5 PF03748.19 FliL 24.6 24.6 103 domain Y Y N flagellar basal body-associated FliL family protein GO:0006935,GO:0009425,GO:0071973 10439416,30890608,35046042,3519573 2 Bacteria superkingdom 32789 EBI-EMBL Flagellar basal body-associated protein FliL flagellar basal body-associated FliL family protein The FliL protein controls the rotational direction of the flagella during chemotaxis [1]. FliL is a cytoplasmic membrane protein associated with the basal body [2]. This protein is a component of the flagellar motor and it is known to enhance the motor performance under high-load conditions in some bacteria. The periplasmic domain of FliL (Flil_C) share significant structural similarity with stomatin/prohibitin/flotillin/HflK/C domains of scaffolding proteins, suggesting that FliL acts as a scaffold [3]. The Flil_C domain is capable of forming a ring assembly with an inner diameter that is comparable in size to the stator unit [3,4]. [1]. 3519573. Sequence of the flaA (cheC) locus of Escherichia coli and discovery of a new gene. Kuo SC, Koshland DE Jr;. J Bacteriol 1986;166:1007-1012. [2]. 10439416. FliL is a membrane-associated component of the flagellar basal body of Salmonella. Schoenhals GJ, Macnab RM;. Microbiology 1999;145:1769-1775. [3]. 35046042. The flagellar motor protein FliL forms a scaffold of circumferentially positioned rings required for stator activation. Tachiyama S, Chan KL, Liu X, Hathroubi S, Peterson B, Khan MF, Ottemann KM, Liu J, Roujeinikova A;. Proc Natl Acad Sci U S A. 2022;119:e2118401119. [4]. 30890608. Structure of Vibrio FliL, a New Stomatin-like Protein That Assists the Bacterial Flagellar Motor Function. Takekawa N, Isumi M, Terashima H, Zhu S, Nishino Y, Sakuma M, Kojima S, Homma M, Imada K;. mBio. 2019;10:e00292-e00219. (from Pfam) NF015699.5 PF03755.18 YicC-like_N 25 25 156 domain Y Y N YicC/YloC family endoribonuclease GO:0016788 1925027,34210798,34815358 2 Bacteria superkingdom 36865 EBI-EMBL Endoribonuclease YicC-like, N-terminal region YicC/YloC family endoribonuclease, N-terminal domain This domain is found at the N-terminal end of Endoribonuclease YicC from Escherichia coli and similar bacterial sequences. YicC, which is important for cells in the stationary phase, and essential for growth at high temperatures [1], contributes to degradation of the small RNA (sRNA) RhyB via collaboration with the exoribonuclease PNPase [2] and seems to generate a 3'-OH and a 5'-phosphate group [3]. [1]. 1925027. Three genes preceding pyrE on the Escherichia coli chromosome are essential for survival and normal cell morphology in stationary culture and at high temperature. Poulsen P, Jensen KF;. Res Microbiol 1991;142:283-288. [2]. 34210798. A fluorescence-based genetic screen reveals diverse mechanisms silencing small RNA signaling in E. coli. Chen J, To L, de Mets F, Luo X, Majdalani N, Tai CH, Gottesman S;. Proc Natl Acad Sci U S A. 2021;118:e2106964118. [3]. 34815358. Discovery and initial characterization of YloC, a novel endoribonuclease in Bacillus subtilis. Ingle S, Chhabra S, Chen J, Lazarus MB, Luo X, Bechhofer DH;. RNA. 2022;28:227-238. (from Pfam) NF015700.5 PF03756.18 AfsA 24 24 133 domain Y Y N AfsA-related hotdog domain-containing protein 12625841,15307895 2 Bacteria superkingdom 16973 EBI-EMBL A-factor biosynthesis hotdog domain A-factor biosynthesis hotdog domain The AfsA family are key enzymes in A-factor biosynthesis, which is essential for streptomycin production and resistance. This domain is distantly related to the thioester dehydratase FabZ family and therefore has a HotDog domain [2]. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. [2]. 15307895. The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases. Dillon SC, Bateman A;. BMC Bioinformatics 2004;5:109-109. (from Pfam) NF015704.5 PF03762.22 VOMI 25 25 167 PfamEq Y N N Vitelline membrane outer layer protein I (VOMI) 8131734,8848836 2 Bacteria superkingdom 174 EBI-EMBL Vitelline membrane outer layer protein I (VOMI) Vitelline membrane outer layer protein I (VOMI) VOMI binds tightly to ovomucin fibrils of the egg yolk membrane. The structure [1] that consists of three beta-sheets forming Greek key motifs, which are related by an internal pseudo three-fold symmetry. Furthermore, the structure of VOMI has strong similarity to the structure of the delta-endotoxin, as well as a carbohydrate-binding site in the top region of the common fold [2]. [1]. 8131734. Crystal structure of vitelline membrane outer layer protein I (VMO-I): a folding motif with homologous Greek key structures related by an internal three-fold symmetry. Shimizu T, Vassylyev DG, Kido S, Doi Y, Morikawa K;. EMBO J 1994;13:1003-1010. [2]. 8848836. The beta-prism: a new folding motif. Shimizu T, Morikawa K;. Trends Biochem Sci 1996;21:3-6. (from Pfam) NF015712.5 PF03770.21 IPK 22.2 22.2 190 PfamEq Y Y N inositol polyphosphate kinase family protein GO:0016301,GO:0032958 10574768 2 Bacteria superkingdom 408 EBI-EMBL Inositol polyphosphate kinase inositol polyphosphate kinase family protein ArgRIII has has been demonstrated to be an inositol polyphosphate kinase [1]. [1]. 10574768. Synthesis of diphosphoinositol pentakisphosphate by a newly identified family of higher inositol polyphosphate kinases. Saiardi A, Erdjument-Bromage H, Snowman AM, Tempst P, Snyder SH;. Curr Biol 1999;9:1323-1326. (from Pfam) NF015716.5 PF03775.21 MinC_C 33.2 33.2 102 domain Y Y N septum site-determining protein MinC GO:0000902 10611296,10869074 2 Bacteria superkingdom 27124 EBI-EMBL Septum formation inhibitor MinC, C-terminal domain Septum formation inhibitor MinC, C-terminal domain In Escherichia coli Swiss:P06138 assembles into a Z ring at midcell while assembly at polar sites is prevented by the min system. MinC Swiss:P18196 a component of this system, is an inhibitor of FtsZ assembly that is positioned within the cell by interaction with MinDE. MinC is an oligomer, probably a dimer [1]. The C terminal half of MinC is the most conserved and interacts with MinD. The N terminal half is thought interact with FtsZ. [1]. 10869074. Analysis of MinC reveals two independent domains involved in interaction with MinD and FtsZ. Hu Z, Lutkenhaus J;. J Bacteriol 2000;182:3965-3971. [2]. 10611296. The MinC component of the division site selection system in Escherichia coli interacts with FtsZ to prevent polymerization. Hu Z, Mukherjee A, Pichoff S, Lutkenhaus J;. Proc Natl Acad Sci U S A 1999;96:14819-14824. (from Pfam) NF015717.5 PF03776.19 MinE 25 25 68 PfamEq Y Y N cell division topological specificity factor MinE GO:0032955,GO:0051301 2645057 2 Bacteria superkingdom 10666 EBI-EMBL Septum formation topological specificity factor MinE cell division topological specificity factor MinE The E. coli minicell locus was shown to code for three gene products (MinC, MinD, and MinE) whose coordinate action is required for proper placement of the division septum. The minE gene codes for a topological specificity factor that, in wild-type cells, prevents the division inhibitor from acting at internal division sites while permitting it to block septation at polar sites [1]. [1]. 2645057. A division inhibitor and a topological specificity factor coded for by the minicell locus determine proper placement of the division septum in E. coli. de Boer PA, Crossley RE, Rothfield LI;. Cell 1989;56:641-649. (from Pfam) NF015718.5 PF03777.18 ChpA-C 21 21 57 domain Y Y N chaplin family protein 12625841,28783117 2 Bacteria superkingdom 38774 EBI-EMBL ChpA-C chaplin domain Some but not all chaplins (coelicolor hydrophobic aerial proteins) have an additional region, C-terminal to the chaplin domain(s), with an LAXTG motif for recognition, cleave, surface attachment by sortase, a transpeptidase. NF015721.5 PF03780.18 Asp23 28 28 108 domain Y Y N Asp23/Gls24 family envelope stress response protein 25074408,7864904 2 Bacteria superkingdom 42192 EBI-EMBL Asp23 family, cell envelope-related function Asp23/Gls24 family envelope stress response protein The alkaline shock protein Asp23 was identified as an alkaline shock protein that was expressed in a sigmaB-dependent manner in Staphylococcus aureus [1]. Following an alkaline shock Asp23 accumulates in the soluble protein fraction of the S. aureus cell. Asp23 is one of the most abundant proteins in the cytosolic protein fraction of stationary S. aureus cells, with a copy-number of >25000 per cell. A second Asp23-family protein, AmaP, which is encoded within the asp23-operon, is required to localise Asp23 to the cell membrane [2]. The overall function for the family is thus a cell envelope-related one in Gram-positive bacteria. UniProtKB:Q2FW64 [2]. [1]. 7864904. Isolation and the gene cloning of an alkaline shock protein in methicillin resistant Staphylococcus aureus. Kuroda M, Ohta T, Hayashi H;. Biochem Biophys Res Commun 1995;207:978-984. [2]. 25074408. Deletion of membrane-associated Asp23 leads to upregulation of cell wall stress genes in Staphylococcus aureus. Muller M, Reiss S, Schluter R, Mader U, Beyer A, Reiss W, Marles-Wright J, Lewis RJ, Pfortner H, Volker U, Riedel K, Hecker M, Engelmann S, Pane-Farre J;. Mol Microbiol. 2014;93:1259-1268. (from Pfam) NF015724.5 PF03783.19 CsgG 20.8 20.8 210 domain Y Y N CsgG/HfaB family protein GO:0030288 9383186 2 Bacteria superkingdom 17623 EBI-EMBL Curli production assembly/transport component CsgG CsgG/HfaB family protein CsgG is an outer membrane-located lipoprotein that is highly resistant to protease digestion. During curli assembly, an adhesive surface fibre, CsgG is required to maintain the stability of CsgA and CsgB [1]. [1]. 9383186. Availability of the fibre subunit CsgA and the nucleator protein CsgB during assembly of fibronectin-binding curli is limited by the intracellular concentration of the novel lipoprotein CsgG. Loferer H, Hammar M, Normark S;. Mol Microbiol 1997;26:11-23. (from Pfam) NF015738.5 PF03798.21 TRAM_LAG1_CLN8 24.6 24.6 198 domain Y Y N TLC domain-containing protein GO:0016020 12151215 2 Bacteria superkingdom 10 EBI-EMBL TLC domain TLC domain NF015739.5 PF03799.20 FtsQ_DivIB_C 21 21 114 PfamEq Y Y N cell division protein FtsQ/DivIB 10792716,16936019,16936026,17185541,19233928,20870765 2 Bacteria superkingdom 47239 EBI-EMBL Cell division protein FtsQ/DivIB, C-terminal cell division protein FtsQ/DivIB Members of this cell division protein family are known as FtsQ in Gram-negative organisms, DivIB in Gram-positive organisms. NF015742.5 PF03802.19 CitX 25 25 165 domain Y Y N citrate lyase holo-[acyl-carrier protein] synthase GO:0051191 10924139,11042274 2 Bacteria superkingdom 8505 EBI-EMBL Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase citrate lyase holo-[acyl-carrier protein] synthase NF015748.5 PF03808.18 Glyco_tran_WecG 27.4 27.4 168 domain Y Y N WecB/TagA/CpsF family glycosyltransferase 2.4.1.- GO:0009058,GO:0016740 11673418,12618464,16953575,18156271,3275612,8830246,9537354 2 Bacteria superkingdom 41973 EBI-EMBL Glycosyl transferase WecG/TagA/CpsF family WecB/TagA/CpsF family glycosyltransferase The WecG member of this family, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan [1, 2, 3, 4, 5, 6, 7]. [1]. 8830246. Characterization of cpsF and its product CMP-N-acetylneuraminic acid synthetase, a group B streptococcal enzyme that can function in K1 capsular polysaccharide biosynthesis in Escherichia coli. Haft RF, Wessels MR, Mebane MF, Conaty N, Rubens CE;. Mol Microbiol. 1996;19:555-563. [2]. 11673418. Identification of the structural gene for the TDP-Fuc4NAc:lipid II Fuc4NAc transferase involved in synthesis of enterobacterial common antigen in Escherichia coli K-12. Rahman A, Barr K, Rick PD;. J Bacteriol 2001;183:6509-6516. [3]. 12618464. Identification and biosynthesis of cyclic enterobacterial common antigen in Escherichia coli. Erbel PJ, Barr K, Gao N, Gerwig GJ, Rick PD, Gardner KH;. J Bacteriol. 2003;185:1995-2004. [4]. 18156271. Localization and interactions of teichoic acid synthetic enzymes in Bacillus subtilis. Formstone A, Carballido-Lopez R, Noirot P, Errington J, Scheffers DJ;. J Bacteriol. 2008;190:1812-1821. [5]. 16953575. Acceptor substrate selectivity and kinetic mec. TRUNCATED at 1650 bytes (from Pfam) NF015751.5 PF03812.18 KdgT 25 25 305 domain Y Y N 2-keto-3-deoxygluconate permease GO:0008643,GO:0015649,GO:0016020,GO:0046411 2 Bacteria superkingdom 11951 EBI-EMBL 2-keto-3-deoxygluconate permease 2-keto-3-deoxygluconate permease NF015754.5 PF03815.24 LCCL 22.6 22.6 96 domain Y Y N LCCL domain-containing protein 11574466 2 Bacteria superkingdom 605 EBI-EMBL LCCL domain LCCL domain NF015756.5 PF03817.18 MadL 25 25 118 PfamEq Y Y N malonate transporter subunit MadL GO:0016020 2 Bacteria superkingdom 3335 EBI-EMBL Malonate transporter MadL subunit malonate transporter subunit MadL NF015757.5 PF03818.18 MadM 24.8 24.8 249 PfamEq Y N N Malonate/sodium symporter MadM subunit 2 Bacteria superkingdom 3677 EBI-EMBL Malonate/sodium symporter MadM subunit Malonate/sodium symporter MadM subunit NF015759.5 PF03820.22 SFXNs 22 22 319 domain Y Y N sideroflexin GO:0006811,GO:0015075,GO:0016020,GO:0055085 30442778 2 Bacteria superkingdom 2 EBI-EMBL Sideroflexins sideroflexin This family contains sideroflexin 1, 2 and 3 (SFXN1/2/3). SFXN1 is a multipass mitochondrial membrane protein and is part of the sideroflexin family of proteins conserved throughout eukaryotes. In humans, SFXN1 is highly expressed in the blood, liver, and kidney, which are tissues with high one-carbon metabolism activity. SFXN1 functions as a mitochondrial serine transporter in one-carbon metabolism. SFXN1 and SFXN3 (and perhaps SFXN2) are the main mitochondrial serine transporters in human cells and Sfxn1-3 also have this function in D. melanogaster. SFXN1 and SFXN3 likely have other physiologically relevant substrates besides serine, such as alanine or cysteine. Because SFXN1 is expressed in many cancers most highly in leukemias and lymphomas and its expression is likely regulated by the Myc transcription factor, it is suggested that it may have roles in cancer cell growth. Furthermore, Myc-binding sites were found in the promoters of SFXN1, SFXN2, and SFXN3 [1]. [1]. 30442778. SFXN1 is a mitochondrial serine transporter required for one-carbon metabolism. Kory N, Wyant GA, Prakash G, Uit de Bos J, Bottanelli F, Pacold ME, Chan SH, Lewis CA, Wang T, Keys HR, Guo YE, Sabatini DM;. Science. 2018; [Epub ahead of print] (from Pfam) NF015764.5 PF03825.21 Nuc_H_symport 25.9 25.9 400 domain Y N N Nucleoside H+ symporter GO:0005337,GO:0015858,GO:0016020 2 Bacteria superkingdom 45165 EBI-EMBL Nucleoside H+ symporter Nucleoside H+ symporter NF015768.5 PF03829.18 PTSIIA_gutA 25 25 113 domain Y Y N PTS glucitol/sorbitol transporter subunit IIA GO:0005737,GO:0008982,GO:0009401 3062173 2 Bacteria superkingdom 6416 EBI-EMBL PTS system glucitol/sorbitol-specific IIA component PTS glucitol/sorbitol transporter subunit IIA This entry consists of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria. The system in Escherichia coli consists of a IIA protein and a IIBC protein. This family is specific for the IIA component. (from Pfam) NF015769.5 PF03830.20 PTSIIB_sorb 27 27 148 domain Y Y N PTS sugar transporter subunit IIB GO:0005737,GO:0008982,GO:0009401 2 Bacteria superkingdom 27837 EBI-EMBL PTS system sorbose subfamily IIB component PTS sugar transporter subunit IIB NF015770.5 PF03831.19 YjdM 23.2 23.2 69 domain Y Y N PhnA domain-containing protein 2 Bacteria superkingdom 29177 EBI-EMBL PhnA domain PhnA domain NF015776.5 PF03837.19 RecT 24 24 198 domain Y Y N recombinase RecT GO:0003677,GO:0006259 11914131 2 Bacteria superkingdom 30776 EBI-EMBL RecT family recombinase RecT The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to RecT [1]. [1]. 11914131. Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52. Iyer LM, Koonin EV, Aravind L;. BMC Genomics 2002;3:8-8. (from Pfam) NF015779.5 PF03840.19 SecG 29.2 29.2 70 PfamEq Y Y N preprotein translocase subunit SecG GO:0009306,GO:0015450,GO:0016020 2 Bacteria superkingdom 42319 EBI-EMBL Preprotein translocase SecG subunit preprotein translocase subunit SecG NF015799.5 PF03861.19 ANTAR 27.3 27.3 54 domain Y Y N ANTAR domain-containing protein GO:0003723 11796212 2 Bacteria superkingdom 101887 EBI-EMBL ANTAR domain ANTAR domain ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins. The majority of the domain consists of a coiled-coil. [1]. 11796212. ANTAR: an RNA-binding domain in transcription antitermination regulatory proteins. Shu CJ, Zhulin IB;. Trends Biochem Sci 2002;27:3-5. (from Pfam) NF015802.5 PF03864.20 Phage_cap_E 22.9 22.9 330 domain Y Y N major capsid protein 2522554 2 Bacteria superkingdom 26806 EBI-EMBL Phage major capsid protein E major capsid protein Major capsid protein E is involved with the stabilisation of the condensed form of the DNA molecule in phage heads [1]. [1]. 2522554. Structure and inherent properties of the bacteriophage lambda head shell. VI. DNA-packaging-defective mutants in the major capsid protein. Katsura I;. J Mol Biol 1989;205:397-405. (from Pfam) NF015803.5 PF03865.18 ShlB 22.7 22.7 311 domain Y Y N ShlB/FhaC/HecB family hemolysin secretion/activation protein 11309114,14688146,15119822 2 Bacteria superkingdom 65314 EBI-EMBL Haemolysin secretion/activation protein ShlB/FhaC/HecB ShlB/FhaC/HecB family hemolysin secretion/activation protein This family represents a group of sequences that are related to ShlB from Serratia marcescens. ShlB is an outer membrane protein pore involved in the Type Vb or Two-partner secretion system where it is functions to secrete and activate the haemolysin ShlA. The activation of ShlA occurs during secretion when ShlB imposes a conformational change in the inactive haemolysin to form the active protein [1]. [1]. 14688146. Activation of Serratia marcescens hemolysin through a conformational change. Walker G, Hertle R, Braun V;. Infect Immun 2004;72:611-614. [2]. 15119822. Type V protein secretion: simplicity gone awry?. Desvaux M, Parham NJ, Henderson IR;. Curr Issues Mol Biol 2004;6:111-124. [3]. 11309114. Two-partner secretion in Gram-negative bacteria: a thrifty, specific pathway for large virulence proteins. Jacob-Dubuisson F, Locht C, Antoine R;. Mol Microbiol 2001;40:306-313. (from Pfam) NF015807.5 PF03869.19 Arc 20.4 20.4 50 domain Y Y N Arc family DNA-binding protein GO:0003677 8107872 2 Bacteria superkingdom 18860 EBI-EMBL Arc-like DNA binding domain Arc-like DNA binding domain Arc repressor act by he cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [1]. [1]. 8107872. DNA recognition by beta-sheets in the Arc repressor-operator crystal structure. Raumann BE, Rould MA, Pabo CO, Sauer RT;. Nature 1994;367:754-757. (from Pfam) NF015810.5 PF03872.18 RseA_N 24 24 87 domain Y Y N RseA family anti-sigma factor GO:0016989 9159523 2 Bacteria superkingdom 14066 EBI-EMBL Anti sigma-E protein RseA, N-terminal domain Anti sigma-E protein RseA, N-terminal domain Sigma-E is important for the induction of proteins involved in heat shock response. RseA binds sigma-E via its N-terminal domain, sequestering sigma-E and preventing transcription from heat-shock promoters [1]. The C-terminal domain is located in the periplasm, and may interact with other protein that signal periplasmic stress. [1]. 9159523. The sigmaE-mediated response to extracytoplasmic stress in Escherichia coli is transduced by RseA and RseB, two negative regulators of sigmaE. De Las Penas A, Connolly L, Gross CA;. Mol Microbiol 1997;24:373-385. (from Pfam) NF015821.5 PF03884.19 YacG 25.5 25.5 52 PfamAutoEq Y Y N DNA gyrase inhibitor YacG yacG GO:0008270 12211008,18586829 2 Bacteria superkingdom 16595 EBI-EMBL DNA gyrase inhibitor YacG DNA gyrase inhibitor YacG YacG inhibits all the catalytic activities of DNA gyrase by preventing its interaction with DNA. It acts by binding directly to the C-terminal domain of GyrB, which probably disrupts DNA binding by the gyrase [1]. YacG has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins [2]. The conserved four cysteine motif in this protein (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures. [1]. 18586829. YacG from Escherichia coli is a specific endogenous inhibitor of DNA gyrase. Sengupta S, Nagaraja V;. Nucleic Acids Res. 2008;36:4310-4316. [2]. 12211008. NMR structure of the Escherichia coli protein YacG: a novel sequence motif in the zinc-finger family of proteins. Ramelot TA, Cort JR, Yee AA, Semesi A, Edwards AM, Arrowsmith CH, Kennedy MA;. Proteins. 2002;49:289-293. (from Pfam) NF015823.5 PF03886.18 ABC_trans_aux 26 26 161 subfamily Y Y N ABC-type transport auxiliary lipoprotein family protein 17369300 2 Bacteria superkingdom 35707 EBI-EMBL ABC-type transport auxiliary lipoprotein component ABC-type transport auxiliary lipoprotein family protein ABC_trans_aux is a family of bacterial proteins that act as auxiliarires to the ABC-transporter in the gamma-hexachlorocyclohexane uptake permease system in Sphingobium japonicum. Gamma-hexachlorocyclohexane, or Lindane, can be used as the sole source of carbon in S.japonicum in aerobic conditions. Lindane is an insecticide [1]. [1]. 17369300. Identification and characterization of genes encoding a putative ABC-type transporter essential for utilization of gamma-hexachlorocyclohexane in Sphingobium japonicum UT26. Endo R, Ohtsubo Y, Tsuda M, Nagata Y;. J Bacteriol. 2007;189:3712-3720. (from Pfam) NF015824.5 PF03887.19 YfbU 25 25 166 PfamEq Y Y N YfbU family protein 2 Bacteria superkingdom 4520 EBI-EMBL YfbU domain YfbU domain This presumed domain is about 160 residues long. It is found in archaebacteria and eubacteria. In Swiss:Q9EUM2 it is associated with a helix-turn-helix domain. This suggests that this may be a ligand binding domain. (from Pfam) NF015826.5 PF03889.18 ArfA 25.5 25.5 44 PfamEq Y Y N alternative ribosome rescue factor ArfA arfA GO:0072344 27906160,28077875 2 Bacteria superkingdom 4977 EBI-EMBL Alternative ribosome-rescue factor A alternative ribosome rescue factor ArfA During translation of messenger RNAs by ribosomes, translation sometimes pauses or stalls. Ribosomes stalled on mRNAs need to be rescued for reuse in order to maintain proper translation capacity. Rescue systems such as ArfA-RF2 and ArfB (formerly known as YaeJ) are present in many bacterial species. Family members such as ArfA cooperates with the canonical peptide release factor RF2 to hydrolyse the peptidyl-tRNA in the non-stop complex. Structural and biochemical analysis show that ArfA anchors its positively charged C-terminal in the mRNA entry channel of the ribosome. Whereas its N terminus is sandwiched between the decoding centre and the switch loop of RF2, leading to marked conformational changes in both the decoding centre and RF2 thereby triggering RF2 peptidyl-hydrolysing activity [1] [2]. [1]. 27906160. Mechanistic insights into the alternative translation termination by ArfA and RF2. Ma C, Kurita D, Li N, Chen Y, Himeno H, Gao N;. Nature. 2017;541:550-553. [2]. 28077875. Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome. Zeng F, Chen Y, Remis J, Shekhar M, Phillips JC, Tajkhorshid E, Jin H;. Nature. 2017;541:554-557. (from Pfam) NF015828.5 PF03892.19 NapB 25.1 25.1 127 PfamEq Y Y N nitrate reductase cytochrome c-type subunit 1.9.6.1 GO:0009061 11389694 2 Bacteria superkingdom 6703 EBI-EMBL Nitrate reductase cytochrome c-type subunit (NapB) nitrate reductase cytochrome c-type subunit The napB gene encodes a dihaem cytochrome c, the small subunit of a heterodimeric periplasmic nitrate reductase [1]. [1]. 11389694. Overproduction, purification and novel redox properties of the dihaem cytochrome c, NapB, from Haemophilus influenzae. Brige A, Cole JA, Hagen WR, Guisez Y, Van Beeumen JJ;. Biochem J 2001;356:851-858. (from Pfam) NF015830.5 PF03894.20 XFP 22 22 177 domain Y N N D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase GO:0005975,GO:0016832 11292814 2 Bacteria superkingdom 31063 EBI-EMBL D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase Bacterial enzyme splits fructose-6-P and/or xylulose-5-P with the aid of inorganic phosphate into either acetyl-P and erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P EC:4.1.2.9, EC:4.1.2.22 [1]. This family is distantly related to transketolases e.g. Pfam:PF02779. [1]. 11292814. Characterization of the D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase gene (xfp) from Bifidobacterium lactis. Meile L, Rohr LM, Geissmann TA, Herensperger M, Teuber M;. J Bacteriol 2001;183:2929-2936. (from Pfam) NF015831.5 PF03895.20 YadA_anchor 22.7 22.7 60 domain Y Y N YadA-like family protein 11080146,11705900 2 Bacteria superkingdom 62554 EBI-EMBL YadA-like membrane anchor domain YadA-like membrane anchor domain This region represents the C-terminal 120 amino acids of a family of surface-exposed bacterial proteins. YadA, an adhesin from Yersinia, was the first member of this family to be characterised. UspA2 from Moraxella was second. The Eib immunoglobulin-binding proteins from E. coli were third, followed by the DsrA proteins of Haemophilus ducreyi and others. These proteins are homologous at their C-terminal and have predicted signal sequences, but they diverge elsewhere. The C-terminal 9 amino acids, consisting of alternating hydrophobic amino acids ending in F or W, comprise a targeting motif for the outer membrane of the Gram negative cell envelope. This region is important for oligomerisation [1]. [1]. 11705900. Nonimmune binding of human immunoglobulin A (IgA) and IgG Fc by distinct sequence segments of the EibF cell surface protein of Escherichia coli. Sandt CH, Hill CW;. Infect Immun 2001;69:7293-7303. [2]. 11080146. Structure and sequence analysis of Yersinia YadA and Moraxella UspAs reveal a novel class of adhesins. Hoiczyk E, Roggenkamp A, Reichenbecher M, Lupas A, Heesemann J;. EMBO J 2000;19:5989-5999. (from Pfam) NF015834.5 PF03899.20 ATP-synt_I 25.1 25.1 99 PfamEq Y Y N ATP synthase subunit I 12917488,6301339,7961438 2 Bacteria superkingdom 18014 EBI-EMBL ATP synthase I chain ATP synthase subunit I The atp operon of alkaliphilic Bacillus pseudofirmus OF4, as in most prokaryotes, contains the eight structural genes for the F-ATPase (ATP synthase), which are preceded by an atpI gene that encodes a membrane protein with 2 TMSs. A tenth gene, atpZ, has been found in this operon, which is upstream of and overlapping with atpI. AtpI is a Ca2+/Mg2+ transporter [3]. [1]. 6301339. Structure and function of H+-ATPase: what we have learned from Escherichia coli H+-ATPase. Kanazawa H, Futai M;. Ann N Y Acad Sci 1982;402:45-64. [2]. 7961438. Bacillus subtilis F0F1 ATPase: DNA sequence of the atp operon and characterization of atp mutants. Santana M, Ionescu MS, Vertes A, Longin R, Kunst F, Danchin A, Glaser P;. J Bacteriol 1994;176:6802-6811. [3]. 12917488. A tenth atp gene and the conserved atpI gene of a Bacillus atp operon have a role in Mg2+ uptake. Hicks DB, Wang Z, Wei Y, Kent R, Guffanti AA, Banciu H, Bechhofer DH, Krulwich TA;. Proc Natl Acad Sci U S A. 2003;100:10213-10218. (from Pfam) NF015838.5 PF03903.18 Phage_T4_gp36 26 26 131 domain Y Y N tail fiber protein 29204885 2 Bacteria superkingdom 676 EBI-EMBL Phage T4 tail fibre tail fiber protein Irreversible binding of T-even bacteriophages to Escherichia coli is mediated by the short and long tail fibres, important for DNA injection. Long tail fibres consist of a phage-proximal (gp34) and a phage-distal rod, the latter containing two protein trimers (gp36 and gp37). Gp36 is present in the upper part of the distal rod, it forms a complex with gp35 and gp37, binding them through the N-terminal and C-terminal regions, respectively. The upper part of the distal rod has a beta-structure [1]. [1]. 29204885. Bacteriophage T4 long tail fiber domains. Hyman P, van Raaij M;. Biophys Rev. 2018;10:463-471. (from Pfam) NF015839.5 PF03904.18 DUF334 30 30 123 domain Y Y N DUF334 domain-containing protein 2 Bacteria superkingdom 694 EBI-EMBL Domain of unknown function (DUF334) Domain of unknown function (DUF334) Staphylococcus aureus plasmid proteins with no characterised function. (from Pfam) NF015841.5 PF03906.19 Phage_T7_tail 25.2 25.2 157 PfamEq Y Y N phage tail fiber protein 3259634 2 Bacteria superkingdom 2150 EBI-EMBL Phage T7 tail fibre protein phage tail fiber protein This HMM describes the N-terminal domain of tail fiber proteins such as gp17 of phage T7. NF015847.5 PF03912.19 Psb28 25 25 106 subfamily Y Y N photosystem II reaction center protein Psb28 psb28 GO:0009523,GO:0009654,GO:0015979,GO:0016020 11904154 2 Bacteria superkingdom 1077 EBI-EMBL Psb28 protein photosystem II reaction center protein Psb28 Psb28 is a 13 kDa soluble protein that is directly assembled in dimeric PSII supercomplexes. The negatively charged N-terminal region is essential for this process [1]. This protein was formerly known as PsbW, but PsbW is now reserved for Pfam:PF07123. [1]. 11904154. Novel approach reveals localisation and assembly pathway of the PsbS and PsbW proteins into the photosystem II dimer. Thidholm E, Lindstrom V, Tissier C, Robinson C, P Schroder W, Funk C;. FEBS Lett 2002;513:217-222. (from Pfam) NF015852.5 PF03917.22 GSH_synth_ATP 25 25 363 PfamEq Y N N Eukaryotic glutathione synthase, ATP binding domain GO:0004363,GO:0005524,GO:0006750 10369661 2 Bacteria superkingdom 1062 EBI-EMBL Eukaryotic glutathione synthase, ATP binding domain Eukaryotic glutathione synthase, ATP binding domain NF015857.5 PF03922.19 OmpW 24 24 195 subfamily Y Y N OmpW family outer membrane protein GO:0019867 10348872,2336399 2 Bacteria superkingdom 27845 EBI-EMBL OmpW family OmpW family outer membrane protein This family includes outer membrane protein W (OmpW) proteins from a variety of bacterial species. This protein may form the receptor for S4 colicins in E. coli [1]. [1]. 10348872. Characterization of colicin S4 and its receptor, OmpW, a minor protein of the Escherichia coli outer membrane. Pilsl H, Smajs D, Braun V;. J Bacteriol 1999;181:3578-3581. [2]. 2336399. Nucleotide sequence of the gene, ompW, encoding a 22kDa immunogenic outer membrane protein of Vibrio cholerae. Jalajakumari MB, Manning PA;. Nucleic Acids Res 1990;18:2180-2180. (from Pfam) NF015861.5 PF03927.18 NapD 28 28 76 PfamEq Y Y N chaperone NapD 10548535,7639719 2 Bacteria superkingdom 6596 EBI-EMBL NapD protein chaperone NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase. [1]. 7639719. The napEDABC gene cluster encoding the periplasmic nitrate reductase system of Thiosphaera pantotropha. Berks BC, Richardson DJ, Reilly A, Willis AC, Ferguson SJ;. Biochem J 1995;309:983-992. [2]. 10548535. Essential roles for the products of the napABCD genes, but not napFGH, in periplasmic nitrate reduction by Escherichia coli K-12. Potter LC, Cole JA;. Biochem J 1999;344:69-76. (from Pfam) NF015863.5 PF03929.21 PepSY_TM 28.8 28.8 295 domain Y Y N PepSY domain-containing protein 2 Bacteria superkingdom 131235 EBI-EMBL PepSY-associated TM region PepSY-associated TM region The PepSY_TM family is so named because it is an alignment of up to five transmembranes helices found in bacterial species some of which carry a nested PepSY domain, Pfam:PF03413. (from Pfam) NF015866.5 PF03932.19 CutC 23.3 23.3 202 PfamEq Y Y N copper homeostasis protein CutC GO:0005507,GO:0055070 15624211,19878721,25030700,26660891,34616378,7635807 2 Bacteria superkingdom 40370 EBI-EMBL CutC family copper homeostasis protein CutC Copper homeostasis protein CutC was originally thought to be involved in copper tolerance in Escherichia coli, as mutation in the corresponding gene lead to an increased copper sensitivity [1]. However, this phenotype has been later reported to depend on the levels of he mRNA-interfering complementary RNA regulator MicL, which is transcribed from a promoter located within the coding sequence of the cutC gene in enterobacteria [2]. In the plant pathogen Xylella fastidiosa, this protein has been reported as specific for copper efflux [3]. The structure of this protein in the bacteria Shigella flexneri showed a monomer structure that adopts a common TIM beta/alpha barrel with eight beta strands surrounded by eight alpha-helices [4]. The human homologue of this protein, whose structure showed a potential copper-binding site, has an important role in intracellular copper homeostasis [5,6]. [1]. 7635807. Identification of cutC and cutF (nlpE) genes involved in copper tolerance in Escherichia coli. Gupta SD, Lee BT, Camakaris J, Wu HC;. J Bacteriol 1995;177:4207-4215. [2]. 25030700. MicL, a new sigmaE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein. Guo MS, Updegrove TB, Gogol EB, Shabalina SA, Gross CA, Storz G;. Genes Dev. 2014;28:1620-1634. [3]. 34616378. Overexpression of mqsR in Xylella fastidiosa Leads to a Priming Effect of Cells to Copper Stress Tolerance. Carvalho IGB, Merfa MV, Teixeira-Silva NS, Martins PMM, Takita MA, de Souza AA;. Front Microbiol. 2021;12:712564. [4]. 15624211. Crystal structure of the copper homeostasis protein (CutCm) from Shigella flexne. TRUNCATED at 1650 bytes (from Pfam) NF015867.5 PF03934.18 T2SSK 24.2 24.2 63 domain Y Y N type II secretion system protein GspK GO:0009306,GO:0016020 14600218,15223057,19299134 2 Bacteria superkingdom 47899 EBI-EMBL Type II secretion system (T2SS), protein K type II secretion system protein GspK Members of this family are involved in the Type II protein secretion system. The T2SK family includes proteins such as ExeK, PulK, OutX and XcpX. They consist of two tandem SAM-like domains, this entry represents the second one. [1]. 15223057. The general secretory pathway: a general misnomer?. Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR;. Trends Microbiol. 2004;12:306-309. [2]. 14600218. Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella. Peabody CR, Chung YJ, Yen MR, Vidal-Ingigliardi D, Pugsley AP, Saier MH Jr;. Microbiology. 2003;149:3051-3072. [3]. 19299134. Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Desvaux M, Hebraud M, Talon R, Henderson IR;. Trends Microbiol. 2009;17:139-145. (from Pfam) NF015869.5 PF03936.21 Terpene_synth_C 26.3 26.3 241 domain Y N N Terpene synthase family, metal binding domain GO:0000287,GO:0010333,GO:0016829 9268308 2 Bacteria superkingdom 1573 EBI-EMBL Terpene synthase family, metal binding domain Terpene synthase family, metal binding domain It has been suggested that this gene family be designated tps (for terpene synthase) [1]. It has been split into six subgroups on the basis of phylogeny, called tpsa-tpsf. tpsa includes vetispiridiene synthase Swiss:Q39979, 5-epi- aristolochene synthase, Swiss:Q40577 and (+)-delta-cadinene synthase Swiss:P93665. tpsb includes (-)-limonene synthase, Swiss:Q40322. tpsc includes kaurene synthase A, Swiss:O04408. tpsd includes taxadiene synthase, Swiss:Q41594, pinene synthase, Swiss:O24475 and myrcene synthase, Swiss:O24474. tpse includes kaurene synthase B. tpsf includes linalool synthase. [1]. 9268308. Monoterpene synthases from grand fir (Abies grandis). cDNA isolation, characterization, and functional expression of myrcene synthase, (-)-(4S)-limonene synthase, and (-)-(1S,5S)-pinene synthase. Bohlmann J, Steele CL, Croteau R;. J Biol Chem 1997;272:21784-21792. (from Pfam) NF015870.5 PF03937.21 Sdh5 27 27 76 PfamEq Y Y N succinate dehydrogenase assembly factor 2 19628817,22239607,22474332,22985599 2 Bacteria superkingdom 16492 EBI-EMBL Flavinator of succinate dehydrogenase succinate dehydrogenase assembly factor 2 This family includes the highly conserved mitochondrial and bacterial proteins Sdh5/SDHAF2/SdhE. Both yeast and human Sdh5/SDHAF2 interact with the catalytic subunit of the succinate dehydrogenase (SDH) complex, a component of both the electron transport chain and the tricarboxylic acid cycle. Sdh5 is required for SDH-dependent respiration and for Sdh1 flavination (incorporation of the flavin adenine dinucleotide cofactor). Mutational inactivation of Sdh5 confers tumor susceptibility in humans [1]. Bacterial homologues of Sdh5, termed SdhE, are functionally conserved being required for the flavinylation of SdhA and succinate dehydrogenase activity. Like Sdh5, SdhE interacts with SdhA. Furthermore, SdhE was characterised as a FAD co-factor chaperone that directly binds FAD to facilitate the flavinylation of SdhA. Phylogenetic analysis demonstrates that SdhE/Sdh5 proteins evolved only once in an ancestral alpha-proteobacteria prior to the evolution of the mitochondria and now remain in subsequent descendants including eukaryotic mitochondria and the alpha, beta and gamma proteobacteria [2]. This family was previously annotated in Pfam as being a divergent TPR repeat but structural evidence has indicated this is not true. The E. coli protein, YgfY also acts as the antitoxin to the membrane-bound toxin family Cpta, Pfam:PF13166, whose E. coli member YgfX, expressed from the same operon as YgfY [3]. [1]. 19628817. SDH5, a gene required for flavination of succinate dehydrogenase, is mutated in paraganglioma. Hao HX, Khalimonchuk O, Schraders M, Dephoure N, Bayley JP, Kunst H, Devilee P, Cremers CW, Schiffman JD, Bentz BG, Gygi S. TRUNCATED at 1650 bytes (from Pfam) NF015871.5 PF03938.19 OmpH 32.4 32.4 141 domain Y Y N OmpH family outer membrane protein GO:0051082 15304217,2318304 2 Bacteria superkingdom 35619 EBI-EMBL Outer membrane protein (OmpH-like) OmpH family outer membrane protein This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterised as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery [2]. [1]. 2318304. Bacterial 'histone-like protein I' (HLP-I) is an outer membrane constituent?. Hirvas L, Coleman J, Koski P, Vaara M;. FEBS Lett 1990;262:123-126. [2]. 15304217. Crystal structure of Skp, a prefoldin-like chaperone that protects soluble and membrane proteins from aggregation. Walton TA, Sousa MC;. Mol Cell 2004;15:367-374. (from Pfam) NF015875.5 PF03942.20 DTW 33.7 33.7 195 domain Y Y N DTW domain-containing protein 2 Bacteria superkingdom 24808 EBI-EMBL DTW domain DTW domain This presumed domain is found in bacterial and eukaryotic proteins. Its function is unknown. The domain contains multiple conserved motifs including a DTXW motif that this domain has been named after. (from Pfam) NF015878.5 PF03945.19 Endotoxin_N 21.3 21.3 223 subfamily_domain Y Y N insecticidal delta-endotoxin Cry8Ea1 family protein GO:0001907,GO:0090729 1658659,9729609 2 Bacteria superkingdom 2322 EBI-EMBL delta endotoxin, N-terminal domain insecticidal delta-endotoxin N-terminal domain This family contains insecticidal toxins produced by Bacillus species of bacteria. During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins they are activated by proteolytic cleavage. The N terminus is cleaved in all of the proteins and a C terminal extension is cleaved in some members. Once activated the endotoxin binds to the gut epithelium and causes cell lysis leading to death. This activated region of the delta endotoxin is composed of three structural domains. The N-terminal helical domain is involved in membrane insertion and pore formation. The second and third domains are involved in receptor binding. [1]. 1658659. Crystal structure of insecticidal delta-endotoxin from Bacillus thuringiensis at 2.5 angstroms resolution. Li J, Carroll J, Ellar DJ;. Nature 1991;353:815-821. [2]. 9729609. Bacillus thuringiensis and its pesticidal crystal proteins. Schnepf E, Crickmore N, Van Rie J, Lereclus D, Baum J, Feitelson J, Zeigler DR, Dean DH;. Microbiol Mol Biol Rev 1998;62:775-806. (from Pfam) NF015881.5 PF03948.19 Ribosomal_L9_C 23.2 23.2 86 domain Y Y N 50S ribosomal L9 C-terminal domain-containing protein 8306963 2 Bacteria superkingdom 42463 EBI-EMBL Ribosomal protein L9, C-terminal domain Ribosomal protein L9, C-terminal domain NF015886.5 PF03953.22 Tubulin_C 26.6 26.6 126 domain Y N N Tubulin C-terminal domain 9428769,9428770,9628483 2 Bacteria superkingdom 75 EBI-EMBL Tubulin C-terminal domain Tubulin C-terminal domain This family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules. (The FtsZ GTPases have been split into their won family). [1]. 9428769. Structure of the alphabeta tubulin dimer by electron crystallography. Nogales E, Wolf SG, Downing KH;. Nature 1998;391:199-203. [2]. 9628483. Tubulin and FtsZ form a distinct family of GTPases. Nogales E, Downing KH, Amos LA, Lowe J;. Nat Struct Biol 1998;5:451-458. [3]. 9428770. Crystal structure of the bacterial cell-division protein FtsZ [see comments]. Lowe J, Amos LA;. Nature 1998;391:203-206. (from Pfam) NF015891.5 PF03958.22 Secretin_N 28.2 28.2 69 domain Y Y N secretin N-terminal domain-containing protein 29632366 2 Bacteria superkingdom 77188 EBI-EMBL Bacterial type II/III secretion system short domain Bacterial type II/III secretion system short domain This is a short, often repeated, domain found in bacterial type II/III secretory system proteins. All previous NolW-like domains fall into this family. (from Pfam) NF015894.5 PF03961.18 FapA 31 31 272 domain Y Y N FapA family protein 27218601 2 Bacteria superkingdom 12657 EBI-EMBL Flagellar Assembly Protein A beta solenoid domain Flagellar Assembly Protein A beta solenoid domain This entry represents the C-terminal beta solenoid domain of FapA and its homologues. Members of this family include FapA (flagellar assembly protein A) Swiss:Q7MBR0 found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction [1]. This entry shows similarity to Pfam:PF03775 suggesting a similar functional role. [1]. 27218601. Glucose induces delocalization of a flagellar biosynthesis protein from the flagellated pole. Park S, Park YH, Lee CR, Kim YR, Seok YJ;. Mol Microbiol. 2016;101:795-808. (from Pfam) NF015896.5 PF03963.19 FlgD 27 27 75 domain Y Y N flagellar hook capping FlgD N-terminal domain-containing protein 18599076,19652342,8157595 2 Bacteria superkingdom 35585 EBI-EMBL Flagellar hook capping protein - N-terminal region Flagellar hook capping protein - N-terminal region FlgD is known to be absolutely required for hook assembly, yet it has not been detected in the mature flagellum [1]. It appears to act as a hook-capping protein to enable assembly of hook protein subunits [1]. FlgD regulates the assembly of the hook cap structure to prevent leakage of hook monomers into the medium and hook monomer polymerisation and also plays a role in determination of the correct hook length, with the help of the FliK protein [2]. This family represents the N-terminal conserved region of FlgD. A recent crystal structure showed that this region was likely to be flexible and was cleaved off during crystallisation [3]. [1]. 8157595. FlgD is a scaffolding protein needed for flagellar hook assembly in Salmonella typhimurium. Ohnishi K, Ohto Y, Aizawa S, Macnab RM, Iino T;. J Bacteriol 1994;176:2272-2281. [2]. 19652342. Cloning, purification, crystallization and preliminary X-ray studies of flagellar hook scaffolding protein FlgD from Pseudomonas aeruginosa PAO1. Luo M, Niu S, Yin Y, Huang A, Wang D;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65:795-797. [3]. 18599076. Crystal structure of the C-terminal domain of a flagellar hook-capping protein from Xanthomonas campestris. Kuo WT, Chin KH, Lo WT, Wang AH, Chou SH;. J Mol Biol. 2008;381:189-199. (from Pfam) NF015900.5 PF03967.18 PRCH 27 27 134 PfamEq Y N N Photosynthetic reaction centre, H-chain N-terminal region GO:0019684,GO:0030077,GO:0045156 10024457 2 Bacteria superkingdom 1673 EBI-EMBL Photosynthetic reaction centre, H-chain N-terminal region Photosynthetic reaction centre, H-chain N-terminal region The family corresponds the N-terminal cytoplasmic domain. [1]. 10024457. Refined crystal structures of reaction centres from Rhodopseudomonas viridis in complexes with the herbicide atrazine and two chiral atrazine derivatives also lead to a new model of the bound carotenoid. Lancaster CR, Michel H;. J Mol Biol 1999;286:883-898. (from Pfam) NF015901.5 PF03968.19 LptD_N 20.4 20.4 113 domain Y Y N LptA/OstA family protein 18424520 2 Bacteria superkingdom 48779 EBI-EMBL LptA/(LptD N-terminal domain) LPS transport protein LptA/OstA family protein This family of proteins are involved in lipopolysaccharide transport across the gram negative inner and outer membranes. The type examples for this family are E. coli LptA Swiss:P0ADV1 and the N-terminal domain of LptD Swiss:P31554. [1]. 18424520. Functional analysis of the protein machinery required for transport of lipopolysaccharide to the outer membrane of Escherichia coli. Sperandeo P, Lau FK, Carpentieri A, De Castro C, Molinaro A, Deho G, Silhavy TJ, Polissi A;. J Bacteriol. 2008;190:4460-4469. (from Pfam) NF015902.6 PF03969.21 AFG1_ATPase 27 27 361 subfamily Y Y N AFG1/ZapE family ATPase zapE GO:0005524,GO:0016887 1441755,24595368,26759378 2 Bacteria superkingdom 52711 EBI-EMBL AFG1-like ATPase AFG1/ZapE family ATPase This P-loop motif-containing family of proteins includes AFG1, LACE1 and ZapE. ATPase family gene 1 (AFG1) is a 377 amino acid yeast protein with an ATPase motif typical of the family [1]. LACE1, the mammalian homologue of AFG1, is a mitochondrial integral membrane protein that is essential for maintenance of fused mitochondrial reticulum and lamellar cristae morphology. It has also been demonstrated that LACE1 mediates degradation of nuclear-encoded complex IV subunits COX4 (cytochrome c oxidase 4), COX5A and COX6A, and is required for normal activity of complexes III and IV of the respiratory chain [2]. ZapE is a cell division protein found in Gram-negative bacteria. The bacterial cell division process relies on the assembly, positioning, and constriction of FtsZ ring (the so-called Z-ring), a ring-like network that marks the future site of the septum of bacterial cell division. ZapE is a Z-ring associated protein required for cell division under low-oxygen conditions. It is an ATPase that appears at the constricting Z-ring late in cell division. It reduces the stability of FtsZ polymers in the presence of ATP in vitro [3]. [1]. 1441755. AFG1, a new member of the SEC18-NSF, PAS1, CDC48-VCP, TBP family of ATPases. Lee YJ, Wickner RB;. Yeast 1992;8:787-790. [2]. 26759378. The mammalian homologue of yeast Afg1 ATPase (lactation elevated 1) mediates degradation of nuclear-encoded complex IV subunits. Cesnekova J, Rodinova M, Hansikova H, Houstek J, Zeman J, Stiburek L;. Biochem J. 2016;473:797-804. [3]. 24595368. ZapE is a novel cell division protein interacting with FtsZ and modulating the Z-ring dynamics. Marteyn BS, Kar. TRUNCATED at 1650 bytes (from Pfam) NF015907.5 PF03974.18 Ecotin 22.2 22.2 122 domain Y Y N ecotin family protein GO:0004867 11352586,11513582,7757004,8156987,9642073 2 Bacteria superkingdom 6394 EBI-EMBL Ecotin ecotin family protein Ecotin is a broad range serine protease inhibitor, which forms homodimers. The C-terminal region contains the dimerisation motif [2]. Interestingly, the binding sites show a fluidity of protein contacts binding sites show a fluidity of protein contacts derived from ecotin's innate flexibility in fitting itself to proteases while [4,5]. [1]. 11513582. Crystal structure of thrombin-ecotin reveals conformational changes and extended interactions. Wang SX, Esmon CT, Fletterick RJ;. Biochemistry 2001;40:10038-10046. [2]. 11352586. The role of ecotin dimerization in protease inhibition. Eggers CT, Wang SX, Fletterick RJ, Craik CS;. J Mol Biol 2001;308:975-991. [3]. 9642073. Ecotin: a serine protease inhibitor with two distinct and interacting binding sites. Yang SQ, Wang CI, Gillmor SA, Fletterick RJ, Craik CS;. J Mol Biol 1998;279:945-957. [4]. 7757004. Ecotin: lessons on survival in a protease-filled world. McGrath ME, Gillmor SA, Fletterick RJ;. Protein Sci 1995;4:141-148. [5]. 8156987. Macromolecular chelation as an improved mechanism of protease inhibition: structure of the ecotin-trypsin complex. McGrath ME, Erpel T, Bystroff C, Fletterick RJ;. EMBO J 1994;13:1502-1507. (from Pfam) NF015914.5 PF03981.17 Ubiq_cyt_C_chap 21.5 21.5 140 domain Y Y N ubiquinol-cytochrome C chaperone family protein 11522252,2544586 2 Bacteria superkingdom 9311 EBI-EMBL Ubiquinol-cytochrome C chaperone ubiquinol-cytochrome C chaperone family protein NF015915.5 PF03982.18 DAGAT 22 22 297 domain Y N N Diacylglycerol acyltransferase GO:0008374 11751830,11751875,12963726,15671038,24799687,27184406,28420705 2 Bacteria superkingdom 5998 EBI-EMBL Diacylglycerol acyltransferase Diacylglycerol acyltransferase The terminal step of triacylglycerol (TAG) formation is catalysed by the enzyme diacylglycerol acyltransferase (DAGAT), required for synthesis and storage of intracellular triglycerides [1,2,3]. In yeast, it is involved in lipid particle synthesis from the endoplasmic reticulum (ER), promoting localised TAG production at discrete ER subdomains, and in ergosterol biosynthesis [1,4]. This family also includes Acyl-CoA wax alcohol acyltransferase 1 and 2 (AWAT1/2) which catalyse the formation of ester bonds between fatty alcohols and fatty acyl-CoAs to form wax monoesters [5,6]. AWAT2 (also known as MFAT) also possesses acyl-CoA retinol acyltransferase (ARAT) activity that catalyses 11-cis-specific retinyl ester synthesis and shows higher catalytic efficiency toward 11-cis-retinol versus 9-cis-retinol, 13-cis-retinol, and all-trans-retinol substrates [7]. [1]. 11751875. The DGA1 gene determines a second triglyceride synthetic pathway in yeast. Oelkers P, Cromley D, Padamsee M, Billheimer JT, Sturley SL;. J Biol Chem 2002;277:8877-8881. [2]. 11751830. Synthesis of triacylglycerols by the acyl-coenzyme A:diacyl-glycerol acyltransferase Dga1p in lipid particles of the yeast Saccharomyces cerevisiae. Sorger D, Daum G;. J Bacteriol 2002;184:519-524. [3]. 27184406. Biochemical characterization of human acyl coenzyme A: 2-monoacylglycerol acyltransferase-3 (MGAT3). Brandt C, McFie PJ, Stone SJ;. Biochem Biophys Res Commun. 2016;475:264-270. [4]. 12963726. Schizosaccharomyces pombe cells deficient in triacylglycerols synthesis undergo apoptosis upon entry into the stationary phase. Zhang Q, Chieu HK, Low CP, Zhang S, Heng CK, Yang H. TRUNCATED at 1650 bytes (from Pfam) NF015923.5 PF03990.19 DUF348 24 11 41 domain Y Y N ubiquitin-like domain-containing protein 11711434,12625841,19799629,26549874 2 Bacteria superkingdom 21851 EBI-EMBL G5-linked-Ubiquitin-like domain G5-linked-Ubiquitin-like domain This domain normally occurs as tandem repeats; however it is found as a single copy in the S. cerevisiae DNA-binding nuclear protein YCR593 (Swiss:P25357). This protein is involved in sporulation part of the SET3C complex, which is required to repress early/middle sporulation genes during meiosis ([2]). The bacterial proteins are likely to be involved in a cell wall function as they are found in conjunction with the Pfam:PF07501 domain, which is involved in various cell surface processes. This domain is also present in the resuscitation-promoting factors RpfB from Mycobacterium tuberculosis and Rpf2 from Corynebacterium glutamicum. These are factors that stimulate resuscitation of dormant cells [3]. This domain has a beta grasp fold. Structural description of this domain revealed a structural conservation between these domains and ubiquitin, hence it is termed UBL-G5 [4]. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. [2]. 11711434. The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program. Pijnappel WW, Schaft D, Roguev A, Shevchenko A, Tekotte H, Wilm M, Rigaut G, Seraphin B, Aasland R, Stewart AF;. Genes Dev 2001;15:2991-3004. [3]. 19799629. Resuscitation-promoting factors as lytic enzymes for bacterial growth and signaling. Kana BD, Mizrahi V;. FEMS Immunol Med Microbiol. 2010;58:39-50. [4]. 26549874. The structure of Resuscitation promoting factor B from M. tuberculosis reveals unexpected ubiquitin-like doma. TRUNCATED at 1650 bytes (from Pfam) NF015926.5 PF03993.17 DUF349 23.9 23.9 75 PfamAutoEq Y Y N DUF349 domain-containing protein 12625841 2 Bacteria superkingdom 27202 EBI-EMBL Domain of Unknown Function (DUF349) Domain of Unknown Function (DUF349) This domain is found singly or as up to five tandem repeats in a small set of bacterial proteins. There are two or three alpha-helices, and possibly a beta-strand. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam) NF015958.5 PF04025.17 RemA-like 26 26 73 domain Y Y N extracellular matrix/biofilm biosynthesis regulator RemA family protein 23646920,34588455 2 Bacteria superkingdom 6153 EBI-EMBL Extracellular matrix regulatory protein A-like extracellular matrix/biofilm biosynthesis regulator RemA family protein This family of mostly uncharacterised proteins includes the extracellular matrix regulatory protein A (RemA) from Bacillus subtilis. RemA is required for biosynthesis of the extracellular matrix and biofilm formation [1,2]. It binds to DNA at multiple sites upstream of the promoters of the operons eps and tapA-sipW-tasA, which are required for the synthesis of the extracellular matrix components, extracellular polysaccharide and TasA amyloid proteins. SinR negatively regulates eps operon expression by occluding RemA binding [1]. Structure of RemA homologue from Geobacillus thermodenitrificans revealed that it forms an unique octameric ring with the potential to form a 16-meric superstructure and suggests that RemA can wrap DNA around its ring-like structure [2]. [1]. 23646920. RemA is a DNA-binding protein that activates biofilm matrix gene expression in Bacillus subtilis. Winkelman JT, Bree AC, Bate AR, Eichenberger P, Gourse RL, Kearns DB;. Mol Microbiol. 2013;88:984-997. [2]. 34588455. Structural and functional characterization of the bacterial biofilm activator RemA. Hoffmann T, Mrusek D, Bedrunka P, Burchert F, Mais CN, Kearns DB, Altegoer F, Bremer E, Bange G;. Nat Commun. 2021;12:5707. (from Pfam) NF015961.5 PF04028.18 DUF374 26.8 26.8 69 domain Y Y N DUF374 domain-containing protein 2 Bacteria superkingdom 8178 EBI-EMBL Domain of unknown function (DUF374) Domain of unknown function (DUF374) Bacterial domain of unknown function. (from Pfam) NF015980.5 PF04052.18 TolB_N 22.4 22.4 106 domain Y N N TolB amino-terminal domain GO:0015031,GO:0042597 10673426 2 Bacteria superkingdom 25125 EBI-EMBL TolB amino-terminal domain TolB amino-terminal domain TolB is an essential periplasmic component of the tol-dependent translocation system. This function of this amino terminal domain is uncertain. [1]. 10673426. The structure of TolB, an essential component of the tol-dependent translocation system, and its protein-protein interaction with the translocation domain of colicin E9. Carr S, Penfold CN, Bamford V, James R, Hemmings AM. Structure Fold Des 2000;8:57-66. (from Pfam) NF016000.5 PF04074.17 DUF386 26.5 26.5 145 subfamily Y Y N YhcH/YjgK/YiaL family protein 16077096,19060153 2 Bacteria superkingdom 25454 EBI-EMBL YhcH/YjgK/YiaL DUF386 family protein This family consists of bacterial proteins. YjgK (TabA) influences biofilm formation by toxin-antitoxin systems [1]. Another member of this family, YhcH, is a possible sugar isomerase of sialic acid catabolism [2]. [1]. 19060153. Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae. Kim Y, Wang X, Ma Q, Zhang XS, Wood TK;. J Bacteriol. 2009;191:1258-1267. [2]. 16077096. Crystal structure of the bacterial YhcH protein indicates a role in sialic acid catabolism. Teplyakov A, Obmolova G, Toedt J, Galperin MY, Gilliland GL;. J Bacteriol. 2005;187:5520-5527. (from Pfam) NF016009.5 PF04083.21 Abhydro_lipase 27 27 63 PfamEq Y N N Partial alpha/beta-hydrolase lipase region GO:0006629 2 Bacteria superkingdom 36 EBI-EMBL Partial alpha/beta-hydrolase lipase region Partial alpha/beta-hydrolase lipase region This family corresponds to a N-terminal part of an alpha/beta hydrolase domain. (from Pfam) NF016011.5 PF04085.19 MreC 28 28 147 domain Y Y N rod shape-determining protein MreC GO:0008360 16484180 2 Bacteria superkingdom 52582 EBI-EMBL rod shape-determining protein MreC rod shape-determining protein MreC MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. (from Pfam) NF016019.5 PF04093.17 MreD 24 24 158 PfamEq Y Y N rod shape-determining protein MreD mreD GO:0008360,GO:0016020 2 Bacteria superkingdom 26157 EBI-EMBL rod shape-determining protein MreD rod shape-determining protein MreD MreD (murein formation D) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. (from Pfam) NF016024.5 PF04098.20 Rad52_Rad22 20.3 20.3 153 domain Y Y N Rad52/Rad22 family DNA repair protein 11914131 2 Bacteria superkingdom 3660 EBI-EMBL Rad52/22 family double-strand break repair protein Rad52/Rad22 family DNA repair protein The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to Rad52 [1]. These proteins contain two helix-hairpin-helix motifs [1]. [1]. 11914131. Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52. Iyer LM, Koonin EV, Aravind L;. BMC Genomics 2002;3:8-8. (from Pfam) NF016029.5 PF04103.20 CD20 27.9 27.9 156 domain Y Y N CD20-like domain-containing protein GO:0016020 10441321,2531187,9922225 2 Bacteria superkingdom 494 EBI-EMBL CD20-like family CD20-like family This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm [1]. This family also includes LR8 like proteins from humans, mice and rats. The function of the human LR8 protein is unknown although it is known to be strongly expressed in the lung fibroblasts [2]. This family also includes sarcospan is a transmembrane component of dystrophin-associated glycoprotein. Loss of the sarcoglycan complex and sarcospan alone is sufficient to cause muscular dystrophy. The role of the sarcoglycan complex and sarcospan is thought to be to strengthen the dystrophin axis connecting the basement membrane with the cytoskeleton [3]. [1]. 2531187. Gene mapping of the three subunits of the high affinity FcR for IgE to mouse chromosomes 1 and 19. Hupp K, Siwarski D, Mock BA, Kinet JP;. J Immunol 1989;143:3787-3791. [2]. 9922225. Isolation of a gene product expressed by a subpopulation of human lung fibroblasts by differential display. Lurton J, Rose TM, Raghu G, Narayanan AS;. Am J Respir Cell Mol Biol 1999;20:327-331. [3]. 10441321. Loss of the sarcoglycan complex and sarcospan leads to . TRUNCATED at 1650 bytes (from Pfam) NF016040.5 PF04115.17 Ureidogly_lyase 23 23 162 domain Y Y N ureidoglycolate lyase 4.3.2.3 GO:0000256,GO:0050385 19935661,24107613 2 Bacteria superkingdom 15162 EBI-EMBL Ureidoglycolate lyase ureidoglycolate lyase Ureidoglycolate lyase (EC:4.3.2.3) is one of the enzymes that acts upon ureidoglycolate, an intermediate of purine catabolism, releasing urea [2]. The enzyme has in the past been wrongly assigned to EC:3.5.3.19, enzymes which release ammonia from ureidoglycolate [1]. [1]. 24107613. Ureidoglycolate hydrolase, amidohydrolase, lyase: how errors in biological databases are incorporated in scientific papers and vice versa. Percudani R, Carnevali D, Puggioni V;. Database (Oxford). 2013;2013:bat071. [2]. 19935661. Ureide catabolism in Arabidopsis thaliana and Escherichia coli. Werner AK, Romeis T, Witte CP;. Nat Chem Biol. 2010;6:19-21. (from Pfam) NF016045.5 PF04120.17 Iron_permease 25 25 128 domain Y Y N low affinity iron permease family protein GO:0055085 11023834 2 Bacteria superkingdom 11027 EBI-EMBL Low affinity iron permease low affinity iron permease family protein NF016066.5 PF04145.20 Ctr 25.3 25.3 151 domain Y Y N copper transporter family protein GO:0005375,GO:0016020,GO:0035434 11983704 2 Bacteria superkingdom 11 EBI-EMBL Ctr copper transporter family copper transporter family protein The redox active metal copper is an essential cofactor in critical biological processes such as respiration, iron transport, oxidative stress protection, hormone production, and pigmentation. A widely conserved family of high-affinity copper transport proteins (Ctr proteins) mediates copper uptake at the plasma membrane. A series of clustered methionine residues in the hydrophilic extracellular domain, and an MXXXM motif in the second transmembrane domain, are important for copper uptake. These methionine probably coordinate copper during the process of metal transport. [1]. 11983704. Biochemical and genetic analyses of yeast and human high-affinity copper transporters suggest a conserved mechanism for copper uptake. Puig S, Lee J, Lau M, Thiele DJ;. J Biol Chem 2002;0:0-0. (from Pfam) NF016067.5 PF04146.20 YTH 22.1 22.1 135 domain Y Y N YTH domain-containing protein GO:0003723 10564280,12368078,16823445,19191354 2 Bacteria superkingdom 2 EBI-EMBL YT521-B-like domain YT521-B-like domain A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells [3]. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or general silencing. The rat protein Swiss:Q9QY02 YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner [1]. The YTH domain has been identified as part of the PUA superfamily [4]. [1]. 10564280. The interaction and colocalization of Sam68 with the splicing- associated factor YT521-B in nuclear dots is regulated by the Src family kinase p59fyn. Hartmann AM, Nayler O, Schwaiger FW, Obermeier A, Stamm S;. Mol Biol Cell 1999;10:3909-3926. [2]. 12368078. YTH: a new domain in nuclear proteins. Stoilov P, Rafalska I, Stamm S;. Trends Biochem Sci 2002;27:495-497. [3]. 16823445. Selective elimination of messenger RNA prevents an incidence of untimely meiosis. Harigaya Y, Tanaka H, Yamanaka S, Tanaka K, Watanabe Y, Tsutsumi C, Chikashige Y, Hiraoka Y, Yamashita A, Yamamoto M;. Nature. 2006;442:45-50. [4]. 19191354. Structural genomics reveals EVE as a new ASCH/PUA-related domain. Bertonati C, Punta M, Fischer M, Yachdav G, Forouhar F, Zhou W, Kuzin AP, Seetharaman J, Abashidze M, Ramelot TA, Kennedy MA, Cort JR, Belachew A, Hunt JF, Tong L, Montelione GT, Rost B;. Prot. TRUNCATED at 1650 bytes (from Pfam) NF016087.5 PF04170.17 NlpE 22 22 86 domain Y Y N copper resistance protein NlpE N-terminal domain-containing protein 11830644,7635807 2 Bacteria superkingdom 12862 EBI-EMBL NlpE N-terminal domain NlpE N-terminal domain This family represents a bacterial outer membrane lipoprotein that is necessary for signalling by the Cpx pathway [1]. This pathway responds to cell envelope disturbances and increases the expression of periplasmic protein folding and degradation factors. While the molecular function of the NlpE protein is unknown, it may be involved in detecting bacterial adhesion to abiotic surfaces. In Escherichia coli and Salmonella typhi, NlpE is also known to confer copper tolerance in copper-sensitive strains of Escherichia coli, and may be involved in copper efflux and delivery of copper to copper-dependent enzymes [2]. [1]. 11830644. Surface sensing and adhesion of Escherichia coli controlled by the Cpx-signaling pathway. Otto K, Silhavy TJ;. Proc Natl Acad Sci U S A 2002;99:2287-2292. [2]. 7635807. Identification of cutC and cutF (nlpE) genes involved in copper tolerance in Escherichia coli. Gupta SD, Lee BT, Camakaris J, Wu HC;. J Bacteriol 1995;177:4207-4215. (from Pfam) NF016103.5 PF04187.18 Cofac_haem_bdg 27.7 27.7 213 PfamEq Y Y N ChaN family lipoprotein 16950397,23868957 2 Bacteria superkingdom 17779 EBI-EMBL Haem-binding uptake, Tiki superfamily, ChaN ChaN family lipoprotein This is a family of putative bacterial lipoproteins necessary for the uptake of haem-iron. The structure of UniProtKB:Q0PBW2, PDB:2g5g, comprises a large parallel beta-sheet with flanking alpha-helices and a smaller domain consisting of alpha-helices. Two cofacial haem groups (~3.5 Angstom apart with an inter-iron distance of 4.4 Angstrom) bind in a pocket formed by a dimer of two ChaN monomers [1,2]. [1]. 23868957. Tiki, at the head of a new superfamily of enzymes. Sanchez-Pulido L, Ponting CP;. Bioinformatics. 2013;29:2371-2374. [2]. 16950397. Cofacial heme binding is linked to dimerization by a bacterial heme transport protein. Chan AC, Lelj-Garolla B, I Rosell F, Pedersen KA, Mauk AG, Murphy ME;. J Mol Biol. 2006;362:1108-1119. (from Pfam) NF016114.5 PF04198.18 Sugar-bind 27 27 257 domain Y Y N sugar-binding domain-containing protein GO:0030246 2 Bacteria superkingdom 53281 EBI-EMBL Putative sugar-binding domain Putative sugar-binding domain This probable domain is found in bacterial transcriptional regulators such as DeoR and SorC. These proteins have an amino-terminal helix-turn-helix Pfam:PF00325 that binds to DNA. This domain is probably the ligand regulator binding region. SorC is regulated by sorbose and other members of this family are likely to be regulated by other sugar substrates. (from Pfam) NF016116.5 PF04200.17 Lipoprotein_17 22.4 11.3 84 domain Y Y N lipoprotein 17-related variable surface protein 21153711,9596719 2 Bacteria superkingdom 1595 EBI-EMBL Lipoprotein associated domain lipoprotein 17-related variable surface domain This domain is found a variable number of times, mostly in Mycoplasma and Ureaplasma, in surface proteins, most of which are lipoproteins. NF016129.5 PF04213.18 HtaA 24 24 164 domain Y Y N HtaA domain-containing protein 10760164 2 Bacteria superkingdom 15227 EBI-EMBL Htaa Htaa This domain is found in HtaA, a secreted protein implicated in iron acquisition and transport [1]. [1]. 10760164. Corynebacterium diphtheriae genes required for acquisition of iron from haemin and haemoglobin are homologous to ABC haemin transporters. Drazek ES, Hammack CA, Schmitt MP;. Mol Microbiol 2000;36:68-84. (from Pfam) NF016137.5 PF04222.17 DUF416 23.7 23.7 188 PfamAutoEq Y Y N DUF416 family protein 2 Bacteria superkingdom 5325 EBI-EMBL Protein of unknown function (DUF416) DUF416 family protein This is a bacterial protein family of unknown function. Proteins in this family adopt an alpha helical structure. Genome context analysis has suggested a high probability of a functional association with histidine kinases, which implicates proteins in this family to play a role in signalling (information from TOPSAN 2Q9R). (from Pfam) NF016138.5 PF04223.17 CitF 27 27 466 domain Y Y N citrate lyase subunit alpha GO:0005737,GO:0006084,GO:0008814,GO:0009346 7830578,9457870 2 Bacteria superkingdom 13463 EBI-EMBL Citrate lyase, alpha subunit (CitF) citrate lyase subunit alpha In citrate-utilising prokaryotes, citrate lyase EC:4.1.3.6 cleaves intracellular citrate into acetate and oxaloacetate, and is organised as a functional complex consisting of alpha, beta, and gamma subunits. The gamma subunit serves as an acyl carrier protein (ACP), and has a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic group. The citrate lyase is active only if this prosthetic group is acetylated; this acetylation is catalysed by an acetate:SH-citrate lyase ligase. The alpha subunit substitutes citryl for the acetyl group to form citryl-S-ACP. The beta subunit completes the reaction by cleaving the citryl to yield oxaloacetate and (regenerated) acetyl-S-ACP. This family represents the alpha subunit EC:2.8.3.10. [1]. 9457870. Purification of Leuconostoc mesenteroides citrate lyase and cloning and characterization of the citCDEFG gene cluster. Bekal S, Van Beeumen J, Samyn B, Garmyn D, Henini S, Divies C, Prevost H;. J Bacteriol 1998;180:647-654. [2]. 7830578. Klebsiella pneumoniae genes for citrate lyase and citrate lyase ligase: localization, sequencing, and expression. Bott M, Dimroth P;. Mol Microbiol 1994;14:347-356. (from Pfam) NF016139.5 PF04224.17 DUF417 22.1 22.1 175 subfamily Y Y N DUF417 family protein 2 Bacteria superkingdom 10556 EBI-EMBL Protein of unknown function, DUF417 DUF417 family protein This family of uncharacterised proteins appears to be restricted to proteobacteria. (from Pfam) NF016140.5 PF04225.17 OapA 22.3 22.3 85 domain Y Y N LysM-like peptidoglycan-binding domain-containing protein GO:0042834 23565292,29686141,8559074,8830271 2 Bacteria superkingdom 18479 EBI-EMBL Opacity-associated protein A LysM-like domain Opacity-associated protein A LysM-like domain The OapA domain gets its name from the Haemophilus influenzae protein OapA, which is required for the expression of colony opacity, thus opacity- associated protein A [1]. The OapA protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [1]. The OapA domain has been shown to bind to peptidoglycan in the E. coli protein YtfB [3]. A screen to identify factors that affect cell division in E. coli discovered that overproducing a fragment of YtfB, including its OapA domain, caused cells to grow as long filaments [3]. OapA domains are commonly associated with other domains that are involved in breaking peptidoglycan cross-links [4]. The OapA domain is distantly related to Pfam:PF01476. [1]. 8559074. Identification and characterization of a cell envelope protein of Haemophilus influenzae contributing to phase variation in colony opacity and nasopharyngeal colonization. Weiser JN, Chong ST, Greenberg D, Fong W;. Mol Microbiol 1995;17:555-564. [2]. 8830271. Phenotypic switching of Haemophilus influenzae. Moxon ER, Gewurz BE, Richards JC, Inzana T, Jennings MP, Hood DW;. Mol Microbiol 1996;19:1149-1150. [3]. 23565292. Harnessing single cell sorting to identify cell division genes and regulators in bacteria. Burke C, Liu M, Britton W, Triccas JA, Thomas T, Smith AL, Allen S, Salomon R, Harry E;. PLoS One. 2013;8:e60964. [4]. 29686141. YtfB, an OapA Domain-Containing Protein, Is a New Cell Division Protein in Escherichia coli. Jorgenson M. TRUNCATED at 1650 bytes (from Pfam) NF016141.5 PF04226.18 Transgly_assoc 25.3 25.3 49 domain Y Y N GlsB/YeaQ/YmgE family stress response membrane protein GO:0016020 2 Bacteria superkingdom 43761 EBI-EMBL Transglycosylase associated protein GlsB/YeaQ/YmgE family stress response membrane protein Bacterial protein, predicted to be an integral membrane protein. Some family members have been annotated as transglycosylase associated proteins, but no experimental evidence is provided. This family was annotated based on the information in Swiss:P76011. (from Pfam) NF016142.5 PF04227.17 Indigoidine_A 25.2 25.2 291 PfamEq Y Y N pseudouridine-5'-phosphate glycosidase GO:0004730 11790734 2 Bacteria superkingdom 21439 EBI-EMBL Indigoidine synthase A like protein pseudouridine-5'-phosphate glycosidase Indigoidine is a blue pigment synthesised by Erwinia chrysanthemi implicated in pathogenicity and protection from oxidative stress. IdgA is involved in indigoidine biosynthesis, but its specific function is unknown [1]. The recommended name for this protein is now pseudouridine-5'-phosphate glycosidase. [1]. 11790734. Characterization of indigoidine biosynthetic genes in Erwinia chrysanthemi and role of this blue pigment in pathogenicity. Reverchon S, Rouanet C, Expert D, Nasser W;. J Bacteriol 2002;184:654-665. (from Pfam) NF016146.5 PF04231.18 Endonuclease_1 25 25 235 domain Y Y N endonuclease GO:0004518 1396690,3036665,7867949 2 Bacteria superkingdom 33291 EBI-EMBL Endonuclease I endonuclease Bacterial periplasmic or secreted endonuclease I (EC:3.1.21.1) E. coli endonuclease I (EndoI) is a sequence independent endonuclease located in the periplasm. It is inhibited by different RNA species. It is thought to normally generate double strand breaks in DNA, except in the presence of high salt concentrations and RNA, when it generates single strand breaks in DNA. Its biological role is unknown [1]. Other family members are known to be extracellular [2]. This family also includes a non-specific, Mg2+ activated ribonuclease precursor (Swiss:Q03091) [3]. [1]. 7867949. The periplasmic endonuclease I of Escherichia coli has amino-acid sequence homology to the extracellular DNases of Vibrio cholerae and Aeromonas hydrophila. Jekel M, Wackernagel W;. Gene 1995;154:55-59. [2]. 3036665. Extracellular proteins of Vibrio cholerae: molecular cloning, nucleotide sequence and characterization of the deoxyribonuclease (DNase) together with its periplasmic localization in Escherichia coli K-12. Focareta T, Manning PA;. Gene 1987;53:31-40. [3]. 1396690. Gene cloning and characterization of a novel extracellular ribonuclease of Bacillus subtilis. Nakamura A, Koide Y, Miyazaki H, Kitamura A, Masaki H, Beppu T, Uozumi T;. Eur J Biochem 1992;209:121-127. (from Pfam) NF016147.5 PF04232.17 SpoVS 24 24 83 domain Y Y N stage V sporulation protein S 7559352 2 Bacteria superkingdom 2581 EBI-EMBL Stage V sporulation protein S (SpoVS) stage V sporulation protein S In Bacillus subtilis this protein interferes with sporulation at an early stage and this inhibitory effect is overcome by SpoIIB and SpoVG. SpoVS seems to play a positive role in allowing progression beyond stage V of sporulation. Null mutations in the spoVS gene block sporulation at stage V, impairing the development of heat resistance and coat assembly [1]. [1]. 7559352. Identification and characterization of sporulation gene spoVS from Bacillus subtilis. Resnekov O, Driks A, Losick R;. J Bacteriol 1995;177:5628-5635. (from Pfam) NF016156.5 PF04241.20 DUF423 25 25 86 PfamAutoEq Y Y N DUF423 domain-containing protein 2 Bacteria superkingdom 26162 EBI-EMBL Protein of unknown function (DUF423) Protein of unknown function (DUF423) This family of proteins with unknown function is a possible integral membrane protein from Caenorhabditis elegans. This family of proteins has GO references indicating the protein is involved in nematode larval development and is a positive regulator of growth rate. (from Pfam) NF016159.5 PF04245.18 NA37 24.6 24.6 325 domain Y Y N nucleoid-associated protein GO:0009295 10368163 2 Bacteria superkingdom 26229 EBI-EMBL 37-kD nucleoid-associated bacterial protein nucleoid-associated protein NF016160.5 PF04246.17 RseC_MucC 24.4 24.4 130 PfamEq Y Y N SoxR reducing system RseC family protein 8264535,9159522,9335303 2 Bacteria superkingdom 12291 EBI-EMBL Positive regulator of sigma(E), RseC/MucC SoxR reducing system RseC family protein This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) [1]. In Pseudomonas aeruginosa, de-repression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonisation in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium [2]. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains an ApbE domain Pfam:PF02424, which is itself involved in thiamine biosynthesis. [1]. 9159522. Modulation of the Escherichia coli sigmaE (RpoE) heat-shock transcription-factor activity by the RseA, RseB and RseC proteins. Missiakas D, Mayer MP, Lemaire M, Georgopoulos C, Raina S;. Mol Microbiol 1997;24:355-371. [2]. 9335303. Evidence that rseC, a gene in the rpoE cluster, has a role in thiamine synthesis in Salmonella typhimurium. Beck BJ, Connolly LE, De Las Penas A, Downs DM;. J Bacteriol 1997;179:6504-6508. [3]. 8264535. Identification of a new class of nitrogen fixation genes in Rhodobacter capsulatus: a putative membrane complex involved in electron transport to nitrogenase. Schmehl M, Jahn A, Meyer zu Vilsendorf A, He. TRUNCATED at 1650 bytes (from Pfam) NF016165.5 PF04253.20 TFR_dimer 27.1 27.1 121 domain Y Y N transferrin receptor-like dimerization domain-containing protein 2 Bacteria superkingdom 1554 EBI-EMBL Transferrin receptor-like dimerisation domain Transferrin receptor-like dimerisation domain This domain is involved in dimerisation of the transferrin receptor as shown in its crystal structure. (from Pfam) NF016169.5 PF04257.19 Exonuc_V_gamma 25 25 314 PfamEq Y Y N exodeoxyribonuclease V subunit gamma 3.1.11.5 31907455,7746848 2 Bacteria superkingdom 39562 EBI-EMBL Exodeoxyribonuclease V, gamma subunit exodeoxyribonuclease V subunit gamma The Exodeoxyribonuclease V enzyme is a multi-subunit enzyme comprised of the proteins RecB, RecC (this family) and RecD. This enzyme plays an important role in homologous genetic recombination, repair of double strand DNA breaks resistance to UV irradiation and chemical DNA-damage. The enzyme (EC:3.1.11.5) catalyses ssDNA or dsDNA-dependent ATP hydrolysis, hydrolysis of ssDNA or dsDNA and unwinding of dsDNA [1]. This subunit recognises and binds DNA forks containing Chi sequences in a sequence specific manner while Chi interactions with the phosphodiester backbone (mainly arginine side chains) stabilise the twisted conformation of the DNA. These interactions induce conformational changes that switch RecBCD from bacteriophage destruction and CRISPR spacer acquisition, to constructive host DNA repair [2]. [1]. 7746848. The initiation and control of homologous recombination in Escherichia coli. Smith GR, Amundsen SK, Dabert P, Taylor AF;. Philos Trans R Soc Lond B Biol Sci 1995;347:13-20. [2]. 31907455. A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair. Cheng K, Wilkinson M, Chaban Y, Wigley DB;. Nat Struct Mol Biol. 2020;27:71-77. (from Pfam) NF016171.5 PF04259.19 SASP_gamma 28.4 28.4 84 subfamily Y Y N gamma-type small acid-soluble spore protein GO:0030435 15468161,3036769 2 Bacteria superkingdom 2217 EBI-EMBL Small, acid-soluble spore protein, gamma-type gamma-type small acid-soluble spore protein The SASP family is a family of small, glutamine and asparagine-rich peptides that store amino acids in the spores of Bacillus subtilis and related bacteria. (from Pfam) NF016172.5 PF04260.17 DUF436 25 25 171 PfamAutoEq Y Y N DUF436 family protein 2 Bacteria superkingdom 9128 EBI-EMBL Protein of unknown function (DUF436) DUF436 family protein Family of bacterial proteins with undetermined function. (from Pfam) NF016173.5 PF04261.17 Dyp_perox_N 20.4 20.4 146 domain Y Y N Dyp-type peroxidase domain-containing protein GO:0004601,GO:0020037 10742277,17654545,21324904,22308037 2 Bacteria superkingdom 67537 EBI-EMBL Dyp-type peroxidase, N-terminal Dyp-type peroxidase, N-terminal Dyp-type (dye-decolorizing) peroxidases are a family of heme proteins found in a wide range of bacteria and fungi [1,2]. They have a wide substrate specificity and lack homology to most other peroxidases, with the ability to function well under much lower pH conditions compared with the other plant peroxidases [2,3,4]. They consist of two domains that adopt a ferredoxin-like fold [2,4], connected by a loop. This entry represents the N-terminal domain [2,3,4]. [1]. 10742277. Efficient heterologous expression in Aspergillus oryzae of a unique dye-decolorizing peroxidase, DyP, of Geotrichum candidum Dec 1. Sugano Y, Nakano R, Sasaki K, Shoda M;. Appl Environ Microbiol 2000;66:1754-1758. [2]. 21324904. Crystal structure and biochemical features of EfeB/YcdB from Escherichia coli O157: ASP235 plays divergent roles in different enzyme-catalyzed processes. Liu X, Du Q, Wang Z, Zhu D, Huang Y, Li N, Wei T, Xu S, Gu L;. J Biol Chem. 2011;286:14922-14931. [3]. 17654545. Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif. Zubieta C, Krishna SS, Kapoor M, Kozbial P, McMullan D, Axelrod HL, Miller MD, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Schimmel P, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA;. Proteins. 2007;69:223-233. [4]. 22308037. Distal heme pocket residues o. TRUNCATED at 1650 bytes (from Pfam) NF016177.5 PF04265.19 TPK_B1_binding 22 22 67 PfamEq Y N N Thiamin pyrophosphokinase, vitamin B1 binding domain GO:0009229,GO:0030975 11435118 2 Bacteria superkingdom 21263 EBI-EMBL Thiamin pyrophosphokinase, vitamin B1 binding domain Thiamin pyrophosphokinase, vitamin B1 binding domain Family of thiamin pyrophosphokinase (EC:2.7.6.2). Thiamin pyrophosphokinase (TPK) catalyses the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggest that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis [1]. [1]. 11435118. The crystal structure of yeast thiamin pyrophosphokinase. Baker LJ, Dorocke JA, Harris RA, Timm DE;. Structure 2001;9:539-546. (from Pfam) NF016179.5 PF04267.17 SoxD 27 27 82 domain Y Y N sarcosine oxidase subunit delta GO:0008115,GO:0046653 11330998,7543100 2 Bacteria superkingdom 16109 EBI-EMBL Sarcosine oxidase, delta subunit family sarcosine oxidase subunit delta Sarcosine oxidase is a hetero-tetrameric enzyme that contains both covalently bound FMN and non-covalently bound FAD and NAD(+). This enzyme catalyses the oxidative demethylation of sarcosine to yield glycine, H2O2, and 5,10-CH2-tetrahydrofolate (H4folate) in a reaction requiring H4folate and O2 [1,2]. [1]. 11330998. Organization of the multiple coenzymes and subunits and role of the covalent flavin link in the complex heterotetrameric sarcosine oxidase. Eschenbrenner M, Chlumsky LJ, Khanna P, Strasser F, Jorns MS;. Biochemistry 2001;40:5352-5367. [2]. 7543100. Sequence analysis of sarcosine oxidase and nearby genes reveals homologies with key enzymes of folate one-carbon metabolism. Chlumsky LJ, Zhang L, Jorns MS;. J Biol Chem 1995;270:18252-18259. (from Pfam) NF016180.5 PF04268.17 SoxG 21 21 152 domain Y Y N sarcosine oxidase subunit gamma family protein 11330998,7543100 2 Bacteria superkingdom 17456 EBI-EMBL Sarcosine oxidase, gamma subunit family sarcosine oxidase subunit gamma family protein Sarcosine oxidase is a hetero-tetrameric enzyme that contains both covalently bound FMN and non-covalently bound FAD and NAD(+). This enzyme catalyses the oxidative demethylation of sarcosine to yield glycine, H2O2, and 5,10-CH2-tetrahydrofolate (H4folate) in a reaction requiring H4folate and O2 [1,2]. [1]. 11330998. Organization of the multiple coenzymes and subunits and role of the covalent flavin link in the complex heterotetrameric sarcosine oxidase. Eschenbrenner M, Chlumsky LJ, Khanna P, Strasser F, Jorns MS;. Biochemistry 2001;40:5352-5367. [2]. 7543100. Sequence analysis of sarcosine oxidase and nearby genes reveals homologies with key enzymes of folate one-carbon metabolism. Chlumsky LJ, Zhang L, Jorns MS;. J Biol Chem 1995;270:18252-18259. (from Pfam) NF016184.5 PF04273.18 BLH_phosphatase 26.1 26.1 110 domain Y Y N beta-lactamase hydrolase domain-containing protein GO:0016787 17586627,17636569 2 Bacteria superkingdom 18522 EBI-EMBL Beta-lactamase hydrolase-like protein, phosphatase-like domain Blh family sulfur transferase domain This domain, once called DUF442, is found as the N-terminal region, a sulfur transferase domain, of the bifunctional protein Blh (from the former name beta-lactamase-like hydrolase). The longer C-terminal domain of Blh is a sulfur dioxygenase domain. An earlier study on the uncharacterized protein NMA1982 showed a structure similar to protein tyrosine phosphatases, and reportedly some activity was detected on the test substrate p-nitrophenyl phosphate. Consequently, proteins annotated by this HMM and the related HMM TIGR01244 have been annotated as phosphatases. NF016185.5 PF04275.19 P-mevalo_kinase 33.8 33.8 114 PfamEq Y N N Phosphomevalonate kinase GO:0004631,GO:0005737,GO:0006695 11243736 2 Bacteria superkingdom 74 EBI-EMBL Phosphomevalonate kinase Phosphomevalonate kinase Phosphomevalonate kinase (EC:2.7.4.2) catalyses the phosphorylation of 5-phosphomevalonate into 5-diphosphomevalonate, an essential step in isoprenoid biosynthesis via the mevalonate pathway [1]. This family represents the animal type of the enzyme. The other is the ERG8 type, found in plants and fungi, and some bacteria (see Pfam:PF00288). [1]. 11243736. Nonorthologous gene displacement of phosphomevalonate kinase. Houten SM, Waterham HR;. Mol Genet Metab 2001;72:273-276. (from Pfam) NF016188.5 PF04278.17 Tic22 23 23 244 domain Y Y N Tic22 family protein GO:0015031 12032074 2 Bacteria superkingdom 847 EBI-EMBL Tic22-like family Tic22 family protein The preprotein translocation at the inner envelope membrane of chloroplasts so far involves five proteins: Tic110, Tic55, Tic40, Tic22 (this family) and Tic20. The molecular function of these proteins has not yet been established [1]. [1]. 12032074. The preprotein conducting channel at the inner envelope membrane of plastids. Heins L, Mehrle A, Hemmler R, Wagner R, Kuchler M, Hormann F, Sveshnikov D, Soll J;. EMBO J 2002;21:2616-2625. (from Pfam) NF016194.5 PF04284.18 DUF441 26.5 26.5 139 PfamAutoEq Y Y N DUF441 family protein 2 Bacteria superkingdom 6535 EBI-EMBL Protein of unknown function (DUF441) DUF441 family protein Predicted to be an integral membrane protein. (from Pfam) NF016197.5 PF04287.17 DUF446 25 25 98 PfamEq Y Y N YqcC family protein 2 Bacteria superkingdom 8525 EBI-EMBL tRNA pseudouridine synthase C YqcC family protein This family is suggested to be the catalytic domain of tRNA pseudouridine synthase C by association. The structure has been solved for one member, as PDB:2HGK, which by inference is designated in this way. (from Pfam) NF016204.5 PF04296.18 YlxR 26.9 26.9 75 PfamAutoEq Y Y N DUF448 domain-containing protein 30355672 2 Bacteria superkingdom 29225 EBI-EMBL Protein of unknown function (DUF448) Protein of unknown function (DUF448) The YlxR family has been demonstrated to regulate metabolic gene expression [1]. [1]. 30355672. Newly Identified Nucleoid-Associated-Like Protein YlxR Regulates Metabolic Gene Expression in Bacillus subtilis. Ogura M, Kanesaki Y;. mSphere. 2018; [Epub ahead of print] (from Pfam) NF016206.5 PF04298.17 Zn_peptidase_2 27 27 218 PfamEq Y Y N zinc metallopeptidase 2 Bacteria superkingdom 14600 EBI-EMBL Putative neutral zinc metallopeptidase zinc metallopeptidase Zinc metallopeptidase zinc binding regions have been predicted in some family members by a pattern match (Prosite:PS00142), of the characteristic HEXXH motif. (from Pfam) NF016208.5 PF04300.18 FBA 32.4 32.4 175 domain Y N N F-box associated region 2 Bacteria superkingdom 100 EBI-EMBL F-box associated region F-box associated region Members of this family are associated with F-box domains, hence the name FBA. This domain is probably involved in binding other proteins that will be targeted for ubiquitination. Swiss:Q9UK22 is involved in binding to N-glycosylated proteins. (from Pfam) NF016209.5 PF04301.18 BioG 27 27 213 PfamAutoEq Y Y N pimeloyl-ACP methyl esterase BioG family protein 27933801 2 Bacteria superkingdom 3487 EBI-EMBL Pimeloyl-ACP methyl esterase BioG DUF452 family protein This protein family includes Pimeloyl-ACP methyl esterase BioG from Haemophilus influenzae (Swiss:P44251) and similar bacterial proteins. This enzyme is involved in the biosynthesis of pymeloyl-ACP and, hence, in biotin biosynthesis. It is organised into a a core domain formed by a seven-stranded beta-sheet and a lid domain consisting of four alpha-helices [1]. [1]. 27933801. An Atypical alpha/beta-Hydrolase Fold Revealed in the Crystal Structure of Pimeloyl-Acyl Carrier Protein Methyl Esterase BioG from Haemophilus influenzae. Shi J, Cao X, Chen Y, Cronan JE, Guo Z;. Biochemistry. 2016;55:6705-6717. (from Pfam) NF016212.5 PF04305.19 DUF455 34.3 34.3 247 PfamAutoEq Y Y N DUF455 family protein 2 Bacteria superkingdom 13833 EBI-EMBL Protein of unknown function (DUF455) DUF455 family protein NF016215.5 PF04308.17 RNaseH_like 25 25 145 PfamEq Y Y N ribonuclease H-like YkuK family protein 16165328 2 Bacteria superkingdom 3097 EBI-EMBL Ribonuclease H-like ribonuclease H-like YkuK family protein RNaseH_like is a family of uncharacterised eubacterial proteins that are distant homologues of Ribonuclease H-like. The family maintains all the core secondary structure elements of the RNase H-like fold and shares several conserved, presumably active site residues with RNase HI. This finding suggests that it functions as a nuclease [1]. [1]. 16165328. Bacillus subtilis YkuK protein is distantly related to RNase H. Knizewski L, Ginalski K;. FEMS Microbiol Lett. 2005;251:341-346. (from Pfam) NF016216.5 PF04309.17 G3P_antiterm 27 27 173 domain Y Y N glycerol-3-phosphate responsive antiterminator GO:0006071,GO:0006355 1809833 2 Bacteria superkingdom 9303 EBI-EMBL Glycerol-3-phosphate responsive antiterminator glycerol-3-phosphate responsive antiterminator Intracellular glycerol is usually converted to glycerol-3-phosphate in an ATP-requiring phosphorylation reaction catalysed by glycerol kinase (GlpK) glycerol-3-phosphate activates the antiterminator GlpP [1]. [1]. 1809833. Expression of the gene encoding glycerol-3-phosphate dehydrogenase (glpD) in Bacillus subtilis is controlled by antitermination. Holmberg C, Rutberg B;. Mol Microbiol 1991;5:2891-2900. (from Pfam) NF016217.5 PF04310.17 MukB 23 23 226 PfamEq Y N N MukB N-terminal GO:0003677,GO:0005524,GO:0007059,GO:0009295,GO:0030261 10545328 2 Bacteria superkingdom 15206 EBI-EMBL MukB N-terminal MukB N-terminal This family represents the N-terminal region of MukB, one of a group of bacterial proteins essential for the movement of nucleoids from mid-cell towards the cell quarters (i.e. chromosome partitioning). The structure of the N-terminal domain consists of an antiparallel six-stranded beta sheet surrounded by one helix on one side and by five helices on the other side [1]. It contains an exposed Walker A loop in an unexpected helix-loop-helix motif (in other proteins, Walker A motifs generally adopt a P loop conformation as part of a strand-loop-helix motif embedded in a conserved topology of alternating helices and (parallel) beta strands)[1]. [1]. 10545328. Crystal structure of the N-terminal domain of MukB: a protein involved in chromosome partitioning. van den Ent F, Lockhart A, Kendrick-Jones J, Lowe J;. Structure Fold Des 1999;7:1181-1187. (from Pfam) NF016218.5 PF04311.18 DUF459 21 21 322 PfamAutoEq Y Y N DUF459 domain-containing protein 2 Bacteria superkingdom 5580 EBI-EMBL Protein of unknown function (DUF459) Protein of unknown function (DUF459) Putative periplasmic protein. (from Pfam) NF016223.5 PF04316.18 FlgM 24 24 55 domain Y Y N flagellar biosynthesis anti-sigma factor FlgM 15068809,9095196 2 Bacteria superkingdom 20074 EBI-EMBL Anti-sigma-28 factor, FlgM flagellar biosynthesis anti-sigma factor FlgM FlgM binds and inhibits the activity of the transcription factor sigma 28. Inhibition of sigma 28 prevents the expression of genes from flagellar transcriptional class 3, which include genes for the filament and chemotaxis. Correctly assembled basal body-hook structures export FlgM, relieving inhibition of sigma 28 and allowing expression of class 3 genes. NMR studies show that free FlgM is mostly unfolded, which may facilitate its export. The C terminal half of FlgM adopts a tertiary structure when it binds to sigma 28. All mutations in FlgM that prevent sigma 28 inhibition affect the C-terminal domain and is the region thought to constitute the binding domain. A minimal binding domain has been identified between Glu 64 and Arg 88 in Salmonella typhimurium (Swiss:P26477). The N-terminal portion remains unstructured and may be necessary for recognition by the export machinery [1]. [1]. 9095196. The C-terminal half of the anti-sigma factor, FlgM, becomes structured when bound to its target, sigma 28. Daughdrill GW, Chadsey MS, Karlinsey JE, Hughes KT, Dahlquist FW;. Nat Struct Biol 1997;4:285-291. [2]. 15068809. Crystal structure of the flagellar sigma/anti-sigma complex sigma(28)/FlgM reveals an intact sigma factor in an inactive conformation. Sorenson MK, Ray SS, Darst SA;. Mol Cell 2004;14:127-138. (from Pfam) NF016224.5 PF04317.17 DUF463 25 25 443 PfamEq Y Y N YcjX family protein 31202886 2 Bacteria superkingdom 17647 EBI-EMBL YcjX-like family, DUF463 GTP-binding protein YcjX This family represents a group of uncharacterised proteins including a bacterial stress protein YcjX. The crystal structure of YcjX from Shewanella oneidensis has now been solved, and shows it to be a Ras-like GTP-binding protein. However, YcjX utilizes a non-canonical switch 2' motif not found in any other G protein [1]. [1]. 31202886. Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein. Tsai JT, Sung N, Lee J, Chang C, Lee S, Tsai FTF;. J Mol Biol. 2019;431:3179-3190. (from Pfam) NF016226.5 PF04319.18 NifZ 27 27 73 domain Y Y N nitrogen fixation protein NifZ GO:0009399 2 Bacteria superkingdom 3551 EBI-EMBL NifZ domain NifZ domain This short protein is found in the nif (nitrogen fixation) operon. Its function is unknown but is probably involved in nitrogen fixation or regulating some component of this process. This 75 residue region is presumed to be a domain. It is found in isolation in some members and in the amino terminal half of the longer NifZ proteins. (from Pfam) NF016231.5 PF04325.18 DUF465 25 25 48 domain Y Y N DUF465 domain-containing protein 16231304 2 Bacteria superkingdom 23154 EBI-EMBL Protein of unknown function (DUF465) Protein of unknown function (DUF465) Family members are found in small bacterial proteins, and also in the heavy chains of fungal proteins that contain the domain kinesin, in which this region is located C-terminal of the motor domain (Pfam:PF00225). It adopts a coiled-coil-like conformation [1]. [1]. 16231304. Solution structure of HP1242 from Helicobacter pylori. Kang SJ, Park SJ, Jung SJ, Lee BJ;. Proteins. 2005;61:1111-1113. (from Pfam) NF016233.5 PF04327.17 Peptidase_Prp 27 27 90 PfamEq Y Y N ribosomal-processing cysteine protease Prp 25388641 2 Bacteria superkingdom 9653 EBI-EMBL Cysteine protease Prp ribosomal-processing cysteine protease Prp This is a family of cysteine protease that are found to cleave the N-terminus extension of ribosomal subunit L27 in eubacteria. Proteins in this family are distinguished by a pair of invariant histidine and cysteine residues with conserved spacing that form the classic catalytic dyad of a cysteine protease [1]. [1]. 25388641. Specific N-terminal cleavage of ribosomal protein L27 in Staphylococcus aureus and related bacteria. Wall EA, Caufield JH, Lyons CE, Manning KA, Dokland T, Christie GE;. Mol Microbiol. 2014; [Epub ahead of print] (from Pfam) NF016234.5 PF04328.18 Sel_put 25 25 61 subfamily Y Y N CstA-like transporter-associated (seleno)protein 21348639,26342139,29769716 2 Bacteria superkingdom 12001 EBI-EMBL Selenoprotein, putative CstA-like transporter-associated (seleno)protein The family of small proteins, previously called DUF466, includes YbdD and YjiX from Escherichia coli K-12, both encoded next to CstA-like transporter proteins involved in proton-driven import of pyruvate. Related proteins in epsilon-proteobacteria are selenoproteins, terminating in CU instead of CC. NF016236.5 PF04333.18 MlaA 25 25 195 domain Y Y N MlaA family lipoprotein GO:0016020 19383799,8145644 2 Bacteria superkingdom 27469 EBI-EMBL MlaA lipoprotein MlaA family lipoprotein MlaA is a component of the Mla pathway, an ABC transport system that functions to maintain the asymmetry of the outer membrane [1]. MlaA is required for the intercellular spreading of Shigella flexneri. It is attached to the outer membrane by a lipid anchor [2]. [1]. 19383799. An ABC transport system that maintains lipid asymmetry in the gram-negative outer membrane. Malinverni JC, Silhavy TJ;. Proc Natl Acad Sci U S A. 2009;106:8009-8014. [2]. 8145644. Identification and characterization of a chromosomal virulence gene, vacJ, required for intercellular spreading of Shigella flexneri. Suzuki T, Murai T, Fukuda I, Tobe T, Yoshikawa M, Sasakawa C;. Mol Microbiol 1994;11:31-41. (from Pfam) NF016238.5 PF04335.18 VirB8 23.2 23.2 213 subfamily Y Y N VirB8/TrbF family protein GO:0016020 11371528,11846762 2 Bacteria superkingdom 24077 EBI-EMBL VirB8 protein VirB8/TrbF family protein This family includes both VirB8-like proteins of type 4 secretion systems (T4SS) and TrbF family conjugal transfer protein. NF016239.5 PF04336.17 ACP_PD 27 27 105 PfamAutoEq Y Y N ACP phosphodiesterase GO:0006633,GO:0008770 16107329 2 Bacteria superkingdom 15689 EBI-EMBL Acyl carrier protein phosphodiesterase ACP phosphodiesterase YajB, now renamed acpH, encodes an ACP hydrolase that converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine prosthetic group from ACP [1]. [1]. 16107329. The enigmatic acyl carrier protein phosphodiesterase of Escherichia coli: genetic and enzymological characterization. Thomas J, Cronan JE;. J Biol Chem. 2005;280:34675-34683. (from Pfam) NF016240.5 PF04337.17 DUF480 25 25 149 PfamAutoEq Y Y N DUF480 domain-containing protein 2 Bacteria superkingdom 14889 EBI-EMBL Protein of unknown function, DUF480 Protein of unknown function, DUF480 This family consists of several proteins of uncharacterised function. (from Pfam) NF016241.5 PF04338.17 DUF481 21.1 21.1 210 domain Y Y N DUF481 domain-containing protein 2 Bacteria superkingdom 20969 EBI-EMBL Protein of unknown function, DUF481 Protein of unknown function, DUF481 This family includes several proteins of uncharacterised function. (from Pfam) NF016249.5 PF04346.17 EutH 25 25 351 PfamEq Y Y N ethanolamine utilization protein EutH eutH GO:0016020,GO:0034228,GO:0034229 10464203 2 Bacteria superkingdom 7016 EBI-EMBL Ethanolamine utilisation protein, EutH ethanolamine utilization protein EutH EutH is a bacterial membrane protein whose molecular function is unknown. It has been suggested that it may act as an ethanolamine transporter, responsible for carrying ethanolamine from the periplasm to the cytoplasm [1]. [1]. 10464203. The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. Kofoid E, Rappleye C, Stojiljkovic I, Roth J;. J Bacteriol 1999;181:5317-5329. (from Pfam) NF016250.5 PF04347.18 FliO 22 22 91 PfamEq Y Y N flagellar biosynthetic protein FliO GO:0016020,GO:0044781 10049367,28771474 2 Bacteria superkingdom 27959 EBI-EMBL Flagellar biosynthesis protein, FliO flagellar biosynthetic protein FliO FliO is an essential component of the flagellum-specific protein export apparatus [1]. It is an integral membrane protein that acts as an assembly chaperone for the flagellar protein FliP (Pfam:PF00813). It is crucial, although not strictly required, for efficient FliP assembly and, thus flagellar assembly and function [2]. [1]. 10049367. Components of the Salmonella flagellar export apparatus and classification of export substrates. Minamino T, Macnab RM;. J Bacteriol 1999;181:1388-1394. [2]. 28771474. A flagellum-specific chaperone facilitates assembly of the core type III export apparatus of the bacterial flagellum. Fabiani FD, Renault TT, Peters B, Dietsche T, Galvez EJC, Guse A, Freier K, Charpentier E, Strowig T, Franz-Wachtel M, Macek B, Wagner S, Hensel M, Erhardt M;. PLoS Biol. 2017;15:e2002267. (from Pfam) NF016252.5 PF04349.17 MdoG 25 25 478 domain Y Y N glucan biosynthesis protein GO:0016051,GO:0042597 10779706 2 Bacteria superkingdom 23209 EBI-EMBL Periplasmic glucan biosynthesis protein, MdoG glucan biosynthesis protein This family represents MdoG, a protein that is necessary for the synthesis of periplasmic glucans. The function of MdoG remains unknown. It has been suggested that it may catalyse the addition of branches to a linear glucan backbone. [1]. 10779706. Osmoregulated periplasmic glucans in Proteobacteria. Bohin JP;. FEMS Microbiol Lett 2000;186:11-19. (from Pfam) NF016253.5 PF04350.18 PilO 22 22 145 subfamily Y Y N type 4a pilus biogenesis protein PilO pilO GO:0043107,GO:0043683 2 Bacteria superkingdom 15897 EBI-EMBL Pilus assembly protein, PilO type 4a pilus biogenesis protein PilO PilO proteins are involved in the assembly of pilin. However, the precise function of this family of proteins is not known. (from Pfam) NF016254.5 PF04351.18 PilP 25.6 25.6 146 PfamEq Y Y N pilus assembly protein PilP 11751821 2 Bacteria superkingdom 11928 EBI-EMBL Pilus assembly protein, PilP pilus assembly protein PilP The PilP family are periplasmic proteins involved in the biogenesis of type IV pili [1]. [1]. 11751821. Genes required for plasmid R64 thin-pilus biogenesis: identification and localization of products of the pilK, pilM, pilO, pilP, pilR, and pilT genes. Sakai D, Komano T;. J Bacteriol 2002;184:444-451. (from Pfam) NF016257.5 PF04354.18 ZipA_C 23 23 128 domain Y Y N cell division protein ZipA C-terminal FtsZ-binding domain-containing protein GO:0090529 10924108 2 Bacteria superkingdom 22029 EBI-EMBL ZipA, C-terminal FtsZ-binding domain ZipA, C-terminal FtsZ-binding domain This family represents the ZipA C-terminal domain. ZipA is involved in septum formation in bacterial cell division. Its C-terminal domain binds FtsZ, a major component of the bacterial septal ring. The structure of this domain is an alpha-beta fold with three alpha helices and a beta sheet of six antiparallel beta strands. The major loops protruding from the beta sheet surface are thought to form a binding site for FtsZ [1]. [1]. 10924108. Solution structure of ZipA, a crucial component of Escherichia coli cell division. Moy FJ, Glasfeld E, Mosyak L, Powers R;. Biochemistry 2000;39:9146-9156. (from Pfam) NF016258.5 PF04355.18 SmpA_OmlA 23.2 23.2 71 domain Y Y N outer membrane protein assembly factor BamE bamE GO:0019867 9973334 2 Bacteria superkingdom 30632 EBI-EMBL SmpA / OmlA family outer membrane protein assembly factor BamE Lipoprotein Bacterial outer membrane lipoprotein, possibly involved in in maintaining the structural integrity of the cell envelope [1]. Lipid attachment site is a conserved N terminal cysteine residue. Sometimes found adjacent to the OmpA domain (Pfam:PF00691). [1]. 9973334. Pseudomonas aeruginosa fur overlaps with a gene encoding a novel outer membrane lipoprotein, OmlA. Ochsner UA, Vasil AI, Johnson Z, Vasil ML;. J Bacteriol 1999;181:1099-1109. (from Pfam) NF016266.5 PF04363.17 DUF496 23.2 23.2 93 PfamAutoEq Y Y N DUF496 family protein 2 Bacteria superkingdom 1638 EBI-EMBL Protein of unknown function (DUF496) DUF496 family protein NF016267.5 PF04364.18 DNA_pol3_chi 25.4 25.4 135 PfamEq Y Y N DNA polymerase III subunit chi 2.7.7.7 GO:0003677,GO:0003887,GO:0006260 7494000 2 Bacteria superkingdom 22243 EBI-EMBL DNA polymerase III chi subunit, HolC DNA polymerase III subunit chi The DNA polymerase III holoenzyme (EC:2.7.7.7) is the polymerase responsible for the replication of the Escherichia coli chromosome. The holoenzyme is composed of the DNA polymerase III core, the sliding clamp, and the DnaX clamp loading complex. The DnaX complex contains either either the tau or gamma product of gene dnax, complexed to delta.delta' and to chi psi. Chi forms a 1:1 heterodimer with psi. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta' allowing a functional clamp-loading complex to form at physiological subunit concentrations. Psi is responsible for the interaction with DnaX (gamma/tau), but psi is insoluble unless it is in a complex with chi [1]. [1]. 7494000. DnaX complex of Escherichia coli DNA polymerase III holoenzyme. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta' to a physiologically relevant range. Olson MW, Dallmann HG, McHenry CS;. J Biol Chem 1995;270:29570-29577. (from Pfam) NF016269.5 PF04366.17 Ysc84 25.1 25.1 127 domain Y Y N YSC84-related protein 19158382 2 Bacteria superkingdom 11863 EBI-EMBL Las17-binding protein actin regulator YSC84-related protein This family is named for yeast protein YSC84. Roughly one third of currently known family members occur in bacteria, but their function is unknown. NF016271.5 PF04368.18 DUF507 24.7 24.7 182 PfamAutoEq Y Y N DUF507 family protein 37596303 2 Bacteria superkingdom 1511 EBI-EMBL Protein of unknown function (DUF507) DUF507 family protein This entry represents a bacterial domain with an unknown function. It folds into a Y-shaped alpha-helical structure, comprising an anti- parallel 4-helix bundle at the base and two helical arms [1]. [1]. 37596303. Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold. McKay CE, Cheng J, Tanner JJ;. Sci Rep. 2023;13:13496. (from Pfam) NF016272.5 PF04369.18 Lactococcin 23.1 23.1 60 subfamily Y Y N lactococcin family bacteriocin GO:0005576,GO:0042742 2 Bacteria superkingdom 198 EBI-EMBL Lactococcin-like family lactococcin family bacteriocin Family of bacteriocins from lactic acid bacteria. (from Pfam) NF016276.5 PF04376.18 ATE_N 27 27 72 PfamEq Y N N Arginine-tRNA-protein transferase, N terminus GO:0004057,GO:0016598 7495814,9858543 2 Bacteria superkingdom 19770 EBI-EMBL Arginine-tRNA-protein transferase, N terminus Arginine-tRNA-protein transferase, N terminus This family represents the N terminal region of the enzyme arginine-tRNA-protein transferase (EC 2.3.2.8), which catalyses the post-translational conjugation of arginine to the N terminus of a protein. In eukaryotes, this functions as part of the N-end rule pathway of protein degradation by conjugating a de-stabilising amino acid to the amino terminal aspartate or glutamate of a protein, targeting the protein for ubiquitin-dependent proteolysis. N terminal cysteine is sometimes modified [1]. In S cerevisiae, Cys20, 23, 94 and/or 95 are thought to be important for activity [2]. Of these, only Cys 94 appears to be completely conserved in this family. [1]. 9858543. Alternative splicing results in differential expression, activity, and localization of the two forms of arginyl-tRNA-protein transferase, a component of the N-end rule pathway. Kwon YT, Kashina AS, Varshavsky A;. Mol Cell Biol 1999;19:182-193. [2]. 7495814. Binding of phenylarsenoxide to Arg-tRNA protein transferase is independent of vicinal thiols. Li J, Pickart CM;. Biochemistry 1995;34:15829-15837. (from Pfam) NF016277.5 PF04377.20 ATE_C 25 25 122 PfamEq Y N N Arginine-tRNA-protein transferase, C terminus GO:0004057,GO:0016598 9858543 2 Bacteria superkingdom 20381 EBI-EMBL Arginine-tRNA-protein transferase, C terminus Arginine-tRNA-protein transferase, C terminus This family represents the C terminal region of the enzyme arginine-tRNA-protein transferase (EC 2.3.2.8), which catalyses the post-translational conjugation of arginine to the N terminus of a protein. In eukaryotes, this functions as part of the N-end rule pathway of protein degradation by conjugating a destabilising amino acid to the amino terminal aspartate or glutamate of a protein, targeting the protein for ubiquitin-dependent proteolysis. N terminal cysteine is sometimes modified [1]. [1]. 9858543. Alternative splicing results in differential expression, activity, and localization of the two forms of arginyl-tRNA-protein transferase, a component of the N-end rule pathway. Kwon YT, Kashina AS, Varshavsky A;. Mol Cell Biol 1999;19:182-193. (from Pfam) NF016279.5 PF04379.19 DUF525 27 27 87 PfamEq Y Y N ApaG domain 10945468,12522211,15213450,1779764 2 Bacteria superkingdom 16962 EBI-EMBL ApaG domain ApaG domain The apaG domain is a ~125 amino acids domain present in bacterial apaG proteins and in eukaryotic F-box proteins. The domain is named after the bacterial apaG protein, of which it forms the core. The domain also occurs in the C-terminal part of eukaryotic proteins with an N-terminal F-box domain. The Salmonella typhimurium apaG domain protein corD is involved in Co(2+) resistance and Mg(2+) efflux. Tertiary structures from different apaG proteins show a fold of several beta-sheets. The apaG domain may be involved in protein-protein interactions which could be implicated in substrate-specificity [1,2,3,4]. [1]. 1779764. Magnesium transport in Salmonella typhimurium: the influence of new mutations conferring Co2+ resistance on the CorA Mg2+ transport system. Gibson MM, Bagga DA, Miller CG, Maguire ME;. Mol Microbiol 1991;5:2753-2762. [2]. 10945468. cDNA cloning and expression analysis of new members of the mammalian F-box protein family. Ilyin GP, Rialland M, Pigeon C, Guguen-Guillouzo C;. Genomics. 2000;67:40-47. [3]. 12522211. Identification of a novel protein, PDIP38, that interacts with the p50 subunit of DNA polymerase delta and proliferating cell nuclear antigen. Liu L, Rodriguez-Belmonte EM, Mazloum N, Xie B, Lee MY;. J Biol Chem. 2003;278:10041-10047. [4]. 15213450. 1H, 15N and 13C resonance assignments of the ApaG protein of the phytopathogen Xanthomonas axonopodis pv. citri. Katsuyama AM, Cicero DO, Spisni A, Paci M, Farah CS, Pertinhez TA;. J Biomol NMR. 2004;29:423-424. (from Pfam) NF016280.5 PF04380.18 BMFP 37.2 37.2 77 subfamily Y Y N accessory factor UbiK family protein 18616282 2 Bacteria superkingdom 15912 EBI-EMBL Membrane fusogenic activity accessory factor UbiK family protein BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro. [1]. 18616282. Brucella abortus MFP: a trimeric coiled-coil protein with membrane fusogenic activity. Carrica Mdel C, Craig PO, Alonso Sdel V, Goldbaum FA, Cravero SL;. Biochemistry. 2008;47:8165-8175. (from Pfam) NF016281.5 PF04381.17 RdgC 25 25 298 domain Y Y N recombination-associated protein RdgC rdgC GO:0006310 10655208,8807285 2 Bacteria superkingdom 19403 EBI-EMBL Putative exonuclease, RdgC recombination-associated protein RdgC Members of the RdgC family may have exonuclease activity. RdgC is required for efficient pilin variation in Neisseria gonorrhoeae, suggesting that it may be involved in recombination reactions [1]. In Escherichia coli, RdgC is required for growth in recombination-deficient exonuclease-depleted strains. Under these conditions, RdgC may act as an exonuclease to remove collapsed replication forks, in the absence of the normal repair mechanisms [2]. [1]. 10655208. A homologue of the recombination-dependent growth gene, rdgC, is involved in gonococcal pilin antigenic variation. Mehr IJ, Long CD, Serkin CD, Seifert HS;. Genetics 2000;154:523-532. [2]. 8807285. Recombination-dependent growth in exonuclease-depleted recBC sbcBC strains of Escherichia coli K-12. Ryder L, Sharples GJ, Lloyd RG;. Genetics 1996;143:1101-1114. (from Pfam) NF016286.5 PF04386.18 SspB 27 27 156 PfamEq Y Y N ClpXP protease specificity-enhancing factor SspB 11009422,11535833,11810257 2 Bacteria superkingdom 21409 EBI-EMBL Stringent starvation protein B ClpXP protease specificity-enhancing factor SspB SspB (stringent starvation protein B) binds to incomplete proteins, C-terminally tagged by trans-translation from ssrA (tmRNA) after release from stalled ribosomes, and promotes degradation by ClpXP. NF016290.5 PF04390.17 LptE 23 23 118 PfamEq Y Y N LPS assembly lipoprotein LptE lptE GO:0019867,GO:0043165 18424520 2 Bacteria superkingdom 29439 EBI-EMBL Lipopolysaccharide-assembly LPS assembly lipoprotein LptE LptE (formerly known as RplB) is involved in lipopolysaccharide-assembly on the outer membrane of Gram-negative organisms. The lipopolysaccharide component of the outer bacterial membrane is transported from its source of origin to the outer membrane by a set of proteins constituting a transport machinery that is made up of LptA, LptB, LptC, LptD, LptE. LptD appears to be anchored in the outer membrane, and LptE forms a complex with it. This part of the machinery complex is involved in the assembly of lipopolysaccharide in the outer leaflet of the outer membrane [1]. [1]. 18424520. Functional analysis of the protein machinery required for transport of lipopolysaccharide to the outer membrane of Escherichia coli. Sperandeo P, Lau FK, Carpentieri A, De Castro C, Molinaro A, Deho G, Silhavy TJ, Polissi A;. J Bacteriol. 2008;190:4460-4469. (from Pfam) NF016291.5 PF04391.17 DUF533 29.6 29.6 178 PfamAutoEq Y Y N DUF533 domain-containing protein 2 Bacteria superkingdom 16760 EBI-EMBL Protein of unknown function (DUF533) Protein of unknown function (DUF533) Some family members may be secreted or integral membrane proteins. (from Pfam) NF016293.5 PF04393.18 DUF535 27 27 281 domain Y Y N DUF535 family protein 11115111,1406277 2 Bacteria superkingdom 14634 EBI-EMBL Protein of unknown function (DUF535) DUF535 family protein Family member Shigella flexneri VirK (Swiss:Q99QA5) is a virulence protein required for the expression, or correct membrane localisation of IcsA (VirG) on the bacterial cell surface [1], [2]. This family also includes Pasteurella haemolytica lapB (Swiss:P32181), which is thought to be membrane-associated. [1]. 1406277. Identification and characterization of virK, a virulence-associated large plasmid gene essential for intercellular spreading of Shigella flexneri. Nakata N, Sasakawa C, Okada N, Tobe T, Fukuda I, Suzuki T, Komatsu K, Yoshikawa M;. Mol Microbiol 1992;6:2387-2395. [2]. 11115111. The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri. Buchrieser C, Glaser P, Rusniok C, Nedjari H, D'Hauteville H, Kunst F, Sansonetti P, Parsot C;. Mol Microbiol 2000;38:760-771. (from Pfam) NF016294.5 PF04394.19 DUF536 20.7 20.7 43 PfamAutoEq Y Y N DUF536 domain-containing protein 21822904,32240216,8302939 2 Bacteria superkingdom 3294 EBI-EMBL Protein of unknown function, DUF536 Protein of unknown function, DUF536 This family aligns the C-terminal region from several bacterial proteins of unknown function that may be involved in a theta-type replication mechanism [1,2,3]. [1]. 8302939. Identification and characterization of a mobilization gene in the streptococcal plasmid, pVA380-1. LeBlanc DJ, Chen YY, Lee LN;. Plasmid 1993;30:296-302. [2]. 21822904. Sequencing and analysis of three plasmids from Lactobacillus casei TISTR1341 and development of plasmid-derived Escherichia coli-L. casei shuttle vectors. Panya M, Lulitanond V, Tangphatsornruang S, Namwat W, Wannasutta R, Suebwongsa N, Mayo B;. Appl Microbiol Biotechnol. 2012;93:261-272. [3]. 32240216. Nucleotide sequence and analysis of pRC12 and pRC18, two theta-replicating plasmids harbored by Lactobacillus curvatus CRL 705. Teran LC, Cuozzo SA, Aristimuno Ficoseco MC, Fadda S, Chaillou S, Champomier-Verges MC, Zagorec M, Hebert EM, Raya RR;. PLoS One. 2020;15:e0230857. (from Pfam) NF016297.5 PF04398.17 DUF538 25 25 112 domain Y Y N DUF538 domain-containing protein 2 Bacteria superkingdom 3 EBI-EMBL Protein of unknown function, DUF538 Protein of unknown function, DUF538 This family consists of several plant proteins of unknown function. (from Pfam) NF016303.5 PF04405.19 ScdA_N 32.5 32.5 56 PfamAutoEq Y Y N DUF542 domain-containing protein 2 Bacteria superkingdom 12201 EBI-EMBL Domain of Unknown function (DUF542) Domain of Unknown function (DUF542) This domain is always found in conjunction with the HHE domain (Pfam:PF03794) at the N-terminus. (from Pfam) NF016306.5 PF04408.28 HA2_N 21 21 29 domain Y N N Helicase associated domain (HA2), winged-helix GO:0004386 26545078,31409651,32179686 2 Bacteria superkingdom 51089 EBI-EMBL Helicase associated domain (HA2), winged-helix Helicase associated domain (HA2), winged-helix The helicase associated domain (HA2) has an all alpha-helical fold and consists of a N-terminal winged-helix (WH) domain and a C-terminal degenerate helical-bundle domain, referred to as the ratchet-like domain [1,2,3]. These domains collaborate with RecA domains at the N-terminal in completing an RNA binding channel to allow the helicases to keep a stable grip on the RNA [3] and assure its correct function. This entry represents the WH domain, which connects the N- (RecA domains) and C-terminal domains (ratchet-like and OB-fold) of helicases. [1]. 26545078. Structure of the RNA Helicase MLE Reveals the Molecular Mechanisms for Uridine Specificity and RNA-ATP Coupling. Prabu JR, Muller M, Thomae AW, Schussler S, Bonneau F, Becker PB, Conti E;. Mol Cell. 2015;60:487-499. [2]. 31409651. Structural and functional characterisation of human RNA helicase DHX8 provides insights into the mechanism of RNA-stimulated ADP release. Felisberto-Rodrigues C, Thomas JC, McAndrew C, Le Bihan YV, Burke R, Workman P, van Montfort RLM;. Biochem J. 2019;476:2521-2543. [3]. 32179686. Structural basis for DEAH-helicase activation by G-patch proteins. Studer MK, Ivanovic L, Weber ME, Marti S, Jonas S;. Proc Natl Acad Sci U S A. 2020;117:7159-7170. (from Pfam) NF016311.5 PF04413.21 Glycos_transf_N 23.9 23.9 179 domain Y Y N glycosyltransferase N-terminal domain-containing protein 10952982 2 Bacteria superkingdom 47879 EBI-EMBL 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase) 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase) Members of this family transfer activated sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides. Members of the family transfer UDP, ADP, GDP or CMP linked sugars. The Glycos_transf_N region is flanked at the N-terminus by a signal peptide and at the C-terminus by Glycos_transf_1 (Pfam:PF00534). The eukaryotic glycogen synthases may be distant members of this bacterial family [1]. [1]. 10952982. 3-Deoxy-D-manno-oct-2-ulosonic acid (Kdo) transferase (WaaA) and kdo kinase (KdkA) of Haemophilus influenzae are both required to complement a waaA knockout mutation of Escherichia coli. Brabetz W, Muller-Loennies S, Brade H;. J Biol Chem 2000;275:34954-34962. (from Pfam) NF016314.5 PF04417.17 DUF501 23.8 23.8 139 PfamAutoEq Y Y N DUF501 domain-containing protein 2 Bacteria superkingdom 14584 EBI-EMBL Protein of unknown function (DUF501) Protein of unknown function (DUF501) Family of uncharacterised bacterial proteins. (from Pfam) NF016315.5 PF04418.17 DUF543 24.1 24.1 75 domain Y Y N DUF543 domain-containing protein GO:0005743,GO:0061617 2 Bacteria superkingdom 2 EBI-EMBL Domain of unknown function (DUF543) Domain of unknown function (DUF543) This family of short eukaryotic proteins has no known function. Most of the members of this family are only 80 amino acid residues long. However the Arabidopsis homologue is over 300 residues long. The presumed domain contains a conserved amino terminal cysteine and a conserved motif GXGXGXG in the carboxy terminal half that may be functionally important. (from Pfam) NF016337.5 PF04442.19 CtaG_Cox11 25 25 148 PfamEq Y Y N cytochrome c oxidase assembly protein GO:0005507 10617659,12063264 2 Bacteria superkingdom 16469 EBI-EMBL Cytochrome c oxidase assembly protein CtaG/Cox11 cytochrome c oxidase assembly protein Cytochrome c oxidase assembly protein is essential for the assembly of functional cytochrome oxidase protein. In eukaryotes it is an integral protein of the mitochondrial inner membrane. Cox11 is essential for the insertion of Cu(I) ions to form the CuB site. This is essential for the stability of other structures in subunit I, for example haems a and a3, and the magnesium/manganese centre. Cox11 is probably only required in sub-stoichiometric amounts relative to the structural units [1]. The C terminal region of the protein is known to form a dimer. Each monomer coordinates one Cu(I) ion via three conserved cysteine residues (111, 208 and 210) in Saccharomyces cerevisiae (Swiss:P19516). Met 224 is also thought to play a role in copper transfer or stabilising the copper site [2]. [1]. 10617659. Cox11p is required for stable formation of the Cu(B) and magnesium centers of cytochrome c oxidase. Hiser L, Di Valentin M, Hamer AG, Hosler JP;. J Biol Chem 2000;275:619-623. [2]. 12063264. Yeast Cox11, a protein essential for cytochrome c oxidase assembly, is a Cu(I) binding protein. Carr HS, George GN, Winge DR;. J Biol Chem 2002;277:31237-31242. (from Pfam) NF016339.5 PF04444.19 Dioxygenase_N 27 27 75 domain Y Y N dioxygenase GO:0005506,GO:0009712,GO:0018576 2 Bacteria superkingdom 25704 EBI-EMBL Catechol dioxygenase N terminus dioxygenase This family consists of the N termini of catechol, chlorocatechol or hydroxyquinol 1,2-dioxygenase proteins. This region is always found adjacent to the dioxygenase domain (Pfam:PF00775). (from Pfam) NF016340.5 PF04445.18 SAM_MT 26 26 230 PfamEq Y Y N class I SAM-dependent methyltransferase 2.1.1.- GO:0008990,GO:0031167 10629202 2 Bacteria superkingdom 23470 EBI-EMBL Putative SAM-dependent methyltransferase class I SAM-dependent methyltransferase This is a family of putative SAM-dependent methyltransferases. [1]. 10629202. opdA, a Salmonella enterica serovar Typhimurium gene encoding a protease, is part of an operon regulated by heat shock. Conlin CA, Miller CG;. J Bacteriol 2000;182:518-521. (from Pfam) NF016342.5 PF04447.17 dATP-dGTP_PPHyd 23 23 97 PfamAutoEq Y Y N dATP/dGTP pyrophosphohydrolase domain-containing protein 33926954 2 Bacteria superkingdom 3021 EBI-EMBL dATP/dGTP pyrophosphohydrolase dATP/dGTP pyrophosphohydrolase This domain is found in phage proteins, such as A0A2H5BHG5 from Acinetobacter phage SH-Ab 15497, which are associated with PurZ, an enzyme that catalyses the synthesis of diaminopurine (Z), a DNA modification that gives phages an advantage for evading host restriction enzymes activity [1]. This domain has dATP and dGTP pyrophosphohydrolase activity; it catalyses the hydrolysis of dATP/dGTP to pyrophosphate and dAMP/dGMP, respectively, with little or no activities for NTPs and pyrimidine dNTPs. It is suggested that enzymes containing this domain supply dGMP as the substrate for PurZ, elevating dZTP level to promote Z incorporation [1]. [1]. 33926954. A widespread pathway for substitution of adenine by diaminopurine in phage genomes. Zhou Y, Xu X, Wei Y, Cheng Y, Guo Y, Khudyakov I, Liu F, He P, Song Z, Li Z, Gao Y, Ang EL, Zhao H, Zhang Y, Zhao S;. Science. 2021;372:512-516. (from Pfam) NF016343.5 PF04448.17 DUF551 22 22 68 domain Y Y N DUF551 domain-containing protein 2 Bacteria superkingdom 17928 EBI-EMBL Protein of unknown function (DUF551) Protein of unknown function (DUF551) This family represents the carboxy terminus of a protein of unknown function, found in dsDNA viruses with no RNA stage, including bacteriophages lambda and P22, and also in some Escherichia coli prophages. (from Pfam) NF016347.5 PF04452.19 Methyltrans_RNA 23.9 23.9 165 domain Y Y N 16S rRNA (uracil(1498)-N(3))-methyltransferase GO:0006364,GO:0008168 11763972,16431987 2 Bacteria superkingdom 80951 EBI-EMBL RNA methyltransferase domain RNA methyltransferase domain RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation [1][2]. [1]. 11763972. SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases. Anantharaman V, Koonin EV, Aravind L;. J Mol Microbiol Biotechnol. 2002;4:71-75. [2]. 16431987. Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family. Basturea GN, Rudd KE, Deutscher MP;. RNA. 2006;12:426-434. (from Pfam) NF016348.5 PF04453.19 LptD 22.4 22.4 384 PfamEq Y Y N LPS assembly protein LptD lptD GO:0015920,GO:0019867,GO:0043165,GO:0061024 24990744,27161977,27922123 2 Bacteria superkingdom 38236 EBI-EMBL LPS transport system D LPS assembly protein LptD Lipopolysaccharide (LPS) is essential for most Gram-negative bacteria and has crucial roles in protection of the bacteria from harsh environments and toxic compounds, including antibiotics. This family includes members such as LPTD found in Shigella flexneri and Yersinia pestis. Structural analysis indicates that LptD forms a novel 26-stranded beta-barrel. It interacts with LPTE where LptE adopts a roll-like structure located inside the barrel of LptD. The LPS translocon LptD is unable to fold properly in the absence of LptE and the two proteins form a unique barrel and plug architecture for LPS transport and insertion [1] [2]. LptD is an essential outer membrane protein that mediates the final transport of lipopolysaccharide (LPS) to outer leaflet. It has been suggested that LptD is a promising target for the development of effective vaccines and antibody-based therapies to control Vibrio infection [3]. [1]. 24990744. Structural basis for outer membrane lipopolysaccharide insertion. Dong H, Xiang Q, Gu Y, Wang Z, Paterson NG, Stansfeld PJ, He C, Zhang Y, Wang W, Dong C;. Nature. 2014;511:52-56. [2]. 27161977. Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens. Botos I, Majdalani N, Mayclin SJ, McCarthy JG, Lundquist K, Wojtowicz D, Barnard TJ, Gumbart JC, Buchanan SK;. Structure. 2016;24:965-976. [3]. 27922123. LptD is a promising vaccine antigen and potential immunotherapeutic target for protection against Vibrio species infection. Zha Z, Li C, Li W, Ye Z, Pan J;. Sci Rep. 2016;6:38577. (from Pfam) NF016351.5 PF04456.17 DUF503 22.4 22.4 88 PfamAutoEq Y Y N DUF503 family protein 2 Bacteria superkingdom 10909 EBI-EMBL Protein of unknown function (DUF503) DUF503 family protein Family of hypothetical bacterial proteins. (from Pfam) NF016355.5 PF04461.18 DUF520 23.2 23.2 161 PfamAutoEq Y Y N DUF520 family protein 12943362 2 Bacteria superkingdom 23694 EBI-EMBL Protein of unknown function (DUF520) DUF520 family protein The structure of the DUF520 family of uncharacterised proteins shows that it has composed of two domains each of which has the same topology [1]. [1]. 12943362. Crystal structure of the YajQ protein from Haemophilus influenzae reveals a tandem of RNP-like domains. Teplyakov A, Obmolova G, Bir N, Reddy P, Howard AJ, Gilliland GL;. J Struct Funct Genomics. 2003;4:1-9. (from Pfam) NF016361.5 PF04468.17 PSP1 27 27 86 domain Y Y N PSP1 C-terminal domain-containing protein 9529527 2 Bacteria superkingdom 19279 EBI-EMBL PSP1 C-terminal conserved region PSP1 C-terminal conserved region This region is present in both eukaryotes and eubacteria. The yeast PSP1 protein is involved in suppressing mutations in the DNA polymerase alpha subunit in yeast [1]. [1]. 9529527. Suppressors of the temperature sensitivity of DNA polymerase alpha mutations in Saccharomyces cerevisiae. Formosa T, Nittis T;. Mol Gen Genet 1998;257:461-468. (from Pfam) NF016372.5 PF04483.17 DUF565 27 27 60 domain Y Y N DUF565 domain-containing protein 2 Bacteria superkingdom 1048 EBI-EMBL Protein of unknown function (DUF565) Protein of unknown function (DUF565) Predicted transmembrane protein found in plants, chloroplasts and cyanobacteria. This family is also known as YCF20. (from Pfam) NF016381.5 PF04492.18 Phage_rep_O 28.7 28.7 95 domain Y Y N replication protein GO:0006260 6239082 2 Bacteria superkingdom 14751 EBI-EMBL Bacteriophage replication protein O replication protein Replication protein O is necessary for the initiation of bacteriophage DNA replication. Protein O interacts with the lambda replication origin, and also with replication protein P to form an oligomer [1]. It is speculated that the N-terminal half interacts with the replication origin while the C terminal half mediates protein-protein interaction (annotation of Swiss: P14815). [1]. 6239082. Bacteriophage lambda replication proteins: formation of a mixed oligomer and binding to the origin of lambda DNA. Zylicz M, Gorska I, Taylor K, Georgopoulos C;. Mol Gen Genet 1984;196:401-406. (from Pfam) NF016394.5 PF04505.17 CD225 27.1 27.1 68 domain Y Y N CD225/dispanin family protein GO:0016020 22363774,7559564 2 Bacteria superkingdom 5490 EBI-EMBL Interferon-induced transmembrane protein CD225/dispanin family protein This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression [1]. [1]. 7559564. Expression cloning of an interferon-inducible 17-kDa membrane protein implicated in the control of cell growth. Deblandre GA, Marinx OP, Evans SS, Majjaj S, Leo O, Caput D, Huez GA, Wathelet MG;. J Biol Chem 1995;270:23860-23866. [2]. 22363774. The dispanins: a novel gene family of ancient origin that contains 14 human members. Sallman Almen M, Bringeland N, Fredriksson R, Schioth HB;. PLoS One. 2012;7:e31961. (from Pfam) NF016400.5 PF04511.20 DER1 26.6 26.6 191 PfamEq Y N N Der1-like family 8631297 2 Bacteria superkingdom 106 EBI-EMBL Der1-like family Der1-like family The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae contains of proteolytic system able to selectively degrade misfolded lumenal secretory proteins. For examination of the components involved in this degradation process, mutants were isolated. They could be divided into four complementation groups. The mutations led to stabilisation of two different substrates for this process. The mutant classes were called 'der' for 'degradation in the ER'. DER1 was cloned by complementation of the der1-2 mutation. The DER1 gene codes for a novel, hydrophobic protein, that is localised to the ER. Deletion of DER1 abolished degradation of the substrate proteins. The function of the Der1 protein seems to be specifically required for the degradation process associated with the ER [1]. Interestingly this family seems distantly related to the Rhomboid family of membrane peptidases. Suggesting that this family may also mediate degradation of misfolded proteins (Bateman A pers. obs.). [1]. 8631297. Der1, a novel protein specifically required for endoplasmic reticulum degradation in yeast. Knop M, Finger A, Braun T, Hellmuth K, Wolf DH;. EMBO J 1996;15:753-763. (from Pfam) NF016419.5 PF04531.18 Phage_holin_1 22 22 82 PfamEq Y Y N phage holin 11459934 2 Bacteria superkingdom 6182 EBI-EMBL Bacteriophage holin phage holin This family of holins is found in several staphylococcal and streptococcal bacteriophages. Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis. It is thought that the temporal precision of holin-mediated lysis may occur through the buildup of a holin oligomer which causes the lysis [1]. [1]. 11459934. Holins kill without warning. Grundling A, Manson MD, Young R;. Proc Natl Acad Sci U S A 2001;98:9348-9352. (from Pfam) NF016423.5 PF04535.17 CASP_dom 26.2 26.2 151 domain Y Y N CASP protein domain-containing protein 21593871,24920445 2 Bacteria superkingdom 4 EBI-EMBL Casparian strip membrane protein domain Casparian strip membrane protein domain This domain is found mainly in plant proteins known as Casparian strip membrane proteins (CASPs) and CASP-like proteins (CASPLs). CASPs are four-membrane-span proteins that mediate the deposition of Casparian strips in the endodermis by recruiting the lignin polymerization machinery. Interestingly, the CASP first extracellular loop was found conserved in euphyllophytes but absent in plants lacking Casparian strips [1,2]. [1]. 21593871. A novel protein family mediates Casparian strip formation in the endodermis. Roppolo D, De Rybel B, Denervaud Tendon V, Pfister A, Alassimone J, Vermeer JE, Yamazaki M, Stierhof YD, Beeckman T, Geldner N;. Nature. 2011;473:380-383. [2]. 24920445. Functional and Evolutionary Analysis of the CASPARIAN STRIP MEMBRANE DOMAIN PROTEIN Family. Roppolo D, Boeckmann B, Pfister A, Boutet E, Rubio MC, Denervaud-Tendon V, Vermeer JE, Gheyselinck J, Xenarios I, Geldner N;. Plant Physiol. 2014;165:1709-1722. (from Pfam) NF016427.5 PF04539.21 Sigma70_r3 25.3 25.3 78 domain Y Y N sigma-70 domain-containing protein GO:0003700,GO:0006352,GO:0006355 11931761 2 Bacteria superkingdom 178981 EBI-EMBL Sigma-70 region 3 Sigma-70 region 3 Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [1]. [1]. 11931761. Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA;. Mol Cell 2002;9:527-539. (from Pfam) NF016430.5 PF04542.19 Sigma70_r2 24 24 71 domain Y Y N sigma factor GO:0003700,GO:0006352,GO:0006355 11931761,8858155 2 Bacteria superkingdom 1140895 EBI-EMBL Sigma-70 region 2 sigma factor This HMM hits a core region shared by multiple sigma factors, interchangeable subunits that complete the RNA polymerase holoenzyme and allow transcription to start. In E. coli K-12 alone, this HMM hits RpoD (sigma-70), RpoH (sigma-32), FliA (sigma-28), FecI (sigma-19), RpoS, and RpoE. NF016433.5 PF04546.18 Sigma70_ner 29.7 29.7 210 PfamEq Y N N Sigma-70, non-essential region GO:0003677,GO:0003700,GO:0006352,GO:0006355,GO:0016987 11931761,8858155 2 Bacteria superkingdom 24582 EBI-EMBL Sigma-70, non-essential region Sigma-70, non-essential region The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. [1]. 11931761. Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA;. Mol Cell 2002;9:527-539. [2]. 8858155. Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Malhotra A, Severinova E, Darst SA;. Cell 1996;87:127-136. (from Pfam) NF016438.5 PF04551.19 GcpE 32 32 343 PfamEq Y Y N flavodoxin-dependent (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase 1.17.7.3 GO:0016114,GO:0046429 11274098,1521767 2 Bacteria superkingdom 58663 EBI-EMBL GcpE protein flavodoxin-dependent (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase In a variety of organisms, including plants and several eubacteria, isoprenoids are synthesised by the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Although different enzymes of this pathway have been described, the terminal biosynthetic steps of the MEP pathway have not been fully elucidated. GcpE gene of Escherichia coli is involved in this pathway [2]. [1]. 1521767. Sequence and characterization of the gcpE gene of Escherichia coli. Baker J, Franklin DB, Parker J;. FEMS Microbiol Lett 1992;73:175-180. [2]. 11274098. GcpE is involved in the 2-C-methyl-D-erythritol 4-phosphate pathway of isoprenoid biosynthesis in Escherichia coli. Altincicek B, Kollas AK, Sanderbrand S, Wiesner J, Hintz M, Beck E, Jomaa H;. J Bacteriol 2001;183:2411-2416. (from Pfam) NF016439.5 PF04552.18 Sigma54_DBD 22.8 22.8 160 domain Y N N Sigma-54, DNA binding domain GO:0001216 10894718 2 Bacteria superkingdom 50175 EBI-EMBL Sigma-54, DNA binding domain Sigma-54, DNA binding domain This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore this region contains a putative helix-turn-helix motif. At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [1]. [1]. 10894718. The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor. Buck M, Gallegos MT, Studholme DJ, Guo Y, Gralla JD;. J Bacteriol 2000;182:4129-4136. (from Pfam) NF016459.5 PF04572.17 Gb3_synth 22.3 22.3 131 PfamEq Y N N Alpha 1,4-glycosyltransferase conserved region 10854428 2 Bacteria superkingdom 471 EBI-EMBL Alpha 1,4-glycosyltransferase conserved region Alpha 1,4-glycosyltransferase conserved region The glycosphingolipids (GSL) form part of eukaryotic cell membranes. They consist of a hydrophilic carbohydrate moiety linked to a hydrophobic ceramide tail embedded within the lipid bilayer of the membrane. Lactosylceramide, Gal1,4Glc1Cer (LacCer), is the common synthetic precursor to the majority of GSL found in vertebrates. Alpha 1.4-glycosyltransferases utilise UDP donors and transfer the sugar to a beta-linked acceptor. This region appears to be confined to higher eukaryotes. No function has been yet assigned to this region [1]. [1]. 10854428. Cloning of Gb3 synthase, the key enzyme in globo-series glycosphingolipid synthesis, predicts a family of alpha 1, 4-glycosyltransferases conserved in plants, insects, and mammals. Keusch JJ, Manzella SM, Nyame KA, Cummings RD, Baenziger JU;. J Biol Chem 2000;275:25315-25321. (from Pfam) NF016462.5 PF04575.18 SlipAM 22 22 288 domain Y Y N surface lipoprotein assembly modifier GO:0009279 27572441,28620585 2 Bacteria superkingdom 9874 EBI-EMBL Surface lipoprotein assembly modifier surface lipoprotein assembly modifier Surface lipoprotein assembly modifier (Slam) is a surface lipoprotein that may have a role in virulence [1]. In Neisseria, it is required for the surface display of lipidated virulence factors [2]. Proteins in this family contain an eight-stranded beta-barrel domain [1]. [1]. 28620585. Identification of a Large Family of Slam-Dependent Surface Lipoproteins in Gram-Negative Bacteria. Hooda Y, Lai CCL, Moraes TF;. Front Cell Infect Microbiol. 2017;7:207. [2]. 27572441. Slam is an outer membrane protein that is required for the surface display of lipidated virulence factors in Neisseria. Hooda Y, Lai CC, Judd A, Buckwalter CM, Shin HE, Gray-Owen SD, Moraes TF;. Nat Microbiol. 2016;1:16009. (from Pfam) NF016473.5 PF04588.18 HIG_1_N 22.4 22.4 52 PfamEq Y Y N HIG1 domain-containing protein 11172064 2 Bacteria superkingdom 4973 EBI-EMBL Hypoxia induced protein conserved region Hypoxia induced protein conserved region This family is found in proteins thought to be involved in the response to hypoxia. Family members mostly come from diverse eukaryotic organisms however eubacterial members have been identified. This region is found at the N-terminus of the member proteins which are predicted to be transmembrane [1]. [1]. 11172064. Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Gracey AY, Troll JV, Somero GN;. Proc Natl Acad Sci U S A 2001;98:1993-1998. (from Pfam) NF016486.5 PF04604.18 L_biotic_typeA 21.7 21.7 50 subfamily Y Y N type A2 lanthipeptide GO:0005576,GO:0042742 7601145 2 Bacteria superkingdom 466 EBI-EMBL Type-A lantibiotic type A2 lanthipeptide Lantibiotics are antibiotic peptides distinguished by the presence of the rare thioether amino acids lanthionine and/or methyl-lanthionine. They are produced by Gram-positive bacteria as gene-encoded precursor peptides and undergo post-translational modification to generate the mature peptide. Based on their structural and functional features lantibiotics are currently divided into two major groups: the flexible amphiphilic type-A and the rather rigid and globular type-B. Type-A lantibiotics act primarily by pore formation in the bacterial membrane by a mechanism involving the interaction with specific docking molecules such as the membrane precursor lipid II [1]. [1]. 7601145. Biosynthesis and biological activities of lantibiotics with unique post-translational modifications. Sahl HG, Jack RW, Bierbaum G;. Eur J Biochem 1995;230:827-853. (from Pfam) NF016487.5 PF04606.17 Ogr_Delta 26.3 26.3 47 domain Y Y N ogr/Delta-like zinc finger family protein 1597424,9143285 2 Bacteria superkingdom 14706 EBI-EMBL Ogr/Delta-like zinc finger ogr/Delta-like zinc finger family protein This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes [1]. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [2]. This family also includes zinc fingers in recombinase proteins. [1]. 1597424. Escherichia coli K-12 and B contain functional bacteriophage P2 ogr genes. Slettan A, Gebhardt K, Kristiansen E, Birkeland NK, Lindqvist BH;. J Bacteriol 1992;174:4094-4100. [2]. 9143285. The two P2 Ogr-like domains of the delta protein from bacteriophage P4 are required for activity. Julien B, Lefevre P, Calendar R;. Virology 1997;230:292-299. (from Pfam) NF016491.5 PF04610.19 TrbL 25.9 25.9 215 domain Y Y N type IV secretion system protein GO:0030255 10438776,9679196 2 Bacteria superkingdom 38184 EBI-EMBL TrbL/VirB6 plasmid conjugal transfer protein type IV secretion system protein NF016493.5 PF04612.17 T2SSM 27.8 27.8 160 subfamily Y Y N type II secretion system protein GspM gspM GO:0015627,GO:0015628 10322014,14600218,15223057,19299134 2 Bacteria superkingdom 17776 EBI-EMBL Type II secretion system (T2SS), protein M type II secretion system protein GspM This family of membrane proteins consists of Type II secretion system protein M sequences from several Gram-negative (diderm) bacteria. The precise function of these proteins is unknown, though in Vibrio cholerae, the T2SM (EpsM) protein interacts with the T2SL (EpsL) protein, and also forms homodimers [1]. [1]. 10322014. Direct interaction of the EpsL and EpsM proteins of the general secretion apparatus in Vibrio cholerae. Sandkvist M, Hough LP, Bagdasarian MM, Bagdasarian M;. J Bacteriol 1999;181:3129-3135. [2]. 15223057. The general secretory pathway: a general misnomer?. Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR;. Trends Microbiol. 2004;12:306-309. [3]. 14600218. Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella. Peabody CR, Chung YJ, Yen MR, Vidal-Ingigliardi D, Pugsley AP, Saier MH Jr;. Microbiology. 2003;149:3051-3072. [4]. 19299134. Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Desvaux M, Hebraud M, Talon R, Henderson IR;. Trends Microbiol. 2009;17:139-145. (from Pfam) NF016501.5 PF04620.17 FlaA 25 25 230 domain Y Y N flagellar filament outer layer protein FlaA GO:0030288,GO:0071973 2194955,8990312 2 Bacteria superkingdom 1218 EBI-EMBL Flagellar filament outer layer protein Flaa flagellar filament outer layer protein FlaA Periplasmic flagella are the organelles of spirochete mobility, and are structurally different from the flagella of other motile bacteria. They reside inside the cell within the periplasmic space, and confer mobility in viscous gel-like media such connective tissue [1]. The flagella are composed of an outer sheath of FlaA proteins and a core filament of FlaB proteins. Each species usually has several FlaA protein species [2]. [1]. 2194955. Expression in Escherichia coli of the 37-kilodalton endoflagellar sheath protein of Treponema pallidum by use of the polymerase chain reaction and a T7 expression system. Isaacs RD, Radolf JD;. Infect Immun 1990;58:2025-2034. [2]. 8990312. An unexpected flaA homolog is present and expressed in Borrelia burgdorferi. Ge Y, Charon NW;. J Bacteriol 1997;179:552-556. (from Pfam) NF016511.5 PF04630.17 Phage_TTP_1 22 22 199 domain Y Y N phage tail protein 23542344 2 Bacteria superkingdom 5484 EBI-EMBL Phage tail tube protein phage tail protein This is a family of phage tail tube proteins from Myoviridae. [1]. 23542344. A conserved spiral structure for highly diverged phage tail assembly chaperones. Pell LG, Cumby N, Clark TE, Tuite A, Battaile KP, Edwards AM, Chirgadze NY, Davidson AR, Maxwell KL;. J Mol Biol. 2013;425:2436-2449. (from Pfam) NF016515.5 PF04634.17 YezG-like 21.7 21.7 146 subfamily Y Y N immunity protein YezG family protein 34280190 2 Bacteria superkingdom 11704 EBI-EMBL Immunity protein YezG-like DUF600 family protein This protein family includes the immunity protein YezG from Bacillus subtilis and similar sequences predominantly found in Firmicutes. YezG is the antitoxin component of a LXG toxin-antitoxin (TA) module that promote kin selection, mediate competition in biofilms, and drive spatial segregation of different strains, probably helping to avoid warfare between strains in biofilms [1]. It shows an alpha/beta structure with an antiparallel beta-sheet. [1]. 34280190. Diverse LXG toxin and antitoxin systems specifically mediate intraspecies competition in Bacillus subtilis biofilms. Kobayashi K;. PLoS Genet. 2021;17:e1009682. (from Pfam) NF016524.5 PF04645.17 DUF603 22.6 22.6 181 domain Y Y N DUF603 domain-containing protein 2 Bacteria superkingdom 908 EBI-EMBL Protein of unknown function, DUF603 Protein of unknown function, DUF603 This family includes several uncharacterised proteins from Borrelia species. (from Pfam) NF016526.5 PF04647.20 AgrB 23 23 185 domain Y Y N accessory gene regulator B family protein GO:0008233,GO:0009372,GO:0016020 11195102 2 Bacteria superkingdom 8349 EBI-EMBL Accessory gene regulator B accessory gene regulator B family protein The arg locus consists of two transcripts: RNAII and RNAIII. RNAII encodes four genes (agrA, B, C, and D) whose gene products assemble a quorum sensing system. AgrB and AgrD are essential for the production of the autoinducing peptide which functions as a signal for quorum sensing. AgrB is a transmembrane protein [1]. [1]. 11195102. Inducible expression and cellular location of AgrB, a protein involved in the maturation of the staphylococcal quorum-sensing pheromone. Saenz HL, Augsburger V, Vuong C, Jack RW, Gotz F, Otto M;. Arch Microbiol 2000;174:452-455. (from Pfam) NF016533.5 PF04655.19 APH_6_hur 27 27 252 domain Y Y N aminoglycoside phosphotransferase family protein GO:0006468,GO:0016773,GO:0019748 1316866,3029728,9211644 2 Bacteria superkingdom 33006 EBI-EMBL Aminoglycoside/hydroxyurea antibiotic resistance kinase aminoglycoside phosphotransferase family protein The aminoglycoside phosphotransferases achieve inactivation of their antibiotic substrates by phosphorylation utilising ATP. Likewise hydroxyurea is inactivated by phosphorylation of the hydroxy group in the hydroxylamine moiety [1,2,3]. [1]. 3029728. Nucleotide sequence of the streptomycinphosphotransferase and amidinotransferase genes from Streptomyces griseus. Tohyama H, Okami Y, Umezawa H;. Nucleic Acids Res 1987;15:1819-1833. [2]. 9211644. Bacterial resistance to aminoglycoside antibiotics. Davies J, Wright GD;. Trends Microbiol 1997;5:234-240. [3]. 1316866. A gene (hur) from Streptomyces aureofaciens, conferring resistance to hydroxyurea, is related to genes encoding streptomycin phosphotransferase. Kormanec J, Farkasovsky M, Potuckova L, Godar S;. Gene 1992;114:133-137. (from Pfam) NF016541.5 PF04663.17 Phenol_monoox 27 27 66 domain Y Y N phenol hydroxylase subunit P4 1.14.13.7 GO:0018662 11571188,2254258 2 Bacteria superkingdom 1794 EBI-EMBL Phenol hydroxylase conserved region phenol hydroxylase subunit P4 Under aerobic conditions, phenol is usually hydroxylated to catechol and degraded via the meta or ortho pathways. Two types of phenol hydroxylase are known: one is a multi-component enzyme the other is a single-component monooxygenase. This region is found in both types of enzymes [1,2]. [1]. 2254258. Complete nucleotide sequence and polypeptide analysis of multicomponent phenol hydroxylase from Pseudomonas sp. strain CF600. Nordlund I, Powlowski J, Shingler V;. J Bacteriol 1990;172:6826-6833. [2]. 11571188. Genetic and functional analysis of the tbc operons for catabolism of alkyl- and chloroaromatic compounds in Burkholderia sp. strain JS150. Kahng HY, Malinverni JC, Majko MM, Kukor JJ;. Appl Environ Microbiol 2001;67:4805-4816. (from Pfam) NF016542.5 PF04664.18 OGFr_N 22 22 208 domain Y Y N opioid growth factor receptor-related protein GO:0016020,GO:0038023 11890982 2 Bacteria superkingdom 1270 EBI-EMBL Opioid growth factor receptor (OGFr) conserved region opioid growth factor receptor-related protein Most known members of this family, the opioid growth factor receptor family, are eukaryotic, but more than ten percent are bacterial. NF016550.5 PF04672.17 Methyltransf_19 26 26 268 domain Y Y N SAM-dependent methyltransferase 2.1.1.- 18154359 2 Bacteria superkingdom 75182 EBI-EMBL S-adenosyl methyltransferase SAM-dependent methyltransferase This family contains a SAM (S-adenosyl methyltransferase) domain, with a central beta sheet with 3 alpha-helices on both sides. Crystal packing analysis of the structure PDB:3giw from Swiss:Q82L35 suggests that a monomer is the solution state oligomeric form. An unidentified ligand (UNL, cyan) was found at the putative active site surrounded by the residues His57, His170, Phe171, Tyr216 and Met22 . The UNL is likely to be a phenylalanine or phenylalanine-like molecule. (details derived from TOPSAN). [1]. 18154359. The histamine N-methyltransferase T105I polymorphism affects active site structure and dynamics. Rutherford K, Parson WW, Daggett V;. Biochemistry. 2008;47:893-901. (from Pfam) NF016551.5 PF04673.17 Cyclase_polyket 24.4 24.4 104 subfamily Y Y N TcmI family type II polyketide cyclase GO:0030639 2 Bacteria superkingdom 6344 EBI-EMBL Polyketide synthesis cyclase TcmI family type II polyketide cyclase This family represents a number of cyclases involved in polyketide synthesis in a number of actinobacterial species. (from Pfam) NF016552.5 PF04674.17 Phi_1 25 25 276 PfamEq Y N N Phosphate-induced protein 1 conserved region 10189698 2 Bacteria superkingdom 87 EBI-EMBL Phosphate-induced protein 1 conserved region Phosphate-induced protein 1 conserved region Family of conserved plant proteins. Conserved region identified in a phosphate-induced protein of unknown function [1]. [1]. 10189698. Phosphate as a limiting factor for the cell division of tobacco BY-2 cells. Sano T, Kuraya Y, Amino S, Nagata T;. Plant Cell Physiol 1999;40:1-8. (from Pfam) NF016565.5 PF04687.17 Microvir_H 22.7 22.7 310 PfamEq Y N N Microvirus H protein (pilot protein) GO:0046718 10225278,24336205,8158636,8433365 2 Bacteria superkingdom 28 EBI-EMBL Microvirus H protein (pilot protein) Microvirus H protein (pilot protein) A single molecule of H protein is found on each of the 12 spikes on the microvirus shell. H is involved in the ejection of the phage DNA, and at least one copy is injected into the host's periplasmic space along with the ssDNA viral genome [1]. Part of H is thought to lie outside the shell, where it recognises lipopolysaccharide from virus-sensitive strains [2]. Part of H may lie within the capsid, since mutations in H can influence the DNA ejection mechanism by affecting the DNA-protein interactions [3]. H may span the capsid through the hydrophilic channels formed by G proteins [1]. Elucidation of the DNA-ejection mechanism from the crystal structure of part of the H protein shows that this tail-less icosahedral, single-stranded DNA phiX174-like coliphage bacteriophage requires H as a pilot protein for its DNA-delivery. H oligomerises to form a tube the function of which seems to be the delivery of the DNA genome across the host's periplasmic space into the host cytoplasm. The tube is constructed of ten alpha-helices with their amino termini arrayed in a right-handed super-helical coiled-coil and their carboxy termini arrayed in a left-handed super-helical coiled-coil. The tube spans the periplasmic space and is present while the genome is being delivered into the host cell's cytoplasm [4]. [1]. 8158636. Analysis of the single-stranded DNA bacteriophage phi X174, refined at a resolution of 3.0 A. McKenna R, Ilag LL, Rossmann MG;. J Mol Biol 1994;237:517-543. [2]. 10225278. Specific interaction of fused H protein of bacteriophage phiX174 with receptor lipopolysaccharides. Suzuki R, Inagaki M, Karita S, Kawaura T, Kato . TRUNCATED at 1650 bytes (from Pfam) NF016566.5 PF04688.18 Holin_SPP1 27 27 74 subfamily Y Y N phage holin 11459934,17012400 2 Bacteria superkingdom 4061 EBI-EMBL SPP1 phage holin SPP1-type phage holin This family constitutes holin proteins from the dsDNA Siphidoviridae group bacteriophages with two transmembrane segments. Most bacteriophages require an endolysin and a holin for host lysis. During late gene expression, holins accumulate and oligomerise in the host cell membrane. They then suddenly trigger to permeablise the membrane, which causes lysis by allowing endolysin to attach the peptidoglycan. There are thought to be at least 35 different families of holin genes [1]. [1]. 11459934. Holins kill without warning. Grundling A, Manson MD, Young R;. Proc Natl Acad Sci U S A 2001;98:9348-9352. [2]. 17012400. Abortive phage resistance mechanism AbiZ speeds the lysis clock to cause premature lysis of phage-infected Lactococcus lactis. Durmaz E, Klaenhammer TR;. J Bacteriol. 2007;189:1417-1425. (from Pfam) NF016583.5 PF04705.17 TSNR_N 28.3 28.3 111 PfamEq Y N N Thiostrepton-resistance methylase, N terminus GO:0008649,GO:0046677 2 Bacteria superkingdom 433 EBI-EMBL Thiostrepton-resistance methylase, N terminus Thiostrepton-resistance methylase, N terminus This region is found in some members of the SpoU-type rRNA methylase family (Pfam:PF00588). (from Pfam) NF016584.5 PF04706.17 Dickkopf_N 21.3 21.3 51 domain Y Y N Dickkopf N-terminal cysteine-rich domain-containing protein GO:0005576,GO:0007275,GO:0030178 12167704,9663378 2 Bacteria superkingdom 321 EBI-EMBL Dickkopf N-terminal cysteine-rich region Dickkopf N-terminal cysteine-rich region Dickkopf proteins are a class of Wnt antagonists. They possess two conserved cysteine-rich regions. This family represents the N-terminal one [1]. The C-terminal region has been found to share significant sequence similarity to the colipase fold, Pfam:PF01114, Pfam:PF02740 [2]. [1]. 12167704. Regulation of Wnt/LRP signaling by distinct domains of Dickkopf proteins. Brott BK, Sokol SY;. Mol Cell Biol 2002;22:6100-6110. [2]. 9663378. A colipase fold in the carboxy-terminal domain of the Wnt antagonists--the Dickkopfs. Aravind L, Koonin EV;. Curr Biol 1998;8:477-478. (from Pfam) NF016595.5 PF04717.17 Phage_base_V 23.8 23.8 75 domain Y Y N phage baseplate assembly protein V 22325780,24381728,7483254 2 Bacteria superkingdom 177019 EBI-EMBL Type VI secretion system/phage-baseplate injector OB domain Type VI secretion system/phage-baseplate injector OB domain Family of bacterial and phage baseplate assembly proteins responsible for forming the small spike at the end of the tail or bacterial pathogenic needle-shaft [1]. This entry represents the OB fold part of the structure. This structure contains an unusual extra beta hairpin that forms the foundation of the spike protein's beta helix [3]. [1]. 7483254. Bacteriophage P2: genes involved in baseplate assembly. Haggard-Ljungquist E, Jacobsen E, Rishovd S, Six EW, Nilssen O, Sunshine MG, Lindqvist BH, Kim KJ, Barreiro V, Koonin EV, et al.;. Virology 1995;213:109-121. [2]. 24381728. The rise of the Type VI secretion system. Filloux A;. F1000Prime Rep. 2013;5:52. [3]. 22325780. Phage pierces the host cell membrane with the iron-loaded spike. Browning C, Shneider MM, Bowman VD, Schwarzer D, Leiman PG;. Structure. 2012;20:326-339. (from Pfam) NF016601.5 PF04723.19 GRDA 22 22 147 domain Y N N Glycine reductase complex selenoprotein A GO:0030699,GO:0030700,GO:0050485 11797052,2963330 2 Bacteria superkingdom 1135 EBI-EMBL Glycine reductase complex selenoprotein A Glycine reductase complex selenoprotein A Found in clostridia, this protein contains one active site selenocysteine and catalyses the reductive deamination of glycine, which is coupled to the esterification of orthophosphate resulting in the formation of ATP [1]. A member of this family may also exist in Treponema denticola [2]. [1]. 2963330. Selenoprotein A of the clostridial glycine reductase complex: purification and amino acid sequence of the selenocysteine-containing peptide. Sliwkowski MX, Stadtman TC;. Proc Natl Acad Sci U S A 1988;85:368-371. [2]. 11797052. Selenium-dependent growth of Treponema denticola: evidence for a clostridial-type glycine reductase. Rother M, Bock A, Wyss C;. Arch Microbiol 2001;177:113-116. (from Pfam) NF016603.5 PF04725.17 PsbR 22.5 22.5 98 PfamEq Y Y N photosystem II protein PsbR psbR GO:0009523,GO:0009654,GO:0015979,GO:0042651 2644135 2 Bacteria superkingdom 47 EBI-EMBL Photosystem II 10 kDa polypeptide PsbR photosystem II protein PsbR This protein is associated with the oxygen-evolving complex of photosystem II. Its function in photosynthesis is not known. The C-terminal hydrophobic region functions as a thylakoid transfer signal but is not removed [1]. [1]. 2644135. A 10 kDa polypeptide associated with the oxygen-evolving complex of photosystem II has a putative C-terminal non-cleavable thylakoid transfer domain. Webber AN, Packman LC, Gray JC;. FEBS Lett 1989;242:435-438. (from Pfam) NF016606.5 PF04728.18 LPP 29.1 29.1 53 domain Y Y N LPP leucine zipper domain-containing protein GO:0019867 10843861,12054830,12741822,15520380,16828114 2 Bacteria superkingdom 1831 EBI-EMBL Lipoprotein leucine-zipper Lipoprotein leucine-zipper This is leucine-zipper is found in the enterobacterial outer membrane lipoprotein LPP. It is likely that this domain oligomerises and is involved in protein-protein interactions. As such it is a bundle of alpha-helical coiled-coils, which are known to play key roles in mediating specific protein-protein interactions for in molecular recognition and the assembly of multi-protein complexes. [1]. 10843861. Core structure of the outer membrane lipoprotein from Escherichia coli at 1.9 A resolution. Shu W, Liu J, Ji H, Lu M;. J Mol Biol. 2000;299:1101-1112. [2]. 12054830. Core side-chain packing and backbone conformation in Lpp-56 coiled-coil mutants. Liu J, Cao W, Lu M;. J Mol Biol. 2002;318:877-888. [3]. 12741822. Zinc-mediated helix capping in a triple-helical protein. Liu J, Dai J, Lu M;. Biochemistry. 2003;42:5657-5664. [4]. 15520380. Atomic structure of a tryptophan-zipper pentamer. Liu J, Yong W, Deng Y, Kallenbach NR, Lu M;. Proc Natl Acad Sci U S A. 2004;101:16156-16161. [5]. 16828114. Conformational transition between four and five-stranded phenylalanine zippers determined by a local packing interaction. Liu J, Zheng Q, Deng Y, Kallenbach NR, Lu M;. J Mol Biol. 2006;361:168-179. (from Pfam) NF016608.5 PF04730.17 Agro_virD5 25 25 672 PfamEq Y N N Agrobacterium VirD5 protein 3658701 2 Bacteria superkingdom 125 EBI-EMBL Agrobacterium VirD5 protein Agrobacterium VirD5 protein The virD operon in Agrobacterium encodes a site-specific endonuclease, and a number of other poorly characterised products. This family represents the VirD5 protein. [1]. 3658701. Molecular characterization of the virD operon from Agrobacterium tumefaciens. Porter SG, Yanofsky MF, Nester EW;. Nucleic Acids Res 1987;15:7503-7517. (from Pfam) NF016615.5 PF04738.18 Lant_dehydr_N 28 28 649 domain Y Y N lantibiotic dehydratase 10215865,12127987,1539969,25363770 2 Bacteria superkingdom 24934 EBI-EMBL Lantibiotic dehydratase, N terminus lantibiotic dehydratase Lantibiotics are ribosomally synthesised antimicrobial agents derived from ribosomally synthesised peptides [1]. They are produced by bacteria of the Firmicutes phylum, and include mutacin, subtilin, and nisin. Lantibiotic peptides contain thioether bridges termed lanthionines that are thought to be generated by dehydration of serine and threonine residues followed by addition of cysteine residues [2]. This family constitutes the N-terminus of the enzyme proposed to catalyse the dehydration step [2],[3] via glutamylation of the substrate during lantibiotic biosynthesis. The enzyme dehydrates Ser/Thr residues in the precursor by glutamylation [4]. [1]. 1539969. Analysis of genes involved in biosynthesis of the lantibiotic subtilin. Klein C, Kaletta C, Schnell N, Entian KD;. Appl Environ Microbiol 1992;58:132-142. [2]. 12127987. Heterologous expression and purification of SpaB involved in subtilin biosynthesis. Xie L, Chatterjee C, Balsara R, Okeley NM, van der Donk WA;. Biochem Biophys Res Commun 2002;295:952-957. [3]. 10215865. Post-translational modification of nisin. The involvement of NisB in the dehydration process. Karakas Sen A, Narbad A, Horn N, Dodd HM, Parr AJ, Colquhoun I, Gasson MJ;. Eur J Biochem 1999;261:524-532. [4]. 25363770. Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB. Ortega MA, Hao Y, Zhang Q, Walker MC, van der Donk WA, Nair SK;. Nature. 2014; [Epub ahead of print] (from Pfam) NF016623.5 PF04748.18 Polysacc_deac_2 27.5 27.5 212 PfamEq Y Y N divergent polysaccharide deacetylase family protein 2 Bacteria superkingdom 23694 EBI-EMBL Divergent polysaccharide deacetylase divergent polysaccharide deacetylase family protein This family is divergently related to Pfam:PF01522 (personal obs:Yeats C). (from Pfam) NF016625.5 PF04750.19 Far-17a_AIG1 24.5 24.5 206 PfamEq Y N N FAR-17a/AIG1-like protein GO:0016020 11266118,2045681 2 Bacteria superkingdom 305 EBI-EMBL FAR-17a/AIG1-like protein FAR-17a/AIG1-like protein This family includes the hamster androgen-induced FAR-17a protein (Swiss:Q60534) [1], and its human homologue, the AIG1 protein (Swiss:Q9NVV5) [2]. The function of these proteins is unknown. This family also includes homologous regions from a number of other metazoan proteins. [1]. 2045681. Isolation and characterization of cDNA for an androgen-regulated mRNA in the flank organ of hamsters. Seki T, Ideta R, Shibuya M, Adachi K;. J Invest Dermatol 1991;96:926-931. [2]. 11266118. Cloning of androgen-inducible gene 1 (AIG1) from human dermal papilla cells. Seo J, Kim J, Kim M;. Mol Cells 2001;11:35-40. (from Pfam) NF016627.5 PF04752.17 ChaC 21 21 176 domain Y Y N gamma-glutamylcyclotransferase GO:0003839,GO:0006751,GO:0061928 23070364,25716890 2 Bacteria superkingdom 17673 EBI-EMBL ChaC-like protein gamma-glutamylcyclotransferase The ChaC family of proteins function as gamma-glutamyl cyclotransferases acting specifically to degrade glutathione but not other gamma-glutamyl peptides [1, 2]. It is is conversed across all phyla and represents a new pathway for glutathione degradation in living cells. [1]. 23070364. Mammalian proapoptotic factor ChaC1 and its homologues function as gamma-glutamyl cyclotransferases acting specifically on glutathione. Kumar A, Tikoo S, Maity S, Sengupta S, Sengupta S, Kaur A, Bachhawat AK;. EMBO Rep. 2012;13:1095-1101. [2]. 25716890. Defining the cytosolic pathway of glutathione degradation in Arabidopsis thaliana: role of the ChaC/GCG family of gamma-glutamyl cyclotransferases as glutathione-degrading enzymes and AtLAP1 as the Cys-Gly peptidase. Kumar S, Kaur A, Chattopadhyay B, Bachhawat AK;. Biochem J. 2015;468:73-85. (from Pfam) NF016629.5 PF04754.17 Transposase_31 21 21 203 domain Y Y N Rpn family recombination-promoting nuclease/putative transposase 2 Bacteria superkingdom 32946 EBI-EMBL Putative transposase, YhgA-like Rpn family recombination-promoting nuclease/putative transposase This family of putative transposases includes the YhgA sequence from Escherichia coli (Swiss:P31667) and several prokaryotic homologues. (from Pfam) NF016630.5 PF04755.17 PAP_fibrillin 22 22 198 domain Y Y N PAP/fibrillin family protein 9839468 2 Bacteria superkingdom 1511 EBI-EMBL PAP_fibrillin PAP/fibrillin family protein This family identifies a conserved region found in a number of plastid lipid-associated proteins (PAPs), and in a number of putative fibrillin proteins. [1]. 9839468. Molecular characterization of CDSP 34, a chloroplastic protein induced by water deficit in Solanum tuberosum L. plants, and regulation of CDSP 34 expression by ABA and high illumination. Gillet B, Beyly A, Peltier G, Rey P;. Plant J 1998;16:257-262. (from Pfam) NF016637.5 PF04762.17 IKI3 23.4 23.4 932 domain Y N N IKI3 family GO:0002098,GO:0033588 10024884 2 Bacteria superkingdom 233 EBI-EMBL IKI3 family IKI3 family Members of this family are components of the elongator multi-subunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation [1]. This region contains WD40 like repeats. [1]. 10024884. Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. Otero G, Fellows J, Li Y, de Bizemont T, Dirac AM, Gustafsson CM, Erdjument-Bromage H, Tempst P, Svejstrup JQ;. Mol Cell 1999;3:109-118. (from Pfam) NF016643.5 PF04768.18 NAT 27 27 168 PfamEq Y N N NAT, N-acetyltransferase, of N-acetylglutamate synthase 22174908,22529931,23894642 2 Bacteria superkingdom 1535 EBI-EMBL NAT, N-acetyltransferase, of N-acetylglutamate synthase NAT, N-acetyltransferase, of N-acetylglutamate synthase This is the C-terminal NAT or N-acetyltransferase domain of bifunctional N-acetylglutamate synthase/kinases. It catalyzes the first two steps in arginine biosynthesis. This domain contains the putative NAGS - N-acetylglutamate synthase - active site. It is found at the C-terminus of Neurospora crassa acetylglutamate synthase - amino-acid acetyltransferase, EC: 2.3.1.1. It is also found C-terminal to the amino acid kinase region (Pfam:PF00696) in some fungal acetylglutamate kinase enzymes [1]. it stabilises the yeast NAGK, N-acetyl-L-glutamate kinase, slows catalysis and modulates feed-back inhibition by arginine [2]. This domain is found to be the N-acetyltransferase (NAT) domain, and it has a typical GCN5-related NAT fold and a site that catalyzes NAG synthesis which is located >25 Angstrom away from the L-arginine binding site in the N-temrinal domain Pfam:PF00696 [3]. [1]. 22174908. A novel N-acetylglutamate synthase architecture revealed by the crystal structure of the bifunctional enzyme from Maricaulis maris. Shi D, Li Y, Cabrera-Luque J, Jin Z, Yu X, Zhao G, Haskins N, Allewell NM, Tuchman M;. PLoS One. 2011;6:e28825. [2]. 22529931. Insight on an arginine synthesis metabolon from the tetrameric structure of yeast acetylglutamate kinase. de Cima S, Gil-Ortiz F, Crabeel M, Fita I, Rubio V;. PLoS One. 2012;7:e34734. [3]. 23894642. Crystal structure of the N-acetyltransferase domain of human N-acetyl-L-glutamate synthase in complex with N-acetyl-L-glutamate provides insights into its catalytic and regulatory mechanisms. Zhao G, Jin Z, Allewell NM, Tuchman M, Shi D;. PLoS One. 2013;8:e70369. (from Pfam) NF016648.5 PF04773.18 FecR 24 24 97 domain Y Y N FecR domain-containing protein 2254251 2 Bacteria superkingdom 182378 EBI-EMBL FecR protein FecR protein FecR is involved in regulation of iron dicitrate transport. In the absence of citrate FecR inactivates FecI. FecR is probably a sensor that recognises iron dicitrate in the periplasm. [1]. 2254251. Novel two-component transmembrane transcription control: regulation of iron dicitrate transport in Escherichia coli K-12. Van Hove B, Staudenmaier H, Braun V;. J Bacteriol 1990;172:6749-6758. (from Pfam) NF016652.5 PF04777.18 Evr1_Alr 27.6 27.6 93 domain Y Y N ERV1/ALR-related protein GO:0016972 11493598 2 Bacteria superkingdom 144 EBI-EMBL Erv1 / Alr family ERV1/ALR-related protein Biogenesis of Fe/S clusters involves a number of essential mitochondrial proteins. Erv1p of Saccharomyces cerevisiae mitochondria is required for the maturation of Fe/S proteins in the cytosol. The ALR (augmenter of liver regeneration) represents a mammalian orthologue of yeast Erv1p. Both Erv1p and full-length ALR are located in the mitochondrial intermembrane an d it thought to operate downstream of the mitochondrial ABC transporter [1]. [1]. 11493598. An essential function of the mitochondrial sulfhydryl oxidase Erv1p/ALR in the maturation of cytosolic Fe/S proteins. Lange H, Lisowsky T, Gerber J, Muhlenhoff U, Kispal G, Lill R;. EMBO Rep 2001;2:715-720. (from Pfam) NF016656.5 PF04782.17 DUF632 25 25 317 domain Y Y N DUF632 domain-containing protein 2 Bacteria superkingdom 2 EBI-EMBL Protein of unknown function (DUF632) Protein of unknown function (DUF632) This plant protein may be a leucine zipper, but there is no experimental evidence for this. (from Pfam) NF016663.5 PF04789.20 DUF621 21.3 21.3 306 domain Y Y N DUF621 domain-containing protein 2 Bacteria superkingdom 3 EBI-EMBL Protein of unknown function (DUF621) Protein of unknown function (DUF621) Family of uncharacterised proteins. Some (such as Swiss:O01625) are annotated as having possible G-protein-coupled receptor-like activity. (from Pfam) NF016668.5 PF04794.17 YdjC 29.7 29.7 266 domain Y Y N ChbG/HpnK family deacetylase 8407820 2 Bacteria superkingdom 25088 EBI-EMBL YdjC-like protein ChbG/HpnK family deacetylase Family of YdjC-like proteins. This region is possibly involved in the the cleavage of cellobiose-phosphate [1]. [1]. 8407820. Cloning and sequencing of a cellobiose phosphotransferase system operon from Bacillus stearothermophilus XL-65-6 and functional expression in Escherichia coli. Lai X, Ingram LO;. J Bacteriol 1993;175:6441-6450. (from Pfam) NF016682.5 PF04809.18 HupH_C 23 23 118 domain Y Y N hydrogenase expression/formation C-terminal domain-containing protein 8045431 2 Bacteria superkingdom 4335 EBI-EMBL HupH hydrogenase expression protein, C-terminal conserved region HupH hydrogenase expression protein, C-terminal conserved region This family represents a C-terminal conserved region found in these bacterial proteins necessary for hydrogenase synthesis. Their precise function is unknown [1]. [1]. 8045431. Organization of the hydrogenase gene cluster from Bradyrhizobium japonicum: sequences and analysis of five more hydrogenase-related genes. Fu C, Maier RJ;. Gene 1994;145:91-96. (from Pfam) NF016683.5 PF04810.20 zf-Sec23_Sec24 25 25 39 PfamEq Y Y N Sec23/Sec24 zinc finger-containing protein GO:0006886,GO:0006888,GO:0008270,GO:0030127 11535824 2 Bacteria superkingdom 61 EBI-EMBL Sec23/Sec24 zinc finger Sec23/Sec24 zinc finger COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is found to be zinc binding domain. [1]. 11535824. Structure of the Sec23p/24p and Sec13p/31p complexes of COPII. Lederkremer GZ, Cheng Y, Petre BM, Vogan E, Springer S, Schekman R, Walz T, Kirchhausen T;. Proc Natl Acad Sci USA 2001;98:10704-10709. (from Pfam) NF016701.5 PF04828.20 GFA 24.3 24.3 93 domain Y Y N GFA family protein GO:0016846 25569776 2 Bacteria superkingdom 91625 EBI-EMBL Glutathione-dependent formaldehyde-activating enzyme GFA family protein The GFA enzyme catalyzes the first step in the detoxification of formaldehyde. This domain has a beta-tent fold [1]. [1]. 25569776. The thalidomide-binding domain of cereblon defines the CULT domain family and is a new member of the beta-tent fold. Lupas AN, Zhu H, Korycinski M;. PLoS Comput Biol. 2015;11:e1004023. (from Pfam) NF016702.5 PF04829.18 PT-VENN 20.3 20.3 52 domain Y Y N VENN motif pre-toxin domain-containing protein 21085179,21306995 2 Bacteria superkingdom 30204 EBI-EMBL Pre-toxin domain with VENN motif Pre-toxin domain with VENN motif This family represents a conserved region found in many bacterial porlymorphic toxins which is located before the C-terminal toxin modules [1][2]. [1]. 21306995. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Zhang D, Iyer LM, Aravind L;. Nucleic Acids Res. 2011;39:4532-4552. [2]. 21085179. A widespread family of polymorphic contact-dependent toxin delivery systems in bacteria. Aoki SK, Diner EJ, de Roodenbeke CT, Burgess BR, Poole SJ, Braaten BA, Jones AM, Webb JS, Hayes CS, Cotter PA, Low DA;. Nature. 2010;468:439-442. (from Pfam) NF016704.5 PF04831.18 Popeye 28.1 28.1 140 PfamEq Y N N Popeye protein conserved region GO:0016020 10882522 2 Bacteria superkingdom 234 EBI-EMBL Popeye protein conserved region Popeye protein conserved region The function of Popeye proteins is not well understood. They are predominantly expressed in cardiac and skeletal muscle. This family represents a conserved region which includes three potential transmembrane domains [1]. [1]. 10882522. Isolation and characterization of the novel popeye gene family expressed in skeletal muscle and heart. Andree B, Hillemann T, Kessler-Icekson G, Schmitt-John T, Jockusch H, Arnold HH, Brand T;. Dev Biol 2000;223:371-382. (from Pfam) NF016710.5 PF04837.17 MbeB_N 22 22 52 domain Y Y N MbeB family mobilization protein 2671664 2 Bacteria superkingdom 5589 EBI-EMBL MbeB-like, N-term conserved region MbeB family mobilization protein This family represents an N-terminal conserved region of MbeB/MobB proteins. These proteins are essential for specific plasmid transfer. (from Pfam) NF016718.5 PF04845.18 PurA 25 25 219 domain Y N N PurA ssDNA and RNA-binding protein GO:0000977,GO:0032422 9524214 2 Bacteria superkingdom 137 EBI-EMBL PurA ssDNA and RNA-binding protein PurA ssDNA and RNA-binding protein This family represents most of the length of the protein. [1]. 9524214. The single-stranded DNA binding protein, Pur-alpha, binds HIV-1 TAR RNA and activates HIV-1 transcription. Chepenik LG, Tretiakova AP, Krachmarov CP, Johnson EM, Khalili K;. Gene 1998;210:37-44. (from Pfam) NF016726.5 PF04854.19 DUF624 24.2 24.2 77 domain Y Y N DUF624 domain-containing protein 2 Bacteria superkingdom 20128 EBI-EMBL Protein of unknown function, DUF624 Protein of unknown function, DUF624 This family includes several uncharacterised bacterial proteins. (from Pfam) NF016759.5 PF04888.17 SseC 30.2 30.2 312 PfamEq Y Y N type III secretion system translocon subunit SctE sctE 11580752,26520801 2 Bacteria superkingdom 4719 EBI-EMBL Secretion system effector C (SseC) like family type III secretion system translocon subunit SctE SseC is a secreted protein that forms a complex together with SecB and SecD on the surface of Salmonella. All these proteins are secreted by the type III secretion system [1]. Many mucosal pathogens use type III secretion systems for the injection of effector proteins into target cells. SecB, SseC and SecD are inserted into the target cell membrane. where they form a small pore or translocon [1,2]. In addition to SseC, this family includes the bacterial secreted proteins PopB, PepB, YopB and EspD which are thought to be directly involved in pore formation, and type III secretion system translocon. [1]. 11580752. Characterization of translocation pores inserted into plasma membranes by type III-secreted Esp proteins of enteropathogenic Escherichia coli. Ide T, Laarmann S, Greune L, Schillers H, Oberleithner H, Schmidt MA;. Cell Microbiol 2001;3:669-679. [2]. 26520801. Type III Secretion: Building and Operating a Remarkable Nanomachine. Portaliou AG, Tsolis KC, Loos MS, Zorzini V, Economou A;. Trends Biochem Sci. 2016;41:175-189. (from Pfam) NF016769.5 PF04899.17 MbeD_MobD 21.6 21.6 70 subfamily Y Y N MbeD/MobD family mobilization/exclusion protein 2671664 2 Bacteria superkingdom 3674 EBI-EMBL MbeD/MobD like MbeD/MobD family mobilization/exclusion protein The plasmid mobilization protein MbeD of the ColE1 mobilization region and in similar systems is fully overlapped by MbeA on the same strand. NF016782.5 PF04914.17 DltD 22.7 22.7 348 PfamEq Y Y N D-alanyl-lipoteichoic acid biosynthesis protein DltD 10781555 2 Bacteria superkingdom 10939 EBI-EMBL DltD protein D-alanyl-lipoteichoic acid biosynthesis protein DltD DltD is and integral membrane protein involved in the biosynthesis of D-alanyl-lipoteichoic acid. This is important in controlling the net ionic charge in lipoteichoic acid (LTA). This family is found in bacteria of the Bacillus/Clostridium group. DltD binds Dcp and ligates it with D-alanine. DltD does not ligate acyl carrier protein (ACP) with D-alanine. It also has thioesterase activity for mischarged D-alanyl-acyl carrier protein (ACP). DltD is thought to be responsible for discriminating between Dcp involved in the D-alanylation of LTA, and ACP involved in fatty acid biosynthesis [1]. [1]. 10781555. Biosynthesis of lipoteichoic acid in Lactobacillus rhamnosus: role of DltD in D-alanylation. Debabov DV, Kiriukhin MY, Neuhaus FC;. J Bacteriol 2000;182:2855-2864. (from Pfam) NF016790.5 PF04922.17 DIE2_ALG10 27 27 391 domain Y N N DIE2/ALG10 family GO:0006488,GO:0106073 9597543,9722534 2 Bacteria superkingdom 177 EBI-EMBL DIE2/ALG10 family DIE2/ALG10 family The ALG10 protein from Saccharomyces cerevisiae encodes the alpha-1,2 glucosyltransferase of the endoplasmic reticulum. This protein has been characterised in rat as potassium channel regulator 1 [2]. [1]. 9597543. The ALG10 locus of Saccharomyces cerevisiae encodes the alpha-1,2 glucosyltransferase of the endoplasmic reticulum: the terminal glucose of the lipid-linked oligosaccharide is required for efficient N-linked glycosylation. Burda P, Aebi M;. Glycobiology 1998;8:455-462. [2]. 9722534. KCR1, a membrane protein that facilitates functional expression of non-inactivating K+ currents associates with rat EAG voltage-dependent K+ channels. Hoshi N, Takahashi H, Shahidullah M, Yokoyama S, Higashida H;. J Biol Chem 1998;273:23080-23085. (from Pfam) NF016795.5 PF04927.17 SMP 22 22 59 PfamEq Y N N Seed maturation protein 2 Bacteria superkingdom 227 EBI-EMBL Seed maturation protein Seed maturation protein Plant seed maturation protein. (from Pfam) NF016796.5 PF04928.22 PAP_central 27.1 27.1 146 PfamEq Y Y N poly(A) polymerase 2.7.7.19 GO:1990817 10944102 2 Bacteria superkingdom 1982 EBI-EMBL Poly(A) polymerase central domain Poly(A) polymerase central domain In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA [1]. This entry represents the central domain. [1]. 10944102. Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP. Martin G, Keller W, Doublie S;. EMBO J 2000;19:4193-4203. (from Pfam) NF016803.5 PF04936.17 DUF658 24.4 24.4 186 domain Y Y N DUF658 family protein 2 Bacteria superkingdom 297 EBI-EMBL Protein of unknown function (DUF658) DUF658 family protein Protein of unknown function found in Lactococcus lactis bacteriophages. (from Pfam) NF016804.5 PF04937.20 DUF659 34.7 34.7 152 domain Y Y N DUF domain-containing protein 2 Bacteria superkingdom 10 EBI-EMBL Protein of unknown function (DUF 659) Protein of unknown function (DUF 659) Transposase-like protein with no known function. (from Pfam) NF016807.5 PF04940.17 BLUF 25 25 92 domain Y Y N BLUF domain-containing protein GO:0009882,GO:0071949 2 Bacteria superkingdom 25411 EBI-EMBL Sensors of blue-light using FAD Sensors of blue-light using FAD The BLUF domain has been shown to bind FAD in the AppA protein (Swiss:Q53119). AppA is involved in the repression of photosynthesis genes in response to blue-light. (from Pfam) NF016818.5 PF04954.18 SIP 26.3 26.3 119 domain Y Y N SIP domain-containing protein 8083157 2 Bacteria superkingdom 81264 EBI-EMBL Siderophore-interacting protein Siderophore-interacting protein NF016819.5 PF04955.17 HupE_UreJ 23 23 179 domain Y Y N HupE/UreJ family protein 2 Bacteria superkingdom 20283 EBI-EMBL HupE / UreJ protein HupE/UreJ family protein This family of proteins are hydrogenase / urease accessory proteins. The alignment contains many conserved histidines that are likely to be involved in nickel binding. The members usually have five membrane-spanning regions. (from Pfam) NF016824.5 PF04960.20 Glutaminase 27 27 286 domain Y Y N glutaminase 3.5.1.2 GO:0004359,GO:0006541 2 Bacteria superkingdom 40227 EBI-EMBL Glutaminase glutaminase This family of enzymes deaminates glutamine to glutamate EC:3.5.1.2. (from Pfam) NF016827.5 PF04963.18 Sigma54_CBD 22.9 22.9 185 domain Y N N Sigma-54 factor, core binding domain GO:0003677,GO:0006352 10894718 2 Bacteria superkingdom 49834 EBI-EMBL Sigma-54 factor, core binding domain Sigma-54 factor, core binding domain This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme [1]. The centre of this domain contains a very weak similarity to a helix-turn-helix motif which may represent the other DNA binding domain. [1]. 10894718. The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor. Buck M, Gallegos MT, Studholme DJ, Guo Y, Gralla JD;. J Bacteriol 2000;182:4129-4136. (from Pfam) NF016828.5 PF04964.19 Flp_Fap 32.2 32.2 46 domain Y Y N Flp family type IVb pilin 11359562,9623911 2 Bacteria superkingdom 21528 EBI-EMBL Flp/Fap pilin component Flp family type IVb pilin NF016829.5 PF04965.19 GPW_gp25 27.2 27.2 96 domain Y Y N GPW/gp25 family protein 21639793,21873404,27193680,30975721 2 Bacteria superkingdom 46947 EBI-EMBL Baseplate wedge protein gp25 GPW/gp25 family protein This family represents T4 phage gp25 protein and gp25-like proteins, found in several systems, including contractile tail bacteriophages, the type VI secretion system (T6SS) and R-type pyocins, which constitute a multiprotein tubular apparatus to attach to and penetrate host cell membranes. Gp25 is a component of the conserved wedge in the inner part of the baseplate and serves as a nucleus for sheath polymerisation, playing a critical role in sheath assembly and contraction [1,2]. The EPR motif (Glu-Pro-Arg, residues 85-87 of gp25) is conserved across all members of the family including orthologues from the RpoS-mediated general stress response system (called IraD) [3,4]. This motif interacts with the 'core bundle' composed of orthologues of T4 gp6 and gp7 proteins in contractile injection systems. [1]. 27193680. Structure of the T4 baseplate and its function in triggering sheath contraction. Taylor NM, Prokhorov NS, Guerrero-Ferreira RC, Shneider MM, Browning C, Goldie KN, Stahlberg H, Leiman PG;. Nature. 2016;533:346-352. [2]. 21873404. Structure-function analysis of HsiF, a gp25-like component of the type VI secretion system, in Pseudomonas aeruginosa. Lossi NS, Dajani R, Freemont P, Filloux A;. Microbiology. 2011;157:3292-3305. [3]. 21639793. The RpoS-mediated general stress response in Escherichia coli. Battesti A, Majdalani N, Gottesman S;. Annu Rev Microbiol. 2011;65:189-213. [4]. 30975721. Structural basis for inhibition of a response regulator of sigma(S) stability by a ClpXP antiadaptor. Dorich V, Brugger C, Tripathi A, Hoskins JR, Tong S, Suhanovsky MM, Sastry A, Wickner S, Gottesman S, Deaconescu AM;. Genes D. TRUNCATED at 1650 bytes (from Pfam) NF016830.5 PF04966.17 OprB 22.9 22.9 372 domain Y Y N carbohydrate porin GO:0008643,GO:0015288,GO:0016020 7768797,8132494 2 Bacteria superkingdom 40988 EBI-EMBL Carbohydrate-selective porin, OprB family carbohydrate porin NF016834.5 PF04970.18 LRAT 24.3 24.3 120 domain Y Y N lecithin retinol acyltransferase family protein 20837014,3410848 2 Bacteria superkingdom 5879 EBI-EMBL Lecithin retinol acyltransferase lecithin retinol acyltransferase family protein The full-length members of this family, eg Swiss:P53816, are representatives of a novel class II tumour-suppressor family, designated as H-REV107-like. This domain is the catalytic N-terminal proline-rich region of the protein. The downstream region is a putative C-terminal transmembrane domain which is found to be crucial for cellular localisation, but not necessary for the enzyme activity [1]. H-REV107-like proteins are homologous to lecithin retinol acyltransferase (LRAT), an enzyme that catalyses the transfer of the sn-1 acyl group of phosphatidylcholine to all-trans-retinol and forming a retinyl ester [2]. [1]. 20837014. Solution structure of the N-terminal catalytic domain of human H-REV107--a novel circular permutated NlpC/P60 domain. Ren X, Lin J, Jin C, Xia B;. FEBS Lett. 2010;584:4222-4226. [2]. 3410848. Evidence for a lecithin-retinol acyltransferase activity in the rat small intestine. MacDonald PN, Ong DE;. J Biol Chem. 1988;263:12478-12482. (from Pfam) NF016838.5 PF04976.17 DmsC 22.3 22.3 275 subfamily Y Y N DmsC/YnfH family molybdoenzyme membrane anchor subunit 1.8.5.3 GO:0016020,GO:0019645 8429002 2 Bacteria superkingdom 20796 EBI-EMBL DMSO reductase anchor subunit (DmsC) DmsC/YnfH family molybdoenzyme membrane anchor subunit The terminal electron transfer enzyme Me2SO reductase of Escherichia coli is a heterotrimeric enzyme composed of a membrane extrinsic catalytic dimer (DmsAB) and a membrane intrinsic polytopic anchor subunit (DmsC) [1]. [1]. 8429002. The topology of the anchor subunit of dimethyl sulfoxide reductase of Escherichia coli. Weiner JH, Shaw G, Turner RJ, Trieber CA;. J Biol Chem 1993;268:3238-3244. (from Pfam) NF016839.5 PF04977.20 DivIC 28.9 28.9 80 domain Y Y N septum formation initiator family protein GO:0051301 8113187 2 Bacteria superkingdom 52211 EBI-EMBL Septum formation initiator septum formation initiator family protein DivIC from B. subtilis is necessary for both vegetative and sporulation septum formation [1]. These proteins are mainly composed of an amino terminal coiled-coil. [1]. 8113187. Characterization of a cell division gene from Bacillus subtilis that is required for vegetative and sporulation septum formation. Levin PA, Losick R;. J Bacteriol 1994;176:1451-1459. (from Pfam) NF016840.5 PF04978.17 DUF664 27 27 149 domain Y Y N DUF664 domain-containing protein 2 Bacteria superkingdom 97889 EBI-EMBL Protein of unknown function (DUF664) Protein of unknown function (DUF664) This family is commonly found in Streptomyces coelicolor and is of unknown function. These proteins contain several conserved histidines at their N-terminus that may form a metal binding site. (from Pfam) NF016846.5 PF04985.19 Phage_tube 22.4 22.4 165 domain Y Y N phage major tail tube protein 1825255,23542344,7676633 2 Bacteria superkingdom 16200 EBI-EMBL Phage tail tube protein FII phage major tail tube protein The major structural components of the contractile tail of bacteriophage P2 are proteins FI and FII, which are believed to be the tail sheath and tube proteins, respectively. [1]. 1825255. Nucleotide sequence of the genes encoding the major tail sheath and tail tube proteins of bacteriophage P2. Temple LM, Forsburg SL, Calendar R, Christie GE;. Virology 1991;181:353-358. [2]. 7676633. Tail sheath and tail tube genes of the temperate coliphage 186. Xue Q, Egan JB;. Virology 1995;212:218-221. [3]. 23542344. A conserved spiral structure for highly diverged phage tail assembly chaperones. Pell LG, Cumby N, Clark TE, Tuite A, Battaile KP, Edwards AM, Chirgadze NY, Davidson AR, Maxwell KL;. J Mol Biol. 2013;425:2436-2449. (from Pfam) NF016847.5 PF04986.18 Y2_Tnp 20.9 20.9 183 domain Y Y N transposase GO:0003677,GO:0004803,GO:0006313 14682279 2 Bacteria superkingdom 23203 EBI-EMBL Putative transposase transposase Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases IS1294 and IS801. This is a rolling-circle transposase. [1]. 14682279. The outs and ins of transposition: from mu to kangaroo. Curcio MJ, Derbyshire KM;. Nat Rev Mol Cell Biol. 2003;4:865-877. (from Pfam) NF016848.5 PF04987.19 PigN 25.4 25.4 456 domain Y Y N PigN domain-containing protein GO:0005789,GO:0006506,GO:0016740 10069808,10574991 2 Bacteria superkingdom 2 EBI-EMBL Phosphatidylinositolglycan class N (PIG-N) Phosphatidylinositolglycan class N (PIG-N) Phosphatidylinositolglycan class N (PIG-N) is a mammalian homologue of the yeast protein MCD4P and is expressed in the endoplasmic reticulum [1]. PIG-N is essential for glycosylphosphatidylinositol anchor synthesis. Glycosylphosphatidylinositol (GPI)-anchored proteins are cell surface-localised proteins that serve many important cellular functions [2]. [1]. 10574991. Pig-n, a mammalian homologue of yeast Mcd4p, is involved in transferring phosphoethanolamine to the first mannose of the glycosylphosphatidylinositol. Hong Y, Maeda Y, Watanabe R, Ohishi K, Mishkind M, Riezman H, Kinoshita T;. J Biol Chem 1999;274:35099-35106. [2]. 10069808. MCD4 encodes a conserved endoplasmic reticulum membrane protein essential for glycosylphosphatidylinositol anchor synthesis in yeast. Gaynor EC, Mondesert G, Grimme SJ, Reed SI, Orlean P, Emr SD;. Mol Biol Cell 1999;10:627-648. (from Pfam) NF016856.5 PF04995.19 CcmD 25.6 25.6 44 PfamEq Y Y N heme exporter protein CcmD ccmD GO:0015886,GO:0016020,GO:0017004 10998170,7635817 2 Bacteria superkingdom 14106 EBI-EMBL Heme exporter protein D (CcmD) heme exporter protein CcmD The CcmD protein is part of a C-type cytochrome biogenesis operon [1]. The exact function of this protein is uncertain. It has been proposed that CcmC, CcmD and CcmE interact directly with each other, establishing a cytoplasm to periplasm haem delivery pathway for cytochrome c maturation [2]. This protein is found fused to CcmE in Swiss:P52224. These proteins contain a predicted transmembrane helix. [1]. 7635817. Escherichia coli genes required for cytochrome c maturation. Thony-Meyer L, Fischer F, Kunzler P, Ritz D, Hennecke H;. J Bacteriol 1995;177:4321-4326. [2]. 10998170. New insights into the role of CcmC, CcmD and CcmE in the haem delivery pathway during cytochrome c maturation by a complete mutational analysis of the conserved tryptophan-rich motif of CcmC. Schulz H, Pellicioli EC, Thony-Meyer L;. Mol Microbiol 2000;37:1379-1388. (from Pfam) NF016860.5 PF04999.18 FtsL 22.9 22.9 97 PfamEq Y Y N cell division protein FtsL GO:0016020,GO:0051301 10844672,10986263,11994149,1332942 2 Bacteria superkingdom 10572 EBI-EMBL Cell division protein FtsL cell division protein FtsL In Escherichia coli, nine gene products are known to be essential for assembly of the division septum. One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein Pfam:PF04977 [3], however this interaction may be indirect [4]. [1]. 1332942. FtsL, an essential cytoplasmic membrane protein involved in cell division in Escherichia coli. Guzman LM, Barondess JJ, Beckwith J;. J Bacteriol 1992;174:7716-7728. [2]. 10986263. Analysis of the essential cell division gene ftsL of Bacillus subtilis by mutagenesis and heterologous complementation. Sievers J, Errington J;. J Bacteriol 2000;182:5572-5579. [3]. 10844672. The Bacillus subtilis cell division protein FtsL localizes to sites of septation and interacts with DivIC. Sievers J, Errington J;. Mol Microbiol 2000;36:846-855. [4]. 11994149. The Bacillus subtilis cell division proteins FtsL and DivIC are intrinsically unstable and do not interact with one another in the absence of other septasomal components. Robson SA, Michie KA, Mackay JP, Harry E, King GF;. Mol Microbiol 2002;44:663-674. (from Pfam) NF016875.5 PF05015.18 HigB-like_toxin 27 27 91 domain Y Y N type II toxin-antitoxin system RelE/ParE family toxin 20696400,8645296 2 Bacteria superkingdom 18128 EBI-EMBL RelE-like toxin of type II toxin-antitoxin system HigB type II toxin-antitoxin system RelE/ParE family toxin This family carries several different examples of type II bacterial toxins of toxin-antitoxin systems including many HigB-like ones. The fold is referred to as the RelE/YoeB/Txe/Yeeu fold suggesting all examples of these are present in this family. Several plasmids with proteic killer gene-systems have been reported. All of them encode a stable toxin and an unstable antidote. Upon loss of the plasmid, the less stable inhibitor is inactivated more rapidly than the toxin, allowing the toxin to be activated. The activation of these systems results in cell filamentation and cessation of viable cell production. It has been verified that both the stable killer and the unstable inhibitor of the systems are short polypeptides. This family corresponds to the toxin [1,2]. [1]. 8645296. A new plasmid-encoded proteic killer gene system: cloning, sequencing, and analyzing hig locus of plasmid Rts1. Tian QB, Ohnishi M, Tabuchi A, Terawaki Y;. Biochem Biophys Res Commun 1996;220:280-284. [2]. 20696400. Crystal structures of Phd-Doc, HigA, and YeeU establish multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems. Arbing MA, Handelman SK, Kuzin AP, Verdon G, Wang C, Su M, Rothenbacher FP, Abashidze M, Liu M, Hurley JM, Xiao R, Acton T, Inouye M, Montelione GT, Woychik NA, Hunt JF;. Structure. 2010;18:996-1010. (from Pfam) NF016885.5 PF05025.18 RbsD_FucU 25 25 138 domain Y Y N RbsD/FucU domain-containing protein GO:0005996,GO:0016853,GO:0048029 16731978 2 Bacteria superkingdom 28988 EBI-EMBL RbsD / FucU transport protein family RbsD / FucU transport protein family The Escherichia coli high-affinity ribose-transport system consists of six proteins encoded by the rbs operon (rbsD, rbsA, rbsC, rbsB, rbsK and rbsR). RbsD was originally thought to be a high affinity ribose transport protein, but further analysis [1] shows that it is a D-ribose pyranase . It catalyzes the interconversion of beta-pyran and beta-furan forms of D-ribose. It also catalyzes the conversion between beta-allofuranose and beta-allopyranose. This family also includes FucU a component of the fucose operon and is a L-fucose mutarotase, involved in the anomeric conversion of L-fucose. It also exhibits a pyranase activity for D-ribose [1]. Both have been classified in the RbsD/FucU family of proteins. Members of this family are ubiquitous having been found in organisms from eubacteria to mammals. [1]. 16731978. Stepwise disassembly and apparent nonstepwise reassembly for the oligomeric RbsD protein. Feng Y, Jiao W, Fu X, Chang Z;. Protein Sci. 2006;15:1441-1448. (from Pfam) NF016887.5 PF05028.19 PARG_cat_C 26.3 26.3 207 PfamEq Y N N Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold GO:0004649,GO:0006282 11593040,22609859,23251397 2 Bacteria superkingdom 82 EBI-EMBL Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold Poly(ADP-ribose) glycohydrolase (PARG), is a ubiquitously expressed exo- and endoglycohydrolase which mediates oxidative and excitotoxic neuronal death [1]. It catalyses hydrolysis of the O-glycosidic linkages of ADP-ribose polymers, which reverses the effects of poly(ADP-ribose) [2,3]. This entry represents the Macro domain fold localised in the C-terminal end of PARG catalytic domain from animals and plants [2,3]. [1]. 11593040. Poly(ADP-ribose) glycohydrolase mediates oxidative and excitotoxic neuronal death. Ying W, Sevigny MB, Chen Y, Swanson RA;. Proc Natl Acad Sci U S A 2001;98:12227-12232. [2]. 23251397. Structures of the human poly (ADP-ribose) glycohydrolase catalytic domain confirm catalytic mechanism and explain inhibition by ADP-HPD derivatives. Tucker JA, Bennett N, Brassington C, Durant ST, Hassall G, Holdgate G, McAlister M, Nissink JW, Truman C, Watson M;. PLoS One. 2012;7:e50889. [3]. 22609859. Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element. Kim IK, Kiefer JR, Ho CM, Stegeman RA, Classen S, Tainer JA, Ellenberger T;. Nat Struct Mol Biol. 2012;19:653-656. (from Pfam) NF016894.5 PF05035.17 DGOK 25 25 281 domain Y Y N 2-dehydro-3-deoxygalactonokinase GO:0008671,GO:0034194 6194665,7287628 2 Bacteria superkingdom 21758 EBI-EMBL 2-keto-3-deoxy-galactonokinase 2-dehydro-3-deoxygalactonokinase 2-keto-3-deoxy-galactonokinase EC:2.7.1.58 catalyses the second step in D-galactonate degradation. [1]. 7287628. Pathway for D-galactonate catabolism in nonpathogenic mycobacteria. Szumilo T;. J Bacteriol 1981;148:368-370. [2]. 6194665. Separation and some properties of D-galactonate pathway enzymes from Mycobacterium sp. 607. Szumilo T;. Acta Microbiol Pol 1983;32:47-52. (from Pfam) NF016895.5 PF05036.18 SPOR 21 21 76 domain Y Y N SPOR domain-containing protein GO:0042834 16042392,26305949 2 Bacteria superkingdom 151891 EBI-EMBL SPOR domain SPOR domain Bacterial SPOR domains bind peptidoglycan (PG) and target proteins to the cell division site by binding to denuded glycan strands that lack stem peptides [2]. This 70 residue domain is composed of two 35 residue repeats found in proteins involved in sporulation and cell division such as FtsN, DedD, and CwlM. This domain is involved in binding peptidoglycan [1]. Two tandem repeats fold into a pseudo-2-fold symmetric single-domain structure containing numerous contacts between the repeats [1]. FtsN is an essential cell division protein with a simple bitopic topology, a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. These repeats lay at the periplasmic C-terminus. FtsN localises to the septum ring complex. [1]. 16042392. Solution Structure of the Peptidoglycan Binding Domain of Bacillus subtilis Cell Wall Lytic Enzyme CwlC: Characterization of the Sporulation-Related Repeats by NMR(,). Mishima M, Shida T, Yabuki K, Kato K, Sekiguchi J, Kojima C;. Biochemistry 2005;44:10153-10163. [2]. 26305949. Bacterial SPOR domains are recruited to septal peptidoglycan by binding to glycan strands that lack stem peptides. Yahashiri A, Jorgenson MA, Weiss DS;. Proc Natl Acad Sci U S A. 2015;112:11347-11352. (from Pfam) NF016896.5 PF05037.18 DUF669 21 21 138 domain Y Y N DUF669 domain-containing protein 2 Bacteria superkingdom 3986 EBI-EMBL Protein of unknown function (DUF669) Protein of unknown function (DUF669) Members of this family are found in various phage proteins. (from Pfam) NF016901.5 PF05043.18 Mga 21.1 21.1 87 domain Y Y N helix-turn-helix domain-containing protein 11952907,11988525 2 Bacteria superkingdom 81922 EBI-EMBL Mga helix-turn-helix domain Mga helix-turn-helix domain M regulator protein trans-acting positive regulator (Mga) is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [1]. This domain is found in the centre of the Mga proteins. This family also contains a number of bacterial RofA transcriptional regulators that seem to be largely restricted to streptococci. These proteins have been shown to regulate the expression of important bacterial adhesins [2]. This is presumably a DNA-binding domain. [1]. 11952907. Two DNA-binding domains of Mga are required for virulence gene activation in the group A streptococcus. McIver KS, Myles RL;. Mol Microbiol 2002;43:1591-1601. [2]. 11988525. Group A streptococcal RofA-type global regulators exhibit a strain-specific genomic presence and regulation pattern. Kreikemeyer B, Beckert S, Braun-Kiewnick A, Podbielski A;. Microbiology 2002;148:1501-1511. (from Pfam) NF016907.5 PF05049.18 IIGP 24 24 375 domain Y N N Interferon-inducible GTPase (IIGP) GO:0005525,GO:0016020 11907101 2 Bacteria superkingdom 2125 EBI-EMBL Interferon-inducible GTPase (IIGP) Interferon-inducible GTPase (IIGP) Interferon-inducible GTPase (IIGP) is thought to play a role in in intracellular defence. IIGP is predominantly associated with the Golgi apparatus and also localises to the endoplasmic reticulum and exerts a distinct role in IFN-induced intracellular membrane trafficking or processing [1]. [1]. 11907101. The IFN-inducible Golgi- and endoplasmic reticulum- associated 47-kDa GTPase IIGP is transiently expressed during listeriosis. Zerrahn J, Schaible UE, Brinkmann V, Guhlich U, Kaufmann SH;. J Immunol 2002;168:3428-3436. (from Pfam) NF016910.5 PF05052.17 MerE 22.8 22.8 75 domain Y N N MerE protein GO:0016020 11763242,9479042 2 Bacteria superkingdom 580 EBI-EMBL MerE protein MerE protein The prokaryotic MerE (or URF-1) protein is part of the mercury resistance operon. The protein is thought not to have any direct role in conferring mercury resistance to the organism but may be a mercury resistance transposon [1,2]. [1]. 9479042. Two aberrant mercury resistance transposons in the Pseudomonas stutzeri plasmid pPB. Reniero D, Mozzon E, Galli E, Barbieri P;. Gene 1998;208:37-42. [2]. 11763242. Mercury resistance transposons of gram-negative environmental bacteria and their classification. Mindlin S, Kholodii G, Gorlenko Z, Minakhina S, Minakhin L, Kalyaeva E, Kopteva A, Petrova M, Yurieva O, Nikiforov V;. Res Microbiol 2001;152:811-822. (from Pfam) NF016927.5 PF05069.18 Phage_tail_S 24.3 24.3 148 domain Y Y N phage virion morphogenesis protein 2 Bacteria superkingdom 26081 EBI-EMBL Phage virion morphogenesis family phage virion morphogenesis protein Protein S of phage P2 is thought to be involved in tail completion and stable head joining. (from Pfam) NF016928.5 PF05071.21 NDUFA12 23 23 98 subfamily Y Y N NADH-ubiquinone oxidoreductase subunit NDUFA12 family protein GO:0016020,GO:0032981 9827566 2 Bacteria superkingdom 6686 EBI-EMBL NADH ubiquinone oxidoreductase subunit NDUFA12 NADH-ubiquinone oxidoreductase subunit NDUFA12 family protein This family contains the 17.2 kD subunit of complex I (NDUFA12) and its homologues. The family also contains a second related eukaryotic protein of unknown function, e.g. Swiss:Q9BV02. [1]. 9827566. NADH:ubiquinone oxidoreductase from bovine heart mitochondria: sequence of a novel 17.2-kDa subunit. Skehel JM, Fearnley IM, Walker JE;. FEBS Lett 1998;438:301-305. (from Pfam) NF016930.5 PF05073.17 Baculo_p24 21.3 21.3 160 domain Y Y N capsid protein p24 GO:0019028 11602755,8423444 2 Bacteria superkingdom 5 EBI-EMBL Baculovirus P24 capsid protein capsid protein p24 Baculovirus P24 is associated with nucleocapsids of budded and polyhedra-derived virions [1,2]. [1]. 11602755. Genome sequence of a baculovirus pathogenic for Culex nigripalpus. Afonso CL, Tulman ER, Lu Z, Balinsky CA, Moser BA, Becnel JJ, Rock DL, Kutish GF;. J Virol 2001;75:11157-11165. [2]. 8423444. Immunocytochemical characterization of p24, a baculovirus capsid-associated protein. Wolgamot GM, Gross CH, Russell RL, Rohrmann GF;. J Gen Virol 1993;74:103-107. (from Pfam) NF016938.5 PF05082.18 Rop-like 27 27 64 subfamily Y Y N CCE_0567 family metalloprotein 19336042 2 Bacteria superkingdom 2134 EBI-EMBL Rop-like CCE_0567 family metalloprotein CCE_0567, a small cyanobacterial metalloprotein (78 aa) from a cyanobacterium, has a solved crystal structure with two antiparallel alpha helices and an ability to bind the Ni(2+) cation. This family, previously labeled DUF683, was named Rop-like for an apparent structural similarity to another small protein, Rop, described by Pfam model PF01815. NF016953.5 PF05097.17 DUF688 20.3 20.3 446 domain Y Y N DUF688 domain-containing protein 2 Bacteria superkingdom 4 EBI-EMBL Protein of unknown function (DUF688) Protein of unknown function (DUF688) This family contains several uncharacterised proteins found in Arabidopsis thaliana. (from Pfam) NF016956.5 PF05100.17 Phage_tail_L 25 25 206 domain Y N N Phage minor tail protein L GO:0030430,GO:0046718,GO:0051536,GO:0098015 2 Bacteria superkingdom 31074 EBI-EMBL Phage minor tail protein L Phage minor tail protein L NF016957.5 PF05101.18 VirB3 23.9 23.9 84 domain Y Y N VirB3 family type IV secretion system protein 8405938,8763954,9679196 2 Bacteria superkingdom 17223 EBI-EMBL Type IV secretory pathway, VirB3-like protein VirB3 family type IV secretion system protein This family includes the Type IV secretory pathway VirB3 protein, that is found associated with bacterial inner and outer membranes [2]. The family also includes the conjugal transfer protein TrbD family that contains a nucleotide binding motif and may provide energy for the export of DNA or the export of other Trb proteins [3]. [1]. 9679196. Structural characterization of the virB operon on the hairy-root-inducing plasmid A4. Liang Y, Aoyama T, Oka A;. DNA Res 1998;5:87-93. [2]. 8405938. Membrane location of the Ti plasmid VirB proteins involved in the biosynthesis of a pilin-like conjugative structure on Agrobacterium tumefaciens. Shirasu K, Kado CI;. FEMS Microbiol Lett 1993;111:287-294. [3]. 8763954. The conjugal transfer system of Agrobacterium tumefaciens octopine-type Ti plasmids is closely related to the transfer system of an IncP plasmid and distantly related to Ti plasmid vir genes. Alt-Morbe J, Stryker JL, Fuqua C, Li PL, Farrand SK, Winans SC;. J Bacteriol 1996;178:4248-4257. (from Pfam) NF016959.5 PF05103.18 DivIVA 28 28 131 domain Y Y N DivIVA domain-containing protein 9045828,9846742 2 Bacteria superkingdom 32280 EBI-EMBL DivIVA protein DivIVA protein The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate mini-cells [1]. Inactivation of divIVA produces a mini-cell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype [1]. These proteins appear to contain coiled-coils. [1]. 9045828. The divIVA minicell locus of Bacillus subtilis. Cha JH, Stewart GC;. J Bacteriol 1997;179:1671-1683. [2]. 9846742. Unconventional organization of the division and cell wall gene cluster of Streptococcus pneumoniae. Massidda O, Anderluzzi D, Friedli L, Feger G;. Microbiology 1998;144:3069-3078. (from Pfam) NF016962.5 PF05106.17 Phage_holin_3_1 23.8 23.8 99 domain Y Y N phage holin family protein 2 Bacteria superkingdom 6343 EBI-EMBL Phage holin family (Lysis protein S) phage holin family protein This family represents one of a large number of mutually dissimilar families of phage holins. Holins act against the host cell membrane to allow lytic enzymes of the phage to reach the bacterial cell wall. This family includes the product of the S gene of phage lambda. (from Pfam) NF016971.5 PF05115.19 PetL 30.1 30.1 31 PfamEq Y Y N cytochrome b6-f complex subunit PetL GO:0009055,GO:0009512 11796719 2 Bacteria superkingdom 314 EBI-EMBL Cytochrome B6-F complex subunit VI (PetL) cytochrome b6-f complex subunit PetL This family consists of several Cytochrome B6-F complex subunit VI (PetL) proteins found in several plant species. PetL is one of the small subunits which make up The cytochrome b(6)f complex. PetL is strictly required neither for the accumulation nor for the function of cytochrome b6f; in its absence, however, the complex becomes unstable in vivo in aging cells and labile in vitro. It has been suggested that the N-terminus of the protein is likely to lie in the thylakoid lumen [1]. [1]. 11796719. Chimeric fusions of subunit IV and PetL in the b6f complex of Chlamydomonas reinhardtii: structural implications and consequences on state transitions. Zito F, Vinh J, Popot JL, Finazzi G;. J Biol Chem 2002;277:12446-12455. (from Pfam) NF016973.5 PF05117.17 DUF695 23.1 23.1 134 PfamAutoEq Y Y N DUF695 domain-containing protein 2 Bacteria superkingdom 6313 EBI-EMBL Family of unknown function (DUF695) Family of unknown function (DUF695) Family of uncharacterised bacterial proteins. (from Pfam) NF016974.5 PF05118.20 Asp_Arg_Hydrox 22.6 22.6 157 domain Y Y N aspartyl/asparaginyl beta-hydroxylase domain-containing protein GO:0018193 8041771 2 Bacteria superkingdom 22830 EBI-EMBL Aspartyl/Asparaginyl beta-hydroxylase Aspartyl/Asparaginyl beta-hydroxylase Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyse oxidative reactions in a range of metabolic processes. Proline 3-hydroxylase hydroxylates proline at position 3, the first of a 2-OG oxygenase catalysing oxidation of a free alpha-amino acid. The structure of proline 3-hydroxylase contains the conserved motifs present in other 2-OG oxygenases including a jelly roll strand core and residues binding iron and 2-oxoglutarate, consistent with divergent evolution within the extended family. This family represent the arginine, asparagine and proline hydroxylases. The aspartyl/asparaginyl beta-hydroxylase (EC:1.14.11.16) specifically hydroxylates one aspartic or asparagine residue in certain epidermal growth factor-like domains of a number of proteins [1]. [1]. 8041771. A fully active catalytic domain of bovine aspartyl (asparaginyl) beta-hydroxylase expressed in Escherichia coli: characterization and evidence for the identification of an active-site region in vertebrate alpha-ketoglutarate-dependent dioxygenases. Jia S, McGinnis K, VanDusen WJ, Burke CJ, Kuo A, Griffin PR, Sardana MK, Elliston KO, Stern AM, Friedman PA;. Proc Natl Acad Sci U S A 1994;91:7227-7231. (from Pfam) NF016975.5 PF05119.17 Terminase_4 24.7 24.7 98 domain Y Y N P27 family phage terminase small subunit 2 Bacteria superkingdom 23321 EBI-EMBL Phage terminase, small subunit P27 family phage terminase small subunit NF016981.5 PF05125.17 Phage_cap_P2 27 27 327 domain Y Y N P2 family phage major capsid protein 1837355 2 Bacteria superkingdom 19817 EBI-EMBL Phage major capsid protein, P2 family P2 family phage major capsid protein NF016983.5 PF05128.17 DUF697 27.7 27.7 162 domain Y Y N DUF697 domain-containing protein 2 Bacteria superkingdom 26412 EBI-EMBL Domain of unknown function (DUF697) Domain of unknown function (DUF697) Family of bacterial hypothetical proteins that is sometimes associated with GTPase domains. (from Pfam) NF016985.5 PF05130.17 FlgN 30.5 30.5 147 subfamily Y Y N flagellar export chaperone FlgN flgN GO:0005515,GO:0044780 11169117 2 Bacteria superkingdom 21433 EBI-EMBL FlgN protein flagellar export chaperone FlgN This family includes the FlgN protein and export chaperone involved in flagellar synthesis [1]. [1]. 11169117. Substrate complexes and domain organization of the Salmonella flagellar export chaperones FlgN and FliT. Bennett JC, Thomas J, Fraser GM, Hughes C;. Mol Microbiol 2001;39:781-791. (from Pfam) NF016989.5 PF05134.18 T2SSL 25.5 25.5 231 subfamily Y Y N type II secretion system protein GspL 10322014,14600218,15223057,15533433,19299134 2 Bacteria superkingdom 21840 EBI-EMBL Type II secretion system (T2SS), protein L type II secretion system protein GspL This family consists of Type II secretion system protein L sequences from several Gram-negative (diderm) bacteria. The Type II secretion system, also called Secretion-dependent pathway (SDP), is responsible for extracellular secretion of a number of different proteins, including proteases and toxins. This pathway supports secretion of proteins across the cell envelope in two distinct steps, in which the second step, involving translocation through the outer membrane, is assisted by at least 13 different gene products. T2SL is predicted to contain a large cytoplasmic domain represented by this family and has been shown to interact with the autophosphorylating cytoplasmic membrane protein T2SE. It is thought that the tri-molecular complex of T2SL, T2SE (Pfam:PF00437) and T2SM (Pfam:PF04612) might be involved in regulating the opening and closing of the secretion pore and/or transducing energy to the site of outer membrane translocation [1]. [1]. 10322014. Direct interaction of the EpsL and EpsM proteins of the general secretion apparatus in Vibrio cholerae. Sandkvist M, Hough LP, Bagdasarian MM, Bagdasarian M;. J Bacteriol 1999;181:3129-3135. [2]. 15533433. The structure of the cytoplasmic domain of EpsL, an inner membrane component of the type II secretion system of Vibrio cholerae: an unusual member of the actin-like ATPase superfamily. Abendroth J, Bagdasarian M, Sandkvist M, Hol WG;. J Mol Biol 2004;344:619-633. [2]. 15223057. The general secretory pathway: a general misnomer?. Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR;. Trends Microbiol. 2004;12:306-309. [3]. 14600218. Type II protein secretion and its relation. TRUNCATED at 1650 bytes (from Pfam) NF016990.5 PF05135.18 Phage_connect_1 21.2 21.2 101 domain Y Y N phage head-tail connector protein 19895817 2 Bacteria superkingdom 26220 EBI-EMBL Phage gp6-like head-tail connector protein phage head-tail connector protein This family of proteins contain head-tail connector proteins related to gp6 from bacteriophage HK97 [1]. A structure of this protein shows similarity to gp15 a well characterised connector component of bacteriophage SPP1 [1]. [1]. 19895817. The crystal structure of bacteriophage HK97 gp6: defining a large family of head-tail connector proteins. Cardarelli L, Lam R, Tuite A, Baker LA, Sadowski PD, Radford DR, Rubinstein JL, Battaile KP, Chirgadze N, Maxwell KL, Davidson AR;. J Mol Biol. 2010;395:754-768. (from Pfam) NF016991.5 PF05136.18 Phage_portal_2 32.9 32.9 354 domain Y Y N phage portal protein GO:0005198,GO:0019068 2 Bacteria superkingdom 34184 EBI-EMBL Phage portal protein, lambda family phage portal protein This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage capsid and the tail proteins. (from Pfam) NF016992.5 PF05137.18 PilN 22.8 22.8 78 domain Y Y N PilN domain-containing protein 7565110 2 Bacteria superkingdom 29467 EBI-EMBL Fimbrial assembly protein (PilN) Fimbrial assembly protein (PilN) NF016996.5 PF05141.17 DIT1_PvcA 26.4 26.4 273 subfamily Y Y N L-tyrosine/L-tryptophan isonitrile synthase family protein 18824174,8183942,8704959 2 Bacteria superkingdom 4484 EBI-EMBL Pyoverdine/dityrosine biosynthesis protein L-tyrosine/L-tryptophan isonitrile synthase family protein DIT1 is involved in synthesising dityrosine [1]. Dityrosine is a sporulation-specific component of the yeast ascospore wall that is essential for the resistance of the spores to adverse environmental conditions. Pyoverdine biosynthesis protein PvcA is involved in the biosynthesis of pyoverdine, a cyclized isocyano derivative of tyrosine [2,3]. It has a modified Rossmann fold [3]. [1]. 8183942. The sporulation-specific enzymes encoded by the DIT1 and DIT2 genes catalyze a two-step reaction leading to a soluble LL-dityrosine-containing precursor of the yeast spore wall. Briza P, Eckerstorfer M, Breitenbach M;. Proc Natl Acad Sci U S A 1994;91:4524-4528. [2]. 8704959. Novel pyoverdine biosynthesis gene(s) of Pseudomonas aeruginosa PAO. Stintzi A, Cornelis P, Hohnadel D, Meyer JM, Dean C, Poole K, Kourambas S, Krishnapillai V;. Microbiology 1996;142:1181-1190. [3]. 18824174. Three-dimensional structures of Pseudomonas aeruginosa PvcA and PvcB, two proteins involved in the synthesis of 2-isocyano-6,7-dihydroxycoumarin. Drake EJ, Gulick AM;. J Mol Biol. 2008;384:193-205. (from Pfam) NF016998.5 PF05144.19 Phage_CRI 21.2 21.2 232 domain Y Y N phage/plasmid replication protein GO:0006260 2 Bacteria superkingdom 5628 EBI-EMBL Phage replication protein CRI phage/plasmid replication protein The phage replication protein CRI, is also known as Gene II, is essential for DNA replication. (from Pfam) NF016999.5 PF05145.17 AbrB 29.2 29.2 314 PfamEq Y Y N AbrB family transcriptional regulator GO:0010468,GO:0016020 11101897,11964117,16223496,19000822 2 Bacteria superkingdom 29703 EBI-EMBL Transition state regulatory protein AbrB AbrB family transcriptional regulator Bacillus subtilis respond to a multitude of environmental stimuli by using transcription factors called transition state regulators (TSRs). They play an essential role in cell survival by regulating spore formation, competence, and biofilm development. AbrB is one of the most known TSRs, acting as a pleotropic regulator for over 60 different genes where it directly binds to their promoter or regulatory regions. Many other genes are indirectly controlled by AbrB since it is a regulator of other regulatory proteins, including ScoC, Abh, SinR and SigH [1]. Hence, AbrB is considered a global regulatory protein controlling processes such as Bacillus subtilis growth and cell division as well as production of extracellular degradative enzymes, nitrogen utilization and amino acid metabolism, motility, synthesis of antibiotics and their resistant determinants, development of competence, transport systems, oxidative stress response, phosphate metabolism, cell surface components and sporulation [2]. AbrB is a tetramer consisting of identical 94 residue monomers. Its DNA-binding function resides solely in the N-terminal domain (AbrBN) of 53 residues [3]. Although it does not recognize a well-defined DNA base-pairing sequence, instead, it appears to target a very weak pseudo consensus nucleotide sequence, TGGNA-5bp-TGGNA, which allows it to be rather promiscuous in binding [1]. The N-terminal domains of very similar sequences are present in two more Bacillus subtilis proteins, Abh and SpoVT. Mutagenesis studies suggest that the role of the C-terminal domain is in forming multimers [4]. [1]. 19000822. Insights into the nature of DNA bin. TRUNCATED at 1650 bytes (from Pfam) NF017003.5 PF05150.17 Legionella_OMP 25.4 25.4 281 subfamily Y Y N Lpg1974 family pore-forming outer membrane protein 29787733 2 Bacteria superkingdom 1563 EBI-EMBL Legionella pneumophila major outer membrane protein precursor Lpg1974 family pore-forming outer membrane protein This family consists of major outer membrane protein precursors from Legionella pneumophila. (from Pfam) NF017006.5 PF05153.20 MIOX 25 25 249 domain Y Y N inositol oxygenase family protein GO:0005506,GO:0005737,GO:0019310,GO:0050113 17012379,18364358 2 Bacteria superkingdom 1717 EBI-EMBL Myo-inositol oxygenase inositol oxygenase family protein MIOX is the enzyme myo-inositol oxygenase. It catalyses the first committed step in the glucuronate-xylulose pathway, It is a di-iron oxygenase with a key role in inositol metabolism. The structure reveals a monomeric, single-domain protein with a mostly helical fold that is distantly related to the diverse HD domain superfamily. The structural core is of five alpha-helices that contribute six ligands, four His and two Asp, to the di-iron centre where the two iron atoms are bridged by a putative hydroxide ion and one of the Asp ligands. The substrate is myo-inositol is bound in a terminal substrate-binding mode to a di-iron cluster [1]. Within the structure are two additional proteinous lids that cover and shield the enzyme's active site [2]. [1]. 17012379. Crystal structure of a substrate complex of myo-inositol oxygenase, a di-iron oxygenase with a key role in inositol metabolism. Brown PM, Caradoc-Davies TT, Dickson JM, Cooper GJ, Loomes KM, Baker EN;. Proc Natl Acad Sci U S A. 2006;103:15032-15037. [2]. 18364358. Structural and biophysical characterization of human myo-inositol oxygenase. Thorsell AG, Persson C, Voevodskaya N, Busam RD, Hammarstrom M, Graslund S, Graslund A, Hallberg BM;. J Biol Chem. 2008;283:15209-15216. (from Pfam) NF017008.5 PF05155.20 Phage_X 25 25 88 domain Y Y N phage/plasmid replication protein GO:0006260 2 Bacteria superkingdom 4102 EBI-EMBL Phage X family phage/plasmid replication protein This family is the product of Gene X. The function of this protein is unknown. (from Pfam) NF017009.5 PF05157.20 MshEN 23.1 23.1 90 domain Y N N MshEN domain 14600218,15843017,16162504,27578558,30232337,34903045,34903052 2 Bacteria superkingdom 65203 EBI-EMBL MshEN domain MshEN domain This domain is found at the N-terminus of the Type II secretion secretion system protein E (GspE) and type IV pilus extensin ATPase PilB and near the C-terminus of the glycosyltransferase NfrB. A variant of this domain, called MshEN, binds cyclic di-GMP [4,6,7], which modulates the activity of the respective protein. The structure of this domain is now known [1,2,4]. [1]. 15843017. The X-ray structure of the type II secretion system complex formed by the N-terminal domain of EpsE and the cytoplasmic domain of EpsL of Vibrio cholerae. Abendroth J, Murphy P, Sandkvist M, Bagdasarian M, Hol WG;. J Mol Biol. 2005;348:845-855. Paper describing PDB structure 2d27. [2]. 16162504. Structure and function of the XpsE N-terminal domain, an essential component of the Xanthomonas campestris type II secretion system. Chen Y, Shiue SJ, Huang CW, Chang JL, Chien YL, Hu NT, Chan NL;. J Biol Chem. 2005;280:42356-42363. [3]. 14600218. Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella. Peabody CR, Chung YJ, Yen MR, Vidal-Ingigliardi D, Pugsley AP, Saier MH Jr;. Microbiology. 2003;149:3051-3072. Paper describing PDB structure 5htl. [4]. 27578558. Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain. Wang YC, Chin KH, Tu ZL, He J, Jones CJ, Sanchez DZ, Yildiz FH, Galperin MY, Chou SH;. Nat Commun. 2016;7:12481. Paper describing PDB structure 6ejf. [5]. 30232337. Structural cycle of the Thermus thermophilus PilF ATPase: the powering of type IVa pilus assembly. Collins R, Karuppiah V, Siebert CA, Dajani R, Thistlethwaite A, Derrick JP;. Sci Rep. 2018;8:14022. [6]. 3490. TRUNCATED at 1650 bytes (from Pfam) NF017015.5 PF05163.17 DinB 23 23 165 subfamily Y Y N DinB family protein 1847907 2 Bacteria superkingdom 78837 EBI-EMBL DinB family DinB family protein DNA damage-inducible (din) genes in Bacillus subtilis are coordinately regulated and together compose a global regulatory network that has been termed the SOS-like or SOB regulon. This family includes DinB from B. subtilis [1]. [1]. 1847907. Cloning and characterization of DNA damage-inducible promoter regions from Bacillus subtilis. Cheo DL, Bayles KW, Yasbin RE;. J Bacteriol 1991;173:1696-1703. (from Pfam) NF017016.5 PF05164.18 ZapA 23.8 23.8 88 PfamEq Y Y N cell division protein ZapA zapA GO:0051301 12368265,15288790 2 Bacteria superkingdom 28066 EBI-EMBL Cell division protein ZapA cell division protein ZapA ZapA is a cell division protein which interacts with FtsZ. FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. The interaction of FtsZ with ZapA drives its polymerisation and promotes FtsZ filament bundling thereby contributing to the spatio-temporal tuning of the Z-ring [1][2]. [1]. 15288790. The crystal structure of ZapA and its modulation of FtsZ polymerisation. Low HH, Moncrieffe MC, Lowe J;. J Mol Biol 2004;341:839-852. [2]. 12368265. A widely conserved bacterial cell division protein that promotes assembly of the tubulin-like protein FtsZ. Gueiros-Filho FJ, Losick R;. Genes Dev 2002;16:2544-2556. (from Pfam) NF017021.5 PF05170.19 AsmA 29.8 29.8 607 domain Y Y N AsmA family protein 7476172,8866482 2 Bacteria superkingdom 76329 EBI-EMBL AsmA family AsmA family protein The AsmA gene, whose product is involved in the assembly of outer membrane proteins in Escherichia coli [2]. AsmA mutations were isolated as extragenic suppressors of an OmpF assembly mutant [1]. AsmA may have a role in LPS biogenesis [1]. [1]. 7476172. Molecular analysis of asmA, a locus identified as the suppressor of OmpF assembly mutants of Escherichia coli K-12. Misra R, Miao Y;. Mol Microbiol 1995;16:779-788. [2]. 8866482. Examination of AsmA and its effect on the assembly of Escherichia coli outer membrane proteins. Deng M, Misra R;. Mol Microbiol 1996;21:605-612. (from Pfam) NF017036.5 PF05185.21 PRMT5 22.9 22.9 171 PfamEq Y N N PRMT5 arginine-N-methyltransferase 10531356,11152681,8943016,9843966 2 Bacteria superkingdom 1505 EBI-EMBL PRMT5 arginine-N-methyltransferase PRMT5 arginine-N-methyltransferase The human homologue of yeast Skb1 (Shk1 kinase-binding protein 1) is PRMT5, an arginine-N-methyltransferase [3][4]. These proteins appear to be key mitotic regulators. They play a role in Jak signalling in higher eukaryotes. [1]. 8943016. The highly conserved skb1 gene encodes a protein that interacts with Shk1, a fission yeast Ste20/PAK homolog. Gilbreth M, Yang P, Wang D, Frost J, Polverino A, Cobb MH, Marcus S;. Proc Natl Acad Sci U S A 1996;93:13802-13807. [2]. 9843966. Negative regulation of mitosis in fission yeast by the shk1 interacting protein skb1 and its human homolog, Skb1Hs. Gilbreth M, Yang P, Bartholomeusz G, Pimental RA, Kansra S, Gadiraju R, Marcus S;. Proc Natl Acad Sci U S A 1998;95:14781-14786. [3]. 10531356. The human homologue of the yeast proteins Skb1 and Hsl7p interacts with Jak kinases and contains protein methyltransferase activity. Pollack BP, Kotenko SV, He W, Izotova LS, Barnoski BL, Pestka S;. J Biol Chem 1999;274:31531-31542. [4]. 11152681. Prmt5, which forms distinct homo-oligomers, is a member of the protein-arginine methyltransferase family. Rho J, Choi S, Seong YR, Cho WK, Kim SH, Im DS;. J Biol Chem 2001;276:11393-11401. (from Pfam) NF017049.5 PF05198.21 IF3_N 26.9 26.9 70 PfamEq Y N N Translation initiation factor IF-3, N-terminal domain GO:0003743,GO:0006413 2 Bacteria superkingdom 41825 EBI-EMBL Translation initiation factor IF-3, N-terminal domain Translation initiation factor IF-3, N-terminal domain NF017052.5 PF05202.17 Flp_C 25 25 254 PfamEq Y N N Recombinase Flp protein 8160270 2 Bacteria superkingdom 230 EBI-EMBL Recombinase Flp protein Recombinase Flp protein NF017056.5 PF05206.19 TRM13 26 26 257 PfamEq Y N N Methyltransferase TRM13 GO:0008033,GO:0008168 17242307 2 Bacteria superkingdom 596 EBI-EMBL Methyltransferase TRM13 Methyltransferase TRM13 This is a family of eukaryotic proteins which are responsible for 2'-O-methylation of tRNA at position 4 [1]. TRM13 shows no sequence similarity to other known methyltransferases. [1]. 17242307. The 2'-O-methyltransferase responsible for modification of yeast tRNA at position 4. Wilkinson ML, Crary SM, Jackman JE, Grayhack EJ, Phizicky EM;. RNA. 2007; [Epub ahead of print] (from Pfam) NF017059.5 PF05209.18 MinC_N 27.3 27.3 71 PfamEq Y N N Septum formation inhibitor MinC, N-terminal domain GO:0051302 10611296,10869074,11350934 2 Bacteria superkingdom 18559 EBI-EMBL Septum formation inhibitor MinC, N-terminal domain Septum formation inhibitor MinC, N-terminal domain In Escherichia coli Swiss:P06138 assembles into a Z ring at midcell while assembly at polar sites is prevented by the min system. MinC Swiss:P18196 a component of this system, is an inhibitor of FtsZ assembly that is positioned within the cell by interaction with MinDE. MinC is an oligomer, probably a dimer [1]. The C terminal half of MinC is the most conserved and interacts with MinD. The N terminal half is thought to interact with FtsZ. [1]. 10869074. Analysis of MinC reveals two independent domains involved in interaction with MinD and FtsZ. Hu Z, Lutkenhaus J;. J Bacteriol 2000;182:3965-3971. [2]. 10611296. The MinC component of the division site selection system in Escherichia coli interacts with FtsZ to prevent polymerization. Hu Z, Mukherjee A, Pichoff S, Lutkenhaus J;. Proc Natl Acad Sci U S A 1999;96:14819-14824. [3]. 11350934. Crystal structure of the bacterial cell division inhibitor MinC. Cordell SC, Anderson RE, Lowe J;. EMBO J 2001;20:2454-2461. (from Pfam) NF017062.5 PF05212.17 DUF707 24.1 24.1 299 PfamAutoEq Y Y N DUF707 domain-containing protein 2 Bacteria superkingdom 440 EBI-EMBL Protein of unknown function (DUF707) Protein of unknown function (DUF707) This family consists of several uncharacterised proteins from Arabidopsis thaliana. (from Pfam) NF017068.5 PF05218.19 DUF713 24.5 24.5 185 domain Y Y N DUF713 domain-containing protein 2 Bacteria superkingdom 6 EBI-EMBL Protein of unknown function (DUF713) Protein of unknown function (DUF713) This family contains several proteins of unknown function from C.elegans. The GO annotation suggests that this protein is involved in nematode development and has a positive regulation on growth rate. (from Pfam) NF017076.5 PF05226.16 CHASE2 26.3 26.3 257 domain Y Y N CHASE2 domain-containing protein 12486065 2 Bacteria superkingdom 33439 EBI-EMBL CHASE2 domain CHASE2 domain CHASE2 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in bacteria. Specifically, CHASE2 domains are found in histidine kinases, adenylate cyclases, serine/threonine kinases and predicted diguanylate cyclases/phosphodiesterases. Environmental factors that are recognised by CHASE2 domains are not known at this time [1]. [1]. 12486065. Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea. Zhulin IB, Nikolskaya AN, Galperin MY;. J Bacteriol 2003;185:285-294. (from Pfam) NF017079.5 PF05229.20 SCPU 22.4 22.4 138 subfamily Y Y N spore coat protein U domain-containing protein 14663080,1904442 2 Bacteria superkingdom 28137 EBI-EMBL Spore Coat Protein U domain fimbrial major subunit CsuA/B family protein This domain is found in a bacterial family of spore coat proteins [1], as well as a family of secreted pili proteins involved in motility and biofilm formation ([2]). This family is distantly related to fimbrial proteins. [1]. 1904442. Protein U, a late-developmental spore coat protein of Myxococcus xanthus, is a secretory protein. Gollop R, Inouye M, Inouye S;. J Bacteriol 1991;173:3597-3600. [2]. 14663080. Attachment to and biofilm formation on abiotic surfaces by Acinetobacter baumannii: involvement of a novel chaperone-usher pili assembly system. Tomaras AP, Dorsey CW, Edelmann RE, Actis LA;. Microbiology 2003;149:3473-3484. (from Pfam) NF017080.5 PF05230.16 MASE2 25 25 89 domain Y Y N MASE2 domain-containing protein 12673057,15142243 2 Bacteria superkingdom 10551 EBI-EMBL MASE2 domain MASE2 domain Predicted integral membrane sensory domain found in histidine kinases, diguanylate cyclases and other bacterial signaling proteins. [1]. 12673057. MASE1 and MASE2: two novel integral membrane sensory domains. Nikolskaya AN, Mulkidjanian AY, Beech IB, Galperin MY;. J Mol Microbiol Biotechnol 2003;5:11-16. [2]. 15142243. Bacterial signal transduction network in a genomic perspective. Galperin MY;. Environ Microbiol 2004;6:552-567. (from Pfam) NF017081.5 PF05231.19 MASE1 29.8 29.8 299 domain Y Y N MASE1 domain-containing protein 12673057,23740576,31022167 2 Bacteria superkingdom 54257 EBI-EMBL MASE1 MASE1 Predicted integral membrane sensory domain found in histidine kinases, diguanylate cyclases and other bacterial signaling proteins [1]. This domain has been reported to bind aspartate [2] and participate in protein-protein interactions [3]. [1]. 12673057. MASE1 and MASE2: two novel integral membrane sensory domains. Nikolskaya AN, Mulkidjanian AY, Beech IB, Galperin MY;. J Mol Microbiol Biotechnol 2003;5:11-16. [2]. 23740576. Identification of the YfgF MASE1 domain as a modulator of bacterial responses to aspartate. Lacey M, Agasing A, Lowry R, Green J;. Open Biol. 2013;3:130046. [3]. 31022167. Genetic dissection of Escherichia coli's master diguanylate cyclase DgcE: Role of the N-terminal MASE1 domain and direct signal input from a GTPase partner system. Pfiffer V, Sarenko O, Possling A, Hengge R;. PLoS Genet. 2019;15:e1008059. (from Pfam) NF017082.5 PF05232.17 BTP 25.6 25.6 64 domain Y Y N chlorhexidine efflux transporter 24277845 2 Bacteria superkingdom 15732 EBI-EMBL Chlorhexidine efflux transporter chlorhexidine efflux transporter This family represents a conserved pair of two transmembrane alpha-helices. All members carry the two pairs of TMs. BTP is a form of drug efflux pump, that actively tranports chlorhexidine out of the cell. Chlorhexidine, a bisbiguanide antimicrobial agent, is commonly used as an antiseptic and disinfectant in hospitals, and there is an increasing problem with resistance to it in some pathogenic bacteria. BTP is localised in the cytoplasmic membrane [1]. [1]. 24277845. Transcriptomic and biochemical analyses identify a family of chlorhexidine efflux proteins. Hassan KA, Jackson SM, Penesyan A, Patching SG, Tetu SG, Eijkelkamp BA, Brown MH, Henderson PJ, Paulsen IT;. Proc Natl Acad Sci U S A. 2013;110:20254-20259. (from Pfam) NF017083.5 PF05233.18 PHB_acc 27 27 40 domain Y Y N PHB accumulation regulatory domain-containing protein 12081972 2 Bacteria superkingdom 10404 EBI-EMBL PHB accumulation regulatory domain PHB accumulation regulatory domain The proteins this domain is found in are typically involved in regulating polymer accumulation in bacteria, particularly poly-beta-hydroxybutyrate (PHB) [1]. The N-terminal region is likely to be the DNA-binding domain (Pfam:PF07879) while this domain probably binds PHB (personal obs:C Yeats). [1]. 12081972. A repressor protein, PhaR, regulates polyhydroxyalkanoate (PHA) synthesis via its direct interaction with PHA. Maehara A, Taguchi S, Nishiyama T, Yamane T, Doi Y;. J Bacteriol 2002;184:3992-4002. (from Pfam) NF017090.5 PF05241.17 EBP 25.7 25.7 113 domain Y N N EXPERA (EXPanded EBP superfamily) 25566323 2 Bacteria superkingdom 448 EBI-EMBL EXPERA (EXPanded EBP superfamily) EXPERA (EXPanded EBP superfamily) The EXPERA (EXPanded EBP superfamily) domain is conserved among the following protein families: TM6SF1 (Transmembrane 6 Superfamily Member 1), TM6SF2 (Transmembrane 6 Superfamily Member 2), MAC30 (Meningioma-associated protein 30 also known as TMEM97, or Transmembrane protein 97), and EBP (Emopamil binding protein). EBP is an enzyme with a D8, D7 sterol isomerase activity that catalyzes the transposition of a double bond from C8=C9 to C7=C8 in the sterol B-ring. Mutations of EBP are known to cause the genetic disorder of X-linked dominant chondrodysplasia punctata (CDPX2). This syndrome of humans is lethal in most males, and affected females display asymmetric hyperkeratotic skin and skeletal abnormalities [1]. [1]. 25566323. TM6SF2 and MAC30, new enzyme homologs in sterol metabolism and common metabolic disease. Sanchez-Pulido L, Ponting CP;. Front Genet. 2014;5:439. (from Pfam) NF017101.5 PF05256.17 UPF0223 25 25 86 PfamEq Y Y N UPF0223 family protein 2 Bacteria superkingdom 4741 EBI-EMBL Uncharacterised protein family (UPF0223) UPF0223 family protein This family of proteins is functionally uncharacterised. (from Pfam) NF017102.5 PF05257.21 CHAP 26 26 81 domain Y Y N CHAP domain-containing protein 12765833,12765834,16818874,21226054,7775463 2 Bacteria superkingdom 73181 EBI-EMBL CHAP domain CHAP domain This domain corresponds to an amidase function. Many of these proteins are involved in cell wall metabolism of bacteria. This domain is found at the N-terminus of Swiss:P43675, where it functions as a glutathionylspermidine amidase EC:3.5.1.78 [1]. This domain is found to be the catalytic domain of PlyCA [4]. CHAP is the amidase domain of bifunctional Escherichia coli glutathionylspermidine synthetase/amidase, and it catalyses the hydrolysis of Gsp (glutathionylspermidine) into glutathione and spermidine [5]. [1]. 7775463. Glutathionylspermidine metabolism in Escherichia coli. Purification, cloning, overproduction, and characterization of a bifunctional glutathionylspermidine synthetase/amidase. Bollinger JM Jr, Kwon DS, Huisman GW, Kolter R, Walsh CT;. J Biol Chem 1995;270:14031-14041. [2]. 12765834. The CHAP domain: a large family of amidases including GSP amidase and peptidoglycan hydrolases. Bateman A, Rawlings ND;. Trends Biochem Sci 2003;28:234-237. [3]. 12765833. Amidase domains from bacterial and phage autolysins define a family of gamma-D,L-glutamate-specific amidohydrolases. Rigden DJ, Jedrzejas MJ, Galperin MY;. Trends Biochem Sci 2003;28:230-234. [4]. 16818874. PlyC: a multimeric bacteriophage lysin. Nelson D, Schuch R, Chahales P, Zhu S, Fischetti VA;. Proc Natl Acad Sci U S A. 2006;103:10765-10770. [5]. 21226054. Structure and mechanism of Escherichia coli glutathionylspermidine amidase belonging to the family of cysteine; histidine-dependent amidohydrolases/peptidases. Pai CH, Wu HJ, Lin CH, Wang AH;. Protein Sci. 2011;20:557-566. (from Pfam) NF017103.5 PF05258.17 DciA 24 24 89 PfamAutoEq Y Y N DciA family protein 27830752 2 Bacteria superkingdom 42677 EBI-EMBL Dna[CI] antecedent, DciA DciA family protein This family contains several actinomycete proteins. Family members such as DciA (dna[CI] antecedent) found in Pseudomonas aeruginosa, has been shown to share a common function with DnaC (in Escherichia coli) and DnaI (in Bacillus subtilis), acting as a replicative helicase. Furthermore, functional analysis revealed that DciA is essential for replication initiation and protein depletion resulted in a blockage of the initiation of replication after the formation of the open complex [1]. [1]. 27830752. DciA is an ancestral replicative helicase operator essential for bacterial replication initiation. Brezellec P, Vallet-Gely I, Possoz C, Quevillon-Cheruel S, Ferat JL;. Nat Commun. 2016;7:13271. (from Pfam) NF017106.5 PF05262.16 Borrelia_P83 33.6 33.6 489 subfamily Y Y N P83/100 family protein 26150534 2 Bacteria superkingdom 643 EBI-EMBL Borrelia P83/100 protein P83/100 family protein This family consists of several Borrelia P83/P100 antigen proteins. (from Pfam) NF017113.5 PF05269.16 Phage_CII 21.3 21.3 91 domain Y Y N CII family transcriptional regulator GO:0003677,GO:0006355 12397182 2 Bacteria superkingdom 4915 EBI-EMBL Bacteriophage CII protein phage lambda CII family transcriptional regulator This family consists of several phage CII regulatory proteins. CII plays a key role in the lysis-lysogeny decision in bacteriophage lambda and related phages [1]. [1]. 12397182. The phage lambda CII transcriptional activator carries a C-terminal domain signaling for rapid proteolysis. Kobiler O, Koby S, Teff D, Court D, Oppenheim AB;. Proc Natl Acad Sci U S A 2002;99:14964-14969. (from Pfam) NF017114.5 PF05270.18 AbfB 22.8 22.8 137 domain Y Y N AbfB domain-containing protein GO:0046373,GO:0046556 10217508 2 Bacteria superkingdom 18465 EBI-EMBL Alpha-L-arabinofuranosidase B (ABFB) domain Alpha-L-arabinofuranosidase B (ABFB) domain This family consists of several fungal alpha-L-arabinofuranosidase B proteins. L-Arabinose is a constituent of plant-cell-wall poly-saccharides. It is found in a polymeric form in L-arabinan, in which the backbone is formed by 1,5-a- linked l-arabinose residues that can be branched via 1,2-a- and 1,3-a-linked l-arabinofuranose side chains. AbfB hydrolyses 1,5-a, 1,3-a and 1,2-a linkages in both oligosaccharides and polysaccharides, which contain terminal non-reducing l-arabinofuranoses in side chains [1]. [1]. 10217508. The abfB gene encoding the major alpha-L-arabinofuranosidase of Aspergillus nidulans: nucleotide sequence, regulation and construction of a disrupted strain. Gielkens M, Gonzalez-Candelas L, Sanchez-Torres P, van de Vondervoort P, de Graaff L, Visser J, Ramon D;. Microbiology 1999;145:735-741. (from Pfam) NF017119.5 PF05275.16 CopB 27 27 208 domain Y Y N copper resistance protein B GO:0005507,GO:0006878,GO:0009279 11696373 2 Bacteria superkingdom 15184 EBI-EMBL Copper resistance protein B precursor (CopB) copper resistance protein B This family consists of several bacterial copper resistance proteins. Copper is essential and serves as cofactor for more than 30 enzymes yet a surplus of copper is toxic and leads to radical formation and oxidation of biomolecules. Therefore, copper homeostasis is a key requisite for every organism. CopB serves to extrude copper when it approaches toxic levels [1]. [1]. 11696373. Tetrathiomolybdate inhibition of the Enterococcus hirae CopB copper ATPase. Bissig KD, Voegelin TC, Solioz M;. FEBS Lett 2001;507:367-370. (from Pfam) NF017135.5 PF05292.16 MCD 23.2 23.2 253 domain Y Y N malonyl-CoA decarboxylase domain-containing protein GO:0006633,GO:0050080 12065578 2 Bacteria superkingdom 7157 EBI-EMBL Malonyl-CoA decarboxylase C-terminal domain Malonyl-CoA decarboxylase C-terminal domain This family consists of several eukaryotic malonyl-CoA decarboxylase (MLYCD) proteins. Malonyl-CoA, in addition to being an intermediate in the de novo synthesis of fatty acids, is an inhibitor of carnitine palmitoyltransferase I, the enzyme that regulates the transfer of long-chain fatty acyl-CoA into mitochondria, where they are oxidised. After exercise, malonyl-CoA decarboxylase participates with acetyl-CoA carboxylase in regulating the concentration of malonyl-CoA in liver and adipose tissue, as well as in muscle. Malonyl-CoA decarboxylase is regulated by AMP-activated protein kinase (AMPK) [1]. [1]. 12065578. Coordinate regulation of malonyl-CoA decarboxylase, sn-glycerol-3-phosphate acyltransferase, and acetyl-CoA carboxylase by AMP-activated protein kinase in rat tissues in response to exercise. Park H, Kaushik VK, Constant S, Prentki M, Przybytkowski E, Ruderman NB, Saha AK;. J Biol Chem 2002;277:32571-32577. (from Pfam) NF017146.5 PF05303.17 GSKIP_dom 20.9 20.9 105 domain Y Y N GSKIP domain-containing protein 14617080,16981698,19638420,9601101 2 Bacteria superkingdom 10 EBI-EMBL GSKIP domain GSKIP domain This domain is found in GSK3-beta interaction protein (GSKIP), which binds to GSK3beta [1]. It is also found as a short domain towards the N terminus in clustered mitochondria protein, also known as clueless in Drosophila, which is involved in proper cytoplasmic distribution of mitochondria [2,3,4]. [1]. 16981698. GSKIP is homologous to the Axin GSK3beta interaction domain and functions as a negative regulator of GSK3beta. Chou HY, Howng SL, Cheng TS, Hsiao YL, Lieu AS, Loh JK, Hwang SL, Lin CC, Hsu CM, Wang C, Lee CI, Lu PJ, Chou CK, Huang CY, Hong YR;. Biochemistry. 2006;45:11379-11389. [2]. 19638420. Clueless, a conserved Drosophila gene required for mitochondrial subcellular localization, interacts genetically with parkin. Cox RT, Spradling AC;. Dis Model Mech. 2009;2:490-499. [3]. 14617080. The genetic control of plant mitochondrial morphology and dynamics. Logan DC, Scott I, Tobin AK;. Plant J. 2003;36:500-509. [4]. 9601101. The S. cerevisiae CLU1 and D. discoideum cluA genes are functional homologues that influence mitochondrial morphology and distribution. Fields SD, Conrad MN, Clarke M;. J Cell Sci. 1998;111:1717-1727. (from Pfam) NF017152.5 PF05309.16 TraE 24.8 24.8 182 subfamily Y Y N TraE/TraK family type IV conjugative transfer system protein 10760136 2 Bacteria superkingdom 7327 EBI-EMBL TraE protein TraE/TraK family type IV conjugative transfer system protein This family consists of several bacterial sex pilus assembly and synthesis proteins (TraE). Conjugal transfer of plasmids from donor to recipient cells is a complex process in which a cell-to-cell contact plays a key role. Many genes encoded by self-transmissible plasmids are required for various processes of conjugation, including pilus formation, stabilisation of mating pairs, conjugative DNA metabolism, surface exclusion and regulation of transfer gene expression [1]. The exact function of the TraE protein is unknown. [1]. 10760136. The transfer region of IncI1 plasmid R64: similarities between R64 tra and legionella icm/dot genes. Komano T, Yoshida T, Narahara K, Furuya N;. Mol Microbiol 2000;35:1348-1359. (from Pfam) NF017163.5 PF05322.16 NinE 25 25 58 domain Y Y N NinE family protein 2 Bacteria superkingdom 3426 EBI-EMBL NINE Protein NinE family protein This family consists of NINE proteins from several bacteriophages and from E. coli. (from Pfam) NF017177.5 PF05339.16 DUF739 27 27 69 subfamily Y Y N DUF739 family protein 2 Bacteria superkingdom 1447 EBI-EMBL Protein of unknown function (DUF739) DUF739 family protein This family contains several bacteriophage proteins. Some of the proteins in this family have been labeled putative cro repressor proteins. (from Pfam) NF017192.5 PF05354.16 Phage_attach 22.8 22.8 117 PfamEq Y Y N head-tail joining protein GO:0019068 12083526 2 Bacteria superkingdom 3757 EBI-EMBL Phage Head-Tail Attachment lambda family head-tail joining protein The phage head-tail attachment protein is required for the joining of phage heads and tails at the last step of morphogenesis [1]. [1]. 12083526. The solution structure of the bacteriophage lambda head-tail joining protein, gpFII. Maxwell KL, Yee AA, Arrowsmith CH, Gold M, Davidson AR;. J Mol Biol 2002;318:1395-1404. (from Pfam) NF017194.5 PF05356.16 Phage_Coat_B 23.5 23.5 56 PfamEq Y Y N major capsid protein 10666593,32071243,8289247 2 Bacteria superkingdom 2135 EBI-EMBL Inovirus Coat protein B major capsid protein Members of this family are the major capsid protein of phage such as filamentous bacteriophage Pf1. NF017195.5 PF05357.18 Phage_Coat_A 20.8 20.8 63 PfamEq Y N N Phage Coat Protein A 10329170 2 Bacteria superkingdom 466 EBI-EMBL Phage Coat Protein A Phage Coat Protein A Infection of Escherichia coli by filamentous bacteriophages is mediated by the minor phage coat protein A and involves two distinct cellular receptors, the F' pilus and the periplasmic protein TolA. These two receptors are contacted in a sequential manner, such that binding of TolA by the extreme N-terminal domain is conditional on a primary interaction of the second coat protein A domain with the F' pilus [1]. [1]. 10329170. Crystal structure of the two N-terminal domains of g3p from filamentous phage fd at 1.9 A: evidence for conformational lability. Holliger P, Riechmann L, Williams RL;. J Mol Biol 1999;288:649-657. (from Pfam) NF017197.5 PF05359.16 DUF748 22 22 151 domain Y Y N DUF748 domain-containing protein 2 Bacteria superkingdom 23172 EBI-EMBL Domain of Unknown Function (DUF748) Domain of Unknown Function (DUF748) NF017198.5 PF05360.19 YiaAB 26.6 26.6 53 subfamily Y Y N YiaA/YiaB family inner membrane protein 11867724 2 Bacteria superkingdom 12762 EBI-EMBL yiaA/B two helix domain YiaA/YiaB family inner membrane protein This domain consists of two transmembrane helices and a conserved linking section. A majority of member proteins have two copies of the domain and therefore four predicted transmembrane segments. NF017205.5 PF05367.16 Phage_endo_I 29.1 29.1 149 domain Y N N Phage endonuclease I GO:0008833,GO:0015074,GO:0016032 12093751 2 Bacteria superkingdom 468 EBI-EMBL Phage endonuclease I Phage endonuclease I The bacteriophage endonuclease I is a nuclease that is selective for the structure of the four-way Holliday DNA junction [1]. [1]. 12093751. Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I. Hadden JM, Declais AC, Phillips SE, Lilley DM;. EMBO J 2002;21:3505-3515. (from Pfam) NF017211.5 PF05373.16 Pro_3_hydrox_C 25 25 101 PfamEq Y N N L-proline 3-hydroxylase, C-terminal GO:0016706 11737217 2 Bacteria superkingdom 615 EBI-EMBL L-proline 3-hydroxylase, C-terminal L-proline 3-hydroxylase, C-terminal Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyse oxidative reactions in a range of metabolic processes. Proline 3-hydroxylase hydroxylates proline at position 3, the first of a 2-OG oxygenase catalysing oxidation of a free alpha-amino acid. The structure contains conserved motifs present in other 2-OG oxygenases including a jelly roll strand core and residues binding iron and 2-oxoglutarate, consistent with divergent evolution within the extended family. The structure differs significantly from many other 2-OG oxygenases in possessing a discrete C-terminal helical domain. [1]. 11737217. Structure of proline 3-hydroxylase. Evolution of the family of 2-oxoglutarate dependent oxygenases. Clifton IJ, Hsueh LC, Baldwin JE, Harlos K, Schofield CJ;. Eur J Biochem 2001;268:6625-6636. (from Pfam) NF017219.5 PF05382.18 Amidase_5 21 21 142 domain Y Y N peptidoglycan amidohydrolase family protein 3422470,6146601,9379901 2 Bacteria superkingdom 11620 EBI-EMBL Bacteriophage peptidoglycan hydrolase peptidoglycan amidohydrolase family protein At least one of the members of this family, the Pal protein from the pneumococcal bacteriophage Dp-1 Swiss:O03979 has been shown to be a N-acetylmuramoyl-L-alanine amidase [1]. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside at the N-terminal domain whereas the C-terminal domain binds to the choline residues of the cell wall teichoic acids [2,3]. This family appears to be related to Pfam:PF00877. [1]. 6146601. Biochemical characterization of a murein hydrolase induced by bacteriophage Dp-1 in Streptococcus pneumoniae: comparative study between bacteriophage-associated lysin and the host amidase. Garcia P, Mendez E, Garcia E, Ronda C, Lopez R;. J Bacteriol 1984;159:793-796. [2]. 9379901. The lytic enzyme of the pneumococcal phage Dp-1: a chimeric lysin of intergeneric origin. Sheehan MM, Garcia JL, Lopez R, Garcia P;. Mol Microbiol 1997;25:717-725. [3]. 3422470. Molecular evolution of lytic enzymes of Streptococcus pneumoniae and its bacteriophages. Garcia E, Garcia JL, Garcia P, Arraras A, Sanchez-Puelles JM, Lopez R;. Proc Natl Acad Sci U S A 1988;85:914-918. (from Pfam) NF017226.5 PF05389.17 MecA 22.5 22.5 221 domain Y Y N adaptor protein MecA 11004200,12028382,8412687 2 Bacteria superkingdom 10350 EBI-EMBL Negative regulator of genetic competence (MecA) adaptor protein MecA This family contains several bacterial MecA proteins. The development of competence in Bacillus subtilis is regulated by growth conditions and several regulatory genes. In complex media competence development is poor, and there is little or no expression of late competence genes. Mec mutations permit competence development and late competence gene expression in complex media, bypassing the requirements for many of the competence regulatory genes. The mecA gene product acts negatively in the development of competence. Null mutations in mecA allow expression of a late competence gene comG, under conditions where it is not normally expressed, including in complex media and in cells mutant for several competence regulatory genes. Overexpression of MecA inhibits comG transcription [1,2,3]. [1]. 8412687. Sequence and properties of mecA, a negative regulator of genetic competence in Bacillus subtilis. Kong L, Siranosian KJ, Grossman AD, Dubnau D;. Mol Microbiol 1993;9:365-373. [2]. 12028382. Spx (YjbD), a negative effector of competence in Bacillus subtilis, enhances ClpC-MecA-ComK interaction. Nakano MM, Nakano S, Zuber P;. Mol Microbiol 2002;44:1341-1349. [3]. 11004200. Identification in Listeria monocytogenes of MecA, a homologue of the Bacillus subtilis competence regulatory protein. Borezee E, Msadek T, Durant L, Berche P;. J Bacteriol 2000;182:5931-5934. (from Pfam) NF017233.5 PF05396.16 Phage_T7_Capsid 27.1 27.1 188 PfamEq Y Y N capsid assembly protein GO:0019069 2 Bacteria superkingdom 904 EBI-EMBL Phage T7 capsid assembly protein phage T7 capsid assembly protein NF017237.5 PF05400.18 FliT 29.5 29.5 85 domain Y Y N flagellar protein FliT fliT 11169117 2 Bacteria superkingdom 7668 EBI-EMBL Flagellar protein FliT flagellar protein FliT This family contains several bacterial flagellar FliT proteins. The flagellar proteins FlgN and FliT have been proposed to act as substrate specific export chaperones, facilitating incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum. In Salmonella typhimurium flgN and fliT mutants, the export of target HAPs is reduced, concomitant with loss of unincorporated flagellin into the surrounding medium [1]. [1]. 11169117. Substrate complexes and domain organization of the Salmonella flagellar export chaperones FlgN and FliT. Bennett JC, Thomas J, Fraser GM, Hughes C;. Mol Microbiol 2001;39:781-791. (from Pfam) NF017242.5 PF05405.19 Mt_ATP-synt_B 21.7 21.7 163 domain Y N N Mitochondrial ATP synthase B chain precursor (ATP-synt_B) GO:0015078,GO:0015986,GO:0045263 8011660 2 Bacteria superkingdom 12251 EBI-EMBL Mitochondrial ATP synthase B chain precursor (ATP-synt_B) Mitochondrial ATP synthase B chain precursor (ATP-synt_B) The Fo sector of the ATP synthase is a membrane bound complex which mediates proton transport. It is composed of nine different polypeptide subunits (a, b, c, d, e, f, g F6, A6L) [1]. [1]. 8011660. Fo membrane domain of ATP synthase from bovine heart mitochondria: purification, subunit composition, and reconstitution with F1-ATPase. Collinson IR, Runswick MJ, Buchanan SK, Fearnley IM, Skehel JM, van Raaij MJ, Griffiths DE, Walker JE;. Biochemistry 1994;33:7971-7978. (from Pfam) NF017243.5 PF05406.20 WGR 22 22 79 domain Y Y N WGR domain-containing protein 2 Bacteria superkingdom 22559 EBI-EMBL WGR domain WGR domain This domain is found in a variety of polyA polymerases as well as the E. coli molybdate metabolism regulator Swiss:P33345 and other proteins of unknown function. I have called this domain WGR after the most conserved central motif of the domain. The domain is found in isolation in proteins such as Swiss:Q9JN21 and is between 70 and 80 residues in length. I propose that this may be a nucleic acid binding domain. (from Pfam) NF017256.5 PF05419.17 GUN4 29.2 29.2 141 domain Y Y N GUN4 domain-containing protein 12574634 2 Bacteria superkingdom 7292 EBI-EMBL GUN4-like GUN4-like In Arabidopsis, GUN4 is required for the functioning of the plastid mediated repression of nuclear transcription that is involved in controlling the levels of magnesium- protoporphyrin IX. GUN4 binds the product and substrate of Mg-chelatase, an enzyme that produces Mg-Proto, and activates Mg-chelatase. GUN4 is thought to participates in plastid-to-nucleus signaling by regulating magnesium-protoporphyrin IX synthesis or trafficking. [1]. 12574634. GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Larkin RM, Alonso JM, Ecker JR, Chory J;. Science 2003;299:902-906. (from Pfam) NF017260.5 PF05423.18 Mycobact_memb 21 21 139 subfamily Y Y N MmpS family transport accessory protein 11891304 2 Bacteria superkingdom 12111 EBI-EMBL Mycobacterium membrane protein MmpS family transport accessory protein This family contains several membrane proteins from Mycobacterium species. [1]. 11891304. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Brosch R, Gordon SV, Marmiesse M, Brodin P, Buchrieser C, Eiglmeier K, Garnier T, Gutierrez C, Hewinson G, Kremer K, Parsons LM, Pym AS, Samper S, van Soolingen D, Cole ST;. Proc Natl Acad Sci U S A 2002;99:3684-3689. (from Pfam) NF017267.5 PF05431.16 Toxin_10 28.6 28.6 188 domain Y N N Insecticidal Crystal Toxin, P42 GO:0090729 9500937 2 Bacteria superkingdom 654 EBI-EMBL Insecticidal Crystal Toxin, P42 Insecticidal Crystal Toxin, P42 Family of Bacillus insecticidal crystal toxins. Strains of Bacillus that have this insecticidal activity use a binary toxin comprised of two proteins, P51 and P42 (this family). Members of this family are highly conserved between strains of different serotypes and phage groups [1]. [1]. 9500937. Variants of the Bacillus sphaericus binary toxins: implications for differential toxicity of strains. Humphreys MJ, Berry C;. J Invertebr Pathol 1998;71:184-185. (from Pfam) NF017315.5 PF05488.18 PAAR_motif 27 27 70 domain Y Y N PAAR domain-containing protein 2 Bacteria superkingdom 65852 EBI-EMBL PAAR motif PAAR motif This motif is found usually in pairs in a family of bacterial membrane proteins. It is also found as a triplet of tandem repeats comprising the entire length in a another family of hypothetical proteins. (from Pfam) NF017316.5 PF05489.17 Phage_tail_X 22 22 60 domain Y Y N tail protein X 2 Bacteria superkingdom 14051 EBI-EMBL Phage Tail Protein X tail protein X This domain is found in a family of phage tail proteins. Visual analysis suggests that it is related to Pfam:PF01476 (personal obs: C Yeats). The functional annotation of family members further confirms this hypothesis. (from Pfam) NF017319.5 PF05494.17 MlaC 26 26 166 domain Y Y N ABC transporter substrate-binding protein 19383799,9020089,9658016 2 Bacteria superkingdom 22395 EBI-EMBL MlaC protein ABC transporter substrate-binding protein MlaC is a component of the Mla pathway, an ABC transport system that functions to maintain the asymmetry of the outer membrane [1]. This family of proteins is involved in toluene tolerance, which is mediated by increased cell membrane rigidity resulting from changes in fatty acid and phospholipid compositions, exclusion of toluene from the cell membrane, and removal of intracellular toluene by degradation [2-3]. Many proteins are involved in these processes. [1]. 19383799. An ABC transport system that maintains lipid asymmetry in the gram-negative outer membrane. Malinverni JC, Silhavy TJ;. Proc Natl Acad Sci U S A. 2009;106:8009-8014. [2]. 9020089. Mechanisms for solvent tolerance in bacteria. Ramos JL, Duque E, Rodriguez-Herva JJ, Godoy P, Haidour A, Reyes F, Fernandez-Barrero A;. J Biol Chem 1997;272:3887-3890. [3]. 9658016. Isolation and characterization of toluene-sensitive mutants from the toluene-resistant bacterium Pseudomonas putida GM73. Kim K, Lee S, Lee K, Lim D;. J Bacteriol 1998;180:3692-3696. (from Pfam) NF017328.5 PF05504.16 Spore_GerAC 23.6 23.6 167 domain Y Y N Ger(x)C family spore germination C-terminal domain-containing protein GO:0009847,GO:0016020 11418573 2 Bacteria superkingdom 41804 EBI-EMBL Spore germination B3/ GerAC like, C-terminal Spore germination B3/ GerAC like, C-terminal The GerAC protein of the Bacillus subtilis spore is required for the germination response to L-alanine. Members of this family are thought to be located in the inner spore membrane. Although the function of this family is unclear, they are likely to encode the components of the germination apparatus that respond directly to this germinant, mediating the spore's response [1]. [1]. 11418573. Localization of GerAA and GerAC germination proteins in the Bacillus subtilis spore. Hudson KD, Corfe BM, Kemp EH, Feavers IM, Coote PJ, Moir A;. J Bacteriol 2001;183:4317-4322. (from Pfam) NF017330.5 PF05506.17 PLipase_C_C 24.4 24.4 80 domain Y Y N phospholipase domain-containing protein GO:0004629,GO:0016042 2 Bacteria superkingdom 40964 EBI-EMBL Bacterial phospholipase C, C-terminal domain Bacterial phospholipase C, C-terminal domain This domain is found, normally as a tandem repeat, at the C-terminus of bacterial phospholipase C proteins. (from Pfam) NF017333.5 PF05509.16 TraY 21.3 21.3 49 domain Y Y N TraY domain-containing protein GO:0003677 12003924 2 Bacteria superkingdom 4028 EBI-EMBL TraY domain TraY domain This family consists of several enterobacterial TraY proteins. TraY is involved in bacterial conjugation where it is required for efficient nick formation in the F plasmid [1]. These proteins have a ribbon-helix-helix fold and are likely to be DNA-binding proteins. [1]. 12003924. Nucleotide and amino acid sequences of oriT-traM-traJ-traY-traA-traL regions and mobilization of virulence plasmids of Salmonella enterica serovars enteritidis, gallinarum-pullorum, and typhimurium. Chu C, Chiu CH, Chu CH, Ou JT;. J Bacteriol 2002;184:2857-2862. (from Pfam) NF017347.5 PF05525.18 Branch_AA_trans 22.3 22.3 429 domain Y Y N branched-chain amino acid transport system II carrier protein GO:0015658,GO:0015803,GO:0016020 8544834 2 Bacteria superkingdom 45292 EBI-EMBL Branched-chain amino acid transport protein branched-chain amino acid transport system II carrier protein This family consists of several bacterial branched-chain amino acid transport proteins which are responsible for the transport of leucine, isoleucine and valine via proton motive force [1]. [1]. 8544834. Cloning and characterization of brnQ, a gene encoding a low-affinity, branched-chain amino acid carrier in Lactobacillus delbruckii subsp. lactis DSM7290. Stucky K, Hagting A, Klein JR, Matern H, Henrich B, Konings WN, Plapp R;. Mol Gen Genet 1995;249:682-690. (from Pfam) NF017348.5 PF05526.16 R_equi_Vir 25 25 177 subfamily Y Y N VapA/VapB family virulence-associated protein 11083803 2 Bacteria superkingdom 312 EBI-EMBL Rhodococcus equi virulence-associated protein VapA/VapB family virulence-associated protein This family consists of several virulence-associated proteins from Rhodococcus equi. Rhodococcus equi is an important pulmonary pathogen of foals and is increasingly isolated from pneumonic infections and other infections in human immunodeficiency virus (HIV)-infected patients. Isolates from foals possess a large virulence plasmid, varying in size from 80 to 90 kb. Isolates lacking the plasmid are avirulent to foals. Little is known about the function of the plasmid apart from its encoding a virulence associated surface proteins [1]. [1]. 11083803. DNA sequence and comparison of virulence plasmids from Rhodococcus equi ATCC 33701 and 103. Takai S, Hines SA, Sekizaki T, Nicholson VM, Alperin DA, Osaki M, Takamatsu D, Nakamura M, Suzuki K, Ogino N, Kakuda T, Dan H, Prescott JF;. Infect Immun 2000;68:6840-6847. (from Pfam) NF017349.5 PF05527.16 DUF758 22.3 22.3 181 domain Y Y N DUF758 domain-containing protein GO:0042981 2 Bacteria superkingdom 3 EBI-EMBL Domain of unknown function (DUF758) Domain of unknown function (DUF758) Family of eukaryotic proteins with unknown function, which are induced by tumour necrosis factor. (from Pfam) NF017359.5 PF05538.16 Campylo_MOMP 29.6 29.6 421 domain Y Y N major outer membrane protein 10992471 2 Bacteria superkingdom 3717 EBI-EMBL Campylobacter major outer membrane protein major outer membrane protein This family consists of Campylobacter major outer membrane proteins. The major outer membrane protein (MOMP), a putative porin and a multifunction surface protein of Campylobacter jejuni, may play an important role in the adaptation of the organism to various host environments [1]. [1]. 10992471. Sequence polymorphism, predicted secondary structures, and surface-exposed conformational epitopes of Campylobacter major outer membrane protein. Zhang Q, Meitzler JC, Huang S, Morishita T;. Infect Immun 2000;68:5679-5689. (from Pfam) NF017363.5 PF05542.16 DUF760 20.2 20.2 83 domain Y Y N DUF760 domain-containing protein 2 Bacteria superkingdom 1287 EBI-EMBL Protein of unknown function (DUF760) Protein of unknown function (DUF760) This family contains several uncharacterised plant proteins. (from Pfam) NF017366.5 PF05545.16 FixQ 29 29 49 domain Y Y N CcoQ/FixQ family Cbb3-type cytochrome c oxidase assembly chaperone 11717256 2 Bacteria superkingdom 10734 EBI-EMBL Cbb3-type cytochrome oxidase component FixQ CcoQ/FixQ family Cbb3-type cytochrome c oxidase assembly chaperone This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [1]. [1]. 11717256. Regulation of gene expression in response to oxygen in Rhizobium etli: role of FnrN in fixNOQP expression and in symbiotic nitrogen fixation. Lopez O, Morera C, Miranda-Rios J, Girard L, Romero D, Soberon M;. J Bacteriol 2001;183:6999-7006. (from Pfam) NF017372.5 PF05551.16 zf-His_Me_endon 27 27 131 domain Y N N Zinc-binding loop region of homing endonuclease 10581547,12527760 2 Bacteria superkingdom 415 EBI-EMBL Zinc-binding loop region of homing endonuclease Zinc-binding loop region of homing endonuclease This domain [1] is the short zinc-binding loops region of a number of much longer chain homing endonucleases. Such loops are probably stabilised by the zinc and may be viewed as small but separate domains. The common structural feature of these domains is that at least three zinc ligands lie very close to each other in the sequence and are not incorporated into regular secondary structural elements. The biological roles played by these small zinc-binding domains are presently unknown [2]. [1]. 10581547. A novel endonuclease mechanism directly visualized for I-PpoI. Galburt EA, Chevalier B, Tang W, Jurica MS, Flick KE, Monnat RJ Jr, Stoddard BL;. Nat Struct Biol. 1999;6:1096-1099. [2]. 12527760. Structural classification of zinc fingers: survey and summary. Krishna SS, Majumdar I, Grishin NV;. Nucleic Acids Res. 2003;31:532-550. (from Pfam) NF017388.5 PF05567.16 T4P_PilY1 28.1 28.1 411 subfamily_domain Y Y N PilC/PilY family type IV pilus protein 20080557,25385640 2 Bacteria superkingdom 20223 EBI-EMBL PilY1 beta-propeller domain PilC/PilY family type IV pilus protein beta-propeller domain Proteins with the beta-propeller domain described by this HMM include the closely related paralogs PilC1 and PilC2 from Neisseria and PilY1 from Pseudomonas aeruginosa, both proteins of type IV pili (T4P). Members of the family function both in pilus biogenesis and as a tip adhesin. NF017396.5 PF05576.16 Peptidase_S37 27 27 448 domain Y N N PS-10 peptidase S37 2 Bacteria superkingdom 9942 EBI-EMBL PS-10 peptidase S37 PS-10 peptidase S37 These serine proteases have been found in Streptomyces species. (from Pfam) NF017400.5 PF05580.17 Peptidase_S55 25 25 210 domain Y Y N SpoIVB peptidase S55 domain-containing protein 11418578,11741860 2 Bacteria superkingdom 9260 EBI-EMBL SpoIVB peptidase S55 SpoIVB peptidase S55 The protein SpoIVB plays a key role in signalling in the final sigma-K checkpoint of Bacillus subtilis. [1]. 11741860. The Bacillus subtilis signaling protein SpoIVB defines a new family of serine peptidases. Hoa NT, Brannigan JA, Cutting SM;. J Bacteriol 2002;184:191-199. [2]. 11418578. The PDZ domain of the SpoIVB serine peptidase facilitates multiple functions. Hoa NT, Brannigan JA, Cutting SM;. J Bacteriol 2001;183:4364-4373. (from Pfam) NF017401.5 PF05582.17 Peptidase_U57 25 25 280 PfamEq Y Y N sporulation peptidase YabG 11040425 2 Bacteria superkingdom 3489 EBI-EMBL YabG peptidase U57 sporulation peptidase YabG YabG is a protease involved in the proteolysis and maturation of SpoIVA and YrbA proteins, conserved with the cortex and/or coat assembly by Bacillus subtilis. [1]. 11040425. The yabG gene of Bacillus subtilis encodes a sporulation specific protease which is involved in the processing of several spore coat proteins. Takamatsu H, Imamura A, Kodama T, Asai K, Ogasawara N, Watabe K;. FEMS Microbiol Lett 2000;192:33-38. (from Pfam) NF017409.5 PF05591.17 T6SS_VipA 24 24 155 domain Y Y N type VI secretion system contractile sheath small subunit 18289922,1913969,23289512,25723169,26768901 2 Bacteria superkingdom 18601 EBI-EMBL Type VI secretion system, VipA, VC_A0107 or Hcp2 type VI secretion system contractile sheath small subunit T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex [1]. VipA is a family of Gram-negative bacterial proteins that form part of the type VI pathogenic secretion system. Members have been variously defined as VC_A0107 family, Hcp2, TssB and VipA, for ClpV-interacting proteins. VipB and VipA proteins interact very closely to form the shaft of the pathogenic penetrating needle system [2,3,4]. VipA and VipB (TssB and TssC) proteins were shown to form a cog-wheel like tubular structure in V. cholerae that was noticed to resemble T4 phage gp18 polysheath. Two beta-strands of VipA and four beta-strands of VipB intertwine forming the middle layer of the sheath. The sheath assembles around an inner Hcp tube and is attached to a structure called a baseplate that spans the bacterial membranes. Importantly, VipA/VipB sheath was shown to form a long contractile organelle in V. cholerae and in E. coli, suggesting that sheath contraction powers the secretion [5]. [1]. 26768901. Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements. Coyne MJ, Roelofs KG, Comstock LE;. BMC Genomics. 2016;17:58. [2]. 1913969. [Study on BCG vaccination and incidence of children's tuberculous meningitis in Liaoning province]. Wu QR;. Zhonghua Jie He. TRUNCATED at 1650 bytes (from Pfam) NF017412.5 PF05594.19 Fil_haemagg 21.5 2.3 72 repeat Y N N filamentous hemagglutinin repeat-containing protein 11703654,2539596 2 Bacteria superkingdom 40336 EBI-EMBL Haemagglutinin repeat Haemagglutinin repeat This highly divergent repeat occurs in number of proteins implicated in cell aggregation [1]. The Pfam alignment probably contains three such repeats (personal obs: C Yeats). These are likely to have a beta-helical structure. [1]. 2539596. Filamentous hemagglutinin of Bordetella pertussis: nucleotide sequence and crucial role in adherence. Relman DA, Domenighini M, Tuomanen E, Rappuoli R, Falkow S;. Proc Natl Acad Sci U S A 1989;86:2637-2641. [2]. 11703654. Beta-helix model for the filamentous haemagglutinin adhesin of Bordetella pertussis and related bacterial secretory proteins. Kajava AV, Cheng N, Cleaver R, Kessel M, Simon MN, Willery E, Jacob-Dubuisson F, Locht C, Steven AC;. Mol Microbiol 2001;42:279-292. (from Pfam) NF017413.5 PF05595.16 DUF771 22.9 22.9 90 PfamAutoEq Y Y N DUF771 domain-containing protein 2 Bacteria superkingdom 3447 EBI-EMBL Domain of unknown function (DUF771) Domain of unknown function (DUF771) Family of uncharacterised ORFs found in Bacteriophage and Lactococcus lactis. (from Pfam) NF017418.5 PF05600.17 CDK5RAP3 22.6 22.6 502 domain Y Y N CDK5 domain-containing protein 12054757,12737517,15790566,17785205,19223857,20228063,28027003 2 Bacteria superkingdom 7 EBI-EMBL CDK5 regulatory subunit-associated protein 3 CDK5 regulatory subunit-associated protein 3 This family contains several eukaryotic sequences such as CDK5RAP3 (also known as C53 or LZAP) which serves as a probable tumour suppressor. Initially identified as a CDK5R1 interactor controlling cell proliferation [1, 2]. It negatively regulates NF-kappa-B-mediated gene transcription through the control of RELA phosphorylation [3, 4]. It also regulates mitotic G2/M transition checkpoint and mitotic G2 DNA damage checkpoint [5, 6]. It has been shown to bind Wip1 and stimulates its phosphatase activity [7]. [1]. 12054757. A novel gene IC53 stimulates ECV304 cell proliferation and is upregulated in failing heart. Chen J, Liu B, Liu Y, Han Y, Yu H, Zhang Y, Lu L, Zhen Y, Hui R;. Biochem Biophys Res Commun. 2002;294:161-166. [2]. 12737517. Cloning and characterization of human IC53-2, a novel CDK5 activator binding protein. Xie YH, He XH, Tang YT, Li JJ, Pan ZM, Qin WX, Wan DF, Gu JR;. Cell Res. 2003;13:83-91. [3]. 17785205. LZAP, a putative tumor suppressor, selectively inhibits NF-kappaB. Wang J, An H, Mayo MW, Baldwin AS, Yarbrough WG;. Cancer Cell. 2007;12:239-251. [4]. 20228063. A novel C53/LZAP-interacting protein regulates stability of C53/LZAP and DDRGK domain-containing Protein 1 (DDRGK1) and modulates NF-kappaB signaling. Wu J, Lei G, Mei M, Tang Y, Li H;. J Biol Chem. 2010;285:15126-15136. [5]. 15790566. Cdk5 activator-binding protein C53 regulates apoptosis induced by genotoxic stress via modulating the G2/M DNA damage checkpoint. Jiang H, Luo S, Li H;. J Biol Chem. 2005;280:20651-20659. [6]. 19223857. Tumor suppressor protein C53 antagonizes checkpoint kinases to promote cyclin-dependent kinase 1 activation. Jian. TRUNCATED at 1650 bytes (from Pfam) NF017428.5 PF05612.17 Leg1 25 25 331 subfamily Y Y N Leg1-related protein 21857963 2 Bacteria superkingdom 61 EBI-EMBL Leg1 Leg1-related protein Protein liver-enriched gene 1 (Leg1) has been suggested to function as a novel secreted regulator for the liver development [1]. [1]. 21857963. liver-enriched gene 1a and 1b encode novel secretory proteins essential for normal liver development in zebrafish. Chang C, Hu M, Zhu Z, Lo LJ, Chen J, Peng J;. PLoS One. 2011;6:e22910. (from Pfam). Bacterial members of this family occur in the Actinobacteria, and are related to Leg1 (liver-enriched gene 1) of zebrafish. NF017432.5 PF05616.18 Neisseria_TspB 20 20 517 domain Y Y N IgG-binding virulence factor TspB family protein 25583528 2 Bacteria superkingdom 4016 EBI-EMBL Neisseria meningitidis TspB protein IgG-binding virulence factor TspB family protein The founding member of this family, TspB from Neisseria meningitidis, is encoded within a prophage region. Proteins scoring above 100 to this model, which is 517 residues long, are found exclusively in Neisseria. NCBI model NF041109 describes a short C-terminal domain, about 51 amino acids long, with two invariant Cys residues and an apparent C-terminal transmembrane segment, that this much longer model overlaps. NF017451.5 PF05635.16 23S_rRNA_IVP 23.4 23.4 106 domain Y Y N four helix bundle protein 16948161,17644584,7751314,8341711 2 Bacteria superkingdom 35361 EBI-EMBL 23S rRNA-intervening sequence protein four helix bundle protein This family consists of bacterial proteins encoded within an intervening sequence present within some 23S rRNA genes [1-3]. It folds into an anti-parallel four-helix bundle and forms homopentamers [4]. [1]. 8341711. Intervening sequence with conserved open reading frame in eubacterial 23S rRNA genes. Ralph D, McClelland M;. Proc Natl Acad Sci U S A 1993;90:6864-6868. [2]. 7751314. Characterization of the 23S and 5S rRNA genes of Coxiella burnetii and identification of an intervening sequence within the 23S rRNA gene. Afseth G, Mo YY, Mallavia LP;. J Bacteriol 1995;177:2946-2949. [3]. 17644584. The unusual 23S rRNA gene of Coxiella burnetii: two self-splicing group I introns flank a 34-base-pair exon, and one element lacks the canonical omegaG. Raghavan R, Miller SR, Hicks LD, Minnick MF;. J Bacteriol. 2007;189:6572-6579. [4]. 16948161. Crystal structure of the conserved hypothetical cytosolic protein Xcc0516 from Xanthomonas campestris reveals a novel quaternary structure assembled by five four-helix bundles. Lin LY, Ching CL, Chin KH, Chou SH, Chan NL;. Proteins. 2006;65:783-786. (from Pfam) NF017453.5 PF05637.17 Glyco_transf_34 23 23 238 domain Y N N galactosyl transferase GMA12/MNN10 family GO:0016020,GO:0016757 7522655,8991513,9839953 2 Bacteria superkingdom 890 EBI-EMBL galactosyl transferase GMA12/MNN10 family galactosyl transferase GMA12/MNN10 family This family contains a number of glycosyltransferase enzymes that contain a DXD motif. This family includes a number of C. elegans homologues where the DXD is replaced by DXH. Some members of this family are included in glycosyltransferase family 34. [1]. 7522655. Localization of an alpha 1,2 galactosyltransferase activity to the Golgi apparatus of Schizosaccharomyces pombe. Chappell TG, Hajibagheri MA, Ayscough K, Pierce M, Warren G;. Mol Biol Cell 1994;5:519-528. [2]. 9839953. Differences in in vivo acceptor specificity of two galactosyltransferases, the gmh3+ and gma12+ gene products from Schizosaccharomyces pombe. Yoko-o T, Roy SK, Jigami Y;. Eur J Biochem 1998;257:630-637. [3]. 8991513. Molecular and phenotypic analysis of the S. cerevisiae MNN10 gene identifies a family of related glycosyltransferases. Dean N, Poster JB;. Glycobiology 1996;6:73-81. (from Pfam) NF017455.5 PF05639.16 Pup 27 27 69 PfamEq Y Y N ubiquitin-like protein Pup GO:0010498,GO:0019941,GO:0031386,GO:0070490,GO:0070628 18832610,18980670 2 Bacteria superkingdom 5887 EBI-EMBL Pup-like protein ubiquitin-like protein Pup This family consists of several short bacterial proteins formely known as (DUF797). It was recently shown that Mycobacterium tuberculosis contains a small protein, Pup (Rv2111c), that is covalently conjugated to the e-NH2 groups of lysines on several target proteins (pupylation) such as the malonyl CoA acyl carrier protein (FabD) [2]. Pupylation of FabD was shown to result in its recruitment to the mycobacterial proteasome and subsequent degradation analogous to eukaryotic ubiquitin-conjugated proteins. Searches recovered Pup orthologs in all major actinobacteria lineages including the basal bifidobacteria and also sporadically in certain other bacterial lineages. [1] The Pup proteins were all between 50-90 residues in length and a multiple alignment shows that they all contain a conserved motif with a G [EQ] signature at the C-terminus. Thus, all of them are suitable for conjugation via the terminal glutamate or the deamidated glutamine (as shown in the case of the Mycobacterium Pup [1]). The conserved globular core of Pup is predicted to form a bihelical unit with the extreme C-terminal 6-7 residues forming a tail in the extended conformation. Thus, Pup is structurally unrelated to the ubiquitin fold and has convergently evolved the function of protein modifier. [1]. 18980670. Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination. Iyer LM, Burroughs AM, Aravind L;. Biol Direct. 2008;3:45. [2]. 18832610. Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis. Pearce MJ, Mintseris J, Ferreyra J, Gygi SP, Darwin KH;. Science. 2008;322:1104-1107. (from Pfam) NF017457.5 PF05641.17 Agenet 27 19 61 domain Y Y N agenet domain-containing protein 12575993 2 Bacteria superkingdom 425 EBI-EMBL Agenet domain Agenet domain This domain is related to the TUDOR domain Pfam:PF00567 [1]. The function of the agenet domain is unknown. This family now matches both the two Agenet domains in the FMR proteins [1]. [1]. 12575993. The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains. Maurer-Stroh S, Dickens NJ, Hughes-Davies L, Kouzarides T, Eisenhaber F, Ponting CP;. Trends Biochem Sci 2003;28:69-74. (from Pfam) NF017459.5 PF05643.16 GNA1162-like 25.9 25.9 185 PfamAutoEq Y Y N GNA1162 family protein 23545639 2 Bacteria superkingdom 5069 EBI-EMBL Putative lipoprotein GNA1162-like DUF799 family lipoprotein This family of putative lipoproteins mainly found in Proteobacteria includes GNA1162 from Neisseria meningitidis, which shows five alpha-helices and four beta-strands, three of them forming a beta-sheet [1]. [1]. 23545639. Structure of Neisseria meningitidis lipoprotein GNA1162. Cai X, Lu J, Wu Z, Yang C, Xu H, Lin Z, Shen Y;. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013;69:362-368. (from Pfam) NF017466.5 PF05651.18 Diacid_rec 23.6 23.6 134 domain Y Y N sugar diacid recognition domain-containing protein 2 Bacteria superkingdom 18725 EBI-EMBL Putative sugar diacid recognition Putative sugar diacid recognition This region is found in several proteins characterised as carbohydrate diacid regulators (e.g. Swiss:P36047). An HTH DNA-binding motif is found at the C-terminus of these proteins suggesting that this region includes the sugar recognition region. (from Pfam) NF017469.5 PF05655.16 AvrD 25 25 331 subfamily Y Y N AvrD family protein 10485919,9326365 2 Bacteria superkingdom 1596 EBI-EMBL Pseudomonas avirulence D protein (AvrD) AvrD family protein This family consists of several avirulence D (AvrD) proteins primarily found in Pseudomonas syringae [1,2]. [1]. 10485919. Identification of a pathogenicity island, which contains genes for virulence and avirulence, on a large native plasmid in the bean pathogen Pseudomonas syringae pathovar phaseolicola. Jackson RW, Athanassopoulos E, Tsiamis G, Mansfield JW, Sesma A, Arnold DL, Gibbon MJ, Murillo J, Taylor JD, Vivian A;. Proc Natl Acad Sci U S A 1999;96:10875-10880. [2]. 9326365. Avirulence gene D of Pseudomonas syringae pv. tomato may have undergone horizontal gene transfer. Hanekamp T, Kobayashi D, Hayes S, Stayton MM;. FEBS Lett 1997;415:40-44. (from Pfam) NF017472.5 PF05658.19 YadA_head 25 10 27 repeat Y N N trimeric autotransporter adhesin repeat-containing protein GO:0019867 2 Bacteria superkingdom 59254 EBI-EMBL YadA head domain repeat (2 copies) trimeric autotransporter adhesin repeat This entry represents two copies of a fourteen residue repeat that makes up the head domain of bacterial haemagglutinins and invasins. (from Pfam) NF017475.5 PF05661.17 DUF808 28.4 28.4 302 PfamAutoEq Y Y N DUF808 family protein 2 Bacteria superkingdom 28473 EBI-EMBL Protein of unknown function (DUF808) DUF808 family protein This family consists of several bacterial proteins of unknown function. (from Pfam) NF017476.5 PF05662.19 YadA_stalk 28.4 10 43 repeat Y N N autotransporter adhesin-related protein GO:0019867 2 Bacteria superkingdom 68375 EBI-EMBL Coiled stalk of trimeric autotransporter adhesin trimeric autotransporter adhesin coiled stalk repeat This short motif is found in invasins and haemagglutinins, normally associated with (Pfam:PF05658). (from Pfam) NF017487.5 PF05675.17 DUF817 25.9 25.9 237 PfamAutoEq Y Y N DUF817 family protein 2 Bacteria superkingdom 12693 EBI-EMBL Protein of unknown function (DUF817) DUF817 family protein This family consists of several bacterial proteins of unknown function. (from Pfam) NF017496.5 PF05685.17 Uma2 27 27 172 domain Y Y N Uma2 family endonuclease 15720711,17154156 2 Bacteria superkingdom 138673 EBI-EMBL Putative restriction endonuclease Uma2 family endonuclease This entry includes a group of putative nuclease, including hypothetical protein TT1808 (also known as Uma2 or TTHA1514), an AT-rich DNA-binding protein from Thermus thermophilus. This domain has a 3-layer alpha/beta/alpha topology similar to that found in restriction endonucleases [1]. The nuclease domain is ubiquitously found in enzymes involved in metabolism of nucleic acids, mostly in nucleases with diverse biological functions [2]. [1]. 17154156. Crystal structure of TTHA1657 (AT-rich DNA-binding protein; p25) from Thermus thermophilus HB8 at 2.16 A resolution. Nakamura A, Sosa A, Komori H, Kita A, Miki K;. Proteins. 2007;66:755-759. [2]. 15720711. Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site. Feder M, Bujnicki JM;. BMC Genomics. 2005;6:21-21. (from Pfam) NF017497.5 PF05686.17 Glyco_transf_90 24 24 396 subfamily Y Y N glycosyl transferase family 90 2 Bacteria superkingdom 3911 EBI-EMBL Glycosyl transferase family 90 glycosyl transferase family 90 This family of glycosyl transferases are specifically (mannosyl) glucuronoxylomannan/galactoxylomannan -beta 1,2-xylosyltransferases, EC:2.4.2.-. (from Pfam) NF017506.5 PF05695.17 DUF825 29.2 29.2 1486 domain Y Y N DUF825 domain-containing protein 2 Bacteria superkingdom 4 EBI-EMBL Plant protein of unknown function (DUF825) Plant protein of unknown function (DUF825) This family consists of several plant proteins greater than 1000 residues in length. The function of this family is unknown. (from Pfam) NF017508.5 PF05697.18 Trigger_N 22.2 22.2 144 PfamEq Y Y N trigger factor GO:0006457,GO:0015031 12603737 2 Bacteria superkingdom 68257 EBI-EMBL Bacterial trigger factor protein (TF) trigger factor N-terminal domain In the E. coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains [1]. This family represents the N-terminal region of the protein. [1]. 12603737. Trigger Factor and DnaK possess overlapping substrate pools and binding specificities. Deuerling E, Patzelt H, Vorderwulbecke S, Rauch T, Kramer G, Schaffitzel E, Mogk A, Schulze-Specking A, Langen H, Bukau B;. Mol Microbiol 2003;47:1317-1328. (from Pfam) NF017510.5 PF05699.19 Dimer_Tnp_hAT 21.4 21.4 84 domain Y Y N hAT transposon family protein GO:0046983 10662858,11454746 2 Bacteria superkingdom 20 EBI-EMBL hAT family C-terminal dimerisation region hAT transposon family protein This dimerisation region is found at the C terminus of the transposases of elements belonging to the Activator superfamily (hAT element superfamily). The isolated dimerisation region forms extremely stable dimers in vitro [1]. [1]. 10662858. A highly conserved domain of the maize activator transposase is involved in dimerization. Essers L, Adolphs RH, Kunze R;. Plant Cell 2000;12:211-224. [2]. 11454746. Structure and evolution of the hAT transposon superfamily. Rubin E, Lithwick G, Levy AA;. Genetics 2001;158:949-957. (from Pfam) NF017530.5 PF05719.16 GPP34 29.1 29.1 201 domain Y Y N GPP34 family phosphoprotein GO:0070273 11042173 2 Bacteria superkingdom 25838 EBI-EMBL Golgi phosphoprotein 3 (GPP34) GPP34 family phosphoprotein This family consists of several eukaryotic GPP34 like proteins. GPP34 localises to the Golgi complex and is conserved from yeast to humans. The cytosolic-ally exposed location of GPP34 predict a role for a novel coat protein in Golgi trafficking [1]. [1]. 11042173. Proteomics characterization of abundant Golgi membrane proteins. Bell AW, Ward MA, Blackstock WP, Freeman HN, Choudhary JS, Lewis AP, Chotai D, Fazel A, Gushue JN, Paiement J, Palcy S, Chevet E, Lafreniere-Roula M, Solari R, Thomas DY, Rowley A, Bergeron JJ;. J Biol Chem 2001;276:5152-5165. (from Pfam) NF017535.5 PF05725.17 FNIP 21 21 44 domain Y Y N FNIP repeat-containing protein 16777069 2 Bacteria superkingdom 24 EBI-EMBL FNIP Repeat FNIP repeat This repeat is approximately 22 residues long and is only found in Dictyostelium discoideum. It appears to be related to Pfam:PF00560 (personal obs:C Yeats). The alignment consists of two tandem repeats. It is termed the FNIP repeat after the pattern of conserved residues. (from Pfam) NF017545.5 PF05735.18 TSP_C 25.6 25.6 198 domain Y N N Thrombospondin C-terminal region GO:0005509,GO:0005576,GO:0007155 11376949 2 Bacteria superkingdom 350 EBI-EMBL Thrombospondin C-terminal region Thrombospondin C-terminal region This region is found at the C-terminus of thrombospondin and related proteins. [1]. 11376949. A thrombospondin homologue in Drosophila melanogaster: cDNA and protein structure. Adolph KW;. Gene 2001;269:177-184. (from Pfam) NF017547.5 PF05737.17 Collagen_bind 27.5 27.5 131 domain Y Y N collagen binding domain-containing protein GO:0005518 9334749 2 Bacteria superkingdom 22869 EBI-EMBL Collagen binding domain Collagen binding domain The domain fold is a jelly-roll, composed of two antiparallel beta-sheets and two short alpha-helices [1]. A groove on beta-sheet I exhibited the best surface complementarity to the collagen. This site partially overlaps with the peptide sequence previously shown to be critical for collagen binding. Recombinant proteins containing single amino acid mutations designed to disrupt the surface of the putative binding site exhibited significantly lower affinities for collagen. [1]. 9334749. Structure of the collagen-binding domain from a Staphylococcus aureus adhesin. Symersky J, Patti JM, Carson M, House-Pompeo K, Teale M, Moore D, Jin L, Schneider A, DeLucas LJ, Hook M, Narayana SV;. Nat Struct Biol 1997;4:833-838. (from Pfam) NF017554.5 PF05745.16 CRPA 23.6 23.6 150 subfamily Y Y N cysteine-rich outer membrane protein GO:0019867 1997423,3066701 2 Bacteria superkingdom 89 EBI-EMBL Chlamydia 15 kDa cysteine-rich outer membrane protein (CRPA) cysteine-rich outer membrane protein This family consists of several Chlamydia 15 kDa cysteine-rich outer membrane proteins which are associated with differentiation of reticulate bodies (RBs) into elementary bodies (EBs) [1]. [1]. 3066701. Molecular cloning and sequence analysis of a developmentally regulated cysteine-rich outer membrane protein from Chlamydia trachomatis. Clarke IN, Ward ME, Lambden PR;. Gene 1988;71:307-314. [2]. 1997423. Sequence diversity of the 60-kilodalton protein and of a putative 15-kilodalton protein between the trachoma and lymphogranuloma venereum biovars of Chlamydia trachomatis. de la Maza LM, Fielder TJ, Carlson EJ, Markoff BA, Peterson EM;. Infect Immun 1991;59:1196-1201. (from Pfam) NF017562.5 PF05754.19 DUF834 23 23 52 domain Y Y N DUF834 domain-containing protein 2 Bacteria superkingdom 18 EBI-EMBL Domain of unknown function (DUF834) Domain of unknown function (DUF834) This short presumed domain is found in a large number of hypothetical plant proteins. The domain is quite rich in conserved glycine residues. It occurs in some putative transposons but currently has no known function. (from Pfam) NF017565.5 PF05757.16 PsbQ 26.9 26.9 204 PfamEq Y Y N photosystem II protein PsbQ psbQ GO:0005509,GO:0009523,GO:0009654,GO:0015979,GO:0019898 12549920 2 Bacteria superkingdom 821 EBI-EMBL Oxygen evolving enhancer protein 3 photosystem II protein PsbQ This family consists of the plant specific oxygen evolving enhancer protein 3 (PsbQ). Photosystem II (PSII)1 is a pigment-protein complex, which consists of at least 25 different protein subunits, at present denoted PsbA-Z according to the genes that encode them. PsbQ plays an important role in the lumenal oxygen-evolving activity of PSII from higher plants and green algae [1]. [1]. 12549920. Structural analysis of the PsbQ protein of photosystem II by Fourier transform infrared and circular dichroic spectroscopy and by bioinformatic methods. Balsera M, Arellano JB, Gutierrez JR, Heredia P, Revuelta JL, De Las Rivas J;. Biochemistry 2003;42:1000-1007. (from Pfam) NF017566.5 PF05758.17 Ycf1 29.4 29.4 945 domain Y N N Ycf1 GO:0016020 10792825 2 Bacteria superkingdom 26 EBI-EMBL Ycf1 Ycf1 The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene [1]. [1]. 10792825. The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. Drescher A, Ruf S, Calsa T Jr, Carrer H, Bock R;. Plant J 2000;22:97-104. (from Pfam) NF017568.5 PF05761.19 5_nucleotid 28.5 28.5 460 domain Y Y N 5'-nucleotidase domain-containing protein 9371705 2 Bacteria superkingdom 604 EBI-EMBL 5' nucleotidase family 5' nucleotidase family This family of eukaryotic proteins includes 5' nucleotidase enzymes, such as purine 5'-nucleotidase EC:3.1.3.5. [1]. 9371705. Bovine cytosolic IMP/GMP-specific 5'-nucleotidase: cloning and expression of active enzyme in Escherichia coli. Allegrini S, Pesi R, Tozzi MG, Fiol CJ, Johnson RB, Eriksson S;. Biochem J 1997;328:483-487. (from Pfam) NF017572.5 PF05766.17 NinG 25.4 25.4 193 domain Y Y N recombination protein NinG 11952832 2 Bacteria superkingdom 14800 EBI-EMBL Bacteriophage Lambda NinG protein recombination protein NinG NinG or Rap is involved in recombination. Rap (recombination adept with plasmid) increases lambda-by-plasmid recombination catalysed by Escherichia coli's RecBCD pathway [1]. [1]. 11952832. Gene products encoded in the ninR region of phage lambda participate in Red-mediated recombination. Tarkowski TA, Mooney D, Thomason LC, Stahl FW;. Genes Cells 2002;7:351-363. (from Pfam) NF017576.5 PF05770.16 Ins134_P3_kin 23 23 201 domain Y N N Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain 8662638 2 Bacteria superkingdom 111 EBI-EMBL Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain This family consists of several inositol 1, 3, 4-trisphosphate 5/6-kinase proteins. Inositol 1,3,4-trisphosphate is at a branch point in inositol phosphate metabolism. It is dephosphorylated by specific phosphatases to either inositol 3,4-bisphosphate or inositol 1,3-bisphosphate. Alternatively, it is phosphorylated to inositol 1,3,4,6-tetrakisphosphate or inositol 1,3,4,5-tetrakisphosphate by inositol trisphosphate 5/6-kinase [1]. This entry represents the ATP-grasp domain. [1]. 8662638. Isolation of inositol 1,3,4-trisphosphate 5/6-kinase, cDNA cloning and expression of the recombinant enzyme. Wilson MP, Majerus PW;. J Biol Chem 1996;271:11904-11910. (from Pfam) NF017578.5 PF05772.17 NinB 23.8 23.8 131 domain Y Y N recombination protein NinB 11952832,16076958 2 Bacteria superkingdom 8910 EBI-EMBL NinB protein recombination protein NinB The ninR region of phage lambda contains two recombination genes, orf (ninB) and rap (ninG), that have roles when the RecF and RecBCD recombination pathways of E. coli, respectively, operate on phage lambda [1]. NinB binds to single-stranded DNA [2]. [1]. 11952832. Gene products encoded in the ninR region of phage lambda participate in Red-mediated recombination. Tarkowski TA, Mooney D, Thomason LC, Stahl FW;. Genes Cells 2002;7:351-363. [2]. 16076958. Functional similarities between phage lambda Orf and Escherichia coli RecFOR in initiation of genetic exchange. Maxwell KL, Reed P, Zhang RG, Beasley S, Walmsley AR, Curtis FA, Joachimiak A, Edwards AM, Sharples GJ;. Proc Natl Acad Sci U S A. 2005;102:11260-11265. (from Pfam) NF017595.5 PF05791.16 Bacillus_HBL 29.1 29.1 177 subfamily Y Y N HBL/NHE enterotoxin family protein GO:0016020 12039781 2 Bacteria superkingdom 6763 EBI-EMBL Bacillus haemolytic enterotoxin (HBL) HBL/NHE enterotoxin family protein This family consists of several Bacillus haemolytic enterotoxins (HblC, HblD, HblA, NheA, and NheB) which can cause food poisoning in humans [1]. [1]. 12039781. Enterotoxin production in natural isolates of Bacillaceae outside the Bacillus cereus group. Phelps RJ, McKillip JL;. Appl Environ Microbiol 2002;68:3147-3151. (from Pfam) NF017611.5 PF05810.17 NinF 21 21 57 domain Y Y N protein NinF 2 Bacteria superkingdom 2020 EBI-EMBL NinF protein protein NinF This family consists of several bacteriophage NinF proteins as well as related sequences from E. coli. (from Pfam) NF017619.5 PF05818.17 TraT 31 31 214 domain Y Y N complement resistance protein TraT traT GO:0019867 3323526,9933744 2 Bacteria superkingdom 5104 EBI-EMBL Enterobacterial TraT complement resistance protein complement resistance protein TraT The traT gene is one of the F factor transfer genes and encodes an outer membrane protein which is involved in interactions between an Escherichia coli and its surroundings [1,2]. [1]. 9933744. Expression of foreign antigens on the surface of Escherichia coli by fusion to the outer membrane protein traT. Chang HJ, Sheu SY, Lo SJ;. J Biomed Sci 1999;6:64-70. [2]. 3323526. Surface exclusion genes traS and traT of the F sex factor of Escherichia coli K-12. Determination of the nucleotide sequence and promoter and terminator activities. Jalajakumari MB, Guidolin A, Buhk HJ, Manning PA, Ham LM, Hodgson AL, Cheah KC, Skurray RA;. J Mol Biol 1987;198:1-11. (from Pfam) NF017623.5 PF05822.17 UMPH-1 23.7 23.7 246 PfamEq Y N N Pyrimidine 5'-nucleotidase (UMPH-1) GO:0000287,GO:0005737,GO:0008253 12580951 2 Bacteria superkingdom 504 EBI-EMBL Pyrimidine 5'-nucleotidase (UMPH-1) Pyrimidine 5'-nucleotidase (UMPH-1) This family consists of several eukaryotic pyrimidine 5'-nucleotidase proteins. P5'N-1, also known as uridine monophosphate hydrolase-1 (UMPH-1), is a member of a large functional group of enzymes, characterised by the ability to dephosphorylate nucleic acids. P5'N-1 catalyses the dephosphorylation of pyrimidine nucleoside monophosphates to the corresponding nucleosides. Deficiencies in this proteins function can lead to several different disorders in humans [1]. [1]. 12580951. Pyrimidine 5' nucleotidase deficiency. Rees DC, Duley JA, Marinaki AM;. Br J Haematol 2003;120:375-383. (from Pfam) NF017624.5 PF05823.17 Gp-FAR-1 29.2 29.2 149 domain Y N N Nematode fatty acid retinoid binding protein (Gp-FAR-1) GO:0008289 11368765 2 Bacteria superkingdom 54 EBI-EMBL Nematode fatty acid retinoid binding protein (Gp-FAR-1) Nematode fatty acid retinoid binding protein (Gp-FAR-1) Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localises to the surface of the organism, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems [1]. [1]. 11368765. A surface-associated retinol- and fatty acid-binding protein (Gp-FAR-1) from the potato cyst nematode Globodera pallida: lipid binding activities, structural analysis and expression pattern. Prior A, Jones JT, Blok VC, Beauchamp J, McDermott L, Cooper A, Kennedy MW;. Biochem J 2001;356:387-394. (from Pfam) NF017630.5 PF05830.16 NodZ 28.3 28.3 322 PfamEq Y Y N nodulation protein NodZ GO:0009312,GO:0016758 8300517 2 Bacteria superkingdom 686 EBI-EMBL Nodulation protein Z (NodZ) nodulation protein NodZ The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal [1]. [1]. 8300517. nodZ, a unique host-specific nodulation gene, is involved in the fucosylation of the lipooligosaccharide nodulation signal of Bradyrhizobium japonicum. Stacey G, Luka S, Sanjuan J, Banfalvi Z, Nieuwkoop AJ, Chun JY, Forsberg LS, Carlson R;. J Bacteriol 1994;176:620-633. (from Pfam) NF017632.5 PF05832.17 DUF846 22.6 22.6 139 domain Y Y N DUF846 domain-containing protein GO:0016020 2 Bacteria superkingdom 9 EBI-EMBL Eukaryotic protein of unknown function (DUF846) Eukaryotic protein of unknown function (DUF846) This family consists of several of unknown function from a variety of eukaryotic organisms. (from Pfam) NF017638.5 PF05838.17 Glyco_hydro_108 21.2 21.2 85 domain Y Y N glycosyl hydrolase 108 family protein 16155206,17174325,7764692 2 Bacteria superkingdom 18058 EBI-EMBL Glycosyl hydrolase 108 glycosyl hydrolase 108 family protein This family acts as a lysozyme (N-acetylmuramidase), EC:3.2.1.17. It contains a conserved EGGY motif near the N-terminus, the glutamic acid within this motif is essential for catalytic activity [1]. In bacteria, it may activate the secretion of large proteins via the breaking and rearrangement of the peptidoglycan layer during secretion [2,3]. It is frequently found at the N-terminus of proteins containing a C-terminal Pfam:PF09374 domain. [1]. 17174325. Coliphage N4 N-acetylmuramidase defines a new family of murein hydrolases. Stojkovic EA, Rothman-Denes LB;. J Mol Biol. 2007;366:406-419. [2]. 16155206. COG3926 and COG5526: A tale of two new lysozyme-like protein families. Pei J, Grishin NV;. Protein Sci 2005; [Epub ahead of print]. [3]. 7764692. Cloning and characterization of a pair of genes that stimulate the production and secretion of Zymomonas mobilis extracellular levansucrase and invertase. Kondo Y, Toyoda A, Fukushi H, Yanase H, Tonomura K, Kawasaki H, Sakai T;. Biosci Biotechnol Biochem. 1994;58:526-530. (from Pfam) NF017640.5 PF05840.18 Phage_GPA 31.4 31.4 321 domain Y Y N replication endonuclease GO:0006260 158588,1701261,2940511,7997180,8510152 2 Bacteria superkingdom 35512 EBI-EMBL Bacteriophage replication gene A protein (GPA) replication endonuclease This family consists of a group of bacteriophage replication gene A protein (GPA) like sequences from both viruses and bacteria. The members of this family are likely to be endonucleases [1,2,3]. [1]. 8510152. Studies of bacteriophage P2 DNA replication. The DNA sequence of the cis-acting gene A and ori region and construction of a P2 mini-chromosome. Liu Y, Saha S, Haggard-Ljungquist E;. J Mol Biol 1993;231:361-374. [2]. 7997180. Identification of an HP1 phage protein required for site-specific excision. Esposito D, Scocca JJ;. Mol Microbiol 1994;13:685-695. [3]. 1701261. Retron for the 67-base multicopy single-stranded DNA from Escherichia coli: a potential transposable element encoding both reverse transcriptase and Dam methylase functions. Hsu MY, Inouye M, Inouye S;. Proc Natl Acad Sci U S A 1990;87:9454-9458. [4]. 158588. Role of polymeric forms of the bacteriophage phi X174 coded gene A protein in phi XRFI DNA cleavage. Ikeda JE, Yudelevich A, Shimamoto N, Hurwitz J;. J Biol Chem 1979;254:9416-9428. [5]. 2940511. Two juxtaposed tyrosyl-OH groups participate in phi X174 gene A protein catalysed cleavage and ligation of DNA. van Mansfeld AD, van Teeffelen HA, Baas PD, Jansz HS;. Nucleic Acids Res 1986;14:4229-4238. (from Pfam) NF017648.5 PF05848.16 CtsR 23.1 23.1 72 PfamEq Y Y N CtsR family transcriptional regulator 10692157 2 Bacteria superkingdom 6201 EBI-EMBL CtsR N-terminal HTH domain CtsR N-terminal HTH domain This family consists of several Firmicute transcriptional repressor of class III stress genes (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [1]. This entry is the N-terminal HTH domain. [1]. 10692157. CtsR controls class III heat shock gene expression in the human pathogen Listeria monocytogenes. Nair S, Derre I, Msadek T, Gaillot O, Berche P;. Mol Microbiol 2000;35:800-811. (from Pfam) NF017658.5 PF05860.18 TPS 33.5 33.5 252 domain Y N N TPS secretion domain 15079085 2 Bacteria superkingdom 90972 EBI-EMBL TPS secretion domain TPS secretion domain Filamentous hemagglutinin (FHA), the major 230-kDa adhesin of the whooping cough agent Bordetella pertussis, is one of the most efficiently secreted proteins in Gram-negative bacteria. FHA is secreted by means of the two-partner secretion (TPS) pathway. A TPS system is composed of two separate proteins, with TpsA the secreted protein and TpsB its associated specific outer-membrane transporter. All TPS-secreted proteins contain a distinctive N-proximal module essential for secretion, the TPS domain. The TPS domain folds into a beta-helix. This domain is found in a wide variety of secreted proteins from bacterial pathogens. [1]. 15079085. The crystal structure of filamentous hemagglutinin secretion domain and its implications for the two-partner secretion pathway. Clantin B, Hodak H, Willery E, Locht C, Jacob-Dubuisson F, Villeret V;. Proc Natl Acad Sci U S A. 2004;101:6194-6199. (from Pfam) NF017663.5 PF05866.16 RusA 22.8 22.8 124 domain Y Y N RusA family crossover junction endodeoxyribonuclease 3.1.21.10 GO:0000287,GO:0006281,GO:0006310 7813450,8648624 2 Bacteria superkingdom 30342 EBI-EMBL Endodeoxyribonuclease RusA RusA family crossover junction endodeoxyribonuclease This family consists of several bacterial and phage Holliday junction resolvase (RusA) like proteins. The RusA protein of Escherichia coli is an endonuclease that can resolve Holliday intermediates and correct the defects in genetic recombination and DNA repair associated with inactivation of RuvAB or RuvC [1,2]. [1]. 8648624. Holliday junction resolvases encoded by homologous rusA genes in Escherichia coli K-12 and phage 82. Mahdi AA, Sharples GJ, Mandal TN, Lloyd RG;. J Mol Biol 1996;257:561-573. [2]. 7813450. Processing of intermediates in recombination and DNA repair: identification of a new endonuclease that specifically cleaves Holliday junctions. Sharples GJ, Chan SN, Mahdi AA, Whitby MC, Lloyd RG;. EMBO J 1994;13:6133-6142. (from Pfam) NF017666.5 PF05869.16 Dam 28.1 28.1 169 subfamily Y Y N DNA N-6-adenine-methyltransferase GO:0003677,GO:0009007 2180941 2 Bacteria superkingdom 15742 EBI-EMBL DNA N-6-adenine-methyltransferase (Dam) DNA N-6-adenine-methyltransferase This family consists of several bacterial and phage DNA N-6-adenine-methyltransferase (Dam) like sequences [1]. [1]. 2180941. Primary structure of a DNA (N6-adenine)-methyltransferase from Escherichia coli virus T1. DNA sequence, genomic organization, and comparative analysis. Schneider-Scherzer E, Auer B, de Groot EJ, Schweiger M;. J Biol Chem 1990;265:6086-6091. (from Pfam) NF017667.5 PF05870.16 PA_decarbox 24.6 24.6 158 PfamEq Y Y N phenolic acid decarboxylase GO:0016831 9546183 2 Bacteria superkingdom 3989 EBI-EMBL Phenolic acid decarboxylase (PAD) phenolic acid decarboxylase This family consists of several bacterial phenolic acid decarboxylase proteins. Phenolic acids, also called substituted cinnamic acids, are important lignin-related aromatic acids and natural constituents of plant cell walls. These acids (particularly ferulic, p-coumaric, and caffeic acids) bind the complex lignin polymer to the hemicellulose and cellulose in plants. The Phenolic acid decarboxylase (PAD) gene (pad) is transcriptionally regulated by p-coumaric, ferulic, or caffeic acid; these three acids are the three substrates of PAD [1]. [1]. 9546183. Gene cloning, transcriptional analysis, purification, and characterization of phenolic acid decarboxylase from Bacillus subtilis. Cavin JF, Dartois V, Divies C;. Appl Environ Microbiol 1998;64:1466-1471. (from Pfam) NF017672.5 PF05875.17 Ceramidase 32.5 32.5 259 domain Y Y N ceramidase domain-containing protein GO:0006672,GO:0016020,GO:0016811 11356846,21733186 2 Bacteria superkingdom 2736 EBI-EMBL Ceramidase Ceramidase This family consists of several ceramidases. Ceramidases are enzymes involved in regulating cellular levels of ceramides, sphingoid bases, and their phosphates, EC:3.5.1.23. This family belongs to the CREST superfamily [2], which are distantly related to the GPCRs. [1]. 11356846. Cloning and characterization of a novel human alkaline ceramidase. A mammalian enzyme that hydrolyzes phytoceramide. Mao C, Xu R, Szulc ZM, Bielawska A, Galadari SH, Obeid LM;. J Biol Chem 2001;276:26577-26588. [2]. 21733186. CREST--a large and diverse superfamily of putative transmembrane hydrolases. Pei J, Millay DP, Olson EN, Grishin NV;. Biol Direct. 2011;6:37. (from Pfam) NF017673.5 PF05876.17 GpA_ATPase 25.6 25.6 247 domain Y Y N phage terminase large subunit family protein GO:0016887 11866517,17870092,23134123,30541105 2 Bacteria superkingdom 37622 EBI-EMBL Phage terminase large subunit gpA, ATPase domain Phage terminase large subunit gpA, ATPase domain This family consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, TerL (gpA), products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA during the DNA packaging process. TerL contains all the catalytic activities required for for DNA maturation and packaging. At the N-terminal (represented in this entry) reside the DNA translocase (packaging) and ATPase activities, while at the C-terminal resides the DNA maturation (nuclease/helicase) catalytic activity [1,2,3,4]. [1]. 11866517. The large subunit of bacteriophage lambda's terminase plays a role in DNA translocation and packaging termination. Duffy C, Feiss M;. J Mol Biol 2002;316:547-561. [2]. 23134123. The enzymology of a viral genome packaging motor is influenced by the assembly state of the motor subunits. Andrews BT, Catalano CE;. Biochemistry. 2012;51:9342-9353. [3]. 30541105. Evidence that a catalytic glutamate and an 'Arginine Toggle' act in concert to mediate ATP hydrolysis and mechanochemical coupling in a viral DNA packaging motor. Ortiz D, delToro D, Ordyan M, Pajak J, Sippy J, Catala A, Oh CS, Vu A, Arya G, Feiss M, Smith DE, Catalano CE;. Nucleic Acids Res. 2019;47:1404-1415. [4]. 17870092. The DNA maturation domain of gpA, the DNA packaging motor protein of bacteriophage lambda, contains an ATPase site associated with endonuclease activity. Ortega ME, Gaussier H, Catalano CE;. J Mol Biol. 2007;373. TRUNCATED at 1650 bytes (from Pfam) NF017688.5 PF05895.17 DUF859 28.8 28.8 626 subfamily Y Y N DUF859 family phage minor structural protein 2 Bacteria superkingdom 2326 EBI-EMBL Siphovirus protein of unknown function (DUF859) DUF859 family Siphovirus minor structural protein This family consists of several uncharacterised proteins from the Siphoviruses and other bacterial viruses. Some members of this family are described as putative minor structural proteins. (from Pfam) NF017696.5 PF05907.18 CXXC_Zn-b_euk 22.9 22.9 155 domain Y Y N CXXC-containing zinc-binding protein 30260988 2 Bacteria superkingdom 5 EBI-EMBL CXXC motif containing zinc binding protein, eukaryotic CXXC motif containing zinc binding protein, eukaryotic This family consists of a number of eukaryotic proteins including CXXC motif containing zinc binding protein (previously known as UPF0587 protein C1orf123). The crystal structure reveals that the protein binds a Zn2+ ion in a tetrahedral coordination with four Cys residues from two CxxC motifs. CXXC motif containing zinc binding protein was initially identified as an interaction partner for the heavy metal-associated (HMA) domain of CCS (copper chaperone for superoxide dismutase). However, it was shown that only misfolded mutant forms, lacking part of the zinc-binding sites, interact with CCS [1]. [1]. 30260988. Identification of a novel zinc-binding protein, C1orf123, as an interactor with a heavy metal-associated domain. Furukawa Y, Lim C, Tosha T, Yoshida K, Hagai T, Akiyama S, Watanabe S, Nakagome K, Shiro Y;. PLoS One. 2018;13:e0204355. (from Pfam) NF017717.5 PF05930.17 Phage_AlpA 21 21 51 domain Y Y N AlpA family phage regulatory protein 7511582 2 Bacteria superkingdom 51064 EBI-EMBL Prophage CP4-57 regulatory protein (AlpA) AlpA family phage regulatory protein This family consists of several short bacterial and phage proteins which are related to the E. coli protein AlpA. AlpA suppress two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light [1]. Several of the sequences in this family are thought to be DNA-binding proteins. [1]. 7511582. Alp suppression of Lon: dependence on the slpA gene. Trempy JE, Kirby JE, Gottesman S;. J Bacteriol 1994;176:2061-2067. (from Pfam) NF017719.5 PF05932.18 CesT 22 22 119 domain Y Y N CesT family type III secretion system chaperone GO:0030254 11849537,9448330 2 Bacteria superkingdom 10570 EBI-EMBL Tir chaperone protein (CesT) family CesT family type III secretion system chaperone This family consists of a number of bacterial sequences which are highly similar to the Tir chaperone protein in E. Coli. In many Gram-negative bacteria, a key indicator of pathogenic potential is the possession of a specialised type III secretion system, which is utilised to deliver virulence effector proteins directly into the host cell cytosol. Many of the proteins secreted from such systems require small cytosolic chaperones to maintain the secreted substrates in a secretion-competent state. CesT serves a chaperone function for the enteropathogenic Escherichia coli (EPEC) translocated intimin receptor (Tir) protein, which confers upon EPEC the ability to alter host cell morphology following intimate bacterial attachment [1]. This family also contains several DspF and related sequences from several plant pathogenic bacteria. The "disease-specific" (dsp) region next to the hrp gene cluster of Erwinia amylovora is required for pathogenicity but not for elicitation of the hypersensitive reaction. DspF and AvrF are small (16 kDa and 14 kDa) and acidic with predicted amphipathic alpha helices in their C termini; they resemble chaperones for virulence factors secreted by type III secretion systems of animal pathogens [2]. [1]. 11849537. Functional analysis of the enteropathogenic Escherichia coli type III secretion system chaperone CesT identifies domains that mediate substrate interactions. Delahay RM, Shaw RK, Elliott SJ, Kaper JB, Knutton S, Frankel G;. Mol Microbiol 2002;43:61-73. [2]. 9448330. Homology and functional similarity of an hrp-linked pathogenicity locus, dspEF, of Erwinia amylovora and the avirulence l. TRUNCATED at 1650 bytes (from Pfam) NF017726.5 PF05939.18 Phage_min_tail 39 39 108 domain Y Y N phage tail protein 6221115 2 Bacteria superkingdom 13515 EBI-EMBL Phage minor tail protein phage tail protein This family consists of a series of phage minor tail proteins and related sequences from several bacterial species. [1]. 6221115. Nucleotide sequence of bacteriophage lambda DNA. Sanger F, Coulson AR, Hong GF, Hill DF, Petersen GB;. J Mol Biol 1982;162:729-773. (from Pfam) NF017731.5 PF05944.17 Phage_term_smal 29.4 29.4 130 PfamEq Y Y N phage terminase small subunit gpM GO:0003677,GO:0004519,GO:0019069 1837355 2 Bacteria superkingdom 17792 EBI-EMBL Phage small terminase subunit phage terminase small subunit This family consists of several phage small terminase subunit proteins as well as some related bacter